Multiple sequence alignment - TraesCS4D01G142300

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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 TraesCS4D01G142300 chr4D 100.000 2935 0 0 1 2935 127565144 127568078 0.000000e+00 5421.0
1 TraesCS4D01G142300 chr4D 91.509 106 9 0 2820 2925 127567867 127567972 2.360000e-31 147.0
2 TraesCS4D01G142300 chr4D 91.509 106 9 0 2724 2829 127567963 127568068 2.360000e-31 147.0
3 TraesCS4D01G142300 chr4D 96.386 83 2 1 173 255 40819752 40819671 5.100000e-28 135.0
4 TraesCS4D01G142300 chr4B 98.642 2578 33 2 359 2935 191662451 191665027 0.000000e+00 4566.0
5 TraesCS4D01G142300 chr4B 91.509 106 9 0 2820 2925 191664816 191664921 2.360000e-31 147.0
6 TraesCS4D01G142300 chr4B 91.509 106 9 0 2724 2829 191664912 191665017 2.360000e-31 147.0
7 TraesCS4D01G142300 chr4A 96.842 2692 72 5 254 2935 440870007 440867319 0.000000e+00 4488.0
8 TraesCS4D01G142300 chr4A 89.423 104 11 0 2726 2829 440867432 440867329 6.600000e-27 132.0
9 TraesCS4D01G142300 chr4A 95.000 80 4 0 173 252 607239918 607239997 3.070000e-25 126.0
10 TraesCS4D01G142300 chr4A 87.736 106 13 0 2820 2925 440867530 440867425 1.100000e-24 124.0
11 TraesCS4D01G142300 chr1D 97.674 172 4 0 1 172 430961933 430962104 2.210000e-76 296.0
12 TraesCS4D01G142300 chr1D 97.110 173 5 0 1 173 461157081 461157253 2.860000e-75 292.0
13 TraesCS4D01G142300 chr1D 96.512 172 6 0 1 172 495272501 495272672 4.790000e-73 285.0
14 TraesCS4D01G142300 chr6D 96.591 176 6 0 1 176 209915789 209915614 2.860000e-75 292.0
15 TraesCS4D01G142300 chr6D 97.093 172 5 0 1 172 158211596 158211767 1.030000e-74 291.0
16 TraesCS4D01G142300 chr6D 97.093 172 5 0 1 172 291374082 291373911 1.030000e-74 291.0
17 TraesCS4D01G142300 chr6D 89.796 49 4 1 1483 1531 90869470 90869423 8.780000e-06 62.1
18 TraesCS4D01G142300 chr3D 96.591 176 6 0 1 176 39033722 39033547 2.860000e-75 292.0
19 TraesCS4D01G142300 chrUn 97.093 172 5 0 1 172 298431187 298431016 1.030000e-74 291.0
20 TraesCS4D01G142300 chrUn 97.093 172 5 0 1 172 317523482 317523653 1.030000e-74 291.0
21 TraesCS4D01G142300 chr2A 96.629 89 2 1 173 261 48551874 48551787 2.360000e-31 147.0
22 TraesCS4D01G142300 chr2A 95.238 84 3 1 170 252 769557131 769557048 6.600000e-27 132.0
23 TraesCS4D01G142300 chr5D 98.765 81 1 0 173 253 548627517 548627597 8.480000e-31 145.0
24 TraesCS4D01G142300 chr5D 97.500 80 2 0 173 252 46616315 46616394 1.420000e-28 137.0
25 TraesCS4D01G142300 chr5B 93.750 96 5 1 173 267 513852935 513852840 3.050000e-30 143.0
26 TraesCS4D01G142300 chr3A 94.382 89 5 0 173 261 13511437 13511349 1.420000e-28 137.0
27 TraesCS4D01G142300 chr1B 96.429 84 1 2 170 252 648680931 648681013 1.420000e-28 137.0
28 TraesCS4D01G142300 chr3B 82.895 76 9 4 1468 1541 653152434 653152507 6.790000e-07 65.8
29 TraesCS4D01G142300 chr6B 89.796 49 4 1 1483 1531 172990136 172990089 8.780000e-06 62.1
30 TraesCS4D01G142300 chr6A 89.796 49 4 1 1483 1531 109114240 109114193 8.780000e-06 62.1
31 TraesCS4D01G142300 chr2B 89.362 47 5 0 1504 1550 663180748 663180702 3.160000e-05 60.2


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 TraesCS4D01G142300 chr4D 127565144 127568078 2934 False 1905.000000 5421 94.339333 1 2935 3 chr4D.!!$F1 2934
1 TraesCS4D01G142300 chr4B 191662451 191665027 2576 False 1620.000000 4566 93.886667 359 2935 3 chr4B.!!$F1 2576
2 TraesCS4D01G142300 chr4A 440867319 440870007 2688 True 1581.333333 4488 91.333667 254 2935 3 chr4A.!!$R1 2681

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
20 21 0.325954 ACCCTAAACCCTAGGACCGG 60.326 60.000 11.48 0.00 36.85 5.28 F
21 22 0.325954 CCCTAAACCCTAGGACCGGT 60.326 60.000 6.92 6.92 36.85 5.28 F
22 23 1.062962 CCCTAAACCCTAGGACCGGTA 60.063 57.143 7.34 0.00 36.85 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 1339 5.685728 AGCTCAATAATAAGGTGTTCCTCC 58.314 41.667 0.0 0.0 44.35 4.30 R
1420 1423 6.491394 CGTTTCACCTGTTGTAGATGAAAAA 58.509 36.000 0.0 0.0 40.06 1.94 R
2199 2202 8.851541 TGTATCATGCATATAAATTGCTCTCA 57.148 30.769 0.0 0.0 40.77 3.27 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
19 20 2.459555 TACCCTAAACCCTAGGACCG 57.540 55.000 11.48 0.00 36.85 4.79
20 21 0.325954 ACCCTAAACCCTAGGACCGG 60.326 60.000 11.48 0.00 36.85 5.28
