Multiple sequence alignment - TraesCS2D01G146500

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 TraesCS2D01G146500 chr2D 100.000 3455 0 0 1 3455 87805089 87808543 0.000000e+00 6381.0
1 TraesCS2D01G146500 chr2D 75.714 210 29 19 1451 1643 593523754 593523550 6.140000e-13 86.1
2 TraesCS2D01G146500 chr2B 89.196 2601 170 48 918 3455 141147258 141149810 0.000000e+00 3144.0
3 TraesCS2D01G146500 chr2B 78.112 233 31 9 2674 2903 65131710 65131925 2.800000e-26 130.0
4 TraesCS2D01G146500 chr2A 94.641 1157 50 5 995 2150 88280779 88281924 0.000000e+00 1783.0
5 TraesCS2D01G146500 chr2A 80.556 576 80 17 2352 2914 133980450 133981006 6.900000e-112 414.0
6 TraesCS2D01G146500 chr2A 75.751 466 92 15 1102 1564 88290420 88289973 7.510000e-52 215.0
7 TraesCS2D01G146500 chr2A 94.853 136 6 1 2176 2311 88281981 88282115 9.710000e-51 211.0
8 TraesCS2D01G146500 chr4D 97.571 700 16 1 1 700 456041733 456041035 0.000000e+00 1197.0
9 TraesCS2D01G146500 chrUn 92.879 660 35 6 49 700 26522421 26523076 0.000000e+00 948.0
10 TraesCS2D01G146500 chr7D 88.736 728 49 16 1 700 81656502 81657224 0.000000e+00 859.0
11 TraesCS2D01G146500 chr7D 88.308 727 53 14 1 700 81364773 81364052 0.000000e+00 843.0
12 TraesCS2D01G146500 chr7D 89.286 504 43 6 204 700 81253545 81254044 3.790000e-174 621.0
13 TraesCS2D01G146500 chr5A 91.401 628 44 6 80 700 578834812 578835436 0.000000e+00 852.0
14 TraesCS2D01G146500 chr5A 75.000 216 34 14 1446 1642 619454671 619454885 7.950000e-12 82.4
15 TraesCS2D01G146500 chr6A 90.094 636 39 10 80 706 583384802 583384182 0.000000e+00 804.0
16 TraesCS2D01G146500 chr7B 89.446 578 38 14 136 700 645201317 645201884 0.000000e+00 708.0
17 TraesCS2D01G146500 chr7B 79.479 999 170 26 1102 2093 61113834 61112864 0.000000e+00 676.0
18 TraesCS2D01G146500 chr7A 92.736 413 28 2 289 700 10847422 10847011 2.300000e-166 595.0
19 TraesCS2D01G146500 chr7A 79.677 866 132 32 1249 2093 107798654 107797812 4.970000e-163 584.0
20 TraesCS2D01G146500 chr7A 90.909 198 11 2 80 270 725324884 725324687 3.420000e-65 259.0
21 TraesCS2D01G146500 chr3B 78.622 421 66 10 2352 2750 167464570 167464152 1.230000e-64 257.0
22 TraesCS2D01G146500 chr3D 78.487 423 59 13 2352 2750 113571637 113572051 7.400000e-62 248.0
23 TraesCS2D01G146500 chr5B 76.471 204 32 14 1438 1634 419727786 419727980 2.840000e-16 97.1
24 TraesCS2D01G146500 chr5B 79.339 121 21 4 1524 1642 611953327 611953445 7.950000e-12 82.4
25 TraesCS2D01G146500 chr5D 85.526 76 11 0 1567 1642 495309042 495309117 2.860000e-11 80.5


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 TraesCS2D01G146500 chr2D 87805089 87808543 3454 False 6381 6381 100.000 1 3455 1 chr2D.!!$F1 3454
1 TraesCS2D01G146500 chr2B 141147258 141149810 2552 False 3144 3144 89.196 918 3455 1 chr2B.!!$F2 2537
2 TraesCS2D01G146500 chr2A 88280779 88282115 1336 False 997 1783 94.747 995 2311 2 chr2A.!!$F2 1316
3 TraesCS2D01G146500 chr2A 133980450 133981006 556 False 414 414 80.556 2352 2914 1 chr2A.!!$F1 562
4 TraesCS2D01G146500 chr4D 456041035 456041733 698 True 1197 1197 97.571 1 700 1 chr4D.!!$R1 699
5 TraesCS2D01G146500 chrUn 26522421 26523076 655 False 948 948 92.879 49 700 1 chrUn.!!$F1 651
6 TraesCS2D01G146500 chr7D 81656502 81657224 722 False 859 859 88.736 1 700 1 chr7D.!!$F2 699
7 TraesCS2D01G146500 chr7D 81364052 81364773 721 True 843 843 88.308 1 700 1 chr7D.!!$R1 699
8 TraesCS2D01G146500 chr5A 578834812 578835436 624 False 852 852 91.401 80 700 1 chr5A.!!$F1 620
9 TraesCS2D01G146500 chr6A 583384182 583384802 620 True 804 804 90.094 80 706 1 chr6A.!!$R1 626
10 TraesCS2D01G146500 chr7B 645201317 645201884 567 False 708 708 89.446 136 700 1 chr7B.!!$F1 564
11 TraesCS2D01G146500 chr7B 61112864 61113834 970 True 676 676 79.479 1102 2093 1 chr7B.!!$R1 991
12 TraesCS2D01G146500 chr7A 107797812 107798654 842 True 584 584 79.677 1249 2093 1 chr7A.!!$R2 844

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
862 901 0.110056 GCTGCAGTGACACCGATTTG 60.11 55.0 16.64 0.0 0.0 2.32 F
865 904 0.110056 GCAGTGACACCGATTTGCTG 60.11 55.0 0.84 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2233 0.103937 TGACAGTGACACATGCACGA 59.896 50.0 8.59 0.0 41.04 4.35 R
2508 2610 0.899019 TGGCGTATGACTTGGTGCTA 59.101 50.0 0.00 0.0 0.00 3.49 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
363 398 3.515602 ACTGAAAAGGACCTGATTGCT 57.484 42.857 0.00 0.00 0.00 3.91
577 616 6.128117 TGTTTAAATCGTCTAAACTGGCCATC 60.128 38.462 5.51 0.00 39.14 3.51
580 619 3.247006 TCGTCTAAACTGGCCATCTTC 57.753 47.619 5.51 0.00 0.00 2.87
683 722 1.946768 CGCGAACCCCAATTGTGATAT 59.053 47.619 0.00 0.00 0.00 1.63
707 746 2.772568 TTGTCAAACACTTGCGATGG 57.227 45.000 0.00 0.00 32.14 3.51
708 747 0.310543 TGTCAAACACTTGCGATGGC 59.689 50.000 0.00 0.00 40.52 4.40
717 756 2.747460 TGCGATGGCAGCTTCACC 60.747 61.111 0.00 0.00 46.21 4.02
718 757 3.512516 GCGATGGCAGCTTCACCC 61.513 66.667 0.00 0.00 39.62 4.61
719 758 2.046023 CGATGGCAGCTTCACCCA 60.046 61.111 0.00 0.00 0.00 4.51
720 759 1.452651 CGATGGCAGCTTCACCCAT 60.453 57.895 0.00 5.01 41.83 4.00
721 760 2.412605 GATGGCAGCTTCACCCATC 58.587 57.895 13.57 13.57 45.65 3.51
722 761 1.693034 ATGGCAGCTTCACCCATCA 59.307 52.632 0.00 0.00 34.33 3.07
