Multiple sequence alignment - TraesCS4A01G066500

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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 TraesCS4A01G066500 chr4A 100.000 2369 0 0 1 2369 63813120 63815488 0.000000e+00 4375.0
1 TraesCS4A01G066500 chr4B 91.646 1604 65 17 655 2246 505497825 505499371 0.000000e+00 2156.0
2 TraesCS4A01G066500 chr4D 93.353 1038 38 15 655 1689 406201307 406202316 0.000000e+00 1506.0
3 TraesCS4A01G066500 chr4D 90.879 603 28 9 1751 2334 406202330 406202924 0.000000e+00 784.0
4 TraesCS4A01G066500 chr7D 94.085 541 17 1 120 660 583338701 583338176 0.000000e+00 808.0
5 TraesCS4A01G066500 chr7D 96.800 125 4 0 1 125 583387557 583387433 2.390000e-50 209.0
6 TraesCS4A01G066500 chr1A 80.602 299 54 4 29 325 353658031 353657735 6.590000e-56 228.0
7 TraesCS4A01G066500 chr7A 79.430 316 62 3 10 323 170626607 170626921 1.100000e-53 220.0
8 TraesCS4A01G066500 chr7A 80.709 254 41 7 134 383 403984935 403985184 8.640000e-45 191.0
9 TraesCS4A01G066500 chr2A 80.078 256 43 7 134 386 772014959 772014709 1.450000e-42 183.0
10 TraesCS4A01G066500 chr2A 79.842 253 44 7 134 383 18063541 18063789 6.730000e-41 178.0
11 TraesCS4A01G066500 chr2A 77.632 152 34 0 31 182 57973371 57973522 2.510000e-15 93.5
12 TraesCS4A01G066500 chrUn 80.085 236 47 0 2 237 318679710 318679945 2.420000e-40 176.0
13 TraesCS4A01G066500 chrUn 80.085 236 47 0 2 237 389625690 389625925 2.420000e-40 176.0
14 TraesCS4A01G066500 chr2D 76.115 314 75 0 2 315 607437595 607437908 5.240000e-37 165.0
15 TraesCS4A01G066500 chr1B 79.237 236 49 0 2 237 633338042 633338277 5.240000e-37 165.0
16 TraesCS4A01G066500 chr5D 95.000 60 3 0 2146 2205 219452693 219452752 6.970000e-16 95.3
17 TraesCS4A01G066500 chr3D 100.000 28 0 0 1941 1968 581548490 581548463 4.000000e-03 52.8


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 TraesCS4A01G066500 chr4A 63813120 63815488 2368 False 4375 4375 100.000 1 2369 1 chr4A.!!$F1 2368
1 TraesCS4A01G066500 chr4B 505497825 505499371 1546 False 2156 2156 91.646 655 2246 1 chr4B.!!$F1 1591
2 TraesCS4A01G066500 chr4D 406201307 406202924 1617 False 1145 1506 92.116 655 2334 2 chr4D.!!$F1 1679
3 TraesCS4A01G066500 chr7D 583338176 583338701 525 True 808 808 94.085 120 660 1 chr7D.!!$R1 540

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
180 181 0.110295 TGGGCTTGTATGTGTGCACT 59.89 50.0 19.41 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2101 0.318445 GCAAGCTGCACACCTTCAAG 60.318 55.0 1.02 0.0 44.26 3.02 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
21 22 2.190981 ACGGCGAGCTTTATTACTTCG 58.809 47.619 16.62 0.00 0.00 3.79
22 23 2.159338 ACGGCGAGCTTTATTACTTCGA 60.159 45.455 16.62 0.00 0.00 3.71
23 24 3.050619 CGGCGAGCTTTATTACTTCGAT 58.949 45.455 0.00 0.00 0.00 3.59
24 25 3.121328 CGGCGAGCTTTATTACTTCGATG 60.121 47.826 0.00 0.00 0.00 3.84
25 26 3.363084 GGCGAGCTTTATTACTTCGATGC 60.363 47.826 0.00 0.00 0.00 3.91
26 27 3.491267 GCGAGCTTTATTACTTCGATGCT 59.509 43.478 0.00 0.00 0.00 3.79
27 28 4.025647 GCGAGCTTTATTACTTCGATGCTT 60.026 41.667 0.00 0.00 0.00 3.91
28 29 5.502544 GCGAGCTTTATTACTTCGATGCTTT 60.503 40.000 0.00 0.00 0.00 3.51
29 30 6.123441 CGAGCTTTATTACTTCGATGCTTTC 58.877 40.000 0.00 0.00 0.00 2.62
30 31 6.237835 CGAGCTTTATTACTTCGATGCTTTCA 60.238 38.462 0.00 0.00 0.00 2.69
31 32 7.517417 CGAGCTTTATTACTTCGATGCTTTCAT 60.517 37.037 0.00 0.00 35.17 2.57
32 33 7.634522 AGCTTTATTACTTCGATGCTTTCATC 58.365 34.615 0.00 0.00 44.34 2.92
45 46 7.430992 GATGCTTTCATCATAATAGAGTGCA 57.569 36.000 0.81 0.00 46.44 4.57
46 47 7.812690 ATGCTTTCATCATAATAGAGTGCAA 57.187 32.000 0.00 0.00 0.00 4.08
47 48 7.812690 TGCTTTCATCATAATAGAGTGCAAT 57.187 32.000 0.00 0.00 0.00 3.56
48 49 7.645402 TGCTTTCATCATAATAGAGTGCAATG 58.355 34.615 0.00 0.00 0.00 2.82
49 50 7.283807 TGCTTTCATCATAATAGAGTGCAATGT 59.716 33.333 0.00 0.00 0.00 2.71
50 51 7.802251 GCTTTCATCATAATAGAGTGCAATGTC 59.198 37.037 0.00 0.00 0.00 3.06
51 52 7.412137 TTCATCATAATAGAGTGCAATGTCG 57.588 36.000 0.00 0.00 0.00 4.35
