Multiple sequence alignment - TraesCS4B01G193600

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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 TraesCS4B01G193600 chr4B 100.000 4600 0 0 1 4600 416539262 416543861 0.000000e+00 8495.0
1 TraesCS4B01G193600 chr4B 91.892 74 6 0 1087 1160 395824616 395824689 2.260000e-18 104.0
2 TraesCS4B01G193600 chr4D 92.920 1356 45 14 842 2181 337410734 337412054 0.000000e+00 1925.0
3 TraesCS4B01G193600 chr4D 93.376 1087 55 4 3007 4090 337412783 337413855 0.000000e+00 1592.0
4 TraesCS4B01G193600 chr4D 94.673 413 17 5 2464 2875 337412401 337412809 1.810000e-178 636.0
5 TraesCS4B01G193600 chr4D 91.133 406 29 5 410 812 337410101 337410502 1.130000e-150 544.0
6 TraesCS4B01G193600 chr4D 90.418 407 39 0 2 408 337409586 337409992 1.880000e-148 536.0
7 TraesCS4B01G193600 chr4D 93.173 249 13 2 2219 2466 337412042 337412287 3.380000e-96 363.0
8 TraesCS4B01G193600 chr4D 91.463 246 18 3 4355 4600 337415347 337415589 7.370000e-88 335.0
9 TraesCS4B01G193600 chr4D 90.763 249 20 2 4352 4600 337424576 337424821 3.430000e-86 329.0
10 TraesCS4B01G193600 chr4D 83.898 236 9 7 4089 4320 337414073 337414283 1.010000e-46 198.0
11 TraesCS4B01G193600 chr4D 92.453 53 3 1 4038 4090 337413871 337413922 1.770000e-09 75.0
12 TraesCS4B01G193600 chr4D 97.222 36 1 0 2183 2218 165592342 165592377 1.380000e-05 62.1
13 TraesCS4B01G193600 chr4A 93.951 1025 36 5 849 1870 134636843 134635842 0.000000e+00 1526.0
14 TraesCS4B01G193600 chr4A 93.121 1003 49 9 3031 4031 134634724 134633740 0.000000e+00 1452.0
15 TraesCS4B01G193600 chr4A 92.943 666 33 8 2219 2875 134635381 134634721 0.000000e+00 957.0
16 TraesCS4B01G193600 chr4A 86.712 587 46 14 4032 4600 134632177 134631605 1.410000e-174 623.0
17 TraesCS4B01G193600 chr4A 85.984 371 44 8 441 805 134638968 134638600 1.550000e-104 390.0
18 TraesCS4B01G193600 chr4A 96.257 187 7 0 1995 2181 134635555 134635369 1.610000e-79 307.0
19 TraesCS4B01G193600 chr4A 95.455 110 3 1 1907 2016 134635840 134635733 1.700000e-39 174.0
20 TraesCS4B01G193600 chr4A 95.775 71 1 1 4242 4310 134632044 134631974 3.760000e-21 113.0
21 TraesCS4B01G193600 chr4A 90.588 85 6 1 4164 4246 134631974 134631890 1.350000e-20 111.0
22 TraesCS4B01G193600 chr4A 98.077 52 1 0 790 841 134638586 134638535 1.760000e-14 91.6
23 TraesCS4B01G193600 chr2D 93.252 163 10 1 2874 3035 520539404 520539242 5.950000e-59 239.0
24 TraesCS4B01G193600 chr2D 92.683 164 11 1 2872 3034 87407527 87407364 7.690000e-58 235.0
25 TraesCS4B01G193600 chr2D 100.000 37 0 0 2183 2219 36768709 36768673 8.260000e-08 69.4
26 TraesCS4B01G193600 chr5D 91.813 171 12 2 2866 3035 53583070 53583239 2.140000e-58 237.0
27 TraesCS4B01G193600 chr5D 91.228 171 13 2 2868 3036 18177649 18177819 9.950000e-57 231.0
28 TraesCS4B01G193600 chr5D 100.000 37 0 0 2183 2219 10986493 10986529 8.260000e-08 69.4
29 TraesCS4B01G193600 chr1D 93.210 162 10 1 2874 3034 338937212 338937373 2.140000e-58 237.0
30 TraesCS4B01G193600 chr1D 82.883 222 30 6 1457 1678 453052670 453052883 4.700000e-45 193.0
31 TraesCS4B01G193600 chr6B 91.860 172 9 5 2872 3039 119526972 119526802 7.690000e-58 235.0
32 TraesCS4B01G193600 chr7D 91.716 169 12 2 2866 3034 530858141 530857975 2.770000e-57 233.0
33 TraesCS4B01G193600 chr5B 92.121 165 12 1 2874 3037 341533895 341533731 9.950000e-57 231.0
34 TraesCS4B01G193600 chr5B 89.610 77 8 0 1087 1163 505690821 505690745 1.050000e-16 99.0
35 TraesCS4B01G193600 chr3A 91.228 171 13 2 2866 3035 648037279 648037448 9.950000e-57 231.0
36 TraesCS4B01G193600 chr5A 82.449 245 31 11 1457 1699 631086715 631086481 2.170000e-48 204.0
37 TraesCS4B01G193600 chr5A 82.083 240 34 8 1457 1695 34327756 34327525 3.630000e-46 196.0
38 TraesCS4B01G193600 chr7B 89.610 77 8 0 1087 1163 51620542 51620466 1.050000e-16 99.0
39 TraesCS4B01G193600 chr1A 89.610 77 8 0 1087 1163 537061249 537061173 1.050000e-16 99.0
40 TraesCS4B01G193600 chr1A 97.297 37 1 0 2183 2219 569856491 569856527 3.840000e-06 63.9
41 TraesCS4B01G193600 chr3D 97.368 38 1 0 2183 2220 526261699 526261662 1.070000e-06 65.8
42 TraesCS4B01G193600 chr3D 91.304 46 3 1 2179 2224 23054070 23054026 1.380000e-05 62.1
43 TraesCS4B01G193600 chr2B 97.297 37 1 0 2183 2219 246954297 246954261 3.840000e-06 63.9
44 TraesCS4B01G193600 chrUn 97.222 36 0 1 2183 2218 332381188 332381222 4.970000e-05 60.2
45 TraesCS4B01G193600 chr3B 90.909 44 3 1 2183 2225 763294712 763294755 1.790000e-04 58.4


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 TraesCS4B01G193600 chr4B 416539262 416543861 4599 False 8495.000000 8495 100.000000 1 4600 1 chr4B.!!$F2 4599
1 TraesCS4B01G193600 chr4D 337409586 337415589 6003 False 689.333333 1925 91.500778 2 4600 9 chr4D.!!$F3 4598
2 TraesCS4B01G193600 chr4A 134631605 134638968 7363 True 574.460000 1526 92.886300 441 4600 10 chr4A.!!$R1 4159

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
258 259 0.107643 TTGTCCAATGGCAGTCACGA 59.892 50.0 0.00 0.0 0.0 4.35 F
