Multiple sequence alignment - TraesCS5D01G196400

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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 TraesCS5D01G196400 chr5D 100.000 3185 0 0 1 3185 299838744 299835560 0.000000e+00 5882
1 TraesCS5D01G196400 chr5D 100.000 294 0 0 3526 3819 299835219 299834926 9.330000e-151 544
2 TraesCS5D01G196400 chr5B 86.229 1721 92 59 262 1910 341072128 341070481 0.000000e+00 1731
3 TraesCS5D01G196400 chr5B 87.488 1023 84 20 2165 3185 341070183 341069203 0.000000e+00 1140
4 TraesCS5D01G196400 chr5B 93.130 262 15 1 5 263 341092564 341092303 7.740000e-102 381
5 TraesCS5D01G196400 chr5B 88.991 218 17 6 3607 3819 341068710 341068495 2.930000e-66 263
6 TraesCS5D01G196400 chr5B 77.586 464 83 19 220 668 544944902 544945359 1.050000e-65 261
7 TraesCS5D01G196400 chr5B 89.189 185 10 6 1959 2135 341070350 341070168 4.970000e-54 222
8 TraesCS5D01G196400 chr5B 97.674 43 1 0 1 43 341092596 341092554 1.470000e-09 75
9 TraesCS5D01G196400 chr5A 93.288 1028 62 6 2159 3185 397253284 397252263 0.000000e+00 1509
10 TraesCS5D01G196400 chr5A 86.389 1271 83 31 685 1908 397254885 397253658 0.000000e+00 1306
11 TraesCS5D01G196400 chr5A 85.294 408 55 3 1 403 397334668 397334261 2.120000e-112 416
12 TraesCS5D01G196400 chr5A 90.667 225 11 3 1920 2135 397253486 397253263 1.340000e-74 291
13 TraesCS5D01G196400 chr5A 89.744 117 5 4 3704 3819 397251799 397251689 3.980000e-30 143
14 TraesCS5D01G196400 chr3D 79.188 591 112 8 60 641 90832274 90831686 2.140000e-107 399
15 TraesCS5D01G196400 chr2B 79.287 589 104 17 65 641 800988936 800988354 2.760000e-106 396
16 TraesCS5D01G196400 chr2B 78.401 588 105 17 73 641 603424549 603425133 2.800000e-96 363
17 TraesCS5D01G196400 chr2B 76.329 583 122 12 73 642 51662697 51662118 8.020000e-77 298
18 TraesCS5D01G196400 chr1D 78.469 627 111 19 36 642 466406491 466407113 4.630000e-104 388
19 TraesCS5D01G196400 chr1D 77.449 541 109 12 70 603 193450404 193449870 1.030000e-80 311
20 TraesCS5D01G196400 chr6D 86.686 353 39 6 2159 2511 438545049 438544705 5.980000e-103 385
21 TraesCS5D01G196400 chr6D 86.957 138 8 6 2006 2135 438545163 438545028 3.070000e-31 147
22 TraesCS5D01G196400 chr4D 82.133 347 54 7 250 591 414044081 414044424 1.340000e-74 291
23 TraesCS5D01G196400 chr3A 76.626 569 95 20 37 591 206622001 206622545 2.910000e-71 279
24 TraesCS5D01G196400 chr1B 75.203 617 123 20 35 628 638933650 638933041 8.130000e-67 265
25 TraesCS5D01G196400 chr6B 84.810 158 16 5 2351 2508 471227662 471227811 6.610000e-33 152
26 TraesCS5D01G196400 chr6B 84.211 133 12 5 2011 2135 471227277 471227408 1.860000e-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 TraesCS5D01G196400 chr5D 299834926 299838744 3818 True 3213.00 5882 100.00000 1 3819 2 chr5D.!!$R1 3818
1 TraesCS5D01G196400 chr5B 341068495 341072128 3633 True 839.00 1731 87.97425 262 3819 4 chr5B.!!$R1 3557
2 TraesCS5D01G196400 chr5A 397251689 397254885 3196 True 812.25 1509 90.02200 685 3819 4 chr5A.!!$R2 3134
3 TraesCS5D01G196400 chr3D 90831686 90832274 588 True 399.00 399 79.18800 60 641 1 chr3D.!!$R1 581
4 TraesCS5D01G196400 chr2B 800988354 800988936 582 True 396.00 396 79.28700 65 641 1 chr2B.!!$R2 576
5 TraesCS5D01G196400 chr2B 603424549 603425133 584 False 363.00 363 78.40100 73 641 1 chr2B.!!$F1 568
6 TraesCS5D01G196400 chr2B 51662118 51662697 579 True 298.00 298 76.32900 73 642 1 chr2B.!!$R1 569
7 TraesCS5D01G196400 chr1D 466406491 466407113 622 False 388.00 388 78.46900 36 642 1 chr1D.!!$F1 606
8 TraesCS5D01G196400 chr1D 193449870 193450404 534 True 311.00 311 77.44900 70 603 1 chr1D.!!$R1 533
9 TraesCS5D01G196400 chr3A 206622001 206622545 544 False 279.00 279 76.62600 37 591 1 chr3A.!!$F1 554
10 TraesCS5D01G196400 chr1B 638933041 638933650 609 True 265.00 265 75.20300 35 628 1 chr1B.!!$R1 593

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
20 21 0.099436 CTGCGCTAGGGTTTTCATGC 59.901 55.0 9.73 0.0 0.0 4.06 F
53 54 0.107459 CTAGGGTTTCTGCTGCCTCC 60.107 60.0 0.00 0.0 0.0 4.30 F
1651 1779 0.179062 GGCAGTCCAGAGCACCTATG 60.179 60.0 0.00 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1292 1374 0.035458 CAATGGCGGGGATCTCTACC 59.965 60.0 0.00 0.0 0.0 3.18 R
1842 1970 0.177604 GACTGAGCTCCCCTGTGATG 59.822 60.0 12.15 0.0 0.0 3.07 R
3089 3405 0.384353 GAAGAAGCGTGCGTGAAACC 60.384 55.0 0.00 0.0 0.0 3.27 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
18 19 3.957288 ACTGCGCTAGGGTTTTCAT 57.043 47.368 9.73 0.00 0.00 2.57
19 20 1.453155 ACTGCGCTAGGGTTTTCATG 58.547 50.000 9.73 0.00 0.00 3.07
