Multiple sequence alignment - TraesCS6B01G159000

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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 TraesCS6B01G159000 chr6B 100.000 3510 0 0 1 3510 161586408 161589917 0.000000e+00 6482.0
1 TraesCS6B01G159000 chr6B 86.538 208 27 1 550 756 159697691 159697898 9.800000e-56 228.0
2 TraesCS6B01G159000 chr6A 93.484 1857 84 12 969 2803 102104971 102106812 0.000000e+00 2724.0
3 TraesCS6B01G159000 chr6A 86.732 716 48 25 2820 3494 102107479 102108188 0.000000e+00 752.0
4 TraesCS6B01G159000 chr6A 82.222 90 13 3 2540 2627 102001111 102001199 1.350000e-09 75.0
5 TraesCS6B01G159000 chr6D 88.611 2160 137 46 972 3104 85041341 85039264 0.000000e+00 2525.0
6 TraesCS6B01G159000 chr6D 94.602 389 19 1 3122 3510 85039152 85038766 5.010000e-168 601.0
7 TraesCS6B01G159000 chr6D 85.981 214 23 6 550 760 65107740 65107531 4.560000e-54 222.0
8 TraesCS6B01G159000 chr7D 87.748 555 60 5 1 551 4239532 4240082 2.950000e-180 641.0
9 TraesCS6B01G159000 chr7D 88.626 211 20 4 550 758 538893339 538893131 1.620000e-63 254.0
10 TraesCS6B01G159000 chr4D 87.004 554 55 9 15 551 319338125 319337572 3.000000e-170 608.0
11 TraesCS6B01G159000 chr4D 86.372 543 65 8 14 552 343059032 343058495 5.050000e-163 584.0
12 TraesCS6B01G159000 chr4D 85.918 561 61 12 8 553 29871298 29871855 1.820000e-162 582.0
13 TraesCS6B01G159000 chr3D 86.042 566 54 13 1 552 412820027 412820581 5.050000e-163 584.0
14 TraesCS6B01G159000 chr3D 84.725 563 67 13 1 555 551003405 551003956 2.380000e-151 545.0
15 TraesCS6B01G159000 chr3D 82.472 542 87 8 16 552 183736602 183737140 5.310000e-128 468.0
16 TraesCS6B01G159000 chr3D 86.190 210 27 2 550 758 551004001 551004209 3.530000e-55 226.0
17 TraesCS6B01G159000 chr3D 86.124 209 27 2 551 758 120104607 120104400 1.270000e-54 224.0
18 TraesCS6B01G159000 chr3D 86.058 208 28 1 550 756 412820628 412820835 4.560000e-54 222.0
19 TraesCS6B01G159000 chr3D 85.321 218 28 4 550 764 520810357 520810573 4.560000e-54 222.0
20 TraesCS6B01G159000 chr3D 90.566 53 3 2 2963 3014 228201755 228201806 6.290000e-08 69.4
21 TraesCS6B01G159000 chr7B 81.087 497 81 11 16 502 637867471 637867964 5.500000e-103 385.0
22 TraesCS6B01G159000 chr3A 81.128 461 77 9 61 516 649824506 649824961 9.260000e-96 361.0
23 TraesCS6B01G159000 chr1D 81.297 401 63 11 26 422 447450197 447450589 7.310000e-82 315.0
24 TraesCS6B01G159000 chr1D 82.222 360 48 11 203 553 307355049 307354697 2.650000e-76 296.0
25 TraesCS6B01G159000 chr1D 86.408 206 27 1 552 756 52738667 52738462 1.270000e-54 224.0
26 TraesCS6B01G159000 chr3B 79.864 442 65 17 15 443 22892108 22891678 5.690000e-78 302.0
27 TraesCS6B01G159000 chr2D 86.916 214 25 3 551 762 43279162 43279374 1.630000e-58 237.0
28 TraesCS6B01G159000 chr2D 95.238 42 1 1 2974 3014 29821426 29821385 8.130000e-07 65.8
29 TraesCS6B01G159000 chr1B 97.143 35 1 0 2986 3020 438699850 438699816 3.780000e-05 60.2


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 TraesCS6B01G159000 chr6B 161586408 161589917 3509 False 6482.0 6482 100.0000 1 3510 1 chr6B.!!$F2 3509
1 TraesCS6B01G159000 chr6A 102104971 102108188 3217 False 1738.0 2724 90.1080 969 3494 2 chr6A.!!$F2 2525
2 TraesCS6B01G159000 chr6D 85038766 85041341 2575 True 1563.0 2525 91.6065 972 3510 2 chr6D.!!$R2 2538
3 TraesCS6B01G159000 chr7D 4239532 4240082 550 False 641.0 641 87.7480 1 551 1 chr7D.!!$F1 550
4 TraesCS6B01G159000 chr4D 319337572 319338125 553 True 608.0 608 87.0040 15 551 1 chr4D.!!$R1 536
5 TraesCS6B01G159000 chr4D 343058495 343059032 537 True 584.0 584 86.3720 14 552 1 chr4D.!!$R2 538
6 TraesCS6B01G159000 chr4D 29871298 29871855 557 False 582.0 582 85.9180 8 553 1 chr4D.!!$F1 545
7 TraesCS6B01G159000 chr3D 183736602 183737140 538 False 468.0 468 82.4720 16 552 1 chr3D.!!$F1 536
8 TraesCS6B01G159000 chr3D 412820027 412820835 808 False 403.0 584 86.0500 1 756 2 chr3D.!!$F4 755
9 TraesCS6B01G159000 chr3D 551003405 551004209 804 False 385.5 545 85.4575 1 758 2 chr3D.!!$F5 757

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
832 963 0.035439 CTGGGAATAACTGCCGTGGT 60.035 55.0 0.0 0.0 38.74 4.16 F
2034 2201 0.030638 CCAACTTCAAGCAACCACCG 59.969 55.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2321 1.098712 AGCCAGTCGAGAGATCGTCC 61.099 60.0 0.00 0.0 45.19 4.79 R
2991 3833 0.879400 CATCACTCGATGCAGAGGCC 60.879 60.0 7.77 0.0 42.54 5.19 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
61 69 0.178990 GCTCACCTTGGGGAGTGTTT 60.179 55.000 18.92 0.00 35.45 2.83
154 162 2.685017 AGGCAGCACCATCCGAGA 60.685 61.111 0.00 0.00 43.14 4.04
325 351 2.578713 CGTCGTTGCGTCCGCTAT 60.579 61.111 13.31 0.00 42.51 2.97
370 396 3.721706 CTCCCTTGCCCGCTCCTT 61.722 66.667 0.00 0.00 0.00 3.36
386 412 1.695242 TCCTTGGGCGTCAACTTCTTA 59.305 47.619 0.00 0.00 0.00 2.10
443 472 3.130160 GGCTTGCCTTCGCCAGAG 61.130 66.667 4.11 0.00 45.59 3.35
450 480 3.003173 CTTCGCCAGAGGGGGTGA 61.003 66.667 0.01 0.00 46.73 4.02
459 489 1.050988 AGAGGGGGTGATCGTGATGG 61.051 60.000 0.00 0.00 0.00 3.51
559 689 2.037367 GGGTTTTGGGGGAGGAGC 59.963 66.667 0.00 0.00 0.00 4.70
612 742 3.093278 CCGACGCAAATGAGGCTC 58.907 61.111 7.79 7.79 0.00 4.70