1787 3642 0.174617 GTTGTGGGTTGTGGGTTGTG 59.825 55.0 0.00 0.0 0.0 3.33 F
1840 3695 0.398696 TGTGTCATACCCGCCTTTGT 59.601 50.0 0.00 0.0 0.0 2.83 F
3335 5512 0.531974 TGAGAAAACAAGCGCCGAGT 60.532 50.0 2.29 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 4276 0.034089 ATCAAGGGGTAAGGCAGTGC 60.034 55.000 6.55 6.55 0.00 4.40 R
3098 5274 0.847373 TTGTTGGACCACAAGCCCTA 59.153 50.000 0.00 0.00 40.38 3.53 R
3548 5725 1.899142 GCAGGAGTCTCCACTTTCTCT 59.101 52.381 21.26 0.00 39.61 3.10 R
4332 8303 0.386838 CGACCAGTAACCGTATCCCC 59.613 60.000 0.00 0.00 0.00 4.81 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.326595 TGAGTTCCTATTGGCCGCAA 59.673 50.000 0.00 0.00 0.00 4.85
40 41 1.354368 CAGGTTCCACTAACACCCCAT 59.646 52.381 0.00 0.00 40.08 4.00
53 54 2.109799 CCCATGCTAGCGGTGGAG 59.890 66.667 30.24 20.00 34.94 3.86
138 139 2.159310 GCACAAGACTACGAGAGATGCT 60.159 50.000 0.00 0.00 0.00 3.79
150 151 2.165437 GAGAGATGCTCGATCCCATACC 59.835 54.545 0.00 0.00 35.36 2.73
155 156 2.046292 TGCTCGATCCCATACCAATCA 58.954 47.619 0.00 0.00 0.00 2.57
161 162 3.672808 GATCCCATACCAATCAGCTCTG 58.327 50.000 0.00 0.00 0.00 3.35
162 163 1.141657 TCCCATACCAATCAGCTCTGC 59.858 52.381 0.00 0.00 0.00 4.26
169 170 2.291411 ACCAATCAGCTCTGCTTTCCAT 60.291 45.455 0.00 0.00 36.40 3.41
176 177 1.542492 CTCTGCTTTCCATGGTTGCT 58.458 50.000 12.58 0.00 0.00 3.91
212 213 0.522626 TAGAATTCACCACGCGTCGA 59.477 50.000 9.86 3.08 0.00 4.20
229 230 1.153429 GACATGTGGTAGGCGGTCC 60.153 63.158 1.15 0.00 0.00 4.46
239 240 1.264749 TAGGCGGTCCATCTGTGCTT 61.265 55.000 0.00 0.00 33.74 3.91
253 254 0.675633 GTGCTTTGTCCAATGGCAGT 59.324 50.000 0.00 0.00 32.91 4.40
257 258 0.950836 TTTGTCCAATGGCAGTCACG 59.049 50.000 0.00 0.00 0.00 4.35
258 259 0.107643 TTGTCCAATGGCAGTCACGA 59.892 50.000 0.00 0.00 0.00 4.35
261 262 1.026182 TCCAATGGCAGTCACGATGC 61.026 55.000 0.00 0.00 43.09 3.91
264 265 1.361668 AATGGCAGTCACGATGCGAC 61.362 55.000 0.00 0.00 44.80 5.19
303 304 1.968017 TCTTGGCAGCTGGAAAGCG 60.968 57.895 17.12 0.00 40.27 4.68
310 311 2.433318 GCTGGAAAGCGCGAGACT 60.433 61.111 12.10 0.00 0.00 3.24
324 325 1.816863 GAGACTCTCCGCAACCACCA 61.817 60.000 0.00 0.00 0.00 4.17
336 337 3.123050 GCAACCACCAGTGTTTGAAATC 58.877 45.455 11.71 0.00 35.36 2.17
367 368 1.592110 CGCGAACGATGCCTGTATTTG 60.592 52.381 0.00 0.00 43.93 2.32
408 409 1.377725 GTGGACGACGAGGACCCTA 60.378 63.158 0.00 0.00 0.00 3.53
455 563 1.067416 GCGGTGGATCGTCAGCATA 59.933 57.895 6.16 0.00 35.11 3.14
480 588 1.626356 CCGAGTCATCCACCATGGGT 61.626 60.000 18.09 0.00 38.32 4.51
486 594 1.692749 ATCCACCATGGGTAGGCGT 60.693 57.895 18.09 4.61 38.32 5.68
509 619 2.365582 CCAACTACACCACCCTAATGC 58.634 52.381 0.00 0.00 0.00 3.56
513 623 2.303600 ACTACACCACCCTAATGCGAAA 59.696 45.455 0.00 0.00 0.00 3.46
530 640 3.631144 CGAAACACACTTCATGTTGCAT 58.369 40.909 0.00 0.00 40.64 3.96
536 646 8.519492 AAACACACTTCATGTTGCATTAATAC 57.481 30.769 0.00 0.00 40.64 1.89
616 729 3.953612 TGGATATTGCAATCACACTTCCC 59.046 43.478 16.86 7.19 0.00 3.97
669 782 6.708054 ACACCAAAACTTGAACATGTGAAAAA 59.292 30.769 0.00 0.00 0.00 1.94
671 784 7.117523 CACCAAAACTTGAACATGTGAAAAAGA 59.882 33.333 0.00 0.00 0.00 2.52
761 874 7.552050 TGAATTTTCTGACATTAACCCCATT 57.448 32.000 0.00 0.00 0.00 3.16
841 987 2.370849 GACTCAAAACCCTACCAGGACA 59.629 50.000 0.00 0.00 37.67 4.02
842 988 2.105993 ACTCAAAACCCTACCAGGACAC 59.894 50.000 0.00 0.00 37.67 3.67
843 989 1.422402 TCAAAACCCTACCAGGACACC 59.578 52.381 0.00 0.00 37.67 4.16
847 2677 2.058595 CCCTACCAGGACACCGGAG 61.059 68.421 9.46 1.26 37.67 4.63
919 2749 2.740580 CGCTGCTTTTATAACCCCTCGA 60.741 50.000 0.00 0.00 0.00 4.04
940 2770 2.239681 TTTCTCTCTCCTCTCCACCC 57.760 55.000 0.00 0.00 0.00 4.61
1137 2970 2.482333 CGGCGAAGAGGACGAGGAT 61.482 63.158 0.00 0.00 0.00 3.24
1388 3233 1.376424 CATGCGACAGGCCAAGACT 60.376 57.895 5.01 0.00 42.61 3.24
1430 3275 2.480419 CCTCGGTACTTCTTTGCTTGTG 59.520 50.000 0.00 0.00 0.00 3.33
1431 3276 1.871039 TCGGTACTTCTTTGCTTGTGC 59.129 47.619 0.00 0.00 40.20 4.57
1433 3278 2.096218 CGGTACTTCTTTGCTTGTGCTC 60.096 50.000 0.00 0.00 40.48 4.26
1454 3299 1.682740 TTCGGGGGATAATTTTCGGC 58.317 50.000 0.00 0.00 0.00 5.54
1463 3308 4.287720 GGATAATTTTCGGCGGTGATTTC 58.712 43.478 7.21 5.65 0.00 2.17
1470 3315 2.619147 TCGGCGGTGATTTCGATTTAA 58.381 42.857 7.21 0.00 0.00 1.52
1471 3316 2.605818 TCGGCGGTGATTTCGATTTAAG 59.394 45.455 7.21 0.00 0.00 1.85
1488 3333 7.678598 TCGATTTAAGGATTAGATAGATGGGGT 59.321 37.037 0.00 0.00 25.49 4.95
1493 3339 4.594920 AGGATTAGATAGATGGGGTGTGTG 59.405 45.833 0.00 0.00 0.00 3.82
1529 3375 2.276863 TTTGGTGTGCAGTTGTGGCG 62.277 55.000 0.00 0.00 0.00 5.69
1669 3515 4.865865 GCACTGAGCACCCTATCC 57.134 61.111 0.00 0.00 44.79 2.59
1686 3532 5.338381 CCCTATCCTCTGTGCAACTTTTCTA 60.338 44.000 0.00 0.00 38.04 2.10
1727 3575 3.006752 TGCATCATTCAAAAGGGTTGGTC 59.993 43.478 0.00 0.00 0.00 4.02
1728 3576 3.259123 GCATCATTCAAAAGGGTTGGTCT 59.741 43.478 0.00 0.00 0.00 3.85
