Multiple sequence alignment - TraesCS5B01G070500

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 TraesCS5B01G070500 chr5B 100.000 3703 0 0 1 3703 81481443 81485145 0.000000e+00 6839.0
1 TraesCS5B01G070500 chr5B 93.182 176 8 2 3528 3703 81518089 81518260 4.750000e-64 255.0
2 TraesCS5B01G070500 chr5B 100.000 36 0 0 906 941 81482278 81482243 2.390000e-07 67.6
3 TraesCS5B01G070500 chr5B 97.436 39 1 0 801 839 81482383 81482345 2.390000e-07 67.6
4 TraesCS5B01G070500 chr5A 93.958 2698 83 30 882 3527 64960846 64958177 0.000000e+00 4006.0
5 TraesCS5B01G070500 chr5A 87.980 391 40 6 303 690 64961333 64960947 4.360000e-124 455.0
6 TraesCS5B01G070500 chr5A 93.972 282 16 1 8 288 64961599 64961318 3.420000e-115 425.0
7 TraesCS5B01G070500 chr5A 91.667 72 6 0 717 788 64960952 64960881 2.350000e-17 100.0
8 TraesCS5B01G070500 chr5D 95.533 2149 44 8 882 3014 72502415 72500303 0.000000e+00 3389.0
9 TraesCS5B01G070500 chr5D 94.947 376 16 2 415 787 72502826 72502451 1.480000e-163 586.0
10 TraesCS5B01G070500 chr5D 96.119 335 10 1 1 335 72503158 72502827 9.040000e-151 544.0
11 TraesCS5B01G070500 chr5D 87.365 277 18 7 3064 3328 72500302 72500031 6.010000e-78 302.0
12 TraesCS5B01G070500 chr5D 93.785 177 9 2 3528 3703 77663241 77663416 7.890000e-67 265.0
13 TraesCS5B01G070500 chr5D 79.874 318 54 8 983 1298 463370466 463370157 1.340000e-54 224.0
14 TraesCS5B01G070500 chr5D 84.579 214 16 7 3328 3527 72499927 72499717 2.920000e-46 196.0
15 TraesCS5B01G070500 chr5D 96.226 53 2 0 835 887 72502426 72502478 1.830000e-13 87.9
16 TraesCS5B01G070500 chr5D 100.000 36 0 0 801 836 72502356 72502391 2.390000e-07 67.6
17 TraesCS5B01G070500 chr2D 79.777 806 120 29 983 1780 168148083 168147313 2.510000e-151 545.0
18 TraesCS5B01G070500 chr2D 92.655 177 11 2 3528 3703 289093255 289093080 1.710000e-63 254.0
19 TraesCS5B01G070500 chr6D 79.379 805 128 27 983 1780 441966569 441965796 1.960000e-147 532.0
20 TraesCS5B01G070500 chr3A 80.236 678 102 22 983 1653 647019122 647019774 7.190000e-132 481.0
21 TraesCS5B01G070500 chr7D 93.182 176 8 2 3528 3703 206070226 206070055 4.750000e-64 255.0
22 TraesCS5B01G070500 chr4D 92.655 177 11 2 3528 3703 111056908 111057083 1.710000e-63 254.0
23 TraesCS5B01G070500 chr4D 92.614 176 10 2 3528 3703 470809489 470809317 2.210000e-62 250.0
24 TraesCS5B01G070500 chr1D 93.064 173 10 2 3532 3703 202586077 202586248 6.140000e-63 252.0
25 TraesCS5B01G070500 chr4A 89.848 197 17 3 3509 3703 558244847 558245042 2.210000e-62 250.0
26 TraesCS5B01G070500 chr1A 92.135 178 12 1 3528 3703 323444125 323444302 2.210000e-62 250.0


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 TraesCS5B01G070500 chr5B 81481443 81485145 3702 False 6839.0 6839 100.00000 1 3703 1 chr5B.!!$F1 3702
1 TraesCS5B01G070500 chr5A 64958177 64961599 3422 True 1246.5 4006 91.89425 8 3527 4 chr5A.!!$R1 3519
2 TraesCS5B01G070500 chr5D 72499717 72503158 3441 True 1003.4 3389 91.70860 1 3527 5 chr5D.!!$R2 3526
3 TraesCS5B01G070500 chr2D 168147313 168148083 770 True 545.0 545 79.77700 983 1780 1 chr2D.!!$R1 797
4 TraesCS5B01G070500 chr6D 441965796 441966569 773 True 532.0 532 79.37900 983 1780 1 chr6D.!!$R1 797
5 TraesCS5B01G070500 chr3A 647019122 647019774 652 False 481.0 481 80.23600 983 1653 1 chr3A.!!$F1 670

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
875 882 0.038892 CAGCAATGCTTTCTGCGGTT 60.039 50.0 4.36 0.0 46.63 4.44 F
1231 1249 0.179045 CTATGAAGGCCGACCCAAGG 60.179 60.0 0.00 0.0 36.11 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2490 0.183492 ACAGTTTGGCTTGCCTCTGA 59.817 50.0 25.03 3.07 0.00 3.27 R
2703 2736 1.053264 CAGGCTACTGGATGCTCCCT 61.053 60.0 0.00 0.00 41.13 4.20 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
69 70 3.479203 CCGCCCCTGCATCCTACA 61.479 66.667 0.00 0.00 37.32 2.74
73 74 2.377810 CCCCTGCATCCTACAGCCA 61.378 63.158 0.00 0.00 33.65 4.75
246 248 4.317530 GGTTTTCCTCCCCAACTATTCT 57.682 45.455 0.00 0.00 36.94 2.40
271 273 4.584325 TCAACAGCTTAGCATCTTTGGTTT 59.416 37.500 7.07 0.00 34.79 3.27
347 349 2.487265 GGTTTGTCTGGTCAGTGGTCAT 60.487 50.000 0.00 0.00 0.00 3.06
352 354 2.832129 GTCTGGTCAGTGGTCATTAGGA 59.168 50.000 0.00 0.00 0.00 2.94
364 366 5.406780 GTGGTCATTAGGATCGATTTGCTAG 59.593 44.000 0.00 0.00 0.00 3.42
373 375 6.759272 AGGATCGATTTGCTAGCAGTTTATA 58.241 36.000 18.45 0.00 0.00 0.98
374 376 7.390027 AGGATCGATTTGCTAGCAGTTTATAT 58.610 34.615 18.45 8.68 0.00 0.86
384 386 8.763049 TGCTAGCAGTTTATATACACATGATC 57.237 34.615 14.93 0.00 0.00 2.92
385 387 7.819415 TGCTAGCAGTTTATATACACATGATCC 59.181 37.037 14.93 0.00 0.00 3.36
444 446 6.866770 TGTTATCACTCTTTTCGGAACTAGTG 59.133 38.462 15.18 15.18 36.52 2.74
449 451 5.701290 CACTCTTTTCGGAACTAGTGGAATT 59.299 40.000 14.17 0.00 32.60 2.17
