Multiple sequence alignment - TraesCS5A01G410400

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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 TraesCS5A01G410400 chr5A 100.000 4095 0 0 1 4095 599450243 599454337 0.000000e+00 7563.0
1 TraesCS5A01G410400 chr5A 86.923 910 76 18 975 1869 599390793 599391674 0.000000e+00 981.0
2 TraesCS5A01G410400 chr5A 85.714 882 98 11 3230 4090 599393252 599394126 0.000000e+00 905.0
3 TraesCS5A01G410400 chr5A 86.945 766 87 5 2409 3174 599392198 599392950 0.000000e+00 848.0
4 TraesCS5A01G410400 chr5A 86.101 813 78 12 135 922 312276032 312275230 0.000000e+00 843.0
5 TraesCS5A01G410400 chr5A 95.364 151 7 0 1 151 312276136 312275986 1.470000e-59 241.0
6 TraesCS5A01G410400 chr5A 95.302 149 7 0 1 149 320795596 320795448 1.900000e-58 237.0
7 TraesCS5A01G410400 chr5A 97.297 37 1 0 945 981 599390710 599390746 3.420000e-06 63.9
8 TraesCS5A01G410400 chr5B 87.719 1995 202 26 2126 4095 588779627 588781603 0.000000e+00 2287.0
9 TraesCS5A01G410400 chr5B 87.803 1443 136 22 2124 3555 588833739 588835152 0.000000e+00 1653.0
10 TraesCS5A01G410400 chr5B 91.101 899 50 20 996 1882 588832799 588833679 0.000000e+00 1190.0
11 TraesCS5A01G410400 chr5B 87.797 926 70 9 975 1864 588778586 588779504 0.000000e+00 1044.0
12 TraesCS5A01G410400 chr5B 82.989 435 44 9 3553 3957 588840346 588840780 2.330000e-97 366.0
13 TraesCS5A01G410400 chr5B 85.207 169 24 1 1964 2132 62942827 62942994 5.440000e-39 172.0
14 TraesCS5A01G410400 chr5B 83.030 165 18 4 1964 2119 382897248 382897411 1.530000e-29 141.0
15 TraesCS5A01G410400 chr5B 92.982 57 2 2 919 975 588832702 588832756 9.430000e-12 82.4
16 TraesCS5A01G410400 chr7D 88.738 808 60 10 133 922 3376123 3375329 0.000000e+00 959.0
17 TraesCS5A01G410400 chr7D 96.026 151 6 0 1 151 3376225 3376075 3.160000e-61 246.0
18 TraesCS5A01G410400 chr2B 88.514 801 79 4 3 800 757534863 757534073 0.000000e+00 957.0
19 TraesCS5A01G410400 chr2B 81.579 152 27 1 1973 2124 527974916 527975066 1.550000e-24 124.0
20 TraesCS5A01G410400 chr1D 90.523 707 48 9 133 836 474123915 474123225 0.000000e+00 917.0
21 TraesCS5A01G410400 chr1D 87.636 736 66 12 203 915 287648795 287648062 0.000000e+00 832.0
22 TraesCS5A01G410400 chr1D 92.857 154 8 2 1 151 204794085 204794238 1.920000e-53 220.0
23 TraesCS5A01G410400 chr1D 92.771 83 6 0 839 921 156011905 156011987 2.000000e-23 121.0
24 TraesCS5A01G410400 chr3A 91.908 655 49 3 142 796 658325738 658326388 0.000000e+00 913.0
25 TraesCS5A01G410400 chr2A 86.224 813 85 13 123 921 128257877 128257078 0.000000e+00 856.0
26 TraesCS5A01G410400 chr2A 81.174 409 41 16 3618 3993 734968240 734968645 3.100000e-76 296.0
27 TraesCS5A01G410400 chr4D 89.970 658 57 4 149 800 478732524 478733178 0.000000e+00 841.0
28 TraesCS5A01G410400 chr1A 85.302 796 86 16 152 919 375096921 375096129 0.000000e+00 793.0
29 TraesCS5A01G410400 chr2D 82.973 787 81 22 149 919 649804791 649804042 0.000000e+00 662.0
30 TraesCS5A01G410400 chr2D 90.698 172 12 2 1 168 195720297 195720468 4.120000e-55 226.0
31 TraesCS5A01G410400 chr2D 84.091 176 26 2 1926 2100 448194281 448194455 7.040000e-38 169.0
32 TraesCS5A01G410400 chr2D 92.593 81 6 0 839 919 639103541 639103621 2.590000e-22 117.0
33 TraesCS5A01G410400 chr2D 97.436 39 1 0 1964 2002 182734666 182734704 2.640000e-07 67.6
34 TraesCS5A01G410400 chr5D 79.674 797 121 20 161 922 221309996 221310786 1.680000e-148 536.0
35 TraesCS5A01G410400 chr3D 78.809 571 76 22 388 921 378202385 378201823 3.920000e-90 342.0
36 TraesCS5A01G410400 chr3D 92.857 154 8 1 1 151 362041545 362041392 1.920000e-53 220.0
37 TraesCS5A01G410400 chr3D 81.250 160 26 4 1964 2121 19326791 19326634 4.300000e-25 126.0
38 TraesCS5A01G410400 chr6A 93.377 151 10 0 1 151 616225516 616225366 1.480000e-54 224.0
39 TraesCS5A01G410400 chr6A 86.335 161 21 1 1964 2123 106983890 106984050 1.510000e-39 174.0
40 TraesCS5A01G410400 chr6D 93.377 151 9 1 1 151 346560915 346560766 5.330000e-54 222.0
41 TraesCS5A01G410400 chr6D 88.496 113 13 0 1037 1149 456251650 456251762 1.990000e-28 137.0
42 TraesCS5A01G410400 chr6D 92.771 83 6 0 839 921 80474060 80474142 2.000000e-23 121.0
43 TraesCS5A01G410400 chr6D 90.588 85 8 0 839 923 347766584 347766668 3.350000e-21 113.0
44 TraesCS5A01G410400 chr6D 90.588 85 8 0 839 923 361486547 361486631 3.350000e-21 113.0
45 TraesCS5A01G410400 chr7A 84.146 164 24 2 1962 2124 215185157 215185319 1.520000e-34 158.0
46 TraesCS5A01G410400 chr7A 88.034 117 11 3 723 836 129254551 129254667 7.140000e-28 135.0
47 TraesCS5A01G410400 chr7A 92.857 84 6 0 839 922 598214118 598214035 5.560000e-24 122.0
48 TraesCS5A01G410400 chr7B 82.162 185 25 7 1942 2124 166988575 166988753 7.090000e-33 152.0
49 TraesCS5A01G410400 chr3B 82.390 159 26 2 1964 2121 31079953 31079796 1.990000e-28 137.0
50 TraesCS5A01G410400 chr1B 84.559 136 20 1 1964 2099 633057787 633057921 2.570000e-27 134.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G410400 chr5A 599450243 599454337 4094 False 7563.000000 7563 100.000000 1 4095 1 chr5A.!!$F1 4094
1 TraesCS5A01G410400 chr5A 599390710 599394126 3416 False 699.475000 981 89.219750 945 4090 4 chr5A.!!$F2 3145
