Multiple sequence alignment - TraesCS2B01G289200

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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 TraesCS2B01G289200 chr2B 100.000 4479 0 0 1 4479 399929707 399934185 0.000000e+00 8272.0
1 TraesCS2B01G289200 chr2D 93.195 3424 130 37 1100 4479 331734231 331737595 0.000000e+00 4937.0
2 TraesCS2B01G289200 chr2D 91.013 790 64 7 1 788 472590791 472590007 0.000000e+00 1059.0
3 TraesCS2B01G289200 chr2D 89.076 119 12 1 3996 4113 607675860 607675742 3.610000e-31 147.0
4 TraesCS2B01G289200 chr2D 90.722 97 2 4 1013 1109 331734035 331734124 6.080000e-24 122.0
5 TraesCS2B01G289200 chr2A 92.387 2417 131 29 1105 3498 439192949 439195335 0.000000e+00 3395.0
6 TraesCS2B01G289200 chr2A 94.712 208 9 2 4270 4476 439199529 439199735 5.590000e-84 322.0
7 TraesCS2B01G289200 chr2A 84.536 194 8 11 995 1168 439192737 439192928 5.960000e-39 172.0
8 TraesCS2B01G289200 chr2A 91.379 58 5 0 842 899 20243203 20243260 3.710000e-11 80.5
9 TraesCS2B01G289200 chr5D 91.635 789 62 3 1 788 434857658 434856873 0.000000e+00 1088.0
10 TraesCS2B01G289200 chr5D 91.381 789 55 7 1 788 351637796 351638572 0.000000e+00 1068.0
11 TraesCS2B01G289200 chr7B 91.392 790 60 6 1 788 492667075 492666292 0.000000e+00 1075.0
12 TraesCS2B01G289200 chr7B 85.385 130 17 2 3997 4125 453316528 453316656 2.810000e-27 134.0
13 TraesCS2B01G289200 chr4D 91.255 789 62 5 1 788 89446793 89446011 0.000000e+00 1068.0
14 TraesCS2B01G289200 chr7D 91.327 784 63 5 6 788 168033748 168034527 0.000000e+00 1066.0
15 TraesCS2B01G289200 chr7D 91.128 789 65 3 1 788 242759994 242759210 0.000000e+00 1064.0
16 TraesCS2B01G289200 chr3B 91.128 789 63 6 1 788 155374522 155375304 0.000000e+00 1062.0
17 TraesCS2B01G289200 chr3B 83.119 622 92 10 2039 2652 752491070 752491686 5.060000e-154 555.0
18 TraesCS2B01G289200 chr3B 87.558 217 23 4 2845 3060 798221937 798221724 9.620000e-62 248.0
19 TraesCS2B01G289200 chr3B 79.357 373 48 23 2909 3264 752492352 752492712 7.490000e-58 235.0
20 TraesCS2B01G289200 chr3B 95.890 73 2 1 2860 2932 798225119 798225048 2.830000e-22 117.0
21 TraesCS2B01G289200 chr1D 91.024 791 62 8 1 788 38475132 38474348 0.000000e+00 1059.0
22 TraesCS2B01G289200 chr1D 83.810 210 30 3 3058 3264 425573526 425573734 3.530000e-46 196.0
23 TraesCS2B01G289200 chr3D 83.361 613 85 12 2048 2652 564929342 564929945 6.550000e-153 551.0
24 TraesCS2B01G289200 chr3A 89.535 172 15 3 3096 3264 699484513 699484684 9.760000e-52 215.0
25 TraesCS2B01G289200 chr6A 89.916 119 11 1 3996 4113 144266676 144266558 7.760000e-33 152.0
26 TraesCS2B01G289200 chr6A 86.567 67 9 0 842 908 608314282 608314348 1.730000e-09 75.0
27 TraesCS2B01G289200 chr6B 89.256 121 8 4 3996 4113 205267344 205267226 3.610000e-31 147.0
28 TraesCS2B01G289200 chr4A 90.090 111 10 1 3996 4106 157206829 157206938 4.670000e-30 143.0
29 TraesCS2B01G289200 chr4A 86.567 67 9 0 842 908 366538993 366539059 1.730000e-09 75.0
30 TraesCS2B01G289200 chr6D 85.714 119 16 1 3996 4113 115788449 115788331 1.690000e-24 124.0
31 TraesCS2B01G289200 chr4B 85.714 119 15 2 3996 4113 19007507 19007624 1.690000e-24 124.0
32 TraesCS2B01G289200 chr4B 88.235 68 5 2 841 907 629372749 629372684 1.340000e-10 78.7
33 TraesCS2B01G289200 chrUn 83.846 130 17 4 3987 4113 29857405 29857277 2.190000e-23 121.0
34 TraesCS2B01G289200 chr5A 89.552 67 7 0 842 908 504717320 504717386 7.980000e-13 86.1
35 TraesCS2B01G289200 chr5B 87.324 71 7 2 839 908 663242169 663242238 3.710000e-11 80.5
36 TraesCS2B01G289200 chr1A 90.164 61 6 0 845 905 512645261 512645321 3.710000e-11 80.5
37 TraesCS2B01G289200 chr1A 87.500 64 8 0 845 908 565121761 565121698 1.730000e-09 75.0
38 TraesCS2B01G289200 chr1B 87.500 64 8 0 845 908 148890100 148890037 1.730000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G289200 chr2B 399929707 399934185 4478 False 8272.0 8272 100.0000 1 4479 1 chr2B.!!$F1 4478
1 TraesCS2B01G289200 chr2D 331734035 331737595 3560 False 2529.5 4937 91.9585 1013 4479 2 chr2D.!!$F1 3466
2 TraesCS2B01G289200 chr2D 472590007 472590791 784 True 1059.0 1059 91.0130 1 788 1 chr2D.!!$R1 787
3 TraesCS2B01G289200 chr2A 439192737 439195335 2598 False 1783.5 3395 88.4615 995 3498 2 chr2A.!!$F3 2503
4 TraesCS2B01G289200 chr5D 434856873 434857658 785 True 1088.0 1088 91.6350 1 788 1 chr5D.!!$R1 787
5 TraesCS2B01G289200 chr5D 351637796 351638572 776 False 1068.0 1068 91.3810 1 788 1 chr5D.!!$F1 787
6 TraesCS2B01G289200 chr7B 492666292 492667075 783 True 1075.0 1075 91.3920 1 788 1 chr7B.!!$R1 787
7 TraesCS2B01G289200 chr4D 89446011 89446793 782 True 1068.0 1068 91.2550 1 788 1 chr4D.!!$R1 787
8 TraesCS2B01G289200 chr7D 168033748 168034527 779 False 1066.0 1066 91.3270 6 788 1 chr7D.!!$F1 782
