Multiple sequence alignment - TraesCS5B01G220300

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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 TraesCS5B01G220300 chr5B 100.000 2896 0 0 1 2896 394629055 394626160 0.000000e+00 5349.0
1 TraesCS5B01G220300 chr5B 86.755 1744 131 46 314 1991 394581762 394580053 0.000000e+00 1849.0
2 TraesCS5B01G220300 chr5B 88.825 1226 103 19 828 2046 394572568 394571370 0.000000e+00 1474.0
3 TraesCS5B01G220300 chr5B 82.712 295 29 11 303 587 394573020 394572738 2.880000e-60 243.0
4 TraesCS5B01G220300 chr5B 88.095 126 10 4 642 763 394572718 394572594 8.360000e-31 145.0
5 TraesCS5B01G220300 chr5D 87.097 1891 149 45 303 2158 336314285 336316115 0.000000e+00 2052.0
6 TraesCS5B01G220300 chr5D 87.414 1748 122 49 314 2034 336337954 336339630 0.000000e+00 1919.0
7 TraesCS5B01G220300 chr5D 88.091 1629 127 38 314 1910 336240452 336238859 0.000000e+00 1871.0
8 TraesCS5B01G220300 chr5D 90.352 1306 85 13 854 2158 336381453 336380188 0.000000e+00 1676.0
9 TraesCS5B01G220300 chr5D 87.344 719 58 17 80 791 336382232 336381540 0.000000e+00 793.0
10 TraesCS5B01G220300 chr5D 91.724 580 33 6 1583 2158 336257245 336256677 0.000000e+00 791.0
11 TraesCS5B01G220300 chr5D 81.545 932 92 39 303 1203 336258523 336257641 0.000000e+00 695.0
12 TraesCS5B01G220300 chr5D 82.200 691 70 15 2206 2850 336380204 336379521 1.960000e-151 545.0
13 TraesCS5B01G220300 chr5D 81.370 365 53 10 2412 2772 548210893 548210540 1.700000e-72 283.0
14 TraesCS5B01G220300 chr5A 86.546 1821 114 60 316 2113 437413300 437411588 0.000000e+00 1884.0
15 TraesCS5B01G220300 chr5A 85.956 1773 155 44 303 2046 437393829 437392122 0.000000e+00 1808.0
16 TraesCS5B01G220300 chr5A 86.328 1675 124 46 323 1937 437400668 437399039 0.000000e+00 1727.0
17 TraesCS5B01G220300 chr5A 79.464 448 47 17 2206 2613 437411300 437410858 2.840000e-70 276.0
18 TraesCS5B01G220300 chr5A 93.750 48 3 0 2111 2158 437411331 437411284 4.000000e-09 73.1
19 TraesCS5B01G220300 chr7B 86.667 270 25 10 2414 2678 714674432 714674169 3.650000e-74 289.0
20 TraesCS5B01G220300 chr7B 83.688 282 32 9 2414 2690 714681917 714681645 1.330000e-63 254.0
21 TraesCS5B01G220300 chr3D 79.452 365 59 13 2424 2782 587568585 587568231 8.020000e-61 244.0
22 TraesCS5B01G220300 chr3D 95.000 80 4 0 80 159 58109668 58109747 3.030000e-25 126.0
23 TraesCS5B01G220300 chr3D 78.283 198 28 12 71 263 304353098 304352911 2.360000e-21 113.0
24 TraesCS5B01G220300 chr3D 90.805 87 3 4 77 159 32704296 32704381 8.480000e-21 111.0
25 TraesCS5B01G220300 chr3D 79.021 143 14 6 85 227 582059431 582059305 1.850000e-12 84.2
26 TraesCS5B01G220300 chr3B 84.472 161 17 5 2424 2580 252398854 252398698 5.000000e-33 152.0
27 TraesCS5B01G220300 chr1D 85.333 150 12 9 80 227 63427582 63427441 2.330000e-31 147.0
28 TraesCS5B01G220300 chr4B 83.234 167 18 9 2424 2583 93292886 93293049 8.360000e-31 145.0
29 TraesCS5B01G220300 chr6D 77.647 255 29 18 1 238 432895120 432894877 2.340000e-26 130.0
30 TraesCS5B01G220300 chr1A 79.793 193 26 11 76 265 554341588 554341770 8.420000e-26 128.0
31 TraesCS5B01G220300 chr1A 92.683 82 5 1 80 161 405089796 405089716 1.820000e-22 117.0
32 TraesCS5B01G220300 chr7A 81.944 144 16 10 85 226 538957804 538957939 2.360000e-21 113.0
33 TraesCS5B01G220300 chr6B 91.358 81 5 2 80 159 653057548 653057469 3.050000e-20 110.0
34 TraesCS5B01G220300 chr2B 85.000 60 7 2 2618 2676 716591059 716591117 3.120000e-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 TraesCS5B01G220300 chr5B 394626160 394629055 2895 True 5349.000000 5349 100.000000 1 2896 1 chr5B.!!$R2 2895
1 TraesCS5B01G220300 chr5B 394580053 394581762 1709 True 1849.000000 1849 86.755000 314 1991 1 chr5B.!!$R1 1677
2 TraesCS5B01G220300 chr5B 394571370 394573020 1650 True 620.666667 1474 86.544000 303 2046 3 chr5B.!!$R3 1743
3 TraesCS5B01G220300 chr5D 336314285 336316115 1830 False 2052.000000 2052 87.097000 303 2158 1 chr5D.!!$F1 1855
4 TraesCS5B01G220300 chr5D 336337954 336339630 1676 False 1919.000000 1919 87.414000 314 2034 1 chr5D.!!$F2 1720
5 TraesCS5B01G220300 chr5D 336238859 336240452 1593 True 1871.000000 1871 88.091000 314 1910 1 chr5D.!!$R1 1596
6 TraesCS5B01G220300 chr5D 336379521 336382232 2711 True 1004.666667 1676 86.632000 80 2850 3 chr5D.!!$R4 2770
7 TraesCS5B01G220300 chr5D 336256677 336258523 1846 True 743.000000 791 86.634500 303 2158 2 chr5D.!!$R3 1855
8 TraesCS5B01G220300 chr5A 437392122 437393829 1707 True 1808.000000 1808 85.956000 303 2046 1 chr5A.!!$R1 1743
9 TraesCS5B01G220300 chr5A 437399039 437400668 1629 True 1727.000000 1727 86.328000 323 1937 1 chr5A.!!$R2 1614
