Multiple sequence alignment - TraesCS1B01G347000

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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 TraesCS1B01G347000 chr1B 100.000 3674 0 0 1 3674 575922497 575926170 0.000000e+00 6785
1 TraesCS1B01G347000 chr1D 87.652 3280 202 93 275 3429 426404136 426407337 0.000000e+00 3626
2 TraesCS1B01G347000 chr1D 87.857 140 9 4 126 264 426402626 426402758 1.370000e-34 158
3 TraesCS1B01G347000 chr1D 90.217 92 7 2 3584 3674 426407579 426407669 6.450000e-23 119
4 TraesCS1B01G347000 chr1A 89.863 1904 115 29 1251 3105 521332145 521334019 0.000000e+00 2375
5 TraesCS1B01G347000 chr1A 83.292 401 39 16 3098 3487 521334203 521334586 9.770000e-91 344
6 TraesCS1B01G347000 chr1A 83.175 422 18 25 739 1144 521331713 521332097 1.630000e-88 337
7 TraesCS1B01G347000 chr1A 82.812 384 49 13 2 371 521330971 521331351 9.840000e-86 327
8 TraesCS1B01G347000 chr1A 81.749 263 10 13 490 737 521331439 521331678 6.270000e-43 185
9 TraesCS1B01G347000 chr6A 96.552 87 3 0 1015 1101 544174185 544174271 1.060000e-30 145
10 TraesCS1B01G347000 chr6D 95.402 87 4 0 1015 1101 398178701 398178787 4.950000e-29 139
11 TraesCS1B01G347000 chr7B 96.386 83 3 0 1015 1097 111312962 111313044 1.780000e-28 137
12 TraesCS1B01G347000 chr7D 94.318 88 5 0 1015 1102 148148070 148148157 6.400000e-28 135
13 TraesCS1B01G347000 chr7A 94.318 88 5 0 1015 1102 149303044 149303131 6.400000e-28 135
14 TraesCS1B01G347000 chr3A 83.969 131 17 4 1007 1134 146395813 146395684 4.980000e-24 122
15 TraesCS1B01G347000 chr3D 89.474 95 10 0 1007 1101 132608063 132607969 1.790000e-23 121


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 TraesCS1B01G347000 chr1B 575922497 575926170 3673 False 6785.0 6785 100.000000 1 3674 1 chr1B.!!$F1 3673
1 TraesCS1B01G347000 chr1D 426402626 426407669 5043 False 1301.0 3626 88.575333 126 3674 3 chr1D.!!$F1 3548
2 TraesCS1B01G347000 chr1A 521330971 521334586 3615 False 713.6 2375 84.178200 2 3487 5 chr1A.!!$F1 3485

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
924 2378 0.036010 TGAGCAGTAGCAAAGGGAGC 60.036 55.0 0.00 0.00 45.49 4.70 F
1846 3370 0.101219 GTCCCGATAGTTAACGGCGT 59.899 55.0 6.77 6.77 46.59 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 3970 0.394565 AGGTGACCAGTGAGCAAGAC 59.605 55.0 3.63 0.0 0.0 3.01 R
3424 5208 0.179018 AACCTTTGAGACGCTGCCTT 60.179 50.0 0.00 0.0 0.0 4.35 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
27 28 4.275810 TCACTCCTGCTAATAGTAACCGT 58.724 43.478 0.00 0.00 0.00 4.83
31 32 6.474751 CACTCCTGCTAATAGTAACCGTTTAC 59.525 42.308 0.00 0.00 38.34 2.01
36 37 6.258160 TGCTAATAGTAACCGTTTACGACTC 58.742 40.000 3.46 0.00 42.28 3.36
46 47 2.414293 CGTTTACGACTCTACTGCTGCT 60.414 50.000 0.00 0.00 43.02 4.24
53 54 1.071385 ACTCTACTGCTGCTGTTTGCT 59.929 47.619 17.29 0.00 43.37 3.91
54 55 2.149578 CTCTACTGCTGCTGTTTGCTT 58.850 47.619 17.29 0.00 43.37 3.91
56 57 2.149578 CTACTGCTGCTGTTTGCTTCT 58.850 47.619 17.29 0.00 43.37 2.85
64 65 1.538950 GCTGTTTGCTTCTTGGAGAGG 59.461 52.381 0.00 0.00 38.95 3.69
66 67 3.072944 CTGTTTGCTTCTTGGAGAGGAG 58.927 50.000 0.00 0.00 33.71 3.69
68 69 2.810852 GTTTGCTTCTTGGAGAGGAGTG 59.189 50.000 0.00 0.00 33.07 3.51
70 71 0.980423 GCTTCTTGGAGAGGAGTGGT 59.020 55.000 0.00 0.00 33.07 4.16
72 73 2.567615 GCTTCTTGGAGAGGAGTGGTAA 59.432 50.000 0.00 0.00 33.07 2.85
73 74 3.008049 GCTTCTTGGAGAGGAGTGGTAAA 59.992 47.826 0.00 0.00 33.07 2.01
74 75 4.323868 GCTTCTTGGAGAGGAGTGGTAAAT 60.324 45.833 0.00 0.00 33.07 1.40
75 76 5.422214 TTCTTGGAGAGGAGTGGTAAATC 57.578 43.478 0.00 0.00 0.00 2.17
76 77 3.447586 TCTTGGAGAGGAGTGGTAAATCG 59.552 47.826 0.00 0.00 0.00 3.34
77 78 2.108168 TGGAGAGGAGTGGTAAATCGG 58.892 52.381 0.00 0.00 0.00 4.18
86 87 2.531376 GGTAAATCGGAAGCGGGCG 61.531 63.158 0.00 0.00 0.00 6.13
97 98 4.919987 GCGGGCGCGTACTACTCC 62.920 72.222 24.70 0.00 0.00 3.85
98 99 3.207669 CGGGCGCGTACTACTCCT 61.208 66.667 15.94 0.00 0.00 3.69
105 106 1.063174 CGCGTACTACTCCTGGTACAC 59.937 57.143 0.00 0.00 38.42 2.90
117 118 0.324368 TGGTACACGCCAGGAGATCT 60.324 55.000 0.00 0.00 33.97 2.75
120 121 2.541556 GTACACGCCAGGAGATCTTTC 58.458 52.381 0.00 0.00 0.00 2.62
121 122 1.270907 ACACGCCAGGAGATCTTTCT 58.729 50.000 0.00 0.00 33.88 2.52
124 125 2.675348 CACGCCAGGAGATCTTTCTTTC 59.325 50.000 0.00 0.00 30.30 2.62
199 205 4.862574 TCGAATTCGAAATCAGGTGTACAG 59.137 41.667 27.36 0.00 46.30 2.74
234 240 2.547211 CGTACTACCGCTAGCACTACAT 59.453 50.000 16.45 0.00 0.00 2.29
268 1640 3.375911 GTACTACTCGTACTCGCGTTT 57.624 47.619 5.77 0.00 44.09 3.60
271 1643 2.349886 ACTACTCGTACTCGCGTTTAGG 59.650 50.000 5.77 4.59 36.42 2.69
272 1644 1.442769 ACTCGTACTCGCGTTTAGGA 58.557 50.000 5.77 8.78 30.66 2.94
273 1645 2.012673 ACTCGTACTCGCGTTTAGGAT 58.987 47.619 5.77 0.00 30.66 3.24
279 1651 3.107642 ACTCGCGTTTAGGATATTGGG 57.892 47.619 5.77 0.00 0.00 4.12
292 1667 6.018433 AGGATATTGGGAGCTGTACATTTT 57.982 37.500 0.00 0.00 0.00 1.82