9 TraesCS2B01G289200 chr7D 242759210 242759994 784 True 1064.0 1064 91.1280 1 788 1 chr7D.!!$R1 787
10 TraesCS2B01G289200 chr3B 155374522 155375304 782 False 1062.0 1062 91.1280 1 788 1 chr3B.!!$F1 787
11 TraesCS2B01G289200 chr3B 752491070 752492712 1642 False 395.0 555 81.2380 2039 3264 2 chr3B.!!$F2 1225
12 TraesCS2B01G289200 chr1D 38474348 38475132 784 True 1059.0 1059 91.0240 1 788 1 chr1D.!!$R1 787
13 TraesCS2B01G289200 chr3D 564929342 564929945 603 False 551.0 551 83.3610 2048 2652 1 chr3D.!!$F1 604


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
704 714 0.178767 CCATTGAGATGCGTGAGGGA 59.821 55.0 0.0 0.0 31.67 4.20 F
2038 2206 0.105408 ACGGAAAACTGTAGCGGTGT 59.895 50.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2255 0.255890 GCAGTAAGGATCCAGGCCAA 59.744 55.0 15.82 0.0 0.0 4.52 R
4001 4683 0.107848 CAAGTAATTCGGGGCGGAGT 60.108 55.0 0.00 0.0 0.0 3.85 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
102 104 4.025979 GTCTATCGTTTCGGTGCCATAAAG 60.026 45.833 0.00 0.00 0.00 1.85
119 121 2.163818 AAGATCAACAACGCCGAAGA 57.836 45.000 0.00 0.00 0.00 2.87
163 165 7.807433 TGAACGGTCAAAGAATCAAACATTATG 59.193 33.333 0.00 0.00 0.00 1.90
197 199 8.947055 AATCCCATAAATGTTGAAACTAATGC 57.053 30.769 0.00 0.00 0.00 3.56
212 214 7.388224 TGAAACTAATGCTATTGACACCGTAAA 59.612 33.333 0.00 0.00 0.00 2.01
240 242 5.785940 AGAGGAGTACATAAGGGACACTTTT 59.214 40.000 0.00 0.00 40.64 2.27
334 337 8.735315 TCAAATAGCAATTTTTCTCCGTATTGA 58.265 29.630 0.00 0.00 32.87 2.57
471 478 4.459089 GTGCCCTCTGGACTCCGC 62.459 72.222 0.00 0.00 0.00 5.54
492 499 4.642953 GCTTTCTTGCACGATACTTCTTC 58.357 43.478 0.00 0.00 0.00 2.87
580 587 3.178267 TGCTTTTGTTTCGAGCTGTTTG 58.822 40.909 0.00 0.00 37.32 2.93
612 620 5.697473 TCTAGATCATCATGACGTCTTCC 57.303 43.478 17.92 0.00 0.00 3.46
617 627 0.532573 ATCATGACGTCTTCCAGCGT 59.467 50.000 17.92 0.00 44.50 5.07
704 714 0.178767 CCATTGAGATGCGTGAGGGA 59.821 55.000 0.00 0.00 31.67 4.20
734 744 1.811266 CTGCGATGTTGAGGGACCG 60.811 63.158 0.00 0.00 0.00 4.79
741 751 2.038975 TTGAGGGACCGAGGAGGG 59.961 66.667 0.00 0.00 46.96 4.30
765 775 1.000163 GAAGCGTGGAGACAAGACTCA 60.000 52.381 0.00 0.00 46.06 3.41
768 778 2.037772 AGCGTGGAGACAAGACTCAAAT 59.962 45.455 0.00 0.00 46.06 2.32
788 798 7.495901 TCAAATCAATGGAGCAACAAGTTTTA 58.504 30.769 0.00 0.00 0.00 1.52
789 799 7.652909 TCAAATCAATGGAGCAACAAGTTTTAG 59.347 33.333 0.00 0.00 0.00 1.85
790 800 6.899393 ATCAATGGAGCAACAAGTTTTAGA 57.101 33.333 0.00 0.00 0.00 2.10
791 801 6.317789 TCAATGGAGCAACAAGTTTTAGAG 57.682 37.500 0.00 0.00 0.00 2.43
792 802 6.061441 TCAATGGAGCAACAAGTTTTAGAGA 58.939 36.000 0.00 0.00 0.00 3.10
793 803 6.205464 TCAATGGAGCAACAAGTTTTAGAGAG 59.795 38.462 0.00 0.00 0.00 3.20
794 804 4.389374 TGGAGCAACAAGTTTTAGAGAGG 58.611 43.478 0.00 0.00 0.00 3.69
795 805 3.753797 GGAGCAACAAGTTTTAGAGAGGG 59.246 47.826 0.00 0.00 0.00 4.30
796 806 4.505039 GGAGCAACAAGTTTTAGAGAGGGA 60.505 45.833 0.00 0.00 0.00 4.20
797 807 4.646572 AGCAACAAGTTTTAGAGAGGGAG 58.353 43.478 0.00 0.00 0.00 4.30
798 808 4.348168 AGCAACAAGTTTTAGAGAGGGAGA 59.652 41.667 0.00 0.00 0.00 3.71
799 809 4.693095 GCAACAAGTTTTAGAGAGGGAGAG 59.307 45.833 0.00 0.00 0.00 3.20
800 810 5.511545 GCAACAAGTTTTAGAGAGGGAGAGA 60.512 44.000 0.00 0.00 0.00 3.10
801 811 5.993748 ACAAGTTTTAGAGAGGGAGAGAG 57.006 43.478 0.00 0.00 0.00 3.20
802 812 5.646215 ACAAGTTTTAGAGAGGGAGAGAGA 58.354 41.667 0.00 0.00 0.00 3.10
803 813 5.714806 ACAAGTTTTAGAGAGGGAGAGAGAG 59.285 44.000 0.00 0.00 0.00 3.20
804 814 5.789574 AGTTTTAGAGAGGGAGAGAGAGA 57.210 43.478 0.00 0.00 0.00 3.10
805 815 6.341408 AGTTTTAGAGAGGGAGAGAGAGAT 57.659 41.667 0.00 0.00 0.00 2.75
806 816 6.741724 AGTTTTAGAGAGGGAGAGAGAGATT 58.258 40.000 0.00 0.00 0.00 2.40
807 817 6.607198 AGTTTTAGAGAGGGAGAGAGAGATTG 59.393 42.308 0.00 0.00 0.00 2.67
808 818 3.600448 AGAGAGGGAGAGAGAGATTGG 57.400 52.381 0.00 0.00 0.00 3.16
809 819 1.963515 GAGAGGGAGAGAGAGATTGGC 59.036 57.143 0.00 0.00 0.00 4.52
810 820 1.047801 GAGGGAGAGAGAGATTGGCC 58.952 60.000 0.00 0.00 0.00 5.36
811 821 0.399806 AGGGAGAGAGAGATTGGCCC 60.400 60.000 0.00 0.00 0.00 5.80
812 822 1.414866 GGGAGAGAGAGATTGGCCCC 61.415 65.000 0.00 0.00 0.00 5.80
813 823 0.692419 GGAGAGAGAGATTGGCCCCA 60.692 60.000 0.00 0.00 0.00 4.96
814 824 1.207791 GAGAGAGAGATTGGCCCCAA 58.792 55.000 0.00 1.67 40.47 4.12
815 825 1.140652 GAGAGAGAGATTGGCCCCAAG 59.859 57.143 0.00 0.00 39.47 3.61
816 826 0.182299 GAGAGAGATTGGCCCCAAGG 59.818 60.000 0.00 0.00 39.47 3.61
817 827 0.551131 AGAGAGATTGGCCCCAAGGT 60.551 55.000 0.00 0.00 39.47 3.50
818 828 0.394899 GAGAGATTGGCCCCAAGGTG 60.395 60.000 0.00 0.00 39.47 4.00
819 829 1.142688 AGAGATTGGCCCCAAGGTGT 61.143 55.000 0.00 0.00 39.47 4.16
820 830 0.681243 GAGATTGGCCCCAAGGTGTC 60.681 60.000 0.00 0.00 39.47 3.67