10 TraesCS5B01G220300 chr5A 437410858 437413300 2442 True 744.366667 1884 86.586667 316 2613 3 chr5A.!!$R3 2297

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
228 229 0.028902 GGCTCAAAACGAACACGCTT 59.971 50.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2742 0.108019 GGGAACGGTCTGTTTGTCCT 59.892 55.0 0.0 0.0 42.09 3.85 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
29 30 6.802608 TCGTATTGAGACTAAATGTAGGGTG 58.197 40.000 0.00 0.00 0.00 4.61
30 31 5.983720 CGTATTGAGACTAAATGTAGGGTGG 59.016 44.000 0.00 0.00 0.00 4.61
31 32 3.906720 TGAGACTAAATGTAGGGTGGC 57.093 47.619 0.00 0.00 0.00 5.01
32 33 3.450904 TGAGACTAAATGTAGGGTGGCT 58.549 45.455 0.00 0.00 0.00 4.75
33 34 4.616553 TGAGACTAAATGTAGGGTGGCTA 58.383 43.478 0.00 0.00 0.00 3.93
34 35 5.216622 TGAGACTAAATGTAGGGTGGCTAT 58.783 41.667 0.00 0.00 0.00 2.97
35 36 5.070446 TGAGACTAAATGTAGGGTGGCTATG 59.930 44.000 0.00 0.00 0.00 2.23
36 37 5.216622 AGACTAAATGTAGGGTGGCTATGA 58.783 41.667 0.00 0.00 0.00 2.15
37 38 5.305644 AGACTAAATGTAGGGTGGCTATGAG 59.694 44.000 0.00 0.00 0.00 2.90
38 39 3.864789 AAATGTAGGGTGGCTATGAGG 57.135 47.619 0.00 0.00 0.00 3.86
39 40 2.496679 ATGTAGGGTGGCTATGAGGT 57.503 50.000 0.00 0.00 0.00 3.85
40 41 1.789523 TGTAGGGTGGCTATGAGGTC 58.210 55.000 0.00 0.00 0.00 3.85
41 42 1.291033 TGTAGGGTGGCTATGAGGTCT 59.709 52.381 0.00 0.00 0.00 3.85
42 43 1.964933 GTAGGGTGGCTATGAGGTCTC 59.035 57.143 0.00 0.00 0.00 3.36
43 44 0.757188 AGGGTGGCTATGAGGTCTCG 60.757 60.000 0.00 0.00 0.00 4.04
44 45 1.068250 GGTGGCTATGAGGTCTCGC 59.932 63.158 0.00 0.00 0.00 5.03
45 46 1.299468 GTGGCTATGAGGTCTCGCG 60.299 63.158 0.00 0.00 0.00 5.87
46 47 1.453197 TGGCTATGAGGTCTCGCGA 60.453 57.895 9.26 9.26 0.00 5.87
47 48 1.035385 TGGCTATGAGGTCTCGCGAA 61.035 55.000 11.33 0.00 0.00 4.70
48 49 0.595310 GGCTATGAGGTCTCGCGAAC 60.595 60.000 11.33 11.39 0.00 3.95
49 50 0.930742 GCTATGAGGTCTCGCGAACG 60.931 60.000 11.33 0.00 42.01 3.95
50 51 0.930742 CTATGAGGTCTCGCGAACGC 60.931 60.000 11.33 9.20 39.84 4.84
68 69 4.922026 GGCCGGACACAACACCGT 62.922 66.667 5.05 0.00 46.53 4.83
69 70 3.645975 GCCGGACACAACACCGTG 61.646 66.667 5.05 0.00 46.53 4.94
70 71 3.645975 CCGGACACAACACCGTGC 61.646 66.667 0.00 0.00 46.53 5.34
71 72 2.892914 CGGACACAACACCGTGCA 60.893 61.111 0.00 0.00 43.53 4.57
72 73 2.713154 GGACACAACACCGTGCAC 59.287 61.111 6.82 6.82 40.73 4.57
73 74 2.713154 GACACAACACCGTGCACC 59.287 61.111 12.15 0.00 40.73 5.01
74 75 2.045829 ACACAACACCGTGCACCA 60.046 55.556 12.15 0.00 40.73 4.17
75 76 1.444119 GACACAACACCGTGCACCAT 61.444 55.000 12.15 0.00 40.73 3.55
76 77 1.008652 CACAACACCGTGCACCATG 60.009 57.895 12.15 12.24 0.00 3.66
77 78 2.192861 ACAACACCGTGCACCATGG 61.193 57.895 11.19 11.19 45.34 3.66
78 79 2.597217 AACACCGTGCACCATGGG 60.597 61.111 18.09 9.20 44.23 4.00
84 85 2.601367 GTGCACCATGGGCCACTT 60.601 61.111 22.60 0.00 0.00 3.16
131 132 5.913137 TCTTTCTCTCTCTTCATCTCCAC 57.087 43.478 0.00 0.00 0.00 4.02
136 137 4.648762 TCTCTCTCTTCATCTCCACCAATC 59.351 45.833 0.00 0.00 0.00 2.67
152 153 4.377370 TCACATGCAAGTGACCGG 57.623 55.556 20.17 0.00 43.18 5.28
159 160 3.133901 ACATGCAAGTGACCGGACATATA 59.866 43.478 9.46 0.00 0.00 0.86
160 161 3.897141 TGCAAGTGACCGGACATATAA 57.103 42.857 9.46 0.00 0.00 0.98
161 162 4.209307 TGCAAGTGACCGGACATATAAA 57.791 40.909 9.46 0.00 0.00 1.40
162 163 4.776349 TGCAAGTGACCGGACATATAAAT 58.224 39.130 9.46 0.00 0.00 1.40
163 164 5.919755 TGCAAGTGACCGGACATATAAATA 58.080 37.500 9.46 0.00 0.00 1.40
164 165 6.530120 TGCAAGTGACCGGACATATAAATAT 58.470 36.000 9.46 0.00 0.00 1.28
191 192 7.104290 AGTAAGAAAAGGTGGAGTATACTTGC 58.896 38.462 6.88 0.65 0.00 4.01
192 193 5.499004 AGAAAAGGTGGAGTATACTTGCA 57.501 39.130 6.88 0.00 0.00 4.08
193 194 6.067217 AGAAAAGGTGGAGTATACTTGCAT 57.933 37.500 6.88 0.00 0.00 3.96
211 212 1.676006 CATGGACGGACAAATAAGGGC 59.324 52.381 0.00 0.00 0.00 5.19
213 214 1.065709 TGGACGGACAAATAAGGGCTC 60.066 52.381 0.00 0.00 0.00 4.70
218 219 3.254903 ACGGACAAATAAGGGCTCAAAAC 59.745 43.478 0.00 0.00 0.00 2.43
220 221 3.504520 GGACAAATAAGGGCTCAAAACGA 59.495 43.478 0.00 0.00 0.00 3.85
228 229 0.028902 GGCTCAAAACGAACACGCTT 59.971 50.000 0.00 0.00 0.00 4.68
229 230 1.533129 GGCTCAAAACGAACACGCTTT 60.533 47.619 0.00 0.00 0.00 3.51
238 239 1.526887 CGAACACGCTTTGACACTGAT 59.473 47.619 0.00 0.00 0.00 2.90
240 241 2.238942 ACACGCTTTGACACTGATCA 57.761 45.000 0.00 0.00 0.00 2.92
245 246 1.198637 GCTTTGACACTGATCAGGCAC 59.801 52.381 26.08 15.90 32.77 5.01
246 247 1.462283 CTTTGACACTGATCAGGCACG 59.538 52.381 26.08 13.67 0.00 5.34
247 248 0.392706 TTGACACTGATCAGGCACGT 59.607 50.000 26.08 16.57 0.00 4.49
