Multiple sequence alignment - TraesCS4B01G365200

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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 TraesCS4B01G365200 chr4B 100.000 4547 0 0 1 4547 653215461 653220007 0.000000e+00 8397.0
1 TraesCS4B01G365200 chr4B 80.731 1313 194 32 1099 2389 82277294 82276019 0.000000e+00 968.0
2 TraesCS4B01G365200 chr4B 80.186 1292 212 32 1126 2399 653277710 653278975 0.000000e+00 928.0
3 TraesCS4B01G365200 chr4B 82.011 189 28 6 3430 3615 82257951 82257766 6.090000e-34 156.0
4 TraesCS4B01G365200 chr4B 83.007 153 22 1 273 425 653215695 653215843 7.930000e-28 135.0
5 TraesCS4B01G365200 chr4B 83.007 153 22 1 235 383 653215733 653215885 7.930000e-28 135.0
6 TraesCS4B01G365200 chr5A 89.118 3198 221 34 1394 4547 691311972 691315086 0.000000e+00 3860.0
7 TraesCS4B01G365200 chr5A 87.712 765 69 11 2 761 691293306 691294050 0.000000e+00 869.0
8 TraesCS4B01G365200 chr5A 80.778 848 143 13 1563 2402 691054503 691053668 0.000000e+00 645.0
9 TraesCS4B01G365200 chr5A 80.999 721 103 17 2441 3141 691053585 691052879 4.000000e-150 542.0
10 TraesCS4B01G365200 chr5A 88.254 315 31 6 1068 1379 691298961 691299272 5.560000e-99 372.0
11 TraesCS4B01G365200 chr5A 76.399 411 68 19 3256 3662 691052829 691052444 1.290000e-45 195.0
12 TraesCS4B01G365200 chr5A 86.014 143 20 0 286 428 691293543 691293685 2.190000e-33 154.0
13 TraesCS4B01G365200 chr5A 75.896 307 58 13 2542 2843 691445387 691445092 4.740000e-30 143.0
14 TraesCS4B01G365200 chrUn 91.321 1302 74 13 3280 4547 126854543 126855839 0.000000e+00 1742.0
15 TraesCS4B01G365200 chrUn 90.759 1028 68 6 1379 2402 126842618 126843622 0.000000e+00 1347.0
16 TraesCS4B01G365200 chrUn 93.860 798 43 5 2487 3283 126843679 126844471 0.000000e+00 1197.0
17 TraesCS4B01G365200 chrUn 90.000 760 51 10 2 759 126840431 126841167 0.000000e+00 959.0
18 TraesCS4B01G365200 chrUn 92.829 251 17 1 1130 1379 126841569 126841819 3.340000e-96 363.0
19 TraesCS4B01G365200 chrUn 88.312 77 4 2 753 824 126841198 126841274 2.250000e-13 87.9
20 TraesCS4B01G365200 chrUn 80.165 121 19 2 232 348 126840736 126840855 8.100000e-13 86.1
21 TraesCS4B01G365200 chrUn 97.297 37 1 0 1900 1936 388948117 388948153 3.800000e-06 63.9
22 TraesCS4B01G365200 chr4D 82.035 796 107 15 1099 1878 55277423 55276648 0.000000e+00 645.0
23 TraesCS4B01G365200 chr4D 86.214 486 51 8 2536 3013 55276627 55276150 3.140000e-141 512.0
24 TraesCS4B01G365200 chr4D 83.058 242 33 6 3433 3666 55275429 55275188 3.560000e-51 213.0
25 TraesCS4B01G365200 chr4A 82.692 520 79 8 1565 2080 541922277 541922789 6.940000e-123 451.0
26 TraesCS4B01G365200 chr4A 80.679 471 76 14 1031 1492 541921771 541922235 7.240000e-93 351.0
27 TraesCS4B01G365200 chr4A 81.522 184 27 6 3430 3611 541965172 541965350 1.320000e-30 145.0
28 TraesCS4B01G365200 chr6A 85.948 306 41 2 2560 2864 3543088 3543392 4.390000e-85 326.0
29 TraesCS4B01G365200 chr6A 82.105 380 66 2 2563 2941 595560435 595560057 1.580000e-84 324.0
30 TraesCS4B01G365200 chr6D 85.957 235 23 5 438 672 456003174 456003398 4.540000e-60 243.0
31 TraesCS4B01G365200 chr2B 77.778 324 65 5 1130 1448 683309965 683309644 4.640000e-45 193.0
32 TraesCS4B01G365200 chr2B 76.852 324 68 7 1130 1448 683487410 683487089 4.680000e-40 176.0
33 TraesCS4B01G365200 chr2A 76.803 319 65 7 1136 1448 710275594 710275279 2.180000e-38 171.0
34 TraesCS4B01G365200 chr2D 76.000 325 73 3 1134 1454 571662292 571661969 3.640000e-36 163.0
35 TraesCS4B01G365200 chr5D 100.000 28 0 0 4186 4213 36757573 36757600 8.000000e-03 52.8
36 TraesCS4B01G365200 chr5B 100.000 28 0 0 4186 4213 514801722 514801695 8.000000e-03 52.8


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 TraesCS4B01G365200 chr4B 653215461 653220007 4546 False 8397.000000 8397 100.000000 1 4547 1 chr4B.!!$F1 4546
1 TraesCS4B01G365200 chr4B 82276019 82277294 1275 True 968.000000 968 80.731000 1099 2389 1 chr4B.!!$R2 1290
2 TraesCS4B01G365200 chr4B 653277710 653278975 1265 False 928.000000 928 80.186000 1126 2399 1 chr4B.!!$F2 1273
3 TraesCS4B01G365200 chr5A 691311972 691315086 3114 False 3860.000000 3860 89.118000 1394 4547 1 chr5A.!!$F2 3153
4 TraesCS4B01G365200 chr5A 691293306 691294050 744 False 511.500000 869 86.863000 2 761 2 chr5A.!!$F3 759
5 TraesCS4B01G365200 chr5A 691052444 691054503 2059 True 460.666667 645 79.392000 1563 3662 3 chr5A.!!$R2 2099
6 TraesCS4B01G365200 chrUn 126854543 126855839 1296 False 1742.000000 1742 91.321000 3280 4547 1 chrUn.!!$F1 1267
7 TraesCS4B01G365200 chrUn 126840431 126844471 4040 False 673.333333 1347 89.320833 2 3283 6 chrUn.!!$F3 3281
8 TraesCS4B01G365200 chr4D 55275188 55277423 2235 True 456.666667 645 83.769000 1099 3666 3 chr4D.!!$R1 2567
9 TraesCS4B01G365200 chr4A 541921771 541922789 1018 False 401.000000 451 81.685500 1031 2080 2 chr4A.!!$F2 1049

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
823 870 0.035915 TTGGCGTCGATTTCCATGGA 60.036 50.0 11.44 11.44 0.0 3.41 F
2408 3323 0.038310 GCTTTGCTTACACCCCCTCT 59.962 55.0 0.00 0.00 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 3554 0.954452 GGGCTCACCACAGAAACAAG 59.046 55.000 0.00 0.00 39.85 3.16 R
