Multiple sequence alignment - TraesCS2A01G193300

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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 TraesCS2A01G193300 chr2A 100.000 6114 0 0 1 6114 161849198 161855311 0.000000e+00 11291.0
1 TraesCS2A01G193300 chr2D 88.040 2709 161 66 1 2631 139114044 139111421 0.000000e+00 3057.0
2 TraesCS2A01G193300 chr2D 97.794 1269 25 2 2614 3881 139111406 139110140 0.000000e+00 2185.0
3 TraesCS2A01G193300 chr2D 97.425 699 9 4 4045 4735 139110105 139109408 0.000000e+00 1182.0
4 TraesCS2A01G193300 chr2D 94.859 603 25 3 4737 5338 139109322 139108725 0.000000e+00 937.0
5 TraesCS2A01G193300 chr2D 95.122 123 6 0 5992 6114 139061106 139060984 1.740000e-45 195.0
6 TraesCS2A01G193300 chr2B 90.154 2407 143 41 1811 4197 197725478 197723146 0.000000e+00 3046.0
7 TraesCS2A01G193300 chr2B 87.848 1794 101 49 32 1779 197727204 197725482 0.000000e+00 1997.0
8 TraesCS2A01G193300 chr2B 87.138 622 40 24 4955 5550 197722148 197721541 0.000000e+00 669.0
9 TraesCS2A01G193300 chr2B 88.915 424 31 5 5694 6114 197721010 197720600 5.470000e-140 508.0
10 TraesCS2A01G193300 chr2B 88.261 230 16 7 4502 4721 197722647 197722419 1.310000e-66 265.0
11 TraesCS2A01G193300 chr2B 91.919 99 8 0 3706 3804 314750366 314750268 8.260000e-29 139.0
12 TraesCS2A01G193300 chr2B 83.108 148 16 5 5548 5695 197721217 197721079 6.430000e-25 126.0
13 TraesCS2A01G193300 chr2B 87.719 57 4 2 4453 4509 122010797 122010850 5.120000e-06 63.9
14 TraesCS2A01G193300 chr3B 94.737 57 3 0 3710 3766 309518231 309518287 8.440000e-14 89.8
15 TraesCS2A01G193300 chr4D 97.727 44 1 0 4457 4500 347523985 347523942 6.570000e-10 76.8
16 TraesCS2A01G193300 chr7D 95.556 45 2 0 4456 4500 401789619 401789663 8.500000e-09 73.1
17 TraesCS2A01G193300 chrUn 95.455 44 2 0 4457 4500 12289435 12289392 3.060000e-08 71.3
18 TraesCS2A01G193300 chr4A 95.455 44 2 0 4457 4500 692915994 692915951 3.060000e-08 71.3
19 TraesCS2A01G193300 chr1D 95.455 44 2 0 4457 4500 378551908 378551865 3.060000e-08 71.3
20 TraesCS2A01G193300 chr1A 95.455 44 2 0 4457 4500 67695598 67695555 3.060000e-08 71.3
21 TraesCS2A01G193300 chr1A 90.566 53 5 0 4457 4509 529327101 529327049 3.060000e-08 71.3


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 TraesCS2A01G193300 chr2A 161849198 161855311 6113 False 11291.000000 11291 100.000000 1 6114 1 chr2A.!!$F1 6113
1 TraesCS2A01G193300 chr2D 139108725 139114044 5319 True 1840.250000 3057 94.529500 1 5338 4 chr2D.!!$R2 5337
2 TraesCS2A01G193300 chr2B 197720600 197727204 6604 True 1101.833333 3046 87.570667 32 6114 6 chr2B.!!$R2 6082

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
360 388 0.042448 GTGAAACGCACGTCCTTGAC 60.042 55.000 0.00 0.0 37.83 3.18 F
361 389 0.179094 TGAAACGCACGTCCTTGACT 60.179 50.000 0.00 0.0 0.00 3.41 F
367 395 0.249911 GCACGTCCTTGACTCCTTGT 60.250 55.000 0.00 0.0 0.00 3.16 F
1437 1518 0.324943 TTTGGCAGCTGGTCCTAGTC 59.675 55.000 17.12 0.0 0.00 2.59 F
1961 2057 0.898320 GGTCTACAAGAGAGGCAGCA 59.102 55.000 0.00 0.0 33.72 4.41 F
2353 2472 1.353103 CATCTCGCGCCATTGGTTC 59.647 57.895 0.00 0.0 0.00 3.62 F
3269 3422 2.303890 TCTTGCCTCAAATCTCTCTGCA 59.696 45.455 0.00 0.0 0.00 4.41 F
3925 4080 0.031111 TATGCCTACCCCAGCAGTCT 60.031 55.000 0.00 0.0 43.38 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1948 0.032912 ACATGATGGGGCTGATGCAA 60.033 50.000 0.00 0.0 41.91 4.08 R
1933 2029 0.116342 TCTTGTAGACCCCCTGCTCA 59.884 55.000 0.00 0.0 0.00 4.26 R
1961 2057 1.067635 GCATCAACCAACGAAGCCAAT 60.068 47.619 0.00 0.0 0.00 3.16 R
3269 3422 3.665971 CCTTTGCCCCCTGCCTCT 61.666 66.667 0.00 0.0 40.16 3.69 R
3908 4063 0.252513 TAAGACTGCTGGGGTAGGCA 60.253 55.000 0.00 0.0 35.55 4.75 R
3909 4064 0.466124 CTAAGACTGCTGGGGTAGGC 59.534 60.000 0.00 0.0 33.15 3.93 R
4777 5332 0.189327 ATGATCAAGGAATGGCCCCC 59.811 55.000 0.00 0.0 37.37 5.40 R
5419 6050 0.030369 GATCGAATACACCGGACGCT 59.970 55.000 9.46 0.0 0.00 5.07 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
38 39 1.134610 GGAAAAAGATGCCATGCAGGG 60.135 52.381 14.45 14.45 43.65 4.45
76 80 0.458889 CCGATCCGGCGTAAGTTTGA 60.459 55.000 6.01 0.00 41.17 2.69
99 103 0.676466 CCAAACATCACGCCTAGCCA 60.676 55.000 0.00 0.00 0.00 4.75
105 109 0.972983 ATCACGCCTAGCCAGTGAGT 60.973 55.000 15.06 5.22 46.29 3.41
106 110 1.153745 CACGCCTAGCCAGTGAGTC 60.154 63.158 0.00 0.00 38.06 3.36
107 111 1.606601 ACGCCTAGCCAGTGAGTCA 60.607 57.895 0.00 0.00 0.00 3.41
108 112 1.153745 CGCCTAGCCAGTGAGTCAC 60.154 63.158 15.78 15.78 34.10 3.67
109 113 1.599606 CGCCTAGCCAGTGAGTCACT 61.600 60.000 20.34 20.34 46.51 3.41
110 114 0.174617 GCCTAGCCAGTGAGTCACTC 59.825 60.000 23.08 12.94 43.43 3.51
111 115 0.820871 CCTAGCCAGTGAGTCACTCC 59.179 60.000 23.08 16.14 43.43 3.85
112 116 1.550327 CTAGCCAGTGAGTCACTCCA 58.450 55.000 23.08 7.52 43.43 3.86
113 117 2.106566 CTAGCCAGTGAGTCACTCCAT 58.893 52.381 23.08 13.30 43.43 3.41