21 22 0.325954 CCCTAAACCCTAGGACCGGT 60.326 60.000 6.92 6.92 36.85 5.28
22 23 1.062962 CCCTAAACCCTAGGACCGGTA 60.063 57.143 7.34 0.00 36.85 4.02
23 24 2.426855 CCCTAAACCCTAGGACCGGTAT 60.427 54.545 7.34 0.96 36.85 2.73
24 25 2.896044 CCTAAACCCTAGGACCGGTATC 59.104 54.545 7.34 2.53 36.85 2.24
25 26 2.862850 AAACCCTAGGACCGGTATCT 57.137 50.000 7.34 11.41 0.00 1.98
26 27 2.083628 AACCCTAGGACCGGTATCTG 57.916 55.000 7.34 0.00 0.00 2.90
27 28 1.229131 ACCCTAGGACCGGTATCTGA 58.771 55.000 7.34 0.00 0.00 3.27
28 29 1.787676 ACCCTAGGACCGGTATCTGAT 59.212 52.381 7.34 0.00 0.00 2.90
29 30 2.991713 ACCCTAGGACCGGTATCTGATA 59.008 50.000 7.34 0.00 0.00 2.15
30 31 3.245193 ACCCTAGGACCGGTATCTGATAC 60.245 52.174 17.52 17.52 35.00 2.24
44 45 7.976135 GTATCTGATACCATGAAAGCTGAAT 57.024 36.000 15.40 0.00 0.00 2.57
46 47 9.494271 GTATCTGATACCATGAAAGCTGAATAA 57.506 33.333 15.40 0.00 0.00 1.40
47 48 8.985315 ATCTGATACCATGAAAGCTGAATAAA 57.015 30.769 0.00 0.00 0.00 1.40
48 49 8.806429 TCTGATACCATGAAAGCTGAATAAAA 57.194 30.769 0.00 0.00 0.00 1.52
49 50 8.677300 TCTGATACCATGAAAGCTGAATAAAAC 58.323 33.333 0.00 0.00 0.00 2.43
50 51 8.579850 TGATACCATGAAAGCTGAATAAAACT 57.420 30.769 0.00 0.00 0.00 2.66
51 52 8.461222 TGATACCATGAAAGCTGAATAAAACTG 58.539 33.333 0.00 0.00 0.00 3.16
52 53 6.655078 ACCATGAAAGCTGAATAAAACTGT 57.345 33.333 0.00 0.00 0.00 3.55
53 54 7.054491 ACCATGAAAGCTGAATAAAACTGTT 57.946 32.000 0.00 0.00 0.00 3.16
54 55 6.925165 ACCATGAAAGCTGAATAAAACTGTTG 59.075 34.615 0.00 0.00 0.00 3.33
55 56 6.128742 CCATGAAAGCTGAATAAAACTGTTGC 60.129 38.462 0.00 0.00 0.00 4.17
56 57 6.147864 TGAAAGCTGAATAAAACTGTTGCT 57.852 33.333 0.00 0.00 0.00 3.91
57 58 6.572519 TGAAAGCTGAATAAAACTGTTGCTT 58.427 32.000 6.28 6.28 40.59 3.91
58 59 6.476380 TGAAAGCTGAATAAAACTGTTGCTTG 59.524 34.615 11.24 0.00 39.11 4.01
59 60 5.520376 AGCTGAATAAAACTGTTGCTTGT 57.480 34.783 0.00 0.00 0.00 3.16
60 61 5.906073 AGCTGAATAAAACTGTTGCTTGTT 58.094 33.333 0.00 0.00 0.00 2.83
61 62 5.750067 AGCTGAATAAAACTGTTGCTTGTTG 59.250 36.000 0.00 0.00 0.00 3.33
62 63 5.748152 GCTGAATAAAACTGTTGCTTGTTGA 59.252 36.000 0.00 0.00 0.00 3.18
63 64 6.421801 GCTGAATAAAACTGTTGCTTGTTGAT 59.578 34.615 0.00 0.00 0.00 2.57
64 65 7.568134 GCTGAATAAAACTGTTGCTTGTTGATG 60.568 37.037 0.00 0.00 0.00 3.07
65 66 7.487484 TGAATAAAACTGTTGCTTGTTGATGA 58.513 30.769 0.00 0.00 0.00 2.92
66 67 8.143193 TGAATAAAACTGTTGCTTGTTGATGAT 58.857 29.630 0.00 0.00 0.00 2.45
67 68 8.891671 AATAAAACTGTTGCTTGTTGATGATT 57.108 26.923 0.00 0.00 0.00 2.57
68 69 8.891671 ATAAAACTGTTGCTTGTTGATGATTT 57.108 26.923 0.00 0.00 0.00 2.17
69 70 6.592798 AAACTGTTGCTTGTTGATGATTTG 57.407 33.333 0.00 0.00 0.00 2.32
70 71 4.624015 ACTGTTGCTTGTTGATGATTTGG 58.376 39.130 0.00 0.00 0.00 3.28
71 72 4.099881 ACTGTTGCTTGTTGATGATTTGGT 59.900 37.500 0.00 0.00 0.00 3.67
72 73 4.370049 TGTTGCTTGTTGATGATTTGGTG 58.630 39.130 0.00 0.00 0.00 4.17
73 74 3.029320 TGCTTGTTGATGATTTGGTGC 57.971 42.857 0.00 0.00 0.00 5.01
74 75 1.987770 GCTTGTTGATGATTTGGTGCG 59.012 47.619 0.00 0.00 0.00 5.34
75 76 2.598589 CTTGTTGATGATTTGGTGCGG 58.401 47.619 0.00 0.00 0.00 5.69
76 77 1.614996 TGTTGATGATTTGGTGCGGT 58.385 45.000 0.00 0.00 0.00 5.68
77 78 2.784347 TGTTGATGATTTGGTGCGGTA 58.216 42.857 0.00 0.00 0.00 4.02
78 79 3.351740 TGTTGATGATTTGGTGCGGTAT 58.648 40.909 0.00 0.00 0.00 2.73
79 80 4.518249 TGTTGATGATTTGGTGCGGTATA 58.482 39.130 0.00 0.00 0.00 1.47
80 81 4.334203 TGTTGATGATTTGGTGCGGTATAC 59.666 41.667 0.00 0.00 0.00 1.47
81 82 4.143986 TGATGATTTGGTGCGGTATACA 57.856 40.909 5.01 0.00 0.00 2.29
82 83 4.518249 TGATGATTTGGTGCGGTATACAA 58.482 39.130 5.01 0.00 0.00 2.41
83 84 4.574421 TGATGATTTGGTGCGGTATACAAG 59.426 41.667 5.01 0.00 0.00 3.16
84 85 4.209307 TGATTTGGTGCGGTATACAAGA 57.791 40.909 5.01 0.00 0.00 3.02
85 86 4.188462 TGATTTGGTGCGGTATACAAGAG 58.812 43.478 5.01 0.00 0.00 2.85
86 87 3.688694 TTTGGTGCGGTATACAAGAGT 57.311 42.857 5.01 0.00 0.00 3.24
87 88 4.804868 TTTGGTGCGGTATACAAGAGTA 57.195 40.909 5.01 0.00 34.10 2.59
88 89 5.347620 TTTGGTGCGGTATACAAGAGTAT 57.652 39.130 5.01 0.00 43.23 2.12
89 90 6.468333 TTTGGTGCGGTATACAAGAGTATA 57.532 37.500 5.01 0.00 41.15 1.47
90 91 6.659745 TTGGTGCGGTATACAAGAGTATAT 57.340 37.500 5.01 0.00 43.17 0.86
