Multiple sequence alignment - TraesCS6B01G117000

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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 TraesCS6B01G117000 chr6B 100.000 4624 0 0 1 4624 106476702 106472079 0.000000e+00 8540.0
1 TraesCS6B01G117000 chr6B 98.858 788 9 0 1 788 412164119 412164906 0.000000e+00 1406.0
2 TraesCS6B01G117000 chr6B 95.396 847 30 8 3781 4624 352214506 352213666 0.000000e+00 1339.0
3 TraesCS6B01G117000 chr6B 93.898 295 16 2 151 444 655893237 655892944 1.180000e-120 444.0
4 TraesCS6B01G117000 chr6B 93.559 295 17 2 151 444 655766125 655765832 5.490000e-119 438.0
5 TraesCS6B01G117000 chr6B 83.268 257 40 3 534 790 619035678 619035425 2.780000e-57 233.0
6 TraesCS6B01G117000 chr6B 94.030 67 3 1 444 510 655892843 655892778 2.940000e-17 100.0
7 TraesCS6B01G117000 chrUn 88.690 2016 148 46 897 2864 97743954 97741971 0.000000e+00 2386.0
8 TraesCS6B01G117000 chrUn 88.243 757 66 15 2910 3658 97741662 97740921 0.000000e+00 883.0
9 TraesCS6B01G117000 chrUn 88.616 571 53 5 1456 2024 36454534 36453974 0.000000e+00 684.0
10 TraesCS6B01G117000 chr6A 88.411 2045 134 45 898 2864 53136362 53134343 0.000000e+00 2368.0
11 TraesCS6B01G117000 chr6A 91.294 827 52 10 2910 3727 53133963 53133148 0.000000e+00 1110.0
12 TraesCS6B01G117000 chr3B 98.471 850 12 1 3776 4624 798689771 798688922 0.000000e+00 1496.0
13 TraesCS6B01G117000 chr3B 84.810 79 11 1 235 313 81531510 81531433 1.380000e-10 78.7
14 TraesCS6B01G117000 chr7A 98.129 855 14 2 3772 4624 49900697 49899843 0.000000e+00 1489.0
15 TraesCS6B01G117000 chr7A 93.960 298 13 3 151 444 668309476 668309180 3.280000e-121 446.0
16 TraesCS6B01G117000 chr7A 88.889 198 11 5 1456 1653 728276257 728276443 2.780000e-57 233.0
17 TraesCS6B01G117000 chr7A 95.890 73 3 0 452 524 668309072 668309000 8.130000e-23 119.0
18 TraesCS6B01G117000 chr4A 98.235 850 12 3 3776 4624 743747683 743746836 0.000000e+00 1483.0
19 TraesCS6B01G117000 chr4A 95.176 850 36 5 3776 4624 641827530 641826685 0.000000e+00 1338.0
20 TraesCS6B01G117000 chr4A 95.065 851 38 4 3776 4624 718427361 718428209 0.000000e+00 1336.0
21 TraesCS6B01G117000 chr4A 83.815 173 26 2 151 322 731593923 731593752 3.700000e-36 163.0
22 TraesCS6B01G117000 chr4A 100.000 28 0 0 489 516 625073490 625073463 8.000000e-03 52.8
23 TraesCS6B01G117000 chr2B 96.853 858 22 5 3770 4624 5073558 5072703 0.000000e+00 1430.0
24 TraesCS6B01G117000 chr2B 94.830 851 38 5 3776 4624 461572557 461573403 0.000000e+00 1323.0
25 TraesCS6B01G117000 chr1B 94.836 852 36 7 3776 4624 684678669 684677823 0.000000e+00 1323.0
26 TraesCS6B01G117000 chr7B 97.407 540 11 3 1 539 320268639 320269176 0.000000e+00 917.0
27 TraesCS6B01G117000 chr7B 88.761 347 33 5 1658 2000 669608086 669607742 1.990000e-113 420.0
28 TraesCS6B01G117000 chr1A 97.407 540 10 4 1 538 412784104 412783567 0.000000e+00 917.0
29 TraesCS6B01G117000 chr1A 78.498 293 37 8 155 444 36189669 36189400 7.960000e-38 169.0
30 TraesCS6B01G117000 chr5B 88.139 548 47 11 1456 2000 62546135 62546667 1.810000e-178 636.0
31 TraesCS6B01G117000 chr4B 87.963 540 53 5 1462 2000 291449662 291449134 1.090000e-175 627.0
32 TraesCS6B01G117000 chr4B 94.071 253 13 1 534 786 109224275 109224525 2.610000e-102 383.0
33 TraesCS6B01G117000 chr3A 94.479 163 7 2 1 163 19781574 19781734 2.760000e-62 250.0
34 TraesCS6B01G117000 chr2A 95.541 157 6 1 7 163 17119999 17120154 2.760000e-62 250.0
35 TraesCS6B01G117000 chr7D 88.344 163 18 1 1 163 634562888 634562727 1.310000e-45 195.0
36 TraesCS6B01G117000 chr2D 83.168 101 12 4 1241 1340 381299754 381299850 2.290000e-13 87.9


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 TraesCS6B01G117000 chr6B 106472079 106476702 4623 True 8540.0 8540 100.0000 1 4624 1 chr6B.!!$R1 4623
1 TraesCS6B01G117000 chr6B 412164119 412164906 787 False 1406.0 1406 98.8580 1 788 1 chr6B.!!$F1 787
2 TraesCS6B01G117000 chr6B 352213666 352214506 840 True 1339.0 1339 95.3960 3781 4624 1 chr6B.!!$R2 843
3 TraesCS6B01G117000 chrUn 97740921 97743954 3033 True 1634.5 2386 88.4665 897 3658 2 chrUn.!!$R2 2761
4 TraesCS6B01G117000 chrUn 36453974 36454534 560 True 684.0 684 88.6160 1456 2024 1 chrUn.!!$R1 568
5 TraesCS6B01G117000 chr6A 53133148 53136362 3214 True 1739.0 2368 89.8525 898 3727 2 chr6A.!!$R1 2829
6 TraesCS6B01G117000 chr3B 798688922 798689771 849 True 1496.0 1496 98.4710 3776 4624 1 chr3B.!!$R2 848
7 TraesCS6B01G117000 chr7A 49899843 49900697 854 True 1489.0 1489 98.1290 3772 4624 1 chr7A.!!$R1 852
8 TraesCS6B01G117000 chr4A 743746836 743747683 847 True 1483.0 1483 98.2350 3776 4624 1 chr4A.!!$R4 848
9 TraesCS6B01G117000 chr4A 641826685 641827530 845 True 1338.0 1338 95.1760 3776 4624 1 chr4A.!!$R2 848
10 TraesCS6B01G117000 chr4A 718427361 718428209 848 False 1336.0 1336 95.0650 3776 4624 1 chr4A.!!$F1 848
11 TraesCS6B01G117000 chr2B 5072703 5073558 855 True 1430.0 1430 96.8530 3770 4624 1 chr2B.!!$R1 854
12 TraesCS6B01G117000 chr2B 461572557 461573403 846 False 1323.0 1323 94.8300 3776 4624 1 chr2B.!!$F1 848
13 TraesCS6B01G117000 chr1B 684677823 684678669 846 True 1323.0 1323 94.8360 3776 4624 1 chr1B.!!$R1 848
