Multiple sequence alignment - TraesCS1B01G233600

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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 TraesCS1B01G233600 chr1B 100.000 4583 0 0 1 4583 419401150 419405732 0.000000e+00 8464.0
1 TraesCS1B01G233600 chr1D 92.700 1959 95 18 1 1938 309582926 309584857 0.000000e+00 2782.0
2 TraesCS1B01G233600 chr1D 97.028 673 16 1 2945 3617 309585594 309586262 0.000000e+00 1129.0
3 TraesCS1B01G233600 chr1D 96.010 401 14 1 2061 2461 309584860 309585258 0.000000e+00 651.0
4 TraesCS1B01G233600 chr1D 92.353 170 12 1 2484 2653 309585251 309585419 1.650000e-59 241.0
5 TraesCS1B01G233600 chr1A 93.995 1149 28 11 2490 3617 389130512 389131640 0.000000e+00 1701.0
6 TraesCS1B01G233600 chr1A 91.574 1175 54 19 760 1924 389128942 389130081 0.000000e+00 1580.0
7 TraesCS1B01G233600 chr1A 95.226 398 13 3 2071 2464 389130122 389130517 3.890000e-175 625.0
8 TraesCS1B01G233600 chr4A 93.936 973 54 4 3616 4583 737736541 737735569 0.000000e+00 1465.0
9 TraesCS1B01G233600 chr4A 91.241 137 11 1 1941 2076 236160494 236160630 7.830000e-43 185.0
10 TraesCS1B01G233600 chr7B 95.048 929 39 6 3616 4539 446670649 446671575 0.000000e+00 1454.0
11 TraesCS1B01G233600 chr7B 84.176 752 111 6 5 754 592179455 592180200 0.000000e+00 723.0
12 TraesCS1B01G233600 chr3B 91.429 980 72 10 3615 4583 13735252 13736230 0.000000e+00 1334.0
13 TraesCS1B01G233600 chr3B 84.503 755 110 5 1 752 614910664 614911414 0.000000e+00 739.0
14 TraesCS1B01G233600 chr3B 91.304 138 10 2 1947 2082 748784614 748784751 2.180000e-43 187.0
15 TraesCS1B01G233600 chr3B 76.062 259 32 18 2579 2821 246164861 246165105 1.740000e-19 108.0
16 TraesCS1B01G233600 chr6B 91.122 980 73 12 3616 4583 687058613 687059590 0.000000e+00 1315.0
17 TraesCS1B01G233600 chr6B 90.437 983 77 13 3616 4583 46663168 46664148 0.000000e+00 1279.0
18 TraesCS1B01G233600 chr6B 92.481 133 9 1 1946 2077 159156797 159156929 6.050000e-44 189.0
19 TraesCS1B01G233600 chr6B 91.912 136 10 1 1946 2080 207510900 207511035 6.050000e-44 189.0
20 TraesCS1B01G233600 chr7A 90.798 978 78 10 3617 4583 611317463 611318439 0.000000e+00 1297.0
21 TraesCS1B01G233600 chr7A 92.537 134 9 1 1945 2077 495545849 495545716 1.680000e-44 191.0
22 TraesCS1B01G233600 chr7A 100.000 29 0 0 2754 2782 136464665 136464693 2.000000e-03 54.7
23 TraesCS1B01G233600 chrUn 90.695 978 79 10 3617 4583 8798102 8799078 0.000000e+00 1291.0
24 TraesCS1B01G233600 chrUn 85.169 681 93 3 72 752 74562479 74563151 0.000000e+00 691.0
25 TraesCS1B01G233600 chrUn 93.284 134 8 1 1941 2073 103517779 103517646 3.620000e-46 196.0
26 TraesCS1B01G233600 chr5B 90.612 980 80 10 3615 4583 437922169 437923147 0.000000e+00 1290.0
27 TraesCS1B01G233600 chr5B 84.707 752 104 5 1 751 590241882 590241141 0.000000e+00 741.0
28 TraesCS1B01G233600 chr5B 93.182 132 7 2 1942 2072 125229813 125229943 4.680000e-45 193.0
29 TraesCS1B01G233600 chr5B 95.000 60 3 0 2590 2649 313143085 313143144 1.360000e-15 95.3
30 TraesCS1B01G233600 chr5B 93.333 45 2 1 2750 2794 600338814 600338857 1.060000e-06 65.8
31 TraesCS1B01G233600 chr2B 90.082 978 84 11 3617 4583 30563908 30564883 0.000000e+00 1256.0
32 TraesCS1B01G233600 chr2B 84.016 757 109 12 1 752 576807252 576806503 0.000000e+00 717.0
33 TraesCS1B01G233600 chr2B 86.801 644 81 2 1 643 64062066 64062706 0.000000e+00 715.0
34 TraesCS1B01G233600 chr2B 93.233 133 8 1 1943 2074 77137381 77137513 1.300000e-45 195.0
35 TraesCS1B01G233600 chr2B 81.395 215 25 10 2581 2782 657063351 657063139 1.320000e-35 161.0
36 TraesCS1B01G233600 chr3D 85.401 685 92 6 72 752 576318612 576319292 0.000000e+00 704.0
37 TraesCS1B01G233600 chr5A 83.709 755 110 11 1 752 69218640 69219384 0.000000e+00 701.0