293 1668 6.435164 AGGATATTGGGAGCTGTACATTTTT 58.565 36.000 0.00 0.00 0.00 1.94
294 1669 7.582719 AGGATATTGGGAGCTGTACATTTTTA 58.417 34.615 0.00 0.00 0.00 1.52
295 1670 7.502561 AGGATATTGGGAGCTGTACATTTTTAC 59.497 37.037 0.00 0.00 0.00 2.01
297 1672 5.957842 TTGGGAGCTGTACATTTTTACTG 57.042 39.130 0.00 0.00 0.00 2.74
298 1673 4.980573 TGGGAGCTGTACATTTTTACTGT 58.019 39.130 0.00 0.00 0.00 3.55
299 1674 5.001232 TGGGAGCTGTACATTTTTACTGTC 58.999 41.667 0.00 0.00 0.00 3.51
300 1675 5.001232 GGGAGCTGTACATTTTTACTGTCA 58.999 41.667 0.00 0.00 0.00 3.58
302 1677 5.932303 GGAGCTGTACATTTTTACTGTCAGA 59.068 40.000 6.91 0.00 30.25 3.27
303 1678 6.128526 GGAGCTGTACATTTTTACTGTCAGAC 60.129 42.308 6.91 0.00 30.25 3.51
304 1679 5.405571 AGCTGTACATTTTTACTGTCAGACG 59.594 40.000 6.91 0.00 30.25 4.18
306 1681 6.615839 GCTGTACATTTTTACTGTCAGACGTC 60.616 42.308 7.70 7.70 30.25 4.34
307 1682 4.966850 ACATTTTTACTGTCAGACGTCG 57.033 40.909 10.46 5.48 0.00 5.12
309 1684 1.401530 TTTTACTGTCAGACGTCGCG 58.598 50.000 10.46 0.00 0.00 5.87
330 1707 3.421844 GCATTGGGACTCTAAACAAGGT 58.578 45.455 0.00 0.00 0.00 3.50
332 1709 3.782656 TTGGGACTCTAAACAAGGTCC 57.217 47.619 0.00 0.00 41.38 4.46
352 1729 2.606795 CCGTCTCGTTTAACCCGTTGTA 60.607 50.000 0.00 0.00 0.00 2.41
354 1731 2.731451 GTCTCGTTTAACCCGTTGTACC 59.269 50.000 0.00 0.00 0.00 3.34
394 1772 5.079998 AGGTGGGAGAAAAAGAAAATCCT 57.920 39.130 0.00 0.00 0.00 3.24
416 1795 5.981915 CCTCTTGAAAGAAAAAGAAGGCTTG 59.018 40.000 3.46 0.00 34.03 4.01
453 1832 3.715097 GCTCCTGGTCTGCTGCCT 61.715 66.667 0.00 0.00 0.00 4.75
454 1833 2.583520 CTCCTGGTCTGCTGCCTC 59.416 66.667 0.00 0.00 0.00 4.70
455 1834 2.203832 TCCTGGTCTGCTGCCTCA 60.204 61.111 0.00 0.00 0.00 3.86
456 1835 2.046507 CCTGGTCTGCTGCCTCAC 60.047 66.667 0.00 0.00 0.00 3.51
457 1836 2.591072 CCTGGTCTGCTGCCTCACT 61.591 63.158 0.00 0.00 0.00 3.41
470 1849 1.085091 CCTCACTCAGCTTCACATGC 58.915 55.000 0.00 0.00 0.00 4.06
471 1850 0.720027 CTCACTCAGCTTCACATGCG 59.280 55.000 0.00 0.00 35.28 4.73
472 1851 0.318120 TCACTCAGCTTCACATGCGA 59.682 50.000 0.00 0.00 35.28 5.10
473 1852 0.720027 CACTCAGCTTCACATGCGAG 59.280 55.000 0.00 0.00 37.23 5.03
474 1853 0.605083 ACTCAGCTTCACATGCGAGA 59.395 50.000 0.00 0.00 36.11 4.04
475 1854 1.001293 ACTCAGCTTCACATGCGAGAA 59.999 47.619 0.00 0.00 36.11 2.87
476 1855 1.392853 CTCAGCTTCACATGCGAGAAC 59.607 52.381 0.00 0.00 35.09 3.01
477 1856 0.094216 CAGCTTCACATGCGAGAACG 59.906 55.000 0.00 0.00 42.93 3.95
478 1857 0.038251 AGCTTCACATGCGAGAACGA 60.038 50.000 0.00 0.00 42.66 3.85
479 1858 0.368227 GCTTCACATGCGAGAACGAG 59.632 55.000 0.00 0.00 42.66 4.18
480 1859 0.368227 CTTCACATGCGAGAACGAGC 59.632 55.000 0.00 0.00 42.66 5.03
486 1865 1.369839 ATGCGAGAACGAGCGAGAGA 61.370 55.000 0.00 0.00 42.66 3.10
512 1891 2.358003 GAGACCTGCGCAGTGCTT 60.358 61.111 33.75 17.41 46.63 3.91
513 1892 1.963338 GAGACCTGCGCAGTGCTTT 60.963 57.895 33.75 15.65 46.63 3.51
514 1893 1.905922 GAGACCTGCGCAGTGCTTTC 61.906 60.000 33.75 20.75 46.63 2.62
515 1894 2.203195 ACCTGCGCAGTGCTTTCA 60.203 55.556 33.75 7.42 46.63 2.69
557 1936 3.058160 GCCTGTGCGCCTGTGATT 61.058 61.111 4.18 0.00 0.00 2.57
558 1937 2.872557 CCTGTGCGCCTGTGATTG 59.127 61.111 4.18 0.00 0.00 2.67
559 1938 1.968017 CCTGTGCGCCTGTGATTGT 60.968 57.895 4.18 0.00 0.00 2.71
560 1939 1.499056 CTGTGCGCCTGTGATTGTC 59.501 57.895 4.18 0.00 0.00 3.18
561 1940 0.952497 CTGTGCGCCTGTGATTGTCT 60.952 55.000 4.18 0.00 0.00 3.41
731 2136 3.422303 GCATTCACGCCACGCTCA 61.422 61.111 0.00 0.00 0.00 4.26
774 2212 0.602905 CAGAGGCCGGTCGTTTCTTT 60.603 55.000 1.90 0.00 0.00 2.52
829 2272 2.034221 ACGGCTCCCCTTGCTTTC 59.966 61.111 0.00 0.00 0.00 2.62
830 2273 2.751837 CGGCTCCCCTTGCTTTCC 60.752 66.667 0.00 0.00 0.00 3.13
832 2275 2.766660 GCTCCCCTTGCTTTCCCT 59.233 61.111 0.00 0.00 0.00 4.20
867 2310 2.393646 AGTATCCTTGTCTCTGGCTCC 58.606 52.381 0.00 0.00 0.00 4.70
868 2311 1.414550 GTATCCTTGTCTCTGGCTCCC 59.585 57.143 0.00 0.00 0.00 4.30
916 2370 3.390521 CCCCCGTGAGCAGTAGCA 61.391 66.667 0.00 0.00 45.49 3.49
917 2371 2.662596 CCCCGTGAGCAGTAGCAA 59.337 61.111 0.00 0.00 45.49 3.91
918 2372 1.003839 CCCCGTGAGCAGTAGCAAA 60.004 57.895 0.00 0.00 45.49 3.68
919 2373 1.021390 CCCCGTGAGCAGTAGCAAAG 61.021 60.000 0.00 0.00 45.49 2.77
920 2374 1.021390 CCCGTGAGCAGTAGCAAAGG 61.021 60.000 0.00 0.00 45.49 3.11
921 2375 1.021390 CCGTGAGCAGTAGCAAAGGG 61.021 60.000 0.00 0.00 45.49 3.95
922 2376 0.037326 CGTGAGCAGTAGCAAAGGGA 60.037 55.000 0.00 0.00 45.49 4.20
923 2377 1.731720 GTGAGCAGTAGCAAAGGGAG 58.268 55.000 0.00 0.00 45.49 4.30
924 2378 0.036010 TGAGCAGTAGCAAAGGGAGC 60.036 55.000 0.00 0.00 45.49 4.70
925 2379 1.078848 AGCAGTAGCAAAGGGAGCG 60.079 57.895 0.00 0.00 45.49 5.03
926 2380 1.079127 GCAGTAGCAAAGGGAGCGA 60.079 57.895 0.00 0.00 41.58 4.93
927 2381 1.086634 GCAGTAGCAAAGGGAGCGAG 61.087 60.000 0.00 0.00 41.58 5.03
928 2382 1.086634 CAGTAGCAAAGGGAGCGAGC 61.087 60.000 0.00 0.00 37.01 5.03
