Multiple sequence alignment - TraesCS6A01G280500

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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 TraesCS6A01G280500 chr6A 100.000 3651 0 0 1 3651 508849616 508853266 0.000000e+00 6743.0
1 TraesCS6A01G280500 chr6D 91.002 3601 173 67 122 3651 368303862 368307382 0.000000e+00 4715.0
2 TraesCS6A01G280500 chr6B 89.798 2519 145 48 455 2916 553374970 553372507 0.000000e+00 3125.0
3 TraesCS6A01G280500 chr6B 92.220 617 32 5 3048 3651 553372135 553371522 0.000000e+00 859.0
4 TraesCS6A01G280500 chr6B 93.373 332 15 3 122 453 553375370 553375046 5.480000e-133 484.0
5 TraesCS6A01G280500 chr6B 94.286 70 4 0 2949 3018 553372504 553372435 1.390000e-19 108.0
6 TraesCS6A01G280500 chr6B 100.000 30 0 0 524 553 396544459 396544488 5.090000e-04 56.5


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 TraesCS6A01G280500 chr6A 508849616 508853266 3650 False 6743 6743 100.00000 1 3651 1 chr6A.!!$F1 3650
1 TraesCS6A01G280500 chr6D 368303862 368307382 3520 False 4715 4715 91.00200 122 3651 1 chr6D.!!$F1 3529
2 TraesCS6A01G280500 chr6B 553371522 553375370 3848 True 1144 3125 92.41925 122 3651 4 chr6B.!!$R1 3529

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
78 79 0.034896 GAAACCTCTGGGACGAGCAA 59.965 55.0 0.0 0.0 36.25 3.91 F
1403 1512 0.103937 ATCCAGAAGTAGCAGAGCGC 59.896 55.0 0.0 0.0 42.91 5.92 F
2073 2214 0.167470 CGCTGTTCTTCATGCCACTG 59.833 55.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1653 0.249398 TCCTGGCGCTAGAGGAAAAC 59.751 55.0 23.73 0.0 35.33 2.43 R
2332 2485 0.603707 TCCTCTTTCTTGCAGGCACG 60.604 55.0 0.00 0.0 0.00 5.34 R
3103 3532 0.807667 CTGCCGACGAGGAGGAATTG 60.808 60.0 0.00 0.0 45.00 2.32 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
23 24 6.927933 AAACTCGTTTTCAACTTTCAACAG 57.072 33.333 0.00 0.00 0.00 3.16
24 25 5.873179 ACTCGTTTTCAACTTTCAACAGA 57.127 34.783 0.00 0.00 0.00 3.41
25 26 6.436843 ACTCGTTTTCAACTTTCAACAGAT 57.563 33.333 0.00 0.00 0.00 2.90
26 27 6.852664 ACTCGTTTTCAACTTTCAACAGATT 58.147 32.000 0.00 0.00 0.00 2.40
27 28 7.312899 ACTCGTTTTCAACTTTCAACAGATTT 58.687 30.769 0.00 0.00 0.00 2.17
28 29 7.273381 ACTCGTTTTCAACTTTCAACAGATTTG 59.727 33.333 0.00 0.00 0.00 2.32
29 30 6.529829 TCGTTTTCAACTTTCAACAGATTTGG 59.470 34.615 0.00 0.00 0.00 3.28
30 31 6.310224 CGTTTTCAACTTTCAACAGATTTGGT 59.690 34.615 0.00 0.00 0.00 3.67
31 32 7.148656 CGTTTTCAACTTTCAACAGATTTGGTT 60.149 33.333 0.00 0.00 0.00 3.67
32 33 8.503196 GTTTTCAACTTTCAACAGATTTGGTTT 58.497 29.630 0.00 0.00 0.00 3.27
33 34 7.826260 TTCAACTTTCAACAGATTTGGTTTC 57.174 32.000 0.00 0.00 0.00 2.78
34 35 6.033341 TCAACTTTCAACAGATTTGGTTTCG 58.967 36.000 0.00 0.00 0.00 3.46
35 36 4.932146 ACTTTCAACAGATTTGGTTTCGG 58.068 39.130 0.00 0.00 0.00 4.30
36 37 4.202111 ACTTTCAACAGATTTGGTTTCGGG 60.202 41.667 0.00 0.00 0.00 5.14
37 38 2.235016 TCAACAGATTTGGTTTCGGGG 58.765 47.619 0.00 0.00 0.00 5.73
38 39 1.272212 CAACAGATTTGGTTTCGGGGG 59.728 52.381 0.00 0.00 0.00 5.40
39 40 0.774908 ACAGATTTGGTTTCGGGGGA 59.225 50.000 0.00 0.00 0.00 4.81
40 41 1.357761 ACAGATTTGGTTTCGGGGGAT 59.642 47.619 0.00 0.00 0.00 3.85
41 42 2.225267 ACAGATTTGGTTTCGGGGGATT 60.225 45.455 0.00 0.00 0.00 3.01
42 43 2.831526 CAGATTTGGTTTCGGGGGATTT 59.168 45.455 0.00 0.00 0.00 2.17
43 44 3.096852 AGATTTGGTTTCGGGGGATTTC 58.903 45.455 0.00 0.00 0.00 2.17
44 45 2.383442 TTTGGTTTCGGGGGATTTCA 57.617 45.000 0.00 0.00 0.00 2.69
45 46 2.614134 TTGGTTTCGGGGGATTTCAT 57.386 45.000 0.00 0.00 0.00 2.57
46 47 2.137810 TGGTTTCGGGGGATTTCATC 57.862 50.000 0.00 0.00 0.00 2.92
47 48 1.356059 TGGTTTCGGGGGATTTCATCA 59.644 47.619 0.00 0.00 0.00 3.07
48 49 2.024464 TGGTTTCGGGGGATTTCATCAT 60.024 45.455 0.00 0.00 0.00 2.45
49 50 2.623416 GGTTTCGGGGGATTTCATCATC 59.377 50.000 0.00 0.00 0.00 2.92
50 51 3.287222 GTTTCGGGGGATTTCATCATCA 58.713 45.455 0.00 0.00 0.00 3.07
51 52 2.936919 TCGGGGGATTTCATCATCAG 57.063 50.000 0.00 0.00 0.00 2.90
52 53 1.202806 TCGGGGGATTTCATCATCAGC 60.203 52.381 0.00 0.00 0.00 4.26