52 53 5.928264 TCATCATAATAGAGTGCAATGTCGG 59.072 40.000 0.00 0.00 0.00 4.79
53 54 4.058124 TCATAATAGAGTGCAATGTCGGC 58.942 43.478 0.00 0.00 0.00 5.54
54 55 2.401583 AATAGAGTGCAATGTCGGCA 57.598 45.000 0.00 0.00 39.32 5.69
59 60 4.172625 TGCAATGTCGGCACCTTT 57.827 50.000 0.00 0.00 36.11 3.11
60 61 1.956043 TGCAATGTCGGCACCTTTC 59.044 52.632 0.00 0.00 36.11 2.62
61 62 1.212751 GCAATGTCGGCACCTTTCC 59.787 57.895 0.00 0.00 0.00 3.13
62 63 1.883021 CAATGTCGGCACCTTTCCC 59.117 57.895 0.00 0.00 0.00 3.97
63 64 0.893270 CAATGTCGGCACCTTTCCCA 60.893 55.000 0.00 0.00 0.00 4.37
64 65 0.609131 AATGTCGGCACCTTTCCCAG 60.609 55.000 0.00 0.00 0.00 4.45
65 66 1.779061 ATGTCGGCACCTTTCCCAGT 61.779 55.000 0.00 0.00 0.00 4.00
66 67 1.966451 GTCGGCACCTTTCCCAGTG 60.966 63.158 0.00 0.00 37.05 3.66
70 71 2.672996 CACCTTTCCCAGTGCCGG 60.673 66.667 0.00 0.00 0.00 6.13
71 72 3.175710 ACCTTTCCCAGTGCCGGT 61.176 61.111 1.90 0.00 0.00 5.28
72 73 2.115266 CCTTTCCCAGTGCCGGTT 59.885 61.111 1.90 0.00 0.00 4.44
73 74 1.530655 CCTTTCCCAGTGCCGGTTT 60.531 57.895 1.90 0.00 0.00 3.27
74 75 1.659794 CTTTCCCAGTGCCGGTTTG 59.340 57.895 1.90 0.00 0.00 2.93
75 76 2.420466 CTTTCCCAGTGCCGGTTTGC 62.420 60.000 1.90 0.00 0.00 3.68
78 79 4.326766 CCAGTGCCGGTTTGCGTG 62.327 66.667 1.90 0.00 0.00 5.34
79 80 3.276091 CAGTGCCGGTTTGCGTGA 61.276 61.111 1.90 0.00 0.00 4.35
80 81 2.281484 AGTGCCGGTTTGCGTGAT 60.281 55.556 1.90 0.00 0.00 3.06
81 82 1.004320 AGTGCCGGTTTGCGTGATA 60.004 52.632 1.90 0.00 0.00 2.15
82 83 1.133869 GTGCCGGTTTGCGTGATAC 59.866 57.895 1.90 0.00 0.00 2.24
83 84 1.301795 TGCCGGTTTGCGTGATACA 60.302 52.632 1.90 0.00 0.00 2.29
84 85 0.885150 TGCCGGTTTGCGTGATACAA 60.885 50.000 1.90 0.00 0.00 2.41
85 86 0.450184 GCCGGTTTGCGTGATACAAT 59.550 50.000 1.90 0.00 0.00 2.71
86 87 1.793714 GCCGGTTTGCGTGATACAATG 60.794 52.381 1.90 0.00 0.00 2.82
87 88 1.534028 CGGTTTGCGTGATACAATGC 58.466 50.000 0.00 0.00 0.00 3.56
88 89 1.793714 CGGTTTGCGTGATACAATGCC 60.794 52.381 0.00 0.00 0.00 4.40
89 90 1.534028 GTTTGCGTGATACAATGCCG 58.466 50.000 0.00 0.00 0.00 5.69
90 91 0.449786 TTTGCGTGATACAATGCCGG 59.550 50.000 0.00 0.00 0.00 6.13
91 92 0.391793 TTGCGTGATACAATGCCGGA 60.392 50.000 5.05 0.00 0.00 5.14
92 93 0.809636 TGCGTGATACAATGCCGGAG 60.810 55.000 5.05 0.00 0.00 4.63
93 94 0.529773 GCGTGATACAATGCCGGAGA 60.530 55.000 5.05 0.00 0.00 3.71
94 95 1.209128 CGTGATACAATGCCGGAGAC 58.791 55.000 5.05 0.00 0.00 3.36
95 96 1.583054 GTGATACAATGCCGGAGACC 58.417 55.000 5.05 0.00 0.00 3.85
96 97 1.139058 GTGATACAATGCCGGAGACCT 59.861 52.381 5.05 0.00 0.00 3.85
97 98 2.364324 GTGATACAATGCCGGAGACCTA 59.636 50.000 5.05 0.00 0.00 3.08
98 99 2.628178 TGATACAATGCCGGAGACCTAG 59.372 50.000 5.05 0.00 0.00 3.02
99 100 2.154567 TACAATGCCGGAGACCTAGT 57.845 50.000 5.05 0.00 0.00 2.57
100 101 0.824759 ACAATGCCGGAGACCTAGTC 59.175 55.000 5.05 0.00 0.00 2.59
101 102 1.115467 CAATGCCGGAGACCTAGTCT 58.885 55.000 5.05 0.00 46.42 3.24
111 112 3.593442 AGACCTAGTCTCCATCTCAGG 57.407 52.381 0.00 0.00 38.71 3.86
112 113 2.856231 AGACCTAGTCTCCATCTCAGGT 59.144 50.000 0.00 0.00 38.71 4.00
113 114 3.270960 AGACCTAGTCTCCATCTCAGGTT 59.729 47.826 0.00 0.00 38.71 3.50
114 115 4.479056 AGACCTAGTCTCCATCTCAGGTTA 59.521 45.833 0.00 0.00 38.71 2.85
115 116 5.135362 AGACCTAGTCTCCATCTCAGGTTAT 59.865 44.000 0.00 0.00 38.71 1.89
116 117 5.782925 ACCTAGTCTCCATCTCAGGTTATT 58.217 41.667 0.00 0.00 32.49 1.40
117 118 5.600484 ACCTAGTCTCCATCTCAGGTTATTG 59.400 44.000 0.00 0.00 32.49 1.90
118 119 5.835819 CCTAGTCTCCATCTCAGGTTATTGA 59.164 44.000 0.00 0.00 0.00 2.57
144 145 1.640428 TATTGCTCTGCCGAGTTTCG 58.360 50.000 7.01 0.00 39.53 3.46
179 180 0.958091 TTGGGCTTGTATGTGTGCAC 59.042 50.000 10.75 10.75 0.00 4.57
180 181 0.110295 TGGGCTTGTATGTGTGCACT 59.890 50.000 19.41 0.00 0.00 4.40
183 184 2.420022 GGGCTTGTATGTGTGCACTAAG 59.580 50.000 19.41 12.75 0.00 2.18
244 245 1.307097 GCAGTTCCAGCTGATGATCC 58.693 55.000 17.39 0.00 38.70 3.36
250 251 2.686119 TCCAGCTGATGATCCTCATGA 58.314 47.619 17.39 0.00 37.20 3.07
