Multiple sequence alignment - TraesCS4A01G117700

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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 TraesCS4A01G117700 chr4A 100.000 8668 0 0 1 8668 143704532 143695865 0.000000e+00 16007.0
1 TraesCS4A01G117700 chr4A 81.265 427 55 14 3022 3426 452349121 452348698 1.090000e-83 322.0
2 TraesCS4A01G117700 chr4D 95.731 6747 175 55 308 7004 327376808 327383491 0.000000e+00 10759.0
3 TraesCS4A01G117700 chr4D 97.137 1502 38 4 7171 8668 327383620 327385120 0.000000e+00 2531.0
4 TraesCS4A01G117700 chr4D 79.582 431 59 17 3022 3426 120884791 120884364 1.840000e-71 281.0
5 TraesCS4A01G117700 chr4D 86.058 208 25 4 8405 8611 461413476 461413272 4.070000e-53 220.0
6 TraesCS4A01G117700 chr4D 90.769 130 11 1 1 129 327376422 327376551 1.160000e-38 172.0
7 TraesCS4A01G117700 chr4D 88.489 139 12 2 120 254 401368556 401368418 1.940000e-36 165.0
8 TraesCS4A01G117700 chr4D 94.595 74 4 0 249 322 327376549 327376622 1.980000e-21 115.0
9 TraesCS4A01G117700 chr4B 95.482 6330 185 48 582 6859 406675312 406681592 0.000000e+00 10011.0
10 TraesCS4A01G117700 chr4B 91.960 1194 70 13 7480 8667 406682399 406683572 0.000000e+00 1650.0
11 TraesCS4A01G117700 chr4B 90.962 343 20 4 249 584 406674661 406674999 1.330000e-122 451.0
12 TraesCS4A01G117700 chr4B 87.179 273 19 5 7217 7488 406681822 406682079 6.580000e-76 296.0
13 TraesCS4A01G117700 chr4B 92.800 125 9 0 5 129 406674539 406674663 1.920000e-41 182.0
14 TraesCS4A01G117700 chr4B 96.552 87 3 0 7171 7257 406681737 406681823 2.520000e-30 145.0
15 TraesCS4A01G117700 chr5B 83.014 418 49 15 3023 3423 340615291 340615703 8.270000e-95 359.0
16 TraesCS4A01G117700 chr5B 78.520 419 61 21 3024 3432 293509201 293508802 1.870000e-61 248.0
17 TraesCS4A01G117700 chr5B 91.453 117 9 1 119 235 587718385 587718500 9.010000e-35 159.0
18 TraesCS4A01G117700 chr5B 87.302 126 12 4 3299 3423 391638988 391638866 3.260000e-29 141.0
19 TraesCS4A01G117700 chr5B 94.444 54 0 3 6806 6859 215889683 215889733 7.210000e-11 80.5
20 TraesCS4A01G117700 chr5B 92.727 55 3 1 6798 6852 694237506 694237559 2.590000e-10 78.7
21 TraesCS4A01G117700 chr5D 82.767 412 49 16 3022 3415 350373564 350373971 1.790000e-91 348.0
22 TraesCS4A01G117700 chr5D 82.185 421 37 18 3023 3422 281011055 281011458 2.330000e-85 327.0
23 TraesCS4A01G117700 chr5D 92.000 100 6 2 7081 7179 77746218 77746316 1.170000e-28 139.0
24 TraesCS4A01G117700 chr3B 82.775 418 45 15 3026 3423 544546254 544545844 1.790000e-91 348.0
25 TraesCS4A01G117700 chr3B 88.824 170 16 3 8492 8659 534107120 534106952 1.140000e-48 206.0
26 TraesCS4A01G117700 chr3B 91.453 117 9 1 119 235 633678228 633678343 9.010000e-35 159.0
27 TraesCS4A01G117700 chr3B 88.321 137 11 3 119 251 643759010 643758875 9.010000e-35 159.0
28 TraesCS4A01G117700 chr3B 88.321 137 11 3 119 251 677859836 677859701 9.010000e-35 159.0
29 TraesCS4A01G117700 chr2B 82.118 425 52 15 3017 3422 415997287 415996868 8.330000e-90 342.0
30 TraesCS4A01G117700 chr2B 93.258 89 6 0 7084 7172 453811095 453811183 1.960000e-26 132.0
31 TraesCS4A01G117700 chr2B 92.727 55 1 3 6805 6859 764153227 764153278 9.330000e-10 76.8
32 TraesCS4A01G117700 chr5A 81.418 409 53 17 3026 3417 564772269 564772671 6.530000e-81 313.0
33 TraesCS4A01G117700 chr2A 85.765 281 34 5 3024 3299 619858023 619858302 8.510000e-75 292.0
34 TraesCS4A01G117700 chr7A 79.707 409 65 12 3021 3422 596690171 596689774 6.630000e-71 279.0
35 TraesCS4A01G117700 chr3D 91.620 179 12 3 8492 8668 28378539 28378362 2.420000e-60 244.0
36 TraesCS4A01G117700 chr3D 93.750 96 5 1 7079 7173 135380742 135380837 9.070000e-30 143.0
37 TraesCS4A01G117700 chr6B 78.014 423 63 15 3023 3427 68295111 68294701 1.120000e-58 239.0
38 TraesCS4A01G117700 chr2D 78.734 395 57 18 3044 3419 137813641 137813255 1.120000e-58 239.0
39 TraesCS4A01G117700 chr2D 90.000 140 8 3 117 251 451959036 451958898 8.940000e-40 176.0
40 TraesCS4A01G117700 chr1D 90.299 134 9 1 124 253 299268551 299268418 1.160000e-38 172.0
41 TraesCS4A01G117700 chr1D 92.174 115 9 0 121 235 47651446 47651560 6.960000e-36 163.0
42 TraesCS4A01G117700 chr1D 94.624 93 5 0 7087 7179 93124875 93124783 2.520000e-30 145.0
43 TraesCS4A01G117700 chrUn 90.769 130 8 1 127 252 108731160 108731289 4.160000e-38 171.0
44 TraesCS4A01G117700 chrUn 90.090 111 10 1 7081 7190 222975763 222975873 9.070000e-30 143.0
45 TraesCS4A01G117700 chrUn 90.090 111 10 1 7081 7190 303647897 303648007 9.070000e-30 143.0