20 21 0.099436 CTGCGCTAGGGTTTTCATGC 59.901 55.000 9.73 0.00 0.00 4.06
21 22 0.607762 TGCGCTAGGGTTTTCATGCA 60.608 50.000 9.73 0.00 0.00 3.96
22 23 0.525761 GCGCTAGGGTTTTCATGCAA 59.474 50.000 8.77 0.00 0.00 4.08
23 24 1.468054 GCGCTAGGGTTTTCATGCAAG 60.468 52.381 8.77 0.00 0.00 4.01
24 25 1.812571 CGCTAGGGTTTTCATGCAAGT 59.187 47.619 0.00 0.00 0.00 3.16
25 26 2.414559 CGCTAGGGTTTTCATGCAAGTG 60.415 50.000 0.00 0.00 0.00 3.16
26 27 2.672195 GCTAGGGTTTTCATGCAAGTGC 60.672 50.000 0.00 0.00 42.50 4.40
45 46 1.148310 CACACACGCTAGGGTTTCTG 58.852 55.000 10.17 8.36 0.00 3.02
53 54 0.107459 CTAGGGTTTCTGCTGCCTCC 60.107 60.000 0.00 0.00 0.00 4.30
55 56 2.436109 GGTTTCTGCTGCCTCCCA 59.564 61.111 0.00 0.00 0.00 4.37
56 57 1.000396 GGTTTCTGCTGCCTCCCAT 60.000 57.895 0.00 0.00 0.00 4.00
59 60 1.841302 TTTCTGCTGCCTCCCATCGT 61.841 55.000 0.00 0.00 0.00 3.73
60 61 2.513204 CTGCTGCCTCCCATCGTG 60.513 66.667 0.00 0.00 0.00 4.35
61 62 4.783621 TGCTGCCTCCCATCGTGC 62.784 66.667 0.00 0.00 0.00 5.34
62 63 4.783621 GCTGCCTCCCATCGTGCA 62.784 66.667 0.00 0.00 0.00 4.57
63 64 2.513204 CTGCCTCCCATCGTGCAG 60.513 66.667 0.00 0.00 44.43 4.41
83 88 1.321074 CCGGCCTACCTCGTCTTCTT 61.321 60.000 0.00 0.00 0.00 2.52
102 107 1.128809 TTGGCCTTAGGACCGTGGAA 61.129 55.000 0.00 0.00 0.00 3.53
117 122 2.668632 GAAGTGCGGTGGATCCCA 59.331 61.111 9.90 0.00 0.00 4.37
150 159 2.511659 GGGAGGGCTTCGTTTTTAGTT 58.488 47.619 0.00 0.00 0.00 2.24
166 175 9.754351 CGTTTTTAGTTTATTTACGAGTTTTGC 57.246 29.630 0.00 0.00 0.00 3.68
188 197 1.269778 CGAGTTTGTGTCCTGCTCAGA 60.270 52.381 0.00 0.00 0.00 3.27
195 204 1.743252 GTCCTGCTCAGAAAGGCGG 60.743 63.158 0.00 0.00 33.25 6.13
198 207 1.743252 CTGCTCAGAAAGGCGGGAC 60.743 63.158 0.00 0.00 0.00 4.46
199 208 2.347490 GCTCAGAAAGGCGGGACA 59.653 61.111 0.00 0.00 0.00 4.02
200 209 1.302511 GCTCAGAAAGGCGGGACAA 60.303 57.895 0.00 0.00 0.00 3.18
201 210 1.578206 GCTCAGAAAGGCGGGACAAC 61.578 60.000 0.00 0.00 0.00 3.32
203 212 1.301401 CAGAAAGGCGGGACAACGA 60.301 57.895 0.00 0.00 35.47 3.85
206 232 1.838568 GAAAGGCGGGACAACGACAC 61.839 60.000 0.00 0.00 46.48 3.67
214 240 0.586802 GGACAACGACACCTTCTTGC 59.413 55.000 0.00 0.00 0.00 4.01
227 253 5.188434 CACCTTCTTGCAGATGGAATAAGA 58.812 41.667 18.52 0.97 40.83 2.10
252 279 2.432300 CCGCCTACCTCCATTCCGT 61.432 63.158 0.00 0.00 0.00 4.69
308 335 3.314553 GTTTGTCTTCGACGGATCTCAA 58.685 45.455 0.00 0.00 34.95 3.02
320 347 2.432146 CGGATCTCAAGGGATTCAGTCA 59.568 50.000 0.00 0.00 0.00 3.41
327 354 2.554032 CAAGGGATTCAGTCAGCGTTTT 59.446 45.455 0.00 0.00 0.00 2.43
328 355 2.427506 AGGGATTCAGTCAGCGTTTTC 58.572 47.619 0.00 0.00 0.00 2.29
356 384 3.607871 TCCGCTTGGATCCAGTCTA 57.392 52.632 15.53 0.00 36.65 2.59
433 471 2.543031 CGGTTGCTATTCTAGTGCGCTA 60.543 50.000 9.73 6.84 0.00 4.26
642 688 7.961283 AGGCGACGAATAAATTAGAAGTTTTTC 59.039 33.333 0.00 0.00 0.00 2.29
899 964 0.914902 TGGGACGGGAGAGAGAGAGA 60.915 60.000 0.00 0.00 0.00 3.10
902 967 1.202651 GGACGGGAGAGAGAGAGAGAG 60.203 61.905 0.00 0.00 0.00 3.20
903 968 1.760613 GACGGGAGAGAGAGAGAGAGA 59.239 57.143 0.00 0.00 0.00 3.10
904 969 1.762957 ACGGGAGAGAGAGAGAGAGAG 59.237 57.143 0.00 0.00 0.00 3.20
905 970 2.039418 CGGGAGAGAGAGAGAGAGAGA 58.961 57.143 0.00 0.00 0.00 3.10
906 971 2.036475 CGGGAGAGAGAGAGAGAGAGAG 59.964 59.091 0.00 0.00 0.00 3.20
907 972 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
908 973 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
909 974 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
910 975 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
911 976 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
912 977 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
913 978 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
914 979 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
915 980 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
916 981 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
917 982 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
918 983 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
919 984 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
920 985 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
921 986 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
922 987 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
923 988 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
924 989 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
925 990 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
926 991 3.711704 GAGAGAGAGAGAGAGAGAGGGAA 59.288 52.174 0.00 0.00 0.00 3.97
