Multiple sequence alignment - TraesCS7D01G472400

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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 TraesCS7D01G472400 chr7D 100.000 3802 0 0 1 3802 585565255 585561454 0.000000e+00 7022
1 TraesCS7D01G472400 chr7D 85.135 1332 126 30 1599 2889 612930808 612932108 0.000000e+00 1297
2 TraesCS7D01G472400 chr7D 74.664 446 56 19 1016 1449 612930352 612930752 1.100000e-30 145
3 TraesCS7D01G472400 chr7A 92.440 2156 114 25 1456 3571 675596301 675594155 0.000000e+00 3033
4 TraesCS7D01G472400 chr7A 88.043 1380 109 16 1018 2364 675921971 675920615 0.000000e+00 1583
5 TraesCS7D01G472400 chr7A 87.004 908 66 21 122 1014 675597702 675596832 0.000000e+00 976
6 TraesCS7D01G472400 chr7A 88.714 824 49 18 225 1014 675922889 675922076 0.000000e+00 966
7 TraesCS7D01G472400 chr7A 85.432 961 90 21 1601 2528 704292959 704293902 0.000000e+00 953
8 TraesCS7D01G472400 chr7A 83.640 489 68 7 2645 3125 704294110 704294594 2.080000e-122 449
9 TraesCS7D01G472400 chr7A 84.788 401 30 6 1016 1415 675596673 675596303 1.290000e-99 374
10 TraesCS7D01G472400 chr7B 90.383 1591 109 14 1018 2578 654927430 654925854 0.000000e+00 2050
11 TraesCS7D01G472400 chr7B 94.188 998 49 5 2580 3571 654925769 654924775 0.000000e+00 1513
12 TraesCS7D01G472400 chr7B 83.421 1719 178 54 1599 3270 702453762 702455420 0.000000e+00 1496
13 TraesCS7D01G472400 chr7B 88.610 439 36 8 122 559 654928574 654928149 4.350000e-144 521
14 TraesCS7D01G472400 chr7B 86.829 410 51 2 608 1014 654928006 654927597 4.480000e-124 455
15 TraesCS7D01G472400 chr3B 83.621 1276 119 46 1599 2837 172871032 172872254 0.000000e+00 1116
16 TraesCS7D01G472400 chr5A 85.274 1005 84 28 1840 2832 703136591 703135639 0.000000e+00 977
17 TraesCS7D01G472400 chr4B 85.438 982 83 26 1840 2809 389845197 389846130 0.000000e+00 966
18 TraesCS7D01G472400 chr4B 84.848 165 18 6 2457 2615 433663747 433663584 3.930000e-35 159
19 TraesCS7D01G472400 chr4B 84.524 168 19 6 2454 2615 662500332 662500498 3.930000e-35 159
20 TraesCS7D01G472400 chrUn 96.000 225 5 2 3582 3802 327661603 327661379 2.790000e-96 363
21 TraesCS7D01G472400 chrUn 96.000 225 4 3 3582 3802 93418072 93417849 1.000000e-95 361
22 TraesCS7D01G472400 chrUn 96.000 225 4 3 3582 3802 407707139 407706916 1.000000e-95 361
23 TraesCS7D01G472400 chr5D 96.000 225 5 2 3582 3802 503212182 503212406 2.790000e-96 363
24 TraesCS7D01G472400 chr5D 96.000 225 4 3 3582 3802 560878744 560878967 1.000000e-95 361
25 TraesCS7D01G472400 chr2D 96.000 225 5 2 3582 3802 272799957 272799733 2.790000e-96 363
26 TraesCS7D01G472400 chr4A 95.556 225 6 2 3582 3802 722780613 722780389 1.300000e-94 357
27 TraesCS7D01G472400 chr4A 80.952 294 24 15 2454 2741 612154128 612154395 1.790000e-48 204
28 TraesCS7D01G472400 chr3A 95.556 225 4 4 3582 3802 692572082 692572304 4.670000e-94 355
29 TraesCS7D01G472400 chr1D 95.556 225 5 3 3582 3802 144236980 144237203 4.670000e-94 355


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 TraesCS7D01G472400 chr7D 585561454 585565255 3801 True 7022.00 7022 100.000000 1 3802 1 chr7D.!!$R1 3801
1 TraesCS7D01G472400 chr7D 612930352 612932108 1756 False 721.00 1297 79.899500 1016 2889 2 chr7D.!!$F1 1873
2 TraesCS7D01G472400 chr7A 675594155 675597702 3547 True 1461.00 3033 88.077333 122 3571 3 chr7A.!!$R1 3449
3 TraesCS7D01G472400 chr7A 675920615 675922889 2274 True 1274.50 1583 88.378500 225 2364 2 chr7A.!!$R2 2139
4 TraesCS7D01G472400 chr7A 704292959 704294594 1635 False 701.00 953 84.536000 1601 3125 2 chr7A.!!$F1 1524
5 TraesCS7D01G472400 chr7B 702453762 702455420 1658 False 1496.00 1496 83.421000 1599 3270 1 chr7B.!!$F1 1671
6 TraesCS7D01G472400 chr7B 654924775 654928574 3799 True 1134.75 2050 90.002500 122 3571 4 chr7B.!!$R1 3449
7 TraesCS7D01G472400 chr3B 172871032 172872254 1222 False 1116.00 1116 83.621000 1599 2837 1 chr3B.!!$F1 1238
8 TraesCS7D01G472400 chr5A 703135639 703136591 952 True 977.00 977 85.274000 1840 2832 1 chr5A.!!$R1 992
9 TraesCS7D01G472400 chr4B 389845197 389846130 933 False 966.00 966 85.438000 1840 2809 1 chr4B.!!$F1 969

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
101 102 0.171903 GTGTAGTACGCCCGTGACAT 59.828 55.0 2.2 0.0 0.0 3.06 F
203 204 0.460987 GCCACGACCTCTTCCTCATG 60.461 60.0 0.0 0.0 0.0 3.07 F
587 610 0.464036 CCGCCTCCTATGTGTTGCTA 59.536 55.0 0.0 0.0 0.0 3.49 F
931 1070 1.052694 GCCGGTAGGGGGTATCAACT 61.053 60.0 1.9 0.0 38.2 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2297 0.172578 TGTGATCCCGTCATCGTCAC 59.827 55.000 0.0 0.0 39.48 3.67 R
2072 2439 4.166011 GCAGTTCGGCATGGTCGC 62.166 66.667 0.0 0.0 0.00 5.19 R
2512 2888 2.631062 TGCTCGTTTCTCCCAAGAAGTA 59.369 45.455 0.0 0.0 42.36 2.24 R
2844 3418 3.740832 TGTGCGAGCGAAATAAGGATATG 59.259 43.478 0.0 0.0 0.00 1.78 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
19 20 1.873698 GGTGAACGTGCTAGTTTGGA 58.126 50.000 0.00 0.00 34.00 3.53
20 21 1.529865 GGTGAACGTGCTAGTTTGGAC 59.470 52.381 0.00 0.00 34.00 4.02
21 22 2.206750 GTGAACGTGCTAGTTTGGACA 58.793 47.619 0.00 0.00 34.00 4.02
22 23 2.610374 GTGAACGTGCTAGTTTGGACAA 59.390 45.455 0.00 0.00 34.00 3.18
23 24 3.064271 GTGAACGTGCTAGTTTGGACAAA 59.936 43.478 0.00 0.00 34.00 2.83
24 25 3.690139 TGAACGTGCTAGTTTGGACAAAA 59.310 39.130 0.00 0.00 34.00 2.44
