Multiple sequence alignment - TraesCS6B01G017800

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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 TraesCS6B01G017800 chr6B 100.000 2675 0 0 1 2675 11300302 11297628 0.000000e+00 4940.0
1 TraesCS6B01G017800 chr6B 96.629 89 3 0 1 89 9192191 9192279 5.970000e-32 148.0
2 TraesCS6B01G017800 chr6A 88.659 2081 145 48 258 2313 5327799 5325785 0.000000e+00 2451.0
3 TraesCS6B01G017800 chr6A 77.848 474 55 25 1803 2260 5323624 5323185 5.720000e-62 248.0
4 TraesCS6B01G017800 chr6A 89.385 179 17 2 87 265 5328019 5327843 9.640000e-55 224.0
5 TraesCS6B01G017800 chr6D 91.457 1791 90 26 277 2042 5988606 5986854 0.000000e+00 2401.0
6 TraesCS6B01G017800 chr6D 86.572 849 71 23 1578 2421 5984016 5983206 0.000000e+00 896.0
7 TraesCS6B01G017800 chr6D 89.062 256 28 0 1066 1321 5981428 5981173 4.300000e-83 318.0
8 TraesCS6B01G017800 chr6D 77.057 632 80 39 1653 2265 5981162 5980577 1.200000e-78 303.0
9 TraesCS6B01G017800 chr6D 91.620 179 12 1 87 265 5988840 5988665 7.400000e-61 244.0
10 TraesCS6B01G017800 chr7A 84.483 290 42 2 993 1282 7920619 7920905 1.570000e-72 283.0
11 TraesCS6B01G017800 chr7D 83.103 290 46 2 993 1282 7078649 7078935 7.350000e-66 261.0
12 TraesCS6B01G017800 chrUn 82.007 289 49 1 993 1281 51199641 51199356 2.660000e-60 243.0
13 TraesCS6B01G017800 chr2A 96.703 91 3 0 1 91 364235234 364235324 4.610000e-33 152.0
14 TraesCS6B01G017800 chr4A 97.701 87 2 0 2 88 613249309 613249395 1.660000e-32 150.0
15 TraesCS6B01G017800 chr1A 96.703 91 2 1 1 91 257769283 257769194 1.660000e-32 150.0
16 TraesCS6B01G017800 chr7B 96.629 89 3 0 1 89 539652504 539652416 5.970000e-32 148.0
17 TraesCS6B01G017800 chr2D 96.591 88 3 0 1 88 583899096 583899183 2.150000e-31 147.0
18 TraesCS6B01G017800 chr1B 96.591 88 3 0 1 88 555003298 555003385 2.150000e-31 147.0
19 TraesCS6B01G017800 chr1B 96.591 88 3 0 1 88 555055640 555055727 2.150000e-31 147.0
20 TraesCS6B01G017800 chr3A 91.346 104 7 2 1 104 535225654 535225755 9.980000e-30 141.0
21 TraesCS6B01G017800 chr4D 96.970 33 0 1 2564 2595 373639811 373639779 1.000000e-03 54.7


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 TraesCS6B01G017800 chr6B 11297628 11300302 2674 True 4940.000000 4940 100.000000 1 2675 1 chr6B.!!$R1 2674
1 TraesCS6B01G017800 chr6A 5323185 5328019 4834 True 974.333333 2451 85.297333 87 2313 3 chr6A.!!$R1 2226
2 TraesCS6B01G017800 chr6D 5980577 5988840 8263 True 832.400000 2401 87.153600 87 2421 5 chr6D.!!$R1 2334

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
814 889 0.247736 GACCTGAGTGGGTGTAGCAG 59.752 60.0 0.0 0.0 40.06 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1813 0.537188 ATAGTCAGCACACCTTCGGG 59.463 55.0 0.0 0.0 41.87 5.14 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
51 52 8.329203 AGTTCTTCAAATCAATGACCTAGAAC 57.671 34.615 13.10 13.10 41.08 3.01
52 53 8.160106 AGTTCTTCAAATCAATGACCTAGAACT 58.840 33.333 15.76 15.76 43.47 3.01
53 54 9.436957 GTTCTTCAAATCAATGACCTAGAACTA 57.563 33.333 13.44 0.00 39.42 2.24
54 55 9.436957 TTCTTCAAATCAATGACCTAGAACTAC 57.563 33.333 0.00 0.00 0.00 2.73
55 56 7.759886 TCTTCAAATCAATGACCTAGAACTACG 59.240 37.037 0.00 0.00 0.00 3.51
56 57 5.810587 TCAAATCAATGACCTAGAACTACGC 59.189 40.000 0.00 0.00 0.00 4.42
57 58 3.416119 TCAATGACCTAGAACTACGCG 57.584 47.619 3.53 3.53 0.00 6.01
58 59 3.011818 TCAATGACCTAGAACTACGCGA 58.988 45.455 15.93 0.00 0.00 5.87
59 60 3.441222 TCAATGACCTAGAACTACGCGAA 59.559 43.478 15.93 0.00 0.00 4.70
60 61 4.097437 TCAATGACCTAGAACTACGCGAAT 59.903 41.667 15.93 0.00 0.00 3.34
61 62 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
62 63 3.011818 TGACCTAGAACTACGCGAATGA 58.988 45.455 15.93 0.00 0.00 2.57
63 64 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
64 65 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
65 66 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
66 67 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
67 68 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
68 69 6.183360 ACCTAGAACTACGCGAATGACTTATT 60.183 38.462 15.93 0.00 0.00 1.40
69 70 6.360148 CCTAGAACTACGCGAATGACTTATTC 59.640 42.308 15.93 3.24 41.46 1.75
70 71 5.647589 AGAACTACGCGAATGACTTATTCA 58.352 37.500 15.93 0.00 44.42 2.57
71 72 5.515626 AGAACTACGCGAATGACTTATTCAC 59.484 40.000 15.93 0.00 44.42 3.18
72 73 4.110482 ACTACGCGAATGACTTATTCACC 58.890 43.478 15.93 0.00 44.42 4.02
73 74 3.247006 ACGCGAATGACTTATTCACCT 57.753 42.857 15.93 0.00 44.42 4.00
74 75 4.380841 ACGCGAATGACTTATTCACCTA 57.619 40.909 15.93 0.00 44.42 3.08