46 TraesCS4A01G117700 chr1B 82.609 207 22 7 8451 8655 302792280 302792474 4.160000e-38 171.0
47 TraesCS4A01G117700 chr7D 94.898 98 4 1 7087 7184 22964342 22964246 1.510000e-32 152.0
48 TraesCS4A01G117700 chr7D 90.090 111 10 1 7081 7190 624842027 624842137 9.070000e-30 143.0
49 TraesCS4A01G117700 chr7D 92.079 101 6 1 7076 7176 79628438 79628340 3.260000e-29 141.0
50 TraesCS4A01G117700 chr6D 94.444 54 0 3 6806 6859 304279412 304279462 7.210000e-11 80.5
51 TraesCS4A01G117700 chr6D 94.340 53 0 3 6806 6858 292073372 292073421 2.590000e-10 78.7
52 TraesCS4A01G117700 chr6D 92.727 55 1 3 6805 6859 292073458 292073407 9.330000e-10 76.8
53 TraesCS4A01G117700 chr1A 92.593 54 3 1 6806 6859 245526650 245526598 9.330000e-10 76.8
54 TraesCS4A01G117700 chr1A 91.379 58 2 3 6802 6859 298608495 298608441 9.330000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G117700 chr4A 143695865 143704532 8667 True 16007.00 16007 100.000000 1 8668 1 chr4A.!!$R1 8667
1 TraesCS4A01G117700 chr4D 327376422 327385120 8698 False 3394.25 10759 94.558000 1 8668 4 chr4D.!!$F1 8667
2 TraesCS4A01G117700 chr4B 406674539 406683572 9033 False 2122.50 10011 92.489167 5 8667 6 chr4B.!!$F1 8662

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
726 1262 0.036875 AAGACAAGGAAAGGCGGAGG 59.963 55.000 0.00 0.0 0.00 4.30 F
728 1264 0.391793 GACAAGGAAAGGCGGAGGAG 60.392 60.000 0.00 0.0 0.00 3.69 F
1981 2538 0.322456 CAATGAACGAGGGGGAAGCA 60.322 55.000 0.00 0.0 0.00 3.91 F
3141 3708 0.835971 AAAACCTGGGTGCCCAATCC 60.836 55.000 11.54 0.0 46.63 3.01 F
3159 3726 1.210967 TCCACTCCCGTGTGAAGTTTT 59.789 47.619 0.00 0.0 40.12 2.43 F
4020 4607 4.265073 GCTCTGTTCTTGATGGGTACAAT 58.735 43.478 0.00 0.0 0.00 2.71 F
5317 5914 3.009723 ACAATCGCTGTTACCATTCAGG 58.990 45.455 0.00 0.0 38.20 3.86 F
5764 6361 1.115467 CTCCTTCGTGGCCAGATAGT 58.885 55.000 5.11 0.0 35.26 2.12 F
7004 7689 1.475403 AGTACTCACTCCGTCCCATG 58.525 55.000 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2484 1.353091 AAGGCTCCGAGTTCTTCCTT 58.647 50.000 0.00 0.00 0.00 3.36 R
2014 2571 1.452110 TGTCACCGCAATCAAGATGG 58.548 50.000 0.00 0.00 0.00 3.51 R
3186 3753 3.526931 TCAGACTATTTCCTTCGCCAG 57.473 47.619 0.00 0.00 0.00 4.85 R
4764 5359 2.682563 GCCACGGATAATGTTCCCTGAA 60.683 50.000 0.00 0.00 31.61 3.02 R
5310 5907 5.007626 TGTTTTCAGTCGAGAAACCTGAATG 59.992 40.000 14.07 0.00 42.84 2.67 R
5452 6049 0.178964 AAGTTAGCTTGGCCAGGCAA 60.179 50.000 37.69 26.34 35.69 4.52 R
6999 7684 0.031111 TACTCCCTCTGTCCCATGGG 60.031 60.000 26.30 26.30 40.95 4.00 R
7151 7880 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.000 0.00 0.00 0.00 0.98 R
8537 9626 0.722848 CCGAACCGAACGTAAATGGG 59.277 55.000 0.00 0.00 0.00 4.00 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
22 24 4.397420 TGGCAAAAGCATCTTGACTAAGA 58.603 39.130 0.00 0.00 46.32 2.10
53 55 7.468084 GCTTGAACCAAACACACTCATAAGTTA 60.468 37.037 0.00 0.00 31.71 2.24
55 57 8.282455 TGAACCAAACACACTCATAAGTTAAA 57.718 30.769 0.00 0.00 31.71 1.52
60 62 7.586300 CCAAACACACTCATAAGTTAAACGAAG 59.414 37.037 0.00 0.00 31.71 3.79
68 70 7.117379 ACTCATAAGTTAAACGAAGTTGCCTAC 59.883 37.037 0.00 0.00 41.51 3.18
81 83 3.291611 CCTACGGTTAGGCGTGGT 58.708 61.111 0.00 0.00 38.72 4.16
126 128 8.256605 TCACAAACCAAACATCCCATTAATATG 58.743 33.333 0.00 0.00 0.00 1.78
127 129 8.040132 CACAAACCAAACATCCCATTAATATGT 58.960 33.333 0.00 0.00 35.40 2.29
128 130 9.261035 ACAAACCAAACATCCCATTAATATGTA 57.739 29.630 3.36 0.00 33.59 2.29
132 134 9.088987 ACCAAACATCCCATTAATATGTATTCC 57.911 33.333 3.36 0.00 33.59 3.01
133 135 8.531146 CCAAACATCCCATTAATATGTATTCCC 58.469 37.037 3.36 0.00 33.59 3.97
134 136 9.312904 CAAACATCCCATTAATATGTATTCCCT 57.687 33.333 3.36 0.00 33.59 4.20
135 137 9.897040 AAACATCCCATTAATATGTATTCCCTT 57.103 29.630 3.36 0.00 33.59 3.95
136 138 9.533831 AACATCCCATTAATATGTATTCCCTTC 57.466 33.333 3.36 0.00 33.59 3.46
137 139 7.829211 ACATCCCATTAATATGTATTCCCTTCG 59.171 37.037 1.28 0.00 32.21 3.79
138 140 7.324388 TCCCATTAATATGTATTCCCTTCGT 57.676 36.000 0.00 0.00 0.00 3.85
139 141 7.751646 TCCCATTAATATGTATTCCCTTCGTT 58.248 34.615 0.00 0.00 0.00 3.85
140 142 7.881232 TCCCATTAATATGTATTCCCTTCGTTC 59.119 37.037 0.00 0.00 0.00 3.95
141 143 7.120726 CCCATTAATATGTATTCCCTTCGTTCC 59.879 40.741 0.00 0.00 0.00 3.62
142 144 7.663905 CCATTAATATGTATTCCCTTCGTTCCA 59.336 37.037 0.00 0.00 0.00 3.53
143 145 8.504005 CATTAATATGTATTCCCTTCGTTCCAC 58.496 37.037 0.00 0.00 0.00 4.02
144 146 3.992943 ATGTATTCCCTTCGTTCCACA 57.007 42.857 0.00 0.00 0.00 4.17