14 TraesCS6B01G117000 chr7B 320268639 320269176 537 False 917.0 917 97.4070 1 539 1 chr7B.!!$F1 538
15 TraesCS6B01G117000 chr1A 412783567 412784104 537 True 917.0 917 97.4070 1 538 1 chr1A.!!$R2 537
16 TraesCS6B01G117000 chr5B 62546135 62546667 532 False 636.0 636 88.1390 1456 2000 1 chr5B.!!$F1 544
17 TraesCS6B01G117000 chr4B 291449134 291449662 528 True 627.0 627 87.9630 1462 2000 1 chr4B.!!$R1 538

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
942 945 0.036875 AGTTTTCCTTCCAGAGGCGG 59.963 55.0 0.00 0.0 45.87 6.13 F
1993 2041 0.036671 CTCCCCACCTGTACGGTTTC 60.037 60.0 6.65 0.0 46.37 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2908 3355 0.033781 TTGATGCCTTGGCACTTTGC 59.966 50.0 17.22 5.12 44.08 3.68 R
3733 4204 0.247460 CGCCTGACCTGAGACATTCA 59.753 55.0 0.00 0.00 0.00 2.57 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
599 602 3.555168 GCTCTCGTTGGGAAAGAAGAGAA 60.555 47.826 0.00 0.00 34.81 2.87
678 681 0.545787 ATAAGGTGTCGTGGGTGGGA 60.546 55.000 0.00 0.00 0.00 4.37
703 706 3.323136 GCGCGTGATACGGCTCTG 61.323 66.667 8.43 0.00 42.82 3.35
792 795 4.799419 CGTAAAACGTTTCCCTTCTCAA 57.201 40.909 15.01 0.00 36.74 3.02
793 796 5.352643 CGTAAAACGTTTCCCTTCTCAAT 57.647 39.130 15.01 0.00 36.74 2.57
794 797 5.754778 CGTAAAACGTTTCCCTTCTCAATT 58.245 37.500 15.01 0.00 36.74 2.32
795 798 5.849604 CGTAAAACGTTTCCCTTCTCAATTC 59.150 40.000 15.01 0.00 36.74 2.17
796 799 4.483476 AAACGTTTCCCTTCTCAATTCG 57.517 40.909 7.96 0.00 0.00 3.34
797 800 3.121738 ACGTTTCCCTTCTCAATTCGT 57.878 42.857 0.00 0.00 0.00 3.85
798 801 3.473625 ACGTTTCCCTTCTCAATTCGTT 58.526 40.909 0.00 0.00 0.00 3.85
799 802 3.250040 ACGTTTCCCTTCTCAATTCGTTG 59.750 43.478 0.00 0.00 0.00 4.10
800 803 3.565516 GTTTCCCTTCTCAATTCGTTGC 58.434 45.455 0.00 0.00 0.00 4.17
801 804 2.859165 TCCCTTCTCAATTCGTTGCT 57.141 45.000 0.00 0.00 0.00 3.91
802 805 2.699954 TCCCTTCTCAATTCGTTGCTC 58.300 47.619 0.00 0.00 0.00 4.26
803 806 2.303022 TCCCTTCTCAATTCGTTGCTCT 59.697 45.455 0.00 0.00 0.00 4.09
804 807 2.675348 CCCTTCTCAATTCGTTGCTCTC 59.325 50.000 0.00 0.00 0.00 3.20
805 808 2.675348 CCTTCTCAATTCGTTGCTCTCC 59.325 50.000 0.00 0.00 0.00 3.71
806 809 1.996292 TCTCAATTCGTTGCTCTCCG 58.004 50.000 0.00 0.00 0.00 4.63
807 810 0.371645 CTCAATTCGTTGCTCTCCGC 59.628 55.000 0.00 0.00 39.77 5.54
808 811 1.019278 TCAATTCGTTGCTCTCCGCC 61.019 55.000 0.00 0.00 38.05 6.13
809 812 2.100631 AATTCGTTGCTCTCCGCCG 61.101 57.895 0.00 0.00 38.05 6.46
810 813 2.781595 AATTCGTTGCTCTCCGCCGT 62.782 55.000 0.00 0.00 38.05 5.68
811 814 4.717629 TCGTTGCTCTCCGCCGTG 62.718 66.667 0.00 0.00 38.05 4.94
814 817 4.742201 TTGCTCTCCGCCGTGCTC 62.742 66.667 0.00 0.00 38.05 4.26
816 819 4.863925 GCTCTCCGCCGTGCTCTC 62.864 72.222 0.00 0.00 0.00 3.20
817 820 3.137459 CTCTCCGCCGTGCTCTCT 61.137 66.667 0.00 0.00 0.00 3.10
818 821 3.119709 CTCTCCGCCGTGCTCTCTC 62.120 68.421 0.00 0.00 0.00 3.20
819 822 3.443925 CTCCGCCGTGCTCTCTCA 61.444 66.667 0.00 0.00 0.00 3.27
820 823 2.989253 TCCGCCGTGCTCTCTCAA 60.989 61.111 0.00 0.00 0.00 3.02
821 824 2.185350 CCGCCGTGCTCTCTCAAT 59.815 61.111 0.00 0.00 0.00 2.57
822 825 1.880340 CCGCCGTGCTCTCTCAATC 60.880 63.158 0.00 0.00 0.00 2.67
823 826 1.140589 CGCCGTGCTCTCTCAATCT 59.859 57.895 0.00 0.00 0.00 2.40
824 827 1.144565 CGCCGTGCTCTCTCAATCTG 61.145 60.000 0.00 0.00 0.00 2.90
825 828 0.174389 GCCGTGCTCTCTCAATCTGA 59.826 55.000 0.00 0.00 0.00 3.27
826 829 1.404717 GCCGTGCTCTCTCAATCTGAA 60.405 52.381 0.00 0.00 0.00 3.02
827 830 2.741228 GCCGTGCTCTCTCAATCTGAAT 60.741 50.000 0.00 0.00 0.00 2.57
828 831 3.122297 CCGTGCTCTCTCAATCTGAATC 58.878 50.000 0.00 0.00 0.00 2.52
829 832 3.122297 CGTGCTCTCTCAATCTGAATCC 58.878 50.000 0.00 0.00 0.00 3.01
830 833 3.465871 GTGCTCTCTCAATCTGAATCCC 58.534 50.000 0.00 0.00 0.00 3.85
831 834 3.134442 GTGCTCTCTCAATCTGAATCCCT 59.866 47.826 0.00 0.00 0.00 4.20
832 835 3.779183 TGCTCTCTCAATCTGAATCCCTT 59.221 43.478 0.00 0.00 0.00 3.95
833 836 4.141756 TGCTCTCTCAATCTGAATCCCTTC 60.142 45.833 0.00 0.00 0.00 3.46
834 837 4.141756 GCTCTCTCAATCTGAATCCCTTCA 60.142 45.833 0.00 0.00 39.07 3.02
835 838 5.628666 GCTCTCTCAATCTGAATCCCTTCAA 60.629 44.000 0.00 0.00 40.78 2.69
836 839 6.572182 TCTCTCAATCTGAATCCCTTCAAT 57.428 37.500 0.00 0.00 40.78 2.57
837 840 6.966751 TCTCTCAATCTGAATCCCTTCAATT 58.033 36.000 0.00 0.00 40.78 2.32
838 841 7.408543 TCTCTCAATCTGAATCCCTTCAATTT 58.591 34.615 0.00 0.00 40.78 1.82
839 842 7.555554 TCTCTCAATCTGAATCCCTTCAATTTC 59.444 37.037 0.00 0.00 40.78 2.17
840 843 6.604795 TCTCAATCTGAATCCCTTCAATTTCC 59.395 38.462 0.00 0.00 40.78 3.13
841 844 5.658190 TCAATCTGAATCCCTTCAATTTCCC 59.342 40.000 0.00 0.00 40.78 3.97
842 845 4.953781 TCTGAATCCCTTCAATTTCCCT 57.046 40.909 0.00 0.00 40.78 4.20
843 846 5.275263 TCTGAATCCCTTCAATTTCCCTT 57.725 39.130 0.00 0.00 40.78 3.95
844 847 5.654370 TCTGAATCCCTTCAATTTCCCTTT 58.346 37.500 0.00 0.00 40.78 3.11
845 848 6.084060 TCTGAATCCCTTCAATTTCCCTTTT 58.916 36.000 0.00 0.00 40.78 2.27
846 849 6.558394 TCTGAATCCCTTCAATTTCCCTTTTT 59.442 34.615 0.00 0.00 40.78 1.94
863 866 1.761449 TTTTTGCACAGCCTCACAGA 58.239 45.000 0.00 0.00 0.00 3.41
864 867 1.024271 TTTTGCACAGCCTCACAGAC 58.976 50.000 0.00 0.00 0.00 3.51
865 868 0.107263 TTTGCACAGCCTCACAGACA 60.107 50.000 0.00 0.00 0.00 3.41