821 831 1.076549 GATTGGCCCCAAGGTGTCA 59.923 57.895 0.00 0.00 39.47 3.58
822 832 0.967380 GATTGGCCCCAAGGTGTCAG 60.967 60.000 0.00 0.00 39.47 3.51
823 833 2.445492 ATTGGCCCCAAGGTGTCAGG 62.445 60.000 0.00 0.00 39.47 3.86
824 834 3.256960 GGCCCCAAGGTGTCAGGA 61.257 66.667 0.00 0.00 34.57 3.86
825 835 2.840753 GGCCCCAAGGTGTCAGGAA 61.841 63.158 0.00 0.00 34.57 3.36
826 836 1.303643 GCCCCAAGGTGTCAGGAAG 60.304 63.158 0.00 0.00 34.57 3.46
827 837 1.303643 CCCCAAGGTGTCAGGAAGC 60.304 63.158 0.00 0.00 0.00 3.86
828 838 1.303643 CCCAAGGTGTCAGGAAGCC 60.304 63.158 0.00 0.00 0.00 4.35
829 839 1.763770 CCAAGGTGTCAGGAAGCCT 59.236 57.895 0.00 0.00 0.00 4.58
830 840 0.984230 CCAAGGTGTCAGGAAGCCTA 59.016 55.000 0.00 0.00 29.64 3.93
831 841 1.561542 CCAAGGTGTCAGGAAGCCTAT 59.438 52.381 0.00 0.00 29.64 2.57
832 842 2.025887 CCAAGGTGTCAGGAAGCCTATT 60.026 50.000 0.00 0.00 29.64 1.73
833 843 3.562176 CCAAGGTGTCAGGAAGCCTATTT 60.562 47.826 0.00 0.00 29.64 1.40
834 844 4.082125 CAAGGTGTCAGGAAGCCTATTTT 58.918 43.478 0.00 0.00 29.64 1.82
835 845 5.253330 CAAGGTGTCAGGAAGCCTATTTTA 58.747 41.667 0.00 0.00 29.64 1.52
836 846 4.844884 AGGTGTCAGGAAGCCTATTTTAC 58.155 43.478 0.00 0.00 29.64 2.01
837 847 3.945921 GGTGTCAGGAAGCCTATTTTACC 59.054 47.826 0.00 0.00 29.64 2.85
838 848 4.324331 GGTGTCAGGAAGCCTATTTTACCT 60.324 45.833 0.00 0.00 29.64 3.08
839 849 5.104652 GGTGTCAGGAAGCCTATTTTACCTA 60.105 44.000 0.00 0.00 29.64 3.08
840 850 6.409349 GGTGTCAGGAAGCCTATTTTACCTAT 60.409 42.308 0.00 0.00 29.64 2.57
841 851 7.054751 GTGTCAGGAAGCCTATTTTACCTATT 58.945 38.462 0.00 0.00 29.64 1.73
842 852 8.208903 GTGTCAGGAAGCCTATTTTACCTATTA 58.791 37.037 0.00 0.00 29.64 0.98
843 853 8.945193 TGTCAGGAAGCCTATTTTACCTATTAT 58.055 33.333 0.00 0.00 29.64 1.28
960 970 9.941664 TTTCTCTACTTTATCGTTTATCCTACG 57.058 33.333 0.00 0.00 40.23 3.51
961 971 8.668510 TCTCTACTTTATCGTTTATCCTACGT 57.331 34.615 0.00 0.00 39.84 3.57
962 972 8.554528 TCTCTACTTTATCGTTTATCCTACGTG 58.445 37.037 0.00 0.00 39.84 4.49
963 973 7.642669 TCTACTTTATCGTTTATCCTACGTGG 58.357 38.462 0.00 0.00 39.84 4.94
964 974 5.045872 ACTTTATCGTTTATCCTACGTGGC 58.954 41.667 0.00 0.00 39.84 5.01
965 975 4.652421 TTATCGTTTATCCTACGTGGCA 57.348 40.909 0.00 0.00 39.84 4.92
966 976 2.282701 TCGTTTATCCTACGTGGCAC 57.717 50.000 7.79 7.79 39.84 5.01
967 977 1.820519 TCGTTTATCCTACGTGGCACT 59.179 47.619 16.72 5.47 39.84 4.40
968 978 2.159338 TCGTTTATCCTACGTGGCACTC 60.159 50.000 16.72 0.00 39.84 3.51
969 979 2.416296 CGTTTATCCTACGTGGCACTCA 60.416 50.000 16.72 1.82 34.47 3.41
970 980 3.737047 CGTTTATCCTACGTGGCACTCAT 60.737 47.826 16.72 3.60 34.47 2.90
971 981 4.498513 CGTTTATCCTACGTGGCACTCATA 60.499 45.833 16.72 4.63 34.47 2.15
972 982 4.848562 TTATCCTACGTGGCACTCATAG 57.151 45.455 16.72 13.52 35.26 2.23
973 983 1.399714 TCCTACGTGGCACTCATAGG 58.600 55.000 23.34 23.34 32.11 2.57
974 984 1.064240 TCCTACGTGGCACTCATAGGA 60.064 52.381 25.93 25.93 35.72 2.94
975 985 1.964223 CCTACGTGGCACTCATAGGAT 59.036 52.381 24.31 2.92 32.41 3.24
976 986 3.154710 CCTACGTGGCACTCATAGGATA 58.845 50.000 24.31 3.73 32.41 2.59
977 987 3.191581 CCTACGTGGCACTCATAGGATAG 59.808 52.174 24.31 6.89 32.41 2.08
978 988 1.341531 ACGTGGCACTCATAGGATAGC 59.658 52.381 16.72 0.00 0.00 2.97
979 989 1.341209 CGTGGCACTCATAGGATAGCA 59.659 52.381 16.72 0.00 0.00 3.49
980 990 2.028658 CGTGGCACTCATAGGATAGCAT 60.029 50.000 16.72 0.00 0.00 3.79
981 991 3.594134 GTGGCACTCATAGGATAGCATC 58.406 50.000 11.13 0.00 0.00 3.91
982 992 3.007290 GTGGCACTCATAGGATAGCATCA 59.993 47.826 11.13 0.00 0.00 3.07
983 993 3.007290 TGGCACTCATAGGATAGCATCAC 59.993 47.826 4.05 0.00 0.00 3.06
984 994 3.260380 GGCACTCATAGGATAGCATCACT 59.740 47.826 4.05 0.00 0.00 3.41
985 995 4.464244 GGCACTCATAGGATAGCATCACTA 59.536 45.833 4.05 0.00 34.64 2.74
986 996 5.128499 GGCACTCATAGGATAGCATCACTAT 59.872 44.000 4.05 0.00 44.62 2.12
987 997 6.322456 GGCACTCATAGGATAGCATCACTATA 59.678 42.308 4.05 0.00 41.87 1.31
988 998 7.199766 GCACTCATAGGATAGCATCACTATAC 58.800 42.308 0.00 0.00 41.87 1.47
989 999 7.148000 GCACTCATAGGATAGCATCACTATACA 60.148 40.741 0.00 0.00 43.86 2.29
990 1000 8.911965 CACTCATAGGATAGCATCACTATACAT 58.088 37.037 0.00 0.00 43.86 2.29
991 1001 8.911965 ACTCATAGGATAGCATCACTATACATG 58.088 37.037 0.00 0.00 43.86 3.21
992 1002 8.242729 TCATAGGATAGCATCACTATACATGG 57.757 38.462 0.00 0.00 43.86 3.66
993 1003 5.350504 AGGATAGCATCACTATACATGGC 57.649 43.478 0.00 0.00 43.86 4.40
994 1004 4.163078 AGGATAGCATCACTATACATGGCC 59.837 45.833 0.00 0.00 43.86 5.36
995 1005 4.163078 GGATAGCATCACTATACATGGCCT 59.837 45.833 3.32 0.00 41.37 5.19
996 1006 3.692257 AGCATCACTATACATGGCCTC 57.308 47.619 3.32 0.00 0.00 4.70
997 1007 2.974794 AGCATCACTATACATGGCCTCA 59.025 45.455 3.32 0.00 0.00 3.86