25 26 3.963383 ACGTGCTAGTTTGGACAAAAG 57.037 42.857 0.00 0.00 31.33 2.27
26 27 3.275999 ACGTGCTAGTTTGGACAAAAGT 58.724 40.909 0.00 0.00 35.53 2.66
27 28 4.444536 ACGTGCTAGTTTGGACAAAAGTA 58.555 39.130 0.00 0.00 33.37 2.24
28 29 4.271776 ACGTGCTAGTTTGGACAAAAGTAC 59.728 41.667 0.00 3.86 33.37 2.73
29 30 4.271533 CGTGCTAGTTTGGACAAAAGTACA 59.728 41.667 13.95 4.21 33.37 2.90
30 31 5.220700 CGTGCTAGTTTGGACAAAAGTACAA 60.221 40.000 13.95 0.00 33.37 2.41
31 32 6.199393 GTGCTAGTTTGGACAAAAGTACAAG 58.801 40.000 10.70 1.45 33.37 3.16
32 33 5.298276 TGCTAGTTTGGACAAAAGTACAAGG 59.702 40.000 0.00 0.00 33.37 3.61
33 34 5.529800 GCTAGTTTGGACAAAAGTACAAGGA 59.470 40.000 0.00 0.00 33.37 3.36
34 35 6.038936 GCTAGTTTGGACAAAAGTACAAGGAA 59.961 38.462 0.00 0.00 33.37 3.36
35 36 6.844097 AGTTTGGACAAAAGTACAAGGAAA 57.156 33.333 0.00 0.00 29.21 3.13
36 37 7.234661 AGTTTGGACAAAAGTACAAGGAAAA 57.765 32.000 0.00 0.00 29.21 2.29
37 38 7.320399 AGTTTGGACAAAAGTACAAGGAAAAG 58.680 34.615 0.00 0.00 29.21 2.27
38 39 5.845391 TGGACAAAAGTACAAGGAAAAGG 57.155 39.130 0.00 0.00 0.00 3.11
39 40 5.265989 TGGACAAAAGTACAAGGAAAAGGT 58.734 37.500 0.00 0.00 0.00 3.50
40 41 6.424883 TGGACAAAAGTACAAGGAAAAGGTA 58.575 36.000 0.00 0.00 0.00 3.08
41 42 6.544564 TGGACAAAAGTACAAGGAAAAGGTAG 59.455 38.462 0.00 0.00 0.00 3.18
42 43 6.769341 GGACAAAAGTACAAGGAAAAGGTAGA 59.231 38.462 0.00 0.00 0.00 2.59
43 44 7.283807 GGACAAAAGTACAAGGAAAAGGTAGAA 59.716 37.037 0.00 0.00 0.00 2.10
44 45 8.584063 ACAAAAGTACAAGGAAAAGGTAGAAA 57.416 30.769 0.00 0.00 0.00 2.52
45 46 8.683615 ACAAAAGTACAAGGAAAAGGTAGAAAG 58.316 33.333 0.00 0.00 0.00 2.62
46 47 8.899771 CAAAAGTACAAGGAAAAGGTAGAAAGA 58.100 33.333 0.00 0.00 0.00 2.52
47 48 9.470399 AAAAGTACAAGGAAAAGGTAGAAAGAA 57.530 29.630 0.00 0.00 0.00 2.52
48 49 9.470399 AAAGTACAAGGAAAAGGTAGAAAGAAA 57.530 29.630 0.00 0.00 0.00 2.52
49 50 9.470399 AAGTACAAGGAAAAGGTAGAAAGAAAA 57.530 29.630 0.00 0.00 0.00 2.29
50 51 8.900781 AGTACAAGGAAAAGGTAGAAAGAAAAC 58.099 33.333 0.00 0.00 0.00 2.43
51 52 7.712204 ACAAGGAAAAGGTAGAAAGAAAACA 57.288 32.000 0.00 0.00 0.00 2.83
52 53 8.129496 ACAAGGAAAAGGTAGAAAGAAAACAA 57.871 30.769 0.00 0.00 0.00 2.83
53 54 8.251026 ACAAGGAAAAGGTAGAAAGAAAACAAG 58.749 33.333 0.00 0.00 0.00 3.16
54 55 7.956328 AGGAAAAGGTAGAAAGAAAACAAGT 57.044 32.000 0.00 0.00 0.00 3.16
55 56 8.362464 AGGAAAAGGTAGAAAGAAAACAAGTT 57.638 30.769 0.00 0.00 0.00 2.66
56 57 9.470399 AGGAAAAGGTAGAAAGAAAACAAGTTA 57.530 29.630 0.00 0.00 0.00 2.24
57 58 9.731819 GGAAAAGGTAGAAAGAAAACAAGTTAG 57.268 33.333 0.00 0.00 0.00 2.34
61 62 9.847224 AAGGTAGAAAGAAAACAAGTTAGATCA 57.153 29.630 0.00 0.00 0.00 2.92
62 63 9.847224 AGGTAGAAAGAAAACAAGTTAGATCAA 57.153 29.630 0.00 0.00 0.00 2.57
74 75 9.930693 AACAAGTTAGATCAAAACTACTAGGAG 57.069 33.333 12.34 0.00 36.17 3.69
75 76 9.091220 ACAAGTTAGATCAAAACTACTAGGAGT 57.909 33.333 0.17 0.17 36.17 3.85
85 86 9.750783 TCAAAACTACTAGGAGTATCTAAGTGT 57.249 33.333 8.40 0.00 33.37 3.55
91 92 9.624697 CTACTAGGAGTATCTAAGTGTAGTACG 57.375 40.741 0.00 0.00 33.37 3.67
92 93 6.928492 ACTAGGAGTATCTAAGTGTAGTACGC 59.072 42.308 5.68 5.68 30.79 4.42
93 94 5.062528 AGGAGTATCTAAGTGTAGTACGCC 58.937 45.833 10.23 0.00 35.93 5.68
94 95 4.215185 GGAGTATCTAAGTGTAGTACGCCC 59.785 50.000 10.23 0.00 33.19 6.13
95 96 3.812053 AGTATCTAAGTGTAGTACGCCCG 59.188 47.826 10.23 0.00 0.00 6.13
96 97 2.113860 TCTAAGTGTAGTACGCCCGT 57.886 50.000 10.23 0.00 0.00 5.28
97 98 1.739466 TCTAAGTGTAGTACGCCCGTG 59.261 52.381 10.23 0.00 0.00 4.94
98 99 1.739466 CTAAGTGTAGTACGCCCGTGA 59.261 52.381 10.23 0.00 0.00 4.35
99 100 0.242017 AAGTGTAGTACGCCCGTGAC 59.758 55.000 10.23 0.15 0.00 3.67
100 101 0.890542 AGTGTAGTACGCCCGTGACA 60.891 55.000 10.23 2.70 0.00 3.58
101 102 0.171903 GTGTAGTACGCCCGTGACAT 59.828 55.000 2.20 0.00 0.00 3.06
102 103 0.889994 TGTAGTACGCCCGTGACATT 59.110 50.000 3.22 0.00 0.00 2.71
103 104 1.273048 TGTAGTACGCCCGTGACATTT 59.727 47.619 3.22 0.00 0.00 2.32
104 105 2.288948 TGTAGTACGCCCGTGACATTTT 60.289 45.455 3.22 0.00 0.00 1.82
105 106 1.886886 AGTACGCCCGTGACATTTTT 58.113 45.000 3.22 0.00 0.00 1.94
130 131 1.448922 TTTTGAGGAAACGCCCGTGG 61.449 55.000 0.00 0.00 37.37 4.94
164 165 1.225745 GAAGGACGCACGCAAATCG 60.226 57.895 0.00 0.00 45.38 3.34
201 202 1.228894 AGCCACGACCTCTTCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
203 204 0.460987 GCCACGACCTCTTCCTCATG 60.461 60.000 0.00 0.00 0.00 3.07
208 209 2.244117 GACCTCTTCCTCATGCGCCA 62.244 60.000 4.18 0.00 0.00 5.69
209 210 1.817099 CCTCTTCCTCATGCGCCAC 60.817 63.158 4.18 0.00 0.00 5.01
211 212 3.197790 CTTCCTCATGCGCCACGG 61.198 66.667 4.18 0.00 0.00 4.94
249 250 4.468689 CCGACCCGCTTTCCTCCC 62.469 72.222 0.00 0.00 0.00 4.30
440 452 1.152419 TCACGACCTCACCTCCCAA 60.152 57.895 0.00 0.00 0.00 4.12
489 502 1.736696 GCCCATTGCTCCGTTCAATTG 60.737 52.381 0.00 0.00 36.87 2.32
514 527 1.430075 CCATCCCATTCCATCCCATCA 59.570 52.381 0.00 0.00 0.00 3.07
572 595 0.741221 GAGTCCACAAGATGACCGCC 60.741 60.000 0.00 0.00 31.76 6.13
586 609 1.221840 CCGCCTCCTATGTGTTGCT 59.778 57.895 0.00 0.00 0.00 3.91
587 610 0.464036 CCGCCTCCTATGTGTTGCTA 59.536 55.000 0.00 0.00 0.00 3.49
596 632 3.129287 CCTATGTGTTGCTAAGCCCTTTG 59.871 47.826 0.00 0.00 0.00 2.77
714 848 5.859205 AATCCTTGTGAATATTGGGCTTC 57.141 39.130 0.00 0.00 0.00 3.86
741 876 6.810182 AGCTTGATTTCATTTCAATCCTTTCG 59.190 34.615 0.00 0.00 32.94 3.46