145 147 3.773418 TGTATTCCCTTCGTTCCACAA 57.227 42.857 0.00 0.00 0.00 3.33
146 148 4.295141 TGTATTCCCTTCGTTCCACAAT 57.705 40.909 0.00 0.00 0.00 2.71
147 149 5.423704 TGTATTCCCTTCGTTCCACAATA 57.576 39.130 0.00 0.00 0.00 1.90
148 150 5.180271 TGTATTCCCTTCGTTCCACAATAC 58.820 41.667 0.00 0.00 0.00 1.89
149 151 3.773418 TTCCCTTCGTTCCACAATACA 57.227 42.857 0.00 0.00 0.00 2.29
150 152 3.992943 TCCCTTCGTTCCACAATACAT 57.007 42.857 0.00 0.00 0.00 2.29
151 153 3.605634 TCCCTTCGTTCCACAATACATG 58.394 45.455 0.00 0.00 0.00 3.21
152 154 2.097466 CCCTTCGTTCCACAATACATGC 59.903 50.000 0.00 0.00 0.00 4.06
153 155 2.097466 CCTTCGTTCCACAATACATGCC 59.903 50.000 0.00 0.00 0.00 4.40
154 156 2.779755 TCGTTCCACAATACATGCCT 57.220 45.000 0.00 0.00 0.00 4.75
155 157 3.066291 TCGTTCCACAATACATGCCTT 57.934 42.857 0.00 0.00 0.00 4.35
156 158 3.417101 TCGTTCCACAATACATGCCTTT 58.583 40.909 0.00 0.00 0.00 3.11
157 159 3.438781 TCGTTCCACAATACATGCCTTTC 59.561 43.478 0.00 0.00 0.00 2.62
158 160 3.190327 CGTTCCACAATACATGCCTTTCA 59.810 43.478 0.00 0.00 0.00 2.69
159 161 4.142403 CGTTCCACAATACATGCCTTTCAT 60.142 41.667 0.00 0.00 35.31 2.57
160 162 5.622007 CGTTCCACAATACATGCCTTTCATT 60.622 40.000 0.00 0.00 31.79 2.57
161 163 5.999205 TCCACAATACATGCCTTTCATTT 57.001 34.783 0.00 0.00 31.79 2.32
162 164 7.319646 GTTCCACAATACATGCCTTTCATTTA 58.680 34.615 0.00 0.00 31.79 1.40
163 165 7.658525 TCCACAATACATGCCTTTCATTTAT 57.341 32.000 0.00 0.00 31.28 1.40
164 166 7.715657 TCCACAATACATGCCTTTCATTTATC 58.284 34.615 0.00 0.00 29.29 1.75
165 167 7.341512 TCCACAATACATGCCTTTCATTTATCA 59.658 33.333 0.00 0.00 29.29 2.15
166 168 7.980662 CCACAATACATGCCTTTCATTTATCAA 59.019 33.333 0.00 0.00 29.29 2.57
167 169 9.368674 CACAATACATGCCTTTCATTTATCAAA 57.631 29.630 0.00 0.00 29.29 2.69
168 170 9.941325 ACAATACATGCCTTTCATTTATCAAAA 57.059 25.926 0.00 0.00 29.29 2.44
224 226 9.874205 ATAGGTACATCCATTTTTGAACAAATG 57.126 29.630 0.00 0.04 41.86 2.32
234 236 8.200364 CATTTTTGAACAAATGGAAGTCAAGT 57.800 30.769 0.82 0.00 39.53 3.16
235 237 8.667463 CATTTTTGAACAAATGGAAGTCAAGTT 58.333 29.630 0.82 0.00 39.53 2.66
236 238 7.593875 TTTTGAACAAATGGAAGTCAAGTTG 57.406 32.000 0.00 0.00 33.33 3.16
237 239 5.261209 TGAACAAATGGAAGTCAAGTTGG 57.739 39.130 2.34 0.00 32.14 3.77
238 240 4.952957 TGAACAAATGGAAGTCAAGTTGGA 59.047 37.500 2.34 0.00 32.14 3.53
239 241 5.420421 TGAACAAATGGAAGTCAAGTTGGAA 59.580 36.000 2.34 0.00 32.14 3.53
240 242 5.262588 ACAAATGGAAGTCAAGTTGGAAC 57.737 39.130 2.34 0.00 32.14 3.62
241 243 4.709397 ACAAATGGAAGTCAAGTTGGAACA 59.291 37.500 2.34 0.00 32.14 3.18
242 244 5.163519 ACAAATGGAAGTCAAGTTGGAACAG 60.164 40.000 2.34 0.00 42.39 3.16
243 245 3.924114 TGGAAGTCAAGTTGGAACAGA 57.076 42.857 2.34 0.00 42.39 3.41
244 246 3.808728 TGGAAGTCAAGTTGGAACAGAG 58.191 45.455 2.34 0.00 42.39 3.35
245 247 3.142174 GGAAGTCAAGTTGGAACAGAGG 58.858 50.000 2.34 0.00 42.39 3.69
246 248 2.938956 AGTCAAGTTGGAACAGAGGG 57.061 50.000 2.34 0.00 42.39 4.30
247 249 2.408565 AGTCAAGTTGGAACAGAGGGA 58.591 47.619 2.34 0.00 42.39 4.20
416 620 6.980051 AAAATTAACTCCACGTCCTACATC 57.020 37.500 0.00 0.00 0.00 3.06
422 626 3.513912 ACTCCACGTCCTACATCATTGAA 59.486 43.478 0.00 0.00 0.00 2.69
496 707 5.618056 TCAAGAGTCAAATCATCTGTTGC 57.382 39.130 0.00 0.00 34.14 4.17
548 764 9.778741 ATCGGAAAAGAATCATAATAACTGCTA 57.221 29.630 0.00 0.00 0.00 3.49
659 1195 2.564062 AGAGCAACCAAATCAACATGGG 59.436 45.455 0.00 0.00 41.17 4.00
726 1262 0.036875 AAGACAAGGAAAGGCGGAGG 59.963 55.000 0.00 0.00 0.00 4.30
727 1263 0.836400 AGACAAGGAAAGGCGGAGGA 60.836 55.000 0.00 0.00 0.00 3.71
728 1264 0.391793 GACAAGGAAAGGCGGAGGAG 60.392 60.000 0.00 0.00 0.00 3.69
935 1481 2.311542 AGAGAAAGAGAGAGGGAGAGCA 59.688 50.000 0.00 0.00 0.00 4.26
1059 1606 2.632544 CGTGGTGGAGGACGTGCTA 61.633 63.158 10.47 0.00 0.00 3.49
1465 2018 1.447489 CCTCTGCTCGGCTGACAAG 60.447 63.158 0.00 0.00 33.27 3.16
1466 2019 1.291588 CTCTGCTCGGCTGACAAGT 59.708 57.895 0.00 0.00 33.27 3.16
1855 2412 3.353600 TCGTACGGCGACTGGAAA 58.646 55.556 16.62 0.00 45.68 3.13
1927 2484 0.323629 CTTCCGGCAAGTCCTTGGTA 59.676 55.000 8.97 0.00 40.74 3.25
1981 2538 0.322456 CAATGAACGAGGGGGAAGCA 60.322 55.000 0.00 0.00 0.00 3.91
2081 2638 9.719279 ACGTTTGTTTTTCGTCTTAATTTGATA 57.281 25.926 0.00 0.00 32.26 2.15
2232 2790 1.272092 TGGTCAATCTGCTTCCCCAAG 60.272 52.381 0.00 0.00 0.00 3.61
2248 2806 3.306294 CCCCAAGTTTCTTTTGATGGCTC 60.306 47.826 0.00 0.00 0.00 4.70
2291 2851 2.091885 ACGTATGCCAATTGGATTCCCT 60.092 45.455 29.02 5.80 37.39 4.20