723 762 0.260816 ATGGCAGCTTCACCCATCAT 59.739 50.000 0.00 0.00 34.33 2.45
724 763 0.681887 TGGCAGCTTCACCCATCATG 60.682 55.000 0.00 0.00 0.00 3.07
725 764 1.436336 GCAGCTTCACCCATCATGC 59.564 57.895 0.00 0.00 0.00 4.06
726 765 1.317431 GCAGCTTCACCCATCATGCA 61.317 55.000 0.00 0.00 32.58 3.96
727 766 1.399714 CAGCTTCACCCATCATGCAT 58.600 50.000 0.00 0.00 0.00 3.96
728 767 1.337071 CAGCTTCACCCATCATGCATC 59.663 52.381 0.00 0.00 0.00 3.91
729 768 1.214673 AGCTTCACCCATCATGCATCT 59.785 47.619 0.00 0.00 0.00 2.90
730 769 2.029623 GCTTCACCCATCATGCATCTT 58.970 47.619 0.00 0.00 0.00 2.40
731 770 3.117776 AGCTTCACCCATCATGCATCTTA 60.118 43.478 0.00 0.00 0.00 2.10
732 771 3.825014 GCTTCACCCATCATGCATCTTAT 59.175 43.478 0.00 0.00 0.00 1.73
733 772 4.082895 GCTTCACCCATCATGCATCTTATC 60.083 45.833 0.00 0.00 0.00 1.75
734 773 4.987963 TCACCCATCATGCATCTTATCT 57.012 40.909 0.00 0.00 0.00 1.98
735 774 5.314718 TCACCCATCATGCATCTTATCTT 57.685 39.130 0.00 0.00 0.00 2.40
736 775 5.311265 TCACCCATCATGCATCTTATCTTC 58.689 41.667 0.00 0.00 0.00 2.87
737 776 4.153655 CACCCATCATGCATCTTATCTTCG 59.846 45.833 0.00 0.00 0.00 3.79
738 777 4.202398 ACCCATCATGCATCTTATCTTCGT 60.202 41.667 0.00 0.00 0.00 3.85
739 778 4.758674 CCCATCATGCATCTTATCTTCGTT 59.241 41.667 0.00 0.00 0.00 3.85
740 779 5.334646 CCCATCATGCATCTTATCTTCGTTG 60.335 44.000 0.00 0.00 0.00 4.10
741 780 5.467735 CCATCATGCATCTTATCTTCGTTGA 59.532 40.000 0.00 0.00 0.00 3.18
742 781 5.973651 TCATGCATCTTATCTTCGTTGAC 57.026 39.130 0.00 0.00 0.00 3.18
743 782 5.418676 TCATGCATCTTATCTTCGTTGACA 58.581 37.500 0.00 0.00 0.00 3.58
744 783 5.874261 TCATGCATCTTATCTTCGTTGACAA 59.126 36.000 0.00 0.00 0.00 3.18
745 784 5.784750 TGCATCTTATCTTCGTTGACAAG 57.215 39.130 0.00 0.00 0.00 3.16
746 785 4.093408 TGCATCTTATCTTCGTTGACAAGC 59.907 41.667 0.00 0.00 0.00 4.01
747 786 4.780324 GCATCTTATCTTCGTTGACAAGCG 60.780 45.833 0.00 0.00 0.00 4.68
748 787 4.168922 TCTTATCTTCGTTGACAAGCGA 57.831 40.909 8.23 8.23 35.17 4.93
749 788 3.918591 TCTTATCTTCGTTGACAAGCGAC 59.081 43.478 10.89 0.00 36.82 5.19
750 789 2.148916 ATCTTCGTTGACAAGCGACA 57.851 45.000 10.89 4.03 36.82 4.35
751 790 1.929230 TCTTCGTTGACAAGCGACAA 58.071 45.000 10.89 0.00 36.82 3.18
752 791 1.858458 TCTTCGTTGACAAGCGACAAG 59.142 47.619 10.89 8.18 36.82 3.16
765 804 0.647410 CGACAAGCAAGCACCTATCG 59.353 55.000 0.00 0.00 0.00 2.92
766 805 1.726853 GACAAGCAAGCACCTATCGT 58.273 50.000 0.00 0.00 0.00 3.73
767 806 1.661112 GACAAGCAAGCACCTATCGTC 59.339 52.381 0.00 0.00 0.00 4.20
768 807 0.647410 CAAGCAAGCACCTATCGTCG 59.353 55.000 0.00 0.00 0.00 5.12
769 808 1.084370 AAGCAAGCACCTATCGTCGC 61.084 55.000 0.00 0.00 0.00 5.19
770 809 2.860628 GCAAGCACCTATCGTCGCG 61.861 63.158 0.00 0.00 0.00 5.87
771 810 1.516386 CAAGCACCTATCGTCGCGT 60.516 57.895 5.77 0.00 0.00 6.01
772 811 1.076533 CAAGCACCTATCGTCGCGTT 61.077 55.000 5.77 0.00 0.00 4.84
773 812 0.801067 AAGCACCTATCGTCGCGTTC 60.801 55.000 5.77 0.00 0.00 3.95
774 813 2.565394 GCACCTATCGTCGCGTTCG 61.565 63.158 5.77 12.96 0.00 3.95
775 814 1.937846 CACCTATCGTCGCGTTCGG 60.938 63.158 20.86 10.90 36.13 4.30
776 815 3.022914 CCTATCGTCGCGTTCGGC 61.023 66.667 20.86 2.89 36.88 5.54
793 832 3.501396 CGGATCACGCCATTGCTT 58.499 55.556 0.00 0.00 34.82 3.91
794 833 1.353103 CGGATCACGCCATTGCTTC 59.647 57.895 0.00 0.00 34.82 3.86
795 834 1.091771 CGGATCACGCCATTGCTTCT 61.092 55.000 0.00 0.00 34.82 2.85
796 835 1.806247 CGGATCACGCCATTGCTTCTA 60.806 52.381 0.00 0.00 34.82 2.10
797 836 1.599542 GGATCACGCCATTGCTTCTAC 59.400 52.381 0.00 0.00 34.43 2.59
798 837 2.279741 GATCACGCCATTGCTTCTACA 58.720 47.619 0.00 0.00 34.43 2.74
799 838 2.401583 TCACGCCATTGCTTCTACAT 57.598 45.000 0.00 0.00 34.43 2.29
800 839 2.279741 TCACGCCATTGCTTCTACATC 58.720 47.619 0.00 0.00 34.43 3.06
801 840 1.331756 CACGCCATTGCTTCTACATCC 59.668 52.381 0.00 0.00 34.43 3.51
802 841 0.583438 CGCCATTGCTTCTACATCCG 59.417 55.000 0.00 0.00 34.43 4.18
803 842 0.308993 GCCATTGCTTCTACATCCGC 59.691 55.000 0.00 0.00 33.53 5.54
804 843 1.667236 CCATTGCTTCTACATCCGCA 58.333 50.000 0.00 0.00 0.00 5.69
805 844 1.331756 CCATTGCTTCTACATCCGCAC 59.668 52.381 0.00 0.00 31.24 5.34
806 845 2.009051 CATTGCTTCTACATCCGCACA 58.991 47.619 0.00 0.00 31.24 4.57
807 846 2.401583 TTGCTTCTACATCCGCACAT 57.598 45.000 0.00 0.00 31.24 3.21
808 847 1.655484 TGCTTCTACATCCGCACATG 58.345 50.000 0.00 0.00 0.00 3.21
809 848 0.305922 GCTTCTACATCCGCACATGC 59.694 55.000 0.00 0.00 37.78 4.06
810 849 1.945387 CTTCTACATCCGCACATGCT 58.055 50.000 1.82 0.00 39.32 3.79
811 850 1.863454 CTTCTACATCCGCACATGCTC 59.137 52.381 1.82 0.00 39.32 4.26
812 851 0.249031 TCTACATCCGCACATGCTCG 60.249 55.000 1.82 0.00 39.32 5.03
813 852 0.528466 CTACATCCGCACATGCTCGT 60.528 55.000 1.82 0.00 39.32 4.18
814 853 0.805711 TACATCCGCACATGCTCGTG 60.806 55.000 1.82 2.13 40.00 4.35
815 854 2.512286 ATCCGCACATGCTCGTGG 60.512 61.111 1.82 0.00 37.37 4.94
816 855 3.315142 ATCCGCACATGCTCGTGGT 62.315 57.895 1.82 0.00 37.37 4.16
817 856 3.792047 CCGCACATGCTCGTGGTG 61.792 66.667 1.82 0.00 37.37 4.17
820 859 2.359107 CACATGCTCGTGGTGCCT 60.359 61.111 0.00 0.00 33.05 4.75
821 860 2.359107 ACATGCTCGTGGTGCCTG 60.359 61.111 0.00 0.00 33.40 4.85