929 2383 1.219393 GTAGCAAAGGGAGCGAGCT 59.781 57.895 0.00 0.00 39.22 4.09
951 2428 1.964891 GCTGCTGCTCTTGCTGTGA 60.965 57.895 8.53 0.00 39.81 3.58
979 2456 1.337260 CCGTGGAAGTGAAGTGAGGAG 60.337 57.143 0.00 0.00 0.00 3.69
981 2458 0.687354 TGGAAGTGAAGTGAGGAGGC 59.313 55.000 0.00 0.00 0.00 4.70
983 2460 1.004440 AAGTGAAGTGAGGAGGCGC 60.004 57.895 0.00 0.00 0.00 6.53
1017 2497 2.037772 AGAGATGAGCGTGACCAAGTTT 59.962 45.455 0.00 0.00 0.00 2.66
1121 2601 3.216371 TCCCTCCCCCAACCCTCT 61.216 66.667 0.00 0.00 0.00 3.69
1146 2626 2.438763 TCCTCTTCTCCTCCTACCTACG 59.561 54.545 0.00 0.00 0.00 3.51
1148 2628 1.493871 TCTTCTCCTCCTACCTACGGG 59.506 57.143 0.00 0.00 38.88 5.28
1149 2629 0.106318 TTCTCCTCCTACCTACGGGC 60.106 60.000 0.00 0.00 35.63 6.13
1150 2630 0.992431 TCTCCTCCTACCTACGGGCT 60.992 60.000 0.00 0.00 35.63 5.19
1151 2631 0.769873 CTCCTCCTACCTACGGGCTA 59.230 60.000 0.00 0.00 35.63 3.93
1152 2632 0.769873 TCCTCCTACCTACGGGCTAG 59.230 60.000 0.00 0.00 35.63 3.42
1162 2642 0.630673 TACGGGCTAGGTAGTTCCCA 59.369 55.000 2.29 0.00 38.68 4.37
1181 2661 1.953686 CATCTTCCTCCTCTCGACCTC 59.046 57.143 0.00 0.00 0.00 3.85
1186 2666 1.921049 TCCTCCTCTCGACCTCCTTTA 59.079 52.381 0.00 0.00 0.00 1.85
1187 2667 2.025898 CCTCCTCTCGACCTCCTTTAC 58.974 57.143 0.00 0.00 0.00 2.01
1188 2668 2.025898 CTCCTCTCGACCTCCTTTACC 58.974 57.143 0.00 0.00 0.00 2.85
1236 2717 3.557903 TTGGGCTCACTCTGCTGGC 62.558 63.158 0.00 0.00 0.00 4.85
1347 2828 4.139234 GGGACACCGCCGGTACTC 62.139 72.222 9.25 6.52 32.11 2.59
1360 2841 1.415200 GGTACTCACTCCATCCCTCC 58.585 60.000 0.00 0.00 0.00 4.30
1374 2855 0.698238 CCCTCCTCATTTCCACCACA 59.302 55.000 0.00 0.00 0.00 4.17
1381 2862 3.197766 CCTCATTTCCACCACAGCTACTA 59.802 47.826 0.00 0.00 0.00 1.82
1437 2940 0.308993 GGTCTGTGCTGTGTTTGCTC 59.691 55.000 0.00 0.00 0.00 4.26
1611 3123 6.528072 GGCACATTAGTTCAGAAATTACTTGC 59.472 38.462 0.00 0.00 0.00 4.01
1623 3135 7.613022 TCAGAAATTACTTGCTCCAGATTTGAT 59.387 33.333 0.00 0.00 0.00 2.57
1634 3146 3.760151 TCCAGATTTGATTGTGCTTGAGG 59.240 43.478 0.00 0.00 0.00 3.86
1655 3167 5.262588 GGTTTCACCTGAACTGAATGTTT 57.737 39.130 0.00 0.00 35.54 2.83
1657 3169 5.519927 GGTTTCACCTGAACTGAATGTTTTG 59.480 40.000 0.00 0.00 35.54 2.44
1684 3204 3.710326 TGATAATTCGGTCTCTGGTCG 57.290 47.619 0.00 0.00 0.00 4.79
1737 3257 1.877443 CCGAACGTTCCCATTGTTCTT 59.123 47.619 22.07 0.00 39.78 2.52
1759 3279 0.116342 TGGGACCAAGCTAGGTGAGA 59.884 55.000 0.00 0.00 43.38 3.27
1805 3329 2.422597 TCGATGAACTTTCCGCAATGT 58.577 42.857 0.00 0.00 0.00 2.71
1841 3365 4.873827 TGCATCTTTGTCCCGATAGTTAAC 59.126 41.667 0.00 0.00 0.00 2.01
1842 3366 4.025979 GCATCTTTGTCCCGATAGTTAACG 60.026 45.833 0.00 0.00 0.00 3.18
1846 3370 0.101219 GTCCCGATAGTTAACGGCGT 59.899 55.000 6.77 6.77 46.59 5.68
2010 3538 3.011144 TGCCATCTTCTTCCCCATTGTTA 59.989 43.478 0.00 0.00 0.00 2.41
2013 3541 5.221322 GCCATCTTCTTCCCCATTGTTATTC 60.221 44.000 0.00 0.00 0.00 1.75
2259 3795 1.671054 CGACACCGCCATCAAGGTT 60.671 57.895 0.00 0.00 39.00 3.50
2345 3881 2.785540 TGCTCCATCATGTAAGCACA 57.214 45.000 7.67 0.00 39.69 4.57
2357 3894 0.690762 TAAGCACACCCCACCTCTTC 59.309 55.000 0.00 0.00 0.00 2.87
2367 3904 3.107601 CCCCACCTCTTCTCATTCACTA 58.892 50.000 0.00 0.00 0.00 2.74
2374 3911 4.441356 CCTCTTCTCATTCACTAGCTCCAC 60.441 50.000 0.00 0.00 0.00 4.02
2402 3944 4.700213 ACTGTATAATGGTGTGAGCAAACC 59.300 41.667 2.77 2.77 36.96 3.27
2428 3970 4.703575 TCTCCAGATTTGCTCCATGAAAAG 59.296 41.667 0.00 0.00 0.00 2.27
2447 3989 0.394565 GTCTTGCTCACTGGTCACCT 59.605 55.000 0.00 0.00 0.00 4.00
2448 3990 1.131638 TCTTGCTCACTGGTCACCTT 58.868 50.000 0.00 0.00 0.00 3.50
2449 3991 2.037251 GTCTTGCTCACTGGTCACCTTA 59.963 50.000 0.00 0.00 0.00 2.69
2470 4012 7.038373 ACCTTATTACCTCAAAATTGGCACATT 60.038 33.333 0.00 0.00 39.30 2.71
2471 4013 7.492344 CCTTATTACCTCAAAATTGGCACATTC 59.508 37.037 0.00 0.00 39.30 2.67
2472 4014 5.798125 TTACCTCAAAATTGGCACATTCA 57.202 34.783 0.00 0.00 39.30 2.57
2488 4030 6.072838 GGCACATTCATCAGTTCGATTATGAT 60.073 38.462 2.62 2.62 34.02 2.45
2526 4083 6.423604 GCTGCTTAGATCAGATTTTAGAGGTC 59.576 42.308 0.00 0.00 33.54 3.85
2531 4088 9.528018 CTTAGATCAGATTTTAGAGGTCAACTC 57.472 37.037 0.00 0.00 46.98 3.01
2574 4134 7.923888 TGATTTTCCAAAATTTCAAATTCGCA 58.076 26.923 0.00 0.00 38.64 5.10
2600 4161 2.849942 TGCAGTGTTCTTGCACAGTAT 58.150 42.857 0.00 0.00 41.52 2.12
2619 4180 2.350057 TAGGAGTCCTGATCCTGTCG 57.650 55.000 22.69 0.00 46.81 4.35
2625 4186 1.135333 GTCCTGATCCTGTCGTTCTCC 59.865 57.143 0.00 0.00 0.00 3.71
2676 4237 3.373020 CACGTGTGCTGCTTGAATC 57.627 52.632 7.58 0.00 0.00 2.52
2726 4287 2.354704 GCATGGTGTAGTAGGCAAGTCA 60.355 50.000 0.00 0.00 0.00 3.41
2781 4342 6.340962 TGCTTCTGTTCTGTTTAGCTACTA 57.659 37.500 0.00 0.00 0.00 1.82
2782 4343 6.390721 TGCTTCTGTTCTGTTTAGCTACTAG 58.609 40.000 0.00 0.00 0.00 2.57
2783 4344 5.289917 GCTTCTGTTCTGTTTAGCTACTAGC 59.710 44.000 0.00 0.00 42.84 3.42