2 TraesCS5A01G410400 chr5A 312275230 312276136 906 True 542.000000 843 90.732500 1 922 2 chr5A.!!$R2 921
3 TraesCS5A01G410400 chr5B 588778586 588781603 3017 False 1665.500000 2287 87.758000 975 4095 2 chr5B.!!$F4 3120
4 TraesCS5A01G410400 chr5B 588832702 588835152 2450 False 975.133333 1653 90.628667 919 3555 3 chr5B.!!$F5 2636
5 TraesCS5A01G410400 chr7D 3375329 3376225 896 True 602.500000 959 92.382000 1 922 2 chr7D.!!$R1 921
6 TraesCS5A01G410400 chr2B 757534073 757534863 790 True 957.000000 957 88.514000 3 800 1 chr2B.!!$R1 797
7 TraesCS5A01G410400 chr1D 474123225 474123915 690 True 917.000000 917 90.523000 133 836 1 chr1D.!!$R2 703
8 TraesCS5A01G410400 chr1D 287648062 287648795 733 True 832.000000 832 87.636000 203 915 1 chr1D.!!$R1 712
9 TraesCS5A01G410400 chr3A 658325738 658326388 650 False 913.000000 913 91.908000 142 796 1 chr3A.!!$F1 654
10 TraesCS5A01G410400 chr2A 128257078 128257877 799 True 856.000000 856 86.224000 123 921 1 chr2A.!!$R1 798
11 TraesCS5A01G410400 chr4D 478732524 478733178 654 False 841.000000 841 89.970000 149 800 1 chr4D.!!$F1 651
12 TraesCS5A01G410400 chr1A 375096129 375096921 792 True 793.000000 793 85.302000 152 919 1 chr1A.!!$R1 767
13 TraesCS5A01G410400 chr2D 649804042 649804791 749 True 662.000000 662 82.973000 149 919 1 chr2D.!!$R1 770
14 TraesCS5A01G410400 chr5D 221309996 221310786 790 False 536.000000 536 79.674000 161 922 1 chr5D.!!$F1 761
15 TraesCS5A01G410400 chr3D 378201823 378202385 562 True 342.000000 342 78.809000 388 921 1 chr3D.!!$R3 533

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
159 161 0.041833 CCCACTCTTCCTCCTCCTCA 59.958 60.0 0.00 0.0 0.00 3.86 F
536 554 0.179134 GGAGACATTGTCGTCCTCGG 60.179 60.0 19.62 0.0 37.67 4.63 F
1668 1876 0.457851 AGACATGCTGGAGCGACTAC 59.542 55.0 0.00 0.0 45.83 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2136 1.679032 GGGGCTGTACTGAATTTCGCT 60.679 52.381 3.61 0.0 0.0 4.93 R
2191 2413 1.098712 GGAACAAACACGCACCTCCA 61.099 55.000 0.00 0.0 0.0 3.86 R
3111 3471 0.251916 CTGGGTATGCGGAAGTTGGA 59.748 55.000 0.00 0.0 0.0 3.53 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
95 96 3.637273 GGTGCCCAGGAGGTTCGT 61.637 66.667 0.00 0.00 38.26 3.85
130 131 0.689412 CCACTCTTCCTCCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
131 132 1.040339 CACTCTTCCTCCTCCTCCCG 61.040 65.000 0.00 0.00 0.00 5.14
159 161 0.041833 CCCACTCTTCCTCCTCCTCA 59.958 60.000 0.00 0.00 0.00 3.86
454 472 2.910479 ACGACTGGGTGCAGACGA 60.910 61.111 2.20 0.00 41.40 4.20
521 539 1.928567 ATGGCCGGGAAAAGGGAGA 60.929 57.895 2.18 0.00 0.00 3.71
525 543 0.323451 GCCGGGAAAAGGGAGACATT 60.323 55.000 2.18 0.00 34.57 2.71
536 554 0.179134 GGAGACATTGTCGTCCTCGG 60.179 60.000 19.62 0.00 37.67 4.63
645 672 2.125106 GAGAAGGCCGCCGACAAT 60.125 61.111 3.05 0.00 0.00 2.71
660 687 1.215382 CAATGACGAGGACAGCGGA 59.785 57.895 0.00 0.00 0.00 5.54
698 725 1.917955 CGCGCTAATCAACTTCTTCGA 59.082 47.619 5.56 0.00 0.00 3.71
790 838 3.752222 TGCCGAATTTTAGCCGAACTTTA 59.248 39.130 0.00 0.00 0.00 1.85
796 844 5.945466 ATTTTAGCCGAACTTTACCGAAA 57.055 34.783 0.00 0.00 0.00 3.46
805 862 5.623673 CCGAACTTTACCGAAATCAGTTTTG 59.376 40.000 0.00 0.00 0.00 2.44
887 986 1.078001 AGGGGGCACGTAAAATCGG 60.078 57.895 0.00 0.00 34.94 4.18
894 993 1.079681 ACGTAAAATCGGCGCCTGA 60.080 52.632 26.68 23.03 34.94 3.86
922 1021 3.258971 ACAGCTGGAGATGTTCTTAGC 57.741 47.619 19.93 0.00 42.67 3.09
923 1022 2.568956 ACAGCTGGAGATGTTCTTAGCA 59.431 45.455 19.93 0.00 42.67 3.49
924 1023 3.199508 ACAGCTGGAGATGTTCTTAGCAT 59.800 43.478 19.93 0.00 42.67 3.79
925 1024 4.197750 CAGCTGGAGATGTTCTTAGCATT 58.802 43.478 5.57 0.00 38.57 3.56
926 1025 5.104776 ACAGCTGGAGATGTTCTTAGCATTA 60.105 40.000 19.93 0.00 42.67 1.90
927 1026 5.466058 CAGCTGGAGATGTTCTTAGCATTAG 59.534 44.000 5.57 0.00 38.57 1.73
928 1027 4.754114 GCTGGAGATGTTCTTAGCATTAGG 59.246 45.833 8.79 0.00 37.13 2.69
929 1028 5.296151 TGGAGATGTTCTTAGCATTAGGG 57.704 43.478 0.00 0.00 0.00 3.53
930 1029 4.968719 TGGAGATGTTCTTAGCATTAGGGA 59.031 41.667 0.00 0.00 0.00 4.20
931 1030 5.163301 TGGAGATGTTCTTAGCATTAGGGAC 60.163 44.000 0.00 0.00 0.00 4.46
932 1031 5.297569 AGATGTTCTTAGCATTAGGGACC 57.702 43.478 0.00 0.00 0.00 4.46
981 1133 0.530431 GCAACCCACAAGGCAAGTTG 60.530 55.000 0.00 0.00 40.58 3.16
1148 1300 1.133976 GGCTAGAGACCCAGGTACGTA 60.134 57.143 0.00 0.00 0.00 3.57
1171 1343 9.248291 CGTATAAGCACATGCATCATATATACA 57.752 33.333 6.64 0.00 45.16 2.29
1182 1358 9.599056 ATGCATCATATATACATCCTAGCTACT 57.401 33.333 0.00 0.00 0.00 2.57
1211 1387 1.355381 TCCATCACCTGCTTCAATGGT 59.645 47.619 0.00 0.00 38.41 3.55
1465 1669 3.922850 GGAAGAAATGCTTGCTTGCTAAC 59.077 43.478 3.47 0.00 41.29 2.34
1494 1702 2.164865 CTGTTCTCGGCTGACTGGCT 62.165 60.000 0.00 0.00 39.32 4.75
1495 1703 1.446966 GTTCTCGGCTGACTGGCTC 60.447 63.158 0.00 0.00 39.32 4.70
1496 1704 2.994671 TTCTCGGCTGACTGGCTCG 61.995 63.158 0.00 1.32 39.32 5.03
1497 1705 3.443925 CTCGGCTGACTGGCTCGA 61.444 66.667 0.00 0.00 39.32 4.04
1594 1802 1.877443 GCCGCCTTGTTTTCACTTCTA 59.123 47.619 0.00 0.00 0.00 2.10
1668 1876 0.457851 AGACATGCTGGAGCGACTAC 59.542 55.000 0.00 0.00 45.83 2.73
