Multiple sequence alignment - TraesCS6B01G316200

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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 TraesCS6B01G316200 chr6B 100.000 2735 0 0 1 2735 564145189 564142455 0.000000e+00 5051
1 TraesCS6B01G316200 chr6B 90.502 916 75 5 990 1893 530851990 530851075 0.000000e+00 1199
2 TraesCS6B01G316200 chr6B 90.066 916 79 3 990 1893 529890077 529890992 0.000000e+00 1177
3 TraesCS6B01G316200 chr6B 85.974 991 131 5 1 989 617653092 617654076 0.000000e+00 1053
4 TraesCS6B01G316200 chr6B 93.750 640 37 3 2096 2734 133195527 133196164 0.000000e+00 957
5 TraesCS6B01G316200 chr6D 90.830 916 72 6 990 1893 349031626 349032541 0.000000e+00 1216
6 TraesCS6B01G316200 chr6D 90.185 917 76 8 990 1893 348861563 348862478 0.000000e+00 1182
7 TraesCS6B01G316200 chr6D 89.301 916 85 4 990 1893 350083738 350082824 0.000000e+00 1136
8 TraesCS6B01G316200 chr6A 89.847 916 81 7 990 1893 495153875 495152960 0.000000e+00 1166
9 TraesCS6B01G316200 chr6A 89.629 916 83 3 990 1893 494047203 494048118 0.000000e+00 1155
10 TraesCS6B01G316200 chr6A 89.531 917 83 4 990 1893 494880434 494879518 0.000000e+00 1149
11 TraesCS6B01G316200 chr6A 88.974 916 89 3 990 1893 493842693 493843608 0.000000e+00 1122
12 TraesCS6B01G316200 chr6A 87.882 916 96 4 990 1893 493756513 493757425 0.000000e+00 1062
13 TraesCS6B01G316200 chr1D 87.891 991 107 10 1 989 175895639 175894660 0.000000e+00 1153
14 TraesCS6B01G316200 chr1D 93.760 641 35 4 2098 2735 303709143 303709781 0.000000e+00 957
15 TraesCS6B01G316200 chr1D 88.889 207 16 5 1895 2098 235664700 235664902 5.850000e-62 248
16 TraesCS6B01G316200 chr7D 87.374 990 122 3 1 989 457191555 457192542 0.000000e+00 1133
17 TraesCS6B01G316200 chr7D 93.906 640 33 4 2099 2735 569741593 569742229 0.000000e+00 961
18 TraesCS6B01G316200 chr7D 93.906 640 34 4 2099 2735 622675905 622676542 0.000000e+00 961
19 TraesCS6B01G316200 chr2D 87.172 990 116 9 1 989 637477772 637476793 0.000000e+00 1114
20 TraesCS6B01G316200 chr2D 93.944 644 33 5 2095 2734 108649100 108649741 0.000000e+00 968
21 TraesCS6B01G316200 chr2D 94.072 641 32 5 2099 2735 650099506 650100144 0.000000e+00 968
22 TraesCS6B01G316200 chr2D 90.104 192 16 3 1893 2082 411263325 411263515 2.100000e-61 246
23 TraesCS6B01G316200 chr5B 86.424 987 126 6 4 989 293415116 293414137 0.000000e+00 1074
24 TraesCS6B01G316200 chr5B 85.368 991 120 21 1 979 686313571 686314548 0.000000e+00 1003
25 TraesCS6B01G316200 chr1A 86.176 991 124 8 1 989 579430308 579431287 0.000000e+00 1059
26 TraesCS6B01G316200 chr7B 85.816 987 138 2 4 989 706739131 706738146 0.000000e+00 1046
27 TraesCS6B01G316200 chr7B 93.887 638 36 3 2099 2735 666408921 666408286 0.000000e+00 959
28 TraesCS6B01G316200 chr7B 83.412 639 83 14 1262 1882 693965769 693965136 3.060000e-159 571
29 TraesCS6B01G316200 chr3A 86.489 940 122 5 1 938 175800445 175801381 0.000000e+00 1027
30 TraesCS6B01G316200 chr3D 93.779 643 34 5 2097 2735 174930248 174930888 0.000000e+00 961
31 TraesCS6B01G316200 chr3D 93.519 648 36 4 2092 2735 278389718 278390363 0.000000e+00 959
32 TraesCS6B01G316200 chr3D 92.347 196 13 2 1895 2088 230799671 230799476 7.460000e-71 278
33 TraesCS6B01G316200 chr3D 90.050 201 13 6 1895 2091 601932218 601932021 1.260000e-63 254
34 TraesCS6B01G316200 chr2A 84.477 889 124 3 101 989 428159370 428160244 0.000000e+00 865
35 TraesCS6B01G316200 chr4D 90.355 197 18 1 1895 2090 85826464 85826268 9.720000e-65 257
36 TraesCS6B01G316200 chr4D 88.038 209 20 5 1894 2099 261589156 261589362 2.720000e-60 243
37 TraesCS6B01G316200 chr3B 89.950 199 18 2 1894 2090 765737154 765737352 3.490000e-64 255
38 TraesCS6B01G316200 chr2B 89.447 199 19 2 1895 2092 47359158 47358961 1.630000e-62 250
39 TraesCS6B01G316200 chr5D 88.406 207 23 1 1895 2101 254632966 254633171 5.850000e-62 248


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 TraesCS6B01G316200 chr6B 564142455 564145189 2734 True 5051 5051 100.000 1 2735 1 chr6B.!!$R2 2734
1 TraesCS6B01G316200 chr6B 530851075 530851990 915 True 1199 1199 90.502 990 1893 1 chr6B.!!$R1 903
2 TraesCS6B01G316200 chr6B 529890077 529890992 915 False 1177 1177 90.066 990 1893 1 chr6B.!!$F2 903
3 TraesCS6B01G316200 chr6B 617653092 617654076 984 False 1053 1053 85.974 1 989 1 chr6B.!!$F3 988
4 TraesCS6B01G316200 chr6B 133195527 133196164 637 False 957 957 93.750 2096 2734 1 chr6B.!!$F1 638
5 TraesCS6B01G316200 chr6D 349031626 349032541 915 False 1216 1216 90.830 990 1893 1 chr6D.!!$F2 903
6 TraesCS6B01G316200 chr6D 348861563 348862478 915 False 1182 1182 90.185 990 1893 1 chr6D.!!$F1 903
7 TraesCS6B01G316200 chr6D 350082824 350083738 914 True 1136 1136 89.301 990 1893 1 chr6D.!!$R1 903
8 TraesCS6B01G316200 chr6A 495152960 495153875 915 True 1166 1166 89.847 990 1893 1 chr6A.!!$R2 903
9 TraesCS6B01G316200 chr6A 494047203 494048118 915 False 1155 1155 89.629 990 1893 1 chr6A.!!$F3 903
10 TraesCS6B01G316200 chr6A 494879518 494880434 916 True 1149 1149 89.531 990 1893 1 chr6A.!!$R1 903