91 92 7.764141 TTGGTGCGGTATACAAGAGTATATA 57.236 36.000 5.01 0.00 43.17 0.86
92 93 7.764141 TGGTGCGGTATACAAGAGTATATAA 57.236 36.000 5.01 0.00 43.17 0.98
93 94 7.823665 TGGTGCGGTATACAAGAGTATATAAG 58.176 38.462 5.01 0.00 43.17 1.73
94 95 7.666804 TGGTGCGGTATACAAGAGTATATAAGA 59.333 37.037 5.01 0.00 43.17 2.10
95 96 8.182881 GGTGCGGTATACAAGAGTATATAAGAG 58.817 40.741 5.01 0.00 43.17 2.85
96 97 8.182881 GTGCGGTATACAAGAGTATATAAGAGG 58.817 40.741 5.01 0.00 43.17 3.69
97 98 7.338703 TGCGGTATACAAGAGTATATAAGAGGG 59.661 40.741 5.01 0.00 43.17 4.30
98 99 7.338957 GCGGTATACAAGAGTATATAAGAGGGT 59.661 40.741 5.01 0.00 43.17 4.34
99 100 9.896645 CGGTATACAAGAGTATATAAGAGGGTA 57.103 37.037 5.01 0.00 43.17 3.69
105 106 8.702819 ACAAGAGTATATAAGAGGGTACAAACC 58.297 37.037 0.00 0.00 45.97 3.27
118 119 3.992427 GGTACAAACCGACTTGAAGTAGG 59.008 47.826 20.77 20.77 45.15 3.18
119 120 3.121738 ACAAACCGACTTGAAGTAGGG 57.878 47.619 24.90 18.39 44.12 3.53
120 121 2.224450 ACAAACCGACTTGAAGTAGGGG 60.224 50.000 24.90 16.88 44.12 4.79
121 122 1.725803 AACCGACTTGAAGTAGGGGT 58.274 50.000 24.90 16.75 44.12 4.95
122 123 2.610438 ACCGACTTGAAGTAGGGGTA 57.390 50.000 24.90 0.00 44.12 3.69
123 124 2.174360 ACCGACTTGAAGTAGGGGTAC 58.826 52.381 24.90 0.00 44.12 3.34
124 125 2.173519 CCGACTTGAAGTAGGGGTACA 58.826 52.381 15.65 0.00 37.35 2.90
125 126 2.564062 CCGACTTGAAGTAGGGGTACAA 59.436 50.000 15.65 0.00 37.35 2.41
126 127 3.007182 CCGACTTGAAGTAGGGGTACAAA 59.993 47.826 15.65 0.00 37.35 2.83
127 128 4.503643 CCGACTTGAAGTAGGGGTACAAAA 60.504 45.833 15.65 0.00 37.35 2.44
128 129 4.450080 CGACTTGAAGTAGGGGTACAAAAC 59.550 45.833 0.00 0.00 0.00 2.43
129 130 5.618236 GACTTGAAGTAGGGGTACAAAACT 58.382 41.667 0.00 0.00 0.00 2.66
130 131 5.374071 ACTTGAAGTAGGGGTACAAAACTG 58.626 41.667 0.00 0.00 0.00 3.16
131 132 5.131475 ACTTGAAGTAGGGGTACAAAACTGA 59.869 40.000 0.00 0.00 0.00 3.41
132 133 4.964593 TGAAGTAGGGGTACAAAACTGAC 58.035 43.478 0.00 0.00 0.00 3.51
133 134 4.657039 TGAAGTAGGGGTACAAAACTGACT 59.343 41.667 0.00 0.00 0.00 3.41
134 135 5.131475 TGAAGTAGGGGTACAAAACTGACTT 59.869 40.000 0.00 0.00 0.00 3.01
135 136 4.969484 AGTAGGGGTACAAAACTGACTTG 58.031 43.478 0.00 0.00 0.00 3.16
136 137 3.223674 AGGGGTACAAAACTGACTTGG 57.776 47.619 0.00 0.00 0.00 3.61
137 138 2.781174 AGGGGTACAAAACTGACTTGGA 59.219 45.455 0.00 0.00 0.00 3.53
138 139 2.882761 GGGGTACAAAACTGACTTGGAC 59.117 50.000 0.00 1.73 36.96 4.02
139 140 3.434596 GGGGTACAAAACTGACTTGGACT 60.435 47.826 0.00 0.00 37.69 3.85
140 141 4.202388 GGGGTACAAAACTGACTTGGACTA 60.202 45.833 0.00 0.00 37.69 2.59
141 142 4.995487 GGGTACAAAACTGACTTGGACTAG 59.005 45.833 0.00 0.00 37.69 2.57
142 143 5.221581 GGGTACAAAACTGACTTGGACTAGA 60.222 44.000 0.00 0.00 37.69 2.43
143 144 6.285990 GGTACAAAACTGACTTGGACTAGAA 58.714 40.000 0.00 0.00 37.69 2.10
144 145 6.424207 GGTACAAAACTGACTTGGACTAGAAG 59.576 42.308 0.00 0.00 37.69 2.85
145 146 5.990668 ACAAAACTGACTTGGACTAGAAGT 58.009 37.500 0.00 0.00 36.33 3.01
146 147 6.049790 ACAAAACTGACTTGGACTAGAAGTC 58.950 40.000 13.36 13.36 46.45 3.01
154 155 7.493743 GACTTGGACTAGAAGTCGTATATCA 57.506 40.000 6.96 0.00 45.96 2.15
155 156 8.101654 GACTTGGACTAGAAGTCGTATATCAT 57.898 38.462 6.96 0.00 45.96 2.45
156 157 9.217278 GACTTGGACTAGAAGTCGTATATCATA 57.783 37.037 6.96 0.00 45.96 2.15
157 158 9.570468 ACTTGGACTAGAAGTCGTATATCATAA 57.430 33.333 0.00 0.00 45.96 1.90
160 161 9.734984 TGGACTAGAAGTCGTATATCATAATGA 57.265 33.333 0.00 0.00 45.96 2.57
161 162 9.991388 GGACTAGAAGTCGTATATCATAATGAC 57.009 37.037 0.00 0.00 45.96 3.06
177 178 8.768501 TCATAATGACTACTCTAACATGGAGT 57.231 34.615 8.01 8.01 44.83 3.85
178 179 9.862149 TCATAATGACTACTCTAACATGGAGTA 57.138 33.333 9.20 9.20 42.96 2.59
179 180 9.900710 CATAATGACTACTCTAACATGGAGTAC 57.099 37.037 6.30 0.00 42.96 2.73
180 181 6.963083 ATGACTACTCTAACATGGAGTACC 57.037 41.667 6.30 3.63 42.96 3.34
195 196 5.842907 TGGAGTACCAATAGACATCAATCG 58.157 41.667 0.00 0.00 43.91 3.34
196 197 5.362717 TGGAGTACCAATAGACATCAATCGT 59.637 40.000 0.00 0.00 43.91 3.73
197 198 6.127168 TGGAGTACCAATAGACATCAATCGTT 60.127 38.462 0.00 0.00 43.91 3.85
198 199 6.201044 GGAGTACCAATAGACATCAATCGTTG 59.799 42.308 0.00 0.00 35.97 4.10