620 750 3.005684 ACGCAAATGAGGCTCAAAAATGA 59.994 39.130 22.84 0.00 0.00 2.57
622 752 4.563061 GCAAATGAGGCTCAAAAATGAGT 58.437 39.130 22.84 0.00 38.16 3.41
630 760 3.945285 GGCTCAAAAATGAGTCGGGAATA 59.055 43.478 7.59 0.00 38.16 1.75
636 766 2.359981 ATGAGTCGGGAATAGGTCGA 57.640 50.000 0.00 0.00 0.00 4.20
640 770 3.888424 TCGGGAATAGGTCGACAGA 57.112 52.632 18.91 4.30 0.00 3.41
658 788 1.005394 ACGGATGAAAAGCGGACGT 60.005 52.632 0.00 0.00 0.00 4.34
663 793 0.447801 ATGAAAAGCGGACGTGCATC 59.552 50.000 8.11 0.00 37.31 3.91
671 801 3.429043 GGACGTGCATCCGTTTAGA 57.571 52.632 0.63 0.00 41.98 2.10
682 812 0.866906 CCGTTTAGATCGGCGCGTTA 60.867 55.000 8.43 0.00 41.48 3.18
698 829 2.673833 CGTTAGCCGACTTTTCTGTCT 58.326 47.619 0.00 0.00 39.56 3.41
706 837 0.320771 ACTTTTCTGTCTGCGCCGAT 60.321 50.000 4.18 0.00 0.00 4.18
712 843 1.078497 TGTCTGCGCCGATCCAAAT 60.078 52.632 4.18 0.00 0.00 2.32
713 844 0.176910 TGTCTGCGCCGATCCAAATA 59.823 50.000 4.18 0.00 0.00 1.40
758 889 1.359848 CGCGTTGGAGTTGCTCTAAT 58.640 50.000 0.00 0.00 33.81 1.73
759 890 2.536365 CGCGTTGGAGTTGCTCTAATA 58.464 47.619 0.00 0.00 33.81 0.98
760 891 2.281762 CGCGTTGGAGTTGCTCTAATAC 59.718 50.000 0.00 0.00 33.81 1.89
761 892 2.608090 GCGTTGGAGTTGCTCTAATACC 59.392 50.000 0.00 0.00 33.81 2.73
762 893 2.858344 CGTTGGAGTTGCTCTAATACCG 59.142 50.000 0.00 0.00 33.81 4.02
763 894 3.675228 CGTTGGAGTTGCTCTAATACCGT 60.675 47.826 0.00 0.00 33.81 4.83
764 895 4.251268 GTTGGAGTTGCTCTAATACCGTT 58.749 43.478 0.00 0.00 33.81 4.44
765 896 4.546829 TGGAGTTGCTCTAATACCGTTT 57.453 40.909 0.00 0.00 0.00 3.60
766 897 4.901868 TGGAGTTGCTCTAATACCGTTTT 58.098 39.130 0.00 0.00 0.00 2.43
767 898 5.310451 TGGAGTTGCTCTAATACCGTTTTT 58.690 37.500 0.00 0.00 0.00 1.94
768 899 5.180492 TGGAGTTGCTCTAATACCGTTTTTG 59.820 40.000 0.00 0.00 0.00 2.44
769 900 5.410439 GGAGTTGCTCTAATACCGTTTTTGA 59.590 40.000 0.00 0.00 0.00 2.69
770 901 6.237313 AGTTGCTCTAATACCGTTTTTGAC 57.763 37.500 0.00 0.00 0.00 3.18
771 902 5.761234 AGTTGCTCTAATACCGTTTTTGACA 59.239 36.000 0.00 0.00 0.00 3.58
772 903 5.600908 TGCTCTAATACCGTTTTTGACAC 57.399 39.130 0.00 0.00 0.00 3.67
773 904 5.302360 TGCTCTAATACCGTTTTTGACACT 58.698 37.500 0.00 0.00 0.00 3.55
774 905 6.457355 TGCTCTAATACCGTTTTTGACACTA 58.543 36.000 0.00 0.00 0.00 2.74
775 906 6.588756 TGCTCTAATACCGTTTTTGACACTAG 59.411 38.462 0.00 0.00 0.00 2.57
776 907 6.035758 GCTCTAATACCGTTTTTGACACTAGG 59.964 42.308 0.00 0.00 0.00 3.02
777 908 6.996509 TCTAATACCGTTTTTGACACTAGGT 58.003 36.000 0.00 0.00 0.00 3.08
778 909 7.444299 TCTAATACCGTTTTTGACACTAGGTT 58.556 34.615 0.00 0.00 0.00 3.50
779 910 5.934935 ATACCGTTTTTGACACTAGGTTG 57.065 39.130 0.00 0.00 0.00 3.77
780 911 3.876341 ACCGTTTTTGACACTAGGTTGA 58.124 40.909 0.00 0.00 0.00 3.18
781 912 4.263435 ACCGTTTTTGACACTAGGTTGAA 58.737 39.130 0.00 0.00 0.00 2.69
782 913 4.885325 ACCGTTTTTGACACTAGGTTGAAT 59.115 37.500 0.00 0.00 0.00 2.57
783 914 5.358725 ACCGTTTTTGACACTAGGTTGAATT 59.641 36.000 0.00 0.00 0.00 2.17
784 915 5.685511 CCGTTTTTGACACTAGGTTGAATTG 59.314 40.000 0.00 0.00 0.00 2.32
785 916 6.459024 CCGTTTTTGACACTAGGTTGAATTGA 60.459 38.462 0.00 0.00 0.00 2.57
786 917 6.970043 CGTTTTTGACACTAGGTTGAATTGAA 59.030 34.615 0.00 0.00 0.00 2.69
787 918 7.044314 CGTTTTTGACACTAGGTTGAATTGAAC 60.044 37.037 0.00 0.00 0.00 3.18
788 919 7.397892 TTTTGACACTAGGTTGAATTGAACA 57.602 32.000 10.02 0.00 0.00 3.18
789 920 7.397892 TTTGACACTAGGTTGAATTGAACAA 57.602 32.000 10.02 0.00 0.00 2.83
790 921 7.397892 TTGACACTAGGTTGAATTGAACAAA 57.602 32.000 10.02 0.00 0.00 2.83
791 922 7.397892 TGACACTAGGTTGAATTGAACAAAA 57.602 32.000 10.02 0.00 0.00 2.44
792 923 7.254852 TGACACTAGGTTGAATTGAACAAAAC 58.745 34.615 10.02 0.00 0.00 2.43
793 924 7.094162 TGACACTAGGTTGAATTGAACAAAACA 60.094 33.333 10.02 0.00 0.00 2.83
794 925 7.781056 ACACTAGGTTGAATTGAACAAAACAT 58.219 30.769 10.02 0.00 0.00 2.71
795 926 7.706179 ACACTAGGTTGAATTGAACAAAACATG 59.294 33.333 10.02 0.00 0.00 3.21
796 927 7.706179 CACTAGGTTGAATTGAACAAAACATGT 59.294 33.333 10.02 0.00 46.82 3.21
816 947 9.537192 AACATGTTATGAATATTGAATTGCTGG 57.463 29.630 9.97 0.00 0.00 4.85
817 948 8.145767 ACATGTTATGAATATTGAATTGCTGGG 58.854 33.333 0.00 0.00 0.00 4.45
818 949 7.894753 TGTTATGAATATTGAATTGCTGGGA 57.105 32.000 0.00 0.00 0.00 4.37
819 950 8.303780 TGTTATGAATATTGAATTGCTGGGAA 57.696 30.769 0.00 0.00 0.00 3.97
820 951 8.926374 TGTTATGAATATTGAATTGCTGGGAAT 58.074 29.630 0.00 0.00 0.00 3.01
824 955 8.537728 TGAATATTGAATTGCTGGGAATAACT 57.462 30.769 0.00 0.00 0.00 2.24
825 956 8.415553 TGAATATTGAATTGCTGGGAATAACTG 58.584 33.333 0.00 0.00 0.00 3.16
826 957 4.454728 TTGAATTGCTGGGAATAACTGC 57.545 40.909 0.00 0.00 0.00 4.40
827 958 2.760092 TGAATTGCTGGGAATAACTGCC 59.240 45.455 0.00 0.00 35.64 4.85
828 959 1.392589 ATTGCTGGGAATAACTGCCG 58.607 50.000 0.00 0.00 38.74 5.69
829 960 0.037590 TTGCTGGGAATAACTGCCGT 59.962 50.000 0.00 0.00 38.74 5.68
830 961 0.676466 TGCTGGGAATAACTGCCGTG 60.676 55.000 0.00 0.00 38.74 4.94
831 962 1.376609 GCTGGGAATAACTGCCGTGG 61.377 60.000 0.00 0.00 38.74 4.94
832 963 0.035439 CTGGGAATAACTGCCGTGGT 60.035 55.000 0.00 0.00 38.74 4.16
833 964 0.035820 TGGGAATAACTGCCGTGGTC 60.036 55.000 0.00 0.00 38.74 4.02