2828 4389 6.768381 GGTTTCTACTTCCAATCCAATCCTAG 59.232 42.308 0.00 0.00 0.00 3.02
2934 4508 9.736023 GCAAGCTATAAGTTTATTGTTAGCATT 57.264 29.630 0.00 0.00 0.00 3.56
2981 4556 2.997986 GCAATTGGTGGCAGATTGAAAG 59.002 45.455 17.43 0.00 33.67 2.62
2986 4561 2.092323 GGTGGCAGATTGAAAGGTACC 58.908 52.381 2.73 2.73 0.00 3.34
3012 4587 4.847757 CACAAGTGTGCTGAATATCAAACG 59.152 41.667 0.00 0.00 39.39 3.60
3025 4600 0.250727 TCAAACGGCAAGAAGGGAGG 60.251 55.000 0.00 0.00 0.00 4.30
3079 4655 1.065854 TCTTGCTAGCTGCCTCCTTTC 60.066 52.381 17.23 0.00 42.00 2.62
3113 4689 3.686726 GCCATTGGTGAAGTAGACTTGAG 59.313 47.826 4.26 0.00 36.11 3.02
3115 4691 4.318332 CATTGGTGAAGTAGACTTGAGCA 58.682 43.478 9.27 9.27 43.64 4.26
3125 4891 6.305693 AGTAGACTTGAGCAAATGTTGAAC 57.694 37.500 0.00 0.00 0.00 3.18
3137 4903 0.482446 TGTTGAACAAGGGGGCATCT 59.518 50.000 0.00 0.00 0.00 2.90
3138 4904 0.890683 GTTGAACAAGGGGGCATCTG 59.109 55.000 0.00 0.00 0.00 2.90
3139 4905 0.482446 TTGAACAAGGGGGCATCTGT 59.518 50.000 0.00 0.00 0.00 3.41
3140 4906 0.038166 TGAACAAGGGGGCATCTGTC 59.962 55.000 0.00 0.00 0.00 3.51
3142 4908 0.482446 AACAAGGGGGCATCTGTCAA 59.518 50.000 0.00 0.00 0.00 3.18
3162 4929 1.875009 AGTAGTCGTCGTCACAGTCA 58.125 50.000 0.00 0.00 0.00 3.41
3163 4930 1.799403 AGTAGTCGTCGTCACAGTCAG 59.201 52.381 0.00 0.00 0.00 3.51
3206 4978 0.035630 CTGGAAGGAGCAAGTGAGGG 60.036 60.000 0.00 0.00 0.00 4.30
3221 4993 3.118038 AGTGAGGGTGTAGCAGAAAAACA 60.118 43.478 0.00 0.00 0.00 2.83
3230 5002 0.234884 GCAGAAAAACAGGTCGACGG 59.765 55.000 9.92 6.90 0.00 4.79
3234 5006 3.250040 CAGAAAAACAGGTCGACGGAATT 59.750 43.478 9.92 0.00 0.00 2.17
3277 5049 2.093235 CCCTCCTTTAGCTTCAGTCTGG 60.093 54.545 0.00 0.00 0.00 3.86
3278 5050 2.569404 CCTCCTTTAGCTTCAGTCTGGT 59.431 50.000 0.00 0.00 0.00 4.00
3289 5061 1.762370 TCAGTCTGGTTGAAGTGCTCA 59.238 47.619 0.00 0.00 0.00 4.26
3302 5074 4.156556 TGAAGTGCTCATCAAATACCTTGC 59.843 41.667 0.00 0.00 34.76 4.01
3340 5124 1.271597 GGCATCTCCAGAACAAGTGGT 60.272 52.381 0.00 0.00 36.37 4.16
3361 5145 5.047377 TGGTAACATGAAAATTGGAGGAAGC 60.047 40.000 0.00 0.00 46.17 3.86
3388 5172 2.238521 TCCCTGAAAATGTCACCTTGC 58.761 47.619 0.00 0.00 31.13 4.01
3389 5173 1.273327 CCCTGAAAATGTCACCTTGCC 59.727 52.381 0.00 0.00 31.13 4.52
3393 5177 1.615392 GAAAATGTCACCTTGCCTGCT 59.385 47.619 0.00 0.00 0.00 4.24
3397 5181 0.250467 TGTCACCTTGCCTGCTCTTC 60.250 55.000 0.00 0.00 0.00 2.87
3398 5182 0.957888 GTCACCTTGCCTGCTCTTCC 60.958 60.000 0.00 0.00 0.00 3.46
3418 5202 5.528600 TCCCATTGGAATAACTCCTGAAA 57.471 39.130 3.62 0.00 45.64 2.69
3424 5208 3.325425 TGGAATAACTCCTGAAACCGACA 59.675 43.478 0.00 0.00 45.64 4.35
3429 5213 0.250295 CTCCTGAAACCGACAAGGCA 60.250 55.000 0.00 0.00 46.52 4.75
3431 5215 1.576421 CTGAAACCGACAAGGCAGC 59.424 57.895 0.00 0.00 46.52 5.25
3433 5217 2.203153 AAACCGACAAGGCAGCGT 60.203 55.556 0.00 0.00 46.52 5.07
3437 5221 2.049156 CGACAAGGCAGCGTCTCA 60.049 61.111 0.00 0.00 0.00 3.27
3438 5222 1.664649 CGACAAGGCAGCGTCTCAA 60.665 57.895 0.00 0.00 0.00 3.02
3439 5223 1.221466 CGACAAGGCAGCGTCTCAAA 61.221 55.000 0.00 0.00 0.00 2.69
3440 5224 0.514691 GACAAGGCAGCGTCTCAAAG 59.485 55.000 0.00 0.00 0.00 2.77
3441 5225 0.886490 ACAAGGCAGCGTCTCAAAGG 60.886 55.000 0.00 0.00 0.00 3.11
3442 5226 0.886490 CAAGGCAGCGTCTCAAAGGT 60.886 55.000 0.00 0.00 0.00 3.50
3443 5227 0.179018 AAGGCAGCGTCTCAAAGGTT 60.179 50.000 0.00 0.00 0.00 3.50
3444 5228 0.179018 AGGCAGCGTCTCAAAGGTTT 60.179 50.000 0.00 0.00 0.00 3.27
3466 5250 1.596260 CGTAGCAGCATGGATCAACAG 59.404 52.381 0.00 0.00 35.86 3.16
3491 5275 4.024893 GTCCATACTGTTATGTGCATTCCG 60.025 45.833 0.00 0.00 34.27 4.30
3505 5289 2.666619 GCATTCCGTTGTTGAGCTCAAG 60.667 50.000 29.13 16.86 36.39 3.02
3506 5290 0.944386 TTCCGTTGTTGAGCTCAAGC 59.056 50.000 29.13 22.00 36.39 4.01
3507 5291 0.179059 TCCGTTGTTGAGCTCAAGCA 60.179 50.000 29.13 24.07 45.16 3.91
3510 5294 2.287788 CCGTTGTTGAGCTCAAGCAAAT 60.288 45.455 29.43 0.00 45.16 2.32
3511 5295 3.374745 CGTTGTTGAGCTCAAGCAAATT 58.625 40.909 29.43 0.00 45.16 1.82
3513 5297 4.614946 GTTGTTGAGCTCAAGCAAATTCT 58.385 39.130 29.43 0.00 45.16 2.40
3514 5298 4.233123 TGTTGAGCTCAAGCAAATTCTG 57.767 40.909 29.13 0.00 45.16 3.02
3527 5311 4.843220 CAAATTCTGCACTCCAAGAGTT 57.157 40.909 0.00 0.00 41.37 3.01
3528 5312 4.791974 CAAATTCTGCACTCCAAGAGTTC 58.208 43.478 0.00 0.00 41.37 3.01
3529 5313 4.363991 AATTCTGCACTCCAAGAGTTCT 57.636 40.909 0.00 0.00 41.37 3.01
3530 5314 2.827800 TCTGCACTCCAAGAGTTCTG 57.172 50.000 0.00 0.00 41.37 3.02
3531 5315 2.042464 TCTGCACTCCAAGAGTTCTGT 58.958 47.619 0.00 0.00 41.37 3.41
3532 5316 2.141517 CTGCACTCCAAGAGTTCTGTG 58.858 52.381 0.00 0.00 41.37 3.66
3533 5317 0.871057 GCACTCCAAGAGTTCTGTGC 59.129 55.000 6.57 6.57 41.37 4.57
3534 5318 1.811558 GCACTCCAAGAGTTCTGTGCA 60.812 52.381 14.03 0.00 46.64 4.57
3535 5319 2.141517 CACTCCAAGAGTTCTGTGCAG 58.858 52.381 0.00 0.00 41.37 4.41
