Multiple sequence alignment - TraesCS7D01G532600

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 TraesCS7D01G532600 chr7D 100.000 5065 0 0 1 5065 626355450 626360514 0.000000e+00 9354.0
1 TraesCS7D01G532600 chr7D 94.915 118 6 0 1977 2094 301329741 301329624 8.660000e-43 185.0
2 TraesCS7D01G532600 chr7B 93.354 2904 135 22 877 3753 726136232 726139104 0.000000e+00 4241.0
3 TraesCS7D01G532600 chr7B 95.472 1060 31 9 4017 5065 726139097 726140150 0.000000e+00 1676.0
4 TraesCS7D01G532600 chr7B 84.311 631 78 16 95 716 726134051 726134669 9.390000e-167 597.0
5 TraesCS7D01G532600 chr7A 94.607 1780 75 6 2091 3861 721914316 721916083 0.000000e+00 2736.0
6 TraesCS7D01G532600 chr7A 94.745 685 35 1 1290 1973 721913632 721914316 0.000000e+00 1064.0
7 TraesCS7D01G532600 chr7A 95.938 517 20 1 3864 4379 721916250 721916766 0.000000e+00 837.0
8 TraesCS7D01G532600 chr7A 91.183 465 33 5 13 470 721909584 721910047 4.310000e-175 625.0
9 TraesCS7D01G532600 chr7A 88.372 387 15 14 870 1251 721913271 721913632 6.020000e-119 438.0
10 TraesCS7D01G532600 chr7A 95.392 217 8 2 4335 4550 721917119 721917334 1.350000e-90 344.0
11 TraesCS7D01G532600 chr7A 98.131 107 2 0 610 716 721910433 721910539 2.410000e-43 187.0
12 TraesCS7D01G532600 chr7A 87.500 128 8 2 741 860 721910837 721910964 1.900000e-29 141.0
13 TraesCS7D01G532600 chr7A 85.567 97 1 3 487 583 721910354 721910437 6.980000e-14 89.8
14 TraesCS7D01G532600 chr2D 82.197 264 33 10 4037 4298 130437443 130437694 1.100000e-51 215.0
15 TraesCS7D01G532600 chr5B 95.833 120 3 2 1976 2094 619116729 619116611 5.180000e-45 193.0
16 TraesCS7D01G532600 chr5B 95.000 120 4 2 1976 2094 619080105 619079987 2.410000e-43 187.0
17 TraesCS7D01G532600 chr6B 93.750 128 5 2 1970 2094 293966297 293966170 6.690000e-44 189.0
18 TraesCS7D01G532600 chr6B 86.364 132 14 4 4028 4157 662150374 662150503 1.900000e-29 141.0
19 TraesCS7D01G532600 chr5D 94.915 118 6 0 1977 2094 2138693 2138576 8.660000e-43 185.0
20 TraesCS7D01G532600 chr5D 93.333 75 4 1 741 814 335224568 335224642 5.360000e-20 110.0
21 TraesCS7D01G532600 chr4D 94.915 118 6 0 1977 2094 367720770 367720887 8.660000e-43 185.0
22 TraesCS7D01G532600 chr3B 94.215 121 7 0 1974 2094 658489670 658489550 8.660000e-43 185.0
23 TraesCS7D01G532600 chr6D 93.023 129 4 3 1970 2094 178852191 178852318 3.110000e-42 183.0
24 TraesCS7D01G532600 chr6D 76.471 187 32 7 4041 4217 437403354 437403538 1.940000e-14 91.6


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 TraesCS7D01G532600 chr7D 626355450 626360514 5064 False 9354.000000 9354 100.000000 1 5065 1 chr7D.!!$F1 5064
1 TraesCS7D01G532600 chr7B 726134051 726140150 6099 False 2171.333333 4241 91.045667 95 5065 3 chr7B.!!$F1 4970
2 TraesCS7D01G532600 chr7A 721909584 721917334 7750 False 717.977778 2736 92.381667 13 4550 9 chr7A.!!$F1 4537

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
850 2202 0.321653 AGAACAGGGCCGCTAACAAG 60.322 55.0 0.00 0.0 0.00 3.16 F
1389 5175 0.179134 CGTCTGTCCGATCTGGTTCC 60.179 60.0 3.97 0.0 39.52 3.62 F
2084 5880 0.110823 CGGACAAGCTTTTTCGGACG 60.111 55.0 5.34 0.0 0.00 4.79 F
2085 5881 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.0 0.00 0.0 0.00 4.79 F
2088 5884 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 5861 0.110823 CGTCCGAAAAAGCTTGTCCG 60.111 55.000 0.00 0.0 0.00 4.79 R
2886 6804 0.234884 GAACGAAACAGGAGCAACCG 59.765 55.000 0.00 0.0 44.74 4.44 R
3509 7429 0.247262 CATCGAAACATGCGACGTGG 60.247 55.000 0.00 0.0 40.94 4.94 R
3946 8035 4.353777 TGGTGATATATCCACTAGGCTCC 58.646 47.826 10.25 0.0 35.05 4.70 R
4180 8273 0.535553 TAACTGGTGCCCGGTGTTTC 60.536 55.000 0.00 0.0 43.15 2.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 7.162546 CGATGAGAAATATAAAGCAAACACACG 59.837 37.037 0.00 0.00 0.00 4.49
66 67 6.086222 AGAAATATAAAGCAAACACACGCAG 58.914 36.000 0.00 0.00 0.00 5.18
70 71 2.869233 AAGCAAACACACGCAGAAAT 57.131 40.000 0.00 0.00 0.00 2.17
83 84 6.019640 CACACGCAGAAATGAGAAAACAAATT 60.020 34.615 0.00 0.00 0.00 1.82
123 128 4.615949 GTTTGTGTGCCATGTATTTCACA 58.384 39.130 0.00 0.00 42.69 3.58
145 150 5.536161 ACATGGACATAAAGAGTTGCAACTT 59.464 36.000 31.58 19.16 39.88 2.66
399 409 9.838975 TTATGTTGTGTTACAGCTTGAAATATG 57.161 29.630 0.00 0.00 30.20 1.78
461 471 9.688592 GAGTGCGGTGTACTAATAAGTATATTT 57.311 33.333 0.00 0.00 40.30 1.40
523 823 9.677567 AAACAAAGAATCATGTATAACACACAC 57.322 29.630 0.00 0.00 40.86 3.82
524 824 8.389779 ACAAAGAATCATGTATAACACACACA 57.610 30.769 0.00 0.00 40.86 3.72
525 825 8.289618 ACAAAGAATCATGTATAACACACACAC 58.710 33.333 0.00 0.00 40.86 3.82
