Multiple sequence alignment - TraesCS3A01G156500

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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 TraesCS3A01G156500 chr3A 100.000 7681 0 0 1 7681 151649636 151641956 0.000000e+00 14185.0
1 TraesCS3A01G156500 chr3A 89.947 189 14 4 156 341 124370763 124370577 9.960000e-59 239.0
2 TraesCS3A01G156500 chr3A 92.405 158 12 0 1 158 303149174 303149331 7.760000e-55 226.0
3 TraesCS3A01G156500 chr3A 84.043 94 14 1 7254 7347 329500985 329501077 1.060000e-13 89.8
4 TraesCS3A01G156500 chr3D 96.409 4539 115 21 156 4665 135873628 135869109 0.000000e+00 7435.0
5 TraesCS3A01G156500 chr3D 96.129 2790 54 9 4757 7504 135869055 135866278 0.000000e+00 4505.0
6 TraesCS3A01G156500 chr3D 87.245 196 24 1 4 198 30320460 30320265 1.000000e-53 222.0
7 TraesCS3A01G156500 chr3D 91.195 159 13 1 1 158 585980116 585979958 1.680000e-51 215.0
8 TraesCS3A01G156500 chr3D 89.431 123 8 2 7559 7681 135866281 135866164 4.800000e-32 150.0
9 TraesCS3A01G156500 chr3D 93.182 88 6 0 4866 4953 370115711 370115798 6.260000e-26 130.0
10 TraesCS3A01G156500 chr3D 85.106 94 13 1 7254 7347 228192956 228192864 2.280000e-15 95.3
11 TraesCS3A01G156500 chr3D 97.368 38 1 0 4665 4702 135869076 135869039 1.790000e-06 65.8
12 TraesCS3A01G156500 chr3B 94.840 1880 66 16 324 2179 194079424 194077552 0.000000e+00 2905.0
13 TraesCS3A01G156500 chr3B 96.952 1345 34 2 2176 3514 194077476 194076133 0.000000e+00 2250.0
14 TraesCS3A01G156500 chr3B 96.575 1197 28 4 6031 7216 194073714 194072520 0.000000e+00 1971.0
15 TraesCS3A01G156500 chr3B 94.528 1261 31 7 4756 5981 194074967 194073710 0.000000e+00 1912.0
16 TraesCS3A01G156500 chr3B 95.524 1117 43 7 3554 4665 194076134 194075020 0.000000e+00 1779.0
17 TraesCS3A01G156500 chr3B 87.555 458 37 8 7235 7681 194072251 194071803 5.320000e-141 512.0
18 TraesCS3A01G156500 chr7A 90.526 190 11 6 156 341 530471204 530471018 2.140000e-60 244.0
19 TraesCS3A01G156500 chr7A 89.947 189 14 4 156 341 184386168 184386354 9.960000e-59 239.0
20 TraesCS3A01G156500 chr7A 89.231 65 5 2 7250 7313 715942357 715942420 6.390000e-11 80.5
21 TraesCS3A01G156500 chr5A 89.947 189 14 4 156 341 166844029 166843843 9.960000e-59 239.0
22 TraesCS3A01G156500 chr4A 89.947 189 14 4 156 341 338991696 338991510 9.960000e-59 239.0
23 TraesCS3A01G156500 chr4A 89.418 189 15 4 156 341 455813981 455814167 4.630000e-57 233.0
24 TraesCS3A01G156500 chr2A 89.947 189 14 4 156 341 551029153 551028967 9.960000e-59 239.0
25 TraesCS3A01G156500 chr2A 85.345 116 14 3 4840 4954 726424209 726424322 4.870000e-22 117.0
26 TraesCS3A01G156500 chr2A 86.364 88 12 0 4868 4955 385979346 385979259 6.340000e-16 97.1
27 TraesCS3A01G156500 chr1D 93.711 159 10 0 1 159 306669687 306669845 9.960000e-59 239.0
28 TraesCS3A01G156500 chr1D 92.994 157 10 1 1 157 318557429 318557274 2.160000e-55 228.0
29 TraesCS3A01G156500 chr1D 94.186 86 5 0 4869 4954 279101376 279101461 1.740000e-26 132.0
30 TraesCS3A01G156500 chr1A 89.418 189 15 4 156 341 102588822 102588636 4.630000e-57 233.0
31 TraesCS3A01G156500 chr6A 93.548 155 10 0 1 155 550062786 550062940 1.670000e-56 231.0
32 TraesCS3A01G156500 chr6A 91.139 158 14 0 1 158 350839528 350839685 1.680000e-51 215.0
33 TraesCS3A01G156500 chr2B 91.772 158 13 0 1 158 470786212 470786055 3.610000e-53 220.0
34 TraesCS3A01G156500 chr5B 91.139 158 14 0 1 158 496093683 496093526 1.680000e-51 215.0
35 TraesCS3A01G156500 chr6D 94.186 86 4 1 4869 4954 344209392 344209476 6.260000e-26 130.0
36 TraesCS3A01G156500 chr6B 91.398 93 7 1 4863 4954 172738936 172738844 8.090000e-25 126.0
37 TraesCS3A01G156500 chr2D 92.941 85 5 1 4869 4953 425742569 425742652 1.050000e-23 122.0


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 TraesCS3A01G156500 chr3A 151641956 151649636 7680 True 14185.000000 14185 100.00000 1 7681 1 chr3A.!!$R2 7680
1 TraesCS3A01G156500 chr3D 135866164 135873628 7464 True 3038.950000 7435 94.83425 156 7681 4 chr3D.!!$R4 7525
2 TraesCS3A01G156500 chr3B 194071803 194079424 7621 True 1888.166667 2905 94.32900 324 7681 6 chr3B.!!$R1 7357

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
802 821 0.247736 GGCCGGCCTGATAGACATAG 59.752 60.000 38.76 0.0 0.00 2.23 F
803 822 0.390472 GCCGGCCTGATAGACATAGC 60.390 60.000 18.11 0.0 0.00 2.97 F
1266 1293 0.666913 GCTCCTACTTCGCCGTATCA 59.333 55.000 0.00 0.0 0.00 2.15 F
1438 1465 2.058593 TCTGCGCTTAGAGATCCTCA 57.941 50.000 9.73 0.0 32.06 3.86 F
2455 2563 2.906691 TGCCAAAATCAAACCACAGG 57.093 45.000 0.00 0.0 0.00 4.00 F