53 54 1.202855 CGGGGGATTTCATCATCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
54 55 2.750807 CGGGGGATTTCATCATCAGCTT 60.751 50.000 0.00 0.00 0.00 3.74
55 56 3.303049 GGGGGATTTCATCATCAGCTTT 58.697 45.455 0.00 0.00 0.00 3.51
56 57 3.069158 GGGGGATTTCATCATCAGCTTTG 59.931 47.826 0.00 0.00 0.00 2.77
57 58 3.069158 GGGGATTTCATCATCAGCTTTGG 59.931 47.826 0.00 0.00 0.00 3.28
58 59 3.956199 GGGATTTCATCATCAGCTTTGGA 59.044 43.478 0.00 0.00 0.00 3.53
59 60 4.037684 GGGATTTCATCATCAGCTTTGGAG 59.962 45.833 0.00 0.00 0.00 3.86
60 61 4.885907 GGATTTCATCATCAGCTTTGGAGA 59.114 41.667 0.00 0.00 0.00 3.71
61 62 5.359009 GGATTTCATCATCAGCTTTGGAGAA 59.641 40.000 0.00 0.00 0.00 2.87
62 63 6.127535 GGATTTCATCATCAGCTTTGGAGAAA 60.128 38.462 12.36 12.36 0.00 2.52
63 64 5.633830 TTCATCATCAGCTTTGGAGAAAC 57.366 39.130 0.00 0.00 0.00 2.78
64 65 4.012374 TCATCATCAGCTTTGGAGAAACC 58.988 43.478 0.00 0.00 39.54 3.27
65 66 3.795688 TCATCAGCTTTGGAGAAACCT 57.204 42.857 0.00 0.00 39.86 3.50
66 67 3.679389 TCATCAGCTTTGGAGAAACCTC 58.321 45.455 0.00 0.00 39.86 3.85
67 68 3.328931 TCATCAGCTTTGGAGAAACCTCT 59.671 43.478 0.00 0.00 39.86 3.69
68 69 3.131709 TCAGCTTTGGAGAAACCTCTG 57.868 47.619 0.00 0.00 39.86 3.35
69 70 2.157738 CAGCTTTGGAGAAACCTCTGG 58.842 52.381 0.00 0.00 39.86 3.86
70 71 1.074566 AGCTTTGGAGAAACCTCTGGG 59.925 52.381 0.00 0.00 39.86 4.45
71 72 1.073923 GCTTTGGAGAAACCTCTGGGA 59.926 52.381 0.00 0.00 39.86 4.37
72 73 2.784347 CTTTGGAGAAACCTCTGGGAC 58.216 52.381 0.00 0.00 39.86 4.46
73 74 0.685097 TTGGAGAAACCTCTGGGACG 59.315 55.000 0.00 0.00 39.86 4.79
74 75 0.178944 TGGAGAAACCTCTGGGACGA 60.179 55.000 0.00 0.00 39.86 4.20
75 76 0.533032 GGAGAAACCTCTGGGACGAG 59.467 60.000 0.00 0.00 36.25 4.18
76 77 0.108567 GAGAAACCTCTGGGACGAGC 60.109 60.000 0.00 0.00 36.25 5.03
77 78 0.832135 AGAAACCTCTGGGACGAGCA 60.832 55.000 0.00 0.00 36.25 4.26
78 79 0.034896 GAAACCTCTGGGACGAGCAA 59.965 55.000 0.00 0.00 36.25 3.91
79 80 0.250338 AAACCTCTGGGACGAGCAAC 60.250 55.000 0.00 0.00 36.25 4.17
80 81 2.113243 AACCTCTGGGACGAGCAACC 62.113 60.000 0.00 0.00 36.25 3.77
81 82 2.286523 CCTCTGGGACGAGCAACCT 61.287 63.158 0.00 0.00 33.58 3.50
82 83 1.079543 CTCTGGGACGAGCAACCTG 60.080 63.158 0.00 0.00 0.00 4.00
83 84 2.046892 CTGGGACGAGCAACCTGG 60.047 66.667 0.00 0.00 0.00 4.45
84 85 2.525629 TGGGACGAGCAACCTGGA 60.526 61.111 0.00 0.00 0.00 3.86
85 86 2.266055 GGGACGAGCAACCTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
86 87 2.266055 GGACGAGCAACCTGGAGG 59.734 66.667 0.00 0.00 42.17 4.30
96 97 3.648694 CCTGGAGGTAGGGGAAGC 58.351 66.667 0.00 0.00 34.06 3.86
97 98 1.306997 CCTGGAGGTAGGGGAAGCA 60.307 63.158 0.00 0.00 34.06 3.91
98 99 0.695803 CCTGGAGGTAGGGGAAGCAT 60.696 60.000 0.00 0.00 34.06 3.79
99 100 0.471617 CTGGAGGTAGGGGAAGCATG 59.528 60.000 0.00 0.00 0.00 4.06
100 101 1.149401 GGAGGTAGGGGAAGCATGC 59.851 63.158 10.51 10.51 0.00 4.06
101 102 1.635817 GGAGGTAGGGGAAGCATGCA 61.636 60.000 21.98 0.00 0.00 3.96
102 103 0.255890 GAGGTAGGGGAAGCATGCAA 59.744 55.000 21.98 0.00 0.00 4.08
103 104 0.929244 AGGTAGGGGAAGCATGCAAT 59.071 50.000 21.98 8.26 0.00 3.56
118 119 2.865343 GCAATGAGCATTCTGAAGGG 57.135 50.000 4.09 0.00 44.79 3.95
119 120 1.407979 GCAATGAGCATTCTGAAGGGG 59.592 52.381 4.09 0.00 44.79 4.79
120 121 2.029623 CAATGAGCATTCTGAAGGGGG 58.970 52.381 4.09 0.00 0.00 5.40
153 154 5.636543 GGATTTGATTTGAGCTGAAACAAGG 59.363 40.000 0.00 0.00 0.00 3.61
172 174 3.871395 GCAGAGGGGGCCTAGCTG 61.871 72.222 0.84 9.49 33.66 4.24
228 230 5.189180 GTCTGCACCTAGATCATTTTTCCT 58.811 41.667 0.00 0.00 0.00 3.36
308 310 2.381911 GTACGTGGTCCTAATCTCCCA 58.618 52.381 0.00 0.00 0.00 4.37
352 354 2.093658 CGTAAACTGTACCCCAGCTGAT 60.094 50.000 17.39 2.50 45.68 2.90
359 361 1.340399 TACCCCAGCTGATGCCTCTG 61.340 60.000 17.39 0.00 40.80 3.35
374 376 2.113774 CTGGTGCTGCTGGTGGAA 59.886 61.111 0.00 0.00 0.00 3.53
393 395 1.005275 CGCAGATGCAGATCCGGAT 60.005 57.895 19.21 19.21 42.21 4.18
433 435 2.426522 TCTTTTGCTGCGCTGAGTTAT 58.573 42.857 19.32 0.00 0.00 1.89
443 445 4.754322 TGCGCTGAGTTATTGTAGAATGA 58.246 39.130 9.73 0.00 0.00 2.57