75 76 4.360563 ACGCGAATGACTTATTCACCTAG 58.639 43.478 15.93 0.00 44.42 3.02
76 77 4.097437 ACGCGAATGACTTATTCACCTAGA 59.903 41.667 15.93 0.00 44.42 2.43
77 78 4.441415 CGCGAATGACTTATTCACCTAGAC 59.559 45.833 0.00 0.00 44.42 2.59
78 79 4.441415 GCGAATGACTTATTCACCTAGACG 59.559 45.833 0.00 0.00 44.42 4.18
79 80 4.976731 CGAATGACTTATTCACCTAGACGG 59.023 45.833 0.00 0.00 44.42 4.79
80 81 5.220989 CGAATGACTTATTCACCTAGACGGA 60.221 44.000 0.00 0.00 44.42 4.69
81 82 5.776173 ATGACTTATTCACCTAGACGGAG 57.224 43.478 0.00 0.00 36.92 4.63
82 83 3.952323 TGACTTATTCACCTAGACGGAGG 59.048 47.826 0.00 0.00 42.89 4.30
106 107 2.685850 ACTGCCGTTTAGATACACCC 57.314 50.000 0.00 0.00 0.00 4.61
112 113 3.001939 GCCGTTTAGATACACCCGAATTG 59.998 47.826 0.00 0.00 0.00 2.32
137 138 3.066760 GGCAAGTTGAGTTAAACTGTGCT 59.933 43.478 7.16 0.00 40.28 4.40
218 219 6.091441 CGGACCATTTCTCTTCTTCTACAAAG 59.909 42.308 0.00 0.00 0.00 2.77
238 239 1.005450 GAGAAACCAAGGCCCATACCA 59.995 52.381 0.00 0.00 0.00 3.25
252 253 2.238646 CCATACCAACACTCCAAGCCTA 59.761 50.000 0.00 0.00 0.00 3.93
256 257 2.108250 ACCAACACTCCAAGCCTATGTT 59.892 45.455 0.00 0.00 33.86 2.71
268 321 5.641209 CCAAGCCTATGTTATCTGTATCTGC 59.359 44.000 0.00 0.00 0.00 4.26
271 324 4.223923 GCCTATGTTATCTGTATCTGCCCT 59.776 45.833 0.00 0.00 0.00 5.19
291 344 3.659334 TGCTTTTGGAGAGCAGCG 58.341 55.556 0.00 0.00 44.63 5.18
324 377 6.405842 GCGAATTCAAATCCTTAGAATTGGGT 60.406 38.462 6.22 0.00 40.83 4.51
385 457 0.524862 CTTGCTCACTGGTTGCCATC 59.475 55.000 0.00 0.00 30.82 3.51
388 460 0.454600 GCTCACTGGTTGCCATCATG 59.545 55.000 0.00 0.00 30.82 3.07
395 467 2.289820 CTGGTTGCCATCATGATTCGAG 59.710 50.000 5.16 0.00 30.82 4.04
411 483 5.800438 TGATTCGAGTACTGAAAATCTGTCG 59.200 40.000 0.00 0.00 31.00 4.35
431 503 4.026804 GTCGCGAGATCATTTTTCGTACAT 60.027 41.667 10.24 0.00 45.19 2.29
441 513 9.767684 GATCATTTTTCGTACATGATGTGTTAA 57.232 29.630 8.61 0.00 42.29 2.01
443 515 9.952188 TCATTTTTCGTACATGATGTGTTAAAA 57.048 25.926 8.61 8.63 42.29 1.52
491 563 9.480053 GTAACATTATTATTGCATTGCCTGAAT 57.520 29.630 6.12 5.37 0.00 2.57
492 564 8.597662 AACATTATTATTGCATTGCCTGAATC 57.402 30.769 6.12 0.00 0.00 2.52
497 569 2.502142 TGCATTGCCTGAATCTCACT 57.498 45.000 6.12 0.00 0.00 3.41
510 582 7.202011 GCCTGAATCTCACTAAAGGGTCTATTA 60.202 40.741 0.00 0.00 0.00 0.98
526 598 7.570607 AGGGTCTATTATTCTTCTTCACCATCT 59.429 37.037 0.00 0.00 0.00 2.90
557 629 9.573133 CTGTTCATTTTTCAAAAGTTGACTAGT 57.427 29.630 0.00 0.00 39.87 2.57
730 805 0.736053 CGAGCGCCTTCTACTTCTCT 59.264 55.000 2.29 0.00 0.00 3.10
756 831 1.650528 CTCTCCCCTGTTGTCTCCTT 58.349 55.000 0.00 0.00 0.00 3.36
799 874 6.041523 GCAAGATAAGATACTCCTTCAGACCT 59.958 42.308 0.00 0.00 0.00 3.85
814 889 0.247736 GACCTGAGTGGGTGTAGCAG 59.752 60.000 0.00 0.00 40.06 4.24
815 890 1.078848 CCTGAGTGGGTGTAGCAGC 60.079 63.158 0.00 0.00 0.00 5.25
816 891 1.673477 CTGAGTGGGTGTAGCAGCA 59.327 57.895 0.00 0.00 33.07 4.41
817 892 0.251354 CTGAGTGGGTGTAGCAGCAT 59.749 55.000 0.00 0.00 33.07 3.79
818 893 0.692476 TGAGTGGGTGTAGCAGCATT 59.308 50.000 0.00 0.00 33.07 3.56
860 935 0.819582 GTCGGTCCGGGAGTAAATCA 59.180 55.000 12.29 0.00 0.00 2.57
928 1003 6.849588 ATGAACTTTGCAGATTTTGGTTTC 57.150 33.333 0.00 0.00 0.00 2.78
964 1039 4.274147 TGGTAGAGGAGTTTAGCTGAGAG 58.726 47.826 0.00 0.00 0.00 3.20
965 1040 4.018324 TGGTAGAGGAGTTTAGCTGAGAGA 60.018 45.833 0.00 0.00 0.00 3.10
986 1062 9.496873 GAGAGATAGTAGTAGTCAATAGCAAGA 57.503 37.037 0.00 0.00 0.00 3.02
1110 1186 1.813337 GGCTGAGAAGAAGAGGCGC 60.813 63.158 0.00 0.00 0.00 6.53
1152 1228 0.104487 ACTCTGCTGCCATCATCTCG 59.896 55.000 0.00 0.00 0.00 4.04
1174 1250 1.085893 GCTGGAGAAGAAGAAGCAGC 58.914 55.000 0.00 0.00 34.01 5.25
1188 1264 2.766345 AGCAGCAGAAGAAAGAGGAG 57.234 50.000 0.00 0.00 0.00 3.69
1206 1282 1.302511 GCAGGAAAGGCTGGACGAA 60.303 57.895 0.00 0.00 0.00 3.85
1245 1321 3.389206 GCGGTCGCTCTTCATGTC 58.611 61.111 8.20 0.00 38.26 3.06
1339 1415 2.890474 CGGCCGGTCTGGATTTCG 60.890 66.667 20.10 0.00 42.00 3.46
1377 1453 1.187087 CAGCCGATATCTACTCCCCC 58.813 60.000 0.34 0.00 0.00 5.40
1420 1496 3.102090 GCTTATGCTTCCAGGGGTC 57.898 57.895 0.00 0.00 36.03 4.46
1421 1497 0.255890 GCTTATGCTTCCAGGGGTCA 59.744 55.000 0.00 0.00 36.03 4.02
1422 1498 1.133668 GCTTATGCTTCCAGGGGTCAT 60.134 52.381 0.00 0.00 36.03 3.06
1423 1499 2.856222 CTTATGCTTCCAGGGGTCATC 58.144 52.381 0.00 0.00 0.00 2.92
1440 1516 4.530857 CGGTGGATCGACTGGGGC 62.531 72.222 8.73 0.00 0.00 5.80
1444 1520 2.220586 TGGATCGACTGGGGCAACA 61.221 57.895 0.00 0.00 39.74 3.33
1445 1521 1.224592 GGATCGACTGGGGCAACAT 59.775 57.895 0.00 0.00 39.74 2.71