38 TraesCS1B01G233600 chr5A 83.004 759 120 8 1 754 451256026 451255272 0.000000e+00 678.0
39 TraesCS1B01G233600 chr5A 78.992 119 19 6 2670 2785 527904010 527903895 4.920000e-10 76.8
40 TraesCS1B01G233600 chr7D 88.514 148 15 2 1927 2073 333908219 333908073 1.310000e-40 178.0
41 TraesCS1B01G233600 chr5D 76.096 251 35 16 2581 2816 450543999 450543759 1.740000e-19 108.0
42 TraesCS1B01G233600 chr5D 94.286 35 2 0 2754 2788 544792524 544792490 2.000000e-03 54.7
43 TraesCS1B01G233600 chr2D 95.455 66 3 0 2581 2646 551860256 551860191 6.270000e-19 106.0
44 TraesCS1B01G233600 chr2D 77.174 184 27 9 2579 2749 138176675 138176856 4.880000e-15 93.5
45 TraesCS1B01G233600 chr2A 92.424 66 5 0 2581 2646 692629681 692629616 1.360000e-15 95.3
46 TraesCS1B01G233600 chr4D 88.462 78 8 1 2574 2650 405765085 405765162 4.880000e-15 93.5
47 TraesCS1B01G233600 chr6A 84.146 82 12 1 2735 2816 163185575 163185655 1.370000e-10 78.7
48 TraesCS1B01G233600 chr6A 89.130 46 4 1 2747 2792 562697900 562697944 6.410000e-04 56.5


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 TraesCS1B01G233600 chr1B 419401150 419405732 4582 False 8464.00 8464 100.000000 1 4583 1 chr1B.!!$F1 4582
1 TraesCS1B01G233600 chr1D 309582926 309586262 3336 False 1200.75 2782 94.522750 1 3617 4 chr1D.!!$F1 3616
2 TraesCS1B01G233600 chr1A 389128942 389131640 2698 False 1302.00 1701 93.598333 760 3617 3 chr1A.!!$F1 2857
3 TraesCS1B01G233600 chr4A 737735569 737736541 972 True 1465.00 1465 93.936000 3616 4583 1 chr4A.!!$R1 967
4 TraesCS1B01G233600 chr7B 446670649 446671575 926 False 1454.00 1454 95.048000 3616 4539 1 chr7B.!!$F1 923
5 TraesCS1B01G233600 chr7B 592179455 592180200 745 False 723.00 723 84.176000 5 754 1 chr7B.!!$F2 749
6 TraesCS1B01G233600 chr3B 13735252 13736230 978 False 1334.00 1334 91.429000 3615 4583 1 chr3B.!!$F1 968
7 TraesCS1B01G233600 chr3B 614910664 614911414 750 False 739.00 739 84.503000 1 752 1 chr3B.!!$F3 751
8 TraesCS1B01G233600 chr6B 687058613 687059590 977 False 1315.00 1315 91.122000 3616 4583 1 chr6B.!!$F4 967
9 TraesCS1B01G233600 chr6B 46663168 46664148 980 False 1279.00 1279 90.437000 3616 4583 1 chr6B.!!$F1 967
10 TraesCS1B01G233600 chr7A 611317463 611318439 976 False 1297.00 1297 90.798000 3617 4583 1 chr7A.!!$F2 966
11 TraesCS1B01G233600 chrUn 8798102 8799078 976 False 1291.00 1291 90.695000 3617 4583 1 chrUn.!!$F1 966
12 TraesCS1B01G233600 chrUn 74562479 74563151 672 False 691.00 691 85.169000 72 752 1 chrUn.!!$F2 680
13 TraesCS1B01G233600 chr5B 437922169 437923147 978 False 1290.00 1290 90.612000 3615 4583 1 chr5B.!!$F3 968
14 TraesCS1B01G233600 chr5B 590241141 590241882 741 True 741.00 741 84.707000 1 751 1 chr5B.!!$R1 750
15 TraesCS1B01G233600 chr2B 30563908 30564883 975 False 1256.00 1256 90.082000 3617 4583 1 chr2B.!!$F1 966
16 TraesCS1B01G233600 chr2B 576806503 576807252 749 True 717.00 717 84.016000 1 752 1 chr2B.!!$R1 751
17 TraesCS1B01G233600 chr2B 64062066 64062706 640 False 715.00 715 86.801000 1 643 1 chr2B.!!$F2 642
18 TraesCS1B01G233600 chr3D 576318612 576319292 680 False 704.00 704 85.401000 72 752 1 chr3D.!!$F1 680
19 TraesCS1B01G233600 chr5A 69218640 69219384 744 False 701.00 701 83.709000 1 752 1 chr5A.!!$F1 751
20 TraesCS1B01G233600 chr5A 451255272 451256026 754 True 678.00 678 83.004000 1 754 1 chr5A.!!$R1 753

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
30 31 0.749818 TTCTTCACAAAGCGGGTGCA 60.750 50.0 1.25 0.0 46.23 4.57 F
390 400 0.898789 ACACCCCAGTCGACGAATCT 60.899 55.0 10.46 0.0 0.00 2.40 F
1956 2012 0.033699 GTCAGGTAGTACTCCCCCGT 60.034 60.0 0.00 0.0 0.00 5.28 F
1970 2026 0.251073 CCCCGTCCGGAAATACTTGT 59.749 55.0 5.23 0.0 37.50 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1213 0.397254 TGAGCTAGCTACCACTCCCC 60.397 60.0 19.38 1.94 0.00 4.81 R