927 992 4.310740 AGAGAGAGAGAGAGAGAGGGAAT 58.689 47.826 0.00 0.00 0.00 3.01
928 993 4.349342 AGAGAGAGAGAGAGAGAGGGAATC 59.651 50.000 0.00 0.00 0.00 2.52
929 994 4.047166 AGAGAGAGAGAGAGAGGGAATCA 58.953 47.826 0.00 0.00 0.00 2.57
930 995 4.103785 AGAGAGAGAGAGAGAGGGAATCAG 59.896 50.000 0.00 0.00 0.00 2.90
931 996 3.788142 AGAGAGAGAGAGAGGGAATCAGT 59.212 47.826 0.00 0.00 0.00 3.41
932 997 4.137543 GAGAGAGAGAGAGGGAATCAGTC 58.862 52.174 0.00 0.00 0.00 3.51
933 998 3.527253 AGAGAGAGAGAGGGAATCAGTCA 59.473 47.826 0.00 0.00 0.00 3.41
934 999 3.885297 GAGAGAGAGAGGGAATCAGTCAG 59.115 52.174 0.00 0.00 0.00 3.51
935 1000 2.958355 GAGAGAGAGGGAATCAGTCAGG 59.042 54.545 0.00 0.00 0.00 3.86
936 1001 2.038659 GAGAGAGGGAATCAGTCAGGG 58.961 57.143 0.00 0.00 0.00 4.45
937 1002 1.648568 AGAGAGGGAATCAGTCAGGGA 59.351 52.381 0.00 0.00 0.00 4.20
1255 1337 2.141517 CTCCTCGCTATCATTGCTTGG 58.858 52.381 0.00 0.00 0.00 3.61
1272 1354 3.887716 GCTTGGCACTTAGATTGGATCAT 59.112 43.478 0.00 0.00 0.00 2.45
1281 1363 1.942657 AGATTGGATCATCGGTTTGCG 59.057 47.619 0.00 0.00 0.00 4.85
1315 1397 1.983119 GAGATCCCCGCCATTGACCA 61.983 60.000 0.00 0.00 0.00 4.02
1329 1411 5.570844 GCCATTGACCACCTAGTTTTCTCTA 60.571 44.000 0.00 0.00 0.00 2.43
1336 1418 4.473559 CCACCTAGTTTTCTCTAATGGGGA 59.526 45.833 0.00 0.00 0.00 4.81
1360 1442 3.308688 CCCTGAGGTGATGTTTTCCAGAT 60.309 47.826 0.00 0.00 0.00 2.90
1366 1448 8.033178 TGAGGTGATGTTTTCCAGATATATGA 57.967 34.615 0.00 0.00 0.00 2.15
1407 1489 6.328641 TCTTGTATCTTAGGCCGAGATAAC 57.671 41.667 24.58 19.74 37.73 1.89
1477 1572 5.488919 AGGAAGATATTTTGAGGGACTGTCA 59.511 40.000 10.38 0.00 41.55 3.58
1502 1597 2.839486 ATGTCGCTTCTTTGACTGGA 57.161 45.000 0.00 0.00 36.10 3.86
1508 1603 1.203287 GCTTCTTTGACTGGATTGGCC 59.797 52.381 0.00 0.00 37.10 5.36
1591 1696 6.763135 TCAGGTGTTATGTTGCTTATGATCTC 59.237 38.462 0.00 0.00 0.00 2.75
1619 1747 0.251698 TGCAAATGTGGGATCTGGCA 60.252 50.000 0.00 0.00 0.00 4.92
1633 1761 0.457166 CTGGCAATCGTGTGCAATGG 60.457 55.000 13.60 0.00 46.81 3.16
1650 1778 0.618680 TGGCAGTCCAGAGCACCTAT 60.619 55.000 0.00 0.00 37.47 2.57
1651 1779 0.179062 GGCAGTCCAGAGCACCTATG 60.179 60.000 0.00 0.00 0.00 2.23
1699 1827 5.796935 CGAGGATGCTGTTTCTTGTTAATTG 59.203 40.000 0.00 0.00 0.00 2.32
1767 1895 9.408069 CACGAGTTATTAACCTTGTATATCCTC 57.592 37.037 2.92 0.00 0.00 3.71
1769 1897 9.843334 CGAGTTATTAACCTTGTATATCCTCTC 57.157 37.037 2.92 0.00 0.00 3.20
1814 1942 1.883638 GCAAGACTGCCAGTTCCATCA 60.884 52.381 0.00 0.00 43.26 3.07
1842 1970 5.221880 TGCATGACAAAGCAGTTAATTGAC 58.778 37.500 1.56 0.00 35.51 3.18
1846 1974 6.631971 TGACAAAGCAGTTAATTGACATCA 57.368 33.333 1.56 0.00 0.00 3.07
1915 2043 4.396357 TTTTGGATAAAAGGGGAGCTCA 57.604 40.909 17.19 0.00 32.31 4.26
1916 2044 3.652057 TTGGATAAAAGGGGAGCTCAG 57.348 47.619 17.19 0.00 0.00 3.35
1918 2046 2.505819 TGGATAAAAGGGGAGCTCAGAC 59.494 50.000 17.19 4.86 0.00 3.51
1927 2215 3.401002 AGGGGAGCTCAGACTGATAGTAT 59.599 47.826 17.19 0.00 0.00 2.12
1982 2271 3.897141 TTGGTCATAACTGGTGCGATA 57.103 42.857 0.00 0.00 0.00 2.92
1997 2286 4.574828 GGTGCGATACTGGTGATAATTTGT 59.425 41.667 0.00 0.00 0.00 2.83
2009 2298 4.864247 GTGATAATTTGTGACATGGTTGGC 59.136 41.667 0.00 0.00 0.00 4.52
2135 2432 2.294233 TGCAGAGTTGGAAGTCAATTGC 59.706 45.455 0.00 0.00 38.91 3.56
2136 2433 2.352127 GCAGAGTTGGAAGTCAATTGCC 60.352 50.000 0.00 0.00 37.73 4.52
2137 2434 3.152341 CAGAGTTGGAAGTCAATTGCCT 58.848 45.455 0.00 0.00 37.73 4.75
2138 2435 4.326826 CAGAGTTGGAAGTCAATTGCCTA 58.673 43.478 0.00 0.00 37.73 3.93
2141 2438 2.492088 GTTGGAAGTCAATTGCCTACCC 59.508 50.000 0.00 0.80 37.73 3.69
2142 2439 1.005450 TGGAAGTCAATTGCCTACCCC 59.995 52.381 0.00 0.00 0.00 4.95
2143 2440 1.005450 GGAAGTCAATTGCCTACCCCA 59.995 52.381 0.00 0.00 0.00 4.96
2146 2443 1.710809 AGTCAATTGCCTACCCCAACT 59.289 47.619 0.00 0.00 0.00 3.16
2147 2444 2.110011 AGTCAATTGCCTACCCCAACTT 59.890 45.455 0.00 0.00 0.00 2.66
2148 2445 2.231235 GTCAATTGCCTACCCCAACTTG 59.769 50.000 0.00 0.00 0.00 3.16
2149 2446 2.158385 TCAATTGCCTACCCCAACTTGT 60.158 45.455 0.00 0.00 0.00 3.16
2150 2447 2.632512 CAATTGCCTACCCCAACTTGTT 59.367 45.455 0.00 0.00 0.00 2.83
2151 2448 2.463047 TTGCCTACCCCAACTTGTTT 57.537 45.000 0.00 0.00 0.00 2.83
2152 2449 1.698506 TGCCTACCCCAACTTGTTTG 58.301 50.000 0.00 0.00 34.63 2.93
2153 2450 1.063567 TGCCTACCCCAACTTGTTTGT 60.064 47.619 0.00 0.00 32.71 2.83
2154 2451 2.036387 GCCTACCCCAACTTGTTTGTT 58.964 47.619 0.00 0.00 32.71 2.83
2155 2452 2.432874 GCCTACCCCAACTTGTTTGTTT 59.567 45.455 0.00 0.00 32.71 2.83