2963 3077 3.809832 GTGACATGCTCAACAGTTACACT 59.190 43.478 0.00 0.0 0.00 3.55 F
4486 4607 0.669619 GGAGTACTCTCTTAGGCGGC 59.330 60.000 21.88 0.0 40.29 6.53 F
5167 5364 0.320374 CACCTTAACTGCCAGGTCGA 59.680 55.000 0.00 0.0 41.86 4.20 F
6531 6737 1.493022 TCCACACCAAAGTAACAGCCT 59.507 47.619 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2431 3.117888 TGCCTAAAGTCCCATCCATCTTC 60.118 47.826 0.00 0.00 0.00 2.87 R
2574 2688 6.520272 GGTGCTCATCAAGACTTAGATATGT 58.480 40.000 0.00 0.00 0.00 2.29 R
3089 3203 6.270815 ACTGTCAGAATTTATCAATGCATGC 58.729 36.000 11.82 11.82 0.00 4.06 R
3497 3611 9.716507 GCGCTTTCTTCTAATACAAAATGATAA 57.283 29.630 0.00 0.00 0.00 1.75 R
3767 3881 5.049167 GCCAGTGTTTGTGAATGAAATGAA 58.951 37.500 0.00 0.00 0.00 2.57 R
4735 4890 0.747852 TTTGGAACGAAAGGGGTTGC 59.252 50.000 0.00 0.00 36.42 4.17 R
6531 6737 0.179234 TTCAAGGTTGTGGTCTGCGA 59.821 50.000 0.00 0.00 0.00 5.10 R
6537 6743 2.031870 GCCTTCTTTCAAGGTTGTGGT 58.968 47.619 2.42 0.00 39.60 4.16 R
7652 8149 0.466124 GTCAGCATCCTAGTCACCCC 59.534 60.000 0.00 0.00 0.00 4.95 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
45 46 9.952030 TGTAGTACACATGATTCCATAGAAAAA 57.048 29.630 0.00 0.00 31.04 1.94
74 75 8.972662 TCTATAGGGTTCAATCCTATGAATGA 57.027 34.615 18.45 8.86 44.68 2.57
75 76 9.392506 TCTATAGGGTTCAATCCTATGAATGAA 57.607 33.333 18.45 0.00 44.68 2.57
77 78 8.697507 ATAGGGTTCAATCCTATGAATGAAAC 57.302 34.615 8.58 5.53 44.13 2.78
78 79 5.590259 AGGGTTCAATCCTATGAATGAAACG 59.410 40.000 7.50 0.00 45.26 3.60
79 80 5.588648 GGGTTCAATCCTATGAATGAAACGA 59.411 40.000 7.50 0.00 45.26 3.85
80 81 6.458342 GGGTTCAATCCTATGAATGAAACGAC 60.458 42.308 7.50 0.00 45.26 4.34
81 82 6.458342 GGTTCAATCCTATGAATGAAACGACC 60.458 42.308 0.68 0.00 40.98 4.79
82 83 5.739959 TCAATCCTATGAATGAAACGACCA 58.260 37.500 0.00 0.00 27.44 4.02
83 84 6.176896 TCAATCCTATGAATGAAACGACCAA 58.823 36.000 0.00 0.00 27.44 3.67
84 85 6.828273 TCAATCCTATGAATGAAACGACCAAT 59.172 34.615 0.00 0.00 27.44 3.16
85 86 6.624352 ATCCTATGAATGAAACGACCAATG 57.376 37.500 0.00 0.00 0.00 2.82
86 87 5.496556 TCCTATGAATGAAACGACCAATGT 58.503 37.500 0.00 0.00 0.00 2.71
87 88 6.645306 TCCTATGAATGAAACGACCAATGTA 58.355 36.000 0.00 0.00 0.00 2.29
88 89 6.761242 TCCTATGAATGAAACGACCAATGTAG 59.239 38.462 0.00 0.00 0.00 2.74
89 90 5.818136 ATGAATGAAACGACCAATGTAGG 57.182 39.130 0.00 0.00 0.00 3.18
90 91 4.900684 TGAATGAAACGACCAATGTAGGA 58.099 39.130 0.00 0.00 0.00 2.94
91 92 5.309638 TGAATGAAACGACCAATGTAGGAA 58.690 37.500 0.00 0.00 0.00 3.36
92 93 5.765677 TGAATGAAACGACCAATGTAGGAAA 59.234 36.000 0.00 0.00 0.00 3.13
93 94 6.263392 TGAATGAAACGACCAATGTAGGAAAA 59.737 34.615 0.00 0.00 0.00 2.29
94 95 6.642707 ATGAAACGACCAATGTAGGAAAAA 57.357 33.333 0.00 0.00 0.00 1.94
95 96 6.642707 TGAAACGACCAATGTAGGAAAAAT 57.357 33.333 0.00 0.00 0.00 1.82
96 97 7.045126 TGAAACGACCAATGTAGGAAAAATT 57.955 32.000 0.00 0.00 0.00 1.82
97 98 7.142680 TGAAACGACCAATGTAGGAAAAATTC 58.857 34.615 0.00 0.00 0.00 2.17
118 119 6.963117 TTCCTAAGAATTCTAACCCTCCAA 57.037 37.500 8.75 0.00 0.00 3.53
119 120 6.963117 TCCTAAGAATTCTAACCCTCCAAA 57.037 37.500 8.75 0.00 0.00 3.28
120 121 6.718294 TCCTAAGAATTCTAACCCTCCAAAC 58.282 40.000 8.75 0.00 0.00 2.93
121 122 6.273730 TCCTAAGAATTCTAACCCTCCAAACA 59.726 38.462 8.75 0.00 0.00 2.83
122 123 7.036863 TCCTAAGAATTCTAACCCTCCAAACAT 60.037 37.037 8.75 0.00 0.00 2.71
123 124 7.283354 CCTAAGAATTCTAACCCTCCAAACATC 59.717 40.741 8.75 0.00 0.00 3.06
124 125 5.510430 AGAATTCTAACCCTCCAAACATCC 58.490 41.667 6.06 0.00 0.00 3.51
125 126 5.254032 AGAATTCTAACCCTCCAAACATCCT 59.746 40.000 6.06 0.00 0.00 3.24
126 127 6.447084 AGAATTCTAACCCTCCAAACATCCTA 59.553 38.462 6.06 0.00 0.00 2.94
127 128 6.848562 ATTCTAACCCTCCAAACATCCTAT 57.151 37.500 0.00 0.00 0.00 2.57
128 129 5.630415 TCTAACCCTCCAAACATCCTATG 57.370 43.478 0.00 0.00 0.00 2.23
129 130 3.669939 AACCCTCCAAACATCCTATGG 57.330 47.619 0.00 0.00 35.49 2.74
130 131 2.858644 ACCCTCCAAACATCCTATGGA 58.141 47.619 0.00 0.00 40.84 3.41
131 132 3.197983 ACCCTCCAAACATCCTATGGAA 58.802 45.455 0.00 0.00 42.41 3.53
132 133 3.793827 ACCCTCCAAACATCCTATGGAAT 59.206 43.478 0.00 0.00 42.41 3.01
133 134 4.232820 ACCCTCCAAACATCCTATGGAATT 59.767 41.667 0.00 0.00 42.41 2.17
134 135 4.829492 CCCTCCAAACATCCTATGGAATTC 59.171 45.833 0.00 0.00 42.41 2.17
135 136 4.829492 CCTCCAAACATCCTATGGAATTCC 59.171 45.833 18.17 18.17 42.41 3.01
136 137 5.399497 CCTCCAAACATCCTATGGAATTCCT 60.399 44.000 24.73 12.90 42.41 3.36
137 138 6.091076 TCCAAACATCCTATGGAATTCCTT 57.909 37.500 24.73 20.40 40.19 3.36