2049 2105 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 R
3434 3575 0.317020 CATGCATGCACGCAGATGAG 60.317 55.0 25.37 0.00 46.99 2.90 R
3793 3940 0.462047 GATGGTCCGTTACAGGGCTG 60.462 60.0 0.00 0.00 35.87 4.85 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
21 22 1.000385 CCGCTGCCATTTCTTCACAAA 60.000 47.619 0.00 0.00 0.00 2.83
30 31 0.749818 TTCTTCACAAAGCGGGTGCA 60.750 50.000 1.25 0.00 46.23 4.57
50 52 1.965754 GATGGCTTCCTCCTCTGCGT 61.966 60.000 0.00 0.00 0.00 5.24
106 108 2.354510 CACCATTTTCGCCATGATACGT 59.645 45.455 0.00 0.00 0.00 3.57
192 196 3.849951 CCGACCGGTGATGGGGAG 61.850 72.222 14.63 0.00 0.00 4.30
322 332 2.752238 CTGTCCTCTCGGGAGCGT 60.752 66.667 6.84 0.00 46.10 5.07
334 344 2.355837 GAGCGTCGGAGTGCAACA 60.356 61.111 0.00 0.00 41.43 3.33
386 396 1.592400 GATGACACCCCAGTCGACGA 61.592 60.000 10.46 0.00 41.41 4.20
390 400 0.898789 ACACCCCAGTCGACGAATCT 60.899 55.000 10.46 0.00 0.00 2.40
412 422 2.451490 GACTGGTCAGAGTCTGATCCA 58.549 52.381 26.94 27.59 42.73 3.41
419 429 1.554160 CAGAGTCTGATCCACTGCCTT 59.446 52.381 15.46 0.00 32.44 4.35
442 452 1.077429 GGCAGAGAAGGCCGGAAAT 60.077 57.895 5.05 0.00 42.39 2.17
467 487 3.838271 GGTGAGCTCGGATGGCGA 61.838 66.667 9.64 0.00 34.52 5.54
518 539 3.933722 CAGCGAGCGGATGGGGAT 61.934 66.667 0.00 0.00 0.00 3.85
595 618 2.427320 GGCGCCCTCATATCTGCA 59.573 61.111 18.11 0.00 0.00 4.41
620 645 1.607225 TTTGGGCTGGATATGAGGGT 58.393 50.000 0.00 0.00 0.00 4.34
819 852 1.334869 GCACATGTATAGCCAGGTTGC 59.665 52.381 0.00 0.00 0.00 4.17
1176 1210 4.747529 GCCACACGTACCGGGGTC 62.748 72.222 6.32 0.00 32.94 4.46
1177 1211 4.073200 CCACACGTACCGGGGTCC 62.073 72.222 6.32 0.00 32.94 4.46
1197 1234 1.116536 GGGGGAGTGGTAGCTAGCTC 61.117 65.000 23.26 18.93 0.00 4.09
1198 1235 0.397254 GGGGAGTGGTAGCTAGCTCA 60.397 60.000 23.26 11.64 0.00 4.26
1199 1236 1.036707 GGGAGTGGTAGCTAGCTCAG 58.963 60.000 23.26 0.00 0.00 3.35
1202 1242 0.336737 AGTGGTAGCTAGCTCAGGGT 59.663 55.000 23.26 1.33 0.00 4.34
1231 1271 0.250513 GCTTAGTGTGTGGAGGGAGG 59.749 60.000 0.00 0.00 0.00 4.30
1232 1272 0.250513 CTTAGTGTGTGGAGGGAGGC 59.749 60.000 0.00 0.00 0.00 4.70
1233 1273 1.541310 TTAGTGTGTGGAGGGAGGCG 61.541 60.000 0.00 0.00 0.00 5.52
1315 1355 3.897856 AGGACTGCTCCTGCTTGT 58.102 55.556 0.00 0.00 46.24 3.16
1399 1439 4.467084 GGATGTTCGGCCAGGCGA 62.467 66.667 12.67 12.67 0.00 5.54
1857 1898 4.756084 AGAGAACACACTTGCAAATAGC 57.244 40.909 0.00 0.00 45.96 2.97
1917 1961 6.264088 CAATTACTCCCTCTGTACGTAACTC 58.736 44.000 0.00 0.00 0.00 3.01
1952 2008 1.848652 TGCAGTCAGGTAGTACTCCC 58.151 55.000 0.00 0.00 0.00 4.30
1953 2009 1.112950 GCAGTCAGGTAGTACTCCCC 58.887 60.000 0.00 0.28 0.00 4.81
1954 2010 1.777941 CAGTCAGGTAGTACTCCCCC 58.222 60.000 0.00 0.00 0.00 5.40
1955 2011 0.258194 AGTCAGGTAGTACTCCCCCG 59.742 60.000 0.00 0.00 0.00 5.73
1956 2012 0.033699 GTCAGGTAGTACTCCCCCGT 60.034 60.000 0.00 0.00 0.00 5.28
1957 2013 0.257039 TCAGGTAGTACTCCCCCGTC 59.743 60.000 0.00 0.00 0.00 4.79
1958 2014 0.754587 CAGGTAGTACTCCCCCGTCC 60.755 65.000 0.00 0.00 0.00 4.79
1959 2015 1.825622 GGTAGTACTCCCCCGTCCG 60.826 68.421 0.00 0.00 0.00 4.79
1960 2016 1.825622 GTAGTACTCCCCCGTCCGG 60.826 68.421 0.00 0.00 0.00 5.14
1961 2017 2.000701 TAGTACTCCCCCGTCCGGA 61.001 63.158 0.00 0.00 37.50 5.14
1962 2018 1.570857 TAGTACTCCCCCGTCCGGAA 61.571 60.000 5.23 0.00 37.50 4.30
1963 2019 1.984026 GTACTCCCCCGTCCGGAAA 60.984 63.158 5.23 0.00 37.50 3.13
1964 2020 1.002017 TACTCCCCCGTCCGGAAAT 59.998 57.895 5.23 0.00 37.50 2.17
1965 2021 0.261402 TACTCCCCCGTCCGGAAATA 59.739 55.000 5.23 0.00 37.50 1.40
1966 2022 1.332889 ACTCCCCCGTCCGGAAATAC 61.333 60.000 5.23 0.00 37.50 1.89
1967 2023 1.002017 TCCCCCGTCCGGAAATACT 59.998 57.895 5.23 0.00 37.50 2.12