3536 5320 1.765314 ACTCCAAGAGTTCTGTGCAGT 59.235 47.619 0.00 0.00 40.28 4.40
3537 5321 2.141517 CTCCAAGAGTTCTGTGCAGTG 58.858 52.381 0.00 0.00 0.00 3.66
3538 5322 0.590195 CCAAGAGTTCTGTGCAGTGC 59.410 55.000 8.58 8.58 0.00 4.40
3539 5323 1.302366 CAAGAGTTCTGTGCAGTGCA 58.698 50.000 15.37 15.37 35.60 4.57
3571 5355 6.961360 ATACTTGATCAACGAGGATGTCTA 57.039 37.500 3.38 0.00 32.59 2.59
3572 5356 5.255710 ACTTGATCAACGAGGATGTCTAG 57.744 43.478 3.38 0.00 34.46 2.43
3598 5540 3.009115 CGCCCCTCCCTCCTTGAA 61.009 66.667 0.00 0.00 0.00 2.69
3635 5577 4.498682 GCAAGTTGCAATCCAATAGCCTAG 60.499 45.833 22.90 0.00 44.26 3.02
3642 5584 2.820059 TCCAATAGCCTAGCATGACG 57.180 50.000 0.00 0.00 0.00 4.35
3645 5587 3.255888 TCCAATAGCCTAGCATGACGTAG 59.744 47.826 0.00 0.00 0.00 3.51
3648 5590 5.473931 CAATAGCCTAGCATGACGTAGATT 58.526 41.667 0.00 0.00 0.00 2.40
3649 5591 3.377346 AGCCTAGCATGACGTAGATTG 57.623 47.619 0.00 0.00 0.00 2.67
3650 5592 2.959030 AGCCTAGCATGACGTAGATTGA 59.041 45.455 0.00 0.00 0.00 2.57
3658 5600 1.822990 TGACGTAGATTGAGGTCACCC 59.177 52.381 0.00 0.00 38.84 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.428799 GTTACTATTAGCAGGAGTGAGTACG 58.571 44.000 0.00 0.00 0.00 3.67
3 4 4.338682 CGGTTACTATTAGCAGGAGTGAGT 59.661 45.833 0.00 0.00 0.00 3.41
9 10 5.356751 TCGTAAACGGTTACTATTAGCAGGA 59.643 40.000 20.45 4.93 37.97 3.86
27 28 2.557056 ACAGCAGCAGTAGAGTCGTAAA 59.443 45.455 0.00 0.00 0.00 2.01
31 32 1.723542 CAAACAGCAGCAGTAGAGTCG 59.276 52.381 0.00 0.00 0.00 4.18
46 47 2.439507 ACTCCTCTCCAAGAAGCAAACA 59.560 45.455 0.00 0.00 0.00 2.83
53 54 4.081642 CGATTTACCACTCCTCTCCAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
54 55 3.447586 CGATTTACCACTCCTCTCCAAGA 59.552 47.826 0.00 0.00 0.00 3.02
56 57 2.500098 CCGATTTACCACTCCTCTCCAA 59.500 50.000 0.00 0.00 0.00 3.53
64 65 1.287425 CCGCTTCCGATTTACCACTC 58.713 55.000 0.00 0.00 36.29 3.51
66 67 1.712018 GCCCGCTTCCGATTTACCAC 61.712 60.000 0.00 0.00 36.29 4.16
68 69 2.531376 CGCCCGCTTCCGATTTACC 61.531 63.158 0.00 0.00 36.29 2.85
70 71 2.893404 GCGCCCGCTTCCGATTTA 60.893 61.111 5.27 0.00 38.26 1.40
76 77 4.197498 TAGTACGCGCCCGCTTCC 62.197 66.667 5.73 0.00 39.32 3.46
77 78 2.953303 GTAGTACGCGCCCGCTTC 60.953 66.667 5.73 1.42 39.32 3.86
86 87 1.063174 CGTGTACCAGGAGTAGTACGC 59.937 57.143 0.00 0.00 43.34 4.42
98 99 0.324368 AGATCTCCTGGCGTGTACCA 60.324 55.000 0.00 0.00 38.29 3.25
105 106 2.284190 GGAAAGAAAGATCTCCTGGCG 58.716 52.381 0.00 0.00 33.77 5.69
117 118 5.825593 AGCATATCTATCCGGGAAAGAAA 57.174 39.130 0.00 0.00 0.00 2.52
120 121 5.413309 AGAAGCATATCTATCCGGGAAAG 57.587 43.478 0.00 0.00 0.00 2.62
121 122 4.082190 CGAGAAGCATATCTATCCGGGAAA 60.082 45.833 0.00 0.00 0.00 3.13
124 125 2.099921 CCGAGAAGCATATCTATCCGGG 59.900 54.545 0.00 0.00 0.00 5.73
191 196 2.264794 CCCTCGTGGCTGTACACC 59.735 66.667 0.00 0.00 38.11 4.16
222 228 4.724303 CACCTCGTATATGTAGTGCTAGC 58.276 47.826 8.10 8.10 0.00 3.42
234 240 5.010112 ACGAGTAGTACTAGCACCTCGTATA 59.990 44.000 29.90 0.00 43.10 1.47
264 1636 4.073293 ACAGCTCCCAATATCCTAAACG 57.927 45.455 0.00 0.00 0.00 3.60
268 1640 6.763715 AAATGTACAGCTCCCAATATCCTA 57.236 37.500 0.33 0.00 0.00 2.94
271 1643 8.345565 CAGTAAAAATGTACAGCTCCCAATATC 58.654 37.037 0.33 0.00 0.00 1.63
272 1644 7.834181 ACAGTAAAAATGTACAGCTCCCAATAT 59.166 33.333 0.33 0.00 0.00 1.28
273 1645 7.172342 ACAGTAAAAATGTACAGCTCCCAATA 58.828 34.615 0.33 0.00 0.00 1.90
279 1651 6.400091 CGTCTGACAGTAAAAATGTACAGCTC 60.400 42.308 8.73 0.00 31.55 4.09
292 1667 1.441515 GCGCGACGTCTGACAGTAA 60.442 57.895 12.10 0.00 0.00 2.24
293 1668 1.918868 ATGCGCGACGTCTGACAGTA 61.919 55.000 12.10 0.25 0.00 2.74
294 1669 2.749110 AATGCGCGACGTCTGACAGT 62.749 55.000 12.10 4.89 0.00 3.55
295 1670 2.088763 AATGCGCGACGTCTGACAG 61.089 57.895 12.10 0.00 0.00 3.51
297 1672 2.391821 CAATGCGCGACGTCTGAC 59.608 61.111 12.10 2.79 0.00 3.51
298 1673 2.809174 CCAATGCGCGACGTCTGA 60.809 61.111 12.10 0.00 0.00 3.27
299 1674 3.853330 CCCAATGCGCGACGTCTG 61.853 66.667 12.10 8.46 0.00 3.51
300 1675 4.063967 TCCCAATGCGCGACGTCT 62.064 61.111 12.10 0.00 0.00 4.18
302 1677 4.373116 AGTCCCAATGCGCGACGT 62.373 61.111 12.10 0.00 0.00 4.34
303 1678 2.607668 TAGAGTCCCAATGCGCGACG 62.608 60.000 12.10 0.00 0.00 5.12
304 1679 0.459585 TTAGAGTCCCAATGCGCGAC 60.460 55.000 12.10 3.24 0.00 5.19
306 1681 0.373716 GTTTAGAGTCCCAATGCGCG 59.626 55.000 0.00 0.00 0.00 6.86
307 1682 1.448985 TGTTTAGAGTCCCAATGCGC 58.551 50.000 0.00 0.00 0.00 6.09
309 1684 3.421844 ACCTTGTTTAGAGTCCCAATGC 58.578 45.455 0.00 0.00 0.00 3.56
320 1697 2.719426 ACGAGACGGACCTTGTTTAG 57.281 50.000 0.00 0.00 0.00 1.85
321 1698 3.457610 AAACGAGACGGACCTTGTTTA 57.542 42.857 14.44 0.00 44.60 2.01
330 1707 0.673437 AACGGGTTAAACGAGACGGA 59.327 50.000 7.70 0.00 34.93 4.69
332 1709 1.490621 ACAACGGGTTAAACGAGACG 58.509 50.000 7.70 0.00 34.93 4.18
352 1729 5.067936 CACCTCGTAATGATTCTCTAGTGGT 59.932 44.000 0.00 0.00 0.00 4.16
354 1731 5.508153 CCCACCTCGTAATGATTCTCTAGTG 60.508 48.000 0.00 0.00 0.00 2.74