119 123 4.444022 GCCAGTGAGTCACTCCATCATTAT 60.444 45.833 23.08 0.00 43.43 1.28
120 124 5.678583 CCAGTGAGTCACTCCATCATTATT 58.321 41.667 23.08 0.00 43.43 1.40
121 125 6.686378 GCCAGTGAGTCACTCCATCATTATTA 60.686 42.308 23.08 0.00 43.43 0.98
159 163 3.569250 TTCAACGCTCTATTTTTGGGC 57.431 42.857 0.00 0.00 0.00 5.36
162 166 3.897819 CGCTCTATTTTTGGGCGTC 57.102 52.632 0.00 0.00 40.78 5.19
196 208 3.786635 CTCTCCCACTTGATTTAGGTCG 58.213 50.000 0.00 0.00 0.00 4.79
198 210 3.056107 TCTCCCACTTGATTTAGGTCGTG 60.056 47.826 0.00 0.00 0.00 4.35
215 229 2.359478 GGTAACACGGCAGGGTGG 60.359 66.667 0.00 0.00 42.23 4.61
273 290 0.593773 CACCAACGCTTTTTCCGGTG 60.594 55.000 0.00 0.00 42.68 4.94
276 303 1.000717 CCAACGCTTTTTCCGGTGAAT 60.001 47.619 0.00 0.00 45.69 2.57
285 312 5.476752 TTTTTCCGGTGAATTTTGCTTTG 57.523 34.783 0.00 0.00 0.00 2.77
299 326 4.301072 TTGCTTTGCAGTATACCCTTCT 57.699 40.909 0.00 0.00 40.61 2.85
321 349 0.818938 TTGCCCACAAGCTATGCATG 59.181 50.000 10.16 0.26 33.24 4.06
347 375 1.808411 TTCGCTCCATGAGGTGAAAC 58.192 50.000 10.05 0.00 35.89 2.78
359 387 2.303452 GTGAAACGCACGTCCTTGA 58.697 52.632 0.00 0.00 37.83 3.02
360 388 0.042448 GTGAAACGCACGTCCTTGAC 60.042 55.000 0.00 0.00 37.83 3.18
361 389 0.179094 TGAAACGCACGTCCTTGACT 60.179 50.000 0.00 0.00 0.00 3.41
362 390 0.507358 GAAACGCACGTCCTTGACTC 59.493 55.000 0.00 0.00 0.00 3.36
363 391 0.878961 AAACGCACGTCCTTGACTCC 60.879 55.000 0.00 0.00 0.00 3.85
364 392 1.745320 AACGCACGTCCTTGACTCCT 61.745 55.000 0.00 0.00 0.00 3.69
365 393 1.006102 CGCACGTCCTTGACTCCTT 60.006 57.895 0.00 0.00 0.00 3.36
366 394 1.284982 CGCACGTCCTTGACTCCTTG 61.285 60.000 0.00 0.00 0.00 3.61
367 395 0.249911 GCACGTCCTTGACTCCTTGT 60.250 55.000 0.00 0.00 0.00 3.16
368 396 1.502231 CACGTCCTTGACTCCTTGTG 58.498 55.000 0.00 0.00 0.00 3.33
400 431 4.574828 GGCGGTGTATTGTATGAGTTTGAT 59.425 41.667 0.00 0.00 0.00 2.57
435 466 1.611977 TCCGTCTGAGTTCATCACGTT 59.388 47.619 10.85 0.00 33.00 3.99
710 778 0.598680 CGCTACTACATGGCAGCTCC 60.599 60.000 0.00 0.00 33.46 4.70
816 884 3.706668 GCCGCGCATCTCGATTCC 61.707 66.667 8.75 0.00 41.67 3.01
817 885 3.398134 CCGCGCATCTCGATTCCG 61.398 66.667 8.75 0.00 41.67 4.30
818 886 4.051963 CGCGCATCTCGATTCCGC 62.052 66.667 8.75 9.04 41.67 5.54
889 957 2.574399 GCGTCCTGACTCCTGACC 59.426 66.667 0.00 0.00 0.00 4.02
946 1014 2.414691 GGTTTCTTGCTGCGATTCTTCC 60.415 50.000 0.00 0.00 0.00 3.46
975 1043 1.804601 GTCCGTTTCTTGATTCCGGT 58.195 50.000 0.00 0.00 39.62 5.28
1128 1198 0.607489 TCAGGCAAGAAGAGCAAGGC 60.607 55.000 0.00 0.00 0.00 4.35
1293 1363 2.011222 CGCTCTCTACGAGAAGAGGTT 58.989 52.381 12.12 0.00 42.78 3.50
1295 1365 3.011119 GCTCTCTACGAGAAGAGGTTGA 58.989 50.000 12.12 0.00 42.78 3.18
1297 1367 3.011119 TCTCTACGAGAAGAGGTTGAGC 58.989 50.000 12.12 0.00 42.78 4.26
1301 1374 3.074675 ACGAGAAGAGGTTGAGCTCTA 57.925 47.619 16.19 4.09 0.00 2.43
1369 1442 3.561310 ACGTGTGCTATGCAAATAGATGG 59.439 43.478 0.00 0.00 41.47 3.51
1390 1463 2.608752 GGTCGTTACTGGTGTAGTGTGG 60.609 54.545 0.00 0.00 40.65 4.17
1407 1488 4.711846 AGTGTGGTAGCATCACAATAGAGA 59.288 41.667 21.38 0.00 45.24 3.10
1408 1489 5.046529 GTGTGGTAGCATCACAATAGAGAG 58.953 45.833 17.19 0.00 45.24 3.20
1437 1518 0.324943 TTTGGCAGCTGGTCCTAGTC 59.675 55.000 17.12 0.00 0.00 2.59
1443 1524 3.082579 GCTGGTCCTAGTCGGCTGG 62.083 68.421 0.00 0.00 32.87 4.85
1486 1567 9.220767 GGATAGATTAGGATGATGTTGTTAACC 57.779 37.037 2.48 0.00 0.00 2.85
1511 1594 8.285394 CCTGACATTTGATATACAATGCTACAC 58.715 37.037 6.34 0.00 38.36 2.90
1624 1710 9.160496 CAGTCTATATCTGATTGAATTTAGGCC 57.840 37.037 0.00 0.00 35.20 5.19
1636 1722 7.606135 TTGAATTTAGGCCATGATGATTGAT 57.394 32.000 5.01 0.00 0.00 2.57
1637 1723 7.606135 TGAATTTAGGCCATGATGATTGATT 57.394 32.000 5.01 0.00 0.00 2.57
1638 1724 7.438564 TGAATTTAGGCCATGATGATTGATTG 58.561 34.615 5.01 0.00 0.00 2.67
1639 1725 7.288158 TGAATTTAGGCCATGATGATTGATTGA 59.712 33.333 5.01 0.00 0.00 2.57
1640 1726 7.606135 ATTTAGGCCATGATGATTGATTGAA 57.394 32.000 5.01 0.00 0.00 2.69
1669 1755 5.439721 TGCATTATCCTGTAGCTCATGTTT 58.560 37.500 0.00 0.00 0.00 2.83
1738 1834 3.904339 TCAAGTTCTACTCAGGAAGCCTT 59.096 43.478 0.00 0.00 0.00 4.35
1750 1846 3.135530 CAGGAAGCCTTTCATAGGTAGCT 59.864 47.826 0.00 0.00 46.61 3.32
1772 1868 6.921857 AGCTCATTTGTGAAATTTGACTTCTG 59.078 34.615 9.24 4.08 0.00 3.02
1789 1885 9.731819 TTGACTTCTGATAAGTAATAACTAGCG 57.268 33.333 0.00 0.00 33.75 4.26
1799 1895 6.651975 AGTAATAACTAGCGAGTATGCCTT 57.348 37.500 0.00 0.00 33.58 4.35
1817 1913 5.243426 GCCTTTCATAGTCGGCAAATTTA 57.757 39.130 0.00 0.00 42.06 1.40
1831 1927 6.980978 TCGGCAAATTTAACTTCATGTTTTGA 59.019 30.769 0.00 0.00 39.89 2.69
1846 1942 5.379732 TGTTTTGATTAACCGGACATTCC 57.620 39.130 9.46 0.00 0.00 3.01
1851 1947 1.364269 TTAACCGGACATTCCACCCT 58.636 50.000 9.46 0.00 35.91 4.34
1852 1948 1.364269 TAACCGGACATTCCACCCTT 58.636 50.000 9.46 0.00 35.91 3.95
1859 1955 2.170166 GACATTCCACCCTTTGCATCA 58.830 47.619 0.00 0.00 0.00 3.07