2476 3036 3.866910 GCAATTGGCAATGTGATAACCAG 59.133 43.478 14.47 0.00 43.97 4.00
2561 3121 5.740290 TCTCCAAATCTAAGGTTCTCGTT 57.260 39.130 0.00 0.00 0.00 3.85
2733 3298 8.576936 TTTCACCCAACGTTAAATTTTGTATC 57.423 30.769 0.00 0.00 0.00 2.24
3122 3689 7.232534 CGGAAAAATCTGGAATTTGGGGATATA 59.767 37.037 0.00 0.00 0.00 0.86
3141 3708 0.835971 AAAACCTGGGTGCCCAATCC 60.836 55.000 11.54 0.00 46.63 3.01
3159 3726 1.210967 TCCACTCCCGTGTGAAGTTTT 59.789 47.619 0.00 0.00 40.12 2.43
3311 3894 4.900684 TCACGAAATTAGATTGGACACCA 58.099 39.130 0.00 0.00 0.00 4.17
3339 3922 9.039165 AGTTTGATATCCCAAAATCACAGATTT 57.961 29.630 0.00 0.00 37.72 2.17
3439 4023 6.918569 CCTCTTCCGTATATGAGTGTACTTTG 59.081 42.308 0.00 0.00 0.00 2.77
3650 4235 6.434028 CACCCAGTTTCTGATTCAATTAAGGA 59.566 38.462 0.00 0.00 32.44 3.36
4020 4607 4.265073 GCTCTGTTCTTGATGGGTACAAT 58.735 43.478 0.00 0.00 0.00 2.71
4331 4918 5.762179 ACAATGAACAAGTCAGGGATCTA 57.238 39.130 0.00 0.00 40.43 1.98
4764 5359 6.070656 TCATGTCCAAGGAAAAGATTTGACT 58.929 36.000 0.00 0.00 0.00 3.41
5305 5902 4.408993 TTCAAGACATTCACAATCGCTG 57.591 40.909 0.00 0.00 0.00 5.18
5310 5907 3.684788 AGACATTCACAATCGCTGTTACC 59.315 43.478 0.00 0.00 35.47 2.85
5317 5914 3.009723 ACAATCGCTGTTACCATTCAGG 58.990 45.455 0.00 0.00 38.20 3.86
5452 6049 1.956477 GACAGGGCAGTTGTGATTTGT 59.044 47.619 0.00 0.00 0.00 2.83
5574 6171 8.737168 TGAATGATCCACATAGAAGTAAAAGG 57.263 34.615 0.00 0.00 38.38 3.11
5764 6361 1.115467 CTCCTTCGTGGCCAGATAGT 58.885 55.000 5.11 0.00 35.26 2.12
6038 6635 2.796593 GCACTTTGGCAGTTCAATGTTC 59.203 45.455 0.00 0.00 34.27 3.18
6092 6689 6.183360 TGGGTCAAAGATAAAGAAACCACAAC 60.183 38.462 0.00 0.00 0.00 3.32
6132 6729 6.542370 GCCTCAGATACAAGGTAAGCATTTTA 59.458 38.462 0.00 0.00 34.96 1.52
6133 6730 7.229506 GCCTCAGATACAAGGTAAGCATTTTAT 59.770 37.037 0.00 0.00 34.96 1.40
6167 6765 8.868916 CAGTTAACATTACAGCAAACAAAGTTT 58.131 29.630 8.61 0.00 0.00 2.66
6300 6898 6.445357 TTCATTGATGAACATGGATGACAG 57.555 37.500 2.39 0.00 41.51 3.51
6333 6931 4.869861 AGAATGTTGTTTGCCAAGTTTGAC 59.130 37.500 0.00 0.00 32.51 3.18
6368 6966 8.083828 TCTAGACTTCTGGAATTTCATTAGCT 57.916 34.615 0.00 0.00 30.21 3.32
6408 7006 8.064222 CGCAAGTACATATTGTTTCATCTAAGG 58.936 37.037 0.00 0.00 0.00 2.69
6421 7019 7.400339 TGTTTCATCTAAGGTCTCTGTTAGGAT 59.600 37.037 0.00 0.00 0.00 3.24
6574 7172 7.283127 GCTCTAATTGTTCCTTTCCATCATGTA 59.717 37.037 0.00 0.00 0.00 2.29
6830 7429 4.489737 TCCCTCCGATCCATAATAAGTGT 58.510 43.478 0.00 0.00 0.00 3.55
6979 7664 6.790285 AATATTAGGTTACCATTTACGGCG 57.210 37.500 4.80 4.80 0.00 6.46
6988 7673 6.257630 GGTTACCATTTACGGCGAAATTAGTA 59.742 38.462 16.62 14.60 0.00 1.82
6992 7677 5.521010 CCATTTACGGCGAAATTAGTACTCA 59.479 40.000 16.62 0.00 0.00 3.41
6999 7684 3.790288 GCGAAATTAGTACTCACTCCGTC 59.210 47.826 0.00 0.00 36.14 4.79
7004 7689 1.475403 AGTACTCACTCCGTCCCATG 58.525 55.000 0.00 0.00 0.00 3.66
7096 7825 7.604657 TTTTCTATTGAGATCTACTCCCTCC 57.395 40.000 0.00 0.00 44.34 4.30
7097 7826 5.932027 TCTATTGAGATCTACTCCCTCCA 57.068 43.478 0.00 0.00 44.34 3.86
7098 7827 6.476409 TCTATTGAGATCTACTCCCTCCAT 57.524 41.667 0.00 0.00 44.34 3.41
7099 7828 6.489603 TCTATTGAGATCTACTCCCTCCATC 58.510 44.000 0.00 0.00 44.34 3.51
7100 7829 3.534357 TGAGATCTACTCCCTCCATCC 57.466 52.381 0.00 0.00 44.34 3.51
7101 7830 2.110899 TGAGATCTACTCCCTCCATCCC 59.889 54.545 0.00 0.00 44.34 3.85
7102 7831 2.110899 GAGATCTACTCCCTCCATCCCA 59.889 54.545 0.00 0.00 39.53 4.37
7103 7832 2.732507 AGATCTACTCCCTCCATCCCAT 59.267 50.000 0.00 0.00 0.00 4.00
7104 7833 3.932562 AGATCTACTCCCTCCATCCCATA 59.067 47.826 0.00 0.00 0.00 2.74
7105 7834 3.835478 TCTACTCCCTCCATCCCATAG 57.165 52.381 0.00 0.00 0.00 2.23
7106 7835 3.072086 TCTACTCCCTCCATCCCATAGT 58.928 50.000 0.00 0.00 0.00 2.12
7107 7836 4.257078 TCTACTCCCTCCATCCCATAGTA 58.743 47.826 0.00 0.00 0.00 1.82
7108 7837 4.864406 TCTACTCCCTCCATCCCATAGTAT 59.136 45.833 0.00 0.00 0.00 2.12
7109 7838 6.043251 TCTACTCCCTCCATCCCATAGTATA 58.957 44.000 0.00 0.00 0.00 1.47
7110 7839 5.633473 ACTCCCTCCATCCCATAGTATAA 57.367 43.478 0.00 0.00 0.00 0.98
7111 7840 5.594777 ACTCCCTCCATCCCATAGTATAAG 58.405 45.833 0.00 0.00 0.00 1.73
7112 7841 5.318889 ACTCCCTCCATCCCATAGTATAAGA 59.681 44.000 0.00 0.00 0.00 2.10
7113 7842 5.843469 TCCCTCCATCCCATAGTATAAGAG 58.157 45.833 0.00 0.00 0.00 2.85
7114 7843 4.407296 CCCTCCATCCCATAGTATAAGAGC 59.593 50.000 0.00 0.00 0.00 4.09
7115 7844 4.098654 CCTCCATCCCATAGTATAAGAGCG 59.901 50.000 0.00 0.00 0.00 5.03