578 652 3.937706 GACATCAAGAGCAGCAAGTACAT 59.062 43.478 0.00 0.00 0.00 2.29
584 658 2.158842 AGAGCAGCAAGTACATCCATCC 60.159 50.000 0.00 0.00 0.00 3.51
661 735 1.275291 TCCTCGCTAGTTTGGTCCTTG 59.725 52.381 0.00 0.00 0.00 3.61
663 737 2.338500 CTCGCTAGTTTGGTCCTTGAC 58.662 52.381 0.00 0.00 0.00 3.18
748 823 2.012673 CGAATTCAAAGCAGAGAGGGG 58.987 52.381 6.22 0.00 0.00 4.79
749 824 2.355108 CGAATTCAAAGCAGAGAGGGGA 60.355 50.000 6.22 0.00 0.00 4.81
750 825 3.690460 GAATTCAAAGCAGAGAGGGGAA 58.310 45.455 0.00 0.00 0.00 3.97
825 900 3.557903 TTGCCACAGGAGCTGGAGC 62.558 63.158 0.00 0.00 42.49 4.70
844 919 1.017701 CGGGGTCGGCTTTGTCTAAC 61.018 60.000 0.00 0.00 0.00 2.34
845 920 0.675837 GGGGTCGGCTTTGTCTAACC 60.676 60.000 0.00 0.00 0.00 2.85
852 934 2.152016 GGCTTTGTCTAACCACTGTCC 58.848 52.381 0.00 0.00 0.00 4.02
858 940 1.135170 GTCTAACCACTGTCCGGTAGC 60.135 57.143 0.00 0.00 34.99 3.58
864 946 0.179145 CACTGTCCGGTAGCGGTAAG 60.179 60.000 30.74 27.82 0.00 2.34
873 955 1.553308 GTAGCGGTAAGTAAGTGCCG 58.447 55.000 0.00 0.00 46.17 5.69
894 979 8.062448 GTGCCGTTTCACTGTAGATAATTAATC 58.938 37.037 0.00 0.00 34.29 1.75
909 994 8.755941 AGATAATTAATCAATGACGTTCACTCG 58.244 33.333 0.00 0.00 37.03 4.18
910 995 4.577687 TTAATCAATGACGTTCACTCGC 57.422 40.909 0.00 0.00 0.00 5.03
911 996 2.078849 ATCAATGACGTTCACTCGCA 57.921 45.000 0.00 0.00 0.00 5.10
912 997 1.136690 TCAATGACGTTCACTCGCAC 58.863 50.000 0.00 0.00 0.00 5.34
916 1001 1.232119 TGACGTTCACTCGCACTCTA 58.768 50.000 0.00 0.00 0.00 2.43
917 1002 1.069432 TGACGTTCACTCGCACTCTAC 60.069 52.381 0.00 0.00 0.00 2.59
918 1003 1.197264 GACGTTCACTCGCACTCTACT 59.803 52.381 0.00 0.00 0.00 2.57
920 1005 3.008330 ACGTTCACTCGCACTCTACTAT 58.992 45.455 0.00 0.00 0.00 2.12
921 1006 3.439476 ACGTTCACTCGCACTCTACTATT 59.561 43.478 0.00 0.00 0.00 1.73
922 1007 4.633126 ACGTTCACTCGCACTCTACTATTA 59.367 41.667 0.00 0.00 0.00 0.98
923 1008 5.199000 CGTTCACTCGCACTCTACTATTAG 58.801 45.833 0.00 0.00 0.00 1.73
924 1009 5.006455 CGTTCACTCGCACTCTACTATTAGA 59.994 44.000 0.00 0.00 33.05 2.10
925 1010 5.987777 TCACTCGCACTCTACTATTAGAC 57.012 43.478 0.00 0.00 30.67 2.59
942 1027 3.533606 AGACACTGCATAAGCTGGTAG 57.466 47.619 1.89 0.00 43.24 3.18
967 1052 1.009829 CGAGTAGAAACATGCAGGGC 58.990 55.000 2.31 0.00 0.00 5.19
1046 1135 3.640407 GAGGCACAGGCACAGGGA 61.640 66.667 0.00 0.00 43.71 4.20
1050 1139 2.353958 CACAGGCACAGGGATGCT 59.646 61.111 0.00 0.00 45.38 3.79
1051 1140 2.044555 CACAGGCACAGGGATGCTG 61.045 63.158 0.00 0.00 45.38 4.41
1076 1170 4.063529 TGTCGAAAGGCAGGCAAG 57.936 55.556 0.00 0.00 43.37 4.01
1077 1171 1.600636 TGTCGAAAGGCAGGCAAGG 60.601 57.895 0.00 0.00 43.37 3.61
1078 1172 2.672996 TCGAAAGGCAGGCAAGGC 60.673 61.111 0.00 0.00 0.00 4.35
1079 1173 2.985282 CGAAAGGCAGGCAAGGCA 60.985 61.111 0.00 0.00 36.37 4.75
1080 1174 2.563798 CGAAAGGCAGGCAAGGCAA 61.564 57.895 0.00 0.00 36.37 4.52
1081 1175 1.005748 GAAAGGCAGGCAAGGCAAC 60.006 57.895 0.00 0.00 36.37 4.17
1124 1218 4.201589 CGTTAAACATCCGCTAACACTGAG 60.202 45.833 0.00 0.00 0.00 3.35
1192 1286 3.095738 CGCCGATTAACTTTTTAAGCCG 58.904 45.455 0.00 0.00 31.05 5.52
1202 1296 3.323691 ACTTTTTAAGCCGGGAAATTGCT 59.676 39.130 2.18 0.00 36.79 3.91
1203 1297 3.311486 TTTTAAGCCGGGAAATTGCTG 57.689 42.857 2.18 0.00 35.08 4.41
1245 1339 1.895020 CGGTGGGTAGGCTGCAAGTA 61.895 60.000 4.64 0.00 35.30 2.24
1246 1340 0.326927 GGTGGGTAGGCTGCAAGTAA 59.673 55.000 4.64 0.00 35.30 2.24
1247 1341 1.271707 GGTGGGTAGGCTGCAAGTAAA 60.272 52.381 4.64 0.00 35.30 2.01
1248 1342 2.510613 GTGGGTAGGCTGCAAGTAAAA 58.489 47.619 4.64 0.00 35.30 1.52
1394 1503 1.759445 GAGCTCAGCCATCCAGAAGTA 59.241 52.381 9.40 0.00 0.00 2.24
1395 1504 1.761784 AGCTCAGCCATCCAGAAGTAG 59.238 52.381 0.00 0.00 0.00 2.57
1402 1511 1.537776 CCATCCAGAAGTAGCAGAGCG 60.538 57.143 0.00 0.00 0.00 5.03
1403 1512 0.103937 ATCCAGAAGTAGCAGAGCGC 59.896 55.000 0.00 0.00 42.91 5.92
1514 1624 1.148157 CTGTACTTCCGGCATCGCAG 61.148 60.000 0.00 0.00 34.56 5.18
1879 1990 3.436015 GCCATGGATCTCAATGAGAATCG 59.564 47.826 18.40 0.61 42.27 3.34