465 467 4.636206 GTGGAATTGCCGAGTTTTCTAGAT 59.364 41.667 0.00 0.00 40.66 1.98
567 570 8.921353 TTACTAGTTTTAGTAAATTGGTGCCA 57.079 30.769 0.00 0.00 45.05 4.92
593 596 5.117584 ACAGCTCAGAGAAGATGCATTTAG 58.882 41.667 0.00 0.00 36.11 1.85
670 677 3.731652 TGCCAAAACAAAGTGGATGAG 57.268 42.857 0.00 0.00 37.03 2.90
700 707 6.484643 CCAAATTGATAGAGGTGATGTAGTGG 59.515 42.308 0.00 0.00 0.00 4.00
704 711 1.944177 AGAGGTGATGTAGTGGCAGT 58.056 50.000 0.00 0.00 0.00 4.40
732 739 6.739331 AGAGAATATAAGGTGGACTGGAAG 57.261 41.667 0.00 0.00 42.29 3.46
795 802 4.703899 GCAGAAAGCATTGTCACAAAAG 57.296 40.909 0.00 0.00 44.79 2.27
796 803 3.492011 GCAGAAAGCATTGTCACAAAAGG 59.508 43.478 0.00 0.00 44.79 3.11
797 804 4.053295 CAGAAAGCATTGTCACAAAAGGG 58.947 43.478 0.00 0.00 0.00 3.95
800 807 3.228188 AGCATTGTCACAAAAGGGAGA 57.772 42.857 0.00 0.00 0.00 3.71
801 808 3.565307 AGCATTGTCACAAAAGGGAGAA 58.435 40.909 0.00 0.00 0.00 2.87
803 810 3.068024 GCATTGTCACAAAAGGGAGAACA 59.932 43.478 0.00 0.00 0.00 3.18
804 811 4.441356 GCATTGTCACAAAAGGGAGAACAA 60.441 41.667 0.00 0.00 0.00 2.83
806 813 3.691575 TGTCACAAAAGGGAGAACAACA 58.308 40.909 0.00 0.00 0.00 3.33
807 814 3.694072 TGTCACAAAAGGGAGAACAACAG 59.306 43.478 0.00 0.00 0.00 3.16
808 815 2.687935 TCACAAAAGGGAGAACAACAGC 59.312 45.455 0.00 0.00 0.00 4.40
810 817 2.952310 ACAAAAGGGAGAACAACAGCTC 59.048 45.455 0.00 0.00 0.00 4.09
811 818 2.951642 CAAAAGGGAGAACAACAGCTCA 59.048 45.455 0.00 0.00 32.83 4.26
812 819 2.262423 AAGGGAGAACAACAGCTCAC 57.738 50.000 0.00 0.00 34.77 3.51
813 820 1.428869 AGGGAGAACAACAGCTCACT 58.571 50.000 0.00 0.00 39.96 3.41
816 823 2.485479 GGGAGAACAACAGCTCACTTCA 60.485 50.000 0.00 0.00 31.87 3.02
817 824 3.206150 GGAGAACAACAGCTCACTTCAA 58.794 45.455 0.00 0.00 32.83 2.69
819 826 4.083590 GGAGAACAACAGCTCACTTCAATC 60.084 45.833 0.00 0.00 32.83 2.67
820 827 4.454678 AGAACAACAGCTCACTTCAATCA 58.545 39.130 0.00 0.00 0.00 2.57
821 828 4.514441 AGAACAACAGCTCACTTCAATCAG 59.486 41.667 0.00 0.00 0.00 2.90
822 829 4.077300 ACAACAGCTCACTTCAATCAGA 57.923 40.909 0.00 0.00 0.00 3.27
823 830 4.454678 ACAACAGCTCACTTCAATCAGAA 58.545 39.130 0.00 0.00 34.41 3.02
824 831 4.883585 ACAACAGCTCACTTCAATCAGAAA 59.116 37.500 0.00 0.00 35.40 2.52
825 832 5.533903 ACAACAGCTCACTTCAATCAGAAAT 59.466 36.000 0.00 0.00 35.40 2.17
826 833 5.624344 ACAGCTCACTTCAATCAGAAATG 57.376 39.130 0.00 0.00 34.87 2.32
827 834 5.068636 ACAGCTCACTTCAATCAGAAATGT 58.931 37.500 0.00 0.00 35.11 2.71
828 835 6.233434 ACAGCTCACTTCAATCAGAAATGTA 58.767 36.000 0.00 0.00 35.11 2.29
829 836 6.712095 ACAGCTCACTTCAATCAGAAATGTAA 59.288 34.615 0.00 0.00 35.11 2.41
830 837 7.392673 ACAGCTCACTTCAATCAGAAATGTAAT 59.607 33.333 0.00 0.00 35.11 1.89
831 838 8.886719 CAGCTCACTTCAATCAGAAATGTAATA 58.113 33.333 0.00 0.00 35.11 0.98
832 839 9.107177 AGCTCACTTCAATCAGAAATGTAATAG 57.893 33.333 0.00 0.00 35.11 1.73
833 840 8.887717 GCTCACTTCAATCAGAAATGTAATAGT 58.112 33.333 0.00 0.00 35.11 2.12
835 842 9.942850 TCACTTCAATCAGAAATGTAATAGTGA 57.057 29.630 0.00 0.00 35.11 3.41
848 855 9.875708 AAATGTAATAGTGATATAAAAGGCCCA 57.124 29.630 0.00 0.00 0.00 5.36
849 856 9.875708 AATGTAATAGTGATATAAAAGGCCCAA 57.124 29.630 0.00 0.00 0.00 4.12
850 857 9.875708 ATGTAATAGTGATATAAAAGGCCCAAA 57.124 29.630 0.00 0.00 0.00 3.28
851 858 9.875708 TGTAATAGTGATATAAAAGGCCCAAAT 57.124 29.630 0.00 0.00 0.00 2.32
854 861 9.605951 AATAGTGATATAAAAGGCCCAAATGAT 57.394 29.630 0.00 0.00 0.00 2.45
855 862 7.294017 AGTGATATAAAAGGCCCAAATGATG 57.706 36.000 0.00 0.00 0.00 3.07
856 863 5.928264 GTGATATAAAAGGCCCAAATGATGC 59.072 40.000 0.00 0.00 0.00 3.91
857 864 5.601729 TGATATAAAAGGCCCAAATGATGCA 59.398 36.000 0.00 0.00 0.00 3.96
858 865 2.773993 AAAAGGCCCAAATGATGCAG 57.226 45.000 0.00 0.00 0.00 4.41
859 866 0.251073 AAAGGCCCAAATGATGCAGC 59.749 50.000 0.00 0.00 0.00 5.25
860 867 0.905809 AAGGCCCAAATGATGCAGCA 60.906 50.000 7.31 7.31 0.00 4.41
861 868 0.905809 AGGCCCAAATGATGCAGCAA 60.906 50.000 9.54 0.00 0.00 3.91
862 869 0.179468 GGCCCAAATGATGCAGCAAT 59.821 50.000 9.54 0.00 0.00 3.56
863 870 1.295792 GCCCAAATGATGCAGCAATG 58.704 50.000 9.54 11.49 0.00 2.82
864 871 1.295792 CCCAAATGATGCAGCAATGC 58.704 50.000 9.54 0.00 0.00 3.56
865 872 1.134521 CCCAAATGATGCAGCAATGCT 60.135 47.619 9.54 0.00 40.77 3.79
866 873 2.627945 CCAAATGATGCAGCAATGCTT 58.372 42.857 9.54 0.00 36.40 3.91
867 874 3.006940 CCAAATGATGCAGCAATGCTTT 58.993 40.909 9.54 1.44 36.40 3.51
868 875 3.063452 CCAAATGATGCAGCAATGCTTTC 59.937 43.478 9.54 3.78 36.40 2.62
869 876 3.887621 AATGATGCAGCAATGCTTTCT 57.112 38.095 9.54 0.00 36.40 2.52
870 877 2.647529 TGATGCAGCAATGCTTTCTG 57.352 45.000 4.36 0.00 36.40 3.02
872 879 3.763319 GCAGCAATGCTTTCTGCG 58.237 55.556 4.36 0.00 46.63 5.18
