Multiple sequence alignment - TraesCS5B01G446500

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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 TraesCS5B01G446500 chr5B 100.000 5743 0 0 1 5743 617837284 617831542 0.000000e+00 10539
1 TraesCS5B01G446500 chr5B 99.033 1448 12 1 1520 2967 136674241 136672796 0.000000e+00 2595
2 TraesCS5B01G446500 chr5B 99.099 777 7 0 1 777 617845478 617844702 0.000000e+00 1397
3 TraesCS5B01G446500 chr5A 90.778 2494 162 42 3282 5743 622782497 622780040 0.000000e+00 3269
4 TraesCS5B01G446500 chr5A 98.820 1441 17 0 1520 2960 182536743 182538183 0.000000e+00 2567
5 TraesCS5B01G446500 chr5A 90.172 641 23 6 883 1520 622783439 622782836 0.000000e+00 798
6 TraesCS5B01G446500 chr5A 96.759 216 7 0 2967 3182 622782844 622782629 1.520000e-95 361
7 TraesCS5B01G446500 chr5A 91.765 85 7 0 779 863 622821761 622821677 1.010000e-22 119
8 TraesCS5B01G446500 chr1B 99.447 1447 8 0 1520 2966 630569976 630568530 0.000000e+00 2628
9 TraesCS5B01G446500 chr1A 99.378 1447 9 0 1520 2966 44330933 44329487 0.000000e+00 2623
10 TraesCS5B01G446500 chr1A 99.033 1448 14 0 1520 2967 108801652 108803099 0.000000e+00 2597
11 TraesCS5B01G446500 chr1A 96.685 1448 45 3 1520 2966 185850567 185852012 0.000000e+00 2405
12 TraesCS5B01G446500 chr1A 99.426 1046 5 1 1520 2565 44361007 44359963 0.000000e+00 1897
13 TraesCS5B01G446500 chr4A 99.034 1450 14 0 1520 2969 725883264 725881815 0.000000e+00 2601
14 TraesCS5B01G446500 chr4A 98.464 781 9 3 1 778 400798904 400799684 0.000000e+00 1373
15 TraesCS5B01G446500 chr2B 98.894 1447 16 0 1520 2966 73396860 73398306 0.000000e+00 2584
16 TraesCS5B01G446500 chr2B 84.228 1547 210 17 3280 4804 762520019 762518485 0.000000e+00 1474
17 TraesCS5B01G446500 chr2B 98.331 779 11 2 1 778 89051441 89052218 0.000000e+00 1365
18 TraesCS5B01G446500 chr2B 84.415 1341 187 12 3317 4646 762533358 762532029 0.000000e+00 1299
19 TraesCS5B01G446500 chr2B 90.766 444 26 5 995 1438 762520847 762520419 3.860000e-161 579
20 TraesCS5B01G446500 chr2B 90.766 444 26 5 995 1438 762537163 762536735 3.860000e-161 579
21 TraesCS5B01G446500 chr2B 94.907 216 11 0 2967 3182 762520367 762520152 7.130000e-89 339
22 TraesCS5B01G446500 chr2B 94.907 216 11 0 2967 3182 762536683 762536468 7.130000e-89 339
23 TraesCS5B01G446500 chr2B 96.875 64 2 0 1457 1520 762520422 762520359 2.190000e-19 108
24 TraesCS5B01G446500 chr2B 96.875 64 2 0 1457 1520 762536738 762536675 2.190000e-19 108
25 TraesCS5B01G446500 chr5D 90.407 1647 102 20 3280 4919 498556204 498554607 0.000000e+00 2115
26 TraesCS5B01G446500 chr5D 91.223 638 19 5 883 1520 498557145 498556545 0.000000e+00 833
27 TraesCS5B01G446500 chr5D 93.694 222 8 1 2967 3182 498556553 498556332 1.540000e-85 327
28 TraesCS5B01G446500 chr5D 96.032 126 5 0 5618 5743 498551145 498551020 7.540000e-49 206
29 TraesCS5B01G446500 chr2D 85.536 1521 205 11 3286 4804 621559701 621558194 0.000000e+00 1576
30 TraesCS5B01G446500 chr2D 89.734 526 23 5 995 1520 621560565 621560071 1.350000e-180 643
31 TraesCS5B01G446500 chr2D 93.981 216 13 0 2967 3182 621560079 621559864 1.540000e-85 327
32 TraesCS5B01G446500 chr4B 98.845 779 8 1 1 778 65128316 65129094 0.000000e+00 1387
33 TraesCS5B01G446500 chr6B 98.464 781 9 3 1 778 92876994 92876214 0.000000e+00 1373
34 TraesCS5B01G446500 chrUn 98.331 779 11 2 1 777 308761286 308760508 0.000000e+00 1365
35 TraesCS5B01G446500 chr3B 98.333 780 10 3 1 778 149962803 149963581 0.000000e+00 1365
36 TraesCS5B01G446500 chr3B 89.755 654 57 4 2315 2966 766911745 766912390 0.000000e+00 828
37 TraesCS5B01G446500 chr3A 98.331 779 11 2 1 777 198387546 198386768 0.000000e+00 1365
38 TraesCS5B01G446500 chr2A 98.214 784 9 5 1 781 423517653 423516872 0.000000e+00 1365


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 TraesCS5B01G446500 chr5B 617831542 617837284 5742 True 10539.000000 10539 100.000000 1 5743 1 chr5B.!!$R2 5742
1 TraesCS5B01G446500 chr5B 136672796 136674241 1445 True 2595.000000 2595 99.033000 1520 2967 1 chr5B.!!$R1 1447
2 TraesCS5B01G446500 chr5B 617844702 617845478 776 True 1397.000000 1397 99.099000 1 777 1 chr5B.!!$R3 776
3 TraesCS5B01G446500 chr5A 182536743 182538183 1440 False 2567.000000 2567 98.820000 1520 2960 1 chr5A.!!$F1 1440
4 TraesCS5B01G446500 chr5A 622780040 622783439 3399 True 1476.000000 3269 92.569667 883 5743 3 chr5A.!!$R2 4860
5 TraesCS5B01G446500 chr1B 630568530 630569976 1446 True 2628.000000 2628 99.447000 1520 2966 1 chr1B.!!$R1 1446
6 TraesCS5B01G446500 chr1A 44329487 44330933 1446 True 2623.000000 2623 99.378000 1520 2966 1 chr1A.!!$R1 1446
7 TraesCS5B01G446500 chr1A 108801652 108803099 1447 False 2597.000000 2597 99.033000 1520 2967 1 chr1A.!!$F1 1447
8 TraesCS5B01G446500 chr1A 185850567 185852012 1445 False 2405.000000 2405 96.685000 1520 2966 1 chr1A.!!$F2 1446
9 TraesCS5B01G446500 chr1A 44359963 44361007 1044 True 1897.000000 1897 99.426000 1520 2565 1 chr1A.!!$R2 1045
10 TraesCS5B01G446500 chr4A 725881815 725883264 1449 True 2601.000000 2601 99.034000 1520 2969 1 chr4A.!!$R1 1449
11 TraesCS5B01G446500 chr4A 400798904 400799684 780 False 1373.000000 1373 98.464000 1 778 1 chr4A.!!$F1 777
12 TraesCS5B01G446500 chr2B 73396860 73398306 1446 False 2584.000000 2584 98.894000 1520 2966 1 chr2B.!!$F1 1446
13 TraesCS5B01G446500 chr2B 89051441 89052218 777 False 1365.000000 1365 98.331000 1 778 1 chr2B.!!$F2 777