526 826 7.977789 AAGAATCATGTATAACACACACACA 57.022 32.000 0.00 0.00 40.86 3.72
527 827 7.364522 AGAATCATGTATAACACACACACAC 57.635 36.000 0.00 0.00 40.86 3.82
528 828 6.934083 AGAATCATGTATAACACACACACACA 59.066 34.615 0.00 0.00 40.86 3.72
529 829 5.915812 TCATGTATAACACACACACACAC 57.084 39.130 0.00 0.00 40.86 3.82
716 1020 2.900122 AACGTCGCAGAATGAAATGG 57.100 45.000 0.00 0.00 39.69 3.16
717 1021 1.086696 ACGTCGCAGAATGAAATGGG 58.913 50.000 0.00 0.00 39.69 4.00
720 1024 2.355756 CGTCGCAGAATGAAATGGGATT 59.644 45.455 0.00 0.00 39.69 3.01
722 1026 2.689471 TCGCAGAATGAAATGGGATTGG 59.311 45.455 0.00 0.00 39.69 3.16
723 1027 2.223876 CGCAGAATGAAATGGGATTGGG 60.224 50.000 0.00 0.00 39.69 4.12
724 1028 2.767960 GCAGAATGAAATGGGATTGGGT 59.232 45.455 0.00 0.00 39.69 4.51
726 1030 4.681512 GCAGAATGAAATGGGATTGGGTTC 60.682 45.833 0.00 0.00 39.69 3.62
728 1032 5.046448 CAGAATGAAATGGGATTGGGTTCAA 60.046 40.000 0.00 0.00 39.69 2.69
729 1033 5.547276 AGAATGAAATGGGATTGGGTTCAAA 59.453 36.000 0.00 0.00 36.36 2.69
730 1034 5.839517 ATGAAATGGGATTGGGTTCAAAA 57.160 34.783 0.00 0.00 36.36 2.44
808 2152 4.449131 ACATGAGCCATATGACTCAAGTG 58.551 43.478 23.47 19.89 45.49 3.16
809 2153 2.910199 TGAGCCATATGACTCAAGTGC 58.090 47.619 18.21 3.93 39.89 4.40
810 2154 2.236893 TGAGCCATATGACTCAAGTGCA 59.763 45.455 18.21 0.00 39.89 4.57
813 2157 5.039920 AGCCATATGACTCAAGTGCAATA 57.960 39.130 3.65 0.00 0.00 1.90
850 2202 0.321653 AGAACAGGGCCGCTAACAAG 60.322 55.000 0.00 0.00 0.00 3.16
880 4654 3.787001 CACGGGCCCTCCTTCTCC 61.787 72.222 22.43 0.00 0.00 3.71
934 4710 3.138728 GCCAGATCCATCCCACCCC 62.139 68.421 0.00 0.00 0.00 4.95
935 4711 1.697394 CCAGATCCATCCCACCCCA 60.697 63.158 0.00 0.00 0.00 4.96
938 4714 2.699938 ATCCATCCCACCCCACCC 60.700 66.667 0.00 0.00 0.00 4.61
939 4715 3.611974 ATCCATCCCACCCCACCCA 62.612 63.158 0.00 0.00 0.00 4.51
1178 4964 2.784654 CGATCCCCTCTCCTCCCCT 61.785 68.421 0.00 0.00 0.00 4.79
1389 5175 0.179134 CGTCTGTCCGATCTGGTTCC 60.179 60.000 3.97 0.00 39.52 3.62
1394 5180 0.179134 GTCCGATCTGGTTCCGTCTG 60.179 60.000 3.97 0.00 39.52 3.51
1445 5231 1.740380 CGGAGCAGTGGTGATTGTAGG 60.740 57.143 0.00 0.00 0.00 3.18
1482 5268 4.584743 GGGAGTTGTTCAGATTTGGTCTTT 59.415 41.667 0.00 0.00 34.00 2.52
1492 5278 5.532406 TCAGATTTGGTCTTTCAGGTTCTTG 59.468 40.000 0.00 0.00 34.00 3.02
1507 5293 4.536489 AGGTTCTTGTACTAGGAAGGCAAT 59.464 41.667 4.46 0.00 0.00 3.56
1555 5343 6.417930 GTGCTATTCTTGAACAAAGACCAAAC 59.582 38.462 0.00 0.00 44.77 2.93
1565 5353 5.424121 ACAAAGACCAAACAGAAATCTCG 57.576 39.130 0.00 0.00 0.00 4.04
1590 5378 4.827481 CCGTAGCAAGCGGTGTAT 57.173 55.556 5.61 0.00 43.84 2.29
1591 5379 2.589890 CCGTAGCAAGCGGTGTATC 58.410 57.895 5.61 0.00 43.84 2.24
1619 5407 4.907582 CGTTTTTATCAGTTCCCAACGTTC 59.092 41.667 0.00 0.00 36.23 3.95
1633 5421 1.881252 CGTTCCGACAATAGGGCGG 60.881 63.158 1.30 1.30 46.08 6.13
1674 5462 1.837439 ACAAGCGGGGTTGATCATCTA 59.163 47.619 16.61 0.00 0.00 1.98
1801 5596 5.912955 GGTTAGCAAACAAGTGTGTAATCAC 59.087 40.000 0.00 0.00 39.84 3.06
1874 5670 6.644592 GCATTAAATTTGAGCAAACTGGTACA 59.355 34.615 0.00 0.00 32.51 2.90
1908 5704 7.504924 TTACAACCTTATGTGAAGTGAAAGG 57.495 36.000 0.00 0.00 42.01 3.11
1923 5719 0.250597 AAAGGGGCGTCTGGTGTTAC 60.251 55.000 0.00 0.00 0.00 2.50
1972 5768 7.727578 TTACACAAGACATCTGGAACCTATA 57.272 36.000 0.00 0.00 0.00 1.31
1973 5769 6.814954 ACACAAGACATCTGGAACCTATAT 57.185 37.500 0.00 0.00 0.00 0.86
1974 5770 7.200434 ACACAAGACATCTGGAACCTATATT 57.800 36.000 0.00 0.00 0.00 1.28
1975 5771 8.319057 ACACAAGACATCTGGAACCTATATTA 57.681 34.615 0.00 0.00 0.00 0.98
1976 5772 8.938883 ACACAAGACATCTGGAACCTATATTAT 58.061 33.333 0.00 0.00 0.00 1.28
1981 5777 9.482175 AGACATCTGGAACCTATATTATACTCC 57.518 37.037 0.00 0.00 0.00 3.85
1982 5778 8.611051 ACATCTGGAACCTATATTATACTCCC 57.389 38.462 0.00 0.00 0.00 4.30
1983 5779 8.410623 ACATCTGGAACCTATATTATACTCCCT 58.589 37.037 0.00 0.00 0.00 4.20
1984 5780 8.919145 CATCTGGAACCTATATTATACTCCCTC 58.081 40.741 0.00 0.00 0.00 4.30
1985 5781 8.245929 TCTGGAACCTATATTATACTCCCTCT 57.754 38.462 0.00 0.00 0.00 3.69
1986 5782 8.116669 TCTGGAACCTATATTATACTCCCTCTG 58.883 40.741 0.00 0.00 0.00 3.35
1987 5783 7.776745 TGGAACCTATATTATACTCCCTCTGT 58.223 38.462 0.00 0.00 0.00 3.41
1988 5784 7.894364 TGGAACCTATATTATACTCCCTCTGTC 59.106 40.741 0.00 0.00 0.00 3.51
1989 5785 7.342541 GGAACCTATATTATACTCCCTCTGTCC 59.657 44.444 0.00 0.00 0.00 4.02
1990 5786 6.424883 ACCTATATTATACTCCCTCTGTCCG 58.575 44.000 0.00 0.00 0.00 4.79