11 TraesCS6B01G316200 chr6A 493842693 493843608 915 False 1122 1122 88.974 990 1893 1 chr6A.!!$F2 903
12 TraesCS6B01G316200 chr6A 493756513 493757425 912 False 1062 1062 87.882 990 1893 1 chr6A.!!$F1 903
13 TraesCS6B01G316200 chr1D 175894660 175895639 979 True 1153 1153 87.891 1 989 1 chr1D.!!$R1 988
14 TraesCS6B01G316200 chr1D 303709143 303709781 638 False 957 957 93.760 2098 2735 1 chr1D.!!$F2 637
15 TraesCS6B01G316200 chr7D 457191555 457192542 987 False 1133 1133 87.374 1 989 1 chr7D.!!$F1 988
16 TraesCS6B01G316200 chr7D 569741593 569742229 636 False 961 961 93.906 2099 2735 1 chr7D.!!$F2 636
17 TraesCS6B01G316200 chr7D 622675905 622676542 637 False 961 961 93.906 2099 2735 1 chr7D.!!$F3 636
18 TraesCS6B01G316200 chr2D 637476793 637477772 979 True 1114 1114 87.172 1 989 1 chr2D.!!$R1 988
19 TraesCS6B01G316200 chr2D 108649100 108649741 641 False 968 968 93.944 2095 2734 1 chr2D.!!$F1 639
20 TraesCS6B01G316200 chr2D 650099506 650100144 638 False 968 968 94.072 2099 2735 1 chr2D.!!$F3 636
21 TraesCS6B01G316200 chr5B 293414137 293415116 979 True 1074 1074 86.424 4 989 1 chr5B.!!$R1 985
22 TraesCS6B01G316200 chr5B 686313571 686314548 977 False 1003 1003 85.368 1 979 1 chr5B.!!$F1 978
23 TraesCS6B01G316200 chr1A 579430308 579431287 979 False 1059 1059 86.176 1 989 1 chr1A.!!$F1 988
24 TraesCS6B01G316200 chr7B 706738146 706739131 985 True 1046 1046 85.816 4 989 1 chr7B.!!$R3 985
25 TraesCS6B01G316200 chr7B 666408286 666408921 635 True 959 959 93.887 2099 2735 1 chr7B.!!$R1 636
26 TraesCS6B01G316200 chr7B 693965136 693965769 633 True 571 571 83.412 1262 1882 1 chr7B.!!$R2 620
27 TraesCS6B01G316200 chr3A 175800445 175801381 936 False 1027 1027 86.489 1 938 1 chr3A.!!$F1 937
28 TraesCS6B01G316200 chr3D 174930248 174930888 640 False 961 961 93.779 2097 2735 1 chr3D.!!$F1 638
29 TraesCS6B01G316200 chr3D 278389718 278390363 645 False 959 959 93.519 2092 2735 1 chr3D.!!$F2 643
30 TraesCS6B01G316200 chr2A 428159370 428160244 874 False 865 865 84.477 101 989 1 chr2A.!!$F1 888

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
574 576 0.036388 ATGACAATGTCTCCGCGGTT 60.036 50.0 27.15 8.84 33.15 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 1973 0.045008 TAGGAGGTGGGCCCAATACA 59.955 55.0 30.64 7.04 34.66 2.29 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
20 21 1.195115 ATGCCTACGAGCTTCTGGAA 58.805 50.000 0.00 0.00 0.00 3.53
57 59 4.093952 CAAGCCTGCTTCCACGCG 62.094 66.667 3.53 3.53 33.42 6.01
123 125 2.169330 GTCCGACACTCCTTTCTACCT 58.831 52.381 0.00 0.00 0.00 3.08
140 142 2.889512 ACCTATCCATCATCGGTGCTA 58.110 47.619 0.00 0.00 29.11 3.49
161 163 1.977056 TCAGTACCTCACACTGACGT 58.023 50.000 1.17 0.00 45.68 4.34
232 234 1.003839 TCGTGACACTCATTGGGCC 60.004 57.895 3.68 0.00 0.00 5.80
233 235 1.003355 CGTGACACTCATTGGGCCT 60.003 57.895 4.53 0.00 0.00 5.19
301 303 1.454479 CACCCTGATGGCATCACCC 60.454 63.158 25.63 1.15 37.83 4.61
306 308 0.812811 CTGATGGCATCACCCGACAG 60.813 60.000 25.63 10.84 37.83 3.51
316 318 4.379243 CCCGACAGCAGCCTCGTT 62.379 66.667 8.82 0.00 0.00 3.85
318 320 3.114616 CGACAGCAGCCTCGTTGG 61.115 66.667 2.44 0.00 39.35 3.77
331 333 2.572284 GTTGGCTACTCCGACGCT 59.428 61.111 0.00 0.00 39.36 5.07
361 363 2.889617 TGTCCCGACACTATGCGG 59.110 61.111 0.00 0.00 46.80 5.69
463 465 2.005960 GCGCCGAGGATGAGTACAGT 62.006 60.000 0.00 0.00 0.00 3.55
544 546 2.081787 TGAGGTTCCCAAGGCCACA 61.082 57.895 5.01 0.00 0.00 4.17
548 550 0.111639 GGTTCCCAAGGCCACACTTA 59.888 55.000 5.01 0.00 0.00 2.24
574 576 0.036388 ATGACAATGTCTCCGCGGTT 60.036 50.000 27.15 8.84 33.15 4.44
592 594 0.183014 TTTACCTCGTTGCCAACCCA 59.817 50.000 1.21 0.00 0.00 4.51
604 606 0.250727 CCAACCCAGTTCATCACCGT 60.251 55.000 0.00 0.00 0.00 4.83
615 617 3.352338 ATCACCGTCGGACGAAGCC 62.352 63.158 30.33 0.00 46.05 4.35
626 628 1.137086 GGACGAAGCCTATTGAGCTCA 59.863 52.381 13.74 13.74 40.49 4.26
652 654 0.463116 ACTTTGTTCGGGAGCACGTT 60.463 50.000 0.00 0.00 34.94 3.99
702 711 1.079819 CCACCGATCAGCAGTTCGT 60.080 57.895 8.50 0.00 35.69 3.85
705 714 1.874019 CCGATCAGCAGTTCGTCGG 60.874 63.158 8.50 0.00 44.72 4.79
783 792 2.347630 TCACCGGTGACACTTCGAT 58.652 52.632 33.23 0.00 34.14 3.59
794 803 2.627945 ACACTTCGATTGTGTGTGTGT 58.372 42.857 19.44 7.64 45.57 3.72
798 807 2.017138 TCGATTGTGTGTGTGTGTGT 57.983 45.000 0.00 0.00 0.00 3.72
973 998 5.466393 ACGATCAATGAAATATCGATGCACA 59.534 36.000 8.54 3.66 43.96 4.57
974 999 5.787062 CGATCAATGAAATATCGATGCACAC 59.213 40.000 8.54 0.00 43.96 3.82
1016 1041 0.684479 CACCATCCTCGTCTCCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
1084 1109 2.358247 ACGACCATGGTGGCGTTC 60.358 61.111 25.52 5.40 43.79 3.95
1085 1110 3.124921 CGACCATGGTGGCGTTCC 61.125 66.667 25.52 4.57 42.67 3.62
1144 1170 2.587247 GGGGCTGAGCTCACAGACA 61.587 63.158 13.74 0.00 46.67 3.41
1168 1194 1.005924 CCTTTCATGGGGCTGTACCTT 59.994 52.381 0.00 0.00 39.10 3.50
1209 1235 3.121030 GCGGTCATCGTTGCTGCT 61.121 61.111 0.00 0.00 41.72 4.24