1683 1891 3.722123 CGACTACGAATTCTGCAAACAC 58.278 45.455 3.52 0.00 42.66 3.32
1712 1920 4.618912 CGTATGATATTTCTGGAGCGACTG 59.381 45.833 0.00 0.00 0.00 3.51
1731 1946 6.254157 GCGACTGAACATTCATTGCAATAATT 59.746 34.615 12.53 2.25 36.46 1.40
1745 1960 9.757859 CATTGCAATAATTTTTAAGCACGAAAT 57.242 25.926 12.53 0.00 0.00 2.17
1760 1975 5.099575 GCACGAAATGGTAAATTAAGGTGG 58.900 41.667 0.00 0.00 0.00 4.61
1847 2069 4.002316 GCAATCAGCTGGGATAGATTCTC 58.998 47.826 15.13 0.00 41.15 2.87
1882 2104 4.697352 CCGATCCTTTATCCTATGGCTTTG 59.303 45.833 0.00 0.00 0.00 2.77
1885 2107 3.118038 TCCTTTATCCTATGGCTTTGCGT 60.118 43.478 0.00 0.00 0.00 5.24
1886 2108 3.632145 CCTTTATCCTATGGCTTTGCGTT 59.368 43.478 0.00 0.00 0.00 4.84
1887 2109 4.097892 CCTTTATCCTATGGCTTTGCGTTT 59.902 41.667 0.00 0.00 0.00 3.60
1888 2110 4.893424 TTATCCTATGGCTTTGCGTTTC 57.107 40.909 0.00 0.00 0.00 2.78
1889 2111 1.083489 TCCTATGGCTTTGCGTTTCG 58.917 50.000 0.00 0.00 0.00 3.46
1890 2112 1.083489 CCTATGGCTTTGCGTTTCGA 58.917 50.000 0.00 0.00 0.00 3.71
1891 2113 1.670811 CCTATGGCTTTGCGTTTCGAT 59.329 47.619 0.00 0.00 0.00 3.59
1892 2114 2.097466 CCTATGGCTTTGCGTTTCGATT 59.903 45.455 0.00 0.00 0.00 3.34
1893 2115 2.723124 ATGGCTTTGCGTTTCGATTT 57.277 40.000 0.00 0.00 0.00 2.17
1894 2116 2.500509 TGGCTTTGCGTTTCGATTTT 57.499 40.000 0.00 0.00 0.00 1.82
1895 2117 2.815478 TGGCTTTGCGTTTCGATTTTT 58.185 38.095 0.00 0.00 0.00 1.94
1896 2118 3.966154 TGGCTTTGCGTTTCGATTTTTA 58.034 36.364 0.00 0.00 0.00 1.52
1897 2119 4.360563 TGGCTTTGCGTTTCGATTTTTAA 58.639 34.783 0.00 0.00 0.00 1.52
1900 2122 6.018669 TGGCTTTGCGTTTCGATTTTTAAAAT 60.019 30.769 2.23 2.23 0.00 1.82
1903 2125 9.523730 GCTTTGCGTTTCGATTTTTAAAATATT 57.476 25.926 2.65 0.00 0.00 1.28
1931 2153 4.404507 TTTCAGCGAAATTCAGTACAGC 57.595 40.909 0.00 0.00 0.00 4.40
1932 2154 2.346803 TCAGCGAAATTCAGTACAGCC 58.653 47.619 0.00 0.00 0.00 4.85
1933 2155 1.398390 CAGCGAAATTCAGTACAGCCC 59.602 52.381 0.00 0.00 0.00 5.19
1934 2156 0.733150 GCGAAATTCAGTACAGCCCC 59.267 55.000 0.00 0.00 0.00 5.80
1935 2157 1.379527 CGAAATTCAGTACAGCCCCC 58.620 55.000 0.00 0.00 0.00 5.40
1936 2158 1.065418 CGAAATTCAGTACAGCCCCCT 60.065 52.381 0.00 0.00 0.00 4.79
1937 2159 2.169769 CGAAATTCAGTACAGCCCCCTA 59.830 50.000 0.00 0.00 0.00 3.53
1941 2163 2.634639 TCAGTACAGCCCCCTAGAAA 57.365 50.000 0.00 0.00 0.00 2.52
1942 2164 2.910544 TCAGTACAGCCCCCTAGAAAA 58.089 47.619 0.00 0.00 0.00 2.29
1943 2165 2.838202 TCAGTACAGCCCCCTAGAAAAG 59.162 50.000 0.00 0.00 0.00 2.27
1945 2167 3.009143 CAGTACAGCCCCCTAGAAAAGTT 59.991 47.826 0.00 0.00 0.00 2.66
1946 2168 3.656264 AGTACAGCCCCCTAGAAAAGTTT 59.344 43.478 0.00 0.00 0.00 2.66
1948 2170 4.302559 ACAGCCCCCTAGAAAAGTTTAG 57.697 45.455 0.00 0.00 0.00 1.85
1978 2200 8.865244 TTAGATACAAATTAGAAGGTACCCCT 57.135 34.615 8.74 8.98 45.63 4.79
1991 2213 4.416516 AGGTACCCCTTCAATCAAAAAGG 58.583 43.478 8.74 0.00 38.13 3.11
1992 2214 4.107311 AGGTACCCCTTCAATCAAAAAGGA 59.893 41.667 8.74 0.00 44.02 3.36
1995 2217 6.666113 GGTACCCCTTCAATCAAAAAGGATAA 59.334 38.462 0.00 0.00 44.02 1.75
1996 2218 7.344612 GGTACCCCTTCAATCAAAAAGGATAAT 59.655 37.037 0.00 0.00 44.02 1.28
1999 2221 7.898636 ACCCCTTCAATCAAAAAGGATAATGTA 59.101 33.333 2.74 0.00 44.02 2.29
2000 2222 8.416329 CCCCTTCAATCAAAAAGGATAATGTAG 58.584 37.037 2.74 0.00 44.02 2.74
2001 2223 8.971073 CCCTTCAATCAAAAAGGATAATGTAGT 58.029 33.333 2.74 0.00 44.02 2.73
2042 2264 8.551205 TCAATCTATTCAATACGTTTGATCTGC 58.449 33.333 11.98 0.00 0.00 4.26
2043 2265 8.337532 CAATCTATTCAATACGTTTGATCTGCA 58.662 33.333 11.98 0.00 0.00 4.41
2044 2266 8.613060 ATCTATTCAATACGTTTGATCTGCAT 57.387 30.769 11.98 6.81 0.00 3.96
2045 2267 7.854534 TCTATTCAATACGTTTGATCTGCATG 58.145 34.615 11.98 0.00 0.00 4.06
2046 2268 4.277257 TCAATACGTTTGATCTGCATGC 57.723 40.909 11.82 11.82 0.00 4.06
2047 2269 3.940852 TCAATACGTTTGATCTGCATGCT 59.059 39.130 20.33 0.00 0.00 3.79
2048 2270 5.115480 TCAATACGTTTGATCTGCATGCTA 58.885 37.500 20.33 7.56 0.00 3.49
2049 2271 5.584251 TCAATACGTTTGATCTGCATGCTAA 59.416 36.000 20.33 7.17 0.00 3.09
2050 2272 6.260714 TCAATACGTTTGATCTGCATGCTAAT 59.739 34.615 20.33 12.06 0.00 1.73
2051 2273 7.440856 TCAATACGTTTGATCTGCATGCTAATA 59.559 33.333 20.33 1.63 0.00 0.98
2052 2274 7.912056 ATACGTTTGATCTGCATGCTAATAT 57.088 32.000 20.33 6.79 0.00 1.28
2053 2275 5.993891 ACGTTTGATCTGCATGCTAATATG 58.006 37.500 20.33 5.69 0.00 1.78
2054 2276 5.759763 ACGTTTGATCTGCATGCTAATATGA 59.240 36.000 20.33 7.75 0.00 2.15
2055 2277 6.429078 ACGTTTGATCTGCATGCTAATATGAT 59.571 34.615 20.33 11.90 0.00 2.45
2056 2278 6.741358 CGTTTGATCTGCATGCTAATATGATG 59.259 38.462 20.33 2.41 0.00 3.07
2057 2279 7.360607 CGTTTGATCTGCATGCTAATATGATGA 60.361 37.037 20.33 4.65 0.00 2.92
2058 2280 6.980051 TGATCTGCATGCTAATATGATGAC 57.020 37.500 20.33 0.00 0.00 3.06
2059 2281 6.469410 TGATCTGCATGCTAATATGATGACA 58.531 36.000 20.33 2.25 0.00 3.58
2060 2282 6.938030 TGATCTGCATGCTAATATGATGACAA 59.062 34.615 20.33 0.00 0.00 3.18
2061 2283 6.549912 TCTGCATGCTAATATGATGACAAC 57.450 37.500 20.33 0.00 0.00 3.32
2062 2284 5.471116 TCTGCATGCTAATATGATGACAACC 59.529 40.000 20.33 0.00 0.00 3.77