1968 2024 0.618393 TCCCCCGTCCGGAAATACTT 60.618 55.000 5.23 0.00 37.50 2.24
1969 2025 0.463116 CCCCCGTCCGGAAATACTTG 60.463 60.000 5.23 0.00 37.50 3.16
1970 2026 0.251073 CCCCGTCCGGAAATACTTGT 59.749 55.000 5.23 0.00 37.50 3.16
1971 2027 1.648504 CCCGTCCGGAAATACTTGTC 58.351 55.000 5.23 0.00 37.50 3.18
1972 2028 1.066716 CCCGTCCGGAAATACTTGTCA 60.067 52.381 5.23 0.00 37.50 3.58
1973 2029 2.419574 CCCGTCCGGAAATACTTGTCAT 60.420 50.000 5.23 0.00 37.50 3.06
1974 2030 3.267483 CCGTCCGGAAATACTTGTCATT 58.733 45.455 5.23 0.00 37.50 2.57
1975 2031 4.435425 CCGTCCGGAAATACTTGTCATTA 58.565 43.478 5.23 0.00 37.50 1.90
1976 2032 4.871557 CCGTCCGGAAATACTTGTCATTAA 59.128 41.667 5.23 0.00 37.50 1.40
1977 2033 5.352016 CCGTCCGGAAATACTTGTCATTAAA 59.648 40.000 5.23 0.00 37.50 1.52
1978 2034 6.128227 CCGTCCGGAAATACTTGTCATTAAAA 60.128 38.462 5.23 0.00 37.50 1.52
1979 2035 7.414762 CCGTCCGGAAATACTTGTCATTAAAAT 60.415 37.037 5.23 0.00 37.50 1.82
1980 2036 7.428183 CGTCCGGAAATACTTGTCATTAAAATG 59.572 37.037 5.23 0.00 37.75 2.32
1981 2037 7.700656 GTCCGGAAATACTTGTCATTAAAATGG 59.299 37.037 5.23 0.00 37.03 3.16
1982 2038 7.612244 TCCGGAAATACTTGTCATTAAAATGGA 59.388 33.333 0.00 0.00 37.03 3.41
1983 2039 8.413229 CCGGAAATACTTGTCATTAAAATGGAT 58.587 33.333 0.00 0.00 37.03 3.41
1984 2040 9.236691 CGGAAATACTTGTCATTAAAATGGATG 57.763 33.333 3.00 0.00 37.03 3.51
1991 2047 9.918630 ACTTGTCATTAAAATGGATGAAAAGAG 57.081 29.630 18.27 0.33 44.74 2.85
2036 2092 7.833285 TGCCTAAATACATCCCTTTTTATCC 57.167 36.000 0.00 0.00 0.00 2.59
2037 2093 7.358263 TGCCTAAATACATCCCTTTTTATCCA 58.642 34.615 0.00 0.00 0.00 3.41
2038 2094 7.505585 TGCCTAAATACATCCCTTTTTATCCAG 59.494 37.037 0.00 0.00 0.00 3.86
2039 2095 7.505923 GCCTAAATACATCCCTTTTTATCCAGT 59.494 37.037 0.00 0.00 0.00 4.00
2040 2096 9.421399 CCTAAATACATCCCTTTTTATCCAGTT 57.579 33.333 0.00 0.00 0.00 3.16
2043 2099 8.893563 AATACATCCCTTTTTATCCAGTTTGA 57.106 30.769 0.00 0.00 0.00 2.69
2044 2100 9.492730 AATACATCCCTTTTTATCCAGTTTGAT 57.507 29.630 0.00 0.00 0.00 2.57
2045 2101 7.174107 ACATCCCTTTTTATCCAGTTTGATG 57.826 36.000 0.00 0.00 33.80 3.07
2046 2102 6.953520 ACATCCCTTTTTATCCAGTTTGATGA 59.046 34.615 0.00 0.00 32.39 2.92
2047 2103 6.834168 TCCCTTTTTATCCAGTTTGATGAC 57.166 37.500 0.00 0.00 0.00 3.06
2048 2104 6.310941 TCCCTTTTTATCCAGTTTGATGACA 58.689 36.000 0.00 0.00 0.00 3.58
2049 2105 6.780031 TCCCTTTTTATCCAGTTTGATGACAA 59.220 34.615 0.00 0.00 0.00 3.18
2050 2106 7.039784 TCCCTTTTTATCCAGTTTGATGACAAG 60.040 37.037 0.00 0.00 37.32 3.16
2051 2107 7.255942 CCCTTTTTATCCAGTTTGATGACAAGT 60.256 37.037 0.00 0.00 37.32 3.16
2052 2108 8.792633 CCTTTTTATCCAGTTTGATGACAAGTA 58.207 33.333 0.00 0.00 37.32 2.24
2057 2113 6.817765 TCCAGTTTGATGACAAGTATTTCC 57.182 37.500 0.00 0.00 37.32 3.13
2058 2114 5.411361 TCCAGTTTGATGACAAGTATTTCCG 59.589 40.000 0.00 0.00 37.32 4.30
2059 2115 5.391950 CCAGTTTGATGACAAGTATTTCCGG 60.392 44.000 0.00 0.00 37.32 5.14
2062 2118 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2067 2123 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2131 2187 2.524306 AGAGCTAGCTAGGCCATGTAG 58.476 52.381 19.38 0.00 0.00 2.74
2148 2204 6.183360 GCCATGTAGATATGCGTGAATAGTTC 60.183 42.308 0.00 0.00 0.00 3.01
2212 2268 5.242615 TGATGAGCTATAGTAGTGGCAAGAG 59.757 44.000 0.84 0.00 0.00 2.85
2235 2291 9.914131 AGAGCATAATTTCTTTGGAAAAACTAC 57.086 29.630 0.00 0.00 43.51 2.73
2375 2435 2.781174 ACTGACTTTTCCACCCTTGGTA 59.219 45.455 0.00 0.00 44.35 3.25
2378 2438 4.611367 TGACTTTTCCACCCTTGGTAAAA 58.389 39.130 0.00 0.00 40.52 1.52
2452 2512 5.949952 ACAATGTGGATAAACTAAACCCTCC 59.050 40.000 0.00 0.00 0.00 4.30
2455 2515 4.354387 TGTGGATAAACTAAACCCTCCCAA 59.646 41.667 0.00 0.00 0.00 4.12
2461 2521 7.147897 GGATAAACTAAACCCTCCCAAAGAATG 60.148 40.741 0.00 0.00 0.00 2.67