1729 3577 4.619160 GCATCATTCAAAAGGGTTGGTCTC 60.619 45.833 0.00 0.00 0.00 3.36
1730 3578 4.453480 TCATTCAAAAGGGTTGGTCTCT 57.547 40.909 0.00 0.00 0.00 3.10
1731 3579 4.144297 TCATTCAAAAGGGTTGGTCTCTG 58.856 43.478 0.00 0.00 0.00 3.35
1732 3580 3.662759 TTCAAAAGGGTTGGTCTCTGT 57.337 42.857 0.00 0.00 0.00 3.41
1733 3581 3.208747 TCAAAAGGGTTGGTCTCTGTC 57.791 47.619 0.00 0.00 0.00 3.51
1734 3582 2.507886 TCAAAAGGGTTGGTCTCTGTCA 59.492 45.455 0.00 0.00 0.00 3.58
1735 3583 2.880890 CAAAAGGGTTGGTCTCTGTCAG 59.119 50.000 0.00 0.00 0.00 3.51
1736 3584 1.059913 AAGGGTTGGTCTCTGTCAGG 58.940 55.000 0.00 0.00 0.00 3.86
1737 3585 1.003233 GGGTTGGTCTCTGTCAGGC 60.003 63.158 0.00 0.00 0.00 4.85
1738 3586 1.484444 GGGTTGGTCTCTGTCAGGCT 61.484 60.000 0.00 0.00 0.00 4.58
1739 3587 1.267121 GGTTGGTCTCTGTCAGGCTA 58.733 55.000 0.00 0.00 0.00 3.93
1740 3588 1.066787 GGTTGGTCTCTGTCAGGCTAC 60.067 57.143 0.00 0.00 0.00 3.58
1741 3589 0.888619 TTGGTCTCTGTCAGGCTACG 59.111 55.000 0.00 0.00 0.00 3.51
1782 3637 1.190643 AGTTTGTTGTGGGTTGTGGG 58.809 50.000 0.00 0.00 0.00 4.61
1783 3638 0.899019 GTTTGTTGTGGGTTGTGGGT 59.101 50.000 0.00 0.00 0.00 4.51
1784 3639 1.276705 GTTTGTTGTGGGTTGTGGGTT 59.723 47.619 0.00 0.00 0.00 4.11
1785 3640 0.898320 TTGTTGTGGGTTGTGGGTTG 59.102 50.000 0.00 0.00 0.00 3.77
1786 3641 0.251832 TGTTGTGGGTTGTGGGTTGT 60.252 50.000 0.00 0.00 0.00 3.32
1787 3642 0.174617 GTTGTGGGTTGTGGGTTGTG 59.825 55.000 0.00 0.00 0.00 3.33
1788 3643 0.972983 TTGTGGGTTGTGGGTTGTGG 60.973 55.000 0.00 0.00 0.00 4.17
1826 3681 5.140747 ACTTCAGGTTGATCTAGTGTGTC 57.859 43.478 0.00 0.00 0.00 3.67
1832 3687 4.406003 AGGTTGATCTAGTGTGTCATACCC 59.594 45.833 0.00 0.00 0.00 3.69
1840 3695 0.398696 TGTGTCATACCCGCCTTTGT 59.601 50.000 0.00 0.00 0.00 2.83
1855 3710 5.182380 CCGCCTTTGTCTTTAAACTCCATAA 59.818 40.000 0.00 0.00 0.00 1.90
2115 4170 6.690194 ACCTATCATTCAGCAACTGATTTC 57.310 37.500 0.00 0.00 40.39 2.17
2132 4187 0.685660 TTCCATGGCATTGCTTTGCA 59.314 45.000 6.96 0.00 44.59 4.08
2177 4232 6.638873 CAGTAGTCAGTAATGTATAGCACTGC 59.361 42.308 0.00 0.00 38.60 4.40
2178 4233 4.950050 AGTCAGTAATGTATAGCACTGCC 58.050 43.478 0.00 0.00 38.60 4.85
2179 4234 4.651503 AGTCAGTAATGTATAGCACTGCCT 59.348 41.667 0.00 0.00 38.60 4.75
2180 4235 5.129485 AGTCAGTAATGTATAGCACTGCCTT 59.871 40.000 0.00 0.00 38.60 4.35
2181 4236 5.817816 GTCAGTAATGTATAGCACTGCCTTT 59.182 40.000 0.00 0.00 38.60 3.11
2182 4237 6.316390 GTCAGTAATGTATAGCACTGCCTTTT 59.684 38.462 0.00 0.00 38.60 2.27
2183 4238 6.538742 TCAGTAATGTATAGCACTGCCTTTTC 59.461 38.462 0.00 0.00 38.60 2.29
2184 4239 6.540189 CAGTAATGTATAGCACTGCCTTTTCT 59.460 38.462 0.00 0.00 32.72 2.52
2185 4240 6.763610 AGTAATGTATAGCACTGCCTTTTCTC 59.236 38.462 0.00 0.00 0.00 2.87
2186 4241 3.873910 TGTATAGCACTGCCTTTTCTCC 58.126 45.455 0.00 0.00 0.00 3.71
2187 4242 2.029838 ATAGCACTGCCTTTTCTCCG 57.970 50.000 0.00 0.00 0.00 4.63
2188 4243 0.673644 TAGCACTGCCTTTTCTCCGC 60.674 55.000 0.00 0.00 0.00 5.54
2189 4244 2.863153 CACTGCCTTTTCTCCGCG 59.137 61.111 0.00 0.00 0.00 6.46
2190 4245 1.667830 CACTGCCTTTTCTCCGCGA 60.668 57.895 8.23 0.00 0.00 5.87
2191 4246 1.021390 CACTGCCTTTTCTCCGCGAT 61.021 55.000 8.23 0.00 0.00 4.58
2192 4247 0.535335 ACTGCCTTTTCTCCGCGATA 59.465 50.000 8.23 0.00 0.00 2.92
2193 4248 1.139058 ACTGCCTTTTCTCCGCGATAT 59.861 47.619 8.23 0.00 0.00 1.63
2194 4249 2.213499 CTGCCTTTTCTCCGCGATATT 58.787 47.619 8.23 0.00 0.00 1.28
2195 4250 3.181469 ACTGCCTTTTCTCCGCGATATTA 60.181 43.478 8.23 0.00 0.00 0.98
2196 4251 3.799366 TGCCTTTTCTCCGCGATATTAA 58.201 40.909 8.23 0.00 0.00 1.40
2197 4252 4.385825 TGCCTTTTCTCCGCGATATTAAT 58.614 39.130 8.23 0.00 0.00 1.40
2198 4253 5.543714 TGCCTTTTCTCCGCGATATTAATA 58.456 37.500 8.23 0.00 0.00 0.98
2199 4254 6.170506 TGCCTTTTCTCCGCGATATTAATAT 58.829 36.000 8.23 7.72 0.00 1.28
2200 4255 7.324935 TGCCTTTTCTCCGCGATATTAATATA 58.675 34.615 8.23 0.00 0.00 0.86
2201 4256 7.985184 TGCCTTTTCTCCGCGATATTAATATAT 59.015 33.333 8.23 0.00 0.00 0.86
2202 4257 8.827677 GCCTTTTCTCCGCGATATTAATATATT 58.172 33.333 8.23 2.97 0.00 1.28
2205 4260 8.882415 TTTCTCCGCGATATTAATATATTCCC 57.118 34.615 8.23 0.00 0.00 3.97
2206 4261 7.834881 TCTCCGCGATATTAATATATTCCCT 57.165 36.000 8.23 0.00 0.00 4.20
2207 4262 8.246430 TCTCCGCGATATTAATATATTCCCTT 57.754 34.615 8.23 0.00 0.00 3.95
2208 4263 8.701895 TCTCCGCGATATTAATATATTCCCTTT 58.298 33.333 8.23 0.00 0.00 3.11
2209 4264 9.976511 CTCCGCGATATTAATATATTCCCTTTA 57.023 33.333 8.23 0.00 0.00 1.85
2251 4306 2.242043 ACCCCTTGATCTTTTGCACTG 58.758 47.619 0.00 0.00 0.00 3.66
2252 4307 2.158475 ACCCCTTGATCTTTTGCACTGA 60.158 45.455 0.00 0.00 0.00 3.41
2253 4308 3.094572 CCCCTTGATCTTTTGCACTGAT 58.905 45.455 0.00 0.00 0.00 2.90
2270 4325 6.489700 TGCACTGATGTAGGATTTTTCTTTGA 59.510 34.615 0.00 0.00 0.00 2.69
2423 4484 2.769663 TGTAGTAGTGGCCCTGGTTATG 59.230 50.000 0.00 0.00 0.00 1.90
2567 4742 7.761249 AGGTCAGTTCAGTTTTTCATTTTTCAG 59.239 33.333 0.00 0.00 0.00 3.02
2570 4745 9.304731 TCAGTTCAGTTTTTCATTTTTCAGATG 57.695 29.630 0.00 0.00 0.00 2.90