1862 1958 0.899717 TTCCACCCTTTGCATCAGCC 60.900 55.000 0.00 0.00 41.13 4.85
1867 1963 1.397390 CCCTTTGCATCAGCCCCATC 61.397 60.000 0.00 0.00 41.13 3.51
1886 1982 7.041098 GCCCCATCATGTAAAATGTAGAAGTAG 60.041 40.741 0.00 0.00 0.00 2.57
1900 1996 7.490962 TGTAGAAGTAGTCATGTTGGTTTTG 57.509 36.000 0.00 0.00 0.00 2.44
1908 2004 5.348164 AGTCATGTTGGTTTTGTTTAGTGC 58.652 37.500 0.00 0.00 0.00 4.40
1961 2057 0.898320 GGTCTACAAGAGAGGCAGCA 59.102 55.000 0.00 0.00 33.72 4.41
2051 2147 9.654663 GTTAGTACATTCTACTGACCAATCTTT 57.345 33.333 0.00 0.00 30.64 2.52
2162 2268 7.964559 TCACATCTCAAGCTCAAAATTTTATCG 59.035 33.333 2.44 0.00 0.00 2.92
2184 2290 3.945921 GCTAACCCCTGTCCTTTTACATC 59.054 47.826 0.00 0.00 0.00 3.06
2192 2298 3.620488 TGTCCTTTTACATCATGGCTCC 58.380 45.455 0.00 0.00 0.00 4.70
2203 2322 4.101741 ACATCATGGCTCCCTCTTAACTAC 59.898 45.833 0.00 0.00 0.00 2.73
2353 2472 1.353103 CATCTCGCGCCATTGGTTC 59.647 57.895 0.00 0.00 0.00 3.62
2566 2686 6.815641 GCTTCAAAGATGATCTCTGTAAGTGA 59.184 38.462 0.00 0.00 41.16 3.41
2784 2936 9.162764 GTATAGGTGCCGTTGATTTATTATCAT 57.837 33.333 0.00 0.00 0.00 2.45
3269 3422 2.303890 TCTTGCCTCAAATCTCTCTGCA 59.696 45.455 0.00 0.00 0.00 4.41
3373 3526 7.454260 AGGTCTGTTTCATTTCCATTCTTAC 57.546 36.000 0.00 0.00 0.00 2.34
3376 3529 9.010029 GGTCTGTTTCATTTCCATTCTTACTTA 57.990 33.333 0.00 0.00 0.00 2.24
3548 3702 2.957402 TCAGTGGTTCCTGAATTGCT 57.043 45.000 0.00 0.00 38.49 3.91
3568 3722 3.918591 GCTCTGCATTTTCACATGTCTTG 59.081 43.478 0.00 0.00 0.00 3.02
3577 3731 7.412237 GCATTTTCACATGTCTTGGCTAATTTC 60.412 37.037 0.00 0.00 0.00 2.17
3594 3748 6.772716 GCTAATTTCCCCTTGATCATCAGTTA 59.227 38.462 0.00 0.00 0.00 2.24
3609 3763 7.780008 TCATCAGTTAAACTTCTTCAAACGA 57.220 32.000 0.00 0.00 0.00 3.85
3696 3850 5.459768 TGTGCTAATTTACTTGTGCATGTG 58.540 37.500 0.00 0.00 32.82 3.21
3817 3971 5.948992 AGGTAAAACTGAGACATTGAAGC 57.051 39.130 0.00 0.00 0.00 3.86
3858 4012 7.283625 TGGTTGCTTTGAAGAGCTTTAATAA 57.716 32.000 0.00 0.00 43.11 1.40
3894 4049 9.675464 ATTTGGTCTATGGAGTTATTTACGAAA 57.325 29.630 0.00 0.00 0.00 3.46
3911 4066 8.627487 TTTACGAAATGTGAATGAATTATGCC 57.373 30.769 0.00 0.00 0.00 4.40
3913 4068 7.566760 ACGAAATGTGAATGAATTATGCCTA 57.433 32.000 0.00 0.00 0.00 3.93
3914 4069 7.417612 ACGAAATGTGAATGAATTATGCCTAC 58.582 34.615 0.00 0.00 0.00 3.18
3915 4070 6.857964 CGAAATGTGAATGAATTATGCCTACC 59.142 38.462 0.00 0.00 0.00 3.18
3916 4071 6.655078 AATGTGAATGAATTATGCCTACCC 57.345 37.500 0.00 0.00 0.00 3.69
3917 4072 4.469657 TGTGAATGAATTATGCCTACCCC 58.530 43.478 0.00 0.00 0.00 4.95
3918 4073 4.079500 TGTGAATGAATTATGCCTACCCCA 60.080 41.667 0.00 0.00 0.00 4.96
3919 4074 4.520492 GTGAATGAATTATGCCTACCCCAG 59.480 45.833 0.00 0.00 0.00 4.45
3920 4075 2.656947 TGAATTATGCCTACCCCAGC 57.343 50.000 0.00 0.00 0.00 4.85
3921 4076 1.849692 TGAATTATGCCTACCCCAGCA 59.150 47.619 0.00 0.00 44.45 4.41
3922 4077 2.158623 TGAATTATGCCTACCCCAGCAG 60.159 50.000 0.00 0.00 43.38 4.24
3923 4078 1.522900 ATTATGCCTACCCCAGCAGT 58.477 50.000 0.00 0.00 43.38 4.40
3924 4079 0.837272 TTATGCCTACCCCAGCAGTC 59.163 55.000 0.00 0.00 43.38 3.51
3925 4080 0.031111 TATGCCTACCCCAGCAGTCT 60.031 55.000 0.00 0.00 43.38 3.24
3926 4081 0.916358 ATGCCTACCCCAGCAGTCTT 60.916 55.000 0.00 0.00 43.38 3.01
3927 4082 0.252513 TGCCTACCCCAGCAGTCTTA 60.253 55.000 0.00 0.00 33.08 2.10
3928 4083 0.466124 GCCTACCCCAGCAGTCTTAG 59.534 60.000 0.00 0.00 0.00 2.18
3929 4084 1.965318 GCCTACCCCAGCAGTCTTAGA 60.965 57.143 0.00 0.00 0.00 2.10
3930 4085 1.757699 CCTACCCCAGCAGTCTTAGAC 59.242 57.143 3.85 3.85 0.00 2.59
3931 4086 2.624557 CCTACCCCAGCAGTCTTAGACT 60.625 54.545 9.37 9.37 44.44 3.24
3932 4087 2.031495 ACCCCAGCAGTCTTAGACTT 57.969 50.000 12.76 0.00 41.37 3.01
3933 4088 1.903183 ACCCCAGCAGTCTTAGACTTC 59.097 52.381 12.76 8.12 41.37 3.01
3954 4109 9.553064 GACTTCTGACCTGTTATATGATTGATT 57.447 33.333 0.00 0.00 0.00 2.57
3955 4110 9.553064 ACTTCTGACCTGTTATATGATTGATTC 57.447 33.333 0.00 0.00 0.00 2.52
3956 4111 8.908786 TTCTGACCTGTTATATGATTGATTCC 57.091 34.615 0.00 0.00 0.00 3.01
3987 4142 3.367630 CCAACAGCAAAGACACAAAACAC 59.632 43.478 0.00 0.00 0.00 3.32
4010 4165 3.325135 GCTTAGCAAGGGATTAGGCTAGA 59.675 47.826 0.00 0.00 39.72 2.43
4018 4173 6.205658 GCAAGGGATTAGGCTAGATTAAACAG 59.794 42.308 0.00 0.00 0.00 3.16
4038 4193 7.865706 AACAGTTAAGGTATGATTGATGGTC 57.134 36.000 0.00 0.00 0.00 4.02
4238 4396 1.479709 CTGTACCACTAGAGCCTGCT 58.520 55.000 0.00 0.00 0.00 4.24
4626 5088 9.170734 TGATAGATTCCTGAACTTGAGAAATTG 57.829 33.333 0.00 0.00 0.00 2.32
4636 5098 6.091986 TGAACTTGAGAAATTGCAAAAACACC 59.908 34.615 1.71 0.00 0.00 4.16
4714 5176 0.319211 TCGTCGTTTAGCACAGGTGG 60.319 55.000 1.10 0.00 0.00 4.61
4735 5197 7.447545 AGGTGGATAACTTGTTTCCTTTACTTC 59.552 37.037 12.37 0.00 0.00 3.01
4776 5331 6.043411 GGTGCTTAAGGACTATAACTCAGTG 58.957 44.000 24.08 0.00 36.56 3.66
