Multiple sequence alignment - TraesCS5A01G047200

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 TraesCS5A01G047200 chr5A 100.000 4227 0 0 1 4227 42344969 42349195 0.000000e+00 7806.0
1 TraesCS5A01G047200 chr5A 98.446 193 3 0 1 193 292287592 292287784 1.460000e-89 340.0
2 TraesCS5A01G047200 chr5A 97.938 194 4 0 1 194 304194768 304194961 1.880000e-88 337.0
3 TraesCS5A01G047200 chr5A 97.938 194 4 0 1 194 476492927 476493120 1.880000e-88 337.0
4 TraesCS5A01G047200 chr5A 97.938 194 4 0 1 194 480617284 480617091 1.880000e-88 337.0
5 TraesCS5A01G047200 chr5A 100.000 85 0 0 192 276 630075117 630075201 1.570000e-34 158.0
6 TraesCS5A01G047200 chr7A 97.716 3985 69 8 262 4227 191296134 191300115 0.000000e+00 6835.0
7 TraesCS5A01G047200 chr7A 95.490 1419 38 7 2021 3417 118477489 118478903 0.000000e+00 2242.0
8 TraesCS5A01G047200 chr7A 96.575 730 23 1 3500 4227 118479389 118480118 0.000000e+00 1208.0
9 TraesCS5A01G047200 chr7A 98.969 194 2 0 1 194 397089067 397089260 8.700000e-92 348.0
10 TraesCS5A01G047200 chr7A 93.939 99 5 1 1909 2007 118477124 118477221 9.470000e-32 148.0
11 TraesCS5A01G047200 chr1A 97.390 3985 81 10 262 4227 74340440 74344420 0.000000e+00 6761.0
12 TraesCS5A01G047200 chr1A 97.938 194 4 0 1 194 134593353 134593160 1.880000e-88 337.0
13 TraesCS5A01G047200 chr1A 79.008 262 34 16 186 438 39514874 39515123 4.370000e-35 159.0
14 TraesCS5A01G047200 chr6A 97.082 3976 74 10 262 4227 142478266 142482209 0.000000e+00 6661.0
15 TraesCS5A01G047200 chr6A 96.864 3986 100 12 262 4227 441728973 441724993 0.000000e+00 6645.0
16 TraesCS5A01G047200 chr6A 96.764 3986 75 18 262 4227 238108855 238104904 0.000000e+00 6597.0
17 TraesCS5A01G047200 chr4A 95.089 3136 94 18 404 3502 510499640 510496528 0.000000e+00 4883.0
18 TraesCS5A01G047200 chr4A 95.342 1653 70 6 262 1909 272795070 272793420 0.000000e+00 2619.0
19 TraesCS5A01G047200 chr4A 97.938 194 4 0 1 194 213942801 213942994 1.880000e-88 337.0
20 TraesCS5A01G047200 chr4A 80.488 246 30 13 194 431 691800014 691800249 5.620000e-39 172.0
21 TraesCS5A01G047200 chr4A 100.000 31 0 0 4039 4069 706294885 706294915 1.640000e-04 58.4
22 TraesCS5A01G047200 chr7B 95.039 1653 75 6 262 1909 545724453 545726103 0.000000e+00 2591.0
23 TraesCS5A01G047200 chr6B 96.342 1285 44 3 627 1909 428248555 428249838 0.000000e+00 2109.0
24 TraesCS5A01G047200 chr6B 100.000 83 0 0 194 276 360457281 360457199 2.040000e-33 154.0
25 TraesCS5A01G047200 chr5B 95.020 1024 45 5 262 1283 534562273 534561254 0.000000e+00 1604.0
26 TraesCS5A01G047200 chr7D 87.622 1333 80 48 606 1909 4897506 4896230 0.000000e+00 1469.0
27 TraesCS5A01G047200 chrUn 93.065 620 30 10 262 877 8292336 8291726 0.000000e+00 894.0
28 TraesCS5A01G047200 chr1B 85.503 745 73 26 1120 1850 570473747 570474470 0.000000e+00 745.0
29 TraesCS5A01G047200 chr1B 100.000 85 0 0 192 276 78174435 78174351 1.570000e-34 158.0
30 TraesCS5A01G047200 chr1B 97.802 91 1 1 186 276 28267681 28267770 5.660000e-34 156.0
31 TraesCS5A01G047200 chr4B 83.416 802 91 27 1120 1909 428908929 428909700 0.000000e+00 706.0
32 TraesCS5A01G047200 chr4B 98.864 88 0 1 189 276 160225745 160225659 5.660000e-34 156.0
33 TraesCS5A01G047200 chr1D 80.092 653 103 19 2024 2660 18291694 18292335 1.070000e-125 460.0
34 TraesCS5A01G047200 chr3A 98.454 194 2 1 1 194 673773037 673773229 1.460000e-89 340.0
35 TraesCS5A01G047200 chr3A 97.938 194 4 0 1 194 373371614 373371421 1.880000e-88 337.0
36 TraesCS5A01G047200 chr2B 100.000 85 0 0 192 276 729786669 729786585 1.570000e-34 158.0
37 TraesCS5A01G047200 chr2B 97.778 90 2 0 187 276 58275572 58275661 5.660000e-34 156.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G047200 chr5A 42344969 42349195 4226 False 7806.000000 7806 100.000000 1 4227 1 chr5A.!!$F1 4226
1 TraesCS5A01G047200 chr7A 191296134 191300115 3981 False 6835.000000 6835 97.716000 262 4227 1 chr7A.!!$F1 3965
2 TraesCS5A01G047200 chr7A 118477124 118480118 2994 False 1199.333333 2242 95.334667 1909 4227 3 chr7A.!!$F3 2318
3 TraesCS5A01G047200 chr1A 74340440 74344420 3980 False 6761.000000 6761 97.390000 262 4227 1 chr1A.!!$F2 3965