4329 5684 1.064060 GTTGAGTTGTCACTGTGGCAC 59.936 52.381 15.64 11.55 28.02 5.01 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
37 38 1.832167 GGCCTGTGAGGGTTGCAAA 60.832 57.895 0.00 0.00 35.37 3.68
38 39 1.187567 GGCCTGTGAGGGTTGCAAAT 61.188 55.000 0.00 0.00 35.37 2.32
39 40 0.037975 GCCTGTGAGGGTTGCAAATG 60.038 55.000 0.00 0.00 35.37 2.32
40 41 0.037975 CCTGTGAGGGTTGCAAATGC 60.038 55.000 0.00 0.00 42.50 3.56
99 100 4.222847 GAGGAAGCGGGGTAGCCG 62.223 72.222 4.56 1.59 38.01 5.52
188 189 3.532155 GGAGCACCGCGGAGAGAT 61.532 66.667 35.90 20.11 0.00 2.75
230 231 1.927487 TGAGAAATTGGTGCCAGCAT 58.073 45.000 0.00 0.00 0.00 3.79
235 236 1.094785 AATTGGTGCCAGCATCGTAC 58.905 50.000 0.00 0.00 0.00 3.67
316 321 3.980989 CGACGGGTGGGACGAACA 61.981 66.667 0.00 0.00 34.93 3.18
317 322 2.422591 GACGGGTGGGACGAACAA 59.577 61.111 0.00 0.00 34.93 2.83
322 327 2.686816 GGTGGGACGAACAATGGCG 61.687 63.158 0.00 0.00 0.00 5.69
358 363 3.980989 CGACGGGTGGGACGAACA 61.981 66.667 0.00 0.00 34.93 3.18
359 364 2.660802 GACGGGTGGGACGAACAT 59.339 61.111 0.00 0.00 34.93 2.71
444 449 2.994995 AGGGCGACGTGGATGTCA 60.995 61.111 0.11 0.00 38.84 3.58
457 462 3.628646 ATGTCAAGGAGGCGCACCC 62.629 63.158 10.83 9.77 36.11 4.61
637 642 1.079438 GAGGAGGACCAGGTGGAGT 59.921 63.158 0.00 0.00 38.94 3.85
674 679 4.758251 TGATGCGGTCGGCTGGTG 62.758 66.667 0.00 0.00 44.05 4.17
675 680 4.451150 GATGCGGTCGGCTGGTGA 62.451 66.667 0.00 0.00 44.05 4.02
676 681 4.760047 ATGCGGTCGGCTGGTGAC 62.760 66.667 0.00 0.00 44.05 3.67
733 738 0.043053 CAATACTGCGACGCGATTGG 60.043 55.000 23.61 12.14 0.00 3.16
771 814 1.821336 CGAGAGAAAGCGAGCACTAG 58.179 55.000 0.00 0.00 0.00 2.57
806 853 1.648504 GGGAATACGAACCGGAGTTG 58.351 55.000 9.46 1.35 35.94 3.16
808 855 1.004595 GAATACGAACCGGAGTTGGC 58.995 55.000 9.46 0.00 35.94 4.52
821 868 1.062587 GAGTTGGCGTCGATTTCCATG 59.937 52.381 0.00 0.00 0.00 3.66
823 870 0.035915 TTGGCGTCGATTTCCATGGA 60.036 50.000 11.44 11.44 0.00 3.41
824 871 0.180171 TGGCGTCGATTTCCATGGAT 59.820 50.000 17.06 0.06 0.00 3.41
825 872 0.868406 GGCGTCGATTTCCATGGATC 59.132 55.000 17.06 10.42 0.00 3.36
827 874 1.139989 CGTCGATTTCCATGGATCGG 58.860 55.000 28.69 15.50 43.85 4.18
829 876 2.287970 CGTCGATTTCCATGGATCGGTA 60.288 50.000 28.69 14.15 43.85 4.02
830 877 3.724374 GTCGATTTCCATGGATCGGTAA 58.276 45.455 28.69 16.06 43.85 2.85
831 878 3.741344 GTCGATTTCCATGGATCGGTAAG 59.259 47.826 28.69 13.06 43.85 2.34
832 879 3.386726 TCGATTTCCATGGATCGGTAAGT 59.613 43.478 28.69 7.17 43.85 2.24
833 880 4.127171 CGATTTCCATGGATCGGTAAGTT 58.873 43.478 24.15 0.20 40.94 2.66
834 881 4.574828 CGATTTCCATGGATCGGTAAGTTT 59.425 41.667 24.15 0.00 40.94 2.66
835 882 5.504010 CGATTTCCATGGATCGGTAAGTTTG 60.504 44.000 24.15 0.97 40.94 2.93
837 884 2.092646 TCCATGGATCGGTAAGTTTGGG 60.093 50.000 11.44 0.00 0.00 4.12
838 885 2.092646 CCATGGATCGGTAAGTTTGGGA 60.093 50.000 5.56 0.00 0.00 4.37
839 886 2.773993 TGGATCGGTAAGTTTGGGAC 57.226 50.000 0.00 0.00 0.00 4.46
840 887 1.279846 TGGATCGGTAAGTTTGGGACC 59.720 52.381 0.00 0.00 0.00 4.46
846 893 3.631145 GGTAAGTTTGGGACCGAAAAC 57.369 47.619 2.90 8.09 36.69 2.43
847 894 3.216800 GGTAAGTTTGGGACCGAAAACT 58.783 45.455 14.97 14.97 46.03 2.66
849 896 1.977056 AGTTTGGGACCGAAAACTCC 58.023 50.000 14.97 0.05 41.61 3.85
850 897 1.493446 AGTTTGGGACCGAAAACTCCT 59.507 47.619 14.97 2.10 41.61 3.69
851 898 1.878088 GTTTGGGACCGAAAACTCCTC 59.122 52.381 2.90 0.00 34.22 3.71
853 900 1.133363 TGGGACCGAAAACTCCTCAA 58.867 50.000 0.00 0.00 0.00 3.02
854 901 1.202722 TGGGACCGAAAACTCCTCAAC 60.203 52.381 0.00 0.00 0.00 3.18
855 902 1.071857 GGGACCGAAAACTCCTCAACT 59.928 52.381 0.00 0.00 0.00 3.16
856 903 2.414806 GGACCGAAAACTCCTCAACTC 58.585 52.381 0.00 0.00 0.00 3.01
857 904 2.414806 GACCGAAAACTCCTCAACTCC 58.585 52.381 0.00 0.00 0.00 3.85
858 905 1.766496 ACCGAAAACTCCTCAACTCCA 59.234 47.619 0.00 0.00 0.00 3.86
859 906 2.224305 ACCGAAAACTCCTCAACTCCAG 60.224 50.000 0.00 0.00 0.00 3.86
860 907 1.801178 CGAAAACTCCTCAACTCCAGC 59.199 52.381 0.00 0.00 0.00 4.85
863 910 2.125350 CTCCTCAACTCCAGCGCC 60.125 66.667 2.29 0.00 0.00 6.53
864 911 2.922503 TCCTCAACTCCAGCGCCA 60.923 61.111 2.29 0.00 0.00 5.69
865 912 2.435586 CCTCAACTCCAGCGCCAG 60.436 66.667 2.29 0.00 0.00 4.85
866 913 2.435586 CTCAACTCCAGCGCCAGG 60.436 66.667 2.29 7.04 0.00 4.45
867 914 2.922503 TCAACTCCAGCGCCAGGA 60.923 61.111 17.21 17.21 0.00 3.86
868 915 2.032528 CAACTCCAGCGCCAGGAA 59.967 61.111 18.51 4.94 34.08 3.36
869 916 2.032681 AACTCCAGCGCCAGGAAC 59.967 61.111 18.51 0.00 34.08 3.62
870 917 3.883744 AACTCCAGCGCCAGGAACG 62.884 63.158 18.51 11.32 34.08 3.95
871 918 4.069232 CTCCAGCGCCAGGAACGA 62.069 66.667 18.51 0.00 34.08 3.85
872 919 3.589654 CTCCAGCGCCAGGAACGAA 62.590 63.158 18.51 0.00 34.08 3.85
874 921 2.040544 CCAGCGCCAGGAACGAAAT 61.041 57.895 10.82 0.00 0.00 2.17
875 922 1.425428 CAGCGCCAGGAACGAAATC 59.575 57.895 2.29 0.00 0.00 2.17
876 923 1.745489 AGCGCCAGGAACGAAATCC 60.745 57.895 2.29 0.00 39.96 3.01
885 932 1.356938 GAACGAAATCCTCCACGGTC 58.643 55.000 0.00 0.00 35.47 4.79