248 249 0.038251 TGACACTGATCAGGCACGTC 60.038 55.000 26.08 22.94 0.00 4.34
249 250 0.737715 GACACTGATCAGGCACGTCC 60.738 60.000 26.08 8.45 0.00 4.79
250 251 1.448540 CACTGATCAGGCACGTCCC 60.449 63.158 26.08 0.00 34.51 4.46
251 252 2.187946 CTGATCAGGCACGTCCCC 59.812 66.667 15.38 0.00 34.51 4.81
252 253 3.723235 CTGATCAGGCACGTCCCCG 62.723 68.421 15.38 0.00 40.83 5.73
253 254 4.530857 GATCAGGCACGTCCCCGG 62.531 72.222 0.00 0.00 38.78 5.73
278 279 3.433615 GTCTGAGGGACAAGATTTGTTCG 59.566 47.826 0.00 0.00 45.52 3.95
280 281 3.815401 CTGAGGGACAAGATTTGTTCGTT 59.185 43.478 0.00 0.00 45.52 3.85
292 293 2.605837 TGTTCGTTGTGGCTGTAGAA 57.394 45.000 0.00 0.00 0.00 2.10
294 295 1.798813 GTTCGTTGTGGCTGTAGAAGG 59.201 52.381 0.00 0.00 0.00 3.46
297 298 1.000955 CGTTGTGGCTGTAGAAGGTCT 59.999 52.381 0.00 0.00 0.00 3.85
307 308 2.248487 GTAGAAGGTCTTACGTGTGCG 58.752 52.381 0.00 0.00 44.93 5.34
312 313 1.296056 GGTCTTACGTGTGCGCCAAT 61.296 55.000 4.18 0.00 42.83 3.16
431 455 5.621193 TCAGGCTGCTAATTATTACTTCCC 58.379 41.667 10.34 0.00 0.00 3.97
461 486 3.432252 TGAGAAAGCCGACGATTTCTTTC 59.568 43.478 21.30 18.82 43.88 2.62
480 505 1.068417 ACGTACGTGCAGAGCCAAA 59.932 52.632 22.14 0.00 0.00 3.28
481 506 0.531090 ACGTACGTGCAGAGCCAAAA 60.531 50.000 22.14 0.00 0.00 2.44
547 577 2.183679 AGTCTCCTCCACAAGACCATC 58.816 52.381 0.00 0.00 42.34 3.51
554 609 3.431905 CCTCCACAAGACCATCATCAGAG 60.432 52.174 0.00 0.00 0.00 3.35
587 669 1.952102 TATGGCGACCAAGACGACCC 61.952 60.000 2.68 0.00 36.95 4.46
589 671 4.353437 GCGACCAAGACGACCCGT 62.353 66.667 0.00 0.00 45.10 5.28
622 726 0.036765 AAGCTTGCCGTACCGATCAA 60.037 50.000 0.00 0.00 0.00 2.57
713 853 2.036217 CTGCCAATGGATGTTGTGTTGT 59.964 45.455 2.05 0.00 0.00 3.32
797 960 0.248054 CAAAGCGTGCTTGTTGTCGT 60.248 50.000 8.03 0.00 36.26 4.34
963 1203 1.531602 GCTTGGTCTGGTGCCCTTT 60.532 57.895 0.00 0.00 0.00 3.11
971 1211 0.969149 CTGGTGCCCTTTTTCTTCCC 59.031 55.000 0.00 0.00 0.00 3.97
997 1237 1.348064 AGAACTGATCCGGTTGTCCA 58.652 50.000 0.00 0.00 32.62 4.02
1056 1296 3.382832 AGGAGGTACGCGCTGCTT 61.383 61.111 5.73 0.00 0.00 3.91
1062 1302 2.104331 TACGCGCTGCTTCTAGCC 59.896 61.111 5.73 0.00 41.51 3.93
1074 1314 3.449227 CTAGCCGCACGGGACTCA 61.449 66.667 11.65 0.00 38.47 3.41
1116 1356 2.609737 CGGAGGCTACTTCAACGTCTTT 60.610 50.000 0.00 0.00 0.00 2.52
1287 1548 1.671979 CCGACGACCTGTGGATACTA 58.328 55.000 0.00 0.00 37.61 1.82
1288 1549 2.019249 CCGACGACCTGTGGATACTAA 58.981 52.381 0.00 0.00 37.61 2.24
1446 1707 3.134127 GAGGTGGTCATTGCGGCC 61.134 66.667 0.00 0.00 0.00 6.13
1470 1731 4.016706 CCGCCGTGGAGGTTCCTT 62.017 66.667 0.00 0.00 43.70 3.36
1605 1882 0.532573 AGATGTTCTGTGTCGGCGAT 59.467 50.000 14.79 0.00 0.00 4.58
1676 1953 4.180946 CCTCGTCGACCGCCTCTG 62.181 72.222 10.58 0.00 36.19 3.35
1744 2037 1.262417 CATGATGCCATCGTTCTTCCG 59.738 52.381 0.00 0.00 0.00 4.30
1745 2038 0.249120 TGATGCCATCGTTCTTCCGT 59.751 50.000 0.00 0.00 0.00 4.69
1750 2043 2.128035 GCCATCGTTCTTCCGTGATAG 58.872 52.381 0.00 0.00 0.00 2.08
1751 2044 2.743938 CCATCGTTCTTCCGTGATAGG 58.256 52.381 0.00 0.00 0.00 2.57
1754 2047 3.984508 TCGTTCTTCCGTGATAGGATC 57.015 47.619 0.00 0.00 40.48 3.36
1820 2113 0.612174 AGGACGTGAAGAGGCAGCTA 60.612 55.000 0.00 0.00 0.00 3.32
1876 2169 3.217626 ACCTCTGCAAAAGTTTCCTCAG 58.782 45.455 0.00 0.00 0.00 3.35
2158 2725 0.468226 TCAAGGACAAGCAGACCGTT 59.532 50.000 0.00 0.00 37.13 4.44
2159 2726 0.868406 CAAGGACAAGCAGACCGTTC 59.132 55.000 0.00 0.00 37.13 3.95
2160 2727 0.250338 AAGGACAAGCAGACCGTTCC 60.250 55.000 0.00 0.00 37.13 3.62
2161 2728 1.671379 GGACAAGCAGACCGTTCCC 60.671 63.158 0.00 0.00 0.00 3.97
2162 2729 1.371558 GACAAGCAGACCGTTCCCT 59.628 57.895 0.00 0.00 0.00 4.20
2163 2730 0.670854 GACAAGCAGACCGTTCCCTC 60.671 60.000 0.00 0.00 0.00 4.30
2164 2731 1.371183 CAAGCAGACCGTTCCCTCA 59.629 57.895 0.00 0.00 0.00 3.86
2165 2732 0.250295 CAAGCAGACCGTTCCCTCAA 60.250 55.000 0.00 0.00 0.00 3.02
2166 2733 0.472471 AAGCAGACCGTTCCCTCAAA 59.528 50.000 0.00 0.00 0.00 2.69
2167 2734 0.472471 AGCAGACCGTTCCCTCAAAA 59.528 50.000 0.00 0.00 0.00 2.44
2168 2735 1.133915 AGCAGACCGTTCCCTCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
2192 2759 4.365899 AAAAAGGACAAACAGACCGTTC 57.634 40.909 0.00 0.00 36.59 3.95
2193 2760 1.963172 AAGGACAAACAGACCGTTCC 58.037 50.000 0.00 0.00 36.59 3.62
2194 2761 0.108019 AGGACAAACAGACCGTTCCC 59.892 55.000 0.00 0.00 36.59 3.97
2195 2762 0.108019 GGACAAACAGACCGTTCCCT 59.892 55.000 0.00 0.00 36.59 4.20
2196 2763 1.509703 GACAAACAGACCGTTCCCTC 58.490 55.000 0.00 0.00 36.59 4.30