998 1008 3.392285 AGCATCACTATACATGGCCTCAA 59.608 43.478 3.32 0.00 0.00 3.02
1042 1052 1.403814 CAATAGACGGCCCAGAGAGA 58.596 55.000 0.00 0.00 0.00 3.10
1044 1054 0.825840 ATAGACGGCCCAGAGAGAGC 60.826 60.000 0.00 0.00 0.00 4.09
1045 1055 2.211468 TAGACGGCCCAGAGAGAGCA 62.211 60.000 0.00 0.00 0.00 4.26
1183 1323 4.880537 CTCAGCTGCGCTACCCGG 62.881 72.222 9.47 0.00 36.40 5.73
1258 1399 1.340405 CCATCAAGCACTAGCCTGGTT 60.340 52.381 0.00 0.00 43.56 3.67
1592 1751 5.036737 CCTTTAATCTGTTTATGCTTGCCG 58.963 41.667 0.00 0.00 0.00 5.69
1606 1765 2.506444 CTTGCCGTGGGGTACTTTTTA 58.494 47.619 0.00 0.00 34.97 1.52
1634 1793 6.293004 AGTTCTAACTTCTAGCTGCTTGAT 57.707 37.500 14.23 3.12 35.21 2.57
1676 1835 2.953284 ATCCTGGCTCCATGAATCTG 57.047 50.000 0.00 0.00 0.00 2.90
1677 1836 0.182061 TCCTGGCTCCATGAATCTGC 59.818 55.000 0.00 0.00 0.00 4.26
1678 1837 0.183014 CCTGGCTCCATGAATCTGCT 59.817 55.000 0.00 0.00 0.00 4.24
1679 1838 1.419012 CCTGGCTCCATGAATCTGCTA 59.581 52.381 0.00 0.00 0.00 3.49
1684 1843 3.055240 GGCTCCATGAATCTGCTAGCTAT 60.055 47.826 17.23 6.80 0.00 2.97
1777 1940 5.490139 TTGATTCATAGCAGCAAGTTAGC 57.510 39.130 0.00 0.00 0.00 3.09
1993 2161 4.937201 GAACAAGGGTGGTTCTTTGATT 57.063 40.909 0.00 0.00 41.05 2.57
2035 2203 1.069500 CCAAACGGAAAACTGTAGCGG 60.069 52.381 0.00 0.00 0.00 5.52
2036 2204 1.600485 CAAACGGAAAACTGTAGCGGT 59.400 47.619 0.00 0.00 0.00 5.68
2037 2205 1.223187 AACGGAAAACTGTAGCGGTG 58.777 50.000 0.00 0.00 0.00 4.94
2038 2206 0.105408 ACGGAAAACTGTAGCGGTGT 59.895 50.000 0.00 0.00 0.00 4.16
2039 2207 0.511221 CGGAAAACTGTAGCGGTGTG 59.489 55.000 0.00 0.00 0.00 3.82
2040 2208 1.589803 GGAAAACTGTAGCGGTGTGT 58.410 50.000 0.00 0.00 0.00 3.72
2041 2209 2.758009 GGAAAACTGTAGCGGTGTGTA 58.242 47.619 0.00 0.00 0.00 2.90
2042 2210 2.477754 GGAAAACTGTAGCGGTGTGTAC 59.522 50.000 0.00 0.00 0.00 2.90
2043 2211 3.387397 GAAAACTGTAGCGGTGTGTACT 58.613 45.455 0.00 0.00 0.00 2.73
2044 2212 3.464111 AAACTGTAGCGGTGTGTACTT 57.536 42.857 0.00 0.00 0.00 2.24
2059 2227 6.245724 GTGTGTACTTGTGTGTACTTTTGAC 58.754 40.000 6.41 0.00 42.22 3.18
2111 2284 1.952296 CCTGGATCCTTACTGCATTGC 59.048 52.381 14.23 0.46 0.00 3.56
2165 2339 6.594284 TTGATCATCGTTCATCTTCATGAC 57.406 37.500 0.00 0.00 38.86 3.06
2205 2379 1.176619 GGGGCGCAAGTGGTTTTACT 61.177 55.000 10.83 0.00 41.68 2.24
2249 2423 3.054361 GGTACATGGTGATGGAGGTCTTT 60.054 47.826 0.00 0.00 33.39 2.52
2449 2623 0.818296 TGTTTGGGGTGTGTTTTCCG 59.182 50.000 0.00 0.00 0.00 4.30
2778 3435 4.574013 GCAATCACATGACCTCCTTTCTAG 59.426 45.833 0.00 0.00 0.00 2.43
3007 3679 5.411977 GCTCATCCTCATATCCTTTGATGTG 59.588 44.000 0.00 0.00 40.41 3.21
3024 3696 6.677781 TGATGTGCTAGTTATTTTACTGCC 57.322 37.500 0.00 0.00 0.00 4.85
3056 3729 2.153366 AAGAATGTTTTGCAAGGCCG 57.847 45.000 0.00 0.00 0.00 6.13
3322 4003 2.096406 CGGCATTGTCGTTGCTCG 59.904 61.111 1.71 0.00 40.03 5.03
3343 4025 2.256461 CAAGGCGCCACAAGAAGC 59.744 61.111 31.54 0.00 0.00 3.86
3385 4067 3.491208 CCATTCTGGAGGGAGCTTG 57.509 57.895 0.00 0.00 40.96 4.01
3386 4068 0.622665 CCATTCTGGAGGGAGCTTGT 59.377 55.000 0.00 0.00 40.96 3.16
3406 4088 4.619973 TGTGGAAAATGATGTTCTTGTGC 58.380 39.130 0.00 0.00 0.00 4.57
3511 4193 6.042322 TCCTGTTTCTTTAAGCTGGTACTACA 59.958 38.462 0.00 0.00 36.63 2.74
3572 4254 2.245096 CGCTTTGCAACAAGAGCATAC 58.755 47.619 18.29 0.00 42.33 2.39
3591 4273 5.692204 GCATACGCTACATGATAGTTTCACT 59.308 40.000 0.00 0.00 34.00 3.41
3622 4304 6.428385 AGCAGAAAGTGAATAGTACAATGC 57.572 37.500 0.00 0.00 0.00 3.56
3640 4322 0.037882 GCCCTCAAAGGAAGCAAAGC 60.038 55.000 0.00 0.00 37.67 3.51
3641 4323 0.242017 CCCTCAAAGGAAGCAAAGCG 59.758 55.000 0.00 0.00 37.67 4.68
3642 4324 1.238439 CCTCAAAGGAAGCAAAGCGA 58.762 50.000 0.00 0.00 37.67 4.93
3643 4325 1.198637 CCTCAAAGGAAGCAAAGCGAG 59.801 52.381 0.00 0.00 37.67 5.03
3655 4337 7.040686 AGGAAGCAAAGCGAGAGTAAAATTTTA 60.041 33.333 6.54 6.54 0.00 1.52
3691 4373 1.272592 TGGGGCATGAGAAGCAAATCA 60.273 47.619 0.00 0.00 0.00 2.57
3693 4375 2.433239 GGGGCATGAGAAGCAAATCAAT 59.567 45.455 0.00 0.00 0.00 2.57
3694 4376 3.492137 GGGGCATGAGAAGCAAATCAATC 60.492 47.826 0.00 0.00 0.00 2.67
3695 4377 3.492137 GGGCATGAGAAGCAAATCAATCC 60.492 47.826 0.00 0.00 0.00 3.01
3697 4379 4.360563 GCATGAGAAGCAAATCAATCCAG 58.639 43.478 0.00 0.00 0.00 3.86
3699 4381 5.579718 CATGAGAAGCAAATCAATCCAGAC 58.420 41.667 0.00 0.00 0.00 3.51
3700 4382 4.654915 TGAGAAGCAAATCAATCCAGACA 58.345 39.130 0.00 0.00 0.00 3.41
3701 4383 4.698780 TGAGAAGCAAATCAATCCAGACAG 59.301 41.667 0.00 0.00 0.00 3.51
3702 4384 3.442977 AGAAGCAAATCAATCCAGACAGC 59.557 43.478 0.00 0.00 0.00 4.40
3703 4385 2.799017 AGCAAATCAATCCAGACAGCA 58.201 42.857 0.00 0.00 0.00 4.41
3704 4386 3.159472 AGCAAATCAATCCAGACAGCAA 58.841 40.909 0.00 0.00 0.00 3.91