866 869 0.533531 TTGCACAGCCTCACAGACAG 60.534 55.000 0.00 0.00 0.00 3.51
867 870 1.670406 GCACAGCCTCACAGACAGG 60.670 63.158 0.00 0.00 0.00 4.00
868 871 1.004080 CACAGCCTCACAGACAGGG 60.004 63.158 0.00 0.00 0.00 4.45
869 872 2.219875 ACAGCCTCACAGACAGGGG 61.220 63.158 0.00 0.00 0.00 4.79
870 873 2.205462 AGCCTCACAGACAGGGGT 59.795 61.111 0.00 0.00 0.00 4.95
871 874 1.915769 AGCCTCACAGACAGGGGTC 60.916 63.158 0.00 0.00 44.66 4.46
872 875 2.217038 GCCTCACAGACAGGGGTCA 61.217 63.158 0.00 0.00 46.80 4.02
873 876 1.674057 CCTCACAGACAGGGGTCAC 59.326 63.158 0.00 0.00 46.80 3.67
874 877 1.290324 CTCACAGACAGGGGTCACG 59.710 63.158 0.00 0.00 46.80 4.35
875 878 2.357517 CACAGACAGGGGTCACGC 60.358 66.667 0.00 0.00 46.80 5.34
876 879 3.626924 ACAGACAGGGGTCACGCC 61.627 66.667 1.61 1.61 46.80 5.68
885 888 2.112297 GGTCACGCCCCAACAGAA 59.888 61.111 0.00 0.00 0.00 3.02
886 889 1.966451 GGTCACGCCCCAACAGAAG 60.966 63.158 0.00 0.00 0.00 2.85
887 890 1.070786 GTCACGCCCCAACAGAAGA 59.929 57.895 0.00 0.00 0.00 2.87
888 891 0.534203 GTCACGCCCCAACAGAAGAA 60.534 55.000 0.00 0.00 0.00 2.52
889 892 0.400213 TCACGCCCCAACAGAAGAAT 59.600 50.000 0.00 0.00 0.00 2.40
890 893 0.523072 CACGCCCCAACAGAAGAATG 59.477 55.000 0.00 0.00 0.00 2.67
891 894 1.244019 ACGCCCCAACAGAAGAATGC 61.244 55.000 0.00 0.00 0.00 3.56
892 895 0.962356 CGCCCCAACAGAAGAATGCT 60.962 55.000 0.00 0.00 0.00 3.79
893 896 1.260544 GCCCCAACAGAAGAATGCTT 58.739 50.000 0.00 0.00 36.96 3.91
894 897 2.446435 GCCCCAACAGAAGAATGCTTA 58.554 47.619 0.00 0.00 33.61 3.09
895 898 3.026694 GCCCCAACAGAAGAATGCTTAT 58.973 45.455 0.00 0.00 33.61 1.73
910 913 1.565156 CTTATGCGCACACACACCGT 61.565 55.000 14.90 0.00 0.00 4.83
942 945 0.036875 AGTTTTCCTTCCAGAGGCGG 59.963 55.000 0.00 0.00 45.87 6.13
944 947 0.768622 TTTTCCTTCCAGAGGCGGAA 59.231 50.000 0.00 0.00 45.87 4.30
1105 1116 1.453197 CCAGTTAATCACCGCCCCC 60.453 63.158 0.00 0.00 0.00 5.40
1119 1130 3.157949 CCCCTCCCTCTTCGCTCC 61.158 72.222 0.00 0.00 0.00 4.70
1121 1132 1.687493 CCCTCCCTCTTCGCTCCTT 60.687 63.158 0.00 0.00 0.00 3.36
1122 1133 1.268283 CCCTCCCTCTTCGCTCCTTT 61.268 60.000 0.00 0.00 0.00 3.11
1126 1137 1.978580 TCCCTCTTCGCTCCTTTTCTT 59.021 47.619 0.00 0.00 0.00 2.52
1127 1138 2.028020 TCCCTCTTCGCTCCTTTTCTTC 60.028 50.000 0.00 0.00 0.00 2.87
1128 1139 2.027653 CCCTCTTCGCTCCTTTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
1129 1140 3.258228 CCTCTTCGCTCCTTTTCTTCTC 58.742 50.000 0.00 0.00 0.00 2.87
1130 1141 3.306364 CCTCTTCGCTCCTTTTCTTCTCA 60.306 47.826 0.00 0.00 0.00 3.27
1131 1142 3.919216 TCTTCGCTCCTTTTCTTCTCAG 58.081 45.455 0.00 0.00 0.00 3.35
1133 1144 3.753294 TCGCTCCTTTTCTTCTCAGTT 57.247 42.857 0.00 0.00 0.00 3.16
1134 1145 3.393800 TCGCTCCTTTTCTTCTCAGTTG 58.606 45.455 0.00 0.00 0.00 3.16
1136 1147 3.185391 CGCTCCTTTTCTTCTCAGTTGTC 59.815 47.826 0.00 0.00 0.00 3.18
1137 1148 4.130118 GCTCCTTTTCTTCTCAGTTGTCA 58.870 43.478 0.00 0.00 0.00 3.58
1138 1149 4.213059 GCTCCTTTTCTTCTCAGTTGTCAG 59.787 45.833 0.00 0.00 0.00 3.51
1140 1151 3.059325 CCTTTTCTTCTCAGTTGTCAGCG 60.059 47.826 0.00 0.00 0.00 5.18
1141 1152 1.502231 TTCTTCTCAGTTGTCAGCGC 58.498 50.000 0.00 0.00 0.00 5.92
1142 1153 0.664466 TCTTCTCAGTTGTCAGCGCG 60.664 55.000 0.00 0.00 0.00 6.86
1371 1392 0.096976 CGACTGGTAAAATGCAGCCG 59.903 55.000 0.00 0.00 0.00 5.52
1414 1459 2.571212 TGATTTTGTGACTTGAGGCGT 58.429 42.857 0.00 0.00 0.00 5.68
1425 1470 1.161563 TTGAGGCGTTCGTTTCACCC 61.162 55.000 0.00 0.00 0.00 4.61
1447 1492 3.677648 CCTTGCCTGCACTGCACC 61.678 66.667 5.68 0.00 38.72 5.01
1547 1592 2.923020 GGTGCAATTTCGCAATTTCGAT 59.077 40.909 0.00 0.00 45.14 3.59
1584 1629 1.857837 GCGATTGAAGCTCTAGCAGTC 59.142 52.381 4.54 2.01 45.16 3.51
1606 1651 4.340666 TCTTACTGCTTTTGTGCCATTGAA 59.659 37.500 0.00 0.00 0.00 2.69
1609 1654 2.798283 CTGCTTTTGTGCCATTGAACAG 59.202 45.455 0.00 0.00 0.00 3.16
1688 1733 8.905702 CATCTAAAATTCGTTTGTTTCTTCCAG 58.094 33.333 0.00 0.00 0.00 3.86
1746 1793 3.012518 GTGACTGATTCAGATTGTGGGG 58.987 50.000 20.33 0.00 33.71 4.96
1773 1820 9.850198 TGTATTCTCAATTGTCCATGATATTGA 57.150 29.630 5.13 3.29 36.08 2.57
1814 1862 7.225341 GCAGAAAACCATGGAATAAAATGATCC 59.775 37.037 21.47 0.00 0.00 3.36
1936 1984 1.327460 CGCGTGTACATGGAGGAATTG 59.673 52.381 16.68 0.00 0.00 2.32
1993 2041 0.036671 CTCCCCACCTGTACGGTTTC 60.037 60.000 6.65 0.00 46.37 2.78
2002 2050 3.446516 ACCTGTACGGTTTCCTATCTGAC 59.553 47.826 0.00 0.00 46.37 3.51
2011 2059 5.391950 CGGTTTCCTATCTGACCATTGTTTG 60.392 44.000 0.00 0.00 32.41 2.93
2015 2063 6.126863 TCCTATCTGACCATTGTTTGAACT 57.873 37.500 0.00 0.00 0.00 3.01
2020 2068 5.375773 TCTGACCATTGTTTGAACTCATGA 58.624 37.500 0.00 0.00 0.00 3.07
2024 2072 8.352137 TGACCATTGTTTGAACTCATGAATAT 57.648 30.769 0.00 0.00 0.00 1.28
2025 2073 9.460019 TGACCATTGTTTGAACTCATGAATATA 57.540 29.630 0.00 0.00 0.00 0.86
2066 2133 0.666274 TCGCAGTTGGAGTAACGCAG 60.666 55.000 0.00 0.00 44.15 5.18
2093 2161 7.626452 GCTTAGTGGCTTGTATTCTTAGTTTGG 60.626 40.741 0.00 0.00 0.00 3.28
2104 2172 6.715347 ATTCTTAGTTTGGCAAGTTCTTGT 57.285 33.333 13.04 0.00 0.00 3.16
2110 2178 6.136541 AGTTTGGCAAGTTCTTGTAGAAAG 57.863 37.500 13.04 0.00 35.75 2.62