2627 4802 4.768583 TGAAATCGATCATCATGTGACCA 58.231 39.130 0.00 0.00 40.28 4.02
2879 5055 3.400255 GTGGAACTGTGAAAGTACTCCC 58.600 50.000 0.00 0.00 38.56 4.30
2880 5056 3.071167 GTGGAACTGTGAAAGTACTCCCT 59.929 47.826 0.00 0.00 38.56 4.20
2881 5057 3.323979 TGGAACTGTGAAAGTACTCCCTC 59.676 47.826 0.00 0.00 38.56 4.30
2882 5058 3.306849 GGAACTGTGAAAGTACTCCCTCC 60.307 52.174 0.00 0.00 38.56 4.30
2883 5059 1.893801 ACTGTGAAAGTACTCCCTCCG 59.106 52.381 0.00 0.00 37.36 4.63
2884 5060 1.893801 CTGTGAAAGTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
2885 5061 2.299297 CTGTGAAAGTACTCCCTCCGTT 59.701 50.000 0.00 0.00 0.00 4.44
2886 5062 2.298163 TGTGAAAGTACTCCCTCCGTTC 59.702 50.000 0.00 0.00 0.00 3.95
2887 5063 1.897802 TGAAAGTACTCCCTCCGTTCC 59.102 52.381 0.00 0.00 0.00 3.62
2888 5064 2.177734 GAAAGTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
2889 5065 3.245371 TGAAAGTACTCCCTCCGTTCCTA 60.245 47.826 0.00 0.00 0.00 2.94
2890 5066 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2891 5067 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2892 5068 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2893 5069 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2894 5070 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2895 5071 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2896 5072 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2897 5073 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2898 5074 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2899 5075 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2900 5076 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2901 5077 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2902 5078 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2903 5079 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2904 5080 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2930 5106 8.433421 AGGATTTCAATACAAACTACATACGG 57.567 34.615 0.00 0.00 0.00 4.02
2931 5107 8.262227 AGGATTTCAATACAAACTACATACGGA 58.738 33.333 0.00 0.00 0.00 4.69
2932 5108 9.052759 GGATTTCAATACAAACTACATACGGAT 57.947 33.333 0.00 0.00 0.00 4.18
2933 5109 9.864034 GATTTCAATACAAACTACATACGGATG 57.136 33.333 5.94 5.94 39.16 3.51
2935 5111 9.872721 TTTCAATACAAACTACATACGGATGTA 57.127 29.630 19.32 19.32 44.77 2.29
2973 5149 9.630098 TTTAGAATGAAGATTCACTCATTTTGC 57.370 29.630 6.78 4.25 40.59 3.68
2974 5150 7.463961 AGAATGAAGATTCACTCATTTTGCT 57.536 32.000 6.78 5.84 40.59 3.91
2975 5151 8.571461 AGAATGAAGATTCACTCATTTTGCTA 57.429 30.769 6.78 0.00 40.59 3.49
2976 5152 8.457261 AGAATGAAGATTCACTCATTTTGCTAC 58.543 33.333 6.78 3.26 40.59 3.58
2977 5153 6.169419 TGAAGATTCACTCATTTTGCTACG 57.831 37.500 0.00 0.00 31.01 3.51
2978 5154 5.700832 TGAAGATTCACTCATTTTGCTACGT 59.299 36.000 0.00 0.00 31.01 3.57
2979 5155 6.871492 TGAAGATTCACTCATTTTGCTACGTA 59.129 34.615 0.00 0.00 31.01 3.57
2980 5156 7.549134 TGAAGATTCACTCATTTTGCTACGTAT 59.451 33.333 0.00 0.00 31.01 3.06
2981 5157 7.239166 AGATTCACTCATTTTGCTACGTATG 57.761 36.000 0.00 0.00 0.00 2.39
2982 5158 6.818644 AGATTCACTCATTTTGCTACGTATGT 59.181 34.615 0.00 0.00 0.00 2.29
2983 5159 7.979537 AGATTCACTCATTTTGCTACGTATGTA 59.020 33.333 0.00 0.00 0.00 2.29
2999 5175 7.584122 ACGTATGTAGACCATAGTGAAATCT 57.416 36.000 0.00 0.00 36.71 2.40
3000 5176 8.008513 ACGTATGTAGACCATAGTGAAATCTT 57.991 34.615 0.00 0.00 36.71 2.40
3001 5177 8.475639 ACGTATGTAGACCATAGTGAAATCTTT 58.524 33.333 0.00 0.00 36.71 2.52
3002 5178 9.961265 CGTATGTAGACCATAGTGAAATCTTTA 57.039 33.333 0.00 0.00 36.71 1.85
3029 5205 7.619512 AGGACTTATATTTAGGAACAGAGGG 57.380 40.000 0.00 0.00 0.00 4.30
3030 5206 7.371043 AGGACTTATATTTAGGAACAGAGGGA 58.629 38.462 0.00 0.00 0.00 4.20
3031 5207 7.511028 AGGACTTATATTTAGGAACAGAGGGAG 59.489 40.741 0.00 0.00 0.00 4.30
3032 5208 7.290481 GGACTTATATTTAGGAACAGAGGGAGT 59.710 40.741 0.00 0.00 0.00 3.85
3033 5209 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
3045 5221 7.235812 GGAACAGAGGGAGTATATTACAAGGAT 59.764 40.741 0.00 0.00 0.00 3.24
3098 5274 5.997746 TGTAATTGACACTGCTAAAAGCTCT 59.002 36.000 0.03 0.00 36.04 4.09
3115 5291 0.690762 TCTAGGGCTTGTGGTCCAAC 59.309 55.000 0.00 0.00 43.45 3.77
3267 5444 9.760077 AAGTTTCTAAGACTGAGATTTAAACGA 57.240 29.630 0.00 0.00 0.00 3.85
3328 5505 3.667960 CGCACCTACATGAGAAAACAAGC 60.668 47.826 0.00 0.00 0.00 4.01
3335 5512 0.531974 TGAGAAAACAAGCGCCGAGT 60.532 50.000 2.29 0.00 0.00 4.18
3360 5537 7.389053 GTCATTATGCTATTTTAGTCAGGAGGG 59.611 40.741 0.00 0.00 0.00 4.30
3437 5614 2.743636 TCAAGGATCTTGTGGACGAC 57.256 50.000 7.42 0.00 0.00 4.34
3476 5653 6.846988 AGGAAAGAATGAGGAGAAAGAAAGT 58.153 36.000 0.00 0.00 0.00 2.66
3529 5706 2.299297 AGAAGTTAACTGTGACGGAGGG 59.701 50.000 9.34 0.00 0.00 4.30
3548 5725 2.169561 GGGCAAAAAGGAGGAACAAACA 59.830 45.455 0.00 0.00 0.00 2.83
3608 5785 3.620488 TGCTGAAGAGTGAAAACAAGGT 58.380 40.909 0.00 0.00 0.00 3.50
3652 5832 3.932545 AGGAGCATTGCTATACTCGAG 57.067 47.619 11.96 11.84 39.88 4.04