2462 2522 3.431415 ACTAAACCCTCCCAAAGAATGC 58.569 45.455 0.00 0.00 0.00 3.56
2463 2523 2.397044 AAACCCTCCCAAAGAATGCA 57.603 45.000 0.00 0.00 0.00 3.96
2464 2524 1.928868 AACCCTCCCAAAGAATGCAG 58.071 50.000 0.00 0.00 0.00 4.41
2465 2525 0.613012 ACCCTCCCAAAGAATGCAGC 60.613 55.000 0.00 0.00 0.00 5.25
2466 2526 1.325476 CCCTCCCAAAGAATGCAGCC 61.325 60.000 0.00 0.00 0.00 4.85
2467 2527 0.324091 CCTCCCAAAGAATGCAGCCT 60.324 55.000 0.00 0.00 0.00 4.58
2468 2528 1.553706 CTCCCAAAGAATGCAGCCTT 58.446 50.000 0.00 0.00 0.00 4.35
2469 2529 1.897802 CTCCCAAAGAATGCAGCCTTT 59.102 47.619 9.52 9.52 33.29 3.11
2470 2530 2.301009 CTCCCAAAGAATGCAGCCTTTT 59.699 45.455 11.91 0.00 30.89 2.27
2471 2531 2.705127 TCCCAAAGAATGCAGCCTTTTT 59.295 40.909 11.91 0.00 30.89 1.94
2488 2548 2.613026 TTTTTGTGCGAGGACAGAGA 57.387 45.000 0.00 0.00 0.00 3.10
2489 2549 2.613026 TTTTGTGCGAGGACAGAGAA 57.387 45.000 0.00 0.00 0.00 2.87
2490 2550 2.613026 TTTGTGCGAGGACAGAGAAA 57.387 45.000 0.00 0.00 0.00 2.52
2491 2551 2.839486 TTGTGCGAGGACAGAGAAAT 57.161 45.000 0.00 0.00 0.00 2.17
2571 2631 2.966324 GGTGCAAACGAAAACACCC 58.034 52.632 10.08 0.00 45.56 4.61
2627 2688 7.116090 TGTCAGATTTTTAAACATGGCAAATCG 59.884 33.333 0.00 1.77 38.39 3.34
2653 2714 5.744345 ACGTTTTTCATGACAAATTACGCAA 59.256 32.000 14.18 0.00 31.75 4.85
2785 2920 7.507733 AAAAACATTTGATTTGCCATGCTTA 57.492 28.000 0.00 0.00 0.00 3.09
2795 2930 5.726980 TTTGCCATGCTTAAAAGATCTGT 57.273 34.783 0.00 0.00 0.00 3.41
2826 2961 9.519191 AGGCTTTTAGCATTTCCATTTAATTTT 57.481 25.926 0.67 0.00 44.75 1.82
2834 2969 8.575589 AGCATTTCCATTTAATTTTGGTTTTCC 58.424 29.630 0.00 0.00 41.14 3.13
2835 2970 8.575589 GCATTTCCATTTAATTTTGGTTTTCCT 58.424 29.630 0.00 0.00 41.38 3.36
2852 2987 6.462909 GGTTTTCCTTCACATTCTTCCATGTT 60.463 38.462 0.00 0.00 34.49 2.71
2856 2991 2.806434 TCACATTCTTCCATGTTGGGG 58.194 47.619 0.00 0.00 38.32 4.96
2879 3014 5.302059 GGAGAGGTATGCATTGTACTGACTA 59.698 44.000 3.54 0.00 0.00 2.59
2884 3019 5.980116 GGTATGCATTGTACTGACTACTGAG 59.020 44.000 3.54 0.00 0.00 3.35
2938 3073 2.449137 AATAAGGAGCCAGCTGCATT 57.551 45.000 13.86 1.25 44.83 3.56
3439 3580 0.455972 GCGGCTAGCTCGATCTCATC 60.456 60.000 23.94 5.83 44.04 2.92
3450 3591 0.235144 GATCTCATCTGCGTGCATGC 59.765 55.000 24.20 24.20 0.00 4.06
3451 3592 0.463116 ATCTCATCTGCGTGCATGCA 60.463 50.000 30.58 30.58 43.95 3.96
3452 3593 0.463116 TCTCATCTGCGTGCATGCAT 60.463 50.000 32.45 17.41 45.26 3.96
3453 3594 0.317020 CTCATCTGCGTGCATGCATG 60.317 55.000 32.45 31.36 45.26 4.06
3793 3940 1.270550 CCAGAAAACCCACTGCATGAC 59.729 52.381 0.00 0.00 33.40 3.06
3903 4055 5.584551 AAACTTAACAAGGAGAGGACCAT 57.415 39.130 0.00 0.00 0.00 3.55
3917 4070 2.042162 AGGACCATCAGCACCAAAAGAT 59.958 45.455 0.00 0.00 0.00 2.40
3920 4073 3.087031 ACCATCAGCACCAAAAGATCAG 58.913 45.455 0.00 0.00 0.00 2.90
3993 4148 8.375493 ACTAACAGGATCTAACCAATCTGTAA 57.625 34.615 0.00 0.00 0.00 2.41
4080 4235 1.123861 TGAGCCAGCCTCTTCACACT 61.124 55.000 0.00 0.00 41.35 3.55
4083 4238 0.610687 GCCAGCCTCTTCACACTAGT 59.389 55.000 0.00 0.00 0.00 2.57
4157 4312 0.106708 AGAGCAAGCGGTGAAGACAA 59.893 50.000 0.00 0.00 0.00 3.18
4316 4471 2.619697 TTGCCAAATGGATCTGGGAA 57.380 45.000 2.98 2.07 40.33 3.97
4331 4486 1.384191 GGAACACAAGAGGCCCCAT 59.616 57.895 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.984193 GAAGCCATCTGCACCCGCT 62.984 63.158 0.00 0.00 44.83 5.52
30 31 1.684386 CGCAGAGGAGGAAGCCATCT 61.684 60.000 0.00 0.00 0.00 2.90
106 108 2.762459 ATAAGGGACGCCGAGGCA 60.762 61.111 15.03 0.00 42.06 4.75
158 160 0.757188 CGGGCAGACTATCAGTCCCT 60.757 60.000 2.74 0.00 46.18 4.20
192 196 1.592223 CAGTCGGAACACCTCTCCC 59.408 63.158 0.00 0.00 0.00 4.30
334 344 4.740822 GGGGCAATGGCAGTCGGT 62.741 66.667 9.51 0.00 43.71 4.69