4 TraesCS5A01G047200 chr6A 142478266 142482209 3943 False 6661.000000 6661 97.082000 262 4227 1 chr6A.!!$F1 3965
5 TraesCS5A01G047200 chr6A 441724993 441728973 3980 True 6645.000000 6645 96.864000 262 4227 1 chr6A.!!$R2 3965
6 TraesCS5A01G047200 chr6A 238104904 238108855 3951 True 6597.000000 6597 96.764000 262 4227 1 chr6A.!!$R1 3965
7 TraesCS5A01G047200 chr4A 510496528 510499640 3112 True 4883.000000 4883 95.089000 404 3502 1 chr4A.!!$R2 3098
8 TraesCS5A01G047200 chr4A 272793420 272795070 1650 True 2619.000000 2619 95.342000 262 1909 1 chr4A.!!$R1 1647
9 TraesCS5A01G047200 chr7B 545724453 545726103 1650 False 2591.000000 2591 95.039000 262 1909 1 chr7B.!!$F1 1647
10 TraesCS5A01G047200 chr6B 428248555 428249838 1283 False 2109.000000 2109 96.342000 627 1909 1 chr6B.!!$F1 1282
11 TraesCS5A01G047200 chr5B 534561254 534562273 1019 True 1604.000000 1604 95.020000 262 1283 1 chr5B.!!$R1 1021
12 TraesCS5A01G047200 chr7D 4896230 4897506 1276 True 1469.000000 1469 87.622000 606 1909 1 chr7D.!!$R1 1303
13 TraesCS5A01G047200 chrUn 8291726 8292336 610 True 894.000000 894 93.065000 262 877 1 chrUn.!!$R1 615
14 TraesCS5A01G047200 chr1B 570473747 570474470 723 False 745.000000 745 85.503000 1120 1850 1 chr1B.!!$F2 730
15 TraesCS5A01G047200 chr4B 428908929 428909700 771 False 706.000000 706 83.416000 1120 1909 1 chr4B.!!$F1 789
16 TraesCS5A01G047200 chr1D 18291694 18292335 641 False 460.000000 460 80.092000 2024 2660 1 chr1D.!!$F1 636

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
230 231 0.033405 ATTTGCCATCAGCCAGCTCT 60.033 50.000 0.00 0.0 42.71 4.09 F
260 261 0.169672 CCAGCTGATGGCAAAGAACG 59.830 55.000 17.39 0.0 43.83 3.95 F
1499 1603 0.174845 TATGTGTACTGACCGCCTGC 59.825 55.000 0.00 0.0 0.00 4.85 F
1505 1609 0.906066 TACTGACCGCCTGCCATTTA 59.094 50.000 0.00 0.0 0.00 1.40 F
2592 3000 4.547671 CTCCTATAGTCCCCTTCAGAACA 58.452 47.826 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 1096 1.419107 CTCATCCTCGTCGTCGTCGA 61.419 60.000 13.59 13.59 44.12 4.20 R
1812 1924 2.006888 CAATCGTAAACAGCCCGTGAT 58.993 47.619 0.00 0.00 0.00 3.06 R
2526 2934 1.808945 CGCACTTCTCCAAATCTGCTT 59.191 47.619 0.00 0.00 0.00 3.91 R
2785 3201 2.035704 TGCAAATGGTTTCGCATCTTGT 59.964 40.909 0.00 0.00 0.00 3.16 R
3970 4827 3.951775 AAACAACCTGAAGCAACAACA 57.048 38.095 0.00 0.00 0.00 3.33 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
17 18 2.828868 GGGGCCACATAGCGATGA 59.171 61.111 14.19 0.00 36.48 2.92
18 19 1.598130 GGGGCCACATAGCGATGAC 60.598 63.158 14.19 2.62 36.48 3.06
19 20 1.956170 GGGCCACATAGCGATGACG 60.956 63.158 14.19 4.12 42.93 4.35
20 21 1.067416 GGCCACATAGCGATGACGA 59.933 57.895 14.19 0.00 42.66 4.20
21 22 0.941463 GGCCACATAGCGATGACGAG 60.941 60.000 14.19 0.48 42.66 4.18
22 23 0.941463 GCCACATAGCGATGACGAGG 60.941 60.000 14.19 10.13 42.66 4.63
23 24 0.668535 CCACATAGCGATGACGAGGA 59.331 55.000 14.19 0.00 42.66 3.71
24 25 1.335415 CCACATAGCGATGACGAGGAG 60.335 57.143 14.19 0.00 42.66 3.69
25 26 0.955178 ACATAGCGATGACGAGGAGG 59.045 55.000 14.19 0.00 42.66 4.30
26 27 1.239347 CATAGCGATGACGAGGAGGA 58.761 55.000 0.00 0.00 42.66 3.71
27 28 1.198867 CATAGCGATGACGAGGAGGAG 59.801 57.143 0.00 0.00 42.66 3.69
28 29 1.167155 TAGCGATGACGAGGAGGAGC 61.167 60.000 0.00 0.00 42.66 4.70
29 30 2.725008 CGATGACGAGGAGGAGCC 59.275 66.667 0.00 0.00 42.66 4.70
30 31 2.851071 CGATGACGAGGAGGAGCCC 61.851 68.421 0.00 0.00 42.66 5.19
31 32 2.444895 ATGACGAGGAGGAGCCCC 60.445 66.667 0.00 0.00 37.37 5.80
64 65 2.943449 CGGAGGACAGAAGAGGTTAC 57.057 55.000 0.00 0.00 0.00 2.50
65 66 1.477295 CGGAGGACAGAAGAGGTTACC 59.523 57.143 0.00 0.00 0.00 2.85
66 67 1.832366 GGAGGACAGAAGAGGTTACCC 59.168 57.143 0.00 0.00 0.00 3.69
67 68 1.832366 GAGGACAGAAGAGGTTACCCC 59.168 57.143 0.00 0.00 0.00 4.95
68 69 0.910338 GGACAGAAGAGGTTACCCCC 59.090 60.000 0.00 0.00 0.00 5.40
69 70 1.652947 GACAGAAGAGGTTACCCCCA 58.347 55.000 0.00 0.00 0.00 4.96
70 71 1.278413 GACAGAAGAGGTTACCCCCAC 59.722 57.143 0.00 0.00 0.00 4.61
71 72 1.358152 CAGAAGAGGTTACCCCCACA 58.642 55.000 0.00 0.00 0.00 4.17