2063 2285 5.379187 TGCATGCTAATATGATGACAACCT 58.621 37.500 20.33 0.00 0.00 3.50
2064 2286 5.829391 TGCATGCTAATATGATGACAACCTT 59.171 36.000 20.33 0.00 0.00 3.50
2065 2287 6.321945 TGCATGCTAATATGATGACAACCTTT 59.678 34.615 20.33 0.00 0.00 3.11
2066 2288 7.147863 TGCATGCTAATATGATGACAACCTTTT 60.148 33.333 20.33 0.00 0.00 2.27
2067 2289 7.707893 GCATGCTAATATGATGACAACCTTTTT 59.292 33.333 11.37 0.00 0.00 1.94
2071 2293 9.237846 GCTAATATGATGACAACCTTTTTAAGC 57.762 33.333 0.00 0.00 0.00 3.09
2074 2296 8.986477 ATATGATGACAACCTTTTTAAGCAAC 57.014 30.769 0.00 0.00 0.00 4.17
2075 2297 6.463995 TGATGACAACCTTTTTAAGCAACT 57.536 33.333 0.00 0.00 0.00 3.16
2076 2298 6.272318 TGATGACAACCTTTTTAAGCAACTG 58.728 36.000 0.00 0.00 0.00 3.16
2077 2299 5.652994 TGACAACCTTTTTAAGCAACTGT 57.347 34.783 0.00 0.00 0.00 3.55
2078 2300 5.406649 TGACAACCTTTTTAAGCAACTGTG 58.593 37.500 0.00 0.00 0.00 3.66
2079 2301 5.184096 TGACAACCTTTTTAAGCAACTGTGA 59.816 36.000 0.00 0.00 0.00 3.58
2080 2302 5.650543 ACAACCTTTTTAAGCAACTGTGAG 58.349 37.500 0.00 0.00 0.00 3.51
2081 2303 5.417580 ACAACCTTTTTAAGCAACTGTGAGA 59.582 36.000 0.00 0.00 0.00 3.27
2082 2304 6.096846 ACAACCTTTTTAAGCAACTGTGAGAT 59.903 34.615 0.00 0.00 0.00 2.75
2083 2305 6.715347 ACCTTTTTAAGCAACTGTGAGATT 57.285 33.333 0.00 0.00 0.00 2.40
2084 2306 6.739112 ACCTTTTTAAGCAACTGTGAGATTC 58.261 36.000 0.00 0.00 0.00 2.52
2085 2307 6.321181 ACCTTTTTAAGCAACTGTGAGATTCA 59.679 34.615 0.00 0.00 0.00 2.57
2086 2308 7.014615 ACCTTTTTAAGCAACTGTGAGATTCAT 59.985 33.333 0.00 0.00 0.00 2.57
2087 2309 8.514594 CCTTTTTAAGCAACTGTGAGATTCATA 58.485 33.333 0.00 0.00 0.00 2.15
2088 2310 9.334693 CTTTTTAAGCAACTGTGAGATTCATAC 57.665 33.333 0.00 0.00 0.00 2.39
2089 2311 7.977789 TTTAAGCAACTGTGAGATTCATACA 57.022 32.000 0.00 0.00 0.00 2.29
2090 2312 7.977789 TTAAGCAACTGTGAGATTCATACAA 57.022 32.000 0.00 0.00 0.00 2.41
2091 2313 6.882610 AAGCAACTGTGAGATTCATACAAA 57.117 33.333 0.00 0.00 0.00 2.83
2092 2314 6.246420 AGCAACTGTGAGATTCATACAAAC 57.754 37.500 0.00 0.00 0.00 2.93
2093 2315 6.000219 AGCAACTGTGAGATTCATACAAACT 59.000 36.000 0.00 0.00 0.00 2.66
2094 2316 6.488006 AGCAACTGTGAGATTCATACAAACTT 59.512 34.615 0.00 0.00 0.00 2.66
2095 2317 7.013655 AGCAACTGTGAGATTCATACAAACTTT 59.986 33.333 0.00 0.00 0.00 2.66
2096 2318 7.649306 GCAACTGTGAGATTCATACAAACTTTT 59.351 33.333 0.00 0.00 0.00 2.27
2105 2327 9.588096 AGATTCATACAAACTTTTAAGAAGGGT 57.412 29.630 0.00 0.00 0.00 4.34
2106 2328 9.626045 GATTCATACAAACTTTTAAGAAGGGTG 57.374 33.333 0.00 0.00 0.00 4.61
2107 2329 8.528044 TTCATACAAACTTTTAAGAAGGGTGT 57.472 30.769 0.00 10.24 0.00 4.16
2108 2330 9.629878 TTCATACAAACTTTTAAGAAGGGTGTA 57.370 29.630 0.00 12.34 0.00 2.90
2109 2331 9.059260 TCATACAAACTTTTAAGAAGGGTGTAC 57.941 33.333 0.00 0.00 0.00 2.90
2110 2332 9.063615 CATACAAACTTTTAAGAAGGGTGTACT 57.936 33.333 0.00 0.00 0.00 2.73
2111 2333 7.329588 ACAAACTTTTAAGAAGGGTGTACTG 57.670 36.000 0.00 0.00 0.00 2.74
2112 2334 7.114095 ACAAACTTTTAAGAAGGGTGTACTGA 58.886 34.615 0.00 0.00 0.00 3.41
2113 2335 7.612633 ACAAACTTTTAAGAAGGGTGTACTGAA 59.387 33.333 0.00 0.00 0.00 3.02
2114 2336 7.803279 AACTTTTAAGAAGGGTGTACTGAAG 57.197 36.000 0.00 0.00 0.00 3.02
2115 2337 5.763698 ACTTTTAAGAAGGGTGTACTGAAGC 59.236 40.000 0.00 0.00 0.00 3.86
2116 2338 4.967084 TTAAGAAGGGTGTACTGAAGCA 57.033 40.909 0.00 0.00 0.00 3.91
2117 2339 3.857157 AAGAAGGGTGTACTGAAGCAA 57.143 42.857 0.00 0.00 0.00 3.91
2118 2340 3.857157 AGAAGGGTGTACTGAAGCAAA 57.143 42.857 0.00 0.00 0.00 3.68
2119 2341 4.164843 AGAAGGGTGTACTGAAGCAAAA 57.835 40.909 0.00 0.00 0.00 2.44
2120 2342 3.883489 AGAAGGGTGTACTGAAGCAAAAC 59.117 43.478 0.00 0.00 0.00 2.43
2121 2343 3.577805 AGGGTGTACTGAAGCAAAACT 57.422 42.857 0.00 0.00 0.00 2.66
2122 2344 3.477530 AGGGTGTACTGAAGCAAAACTC 58.522 45.455 0.00 0.00 0.00 3.01
2152 2374 8.934023 TCTAAATGAAAGTGATACCAAAAGGT 57.066 30.769 0.00 0.00 0.00 3.50
2169 2391 4.592485 AAGGTCATCATAGCGTCTTAGG 57.408 45.455 0.00 0.00 0.00 2.69
2191 2413 4.811557 GGAACTTGCTACGCATATCTTTCT 59.188 41.667 0.00 0.00 38.76 2.52
2193 2415 4.122776 ACTTGCTACGCATATCTTTCTGG 58.877 43.478 0.00 0.00 38.76 3.86
2217 2440 1.268794 TGCGTGTTTGTTCCCAATTCG 60.269 47.619 0.00 0.00 0.00 3.34
2232 2455 5.105716 TCCCAATTCGACAGTTTGTTTTTGA 60.106 36.000 0.00 0.00 0.00 2.69
2267 2490 0.178975 AATTTGTGGCACCCGGAAGA 60.179 50.000 16.26 0.00 0.00 2.87
2270 2493 2.063015 TTGTGGCACCCGGAAGACAT 62.063 55.000 16.26 0.00 0.00 3.06
2272 2495 0.743345 GTGGCACCCGGAAGACATAC 60.743 60.000 6.29 0.00 0.00 2.39
2277 2503 2.629051 CACCCGGAAGACATACCTTTC 58.371 52.381 0.73 0.00 0.00 2.62
2335 2561 1.231963 AACCCAAGACCTCCCAAACT 58.768 50.000 0.00 0.00 0.00 2.66
2355 2588 3.947834 ACTGATAGGAAAAGGCCAATTCG 59.052 43.478 5.01 0.00 0.00 3.34
2404 2646 2.038033 TGCCCCGAAGCTACATAATACC 59.962 50.000 0.00 0.00 0.00 2.73
2421 2768 9.474313 ACATAATACCCATGTATGAAACAAACT 57.526 29.630 7.14 0.00 42.70 2.66
2435 2782 5.294306 TGAAACAAACTGTGTCTGTCATCTC 59.706 40.000 0.00 0.00 40.60 2.75
2444 2791 4.999311 TGTGTCTGTCATCTCAGGAAATTG 59.001 41.667 0.00 0.00 36.25 2.32
2451 2798 9.770097 TCTGTCATCTCAGGAAATTGATAATAC 57.230 33.333 0.00 0.00 36.25 1.89