873 880 1.804326 GCAGCAATGCTTTCTGCGG 60.804 57.895 4.36 0.00 46.63 5.69
874 881 1.582968 CAGCAATGCTTTCTGCGGT 59.417 52.632 4.36 0.00 46.63 5.68
875 882 0.038892 CAGCAATGCTTTCTGCGGTT 60.039 50.000 4.36 0.00 46.63 4.44
876 883 0.675633 AGCAATGCTTTCTGCGGTTT 59.324 45.000 0.00 0.00 46.63 3.27
877 884 0.785979 GCAATGCTTTCTGCGGTTTG 59.214 50.000 0.00 0.00 46.63 2.93
878 885 0.785979 CAATGCTTTCTGCGGTTTGC 59.214 50.000 0.00 0.00 46.63 3.68
879 886 0.675633 AATGCTTTCTGCGGTTTGCT 59.324 45.000 0.00 0.00 46.63 3.91
880 887 0.675633 ATGCTTTCTGCGGTTTGCTT 59.324 45.000 0.00 0.00 46.63 3.91
971 989 5.796424 AGTGAGCATTTGTTTCTGGATTT 57.204 34.783 0.00 0.00 0.00 2.17
1117 1135 9.438291 GTGTGTCATGCTCATATAAATGTTAAC 57.562 33.333 0.00 0.00 34.50 2.01
1231 1249 0.179045 CTATGAAGGCCGACCCAAGG 60.179 60.000 0.00 0.00 36.11 3.61
1572 1599 2.957402 TTGCAACAGAGGAGTCCAAT 57.043 45.000 12.86 0.00 0.00 3.16
1803 1830 5.495926 ACCATCTGTCTTGTCTGATCTTT 57.504 39.130 0.00 0.00 0.00 2.52
1853 1880 4.010349 CAGGGTAGTAAGCTTTTCCCTTG 58.990 47.826 20.30 12.21 42.70 3.61
1884 1911 5.582550 TCTCTATATGCAGACAAGAACACG 58.417 41.667 0.00 0.00 0.00 4.49
1971 2001 5.979993 TCAAATAGGGAGTTATACGCACAA 58.020 37.500 0.00 0.00 0.00 3.33
2183 2213 3.686726 AGAATTGCTAAGCTGTGTAGTGC 59.313 43.478 0.00 0.00 0.00 4.40
2184 2214 2.839486 TTGCTAAGCTGTGTAGTGCT 57.161 45.000 0.00 0.00 41.82 4.40
2185 2215 2.084610 TGCTAAGCTGTGTAGTGCTG 57.915 50.000 0.00 0.00 39.71 4.41
2186 2216 1.338105 TGCTAAGCTGTGTAGTGCTGG 60.338 52.381 0.00 0.00 39.71 4.85
2187 2217 1.363744 CTAAGCTGTGTAGTGCTGGC 58.636 55.000 0.00 0.00 39.71 4.85
2188 2218 0.389817 TAAGCTGTGTAGTGCTGGCG 60.390 55.000 0.00 0.00 39.71 5.69
2189 2219 3.793144 GCTGTGTAGTGCTGGCGC 61.793 66.667 0.00 0.00 0.00 6.53
2457 2490 2.958818 TGACCCTATCGCTATCCTTGT 58.041 47.619 0.00 0.00 0.00 3.16
2663 2696 5.238650 AGAATTCCATGACGAAAACGAAACT 59.761 36.000 0.65 0.00 0.00 2.66
2735 2768 4.318332 CAGTAGCCTGTGAATGACTGAAA 58.682 43.478 0.00 0.00 37.14 2.69
2794 2827 0.904649 ATCGACATTGGGCTGACTCA 59.095 50.000 0.00 0.00 0.00 3.41
2885 2918 7.703058 AGTTCTATTTTGGTCGGATGAAATT 57.297 32.000 0.00 0.00 0.00 1.82
2973 3019 3.203716 CATGCTTCTATTGAGCTGCTCA 58.796 45.455 27.35 27.35 38.87 4.26
3014 3060 3.484407 GCATAGGCCATTGAACATCTCT 58.516 45.455 5.01 0.00 0.00 3.10
3015 3061 3.252701 GCATAGGCCATTGAACATCTCTG 59.747 47.826 5.01 0.00 0.00 3.35
3129 3179 4.870363 TGAAAAGCACACCATAGAAAAGC 58.130 39.130 0.00 0.00 0.00 3.51
3142 3192 9.079833 CACCATAGAAAAGCAAAGTCATAAATG 57.920 33.333 0.00 0.00 0.00 2.32
3324 3387 7.385205 CGGACTAGACGATGATGGATTATTTTT 59.615 37.037 0.00 0.00 0.00 1.94
3325 3388 8.713271 GGACTAGACGATGATGGATTATTTTTC 58.287 37.037 0.00 0.00 0.00 2.29
3326 3389 9.482627 GACTAGACGATGATGGATTATTTTTCT 57.517 33.333 0.00 0.00 0.00 2.52
3373 3543 2.108970 GTTCGTCCTCCCATCCTTACT 58.891 52.381 0.00 0.00 0.00 2.24
3374 3544 2.500504 GTTCGTCCTCCCATCCTTACTT 59.499 50.000 0.00 0.00 0.00 2.24
3375 3545 2.385803 TCGTCCTCCCATCCTTACTTC 58.614 52.381 0.00 0.00 0.00 3.01
3422 3612 5.590259 ACTCACAGATATTTATTTGCGCCTT 59.410 36.000 4.18 0.00 0.00 4.35
3459 3649 6.270231 ACCTGGATCTGTTTAACTTGAGTAGT 59.730 38.462 0.00 0.00 39.32 2.73
3462 3652 7.907389 TGGATCTGTTTAACTTGAGTAGTCAT 58.093 34.615 0.00 0.00 35.54 3.06
3503 3706 5.497474 ACTACCGGAGTTGAAGCATTAATT 58.503 37.500 9.46 0.00 33.13 1.40
3505 3708 7.280356 ACTACCGGAGTTGAAGCATTAATTAT 58.720 34.615 9.46 0.00 33.13 1.28
3527 3730 9.705471 ATTATCAATAATTTTTGTTTGCGCATG 57.295 25.926 12.75 0.85 28.99 4.06
3528 3731 6.536731 TCAATAATTTTTGTTTGCGCATGT 57.463 29.167 12.75 0.00 0.00 3.21
3529 3732 6.361114 TCAATAATTTTTGTTTGCGCATGTG 58.639 32.000 12.75 0.66 0.00 3.21
3530 3733 5.921004 ATAATTTTTGTTTGCGCATGTGT 57.079 30.435 12.75 0.00 0.00 3.72
3531 3734 4.612932 AATTTTTGTTTGCGCATGTGTT 57.387 31.818 12.75 0.00 0.00 3.32
3532 3735 5.725110 AATTTTTGTTTGCGCATGTGTTA 57.275 30.435 12.75 0.00 0.00 2.41
3533 3736 4.768659 TTTTTGTTTGCGCATGTGTTAG 57.231 36.364 12.75 0.00 0.00 2.34
3534 3737 3.428746 TTTGTTTGCGCATGTGTTAGT 57.571 38.095 12.75 0.00 0.00 2.24
3535 3738 3.428746 TTGTTTGCGCATGTGTTAGTT 57.571 38.095 12.75 0.00 0.00 2.24
3536 3739 4.553756 TTGTTTGCGCATGTGTTAGTTA 57.446 36.364 12.75 0.00 0.00 2.24
3537 3740 4.757799 TGTTTGCGCATGTGTTAGTTAT 57.242 36.364 12.75 0.00 0.00 1.89
3538 3741 4.717991 TGTTTGCGCATGTGTTAGTTATC 58.282 39.130 12.75 0.00 0.00 1.75
3539 3742 3.649870 TTGCGCATGTGTTAGTTATCG 57.350 42.857 12.75 0.00 0.00 2.92
3540 3743 2.882324 TGCGCATGTGTTAGTTATCGA 58.118 42.857 5.66 0.00 0.00 3.59
3541 3744 2.601314 TGCGCATGTGTTAGTTATCGAC 59.399 45.455 5.66 0.00 0.00 4.20
3542 3745 2.858344 GCGCATGTGTTAGTTATCGACT 59.142 45.455 0.30 0.00 42.55 4.18
