Multiple sequence alignment - TraesCS5A01G111300

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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 TraesCS5A01G111300 chr5A 100.000 2962 0 0 1 2962 214165404 214168365 0.000000e+00 5470.0
1 TraesCS5A01G111300 chr5D 91.650 1988 89 41 1 1951 200500056 200502003 0.000000e+00 2680.0
2 TraesCS5A01G111300 chr5D 93.706 286 13 2 2171 2452 200502368 200502652 9.810000e-115 424.0
3 TraesCS5A01G111300 chr5D 85.973 221 20 8 1952 2167 200502054 200502268 2.970000e-55 226.0
4 TraesCS5A01G111300 chr5D 89.231 130 12 2 2773 2901 200503371 200503499 8.500000e-36 161.0
5 TraesCS5A01G111300 chr5D 85.075 134 20 0 1001 1134 425077485 425077352 1.430000e-28 137.0
6 TraesCS5A01G111300 chr5D 83.217 143 21 3 1235 1375 425077353 425077212 8.620000e-26 128.0
7 TraesCS5A01G111300 chr5B 92.742 1860 75 28 96 1951 211145171 211146974 0.000000e+00 2632.0
8 TraesCS5A01G111300 chr5B 93.080 289 15 2 2171 2455 211147334 211147621 4.570000e-113 418.0
9 TraesCS5A01G111300 chr5B 85.646 209 19 8 1953 2156 211147026 211147228 2.990000e-50 209.0
10 TraesCS5A01G111300 chr5B 85.075 134 20 0 1001 1134 514279627 514279494 1.430000e-28 137.0
11 TraesCS5A01G111300 chr5B 83.217 143 21 3 1235 1375 514279495 514279354 8.620000e-26 128.0
12 TraesCS5A01G111300 chr4B 78.261 644 87 42 993 1619 100576433 100577040 6.030000e-97 364.0
13 TraesCS5A01G111300 chr4A 80.263 380 45 19 993 1369 517884376 517884728 2.930000e-65 259.0
14 TraesCS5A01G111300 chr4A 93.525 139 8 1 1481 1619 517884841 517884978 3.870000e-49 206.0
15 TraesCS5A01G111300 chr4A 100.000 37 0 0 2470 2506 17258510 17258546 5.300000e-08 69.4
16 TraesCS5A01G111300 chr4A 97.368 38 1 0 2470 2507 121501312 121501275 6.850000e-07 65.8
17 TraesCS5A01G111300 chr4D 93.525 139 8 1 1481 1619 68053661 68053798 3.870000e-49 206.0
18 TraesCS5A01G111300 chr4D 90.278 144 13 1 993 1136 68053182 68053324 1.400000e-43 187.0
19 TraesCS5A01G111300 chr4D 88.571 140 16 0 1230 1369 68053409 68053548 1.410000e-38 171.0
20 TraesCS5A01G111300 chr1D 91.339 127 11 0 1489 1615 364624919 364624793 1.090000e-39 174.0
21 TraesCS5A01G111300 chr1B 90.769 130 12 0 1486 1615 487951130 487951001 1.090000e-39 174.0
22 TraesCS5A01G111300 chr1A 90.551 127 12 0 1489 1615 463461337 463461211 5.080000e-38 169.0
23 TraesCS5A01G111300 chr1A 85.714 56 5 3 2452 2507 23234759 23234811 4.120000e-04 56.5
24 TraesCS5A01G111300 chr3D 88.800 125 14 0 1486 1610 492131786 492131910 1.420000e-33 154.0
25 TraesCS5A01G111300 chr3A 85.507 138 19 1 988 1125 633922089 633922225 3.080000e-30 143.0
26 TraesCS5A01G111300 chr3A 77.941 136 30 0 1234 1369 470829759 470829624 5.260000e-13 86.1
27 TraesCS5A01G111300 chr3A 92.982 57 3 1 2906 2962 107068579 107068524 6.800000e-12 82.4
28 TraesCS5A01G111300 chr3B 85.714 133 18 1 993 1125 653152044 653152175 3.980000e-29 139.0
29 TraesCS5A01G111300 chr2B 80.519 154 27 3 1 153 42498458 42498307 6.710000e-22 115.0
30 TraesCS5A01G111300 chr2B 78.431 153 33 0 1 153 42491141 42490989 1.880000e-17 100.0
31 TraesCS5A01G111300 chr2B 77.778 153 34 0 1 153 42492965 42492813 8.740000e-16 95.3
32 TraesCS5A01G111300 chr2B 77.778 153 34 0 1 153 42494803 42494651 8.740000e-16 95.3
33 TraesCS5A01G111300 chr2B 77.778 153 34 0 1 153 42496629 42496477 8.740000e-16 95.3
34 TraesCS5A01G111300 chr7D 82.883 111 17 2 1231 1340 380145182 380145291 6.760000e-17 99.0
35 TraesCS5A01G111300 chr6D 84.536 97 13 2 1481 1576 309719541 309719636 8.740000e-16 95.3
36 TraesCS5A01G111300 chr6D 95.000 40 2 0 2475 2514 436760990 436760951 2.460000e-06 63.9
37 TraesCS5A01G111300 chr6B 84.536 97 13 2 1481 1576 477691815 477691910 8.740000e-16 95.3
38 TraesCS5A01G111300 chr6B 97.368 38 1 0 2470 2507 691119386 691119423 6.850000e-07 65.8
39 TraesCS5A01G111300 chr6A 84.536 97 13 2 1481 1576 446521686 446521781 8.740000e-16 95.3
40 TraesCS5A01G111300 chr6A 97.368 38 1 0 2470 2507 447635281 447635244 6.850000e-07 65.8
41 TraesCS5A01G111300 chr2D 86.076 79 11 0 1488 1566 466723987 466723909 5.260000e-13 86.1
42 TraesCS5A01G111300 chr2D 97.368 38 1 0 2470 2507 116513228 116513265 6.850000e-07 65.8
43 TraesCS5A01G111300 chr7A 97.368 38 1 0 2470 2507 194457039 194457002 6.850000e-07 65.8
44 TraesCS5A01G111300 chr2A 100.000 31 0 0 2475 2505 173354840 173354870 1.150000e-04 58.4


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 TraesCS5A01G111300 chr5A 214165404 214168365 2961 False 5470.000000 5470 100.000000 1 2962 1 chr5A.!!$F1 2961