2454 2801 9.512588 GTCATCTCAGGAAATTGATAATACCAT 57.487 33.333 0.00 0.00 0.00 3.55
2506 2854 1.676635 GGCAGAGATGGCAGCAACA 60.677 57.895 5.19 0.00 0.00 3.33
2610 2958 0.673644 GGCAGCAACTACCATGTCGT 60.674 55.000 0.00 0.00 0.00 4.34
2613 2961 2.739913 GCAGCAACTACCATGTCGTAAA 59.260 45.455 0.00 0.00 0.00 2.01
2692 3040 3.252484 GATGTCGTACGCGCCCAC 61.252 66.667 11.24 3.54 38.14 4.61
2765 3113 2.738521 CGCTACACCGCAGTTGCT 60.739 61.111 2.29 0.00 37.96 3.91
2796 3144 1.523758 CTCAGGGGTCTTTTTCCACG 58.476 55.000 0.00 0.00 32.92 4.94
2856 3207 2.886523 TGAATTGTCAACCTTCTGCCTG 59.113 45.455 0.00 0.00 0.00 4.85
2885 3242 5.473846 CGCCCATATCTATATCTGTACCGAT 59.526 44.000 5.09 5.09 0.00 4.18
2886 3243 6.348622 CGCCCATATCTATATCTGTACCGATC 60.349 46.154 2.74 0.00 0.00 3.69
2887 3244 6.348622 GCCCATATCTATATCTGTACCGATCG 60.349 46.154 8.51 8.51 0.00 3.69
2888 3245 6.935208 CCCATATCTATATCTGTACCGATCGA 59.065 42.308 18.66 0.00 0.00 3.59
2899 3256 5.075858 TGTACCGATCGACTACCATTTTT 57.924 39.130 18.66 0.00 0.00 1.94
2944 3301 4.066139 AAGCCCATGGTGAGCCCC 62.066 66.667 11.73 0.00 0.00 5.80
3000 3360 4.636206 GGGGTTAGAATTCACTGACATGAC 59.364 45.833 8.44 0.00 0.00 3.06
3078 3438 3.678548 CAGTGTCTCATCATGCCATATCG 59.321 47.826 0.00 0.00 0.00 2.92
3105 3465 6.451393 GTTCGAGCTTATAGATCAGGATGTT 58.549 40.000 0.00 0.00 37.40 2.71
3110 3470 5.071519 AGCTTATAGATCAGGATGTTGTGCT 59.928 40.000 0.00 0.00 37.40 4.40
3111 3471 5.762218 GCTTATAGATCAGGATGTTGTGCTT 59.238 40.000 0.00 0.00 37.40 3.91
3121 3481 1.021202 TGTTGTGCTTCCAACTTCCG 58.979 50.000 13.13 0.00 44.01 4.30
3129 3489 0.693622 TTCCAACTTCCGCATACCCA 59.306 50.000 0.00 0.00 0.00 4.51
3134 3494 1.276622 ACTTCCGCATACCCAGAAGT 58.723 50.000 0.00 0.00 43.06 3.01
3161 3521 7.898014 ACAAATAAGGTCCTTCTCAAAAGTT 57.102 32.000 7.61 0.00 0.00 2.66
3181 3541 9.802039 AAAAGTTATTGTATGGACTTGTAAGGA 57.198 29.630 0.00 0.00 33.02 3.36
3261 3876 9.781834 GACATACCATGACGAAATTATGAAAAA 57.218 29.630 0.00 0.00 0.00 1.94
3266 3881 9.487790 ACCATGACGAAATTATGAAAAATTTGT 57.512 25.926 0.00 0.00 38.77 2.83
3294 3909 5.456497 CAGCGCAGTATGTTATGAAAATTGG 59.544 40.000 11.47 0.00 39.31 3.16
3302 3917 5.621197 TGTTATGAAAATTGGAGACACGG 57.379 39.130 0.00 0.00 42.67 4.94
3303 3918 4.457603 TGTTATGAAAATTGGAGACACGGG 59.542 41.667 0.00 0.00 42.67 5.28
3313 3928 2.564062 TGGAGACACGGGTACTAAAAGG 59.436 50.000 0.00 0.00 33.40 3.11
3315 3930 3.450096 GGAGACACGGGTACTAAAAGGAT 59.550 47.826 0.00 0.00 0.00 3.24
3318 3933 1.931172 CACGGGTACTAAAAGGATGCG 59.069 52.381 0.00 0.00 0.00 4.73
3349 3964 2.805295 GCAAGGGGTTACAAAAGGTTGC 60.805 50.000 0.00 0.00 38.39 4.17
3352 3967 2.698274 AGGGGTTACAAAAGGTTGCAAG 59.302 45.455 0.00 0.00 38.39 4.01
3362 3977 0.897621 AGGTTGCAAGCCAATTAGCC 59.102 50.000 24.26 6.92 35.55 3.93
3363 3978 0.607620 GGTTGCAAGCCAATTAGCCA 59.392 50.000 17.84 0.00 35.55 4.75
3366 3982 3.337358 GTTGCAAGCCAATTAGCCAAAT 58.663 40.909 0.00 0.00 35.55 2.32
3432 4049 5.157395 TCCATCATATCCACTGATCTTCCA 58.843 41.667 0.00 0.00 31.00 3.53
3439 4056 3.754965 TCCACTGATCTTCCAAACAAGG 58.245 45.455 0.00 0.00 0.00 3.61
3447 4064 1.144913 CTTCCAAACAAGGACCTCCCA 59.855 52.381 0.00 0.00 37.42 4.37
3455 4072 4.741928 ACAAGGACCTCCCAAATAAAGT 57.258 40.909 0.00 0.00 37.41 2.66
3474 4091 3.356290 AGTGCCTGAACATCAATAACCC 58.644 45.455 0.00 0.00 0.00 4.11
3478 4095 4.776837 TGCCTGAACATCAATAACCCAAAT 59.223 37.500 0.00 0.00 0.00 2.32
3520 4137 5.068329 GGGAAAATGAAGGGAATCTAAGCAG 59.932 44.000 0.00 0.00 0.00 4.24
3589 4210 3.238108 ACTAACAGCGACATCAGAAGG 57.762 47.619 0.00 0.00 0.00 3.46
3590 4211 2.826128 ACTAACAGCGACATCAGAAGGA 59.174 45.455 0.00 0.00 0.00 3.36
3591 4212 2.086054 AACAGCGACATCAGAAGGAC 57.914 50.000 0.00 0.00 0.00 3.85
3592 4213 0.109086 ACAGCGACATCAGAAGGACG 60.109 55.000 0.00 0.00 0.00 4.79
3655 4276 6.058183 AGTCATTCAAAAGAAGTAGCACACT 58.942 36.000 0.00 0.00 40.05 3.55
3663 4284 0.905357 AAGTAGCACACTGGCTAGGG 59.095 55.000 0.00 0.00 46.34 3.53
3687 4308 2.609747 AGCAAGACTACCCACTTGAGA 58.390 47.619 0.00 0.00 43.98 3.27
3728 4352 2.584835 ACAGCAAGGCAAACTGGATA 57.415 45.000 5.79 0.00 35.70 2.59
3859 4500 6.759497 ACTTACTGTATCAATCCCAAAAGC 57.241 37.500 0.00 0.00 0.00 3.51
3860 4501 5.354234 ACTTACTGTATCAATCCCAAAAGCG 59.646 40.000 0.00 0.00 0.00 4.68
3862 4503 3.689649 ACTGTATCAATCCCAAAAGCGTC 59.310 43.478 0.00 0.00 0.00 5.19
3876 4517 4.803098 AAAGCGTCAGTTCTATGTACCT 57.197 40.909 0.00 0.00 0.00 3.08
3888 4529 9.035607 CAGTTCTATGTACCTACATCAATCAAC 57.964 37.037 1.09 0.90 45.11 3.18
3924 4565 0.037160 GAAAGGCTCCGGGGTTACAA 59.963 55.000 1.62 0.00 0.00 2.41
3958 4599 5.297029 AGAAACTGCACAGGAAAGAACTTAC 59.703 40.000 2.21 0.00 0.00 2.34
4016 4657 2.309136 ACTAAAGGGCATGGCAAAGT 57.691 45.000 22.06 14.24 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 4.144727 GGGAGGAGGAGGAGGCGA 62.145 72.222 0.00 0.00 0.00 5.54
130 131 1.671901 GAAGAGTGGGAGGAGGAGCG 61.672 65.000 0.00 0.00 0.00 5.03
131 132 1.334384 GGAAGAGTGGGAGGAGGAGC 61.334 65.000 0.00 0.00 0.00 4.70
159 161 2.363147 GAGTGGGAGGAGGAGCGT 60.363 66.667 0.00 0.00 0.00 5.07
261 264 2.264480 CCGCCCTCGTTGATGACA 59.736 61.111 0.00 0.00 0.00 3.58
513 531 1.978580 AGGACGACAATGTCTCCCTTT 59.021 47.619 20.48 7.06 38.91 3.11