199 200 6.049149 AGTACCAATAGACATCAATCGTTGG 58.951 40.000 9.82 9.82 41.33 3.77
200 201 5.097742 ACCAATAGACATCAATCGTTGGA 57.902 39.130 15.33 0.00 39.57 3.53
201 202 5.684704 ACCAATAGACATCAATCGTTGGAT 58.315 37.500 15.33 0.00 39.57 3.41
202 203 5.760253 ACCAATAGACATCAATCGTTGGATC 59.240 40.000 15.33 0.00 39.57 3.36
203 204 5.759763 CCAATAGACATCAATCGTTGGATCA 59.240 40.000 0.00 0.00 39.57 2.92
204 205 6.260714 CCAATAGACATCAATCGTTGGATCAA 59.739 38.462 0.00 0.00 39.57 2.57
205 206 7.350467 CAATAGACATCAATCGTTGGATCAAG 58.650 38.462 0.00 0.00 30.81 3.02
206 207 5.089970 AGACATCAATCGTTGGATCAAGA 57.910 39.130 0.00 0.00 30.81 3.02
207 208 5.114780 AGACATCAATCGTTGGATCAAGAG 58.885 41.667 0.00 0.00 30.81 2.85
208 209 5.089970 ACATCAATCGTTGGATCAAGAGA 57.910 39.130 0.00 0.00 30.81 3.10
209 210 5.491070 ACATCAATCGTTGGATCAAGAGAA 58.509 37.500 0.00 0.00 30.81 2.87
210 211 5.939883 ACATCAATCGTTGGATCAAGAGAAA 59.060 36.000 0.00 0.00 30.81 2.52
211 212 6.600822 ACATCAATCGTTGGATCAAGAGAAAT 59.399 34.615 0.00 0.00 30.81 2.17
212 213 6.426980 TCAATCGTTGGATCAAGAGAAATG 57.573 37.500 0.00 0.00 30.81 2.32
213 214 6.172630 TCAATCGTTGGATCAAGAGAAATGA 58.827 36.000 0.00 0.00 30.81 2.57
214 215 6.654582 TCAATCGTTGGATCAAGAGAAATGAA 59.345 34.615 0.00 0.00 30.81 2.57
215 216 7.174772 TCAATCGTTGGATCAAGAGAAATGAAA 59.825 33.333 0.00 0.00 30.81 2.69
216 217 6.486253 TCGTTGGATCAAGAGAAATGAAAG 57.514 37.500 0.00 0.00 0.00 2.62
217 218 5.412594 TCGTTGGATCAAGAGAAATGAAAGG 59.587 40.000 0.00 0.00 0.00 3.11
218 219 5.405797 GTTGGATCAAGAGAAATGAAAGGC 58.594 41.667 0.00 0.00 0.00 4.35
219 220 4.927049 TGGATCAAGAGAAATGAAAGGCT 58.073 39.130 0.00 0.00 0.00 4.58
220 221 4.946157 TGGATCAAGAGAAATGAAAGGCTC 59.054 41.667 0.00 0.00 0.00 4.70
221 222 4.946157 GGATCAAGAGAAATGAAAGGCTCA 59.054 41.667 0.00 0.00 38.81 4.26
223 224 6.769822 GGATCAAGAGAAATGAAAGGCTCATA 59.230 38.462 0.00 0.00 44.43 2.15
224 225 7.447853 GGATCAAGAGAAATGAAAGGCTCATAT 59.552 37.037 0.00 0.00 44.43 1.78
225 226 8.763984 ATCAAGAGAAATGAAAGGCTCATATT 57.236 30.769 0.00 0.00 44.43 1.28
226 227 8.218338 TCAAGAGAAATGAAAGGCTCATATTC 57.782 34.615 0.00 0.00 44.43 1.75
227 228 7.830697 TCAAGAGAAATGAAAGGCTCATATTCA 59.169 33.333 2.10 2.10 44.43 2.57
228 229 8.630917 CAAGAGAAATGAAAGGCTCATATTCAT 58.369 33.333 6.37 6.37 44.43 2.57
234 235 7.771927 ATGAAAGGCTCATATTCATTTAGGG 57.228 36.000 6.37 0.00 43.32 3.53
235 236 6.070656 TGAAAGGCTCATATTCATTTAGGGG 58.929 40.000 0.00 0.00 0.00 4.79
236 237 5.669798 AAGGCTCATATTCATTTAGGGGT 57.330 39.130 0.00 0.00 0.00 4.95
237 238 6.780198 AAGGCTCATATTCATTTAGGGGTA 57.220 37.500 0.00 0.00 0.00 3.69
238 239 6.128138 AGGCTCATATTCATTTAGGGGTAC 57.872 41.667 0.00 0.00 0.00 3.34
239 240 5.852250 AGGCTCATATTCATTTAGGGGTACT 59.148 40.000 0.00 0.00 0.00 2.73
240 241 5.940470 GGCTCATATTCATTTAGGGGTACTG 59.060 44.000 0.00 0.00 0.00 2.74
241 242 6.465894 GGCTCATATTCATTTAGGGGTACTGT 60.466 42.308 0.00 0.00 0.00 3.55
242 243 7.256547 GGCTCATATTCATTTAGGGGTACTGTA 60.257 40.741 0.00 0.00 0.00 2.74
243 244 8.154856 GCTCATATTCATTTAGGGGTACTGTAA 58.845 37.037 0.00 0.00 0.00 2.41
246 247 9.284968 CATATTCATTTAGGGGTACTGTAAAGG 57.715 37.037 0.00 0.00 0.00 3.11
247 248 6.956102 TTCATTTAGGGGTACTGTAAAGGA 57.044 37.500 0.00 0.00 0.00 3.36
248 249 6.555463 TCATTTAGGGGTACTGTAAAGGAG 57.445 41.667 0.00 0.00 0.00 3.69
249 250 4.831674 TTTAGGGGTACTGTAAAGGAGC 57.168 45.455 0.00 0.00 0.00 4.70
250 251 2.644060 AGGGGTACTGTAAAGGAGCT 57.356 50.000 0.00 0.00 0.00 4.09
251 252 2.468915 AGGGGTACTGTAAAGGAGCTC 58.531 52.381 4.71 4.71 0.00 4.09
252 253 1.136500 GGGGTACTGTAAAGGAGCTCG 59.864 57.143 7.83 0.00 0.00 5.03
281 282 1.844357 CGTAACAATACCTGCTCGTCG 59.156 52.381 0.00 0.00 0.00 5.12
291 292 3.423154 GCTCGTCGTGCCTTTGGG 61.423 66.667 8.06 0.00 0.00 4.12
414 415 6.815641 ACAAACAGTTGCAAAAATACATCACA 59.184 30.769 0.00 0.00 38.39 3.58
473 474 3.276857 ACAAAATTGCATGTGTTTGCCA 58.723 36.364 10.21 0.00 42.06 4.92
635 636 2.604614 CCGGCAACAAACAAGAGTTAGC 60.605 50.000 0.00 0.00 36.84 3.09
783 784 1.079621 TAAAGAGGCCCCACGAGGA 59.920 57.895 0.00 0.00 38.24 3.71
899 900 1.579698 CATCAGGCTGGAGTTCATCG 58.420 55.000 15.73 0.00 0.00 3.84
1419 1422 6.299922 AGAAGACCTTACTAAAGCAGCTTTT 58.700 36.000 25.29 11.27 35.21 2.27