251 252 2.633481 TCCAGCTGATGATCCTCATGAG 59.367 50.000 17.39 16.24 40.40 2.90
312 313 4.096003 CCCCATGACCGGTCGCTT 62.096 66.667 28.70 13.97 0.00 4.68
313 314 2.511600 CCCATGACCGGTCGCTTC 60.512 66.667 28.70 6.70 0.00 3.86
314 315 2.511600 CCATGACCGGTCGCTTCC 60.512 66.667 28.70 5.90 0.00 3.46
315 316 2.579201 CATGACCGGTCGCTTCCT 59.421 61.111 28.70 6.92 0.00 3.36
316 317 1.811266 CATGACCGGTCGCTTCCTG 60.811 63.158 28.70 14.69 0.00 3.86
317 318 2.283529 ATGACCGGTCGCTTCCTGT 61.284 57.895 28.70 5.09 0.00 4.00
318 319 2.126031 GACCGGTCGCTTCCTGTC 60.126 66.667 20.85 0.00 35.34 3.51
319 320 3.644399 GACCGGTCGCTTCCTGTCC 62.644 68.421 20.85 0.00 36.28 4.02
320 321 3.382832 CCGGTCGCTTCCTGTCCT 61.383 66.667 0.00 0.00 0.00 3.85
321 322 2.182030 CGGTCGCTTCCTGTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
322 323 2.579738 GGTCGCTTCCTGTCCTCC 59.420 66.667 0.00 0.00 0.00 4.30
323 324 2.579738 GTCGCTTCCTGTCCTCCC 59.420 66.667 0.00 0.00 0.00 4.30
324 325 2.119611 TCGCTTCCTGTCCTCCCA 59.880 61.111 0.00 0.00 0.00 4.37
508 509 3.815856 TGCCTTGTTCTGAATTTTGCA 57.184 38.095 0.00 0.00 0.00 4.08
573 574 1.304052 TTGGGATTGGGTTCGGCTG 60.304 57.895 0.00 0.00 0.00 4.85
618 619 2.173569 GCCACATTCCTACCTTCCTGAT 59.826 50.000 0.00 0.00 0.00 2.90
633 634 4.613925 TCCTGATAGAGATCCAATGCAC 57.386 45.455 0.00 0.00 0.00 4.57
635 636 3.558746 CCTGATAGAGATCCAATGCACCC 60.559 52.174 0.00 0.00 0.00 4.61
638 639 1.293062 AGAGATCCAATGCACCCAGT 58.707 50.000 0.00 0.00 0.00 4.00
646 647 0.257039 AATGCACCCAGTCCAGGATC 59.743 55.000 0.00 0.00 0.00 3.36
746 747 3.330267 CAGTAGAGTCCTGCTGTTTTCC 58.670 50.000 0.00 0.00 44.73 3.13
752 753 5.066593 AGAGTCCTGCTGTTTTCCTAAAAG 58.933 41.667 0.00 0.00 0.00 2.27
755 756 5.532779 AGTCCTGCTGTTTTCCTAAAAGAAG 59.467 40.000 0.00 0.00 0.00 2.85
781 782 7.823745 AATCTAGTGTGATTTTGACCAAGTT 57.176 32.000 0.00 0.00 33.33 2.66
782 783 6.618287 TCTAGTGTGATTTTGACCAAGTTG 57.382 37.500 0.00 0.00 0.00 3.16
783 784 6.119536 TCTAGTGTGATTTTGACCAAGTTGT 58.880 36.000 1.45 0.00 0.00 3.32
784 785 7.276658 TCTAGTGTGATTTTGACCAAGTTGTA 58.723 34.615 1.45 0.00 0.00 2.41
785 786 6.131544 AGTGTGATTTTGACCAAGTTGTAC 57.868 37.500 1.45 0.00 0.00 2.90
857 858 0.515127 TTGCCGCTAAATGACACACG 59.485 50.000 0.00 0.00 0.00 4.49
923 924 4.142227 GCTACTTATCCTCTCGTGTTGGAA 60.142 45.833 6.20 0.00 33.20 3.53
935 936 4.062293 TCGTGTTGGAAAACTCCACATAG 58.938 43.478 0.00 0.00 39.90 2.23
936 937 4.062293 CGTGTTGGAAAACTCCACATAGA 58.938 43.478 0.00 0.00 39.90 1.98
937 938 4.084013 CGTGTTGGAAAACTCCACATAGAC 60.084 45.833 0.00 0.00 39.90 2.59
938 939 4.819630 GTGTTGGAAAACTCCACATAGACA 59.180 41.667 0.00 0.00 39.90 3.41
940 941 4.015872 TGGAAAACTCCACATAGACACC 57.984 45.455 0.00 0.00 34.33 4.16
941 942 3.392947 TGGAAAACTCCACATAGACACCA 59.607 43.478 0.00 0.00 34.33 4.17
943 944 5.010282 GGAAAACTCCACATAGACACCAAT 58.990 41.667 0.00 0.00 0.00 3.16
944 945 6.177610 GGAAAACTCCACATAGACACCAATA 58.822 40.000 0.00 0.00 0.00 1.90
946 947 5.755409 AACTCCACATAGACACCAATACA 57.245 39.130 0.00 0.00 0.00 2.29
947 948 5.086104 ACTCCACATAGACACCAATACAC 57.914 43.478 0.00 0.00 0.00 2.90
948 949 4.081087 ACTCCACATAGACACCAATACACC 60.081 45.833 0.00 0.00 0.00 4.16
949 950 3.841255 TCCACATAGACACCAATACACCA 59.159 43.478 0.00 0.00 0.00 4.17
950 951 4.473196 TCCACATAGACACCAATACACCAT 59.527 41.667 0.00 0.00 0.00 3.55
951 952 5.663556 TCCACATAGACACCAATACACCATA 59.336 40.000 0.00 0.00 0.00 2.74
963 964 5.070981 CCAATACACCATAGATCACACCTCT 59.929 44.000 0.00 0.00 0.00 3.69
965 966 6.902771 ATACACCATAGATCACACCTCTAC 57.097 41.667 0.00 0.00 0.00 2.59
967 968 4.890581 ACACCATAGATCACACCTCTACTC 59.109 45.833 0.00 0.00 0.00 2.59
977 978 1.133606 CACCTCTACTCCTCCTCCTCC 60.134 61.905 0.00 0.00 0.00 4.30
978 979 1.275357 ACCTCTACTCCTCCTCCTCCT 60.275 57.143 0.00 0.00 0.00 3.69
979 980 1.423921 CCTCTACTCCTCCTCCTCCTC 59.576 61.905 0.00 0.00 0.00 3.71
981 982 2.106511 CTCTACTCCTCCTCCTCCTCAG 59.893 59.091 0.00 0.00 0.00 3.35