386 396 2.830923 CAGACTCTGACCAGTCCAGATT 59.169 50.000 0.00 0.00 43.53 2.40
390 400 2.451490 GATCAGACTCTGACCAGTCCA 58.549 52.381 11.07 0.00 43.63 4.02
467 487 1.490490 TCACTTCACTCAACTGCCCTT 59.510 47.619 0.00 0.00 0.00 3.95
472 492 3.322254 ACCCTAGTCACTTCACTCAACTG 59.678 47.826 0.00 0.00 0.00 3.16
476 496 3.494398 GCAAACCCTAGTCACTTCACTCA 60.494 47.826 0.00 0.00 0.00 3.41
518 539 2.436542 CACCCGACCCCACTTATATTCA 59.563 50.000 0.00 0.00 0.00 2.57
573 595 4.954118 ATATGAGGGCGCCCGGGA 62.954 66.667 38.88 26.52 41.95 5.14
595 618 4.264083 CCTCATATCCAGCCCAAATATGGT 60.264 45.833 0.00 0.00 46.01 3.55
775 808 3.244561 GGGTTCTCTCATGGTCTTGTTGA 60.245 47.826 0.00 0.00 0.00 3.18
835 868 6.466038 CCCTAGGCTGTAGTCTGTAGATCTTA 60.466 46.154 2.05 0.00 0.00 2.10
843 876 1.619977 CCACCCTAGGCTGTAGTCTGT 60.620 57.143 2.05 0.00 0.00 3.41
844 877 1.115467 CCACCCTAGGCTGTAGTCTG 58.885 60.000 2.05 0.00 0.00 3.51
845 878 3.617535 CCACCCTAGGCTGTAGTCT 57.382 57.895 2.05 0.00 0.00 3.24
1020 1053 1.301716 GTGTGCGTGTGTGGAGGAT 60.302 57.895 0.00 0.00 0.00 3.24
1173 1207 2.762875 CTACCACTCCCCCGGACC 60.763 72.222 0.73 0.00 0.00 4.46
1174 1208 2.578586 TAGCTACCACTCCCCCGGAC 62.579 65.000 0.73 0.00 0.00 4.79
1175 1209 2.294170 CTAGCTACCACTCCCCCGGA 62.294 65.000 0.73 0.00 0.00 5.14
1176 1210 1.833049 CTAGCTACCACTCCCCCGG 60.833 68.421 0.00 0.00 0.00 5.73
1177 1211 2.499827 GCTAGCTACCACTCCCCCG 61.500 68.421 7.70 0.00 0.00 5.73
1178 1212 1.075151 AGCTAGCTACCACTCCCCC 60.075 63.158 17.69 0.00 0.00 5.40
1179 1213 0.397254 TGAGCTAGCTACCACTCCCC 60.397 60.000 19.38 1.94 0.00 4.81
1180 1214 1.036707 CTGAGCTAGCTACCACTCCC 58.963 60.000 19.38 2.75 0.00 4.30
1371 1411 4.109675 AACATCCCGGGGAAGCCG 62.110 66.667 23.50 11.45 34.34 5.52
1562 1602 3.286751 GCAGTTGCTCGGTTGCCA 61.287 61.111 0.00 0.00 38.21 4.92
1564 1604 2.253452 CTGCAGTTGCTCGGTTGC 59.747 61.111 5.25 0.00 42.66 4.17
1566 1606 3.349006 CGCTGCAGTTGCTCGGTT 61.349 61.111 16.64 0.00 42.66 4.44
1820 1861 8.221766 GTGTGTTCTCTAAGCTGTATTTGTTAC 58.778 37.037 0.00 0.00 0.00 2.50
1857 1898 9.574458 ACGCTATGCAGAAATATAGTAATACTG 57.426 33.333 2.68 0.00 0.00 2.74
1877 1921 4.761739 AGTAATTGCCAATATGCACGCTAT 59.238 37.500 0.00 0.00 41.88 2.97
1917 1961 6.324522 TGACTGCAAAAACGTTTTACATTG 57.675 33.333 25.44 19.89 0.00 2.82
1952 2008 1.066716 TGACAAGTATTTCCGGACGGG 60.067 52.381 1.83 1.55 35.59 5.28
1953 2009 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1954 2010 6.411630 TTTAATGACAAGTATTTCCGGACG 57.588 37.500 1.83 0.00 0.00 4.79
1955 2011 7.700656 CCATTTTAATGACAAGTATTTCCGGAC 59.299 37.037 1.83 0.00 38.70 4.79
1956 2012 7.612244 TCCATTTTAATGACAAGTATTTCCGGA 59.388 33.333 0.00 0.00 38.70 5.14
1957 2013 7.767261 TCCATTTTAATGACAAGTATTTCCGG 58.233 34.615 0.00 0.00 38.70 5.14
1958 2014 9.236691 CATCCATTTTAATGACAAGTATTTCCG 57.763 33.333 4.07 0.00 38.70 4.30
1965 2021 9.918630 CTCTTTTCATCCATTTTAATGACAAGT 57.081 29.630 4.07 0.00 39.24 3.16
2010 2066 9.528489 GGATAAAAAGGGATGTATTTAGGCATA 57.472 33.333 0.00 0.00 0.00 3.14
2011 2067 8.010105 TGGATAAAAAGGGATGTATTTAGGCAT 58.990 33.333 0.00 0.00 0.00 4.40
2012 2068 7.358263 TGGATAAAAAGGGATGTATTTAGGCA 58.642 34.615 0.00 0.00 0.00 4.75
2013 2069 7.505923 ACTGGATAAAAAGGGATGTATTTAGGC 59.494 37.037 0.00 0.00 0.00 3.93
2014 2070 8.996651 ACTGGATAAAAAGGGATGTATTTAGG 57.003 34.615 0.00 0.00 0.00 2.69
2017 2073 9.320295 TCAAACTGGATAAAAAGGGATGTATTT 57.680 29.630 0.00 0.00 0.00 1.40
2018 2074 8.893563 TCAAACTGGATAAAAAGGGATGTATT 57.106 30.769 0.00 0.00 0.00 1.89
2019 2075 8.917088 CATCAAACTGGATAAAAAGGGATGTAT 58.083 33.333 0.00 0.00 0.00 2.29
2020 2076 8.112822 TCATCAAACTGGATAAAAAGGGATGTA 58.887 33.333 0.00 0.00 32.47 2.29
2021 2077 6.953520 TCATCAAACTGGATAAAAAGGGATGT 59.046 34.615 0.00 0.00 32.47 3.06
2022 2078 7.093814 TGTCATCAAACTGGATAAAAAGGGATG 60.094 37.037 0.00 0.00 0.00 3.51