7116 7845 4.673968 TCCATCCCATAGTATAAGAGCGT 58.326 43.478 0.00 0.00 0.00 5.07
7117 7846 5.084519 TCCATCCCATAGTATAAGAGCGTT 58.915 41.667 0.00 0.00 0.00 4.84
7118 7847 5.542635 TCCATCCCATAGTATAAGAGCGTTT 59.457 40.000 0.00 0.00 0.00 3.60
7119 7848 6.042781 TCCATCCCATAGTATAAGAGCGTTTT 59.957 38.462 0.00 0.00 0.00 2.43
7120 7849 6.710744 CCATCCCATAGTATAAGAGCGTTTTT 59.289 38.462 0.00 0.00 0.00 1.94
7121 7850 7.307989 CCATCCCATAGTATAAGAGCGTTTTTG 60.308 40.741 0.00 0.00 0.00 2.44
7122 7851 6.880484 TCCCATAGTATAAGAGCGTTTTTGA 58.120 36.000 0.00 0.00 0.00 2.69
7123 7852 6.759827 TCCCATAGTATAAGAGCGTTTTTGAC 59.240 38.462 0.00 0.00 0.00 3.18
7124 7853 6.537301 CCCATAGTATAAGAGCGTTTTTGACA 59.463 38.462 0.00 0.00 0.00 3.58
7125 7854 7.399523 CCATAGTATAAGAGCGTTTTTGACAC 58.600 38.462 0.00 0.00 0.00 3.67
7126 7855 7.277981 CCATAGTATAAGAGCGTTTTTGACACT 59.722 37.037 0.00 0.00 0.00 3.55
7127 7856 9.297586 CATAGTATAAGAGCGTTTTTGACACTA 57.702 33.333 0.00 0.00 0.00 2.74
7128 7857 7.578169 AGTATAAGAGCGTTTTTGACACTAC 57.422 36.000 0.00 0.00 0.00 2.73
7129 7858 7.149973 AGTATAAGAGCGTTTTTGACACTACA 58.850 34.615 0.00 0.00 0.00 2.74
7130 7859 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
7131 7860 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
7132 7861 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
7133 7862 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
7134 7863 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
7161 7890 5.959618 AAAACGCTCTTATATTATGGGGC 57.040 39.130 0.00 0.00 0.00 5.80
7162 7891 3.247006 ACGCTCTTATATTATGGGGCG 57.753 47.619 17.85 17.85 45.49 6.13
7163 7892 2.093658 ACGCTCTTATATTATGGGGCGG 60.094 50.000 21.13 9.94 44.53 6.13
7164 7893 2.167693 CGCTCTTATATTATGGGGCGGA 59.832 50.000 14.03 0.00 38.12 5.54
7165 7894 3.738281 CGCTCTTATATTATGGGGCGGAG 60.738 52.174 14.03 0.00 38.12 4.63
7166 7895 3.432326 GCTCTTATATTATGGGGCGGAGG 60.432 52.174 0.00 0.00 0.00 4.30
7167 7896 3.112263 TCTTATATTATGGGGCGGAGGG 58.888 50.000 0.00 0.00 0.00 4.30
7168 7897 2.953093 TATATTATGGGGCGGAGGGA 57.047 50.000 0.00 0.00 0.00 4.20
7169 7898 1.584724 ATATTATGGGGCGGAGGGAG 58.415 55.000 0.00 0.00 0.00 4.30
7262 7991 6.376018 GCCCTTGAATGGTAGTAAATGTTACA 59.624 38.462 1.33 0.00 0.00 2.41
7327 8083 9.912634 TTTTAATGTTGGATCTTCTGAATGAAC 57.087 29.630 0.00 0.00 0.00 3.18
7362 8118 6.827586 AATTGGACACGCCTTTAGAAAATA 57.172 33.333 0.00 0.00 37.63 1.40
7572 8654 5.957842 AATACCATCAGCGTCAAGAAAAA 57.042 34.783 0.00 0.00 0.00 1.94
7738 8821 0.460987 GTCATGAGGGGTTGCGAGAG 60.461 60.000 0.00 0.00 0.00 3.20
8173 9261 5.008118 GCTGGTTTATGTTAGCATTCTCTCC 59.992 44.000 0.00 0.00 36.58 3.71
8191 9279 7.055667 TCTCTCCGTGCTAATATTTCTCATT 57.944 36.000 0.00 0.00 0.00 2.57
8340 9428 5.869344 TCATACAAGAGAGAAACATCCAACG 59.131 40.000 0.00 0.00 0.00 4.10
8384 9473 0.837940 GAGGGCCCAAACCTAGGTAG 59.162 60.000 27.56 11.09 38.79 3.18
8537 9626 6.603095 AGATACGATACGGTTTCGGTAATAC 58.397 40.000 21.65 9.22 40.83 1.89
8562 9651 0.309302 TACGTTCGGTTCGGTTTCGA 59.691 50.000 0.00 0.00 44.44 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 24 4.215109 AGTGTGTTTGGTTCAAGCCTTAT 58.785 39.130 0.00 0.00 0.00 1.73
68 70 2.652941 TAACTTACCACGCCTAACCG 57.347 50.000 0.00 0.00 0.00 4.44
69 71 3.928992 GTCTTAACTTACCACGCCTAACC 59.071 47.826 0.00 0.00 0.00 2.85
126 128 5.180271 TGTATTGTGGAACGAAGGGAATAC 58.820 41.667 0.00 0.00 42.39 1.89
127 129 5.423704 TGTATTGTGGAACGAAGGGAATA 57.576 39.130 0.00 0.00 42.39 1.75
128 130 4.295141 TGTATTGTGGAACGAAGGGAAT 57.705 40.909 0.00 0.00 42.39 3.01
129 131 3.773418 TGTATTGTGGAACGAAGGGAA 57.227 42.857 0.00 0.00 42.39 3.97
130 132 3.605634 CATGTATTGTGGAACGAAGGGA 58.394 45.455 0.00 0.00 42.39 4.20
131 133 2.097466 GCATGTATTGTGGAACGAAGGG 59.903 50.000 0.00 0.00 42.39 3.95
132 134 2.097466 GGCATGTATTGTGGAACGAAGG 59.903 50.000 0.00 0.00 42.39 3.46
133 135 3.009723 AGGCATGTATTGTGGAACGAAG 58.990 45.455 0.00 0.00 42.39 3.79
134 136 3.066291 AGGCATGTATTGTGGAACGAA 57.934 42.857 0.00 0.00 42.39 3.85
135 137 2.779755 AGGCATGTATTGTGGAACGA 57.220 45.000 0.00 0.00 42.39 3.85
136 138 3.190327 TGAAAGGCATGTATTGTGGAACG 59.810 43.478 0.00 0.00 42.39 3.95
137 139 4.782019 TGAAAGGCATGTATTGTGGAAC 57.218 40.909 0.00 0.00 37.35 3.62
138 140 5.999205 AATGAAAGGCATGTATTGTGGAA 57.001 34.783 0.00 0.00 37.28 3.53
139 141 5.999205 AAATGAAAGGCATGTATTGTGGA 57.001 34.783 0.00 0.00 37.28 4.02
140 142 7.490840 TGATAAATGAAAGGCATGTATTGTGG 58.509 34.615 0.00 0.00 37.50 4.17
141 143 8.929827 TTGATAAATGAAAGGCATGTATTGTG 57.070 30.769 0.00 0.00 37.50 3.33