1991 5787 6.217074 ACCTATATTATACTCCCTCTGTCCGA 59.783 42.308 0.00 0.00 0.00 4.55
1992 5788 7.117397 CCTATATTATACTCCCTCTGTCCGAA 58.883 42.308 0.00 0.00 0.00 4.30
1993 5789 7.614583 CCTATATTATACTCCCTCTGTCCGAAA 59.385 40.741 0.00 0.00 0.00 3.46
1994 5790 7.850935 ATATTATACTCCCTCTGTCCGAAAA 57.149 36.000 0.00 0.00 0.00 2.29
1995 5791 6.555463 ATTATACTCCCTCTGTCCGAAAAA 57.445 37.500 0.00 0.00 0.00 1.94
1996 5792 2.841442 ACTCCCTCTGTCCGAAAAAG 57.159 50.000 0.00 0.00 0.00 2.27
1997 5793 1.270893 ACTCCCTCTGTCCGAAAAAGC 60.271 52.381 0.00 0.00 0.00 3.51
1998 5794 1.002544 CTCCCTCTGTCCGAAAAAGCT 59.997 52.381 0.00 0.00 0.00 3.74
1999 5795 1.420138 TCCCTCTGTCCGAAAAAGCTT 59.580 47.619 0.00 0.00 0.00 3.74
2000 5796 1.537202 CCCTCTGTCCGAAAAAGCTTG 59.463 52.381 0.00 0.00 0.00 4.01
2001 5797 2.222027 CCTCTGTCCGAAAAAGCTTGT 58.778 47.619 0.00 0.00 0.00 3.16
2002 5798 2.224314 CCTCTGTCCGAAAAAGCTTGTC 59.776 50.000 0.00 0.00 0.00 3.18
2003 5799 2.218603 TCTGTCCGAAAAAGCTTGTCC 58.781 47.619 0.00 0.00 0.00 4.02
2004 5800 1.266989 CTGTCCGAAAAAGCTTGTCCC 59.733 52.381 0.00 0.00 0.00 4.46
2005 5801 1.133915 TGTCCGAAAAAGCTTGTCCCT 60.134 47.619 0.00 0.00 0.00 4.20
2006 5802 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
2007 5803 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
2008 5804 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
2009 5805 2.360801 CCGAAAAAGCTTGTCCCTCAAA 59.639 45.455 0.00 0.00 35.48 2.69
2010 5806 3.005791 CCGAAAAAGCTTGTCCCTCAAAT 59.994 43.478 0.00 0.00 35.48 2.32
2011 5807 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
2012 5808 4.309933 GAAAAAGCTTGTCCCTCAAATGG 58.690 43.478 0.00 0.00 35.48 3.16
2013 5809 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
2014 5810 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
2015 5811 3.463048 AGCTTGTCCCTCAAATGGATT 57.537 42.857 0.00 0.00 35.48 3.01
2016 5812 3.782992 AGCTTGTCCCTCAAATGGATTT 58.217 40.909 0.00 0.00 35.48 2.17
2017 5813 4.934356 AGCTTGTCCCTCAAATGGATTTA 58.066 39.130 0.00 0.00 35.48 1.40
2018 5814 5.522641 AGCTTGTCCCTCAAATGGATTTAT 58.477 37.500 0.00 0.00 35.48 1.40
2019 5815 5.595952 AGCTTGTCCCTCAAATGGATTTATC 59.404 40.000 0.00 0.00 35.48 1.75
2020 5816 5.595952 GCTTGTCCCTCAAATGGATTTATCT 59.404 40.000 0.00 0.00 35.48 1.98
2021 5817 6.772716 GCTTGTCCCTCAAATGGATTTATCTA 59.227 38.462 0.00 0.00 35.48 1.98
2022 5818 7.040823 GCTTGTCCCTCAAATGGATTTATCTAG 60.041 40.741 0.00 0.00 35.48 2.43
2023 5819 6.299141 TGTCCCTCAAATGGATTTATCTAGC 58.701 40.000 0.00 0.00 33.65 3.42
2024 5820 6.126507 TGTCCCTCAAATGGATTTATCTAGCA 60.127 38.462 0.00 0.00 33.65 3.49
2025 5821 6.205658 GTCCCTCAAATGGATTTATCTAGCAC 59.794 42.308 0.00 0.00 33.65 4.40
2026 5822 5.474876 CCCTCAAATGGATTTATCTAGCACC 59.525 44.000 0.00 0.00 0.00 5.01
2027 5823 6.064060 CCTCAAATGGATTTATCTAGCACCA 58.936 40.000 0.00 0.00 0.00 4.17
2028 5824 6.547141 CCTCAAATGGATTTATCTAGCACCAA 59.453 38.462 0.00 0.00 0.00 3.67
2029 5825 7.255381 CCTCAAATGGATTTATCTAGCACCAAG 60.255 40.741 0.00 0.00 0.00 3.61
2030 5826 7.118723 TCAAATGGATTTATCTAGCACCAAGT 58.881 34.615 0.00 0.00 0.00 3.16
2031 5827 7.615365 TCAAATGGATTTATCTAGCACCAAGTT 59.385 33.333 0.00 0.00 0.00 2.66
2032 5828 8.902806 CAAATGGATTTATCTAGCACCAAGTTA 58.097 33.333 0.00 0.00 0.00 2.24
2033 5829 8.682936 AATGGATTTATCTAGCACCAAGTTAG 57.317 34.615 0.00 0.00 32.79 2.34
2034 5830 7.195374 TGGATTTATCTAGCACCAAGTTAGT 57.805 36.000 0.00 0.00 33.25 2.24
2035 5831 7.047891 TGGATTTATCTAGCACCAAGTTAGTG 58.952 38.462 0.00 0.00 38.30 2.74
2047 5843 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2048 5844 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2049 5845 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
2050 5846 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
2051 5847 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
2052 5848 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
2053 5849 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
2054 5850 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2055 5851 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
2056 5852 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
2057 5853 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
2058 5854 5.549228 TGCTAGATACATCCATTTGAGGGAT 59.451 40.000 0.00 0.00 45.98 3.85
2064 5860 3.967467 ATCCATTTGAGGGATGAGCTT 57.033 42.857 0.00 0.00 43.44 3.74
2065 5861 3.287867 TCCATTTGAGGGATGAGCTTC 57.712 47.619 0.00 0.00 0.00 3.86
2066 5862 1.945394 CCATTTGAGGGATGAGCTTCG 59.055 52.381 0.00 0.00 0.00 3.79