822 861 3.129502 CATGCTCGTGGTGCCTGG 61.130 66.667 0.00 0.00 0.00 4.45
825 864 4.082523 GCTCGTGGTGCCTGGCTA 62.083 66.667 21.03 3.30 0.00 3.93
826 865 2.903357 CTCGTGGTGCCTGGCTAT 59.097 61.111 21.03 0.00 0.00 2.97
827 866 1.227380 CTCGTGGTGCCTGGCTATC 60.227 63.158 21.03 10.08 0.00 2.08
828 867 1.680522 CTCGTGGTGCCTGGCTATCT 61.681 60.000 21.03 0.00 0.00 1.98
829 868 1.522355 CGTGGTGCCTGGCTATCTG 60.522 63.158 21.03 3.33 0.00 2.90
830 869 1.821332 GTGGTGCCTGGCTATCTGC 60.821 63.158 21.03 1.71 41.94 4.26
831 870 2.590007 GGTGCCTGGCTATCTGCG 60.590 66.667 21.03 0.00 44.05 5.18
832 871 2.501128 GTGCCTGGCTATCTGCGA 59.499 61.111 21.03 0.00 44.05 5.10
833 872 1.884926 GTGCCTGGCTATCTGCGAC 60.885 63.158 21.03 2.80 44.05 5.19
834 873 2.280457 GCCTGGCTATCTGCGACC 60.280 66.667 12.43 0.00 44.05 4.79
835 874 2.801631 GCCTGGCTATCTGCGACCT 61.802 63.158 12.43 0.00 44.05 3.85
836 875 1.068753 CCTGGCTATCTGCGACCTG 59.931 63.158 0.00 0.00 44.05 4.00
837 876 1.593750 CTGGCTATCTGCGACCTGC 60.594 63.158 0.00 0.00 44.05 4.85
858 897 3.601685 TCGCTGCAGTGACACCGA 61.602 61.111 25.69 16.12 0.00 4.69
859 898 2.433145 CGCTGCAGTGACACCGAT 60.433 61.111 22.94 0.00 0.00 4.18
860 899 2.029288 CGCTGCAGTGACACCGATT 61.029 57.895 22.94 0.00 0.00 3.34
861 900 1.568612 CGCTGCAGTGACACCGATTT 61.569 55.000 22.94 0.00 0.00 2.17
862 901 0.110056 GCTGCAGTGACACCGATTTG 60.110 55.000 16.64 0.00 0.00 2.32
863 902 0.110056 CTGCAGTGACACCGATTTGC 60.110 55.000 5.25 9.23 0.00 3.68
864 903 0.534877 TGCAGTGACACCGATTTGCT 60.535 50.000 15.29 0.00 33.00 3.91
865 904 0.110056 GCAGTGACACCGATTTGCTG 60.110 55.000 0.84 0.00 0.00 4.41
866 905 0.518636 CAGTGACACCGATTTGCTGG 59.481 55.000 0.84 0.00 0.00 4.85
867 906 1.210155 GTGACACCGATTTGCTGGC 59.790 57.895 0.00 0.00 0.00 4.85
868 907 1.073025 TGACACCGATTTGCTGGCT 59.927 52.632 0.00 0.00 0.00 4.75
869 908 1.236616 TGACACCGATTTGCTGGCTG 61.237 55.000 0.00 0.00 0.00 4.85
870 909 1.926511 GACACCGATTTGCTGGCTGG 61.927 60.000 0.00 0.00 0.00 4.85
871 910 1.675310 CACCGATTTGCTGGCTGGA 60.675 57.895 0.00 0.00 0.00 3.86
872 911 1.074775 ACCGATTTGCTGGCTGGAA 59.925 52.632 0.00 0.00 0.00 3.53
873 912 0.539438 ACCGATTTGCTGGCTGGAAA 60.539 50.000 12.95 12.95 40.18 3.13
874 913 0.602562 CCGATTTGCTGGCTGGAAAA 59.397 50.000 14.38 1.33 39.36 2.29
875 914 1.205417 CCGATTTGCTGGCTGGAAAAT 59.795 47.619 14.38 6.01 39.36 1.82
876 915 2.533266 CGATTTGCTGGCTGGAAAATC 58.467 47.619 14.38 12.83 39.36 2.17
877 916 2.165030 CGATTTGCTGGCTGGAAAATCT 59.835 45.455 14.38 0.00 38.46 2.40
878 917 3.518590 GATTTGCTGGCTGGAAAATCTG 58.481 45.455 14.38 0.00 39.36 2.90
879 918 2.291209 TTGCTGGCTGGAAAATCTGA 57.709 45.000 0.00 0.00 0.00 3.27
880 919 1.830279 TGCTGGCTGGAAAATCTGAG 58.170 50.000 0.00 0.00 0.00 3.35
881 920 1.352017 TGCTGGCTGGAAAATCTGAGA 59.648 47.619 0.00 0.00 0.00 3.27
882 921 2.015587 GCTGGCTGGAAAATCTGAGAG 58.984 52.381 0.00 0.00 0.00 3.20
883 922 2.355513 GCTGGCTGGAAAATCTGAGAGA 60.356 50.000 0.00 0.00 0.00 3.10
884 923 3.871463 GCTGGCTGGAAAATCTGAGAGAA 60.871 47.826 0.00 0.00 0.00 2.87
885 924 3.940221 CTGGCTGGAAAATCTGAGAGAAG 59.060 47.826 0.00 0.00 0.00 2.85
886 925 3.584406 TGGCTGGAAAATCTGAGAGAAGA 59.416 43.478 0.00 0.00 0.00 2.87
887 926 4.226846 TGGCTGGAAAATCTGAGAGAAGAT 59.773 41.667 0.00 0.00 38.59 2.40
888 927 4.575645 GGCTGGAAAATCTGAGAGAAGATG 59.424 45.833 0.00 0.00 36.99 2.90
889 928 5.426504 GCTGGAAAATCTGAGAGAAGATGA 58.573 41.667 0.00 0.00 36.99 2.92
890 929 5.294060 GCTGGAAAATCTGAGAGAAGATGAC 59.706 44.000 0.00 0.00 36.99 3.06
891 930 6.617782 TGGAAAATCTGAGAGAAGATGACT 57.382 37.500 0.00 0.00 36.99 3.41
892 931 6.638610 TGGAAAATCTGAGAGAAGATGACTC 58.361 40.000 0.00 0.00 36.99 3.36
893 932 5.748152 GGAAAATCTGAGAGAAGATGACTCG 59.252 44.000 0.00 0.00 36.99 4.18
894 933 6.405286 GGAAAATCTGAGAGAAGATGACTCGA 60.405 42.308 0.00 0.00 36.99 4.04
895 934 6.713762 AAATCTGAGAGAAGATGACTCGAT 57.286 37.500 0.00 0.00 36.99 3.59
896 935 7.815840 AAATCTGAGAGAAGATGACTCGATA 57.184 36.000 0.00 0.00 36.99 2.92
897 936 7.815840 AATCTGAGAGAAGATGACTCGATAA 57.184 36.000 0.00 0.00 36.99 1.75
898 937 6.859420 TCTGAGAGAAGATGACTCGATAAG 57.141 41.667 0.00 0.00 39.12 1.73
899 938 5.762711 TCTGAGAGAAGATGACTCGATAAGG 59.237 44.000 0.00 0.00 39.12 2.69
900 939 5.685728 TGAGAGAAGATGACTCGATAAGGA 58.314 41.667 0.00 0.00 39.12 3.36
901 940 5.762711 TGAGAGAAGATGACTCGATAAGGAG 59.237 44.000 0.00 0.00 39.12 3.69
902 941 5.070001 AGAGAAGATGACTCGATAAGGAGG 58.930 45.833 0.00 0.00 38.39 4.30
903 942 5.055265 AGAAGATGACTCGATAAGGAGGA 57.945 43.478 0.00 0.00 38.39 3.71
904 943 5.640147 AGAAGATGACTCGATAAGGAGGAT 58.360 41.667 0.00 0.00 38.39 3.24
905 944 5.476599 AGAAGATGACTCGATAAGGAGGATG 59.523 44.000 0.00 0.00 38.39 3.51
906 945 4.991776 AGATGACTCGATAAGGAGGATGA 58.008 43.478 0.00 0.00 38.39 2.92
907 946 5.389520 AGATGACTCGATAAGGAGGATGAA 58.610 41.667 0.00 0.00 38.39 2.57
908 947 5.476599 AGATGACTCGATAAGGAGGATGAAG 59.523 44.000 0.00 0.00 38.39 3.02
909 948 3.891977 TGACTCGATAAGGAGGATGAAGG 59.108 47.826 0.00 0.00 38.39 3.46
910 949 3.892588 GACTCGATAAGGAGGATGAAGGT 59.107 47.826 0.00 0.00 38.39 3.50
911 950 5.063017 ACTCGATAAGGAGGATGAAGGTA 57.937 43.478 0.00 0.00 38.39 3.08
912 951 5.074115 ACTCGATAAGGAGGATGAAGGTAG 58.926 45.833 0.00 0.00 38.39 3.18