394 1772 6.773976 TCAAGCCTTCTTTTTCTTTCAAGA 57.226 33.333 0.00 0.00 0.00 3.02
453 1832 0.318120 TCGCATGTGAAGCTGAGTGA 59.682 50.000 6.47 0.00 0.00 3.41
454 1833 0.720027 CTCGCATGTGAAGCTGAGTG 59.280 55.000 10.71 0.00 32.21 3.51
455 1834 0.605083 TCTCGCATGTGAAGCTGAGT 59.395 50.000 10.71 0.00 35.59 3.41
456 1835 1.392853 GTTCTCGCATGTGAAGCTGAG 59.607 52.381 10.71 0.00 35.49 3.35
457 1836 1.432514 GTTCTCGCATGTGAAGCTGA 58.567 50.000 10.71 1.03 0.00 4.26
470 1849 0.300491 CTCTCTCTCGCTCGTTCTCG 59.700 60.000 0.00 0.00 38.55 4.04
471 1850 1.593006 CTCTCTCTCTCGCTCGTTCTC 59.407 57.143 0.00 0.00 0.00 2.87
472 1851 1.206132 TCTCTCTCTCTCGCTCGTTCT 59.794 52.381 0.00 0.00 0.00 3.01
473 1852 1.593006 CTCTCTCTCTCTCGCTCGTTC 59.407 57.143 0.00 0.00 0.00 3.95
474 1853 1.206132 TCTCTCTCTCTCTCGCTCGTT 59.794 52.381 0.00 0.00 0.00 3.85
475 1854 0.821517 TCTCTCTCTCTCTCGCTCGT 59.178 55.000 0.00 0.00 0.00 4.18
476 1855 1.067060 TCTCTCTCTCTCTCTCGCTCG 59.933 57.143 0.00 0.00 0.00 5.03
477 1856 2.362397 TCTCTCTCTCTCTCTCTCGCTC 59.638 54.545 0.00 0.00 0.00 5.03
478 1857 2.101582 GTCTCTCTCTCTCTCTCTCGCT 59.898 54.545 0.00 0.00 0.00 4.93
479 1858 2.474816 GTCTCTCTCTCTCTCTCTCGC 58.525 57.143 0.00 0.00 0.00 5.03
480 1859 2.695666 AGGTCTCTCTCTCTCTCTCTCG 59.304 54.545 0.00 0.00 0.00 4.04
486 1865 0.748005 GCGCAGGTCTCTCTCTCTCT 60.748 60.000 0.30 0.00 0.00 3.10
512 1891 2.023673 GGACGGCCATGAATGAATGAA 58.976 47.619 0.00 0.00 0.00 2.57
513 1892 1.064832 TGGACGGCCATGAATGAATGA 60.065 47.619 5.41 0.00 39.92 2.57
514 1893 1.391577 TGGACGGCCATGAATGAATG 58.608 50.000 5.41 0.00 39.92 2.67
515 1894 3.901087 TGGACGGCCATGAATGAAT 57.099 47.368 5.41 0.00 39.92 2.57
557 1936 1.447217 CACTGTGGGCAGACAGACA 59.553 57.895 19.40 0.00 45.39 3.41
558 1937 1.302033 CCACTGTGGGCAGACAGAC 60.302 63.158 19.23 0.00 45.39 3.51
559 1938 3.150949 CCACTGTGGGCAGACAGA 58.849 61.111 19.23 0.00 45.39 3.41
632 2018 1.469079 GGTTTTGTTTGACGTGCAGCT 60.469 47.619 0.00 0.00 0.00 4.24
731 2136 1.003718 GTTTACTGCTGCCCTCGGT 60.004 57.895 0.00 0.00 0.00 4.69
766 2204 5.432885 TGCCTCCTTAAAAGAAAGAAACG 57.567 39.130 0.00 0.00 0.00 3.60
774 2212 2.290323 GGTCTGCTGCCTCCTTAAAAGA 60.290 50.000 0.00 0.00 0.00 2.52
832 2275 2.235402 GGATACTTGTCTTCCGTGGGAA 59.765 50.000 0.00 0.00 39.66 3.97
867 2310 2.670148 CGTGGGGAAGAAGGGGAGG 61.670 68.421 0.00 0.00 0.00 4.30
868 2311 2.990479 CGTGGGGAAGAAGGGGAG 59.010 66.667 0.00 0.00 0.00 4.30
903 2357 0.037326 TCCCTTTGCTACTGCTCACG 60.037 55.000 0.00 0.00 40.48 4.35
904 2358 1.731720 CTCCCTTTGCTACTGCTCAC 58.268 55.000 0.00 0.00 40.48 3.51
905 2359 0.036010 GCTCCCTTTGCTACTGCTCA 60.036 55.000 0.00 0.00 40.48 4.26
906 2360 1.086634 CGCTCCCTTTGCTACTGCTC 61.087 60.000 0.00 0.00 40.48 4.26
907 2361 1.078848 CGCTCCCTTTGCTACTGCT 60.079 57.895 0.00 0.00 40.48 4.24
908 2362 1.079127 TCGCTCCCTTTGCTACTGC 60.079 57.895 0.00 0.00 40.20 4.40
909 2363 1.086634 GCTCGCTCCCTTTGCTACTG 61.087 60.000 0.00 0.00 0.00 2.74
910 2364 1.219393 GCTCGCTCCCTTTGCTACT 59.781 57.895 0.00 0.00 0.00 2.57
911 2365 1.086634 CAGCTCGCTCCCTTTGCTAC 61.087 60.000 0.00 0.00 32.29 3.58
912 2366 1.219124 CAGCTCGCTCCCTTTGCTA 59.781 57.895 0.00 0.00 32.29 3.49
913 2367 2.046507 CAGCTCGCTCCCTTTGCT 60.047 61.111 0.00 0.00 0.00 3.91
914 2368 3.808656 GCAGCTCGCTCCCTTTGC 61.809 66.667 1.48 0.00 37.77 3.68
928 2382 2.871099 CAAGAGCAGCAGCAGCAG 59.129 61.111 12.92 0.00 45.49 4.24
929 2383 3.362797 GCAAGAGCAGCAGCAGCA 61.363 61.111 12.92 0.00 45.49 4.41
933 2402 1.913451 CTCACAGCAAGAGCAGCAGC 61.913 60.000 0.00 0.00 45.49 5.25
935 2404 1.302271 CCTCACAGCAAGAGCAGCA 60.302 57.895 0.00 0.00 45.49 4.41
951 2428 1.052124 TCACTTCCACGGTTCCACCT 61.052 55.000 0.00 0.00 35.66 4.00
960 2437 1.337260 CCTCCTCACTTCACTTCCACG 60.337 57.143 0.00 0.00 0.00 4.94
961 2438 1.609320 GCCTCCTCACTTCACTTCCAC 60.609 57.143 0.00 0.00 0.00 4.02
962 2439 0.687354 GCCTCCTCACTTCACTTCCA 59.313 55.000 0.00 0.00 0.00 3.53
963 2440 0.390472 CGCCTCCTCACTTCACTTCC 60.390 60.000 0.00 0.00 0.00 3.46
964 2441 1.016653 GCGCCTCCTCACTTCACTTC 61.017 60.000 0.00 0.00 0.00 3.01
986 2463 1.358402 CTCATCTCTGACGCTCCCG 59.642 63.158 0.00 0.00 41.14 5.14
987 2464 1.067250 GCTCATCTCTGACGCTCCC 59.933 63.158 0.00 0.00 0.00 4.30
988 2465 1.299014 CGCTCATCTCTGACGCTCC 60.299 63.158 0.00 0.00 0.00 4.70
989 2466 0.865218 CACGCTCATCTCTGACGCTC 60.865 60.000 0.00 0.00 32.64 5.03
993 2470 0.528017 TGGTCACGCTCATCTCTGAC 59.472 55.000 0.00 0.00 33.61 3.51
994 2471 1.203287 CTTGGTCACGCTCATCTCTGA 59.797 52.381 0.00 0.00 0.00 3.27
995 2472 1.067283 ACTTGGTCACGCTCATCTCTG 60.067 52.381 0.00 0.00 0.00 3.35
1017 2497 0.389296 CCACCGTGACGCACTTGATA 60.389 55.000 0.00 0.00 31.34 2.15
1121 2601 2.245287 GGTAGGAGGAGAAGAGGAAGGA 59.755 54.545 0.00 0.00 0.00 3.36
1146 2626 2.104669 AGATGGGAACTACCTAGCCC 57.895 55.000 0.00 0.00 36.15 5.19
1148 2628 3.310193 AGGAAGATGGGAACTACCTAGC 58.690 50.000 0.00 0.00 38.98 3.42