1217 1243 0.602638 ATCGTTGCTGCTGTTCGGAA 60.603 50.000 0.00 0.00 0.00 4.30
1219 1245 1.771073 CGTTGCTGCTGTTCGGAACA 61.771 55.000 21.30 21.30 39.52 3.18
1234 1260 1.402984 GGAACAGAGCAGTTCGACGAT 60.403 52.381 0.00 0.00 46.81 3.73
1315 1341 2.049627 GCTTCGGCCCCATCATCTCT 62.050 60.000 0.00 0.00 34.32 3.10
1373 1399 4.838152 GCCTCGGCTTCGGCATCA 62.838 66.667 0.00 0.00 45.59 3.07
1435 1470 2.100631 GTACAAGCGTCGCATGCCT 61.101 57.895 21.32 6.58 29.81 4.75
1472 1507 2.435059 GCCTCTGCCAAGTCGTCC 60.435 66.667 0.00 0.00 0.00 4.79
1473 1508 2.948720 GCCTCTGCCAAGTCGTCCT 61.949 63.158 0.00 0.00 0.00 3.85
1493 1530 2.125552 CCGCGTGCAAGGATCAGA 60.126 61.111 4.92 0.00 0.00 3.27
1505 1542 0.615331 GGATCAGAGTCAAGGTGCCA 59.385 55.000 0.00 0.00 0.00 4.92
1509 1546 2.149383 AGAGTCAAGGTGCCAGCCA 61.149 57.895 0.00 0.00 0.00 4.75
1513 1550 1.531365 TCAAGGTGCCAGCCAAAGG 60.531 57.895 0.00 0.00 0.00 3.11
1553 1596 0.732880 ACAACAAGATCGACTCGCCG 60.733 55.000 0.00 0.00 0.00 6.46
1576 1619 0.888736 CCCAAGATCGTGCACACCAA 60.889 55.000 18.64 0.00 0.00 3.67
1577 1620 1.167851 CCAAGATCGTGCACACCAAT 58.832 50.000 18.64 4.16 0.00 3.16
1601 1644 0.756294 TCAAGTTCCTCGACAAGGCA 59.244 50.000 0.00 0.00 45.78 4.75
1602 1645 1.140052 TCAAGTTCCTCGACAAGGCAA 59.860 47.619 0.00 0.00 45.78 4.52
1608 1651 0.321564 CCTCGACAAGGCAACCATCA 60.322 55.000 0.00 0.00 38.67 3.07
1616 1659 0.548031 AGGCAACCATCATCACGGAT 59.452 50.000 0.00 0.00 37.17 4.18
1620 1663 2.223340 GCAACCATCATCACGGATTCAC 60.223 50.000 0.00 0.00 0.00 3.18
1666 1709 1.220206 CCTCGTGGAAGCTCTGCAT 59.780 57.895 0.00 0.00 34.57 3.96
1667 1710 0.392193 CCTCGTGGAAGCTCTGCATT 60.392 55.000 0.00 0.00 34.57 3.56
1670 1713 0.877071 CGTGGAAGCTCTGCATTGTT 59.123 50.000 0.00 0.00 0.00 2.83
1750 1801 1.215382 CGTGTCATCGGCCTTCTCA 59.785 57.895 0.00 0.00 0.00 3.27
1753 1804 0.904649 TGTCATCGGCCTTCTCACAT 59.095 50.000 0.00 0.00 0.00 3.21
1765 1816 4.578871 CCTTCTCACATATGAACACCACA 58.421 43.478 10.38 0.00 33.30 4.17
1805 1856 1.684983 CCATGGAAATGACCATCCTGC 59.315 52.381 5.56 0.00 46.24 4.85
1893 1944 2.299013 TCTACAACAAGGTGATCGTGCT 59.701 45.455 0.00 0.00 0.00 4.40
1894 1945 1.967319 ACAACAAGGTGATCGTGCTT 58.033 45.000 0.00 0.00 0.00 3.91
1895 1946 1.603802 ACAACAAGGTGATCGTGCTTG 59.396 47.619 0.00 0.00 0.00 4.01
1896 1947 1.603802 CAACAAGGTGATCGTGCTTGT 59.396 47.619 0.00 0.00 39.55 3.16
1897 1948 1.967319 ACAAGGTGATCGTGCTTGTT 58.033 45.000 0.00 0.00 35.05 2.83
1898 1949 1.603802 ACAAGGTGATCGTGCTTGTTG 59.396 47.619 0.00 0.00 35.05 3.33
1899 1950 1.872952 CAAGGTGATCGTGCTTGTTGA 59.127 47.619 0.00 0.00 0.00 3.18
1900 1951 1.800805 AGGTGATCGTGCTTGTTGAG 58.199 50.000 0.00 0.00 0.00 3.02
1901 1952 1.070758 AGGTGATCGTGCTTGTTGAGT 59.929 47.619 0.00 0.00 0.00 3.41
1902 1953 2.299013 AGGTGATCGTGCTTGTTGAGTA 59.701 45.455 0.00 0.00 0.00 2.59
1903 1954 3.055819 AGGTGATCGTGCTTGTTGAGTAT 60.056 43.478 0.00 0.00 0.00 2.12
1904 1955 4.159693 AGGTGATCGTGCTTGTTGAGTATA 59.840 41.667 0.00 0.00 0.00 1.47
1905 1956 5.050490 GGTGATCGTGCTTGTTGAGTATAT 58.950 41.667 0.00 0.00 0.00 0.86
1906 1957 5.050769 GGTGATCGTGCTTGTTGAGTATATG 60.051 44.000 0.00 0.00 0.00 1.78
1907 1958 5.520288 GTGATCGTGCTTGTTGAGTATATGT 59.480 40.000 0.00 0.00 0.00 2.29
1908 1959 5.519927 TGATCGTGCTTGTTGAGTATATGTG 59.480 40.000 0.00 0.00 0.00 3.21
1909 1960 4.816392 TCGTGCTTGTTGAGTATATGTGT 58.184 39.130 0.00 0.00 0.00 3.72
1910 1961 5.234752 TCGTGCTTGTTGAGTATATGTGTT 58.765 37.500 0.00 0.00 0.00 3.32
1911 1962 6.391537 TCGTGCTTGTTGAGTATATGTGTTA 58.608 36.000 0.00 0.00 0.00 2.41
1912 1963 7.039270 TCGTGCTTGTTGAGTATATGTGTTAT 58.961 34.615 0.00 0.00 0.00 1.89
1913 1964 7.010091 TCGTGCTTGTTGAGTATATGTGTTATG 59.990 37.037 0.00 0.00 0.00 1.90
1914 1965 6.907212 GTGCTTGTTGAGTATATGTGTTATGC 59.093 38.462 0.00 0.00 0.00 3.14
1915 1966 6.597280 TGCTTGTTGAGTATATGTGTTATGCA 59.403 34.615 0.00 0.00 0.00 3.96
1916 1967 7.282901 TGCTTGTTGAGTATATGTGTTATGCAT 59.717 33.333 3.79 3.79 0.00 3.96
1917 1968 8.773645 GCTTGTTGAGTATATGTGTTATGCATA 58.226 33.333 1.16 1.16 33.91 3.14
1923 1974 9.643693 TGAGTATATGTGTTATGCATATCTGTG 57.356 33.333 7.36 0.00 39.44 3.66
1924 1975 9.645059 GAGTATATGTGTTATGCATATCTGTGT 57.355 33.333 7.36 0.00 39.44 3.72
1929 1980 7.495135 TGTGTTATGCATATCTGTGTATTGG 57.505 36.000 7.36 0.00 0.00 3.16
1930 1981 6.486320 TGTGTTATGCATATCTGTGTATTGGG 59.514 38.462 7.36 0.00 0.00 4.12
1931 1982 5.473162 TGTTATGCATATCTGTGTATTGGGC 59.527 40.000 7.36 0.00 0.00 5.36
1932 1983 2.862541 TGCATATCTGTGTATTGGGCC 58.137 47.619 0.00 0.00 0.00 5.80
1933 1984 2.162681 GCATATCTGTGTATTGGGCCC 58.837 52.381 17.59 17.59 0.00 5.80
1934 1985 2.488891 GCATATCTGTGTATTGGGCCCA 60.489 50.000 24.45 24.45 0.00 5.36
1935 1986 3.149196 CATATCTGTGTATTGGGCCCAC 58.851 50.000 28.70 14.93 0.00 4.61
1936 1987 0.258774 ATCTGTGTATTGGGCCCACC 59.741 55.000 28.70 16.48 40.81 4.61
1937 1988 0.844661 TCTGTGTATTGGGCCCACCT 60.845 55.000 28.70 18.23 41.11 4.00
1938 1989 0.394352 CTGTGTATTGGGCCCACCTC 60.394 60.000 28.70 17.85 41.11 3.85