3705 4387 3.575256 AGCAAATCAATCCAGACAGCAAA 59.425 39.130 0.00 0.00 0.00 3.68
3706 4388 3.676646 GCAAATCAATCCAGACAGCAAAC 59.323 43.478 0.00 0.00 0.00 2.93
3707 4389 4.560108 GCAAATCAATCCAGACAGCAAACT 60.560 41.667 0.00 0.00 0.00 2.66
3708 4390 5.535333 CAAATCAATCCAGACAGCAAACTT 58.465 37.500 0.00 0.00 0.00 2.66
3709 4391 5.796424 AATCAATCCAGACAGCAAACTTT 57.204 34.783 0.00 0.00 0.00 2.66
3710 4392 4.572985 TCAATCCAGACAGCAAACTTTG 57.427 40.909 0.00 0.00 0.00 2.77
3711 4393 4.206375 TCAATCCAGACAGCAAACTTTGA 58.794 39.130 5.65 0.00 0.00 2.69
3712 4394 4.036734 TCAATCCAGACAGCAAACTTTGAC 59.963 41.667 5.65 0.00 0.00 3.18
3713 4395 1.939934 TCCAGACAGCAAACTTTGACG 59.060 47.619 5.65 0.00 0.00 4.35
3714 4396 1.002468 CCAGACAGCAAACTTTGACGG 60.002 52.381 5.65 1.11 0.00 4.79
3715 4397 1.939934 CAGACAGCAAACTTTGACGGA 59.060 47.619 5.65 0.00 0.00 4.69
3716 4398 1.940613 AGACAGCAAACTTTGACGGAC 59.059 47.619 5.65 0.00 0.00 4.79
3717 4399 1.940613 GACAGCAAACTTTGACGGACT 59.059 47.619 5.65 0.00 0.00 3.85
3721 4403 3.311322 CAGCAAACTTTGACGGACTTGTA 59.689 43.478 5.65 0.00 0.00 2.41
3758 4440 3.385115 AGGTTAACCAGCTAGCCTATGT 58.615 45.455 26.26 0.27 38.89 2.29
3899 4581 2.905415 TTGTGCAAGAGGGAATGGAT 57.095 45.000 0.00 0.00 0.00 3.41
3944 4626 1.152756 AGTCCCACAAGCCACAACC 60.153 57.895 0.00 0.00 0.00 3.77
3970 4652 9.896645 CATGCATACCTATCAATTATCTTACCT 57.103 33.333 0.00 0.00 0.00 3.08
4001 4683 9.753674 AATTCAGTCCCTTCAAATTAATACTCA 57.246 29.630 0.00 0.00 0.00 3.41
4023 4705 0.391927 CCGCCCCGAATTACTTGTCA 60.392 55.000 0.00 0.00 0.00 3.58
4041 4723 6.596888 ACTTGTCACAGAAATGGATGTATCTG 59.403 38.462 0.00 0.00 43.79 2.90
4042 4724 4.877823 TGTCACAGAAATGGATGTATCTGC 59.122 41.667 1.77 0.00 42.34 4.26
4044 4726 5.530171 GTCACAGAAATGGATGTATCTGCAT 59.470 40.000 1.77 0.00 42.34 3.96
4089 4771 8.246180 ACATCAATTTCTATCCATTTGTGTGAC 58.754 33.333 0.00 0.00 0.00 3.67
4091 4773 8.175925 TCAATTTCTATCCATTTGTGTGACAA 57.824 30.769 0.00 0.00 36.11 3.18
4138 4821 6.095860 CCAGATAAGAGCAAAACCATGAATCA 59.904 38.462 0.00 0.00 0.00 2.57
4168 4851 1.933181 CACAACGACTGAGCACAAGAA 59.067 47.619 0.00 0.00 0.00 2.52
4243 4926 4.698304 CCGTGTTTACCACAAATACCATCT 59.302 41.667 0.00 0.00 44.78 2.90
4245 4928 5.180492 CGTGTTTACCACAAATACCATCTGT 59.820 40.000 0.00 0.00 44.78 3.41
4263 4946 3.802139 TCTGTTTCTGTGTAAGCAAGTCG 59.198 43.478 0.00 0.00 0.00 4.18
4264 4947 2.286833 TGTTTCTGTGTAAGCAAGTCGC 59.713 45.455 0.00 0.00 42.91 5.19
4316 4999 5.348451 ACAAAATTGACAAGCAACTTCACAC 59.652 36.000 0.00 0.00 39.78 3.82
4342 5025 6.889177 TCAAAGCATTACTTGAATCCCATACA 59.111 34.615 0.00 0.00 39.09 2.29
4353 5036 7.399765 ACTTGAATCCCATACATTGATTTTGGA 59.600 33.333 0.00 0.00 0.00 3.53
4358 5041 5.299028 TCCCATACATTGATTTTGGATGACG 59.701 40.000 0.00 0.00 37.58 4.35
4372 5055 2.420022 GGATGACGGGAACATTCAACAG 59.580 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 1.136336 GTGTCTTCGGCGTTGTTGATC 60.136 52.381 6.85 0.00 0.00 2.92
197 199 4.181578 CTCTGGGTTTACGGTGTCAATAG 58.818 47.826 0.00 0.00 0.00 1.73
212 214 2.590611 TCCCTTATGTACTCCTCTGGGT 59.409 50.000 0.00 0.00 35.20 4.51
240 242 1.951602 TCGGAGTCTGAAACGTTCTGA 59.048 47.619 0.00 2.41 35.61 3.27
349 353 9.819267 CTTCGGACTACTTCTTATTTTCCTAAT 57.181 33.333 0.00 0.00 0.00 1.73
350 354 8.255905 CCTTCGGACTACTTCTTATTTTCCTAA 58.744 37.037 0.00 0.00 0.00 2.69
431 438 2.273449 GTGTCCATGAGGCAGGGG 59.727 66.667 0.00 0.00 35.84 4.79
471 478 5.163913 CCAGAAGAAGTATCGTGCAAGAAAG 60.164 44.000 6.39 0.00 0.00 2.62
521 528 4.628333 GGTACGATGGTCAAAATCTTCGAA 59.372 41.667 0.00 0.00 35.47 3.71
528 535 3.322211 TCGTGGTACGATGGTCAAAAT 57.678 42.857 0.00 0.00 46.73 1.82
580 587 7.307694 GTCATGATGATCTAGATCTGTCAGAC 58.692 42.308 28.70 27.65 36.96 3.51
617 627 3.118186 TCTCGAAAAACTTGTCCTTGGGA 60.118 43.478 0.00 0.00 0.00 4.37
741 751 3.876589 TTGTCTCCACGCTTCCGGC 62.877 63.158 0.00 0.00 39.22 6.13
765 775 7.725251 TCTAAAACTTGTTGCTCCATTGATTT 58.275 30.769 0.00 0.00 0.00 2.17
768 778 6.061441 TCTCTAAAACTTGTTGCTCCATTGA 58.939 36.000 0.00 0.00 0.00 2.57
788 798 2.424812 GCCAATCTCTCTCTCCCTCTCT 60.425 54.545 0.00 0.00 0.00 3.10
789 799 1.963515 GCCAATCTCTCTCTCCCTCTC 59.036 57.143 0.00 0.00 0.00 3.20
790 800 1.412937 GGCCAATCTCTCTCTCCCTCT 60.413 57.143 0.00 0.00 0.00 3.69
791 801 1.047801 GGCCAATCTCTCTCTCCCTC 58.952 60.000 0.00 0.00 0.00 4.30
792 802 0.399806 GGGCCAATCTCTCTCTCCCT 60.400 60.000 4.39 0.00 0.00 4.20
793 803 1.414866 GGGGCCAATCTCTCTCTCCC 61.415 65.000 4.39 0.00 0.00 4.30
794 804 0.692419 TGGGGCCAATCTCTCTCTCC 60.692 60.000 4.39 0.00 0.00 3.71
795 805 1.140652 CTTGGGGCCAATCTCTCTCTC 59.859 57.143 4.39 0.00 35.20 3.20
796 806 1.211456 CTTGGGGCCAATCTCTCTCT 58.789 55.000 4.39 0.00 35.20 3.10
797 807 0.182299 CCTTGGGGCCAATCTCTCTC 59.818 60.000 4.39 0.00 35.20 3.20