2067 5863 1.945394 CATTTGAGGGATGAGCTTCGG 59.055 52.381 0.00 0.00 0.00 4.30
2068 5864 1.275666 TTTGAGGGATGAGCTTCGGA 58.724 50.000 0.00 0.00 0.00 4.55
2069 5865 0.537188 TTGAGGGATGAGCTTCGGAC 59.463 55.000 0.00 0.00 0.00 4.79
2070 5866 0.614697 TGAGGGATGAGCTTCGGACA 60.615 55.000 0.00 0.00 0.00 4.02
2071 5867 0.537188 GAGGGATGAGCTTCGGACAA 59.463 55.000 0.00 0.00 0.00 3.18
2072 5868 0.539051 AGGGATGAGCTTCGGACAAG 59.461 55.000 0.00 0.00 0.00 3.16
2073 5869 1.092345 GGGATGAGCTTCGGACAAGC 61.092 60.000 0.00 0.00 43.31 4.01
2080 5876 1.674908 GCTTCGGACAAGCTTTTTCG 58.325 50.000 6.98 6.98 40.01 3.46
2081 5877 1.663161 GCTTCGGACAAGCTTTTTCGG 60.663 52.381 13.16 9.25 40.01 4.30
2082 5878 1.871039 CTTCGGACAAGCTTTTTCGGA 59.129 47.619 13.16 11.24 0.00 4.55
2083 5879 1.223187 TCGGACAAGCTTTTTCGGAC 58.777 50.000 13.16 0.00 0.00 4.79
2084 5880 0.110823 CGGACAAGCTTTTTCGGACG 60.111 55.000 5.34 0.00 0.00 4.79
2085 5881 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
2086 5882 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
2087 5883 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
2088 5884 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
2089 5885 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
2096 6010 1.308069 TTCGGACGGAGGGAGTAACG 61.308 60.000 0.00 0.00 0.00 3.18
2118 6032 8.561738 AACGACCAATCAACTATACAAGAAAT 57.438 30.769 0.00 0.00 0.00 2.17
2151 6065 2.882927 TCCATTGACCGTTATCTCCG 57.117 50.000 0.00 0.00 0.00 4.63
2165 6079 5.450137 CGTTATCTCCGTCATAACTGGAGTT 60.450 44.000 7.32 0.00 42.17 3.01
2209 6123 4.214310 TGCCATGACTTCAGGAAAAAGAA 58.786 39.130 0.00 0.00 0.00 2.52
2210 6124 4.037923 TGCCATGACTTCAGGAAAAAGAAC 59.962 41.667 0.00 0.00 0.00 3.01
2242 6156 3.888323 TGCCACAAAGAAGCATGTTAAGA 59.112 39.130 0.00 0.00 0.00 2.10
2284 6198 4.356405 TCTTCTTCAACCTGCTGAATCA 57.644 40.909 0.00 0.00 34.86 2.57
2354 6268 5.131642 TCCAGATTCTTCCAGCATAGTTCAT 59.868 40.000 0.00 0.00 0.00 2.57
2367 6281 4.637534 GCATAGTTCATCATGACCACACTT 59.362 41.667 0.00 0.00 0.00 3.16
2422 6336 3.473923 AAAGTTGGCCATGTTTTCCAG 57.526 42.857 6.09 0.00 0.00 3.86
2460 6374 7.541162 CATCTTCCATTGTATGTTGATTGTGT 58.459 34.615 0.00 0.00 0.00 3.72
2480 6394 7.744087 TGTGTCAGTGCTCTGTATTTTTAAT 57.256 32.000 15.01 0.00 41.91 1.40
2488 6402 9.851686 AGTGCTCTGTATTTTTAATCATATCCA 57.148 29.630 0.00 0.00 0.00 3.41
2515 6429 9.539825 GTCCAGGCATAAGTATCATTCTATATG 57.460 37.037 0.00 0.00 0.00 1.78
2526 6444 9.482175 AGTATCATTCTATATGTCCTTAGACCC 57.518 37.037 0.00 0.00 42.81 4.46
2529 6447 8.138928 TCATTCTATATGTCCTTAGACCCATG 57.861 38.462 0.00 0.00 42.81 3.66
2531 6449 8.766476 CATTCTATATGTCCTTAGACCCATGAT 58.234 37.037 0.00 0.00 42.81 2.45
2550 6468 8.152246 CCCATGATCCATTTATTTTAACAGCAT 58.848 33.333 0.00 0.00 0.00 3.79
2622 6540 6.014925 GGTTTTGGATTTTCTACAGGGCTAAA 60.015 38.462 0.00 0.00 0.00 1.85
2690 6608 3.162666 TCGTCCTTCCACTCTACACATT 58.837 45.455 0.00 0.00 0.00 2.71
2851 6769 7.500892 TCTCCACTCTTTTTGTATGTGCTTTAA 59.499 33.333 0.00 0.00 0.00 1.52
2886 6804 8.609478 TTAACTTTCTGTGAACGAATTGAAAC 57.391 30.769 0.00 0.00 0.00 2.78
2920 6838 2.746269 TCGTTCCTGGTCTTGTTAACG 58.254 47.619 7.91 7.91 40.61 3.18
3129 7047 6.428159 AGACTTGTTGACAGATCATTACAACC 59.572 38.462 16.33 6.72 39.66 3.77
3155 7073 6.088085 CAGGAAAGCAAATTTATCACGTGTTC 59.912 38.462 16.51 6.98 0.00 3.18
3169 7087 4.152223 TCACGTGTTCTGAGTTGCATAATG 59.848 41.667 16.51 0.00 0.00 1.90
3231 7149 4.804139 GCTATGTTTATGCGTGTCTGTAGT 59.196 41.667 0.00 0.00 0.00 2.73
3245 7163 5.411977 GTGTCTGTAGTGAGTTAGAGCTACA 59.588 44.000 0.00 0.00 40.71 2.74
3303 7221 7.811236 TGGTAGTTCTTAGACAGTTTATCAACG 59.189 37.037 0.00 0.00 38.03 4.10
3315 7233 5.929992 CAGTTTATCAACGGAGGTCAAAGTA 59.070 40.000 0.00 0.00 38.03 2.24
3395 7315 4.421058 ACGTCTTTCTTTTGTTTGCCTTC 58.579 39.130 0.00 0.00 0.00 3.46
3441 7361 2.359975 CCCGGCCTGTTCTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
3509 7429 2.267324 GGCTGACAGAGACCCTGC 59.733 66.667 6.65 0.00 46.81 4.85
3527 7447 1.966493 GCCACGTCGCATGTTTCGAT 61.966 55.000 0.00 0.00 38.29 3.59
3594 7519 3.126686 CCCCTGTTGTTTGCAAGTTTTTG 59.873 43.478 0.00 0.00 34.94 2.44
3603 7528 5.641209 TGTTTGCAAGTTTTTGTTAGCACAT 59.359 32.000 0.00 0.00 36.65 3.21
3717 7642 2.049156 TTGTCGCACGCTCTGAGG 60.049 61.111 6.83 0.00 0.00 3.86
3815 7740 7.659186 CACTCTTAACTTCCAGTAGTTAGTGT 58.341 38.462 8.97 3.54 40.59 3.55
3874 7923 4.767255 CCTGACGCAGCCCCTGAC 62.767 72.222 0.00 0.00 32.44 3.51
3900 7949 4.617454 GCGTGCGTGCATCGATCG 62.617 66.667 9.36 9.36 42.86 3.69
3901 7950 3.247455 CGTGCGTGCATCGATCGT 61.247 61.111 15.94 0.00 42.86 3.73