2197 2764 0.834612 ACAAACAGACCGTTCCCTCA 59.165 50.000 0.00 0.00 36.59 3.86
2198 2765 1.210967 ACAAACAGACCGTTCCCTCAA 59.789 47.619 0.00 0.00 36.59 3.02
2199 2766 2.294074 CAAACAGACCGTTCCCTCAAA 58.706 47.619 0.00 0.00 36.59 2.69
2200 2767 2.685897 CAAACAGACCGTTCCCTCAAAA 59.314 45.455 0.00 0.00 36.59 2.44
2201 2768 2.721425 ACAGACCGTTCCCTCAAAAA 57.279 45.000 0.00 0.00 0.00 1.94
2241 2808 4.319549 CCGTAAGCTGACTTTTGGTTCTTC 60.320 45.833 0.00 0.00 37.33 2.87
2289 2856 9.260002 CCGGCATATAAATTTATGAAAAAGCTT 57.740 29.630 18.98 0.00 32.36 3.74
2307 2895 5.064441 AGCTTGAGTATGGCATTTCAAAC 57.936 39.130 20.44 17.57 0.00 2.93
2319 2907 4.331443 GGCATTTCAAACGTTTTTCTTGGT 59.669 37.500 11.66 0.00 0.00 3.67
2348 2936 2.279935 TGTATTGGGGCGACAGTTTT 57.720 45.000 0.00 0.00 0.00 2.43
2404 2992 0.365523 CACACGAGTAATTCACCGCG 59.634 55.000 0.00 0.00 0.00 6.46
2406 2994 0.365523 CACGAGTAATTCACCGCGTG 59.634 55.000 4.92 12.08 44.53 5.34
2407 2995 0.038892 ACGAGTAATTCACCGCGTGT 60.039 50.000 4.92 0.00 37.31 4.49
2408 2996 1.199789 ACGAGTAATTCACCGCGTGTA 59.800 47.619 4.92 0.00 37.31 2.90
2409 2997 2.252747 CGAGTAATTCACCGCGTGTAA 58.747 47.619 4.92 0.00 34.79 2.41
2410 2998 2.662637 CGAGTAATTCACCGCGTGTAAA 59.337 45.455 4.92 0.00 34.79 2.01
2411 2999 3.305094 CGAGTAATTCACCGCGTGTAAAT 59.695 43.478 4.92 0.00 34.79 1.40
2413 3001 4.965062 AGTAATTCACCGCGTGTAAATTG 58.035 39.130 15.09 0.00 34.79 2.32
2422 3029 1.266404 GCGTGTAAATTGCGTCTCTCG 60.266 52.381 0.00 0.00 43.12 4.04
2438 3045 0.110056 CTCGTTCTGCAACACCATGC 60.110 55.000 0.00 0.00 46.58 4.06
2489 3096 5.639757 TCCATGTTGCATAAAATGAAGACG 58.360 37.500 0.00 0.00 0.00 4.18
2533 3141 5.903764 GCAATATTGTCTGTGTTGCAAAA 57.096 34.783 16.61 0.00 43.33 2.44
2534 3142 5.908106 GCAATATTGTCTGTGTTGCAAAAG 58.092 37.500 16.61 0.00 43.33 2.27
2539 3148 5.837586 TTGTCTGTGTTGCAAAAGTTTTC 57.162 34.783 0.00 0.00 0.00 2.29
2560 3169 2.370349 CCCGCAACAACACCCATATTA 58.630 47.619 0.00 0.00 0.00 0.98
2606 3215 5.886960 AAAACTTCAGCATCACCTATGTC 57.113 39.130 0.00 0.00 37.93 3.06
2618 3227 5.545658 TCACCTATGTCGCAAAAGATTTC 57.454 39.130 0.00 0.00 0.00 2.17
2633 3242 8.006027 GCAAAAGATTTCTGCAACATAAACTTC 58.994 33.333 0.00 0.00 36.09 3.01
2646 3258 8.280909 CAACATAAACTTCGTTGCAAAGTATT 57.719 30.769 12.18 7.16 35.96 1.89
2650 3262 5.751243 AACTTCGTTGCAAAGTATTCTGT 57.249 34.783 12.18 1.69 35.96 3.41
2658 3270 7.007697 CGTTGCAAAGTATTCTGTAACACTAC 58.992 38.462 0.00 0.00 37.83 2.73
2676 3288 4.218200 CACTACCCTTGTTGCAATGATGAA 59.782 41.667 0.59 0.00 0.00 2.57
2679 3291 5.231702 ACCCTTGTTGCAATGATGAAAAT 57.768 34.783 0.59 0.00 0.00 1.82
2680 3292 5.623169 ACCCTTGTTGCAATGATGAAAATT 58.377 33.333 0.59 0.00 0.00 1.82
2691 3303 2.029470 TGATGAAAATTGCCGTTGGACC 60.029 45.455 0.00 0.00 0.00 4.46
2694 3306 0.678950 AAAATTGCCGTTGGACCCTG 59.321 50.000 0.00 0.00 0.00 4.45
2703 3315 1.971357 CGTTGGACCCTGGATAGCTAT 59.029 52.381 5.76 5.76 0.00 2.97
2714 3326 5.481824 CCCTGGATAGCTATACATCTTGACA 59.518 44.000 19.14 0.00 0.00 3.58
2721 3333 9.497030 GATAGCTATACATCTTGACAGTTATCG 57.503 37.037 6.13 0.00 0.00 2.92
2725 3337 3.786635 ACATCTTGACAGTTATCGAGGC 58.213 45.455 0.00 0.00 31.74 4.70
2735 3347 2.142357 TTATCGAGGCGGCGGATCTG 62.142 60.000 18.91 0.00 0.00 2.90
2743 3355 0.931005 GCGGCGGATCTGTTAGAAAG 59.069 55.000 9.78 0.00 0.00 2.62
2754 3366 3.764434 TCTGTTAGAAAGATCTGTCGGCT 59.236 43.478 7.27 0.00 37.10 5.52
2767 3379 3.172575 CGGCTGACGTGTAGTGCG 61.173 66.667 0.00 0.00 37.93 5.34
2776 3388 3.390521 TGTAGTGCGCCCCCTCTG 61.391 66.667 4.18 0.00 0.00 3.35
2782 3394 4.056125 GCGCCCCCTCTGCAAAAC 62.056 66.667 0.00 0.00 0.00 2.43
2792 3404 4.142315 CCCCTCTGCAAAACAACATGATAG 60.142 45.833 0.00 0.00 0.00 2.08
2799 3411 7.978414 TCTGCAAAACAACATGATAGTTCAAAA 59.022 29.630 0.00 0.00 34.96 2.44
2850 3463 2.894765 CCCCCGACCAACTAAAATTGTT 59.105 45.455 0.00 0.00 0.00 2.83
2851 3464 4.080687 CCCCCGACCAACTAAAATTGTTA 58.919 43.478 0.00 0.00 0.00 2.41
2852 3465 4.707934 CCCCCGACCAACTAAAATTGTTAT 59.292 41.667 0.00 0.00 0.00 1.89
2853 3466 5.163591 CCCCCGACCAACTAAAATTGTTATC 60.164 44.000 0.00 0.00 0.00 1.75
2854 3467 5.416326 CCCCGACCAACTAAAATTGTTATCA 59.584 40.000 0.00 0.00 0.00 2.15
2855 3468 6.071840 CCCCGACCAACTAAAATTGTTATCAA 60.072 38.462 0.00 0.00 37.98 2.57
2856 3469 7.371936 CCCGACCAACTAAAATTGTTATCAAA 58.628 34.615 0.00 0.00 37.11 2.69
2857 3470 7.868415 CCCGACCAACTAAAATTGTTATCAAAA 59.132 33.333 0.00 0.00 37.11 2.44
2858 3471 8.696175 CCGACCAACTAAAATTGTTATCAAAAC 58.304 33.333 0.00 0.00 37.11 2.43
2859 3472 9.239002 CGACCAACTAAAATTGTTATCAAAACA 57.761 29.630 0.00 0.00 37.11 2.83
2877 3490 8.828688 TCAAAACATTCACAAATATCATGCAA 57.171 26.923 0.00 0.00 0.00 4.08