749 884 7.539712 TCATTTCAATCCTTTCGAGTATGAC 57.460 36.000 0.00 0.00 0.00 3.06
849 987 3.375299 GTGCTTATCATCACACAACTCCC 59.625 47.826 0.00 0.00 33.63 4.30
868 1006 9.204570 CAACTCCCAACTTATATTCCTATAACG 57.795 37.037 0.00 0.00 0.00 3.18
886 1024 8.167985 CCTATAACGTACGTAGCTTCTATCTTC 58.832 40.741 23.12 0.00 0.00 2.87
906 1045 3.555966 TCGATGCAGAGTCCTGAATAGA 58.444 45.455 0.00 0.00 38.79 1.98
908 1047 4.217334 TCGATGCAGAGTCCTGAATAGATC 59.783 45.833 0.00 0.00 38.79 2.75
927 1066 2.880380 GCTGCCGGTAGGGGGTATC 61.880 68.421 21.82 0.00 38.20 2.24
931 1070 1.052694 GCCGGTAGGGGGTATCAACT 61.053 60.000 1.90 0.00 38.20 3.16
933 1072 2.681422 CCGGTAGGGGGTATCAACTAA 58.319 52.381 0.00 0.00 0.00 2.24
961 1100 4.187694 GAGGAAACTATTCAGAGCCAGTG 58.812 47.826 0.00 0.00 44.43 3.66
1014 1153 3.124297 GCTTCTGTATGCAGTCTGTTGAC 59.876 47.826 10.80 0.00 43.05 3.18
1067 1374 1.623811 GGTGAGTTACTTGCCCTCTCA 59.376 52.381 0.00 0.00 33.60 3.27
1188 1503 9.967346 TTGAACGTTTAATCATTTAATGTTGGA 57.033 25.926 10.68 0.00 31.63 3.53
1189 1504 9.619316 TGAACGTTTAATCATTTAATGTTGGAG 57.381 29.630 10.68 0.00 31.63 3.86
1190 1505 9.834628 GAACGTTTAATCATTTAATGTTGGAGA 57.165 29.630 10.68 0.00 31.63 3.71
1244 1561 7.801315 CCATTTTGAATGCTCTGTTTTTCATTG 59.199 33.333 0.00 0.00 30.19 2.82
1251 1568 4.338964 TGCTCTGTTTTTCATTGCTGAAGA 59.661 37.500 0.00 0.00 42.19 2.87
1288 1607 1.542472 CAATGCAGTGCACCTCAATGA 59.458 47.619 22.44 0.00 42.95 2.57
1289 1608 1.913778 ATGCAGTGCACCTCAATGAA 58.086 45.000 22.44 0.00 42.95 2.57
1346 1665 4.021368 TCTGGTTACTTACCTGAGCAAGTC 60.021 45.833 1.61 0.00 46.41 3.01
1348 1667 4.895961 GGTTACTTACCTGAGCAAGTCTT 58.104 43.478 1.61 0.00 44.10 3.01
1355 1675 2.173569 ACCTGAGCAAGTCTTGAAGGTT 59.826 45.455 20.88 11.08 37.27 3.50
1422 1743 3.494048 GGTTTGGTGCCATCACATTTTGA 60.494 43.478 0.00 0.00 44.87 2.69
1432 1753 4.158209 CCATCACATTTTGACAGCCATACA 59.842 41.667 0.00 0.00 36.92 2.29
1503 1824 4.584327 ATGAAGCAAAACGTTAAGCCTT 57.416 36.364 17.95 10.91 0.00 4.35
1553 1874 7.829706 GTCTCATAGTAATGGAAACCCTTTCTT 59.170 37.037 0.00 0.00 39.59 2.52
1568 1902 9.503399 AAACCCTTTCTTAGAAGTACAACTATG 57.497 33.333 0.00 1.38 0.00 2.23
1698 2036 2.158726 AGGTAGTCCAAACAGGCGAAAA 60.159 45.455 0.00 0.00 37.29 2.29
1764 2103 9.449719 CAATTAGAGTTACACCTTTAGGAACAT 57.550 33.333 2.06 0.00 38.94 2.71
1773 2112 6.306987 ACACCTTTAGGAACATCTTTCATGT 58.693 36.000 2.06 0.00 38.94 3.21
1793 2132 3.064271 TGTGTTTAGGTGTTTGACGAAGC 59.936 43.478 0.00 0.00 0.00 3.86
1813 2152 6.204688 CGAAGCTAATATGGATGGTAGCAAAA 59.795 38.462 0.00 0.00 41.17 2.44
1934 2297 6.814146 GGACAGGTTTATCACTCTAGTTTCAG 59.186 42.308 0.00 0.00 0.00 3.02
2035 2398 3.021695 TCAGATTCAGGTACCGGTACAG 58.978 50.000 38.26 30.38 37.78 2.74
2072 2439 1.278238 GATGTACTTCCGTTCCTGCG 58.722 55.000 0.00 0.00 0.00 5.18
2151 2520 7.440523 AGTTGATGAAGCGATAACTTTCTTT 57.559 32.000 0.00 0.00 0.00 2.52
2192 2561 5.104982 TCAAAAACTTCCATGTCAAAAGCCT 60.105 36.000 0.00 0.00 0.00 4.58
2223 2592 6.989169 ACAAGTTGCTTATCTATCTGACATCC 59.011 38.462 1.81 0.00 0.00 3.51
2512 2888 7.714377 TGTTTGCTTGGTATTTCATGTGATTTT 59.286 29.630 0.00 0.00 0.00 1.82
2521 2897 9.573133 GGTATTTCATGTGATTTTACTTCTTGG 57.427 33.333 0.00 0.00 0.00 3.61
2546 3029 7.332678 GGGAGAAACGAGCAGTAGTATTTTAAA 59.667 37.037 0.00 0.00 0.00 1.52
2578 3061 3.878245 GCTCGTTCAGCTATAAATTGGC 58.122 45.455 0.00 0.00 45.83 4.52
2798 3368 4.583871 AGTTCATGAACCTTGTCATCCTC 58.416 43.478 30.34 5.47 42.06 3.71
2844 3418 1.202891 ACAGGTTAGGGGTGTTCTTGC 60.203 52.381 0.00 0.00 0.00 4.01
2925 3499 9.066892 TCTGATGTATTGAAGTATAAAATGCCC 57.933 33.333 0.00 0.00 0.00 5.36
3017 3593 1.218047 CTGGCTCGAAATCGGACCA 59.782 57.895 14.17 14.17 40.54 4.02
3042 3618 4.374843 TTGCCATTGATGCACTGTTATC 57.625 40.909 0.00 0.00 38.72 1.75
3126 3707 6.706716 AGAAGAACTGGCTAGTTAACAAGTTC 59.293 38.462 16.16 19.56 46.79 3.01
3151 3733 4.340617 TCTTTGGGGCTAGGTTAACAATG 58.659 43.478 8.10 0.00 0.00 2.82
3280 3862 4.280929 GGTTTACCTTCTTTTCCATGCAGT 59.719 41.667 0.00 0.00 0.00 4.40
3309 3891 2.533916 AGTCATTGCACTCCAGAGAGA 58.466 47.619 0.70 0.00 43.39 3.10
3400 3982 5.246307 GTGCTATCTCCTTTAAACACTGGT 58.754 41.667 0.00 0.00 0.00 4.00
3413 3995 0.962356 CACTGGTCCAGGGATGCAAC 60.962 60.000 23.06 0.00 36.97 4.17
3480 4062 3.823873 AGTTTTAATTGCGATGGTGACCA 59.176 39.130 6.84 6.84 38.19 4.02
3511 4093 6.476706 GCTTTATTTTGCTTTCAGTGTTGACT 59.523 34.615 0.00 0.00 31.71 3.41
3566 4148 4.576463 GGACGAGGCATTCTCATAAAACAT 59.424 41.667 0.00 0.00 42.55 2.71
3567 4149 5.758296 GGACGAGGCATTCTCATAAAACATA 59.242 40.000 0.00 0.00 42.55 2.29
3568 4150 6.428159 GGACGAGGCATTCTCATAAAACATAT 59.572 38.462 0.00 0.00 42.55 1.78
3570 4152 6.205464 ACGAGGCATTCTCATAAAACATATGG 59.795 38.462 7.80 0.00 42.55 2.74
3571 4153 6.336842 AGGCATTCTCATAAAACATATGGC 57.663 37.500 7.80 0.00 37.36 4.40
3572 4154 5.834742 AGGCATTCTCATAAAACATATGGCA 59.165 36.000 7.80 0.00 38.92 4.92
3573 4155 6.495872 AGGCATTCTCATAAAACATATGGCAT 59.504 34.615 4.88 4.88 38.92 4.40
3574 4156 7.015877 AGGCATTCTCATAAAACATATGGCATT 59.984 33.333 4.78 1.70 38.92 3.56
3575 4157 7.330208 GGCATTCTCATAAAACATATGGCATTC 59.670 37.037 4.78 0.00 37.14 2.67
3576 4158 8.086522 GCATTCTCATAAAACATATGGCATTCT 58.913 33.333 4.78 0.00 0.00 2.40
3579 4161 9.625747 TTCTCATAAAACATATGGCATTCTACA 57.374 29.630 4.78 0.00 0.00 2.74