1420 1423 6.773200 AGAAGACCTTACTAAAGCAGCTTTTT 59.227 34.615 25.29 14.97 35.21 1.94
2032 2035 9.978044 ATGTAGCTATGTCTGCATATACATATG 57.022 33.333 13.82 0.00 39.50 1.78
2199 2202 4.524802 TGCCCTTCACAGAATGGAATAT 57.475 40.909 5.42 0.00 43.62 1.28
2540 2554 6.205853 ACAAGTATTTCTCCAATAAACACGCA 59.794 34.615 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.062962 CCGGTCCTAGGGTTTAGGGTA 60.063 57.143 9.46 0.00 35.45 3.69
1 2 0.325954 CCGGTCCTAGGGTTTAGGGT 60.326 60.000 9.46 0.00 35.45 4.34
2 3 0.325954 ACCGGTCCTAGGGTTTAGGG 60.326 60.000 9.46 4.92 35.45 3.53
3 4 2.459555 TACCGGTCCTAGGGTTTAGG 57.540 55.000 12.40 8.37 37.75 2.69
4 5 3.573110 CAGATACCGGTCCTAGGGTTTAG 59.427 52.174 12.40 0.00 37.75 1.85
5 6 3.205056 TCAGATACCGGTCCTAGGGTTTA 59.795 47.826 12.40 0.00 37.75 2.01
6 7 2.023695 TCAGATACCGGTCCTAGGGTTT 60.024 50.000 12.40 0.00 37.75 3.27
7 8 1.572415 TCAGATACCGGTCCTAGGGTT 59.428 52.381 12.40 0.00 37.75 4.11
8 9 1.229131 TCAGATACCGGTCCTAGGGT 58.771 55.000 12.40 0.83 40.35 4.34
9 10 2.606751 ATCAGATACCGGTCCTAGGG 57.393 55.000 12.40 0.00 0.00 3.53
10 11 3.354467 GGTATCAGATACCGGTCCTAGG 58.646 54.545 21.68 0.82 45.20 3.02
20 21 7.976135 ATTCAGCTTTCATGGTATCAGATAC 57.024 36.000 11.71 11.71 35.00 2.24
22 23 8.985315 TTTATTCAGCTTTCATGGTATCAGAT 57.015 30.769 0.00 0.00 0.00 2.90
23 24 8.677300 GTTTTATTCAGCTTTCATGGTATCAGA 58.323 33.333 0.00 0.00 0.00 3.27
24 25 8.680903 AGTTTTATTCAGCTTTCATGGTATCAG 58.319 33.333 0.00 0.00 0.00 2.90
25 26 8.461222 CAGTTTTATTCAGCTTTCATGGTATCA 58.539 33.333 0.00 0.00 0.00 2.15
26 27 8.462016 ACAGTTTTATTCAGCTTTCATGGTATC 58.538 33.333 0.00 0.00 0.00 2.24
27 28 8.353423 ACAGTTTTATTCAGCTTTCATGGTAT 57.647 30.769 0.00 0.00 0.00 2.73
28 29 7.759489 ACAGTTTTATTCAGCTTTCATGGTA 57.241 32.000 0.00 0.00 0.00 3.25
29 30 6.655078 ACAGTTTTATTCAGCTTTCATGGT 57.345 33.333 0.00 0.00 0.00 3.55
30 31 6.128742 GCAACAGTTTTATTCAGCTTTCATGG 60.129 38.462 0.00 0.00 0.00 3.66
31 32 6.643770 AGCAACAGTTTTATTCAGCTTTCATG 59.356 34.615 0.00 0.00 0.00 3.07
32 33 6.752168 AGCAACAGTTTTATTCAGCTTTCAT 58.248 32.000 0.00 0.00 0.00 2.57
33 34 6.147864 AGCAACAGTTTTATTCAGCTTTCA 57.852 33.333 0.00 0.00 0.00 2.69
34 35 6.476706 ACAAGCAACAGTTTTATTCAGCTTTC 59.523 34.615 2.78 0.00 38.86 2.62
35 36 6.340522 ACAAGCAACAGTTTTATTCAGCTTT 58.659 32.000 2.78 0.00 38.86 3.51
36 37 5.906073 ACAAGCAACAGTTTTATTCAGCTT 58.094 33.333 0.00 0.00 41.27 3.74
37 38 5.520376 ACAAGCAACAGTTTTATTCAGCT 57.480 34.783 0.00 0.00 0.00 4.24
38 39 5.748152 TCAACAAGCAACAGTTTTATTCAGC 59.252 36.000 0.00 0.00 0.00 4.26
39 40 7.648908 TCATCAACAAGCAACAGTTTTATTCAG 59.351 33.333 0.00 0.00 0.00 3.02
40 41 7.487484 TCATCAACAAGCAACAGTTTTATTCA 58.513 30.769 0.00 0.00 0.00 2.57
41 42 7.928908 TCATCAACAAGCAACAGTTTTATTC 57.071 32.000 0.00 0.00 0.00 1.75
42 43 8.891671 AATCATCAACAAGCAACAGTTTTATT 57.108 26.923 0.00 0.00 0.00 1.40
43 44 8.767085 CAAATCATCAACAAGCAACAGTTTTAT 58.233 29.630 0.00 0.00 0.00 1.40
44 45 7.224362 CCAAATCATCAACAAGCAACAGTTTTA 59.776 33.333 0.00 0.00 0.00 1.52
45 46 6.037391 CCAAATCATCAACAAGCAACAGTTTT 59.963 34.615 0.00 0.00 0.00 2.43
46 47 5.524646 CCAAATCATCAACAAGCAACAGTTT 59.475 36.000 0.00 0.00 0.00 2.66
47 48 5.051816 CCAAATCATCAACAAGCAACAGTT 58.948 37.500 0.00 0.00 0.00 3.16
48 49 4.099881 ACCAAATCATCAACAAGCAACAGT 59.900 37.500 0.00 0.00 0.00 3.55
49 50 4.446385 CACCAAATCATCAACAAGCAACAG 59.554 41.667 0.00 0.00 0.00 3.16
50 51 4.370049 CACCAAATCATCAACAAGCAACA 58.630 39.130 0.00 0.00 0.00 3.33
51 52 3.184986 GCACCAAATCATCAACAAGCAAC 59.815 43.478 0.00 0.00 0.00 4.17
52 53 3.391965 GCACCAAATCATCAACAAGCAA 58.608 40.909 0.00 0.00 0.00 3.91
53 54 2.607526 CGCACCAAATCATCAACAAGCA 60.608 45.455 0.00 0.00 0.00 3.91
54 55 1.987770 CGCACCAAATCATCAACAAGC 59.012 47.619 0.00 0.00 0.00 4.01
55 56 2.030007 ACCGCACCAAATCATCAACAAG 60.030 45.455 0.00 0.00 0.00 3.16
56 57 1.959985 ACCGCACCAAATCATCAACAA 59.040 42.857 0.00 0.00 0.00 2.83
57 58 1.614996 ACCGCACCAAATCATCAACA 58.385 45.000 0.00 0.00 0.00 3.33
58 59 4.334203 TGTATACCGCACCAAATCATCAAC 59.666 41.667 0.00 0.00 0.00 3.18
59 60 4.518249 TGTATACCGCACCAAATCATCAA 58.482 39.130 0.00 0.00 0.00 2.57
60 61 4.143986 TGTATACCGCACCAAATCATCA 57.856 40.909 0.00 0.00 0.00 3.07