1887 1998 7.492669 TGGATCTCAATGAGAATCGTACTTTTC 59.507 37.037 17.59 5.90 42.27 2.29
1899 2010 6.872670 ATCGTACTTTTCTCGAGAATGAAC 57.127 37.500 27.51 20.09 37.04 3.18
1910 2021 9.435688 TTTCTCGAGAATGAACAAGAATCATAA 57.564 29.630 27.51 4.50 36.53 1.90
1936 2047 4.437682 AGTTCATTCTCACCTCCACAAA 57.562 40.909 0.00 0.00 0.00 2.83
1961 2072 9.574516 AACCAAGAACTCAATAGAACATTTACT 57.425 29.630 0.00 0.00 0.00 2.24
1962 2073 9.003658 ACCAAGAACTCAATAGAACATTTACTG 57.996 33.333 0.00 0.00 0.00 2.74
1963 2074 9.219603 CCAAGAACTCAATAGAACATTTACTGA 57.780 33.333 0.00 0.00 0.00 3.41
1973 2089 6.428385 AGAACATTTACTGATGTAGCTTGC 57.572 37.500 0.00 0.00 39.25 4.01
1976 2092 6.187125 ACATTTACTGATGTAGCTTGCTTG 57.813 37.500 0.00 0.00 38.43 4.01
1994 2110 5.606505 TGCTTGATAACGGCATGTAGATTA 58.393 37.500 0.00 0.00 0.00 1.75
1996 2112 5.389935 GCTTGATAACGGCATGTAGATTAGC 60.390 44.000 0.00 0.00 0.00 3.09
2000 2116 3.099267 ACGGCATGTAGATTAGCTCAC 57.901 47.619 0.00 0.00 0.00 3.51
2005 2128 4.260948 GGCATGTAGATTAGCTCACTTTGC 60.261 45.833 0.00 0.00 0.00 3.68
2017 2140 9.618890 ATTAGCTCACTTTGCTGATTTCTATTA 57.381 29.630 0.00 0.00 41.32 0.98
2018 2141 7.313951 AGCTCACTTTGCTGATTTCTATTAC 57.686 36.000 0.00 0.00 39.56 1.89
2019 2142 6.317391 AGCTCACTTTGCTGATTTCTATTACC 59.683 38.462 0.00 0.00 39.56 2.85
2069 2210 1.130561 GTAACCGCTGTTCTTCATGCC 59.869 52.381 0.00 0.00 35.87 4.40
2073 2214 0.167470 CGCTGTTCTTCATGCCACTG 59.833 55.000 0.00 0.00 0.00 3.66
2167 2311 8.299990 AGTAAGCAAACTGATACTGATAGAGT 57.700 34.615 0.00 0.00 38.88 3.24
2234 2378 2.358860 CTGCTGCTGCTGCTGAGT 60.359 61.111 27.67 0.00 40.01 3.41
2332 2485 1.004440 AAGCAGCGGTGAAGAGGTC 60.004 57.895 20.69 0.00 0.00 3.85
2385 2538 2.415512 AGAAGCACTTCGCCGATAAAAC 59.584 45.455 4.81 0.00 43.97 2.43
2419 2572 8.660373 GTTGATGTTGAGAATTTCGTAGAAGAT 58.340 33.333 0.00 0.00 45.90 2.40
2512 2665 0.329261 TGAAGGAGAGCCCCAACATG 59.671 55.000 0.00 0.00 34.66 3.21
2649 2802 0.680921 GCAGGGCTGGAATGCAAGTA 60.681 55.000 0.00 0.00 39.75 2.24
2650 2803 1.386533 CAGGGCTGGAATGCAAGTAG 58.613 55.000 0.00 0.00 34.04 2.57
2677 2833 0.387929 CAGTGCCATGCCAATCCATC 59.612 55.000 0.00 0.00 0.00 3.51
2680 2836 0.105401 TGCCATGCCAATCCATCCAT 60.105 50.000 0.00 0.00 0.00 3.41
2681 2837 0.320374 GCCATGCCAATCCATCCATG 59.680 55.000 0.00 0.00 35.90 3.66
2682 2838 0.320374 CCATGCCAATCCATCCATGC 59.680 55.000 0.00 0.00 35.06 4.06
2683 2839 0.038618 CATGCCAATCCATCCATGCG 60.039 55.000 0.00 0.00 0.00 4.73
2740 2896 5.468592 TCAAATGTAAACATGACATGCACC 58.531 37.500 15.49 2.14 37.59 5.01
2813 2969 5.421056 TGATAGAACACCTACGGAATCTTGT 59.579 40.000 0.00 0.00 0.00 3.16
2863 3022 5.591099 AGTATTTTGGTCTGCTTGTTTGTG 58.409 37.500 0.00 0.00 0.00 3.33
2941 3100 3.197766 TGTTGGTGCTACTCAGGATAAGG 59.802 47.826 0.00 0.00 0.00 2.69
2978 3137 6.092748 AGCAGTTTTATGTATTTTTGGCTCG 58.907 36.000 0.00 0.00 0.00 5.03
3018 3177 4.933400 TCTTATCCAAACGAAACTGCTACC 59.067 41.667 0.00 0.00 0.00 3.18
3088 3517 2.042831 AGAAGCCATCGTGCCAAGC 61.043 57.895 0.00 0.00 0.00 4.01
3102 3531 1.079819 CAAGCTGTGGGACGACGAT 60.080 57.895 0.00 0.00 0.00 3.73
3103 3532 1.078759 CAAGCTGTGGGACGACGATC 61.079 60.000 0.00 0.00 0.00 3.69
3118 3547 1.065701 ACGATCAATTCCTCCTCGTCG 59.934 52.381 0.00 0.00 38.05 5.12
3125 3554 2.752238 CCTCCTCGTCGGCAGAGT 60.752 66.667 7.82 0.00 34.08 3.24
3134 3563 2.278206 CGGCAGAGTCGATCGTGG 60.278 66.667 15.94 2.70 29.41 4.94
3172 3601 4.488126 ACTGATGCATTGTGTGTGTAAC 57.512 40.909 0.00 0.00 37.35 2.50
3201 3631 2.165030 AGTAGCATTGCATTTGGACAGC 59.835 45.455 11.91 0.00 0.00 4.40
3233 3663 3.006859 TGCATATCATCTACTCCCAACCG 59.993 47.826 0.00 0.00 0.00 4.44
3300 3734 3.444805 AGGAGCCTCGACGCAGAC 61.445 66.667 9.10 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.614469 AAACCAAATCTGTTGAAAGTTGAAAA 57.386 26.923 0.00 0.00 0.00 2.29
8 9 7.062839 CGAAACCAAATCTGTTGAAAGTTGAAA 59.937 33.333 0.00 0.00 0.00 2.69
9 10 6.529829 CGAAACCAAATCTGTTGAAAGTTGAA 59.470 34.615 0.00 0.00 0.00 2.69
10 11 6.033341 CGAAACCAAATCTGTTGAAAGTTGA 58.967 36.000 0.00 0.00 0.00 3.18