3580 4162 9.276590 TCTCATAAAACATATGGCATTCTACAG 57.723 33.333 4.78 0.00 0.00 2.74
3581 4163 9.276590 CTCATAAAACATATGGCATTCTACAGA 57.723 33.333 4.78 0.00 0.00 3.41
3582 4164 9.797642 TCATAAAACATATGGCATTCTACAGAT 57.202 29.630 4.78 0.00 0.00 2.90
3636 4218 4.841443 GAACATTTCCACGGGTACTTTT 57.159 40.909 0.00 0.00 0.00 2.27
3637 4219 5.190992 GAACATTTCCACGGGTACTTTTT 57.809 39.130 0.00 0.00 0.00 1.94
3682 4264 7.803279 AGTTCTTTTTCGAAAGATTACCTGT 57.197 32.000 10.98 0.00 41.60 4.00
3683 4265 7.862648 AGTTCTTTTTCGAAAGATTACCTGTC 58.137 34.615 10.98 0.00 41.60 3.51
3684 4266 7.715686 AGTTCTTTTTCGAAAGATTACCTGTCT 59.284 33.333 10.98 0.00 41.60 3.41
3685 4267 8.343366 GTTCTTTTTCGAAAGATTACCTGTCTT 58.657 33.333 10.98 0.00 41.60 3.01
3686 4268 8.446599 TCTTTTTCGAAAGATTACCTGTCTTT 57.553 30.769 10.98 1.12 45.77 2.52
3687 4269 8.342634 TCTTTTTCGAAAGATTACCTGTCTTTG 58.657 33.333 10.98 0.55 43.80 2.77
3688 4270 7.562454 TTTTCGAAAGATTACCTGTCTTTGT 57.438 32.000 10.98 0.00 43.80 2.83
3689 4271 7.562454 TTTCGAAAGATTACCTGTCTTTGTT 57.438 32.000 6.47 0.00 43.80 2.83
3690 4272 7.562454 TTCGAAAGATTACCTGTCTTTGTTT 57.438 32.000 5.91 0.00 43.80 2.83
3691 4273 8.665643 TTCGAAAGATTACCTGTCTTTGTTTA 57.334 30.769 5.91 0.00 43.80 2.01
3692 4274 8.842358 TCGAAAGATTACCTGTCTTTGTTTAT 57.158 30.769 5.91 0.00 43.80 1.40
3693 4275 8.717821 TCGAAAGATTACCTGTCTTTGTTTATG 58.282 33.333 5.91 0.00 43.80 1.90
3694 4276 7.481798 CGAAAGATTACCTGTCTTTGTTTATGC 59.518 37.037 5.91 0.00 43.80 3.14
3695 4277 8.409358 AAAGATTACCTGTCTTTGTTTATGCT 57.591 30.769 0.73 0.00 42.58 3.79
3696 4278 8.409358 AAGATTACCTGTCTTTGTTTATGCTT 57.591 30.769 0.00 0.00 32.17 3.91
3697 4279 8.045176 AGATTACCTGTCTTTGTTTATGCTTC 57.955 34.615 0.00 0.00 0.00 3.86
3698 4280 4.749245 ACCTGTCTTTGTTTATGCTTCG 57.251 40.909 0.00 0.00 0.00 3.79
3699 4281 3.502211 ACCTGTCTTTGTTTATGCTTCGG 59.498 43.478 0.00 0.00 0.00 4.30
3700 4282 3.751175 CCTGTCTTTGTTTATGCTTCGGA 59.249 43.478 0.00 0.00 0.00 4.55
3701 4283 4.396166 CCTGTCTTTGTTTATGCTTCGGAT 59.604 41.667 0.00 0.00 0.00 4.18
3702 4284 5.106157 CCTGTCTTTGTTTATGCTTCGGATT 60.106 40.000 0.00 0.00 0.00 3.01
3703 4285 6.093495 CCTGTCTTTGTTTATGCTTCGGATTA 59.907 38.462 0.00 0.00 0.00 1.75
3704 4286 7.072177 TGTCTTTGTTTATGCTTCGGATTAG 57.928 36.000 0.00 0.00 0.00 1.73
3705 4287 6.876789 TGTCTTTGTTTATGCTTCGGATTAGA 59.123 34.615 0.00 0.00 0.00 2.10
3706 4288 7.064609 TGTCTTTGTTTATGCTTCGGATTAGAG 59.935 37.037 0.00 0.00 0.00 2.43
3707 4289 5.734855 TTGTTTATGCTTCGGATTAGAGC 57.265 39.130 0.00 0.00 0.00 4.09
3708 4290 4.765273 TGTTTATGCTTCGGATTAGAGCA 58.235 39.130 4.71 4.71 39.91 4.26
3709 4291 5.182487 TGTTTATGCTTCGGATTAGAGCAA 58.818 37.500 6.22 0.00 39.04 3.91
3710 4292 5.645929 TGTTTATGCTTCGGATTAGAGCAAA 59.354 36.000 6.22 1.18 39.04 3.68
3711 4293 6.318648 TGTTTATGCTTCGGATTAGAGCAAAT 59.681 34.615 6.22 0.00 39.04 2.32
3712 4294 4.825546 ATGCTTCGGATTAGAGCAAATG 57.174 40.909 6.22 0.00 39.04 2.32
3713 4295 3.872696 TGCTTCGGATTAGAGCAAATGA 58.127 40.909 0.00 0.00 32.17 2.57
3714 4296 3.623060 TGCTTCGGATTAGAGCAAATGAC 59.377 43.478 0.00 0.00 32.17 3.06
3715 4297 3.873952 GCTTCGGATTAGAGCAAATGACT 59.126 43.478 0.00 0.00 0.00 3.41
3716 4298 5.050490 GCTTCGGATTAGAGCAAATGACTA 58.950 41.667 0.00 0.00 0.00 2.59
3717 4299 5.523916 GCTTCGGATTAGAGCAAATGACTAA 59.476 40.000 0.00 0.00 0.00 2.24
3718 4300 6.203723 GCTTCGGATTAGAGCAAATGACTAAT 59.796 38.462 0.00 0.00 38.83 1.73
3719 4301 7.254932 GCTTCGGATTAGAGCAAATGACTAATT 60.255 37.037 0.00 0.00 37.09 1.40
3720 4302 7.715265 TCGGATTAGAGCAAATGACTAATTC 57.285 36.000 0.00 0.00 37.09 2.17
3721 4303 6.584954 CGGATTAGAGCAAATGACTAATTCG 58.415 40.000 17.86 17.86 43.83 3.34
3722 4304 6.201044 CGGATTAGAGCAAATGACTAATTCGT 59.799 38.462 20.44 0.00 44.06 3.85
3723 4305 7.567771 CGGATTAGAGCAAATGACTAATTCGTC 60.568 40.741 20.44 3.23 44.06 4.20
3724 4306 6.903883 TTAGAGCAAATGACTAATTCGTCC 57.096 37.500 7.58 0.00 32.97 4.79
3725 4307 4.832248 AGAGCAAATGACTAATTCGTCCA 58.168 39.130 7.58 0.00 32.97 4.02
3726 4308 4.631813 AGAGCAAATGACTAATTCGTCCAC 59.368 41.667 7.58 0.00 32.97 4.02
3727 4309 3.370978 AGCAAATGACTAATTCGTCCACG 59.629 43.478 7.58 0.00 41.45 4.94
3728 4310 3.670203 CAAATGACTAATTCGTCCACGC 58.330 45.455 7.58 0.00 39.60 5.34
3729 4311 1.935933 ATGACTAATTCGTCCACGCC 58.064 50.000 7.58 0.00 39.60 5.68
3730 4312 0.892755 TGACTAATTCGTCCACGCCT 59.107 50.000 7.58 0.00 39.60 5.52
3731 4313 2.093890 TGACTAATTCGTCCACGCCTA 58.906 47.619 7.58 0.00 39.60 3.93
3732 4314 2.159338 TGACTAATTCGTCCACGCCTAC 60.159 50.000 7.58 0.00 39.60 3.18
3733 4315 5.561148 TGACTAATTCGTCCACGCCTACG 62.561 52.174 7.58 0.00 40.40 3.51
3734 4316 1.064505 CTAATTCGTCCACGCCTACGA 59.935 52.381 2.99 2.99 45.64 3.43
3736 4318 2.562912 TCGTCCACGCCTACGAAC 59.437 61.111 4.49 0.00 44.47 3.95
3737 4319 2.505557 CGTCCACGCCTACGAACC 60.506 66.667 0.00 0.00 43.93 3.62
3738 4320 2.652530 GTCCACGCCTACGAACCA 59.347 61.111 0.00 0.00 43.93 3.67
3739 4321 1.445582 GTCCACGCCTACGAACCAG 60.446 63.158 0.00 0.00 43.93 4.00
3740 4322 1.904865 TCCACGCCTACGAACCAGT 60.905 57.895 0.00 0.00 43.93 4.00
3741 4323 1.445582 CCACGCCTACGAACCAGTC 60.446 63.158 0.00 0.00 43.93 3.51
3755 4337 5.412526 GAACCAGTCGACATTTTGTACAA 57.587 39.130 19.50 3.59 0.00 2.41
3756 4338 5.812652 GAACCAGTCGACATTTTGTACAAA 58.187 37.500 19.50 17.01 0.00 2.83