3902 7951 1.937362 CGTGCGTGCATCGATCGTA 60.937 57.895 15.94 2.15 42.86 3.43
3903 7952 1.553654 GTGCGTGCATCGATCGTAC 59.446 57.895 15.94 9.68 42.86 3.67
3904 7953 0.866061 GTGCGTGCATCGATCGTACT 60.866 55.000 15.94 0.00 42.86 2.73
3907 7956 1.951792 CGTGCATCGATCGTACTAGG 58.048 55.000 15.94 0.00 42.86 3.02
4118 8207 9.914923 GTTTATGTGAAAAACTGGATCAAAAAC 57.085 29.630 0.00 0.00 34.66 2.43
4180 8273 3.497118 ACATGAAAACACACACACAACG 58.503 40.909 0.00 0.00 0.00 4.10
4218 8311 4.338118 AGTTACAACACAACACAAGGATGG 59.662 41.667 0.00 0.00 0.00 3.51
4367 8465 2.237751 CGCATTAGGCCCGTCGAAG 61.238 63.158 0.00 0.00 40.31 3.79
4448 8943 2.095718 GCCGCAAGAGAACGAGATTTTT 60.096 45.455 0.00 0.00 43.02 1.94
4496 8991 2.747396 TGCTGCCATTTGGTCATTTC 57.253 45.000 0.00 0.00 37.57 2.17
4659 9155 7.519008 CGACTCTTAGCAGTTTTGTTGAGAATT 60.519 37.037 0.00 0.00 31.51 2.17
4771 9267 5.245301 TCTTTCCTTTCGGACAAGAGTCATA 59.755 40.000 0.00 0.00 46.80 2.15
4796 9292 7.712204 TCGATTATATAGATGTAACAGCCCA 57.288 36.000 0.00 0.00 0.00 5.36
4823 9319 4.076394 TGTTACCCTGCCATCTTTGTAAC 58.924 43.478 0.00 0.00 38.82 2.50
4941 9438 7.039313 ACTTCCAAAGTTTCCAATACAACTC 57.961 36.000 0.00 0.00 39.04 3.01
4943 9440 5.450453 TCCAAAGTTTCCAATACAACTCCA 58.550 37.500 0.00 0.00 31.79 3.86
4944 9441 6.074648 TCCAAAGTTTCCAATACAACTCCAT 58.925 36.000 0.00 0.00 31.79 3.41
4956 9454 9.196552 CCAATACAACTCCATTTCTTTCTTTTC 57.803 33.333 0.00 0.00 0.00 2.29
5009 9507 8.754991 TTACTTCTTCCAAAAATGTCCAACTA 57.245 30.769 0.00 0.00 0.00 2.24
5058 9556 4.335416 TGAGCCACCCTCTTAAATTTCAG 58.665 43.478 0.00 0.00 41.35 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.533153 TCGGTTTTATTTCATTTCACGTTTTTC 58.467 29.630 0.00 0.00 0.00 2.29
14 15 8.408743 TCGGTTTTATTTCATTTCACGTTTTT 57.591 26.923 0.00 0.00 0.00 1.94
16 17 7.863375 TCATCGGTTTTATTTCATTTCACGTTT 59.137 29.630 0.00 0.00 0.00 3.60
17 18 7.364200 TCATCGGTTTTATTTCATTTCACGTT 58.636 30.769 0.00 0.00 0.00 3.99
18 19 6.904498 TCATCGGTTTTATTTCATTTCACGT 58.096 32.000 0.00 0.00 0.00 4.49
19 20 7.240674 TCTCATCGGTTTTATTTCATTTCACG 58.759 34.615 0.00 0.00 0.00 4.35
20 21 8.964420 TTCTCATCGGTTTTATTTCATTTCAC 57.036 30.769 0.00 0.00 0.00 3.18
48 49 3.980646 TTCTGCGTGTGTTTGCTTTAT 57.019 38.095 0.00 0.00 0.00 1.40
54 55 3.607422 TCTCATTTCTGCGTGTGTTTG 57.393 42.857 0.00 0.00 0.00 2.93
123 128 6.942576 ACTAAGTTGCAACTCTTTATGTCCAT 59.057 34.615 31.20 14.04 38.57 3.41
145 150 8.962884 ATGTATAGAATGTCAAATGTGCACTA 57.037 30.769 19.41 4.84 0.00 2.74
341 350 8.632679 TCAATTACACTGCTCTGAAAGAAAAAT 58.367 29.630 0.00 0.00 46.34 1.82
470 480 9.905713 ATCCAACAGTGTATGTGTAATTTATCT 57.094 29.630 0.00 0.00 43.00 1.98
484 496 8.684386 TGATTCTTTGTTTATCCAACAGTGTA 57.316 30.769 0.00 0.00 46.37 2.90
517 817 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
518 818 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
519 819 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
520 820 1.535028 CTTGTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
521 821 1.135717 CCTTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
522 822 1.164411 CCTTGTGTGTGTGTGTGTGT 58.836 50.000 0.00 0.00 0.00 3.72
523 823 0.179166 GCCTTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
524 824 1.312371 GGCCTTGTGTGTGTGTGTGT 61.312 55.000 0.00 0.00 0.00 3.72
525 825 1.311651 TGGCCTTGTGTGTGTGTGTG 61.312 55.000 3.32 0.00 0.00 3.82
526 826 0.395586 ATGGCCTTGTGTGTGTGTGT 60.396 50.000 3.32 0.00 0.00 3.72
527 827 0.746063 AATGGCCTTGTGTGTGTGTG 59.254 50.000 3.32 0.00 0.00 3.82
528 828 0.746063 CAATGGCCTTGTGTGTGTGT 59.254 50.000 3.32 0.00 0.00 3.72
529 829 1.031235 TCAATGGCCTTGTGTGTGTG 58.969 50.000 3.32 0.00 36.20 3.82
562 864 6.968263 TCACAAATTACCTGATTTGGTCAA 57.032 33.333 13.10 0.00 46.36 3.18
563 865 6.718912 TCATCACAAATTACCTGATTTGGTCA 59.281 34.615 13.10 0.12 46.36 4.02
700 1003 3.489738 CCAATCCCATTTCATTCTGCGAC 60.490 47.826 0.00 0.00 0.00 5.19
808 2152 8.079211 TCTATGTGTCCCCTAGATATTATTGC 57.921 38.462 0.00 0.00 0.00 3.56
809 2153 9.877178 GTTCTATGTGTCCCCTAGATATTATTG 57.123 37.037 0.00 0.00 0.00 1.90
810 2154 9.615660 TGTTCTATGTGTCCCCTAGATATTATT 57.384 33.333 0.00 0.00 0.00 1.40
813 2157 6.498651 CCTGTTCTATGTGTCCCCTAGATATT 59.501 42.308 0.00 0.00 0.00 1.28
850 2202 4.410400 CCGTGGAGGGAGGTTGCC 62.410 72.222 0.00 0.00 35.97 4.52
880 4654 2.364317 TTGGGCCCGAGAGAGAGG 60.364 66.667 19.37 0.00 0.00 3.69
966 4742 2.740055 CCGCCTCTCTGTGTGTGC 60.740 66.667 0.00 0.00 0.00 4.57
1277 5063 5.983333 AATCCACCATGACCTAGAGAAAT 57.017 39.130 0.00 0.00 0.00 2.17