982 983 1.144913 CTACTCCTCCTCCTCCTCAGG 59.855 61.905 0.00 0.00 42.01 3.86
989 990 4.266962 TCCTCCTCAGGATCGCAG 57.733 61.111 0.00 0.00 44.75 5.18
990 991 2.130426 TCCTCCTCAGGATCGCAGC 61.130 63.158 0.00 0.00 44.75 5.25
991 992 2.420890 CTCCTCAGGATCGCAGCC 59.579 66.667 0.00 0.00 0.00 4.85
992 993 2.042537 TCCTCAGGATCGCAGCCT 60.043 61.111 0.00 0.00 35.75 4.58
993 994 2.086251 CTCCTCAGGATCGCAGCCTC 62.086 65.000 0.00 0.00 32.12 4.70
1044 1045 1.406065 CCGCTCCACATCTCTCCCAT 61.406 60.000 0.00 0.00 0.00 4.00
1156 1160 1.152839 GACGGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
1157 1161 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
1158 1162 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
1315 1319 0.041488 CGCCGTCTACGTCTACATCC 60.041 60.000 0.00 0.00 37.74 3.51
1322 1326 2.158652 TCTACGTCTACATCCCCCAGAG 60.159 54.545 0.00 0.00 0.00 3.35
1377 1381 7.558807 TCCATGATCAATCACTAGCTCAAATTT 59.441 33.333 0.00 0.00 40.03 1.82
1414 1418 2.931512 TATTTAGCGCCAACAAAGCC 57.068 45.000 2.29 0.00 0.00 4.35
1419 1423 2.260869 GCGCCAACAAAGCCTCTGA 61.261 57.895 0.00 0.00 0.00 3.27
1422 1426 0.108945 GCCAACAAAGCCTCTGATGC 60.109 55.000 0.00 0.00 0.00 3.91
1545 1549 4.751600 GGAAGAAGCAGGAAACAAAATTGG 59.248 41.667 0.00 0.00 0.00 3.16
1595 1601 2.165641 CGCCTTACATACACCTCTGACA 59.834 50.000 0.00 0.00 0.00 3.58
1788 1797 0.833949 GTTCATCTCTCCCCACTCCC 59.166 60.000 0.00 0.00 0.00 4.30
1823 1846 0.041238 TCCGGAAGAGGATGGTCAGT 59.959 55.000 0.00 0.00 34.92 3.41
1830 1853 0.459237 GAGGATGGTCAGTGCTCACG 60.459 60.000 0.00 0.00 34.58 4.35
2036 2068 1.378250 GCAAGCCTCAGACCATGCT 60.378 57.895 0.00 0.00 35.08 3.79
2038 2070 0.252479 CAAGCCTCAGACCATGCTCT 59.748 55.000 0.00 0.00 32.62 4.09
2069 2101 2.100525 TTGGGGTGGGGAAATGGGAC 62.101 60.000 0.00 0.00 0.00 4.46
2093 2125 2.355481 GTGTGCAGCTTGCCTTGC 60.355 61.111 5.82 0.71 44.23 4.01
2114 2146 1.178276 GCTCCGAGACCTTCTTCTGA 58.822 55.000 0.00 0.00 0.00 3.27
2224 2257 4.644685 ACAAGTTAACAACATCACTGGCTT 59.355 37.500 8.61 0.00 0.00 4.35
2260 2293 5.248248 TCTGAAAATGTGTAGGTCTGGATCA 59.752 40.000 0.00 0.00 0.00 2.92
2282 2316 1.165270 AGCAATACGAAAGGGTGTGC 58.835 50.000 0.00 0.00 34.39 4.57
2304 2338 7.066887 TGTGCTCAACTCATTCTGAAACTTTTA 59.933 33.333 0.00 0.00 0.00 1.52
2306 2340 9.283768 TGCTCAACTCATTCTGAAACTTTTATA 57.716 29.630 0.00 0.00 0.00 0.98
2339 2376 5.296151 AGTCAGAAACTGAGATTTGTCCA 57.704 39.130 1.53 0.00 41.46 4.02
2340 2377 5.303971 AGTCAGAAACTGAGATTTGTCCAG 58.696 41.667 1.53 0.00 41.46 3.86
2341 2378 5.070981 AGTCAGAAACTGAGATTTGTCCAGA 59.929 40.000 1.53 0.00 41.46 3.86
2342 2379 5.407995 GTCAGAAACTGAGATTTGTCCAGAG 59.592 44.000 1.53 0.00 41.46 3.35
2343 2380 4.153835 CAGAAACTGAGATTTGTCCAGAGC 59.846 45.833 0.00 0.00 32.44 4.09
2344 2381 2.777832 ACTGAGATTTGTCCAGAGCC 57.222 50.000 0.00 0.00 0.00 4.70
2345 2382 1.980765 ACTGAGATTTGTCCAGAGCCA 59.019 47.619 0.00 0.00 0.00 4.75
2346 2383 2.575279 ACTGAGATTTGTCCAGAGCCAT 59.425 45.455 0.00 0.00 0.00 4.40
2347 2384 2.943690 CTGAGATTTGTCCAGAGCCATG 59.056 50.000 0.00 0.00 0.00 3.66
2348 2385 2.573009 TGAGATTTGTCCAGAGCCATGA 59.427 45.455 0.00 0.00 0.00 3.07
2349 2386 3.009363 TGAGATTTGTCCAGAGCCATGAA 59.991 43.478 0.00 0.00 0.00 2.57
2350 2387 3.350833 AGATTTGTCCAGAGCCATGAAC 58.649 45.455 0.00 0.00 0.00 3.18
2351 2388 2.655090 TTTGTCCAGAGCCATGAACA 57.345 45.000 0.00 0.00 0.00 3.18
2352 2389 2.885135 TTGTCCAGAGCCATGAACAT 57.115 45.000 0.00 0.00 0.00 2.71
2353 2390 2.118313 TGTCCAGAGCCATGAACATG 57.882 50.000 7.70 7.70 38.51 3.21
2354 2391 1.352017 TGTCCAGAGCCATGAACATGT 59.648 47.619 12.74 0.00 37.11 3.21
2355 2392 2.571202 TGTCCAGAGCCATGAACATGTA 59.429 45.455 12.74 0.00 37.11 2.29
2356 2393 3.201290 GTCCAGAGCCATGAACATGTAG 58.799 50.000 12.74 1.43 37.11 2.74
2357 2394 2.840038 TCCAGAGCCATGAACATGTAGT 59.160 45.455 12.74 0.00 37.11 2.73
2358 2395 3.118629 TCCAGAGCCATGAACATGTAGTC 60.119 47.826 12.74 0.00 37.11 2.59
2359 2396 3.201290 CAGAGCCATGAACATGTAGTCC 58.799 50.000 12.74 0.00 37.11 3.85