2156 2453 3.739830 GCCTACCCCAACTTGTTTGTTTG 60.740 47.826 0.00 0.00 32.71 2.93
2157 2454 3.449377 CCTACCCCAACTTGTTTGTTTGT 59.551 43.478 0.00 0.00 32.71 2.83
2158 2455 4.081365 CCTACCCCAACTTGTTTGTTTGTT 60.081 41.667 0.00 0.00 32.71 2.83
2159 2456 4.359434 ACCCCAACTTGTTTGTTTGTTT 57.641 36.364 0.00 0.00 32.71 2.83
2160 2457 4.068599 ACCCCAACTTGTTTGTTTGTTTG 58.931 39.130 0.00 0.00 32.71 2.93
2161 2458 4.068599 CCCCAACTTGTTTGTTTGTTTGT 58.931 39.130 0.00 0.00 32.71 2.83
2162 2459 5.221661 ACCCCAACTTGTTTGTTTGTTTGTA 60.222 36.000 0.00 0.00 32.71 2.41
2163 2460 5.350091 CCCCAACTTGTTTGTTTGTTTGTAG 59.650 40.000 0.00 0.00 32.71 2.74
2164 2461 6.159988 CCCAACTTGTTTGTTTGTTTGTAGA 58.840 36.000 0.00 0.00 32.71 2.59
2165 2462 6.310224 CCCAACTTGTTTGTTTGTTTGTAGAG 59.690 38.462 0.00 0.00 32.71 2.43
2166 2463 6.866248 CCAACTTGTTTGTTTGTTTGTAGAGT 59.134 34.615 0.00 0.00 32.71 3.24
2167 2464 7.383843 CCAACTTGTTTGTTTGTTTGTAGAGTT 59.616 33.333 0.00 0.00 32.71 3.01
2168 2465 7.867445 ACTTGTTTGTTTGTTTGTAGAGTTG 57.133 32.000 0.00 0.00 0.00 3.16
2169 2466 6.866248 ACTTGTTTGTTTGTTTGTAGAGTTGG 59.134 34.615 0.00 0.00 0.00 3.77
2170 2467 6.576662 TGTTTGTTTGTTTGTAGAGTTGGA 57.423 33.333 0.00 0.00 0.00 3.53
2171 2468 6.982852 TGTTTGTTTGTTTGTAGAGTTGGAA 58.017 32.000 0.00 0.00 0.00 3.53
2172 2469 7.087639 TGTTTGTTTGTTTGTAGAGTTGGAAG 58.912 34.615 0.00 0.00 0.00 3.46
2173 2470 6.827586 TTGTTTGTTTGTAGAGTTGGAAGT 57.172 33.333 0.00 0.00 0.00 3.01
2174 2471 6.431198 TGTTTGTTTGTAGAGTTGGAAGTC 57.569 37.500 0.00 0.00 0.00 3.01
2175 2472 5.941058 TGTTTGTTTGTAGAGTTGGAAGTCA 59.059 36.000 0.00 0.00 0.00 3.41
2176 2473 6.093495 TGTTTGTTTGTAGAGTTGGAAGTCAG 59.907 38.462 0.00 0.00 0.00 3.51
2227 2524 4.733230 GCAAATAGCAATGCCGTGTATTCA 60.733 41.667 0.00 0.00 44.79 2.57
2263 2560 7.870954 GTGGTTATATCAAATCGTACCAGATCA 59.129 37.037 0.00 0.00 35.08 2.92
2318 2616 8.482598 AGCAATTTGCCATTACTGCAAGGAAT 62.483 38.462 17.51 0.00 45.23 3.01
2329 2627 3.571401 ACTGCAAGGAATGAAACCTTCTG 59.429 43.478 0.00 0.00 44.65 3.02
2337 2635 3.884037 ATGAAACCTTCTGAACACCCT 57.116 42.857 0.00 0.00 0.00 4.34
2530 2828 6.486657 ACATAATCACAAAGCACTGTTGTACT 59.513 34.615 0.00 0.00 37.09 2.73
2531 2829 7.659799 ACATAATCACAAAGCACTGTTGTACTA 59.340 33.333 0.00 0.00 37.09 1.82
2532 2830 8.668353 CATAATCACAAAGCACTGTTGTACTAT 58.332 33.333 0.00 0.00 37.09 2.12
2533 2831 6.727824 ATCACAAAGCACTGTTGTACTATC 57.272 37.500 0.00 0.00 37.09 2.08
2534 2832 5.606505 TCACAAAGCACTGTTGTACTATCA 58.393 37.500 0.00 0.00 37.09 2.15
2535 2833 5.465390 TCACAAAGCACTGTTGTACTATCAC 59.535 40.000 0.00 0.00 37.09 3.06
2536 2834 4.447724 ACAAAGCACTGTTGTACTATCACG 59.552 41.667 0.00 0.00 37.44 4.35
2567 2865 1.423541 TCAACATGCACCAGTACCCTT 59.576 47.619 0.00 0.00 0.00 3.95
2599 2897 7.337938 TCATTTCCACATAAGCAATCTGTCTA 58.662 34.615 0.00 0.00 0.00 2.59
2618 2916 3.696051 TCTAATCTTGCATTTCACAGCCC 59.304 43.478 0.00 0.00 0.00 5.19
2678 2976 3.632643 TGCTTGTCTAATGGCTGATCA 57.367 42.857 0.00 0.00 0.00 2.92
2684 2982 4.454678 TGTCTAATGGCTGATCATTCCAC 58.545 43.478 16.33 6.80 38.24 4.02
2685 2983 4.080413 TGTCTAATGGCTGATCATTCCACA 60.080 41.667 16.33 8.81 38.24 4.17
2791 3089 2.120232 CTTGATCCCGATTCTTCGTCG 58.880 52.381 0.00 0.00 43.97 5.12
2822 3120 1.205417 CCACCCCATCAAAATGACAGC 59.795 52.381 0.00 0.00 34.61 4.40
2988 3304 5.363562 TGCTTGGATCTGATTGTACTCAT 57.636 39.130 0.00 0.00 0.00 2.90
2989 3305 5.363101 TGCTTGGATCTGATTGTACTCATC 58.637 41.667 0.00 0.00 0.00 2.92
2990 3306 5.129980 TGCTTGGATCTGATTGTACTCATCT 59.870 40.000 0.00 0.00 0.00 2.90
2991 3307 6.054295 GCTTGGATCTGATTGTACTCATCTT 58.946 40.000 0.00 0.00 0.00 2.40
2992 3308 7.147672 TGCTTGGATCTGATTGTACTCATCTTA 60.148 37.037 0.00 0.00 0.00 2.10
2993 3309 7.170658 GCTTGGATCTGATTGTACTCATCTTAC 59.829 40.741 0.00 0.00 0.00 2.34
2994 3310 7.660030 TGGATCTGATTGTACTCATCTTACA 57.340 36.000 0.00 0.00 0.00 2.41
2995 3311 8.078060 TGGATCTGATTGTACTCATCTTACAA 57.922 34.615 0.00 0.00 42.23 2.41
2996 3312 8.539544 TGGATCTGATTGTACTCATCTTACAAA 58.460 33.333 0.00 0.00 41.55 2.83
2997 3313 9.039870 GGATCTGATTGTACTCATCTTACAAAG 57.960 37.037 0.00 0.00 41.55 2.77
2998 3314 9.593134 GATCTGATTGTACTCATCTTACAAAGT 57.407 33.333 0.00 0.00 41.55 2.66
3009 3325 7.974501 ACTCATCTTACAAAGTATACTCAACCG 59.025 37.037 5.70 0.00 0.00 4.44
3080 3396 5.189736 TGAATAGTATCAGCTGTCCAGGTTT 59.810 40.000 14.67 1.09 36.98 3.27
3089 3405 2.286772 GCTGTCCAGGTTTTGTAACACG 60.287 50.000 0.00 0.00 35.92 4.49
3122 3438 4.220821 ACGCTTCTTCTAGTCAAAGGATGA 59.779 41.667 0.00 0.00 35.05 2.92
3569 3887 0.174845 CCCAGATGTAGGCGAACGAA 59.825 55.000 0.00 0.00 0.00 3.85