521 539 2.126071 CGCCGAGGACGACAATGT 60.126 61.111 0.00 0.00 42.66 2.71
643 670 0.965866 TCTCCGCTGTCCTCGTCATT 60.966 55.000 0.00 0.00 0.00 2.57
645 672 2.033602 TCTCCGCTGTCCTCGTCA 59.966 61.111 0.00 0.00 0.00 4.35
670 697 0.878416 TTGATTAGCGCGGCAAAGTT 59.122 45.000 8.83 0.00 0.00 2.66
684 711 2.833631 ACGGGTCGAAGAAGTTGATT 57.166 45.000 0.00 0.00 39.69 2.57
837 907 2.162754 CGCTAAAATCGACGCGGGT 61.163 57.895 12.47 4.12 41.72 5.28
844 931 2.185867 AGCCGGCGCTAAAATCGA 59.814 55.556 23.20 0.00 46.08 3.59
915 1014 2.777692 CCTGGGTCCCTAATGCTAAGAA 59.222 50.000 10.00 0.00 0.00 2.52
922 1021 2.039084 GCTCATACCTGGGTCCCTAATG 59.961 54.545 10.00 7.62 0.00 1.90
923 1022 2.089925 AGCTCATACCTGGGTCCCTAAT 60.090 50.000 10.00 0.00 0.00 1.73
924 1023 1.294068 AGCTCATACCTGGGTCCCTAA 59.706 52.381 10.00 0.00 0.00 2.69
925 1024 0.941963 AGCTCATACCTGGGTCCCTA 59.058 55.000 10.00 0.00 0.00 3.53
926 1025 0.044855 AAGCTCATACCTGGGTCCCT 59.955 55.000 10.00 0.00 0.00 4.20
927 1026 0.181350 CAAGCTCATACCTGGGTCCC 59.819 60.000 0.00 0.00 0.00 4.46
928 1027 0.464554 GCAAGCTCATACCTGGGTCC 60.465 60.000 0.00 0.00 0.00 4.46
929 1028 0.253044 TGCAAGCTCATACCTGGGTC 59.747 55.000 0.00 0.00 0.00 4.46
930 1029 0.921896 ATGCAAGCTCATACCTGGGT 59.078 50.000 0.00 0.00 0.00 4.51
931 1030 2.062971 AATGCAAGCTCATACCTGGG 57.937 50.000 0.00 0.00 0.00 4.45
932 1031 6.882610 TTTATAATGCAAGCTCATACCTGG 57.117 37.500 0.00 0.00 0.00 4.45
981 1133 3.454375 CATGGAATCAATTTCTGGCTGC 58.546 45.455 0.00 0.00 34.56 5.25
1148 1300 9.281371 GGATGTATATATGATGCATGTGCTTAT 57.719 33.333 2.46 0.85 42.66 1.73
1171 1343 8.938883 TGATGGATTAGAAAAAGTAGCTAGGAT 58.061 33.333 0.00 0.00 0.00 3.24
1182 1358 6.009589 TGAAGCAGGTGATGGATTAGAAAAA 58.990 36.000 0.00 0.00 0.00 1.94
1211 1387 2.697654 TCACATGATTGATGCACGACA 58.302 42.857 0.00 0.00 35.15 4.35
1486 1694 1.745653 CTACACAGATCGAGCCAGTCA 59.254 52.381 0.00 0.00 0.00 3.41
1494 1702 3.181486 GCATGAGTTCCTACACAGATCGA 60.181 47.826 0.00 0.00 0.00 3.59
1495 1703 3.119291 GCATGAGTTCCTACACAGATCG 58.881 50.000 0.00 0.00 0.00 3.69
1496 1704 3.462021 GGCATGAGTTCCTACACAGATC 58.538 50.000 0.00 0.00 0.00 2.75
1497 1705 2.159043 CGGCATGAGTTCCTACACAGAT 60.159 50.000 0.00 0.00 0.00 2.90
1594 1802 3.118454 GTGCACTGCGCCATACGT 61.118 61.111 10.32 0.00 46.11 3.57
1668 1876 2.653890 CCTGTGTGTTTGCAGAATTCG 58.346 47.619 0.00 0.00 34.87 3.34
1683 1891 4.631131 TCCAGAAATATCATACGCCTGTG 58.369 43.478 0.00 0.00 0.00 3.66
1731 1946 9.413048 CCTTAATTTACCATTTCGTGCTTAAAA 57.587 29.630 0.00 0.00 0.00 1.52
1847 2069 4.530857 GATCGGAGGTGGCCGGTG 62.531 72.222 1.90 0.00 46.55 4.94
1914 2136 1.679032 GGGGCTGTACTGAATTTCGCT 60.679 52.381 3.61 0.00 0.00 4.93
1921 2143 2.634639 TTCTAGGGGGCTGTACTGAA 57.365 50.000 3.61 0.00 0.00 3.02
1925 2147 3.715638 AACTTTTCTAGGGGGCTGTAC 57.284 47.619 0.00 0.00 0.00 2.90
1926 2148 4.226620 CCTAAACTTTTCTAGGGGGCTGTA 59.773 45.833 0.00 0.00 32.46 2.74
1927 2149 3.010250 CCTAAACTTTTCTAGGGGGCTGT 59.990 47.826 0.00 0.00 32.46 4.40
1928 2150 3.621558 CCTAAACTTTTCTAGGGGGCTG 58.378 50.000 0.00 0.00 32.46 4.85
1971 2193 7.712204 TTATCCTTTTTGATTGAAGGGGTAC 57.288 36.000 2.61 0.00 42.17 3.34
1973 2195 6.730507 ACATTATCCTTTTTGATTGAAGGGGT 59.269 34.615 2.61 0.00 42.17 4.95
1974 2196 7.186570 ACATTATCCTTTTTGATTGAAGGGG 57.813 36.000 2.61 0.00 42.17 4.79
2016 2238 8.551205 GCAGATCAAACGTATTGAATAGATTGA 58.449 33.333 14.24 6.00 31.55 2.57
2017 2239 8.337532 TGCAGATCAAACGTATTGAATAGATTG 58.662 33.333 14.24 1.13 31.55 2.67
2018 2240 8.437360 TGCAGATCAAACGTATTGAATAGATT 57.563 30.769 14.24 1.36 31.55 2.40
2019 2241 8.501580 CATGCAGATCAAACGTATTGAATAGAT 58.498 33.333 14.24 1.91 31.55 1.98
2020 2242 7.518848 GCATGCAGATCAAACGTATTGAATAGA 60.519 37.037 14.21 2.98 31.55 1.98
2021 2243 6.576313 GCATGCAGATCAAACGTATTGAATAG 59.424 38.462 14.21 9.47 31.55 1.73
2022 2244 6.260714 AGCATGCAGATCAAACGTATTGAATA 59.739 34.615 21.98 0.00 31.55 1.75
2023 2245 5.066893 AGCATGCAGATCAAACGTATTGAAT 59.933 36.000 21.98 6.53 31.55 2.57
2024 2246 4.395854 AGCATGCAGATCAAACGTATTGAA 59.604 37.500 21.98 2.37 31.55 2.69
2025 2247 3.940852 AGCATGCAGATCAAACGTATTGA 59.059 39.130 21.98 13.12 0.00 2.57
2026 2248 4.282950 AGCATGCAGATCAAACGTATTG 57.717 40.909 21.98 0.00 0.00 1.90
2027 2249 6.624352 ATTAGCATGCAGATCAAACGTATT 57.376 33.333 21.98 0.00 0.00 1.89
2028 2250 7.603784 TCATATTAGCATGCAGATCAAACGTAT 59.396 33.333 21.98 0.00 0.00 3.06
2029 2251 6.928492 TCATATTAGCATGCAGATCAAACGTA 59.072 34.615 21.98 0.00 0.00 3.57
2030 2252 5.759763 TCATATTAGCATGCAGATCAAACGT 59.240 36.000 21.98 0.00 0.00 3.99
2031 2253 6.232139 TCATATTAGCATGCAGATCAAACG 57.768 37.500 21.98 0.00 0.00 3.60
2032 2254 7.749570 GTCATCATATTAGCATGCAGATCAAAC 59.250 37.037 21.98 2.39 0.00 2.93
2033 2255 7.446013 TGTCATCATATTAGCATGCAGATCAAA 59.554 33.333 21.98 4.37 0.00 2.69
2034 2256 6.938030 TGTCATCATATTAGCATGCAGATCAA 59.062 34.615 21.98 5.84 0.00 2.57
2035 2257 6.469410 TGTCATCATATTAGCATGCAGATCA 58.531 36.000 21.98 0.59 0.00 2.92
2036 2258 6.980051 TGTCATCATATTAGCATGCAGATC 57.020 37.500 21.98 3.45 0.00 2.75
2037 2259 6.150641 GGTTGTCATCATATTAGCATGCAGAT 59.849 38.462 21.98 15.13 0.00 2.90