1495 1571 0.108281 GGACCTGAAAGCGTCCTACC 60.108 60.000 0.00 0.00 45.29 3.18
1518 1594 3.946907 GGAACGTTCCACCAGTCG 58.053 61.111 36.67 0.00 46.76 4.18
1593 1669 1.011333 GAGAAGACTCGTCCTCTCCG 58.989 60.000 12.55 0.00 39.89 4.63
1671 1747 3.274288 GCTCAACCTTTACAGGGAGATG 58.726 50.000 0.00 0.00 46.01 2.90
1689 1765 8.953665 AGGGAGATGTGAAAAAGGAAGATATAT 58.046 33.333 0.00 0.00 0.00 0.86
1720 1796 0.809385 ACCTCGTCGTCATAGTGGTG 59.191 55.000 0.00 0.00 31.48 4.17
1737 1813 9.031360 CATAGTGGTGTTGTACATAATAGTCAC 57.969 37.037 0.00 0.24 0.00 3.67
1770 1846 0.804989 GACTATTTTGCCTGCGTGCT 59.195 50.000 0.00 0.00 0.00 4.40
1771 1847 0.523072 ACTATTTTGCCTGCGTGCTG 59.477 50.000 0.00 0.00 0.00 4.41
1772 1848 0.179156 CTATTTTGCCTGCGTGCTGG 60.179 55.000 12.87 12.87 37.98 4.85
1773 1849 0.607762 TATTTTGCCTGCGTGCTGGA 60.608 50.000 20.34 4.27 37.23 3.86
1792 1868 1.841302 AAGCTGTTCCGGCCATCAGA 61.841 55.000 2.24 0.00 36.20 3.27
1793 1869 1.153086 GCTGTTCCGGCCATCAGAT 60.153 57.895 2.24 0.00 0.00 2.90
1794 1870 0.749454 GCTGTTCCGGCCATCAGATT 60.749 55.000 2.24 0.00 0.00 2.40
1846 1922 1.146957 TGTTTTCGTCGGTCGGTGTG 61.147 55.000 0.00 0.00 40.32 3.82
1856 1932 2.817844 TCGGTCGGTGTGATAGGATATG 59.182 50.000 0.00 0.00 0.00 1.78
1859 1935 4.500887 CGGTCGGTGTGATAGGATATGTTT 60.501 45.833 0.00 0.00 0.00 2.83
1860 1936 5.365619 GGTCGGTGTGATAGGATATGTTTT 58.634 41.667 0.00 0.00 0.00 2.43
1862 1938 4.814234 TCGGTGTGATAGGATATGTTTTGC 59.186 41.667 0.00 0.00 0.00 3.68
1863 1939 4.318760 CGGTGTGATAGGATATGTTTTGCG 60.319 45.833 0.00 0.00 0.00 4.85
1864 1940 4.574828 GGTGTGATAGGATATGTTTTGCGT 59.425 41.667 0.00 0.00 0.00 5.24
1865 1941 5.277345 GGTGTGATAGGATATGTTTTGCGTC 60.277 44.000 0.00 0.00 0.00 5.19
1866 1942 5.523916 GTGTGATAGGATATGTTTTGCGTCT 59.476 40.000 0.00 0.00 0.00 4.18
1867 1943 5.523552 TGTGATAGGATATGTTTTGCGTCTG 59.476 40.000 0.00 0.00 0.00 3.51
1868 1944 5.523916 GTGATAGGATATGTTTTGCGTCTGT 59.476 40.000 0.00 0.00 0.00 3.41
1920 1999 8.792538 CAAATATGATTTTCGTTTCTCTTGCTC 58.207 33.333 0.00 0.00 0.00 4.26
1938 2017 2.026729 GCTCCTAGCTGGGTTTTCTCTT 60.027 50.000 16.69 0.00 38.45 2.85
1976 5338 8.873215 ATATAGTTCTTATTTGTGTGTCCTCG 57.127 34.615 0.00 0.00 0.00 4.63
1993 5355 3.438781 TCCTCGCGAAATAAAAATGTGCT 59.561 39.130 11.33 0.00 0.00 4.40
2004 5366 3.405823 AAAATGTGCTTGTGGAATGGG 57.594 42.857 0.00 0.00 0.00 4.00
2027 5391 5.411361 GGAACTTTTTGTGTTTTTGCCTTCT 59.589 36.000 0.00 0.00 0.00 2.85
2059 5423 6.223120 GTGCATTGTTCCCAAGAGTATTTTT 58.777 36.000 0.00 0.00 33.17 1.94
2060 5424 6.146021 GTGCATTGTTCCCAAGAGTATTTTTG 59.854 38.462 0.00 0.00 33.17 2.44
2062 5426 6.705825 GCATTGTTCCCAAGAGTATTTTTGTT 59.294 34.615 0.00 0.00 33.17 2.83
2063 5427 7.307337 GCATTGTTCCCAAGAGTATTTTTGTTG 60.307 37.037 0.00 0.00 33.17 3.33
2064 5428 6.783708 TGTTCCCAAGAGTATTTTTGTTGT 57.216 33.333 0.00 0.00 0.00 3.32
2065 5429 6.568869 TGTTCCCAAGAGTATTTTTGTTGTG 58.431 36.000 0.00 0.00 0.00 3.33
2067 5431 4.038642 TCCCAAGAGTATTTTTGTTGTGCC 59.961 41.667 0.00 0.00 0.00 5.01
2119 5483 3.588210 TGATCATTGCACTGGATGGAT 57.412 42.857 4.01 0.00 0.00 3.41
2120 5484 3.905968 TGATCATTGCACTGGATGGATT 58.094 40.909 4.01 0.00 0.00 3.01
2121 5485 4.283337 TGATCATTGCACTGGATGGATTT 58.717 39.130 4.01 0.00 0.00 2.17
2122 5486 4.098807 TGATCATTGCACTGGATGGATTTG 59.901 41.667 4.01 0.00 0.00 2.32
2123 5487 3.433343 TCATTGCACTGGATGGATTTGT 58.567 40.909 4.01 0.00 0.00 2.83
2124 5488 3.444742 TCATTGCACTGGATGGATTTGTC 59.555 43.478 4.01 0.00 0.00 3.18
2167 5531 8.874744 TGTAGAGTTATGTACAGGTAAGAACT 57.125 34.615 0.33 4.04 30.69 3.01
2171 5535 9.750783 AGAGTTATGTACAGGTAAGAACTAGAA 57.249 33.333 0.33 0.00 0.00 2.10
2172 5536 9.786105 GAGTTATGTACAGGTAAGAACTAGAAC 57.214 37.037 0.33 0.00 0.00 3.01
2173 5537 9.305555 AGTTATGTACAGGTAAGAACTAGAACA 57.694 33.333 0.33 0.00 0.00 3.18
2174 5538 9.570488 GTTATGTACAGGTAAGAACTAGAACAG 57.430 37.037 0.33 0.00 0.00 3.16
2185 5549 6.926630 AGAACTAGAACAGGAACAGATTCT 57.073 37.500 0.00 0.00 34.98 2.40
2191 5555 1.081892 CAGGAACAGATTCTGCCGTG 58.918 55.000 13.64 12.66 34.37 4.94
2203 5567 1.071605 CTGCCGTGCTGAAGACTTAC 58.928 55.000 0.00 0.00 0.00 2.34
2213 5577 4.284490 TGCTGAAGACTTACTGACCAATCT 59.716 41.667 0.00 0.00 0.00 2.40
2231 5595 2.691927 TCTCTGCACAGTACTGCATTG 58.308 47.619 22.90 14.45 46.05 2.82
2261 5626 1.066215 CGATGGTGACCCAACTGATCA 60.066 52.381 0.00 0.00 46.04 2.92
2265 5630 2.976185 TGGTGACCCAACTGATCAGTAA 59.024 45.455 28.10 7.81 41.58 2.24
2266 5631 3.587061 TGGTGACCCAACTGATCAGTAAT 59.413 43.478 28.10 11.56 41.58 1.89
2296 5697 8.825667 TTTGATAAAAGGGTGAACTTTATTGC 57.174 30.769 0.00 0.00 39.63 3.56