72 73 1.702957 CAGAAGAGGTTACCCCCACAA 59.297 52.381 0.00 0.00 0.00 3.33
73 74 1.985895 AGAAGAGGTTACCCCCACAAG 59.014 52.381 0.00 0.00 0.00 3.16
74 75 1.703513 GAAGAGGTTACCCCCACAAGT 59.296 52.381 0.00 0.00 0.00 3.16
75 76 1.064825 AGAGGTTACCCCCACAAGTG 58.935 55.000 0.00 0.00 0.00 3.16
76 77 0.608308 GAGGTTACCCCCACAAGTGC 60.608 60.000 0.00 0.00 0.00 4.40
77 78 1.969589 GGTTACCCCCACAAGTGCG 60.970 63.158 0.00 0.00 0.00 5.34
78 79 1.969589 GTTACCCCCACAAGTGCGG 60.970 63.158 0.00 0.00 0.00 5.69
79 80 2.148052 TTACCCCCACAAGTGCGGA 61.148 57.895 5.49 0.00 30.18 5.54
80 81 2.400269 TTACCCCCACAAGTGCGGAC 62.400 60.000 0.00 0.00 30.18 4.79
83 84 4.619227 CCCACAAGTGCGGACGGT 62.619 66.667 0.00 1.01 0.00 4.83
84 85 3.345808 CCACAAGTGCGGACGGTG 61.346 66.667 21.69 21.69 34.13 4.94
85 86 2.279851 CACAAGTGCGGACGGTGA 60.280 61.111 23.37 0.00 35.48 4.02
86 87 1.885388 CACAAGTGCGGACGGTGAA 60.885 57.895 23.37 0.00 35.48 3.18
87 88 1.885850 ACAAGTGCGGACGGTGAAC 60.886 57.895 18.00 0.00 0.00 3.18
88 89 1.885388 CAAGTGCGGACGGTGAACA 60.885 57.895 7.83 0.00 0.00 3.18
89 90 1.070786 AAGTGCGGACGGTGAACAT 59.929 52.632 0.00 0.00 0.00 2.71
90 91 1.227999 AAGTGCGGACGGTGAACATG 61.228 55.000 0.00 0.00 0.00 3.21
91 92 1.666553 GTGCGGACGGTGAACATGA 60.667 57.895 0.00 0.00 0.00 3.07
92 93 1.019278 GTGCGGACGGTGAACATGAT 61.019 55.000 0.00 0.00 0.00 2.45
93 94 0.533032 TGCGGACGGTGAACATGATA 59.467 50.000 0.00 0.00 0.00 2.15
94 95 1.138069 TGCGGACGGTGAACATGATAT 59.862 47.619 0.00 0.00 0.00 1.63
95 96 2.362717 TGCGGACGGTGAACATGATATA 59.637 45.455 0.00 0.00 0.00 0.86
96 97 2.729882 GCGGACGGTGAACATGATATAC 59.270 50.000 0.00 0.00 0.00 1.47
97 98 2.977829 CGGACGGTGAACATGATATACG 59.022 50.000 0.00 0.77 0.00 3.06
98 99 2.729882 GGACGGTGAACATGATATACGC 59.270 50.000 0.00 0.00 0.00 4.42
99 100 3.377439 GACGGTGAACATGATATACGCA 58.623 45.455 0.00 0.00 0.00 5.24
100 101 3.787785 ACGGTGAACATGATATACGCAA 58.212 40.909 0.00 0.00 0.00 4.85
101 102 3.554324 ACGGTGAACATGATATACGCAAC 59.446 43.478 0.00 0.00 0.00 4.17
102 103 3.059868 CGGTGAACATGATATACGCAACC 60.060 47.826 0.00 0.00 0.00 3.77
103 104 3.250040 GGTGAACATGATATACGCAACCC 59.750 47.826 0.00 0.00 0.00 4.11
104 105 3.874543 GTGAACATGATATACGCAACCCA 59.125 43.478 0.00 0.00 0.00 4.51
105 106 3.874543 TGAACATGATATACGCAACCCAC 59.125 43.478 0.00 0.00 0.00 4.61
106 107 3.552132 ACATGATATACGCAACCCACA 57.448 42.857 0.00 0.00 0.00 4.17
107 108 4.085357 ACATGATATACGCAACCCACAT 57.915 40.909 0.00 0.00 0.00 3.21
108 109 4.065088 ACATGATATACGCAACCCACATC 58.935 43.478 0.00 0.00 0.00 3.06
109 110 3.120321 TGATATACGCAACCCACATCC 57.880 47.619 0.00 0.00 0.00 3.51
110 111 2.224426 TGATATACGCAACCCACATCCC 60.224 50.000 0.00 0.00 0.00 3.85
111 112 0.470766 TATACGCAACCCACATCCCC 59.529 55.000 0.00 0.00 0.00 4.81
112 113 1.567208 ATACGCAACCCACATCCCCA 61.567 55.000 0.00 0.00 0.00 4.96
113 114 1.780107 TACGCAACCCACATCCCCAA 61.780 55.000 0.00 0.00 0.00 4.12
114 115 2.342650 CGCAACCCACATCCCCAAG 61.343 63.158 0.00 0.00 0.00 3.61
115 116 1.076549 GCAACCCACATCCCCAAGA 59.923 57.895 0.00 0.00 0.00 3.02
116 117 0.967380 GCAACCCACATCCCCAAGAG 60.967 60.000 0.00 0.00 0.00 2.85
117 118 0.323725 CAACCCACATCCCCAAGAGG 60.324 60.000 0.00 0.00 0.00 3.69
128 129 1.078848 CCAAGAGGGAGTGGAAGCG 60.079 63.158 0.00 0.00 40.01 4.68
129 130 1.674057 CAAGAGGGAGTGGAAGCGT 59.326 57.895 0.00 0.00 0.00 5.07
130 131 0.671781 CAAGAGGGAGTGGAAGCGTG 60.672 60.000 0.00 0.00 0.00 5.34
131 132 2.435059 GAGGGAGTGGAAGCGTGC 60.435 66.667 0.00 0.00 0.00 5.34
132 133 4.379243 AGGGAGTGGAAGCGTGCG 62.379 66.667 0.00 0.00 0.00 5.34
144 145 4.111016 CGTGCGCTCAGGGACGTA 62.111 66.667 9.73 0.00 0.00 3.57
145 146 2.494918 GTGCGCTCAGGGACGTAT 59.505 61.111 9.73 0.00 0.00 3.06
146 147 1.731700 GTGCGCTCAGGGACGTATA 59.268 57.895 9.73 0.00 0.00 1.47
147 148 0.314302 GTGCGCTCAGGGACGTATAT 59.686 55.000 9.73 0.00 0.00 0.86
148 149 0.313987 TGCGCTCAGGGACGTATATG 59.686 55.000 9.73 0.00 0.00 1.78
149 150 1.009389 GCGCTCAGGGACGTATATGC 61.009 60.000 0.00 0.00 0.00 3.14
150 151 0.729478 CGCTCAGGGACGTATATGCG 60.729 60.000 11.90 11.90 36.41 4.73