14 TraesCS5B01G446500 chr2B 762518485 762520847 2362 True 625.000000 1474 91.694000 995 4804 4 chr2B.!!$R1 3809
15 TraesCS5B01G446500 chr2B 762532029 762537163 5134 True 581.250000 1299 91.740750 995 4646 4 chr2B.!!$R2 3651
16 TraesCS5B01G446500 chr5D 498551020 498557145 6125 True 870.250000 2115 92.839000 883 5743 4 chr5D.!!$R1 4860
17 TraesCS5B01G446500 chr2D 621558194 621560565 2371 True 848.666667 1576 89.750333 995 4804 3 chr2D.!!$R1 3809
18 TraesCS5B01G446500 chr4B 65128316 65129094 778 False 1387.000000 1387 98.845000 1 778 1 chr4B.!!$F1 777
19 TraesCS5B01G446500 chr6B 92876214 92876994 780 True 1373.000000 1373 98.464000 1 778 1 chr6B.!!$R1 777
20 TraesCS5B01G446500 chrUn 308760508 308761286 778 True 1365.000000 1365 98.331000 1 777 1 chrUn.!!$R1 776
21 TraesCS5B01G446500 chr3B 149962803 149963581 778 False 1365.000000 1365 98.333000 1 778 1 chr3B.!!$F1 777
22 TraesCS5B01G446500 chr3B 766911745 766912390 645 False 828.000000 828 89.755000 2315 2966 1 chr3B.!!$F2 651
23 TraesCS5B01G446500 chr3A 198386768 198387546 778 True 1365.000000 1365 98.331000 1 777 1 chr3A.!!$R1 776
24 TraesCS5B01G446500 chr2A 423516872 423517653 781 True 1365.000000 1365 98.214000 1 781 1 chr2A.!!$R1 780

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
842 846 0.795698 CACGCCAACGATGACATCAA 59.204 50.000 15.58 0.0 43.93 2.57 F
1318 1325 1.187087 CTACCAGTTCCGCCTCTTCT 58.813 55.000 0.00 0.0 0.00 2.85 F
2969 2979 2.603473 TAGCTCCGCCACTGGTGT 60.603 61.111 7.86 0.0 0.00 4.16 F
3278 3369 0.112412 GGGGCCTCAAAAGAACCAGA 59.888 55.000 0.84 0.0 0.00 3.86 F
3810 6858 0.901827 ACCATACCACGTCTGCATCA 59.098 50.000 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 1961 1.070601 GGTTTTGGCCAGATTTGCAGT 59.929 47.619 5.11 0.00 0.00 4.40 R
3258 3274 0.178964 CTGGTTCTTTTGAGGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96 R
4175 7228 0.108207 GGATCATCTGCTCCCTGTGG 59.892 60.000 0.00 0.00 0.00 4.17 R
4281 7334 1.255667 TTGAGGCACCGGTAGTCCTC 61.256 60.000 28.96 28.96 40.46 3.71 R
5514 11825 1.004595 GATACCGGAAACAAGCGACC 58.995 55.000 9.46 0.00 0.00 4.79 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
38 41 5.540337 CAGGATTGGTAGATAGTCAGGCTTA 59.460 44.000 0.00 0.00 0.00 3.09
440 444 3.498397 GGGAAATGTCACGCGATGAATAT 59.502 43.478 15.93 8.28 39.72 1.28
533 537 1.282248 CGCTGATGACCGACACGTTT 61.282 55.000 0.00 0.00 0.00 3.60
780 784 2.122769 TCGGGGTCCTGACAACCA 60.123 61.111 9.84 0.00 38.62 3.67
781 785 2.032071 CGGGGTCCTGACAACCAC 59.968 66.667 9.84 0.00 38.62 4.16
782 786 2.032071 GGGGTCCTGACAACCACG 59.968 66.667 0.00 0.00 38.62 4.94
783 787 2.668550 GGGTCCTGACAACCACGC 60.669 66.667 0.00 0.00 38.62 5.34
784 788 2.668550 GGTCCTGACAACCACGCC 60.669 66.667 0.00 0.00 36.75 5.68
785 789 3.041940 GTCCTGACAACCACGCCG 61.042 66.667 0.00 0.00 0.00 6.46
786 790 4.308458 TCCTGACAACCACGCCGG 62.308 66.667 0.00 0.00 42.50 6.13
791 795 3.869473 GACAACCACGCCGGCAGTA 62.869 63.158 28.98 0.00 39.03 2.74
792 796 2.666862 CAACCACGCCGGCAGTAA 60.667 61.111 28.98 0.00 39.03 2.24
793 797 2.667199 AACCACGCCGGCAGTAAC 60.667 61.111 28.98 0.00 39.03 2.50
794 798 3.463728 AACCACGCCGGCAGTAACA 62.464 57.895 28.98 0.00 39.03 2.41
795 799 3.419759 CCACGCCGGCAGTAACAC 61.420 66.667 28.98 0.00 0.00 3.32
796 800 2.663520 CACGCCGGCAGTAACACA 60.664 61.111 28.98 0.00 0.00 3.72
797 801 2.032634 CACGCCGGCAGTAACACAT 61.033 57.895 28.98 0.00 0.00 3.21
798 802 1.302192 ACGCCGGCAGTAACACATT 60.302 52.632 28.98 0.00 0.00 2.71
799 803 1.296056 ACGCCGGCAGTAACACATTC 61.296 55.000 28.98 0.00 0.00 2.67
800 804 1.423845 GCCGGCAGTAACACATTCG 59.576 57.895 24.80 0.00 0.00 3.34
801 805 1.017177 GCCGGCAGTAACACATTCGA 61.017 55.000 24.80 0.00 0.00 3.71
802 806 1.651987 CCGGCAGTAACACATTCGAT 58.348 50.000 0.00 0.00 0.00 3.59
803 807 1.327460 CCGGCAGTAACACATTCGATG 59.673 52.381 0.00 0.00 0.00 3.84
804 808 1.999735 CGGCAGTAACACATTCGATGT 59.000 47.619 0.00 0.00 46.22 3.06
805 809 2.415168 CGGCAGTAACACATTCGATGTT 59.585 45.455 7.91 7.91 42.70 2.71
806 810 3.724716 CGGCAGTAACACATTCGATGTTG 60.725 47.826 12.09 1.69 42.70 3.33
807 811 3.163594 GCAGTAACACATTCGATGTTGC 58.836 45.455 12.09 10.81 42.70 4.17
808 812 3.407252 CAGTAACACATTCGATGTTGCG 58.593 45.455 12.09 5.07 44.48 4.85
809 813 3.064207 AGTAACACATTCGATGTTGCGT 58.936 40.909 12.09 0.00 44.48 5.24
810 814 2.314561 AACACATTCGATGTTGCGTG 57.685 45.000 2.18 0.00 42.70 5.34
811 815 1.507562 ACACATTCGATGTTGCGTGA 58.492 45.000 0.00 0.00 42.70 4.35
812 816 1.194547 ACACATTCGATGTTGCGTGAC 59.805 47.619 0.00 0.00 42.70 3.67
813 817 1.194322 CACATTCGATGTTGCGTGACA 59.806 47.619 0.00 0.00 42.70 3.58
814 818 1.870402 ACATTCGATGTTGCGTGACAA 59.130 42.857 0.00 0.00 41.63 3.18
824 828 3.276091 CGTGACAACGGCTTGCCA 61.276 61.111 12.45 0.00 46.25 4.92
825 829 2.331451 GTGACAACGGCTTGCCAC 59.669 61.111 12.45 0.00 34.16 5.01
826 830 3.276091 TGACAACGGCTTGCCACG 61.276 61.111 12.45 1.22 0.00 4.94
827 831 4.683334 GACAACGGCTTGCCACGC 62.683 66.667 12.45 0.00 0.00 5.34
834 838 3.737172 GCTTGCCACGCCAACGAT 61.737 61.111 0.00 0.00 43.93 3.73
835 839 2.176546 CTTGCCACGCCAACGATG 59.823 61.111 0.00 0.00 43.93 3.84
836 840 2.281139 TTGCCACGCCAACGATGA 60.281 55.556 0.00 0.00 43.93 2.92
837 841 2.513065 CTTGCCACGCCAACGATGAC 62.513 60.000 0.00 0.00 43.93 3.06
838 842 3.047280 GCCACGCCAACGATGACA 61.047 61.111 0.00 0.00 43.93 3.58
839 843 2.398554 GCCACGCCAACGATGACAT 61.399 57.895 0.00 0.00 43.93 3.06
840 844 1.715585 CCACGCCAACGATGACATC 59.284 57.895 5.28 5.28 43.93 3.06