61 62 4.814234 TCTTGTATACCGCACCAAATCATC 59.186 41.667 0.00 0.00 0.00 2.92
62 63 4.776349 TCTTGTATACCGCACCAAATCAT 58.224 39.130 0.00 0.00 0.00 2.45
63 64 4.188462 CTCTTGTATACCGCACCAAATCA 58.812 43.478 0.00 0.00 0.00 2.57
64 65 4.189231 ACTCTTGTATACCGCACCAAATC 58.811 43.478 0.00 0.00 0.00 2.17
65 66 4.216411 ACTCTTGTATACCGCACCAAAT 57.784 40.909 0.00 0.00 0.00 2.32
66 67 3.688694 ACTCTTGTATACCGCACCAAA 57.311 42.857 0.00 0.00 0.00 3.28
67 68 6.659745 ATATACTCTTGTATACCGCACCAA 57.340 37.500 0.00 0.00 42.38 3.67
68 69 7.666804 TCTTATATACTCTTGTATACCGCACCA 59.333 37.037 0.00 0.00 42.38 4.17
69 70 8.048534 TCTTATATACTCTTGTATACCGCACC 57.951 38.462 0.00 0.00 42.38 5.01
70 71 8.182881 CCTCTTATATACTCTTGTATACCGCAC 58.817 40.741 0.00 0.00 42.38 5.34
71 72 7.338703 CCCTCTTATATACTCTTGTATACCGCA 59.661 40.741 0.00 0.00 42.38 5.69
72 73 7.338957 ACCCTCTTATATACTCTTGTATACCGC 59.661 40.741 0.00 0.00 42.38 5.68
73 74 8.804912 ACCCTCTTATATACTCTTGTATACCG 57.195 38.462 0.00 0.00 42.38 4.02
79 80 8.702819 GGTTTGTACCCTCTTATATACTCTTGT 58.297 37.037 0.00 0.00 38.60 3.16
80 81 7.866393 CGGTTTGTACCCTCTTATATACTCTTG 59.134 40.741 0.00 0.00 41.75 3.02
81 82 7.781693 TCGGTTTGTACCCTCTTATATACTCTT 59.218 37.037 0.00 0.00 41.75 2.85
82 83 7.230309 GTCGGTTTGTACCCTCTTATATACTCT 59.770 40.741 0.00 0.00 41.75 3.24
83 84 7.230309 AGTCGGTTTGTACCCTCTTATATACTC 59.770 40.741 0.00 0.00 41.75 2.59
84 85 7.065504 AGTCGGTTTGTACCCTCTTATATACT 58.934 38.462 0.00 0.00 41.75 2.12
85 86 7.282332 AGTCGGTTTGTACCCTCTTATATAC 57.718 40.000 0.00 0.00 41.75 1.47
86 87 7.560991 TCAAGTCGGTTTGTACCCTCTTATATA 59.439 37.037 0.00 0.00 41.75 0.86
87 88 6.381994 TCAAGTCGGTTTGTACCCTCTTATAT 59.618 38.462 0.00 0.00 41.75 0.86
88 89 5.716228 TCAAGTCGGTTTGTACCCTCTTATA 59.284 40.000 0.00 0.00 41.75 0.98
89 90 4.529377 TCAAGTCGGTTTGTACCCTCTTAT 59.471 41.667 0.00 0.00 41.75 1.73
90 91 3.896888 TCAAGTCGGTTTGTACCCTCTTA 59.103 43.478 0.00 0.00 41.75 2.10
91 92 2.701951 TCAAGTCGGTTTGTACCCTCTT 59.298 45.455 0.00 0.00 41.75 2.85
92 93 2.322658 TCAAGTCGGTTTGTACCCTCT 58.677 47.619 0.00 0.00 41.75 3.69
93 94 2.825861 TCAAGTCGGTTTGTACCCTC 57.174 50.000 0.00 0.00 41.75 4.30
94 95 2.436911 ACTTCAAGTCGGTTTGTACCCT 59.563 45.455 0.00 0.00 41.75 4.34
95 96 2.842457 ACTTCAAGTCGGTTTGTACCC 58.158 47.619 0.00 0.00 41.75 3.69
96 97 3.992427 CCTACTTCAAGTCGGTTTGTACC 59.008 47.826 0.00 0.00 41.33 3.34
97 98 3.992427 CCCTACTTCAAGTCGGTTTGTAC 59.008 47.826 7.32 0.00 29.69 2.90
98 99 3.007182 CCCCTACTTCAAGTCGGTTTGTA 59.993 47.826 7.32 0.00 29.69 2.41
99 100 2.224450 CCCCTACTTCAAGTCGGTTTGT 60.224 50.000 7.32 0.00 29.69 2.83
100 101 2.224450 ACCCCTACTTCAAGTCGGTTTG 60.224 50.000 7.32 0.00 29.69 2.93
101 102 2.052468 ACCCCTACTTCAAGTCGGTTT 58.948 47.619 7.32 0.00 29.69 3.27
102 103 1.725803 ACCCCTACTTCAAGTCGGTT 58.274 50.000 7.32 0.00 29.69 4.44
103 104 2.174360 GTACCCCTACTTCAAGTCGGT 58.826 52.381 7.32 7.98 29.69 4.69
104 105 2.173519 TGTACCCCTACTTCAAGTCGG 58.826 52.381 0.82 0.82 31.38 4.79
105 106 3.947910 TTGTACCCCTACTTCAAGTCG 57.052 47.619 0.00 0.00 0.00 4.18
106 107 5.469084 CAGTTTTGTACCCCTACTTCAAGTC 59.531 44.000 0.00 0.00 0.00 3.01
107 108 5.131475 TCAGTTTTGTACCCCTACTTCAAGT 59.869 40.000 0.00 0.00 0.00 3.16
108 109 5.469084 GTCAGTTTTGTACCCCTACTTCAAG 59.531 44.000 0.00 0.00 0.00 3.02
109 110 5.131475 AGTCAGTTTTGTACCCCTACTTCAA 59.869 40.000 0.00 0.00 0.00 2.69
110 111 4.657039 AGTCAGTTTTGTACCCCTACTTCA 59.343 41.667 0.00 0.00 0.00 3.02
111 112 5.224821 AGTCAGTTTTGTACCCCTACTTC 57.775 43.478 0.00 0.00 0.00 3.01
112 113 5.374071 CAAGTCAGTTTTGTACCCCTACTT 58.626 41.667 0.00 0.00 0.00 2.24
113 114 4.202430 CCAAGTCAGTTTTGTACCCCTACT 60.202 45.833 0.00 0.00 0.00 2.57
114 115 4.070009 CCAAGTCAGTTTTGTACCCCTAC 58.930 47.826 0.00 0.00 0.00 3.18
115 116 3.975312 TCCAAGTCAGTTTTGTACCCCTA 59.025 43.478 0.00 0.00 0.00 3.53
116 117 2.781174 TCCAAGTCAGTTTTGTACCCCT 59.219 45.455 0.00 0.00 0.00 4.79
117 118 2.882761 GTCCAAGTCAGTTTTGTACCCC 59.117 50.000 0.00 0.00 0.00 4.95
118 119 3.816994 AGTCCAAGTCAGTTTTGTACCC 58.183 45.455 0.00 0.00 0.00 3.69
119 120 5.850614 TCTAGTCCAAGTCAGTTTTGTACC 58.149 41.667 0.00 0.00 0.00 3.34
120 121 6.985059 ACTTCTAGTCCAAGTCAGTTTTGTAC 59.015 38.462 0.00 0.00 27.00 2.90