152 153 1.269621 GCTCAGGGACGTATATGCGTT 60.270 52.381 19.91 1.62 45.79 4.84
153 154 2.394708 CTCAGGGACGTATATGCGTTG 58.605 52.381 19.91 14.12 45.79 4.10
154 155 1.067974 TCAGGGACGTATATGCGTTGG 59.932 52.381 19.91 9.99 45.79 3.77
155 156 1.067974 CAGGGACGTATATGCGTTGGA 59.932 52.381 19.91 0.00 45.79 3.53
156 157 1.340248 AGGGACGTATATGCGTTGGAG 59.660 52.381 19.91 0.00 45.79 3.86
157 158 1.137513 GGACGTATATGCGTTGGAGC 58.862 55.000 19.91 6.85 45.79 4.70
158 159 1.137513 GACGTATATGCGTTGGAGCC 58.862 55.000 19.91 2.66 45.79 4.70
159 160 0.462375 ACGTATATGCGTTGGAGCCA 59.538 50.000 13.39 0.00 43.04 4.75
160 161 1.139989 CGTATATGCGTTGGAGCCAG 58.860 55.000 4.91 0.00 36.02 4.85
161 162 1.538204 CGTATATGCGTTGGAGCCAGT 60.538 52.381 4.91 0.00 36.02 4.00
162 163 2.135933 GTATATGCGTTGGAGCCAGTC 58.864 52.381 0.00 0.00 36.02 3.51
163 164 0.530650 ATATGCGTTGGAGCCAGTCG 60.531 55.000 10.32 10.32 36.02 4.18
170 171 4.344865 GGAGCCAGTCGCCCCAAA 62.345 66.667 0.00 0.00 38.78 3.28
171 172 2.747855 GAGCCAGTCGCCCCAAAG 60.748 66.667 0.00 0.00 38.78 2.77
172 173 3.553095 GAGCCAGTCGCCCCAAAGT 62.553 63.158 0.00 0.00 38.78 2.66
173 174 2.597510 GCCAGTCGCCCCAAAGTT 60.598 61.111 0.00 0.00 0.00 2.66
174 175 2.626780 GCCAGTCGCCCCAAAGTTC 61.627 63.158 0.00 0.00 0.00 3.01
175 176 1.228124 CCAGTCGCCCCAAAGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
176 177 0.821711 CCAGTCGCCCCAAAGTTCAA 60.822 55.000 0.00 0.00 0.00 2.69
177 178 0.310854 CAGTCGCCCCAAAGTTCAAC 59.689 55.000 0.00 0.00 0.00 3.18
178 179 0.822121 AGTCGCCCCAAAGTTCAACC 60.822 55.000 0.00 0.00 0.00 3.77
179 180 1.529713 TCGCCCCAAAGTTCAACCC 60.530 57.895 0.00 0.00 0.00 4.11
180 181 2.914908 CGCCCCAAAGTTCAACCCG 61.915 63.158 0.00 0.00 0.00 5.28
181 182 1.830847 GCCCCAAAGTTCAACCCGT 60.831 57.895 0.00 0.00 0.00 5.28
182 183 2.037871 CCCCAAAGTTCAACCCGTG 58.962 57.895 0.00 0.00 0.00 4.94
183 184 1.460273 CCCCAAAGTTCAACCCGTGG 61.460 60.000 0.00 0.00 0.00 4.94
184 185 0.753848 CCCAAAGTTCAACCCGTGGT 60.754 55.000 2.05 0.00 37.65 4.16
185 186 0.666374 CCAAAGTTCAACCCGTGGTC 59.334 55.000 0.00 0.00 33.12 4.02
186 187 0.666374 CAAAGTTCAACCCGTGGTCC 59.334 55.000 0.00 0.00 33.12 4.46
187 188 0.549469 AAAGTTCAACCCGTGGTCCT 59.451 50.000 0.00 0.00 33.12 3.85
188 189 0.108019 AAGTTCAACCCGTGGTCCTC 59.892 55.000 0.00 0.00 33.12 3.71
189 190 1.302271 GTTCAACCCGTGGTCCTCC 60.302 63.158 0.00 0.00 33.12 4.30
190 191 1.460689 TTCAACCCGTGGTCCTCCT 60.461 57.895 0.00 0.00 33.12 3.69
191 192 0.178926 TTCAACCCGTGGTCCTCCTA 60.179 55.000 0.00 0.00 33.12 2.94
192 193 0.042131 TCAACCCGTGGTCCTCCTAT 59.958 55.000 0.00 0.00 33.12 2.57
193 194 0.464452 CAACCCGTGGTCCTCCTATC 59.536 60.000 0.00 0.00 33.12 2.08
194 195 0.042131 AACCCGTGGTCCTCCTATCA 59.958 55.000 0.00 0.00 33.12 2.15
195 196 0.686769 ACCCGTGGTCCTCCTATCAC 60.687 60.000 0.00 0.00 34.23 3.06
196 197 0.397254 CCCGTGGTCCTCCTATCACT 60.397 60.000 0.00 0.00 34.23 3.41
197 198 1.133575 CCCGTGGTCCTCCTATCACTA 60.134 57.143 0.00 0.00 34.23 2.74
198 199 1.955080 CCGTGGTCCTCCTATCACTAC 59.045 57.143 0.00 0.00 34.23 2.73
199 200 2.423088 CCGTGGTCCTCCTATCACTACT 60.423 54.545 0.00 0.00 34.23 2.57
200 201 2.619177 CGTGGTCCTCCTATCACTACTG 59.381 54.545 0.00 0.00 34.23 2.74
201 202 2.959707 GTGGTCCTCCTATCACTACTGG 59.040 54.545 0.00 0.00 34.23 4.00
202 203 2.856864 TGGTCCTCCTATCACTACTGGA 59.143 50.000 0.00 0.00 34.23 3.86
203 204 3.271225 TGGTCCTCCTATCACTACTGGAA 59.729 47.826 0.00 0.00 34.23 3.53
204 205 4.264668 TGGTCCTCCTATCACTACTGGAAA 60.265 45.833 0.00 0.00 34.23 3.13
205 206 4.099727 GGTCCTCCTATCACTACTGGAAAC 59.900 50.000 0.00 0.00 0.00 2.78
206 207 4.710375 GTCCTCCTATCACTACTGGAAACA 59.290 45.833 0.00 0.00 39.59 2.83
218 219 2.094100 TGGAAACAGGGAATTTGCCA 57.906 45.000 9.80 0.00 35.01 4.92
219 220 2.618794 TGGAAACAGGGAATTTGCCAT 58.381 42.857 9.80 0.00 35.01 4.40
220 221 2.566724 TGGAAACAGGGAATTTGCCATC 59.433 45.455 9.80 2.27 35.01 3.51
221 222 2.566724 GGAAACAGGGAATTTGCCATCA 59.433 45.455 9.80 0.00 0.00 3.07
222 223 3.368739 GGAAACAGGGAATTTGCCATCAG 60.369 47.826 9.80 0.00 0.00 2.90
223 224 1.188863 ACAGGGAATTTGCCATCAGC 58.811 50.000 9.80 0.00 44.14 4.26