2302 5703 5.453567 AGGGTGAACTTTATTGCTTCAAC 57.546 39.130 0.00 0.00 31.85 3.18
2322 5754 8.515695 TTCAACATGAAGCATCAAGAAGATAT 57.484 30.769 0.00 0.00 39.49 1.63
2343 5775 8.314751 AGATATAAACACTATGAGCATACACCC 58.685 37.037 0.00 0.00 0.00 4.61
2344 5776 2.890808 ACACTATGAGCATACACCCG 57.109 50.000 0.00 0.00 0.00 5.28
2362 5794 1.302832 GGGCCTCCGCATTGATAGG 60.303 63.158 0.84 0.00 36.38 2.57
2363 5795 1.754745 GGCCTCCGCATTGATAGGA 59.245 57.895 0.00 1.02 36.38 2.94
2365 5797 1.555075 GGCCTCCGCATTGATAGGATA 59.445 52.381 0.00 0.00 36.38 2.59
2367 5799 3.201290 GCCTCCGCATTGATAGGATATG 58.799 50.000 0.00 0.00 33.04 1.78
2370 5802 3.599343 TCCGCATTGATAGGATATGCAC 58.401 45.455 0.00 0.00 43.66 4.57
2372 5804 3.752747 CCGCATTGATAGGATATGCACAA 59.247 43.478 0.00 0.89 43.66 3.33
2373 5805 4.216042 CCGCATTGATAGGATATGCACAAA 59.784 41.667 0.00 0.00 43.66 2.83
2374 5806 5.278414 CCGCATTGATAGGATATGCACAAAA 60.278 40.000 0.00 0.00 43.66 2.44
2375 5807 6.384224 CGCATTGATAGGATATGCACAAAAT 58.616 36.000 0.00 0.00 43.66 1.82
2376 5808 6.525628 CGCATTGATAGGATATGCACAAAATC 59.474 38.462 0.00 0.00 43.66 2.17
2377 5809 7.574404 CGCATTGATAGGATATGCACAAAATCT 60.574 37.037 0.00 0.00 43.66 2.40
2388 5832 4.930963 TGCACAAAATCTAACACCAACAG 58.069 39.130 0.00 0.00 0.00 3.16
2390 5834 5.215160 GCACAAAATCTAACACCAACAGAG 58.785 41.667 0.00 0.00 0.00 3.35
2397 5843 5.092554 TCTAACACCAACAGAGAAACACA 57.907 39.130 0.00 0.00 0.00 3.72
2398 5844 4.873827 TCTAACACCAACAGAGAAACACAC 59.126 41.667 0.00 0.00 0.00 3.82
2400 5846 2.290641 ACACCAACAGAGAAACACACCA 60.291 45.455 0.00 0.00 0.00 4.17
2401 5847 2.097466 CACCAACAGAGAAACACACCAC 59.903 50.000 0.00 0.00 0.00 4.16
2404 5850 2.038387 ACAGAGAAACACACCACCAC 57.962 50.000 0.00 0.00 0.00 4.16
2405 5851 1.308998 CAGAGAAACACACCACCACC 58.691 55.000 0.00 0.00 0.00 4.61
2406 5852 1.134098 CAGAGAAACACACCACCACCT 60.134 52.381 0.00 0.00 0.00 4.00
2407 5853 2.104111 CAGAGAAACACACCACCACCTA 59.896 50.000 0.00 0.00 0.00 3.08
2408 5854 2.368875 AGAGAAACACACCACCACCTAG 59.631 50.000 0.00 0.00 0.00 3.02
2409 5855 2.104281 GAGAAACACACCACCACCTAGT 59.896 50.000 0.00 0.00 0.00 2.57
2410 5856 3.311091 AGAAACACACCACCACCTAGTA 58.689 45.455 0.00 0.00 0.00 1.82
2411 5857 3.712733 AGAAACACACCACCACCTAGTAA 59.287 43.478 0.00 0.00 0.00 2.24
2412 5858 4.164604 AGAAACACACCACCACCTAGTAAA 59.835 41.667 0.00 0.00 0.00 2.01
2413 5859 3.764237 ACACACCACCACCTAGTAAAG 57.236 47.619 0.00 0.00 0.00 1.85
2414 5860 3.043418 ACACACCACCACCTAGTAAAGT 58.957 45.455 0.00 0.00 0.00 2.66
2415 5861 3.070590 ACACACCACCACCTAGTAAAGTC 59.929 47.826 0.00 0.00 0.00 3.01
2416 5862 3.070446 CACACCACCACCTAGTAAAGTCA 59.930 47.826 0.00 0.00 0.00 3.41
2417 5863 3.908103 ACACCACCACCTAGTAAAGTCAT 59.092 43.478 0.00 0.00 0.00 3.06
2418 5864 5.046878 CACACCACCACCTAGTAAAGTCATA 60.047 44.000 0.00 0.00 0.00 2.15
2419 5865 5.724854 ACACCACCACCTAGTAAAGTCATAT 59.275 40.000 0.00 0.00 0.00 1.78
2420 5866 6.899075 ACACCACCACCTAGTAAAGTCATATA 59.101 38.462 0.00 0.00 0.00 0.86
2421 5867 7.147776 ACACCACCACCTAGTAAAGTCATATAC 60.148 40.741 0.00 0.00 0.00 1.47
2422 5868 6.325804 ACCACCACCTAGTAAAGTCATATACC 59.674 42.308 0.00 0.00 0.00 2.73
2423 5869 6.239515 CCACCACCTAGTAAAGTCATATACCC 60.240 46.154 0.00 0.00 0.00 3.69
2424 5870 5.842874 ACCACCTAGTAAAGTCATATACCCC 59.157 44.000 0.00 0.00 0.00 4.95
2425 5871 6.082707 CCACCTAGTAAAGTCATATACCCCT 58.917 44.000 0.00 0.00 0.00 4.79
2426 5872 7.146888 ACCACCTAGTAAAGTCATATACCCCTA 60.147 40.741 0.00 0.00 0.00 3.53
2427 5873 7.731688 CCACCTAGTAAAGTCATATACCCCTAA 59.268 40.741 0.00 0.00 0.00 2.69
2428 5874 9.151177 CACCTAGTAAAGTCATATACCCCTAAA 57.849 37.037 0.00 0.00 0.00 1.85
2429 5875 9.377238 ACCTAGTAAAGTCATATACCCCTAAAG 57.623 37.037 0.00 0.00 0.00 1.85
2430 5876 8.813951 CCTAGTAAAGTCATATACCCCTAAAGG 58.186 40.741 0.00 0.00 0.00 3.11
2431 5877 9.597681 CTAGTAAAGTCATATACCCCTAAAGGA 57.402 37.037 0.00 0.00 38.24 3.36
2432 5878 8.865244 AGTAAAGTCATATACCCCTAAAGGAA 57.135 34.615 0.00 0.00 38.24 3.36
2433 5879 9.287818 AGTAAAGTCATATACCCCTAAAGGAAA 57.712 33.333 0.00 0.00 38.24 3.13
2434 5880 9.910267 GTAAAGTCATATACCCCTAAAGGAAAA 57.090 33.333 0.00 0.00 38.24 2.29
2435 5881 8.818622 AAAGTCATATACCCCTAAAGGAAAAC 57.181 34.615 0.00 0.00 38.24 2.43
2458 5904 6.821388 ACCTAGCAAAGTCATATAAGACCAG 58.179 40.000 4.52 0.00 39.34 4.00
2466 5912 4.524714 AGTCATATAAGACCAGCGCTATGT 59.475 41.667 10.99 11.11 39.34 2.29
2472 5918 3.264897 CCAGCGCTATGTGTCGGC 61.265 66.667 10.99 0.00 0.00 5.54
2477 5925 2.805546 GCTATGTGTCGGCGAGGA 59.194 61.111 11.20 0.00 0.00 3.71