3570 3888 1.278238 CCAGATGTAGGCGAACGAAC 58.722 55.000 0.00 0.00 0.00 3.95
3571 3889 1.135083 CCAGATGTAGGCGAACGAACT 60.135 52.381 0.00 0.00 0.00 3.01
3572 3890 2.098607 CCAGATGTAGGCGAACGAACTA 59.901 50.000 0.00 0.00 0.00 2.24
3576 3894 3.581024 TGTAGGCGAACGAACTATGTT 57.419 42.857 0.00 0.00 0.00 2.71
3586 3904 7.483691 GGCGAACGAACTATGTTGAAATAAATT 59.516 33.333 0.00 0.00 0.00 1.82
3587 3905 8.304138 GCGAACGAACTATGTTGAAATAAATTG 58.696 33.333 0.00 0.00 0.00 2.32
3646 4360 2.097466 CCGCAAATTAATCGAGCAACCT 59.903 45.455 0.00 0.00 0.00 3.50
3661 4375 6.073222 TCGAGCAACCTTCTTCTGTTTATTTC 60.073 38.462 0.00 0.00 0.00 2.17
3667 4381 9.185192 CAACCTTCTTCTGTTTATTTCATGAAC 57.815 33.333 7.89 0.00 0.00 3.18
3680 4396 2.108168 TCATGAACCGGAGTCCTAAGG 58.892 52.381 9.46 3.67 0.00 2.69
3684 4400 3.537874 CCGGAGTCCTAAGGGGCG 61.538 72.222 7.77 0.00 43.12 6.13
3687 4403 2.732619 GGAGTCCTAAGGGGCGTGG 61.733 68.421 0.41 0.00 43.12 4.94
3733 4491 7.097192 AGAGGTAATACATGTGTGTTGTAGTG 58.903 38.462 9.11 0.00 39.77 2.74
3765 4523 0.915364 GGGATGAAGAAGAGCCAGGT 59.085 55.000 0.00 0.00 0.00 4.00
3778 4536 1.770294 GCCAGGTGCTCTACTCTACT 58.230 55.000 0.00 0.00 36.87 2.57
3779 4537 1.679153 GCCAGGTGCTCTACTCTACTC 59.321 57.143 0.00 0.00 36.87 2.59
3780 4538 2.946341 GCCAGGTGCTCTACTCTACTCA 60.946 54.545 0.00 0.00 36.87 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.453155 CATGAAAACCCTAGCGCAGT 58.547 50.000 11.47 0.00 0.00 4.40
1 2 0.099436 GCATGAAAACCCTAGCGCAG 59.901 55.000 11.47 4.88 0.00 5.18
2 3 0.607762 TGCATGAAAACCCTAGCGCA 60.608 50.000 11.47 0.00 0.00 6.09
3 4 0.525761 TTGCATGAAAACCCTAGCGC 59.474 50.000 0.00 0.00 0.00 5.92
4 5 1.812571 ACTTGCATGAAAACCCTAGCG 59.187 47.619 6.60 0.00 0.00 4.26
5 6 2.672195 GCACTTGCATGAAAACCCTAGC 60.672 50.000 6.60 0.00 41.59 3.42
6 7 3.221964 GCACTTGCATGAAAACCCTAG 57.778 47.619 6.60 0.00 41.59 3.02
19 20 1.205064 CTAGCGTGTGTGCACTTGC 59.795 57.895 19.41 15.58 43.16 4.01
20 21 1.568612 CCCTAGCGTGTGTGCACTTG 61.569 60.000 19.41 6.13 43.16 3.16
21 22 1.301716 CCCTAGCGTGTGTGCACTT 60.302 57.895 19.41 0.00 43.16 3.16
22 23 2.040009 AACCCTAGCGTGTGTGCACT 62.040 55.000 19.41 0.00 43.16 4.40
23 24 1.164041 AAACCCTAGCGTGTGTGCAC 61.164 55.000 10.75 10.75 41.97 4.57
24 25 0.882927 GAAACCCTAGCGTGTGTGCA 60.883 55.000 0.00 0.00 37.31 4.57
25 26 0.602905 AGAAACCCTAGCGTGTGTGC 60.603 55.000 0.00 0.00 0.00 4.57
26 27 1.148310 CAGAAACCCTAGCGTGTGTG 58.852 55.000 0.00 0.00 0.00 3.82
27 28 0.602905 GCAGAAACCCTAGCGTGTGT 60.603 55.000 0.00 0.00 0.00 3.72
28 29 0.320771 AGCAGAAACCCTAGCGTGTG 60.321 55.000 0.00 0.00 0.00 3.82
29 30 0.320771 CAGCAGAAACCCTAGCGTGT 60.321 55.000 0.00 0.00 0.00 4.49
30 31 1.639298 GCAGCAGAAACCCTAGCGTG 61.639 60.000 0.00 0.00 0.00 5.34
31 32 1.376037 GCAGCAGAAACCCTAGCGT 60.376 57.895 0.00 0.00 0.00 5.07
32 33 2.109126 GGCAGCAGAAACCCTAGCG 61.109 63.158 0.00 0.00 0.00 4.26
33 34 0.746204 GAGGCAGCAGAAACCCTAGC 60.746 60.000 0.00 0.00 0.00 3.42
45 46 4.783621 TGCACGATGGGAGGCAGC 62.784 66.667 0.00 0.00 0.00 5.25
55 56 4.530857 GTAGGCCGGCTGCACGAT 62.531 66.667 28.56 6.33 43.89 3.73
61 62 4.208686 GACGAGGTAGGCCGGCTG 62.209 72.222 28.56 9.94 40.50 4.85
62 63 4.444081 AGACGAGGTAGGCCGGCT 62.444 66.667 28.56 15.07 39.67 5.52
63 64 3.427598 GAAGACGAGGTAGGCCGGC 62.428 68.421 21.18 21.18 40.50 6.13
83 88 1.128809 TTCCACGGTCCTAAGGCCAA 61.129 55.000 5.01 0.00 0.00 4.52
102 107 1.224592 GATTGGGATCCACCGCACT 59.775 57.895 15.23 0.00 40.11 4.40
117 122 1.078426 CCTCCCGTCGGCAAAGATT 60.078 57.895 5.50 0.00 0.00 2.40
166 175 1.269778 TGAGCAGGACACAAACTCGAG 60.270 52.381 11.84 11.84 0.00 4.04
168 177 1.143305 CTGAGCAGGACACAAACTCG 58.857 55.000 0.00 0.00 0.00 4.18
170 179 3.209410 CTTTCTGAGCAGGACACAAACT 58.791 45.455 0.00 0.00 0.00 2.66
188 197 1.890510 GTGTCGTTGTCCCGCCTTT 60.891 57.895 0.00 0.00 0.00 3.11
195 204 0.586802 GCAAGAAGGTGTCGTTGTCC 59.413 55.000 0.00 0.00 0.00 4.02
198 207 1.581934 TCTGCAAGAAGGTGTCGTTG 58.418 50.000 0.00 0.00 42.31 4.10
227 253 0.261991 TGGAGGTAGGCGGAGAGAAT 59.738 55.000 0.00 0.00 0.00 2.40
308 335 2.039084 AGAAAACGCTGACTGAATCCCT 59.961 45.455 0.00 0.00 0.00 4.20
320 347 2.280628 GGATCCATCGAAGAAAACGCT 58.719 47.619 6.95 0.00 43.58 5.07
327 354 0.104855 CCAAGCGGATCCATCGAAGA 59.895 55.000 13.41 0.00 45.75 2.87
328 355 0.104855 TCCAAGCGGATCCATCGAAG 59.895 55.000 13.41 0.00 35.91 3.79
356 384 4.041567 TCCAATCTGTAGACACACCAACAT 59.958 41.667 0.00 0.00 0.00 2.71
433 471 5.067936 CGTCATGTTAAGACCTCATAGGACT 59.932 44.000 0.00 0.00 42.06 3.85