841 845 1.018752 CCACGCCAACGATGACATCA 61.019 55.000 15.58 0.00 43.93 3.07
842 846 0.795698 CACGCCAACGATGACATCAA 59.204 50.000 15.58 0.00 43.93 2.57
843 847 1.398041 CACGCCAACGATGACATCAAT 59.602 47.619 15.58 0.00 43.93 2.57
844 848 1.398041 ACGCCAACGATGACATCAATG 59.602 47.619 15.58 12.16 43.93 2.82
845 849 1.398041 CGCCAACGATGACATCAATGT 59.602 47.619 15.58 2.71 42.80 2.71
846 850 2.159531 CGCCAACGATGACATCAATGTT 60.160 45.455 15.58 8.50 41.00 2.71
847 851 3.173599 GCCAACGATGACATCAATGTTG 58.826 45.455 19.65 19.65 41.95 3.33
848 852 3.173599 CCAACGATGACATCAATGTTGC 58.826 45.455 20.55 0.00 41.95 4.17
849 853 3.119743 CCAACGATGACATCAATGTTGCT 60.120 43.478 20.55 0.00 41.95 3.91
850 854 4.094739 CCAACGATGACATCAATGTTGCTA 59.905 41.667 20.55 0.00 41.95 3.49
851 855 5.260900 CAACGATGACATCAATGTTGCTAG 58.739 41.667 15.58 0.00 41.95 3.42
852 856 4.758688 ACGATGACATCAATGTTGCTAGA 58.241 39.130 15.58 0.00 41.95 2.43
853 857 4.807834 ACGATGACATCAATGTTGCTAGAG 59.192 41.667 15.58 0.00 41.95 2.43
854 858 4.210746 CGATGACATCAATGTTGCTAGAGG 59.789 45.833 15.58 0.00 41.95 3.69
855 859 4.558226 TGACATCAATGTTGCTAGAGGT 57.442 40.909 0.00 0.00 41.95 3.85
856 860 5.675684 TGACATCAATGTTGCTAGAGGTA 57.324 39.130 0.00 0.00 41.95 3.08
857 861 6.048732 TGACATCAATGTTGCTAGAGGTAA 57.951 37.500 0.00 0.00 41.95 2.85
858 862 6.108687 TGACATCAATGTTGCTAGAGGTAAG 58.891 40.000 0.00 0.00 41.95 2.34
859 863 6.054860 ACATCAATGTTGCTAGAGGTAAGT 57.945 37.500 0.00 0.00 37.90 2.24
860 864 5.877012 ACATCAATGTTGCTAGAGGTAAGTG 59.123 40.000 0.00 0.00 37.90 3.16
861 865 5.483685 TCAATGTTGCTAGAGGTAAGTGT 57.516 39.130 0.00 0.00 0.00 3.55
862 866 6.599356 TCAATGTTGCTAGAGGTAAGTGTA 57.401 37.500 0.00 0.00 0.00 2.90
863 867 7.182817 TCAATGTTGCTAGAGGTAAGTGTAT 57.817 36.000 0.00 0.00 0.00 2.29
864 868 7.041721 TCAATGTTGCTAGAGGTAAGTGTATG 58.958 38.462 0.00 0.00 0.00 2.39
865 869 6.791867 ATGTTGCTAGAGGTAAGTGTATGA 57.208 37.500 0.00 0.00 0.00 2.15
866 870 6.208988 TGTTGCTAGAGGTAAGTGTATGAG 57.791 41.667 0.00 0.00 0.00 2.90
867 871 5.715279 TGTTGCTAGAGGTAAGTGTATGAGT 59.285 40.000 0.00 0.00 0.00 3.41
868 872 5.836821 TGCTAGAGGTAAGTGTATGAGTG 57.163 43.478 0.00 0.00 0.00 3.51
869 873 4.098044 TGCTAGAGGTAAGTGTATGAGTGC 59.902 45.833 0.00 0.00 0.00 4.40
870 874 4.098044 GCTAGAGGTAAGTGTATGAGTGCA 59.902 45.833 0.00 0.00 0.00 4.57
871 875 5.394224 GCTAGAGGTAAGTGTATGAGTGCAA 60.394 44.000 0.00 0.00 0.00 4.08
872 876 5.078411 AGAGGTAAGTGTATGAGTGCAAG 57.922 43.478 0.00 0.00 0.00 4.01
873 877 4.772624 AGAGGTAAGTGTATGAGTGCAAGA 59.227 41.667 0.00 0.00 0.00 3.02
874 878 4.822026 AGGTAAGTGTATGAGTGCAAGAC 58.178 43.478 0.00 0.00 0.00 3.01
875 879 3.612860 GGTAAGTGTATGAGTGCAAGACG 59.387 47.826 0.00 0.00 0.00 4.18
876 880 3.660501 AAGTGTATGAGTGCAAGACGA 57.339 42.857 0.00 0.00 0.00 4.20
877 881 3.876274 AGTGTATGAGTGCAAGACGAT 57.124 42.857 0.00 0.00 0.00 3.73
878 882 3.515630 AGTGTATGAGTGCAAGACGATG 58.484 45.455 0.00 0.00 0.00 3.84
879 883 3.056536 AGTGTATGAGTGCAAGACGATGT 60.057 43.478 0.00 0.00 0.00 3.06
880 884 4.157840 AGTGTATGAGTGCAAGACGATGTA 59.842 41.667 0.00 0.00 0.00 2.29
881 885 4.500837 GTGTATGAGTGCAAGACGATGTAG 59.499 45.833 0.00 0.00 0.00 2.74
955 959 6.116680 CTTCCTGAGCACAGTCATTAATTC 57.883 41.667 10.37 0.00 42.05 2.17
956 960 5.164620 TCCTGAGCACAGTCATTAATTCA 57.835 39.130 10.37 0.00 42.05 2.57
957 961 5.559770 TCCTGAGCACAGTCATTAATTCAA 58.440 37.500 10.37 0.00 42.05 2.69
958 962 5.645067 TCCTGAGCACAGTCATTAATTCAAG 59.355 40.000 10.37 0.00 42.05 3.02
959 963 5.300969 TGAGCACAGTCATTAATTCAAGC 57.699 39.130 0.00 0.00 0.00 4.01
960 964 4.156556 TGAGCACAGTCATTAATTCAAGCC 59.843 41.667 0.00 0.00 0.00 4.35
972 976 8.677300 TCATTAATTCAAGCCTAAGTTAAGCTG 58.323 33.333 6.77 2.52 36.84 4.24
1318 1325 1.187087 CTACCAGTTCCGCCTCTTCT 58.813 55.000 0.00 0.00 0.00 2.85
2969 2979 2.603473 TAGCTCCGCCACTGGTGT 60.603 61.111 7.86 0.00 0.00 4.16
2970 2980 2.842394 CTAGCTCCGCCACTGGTGTG 62.842 65.000 7.86 1.78 43.45 3.82
3182 3198 4.159321 GGACAAGGTACTCCTACAAGGTAC 59.841 50.000 0.00 0.00 44.35 3.34
3183 3199 4.744237 ACAAGGTACTCCTACAAGGTACA 58.256 43.478 0.00 0.00 44.35 2.90
3184 3200 4.525874 ACAAGGTACTCCTACAAGGTACAC 59.474 45.833 0.00 0.00 44.35 2.90
3185 3201 4.671596 AGGTACTCCTACAAGGTACACT 57.328 45.455 0.00 0.00 43.12 3.55
3186 3202 5.786121 AGGTACTCCTACAAGGTACACTA 57.214 43.478 0.00 0.00 43.12 2.74
3187 3203 5.753716 AGGTACTCCTACAAGGTACACTAG 58.246 45.833 0.00 0.00 43.12 2.57
3188 3204 5.490357 AGGTACTCCTACAAGGTACACTAGA 59.510 44.000 0.00 0.00 43.12 2.43
3189 3205 5.588246 GGTACTCCTACAAGGTACACTAGAC 59.412 48.000 0.00 0.00 37.95 2.59
3190 3206 5.252586 ACTCCTACAAGGTACACTAGACA 57.747 43.478 0.00 0.00 36.53 3.41
3191 3207 5.008980 ACTCCTACAAGGTACACTAGACAC 58.991 45.833 0.00 0.00 36.53 3.67
3192 3208 4.989277 TCCTACAAGGTACACTAGACACA 58.011 43.478 0.00 0.00 36.53 3.72
3193 3209 5.577100 TCCTACAAGGTACACTAGACACAT 58.423 41.667 0.00 0.00 36.53 3.21
3195 3211 7.177184 TCCTACAAGGTACACTAGACACATAA 58.823 38.462 0.00 0.00 36.53 1.90
3196 3212 7.121759 TCCTACAAGGTACACTAGACACATAAC 59.878 40.741 0.00 0.00 36.53 1.89
3197 3213 6.912951 ACAAGGTACACTAGACACATAACT 57.087 37.500 0.00 0.00 0.00 2.24
3199 3215 7.376615 ACAAGGTACACTAGACACATAACTTC 58.623 38.462 0.00 0.00 0.00 3.01
3201 3217 6.014647 AGGTACACTAGACACATAACTTCCA 58.985 40.000 0.00 0.00 0.00 3.53
3203 3219 6.071503 GGTACACTAGACACATAACTTCCACT 60.072 42.308 0.00 0.00 0.00 4.00