11 12 5.231991 CCGAAACCAAATCTGTTGAAAGTTG 59.768 40.000 0.00 0.00 0.00 3.16
12 13 5.348164 CCGAAACCAAATCTGTTGAAAGTT 58.652 37.500 0.00 0.00 0.00 2.66
13 14 4.202111 CCCGAAACCAAATCTGTTGAAAGT 60.202 41.667 0.00 0.00 0.00 2.66
14 15 4.298332 CCCGAAACCAAATCTGTTGAAAG 58.702 43.478 0.00 0.00 0.00 2.62
15 16 3.068873 CCCCGAAACCAAATCTGTTGAAA 59.931 43.478 0.00 0.00 0.00 2.69
16 17 2.625790 CCCCGAAACCAAATCTGTTGAA 59.374 45.455 0.00 0.00 0.00 2.69
17 18 2.235016 CCCCGAAACCAAATCTGTTGA 58.765 47.619 0.00 0.00 0.00 3.18
18 19 1.272212 CCCCCGAAACCAAATCTGTTG 59.728 52.381 0.00 0.00 0.00 3.33
19 20 1.146152 TCCCCCGAAACCAAATCTGTT 59.854 47.619 0.00 0.00 0.00 3.16
20 21 0.774908 TCCCCCGAAACCAAATCTGT 59.225 50.000 0.00 0.00 0.00 3.41
21 22 2.143876 ATCCCCCGAAACCAAATCTG 57.856 50.000 0.00 0.00 0.00 2.90
22 23 2.919772 AATCCCCCGAAACCAAATCT 57.080 45.000 0.00 0.00 0.00 2.40
23 24 2.829120 TGAAATCCCCCGAAACCAAATC 59.171 45.455 0.00 0.00 0.00 2.17
24 25 2.896039 TGAAATCCCCCGAAACCAAAT 58.104 42.857 0.00 0.00 0.00 2.32
25 26 2.383442 TGAAATCCCCCGAAACCAAA 57.617 45.000 0.00 0.00 0.00 3.28
26 27 2.225142 TGATGAAATCCCCCGAAACCAA 60.225 45.455 0.00 0.00 44.73 3.67
27 28 1.356059 TGATGAAATCCCCCGAAACCA 59.644 47.619 0.00 0.00 44.73 3.67
28 29 2.137810 TGATGAAATCCCCCGAAACC 57.862 50.000 0.00 0.00 44.73 3.27
29 30 3.287222 TGATGATGAAATCCCCCGAAAC 58.713 45.455 0.00 0.00 44.73 2.78
30 31 3.554934 CTGATGATGAAATCCCCCGAAA 58.445 45.455 0.00 0.00 44.73 3.46
31 32 2.749466 GCTGATGATGAAATCCCCCGAA 60.749 50.000 0.00 0.00 44.73 4.30
32 33 1.202806 GCTGATGATGAAATCCCCCGA 60.203 52.381 0.00 0.00 44.73 5.14
33 34 1.202855 AGCTGATGATGAAATCCCCCG 60.203 52.381 0.00 0.00 44.73 5.73
34 35 2.671896 AGCTGATGATGAAATCCCCC 57.328 50.000 0.00 0.00 44.73 5.40
35 36 3.069158 CCAAAGCTGATGATGAAATCCCC 59.931 47.826 1.45 0.00 44.73 4.81
36 37 3.956199 TCCAAAGCTGATGATGAAATCCC 59.044 43.478 1.45 0.00 44.73 3.85
37 38 4.885907 TCTCCAAAGCTGATGATGAAATCC 59.114 41.667 1.45 0.00 44.73 3.01
38 39 6.446781 TTCTCCAAAGCTGATGATGAAATC 57.553 37.500 1.45 0.00 45.83 2.17
39 40 6.350780 GGTTTCTCCAAAGCTGATGATGAAAT 60.351 38.462 15.71 0.00 37.09 2.17
40 41 5.047802 GGTTTCTCCAAAGCTGATGATGAAA 60.048 40.000 1.45 8.10 37.09 2.69
41 42 4.460382 GGTTTCTCCAAAGCTGATGATGAA 59.540 41.667 1.45 3.31 37.09 2.57
42 43 4.012374 GGTTTCTCCAAAGCTGATGATGA 58.988 43.478 1.45 0.00 37.09 2.92
43 44 4.015084 AGGTTTCTCCAAAGCTGATGATG 58.985 43.478 1.45 0.00 46.41 3.07
44 45 4.313020 AGGTTTCTCCAAAGCTGATGAT 57.687 40.909 1.45 0.00 46.41 2.45
45 46 3.795688 AGGTTTCTCCAAAGCTGATGA 57.204 42.857 1.45 0.00 46.41 2.92
51 52 1.073923 TCCCAGAGGTTTCTCCAAAGC 59.926 52.381 0.00 0.00 40.83 3.51
52 53 2.784347 GTCCCAGAGGTTTCTCCAAAG 58.216 52.381 0.00 0.00 40.83 2.77
53 54 1.071699 CGTCCCAGAGGTTTCTCCAAA 59.928 52.381 0.00 0.00 40.83 3.28
54 55 0.685097 CGTCCCAGAGGTTTCTCCAA 59.315 55.000 0.00 0.00 40.83 3.53
55 56 0.178944 TCGTCCCAGAGGTTTCTCCA 60.179 55.000 0.00 0.00 40.83 3.86
56 57 0.533032 CTCGTCCCAGAGGTTTCTCC 59.467 60.000 0.00 0.00 40.83 3.71
57 58 0.108567 GCTCGTCCCAGAGGTTTCTC 60.109 60.000 0.00 0.00 38.63 2.87
58 59 0.832135 TGCTCGTCCCAGAGGTTTCT 60.832 55.000 0.00 0.00 38.63 2.52
59 60 0.034896 TTGCTCGTCCCAGAGGTTTC 59.965 55.000 0.00 0.00 38.63 2.78
60 61 0.250338 GTTGCTCGTCCCAGAGGTTT 60.250 55.000 0.00 0.00 38.63 3.27
61 62 1.371558 GTTGCTCGTCCCAGAGGTT 59.628 57.895 0.00 0.00 38.63 3.50
62 63 2.584391 GGTTGCTCGTCCCAGAGGT 61.584 63.158 0.00 0.00 38.63 3.85
63 64 2.266055 GGTTGCTCGTCCCAGAGG 59.734 66.667 0.00 0.00 38.63 3.69
64 65 1.079543 CAGGTTGCTCGTCCCAGAG 60.080 63.158 0.00 0.00 41.03 3.35
65 66 2.583441 CCAGGTTGCTCGTCCCAGA 61.583 63.158 0.00 0.00 0.00 3.86
66 67 2.046892 CCAGGTTGCTCGTCCCAG 60.047 66.667 0.00 0.00 0.00 4.45
67 68 2.525629 TCCAGGTTGCTCGTCCCA 60.526 61.111 0.00 0.00 0.00 4.37
68 69 2.266055 CTCCAGGTTGCTCGTCCC 59.734 66.667 0.00 0.00 0.00 4.46
69 70 2.266055 CCTCCAGGTTGCTCGTCC 59.734 66.667 0.00 0.00 0.00 4.79
79 80 0.695803 ATGCTTCCCCTACCTCCAGG 60.696 60.000 0.00 0.00 42.17 4.45
