Multiple sequence alignment - TraesCS1D01G214700

Loading Multiple Alignment...

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 TraesCS1D01G214700 chr1D 100.000 5027 0 0 1 5027 299925840 299930866 0.000000e+00 9284.0
1 TraesCS1D01G214700 chr1B 92.105 2584 147 21 2452 5026 404513715 404516250 0.000000e+00 3589.0
2 TraesCS1D01G214700 chr1B 89.668 1655 71 42 769 2359 404512091 404513709 0.000000e+00 2017.0
3 TraesCS1D01G214700 chr1B 95.370 216 10 0 324 539 404509904 404510119 1.340000e-90 344.0
4 TraesCS1D01G214700 chr1B 94.836 213 11 0 324 536 404509306 404509518 2.900000e-87 333.0
5 TraesCS1D01G214700 chr1B 88.446 251 8 10 538 771 404511786 404512032 2.960000e-72 283.0
6 TraesCS1D01G214700 chr1B 89.674 184 8 5 80 258 404507265 404507442 1.820000e-54 224.0
7 TraesCS1D01G214700 chr1B 94.059 101 3 1 538 638 404511405 404511502 3.140000e-32 150.0
8 TraesCS1D01G214700 chr1B 93.220 59 4 0 275 333 404508847 404508905 2.490000e-13 87.9
9 TraesCS1D01G214700 chr1A 92.842 1844 82 21 2452 4261 374215701 374217528 0.000000e+00 2628.0
10 TraesCS1D01G214700 chr1A 84.350 2409 126 90 146 2369 374213360 374215702 0.000000e+00 2128.0
11 TraesCS1D01G214700 chr1A 88.949 742 53 10 4288 5027 374217583 374218297 0.000000e+00 889.0
12 TraesCS1D01G214700 chr1A 85.621 153 18 4 80 229 580835621 580835772 1.870000e-34 158.0
13 TraesCS1D01G214700 chr7A 85.542 166 20 4 80 244 303959763 303959925 2.410000e-38 171.0
14 TraesCS1D01G214700 chr2D 85.350 157 19 4 1150 1304 524144890 524145044 5.210000e-35 159.0
15 TraesCS1D01G214700 chr2A 84.713 157 20 4 1150 1304 669841286 669841440 2.420000e-33 154.0
16 TraesCS1D01G214700 chr2A 90.588 85 7 1 2371 2455 768095513 768095430 1.480000e-20 111.0
17 TraesCS1D01G214700 chr2B 84.076 157 21 4 1150 1304 619749392 619749546 1.130000e-31 148.0
18 TraesCS1D01G214700 chr7B 88.525 122 13 1 119 240 267334066 267333946 4.060000e-31 147.0
19 TraesCS1D01G214700 chr3B 94.118 85 4 1 2371 2455 284678925 284678842 1.470000e-25 128.0
20 TraesCS1D01G214700 chr5D 92.135 89 4 3 2368 2455 40719349 40719435 6.830000e-24 122.0
21 TraesCS1D01G214700 chr3D 92.941 85 5 1 2371 2455 206978514 206978597 6.830000e-24 122.0
22 TraesCS1D01G214700 chr3A 92.941 85 4 2 2371 2455 265542789 265542707 6.830000e-24 122.0
23 TraesCS1D01G214700 chr5B 92.857 84 5 1 2371 2454 322144334 322144416 2.460000e-23 121.0
24 TraesCS1D01G214700 chr6A 90.805 87 7 1 2368 2454 35578017 35578102 1.140000e-21 115.0
25 TraesCS1D01G214700 chr4A 91.667 84 6 1 2371 2454 737710847 737710765 1.140000e-21 115.0
26 TraesCS1D01G214700 chr6B 89.535 86 8 1 2367 2452 398012672 398012756 1.910000e-19 108.0


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 TraesCS1D01G214700 chr1D 299925840 299930866 5026 False 9284.000000 9284 100.000000 1 5027 1 chr1D.!!$F1 5026
1 TraesCS1D01G214700 chr1B 404507265 404516250 8985 False 878.487500 3589 92.172250 80 5026 8 chr1B.!!$F1 4946
2 TraesCS1D01G214700 chr1A 374213360 374218297 4937 False 1881.666667 2628 88.713667 146 5027 3 chr1A.!!$F2 4881

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
617 4698 0.034896 ACTTTAGCAGTCCACCACGG 59.965 55.0 0.00 0.0 0.00 4.94 F
1728 5977 0.391263 TGCATGCTCAGTCTGCTCAG 60.391 55.0 20.33 0.0 36.84 3.35 F
2381 6690 0.035739 GGTTTGTGCTCCCTCCGTAA 59.964 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 6226 0.804989 GGCGGAGTCATGGTTCAAAG 59.195 55.0 0.0 0.0 0.00 2.77 R
2959 7304 0.030235 CACCGTCAGAGTTGTCACGA 59.970 55.0 0.0 0.0 34.06 4.35 R
4236 8602 0.114364 ACAACAGTTCCCATTCCCCC 59.886 55.0 0.0 0.0 0.00 5.40 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 9.944376 ACTTATGATATTATGCACTACGGATTT 57.056 29.630 0.00 0.00 0.00 2.17
74 75 8.863872 ATTAGTATATGCTTCCCATTACAACC 57.136 34.615 0.00 0.00 35.34 3.77
75 76 6.260700 AGTATATGCTTCCCATTACAACCA 57.739 37.500 0.00 0.00 35.34 3.67
76 77 6.668645 AGTATATGCTTCCCATTACAACCAA 58.331 36.000 0.00 0.00 35.34 3.67
77 78 5.852282 ATATGCTTCCCATTACAACCAAC 57.148 39.130 0.00 0.00 35.34 3.77
78 79 2.243810 TGCTTCCCATTACAACCAACC 58.756 47.619 0.00 0.00 0.00 3.77
79 80 2.158385 TGCTTCCCATTACAACCAACCT 60.158 45.455 0.00 0.00 0.00 3.50
80 81 3.074687 TGCTTCCCATTACAACCAACCTA 59.925 43.478 0.00 0.00 0.00 3.08
81 82 4.083565 GCTTCCCATTACAACCAACCTAA 58.916 43.478 0.00 0.00 0.00 2.69
82 83 4.082408 GCTTCCCATTACAACCAACCTAAC 60.082 45.833 0.00 0.00 0.00 2.34
83 84 4.726035 TCCCATTACAACCAACCTAACA 57.274 40.909 0.00 0.00 0.00 2.41
84 85 5.063017 TCCCATTACAACCAACCTAACAA 57.937 39.130 0.00 0.00 0.00 2.83
85 86 5.455872 TCCCATTACAACCAACCTAACAAA 58.544 37.500 0.00 0.00 0.00 2.83
86 87 6.078664 TCCCATTACAACCAACCTAACAAAT 58.921 36.000 0.00 0.00 0.00 2.32
87 88 6.209788 TCCCATTACAACCAACCTAACAAATC 59.790 38.462 0.00 0.00 0.00 2.17
88 89 6.210584 CCCATTACAACCAACCTAACAAATCT 59.789 38.462 0.00 0.00 0.00 2.40
96 97 9.173021 CAACCAACCTAACAAATCTATATGACA 57.827 33.333 0.00 0.00 0.00 3.58
298 1706 2.866085 CTAGACCAGCCACTGCCAGC 62.866 65.000 0.00 0.00 38.69 4.85
330 2746 3.819337 GGAAGAGTTACTTTCAACACCCC 59.181 47.826 8.62 0.00 39.13 4.95