2125 2194 6.630203 TGTAGAAAGTTATGGGCCTCTTAA 57.370 37.500 4.53 0.00 0.00 1.85
2128 2197 8.113462 TGTAGAAAGTTATGGGCCTCTTAAATT 58.887 33.333 4.53 4.90 0.00 1.82
2129 2198 8.967918 GTAGAAAGTTATGGGCCTCTTAAATTT 58.032 33.333 17.19 17.19 36.59 1.82
2131 2200 7.895962 AGAAAGTTATGGGCCTCTTAAATTTCT 59.104 33.333 27.00 27.00 45.18 2.52
2134 2203 3.825908 TGGGCCTCTTAAATTTCTGGT 57.174 42.857 4.53 0.00 0.00 4.00
2137 2206 6.584471 TGGGCCTCTTAAATTTCTGGTATA 57.416 37.500 4.53 0.00 0.00 1.47
2141 2210 8.360390 GGGCCTCTTAAATTTCTGGTATAAATG 58.640 37.037 0.84 0.00 0.00 2.32
2184 2253 6.891908 AGATTTGGCACCTATTGTTACATTCT 59.108 34.615 0.00 0.00 0.00 2.40
2186 2255 4.188462 TGGCACCTATTGTTACATTCTCG 58.812 43.478 0.00 0.00 0.00 4.04
2192 2261 6.590292 CACCTATTGTTACATTCTCGTTCTGT 59.410 38.462 0.00 0.00 0.00 3.41
2197 2266 8.782533 ATTGTTACATTCTCGTTCTGTTTTTC 57.217 30.769 0.00 0.00 0.00 2.29
2210 2279 6.204882 CGTTCTGTTTTTCCTCCTAGAACATT 59.795 38.462 13.32 0.00 42.34 2.71
2251 2320 8.150945 CCCAGCTTACAACAATGTAGATATACT 58.849 37.037 0.00 0.00 42.72 2.12
2296 2365 4.336433 CAGACTTGTGTGTGGATTTCAGTT 59.664 41.667 0.00 0.00 34.29 3.16
2335 2404 3.756082 ATGATTAGGCCTTGTTTGGGA 57.244 42.857 12.58 0.00 0.00 4.37
2347 2416 4.262164 CCTTGTTTGGGAAGGTGAGAAATG 60.262 45.833 0.00 0.00 36.05 2.32
2358 2427 5.061721 AGGTGAGAAATGTTACCCTGTTT 57.938 39.130 0.00 0.00 33.67 2.83
2365 2434 6.133356 AGAAATGTTACCCTGTTTCCTTTGA 58.867 36.000 0.00 0.00 32.43 2.69
2371 2440 3.909732 ACCCTGTTTCCTTTGAATGTGA 58.090 40.909 0.00 0.00 0.00 3.58
2377 2446 8.096414 CCCTGTTTCCTTTGAATGTGAAAATAT 58.904 33.333 0.00 0.00 0.00 1.28
2423 2493 7.280205 ACCAAAGGAATTGAGCTTAATACGTAG 59.720 37.037 3.88 0.00 41.85 3.51
2430 2500 3.639561 TGAGCTTAATACGTAGCCATCCA 59.360 43.478 0.08 0.00 38.14 3.41
2431 2501 4.100344 TGAGCTTAATACGTAGCCATCCAA 59.900 41.667 0.08 0.00 38.14 3.53
2432 2502 5.031066 AGCTTAATACGTAGCCATCCAAA 57.969 39.130 0.08 0.00 38.14 3.28
2433 2503 4.814771 AGCTTAATACGTAGCCATCCAAAC 59.185 41.667 0.08 0.00 38.14 2.93
2434 2504 4.573201 GCTTAATACGTAGCCATCCAAACA 59.427 41.667 0.08 0.00 0.00 2.83
2462 2537 4.337264 AGCCCTGTAAAAATCTCCCAAT 57.663 40.909 0.00 0.00 0.00 3.16
2500 2605 9.733556 TTTACATGTGGTTTGATACATAGAAGT 57.266 29.630 9.11 0.00 35.86 3.01
2501 2606 7.849804 ACATGTGGTTTGATACATAGAAGTC 57.150 36.000 0.00 0.00 35.86 3.01
2502 2607 7.394016 ACATGTGGTTTGATACATAGAAGTCA 58.606 34.615 0.00 0.00 35.86 3.41
2503 2608 8.049117 ACATGTGGTTTGATACATAGAAGTCAT 58.951 33.333 0.00 0.00 35.86 3.06
2504 2609 7.848223 TGTGGTTTGATACATAGAAGTCATG 57.152 36.000 0.00 0.00 0.00 3.07
2505 2610 6.316140 TGTGGTTTGATACATAGAAGTCATGC 59.684 38.462 0.00 0.00 0.00 4.06
2506 2611 6.316140 GTGGTTTGATACATAGAAGTCATGCA 59.684 38.462 0.00 0.00 0.00 3.96
2507 2612 6.316140 TGGTTTGATACATAGAAGTCATGCAC 59.684 38.462 0.00 0.00 0.00 4.57
2561 2667 6.757897 TTAACTTGATAGCAGGTGGAATTG 57.242 37.500 0.00 0.00 34.23 2.32
2764 2883 3.622455 GCATTGCTGGAAGGTACCTTACT 60.622 47.826 32.39 13.40 37.74 2.24
2779 2898 9.109246 AGGTACCTTACTTTATAGTTCAGGTTT 57.891 33.333 9.21 6.27 41.04 3.27
2842 2961 7.211966 AGGCTTATGCATTACATTTCATCTC 57.788 36.000 3.54 0.00 40.38 2.75
2844 2963 6.208204 GGCTTATGCATTACATTTCATCTCCT 59.792 38.462 3.54 0.00 40.38 3.69
2971 3428 8.500753 TCTTGGCGTTGAAAATATGTAATACT 57.499 30.769 0.00 0.00 0.00 2.12
3003 3460 3.373439 GCTCTTGCCAGACTTGAACATAG 59.627 47.826 0.00 0.00 0.00 2.23
3038 3498 3.309296 TCCTGGGTTGGCAAAAATTACA 58.691 40.909 0.00 0.00 0.00 2.41
3047 3509 7.351981 GGTTGGCAAAAATTACAAACATTCTC 58.648 34.615 0.00 0.00 31.15 2.87
3074 3536 5.924254 TGAAAATGTAGTCCTGTAGAACACG 59.076 40.000 0.00 0.00 0.00 4.49
3080 3542 1.792949 GTCCTGTAGAACACGCACTTG 59.207 52.381 0.00 0.00 0.00 3.16
3092 3554 3.563808 ACACGCACTTGCTCTTATTTTGA 59.436 39.130 0.00 0.00 39.32 2.69
3135 3597 2.809446 CTAGATGGACGAATGAACGCA 58.191 47.619 0.00 0.00 36.70 5.24
3149 3611 6.472163 CGAATGAACGCAAATTTTATAGCCTT 59.528 34.615 0.00 0.00 0.00 4.35
3195 3657 4.134563 GTGCTCCTTTAACTGGAAACTCA 58.865 43.478 0.00 0.00 32.61 3.41
3196 3658 4.578928 GTGCTCCTTTAACTGGAAACTCAA 59.421 41.667 0.00 0.00 32.61 3.02
3198 3660 5.833131 TGCTCCTTTAACTGGAAACTCAATT 59.167 36.000 0.00 0.00 32.61 2.32
3200 3662 6.084326 TCCTTTAACTGGAAACTCAATTGC 57.916 37.500 0.00 0.00 0.00 3.56
3201 3663 5.833131 TCCTTTAACTGGAAACTCAATTGCT 59.167 36.000 0.00 0.00 0.00 3.91
3202 3664 7.001674 TCCTTTAACTGGAAACTCAATTGCTA 58.998 34.615 0.00 0.00 0.00 3.49
3210 3672 7.038941 ACTGGAAACTCAATTGCTACTACTACT 60.039 37.037 0.00 0.00 0.00 2.57
3226 3688 6.181190 ACTACTACTACAGATGAGCTTGTCA 58.819 40.000 0.00 0.00 40.38 3.58
3228 3690 4.767409 ACTACTACAGATGAGCTTGTCACA 59.233 41.667 0.00 0.00 38.28 3.58
3231 3693 4.767409 ACTACAGATGAGCTTGTCACAGTA 59.233 41.667 0.00 0.00 38.28 2.74
3235 3697 3.829026 AGATGAGCTTGTCACAGTAGACA 59.171 43.478 0.00 0.00 46.12 3.41
3266 3728 1.905215 AGTAGCTGAAGCAGTCATGGT 59.095 47.619 4.90 0.00 45.16 3.55
3283 3745 0.951558 GGTCAGTGCCGACAACAAAT 59.048 50.000 0.00 0.00 37.66 2.32
3291 3753 0.953471 CCGACAACAAATCCGCTCCA 60.953 55.000 0.00 0.00 0.00 3.86
3344 3806 2.548480 GACAAGGCTACAAACAGGTGAC 59.452 50.000 0.00 0.00 0.00 3.67