138 139 6.502138 TCCAAACATCCTATGGAATTCCTTT 58.498 36.000 24.73 14.64 40.19 3.11
139 140 6.380846 TCCAAACATCCTATGGAATTCCTTTG 59.619 38.462 24.73 20.75 40.19 2.77
140 141 6.380846 CCAAACATCCTATGGAATTCCTTTGA 59.619 38.462 24.73 17.31 36.27 2.69
141 142 7.093377 CCAAACATCCTATGGAATTCCTTTGAA 60.093 37.037 24.73 4.63 36.27 2.69
142 143 8.480501 CAAACATCCTATGGAATTCCTTTGAAT 58.519 33.333 24.73 12.14 37.41 2.57
143 144 7.830099 ACATCCTATGGAATTCCTTTGAATC 57.170 36.000 24.73 0.00 35.90 2.52
144 145 7.356680 ACATCCTATGGAATTCCTTTGAATCA 58.643 34.615 24.73 2.61 35.90 2.57
145 146 7.504911 ACATCCTATGGAATTCCTTTGAATCAG 59.495 37.037 24.73 11.36 35.90 2.90
146 147 7.211897 TCCTATGGAATTCCTTTGAATCAGA 57.788 36.000 24.73 9.17 40.34 3.27
147 148 7.285566 TCCTATGGAATTCCTTTGAATCAGAG 58.714 38.462 24.73 8.67 40.34 3.35
148 149 6.489361 CCTATGGAATTCCTTTGAATCAGAGG 59.511 42.308 24.73 13.16 40.34 3.69
149 150 5.519183 TGGAATTCCTTTGAATCAGAGGA 57.481 39.130 24.73 17.42 41.96 3.71
150 151 5.503927 TGGAATTCCTTTGAATCAGAGGAG 58.496 41.667 24.73 1.27 43.90 3.69
151 152 4.337836 GGAATTCCTTTGAATCAGAGGAGC 59.662 45.833 19.86 14.01 43.90 4.70
152 153 3.356529 TTCCTTTGAATCAGAGGAGCC 57.643 47.619 19.86 0.00 43.90 4.70
153 154 1.561542 TCCTTTGAATCAGAGGAGCCC 59.438 52.381 17.42 0.00 39.39 5.19
154 155 1.563410 CCTTTGAATCAGAGGAGCCCT 59.437 52.381 14.05 0.00 37.88 5.19
155 156 2.774234 CCTTTGAATCAGAGGAGCCCTA 59.226 50.000 14.05 0.00 37.88 3.53
156 157 3.200825 CCTTTGAATCAGAGGAGCCCTAA 59.799 47.826 14.05 0.00 37.88 2.69
157 158 4.324563 CCTTTGAATCAGAGGAGCCCTAAA 60.325 45.833 14.05 0.00 37.88 1.85
158 159 4.494091 TTGAATCAGAGGAGCCCTAAAG 57.506 45.455 0.00 0.00 31.76 1.85
159 160 2.774234 TGAATCAGAGGAGCCCTAAAGG 59.226 50.000 0.00 0.00 31.76 3.11
160 161 2.877154 ATCAGAGGAGCCCTAAAGGA 57.123 50.000 0.00 0.00 38.24 3.36
161 162 2.877154 TCAGAGGAGCCCTAAAGGAT 57.123 50.000 0.00 0.00 38.24 3.24
162 163 3.136641 TCAGAGGAGCCCTAAAGGATT 57.863 47.619 0.00 0.00 38.24 3.01
163 164 3.464828 TCAGAGGAGCCCTAAAGGATTT 58.535 45.455 0.00 0.00 43.42 2.17
164 165 3.456277 TCAGAGGAGCCCTAAAGGATTTC 59.544 47.826 0.00 0.00 40.09 2.17
165 166 3.457749 CAGAGGAGCCCTAAAGGATTTCT 59.542 47.826 0.00 0.00 40.09 2.52
166 167 4.080072 CAGAGGAGCCCTAAAGGATTTCTT 60.080 45.833 0.00 0.00 40.09 2.52
167 168 4.165180 AGAGGAGCCCTAAAGGATTTCTTC 59.835 45.833 0.00 0.00 40.09 2.87
183 184 4.771114 TTCTTCCAAGAGGTTGAAGTGA 57.229 40.909 0.00 0.00 36.22 3.41
196 197 8.360390 AGAGGTTGAAGTGAATGTTAAAATTCC 58.640 33.333 14.54 7.17 35.98 3.01
218 219 5.874810 TCCTGTGAAATGTAGTACAAGATGC 59.125 40.000 7.16 0.00 0.00 3.91
226 227 8.668510 AAATGTAGTACAAGATGCATCCTTAG 57.331 34.615 23.06 12.56 0.00 2.18
227 228 6.161855 TGTAGTACAAGATGCATCCTTAGG 57.838 41.667 23.06 10.53 0.00 2.69
233 234 7.836183 AGTACAAGATGCATCCTTAGGAAAAAT 59.164 33.333 23.06 0.00 34.34 1.82
235 236 7.550712 ACAAGATGCATCCTTAGGAAAAATTC 58.449 34.615 23.06 0.00 34.34 2.17
405 407 0.675837 TCAGCGACGCCTACTACTGT 60.676 55.000 17.79 0.00 0.00 3.55
408 410 0.381089 GCGACGCCTACTACTGTGAT 59.619 55.000 9.14 0.00 0.00 3.06
468 470 7.346175 TGCTATCAGGGTTATGGTTTTACTCTA 59.654 37.037 0.00 0.00 0.00 2.43
584 586 9.193133 CTCGGATAATCTGTAAAAACATATCGT 57.807 33.333 0.00 0.00 0.00 3.73
636 638 3.451178 ACCATATCCACTATCATACCCGC 59.549 47.826 0.00 0.00 0.00 6.13
637 639 3.181465 CCATATCCACTATCATACCCGCC 60.181 52.174 0.00 0.00 0.00 6.13
703 705 8.023128 CCGATGAATTAGTGCAAATAATAAGGG 58.977 37.037 5.99 2.03 35.85 3.95
797 816 0.472925 TAATGGGCCGGCCTGATAGA 60.473 55.000 42.70 22.69 36.10 1.98
799 818 3.161450 GGGCCGGCCTGATAGACA 61.161 66.667 42.70 0.00 36.10 3.41
800 819 2.520536 GGGCCGGCCTGATAGACAT 61.521 63.158 42.70 0.00 36.10 3.06
801 820 1.192146 GGGCCGGCCTGATAGACATA 61.192 60.000 42.70 0.00 36.10 2.29
802 821 0.247736 GGCCGGCCTGATAGACATAG 59.752 60.000 38.76 0.00 0.00 2.23
803 822 0.390472 GCCGGCCTGATAGACATAGC 60.390 60.000 18.11 0.00 0.00 2.97
830 854 4.489771 CTCCACCGGCCCATGGAC 62.490 72.222 15.22 0.00 40.17 4.02
844 868 1.061131 CATGGACAATTCGTCGACTGC 59.939 52.381 14.70 0.00 46.42 4.40
994 1021 2.743718 CAACCTGCCACCGACTCT 59.256 61.111 0.00 0.00 0.00 3.24
1263 1290 3.518003 GGCTCCTACTTCGCCGTA 58.482 61.111 0.00 0.00 33.64 4.02
1266 1293 0.666913 GCTCCTACTTCGCCGTATCA 59.333 55.000 0.00 0.00 0.00 2.15
1366 1393 2.973899 GAGGCTGGAGCTTCGACA 59.026 61.111 0.00 0.00 37.41 4.35
1438 1465 2.058593 TCTGCGCTTAGAGATCCTCA 57.941 50.000 9.73 0.00 32.06 3.86
1522 1549 4.679106 CGAGGAGTTGTCATATTGAGCTGT 60.679 45.833 0.00 0.00 0.00 4.40