3757 4339 6.385649 AACCAGTCGACATTTTGTACAAAT 57.614 33.333 21.17 7.24 0.00 2.32
3758 4340 6.385649 ACCAGTCGACATTTTGTACAAATT 57.614 33.333 21.17 14.93 0.00 1.82
3759 4341 6.801575 ACCAGTCGACATTTTGTACAAATTT 58.198 32.000 21.17 9.77 0.00 1.82
3760 4342 7.262048 ACCAGTCGACATTTTGTACAAATTTT 58.738 30.769 21.17 11.18 0.00 1.82
3761 4343 8.407064 ACCAGTCGACATTTTGTACAAATTTTA 58.593 29.630 21.17 7.35 0.00 1.52
3762 4344 9.405587 CCAGTCGACATTTTGTACAAATTTTAT 57.594 29.630 21.17 9.37 0.00 1.40
3767 4349 9.706996 CGACATTTTGTACAAATTTTATGAACG 57.293 29.630 26.29 24.21 0.00 3.95
3769 4351 9.751542 ACATTTTGTACAAATTTTATGAACGGA 57.248 25.926 26.29 9.44 0.00 4.69
3772 4354 7.861176 TTGTACAAATTTTATGAACGGAAGC 57.139 32.000 5.64 0.00 0.00 3.86
3773 4355 7.209471 TGTACAAATTTTATGAACGGAAGCT 57.791 32.000 0.00 0.00 0.00 3.74
3774 4356 7.302524 TGTACAAATTTTATGAACGGAAGCTC 58.697 34.615 0.00 0.00 0.00 4.09
3775 4357 6.575162 ACAAATTTTATGAACGGAAGCTCT 57.425 33.333 0.00 0.00 0.00 4.09
3776 4358 6.981722 ACAAATTTTATGAACGGAAGCTCTT 58.018 32.000 0.00 0.00 0.00 2.85
3777 4359 8.106247 ACAAATTTTATGAACGGAAGCTCTTA 57.894 30.769 0.00 0.00 0.00 2.10
3778 4360 8.739972 ACAAATTTTATGAACGGAAGCTCTTAT 58.260 29.630 0.00 0.00 0.00 1.73
3779 4361 9.573133 CAAATTTTATGAACGGAAGCTCTTATT 57.427 29.630 0.00 0.00 0.00 1.40
3782 4364 9.788960 ATTTTATGAACGGAAGCTCTTATTTTC 57.211 29.630 0.00 0.00 0.00 2.29
3783 4365 7.915293 TTATGAACGGAAGCTCTTATTTTCA 57.085 32.000 0.00 0.00 0.00 2.69
3784 4366 8.506168 TTATGAACGGAAGCTCTTATTTTCAT 57.494 30.769 10.97 10.97 36.61 2.57
3785 4367 9.607988 TTATGAACGGAAGCTCTTATTTTCATA 57.392 29.630 9.59 9.59 34.92 2.15
3786 4368 8.682936 ATGAACGGAAGCTCTTATTTTCATAT 57.317 30.769 0.00 0.00 32.13 1.78
3787 4369 8.506168 TGAACGGAAGCTCTTATTTTCATATT 57.494 30.769 0.00 0.00 0.00 1.28
3788 4370 8.956426 TGAACGGAAGCTCTTATTTTCATATTT 58.044 29.630 0.00 0.00 0.00 1.40
3789 4371 9.439537 GAACGGAAGCTCTTATTTTCATATTTC 57.560 33.333 0.00 0.00 0.00 2.17
3790 4372 7.931275 ACGGAAGCTCTTATTTTCATATTTCC 58.069 34.615 0.00 0.00 0.00 3.13
3791 4373 7.072030 CGGAAGCTCTTATTTTCATATTTCCG 58.928 38.462 0.00 0.00 44.60 4.30
3792 4374 7.254795 CGGAAGCTCTTATTTTCATATTTCCGT 60.255 37.037 0.00 0.00 44.79 4.69
3793 4375 9.052759 GGAAGCTCTTATTTTCATATTTCCGTA 57.947 33.333 0.00 0.00 0.00 4.02
3796 4378 9.220767 AGCTCTTATTTTCATATTTCCGTATCC 57.779 33.333 0.00 0.00 0.00 2.59
3797 4379 9.220767 GCTCTTATTTTCATATTTCCGTATCCT 57.779 33.333 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.529865 GTCCAAACTAGCACGTTCACC 59.470 52.381 0.00 0.00 0.00 4.02
2 3 2.605837 TGTCCAAACTAGCACGTTCA 57.394 45.000 0.00 0.00 0.00 3.18
4 5 3.692593 ACTTTTGTCCAAACTAGCACGTT 59.307 39.130 0.00 0.00 0.00 3.99
5 6 3.275999 ACTTTTGTCCAAACTAGCACGT 58.724 40.909 0.00 0.00 0.00 4.49
6 7 3.963383 ACTTTTGTCCAAACTAGCACG 57.037 42.857 0.00 0.00 0.00 5.34
7 8 5.744666 TGTACTTTTGTCCAAACTAGCAC 57.255 39.130 0.00 0.00 0.00 4.40
8 9 5.298276 CCTTGTACTTTTGTCCAAACTAGCA 59.702 40.000 0.00 0.00 27.93 3.49
9 10 5.529800 TCCTTGTACTTTTGTCCAAACTAGC 59.470 40.000 0.00 0.00 27.93 3.42
10 11 7.562454 TTCCTTGTACTTTTGTCCAAACTAG 57.438 36.000 0.00 0.00 27.93 2.57
11 12 7.941431 TTTCCTTGTACTTTTGTCCAAACTA 57.059 32.000 0.00 0.00 27.93 2.24
12 13 6.844097 TTTCCTTGTACTTTTGTCCAAACT 57.156 33.333 0.00 0.00 27.93 2.66
13 14 6.533723 CCTTTTCCTTGTACTTTTGTCCAAAC 59.466 38.462 0.00 0.00 27.93 2.93
14 15 6.211785 ACCTTTTCCTTGTACTTTTGTCCAAA 59.788 34.615 0.00 0.00 27.93 3.28
15 16 5.717654 ACCTTTTCCTTGTACTTTTGTCCAA 59.282 36.000 0.00 0.00 0.00 3.53
16 17 5.265989 ACCTTTTCCTTGTACTTTTGTCCA 58.734 37.500 0.00 0.00 0.00 4.02
17 18 5.847111 ACCTTTTCCTTGTACTTTTGTCC 57.153 39.130 0.00 0.00 0.00 4.02
18 19 7.797038 TCTACCTTTTCCTTGTACTTTTGTC 57.203 36.000 0.00 0.00 0.00 3.18
19 20 8.584063 TTTCTACCTTTTCCTTGTACTTTTGT 57.416 30.769 0.00 0.00 0.00 2.83
20 21 8.899771 TCTTTCTACCTTTTCCTTGTACTTTTG 58.100 33.333 0.00 0.00 0.00 2.44
21 22 9.470399 TTCTTTCTACCTTTTCCTTGTACTTTT 57.530 29.630 0.00 0.00 0.00 2.27
22 23 9.470399 TTTCTTTCTACCTTTTCCTTGTACTTT 57.530 29.630 0.00 0.00 0.00 2.66
23 24 9.470399 TTTTCTTTCTACCTTTTCCTTGTACTT 57.530 29.630 0.00 0.00 0.00 2.24
24 25 8.900781 GTTTTCTTTCTACCTTTTCCTTGTACT 58.099 33.333 0.00 0.00 0.00 2.73
25 26 8.680001 TGTTTTCTTTCTACCTTTTCCTTGTAC 58.320 33.333 0.00 0.00 0.00 2.90
26 27 8.810990 TGTTTTCTTTCTACCTTTTCCTTGTA 57.189 30.769 0.00 0.00 0.00 2.41
27 28 7.712204 TGTTTTCTTTCTACCTTTTCCTTGT 57.288 32.000 0.00 0.00 0.00 3.16
28 29 8.251026 ACTTGTTTTCTTTCTACCTTTTCCTTG 58.749 33.333 0.00 0.00 0.00 3.61
29 30 8.362464 ACTTGTTTTCTTTCTACCTTTTCCTT 57.638 30.769 0.00 0.00 0.00 3.36
30 31 7.956328 ACTTGTTTTCTTTCTACCTTTTCCT 57.044 32.000 0.00 0.00 0.00 3.36
31 32 9.731819 CTAACTTGTTTTCTTTCTACCTTTTCC 57.268 33.333 0.00 0.00 0.00 3.13
35 36 9.847224 TGATCTAACTTGTTTTCTTTCTACCTT 57.153 29.630 0.00 0.00 0.00 3.50
36 37 9.847224 TTGATCTAACTTGTTTTCTTTCTACCT 57.153 29.630 0.00 0.00 0.00 3.08
48 49 9.930693 CTCCTAGTAGTTTTGATCTAACTTGTT 57.069 33.333 15.70 7.58 37.12 2.83
49 50 9.091220 ACTCCTAGTAGTTTTGATCTAACTTGT 57.909 33.333 15.70 8.65 37.12 3.16
59 60 9.750783 ACACTTAGATACTCCTAGTAGTTTTGA 57.249 33.333 0.00 0.00 33.66 2.69
65 66 9.624697 CGTACTACACTTAGATACTCCTAGTAG 57.375 40.741 0.00 0.00 33.66 2.57
66 67 8.085296 GCGTACTACACTTAGATACTCCTAGTA 58.915 40.741 0.00 0.00 34.82 1.82