2023 2079 6.953520 TGTCATCAAACTGGATAAAAAGGGAT 59.046 34.615 0.00 0.00 0.00 3.85
2024 2080 6.310941 TGTCATCAAACTGGATAAAAAGGGA 58.689 36.000 0.00 0.00 0.00 4.20
2025 2081 6.588719 TGTCATCAAACTGGATAAAAAGGG 57.411 37.500 0.00 0.00 0.00 3.95
2026 2082 7.661040 ACTTGTCATCAAACTGGATAAAAAGG 58.339 34.615 0.00 0.00 32.87 3.11
2031 2087 8.956426 GGAAATACTTGTCATCAAACTGGATAA 58.044 33.333 0.00 0.00 32.87 1.75
2032 2088 7.279981 CGGAAATACTTGTCATCAAACTGGATA 59.720 37.037 0.00 0.00 32.87 2.59
2033 2089 6.094048 CGGAAATACTTGTCATCAAACTGGAT 59.906 38.462 0.00 0.00 32.87 3.41
2034 2090 5.411361 CGGAAATACTTGTCATCAAACTGGA 59.589 40.000 0.00 0.00 32.87 3.86
2035 2091 5.391950 CCGGAAATACTTGTCATCAAACTGG 60.392 44.000 0.00 0.00 32.87 4.00
2036 2092 5.411361 TCCGGAAATACTTGTCATCAAACTG 59.589 40.000 0.00 0.00 32.87 3.16
2037 2093 5.411669 GTCCGGAAATACTTGTCATCAAACT 59.588 40.000 5.23 0.00 32.87 2.66
2038 2094 5.628134 GTCCGGAAATACTTGTCATCAAAC 58.372 41.667 5.23 0.00 32.87 2.93
2039 2095 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2040 2096 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2041 2097 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2042 2098 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2043 2099 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2044 2100 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2045 2101 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2046 2102 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2047 2103 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2048 2104 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2049 2105 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2050 2106 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2051 2107 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2052 2108 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2053 2109 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2054 2110 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2055 2111 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2056 2112 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
2057 2113 1.978454 ATTAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2058 2114 4.277921 CACTAATTAGTACTCCCTCCGTCC 59.722 50.000 17.62 0.00 34.13 4.79
2059 2115 4.277921 CCACTAATTAGTACTCCCTCCGTC 59.722 50.000 17.62 0.00 34.13 4.79
2062 2118 4.277921 CGACCACTAATTAGTACTCCCTCC 59.722 50.000 17.62 1.97 34.13 4.30
2067 2123 8.619546 AGTGTAATCGACCACTAATTAGTACTC 58.380 37.037 17.62 13.11 40.03 2.59
2131 2187 6.477033 ACAAGACAGAACTATTCACGCATATC 59.523 38.462 0.00 0.00 0.00 1.63
2148 2204 6.261158 TCGATGGTAGAGATAAGACAAGACAG 59.739 42.308 0.00 0.00 0.00 3.51
2212 2268 9.691362 TCTGTAGTTTTTCCAAAGAAATTATGC 57.309 29.630 0.00 0.00 41.55 3.14
2235 2291 4.750098 CCGGTAATTACAGCTGGTTATCTG 59.250 45.833 19.93 7.26 36.45 2.90
2303 2363 6.815089 TGTGTACATTTTGCCAATTTCTTCT 58.185 32.000 0.00 0.00 0.00 2.85
2378 2438 8.954350 ACGTCTTACATACAGACATTACTAGTT 58.046 33.333 0.00 0.00 40.78 2.24
2469 2529 2.613026 TCTCTGTCCTCGCACAAAAA 57.387 45.000 0.00 0.00 0.00 1.94
2470 2530 2.613026 TTCTCTGTCCTCGCACAAAA 57.387 45.000 0.00 0.00 0.00 2.44
2471 2531 2.613026 TTTCTCTGTCCTCGCACAAA 57.387 45.000 0.00 0.00 0.00 2.83
2472 2532 2.416747 CATTTCTCTGTCCTCGCACAA 58.583 47.619 0.00 0.00 0.00 3.33
2473 2533 1.941209 GCATTTCTCTGTCCTCGCACA 60.941 52.381 0.00 0.00 0.00 4.57
2474 2534 0.723981 GCATTTCTCTGTCCTCGCAC 59.276 55.000 0.00 0.00 0.00 5.34
2475 2535 0.321346 TGCATTTCTCTGTCCTCGCA 59.679 50.000 0.00 0.00 0.00 5.10
2476 2536 1.396301 CTTGCATTTCTCTGTCCTCGC 59.604 52.381 0.00 0.00 0.00 5.03
2477 2537 1.396301 GCTTGCATTTCTCTGTCCTCG 59.604 52.381 0.00 0.00 0.00 4.63