4777 5332 6.043411 GTGCTTAAGGACTATAACTCAGTGG 58.957 44.000 18.90 0.00 33.32 4.00
4800 5355 4.162651 GGGGCCATTCCTTGATCATTTAT 58.837 43.478 4.39 0.00 34.39 1.40
4926 5504 7.806409 TTGGGACTTGATAATCATGTGTATG 57.194 36.000 0.00 0.00 35.29 2.39
4950 5528 7.304735 TGTTTGGAACTCGAAAATCATATGTG 58.695 34.615 1.90 0.00 0.00 3.21
5022 5647 2.045340 GGGTGCATTGCTACCCGT 60.045 61.111 24.17 0.00 46.42 5.28
5024 5649 2.112815 GGTGCATTGCTACCCGTCC 61.113 63.158 10.49 0.00 0.00 4.79
5037 5662 0.255890 CCCGTCCCCACATCATTTCT 59.744 55.000 0.00 0.00 0.00 2.52
5038 5663 1.668419 CCGTCCCCACATCATTTCTC 58.332 55.000 0.00 0.00 0.00 2.87
5041 5666 1.566231 GTCCCCACATCATTTCTCCCT 59.434 52.381 0.00 0.00 0.00 4.20
5140 5766 3.502123 AGGAAACAAAACCTCATCGGA 57.498 42.857 0.00 0.00 36.31 4.55
5144 5770 0.395312 ACAAAACCTCATCGGACCGT 59.605 50.000 14.79 0.00 36.31 4.83
5149 5775 0.175760 ACCTCATCGGACCGTCATTG 59.824 55.000 14.79 8.01 36.31 2.82
5232 5858 1.892474 AGTCTGCTCTCCTTGACTGTC 59.108 52.381 0.00 0.00 38.22 3.51
5294 5920 2.423538 ACTTGGCCGAAATGATTACTGC 59.576 45.455 0.00 0.00 0.00 4.40
5362 5991 7.137426 TCTCTTAGTTTAGTTCAACGAGTGTC 58.863 38.462 0.00 0.00 0.00 3.67
5393 6024 2.577449 AAAAAGACACCCAAAGCGTG 57.423 45.000 0.00 0.00 37.26 5.34
5394 6025 1.470051 AAAAGACACCCAAAGCGTGT 58.530 45.000 0.00 0.00 46.91 4.49
5395 6026 1.470051 AAAGACACCCAAAGCGTGTT 58.530 45.000 0.00 0.00 44.34 3.32
5398 6029 2.645802 AGACACCCAAAGCGTGTTAAA 58.354 42.857 0.00 0.00 44.34 1.52
5400 6031 3.444388 AGACACCCAAAGCGTGTTAAAAA 59.556 39.130 0.00 0.00 44.34 1.94
5417 6048 2.713828 AAAACTAAACCATGGGGCCT 57.286 45.000 18.09 0.00 37.90 5.19
5419 6050 1.080638 AACTAAACCATGGGGCCTGA 58.919 50.000 18.09 0.00 37.90 3.86
5420 6051 0.625849 ACTAAACCATGGGGCCTGAG 59.374 55.000 18.09 6.74 37.90 3.35
5421 6052 0.753111 CTAAACCATGGGGCCTGAGC 60.753 60.000 18.09 0.00 37.90 4.26
5424 6055 4.864334 CCATGGGGCCTGAGCGTC 62.864 72.222 2.85 0.00 41.24 5.19
5431 6063 3.755628 GCCTGAGCGTCCGGTGTA 61.756 66.667 0.00 0.00 0.00 2.90
5464 6096 1.671166 CCATCGCGGGACATCCATA 59.329 57.895 6.13 0.00 37.91 2.74
5515 6154 0.323360 GCTTAACCAGGGCCACATGA 60.323 55.000 6.18 0.00 0.00 3.07
5550 6190 3.876309 AACGGCATATATTCCTTGGGT 57.124 42.857 0.00 0.00 0.00 4.51
5563 6528 3.479489 TCCTTGGGTTTCGAAGTTTACC 58.521 45.455 8.02 8.02 0.00 2.85
5564 6529 2.224784 CCTTGGGTTTCGAAGTTTACCG 59.775 50.000 9.96 0.00 0.00 4.02
5567 6532 1.800586 GGGTTTCGAAGTTTACCGTCC 59.199 52.381 9.96 0.00 0.00 4.79
5573 6538 2.364970 TCGAAGTTTACCGTCCAAAGGA 59.635 45.455 0.00 0.00 0.00 3.36
5575 6540 2.853235 AGTTTACCGTCCAAAGGAGG 57.147 50.000 0.00 0.00 37.34 4.30
5580 6545 4.225497 CGTCCAAAGGAGGGCATC 57.775 61.111 0.00 0.00 34.37 3.91
5581 6546 1.815421 CGTCCAAAGGAGGGCATCG 60.815 63.158 0.00 0.00 34.37 3.84
5610 6575 0.438830 GAACGAGCAAAGGTACAGCG 59.561 55.000 0.00 0.00 0.00 5.18
5615 6580 1.966451 GCAAAGGTACAGCGTGGCT 60.966 57.895 0.00 0.00 40.77 4.75
5621 6586 0.815734 GGTACAGCGTGGCTTCTCTA 59.184 55.000 0.00 0.00 36.40 2.43
5628 6593 4.100189 ACAGCGTGGCTTCTCTATTTATCT 59.900 41.667 0.00 0.00 36.40 1.98
5639 6604 4.583073 TCTCTATTTATCTGCGTGCTGGTA 59.417 41.667 0.00 0.00 0.00 3.25
5640 6605 4.871513 TCTATTTATCTGCGTGCTGGTAG 58.128 43.478 0.00 0.00 0.00 3.18
5641 6606 2.309528 TTTATCTGCGTGCTGGTAGG 57.690 50.000 0.00 0.00 0.00 3.18
5642 6607 1.480789 TTATCTGCGTGCTGGTAGGA 58.519 50.000 0.00 0.00 0.00 2.94
5643 6608 1.032794 TATCTGCGTGCTGGTAGGAG 58.967 55.000 0.00 0.00 0.00 3.69
5644 6609 0.972983 ATCTGCGTGCTGGTAGGAGT 60.973 55.000 0.00 0.00 0.00 3.85
5645 6610 0.323087 TCTGCGTGCTGGTAGGAGTA 60.323 55.000 0.00 0.00 0.00 2.59
5654 6619 3.069872 TGCTGGTAGGAGTACGTCAAAAA 59.930 43.478 0.00 0.00 0.00 1.94
5655 6620 3.431233 GCTGGTAGGAGTACGTCAAAAAC 59.569 47.826 0.00 0.00 0.00 2.43
5657 6622 4.624015 TGGTAGGAGTACGTCAAAAACAG 58.376 43.478 0.00 0.00 0.00 3.16
5687 6652 5.183969 GGTAGTTTCTAAGGAAAGGCGAAT 58.816 41.667 0.00 0.00 41.43 3.34
5704 6739 6.729187 AGGCGAATAGAAATAAAACAGATGC 58.271 36.000 0.00 0.00 0.00 3.91
5735 6770 4.212636 GGCACTAAATTATGTATTCGCCGT 59.787 41.667 0.00 0.00 0.00 5.68
5747 6782 5.834169 TGTATTCGCCGTTGATGAAGTATA 58.166 37.500 0.00 0.00 0.00 1.47
5753 6788 4.270084 CGCCGTTGATGAAGTATACACAAT 59.730 41.667 5.50 0.00 0.00 2.71
5757 6792 6.535150 CCGTTGATGAAGTATACACAATCAGT 59.465 38.462 5.50 0.00 0.00 3.41
5759 6794 7.899841 CGTTGATGAAGTATACACAATCAGTTG 59.100 37.037 5.50 2.02 41.20 3.16
5761 6796 9.936759 TTGATGAAGTATACACAATCAGTTGTA 57.063 29.630 5.50 0.00 46.49 2.41
5762 6797 9.366216 TGATGAAGTATACACAATCAGTTGTAC 57.634 33.333 5.50 0.00 46.49 2.90
5763 6798 8.718102 ATGAAGTATACACAATCAGTTGTACC 57.282 34.615 5.50 0.00 46.49 3.34
5765 6800 8.372459 TGAAGTATACACAATCAGTTGTACCTT 58.628 33.333 5.50 0.00 46.49 3.50
5767 6802 7.328737 AGTATACACAATCAGTTGTACCTTCC 58.671 38.462 5.50 0.00 46.49 3.46
5768 6803 4.431416 ACACAATCAGTTGTACCTTCCA 57.569 40.909 0.00 0.00 46.49 3.53