913 952 4.408276 TCGATAAGGAGGATGAAGGTAGG 58.592 47.826 0.00 0.00 0.00 3.18
914 953 3.056465 CGATAAGGAGGATGAAGGTAGGC 60.056 52.174 0.00 0.00 0.00 3.93
915 954 2.270434 AAGGAGGATGAAGGTAGGCA 57.730 50.000 0.00 0.00 0.00 4.75
916 955 2.270434 AGGAGGATGAAGGTAGGCAA 57.730 50.000 0.00 0.00 0.00 4.52
917 956 2.781667 AGGAGGATGAAGGTAGGCAAT 58.218 47.619 0.00 0.00 0.00 3.56
918 957 2.441001 AGGAGGATGAAGGTAGGCAATG 59.559 50.000 0.00 0.00 0.00 2.82
919 958 2.173569 GGAGGATGAAGGTAGGCAATGT 59.826 50.000 0.00 0.00 0.00 2.71
920 959 3.471680 GAGGATGAAGGTAGGCAATGTC 58.528 50.000 0.00 0.00 0.00 3.06
921 960 3.118531 AGGATGAAGGTAGGCAATGTCT 58.881 45.455 0.00 0.00 0.00 3.41
922 961 3.525199 AGGATGAAGGTAGGCAATGTCTT 59.475 43.478 0.00 0.00 0.00 3.01
961 1000 4.457496 CGCTGCAGTGACCCCGAT 62.457 66.667 22.94 0.00 0.00 4.18
962 1001 2.900273 GCTGCAGTGACCCCGATA 59.100 61.111 16.64 0.00 0.00 2.92
976 1020 3.132289 ACCCCGATATTGTCACTACAGTG 59.868 47.826 2.84 2.84 46.91 3.66
990 1034 3.911698 AGTGACGCGGACACTGCA 61.912 61.111 29.81 7.95 45.19 4.41
993 1037 2.355837 GACGCGGACACTGCAAGA 60.356 61.111 12.47 0.00 37.43 3.02
1316 1369 3.664244 GCGTCTACTTCGCGACAG 58.336 61.111 9.15 12.49 43.94 3.51
1317 1370 1.868251 GCGTCTACTTCGCGACAGG 60.868 63.158 9.15 4.67 43.94 4.00
1318 1371 1.868251 CGTCTACTTCGCGACAGGC 60.868 63.158 9.15 7.24 38.69 4.85
1480 1549 3.066190 TCCGTGACCTACCGCCTG 61.066 66.667 0.00 0.00 0.00 4.85
2017 2086 1.374758 GGAGTTCACGGAGGCTGTG 60.375 63.158 0.00 0.00 41.65 3.66
2135 2204 5.693104 ACGTAGAGAAGTAGAGACGATGATC 59.307 44.000 0.00 0.00 34.54 2.92
2156 2225 1.132232 GACCACTCGTCGACTCGTC 59.868 63.158 14.70 7.65 0.00 4.20
2166 2235 1.580385 CGACTCGTCGTGGATGTCG 60.580 63.158 11.05 0.00 46.99 4.35
2167 2236 1.500844 GACTCGTCGTGGATGTCGT 59.499 57.895 0.00 0.00 0.00 4.34
2169 2238 2.126618 TCGTCGTGGATGTCGTGC 60.127 61.111 0.00 0.00 0.00 5.34
2170 2239 2.430075 CGTCGTGGATGTCGTGCA 60.430 61.111 0.00 0.00 0.00 4.57
2172 2241 1.709760 GTCGTGGATGTCGTGCATG 59.290 57.895 0.00 0.00 38.06 4.06
2327 2428 3.181449 GGCACCCCCAAAGTTAAATGTTT 60.181 43.478 0.00 0.00 0.00 2.83
2375 2476 6.015350 TGAGAGAAGTTCATTTTACGACCTCT 60.015 38.462 5.50 0.00 0.00 3.69
2378 2479 7.813627 AGAGAAGTTCATTTTACGACCTCTAAC 59.186 37.037 5.50 0.00 0.00 2.34
2383 2484 5.883661 TCATTTTACGACCTCTAACTACCG 58.116 41.667 0.00 0.00 0.00 4.02
2401 2502 1.737793 CCGCCTAAGCCTAAAACACAG 59.262 52.381 0.00 0.00 34.57 3.66
2413 2514 6.070767 AGCCTAAAACACAGCTCTGAACTATA 60.071 38.462 3.60 0.00 0.00 1.31
2428 2529 9.804758 CTCTGAACTATAAGACCGTCTAATTTT 57.195 33.333 0.26 0.00 0.00 1.82
2443 2544 6.856426 CGTCTAATTTTCAACCCTCAACTTTC 59.144 38.462 0.00 0.00 0.00 2.62
2450 2551 4.090090 TCAACCCTCAACTTTCAAAACCA 58.910 39.130 0.00 0.00 0.00 3.67
2508 2610 3.728076 TGACGAGTCAACAGCTTAGTT 57.272 42.857 3.11 0.00 36.53 2.24
2539 2641 1.869132 CATACGCCATGTCACCATCTG 59.131 52.381 0.00 0.00 0.00 2.90
2550 2652 5.169992 TGTCACCATCTGTTGAATCTGAT 57.830 39.130 0.00 0.00 0.00 2.90
2624 2726 3.788227 TTGAATCTAAGGGCTGTGTGT 57.212 42.857 0.00 0.00 0.00 3.72
2626 2728 4.202245 TGAATCTAAGGGCTGTGTGTAC 57.798 45.455 0.00 0.00 0.00 2.90
2749 2865 4.645535 TGTTGAGACTTTCCCAGATTGAG 58.354 43.478 0.00 0.00 0.00 3.02
2750 2866 3.340814 TGAGACTTTCCCAGATTGAGC 57.659 47.619 0.00 0.00 0.00 4.26
2779 2895 6.472887 TGGTTGTGTGGGTTTTTGAAAATTA 58.527 32.000 0.00 0.00 0.00 1.40
2845 2961 7.992033 TGACCCAAAAATGTCTTTGAATTTGAT 59.008 29.630 0.00 0.00 38.35 2.57
2920 3037 7.293073 CCAGATTTAATATAGGGGCATGCTAT 58.707 38.462 18.92 10.26 0.00 2.97
2967 3084 1.194772 GCTGCCGTTAGATTTATCGCC 59.805 52.381 0.00 0.00 0.00 5.54
2976 3093 7.328680 CGTTAGATTTATCGCCATCGAACGG 62.329 48.000 15.47 3.22 46.28 4.44
2984 3101 3.914984 CCATCGAACGGCATATCCT 57.085 52.632 0.00 0.00 0.00 3.24
2997 3114 3.682696 GCATATCCTGCCTTCATCATCA 58.317 45.455 0.00 0.00 45.66 3.07
3017 3134 5.330455 TCACAACAAAGGCAATGTTACAA 57.670 34.783 7.47 0.00 38.90 2.41
3021 3138 5.352846 ACAACAAAGGCAATGTTACAAAACC 59.647 36.000 7.47 0.00 38.90 3.27
3033 3150 5.784177 TGTTACAAAACCTTTTGCAACTGA 58.216 33.333 19.94 5.76 46.75 3.41
3039 3156 5.535753 AAACCTTTTGCAACTGAGCTAAT 57.464 34.783 0.00 0.00 34.99 1.73
3040 3157 6.648879 AAACCTTTTGCAACTGAGCTAATA 57.351 33.333 0.00 0.00 34.99 0.98
3041 3158 5.629079 ACCTTTTGCAACTGAGCTAATAC 57.371 39.130 0.00 0.00 34.99 1.89
3074 3191 8.462016 AGAAATATTTGCAATAGAGGTTGTGTC 58.538 33.333 5.17 0.00 0.00 3.67
3076 3193 1.438651 TGCAATAGAGGTTGTGTCGC 58.561 50.000 0.00 0.00 0.00 5.19
3190 3321 0.250684 ATGATGTCGCAACACCACCA 60.251 50.000 0.00 0.00 38.48 4.17
3195 3326 1.666553 TCGCAACACCACCATCGTC 60.667 57.895 0.00 0.00 0.00 4.20
3209 3356 1.792367 CATCGTCGTTTGCAACTCTGA 59.208 47.619 0.00 0.00 0.00 3.27
3228 3375 4.763279 TCTGATGTTGTTGCATGAACTCAT 59.237 37.500 0.00 7.66 35.37 2.90
3229 3376 5.242171 TCTGATGTTGTTGCATGAACTCATT 59.758 36.000 0.00 0.00 35.37 2.57
3242 3389 2.183478 ACTCATTTGTGCATGGACGA 57.817 45.000 13.03 8.16 0.00 4.20
3260 3407 1.007011 CGATCGTTGACTCATCGTTGC 60.007 52.381 7.03 1.16 35.70 4.17
3267 3414 2.180769 CTCATCGTTGCCGTCCGA 59.819 61.111 0.00 0.00 37.51 4.55
3273 3420 3.103911 GTTGCCGTCCGAGTCACG 61.104 66.667 0.00 0.00 42.18 4.35