1149 2629 3.898741 GGAGGAAGATGGGAACTACCTAG 59.101 52.174 0.00 0.00 38.98 3.02
1150 2630 3.536434 AGGAGGAAGATGGGAACTACCTA 59.464 47.826 0.00 0.00 38.98 3.08
1151 2631 2.319438 AGGAGGAAGATGGGAACTACCT 59.681 50.000 0.00 0.00 38.98 3.08
1152 2632 2.701423 GAGGAGGAAGATGGGAACTACC 59.299 54.545 0.00 0.00 38.08 3.18
1155 2635 2.758130 GAGAGGAGGAAGATGGGAACT 58.242 52.381 0.00 0.00 0.00 3.01
1162 2642 1.133606 GGAGGTCGAGAGGAGGAAGAT 60.134 57.143 0.00 0.00 0.00 2.40
1181 2661 4.496670 CCGAGTGAGCGGTAAAGG 57.503 61.111 0.00 0.00 46.07 3.11
1347 2828 2.158696 GGAAATGAGGAGGGATGGAGTG 60.159 54.545 0.00 0.00 0.00 3.51
1360 2841 3.340814 AGTAGCTGTGGTGGAAATGAG 57.659 47.619 0.00 0.00 0.00 2.90
1374 2855 4.404640 TGTGAACACCAGTAGTAGTAGCT 58.595 43.478 2.46 0.00 0.00 3.32
1381 2862 1.808891 GCGGTTGTGAACACCAGTAGT 60.809 52.381 2.46 0.00 0.00 2.73
1421 2924 1.280746 CGGAGCAAACACAGCACAG 59.719 57.895 0.00 0.00 0.00 3.66
1437 2940 1.376037 GTCCTCTTGCCCTGAACGG 60.376 63.158 0.00 0.00 0.00 4.44
1611 3123 4.142447 CCTCAAGCACAATCAAATCTGGAG 60.142 45.833 0.00 0.00 0.00 3.86
1634 3146 6.329496 TCAAAACATTCAGTTCAGGTGAAAC 58.671 36.000 0.00 0.00 40.26 2.78
1647 3159 9.558648 CGAATTATCATCAGTTCAAAACATTCA 57.441 29.630 0.00 0.00 0.00 2.57
1648 3160 9.013490 CCGAATTATCATCAGTTCAAAACATTC 57.987 33.333 0.00 0.00 0.00 2.67
1649 3161 8.522830 ACCGAATTATCATCAGTTCAAAACATT 58.477 29.630 0.00 0.00 0.00 2.71
1650 3162 8.055279 ACCGAATTATCATCAGTTCAAAACAT 57.945 30.769 0.00 0.00 0.00 2.71
1655 3167 6.758416 CAGAGACCGAATTATCATCAGTTCAA 59.242 38.462 0.00 0.00 0.00 2.69
1657 3169 5.694006 CCAGAGACCGAATTATCATCAGTTC 59.306 44.000 0.00 0.00 0.00 3.01
1719 3239 3.982576 ACAAGAACAATGGGAACGTTC 57.017 42.857 20.14 20.14 37.50 3.95
1737 3257 0.400213 CACCTAGCTTGGTCCCAACA 59.600 55.000 17.51 0.00 38.45 3.33
1759 3279 3.591835 CGCGTTGGGTGCAGGTTT 61.592 61.111 0.00 0.00 0.00 3.27
1780 3300 2.223144 TGCGGAAAGTTCATCGAAACAG 59.777 45.455 3.01 0.00 0.00 3.16
1805 3329 1.375908 GATGCAGAGCAACCCGTGA 60.376 57.895 0.00 0.00 43.62 4.35
1841 3365 1.265635 TCTGAACAATGGAAAACGCCG 59.734 47.619 0.00 0.00 0.00 6.46
1842 3366 3.191371 AGATCTGAACAATGGAAAACGCC 59.809 43.478 0.00 0.00 0.00 5.68
1843 3367 4.161333 CAGATCTGAACAATGGAAAACGC 58.839 43.478 18.34 0.00 0.00 4.84
1846 3370 3.820467 ACGCAGATCTGAACAATGGAAAA 59.180 39.130 27.04 0.00 0.00 2.29
1907 3433 0.956633 CCTGTGCAGTTGTGATTGCT 59.043 50.000 0.00 0.00 39.10 3.91
2259 3795 2.342279 CTCGGCGGTTGAAGGACA 59.658 61.111 7.21 0.00 0.00 4.02
2345 3881 1.630878 GTGAATGAGAAGAGGTGGGGT 59.369 52.381 0.00 0.00 0.00 4.95
2357 3894 2.499289 ACCAGTGGAGCTAGTGAATGAG 59.501 50.000 18.40 0.00 0.00 2.90
2367 3904 4.345257 CCATTATACAGTACCAGTGGAGCT 59.655 45.833 18.40 10.30 0.00 4.09
2374 3911 5.050490 GCTCACACCATTATACAGTACCAG 58.950 45.833 0.00 0.00 0.00 4.00
2402 3944 4.204799 TCATGGAGCAAATCTGGAGAATG 58.795 43.478 0.00 0.00 0.00 2.67
2428 3970 0.394565 AGGTGACCAGTGAGCAAGAC 59.605 55.000 3.63 0.00 0.00 3.01
2447 3989 7.901029 TGAATGTGCCAATTTTGAGGTAATAA 58.099 30.769 0.00 0.00 0.00 1.40
2448 3990 7.473735 TGAATGTGCCAATTTTGAGGTAATA 57.526 32.000 0.00 0.00 0.00 0.98
2449 3991 6.357579 TGAATGTGCCAATTTTGAGGTAAT 57.642 33.333 0.00 0.00 0.00 1.89
2488 4030 5.027293 TCTAAGCAGCAGCATTTCATAGA 57.973 39.130 3.17 0.00 45.49 1.98
2526 4083 1.262950 TGTTTGCATCGGTTCGAGTTG 59.737 47.619 0.00 0.00 39.91 3.16
2531 4088 0.453282 CAGCTGTTTGCATCGGTTCG 60.453 55.000 5.25 0.00 45.94 3.95
2532 4089 0.874390 TCAGCTGTTTGCATCGGTTC 59.126 50.000 14.67 0.00 45.94 3.62
2600 4161 1.564818 ACGACAGGATCAGGACTCCTA 59.435 52.381 0.00 0.00 41.29 2.94
2619 4180 3.057245 GCCTGTGGATTCAAAAGGAGAAC 60.057 47.826 0.88 0.00 33.20 3.01
2625 4186 3.318839 TCAAGTGCCTGTGGATTCAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
2676 4237 3.302347 GAGTCAGTCCGGGGTGCTG 62.302 68.421 0.00 5.77 0.00 4.41
2781 4342 4.379394 CCAAAACACGCAACATATAGTGCT 60.379 41.667 7.87 0.00 38.08 4.40
2782 4343 3.851403 CCAAAACACGCAACATATAGTGC 59.149 43.478 0.63 0.63 38.08 4.40
2783 4344 5.041951 ACCAAAACACGCAACATATAGTG 57.958 39.130 0.00 0.00 40.17 2.74
2925 4499 4.116961 CGAATCCCTACGAAATGCTAACA 58.883 43.478 0.00 0.00 0.00 2.41
2934 4508 1.097232 TCGAAGCGAATCCCTACGAA 58.903 50.000 0.00 0.00 31.06 3.85
2959 4533 0.896923 TCAATCTGCCACCAATTGCC 59.103 50.000 0.00 0.00 31.84 4.52
3004 4579 2.355716 CCTCCCTTCTTGCCGTTTGATA 60.356 50.000 0.00 0.00 0.00 2.15
3012 4587 1.584717 ATTCCCCCTCCCTTCTTGCC 61.585 60.000 0.00 0.00 0.00 4.52
3079 4655 2.030007 CACCAATGGCTACAAACACAGG 60.030 50.000 0.00 0.00 0.00 4.00
3113 4689 1.877680 GCCCCCTTGTTCAACATTTGC 60.878 52.381 0.00 0.00 0.00 3.68
3115 4691 1.799933 TGCCCCCTTGTTCAACATTT 58.200 45.000 0.00 0.00 0.00 2.32
3125 4891 1.180029 CTTTGACAGATGCCCCCTTG 58.820 55.000 0.00 0.00 0.00 3.61
3137 4903 2.355444 TGTGACGACGACTACTTTGACA 59.645 45.455 0.00 0.00 0.00 3.58
3138 4904 2.971915 CTGTGACGACGACTACTTTGAC 59.028 50.000 0.00 0.00 0.00 3.18