618 664 8.649810 TGAAAAACTTCTAATTTATTCGTCGC 57.350 30.769 0.00 0.00 0.00 5.19
852 901 4.083003 CCTGCGCAAAGACAGGTTTATTTA 60.083 41.667 13.05 0.00 46.95 1.40
853 902 3.305335 CCTGCGCAAAGACAGGTTTATTT 60.305 43.478 13.05 0.00 46.95 1.40
856 905 1.234821 CCTGCGCAAAGACAGGTTTA 58.765 50.000 13.05 0.00 46.95 2.01
857 906 2.032981 CCTGCGCAAAGACAGGTTT 58.967 52.632 13.05 0.00 46.95 3.27
858 907 3.749981 CCTGCGCAAAGACAGGTT 58.250 55.556 13.05 0.00 46.95 3.50
888 941 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
899 964 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
902 967 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
903 968 3.051803 TCCCTCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
904 969 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
905 970 3.421394 TCCCTCTCTCTCTCTCTCTCT 57.579 52.381 0.00 0.00 0.00 3.10
906 971 4.103153 TGATTCCCTCTCTCTCTCTCTCTC 59.897 50.000 0.00 0.00 0.00 3.20
907 972 4.047166 TGATTCCCTCTCTCTCTCTCTCT 58.953 47.826 0.00 0.00 0.00 3.10
908 973 4.141390 ACTGATTCCCTCTCTCTCTCTCTC 60.141 50.000 0.00 0.00 0.00 3.20
909 974 3.788142 ACTGATTCCCTCTCTCTCTCTCT 59.212 47.826 0.00 0.00 0.00 3.10
910 975 4.137543 GACTGATTCCCTCTCTCTCTCTC 58.862 52.174 0.00 0.00 0.00 3.20
911 976 3.527253 TGACTGATTCCCTCTCTCTCTCT 59.473 47.826 0.00 0.00 0.00 3.10
912 977 3.885297 CTGACTGATTCCCTCTCTCTCTC 59.115 52.174 0.00 0.00 0.00 3.20
913 978 3.373001 CCTGACTGATTCCCTCTCTCTCT 60.373 52.174 0.00 0.00 0.00 3.10
914 979 2.958355 CCTGACTGATTCCCTCTCTCTC 59.042 54.545 0.00 0.00 0.00 3.20
915 980 2.359143 CCCTGACTGATTCCCTCTCTCT 60.359 54.545 0.00 0.00 0.00 3.10
916 981 2.038659 CCCTGACTGATTCCCTCTCTC 58.961 57.143 0.00 0.00 0.00 3.20
917 982 1.648568 TCCCTGACTGATTCCCTCTCT 59.351 52.381 0.00 0.00 0.00 3.10
918 983 2.166907 TCCCTGACTGATTCCCTCTC 57.833 55.000 0.00 0.00 0.00 3.20
919 984 2.476199 CTTCCCTGACTGATTCCCTCT 58.524 52.381 0.00 0.00 0.00 3.69
920 985 1.488393 CCTTCCCTGACTGATTCCCTC 59.512 57.143 0.00 0.00 0.00 4.30
921 986 1.081174 TCCTTCCCTGACTGATTCCCT 59.919 52.381 0.00 0.00 0.00 4.20
922 987 1.210722 GTCCTTCCCTGACTGATTCCC 59.789 57.143 0.00 0.00 0.00 3.97
923 988 1.909302 TGTCCTTCCCTGACTGATTCC 59.091 52.381 0.00 0.00 33.83 3.01
924 989 2.834549 TCTGTCCTTCCCTGACTGATTC 59.165 50.000 0.00 0.00 36.26 2.52
925 990 2.836981 CTCTGTCCTTCCCTGACTGATT 59.163 50.000 0.00 0.00 39.14 2.57
926 991 2.465813 CTCTGTCCTTCCCTGACTGAT 58.534 52.381 0.00 0.00 39.14 2.90
927 992 1.930251 CTCTGTCCTTCCCTGACTGA 58.070 55.000 0.00 0.00 38.05 3.41
928 993 0.248843 GCTCTGTCCTTCCCTGACTG 59.751 60.000 0.00 0.00 33.83 3.51
929 994 1.254284 CGCTCTGTCCTTCCCTGACT 61.254 60.000 0.00 0.00 33.83 3.41
930 995 1.216710 CGCTCTGTCCTTCCCTGAC 59.783 63.158 0.00 0.00 0.00 3.51
931 996 0.967887 CTCGCTCTGTCCTTCCCTGA 60.968 60.000 0.00 0.00 0.00 3.86
932 997 0.967887 TCTCGCTCTGTCCTTCCCTG 60.968 60.000 0.00 0.00 0.00 4.45
933 998 0.251832 TTCTCGCTCTGTCCTTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
934 999 0.108567 GTTCTCGCTCTGTCCTTCCC 60.109 60.000 0.00 0.00 0.00 3.97
935 1000 0.603569 TGTTCTCGCTCTGTCCTTCC 59.396 55.000 0.00 0.00 0.00 3.46
936 1001 1.000163 TGTGTTCTCGCTCTGTCCTTC 60.000 52.381 0.00 0.00 0.00 3.46
937 1002 1.040646 TGTGTTCTCGCTCTGTCCTT 58.959 50.000 0.00 0.00 0.00 3.36
1236 1318 1.811558 GCCAAGCAATGATAGCGAGGA 60.812 52.381 0.00 0.00 37.01 3.71
1255 1337 3.733337 ACCGATGATCCAATCTAAGTGC 58.267 45.455 0.00 0.00 0.00 4.40
1292 1374 0.035458 CAATGGCGGGGATCTCTACC 59.965 60.000 0.00 0.00 0.00 3.18
1293 1375 1.048601 TCAATGGCGGGGATCTCTAC 58.951 55.000 0.00 0.00 0.00 2.59
1294 1376 1.048601 GTCAATGGCGGGGATCTCTA 58.951 55.000 0.00 0.00 0.00 2.43
1298 1380 1.823899 GTGGTCAATGGCGGGGATC 60.824 63.158 0.00 0.00 0.00 3.36
1299 1381 2.275418 GTGGTCAATGGCGGGGAT 59.725 61.111 0.00 0.00 0.00 3.85
1300 1382 4.041762 GGTGGTCAATGGCGGGGA 62.042 66.667 0.00 0.00 0.00 4.81
1315 1397 5.369993 GGATCCCCATTAGAGAAAACTAGGT 59.630 44.000 0.00 0.00 0.00 3.08
1336 1418 2.649312 TGGAAAACATCACCTCAGGGAT 59.351 45.455 0.00 0.00 36.25 3.85
1391 1473 3.223435 CTGGAGTTATCTCGGCCTAAGA 58.777 50.000 0.00 3.87 41.26 2.10
1392 1474 2.297597 CCTGGAGTTATCTCGGCCTAAG 59.702 54.545 0.00 0.00 41.26 2.18
1407 1489 6.605119 ACATGAAATTTATACCTCCCTGGAG 58.395 40.000 6.20 6.20 41.63 3.86
1444 1537 7.340487 CCCTCAAAATATCTTCCTAAACAAGCT 59.660 37.037 0.00 0.00 0.00 3.74
1496 1591 0.181350 CCACCTAGGCCAATCCAGTC 59.819 60.000 9.30 0.00 37.29 3.51
1502 1597 2.443255 CAGAATACCCACCTAGGCCAAT 59.557 50.000 9.30 0.00 35.39 3.16
1508 1603 2.090719 TCTCCCCAGAATACCCACCTAG 60.091 54.545 0.00 0.00 0.00 3.02