5770 6805 5.385198 ACACAATCAGTTGTACCTTCCATT 58.615 37.500 0.00 0.00 46.49 3.16
5771 6806 5.241506 ACACAATCAGTTGTACCTTCCATTG 59.758 40.000 0.00 0.00 46.49 2.82
5774 6809 4.015872 TCAGTTGTACCTTCCATTGTCC 57.984 45.455 0.00 0.00 0.00 4.02
5775 6810 2.742053 CAGTTGTACCTTCCATTGTCCG 59.258 50.000 0.00 0.00 0.00 4.79
5776 6811 2.081462 GTTGTACCTTCCATTGTCCGG 58.919 52.381 0.00 0.00 0.00 5.14
5777 6812 0.616371 TGTACCTTCCATTGTCCGGG 59.384 55.000 0.00 0.00 0.00 5.73
5786 6823 1.026718 CATTGTCCGGGGAGCTCAAC 61.027 60.000 17.19 7.62 0.00 3.18
5801 6838 2.349886 GCTCAACGCAGTATCTTTCCAG 59.650 50.000 0.00 0.00 45.00 3.86
5806 6843 1.134699 CGCAGTATCTTTCCAGCCTCA 60.135 52.381 0.00 0.00 0.00 3.86
5807 6844 2.484417 CGCAGTATCTTTCCAGCCTCAT 60.484 50.000 0.00 0.00 0.00 2.90
5853 6890 4.201950 GGAAACCCATTCACGATTCATCTG 60.202 45.833 0.00 0.00 39.98 2.90
5854 6891 2.292267 ACCCATTCACGATTCATCTGC 58.708 47.619 0.00 0.00 0.00 4.26
5855 6892 2.092753 ACCCATTCACGATTCATCTGCT 60.093 45.455 0.00 0.00 0.00 4.24
5856 6893 2.289820 CCCATTCACGATTCATCTGCTG 59.710 50.000 0.00 0.00 0.00 4.41
5857 6894 2.941064 CCATTCACGATTCATCTGCTGT 59.059 45.455 0.00 0.00 0.00 4.40
5858 6895 4.122046 CCATTCACGATTCATCTGCTGTA 58.878 43.478 0.00 0.00 0.00 2.74
5859 6896 4.571984 CCATTCACGATTCATCTGCTGTAA 59.428 41.667 0.00 0.00 0.00 2.41
5860 6897 5.496387 CATTCACGATTCATCTGCTGTAAC 58.504 41.667 0.00 0.00 0.00 2.50
5861 6898 3.179048 TCACGATTCATCTGCTGTAACG 58.821 45.455 0.00 0.00 0.00 3.18
5862 6899 1.927174 ACGATTCATCTGCTGTAACGC 59.073 47.619 0.00 0.00 0.00 4.84
5940 6977 7.384524 TTCATCTCCTTATCCATTGTCTCAT 57.615 36.000 0.00 0.00 0.00 2.90
5947 6984 6.064060 CCTTATCCATTGTCTCATTTAGGCA 58.936 40.000 0.00 0.00 38.31 4.75
5952 6989 6.057533 TCCATTGTCTCATTTAGGCACTATG 58.942 40.000 0.00 0.00 40.31 2.23
5961 6998 5.527214 TCATTTAGGCACTATGAATGGAACG 59.473 40.000 0.00 0.00 42.38 3.95
5964 7001 1.064060 GGCACTATGAATGGAACGTGC 59.936 52.381 0.00 0.00 44.97 5.34
6003 7040 7.442666 ACTTAACCAAAGAGAAGAAAGCTACTG 59.557 37.037 0.00 0.00 38.67 2.74
6009 7046 2.999355 GAGAAGAAAGCTACTGTGCCTG 59.001 50.000 0.00 0.00 0.00 4.85
6040 7077 2.157640 TTGGTCCAAATAGGCCATGG 57.842 50.000 7.63 7.63 41.29 3.66
6092 7129 1.212688 TGACCCCAATATCTGTGGCAG 59.787 52.381 0.00 0.00 34.56 4.85
6109 7146 2.648059 GCAGAATTAGCACACCCATCT 58.352 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.350780 GGCATCTTTTTCCTTGTGATGAGAAT 60.351 38.462 0.00 0.00 37.33 2.40
15 16 3.259064 CTGCATGGCATCTTTTTCCTTG 58.741 45.455 0.00 0.00 38.13 3.61
20 21 1.551883 GTCCCTGCATGGCATCTTTTT 59.448 47.619 2.62 0.00 38.13 1.94
38 39 3.041940 CACGGACCCTTGCACGTC 61.042 66.667 0.00 0.00 37.48 4.34
72 76 0.309302 CGTGATGTTTGGCCGTCAAA 59.691 50.000 0.00 0.00 42.50 2.69
76 80 3.361977 GGCGTGATGTTTGGCCGT 61.362 61.111 0.00 0.00 35.59 5.68
85 89 0.529337 CTCACTGGCTAGGCGTGATG 60.529 60.000 29.46 22.56 37.09 3.07
87 91 1.595993 GACTCACTGGCTAGGCGTGA 61.596 60.000 28.34 28.34 36.37 4.35
90 94 1.153745 GTGACTCACTGGCTAGGCG 60.154 63.158 12.19 9.02 0.00 5.52
105 109 7.770433 CCTTCTGTGTTAATAATGATGGAGTGA 59.230 37.037 0.00 0.00 0.00 3.41
106 110 7.012704 CCCTTCTGTGTTAATAATGATGGAGTG 59.987 40.741 8.26 0.00 0.00 3.51
107 111 7.056635 CCCTTCTGTGTTAATAATGATGGAGT 58.943 38.462 8.26 0.00 0.00 3.85
108 112 6.488006 CCCCTTCTGTGTTAATAATGATGGAG 59.512 42.308 8.26 0.00 0.00 3.86
109 113 6.364701 CCCCTTCTGTGTTAATAATGATGGA 58.635 40.000 8.26 0.00 0.00 3.41
110 114 5.010012 GCCCCTTCTGTGTTAATAATGATGG 59.990 44.000 0.00 0.00 0.00 3.51
111 115 5.277974 CGCCCCTTCTGTGTTAATAATGATG 60.278 44.000 0.00 0.00 0.00 3.07
112 116 4.821805 CGCCCCTTCTGTGTTAATAATGAT 59.178 41.667 0.00 0.00 0.00 2.45
113 117 4.196193 CGCCCCTTCTGTGTTAATAATGA 58.804 43.478 0.00 0.00 0.00 2.57
119 123 0.759959 TCACGCCCCTTCTGTGTTAA 59.240 50.000 0.00 0.00 35.20 2.01
120 124 0.981183 ATCACGCCCCTTCTGTGTTA 59.019 50.000 0.00 0.00 35.20 2.41
121 125 0.110486 AATCACGCCCCTTCTGTGTT 59.890 50.000 0.00 0.00 35.20 3.32
159 163 3.550678 GGGAGAGCGTGTTTAAATAGACG 59.449 47.826 11.08 11.08 34.93 4.18
162 166 4.504858 AGTGGGAGAGCGTGTTTAAATAG 58.495 43.478 0.00 0.00 0.00 1.73
196 208 1.964373 CACCCTGCCGTGTTACCAC 60.964 63.158 0.00 0.00 38.27 4.16
198 210 2.359478 CCACCCTGCCGTGTTACC 60.359 66.667 0.00 0.00 31.47 2.85
211 225 2.200170 GATTCGCAACACAGGCCACC 62.200 60.000 5.01 0.00 0.00 4.61
215 229 0.110056 CACTGATTCGCAACACAGGC 60.110 55.000 0.00 0.00 35.08 4.85
217 231 1.866601 TGACACTGATTCGCAACACAG 59.133 47.619 0.00 0.00 36.58 3.66
221 235 3.609103 ACTTTGACACTGATTCGCAAC 57.391 42.857 0.00 0.00 0.00 4.17
252 269 0.593773 CCGGAAAAAGCGTTGGTGTG 60.594 55.000 0.00 0.00 0.00 3.82
273 290 5.965922 AGGGTATACTGCAAAGCAAAATTC 58.034 37.500 2.25 0.00 38.41 2.17
276 303 5.076873 AGAAGGGTATACTGCAAAGCAAAA 58.923 37.500 2.25 0.00 38.41 2.44
285 312 2.683362 GGCAACAAGAAGGGTATACTGC 59.317 50.000 2.25 1.32 0.00 4.40
299 326 0.602562 GCATAGCTTGTGGGCAACAA 59.397 50.000 7.34 7.34 46.66 2.83