834 965 0.035820 GGGAATAACTGCCGTGGTCA 60.036 55.000 0.00 0.00 0.00 4.02
835 966 1.612199 GGGAATAACTGCCGTGGTCAA 60.612 52.381 0.00 0.00 0.00 3.18
836 967 2.365582 GGAATAACTGCCGTGGTCAAT 58.634 47.619 0.00 0.00 0.00 2.57
837 968 2.097466 GGAATAACTGCCGTGGTCAATG 59.903 50.000 0.00 0.00 0.00 2.82
838 969 2.779755 ATAACTGCCGTGGTCAATGA 57.220 45.000 0.00 0.00 0.00 2.57
839 970 1.803334 TAACTGCCGTGGTCAATGAC 58.197 50.000 4.51 4.51 0.00 3.06
840 971 0.179032 AACTGCCGTGGTCAATGACA 60.179 50.000 15.86 0.00 33.68 3.58
841 972 0.179032 ACTGCCGTGGTCAATGACAA 60.179 50.000 15.86 0.00 33.68 3.18
842 973 0.518636 CTGCCGTGGTCAATGACAAG 59.481 55.000 15.86 5.46 33.68 3.16
843 974 1.210155 GCCGTGGTCAATGACAAGC 59.790 57.895 15.86 7.92 33.68 4.01
844 975 1.497278 CCGTGGTCAATGACAAGCG 59.503 57.895 15.86 14.45 33.68 4.68
845 976 0.948623 CCGTGGTCAATGACAAGCGA 60.949 55.000 15.86 0.00 33.68 4.93
846 977 0.439985 CGTGGTCAATGACAAGCGAG 59.560 55.000 15.86 0.00 33.68 5.03
847 978 1.795768 GTGGTCAATGACAAGCGAGA 58.204 50.000 15.86 0.00 33.68 4.04
848 979 1.728971 GTGGTCAATGACAAGCGAGAG 59.271 52.381 15.86 0.00 33.68 3.20
849 980 1.618343 TGGTCAATGACAAGCGAGAGA 59.382 47.619 15.86 0.00 33.68 3.10
850 981 1.996191 GGTCAATGACAAGCGAGAGAC 59.004 52.381 15.86 0.00 33.68 3.36
851 982 2.353208 GGTCAATGACAAGCGAGAGACT 60.353 50.000 15.86 0.00 33.68 3.24
852 983 3.119459 GGTCAATGACAAGCGAGAGACTA 60.119 47.826 15.86 0.00 33.68 2.59
853 984 3.854809 GTCAATGACAAGCGAGAGACTAC 59.145 47.826 8.74 0.00 32.09 2.73
854 985 3.759086 TCAATGACAAGCGAGAGACTACT 59.241 43.478 0.00 0.00 0.00 2.57
855 986 4.218635 TCAATGACAAGCGAGAGACTACTT 59.781 41.667 0.00 0.00 0.00 2.24
856 987 4.792521 ATGACAAGCGAGAGACTACTTT 57.207 40.909 0.00 0.00 0.00 2.66
857 988 4.585955 TGACAAGCGAGAGACTACTTTT 57.414 40.909 0.00 0.00 0.00 2.27
858 989 5.700722 TGACAAGCGAGAGACTACTTTTA 57.299 39.130 0.00 0.00 0.00 1.52
859 990 6.268825 TGACAAGCGAGAGACTACTTTTAT 57.731 37.500 0.00 0.00 0.00 1.40
860 991 6.093404 TGACAAGCGAGAGACTACTTTTATG 58.907 40.000 0.00 0.00 0.00 1.90
861 992 6.072119 TGACAAGCGAGAGACTACTTTTATGA 60.072 38.462 0.00 0.00 0.00 2.15
862 993 6.688578 ACAAGCGAGAGACTACTTTTATGAA 58.311 36.000 0.00 0.00 0.00 2.57
863 994 7.324178 ACAAGCGAGAGACTACTTTTATGAAT 58.676 34.615 0.00 0.00 0.00 2.57
864 995 7.276658 ACAAGCGAGAGACTACTTTTATGAATG 59.723 37.037 0.00 0.00 0.00 2.67
865 996 6.868622 AGCGAGAGACTACTTTTATGAATGT 58.131 36.000 0.00 0.00 0.00 2.71
866 997 7.324178 AGCGAGAGACTACTTTTATGAATGTT 58.676 34.615 0.00 0.00 0.00 2.71
867 998 7.819900 AGCGAGAGACTACTTTTATGAATGTTT 59.180 33.333 0.00 0.00 0.00 2.83
868 999 9.084164 GCGAGAGACTACTTTTATGAATGTTTA 57.916 33.333 0.00 0.00 0.00 2.01
885 1016 9.932207 TGAATGTTTATGAATCTGAATTTGCTT 57.068 25.926 0.00 0.00 0.00 3.91
892 1023 9.985730 TTATGAATCTGAATTTGCTTTTTGACT 57.014 25.926 0.00 0.00 0.00 3.41
893 1024 8.897872 ATGAATCTGAATTTGCTTTTTGACTT 57.102 26.923 0.00 0.00 0.00 3.01
894 1025 8.133754 TGAATCTGAATTTGCTTTTTGACTTG 57.866 30.769 0.00 0.00 0.00 3.16
895 1026 5.971895 TCTGAATTTGCTTTTTGACTTGC 57.028 34.783 0.00 0.00 0.00 4.01
896 1027 4.503734 TCTGAATTTGCTTTTTGACTTGCG 59.496 37.500 0.00 0.00 0.00 4.85
897 1028 4.428209 TGAATTTGCTTTTTGACTTGCGA 58.572 34.783 0.00 0.00 0.00 5.10
898 1029 4.867047 TGAATTTGCTTTTTGACTTGCGAA 59.133 33.333 0.00 0.00 33.95 4.70
899 1030 4.777140 ATTTGCTTTTTGACTTGCGAAC 57.223 36.364 0.00 0.00 32.49 3.95
900 1031 3.502191 TTGCTTTTTGACTTGCGAACT 57.498 38.095 0.00 0.00 0.00 3.01
901 1032 3.502191 TGCTTTTTGACTTGCGAACTT 57.498 38.095 0.00 0.00 0.00 2.66
902 1033 3.434637 TGCTTTTTGACTTGCGAACTTC 58.565 40.909 0.00 0.00 0.00 3.01
903 1034 3.119673 TGCTTTTTGACTTGCGAACTTCA 60.120 39.130 0.00 0.00 0.00 3.02
904 1035 3.857093 GCTTTTTGACTTGCGAACTTCAA 59.143 39.130 0.00 0.00 0.00 2.69
905 1036 4.326009 GCTTTTTGACTTGCGAACTTCAAA 59.674 37.500 0.00 0.00 36.43 2.69
906 1037 5.164002 GCTTTTTGACTTGCGAACTTCAAAA 60.164 36.000 7.10 7.10 43.04 2.44
907 1038 6.455513 GCTTTTTGACTTGCGAACTTCAAAAT 60.456 34.615 10.73 0.00 43.74 1.82
908 1039 5.947503 TTTGACTTGCGAACTTCAAAATG 57.052 34.783 0.00 0.00 35.54 2.32
909 1040 3.963665 TGACTTGCGAACTTCAAAATGG 58.036 40.909 0.00 0.00 0.00 3.16
910 1041 3.629855 TGACTTGCGAACTTCAAAATGGA 59.370 39.130 0.00 0.00 0.00 3.41
911 1042 4.222114 GACTTGCGAACTTCAAAATGGAG 58.778 43.478 0.00 0.00 0.00 3.86
912 1043 3.004734 ACTTGCGAACTTCAAAATGGAGG 59.995 43.478 0.00 0.00 0.00 4.30
913 1044 1.269448 TGCGAACTTCAAAATGGAGGC 59.731 47.619 0.00 0.00 0.00 4.70
914 1045 1.541588 GCGAACTTCAAAATGGAGGCT 59.458 47.619 0.00 0.00 0.00 4.58
915 1046 2.669391 GCGAACTTCAAAATGGAGGCTG 60.669 50.000 0.00 0.00 0.00 4.85
916 1047 2.669391 CGAACTTCAAAATGGAGGCTGC 60.669 50.000 0.00 0.00 0.00 5.25
917 1048 2.299326 ACTTCAAAATGGAGGCTGCT 57.701 45.000 7.74 0.00 0.00 4.24
918 1049 2.165998 ACTTCAAAATGGAGGCTGCTC 58.834 47.619 7.74 0.00 0.00 4.26
919 1050 1.475682 CTTCAAAATGGAGGCTGCTCC 59.524 52.381 7.74 5.42 43.60 4.70
927 1058 2.037367 AGGCTGCTCCTACGACCA 59.963 61.111 0.00 0.00 45.41 4.02
928 1059 2.184579 GGCTGCTCCTACGACCAC 59.815 66.667 0.00 0.00 0.00 4.16
929 1060 2.352032 GGCTGCTCCTACGACCACT 61.352 63.158 0.00 0.00 0.00 4.00
930 1061 1.139947 GCTGCTCCTACGACCACTC 59.860 63.158 0.00 0.00 0.00 3.51