2878 3491 9.269453 TCAAAACATTCACAAATATCATGCAAA 57.731 25.926 0.00 0.00 0.00 3.68
2879 3492 9.880064 CAAAACATTCACAAATATCATGCAAAA 57.120 25.926 0.00 0.00 0.00 2.44
2880 3493 9.881529 AAAACATTCACAAATATCATGCAAAAC 57.118 25.926 0.00 0.00 0.00 2.43
2881 3494 8.836268 AACATTCACAAATATCATGCAAAACT 57.164 26.923 0.00 0.00 0.00 2.66
2882 3495 8.836268 ACATTCACAAATATCATGCAAAACTT 57.164 26.923 0.00 0.00 0.00 2.66
2883 3496 8.714179 ACATTCACAAATATCATGCAAAACTTG 58.286 29.630 0.00 0.00 0.00 3.16
2884 3497 8.714179 CATTCACAAATATCATGCAAAACTTGT 58.286 29.630 0.00 0.00 0.00 3.16
2885 3498 7.640616 TCACAAATATCATGCAAAACTTGTG 57.359 32.000 17.01 17.01 42.25 3.33
2886 3499 6.145858 TCACAAATATCATGCAAAACTTGTGC 59.854 34.615 17.77 0.00 41.22 4.57
2887 3500 5.118971 ACAAATATCATGCAAAACTTGTGCG 59.881 36.000 0.00 0.00 45.27 5.34
2888 3501 4.700268 ATATCATGCAAAACTTGTGCGA 57.300 36.364 0.00 0.00 45.27 5.10
2889 3502 2.859526 TCATGCAAAACTTGTGCGAA 57.140 40.000 0.00 0.00 45.27 4.70
2890 3503 2.458951 TCATGCAAAACTTGTGCGAAC 58.541 42.857 0.00 0.00 45.27 3.95
2891 3504 2.159324 TCATGCAAAACTTGTGCGAACA 60.159 40.909 0.00 0.00 45.27 3.18
2892 3505 1.623359 TGCAAAACTTGTGCGAACAC 58.377 45.000 0.00 0.00 45.27 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.448006 CCTACATTTAGTCTCAATACGAGGG 58.552 44.000 0.00 0.00 42.55 4.30
3 4 6.040616 ACCCTACATTTAGTCTCAATACGAGG 59.959 42.308 0.00 0.00 42.55 4.63
4 5 6.918569 CACCCTACATTTAGTCTCAATACGAG 59.081 42.308 0.00 0.00 43.80 4.18
5 6 6.183360 CCACCCTACATTTAGTCTCAATACGA 60.183 42.308 0.00 0.00 0.00 3.43
6 7 5.983720 CCACCCTACATTTAGTCTCAATACG 59.016 44.000 0.00 0.00 0.00 3.06
7 8 5.758784 GCCACCCTACATTTAGTCTCAATAC 59.241 44.000 0.00 0.00 0.00 1.89
9 10 4.475016 AGCCACCCTACATTTAGTCTCAAT 59.525 41.667 0.00 0.00 0.00 2.57
10 11 3.844211 AGCCACCCTACATTTAGTCTCAA 59.156 43.478 0.00 0.00 0.00 3.02
11 12 3.450904 AGCCACCCTACATTTAGTCTCA 58.549 45.455 0.00 0.00 0.00 3.27
12 13 5.304614 TCATAGCCACCCTACATTTAGTCTC 59.695 44.000 0.00 0.00 0.00 3.36
13 14 5.216622 TCATAGCCACCCTACATTTAGTCT 58.783 41.667 0.00 0.00 0.00 3.24
14 15 5.511545 CCTCATAGCCACCCTACATTTAGTC 60.512 48.000 0.00 0.00 0.00 2.59
15 16 4.348168 CCTCATAGCCACCCTACATTTAGT 59.652 45.833 0.00 0.00 0.00 2.24
16 17 4.348168 ACCTCATAGCCACCCTACATTTAG 59.652 45.833 0.00 0.00 0.00 1.85
17 18 4.303794 ACCTCATAGCCACCCTACATTTA 58.696 43.478 0.00 0.00 0.00 1.40
18 19 3.123273 ACCTCATAGCCACCCTACATTT 58.877 45.455 0.00 0.00 0.00 2.32
19 20 2.706190 GACCTCATAGCCACCCTACATT 59.294 50.000 0.00 0.00 0.00 2.71
20 21 2.090494 AGACCTCATAGCCACCCTACAT 60.090 50.000 0.00 0.00 0.00 2.29
21 22 1.291033 AGACCTCATAGCCACCCTACA 59.709 52.381 0.00 0.00 0.00 2.74
22 23 1.964933 GAGACCTCATAGCCACCCTAC 59.035 57.143 0.00 0.00 0.00 3.18
23 24 1.478837 CGAGACCTCATAGCCACCCTA 60.479 57.143 0.00 0.00 0.00 3.53
24 25 0.757188 CGAGACCTCATAGCCACCCT 60.757 60.000 0.00 0.00 0.00 4.34
25 26 1.742768 CGAGACCTCATAGCCACCC 59.257 63.158 0.00 0.00 0.00 4.61
26 27 1.068250 GCGAGACCTCATAGCCACC 59.932 63.158 0.00 0.00 0.00 4.61
27 28 1.299468 CGCGAGACCTCATAGCCAC 60.299 63.158 0.00 0.00 0.00 5.01
28 29 1.035385 TTCGCGAGACCTCATAGCCA 61.035 55.000 9.59 0.00 41.84 4.75
29 30 0.595310 GTTCGCGAGACCTCATAGCC 60.595 60.000 9.59 0.00 41.84 3.93
30 31 0.930742 CGTTCGCGAGACCTCATAGC 60.931 60.000 9.59 0.00 44.71 2.97
31 32 0.930742 GCGTTCGCGAGACCTCATAG 60.931 60.000 9.59 0.00 44.71 2.23
32 33 1.063649 GCGTTCGCGAGACCTCATA 59.936 57.895 9.59 0.00 44.71 2.15
33 34 2.202623 GCGTTCGCGAGACCTCAT 60.203 61.111 9.59 0.00 44.71 2.90
55 56 2.713154 GTGCACGGTGTTGTGTCC 59.287 61.111 10.24 0.00 41.94 4.02
56 57 1.444119 ATGGTGCACGGTGTTGTGTC 61.444 55.000 11.45 0.00 41.94 3.67
57 58 1.453015 ATGGTGCACGGTGTTGTGT 60.453 52.632 11.45 0.00 41.94 3.72
58 59 1.008652 CATGGTGCACGGTGTTGTG 60.009 57.895 11.45 0.00 42.81 3.33
59 60 2.192861 CCATGGTGCACGGTGTTGT 61.193 57.895 11.45 0.00 0.00 3.32
60 61 2.644418 CCATGGTGCACGGTGTTG 59.356 61.111 11.45 3.64 0.00 3.33
61 62 2.597217 CCCATGGTGCACGGTGTT 60.597 61.111 11.73 0.00 0.00 3.32
67 68 1.757423 AAAAGTGGCCCATGGTGCAC 61.757 55.000 21.92 8.80 0.00 4.57
68 69 1.053264 AAAAAGTGGCCCATGGTGCA 61.053 50.000 21.92 9.36 0.00 4.57
69 70 0.320683 GAAAAAGTGGCCCATGGTGC 60.321 55.000 11.73 13.54 0.00 5.01
70 71 1.273327 GAGAAAAAGTGGCCCATGGTG 59.727 52.381 11.73 3.26 0.00 4.17
71 72 1.147817 AGAGAAAAAGTGGCCCATGGT 59.852 47.619 11.73 0.00 0.00 3.55
72 73 1.928868 AGAGAAAAAGTGGCCCATGG 58.071 50.000 4.14 4.14 0.00 3.66
73 74 3.575687 AGAAAGAGAAAAAGTGGCCCATG 59.424 43.478 0.00 0.00 0.00 3.66