1939 1990 1.076995 GTGTATTGGGCCCACCTCC 60.077 63.158 28.70 13.64 41.11 4.30
1940 1991 1.230149 TGTATTGGGCCCACCTCCT 60.230 57.895 28.70 9.67 41.11 3.69
1941 1992 0.045008 TGTATTGGGCCCACCTCCTA 59.955 55.000 28.70 9.60 41.11 2.94
1942 1993 0.765510 GTATTGGGCCCACCTCCTAG 59.234 60.000 28.70 0.00 41.11 3.02
1943 1994 0.345502 TATTGGGCCCACCTCCTAGT 59.654 55.000 28.70 0.00 41.11 2.57
1944 1995 0.552615 ATTGGGCCCACCTCCTAGTT 60.553 55.000 28.70 0.00 41.11 2.24
1945 1996 1.205460 TTGGGCCCACCTCCTAGTTC 61.205 60.000 28.70 0.00 41.11 3.01
1946 1997 2.376165 GGGCCCACCTCCTAGTTCC 61.376 68.421 19.95 0.00 35.85 3.62
1947 1998 1.307084 GGCCCACCTCCTAGTTCCT 60.307 63.158 0.00 0.00 0.00 3.36
1948 1999 0.914902 GGCCCACCTCCTAGTTCCTT 60.915 60.000 0.00 0.00 0.00 3.36
1949 2000 0.253327 GCCCACCTCCTAGTTCCTTG 59.747 60.000 0.00 0.00 0.00 3.61
1950 2001 1.657804 CCCACCTCCTAGTTCCTTGT 58.342 55.000 0.00 0.00 0.00 3.16
1951 2002 2.829023 CCCACCTCCTAGTTCCTTGTA 58.171 52.381 0.00 0.00 0.00 2.41
1952 2003 3.385115 CCCACCTCCTAGTTCCTTGTAT 58.615 50.000 0.00 0.00 0.00 2.29
1953 2004 4.553678 CCCACCTCCTAGTTCCTTGTATA 58.446 47.826 0.00 0.00 0.00 1.47
1954 2005 4.589374 CCCACCTCCTAGTTCCTTGTATAG 59.411 50.000 0.00 0.00 0.00 1.31
1955 2006 5.209659 CCACCTCCTAGTTCCTTGTATAGT 58.790 45.833 0.00 0.00 0.00 2.12
1956 2007 5.661759 CCACCTCCTAGTTCCTTGTATAGTT 59.338 44.000 0.00 0.00 0.00 2.24
1957 2008 6.837568 CCACCTCCTAGTTCCTTGTATAGTTA 59.162 42.308 0.00 0.00 0.00 2.24
1958 2009 7.343833 CCACCTCCTAGTTCCTTGTATAGTTAA 59.656 40.741 0.00 0.00 0.00 2.01
1959 2010 8.414778 CACCTCCTAGTTCCTTGTATAGTTAAG 58.585 40.741 0.00 0.00 0.00 1.85
1960 2011 7.564292 ACCTCCTAGTTCCTTGTATAGTTAAGG 59.436 40.741 0.00 0.00 43.83 2.69
1961 2012 7.564292 CCTCCTAGTTCCTTGTATAGTTAAGGT 59.436 40.741 0.00 0.00 43.14 3.50
1962 2013 8.530804 TCCTAGTTCCTTGTATAGTTAAGGTC 57.469 38.462 0.00 0.00 43.14 3.85
1963 2014 7.284034 TCCTAGTTCCTTGTATAGTTAAGGTCG 59.716 40.741 0.00 0.00 43.14 4.79
1964 2015 6.847421 AGTTCCTTGTATAGTTAAGGTCGT 57.153 37.500 0.00 0.00 43.14 4.34
1965 2016 6.628185 AGTTCCTTGTATAGTTAAGGTCGTG 58.372 40.000 0.00 0.00 43.14 4.35
1966 2017 5.587388 TCCTTGTATAGTTAAGGTCGTGG 57.413 43.478 0.00 0.00 43.14 4.94
1967 2018 4.117685 CCTTGTATAGTTAAGGTCGTGGC 58.882 47.826 0.00 0.00 38.87 5.01
1968 2019 3.806625 TGTATAGTTAAGGTCGTGGCC 57.193 47.619 0.00 0.00 0.00 5.36
1969 2020 2.431782 TGTATAGTTAAGGTCGTGGCCC 59.568 50.000 0.00 0.00 0.00 5.80
1970 2021 1.575419 ATAGTTAAGGTCGTGGCCCA 58.425 50.000 0.00 0.00 0.00 5.36
1971 2022 0.609662 TAGTTAAGGTCGTGGCCCAC 59.390 55.000 2.98 2.98 0.00 4.61
1972 2023 1.673337 GTTAAGGTCGTGGCCCACC 60.673 63.158 8.62 3.51 0.00 4.61
1973 2024 1.844289 TTAAGGTCGTGGCCCACCT 60.844 57.895 8.62 11.56 45.59 4.00
1974 2025 1.833787 TTAAGGTCGTGGCCCACCTC 61.834 60.000 16.51 1.15 42.61 3.85
1975 2026 2.741878 TAAGGTCGTGGCCCACCTCT 62.742 60.000 16.51 10.46 42.61 3.69
1976 2027 3.637273 GGTCGTGGCCCACCTCTT 61.637 66.667 8.62 0.00 36.63 2.85
1977 2028 2.358737 GTCGTGGCCCACCTCTTG 60.359 66.667 8.62 0.00 36.63 3.02
1978 2029 2.847234 TCGTGGCCCACCTCTTGT 60.847 61.111 8.62 0.00 36.63 3.16
1979 2030 1.534476 TCGTGGCCCACCTCTTGTA 60.534 57.895 8.62 0.00 36.63 2.41
1980 2031 1.375523 CGTGGCCCACCTCTTGTAC 60.376 63.158 8.62 0.00 36.63 2.90
1981 2032 1.758592 GTGGCCCACCTCTTGTACA 59.241 57.895 1.17 0.00 36.63 2.90
1982 2033 0.328258 GTGGCCCACCTCTTGTACAT 59.672 55.000 1.17 0.00 36.63 2.29
1983 2034 0.618458 TGGCCCACCTCTTGTACATC 59.382 55.000 0.00 0.00 36.63 3.06
1984 2035 0.618458 GGCCCACCTCTTGTACATCA 59.382 55.000 0.00 0.00 0.00 3.07
1985 2036 1.212935 GGCCCACCTCTTGTACATCAT 59.787 52.381 0.00 0.00 0.00 2.45
1986 2037 2.438021 GGCCCACCTCTTGTACATCATA 59.562 50.000 0.00 0.00 0.00 2.15
1987 2038 3.073062 GGCCCACCTCTTGTACATCATAT 59.927 47.826 0.00 0.00 0.00 1.78
1988 2039 4.286032 GGCCCACCTCTTGTACATCATATA 59.714 45.833 0.00 0.00 0.00 0.86
1989 2040 5.045578 GGCCCACCTCTTGTACATCATATAT 60.046 44.000 0.00 0.00 0.00 0.86
1990 2041 6.156256 GGCCCACCTCTTGTACATCATATATA 59.844 42.308 0.00 0.00 0.00 0.86
1991 2042 7.147479 GGCCCACCTCTTGTACATCATATATAT 60.147 40.741 0.00 0.00 0.00 0.86
1992 2043 7.712639 GCCCACCTCTTGTACATCATATATATG 59.287 40.741 15.47 15.47 35.04 1.78
1993 2044 8.762645 CCCACCTCTTGTACATCATATATATGT 58.237 37.037 19.78 8.43 40.57 2.29
1994 2045 9.591792 CCACCTCTTGTACATCATATATATGTG 57.408 37.037 19.78 18.15 38.05 3.21
1995 2046 9.091784 CACCTCTTGTACATCATATATATGTGC 57.908 37.037 19.78 9.72 38.05 4.57
1996 2047 8.260818 ACCTCTTGTACATCATATATATGTGCC 58.739 37.037 19.78 12.47 38.66 5.01
1997 2048 8.481314 CCTCTTGTACATCATATATATGTGCCT 58.519 37.037 19.78 7.67 38.66 4.75
1998 2049 9.881649 CTCTTGTACATCATATATATGTGCCTT 57.118 33.333 19.78 6.50 38.66 4.35
2001 2052 8.267620 TGTACATCATATATATGTGCCTTTGC 57.732 34.615 19.78 8.00 38.66 3.68
2002 2053 7.882271 TGTACATCATATATATGTGCCTTTGCA 59.118 33.333 19.78 9.82 38.66 4.08
2010 2061 4.177673 TGCCTTTGCACATGAGCA 57.822 50.000 14.17 14.17 44.23 4.26
2020 2071 4.099380 TGCACATGAGCAATACAACATG 57.901 40.909 15.81 0.00 42.46 3.21