224 225 0.462789 CAGGGAATTTGCCATCAGCC 59.537 55.000 9.80 0.00 42.71 4.85
225 226 0.041535 AGGGAATTTGCCATCAGCCA 59.958 50.000 9.80 0.00 42.71 4.75
226 227 0.462789 GGGAATTTGCCATCAGCCAG 59.537 55.000 1.50 0.00 42.71 4.85
227 228 0.179092 GGAATTTGCCATCAGCCAGC 60.179 55.000 0.00 0.00 42.71 4.85
228 229 0.822164 GAATTTGCCATCAGCCAGCT 59.178 50.000 0.00 0.00 42.71 4.24
229 230 0.822164 AATTTGCCATCAGCCAGCTC 59.178 50.000 0.00 0.00 42.71 4.09
230 231 0.033405 ATTTGCCATCAGCCAGCTCT 60.033 50.000 0.00 0.00 42.71 4.09
231 232 0.251474 TTTGCCATCAGCCAGCTCTT 60.251 50.000 0.00 0.00 42.71 2.85
232 233 0.251474 TTGCCATCAGCCAGCTCTTT 60.251 50.000 0.00 0.00 42.71 2.52
233 234 0.963856 TGCCATCAGCCAGCTCTTTG 60.964 55.000 0.00 0.00 42.71 2.77
234 235 1.807886 CCATCAGCCAGCTCTTTGC 59.192 57.895 0.00 0.00 43.29 3.68
235 236 1.664321 CCATCAGCCAGCTCTTTGCC 61.664 60.000 0.00 0.00 44.23 4.52
236 237 0.963856 CATCAGCCAGCTCTTTGCCA 60.964 55.000 0.00 0.00 44.23 4.92
237 238 0.033405 ATCAGCCAGCTCTTTGCCAT 60.033 50.000 0.00 0.00 44.23 4.40
238 239 0.679002 TCAGCCAGCTCTTTGCCATC 60.679 55.000 0.00 0.00 44.23 3.51
239 240 0.680280 CAGCCAGCTCTTTGCCATCT 60.680 55.000 0.00 0.00 44.23 2.90
240 241 0.680280 AGCCAGCTCTTTGCCATCTG 60.680 55.000 0.00 0.00 44.23 2.90
241 242 1.807886 CCAGCTCTTTGCCATCTGC 59.192 57.895 0.00 0.00 44.23 4.26
242 243 1.664321 CCAGCTCTTTGCCATCTGCC 61.664 60.000 0.00 0.00 44.23 4.85
243 244 0.963856 CAGCTCTTTGCCATCTGCCA 60.964 55.000 0.00 0.00 44.23 4.92
244 245 0.680280 AGCTCTTTGCCATCTGCCAG 60.680 55.000 0.00 0.00 44.23 4.85
245 246 1.807886 CTCTTTGCCATCTGCCAGC 59.192 57.895 0.00 0.00 40.16 4.85
246 247 0.680280 CTCTTTGCCATCTGCCAGCT 60.680 55.000 0.00 0.00 40.16 4.24
247 248 0.963856 TCTTTGCCATCTGCCAGCTG 60.964 55.000 6.78 6.78 40.16 4.24
248 249 0.963856 CTTTGCCATCTGCCAGCTGA 60.964 55.000 17.39 1.51 40.16 4.26
249 250 0.323999 TTTGCCATCTGCCAGCTGAT 60.324 50.000 17.39 6.23 40.16 2.90
250 251 1.035385 TTGCCATCTGCCAGCTGATG 61.035 55.000 24.57 24.57 45.69 3.07
260 261 0.169672 CCAGCTGATGGCAAAGAACG 59.830 55.000 17.39 0.00 43.83 3.95
342 344 3.763671 GGCAAATCCTATGGCCGG 58.236 61.111 0.00 0.00 36.58 6.13
378 380 0.474854 TACCAGCCCCACCTCTTTGA 60.475 55.000 0.00 0.00 0.00 2.69
389 391 1.701847 ACCTCTTTGACATCTGCCAGT 59.298 47.619 0.00 0.00 0.00 4.00
697 713 1.987855 CCCACACGCCTTCCTCCTA 60.988 63.158 0.00 0.00 0.00 2.94
1040 1096 1.545706 GGAGGAGGACTTCACGCCTT 61.546 60.000 0.00 0.00 33.84 4.35
1275 1356 0.759060 GGTTTGGGTTCTGTGGCCTT 60.759 55.000 3.32 0.00 0.00 4.35
1499 1603 0.174845 TATGTGTACTGACCGCCTGC 59.825 55.000 0.00 0.00 0.00 4.85
1505 1609 0.906066 TACTGACCGCCTGCCATTTA 59.094 50.000 0.00 0.00 0.00 1.40
2039 2438 7.348274 TCCTAACCAACAGATCCTAAGAATGAT 59.652 37.037 0.00 0.00 0.00 2.45
2526 2934 7.857456 ACAACATAGTGGTAGAACATGGATAA 58.143 34.615 0.00 0.00 0.00 1.75
2592 3000 4.547671 CTCCTATAGTCCCCTTCAGAACA 58.452 47.826 0.00 0.00 0.00 3.18
3431 3931 4.727507 ATCAGTTAAGAGCAGTCGATGT 57.272 40.909 0.00 0.00 0.00 3.06
3443 3943 2.099756 CAGTCGATGTAGCTGGTCATGA 59.900 50.000 0.00 0.00 0.00 3.07
3884 4739 3.441572 GCAATACACTCCTTGAGCACATT 59.558 43.478 0.00 0.00 32.04 2.71
4197 5054 5.106277 GGCTTTTATTTCTTCTACAGCCGTT 60.106 40.000 0.00 0.00 36.49 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.598130 GTCATCGCTATGTGGCCCC 60.598 63.158 0.00 0.00 34.50 5.80
1 2 1.956170 CGTCATCGCTATGTGGCCC 60.956 63.158 0.00 0.00 34.50 5.80
2 3 0.941463 CTCGTCATCGCTATGTGGCC 60.941 60.000 0.00 0.00 36.96 5.36
3 4 0.941463 CCTCGTCATCGCTATGTGGC 60.941 60.000 0.00 0.00 36.96 5.01
4 5 0.668535 TCCTCGTCATCGCTATGTGG 59.331 55.000 0.00 0.00 36.96 4.17
5 6 1.335415 CCTCCTCGTCATCGCTATGTG 60.335 57.143 0.00 0.00 36.96 3.21
6 7 0.955178 CCTCCTCGTCATCGCTATGT 59.045 55.000 0.00 0.00 36.96 2.29
7 8 1.198867 CTCCTCCTCGTCATCGCTATG 59.801 57.143 0.00 0.00 36.96 2.23
8 9 1.529226 CTCCTCCTCGTCATCGCTAT 58.471 55.000 0.00 0.00 36.96 2.97
9 10 1.167155 GCTCCTCCTCGTCATCGCTA 61.167 60.000 0.00 0.00 36.96 4.26
10 11 2.485795 GCTCCTCCTCGTCATCGCT 61.486 63.158 0.00 0.00 36.96 4.93