798 808 0.551131 ACCTTGGGGCCAATCTCTCT 60.551 55.000 4.39 0.00 35.20 3.10
799 809 0.394899 CACCTTGGGGCCAATCTCTC 60.395 60.000 4.39 0.00 35.20 3.20
800 810 1.142688 ACACCTTGGGGCCAATCTCT 61.143 55.000 4.39 0.00 35.20 3.10
801 811 0.681243 GACACCTTGGGGCCAATCTC 60.681 60.000 4.39 0.00 35.20 2.75
802 812 1.384191 GACACCTTGGGGCCAATCT 59.616 57.895 4.39 0.00 35.20 2.40
803 813 0.967380 CTGACACCTTGGGGCCAATC 60.967 60.000 4.39 0.00 35.20 2.67
804 814 1.077265 CTGACACCTTGGGGCCAAT 59.923 57.895 4.39 0.00 35.20 3.16
805 815 2.520458 CTGACACCTTGGGGCCAA 59.480 61.111 4.39 0.00 35.63 4.52
806 816 3.579302 CCTGACACCTTGGGGCCA 61.579 66.667 4.39 0.00 35.63 5.36
807 817 2.771328 CTTCCTGACACCTTGGGGCC 62.771 65.000 0.00 0.00 35.63 5.80
808 818 1.303643 CTTCCTGACACCTTGGGGC 60.304 63.158 0.00 0.00 35.63 5.80
809 819 1.303643 GCTTCCTGACACCTTGGGG 60.304 63.158 0.00 0.00 38.88 4.96
810 820 1.303643 GGCTTCCTGACACCTTGGG 60.304 63.158 0.00 0.00 0.00 4.12
811 821 0.984230 TAGGCTTCCTGACACCTTGG 59.016 55.000 0.00 0.00 34.61 3.61
812 822 3.356529 AATAGGCTTCCTGACACCTTG 57.643 47.619 0.00 0.00 34.61 3.61
813 823 4.388577 AAAATAGGCTTCCTGACACCTT 57.611 40.909 0.00 0.00 34.61 3.50
814 824 4.324331 GGTAAAATAGGCTTCCTGACACCT 60.324 45.833 0.00 0.00 34.61 4.00
815 825 3.945921 GGTAAAATAGGCTTCCTGACACC 59.054 47.826 0.00 0.00 34.61 4.16
816 826 4.844884 AGGTAAAATAGGCTTCCTGACAC 58.155 43.478 0.00 0.00 34.61 3.67
817 827 6.824958 ATAGGTAAAATAGGCTTCCTGACA 57.175 37.500 0.00 0.00 34.61 3.58
934 944 9.941664 CGTAGGATAAACGATAAAGTAGAGAAA 57.058 33.333 0.00 0.00 42.90 2.52
935 945 9.113838 ACGTAGGATAAACGATAAAGTAGAGAA 57.886 33.333 2.27 0.00 42.90 2.87
936 946 8.554528 CACGTAGGATAAACGATAAAGTAGAGA 58.445 37.037 2.27 0.00 42.90 3.10
937 947 7.802251 CCACGTAGGATAAACGATAAAGTAGAG 59.198 40.741 2.27 0.00 42.90 2.43
938 948 7.642669 CCACGTAGGATAAACGATAAAGTAGA 58.357 38.462 2.27 0.00 42.90 2.59
939 949 6.361748 GCCACGTAGGATAAACGATAAAGTAG 59.638 42.308 8.04 0.00 42.90 2.57
940 950 6.183360 TGCCACGTAGGATAAACGATAAAGTA 60.183 38.462 8.04 0.00 42.90 2.24
941 951 5.045872 GCCACGTAGGATAAACGATAAAGT 58.954 41.667 8.04 0.00 42.90 2.66
942 952 5.045215 TGCCACGTAGGATAAACGATAAAG 58.955 41.667 8.04 0.00 42.90 1.85
943 953 4.805192 GTGCCACGTAGGATAAACGATAAA 59.195 41.667 8.04 0.00 42.90 1.40
944 954 4.098349 AGTGCCACGTAGGATAAACGATAA 59.902 41.667 8.04 0.00 42.90 1.75
945 955 3.633525 AGTGCCACGTAGGATAAACGATA 59.366 43.478 8.04 0.00 42.90 2.92
946 956 2.429610 AGTGCCACGTAGGATAAACGAT 59.570 45.455 8.04 0.00 42.90 3.73
947 957 1.820519 AGTGCCACGTAGGATAAACGA 59.179 47.619 8.04 0.00 42.90 3.85
948 958 2.190981 GAGTGCCACGTAGGATAAACG 58.809 52.381 8.04 0.00 45.64 3.60
949 959 3.241067 TGAGTGCCACGTAGGATAAAC 57.759 47.619 8.04 1.53 41.22 2.01
950 960 4.038763 CCTATGAGTGCCACGTAGGATAAA 59.961 45.833 14.81 0.00 44.95 1.40
951 961 3.572682 CCTATGAGTGCCACGTAGGATAA 59.427 47.826 14.81 0.00 44.95 1.75
952 962 3.154710 CCTATGAGTGCCACGTAGGATA 58.845 50.000 14.81 0.00 44.95 2.59
953 963 1.964223 CCTATGAGTGCCACGTAGGAT 59.036 52.381 14.81 0.00 44.95 3.24
954 964 1.064240 TCCTATGAGTGCCACGTAGGA 60.064 52.381 17.20 17.20 46.96 2.94
955 965 1.399714 TCCTATGAGTGCCACGTAGG 58.600 55.000 14.15 14.15 44.08 3.18
956 966 3.366476 GCTATCCTATGAGTGCCACGTAG 60.366 52.174 0.00 0.00 0.00 3.51
957 967 2.557056 GCTATCCTATGAGTGCCACGTA 59.443 50.000 0.00 0.00 0.00 3.57
958 968 1.341531 GCTATCCTATGAGTGCCACGT 59.658 52.381 0.00 0.00 0.00 4.49
959 969 1.341209 TGCTATCCTATGAGTGCCACG 59.659 52.381 0.00 0.00 0.00 4.94
960 970 3.007290 TGATGCTATCCTATGAGTGCCAC 59.993 47.826 0.00 0.00 0.00 5.01
961 971 3.007290 GTGATGCTATCCTATGAGTGCCA 59.993 47.826 0.00 0.00 0.00 4.92
962 972 3.260380 AGTGATGCTATCCTATGAGTGCC 59.740 47.826 0.00 0.00 0.00 5.01
963 973 4.533919 AGTGATGCTATCCTATGAGTGC 57.466 45.455 0.00 0.00 0.00 4.40
964 974 8.286191 TGTATAGTGATGCTATCCTATGAGTG 57.714 38.462 0.00 0.00 40.61 3.51
965 975 8.911965 CATGTATAGTGATGCTATCCTATGAGT 58.088 37.037 0.00 0.00 40.61 3.41
966 976 8.358895 CCATGTATAGTGATGCTATCCTATGAG 58.641 40.741 0.00 0.00 40.61 2.90
967 977 7.201947 GCCATGTATAGTGATGCTATCCTATGA 60.202 40.741 0.00 0.00 40.61 2.15
968 978 6.927936 GCCATGTATAGTGATGCTATCCTATG 59.072 42.308 0.00 0.00 40.61 2.23
969 979 6.042552 GGCCATGTATAGTGATGCTATCCTAT 59.957 42.308 0.00 0.00 40.61 2.57
970 980 5.363868 GGCCATGTATAGTGATGCTATCCTA 59.636 44.000 0.00 0.00 40.61 2.94
971 981 4.163078 GGCCATGTATAGTGATGCTATCCT 59.837 45.833 0.00 0.00 40.61 3.24
972 982 4.163078 AGGCCATGTATAGTGATGCTATCC 59.837 45.833 5.01 0.00 40.61 2.59
973 983 5.105187 TGAGGCCATGTATAGTGATGCTATC 60.105 44.000 5.01 0.00 40.61 2.08
974 984 4.779489 TGAGGCCATGTATAGTGATGCTAT 59.221 41.667 5.01 0.00 42.63 2.97
975 985 4.159557 TGAGGCCATGTATAGTGATGCTA 58.840 43.478 5.01 0.00 0.00 3.49