142 144 9.941325 TTTTGATAAATGAAAGGCATGTATTGT 57.059 25.926 0.00 0.00 37.50 2.71
198 200 9.874205 CATTTGTTCAAAAATGGATGTACCTAT 57.126 29.630 2.11 0.00 41.71 2.57
209 211 8.200364 ACTTGACTTCCATTTGTTCAAAAATG 57.800 30.769 2.11 3.25 43.94 2.32
210 212 8.667463 CAACTTGACTTCCATTTGTTCAAAAAT 58.333 29.630 2.11 0.00 0.00 1.82
211 213 7.118971 CCAACTTGACTTCCATTTGTTCAAAAA 59.881 33.333 2.11 0.00 0.00 1.94
212 214 6.593382 CCAACTTGACTTCCATTTGTTCAAAA 59.407 34.615 2.11 0.00 0.00 2.44
213 215 6.071108 TCCAACTTGACTTCCATTTGTTCAAA 60.071 34.615 0.44 0.44 0.00 2.69
214 216 5.420421 TCCAACTTGACTTCCATTTGTTCAA 59.580 36.000 0.00 0.00 0.00 2.69
215 217 4.952957 TCCAACTTGACTTCCATTTGTTCA 59.047 37.500 0.00 0.00 0.00 3.18
216 218 5.514274 TCCAACTTGACTTCCATTTGTTC 57.486 39.130 0.00 0.00 0.00 3.18
217 219 5.186797 TGTTCCAACTTGACTTCCATTTGTT 59.813 36.000 0.00 0.00 0.00 2.83
218 220 4.709397 TGTTCCAACTTGACTTCCATTTGT 59.291 37.500 0.00 0.00 0.00 2.83
219 221 5.067674 TCTGTTCCAACTTGACTTCCATTTG 59.932 40.000 0.00 0.00 0.00 2.32
220 222 5.200483 TCTGTTCCAACTTGACTTCCATTT 58.800 37.500 0.00 0.00 0.00 2.32
221 223 4.792068 TCTGTTCCAACTTGACTTCCATT 58.208 39.130 0.00 0.00 0.00 3.16
222 224 4.392940 CTCTGTTCCAACTTGACTTCCAT 58.607 43.478 0.00 0.00 0.00 3.41
223 225 3.433598 CCTCTGTTCCAACTTGACTTCCA 60.434 47.826 0.00 0.00 0.00 3.53
224 226 3.142174 CCTCTGTTCCAACTTGACTTCC 58.858 50.000 0.00 0.00 0.00 3.46
225 227 3.142174 CCCTCTGTTCCAACTTGACTTC 58.858 50.000 0.00 0.00 0.00 3.01
226 228 2.777692 TCCCTCTGTTCCAACTTGACTT 59.222 45.455 0.00 0.00 0.00 3.01
227 229 2.370189 CTCCCTCTGTTCCAACTTGACT 59.630 50.000 0.00 0.00 0.00 3.41
228 230 2.104963 ACTCCCTCTGTTCCAACTTGAC 59.895 50.000 0.00 0.00 0.00 3.18
229 231 2.408565 ACTCCCTCTGTTCCAACTTGA 58.591 47.619 0.00 0.00 0.00 3.02
230 232 2.938956 ACTCCCTCTGTTCCAACTTG 57.061 50.000 0.00 0.00 0.00 3.16
231 233 3.588569 ACTACTCCCTCTGTTCCAACTT 58.411 45.455 0.00 0.00 0.00 2.66
232 234 3.261818 ACTACTCCCTCTGTTCCAACT 57.738 47.619 0.00 0.00 0.00 3.16
233 235 4.065789 CAAACTACTCCCTCTGTTCCAAC 58.934 47.826 0.00 0.00 0.00 3.77
234 236 3.496160 GCAAACTACTCCCTCTGTTCCAA 60.496 47.826 0.00 0.00 0.00 3.53
235 237 2.038557 GCAAACTACTCCCTCTGTTCCA 59.961 50.000 0.00 0.00 0.00 3.53
236 238 2.038557 TGCAAACTACTCCCTCTGTTCC 59.961 50.000 0.00 0.00 0.00 3.62
237 239 3.067833 GTGCAAACTACTCCCTCTGTTC 58.932 50.000 0.00 0.00 0.00 3.18
238 240 2.224548 GGTGCAAACTACTCCCTCTGTT 60.225 50.000 0.00 0.00 0.00 3.16
239 241 1.348036 GGTGCAAACTACTCCCTCTGT 59.652 52.381 0.00 0.00 0.00 3.41
240 242 1.347707 TGGTGCAAACTACTCCCTCTG 59.652 52.381 0.00 0.00 0.00 3.35
241 243 1.729586 TGGTGCAAACTACTCCCTCT 58.270 50.000 0.00 0.00 0.00 3.69
242 244 2.561478 TTGGTGCAAACTACTCCCTC 57.439 50.000 0.00 0.00 0.00 4.30
243 245 2.956333 GTTTTGGTGCAAACTACTCCCT 59.044 45.455 0.00 0.00 32.79 4.20
244 246 2.691011 TGTTTTGGTGCAAACTACTCCC 59.309 45.455 0.00 0.00 32.79 4.30
245 247 3.129638 TGTGTTTTGGTGCAAACTACTCC 59.870 43.478 0.00 0.00 32.79 3.85
246 248 4.364415 TGTGTTTTGGTGCAAACTACTC 57.636 40.909 0.00 0.00 32.79 2.59
247 249 5.337578 AATGTGTTTTGGTGCAAACTACT 57.662 34.783 0.00 0.00 32.79 2.57
416 620 8.190784 GGGATCAAGTACTAAACCAATTCAATG 58.809 37.037 0.00 0.00 0.00 2.82
422 626 4.542525 TGGGGGATCAAGTACTAAACCAAT 59.457 41.667 0.00 0.00 0.00 3.16
496 707 2.187946 CCTTGCAGGTAGGAGCGG 59.812 66.667 0.00 0.00 34.56 5.52
515 726 7.884816 TTATGATTCTTTTCCGATACGATCC 57.115 36.000 0.00 0.00 0.00 3.36
520 731 9.813080 GCAGTTATTATGATTCTTTTCCGATAC 57.187 33.333 0.00 0.00 0.00 2.24
548 764 7.284489 TCAGCTAAAAGACAACAACCAACTATT 59.716 33.333 0.00 0.00 0.00 1.73
551 767 4.947388 TCAGCTAAAAGACAACAACCAACT 59.053 37.500 0.00 0.00 0.00 3.16
617 1153 2.084546 GGCTCCGCAACTATTCACTTT 58.915 47.619 0.00 0.00 0.00 2.66
618 1154 1.003118 TGGCTCCGCAACTATTCACTT 59.997 47.619 0.00 0.00 0.00 3.16
645 1181 2.231964 CTCCACACCCATGTTGATTTGG 59.768 50.000 0.00 0.00 36.72 3.28
659 1195 0.948141 GTGCACTCTGCTCTCCACAC 60.948 60.000 10.32 0.00 45.31 3.82
726 1262 0.108089 GTCTTCCCTTTCGCCTCCTC 60.108 60.000 0.00 0.00 0.00 3.71
727 1263 1.889530 CGTCTTCCCTTTCGCCTCCT 61.890 60.000 0.00 0.00 0.00 3.69
728 1264 1.448013 CGTCTTCCCTTTCGCCTCC 60.448 63.158 0.00 0.00 0.00 4.30
801 1337 0.686224 TTTCGGCTCCTTCGGGTTTA 59.314 50.000 0.00 0.00 36.28 2.01
935 1481 1.226974 CGTCGCCGAGTCCATCAAT 60.227 57.895 0.00 0.00 35.63 2.57
1200 1747 2.693797 AGCAAACTCATTCAGCAACG 57.306 45.000 0.00 0.00 0.00 4.10