2021 2072 2.855963 GCACATGAGCAATACAACATGC 59.144 45.455 10.48 0.00 42.28 4.06
2022 2073 3.673866 GCACATGAGCAATACAACATGCA 60.674 43.478 10.48 0.00 44.95 3.96
2023 2074 4.487019 CACATGAGCAATACAACATGCAA 58.513 39.130 0.00 0.00 44.95 4.08
2024 2075 5.106442 CACATGAGCAATACAACATGCAAT 58.894 37.500 0.00 0.00 44.95 3.56
2025 2076 5.579119 CACATGAGCAATACAACATGCAATT 59.421 36.000 0.00 0.00 44.95 2.32
2026 2077 5.808540 ACATGAGCAATACAACATGCAATTC 59.191 36.000 0.00 0.00 44.95 2.17
2027 2078 5.388408 TGAGCAATACAACATGCAATTCA 57.612 34.783 0.00 0.00 44.95 2.57
2028 2079 5.162794 TGAGCAATACAACATGCAATTCAC 58.837 37.500 0.00 0.00 44.95 3.18
2029 2080 5.136816 AGCAATACAACATGCAATTCACA 57.863 34.783 0.00 0.00 44.95 3.58
2030 2081 5.726397 AGCAATACAACATGCAATTCACAT 58.274 33.333 0.00 0.00 44.95 3.21
2031 2082 6.865411 AGCAATACAACATGCAATTCACATA 58.135 32.000 0.00 0.00 44.95 2.29
2032 2083 7.494211 AGCAATACAACATGCAATTCACATAT 58.506 30.769 0.00 0.00 44.95 1.78
2033 2084 7.982919 AGCAATACAACATGCAATTCACATATT 59.017 29.630 0.00 0.00 44.95 1.28
2034 2085 8.270799 GCAATACAACATGCAATTCACATATTC 58.729 33.333 0.00 0.00 42.12 1.75
2035 2086 9.524106 CAATACAACATGCAATTCACATATTCT 57.476 29.630 0.00 0.00 0.00 2.40
2038 2089 8.054152 ACAACATGCAATTCACATATTCTACA 57.946 30.769 0.00 0.00 0.00 2.74
2039 2090 8.689061 ACAACATGCAATTCACATATTCTACAT 58.311 29.630 0.00 0.00 0.00 2.29
2040 2091 8.964150 CAACATGCAATTCACATATTCTACATG 58.036 33.333 0.00 0.00 37.70 3.21
2041 2092 7.654568 ACATGCAATTCACATATTCTACATGG 58.345 34.615 0.00 0.00 36.40 3.66
2042 2093 7.286087 ACATGCAATTCACATATTCTACATGGT 59.714 33.333 0.00 0.00 36.40 3.55
2043 2094 8.785946 CATGCAATTCACATATTCTACATGGTA 58.214 33.333 0.00 0.00 0.00 3.25
2044 2095 8.922931 TGCAATTCACATATTCTACATGGTAT 57.077 30.769 0.00 0.00 0.00 2.73
2045 2096 9.002600 TGCAATTCACATATTCTACATGGTATC 57.997 33.333 0.00 0.00 0.00 2.24
2046 2097 9.002600 GCAATTCACATATTCTACATGGTATCA 57.997 33.333 0.00 0.00 0.00 2.15
2051 2102 9.764363 TCACATATTCTACATGGTATCAGTTTC 57.236 33.333 0.00 0.00 0.00 2.78
2052 2103 8.993121 CACATATTCTACATGGTATCAGTTTCC 58.007 37.037 0.00 0.00 0.00 3.13
2053 2104 7.872993 ACATATTCTACATGGTATCAGTTTCCG 59.127 37.037 0.00 0.00 0.00 4.30
2054 2105 4.665833 TCTACATGGTATCAGTTTCCGG 57.334 45.455 0.00 0.00 0.00 5.14
2055 2106 2.710096 ACATGGTATCAGTTTCCGGG 57.290 50.000 0.00 0.00 0.00 5.73
2056 2107 1.913419 ACATGGTATCAGTTTCCGGGT 59.087 47.619 0.00 0.00 0.00 5.28
2057 2108 2.307686 ACATGGTATCAGTTTCCGGGTT 59.692 45.455 0.00 0.00 0.00 4.11
2058 2109 2.773993 TGGTATCAGTTTCCGGGTTC 57.226 50.000 0.00 0.00 0.00 3.62
2059 2110 2.262637 TGGTATCAGTTTCCGGGTTCT 58.737 47.619 0.00 0.00 0.00 3.01
2060 2111 3.443052 TGGTATCAGTTTCCGGGTTCTA 58.557 45.455 0.00 0.00 0.00 2.10
2061 2112 3.839490 TGGTATCAGTTTCCGGGTTCTAA 59.161 43.478 0.00 0.00 0.00 2.10
2062 2113 4.186926 GGTATCAGTTTCCGGGTTCTAAC 58.813 47.826 0.00 0.00 0.00 2.34
2075 2126 3.005554 GGTTCTAACCCTAGTTTTCGCC 58.994 50.000 0.02 0.00 43.43 5.54
2076 2127 2.660189 TCTAACCCTAGTTTTCGCCG 57.340 50.000 0.00 0.00 37.42 6.46
2077 2128 1.004595 CTAACCCTAGTTTTCGCCGC 58.995 55.000 0.00 0.00 37.42 6.53
2078 2129 0.609662 TAACCCTAGTTTTCGCCGCT 59.390 50.000 0.00 0.00 37.42 5.52
2079 2130 0.953960 AACCCTAGTTTTCGCCGCTG 60.954 55.000 0.00 0.00 29.61 5.18
2080 2131 2.750888 CCCTAGTTTTCGCCGCTGC 61.751 63.158 0.00 0.00 0.00 5.25
2081 2132 2.750888 CCTAGTTTTCGCCGCTGCC 61.751 63.158 0.00 0.00 0.00 4.85
2082 2133 3.083600 CTAGTTTTCGCCGCTGCCG 62.084 63.158 0.00 0.00 0.00 5.69
2195 2248 4.822350 TGACGATAATTGTGACAAAACCCA 59.178 37.500 0.62 0.00 0.00 4.51
2239 2292 5.586643 GGGCTCCTACTTCTATGACAAAAAG 59.413 44.000 0.00 0.00 0.00 2.27
2356 2409 3.586100 GCAAGGGCGAGGAAAATTTTA 57.414 42.857 2.75 0.00 0.00 1.52
2415 2468 1.132199 ATGCGCGTTTCTCTCGTACG 61.132 55.000 9.53 9.53 38.26 3.67
2441 2494 2.731721 CGTGTGTGCGAGGCGTTA 60.732 61.111 0.00 0.00 0.00 3.18
2579 2632 2.594541 CGATTCCTTCGCTACTGCC 58.405 57.895 0.00 0.00 41.69 4.85
2618 2671 0.540454 TGCTGCCTCTCTGGATGAAG 59.460 55.000 0.00 0.00 38.35 3.02
2626 2679 2.759535 CTCTCTGGATGAAGAGTGAGCA 59.240 50.000 1.44 0.00 43.57 4.26
2633 2686 0.035317 TGAAGAGTGAGCATTGCGGT 59.965 50.000 2.38 0.00 0.00 5.68
2640 2695 2.676471 AGCATTGCGGTGGGGTTC 60.676 61.111 2.38 0.00 0.00 3.62
2680 2736 1.280457 GAGTGGATGAACAGGACCCT 58.720 55.000 0.00 0.00 0.00 4.34
2695 2751 2.270986 CCCTTGGTGTTGCCTCTGC 61.271 63.158 0.00 0.00 38.35 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.956633 CAATAAGCATGCCGGCTCAT 59.043 50.000 29.70 11.29 45.07 2.90
57 59 1.337821 CTTAGCCTTCGTGTCGACAC 58.662 55.000 33.76 33.76 43.15 3.67
115 117 4.262463 GCACCGATGATGGATAGGTAGAAA 60.262 45.833 0.00 0.00 37.95 2.52
123 125 4.528206 ACTGAATAGCACCGATGATGGATA 59.472 41.667 0.00 0.00 0.00 2.59
232 234 5.880054 ACCGAAGAATACATTTCACCAAG 57.120 39.130 0.00 0.00 0.00 3.61
301 303 3.114616 CCAACGAGGCTGCTGTCG 61.115 66.667 18.79 18.79 42.04 4.35
316 318 0.679002 AGTTAGCGTCGGAGTAGCCA 60.679 55.000 0.00 0.00 35.94 4.75