67 68 6.928492 GCGTACTACACTTAGATACTCCTAGT 59.072 42.308 0.00 0.00 0.00 2.57
68 69 6.368516 GGCGTACTACACTTAGATACTCCTAG 59.631 46.154 0.00 0.00 0.00 3.02
69 70 6.226787 GGCGTACTACACTTAGATACTCCTA 58.773 44.000 0.00 0.00 0.00 2.94
70 71 5.062528 GGCGTACTACACTTAGATACTCCT 58.937 45.833 0.00 0.00 0.00 3.69
71 72 4.215185 GGGCGTACTACACTTAGATACTCC 59.785 50.000 0.00 0.00 0.00 3.85
72 73 4.084118 CGGGCGTACTACACTTAGATACTC 60.084 50.000 0.00 0.00 0.00 2.59
73 74 3.812053 CGGGCGTACTACACTTAGATACT 59.188 47.826 0.00 0.00 0.00 2.12
74 75 3.561725 ACGGGCGTACTACACTTAGATAC 59.438 47.826 0.00 0.00 0.00 2.24
75 76 3.561310 CACGGGCGTACTACACTTAGATA 59.439 47.826 0.00 0.00 0.00 1.98
76 77 2.357009 CACGGGCGTACTACACTTAGAT 59.643 50.000 0.00 0.00 0.00 1.98
77 78 1.739466 CACGGGCGTACTACACTTAGA 59.261 52.381 0.00 0.00 0.00 2.10
78 79 1.739466 TCACGGGCGTACTACACTTAG 59.261 52.381 0.00 0.00 0.00 2.18
79 80 1.468520 GTCACGGGCGTACTACACTTA 59.531 52.381 0.00 0.00 0.00 2.24
80 81 0.242017 GTCACGGGCGTACTACACTT 59.758 55.000 0.00 0.00 0.00 3.16
81 82 0.890542 TGTCACGGGCGTACTACACT 60.891 55.000 0.00 0.00 0.00 3.55
82 83 0.171903 ATGTCACGGGCGTACTACAC 59.828 55.000 0.00 0.00 0.00 2.90
83 84 0.889994 AATGTCACGGGCGTACTACA 59.110 50.000 0.00 0.00 0.00 2.74
84 85 2.000429 AAATGTCACGGGCGTACTAC 58.000 50.000 0.00 0.00 0.00 2.73
85 86 2.747396 AAAATGTCACGGGCGTACTA 57.253 45.000 0.00 0.00 0.00 1.82
86 87 1.886886 AAAAATGTCACGGGCGTACT 58.113 45.000 0.00 0.00 0.00 2.73
110 111 0.382515 CACGGGCGTTTCCTCAAAAA 59.617 50.000 0.00 0.00 34.39 1.94
111 112 1.448922 CCACGGGCGTTTCCTCAAAA 61.449 55.000 0.00 0.00 34.39 2.44
112 113 1.894756 CCACGGGCGTTTCCTCAAA 60.895 57.895 0.00 0.00 34.39 2.69
113 114 2.281208 CCACGGGCGTTTCCTCAA 60.281 61.111 0.00 0.00 34.39 3.02
130 131 4.838152 TCGCGGCTCCCAAGATGC 62.838 66.667 6.13 0.00 0.00 3.91
135 136 4.388499 GTCCTTCGCGGCTCCCAA 62.388 66.667 6.13 0.00 0.00 4.12
145 146 1.225745 GATTTGCGTGCGTCCTTCG 60.226 57.895 0.00 0.00 43.12 3.79
249 250 3.077556 CAGGAGGGAGACGGGGTG 61.078 72.222 0.00 0.00 0.00 4.61
333 338 4.148825 CTCACCGGAGAAGGCCCG 62.149 72.222 9.46 0.00 44.26 6.13
334 339 3.787001 CCTCACCGGAGAAGGCCC 61.787 72.222 9.46 0.00 44.26 5.80
335 340 2.683933 TCCTCACCGGAGAAGGCC 60.684 66.667 9.46 0.00 44.26 5.19
440 452 1.158904 TAGATCTGGACGGAGGGGAT 58.841 55.000 5.18 0.00 0.00 3.85
514 527 4.202441 CAACCAAATCGAATCCCAGAGAT 58.798 43.478 0.00 0.00 36.48 2.75
560 583 1.414181 ACATAGGAGGCGGTCATCTTG 59.586 52.381 0.00 0.00 0.00 3.02
572 595 2.171448 AGGGCTTAGCAACACATAGGAG 59.829 50.000 6.53 0.00 0.00 3.69
596 632 6.600427 TCAGATTTAAAACTAACGGATTCCCC 59.400 38.462 0.00 0.00 0.00 4.81
686 820 5.581874 CCCAATATTCACAAGGATTTGTTGC 59.418 40.000 0.00 0.00 45.01 4.17
714 848 9.298774 GAAAGGATTGAAATGAAATCAAGCTAG 57.701 33.333 4.77 0.00 41.61 3.42
741 876 5.911752 ACATCATCCAAGACAGTCATACTC 58.088 41.667 2.66 0.00 0.00 2.59
749 884 4.700700 TGCATCTACATCATCCAAGACAG 58.299 43.478 0.00 0.00 0.00 3.51
814 951 4.050553 TGATAAGCACAAAAGCAGCAAAC 58.949 39.130 0.00 0.00 36.85 2.93
868 1006 4.847217 GCATCGAAGATAGAAGCTACGTAC 59.153 45.833 0.00 0.00 45.12 3.67
886 1024 3.998099 TCTATTCAGGACTCTGCATCG 57.002 47.619 0.00 0.00 40.69 3.84
927 1066 8.833231 TGAATAGTTTCCTCAGAAGTTAGTTG 57.167 34.615 0.00 0.00 32.35 3.16
931 1070 7.324178 GCTCTGAATAGTTTCCTCAGAAGTTA 58.676 38.462 2.92 0.00 43.69 2.24
933 1072 5.337975 GGCTCTGAATAGTTTCCTCAGAAGT 60.338 44.000 2.92 0.00 43.69 3.01
1014 1153 3.112075 CGCCAGGTACAGTGCACG 61.112 66.667 12.01 9.15 0.00 5.34
1067 1374 3.600388 GAATGACAAGGTCTGGACGAAT 58.400 45.455 0.00 0.00 33.15 3.34
1175 1490 7.362401 CCAACTTCTCCTCTCCAACATTAAATG 60.362 40.741 0.00 0.00 0.00 2.32
1176 1491 6.660949 CCAACTTCTCCTCTCCAACATTAAAT 59.339 38.462 0.00 0.00 0.00 1.40
1178 1493 5.073144 ACCAACTTCTCCTCTCCAACATTAA 59.927 40.000 0.00 0.00 0.00 1.40
1179 1494 4.597507 ACCAACTTCTCCTCTCCAACATTA 59.402 41.667 0.00 0.00 0.00 1.90
1180 1495 3.395941 ACCAACTTCTCCTCTCCAACATT 59.604 43.478 0.00 0.00 0.00 2.71
1181 1496 2.982488 ACCAACTTCTCCTCTCCAACAT 59.018 45.455 0.00 0.00 0.00 2.71
1182 1497 2.408565 ACCAACTTCTCCTCTCCAACA 58.591 47.619 0.00 0.00 0.00 3.33
1183 1498 3.579151 AGTACCAACTTCTCCTCTCCAAC 59.421 47.826 0.00 0.00 29.00 3.77
1184 1499 3.858135 AGTACCAACTTCTCCTCTCCAA 58.142 45.455 0.00 0.00 29.00 3.53
1185 1500 3.544698 AGTACCAACTTCTCCTCTCCA 57.455 47.619 0.00 0.00 29.00 3.86
1186 1501 5.997384 TTAAGTACCAACTTCTCCTCTCC 57.003 43.478 0.00 0.00 42.42 3.71
1187 1502 7.229581 TCTTTAAGTACCAACTTCTCCTCTC 57.770 40.000 0.00 0.00 42.42 3.20
1188 1503 7.800300 ATCTTTAAGTACCAACTTCTCCTCT 57.200 36.000 0.00 0.00 42.42 3.69
1189 1504 7.334671 CCAATCTTTAAGTACCAACTTCTCCTC 59.665 40.741 0.00 0.00 42.42 3.71
1190 1505 7.168905 CCAATCTTTAAGTACCAACTTCTCCT 58.831 38.462 0.00 0.00 42.42 3.69
1244 1561 3.495670 AGTGACAGTATCGTCTTCAGC 57.504 47.619 0.00 0.00 36.82 4.26
1251 1568 4.181578 GCATTGGTTAGTGACAGTATCGT 58.818 43.478 0.00 0.00 0.00 3.73
1288 1607 7.177921 ACAGGAATTTTGTGATGACTGATGATT 59.822 33.333 0.00 0.00 0.00 2.57
1289 1608 6.662234 ACAGGAATTTTGTGATGACTGATGAT 59.338 34.615 0.00 0.00 0.00 2.45
1337 1656 3.470709 CAGAACCTTCAAGACTTGCTCA 58.529 45.455 10.50 0.00 0.00 4.26
1346 1665 3.131709 TCAGCTTCCAGAACCTTCAAG 57.868 47.619 0.00 0.00 0.00 3.02