3204 3220 6.420913 ACACTAGACACATAACTTCCACTT 57.579 37.500 0.00 0.00 0.00 3.16
3205 3221 6.456501 ACACTAGACACATAACTTCCACTTC 58.543 40.000 0.00 0.00 0.00 3.01
3209 3225 7.819900 ACTAGACACATAACTTCCACTTCAATC 59.180 37.037 0.00 0.00 0.00 2.67
3210 3226 6.533730 AGACACATAACTTCCACTTCAATCA 58.466 36.000 0.00 0.00 0.00 2.57
3213 3229 8.862325 ACACATAACTTCCACTTCAATCATAA 57.138 30.769 0.00 0.00 0.00 1.90
3238 3254 7.585286 TTTGAATCATTTGAACTAGCAATGC 57.415 32.000 0.00 0.00 0.00 3.56
3242 3258 6.956299 ATCATTTGAACTAGCAATGCAAAC 57.044 33.333 8.35 0.00 32.09 2.93
3243 3259 5.840715 TCATTTGAACTAGCAATGCAAACA 58.159 33.333 8.35 0.00 32.09 2.83
3245 3261 6.587226 TCATTTGAACTAGCAATGCAAACATC 59.413 34.615 8.35 0.00 34.62 3.06
3246 3262 4.439305 TGAACTAGCAATGCAAACATCC 57.561 40.909 8.35 0.00 34.62 3.51
3249 3265 5.355071 TGAACTAGCAATGCAAACATCCTAG 59.645 40.000 8.35 0.00 34.62 3.02
3250 3266 3.629398 ACTAGCAATGCAAACATCCTAGC 59.371 43.478 8.35 0.00 34.62 3.42
3252 3268 3.094572 AGCAATGCAAACATCCTAGCTT 58.905 40.909 8.35 0.00 34.62 3.74
3258 3274 3.008375 TGCAAACATCCTAGCTTCAGTCT 59.992 43.478 0.00 0.00 0.00 3.24
3260 3276 3.902881 AACATCCTAGCTTCAGTCTGG 57.097 47.619 0.00 0.00 0.00 3.86
3261 3277 2.114616 ACATCCTAGCTTCAGTCTGGG 58.885 52.381 0.00 0.00 33.96 4.45
3262 3278 1.415659 CATCCTAGCTTCAGTCTGGGG 59.584 57.143 0.00 0.00 33.54 4.96
3263 3279 0.978146 TCCTAGCTTCAGTCTGGGGC 60.978 60.000 0.00 5.04 33.54 5.80
3264 3280 1.524482 CTAGCTTCAGTCTGGGGCC 59.476 63.158 0.00 0.00 0.00 5.80
3266 3282 0.978146 TAGCTTCAGTCTGGGGCCTC 60.978 60.000 0.84 0.00 0.00 4.70
3267 3283 2.596851 GCTTCAGTCTGGGGCCTCA 61.597 63.158 4.49 4.49 0.00 3.86
3268 3284 2.069776 CTTCAGTCTGGGGCCTCAA 58.930 57.895 6.84 0.00 0.00 3.02
3269 3285 0.401738 CTTCAGTCTGGGGCCTCAAA 59.598 55.000 6.84 0.00 0.00 2.69
3270 3286 0.850100 TTCAGTCTGGGGCCTCAAAA 59.150 50.000 6.84 0.00 0.00 2.44
3271 3287 0.401738 TCAGTCTGGGGCCTCAAAAG 59.598 55.000 6.84 0.00 0.00 2.27
3272 3288 0.401738 CAGTCTGGGGCCTCAAAAGA 59.598 55.000 6.84 0.00 0.00 2.52
3273 3289 1.149101 AGTCTGGGGCCTCAAAAGAA 58.851 50.000 6.84 0.00 0.00 2.52
3277 3368 0.178964 TGGGGCCTCAAAAGAACCAG 60.179 55.000 0.25 0.00 0.00 4.00
3278 3369 0.112412 GGGGCCTCAAAAGAACCAGA 59.888 55.000 0.84 0.00 0.00 3.86
3309 3401 3.414549 TCGTCTGAAAGTTGGCAAAAC 57.585 42.857 0.00 0.00 33.76 2.43
3321 3413 8.424274 AAAGTTGGCAAAACTTCATTTTAGAG 57.576 30.769 14.89 0.00 38.50 2.43
3363 6399 9.894783 GATATCTAGTCTAGTTTATGACGCAAA 57.105 33.333 6.77 0.00 38.16 3.68
3393 6435 3.628008 TCCATAGCTCGTAGTTCCAAGA 58.372 45.455 0.00 0.00 0.00 3.02
3405 6449 5.293569 CGTAGTTCCAAGATCCAACCATAAC 59.706 44.000 0.00 0.00 0.00 1.89
3411 6455 2.906354 AGATCCAACCATAACGAGCAC 58.094 47.619 0.00 0.00 0.00 4.40
3434 6478 3.002656 CCAACATCATCAGCATTCGGTAC 59.997 47.826 0.00 0.00 0.00 3.34
3438 6482 4.699735 ACATCATCAGCATTCGGTACAAAA 59.300 37.500 0.00 0.00 0.00 2.44
3461 6508 3.634504 AGCCATTCTATGCCACATTCAA 58.365 40.909 0.00 0.00 0.00 2.69
3809 6857 1.290203 CACCATACCACGTCTGCATC 58.710 55.000 0.00 0.00 0.00 3.91
3810 6858 0.901827 ACCATACCACGTCTGCATCA 59.098 50.000 0.00 0.00 0.00 3.07
3926 6979 2.357009 GCCATACAGCATCAAGTTCAGG 59.643 50.000 0.00 0.00 0.00 3.86
4004 7057 2.338577 ACTACTCCATTGATGCAGGC 57.661 50.000 0.00 0.00 0.00 4.85
4037 7090 2.344025 GTCTACATGTCCACCGAAACC 58.656 52.381 0.00 0.00 0.00 3.27
4055 7108 3.050275 GACTTCACCCGTGGCAGC 61.050 66.667 0.00 0.00 0.00 5.25
4067 7120 1.002366 GTGGCAGCGATCAGTACAAG 58.998 55.000 0.00 0.00 0.00 3.16
4281 7334 1.315257 CGAGAGGTTTTGCCCCATGG 61.315 60.000 4.14 4.14 38.26 3.66
4284 7337 0.972471 GAGGTTTTGCCCCATGGAGG 60.972 60.000 15.22 14.13 38.26 4.30
4302 7355 1.445582 GACTACCGGTGCCTCAACG 60.446 63.158 19.93 0.00 44.86 4.10
4412 7465 2.584608 GACCACCCTGATGTCCCG 59.415 66.667 0.00 0.00 0.00 5.14
4429 7482 1.734477 CGATATTCCCTCAGCCGCG 60.734 63.158 0.00 0.00 0.00 6.46
4500 7553 0.610687 GAGGGAGAGGTTGACACTGG 59.389 60.000 0.00 0.00 0.00 4.00
4551 7604 3.561310 CCATGACATGGTCGAAATACTGG 59.439 47.826 24.15 0.00 45.54 4.00
4559 7612 2.709475 GAAATACTGGCGCCGCAG 59.291 61.111 23.90 17.51 0.00 5.18
4623 7676 0.030908 GCCGGAGAAGATGAGGTACG 59.969 60.000 5.05 0.00 0.00 3.67
4699 7752 6.369799 GCTTTGCTGTTAGAAAGAAGAAGAG 58.630 40.000 0.00 0.00 31.89 2.85
4735 7791 2.432510 GGAGTCCTGTACAAGATGAGGG 59.567 54.545 0.41 0.00 0.00 4.30
4760 7817 2.163613 CTGATTGGTTCGCCCTTTTACC 59.836 50.000 0.00 0.00 36.08 2.85
4773 7830 2.427812 CCTTTTACCCGTTTGTGTTGGT 59.572 45.455 0.00 0.00 34.85 3.67
4774 7831 3.631227 CCTTTTACCCGTTTGTGTTGGTA 59.369 43.478 0.00 0.00 32.27 3.25
4775 7832 4.097589 CCTTTTACCCGTTTGTGTTGGTAA 59.902 41.667 0.00 0.00 40.59 2.85
4804 7862 4.023963 GCTCTTCCTTTTCCACTGTAACAC 60.024 45.833 0.00 0.00 0.00 3.32
4807 7865 6.126409 TCTTCCTTTTCCACTGTAACACATT 58.874 36.000 0.00 0.00 0.00 2.71
4842 7900 3.660501 ATGTCTAGACACGACAGCAAA 57.339 42.857 27.41 1.00 45.05 3.68
4843 7901 3.446310 TGTCTAGACACGACAGCAAAA 57.554 42.857 21.74 0.00 36.54 2.44
4845 7903 4.377021 TGTCTAGACACGACAGCAAAAAT 58.623 39.130 21.74 0.00 36.54 1.82
4846 7904 4.211164 TGTCTAGACACGACAGCAAAAATG 59.789 41.667 21.74 0.00 36.54 2.32
4847 7905 4.447724 GTCTAGACACGACAGCAAAAATGA 59.552 41.667 18.20 0.00 0.00 2.57
4848 7906 3.609103 AGACACGACAGCAAAAATGAC 57.391 42.857 0.00 0.00 0.00 3.06
4911 7976 2.300597 TACGATCTCGACACGCGGTG 62.301 60.000 12.47 9.20 43.02 4.94
4957 11264 2.531912 CAGCGCTTACTGATGTCTTACG 59.468 50.000 7.50 0.00 40.25 3.18