2360 2397 2.840038 AGAGCCATGAACATGTAGTCCA 59.160 45.455 12.74 0.00 37.11 4.02
2361 2398 3.457380 AGAGCCATGAACATGTAGTCCAT 59.543 43.478 12.74 0.00 37.11 3.41
2362 2399 4.080129 AGAGCCATGAACATGTAGTCCATT 60.080 41.667 12.74 0.00 37.11 3.16
2363 2400 4.202441 AGCCATGAACATGTAGTCCATTC 58.798 43.478 12.74 0.00 37.11 2.67
2364 2401 3.316308 GCCATGAACATGTAGTCCATTCC 59.684 47.826 12.74 0.00 37.11 3.01
2365 2402 4.525996 CCATGAACATGTAGTCCATTCCA 58.474 43.478 12.74 0.00 37.11 3.53
2366 2403 4.949238 CCATGAACATGTAGTCCATTCCAA 59.051 41.667 12.74 0.00 37.11 3.53
2367 2404 5.418524 CCATGAACATGTAGTCCATTCCAAA 59.581 40.000 12.74 0.00 37.11 3.28
2368 2405 6.097270 CCATGAACATGTAGTCCATTCCAAAT 59.903 38.462 12.74 0.00 37.11 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.601763 CGAAGTAATAAAGCTCGCCGTT 59.398 45.455 0.00 0.00 0.00 4.44
1 2 2.159338 TCGAAGTAATAAAGCTCGCCGT 60.159 45.455 0.00 0.00 0.00 5.68
2 3 2.456989 TCGAAGTAATAAAGCTCGCCG 58.543 47.619 0.00 0.00 0.00 6.46
3 4 3.363084 GCATCGAAGTAATAAAGCTCGCC 60.363 47.826 0.00 0.00 0.00 5.54
4 5 3.491267 AGCATCGAAGTAATAAAGCTCGC 59.509 43.478 0.00 0.00 0.00 5.03
5 6 5.643339 AAGCATCGAAGTAATAAAGCTCG 57.357 39.130 0.00 0.00 0.00 5.03
6 7 7.005062 TGAAAGCATCGAAGTAATAAAGCTC 57.995 36.000 0.00 0.00 0.00 4.09
7 8 6.985188 TGAAAGCATCGAAGTAATAAAGCT 57.015 33.333 0.00 0.00 0.00 3.74
8 9 7.828685 GATGAAAGCATCGAAGTAATAAAGC 57.171 36.000 0.00 0.00 41.31 3.51
14 15 9.981114 TCTATTATGATGAAAGCATCGAAGTAA 57.019 29.630 0.00 0.00 39.99 2.24
15 16 9.631452 CTCTATTATGATGAAAGCATCGAAGTA 57.369 33.333 0.00 0.00 39.99 2.24
16 17 8.147058 ACTCTATTATGATGAAAGCATCGAAGT 58.853 33.333 0.00 0.00 39.99 3.01
17 18 8.433893 CACTCTATTATGATGAAAGCATCGAAG 58.566 37.037 0.00 0.00 39.99 3.79
18 19 7.095481 GCACTCTATTATGATGAAAGCATCGAA 60.095 37.037 0.00 0.00 39.99 3.71
19 20 6.367149 GCACTCTATTATGATGAAAGCATCGA 59.633 38.462 0.00 0.00 39.99 3.59
20 21 6.146673 TGCACTCTATTATGATGAAAGCATCG 59.853 38.462 0.00 0.00 39.99 3.84
21 22 7.430992 TGCACTCTATTATGATGAAAGCATC 57.569 36.000 0.00 0.00 39.99 3.91
23 24 7.283807 ACATTGCACTCTATTATGATGAAAGCA 59.716 33.333 0.00 0.00 35.55 3.91
24 25 7.646314 ACATTGCACTCTATTATGATGAAAGC 58.354 34.615 0.00 0.00 0.00 3.51
25 26 8.008279 CGACATTGCACTCTATTATGATGAAAG 58.992 37.037 0.00 0.00 0.00 2.62
26 27 7.041848 CCGACATTGCACTCTATTATGATGAAA 60.042 37.037 0.00 0.00 0.00 2.69
27 28 6.424812 CCGACATTGCACTCTATTATGATGAA 59.575 38.462 0.00 0.00 0.00 2.57
28 29 5.928264 CCGACATTGCACTCTATTATGATGA 59.072 40.000 0.00 0.00 0.00 2.92
29 30 5.390251 GCCGACATTGCACTCTATTATGATG 60.390 44.000 0.00 0.00 0.00 3.07
30 31 4.692625 GCCGACATTGCACTCTATTATGAT 59.307 41.667 0.00 0.00 0.00 2.45
31 32 4.058124 GCCGACATTGCACTCTATTATGA 58.942 43.478 0.00 0.00 0.00 2.15
32 33 3.809279 TGCCGACATTGCACTCTATTATG 59.191 43.478 0.00 0.00 32.85 1.90
33 34 4.071961 TGCCGACATTGCACTCTATTAT 57.928 40.909 0.00 0.00 32.85 1.28
34 35 3.535280 TGCCGACATTGCACTCTATTA 57.465 42.857 0.00 0.00 32.85 0.98
35 36 2.401583 TGCCGACATTGCACTCTATT 57.598 45.000 0.00 0.00 32.85 1.73
42 43 1.523154 GGAAAGGTGCCGACATTGCA 61.523 55.000 0.00 0.00 36.12 4.08
43 44 1.212751 GGAAAGGTGCCGACATTGC 59.787 57.895 0.00 0.00 0.00 3.56
44 45 0.893270 TGGGAAAGGTGCCGACATTG 60.893 55.000 0.00 0.00 38.32 2.82
45 46 0.609131 CTGGGAAAGGTGCCGACATT 60.609 55.000 0.00 0.00 38.32 2.71
46 47 1.002134 CTGGGAAAGGTGCCGACAT 60.002 57.895 0.00 0.00 38.32 3.06
47 48 2.429930 CTGGGAAAGGTGCCGACA 59.570 61.111 0.00 0.00 38.32 4.35
48 49 1.966451 CACTGGGAAAGGTGCCGAC 60.966 63.158 0.00 0.00 38.32 4.79
49 50 2.429930 CACTGGGAAAGGTGCCGA 59.570 61.111 0.00 0.00 38.32 5.54
53 54 2.672996 CCGGCACTGGGAAAGGTG 60.673 66.667 0.00 0.00 36.62 4.00
54 55 2.292785 AAACCGGCACTGGGAAAGGT 62.293 55.000 0.00 0.00 0.00 3.50
55 56 1.530655 AAACCGGCACTGGGAAAGG 60.531 57.895 0.00 0.00 0.00 3.11
56 57 1.659794 CAAACCGGCACTGGGAAAG 59.340 57.895 0.00 0.00 0.00 2.62
57 58 2.494530 GCAAACCGGCACTGGGAAA 61.495 57.895 0.00 0.00 0.00 3.13
58 59 2.909965 GCAAACCGGCACTGGGAA 60.910 61.111 0.00 0.00 0.00 3.97