931 1062 1.810532 CTGCTCCTACGACCACTCC 59.189 63.158 0.00 0.00 0.00 3.85
932 1063 0.681564 CTGCTCCTACGACCACTCCT 60.682 60.000 0.00 0.00 0.00 3.69
933 1064 0.680280 TGCTCCTACGACCACTCCTC 60.680 60.000 0.00 0.00 0.00 3.71
934 1065 0.394625 GCTCCTACGACCACTCCTCT 60.395 60.000 0.00 0.00 0.00 3.69
935 1066 1.956159 GCTCCTACGACCACTCCTCTT 60.956 57.143 0.00 0.00 0.00 2.85
936 1067 2.018515 CTCCTACGACCACTCCTCTTC 58.981 57.143 0.00 0.00 0.00 2.87
937 1068 1.353358 TCCTACGACCACTCCTCTTCA 59.647 52.381 0.00 0.00 0.00 3.02
938 1069 1.746220 CCTACGACCACTCCTCTTCAG 59.254 57.143 0.00 0.00 0.00 3.02
939 1070 2.438411 CTACGACCACTCCTCTTCAGT 58.562 52.381 0.00 0.00 0.00 3.41
940 1071 1.705873 ACGACCACTCCTCTTCAGTT 58.294 50.000 0.00 0.00 0.00 3.16
941 1072 1.341531 ACGACCACTCCTCTTCAGTTG 59.658 52.381 0.00 0.00 0.00 3.16
942 1073 1.802069 GACCACTCCTCTTCAGTTGC 58.198 55.000 0.00 0.00 0.00 4.17
943 1074 1.346068 GACCACTCCTCTTCAGTTGCT 59.654 52.381 0.00 0.00 0.00 3.91
944 1075 1.346068 ACCACTCCTCTTCAGTTGCTC 59.654 52.381 0.00 0.00 0.00 4.26
945 1076 1.622811 CCACTCCTCTTCAGTTGCTCT 59.377 52.381 0.00 0.00 0.00 4.09
946 1077 2.038295 CCACTCCTCTTCAGTTGCTCTT 59.962 50.000 0.00 0.00 0.00 2.85
947 1078 3.495806 CCACTCCTCTTCAGTTGCTCTTT 60.496 47.826 0.00 0.00 0.00 2.52
948 1079 4.133078 CACTCCTCTTCAGTTGCTCTTTT 58.867 43.478 0.00 0.00 0.00 2.27
949 1080 4.213059 CACTCCTCTTCAGTTGCTCTTTTC 59.787 45.833 0.00 0.00 0.00 2.29
950 1081 3.393800 TCCTCTTCAGTTGCTCTTTTCG 58.606 45.455 0.00 0.00 0.00 3.46
951 1082 2.481952 CCTCTTCAGTTGCTCTTTTCGG 59.518 50.000 0.00 0.00 0.00 4.30
952 1083 3.393800 CTCTTCAGTTGCTCTTTTCGGA 58.606 45.455 0.00 0.00 0.00 4.55
953 1084 3.999663 CTCTTCAGTTGCTCTTTTCGGAT 59.000 43.478 0.00 0.00 0.00 4.18
954 1085 3.748048 TCTTCAGTTGCTCTTTTCGGATG 59.252 43.478 0.00 0.00 0.00 3.51
955 1086 2.426522 TCAGTTGCTCTTTTCGGATGG 58.573 47.619 0.00 0.00 0.00 3.51
956 1087 2.154462 CAGTTGCTCTTTTCGGATGGT 58.846 47.619 0.00 0.00 0.00 3.55
957 1088 3.007506 TCAGTTGCTCTTTTCGGATGGTA 59.992 43.478 0.00 0.00 0.00 3.25
958 1089 3.751175 CAGTTGCTCTTTTCGGATGGTAA 59.249 43.478 0.00 0.00 0.00 2.85
959 1090 4.215399 CAGTTGCTCTTTTCGGATGGTAAA 59.785 41.667 0.00 0.00 0.00 2.01
960 1091 4.215613 AGTTGCTCTTTTCGGATGGTAAAC 59.784 41.667 0.00 0.00 0.00 2.01
961 1092 3.745799 TGCTCTTTTCGGATGGTAAACA 58.254 40.909 0.00 0.00 0.00 2.83
962 1093 3.751175 TGCTCTTTTCGGATGGTAAACAG 59.249 43.478 0.00 0.00 0.00 3.16
963 1094 4.000988 GCTCTTTTCGGATGGTAAACAGA 58.999 43.478 0.00 0.00 0.00 3.41
964 1095 4.142881 GCTCTTTTCGGATGGTAAACAGAC 60.143 45.833 0.00 0.00 0.00 3.51
965 1096 4.320870 TCTTTTCGGATGGTAAACAGACC 58.679 43.478 0.00 0.00 40.21 3.85
966 1097 2.773993 TTCGGATGGTAAACAGACCC 57.226 50.000 0.00 0.00 38.89 4.46
967 1098 1.946984 TCGGATGGTAAACAGACCCT 58.053 50.000 0.00 0.00 38.89 4.34
968 1099 1.829222 TCGGATGGTAAACAGACCCTC 59.171 52.381 0.00 0.00 38.89 4.30
969 1100 1.831736 CGGATGGTAAACAGACCCTCT 59.168 52.381 0.00 0.00 38.89 3.69
970 1101 2.236395 CGGATGGTAAACAGACCCTCTT 59.764 50.000 0.00 0.00 38.89 2.85
971 1102 3.679083 CGGATGGTAAACAGACCCTCTTC 60.679 52.174 0.00 0.00 38.89 2.87
972 1103 3.370633 GGATGGTAAACAGACCCTCTTCC 60.371 52.174 0.00 0.00 38.89 3.46
973 1104 2.986050 TGGTAAACAGACCCTCTTCCT 58.014 47.619 0.00 0.00 38.89 3.36
974 1105 2.904434 TGGTAAACAGACCCTCTTCCTC 59.096 50.000 0.00 0.00 38.89 3.71
975 1106 3.174779 GGTAAACAGACCCTCTTCCTCT 58.825 50.000 0.00 0.00 32.88 3.69
1005 1136 2.355481 GAACCCGACGACGTGCTT 60.355 61.111 4.58 0.00 37.88 3.91
1060 1191 3.706373 ACGATGAGGCCGTGGCTT 61.706 61.111 11.25 2.20 38.98 4.35
1061 1192 2.892425 CGATGAGGCCGTGGCTTC 60.892 66.667 15.45 15.45 45.73 3.86
1131 1277 4.332543 AACGGAGGGGAGGGCTCA 62.333 66.667 0.00 0.00 0.00 4.26
1283 1429 3.119096 GGCCGCGAAGACCAACTC 61.119 66.667 8.23 0.00 0.00 3.01
1405 1572 3.522731 CCGAGGAGGCCGACAGAG 61.523 72.222 0.00 0.00 0.00 3.35
1406 1573 4.200283 CGAGGAGGCCGACAGAGC 62.200 72.222 0.00 0.00 0.00 4.09
1407 1574 4.200283 GAGGAGGCCGACAGAGCG 62.200 72.222 0.00 0.00 0.00 5.03
1415 1582 3.432588 CGACAGAGCGGACGAGGT 61.433 66.667 0.00 0.00 0.00 3.85
1416 1583 2.179517 GACAGAGCGGACGAGGTG 59.820 66.667 0.00 0.00 0.00 4.00
1417 1584 3.343788 GACAGAGCGGACGAGGTGG 62.344 68.421 0.00 0.00 0.00 4.61
1418 1585 4.803426 CAGAGCGGACGAGGTGGC 62.803 72.222 0.00 0.00 0.00 5.01
1539 1706 3.221389 CCGGGGAACGCCGATAGA 61.221 66.667 27.00 0.00 43.13 1.98
1665 1832 2.659016 CTGTTCTGGCTCGGCAGA 59.341 61.111 17.85 17.85 0.00 4.26
1757 1924 2.094659 CCAACTACGAGCAGCCACG 61.095 63.158 7.86 7.86 0.00 4.94
1761 1928 3.633094 CTACGAGCAGCCACGCACT 62.633 63.158 9.12 0.00 0.00 4.40
1915 2082 1.990060 CAGATCTGGGACCCGGTGT 60.990 63.158 19.40 9.36 0.00 4.16
1997 2164 4.827087 AGCGGCTGTCAGGATGCG 62.827 66.667 0.00 0.00 34.76 4.73
2034 2201 0.030638 CCAACTTCAAGCAACCACCG 59.969 55.000 0.00 0.00 0.00 4.94
2098 2265 0.247736 CCTCAACGACTTCCTGGAGG 59.752 60.000 3.99 3.99 36.33 4.30
2099 2266 0.969894 CTCAACGACTTCCTGGAGGT 59.030 55.000 11.68 11.68 36.34 3.85
2100 2267 0.679505 TCAACGACTTCCTGGAGGTG 59.320 55.000 16.93 10.84 36.34 4.00
2101 2268 0.320771 CAACGACTTCCTGGAGGTGG 60.321 60.000 16.93 17.16 36.34 4.61