3543 3746 4.039703 GCGCATGTGTTAGTTATCGACTA 58.960 43.478 0.30 0.00 39.86 2.59
3544 3747 4.146616 GCGCATGTGTTAGTTATCGACTAG 59.853 45.833 0.30 0.00 41.68 2.57
3545 3748 4.675565 CGCATGTGTTAGTTATCGACTAGG 59.324 45.833 0.00 0.00 41.68 3.02
3546 3749 4.982916 GCATGTGTTAGTTATCGACTAGGG 59.017 45.833 0.00 0.00 41.68 3.53
3547 3750 5.529791 CATGTGTTAGTTATCGACTAGGGG 58.470 45.833 0.00 0.00 41.68 4.79
3548 3751 3.956199 TGTGTTAGTTATCGACTAGGGGG 59.044 47.826 0.00 0.00 41.68 5.40
3574 3777 7.410120 GGGGGATGAATAGGCTATTTTTATG 57.590 40.000 20.12 0.00 0.00 1.90
3575 3778 7.182060 GGGGGATGAATAGGCTATTTTTATGA 58.818 38.462 20.12 2.68 0.00 2.15
3576 3779 7.673926 GGGGGATGAATAGGCTATTTTTATGAA 59.326 37.037 20.12 2.68 0.00 2.57
3577 3780 9.088987 GGGGATGAATAGGCTATTTTTATGAAA 57.911 33.333 20.12 1.47 0.00 2.69
3592 3795 7.979115 TTTTATGAAAGTCTTCAAAACACGG 57.021 32.000 0.00 0.00 44.64 4.94
3593 3796 4.568152 ATGAAAGTCTTCAAAACACGGG 57.432 40.909 0.00 0.00 44.64 5.28
3594 3797 2.685897 TGAAAGTCTTCAAAACACGGGG 59.314 45.455 0.00 0.00 38.65 5.73
3595 3798 1.687563 AAGTCTTCAAAACACGGGGG 58.312 50.000 0.00 0.00 0.00 5.40
3596 3799 0.822121 AGTCTTCAAAACACGGGGGC 60.822 55.000 0.00 0.00 0.00 5.80
3597 3800 0.822121 GTCTTCAAAACACGGGGGCT 60.822 55.000 0.00 0.00 0.00 5.19
3598 3801 0.106419 TCTTCAAAACACGGGGGCTT 60.106 50.000 0.00 0.00 0.00 4.35
3599 3802 0.750249 CTTCAAAACACGGGGGCTTT 59.250 50.000 0.00 0.00 0.00 3.51
3600 3803 0.461961 TTCAAAACACGGGGGCTTTG 59.538 50.000 0.00 0.00 0.00 2.77
3601 3804 0.395862 TCAAAACACGGGGGCTTTGA 60.396 50.000 7.51 7.51 35.88 2.69
3602 3805 0.461961 CAAAACACGGGGGCTTTGAA 59.538 50.000 3.76 0.00 31.77 2.69
3603 3806 0.750249 AAAACACGGGGGCTTTGAAG 59.250 50.000 0.00 0.00 0.00 3.02
3604 3807 0.106419 AAACACGGGGGCTTTGAAGA 60.106 50.000 0.00 0.00 0.00 2.87
3605 3808 0.822121 AACACGGGGGCTTTGAAGAC 60.822 55.000 0.00 0.00 0.00 3.01
3606 3809 1.228124 CACGGGGGCTTTGAAGACA 60.228 57.895 0.00 0.00 35.04 3.41
3607 3810 0.821711 CACGGGGGCTTTGAAGACAA 60.822 55.000 0.00 0.00 35.04 3.18
3608 3811 0.106419 ACGGGGGCTTTGAAGACAAA 60.106 50.000 0.00 0.00 42.66 2.83
3609 3812 1.256812 CGGGGGCTTTGAAGACAAAT 58.743 50.000 0.00 0.00 43.64 2.32
3610 3813 1.067635 CGGGGGCTTTGAAGACAAATG 60.068 52.381 0.00 0.00 43.64 2.32
3611 3814 2.247358 GGGGGCTTTGAAGACAAATGA 58.753 47.619 0.00 0.00 43.64 2.57
3612 3815 2.833943 GGGGGCTTTGAAGACAAATGAT 59.166 45.455 0.00 0.00 43.64 2.45
3613 3816 4.023291 GGGGGCTTTGAAGACAAATGATA 58.977 43.478 0.00 0.00 43.64 2.15
3614 3817 4.098501 GGGGGCTTTGAAGACAAATGATAG 59.901 45.833 0.00 0.00 43.64 2.08
3615 3818 4.949856 GGGGCTTTGAAGACAAATGATAGA 59.050 41.667 0.00 0.00 43.64 1.98
3616 3819 5.418840 GGGGCTTTGAAGACAAATGATAGAA 59.581 40.000 0.00 0.00 43.64 2.10
3617 3820 6.071391 GGGGCTTTGAAGACAAATGATAGAAA 60.071 38.462 0.00 0.00 43.64 2.52
3618 3821 7.364144 GGGGCTTTGAAGACAAATGATAGAAAT 60.364 37.037 0.00 0.00 43.64 2.17
3619 3822 7.490402 GGGCTTTGAAGACAAATGATAGAAATG 59.510 37.037 0.00 0.00 43.64 2.32
3620 3823 8.246180 GGCTTTGAAGACAAATGATAGAAATGA 58.754 33.333 0.00 0.00 43.64 2.57
3621 3824 9.630098 GCTTTGAAGACAAATGATAGAAATGAA 57.370 29.630 0.00 0.00 43.64 2.57
3623 3826 9.630098 TTTGAAGACAAATGATAGAAATGAAGC 57.370 29.630 0.00 0.00 40.47 3.86
3624 3827 8.571461 TGAAGACAAATGATAGAAATGAAGCT 57.429 30.769 0.00 0.00 0.00 3.74
3625 3828 9.671279 TGAAGACAAATGATAGAAATGAAGCTA 57.329 29.630 0.00 0.00 0.00 3.32
3635 3838 9.729281 TGATAGAAATGAAGCTATTGATATGCA 57.271 29.630 0.00 0.00 0.00 3.96
3637 3840 6.910995 AGAAATGAAGCTATTGATATGCAGC 58.089 36.000 0.00 0.00 0.00 5.25
3638 3841 4.941325 ATGAAGCTATTGATATGCAGCG 57.059 40.909 0.00 0.00 39.04 5.18
3639 3842 3.069289 TGAAGCTATTGATATGCAGCGG 58.931 45.455 0.00 0.00 39.04 5.52
3640 3843 3.244181 TGAAGCTATTGATATGCAGCGGA 60.244 43.478 0.00 0.00 39.04 5.54
3641 3844 3.407424 AGCTATTGATATGCAGCGGAA 57.593 42.857 0.00 0.00 39.04 4.30
3642 3845 3.332919 AGCTATTGATATGCAGCGGAAG 58.667 45.455 0.00 0.00 39.04 3.46
3643 3846 2.417933 GCTATTGATATGCAGCGGAAGG 59.582 50.000 0.00 0.00 0.00 3.46
3644 3847 2.645838 ATTGATATGCAGCGGAAGGT 57.354 45.000 0.00 0.00 46.81 3.50
3645 3848 3.769739 ATTGATATGCAGCGGAAGGTA 57.230 42.857 0.00 0.00 41.81 3.08
3646 3849 2.820059 TGATATGCAGCGGAAGGTAG 57.180 50.000 0.00 0.00 41.81 3.18
3647 3850 2.316108 TGATATGCAGCGGAAGGTAGA 58.684 47.619 0.00 0.00 41.81 2.59
3648 3851 2.035961 TGATATGCAGCGGAAGGTAGAC 59.964 50.000 0.00 0.00 41.81 2.59
3649 3852 1.776662 TATGCAGCGGAAGGTAGACT 58.223 50.000 0.00 0.00 41.81 3.24
3650 3853 1.776662 ATGCAGCGGAAGGTAGACTA 58.223 50.000 0.00 0.00 41.81 2.59
3651 3854 1.776662 TGCAGCGGAAGGTAGACTAT 58.223 50.000 0.00 0.00 41.81 2.12
3652 3855 2.940158 TGCAGCGGAAGGTAGACTATA 58.060 47.619 0.00 0.00 41.81 1.31