74 75 3.849527 AGAAAGAGAAAAAGTGGCCCAT 58.150 40.909 0.00 0.00 0.00 4.00
75 76 3.312736 AGAAAGAGAAAAAGTGGCCCA 57.687 42.857 0.00 0.00 0.00 5.36
76 77 4.672587 AAAGAAAGAGAAAAAGTGGCCC 57.327 40.909 0.00 0.00 0.00 5.80
77 78 7.661968 AGAATAAAGAAAGAGAAAAAGTGGCC 58.338 34.615 0.00 0.00 0.00 5.36
78 79 9.534565 AAAGAATAAAGAAAGAGAAAAAGTGGC 57.465 29.630 0.00 0.00 0.00 5.01
105 106 7.823799 GTGGAGATGAAGAGAGAGAAAGAAAAT 59.176 37.037 0.00 0.00 0.00 1.82
124 125 2.812836 TGCATGTGATTGGTGGAGAT 57.187 45.000 0.00 0.00 0.00 2.75
128 129 1.887854 TCACTTGCATGTGATTGGTGG 59.112 47.619 26.52 4.09 41.43 4.61
131 132 1.135603 CGGTCACTTGCATGTGATTGG 60.136 52.381 30.91 20.98 46.77 3.16
136 137 0.884259 TGTCCGGTCACTTGCATGTG 60.884 55.000 23.12 23.12 39.15 3.21
169 170 5.876357 TGCAAGTATACTCCACCTTTTCTT 58.124 37.500 5.70 0.00 0.00 2.52
176 177 3.467803 GTCCATGCAAGTATACTCCACC 58.532 50.000 5.70 0.00 0.00 4.61
178 179 2.102420 CCGTCCATGCAAGTATACTCCA 59.898 50.000 5.70 7.22 0.00 3.86
183 184 3.897141 TTGTCCGTCCATGCAAGTATA 57.103 42.857 0.00 0.00 0.00 1.47
186 187 1.909700 ATTTGTCCGTCCATGCAAGT 58.090 45.000 0.00 0.00 0.00 3.16
187 188 3.181497 CCTTATTTGTCCGTCCATGCAAG 60.181 47.826 0.00 0.00 0.00 4.01
188 189 2.752354 CCTTATTTGTCCGTCCATGCAA 59.248 45.455 0.00 0.00 0.00 4.08
189 190 2.364632 CCTTATTTGTCCGTCCATGCA 58.635 47.619 0.00 0.00 0.00 3.96
190 191 1.676006 CCCTTATTTGTCCGTCCATGC 59.324 52.381 0.00 0.00 0.00 4.06
191 192 1.676006 GCCCTTATTTGTCCGTCCATG 59.324 52.381 0.00 0.00 0.00 3.66
192 193 1.564348 AGCCCTTATTTGTCCGTCCAT 59.436 47.619 0.00 0.00 0.00 3.41
193 194 0.988832 AGCCCTTATTTGTCCGTCCA 59.011 50.000 0.00 0.00 0.00 4.02
218 219 0.927537 TCAGTGTCAAAGCGTGTTCG 59.072 50.000 0.00 0.00 40.37 3.95
220 221 2.545526 CTGATCAGTGTCAAAGCGTGTT 59.454 45.455 14.95 0.00 0.00 3.32
228 229 0.392706 ACGTGCCTGATCAGTGTCAA 59.607 50.000 21.11 0.00 0.00 3.18
229 230 0.038251 GACGTGCCTGATCAGTGTCA 60.038 55.000 21.11 12.68 0.00 3.58
246 247 3.450115 CCTCAGACGTCCGGGGAC 61.450 72.222 12.73 7.82 41.40 4.46
247 248 4.753662 CCCTCAGACGTCCGGGGA 62.754 72.222 19.75 7.86 39.42 4.81
248 249 4.753662 TCCCTCAGACGTCCGGGG 62.754 72.222 26.00 24.94 37.30 5.73
249 250 3.450115 GTCCCTCAGACGTCCGGG 61.450 72.222 22.65 22.65 35.30 5.73
278 279 2.841442 AGACCTTCTACAGCCACAAC 57.159 50.000 0.00 0.00 0.00 3.32
280 281 2.230508 CGTAAGACCTTCTACAGCCACA 59.769 50.000 0.00 0.00 43.02 4.17
292 293 2.048503 GGCGCACACGTAAGACCT 60.049 61.111 10.83 0.00 42.83 3.85
294 295 1.352114 TATTGGCGCACACGTAAGAC 58.648 50.000 10.83 0.00 42.83 3.01
297 298 3.783191 TCTTATATTGGCGCACACGTAA 58.217 40.909 10.83 1.62 42.83 3.18
307 308 9.732130 AGAGTTCTCCATTTATCTTATATTGGC 57.268 33.333 0.00 0.00 0.00 4.52
431 455 2.973224 CGTCGGCTTTCTCATTTGTTTG 59.027 45.455 0.00 0.00 0.00 2.93
554 609 1.528129 GCCATATTAGTCAGCAGCCC 58.472 55.000 0.00 0.00 0.00 5.19
591 673 1.211709 CAAGCTTTTTACCGGGCCG 59.788 57.895 21.46 21.46 0.00 6.13
592 674 1.080093 GCAAGCTTTTTACCGGGCC 60.080 57.895 6.32 0.00 0.00 5.80
593 675 1.080093 GGCAAGCTTTTTACCGGGC 60.080 57.895 6.32 0.00 0.00 6.13
594 676 1.211709 CGGCAAGCTTTTTACCGGG 59.788 57.895 6.32 0.00 40.18 5.73
595 677 4.859784 CGGCAAGCTTTTTACCGG 57.140 55.556 15.67 0.00 40.18 5.28
597 679 2.624316 GGTACGGCAAGCTTTTTACC 57.376 50.000 0.00 1.51 0.00 2.85
622 726 2.073056 TGCAGCACGTACGAAATGATT 58.927 42.857 24.41 0.00 0.00 2.57
697 821 3.380004 ACACGAACAACACAACATCCATT 59.620 39.130 0.00 0.00 0.00 3.16
713 853 6.255215 GTTGAAATTCTTTGTCTGACACGAA 58.745 36.000 10.56 15.50 0.00 3.85
778 941 0.248054 ACGACAACAAGCACGCTTTG 60.248 50.000 0.44 1.73 33.42 2.77
971 1211 1.699656 CCGGATCAGTTCTTGCAGCG 61.700 60.000 0.00 0.00 0.00 5.18
997 1237 1.180029 GCTGCCACAATCTTCATGGT 58.820 50.000 0.00 0.00 35.79 3.55
1030 1270 2.010582 GCGTACCTCCTGCTCCTCTG 62.011 65.000 0.00 0.00 0.00 3.35
1031 1271 1.755008 GCGTACCTCCTGCTCCTCT 60.755 63.158 0.00 0.00 0.00 3.69
1056 1296 3.138798 GAGTCCCGTGCGGCTAGA 61.139 66.667 4.91 0.00 0.00 2.43
1062 1302 1.136984 GTACTCTGAGTCCCGTGCG 59.863 63.158 14.62 0.00 0.00 5.34
1065 1305 1.584380 GCACGTACTCTGAGTCCCGT 61.584 60.000 22.15 22.15 36.69 5.28
1074 1314 1.912417 AGACCTTGAGCACGTACTCT 58.088 50.000 16.53 0.59 37.58 3.24
1219 1480 1.908089 CGAAGCCGTCGTATCGTTG 59.092 57.895 0.00 0.00 45.09 4.10
1220 1481 4.372235 CGAAGCCGTCGTATCGTT 57.628 55.556 0.00 0.00 45.09 3.85
1275 1536 2.743183 GCACAGCCTTAGTATCCACAGG 60.743 54.545 0.00 0.00 0.00 4.00
1389 1650 2.041928 CCTCTCCTGGCCTTCCCT 59.958 66.667 3.32 0.00 0.00 4.20
1496 1757 2.125512 ACTCGGTGATCTTGGCGC 60.126 61.111 0.00 0.00 0.00 6.53
1569 1830 2.915659 TCCACGCCGGTCTTGTCT 60.916 61.111 1.90 0.00 35.57 3.41