886 933 0.389426 AACGAAATCCTCCACGGTCG 60.389 55.000 0.00 0.00 35.56 4.79
887 934 1.246056 ACGAAATCCTCCACGGTCGA 61.246 55.000 0.00 0.00 34.11 4.20
889 936 1.854227 GAAATCCTCCACGGTCGATC 58.146 55.000 0.00 0.00 0.00 3.69
890 937 0.464452 AAATCCTCCACGGTCGATCC 59.536 55.000 0.00 0.00 0.00 3.36
891 938 1.400530 AATCCTCCACGGTCGATCCC 61.401 60.000 0.00 0.00 0.00 3.85
898 945 3.138798 CGGTCGATCCCGGAGTGT 61.139 66.667 0.73 0.00 44.32 3.55
899 946 2.494918 GGTCGATCCCGGAGTGTG 59.505 66.667 0.73 0.00 36.24 3.82
901 948 1.433879 GTCGATCCCGGAGTGTGAG 59.566 63.158 0.73 0.00 36.24 3.51
902 949 1.030488 GTCGATCCCGGAGTGTGAGA 61.030 60.000 0.73 0.00 36.24 3.27
903 950 0.106669 TCGATCCCGGAGTGTGAGAT 60.107 55.000 0.73 0.00 36.24 2.75
904 951 0.312416 CGATCCCGGAGTGTGAGATC 59.688 60.000 0.73 3.56 0.00 2.75
905 952 0.676736 GATCCCGGAGTGTGAGATCC 59.323 60.000 0.73 0.00 0.00 3.36
910 957 3.330766 GGAGTGTGAGATCCGTTCG 57.669 57.895 0.00 0.00 0.00 3.95
911 958 0.179134 GGAGTGTGAGATCCGTTCGG 60.179 60.000 4.74 4.74 0.00 4.30
912 959 0.802607 GAGTGTGAGATCCGTTCGGC 60.803 60.000 6.35 0.00 0.00 5.54
913 960 2.158959 GTGTGAGATCCGTTCGGCG 61.159 63.158 0.00 0.00 40.95 6.46
915 962 1.586564 GTGAGATCCGTTCGGCGAG 60.587 63.158 10.46 0.00 44.77 5.03
918 965 2.278661 GATCCGTTCGGCGAGACC 60.279 66.667 10.46 1.21 44.77 3.85
930 977 2.277628 GAGACCGCTTCTCGCTCG 60.278 66.667 0.00 0.00 41.63 5.03
931 978 2.746671 AGACCGCTTCTCGCTCGA 60.747 61.111 0.00 0.00 36.73 4.04
933 980 1.870016 GACCGCTTCTCGCTCGAAG 60.870 63.158 7.31 7.31 42.52 3.79
938 985 1.142748 CTTCTCGCTCGAAGCCCAT 59.857 57.895 0.00 0.00 38.18 4.00
939 986 0.873743 CTTCTCGCTCGAAGCCCATC 60.874 60.000 0.00 0.00 38.18 3.51
940 987 1.604147 TTCTCGCTCGAAGCCCATCA 61.604 55.000 0.00 0.00 38.18 3.07
941 988 1.153568 CTCGCTCGAAGCCCATCAA 60.154 57.895 0.00 0.00 38.18 2.57
942 989 0.740868 CTCGCTCGAAGCCCATCAAA 60.741 55.000 0.00 0.00 38.18 2.69
943 990 0.107703 TCGCTCGAAGCCCATCAAAT 60.108 50.000 0.00 0.00 38.18 2.32
944 991 0.305922 CGCTCGAAGCCCATCAAATC 59.694 55.000 0.00 0.00 38.18 2.17
945 992 0.305922 GCTCGAAGCCCATCAAATCG 59.694 55.000 0.00 0.00 34.48 3.34
946 993 0.305922 CTCGAAGCCCATCAAATCGC 59.694 55.000 0.00 0.00 33.76 4.58
948 995 1.735973 GAAGCCCATCAAATCGCCC 59.264 57.895 0.00 0.00 0.00 6.13
951 998 1.150536 GCCCATCAAATCGCCCCTA 59.849 57.895 0.00 0.00 0.00 3.53
952 999 0.251341 GCCCATCAAATCGCCCCTAT 60.251 55.000 0.00 0.00 0.00 2.57
953 1000 1.538047 CCCATCAAATCGCCCCTATG 58.462 55.000 0.00 0.00 0.00 2.23
954 1001 0.883833 CCATCAAATCGCCCCTATGC 59.116 55.000 0.00 0.00 0.00 3.14
964 1011 4.609018 CCCTATGCGGCCCTCGTG 62.609 72.222 0.00 0.00 41.72 4.35
965 1012 3.849951 CCTATGCGGCCCTCGTGT 61.850 66.667 0.00 0.00 41.72 4.49
966 1013 2.279517 CTATGCGGCCCTCGTGTC 60.280 66.667 0.00 0.00 41.72 3.67
969 1016 2.173758 TATGCGGCCCTCGTGTCAAA 62.174 55.000 0.00 0.00 41.72 2.69
1019 1066 9.696572 AAAAAGGAGTCCTATTCCCTAAATTAC 57.303 33.333 13.43 0.00 35.20 1.89
1020 1067 6.667558 AGGAGTCCTATTCCCTAAATTACG 57.332 41.667 10.94 0.00 35.20 3.18
1021 1068 6.141790 AGGAGTCCTATTCCCTAAATTACGT 58.858 40.000 10.94 0.00 35.20 3.57
1022 1069 7.300658 AGGAGTCCTATTCCCTAAATTACGTA 58.699 38.462 10.94 0.00 35.20 3.57
1023 1070 7.954620 AGGAGTCCTATTCCCTAAATTACGTAT 59.045 37.037 10.94 0.00 35.20 3.06
1024 1071 8.591940 GGAGTCCTATTCCCTAAATTACGTATT 58.408 37.037 0.41 0.00 0.00 1.89
1025 1072 9.993454 GAGTCCTATTCCCTAAATTACGTATTT 57.007 33.333 0.00 0.00 39.69 1.40
1026 1073 9.993454 AGTCCTATTCCCTAAATTACGTATTTC 57.007 33.333 0.00 0.00 37.60 2.17
1027 1074 9.993454 GTCCTATTCCCTAAATTACGTATTTCT 57.007 33.333 0.00 0.00 37.60 2.52
1028 1075 9.991906 TCCTATTCCCTAAATTACGTATTTCTG 57.008 33.333 0.00 0.00 37.60 3.02
1029 1076 9.774413 CCTATTCCCTAAATTACGTATTTCTGT 57.226 33.333 0.00 0.00 37.60 3.41
1032 1079 7.311364 TCCCTAAATTACGTATTTCTGTTGC 57.689 36.000 0.00 0.00 37.60 4.17
1033 1080 7.107542 TCCCTAAATTACGTATTTCTGTTGCT 58.892 34.615 0.00 0.00 37.60 3.91
1034 1081 7.608761 TCCCTAAATTACGTATTTCTGTTGCTT 59.391 33.333 0.00 0.00 37.60 3.91
1035 1082 8.241367 CCCTAAATTACGTATTTCTGTTGCTTT 58.759 33.333 0.00 0.00 37.60 3.51
1057 1104 0.178926 TTACTGTCTCCGTCCCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
1058 1105 0.901580 TACTGTCTCCGTCCCCCAAC 60.902 60.000 0.00 0.00 0.00 3.77
1060 1107 2.606826 GTCTCCGTCCCCCAACCT 60.607 66.667 0.00 0.00 0.00 3.50
1062 1109 3.771160 CTCCGTCCCCCAACCTCG 61.771 72.222 0.00 0.00 0.00 4.63
1067 1114 4.995058 TCCCCCAACCTCGGGCTT 62.995 66.667 0.00 0.00 45.90 4.35
1068 1115 3.012722 CCCCCAACCTCGGGCTTA 61.013 66.667 0.00 0.00 45.90 3.09
1069 1116 2.590092 CCCCAACCTCGGGCTTAG 59.410 66.667 0.00 0.00 45.90 2.18
1070 1117 2.298661 CCCCAACCTCGGGCTTAGT 61.299 63.158 0.00 0.00 45.90 2.24
1090 1149 0.762082 TTGCAGCATTGGGGTTTCCA 60.762 50.000 0.00 0.00 45.43 3.53
1285 1368 2.123208 TCACCGTCACCCTCCACA 60.123 61.111 0.00 0.00 0.00 4.17
1297 1380 1.674057 CTCCACAAAGTCCCGCTCT 59.326 57.895 0.00 0.00 0.00 4.09
1359 1442 3.514309 GGGTATGCCATTACTACCTCGAT 59.486 47.826 1.04 0.00 36.09 3.59
1363 1446 6.321690 GGTATGCCATTACTACCTCGATATCT 59.678 42.308 0.34 0.00 33.57 1.98