1 TraesCS5A01G111300 chr5D 200500056 200503499 3443 False 872.750000 2680 90.140000 1 2901 4 chr5D.!!$F1 2900
2 TraesCS5A01G111300 chr5B 211145171 211147621 2450 False 1086.333333 2632 90.489333 96 2455 3 chr5B.!!$F1 2359
3 TraesCS5A01G111300 chr4B 100576433 100577040 607 False 364.000000 364 78.261000 993 1619 1 chr4B.!!$F1 626
4 TraesCS5A01G111300 chr4A 517884376 517884978 602 False 232.500000 259 86.894000 993 1619 2 chr4A.!!$F2 626

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
899 934 0.108615 CAGTCGTCACTTGCCTAGGG 60.109 60.0 11.72 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 3449 0.036388 GTCATTGTGGAAGCGGAGGA 60.036 55.0 0.0 0.0 0.0 3.71 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
42 43 9.935682 AAATGACACGTAAATCATGATGATTAC 57.064 29.630 19.93 13.52 45.57 1.89
43 44 7.160633 TGACACGTAAATCATGATGATTACG 57.839 36.000 31.89 31.89 45.57 3.18
44 45 6.754675 TGACACGTAAATCATGATGATTACGT 59.245 34.615 32.79 32.79 45.57 3.57
45 46 7.916450 TGACACGTAAATCATGATGATTACGTA 59.084 33.333 35.11 25.72 45.57 3.57
46 47 8.812147 ACACGTAAATCATGATGATTACGTAT 57.188 30.769 35.11 29.03 45.57 3.06
47 48 8.912658 ACACGTAAATCATGATGATTACGTATC 58.087 33.333 35.11 16.70 45.57 2.24
107 108 3.955650 ACGTGTAGTCACAGGCTAATT 57.044 42.857 0.00 0.00 42.93 1.40
129 130 8.574251 AATTTACTAGCATGTGTATGTTTCCA 57.426 30.769 0.00 0.00 36.65 3.53
162 163 6.926272 GCACGAGAAATTATCTTCTGGTCTAT 59.074 38.462 0.00 0.00 40.95 1.98
177 178 9.582431 CTTCTGGTCTATTCGTAAAAGACATTA 57.418 33.333 9.18 0.00 41.15 1.90
179 180 9.932207 TCTGGTCTATTCGTAAAAGACATTAAA 57.068 29.630 9.18 0.00 41.15 1.52
266 269 8.752766 TGTACTTCAAAAGAGTATAAGGTTCG 57.247 34.615 0.00 0.00 32.67 3.95
270 273 8.311836 ACTTCAAAAGAGTATAAGGTTCGATCA 58.688 33.333 0.00 0.00 0.00 2.92
276 279 6.071984 AGAGTATAAGGTTCGATCATCCACT 58.928 40.000 0.00 0.00 0.00 4.00
285 288 2.159240 TCGATCATCCACTTCGTCCTTG 60.159 50.000 0.00 0.00 34.60 3.61
294 297 0.951040 CTTCGTCCTTGGTCCAGCAC 60.951 60.000 0.00 0.00 0.00 4.40
312 315 2.724454 CACTCCTCTTTCCCTCTCGTA 58.276 52.381 0.00 0.00 0.00 3.43
391 394 9.076596 GTTCTTGCCAAATAAGTGATTATCAAC 57.923 33.333 0.00 0.00 0.00 3.18
510 527 2.332514 CACAGGTTGCAAGTGCGG 59.667 61.111 0.00 0.00 45.83 5.69
567 584 2.317900 TGAGATAGGACAAGGGAGGGAA 59.682 50.000 0.00 0.00 0.00 3.97
569 586 3.388913 AGATAGGACAAGGGAGGGAAAG 58.611 50.000 0.00 0.00 0.00 2.62
615 648 6.303054 AGAAAGAAAGAAAGAAGAAGAGGGG 58.697 40.000 0.00 0.00 0.00 4.79
715 750 0.465460 CACCCTCCTCTCTCTCCTCG 60.465 65.000 0.00 0.00 0.00 4.63
855 890 0.476771 CCGCCACCATATAACCCCTT 59.523 55.000 0.00 0.00 0.00 3.95
858 893 2.594131 GCCACCATATAACCCCTTTCC 58.406 52.381 0.00 0.00 0.00 3.13
896 931 0.240145 CGACAGTCGTCACTTGCCTA 59.760 55.000 15.21 0.00 42.74 3.93
897 932 1.729472 CGACAGTCGTCACTTGCCTAG 60.729 57.143 15.21 0.00 42.74 3.02
898 933 0.603569 ACAGTCGTCACTTGCCTAGG 59.396 55.000 3.67 3.67 0.00 3.02
899 934 0.108615 CAGTCGTCACTTGCCTAGGG 60.109 60.000 11.72 0.00 0.00 3.53
913 948 1.618345 CCTAGGGCTGTGTCTGTCTCT 60.618 57.143 0.00 0.00 0.00 3.10
914 949 1.748493 CTAGGGCTGTGTCTGTCTCTC 59.252 57.143 0.00 0.00 0.00 3.20
915 950 0.114168 AGGGCTGTGTCTGTCTCTCT 59.886 55.000 0.00 0.00 0.00 3.10
917 952 1.544724 GGCTGTGTCTGTCTCTCTCT 58.455 55.000 0.00 0.00 0.00 3.10
918 953 1.472480 GGCTGTGTCTGTCTCTCTCTC 59.528 57.143 0.00 0.00 0.00 3.20
919 954 2.436417 GCTGTGTCTGTCTCTCTCTCT 58.564 52.381 0.00 0.00 0.00 3.10
920 955 2.420022 GCTGTGTCTGTCTCTCTCTCTC 59.580 54.545 0.00 0.00 0.00 3.20
921 956 3.869912 GCTGTGTCTGTCTCTCTCTCTCT 60.870 52.174 0.00 0.00 0.00 3.10
923 958 2.930040 GTGTCTGTCTCTCTCTCTCTCG 59.070 54.545 0.00 0.00 0.00 4.04
924 959 1.933853 GTCTGTCTCTCTCTCTCTCGC 59.066 57.143 0.00 0.00 0.00 5.03
925 960 1.831106 TCTGTCTCTCTCTCTCTCGCT 59.169 52.381 0.00 0.00 0.00 4.93
926 961 2.159099 TCTGTCTCTCTCTCTCTCGCTC 60.159 54.545 0.00 0.00 0.00 5.03
927 962 1.831106 TGTCTCTCTCTCTCTCGCTCT 59.169 52.381 0.00 0.00 0.00 4.09
929 964 2.101582 GTCTCTCTCTCTCTCGCTCTCT 59.898 54.545 0.00 0.00 0.00 3.10
930 965 2.362397 TCTCTCTCTCTCTCGCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
931 966 2.363680 CTCTCTCTCTCTCGCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
932 967 2.362397 TCTCTCTCTCTCGCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
933 968 2.363680 CTCTCTCTCTCGCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