1278 5064 5.250543 TCAAATCCACCATGACCTAGAGAAA 59.749 40.000 0.00 0.00 0.00 2.52
1281 5067 4.760530 TCAAATCCACCATGACCTAGAG 57.239 45.455 0.00 0.00 0.00 2.43
1282 5068 5.439721 CAATCAAATCCACCATGACCTAGA 58.560 41.667 0.00 0.00 0.00 2.43
1283 5069 4.581824 CCAATCAAATCCACCATGACCTAG 59.418 45.833 0.00 0.00 0.00 3.02
1284 5070 4.535781 CCAATCAAATCCACCATGACCTA 58.464 43.478 0.00 0.00 0.00 3.08
1285 5071 3.368248 CCAATCAAATCCACCATGACCT 58.632 45.455 0.00 0.00 0.00 3.85
1287 5073 3.364549 TCCCAATCAAATCCACCATGAC 58.635 45.455 0.00 0.00 0.00 3.06
1288 5074 3.754219 TCCCAATCAAATCCACCATGA 57.246 42.857 0.00 0.00 0.00 3.07
1289 5075 3.770933 AGTTCCCAATCAAATCCACCATG 59.229 43.478 0.00 0.00 0.00 3.66
1290 5076 4.026052 GAGTTCCCAATCAAATCCACCAT 58.974 43.478 0.00 0.00 0.00 3.55
1291 5077 3.075882 AGAGTTCCCAATCAAATCCACCA 59.924 43.478 0.00 0.00 0.00 4.17
1368 5154 0.898789 AACCAGATCGGACAGACGGT 60.899 55.000 10.05 0.00 38.63 4.83
1389 5175 2.514592 AATCGCATGGCCCAGACG 60.515 61.111 0.00 1.93 0.00 4.18
1445 5231 5.167303 ACAACTCCCTATGAAACTTCCTC 57.833 43.478 0.00 0.00 0.00 3.71
1482 5268 3.514309 GCCTTCCTAGTACAAGAACCTGA 59.486 47.826 0.00 0.00 0.00 3.86
1492 5278 3.181464 GGAGGTGATTGCCTTCCTAGTAC 60.181 52.174 0.00 0.00 39.34 2.73
1507 5293 0.961019 GCAAATGCAACTGGAGGTGA 59.039 50.000 0.00 0.00 41.59 4.02
1555 5343 1.012841 GGCTGAAGGCGAGATTTCTG 58.987 55.000 0.00 0.00 42.94 3.02
1565 5353 2.754995 GCTTGCTACGGCTGAAGGC 61.755 63.158 0.00 0.54 39.59 4.35
1633 5421 3.906720 TTGCTAACCTGGGTAGATGAC 57.093 47.619 22.83 5.12 0.00 3.06
1674 5462 7.232941 GGTACCAGAGTATATGATAACCTGTGT 59.767 40.741 7.15 0.00 0.00 3.72
1801 5596 0.249398 CTACCCTGAACCTGGGAACG 59.751 60.000 14.65 0.00 44.09 3.95
1874 5670 7.573710 TCACATAAGGTTGTAAAGATATGCCT 58.426 34.615 0.00 0.00 0.00 4.75
1908 5704 1.445582 CTCGTAACACCAGACGCCC 60.446 63.158 0.00 0.00 38.93 6.13
1923 5719 8.873215 ATGAAGATACAAAGGTTATACACTCG 57.127 34.615 0.00 0.00 0.00 4.18
1972 5768 6.555463 TTTTTCGGACAGAGGGAGTATAAT 57.445 37.500 0.00 0.00 0.00 1.28
1973 5769 5.626116 GCTTTTTCGGACAGAGGGAGTATAA 60.626 44.000 0.00 0.00 0.00 0.98
1974 5770 4.142004 GCTTTTTCGGACAGAGGGAGTATA 60.142 45.833 0.00 0.00 0.00 1.47
1975 5771 3.369576 GCTTTTTCGGACAGAGGGAGTAT 60.370 47.826 0.00 0.00 0.00 2.12
1976 5772 2.028385 GCTTTTTCGGACAGAGGGAGTA 60.028 50.000 0.00 0.00 0.00 2.59
1977 5773 1.270893 GCTTTTTCGGACAGAGGGAGT 60.271 52.381 0.00 0.00 0.00 3.85
1978 5774 1.002544 AGCTTTTTCGGACAGAGGGAG 59.997 52.381 0.00 0.00 0.00 4.30
1979 5775 1.056660 AGCTTTTTCGGACAGAGGGA 58.943 50.000 0.00 0.00 0.00 4.20
1980 5776 1.537202 CAAGCTTTTTCGGACAGAGGG 59.463 52.381 0.00 0.00 0.00 4.30
1981 5777 2.222027 ACAAGCTTTTTCGGACAGAGG 58.778 47.619 0.00 0.00 0.00 3.69
1982 5778 2.224314 GGACAAGCTTTTTCGGACAGAG 59.776 50.000 0.00 0.00 0.00 3.35
1983 5779 2.218603 GGACAAGCTTTTTCGGACAGA 58.781 47.619 0.00 0.00 0.00 3.41
1984 5780 1.266989 GGGACAAGCTTTTTCGGACAG 59.733 52.381 0.00 0.00 0.00 3.51
1985 5781 1.133915 AGGGACAAGCTTTTTCGGACA 60.134 47.619 0.00 0.00 0.00 4.02
1986 5782 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
1987 5783 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
1988 5784 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
1989 5785 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
1990 5786 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
1991 5787 3.966665 TCCATTTGAGGGACAAGCTTTTT 59.033 39.130 0.00 0.00 39.77 1.94
1992 5788 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
1993 5789 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
1994 5790 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
1995 5791 3.463048 AATCCATTTGAGGGACAAGCT 57.537 42.857 0.00 0.00 39.77 3.74
1996 5792 5.595952 AGATAAATCCATTTGAGGGACAAGC 59.404 40.000 0.00 0.00 39.77 4.01
1997 5793 7.040823 GCTAGATAAATCCATTTGAGGGACAAG 60.041 40.741 0.00 0.00 39.77 3.16
1998 5794 6.772716 GCTAGATAAATCCATTTGAGGGACAA 59.227 38.462 0.00 0.00 37.23 3.18
1999 5795 6.126507 TGCTAGATAAATCCATTTGAGGGACA 60.127 38.462 0.00 0.00 37.23 4.02
2000 5796 6.205658 GTGCTAGATAAATCCATTTGAGGGAC 59.794 42.308 0.00 0.00 37.23 4.46
2001 5797 6.299141 GTGCTAGATAAATCCATTTGAGGGA 58.701 40.000 0.00 0.00 39.14 4.20
2002 5798 5.474876 GGTGCTAGATAAATCCATTTGAGGG 59.525 44.000 0.00 0.00 0.00 4.30
2003 5799 6.064060 TGGTGCTAGATAAATCCATTTGAGG 58.936 40.000 0.00 0.00 0.00 3.86
2004 5800 7.284034 ACTTGGTGCTAGATAAATCCATTTGAG 59.716 37.037 0.00 0.00 0.00 3.02
2005 5801 7.118723 ACTTGGTGCTAGATAAATCCATTTGA 58.881 34.615 0.00 0.00 0.00 2.69