11 12 2.026879 GCTCCTCCTCGTCATCGC 59.973 66.667 0.00 0.00 36.96 4.58
12 13 2.725008 GGCTCCTCCTCGTCATCG 59.275 66.667 0.00 0.00 38.55 3.84
13 14 2.503382 GGGGCTCCTCCTCGTCATC 61.503 68.421 0.00 0.00 34.39 2.92
14 15 2.444895 GGGGCTCCTCCTCGTCAT 60.445 66.667 0.00 0.00 34.39 3.06
34 35 3.625897 TCCTCCGGTGTGTGGCTG 61.626 66.667 0.00 0.00 0.00 4.85
35 36 3.626924 GTCCTCCGGTGTGTGGCT 61.627 66.667 0.00 0.00 0.00 4.75
36 37 3.883744 CTGTCCTCCGGTGTGTGGC 62.884 68.421 0.00 0.00 0.00 5.01
37 38 1.754380 TTCTGTCCTCCGGTGTGTGG 61.754 60.000 0.00 0.00 0.00 4.17
38 39 0.319900 CTTCTGTCCTCCGGTGTGTG 60.320 60.000 0.00 0.00 0.00 3.82
39 40 0.469331 TCTTCTGTCCTCCGGTGTGT 60.469 55.000 0.00 0.00 0.00 3.72
40 41 0.244994 CTCTTCTGTCCTCCGGTGTG 59.755 60.000 0.00 0.00 0.00 3.82
41 42 0.900647 CCTCTTCTGTCCTCCGGTGT 60.901 60.000 0.00 0.00 0.00 4.16
42 43 0.900647 ACCTCTTCTGTCCTCCGGTG 60.901 60.000 0.00 0.00 0.00 4.94
43 44 0.178929 AACCTCTTCTGTCCTCCGGT 60.179 55.000 0.00 0.00 0.00 5.28
44 45 1.477295 GTAACCTCTTCTGTCCTCCGG 59.523 57.143 0.00 0.00 0.00 5.14
45 46 1.477295 GGTAACCTCTTCTGTCCTCCG 59.523 57.143 0.00 0.00 0.00 4.63
60 61 1.969589 CCGCACTTGTGGGGGTAAC 60.970 63.158 23.74 0.00 41.84 2.50
61 62 2.148052 TCCGCACTTGTGGGGGTAA 61.148 57.895 28.38 12.98 45.45 2.85
62 63 2.527123 TCCGCACTTGTGGGGGTA 60.527 61.111 28.38 13.58 45.45 3.69
63 64 4.265056 GTCCGCACTTGTGGGGGT 62.265 66.667 28.38 0.00 45.45 4.95
66 67 4.619227 ACCGTCCGCACTTGTGGG 62.619 66.667 8.95 10.32 45.45 4.61
67 68 3.345808 CACCGTCCGCACTTGTGG 61.346 66.667 2.11 2.11 46.72 4.17
68 69 1.885388 TTCACCGTCCGCACTTGTG 60.885 57.895 0.00 0.00 0.00 3.33
69 70 1.885850 GTTCACCGTCCGCACTTGT 60.886 57.895 0.00 0.00 0.00 3.16
70 71 1.227999 ATGTTCACCGTCCGCACTTG 61.228 55.000 0.00 0.00 0.00 3.16
71 72 1.070786 ATGTTCACCGTCCGCACTT 59.929 52.632 0.00 0.00 0.00 3.16
72 73 1.667830 CATGTTCACCGTCCGCACT 60.668 57.895 0.00 0.00 0.00 4.40
73 74 1.019278 ATCATGTTCACCGTCCGCAC 61.019 55.000 0.00 0.00 0.00 5.34
74 75 0.533032 TATCATGTTCACCGTCCGCA 59.467 50.000 0.00 0.00 0.00 5.69
75 76 1.865865 ATATCATGTTCACCGTCCGC 58.134 50.000 0.00 0.00 0.00 5.54
76 77 2.977829 CGTATATCATGTTCACCGTCCG 59.022 50.000 0.00 0.00 0.00 4.79
77 78 2.729882 GCGTATATCATGTTCACCGTCC 59.270 50.000 0.00 0.00 0.00 4.79
78 79 3.377439 TGCGTATATCATGTTCACCGTC 58.623 45.455 0.00 0.00 0.00 4.79
79 80 3.446310 TGCGTATATCATGTTCACCGT 57.554 42.857 0.00 0.00 0.00 4.83
80 81 3.059868 GGTTGCGTATATCATGTTCACCG 60.060 47.826 0.00 0.00 0.00 4.94
81 82 3.250040 GGGTTGCGTATATCATGTTCACC 59.750 47.826 0.00 0.00 0.00 4.02
82 83 3.874543 TGGGTTGCGTATATCATGTTCAC 59.125 43.478 0.00 0.00 0.00 3.18
83 84 3.874543 GTGGGTTGCGTATATCATGTTCA 59.125 43.478 0.00 0.00 0.00 3.18
84 85 3.874543 TGTGGGTTGCGTATATCATGTTC 59.125 43.478 0.00 0.00 0.00 3.18
85 86 3.879998 TGTGGGTTGCGTATATCATGTT 58.120 40.909 0.00 0.00 0.00 2.71
86 87 3.552132 TGTGGGTTGCGTATATCATGT 57.448 42.857 0.00 0.00 0.00 3.21
87 88 3.436704 GGATGTGGGTTGCGTATATCATG 59.563 47.826 0.00 0.00 0.00 3.07
88 89 3.559171 GGGATGTGGGTTGCGTATATCAT 60.559 47.826 0.00 0.00 0.00 2.45
89 90 2.224426 GGGATGTGGGTTGCGTATATCA 60.224 50.000 0.00 0.00 0.00 2.15
90 91 2.423577 GGGATGTGGGTTGCGTATATC 58.576 52.381 0.00 0.00 0.00 1.63
91 92 1.073284 GGGGATGTGGGTTGCGTATAT 59.927 52.381 0.00 0.00 0.00 0.86
92 93 0.470766 GGGGATGTGGGTTGCGTATA 59.529 55.000 0.00 0.00 0.00 1.47
93 94 1.226262 GGGGATGTGGGTTGCGTAT 59.774 57.895 0.00 0.00 0.00 3.06
94 95 1.780107 TTGGGGATGTGGGTTGCGTA 61.780 55.000 0.00 0.00 0.00 4.42
95 96 3.140073 TTGGGGATGTGGGTTGCGT 62.140 57.895 0.00 0.00 0.00 5.24
96 97 2.282816 TTGGGGATGTGGGTTGCG 60.283 61.111 0.00 0.00 0.00 4.85
97 98 0.967380 CTCTTGGGGATGTGGGTTGC 60.967 60.000 0.00 0.00 0.00 4.17
98 99 0.323725 CCTCTTGGGGATGTGGGTTG 60.324 60.000 0.00 0.00 0.00 3.77
99 100 2.087248 CCTCTTGGGGATGTGGGTT 58.913 57.895 0.00 0.00 0.00 4.11
100 101 3.841078 CCTCTTGGGGATGTGGGT 58.159 61.111 0.00 0.00 0.00 4.51
110 111 1.078848 CGCTTCCACTCCCTCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
111 112 0.671781 CACGCTTCCACTCCCTCTTG 60.672 60.000 0.00 0.00 0.00 3.02