1549 1576 4.037208 CAGAGAATTTGAAGTTGCACTGGT 59.963 41.667 0.00 0.00 0.00 4.00
1559 1586 5.711506 TGAAGTTGCACTGGTGATATGATTT 59.288 36.000 4.79 0.00 0.00 2.17
1601 1629 5.825593 TTGTGGGGAAGAGATCATATACC 57.174 43.478 0.00 0.00 0.00 2.73
1635 1663 9.809395 AGTAGCACTTAGTAATATACTCATGGA 57.191 33.333 0.00 0.00 40.14 3.41
1650 1678 4.785376 ACTCATGGAAGGGTCTTGAATAGT 59.215 41.667 0.00 0.00 0.00 2.12
1827 1855 3.887352 TGCGATCTAGAGGTCAGTAGTT 58.113 45.455 0.00 0.00 0.00 2.24
1886 1915 4.842531 TCTATGAACTTGGATGCCAGAA 57.157 40.909 0.00 0.00 33.81 3.02
2044 2073 7.054751 ACTTAGGAAGTCAAATATTAGGTGCC 58.945 38.462 0.00 0.00 37.02 5.01
2455 2563 2.906691 TGCCAAAATCAAACCACAGG 57.093 45.000 0.00 0.00 0.00 4.00
2574 2688 8.389779 TGTTTTAATTGTGAGAATCTAGTGCA 57.610 30.769 0.00 0.00 34.92 4.57
2591 2705 8.470657 TCTAGTGCACATATCTAAGTCTTGAT 57.529 34.615 21.04 0.00 0.00 2.57
2592 2706 8.355913 TCTAGTGCACATATCTAAGTCTTGATG 58.644 37.037 21.04 0.00 0.00 3.07
2664 2778 3.945285 TCGTGACACTGCAGATCTGTATA 59.055 43.478 23.35 9.92 0.00 1.47
2963 3077 3.809832 GTGACATGCTCAACAGTTACACT 59.190 43.478 0.00 0.00 0.00 3.55
3497 3611 4.235762 AACACGCACCTGACCGCT 62.236 61.111 0.00 0.00 0.00 5.52
3812 3926 6.043411 GGCTCTCTTCGTGTTATCTATTGTT 58.957 40.000 0.00 0.00 0.00 2.83
4183 4304 5.299531 GCCCAAATCTCTACTTCCATTAACC 59.700 44.000 0.00 0.00 0.00 2.85
4277 4398 6.706270 AGTTTACATCAGTCACTTGGTTACAG 59.294 38.462 0.00 0.00 0.00 2.74
4295 4416 9.126151 TGGTTACAGACATCACAAGATTTTAAA 57.874 29.630 0.00 0.00 30.20 1.52
4486 4607 0.669619 GGAGTACTCTCTTAGGCGGC 59.330 60.000 21.88 0.00 40.29 6.53
4570 4692 5.048224 AGAGCTGATCTGTTGTTGAATTTGG 60.048 40.000 0.00 0.00 36.69 3.28
4571 4693 3.676646 GCTGATCTGTTGTTGAATTTGGC 59.323 43.478 1.27 0.00 0.00 4.52
4694 4849 7.410800 CGTAATCCACGCTATAAAATACCAA 57.589 36.000 0.00 0.00 45.03 3.67
4695 4850 8.025243 CGTAATCCACGCTATAAAATACCAAT 57.975 34.615 0.00 0.00 45.03 3.16
4696 4851 8.166706 CGTAATCCACGCTATAAAATACCAATC 58.833 37.037 0.00 0.00 45.03 2.67
4697 4852 7.448748 AATCCACGCTATAAAATACCAATCC 57.551 36.000 0.00 0.00 0.00 3.01
4698 4853 6.182507 TCCACGCTATAAAATACCAATCCT 57.817 37.500 0.00 0.00 0.00 3.24
4699 4854 6.597562 TCCACGCTATAAAATACCAATCCTT 58.402 36.000 0.00 0.00 0.00 3.36
4700 4855 7.737869 TCCACGCTATAAAATACCAATCCTTA 58.262 34.615 0.00 0.00 0.00 2.69
4701 4856 8.380099 TCCACGCTATAAAATACCAATCCTTAT 58.620 33.333 0.00 0.00 0.00 1.73
4702 4857 9.010029 CCACGCTATAAAATACCAATCCTTATT 57.990 33.333 0.00 0.00 0.00 1.40
4710 4865 8.593945 AAAATACCAATCCTTATTCTGCTTCA 57.406 30.769 0.00 0.00 0.00 3.02
4711 4866 8.593945 AAATACCAATCCTTATTCTGCTTCAA 57.406 30.769 0.00 0.00 0.00 2.69
4712 4867 8.773033 AATACCAATCCTTATTCTGCTTCAAT 57.227 30.769 0.00 0.00 0.00 2.57
4713 4868 8.773033 ATACCAATCCTTATTCTGCTTCAATT 57.227 30.769 0.00 0.00 0.00 2.32
4714 4869 7.486407 ACCAATCCTTATTCTGCTTCAATTT 57.514 32.000 0.00 0.00 0.00 1.82
4715 4870 8.593945 ACCAATCCTTATTCTGCTTCAATTTA 57.406 30.769 0.00 0.00 0.00 1.40
4716 4871 9.205513 ACCAATCCTTATTCTGCTTCAATTTAT 57.794 29.630 0.00 0.00 0.00 1.40
4726 4881 9.617523 ATTCTGCTTCAATTTATAAAATTGGGG 57.382 29.630 19.58 14.69 38.00 4.96
4727 4882 7.047271 TCTGCTTCAATTTATAAAATTGGGGC 58.953 34.615 19.58 20.75 38.00 5.80
4728 4883 6.715280 TGCTTCAATTTATAAAATTGGGGCA 58.285 32.000 24.21 24.21 39.92 5.36
4729 4884 6.822676 TGCTTCAATTTATAAAATTGGGGCAG 59.177 34.615 24.21 16.71 38.78 4.85
4730 4885 6.260714 GCTTCAATTTATAAAATTGGGGCAGG 59.739 38.462 19.58 7.07 38.00 4.85
4731 4886 6.245890 TCAATTTATAAAATTGGGGCAGGG 57.754 37.500 19.58 0.00 38.00 4.45
4732 4887 5.131809 TCAATTTATAAAATTGGGGCAGGGG 59.868 40.000 19.58 0.00 38.00 4.79
4733 4888 2.785357 TATAAAATTGGGGCAGGGGG 57.215 50.000 0.00 0.00 0.00 5.40
4751 4906 3.362262 GGCAACCCCTTTCGTTCC 58.638 61.111 0.00 0.00 0.00 3.62
4752 4907 1.529713 GGCAACCCCTTTCGTTCCA 60.530 57.895 0.00 0.00 0.00 3.53
4753 4908 1.110518 GGCAACCCCTTTCGTTCCAA 61.111 55.000 0.00 0.00 0.00 3.53
4754 4909 0.747852 GCAACCCCTTTCGTTCCAAA 59.252 50.000 0.00 0.00 0.00 3.28
4755 4910 1.137282 GCAACCCCTTTCGTTCCAAAA 59.863 47.619 0.00 0.00 0.00 2.44
4756 4911 2.418884 GCAACCCCTTTCGTTCCAAAAA 60.419 45.455 0.00 0.00 0.00 1.94
4905 5066 8.902540 ATCATAATATAAGACGCCTTTTGACA 57.097 30.769 0.00 0.00 33.94 3.58
4906 5067 8.138365 TCATAATATAAGACGCCTTTTGACAC 57.862 34.615 0.00 0.00 33.94 3.67
4907 5068 7.985184 TCATAATATAAGACGCCTTTTGACACT 59.015 33.333 0.00 0.00 33.94 3.55
4908 5069 9.256477 CATAATATAAGACGCCTTTTGACACTA 57.744 33.333 0.00 0.00 33.94 2.74
4909 5070 9.998106 ATAATATAAGACGCCTTTTGACACTAT 57.002 29.630 0.00 0.00 33.94 2.12