321 349 0.379669 CTCATGGAGCGAAACATGGC 59.620 55.000 11.85 0.00 43.49 4.40
347 375 1.006102 AAGGAGTCAAGGACGTGCG 60.006 57.895 0.00 0.00 37.67 5.34
352 380 2.544267 CGTTTCACAAGGAGTCAAGGAC 59.456 50.000 0.00 0.00 0.00 3.85
400 431 7.275183 ACTCAGACGGATCATCATCATTTTTA 58.725 34.615 0.00 0.00 0.00 1.52
406 437 3.701040 TGAACTCAGACGGATCATCATCA 59.299 43.478 0.00 0.00 0.00 3.07
407 438 4.313277 TGAACTCAGACGGATCATCATC 57.687 45.455 0.00 0.00 0.00 2.92
435 466 5.056480 TGCTTTTTCTGATGAGAAACTCGA 58.944 37.500 6.87 0.00 45.90 4.04
535 585 2.040359 GGGGAAGAGGGAGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
624 674 4.521062 CTCTCTTGGGCTCGGCGG 62.521 72.222 7.21 0.00 0.00 6.13
1007 1075 2.157085 CGGCGAAACAAAGACTTACTCC 59.843 50.000 0.00 0.00 0.00 3.85
1318 1391 0.392193 ACTGCTGCAGGTGATAGCAC 60.392 55.000 31.00 1.50 42.05 4.40
1322 1395 3.740631 CATAGACTGCTGCAGGTGATA 57.259 47.619 31.00 18.13 35.51 2.15
1369 1442 2.608752 CCACACTACACCAGTAACGACC 60.609 54.545 0.00 0.00 34.98 4.79
1390 1463 6.753180 TCATTCCTCTCTATTGTGATGCTAC 58.247 40.000 0.00 0.00 0.00 3.58
1407 1488 1.188863 GCTGCCAAACCATCATTCCT 58.811 50.000 0.00 0.00 0.00 3.36
1408 1489 1.134907 CAGCTGCCAAACCATCATTCC 60.135 52.381 0.00 0.00 0.00 3.01
1437 1518 1.203052 AGAATCAACATTTGCCAGCCG 59.797 47.619 0.00 0.00 0.00 5.52
1443 1524 6.441093 TCTATCCACAGAATCAACATTTGC 57.559 37.500 0.00 0.00 0.00 3.68
1486 1567 8.006027 CGTGTAGCATTGTATATCAAATGTCAG 58.994 37.037 10.41 0.00 39.62 3.51
1511 1594 2.271800 GTCTAGTCCAACATGAAGCCG 58.728 52.381 0.00 0.00 0.00 5.52
1598 1681 9.160496 GGCCTAAATTCAATCAGATATAGACTG 57.840 37.037 0.00 0.00 36.80 3.51
1601 1684 9.676861 CATGGCCTAAATTCAATCAGATATAGA 57.323 33.333 3.32 0.00 0.00 1.98
1605 1688 8.165397 TCATCATGGCCTAAATTCAATCAGATA 58.835 33.333 3.32 0.00 0.00 1.98
1640 1726 5.945784 TGAGCTACAGGATAATGCAGTTTTT 59.054 36.000 0.00 0.00 0.00 1.94
1669 1755 5.092554 TCGATGACCCAGCAAGTAATAAA 57.907 39.130 0.00 0.00 0.00 1.40
1738 1834 8.579850 AATTTCACAAATGAGCTACCTATGAA 57.420 30.769 0.00 0.00 35.83 2.57
1772 1868 8.460428 AGGCATACTCGCTAGTTATTACTTATC 58.540 37.037 0.00 0.00 37.15 1.75
1784 1880 5.127693 ACTATGAAAGGCATACTCGCTAG 57.872 43.478 0.00 0.00 38.44 3.42
1799 1895 7.441890 TGAAGTTAAATTTGCCGACTATGAA 57.558 32.000 0.00 0.00 0.00 2.57
1817 1913 6.039941 TGTCCGGTTAATCAAAACATGAAGTT 59.960 34.615 0.00 0.00 42.54 2.66
1831 1927 1.920351 AGGGTGGAATGTCCGGTTAAT 59.080 47.619 0.00 0.00 40.17 1.40
1836 1932 1.595093 GCAAAGGGTGGAATGTCCGG 61.595 60.000 0.00 0.00 40.17 5.14
1846 1942 2.353610 GGGGCTGATGCAAAGGGTG 61.354 63.158 0.00 0.00 41.91 4.61
1851 1947 1.116308 CATGATGGGGCTGATGCAAA 58.884 50.000 0.00 0.00 41.91 3.68
1852 1948 0.032912 ACATGATGGGGCTGATGCAA 60.033 50.000 0.00 0.00 41.91 4.08
1859 1955 5.387113 TCTACATTTTACATGATGGGGCT 57.613 39.130 0.00 0.00 0.00 5.19
1862 1958 8.964476 ACTACTTCTACATTTTACATGATGGG 57.036 34.615 0.00 0.00 0.00 4.00
1886 1982 5.005299 GTGCACTAAACAAAACCAACATGAC 59.995 40.000 10.32 0.00 0.00 3.06
1933 2029 0.116342 TCTTGTAGACCCCCTGCTCA 59.884 55.000 0.00 0.00 0.00 4.26
1961 2057 1.067635 GCATCAACCAACGAAGCCAAT 60.068 47.619 0.00 0.00 0.00 3.16
1970 2066 3.964909 ACTTTCGAAAGCATCAACCAAC 58.035 40.909 32.49 0.00 39.63 3.77
2051 2147 6.578944 ACTACCGACTTCACATGCAATAATA 58.421 36.000 0.00 0.00 0.00 0.98
2162 2268 3.428413 TGTAAAAGGACAGGGGTTAGC 57.572 47.619 0.00 0.00 0.00 3.09
2184 2290 3.706594 TCTGTAGTTAAGAGGGAGCCATG 59.293 47.826 0.00 0.00 0.00 3.66
2203 2322 6.094048 AGTGGATTCGGACAAAAATACATCTG 59.906 38.462 0.00 0.00 28.83 2.90
2353 2472 8.438676 AAAAGAACATTAATGGATAGGAGACG 57.561 34.615 19.37 0.00 0.00 4.18
2566 2686 9.574458 GAAGCTTAGAAGAACAGAAAAACTTTT 57.426 29.630 0.00 0.00 0.00 2.27
2784 2936 8.740123 TCTTTGTAGAACCAGTTCACAAAATA 57.260 30.769 24.56 18.51 42.51 1.40
3269 3422 3.665971 CCTTTGCCCCCTGCCTCT 61.666 66.667 0.00 0.00 40.16 3.69
3373 3526 9.670719 GAAGAGAGACCAAAACTGAAAATTAAG 57.329 33.333 0.00 0.00 0.00 1.85
3376 3529 6.607198 TGGAAGAGAGACCAAAACTGAAAATT 59.393 34.615 0.00 0.00 32.93 1.82
3516 3670 4.097892 GGAACCACTGAAAGAAAGAAGCAA 59.902 41.667 0.00 0.00 37.43 3.91
3547 3701 4.482386 CCAAGACATGTGAAAATGCAGAG 58.518 43.478 1.15 0.00 0.00 3.35
3548 3702 3.305539 GCCAAGACATGTGAAAATGCAGA 60.306 43.478 1.15 0.00 0.00 4.26
3568 3722 4.473444 TGATGATCAAGGGGAAATTAGCC 58.527 43.478 0.00 0.00 0.00 3.93
3577 3731 6.183347 AGAAGTTTAACTGATGATCAAGGGG 58.817 40.000 0.00 0.00 0.00 4.79
3594 3748 5.221244 CCCAAGGAATCGTTTGAAGAAGTTT 60.221 40.000 0.00 0.00 0.00 2.66
3609 3763 0.922626 GGAAGCCTCTCCCAAGGAAT 59.077 55.000 0.00 0.00 38.87 3.01
3696 3850 9.237846 GTATAGAAAACAAATCTAGCATTTGCC 57.762 33.333 19.18 11.11 41.36 4.52
3858 4012 9.927081 AACTCCATAGACCAAATCAATTATCTT 57.073 29.630 0.00 0.00 0.00 2.40
3886 4040 8.465999 AGGCATAATTCATTCACATTTCGTAAA 58.534 29.630 0.00 0.00 0.00 2.01
3889 4043 6.455360 AGGCATAATTCATTCACATTTCGT 57.545 33.333 0.00 0.00 0.00 3.85