80 81 0.471617 CATGCTTCCCCTACCTCCAG 59.528 60.000 0.00 0.00 0.00 3.86
81 82 1.635817 GCATGCTTCCCCTACCTCCA 61.636 60.000 11.37 0.00 0.00 3.86
82 83 1.149401 GCATGCTTCCCCTACCTCC 59.851 63.158 11.37 0.00 0.00 4.30
83 84 0.255890 TTGCATGCTTCCCCTACCTC 59.744 55.000 20.33 0.00 0.00 3.85
84 85 0.929244 ATTGCATGCTTCCCCTACCT 59.071 50.000 20.33 0.00 0.00 3.08
85 86 1.035139 CATTGCATGCTTCCCCTACC 58.965 55.000 20.33 0.00 0.00 3.18
86 87 1.952296 CTCATTGCATGCTTCCCCTAC 59.048 52.381 20.33 0.00 0.00 3.18
87 88 1.751733 GCTCATTGCATGCTTCCCCTA 60.752 52.381 20.33 0.00 42.31 3.53
88 89 1.041447 GCTCATTGCATGCTTCCCCT 61.041 55.000 20.33 0.00 42.31 4.79
89 90 1.440476 GCTCATTGCATGCTTCCCC 59.560 57.895 20.33 0.00 42.31 4.81
99 100 1.407979 CCCCTTCAGAATGCTCATTGC 59.592 52.381 0.00 0.00 43.25 3.56
100 101 2.029623 CCCCCTTCAGAATGCTCATTG 58.970 52.381 0.00 0.00 34.76 2.82
101 102 1.925255 TCCCCCTTCAGAATGCTCATT 59.075 47.619 0.00 0.00 34.76 2.57
102 103 1.600058 TCCCCCTTCAGAATGCTCAT 58.400 50.000 0.00 0.00 34.76 2.90
103 104 1.004745 GTTCCCCCTTCAGAATGCTCA 59.995 52.381 0.00 0.00 34.76 4.26
104 105 1.756430 GTTCCCCCTTCAGAATGCTC 58.244 55.000 0.00 0.00 34.76 4.26
105 106 0.035056 CGTTCCCCCTTCAGAATGCT 60.035 55.000 0.00 0.00 34.76 3.79
106 107 0.322546 ACGTTCCCCCTTCAGAATGC 60.323 55.000 0.00 0.00 33.20 3.56
107 108 1.271379 ACACGTTCCCCCTTCAGAATG 60.271 52.381 0.00 0.00 35.54 2.67
108 109 1.064825 ACACGTTCCCCCTTCAGAAT 58.935 50.000 0.00 0.00 0.00 2.40
109 110 0.841289 AACACGTTCCCCCTTCAGAA 59.159 50.000 0.00 0.00 0.00 3.02
110 111 0.107831 CAACACGTTCCCCCTTCAGA 59.892 55.000 0.00 0.00 0.00 3.27
111 112 0.889186 CCAACACGTTCCCCCTTCAG 60.889 60.000 0.00 0.00 0.00 3.02
112 113 1.149627 CCAACACGTTCCCCCTTCA 59.850 57.895 0.00 0.00 0.00 3.02
113 114 0.037734 ATCCAACACGTTCCCCCTTC 59.962 55.000 0.00 0.00 0.00 3.46
114 115 0.481128 AATCCAACACGTTCCCCCTT 59.519 50.000 0.00 0.00 0.00 3.95
115 116 0.481128 AAATCCAACACGTTCCCCCT 59.519 50.000 0.00 0.00 0.00 4.79
116 117 0.601057 CAAATCCAACACGTTCCCCC 59.399 55.000 0.00 0.00 0.00 5.40
117 118 1.611519 TCAAATCCAACACGTTCCCC 58.388 50.000 0.00 0.00 0.00 4.81
118 119 3.934457 AATCAAATCCAACACGTTCCC 57.066 42.857 0.00 0.00 0.00 3.97
119 120 4.865776 TCAAATCAAATCCAACACGTTCC 58.134 39.130 0.00 0.00 0.00 3.62
120 121 4.382754 GCTCAAATCAAATCCAACACGTTC 59.617 41.667 0.00 0.00 0.00 3.95
172 174 0.318762 GATCAGACCTACCGATGCCC 59.681 60.000 0.00 0.00 0.00 5.36
228 230 2.912771 TCTGCTGACACGAAAAAGGAA 58.087 42.857 0.00 0.00 0.00 3.36
272 274 3.709880 TACGGCCCTTGATGACGCG 62.710 63.158 3.53 3.53 0.00 6.01
308 310 4.298332 CTGAGGTTTTGCAAATAAAGCGT 58.702 39.130 13.65 3.33 37.88 5.07
352 354 4.340246 CCAGCAGCACCAGAGGCA 62.340 66.667 0.00 0.00 0.00 4.75
359 361 3.357079 CGTTCCACCAGCAGCACC 61.357 66.667 0.00 0.00 0.00 5.01
374 376 1.752358 ATCCGGATCTGCATCTGCGT 61.752 55.000 12.38 0.00 45.83 5.24
393 395 3.692101 AGATTTTGTGTTTCGTCACCACA 59.308 39.130 0.00 0.00 37.32 4.17
495 569 0.445436 CTTGTGAACTCGGCATGCTC 59.555 55.000 18.92 7.32 0.00 4.26
578 652 3.245016 ACACAAGCATGAAAGAGGATGGA 60.245 43.478 0.00 0.00 0.00 3.41
584 658 6.198029 CGTATCTCTACACAAGCATGAAAGAG 59.802 42.308 0.00 4.96 35.95 2.85
748 823 2.808543 ACTGCACCGTGATTTCTTCTTC 59.191 45.455 1.65 0.00 0.00 2.87
749 824 2.549754 CACTGCACCGTGATTTCTTCTT 59.450 45.455 1.65 0.00 37.06 2.52
750 825 2.146342 CACTGCACCGTGATTTCTTCT 58.854 47.619 1.65 0.00 37.06 2.85
825 900 1.017701 GTTAGACAAAGCCGACCCCG 61.018 60.000 0.00 0.00 0.00 5.73
829 904 1.798813 CAGTGGTTAGACAAAGCCGAC 59.201 52.381 0.00 0.00 34.56 4.79
852 934 1.553308 GCACTTACTTACCGCTACCG 58.447 55.000 0.00 0.00 0.00 4.02
858 940 4.103836 AGTGAAACGGCACTTACTTACCG 61.104 47.826 0.00 0.00 46.42 4.02
864 946 3.645884 TCTACAGTGAAACGGCACTTAC 58.354 45.455 0.00 0.00 46.42 2.34
894 979 1.125021 GAGTGCGAGTGAACGTCATTG 59.875 52.381 0.00 0.00 35.59 2.82
898 983 1.197264 AGTAGAGTGCGAGTGAACGTC 59.803 52.381 0.00 0.00 35.59 4.34
904 989 5.294799 AGTGTCTAATAGTAGAGTGCGAGTG 59.705 44.000 0.00 0.00 37.02 3.51