3345 3807 1.880027 CAAGGCTACAAACAGGTGACC 59.120 52.381 0.00 0.00 0.00 4.02
3346 3808 1.136828 AGGCTACAAACAGGTGACCA 58.863 50.000 3.63 0.00 0.00 4.02
3348 3810 1.202770 GGCTACAAACAGGTGACCACT 60.203 52.381 3.63 0.00 0.00 4.00
3350 3812 2.484770 GCTACAAACAGGTGACCACTGA 60.485 50.000 3.63 0.00 39.24 3.41
3351 3813 2.799126 ACAAACAGGTGACCACTGAA 57.201 45.000 3.63 0.00 39.24 3.02
3352 3814 3.080300 ACAAACAGGTGACCACTGAAA 57.920 42.857 3.63 0.00 39.24 2.69
3363 3825 3.153919 GACCACTGAAACCCAAGCAATA 58.846 45.455 0.00 0.00 0.00 1.90
3367 3829 2.890945 ACTGAAACCCAAGCAATACCAC 59.109 45.455 0.00 0.00 0.00 4.16
3374 3836 1.155889 CAAGCAATACCACGCTGTGA 58.844 50.000 9.75 0.00 38.82 3.58
3384 3846 3.417101 ACCACGCTGTGAAATATTCCAA 58.583 40.909 9.75 0.00 35.23 3.53
3386 3848 4.279671 ACCACGCTGTGAAATATTCCAAAA 59.720 37.500 9.75 0.00 35.23 2.44
3389 3851 6.368516 CCACGCTGTGAAATATTCCAAAATTT 59.631 34.615 9.75 0.00 35.23 1.82
3390 3852 7.228840 CACGCTGTGAAATATTCCAAAATTTG 58.771 34.615 0.00 0.00 35.23 2.32
3391 3853 7.116090 CACGCTGTGAAATATTCCAAAATTTGA 59.884 33.333 7.37 0.00 35.23 2.69
3404 3866 9.835389 ATTCCAAAATTTGATTTCTGAACAGAA 57.165 25.926 12.40 12.40 44.94 3.02
3422 3893 4.274950 ACAGAAACCACTGAAACAATACCG 59.725 41.667 0.00 0.00 40.63 4.02
3569 4040 3.043465 TCTGATGATGAAGAGAGGCCT 57.957 47.619 3.86 3.86 0.00 5.19
3697 4168 3.393278 ACCAAGCCCTTTTCACTAGTACA 59.607 43.478 0.00 0.00 0.00 2.90
3698 4169 4.141344 ACCAAGCCCTTTTCACTAGTACAA 60.141 41.667 0.00 0.00 0.00 2.41
3699 4170 4.825085 CCAAGCCCTTTTCACTAGTACAAA 59.175 41.667 0.00 0.00 0.00 2.83
3700 4171 5.476945 CCAAGCCCTTTTCACTAGTACAAAT 59.523 40.000 0.00 0.00 0.00 2.32
3727 4198 6.594159 GCACGGGATAGCAATATACAGTAATT 59.406 38.462 0.00 0.00 0.00 1.40
3728 4199 7.413000 GCACGGGATAGCAATATACAGTAATTG 60.413 40.741 0.00 9.44 36.40 2.32
3729 4200 7.602644 CACGGGATAGCAATATACAGTAATTGT 59.397 37.037 12.92 0.00 43.96 2.71
3730 4201 7.602644 ACGGGATAGCAATATACAGTAATTGTG 59.397 37.037 12.92 0.00 41.10 3.33
3731 4202 7.602644 CGGGATAGCAATATACAGTAATTGTGT 59.397 37.037 12.92 1.41 41.10 3.72
3732 4203 8.936864 GGGATAGCAATATACAGTAATTGTGTC 58.063 37.037 12.92 9.90 41.10 3.67
3733 4204 9.712305 GGATAGCAATATACAGTAATTGTGTCT 57.288 33.333 12.92 7.58 41.10 3.41
3737 4208 9.618890 AGCAATATACAGTAATTGTGTCTGAAT 57.381 29.630 12.92 0.00 41.10 2.57
3738 4209 9.655769 GCAATATACAGTAATTGTGTCTGAATG 57.344 33.333 12.92 0.00 41.10 2.67
3742 4213 8.709386 ATACAGTAATTGTGTCTGAATGTCTC 57.291 34.615 0.00 0.00 41.10 3.36
3743 4214 6.524734 ACAGTAATTGTGTCTGAATGTCTCA 58.475 36.000 0.00 0.00 38.99 3.27
3744 4215 6.648310 ACAGTAATTGTGTCTGAATGTCTCAG 59.352 38.462 0.00 0.00 44.99 3.35
3745 4216 8.220375 ACAGTAATTGTGTCTGAATGTCTCAGG 61.220 40.741 2.11 0.00 44.35 3.86
3751 4222 2.021355 CTGAATGTCTCAGGTCAGGC 57.979 55.000 0.00 0.00 46.89 4.85
3752 4223 0.247460 TGAATGTCTCAGGTCAGGCG 59.753 55.000 0.00 0.00 0.00 5.52
3753 4224 1.078848 AATGTCTCAGGTCAGGCGC 60.079 57.895 0.00 0.00 0.00 6.53
3754 4225 2.527951 AATGTCTCAGGTCAGGCGCC 62.528 60.000 21.89 21.89 0.00 6.53
3755 4226 4.803426 GTCTCAGGTCAGGCGCCG 62.803 72.222 23.20 16.49 0.00 6.46
3768 4239 3.484547 CGCCGCCGTTCCTTGTAC 61.485 66.667 0.00 0.00 0.00 2.90
3774 4245 1.338011 CGCCGTTCCTTGTACCCTTTA 60.338 52.381 0.00 0.00 0.00 1.85
4361 4837 2.775032 GAAGGCAGGCGTCGGTGTTA 62.775 60.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 8.431593 GCACAACGATATTTTGATTTTTGCTAA 58.568 29.630 0.00 0.00 0.00 3.09
532 535 4.776322 TCCAACCTCATGCCGCCG 62.776 66.667 0.00 0.00 0.00 6.46
599 602 0.911769 TGAACGCAATCCCCTCATCT 59.088 50.000 0.00 0.00 0.00 2.90
678 681 1.205657 CGTATCACGCGCTTTATGGT 58.794 50.000 5.73 0.00 33.65 3.55
710 713 5.154932 GGACGTTGGATCGATCTGTATTAG 58.845 45.833 23.96 11.85 34.70 1.73
715 718 0.460311 GGGACGTTGGATCGATCTGT 59.540 55.000 23.96 16.74 34.70 3.41
800 803 3.119709 GAGAGAGCACGGCGGAGAG 62.120 68.421 13.24 0.00 0.00 3.20
801 804 3.134792 GAGAGAGCACGGCGGAGA 61.135 66.667 13.24 0.00 0.00 3.71
802 805 2.290122 ATTGAGAGAGCACGGCGGAG 62.290 60.000 13.24 4.25 0.00 4.63
803 806 2.284798 GATTGAGAGAGCACGGCGGA 62.285 60.000 13.24 0.00 0.00 5.54
804 807 1.880340 GATTGAGAGAGCACGGCGG 60.880 63.158 13.24 0.66 0.00 6.13
805 808 1.140589 AGATTGAGAGAGCACGGCG 59.859 57.895 4.80 4.80 0.00 6.46
806 809 0.174389 TCAGATTGAGAGAGCACGGC 59.826 55.000 0.00 0.00 0.00 5.68
807 810 2.662006 TTCAGATTGAGAGAGCACGG 57.338 50.000 0.00 0.00 0.00 4.94
808 811 3.122297 GGATTCAGATTGAGAGAGCACG 58.878 50.000 0.00 0.00 0.00 5.34
809 812 3.134442 AGGGATTCAGATTGAGAGAGCAC 59.866 47.826 0.00 0.00 0.00 4.40
810 813 3.382278 AGGGATTCAGATTGAGAGAGCA 58.618 45.455 0.00 0.00 0.00 4.26
811 814 4.141756 TGAAGGGATTCAGATTGAGAGAGC 60.142 45.833 0.00 0.00 0.00 4.09
812 815 5.611128 TGAAGGGATTCAGATTGAGAGAG 57.389 43.478 0.00 0.00 0.00 3.20
813 816 6.572182 ATTGAAGGGATTCAGATTGAGAGA 57.428 37.500 0.00 0.00 31.87 3.10
814 817 7.201803 GGAAATTGAAGGGATTCAGATTGAGAG 60.202 40.741 0.00 0.00 31.87 3.20
815 818 6.604795 GGAAATTGAAGGGATTCAGATTGAGA 59.395 38.462 0.00 0.00 31.87 3.27
816 819 6.183360 GGGAAATTGAAGGGATTCAGATTGAG 60.183 42.308 0.00 0.00 31.87 3.02
817 820 5.658190 GGGAAATTGAAGGGATTCAGATTGA 59.342 40.000 0.00 0.00 31.87 2.57