934 969 2.362397 TCTCTCTCTCGCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
935 970 2.363680 CTCTCTCTCGCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
936 971 2.362397 TCTCTCTCGCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
937 972 2.363680 CTCTCTCGCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
938 973 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
939 974 2.363680 CTCTCGCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
940 975 2.362397 TCTCGCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
941 976 2.363680 CTCGCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
942 977 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
943 978 2.546795 CGCTCTCTCTCTCTCTCTCTCC 60.547 59.091 0.00 0.00 0.00 3.71
944 979 2.224402 GCTCTCTCTCTCTCTCTCTCCC 60.224 59.091 0.00 0.00 0.00 4.30
945 980 3.312890 CTCTCTCTCTCTCTCTCTCCCT 58.687 54.545 0.00 0.00 0.00 4.20
946 981 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
947 982 3.051803 TCTCTCTCTCTCTCTCTCCCTCT 60.052 52.174 0.00 0.00 0.00 3.69
948 983 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
949 984 2.370189 CTCTCTCTCTCTCTCCCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
950 985 1.421646 CTCTCTCTCTCTCCCTCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
951 986 1.010793 TCTCTCTCTCTCCCTCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
952 987 1.421646 CTCTCTCTCTCCCTCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
955 990 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
965 1000 1.010793 TCTCCCTCTCCCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
970 1005 2.370189 CCTCTCCCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
971 1006 3.312890 CTCTCCCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
972 1007 3.713764 CTCTCCCTCTCTCTCTCTCTCTT 59.286 52.174 0.00 0.00 0.00 2.85
1059 1103 4.344865 GGCGCCTGGACCAAGGAA 62.345 66.667 22.15 0.00 40.02 3.36
1091 1135 0.178767 CTCATCGCCCACATCAAGGA 59.821 55.000 0.00 0.00 0.00 3.36
1143 1187 3.127548 CCAAAGCAGCAGGTACAACATAG 59.872 47.826 0.00 0.00 0.00 2.23
1226 1271 5.007039 GTGATGTTGATTCGTCTGCATGTAT 59.993 40.000 0.00 0.00 0.00 2.29
1312 1359 0.451783 CCTTAAGCGCGGCAATTTCT 59.548 50.000 8.83 0.00 0.00 2.52
1376 1423 4.382685 CCTCGGAAACAAGTAAGCCATCTA 60.383 45.833 0.00 0.00 0.00 1.98
1441 1498 5.931724 TGAAATATATGTGTCGGATGCGATT 59.068 36.000 13.85 0.00 0.00 3.34
1443 1500 5.784750 ATATATGTGTCGGATGCGATTTG 57.215 39.130 13.85 0.00 0.00 2.32
1469 1526 1.798813 GGACGGCGGTGATATTGATTC 59.201 52.381 13.24 0.00 0.00 2.52
1626 1697 3.057548 CGCTCAATGCTGGCACCA 61.058 61.111 0.00 0.00 40.11 4.17
1831 1902 1.383386 TGTCCATAAGCCCGCCCTA 60.383 57.895 0.00 0.00 0.00 3.53
1957 2078 1.364626 GGGTGCAGCTGTGAGATTCG 61.365 60.000 16.64 0.00 0.00 3.34
1971 2092 1.009829 GATTCGTTGATGCCTCGCTT 58.990 50.000 0.00 0.00 0.00 4.68
1972 2093 1.004504 GATTCGTTGATGCCTCGCTTC 60.005 52.381 0.00 0.00 34.04 3.86
2053 2177 8.509690 CAGAGCTCAGATTAATTAGAGAGAGAG 58.490 40.741 17.77 6.30 0.00 3.20
2054 2178 8.439971 AGAGCTCAGATTAATTAGAGAGAGAGA 58.560 37.037 17.77 0.00 0.00 3.10
2056 2180 8.439971 AGCTCAGATTAATTAGAGAGAGAGAGA 58.560 37.037 17.42 0.00 0.00 3.10
2057 2181 9.236006 GCTCAGATTAATTAGAGAGAGAGAGAT 57.764 37.037 17.42 0.00 0.00 2.75
2066 2190 9.607333 AATTAGAGAGAGAGAGATAGAGAGAGA 57.393 37.037 0.00 0.00 0.00 3.10
2067 2191 8.642935 TTAGAGAGAGAGAGATAGAGAGAGAG 57.357 42.308 0.00 0.00 0.00 3.20
2069 2193 6.947733 AGAGAGAGAGAGATAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2071 2195 6.947733 AGAGAGAGAGATAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2072 2196 6.015918 AGAGAGAGATAGAGAGAGAGAGAGG 58.984 48.000 0.00 0.00 0.00 3.69
2073 2197 5.090139 AGAGAGATAGAGAGAGAGAGAGGG 58.910 50.000 0.00 0.00 0.00 4.30
2088 2212 7.831690 AGAGAGAGAGGGGAAATTTATGTTTTC 59.168 37.037 0.00 0.00 33.31 2.29
2116 2240 6.072112 AGCATTTTTGTGTAAGTTGATCGT 57.928 33.333 0.00 0.00 0.00 3.73
2146 2270 5.596836 TTTGTGTTTGCCTTCATTCTCTT 57.403 34.783 0.00 0.00 0.00 2.85
2156 2280 4.530875 CCTTCATTCTCTTATGCCTGGTT 58.469 43.478 0.00 0.00 0.00 3.67
2167 2291 0.392336 TGCCTGGTTTGGATTGCAAC 59.608 50.000 0.00 0.00 0.00 4.17
2168 2292 0.667184 GCCTGGTTTGGATTGCAACG 60.667 55.000 0.00 0.00 0.00 4.10
2340 2564 0.886490 GCTGTGGGTGGTGAAGTCAG 60.886 60.000 0.00 0.00 0.00 3.51
2343 2567 2.567169 CTGTGGGTGGTGAAGTCAGATA 59.433 50.000 0.00 0.00 0.00 1.98