4910 5071 7.715265 ATATAAGACGCCTTTTGACACTATG 57.285 36.000 0.00 0.00 33.94 2.23
4911 5072 3.678056 AGACGCCTTTTGACACTATGA 57.322 42.857 0.00 0.00 0.00 2.15
4912 5073 4.207891 AGACGCCTTTTGACACTATGAT 57.792 40.909 0.00 0.00 0.00 2.45
4999 5166 2.000447 GGTACTTTGTAGCCTTGCTCG 59.000 52.381 0.00 0.00 40.44 5.03
5167 5364 0.320374 CACCTTAACTGCCAGGTCGA 59.680 55.000 0.00 0.00 41.86 4.20
5495 5693 4.522405 TGGCATAATTACATGAAATCCCCG 59.478 41.667 0.00 0.00 0.00 5.73
5506 5704 3.476552 TGAAATCCCCGAAGTATGATGC 58.523 45.455 0.00 0.00 0.00 3.91
5518 5716 6.406737 CCGAAGTATGATGCCAGATATCTGAT 60.407 42.308 30.40 18.41 46.59 2.90
5832 6033 3.304911 TTTGGTCACCTGATCAAACCA 57.695 42.857 9.26 12.48 46.65 3.67
5925 6127 8.902540 AGAATAGTATGACACAGAACAAAACA 57.097 30.769 0.00 0.00 0.00 2.83
5945 6147 8.562892 CAAAACAAGCTCTTAAGAATGAGAAGA 58.437 33.333 15.63 0.00 0.00 2.87
6137 6339 6.012337 TCCCTTATTATCCATCTGCACAAA 57.988 37.500 0.00 0.00 0.00 2.83
6363 6569 7.687941 AATGAAGGAATTGACTCATAAACGT 57.312 32.000 0.00 0.00 0.00 3.99
6521 6727 5.241403 ACAATGAGTCTATCCACACCAAA 57.759 39.130 0.00 0.00 0.00 3.28
6531 6737 1.493022 TCCACACCAAAGTAACAGCCT 59.507 47.619 0.00 0.00 0.00 4.58
6533 6739 1.531149 CACACCAAAGTAACAGCCTCG 59.469 52.381 0.00 0.00 0.00 4.63
6537 6743 1.608025 CCAAAGTAACAGCCTCGCAGA 60.608 52.381 0.00 0.00 0.00 4.26
6624 6830 1.266178 TGATGTCCAGGAAGAAGCGA 58.734 50.000 0.00 0.00 0.00 4.93
7061 7267 7.065923 GGAGAAGTTCATATTACAACCCTGAAC 59.934 40.741 5.50 5.77 43.70 3.18
7122 7328 6.589523 TCAAAATTGTCAACTTCACAACCTTG 59.410 34.615 0.00 0.00 36.59 3.61
7147 7353 3.392769 TCCAAAACGTGACAAAAGTCG 57.607 42.857 0.00 0.00 0.00 4.18
7201 7414 3.353557 ACTACCTAGTCAGCATCGTTGA 58.646 45.455 0.00 0.00 0.00 3.18
7202 7415 3.954904 ACTACCTAGTCAGCATCGTTGAT 59.045 43.478 0.00 0.00 0.00 2.57
7218 7431 5.996644 TCGTTGATACCCATCCACTTAATT 58.003 37.500 0.00 0.00 0.00 1.40
7219 7432 5.820423 TCGTTGATACCCATCCACTTAATTG 59.180 40.000 0.00 0.00 0.00 2.32
7349 7812 5.945191 CCATTTTAGGTGAAAATTTGGCCAT 59.055 36.000 6.09 0.00 43.83 4.40
7350 7813 6.127952 CCATTTTAGGTGAAAATTTGGCCATG 60.128 38.462 6.09 0.00 43.83 3.66
7358 7844 6.128309 GGTGAAAATTTGGCCATGTAATGTTC 60.128 38.462 18.86 18.86 44.81 3.18
7419 7905 4.813027 TGAACACTACCCTCGTATTCAAC 58.187 43.478 0.00 0.00 0.00 3.18
7510 8007 7.121759 TCAAAATTGGCCAAAACAAAATCAGAA 59.878 29.630 24.71 0.00 0.00 3.02
7520 8017 9.074443 CCAAAACAAAATCAGAAAAACAAATGG 57.926 29.630 0.00 0.00 0.00 3.16
7562 8059 5.001232 TGAGCACTACCCTTGTATTCAAAC 58.999 41.667 0.00 0.00 32.87 2.93
7633 8130 4.412843 AGGAAAATACACATTCGGGGTTT 58.587 39.130 0.00 0.00 0.00 3.27
7637 8134 6.403964 GGAAAATACACATTCGGGGTTTAGTC 60.404 42.308 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.952030 TTTTTCTATGGAATCATGTGTACTACA 57.048 29.630 0.00 0.00 44.87 2.74
48 49 9.392506 TCATTCATAGGATTGAACCCTATAGAA 57.607 33.333 0.00 5.55 43.25 2.10
49 50 8.972662 TCATTCATAGGATTGAACCCTATAGA 57.027 34.615 0.00 0.00 43.25 1.98
51 52 9.793259 GTTTCATTCATAGGATTGAACCCTATA 57.207 33.333 12.74 0.00 43.25 1.31
52 53 7.445402 CGTTTCATTCATAGGATTGAACCCTAT 59.555 37.037 12.74 0.00 45.32 2.57
53 54 6.765989 CGTTTCATTCATAGGATTGAACCCTA 59.234 38.462 12.74 0.00 40.92 3.53
54 55 5.590259 CGTTTCATTCATAGGATTGAACCCT 59.410 40.000 12.74 0.00 40.92 4.34
55 56 5.588648 TCGTTTCATTCATAGGATTGAACCC 59.411 40.000 12.74 7.25 40.92 4.11
56 57 6.458342 GGTCGTTTCATTCATAGGATTGAACC 60.458 42.308 12.74 8.89 40.92 3.62
57 58 6.093495 TGGTCGTTTCATTCATAGGATTGAAC 59.907 38.462 12.74 8.49 40.92 3.18
58 59 6.176896 TGGTCGTTTCATTCATAGGATTGAA 58.823 36.000 9.88 9.88 40.03 2.69
59 60 5.739959 TGGTCGTTTCATTCATAGGATTGA 58.260 37.500 0.00 0.00 33.00 2.57
60 61 6.435430 TTGGTCGTTTCATTCATAGGATTG 57.565 37.500 0.00 0.00 0.00 2.67
61 62 6.603201 ACATTGGTCGTTTCATTCATAGGATT 59.397 34.615 0.00 0.00 0.00 3.01
62 63 6.122277 ACATTGGTCGTTTCATTCATAGGAT 58.878 36.000 0.00 0.00 0.00 3.24
63 64 5.496556 ACATTGGTCGTTTCATTCATAGGA 58.503 37.500 0.00 0.00 0.00 2.94
64 65 5.818136 ACATTGGTCGTTTCATTCATAGG 57.182 39.130 0.00 0.00 0.00 2.57
65 66 6.761242 TCCTACATTGGTCGTTTCATTCATAG 59.239 38.462 0.00 0.00 0.00 2.23
66 67 6.645306 TCCTACATTGGTCGTTTCATTCATA 58.355 36.000 0.00 0.00 0.00 2.15
67 68 5.496556 TCCTACATTGGTCGTTTCATTCAT 58.503 37.500 0.00 0.00 0.00 2.57
68 69 4.900684 TCCTACATTGGTCGTTTCATTCA 58.099 39.130 0.00 0.00 0.00 2.57
69 70 5.873179 TTCCTACATTGGTCGTTTCATTC 57.127 39.130 0.00 0.00 0.00 2.67
70 71 6.642707 TTTTCCTACATTGGTCGTTTCATT 57.357 33.333 0.00 0.00 0.00 2.57