2006 5802 7.338800 ACTTGGTGCTAGATAAATCCATTTG 57.661 36.000 0.00 0.00 0.00 2.32
2007 5803 7.961326 AACTTGGTGCTAGATAAATCCATTT 57.039 32.000 0.00 0.00 0.00 2.32
2008 5804 8.275040 ACTAACTTGGTGCTAGATAAATCCATT 58.725 33.333 0.00 0.00 0.00 3.16
2009 5805 7.716998 CACTAACTTGGTGCTAGATAAATCCAT 59.283 37.037 0.00 0.00 0.00 3.41
2010 5806 7.047891 CACTAACTTGGTGCTAGATAAATCCA 58.952 38.462 0.00 0.00 0.00 3.41
2011 5807 7.484035 CACTAACTTGGTGCTAGATAAATCC 57.516 40.000 0.00 0.00 0.00 3.01
2023 5819 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
2024 5820 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
2025 5821 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
2026 5822 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
2027 5823 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
2028 5824 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
2029 5825 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
2030 5826 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
2031 5827 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
2032 5828 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
2033 5829 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
2034 5830 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2035 5831 5.489792 TCCCTCAAATGGATGTATCTAGC 57.510 43.478 0.00 0.00 0.00 3.42
2044 5840 3.746751 CGAAGCTCATCCCTCAAATGGAT 60.747 47.826 0.00 0.00 43.46 3.41
2045 5841 2.420547 CGAAGCTCATCCCTCAAATGGA 60.421 50.000 0.00 0.00 36.05 3.41
2046 5842 1.945394 CGAAGCTCATCCCTCAAATGG 59.055 52.381 0.00 0.00 0.00 3.16
2047 5843 1.945394 CCGAAGCTCATCCCTCAAATG 59.055 52.381 0.00 0.00 0.00 2.32
2048 5844 1.839994 TCCGAAGCTCATCCCTCAAAT 59.160 47.619 0.00 0.00 0.00 2.32
2049 5845 1.066143 GTCCGAAGCTCATCCCTCAAA 60.066 52.381 0.00 0.00 0.00 2.69
2050 5846 0.537188 GTCCGAAGCTCATCCCTCAA 59.463 55.000 0.00 0.00 0.00 3.02
2051 5847 0.614697 TGTCCGAAGCTCATCCCTCA 60.615 55.000 0.00 0.00 0.00 3.86
2052 5848 0.537188 TTGTCCGAAGCTCATCCCTC 59.463 55.000 0.00 0.00 0.00 4.30
2053 5849 0.539051 CTTGTCCGAAGCTCATCCCT 59.461 55.000 0.00 0.00 0.00 4.20
2054 5850 1.092345 GCTTGTCCGAAGCTCATCCC 61.092 60.000 0.00 0.00 40.01 3.85
2055 5851 2.388347 GCTTGTCCGAAGCTCATCC 58.612 57.895 0.00 0.00 40.01 3.51
2061 5857 1.663161 CCGAAAAAGCTTGTCCGAAGC 60.663 52.381 0.00 0.00 43.31 3.86
2062 5858 1.871039 TCCGAAAAAGCTTGTCCGAAG 59.129 47.619 0.00 0.00 0.00 3.79
2063 5859 1.600485 GTCCGAAAAAGCTTGTCCGAA 59.400 47.619 0.00 0.00 0.00 4.30
2064 5860 1.223187 GTCCGAAAAAGCTTGTCCGA 58.777 50.000 0.00 0.00 0.00 4.55
2065 5861 0.110823 CGTCCGAAAAAGCTTGTCCG 60.111 55.000 0.00 0.00 0.00 4.79
2066 5862 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
2067 5863 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
2068 5864 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
2069 5865 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
2070 5866 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
2071 5867 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
2072 5868 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
2073 5869 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
2074 5870 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2075 5871 1.273327 GTTACTCCCTCCGTCCGAAAA 59.727 52.381 0.00 0.00 0.00 2.29
2076 5872 0.890683 GTTACTCCCTCCGTCCGAAA 59.109 55.000 0.00 0.00 0.00 3.46
2077 5873 1.308069 CGTTACTCCCTCCGTCCGAA 61.308 60.000 0.00 0.00 0.00 4.30
2078 5874 1.746615 CGTTACTCCCTCCGTCCGA 60.747 63.158 0.00 0.00 0.00 4.55
2079 5875 1.746615 TCGTTACTCCCTCCGTCCG 60.747 63.158 0.00 0.00 0.00 4.79
2080 5876 1.661498 GGTCGTTACTCCCTCCGTCC 61.661 65.000 0.00 0.00 0.00 4.79
2081 5877 0.962356 TGGTCGTTACTCCCTCCGTC 60.962 60.000 0.00 0.00 0.00 4.79
2082 5878 0.540365 TTGGTCGTTACTCCCTCCGT 60.540 55.000 0.00 0.00 0.00 4.69
2083 5879 0.822164 ATTGGTCGTTACTCCCTCCG 59.178 55.000 0.00 0.00 0.00 4.63
2084 5880 1.829222 TGATTGGTCGTTACTCCCTCC 59.171 52.381 0.00 0.00 0.00 4.30
2085 5881 3.056035 AGTTGATTGGTCGTTACTCCCTC 60.056 47.826 0.00 0.00 0.00 4.30
2086 5882 2.904434 AGTTGATTGGTCGTTACTCCCT 59.096 45.455 0.00 0.00 0.00 4.20
2087 5883 3.329929 AGTTGATTGGTCGTTACTCCC 57.670 47.619 0.00 0.00 0.00 4.30
2088 5884 6.567050 TGTATAGTTGATTGGTCGTTACTCC 58.433 40.000 0.00 0.00 0.00 3.85
2089 5885 7.972277 TCTTGTATAGTTGATTGGTCGTTACTC 59.028 37.037 0.00 0.00 0.00 2.59
2151 6065 8.969267 CGAACTGATAATAACTCCAGTTATGAC 58.031 37.037 11.86 7.80 46.98 3.06
2165 6079 6.033341 GCATTTTGGTTGCGAACTGATAATA 58.967 36.000 0.00 0.00 0.00 0.98