2102 2269 0.471211 AACGACTTCCTGGAGGTGGA 60.471 55.000 24.03 0.00 36.34 4.02
2103 2270 0.900647 ACGACTTCCTGGAGGTGGAG 60.901 60.000 24.03 13.90 34.76 3.86
2154 2321 2.044555 CACCCCAGATGCACAGCTG 61.045 63.158 13.48 13.48 43.91 4.24
2212 2379 1.440893 CAGGTGGATGAGCTCCTCG 59.559 63.158 12.15 0.00 45.21 4.63
2236 2403 0.877071 CATGGGCTTCACCGATATGC 59.123 55.000 0.00 0.00 40.62 3.14
2248 2415 1.303155 GATATGCTGGCCAGGGCTC 60.303 63.158 33.46 17.46 41.60 4.70
2284 2454 5.239963 GCTCCTAGTCCTACATAGTGAGTTC 59.760 48.000 0.00 0.00 0.00 3.01
2343 2518 3.047796 GCAACACTATGCATGCTTATGC 58.952 45.455 20.33 17.93 45.70 3.14
2505 2680 6.215121 TGCAATGTCAATTAAGTTGGTCTTG 58.785 36.000 0.00 0.00 38.39 3.02
2553 2729 7.596494 TGAATTCAGCAGGAAAATTTAGTGAG 58.404 34.615 3.38 0.00 39.39 3.51
2632 2809 0.519961 AACGCGCCTAATTTCACCAC 59.480 50.000 5.73 0.00 0.00 4.16
2803 2986 8.374327 TCAGAATGCTGATTTCTACATACATG 57.626 34.615 0.00 0.00 45.88 3.21
2804 2987 7.041576 TCAGAATGCTGATTTCTACATACATGC 60.042 37.037 0.00 0.00 45.88 4.06
2806 2989 6.798315 ATGCTGATTTCTACATACATGCTC 57.202 37.500 0.00 0.00 0.00 4.26
2807 2990 5.673514 TGCTGATTTCTACATACATGCTCA 58.326 37.500 0.00 0.00 0.00 4.26
2809 2992 7.444299 TGCTGATTTCTACATACATGCTCATA 58.556 34.615 0.00 0.00 0.00 2.15
2810 2993 7.933033 TGCTGATTTCTACATACATGCTCATAA 59.067 33.333 0.00 0.00 0.00 1.90
2811 2994 8.944029 GCTGATTTCTACATACATGCTCATAAT 58.056 33.333 0.00 0.00 0.00 1.28
2895 3728 1.817740 GCCTTGTTCAGTGCCCTGTAA 60.818 52.381 0.00 0.00 39.82 2.41
2946 3779 7.273320 AGTTATCTCCAATTCTTCATGCATG 57.727 36.000 21.07 21.07 0.00 4.06
2952 3785 4.768448 TCCAATTCTTCATGCATGACTTGT 59.232 37.500 28.72 12.74 36.36 3.16
2953 3786 5.945191 TCCAATTCTTCATGCATGACTTGTA 59.055 36.000 28.72 13.08 36.36 2.41
2954 3787 6.433716 TCCAATTCTTCATGCATGACTTGTAA 59.566 34.615 28.72 17.28 36.36 2.41
2955 3788 6.529125 CCAATTCTTCATGCATGACTTGTAAC 59.471 38.462 28.72 0.00 36.36 2.50
3016 3858 4.099403 CATCGAGTGATGCACGCT 57.901 55.556 0.00 0.00 45.06 5.07
3059 3901 6.942532 TGGTTGATGATCTGGCTTTATTAC 57.057 37.500 0.00 0.00 0.00 1.89
3068 3910 7.801104 TGATCTGGCTTTATTACAACCTGATA 58.199 34.615 0.00 0.00 38.66 2.15
3294 4251 0.668535 GGCCGTTGAGCACTTTTTCT 59.331 50.000 0.00 0.00 0.00 2.52
3305 4262 3.798337 AGCACTTTTTCTGAATTGTTGCG 59.202 39.130 0.00 0.00 0.00 4.85
3310 4267 7.014702 CACTTTTTCTGAATTGTTGCGTTTTT 58.985 30.769 0.00 0.00 0.00 1.94
3311 4268 7.214263 CACTTTTTCTGAATTGTTGCGTTTTTC 59.786 33.333 0.00 0.00 0.00 2.29
3374 4331 6.294508 GGCAGACTAAAAGGATTAACTTTGCA 60.295 38.462 0.00 0.00 40.36 4.08
3474 4436 6.833933 AGTCAGGATTAACTTTGTGTTTTCCT 59.166 34.615 0.00 0.00 44.18 3.36
3494 4456 6.042638 TCCTTTCCAGTACTTCATCTTGAG 57.957 41.667 0.00 0.00 0.00 3.02
3496 4458 6.724441 TCCTTTCCAGTACTTCATCTTGAGTA 59.276 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 43 1.002134 CCCCAAGGTGAGCGTGATT 60.002 57.895 0.00 0.00 0.00 2.57
38 45 2.525629 TCCCCAAGGTGAGCGTGA 60.526 61.111 0.00 0.00 0.00 4.35
78 86 1.466025 TTCCACGTCTACCCGCAAGT 61.466 55.000 0.00 0.00 0.00 3.16
135 143 3.320879 CTCGGATGGTGCTGCCTGT 62.321 63.158 0.00 0.00 38.35 4.00
154 162 1.302511 ACCGGCTCATCTGCGTTTT 60.303 52.632 0.00 0.00 0.00 2.43
310 321 1.803922 CACATAGCGGACGCAACGA 60.804 57.895 19.48 1.40 44.88 3.85
370 396 2.343101 CGAATAAGAAGTTGACGCCCA 58.657 47.619 0.00 0.00 0.00 5.36
379 405 1.751437 GCCCAAGCCGAATAAGAAGT 58.249 50.000 0.00 0.00 0.00 3.01
436 462 4.227134 CGATCACCCCCTCTGGCG 62.227 72.222 0.00 0.00 0.00 5.69
440 469 1.050988 CCATCACGATCACCCCCTCT 61.051 60.000 0.00 0.00 0.00 3.69
443 472 2.203209 GCCATCACGATCACCCCC 60.203 66.667 0.00 0.00 0.00 5.40
448 478 2.104132 CGTCCGCCATCACGATCA 59.896 61.111 0.00 0.00 38.32 2.92
450 480 2.413351 CTCGTCCGCCATCACGAT 59.587 61.111 0.00 0.00 43.75 3.73
459 489 4.856607 CTTCCTCGCCTCGTCCGC 62.857 72.222 0.00 0.00 0.00 5.54
485 515 4.814294 GACCTCGATGCCGCCGTT 62.814 66.667 0.00 0.00 35.37 4.44
612 742 4.034048 CGACCTATTCCCGACTCATTTTTG 59.966 45.833 0.00 0.00 0.00 2.44
622 752 1.386533 GTCTGTCGACCTATTCCCGA 58.613 55.000 14.12 0.00 33.98 5.14
630 760 1.254026 TTTCATCCGTCTGTCGACCT 58.746 50.000 14.12 0.00 42.86 3.85
636 766 0.320374 TCCGCTTTTCATCCGTCTGT 59.680 50.000 0.00 0.00 0.00 3.41
640 770 1.005394 ACGTCCGCTTTTCATCCGT 60.005 52.632 0.00 0.00 0.00 4.69
698 829 0.874175 CGTCTATTTGGATCGGCGCA 60.874 55.000 10.83 0.00 0.00 6.09
706 837 3.251763 CGCGCGCGTCTATTTGGA 61.252 61.111 42.49 0.00 34.35 3.53
712 843 2.733969 TTTTTCCGCGCGCGTCTA 60.734 55.556 45.51 30.53 37.81 2.59
726 857 2.557372 AACGCGGCGACCCATTTTT 61.557 52.632 30.94 7.11 0.00 1.94
727 858 2.981350 AACGCGGCGACCCATTTT 60.981 55.556 30.94 7.93 0.00 1.82
758 889 5.021033 TCAACCTAGTGTCAAAAACGGTA 57.979 39.130 0.00 0.00 0.00 4.02
759 890 3.876341 TCAACCTAGTGTCAAAAACGGT 58.124 40.909 0.00 0.00 0.00 4.83
760 891 4.886247 TTCAACCTAGTGTCAAAAACGG 57.114 40.909 0.00 0.00 0.00 4.44
761 892 6.491394 TCAATTCAACCTAGTGTCAAAAACG 58.509 36.000 0.00 0.00 0.00 3.60
762 893 7.757624 TGTTCAATTCAACCTAGTGTCAAAAAC 59.242 33.333 0.00 0.00 0.00 2.43
763 894 7.831753 TGTTCAATTCAACCTAGTGTCAAAAA 58.168 30.769 0.00 0.00 0.00 1.94
764 895 7.397892 TGTTCAATTCAACCTAGTGTCAAAA 57.602 32.000 0.00 0.00 0.00 2.44