1605 1882 3.477582 TGGATTCCCAGCACGTGA 58.522 55.556 22.23 0.00 37.58 4.35
1751 2044 5.558818 ACTGGCAAATCAGATCCTATGATC 58.441 41.667 0.01 0.01 46.52 2.92
1754 2047 5.735354 GCAAACTGGCAAATCAGATCCTATG 60.735 44.000 0.00 0.00 38.11 2.23
1840 2133 0.687354 GAGGTTGAGCCAGAACTCCA 59.313 55.000 0.00 0.00 40.61 3.86
1876 2169 3.873910 TGCTAGTACAATTCTTCAGCCC 58.126 45.455 0.00 0.00 0.00 5.19
1937 2233 0.533491 ATTAACACCACGCCGCTAGA 59.467 50.000 0.00 0.00 0.00 2.43
2104 2412 7.453752 GTCCCTCCCTCATAACTATACAACATA 59.546 40.741 0.00 0.00 0.00 2.29
2124 2691 4.257731 GTCCTTGAATCTTTCTGTCCCTC 58.742 47.826 0.00 0.00 0.00 4.30
2171 2738 3.129813 GGAACGGTCTGTTTGTCCTTTTT 59.870 43.478 0.00 0.00 42.09 1.94
2172 2739 2.686405 GGAACGGTCTGTTTGTCCTTTT 59.314 45.455 0.00 0.00 42.09 2.27
2173 2740 2.294979 GGAACGGTCTGTTTGTCCTTT 58.705 47.619 0.00 0.00 42.09 3.11
2174 2741 1.476291 GGGAACGGTCTGTTTGTCCTT 60.476 52.381 0.00 0.00 42.09 3.36
2175 2742 0.108019 GGGAACGGTCTGTTTGTCCT 59.892 55.000 0.00 0.00 42.09 3.85
2176 2743 0.108019 AGGGAACGGTCTGTTTGTCC 59.892 55.000 0.00 2.02 42.09 4.02
2177 2744 1.202604 TGAGGGAACGGTCTGTTTGTC 60.203 52.381 0.00 0.00 42.09 3.18
2178 2745 0.834612 TGAGGGAACGGTCTGTTTGT 59.165 50.000 0.00 0.00 42.09 2.83
2179 2746 1.961793 TTGAGGGAACGGTCTGTTTG 58.038 50.000 0.00 0.00 42.09 2.93
2180 2747 2.721425 TTTGAGGGAACGGTCTGTTT 57.279 45.000 0.00 0.00 42.09 2.83
2181 2748 2.721425 TTTTGAGGGAACGGTCTGTT 57.279 45.000 0.00 0.00 45.61 3.16
2182 2749 2.721425 TTTTTGAGGGAACGGTCTGT 57.279 45.000 0.00 0.00 0.00 3.41
2202 2769 4.201980 GCTTACGGTCTGTTTGTCCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
2203 2770 3.314357 GCTTACGGTCTGTTTGTCCTTTT 59.686 43.478 0.00 0.00 0.00 2.27
2204 2771 2.876550 GCTTACGGTCTGTTTGTCCTTT 59.123 45.455 0.00 0.00 0.00 3.11
2205 2772 2.104281 AGCTTACGGTCTGTTTGTCCTT 59.896 45.455 0.00 0.00 0.00 3.36
2206 2773 1.692519 AGCTTACGGTCTGTTTGTCCT 59.307 47.619 0.00 0.00 0.00 3.85
2207 2774 1.798813 CAGCTTACGGTCTGTTTGTCC 59.201 52.381 0.00 0.00 0.00 4.02
2208 2775 2.475487 GTCAGCTTACGGTCTGTTTGTC 59.525 50.000 0.00 0.00 0.00 3.18
2209 2776 2.102588 AGTCAGCTTACGGTCTGTTTGT 59.897 45.455 0.00 0.00 0.00 2.83
2210 2777 2.755650 AGTCAGCTTACGGTCTGTTTG 58.244 47.619 0.00 0.00 0.00 2.93
2211 2778 3.470645 AAGTCAGCTTACGGTCTGTTT 57.529 42.857 0.00 0.00 32.27 2.83
2212 2779 3.470645 AAAGTCAGCTTACGGTCTGTT 57.529 42.857 0.00 0.00 33.95 3.16
2213 2780 3.131396 CAAAAGTCAGCTTACGGTCTGT 58.869 45.455 0.00 0.00 33.95 3.41
2214 2781 2.480419 CCAAAAGTCAGCTTACGGTCTG 59.520 50.000 0.00 0.00 33.95 3.51
2215 2782 2.104281 ACCAAAAGTCAGCTTACGGTCT 59.896 45.455 0.00 0.00 35.63 3.85
2216 2783 2.490991 ACCAAAAGTCAGCTTACGGTC 58.509 47.619 0.00 0.00 35.63 4.79
2217 2784 2.632987 ACCAAAAGTCAGCTTACGGT 57.367 45.000 0.00 0.00 35.66 4.83
2218 2785 3.139077 AGAACCAAAAGTCAGCTTACGG 58.861 45.455 0.00 0.00 33.95 4.02
2219 2786 4.511826 AGAAGAACCAAAAGTCAGCTTACG 59.488 41.667 0.00 0.00 33.95 3.18
2220 2787 6.378710 AAGAAGAACCAAAAGTCAGCTTAC 57.621 37.500 0.00 0.00 33.95 2.34
2221 2788 6.238374 CGAAAGAAGAACCAAAAGTCAGCTTA 60.238 38.462 0.00 0.00 33.95 3.09
2222 2789 5.449177 CGAAAGAAGAACCAAAAGTCAGCTT 60.449 40.000 0.00 0.00 36.30 3.74
2223 2790 4.035675 CGAAAGAAGAACCAAAAGTCAGCT 59.964 41.667 0.00 0.00 0.00 4.24
2263 2830 8.816640 AGCTTTTTCATAAATTTATATGCCGG 57.183 30.769 10.34 0.00 34.05 6.13
2289 2856 5.446143 AAACGTTTGAAATGCCATACTCA 57.554 34.783 13.81 0.00 0.00 3.41
2307 2895 9.940166 ATACAACTAAAACTACCAAGAAAAACG 57.060 29.630 0.00 0.00 0.00 3.60
2319 2907 4.937015 GTCGCCCCAATACAACTAAAACTA 59.063 41.667 0.00 0.00 0.00 2.24
2348 2936 3.103742 AGGCAAGTGTTTCCCTTTGAAA 58.896 40.909 0.00 0.00 40.64 2.69
2354 2942 1.986882 CTGAAGGCAAGTGTTTCCCT 58.013 50.000 0.00 0.00 0.00 4.20
2357 2945 0.040067 CGGCTGAAGGCAAGTGTTTC 60.040 55.000 4.64 0.00 44.01 2.78
2393 2981 3.725305 CGCAATTTACACGCGGTGAATTA 60.725 43.478 21.13 3.16 42.00 1.40
2394 2982 2.591133 GCAATTTACACGCGGTGAATT 58.409 42.857 12.47 16.26 43.96 2.17
2404 2992 3.673809 AGAACGAGAGACGCAATTTACAC 59.326 43.478 0.00 0.00 46.94 2.90
2406 2994 3.482112 GCAGAACGAGAGACGCAATTTAC 60.482 47.826 0.00 0.00 46.94 2.01
2407 2995 2.666508 GCAGAACGAGAGACGCAATTTA 59.333 45.455 0.00 0.00 46.94 1.40
2408 2996 1.461127 GCAGAACGAGAGACGCAATTT 59.539 47.619 0.00 0.00 46.94 1.82
2409 2997 1.071605 GCAGAACGAGAGACGCAATT 58.928 50.000 0.00 0.00 46.94 2.32
2410 2998 0.038251 TGCAGAACGAGAGACGCAAT 60.038 50.000 0.00 0.00 46.94 3.56
2411 2999 0.249280 TTGCAGAACGAGAGACGCAA 60.249 50.000 0.00 0.00 46.94 4.85