4967 11274 8.687292 TTACTGATGTCTTACGGATGTACTAT 57.313 34.615 0.00 0.00 0.00 2.12
5042 11349 4.998671 TCATTGTGGTGTGTTGATTGTT 57.001 36.364 0.00 0.00 0.00 2.83
5108 11415 7.940137 TGAATAAAAGCCAGTAGGTTTCTGTAA 59.060 33.333 0.00 0.00 45.29 2.41
5136 11443 0.741574 TCGAAGCACGTTGTTGGTGT 60.742 50.000 0.00 0.00 43.13 4.16
5165 11472 8.567948 ACCATGCTTGTAAAAGAATATATTCGG 58.432 33.333 17.69 11.21 41.56 4.30
5166 11473 8.567948 CCATGCTTGTAAAAGAATATATTCGGT 58.432 33.333 17.69 8.87 41.56 4.69
5170 11477 8.609176 GCTTGTAAAAGAATATATTCGGTGTGA 58.391 33.333 17.69 2.42 41.56 3.58
5173 11480 9.309516 TGTAAAAGAATATATTCGGTGTGAGAC 57.690 33.333 17.69 10.45 41.56 3.36
5175 11482 8.425577 AAAAGAATATATTCGGTGTGAGACAG 57.574 34.615 17.69 0.00 41.56 3.51
5182 11489 3.469008 TCGGTGTGAGACAGTCATTTT 57.531 42.857 2.66 0.00 37.56 1.82
5202 11512 9.566530 TCATTTTAACATTTGATTACCATGTCG 57.433 29.630 0.00 0.00 30.58 4.35
5256 11566 4.201990 GCTGGAGATTTTCTTCGCATTCAT 60.202 41.667 0.00 0.00 0.00 2.57
5371 11681 0.394192 CACACCAAGAGCAGGAGTCA 59.606 55.000 0.00 0.00 0.00 3.41
5372 11682 1.131638 ACACCAAGAGCAGGAGTCAA 58.868 50.000 0.00 0.00 0.00 3.18
5384 11694 1.202818 AGGAGTCAAGACAAAGTGGCC 60.203 52.381 0.00 0.00 0.00 5.36
5386 11696 1.604278 GAGTCAAGACAAAGTGGCCAC 59.396 52.381 29.22 29.22 0.00 5.01
5398 11708 1.909302 AGTGGCCACAACTGCTATACT 59.091 47.619 36.39 9.43 0.00 2.12
5399 11709 2.093447 AGTGGCCACAACTGCTATACTC 60.093 50.000 36.39 5.31 0.00 2.59
5412 11722 2.268298 CTATACTCCACACAACACGGC 58.732 52.381 0.00 0.00 0.00 5.68
5430 11740 3.119990 ACGGCGAACAATTTAACCAGATG 60.120 43.478 16.62 0.00 0.00 2.90
5431 11741 3.179048 GGCGAACAATTTAACCAGATGC 58.821 45.455 0.00 0.00 0.00 3.91
5433 11743 4.485163 GCGAACAATTTAACCAGATGCTT 58.515 39.130 0.00 0.00 0.00 3.91
5434 11744 4.324402 GCGAACAATTTAACCAGATGCTTG 59.676 41.667 0.00 0.00 0.00 4.01
5435 11745 5.460646 CGAACAATTTAACCAGATGCTTGT 58.539 37.500 0.00 0.00 0.00 3.16
5436 11746 5.920273 CGAACAATTTAACCAGATGCTTGTT 59.080 36.000 0.00 0.00 37.87 2.83
5437 11747 6.088085 CGAACAATTTAACCAGATGCTTGTTC 59.912 38.462 12.75 12.75 43.50 3.18
5438 11748 6.403866 ACAATTTAACCAGATGCTTGTTCA 57.596 33.333 0.00 0.00 0.00 3.18
5439 11749 6.449698 ACAATTTAACCAGATGCTTGTTCAG 58.550 36.000 0.00 0.00 0.00 3.02
5480 11791 2.296792 CAATGTATGCATCGGTTGGGA 58.703 47.619 0.19 0.00 33.50 4.37
5512 11823 0.937304 CTGTCCACTTGTGTTGTCGG 59.063 55.000 0.00 0.00 0.00 4.79
5514 11825 1.885388 TCCACTTGTGTTGTCGGCG 60.885 57.895 0.00 0.00 0.00 6.46
5517 11828 1.885850 ACTTGTGTTGTCGGCGGTC 60.886 57.895 7.21 1.06 0.00 4.79
5532 11843 0.738412 CGGTCGCTTGTTTCCGGTAT 60.738 55.000 0.00 0.00 39.41 2.73
5540 11851 1.271856 TGTTTCCGGTATCTCTGCCA 58.728 50.000 0.00 0.00 0.00 4.92
5582 11893 0.778815 GCAGCGTATCATGCTACGAC 59.221 55.000 28.02 19.53 45.64 4.34
5609 11920 1.226435 GCTCTGGTACTCAGACGCG 60.226 63.158 3.53 3.53 46.71 6.01
5695 12006 1.138883 TCTCGGCATCGCACACTAC 59.861 57.895 0.00 0.00 36.13 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 9.638176 AGACATCTATAAATGAAAAAGGCTGAT 57.362 29.630 0.00 0.00 0.00 2.90
440 444 2.050350 CGGGCTAACAGGACTCCGA 61.050 63.158 0.00 0.00 39.83 4.55
533 537 0.466739 GCATCCATGACCCAGCATCA 60.467 55.000 0.00 0.00 0.00 3.07
779 783 1.573829 AATGTGTTACTGCCGGCGTG 61.574 55.000 26.82 22.00 0.00 5.34
780 784 1.296056 GAATGTGTTACTGCCGGCGT 61.296 55.000 23.90 23.67 0.00 5.68
781 785 1.423845 GAATGTGTTACTGCCGGCG 59.576 57.895 23.90 18.98 0.00 6.46
782 786 1.017177 TCGAATGTGTTACTGCCGGC 61.017 55.000 22.73 22.73 0.00 6.13
783 787 1.327460 CATCGAATGTGTTACTGCCGG 59.673 52.381 0.00 0.00 0.00 6.13
784 788 1.999735 ACATCGAATGTGTTACTGCCG 59.000 47.619 0.00 0.00 43.01 5.69
785 789 3.747193 CAACATCGAATGTGTTACTGCC 58.253 45.455 2.72 0.00 44.07 4.85
786 790 3.163594 GCAACATCGAATGTGTTACTGC 58.836 45.455 2.72 0.64 44.07 4.40
787 791 3.120683 ACGCAACATCGAATGTGTTACTG 60.121 43.478 2.72 0.00 44.07 2.74
788 792 3.064207 ACGCAACATCGAATGTGTTACT 58.936 40.909 2.72 0.00 44.07 2.24
789 793 3.120820 TCACGCAACATCGAATGTGTTAC 60.121 43.478 11.30 2.47 44.07 2.50
790 794 3.060602 TCACGCAACATCGAATGTGTTA 58.939 40.909 11.30 3.57 44.07 2.41
791 795 1.870402 TCACGCAACATCGAATGTGTT 59.130 42.857 11.30 5.09 44.07 3.32
792 796 1.194547 GTCACGCAACATCGAATGTGT 59.805 47.619 8.94 8.94 44.07 3.72
793 797 1.194322 TGTCACGCAACATCGAATGTG 59.806 47.619 7.86 7.86 44.07 3.21
795 799 2.592796 TTGTCACGCAACATCGAATG 57.407 45.000 0.00 0.00 31.07 2.67
804 808 2.712539 CAAGCCGTTGTCACGCAA 59.287 55.556 0.00 0.00 45.72 4.85
805 809 3.947841 GCAAGCCGTTGTCACGCA 61.948 61.111 0.00 0.00 45.72 5.24
806 810 4.683334 GGCAAGCCGTTGTCACGC 62.683 66.667 0.00 0.00 45.72 5.34
807 811 3.276091 TGGCAAGCCGTTGTCACG 61.276 61.111 6.60 0.00 43.47 4.35
809 813 3.276091 CGTGGCAAGCCGTTGTCA 61.276 61.111 6.60 0.00 46.18 3.58
810 814 4.683334 GCGTGGCAAGCCGTTGTC 62.683 66.667 14.76 0.00 38.89 3.18
817 821 3.737172 ATCGTTGGCGTGGCAAGC 61.737 61.111 17.36 17.36 39.49 4.01
818 822 2.176546 CATCGTTGGCGTGGCAAG 59.823 61.111 9.28 0.00 39.49 4.01
819 823 2.281139 TCATCGTTGGCGTGGCAA 60.281 55.556 4.57 4.57 39.49 4.52
820 824 3.047280 GTCATCGTTGGCGTGGCA 61.047 61.111 0.00 0.00 39.49 4.92
821 825 2.309764 GATGTCATCGTTGGCGTGGC 62.310 60.000 0.00 0.00 39.49 5.01
822 826 1.018752 TGATGTCATCGTTGGCGTGG 61.019 55.000 8.29 0.00 39.49 4.94
823 827 0.795698 TTGATGTCATCGTTGGCGTG 59.204 50.000 8.29 0.00 39.49 5.34
824 828 1.398041 CATTGATGTCATCGTTGGCGT 59.602 47.619 8.29 0.00 39.49 5.68