765 896 7.397892 TTGTTCAATTCAACCTAGTGTCAAA 57.602 32.000 0.00 0.00 0.00 2.69
766 897 7.397892 TTTGTTCAATTCAACCTAGTGTCAA 57.602 32.000 0.00 0.00 0.00 3.18
767 898 7.094162 TGTTTTGTTCAATTCAACCTAGTGTCA 60.094 33.333 0.00 0.00 0.00 3.58
768 899 7.254852 TGTTTTGTTCAATTCAACCTAGTGTC 58.745 34.615 0.00 0.00 0.00 3.67
769 900 7.164230 TGTTTTGTTCAATTCAACCTAGTGT 57.836 32.000 0.00 0.00 0.00 3.55
770 901 7.706179 ACATGTTTTGTTCAATTCAACCTAGTG 59.294 33.333 0.00 0.00 33.74 2.74
771 902 7.781056 ACATGTTTTGTTCAATTCAACCTAGT 58.219 30.769 0.00 0.00 33.74 2.57
772 903 8.647143 AACATGTTTTGTTCAATTCAACCTAG 57.353 30.769 4.92 0.00 45.55 3.02
774 905 9.044150 CATAACATGTTTTGTTCAATTCAACCT 57.956 29.630 17.78 0.00 45.55 3.50
775 906 9.039870 TCATAACATGTTTTGTTCAATTCAACC 57.960 29.630 22.95 0.00 45.55 3.77
790 921 9.537192 CCAGCAATTCAATATTCATAACATGTT 57.463 29.630 16.68 16.68 0.00 2.71
791 922 8.145767 CCCAGCAATTCAATATTCATAACATGT 58.854 33.333 0.00 0.00 0.00 3.21
792 923 8.361889 TCCCAGCAATTCAATATTCATAACATG 58.638 33.333 0.00 0.00 0.00 3.21
793 924 8.481492 TCCCAGCAATTCAATATTCATAACAT 57.519 30.769 0.00 0.00 0.00 2.71
794 925 7.894753 TCCCAGCAATTCAATATTCATAACA 57.105 32.000 0.00 0.00 0.00 2.41
798 929 9.151177 AGTTATTCCCAGCAATTCAATATTCAT 57.849 29.630 0.00 0.00 0.00 2.57
799 930 8.415553 CAGTTATTCCCAGCAATTCAATATTCA 58.584 33.333 0.00 0.00 0.00 2.57
800 931 7.383300 GCAGTTATTCCCAGCAATTCAATATTC 59.617 37.037 0.00 0.00 0.00 1.75
801 932 7.212274 GCAGTTATTCCCAGCAATTCAATATT 58.788 34.615 0.00 0.00 0.00 1.28
802 933 6.239402 GGCAGTTATTCCCAGCAATTCAATAT 60.239 38.462 0.00 0.00 0.00 1.28
803 934 5.068987 GGCAGTTATTCCCAGCAATTCAATA 59.931 40.000 0.00 0.00 0.00 1.90
804 935 4.141869 GGCAGTTATTCCCAGCAATTCAAT 60.142 41.667 0.00 0.00 0.00 2.57
805 936 3.195396 GGCAGTTATTCCCAGCAATTCAA 59.805 43.478 0.00 0.00 0.00 2.69
806 937 2.760092 GGCAGTTATTCCCAGCAATTCA 59.240 45.455 0.00 0.00 0.00 2.57
807 938 2.223572 CGGCAGTTATTCCCAGCAATTC 60.224 50.000 0.00 0.00 0.00 2.17
808 939 1.750778 CGGCAGTTATTCCCAGCAATT 59.249 47.619 0.00 0.00 0.00 2.32
809 940 1.340991 ACGGCAGTTATTCCCAGCAAT 60.341 47.619 0.00 0.00 0.00 3.56
810 941 0.037590 ACGGCAGTTATTCCCAGCAA 59.962 50.000 0.00 0.00 0.00 3.91
811 942 0.676466 CACGGCAGTTATTCCCAGCA 60.676 55.000 0.00 0.00 0.00 4.41
812 943 1.376609 CCACGGCAGTTATTCCCAGC 61.377 60.000 0.00 0.00 0.00 4.85
813 944 0.035439 ACCACGGCAGTTATTCCCAG 60.035 55.000 0.00 0.00 0.00 4.45
814 945 0.035820 GACCACGGCAGTTATTCCCA 60.036 55.000 0.00 0.00 0.00 4.37
815 946 0.035820 TGACCACGGCAGTTATTCCC 60.036 55.000 0.00 0.00 0.00 3.97
816 947 1.816074 TTGACCACGGCAGTTATTCC 58.184 50.000 0.00 0.00 0.00 3.01
817 948 3.006940 TCATTGACCACGGCAGTTATTC 58.993 45.455 0.00 0.00 0.00 1.75
818 949 2.747446 GTCATTGACCACGGCAGTTATT 59.253 45.455 5.44 0.00 0.00 1.40
819 950 2.290008 TGTCATTGACCACGGCAGTTAT 60.290 45.455 14.05 0.00 0.00 1.89
820 951 1.070914 TGTCATTGACCACGGCAGTTA 59.929 47.619 14.05 0.00 0.00 2.24
821 952 0.179032 TGTCATTGACCACGGCAGTT 60.179 50.000 14.05 0.00 0.00 3.16
822 953 0.179032 TTGTCATTGACCACGGCAGT 60.179 50.000 14.05 0.00 0.00 4.40
823 954 0.518636 CTTGTCATTGACCACGGCAG 59.481 55.000 14.05 0.00 0.00 4.85
824 955 1.514678 GCTTGTCATTGACCACGGCA 61.515 55.000 14.05 0.00 0.00 5.69
825 956 1.210155 GCTTGTCATTGACCACGGC 59.790 57.895 14.05 8.93 0.00 5.68
826 957 0.948623 TCGCTTGTCATTGACCACGG 60.949 55.000 14.05 2.13 0.00 4.94
827 958 0.439985 CTCGCTTGTCATTGACCACG 59.560 55.000 14.05 13.87 0.00 4.94
828 959 1.728971 CTCTCGCTTGTCATTGACCAC 59.271 52.381 14.05 2.99 0.00 4.16
829 960 1.618343 TCTCTCGCTTGTCATTGACCA 59.382 47.619 14.05 2.34 0.00 4.02
830 961 1.996191 GTCTCTCGCTTGTCATTGACC 59.004 52.381 14.05 0.00 0.00 4.02
831 962 2.953020 AGTCTCTCGCTTGTCATTGAC 58.047 47.619 9.93 9.93 0.00 3.18
832 963 3.759086 AGTAGTCTCTCGCTTGTCATTGA 59.241 43.478 0.00 0.00 0.00 2.57
833 964 4.103365 AGTAGTCTCTCGCTTGTCATTG 57.897 45.455 0.00 0.00 0.00 2.82
834 965 4.792521 AAGTAGTCTCTCGCTTGTCATT 57.207 40.909 0.00 0.00 0.00 2.57
835 966 4.792521 AAAGTAGTCTCTCGCTTGTCAT 57.207 40.909 0.00 0.00 0.00 3.06
836 967 4.585955 AAAAGTAGTCTCTCGCTTGTCA 57.414 40.909 0.00 0.00 0.00 3.58
837 968 6.323266 TCATAAAAGTAGTCTCTCGCTTGTC 58.677 40.000 0.00 0.00 0.00 3.18
838 969 6.268825 TCATAAAAGTAGTCTCTCGCTTGT 57.731 37.500 0.00 0.00 0.00 3.16
839 970 7.276658 ACATTCATAAAAGTAGTCTCTCGCTTG 59.723 37.037 0.00 0.00 0.00 4.01
840 971 7.324178 ACATTCATAAAAGTAGTCTCTCGCTT 58.676 34.615 0.00 0.00 0.00 4.68
841 972 6.868622 ACATTCATAAAAGTAGTCTCTCGCT 58.131 36.000 0.00 0.00 0.00 4.93
842 973 7.527084 AACATTCATAAAAGTAGTCTCTCGC 57.473 36.000 0.00 0.00 0.00 5.03
859 990 9.932207 AAGCAAATTCAGATTCATAAACATTCA 57.068 25.926 0.00 0.00 0.00 2.57
866 997 9.985730 AGTCAAAAAGCAAATTCAGATTCATAA 57.014 25.926 0.00 0.00 0.00 1.90
867 998 9.985730 AAGTCAAAAAGCAAATTCAGATTCATA 57.014 25.926 0.00 0.00 0.00 2.15
868 999 8.770828 CAAGTCAAAAAGCAAATTCAGATTCAT 58.229 29.630 0.00 0.00 0.00 2.57
869 1000 7.254522 GCAAGTCAAAAAGCAAATTCAGATTCA 60.255 33.333 0.00 0.00 0.00 2.57
870 1001 7.067728 GCAAGTCAAAAAGCAAATTCAGATTC 58.932 34.615 0.00 0.00 0.00 2.52
871 1002 6.292488 CGCAAGTCAAAAAGCAAATTCAGATT 60.292 34.615 0.00 0.00 0.00 2.40