2356 2580 4.046938 AGTCAGATATGCGTTGGTAGTG 57.953 45.455 0.00 0.00 0.00 2.74
2378 2602 0.519077 GCTCAACGCCTTCTTTCCTG 59.481 55.000 0.00 0.00 0.00 3.86
2382 2606 1.001378 CAACGCCTTCTTTCCTGGTTG 60.001 52.381 0.00 0.00 0.00 3.77
2430 2654 5.878116 TCCATTACCACTTCATTTCCGTAAG 59.122 40.000 0.00 0.00 0.00 2.34
2436 2660 4.455877 CCACTTCATTTCCGTAAGCTTCTT 59.544 41.667 0.00 0.00 0.00 2.52
2440 2664 4.894784 TCATTTCCGTAAGCTTCTTCAGT 58.105 39.130 0.00 0.00 0.00 3.41
2442 2666 4.602340 TTTCCGTAAGCTTCTTCAGTCT 57.398 40.909 0.00 0.00 0.00 3.24
2445 2669 1.996191 CGTAAGCTTCTTCAGTCTGCC 59.004 52.381 0.00 0.00 0.00 4.85
2455 2679 0.836606 TCAGTCTGCCCTTTGTCACA 59.163 50.000 0.00 0.00 0.00 3.58
2456 2680 0.947244 CAGTCTGCCCTTTGTCACAC 59.053 55.000 0.00 0.00 0.00 3.82
2461 2685 1.682854 CTGCCCTTTGTCACACATGTT 59.317 47.619 0.00 0.00 0.00 2.71
2462 2686 2.101249 CTGCCCTTTGTCACACATGTTT 59.899 45.455 0.00 0.00 0.00 2.83
2463 2687 2.100584 TGCCCTTTGTCACACATGTTTC 59.899 45.455 0.00 0.00 0.00 2.78
2464 2688 2.100584 GCCCTTTGTCACACATGTTTCA 59.899 45.455 0.00 0.00 0.00 2.69
2466 2690 4.300803 CCCTTTGTCACACATGTTTCATG 58.699 43.478 0.00 7.99 0.00 3.07
2467 2691 4.202141 CCCTTTGTCACACATGTTTCATGT 60.202 41.667 9.21 9.21 0.00 3.21
2468 2692 5.009510 CCCTTTGTCACACATGTTTCATGTA 59.990 40.000 13.76 0.00 0.00 2.29
2469 2693 6.144854 CCTTTGTCACACATGTTTCATGTAG 58.855 40.000 13.76 10.30 0.00 2.74
2470 2694 6.238731 CCTTTGTCACACATGTTTCATGTAGT 60.239 38.462 13.76 11.57 0.00 2.73
2471 2695 5.922739 TGTCACACATGTTTCATGTAGTC 57.077 39.130 13.76 8.91 0.00 2.59
2472 2696 5.610398 TGTCACACATGTTTCATGTAGTCT 58.390 37.500 13.76 0.00 0.00 3.24
2473 2697 6.054941 TGTCACACATGTTTCATGTAGTCTT 58.945 36.000 13.76 0.00 0.00 3.01
2474 2698 7.213678 TGTCACACATGTTTCATGTAGTCTTA 58.786 34.615 13.76 0.00 0.00 2.10
2475 2699 7.713073 TGTCACACATGTTTCATGTAGTCTTAA 59.287 33.333 13.76 0.00 0.00 1.85
2476 2700 8.556194 GTCACACATGTTTCATGTAGTCTTAAA 58.444 33.333 13.76 0.00 0.00 1.52
2477 2701 9.114952 TCACACATGTTTCATGTAGTCTTAAAA 57.885 29.630 13.76 0.00 0.00 1.52
2478 2702 9.897744 CACACATGTTTCATGTAGTCTTAAAAT 57.102 29.630 13.76 0.00 0.00 1.82
2556 2780 9.495572 ACTTAAGACACTTCTTCTAAAATGGAG 57.504 33.333 10.09 0.00 41.48 3.86
2562 2787 7.974504 ACACTTCTTCTAAAATGGAGGAGTAA 58.025 34.615 0.00 0.00 0.00 2.24
2574 2799 9.990868 AAAATGGAGGAGTAATACATAAAAGGT 57.009 29.630 0.00 0.00 0.00 3.50
2577 2802 8.331931 TGGAGGAGTAATACATAAAAGGTCAT 57.668 34.615 0.00 0.00 0.00 3.06
2578 2803 8.778059 TGGAGGAGTAATACATAAAAGGTCATT 58.222 33.333 0.00 0.00 0.00 2.57
2628 2853 9.132521 CCTTAATTTTACAGAACAGAGCAAATG 57.867 33.333 0.00 0.00 0.00 2.32
2636 2861 6.265577 ACAGAACAGAGCAAATGTTGTTTAC 58.734 36.000 6.01 0.00 40.86 2.01
2642 2867 5.174398 CAGAGCAAATGTTGTTTACAAGCAG 59.826 40.000 0.00 0.00 40.89 4.24
2645 2870 4.990426 GCAAATGTTGTTTACAAGCAGGAT 59.010 37.500 0.00 0.00 40.89 3.24
2664 2889 1.921243 TGCGAACATCATCGTAGGTG 58.079 50.000 0.00 0.00 44.49 4.00
2667 2892 2.734175 GCGAACATCATCGTAGGTGACA 60.734 50.000 0.00 0.00 44.49 3.58
2672 2897 1.182667 TCATCGTAGGTGACACCCAG 58.817 55.000 21.32 12.52 39.75 4.45
2687 2912 1.003580 ACCCAGTCCACACAATGCTAG 59.996 52.381 0.00 0.00 0.00 3.42
2692 2917 2.093447 AGTCCACACAATGCTAGCTACC 60.093 50.000 17.23 0.00 0.00 3.18
2695 2920 3.772572 TCCACACAATGCTAGCTACCTAA 59.227 43.478 17.23 0.00 0.00 2.69
2696 2921 4.224147 TCCACACAATGCTAGCTACCTAAA 59.776 41.667 17.23 0.00 0.00 1.85
2698 2923 5.178797 CACACAATGCTAGCTACCTAAACT 58.821 41.667 17.23 0.00 0.00 2.66
2699 2924 5.063944 CACACAATGCTAGCTACCTAAACTG 59.936 44.000 17.23 0.00 0.00 3.16
2700 2925 5.046591 ACACAATGCTAGCTACCTAAACTGA 60.047 40.000 17.23 0.00 0.00 3.41
2701 2926 6.051717 CACAATGCTAGCTACCTAAACTGAT 58.948 40.000 17.23 0.00 0.00 2.90
2702 2927 6.018425 CACAATGCTAGCTACCTAAACTGATG 60.018 42.308 17.23 0.32 0.00 3.07
2703 2928 5.878406 ATGCTAGCTACCTAAACTGATGT 57.122 39.130 17.23 0.00 0.00 3.06
2706 3375 5.067936 TGCTAGCTACCTAAACTGATGTCTC 59.932 44.000 17.23 0.00 0.00 3.36
2725 3394 3.052036 CTCCATTTTGTGCAAGTTTCCG 58.948 45.455 0.00 0.00 0.00 4.30
2726 3395 2.134346 CCATTTTGTGCAAGTTTCCGG 58.866 47.619 0.00 0.00 0.00 5.14
2742 3411 4.577988 TTCCGGTCCTTGATTTTATCCA 57.422 40.909 0.00 0.00 0.00 3.41
2754 3423 9.578439 CCTTGATTTTATCCAAGATTTGAGAAC 57.422 33.333 0.00 0.00 41.56 3.01
2778 3447 0.880278 GACGTGAGCTCCAACTTGCA 60.880 55.000 12.15 0.00 0.00 4.08
2779 3448 0.250467 ACGTGAGCTCCAACTTGCAT 60.250 50.000 12.15 0.00 0.00 3.96