358 2774 1.994779 GCAATCAATCCCAGCGTTTTG 59.005 47.619 0.00 0.00 0.00 2.44
395 2811 1.833049 ATCCGAGTCGTCCATCCCC 60.833 63.158 12.31 0.00 0.00 4.81
399 2815 1.783031 CGAGTCGTCCATCCCCTACG 61.783 65.000 3.82 0.00 37.96 3.51
400 2816 1.453762 GAGTCGTCCATCCCCTACGG 61.454 65.000 0.00 0.00 37.24 4.02
406 2822 2.768344 CATCCCCTACGGCCACCT 60.768 66.667 2.24 0.00 0.00 4.00
408 2824 3.023045 ATCCCCTACGGCCACCTCT 62.023 63.158 2.24 0.00 0.00 3.69
463 2879 2.143925 CTTCACGTTTTCTCCCCTGTC 58.856 52.381 0.00 0.00 0.00 3.51
617 4698 0.034896 ACTTTAGCAGTCCACCACGG 59.965 55.000 0.00 0.00 0.00 4.94
767 4874 3.202706 GAGAATTGCGACCGGGCC 61.203 66.667 6.32 0.00 0.00 5.80
889 5060 8.182881 GTCTACTCTAGAAGCATTAAAGACGAA 58.817 37.037 0.00 0.00 36.40 3.85
908 5079 0.970937 AGGAATTCCCGAGACGAGCA 60.971 55.000 21.22 0.00 40.87 4.26
1345 5553 4.767892 CCCTCCCTCCCTTGGCCT 62.768 72.222 3.32 0.00 0.00 5.19
1421 5630 2.680913 GCTCCATTGCTGACGCGTT 61.681 57.895 15.53 0.00 39.65 4.84
1436 5645 6.369326 TGACGCGTTGCAATTAATTTTTAG 57.631 33.333 15.53 0.00 0.00 1.85
1439 5648 7.751348 TGACGCGTTGCAATTAATTTTTAGTAT 59.249 29.630 15.53 0.00 0.00 2.12
1440 5649 8.455598 ACGCGTTGCAATTAATTTTTAGTATT 57.544 26.923 5.58 0.00 0.00 1.89
1441 5650 9.557338 ACGCGTTGCAATTAATTTTTAGTATTA 57.443 25.926 5.58 0.00 0.00 0.98
1506 5716 3.769536 CAAGCGTTTCTTTCCTTGTGTT 58.230 40.909 0.00 0.00 31.27 3.32
1508 5718 2.099098 AGCGTTTCTTTCCTTGTGTTGG 59.901 45.455 0.00 0.00 0.00 3.77
1509 5719 2.159296 GCGTTTCTTTCCTTGTGTTGGT 60.159 45.455 0.00 0.00 0.00 3.67
1510 5720 3.434637 CGTTTCTTTCCTTGTGTTGGTG 58.565 45.455 0.00 0.00 0.00 4.17
1511 5721 3.733684 CGTTTCTTTCCTTGTGTTGGTGG 60.734 47.826 0.00 0.00 0.00 4.61
1512 5722 2.065899 TCTTTCCTTGTGTTGGTGGG 57.934 50.000 0.00 0.00 0.00 4.61
1513 5723 1.039856 CTTTCCTTGTGTTGGTGGGG 58.960 55.000 0.00 0.00 0.00 4.96
1514 5724 0.631753 TTTCCTTGTGTTGGTGGGGA 59.368 50.000 0.00 0.00 0.00 4.81
1617 5836 4.177026 GGCACCTGCAGATACGATTATAG 58.823 47.826 17.39 0.00 44.36 1.31
1618 5837 4.322049 GGCACCTGCAGATACGATTATAGT 60.322 45.833 17.39 0.00 44.36 2.12
1619 5838 5.105877 GGCACCTGCAGATACGATTATAGTA 60.106 44.000 17.39 0.00 44.36 1.82
1620 5839 5.800941 GCACCTGCAGATACGATTATAGTAC 59.199 44.000 17.39 0.00 41.59 2.73
1621 5840 6.349445 GCACCTGCAGATACGATTATAGTACT 60.349 42.308 17.39 0.00 41.59 2.73
1622 5841 7.148289 GCACCTGCAGATACGATTATAGTACTA 60.148 40.741 17.39 4.77 41.59 1.82
1695 5943 1.145803 GTCTCCGTGCTGTTTACCAC 58.854 55.000 0.00 0.00 0.00 4.16
1697 5945 1.139256 TCTCCGTGCTGTTTACCACAA 59.861 47.619 0.00 0.00 33.87 3.33
1726 5975 0.391395 AGTGCATGCTCAGTCTGCTC 60.391 55.000 20.33 0.00 36.84 4.26
1727 5976 0.672711 GTGCATGCTCAGTCTGCTCA 60.673 55.000 20.33 0.00 36.84 4.26
1728 5977 0.391263 TGCATGCTCAGTCTGCTCAG 60.391 55.000 20.33 0.00 36.84 3.35
1734 5983 2.029560 TGCTCAGTCTGCTCAGTAAGTG 60.030 50.000 0.00 0.00 0.00 3.16
1745 5994 5.368145 TGCTCAGTAAGTGAATGTTCTTGT 58.632 37.500 0.00 0.00 33.60 3.16
1747 5996 5.466728 GCTCAGTAAGTGAATGTTCTTGTCA 59.533 40.000 0.00 0.00 33.60 3.58
1748 5997 6.148480 GCTCAGTAAGTGAATGTTCTTGTCAT 59.852 38.462 0.00 0.00 33.60 3.06
1749 5998 7.308229 GCTCAGTAAGTGAATGTTCTTGTCATT 60.308 37.037 0.00 0.00 38.08 2.57
1750 5999 9.208022 CTCAGTAAGTGAATGTTCTTGTCATTA 57.792 33.333 0.00 0.00 35.94 1.90
1751 6000 9.208022 TCAGTAAGTGAATGTTCTTGTCATTAG 57.792 33.333 0.00 0.00 35.94 1.73
1752 6001 8.993121 CAGTAAGTGAATGTTCTTGTCATTAGT 58.007 33.333 0.00 0.00 35.94 2.24
1753 6002 9.561069 AGTAAGTGAATGTTCTTGTCATTAGTT 57.439 29.630 0.00 0.00 35.94 2.24
1754 6003 9.813080 GTAAGTGAATGTTCTTGTCATTAGTTC 57.187 33.333 0.00 0.00 35.94 3.01
1755 6004 8.682936 AAGTGAATGTTCTTGTCATTAGTTCT 57.317 30.769 0.00 0.00 35.94 3.01
1756 6005 8.682936 AGTGAATGTTCTTGTCATTAGTTCTT 57.317 30.769 0.00 0.00 35.94 2.52
1757 6006 9.125026 AGTGAATGTTCTTGTCATTAGTTCTTT 57.875 29.630 0.00 0.00 35.94 2.52
1768 6040 9.581289 TTGTCATTAGTTCTTTATTTCCCTCAA 57.419 29.630 0.00 0.00 0.00 3.02
1769 6041 9.231297 TGTCATTAGTTCTTTATTTCCCTCAAG 57.769 33.333 0.00 0.00 0.00 3.02
1783 6055 5.708736 TCCCTCAAGGAATATGCTGTTTA 57.291 39.130 0.00 0.00 43.78 2.01
1784 6056 6.073447 TCCCTCAAGGAATATGCTGTTTAA 57.927 37.500 0.00 0.00 43.78 1.52
1785 6057 5.885912 TCCCTCAAGGAATATGCTGTTTAAC 59.114 40.000 0.00 0.00 43.78 2.01
1806 6078 5.425577 ACGTGAGTACATGCTACTATGAG 57.574 43.478 7.63 4.32 46.88 2.90
1807 6079 4.276183 ACGTGAGTACATGCTACTATGAGG 59.724 45.833 7.63 4.89 46.88 3.86
1808 6080 4.276183 CGTGAGTACATGCTACTATGAGGT 59.724 45.833 7.63 0.00 0.00 3.85
1809 6081 5.221067 CGTGAGTACATGCTACTATGAGGTT 60.221 44.000 7.63 0.00 0.00 3.50
1810 6082 6.574350 GTGAGTACATGCTACTATGAGGTTT 58.426 40.000 7.63 0.00 0.00 3.27
1813 6085 6.574350 AGTACATGCTACTATGAGGTTTGAC 58.426 40.000 0.00 0.00 0.00 3.18
1849 6124 6.957631 TGGTGGCTTCTCTTATAAGAAATCA 58.042 36.000 15.85 7.77 34.95 2.57
1861 6136 9.231297 TCTTATAAGAAATCAGTTGGTTTCCAG 57.769 33.333 12.87 4.20 35.46 3.86
1887 6162 2.106684 AGTGGTCAACTTTCCTTCCTCC 59.893 50.000 0.00 0.00 34.57 4.30