872 1003 5.176223 CGCAAGTCAAAAAGCAAATTCAGAT 59.824 36.000 0.00 0.00 0.00 2.90
873 1004 4.503734 CGCAAGTCAAAAAGCAAATTCAGA 59.496 37.500 0.00 0.00 0.00 3.27
874 1005 4.503734 TCGCAAGTCAAAAAGCAAATTCAG 59.496 37.500 0.00 0.00 39.48 3.02
875 1006 4.428209 TCGCAAGTCAAAAAGCAAATTCA 58.572 34.783 0.00 0.00 39.48 2.57
876 1007 5.005682 AGTTCGCAAGTCAAAAAGCAAATTC 59.994 36.000 0.00 0.00 39.48 2.17
877 1008 4.869861 AGTTCGCAAGTCAAAAAGCAAATT 59.130 33.333 0.00 0.00 39.48 1.82
878 1009 4.432712 AGTTCGCAAGTCAAAAAGCAAAT 58.567 34.783 0.00 0.00 39.48 2.32
879 1010 3.843999 AGTTCGCAAGTCAAAAAGCAAA 58.156 36.364 0.00 0.00 39.48 3.68
880 1011 3.502191 AGTTCGCAAGTCAAAAAGCAA 57.498 38.095 0.00 0.00 39.48 3.91
881 1012 3.119673 TGAAGTTCGCAAGTCAAAAAGCA 60.120 39.130 0.00 0.00 39.48 3.91
882 1013 3.434637 TGAAGTTCGCAAGTCAAAAAGC 58.565 40.909 0.00 0.00 39.48 3.51
883 1014 6.388259 TTTTGAAGTTCGCAAGTCAAAAAG 57.612 33.333 7.71 0.00 35.17 2.27
884 1015 6.183360 CCATTTTGAAGTTCGCAAGTCAAAAA 60.183 34.615 12.75 0.00 39.44 1.94
885 1016 5.290643 CCATTTTGAAGTTCGCAAGTCAAAA 59.709 36.000 11.52 11.52 40.01 2.44
886 1017 4.803088 CCATTTTGAAGTTCGCAAGTCAAA 59.197 37.500 0.00 0.00 39.48 2.69
887 1018 4.097135 TCCATTTTGAAGTTCGCAAGTCAA 59.903 37.500 0.00 0.00 39.48 3.18
888 1019 3.629855 TCCATTTTGAAGTTCGCAAGTCA 59.370 39.130 0.00 0.00 39.48 3.41
889 1020 4.222114 CTCCATTTTGAAGTTCGCAAGTC 58.778 43.478 0.00 0.00 39.48 3.01
890 1021 3.004734 CCTCCATTTTGAAGTTCGCAAGT 59.995 43.478 0.00 0.00 39.48 3.16
891 1022 3.568538 CCTCCATTTTGAAGTTCGCAAG 58.431 45.455 0.00 0.00 0.00 4.01
892 1023 2.288152 GCCTCCATTTTGAAGTTCGCAA 60.288 45.455 0.00 0.00 0.00 4.85
893 1024 1.269448 GCCTCCATTTTGAAGTTCGCA 59.731 47.619 0.00 0.00 0.00 5.10
894 1025 1.541588 AGCCTCCATTTTGAAGTTCGC 59.458 47.619 0.00 0.00 0.00 4.70
895 1026 2.669391 GCAGCCTCCATTTTGAAGTTCG 60.669 50.000 0.00 0.00 0.00 3.95
896 1027 2.560105 AGCAGCCTCCATTTTGAAGTTC 59.440 45.455 0.00 0.00 0.00 3.01
897 1028 2.560105 GAGCAGCCTCCATTTTGAAGTT 59.440 45.455 0.00 0.00 31.68 2.66
898 1029 2.165998 GAGCAGCCTCCATTTTGAAGT 58.834 47.619 0.00 0.00 31.68 3.01
899 1030 2.935481 GAGCAGCCTCCATTTTGAAG 57.065 50.000 0.00 0.00 31.68 3.02
909 1040 2.052690 TGGTCGTAGGAGCAGCCTC 61.053 63.158 12.97 0.00 46.97 4.70
915 1046 0.394625 AGAGGAGTGGTCGTAGGAGC 60.395 60.000 7.66 7.66 41.07 4.70
916 1047 2.018515 GAAGAGGAGTGGTCGTAGGAG 58.981 57.143 0.00 0.00 0.00 3.69
917 1048 1.353358 TGAAGAGGAGTGGTCGTAGGA 59.647 52.381 0.00 0.00 0.00 2.94
918 1049 1.746220 CTGAAGAGGAGTGGTCGTAGG 59.254 57.143 0.00 0.00 0.00 3.18
919 1050 2.438411 ACTGAAGAGGAGTGGTCGTAG 58.562 52.381 0.00 0.00 0.00 3.51
920 1051 2.557056 CAACTGAAGAGGAGTGGTCGTA 59.443 50.000 0.00 0.00 0.00 3.43
921 1052 1.341531 CAACTGAAGAGGAGTGGTCGT 59.658 52.381 0.00 0.00 0.00 4.34
922 1053 1.937108 GCAACTGAAGAGGAGTGGTCG 60.937 57.143 0.00 0.00 0.00 4.79
923 1054 1.346068 AGCAACTGAAGAGGAGTGGTC 59.654 52.381 0.00 0.00 0.00 4.02
924 1055 1.346068 GAGCAACTGAAGAGGAGTGGT 59.654 52.381 0.00 0.00 0.00 4.16
925 1056 1.622811 AGAGCAACTGAAGAGGAGTGG 59.377 52.381 0.00 0.00 0.00 4.00
926 1057 3.399440 AAGAGCAACTGAAGAGGAGTG 57.601 47.619 0.00 0.00 0.00 3.51
927 1058 4.384940 GAAAAGAGCAACTGAAGAGGAGT 58.615 43.478 0.00 0.00 0.00 3.85
928 1059 3.431572 CGAAAAGAGCAACTGAAGAGGAG 59.568 47.826 0.00 0.00 0.00 3.69
929 1060 3.393800 CGAAAAGAGCAACTGAAGAGGA 58.606 45.455 0.00 0.00 0.00 3.71
930 1061 2.481952 CCGAAAAGAGCAACTGAAGAGG 59.518 50.000 0.00 0.00 0.00 3.69
931 1062 3.393800 TCCGAAAAGAGCAACTGAAGAG 58.606 45.455 0.00 0.00 0.00 2.85
932 1063 3.469008 TCCGAAAAGAGCAACTGAAGA 57.531 42.857 0.00 0.00 0.00 2.87
933 1064 3.120060 CCATCCGAAAAGAGCAACTGAAG 60.120 47.826 0.00 0.00 0.00 3.02
934 1065 2.813754 CCATCCGAAAAGAGCAACTGAA 59.186 45.455 0.00 0.00 0.00 3.02
935 1066 2.224523 ACCATCCGAAAAGAGCAACTGA 60.225 45.455 0.00 0.00 0.00 3.41
936 1067 2.154462 ACCATCCGAAAAGAGCAACTG 58.846 47.619 0.00 0.00 0.00 3.16
937 1068 2.568623 ACCATCCGAAAAGAGCAACT 57.431 45.000 0.00 0.00 0.00 3.16
938 1069 4.023536 TGTTTACCATCCGAAAAGAGCAAC 60.024 41.667 0.00 0.00 0.00 4.17
939 1070 4.138290 TGTTTACCATCCGAAAAGAGCAA 58.862 39.130 0.00 0.00 0.00 3.91
940 1071 3.745799 TGTTTACCATCCGAAAAGAGCA 58.254 40.909 0.00 0.00 0.00 4.26
941 1072 4.000988 TCTGTTTACCATCCGAAAAGAGC 58.999 43.478 0.00 0.00 0.00 4.09
942 1073 4.392138 GGTCTGTTTACCATCCGAAAAGAG 59.608 45.833 0.00 0.00 39.50 2.85
943 1074 4.320870 GGTCTGTTTACCATCCGAAAAGA 58.679 43.478 0.00 0.00 39.50 2.52
944 1075 3.439129 GGGTCTGTTTACCATCCGAAAAG 59.561 47.826 0.00 0.00 41.67 2.27
945 1076 3.073356 AGGGTCTGTTTACCATCCGAAAA 59.927 43.478 0.00 0.00 41.67 2.29
946 1077 2.640826 AGGGTCTGTTTACCATCCGAAA 59.359 45.455 0.00 0.00 41.67 3.46
947 1078 2.235402 GAGGGTCTGTTTACCATCCGAA 59.765 50.000 0.00 0.00 43.06 4.30
948 1079 1.829222 GAGGGTCTGTTTACCATCCGA 59.171 52.381 0.00 0.00 43.06 4.55
949 1080 2.311124 GAGGGTCTGTTTACCATCCG 57.689 55.000 0.00 0.00 43.06 4.18
952 1083 3.519913 GAGGAAGAGGGTCTGTTTACCAT 59.480 47.826 0.00 0.00 41.67 3.55
953 1084 2.904434 GAGGAAGAGGGTCTGTTTACCA 59.096 50.000 0.00 0.00 41.67 3.25
954 1085 3.174779 AGAGGAAGAGGGTCTGTTTACC 58.825 50.000 0.00 0.00 38.94 2.85