2413 3001 0.939577 TGTTGCAGAACGAGAGACGC 60.940 55.000 0.00 0.00 46.94 5.19
2422 3029 0.661187 CACGCATGGTGTTGCAGAAC 60.661 55.000 0.00 0.00 42.91 3.01
2438 3045 1.003262 CGGAAGGCAATTGCAACACG 61.003 55.000 30.32 23.24 44.36 4.49
2439 3046 1.284297 GCGGAAGGCAATTGCAACAC 61.284 55.000 30.32 17.56 44.36 3.32
2466 3073 5.392919 CCGTCTTCATTTTATGCAACATGGA 60.393 40.000 0.00 0.00 0.00 3.41
2515 3123 6.533367 GGAAAACTTTTGCAACACAGACAATA 59.467 34.615 0.00 0.00 0.00 1.90
2530 3138 2.028020 TGTTGTTGCGGGGAAAACTTTT 60.028 40.909 0.00 0.00 0.00 2.27
2533 3141 0.458260 GTGTTGTTGCGGGGAAAACT 59.542 50.000 0.00 0.00 0.00 2.66
2534 3142 0.528901 GGTGTTGTTGCGGGGAAAAC 60.529 55.000 0.00 0.00 0.00 2.43
2539 3148 0.682855 ATATGGGTGTTGTTGCGGGG 60.683 55.000 0.00 0.00 0.00 5.73
2583 3192 5.106555 CGACATAGGTGATGCTGAAGTTTTT 60.107 40.000 0.00 0.00 39.39 1.94
2584 3193 4.393062 CGACATAGGTGATGCTGAAGTTTT 59.607 41.667 0.00 0.00 39.39 2.43
2585 3194 3.935203 CGACATAGGTGATGCTGAAGTTT 59.065 43.478 0.00 0.00 39.39 2.66
2593 3202 2.677836 TCTTTTGCGACATAGGTGATGC 59.322 45.455 0.00 0.00 39.39 3.91
2606 3215 6.144402 AGTTTATGTTGCAGAAATCTTTTGCG 59.856 34.615 0.00 0.00 40.62 4.85
2633 3242 5.985781 AGTGTTACAGAATACTTTGCAACG 58.014 37.500 0.00 0.00 33.57 4.10
2646 3258 3.134985 TGCAACAAGGGTAGTGTTACAGA 59.865 43.478 0.00 0.00 37.09 3.41
2650 3262 4.720046 TCATTGCAACAAGGGTAGTGTTA 58.280 39.130 0.00 0.00 37.09 2.41
2658 3270 5.933790 CAATTTTCATCATTGCAACAAGGG 58.066 37.500 0.00 0.00 0.00 3.95
2676 3288 1.184970 CCAGGGTCCAACGGCAATTT 61.185 55.000 0.00 0.00 0.00 1.82
2679 3291 1.202099 TATCCAGGGTCCAACGGCAA 61.202 55.000 0.00 0.00 0.00 4.52
2680 3292 1.613928 TATCCAGGGTCCAACGGCA 60.614 57.895 0.00 0.00 0.00 5.69
2682 3294 1.146263 GCTATCCAGGGTCCAACGG 59.854 63.158 0.00 0.00 0.00 4.44
2691 3303 6.210385 ACTGTCAAGATGTATAGCTATCCAGG 59.790 42.308 10.16 0.00 0.00 4.45
2694 3306 9.796120 GATAACTGTCAAGATGTATAGCTATCC 57.204 37.037 10.16 0.00 0.00 2.59
2703 3315 4.497507 CGCCTCGATAACTGTCAAGATGTA 60.498 45.833 0.00 0.00 0.00 2.29
2714 3326 2.143594 GATCCGCCGCCTCGATAACT 62.144 60.000 0.00 0.00 0.00 2.24
2721 3333 1.300233 CTAACAGATCCGCCGCCTC 60.300 63.158 0.00 0.00 0.00 4.70
2725 3337 2.579207 TCTTTCTAACAGATCCGCCG 57.421 50.000 0.00 0.00 0.00 6.46
2735 3347 3.860536 GTCAGCCGACAGATCTTTCTAAC 59.139 47.826 7.27 0.00 42.13 2.34
2743 3355 0.450583 TACACGTCAGCCGACAGATC 59.549 55.000 0.20 0.00 42.74 2.75
2749 3361 2.257371 GCACTACACGTCAGCCGA 59.743 61.111 0.00 0.00 40.70 5.54
2754 3366 4.367023 GGGGCGCACTACACGTCA 62.367 66.667 10.74 0.00 36.72 4.35
2767 3379 1.367471 GTTGTTTTGCAGAGGGGGC 59.633 57.895 0.00 0.00 0.00 5.80
2851 3464 9.438228 TTGCATGATATTTGTGAATGTTTTGAT 57.562 25.926 0.00 0.00 0.00 2.57
2852 3465 8.828688 TTGCATGATATTTGTGAATGTTTTGA 57.171 26.923 0.00 0.00 0.00 2.69
2853 3466 9.880064 TTTTGCATGATATTTGTGAATGTTTTG 57.120 25.926 0.00 0.00 0.00 2.44
2854 3467 9.881529 GTTTTGCATGATATTTGTGAATGTTTT 57.118 25.926 0.00 0.00 0.00 2.43
2855 3468 9.275398 AGTTTTGCATGATATTTGTGAATGTTT 57.725 25.926 0.00 0.00 0.00 2.83
2856 3469 8.836268 AGTTTTGCATGATATTTGTGAATGTT 57.164 26.923 0.00 0.00 0.00 2.71
2857 3470 8.714179 CAAGTTTTGCATGATATTTGTGAATGT 58.286 29.630 0.00 0.00 0.00 2.71
2858 3471 8.714179 ACAAGTTTTGCATGATATTTGTGAATG 58.286 29.630 0.00 0.00 0.00 2.67
2859 3472 8.714179 CACAAGTTTTGCATGATATTTGTGAAT 58.286 29.630 17.25 0.00 44.02 2.57
2860 3473 7.307278 GCACAAGTTTTGCATGATATTTGTGAA 60.307 33.333 22.40 0.00 44.02 3.18
2861 3474 6.145858 GCACAAGTTTTGCATGATATTTGTGA 59.854 34.615 22.40 0.00 44.02 3.58
2862 3475 6.301108 GCACAAGTTTTGCATGATATTTGTG 58.699 36.000 9.12 17.59 44.08 3.33
2863 3476 5.118971 CGCACAAGTTTTGCATGATATTTGT 59.881 36.000 14.04 0.00 40.20 2.83
2864 3477 5.345472 TCGCACAAGTTTTGCATGATATTTG 59.655 36.000 14.04 0.00 40.20 2.32
2865 3478 5.468592 TCGCACAAGTTTTGCATGATATTT 58.531 33.333 14.04 0.00 40.20 1.40
2866 3479 5.058149 TCGCACAAGTTTTGCATGATATT 57.942 34.783 14.04 0.00 40.20 1.28
2867 3480 4.700268 TCGCACAAGTTTTGCATGATAT 57.300 36.364 14.04 0.00 40.20 1.63
2868 3481 4.225984 GTTCGCACAAGTTTTGCATGATA 58.774 39.130 14.04 0.00 40.20 2.15
2869 3482 3.052036 GTTCGCACAAGTTTTGCATGAT 58.948 40.909 14.04 0.00 40.20 2.45
2870 3483 2.159324 TGTTCGCACAAGTTTTGCATGA 60.159 40.909 14.04 1.62 40.20 3.07
2871 3484 2.034675 GTGTTCGCACAAGTTTTGCATG 60.035 45.455 14.04 0.00 46.85 4.06
2872 3485 2.192624 GTGTTCGCACAAGTTTTGCAT 58.807 42.857 14.04 0.00 46.85 3.96
2873 3486 1.623359 GTGTTCGCACAAGTTTTGCA 58.377 45.000 14.04 0.00 46.85 4.08


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

AutoCloner maintained by Alex Coulton.