818 821 5.659971 AGGGAAATTGAAGGGATTCAGATTG 59.340 40.000 0.00 0.00 31.87 2.67
819 822 5.846868 AGGGAAATTGAAGGGATTCAGATT 58.153 37.500 0.00 0.00 31.87 2.40
820 823 5.478503 AGGGAAATTGAAGGGATTCAGAT 57.521 39.130 0.00 0.00 31.87 2.90
821 824 4.953781 AGGGAAATTGAAGGGATTCAGA 57.046 40.909 0.00 0.00 31.87 3.27
822 825 6.364568 AAAAGGGAAATTGAAGGGATTCAG 57.635 37.500 0.00 0.00 31.87 3.02
823 826 6.762077 AAAAAGGGAAATTGAAGGGATTCA 57.238 33.333 0.00 0.00 0.00 2.57
844 847 1.405105 GTCTGTGAGGCTGTGCAAAAA 59.595 47.619 0.00 0.00 0.00 1.94
845 848 1.024271 GTCTGTGAGGCTGTGCAAAA 58.976 50.000 0.00 0.00 0.00 2.44
846 849 0.107263 TGTCTGTGAGGCTGTGCAAA 60.107 50.000 0.00 0.00 0.00 3.68
847 850 0.533531 CTGTCTGTGAGGCTGTGCAA 60.534 55.000 0.00 0.00 0.00 4.08
848 851 1.070275 CTGTCTGTGAGGCTGTGCA 59.930 57.895 0.00 0.00 0.00 4.57
849 852 1.670406 CCTGTCTGTGAGGCTGTGC 60.670 63.158 0.00 0.00 0.00 4.57
850 853 1.004080 CCCTGTCTGTGAGGCTGTG 60.004 63.158 0.00 0.00 0.00 3.66
851 854 2.219875 CCCCTGTCTGTGAGGCTGT 61.220 63.158 0.00 0.00 0.00 4.40
852 855 2.177594 GACCCCTGTCTGTGAGGCTG 62.178 65.000 0.00 0.00 38.53 4.85
853 856 1.915769 GACCCCTGTCTGTGAGGCT 60.916 63.158 0.00 0.00 38.53 4.58
854 857 2.217038 TGACCCCTGTCTGTGAGGC 61.217 63.158 0.00 0.00 42.28 4.70
855 858 1.674057 GTGACCCCTGTCTGTGAGG 59.326 63.158 0.00 0.00 42.28 3.86
856 859 1.290324 CGTGACCCCTGTCTGTGAG 59.710 63.158 0.00 0.00 42.28 3.51
857 860 2.867855 GCGTGACCCCTGTCTGTGA 61.868 63.158 0.00 0.00 42.28 3.58
858 861 2.357517 GCGTGACCCCTGTCTGTG 60.358 66.667 0.00 0.00 42.28 3.66
859 862 3.626924 GGCGTGACCCCTGTCTGT 61.627 66.667 0.00 0.00 42.28 3.41
868 871 1.966451 CTTCTGTTGGGGCGTGACC 60.966 63.158 0.00 0.00 37.93 4.02
869 872 0.534203 TTCTTCTGTTGGGGCGTGAC 60.534 55.000 0.00 0.00 0.00 3.67
870 873 0.400213 ATTCTTCTGTTGGGGCGTGA 59.600 50.000 0.00 0.00 0.00 4.35
871 874 0.523072 CATTCTTCTGTTGGGGCGTG 59.477 55.000 0.00 0.00 0.00 5.34
872 875 1.244019 GCATTCTTCTGTTGGGGCGT 61.244 55.000 0.00 0.00 0.00 5.68
873 876 0.962356 AGCATTCTTCTGTTGGGGCG 60.962 55.000 0.00 0.00 0.00 6.13
874 877 1.260544 AAGCATTCTTCTGTTGGGGC 58.739 50.000 0.00 0.00 0.00 5.80
875 878 3.181483 GCATAAGCATTCTTCTGTTGGGG 60.181 47.826 0.00 0.00 41.58 4.96
876 879 3.488047 CGCATAAGCATTCTTCTGTTGGG 60.488 47.826 0.00 0.00 42.27 4.12
877 880 3.688272 CGCATAAGCATTCTTCTGTTGG 58.312 45.455 0.00 0.00 42.27 3.77
878 881 3.103738 GCGCATAAGCATTCTTCTGTTG 58.896 45.455 0.30 0.00 42.27 3.33
879 882 2.749076 TGCGCATAAGCATTCTTCTGTT 59.251 40.909 5.66 0.00 42.92 3.16
880 883 2.358957 TGCGCATAAGCATTCTTCTGT 58.641 42.857 5.66 0.00 42.92 3.41
889 892 1.573932 GTGTGTGTGCGCATAAGCA 59.426 52.632 15.91 10.71 45.96 3.91
890 893 1.154225 GGTGTGTGTGCGCATAAGC 60.154 57.895 15.91 7.87 37.46 3.09
891 894 1.132436 CGGTGTGTGTGCGCATAAG 59.868 57.895 15.91 0.00 37.46 1.73
892 895 1.561717 GACGGTGTGTGTGCGCATAA 61.562 55.000 15.91 1.50 37.46 1.90
893 896 2.024868 GACGGTGTGTGTGCGCATA 61.025 57.895 15.91 8.59 37.46 3.14
894 897 3.345808 GACGGTGTGTGTGCGCAT 61.346 61.111 15.91 0.00 37.46 4.73
910 913 0.526954 GAAAACTCTATCCGCCGCGA 60.527 55.000 15.93 0.32 0.00 5.87
1105 1116 1.552792 AGAAAAGGAGCGAAGAGGGAG 59.447 52.381 0.00 0.00 0.00 4.30
1115 1126 4.130118 TGACAACTGAGAAGAAAAGGAGC 58.870 43.478 0.00 0.00 0.00 4.70
1119 1130 3.605692 GCGCTGACAACTGAGAAGAAAAG 60.606 47.826 0.00 0.00 0.00 2.27
1121 1132 1.867233 GCGCTGACAACTGAGAAGAAA 59.133 47.619 0.00 0.00 0.00 2.52
1122 1133 1.502231 GCGCTGACAACTGAGAAGAA 58.498 50.000 0.00 0.00 0.00 2.52
1126 1137 1.661509 CACGCGCTGACAACTGAGA 60.662 57.895 5.73 0.00 0.00 3.27
1127 1138 1.951130 ACACGCGCTGACAACTGAG 60.951 57.895 5.73 0.00 0.00 3.35
1128 1139 2.106131 ACACGCGCTGACAACTGA 59.894 55.556 5.73 0.00 0.00 3.41
1129 1140 2.246397 CACACGCGCTGACAACTG 59.754 61.111 5.73 0.00 0.00 3.16
1130 1141 2.202878 ACACACGCGCTGACAACT 60.203 55.556 5.73 0.00 0.00 3.16
1131 1142 2.053116 CACACACGCGCTGACAAC 60.053 61.111 5.73 0.00 0.00 3.32
1133 1144 3.261216 CACACACACGCGCTGACA 61.261 61.111 5.73 0.00 0.00 3.58
1134 1145 2.959599 TCACACACACGCGCTGAC 60.960 61.111 5.73 0.00 0.00 3.51
1136 1147 4.339809 CGTCACACACACGCGCTG 62.340 66.667 5.73 6.58 0.00 5.18
1155 1176 3.437795 ACTACGACAGACCGCCGG 61.438 66.667 0.00 0.00 0.00 6.13
1344 1365 1.619654 TTTTACCAGTCGAGGACGGA 58.380 50.000 11.61 0.00 37.67 4.69
1371 1392 2.588034 GTACGCATTCGGGGAGGC 60.588 66.667 0.00 0.00 40.69 4.70
1414 1459 1.746220 CAAGGTGTTGGGTGAAACGAA 59.254 47.619 0.00 0.00 38.12 3.85
1425 1470 1.361271 CAGTGCAGGCAAGGTGTTG 59.639 57.895 0.00 0.00 36.67 3.33
1447 1492 0.038526 ACTCGTTTCAGGTACCTGCG 60.039 55.000 33.39 29.08 43.31 5.18
1609 1654 2.195922 CAACTGAAACCAAGCACAAGC 58.804 47.619 0.00 0.00 42.56 4.01
1688 1733 4.209911 GCAGCAACAGAAGGAAATTCAAAC 59.790 41.667 0.00 0.00 40.67 2.93
1746 1793 9.888878 CAATATCATGGACAATTGAGAATACAC 57.111 33.333 13.59 0.00 32.29 2.90
1773 1820 4.405116 TTTCTGCACATTTTTCTGCCTT 57.595 36.364 0.00 0.00 0.00 4.35
1814 1862 5.183713 TGAATGCCCTCACTTTTAGAACATG 59.816 40.000 0.00 0.00 0.00 3.21
1936 1984 3.440522 GCAAACTTATGTCAGAAGTCCCC 59.559 47.826 13.05 1.70 36.10 4.81
1993 2041 5.939883 TGAGTTCAAACAATGGTCAGATAGG 59.060 40.000 0.00 0.00 0.00 2.57