2478 5926 1.141019 GCTATGTGTCGGCGAGGAA 59.859 57.895 11.20 0.00 0.00 3.36
2479 5927 0.459585 GCTATGTGTCGGCGAGGAAA 60.460 55.000 11.20 0.00 0.00 3.13
2480 5928 2.004583 CTATGTGTCGGCGAGGAAAA 57.995 50.000 11.20 0.00 0.00 2.29
2481 5929 2.343101 CTATGTGTCGGCGAGGAAAAA 58.657 47.619 11.20 0.00 0.00 1.94
2502 5950 7.547285 AAAAAGAAAAAGAAAAACAAAGCGC 57.453 28.000 0.00 0.00 0.00 5.92
2503 5951 4.499174 AGAAAAAGAAAAACAAAGCGCG 57.501 36.364 0.00 0.00 0.00 6.86
2504 5952 4.170256 AGAAAAAGAAAAACAAAGCGCGA 58.830 34.783 12.10 0.00 0.00 5.87
2531 6000 3.618594 CCAACTGATCCGTACATGAACAG 59.381 47.826 14.39 14.39 38.27 3.16
2548 6019 2.062636 ACAGGGTTAGGCCTTCTTTGA 58.937 47.619 12.58 0.00 37.43 2.69
2549 6020 2.649816 ACAGGGTTAGGCCTTCTTTGAT 59.350 45.455 12.58 0.00 37.43 2.57
2550 6021 3.076032 ACAGGGTTAGGCCTTCTTTGATT 59.924 43.478 12.58 0.00 37.43 2.57
2551 6022 3.696548 CAGGGTTAGGCCTTCTTTGATTC 59.303 47.826 12.58 0.00 37.43 2.52
2552 6023 3.333680 AGGGTTAGGCCTTCTTTGATTCA 59.666 43.478 12.58 0.00 37.43 2.57
2553 6024 3.444034 GGGTTAGGCCTTCTTTGATTCAC 59.556 47.826 12.58 0.00 37.43 3.18
2554 6025 4.336280 GGTTAGGCCTTCTTTGATTCACT 58.664 43.478 12.58 0.00 0.00 3.41
2555 6026 4.396478 GGTTAGGCCTTCTTTGATTCACTC 59.604 45.833 12.58 0.00 0.00 3.51
2585 6056 5.067674 CGGGATTCTCAAAATGCAGGAATAA 59.932 40.000 0.00 0.00 0.00 1.40
2621 6093 5.163713 GGAAAATAGTGTCATGTCCTCTTGC 60.164 44.000 0.00 0.00 0.00 4.01
2628 6100 4.806247 GTGTCATGTCCTCTTGCATACTAC 59.194 45.833 0.00 0.00 0.00 2.73
2630 6102 5.129320 TGTCATGTCCTCTTGCATACTACAT 59.871 40.000 0.00 0.00 0.00 2.29
2634 6106 6.239217 TGTCCTCTTGCATACTACATGATT 57.761 37.500 0.00 0.00 0.00 2.57
2635 6107 7.360113 TGTCCTCTTGCATACTACATGATTA 57.640 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.436957 GTTCTAGGTCATTGATTTGAAGAACTA 57.563 33.333 15.55 0.00 37.68 2.24
26 27 8.160106 AGTTCTAGGTCATTGATTTGAAGAACT 58.840 33.333 17.70 17.70 41.75 3.01
27 28 8.329203 AGTTCTAGGTCATTGATTTGAAGAAC 57.671 34.615 15.28 15.28 39.28 3.01
28 29 9.436957 GTAGTTCTAGGTCATTGATTTGAAGAA 57.563 33.333 0.00 0.00 0.00 2.52
29 30 7.759886 CGTAGTTCTAGGTCATTGATTTGAAGA 59.240 37.037 0.00 0.00 0.00 2.87
30 31 7.464710 GCGTAGTTCTAGGTCATTGATTTGAAG 60.465 40.741 0.00 0.00 0.00 3.02
31 32 6.312918 GCGTAGTTCTAGGTCATTGATTTGAA 59.687 38.462 0.00 0.00 0.00 2.69
32 33 5.810587 GCGTAGTTCTAGGTCATTGATTTGA 59.189 40.000 0.00 0.00 0.00 2.69
33 34 5.276395 CGCGTAGTTCTAGGTCATTGATTTG 60.276 44.000 0.00 0.00 0.00 2.32
34 35 4.804139 CGCGTAGTTCTAGGTCATTGATTT 59.196 41.667 0.00 0.00 0.00 2.17
35 36 4.097437 TCGCGTAGTTCTAGGTCATTGATT 59.903 41.667 5.77 0.00 0.00 2.57
36 37 3.630769 TCGCGTAGTTCTAGGTCATTGAT 59.369 43.478 5.77 0.00 0.00 2.57
37 38 3.011818 TCGCGTAGTTCTAGGTCATTGA 58.988 45.455 5.77 0.00 0.00 2.57
38 39 3.416119 TCGCGTAGTTCTAGGTCATTG 57.584 47.619 5.77 0.00 0.00 2.82
39 40 4.097437 TCATTCGCGTAGTTCTAGGTCATT 59.903 41.667 5.77 0.00 0.00 2.57
40 41 3.630769 TCATTCGCGTAGTTCTAGGTCAT 59.369 43.478 5.77 0.00 0.00 3.06
41 42 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
42 43 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
43 44 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
44 45 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
45 46 6.910972 TGAATAAGTCATTCGCGTAGTTCTAG 59.089 38.462 5.77 0.00 45.25 2.43
46 47 6.690098 GTGAATAAGTCATTCGCGTAGTTCTA 59.310 38.462 5.77 0.00 45.25 2.10
47 48 5.515626 GTGAATAAGTCATTCGCGTAGTTCT 59.484 40.000 5.77 0.00 45.25 3.01
48 49 5.715264 GTGAATAAGTCATTCGCGTAGTTC 58.285 41.667 5.77 0.29 45.25 3.01
49 50 5.697848 GTGAATAAGTCATTCGCGTAGTT 57.302 39.130 5.77 2.59 45.25 2.24
56 57 4.976731 CCGTCTAGGTGAATAAGTCATTCG 59.023 45.833 0.00 0.00 45.25 3.34
57 58 6.145338 TCCGTCTAGGTGAATAAGTCATTC 57.855 41.667 0.00 0.00 40.27 2.67
58 59 5.069251 CCTCCGTCTAGGTGAATAAGTCATT 59.931 44.000 0.00 0.00 38.90 2.57
59 60 4.585162 CCTCCGTCTAGGTGAATAAGTCAT 59.415 45.833 0.00 0.00 38.90 3.06
60 61 3.952323 CCTCCGTCTAGGTGAATAAGTCA 59.048 47.826 0.00 0.00 41.99 3.41
61 62 4.571372 CCTCCGTCTAGGTGAATAAGTC 57.429 50.000 0.00 0.00 41.99 3.01
71 72 2.220313 GCAGTACTACCTCCGTCTAGG 58.780 57.143 0.00 0.00 42.82 3.02
72 73 2.220313 GGCAGTACTACCTCCGTCTAG 58.780 57.143 4.74 0.00 0.00 2.43
73 74 1.473965 CGGCAGTACTACCTCCGTCTA 60.474 57.143 10.49 0.00 35.75 2.59
74 75 0.747283 CGGCAGTACTACCTCCGTCT 60.747 60.000 10.49 0.00 35.75 4.18
75 76 1.726265 CGGCAGTACTACCTCCGTC 59.274 63.158 10.49 0.00 35.75 4.79
76 77 3.915575 CGGCAGTACTACCTCCGT 58.084 61.111 10.49 0.00 35.75 4.69
77 78 0.529378 AAACGGCAGTACTACCTCCG 59.471 55.000 10.49 14.85 45.04 4.63