1373 1456 1.889829 CCTCGATATCTGTGTCCCCTC 59.110 57.143 0.34 0.00 0.00 4.30
1375 1458 0.039074 CGATATCTGTGTCCCCTCGC 60.039 60.000 0.34 0.00 0.00 5.03
1376 1459 1.040646 GATATCTGTGTCCCCTCGCA 58.959 55.000 0.00 0.00 0.00 5.10
1377 1460 1.000283 GATATCTGTGTCCCCTCGCAG 60.000 57.143 0.00 0.00 44.33 5.18
1410 2293 1.448119 CCGTCAGCATCTCCTCGCTA 61.448 60.000 0.00 0.00 36.50 4.26
1471 2354 4.710167 TCCTCGAGCCGGACGTCA 62.710 66.667 18.91 0.00 0.00 4.35
1482 2365 3.060866 GACGTCAAGGTCCCAGCT 58.939 61.111 11.55 0.00 0.00 4.24
1483 2366 1.374758 GACGTCAAGGTCCCAGCTG 60.375 63.158 11.55 6.78 0.00 4.24
1502 2385 0.391597 GGTCTGGACGTGAACCTGAA 59.608 55.000 0.00 0.00 37.18 3.02
1731 2636 3.234730 ATCCGCATCCTCCGGGTC 61.235 66.667 0.00 0.00 45.60 4.46
1767 2672 1.378911 GGCCATGGACAGCATCACA 60.379 57.895 18.40 0.00 0.00 3.58
1822 2727 3.529533 GAGAGCAGCAACAGATGTACAT 58.470 45.455 8.43 8.43 0.00 2.29
1830 2735 4.587262 AGCAACAGATGTACATCCCGTATA 59.413 41.667 28.26 0.00 38.58 1.47
1834 2739 5.382616 ACAGATGTACATCCCGTATAGACA 58.617 41.667 28.26 0.00 38.58 3.41
1879 2784 1.566018 GAACCTGTCTTTCCGTGCCG 61.566 60.000 0.00 0.00 0.00 5.69
1900 2805 1.456705 GGCGATCTCAGGGTCTCCT 60.457 63.158 0.00 0.00 46.26 3.69
1901 2806 1.460273 GGCGATCTCAGGGTCTCCTC 61.460 65.000 0.00 0.00 42.67 3.71
1902 2807 1.460273 GCGATCTCAGGGTCTCCTCC 61.460 65.000 0.00 0.00 42.67 4.30
1907 2812 1.000771 TCAGGGTCTCCTCCGTCTG 60.001 63.158 0.00 0.00 42.67 3.51
2011 2919 1.571215 CGGCTTAAACACCACCGACC 61.571 60.000 0.00 0.00 46.71 4.79
2012 2920 0.535553 GGCTTAAACACCACCGACCA 60.536 55.000 0.00 0.00 0.00 4.02
2014 2922 1.812708 GCTTAAACACCACCGACCACT 60.813 52.381 0.00 0.00 0.00 4.00
2015 2923 2.140717 CTTAAACACCACCGACCACTC 58.859 52.381 0.00 0.00 0.00 3.51
2016 2924 0.393820 TAAACACCACCGACCACTCC 59.606 55.000 0.00 0.00 0.00 3.85
2017 2925 2.333701 AAACACCACCGACCACTCCC 62.334 60.000 0.00 0.00 0.00 4.30
2020 2928 2.073716 ACCACCGACCACTCCCAAA 61.074 57.895 0.00 0.00 0.00 3.28
2021 2929 1.149627 CCACCGACCACTCCCAAAA 59.850 57.895 0.00 0.00 0.00 2.44
2022 2930 0.466555 CCACCGACCACTCCCAAAAA 60.467 55.000 0.00 0.00 0.00 1.94
2025 2933 1.524008 CCGACCACTCCCAAAAAGGC 61.524 60.000 0.00 0.00 35.39 4.35
2026 2934 1.852067 CGACCACTCCCAAAAAGGCG 61.852 60.000 0.00 0.00 35.39 5.52
2128 3042 0.171007 AATTCACCGGATTTGCTGCG 59.829 50.000 9.46 0.00 38.61 5.18
2148 3062 3.687698 GCGGGCTAAACTGATGAACTTAA 59.312 43.478 0.00 0.00 0.00 1.85
2226 3141 2.980233 ACACCTTTGCGGCAGAGC 60.980 61.111 14.57 0.00 35.61 4.09
2228 3143 2.359230 ACCTTTGCGGCAGAGCTC 60.359 61.111 14.57 5.27 38.13 4.09
2402 3317 5.969435 GGTAATTTATCGCTTTGCTTACACC 59.031 40.000 0.00 0.00 0.00 4.16
2403 3318 4.632538 ATTTATCGCTTTGCTTACACCC 57.367 40.909 0.00 0.00 0.00 4.61
2404 3319 2.032680 TATCGCTTTGCTTACACCCC 57.967 50.000 0.00 0.00 0.00 4.95
2407 3322 1.305930 CGCTTTGCTTACACCCCCTC 61.306 60.000 0.00 0.00 0.00 4.30
2408 3323 0.038310 GCTTTGCTTACACCCCCTCT 59.962 55.000 0.00 0.00 0.00 3.69
2409 3324 1.547901 GCTTTGCTTACACCCCCTCTT 60.548 52.381 0.00 0.00 0.00 2.85
2410 3325 2.290705 GCTTTGCTTACACCCCCTCTTA 60.291 50.000 0.00 0.00 0.00 2.10
2411 3326 3.624959 GCTTTGCTTACACCCCCTCTTAT 60.625 47.826 0.00 0.00 0.00 1.73
2412 3327 4.384868 GCTTTGCTTACACCCCCTCTTATA 60.385 45.833 0.00 0.00 0.00 0.98
2413 3328 5.690364 GCTTTGCTTACACCCCCTCTTATAT 60.690 44.000 0.00 0.00 0.00 0.86
2415 3330 5.987019 TGCTTACACCCCCTCTTATATTT 57.013 39.130 0.00 0.00 0.00 1.40
2417 3332 6.737608 TGCTTACACCCCCTCTTATATTTTT 58.262 36.000 0.00 0.00 0.00 1.94
2494 3459 5.173774 AGAATTGTAGGCGCATTGTTATG 57.826 39.130 10.83 0.00 34.76 1.90
2517 3482 5.047188 GCTTGAGCTAAGGTCTCAATAGTC 58.953 45.833 5.98 0.00 45.96 2.59
2582 3549 3.821033 ACTAGGTGAAAGAAACATGCCAC 59.179 43.478 0.00 0.00 0.00 5.01
2587 3554 3.972502 GTGAAAGAAACATGCCACGTAAC 59.027 43.478 0.00 0.00 0.00 2.50
2906 3875 9.469239 CGAGAACTATTTTATTGTTTTACCGTC 57.531 33.333 0.00 0.00 0.00 4.79
2961 3936 4.211374 CCTACAGTCTTTTGGTCTGAAACG 59.789 45.833 0.00 0.00 33.93 3.60
2986 3961 7.115520 CGTATGCAGTTCTTTCATATCAGTAGG 59.884 40.741 0.00 0.00 0.00 3.18
3025 4094 4.519540 TTCTAAGGCTTTTGGAATGTGC 57.480 40.909 4.45 0.00 0.00 4.57
3125 4224 6.048732 TGCTACACAGATGTTCTTCCATTA 57.951 37.500 0.00 0.00 40.48 1.90
3200 4299 8.519799 AGGTCTAAGACTTCTCTATTCTTCTG 57.480 38.462 0.00 0.00 31.93 3.02
3243 4346 9.249053 ACCATCTACTTCTATATACATGTCAGG 57.751 37.037 0.00 0.00 0.00 3.86
3253 4356 2.275134 ACATGTCAGGTGATTGTGCA 57.725 45.000 0.00 0.00 0.00 4.57
3254 4357 2.799017 ACATGTCAGGTGATTGTGCAT 58.201 42.857 0.00 0.00 0.00 3.96
3373 4492 9.438228 ACTTTTTAGTCTATACAAGCTTCCTTC 57.562 33.333 0.00 0.00 0.00 3.46
3382 4501 4.965200 ACAAGCTTCCTTCACTTAGTCT 57.035 40.909 0.00 0.00 0.00 3.24
3405 4527 4.597507 TCCCTGTCCTGATTGAAACTAAGT 59.402 41.667 0.00 0.00 0.00 2.24
3408 4530 5.182001 CCTGTCCTGATTGAAACTAAGTTGG 59.818 44.000 0.00 0.00 0.00 3.77
3485 4789 2.105477 AGGGTCAATATGTAGCAGCCAG 59.895 50.000 0.00 0.00 0.00 4.85
3507 4811 5.049336 CAGAGATCTGCATTGACATGATTCC 60.049 44.000 0.00 0.00 37.15 3.01
3617 4924 5.528690 TGCTTCATGGCTTCAATCATACTAC 59.471 40.000 0.00 0.00 0.00 2.73