955 1086 4.090819 AGAGAGGAAGAGGGTCTGTTTAC 58.909 47.826 0.00 0.00 0.00 2.01
956 1087 4.405756 AGAGAGGAAGAGGGTCTGTTTA 57.594 45.455 0.00 0.00 0.00 2.01
957 1088 3.268034 AGAGAGGAAGAGGGTCTGTTT 57.732 47.619 0.00 0.00 0.00 2.83
958 1089 4.405756 TTAGAGAGGAAGAGGGTCTGTT 57.594 45.455 0.00 0.00 0.00 3.16
959 1090 4.405756 TTTAGAGAGGAAGAGGGTCTGT 57.594 45.455 0.00 0.00 0.00 3.41
960 1091 4.081365 GGTTTTAGAGAGGAAGAGGGTCTG 60.081 50.000 0.00 0.00 0.00 3.51
961 1092 4.098155 GGTTTTAGAGAGGAAGAGGGTCT 58.902 47.826 0.00 0.00 0.00 3.85
962 1093 3.198200 GGGTTTTAGAGAGGAAGAGGGTC 59.802 52.174 0.00 0.00 0.00 4.46
963 1094 3.182976 GGGTTTTAGAGAGGAAGAGGGT 58.817 50.000 0.00 0.00 0.00 4.34
964 1095 2.506231 GGGGTTTTAGAGAGGAAGAGGG 59.494 54.545 0.00 0.00 0.00 4.30
965 1096 3.182152 TGGGGTTTTAGAGAGGAAGAGG 58.818 50.000 0.00 0.00 0.00 3.69
966 1097 3.198853 CCTGGGGTTTTAGAGAGGAAGAG 59.801 52.174 0.00 0.00 0.00 2.85
967 1098 3.181399 TCCTGGGGTTTTAGAGAGGAAGA 60.181 47.826 0.00 0.00 0.00 2.87
968 1099 3.182152 TCCTGGGGTTTTAGAGAGGAAG 58.818 50.000 0.00 0.00 0.00 3.46
969 1100 3.285290 TCCTGGGGTTTTAGAGAGGAA 57.715 47.619 0.00 0.00 0.00 3.36
970 1101 2.910977 GTTCCTGGGGTTTTAGAGAGGA 59.089 50.000 0.00 0.00 0.00 3.71
971 1102 2.026169 GGTTCCTGGGGTTTTAGAGAGG 60.026 54.545 0.00 0.00 0.00 3.69
972 1103 2.026169 GGGTTCCTGGGGTTTTAGAGAG 60.026 54.545 0.00 0.00 0.00 3.20
973 1104 1.990327 GGGTTCCTGGGGTTTTAGAGA 59.010 52.381 0.00 0.00 0.00 3.10
974 1105 1.339727 CGGGTTCCTGGGGTTTTAGAG 60.340 57.143 0.00 0.00 0.00 2.43
975 1106 0.694196 CGGGTTCCTGGGGTTTTAGA 59.306 55.000 0.00 0.00 0.00 2.10
1005 1136 2.044252 CCGGTTCGAGAGGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
1064 1195 4.680237 TGCTGGCCGTGACCGAAG 62.680 66.667 0.00 0.00 35.63 3.79
1398 1565 3.432588 ACCTCGTCCGCTCTGTCG 61.433 66.667 0.00 0.00 0.00 4.35
1399 1566 2.179517 CACCTCGTCCGCTCTGTC 59.820 66.667 0.00 0.00 0.00 3.51
1400 1567 3.374402 CCACCTCGTCCGCTCTGT 61.374 66.667 0.00 0.00 0.00 3.41
1401 1568 4.803426 GCCACCTCGTCCGCTCTG 62.803 72.222 0.00 0.00 0.00 3.35
1411 1578 4.864334 CCTGATGGCCGCCACCTC 62.864 72.222 16.16 10.34 35.80 3.85
1536 1703 3.740141 CGGCCCGCTTCTTCTTATTTCTA 60.740 47.826 0.00 0.00 0.00 2.10
1539 1706 1.379527 CGGCCCGCTTCTTCTTATTT 58.620 50.000 0.00 0.00 0.00 1.40
1698 1865 3.414700 GTGACAGCCGCCTTGTCG 61.415 66.667 7.92 0.00 46.14 4.35
1915 2082 2.688666 CCCCTGGTCAGCTAGCCA 60.689 66.667 12.13 8.00 0.00 4.75
1919 2086 2.759973 CGAGCCCCTGGTCAGCTA 60.760 66.667 3.43 0.00 38.96 3.32
2122 2289 1.222936 GGGTGATGCTGTCAGGGAG 59.777 63.158 1.14 0.00 37.56 4.30
2154 2321 1.098712 AGCCAGTCGAGAGATCGTCC 61.099 60.000 0.00 0.00 45.19 4.79
2212 2379 1.450312 CGGTGAAGCCCATGTCCTC 60.450 63.158 0.00 0.00 0.00 3.71
2236 2403 2.954684 TACGTTGAGCCCTGGCCAG 61.955 63.158 26.87 26.87 43.17 4.85
2284 2454 5.046529 GCATATATGGTGAAGCCTCTATCG 58.953 45.833 14.51 0.00 38.35 2.92
2290 2460 4.202493 TGTCATGCATATATGGTGAAGCCT 60.202 41.667 14.51 0.00 38.35 4.58
2340 2515 5.018809 AGATCACAAACAAATACCCAGCAT 58.981 37.500 0.00 0.00 0.00 3.79
2341 2516 4.406456 AGATCACAAACAAATACCCAGCA 58.594 39.130 0.00 0.00 0.00 4.41
2342 2517 5.391312 AAGATCACAAACAAATACCCAGC 57.609 39.130 0.00 0.00 0.00 4.85
2343 2518 7.687941 ACTAAGATCACAAACAAATACCCAG 57.312 36.000 0.00 0.00 0.00 4.45
2344 2519 8.356657 CAAACTAAGATCACAAACAAATACCCA 58.643 33.333 0.00 0.00 0.00 4.51
2345 2520 7.812669 CCAAACTAAGATCACAAACAAATACCC 59.187 37.037 0.00 0.00 0.00 3.69
2346 2521 8.357402 ACCAAACTAAGATCACAAACAAATACC 58.643 33.333 0.00 0.00 0.00 2.73
2349 2524 9.131791 ACTACCAAACTAAGATCACAAACAAAT 57.868 29.630 0.00 0.00 0.00 2.32
2350 2525 8.402472 CACTACCAAACTAAGATCACAAACAAA 58.598 33.333 0.00 0.00 0.00 2.83
2505 2680 6.981559 TCAACATTACAAACCTAAAACCTTGC 59.018 34.615 0.00 0.00 0.00 4.01
2632 2809 2.344441 CAGTATGTTTACTGCACCGACG 59.656 50.000 0.60 0.00 46.46 5.12
2682 2859 7.784550 TCCCATCCGAGTAATGATGATGATATA 59.215 37.037 0.00 0.00 40.64 0.86
2684 2861 5.957774 TCCCATCCGAGTAATGATGATGATA 59.042 40.000 0.00 0.00 40.64 2.15
2686 2863 4.159557 TCCCATCCGAGTAATGATGATGA 58.840 43.478 0.00 0.00 40.64 2.92
2701 2884 1.970640 GCCCAACCATTAATCCCATCC 59.029 52.381 0.00 0.00 0.00 3.51
2990 3832 1.332889 ATCACTCGATGCAGAGGCCA 61.333 55.000 5.01 0.00 42.31 5.36
2991 3833 0.879400 CATCACTCGATGCAGAGGCC 60.879 60.000 7.77 0.00 42.54 5.19
2992 3834 2.602738 CATCACTCGATGCAGAGGC 58.397 57.895 7.77 0.00 42.54 4.70
3016 3858 4.843516 ACCATAAAAAGGAAATCAAGGGCA 59.156 37.500 0.00 0.00 0.00 5.36
3059 3901 4.724074 AAATGGTGCACATATCAGGTTG 57.276 40.909 20.43 0.00 39.40 3.77
3068 3910 3.006110 CAGAGTTCCAAAATGGTGCACAT 59.994 43.478 20.43 7.56 43.07 3.21
3294 4251 6.754209 ACATAACAGAAAAACGCAACAATTCA 59.246 30.769 0.00 0.00 0.00 2.57
3305 4262 8.696410 TCAAAGGTTTCACATAACAGAAAAAC 57.304 30.769 0.00 0.00 35.71 2.43
3310 4267 6.068010 ACCATCAAAGGTTTCACATAACAGA 58.932 36.000 0.00 0.00 39.34 3.41
3311 4268 6.331369 ACCATCAAAGGTTTCACATAACAG 57.669 37.500 0.00 0.00 39.34 3.16
3474 4436 6.208007 TCGTACTCAAGATGAAGTACTGGAAA 59.792 38.462 0.00 0.00 33.20 3.13


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

AutoCloner maintained by Alex Coulton.