61 62 4.326766 CACGCAAACCGGCACTGG 62.327 66.667 0.00 0.00 42.52 4.00
62 63 1.295357 TATCACGCAAACCGGCACTG 61.295 55.000 0.00 0.00 42.52 3.66
63 64 1.004320 TATCACGCAAACCGGCACT 60.004 52.632 0.00 0.00 42.52 4.40
64 65 1.133869 GTATCACGCAAACCGGCAC 59.866 57.895 0.00 0.00 42.52 5.01
65 66 0.885150 TTGTATCACGCAAACCGGCA 60.885 50.000 0.00 0.00 42.52 5.69
66 67 0.450184 ATTGTATCACGCAAACCGGC 59.550 50.000 0.00 0.00 42.52 6.13
67 68 1.793714 GCATTGTATCACGCAAACCGG 60.794 52.381 0.00 0.00 42.52 5.28
68 69 1.534028 GCATTGTATCACGCAAACCG 58.466 50.000 0.00 0.00 44.21 4.44
69 70 1.793714 CGGCATTGTATCACGCAAACC 60.794 52.381 0.00 0.00 0.00 3.27
70 71 1.534028 CGGCATTGTATCACGCAAAC 58.466 50.000 0.00 0.00 0.00 2.93
71 72 0.449786 CCGGCATTGTATCACGCAAA 59.550 50.000 0.00 0.00 0.00 3.68
72 73 0.391793 TCCGGCATTGTATCACGCAA 60.392 50.000 0.00 0.00 0.00 4.85
73 74 0.809636 CTCCGGCATTGTATCACGCA 60.810 55.000 0.00 0.00 0.00 5.24
74 75 0.529773 TCTCCGGCATTGTATCACGC 60.530 55.000 0.00 0.00 0.00 5.34
75 76 1.209128 GTCTCCGGCATTGTATCACG 58.791 55.000 0.00 0.00 0.00 4.35
76 77 1.139058 AGGTCTCCGGCATTGTATCAC 59.861 52.381 0.00 0.00 0.00 3.06
77 78 1.496060 AGGTCTCCGGCATTGTATCA 58.504 50.000 0.00 0.00 0.00 2.15
78 79 2.628657 ACTAGGTCTCCGGCATTGTATC 59.371 50.000 0.00 0.00 0.00 2.24
79 80 2.628657 GACTAGGTCTCCGGCATTGTAT 59.371 50.000 0.00 0.00 0.00 2.29
80 81 2.029623 GACTAGGTCTCCGGCATTGTA 58.970 52.381 0.00 0.00 0.00 2.41
81 82 0.824759 GACTAGGTCTCCGGCATTGT 59.175 55.000 0.00 0.00 0.00 2.71
82 83 1.115467 AGACTAGGTCTCCGGCATTG 58.885 55.000 0.00 0.00 38.71 2.82
83 84 3.617535 AGACTAGGTCTCCGGCATT 57.382 52.632 0.00 0.00 38.71 3.56
91 92 2.856231 ACCTGAGATGGAGACTAGGTCT 59.144 50.000 0.00 0.00 46.42 3.85
92 93 3.306472 ACCTGAGATGGAGACTAGGTC 57.694 52.381 0.00 0.00 33.48 3.85
93 94 3.767309 AACCTGAGATGGAGACTAGGT 57.233 47.619 0.00 0.00 40.07 3.08
94 95 5.835819 TCAATAACCTGAGATGGAGACTAGG 59.164 44.000 0.00 0.00 0.00 3.02
95 96 6.322456 TGTCAATAACCTGAGATGGAGACTAG 59.678 42.308 0.00 0.00 0.00 2.57
96 97 6.194967 TGTCAATAACCTGAGATGGAGACTA 58.805 40.000 0.00 0.00 0.00 2.59
97 98 5.026121 TGTCAATAACCTGAGATGGAGACT 58.974 41.667 0.00 0.00 0.00 3.24
98 99 5.344743 TGTCAATAACCTGAGATGGAGAC 57.655 43.478 0.00 0.00 0.00 3.36
99 100 6.841229 AGTATGTCAATAACCTGAGATGGAGA 59.159 38.462 0.00 0.00 32.09 3.71
100 101 7.060383 AGTATGTCAATAACCTGAGATGGAG 57.940 40.000 0.00 0.00 32.09 3.86
101 102 7.437713 AAGTATGTCAATAACCTGAGATGGA 57.562 36.000 0.00 0.00 32.09 3.41
102 103 9.784531 AATAAGTATGTCAATAACCTGAGATGG 57.215 33.333 0.00 0.00 32.09 3.51
104 105 9.277783 GCAATAAGTATGTCAATAACCTGAGAT 57.722 33.333 0.00 0.00 34.06 2.75
105 106 8.486210 AGCAATAAGTATGTCAATAACCTGAGA 58.514 33.333 0.00 0.00 0.00 3.27
106 107 8.668510 AGCAATAAGTATGTCAATAACCTGAG 57.331 34.615 0.00 0.00 0.00 3.35
107 108 8.486210 AGAGCAATAAGTATGTCAATAACCTGA 58.514 33.333 0.00 0.00 0.00 3.86
108 109 8.554528 CAGAGCAATAAGTATGTCAATAACCTG 58.445 37.037 0.00 0.00 0.00 4.00
109 110 7.227512 GCAGAGCAATAAGTATGTCAATAACCT 59.772 37.037 0.00 0.00 0.00 3.50
110 111 7.355778 GCAGAGCAATAAGTATGTCAATAACC 58.644 38.462 0.00 0.00 0.00 2.85
111 112 7.355778 GGCAGAGCAATAAGTATGTCAATAAC 58.644 38.462 0.00 0.00 0.00 1.89
112 113 6.202762 CGGCAGAGCAATAAGTATGTCAATAA 59.797 38.462 0.00 0.00 0.00 1.40
113 114 5.696270 CGGCAGAGCAATAAGTATGTCAATA 59.304 40.000 0.00 0.00 0.00 1.90
114 115 4.512944 CGGCAGAGCAATAAGTATGTCAAT 59.487 41.667 0.00 0.00 0.00 2.57
115 116 3.871006 CGGCAGAGCAATAAGTATGTCAA 59.129 43.478 0.00 0.00 0.00 3.18
116 117 3.132111 TCGGCAGAGCAATAAGTATGTCA 59.868 43.478 0.00 0.00 0.00 3.58
117 118 3.717707 TCGGCAGAGCAATAAGTATGTC 58.282 45.455 0.00 0.00 0.00 3.06
118 119 3.722147 CTCGGCAGAGCAATAAGTATGT 58.278 45.455 0.00 0.00 37.73 2.29
144 145 1.200020 CCCAAGCTCGTGTTCATTTCC 59.800 52.381 0.00 0.00 0.00 3.13
179 180 4.624882 CAGTTCAAGAGCTAGTGTGCTTAG 59.375 45.833 0.00 0.00 44.17 2.18
180 181 4.039245 ACAGTTCAAGAGCTAGTGTGCTTA 59.961 41.667 0.00 0.00 44.17 3.09