1456 2009 0.038159 AGCGTCACTACTTGTCAGCC 60.038 55.000 0.00 0.00 0.00 4.85
1765 2322 3.815401 CTCGGAAAGGCAAAAGAGAAAGA 59.185 43.478 0.00 0.00 0.00 2.52
1784 2341 4.521062 CTTCCCTCCCTGCGCTCG 62.521 72.222 9.73 0.00 0.00 5.03
1927 2484 1.353091 AAGGCTCCGAGTTCTTCCTT 58.647 50.000 0.00 0.00 0.00 3.36
1981 2538 2.429933 ATCCAGCATCCTCATAGGGT 57.570 50.000 0.00 0.00 35.59 4.34
2014 2571 1.452110 TGTCACCGCAATCAAGATGG 58.548 50.000 0.00 0.00 0.00 3.51
2081 2638 6.599445 AGCAATTAAGCAGATTCCATCTAGT 58.401 36.000 0.00 0.00 37.58 2.57
2083 2640 8.213679 ACTAAGCAATTAAGCAGATTCCATCTA 58.786 33.333 0.00 0.00 37.58 1.98
2084 2641 7.013083 CACTAAGCAATTAAGCAGATTCCATCT 59.987 37.037 0.00 0.00 41.15 2.90
2085 2642 7.137426 CACTAAGCAATTAAGCAGATTCCATC 58.863 38.462 0.00 0.00 36.85 3.51
2101 2659 1.908344 TGCATCAAGCCACTAAGCAA 58.092 45.000 0.00 0.00 44.83 3.91
2232 2790 9.860898 AATTAGTAATGAGCCATCAAAAGAAAC 57.139 29.630 0.00 0.00 39.39 2.78
2248 2806 8.378172 ACGTATGTCCCATTGAATTAGTAATG 57.622 34.615 0.00 0.00 34.79 1.90
2291 2851 5.230942 ACAAACAACACAACGGATGAAAAA 58.769 33.333 0.00 0.00 0.00 1.94
2366 2926 1.714541 TCATTTTGGCCCTTCAAGCA 58.285 45.000 0.00 0.00 0.00 3.91
2476 3036 3.382546 CACCTGTCCCAATGGATTGATTC 59.617 47.826 0.00 0.00 44.28 2.52
2561 3121 4.534500 TCACTAAAATTAGGAGTGGCCTCA 59.466 41.667 3.32 0.00 46.97 3.86
2733 3298 6.662663 TCTGATGTATCCATCTACAGAGGATG 59.337 42.308 15.08 0.00 46.38 3.51
2990 3556 4.101741 ACCTAATATGTTGAGGTCCTCAGC 59.898 45.833 24.78 24.78 39.46 4.26
3097 3664 5.698741 ATCCCCAAATTCCAGATTTTTCC 57.301 39.130 0.00 0.00 0.00 3.13
3186 3753 3.526931 TCAGACTATTTCCTTCGCCAG 57.473 47.619 0.00 0.00 0.00 4.85
3311 3894 8.421249 TCTGTGATTTTGGGATATCAAACTTT 57.579 30.769 4.83 0.00 36.49 2.66
3439 4023 4.612264 TCAAAGTAGTAGTGAACCACCC 57.388 45.455 0.00 0.00 34.49 4.61
3640 4225 9.323985 CAGTGAACCAAAATTTTCCTTAATTGA 57.676 29.630 0.00 0.00 0.00 2.57
3700 4286 8.856153 ATACTACCTAGAGACATGACATACAG 57.144 38.462 0.00 0.00 0.00 2.74
3813 4399 6.037610 CCTTTCCAGATTTCGAAGGAGTAATG 59.962 42.308 0.00 0.00 39.33 1.90
4020 4607 3.127895 GGCCGTATGCAAAGATACAAACA 59.872 43.478 0.00 0.00 43.89 2.83
4331 4918 3.580022 TGTTGAGACCATCACTGATGAGT 59.420 43.478 19.04 14.56 42.09 3.41
4538 5125 4.039245 AGTTCCATTACATCCATCGTCGAT 59.961 41.667 0.75 0.75 0.00 3.59
4764 5359 2.682563 GCCACGGATAATGTTCCCTGAA 60.683 50.000 0.00 0.00 31.61 3.02
5310 5907 5.007626 TGTTTTCAGTCGAGAAACCTGAATG 59.992 40.000 14.07 0.00 42.84 2.67
5452 6049 0.178964 AAGTTAGCTTGGCCAGGCAA 60.179 50.000 37.69 26.34 35.69 4.52
5574 6171 4.872691 AGTGCACTAAGATTACATGCAGAC 59.127 41.667 20.16 0.00 46.29 3.51
6038 6635 7.592938 TGAATAACTGAACTGTTTATGCTTGG 58.407 34.615 0.00 0.00 0.00 3.61
6092 6689 3.133003 TCTGAGGCCTCTCTTATTTTCGG 59.867 47.826 32.28 8.98 40.58 4.30
6185 6783 7.353414 TCATGTGTTTTGTTTCCCATTCTAA 57.647 32.000 0.00 0.00 0.00 2.10
6300 6898 4.431599 GCAAACAACATTCTCGAAATTCGC 60.432 41.667 10.93 0.00 40.21 4.70
6333 6931 3.314080 CCAGAAGTCTAGAAGCTCTACGG 59.686 52.174 0.00 0.00 0.00 4.02
6368 6966 0.813610 CTTGCGGATATGCGGTCCAA 60.814 55.000 18.67 12.40 37.81 3.53
6408 7006 1.134371 GTGGGCCATCCTAACAGAGAC 60.134 57.143 10.70 0.00 36.20 3.36
6421 7019 0.988832 CTTAGGTGGTAAGTGGGCCA 59.011 55.000 0.00 0.00 34.42 5.36
6545 7143 6.664816 TGATGGAAAGGAACAATTAGAGCATT 59.335 34.615 0.00 0.00 0.00 3.56
6636 7234 7.681939 ATACACGAAAAATCTTAGCTTCCAA 57.318 32.000 0.00 0.00 0.00 3.53
6803 7402 2.195741 TATGGATCGGAGGGAGTACG 57.804 55.000 0.00 0.00 0.00 3.67
6830 7429 8.610248 TCAAATATCTTGAACTAAAACCACGA 57.390 30.769 0.00 0.00 0.00 4.35
6898 7583 2.165641 AGCATAGACGTCGTTGGAATCA 59.834 45.455 18.37 0.00 0.00 2.57
6905 7590 5.892568 AGAAAGATAAGCATAGACGTCGTT 58.107 37.500 10.46 0.00 0.00 3.85
6975 7660 3.114065 GGAGTGAGTACTAATTTCGCCG 58.886 50.000 0.00 0.00 37.25 6.46
6999 7684 0.031111 TACTCCCTCTGTCCCATGGG 60.031 60.000 26.30 26.30 40.95 4.00
7004 7689 7.560368 CATCAATATATTACTCCCTCTGTCCC 58.440 42.308 0.00 0.00 0.00 4.46
7078 7807 4.424842 GGATGGAGGGAGTAGATCTCAAT 58.575 47.826 0.00 0.00 44.40 2.57
7089 7818 5.843469 TCTTATACTATGGGATGGAGGGAG 58.157 45.833 0.00 0.00 0.00 4.30
7090 7819 5.814712 GCTCTTATACTATGGGATGGAGGGA 60.815 48.000 7.73 0.00 0.00 4.20
7091 7820 4.407296 GCTCTTATACTATGGGATGGAGGG 59.593 50.000 7.73 0.00 0.00 4.30
7092 7821 4.098654 CGCTCTTATACTATGGGATGGAGG 59.901 50.000 7.73 0.00 0.00 4.30
7093 7822 4.707448 ACGCTCTTATACTATGGGATGGAG 59.293 45.833 3.00 3.00 0.00 3.86
7094 7823 4.673968 ACGCTCTTATACTATGGGATGGA 58.326 43.478 0.00 0.00 0.00 3.41