825 829 1.398041 ACATTGATGTCATCGTTGGCG 59.602 47.619 15.41 2.79 35.87 5.69
826 830 3.173599 CAACATTGATGTCATCGTTGGC 58.826 45.455 17.63 0.00 40.80 4.52
827 831 3.119743 AGCAACATTGATGTCATCGTTGG 60.120 43.478 22.72 10.99 40.80 3.77
828 832 4.087510 AGCAACATTGATGTCATCGTTG 57.912 40.909 19.65 19.65 40.80 4.10
829 833 5.178061 TCTAGCAACATTGATGTCATCGTT 58.822 37.500 8.29 3.91 40.80 3.85
830 834 4.758688 TCTAGCAACATTGATGTCATCGT 58.241 39.130 8.29 0.00 40.80 3.73
831 835 4.210746 CCTCTAGCAACATTGATGTCATCG 59.789 45.833 8.29 0.00 40.80 3.84
832 836 5.121811 ACCTCTAGCAACATTGATGTCATC 58.878 41.667 5.83 5.83 40.80 2.92
833 837 5.108187 ACCTCTAGCAACATTGATGTCAT 57.892 39.130 0.00 0.00 40.80 3.06
834 838 4.558226 ACCTCTAGCAACATTGATGTCA 57.442 40.909 0.00 0.00 40.80 3.58
835 839 6.036517 CACTTACCTCTAGCAACATTGATGTC 59.963 42.308 0.00 0.00 40.80 3.06
836 840 5.877012 CACTTACCTCTAGCAACATTGATGT 59.123 40.000 0.00 0.00 44.20 3.06
837 841 5.877012 ACACTTACCTCTAGCAACATTGATG 59.123 40.000 0.00 0.00 0.00 3.07
838 842 6.054860 ACACTTACCTCTAGCAACATTGAT 57.945 37.500 0.00 0.00 0.00 2.57
839 843 5.483685 ACACTTACCTCTAGCAACATTGA 57.516 39.130 0.00 0.00 0.00 2.57
840 844 7.041721 TCATACACTTACCTCTAGCAACATTG 58.958 38.462 0.00 0.00 0.00 2.82
841 845 7.093289 ACTCATACACTTACCTCTAGCAACATT 60.093 37.037 0.00 0.00 0.00 2.71
842 846 6.381420 ACTCATACACTTACCTCTAGCAACAT 59.619 38.462 0.00 0.00 0.00 2.71
843 847 5.715279 ACTCATACACTTACCTCTAGCAACA 59.285 40.000 0.00 0.00 0.00 3.33
844 848 6.037098 CACTCATACACTTACCTCTAGCAAC 58.963 44.000 0.00 0.00 0.00 4.17
845 849 5.394224 GCACTCATACACTTACCTCTAGCAA 60.394 44.000 0.00 0.00 0.00 3.91
846 850 4.098044 GCACTCATACACTTACCTCTAGCA 59.902 45.833 0.00 0.00 0.00 3.49
847 851 4.098044 TGCACTCATACACTTACCTCTAGC 59.902 45.833 0.00 0.00 0.00 3.42
848 852 5.836821 TGCACTCATACACTTACCTCTAG 57.163 43.478 0.00 0.00 0.00 2.43
849 853 5.949952 TCTTGCACTCATACACTTACCTCTA 59.050 40.000 0.00 0.00 0.00 2.43
850 854 4.772624 TCTTGCACTCATACACTTACCTCT 59.227 41.667 0.00 0.00 0.00 3.69
851 855 4.865365 GTCTTGCACTCATACACTTACCTC 59.135 45.833 0.00 0.00 0.00 3.85
852 856 4.618460 CGTCTTGCACTCATACACTTACCT 60.618 45.833 0.00 0.00 0.00 3.08
853 857 3.612860 CGTCTTGCACTCATACACTTACC 59.387 47.826 0.00 0.00 0.00 2.85
854 858 4.482386 TCGTCTTGCACTCATACACTTAC 58.518 43.478 0.00 0.00 0.00 2.34
855 859 4.776795 TCGTCTTGCACTCATACACTTA 57.223 40.909 0.00 0.00 0.00 2.24
856 860 3.660501 TCGTCTTGCACTCATACACTT 57.339 42.857 0.00 0.00 0.00 3.16
857 861 3.056536 ACATCGTCTTGCACTCATACACT 60.057 43.478 0.00 0.00 0.00 3.55
858 862 3.254060 ACATCGTCTTGCACTCATACAC 58.746 45.455 0.00 0.00 0.00 2.90
859 863 3.592898 ACATCGTCTTGCACTCATACA 57.407 42.857 0.00 0.00 0.00 2.29
860 864 4.500837 CACTACATCGTCTTGCACTCATAC 59.499 45.833 0.00 0.00 0.00 2.39
861 865 4.398044 TCACTACATCGTCTTGCACTCATA 59.602 41.667 0.00 0.00 0.00 2.15
862 866 3.193479 TCACTACATCGTCTTGCACTCAT 59.807 43.478 0.00 0.00 0.00 2.90
863 867 2.556622 TCACTACATCGTCTTGCACTCA 59.443 45.455 0.00 0.00 0.00 3.41
864 868 3.217599 TCACTACATCGTCTTGCACTC 57.782 47.619 0.00 0.00 0.00 3.51
865 869 3.005897 AGTTCACTACATCGTCTTGCACT 59.994 43.478 0.00 0.00 0.00 4.40
866 870 3.121944 CAGTTCACTACATCGTCTTGCAC 59.878 47.826 0.00 0.00 0.00 4.57
867 871 3.005367 TCAGTTCACTACATCGTCTTGCA 59.995 43.478 0.00 0.00 0.00 4.08
868 872 3.575630 TCAGTTCACTACATCGTCTTGC 58.424 45.455 0.00 0.00 0.00 4.01
869 873 6.366061 TCATTTCAGTTCACTACATCGTCTTG 59.634 38.462 0.00 0.00 0.00 3.02
870 874 6.455647 TCATTTCAGTTCACTACATCGTCTT 58.544 36.000 0.00 0.00 0.00 3.01
871 875 6.025749 TCATTTCAGTTCACTACATCGTCT 57.974 37.500 0.00 0.00 0.00 4.18
872 876 6.670927 GCTTCATTTCAGTTCACTACATCGTC 60.671 42.308 0.00 0.00 0.00 4.20
873 877 5.120830 GCTTCATTTCAGTTCACTACATCGT 59.879 40.000 0.00 0.00 0.00 3.73
874 878 5.554636 GCTTCATTTCAGTTCACTACATCG 58.445 41.667 0.00 0.00 0.00 3.84
875 879 5.554636 CGCTTCATTTCAGTTCACTACATC 58.445 41.667 0.00 0.00 0.00 3.06
876 880 4.142816 GCGCTTCATTTCAGTTCACTACAT 60.143 41.667 0.00 0.00 0.00 2.29
877 881 3.186409 GCGCTTCATTTCAGTTCACTACA 59.814 43.478 0.00 0.00 0.00 2.74
878 882 3.722082 CGCGCTTCATTTCAGTTCACTAC 60.722 47.826 5.56 0.00 0.00 2.73
879 883 2.411748 CGCGCTTCATTTCAGTTCACTA 59.588 45.455 5.56 0.00 0.00 2.74
880 884 1.195448 CGCGCTTCATTTCAGTTCACT 59.805 47.619 5.56 0.00 0.00 3.41
881 885 1.194547 TCGCGCTTCATTTCAGTTCAC 59.805 47.619 5.56 0.00 0.00 3.18
950 954 5.943416 TGCAGCTTAACTTAGGCTTGAATTA 59.057 36.000 2.73 0.00 39.27 1.40
951 955 4.766891 TGCAGCTTAACTTAGGCTTGAATT 59.233 37.500 2.73 0.00 39.27 2.17
952 956 4.335416 TGCAGCTTAACTTAGGCTTGAAT 58.665 39.130 2.73 0.00 39.27 2.57
953 957 3.750371 TGCAGCTTAACTTAGGCTTGAA 58.250 40.909 2.73 0.00 39.27 2.69
954 958 3.417069 TGCAGCTTAACTTAGGCTTGA 57.583 42.857 2.73 0.00 39.27 3.02
955 959 3.065925 GGATGCAGCTTAACTTAGGCTTG 59.934 47.826 0.22 1.58 39.27 4.01
956 960 3.282885 GGATGCAGCTTAACTTAGGCTT 58.717 45.455 0.22 0.00 39.27 4.35
957 961 2.239654 TGGATGCAGCTTAACTTAGGCT 59.760 45.455 0.22 0.00 42.31 4.58
958 962 2.643551 TGGATGCAGCTTAACTTAGGC 58.356 47.619 0.22 0.00 0.00 3.93
959 963 6.318648 TGTTTATGGATGCAGCTTAACTTAGG 59.681 38.462 0.22 0.00 0.00 2.69
960 964 7.320443 TGTTTATGGATGCAGCTTAACTTAG 57.680 36.000 0.22 0.00 0.00 2.18
972 976 6.854496 ATCAATGCATTTGTTTATGGATGC 57.146 33.333 9.83 0.00 43.83 3.91
990 994 3.381272 CCCAAGGCGACATTGTAATCAAT 59.619 43.478 0.00 0.00 44.02 2.57