121 122 7.120923 ACTTCTAGTCCAAGTCAGTTTTGTA 57.879 36.000 0.00 0.00 27.00 2.41
122 123 5.990668 ACTTCTAGTCCAAGTCAGTTTTGT 58.009 37.500 0.00 0.00 27.00 2.83
123 124 5.175856 CGACTTCTAGTCCAAGTCAGTTTTG 59.824 44.000 18.00 2.79 46.99 2.44
124 125 5.163437 ACGACTTCTAGTCCAAGTCAGTTTT 60.163 40.000 18.00 0.57 46.99 2.43
125 126 4.341520 ACGACTTCTAGTCCAAGTCAGTTT 59.658 41.667 18.00 2.39 46.99 2.66
126 127 3.890147 ACGACTTCTAGTCCAAGTCAGTT 59.110 43.478 18.00 4.22 46.99 3.16
127 128 3.488363 ACGACTTCTAGTCCAAGTCAGT 58.512 45.455 18.00 14.31 46.99 3.41
128 129 5.821516 ATACGACTTCTAGTCCAAGTCAG 57.178 43.478 18.00 13.87 46.99 3.51
129 130 7.052248 TGATATACGACTTCTAGTCCAAGTCA 58.948 38.462 18.00 5.06 46.99 3.41
130 131 7.493743 TGATATACGACTTCTAGTCCAAGTC 57.506 40.000 11.14 11.14 42.12 3.01
131 132 9.570468 TTATGATATACGACTTCTAGTCCAAGT 57.430 33.333 0.00 0.00 42.12 3.16
134 135 9.734984 TCATTATGATATACGACTTCTAGTCCA 57.265 33.333 0.00 0.00 42.12 4.02
135 136 9.991388 GTCATTATGATATACGACTTCTAGTCC 57.009 37.037 0.00 0.00 42.12 3.85
151 152 9.373450 ACTCCATGTTAGAGTAGTCATTATGAT 57.627 33.333 0.00 0.00 42.76 2.45
152 153 8.768501 ACTCCATGTTAGAGTAGTCATTATGA 57.231 34.615 0.00 0.00 42.76 2.15
153 154 9.900710 GTACTCCATGTTAGAGTAGTCATTATG 57.099 37.037 9.72 0.00 45.15 1.90
154 155 9.080097 GGTACTCCATGTTAGAGTAGTCATTAT 57.920 37.037 9.72 0.00 45.15 1.28
155 156 8.057011 TGGTACTCCATGTTAGAGTAGTCATTA 58.943 37.037 9.72 0.00 45.15 1.90
156 157 6.895756 TGGTACTCCATGTTAGAGTAGTCATT 59.104 38.462 9.72 0.00 45.15 2.57
157 158 6.432581 TGGTACTCCATGTTAGAGTAGTCAT 58.567 40.000 9.72 0.00 45.15 3.06
158 159 5.823312 TGGTACTCCATGTTAGAGTAGTCA 58.177 41.667 9.72 8.91 45.15 3.41
159 160 6.770746 TTGGTACTCCATGTTAGAGTAGTC 57.229 41.667 9.72 7.05 45.15 2.59
160 161 8.280084 TCTATTGGTACTCCATGTTAGAGTAGT 58.720 37.037 9.72 0.00 45.15 2.73
161 162 8.569641 GTCTATTGGTACTCCATGTTAGAGTAG 58.430 40.741 9.72 1.65 45.15 2.57
162 163 8.057011 TGTCTATTGGTACTCCATGTTAGAGTA 58.943 37.037 6.30 6.30 42.76 2.59
163 164 6.895756 TGTCTATTGGTACTCCATGTTAGAGT 59.104 38.462 8.01 8.01 46.22 3.24
164 165 7.348080 TGTCTATTGGTACTCCATGTTAGAG 57.652 40.000 0.00 0.00 43.91 2.43
165 166 7.563556 TGATGTCTATTGGTACTCCATGTTAGA 59.436 37.037 0.00 0.00 43.91 2.10
166 167 7.726216 TGATGTCTATTGGTACTCCATGTTAG 58.274 38.462 0.00 0.00 43.91 2.34
167 168 7.669089 TGATGTCTATTGGTACTCCATGTTA 57.331 36.000 0.00 0.00 43.91 2.41
168 169 6.560003 TGATGTCTATTGGTACTCCATGTT 57.440 37.500 0.00 0.00 43.91 2.71
169 170 6.560003 TTGATGTCTATTGGTACTCCATGT 57.440 37.500 0.00 0.00 43.91 3.21
170 171 6.367149 CGATTGATGTCTATTGGTACTCCATG 59.633 42.308 0.00 0.00 43.91 3.66
171 172 6.042093 ACGATTGATGTCTATTGGTACTCCAT 59.958 38.462 0.00 0.00 43.91 3.41
172 173 5.362717 ACGATTGATGTCTATTGGTACTCCA 59.637 40.000 0.00 0.00 42.66 3.86
173 174 5.844004 ACGATTGATGTCTATTGGTACTCC 58.156 41.667 0.00 0.00 0.00 3.85
174 175 6.201044 CCAACGATTGATGTCTATTGGTACTC 59.799 42.308 0.00 0.00 32.01 2.59
175 176 6.049149 CCAACGATTGATGTCTATTGGTACT 58.951 40.000 0.00 0.00 32.01 2.73
176 177 6.046593 TCCAACGATTGATGTCTATTGGTAC 58.953 40.000 0.00 0.00 35.32 3.34
177 178 6.228616 TCCAACGATTGATGTCTATTGGTA 57.771 37.500 0.00 0.00 35.32 3.25
178 179 5.097742 TCCAACGATTGATGTCTATTGGT 57.902 39.130 0.00 0.00 35.32 3.67
179 180 5.759763 TGATCCAACGATTGATGTCTATTGG 59.240 40.000 0.00 0.00 35.21 3.16
180 181 6.849588 TGATCCAACGATTGATGTCTATTG 57.150 37.500 0.00 0.00 0.00 1.90
181 182 7.275183 TCTTGATCCAACGATTGATGTCTATT 58.725 34.615 0.00 0.00 0.00 1.73
182 183 6.820335 TCTTGATCCAACGATTGATGTCTAT 58.180 36.000 0.00 0.00 0.00 1.98
183 184 6.096846 TCTCTTGATCCAACGATTGATGTCTA 59.903 38.462 0.00 0.00 0.00 2.59
184 185 5.089970 TCTTGATCCAACGATTGATGTCT 57.910 39.130 0.00 0.00 0.00 3.41
185 186 5.111989 TCTCTTGATCCAACGATTGATGTC 58.888 41.667 0.00 0.00 0.00 3.06
186 187 5.089970 TCTCTTGATCCAACGATTGATGT 57.910 39.130 0.00 0.00 0.00 3.06
187 188 6.426980 TTTCTCTTGATCCAACGATTGATG 57.573 37.500 0.00 0.00 0.00 3.07
188 189 6.825213 TCATTTCTCTTGATCCAACGATTGAT 59.175 34.615 0.00 0.00 0.00 2.57
189 190 6.172630 TCATTTCTCTTGATCCAACGATTGA 58.827 36.000 0.00 0.00 0.00 2.57
190 191 6.426980 TCATTTCTCTTGATCCAACGATTG 57.573 37.500 0.00 0.00 0.00 2.67