7095 7824 5.407407 AACGCTCTTATACTATGGGATGG 57.593 43.478 0.00 0.00 0.00 3.51
7096 7825 7.441157 TCAAAAACGCTCTTATACTATGGGATG 59.559 37.037 0.00 0.00 0.00 3.51
7097 7826 7.441458 GTCAAAAACGCTCTTATACTATGGGAT 59.559 37.037 0.00 0.00 0.00 3.85
7098 7827 6.759827 GTCAAAAACGCTCTTATACTATGGGA 59.240 38.462 0.00 0.00 0.00 4.37
7099 7828 6.537301 TGTCAAAAACGCTCTTATACTATGGG 59.463 38.462 0.00 0.00 0.00 4.00
7100 7829 7.277981 AGTGTCAAAAACGCTCTTATACTATGG 59.722 37.037 0.00 0.00 45.69 2.74
7101 7830 8.186178 AGTGTCAAAAACGCTCTTATACTATG 57.814 34.615 0.00 0.00 45.69 2.23
7102 7831 9.298774 GTAGTGTCAAAAACGCTCTTATACTAT 57.701 33.333 0.00 0.00 45.69 2.12
7103 7832 8.298854 TGTAGTGTCAAAAACGCTCTTATACTA 58.701 33.333 0.00 0.00 45.69 1.82
7104 7833 7.115947 GTGTAGTGTCAAAAACGCTCTTATACT 59.884 37.037 0.00 0.00 45.69 2.12
7105 7834 7.115947 AGTGTAGTGTCAAAAACGCTCTTATAC 59.884 37.037 0.00 0.00 45.69 1.47
7106 7835 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
7107 7836 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
7108 7837 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
7109 7838 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
7110 7839 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
7111 7840 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
7138 7867 5.048991 CGCCCCATAATATAAGAGCGTTTTT 60.049 40.000 0.00 0.00 37.69 1.94
7139 7868 4.454504 CGCCCCATAATATAAGAGCGTTTT 59.545 41.667 0.00 0.00 37.69 2.43
7140 7869 4.000988 CGCCCCATAATATAAGAGCGTTT 58.999 43.478 0.00 0.00 37.69 3.60
7141 7870 3.596214 CGCCCCATAATATAAGAGCGTT 58.404 45.455 0.00 0.00 37.69 4.84
7142 7871 2.093658 CCGCCCCATAATATAAGAGCGT 60.094 50.000 0.00 0.00 40.66 5.07
7143 7872 2.167693 TCCGCCCCATAATATAAGAGCG 59.832 50.000 0.00 0.00 41.84 5.03
7144 7873 3.432326 CCTCCGCCCCATAATATAAGAGC 60.432 52.174 0.00 0.00 0.00 4.09
7145 7874 3.134804 CCCTCCGCCCCATAATATAAGAG 59.865 52.174 0.00 0.00 0.00 2.85
7146 7875 3.112263 CCCTCCGCCCCATAATATAAGA 58.888 50.000 0.00 0.00 0.00 2.10
7147 7876 3.112263 TCCCTCCGCCCCATAATATAAG 58.888 50.000 0.00 0.00 0.00 1.73
7148 7877 3.112263 CTCCCTCCGCCCCATAATATAA 58.888 50.000 0.00 0.00 0.00 0.98
7149 7878 2.045326 ACTCCCTCCGCCCCATAATATA 59.955 50.000 0.00 0.00 0.00 0.86
7150 7879 1.203440 ACTCCCTCCGCCCCATAATAT 60.203 52.381 0.00 0.00 0.00 1.28
7151 7880 0.192566 ACTCCCTCCGCCCCATAATA 59.807 55.000 0.00 0.00 0.00 0.98
7152 7881 0.192566 TACTCCCTCCGCCCCATAAT 59.807 55.000 0.00 0.00 0.00 1.28
7153 7882 0.761702 GTACTCCCTCCGCCCCATAA 60.762 60.000 0.00 0.00 0.00 1.90
7154 7883 1.152398 GTACTCCCTCCGCCCCATA 60.152 63.158 0.00 0.00 0.00 2.74
7155 7884 2.446036 GTACTCCCTCCGCCCCAT 60.446 66.667 0.00 0.00 0.00 4.00
7156 7885 2.833151 AATGTACTCCCTCCGCCCCA 62.833 60.000 0.00 0.00 0.00 4.96
7157 7886 0.761702 TAATGTACTCCCTCCGCCCC 60.762 60.000 0.00 0.00 0.00 5.80
7158 7887 0.680061 CTAATGTACTCCCTCCGCCC 59.320 60.000 0.00 0.00 0.00 6.13
7159 7888 1.700955 TCTAATGTACTCCCTCCGCC 58.299 55.000 0.00 0.00 0.00 6.13
7160 7889 2.036089 CCTTCTAATGTACTCCCTCCGC 59.964 54.545 0.00 0.00 0.00 5.54
7161 7890 3.563223 TCCTTCTAATGTACTCCCTCCG 58.437 50.000 0.00 0.00 0.00 4.63
7162 7891 6.316513 ACTATCCTTCTAATGTACTCCCTCC 58.683 44.000 0.00 0.00 0.00 4.30
7163 7892 7.842887 AACTATCCTTCTAATGTACTCCCTC 57.157 40.000 0.00 0.00 0.00 4.30
7164 7893 9.900112 ATTAACTATCCTTCTAATGTACTCCCT 57.100 33.333 0.00 0.00 0.00 4.20
7223 7952 3.222603 TCAAGGGCAAGGAAGACTTTTC 58.777 45.455 0.00 0.00 37.29 2.29
7327 8083 6.027749 GGCGTGTCCAATTAATTTTAGACAG 58.972 40.000 18.82 15.09 35.10 3.51
7340 8096 6.827586 TTATTTTCTAAAGGCGTGTCCAAT 57.172 33.333 0.00 0.00 37.29 3.16
7572 8654 5.242393 CAGATCTGTTTTGTCCATTTGAGGT 59.758 40.000 14.95 0.00 0.00 3.85
7693 8776 6.036577 ACACTGAAAGAAAGCCAAGAAAAA 57.963 33.333 0.00 0.00 37.43 1.94
7738 8821 5.463724 CACTCACTCCTGTACTTGAGAAAAC 59.536 44.000 16.05 0.00 38.19 2.43
7985 9071 4.978083 AGAATCAAAGCGCATTGAAGAT 57.022 36.364 29.11 18.92 42.22 2.40
8191 9279 3.554960 GGGTGACGAAGCAGCATGATATA 60.555 47.826 0.00 0.00 39.69 0.86
8340 9428 4.466255 TCTAGGGTAACATCCTACTCCC 57.534 50.000 0.00 0.00 35.92 4.30
8384 9473 1.947456 GGTTTCACACAGTGGAGGTTC 59.053 52.381 5.31 0.00 33.87 3.62
8477 9566 9.294614 ACCGTATAAACCAAAGTATAAAAACCA 57.705 29.630 0.00 0.00 0.00 3.67
8522 9611 3.632643 AATGGGTATTACCGAAACCGT 57.367 42.857 6.77 0.00 39.83 4.83
8537 9626 0.722848 CCGAACCGAACGTAAATGGG 59.277 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.