1900 6175 9.467796 ACTTTCCTTCCTCCTAATAAAATTGAG 57.532 33.333 0.00 0.00 0.00 3.02
1902 6177 8.807948 TTCCTTCCTCCTAATAAAATTGAGTG 57.192 34.615 0.00 0.00 0.00 3.51
1938 6213 3.897239 TGGATATGGTCAAAGCCGAAAT 58.103 40.909 0.00 0.00 0.00 2.17
1939 6214 3.631686 TGGATATGGTCAAAGCCGAAATG 59.368 43.478 0.00 0.00 0.00 2.32
1940 6215 3.882888 GGATATGGTCAAAGCCGAAATGA 59.117 43.478 0.00 0.00 0.00 2.57
1941 6216 4.520492 GGATATGGTCAAAGCCGAAATGAT 59.480 41.667 0.00 0.00 0.00 2.45
1943 6218 3.574284 TGGTCAAAGCCGAAATGATTG 57.426 42.857 0.00 0.00 0.00 2.67
1945 6220 2.231235 GGTCAAAGCCGAAATGATTGGT 59.769 45.455 0.00 0.00 0.00 3.67
1946 6221 3.306019 GGTCAAAGCCGAAATGATTGGTT 60.306 43.478 0.00 0.00 0.00 3.67
1947 6222 4.306600 GTCAAAGCCGAAATGATTGGTTT 58.693 39.130 0.00 0.00 0.00 3.27
1948 6223 4.150451 GTCAAAGCCGAAATGATTGGTTTG 59.850 41.667 10.54 10.54 0.00 2.93
1949 6224 4.038522 TCAAAGCCGAAATGATTGGTTTGA 59.961 37.500 13.73 13.73 33.99 2.69
1950 6225 4.599047 AAGCCGAAATGATTGGTTTGAA 57.401 36.364 0.00 0.00 0.00 2.69
1951 6226 3.913089 AGCCGAAATGATTGGTTTGAAC 58.087 40.909 0.00 0.00 0.00 3.18
2005 6290 7.049026 GCTAATTCGTTTATAAAATGCAACGC 58.951 34.615 0.00 0.00 41.39 4.84
2220 6529 3.955775 TCGACTACGAGCGTGTCA 58.044 55.556 18.31 8.62 43.81 3.58
2344 6653 2.711542 CCTTTTCGTGCTCCAGGTATT 58.288 47.619 0.00 0.00 0.00 1.89
2346 6655 2.851263 TTTCGTGCTCCAGGTATTGT 57.149 45.000 0.00 0.00 0.00 2.71
2367 6676 5.070001 TGTCCCAGTTCTTCTTATGGTTTG 58.930 41.667 0.00 0.00 0.00 2.93
2368 6677 5.070685 GTCCCAGTTCTTCTTATGGTTTGT 58.929 41.667 0.00 0.00 0.00 2.83
2369 6678 5.048713 GTCCCAGTTCTTCTTATGGTTTGTG 60.049 44.000 0.00 0.00 0.00 3.33
2370 6679 4.321230 CCCAGTTCTTCTTATGGTTTGTGC 60.321 45.833 0.00 0.00 0.00 4.57
2371 6680 4.520492 CCAGTTCTTCTTATGGTTTGTGCT 59.480 41.667 0.00 0.00 0.00 4.40
2372 6681 5.335191 CCAGTTCTTCTTATGGTTTGTGCTC 60.335 44.000 0.00 0.00 0.00 4.26
2373 6682 4.762251 AGTTCTTCTTATGGTTTGTGCTCC 59.238 41.667 0.00 0.00 0.00 4.70
2374 6683 3.686016 TCTTCTTATGGTTTGTGCTCCC 58.314 45.455 0.00 0.00 0.00 4.30
2375 6684 3.330701 TCTTCTTATGGTTTGTGCTCCCT 59.669 43.478 0.00 0.00 0.00 4.20
2376 6685 3.350219 TCTTATGGTTTGTGCTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
2377 6686 2.026262 TCTTATGGTTTGTGCTCCCTCC 60.026 50.000 0.00 0.00 0.00 4.30
2378 6687 0.251916 TATGGTTTGTGCTCCCTCCG 59.748 55.000 0.00 0.00 0.00 4.63
2379 6688 1.779061 ATGGTTTGTGCTCCCTCCGT 61.779 55.000 0.00 0.00 0.00 4.69
2380 6689 1.122632 TGGTTTGTGCTCCCTCCGTA 61.123 55.000 0.00 0.00 0.00 4.02
2381 6690 0.035739 GGTTTGTGCTCCCTCCGTAA 59.964 55.000 0.00 0.00 0.00 3.18
2382 6691 1.543871 GGTTTGTGCTCCCTCCGTAAA 60.544 52.381 0.00 0.00 0.00 2.01
2383 6692 1.804748 GTTTGTGCTCCCTCCGTAAAG 59.195 52.381 0.00 0.00 0.00 1.85
2384 6693 1.344065 TTGTGCTCCCTCCGTAAAGA 58.656 50.000 0.00 0.00 0.00 2.52
2385 6694 1.344065 TGTGCTCCCTCCGTAAAGAA 58.656 50.000 0.00 0.00 0.00 2.52
2386 6695 1.695242 TGTGCTCCCTCCGTAAAGAAA 59.305 47.619 0.00 0.00 0.00 2.52
2387 6696 2.304761 TGTGCTCCCTCCGTAAAGAAAT 59.695 45.455 0.00 0.00 0.00 2.17
2388 6697 3.516300 TGTGCTCCCTCCGTAAAGAAATA 59.484 43.478 0.00 0.00 0.00 1.40
2389 6698 4.163458 TGTGCTCCCTCCGTAAAGAAATAT 59.837 41.667 0.00 0.00 0.00 1.28
2390 6699 5.364446 TGTGCTCCCTCCGTAAAGAAATATA 59.636 40.000 0.00 0.00 0.00 0.86
2391 6700 6.126997 TGTGCTCCCTCCGTAAAGAAATATAA 60.127 38.462 0.00 0.00 0.00 0.98
2392 6701 6.202379 GTGCTCCCTCCGTAAAGAAATATAAC 59.798 42.308 0.00 0.00 0.00 1.89
2393 6702 6.126997 TGCTCCCTCCGTAAAGAAATATAACA 60.127 38.462 0.00 0.00 0.00 2.41
2394 6703 6.424207 GCTCCCTCCGTAAAGAAATATAACAG 59.576 42.308 0.00 0.00 0.00 3.16
2395 6704 6.285990 TCCCTCCGTAAAGAAATATAACAGC 58.714 40.000 0.00 0.00 0.00 4.40
2396 6705 5.176958 CCCTCCGTAAAGAAATATAACAGCG 59.823 44.000 0.00 0.00 0.00 5.18
2397 6706 5.751990 CCTCCGTAAAGAAATATAACAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
2398 6707 6.257193 CCTCCGTAAAGAAATATAACAGCGTT 59.743 38.462 0.02 0.02 0.00 4.84
2399 6708 7.201582 CCTCCGTAAAGAAATATAACAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
2400 6709 8.031848 TCCGTAAAGAAATATAACAGCGTTTT 57.968 30.769 0.00 0.00 0.00 2.43
2401 6710 9.149225 TCCGTAAAGAAATATAACAGCGTTTTA 57.851 29.630 0.00 0.00 0.00 1.52
2402 6711 9.417284 CCGTAAAGAAATATAACAGCGTTTTAG 57.583 33.333 0.00 0.00 0.00 1.85
2408 6717 9.601217 AGAAATATAACAGCGTTTTAGATCACT 57.399 29.630 0.00 0.00 0.00 3.41
2416 6725 8.773404 ACAGCGTTTTAGATCACTAAATTAGT 57.227 30.769 0.00 0.00 44.59 2.24
2432 6741 9.303537 ACTAAATTAGTGATCTAAACGCTCTTC 57.696 33.333 4.66 0.00 39.23 2.87
2433 6742 9.522804 CTAAATTAGTGATCTAAACGCTCTTCT 57.477 33.333 0.00 0.00 39.23 2.85
2438 6747 7.763172 AGTGATCTAAACGCTCTTCTATTTG 57.237 36.000 0.00 0.00 0.00 2.32
2439 6748 7.324178 AGTGATCTAAACGCTCTTCTATTTGT 58.676 34.615 0.00 0.00 0.00 2.83
2440 6749 7.819900 AGTGATCTAAACGCTCTTCTATTTGTT 59.180 33.333 0.00 0.00 0.00 2.83
2441 6750 8.443937 GTGATCTAAACGCTCTTCTATTTGTTT 58.556 33.333 0.00 0.00 34.32 2.83
2442 6751 9.647797 TGATCTAAACGCTCTTCTATTTGTTTA 57.352 29.630 0.00 0.00 32.41 2.01