191 192 7.362401 CCTTTCATTTCTCTTGATCCAACGATT 60.362 37.037 0.00 0.00 0.00 3.34
192 193 6.094603 CCTTTCATTTCTCTTGATCCAACGAT 59.905 38.462 0.00 0.00 0.00 3.73
193 194 5.412594 CCTTTCATTTCTCTTGATCCAACGA 59.587 40.000 0.00 0.00 0.00 3.85
194 195 5.634896 CCTTTCATTTCTCTTGATCCAACG 58.365 41.667 0.00 0.00 0.00 4.10
195 196 5.184671 AGCCTTTCATTTCTCTTGATCCAAC 59.815 40.000 0.00 0.00 0.00 3.77
196 197 5.327732 AGCCTTTCATTTCTCTTGATCCAA 58.672 37.500 0.00 0.00 0.00 3.53
197 198 4.927049 AGCCTTTCATTTCTCTTGATCCA 58.073 39.130 0.00 0.00 0.00 3.41
198 199 4.946157 TGAGCCTTTCATTTCTCTTGATCC 59.054 41.667 0.00 0.00 0.00 3.36
199 200 6.696441 ATGAGCCTTTCATTTCTCTTGATC 57.304 37.500 0.00 0.00 44.14 2.92
200 201 8.763984 AATATGAGCCTTTCATTTCTCTTGAT 57.236 30.769 0.00 0.00 44.14 2.57
201 202 7.830697 TGAATATGAGCCTTTCATTTCTCTTGA 59.169 33.333 0.00 0.00 44.14 3.02
202 203 7.993101 TGAATATGAGCCTTTCATTTCTCTTG 58.007 34.615 0.00 0.00 44.14 3.02
203 204 8.763984 ATGAATATGAGCCTTTCATTTCTCTT 57.236 30.769 0.00 0.00 44.14 2.85
204 205 8.763984 AATGAATATGAGCCTTTCATTTCTCT 57.236 30.769 4.70 0.00 44.14 3.10
209 210 7.234166 CCCCTAAATGAATATGAGCCTTTCATT 59.766 37.037 4.70 4.70 46.59 2.57
211 212 6.070656 CCCCTAAATGAATATGAGCCTTTCA 58.929 40.000 0.00 0.00 40.85 2.69
212 213 6.071320 ACCCCTAAATGAATATGAGCCTTTC 58.929 40.000 0.00 0.00 0.00 2.62
213 214 6.030727 ACCCCTAAATGAATATGAGCCTTT 57.969 37.500 0.00 0.00 0.00 3.11
214 215 5.669798 ACCCCTAAATGAATATGAGCCTT 57.330 39.130 0.00 0.00 0.00 4.35
215 216 5.852250 AGTACCCCTAAATGAATATGAGCCT 59.148 40.000 0.00 0.00 0.00 4.58
216 217 5.940470 CAGTACCCCTAAATGAATATGAGCC 59.060 44.000 0.00 0.00 0.00 4.70
217 218 6.534634 ACAGTACCCCTAAATGAATATGAGC 58.465 40.000 0.00 0.00 0.00 4.26
220 221 9.284968 CCTTTACAGTACCCCTAAATGAATATG 57.715 37.037 0.00 0.00 0.00 1.78
221 222 9.232882 TCCTTTACAGTACCCCTAAATGAATAT 57.767 33.333 0.00 0.00 0.00 1.28
222 223 8.626917 TCCTTTACAGTACCCCTAAATGAATA 57.373 34.615 0.00 0.00 0.00 1.75
223 224 7.519347 TCCTTTACAGTACCCCTAAATGAAT 57.481 36.000 0.00 0.00 0.00 2.57
224 225 6.577638 GCTCCTTTACAGTACCCCTAAATGAA 60.578 42.308 0.00 0.00 0.00 2.57
225 226 5.104652 GCTCCTTTACAGTACCCCTAAATGA 60.105 44.000 0.00 0.00 0.00 2.57
226 227 5.104485 AGCTCCTTTACAGTACCCCTAAATG 60.104 44.000 0.00 0.00 0.00 2.32
227 228 5.037598 AGCTCCTTTACAGTACCCCTAAAT 58.962 41.667 0.00 0.00 0.00 1.40
228 229 4.432316 AGCTCCTTTACAGTACCCCTAAA 58.568 43.478 0.00 0.00 0.00 1.85
229 230 4.028825 GAGCTCCTTTACAGTACCCCTAA 58.971 47.826 0.87 0.00 0.00 2.69
230 231 3.639952 GAGCTCCTTTACAGTACCCCTA 58.360 50.000 0.87 0.00 0.00 3.53
231 232 2.468915 GAGCTCCTTTACAGTACCCCT 58.531 52.381 0.87 0.00 0.00 4.79
232 233 1.136500 CGAGCTCCTTTACAGTACCCC 59.864 57.143 8.47 0.00 0.00 4.95
233 234 1.823610 ACGAGCTCCTTTACAGTACCC 59.176 52.381 8.47 0.00 0.00 3.69
234 235 3.057033 TCAACGAGCTCCTTTACAGTACC 60.057 47.826 8.47 0.00 0.00 3.34
235 236 4.082895 TCTCAACGAGCTCCTTTACAGTAC 60.083 45.833 8.47 0.00 0.00 2.73
236 237 4.077108 TCTCAACGAGCTCCTTTACAGTA 58.923 43.478 8.47 0.00 0.00 2.74
237 238 2.891580 TCTCAACGAGCTCCTTTACAGT 59.108 45.455 8.47 0.00 0.00 3.55
238 239 3.577649 TCTCAACGAGCTCCTTTACAG 57.422 47.619 8.47 1.97 0.00 2.74
239 240 4.056050 GTTTCTCAACGAGCTCCTTTACA 58.944 43.478 8.47 0.00 0.00 2.41
240 241 4.648917 GTTTCTCAACGAGCTCCTTTAC 57.351 45.455 8.47 0.00 0.00 2.01
252 253 5.178809 AGCAGGTATTGTTACGTTTCTCAAC 59.821 40.000 0.00 0.00 0.00 3.18
414 415 8.334632 CAAAAGAAATGAAGCAAACCGTAAAAT 58.665 29.630 0.00 0.00 0.00 1.82
635 636 5.371526 ACATATACTGGATTTGGACTGCAG 58.628 41.667 13.48 13.48 37.99 4.41
673 674 8.898761 TCTCTTGCTCTGTGTTACAAATTTTAA 58.101 29.630 0.00 0.00 0.00 1.52
783 784 5.191722 TCATTTATAGGCAGGACAAGAAGGT 59.808 40.000 0.00 0.00 0.00 3.50
899 900 3.452627 TCCAGTTTCAGGCTTAGATCCTC 59.547 47.826 0.00 0.00 0.00 3.71
1338 1339 5.685728 AGCTCAATAATAAGGTGTTCCTCC 58.314 41.667 0.00 0.00 44.35 4.30
1420 1423 6.491394 CGTTTCACCTGTTGTAGATGAAAAA 58.509 36.000 0.00 0.00 40.06 1.94
2199 2202 8.851541 TGTATCATGCATATAAATTGCTCTCA 57.148 30.769 0.00 0.00 40.77 3.27
2658 2672 7.944729 ATGCTCAGCCTTTTTAAGAGAATTA 57.055 32.000 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.