3274 3421 3.289062 TTGCCGTCCGAGTCACGA 61.289 61.111 4.68 0.00 45.77 4.35
3275 3422 3.547249 TTGCCGTCCGAGTCACGAC 62.547 63.158 4.68 1.43 45.77 4.34
3278 3425 4.086178 CGTCCGAGTCACGACGCT 62.086 66.667 14.62 0.00 45.77 5.07
3279 3426 2.202324 GTCCGAGTCACGACGCTC 60.202 66.667 0.00 0.00 45.77 5.03
3282 3429 4.736631 CGAGTCACGACGCTCGCA 62.737 66.667 9.78 0.00 46.01 5.10
3283 3430 2.872001 GAGTCACGACGCTCGCAG 60.872 66.667 0.00 1.98 45.12 5.18
3284 3431 3.310253 GAGTCACGACGCTCGCAGA 62.310 63.158 0.00 3.96 45.12 4.26
3285 3432 2.202492 GTCACGACGCTCGCAGAT 60.202 61.111 0.00 0.00 45.12 2.90
3286 3433 1.062047 GTCACGACGCTCGCAGATA 59.938 57.895 0.00 0.00 45.12 1.98
3288 3435 1.939785 CACGACGCTCGCAGATACC 60.940 63.158 0.00 0.00 45.12 2.73
3290 3437 2.713770 GACGCTCGCAGATACCGA 59.286 61.111 0.00 0.00 33.89 4.69
3297 3444 1.264557 CTCGCAGATACCGAGTACAGG 59.735 57.143 5.93 5.93 45.17 4.00
3304 3451 2.055310 TACCGAGTACAGGCGATGCG 62.055 60.000 7.24 0.00 0.00 4.73
3331 3478 0.801836 GCGGCGGAAATTTGGTGATG 60.802 55.000 9.78 0.00 0.00 3.07
3338 3485 3.430453 GGAAATTTGGTGATGGAGGTCA 58.570 45.455 0.00 0.00 0.00 4.02
3346 3493 1.527844 GATGGAGGTCAGCCATGGC 60.528 63.158 30.12 30.12 45.81 4.40
3358 3505 2.338257 CATGGCGGCGGTTGTTTT 59.662 55.556 9.78 0.00 0.00 2.43
3380 3527 3.705051 TGGATCCGTACCTAGTTGAGTT 58.295 45.455 7.39 0.00 0.00 3.01
3411 3558 2.675423 CCGACGGAGACCTGGTCA 60.675 66.667 27.48 0.00 34.60 4.02
3412 3559 2.567049 CGACGGAGACCTGGTCAC 59.433 66.667 27.48 21.23 34.60 3.67
3447 3594 3.050275 GTCTGCGCCAGGTCAACC 61.050 66.667 4.18 0.00 31.51 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
646 685 1.404391 CGCGTCCTACAGAACTACCAT 59.596 52.381 0.00 0.00 0.00 3.55
659 698 1.674322 CAATTGGGGTTCGCGTCCT 60.674 57.895 18.58 1.25 0.00 3.85
701 740 3.512516 GGGTGAAGCTGCCATCGC 61.513 66.667 7.77 7.77 0.00 4.58
702 741 1.442526 GATGGGTGAAGCTGCCATCG 61.443 60.000 0.00 0.00 30.18 3.84
703 742 0.394762 TGATGGGTGAAGCTGCCATC 60.395 55.000 0.00 0.00 36.83 3.51
704 743 0.260816 ATGATGGGTGAAGCTGCCAT 59.739 50.000 0.00 0.00 0.00 4.40
705 744 0.681887 CATGATGGGTGAAGCTGCCA 60.682 55.000 0.00 0.00 0.00 4.92
706 745 2.012902 GCATGATGGGTGAAGCTGCC 62.013 60.000 0.00 0.00 0.00 4.85
707 746 1.317431 TGCATGATGGGTGAAGCTGC 61.317 55.000 0.00 0.00 0.00 5.25
708 747 1.337071 GATGCATGATGGGTGAAGCTG 59.663 52.381 2.46 0.00 0.00 4.24
709 748 1.214673 AGATGCATGATGGGTGAAGCT 59.785 47.619 2.46 0.00 0.00 3.74
710 749 1.688772 AGATGCATGATGGGTGAAGC 58.311 50.000 2.46 0.00 0.00 3.86
711 750 5.314529 AGATAAGATGCATGATGGGTGAAG 58.685 41.667 2.46 0.00 0.00 3.02
712 751 5.314718 AGATAAGATGCATGATGGGTGAA 57.685 39.130 2.46 0.00 0.00 3.18
713 752 4.987963 AGATAAGATGCATGATGGGTGA 57.012 40.909 2.46 0.00 0.00 4.02
714 753 4.153655 CGAAGATAAGATGCATGATGGGTG 59.846 45.833 2.46 0.00 0.00 4.61
715 754 4.202398 ACGAAGATAAGATGCATGATGGGT 60.202 41.667 2.46 0.00 0.00 4.51
716 755 4.321718 ACGAAGATAAGATGCATGATGGG 58.678 43.478 2.46 0.00 0.00 4.00
717 756 5.467735 TCAACGAAGATAAGATGCATGATGG 59.532 40.000 2.46 0.00 0.00 3.51
718 757 6.018507 TGTCAACGAAGATAAGATGCATGATG 60.019 38.462 2.46 0.00 0.00 3.07
719 758 6.051074 TGTCAACGAAGATAAGATGCATGAT 58.949 36.000 2.46 0.00 0.00 2.45
720 759 5.418676 TGTCAACGAAGATAAGATGCATGA 58.581 37.500 2.46 0.00 0.00 3.07
721 760 5.723492 TGTCAACGAAGATAAGATGCATG 57.277 39.130 2.46 0.00 0.00 4.06
722 761 5.220739 GCTTGTCAACGAAGATAAGATGCAT 60.221 40.000 17.28 0.00 38.54 3.96
723 762 4.093408 GCTTGTCAACGAAGATAAGATGCA 59.907 41.667 17.28 0.00 38.54 3.96
724 763 4.582459 GCTTGTCAACGAAGATAAGATGC 58.418 43.478 17.28 4.76 38.54 3.91
725 764 4.562789 TCGCTTGTCAACGAAGATAAGATG 59.437 41.667 17.28 10.99 38.54 2.90
726 765 4.563184 GTCGCTTGTCAACGAAGATAAGAT 59.437 41.667 17.28 0.00 40.47 2.40
727 766 3.918591 GTCGCTTGTCAACGAAGATAAGA 59.081 43.478 17.28 1.47 40.47 2.10
728 767 3.673338 TGTCGCTTGTCAACGAAGATAAG 59.327 43.478 10.45 11.67 40.47 1.73
729 768 3.644823 TGTCGCTTGTCAACGAAGATAA 58.355 40.909 10.45 0.00 40.47 1.75
730 769 3.291809 TGTCGCTTGTCAACGAAGATA 57.708 42.857 10.45 0.00 40.47 1.98
731 770 2.148916 TGTCGCTTGTCAACGAAGAT 57.851 45.000 10.45 0.00 40.47 2.40
732 771 1.858458 CTTGTCGCTTGTCAACGAAGA 59.142 47.619 10.45 4.14 40.47 2.87
733 772 1.657538 GCTTGTCGCTTGTCAACGAAG 60.658 52.381 10.45 7.77 40.47 3.79
734 773 0.303493 GCTTGTCGCTTGTCAACGAA 59.697 50.000 10.45 0.00 40.47 3.85
735 774 0.808060 TGCTTGTCGCTTGTCAACGA 60.808 50.000 0.00 6.27 40.11 3.85
736 775 0.027455 TTGCTTGTCGCTTGTCAACG 59.973 50.000 2.38 2.38 40.11 4.10
737 776 1.746760 CTTGCTTGTCGCTTGTCAAC 58.253 50.000 0.00 0.00 40.11 3.18
738 777 0.029300 GCTTGCTTGTCGCTTGTCAA 59.971 50.000 0.00 0.00 40.11 3.18
739 778 1.094650 TGCTTGCTTGTCGCTTGTCA 61.095 50.000 0.00 0.00 40.11 3.58
740 779 0.658536 GTGCTTGCTTGTCGCTTGTC 60.659 55.000 0.00 0.00 40.11 3.18
741 780 1.356624 GTGCTTGCTTGTCGCTTGT 59.643 52.632 0.00 0.00 40.11 3.16
742 781 1.370900 GGTGCTTGCTTGTCGCTTG 60.371 57.895 0.00 0.00 40.11 4.01
743 782 0.250295 TAGGTGCTTGCTTGTCGCTT 60.250 50.000 0.00 0.00 40.11 4.68
744 783 0.036010 ATAGGTGCTTGCTTGTCGCT 60.036 50.000 0.00 0.00 40.11 4.93
745 784 0.375106 GATAGGTGCTTGCTTGTCGC 59.625 55.000 0.00 0.00 39.77 5.19