3653 3856 2.621998 TGCAGCGGAAGGTAGACTATAC 59.378 50.000 0.00 0.00 41.81 1.47
3654 3857 2.885894 GCAGCGGAAGGTAGACTATACT 59.114 50.000 0.00 0.00 41.81 2.12
3655 3858 4.070716 GCAGCGGAAGGTAGACTATACTA 58.929 47.826 0.00 0.00 41.81 1.82
3656 3859 4.154556 GCAGCGGAAGGTAGACTATACTAG 59.845 50.000 0.00 0.00 41.81 2.57
3657 3860 5.549347 CAGCGGAAGGTAGACTATACTAGA 58.451 45.833 0.00 0.00 41.81 2.43
3658 3861 5.409214 CAGCGGAAGGTAGACTATACTAGAC 59.591 48.000 0.00 0.00 41.81 2.59
3659 3862 5.071519 AGCGGAAGGTAGACTATACTAGACA 59.928 44.000 0.00 0.00 41.99 3.41
3660 3863 5.762218 GCGGAAGGTAGACTATACTAGACAA 59.238 44.000 0.00 0.00 0.00 3.18
3661 3864 6.073112 GCGGAAGGTAGACTATACTAGACAAG 60.073 46.154 0.00 0.00 0.00 3.16
3662 3865 6.073112 CGGAAGGTAGACTATACTAGACAAGC 60.073 46.154 0.00 0.00 0.00 4.01
3663 3866 6.207221 GGAAGGTAGACTATACTAGACAAGCC 59.793 46.154 0.00 0.00 0.00 4.35
3664 3867 6.263412 AGGTAGACTATACTAGACAAGCCA 57.737 41.667 0.00 0.00 0.00 4.75
3665 3868 6.854578 AGGTAGACTATACTAGACAAGCCAT 58.145 40.000 0.00 0.00 0.00 4.40
3666 3869 7.986704 AGGTAGACTATACTAGACAAGCCATA 58.013 38.462 0.00 0.00 0.00 2.74
3667 3870 8.104566 AGGTAGACTATACTAGACAAGCCATAG 58.895 40.741 0.00 0.00 33.04 2.23
3668 3871 7.884354 GGTAGACTATACTAGACAAGCCATAGT 59.116 40.741 0.00 0.00 38.52 2.12
3669 3872 7.989416 AGACTATACTAGACAAGCCATAGTC 57.011 40.000 10.22 10.22 44.54 2.59
3670 3873 7.519057 AGACTATACTAGACAAGCCATAGTCA 58.481 38.462 17.25 0.00 45.44 3.41
3671 3874 7.999545 AGACTATACTAGACAAGCCATAGTCAA 59.000 37.037 17.25 0.00 45.44 3.18
3672 3875 8.534954 ACTATACTAGACAAGCCATAGTCAAA 57.465 34.615 0.00 0.00 34.16 2.69
3673 3876 9.148879 ACTATACTAGACAAGCCATAGTCAAAT 57.851 33.333 0.00 0.00 34.16 2.32
3676 3879 9.988815 ATACTAGACAAGCCATAGTCAAATAAG 57.011 33.333 0.00 0.00 37.23 1.73
3677 3880 7.852263 ACTAGACAAGCCATAGTCAAATAAGT 58.148 34.615 0.00 0.00 37.23 2.24
3678 3881 8.978472 ACTAGACAAGCCATAGTCAAATAAGTA 58.022 33.333 0.00 0.00 37.23 2.24
3679 3882 9.817809 CTAGACAAGCCATAGTCAAATAAGTAA 57.182 33.333 0.00 0.00 37.23 2.24
3681 3884 9.113838 AGACAAGCCATAGTCAAATAAGTAATG 57.886 33.333 0.00 0.00 37.23 1.90
3682 3885 9.109393 GACAAGCCATAGTCAAATAAGTAATGA 57.891 33.333 0.00 0.00 34.93 2.57
3683 3886 9.461312 ACAAGCCATAGTCAAATAAGTAATGAA 57.539 29.630 0.00 0.00 0.00 2.57
3684 3887 9.941664 CAAGCCATAGTCAAATAAGTAATGAAG 57.058 33.333 0.00 0.00 0.00 3.02
3685 3888 9.905713 AAGCCATAGTCAAATAAGTAATGAAGA 57.094 29.630 0.00 0.00 0.00 2.87
3686 3889 9.553064 AGCCATAGTCAAATAAGTAATGAAGAG 57.447 33.333 0.00 0.00 0.00 2.85
3687 3890 9.547753 GCCATAGTCAAATAAGTAATGAAGAGA 57.452 33.333 0.00 0.00 0.00 3.10
3692 3895 9.507329 AGTCAAATAAGTAATGAAGAGAAAGCA 57.493 29.630 0.00 0.00 0.00 3.91
3698 3901 9.896645 ATAAGTAATGAAGAGAAAGCATGAAGA 57.103 29.630 0.00 0.00 0.00 2.87
3699 3902 7.608308 AGTAATGAAGAGAAAGCATGAAGAC 57.392 36.000 0.00 0.00 0.00 3.01
3700 3903 7.393216 AGTAATGAAGAGAAAGCATGAAGACT 58.607 34.615 0.00 0.00 0.00 3.24
3701 3904 8.535335 AGTAATGAAGAGAAAGCATGAAGACTA 58.465 33.333 0.00 0.00 0.00 2.59
3702 3905 9.323985 GTAATGAAGAGAAAGCATGAAGACTAT 57.676 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.394836 GAGGGCTGGAGGCTTCGT 61.395 66.667 0.00 0.00 41.46 3.85
175 177 1.000496 ACCGGAGAAGAAGAACACGTC 60.000 52.381 9.46 0.00 0.00 4.34
237 239 5.409520 TGCTAAGCTGTTGACAGAATAGTTG 59.590 40.000 14.98 0.00 46.59 3.16
246 248 3.503363 CCAAAGATGCTAAGCTGTTGACA 59.497 43.478 0.00 0.00 0.00 3.58
347 349 4.672587 ACTGCTAGCAAATCGATCCTAA 57.327 40.909 19.86 0.00 0.00 2.69
352 354 8.926710 GTGTATATAAACTGCTAGCAAATCGAT 58.073 33.333 19.86 10.82 0.00 3.59
373 375 7.391554 CCCGATGAAAAATAGGATCATGTGTAT 59.608 37.037 0.00 0.00 34.10 2.29
374 376 6.710295 CCCGATGAAAAATAGGATCATGTGTA 59.290 38.462 0.00 0.00 34.10 2.90
384 386 2.618709 GCAGGACCCGATGAAAAATAGG 59.381 50.000 0.00 0.00 0.00 2.57
385 387 3.278574 TGCAGGACCCGATGAAAAATAG 58.721 45.455 0.00 0.00 0.00 1.73
391 393 1.913951 ATGCTGCAGGACCCGATGAA 61.914 55.000 17.12 0.00 0.00 2.57
397 399 2.112898 CATTCATGCTGCAGGACCC 58.887 57.895 17.37 0.00 0.00 4.46
444 446 7.497925 AATATCTAGAAAACTCGGCAATTCC 57.502 36.000 0.00 0.00 0.00 3.01
465 467 5.382616 TCTGGCCGTCAGTCTAGAATAATA 58.617 41.667 0.00 0.00 43.76 0.98
500 502 2.139917 AGATTACACTGCGCAACGAAA 58.860 42.857 13.05 4.34 0.00 3.46
567 570 4.750021 TGCATCTTCTCTGAGCTGTAAT 57.250 40.909 0.00 0.00 0.00 1.89
700 707 5.462405 CACCTTATATTCTCTACGGACTGC 58.538 45.833 0.00 0.00 0.00 4.40
704 711 5.768662 CAGTCCACCTTATATTCTCTACGGA 59.231 44.000 0.00 0.00 0.00 4.69
732 739 1.609072 GTGGGACTTTTGAGCTTGGTC 59.391 52.381 0.00 0.00 0.00 4.02
788 795 2.689983 AGCTGTTGTTCTCCCTTTTGTG 59.310 45.455 0.00 0.00 0.00 3.33
789 796 2.952310 GAGCTGTTGTTCTCCCTTTTGT 59.048 45.455 0.00 0.00 0.00 2.83