2780 3449 0.877071 CGTGAGCTCCAACTTGCATT 59.123 50.000 12.15 0.00 0.00 3.56
2781 3450 1.135859 CGTGAGCTCCAACTTGCATTC 60.136 52.381 12.15 0.00 0.00 2.67
2783 3452 1.074405 TGAGCTCCAACTTGCATTCCT 59.926 47.619 12.15 0.00 0.00 3.36
2784 3453 1.742268 GAGCTCCAACTTGCATTCCTC 59.258 52.381 0.87 0.00 0.00 3.71
2785 3454 0.813821 GCTCCAACTTGCATTCCTCC 59.186 55.000 0.00 0.00 0.00 4.30
2786 3455 1.089920 CTCCAACTTGCATTCCTCCG 58.910 55.000 0.00 0.00 0.00 4.63
2788 3457 0.962356 CCAACTTGCATTCCTCCGCT 60.962 55.000 0.00 0.00 0.00 5.52
2790 3459 1.135575 CAACTTGCATTCCTCCGCTTC 60.136 52.381 0.00 0.00 0.00 3.86
2801 3495 1.002624 TCCGCTTCCACAATGACCC 60.003 57.895 0.00 0.00 0.00 4.46
2815 3509 1.314534 TGACCCAGCAATGCCAATCG 61.315 55.000 0.00 0.00 0.00 3.34
2816 3510 2.105528 CCCAGCAATGCCAATCGC 59.894 61.111 0.00 0.00 38.31 4.58
2836 3530 3.569200 AAGGAGTCAAAGCCCCGCC 62.569 63.158 0.00 0.00 0.00 6.13
2847 3541 4.840005 CCCCGCCTCTCCGCTTTC 62.840 72.222 0.00 0.00 0.00 2.62
2849 3543 3.775654 CCGCCTCTCCGCTTTCCT 61.776 66.667 0.00 0.00 0.00 3.36
2891 3585 2.086869 CCACCAGTCCATGAATGTGTC 58.913 52.381 0.00 0.00 0.00 3.67
2892 3586 2.086869 CACCAGTCCATGAATGTGTCC 58.913 52.381 0.00 0.00 0.00 4.02
2898 3592 1.307355 CCATGAATGTGTCCGCAGCA 61.307 55.000 0.00 0.00 0.00 4.41
2899 3593 0.736636 CATGAATGTGTCCGCAGCAT 59.263 50.000 0.00 0.00 0.00 3.79
2900 3594 1.019673 ATGAATGTGTCCGCAGCATC 58.980 50.000 0.00 0.00 0.00 3.91
2901 3595 1.349627 GAATGTGTCCGCAGCATCG 59.650 57.895 0.00 0.00 0.00 3.84
2902 3596 1.079197 AATGTGTCCGCAGCATCGA 60.079 52.632 0.00 0.00 0.00 3.59
2903 3597 1.361668 AATGTGTCCGCAGCATCGAC 61.362 55.000 0.00 0.00 0.00 4.20
2904 3598 3.188786 GTGTCCGCAGCATCGACC 61.189 66.667 0.00 0.00 0.00 4.79
2905 3599 4.794439 TGTCCGCAGCATCGACCG 62.794 66.667 0.00 0.00 0.00 4.79
2906 3600 4.492160 GTCCGCAGCATCGACCGA 62.492 66.667 0.00 0.00 0.00 4.69
2907 3601 4.193334 TCCGCAGCATCGACCGAG 62.193 66.667 0.00 0.00 0.00 4.63
2909 3603 4.193334 CGCAGCATCGACCGAGGA 62.193 66.667 8.30 0.00 0.00 3.71
2910 3604 2.184322 GCAGCATCGACCGAGGAA 59.816 61.111 8.30 0.00 0.00 3.36
2911 3605 1.227380 GCAGCATCGACCGAGGAAT 60.227 57.895 8.30 0.00 0.00 3.01
2912 3606 0.032130 GCAGCATCGACCGAGGAATA 59.968 55.000 8.30 0.00 0.00 1.75
2913 3607 1.337260 GCAGCATCGACCGAGGAATAT 60.337 52.381 8.30 0.00 0.00 1.28
2914 3608 2.332104 CAGCATCGACCGAGGAATATG 58.668 52.381 8.30 0.00 0.00 1.78
2915 3609 1.964223 AGCATCGACCGAGGAATATGT 59.036 47.619 8.30 0.00 0.00 2.29
2916 3610 2.365617 AGCATCGACCGAGGAATATGTT 59.634 45.455 8.30 0.00 0.00 2.71
2917 3611 2.476619 GCATCGACCGAGGAATATGTTG 59.523 50.000 8.30 0.00 0.00 3.33
2918 3612 2.882927 TCGACCGAGGAATATGTTGG 57.117 50.000 0.00 0.00 0.00 3.77
2919 3613 1.411246 TCGACCGAGGAATATGTTGGG 59.589 52.381 0.00 0.00 0.00 4.12
2920 3614 1.138266 CGACCGAGGAATATGTTGGGT 59.862 52.381 0.00 0.00 0.00 4.51
2921 3615 2.419574 CGACCGAGGAATATGTTGGGTT 60.420 50.000 0.00 0.00 0.00 4.11
2922 3616 3.617284 GACCGAGGAATATGTTGGGTTT 58.383 45.455 0.00 0.00 0.00 3.27
2923 3617 3.617284 ACCGAGGAATATGTTGGGTTTC 58.383 45.455 0.00 0.00 0.00 2.78
2924 3618 2.612212 CCGAGGAATATGTTGGGTTTCG 59.388 50.000 0.00 0.00 0.00 3.46
2925 3619 3.267483 CGAGGAATATGTTGGGTTTCGT 58.733 45.455 0.00 0.00 0.00 3.85
2926 3620 4.435425 CGAGGAATATGTTGGGTTTCGTA 58.565 43.478 0.00 0.00 0.00 3.43
2927 3621 4.506654 CGAGGAATATGTTGGGTTTCGTAG 59.493 45.833 0.00 0.00 0.00 3.51
2928 3622 5.425630 GAGGAATATGTTGGGTTTCGTAGT 58.574 41.667 0.00 0.00 0.00 2.73
2929 3623 6.549433 AGGAATATGTTGGGTTTCGTAGTA 57.451 37.500 0.00 0.00 0.00 1.82
2930 3624 6.949715 AGGAATATGTTGGGTTTCGTAGTAA 58.050 36.000 0.00 0.00 0.00 2.24
2931 3625 7.571025 AGGAATATGTTGGGTTTCGTAGTAAT 58.429 34.615 0.00 0.00 0.00 1.89
2932 3626 8.050930 AGGAATATGTTGGGTTTCGTAGTAATT 58.949 33.333 0.00 0.00 0.00 1.40
2933 3627 8.680001 GGAATATGTTGGGTTTCGTAGTAATTT 58.320 33.333 0.00 0.00 0.00 1.82
2956 3650 2.325509 AAAATTTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
2957 3651 1.231221 AAATTTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
2958 3652 1.231221 AATTTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
2959 3653 0.796312 ATTTCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
2960 3654 0.249531 TTTCCTACGCACACGCAAGA 60.250 50.000 0.00 0.00 45.53 3.02
2961 3655 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.275632 CGTAATCATCATGATTTACGTGTCATT 58.724 33.333 28.56 11.55 44.03 2.57