2443 6752 9.903185 GATCTAAACGCTCTTCTATTTGTTTAC 57.097 33.333 0.00 0.00 32.41 2.01
2444 6753 8.821147 TCTAAACGCTCTTCTATTTGTTTACA 57.179 30.769 0.00 0.00 32.41 2.41
2445 6754 8.922676 TCTAAACGCTCTTCTATTTGTTTACAG 58.077 33.333 0.00 0.00 32.41 2.74
2446 6755 7.724305 AAACGCTCTTCTATTTGTTTACAGA 57.276 32.000 0.00 0.00 0.00 3.41
2447 6756 6.952935 ACGCTCTTCTATTTGTTTACAGAG 57.047 37.500 0.00 0.00 0.00 3.35
2448 6757 5.869888 ACGCTCTTCTATTTGTTTACAGAGG 59.130 40.000 0.00 0.00 0.00 3.69
2449 6758 5.292101 CGCTCTTCTATTTGTTTACAGAGGG 59.708 44.000 0.00 0.00 0.00 4.30
2450 6759 6.407202 GCTCTTCTATTTGTTTACAGAGGGA 58.593 40.000 0.00 0.00 0.00 4.20
2468 6777 3.014623 GGGAGTACCTTGCAATTGTACC 58.985 50.000 24.60 18.68 36.38 3.34
2469 6778 3.014623 GGAGTACCTTGCAATTGTACCC 58.985 50.000 24.60 21.73 36.38 3.69
2547 6858 4.568956 TGATCATGTGACGATCTGTGTTT 58.431 39.130 0.00 0.00 40.03 2.83
2559 6870 8.471609 TGACGATCTGTGTTTAATTAGATGGTA 58.528 33.333 0.00 0.00 38.27 3.25
2597 6916 5.125417 TGATTATAGTGCAGTTCCTTTTGGC 59.875 40.000 0.00 0.00 40.12 4.52
2602 6921 1.761784 TGCAGTTCCTTTTGGCACATT 59.238 42.857 0.00 0.00 38.23 2.71
2695 7038 4.460382 GGATTGACTCACCAACAATCACAT 59.540 41.667 16.87 0.00 46.38 3.21
2742 7085 4.072131 ACTAAACCACCACAAGCACATAG 58.928 43.478 0.00 0.00 0.00 2.23
2758 7101 4.511082 GCACATAGCCAGAAGATTTCTCTC 59.489 45.833 0.00 0.00 38.11 3.20
2798 7141 3.459232 TTCAGATCGGAAGGTATGCAG 57.541 47.619 4.00 0.00 0.00 4.41
2959 7304 2.356535 GCTTCATGACCTGGAGATTGGT 60.357 50.000 0.00 0.00 39.60 3.67
3085 7430 2.224066 CGGAACATATCGCCTTCCTCTT 60.224 50.000 0.00 0.00 32.63 2.85
3158 7503 5.452077 GCTCCATTCTCTAACCTTCGTATGT 60.452 44.000 0.00 0.00 0.00 2.29
3159 7504 6.540438 TCCATTCTCTAACCTTCGTATGTT 57.460 37.500 0.00 0.00 0.00 2.71
3160 7505 6.942976 TCCATTCTCTAACCTTCGTATGTTT 58.057 36.000 0.00 0.00 0.00 2.83
3166 7514 3.636282 AACCTTCGTATGTTTGTTGCC 57.364 42.857 0.00 0.00 0.00 4.52
3177 7525 6.348950 CGTATGTTTGTTGCCTCCAAAGATAA 60.349 38.462 9.66 0.00 38.77 1.75
3398 7747 6.578944 ACGACCACAATATATACTTGAGCAA 58.421 36.000 10.16 0.00 0.00 3.91
3530 7879 3.797039 TCATGGAGCTGCTAATGTACAC 58.203 45.455 18.83 0.00 0.00 2.90
3544 7893 1.068588 TGTACACAGCGATCATAGCCC 59.931 52.381 0.00 0.00 34.64 5.19
3611 7960 1.810412 GCGACCTGAGAAACAAGGTGT 60.810 52.381 0.00 0.00 32.90 4.16
3755 8104 2.815647 CCTCGCCTTCTCAACGGC 60.816 66.667 0.00 0.00 42.86 5.68
3756 8105 2.262915 CTCGCCTTCTCAACGGCT 59.737 61.111 0.00 0.00 44.11 5.52
3789 8138 4.711949 CTGCTCCCACCGCTTGCT 62.712 66.667 0.00 0.00 0.00 3.91
3825 8174 2.760092 GCTTGGGATTGTTGGAATGCTA 59.240 45.455 0.00 0.00 0.00 3.49
3876 8225 1.884579 GGTATCGCGAGGATTCTGGTA 59.115 52.381 16.66 0.00 36.55 3.25
3891 8240 1.033202 TGGTAGTCGTCGCCTATGCA 61.033 55.000 0.00 0.00 37.32 3.96
3942 8291 1.139734 CGTGAGGGTGATGGACTCG 59.860 63.158 0.00 0.00 34.03 4.18
3968 8317 4.015084 CAAACAATGCTTGAGAGGGATCT 58.985 43.478 0.00 0.00 0.00 2.75
3984 8333 4.351054 CTGCACTTCCCCCGGCTT 62.351 66.667 0.00 0.00 0.00 4.35
4059 8408 8.407832 TGTAAAGGTTTGATATGCTTCATCATG 58.592 33.333 0.00 0.00 32.63 3.07
4096 8459 6.316640 AGCTGATTCTTGATTCATTCTGACTG 59.683 38.462 0.00 0.00 0.00 3.51
4234 8600 0.825410 GGGCATGTTCATTGCATCCA 59.175 50.000 0.00 0.00 41.95 3.41
4236 8602 1.202486 GGCATGTTCATTGCATCCAGG 60.202 52.381 0.00 0.00 41.95 4.45
4262 8628 6.211785 GGGGAATGGGAACTGTTGTAAATTAA 59.788 38.462 0.00 0.00 0.00 1.40
4264 8630 7.039293 GGGAATGGGAACTGTTGTAAATTAACT 60.039 37.037 0.00 0.00 0.00 2.24
4265 8631 9.016438 GGAATGGGAACTGTTGTAAATTAACTA 57.984 33.333 0.00 0.00 0.00 2.24
4306 8700 4.024387 TGCAGACGGTTCAAACTATGTTTC 60.024 41.667 0.00 0.00 0.00 2.78
4329 8723 2.096013 GCAAGTTATTTCCTGTCTCCGC 59.904 50.000 0.00 0.00 0.00 5.54
4332 8726 2.232941 AGTTATTTCCTGTCTCCGCGAA 59.767 45.455 8.23 0.00 0.00 4.70
4349 8743 5.523552 TCCGCGAATGGAAATATGCATATAG 59.476 40.000 19.39 5.59 36.48 1.31
4399 8793 7.736447 TCATTTTTCTGGAAAAGAGAGTCTC 57.264 36.000 12.54 12.54 40.35 3.36
4404 8798 2.558795 CTGGAAAAGAGAGTCTCGTGGA 59.441 50.000 14.47 0.00 35.36 4.02
4419 8813 1.481871 GTGGACTTGGGGACTCGATA 58.518 55.000 0.00 0.00 0.00 2.92
4444 8838 5.390613 CGAACGGTTGAAAGCTATCAAAAT 58.609 37.500 0.00 0.00 40.76 1.82
4524 8918 6.312487 TCTCGAAAACGAAGTGTAGATACAG 58.688 40.000 0.00 0.00 45.00 2.74
4529 8923 7.253684 CGAAAACGAAGTGTAGATACAGAATCC 60.254 40.741 0.00 0.00 45.00 3.01
4543 8937 9.373450 AGATACAGAATCCATAAGAGAGCTAAA 57.627 33.333 0.00 0.00 34.90 1.85
4637 9031 8.691661 ACAGAACACAATGGTTAAATTCTACT 57.308 30.769 0.00 0.00 0.00 2.57
4638 9032 9.787435 ACAGAACACAATGGTTAAATTCTACTA 57.213 29.630 0.00 0.00 0.00 1.82
4640 9034 8.947115 AGAACACAATGGTTAAATTCTACTAGC 58.053 33.333 0.00 0.00 0.00 3.42
4641 9035 8.630054 AACACAATGGTTAAATTCTACTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
4642 9036 8.268850 ACACAATGGTTAAATTCTACTAGCAG 57.731 34.615 0.00 0.00 0.00 4.24
4643 9037 7.883311 ACACAATGGTTAAATTCTACTAGCAGT 59.117 33.333 0.00 0.00 0.00 4.40
4644 9038 9.378551 CACAATGGTTAAATTCTACTAGCAGTA 57.621 33.333 0.00 0.00 0.00 2.74