2038 2260 5.471116 GGTTGTCATCATATTAGCATGCAGA 59.529 40.000 21.98 8.07 0.00 4.26
2039 2261 5.472478 AGGTTGTCATCATATTAGCATGCAG 59.528 40.000 21.98 2.25 0.00 4.41
2040 2262 5.379187 AGGTTGTCATCATATTAGCATGCA 58.621 37.500 21.98 0.00 0.00 3.96
2041 2263 5.954296 AGGTTGTCATCATATTAGCATGC 57.046 39.130 10.51 10.51 0.00 4.06
2045 2267 9.237846 GCTTAAAAAGGTTGTCATCATATTAGC 57.762 33.333 0.00 0.00 0.00 3.09
2048 2270 9.423061 GTTGCTTAAAAAGGTTGTCATCATATT 57.577 29.630 0.00 0.00 0.00 1.28
2049 2271 8.806146 AGTTGCTTAAAAAGGTTGTCATCATAT 58.194 29.630 0.00 0.00 0.00 1.78
2050 2272 8.081633 CAGTTGCTTAAAAAGGTTGTCATCATA 58.918 33.333 0.00 0.00 0.00 2.15
2051 2273 6.925165 CAGTTGCTTAAAAAGGTTGTCATCAT 59.075 34.615 0.00 0.00 0.00 2.45
2052 2274 6.127479 ACAGTTGCTTAAAAAGGTTGTCATCA 60.127 34.615 0.00 0.00 0.00 3.07
2053 2275 6.198966 CACAGTTGCTTAAAAAGGTTGTCATC 59.801 38.462 0.00 0.00 0.00 2.92
2054 2276 6.042143 CACAGTTGCTTAAAAAGGTTGTCAT 58.958 36.000 0.00 0.00 0.00 3.06
2055 2277 5.184096 TCACAGTTGCTTAAAAAGGTTGTCA 59.816 36.000 0.00 0.00 0.00 3.58
2056 2278 5.646606 TCACAGTTGCTTAAAAAGGTTGTC 58.353 37.500 0.00 0.00 0.00 3.18
2057 2279 5.417580 TCTCACAGTTGCTTAAAAAGGTTGT 59.582 36.000 0.00 0.00 0.00 3.32
2058 2280 5.890334 TCTCACAGTTGCTTAAAAAGGTTG 58.110 37.500 0.00 0.00 0.00 3.77
2059 2281 6.715347 ATCTCACAGTTGCTTAAAAAGGTT 57.285 33.333 0.00 0.00 0.00 3.50
2060 2282 6.321181 TGAATCTCACAGTTGCTTAAAAAGGT 59.679 34.615 0.00 0.00 0.00 3.50
2061 2283 6.738114 TGAATCTCACAGTTGCTTAAAAAGG 58.262 36.000 0.00 0.00 0.00 3.11
2062 2284 9.334693 GTATGAATCTCACAGTTGCTTAAAAAG 57.665 33.333 0.00 0.00 0.00 2.27
2063 2285 8.845227 TGTATGAATCTCACAGTTGCTTAAAAA 58.155 29.630 0.00 0.00 0.00 1.94
2064 2286 8.389779 TGTATGAATCTCACAGTTGCTTAAAA 57.610 30.769 0.00 0.00 0.00 1.52
2065 2287 7.977789 TGTATGAATCTCACAGTTGCTTAAA 57.022 32.000 0.00 0.00 0.00 1.52
2066 2288 7.977789 TTGTATGAATCTCACAGTTGCTTAA 57.022 32.000 0.00 0.00 0.00 1.85
2067 2289 7.661437 AGTTTGTATGAATCTCACAGTTGCTTA 59.339 33.333 0.00 0.00 0.00 3.09
2068 2290 6.488006 AGTTTGTATGAATCTCACAGTTGCTT 59.512 34.615 0.00 0.00 0.00 3.91
2069 2291 6.000219 AGTTTGTATGAATCTCACAGTTGCT 59.000 36.000 0.00 0.00 0.00 3.91
2070 2292 6.246420 AGTTTGTATGAATCTCACAGTTGC 57.754 37.500 0.00 0.00 0.00 4.17
2079 2301 9.588096 ACCCTTCTTAAAAGTTTGTATGAATCT 57.412 29.630 0.00 0.00 0.00 2.40
2080 2302 9.626045 CACCCTTCTTAAAAGTTTGTATGAATC 57.374 33.333 0.00 0.00 0.00 2.52
2081 2303 9.143155 ACACCCTTCTTAAAAGTTTGTATGAAT 57.857 29.630 0.00 0.00 0.00 2.57
2082 2304 8.528044 ACACCCTTCTTAAAAGTTTGTATGAA 57.472 30.769 0.00 0.00 0.00 2.57
2083 2305 9.059260 GTACACCCTTCTTAAAAGTTTGTATGA 57.941 33.333 0.00 0.00 0.00 2.15
2084 2306 9.063615 AGTACACCCTTCTTAAAAGTTTGTATG 57.936 33.333 0.00 0.00 0.00 2.39
2085 2307 9.063615 CAGTACACCCTTCTTAAAAGTTTGTAT 57.936 33.333 0.00 0.00 0.00 2.29
2086 2308 8.266473 TCAGTACACCCTTCTTAAAAGTTTGTA 58.734 33.333 0.00 0.00 0.00 2.41
2087 2309 7.114095 TCAGTACACCCTTCTTAAAAGTTTGT 58.886 34.615 0.00 0.00 0.00 2.83
2088 2310 7.562454 TCAGTACACCCTTCTTAAAAGTTTG 57.438 36.000 0.00 0.00 0.00 2.93
2089 2311 7.201794 GCTTCAGTACACCCTTCTTAAAAGTTT 60.202 37.037 0.00 0.00 0.00 2.66
2090 2312 6.262496 GCTTCAGTACACCCTTCTTAAAAGTT 59.738 38.462 0.00 0.00 0.00 2.66
2091 2313 5.763698 GCTTCAGTACACCCTTCTTAAAAGT 59.236 40.000 0.00 0.00 0.00 2.66
2092 2314 5.763204 TGCTTCAGTACACCCTTCTTAAAAG 59.237 40.000 0.00 0.00 0.00 2.27
2093 2315 5.686753 TGCTTCAGTACACCCTTCTTAAAA 58.313 37.500 0.00 0.00 0.00 1.52
2094 2316 5.298989 TGCTTCAGTACACCCTTCTTAAA 57.701 39.130 0.00 0.00 0.00 1.52
2095 2317 4.967084 TGCTTCAGTACACCCTTCTTAA 57.033 40.909 0.00 0.00 0.00 1.85
2096 2318 4.967084 TTGCTTCAGTACACCCTTCTTA 57.033 40.909 0.00 0.00 0.00 2.10
2097 2319 3.857157 TTGCTTCAGTACACCCTTCTT 57.143 42.857 0.00 0.00 0.00 2.52
2098 2320 3.857157 TTTGCTTCAGTACACCCTTCT 57.143 42.857 0.00 0.00 0.00 2.85
2099 2321 3.883489 AGTTTTGCTTCAGTACACCCTTC 59.117 43.478 0.00 0.00 0.00 3.46
2100 2322 3.883489 GAGTTTTGCTTCAGTACACCCTT 59.117 43.478 0.00 0.00 0.00 3.95
2101 2323 3.118038 TGAGTTTTGCTTCAGTACACCCT 60.118 43.478 0.00 0.00 0.00 4.34
2102 2324 3.211045 TGAGTTTTGCTTCAGTACACCC 58.789 45.455 0.00 0.00 0.00 4.61
2103 2325 4.893424 TTGAGTTTTGCTTCAGTACACC 57.107 40.909 0.00 0.00 0.00 4.16
2104 2326 8.034058 AGATATTGAGTTTTGCTTCAGTACAC 57.966 34.615 0.00 0.00 0.00 2.90
2105 2327 9.719355 TTAGATATTGAGTTTTGCTTCAGTACA 57.281 29.630 0.00 0.00 0.00 2.90
2152 2374 5.592054 CAAGTTCCTAAGACGCTATGATGA 58.408 41.667 0.00 0.00 0.00 2.92
2191 2413 1.098712 GGAACAAACACGCACCTCCA 61.099 55.000 0.00 0.00 0.00 3.86
2193 2415 1.098712 TGGGAACAAACACGCACCTC 61.099 55.000 0.00 0.00 37.44 3.85
2335 2561 3.945285 GACGAATTGGCCTTTTCCTATCA 59.055 43.478 3.32 0.00 0.00 2.15
2355 2588 5.537300 TGTGAGCTCCTTATATCCTTGAC 57.463 43.478 12.15 0.00 0.00 3.18
2385 2618 2.635915 TGGGTATTATGTAGCTTCGGGG 59.364 50.000 0.00 0.00 0.00 5.73
2404 2646 6.144854 CAGACACAGTTTGTTTCATACATGG 58.855 40.000 0.00 0.00 39.17 3.66
2421 2768 4.897509 ATTTCCTGAGATGACAGACACA 57.102 40.909 0.00 0.00 39.94 3.72
2435 2782 8.945481 TGCAAAATGGTATTATCAATTTCCTG 57.055 30.769 0.00 0.00 0.00 3.86