31 32 8.982685 AGTAAGCTTTGATACGTAATCATCATG 58.017 33.333 3.20 0.00 44.13 3.07
45 46 8.726988 TGCGTTAAAATCTTAGTAAGCTTTGAT 58.273 29.630 3.20 0.00 28.26 2.57
46 47 8.090250 TGCGTTAAAATCTTAGTAAGCTTTGA 57.910 30.769 3.20 2.92 28.26 2.69
47 48 8.895932 ATGCGTTAAAATCTTAGTAAGCTTTG 57.104 30.769 3.20 2.44 28.26 2.77
51 52 7.960738 TGTTGATGCGTTAAAATCTTAGTAAGC 59.039 33.333 4.93 0.00 0.00 3.09
129 130 2.704725 AATTTCTCGTGCGTTGCAAT 57.295 40.000 0.59 0.00 41.47 3.56
199 202 1.013596 TTCTCGTGTGTTGCAACAGG 58.986 50.000 31.81 22.47 40.05 4.00
201 204 3.773860 AATTTCTCGTGTGTTGCAACA 57.226 38.095 27.96 27.96 36.38 3.33
255 258 5.629849 CGAAGTGGATGATCGAACCTTATAC 59.370 44.000 0.00 0.00 38.82 1.47
276 279 1.070786 GTGCTGGACCAAGGACGAA 59.929 57.895 0.00 0.00 0.00 3.85
285 288 0.035915 GGAAAGAGGAGTGCTGGACC 60.036 60.000 0.00 0.00 0.00 4.46
294 297 3.292460 ACATACGAGAGGGAAAGAGGAG 58.708 50.000 0.00 0.00 0.00 3.69
348 351 6.753897 CAAGAACTTAATGTCTTGCCAAAC 57.246 37.500 12.72 0.00 34.15 2.93
480 483 6.494893 TGCAACCTGTGTCAATATTCTAAC 57.505 37.500 0.00 0.00 0.00 2.34
510 527 7.771183 TGTTTGGTTTCATAGATAATTGCTCC 58.229 34.615 0.00 0.00 0.00 4.70
592 625 5.048364 GCCCCTCTTCTTCTTTCTTTCTTTC 60.048 44.000 0.00 0.00 0.00 2.62
596 629 4.006989 GAGCCCCTCTTCTTCTTTCTTTC 58.993 47.826 0.00 0.00 0.00 2.62
599 632 1.912731 GGAGCCCCTCTTCTTCTTTCT 59.087 52.381 0.00 0.00 0.00 2.52
600 633 1.406205 CGGAGCCCCTCTTCTTCTTTC 60.406 57.143 0.00 0.00 0.00 2.62
606 639 2.364448 GTCCGGAGCCCCTCTTCT 60.364 66.667 3.06 0.00 0.00 2.85
608 641 2.685380 CTGTCCGGAGCCCCTCTT 60.685 66.667 3.06 0.00 0.00 2.85
855 890 2.948889 TGATCTCAGGGAGGAAGGAA 57.051 50.000 0.00 0.00 0.00 3.36
858 893 2.497675 TCGTTTGATCTCAGGGAGGAAG 59.502 50.000 0.00 0.00 0.00 3.46
893 928 0.820871 GAGACAGACACAGCCCTAGG 59.179 60.000 0.06 0.06 0.00 3.02
896 931 0.114168 AGAGAGACAGACACAGCCCT 59.886 55.000 0.00 0.00 0.00 5.19
897 932 0.530288 GAGAGAGACAGACACAGCCC 59.470 60.000 0.00 0.00 0.00 5.19
898 933 1.472480 GAGAGAGAGACAGACACAGCC 59.528 57.143 0.00 0.00 0.00 4.85
899 934 2.420022 GAGAGAGAGAGACAGACACAGC 59.580 54.545 0.00 0.00 0.00 4.40
913 948 2.362397 GAGAGAGAGAGCGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
914 949 2.363680 AGAGAGAGAGAGCGAGAGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
915 950 2.362397 GAGAGAGAGAGAGCGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
917 952 2.362397 GAGAGAGAGAGAGAGCGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
918 953 2.363680 AGAGAGAGAGAGAGAGCGAGAG 59.636 54.545 0.00 0.00 0.00 3.20
919 954 2.362397 GAGAGAGAGAGAGAGAGCGAGA 59.638 54.545 0.00 0.00 0.00 4.04
920 955 2.363680 AGAGAGAGAGAGAGAGAGCGAG 59.636 54.545 0.00 0.00 0.00 5.03
921 956 2.362397 GAGAGAGAGAGAGAGAGAGCGA 59.638 54.545 0.00 0.00 0.00 4.93
923 958 2.224402 GGGAGAGAGAGAGAGAGAGAGC 60.224 59.091 0.00 0.00 0.00 4.09
924 959 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
925 960 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
926 961 3.312890 AGAGGGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
927 962 3.309296 GAGAGGGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
929 964 2.408565 GGAGAGGGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
930 965 1.421646 GGGAGAGGGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
931 966 1.010793 AGGGAGAGGGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
932 967 1.421646 GAGGGAGAGGGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
933 968 1.010793 AGAGGGAGAGGGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
934 969 1.421646 GAGAGGGAGAGGGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
935 970 1.518367 GAGAGGGAGAGGGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
936 971 0.478507 GGAGAGGGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
937 972 0.996762 GGGAGAGGGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
938 973 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
939 974 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
940 975 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
941 976 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
942 977 0.998945 AGAGAGGGAGAGGGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
943 978 0.478507 GAGAGAGGGAGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
944 979 1.421646 GAGAGAGAGGGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
945 980 1.010793 AGAGAGAGAGGGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