792 799 2.173569 AGTGAGCTGTTGTTCTCCCTTT 59.826 45.455 0.00 0.00 0.00 3.11
793 800 1.771255 AGTGAGCTGTTGTTCTCCCTT 59.229 47.619 0.00 0.00 0.00 3.95
795 802 2.147150 GAAGTGAGCTGTTGTTCTCCC 58.853 52.381 0.00 0.00 0.00 4.30
796 803 2.838736 TGAAGTGAGCTGTTGTTCTCC 58.161 47.619 0.00 0.00 0.00 3.71
797 804 4.512944 TGATTGAAGTGAGCTGTTGTTCTC 59.487 41.667 0.00 0.00 0.00 2.87
800 807 4.454678 TCTGATTGAAGTGAGCTGTTGTT 58.545 39.130 0.00 0.00 0.00 2.83
801 808 4.077300 TCTGATTGAAGTGAGCTGTTGT 57.923 40.909 0.00 0.00 0.00 3.32
803 810 5.533903 ACATTTCTGATTGAAGTGAGCTGTT 59.466 36.000 0.00 0.00 42.68 3.16
804 811 5.068636 ACATTTCTGATTGAAGTGAGCTGT 58.931 37.500 0.00 0.00 42.68 4.40
806 813 7.934855 ATTACATTTCTGATTGAAGTGAGCT 57.065 32.000 7.67 0.00 42.68 4.09
807 814 8.887717 ACTATTACATTTCTGATTGAAGTGAGC 58.112 33.333 7.67 0.00 42.68 4.26
822 829 9.875708 TGGGCCTTTTATATCACTATTACATTT 57.124 29.630 4.53 0.00 0.00 2.32
823 830 9.875708 TTGGGCCTTTTATATCACTATTACATT 57.124 29.630 4.53 0.00 0.00 2.71
824 831 9.875708 TTTGGGCCTTTTATATCACTATTACAT 57.124 29.630 4.53 0.00 0.00 2.29
825 832 9.875708 ATTTGGGCCTTTTATATCACTATTACA 57.124 29.630 4.53 0.00 0.00 2.41
828 835 9.605951 ATCATTTGGGCCTTTTATATCACTATT 57.394 29.630 4.53 0.00 0.00 1.73
829 836 9.028284 CATCATTTGGGCCTTTTATATCACTAT 57.972 33.333 4.53 0.00 0.00 2.12
830 837 7.039784 GCATCATTTGGGCCTTTTATATCACTA 60.040 37.037 4.53 0.00 0.00 2.74
831 838 6.239402 GCATCATTTGGGCCTTTTATATCACT 60.239 38.462 4.53 0.00 0.00 3.41
832 839 5.928264 GCATCATTTGGGCCTTTTATATCAC 59.072 40.000 4.53 0.00 0.00 3.06
833 840 5.601729 TGCATCATTTGGGCCTTTTATATCA 59.398 36.000 4.53 0.00 0.00 2.15
834 841 6.100404 TGCATCATTTGGGCCTTTTATATC 57.900 37.500 4.53 0.00 0.00 1.63
835 842 5.511888 GCTGCATCATTTGGGCCTTTTATAT 60.512 40.000 4.53 0.00 0.00 0.86
836 843 4.202243 GCTGCATCATTTGGGCCTTTTATA 60.202 41.667 4.53 0.00 0.00 0.98
837 844 3.432608 GCTGCATCATTTGGGCCTTTTAT 60.433 43.478 4.53 0.00 0.00 1.40
838 845 2.093553 GCTGCATCATTTGGGCCTTTTA 60.094 45.455 4.53 0.00 0.00 1.52
839 846 1.339342 GCTGCATCATTTGGGCCTTTT 60.339 47.619 4.53 0.00 0.00 2.27
840 847 0.251073 GCTGCATCATTTGGGCCTTT 59.749 50.000 4.53 0.00 0.00 3.11
841 848 0.905809 TGCTGCATCATTTGGGCCTT 60.906 50.000 4.53 0.00 0.00 4.35
842 849 0.905809 TTGCTGCATCATTTGGGCCT 60.906 50.000 1.84 0.00 0.00 5.19
843 850 0.179468 ATTGCTGCATCATTTGGGCC 59.821 50.000 1.84 0.00 0.00 5.80
844 851 1.295792 CATTGCTGCATCATTTGGGC 58.704 50.000 1.84 0.00 0.00 5.36
856 863 0.038892 AACCGCAGAAAGCATTGCTG 60.039 50.000 12.82 1.29 46.13 4.41
857 864 0.675633 AAACCGCAGAAAGCATTGCT 59.324 45.000 5.03 5.03 46.13 3.91
858 865 0.785979 CAAACCGCAGAAAGCATTGC 59.214 50.000 0.00 0.00 46.13 3.56
859 866 0.785979 GCAAACCGCAGAAAGCATTG 59.214 50.000 0.00 0.00 46.13 2.82
860 867 0.675633 AGCAAACCGCAGAAAGCATT 59.324 45.000 0.00 0.00 46.13 3.56
861 868 0.675633 AAGCAAACCGCAGAAAGCAT 59.324 45.000 0.00 0.00 46.13 3.79
862 869 0.248990 CAAGCAAACCGCAGAAAGCA 60.249 50.000 0.00 0.00 46.13 3.91
863 870 0.249031 ACAAGCAAACCGCAGAAAGC 60.249 50.000 0.00 0.00 46.13 3.51
864 871 2.119457 GAACAAGCAAACCGCAGAAAG 58.881 47.619 0.00 0.00 46.13 2.62
865 872 1.748493 AGAACAAGCAAACCGCAGAAA 59.252 42.857 0.00 0.00 46.13 2.52
866 873 1.333619 GAGAACAAGCAAACCGCAGAA 59.666 47.619 0.00 0.00 46.13 3.02
867 874 0.944386 GAGAACAAGCAAACCGCAGA 59.056 50.000 0.00 0.00 46.13 4.26
868 875 0.947244 AGAGAACAAGCAAACCGCAG 59.053 50.000 0.00 0.00 46.13 5.18
869 876 0.662619 CAGAGAACAAGCAAACCGCA 59.337 50.000 0.00 0.00 46.13 5.69
870 877 0.944386 TCAGAGAACAAGCAAACCGC 59.056 50.000 0.00 0.00 42.91 5.68
871 878 4.245660 TCTATCAGAGAACAAGCAAACCG 58.754 43.478 0.00 0.00 0.00 4.44
872 879 5.065731 CCATCTATCAGAGAACAAGCAAACC 59.934 44.000 0.00 0.00 37.85 3.27
873 880 5.645497 ACCATCTATCAGAGAACAAGCAAAC 59.355 40.000 0.00 0.00 37.85 2.93
874 881 5.645067 CACCATCTATCAGAGAACAAGCAAA 59.355 40.000 0.00 0.00 37.85 3.68
875 882 5.181009 CACCATCTATCAGAGAACAAGCAA 58.819 41.667 0.00 0.00 37.85 3.91
876 883 4.763073 CACCATCTATCAGAGAACAAGCA 58.237 43.478 0.00 0.00 37.85 3.91
877 884 3.559242 GCACCATCTATCAGAGAACAAGC 59.441 47.826 0.00 0.00 37.85 4.01
878 885 4.125703 GGCACCATCTATCAGAGAACAAG 58.874 47.826 0.00 0.00 37.85 3.16
879 886 4.142609 GGCACCATCTATCAGAGAACAA 57.857 45.455 0.00 0.00 37.85 2.83
880 887 3.827008 GGCACCATCTATCAGAGAACA 57.173 47.619 0.00 0.00 37.85 3.18
971 989 0.739462 CGATGGCAAGCGTGAACCTA 60.739 55.000 2.99 0.00 0.00 3.08
1231 1249 2.408368 GCATAAAAACGCCTGAGTTTGC 59.592 45.455 0.00 0.00 42.81 3.68
1540 1567 5.356190 CCTCTGTTGCAATCACATATTCAGT 59.644 40.000 0.59 0.00 0.00 3.41
1853 1880 8.690884 TCTTGTCTGCATATAGAGAATATAGCC 58.309 37.037 0.00 0.00 30.72 3.93