2451 2798 9.171701 CACAACAATAAAAATTCTGCAAAATGG 57.828 29.630 0.00 0.00 0.00 3.16
2454 2801 7.148188 TGGCACAACAATAAAAATTCTGCAAAA 60.148 29.630 0.00 0.00 31.92 2.44
2506 2854 1.614824 CCTCCTGGTTGCCTCCTCT 60.615 63.158 0.00 0.00 0.00 3.69
2580 2928 0.438830 GTTGCTGCCGTTTAGAGACG 59.561 55.000 0.00 0.00 42.43 4.18
2686 3034 1.828660 ATAGACGAGGAGGTGGGCG 60.829 63.158 0.00 0.00 0.00 6.13
2692 3040 0.671251 GGTGCTCATAGACGAGGAGG 59.329 60.000 0.00 0.00 36.44 4.30
2765 3113 1.492133 CCCCTGAGCAACTGGAGGAA 61.492 60.000 8.05 0.00 39.52 3.36
2796 3144 5.872070 GCATACTTGGAAGTGATAGGATAGC 59.128 44.000 2.14 0.00 40.07 2.97
2825 3174 7.389053 AGAAGGTTGACAATTCATTGAGAGTAC 59.611 37.037 6.53 0.00 40.14 2.73
2832 3181 4.021719 AGGCAGAAGGTTGACAATTCATTG 60.022 41.667 4.74 0.00 43.26 2.82
2856 3207 2.128035 GATATAGATATGGGCGCGCAC 58.872 52.381 34.42 32.34 0.00 5.34
2863 3214 6.935208 TCGATCGGTACAGATATAGATATGGG 59.065 42.308 16.41 0.00 0.00 4.00
2944 3301 5.799213 AGTCTTTGGTTGGAGAATCTGTAG 58.201 41.667 0.00 0.00 33.73 2.74
3051 3411 4.638304 TGGCATGATGAGACACTGATATG 58.362 43.478 0.00 0.00 0.00 1.78
3052 3412 4.968971 TGGCATGATGAGACACTGATAT 57.031 40.909 0.00 0.00 0.00 1.63
3053 3413 4.968971 ATGGCATGATGAGACACTGATA 57.031 40.909 0.00 0.00 0.00 2.15
3054 3414 3.859061 ATGGCATGATGAGACACTGAT 57.141 42.857 0.00 0.00 0.00 2.90
3055 3415 4.560108 CGATATGGCATGATGAGACACTGA 60.560 45.833 10.98 0.00 0.00 3.41
3056 3416 3.678548 CGATATGGCATGATGAGACACTG 59.321 47.826 10.98 0.00 0.00 3.66
3057 3417 3.306571 CCGATATGGCATGATGAGACACT 60.307 47.826 10.98 0.00 0.00 3.55
3058 3418 2.998670 CCGATATGGCATGATGAGACAC 59.001 50.000 10.98 0.00 0.00 3.67
3059 3419 3.323751 CCGATATGGCATGATGAGACA 57.676 47.619 10.98 0.00 0.00 3.41
3078 3438 3.238441 CTGATCTATAAGCTCGAACGCC 58.762 50.000 0.00 0.00 0.00 5.68
3105 3465 0.537143 ATGCGGAAGTTGGAAGCACA 60.537 50.000 0.00 0.00 40.82 4.57
3110 3470 0.693622 TGGGTATGCGGAAGTTGGAA 59.306 50.000 0.00 0.00 0.00 3.53
3111 3471 0.251916 CTGGGTATGCGGAAGTTGGA 59.748 55.000 0.00 0.00 0.00 3.53
3121 3481 7.122204 ACCTTATTTGTTTACTTCTGGGTATGC 59.878 37.037 0.00 0.00 0.00 3.14
3129 3489 8.437575 TGAGAAGGACCTTATTTGTTTACTTCT 58.562 33.333 6.75 0.00 43.21 2.85
3134 3494 9.416284 ACTTTTGAGAAGGACCTTATTTGTTTA 57.584 29.630 6.75 0.00 0.00 2.01
3216 3831 9.899226 GGTATGTCCATTCTAAATTTCTAATGC 57.101 33.333 15.22 7.48 35.97 3.56
3241 3856 9.956797 GACAAATTTTTCATAATTTCGTCATGG 57.043 29.630 0.00 0.00 35.98 3.66
3247 3862 7.685304 GCTGCAGACAAATTTTTCATAATTTCG 59.315 33.333 20.43 0.00 35.98 3.46
3277 3892 7.186804 CCGTGTCTCCAATTTTCATAACATAC 58.813 38.462 0.00 0.00 0.00 2.39
3294 3909 4.430908 CATCCTTTTAGTACCCGTGTCTC 58.569 47.826 0.00 0.00 0.00 3.36
3302 3917 5.353123 TGAATTCACGCATCCTTTTAGTACC 59.647 40.000 3.38 0.00 0.00 3.34
3303 3918 6.417191 TGAATTCACGCATCCTTTTAGTAC 57.583 37.500 3.38 0.00 0.00 2.73
3318 3933 3.572255 TGTAACCCCTTGCTTGAATTCAC 59.428 43.478 7.89 0.00 0.00 3.18
3349 3964 7.387397 TGACTTTTTATTTGGCTAATTGGCTTG 59.613 33.333 13.90 0.00 42.34 4.01
3352 3967 7.518161 GTTGACTTTTTATTTGGCTAATTGGC 58.482 34.615 5.01 5.01 42.18 4.52
3366 3982 9.724839 CTTGGTTATTTTCTCGTTGACTTTTTA 57.275 29.630 0.00 0.00 0.00 1.52
3432 4049 5.304357 CACTTTATTTGGGAGGTCCTTGTTT 59.696 40.000 0.00 0.00 36.20 2.83
3439 4056 2.755103 CAGGCACTTTATTTGGGAGGTC 59.245 50.000 0.00 0.00 34.60 3.85
3447 4064 8.034804 GGTTATTGATGTTCAGGCACTTTATTT 58.965 33.333 0.00 0.00 34.60 1.40
3455 4072 3.448093 TGGGTTATTGATGTTCAGGCA 57.552 42.857 0.00 0.00 0.00 4.75
3474 4091 4.322198 CCCATCTTGGACAGGTTTCATTTG 60.322 45.833 0.00 0.00 40.96 2.32
3478 4095 1.075374 CCCCATCTTGGACAGGTTTCA 59.925 52.381 0.00 0.00 40.96 2.69
3520 4137 8.770438 TGAGGTTTTATACATTTTGCAAATCC 57.230 30.769 13.65 0.00 0.00 3.01
3551 4168 7.386848 GCTGTTAGTACAAAGTTTATGACCTCA 59.613 37.037 0.00 0.00 32.92 3.86
3589 4210 0.668096 TTGTACCGTGGATGCACGTC 60.668 55.000 33.10 23.46 46.04 4.34
3590 4211 0.669318 CTTGTACCGTGGATGCACGT 60.669 55.000 33.10 23.96 46.04 4.49
3591 4212 0.669318 ACTTGTACCGTGGATGCACG 60.669 55.000 30.14 30.14 46.92 5.34
3592 4213 1.519408 AACTTGTACCGTGGATGCAC 58.481 50.000 7.39 7.39 0.00 4.57
3655 4276 1.705186 AGTCTTGCTTTTCCCTAGCCA 59.295 47.619 0.00 0.00 37.85 4.75
3663 4284 4.134563 TCAAGTGGGTAGTCTTGCTTTTC 58.865 43.478 0.00 0.00 40.27 2.29
3687 4308 8.616076 GCTGTAAGTTATGCTGATTATTTCTGT 58.384 33.333 4.30 0.00 35.30 3.41
3859 4500 6.373186 TGATGTAGGTACATAGAACTGACG 57.627 41.667 2.56 0.00 46.20 4.35
3860 4501 8.414003 TGATTGATGTAGGTACATAGAACTGAC 58.586 37.037 2.56 0.00 46.20 3.51
3862 4503 9.035607 GTTGATTGATGTAGGTACATAGAACTG 57.964 37.037 2.56 0.00 46.20 3.16
3876 4517 4.080919 AGTGCCTAGCAGTTGATTGATGTA 60.081 41.667 0.00 0.00 39.37 2.29
3888 4529 4.688021 CCTTTCTTAGTAGTGCCTAGCAG 58.312 47.826 0.00 0.00 40.08 4.24
3924 4565 2.689471 TGTGCAGTTTCTCATTGTTGCT 59.311 40.909 0.00 0.00 33.00 3.91
3958 4599 5.104941 TGGATACCTGAAGTTCCAGTATGTG 60.105 44.000 15.80 0.00 33.44 3.21
4016 4657 2.879756 GCCTAAAAGGGTGACTGCATCA 60.880 50.000 0.00 0.00 35.37 3.07


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

AutoCloner maintained by Alex Coulton.