3618 4925 5.049129 GCTTCATGGCTTCAATCATACTACC 60.049 44.000 0.00 0.00 0.00 3.18
3619 4926 5.894298 TCATGGCTTCAATCATACTACCT 57.106 39.130 0.00 0.00 0.00 3.08
3621 4928 6.291377 TCATGGCTTCAATCATACTACCTTC 58.709 40.000 0.00 0.00 0.00 3.46
3622 4929 5.957771 TGGCTTCAATCATACTACCTTCT 57.042 39.130 0.00 0.00 0.00 2.85
3623 4930 7.290014 TCATGGCTTCAATCATACTACCTTCTA 59.710 37.037 0.00 0.00 0.00 2.10
3626 4933 7.933577 TGGCTTCAATCATACTACCTTCTATTG 59.066 37.037 0.00 0.00 0.00 1.90
3669 4998 2.858868 GCTCGAAGTGCTGCACAG 59.141 61.111 31.90 21.52 44.39 3.66
3682 5011 7.076842 AGTGCTGCACAGTAGTTTATTATTG 57.923 36.000 31.90 0.00 36.74 1.90
3752 5088 7.175467 TCTCCGTATTAGAAGACAGTTGTTGTA 59.825 37.037 0.00 0.00 41.05 2.41
3753 5089 7.660112 TCCGTATTAGAAGACAGTTGTTGTAA 58.340 34.615 0.00 0.00 41.05 2.41
3754 5090 8.308931 TCCGTATTAGAAGACAGTTGTTGTAAT 58.691 33.333 5.06 5.06 41.05 1.89
3755 5091 8.592998 CCGTATTAGAAGACAGTTGTTGTAATC 58.407 37.037 3.52 0.00 41.05 1.75
3756 5092 8.592998 CGTATTAGAAGACAGTTGTTGTAATCC 58.407 37.037 3.52 0.00 41.05 3.01
3757 5093 9.654663 GTATTAGAAGACAGTTGTTGTAATCCT 57.345 33.333 3.52 0.00 41.05 3.24
3758 5094 8.779354 ATTAGAAGACAGTTGTTGTAATCCTC 57.221 34.615 0.00 0.00 41.05 3.71
3759 5095 6.174720 AGAAGACAGTTGTTGTAATCCTCA 57.825 37.500 0.00 0.00 41.05 3.86
3760 5096 6.591935 AGAAGACAGTTGTTGTAATCCTCAA 58.408 36.000 0.00 0.00 41.05 3.02
3792 5137 6.152323 GCCATTGCCATTGATATTCTGACTAT 59.848 38.462 0.00 0.00 0.00 2.12
3805 5150 3.898482 TCTGACTATTCTCATGTCGGGA 58.102 45.455 0.00 0.00 37.60 5.14
3836 5181 2.128771 AAACTATGTGGCGCCATCTT 57.871 45.000 35.23 23.84 0.00 2.40
3837 5182 1.668419 AACTATGTGGCGCCATCTTC 58.332 50.000 35.23 20.58 0.00 2.87
3838 5183 0.541392 ACTATGTGGCGCCATCTTCA 59.459 50.000 35.23 25.97 0.00 3.02
3920 5265 1.847968 AATCGGGGGCCTCCTATGG 60.848 63.158 22.56 3.46 35.33 2.74
3991 5337 2.515901 GCCATATGGACCGCCCTT 59.484 61.111 26.47 0.00 37.39 3.95
4028 5374 2.746279 TTTGTGGCTCTTTTCCTCCA 57.254 45.000 0.00 0.00 0.00 3.86
4118 5464 5.929992 CCATGACAATTCTGCTCAAAACAAT 59.070 36.000 0.00 0.00 0.00 2.71
4122 5468 6.476380 TGACAATTCTGCTCAAAACAATGTTC 59.524 34.615 0.00 0.00 0.00 3.18
4144 5490 3.550678 CGGTCGGTTAGTTCTTATTCAGC 59.449 47.826 0.00 0.00 0.00 4.26
4156 5502 7.217200 AGTTCTTATTCAGCTGTGTAAGACAA 58.783 34.615 27.55 18.54 34.07 3.18
4158 5504 7.421530 TCTTATTCAGCTGTGTAAGACAAAC 57.578 36.000 25.64 0.00 32.80 2.93
4159 5505 4.732285 ATTCAGCTGTGTAAGACAAACG 57.268 40.909 14.67 0.00 32.80 3.60
4161 5507 2.101750 TCAGCTGTGTAAGACAAACGGA 59.898 45.455 14.67 0.00 32.80 4.69
4216 5563 3.610040 ACATTTGAGACGTATCAGGCA 57.390 42.857 13.25 2.27 0.00 4.75
4227 5574 2.680805 CGTATCAGGCAATGTCCTTGGT 60.681 50.000 0.00 0.00 35.25 3.67
4239 5586 0.768622 TCCTTGGTCAACGGTTCCAT 59.231 50.000 2.52 0.00 0.00 3.41
4257 5612 3.117131 TCCATACTGTAGCATCTCCCTCA 60.117 47.826 0.00 0.00 0.00 3.86
4329 5684 4.093998 GCCTCGTCATGCATAATTGATAGG 59.906 45.833 0.00 6.92 33.93 2.57
4338 5693 3.885297 GCATAATTGATAGGTGCCACAGT 59.115 43.478 0.00 0.00 0.00 3.55
4340 5695 3.719268 AATTGATAGGTGCCACAGTGA 57.281 42.857 0.62 0.00 0.00 3.41
4390 5750 5.104527 TGTGTATTAGGAGGGGTTCTTCATG 60.105 44.000 0.00 0.00 0.00 3.07
4504 5864 5.954296 ACTCATGAATTGTTTGAGTGGAG 57.046 39.130 11.68 0.00 46.19 3.86
4520 5880 9.449719 TTTGAGTGGAGTATATTCTTTTCCTTC 57.550 33.333 0.00 0.00 0.00 3.46
4533 5893 6.963083 TCTTTTCCTTCCGTTTAATTTCCA 57.037 33.333 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.270205 CTGGACCTCCGCTTGCAT 59.730 61.111 0.00 0.00 39.43 3.96
38 39 4.704833 GCTGGACCTCCGCTTGCA 62.705 66.667 0.00 0.00 39.43 4.08
40 41 4.785453 GGGCTGGACCTCCGCTTG 62.785 72.222 0.00 0.00 39.43 4.01
99 100 1.449070 CGGGCCCCTTTTCTCGTAC 60.449 63.158 18.66 0.00 0.00 3.67
187 188 4.054671 CAAAATACGTTGTTGGCACCAAT 58.945 39.130 5.22 0.00 38.28 3.16
188 189 3.119101 ACAAAATACGTTGTTGGCACCAA 60.119 39.130 0.00 0.00 38.60 3.67
383 388 4.399395 GGTTCGTTCCCCCGGTCC 62.399 72.222 0.00 0.00 0.00 4.46
436 441 2.268920 GCGCCTCCTTGACATCCA 59.731 61.111 0.00 0.00 0.00 3.41
637 642 1.454976 CTCCCTCCCGGACGATCTA 59.545 63.158 0.73 0.00 34.86 1.98
674 679 2.187946 CATGGAGGACAGCGGGTC 59.812 66.667 3.28 3.28 46.20 4.46
675 680 3.402681 CCATGGAGGACAGCGGGT 61.403 66.667 5.56 0.00 41.22 5.28
676 681 4.864334 GCCATGGAGGACAGCGGG 62.864 72.222 18.40 0.00 41.22 6.13
771 814 2.735237 CCCGGCCGATCCTTCTAC 59.265 66.667 30.73 0.00 0.00 2.59
806 853 0.868406 GATCCATGGAAATCGACGCC 59.132 55.000 20.67 0.00 0.00 5.68
808 855 1.139989 CCGATCCATGGAAATCGACG 58.860 55.000 30.48 21.38 45.83 5.12
821 868 2.034104 GGTCCCAAACTTACCGATCC 57.966 55.000 0.00 0.00 0.00 3.36
827 874 3.251729 GGAGTTTTCGGTCCCAAACTTAC 59.748 47.826 12.94 7.71 42.15 2.34
829 876 2.092049 AGGAGTTTTCGGTCCCAAACTT 60.092 45.455 12.94 0.00 42.15 2.66
830 877 1.493446 AGGAGTTTTCGGTCCCAAACT 59.507 47.619 11.94 11.94 44.26 2.66
831 878 1.878088 GAGGAGTTTTCGGTCCCAAAC 59.122 52.381 3.89 3.89 32.70 2.93
832 879 1.491332 TGAGGAGTTTTCGGTCCCAAA 59.509 47.619 0.00 0.00 32.70 3.28