3770 5951 2.393271 TTGTGTTGGGCAAAGTTTGG 57.607 45.000 17.11 0.00 0.00 3.28
3803 5984 5.010282 GTCATGGGTTTCTTGGTTGATAGT 58.990 41.667 0.00 0.00 0.00 2.12
3954 6135 2.724174 CACGCGTCGCATATCTTCATTA 59.276 45.455 18.75 0.00 0.00 1.90
3984 6165 7.187824 AGAACAATGATATAGACTGTGTGGT 57.812 36.000 0.00 0.00 0.00 4.16
3985 6166 7.624549 AGAACAATGATATAGACTGTGTGGTT 58.375 34.615 0.00 0.00 0.00 3.67
4065 7808 2.012051 GCACATGTTCCCTCTAACCGG 61.012 57.143 0.00 0.00 0.00 5.28
4073 7816 2.579787 CTCTAACCGGCGAGCACG 60.580 66.667 9.30 0.00 42.93 5.34
4107 8068 0.839946 TATCTTTGAGGGGGCTGCTC 59.160 55.000 0.00 0.00 0.00 4.26
4193 8162 4.335400 TGCAGATACACAAGAGTTGACA 57.665 40.909 0.00 0.00 0.00 3.58
4194 8163 4.309933 TGCAGATACACAAGAGTTGACAG 58.690 43.478 0.00 0.00 0.00 3.51
4200 8169 6.926272 AGATACACAAGAGTTGACAGAAGTTC 59.074 38.462 0.00 0.00 0.00 3.01
4321 8292 3.594453 TGGCATCCCCAAGCTTAAG 57.406 52.632 0.00 0.00 41.82 1.85
4323 8294 0.756815 GGCATCCCCAAGCTTAAGGG 60.757 60.000 22.56 22.56 45.04 3.95
4324 8295 0.033109 GCATCCCCAAGCTTAAGGGT 60.033 55.000 25.71 12.60 43.89 4.34
4325 8296 2.024306 GCATCCCCAAGCTTAAGGGTC 61.024 57.143 25.71 15.84 43.89 4.46
4327 8298 2.653543 TCCCCAAGCTTAAGGGTCTA 57.346 50.000 25.71 10.43 43.89 2.59
4329 8300 3.470868 TCCCCAAGCTTAAGGGTCTATT 58.529 45.455 25.71 0.00 43.89 1.73
4330 8301 3.458487 TCCCCAAGCTTAAGGGTCTATTC 59.542 47.826 25.71 0.00 43.89 1.75
4332 8303 3.467803 CCAAGCTTAAGGGTCTATTCCG 58.532 50.000 0.00 0.00 0.00 4.30
4333 8304 3.467803 CAAGCTTAAGGGTCTATTCCGG 58.532 50.000 0.00 0.00 0.00 5.14
4337 8308 3.248888 CTTAAGGGTCTATTCCGGGGAT 58.751 50.000 0.00 0.00 0.00 3.85
4339 8310 2.322339 AGGGTCTATTCCGGGGATAC 57.678 55.000 0.00 0.00 0.00 2.24
4340 8311 0.893447 GGGTCTATTCCGGGGATACG 59.107 60.000 0.00 0.00 37.60 3.06
4382 9382 7.510549 TCCTTCTAACAAGATGGTTCTTTTG 57.489 36.000 7.08 0.00 40.28 2.44
4387 9387 8.110860 TCTAACAAGATGGTTCTTTTGAATCC 57.889 34.615 0.00 0.00 40.28 3.01
4472 9472 9.424319 GATAATCCATACATGTAAGTACTGTGG 57.576 37.037 10.14 11.01 0.00 4.17
4484 9484 2.979678 AGTACTGTGGAAACTCATGGGT 59.020 45.455 0.00 0.00 32.63 4.51
4491 9491 7.007723 ACTGTGGAAACTCATGGGTAAATTAA 58.992 34.615 0.00 0.00 32.63 1.40
4494 9494 8.875168 TGTGGAAACTCATGGGTAAATTAATTT 58.125 29.630 17.18 17.18 0.00 1.82
4495 9495 9.719355 GTGGAAACTCATGGGTAAATTAATTTT 57.281 29.630 18.14 3.85 0.00 1.82
4496 9496 9.936759 TGGAAACTCATGGGTAAATTAATTTTC 57.063 29.630 18.14 13.03 0.00 2.29
4592 9592 5.888412 AAACATGAAGCAAACAACGATTC 57.112 34.783 0.00 0.00 0.00 2.52
4594 9594 5.186996 ACATGAAGCAAACAACGATTCTT 57.813 34.783 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.326595 TTGCGGCCAATAGGAACTCA 59.673 50.000 2.24 0.00 41.75 3.41
1 2 0.733150 GTTGCGGCCAATAGGAACTC 59.267 55.000 2.24 0.00 41.75 3.01
2 3 0.037590 TGTTGCGGCCAATAGGAACT 59.962 50.000 2.24 0.00 46.37 3.01
3 4 0.451783 CTGTTGCGGCCAATAGGAAC 59.548 55.000 2.24 4.54 36.77 3.62
5 6 4.635769 CTGTTGCGGCCAATAGGA 57.364 55.556 2.24 0.00 36.77 2.94
7 8 0.451783 GAACCTGTTGCGGCCAATAG 59.548 55.000 2.24 0.00 39.19 1.73
8 9 0.963355 GGAACCTGTTGCGGCCAATA 60.963 55.000 2.24 0.00 32.75 1.90
19 20 0.769247 GGGGTGTTAGTGGAACCTGT 59.231 55.000 0.00 0.00 37.80 4.00
40 41 1.305465 TTACCCTCCACCGCTAGCA 60.305 57.895 16.45 0.00 0.00 3.49
53 54 1.620739 GGTCCCTTCCTCGGTTACCC 61.621 65.000 0.00 0.00 0.00 3.69
88 89 2.241479 CTCCTGCCAGCAGTCTCAGG 62.241 65.000 17.86 3.11 45.59 3.86
90 91 2.288778 CCTCCTGCCAGCAGTCTCA 61.289 63.158 17.86 0.00 42.15 3.27
91 92 2.583520 CCTCCTGCCAGCAGTCTC 59.416 66.667 17.86 0.00 42.15 3.36
114 115 1.540267 TCTCTCGTAGTCTTGTGCCAC 59.460 52.381 0.00 0.00 0.00 5.01
138 139 2.300152 GAGCTGATTGGTATGGGATCGA 59.700 50.000 0.00 0.00 0.00 3.59
150 151 2.099263 CCATGGAAAGCAGAGCTGATTG 59.901 50.000 5.56 0.00 39.36 2.67
155 156 1.542492 CAACCATGGAAAGCAGAGCT 58.458 50.000 21.47 0.00 42.56 4.09
212 213 1.271840 ATGGACCGCCTACCACATGT 61.272 55.000 0.00 0.00 39.06 3.21
229 230 2.673043 GCCATTGGACAAAGCACAGATG 60.673 50.000 6.95 0.00 0.00 2.90
239 240 0.107643 TCGTGACTGCCATTGGACAA 59.892 50.000 6.95 0.00 0.00 3.18
253 254 4.492160 GGCCTCGTCGCATCGTGA 62.492 66.667 0.00 0.00 0.00 4.35
257 258 2.027751 GGTAGGCCTCGTCGCATC 59.972 66.667 9.68 0.00 0.00 3.91
258 259 3.900892 CGGTAGGCCTCGTCGCAT 61.901 66.667 9.68 0.00 0.00 4.73
261 262 4.189188 CACCGGTAGGCCTCGTCG 62.189 72.222 9.68 12.15 42.76 5.12
264 265 4.189188 CGTCACCGGTAGGCCTCG 62.189 72.222 9.68 7.95 42.76 4.63
284 285 1.583477 GCTTTCCAGCTGCCAAGAC 59.417 57.895 21.41 11.96 43.51 3.01
310 311 1.978455 AACACTGGTGGTTGCGGAGA 61.978 55.000 5.70 0.00 34.19 3.71
324 325 1.241315 CGGCCCCGATTTCAAACACT 61.241 55.000 0.00 0.00 42.83 3.55
351 352 4.949856 AGAATTCCAAATACAGGCATCGTT 59.050 37.500 0.65 0.00 0.00 3.85
356 357 2.682856 GCGAGAATTCCAAATACAGGCA 59.317 45.455 0.65 0.00 0.00 4.75
362 363 2.198406 CCGACGCGAGAATTCCAAATA 58.802 47.619 15.93 0.00 0.00 1.40
367 368 3.262686 GGCCGACGCGAGAATTCC 61.263 66.667 15.93 1.76 35.02 3.01