1921 1951 9.646427 GTATTTGCAAACAACCTGGAATATAAA 57.354 29.630 15.41 0.00 34.87 1.40
1922 1952 9.030452 AGTATTTGCAAACAACCTGGAATATAA 57.970 29.630 15.41 0.00 34.87 0.98
1971 2001 7.498239 GGAAACAGACTAAACTTACCAAGTCTT 59.502 37.037 1.23 0.00 44.81 3.01
2183 2213 1.526686 TGATATTGCCAGGCGCCAG 60.527 57.895 31.54 22.32 36.24 4.85
2184 2214 1.823470 GTGATATTGCCAGGCGCCA 60.823 57.895 31.54 7.75 36.24 5.69
2185 2215 0.250295 TAGTGATATTGCCAGGCGCC 60.250 55.000 21.89 21.89 36.24 6.53
2186 2216 1.813513 ATAGTGATATTGCCAGGCGC 58.186 50.000 7.03 0.00 38.31 6.53
2187 2217 4.820897 TCTTATAGTGATATTGCCAGGCG 58.179 43.478 7.03 0.00 0.00 5.52
2188 2218 6.486657 TGTTTCTTATAGTGATATTGCCAGGC 59.513 38.462 3.66 3.66 0.00 4.85
2189 2219 8.450578 TTGTTTCTTATAGTGATATTGCCAGG 57.549 34.615 0.00 0.00 0.00 4.45
2421 2454 3.157087 GGGTCAATGACAGTTCCAATGT 58.843 45.455 15.86 0.00 33.68 2.71
2457 2490 0.183492 ACAGTTTGGCTTGCCTCTGA 59.817 50.000 25.03 3.07 0.00 3.27
2663 2696 3.953712 TCTAACTCATCAAAGGCGTCA 57.046 42.857 0.00 0.00 0.00 4.35
2703 2736 1.053264 CAGGCTACTGGATGCTCCCT 61.053 60.000 0.00 0.00 41.13 4.20
2735 2768 2.092914 GGCATGAGCAGGGTAGTAGTTT 60.093 50.000 0.00 0.00 44.61 2.66
2794 2827 5.680594 TTCAAGAATATTTTGGGCATGCT 57.319 34.783 18.92 0.00 0.00 3.79
2853 2886 7.788026 TCCGACCAAAATAGAACTACATACAT 58.212 34.615 0.00 0.00 0.00 2.29
2885 2918 6.040729 CCATGGAAATATGTACATCAGGCAAA 59.959 38.462 12.68 0.00 0.00 3.68
3129 3179 9.552114 GAAGACATCTGAACATTTATGACTTTG 57.448 33.333 0.00 0.00 35.51 2.77
3142 3192 6.603201 TCCCCATATTTTGAAGACATCTGAAC 59.397 38.462 0.00 0.00 0.00 3.18
3233 3286 4.303603 CGATGGAATGCGGCGCTG 62.304 66.667 33.26 13.18 0.00 5.18
3297 3360 2.632987 TCCATCATCGTCTAGTCCGA 57.367 50.000 9.13 9.13 38.89 4.55
3422 3612 6.620877 ACAGATCCAGGTTTTATCACAGTA 57.379 37.500 0.00 0.00 0.00 2.74
3459 3649 1.836802 TTTGCCTAGCACATGCATGA 58.163 45.000 32.75 9.69 45.16 3.07
3462 3652 1.962807 AGTTTTTGCCTAGCACATGCA 59.037 42.857 6.64 0.00 45.16 3.96
3503 3706 8.167345 CACATGCGCAAACAAAAATTATTGATA 58.833 29.630 17.11 0.00 34.38 2.15
3505 3708 6.018425 ACACATGCGCAAACAAAAATTATTGA 60.018 30.769 17.11 0.00 34.38 2.57
3527 3730 4.581077 CCCCCTAGTCGATAACTAACAC 57.419 50.000 0.00 0.00 39.98 3.32
3550 3753 7.182060 TCATAAAAATAGCCTATTCATCCCCC 58.818 38.462 0.00 0.00 0.00 5.40
3551 3754 8.650143 TTCATAAAAATAGCCTATTCATCCCC 57.350 34.615 0.00 0.00 0.00 4.81
3566 3769 9.030301 CCGTGTTTTGAAGACTTTCATAAAAAT 57.970 29.630 0.00 0.00 42.60 1.82
3567 3770 7.489757 CCCGTGTTTTGAAGACTTTCATAAAAA 59.510 33.333 0.00 0.00 42.60 1.94
3568 3771 6.975772 CCCGTGTTTTGAAGACTTTCATAAAA 59.024 34.615 0.00 0.00 42.60 1.52
3569 3772 6.460399 CCCCGTGTTTTGAAGACTTTCATAAA 60.460 38.462 0.00 0.00 42.60 1.40
3570 3773 5.009210 CCCCGTGTTTTGAAGACTTTCATAA 59.991 40.000 0.00 0.00 42.60 1.90
3571 3774 4.517453 CCCCGTGTTTTGAAGACTTTCATA 59.483 41.667 0.00 0.00 42.60 2.15
3572 3775 3.317993 CCCCGTGTTTTGAAGACTTTCAT 59.682 43.478 0.00 0.00 42.60 2.57
3573 3776 2.685897 CCCCGTGTTTTGAAGACTTTCA 59.314 45.455 0.00 0.00 41.44 2.69
3574 3777 2.034179 CCCCCGTGTTTTGAAGACTTTC 59.966 50.000 0.00 0.00 0.00 2.62
3575 3778 2.028876 CCCCCGTGTTTTGAAGACTTT 58.971 47.619 0.00 0.00 0.00 2.66
3576 3779 1.687563 CCCCCGTGTTTTGAAGACTT 58.312 50.000 0.00 0.00 0.00 3.01
3577 3780 0.822121 GCCCCCGTGTTTTGAAGACT 60.822 55.000 0.00 0.00 0.00 3.24
3578 3781 0.822121 AGCCCCCGTGTTTTGAAGAC 60.822 55.000 0.00 0.00 0.00 3.01
3579 3782 0.106419 AAGCCCCCGTGTTTTGAAGA 60.106 50.000 0.00 0.00 0.00 2.87
3580 3783 0.750249 AAAGCCCCCGTGTTTTGAAG 59.250 50.000 0.00 0.00 0.00 3.02
3581 3784 0.461961 CAAAGCCCCCGTGTTTTGAA 59.538 50.000 0.00 0.00 33.50 2.69
3582 3785 0.395862 TCAAAGCCCCCGTGTTTTGA 60.396 50.000 5.26 5.26 37.25 2.69
3583 3786 0.461961 TTCAAAGCCCCCGTGTTTTG 59.538 50.000 0.00 0.00 33.09 2.44
3584 3787 0.750249 CTTCAAAGCCCCCGTGTTTT 59.250 50.000 0.00 0.00 0.00 2.43
3585 3788 0.106419 TCTTCAAAGCCCCCGTGTTT 60.106 50.000 0.00 0.00 0.00 2.83
3586 3789 0.822121 GTCTTCAAAGCCCCCGTGTT 60.822 55.000 0.00 0.00 0.00 3.32
3587 3790 1.228154 GTCTTCAAAGCCCCCGTGT 60.228 57.895 0.00 0.00 0.00 4.49
3588 3791 0.821711 TTGTCTTCAAAGCCCCCGTG 60.822 55.000 0.00 0.00 0.00 4.94
3589 3792 0.106419 TTTGTCTTCAAAGCCCCCGT 60.106 50.000 0.00 0.00 38.44 5.28
3590 3793 1.067635 CATTTGTCTTCAAAGCCCCCG 60.068 52.381 0.00 0.00 45.01 5.73
3591 3794 2.247358 TCATTTGTCTTCAAAGCCCCC 58.753 47.619 0.00 0.00 45.01 5.40
3592 3795 4.949856 TCTATCATTTGTCTTCAAAGCCCC 59.050 41.667 0.00 0.00 45.01 5.80
3593 3796 6.515272 TTCTATCATTTGTCTTCAAAGCCC 57.485 37.500 0.00 0.00 45.01 5.19
3594 3797 8.246180 TCATTTCTATCATTTGTCTTCAAAGCC 58.754 33.333 0.00 0.00 45.01 4.35
3595 3798 9.630098 TTCATTTCTATCATTTGTCTTCAAAGC 57.370 29.630 0.00 0.00 45.01 3.51