833 880 1.133363 TGAGGAGTTTTCGGTCCCAA 58.867 50.000 0.00 0.00 32.70 4.12
834 881 1.133363 TTGAGGAGTTTTCGGTCCCA 58.867 50.000 0.00 0.00 32.70 4.37
835 882 1.071857 AGTTGAGGAGTTTTCGGTCCC 59.928 52.381 0.00 0.00 32.70 4.46
837 884 2.224209 TGGAGTTGAGGAGTTTTCGGTC 60.224 50.000 0.00 0.00 0.00 4.79
838 885 1.766496 TGGAGTTGAGGAGTTTTCGGT 59.234 47.619 0.00 0.00 0.00 4.69
839 886 2.417719 CTGGAGTTGAGGAGTTTTCGG 58.582 52.381 0.00 0.00 0.00 4.30
840 887 1.801178 GCTGGAGTTGAGGAGTTTTCG 59.199 52.381 0.00 0.00 0.00 3.46
841 888 1.801178 CGCTGGAGTTGAGGAGTTTTC 59.199 52.381 0.00 0.00 0.00 2.29
843 890 0.603975 GCGCTGGAGTTGAGGAGTTT 60.604 55.000 0.00 0.00 0.00 2.66
844 891 1.004440 GCGCTGGAGTTGAGGAGTT 60.004 57.895 0.00 0.00 0.00 3.01
845 892 2.659610 GCGCTGGAGTTGAGGAGT 59.340 61.111 0.00 0.00 0.00 3.85
846 893 2.125350 GGCGCTGGAGTTGAGGAG 60.125 66.667 7.64 0.00 0.00 3.69
847 894 2.922503 TGGCGCTGGAGTTGAGGA 60.923 61.111 7.64 0.00 0.00 3.71
849 896 2.435586 CCTGGCGCTGGAGTTGAG 60.436 66.667 7.64 0.00 0.00 3.02
850 897 2.515979 TTCCTGGCGCTGGAGTTGA 61.516 57.895 18.72 5.65 33.24 3.18
851 898 2.032528 TTCCTGGCGCTGGAGTTG 59.967 61.111 18.72 0.00 33.24 3.16
853 900 4.379243 CGTTCCTGGCGCTGGAGT 62.379 66.667 18.72 0.00 33.24 3.85
854 901 3.589654 TTCGTTCCTGGCGCTGGAG 62.590 63.158 18.72 11.17 33.24 3.86
855 902 2.463589 ATTTCGTTCCTGGCGCTGGA 62.464 55.000 16.43 16.43 0.00 3.86
856 903 1.982073 GATTTCGTTCCTGGCGCTGG 61.982 60.000 7.64 10.70 0.00 4.85
857 904 1.425428 GATTTCGTTCCTGGCGCTG 59.575 57.895 7.64 0.00 0.00 5.18
858 905 1.745489 GGATTTCGTTCCTGGCGCT 60.745 57.895 7.64 0.00 32.68 5.92
859 906 1.706287 GAGGATTTCGTTCCTGGCGC 61.706 60.000 0.00 0.00 46.35 6.53
860 907 1.090052 GGAGGATTTCGTTCCTGGCG 61.090 60.000 8.67 0.00 46.35 5.69
863 910 1.359848 CGTGGAGGATTTCGTTCCTG 58.640 55.000 8.67 0.00 46.35 3.86
865 912 0.036671 ACCGTGGAGGATTTCGTTCC 60.037 55.000 0.00 0.00 45.00 3.62
866 913 1.356938 GACCGTGGAGGATTTCGTTC 58.643 55.000 0.00 0.00 45.00 3.95
867 914 0.389426 CGACCGTGGAGGATTTCGTT 60.389 55.000 0.00 0.00 45.00 3.85
868 915 1.214589 CGACCGTGGAGGATTTCGT 59.785 57.895 0.00 0.00 45.00 3.85
869 916 0.102481 ATCGACCGTGGAGGATTTCG 59.898 55.000 0.00 0.00 45.00 3.46
870 917 1.538419 GGATCGACCGTGGAGGATTTC 60.538 57.143 0.00 0.00 45.00 2.17
871 918 0.464452 GGATCGACCGTGGAGGATTT 59.536 55.000 0.00 0.00 45.00 2.17
872 919 1.400530 GGGATCGACCGTGGAGGATT 61.401 60.000 0.00 0.00 45.00 3.01
874 921 2.441532 GGGATCGACCGTGGAGGA 60.442 66.667 0.00 0.00 45.00 3.71
882 929 2.005960 CTCACACTCCGGGATCGACC 62.006 65.000 0.00 0.00 39.00 4.79
885 932 0.312416 GATCTCACACTCCGGGATCG 59.688 60.000 0.00 0.00 0.00 3.69
886 933 0.676736 GGATCTCACACTCCGGGATC 59.323 60.000 0.00 3.68 34.00 3.36
887 934 2.827715 GGATCTCACACTCCGGGAT 58.172 57.895 0.00 0.00 0.00 3.85
892 939 0.179134 CCGAACGGATCTCACACTCC 60.179 60.000 7.53 0.00 37.50 3.85
893 940 0.802607 GCCGAACGGATCTCACACTC 60.803 60.000 17.63 0.00 37.50 3.51
894 941 1.215647 GCCGAACGGATCTCACACT 59.784 57.895 17.63 0.00 37.50 3.55
895 942 2.158959 CGCCGAACGGATCTCACAC 61.159 63.158 17.63 0.00 38.44 3.82
896 943 2.180769 CGCCGAACGGATCTCACA 59.819 61.111 17.63 0.00 38.44 3.58
897 944 1.586564 CTCGCCGAACGGATCTCAC 60.587 63.158 17.63 0.00 43.89 3.51
898 945 1.747745 TCTCGCCGAACGGATCTCA 60.748 57.895 17.63 0.00 43.89 3.27
899 946 1.298488 GTCTCGCCGAACGGATCTC 60.298 63.158 17.63 0.00 43.89 2.75
901 948 2.278661 GGTCTCGCCGAACGGATC 60.279 66.667 17.63 0.00 43.89 3.36
921 968 1.141881 GATGGGCTTCGAGCGAGAA 59.858 57.895 0.00 0.00 43.62 2.87
923 970 0.740868 TTTGATGGGCTTCGAGCGAG 60.741 55.000 0.00 0.00 43.62 5.03
924 971 0.107703 ATTTGATGGGCTTCGAGCGA 60.108 50.000 0.00 0.00 43.62 4.93
925 972 0.305922 GATTTGATGGGCTTCGAGCG 59.694 55.000 0.00 0.00 43.62 5.03
926 973 0.305922 CGATTTGATGGGCTTCGAGC 59.694 55.000 0.00 0.00 41.46 5.03
927 974 0.305922 GCGATTTGATGGGCTTCGAG 59.694 55.000 0.00 0.00 31.74 4.04
928 975 1.095228 GGCGATTTGATGGGCTTCGA 61.095 55.000 0.00 0.00 31.74 3.71
929 976 1.356624 GGCGATTTGATGGGCTTCG 59.643 57.895 0.00 0.00 0.00 3.79
930 977 1.735973 GGGCGATTTGATGGGCTTC 59.264 57.895 0.00 0.00 34.03 3.86
931 978 1.758122 GGGGCGATTTGATGGGCTT 60.758 57.895 0.00 0.00 34.03 4.35
933 980 0.251341 ATAGGGGCGATTTGATGGGC 60.251 55.000 0.00 0.00 0.00 5.36
934 981 1.538047 CATAGGGGCGATTTGATGGG 58.462 55.000 0.00 0.00 0.00 4.00
935 982 0.883833 GCATAGGGGCGATTTGATGG 59.116 55.000 0.00 0.00 0.00 3.51
948 995 3.792053 GACACGAGGGCCGCATAGG 62.792 68.421 8.33 0.00 43.32 2.57
951 998 3.545124 TTTGACACGAGGGCCGCAT 62.545 57.895 8.33 0.00 43.32 4.73
952 999 3.758973 TTTTGACACGAGGGCCGCA 62.759 57.895 8.33 0.00 43.32 5.69
953 1000 2.548295 TTTTTGACACGAGGGCCGC 61.548 57.895 0.00 0.00 43.32 6.53
954 1001 3.739167 TTTTTGACACGAGGGCCG 58.261 55.556 0.00 0.00 45.44 6.13
969 1016 8.547481 TTTCAAGGAAAATAGGACTCCTTTTT 57.453 30.769 1.94 5.30 45.37 1.94
993 1040 9.696572 GTAATTTAGGGAATAGGACTCCTTTTT 57.303 33.333 1.94 0.00 34.61 1.94
996 1043 6.614496 ACGTAATTTAGGGAATAGGACTCCTT 59.386 38.462 1.94 0.00 34.61 3.36
998 1045 6.416631 ACGTAATTTAGGGAATAGGACTCC 57.583 41.667 0.00 0.00 0.00 3.85