78 79 3.019564 TCTAAACGGCAGTACTACCTCC 58.980 50.000 10.49 2.13 0.00 4.30
79 80 4.915158 ATCTAAACGGCAGTACTACCTC 57.085 45.455 10.49 0.00 0.00 3.85
80 81 5.067023 GTGTATCTAAACGGCAGTACTACCT 59.933 44.000 10.49 0.00 0.00 3.08
81 82 5.277047 GTGTATCTAAACGGCAGTACTACC 58.723 45.833 1.53 1.53 0.00 3.18
82 83 5.277047 GGTGTATCTAAACGGCAGTACTAC 58.723 45.833 0.00 0.00 0.00 2.73
83 84 4.339247 GGGTGTATCTAAACGGCAGTACTA 59.661 45.833 0.00 0.00 0.00 1.82
84 85 3.131755 GGGTGTATCTAAACGGCAGTACT 59.868 47.826 0.00 0.00 0.00 2.73
85 86 3.451526 GGGTGTATCTAAACGGCAGTAC 58.548 50.000 0.00 0.00 0.00 2.73
106 107 3.837213 ACTCAACTTGCCATCAATTCG 57.163 42.857 0.00 0.00 0.00 3.34
112 113 5.215160 CACAGTTTAACTCAACTTGCCATC 58.785 41.667 0.00 0.00 34.60 3.51
137 138 4.163268 TCCATGGACCGATCTGAATAAACA 59.837 41.667 11.44 0.00 0.00 2.83
218 219 1.005450 TGGTATGGGCCTTGGTTTCTC 59.995 52.381 4.53 0.00 0.00 2.87
222 223 0.485099 TGTTGGTATGGGCCTTGGTT 59.515 50.000 4.53 0.00 0.00 3.67
228 229 0.039035 TTGGAGTGTTGGTATGGGCC 59.961 55.000 0.00 0.00 0.00 5.80
238 239 5.045578 ACAGATAACATAGGCTTGGAGTGTT 60.046 40.000 0.00 0.00 36.94 3.32
252 253 5.300286 GCAAAAGGGCAGATACAGATAACAT 59.700 40.000 0.00 0.00 0.00 2.71
256 257 4.778213 AGCAAAAGGGCAGATACAGATA 57.222 40.909 0.00 0.00 35.83 1.98
268 321 1.688197 TGCTCTCCAAAAGCAAAAGGG 59.312 47.619 0.00 0.00 46.29 3.95
324 377 3.135348 TGAACAAATTCCCAATTGGCACA 59.865 39.130 19.75 4.95 33.49 4.57
377 449 4.025396 CAGTACTCGAATCATGATGGCAAC 60.025 45.833 9.46 3.80 0.00 4.17
385 457 7.514280 CGACAGATTTTCAGTACTCGAATCATG 60.514 40.741 17.80 15.26 30.98 3.07
388 460 5.275974 GCGACAGATTTTCAGTACTCGAATC 60.276 44.000 11.66 11.66 0.00 2.52
395 467 3.499048 TCTCGCGACAGATTTTCAGTAC 58.501 45.455 3.71 0.00 0.00 2.73
411 483 5.389642 TCATGTACGAAAAATGATCTCGC 57.610 39.130 1.59 0.00 36.03 5.03
491 563 9.716556 AGAAGAATAATAGACCCTTTAGTGAGA 57.283 33.333 0.00 0.00 0.00 3.27
497 569 9.053472 TGGTGAAGAAGAATAATAGACCCTTTA 57.947 33.333 0.00 0.00 0.00 1.85
510 582 9.995003 GAACAGATATAGATGGTGAAGAAGAAT 57.005 33.333 0.00 0.00 0.00 2.40
557 629 5.930135 AGAAGAAGCTTCAGGTAAGAAACA 58.070 37.500 27.57 0.00 37.38 2.83
730 805 0.906756 CAACAGGGGAGAGCAGGAGA 60.907 60.000 0.00 0.00 0.00 3.71
799 874 0.692476 AATGCTGCTACACCCACTCA 59.308 50.000 0.00 0.00 0.00 3.41
814 889 0.733909 GAAGCGGTTGGAGCAAATGC 60.734 55.000 3.70 0.00 42.49 3.56
815 890 0.597568 TGAAGCGGTTGGAGCAAATG 59.402 50.000 3.70 0.00 37.01 2.32
816 891 0.883833 CTGAAGCGGTTGGAGCAAAT 59.116 50.000 3.70 0.00 37.01 2.32
817 892 1.795170 GCTGAAGCGGTTGGAGCAAA 61.795 55.000 18.44 0.00 37.01 3.68
818 893 2.260869 GCTGAAGCGGTTGGAGCAA 61.261 57.895 18.44 0.00 37.01 3.91
822 897 0.037326 CTAGTGCTGAAGCGGTTGGA 60.037 55.000 3.70 0.00 45.83 3.53
860 935 1.205460 TTTCTTCCTAAGGGCCCGCT 61.205 55.000 18.44 10.79 0.00 5.52
928 1003 6.492772 ACTCCTCTACCAGTTATAATTACGGG 59.507 42.308 0.00 0.00 36.97 5.28
964 1039 9.887406 GACTTCTTGCTATTGACTACTACTATC 57.113 37.037 0.00 0.00 0.00 2.08
965 1040 9.409918 TGACTTCTTGCTATTGACTACTACTAT 57.590 33.333 0.00 0.00 0.00 2.12
986 1062 2.329267 TCTCCATGACCACTGTGACTT 58.671 47.619 9.86 0.00 0.00 3.01
1110 1186 4.767255 AGCGCTTTCTCCAGCCGG 62.767 66.667 2.64 0.00 36.31 6.13
1152 1228 1.277557 TGCTTCTTCTTCTCCAGCTCC 59.722 52.381 0.00 0.00 0.00 4.70
1174 1250 3.692257 TTCCTGCTCCTCTTTCTTCTG 57.308 47.619 0.00 0.00 0.00 3.02
1188 1264 1.301677 CTTCGTCCAGCCTTTCCTGC 61.302 60.000 0.00 0.00 0.00 4.85
1206 1282 4.740235 GCTATCGAAGCGCCTTCT 57.260 55.556 2.29 0.00 42.53 2.85
1230 1306 0.532573 TGAGGACATGAAGAGCGACC 59.467 55.000 0.00 0.00 0.00 4.79
1326 1402 0.807667 CCAGAGCGAAATCCAGACCG 60.808 60.000 0.00 0.00 0.00 4.79
1330 1406 1.363744 GTGTCCAGAGCGAAATCCAG 58.636 55.000 0.00 0.00 0.00 3.86
1339 1415 3.426568 GCCTTGCGTGTCCAGAGC 61.427 66.667 0.00 0.00 0.00 4.09
1362 1438 1.174783 CACCGGGGGAGTAGATATCG 58.825 60.000 6.32 0.00 0.00 2.92
1383 1459 0.524816 CTTGATTGGCGCACATGAGC 60.525 55.000 10.83 4.89 40.21 4.26
1419 1495 1.391933 CCCAGTCGATCCACCGATGA 61.392 60.000 0.00 0.00 40.91 2.92
1420 1496 1.068083 CCCAGTCGATCCACCGATG 59.932 63.158 0.00 0.00 40.91 3.84
1421 1497 2.134287 CCCCAGTCGATCCACCGAT 61.134 63.158 0.00 0.00 40.91 4.18
1422 1498 2.758327 CCCCAGTCGATCCACCGA 60.758 66.667 0.00 0.00 36.06 4.69
1423 1499 4.530857 GCCCCAGTCGATCCACCG 62.531 72.222 0.00 0.00 0.00 4.94
1648 1724 0.696501 TCCCTGTAAAGGTTGAGCCC 59.303 55.000 0.00 0.00 38.26 5.19
1700 1776 1.093159 ACCACTATGACGACGAGGTC 58.907 55.000 0.00 0.00 37.45 3.85