2039 2105 3.238108 ACTCCAACTGCGAGTAGAATG 57.762 47.619 0.00 0.00 38.82 2.67
2040 2106 4.674623 CGTTACTCCAACTGCGAGTAGAAT 60.675 45.833 0.00 0.00 42.30 2.40
2042 2108 2.161012 CGTTACTCCAACTGCGAGTAGA 59.839 50.000 0.00 0.00 42.30 2.59
2043 2109 2.516923 CGTTACTCCAACTGCGAGTAG 58.483 52.381 0.00 0.00 42.30 2.57
2044 2110 1.401931 GCGTTACTCCAACTGCGAGTA 60.402 52.381 0.00 0.00 40.93 2.59
2052 2118 2.000447 CTAAGCCTGCGTTACTCCAAC 59.000 52.381 0.00 0.00 0.00 3.77
2066 2133 5.429130 ACTAAGAATACAAGCCACTAAGCC 58.571 41.667 0.00 0.00 0.00 4.35
2093 2161 6.612306 CCCATAACTTTCTACAAGAACTTGC 58.388 40.000 13.50 0.00 44.03 4.01
2104 2172 9.185680 GAAATTTAAGAGGCCCATAACTTTCTA 57.814 33.333 18.42 0.00 31.18 2.10
2110 2178 5.656859 ACCAGAAATTTAAGAGGCCCATAAC 59.343 40.000 0.00 0.00 0.00 1.89
2128 2197 8.501904 TCCTCCATTTCATCATTTATACCAGAA 58.498 33.333 0.00 0.00 0.00 3.02
2129 2198 8.044574 TCCTCCATTTCATCATTTATACCAGA 57.955 34.615 0.00 0.00 0.00 3.86
2131 2200 9.659135 ATTTCCTCCATTTCATCATTTATACCA 57.341 29.630 0.00 0.00 0.00 3.25
2141 2210 7.654923 GCCAAATCTAATTTCCTCCATTTCATC 59.345 37.037 0.00 0.00 0.00 2.92
2184 2253 5.163385 TGTTCTAGGAGGAAAAACAGAACGA 60.163 40.000 7.53 0.00 42.94 3.85
2186 2255 7.228706 TGAATGTTCTAGGAGGAAAAACAGAAC 59.771 37.037 5.54 5.54 41.30 3.01
2192 2261 8.533569 AAACTTGAATGTTCTAGGAGGAAAAA 57.466 30.769 8.61 0.00 34.93 1.94
2197 2266 8.454106 CAACATAAACTTGAATGTTCTAGGAGG 58.546 37.037 8.61 0.09 42.83 4.30
2210 2279 4.098914 AGCTGGGACAACATAAACTTGA 57.901 40.909 0.00 0.00 38.70 3.02
2251 2320 5.931294 TGGAGTGTATTGTGAAGGTAACAA 58.069 37.500 0.00 0.00 41.50 2.83
2268 2337 1.138859 TCCACACACAAGTCTGGAGTG 59.861 52.381 3.45 3.45 37.83 3.51
2269 2338 1.496060 TCCACACACAAGTCTGGAGT 58.504 50.000 0.00 0.00 37.83 3.85
2335 2404 4.724279 ACAGGGTAACATTTCTCACCTT 57.276 40.909 0.00 0.00 39.74 3.50
2347 2416 5.300792 TCACATTCAAAGGAAACAGGGTAAC 59.699 40.000 0.00 0.00 36.43 2.50
2385 2454 8.434589 TCAATTCCTTTGGTGGATAGAAATTT 57.565 30.769 0.00 0.00 35.83 1.82
2405 2475 5.701290 GGATGGCTACGTATTAAGCTCAATT 59.299 40.000 7.90 0.00 38.80 2.32
2423 2493 2.290367 GGCTTGTTTTTGTTTGGATGGC 59.710 45.455 0.00 0.00 0.00 4.40
2430 2500 7.609918 AGATTTTTACAGGGCTTGTTTTTGTTT 59.390 29.630 7.82 0.00 41.29 2.83
2431 2501 7.109501 AGATTTTTACAGGGCTTGTTTTTGTT 58.890 30.769 7.82 0.00 41.29 2.83
2432 2502 6.649155 AGATTTTTACAGGGCTTGTTTTTGT 58.351 32.000 7.82 0.00 41.29 2.83
2433 2503 6.202762 GGAGATTTTTACAGGGCTTGTTTTTG 59.797 38.462 7.82 0.00 41.29 2.44
2434 2504 6.288294 GGAGATTTTTACAGGGCTTGTTTTT 58.712 36.000 7.82 0.00 41.29 1.94
2482 2587 6.316140 GTGCATGACTTCTATGTATCAAACCA 59.684 38.462 0.00 0.00 0.00 3.67
2483 2588 6.540189 AGTGCATGACTTCTATGTATCAAACC 59.460 38.462 0.00 0.00 0.00 3.27
2484 2589 7.545362 AGTGCATGACTTCTATGTATCAAAC 57.455 36.000 0.00 0.00 0.00 2.93
2485 2590 8.257306 TGTAGTGCATGACTTCTATGTATCAAA 58.743 33.333 0.00 0.00 35.96 2.69
2486 2591 7.781056 TGTAGTGCATGACTTCTATGTATCAA 58.219 34.615 0.00 0.00 35.96 2.57
2487 2592 7.346751 TGTAGTGCATGACTTCTATGTATCA 57.653 36.000 0.00 0.00 35.96 2.15
2502 2607 4.949238 TGCAGGAATAAACATGTAGTGCAT 59.051 37.500 0.00 0.00 38.60 3.96
2503 2608 4.331108 TGCAGGAATAAACATGTAGTGCA 58.669 39.130 0.00 4.29 36.11 4.57
2504 2609 4.963276 TGCAGGAATAAACATGTAGTGC 57.037 40.909 0.00 1.62 0.00 4.40
2505 2610 5.124457 AGCTTGCAGGAATAAACATGTAGTG 59.876 40.000 0.00 0.00 0.00 2.74
2506 2611 5.256474 AGCTTGCAGGAATAAACATGTAGT 58.744 37.500 0.00 0.00 0.00 2.73
2507 2612 5.824904 AGCTTGCAGGAATAAACATGTAG 57.175 39.130 0.00 0.00 0.00 2.74
2561 2667 3.816523 TCCGGGTTTCATTTTGACACTAC 59.183 43.478 0.00 0.00 28.56 2.73
2618 2737 4.426704 GGAGGTGGCCTAGGAATTATAGA 58.573 47.826 14.75 0.00 31.76 1.98
2621 2740 2.349445 GGGAGGTGGCCTAGGAATTAT 58.651 52.381 14.75 0.00 31.76 1.28
2629 2748 3.835134 CCTTTGGGAGGTGGCCTA 58.165 61.111 3.32 0.00 40.95 3.93
2817 2936 7.255730 GGAGATGAAATGTAATGCATAAGCCTT 60.256 37.037 0.00 0.00 41.13 4.35
2908 3355 0.033781 TTGATGCCTTGGCACTTTGC 59.966 50.000 17.22 5.12 44.08 3.68
2914 3361 5.126222 TCGTTAAATATTTGATGCCTTGGCA 59.874 36.000 17.19 17.19 0.00 4.92
2915 3362 5.458779 GTCGTTAAATATTTGATGCCTTGGC 59.541 40.000 11.05 4.43 0.00 4.52
2917 3364 9.950680 ATAAGTCGTTAAATATTTGATGCCTTG 57.049 29.630 15.02 0.00 0.00 3.61
2949 3403 7.618502 ACAGTATTACATATTTTCAACGCCA 57.381 32.000 0.00 0.00 0.00 5.69
2971 3428 0.250252 TGGCAAGAGCGACATCAACA 60.250 50.000 0.00 0.00 43.41 3.33
2980 3437 0.514691 GTTCAAGTCTGGCAAGAGCG 59.485 55.000 0.00 0.00 43.41 5.03
3003 3460 2.107204 ACCCAGGATGATAAGCACCATC 59.893 50.000 0.00 0.00 39.69 3.51
3038 3498 6.434340 GGACTACATTTTCAGGGAGAATGTTT 59.566 38.462 16.88 7.80 42.15 2.83
3047 3509 5.677319 TCTACAGGACTACATTTTCAGGG 57.323 43.478 0.00 0.00 0.00 4.45
3074 3536 7.596248 TCAAGAATTCAAAATAAGAGCAAGTGC 59.404 33.333 8.44 0.00 42.49 4.40
3080 3542 9.080915 GTTCCATCAAGAATTCAAAATAAGAGC 57.919 33.333 8.44 0.00 0.00 4.09
3092 3554 5.537674 AGCAGAAACTGTTCCATCAAGAATT 59.462 36.000 0.00 0.00 33.92 2.17
3108 3570 4.433615 TCATTCGTCCATCTAGCAGAAAC 58.566 43.478 0.00 0.00 0.00 2.78
3118 3580 2.892373 TTTGCGTTCATTCGTCCATC 57.108 45.000 0.00 0.00 0.00 3.51