746 785 0.647410 CGATAGGTGCTTGCTTGTCG 59.353 55.000 0.00 0.00 0.00 4.35
747 786 1.661112 GACGATAGGTGCTTGCTTGTC 59.339 52.381 0.00 0.00 43.77 3.18
748 787 1.726853 GACGATAGGTGCTTGCTTGT 58.273 50.000 0.00 0.00 43.77 3.16
749 788 0.647410 CGACGATAGGTGCTTGCTTG 59.353 55.000 0.00 0.00 43.77 4.01
750 789 1.084370 GCGACGATAGGTGCTTGCTT 61.084 55.000 0.00 0.00 43.77 3.91
751 790 1.519455 GCGACGATAGGTGCTTGCT 60.519 57.895 0.00 0.00 43.77 3.91
752 791 2.860628 CGCGACGATAGGTGCTTGC 61.861 63.158 0.00 0.00 43.77 4.01
753 792 1.076533 AACGCGACGATAGGTGCTTG 61.077 55.000 15.93 0.00 43.77 4.01
754 793 0.801067 GAACGCGACGATAGGTGCTT 60.801 55.000 15.93 0.00 43.77 3.91
755 794 1.226603 GAACGCGACGATAGGTGCT 60.227 57.895 15.93 0.00 43.77 4.40
756 795 2.565394 CGAACGCGACGATAGGTGC 61.565 63.158 15.93 0.00 40.82 5.01
757 796 1.937846 CCGAACGCGACGATAGGTG 60.938 63.158 25.06 9.03 40.82 4.00
758 797 2.406401 CCGAACGCGACGATAGGT 59.594 61.111 25.06 0.00 40.82 3.08
759 798 3.022914 GCCGAACGCGACGATAGG 61.023 66.667 25.06 14.92 40.82 2.57
784 823 0.308993 GCGGATGTAGAAGCAATGGC 59.691 55.000 0.00 0.00 41.61 4.40
785 824 1.331756 GTGCGGATGTAGAAGCAATGG 59.668 52.381 0.00 0.00 41.56 3.16
786 825 2.009051 TGTGCGGATGTAGAAGCAATG 58.991 47.619 0.00 0.00 41.56 2.82
787 826 2.401583 TGTGCGGATGTAGAAGCAAT 57.598 45.000 0.00 0.00 41.56 3.56
788 827 2.009051 CATGTGCGGATGTAGAAGCAA 58.991 47.619 0.00 0.00 41.56 3.91
789 828 1.655484 CATGTGCGGATGTAGAAGCA 58.345 50.000 0.00 0.00 37.26 3.91
790 829 0.305922 GCATGTGCGGATGTAGAAGC 59.694 55.000 0.00 0.00 0.00 3.86
801 840 4.450122 GCACCACGAGCATGTGCG 62.450 66.667 7.62 7.62 44.95 5.34
803 842 2.359107 AGGCACCACGAGCATGTG 60.359 61.111 0.00 1.64 39.60 3.21
804 843 2.359107 CAGGCACCACGAGCATGT 60.359 61.111 0.00 0.00 38.81 3.21
805 844 3.129502 CCAGGCACCACGAGCATG 61.130 66.667 0.00 0.00 42.86 4.06
808 847 3.391665 ATAGCCAGGCACCACGAGC 62.392 63.158 15.80 0.00 0.00 5.03
809 848 1.227380 GATAGCCAGGCACCACGAG 60.227 63.158 15.80 0.00 0.00 4.18
810 849 1.685765 AGATAGCCAGGCACCACGA 60.686 57.895 15.80 0.00 0.00 4.35
811 850 1.522355 CAGATAGCCAGGCACCACG 60.522 63.158 15.80 0.00 0.00 4.94
812 851 1.821332 GCAGATAGCCAGGCACCAC 60.821 63.158 15.80 1.86 37.23 4.16
813 852 2.591753 GCAGATAGCCAGGCACCA 59.408 61.111 15.80 0.00 37.23 4.17
814 853 2.590007 CGCAGATAGCCAGGCACC 60.590 66.667 15.80 1.52 41.38 5.01
815 854 1.884926 GTCGCAGATAGCCAGGCAC 60.885 63.158 15.80 4.61 40.67 5.01
816 855 2.501128 GTCGCAGATAGCCAGGCA 59.499 61.111 15.80 0.00 40.67 4.75
817 856 2.280457 GGTCGCAGATAGCCAGGC 60.280 66.667 1.84 1.84 40.67 4.85
818 857 1.068753 CAGGTCGCAGATAGCCAGG 59.931 63.158 0.00 0.00 40.67 4.45
819 858 1.593750 GCAGGTCGCAGATAGCCAG 60.594 63.158 0.00 0.00 40.67 4.85
820 859 2.501128 GCAGGTCGCAGATAGCCA 59.499 61.111 0.00 0.00 40.67 4.75
821 860 2.659897 CGCAGGTCGCAGATAGCC 60.660 66.667 0.00 0.00 42.60 3.93
838 877 4.064491 GTGTCACTGCAGCGACGC 62.064 66.667 27.13 27.13 34.78 5.19
839 878 3.406361 GGTGTCACTGCAGCGACG 61.406 66.667 25.39 8.31 34.78 5.12
843 882 0.110056 CAAATCGGTGTCACTGCAGC 60.110 55.000 15.27 0.00 0.00 5.25
844 883 0.110056 GCAAATCGGTGTCACTGCAG 60.110 55.000 13.48 13.48 0.00 4.41
845 884 0.534877 AGCAAATCGGTGTCACTGCA 60.535 50.000 14.44 2.56 32.21 4.41
846 885 0.110056 CAGCAAATCGGTGTCACTGC 60.110 55.000 6.95 6.49 38.36 4.40
847 886 0.518636 CCAGCAAATCGGTGTCACTG 59.481 55.000 5.35 5.35 41.76 3.66
848 887 1.237285 GCCAGCAAATCGGTGTCACT 61.237 55.000 2.35 0.00 41.76 3.41
849 888 1.210155 GCCAGCAAATCGGTGTCAC 59.790 57.895 0.00 0.00 41.76 3.67
850 889 1.073025 AGCCAGCAAATCGGTGTCA 59.927 52.632 0.00 0.00 41.76 3.58
851 890 1.503542 CAGCCAGCAAATCGGTGTC 59.496 57.895 0.00 0.00 41.76 3.67
852 891 1.973281 CCAGCCAGCAAATCGGTGT 60.973 57.895 0.00 0.00 41.76 4.16
853 892 1.243342 TTCCAGCCAGCAAATCGGTG 61.243 55.000 0.00 0.00 43.02 4.94
854 893 0.539438 TTTCCAGCCAGCAAATCGGT 60.539 50.000 0.00 0.00 0.00 4.69
855 894 0.602562 TTTTCCAGCCAGCAAATCGG 59.397 50.000 0.00 0.00 0.00 4.18
856 895 2.165030 AGATTTTCCAGCCAGCAAATCG 59.835 45.455 7.23 0.00 39.58 3.34
857 896 3.194116 TCAGATTTTCCAGCCAGCAAATC 59.806 43.478 5.47 5.47 36.34 2.17
858 897 3.167485 TCAGATTTTCCAGCCAGCAAAT 58.833 40.909 0.00 0.00 0.00 2.32
859 898 2.559668 CTCAGATTTTCCAGCCAGCAAA 59.440 45.455 0.00 0.00 0.00 3.68
860 899 2.165167 CTCAGATTTTCCAGCCAGCAA 58.835 47.619 0.00 0.00 0.00 3.91
861 900 1.352017 TCTCAGATTTTCCAGCCAGCA 59.648 47.619 0.00 0.00 0.00 4.41
862 901 2.015587 CTCTCAGATTTTCCAGCCAGC 58.984 52.381 0.00 0.00 0.00 4.85
863 902 3.623906 TCTCTCAGATTTTCCAGCCAG 57.376 47.619 0.00 0.00 0.00 4.85
864 903 3.584406 TCTTCTCTCAGATTTTCCAGCCA 59.416 43.478 0.00 0.00 0.00 4.75
865 904 4.213564 TCTTCTCTCAGATTTTCCAGCC 57.786 45.455 0.00 0.00 0.00 4.85
866 905 5.294060 GTCATCTTCTCTCAGATTTTCCAGC 59.706 44.000 0.00 0.00 30.50 4.85
867 906 6.642430 AGTCATCTTCTCTCAGATTTTCCAG 58.358 40.000 0.00 0.00 30.50 3.86
868 907 6.617782 AGTCATCTTCTCTCAGATTTTCCA 57.382 37.500 0.00 0.00 30.50 3.53
869 908 5.748152 CGAGTCATCTTCTCTCAGATTTTCC 59.252 44.000 0.00 0.00 30.50 3.13
870 909 6.559810 TCGAGTCATCTTCTCTCAGATTTTC 58.440 40.000 0.00 0.00 30.50 2.29
871 910 6.522625 TCGAGTCATCTTCTCTCAGATTTT 57.477 37.500 0.00 0.00 30.50 1.82