391 392 1.377725 GTAGGGTCCTCGTCGTCCA 60.378 63.158 0.00 0.00 0.00 4.02
392 393 2.467826 CGTAGGGTCCTCGTCGTCC 61.468 68.421 0.00 0.00 0.00 4.79
394 395 1.449246 CTCGTAGGGTCCTCGTCGT 60.449 63.158 0.00 0.00 0.00 4.34
438 546 2.061773 GATTATGCTGACGATCCACCG 58.938 52.381 0.00 0.00 0.00 4.94
455 563 1.123928 GGTGGATGACTCGGAGGATT 58.876 55.000 10.23 0.00 0.00 3.01
486 594 2.627148 TAGGGTGGTGTAGTTGGCTA 57.373 50.000 0.00 0.00 0.00 3.93
499 607 2.151202 AGTGTGTTTCGCATTAGGGTG 58.849 47.619 0.00 0.00 0.00 4.61
501 609 2.811431 TGAAGTGTGTTTCGCATTAGGG 59.189 45.455 0.00 0.00 0.00 3.53
509 619 3.063670 TGCAACATGAAGTGTGTTTCG 57.936 42.857 0.00 0.00 41.14 3.46
513 623 6.148645 TCGTATTAATGCAACATGAAGTGTGT 59.851 34.615 0.00 0.00 41.14 3.72
589 699 4.951715 AGTGTGATTGCAATATCCATGTGT 59.048 37.500 12.97 0.00 0.00 3.72
616 729 1.937223 TGGAAACATTATAGCACCGCG 59.063 47.619 0.00 0.00 33.40 6.46
769 886 7.330208 GGGTGTTGATCTGAATTCATTTTTCTG 59.670 37.037 8.96 0.00 0.00 3.02
818 964 1.439679 CTGGTAGGGTTTTGAGTCGC 58.560 55.000 0.00 0.00 0.00 5.19
841 987 1.551019 GGGGAAAGCACTACTCCGGT 61.551 60.000 0.00 0.00 0.00 5.28
842 988 1.221021 GGGGAAAGCACTACTCCGG 59.779 63.158 0.00 0.00 0.00 5.14
843 989 0.323629 TTGGGGAAAGCACTACTCCG 59.676 55.000 0.00 0.00 0.00 4.63
847 2677 1.065709 TCGGATTGGGGAAAGCACTAC 60.066 52.381 0.00 0.00 0.00 2.73
919 2749 3.111484 GGGTGGAGAGGAGAGAGAAAAT 58.889 50.000 0.00 0.00 0.00 1.82
993 2823 2.192979 GGATCGGCCATTGCTGGA 59.807 61.111 2.24 0.00 46.37 3.86
1165 3010 3.551915 GAGCGAAGTAACGGCGGC 61.552 66.667 13.24 0.00 0.00 6.53
1241 3086 1.986378 CTACGGACACAAGAAGAAGCG 59.014 52.381 0.00 0.00 0.00 4.68
1388 3233 1.207811 TGATTGGCGCAGATCTTGAGA 59.792 47.619 10.83 0.00 0.00 3.27
1430 3275 3.003378 CGAAAATTATCCCCCGAAAGAGC 59.997 47.826 0.00 0.00 0.00 4.09
1431 3276 3.564225 CCGAAAATTATCCCCCGAAAGAG 59.436 47.826 0.00 0.00 0.00 2.85
1433 3278 2.034179 GCCGAAAATTATCCCCCGAAAG 59.966 50.000 0.00 0.00 0.00 2.62
1454 3299 7.709269 TCTAATCCTTAAATCGAAATCACCG 57.291 36.000 0.00 0.00 0.00 4.94
1463 3308 7.766278 CACCCCATCTATCTAATCCTTAAATCG 59.234 40.741 0.00 0.00 0.00 3.34
1470 3315 4.594920 CACACACCCCATCTATCTAATCCT 59.405 45.833 0.00 0.00 0.00 3.24
1471 3316 4.348168 ACACACACCCCATCTATCTAATCC 59.652 45.833 0.00 0.00 0.00 3.01
1488 3333 7.866898 CCAAATATCAAGATGTCAAAACACACA 59.133 33.333 0.00 0.00 38.48 3.72
1493 3339 7.148755 GCACACCAAATATCAAGATGTCAAAAC 60.149 37.037 0.00 0.00 0.00 2.43
1529 3375 1.142778 GCTCCTGCATCTTCGTCGTC 61.143 60.000 0.00 0.00 39.41 4.20
1695 3543 8.729756 CCCTTTTGAATGATGCACGATATATAA 58.270 33.333 0.00 0.00 0.00 0.98
1702 3550 2.513753 ACCCTTTTGAATGATGCACGA 58.486 42.857 0.00 0.00 0.00 4.35
1705 3553 2.971330 ACCAACCCTTTTGAATGATGCA 59.029 40.909 0.00 0.00 0.00 3.96
1727 3575 1.686355 AGATCCGTAGCCTGACAGAG 58.314 55.000 3.32 0.00 0.00 3.35
1728 3576 3.149981 CATAGATCCGTAGCCTGACAGA 58.850 50.000 3.32 0.00 0.00 3.41
1729 3577 3.149981 TCATAGATCCGTAGCCTGACAG 58.850 50.000 0.00 0.00 0.00 3.51
1730 3578 3.223674 TCATAGATCCGTAGCCTGACA 57.776 47.619 0.00 0.00 0.00 3.58
1731 3579 4.792521 ATTCATAGATCCGTAGCCTGAC 57.207 45.455 0.00 0.00 0.00 3.51
1732 3580 4.832823 TGAATTCATAGATCCGTAGCCTGA 59.167 41.667 3.38 0.00 0.00 3.86
1733 3581 4.926238 GTGAATTCATAGATCCGTAGCCTG 59.074 45.833 12.12 0.00 0.00 4.85
1734 3582 4.588951 TGTGAATTCATAGATCCGTAGCCT 59.411 41.667 12.12 0.00 0.00 4.58
1735 3583 4.883083 TGTGAATTCATAGATCCGTAGCC 58.117 43.478 12.12 0.00 0.00 3.93
1736 3584 5.107298 GCTTGTGAATTCATAGATCCGTAGC 60.107 44.000 12.12 8.99 0.00 3.58
1737 3585 5.406780 GGCTTGTGAATTCATAGATCCGTAG 59.593 44.000 12.12 2.64 0.00 3.51
1738 3586 5.163353 TGGCTTGTGAATTCATAGATCCGTA 60.163 40.000 12.12 0.00 0.00 4.02
1739 3587 4.130118 GGCTTGTGAATTCATAGATCCGT 58.870 43.478 12.12 0.00 0.00 4.69
1740 3588 4.129380 TGGCTTGTGAATTCATAGATCCG 58.871 43.478 12.12 0.00 0.00 4.18
1741 3589 5.591877 ACTTGGCTTGTGAATTCATAGATCC 59.408 40.000 12.12 11.04 0.00 3.36
1782 3637 5.761726 AGTACTGCTTAGTTAAACCCACAAC 59.238 40.000 0.00 0.00 0.00 3.32
1783 3638 5.932455 AGTACTGCTTAGTTAAACCCACAA 58.068 37.500 0.00 0.00 0.00 3.33
1784 3639 5.556006 AGTACTGCTTAGTTAAACCCACA 57.444 39.130 0.00 0.00 0.00 4.17
1785 3640 5.993441 TGAAGTACTGCTTAGTTAAACCCAC 59.007 40.000 1.64 0.00 37.59 4.61
1786 3641 6.177310 TGAAGTACTGCTTAGTTAAACCCA 57.823 37.500 1.64 0.00 37.59 4.51
1787 3642 5.642491 CCTGAAGTACTGCTTAGTTAAACCC 59.358 44.000 1.64 0.00 37.59 4.11
1788 3643 6.228995 ACCTGAAGTACTGCTTAGTTAAACC 58.771 40.000 1.64 0.00 37.59 3.27
1826 3681 4.457949 AGTTTAAAGACAAAGGCGGGTATG 59.542 41.667 0.00 0.00 0.00 2.39
1832 3687 4.766404 ATGGAGTTTAAAGACAAAGGCG 57.234 40.909 0.00 0.00 0.00 5.52
1840 3695 7.332557 TGCCGTTCTATTATGGAGTTTAAAGA 58.667 34.615 0.00 0.00 0.00 2.52
1855 3710 1.802880 GCGACACTGATGCCGTTCTAT 60.803 52.381 0.00 0.00 0.00 1.98
1875 3730 5.316987 ACCAGGACATTTTCTTTCTAGGTG 58.683 41.667 0.00 0.00 0.00 4.00