946 981 1.421646 GAGAGAGAGAGGGAGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
947 982 1.010793 AGAGAGAGAGAGGGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
948 983 1.421646 GAGAGAGAGAGAGGGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
949 984 2.370189 GAGAGAGAGAGAGAGGGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
950 985 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
951 986 3.421394 AGAGAGAGAGAGAGAGGGAGA 57.579 52.381 0.00 0.00 0.00 3.71
952 987 3.813443 CAAGAGAGAGAGAGAGAGGGAG 58.187 54.545 0.00 0.00 0.00 4.30
955 990 2.092212 AGGCAAGAGAGAGAGAGAGAGG 60.092 54.545 0.00 0.00 0.00 3.69
1059 1103 1.804396 CGATGAGCCGCTGATCCTCT 61.804 60.000 13.45 0.00 0.00 3.69
1091 1135 1.687612 CAGCACCCTTCTCCATGGT 59.312 57.895 12.58 0.00 0.00 3.55
1162 1207 1.135199 GCATGCCAATGTTGAGTCCTG 60.135 52.381 6.36 0.00 36.08 3.86
1163 1208 1.180029 GCATGCCAATGTTGAGTCCT 58.820 50.000 6.36 0.00 36.08 3.85
1202 1247 3.125829 ACATGCAGACGAATCAACATCAC 59.874 43.478 0.00 0.00 0.00 3.06
1226 1271 1.666553 CGCAGCAACCCTACACGAA 60.667 57.895 0.00 0.00 0.00 3.85
1312 1359 2.125229 CTCGTCCTCCTCGTCGGA 60.125 66.667 0.00 0.00 40.30 4.55
1469 1526 0.390124 TGCAAAGCAAGGAAGCCAAG 59.610 50.000 0.00 0.00 34.76 3.61
1851 1922 2.304761 TCCTAAGAACACCATCCGCTTT 59.695 45.455 0.00 0.00 0.00 3.51
1865 1936 1.770658 TCCGAGTATCCCGTCCTAAGA 59.229 52.381 0.00 0.00 0.00 2.10
1890 1961 5.330295 GTTCAAGCACAAGCATATCTTCTG 58.670 41.667 0.00 0.00 45.49 3.02
1957 2078 4.185413 TCGAAGCGAGGCATCAAC 57.815 55.556 0.00 0.00 0.00 3.18
1971 2092 3.491619 GCTATTGTGCTTCAGGATCTCGA 60.492 47.826 0.00 0.00 0.00 4.04
1972 2093 2.799412 GCTATTGTGCTTCAGGATCTCG 59.201 50.000 0.00 0.00 0.00 4.04
1996 2120 9.679661 TCTGAAGCTAATATCTCGATCTCTAAT 57.320 33.333 0.00 0.00 0.00 1.73
2004 2128 7.283354 TCTGACTTTCTGAAGCTAATATCTCGA 59.717 37.037 0.00 0.00 36.29 4.04
2053 2177 4.168101 TCCCCTCTCTCTCTCTCTATCTC 58.832 52.174 0.00 0.00 0.00 2.75
2054 2178 4.228237 TCCCCTCTCTCTCTCTCTATCT 57.772 50.000 0.00 0.00 0.00 1.98
2056 2180 5.948481 ATTTCCCCTCTCTCTCTCTCTAT 57.052 43.478 0.00 0.00 0.00 1.98
2057 2181 5.742562 AATTTCCCCTCTCTCTCTCTCTA 57.257 43.478 0.00 0.00 0.00 2.43
2058 2182 4.625225 AATTTCCCCTCTCTCTCTCTCT 57.375 45.455 0.00 0.00 0.00 3.10
2059 2183 6.326323 ACATAAATTTCCCCTCTCTCTCTCTC 59.674 42.308 0.00 0.00 0.00 3.20
2061 2185 6.493189 ACATAAATTTCCCCTCTCTCTCTC 57.507 41.667 0.00 0.00 0.00 3.20
2062 2186 6.899892 AACATAAATTTCCCCTCTCTCTCT 57.100 37.500 0.00 0.00 0.00 3.10
2063 2187 7.067615 GGAAAACATAAATTTCCCCTCTCTCTC 59.932 40.741 6.75 0.00 46.61 3.20
2088 2212 2.556622 ACTTACACAAAAATGCTCCGGG 59.443 45.455 0.00 0.00 0.00 5.73
2089 2213 3.915437 ACTTACACAAAAATGCTCCGG 57.085 42.857 0.00 0.00 0.00 5.14
2116 2240 4.707448 TGAAGGCAAACACAAAACTTCCTA 59.293 37.500 0.00 0.00 34.87 2.94
2146 2270 2.228545 TGCAATCCAAACCAGGCATA 57.771 45.000 0.00 0.00 0.00 3.14
2156 2280 0.869068 CGGTACACGTTGCAATCCAA 59.131 50.000 0.59 0.00 37.93 3.53
2167 2291 4.540735 GGCCCCCATCGGTACACG 62.541 72.222 0.00 0.00 46.11 4.49
2168 2292 4.185286 GGGCCCCCATCGGTACAC 62.185 72.222 12.23 0.00 35.81 2.90
2324 2548 3.535561 CATATCTGACTTCACCACCCAC 58.464 50.000 0.00 0.00 0.00 4.61
2326 2550 2.565841 GCATATCTGACTTCACCACCC 58.434 52.381 0.00 0.00 0.00 4.61
2340 2564 2.135933 GCTCCACTACCAACGCATATC 58.864 52.381 0.00 0.00 0.00 1.63
2343 2567 0.108138 GAGCTCCACTACCAACGCAT 60.108 55.000 0.87 0.00 0.00 4.73
2378 2602 2.182014 GTGTCACGAAGCAAAACAACC 58.818 47.619 0.00 0.00 0.00 3.77
2382 2606 2.844122 AAGGTGTCACGAAGCAAAAC 57.156 45.000 0.00 0.00 0.00 2.43
2430 2654 1.538950 CAAAGGGCAGACTGAAGAAGC 59.461 52.381 6.65 0.00 0.00 3.86
2436 2660 0.836606 TGTGACAAAGGGCAGACTGA 59.163 50.000 6.65 0.00 0.00 3.41
2440 2664 1.133823 ACATGTGTGACAAAGGGCAGA 60.134 47.619 0.00 0.00 0.00 4.26
2442 2666 1.774110 AACATGTGTGACAAAGGGCA 58.226 45.000 0.00 0.00 0.00 5.36
2445 2669 4.935702 ACATGAAACATGTGTGACAAAGG 58.064 39.130 15.11 0.00 0.00 3.11
2531 2755 8.940952 CCTCCATTTTAGAAGAAGTGTCTTAAG 58.059 37.037 0.00 0.00 44.42 1.85
2535 2759 6.271159 ACTCCTCCATTTTAGAAGAAGTGTCT 59.729 38.462 0.00 0.00 34.72 3.41
2549 2773 9.628500 GACCTTTTATGTATTACTCCTCCATTT 57.372 33.333 0.00 0.00 0.00 2.32
2550 2774 8.778059 TGACCTTTTATGTATTACTCCTCCATT 58.222 33.333 0.00 0.00 0.00 3.16
2552 2776 7.743116 TGACCTTTTATGTATTACTCCTCCA 57.257 36.000 0.00 0.00 0.00 3.86
2593 2818 9.515226 TGTTCTGTAAAATTAAGGTATGCTCTT 57.485 29.630 0.00 0.00 0.00 2.85