1348 1667 2.373169 ACATCAGCTTCCAGAACCTTCA 59.627 45.455 0.00 0.00 0.00 3.02
1355 1675 6.605471 TCTACTTTAACATCAGCTTCCAGA 57.395 37.500 0.00 0.00 0.00 3.86
1406 1727 2.331194 GCTGTCAAAATGTGATGGCAC 58.669 47.619 0.00 0.00 45.35 5.01
1407 1728 1.273048 GGCTGTCAAAATGTGATGGCA 59.727 47.619 0.00 0.00 38.90 4.92
1422 1743 6.349300 CCTTCTAGTTATGTTGTATGGCTGT 58.651 40.000 0.00 0.00 0.00 4.40
1432 1753 5.514500 TTGCTTCCCCTTCTAGTTATGTT 57.486 39.130 0.00 0.00 0.00 2.71
1527 1848 7.339482 AGAAAGGGTTTCCATTACTATGAGAC 58.661 38.462 0.00 0.00 40.54 3.36
1535 1856 7.997773 ACTTCTAAGAAAGGGTTTCCATTAC 57.002 36.000 0.00 0.00 40.54 1.89
1607 1941 0.586319 ACGTGCAAATGGAAGTGTCG 59.414 50.000 0.00 0.00 0.00 4.35
1698 2036 9.396022 CCACAGAATTTATGTCACCTTATTACT 57.604 33.333 0.00 0.00 0.00 2.24
1719 2058 3.485463 TGAAGTACTTTGACCCCACAG 57.515 47.619 10.02 0.00 0.00 3.66
1764 2103 6.457663 CGTCAAACACCTAAACACATGAAAGA 60.458 38.462 0.00 0.00 0.00 2.52
1773 2112 3.537580 AGCTTCGTCAAACACCTAAACA 58.462 40.909 0.00 0.00 0.00 2.83
1934 2297 0.172578 TGTGATCCCGTCATCGTCAC 59.827 55.000 0.00 0.00 39.48 3.67
2035 2398 5.808042 ACATCATTAACTGTGTCTGATGC 57.192 39.130 18.74 0.00 44.40 3.91
2072 2439 4.166011 GCAGTTCGGCATGGTCGC 62.166 66.667 0.00 0.00 0.00 5.19
2151 2520 6.811170 AGTTTTTGAAGAAAACATTTGCTCGA 59.189 30.769 14.53 0.00 41.29 4.04
2223 2592 8.680903 AGTCTTTTCAAGGCAATATTGATGTAG 58.319 33.333 19.73 11.99 36.60 2.74
2420 2792 4.398673 TGCTATCAATAAAGCACATGCACA 59.601 37.500 6.64 0.00 43.56 4.57
2504 2880 6.017440 CGTTTCTCCCAAGAAGTAAAATCACA 60.017 38.462 0.00 0.00 42.36 3.58
2512 2888 2.631062 TGCTCGTTTCTCCCAAGAAGTA 59.369 45.455 0.00 0.00 42.36 2.24
2521 2897 7.823149 TTAAAATACTACTGCTCGTTTCTCC 57.177 36.000 0.00 0.00 0.00 3.71
2560 3043 4.550831 CGTCTGCCAATTTATAGCTGAACG 60.551 45.833 0.00 0.00 36.43 3.95
2578 3061 5.356882 TCTTTTGTTAGATTTGGCGTCTG 57.643 39.130 0.00 0.00 0.00 3.51
2660 3230 4.997395 TGCTTCAGATAGTTCCTCAACAAC 59.003 41.667 0.00 0.00 34.60 3.32
2798 3368 8.201554 TGCTGAAATGCTTAATTACACTCTAG 57.798 34.615 0.00 0.00 0.00 2.43
2844 3418 3.740832 TGTGCGAGCGAAATAAGGATATG 59.259 43.478 0.00 0.00 0.00 1.78
2904 3478 8.807118 TGTTTGGGCATTTTATACTTCAATACA 58.193 29.630 0.00 0.00 0.00 2.29
2925 3499 5.051508 GCAGTACATTGCAAGAAACTGTTTG 60.052 40.000 25.95 17.57 43.53 2.93
3017 3593 4.010667 ACAGTGCATCAATGGCAAAATT 57.989 36.364 0.00 0.00 43.91 1.82
3042 3618 5.984695 TCGGGATAGATTATTCACTCTGG 57.015 43.478 0.00 0.00 0.00 3.86
3126 3707 3.245122 TGTTAACCTAGCCCCAAAGAAGG 60.245 47.826 2.48 0.00 0.00 3.46
3280 3862 4.020307 TGGAGTGCAATGACTTCTACATCA 60.020 41.667 0.00 0.00 0.00 3.07
3309 3891 1.398692 GCTCTCCAGGAGTTCGAGAT 58.601 55.000 16.65 0.00 43.62 2.75
3362 3944 7.037730 AGGAGATAGCACCTATCAAATTAGCAT 60.038 37.037 13.09 0.00 43.62 3.79
3400 3982 0.400213 AAACGAGTTGCATCCCTGGA 59.600 50.000 0.00 0.00 0.00 3.86
3480 4062 7.177392 ACACTGAAAGCAAAATAAAGCTAGGAT 59.823 33.333 0.00 0.00 40.90 3.24
3615 4197 4.841443 AAAAGTACCCGTGGAAATGTTC 57.159 40.909 0.00 0.00 0.00 3.18
3662 4244 8.129211 ACAAAGACAGGTAATCTTTCGAAAAAG 58.871 33.333 12.41 0.89 43.06 2.27
3663 4245 7.992008 ACAAAGACAGGTAATCTTTCGAAAAA 58.008 30.769 12.41 0.00 43.06 1.94
3664 4246 7.562454 ACAAAGACAGGTAATCTTTCGAAAA 57.438 32.000 12.41 3.81 43.06 2.29
3665 4247 7.562454 AACAAAGACAGGTAATCTTTCGAAA 57.438 32.000 10.71 10.71 43.06 3.46
3666 4248 7.562454 AAACAAAGACAGGTAATCTTTCGAA 57.438 32.000 0.00 0.00 43.06 3.71
3667 4249 8.717821 CATAAACAAAGACAGGTAATCTTTCGA 58.282 33.333 0.00 0.00 43.06 3.71
3668 4250 7.481798 GCATAAACAAAGACAGGTAATCTTTCG 59.518 37.037 0.00 0.00 43.06 3.46
3669 4251 8.515414 AGCATAAACAAAGACAGGTAATCTTTC 58.485 33.333 0.00 0.00 43.06 2.62
3670 4252 8.409358 AGCATAAACAAAGACAGGTAATCTTT 57.591 30.769 0.00 0.00 45.24 2.52
3671 4253 8.409358 AAGCATAAACAAAGACAGGTAATCTT 57.591 30.769 0.00 0.00 38.05 2.40
3672 4254 7.148407 CGAAGCATAAACAAAGACAGGTAATCT 60.148 37.037 0.00 0.00 0.00 2.40
3673 4255 6.961554 CGAAGCATAAACAAAGACAGGTAATC 59.038 38.462 0.00 0.00 0.00 1.75
3674 4256 6.128007 CCGAAGCATAAACAAAGACAGGTAAT 60.128 38.462 0.00 0.00 0.00 1.89
3675 4257 5.180492 CCGAAGCATAAACAAAGACAGGTAA 59.820 40.000 0.00 0.00 0.00 2.85
3676 4258 4.693566 CCGAAGCATAAACAAAGACAGGTA 59.306 41.667 0.00 0.00 0.00 3.08
3677 4259 3.502211 CCGAAGCATAAACAAAGACAGGT 59.498 43.478 0.00 0.00 0.00 4.00
3678 4260 3.751175 TCCGAAGCATAAACAAAGACAGG 59.249 43.478 0.00 0.00 0.00 4.00
3679 4261 5.551760 ATCCGAAGCATAAACAAAGACAG 57.448 39.130 0.00 0.00 0.00 3.51
3680 4262 5.957842 AATCCGAAGCATAAACAAAGACA 57.042 34.783 0.00 0.00 0.00 3.41
3681 4263 7.303634 TCTAATCCGAAGCATAAACAAAGAC 57.696 36.000 0.00 0.00 0.00 3.01
3682 4264 6.037172 GCTCTAATCCGAAGCATAAACAAAGA 59.963 38.462 0.00 0.00 0.00 2.52
3683 4265 6.183360 TGCTCTAATCCGAAGCATAAACAAAG 60.183 38.462 0.00 0.00 0.00 2.77
3684 4266 5.645929 TGCTCTAATCCGAAGCATAAACAAA 59.354 36.000 0.00 0.00 0.00 2.83
3685 4267 5.182487 TGCTCTAATCCGAAGCATAAACAA 58.818 37.500 0.00 0.00 0.00 2.83
3686 4268 4.765273 TGCTCTAATCCGAAGCATAAACA 58.235 39.130 0.00 0.00 0.00 2.83
3687 4269 5.734855 TTGCTCTAATCCGAAGCATAAAC 57.265 39.130 0.00 0.00 35.33 2.01
3688 4270 6.542005 TCATTTGCTCTAATCCGAAGCATAAA 59.458 34.615 0.00 0.00 35.33 1.40
3689 4271 6.017934 GTCATTTGCTCTAATCCGAAGCATAA 60.018 38.462 0.00 0.00 35.33 1.90