991 995 2.752354 CCCAAGGCGACATTGTAATCAA 59.248 45.455 0.00 0.00 37.98 2.57
992 996 2.364632 CCCAAGGCGACATTGTAATCA 58.635 47.619 0.00 0.00 0.00 2.57
993 997 1.065551 GCCCAAGGCGACATTGTAATC 59.934 52.381 0.00 0.00 39.62 1.75
1014 1018 2.394563 GGCGAGCAGGAAGAGCAAC 61.395 63.158 0.00 0.00 0.00 4.17
1954 1961 1.070601 GGTTTTGGCCAGATTTGCAGT 59.929 47.619 5.11 0.00 0.00 4.40
3182 3198 6.455647 TGAAGTGGAAGTTATGTGTCTAGTG 58.544 40.000 0.00 0.00 0.00 2.74
3183 3199 6.665992 TGAAGTGGAAGTTATGTGTCTAGT 57.334 37.500 0.00 0.00 0.00 2.57
3184 3200 7.819415 TGATTGAAGTGGAAGTTATGTGTCTAG 59.181 37.037 0.00 0.00 0.00 2.43
3185 3201 7.676004 TGATTGAAGTGGAAGTTATGTGTCTA 58.324 34.615 0.00 0.00 0.00 2.59
3186 3202 6.533730 TGATTGAAGTGGAAGTTATGTGTCT 58.466 36.000 0.00 0.00 0.00 3.41
3187 3203 6.801539 TGATTGAAGTGGAAGTTATGTGTC 57.198 37.500 0.00 0.00 0.00 3.67
3188 3204 8.862325 TTATGATTGAAGTGGAAGTTATGTGT 57.138 30.769 0.00 0.00 0.00 3.72
3213 3229 7.820386 TGCATTGCTAGTTCAAATGATTCAAAT 59.180 29.630 10.49 0.00 0.00 2.32
3215 3231 6.689554 TGCATTGCTAGTTCAAATGATTCAA 58.310 32.000 10.49 0.00 0.00 2.69
3216 3232 6.270156 TGCATTGCTAGTTCAAATGATTCA 57.730 33.333 10.49 0.00 0.00 2.57
3217 3233 7.116662 TGTTTGCATTGCTAGTTCAAATGATTC 59.883 33.333 10.49 0.00 0.00 2.52
3218 3234 6.930164 TGTTTGCATTGCTAGTTCAAATGATT 59.070 30.769 10.49 0.00 0.00 2.57
3219 3235 6.457355 TGTTTGCATTGCTAGTTCAAATGAT 58.543 32.000 10.49 0.00 0.00 2.45
3221 3237 6.183360 GGATGTTTGCATTGCTAGTTCAAATG 60.183 38.462 10.49 0.00 35.07 2.32
3222 3238 5.870978 GGATGTTTGCATTGCTAGTTCAAAT 59.129 36.000 10.49 0.00 35.07 2.32
3223 3239 5.010922 AGGATGTTTGCATTGCTAGTTCAAA 59.989 36.000 10.49 0.00 35.07 2.69
3224 3240 4.523943 AGGATGTTTGCATTGCTAGTTCAA 59.476 37.500 10.49 0.00 35.07 2.69
3228 3244 3.629398 GCTAGGATGTTTGCATTGCTAGT 59.371 43.478 10.49 0.00 35.07 2.57
3229 3245 3.881688 AGCTAGGATGTTTGCATTGCTAG 59.118 43.478 10.49 9.28 35.07 3.42
3233 3249 4.157289 ACTGAAGCTAGGATGTTTGCATTG 59.843 41.667 0.00 0.00 35.07 2.82
3234 3250 4.338879 ACTGAAGCTAGGATGTTTGCATT 58.661 39.130 0.00 0.00 35.07 3.56
3237 3253 3.373439 CAGACTGAAGCTAGGATGTTTGC 59.627 47.826 0.00 0.00 0.00 3.68
3238 3254 3.937706 CCAGACTGAAGCTAGGATGTTTG 59.062 47.826 3.32 0.00 0.00 2.93
3242 3258 1.415659 CCCCAGACTGAAGCTAGGATG 59.584 57.143 3.32 0.00 0.00 3.51
3243 3259 1.799933 CCCCAGACTGAAGCTAGGAT 58.200 55.000 3.32 0.00 0.00 3.24
3245 3261 1.524482 GCCCCAGACTGAAGCTAGG 59.476 63.158 3.32 0.00 0.00 3.02
3246 3262 0.980231 AGGCCCCAGACTGAAGCTAG 60.980 60.000 3.32 0.00 0.00 3.42
3249 3265 2.129555 TTGAGGCCCCAGACTGAAGC 62.130 60.000 3.32 6.08 0.00 3.86
3250 3266 0.401738 TTTGAGGCCCCAGACTGAAG 59.598 55.000 3.32 0.00 0.00 3.02
3252 3268 0.401738 CTTTTGAGGCCCCAGACTGA 59.598 55.000 3.32 0.00 0.00 3.41
3258 3274 0.178964 CTGGTTCTTTTGAGGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
3260 3276 2.095461 GATCTGGTTCTTTTGAGGCCC 58.905 52.381 0.00 0.00 0.00 5.80
3261 3277 2.751806 CTGATCTGGTTCTTTTGAGGCC 59.248 50.000 0.00 0.00 0.00 5.19
3262 3278 3.679389 TCTGATCTGGTTCTTTTGAGGC 58.321 45.455 0.00 0.00 0.00 4.70
3263 3279 4.639310 CCATCTGATCTGGTTCTTTTGAGG 59.361 45.833 0.00 0.00 0.00 3.86
3264 3280 4.639310 CCCATCTGATCTGGTTCTTTTGAG 59.361 45.833 0.00 0.00 31.44 3.02
3266 3282 4.592942 TCCCATCTGATCTGGTTCTTTTG 58.407 43.478 0.00 0.00 31.44 2.44
3267 3283 4.934797 TCCCATCTGATCTGGTTCTTTT 57.065 40.909 0.00 0.00 31.44 2.27
3268 3284 4.444022 CGATCCCATCTGATCTGGTTCTTT 60.444 45.833 0.00 0.00 39.20 2.52
3269 3285 3.070734 CGATCCCATCTGATCTGGTTCTT 59.929 47.826 0.00 0.00 39.20 2.52
3270 3286 2.632028 CGATCCCATCTGATCTGGTTCT 59.368 50.000 0.00 0.00 39.20 3.01
3271 3287 2.366916 ACGATCCCATCTGATCTGGTTC 59.633 50.000 0.00 4.11 39.20 3.62
3272 3288 2.366916 GACGATCCCATCTGATCTGGTT 59.633 50.000 0.00 0.00 39.20 3.67
3273 3289 1.967066 GACGATCCCATCTGATCTGGT 59.033 52.381 0.00 0.00 39.20 4.00
3321 3413 4.865776 AGATATCGAACTGAAGCTAGTGC 58.134 43.478 0.00 0.00 40.05 4.40
3336 3428 7.740246 TGCGTCATAAACTAGACTAGATATCG 58.260 38.462 16.55 13.50 32.68 2.92
3363 6399 8.837389 GGAACTACGAGCTATGGAAAATATTTT 58.163 33.333 13.24 13.24 0.00 1.82
3373 6409 4.551388 GATCTTGGAACTACGAGCTATGG 58.449 47.826 0.00 0.00 0.00 2.74
3382 6418 5.293569 CGTTATGGTTGGATCTTGGAACTAC 59.706 44.000 0.00 0.00 0.00 2.73
3388 6428 2.614057 GCTCGTTATGGTTGGATCTTGG 59.386 50.000 0.00 0.00 0.00 3.61
3393 6435 1.408266 GGGTGCTCGTTATGGTTGGAT 60.408 52.381 0.00 0.00 0.00 3.41
3405 6449 1.012086 CTGATGATGTTGGGTGCTCG 58.988 55.000 0.00 0.00 0.00 5.03
3411 6455 1.335810 CCGAATGCTGATGATGTTGGG 59.664 52.381 0.00 0.00 0.00 4.12
3461 6508 7.556275 TGACAGTCCAAACTTCAAAAGATTAGT 59.444 33.333 0.00 0.00 31.71 2.24
3516 6563 0.390860 AGCTGTGTGTCTCACTCCAC 59.609 55.000 6.60 0.00 46.27 4.02
3724 6771 0.454285 CATGCGTAACCTTTGGCGTG 60.454 55.000 0.00 0.00 36.25 5.34
3809 6857 3.624861 GCCAGTCATACTCATGGTTTCTG 59.375 47.826 0.00 0.00 35.17 3.02
3810 6858 3.370953 GGCCAGTCATACTCATGGTTTCT 60.371 47.826 0.00 0.00 35.17 2.52
3866 6914 0.668401 CGTCCTTCCCGTTGTACACC 60.668 60.000 0.00 0.00 0.00 4.16
3902 6955 1.755179 ACTTGATGCTGTATGGCACC 58.245 50.000 0.00 0.00 45.36 5.01
3926 6979 2.781911 GGAAGAGTTTCCGGGCATC 58.218 57.895 0.00 0.00 43.27 3.91
4004 7057 3.120683 ACATGTAGACGAAATGCACAACG 60.121 43.478 0.00 0.00 0.00 4.10
4037 7090 2.738521 CTGCCACGGGTGAAGTCG 60.739 66.667 0.00 0.00 0.00 4.18
4055 7108 5.006746 GGCCTTTATGAACTTGTACTGATCG 59.993 44.000 0.00 0.00 0.00 3.69