71 72 6.642707 TTTTTCCTACATTGGTCGTTTCAT 57.357 33.333 0.00 0.00 0.00 2.57
72 73 6.642707 ATTTTTCCTACATTGGTCGTTTCA 57.357 33.333 0.00 0.00 0.00 2.69
73 74 6.584942 GGAATTTTTCCTACATTGGTCGTTTC 59.415 38.462 0.00 0.00 46.57 2.78
74 75 6.452242 GGAATTTTTCCTACATTGGTCGTTT 58.548 36.000 0.00 0.00 46.57 3.60
75 76 6.020971 GGAATTTTTCCTACATTGGTCGTT 57.979 37.500 0.00 0.00 46.57 3.85
76 77 5.638596 GGAATTTTTCCTACATTGGTCGT 57.361 39.130 0.00 0.00 46.57 4.34
94 95 7.525158 TTGGAGGGTTAGAATTCTTAGGAAT 57.475 36.000 14.36 0.00 43.26 3.01
95 96 6.963117 TTGGAGGGTTAGAATTCTTAGGAA 57.037 37.500 14.36 0.00 35.78 3.36
96 97 6.273730 TGTTTGGAGGGTTAGAATTCTTAGGA 59.726 38.462 14.36 0.00 0.00 2.94
97 98 6.481643 TGTTTGGAGGGTTAGAATTCTTAGG 58.518 40.000 14.36 0.00 0.00 2.69
98 99 7.283354 GGATGTTTGGAGGGTTAGAATTCTTAG 59.717 40.741 14.36 0.00 0.00 2.18
99 100 7.036863 AGGATGTTTGGAGGGTTAGAATTCTTA 60.037 37.037 14.36 0.70 0.00 2.10
100 101 5.952347 GGATGTTTGGAGGGTTAGAATTCTT 59.048 40.000 14.36 0.00 0.00 2.52
101 102 5.254032 AGGATGTTTGGAGGGTTAGAATTCT 59.746 40.000 13.56 13.56 0.00 2.40
102 103 5.510430 AGGATGTTTGGAGGGTTAGAATTC 58.490 41.667 0.00 0.00 0.00 2.17
103 104 5.536497 AGGATGTTTGGAGGGTTAGAATT 57.464 39.130 0.00 0.00 0.00 2.17
104 105 6.410853 CCATAGGATGTTTGGAGGGTTAGAAT 60.411 42.308 0.00 0.00 31.94 2.40
105 106 5.104109 CCATAGGATGTTTGGAGGGTTAGAA 60.104 44.000 0.00 0.00 31.94 2.10
106 107 4.412199 CCATAGGATGTTTGGAGGGTTAGA 59.588 45.833 0.00 0.00 31.94 2.10
107 108 4.412199 TCCATAGGATGTTTGGAGGGTTAG 59.588 45.833 0.00 0.00 34.65 2.34
108 109 4.376223 TCCATAGGATGTTTGGAGGGTTA 58.624 43.478 0.00 0.00 34.65 2.85
109 110 3.197983 TCCATAGGATGTTTGGAGGGTT 58.802 45.455 0.00 0.00 34.65 4.11
110 111 2.858644 TCCATAGGATGTTTGGAGGGT 58.141 47.619 0.00 0.00 34.65 4.34
111 112 3.951563 TTCCATAGGATGTTTGGAGGG 57.048 47.619 0.00 0.00 40.48 4.30
112 113 4.829492 GGAATTCCATAGGATGTTTGGAGG 59.171 45.833 20.04 0.00 40.48 4.30
113 114 5.699143 AGGAATTCCATAGGATGTTTGGAG 58.301 41.667 26.22 0.00 40.48 3.86
114 115 5.732331 AGGAATTCCATAGGATGTTTGGA 57.268 39.130 26.22 0.00 37.76 3.53
115 116 6.380846 TCAAAGGAATTCCATAGGATGTTTGG 59.619 38.462 26.22 6.34 38.89 3.28
116 117 7.408756 TCAAAGGAATTCCATAGGATGTTTG 57.591 36.000 26.22 21.64 38.89 2.93
117 118 8.613922 ATTCAAAGGAATTCCATAGGATGTTT 57.386 30.769 26.22 12.04 40.87 2.83
118 119 7.840716 TGATTCAAAGGAATTCCATAGGATGTT 59.159 33.333 26.22 6.40 43.69 2.71
119 120 7.356680 TGATTCAAAGGAATTCCATAGGATGT 58.643 34.615 26.22 9.56 43.69 3.06
120 121 7.722728 TCTGATTCAAAGGAATTCCATAGGATG 59.277 37.037 26.22 14.17 43.69 3.51
121 122 7.819500 TCTGATTCAAAGGAATTCCATAGGAT 58.180 34.615 26.22 14.31 43.69 3.24
122 123 7.211897 TCTGATTCAAAGGAATTCCATAGGA 57.788 36.000 26.22 14.38 43.69 2.94
123 124 6.489361 CCTCTGATTCAAAGGAATTCCATAGG 59.511 42.308 26.22 11.27 43.69 2.57
124 125 7.285566 TCCTCTGATTCAAAGGAATTCCATAG 58.714 38.462 26.22 14.40 43.69 2.23
125 126 7.211897 TCCTCTGATTCAAAGGAATTCCATA 57.788 36.000 26.22 5.67 43.69 2.74
126 127 6.083487 TCCTCTGATTCAAAGGAATTCCAT 57.917 37.500 26.22 12.25 43.69 3.41
127 128 5.503927 CTCCTCTGATTCAAAGGAATTCCA 58.496 41.667 26.22 5.55 43.69 3.53
128 129 4.337836 GCTCCTCTGATTCAAAGGAATTCC 59.662 45.833 17.31 17.31 43.69 3.01
129 130 4.337836 GGCTCCTCTGATTCAAAGGAATTC 59.662 45.833 9.95 0.00 43.69 2.17
130 131 4.276642 GGCTCCTCTGATTCAAAGGAATT 58.723 43.478 9.95 0.00 43.69 2.17
131 132 3.372458 GGGCTCCTCTGATTCAAAGGAAT 60.372 47.826 9.95 0.00 46.27 3.01
132 133 2.025887 GGGCTCCTCTGATTCAAAGGAA 60.026 50.000 9.95 0.00 38.69 3.36
133 134 1.561542 GGGCTCCTCTGATTCAAAGGA 59.438 52.381 8.44 8.44 37.61 3.36
134 135 1.563410 AGGGCTCCTCTGATTCAAAGG 59.437 52.381 0.00 0.00 0.00 3.11
135 136 4.494091 TTAGGGCTCCTCTGATTCAAAG 57.506 45.455 0.00 0.00 34.61 2.77
136 137 4.324563 CCTTTAGGGCTCCTCTGATTCAAA 60.325 45.833 0.00 0.00 34.61 2.69
137 138 3.200825 CCTTTAGGGCTCCTCTGATTCAA 59.799 47.826 0.00 0.00 34.61 2.69
138 139 2.774234 CCTTTAGGGCTCCTCTGATTCA 59.226 50.000 0.00 0.00 34.61 2.57
139 140 3.041946 TCCTTTAGGGCTCCTCTGATTC 58.958 50.000 0.00 0.00 34.61 2.52
140 141 3.136641 TCCTTTAGGGCTCCTCTGATT 57.863 47.619 0.00 0.00 34.61 2.57
141 142 2.877154 TCCTTTAGGGCTCCTCTGAT 57.123 50.000 0.00 0.00 34.61 2.90
142 143 2.877154 ATCCTTTAGGGCTCCTCTGA 57.123 50.000 0.00 0.00 34.61 3.27
143 144 3.457749 AGAAATCCTTTAGGGCTCCTCTG 59.542 47.826 0.00 0.00 34.61 3.35
144 145 3.741955 AGAAATCCTTTAGGGCTCCTCT 58.258 45.455 0.00 0.00 34.61 3.69
145 146 4.456535 GAAGAAATCCTTTAGGGCTCCTC 58.543 47.826 0.00 0.00 34.68 3.71