3890 4044 6.857964 GGTAGGCATAATTCATTCACATTTCG 59.142 38.462 0.00 0.00 0.00 3.46
3894 4049 5.079643 GGGGTAGGCATAATTCATTCACAT 58.920 41.667 0.00 0.00 0.00 3.21
3908 4063 0.252513 TAAGACTGCTGGGGTAGGCA 60.253 55.000 0.00 0.00 35.55 4.75
3909 4064 0.466124 CTAAGACTGCTGGGGTAGGC 59.534 60.000 0.00 0.00 33.15 3.93
3910 4065 1.757699 GTCTAAGACTGCTGGGGTAGG 59.242 57.143 0.00 0.00 0.00 3.18
3911 4066 2.741145 AGTCTAAGACTGCTGGGGTAG 58.259 52.381 0.00 0.00 41.76 3.18
3913 4068 1.903183 GAAGTCTAAGACTGCTGGGGT 59.097 52.381 0.00 0.00 42.59 4.95
3914 4069 2.183679 AGAAGTCTAAGACTGCTGGGG 58.816 52.381 0.00 0.00 45.95 4.96
3919 4074 3.257127 ACAGGTCAGAAGTCTAAGACTGC 59.743 47.826 0.00 0.00 42.59 4.40
3920 4075 5.461032 AACAGGTCAGAAGTCTAAGACTG 57.539 43.478 0.00 0.00 42.59 3.51
3921 4076 8.908903 CATATAACAGGTCAGAAGTCTAAGACT 58.091 37.037 0.00 0.00 45.64 3.24
3922 4077 8.904834 TCATATAACAGGTCAGAAGTCTAAGAC 58.095 37.037 0.00 0.00 0.00 3.01
3923 4078 9.647918 ATCATATAACAGGTCAGAAGTCTAAGA 57.352 33.333 0.00 0.00 0.00 2.10
3926 4081 9.421399 TCAATCATATAACAGGTCAGAAGTCTA 57.579 33.333 0.00 0.00 0.00 2.59
3927 4082 8.311395 TCAATCATATAACAGGTCAGAAGTCT 57.689 34.615 0.00 0.00 0.00 3.24
3928 4083 9.553064 AATCAATCATATAACAGGTCAGAAGTC 57.447 33.333 0.00 0.00 0.00 3.01
3929 4084 9.553064 GAATCAATCATATAACAGGTCAGAAGT 57.447 33.333 0.00 0.00 0.00 3.01
3930 4085 8.997323 GGAATCAATCATATAACAGGTCAGAAG 58.003 37.037 0.00 0.00 0.00 2.85
3931 4086 8.493607 TGGAATCAATCATATAACAGGTCAGAA 58.506 33.333 0.00 0.00 0.00 3.02
3932 4087 8.033178 TGGAATCAATCATATAACAGGTCAGA 57.967 34.615 0.00 0.00 0.00 3.27
3933 4088 8.859236 ATGGAATCAATCATATAACAGGTCAG 57.141 34.615 0.00 0.00 0.00 3.51
3987 4142 1.202698 AGCCTAATCCCTTGCTAAGCG 60.203 52.381 0.00 0.00 30.97 4.68
4018 4173 6.706270 ACATCGACCATCAATCATACCTTAAC 59.294 38.462 0.00 0.00 0.00 2.01
4027 4182 3.893326 AGACACATCGACCATCAATCA 57.107 42.857 0.00 0.00 0.00 2.57
4038 4193 9.914131 CATATATATATACCCCAAGACACATCG 57.086 37.037 4.54 0.00 0.00 3.84
4626 5088 4.122046 AGATTTTCTGCAGGTGTTTTTGC 58.878 39.130 15.13 0.00 40.67 3.68
4636 5098 7.046652 TCTCCAGATCTAAAGATTTTCTGCAG 58.953 38.462 7.63 7.63 34.37 4.41
4735 5197 5.108385 AGCACCAGAAGAAACAAAATACG 57.892 39.130 0.00 0.00 0.00 3.06
4777 5332 0.189327 ATGATCAAGGAATGGCCCCC 59.811 55.000 0.00 0.00 37.37 5.40
4800 5355 3.245984 TGAGGATTTGTAGACTGGAGGGA 60.246 47.826 0.00 0.00 0.00 4.20
4926 5504 7.305474 ACACATATGATTTTCGAGTTCCAAAC 58.695 34.615 10.38 0.00 0.00 2.93
4950 5528 3.127721 GTCAAGAAAATGCCCAGAGCTAC 59.872 47.826 0.00 0.00 44.23 3.58
5022 5647 1.565759 CAGGGAGAAATGATGTGGGGA 59.434 52.381 0.00 0.00 0.00 4.81
5024 5649 2.372264 CACAGGGAGAAATGATGTGGG 58.628 52.381 0.00 0.00 38.04 4.61
5037 5662 4.264253 CAAGATTAGTCAATGCACAGGGA 58.736 43.478 0.00 0.00 0.00 4.20
5038 5663 3.379372 CCAAGATTAGTCAATGCACAGGG 59.621 47.826 0.00 0.00 0.00 4.45
5041 5666 8.523915 AAATATCCAAGATTAGTCAATGCACA 57.476 30.769 0.00 0.00 0.00 4.57
5140 5766 4.315803 CTCAAAAGGAGTACAATGACGGT 58.684 43.478 0.00 0.00 38.90 4.83
5144 5770 4.041567 TCCAGCTCAAAAGGAGTACAATGA 59.958 41.667 0.00 0.00 45.88 2.57
5149 5775 5.966742 AAATTCCAGCTCAAAAGGAGTAC 57.033 39.130 0.00 0.00 45.88 2.73
5215 5841 0.600557 ACGACAGTCAAGGAGAGCAG 59.399 55.000 0.41 0.00 0.00 4.24
5232 5858 7.907045 GCAAGCCATCATAATCATAATTAGACG 59.093 37.037 0.00 0.00 31.02 4.18
5398 6029 2.158234 TCAGGCCCCATGGTTTAGTTTT 60.158 45.455 11.73 0.00 0.00 2.43
5400 6031 1.005924 CTCAGGCCCCATGGTTTAGTT 59.994 52.381 11.73 0.00 0.00 2.24
5401 6032 0.625849 CTCAGGCCCCATGGTTTAGT 59.374 55.000 11.73 0.00 0.00 2.24
5402 6033 0.753111 GCTCAGGCCCCATGGTTTAG 60.753 60.000 11.73 0.45 0.00 1.85
5403 6034 1.306296 GCTCAGGCCCCATGGTTTA 59.694 57.895 11.73 0.00 0.00 2.01
5404 6035 2.037847 GCTCAGGCCCCATGGTTT 59.962 61.111 11.73 0.00 0.00 3.27
5405 6036 4.431131 CGCTCAGGCCCCATGGTT 62.431 66.667 11.73 0.00 34.44 3.67
5407 6038 4.864334 GACGCTCAGGCCCCATGG 62.864 72.222 4.14 4.14 34.44 3.66
5408 6039 4.864334 GGACGCTCAGGCCCCATG 62.864 72.222 0.00 0.00 44.51 3.66
5414 6045 2.573609 AATACACCGGACGCTCAGGC 62.574 60.000 9.46 0.00 34.97 4.85
5415 6046 0.527817 GAATACACCGGACGCTCAGG 60.528 60.000 9.46 3.43 37.75 3.86
5416 6047 0.866061 CGAATACACCGGACGCTCAG 60.866 60.000 9.46 0.00 0.00 3.35
5417 6048 1.138036 CGAATACACCGGACGCTCA 59.862 57.895 9.46 0.00 0.00 4.26
5419 6050 0.030369 GATCGAATACACCGGACGCT 59.970 55.000 9.46 0.00 0.00 5.07
5420 6051 0.030369 AGATCGAATACACCGGACGC 59.970 55.000 9.46 0.00 0.00 5.19
5421 6052 1.599667 CCAGATCGAATACACCGGACG 60.600 57.143 9.46 0.00 0.00 4.79
5423 6054 2.061509 TCCAGATCGAATACACCGGA 57.938 50.000 9.46 0.00 0.00 5.14
5424 6055 2.882927 TTCCAGATCGAATACACCGG 57.117 50.000 0.00 0.00 0.00 5.28
5515 6154 1.223187 CCGTTTTAAGCACGTCTGGT 58.777 50.000 8.08 0.00 35.81 4.00
5550 6190 3.560896 CCTTTGGACGGTAAACTTCGAAA 59.439 43.478 0.00 0.00 0.00 3.46