3597 3800 9.630098 GCTTCATTTCTATCATTTGTCTTCAAA 57.370 29.630 0.00 0.00 45.71 2.69
3598 3801 9.017509 AGCTTCATTTCTATCATTTGTCTTCAA 57.982 29.630 0.00 0.00 0.00 2.69
3599 3802 8.571461 AGCTTCATTTCTATCATTTGTCTTCA 57.429 30.769 0.00 0.00 0.00 3.02
3609 3812 9.729281 TGCATATCAATAGCTTCATTTCTATCA 57.271 29.630 0.00 0.00 0.00 2.15
3611 3814 8.675504 GCTGCATATCAATAGCTTCATTTCTAT 58.324 33.333 0.00 0.00 33.53 1.98
3612 3815 7.148523 CGCTGCATATCAATAGCTTCATTTCTA 60.149 37.037 0.00 0.00 34.13 2.10
3613 3816 6.348295 CGCTGCATATCAATAGCTTCATTTCT 60.348 38.462 0.00 0.00 34.13 2.52
3614 3817 5.793952 CGCTGCATATCAATAGCTTCATTTC 59.206 40.000 0.00 0.00 34.13 2.17
3615 3818 5.335426 CCGCTGCATATCAATAGCTTCATTT 60.335 40.000 0.00 0.00 34.13 2.32
3616 3819 4.155462 CCGCTGCATATCAATAGCTTCATT 59.845 41.667 0.00 0.00 34.13 2.57
3617 3820 3.688185 CCGCTGCATATCAATAGCTTCAT 59.312 43.478 0.00 0.00 34.13 2.57
3618 3821 3.069289 CCGCTGCATATCAATAGCTTCA 58.931 45.455 0.00 0.00 34.13 3.02
3619 3822 3.329386 TCCGCTGCATATCAATAGCTTC 58.671 45.455 0.00 0.00 34.13 3.86
3620 3823 3.407424 TCCGCTGCATATCAATAGCTT 57.593 42.857 0.00 0.00 34.13 3.74
3621 3824 3.332919 CTTCCGCTGCATATCAATAGCT 58.667 45.455 0.00 0.00 34.13 3.32
3622 3825 2.417933 CCTTCCGCTGCATATCAATAGC 59.582 50.000 0.00 0.00 0.00 2.97
3623 3826 3.668447 ACCTTCCGCTGCATATCAATAG 58.332 45.455 0.00 0.00 0.00 1.73
3624 3827 3.769739 ACCTTCCGCTGCATATCAATA 57.230 42.857 0.00 0.00 0.00 1.90
3625 3828 2.645838 ACCTTCCGCTGCATATCAAT 57.354 45.000 0.00 0.00 0.00 2.57
3626 3829 2.698274 TCTACCTTCCGCTGCATATCAA 59.302 45.455 0.00 0.00 0.00 2.57
3627 3830 2.035961 GTCTACCTTCCGCTGCATATCA 59.964 50.000 0.00 0.00 0.00 2.15
3628 3831 2.297597 AGTCTACCTTCCGCTGCATATC 59.702 50.000 0.00 0.00 0.00 1.63
3629 3832 2.320781 AGTCTACCTTCCGCTGCATAT 58.679 47.619 0.00 0.00 0.00 1.78
3630 3833 1.776662 AGTCTACCTTCCGCTGCATA 58.223 50.000 0.00 0.00 0.00 3.14
3631 3834 1.776662 TAGTCTACCTTCCGCTGCAT 58.223 50.000 0.00 0.00 0.00 3.96
3632 3835 1.776662 ATAGTCTACCTTCCGCTGCA 58.223 50.000 0.00 0.00 0.00 4.41
3633 3836 2.885894 AGTATAGTCTACCTTCCGCTGC 59.114 50.000 0.00 0.00 0.00 5.25
3634 3837 5.409214 GTCTAGTATAGTCTACCTTCCGCTG 59.591 48.000 0.00 0.00 40.38 5.18
3635 3838 5.071519 TGTCTAGTATAGTCTACCTTCCGCT 59.928 44.000 0.00 0.00 40.38 5.52
3636 3839 5.303971 TGTCTAGTATAGTCTACCTTCCGC 58.696 45.833 0.00 0.00 40.38 5.54
3637 3840 6.073112 GCTTGTCTAGTATAGTCTACCTTCCG 60.073 46.154 0.00 0.00 40.38 4.30
3638 3841 6.207221 GGCTTGTCTAGTATAGTCTACCTTCC 59.793 46.154 0.00 0.00 40.38 3.46
3639 3842 6.771749 TGGCTTGTCTAGTATAGTCTACCTTC 59.228 42.308 0.00 0.00 40.38 3.46
3640 3843 6.670617 TGGCTTGTCTAGTATAGTCTACCTT 58.329 40.000 0.00 0.00 40.38 3.50
3641 3844 6.263412 TGGCTTGTCTAGTATAGTCTACCT 57.737 41.667 0.00 0.00 40.38 3.08
3642 3845 7.884354 ACTATGGCTTGTCTAGTATAGTCTACC 59.116 40.741 0.00 0.00 40.38 3.18
3643 3846 8.851541 ACTATGGCTTGTCTAGTATAGTCTAC 57.148 38.462 0.00 0.00 40.38 2.59
3644 3847 8.657712 TGACTATGGCTTGTCTAGTATAGTCTA 58.342 37.037 23.70 15.69 43.82 2.59
3645 3848 7.519057 TGACTATGGCTTGTCTAGTATAGTCT 58.481 38.462 23.70 6.53 43.82 3.24
3646 3849 7.747155 TGACTATGGCTTGTCTAGTATAGTC 57.253 40.000 20.48 20.48 43.79 2.59
3647 3850 8.534954 TTTGACTATGGCTTGTCTAGTATAGT 57.465 34.615 10.61 10.61 40.38 2.12
3650 3853 9.988815 CTTATTTGACTATGGCTTGTCTAGTAT 57.011 33.333 0.00 0.00 34.57 2.12
3651 3854 8.978472 ACTTATTTGACTATGGCTTGTCTAGTA 58.022 33.333 0.00 0.00 34.57 1.82
3652 3855 7.852263 ACTTATTTGACTATGGCTTGTCTAGT 58.148 34.615 0.00 0.00 34.57 2.57
3653 3856 9.817809 TTACTTATTTGACTATGGCTTGTCTAG 57.182 33.333 0.00 0.00 34.57 2.43
3655 3858 9.113838 CATTACTTATTTGACTATGGCTTGTCT 57.886 33.333 0.00 0.00 34.57 3.41
3656 3859 9.109393 TCATTACTTATTTGACTATGGCTTGTC 57.891 33.333 0.00 0.00 0.00 3.18
3657 3860 9.461312 TTCATTACTTATTTGACTATGGCTTGT 57.539 29.630 0.00 0.00 0.00 3.16
3658 3861 9.941664 CTTCATTACTTATTTGACTATGGCTTG 57.058 33.333 0.00 0.00 0.00 4.01
3659 3862 9.905713 TCTTCATTACTTATTTGACTATGGCTT 57.094 29.630 0.00 0.00 0.00 4.35
3660 3863 9.553064 CTCTTCATTACTTATTTGACTATGGCT 57.447 33.333 0.00 0.00 0.00 4.75
3661 3864 9.547753 TCTCTTCATTACTTATTTGACTATGGC 57.452 33.333 0.00 0.00 0.00 4.40
3666 3869 9.507329 TGCTTTCTCTTCATTACTTATTTGACT 57.493 29.630 0.00 0.00 0.00 3.41
3672 3875 9.896645 TCTTCATGCTTTCTCTTCATTACTTAT 57.103 29.630 0.00 0.00 0.00 1.73
3673 3876 9.155975 GTCTTCATGCTTTCTCTTCATTACTTA 57.844 33.333 0.00 0.00 0.00 2.24
3674 3877 7.882271 AGTCTTCATGCTTTCTCTTCATTACTT 59.118 33.333 0.00 0.00 0.00 2.24
3675 3878 7.393216 AGTCTTCATGCTTTCTCTTCATTACT 58.607 34.615 0.00 0.00 0.00 2.24
3676 3879 7.608308 AGTCTTCATGCTTTCTCTTCATTAC 57.392 36.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.