3135 3597 8.650143 TGTCAAGAAGGAAGGCTATAAAATTT 57.350 30.769 0.00 0.00 0.00 1.82
3149 3611 4.020218 CCTGAATGTACCTGTCAAGAAGGA 60.020 45.833 0.00 0.00 38.27 3.36
3195 3657 7.504238 AGCTCATCTGTAGTAGTAGTAGCAATT 59.496 37.037 0.00 0.00 0.00 2.32
3196 3658 7.001674 AGCTCATCTGTAGTAGTAGTAGCAAT 58.998 38.462 0.00 0.00 0.00 3.56
3198 3660 5.931294 AGCTCATCTGTAGTAGTAGTAGCA 58.069 41.667 0.00 0.00 0.00 3.49
3200 3662 7.496263 TGACAAGCTCATCTGTAGTAGTAGTAG 59.504 40.741 0.00 0.00 0.00 2.57
3201 3663 7.280428 GTGACAAGCTCATCTGTAGTAGTAGTA 59.720 40.741 0.00 0.00 0.00 1.82
3202 3664 6.094325 GTGACAAGCTCATCTGTAGTAGTAGT 59.906 42.308 0.00 0.00 0.00 2.73
3210 3672 5.010282 TCTACTGTGACAAGCTCATCTGTA 58.990 41.667 0.00 0.00 0.00 2.74
3226 3688 2.623418 TCTGATGGGGTGTCTACTGT 57.377 50.000 0.00 0.00 0.00 3.55
3228 3690 3.191888 ACTTCTGATGGGGTGTCTACT 57.808 47.619 0.00 0.00 0.00 2.57
3231 3693 1.834263 GCTACTTCTGATGGGGTGTCT 59.166 52.381 0.00 0.00 0.00 3.41
3235 3697 2.254152 TCAGCTACTTCTGATGGGGT 57.746 50.000 0.00 0.00 38.11 4.95
3266 3728 1.234821 GGATTTGTTGTCGGCACTGA 58.765 50.000 0.00 0.00 0.00 3.41
3344 3806 2.231235 GGTATTGCTTGGGTTTCAGTGG 59.769 50.000 0.00 0.00 0.00 4.00
3345 3807 2.890311 TGGTATTGCTTGGGTTTCAGTG 59.110 45.455 0.00 0.00 0.00 3.66
3346 3808 2.890945 GTGGTATTGCTTGGGTTTCAGT 59.109 45.455 0.00 0.00 0.00 3.41
3348 3810 1.883275 CGTGGTATTGCTTGGGTTTCA 59.117 47.619 0.00 0.00 0.00 2.69
3350 3812 0.601057 GCGTGGTATTGCTTGGGTTT 59.399 50.000 0.00 0.00 0.00 3.27
3351 3813 0.251165 AGCGTGGTATTGCTTGGGTT 60.251 50.000 0.00 0.00 38.57 4.11
3352 3814 0.960364 CAGCGTGGTATTGCTTGGGT 60.960 55.000 0.00 0.00 40.03 4.51
3363 3825 3.066291 TGGAATATTTCACAGCGTGGT 57.934 42.857 8.46 0.00 33.87 4.16
3367 3829 7.579589 TCAAATTTTGGAATATTTCACAGCG 57.420 32.000 9.18 0.00 0.00 5.18
3384 3846 8.260114 AGTGGTTTCTGTTCAGAAATCAAATTT 58.740 29.630 30.18 18.75 46.46 1.82
3386 3848 7.068593 TCAGTGGTTTCTGTTCAGAAATCAAAT 59.931 33.333 30.18 22.52 46.46 2.32
3389 3851 5.436175 TCAGTGGTTTCTGTTCAGAAATCA 58.564 37.500 26.98 26.98 43.95 2.57
3390 3852 6.377327 TTCAGTGGTTTCTGTTCAGAAATC 57.623 37.500 24.31 23.91 39.58 2.17
3391 3853 6.152661 TGTTTCAGTGGTTTCTGTTCAGAAAT 59.847 34.615 24.31 10.84 39.58 2.17
3394 3856 4.584874 TGTTTCAGTGGTTTCTGTTCAGA 58.415 39.130 0.00 0.00 36.85 3.27
3397 3859 6.206498 GGTATTGTTTCAGTGGTTTCTGTTC 58.794 40.000 0.00 0.00 36.85 3.18
3399 3861 4.274950 CGGTATTGTTTCAGTGGTTTCTGT 59.725 41.667 0.00 0.00 36.85 3.41
3400 3862 4.274950 ACGGTATTGTTTCAGTGGTTTCTG 59.725 41.667 0.00 0.00 36.85 3.02
3401 3863 4.457466 ACGGTATTGTTTCAGTGGTTTCT 58.543 39.130 0.00 0.00 0.00 2.52
3402 3864 4.823790 ACGGTATTGTTTCAGTGGTTTC 57.176 40.909 0.00 0.00 0.00 2.78
3403 3865 6.696441 TTTACGGTATTGTTTCAGTGGTTT 57.304 33.333 0.00 0.00 0.00 3.27
3404 3866 6.072342 GGATTTACGGTATTGTTTCAGTGGTT 60.072 38.462 0.00 0.00 0.00 3.67
3405 3867 5.413523 GGATTTACGGTATTGTTTCAGTGGT 59.586 40.000 0.00 0.00 0.00 4.16
3406 3868 5.163693 GGGATTTACGGTATTGTTTCAGTGG 60.164 44.000 0.00 0.00 0.00 4.00
3407 3869 5.413213 TGGGATTTACGGTATTGTTTCAGTG 59.587 40.000 0.00 0.00 0.00 3.66
3408 3870 5.413523 GTGGGATTTACGGTATTGTTTCAGT 59.586 40.000 0.00 0.00 0.00 3.41
3409 3871 5.413213 TGTGGGATTTACGGTATTGTTTCAG 59.587 40.000 0.00 0.00 0.00 3.02
3410 3872 5.181622 GTGTGGGATTTACGGTATTGTTTCA 59.818 40.000 0.00 0.00 0.00 2.69
3422 3893 3.126343 CGCAAACCTAGTGTGGGATTTAC 59.874 47.826 0.00 0.00 36.04 2.01
3675 4146 3.393278 TGTACTAGTGAAAAGGGCTTGGT 59.607 43.478 5.39 0.00 0.00 3.67
3697 4168 6.707290 TGTATATTGCTATCCCGTGCTATTT 58.293 36.000 0.00 0.00 0.00 1.40
3698 4169 6.070767 ACTGTATATTGCTATCCCGTGCTATT 60.071 38.462 0.00 0.00 0.00 1.73
3699 4170 5.422331 ACTGTATATTGCTATCCCGTGCTAT 59.578 40.000 0.00 0.00 0.00 2.97
3700 4171 4.770531 ACTGTATATTGCTATCCCGTGCTA 59.229 41.667 0.00 0.00 0.00 3.49
3733 4204 0.247460 CGCCTGACCTGAGACATTCA 59.753 55.000 0.00 0.00 0.00 2.57
3734 4205 1.086634 GCGCCTGACCTGAGACATTC 61.087 60.000 0.00 0.00 0.00 2.67
3735 4206 1.078848 GCGCCTGACCTGAGACATT 60.079 57.895 0.00 0.00 0.00 2.71
3736 4207 2.581354 GCGCCTGACCTGAGACAT 59.419 61.111 0.00 0.00 0.00 3.06
3737 4208 3.695606 GGCGCCTGACCTGAGACA 61.696 66.667 22.15 0.00 0.00 3.41
3738 4209 4.803426 CGGCGCCTGACCTGAGAC 62.803 72.222 26.68 0.00 0.00 3.36
3751 4222 3.484547 GTACAAGGAACGGCGGCG 61.485 66.667 31.06 31.06 0.00 6.46
3752 4223 3.122971 GGTACAAGGAACGGCGGC 61.123 66.667 13.24 0.00 0.00 6.53
3753 4224 2.435410 GGGTACAAGGAACGGCGG 60.435 66.667 13.24 0.00 0.00 6.13
3754 4225 0.604511 AAAGGGTACAAGGAACGGCG 60.605 55.000 4.80 4.80 0.00 6.46
3755 4226 2.477845 TAAAGGGTACAAGGAACGGC 57.522 50.000 0.00 0.00 0.00 5.68
3756 4227 3.946606 ACATAAAGGGTACAAGGAACGG 58.053 45.455 0.00 0.00 0.00 4.44
3757 4228 6.400568 TCTAACATAAAGGGTACAAGGAACG 58.599 40.000 0.00 0.00 0.00 3.95
3758 4229 7.336176 CCTTCTAACATAAAGGGTACAAGGAAC 59.664 40.741 0.00 0.00 38.72 3.62
3759 4230 7.399634 CCTTCTAACATAAAGGGTACAAGGAA 58.600 38.462 0.00 0.00 38.72 3.36
3760 4231 6.954232 CCTTCTAACATAAAGGGTACAAGGA 58.046 40.000 0.00 0.00 38.72 3.36
3774 4245 3.533907 TCCTCCTCTCTCCCTTCTAACAT 59.466 47.826 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.