4646 9040 9.046296 CAATGGTTAAATTCTACTAGCAGTAGG 57.954 37.037 17.67 5.54 46.25 3.18
4647 9041 6.579865 TGGTTAAATTCTACTAGCAGTAGGC 58.420 40.000 17.67 0.00 46.25 3.93
4651 9045 4.927978 ATTCTACTAGCAGTAGGCAGTG 57.072 45.455 17.67 0.00 46.25 3.66
4671 9065 6.238759 GCAGTGTCTTGTCTAAAGTTGGAAAT 60.239 38.462 0.00 0.00 0.00 2.17
4717 9111 1.421382 CATCTTGCCTTGGTTTTGCG 58.579 50.000 0.00 0.00 0.00 4.85
4765 9159 3.452474 CCTAGGAAGAACAATCTGAGCG 58.548 50.000 1.05 0.00 35.59 5.03
4866 9260 4.398673 ACACACAAAAGCCGGTAAAAAGTA 59.601 37.500 1.90 0.00 0.00 2.24
4872 9266 8.024285 CACAAAAGCCGGTAAAAAGTATGAATA 58.976 33.333 1.90 0.00 0.00 1.75
4931 9326 2.023414 TTTGTCGTCACGGGCAGACT 62.023 55.000 12.32 0.00 34.92 3.24
4959 9354 2.816087 CACCCCTGAAGAACATGAGTTG 59.184 50.000 0.00 0.00 38.30 3.16
4960 9355 2.443255 ACCCCTGAAGAACATGAGTTGT 59.557 45.455 0.00 0.00 41.53 3.32
4972 9367 3.191581 ACATGAGTTGTAGACCGAGACAG 59.808 47.826 0.00 0.00 36.57 3.51
4991 9386 6.815089 AGACAGCTTCCTAGTGAGATTTATG 58.185 40.000 0.00 0.00 0.00 1.90
5001 9396 7.665559 TCCTAGTGAGATTTATGCAACTTGTTT 59.334 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.944376 AAATCCGTAGTGCATAATATCATAAGT 57.056 29.630 0.00 0.00 0.00 2.24
48 49 9.953565 GGTTGTAATGGGAAGCATATACTAATA 57.046 33.333 0.00 0.00 0.00 0.98
49 50 8.444783 TGGTTGTAATGGGAAGCATATACTAAT 58.555 33.333 0.00 0.00 0.00 1.73
50 51 7.807198 TGGTTGTAATGGGAAGCATATACTAA 58.193 34.615 0.00 0.00 0.00 2.24
51 52 7.381789 TGGTTGTAATGGGAAGCATATACTA 57.618 36.000 0.00 0.00 0.00 1.82
52 53 6.260700 TGGTTGTAATGGGAAGCATATACT 57.739 37.500 0.00 0.00 0.00 2.12
53 54 6.238925 GGTTGGTTGTAATGGGAAGCATATAC 60.239 42.308 0.00 0.00 30.17 1.47
54 55 5.830991 GGTTGGTTGTAATGGGAAGCATATA 59.169 40.000 0.00 0.00 30.17 0.86
55 56 4.649218 GGTTGGTTGTAATGGGAAGCATAT 59.351 41.667 0.00 0.00 30.17 1.78
56 57 4.020543 GGTTGGTTGTAATGGGAAGCATA 58.979 43.478 0.00 0.00 30.17 3.14
57 58 2.831526 GGTTGGTTGTAATGGGAAGCAT 59.168 45.455 0.00 0.00 30.17 3.79
58 59 2.158385 AGGTTGGTTGTAATGGGAAGCA 60.158 45.455 0.00 0.00 0.00 3.91
59 60 2.525368 AGGTTGGTTGTAATGGGAAGC 58.475 47.619 0.00 0.00 0.00 3.86
60 61 5.074115 TGTTAGGTTGGTTGTAATGGGAAG 58.926 41.667 0.00 0.00 0.00 3.46
61 62 5.063017 TGTTAGGTTGGTTGTAATGGGAA 57.937 39.130 0.00 0.00 0.00 3.97
62 63 4.726035 TGTTAGGTTGGTTGTAATGGGA 57.274 40.909 0.00 0.00 0.00 4.37
63 64 5.793030 TTTGTTAGGTTGGTTGTAATGGG 57.207 39.130 0.00 0.00 0.00 4.00
64 65 7.227049 AGATTTGTTAGGTTGGTTGTAATGG 57.773 36.000 0.00 0.00 0.00 3.16
69 70 9.174166 GTCATATAGATTTGTTAGGTTGGTTGT 57.826 33.333 0.00 0.00 0.00 3.32
70 71 9.173021 TGTCATATAGATTTGTTAGGTTGGTTG 57.827 33.333 0.00 0.00 0.00 3.77
71 72 9.920946 ATGTCATATAGATTTGTTAGGTTGGTT 57.079 29.630 0.00 0.00 0.00 3.67
72 73 9.342308 CATGTCATATAGATTTGTTAGGTTGGT 57.658 33.333 0.00 0.00 0.00 3.67
73 74 9.559732 TCATGTCATATAGATTTGTTAGGTTGG 57.440 33.333 0.00 0.00 0.00 3.77
96 97 7.596494 AGATTCGTCATTGAACATGTTTTCAT 58.404 30.769 13.36 2.54 41.78 2.57
129 130 5.948758 TCATCATATACACCACCAAAGCAAA 59.051 36.000 0.00 0.00 0.00 3.68
282 288 4.648626 TGCTGGCAGTGGCTGGTC 62.649 66.667 22.27 9.38 40.87 4.02
298 1706 6.990349 TGAAAGTAACTCTTCCCAAACTACTG 59.010 38.462 0.00 0.00 35.02 2.74
395 2811 2.722201 GGTGGAGAGGTGGCCGTAG 61.722 68.421 0.00 0.00 0.00 3.51
399 2815 2.034221 GTTGGTGGAGAGGTGGCC 59.966 66.667 0.00 0.00 0.00 5.36
400 2816 2.034221 GGTTGGTGGAGAGGTGGC 59.966 66.667 0.00 0.00 0.00 5.01
406 2822 2.112297 GCGGTTGGTTGGTGGAGA 59.888 61.111 0.00 0.00 0.00 3.71
408 2824 4.178169 ACGCGGTTGGTTGGTGGA 62.178 61.111 12.47 0.00 0.00 4.02
546 4249 1.807738 CGAACGCTTCCTAGTCGTAC 58.192 55.000 0.00 0.00 34.59 3.67
552 4255 0.590230 CTCTCGCGAACGCTTCCTAG 60.590 60.000 11.33 0.00 39.84 3.02
767 4874 3.485463 TTATTTATGTGCTCTCCCCCG 57.515 47.619 0.00 0.00 0.00 5.73
770 4877 4.947388 TGGTGTTTATTTATGTGCTCTCCC 59.053 41.667 0.00 0.00 0.00 4.30
771 4878 5.163652 GGTGGTGTTTATTTATGTGCTCTCC 60.164 44.000 0.00 0.00 0.00 3.71
773 4880 4.394920 CGGTGGTGTTTATTTATGTGCTCT 59.605 41.667 0.00 0.00 0.00 4.09
829 4997 2.917713 AGCAGAGGAAGGAAGAGAGA 57.082 50.000 0.00 0.00 0.00 3.10
836 5007 0.837691 TGGCAGAAGCAGAGGAAGGA 60.838 55.000 0.00 0.00 44.61 3.36
889 5060 0.970937 TGCTCGTCTCGGGAATTCCT 60.971 55.000 23.63 0.00 35.95 3.36
961 5151 0.693049 AACTCCCCGATCAACAAGCT 59.307 50.000 0.00 0.00 0.00 3.74
1047 5240 3.370231 AAAATCGCCACCGCCACC 61.370 61.111 0.00 0.00 0.00 4.61
1048 5241 2.126502 CAAAATCGCCACCGCCAC 60.127 61.111 0.00 0.00 0.00 5.01
1263 5471 1.758514 GGAGGAGGCGATGAGGACA 60.759 63.158 0.00 0.00 0.00 4.02
1330 5538 1.617839 AAGAGGCCAAGGGAGGGAG 60.618 63.158 5.01 0.00 0.00 4.30
1343 5551 3.804193 GCAAAGCGGCGGAAGAGG 61.804 66.667 9.78 0.00 0.00 3.69
1344 5552 2.245714 GAAGCAAAGCGGCGGAAGAG 62.246 60.000 9.78 0.00 39.27 2.85
1345 5553 2.281484 AAGCAAAGCGGCGGAAGA 60.281 55.556 9.78 0.00 39.27 2.87
1439 5648 9.296400 GGAAAGAAACGCTTGCATATAATTTAA 57.704 29.630 0.00 0.00 36.80 1.52
1440 5649 8.682710 AGGAAAGAAACGCTTGCATATAATTTA 58.317 29.630 0.00 0.00 36.80 1.40