2209 6123 1.134753 CTTTGTGGCATGTGTGTGTGT 59.865 47.619 0.00 0.00 0.00 3.72
2210 6124 1.404748 TCTTTGTGGCATGTGTGTGTG 59.595 47.619 0.00 0.00 0.00 3.82
2242 6156 4.706962 AGAAAAGCTGAGTGGAACAAAAGT 59.293 37.500 0.00 0.00 44.16 2.66
2354 6268 5.313520 CAATTATGCAAGTGTGGTCATGA 57.686 39.130 0.00 0.00 0.00 3.07
2422 6336 2.756760 TGGAAGATGCCAAGCTTGAATC 59.243 45.455 28.05 25.51 34.31 2.52
2480 6394 4.234550 ACTTATGCCTGGACTGGATATGA 58.765 43.478 0.00 0.00 0.00 2.15
2485 6399 3.653164 TGATACTTATGCCTGGACTGGA 58.347 45.455 0.00 0.00 0.00 3.86
2486 6400 4.630644 ATGATACTTATGCCTGGACTGG 57.369 45.455 0.00 0.00 0.00 4.00
2487 6401 5.862845 AGAATGATACTTATGCCTGGACTG 58.137 41.667 0.00 0.00 0.00 3.51
2488 6402 7.805083 ATAGAATGATACTTATGCCTGGACT 57.195 36.000 0.00 0.00 0.00 3.85
2489 6403 9.539825 CATATAGAATGATACTTATGCCTGGAC 57.460 37.037 0.00 0.00 0.00 4.02
2515 6429 4.713792 AATGGATCATGGGTCTAAGGAC 57.286 45.455 0.00 0.00 41.43 3.85
2524 6442 7.499292 TGCTGTTAAAATAAATGGATCATGGG 58.501 34.615 0.00 0.00 0.00 4.00
2526 6444 8.492748 GCATGCTGTTAAAATAAATGGATCATG 58.507 33.333 11.37 0.00 0.00 3.07
2529 6447 8.422973 TTGCATGCTGTTAAAATAAATGGATC 57.577 30.769 20.33 0.00 0.00 3.36
2531 6449 6.313411 GCTTGCATGCTGTTAAAATAAATGGA 59.687 34.615 20.33 0.00 0.00 3.41
2594 6512 4.321974 CCCTGTAGAAAATCCAAAACCTGC 60.322 45.833 0.00 0.00 0.00 4.85
2690 6608 8.121305 ACCATGTATGCAAGTAAATCAAGAAA 57.879 30.769 0.00 0.00 0.00 2.52
2851 6769 9.498307 CGTTCACAGAAAGTTAAAGTACAAAAT 57.502 29.630 0.00 0.00 0.00 1.82
2886 6804 0.234884 GAACGAAACAGGAGCAACCG 59.765 55.000 0.00 0.00 44.74 4.44
2920 6838 7.173218 TCAAGATGACAAGATAACAAACAGACC 59.827 37.037 0.00 0.00 0.00 3.85
3101 7019 6.870439 TGTAATGATCTGTCAACAAGTCTCTG 59.130 38.462 0.00 0.00 38.01 3.35
3110 7028 4.396166 CCTGGGTTGTAATGATCTGTCAAC 59.604 45.833 11.90 11.90 38.01 3.18
3129 7047 4.858692 CACGTGATAAATTTGCTTTCCTGG 59.141 41.667 10.90 0.00 0.00 4.45
3231 7149 5.773680 ACCACTACTTTGTAGCTCTAACTCA 59.226 40.000 0.00 0.00 0.00 3.41
3303 7221 5.746307 AGAAAAACGTTACTTTGACCTCC 57.254 39.130 0.00 0.00 0.00 4.30
3315 7233 5.648092 AGGCATGCTAGATAAGAAAAACGTT 59.352 36.000 18.92 0.00 0.00 3.99
3395 7315 8.924691 GCATTAGCTCTTATGTTTATCTCTCAG 58.075 37.037 0.00 0.00 37.91 3.35
3426 7346 3.423154 GCGTGGAAGAACAGGCCG 61.423 66.667 0.00 0.00 44.12 6.13
3441 7361 2.507102 ACGACGATGAAGCCTGCG 60.507 61.111 0.00 0.00 0.00 5.18
3509 7429 0.247262 CATCGAAACATGCGACGTGG 60.247 55.000 0.00 0.00 40.94 4.94
3594 7519 5.121221 ACAAAGCCAGTTTATGTGCTAAC 57.879 39.130 0.00 0.00 35.26 2.34
3603 7528 8.643324 ACCAAAATACATAACAAAGCCAGTTTA 58.357 29.630 0.00 0.00 0.00 2.01
3717 7642 7.923344 CGGGATACATATATTGTCAGAGGATTC 59.077 40.741 0.00 0.00 39.87 2.52
3900 7949 9.187996 AGTCACTTCCTATTTAGTTCCTAGTAC 57.812 37.037 0.00 0.00 0.00 2.73
3901 7950 9.186837 CAGTCACTTCCTATTTAGTTCCTAGTA 57.813 37.037 0.00 0.00 0.00 1.82
3902 7951 7.894364 TCAGTCACTTCCTATTTAGTTCCTAGT 59.106 37.037 0.00 0.00 0.00 2.57
3903 7952 8.294954 TCAGTCACTTCCTATTTAGTTCCTAG 57.705 38.462 0.00 0.00 0.00 3.02
3904 7953 8.660295 TTCAGTCACTTCCTATTTAGTTCCTA 57.340 34.615 0.00 0.00 0.00 2.94
3907 7956 8.041323 TGGATTCAGTCACTTCCTATTTAGTTC 58.959 37.037 0.00 0.00 0.00 3.01
3946 8035 4.353777 TGGTGATATATCCACTAGGCTCC 58.646 47.826 10.25 0.00 35.05 4.70
4180 8273 0.535553 TAACTGGTGCCCGGTGTTTC 60.536 55.000 0.00 0.00 43.15 2.78
4218 8311 5.511545 CCAACCACCTACATCTTAGATAGCC 60.512 48.000 0.00 0.00 0.00 3.93
4367 8465 0.388294 GTGGCTACCATACGACCCTC 59.612 60.000 0.00 0.00 35.28 4.30
4659 9155 7.946381 TGAGTACAATTATAAACCATGCCAA 57.054 32.000 0.00 0.00 0.00 4.52
4771 9267 8.306313 TGGGCTGTTACATCTATATAATCGAT 57.694 34.615 0.00 0.00 0.00 3.59
4785 9281 3.495453 GGTAACACTTCTGGGCTGTTACA 60.495 47.826 20.04 0.00 46.44 2.41
4796 9292 2.269940 AGATGGCAGGGTAACACTTCT 58.730 47.619 0.00 0.00 39.74 2.85
4935 9432 6.790232 TGGAAAAGAAAGAAATGGAGTTGT 57.210 33.333 0.00 0.00 0.00 3.32
4968 9466 9.750125 GGAAGAAGTAAAAATGTCACTTGAAAT 57.250 29.630 0.00 0.00 32.79 2.17
4987 9485 7.092716 CCATAGTTGGACATTTTTGGAAGAAG 58.907 38.462 0.00 0.00 46.92 2.85
4988 9486 6.014669 CCCATAGTTGGACATTTTTGGAAGAA 60.015 38.462 0.00 0.00 46.92 2.52
4989 9487 5.480073 CCCATAGTTGGACATTTTTGGAAGA 59.520 40.000 0.00 0.00 46.92 2.87
4992 9490 3.513515 GCCCATAGTTGGACATTTTTGGA 59.486 43.478 0.00 0.00 46.92 3.53
5009 9507 5.898972 ACATTACTTGTGATTTATGGCCCAT 59.101 36.000 0.00 0.00 37.11 4.00
5040 9538 2.760650 GGGCTGAAATTTAAGAGGGTGG 59.239 50.000 6.75 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.