906 991 5.743467 CAGTGTCTAATAGTAGAGTGCGAG 58.257 45.833 0.00 0.00 37.02 5.03
907 992 4.035324 GCAGTGTCTAATAGTAGAGTGCGA 59.965 45.833 11.29 0.00 37.02 5.10
909 994 5.250235 TGCAGTGTCTAATAGTAGAGTGC 57.750 43.478 16.58 16.58 37.02 4.40
910 995 7.593273 GCTTATGCAGTGTCTAATAGTAGAGTG 59.407 40.741 0.00 0.54 36.75 3.51
911 996 7.504238 AGCTTATGCAGTGTCTAATAGTAGAGT 59.496 37.037 0.00 0.00 42.74 3.24
912 997 7.807433 CAGCTTATGCAGTGTCTAATAGTAGAG 59.193 40.741 0.00 0.00 42.74 2.43
916 1001 5.129485 ACCAGCTTATGCAGTGTCTAATAGT 59.871 40.000 3.16 0.00 42.74 2.12
917 1002 5.605534 ACCAGCTTATGCAGTGTCTAATAG 58.394 41.667 3.16 0.00 42.74 1.73
918 1003 5.614324 ACCAGCTTATGCAGTGTCTAATA 57.386 39.130 3.16 0.00 42.74 0.98
920 1005 3.981071 ACCAGCTTATGCAGTGTCTAA 57.019 42.857 3.16 0.00 42.74 2.10
921 1006 3.181475 GCTACCAGCTTATGCAGTGTCTA 60.181 47.826 3.16 0.00 42.74 2.59
922 1007 2.419297 GCTACCAGCTTATGCAGTGTCT 60.419 50.000 3.16 0.00 42.74 3.41
923 1008 1.936547 GCTACCAGCTTATGCAGTGTC 59.063 52.381 3.16 0.00 42.74 3.67
924 1009 1.278985 TGCTACCAGCTTATGCAGTGT 59.721 47.619 3.16 0.00 42.97 3.55
925 1010 1.667724 GTGCTACCAGCTTATGCAGTG 59.332 52.381 3.16 0.00 42.97 3.66
942 1027 0.370273 CATGTTTCTACTCGGCGTGC 59.630 55.000 6.85 0.00 0.00 5.34
967 1052 1.151777 CCGCACAGTATTAGCCGTGG 61.152 60.000 0.00 0.00 0.00 4.94
1046 1135 0.392706 TTCGACACCTGACACAGCAT 59.607 50.000 0.00 0.00 0.00 3.79
1050 1139 0.531974 GCCTTTCGACACCTGACACA 60.532 55.000 0.00 0.00 0.00 3.72
1051 1140 0.531974 TGCCTTTCGACACCTGACAC 60.532 55.000 0.00 0.00 0.00 3.67
1071 1165 2.028020 AGTAGACAGTAGTTGCCTTGCC 60.028 50.000 0.00 0.00 0.00 4.52
1073 1167 2.996621 GCAGTAGACAGTAGTTGCCTTG 59.003 50.000 0.00 0.00 0.00 3.61
1074 1168 2.900546 AGCAGTAGACAGTAGTTGCCTT 59.099 45.455 0.00 0.00 30.00 4.35
1076 1170 3.429135 GGTAGCAGTAGACAGTAGTTGCC 60.429 52.174 0.00 0.00 30.00 4.52
1077 1171 3.731264 CGGTAGCAGTAGACAGTAGTTGC 60.731 52.174 0.00 0.00 0.00 4.17
1078 1172 3.688185 TCGGTAGCAGTAGACAGTAGTTG 59.312 47.826 0.00 0.00 0.00 3.16
1079 1173 3.688673 GTCGGTAGCAGTAGACAGTAGTT 59.311 47.826 0.00 0.00 34.09 2.24
1080 1174 3.269178 GTCGGTAGCAGTAGACAGTAGT 58.731 50.000 0.00 0.00 34.09 2.73
1081 1175 2.284684 CGTCGGTAGCAGTAGACAGTAG 59.715 54.545 0.00 0.00 33.56 2.57
1082 1176 2.274437 CGTCGGTAGCAGTAGACAGTA 58.726 52.381 0.00 0.00 33.56 2.74
1083 1177 1.085091 CGTCGGTAGCAGTAGACAGT 58.915 55.000 0.00 0.00 33.56 3.55
1084 1178 1.085091 ACGTCGGTAGCAGTAGACAG 58.915 55.000 0.00 0.00 33.56 3.51
1085 1179 1.527034 AACGTCGGTAGCAGTAGACA 58.473 50.000 0.00 0.00 33.56 3.41
1086 1180 3.747099 TTAACGTCGGTAGCAGTAGAC 57.253 47.619 0.00 0.00 0.00 2.59
1087 1181 3.501828 TGTTTAACGTCGGTAGCAGTAGA 59.498 43.478 0.00 0.00 0.00 2.59
1124 1218 5.412286 AGTTTTACCATGATGGCATTTTTGC 59.588 36.000 12.25 0.00 42.67 3.68
1202 1296 6.531594 CGTTGAAGATAGTTATGTGCTTCTCA 59.468 38.462 0.00 0.00 36.73 3.27
1203 1297 6.019479 CCGTTGAAGATAGTTATGTGCTTCTC 60.019 42.308 0.00 0.00 36.73 2.87
1453 1563 2.146342 AGATTGCTATATGTGGCGTGC 58.854 47.619 0.00 0.00 34.02 5.34
1480 1590 4.161295 CAGCGGATCGGGAGGCAA 62.161 66.667 2.13 0.00 0.00 4.52
1520 1630 1.230635 CGATGGATCGGTGGCAATCC 61.231 60.000 9.34 9.34 45.93 3.01
1543 1653 0.249398 TCCTGGCGCTAGAGGAAAAC 59.751 55.000 23.73 0.00 35.33 2.43
1765 1876 3.560902 ATACGCATCTGACGGATACAG 57.439 47.619 0.00 0.00 30.65 2.74
1879 1990 7.639162 TCTTGTTCATTCTCGAGAAAAGTAC 57.361 36.000 30.18 25.40 37.61 2.73
1910 2021 5.958380 TGTGGAGGTGAGAATGAACTAGTAT 59.042 40.000 0.00 0.00 0.00 2.12
1912 2023 4.160329 TGTGGAGGTGAGAATGAACTAGT 58.840 43.478 0.00 0.00 0.00 2.57
1913 2024 4.808414 TGTGGAGGTGAGAATGAACTAG 57.192 45.455 0.00 0.00 0.00 2.57
1914 2025 5.305585 GTTTGTGGAGGTGAGAATGAACTA 58.694 41.667 0.00 0.00 0.00 2.24
1915 2026 4.137543 GTTTGTGGAGGTGAGAATGAACT 58.862 43.478 0.00 0.00 0.00 3.01
1916 2027 3.253432 GGTTTGTGGAGGTGAGAATGAAC 59.747 47.826 0.00 0.00 0.00 3.18
1917 2028 3.117701 TGGTTTGTGGAGGTGAGAATGAA 60.118 43.478 0.00 0.00 0.00 2.57
1919 2030 2.862541 TGGTTTGTGGAGGTGAGAATG 58.137 47.619 0.00 0.00 0.00 2.67