1441 5650 7.547227 AGGAAAGAAACGCTTGCATATAATTT 58.453 30.769 0.00 0.00 36.80 1.82
1442 5651 7.100458 AGGAAAGAAACGCTTGCATATAATT 57.900 32.000 0.00 0.00 36.80 1.40
1449 5658 3.130340 AGAAAAGGAAAGAAACGCTTGCA 59.870 39.130 0.00 0.00 36.80 4.08
1476 5686 1.317613 AGAAACGCTTGCCATTGTCA 58.682 45.000 0.00 0.00 0.00 3.58
1508 5718 2.926242 TTCGTCCCCACTCCCCAC 60.926 66.667 0.00 0.00 0.00 4.61
1509 5719 2.606519 CTTCGTCCCCACTCCCCA 60.607 66.667 0.00 0.00 0.00 4.96
1510 5720 3.400054 CCTTCGTCCCCACTCCCC 61.400 72.222 0.00 0.00 0.00 4.81
1511 5721 4.097361 GCCTTCGTCCCCACTCCC 62.097 72.222 0.00 0.00 0.00 4.30
1512 5722 4.452733 CGCCTTCGTCCCCACTCC 62.453 72.222 0.00 0.00 0.00 3.85
1513 5723 2.837371 CTTCGCCTTCGTCCCCACTC 62.837 65.000 0.00 0.00 36.96 3.51
1514 5724 2.920912 TTCGCCTTCGTCCCCACT 60.921 61.111 0.00 0.00 36.96 4.00
1593 5812 1.337384 ATCGTATCTGCAGGTGCCCA 61.337 55.000 15.13 0.00 41.18 5.36
1596 5815 4.810790 ACTATAATCGTATCTGCAGGTGC 58.189 43.478 15.13 9.88 42.50 5.01
1617 5836 8.709272 AATACTCCAGAACCTTCCTATAGTAC 57.291 38.462 0.00 0.00 0.00 2.73
1618 5837 9.725206 AAAATACTCCAGAACCTTCCTATAGTA 57.275 33.333 0.00 0.00 0.00 1.82
1619 5838 8.625467 AAAATACTCCAGAACCTTCCTATAGT 57.375 34.615 0.00 0.00 0.00 2.12
1682 5930 1.975660 TCCCTTGTGGTAAACAGCAC 58.024 50.000 0.19 0.19 40.74 4.40
1695 5943 3.220110 AGCATGCACTGAATATCCCTTG 58.780 45.455 21.98 0.00 0.00 3.61
1697 5945 2.440627 TGAGCATGCACTGAATATCCCT 59.559 45.455 21.98 0.00 0.00 4.20
1726 5975 8.993121 ACTAATGACAAGAACATTCACTTACTG 58.007 33.333 0.00 0.00 38.61 2.74
1727 5976 9.561069 AACTAATGACAAGAACATTCACTTACT 57.439 29.630 0.00 0.00 38.61 2.24
1728 5977 9.813080 GAACTAATGACAAGAACATTCACTTAC 57.187 33.333 0.00 0.00 38.61 2.34
1745 5994 8.611257 TCCTTGAGGGAAATAAAGAACTAATGA 58.389 33.333 0.00 0.00 41.91 2.57
1762 6011 5.220854 CGTTAAACAGCATATTCCTTGAGGG 60.221 44.000 0.00 0.00 35.41 4.30
1763 6012 5.354234 ACGTTAAACAGCATATTCCTTGAGG 59.646 40.000 0.00 0.00 0.00 3.86
1768 6040 5.488341 ACTCACGTTAAACAGCATATTCCT 58.512 37.500 0.00 0.00 0.00 3.36
1769 6041 5.796350 ACTCACGTTAAACAGCATATTCC 57.204 39.130 0.00 0.00 0.00 3.01
1781 6053 7.324354 TCATAGTAGCATGTACTCACGTTAA 57.676 36.000 10.12 0.00 0.00 2.01
1783 6055 5.221067 CCTCATAGTAGCATGTACTCACGTT 60.221 44.000 10.12 0.00 0.00 3.99
1784 6056 4.276183 CCTCATAGTAGCATGTACTCACGT 59.724 45.833 10.12 0.00 0.00 4.49
1785 6057 4.276183 ACCTCATAGTAGCATGTACTCACG 59.724 45.833 10.12 0.00 0.00 4.35
1799 6071 6.698380 ACAAATACTCGTCAAACCTCATAGT 58.302 36.000 0.00 0.00 0.00 2.12
1800 6072 7.596749 AACAAATACTCGTCAAACCTCATAG 57.403 36.000 0.00 0.00 0.00 2.23
1801 6073 7.094975 CCAAACAAATACTCGTCAAACCTCATA 60.095 37.037 0.00 0.00 0.00 2.15
1803 6075 5.008217 CCAAACAAATACTCGTCAAACCTCA 59.992 40.000 0.00 0.00 0.00 3.86
1804 6076 5.008316 ACCAAACAAATACTCGTCAAACCTC 59.992 40.000 0.00 0.00 0.00 3.85
1805 6077 4.885325 ACCAAACAAATACTCGTCAAACCT 59.115 37.500 0.00 0.00 0.00 3.50
1806 6078 4.973663 CACCAAACAAATACTCGTCAAACC 59.026 41.667 0.00 0.00 0.00 3.27
1807 6079 4.973663 CCACCAAACAAATACTCGTCAAAC 59.026 41.667 0.00 0.00 0.00 2.93
1808 6080 4.498345 GCCACCAAACAAATACTCGTCAAA 60.498 41.667 0.00 0.00 0.00 2.69
1809 6081 3.003897 GCCACCAAACAAATACTCGTCAA 59.996 43.478 0.00 0.00 0.00 3.18
1810 6082 2.550606 GCCACCAAACAAATACTCGTCA 59.449 45.455 0.00 0.00 0.00 4.35
1813 6085 3.502211 AGAAGCCACCAAACAAATACTCG 59.498 43.478 0.00 0.00 0.00 4.18
1849 6124 3.458487 ACCACTCTAACTGGAAACCAACT 59.542 43.478 0.00 0.00 30.80 3.16
1861 6136 4.755629 GGAAGGAAAGTTGACCACTCTAAC 59.244 45.833 0.00 0.00 32.94 2.34
1900 6175 8.796475 ACCATATCCAAAACATATATTCTGCAC 58.204 33.333 0.00 0.00 0.00 4.57
1902 6177 9.013229 TGACCATATCCAAAACATATATTCTGC 57.987 33.333 0.00 0.00 0.00 4.26
1943 6218 5.262588 AGTCATGGTTCAAAGTTCAAACC 57.737 39.130 10.88 10.88 42.28 3.27
1945 6220 4.036262 CGGAGTCATGGTTCAAAGTTCAAA 59.964 41.667 0.00 0.00 0.00 2.69
1946 6221 3.563808 CGGAGTCATGGTTCAAAGTTCAA 59.436 43.478 0.00 0.00 0.00 2.69
1947 6222 3.138304 CGGAGTCATGGTTCAAAGTTCA 58.862 45.455 0.00 0.00 0.00 3.18
1948 6223 2.095718 GCGGAGTCATGGTTCAAAGTTC 60.096 50.000 0.00 0.00 0.00 3.01
1949 6224 1.880027 GCGGAGTCATGGTTCAAAGTT 59.120 47.619 0.00 0.00 0.00 2.66
1950 6225 1.523758 GCGGAGTCATGGTTCAAAGT 58.476 50.000 0.00 0.00 0.00 2.66
1951 6226 0.804989 GGCGGAGTCATGGTTCAAAG 59.195 55.000 0.00 0.00 0.00 2.77
2005 6290 7.075741 GGGAACGGAATGAATATATTTGTTCG 58.924 38.462 0.00 1.88 37.01 3.95
2344 6653 4.993705 AACCATAAGAAGAACTGGGACA 57.006 40.909 0.00 0.00 32.89 4.02
2346 6655 5.070001 CACAAACCATAAGAAGAACTGGGA 58.930 41.667 0.00 0.00 32.89 4.37
2367 6676 2.467566 TTTCTTTACGGAGGGAGCAC 57.532 50.000 0.00 0.00 0.00 4.40
2368 6677 6.126997 TGTTATATTTCTTTACGGAGGGAGCA 60.127 38.462 0.00 0.00 0.00 4.26
2369 6678 6.285990 TGTTATATTTCTTTACGGAGGGAGC 58.714 40.000 0.00 0.00 0.00 4.70
2370 6679 6.424207 GCTGTTATATTTCTTTACGGAGGGAG 59.576 42.308 0.00 0.00 0.00 4.30
2371 6680 6.285990 GCTGTTATATTTCTTTACGGAGGGA 58.714 40.000 0.00 0.00 0.00 4.20
2372 6681 5.176958 CGCTGTTATATTTCTTTACGGAGGG 59.823 44.000 0.00 0.00 0.00 4.30