2594 2819 9.167311 CTGTTCTGTAAAATTAAGGTATGCTCT 57.833 33.333 0.00 0.00 0.00 4.09
2595 2820 9.162764 TCTGTTCTGTAAAATTAAGGTATGCTC 57.837 33.333 0.00 0.00 0.00 4.26
2596 2821 9.167311 CTCTGTTCTGTAAAATTAAGGTATGCT 57.833 33.333 0.00 0.00 0.00 3.79
2597 2822 7.910683 GCTCTGTTCTGTAAAATTAAGGTATGC 59.089 37.037 0.00 0.00 0.00 3.14
2598 2823 8.946085 TGCTCTGTTCTGTAAAATTAAGGTATG 58.054 33.333 0.00 0.00 0.00 2.39
2599 2824 9.515226 TTGCTCTGTTCTGTAAAATTAAGGTAT 57.485 29.630 0.00 0.00 0.00 2.73
2600 2825 8.911918 TTGCTCTGTTCTGTAAAATTAAGGTA 57.088 30.769 0.00 0.00 0.00 3.08
2601 2826 7.817418 TTGCTCTGTTCTGTAAAATTAAGGT 57.183 32.000 0.00 0.00 0.00 3.50
2602 2827 9.132521 CATTTGCTCTGTTCTGTAAAATTAAGG 57.867 33.333 0.00 0.00 0.00 2.69
2603 2828 9.683069 ACATTTGCTCTGTTCTGTAAAATTAAG 57.317 29.630 0.00 0.00 0.00 1.85
2613 2838 6.264832 TGTAAACAACATTTGCTCTGTTCTG 58.735 36.000 0.00 0.00 34.69 3.02
2618 2843 5.042593 TGCTTGTAAACAACATTTGCTCTG 58.957 37.500 5.85 0.00 38.10 3.35
2628 2853 2.225491 TCGCATCCTGCTTGTAAACAAC 59.775 45.455 0.00 0.00 42.25 3.32
2636 2861 3.911989 GATGTTCGCATCCTGCTTG 57.088 52.632 0.00 0.00 46.22 4.01
2645 2870 1.474879 TCACCTACGATGATGTTCGCA 59.525 47.619 0.00 0.00 42.82 5.10
2647 2872 2.852413 GTGTCACCTACGATGATGTTCG 59.148 50.000 0.00 0.00 44.56 3.95
2664 2889 1.238439 CATTGTGTGGACTGGGTGTC 58.762 55.000 0.00 0.00 44.63 3.67
2667 2892 1.003580 CTAGCATTGTGTGGACTGGGT 59.996 52.381 0.00 0.00 0.00 4.51
2672 2897 2.093447 AGGTAGCTAGCATTGTGTGGAC 60.093 50.000 24.01 0.00 0.00 4.02
2679 2904 6.051717 ACATCAGTTTAGGTAGCTAGCATTG 58.948 40.000 24.01 11.02 0.00 2.82
2687 2912 4.737855 TGGAGACATCAGTTTAGGTAGC 57.262 45.455 0.00 0.00 33.40 3.58
2702 2927 4.051237 GGAAACTTGCACAAAATGGAGAC 58.949 43.478 0.00 0.00 0.00 3.36
2703 2928 3.243367 CGGAAACTTGCACAAAATGGAGA 60.243 43.478 0.00 0.00 0.00 3.71
2706 3375 2.134346 CCGGAAACTTGCACAAAATGG 58.866 47.619 0.00 0.00 0.00 3.16
2725 3394 8.066612 TCAAATCTTGGATAAAATCAAGGACC 57.933 34.615 0.00 0.00 40.35 4.46
2726 3395 8.960591 TCTCAAATCTTGGATAAAATCAAGGAC 58.039 33.333 0.00 0.00 40.35 3.85
2742 3411 6.097915 TCACGTCTTAGGTTCTCAAATCTT 57.902 37.500 0.00 0.00 0.00 2.40
2754 3423 1.546476 AGTTGGAGCTCACGTCTTAGG 59.454 52.381 17.19 0.00 0.00 2.69
2778 3447 1.281867 TCATTGTGGAAGCGGAGGAAT 59.718 47.619 0.00 0.00 0.00 3.01
2779 3448 0.690192 TCATTGTGGAAGCGGAGGAA 59.310 50.000 0.00 0.00 0.00 3.36
2780 3449 0.036388 GTCATTGTGGAAGCGGAGGA 60.036 55.000 0.00 0.00 0.00 3.71
2781 3450 1.026718 GGTCATTGTGGAAGCGGAGG 61.027 60.000 0.00 0.00 0.00 4.30
2783 3452 1.002624 GGGTCATTGTGGAAGCGGA 60.003 57.895 0.00 0.00 0.00 5.54
2784 3453 1.303236 TGGGTCATTGTGGAAGCGG 60.303 57.895 0.00 0.00 0.00 5.52
2785 3454 1.926511 GCTGGGTCATTGTGGAAGCG 61.927 60.000 0.00 0.00 0.00 4.68
2786 3455 0.895100 TGCTGGGTCATTGTGGAAGC 60.895 55.000 0.00 0.00 0.00 3.86
2788 3457 1.894466 CATTGCTGGGTCATTGTGGAA 59.106 47.619 0.00 0.00 0.00 3.53
2790 3459 0.108520 GCATTGCTGGGTCATTGTGG 60.109 55.000 0.16 0.00 0.00 4.17
2815 3509 1.979155 GGGGCTTTGACTCCTTGGC 60.979 63.158 0.00 0.00 0.00 4.52
2816 3510 1.675641 CGGGGCTTTGACTCCTTGG 60.676 63.158 0.00 0.00 0.00 3.61
2847 3541 2.584608 CACCCCGGTAGCTTCAGG 59.415 66.667 0.00 2.44 0.00 3.86
2849 3543 2.808761 TAGGCACCCCGGTAGCTTCA 62.809 60.000 0.00 0.00 35.76 3.02
2892 3586 2.960957 ATTCCTCGGTCGATGCTGCG 62.961 60.000 0.00 0.00 0.00 5.18
2898 3592 2.037251 CCCAACATATTCCTCGGTCGAT 59.963 50.000 0.00 0.00 0.00 3.59
2899 3593 1.411246 CCCAACATATTCCTCGGTCGA 59.589 52.381 0.00 0.00 0.00 4.20
2900 3594 1.138266 ACCCAACATATTCCTCGGTCG 59.862 52.381 0.00 0.00 0.00 4.79
2901 3595 3.277142 AACCCAACATATTCCTCGGTC 57.723 47.619 0.00 0.00 0.00 4.79
2902 3596 3.617284 GAAACCCAACATATTCCTCGGT 58.383 45.455 0.00 0.00 0.00 4.69
2903 3597 2.612212 CGAAACCCAACATATTCCTCGG 59.388 50.000 0.00 0.00 0.00 4.63
2904 3598 3.267483 ACGAAACCCAACATATTCCTCG 58.733 45.455 0.00 0.00 0.00 4.63
2905 3599 5.425630 ACTACGAAACCCAACATATTCCTC 58.574 41.667 0.00 0.00 0.00 3.71
2906 3600 5.431179 ACTACGAAACCCAACATATTCCT 57.569 39.130 0.00 0.00 0.00 3.36
2907 3601 7.797038 ATTACTACGAAACCCAACATATTCC 57.203 36.000 0.00 0.00 0.00 3.01
2936 3630 2.657184 GCGTGTGCGTAGGAAATTTTT 58.343 42.857 0.00 0.00 40.81 1.94
2937 3631 2.325509 GCGTGTGCGTAGGAAATTTT 57.674 45.000 0.00 0.00 40.81 1.82


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

AutoCloner maintained by Alex Coulton.