1920 2031 3.138283 TCTTGGTTTGTGGAGGTGAGAAT 59.862 43.478 0.00 0.00 0.00 2.40
1936 2047 9.003658 CAGTAAATGTTCTATTGAGTTCTTGGT 57.996 33.333 0.00 0.00 0.00 3.67
1959 2070 4.568359 CGTTATCAAGCAAGCTACATCAGT 59.432 41.667 0.00 0.00 0.00 3.41
1960 2071 4.025396 CCGTTATCAAGCAAGCTACATCAG 60.025 45.833 0.00 0.00 0.00 2.90
1961 2072 3.871006 CCGTTATCAAGCAAGCTACATCA 59.129 43.478 0.00 0.00 0.00 3.07
1962 2073 3.303395 GCCGTTATCAAGCAAGCTACATC 60.303 47.826 0.00 0.00 0.00 3.06
1963 2074 2.614057 GCCGTTATCAAGCAAGCTACAT 59.386 45.455 0.00 0.00 0.00 2.29
1964 2075 2.006888 GCCGTTATCAAGCAAGCTACA 58.993 47.619 0.00 0.00 0.00 2.74
1965 2076 2.006888 TGCCGTTATCAAGCAAGCTAC 58.993 47.619 0.00 0.00 32.56 3.58
1973 2089 5.928839 AGCTAATCTACATGCCGTTATCAAG 59.071 40.000 0.00 0.00 0.00 3.02
1976 2092 5.346281 GTGAGCTAATCTACATGCCGTTATC 59.654 44.000 0.00 0.00 0.00 1.75
1994 2110 6.317391 GGTAATAGAAATCAGCAAAGTGAGCT 59.683 38.462 0.00 0.00 44.62 4.09
1996 2112 7.615582 TGGTAATAGAAATCAGCAAAGTGAG 57.384 36.000 0.00 0.00 0.00 3.51
2000 2116 7.999679 TGGATTGGTAATAGAAATCAGCAAAG 58.000 34.615 0.00 0.00 32.96 2.77
2005 2128 8.292448 CCGATTTGGATTGGTAATAGAAATCAG 58.708 37.037 0.00 0.00 42.00 2.90
2018 2141 2.684881 CTCCTGAACCGATTTGGATTGG 59.315 50.000 0.00 0.00 42.00 3.16
2019 2142 3.347216 ACTCCTGAACCGATTTGGATTG 58.653 45.455 0.00 0.00 42.00 2.67
2069 2210 3.750130 AGTTCTACAAATCTGCAGCAGTG 59.250 43.478 22.10 15.27 32.61 3.66
2073 2214 5.123027 AGCTAAAGTTCTACAAATCTGCAGC 59.877 40.000 9.47 0.00 0.00 5.25
2158 2302 2.606795 GCGGCTGCTTCTACTCTATCAG 60.607 54.545 11.21 0.00 38.39 2.90
2159 2303 1.338337 GCGGCTGCTTCTACTCTATCA 59.662 52.381 11.21 0.00 38.39 2.15
2160 2304 2.058913 GCGGCTGCTTCTACTCTATC 57.941 55.000 11.21 0.00 38.39 2.08
2234 2378 3.499563 CCTCTACCCATTGGTTGGTTCAA 60.500 47.826 1.20 0.00 44.75 2.69
2332 2485 0.603707 TCCTCTTTCTTGCAGGCACG 60.604 55.000 0.00 0.00 0.00 5.34
2338 2491 1.905215 CTCCCTCTCCTCTTTCTTGCA 59.095 52.381 0.00 0.00 0.00 4.08
2341 2494 1.578897 GCCTCCCTCTCCTCTTTCTT 58.421 55.000 0.00 0.00 0.00 2.52
2385 2538 2.766313 TCTCAACATCAACCTGTTCGG 58.234 47.619 0.00 0.00 37.25 4.30
2419 2572 3.363844 TTCATCGCCGCCATCGACA 62.364 57.895 0.00 0.00 38.88 4.35
2512 2665 0.687354 TGCTGTTCTCTTCCAGGACC 59.313 55.000 0.00 0.00 27.33 4.46
2649 2802 1.945354 GCATGGCACTGCTCATTGCT 61.945 55.000 11.13 0.00 43.37 3.91
2650 2803 1.518572 GCATGGCACTGCTCATTGC 60.519 57.895 12.62 3.93 39.12 3.56
2653 2807 0.686441 ATTGGCATGGCACTGCTCAT 60.686 50.000 23.26 8.83 41.95 2.90
2677 2833 1.226660 GGCACCGAAAATCGCATGG 60.227 57.895 0.00 0.00 38.82 3.66
2680 2836 2.331893 CCTGGCACCGAAAATCGCA 61.332 57.895 0.00 0.00 38.82 5.10
2681 2837 1.022451 TACCTGGCACCGAAAATCGC 61.022 55.000 0.00 0.00 38.82 4.58
2682 2838 1.006832 CTACCTGGCACCGAAAATCG 58.993 55.000 0.00 0.00 40.07 3.34
2683 2839 0.733150 GCTACCTGGCACCGAAAATC 59.267 55.000 0.00 0.00 0.00 2.17
2740 2896 1.526887 ACACACGAATTTCAGCACTCG 59.473 47.619 0.00 0.00 37.33 4.18
2863 3022 2.289694 TGTCCTCAAGTAAAGCTCTGCC 60.290 50.000 0.00 0.00 0.00 4.85
2941 3100 8.451908 ACATAAAACTGCTTGGATAGATAACC 57.548 34.615 0.00 0.00 0.00 2.85
2978 3137 5.978322 GGATAAGATTGACGAACCAGAGTAC 59.022 44.000 0.00 0.00 0.00 2.73
3088 3517 1.927174 GAATTGATCGTCGTCCCACAG 59.073 52.381 0.00 0.00 0.00 3.66
3102 3531 1.254975 TGCCGACGAGGAGGAATTGA 61.255 55.000 0.00 0.00 45.00 2.57
3103 3532 0.807667 CTGCCGACGAGGAGGAATTG 60.808 60.000 0.00 0.00 45.00 2.32
3118 3547 1.945354 TTCCCACGATCGACTCTGCC 61.945 60.000 24.34 0.00 0.00 4.85
3125 3554 1.739035 GCATCAAGTTCCCACGATCGA 60.739 52.381 24.34 0.00 0.00 3.59
3134 3563 3.149196 TCAGTTTCCAGCATCAAGTTCC 58.851 45.455 0.00 0.00 0.00 3.62
3172 3601 4.801147 AATGCAATGCTACTACATCACG 57.199 40.909 6.82 0.00 0.00 4.35
3201 3631 4.517952 AGATGATATGCAGAGAGAACGG 57.482 45.455 0.00 0.00 0.00 4.44
3233 3663 2.594592 AGCGCTGGTTGGTTGGTC 60.595 61.111 10.39 0.00 0.00 4.02
3300 3734 2.030562 GACACCACCACCACCTCG 59.969 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.