872 911 6.713762 ATCGAGTCATCTTCTCTCAGATTT 57.286 37.500 0.00 0.00 30.50 2.17
873 912 7.040478 CCTTATCGAGTCATCTTCTCTCAGATT 60.040 40.741 0.00 0.00 30.50 2.40
874 913 6.430925 CCTTATCGAGTCATCTTCTCTCAGAT 59.569 42.308 0.00 0.00 33.44 2.90
875 914 5.762711 CCTTATCGAGTCATCTTCTCTCAGA 59.237 44.000 0.00 0.00 0.00 3.27
876 915 5.762711 TCCTTATCGAGTCATCTTCTCTCAG 59.237 44.000 0.00 0.00 0.00 3.35
877 916 5.685728 TCCTTATCGAGTCATCTTCTCTCA 58.314 41.667 0.00 0.00 0.00 3.27
878 917 5.181245 CCTCCTTATCGAGTCATCTTCTCTC 59.819 48.000 0.00 0.00 0.00 3.20
879 918 5.070001 CCTCCTTATCGAGTCATCTTCTCT 58.930 45.833 0.00 0.00 0.00 3.10
880 919 5.067273 TCCTCCTTATCGAGTCATCTTCTC 58.933 45.833 0.00 0.00 0.00 2.87
881 920 5.055265 TCCTCCTTATCGAGTCATCTTCT 57.945 43.478 0.00 0.00 0.00 2.85
882 921 5.475220 TCATCCTCCTTATCGAGTCATCTTC 59.525 44.000 0.00 0.00 0.00 2.87
883 922 5.389520 TCATCCTCCTTATCGAGTCATCTT 58.610 41.667 0.00 0.00 0.00 2.40
884 923 4.991776 TCATCCTCCTTATCGAGTCATCT 58.008 43.478 0.00 0.00 0.00 2.90
885 924 5.336372 CCTTCATCCTCCTTATCGAGTCATC 60.336 48.000 0.00 0.00 0.00 2.92
886 925 4.526262 CCTTCATCCTCCTTATCGAGTCAT 59.474 45.833 0.00 0.00 0.00 3.06
887 926 3.891977 CCTTCATCCTCCTTATCGAGTCA 59.108 47.826 0.00 0.00 0.00 3.41
888 927 3.892588 ACCTTCATCCTCCTTATCGAGTC 59.107 47.826 0.00 0.00 0.00 3.36
889 928 3.917300 ACCTTCATCCTCCTTATCGAGT 58.083 45.455 0.00 0.00 0.00 4.18
890 929 4.461081 CCTACCTTCATCCTCCTTATCGAG 59.539 50.000 0.00 0.00 0.00 4.04
891 930 4.408276 CCTACCTTCATCCTCCTTATCGA 58.592 47.826 0.00 0.00 0.00 3.59
892 931 3.056465 GCCTACCTTCATCCTCCTTATCG 60.056 52.174 0.00 0.00 0.00 2.92
893 932 3.904339 TGCCTACCTTCATCCTCCTTATC 59.096 47.826 0.00 0.00 0.00 1.75
894 933 3.941629 TGCCTACCTTCATCCTCCTTAT 58.058 45.455 0.00 0.00 0.00 1.73
895 934 3.414759 TGCCTACCTTCATCCTCCTTA 57.585 47.619 0.00 0.00 0.00 2.69
896 935 2.270434 TGCCTACCTTCATCCTCCTT 57.730 50.000 0.00 0.00 0.00 3.36
897 936 2.270434 TTGCCTACCTTCATCCTCCT 57.730 50.000 0.00 0.00 0.00 3.69
898 937 2.173569 ACATTGCCTACCTTCATCCTCC 59.826 50.000 0.00 0.00 0.00 4.30
899 938 3.135530 AGACATTGCCTACCTTCATCCTC 59.864 47.826 0.00 0.00 0.00 3.71
900 939 3.118531 AGACATTGCCTACCTTCATCCT 58.881 45.455 0.00 0.00 0.00 3.24
901 940 3.567478 AGACATTGCCTACCTTCATCC 57.433 47.619 0.00 0.00 0.00 3.51
902 941 3.629398 CCAAGACATTGCCTACCTTCATC 59.371 47.826 0.00 0.00 34.91 2.92
903 942 3.624777 CCAAGACATTGCCTACCTTCAT 58.375 45.455 0.00 0.00 34.91 2.57
904 943 2.879756 GCCAAGACATTGCCTACCTTCA 60.880 50.000 0.00 0.00 34.91 3.02
905 944 1.745653 GCCAAGACATTGCCTACCTTC 59.254 52.381 0.00 0.00 34.91 3.46
906 945 1.616994 GGCCAAGACATTGCCTACCTT 60.617 52.381 0.00 0.00 34.91 3.50
907 946 0.034089 GGCCAAGACATTGCCTACCT 60.034 55.000 0.00 0.00 34.91 3.08
908 947 0.323360 TGGCCAAGACATTGCCTACC 60.323 55.000 0.61 0.00 35.13 3.18
909 948 1.406539 CATGGCCAAGACATTGCCTAC 59.593 52.381 10.96 0.00 35.13 3.18
910 949 1.005805 ACATGGCCAAGACATTGCCTA 59.994 47.619 16.33 0.00 35.13 3.93
911 950 0.251922 ACATGGCCAAGACATTGCCT 60.252 50.000 16.33 0.00 35.13 4.75
912 951 0.108520 CACATGGCCAAGACATTGCC 60.109 55.000 16.33 0.00 34.91 4.52
913 952 0.108520 CCACATGGCCAAGACATTGC 60.109 55.000 16.33 0.00 34.91 3.56
914 953 0.533491 CCCACATGGCCAAGACATTG 59.467 55.000 16.33 7.68 36.09 2.82
915 954 0.409092 TCCCACATGGCCAAGACATT 59.591 50.000 16.33 0.00 0.00 2.71
916 955 0.323725 GTCCCACATGGCCAAGACAT 60.324 55.000 16.33 0.00 0.00 3.06
917 956 1.074775 GTCCCACATGGCCAAGACA 59.925 57.895 16.33 0.00 0.00 3.41
918 957 1.678970 GGTCCCACATGGCCAAGAC 60.679 63.158 16.33 13.84 32.38 3.01
919 958 1.852157 AGGTCCCACATGGCCAAGA 60.852 57.895 16.33 1.65 33.97 3.02
920 959 1.679977 CAGGTCCCACATGGCCAAG 60.680 63.158 10.96 8.43 33.97 3.61
921 960 2.440147 CAGGTCCCACATGGCCAA 59.560 61.111 10.96 0.00 33.97 4.52
922 961 4.365111 GCAGGTCCCACATGGCCA 62.365 66.667 8.56 8.56 33.97 5.36
926 965 1.448540 GACTCGCAGGTCCCACATG 60.449 63.158 0.00 0.00 32.28 3.21
940 979 2.433318 GGGTCACTGCAGCGACTC 60.433 66.667 28.65 24.06 32.57 3.36
952 991 3.367321 TGTAGTGACAATATCGGGGTCA 58.633 45.455 0.00 0.00 39.09 4.02
953 992 3.383825 ACTGTAGTGACAATATCGGGGTC 59.616 47.826 0.00 0.00 34.35 4.46
954 993 3.371965 ACTGTAGTGACAATATCGGGGT 58.628 45.455 0.00 0.00 34.35 4.95
976 1020 1.495584 TTTCTTGCAGTGTCCGCGTC 61.496 55.000 4.92 0.00 0.00 5.19
979 1023 3.936585 TTTTTCTTGCAGTGTCCGC 57.063 47.368 0.00 0.00 0.00 5.54
1021 1068 2.367202 GCTGGGTGGCTACTGGCTA 61.367 63.158 0.00 0.00 41.46 3.93
1022 1069 3.721706 GCTGGGTGGCTACTGGCT 61.722 66.667 0.00 0.00 41.46 4.75
1025 1072 4.393155 TGCGCTGGGTGGCTACTG 62.393 66.667 9.73 0.00 0.00 2.74
1026 1073 4.087892 CTGCGCTGGGTGGCTACT 62.088 66.667 9.73 0.00 0.00 2.57
1351 1407 0.804933 GGAAGTACACGATCACCGGC 60.805 60.000 0.00 0.00 43.93 6.13
2017 2086 1.360820 GGAAGAAGTAGAAGGCGTGC 58.639 55.000 0.00 0.00 0.00 5.34
2156 2225 1.291184 ACACATGCACGACATCCACG 61.291 55.000 0.00 0.00 36.64 4.94
2159 2228 0.443869 GTGACACATGCACGACATCC 59.556 55.000 0.00 0.00 36.64 3.51
2160 2229 1.127397 CAGTGACACATGCACGACATC 59.873 52.381 8.59 0.00 41.04 3.06
2161 2230 1.150827 CAGTGACACATGCACGACAT 58.849 50.000 8.59 0.00 41.04 3.06