1720 1796 5.751990 CCTTCGGGTGACTATTATGTACAAC 59.248 44.000 0.00 0.00 0.00 3.32
1737 1813 0.537188 ATAGTCAGCACACCTTCGGG 59.463 55.000 0.00 0.00 41.87 5.14
1770 1846 2.819984 GATGGCCGGAACAGCTTCCA 62.820 60.000 5.05 0.00 45.99 3.53
1771 1847 2.044946 ATGGCCGGAACAGCTTCC 60.045 61.111 5.05 0.00 42.60 3.46
1772 1848 1.372087 CTGATGGCCGGAACAGCTTC 61.372 60.000 5.05 0.00 0.00 3.86
1773 1849 1.377725 CTGATGGCCGGAACAGCTT 60.378 57.895 5.05 0.00 0.00 3.74
1792 1868 3.813443 AGTTGCGCCATCAGATTCTAAT 58.187 40.909 4.18 0.00 0.00 1.73
1793 1869 3.266510 AGTTGCGCCATCAGATTCTAA 57.733 42.857 4.18 0.00 0.00 2.10
1794 1870 2.938451 CAAGTTGCGCCATCAGATTCTA 59.062 45.455 4.18 0.00 0.00 2.10
1846 1922 6.037172 ACAACAGACGCAAAACATATCCTATC 59.963 38.462 0.00 0.00 0.00 2.08
1856 1932 4.144051 CGACAATAACAACAGACGCAAAAC 59.856 41.667 0.00 0.00 0.00 2.43
1859 1935 2.222213 CCGACAATAACAACAGACGCAA 59.778 45.455 0.00 0.00 0.00 4.85
1860 1936 1.795872 CCGACAATAACAACAGACGCA 59.204 47.619 0.00 0.00 0.00 5.24
1862 1938 5.119588 ACAATACCGACAATAACAACAGACG 59.880 40.000 0.00 0.00 0.00 4.18
1863 1939 6.476243 ACAATACCGACAATAACAACAGAC 57.524 37.500 0.00 0.00 0.00 3.51
1864 1940 8.661257 CATTACAATACCGACAATAACAACAGA 58.339 33.333 0.00 0.00 0.00 3.41
1865 1941 8.661257 TCATTACAATACCGACAATAACAACAG 58.339 33.333 0.00 0.00 0.00 3.16
1866 1942 8.549338 TCATTACAATACCGACAATAACAACA 57.451 30.769 0.00 0.00 0.00 3.33
1867 1943 9.828852 TTTCATTACAATACCGACAATAACAAC 57.171 29.630 0.00 0.00 0.00 3.32
1868 1944 9.828852 GTTTCATTACAATACCGACAATAACAA 57.171 29.630 0.00 0.00 0.00 2.83
1906 1985 2.094494 CAGCTAGGAGCAAGAGAAACGA 60.094 50.000 0.64 0.00 45.56 3.85
1907 1986 2.266554 CAGCTAGGAGCAAGAGAAACG 58.733 52.381 0.64 0.00 45.56 3.60
1908 1987 2.626840 CCAGCTAGGAGCAAGAGAAAC 58.373 52.381 0.64 0.00 45.56 2.78
1909 1988 1.556911 CCCAGCTAGGAGCAAGAGAAA 59.443 52.381 0.00 0.00 45.56 2.52
1920 1999 3.703001 TCAAGAGAAAACCCAGCTAGG 57.297 47.619 0.00 0.00 37.03 3.02
1962 5324 1.588674 TTTCGCGAGGACACACAAAT 58.411 45.000 9.59 0.00 0.00 2.32
1970 5332 3.542310 GCACATTTTTATTTCGCGAGGAC 59.458 43.478 9.59 0.00 0.00 3.85
1976 5338 4.683781 TCCACAAGCACATTTTTATTTCGC 59.316 37.500 0.00 0.00 0.00 4.70
1993 5355 4.223923 ACACAAAAAGTTCCCATTCCACAA 59.776 37.500 0.00 0.00 0.00 3.33
2004 5366 6.480524 AGAAGGCAAAAACACAAAAAGTTC 57.519 33.333 0.00 0.00 0.00 3.01
2027 5391 1.622811 GGGAACAATGCACCAATGGAA 59.377 47.619 6.16 0.00 0.00 3.53
2062 5426 2.601240 TCTGGGATTTCATTGGCACA 57.399 45.000 0.00 0.00 0.00 4.57
2063 5427 3.431207 CCATTCTGGGATTTCATTGGCAC 60.431 47.826 0.00 0.00 32.67 5.01
2064 5428 2.767394 CCATTCTGGGATTTCATTGGCA 59.233 45.455 0.00 0.00 32.67 4.92
2065 5429 3.033184 TCCATTCTGGGATTTCATTGGC 58.967 45.455 0.00 0.00 38.32 4.52
2067 5431 4.713321 AGGTTCCATTCTGGGATTTCATTG 59.287 41.667 0.00 0.00 38.32 2.82
2089 5453 5.462068 CCAGTGCAATGATCAATAAATGCAG 59.538 40.000 17.16 10.84 43.62 4.41
2095 5459 5.447757 TCCATCCAGTGCAATGATCAATAA 58.552 37.500 17.16 0.00 0.00 1.40
2167 5531 3.368427 CGGCAGAATCTGTTCCTGTTCTA 60.368 47.826 12.29 0.00 34.81 2.10
2169 5533 1.734465 CGGCAGAATCTGTTCCTGTTC 59.266 52.381 12.29 0.00 34.81 3.18
2170 5534 1.072331 ACGGCAGAATCTGTTCCTGTT 59.928 47.619 12.29 0.00 34.81 3.16
2171 5535 0.687354 ACGGCAGAATCTGTTCCTGT 59.313 50.000 12.29 3.73 34.81 4.00
2172 5536 1.081892 CACGGCAGAATCTGTTCCTG 58.918 55.000 12.29 3.09 34.81 3.86
2173 5537 0.674895 GCACGGCAGAATCTGTTCCT 60.675 55.000 12.29 0.00 34.81 3.36
2174 5538 0.674895 AGCACGGCAGAATCTGTTCC 60.675 55.000 12.29 4.56 34.81 3.62
2185 5549 0.679505 AGTAAGTCTTCAGCACGGCA 59.320 50.000 0.00 0.00 0.00 5.69
2191 5555 4.826556 AGATTGGTCAGTAAGTCTTCAGC 58.173 43.478 0.00 0.00 0.00 4.26
2203 5567 2.469274 ACTGTGCAGAGATTGGTCAG 57.531 50.000 19.13 5.73 0.00 3.51
2231 5595 2.028930 GGGTCACCATCGATCCATCTAC 60.029 54.545 0.00 0.00 36.09 2.59
2296 5697 7.982224 TATCTTCTTGATGCTTCATGTTGAAG 58.018 34.615 11.92 11.92 44.33 3.02
2302 5703 9.661187 GTGTTTATATCTTCTTGATGCTTCATG 57.339 33.333 2.75 6.16 36.65 3.07
2322 5754 4.442332 CCGGGTGTATGCTCATAGTGTTTA 60.442 45.833 0.00 0.00 0.00 2.01
2344 5776 1.302832 CCTATCAATGCGGAGGCCC 60.303 63.158 0.00 0.00 38.85 5.80
2358 5790 7.998383 TGGTGTTAGATTTTGTGCATATCCTAT 59.002 33.333 0.00 0.00 0.00 2.57
2359 5791 7.342581 TGGTGTTAGATTTTGTGCATATCCTA 58.657 34.615 0.00 0.00 0.00 2.94
2360 5792 6.186957 TGGTGTTAGATTTTGTGCATATCCT 58.813 36.000 0.00 0.00 0.00 3.24
2362 5794 7.312154 TGTTGGTGTTAGATTTTGTGCATATC 58.688 34.615 0.00 0.00 0.00 1.63
2363 5795 7.176515 TCTGTTGGTGTTAGATTTTGTGCATAT 59.823 33.333 0.00 0.00 0.00 1.78