183 184 2.734079 GACAGTTCAAGAGCTAGTGTGC 59.266 50.000 0.00 0.00 0.00 4.57
244 245 1.142748 GCCCGTCAGGACTCATGAG 59.857 63.158 21.37 21.37 41.02 2.90
268 269 1.647346 CAAACTGACGGGCGCTAATA 58.353 50.000 7.64 0.00 0.00 0.98
310 311 1.376037 GCGTTGGGAGGACAGGAAG 60.376 63.158 0.00 0.00 0.00 3.46
311 312 2.144078 TGCGTTGGGAGGACAGGAA 61.144 57.895 0.00 0.00 0.00 3.36
312 313 2.525629 TGCGTTGGGAGGACAGGA 60.526 61.111 0.00 0.00 0.00 3.86
313 314 2.358737 GTGCGTTGGGAGGACAGG 60.359 66.667 0.00 0.00 0.00 4.00
314 315 2.358737 GGTGCGTTGGGAGGACAG 60.359 66.667 0.00 0.00 0.00 3.51
315 316 2.063015 AATGGTGCGTTGGGAGGACA 62.063 55.000 0.00 0.00 0.00 4.02
316 317 1.303317 AATGGTGCGTTGGGAGGAC 60.303 57.895 0.00 0.00 0.00 3.85
317 318 1.303236 CAATGGTGCGTTGGGAGGA 60.303 57.895 0.00 0.00 0.00 3.71
318 319 1.586154 GACAATGGTGCGTTGGGAGG 61.586 60.000 0.00 0.00 34.96 4.30
319 320 0.606401 AGACAATGGTGCGTTGGGAG 60.606 55.000 0.00 0.00 34.96 4.30
320 321 0.605319 GAGACAATGGTGCGTTGGGA 60.605 55.000 0.00 0.00 34.96 4.37
321 322 1.586154 GGAGACAATGGTGCGTTGGG 61.586 60.000 0.00 0.00 34.96 4.12
322 323 0.888736 TGGAGACAATGGTGCGTTGG 60.889 55.000 0.00 0.00 37.44 3.77
323 324 0.238289 GTGGAGACAATGGTGCGTTG 59.762 55.000 0.00 0.00 46.06 4.10
324 325 0.889186 GGTGGAGACAATGGTGCGTT 60.889 55.000 0.00 0.00 46.06 4.84
463 464 0.907230 AGGTGCTGAGGAGAGGGAAC 60.907 60.000 0.00 0.00 0.00 3.62
508 509 3.347216 CTTGAGAAACGGGATGGTCAAT 58.653 45.455 0.00 0.00 0.00 2.57
580 581 2.656069 GCGGTGCAGAAGGGGAGTA 61.656 63.158 0.00 0.00 0.00 2.59
618 619 2.435805 GACTGGGTGCATTGGATCTCTA 59.564 50.000 0.00 0.00 0.00 2.43
633 634 1.222936 GCACTGATCCTGGACTGGG 59.777 63.158 0.00 0.00 0.00 4.45
635 636 0.545171 ATGGCACTGATCCTGGACTG 59.455 55.000 0.00 0.27 0.00 3.51
638 639 0.994247 ACAATGGCACTGATCCTGGA 59.006 50.000 1.60 0.00 0.00 3.86
646 647 7.887996 ATAAAACAACATAACAATGGCACTG 57.112 32.000 0.00 0.00 0.00 3.66
708 709 8.457238 ACTCTACTGCTTTTTCTTCTTCAAAT 57.543 30.769 0.00 0.00 0.00 2.32
712 713 6.147000 CAGGACTCTACTGCTTTTTCTTCTTC 59.853 42.308 0.00 0.00 0.00 2.87
713 714 5.994668 CAGGACTCTACTGCTTTTTCTTCTT 59.005 40.000 0.00 0.00 0.00 2.52
714 715 5.546526 CAGGACTCTACTGCTTTTTCTTCT 58.453 41.667 0.00 0.00 0.00 2.85
715 716 5.854431 CAGGACTCTACTGCTTTTTCTTC 57.146 43.478 0.00 0.00 0.00 2.87
752 753 8.099364 TGGTCAAAATCACACTAGATTTCTTC 57.901 34.615 0.00 0.00 44.96 2.87
755 756 7.875971 ACTTGGTCAAAATCACACTAGATTTC 58.124 34.615 0.00 0.00 44.96 2.17
781 782 8.277490 ACTCTCGAGATATTTTGTACAGTACA 57.723 34.615 17.03 9.51 36.79 2.90
784 785 9.121658 TCATACTCTCGAGATATTTTGTACAGT 57.878 33.333 17.03 8.11 0.00 3.55
785 786 9.605955 CTCATACTCTCGAGATATTTTGTACAG 57.394 37.037 17.03 9.68 0.00 2.74
857 858 1.141053 AGGGAAGACAGTGACAACCAC 59.859 52.381 0.00 0.00 46.03 4.16
923 924 5.938125 GTGTATTGGTGTCTATGTGGAGTTT 59.062 40.000 0.00 0.00 0.00 2.66
935 936 5.523916 GTGTGATCTATGGTGTATTGGTGTC 59.476 44.000 0.00 0.00 0.00 3.67
936 937 5.428253 GTGTGATCTATGGTGTATTGGTGT 58.572 41.667 0.00 0.00 0.00 4.16
937 938 4.816385 GGTGTGATCTATGGTGTATTGGTG 59.184 45.833 0.00 0.00 0.00 4.17
938 939 4.721776 AGGTGTGATCTATGGTGTATTGGT 59.278 41.667 0.00 0.00 0.00 3.67
940 941 6.166984 AGAGGTGTGATCTATGGTGTATTG 57.833 41.667 0.00 0.00 0.00 1.90
941 942 7.069986 AGTAGAGGTGTGATCTATGGTGTATT 58.930 38.462 0.00 0.00 32.15 1.89
943 944 6.014771 AGTAGAGGTGTGATCTATGGTGTA 57.985 41.667 0.00 0.00 32.15 2.90
944 945 4.873010 AGTAGAGGTGTGATCTATGGTGT 58.127 43.478 0.00 0.00 32.15 4.16
946 947 4.169068 AGGAGTAGAGGTGTGATCTATGGT 59.831 45.833 0.00 0.00 32.15 3.55
947 948 4.735369 AGGAGTAGAGGTGTGATCTATGG 58.265 47.826 0.00 0.00 32.15 2.74
948 949 4.764823 GGAGGAGTAGAGGTGTGATCTATG 59.235 50.000 0.00 0.00 32.15 2.23
949 950 4.667858 AGGAGGAGTAGAGGTGTGATCTAT 59.332 45.833 0.00 0.00 32.15 1.98
950 951 4.048600 AGGAGGAGTAGAGGTGTGATCTA 58.951 47.826 0.00 0.00 0.00 1.98
951 952 2.856231 AGGAGGAGTAGAGGTGTGATCT 59.144 50.000 0.00 0.00 0.00 2.75
963 964 1.227249 CCTGAGGAGGAGGAGGAGTA 58.773 60.000 0.00 0.00 42.93 2.59