1934 3790 7.816995 GCAAATTAGTGTGTGATATCCCAAAAA 59.183 33.333 0.00 0.00 0.00 1.94
2115 4170 1.013596 CATGCAAAGCAATGCCATGG 58.986 50.000 7.63 7.63 45.83 3.66
2179 4234 9.321562 GGGAATATATTAATATCGCGGAGAAAA 57.678 33.333 11.28 0.00 0.00 2.29
2180 4235 8.701895 AGGGAATATATTAATATCGCGGAGAAA 58.298 33.333 11.28 0.00 0.00 2.52
2181 4236 8.246430 AGGGAATATATTAATATCGCGGAGAA 57.754 34.615 11.28 0.00 0.00 2.87
2182 4237 7.834881 AGGGAATATATTAATATCGCGGAGA 57.165 36.000 11.28 0.00 0.00 3.71
2183 4238 8.888579 AAAGGGAATATATTAATATCGCGGAG 57.111 34.615 11.28 0.00 0.00 4.63
2214 4269 3.096852 GGGGTAAGGCAGTGCTATTTTT 58.903 45.455 16.11 5.03 0.00 1.94
2215 4270 2.311841 AGGGGTAAGGCAGTGCTATTTT 59.688 45.455 16.11 7.41 0.00 1.82
2216 4271 1.923148 AGGGGTAAGGCAGTGCTATTT 59.077 47.619 16.11 9.83 0.00 1.40
2217 4272 1.596496 AGGGGTAAGGCAGTGCTATT 58.404 50.000 16.11 12.68 0.00 1.73
2218 4273 1.212935 CAAGGGGTAAGGCAGTGCTAT 59.787 52.381 16.11 6.75 0.00 2.97
2219 4274 0.618458 CAAGGGGTAAGGCAGTGCTA 59.382 55.000 16.11 0.00 0.00 3.49
2220 4275 1.133809 TCAAGGGGTAAGGCAGTGCT 61.134 55.000 16.11 0.00 0.00 4.40
2221 4276 0.034089 ATCAAGGGGTAAGGCAGTGC 60.034 55.000 6.55 6.55 0.00 4.40
2222 4277 1.561542 AGATCAAGGGGTAAGGCAGTG 59.438 52.381 0.00 0.00 0.00 3.66
2223 4278 1.972588 AGATCAAGGGGTAAGGCAGT 58.027 50.000 0.00 0.00 0.00 4.40
2224 4279 3.372440 AAAGATCAAGGGGTAAGGCAG 57.628 47.619 0.00 0.00 0.00 4.85
2225 4280 3.430453 CAAAAGATCAAGGGGTAAGGCA 58.570 45.455 0.00 0.00 0.00 4.75
2226 4281 2.166459 GCAAAAGATCAAGGGGTAAGGC 59.834 50.000 0.00 0.00 0.00 4.35
2252 4307 9.918630 CAAGAATGTCAAAGAAAAATCCTACAT 57.081 29.630 0.00 0.00 0.00 2.29
2253 4308 7.867403 GCAAGAATGTCAAAGAAAAATCCTACA 59.133 33.333 0.00 0.00 0.00 2.74
2270 4325 6.815142 GGCTCAAAATCAATTAGCAAGAATGT 59.185 34.615 0.00 0.00 34.85 2.71
2523 4696 6.706270 ACTGACCTACATCACAAAACTTACAG 59.294 38.462 0.00 0.00 0.00 2.74
2567 4742 6.656693 ACTGCCAACTTATATATTCTGCCATC 59.343 38.462 0.00 0.00 0.00 3.51
2570 4745 7.332182 GTCTACTGCCAACTTATATATTCTGCC 59.668 40.741 0.00 0.00 0.00 4.85
2581 4756 8.755028 TCATATTTGTAGTCTACTGCCAACTTA 58.245 33.333 11.28 0.00 0.00 2.24
2840 5016 6.940867 AGTTCCACTTATAGGTCCAAAAACTC 59.059 38.462 0.00 0.00 0.00 3.01
2875 5051 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2876 5052 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2877 5053 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2878 5054 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2904 5080 9.537192 CCGTATGTAGTTTGTATTGAAATCCTA 57.463 33.333 0.00 0.00 0.00 2.94
2905 5081 8.262227 TCCGTATGTAGTTTGTATTGAAATCCT 58.738 33.333 0.00 0.00 0.00 3.24
2906 5082 8.428186 TCCGTATGTAGTTTGTATTGAAATCC 57.572 34.615 0.00 0.00 0.00 3.01
2907 5083 9.864034 CATCCGTATGTAGTTTGTATTGAAATC 57.136 33.333 0.00 0.00 0.00 2.17
2908 5084 9.391006 ACATCCGTATGTAGTTTGTATTGAAAT 57.609 29.630 0.00 0.00 44.66 2.17
2909 5085 8.780846 ACATCCGTATGTAGTTTGTATTGAAA 57.219 30.769 0.00 0.00 44.66 2.69
2947 5123 9.630098 GCAAAATGAGTGAATCTTCATTCTAAA 57.370 29.630 14.16 0.00 42.39 1.85
2948 5124 9.017509 AGCAAAATGAGTGAATCTTCATTCTAA 57.982 29.630 14.16 0.00 42.39 2.10
2949 5125 8.571461 AGCAAAATGAGTGAATCTTCATTCTA 57.429 30.769 14.16 4.41 42.39 2.10
2950 5126 7.463961 AGCAAAATGAGTGAATCTTCATTCT 57.536 32.000 14.16 1.02 42.39 2.40
2951 5127 7.427606 CGTAGCAAAATGAGTGAATCTTCATTC 59.572 37.037 11.75 8.11 42.29 2.67
2952 5128 7.094634 ACGTAGCAAAATGAGTGAATCTTCATT 60.095 33.333 7.43 7.43 39.73 2.57
2953 5129 6.372659 ACGTAGCAAAATGAGTGAATCTTCAT 59.627 34.615 0.00 0.00 39.73 2.57
2954 5130 5.700832 ACGTAGCAAAATGAGTGAATCTTCA 59.299 36.000 0.00 0.00 34.20 3.02
2955 5131 6.170675 ACGTAGCAAAATGAGTGAATCTTC 57.829 37.500 0.00 0.00 0.00 2.87
2956 5132 7.334421 ACATACGTAGCAAAATGAGTGAATCTT 59.666 33.333 0.08 0.00 0.00 2.40
2957 5133 6.818644 ACATACGTAGCAAAATGAGTGAATCT 59.181 34.615 0.08 0.00 0.00 2.40
2958 5134 7.005062 ACATACGTAGCAAAATGAGTGAATC 57.995 36.000 0.08 0.00 0.00 2.52
2959 5135 6.985188 ACATACGTAGCAAAATGAGTGAAT 57.015 33.333 0.08 0.00 0.00 2.57
2960 5136 7.274904 GTCTACATACGTAGCAAAATGAGTGAA 59.725 37.037 0.08 0.00 44.17 3.18
2961 5137 6.750501 GTCTACATACGTAGCAAAATGAGTGA 59.249 38.462 0.08 0.00 44.17 3.41
2962 5138 6.019801 GGTCTACATACGTAGCAAAATGAGTG 60.020 42.308 0.08 0.00 44.17 3.51
2963 5139 6.040878 GGTCTACATACGTAGCAAAATGAGT 58.959 40.000 0.08 0.00 44.17 3.41
2964 5140 6.040247 TGGTCTACATACGTAGCAAAATGAG 58.960 40.000 0.08 0.00 44.17 2.90
2965 5141 5.968254 TGGTCTACATACGTAGCAAAATGA 58.032 37.500 0.08 0.00 44.17 2.57
2966 5142 6.844696 ATGGTCTACATACGTAGCAAAATG 57.155 37.500 0.08 0.00 44.17 2.32
2967 5143 7.652105 CACTATGGTCTACATACGTAGCAAAAT 59.348 37.037 0.08 0.00 44.17 1.82
2968 5144 6.976349 CACTATGGTCTACATACGTAGCAAAA 59.024 38.462 0.08 0.00 44.17 2.44
2969 5145 6.319405 TCACTATGGTCTACATACGTAGCAAA 59.681 38.462 0.08 0.00 44.17 3.68
2970 5146 5.824097 TCACTATGGTCTACATACGTAGCAA 59.176 40.000 0.08 0.00 44.17 3.91
2971 5147 5.370679 TCACTATGGTCTACATACGTAGCA 58.629 41.667 0.08 0.00 44.17 3.49