318 320 0.248539 CCAGTTAGCGTCGGAGTAGC 60.249 60.000 0.00 0.00 0.00 3.58
331 333 2.228480 GGGACACCCAGCCCAGTTA 61.228 63.158 1.54 0.00 44.65 2.24
361 363 0.248539 CGCAGTAGCCGGAAGTAGAC 60.249 60.000 5.05 0.00 37.52 2.59
453 455 2.536066 TGGCCACAGTACTGTACTCAT 58.464 47.619 27.48 6.48 42.83 2.90
496 498 3.890147 ACTCCTGAAGAAGTTGTCGTAGT 59.110 43.478 0.00 0.00 0.00 2.73
544 546 7.522399 GCGGAGACATTGTCATAGTAGATAAGT 60.522 40.741 18.57 0.00 34.60 2.24
548 550 4.320567 CGCGGAGACATTGTCATAGTAGAT 60.321 45.833 18.57 0.00 34.60 1.98
574 576 0.250553 CTGGGTTGGCAACGAGGTAA 60.251 55.000 22.95 4.96 42.51 2.85
592 594 1.211969 CGTCCGACGGTGATGAACT 59.788 57.895 14.79 0.00 38.08 3.01
604 606 0.102481 GCTCAATAGGCTTCGTCCGA 59.898 55.000 0.00 0.00 0.00 4.55
615 617 6.906659 ACAAAGTGAATGTTGAGCTCAATAG 58.093 36.000 30.65 15.92 38.24 1.73
626 628 2.293399 GCTCCCGAACAAAGTGAATGTT 59.707 45.455 0.00 0.00 43.37 2.71
652 654 0.874175 CTCGAACACGACCAAGTGCA 60.874 55.000 0.00 0.00 45.45 4.57
702 711 1.203052 GTCCCTTCGTCATAACACCGA 59.797 52.381 0.00 0.00 0.00 4.69
705 714 3.778618 GGTAGTCCCTTCGTCATAACAC 58.221 50.000 0.00 0.00 0.00 3.32
730 739 2.558359 CCGAAAGCCCTCAAAAGTTGAT 59.442 45.455 0.00 0.00 39.30 2.57
733 742 1.954382 GACCGAAAGCCCTCAAAAGTT 59.046 47.619 0.00 0.00 0.00 2.66
776 785 2.351418 CACACACACACACAATCGAAGT 59.649 45.455 0.00 0.00 0.00 3.01
783 792 0.962855 CCCCACACACACACACACAA 60.963 55.000 0.00 0.00 0.00 3.33
912 937 6.970165 ATATATAGGTACAAGGGGTGCAAT 57.030 37.500 0.00 0.00 33.19 3.56
973 998 8.774586 GTGTTGTAGTTTGTAGAGAATGATTGT 58.225 33.333 0.00 0.00 0.00 2.71
974 999 8.230486 GGTGTTGTAGTTTGTAGAGAATGATTG 58.770 37.037 0.00 0.00 0.00 2.67
1016 1041 2.766263 TCATGCCAAGAAGGTAGACGAT 59.234 45.455 0.00 0.00 40.61 3.73
1138 1164 1.546323 CCCATGAAAGGCACTGTCTGT 60.546 52.381 0.00 0.00 44.67 3.41
1148 1174 0.625849 AGGTACAGCCCCATGAAAGG 59.374 55.000 0.00 0.00 38.26 3.11
1195 1221 0.179240 CGAACAGCAGCAACGATGAC 60.179 55.000 0.00 0.00 0.00 3.06
1198 1224 0.602638 TTCCGAACAGCAGCAACGAT 60.603 50.000 0.00 0.00 0.00 3.73
1202 1228 4.549793 TGTTCCGAACAGCAGCAA 57.450 50.000 9.99 0.00 36.25 3.91
1209 1235 1.865865 GAACTGCTCTGTTCCGAACA 58.134 50.000 13.29 13.29 40.10 3.18
1217 1243 0.881796 TCATCGTCGAACTGCTCTGT 59.118 50.000 0.00 0.00 0.00 3.41
1219 1245 0.881796 TGTCATCGTCGAACTGCTCT 59.118 50.000 0.00 0.00 0.00 4.09
1264 1290 3.198853 GGTAGAACCAGCTGAAGAAGGAT 59.801 47.826 17.39 0.00 38.42 3.24
1315 1341 1.227823 CCAGACAAGGAACACGCCA 60.228 57.895 0.00 0.00 0.00 5.69
1405 1440 1.241315 GCTTGTACATGGGCGTGGTT 61.241 55.000 10.47 0.00 0.00 3.67
1406 1441 1.674322 GCTTGTACATGGGCGTGGT 60.674 57.895 10.47 0.00 0.00 4.16
1443 1478 2.999648 AGAGGCTCTTGAGCGGCA 61.000 61.111 12.24 0.00 35.24 5.69
1493 1530 0.825010 CTTTGGCTGGCACCTTGACT 60.825 55.000 2.29 0.00 0.00 3.41
1509 1546 1.482593 CTCATAGAGGTGTCCGCCTTT 59.517 52.381 0.11 0.00 39.34 3.11
1534 1577 0.732880 CGGCGAGTCGATCTTGTTGT 60.733 55.000 18.61 0.00 0.00 3.32
1536 1579 1.805945 GCGGCGAGTCGATCTTGTT 60.806 57.895 18.61 0.00 0.00 2.83
1553 1596 2.747460 TGCACGATCTTGGGCTGC 60.747 61.111 0.92 0.00 0.00 5.25
1567 1610 2.653726 ACTTGAAGTCATTGGTGTGCA 58.346 42.857 0.00 0.00 0.00 4.57
1601 1644 3.009723 GTGTGAATCCGTGATGATGGTT 58.990 45.455 0.00 0.00 0.00 3.67
1602 1645 2.027285 TGTGTGAATCCGTGATGATGGT 60.027 45.455 0.00 0.00 0.00 3.55
1608 1651 2.420547 CCTCCATGTGTGAATCCGTGAT 60.421 50.000 0.00 0.00 0.00 3.06
1616 1659 0.615331 GCCTCTCCTCCATGTGTGAA 59.385 55.000 0.00 0.00 0.00 3.18
1620 1663 2.503061 CGGCCTCTCCTCCATGTG 59.497 66.667 0.00 0.00 0.00 3.21
1666 1709 1.623811 GCTCCTCCACCTGAGTAACAA 59.376 52.381 0.00 0.00 39.65 2.83
1667 1710 1.203187 AGCTCCTCCACCTGAGTAACA 60.203 52.381 0.00 0.00 39.65 2.41
1670 1713 0.704664 TGAGCTCCTCCACCTGAGTA 59.295 55.000 12.15 0.00 39.65 2.59
1750 1801 3.126858 GCACGAATGTGGTGTTCATATGT 59.873 43.478 1.90 0.00 46.51 2.29
1753 1804 2.741517 CTGCACGAATGTGGTGTTCATA 59.258 45.455 0.00 0.00 46.51 2.15
1782 1833 0.670162 GATGGTCATTTCCATGGCGG 59.330 55.000 6.96 0.00 46.72 6.13
1897 1948 9.643693 CACAGATATGCATAACACATATACTCA 57.356 33.333 11.13 0.00 40.07 3.41
1898 1949 9.645059 ACACAGATATGCATAACACATATACTC 57.355 33.333 11.13 0.00 40.07 2.59
1903 1954 9.218440 CCAATACACAGATATGCATAACACATA 57.782 33.333 11.13 0.42 34.64 2.29
1904 1955 7.175467 CCCAATACACAGATATGCATAACACAT 59.825 37.037 11.13 0.00 0.00 3.21
1905 1956 6.486320 CCCAATACACAGATATGCATAACACA 59.514 38.462 11.13 0.00 0.00 3.72
1906 1957 6.568462 GCCCAATACACAGATATGCATAACAC 60.568 42.308 11.13 5.73 0.00 3.32
1907 1958 5.473162 GCCCAATACACAGATATGCATAACA 59.527 40.000 11.13 0.00 0.00 2.41
1908 1959 5.106157 GGCCCAATACACAGATATGCATAAC 60.106 44.000 11.13 8.30 0.00 1.89
1909 1960 5.009631 GGCCCAATACACAGATATGCATAA 58.990 41.667 11.13 0.00 0.00 1.90
1910 1961 4.567537 GGGCCCAATACACAGATATGCATA 60.568 45.833 19.95 9.27 0.00 3.14
1911 1962 3.424703 GGCCCAATACACAGATATGCAT 58.575 45.455 3.79 3.79 0.00 3.96