146 147 3.203263 GGAAGAAATCCTTTAGGGCTCCT 59.797 47.826 0.00 0.00 45.56 3.69
147 148 3.556999 GGAAGAAATCCTTTAGGGCTCC 58.443 50.000 0.00 0.00 45.56 4.70
159 160 5.765182 TCACTTCAACCTCTTGGAAGAAATC 59.235 40.000 7.54 0.00 34.03 2.17
160 161 5.694995 TCACTTCAACCTCTTGGAAGAAAT 58.305 37.500 7.54 0.00 34.03 2.17
161 162 5.110814 TCACTTCAACCTCTTGGAAGAAA 57.889 39.130 7.54 0.00 34.03 2.52
162 163 4.771114 TCACTTCAACCTCTTGGAAGAA 57.229 40.909 7.54 0.00 34.03 2.52
163 164 4.771114 TTCACTTCAACCTCTTGGAAGA 57.229 40.909 7.54 0.00 37.04 2.87
164 165 4.823989 ACATTCACTTCAACCTCTTGGAAG 59.176 41.667 0.00 0.00 37.04 3.46
165 166 4.792068 ACATTCACTTCAACCTCTTGGAA 58.208 39.130 0.00 0.00 37.04 3.53
166 167 4.437682 ACATTCACTTCAACCTCTTGGA 57.562 40.909 0.00 0.00 37.04 3.53
167 168 6.633500 TTAACATTCACTTCAACCTCTTGG 57.367 37.500 0.00 0.00 39.83 3.61
196 197 6.726258 TGCATCTTGTACTACATTTCACAG 57.274 37.500 0.00 0.00 0.00 3.66
335 336 4.701171 ACTCTTCACTCTACGTCTTTAGGG 59.299 45.833 0.00 0.00 0.00 3.53
336 337 5.632959 CACTCTTCACTCTACGTCTTTAGG 58.367 45.833 0.00 0.00 0.00 2.69
338 339 4.517832 TGCACTCTTCACTCTACGTCTTTA 59.482 41.667 0.00 0.00 0.00 1.85
339 340 3.318275 TGCACTCTTCACTCTACGTCTTT 59.682 43.478 0.00 0.00 0.00 2.52
392 394 1.749634 GGTCATCACAGTAGTAGGCGT 59.250 52.381 0.00 0.00 0.00 5.68
405 407 3.500299 CACAATTACAACCGTGGTCATCA 59.500 43.478 0.00 0.00 0.00 3.07
408 410 2.222886 CCACAATTACAACCGTGGTCA 58.777 47.619 0.00 0.00 43.23 4.02
417 419 7.389330 CACCTTAGTGTATGACCACAATTACAA 59.611 37.037 0.00 0.00 39.30 2.41
584 586 9.529823 AGTAATATCCGACAGGTGAGAATTATA 57.470 33.333 0.00 0.00 39.05 0.98
595 597 5.977489 TGGTATCAGTAATATCCGACAGG 57.023 43.478 0.00 0.00 39.46 4.00
597 599 8.234136 GGATATGGTATCAGTAATATCCGACA 57.766 38.462 5.12 0.00 40.52 4.35
687 689 2.687935 CCGCACCCTTATTATTTGCACT 59.312 45.455 0.00 0.00 32.51 4.40
703 705 5.003804 AGGTATGGATAATTTCATCCGCAC 58.996 41.667 3.35 3.63 46.51 5.34
741 752 7.549134 TCGCTGCTAAATGGTATGGATAATAAG 59.451 37.037 0.00 0.00 0.00 1.73
777 796 0.400213 CTATCAGGCCGGCCCATTAA 59.600 55.000 41.72 22.53 36.58 1.40
797 816 1.028905 GGAGAGCACGAGAGCTATGT 58.971 55.000 0.00 0.00 46.75 2.29
799 818 1.028905 GTGGAGAGCACGAGAGCTAT 58.971 55.000 0.00 0.00 46.75 2.97
800 819 1.032657 GGTGGAGAGCACGAGAGCTA 61.033 60.000 0.00 0.00 46.75 3.32
802 821 2.183046 GGTGGAGAGCACGAGAGC 59.817 66.667 0.00 0.00 0.00 4.09
803 822 2.487428 CGGTGGAGAGCACGAGAG 59.513 66.667 0.00 0.00 0.00 3.20
830 854 0.165944 GTTGGGCAGTCGACGAATTG 59.834 55.000 10.46 3.89 0.00 2.32
844 868 1.526575 AAGTGCGGCAAGATGTTGGG 61.527 55.000 3.23 0.00 33.87 4.12
1438 1465 4.250464 TCACATCGAACCGCTCTAAAAAT 58.750 39.130 0.00 0.00 0.00 1.82
1481 1508 4.138290 CCTCGGATCACATCTACACTAGT 58.862 47.826 0.00 0.00 0.00 2.57
1522 1549 2.297033 GCAACTTCAAATTCTCTGCCCA 59.703 45.455 0.00 0.00 0.00 5.36
1549 1576 4.717877 AGCAACGGGATCAAATCATATCA 58.282 39.130 0.00 0.00 0.00 2.15
1559 1586 2.559698 TCTCAAAAGCAACGGGATCA 57.440 45.000 0.00 0.00 0.00 2.92
1601 1629 1.336887 ACTAAGTGCTACTGTGCCACG 60.337 52.381 6.90 0.00 0.00 4.94
1635 1663 5.514500 TTAGCCAACTATTCAAGACCCTT 57.486 39.130 0.00 0.00 0.00 3.95
1650 1678 6.439375 TGAGTAAAGGTCAGTCTATTAGCCAA 59.561 38.462 0.00 0.00 0.00 4.52
1752 1780 5.581085 AGAAACGGCACATTCTATAACAGTC 59.419 40.000 0.00 0.00 33.31 3.51
1827 1855 4.081406 ACACTTGAAGAAATGGCTATGCA 58.919 39.130 0.00 0.00 0.00 3.96
1996 2025 5.643777 GTCACCACTACAATTCTGCAAGTAT 59.356 40.000 0.00 0.00 33.76 2.12
2323 2431 3.117888 TGCCTAAAGTCCCATCCATCTTC 60.118 47.826 0.00 0.00 0.00 2.87
2455 2563 8.076178 GCGAATTGGGTGATAATATATTATGGC 58.924 37.037 20.31 12.79 33.37 4.40
2574 2688 6.520272 GGTGCTCATCAAGACTTAGATATGT 58.480 40.000 0.00 0.00 0.00 2.29
3089 3203 6.270815 ACTGTCAGAATTTATCAATGCATGC 58.729 36.000 11.82 11.82 0.00 4.06
3497 3611 9.716507 GCGCTTTCTTCTAATACAAAATGATAA 57.283 29.630 0.00 0.00 0.00 1.75
3767 3881 5.049167 GCCAGTGTTTGTGAATGAAATGAA 58.951 37.500 0.00 0.00 0.00 2.57
3812 3926 7.618512 AGAGTTGAAATAGTAAGGTGGTAGCTA 59.381 37.037 0.00 0.00 0.00 3.32
4183 4304 6.141685 CACGACCGGAGTTTCTTTAATTTTTG 59.858 38.462 9.46 0.00 0.00 2.44
4486 4607 5.902613 TTATCAGGAACATCCAAAAGCAG 57.097 39.130 0.00 0.00 39.61 4.24
4570 4692 5.124457 ACCAGTCAGATGTGAAATGTATTGC 59.876 40.000 0.00 0.00 33.27 3.56
4571 4693 6.748333 ACCAGTCAGATGTGAAATGTATTG 57.252 37.500 0.00 0.00 33.27 1.90
4690 4845 7.486407 AAATTGAAGCAGAATAAGGATTGGT 57.514 32.000 0.00 0.00 0.00 3.67
4700 4855 9.617523 CCCCAATTTTATAAATTGAAGCAGAAT 57.382 29.630 20.65 0.00 39.36 2.40