999 1046 9.993454 AAATACGTAATTTAGGGAATAGGACTC 57.007 33.333 0.00 0.00 35.98 3.36
1001 1048 9.993454 AGAAATACGTAATTTAGGGAATAGGAC 57.007 33.333 0.00 0.00 37.93 3.85
1002 1049 9.991906 CAGAAATACGTAATTTAGGGAATAGGA 57.008 33.333 0.00 0.00 37.93 2.94
1003 1050 9.774413 ACAGAAATACGTAATTTAGGGAATAGG 57.226 33.333 0.00 0.00 37.93 2.57
1006 1053 8.403236 GCAACAGAAATACGTAATTTAGGGAAT 58.597 33.333 0.00 0.00 37.93 3.01
1008 1055 7.107542 AGCAACAGAAATACGTAATTTAGGGA 58.892 34.615 0.00 0.00 37.93 4.20
1009 1056 7.316544 AGCAACAGAAATACGTAATTTAGGG 57.683 36.000 0.00 0.00 37.93 3.53
1018 1065 8.780249 ACAGTAATTAAAGCAACAGAAATACGT 58.220 29.630 0.00 0.00 0.00 3.57
1019 1066 9.262472 GACAGTAATTAAAGCAACAGAAATACG 57.738 33.333 0.00 0.00 0.00 3.06
1022 1069 8.515414 GGAGACAGTAATTAAAGCAACAGAAAT 58.485 33.333 0.00 0.00 0.00 2.17
1023 1070 7.307751 CGGAGACAGTAATTAAAGCAACAGAAA 60.308 37.037 0.00 0.00 0.00 2.52
1024 1071 6.147164 CGGAGACAGTAATTAAAGCAACAGAA 59.853 38.462 0.00 0.00 0.00 3.02
1025 1072 5.637810 CGGAGACAGTAATTAAAGCAACAGA 59.362 40.000 0.00 0.00 0.00 3.41
1026 1073 5.408604 ACGGAGACAGTAATTAAAGCAACAG 59.591 40.000 0.00 0.00 0.00 3.16
1027 1074 5.302360 ACGGAGACAGTAATTAAAGCAACA 58.698 37.500 0.00 0.00 0.00 3.33
1028 1075 5.163884 GGACGGAGACAGTAATTAAAGCAAC 60.164 44.000 0.00 0.00 0.00 4.17
1029 1076 4.933400 GGACGGAGACAGTAATTAAAGCAA 59.067 41.667 0.00 0.00 0.00 3.91
1030 1077 4.501071 GGACGGAGACAGTAATTAAAGCA 58.499 43.478 0.00 0.00 0.00 3.91
1031 1078 3.869832 GGGACGGAGACAGTAATTAAAGC 59.130 47.826 0.00 0.00 0.00 3.51
1032 1079 4.439968 GGGGACGGAGACAGTAATTAAAG 58.560 47.826 0.00 0.00 0.00 1.85
1033 1080 3.198417 GGGGGACGGAGACAGTAATTAAA 59.802 47.826 0.00 0.00 0.00 1.52
1034 1081 2.767960 GGGGGACGGAGACAGTAATTAA 59.232 50.000 0.00 0.00 0.00 1.40
1035 1082 2.292389 TGGGGGACGGAGACAGTAATTA 60.292 50.000 0.00 0.00 0.00 1.40
1043 1090 2.606826 AGGTTGGGGGACGGAGAC 60.607 66.667 0.00 0.00 0.00 3.36
1057 1104 0.321653 CTGCAAACTAAGCCCGAGGT 60.322 55.000 0.00 0.00 0.00 3.85
1058 1105 1.648467 GCTGCAAACTAAGCCCGAGG 61.648 60.000 0.00 0.00 33.12 4.63
1060 1107 0.322456 ATGCTGCAAACTAAGCCCGA 60.322 50.000 6.36 0.00 38.71 5.14
1062 1109 1.404583 CCAATGCTGCAAACTAAGCCC 60.405 52.381 6.36 0.00 38.71 5.19
1066 1113 2.008242 ACCCCAATGCTGCAAACTAA 57.992 45.000 6.36 0.00 0.00 2.24
1067 1114 2.008242 AACCCCAATGCTGCAAACTA 57.992 45.000 6.36 0.00 0.00 2.24
1068 1115 1.070601 GAAACCCCAATGCTGCAAACT 59.929 47.619 6.36 0.00 0.00 2.66
1069 1116 1.511850 GAAACCCCAATGCTGCAAAC 58.488 50.000 6.36 0.00 0.00 2.93
1070 1117 0.396060 GGAAACCCCAATGCTGCAAA 59.604 50.000 6.36 0.00 34.14 3.68
1093 1152 0.252057 TCCGTCTCCTCCATGTTGGA 60.252 55.000 4.22 4.22 45.98 3.53
1094 1153 0.176680 CTCCGTCTCCTCCATGTTGG 59.823 60.000 0.00 0.00 39.43 3.77
1095 1154 1.186200 TCTCCGTCTCCTCCATGTTG 58.814 55.000 0.00 0.00 0.00 3.33
1096 1155 1.550976 GTTCTCCGTCTCCTCCATGTT 59.449 52.381 0.00 0.00 0.00 2.71
1097 1156 1.187087 GTTCTCCGTCTCCTCCATGT 58.813 55.000 0.00 0.00 0.00 3.21
1285 1368 2.262915 CGAGCAGAGCGGGACTTT 59.737 61.111 0.00 0.00 0.00 2.66
1359 1442 1.043116 CCTGCGAGGGGACACAGATA 61.043 60.000 0.00 0.00 31.84 1.98
1375 1458 4.489771 GGGGGTGATCGTGCCCTG 62.490 72.222 16.28 0.00 44.25 4.45
1394 2277 1.313772 GAGTAGCGAGGAGATGCTGA 58.686 55.000 0.00 0.00 42.46 4.26
1440 2323 2.665419 TCGAGGACGAAGAGCATCTCG 61.665 57.143 0.00 0.00 42.82 4.04
1471 2354 3.488423 CAGACCAGCTGGGACCTT 58.512 61.111 35.42 15.51 41.07 3.50
1481 2364 0.319900 CAGGTTCACGTCCAGACCAG 60.320 60.000 8.37 0.00 0.00 4.00
1482 2365 0.757561 TCAGGTTCACGTCCAGACCA 60.758 55.000 8.37 0.00 0.00 4.02
1483 2366 0.391597 TTCAGGTTCACGTCCAGACC 59.608 55.000 0.00 0.00 0.00 3.85
1502 2385 0.605589 GTAGAGCAGCGCCATAGGAT 59.394 55.000 2.29 0.00 0.00 3.24
1731 2636 2.353605 GGCCACCATACCATTGTTGTTG 60.354 50.000 0.00 0.00 0.00 3.33
1767 2672 3.760035 AGCGACGCCGAGTGGATT 61.760 61.111 17.79 0.00 37.49 3.01
1822 2727 1.531423 GCCTCGATGTCTATACGGGA 58.469 55.000 0.00 0.00 0.00 5.14
1830 2735 3.071206 ACAGGCGCCTCGATGTCT 61.071 61.111 30.29 0.00 0.00 3.41
1879 2784 4.593864 GACCCTGAGATCGCCGCC 62.594 72.222 0.00 0.00 0.00 6.13
1900 2805 2.350895 CATTGGTGCCCAGACGGA 59.649 61.111 0.00 0.00 33.81 4.69
1901 2806 2.751436 CCATTGGTGCCCAGACGG 60.751 66.667 0.00 0.00 33.81 4.79
1902 2807 3.443045 GCCATTGGTGCCCAGACG 61.443 66.667 4.26 0.00 33.81 4.18
1907 2812 3.936772 TTCTCCGCCATTGGTGCCC 62.937 63.158 10.90 0.00 0.00 5.36
1991 2896 1.301874 TCGGTGGTGTTTAAGCCGG 60.302 57.895 0.00 0.00 42.35 6.13
2011 2919 1.866853 GAGCCGCCTTTTTGGGAGTG 61.867 60.000 0.00 0.00 36.00 3.51
2012 2920 1.603739 GAGCCGCCTTTTTGGGAGT 60.604 57.895 0.00 0.00 36.00 3.85
2014 2922 2.671619 CGAGCCGCCTTTTTGGGA 60.672 61.111 0.00 0.00 36.00 4.37
2128 3042 7.283127 TCATGATTAAGTTCATCAGTTTAGCCC 59.717 37.037 5.97 0.00 34.09 5.19
2183 3098 6.254589 GCTCCGCATTTAGATATCTGTATGAC 59.745 42.308 22.92 16.03 0.00 3.06
2415 3330 6.720288 TCCAAAATGTATTCCCTCCGTAAAAA 59.280 34.615 0.00 0.00 0.00 1.94
2417 3332 5.817784 TCCAAAATGTATTCCCTCCGTAAA 58.182 37.500 0.00 0.00 0.00 2.01
2418 3333 5.438698 TCCAAAATGTATTCCCTCCGTAA 57.561 39.130 0.00 0.00 0.00 3.18