3139 4905 2.615447 ACTGTGACGACGACTACTTTGA 59.385 45.455 0.00 0.00 0.00 2.69
3140 4906 2.971915 GACTGTGACGACGACTACTTTG 59.028 50.000 0.00 0.00 0.00 2.77
3142 4908 2.216046 TGACTGTGACGACGACTACTT 58.784 47.619 0.00 0.00 0.00 2.24
3162 4929 1.422781 TCCCGGTCGACCATATACTCT 59.577 52.381 32.80 0.00 35.14 3.24
3163 4930 1.538950 GTCCCGGTCGACCATATACTC 59.461 57.143 32.80 12.77 35.14 2.59
3206 4978 3.059800 GTCGACCTGTTTTTCTGCTACAC 60.060 47.826 3.51 0.00 0.00 2.90
3221 4993 2.267961 GGCCAATTCCGTCGACCT 59.732 61.111 10.58 0.00 0.00 3.85
3230 5002 0.872388 AACAAGTCGACGGCCAATTC 59.128 50.000 10.46 0.00 0.00 2.17
3234 5006 0.745128 AAACAACAAGTCGACGGCCA 60.745 50.000 10.46 0.00 0.00 5.36
3241 5013 2.143925 GGAGGGAGAAACAACAAGTCG 58.856 52.381 0.00 0.00 0.00 4.18
3277 5049 5.886960 AGGTATTTGATGAGCACTTCAAC 57.113 39.130 11.14 2.78 39.77 3.18
3278 5050 5.335897 GCAAGGTATTTGATGAGCACTTCAA 60.336 40.000 8.12 8.12 39.21 2.69
3285 5057 2.099756 GGTGGCAAGGTATTTGATGAGC 59.900 50.000 0.00 0.00 39.21 4.26
3289 5061 2.311542 TCCTGGTGGCAAGGTATTTGAT 59.688 45.455 5.18 0.00 39.21 2.57
3302 5074 1.324740 CCATTGTGCCATCCTGGTGG 61.325 60.000 9.99 9.99 40.46 4.61
3340 5124 5.007034 TCGCTTCCTCCAATTTTCATGTTA 58.993 37.500 0.00 0.00 0.00 2.41
3411 5195 0.250295 CTGCCTTGTCGGTTTCAGGA 60.250 55.000 0.00 0.00 34.25 3.86
3418 5202 3.575351 GAGACGCTGCCTTGTCGGT 62.575 63.158 0.00 0.00 40.05 4.69
3424 5208 0.179018 AACCTTTGAGACGCTGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
3429 5213 1.949465 ACGAAAACCTTTGAGACGCT 58.051 45.000 0.00 0.00 0.00 5.07
3431 5215 2.798283 TGCTACGAAAACCTTTGAGACG 59.202 45.455 0.00 0.00 0.00 4.18
3433 5217 2.806244 GCTGCTACGAAAACCTTTGAGA 59.194 45.455 0.00 0.00 0.00 3.27
3437 5221 2.228822 CCATGCTGCTACGAAAACCTTT 59.771 45.455 0.00 0.00 0.00 3.11
3438 5222 1.812571 CCATGCTGCTACGAAAACCTT 59.187 47.619 0.00 0.00 0.00 3.50
3439 5223 1.003118 TCCATGCTGCTACGAAAACCT 59.997 47.619 0.00 0.00 0.00 3.50
3440 5224 1.448985 TCCATGCTGCTACGAAAACC 58.551 50.000 0.00 0.00 0.00 3.27
3441 5225 2.677836 TGATCCATGCTGCTACGAAAAC 59.322 45.455 0.00 0.00 0.00 2.43
3442 5226 2.984562 TGATCCATGCTGCTACGAAAA 58.015 42.857 0.00 0.00 0.00 2.29
3443 5227 2.677836 GTTGATCCATGCTGCTACGAAA 59.322 45.455 0.00 0.00 0.00 3.46
3444 5228 2.279741 GTTGATCCATGCTGCTACGAA 58.720 47.619 0.00 0.00 0.00 3.85
3466 5250 5.220854 GGAATGCACATAACAGTATGGACAC 60.221 44.000 0.00 0.00 43.62 3.67
3491 5275 4.443394 CAGAATTTGCTTGAGCTCAACAAC 59.557 41.667 28.52 21.59 42.66 3.32
3505 5289 2.555757 ACTCTTGGAGTGCAGAATTTGC 59.444 45.455 0.00 5.87 41.76 3.68
3506 5290 4.518211 AGAACTCTTGGAGTGCAGAATTTG 59.482 41.667 8.20 0.00 42.59 2.32
3507 5291 4.518211 CAGAACTCTTGGAGTGCAGAATTT 59.482 41.667 8.20 0.00 42.59 1.82
3510 5294 2.435805 ACAGAACTCTTGGAGTGCAGAA 59.564 45.455 8.20 0.00 42.59 3.02
3511 5295 2.042464 ACAGAACTCTTGGAGTGCAGA 58.958 47.619 8.20 0.00 42.59 4.26
3513 5297 2.245159 CACAGAACTCTTGGAGTGCA 57.755 50.000 8.20 0.00 42.59 4.57
3514 5298 0.871057 GCACAGAACTCTTGGAGTGC 59.129 55.000 0.00 0.00 42.59 4.40
3515 5299 2.141517 CTGCACAGAACTCTTGGAGTG 58.858 52.381 0.74 0.00 42.59 3.51
3516 5300 1.765314 ACTGCACAGAACTCTTGGAGT 59.235 47.619 4.31 8.92 45.64 3.85
3517 5301 2.141517 CACTGCACAGAACTCTTGGAG 58.858 52.381 4.31 8.04 35.03 3.86
3518 5302 1.811558 GCACTGCACAGAACTCTTGGA 60.812 52.381 4.31 0.00 0.00 3.53
3519 5303 0.590195 GCACTGCACAGAACTCTTGG 59.410 55.000 4.31 0.00 0.00 3.61
3520 5304 1.302366 TGCACTGCACAGAACTCTTG 58.698 50.000 4.31 0.00 31.71 3.02
3521 5305 3.786656 TGCACTGCACAGAACTCTT 57.213 47.368 4.31 0.00 31.71 2.85
3531 5315 7.003402 TCAAGTATATATATGGTGCACTGCA 57.997 36.000 17.98 7.60 35.60 4.41
3532 5316 7.765819 TGATCAAGTATATATATGGTGCACTGC 59.234 37.037 17.98 0.83 0.00 4.40
3533 5317 9.657419 TTGATCAAGTATATATATGGTGCACTG 57.343 33.333 17.98 2.02 0.00 3.66
3534 5318 9.658799 GTTGATCAAGTATATATATGGTGCACT 57.341 33.333 17.98 0.00 0.00 4.40
3535 5319 8.595533 CGTTGATCAAGTATATATATGGTGCAC 58.404 37.037 8.80 8.80 0.00 4.57
3536 5320 8.527810 TCGTTGATCAAGTATATATATGGTGCA 58.472 33.333 8.80 0.00 0.00 4.57
3537 5321 8.926715 TCGTTGATCAAGTATATATATGGTGC 57.073 34.615 8.80 0.00 0.00 5.01
3538 5322 9.521503 CCTCGTTGATCAAGTATATATATGGTG 57.478 37.037 8.80 1.44 0.00 4.17
3539 5323 9.475620 TCCTCGTTGATCAAGTATATATATGGT 57.524 33.333 8.80 0.00 0.00 3.55
3544 5328 9.249053 AGACATCCTCGTTGATCAAGTATATAT 57.751 33.333 8.80 0.00 0.00 0.86
3545 5329 8.637196 AGACATCCTCGTTGATCAAGTATATA 57.363 34.615 8.80 0.00 0.00 0.86
3571 5355 2.586792 GAGGGGCGTCATTGCTCT 59.413 61.111 0.00 0.00 35.04 4.09
3572 5356 2.514824 GGAGGGGCGTCATTGCTC 60.515 66.667 0.00 0.00 34.52 4.26
3598 5540 4.044426 GCAACTTGCGAACAGAAATCTTT 58.956 39.130 0.00 0.00 31.71 2.52
3635 5577 2.860735 GTGACCTCAATCTACGTCATGC 59.139 50.000 0.00 0.00 37.55 4.06


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

AutoCloner maintained by Alex Coulton.