2972 5148 5.936686 TCACTATGGTCTACATACGTAGC 57.063 43.478 0.08 0.00 44.17 3.58
2973 5149 8.784994 AGATTTCACTATGGTCTACATACGTAG 58.215 37.037 0.08 0.00 45.62 3.51
2974 5150 8.687292 AGATTTCACTATGGTCTACATACGTA 57.313 34.615 0.00 0.00 41.03 3.57
2975 5151 7.584122 AGATTTCACTATGGTCTACATACGT 57.416 36.000 0.00 0.00 41.03 3.57
2976 5152 8.873215 AAAGATTTCACTATGGTCTACATACG 57.127 34.615 0.00 0.00 41.03 3.06
3003 5179 9.155785 CCCTCTGTTCCTAAATATAAGTCCTTA 57.844 37.037 0.00 0.00 0.00 2.69
3004 5180 7.849904 TCCCTCTGTTCCTAAATATAAGTCCTT 59.150 37.037 0.00 0.00 0.00 3.36
3005 5181 7.371043 TCCCTCTGTTCCTAAATATAAGTCCT 58.629 38.462 0.00 0.00 0.00 3.85
3006 5182 7.290481 ACTCCCTCTGTTCCTAAATATAAGTCC 59.710 40.741 0.00 0.00 0.00 3.85
3007 5183 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
3008 5184 9.900112 ATACTCCCTCTGTTCCTAAATATAAGT 57.100 33.333 0.00 0.00 0.00 2.24
3014 5190 9.670442 TGTAATATACTCCCTCTGTTCCTAAAT 57.330 33.333 0.00 0.00 0.00 1.40
3015 5191 9.496710 TTGTAATATACTCCCTCTGTTCCTAAA 57.503 33.333 0.00 0.00 0.00 1.85
3016 5192 9.144298 CTTGTAATATACTCCCTCTGTTCCTAA 57.856 37.037 0.00 0.00 0.00 2.69
3017 5193 7.728981 CCTTGTAATATACTCCCTCTGTTCCTA 59.271 40.741 0.00 0.00 0.00 2.94
3018 5194 6.555360 CCTTGTAATATACTCCCTCTGTTCCT 59.445 42.308 0.00 0.00 0.00 3.36
3019 5195 6.553852 TCCTTGTAATATACTCCCTCTGTTCC 59.446 42.308 0.00 0.00 0.00 3.62
3020 5196 7.598759 TCCTTGTAATATACTCCCTCTGTTC 57.401 40.000 0.00 0.00 0.00 3.18
3021 5197 7.569111 ACATCCTTGTAATATACTCCCTCTGTT 59.431 37.037 0.00 0.00 33.16 3.16
3022 5198 7.076446 ACATCCTTGTAATATACTCCCTCTGT 58.924 38.462 0.00 0.00 33.16 3.41
3023 5199 7.546250 ACATCCTTGTAATATACTCCCTCTG 57.454 40.000 0.00 0.00 33.16 3.35
3024 5200 8.457757 ACTACATCCTTGTAATATACTCCCTCT 58.542 37.037 0.00 0.00 37.86 3.69
3025 5201 8.653036 ACTACATCCTTGTAATATACTCCCTC 57.347 38.462 0.00 0.00 37.86 4.30
3098 5274 0.847373 TTGTTGGACCACAAGCCCTA 59.153 50.000 0.00 0.00 40.38 3.53
3115 5291 7.661040 ACACAGGAAACCTTTATGAGAAATTG 58.339 34.615 0.00 0.00 0.00 2.32
3265 5442 5.403246 AGCAACTCTCACTTTATGTACTCG 58.597 41.667 0.00 0.00 0.00 4.18
3267 5444 7.841956 ACATAGCAACTCTCACTTTATGTACT 58.158 34.615 0.00 0.00 30.82 2.73
3282 5459 1.953686 ACCGCACAAAACATAGCAACT 59.046 42.857 0.00 0.00 0.00 3.16
3328 5505 4.732285 AAAATAGCATAATGACTCGGCG 57.268 40.909 0.00 0.00 0.00 6.46
3335 5512 7.072454 ACCCTCCTGACTAAAATAGCATAATGA 59.928 37.037 0.00 0.00 0.00 2.57
3360 5537 7.389884 ACATGAGGATGACATGATATTTGCTAC 59.610 37.037 13.54 0.00 33.36 3.58
3431 5608 2.084844 CTGCTCAGCAATGTCGTCC 58.915 57.895 0.00 0.00 38.41 4.79
3529 5706 4.097892 TCTCTGTTTGTTCCTCCTTTTTGC 59.902 41.667 0.00 0.00 0.00 3.68
3548 5725 1.899142 GCAGGAGTCTCCACTTTCTCT 59.101 52.381 21.26 0.00 39.61 3.10
3608 5785 2.906389 AGCATAGGATGAAATAGCCGGA 59.094 45.455 5.05 0.00 40.72 5.14
3652 5832 6.073058 TGACACTCATTTGACAATTCACTAGC 60.073 38.462 0.00 0.00 0.00 3.42
3733 5914 3.765511 CACAAACATCCATCCCACAGAAT 59.234 43.478 0.00 0.00 0.00 2.40
3770 5951 3.632145 AGAAACCCATGACTGACACAAAC 59.368 43.478 0.00 0.00 0.00 2.93
3803 5984 5.598005 ACCATCCAGAAAAACAAATGACAGA 59.402 36.000 0.00 0.00 0.00 3.41
3954 6135 7.279536 CACAGTCTATATCATTGTTCTTGCAGT 59.720 37.037 0.00 0.00 0.00 4.40
3984 6165 1.798223 GTCTTGCGTGCTCATGTACAA 59.202 47.619 0.00 0.00 0.00 2.41
3985 6166 1.000843 AGTCTTGCGTGCTCATGTACA 59.999 47.619 0.00 0.00 0.00 2.90
4012 6193 0.608035 TTCGGACAAGACAATGGCCC 60.608 55.000 0.00 0.00 46.56 5.80
4073 7816 3.567478 AAGATAACCATCTGGAGGCAC 57.433 47.619 2.55 0.00 40.81 5.01
4107 8068 5.389859 TTCAAATAAACACTGGATGCCTG 57.610 39.130 0.00 0.00 0.00 4.85
4193 8162 9.434420 CTCTTCATCAAATTCAGTAGAACTTCT 57.566 33.333 0.00 0.00 36.39 2.85
4194 8163 9.213799 ACTCTTCATCAAATTCAGTAGAACTTC 57.786 33.333 0.00 0.00 36.39 3.01
4200 8169 6.875726 TCCACACTCTTCATCAAATTCAGTAG 59.124 38.462 0.00 0.00 0.00 2.57
4320 8291 1.549493 CGTATCCCCGGAATAGACCCT 60.549 57.143 0.73 0.00 0.00 4.34
4321 8292 0.893447 CGTATCCCCGGAATAGACCC 59.107 60.000 0.73 0.00 0.00 4.46
4332 8303 0.386838 CGACCAGTAACCGTATCCCC 59.613 60.000 0.00 0.00 0.00 4.81
4333 8304 1.106285 ACGACCAGTAACCGTATCCC 58.894 55.000 0.00 0.00 34.52 3.85
4337 8308 2.229792 ACTGAACGACCAGTAACCGTA 58.770 47.619 11.53 0.00 44.82 4.02
4339 8310 2.056577 GAACTGAACGACCAGTAACCG 58.943 52.381 13.08 0.00 45.82 4.44
4340 8311 2.036862 AGGAACTGAACGACCAGTAACC 59.963 50.000 18.99 18.99 45.82 2.85
4348 8326 5.287226 TCTTGTTAGAAGGAACTGAACGAC 58.713 41.667 0.00 0.00 40.86 4.34
4382 9382 7.922811 AGTTTGTTGATGAAACTTTCTGGATTC 59.077 33.333 3.22 0.00 40.04 2.52
4494 9494 9.967346 GAAGTATATACTGTAGCAAGTGATGAA 57.033 33.333 16.11 0.00 36.50 2.57
4495 9495 8.577296 GGAAGTATATACTGTAGCAAGTGATGA 58.423 37.037 16.11 0.00 36.50 2.92
4496 9496 8.360390 TGGAAGTATATACTGTAGCAAGTGATG 58.640 37.037 16.11 0.00 36.50 3.07
4572 9572 4.836125 AGAATCGTTGTTTGCTTCATGT 57.164 36.364 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.