2421 3336 8.807948 ATATATTCCAAAATGTATTCCCTCCG 57.192 34.615 0.00 0.00 28.04 4.63
2450 3413 4.698201 TGTTGTTGAAGAGGTGATACCA 57.302 40.909 0.28 0.00 41.95 3.25
2455 3418 5.652014 ACAATTCTTGTTGTTGAAGAGGTGA 59.348 36.000 0.00 0.00 42.22 4.02
2484 3449 9.523755 GAGACCTTAGCTCAAGCATAACAATGC 62.524 44.444 4.59 2.12 45.16 3.56
2489 3454 4.759782 TGAGACCTTAGCTCAAGCATAAC 58.240 43.478 4.59 0.00 45.16 1.89
2582 3549 3.303132 GCTCACCACAGAAACAAGTTACG 60.303 47.826 0.00 0.00 0.00 3.18
2587 3554 0.954452 GGGCTCACCACAGAAACAAG 59.046 55.000 0.00 0.00 39.85 3.16
2705 3672 4.637534 AGCATTCGAGCAGATGTAAACATT 59.362 37.500 0.00 0.00 35.07 2.71
2906 3875 6.978080 GCTAAAGGATGAGTTCAGACTTCTAG 59.022 42.308 2.79 0.00 35.88 2.43
2961 3936 7.095439 GCCTACTGATATGAAAGAACTGCATAC 60.095 40.741 0.00 0.00 0.00 2.39
2986 3961 7.201470 GCCTTAGAAATTTGCAAACTATGAAGC 60.201 37.037 15.41 8.20 0.00 3.86
3125 4224 9.204337 TGAACCCATGAAAAAGATGATCATAAT 57.796 29.630 8.54 0.00 32.73 1.28
3131 4230 6.923199 AACTGAACCCATGAAAAAGATGAT 57.077 33.333 0.00 0.00 0.00 2.45
3145 4244 3.089284 CCACTAATGGGAAACTGAACCC 58.911 50.000 0.00 0.00 43.04 4.11
3363 4482 3.262151 GGGAGACTAAGTGAAGGAAGCTT 59.738 47.826 0.00 0.00 0.00 3.74
3373 4492 2.808919 TCAGGACAGGGAGACTAAGTG 58.191 52.381 0.00 0.00 0.00 3.16
3382 4501 4.597507 ACTTAGTTTCAATCAGGACAGGGA 59.402 41.667 0.00 0.00 0.00 4.20
3405 4527 3.623960 CGTGGAAATATTAAGTCGGCCAA 59.376 43.478 2.24 0.00 0.00 4.52
3408 4530 3.866910 TCACGTGGAAATATTAAGTCGGC 59.133 43.478 17.00 0.00 0.00 5.54
3485 4789 4.215827 GGGAATCATGTCAATGCAGATCTC 59.784 45.833 0.00 0.00 33.47 2.75
3507 4811 1.750193 ATCCACAACCGTAAGCATGG 58.250 50.000 0.00 0.00 36.82 3.66
3617 4924 7.227512 CCCTTATAGTTGCAGAACAATAGAAGG 59.772 40.741 9.11 9.11 41.27 3.46
3618 4925 7.987458 TCCCTTATAGTTGCAGAACAATAGAAG 59.013 37.037 0.00 0.00 41.27 2.85
3619 4926 7.857456 TCCCTTATAGTTGCAGAACAATAGAA 58.143 34.615 0.00 0.00 41.27 2.10
3621 4928 6.203723 GCTCCCTTATAGTTGCAGAACAATAG 59.796 42.308 0.00 0.00 41.27 1.73
3622 4929 6.055588 GCTCCCTTATAGTTGCAGAACAATA 58.944 40.000 0.00 0.00 41.27 1.90
3623 4930 4.884164 GCTCCCTTATAGTTGCAGAACAAT 59.116 41.667 0.00 0.00 41.27 2.71
3626 4933 4.143986 AGCTCCCTTATAGTTGCAGAAC 57.856 45.455 0.00 0.00 0.00 3.01
3631 4943 3.804063 GCCTGTAGCTCCCTTATAGTTGC 60.804 52.174 0.00 0.00 38.99 4.17
3752 5088 5.840149 TGGCAATGGCTATATTTTGAGGATT 59.160 36.000 8.59 0.00 40.87 3.01
3753 5089 5.396485 TGGCAATGGCTATATTTTGAGGAT 58.604 37.500 8.59 0.00 40.87 3.24
3754 5090 4.802307 TGGCAATGGCTATATTTTGAGGA 58.198 39.130 8.59 0.00 40.87 3.71
3755 5091 5.733620 ATGGCAATGGCTATATTTTGAGG 57.266 39.130 8.59 0.00 39.71 3.86
3756 5092 6.751157 TCAATGGCAATGGCTATATTTTGAG 58.249 36.000 8.59 0.00 40.74 3.02
3757 5093 6.728089 TCAATGGCAATGGCTATATTTTGA 57.272 33.333 8.59 5.33 40.74 2.69
3758 5094 9.661563 AATATCAATGGCAATGGCTATATTTTG 57.338 29.630 8.59 3.23 40.74 2.44
3759 5095 9.880157 GAATATCAATGGCAATGGCTATATTTT 57.120 29.630 8.59 0.00 40.74 1.82
3760 5096 9.263446 AGAATATCAATGGCAATGGCTATATTT 57.737 29.630 8.59 0.00 40.74 1.40
3836 5181 3.006537 AGGAGGATTTTTCTTCGACGTGA 59.993 43.478 0.00 0.00 0.00 4.35
3837 5182 3.326747 AGGAGGATTTTTCTTCGACGTG 58.673 45.455 0.00 0.00 0.00 4.49
3838 5183 3.258622 AGAGGAGGATTTTTCTTCGACGT 59.741 43.478 0.00 0.00 0.00 4.34
3924 5269 2.357517 CACGGAGGGAGTGTGTGC 60.358 66.667 0.00 0.00 35.08 4.57
3991 5337 4.161189 CACAAATCTAGAGGAAGGAGCTGA 59.839 45.833 0.00 0.00 0.00 4.26
4087 5433 5.711506 TGAGCAGAATTGTCATGGTATTGTT 59.288 36.000 0.00 0.00 0.00 2.83
4118 5464 4.789012 ATAAGAACTAACCGACCGAACA 57.211 40.909 0.00 0.00 0.00 3.18
4122 5468 3.550678 GCTGAATAAGAACTAACCGACCG 59.449 47.826 0.00 0.00 0.00 4.79
4144 5490 5.632959 TGTTTTTCCGTTTGTCTTACACAG 58.367 37.500 0.00 0.00 35.97 3.66
4156 5502 4.098807 ACACTTTGGCTATGTTTTTCCGTT 59.901 37.500 0.00 0.00 0.00 4.44
4158 5504 4.237349 ACACTTTGGCTATGTTTTTCCG 57.763 40.909 0.00 0.00 0.00 4.30
4159 5505 9.353999 CTATAAACACTTTGGCTATGTTTTTCC 57.646 33.333 5.72 0.00 42.43 3.13
4216 5563 2.227194 GAACCGTTGACCAAGGACATT 58.773 47.619 4.24 0.00 0.00 2.71
4227 5574 2.563620 TGCTACAGTATGGAACCGTTGA 59.436 45.455 0.00 0.00 43.62 3.18
4239 5586 2.950781 CCTGAGGGAGATGCTACAGTA 58.049 52.381 0.00 0.00 33.58 2.74
4257 5612 1.293062 ACAACAGCATGGAGATCCCT 58.707 50.000 0.00 0.00 43.62 4.20
4304 5659 2.874086 TCAATTATGCATGACGAGGCAG 59.126 45.455 10.16 0.00 43.30 4.85
4313 5668 4.278919 TGTGGCACCTATCAATTATGCATG 59.721 41.667 16.26 0.00 38.05 4.06
4314 5669 4.472496 TGTGGCACCTATCAATTATGCAT 58.528 39.130 16.26 3.79 38.05 3.96
4315 5670 3.884693 CTGTGGCACCTATCAATTATGCA 59.115 43.478 16.26 0.00 38.05 3.96
4316 5671 3.885297 ACTGTGGCACCTATCAATTATGC 59.115 43.478 16.26 0.00 35.51 3.14
4329 5684 1.064060 GTTGAGTTGTCACTGTGGCAC 59.936 52.381 15.64 11.55 28.02 5.01
4338 5693 5.029807 TGTAATCACAGGTTGAGTTGTCA 57.970 39.130 0.00 0.00 37.77 3.58
4390 5750 3.539431 TCTCAAACTCGAGAAGTCGTC 57.461 47.619 21.68 0.00 46.85 4.20


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

AutoCloner maintained by Alex Coulton.