3690 4272 5.466728 GTCATTTGCTCTAATCCGAAGCATA 59.533 40.000 0.00 0.00 35.33 3.14
3691 4273 4.274459 GTCATTTGCTCTAATCCGAAGCAT 59.726 41.667 0.00 0.00 35.33 3.79
3692 4274 3.623060 GTCATTTGCTCTAATCCGAAGCA 59.377 43.478 0.00 0.00 0.00 3.91
3693 4275 3.873952 AGTCATTTGCTCTAATCCGAAGC 59.126 43.478 0.00 0.00 0.00 3.86
3694 4276 7.721286 ATTAGTCATTTGCTCTAATCCGAAG 57.279 36.000 0.00 0.00 31.40 3.79
3695 4277 7.042725 CGAATTAGTCATTTGCTCTAATCCGAA 60.043 37.037 0.00 0.00 35.19 4.30
3696 4278 6.420903 CGAATTAGTCATTTGCTCTAATCCGA 59.579 38.462 0.00 0.00 35.19 4.55
3697 4279 6.201044 ACGAATTAGTCATTTGCTCTAATCCG 59.799 38.462 0.00 10.00 37.70 4.18
3698 4280 7.307455 GGACGAATTAGTCATTTGCTCTAATCC 60.307 40.741 18.70 0.00 42.62 3.01
3699 4281 7.224753 TGGACGAATTAGTCATTTGCTCTAATC 59.775 37.037 18.70 0.00 42.62 1.75
3700 4282 7.011482 GTGGACGAATTAGTCATTTGCTCTAAT 59.989 37.037 18.70 0.00 42.62 1.73
3701 4283 6.312918 GTGGACGAATTAGTCATTTGCTCTAA 59.687 38.462 18.70 0.00 42.62 2.10
3702 4284 5.810587 GTGGACGAATTAGTCATTTGCTCTA 59.189 40.000 18.70 0.00 42.62 2.43
3703 4285 4.631813 GTGGACGAATTAGTCATTTGCTCT 59.368 41.667 18.70 0.00 42.62 4.09
3704 4286 4.492570 CGTGGACGAATTAGTCATTTGCTC 60.493 45.833 18.70 2.29 42.62 4.26
3705 4287 3.370978 CGTGGACGAATTAGTCATTTGCT 59.629 43.478 18.70 0.00 42.62 3.91
3706 4288 3.670203 CGTGGACGAATTAGTCATTTGC 58.330 45.455 18.70 3.56 42.62 3.68
3707 4289 3.485216 GGCGTGGACGAATTAGTCATTTG 60.485 47.826 18.70 7.75 42.62 2.32
3708 4290 2.676342 GGCGTGGACGAATTAGTCATTT 59.324 45.455 18.70 0.00 42.62 2.32
3709 4291 2.093658 AGGCGTGGACGAATTAGTCATT 60.094 45.455 18.70 0.00 42.62 2.57
3710 4292 1.480954 AGGCGTGGACGAATTAGTCAT 59.519 47.619 18.70 0.00 42.62 3.06
3711 4293 0.892755 AGGCGTGGACGAATTAGTCA 59.107 50.000 18.70 4.34 42.62 3.41
3712 4294 2.457970 GTAGGCGTGGACGAATTAGTC 58.542 52.381 9.98 9.98 43.02 2.59
3713 4295 1.202222 CGTAGGCGTGGACGAATTAGT 60.202 52.381 2.73 0.00 41.60 2.24
3714 4296 1.064505 TCGTAGGCGTGGACGAATTAG 59.935 52.381 2.73 0.00 44.56 1.73
3715 4297 1.093972 TCGTAGGCGTGGACGAATTA 58.906 50.000 2.73 0.00 44.56 1.40
3716 4298 1.885157 TCGTAGGCGTGGACGAATT 59.115 52.632 2.73 0.00 44.56 2.17
3717 4299 3.594568 TCGTAGGCGTGGACGAAT 58.405 55.556 2.73 0.00 44.56 3.34
3719 4301 2.562912 GTTCGTAGGCGTGGACGA 59.437 61.111 2.73 0.53 45.76 4.20
3720 4302 2.505557 GGTTCGTAGGCGTGGACG 60.506 66.667 0.00 0.00 43.27 4.79
3721 4303 1.445582 CTGGTTCGTAGGCGTGGAC 60.446 63.158 0.00 0.00 39.49 4.02
3722 4304 1.870055 GACTGGTTCGTAGGCGTGGA 61.870 60.000 0.00 0.00 39.49 4.02
3723 4305 1.445582 GACTGGTTCGTAGGCGTGG 60.446 63.158 0.00 0.00 39.49 4.94
3724 4306 1.800315 CGACTGGTTCGTAGGCGTG 60.800 63.158 0.00 0.00 41.64 5.34
3725 4307 2.564975 CGACTGGTTCGTAGGCGT 59.435 61.111 0.00 0.00 41.64 5.68
3731 4313 9.060336 ATTTGTACAAAATGTCGACTGGTTCGT 62.060 37.037 23.97 9.36 40.16 3.85
3732 4314 6.782978 ATTTGTACAAAATGTCGACTGGTTCG 60.783 38.462 23.97 3.66 40.40 3.95
3733 4315 5.412526 TTGTACAAAATGTCGACTGGTTC 57.587 39.130 17.92 6.28 0.00 3.62
3734 4316 5.821516 TTTGTACAAAATGTCGACTGGTT 57.178 34.783 18.54 6.36 0.00 3.67
3735 4317 6.385649 AATTTGTACAAAATGTCGACTGGT 57.614 33.333 23.97 9.77 33.56 4.00
3736 4318 7.692908 AAAATTTGTACAAAATGTCGACTGG 57.307 32.000 23.97 4.20 33.56 4.00
3741 4323 9.706996 CGTTCATAAAATTTGTACAAAATGTCG 57.293 29.630 23.97 21.95 33.56 4.35
3743 4325 9.751542 TCCGTTCATAAAATTTGTACAAAATGT 57.248 25.926 23.97 14.09 33.56 2.71
3746 4328 8.756864 GCTTCCGTTCATAAAATTTGTACAAAA 58.243 29.630 23.97 8.90 33.56 2.44
3747 4329 8.138712 AGCTTCCGTTCATAAAATTTGTACAAA 58.861 29.630 22.58 22.58 34.46 2.83
3748 4330 7.653647 AGCTTCCGTTCATAAAATTTGTACAA 58.346 30.769 3.59 3.59 0.00 2.41
3749 4331 7.174253 AGAGCTTCCGTTCATAAAATTTGTACA 59.826 33.333 0.00 0.00 0.00 2.90
3750 4332 7.527457 AGAGCTTCCGTTCATAAAATTTGTAC 58.473 34.615 0.00 0.00 0.00 2.90
3751 4333 7.681939 AGAGCTTCCGTTCATAAAATTTGTA 57.318 32.000 0.00 0.00 0.00 2.41
3752 4334 6.575162 AGAGCTTCCGTTCATAAAATTTGT 57.425 33.333 0.00 0.00 0.00 2.83
3753 4335 9.573133 AATAAGAGCTTCCGTTCATAAAATTTG 57.427 29.630 0.00 0.00 0.00 2.32
3756 4338 9.788960 GAAAATAAGAGCTTCCGTTCATAAAAT 57.211 29.630 0.00 0.00 0.00 1.82
3757 4339 8.788806 TGAAAATAAGAGCTTCCGTTCATAAAA 58.211 29.630 0.00 0.00 0.00 1.52
3758 4340 8.330466 TGAAAATAAGAGCTTCCGTTCATAAA 57.670 30.769 0.00 0.00 0.00 1.40
3759 4341 7.915293 TGAAAATAAGAGCTTCCGTTCATAA 57.085 32.000 0.00 0.00 0.00 1.90
3760 4342 9.778741 ATATGAAAATAAGAGCTTCCGTTCATA 57.221 29.630 16.35 16.35 39.63 2.15
3761 4343 8.682936 ATATGAAAATAAGAGCTTCCGTTCAT 57.317 30.769 14.32 14.32 37.94 2.57
3762 4344 8.506168 AATATGAAAATAAGAGCTTCCGTTCA 57.494 30.769 0.00 0.00 0.00 3.18
3763 4345 9.439537 GAAATATGAAAATAAGAGCTTCCGTTC 57.560 33.333 0.00 0.00 0.00 3.95
3764 4346 8.406297 GGAAATATGAAAATAAGAGCTTCCGTT 58.594 33.333 0.00 0.00 0.00 4.44
3765 4347 7.254795 CGGAAATATGAAAATAAGAGCTTCCGT 60.255 37.037 0.00 0.00 43.97 4.69
3766 4348 7.072030 CGGAAATATGAAAATAAGAGCTTCCG 58.928 38.462 0.00 0.00 43.67 4.30
3767 4349 7.931275 ACGGAAATATGAAAATAAGAGCTTCC 58.069 34.615 0.00 0.00 0.00 3.46
3770 4352 9.220767 GGATACGGAAATATGAAAATAAGAGCT 57.779 33.333 0.00 0.00 0.00 4.09
3771 4353 9.220767 AGGATACGGAAATATGAAAATAAGAGC 57.779 33.333 0.00 0.00 46.39 4.09


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

AutoCloner maintained by Alex Coulton.