5563 6528 1.815421 CGATGCCCTCCTTTGGACG 60.815 63.158 0.00 0.00 0.00 4.79
5564 6529 0.181350 ATCGATGCCCTCCTTTGGAC 59.819 55.000 0.00 0.00 0.00 4.02
5567 6532 3.692257 ATAGATCGATGCCCTCCTTTG 57.308 47.619 0.54 0.00 0.00 2.77
5573 6538 3.191581 CGTTCTGTATAGATCGATGCCCT 59.808 47.826 12.99 0.00 44.80 5.19
5575 6540 4.421033 TCGTTCTGTATAGATCGATGCC 57.579 45.455 15.96 0.00 45.29 4.40
5579 6544 5.494632 TTTGCTCGTTCTGTATAGATCGA 57.505 39.130 18.04 18.04 46.93 3.59
5580 6545 4.677378 CCTTTGCTCGTTCTGTATAGATCG 59.323 45.833 12.29 12.29 43.88 3.69
5581 6546 5.593010 ACCTTTGCTCGTTCTGTATAGATC 58.407 41.667 0.00 0.00 31.81 2.75
5610 6575 4.210120 CACGCAGATAAATAGAGAAGCCAC 59.790 45.833 0.00 0.00 0.00 5.01
5615 6580 4.141937 ACCAGCACGCAGATAAATAGAGAA 60.142 41.667 0.00 0.00 0.00 2.87
5621 6586 2.434336 TCCTACCAGCACGCAGATAAAT 59.566 45.455 0.00 0.00 0.00 1.40
5628 6593 1.888018 GTACTCCTACCAGCACGCA 59.112 57.895 0.00 0.00 0.00 5.24
5639 6604 2.809299 GCCCTGTTTTTGACGTACTCCT 60.809 50.000 0.00 0.00 0.00 3.69
5640 6605 1.534163 GCCCTGTTTTTGACGTACTCC 59.466 52.381 0.00 0.00 0.00 3.85
5641 6606 2.032290 GTGCCCTGTTTTTGACGTACTC 60.032 50.000 0.00 0.00 0.00 2.59
5642 6607 1.944709 GTGCCCTGTTTTTGACGTACT 59.055 47.619 0.00 0.00 0.00 2.73
5643 6608 1.002142 GGTGCCCTGTTTTTGACGTAC 60.002 52.381 0.00 0.00 0.00 3.67
5644 6609 1.310904 GGTGCCCTGTTTTTGACGTA 58.689 50.000 0.00 0.00 0.00 3.57
5645 6610 1.720694 CGGTGCCCTGTTTTTGACGT 61.721 55.000 0.00 0.00 0.00 4.34
5654 6619 1.125711 AGAAACTACCGGTGCCCTGT 61.126 55.000 19.93 5.27 0.00 4.00
5655 6620 0.899720 TAGAAACTACCGGTGCCCTG 59.100 55.000 19.93 4.60 0.00 4.45
5657 6622 1.406477 CCTTAGAAACTACCGGTGCCC 60.406 57.143 19.93 1.56 0.00 5.36
5668 6633 6.980051 TTCTATTCGCCTTTCCTTAGAAAC 57.020 37.500 0.00 0.00 37.07 2.78
5674 6639 8.117813 TGTTTTATTTCTATTCGCCTTTCCTT 57.882 30.769 0.00 0.00 0.00 3.36
5675 6640 7.610305 TCTGTTTTATTTCTATTCGCCTTTCCT 59.390 33.333 0.00 0.00 0.00 3.36
5687 6652 7.500227 CCTGATCTGGCATCTGTTTTATTTCTA 59.500 37.037 5.61 0.00 0.00 2.10
5704 6739 8.627208 AATACATAATTTAGTGCCTGATCTGG 57.373 34.615 14.07 14.07 0.00 3.86
5721 6756 5.113383 ACTTCATCAACGGCGAATACATAA 58.887 37.500 16.62 0.00 0.00 1.90
5724 6759 2.967362 ACTTCATCAACGGCGAATACA 58.033 42.857 16.62 0.00 0.00 2.29
5726 6761 5.688621 GTGTATACTTCATCAACGGCGAATA 59.311 40.000 16.62 0.00 0.00 1.75
5753 6788 3.556213 CGGACAATGGAAGGTACAACTGA 60.556 47.826 0.00 0.00 0.00 3.41
5757 6792 1.003812 CCCGGACAATGGAAGGTACAA 59.996 52.381 0.73 0.00 0.00 2.41
5759 6794 0.107361 CCCCGGACAATGGAAGGTAC 60.107 60.000 0.73 0.00 0.00 3.34
5760 6795 0.252789 TCCCCGGACAATGGAAGGTA 60.253 55.000 0.73 0.00 0.00 3.08
5761 6796 1.540367 TCCCCGGACAATGGAAGGT 60.540 57.895 0.73 0.00 0.00 3.50
5762 6797 1.224592 CTCCCCGGACAATGGAAGG 59.775 63.158 0.73 0.00 0.00 3.46
5763 6798 1.452108 GCTCCCCGGACAATGGAAG 60.452 63.158 0.73 0.00 0.00 3.46
5765 6800 2.285368 AGCTCCCCGGACAATGGA 60.285 61.111 0.73 0.00 0.00 3.41
5767 6802 1.026718 GTTGAGCTCCCCGGACAATG 61.027 60.000 12.15 0.00 0.00 2.82
5768 6803 1.299976 GTTGAGCTCCCCGGACAAT 59.700 57.895 12.15 0.00 0.00 2.71
5770 6805 3.691342 CGTTGAGCTCCCCGGACA 61.691 66.667 12.15 0.00 0.00 4.02
5786 6823 1.134699 TGAGGCTGGAAAGATACTGCG 60.135 52.381 0.00 0.00 33.07 5.18
5801 6838 1.141019 CACAATGCTGGCATGAGGC 59.859 57.895 8.91 0.00 43.74 4.70
5806 6843 3.259876 AGTCATTTTCACAATGCTGGCAT 59.740 39.130 1.86 1.86 38.46 4.40
5807 6844 2.629137 AGTCATTTTCACAATGCTGGCA 59.371 40.909 0.00 0.00 0.00 4.92
5848 6885 2.100031 TGGCGCGTTACAGCAGATG 61.100 57.895 8.43 0.00 36.85 2.90
5853 6890 3.788766 CTGGTGGCGCGTTACAGC 61.789 66.667 18.13 18.13 35.77 4.40
5854 6891 1.897398 GAACTGGTGGCGCGTTACAG 61.897 60.000 8.43 13.73 35.40 2.74
5855 6892 1.957186 GAACTGGTGGCGCGTTACA 60.957 57.895 8.43 1.47 0.00 2.41
5856 6893 2.674084 GGAACTGGTGGCGCGTTAC 61.674 63.158 8.43 7.19 0.00 2.50
5857 6894 2.357760 GGAACTGGTGGCGCGTTA 60.358 61.111 8.43 0.00 0.00 3.18
5858 6895 3.767630 AAGGAACTGGTGGCGCGTT 62.768 57.895 8.43 0.00 40.86 4.84
5859 6896 4.250305 AAGGAACTGGTGGCGCGT 62.250 61.111 8.43 0.00 40.86 6.01
5860 6897 3.726517 CAAGGAACTGGTGGCGCG 61.727 66.667 0.00 0.00 40.86 6.86
5861 6898 4.043200 GCAAGGAACTGGTGGCGC 62.043 66.667 0.00 0.00 40.86 6.53
5862 6899 2.463589 TAGGCAAGGAACTGGTGGCG 62.464 60.000 0.00 0.00 44.92 5.69
5940 6977 4.634004 CACGTTCCATTCATAGTGCCTAAA 59.366 41.667 0.00 0.00 0.00 1.85
5947 6984 2.356135 GTGGCACGTTCCATTCATAGT 58.644 47.619 10.90 0.00 38.57 2.12
5952 6989 2.867472 CCGTGGCACGTTCCATTC 59.133 61.111 34.74 0.00 40.58 2.67
5964 7001 0.872388 GTTAAGTTCAGGTGCCGTGG 59.128 55.000 0.00 0.00 0.00 4.94
6003 7040 2.288395 CCAATCCAGTTTGTTCAGGCAC 60.288 50.000 0.00 0.00 0.00 5.01
6040 7077 5.733373 GCCGATGTGATTTTCTTTGGTATCC 60.733 44.000 0.00 0.00 0.00 2.59
6092 7129 3.609853 TGACAGATGGGTGTGCTAATTC 58.390 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.