112 113 1.674057 CACGCTTCCACTCCCTCTT 59.326 57.895 0.00 0.00 0.00 2.85
113 114 2.948720 GCACGCTTCCACTCCCTCT 61.949 63.158 0.00 0.00 0.00 3.69
114 115 2.435059 GCACGCTTCCACTCCCTC 60.435 66.667 0.00 0.00 0.00 4.30
115 116 4.379243 CGCACGCTTCCACTCCCT 62.379 66.667 0.00 0.00 0.00 4.20
127 128 2.055310 TATACGTCCCTGAGCGCACG 62.055 60.000 11.47 12.58 38.24 5.34
128 129 0.314302 ATATACGTCCCTGAGCGCAC 59.686 55.000 11.47 3.13 0.00 5.34
129 130 0.313987 CATATACGTCCCTGAGCGCA 59.686 55.000 11.47 0.00 0.00 6.09
130 131 1.009389 GCATATACGTCCCTGAGCGC 61.009 60.000 0.00 0.00 0.00 5.92
131 132 0.729478 CGCATATACGTCCCTGAGCG 60.729 60.000 0.00 0.00 37.91 5.03
132 133 0.314302 ACGCATATACGTCCCTGAGC 59.686 55.000 0.00 0.00 44.43 4.26
141 142 1.139989 CTGGCTCCAACGCATATACG 58.860 55.000 0.00 0.00 39.50 3.06
142 143 2.135933 GACTGGCTCCAACGCATATAC 58.864 52.381 0.00 0.00 0.00 1.47
143 144 1.269569 CGACTGGCTCCAACGCATATA 60.270 52.381 3.18 0.00 0.00 0.86
144 145 0.530650 CGACTGGCTCCAACGCATAT 60.531 55.000 3.18 0.00 0.00 1.78
145 146 1.153647 CGACTGGCTCCAACGCATA 60.154 57.895 3.18 0.00 0.00 3.14
146 147 2.434884 CGACTGGCTCCAACGCAT 60.435 61.111 3.18 0.00 0.00 4.73
154 155 2.747855 CTTTGGGGCGACTGGCTC 60.748 66.667 0.00 0.00 43.39 4.70
155 156 3.133365 AACTTTGGGGCGACTGGCT 62.133 57.895 0.00 0.00 42.94 4.75
156 157 2.597510 AACTTTGGGGCGACTGGC 60.598 61.111 0.00 0.00 42.51 4.85
157 158 0.821711 TTGAACTTTGGGGCGACTGG 60.822 55.000 0.00 0.00 0.00 4.00
158 159 0.310854 GTTGAACTTTGGGGCGACTG 59.689 55.000 0.00 0.00 0.00 3.51
159 160 0.822121 GGTTGAACTTTGGGGCGACT 60.822 55.000 0.00 0.00 0.00 4.18
160 161 1.658114 GGTTGAACTTTGGGGCGAC 59.342 57.895 0.00 0.00 0.00 5.19
161 162 1.529713 GGGTTGAACTTTGGGGCGA 60.530 57.895 0.00 0.00 0.00 5.54
162 163 2.914908 CGGGTTGAACTTTGGGGCG 61.915 63.158 0.00 0.00 0.00 6.13
163 164 1.830847 ACGGGTTGAACTTTGGGGC 60.831 57.895 0.00 0.00 0.00 5.80
164 165 1.460273 CCACGGGTTGAACTTTGGGG 61.460 60.000 0.00 0.00 0.00 4.96
165 166 0.753848 ACCACGGGTTGAACTTTGGG 60.754 55.000 12.65 5.57 27.29 4.12
166 167 0.666374 GACCACGGGTTGAACTTTGG 59.334 55.000 8.27 8.27 35.25 3.28
167 168 0.666374 GGACCACGGGTTGAACTTTG 59.334 55.000 0.00 0.00 35.25 2.77
168 169 0.549469 AGGACCACGGGTTGAACTTT 59.451 50.000 0.00 0.00 35.25 2.66
169 170 0.108019 GAGGACCACGGGTTGAACTT 59.892 55.000 0.00 0.00 35.25 2.66
170 171 1.752833 GAGGACCACGGGTTGAACT 59.247 57.895 0.00 0.00 35.25 3.01
171 172 1.302271 GGAGGACCACGGGTTGAAC 60.302 63.158 0.00 0.00 35.25 3.18
172 173 0.178926 TAGGAGGACCACGGGTTGAA 60.179 55.000 0.00 0.00 35.25 2.69
173 174 0.042131 ATAGGAGGACCACGGGTTGA 59.958 55.000 0.00 0.00 35.25 3.18
174 175 0.464452 GATAGGAGGACCACGGGTTG 59.536 60.000 0.00 0.00 35.25 3.77
175 176 0.042131 TGATAGGAGGACCACGGGTT 59.958 55.000 0.00 0.00 35.25 4.11
176 177 0.686769 GTGATAGGAGGACCACGGGT 60.687 60.000 0.00 0.00 39.44 5.28
177 178 0.397254 AGTGATAGGAGGACCACGGG 60.397 60.000 0.00 0.00 38.94 5.28
178 179 1.955080 GTAGTGATAGGAGGACCACGG 59.045 57.143 0.00 0.00 38.94 4.94
179 180 2.619177 CAGTAGTGATAGGAGGACCACG 59.381 54.545 0.00 0.00 38.94 4.94
180 181 2.959707 CCAGTAGTGATAGGAGGACCAC 59.040 54.545 0.00 0.00 38.94 4.16
181 182 2.856864 TCCAGTAGTGATAGGAGGACCA 59.143 50.000 0.00 0.00 38.94 4.02
182 183 3.596940 TCCAGTAGTGATAGGAGGACC 57.403 52.381 0.00 0.00 0.00 4.46
183 184 4.710375 TGTTTCCAGTAGTGATAGGAGGAC 59.290 45.833 0.00 0.00 0.00 3.85
184 185 4.942944 TGTTTCCAGTAGTGATAGGAGGA 58.057 43.478 0.00 0.00 0.00 3.71
185 186 4.100189 CCTGTTTCCAGTAGTGATAGGAGG 59.900 50.000 0.00 0.00 36.95 4.30
186 187 4.100189 CCCTGTTTCCAGTAGTGATAGGAG 59.900 50.000 0.00 0.00 36.95 3.69
187 188 4.030913 CCCTGTTTCCAGTAGTGATAGGA 58.969 47.826 0.00 0.00 36.95 2.94
188 189 4.030913 TCCCTGTTTCCAGTAGTGATAGG 58.969 47.826 0.00 0.00 36.95 2.57
189 190 5.677319 TTCCCTGTTTCCAGTAGTGATAG 57.323 43.478 0.00 0.00 36.95 2.08
190 191 6.636454 AATTCCCTGTTTCCAGTAGTGATA 57.364 37.500 0.00 0.00 36.95 2.15
191 192 5.520748 AATTCCCTGTTTCCAGTAGTGAT 57.479 39.130 0.00 0.00 36.95 3.06
192 193 4.993705 AATTCCCTGTTTCCAGTAGTGA 57.006 40.909 0.00 0.00 36.95 3.41