976 986 2.974794 TGAGGCCATGTATAGTGATGCT 59.025 45.455 5.01 0.00 0.00 3.79
977 987 3.407424 TGAGGCCATGTATAGTGATGC 57.593 47.619 5.01 0.00 0.00 3.91
978 988 3.750130 GCTTGAGGCCATGTATAGTGATG 59.250 47.826 5.01 0.00 34.27 3.07
979 989 3.392285 TGCTTGAGGCCATGTATAGTGAT 59.608 43.478 5.01 0.00 40.92 3.06
980 990 2.771372 TGCTTGAGGCCATGTATAGTGA 59.229 45.455 5.01 0.00 40.92 3.41
981 991 2.874701 GTGCTTGAGGCCATGTATAGTG 59.125 50.000 5.01 0.00 40.92 2.74
982 992 2.774234 AGTGCTTGAGGCCATGTATAGT 59.226 45.455 5.01 0.00 40.92 2.12
983 993 3.482156 AGTGCTTGAGGCCATGTATAG 57.518 47.619 5.01 0.00 40.92 1.31
984 994 3.931907 AAGTGCTTGAGGCCATGTATA 57.068 42.857 5.01 0.00 40.92 1.47
985 995 2.814805 AAGTGCTTGAGGCCATGTAT 57.185 45.000 5.01 0.00 40.92 2.29
986 996 2.224744 TGAAAGTGCTTGAGGCCATGTA 60.225 45.455 5.01 0.00 40.92 2.29
987 997 1.251251 GAAAGTGCTTGAGGCCATGT 58.749 50.000 5.01 0.00 40.92 3.21
988 998 1.201647 CTGAAAGTGCTTGAGGCCATG 59.798 52.381 5.01 0.00 40.92 3.66
989 999 1.542492 CTGAAAGTGCTTGAGGCCAT 58.458 50.000 5.01 0.00 40.92 4.40
990 1000 1.174712 GCTGAAAGTGCTTGAGGCCA 61.175 55.000 5.01 0.00 40.92 5.36
991 1001 1.583477 GCTGAAAGTGCTTGAGGCC 59.417 57.895 0.00 0.00 40.92 5.19
992 1002 1.583477 GGCTGAAAGTGCTTGAGGC 59.417 57.895 0.00 3.27 42.22 4.70
993 1003 0.538057 TGGGCTGAAAGTGCTTGAGG 60.538 55.000 0.00 0.00 35.30 3.86
994 1004 0.879765 CTGGGCTGAAAGTGCTTGAG 59.120 55.000 0.00 0.00 35.30 3.02
995 1005 0.473755 TCTGGGCTGAAAGTGCTTGA 59.526 50.000 0.00 0.00 35.30 3.02
996 1006 0.595095 GTCTGGGCTGAAAGTGCTTG 59.405 55.000 0.00 0.00 35.30 4.01
997 1007 0.475906 AGTCTGGGCTGAAAGTGCTT 59.524 50.000 0.00 0.00 35.30 3.91
998 1008 0.036022 GAGTCTGGGCTGAAAGTGCT 59.964 55.000 0.00 0.00 35.30 4.40
1042 1052 4.756458 GCGCCTGTCTGCTCTGCT 62.756 66.667 0.00 0.00 0.00 4.24
1183 1323 1.099879 ATGGCAAGCTCGCAGAATCC 61.100 55.000 0.00 0.00 34.09 3.01
1592 1751 6.955364 AGAACTATCCTAAAAAGTACCCCAC 58.045 40.000 0.00 0.00 0.00 4.61
1606 1765 6.133356 AGCAGCTAGAAGTTAGAACTATCCT 58.867 40.000 0.00 0.00 38.57 3.24
1634 1793 2.316108 GAGAAAGTCCCAGGCCAAAAA 58.684 47.619 5.01 0.00 0.00 1.94
1676 1835 6.074249 GGAAACTCGACATAACAATAGCTAGC 60.074 42.308 6.62 6.62 0.00 3.42
1677 1836 6.978659 TGGAAACTCGACATAACAATAGCTAG 59.021 38.462 0.00 0.00 0.00 3.42
1678 1837 6.755141 GTGGAAACTCGACATAACAATAGCTA 59.245 38.462 0.00 0.00 0.00 3.32
1679 1838 5.581085 GTGGAAACTCGACATAACAATAGCT 59.419 40.000 0.00 0.00 0.00 3.32
1684 1843 3.061322 CGGTGGAAACTCGACATAACAA 58.939 45.455 0.00 0.00 0.00 2.83
1847 2010 4.523943 ACAAATGCAGTCAAGGCTAATGAA 59.476 37.500 0.00 0.00 0.00 2.57
1893 2058 5.050227 CCACGATTTCATGTGTGCAATTTTT 60.050 36.000 0.00 0.00 34.28 1.94
1894 2059 4.448395 CCACGATTTCATGTGTGCAATTTT 59.552 37.500 0.00 0.00 34.28 1.82
1895 2060 3.989167 CCACGATTTCATGTGTGCAATTT 59.011 39.130 0.00 0.00 34.28 1.82
1896 2061 3.577667 CCACGATTTCATGTGTGCAATT 58.422 40.909 0.00 0.00 34.28 2.32
1897 2062 2.094597 CCCACGATTTCATGTGTGCAAT 60.095 45.455 0.00 0.00 34.28 3.56
1901 2067 1.199789 CCACCCACGATTTCATGTGTG 59.800 52.381 0.00 0.00 34.28 3.82
1961 2129 3.699038 CCACCCTTGTTCTTCTGTTTTGA 59.301 43.478 0.00 0.00 0.00 2.69
2035 2203 6.245724 GTCAAAAGTACACACAAGTACACAC 58.754 40.000 6.97 0.00 45.25 3.82
2036 2204 5.062433 CGTCAAAAGTACACACAAGTACACA 59.938 40.000 6.97 0.00 45.25 3.72
2037 2205 5.486706 CGTCAAAAGTACACACAAGTACAC 58.513 41.667 6.97 0.00 45.25 2.90
2038 2206 4.567558 CCGTCAAAAGTACACACAAGTACA 59.432 41.667 6.97 0.00 45.25 2.90
2039 2207 4.567959 ACCGTCAAAAGTACACACAAGTAC 59.432 41.667 0.00 0.00 43.61 2.73
2040 2208 4.757594 ACCGTCAAAAGTACACACAAGTA 58.242 39.130 0.00 0.00 0.00 2.24
2041 2209 3.602483 ACCGTCAAAAGTACACACAAGT 58.398 40.909 0.00 0.00 0.00 3.16
2042 2210 5.917541 ATACCGTCAAAAGTACACACAAG 57.082 39.130 0.00 0.00 0.00 3.16
2043 2211 6.421501 CACTATACCGTCAAAAGTACACACAA 59.578 38.462 0.00 0.00 0.00 3.33
2044 2212 5.921976 CACTATACCGTCAAAAGTACACACA 59.078 40.000 0.00 0.00 0.00 3.72
2059 2227 6.621316 AGATATATCTTCGCCACTATACCG 57.379 41.667 9.57 0.00 31.97 4.02
2087 2255 0.255890 GCAGTAAGGATCCAGGCCAA 59.744 55.000 15.82 0.00 0.00 4.52
2111 2284 3.320673 ACGGCACCTCTTTAAGAGAAG 57.679 47.619 22.19 14.56 45.07 2.85
2165 2339 2.868583 CTGCTTATCGTGACCTGGATTG 59.131 50.000 0.00 0.00 0.00 2.67
2191 2365 4.584327 ACCATTGAGTAAAACCACTTGC 57.416 40.909 0.00 0.00 0.00 4.01
2205 2379 5.598005 ACCTGTTCTTGAAATGAACCATTGA 59.402 36.000 0.00 0.00 46.83 2.57
2249 2423 1.070289 TCTCCTCTGCTAGCGTCGATA 59.930 52.381 10.77 0.00 0.00 2.92
2449 2623 8.358895 AGTACTTCTACAAGTCTAAACAGAACC 58.641 37.037 0.00 0.00 42.27 3.62
2481 2658 2.233186 CACTGCAGAAGATGACCAGAGA 59.767 50.000 23.35 0.00 0.00 3.10
2778 3435 3.948196 AACACATGCATGCACAAAAAC 57.052 38.095 25.37 0.00 0.00 2.43