1551 1655 1.224592 CTGACCGCCATAAGCCCTT 59.775 57.895 0.00 0.00 38.78 3.95
1552 1656 2.746375 CCTGACCGCCATAAGCCCT 61.746 63.158 0.00 0.00 38.78 5.19
1591 1696 4.368874 TCCCACATTTGCAACATAATCG 57.631 40.909 0.00 0.00 0.00 3.34
1619 1747 0.523072 GACTGCCATTGCACACGATT 59.477 50.000 0.00 0.00 44.23 3.34
1633 1761 0.539051 ACATAGGTGCTCTGGACTGC 59.461 55.000 0.00 0.00 0.00 4.40
1647 1775 4.333649 CCTACATTGCTTGTCCACACATAG 59.666 45.833 0.00 0.00 39.87 2.23
1650 1778 2.158682 ACCTACATTGCTTGTCCACACA 60.159 45.455 0.00 0.00 39.87 3.72
1651 1779 2.504367 ACCTACATTGCTTGTCCACAC 58.496 47.619 0.00 0.00 39.87 3.82
1699 1827 6.399639 TTTTTGGGTTGAAGAGTGGATAAC 57.600 37.500 0.00 0.00 0.00 1.89
1739 1867 9.538508 GGATATACAAGGTTAATAACTCGTGTT 57.461 33.333 14.15 8.09 39.98 3.32
1741 1869 9.408069 GAGGATATACAAGGTTAATAACTCGTG 57.592 37.037 2.96 4.94 0.00 4.35
1743 1871 9.843334 GAGAGGATATACAAGGTTAATAACTCG 57.157 37.037 2.96 0.00 0.00 4.18
1762 1890 4.730966 TGCTCCGACTATTTAGAGAGGAT 58.269 43.478 0.00 0.00 0.00 3.24
1763 1891 4.166246 TGCTCCGACTATTTAGAGAGGA 57.834 45.455 0.00 0.00 0.00 3.71
1767 1895 5.176590 GCTCAATTGCTCCGACTATTTAGAG 59.823 44.000 0.00 0.00 0.00 2.43
1769 1897 5.053145 AGCTCAATTGCTCCGACTATTTAG 58.947 41.667 0.00 0.00 39.34 1.85
1771 1899 3.878778 AGCTCAATTGCTCCGACTATTT 58.121 40.909 0.00 0.00 39.34 1.40
1804 1932 4.171005 GTCATGCAAATGTGATGGAACTG 58.829 43.478 0.00 0.00 0.00 3.16
1814 1942 3.738830 ACTGCTTTGTCATGCAAATGT 57.261 38.095 13.30 10.61 45.00 2.71
1842 1970 0.177604 GACTGAGCTCCCCTGTGATG 59.822 60.000 12.15 0.00 0.00 3.07
1846 1974 0.409876 TACAGACTGAGCTCCCCTGT 59.590 55.000 25.55 25.55 40.66 4.00
1940 2229 6.176183 CAATACTCCCTCTGTCTCAAAATGT 58.824 40.000 0.00 0.00 0.00 2.71
1982 2271 5.324409 ACCATGTCACAAATTATCACCAGT 58.676 37.500 0.00 0.00 0.00 4.00
1997 2286 0.542467 AATGCCTGCCAACCATGTCA 60.542 50.000 0.00 0.00 0.00 3.58
2009 2298 2.163010 CACTAAGCAACCAGAATGCCTG 59.837 50.000 0.00 0.00 44.91 4.85
2106 2403 4.210331 ACTTCCAACTCTGCAAGTGAAAT 58.790 39.130 2.88 0.00 38.58 2.17
2135 2432 3.449377 ACAAACAAACAAGTTGGGGTAGG 59.551 43.478 7.96 1.54 41.97 3.18
2136 2433 4.729227 ACAAACAAACAAGTTGGGGTAG 57.271 40.909 7.96 2.19 41.97 3.18
2137 2434 5.221661 ACAAACAAACAAACAAGTTGGGGTA 60.222 36.000 7.96 0.00 41.97 3.69
2138 2435 4.068599 CAAACAAACAAACAAGTTGGGGT 58.931 39.130 7.96 0.00 41.97 4.95
2141 2438 6.866248 ACTCTACAAACAAACAAACAAGTTGG 59.134 34.615 7.96 0.00 41.97 3.77
2142 2439 7.867445 ACTCTACAAACAAACAAACAAGTTG 57.133 32.000 0.00 0.00 43.43 3.16
2143 2440 7.383843 CCAACTCTACAAACAAACAAACAAGTT 59.616 33.333 0.00 0.00 0.00 2.66
2146 2443 6.982852 TCCAACTCTACAAACAAACAAACAA 58.017 32.000 0.00 0.00 0.00 2.83
2147 2444 6.576662 TCCAACTCTACAAACAAACAAACA 57.423 33.333 0.00 0.00 0.00 2.83
2148 2445 7.088272 ACTTCCAACTCTACAAACAAACAAAC 58.912 34.615 0.00 0.00 0.00 2.93
2149 2446 7.040340 TGACTTCCAACTCTACAAACAAACAAA 60.040 33.333 0.00 0.00 0.00 2.83
2150 2447 6.431543 TGACTTCCAACTCTACAAACAAACAA 59.568 34.615 0.00 0.00 0.00 2.83
2151 2448 5.941058 TGACTTCCAACTCTACAAACAAACA 59.059 36.000 0.00 0.00 0.00 2.83
2152 2449 6.093633 ACTGACTTCCAACTCTACAAACAAAC 59.906 38.462 0.00 0.00 0.00 2.93
2153 2450 6.177610 ACTGACTTCCAACTCTACAAACAAA 58.822 36.000 0.00 0.00 0.00 2.83
2154 2451 5.741011 ACTGACTTCCAACTCTACAAACAA 58.259 37.500 0.00 0.00 0.00 2.83
2155 2452 5.353394 ACTGACTTCCAACTCTACAAACA 57.647 39.130 0.00 0.00 0.00 2.83
2156 2453 5.585047 ACAACTGACTTCCAACTCTACAAAC 59.415 40.000 0.00 0.00 0.00 2.93
2157 2454 5.741011 ACAACTGACTTCCAACTCTACAAA 58.259 37.500 0.00 0.00 0.00 2.83
2158 2455 5.353394 ACAACTGACTTCCAACTCTACAA 57.647 39.130 0.00 0.00 0.00 2.41
2159 2456 5.128827 AGAACAACTGACTTCCAACTCTACA 59.871 40.000 0.00 0.00 0.00 2.74
2160 2457 5.602628 AGAACAACTGACTTCCAACTCTAC 58.397 41.667 0.00 0.00 0.00 2.59
2161 2458 5.871396 AGAACAACTGACTTCCAACTCTA 57.129 39.130 0.00 0.00 0.00 2.43
2162 2459 4.762289 AGAACAACTGACTTCCAACTCT 57.238 40.909 0.00 0.00 0.00 3.24
2163 2460 4.876107 TGAAGAACAACTGACTTCCAACTC 59.124 41.667 0.00 0.00 39.14 3.01
2164 2461 4.843728 TGAAGAACAACTGACTTCCAACT 58.156 39.130 0.00 0.00 39.14 3.16
2165 2462 5.296780 TCATGAAGAACAACTGACTTCCAAC 59.703 40.000 0.00 0.00 39.14 3.77
2166 2463 5.296780 GTCATGAAGAACAACTGACTTCCAA 59.703 40.000 0.00 0.00 39.14 3.53
2167 2464 4.816385 GTCATGAAGAACAACTGACTTCCA 59.184 41.667 0.00 0.00 39.14 3.53
2168 2465 5.059833 AGTCATGAAGAACAACTGACTTCC 58.940 41.667 0.00 0.00 42.55 3.46
2169 2466 6.610741 AAGTCATGAAGAACAACTGACTTC 57.389 37.500 9.73 0.00 46.71 3.01