2373 6682 5.751990 ACGCTGTTATATTTCTTTACGGAGG 59.248 40.000 0.00 0.00 0.00 4.30
2374 6683 6.823678 ACGCTGTTATATTTCTTTACGGAG 57.176 37.500 0.00 0.00 0.00 4.63
2375 6684 7.599630 AAACGCTGTTATATTTCTTTACGGA 57.400 32.000 0.00 0.00 0.00 4.69
2376 6685 9.417284 CTAAAACGCTGTTATATTTCTTTACGG 57.583 33.333 0.00 0.00 0.00 4.02
2382 6691 9.601217 AGTGATCTAAAACGCTGTTATATTTCT 57.399 29.630 0.00 0.00 0.00 2.52
2390 6699 9.216117 ACTAATTTAGTGATCTAAAACGCTGTT 57.784 29.630 8.27 0.00 45.40 3.16
2391 6700 8.773404 ACTAATTTAGTGATCTAAAACGCTGT 57.227 30.769 8.27 0.00 45.40 4.40
2406 6715 9.303537 GAAGAGCGTTTAGATCACTAATTTAGT 57.696 33.333 3.16 3.16 38.23 2.24
2407 6716 9.522804 AGAAGAGCGTTTAGATCACTAATTTAG 57.477 33.333 1.79 1.79 38.23 1.85
2412 6721 9.302345 CAAATAGAAGAGCGTTTAGATCACTAA 57.698 33.333 0.00 0.00 37.82 2.24
2413 6722 8.467598 ACAAATAGAAGAGCGTTTAGATCACTA 58.532 33.333 0.00 0.00 37.82 2.74
2414 6723 7.324178 ACAAATAGAAGAGCGTTTAGATCACT 58.676 34.615 0.00 0.00 37.82 3.41
2415 6724 7.527084 ACAAATAGAAGAGCGTTTAGATCAC 57.473 36.000 0.00 0.00 37.82 3.06
2416 6725 8.547967 AAACAAATAGAAGAGCGTTTAGATCA 57.452 30.769 0.00 0.00 37.82 2.92
2417 6726 9.903185 GTAAACAAATAGAAGAGCGTTTAGATC 57.097 33.333 0.00 0.00 31.53 2.75
2418 6727 9.431887 TGTAAACAAATAGAAGAGCGTTTAGAT 57.568 29.630 0.00 0.00 31.53 1.98
2419 6728 8.821147 TGTAAACAAATAGAAGAGCGTTTAGA 57.179 30.769 0.00 0.00 31.53 2.10
2420 6729 8.922676 TCTGTAAACAAATAGAAGAGCGTTTAG 58.077 33.333 0.00 0.00 31.53 1.85
2421 6730 8.821147 TCTGTAAACAAATAGAAGAGCGTTTA 57.179 30.769 0.00 0.00 0.00 2.01
2422 6731 7.095187 CCTCTGTAAACAAATAGAAGAGCGTTT 60.095 37.037 0.00 0.00 0.00 3.60
2423 6732 6.369065 CCTCTGTAAACAAATAGAAGAGCGTT 59.631 38.462 0.00 0.00 0.00 4.84
2424 6733 5.869888 CCTCTGTAAACAAATAGAAGAGCGT 59.130 40.000 0.00 0.00 0.00 5.07
2425 6734 5.292101 CCCTCTGTAAACAAATAGAAGAGCG 59.708 44.000 0.00 0.00 0.00 5.03
2426 6735 6.407202 TCCCTCTGTAAACAAATAGAAGAGC 58.593 40.000 0.00 0.00 0.00 4.09
2427 6736 7.616313 ACTCCCTCTGTAAACAAATAGAAGAG 58.384 38.462 0.00 0.00 0.00 2.85
2428 6737 7.554959 ACTCCCTCTGTAAACAAATAGAAGA 57.445 36.000 0.00 0.00 0.00 2.87
2429 6738 7.764901 GGTACTCCCTCTGTAAACAAATAGAAG 59.235 40.741 0.00 0.00 0.00 2.85
2430 6739 7.456902 AGGTACTCCCTCTGTAAACAAATAGAA 59.543 37.037 0.00 0.00 40.71 2.10
2431 6740 6.958192 AGGTACTCCCTCTGTAAACAAATAGA 59.042 38.462 0.00 0.00 40.71 1.98
2432 6741 7.184067 AGGTACTCCCTCTGTAAACAAATAG 57.816 40.000 0.00 0.00 40.71 1.73
2433 6742 7.391620 CAAGGTACTCCCTCTGTAAACAAATA 58.608 38.462 0.00 0.00 45.47 1.40
2434 6743 6.238648 CAAGGTACTCCCTCTGTAAACAAAT 58.761 40.000 0.00 0.00 45.47 2.32
2435 6744 5.617252 CAAGGTACTCCCTCTGTAAACAAA 58.383 41.667 0.00 0.00 45.47 2.83
2436 6745 4.504340 GCAAGGTACTCCCTCTGTAAACAA 60.504 45.833 0.00 0.00 45.47 2.83
2437 6746 3.007614 GCAAGGTACTCCCTCTGTAAACA 59.992 47.826 0.00 0.00 45.47 2.83
2438 6747 3.007614 TGCAAGGTACTCCCTCTGTAAAC 59.992 47.826 0.00 0.00 45.47 2.01
2439 6748 3.244582 TGCAAGGTACTCCCTCTGTAAA 58.755 45.455 0.00 0.00 45.47 2.01
2440 6749 2.897350 TGCAAGGTACTCCCTCTGTAA 58.103 47.619 0.00 0.00 45.47 2.41
2441 6750 2.615986 TGCAAGGTACTCCCTCTGTA 57.384 50.000 0.00 0.00 45.47 2.74
2442 6751 1.729586 TTGCAAGGTACTCCCTCTGT 58.270 50.000 0.00 0.00 45.47 3.41
2443 6752 3.012518 CAATTGCAAGGTACTCCCTCTG 58.987 50.000 4.94 0.00 45.47 3.35
2444 6753 2.644798 ACAATTGCAAGGTACTCCCTCT 59.355 45.455 4.94 0.00 45.47 3.69
2445 6754 3.073274 ACAATTGCAAGGTACTCCCTC 57.927 47.619 4.94 0.00 45.47 4.30
2447 6756 3.014623 GGTACAATTGCAAGGTACTCCC 58.985 50.000 28.64 17.35 38.49 4.30
2448 6757 3.014623 GGGTACAATTGCAAGGTACTCC 58.985 50.000 28.64 24.95 38.49 3.85
2449 6758 3.014623 GGGGTACAATTGCAAGGTACTC 58.985 50.000 28.64 26.95 38.49 2.59
2468 6777 1.605232 GTTTGACGTTTGGTACAGGGG 59.395 52.381 0.00 0.00 42.39 4.79
2469 6778 2.546789 GAGTTTGACGTTTGGTACAGGG 59.453 50.000 0.00 0.00 42.39 4.45
2559 6870 8.597167 TGCACTATAATCAGCATACTAAAGGAT 58.403 33.333 0.00 0.00 31.05 3.24
2582 6901 1.412079 ATGTGCCAAAAGGAACTGCA 58.588 45.000 0.00 0.00 40.86 4.41
2583 6902 2.224018 TGAATGTGCCAAAAGGAACTGC 60.224 45.455 0.00 0.00 40.86 4.40
2597 6916 5.183713 TGGCTCAATTTAGGAACTGAATGTG 59.816 40.000 0.00 0.00 44.07 3.21
2602 6921 6.039717 GCAATATGGCTCAATTTAGGAACTGA 59.960 38.462 0.00 0.00 41.52 3.41
2667 7010 4.163441 TGTTGGTGAGTCAATCCAAAGA 57.837 40.909 14.92 4.65 41.86 2.52
2742 7085 6.019156 CGACTATTTGAGAGAAATCTTCTGGC 60.019 42.308 0.00 0.00 40.87 4.85
2798 7141 2.063266 CAATGCAATGGTGTTGCTCAC 58.937 47.619 13.17 4.47 45.13 3.51
2907 7252 5.435686 AAACACATCCATAGAAGGCTGTA 57.564 39.130 0.00 0.00 35.94 2.74
2908 7253 4.307032 AAACACATCCATAGAAGGCTGT 57.693 40.909 0.00 0.00 38.48 4.40
2959 7304 0.030235 CACCGTCAGAGTTGTCACGA 59.970 55.000 0.00 0.00 34.06 4.35
3085 7430 1.001293 GATGCGTCCATCTGATAGCCA 59.999 52.381 0.00 0.00 43.62 4.75
3158 7503 6.349777 CGGTAATTATCTTTGGAGGCAACAAA 60.350 38.462 6.47 6.47 41.41 2.83
3159 7504 5.124776 CGGTAATTATCTTTGGAGGCAACAA 59.875 40.000 0.00 0.00 41.41 2.83