2478 2538 2.709213 AGCTTGCATTTCTCTGTCCTC 58.291 47.619 0.00 0.00 0.00 3.71
2479 2539 2.875094 AGCTTGCATTTCTCTGTCCT 57.125 45.000 0.00 0.00 0.00 3.85
2480 2540 3.930634 AAAGCTTGCATTTCTCTGTCC 57.069 42.857 0.00 0.00 0.00 4.02
2481 2541 5.362556 TGTAAAGCTTGCATTTCTCTGTC 57.637 39.130 0.00 0.00 0.00 3.51
2482 2542 5.972107 ATGTAAAGCTTGCATTTCTCTGT 57.028 34.783 0.00 0.00 31.69 3.41
2483 2543 6.618811 AGAATGTAAAGCTTGCATTTCTCTG 58.381 36.000 22.40 0.00 44.30 3.35
2484 2544 6.830873 AGAATGTAAAGCTTGCATTTCTCT 57.169 33.333 22.40 15.75 44.30 3.10
2485 2545 9.578439 AATTAGAATGTAAAGCTTGCATTTCTC 57.422 29.630 22.40 14.33 44.30 2.87
2486 2546 9.362539 CAATTAGAATGTAAAGCTTGCATTTCT 57.637 29.630 22.40 20.81 44.30 2.52
2487 2547 9.143631 ACAATTAGAATGTAAAGCTTGCATTTC 57.856 29.630 22.40 17.07 44.30 2.17
2488 2548 9.143631 GACAATTAGAATGTAAAGCTTGCATTT 57.856 29.630 22.40 16.59 44.30 2.32
2489 2549 7.485913 CGACAATTAGAATGTAAAGCTTGCATT 59.514 33.333 21.96 21.96 46.41 3.56
2490 2550 6.968904 CGACAATTAGAATGTAAAGCTTGCAT 59.031 34.615 0.00 5.28 37.60 3.96
2491 2551 6.148645 TCGACAATTAGAATGTAAAGCTTGCA 59.851 34.615 0.00 2.70 0.00 4.08
2551 2611 0.099082 GGTGTTTTCGTTTGCACCGA 59.901 50.000 3.66 3.66 41.37 4.69
2553 2613 4.900992 AACGGGTGTTTTCGTTTGCACC 62.901 50.000 11.45 11.45 45.66 5.01
2571 2631 2.981400 AGCACGGTCCAAATTAAACG 57.019 45.000 0.00 0.00 0.00 3.60
2627 2688 6.075310 TGCGTAATTTGTCATGAAAAACGTTC 60.075 34.615 13.32 3.27 33.85 3.95
2653 2714 5.721876 TGTCATGTTTAAAACGTTCGAGT 57.278 34.783 0.00 0.00 0.00 4.18
2708 2843 0.245539 CCCTTCAACAAGCATGGCAG 59.754 55.000 0.00 0.00 0.00 4.85
2785 2920 5.859205 AAAAGCCTGACAACAGATCTTTT 57.141 34.783 16.17 16.17 46.03 2.27
2795 2930 3.894427 TGGAAATGCTAAAAGCCTGACAA 59.106 39.130 0.00 0.00 41.51 3.18
2826 2961 4.541705 TGGAAGAATGTGAAGGAAAACCA 58.458 39.130 0.00 0.00 0.00 3.67
2829 2964 6.462768 CCAACATGGAAGAATGTGAAGGAAAA 60.463 38.462 0.00 0.00 40.96 2.29
2830 2965 5.010922 CCAACATGGAAGAATGTGAAGGAAA 59.989 40.000 0.00 0.00 40.96 3.13
2831 2966 4.523943 CCAACATGGAAGAATGTGAAGGAA 59.476 41.667 0.00 0.00 40.96 3.36
2832 2967 4.081406 CCAACATGGAAGAATGTGAAGGA 58.919 43.478 0.00 0.00 40.96 3.36
2833 2968 3.194116 CCCAACATGGAAGAATGTGAAGG 59.806 47.826 0.00 0.00 40.96 3.46
2834 2969 3.194116 CCCCAACATGGAAGAATGTGAAG 59.806 47.826 0.00 0.00 40.96 3.02
2835 2970 3.164268 CCCCAACATGGAAGAATGTGAA 58.836 45.455 0.00 0.00 40.96 3.18
2852 2987 1.595311 ACAATGCATACCTCTCCCCA 58.405 50.000 0.00 0.00 0.00 4.96
2856 2991 5.269505 AGTCAGTACAATGCATACCTCTC 57.730 43.478 0.00 0.00 0.00 3.20
2879 3014 2.157738 GAAGCTGTGAATTGCCTCAGT 58.842 47.619 0.00 0.00 32.12 3.41
2938 3073 7.730672 ATGAGGCTATGATAGAAATGAGCTA 57.269 36.000 3.13 0.00 0.00 3.32
2951 3086 6.650427 ATACGTGAAAGTATGAGGCTATGA 57.350 37.500 0.00 0.00 36.10 2.15
3434 3575 0.317020 CATGCATGCACGCAGATGAG 60.317 55.000 25.37 0.00 46.99 2.90
3777 3924 0.675633 GCTGTCATGCAGTGGGTTTT 59.324 50.000 15.48 0.00 46.64 2.43
3793 3940 0.462047 GATGGTCCGTTACAGGGCTG 60.462 60.000 0.00 0.00 35.87 4.85
3903 4055 2.106338 TGGACTGATCTTTTGGTGCTGA 59.894 45.455 0.00 0.00 0.00 4.26
3917 4070 2.123248 TTTGATGCCCGCTGGACTGA 62.123 55.000 0.00 0.00 0.00 3.41
3920 4073 2.700773 GGTTTGATGCCCGCTGGAC 61.701 63.158 0.00 0.00 0.00 4.02
3993 4148 2.575921 TCTGGGAGATGAGGATGGTT 57.424 50.000 0.00 0.00 0.00 3.67
4080 4235 3.181422 TGACAGGAGGAAGTTCCAGACTA 60.181 47.826 23.87 1.35 39.61 2.59
4083 4238 2.398754 TGACAGGAGGAAGTTCCAGA 57.601 50.000 23.87 0.00 39.61 3.86
4265 4420 6.531503 TTGGTTGTACAATTTGTTTCCTGA 57.468 33.333 12.26 0.00 0.00 3.86
4316 4471 1.136329 ACTGATGGGGCCTCTTGTGT 61.136 55.000 3.07 0.00 0.00 3.72
4331 4486 1.555075 GGGTGTGCTAGGATTGACTGA 59.445 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.