2171 2468 8.682936 AATTAAGTCATGAAGAACAACTGACT 57.317 30.769 0.00 0.00 45.19 3.41
2205 2502 4.919206 TGAATACACGGCATTGCTATTTG 58.081 39.130 8.82 3.56 0.00 2.32
2227 2524 8.889717 CGATTTGATATAACCACCAGTTTTACT 58.110 33.333 0.00 0.00 40.05 2.24
2318 2616 4.781775 TTAGGGTGTTCAGAAGGTTTCA 57.218 40.909 0.00 0.00 0.00 2.69
2495 2793 7.543172 GTGCTTTGTGATTATGTGAATGAACAT 59.457 33.333 0.00 0.00 43.21 2.71
2530 2828 4.061596 TGTTGAACACTCATTGCGTGATA 58.938 39.130 13.42 0.00 35.97 2.15
2531 2829 2.877786 TGTTGAACACTCATTGCGTGAT 59.122 40.909 13.42 1.41 35.97 3.06
2532 2830 2.284190 TGTTGAACACTCATTGCGTGA 58.716 42.857 13.42 0.00 36.29 4.35
2533 2831 2.753989 TGTTGAACACTCATTGCGTG 57.246 45.000 5.26 5.26 38.32 5.34
2534 2832 2.605338 GCATGTTGAACACTCATTGCGT 60.605 45.455 0.00 0.00 0.00 5.24
2535 2833 1.980844 GCATGTTGAACACTCATTGCG 59.019 47.619 0.00 0.00 0.00 4.85
2536 2834 2.727798 GTGCATGTTGAACACTCATTGC 59.272 45.455 12.47 12.47 34.95 3.56
2567 2865 9.206870 GATTGCTTATGTGGAAATGAAGAAAAA 57.793 29.630 0.00 0.00 0.00 1.94
2599 2897 2.532843 AGGGCTGTGAAATGCAAGATT 58.467 42.857 0.00 0.00 0.00 2.40
2758 3056 2.225467 GGATCAAGCTGGGCATAAGAC 58.775 52.381 0.00 0.00 0.00 3.01
2822 3120 2.742053 CGACCATGTTGTTAGTCCAAGG 59.258 50.000 0.00 0.00 0.00 3.61
2887 3185 5.414454 TGTATCCAAATACAGACTTTGTGGC 59.586 40.000 0.00 0.00 42.19 5.01
2988 3304 6.071784 TGCTCGGTTGAGTATACTTTGTAAGA 60.072 38.462 6.88 2.85 44.48 2.10
2989 3305 6.097356 TGCTCGGTTGAGTATACTTTGTAAG 58.903 40.000 6.88 2.83 44.48 2.34
2990 3306 6.028146 TGCTCGGTTGAGTATACTTTGTAA 57.972 37.500 6.88 0.00 44.48 2.41
2991 3307 5.648178 TGCTCGGTTGAGTATACTTTGTA 57.352 39.130 6.88 0.00 44.48 2.41
2992 3308 4.530710 TGCTCGGTTGAGTATACTTTGT 57.469 40.909 6.88 0.00 44.48 2.83
2993 3309 6.757010 ACTATTGCTCGGTTGAGTATACTTTG 59.243 38.462 6.88 0.00 44.48 2.77
2994 3310 6.875076 ACTATTGCTCGGTTGAGTATACTTT 58.125 36.000 6.88 0.00 44.48 2.66
2995 3311 6.466885 ACTATTGCTCGGTTGAGTATACTT 57.533 37.500 6.88 0.00 44.48 2.24
2996 3312 6.466885 AACTATTGCTCGGTTGAGTATACT 57.533 37.500 4.68 4.68 44.48 2.12
2997 3313 6.534079 ACAAACTATTGCTCGGTTGAGTATAC 59.466 38.462 0.00 0.00 44.48 1.47
2998 3314 6.636705 ACAAACTATTGCTCGGTTGAGTATA 58.363 36.000 0.00 0.00 44.48 1.47
2999 3315 5.488341 ACAAACTATTGCTCGGTTGAGTAT 58.512 37.500 0.00 0.00 44.48 2.12
3000 3316 4.890088 ACAAACTATTGCTCGGTTGAGTA 58.110 39.130 0.00 0.00 44.48 2.59
3001 3317 3.740115 ACAAACTATTGCTCGGTTGAGT 58.260 40.909 0.00 0.00 44.48 3.41
3002 3318 5.856126 TTACAAACTATTGCTCGGTTGAG 57.144 39.130 0.00 0.00 45.49 3.02
3003 3319 6.811253 ATTTACAAACTATTGCTCGGTTGA 57.189 33.333 0.00 0.00 40.34 3.18
3004 3320 7.692291 CAGTATTTACAAACTATTGCTCGGTTG 59.308 37.037 0.00 0.00 40.34 3.77
3005 3321 7.604927 TCAGTATTTACAAACTATTGCTCGGTT 59.395 33.333 0.00 0.00 40.34 4.44
3009 3325 7.974675 TGCTCAGTATTTACAAACTATTGCTC 58.025 34.615 0.00 0.00 40.34 4.26
3080 3396 1.062294 GTGCGTGAAACCGTGTTACAA 59.938 47.619 0.00 0.00 0.00 2.41
3089 3405 0.384353 GAAGAAGCGTGCGTGAAACC 60.384 55.000 0.00 0.00 0.00 3.27
3122 3438 9.656040 GCAGATGATCAGATTTAATCTACATCT 57.344 33.333 26.14 26.14 44.58 2.90
3603 3921 5.452077 CGGAAACCCAAGTGAAAACCATAAA 60.452 40.000 0.00 0.00 0.00 1.40
3605 3923 3.570550 CGGAAACCCAAGTGAAAACCATA 59.429 43.478 0.00 0.00 0.00 2.74
3606 3924 2.364002 CGGAAACCCAAGTGAAAACCAT 59.636 45.455 0.00 0.00 0.00 3.55
3612 3951 1.475403 TTTGCGGAAACCCAAGTGAA 58.525 45.000 0.00 0.00 0.00 3.18
3619 3958 3.691498 CTCGATTAATTTGCGGAAACCC 58.309 45.455 3.52 0.00 0.00 4.11
3620 3959 3.105937 GCTCGATTAATTTGCGGAAACC 58.894 45.455 3.52 0.00 0.00 3.27
3646 4360 6.712998 TCCGGTTCATGAAATAAACAGAAGAA 59.287 34.615 10.35 0.00 0.00 2.52
3661 4375 1.139058 CCCTTAGGACTCCGGTTCATG 59.861 57.143 0.00 0.00 33.47 3.07
3667 4381 3.537874 CGCCCCTTAGGACTCCGG 61.538 72.222 0.00 0.00 38.24 5.14
3700 4457 7.119262 ACACACATGTATTACCTCTTTGCTTAC 59.881 37.037 0.00 0.00 37.26 2.34
3701 4458 7.165485 ACACACATGTATTACCTCTTTGCTTA 58.835 34.615 0.00 0.00 37.26 3.09
3702 4459 6.003950 ACACACATGTATTACCTCTTTGCTT 58.996 36.000 0.00 0.00 37.26 3.91
3714 4472 6.573664 ATTGCACTACAACACACATGTATT 57.426 33.333 0.00 0.00 42.27 1.89
3733 4491 0.250038 TCATCCCTCGCTGCTATTGC 60.250 55.000 0.00 0.00 40.20 3.56
3765 4523 4.105537 AGGATGGATGAGTAGAGTAGAGCA 59.894 45.833 0.00 0.00 0.00 4.26
3779 4537 1.509703 CTGCGTCATCAGGATGGATG 58.490 55.000 9.25 0.00 44.78 3.51
3780 4538 0.250209 GCTGCGTCATCAGGATGGAT 60.250 55.000 9.25 0.00 39.24 3.41


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

AutoCloner maintained by Alex Coulton.