3007 3679 4.580580 AGGCATGGCAGTAAAATAACTAGC 59.419 41.667 22.64 0.00 0.00 3.42
3019 3691 2.040278 TCTTTCTGTTAGGCATGGCAGT 59.960 45.455 22.64 3.93 0.00 4.40
3024 3696 6.128742 GCAAAACATTCTTTCTGTTAGGCATG 60.129 38.462 0.00 0.00 35.84 4.06
3056 3729 1.467734 CAGCTCTGAACTGCCACAATC 59.532 52.381 0.00 0.00 0.00 2.67
3322 4003 3.365265 CTTGTGGCGCCTTGGACC 61.365 66.667 29.70 8.80 0.00 4.46
3343 4025 0.686224 TTTTTGGGCATGGAAGCTGG 59.314 50.000 0.00 0.00 34.17 4.85
3385 4067 4.619973 TGCACAAGAACATCATTTTCCAC 58.380 39.130 0.00 0.00 0.00 4.02
3386 4068 4.933505 TGCACAAGAACATCATTTTCCA 57.066 36.364 0.00 0.00 0.00 3.53
3453 4135 6.151691 GCTAAACTGCATCATTCTTTTGTGA 58.848 36.000 0.00 0.00 0.00 3.58
3511 4193 7.425606 AGAAACATGAAAACGCTTGATAAAGT 58.574 30.769 0.00 0.00 0.00 2.66
3591 4273 7.750229 ACTATTCACTTTCTGCTTTTCATCA 57.250 32.000 0.00 0.00 0.00 3.07
3600 4282 5.449177 GGGCATTGTACTATTCACTTTCTGC 60.449 44.000 0.00 0.00 0.00 4.26
3622 4304 0.242017 CGCTTTGCTTCCTTTGAGGG 59.758 55.000 0.00 0.00 35.59 4.30
3655 4337 5.922960 TGCCCCATATTTATTGACCTAGT 57.077 39.130 0.00 0.00 0.00 2.57
3657 4339 6.274436 TCTCATGCCCCATATTTATTGACCTA 59.726 38.462 0.00 0.00 0.00 3.08
3675 4357 4.097437 TCTGGATTGATTTGCTTCTCATGC 59.903 41.667 0.00 0.00 0.00 4.06
3691 4373 3.003689 CGTCAAAGTTTGCTGTCTGGATT 59.996 43.478 10.90 0.00 0.00 3.01
3693 4375 1.939934 CGTCAAAGTTTGCTGTCTGGA 59.060 47.619 10.90 0.00 0.00 3.86
3694 4376 1.002468 CCGTCAAAGTTTGCTGTCTGG 60.002 52.381 10.90 2.65 0.00 3.86
3695 4377 1.939934 TCCGTCAAAGTTTGCTGTCTG 59.060 47.619 10.90 0.00 0.00 3.51
3697 4379 1.940613 AGTCCGTCAAAGTTTGCTGTC 59.059 47.619 10.90 1.76 0.00 3.51
3699 4381 2.097466 ACAAGTCCGTCAAAGTTTGCTG 59.903 45.455 10.90 5.45 0.00 4.41
3700 4382 2.365582 ACAAGTCCGTCAAAGTTTGCT 58.634 42.857 10.90 0.00 0.00 3.91
3701 4383 2.844122 ACAAGTCCGTCAAAGTTTGC 57.156 45.000 10.90 5.48 0.00 3.68
3702 4384 3.311322 TGCTACAAGTCCGTCAAAGTTTG 59.689 43.478 9.44 9.44 0.00 2.93
3703 4385 3.537580 TGCTACAAGTCCGTCAAAGTTT 58.462 40.909 0.00 0.00 0.00 2.66
3704 4386 3.188159 TGCTACAAGTCCGTCAAAGTT 57.812 42.857 0.00 0.00 0.00 2.66
3705 4387 2.902705 TGCTACAAGTCCGTCAAAGT 57.097 45.000 0.00 0.00 0.00 2.66
3706 4388 4.527564 CTTTTGCTACAAGTCCGTCAAAG 58.472 43.478 0.00 0.00 0.00 2.77
3707 4389 3.242936 GCTTTTGCTACAAGTCCGTCAAA 60.243 43.478 0.00 0.00 43.35 2.69
3708 4390 2.289547 GCTTTTGCTACAAGTCCGTCAA 59.710 45.455 0.00 0.00 43.35 3.18
3709 4391 1.871039 GCTTTTGCTACAAGTCCGTCA 59.129 47.619 0.00 0.00 43.35 4.35
3710 4392 1.136336 CGCTTTTGCTACAAGTCCGTC 60.136 52.381 0.00 0.00 44.80 4.79
3711 4393 0.865769 CGCTTTTGCTACAAGTCCGT 59.134 50.000 0.00 0.00 44.80 4.69
3712 4394 0.165944 CCGCTTTTGCTACAAGTCCG 59.834 55.000 0.00 0.00 44.80 4.79
3713 4395 1.519408 TCCGCTTTTGCTACAAGTCC 58.481 50.000 0.00 0.00 44.80 3.85
3714 4396 2.289547 TGTTCCGCTTTTGCTACAAGTC 59.710 45.455 0.00 0.00 44.80 3.01
3715 4397 2.290641 CTGTTCCGCTTTTGCTACAAGT 59.709 45.455 0.00 0.00 44.80 3.16
3716 4398 2.548057 TCTGTTCCGCTTTTGCTACAAG 59.452 45.455 0.00 0.00 44.80 3.16
3717 4399 2.548057 CTCTGTTCCGCTTTTGCTACAA 59.452 45.455 0.00 0.00 44.80 2.41
3721 4403 0.179018 ACCTCTGTTCCGCTTTTGCT 60.179 50.000 0.00 0.00 44.80 3.91
3758 4440 2.035704 GCAAATGATGTGGGTTGTGTCA 59.964 45.455 0.00 0.00 0.00 3.58
3899 4581 2.939103 CGCCAACCAAATTTTGTTTCCA 59.061 40.909 4.96 0.00 0.00 3.53
3944 4626 9.896645 AGGTAAGATAATTGATAGGTATGCATG 57.103 33.333 10.16 0.00 0.00 4.06
3970 4652 8.648698 TTAATTTGAAGGGACTGAATTGATCA 57.351 30.769 0.00 0.00 40.86 2.92
4001 4683 0.107848 CAAGTAATTCGGGGCGGAGT 60.108 55.000 0.00 0.00 0.00 3.85
4023 4705 5.443283 ACATGCAGATACATCCATTTCTGT 58.557 37.500 0.00 0.00 38.26 3.41
4089 4771 1.004979 TCCCCCGTCCCAAATTACTTG 59.995 52.381 0.00 0.00 34.52 3.16
4091 4773 0.916809 CTCCCCCGTCCCAAATTACT 59.083 55.000 0.00 0.00 0.00 2.24
4138 4821 0.753262 AGTCGTTGTGGAACTGCTCT 59.247 50.000 0.00 0.00 38.04 4.09
4168 4851 1.808945 CCAGATTGTCGCTTGAGCTTT 59.191 47.619 1.07 0.00 39.32 3.51
4179 4862 5.402398 GTTAAAAGGATGTGCCAGATTGTC 58.598 41.667 0.00 0.00 40.02 3.18
4243 4926 2.286833 GCGACTTGCTTACACAGAAACA 59.713 45.455 0.00 0.00 41.73 2.83
4316 4999 5.902613 TGGGATTCAAGTAATGCTTTGAG 57.097 39.130 0.00 0.00 36.25 3.02
4342 5025 4.085733 TGTTCCCGTCATCCAAAATCAAT 58.914 39.130 0.00 0.00 0.00 2.57
4353 5036 3.417069 TCTGTTGAATGTTCCCGTCAT 57.583 42.857 0.00 0.00 0.00 3.06
4358 5041 3.888930 TGACCTTTCTGTTGAATGTTCCC 59.111 43.478 0.00 0.00 31.56 3.97
4372 5055 5.607119 ACATGTAACATTCGTGACCTTTC 57.393 39.130 0.00 0.00 0.00 2.62
4414 5097 6.554334 TTATTTGCCTGTCTCAGTTGTAAC 57.446 37.500 0.00 0.00 0.00 2.50



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

AutoCloner maintained by Alex Coulton.