2162 2231 0.179086 ACAGTGACACATGCACGACA 60.179 50.000 8.59 0.00 41.04 4.35
2163 2232 0.508641 GACAGTGACACATGCACGAC 59.491 55.000 8.59 0.00 41.04 4.34
2164 2233 0.103937 TGACAGTGACACATGCACGA 59.896 50.000 8.59 0.00 41.04 4.35
2166 2235 2.355756 ACTTTGACAGTGACACATGCAC 59.644 45.455 8.59 0.00 32.83 4.57
2167 2236 2.613595 GACTTTGACAGTGACACATGCA 59.386 45.455 8.59 0.00 35.01 3.96
2169 2238 2.348872 GCGACTTTGACAGTGACACATG 60.349 50.000 8.59 5.98 35.01 3.21
2170 2239 1.867233 GCGACTTTGACAGTGACACAT 59.133 47.619 8.59 0.00 35.01 3.21
2172 2241 1.258982 CAGCGACTTTGACAGTGACAC 59.741 52.381 0.00 0.00 35.01 3.67
2292 2393 2.493030 GTGCCATCACTGCCATGC 59.507 61.111 0.00 0.00 40.03 4.06
2369 2470 2.034432 GCTTAGGCGGTAGTTAGAGGTC 59.966 54.545 0.00 0.00 0.00 3.85
2375 2476 4.222588 TGTTTTAGGCTTAGGCGGTAGTTA 59.777 41.667 0.00 0.00 39.81 2.24
2378 2479 2.934553 GTGTTTTAGGCTTAGGCGGTAG 59.065 50.000 0.00 0.00 39.81 3.18
2383 2484 2.420372 GAGCTGTGTTTTAGGCTTAGGC 59.580 50.000 0.00 0.00 35.01 3.93
2401 2502 4.904253 AGACGGTCTTATAGTTCAGAGC 57.096 45.455 4.45 0.00 34.73 4.09
2413 2514 4.981812 AGGGTTGAAAATTAGACGGTCTT 58.018 39.130 16.95 0.00 0.00 3.01
2428 2529 4.090090 TGGTTTTGAAAGTTGAGGGTTGA 58.910 39.130 0.00 0.00 0.00 3.18
2464 2565 2.564947 ACCAGTCAAAAACCACTGCAAA 59.435 40.909 0.00 0.00 39.03 3.68
2466 2567 1.846007 ACCAGTCAAAAACCACTGCA 58.154 45.000 0.00 0.00 39.03 4.41
2467 2568 2.959507 AACCAGTCAAAAACCACTGC 57.040 45.000 0.00 0.00 39.03 4.40
2468 2569 4.625311 GTCAAAACCAGTCAAAAACCACTG 59.375 41.667 0.00 0.00 39.90 3.66
2508 2610 0.899019 TGGCGTATGACTTGGTGCTA 59.101 50.000 0.00 0.00 0.00 3.49
2539 2641 7.093322 AGTGGAAGCAAATATCAGATTCAAC 57.907 36.000 5.26 5.26 35.00 3.18
2707 2821 5.869649 ACAAGTTTTGCCAAGTAGGAAAT 57.130 34.783 0.00 0.00 41.22 2.17
2711 2827 4.338118 TCTCAACAAGTTTTGCCAAGTAGG 59.662 41.667 0.00 0.00 41.84 3.18
2749 2865 3.676291 AAACCCACACAACCATTATGC 57.324 42.857 0.00 0.00 0.00 3.14
2750 2866 5.605534 TCAAAAACCCACACAACCATTATG 58.394 37.500 0.00 0.00 0.00 1.90
2832 2948 6.748132 AGAGCGGAAAAATCAAATTCAAAGA 58.252 32.000 0.00 0.00 0.00 2.52
2867 2983 5.536161 ACTTTCAACATGTTCTGCCAAGTAT 59.464 36.000 8.48 0.00 0.00 2.12
2920 3037 3.838271 GGATCTCTGGCCGACGCA 61.838 66.667 0.00 0.00 36.38 5.24
2978 3095 4.987963 TGTGATGATGAAGGCAGGATAT 57.012 40.909 0.00 0.00 0.00 1.63
2984 3101 3.256383 CCTTTGTTGTGATGATGAAGGCA 59.744 43.478 0.00 0.00 0.00 4.75
2997 3114 5.352846 GGTTTTGTAACATTGCCTTTGTTGT 59.647 36.000 6.34 0.00 37.81 3.32
3017 3134 5.535753 ATTAGCTCAGTTGCAAAAGGTTT 57.464 34.783 0.00 0.00 34.99 3.27
3021 3138 9.495754 GAAATAGTATTAGCTCAGTTGCAAAAG 57.504 33.333 0.00 0.05 34.99 2.27
3084 3203 4.103365 TGTTGCAAAAAGTGATGACGTT 57.897 36.364 0.00 0.00 0.00 3.99
3185 3316 0.385473 GTTGCAAACGACGATGGTGG 60.385 55.000 0.00 0.00 36.92 4.61
3209 3356 5.464057 CACAAATGAGTTCATGCAACAACAT 59.536 36.000 12.32 10.47 37.48 2.71
3221 3368 2.483877 TCGTCCATGCACAAATGAGTTC 59.516 45.455 0.00 0.00 0.00 3.01
3228 3375 1.196581 CAACGATCGTCCATGCACAAA 59.803 47.619 22.98 0.00 0.00 2.83
3229 3376 0.795698 CAACGATCGTCCATGCACAA 59.204 50.000 22.98 0.00 0.00 3.33
3242 3389 1.359848 GGCAACGATGAGTCAACGAT 58.640 50.000 26.94 14.31 33.96 3.73
3267 3414 1.366854 TATCTGCGAGCGTCGTGACT 61.367 55.000 8.72 0.00 42.81 3.41
3273 3420 1.369448 CTCGGTATCTGCGAGCGTC 60.369 63.158 0.00 0.00 38.84 5.19
3274 3421 0.812811 TACTCGGTATCTGCGAGCGT 60.813 55.000 0.00 0.00 38.84 5.07
3275 3422 0.384477 GTACTCGGTATCTGCGAGCG 60.384 60.000 0.00 0.00 39.10 5.03
3276 3423 0.661552 TGTACTCGGTATCTGCGAGC 59.338 55.000 0.00 0.00 33.53 5.03
3277 3424 1.264557 CCTGTACTCGGTATCTGCGAG 59.735 57.143 0.00 0.00 36.03 5.03
3278 3425 1.306148 CCTGTACTCGGTATCTGCGA 58.694 55.000 0.00 0.00 0.00 5.10
3279 3426 0.317938 GCCTGTACTCGGTATCTGCG 60.318 60.000 0.00 0.00 0.00 5.18
3280 3427 0.317938 CGCCTGTACTCGGTATCTGC 60.318 60.000 0.00 0.00 0.00 4.26
3281 3428 1.306148 TCGCCTGTACTCGGTATCTG 58.694 55.000 0.00 0.00 0.00 2.90
3282 3429 1.880675 CATCGCCTGTACTCGGTATCT 59.119 52.381 0.00 0.00 0.00 1.98
3283 3430 1.666311 GCATCGCCTGTACTCGGTATC 60.666 57.143 0.00 0.00 0.00 2.24
3284 3431 0.314302 GCATCGCCTGTACTCGGTAT 59.686 55.000 0.00 0.00 0.00 2.73
3285 3432 1.731700 GCATCGCCTGTACTCGGTA 59.268 57.895 0.00 0.00 0.00 4.02
3286 3433 2.494918 GCATCGCCTGTACTCGGT 59.505 61.111 0.00 0.00 0.00 4.69
3308 3455 2.202427 CAAATTTCCGCCGCCGTC 60.202 61.111 0.00 0.00 0.00 4.79
3310 3457 3.743636 ACCAAATTTCCGCCGCCG 61.744 61.111 0.00 0.00 0.00 6.46
3314 3461 1.134946 CTCCATCACCAAATTTCCGCC 59.865 52.381 0.00 0.00 0.00 6.13
3318 3465 3.119352 GCTGACCTCCATCACCAAATTTC 60.119 47.826 0.00 0.00 0.00 2.17
3331 3478 4.864334 CCGCCATGGCTGACCTCC 62.864 72.222 33.07 3.30 39.32 4.30
3346 3493 0.388006 GGATCCAAAAACAACCGCCG 60.388 55.000 6.95 0.00 0.00 6.46
3349 3496 2.095617 GGTACGGATCCAAAAACAACCG 60.096 50.000 13.41 0.00 44.77 4.44
3350 3497 3.151554 AGGTACGGATCCAAAAACAACC 58.848 45.455 13.41 7.65 0.00 3.77
3358 3505 3.705051 ACTCAACTAGGTACGGATCCAA 58.295 45.455 13.41 0.00 0.00 3.53
3396 3543 2.971452 GGTGACCAGGTCTCCGTC 59.029 66.667 22.35 7.59 36.66 4.79


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

AutoCloner maintained by Alex Coulton.