1912 1963 2.488891 GGGCCCAATACACAGATATGCA 60.489 50.000 19.95 0.00 0.00 3.96
1913 1964 2.162681 GGGCCCAATACACAGATATGC 58.837 52.381 19.95 0.00 0.00 3.14
1914 1965 3.149196 GTGGGCCCAATACACAGATATG 58.851 50.000 30.64 0.00 35.30 1.78
1915 1966 2.108250 GGTGGGCCCAATACACAGATAT 59.892 50.000 30.64 0.00 36.87 1.63
1916 1967 1.493022 GGTGGGCCCAATACACAGATA 59.507 52.381 30.64 0.00 36.87 1.98
1917 1968 0.258774 GGTGGGCCCAATACACAGAT 59.741 55.000 30.64 0.00 36.87 2.90
1918 1969 0.844661 AGGTGGGCCCAATACACAGA 60.845 55.000 30.64 0.00 36.87 3.41
1919 1970 0.394352 GAGGTGGGCCCAATACACAG 60.394 60.000 30.64 0.00 36.87 3.66
1920 1971 1.688811 GAGGTGGGCCCAATACACA 59.311 57.895 30.64 0.00 36.87 3.72
1921 1972 1.076995 GGAGGTGGGCCCAATACAC 60.077 63.158 30.64 18.03 34.66 2.90
1922 1973 0.045008 TAGGAGGTGGGCCCAATACA 59.955 55.000 30.64 7.04 34.66 2.29
1923 1974 0.765510 CTAGGAGGTGGGCCCAATAC 59.234 60.000 30.64 19.98 34.66 1.89
1924 1975 0.345502 ACTAGGAGGTGGGCCCAATA 59.654 55.000 30.64 13.47 34.66 1.90
1925 1976 0.552615 AACTAGGAGGTGGGCCCAAT 60.553 55.000 30.64 19.67 34.66 3.16
1926 1977 1.151677 AACTAGGAGGTGGGCCCAA 60.152 57.895 30.64 9.14 34.66 4.12
1927 1978 1.615424 GAACTAGGAGGTGGGCCCA 60.615 63.158 24.45 24.45 34.66 5.36
1928 1979 2.376165 GGAACTAGGAGGTGGGCCC 61.376 68.421 17.59 17.59 34.57 5.80
1929 1980 0.914902 AAGGAACTAGGAGGTGGGCC 60.915 60.000 0.00 0.00 38.49 5.80
1930 1981 0.253327 CAAGGAACTAGGAGGTGGGC 59.747 60.000 0.00 0.00 38.49 5.36
1931 1982 1.657804 ACAAGGAACTAGGAGGTGGG 58.342 55.000 0.00 0.00 38.49 4.61
1932 1983 5.209659 ACTATACAAGGAACTAGGAGGTGG 58.790 45.833 0.00 0.00 38.49 4.61
1933 1984 6.793505 AACTATACAAGGAACTAGGAGGTG 57.206 41.667 0.00 0.00 38.49 4.00
1934 1985 7.564292 CCTTAACTATACAAGGAACTAGGAGGT 59.436 40.741 0.00 0.00 43.44 3.85
1935 1986 7.564292 ACCTTAACTATACAAGGAACTAGGAGG 59.436 40.741 7.34 0.00 43.44 4.30
1936 1987 8.536340 ACCTTAACTATACAAGGAACTAGGAG 57.464 38.462 7.34 0.00 43.44 3.69
1937 1988 7.284034 CGACCTTAACTATACAAGGAACTAGGA 59.716 40.741 7.34 0.00 43.44 2.94
1938 1989 7.067981 ACGACCTTAACTATACAAGGAACTAGG 59.932 40.741 7.34 0.00 43.44 3.02
1939 1990 7.914346 CACGACCTTAACTATACAAGGAACTAG 59.086 40.741 7.34 0.00 43.44 2.57
1940 1991 7.148018 CCACGACCTTAACTATACAAGGAACTA 60.148 40.741 7.34 0.00 43.44 2.24
1941 1992 6.350780 CCACGACCTTAACTATACAAGGAACT 60.351 42.308 7.34 0.00 43.44 3.01
1942 1993 5.809051 CCACGACCTTAACTATACAAGGAAC 59.191 44.000 7.34 1.12 43.44 3.62
1943 1994 5.625197 GCCACGACCTTAACTATACAAGGAA 60.625 44.000 7.34 0.00 43.44 3.36
1944 1995 4.142093 GCCACGACCTTAACTATACAAGGA 60.142 45.833 7.34 0.00 43.44 3.36
1945 1996 4.117685 GCCACGACCTTAACTATACAAGG 58.882 47.826 0.00 0.00 45.73 3.61
1946 1997 4.117685 GGCCACGACCTTAACTATACAAG 58.882 47.826 0.00 0.00 0.00 3.16
1947 1998 3.118665 GGGCCACGACCTTAACTATACAA 60.119 47.826 4.39 0.00 0.00 2.41
1948 1999 2.431782 GGGCCACGACCTTAACTATACA 59.568 50.000 4.39 0.00 0.00 2.29
1949 2000 2.431782 TGGGCCACGACCTTAACTATAC 59.568 50.000 0.00 0.00 0.00 1.47
1950 2001 2.431782 GTGGGCCACGACCTTAACTATA 59.568 50.000 22.83 0.00 0.00 1.31
1951 2002 1.208776 GTGGGCCACGACCTTAACTAT 59.791 52.381 22.83 0.00 0.00 2.12
1952 2003 0.609662 GTGGGCCACGACCTTAACTA 59.390 55.000 22.83 0.00 0.00 2.24
1953 2004 1.373812 GTGGGCCACGACCTTAACT 59.626 57.895 22.83 0.00 0.00 2.24
1954 2005 1.673337 GGTGGGCCACGACCTTAAC 60.673 63.158 29.18 9.97 41.76 2.01
1955 2006 2.751688 GGTGGGCCACGACCTTAA 59.248 61.111 29.18 0.00 41.76 1.85
1959 2010 3.637273 AAGAGGTGGGCCACGACC 61.637 66.667 29.18 19.73 44.99 4.79
1960 2011 1.823169 TACAAGAGGTGGGCCACGAC 61.823 60.000 29.18 23.66 34.83 4.34
1961 2012 1.534476 TACAAGAGGTGGGCCACGA 60.534 57.895 29.18 6.37 34.83 4.35
1962 2013 1.375523 GTACAAGAGGTGGGCCACG 60.376 63.158 29.18 17.74 34.83 4.94
1963 2014 0.328258 ATGTACAAGAGGTGGGCCAC 59.672 55.000 28.69 28.69 37.19 5.01
1964 2015 0.618458 GATGTACAAGAGGTGGGCCA 59.382 55.000 0.00 0.00 37.19 5.36
1965 2016 0.618458 TGATGTACAAGAGGTGGGCC 59.382 55.000 0.00 0.00 0.00 5.80
1966 2017 2.717639 ATGATGTACAAGAGGTGGGC 57.282 50.000 0.00 0.00 0.00 5.36
1967 2018 8.762645 ACATATATATGATGTACAAGAGGTGGG 58.237 37.037 26.05 0.00 35.75 4.61
1968 2019 9.591792 CACATATATATGATGTACAAGAGGTGG 57.408 37.037 26.05 0.00 35.75 4.61
1969 2020 9.091784 GCACATATATATGATGTACAAGAGGTG 57.908 37.037 26.05 11.74 35.75 4.00
1970 2021 8.260818 GGCACATATATATGATGTACAAGAGGT 58.739 37.037 26.05 0.00 35.75 3.85
1971 2022 8.481314 AGGCACATATATATGATGTACAAGAGG 58.519 37.037 26.05 0.00 35.75 3.69
1972 2023 9.881649 AAGGCACATATATATGATGTACAAGAG 57.118 33.333 26.05 0.00 35.75 2.85
1975 2026 8.729756 GCAAAGGCACATATATATGATGTACAA 58.270 33.333 26.05 0.00 40.72 2.41
1976 2027 8.267620 GCAAAGGCACATATATATGATGTACA 57.732 34.615 26.05 0.00 40.72 2.90
1999 2050 3.673866 GCATGTTGTATTGCTCATGTGCA 60.674 43.478 18.04 18.04 39.54 4.57
2000 2051 2.855963 GCATGTTGTATTGCTCATGTGC 59.144 45.455 12.78 12.78 39.54 4.57
2001 2052 4.099380 TGCATGTTGTATTGCTCATGTG 57.901 40.909 0.00 0.00 39.54 3.21