965 966 2.326992 TCCTGAGGAGGAGGAGGAG 58.673 63.158 0.00 0.00 44.13 3.69
977 978 1.756408 ATGGAGGCTGCGATCCTGAG 61.756 60.000 19.36 0.00 36.50 3.35
978 979 1.763655 ATGGAGGCTGCGATCCTGA 60.764 57.895 19.36 4.98 36.50 3.86
979 980 1.597302 CATGGAGGCTGCGATCCTG 60.597 63.158 19.36 12.78 36.50 3.86
981 982 2.976903 GCATGGAGGCTGCGATCC 60.977 66.667 13.82 13.82 36.05 3.36
982 983 1.170919 ATTGCATGGAGGCTGCGATC 61.171 55.000 0.35 0.00 39.05 3.69
983 984 1.152819 ATTGCATGGAGGCTGCGAT 60.153 52.632 0.35 0.00 42.62 4.58
984 985 2.116533 CATTGCATGGAGGCTGCGA 61.117 57.895 0.35 0.00 42.62 5.10
985 986 2.411701 CATTGCATGGAGGCTGCG 59.588 61.111 0.35 0.00 42.62 5.18
1005 1006 2.751688 GCGGTGGTGGTAAGGGAA 59.248 61.111 0.00 0.00 0.00 3.97
1156 1160 0.955919 CACCACGCCCTCTTCTTTCC 60.956 60.000 0.00 0.00 0.00 3.13
1157 1161 0.955919 CCACCACGCCCTCTTCTTTC 60.956 60.000 0.00 0.00 0.00 2.62
1158 1162 1.073199 CCACCACGCCCTCTTCTTT 59.927 57.895 0.00 0.00 0.00 2.52
1315 1319 2.187946 GCACACGATCCTCTGGGG 59.812 66.667 0.00 0.00 0.00 4.96
1392 1396 4.081697 AGGCTTTGTTGGCGCTAAATATTT 60.082 37.500 8.12 5.89 37.59 1.40
1393 1397 3.447229 AGGCTTTGTTGGCGCTAAATATT 59.553 39.130 8.12 0.00 37.59 1.28
1414 1418 8.140628 ACTACAAGTACAATGATAGCATCAGAG 58.859 37.037 0.00 3.36 43.53 3.35
1419 1423 9.265901 GATGAACTACAAGTACAATGATAGCAT 57.734 33.333 5.77 0.00 35.92 3.79
1422 1426 9.809096 AGTGATGAACTACAAGTACAATGATAG 57.191 33.333 5.77 6.33 37.36 2.08
1595 1601 0.889638 TCGAGGAATAGGCGCGATCT 60.890 55.000 12.10 9.21 0.00 2.75
1788 1797 2.622962 GGAACCAAGGTTTCCGGCG 61.623 63.158 5.87 0.00 38.60 6.46
1807 1817 0.908198 AGCACTGACCATCCTCTTCC 59.092 55.000 0.00 0.00 0.00 3.46
2038 2070 4.619320 CCCCAAACCTGCCCAGCA 62.619 66.667 0.00 0.00 36.92 4.41
2069 2101 0.318445 GCAAGCTGCACACCTTCAAG 60.318 55.000 1.02 0.00 44.26 3.02
2093 2125 1.135141 CAGAAGAAGGTCTCGGAGCTG 60.135 57.143 0.00 0.00 39.62 4.24
2205 2238 7.114811 CACATTAAAGCCAGTGATGTTGTTAAC 59.885 37.037 0.00 0.00 33.99 2.01
2206 2239 7.013750 TCACATTAAAGCCAGTGATGTTGTTAA 59.986 33.333 0.00 0.00 36.20 2.01
2207 2240 6.488344 TCACATTAAAGCCAGTGATGTTGTTA 59.512 34.615 0.00 0.00 36.20 2.41
2208 2241 5.301551 TCACATTAAAGCCAGTGATGTTGTT 59.698 36.000 0.00 0.00 36.20 2.83
2209 2242 4.826733 TCACATTAAAGCCAGTGATGTTGT 59.173 37.500 0.00 0.00 36.20 3.32
2210 2243 5.375417 TCACATTAAAGCCAGTGATGTTG 57.625 39.130 0.00 0.00 36.20 3.33
2211 2244 5.301551 TGTTCACATTAAAGCCAGTGATGTT 59.698 36.000 0.00 0.00 40.32 2.71
2212 2245 4.826733 TGTTCACATTAAAGCCAGTGATGT 59.173 37.500 0.00 0.00 40.32 3.06
2260 2293 2.552315 CACACCCTTTCGTATTGCTTGT 59.448 45.455 0.00 0.00 0.00 3.16
2321 2358 4.322567 GCTCTGGACAAATCTCAGTTTCT 58.677 43.478 0.00 0.00 0.00 2.52
2328 2365 3.272574 TCATGGCTCTGGACAAATCTC 57.727 47.619 0.00 0.00 32.29 2.75
2329 2366 3.245016 TGTTCATGGCTCTGGACAAATCT 60.245 43.478 0.00 0.00 31.60 2.40
2330 2367 3.084039 TGTTCATGGCTCTGGACAAATC 58.916 45.455 0.00 0.00 31.60 2.17
2331 2368 3.159213 TGTTCATGGCTCTGGACAAAT 57.841 42.857 0.00 0.00 31.60 2.32
2332 2369 2.655090 TGTTCATGGCTCTGGACAAA 57.345 45.000 0.00 0.00 31.60 2.83
2335 2372 2.119801 ACATGTTCATGGCTCTGGAC 57.880 50.000 15.71 0.00 0.00 4.02
2336 2373 2.840038 ACTACATGTTCATGGCTCTGGA 59.160 45.455 2.30 0.00 0.00 3.86
2337 2374 3.201290 GACTACATGTTCATGGCTCTGG 58.799 50.000 2.30 1.54 0.00 3.86
2338 2375 3.201290 GGACTACATGTTCATGGCTCTG 58.799 50.000 2.30 5.06 0.00 3.35
2339 2376 2.840038 TGGACTACATGTTCATGGCTCT 59.160 45.455 2.30 0.00 0.00 4.09
2340 2377 3.266510 TGGACTACATGTTCATGGCTC 57.733 47.619 2.30 7.56 0.00 4.70
2341 2378 3.939740 ATGGACTACATGTTCATGGCT 57.060 42.857 2.30 0.49 42.99 4.75
2342 2379 3.316308 GGAATGGACTACATGTTCATGGC 59.684 47.826 2.30 0.00 43.79 4.40
2343 2380 4.525996 TGGAATGGACTACATGTTCATGG 58.474 43.478 2.30 3.34 43.79 3.66
2344 2381 6.513806 TTTGGAATGGACTACATGTTCATG 57.486 37.500 2.30 10.72 43.79 3.07


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

AutoCloner maintained by Alex Coulton.