4701 4856 7.552330 GCCCCAATTTTATAAATTGAAGCAGAA 59.448 33.333 20.65 0.00 39.36 3.02
4702 4857 7.047271 GCCCCAATTTTATAAATTGAAGCAGA 58.953 34.615 20.65 0.00 39.36 4.26
4703 4858 6.822676 TGCCCCAATTTTATAAATTGAAGCAG 59.177 34.615 22.99 11.22 38.88 4.24
4704 4859 6.715280 TGCCCCAATTTTATAAATTGAAGCA 58.285 32.000 22.99 22.99 40.12 3.91
4705 4860 6.260714 CCTGCCCCAATTTTATAAATTGAAGC 59.739 38.462 20.65 20.41 39.36 3.86
4706 4861 6.767423 CCCTGCCCCAATTTTATAAATTGAAG 59.233 38.462 20.65 14.07 39.36 3.02
4707 4862 6.353429 CCCCTGCCCCAATTTTATAAATTGAA 60.353 38.462 20.65 7.46 39.36 2.69
4708 4863 5.131809 CCCCTGCCCCAATTTTATAAATTGA 59.868 40.000 20.65 5.54 39.36 2.57
4709 4864 5.375773 CCCCTGCCCCAATTTTATAAATTG 58.624 41.667 14.79 14.79 37.38 2.32
4710 4865 4.415179 CCCCCTGCCCCAATTTTATAAATT 59.585 41.667 0.00 0.00 0.00 1.82
4711 4866 3.980022 CCCCCTGCCCCAATTTTATAAAT 59.020 43.478 0.00 0.00 0.00 1.40
4712 4867 3.388913 CCCCCTGCCCCAATTTTATAAA 58.611 45.455 0.00 0.00 0.00 1.40
4713 4868 3.053359 CCCCCTGCCCCAATTTTATAA 57.947 47.619 0.00 0.00 0.00 0.98
4714 4869 2.785357 CCCCCTGCCCCAATTTTATA 57.215 50.000 0.00 0.00 0.00 0.98
4715 4870 3.652886 CCCCCTGCCCCAATTTTAT 57.347 52.632 0.00 0.00 0.00 1.40
4733 4888 2.273179 GGAACGAAAGGGGTTGCCC 61.273 63.158 0.00 0.00 44.51 5.36
4734 4889 1.110518 TTGGAACGAAAGGGGTTGCC 61.111 55.000 0.00 0.00 35.19 4.52
4735 4890 0.747852 TTTGGAACGAAAGGGGTTGC 59.252 50.000 0.00 0.00 36.42 4.17
4736 4891 3.528597 TTTTTGGAACGAAAGGGGTTG 57.471 42.857 0.00 0.00 0.00 3.77
4854 5009 7.057894 ACGGAGGGAGTATAAATTAATTGCAA 58.942 34.615 0.00 0.00 0.00 4.08
4999 5166 7.973944 GGATATTTGTAAGGTTCCAAACACATC 59.026 37.037 0.00 0.00 33.73 3.06
5495 5693 8.789825 AAATCAGATATCTGGCATCATACTTC 57.210 34.615 28.30 0.00 43.91 3.01
5506 5704 7.636150 AAACTCCACAAAATCAGATATCTGG 57.364 36.000 28.30 16.32 43.91 3.86
5518 5716 9.855021 CTAGAAGAAAAGAAAAACTCCACAAAA 57.145 29.630 0.00 0.00 0.00 2.44
5831 6032 7.292292 CACTCCAATAAACAAAAATGCATGTG 58.708 34.615 0.00 1.49 0.00 3.21
5832 6033 6.427547 CCACTCCAATAAACAAAAATGCATGT 59.572 34.615 0.00 0.00 0.00 3.21
5923 6125 9.377312 GTTATCTTCTCATTCTTAAGAGCTTGT 57.623 33.333 5.12 0.00 33.05 3.16
5925 6127 8.767436 AGGTTATCTTCTCATTCTTAAGAGCTT 58.233 33.333 5.12 0.00 33.05 3.74
6137 6339 2.239907 GGTAGGAAGGGAAGAACTGCAT 59.760 50.000 0.00 0.00 0.00 3.96
6363 6569 4.136796 AGCAGCATTCAAGTAACTTGTCA 58.863 39.130 0.00 0.00 41.66 3.58
6521 6727 1.185618 TGGTCTGCGAGGCTGTTACT 61.186 55.000 0.00 0.00 0.00 2.24
6531 6737 0.179234 TTCAAGGTTGTGGTCTGCGA 59.821 50.000 0.00 0.00 0.00 5.10
6533 6739 2.297701 TCTTTCAAGGTTGTGGTCTGC 58.702 47.619 0.00 0.00 0.00 4.26
6537 6743 2.031870 GCCTTCTTTCAAGGTTGTGGT 58.968 47.619 2.42 0.00 39.60 4.16
6624 6830 2.755469 GGGTGACATTGGCGGCAT 60.755 61.111 14.32 0.00 0.00 4.40
6758 6964 4.177026 AGACGAGATGTATGTGCTCAAAC 58.823 43.478 0.00 0.00 0.00 2.93
7089 7295 7.754924 GTGAAGTTGACAATTTTGAAGTTCAGA 59.245 33.333 12.49 0.00 36.17 3.27
7091 7297 7.374272 TGTGAAGTTGACAATTTTGAAGTTCA 58.626 30.769 9.21 9.21 34.59 3.18
7122 7328 5.158494 ACTTTTGTCACGTTTTGGAACTTC 58.842 37.500 0.00 0.00 33.51 3.01
7147 7353 5.830000 AACCAGTCAAAACTAAACCAGTC 57.170 39.130 0.00 0.00 36.04 3.51
7520 8017 9.038803 AGTGCTCATTTTTGAGATTTTTCTTTC 57.961 29.630 7.16 0.00 38.13 2.62
7524 8021 7.329471 GGGTAGTGCTCATTTTTGAGATTTTTC 59.671 37.037 7.16 0.00 38.13 2.29
7533 8030 4.853924 ACAAGGGTAGTGCTCATTTTTG 57.146 40.909 0.00 0.00 0.00 2.44
7534 8031 6.719370 TGAATACAAGGGTAGTGCTCATTTTT 59.281 34.615 0.00 0.00 31.88 1.94
7542 8039 4.156008 CCAGTTTGAATACAAGGGTAGTGC 59.844 45.833 0.00 0.00 37.32 4.40
7547 8044 4.463050 TTCCCAGTTTGAATACAAGGGT 57.537 40.909 0.00 0.00 38.97 4.34
7602 8099 9.855021 CCGAATGTGTATTTTCCTTCTAATTTT 57.145 29.630 0.00 0.00 0.00 1.82
7603 8100 8.466798 CCCGAATGTGTATTTTCCTTCTAATTT 58.533 33.333 0.00 0.00 0.00 1.82
7606 8103 5.883673 CCCCGAATGTGTATTTTCCTTCTAA 59.116 40.000 0.00 0.00 0.00 2.10
7607 8104 5.045432 ACCCCGAATGTGTATTTTCCTTCTA 60.045 40.000 0.00 0.00 0.00 2.10
7608 8105 4.263771 ACCCCGAATGTGTATTTTCCTTCT 60.264 41.667 0.00 0.00 0.00 2.85
7609 8106 4.014406 ACCCCGAATGTGTATTTTCCTTC 58.986 43.478 0.00 0.00 0.00 3.46
7627 8124 0.906282 TCACCCTCCGACTAAACCCC 60.906 60.000 0.00 0.00 0.00 4.95
7633 8130 1.592400 CGCAAGTCACCCTCCGACTA 61.592 60.000 0.00 0.00 42.90 2.59
7637 8134 4.760047 CCCGCAAGTCACCCTCCG 62.760 72.222 0.00 0.00 0.00 4.63
7652 8149 0.466124 GTCAGCATCCTAGTCACCCC 59.534 60.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.