3160 7505 4.638421 CGGTAATTATCTTTGGAGGCAACA 59.362 41.667 0.00 0.00 41.41 3.33
3166 7514 9.931210 GTAAAATGTCGGTAATTATCTTTGGAG 57.069 33.333 0.00 0.00 0.00 3.86
3177 7525 9.730420 GCAATATTTCAGTAAAATGTCGGTAAT 57.270 29.630 0.00 0.00 38.08 1.89
3398 7747 9.976511 CATGCCACATATGATTTCTTTTCTATT 57.023 29.630 10.38 0.00 0.00 1.73
3530 7879 0.320247 GGTGAGGGCTATGATCGCTG 60.320 60.000 0.00 0.00 0.00 5.18
3544 7893 2.187073 GCCTTGCCAATCTGGTGAG 58.813 57.895 0.00 0.00 40.46 3.51
3611 7960 0.253044 GATTAGCCACTGCACCAGGA 59.747 55.000 0.00 0.00 41.13 3.86
3755 8104 2.688446 AGCAGGAATGCATTGATCACAG 59.312 45.455 18.59 0.74 37.25 3.66
3756 8105 2.686405 GAGCAGGAATGCATTGATCACA 59.314 45.455 18.59 0.00 37.25 3.58
3825 8174 2.436542 CCATGGGAATGCCATGACAAAT 59.563 45.455 31.31 0.00 45.40 2.32
3858 8207 2.812591 GACTACCAGAATCCTCGCGATA 59.187 50.000 10.36 0.38 0.00 2.92
3876 8225 1.665679 CAAAATGCATAGGCGACGACT 59.334 47.619 8.97 8.97 45.35 4.18
3891 8240 2.232941 CAGGAATGGTGCAGAGCAAAAT 59.767 45.455 0.00 0.00 41.47 1.82
3968 8317 4.659172 CAAGCCGGGGGAAGTGCA 62.659 66.667 2.18 0.00 0.00 4.57
4059 8408 6.228995 TCAAGAATCAGCTGTCCATATGATC 58.771 40.000 14.67 0.00 31.31 2.92
4096 8459 2.938869 GCAGATTGCTGGAGACAAAAC 58.061 47.619 0.00 0.00 42.53 2.43
4164 8527 9.842775 TGATCTATCTTTTCTGTATCTGCATTT 57.157 29.630 0.00 0.00 0.00 2.32
4236 8602 0.114364 ACAACAGTTCCCATTCCCCC 59.886 55.000 0.00 0.00 0.00 5.40
4266 8632 5.422145 GTCTGCAATGAATATGCCCTTTTT 58.578 37.500 0.00 0.00 43.16 1.94
4267 8633 4.440525 CGTCTGCAATGAATATGCCCTTTT 60.441 41.667 0.00 0.00 43.16 2.27
4268 8634 3.067180 CGTCTGCAATGAATATGCCCTTT 59.933 43.478 0.00 0.00 43.16 3.11
4269 8635 2.620115 CGTCTGCAATGAATATGCCCTT 59.380 45.455 0.00 0.00 43.16 3.95
4270 8636 2.224606 CGTCTGCAATGAATATGCCCT 58.775 47.619 0.00 0.00 43.16 5.19
4271 8637 1.267806 CCGTCTGCAATGAATATGCCC 59.732 52.381 0.00 0.00 43.16 5.36
4274 8640 4.880886 TGAACCGTCTGCAATGAATATG 57.119 40.909 0.00 0.00 0.00 1.78
4275 8641 5.415701 AGTTTGAACCGTCTGCAATGAATAT 59.584 36.000 0.00 0.00 0.00 1.28
4276 8642 4.759693 AGTTTGAACCGTCTGCAATGAATA 59.240 37.500 0.00 0.00 0.00 1.75
4277 8643 3.569701 AGTTTGAACCGTCTGCAATGAAT 59.430 39.130 0.00 0.00 0.00 2.57
4279 8645 2.571212 AGTTTGAACCGTCTGCAATGA 58.429 42.857 0.00 0.00 0.00 2.57
4281 8647 4.072131 ACATAGTTTGAACCGTCTGCAAT 58.928 39.130 0.00 0.00 0.00 3.56
4282 8648 3.472652 ACATAGTTTGAACCGTCTGCAA 58.527 40.909 0.00 0.00 0.00 4.08
4285 8651 5.666969 TGAAACATAGTTTGAACCGTCTG 57.333 39.130 0.00 0.00 0.00 3.51
4286 8652 4.213482 GCTGAAACATAGTTTGAACCGTCT 59.787 41.667 0.00 0.00 0.00 4.18
4375 8769 6.425114 CGAGACTCTCTTTTCCAGAAAAATGA 59.575 38.462 6.98 7.01 39.49 2.57
4399 8793 1.605058 ATCGAGTCCCCAAGTCCACG 61.605 60.000 0.00 0.00 0.00 4.94
4404 8798 0.033796 TCGGTATCGAGTCCCCAAGT 60.034 55.000 0.00 0.00 40.88 3.16
4406 8800 0.819582 GTTCGGTATCGAGTCCCCAA 59.180 55.000 0.00 0.00 46.75 4.12
4419 8813 2.289195 TGATAGCTTTCAACCGTTCGGT 60.289 45.455 11.27 11.27 40.78 4.69
4444 8838 4.707030 ACGTTATGATGAACCGTCTACA 57.293 40.909 0.00 0.00 0.00 2.74
4524 8918 8.584157 TCTCATCTTTAGCTCTCTTATGGATTC 58.416 37.037 0.00 0.00 0.00 2.52
4529 8923 7.656542 TGCAATCTCATCTTTAGCTCTCTTATG 59.343 37.037 0.00 0.00 0.00 1.90
4543 8937 7.774157 ACTTCAATTGACTATGCAATCTCATCT 59.226 33.333 7.89 0.00 37.50 2.90
4636 9030 2.232452 ACAAGACACTGCCTACTGCTAG 59.768 50.000 0.00 0.00 42.00 3.42
4637 9031 2.231478 GACAAGACACTGCCTACTGCTA 59.769 50.000 0.00 0.00 42.00 3.49
4638 9032 1.001406 GACAAGACACTGCCTACTGCT 59.999 52.381 0.00 0.00 42.00 4.24
4639 9033 1.001406 AGACAAGACACTGCCTACTGC 59.999 52.381 0.00 0.00 41.77 4.40
4640 9034 4.521130 TTAGACAAGACACTGCCTACTG 57.479 45.455 0.00 0.00 0.00 2.74
4641 9035 4.589374 ACTTTAGACAAGACACTGCCTACT 59.411 41.667 0.00 0.00 0.00 2.57
4642 9036 4.884247 ACTTTAGACAAGACACTGCCTAC 58.116 43.478 0.00 0.00 0.00 3.18
4643 9037 5.297547 CAACTTTAGACAAGACACTGCCTA 58.702 41.667 0.00 0.00 0.00 3.93
4644 9038 4.130118 CAACTTTAGACAAGACACTGCCT 58.870 43.478 0.00 0.00 0.00 4.75
4645 9039 3.251004 CCAACTTTAGACAAGACACTGCC 59.749 47.826 0.00 0.00 0.00 4.85
4646 9040 4.127171 TCCAACTTTAGACAAGACACTGC 58.873 43.478 0.00 0.00 0.00 4.40
4647 9041 6.677781 TTTCCAACTTTAGACAAGACACTG 57.322 37.500 0.00 0.00 0.00 3.66
4651 9045 6.438763 CACCATTTCCAACTTTAGACAAGAC 58.561 40.000 0.00 0.00 0.00 3.01
4717 9111 5.904362 AGGAACTGCAGGACAAATTAATC 57.096 39.130 19.93 0.45 37.18 1.75
4765 9159 0.532573 TCTCGTCATCAGGTCAAGGC 59.467 55.000 0.00 0.00 0.00 4.35
4866 9260 7.037370 TGGTACATATCATTCTGGCCTATTCAT 60.037 37.037 3.32 0.00 0.00 2.57
4872 9266 3.716353 TGTGGTACATATCATTCTGGCCT 59.284 43.478 3.32 0.00 44.52 5.19
4931 9326 4.781775 TGTTCTTCAGGGGTGTTAAGAA 57.218 40.909 0.00 0.00 36.02 2.52
4959 9354 1.465794 AGGAAGCTGTCTCGGTCTAC 58.534 55.000 0.00 0.00 0.00 2.59
4960 9355 2.239150 ACTAGGAAGCTGTCTCGGTCTA 59.761 50.000 0.00 0.00 0.00 2.59
4972 9367 5.819901 AGTTGCATAAATCTCACTAGGAAGC 59.180 40.000 0.00 0.00 0.00 3.86
5001 9396 5.185442 ACTTTACTCCGAAAACCACCAAAAA 59.815 36.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.