193 194 4.321230 GCAAATTCCCTGTTTCCAGTAGTG 60.321 45.833 0.00 0.00 36.95 2.74
194 195 3.826729 GCAAATTCCCTGTTTCCAGTAGT 59.173 43.478 0.00 0.00 36.95 2.73
195 196 3.193479 GGCAAATTCCCTGTTTCCAGTAG 59.807 47.826 0.00 0.00 36.95 2.57
196 197 3.161866 GGCAAATTCCCTGTTTCCAGTA 58.838 45.455 0.00 0.00 36.95 2.74
197 198 1.970640 GGCAAATTCCCTGTTTCCAGT 59.029 47.619 0.00 0.00 36.95 4.00
198 199 1.969923 TGGCAAATTCCCTGTTTCCAG 59.030 47.619 0.00 0.00 38.50 3.86
199 200 2.094100 TGGCAAATTCCCTGTTTCCA 57.906 45.000 0.00 0.00 0.00 3.53
200 201 2.566724 TGATGGCAAATTCCCTGTTTCC 59.433 45.455 0.00 0.00 0.00 3.13
201 202 3.853475 CTGATGGCAAATTCCCTGTTTC 58.147 45.455 0.00 0.00 0.00 2.78
202 203 2.027837 GCTGATGGCAAATTCCCTGTTT 60.028 45.455 0.00 0.00 41.35 2.83
203 204 1.551883 GCTGATGGCAAATTCCCTGTT 59.448 47.619 0.00 0.00 41.35 3.16
204 205 1.188863 GCTGATGGCAAATTCCCTGT 58.811 50.000 0.00 0.00 41.35 4.00
205 206 0.462789 GGCTGATGGCAAATTCCCTG 59.537 55.000 0.00 0.00 44.01 4.45
206 207 0.041535 TGGCTGATGGCAAATTCCCT 59.958 50.000 0.00 0.00 46.03 4.20
207 208 2.594342 TGGCTGATGGCAAATTCCC 58.406 52.632 0.00 0.00 46.03 3.97
214 215 0.963856 CAAAGAGCTGGCTGATGGCA 60.964 55.000 0.00 0.00 46.87 4.92
215 216 1.807886 CAAAGAGCTGGCTGATGGC 59.192 57.895 0.00 0.00 40.90 4.40
216 217 1.664321 GGCAAAGAGCTGGCTGATGG 61.664 60.000 0.00 0.00 44.79 3.51
217 218 0.963856 TGGCAAAGAGCTGGCTGATG 60.964 55.000 0.00 0.00 44.79 3.07
218 219 0.033405 ATGGCAAAGAGCTGGCTGAT 60.033 50.000 0.00 0.00 44.79 2.90
219 220 0.679002 GATGGCAAAGAGCTGGCTGA 60.679 55.000 0.00 0.00 44.79 4.26
220 221 0.680280 AGATGGCAAAGAGCTGGCTG 60.680 55.000 0.00 0.00 44.79 4.85
221 222 0.680280 CAGATGGCAAAGAGCTGGCT 60.680 55.000 0.00 0.00 44.79 4.75
222 223 1.807886 CAGATGGCAAAGAGCTGGC 59.192 57.895 0.00 0.00 44.79 4.85
223 224 1.807886 GCAGATGGCAAAGAGCTGG 59.192 57.895 0.00 0.00 44.79 4.85
233 234 3.433319 CATCAGCTGGCAGATGGC 58.567 61.111 30.21 10.71 36.65 4.40
242 243 0.877071 ACGTTCTTTGCCATCAGCTG 59.123 50.000 7.63 7.63 44.23 4.24
243 244 1.160137 GACGTTCTTTGCCATCAGCT 58.840 50.000 0.00 0.00 44.23 4.24
244 245 1.160137 AGACGTTCTTTGCCATCAGC 58.840 50.000 0.00 0.00 44.14 4.26
245 246 3.904136 AAAGACGTTCTTTGCCATCAG 57.096 42.857 10.79 0.00 44.34 2.90
253 254 2.030805 GCAGATGGCAAAGACGTTCTTT 60.031 45.455 0.00 7.04 46.75 2.52
254 255 1.537202 GCAGATGGCAAAGACGTTCTT 59.463 47.619 0.00 0.00 43.97 2.52
255 256 1.160137 GCAGATGGCAAAGACGTTCT 58.840 50.000 0.00 0.00 43.97 3.01
256 257 3.683581 GCAGATGGCAAAGACGTTC 57.316 52.632 0.00 0.00 43.97 3.95
342 344 0.247537 GTACGCCGTTACATGCTTGC 60.248 55.000 0.00 0.00 0.00 4.01
480 485 1.314867 GATGGGTGGGGAGAGAGGA 59.685 63.158 0.00 0.00 0.00 3.71
697 713 3.667282 CGGTCGGTGAGGTCGTGT 61.667 66.667 0.00 0.00 0.00 4.49
1040 1096 1.419107 CTCATCCTCGTCGTCGTCGA 61.419 60.000 13.59 13.59 44.12 4.20
1082 1138 2.269023 TGATCTTCTTGGGCTTCTCCA 58.731 47.619 0.00 0.00 36.21 3.86
1275 1356 6.652900 TGGAAATCACACATTTCGTTCAGATA 59.347 34.615 1.91 0.00 38.53 1.98
1499 1603 7.444487 TGCATCATCAGAAAGAGAGATAAATGG 59.556 37.037 0.00 0.00 0.00 3.16
1505 1609 4.744259 GCCTGCATCATCAGAAAGAGAGAT 60.744 45.833 0.00 0.00 36.19 2.75
1812 1924 2.006888 CAATCGTAAACAGCCCGTGAT 58.993 47.619 0.00 0.00 0.00 3.06
1819 1931 2.440501 CAATCGGCAATCGTAAACAGC 58.559 47.619 0.00 0.00 40.32 4.40
1911 2031 3.708734 CGCACGGGTTTGACGACC 61.709 66.667 0.00 0.00 39.04 4.79
2496 2901 6.268825 TGTTCTACCACTATGTTGTCTCTC 57.731 41.667 0.00 0.00 0.00 3.20
2497 2902 6.351371 CCATGTTCTACCACTATGTTGTCTCT 60.351 42.308 0.00 0.00 0.00 3.10
2526 2934 1.808945 CGCACTTCTCCAAATCTGCTT 59.191 47.619 0.00 0.00 0.00 3.91
2785 3201 2.035704 TGCAAATGGTTTCGCATCTTGT 59.964 40.909 0.00 0.00 0.00 3.16
3356 3805 7.124901 AGTGTTCATCTGATACCTATTGACTGT 59.875 37.037 0.00 0.00 0.00 3.55
3431 3931 7.071196 ACAGGTTAAATAGATCATGACCAGCTA 59.929 37.037 0.00 0.00 0.00 3.32
3970 4827 3.951775 AAACAACCTGAAGCAACAACA 57.048 38.095 0.00 0.00 0.00 3.33
4178 5035 8.500773 CAGTTTTAACGGCTGTAGAAGAAATAA 58.499 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.