4175 7228 0.108207 GGATCATCTGCTCCCTGTGG 59.892 60.000 0.00 0.00 0.00 4.17
4281 7334 1.255667 TTGAGGCACCGGTAGTCCTC 61.256 60.000 28.96 28.96 40.46 3.71
4284 7337 1.445582 CGTTGAGGCACCGGTAGTC 60.446 63.158 6.87 3.20 0.00 2.59
4302 7355 2.823119 TACACGAAGCTCGACGACGC 62.823 60.000 13.25 10.17 43.74 5.19
4340 7393 2.658593 GCCATCCCGATCACGACG 60.659 66.667 0.00 0.00 42.66 5.12
4394 7447 2.584608 GGGACATCAGGGTGGTCG 59.415 66.667 0.00 0.00 32.39 4.79
4412 7465 1.374758 CCGCGGCTGAGGGAATATC 60.375 63.158 14.67 0.00 0.00 1.63
4429 7482 4.201951 CACGGTACATGGACTGCC 57.798 61.111 17.33 0.00 0.00 4.85
4500 7553 2.172851 TCATGGTTCCCAACGTACAC 57.827 50.000 0.00 0.00 36.95 2.90
4699 7752 3.092511 TCCATCCTGCAGAGCCCC 61.093 66.667 17.39 0.00 0.00 5.80
4735 7791 1.749258 GGGCGAACCAATCAGGACC 60.749 63.158 0.00 0.00 41.22 4.46
4760 7817 5.465935 AGCAATTATTACCAACACAAACGG 58.534 37.500 0.00 0.00 0.00 4.44
4773 7830 7.669722 ACAGTGGAAAAGGAAGAGCAATTATTA 59.330 33.333 0.00 0.00 0.00 0.98
4774 7831 6.494835 ACAGTGGAAAAGGAAGAGCAATTATT 59.505 34.615 0.00 0.00 0.00 1.40
4775 7832 6.012745 ACAGTGGAAAAGGAAGAGCAATTAT 58.987 36.000 0.00 0.00 0.00 1.28
4842 7900 6.102663 CGGTGAATCTGAAGACTAGTCATTT 58.897 40.000 24.44 11.17 0.00 2.32
4843 7901 5.186021 ACGGTGAATCTGAAGACTAGTCATT 59.814 40.000 24.44 14.31 0.00 2.57
4845 7903 4.079970 ACGGTGAATCTGAAGACTAGTCA 58.920 43.478 24.44 3.92 0.00 3.41
4846 7904 4.156190 TGACGGTGAATCTGAAGACTAGTC 59.844 45.833 15.41 15.41 0.00 2.59
4847 7905 4.079970 TGACGGTGAATCTGAAGACTAGT 58.920 43.478 0.00 0.00 0.00 2.57
4848 7906 4.703645 TGACGGTGAATCTGAAGACTAG 57.296 45.455 0.00 0.00 0.00 2.57
4888 7953 2.223444 CGCGTGTCGAGATCGTATTAG 58.777 52.381 0.00 0.00 41.67 1.73
4911 7976 4.602340 ACCACTCATCGGTAATACATCC 57.398 45.455 0.00 0.00 34.02 3.51
4957 11264 8.939929 CAATACATCAACCATCATAGTACATCC 58.060 37.037 0.00 0.00 0.00 3.51
4967 11274 5.438833 TCATCAGCAATACATCAACCATCA 58.561 37.500 0.00 0.00 0.00 3.07
5042 11349 5.541845 CACTGGACTAGAAGAATCACAACA 58.458 41.667 0.00 0.00 0.00 3.33
5108 11415 1.935933 ACGTGCTTCGACAAGAAAGT 58.064 45.000 8.63 0.00 42.86 2.66
5163 11470 4.509970 TGTTAAAATGACTGTCTCACACCG 59.490 41.667 9.51 0.00 0.00 4.94
5165 11472 8.128582 TCAAATGTTAAAATGACTGTCTCACAC 58.871 33.333 9.51 0.00 0.00 3.82
5166 11473 8.219546 TCAAATGTTAAAATGACTGTCTCACA 57.780 30.769 9.51 3.61 0.00 3.58
5202 11512 6.259550 CCTTTGGGCAGCAGTAAATATATC 57.740 41.667 0.00 0.00 0.00 1.63
5234 11544 4.952262 TGAATGCGAAGAAAATCTCCAG 57.048 40.909 0.00 0.00 0.00 3.86
5305 11615 6.488006 TTCGGAGACTACAAAGTACAGTACTT 59.512 38.462 18.79 18.79 44.19 2.24
5307 11617 5.869753 TCGGAGACTACAAAGTACAGTAC 57.130 43.478 2.05 2.05 35.56 2.73
5309 11619 5.779529 TTTCGGAGACTACAAAGTACAGT 57.220 39.130 0.00 0.00 35.56 3.55
5311 11621 9.715121 ATTATTTTTCGGAGACTACAAAGTACA 57.285 29.630 0.00 0.00 35.56 2.90
5342 11652 2.796032 GCTCTTGGTGTGAGTTTGTTGC 60.796 50.000 0.00 0.00 34.30 4.17
5371 11681 1.750778 CAGTTGTGGCCACTTTGTCTT 59.249 47.619 34.75 11.88 0.00 3.01
5372 11682 1.392589 CAGTTGTGGCCACTTTGTCT 58.607 50.000 34.75 21.22 0.00 3.41
5384 11694 3.925379 TGTGTGGAGTATAGCAGTTGTG 58.075 45.455 0.00 0.00 0.00 3.33
5386 11696 4.152402 GTGTTGTGTGGAGTATAGCAGTTG 59.848 45.833 0.00 0.00 0.00 3.16
5398 11708 2.174969 GTTCGCCGTGTTGTGTGGA 61.175 57.895 0.00 0.00 0.00 4.02
5399 11709 1.983196 TTGTTCGCCGTGTTGTGTGG 61.983 55.000 0.00 0.00 0.00 4.17
5412 11722 5.460646 ACAAGCATCTGGTTAAATTGTTCG 58.539 37.500 0.00 0.00 33.98 3.95
5431 11741 5.641209 AGAATACTTGCTACAGCTGAACAAG 59.359 40.000 29.33 29.33 42.63 3.16
5433 11743 4.931601 CAGAATACTTGCTACAGCTGAACA 59.068 41.667 23.35 12.29 42.66 3.18
5434 11744 4.932200 ACAGAATACTTGCTACAGCTGAAC 59.068 41.667 23.35 9.58 42.66 3.18
5435 11745 4.931601 CACAGAATACTTGCTACAGCTGAA 59.068 41.667 23.35 2.64 42.66 3.02
5436 11746 4.498241 CACAGAATACTTGCTACAGCTGA 58.502 43.478 23.35 2.95 42.66 4.26
5437 11747 3.620374 CCACAGAATACTTGCTACAGCTG 59.380 47.826 13.48 13.48 42.66 4.24
5438 11748 3.866651 CCACAGAATACTTGCTACAGCT 58.133 45.455 2.44 0.00 42.66 4.24
5439 11749 2.352960 GCCACAGAATACTTGCTACAGC 59.647 50.000 0.00 0.00 42.50 4.40
5440 11750 3.599343 TGCCACAGAATACTTGCTACAG 58.401 45.455 0.00 0.00 0.00 2.74
5441 11751 3.694043 TGCCACAGAATACTTGCTACA 57.306 42.857 0.00 0.00 0.00 2.74
5442 11752 4.396166 ACATTGCCACAGAATACTTGCTAC 59.604 41.667 0.00 0.00 0.00 3.58
5443 11753 4.588899 ACATTGCCACAGAATACTTGCTA 58.411 39.130 0.00 0.00 0.00 3.49
5444 11754 3.424703 ACATTGCCACAGAATACTTGCT 58.575 40.909 0.00 0.00 0.00 3.91
5445 11755 3.855689 ACATTGCCACAGAATACTTGC 57.144 42.857 0.00 0.00 0.00 4.01
5446 11756 5.276270 GCATACATTGCCACAGAATACTTG 58.724 41.667 0.00 0.00 46.15 3.16
5447 11757 5.505173 GCATACATTGCCACAGAATACTT 57.495 39.130 0.00 0.00 46.15 2.24
5473 11784 1.542328 GGTTTGGTGCAAATCCCAACC 60.542 52.381 10.85 10.85 41.33 3.77
5480 11791 1.412343 GTGGACAGGTTTGGTGCAAAT 59.588 47.619 0.00 0.00 38.35 2.32
5491 11802 1.742411 CGACAACACAAGTGGACAGGT 60.742 52.381 5.08 0.00 34.19 4.00
5512 11823 4.084888 CCGGAAACAAGCGACCGC 62.085 66.667 6.25 6.25 43.37 5.68
5514 11825 1.004595 GATACCGGAAACAAGCGACC 58.995 55.000 9.46 0.00 0.00 4.79
5517 11828 1.927174 CAGAGATACCGGAAACAAGCG 59.073 52.381 9.46 0.00 0.00 4.68
5532 11843 4.819761 GCGCGACCATGGCAGAGA 62.820 66.667 12.10 0.00 0.00 3.10
5609 11920 1.516603 GAACGGCGAGTACCTGAGC 60.517 63.158 16.62 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.