2002 2053 4.787260 TTGCATGTTGTATTGCTCATGT 57.213 36.364 0.00 0.00 39.54 3.21
2003 2054 5.808030 TGAATTGCATGTTGTATTGCTCATG 59.192 36.000 0.00 0.00 39.60 3.07
2004 2055 5.808540 GTGAATTGCATGTTGTATTGCTCAT 59.191 36.000 0.00 0.00 39.60 2.90
2005 2056 5.162794 GTGAATTGCATGTTGTATTGCTCA 58.837 37.500 0.00 0.00 39.60 4.26
2006 2057 5.162794 TGTGAATTGCATGTTGTATTGCTC 58.837 37.500 0.00 0.00 39.60 4.26
2007 2058 5.136816 TGTGAATTGCATGTTGTATTGCT 57.863 34.783 0.00 0.00 39.60 3.91
2008 2059 7.703298 ATATGTGAATTGCATGTTGTATTGC 57.297 32.000 0.00 0.00 39.33 3.56
2009 2060 9.524106 AGAATATGTGAATTGCATGTTGTATTG 57.476 29.630 6.39 0.00 29.87 1.90
2012 2063 9.171877 TGTAGAATATGTGAATTGCATGTTGTA 57.828 29.630 6.39 4.88 29.87 2.41
2013 2064 8.054152 TGTAGAATATGTGAATTGCATGTTGT 57.946 30.769 6.39 5.60 29.87 3.32
2014 2065 8.964150 CATGTAGAATATGTGAATTGCATGTTG 58.036 33.333 6.39 0.00 29.87 3.33
2015 2066 8.139350 CCATGTAGAATATGTGAATTGCATGTT 58.861 33.333 0.00 2.89 31.86 2.71
2016 2067 7.286087 ACCATGTAGAATATGTGAATTGCATGT 59.714 33.333 0.00 0.00 0.00 3.21
2017 2068 7.654568 ACCATGTAGAATATGTGAATTGCATG 58.345 34.615 0.00 0.00 0.00 4.06
2018 2069 7.828508 ACCATGTAGAATATGTGAATTGCAT 57.171 32.000 0.00 0.00 0.00 3.96
2019 2070 8.922931 ATACCATGTAGAATATGTGAATTGCA 57.077 30.769 0.00 0.00 0.00 4.08
2020 2071 9.002600 TGATACCATGTAGAATATGTGAATTGC 57.997 33.333 0.00 0.00 0.00 3.56
2025 2076 9.764363 GAAACTGATACCATGTAGAATATGTGA 57.236 33.333 0.00 0.00 0.00 3.58
2026 2077 8.993121 GGAAACTGATACCATGTAGAATATGTG 58.007 37.037 0.00 0.00 0.00 3.21
2027 2078 7.872993 CGGAAACTGATACCATGTAGAATATGT 59.127 37.037 0.00 0.00 0.00 2.29
2028 2079 7.331934 CCGGAAACTGATACCATGTAGAATATG 59.668 40.741 0.00 0.00 0.00 1.78
2029 2080 7.386851 CCGGAAACTGATACCATGTAGAATAT 58.613 38.462 0.00 0.00 0.00 1.28
2030 2081 6.239487 CCCGGAAACTGATACCATGTAGAATA 60.239 42.308 0.73 0.00 0.00 1.75
2031 2082 5.454755 CCCGGAAACTGATACCATGTAGAAT 60.455 44.000 0.73 0.00 0.00 2.40
2032 2083 4.141801 CCCGGAAACTGATACCATGTAGAA 60.142 45.833 0.73 0.00 0.00 2.10
2033 2084 3.386726 CCCGGAAACTGATACCATGTAGA 59.613 47.826 0.73 0.00 0.00 2.59
2034 2085 3.134081 ACCCGGAAACTGATACCATGTAG 59.866 47.826 0.73 0.00 0.00 2.74
2035 2086 3.109151 ACCCGGAAACTGATACCATGTA 58.891 45.455 0.73 0.00 0.00 2.29
2036 2087 1.913419 ACCCGGAAACTGATACCATGT 59.087 47.619 0.73 0.00 0.00 3.21
2037 2088 2.710096 ACCCGGAAACTGATACCATG 57.290 50.000 0.73 0.00 0.00 3.66
2038 2089 2.844348 AGAACCCGGAAACTGATACCAT 59.156 45.455 0.73 0.00 0.00 3.55
2039 2090 2.262637 AGAACCCGGAAACTGATACCA 58.737 47.619 0.73 0.00 0.00 3.25
2040 2091 4.186926 GTTAGAACCCGGAAACTGATACC 58.813 47.826 0.73 0.00 0.00 2.73
2041 2092 4.186926 GGTTAGAACCCGGAAACTGATAC 58.813 47.826 0.73 0.00 43.43 2.24
2042 2093 4.476628 GGTTAGAACCCGGAAACTGATA 57.523 45.455 0.73 0.00 43.43 2.15
2043 2094 3.345508 GGTTAGAACCCGGAAACTGAT 57.654 47.619 0.73 0.00 43.43 2.90
2044 2095 2.845363 GGTTAGAACCCGGAAACTGA 57.155 50.000 0.73 0.00 43.43 3.41
2055 2106 2.669924 CGGCGAAAACTAGGGTTAGAAC 59.330 50.000 0.00 0.00 34.90 3.01
2056 2107 2.932187 GCGGCGAAAACTAGGGTTAGAA 60.932 50.000 12.98 0.00 34.90 2.10
2057 2108 1.404583 GCGGCGAAAACTAGGGTTAGA 60.405 52.381 12.98 0.00 34.90 2.10
2058 2109 1.004595 GCGGCGAAAACTAGGGTTAG 58.995 55.000 12.98 0.00 34.90 2.34
2059 2110 0.609662 AGCGGCGAAAACTAGGGTTA 59.390 50.000 12.98 0.00 34.90 2.85
2060 2111 0.953960 CAGCGGCGAAAACTAGGGTT 60.954 55.000 12.98 0.00 37.24 4.11
2061 2112 1.375523 CAGCGGCGAAAACTAGGGT 60.376 57.895 12.98 0.00 0.00 4.34
2062 2113 2.750888 GCAGCGGCGAAAACTAGGG 61.751 63.158 12.98 0.00 0.00 3.53
2063 2114 2.750888 GGCAGCGGCGAAAACTAGG 61.751 63.158 12.98 0.00 42.47 3.02
2064 2115 2.785258 GGCAGCGGCGAAAACTAG 59.215 61.111 12.98 0.00 42.47 2.57
2085 2136 4.752879 TAGTGGGAGTTGCGCGGC 62.753 66.667 8.83 0.00 0.00 6.53
2086 2137 2.813908 GTAGTGGGAGTTGCGCGG 60.814 66.667 8.83 0.00 0.00 6.46
2087 2138 1.225376 TTTGTAGTGGGAGTTGCGCG 61.225 55.000 0.00 0.00 0.00 6.86
2088 2139 0.948678 TTTTGTAGTGGGAGTTGCGC 59.051 50.000 0.00 0.00 0.00 6.09
2195 2248 4.019860 GCCCACCACATCTATGATGATACT 60.020 45.833 13.63 0.00 0.00 2.12
2239 2292 4.525912 AAAGCCCATTTTCTGTCATGAC 57.474 40.909 19.27 19.27 0.00 3.06
2322 2375 2.356741 GCCCTTGCTTCTACCATGGTTA 60.357 50.000 25.38 9.30 33.53 2.85
2367 2420 1.297364 CCGACCACCCACCGTAATT 59.703 57.895 0.00 0.00 0.00 1.40
2368 2421 2.662070 CCCGACCACCCACCGTAAT 61.662 63.158 0.00 0.00 0.00 1.89
2486 2539 2.986306 GCCTGCAGTGCAATCGCTT 61.986 57.895 20.22 0.00 38.41 4.68
2579 2632 0.248498 TCGATCGGCTTCAGTTAGCG 60.248 55.000 16.41 0.00 42.15 4.26
2618 2671 2.401766 CCCACCGCAATGCTCACTC 61.402 63.158 2.94 0.00 0.00 3.51
2626 2679 2.978946 ATCCGAACCCCACCGCAAT 61.979 57.895 0.00 0.00 0.00 3.56
2640 2695 3.257561 CCGCTCGCTGTTCATCCG 61.258 66.667 0.00 0.00 0.00 4.18
2651 2706 3.461773 ATCCACTCCCACCGCTCG 61.462 66.667 0.00 0.00 0.00 5.03
2695 2751 0.530650 CGATCGGGGTCCTGTTCATG 60.531 60.000 7.38 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.