2365 5797 5.301551 TCTGTTGGTGTTAGATTTTGTGCAT 59.698 36.000 0.00 0.00 0.00 3.96
2367 5799 5.008613 TCTCTGTTGGTGTTAGATTTTGTGC 59.991 40.000 0.00 0.00 0.00 4.57
2370 5802 7.432252 GTGTTTCTCTGTTGGTGTTAGATTTTG 59.568 37.037 0.00 0.00 0.00 2.44
2372 5804 6.601613 TGTGTTTCTCTGTTGGTGTTAGATTT 59.398 34.615 0.00 0.00 0.00 2.17
2373 5805 6.038271 GTGTGTTTCTCTGTTGGTGTTAGATT 59.962 38.462 0.00 0.00 0.00 2.40
2374 5806 5.527582 GTGTGTTTCTCTGTTGGTGTTAGAT 59.472 40.000 0.00 0.00 0.00 1.98
2375 5807 4.873827 GTGTGTTTCTCTGTTGGTGTTAGA 59.126 41.667 0.00 0.00 0.00 2.10
2376 5808 4.035208 GGTGTGTTTCTCTGTTGGTGTTAG 59.965 45.833 0.00 0.00 0.00 2.34
2377 5809 3.942748 GGTGTGTTTCTCTGTTGGTGTTA 59.057 43.478 0.00 0.00 0.00 2.41
2388 5832 2.104281 ACTAGGTGGTGGTGTGTTTCTC 59.896 50.000 0.00 0.00 0.00 2.87
2390 5834 2.632987 ACTAGGTGGTGGTGTGTTTC 57.367 50.000 0.00 0.00 0.00 2.78
2397 5843 6.325804 GGTATATGACTTTACTAGGTGGTGGT 59.674 42.308 0.00 0.00 0.00 4.16
2398 5844 6.239515 GGGTATATGACTTTACTAGGTGGTGG 60.240 46.154 0.00 0.00 0.00 4.61
2400 5846 5.842874 GGGGTATATGACTTTACTAGGTGGT 59.157 44.000 0.00 0.00 0.00 4.16
2401 5847 6.082707 AGGGGTATATGACTTTACTAGGTGG 58.917 44.000 0.00 0.00 0.00 4.61
2404 5850 8.813951 CCTTTAGGGGTATATGACTTTACTAGG 58.186 40.741 0.00 0.00 0.00 3.02
2405 5851 9.597681 TCCTTTAGGGGTATATGACTTTACTAG 57.402 37.037 0.00 0.00 35.41 2.57
2406 5852 9.956558 TTCCTTTAGGGGTATATGACTTTACTA 57.043 33.333 0.00 0.00 35.41 1.82
2407 5853 8.865244 TTCCTTTAGGGGTATATGACTTTACT 57.135 34.615 0.00 0.00 35.41 2.24
2408 5854 9.910267 TTTTCCTTTAGGGGTATATGACTTTAC 57.090 33.333 0.00 0.00 35.41 2.01
2409 5855 9.910267 GTTTTCCTTTAGGGGTATATGACTTTA 57.090 33.333 0.00 0.00 35.41 1.85
2410 5856 7.837689 GGTTTTCCTTTAGGGGTATATGACTTT 59.162 37.037 0.00 0.00 36.94 2.66
2411 5857 7.351952 GGTTTTCCTTTAGGGGTATATGACTT 58.648 38.462 0.00 0.00 36.94 3.01
2412 5858 6.907961 GGTTTTCCTTTAGGGGTATATGACT 58.092 40.000 0.00 0.00 36.94 3.41
2429 5875 8.613482 GTCTTATATGACTTTGCTAGGTTTTCC 58.387 37.037 10.70 0.00 35.76 3.13
2430 5876 8.613482 GGTCTTATATGACTTTGCTAGGTTTTC 58.387 37.037 15.98 0.00 37.16 2.29
2431 5877 8.107095 TGGTCTTATATGACTTTGCTAGGTTTT 58.893 33.333 15.98 0.00 37.16 2.43
2432 5878 7.630082 TGGTCTTATATGACTTTGCTAGGTTT 58.370 34.615 15.98 0.00 37.16 3.27
2433 5879 7.195374 TGGTCTTATATGACTTTGCTAGGTT 57.805 36.000 15.98 0.00 37.16 3.50
2434 5880 6.686632 GCTGGTCTTATATGACTTTGCTAGGT 60.687 42.308 15.98 0.00 37.16 3.08
2435 5881 5.698545 GCTGGTCTTATATGACTTTGCTAGG 59.301 44.000 15.98 0.00 37.16 3.02
2478 5926 6.302078 CGCGCTTTGTTTTTCTTTTTCTTTTT 59.698 30.769 5.56 0.00 0.00 1.94
2479 5927 5.788041 CGCGCTTTGTTTTTCTTTTTCTTTT 59.212 32.000 5.56 0.00 0.00 2.27
2480 5928 5.119434 TCGCGCTTTGTTTTTCTTTTTCTTT 59.881 32.000 5.56 0.00 0.00 2.52
2481 5929 4.623595 TCGCGCTTTGTTTTTCTTTTTCTT 59.376 33.333 5.56 0.00 0.00 2.52
2482 5930 4.170256 TCGCGCTTTGTTTTTCTTTTTCT 58.830 34.783 5.56 0.00 0.00 2.52
2483 5931 4.493074 TCGCGCTTTGTTTTTCTTTTTC 57.507 36.364 5.56 0.00 0.00 2.29
2484 5932 4.317069 CGATCGCGCTTTGTTTTTCTTTTT 60.317 37.500 5.56 0.00 0.00 1.94
2492 5940 2.175811 GCCGATCGCGCTTTGTTT 59.824 55.556 10.32 0.00 35.83 2.83
2500 5948 2.586079 ATCAGTTGGCCGATCGCG 60.586 61.111 10.32 0.00 38.94 5.87
2501 5949 2.247437 GGATCAGTTGGCCGATCGC 61.247 63.158 10.32 5.23 39.16 4.58
2502 5950 4.033894 GGATCAGTTGGCCGATCG 57.966 61.111 8.51 8.51 39.16 3.69
2531 6000 3.444034 GTGAATCAAAGAAGGCCTAACCC 59.556 47.826 5.16 0.00 40.58 4.11
2548 6019 4.080919 TGAGAATCCCGTGAATGAGTGAAT 60.081 41.667 0.00 0.00 0.00 2.57
2549 6020 3.260632 TGAGAATCCCGTGAATGAGTGAA 59.739 43.478 0.00 0.00 0.00 3.18
2550 6021 2.831526 TGAGAATCCCGTGAATGAGTGA 59.168 45.455 0.00 0.00 0.00 3.41
2551 6022 3.251479 TGAGAATCCCGTGAATGAGTG 57.749 47.619 0.00 0.00 0.00 3.51
2552 6023 3.981071 TTGAGAATCCCGTGAATGAGT 57.019 42.857 0.00 0.00 0.00 3.41
2553 6024 5.575957 CATTTTGAGAATCCCGTGAATGAG 58.424 41.667 0.00 0.00 0.00 2.90
2554 6025 4.142403 GCATTTTGAGAATCCCGTGAATGA 60.142 41.667 0.00 0.00 0.00 2.57
2555 6026 4.107622 GCATTTTGAGAATCCCGTGAATG 58.892 43.478 0.00 0.00 0.00 2.67
2592 6064 4.641989 GGACATGACACTATTTTCCTGCAT 59.358 41.667 0.00 0.00 0.00 3.96
2593 6065 4.009675 GGACATGACACTATTTTCCTGCA 58.990 43.478 0.00 0.00 0.00 4.41
2598 6070 5.412594 TGCAAGAGGACATGACACTATTTTC 59.587 40.000 0.00 0.00 0.00 2.29
2644 6116 8.691661 AACACTCTTACAACCATGTTAATCTT 57.308 30.769 0.00 0.00 41.05 2.40
2646 6118 7.807907 CCAAACACTCTTACAACCATGTTAATC 59.192 37.037 0.00 0.00 41.05 1.75


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

AutoCloner maintained by Alex Coulton.