Multiple sequence alignment - TraesCS6A01G296100

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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 TraesCS6A01G296100 chr6A 100.000 1661 0 0 745 2405 529573023 529574683 0.000000e+00 3068.0
1 TraesCS6A01G296100 chr6A 100.000 317 0 0 1 317 529572279 529572595 9.580000e-164 586.0
2 TraesCS6A01G296100 chr6A 94.953 317 15 1 1 317 143069542 143069857 1.660000e-136 496.0
3 TraesCS6A01G296100 chr6A 74.212 857 190 27 899 1738 494495364 494496206 1.780000e-86 329.0
4 TraesCS6A01G296100 chr3B 81.039 1155 195 11 757 1907 798315500 798316634 0.000000e+00 898.0
5 TraesCS6A01G296100 chr2A 80.386 984 173 18 1013 1984 71142307 71141332 0.000000e+00 730.0
6 TraesCS6A01G296100 chr2A 93.671 316 17 3 4 317 60095306 60094992 1.010000e-128 470.0
7 TraesCS6A01G296100 chr1B 77.060 1347 251 35 752 2082 89433361 89432057 0.000000e+00 723.0
8 TraesCS6A01G296100 chr5B 75.895 1033 234 13 1380 2401 115434801 115433773 4.580000e-142 514.0
9 TraesCS6A01G296100 chr7B 78.055 843 162 19 982 1813 188595352 188596182 5.930000e-141 510.0
10 TraesCS6A01G296100 chr4A 94.286 315 17 1 4 317 7129622 7129308 4.650000e-132 481.0
11 TraesCS6A01G296100 chr4A 93.691 317 19 1 2 317 452251772 452251456 7.780000e-130 473.0
12 TraesCS6A01G296100 chr7A 93.711 318 19 1 1 317 18386398 18386715 2.160000e-130 475.0
13 TraesCS6A01G296100 chr7A 93.711 318 18 2 2 317 567716607 567716924 2.160000e-130 475.0
14 TraesCS6A01G296100 chr7A 93.651 315 19 1 4 317 637176568 637176254 1.010000e-128 470.0
15 TraesCS6A01G296100 chr1A 93.968 315 18 1 4 317 256020183 256019869 2.160000e-130 475.0
16 TraesCS6A01G296100 chr1A 87.500 48 4 2 1170 1216 45497506 45497460 1.000000e-03 54.7
17 TraesCS6A01G296100 chr3A 93.396 318 20 1 1 317 361336523 361336206 1.010000e-128 470.0
18 TraesCS6A01G296100 chr2D 76.255 518 89 26 900 1408 594571743 594571251 6.640000e-61 244.0
19 TraesCS6A01G296100 chr5D 82.500 80 12 2 1166 1244 487876600 487876522 4.290000e-08 69.4
20 TraesCS6A01G296100 chr7D 80.000 75 13 2 1170 1243 178935320 178935247 1.000000e-03 54.7


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 TraesCS6A01G296100 chr6A 529572279 529574683 2404 False 1827 3068 100.000 1 2405 2 chr6A.!!$F3 2404
1 TraesCS6A01G296100 chr6A 494495364 494496206 842 False 329 329 74.212 899 1738 1 chr6A.!!$F2 839
2 TraesCS6A01G296100 chr3B 798315500 798316634 1134 False 898 898 81.039 757 1907 1 chr3B.!!$F1 1150
3 TraesCS6A01G296100 chr2A 71141332 71142307 975 True 730 730 80.386 1013 1984 1 chr2A.!!$R2 971
4 TraesCS6A01G296100 chr1B 89432057 89433361 1304 True 723 723 77.060 752 2082 1 chr1B.!!$R1 1330
5 TraesCS6A01G296100 chr5B 115433773 115434801 1028 True 514 514 75.895 1380 2401 1 chr5B.!!$R1 1021
6 TraesCS6A01G296100 chr7B 188595352 188596182 830 False 510 510 78.055 982 1813 1 chr7B.!!$F1 831

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
858 860 0.036448 TCGTCTTCCTCGTCCAGAGT 59.964 55.0 0.0 0.0 45.44 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2142 0.038744 ACCAATCTGTTCCTGCCCAG 59.961 55.0 0.0 0.0 0.0 4.45 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
32 33 7.945033 TTACGTTCCGTAAGTTTTGTCTTAT 57.055 32.000 5.21 0.00 45.40 1.73
33 34 6.849588 ACGTTCCGTAAGTTTTGTCTTATT 57.150 33.333 0.00 0.00 38.73 1.40
34 35 7.250445 ACGTTCCGTAAGTTTTGTCTTATTT 57.750 32.000 0.00 0.00 38.73 1.40
35 36 7.696755 ACGTTCCGTAAGTTTTGTCTTATTTT 58.303 30.769 0.00 0.00 38.73 1.82
36 37 7.852454 ACGTTCCGTAAGTTTTGTCTTATTTTC 59.148 33.333 0.00 0.00 38.73 2.29
37 38 7.057566 CGTTCCGTAAGTTTTGTCTTATTTTCG 59.942 37.037 0.00 0.00 33.39 3.46
38 39 7.712264 TCCGTAAGTTTTGTCTTATTTTCGA 57.288 32.000 0.00 0.00 33.39 3.71
39 40 7.566709 TCCGTAAGTTTTGTCTTATTTTCGAC 58.433 34.615 0.00 0.00 33.39 4.20
40 41 6.513991 CCGTAAGTTTTGTCTTATTTTCGACG 59.486 38.462 0.00 0.00 33.39 5.12
41 42 6.029668 CGTAAGTTTTGTCTTATTTTCGACGC 59.970 38.462 0.00 0.00 33.39 5.19
42 43 5.412526 AGTTTTGTCTTATTTTCGACGCA 57.587 34.783 0.00 0.00 32.93 5.24
43 44 5.812652 AGTTTTGTCTTATTTTCGACGCAA 58.187 33.333 0.00 0.00 32.93 4.85
44 45 6.259638 AGTTTTGTCTTATTTTCGACGCAAA 58.740 32.000 0.00 0.00 32.93 3.68
45 46 6.748198 AGTTTTGTCTTATTTTCGACGCAAAA 59.252 30.769 0.00 2.69 33.85 2.44
46 47 7.273815 AGTTTTGTCTTATTTTCGACGCAAAAA 59.726 29.630 0.00 0.00 36.68 1.94
47 48 6.726035 TTGTCTTATTTTCGACGCAAAAAG 57.274 33.333 0.00 3.41 32.93 2.27
48 49 5.209240 TGTCTTATTTTCGACGCAAAAAGG 58.791 37.500 0.00 0.00 32.93 3.11
49 50 4.615541 GTCTTATTTTCGACGCAAAAAGGG 59.384 41.667 0.00 0.00 0.00 3.95
50 51 4.515944 TCTTATTTTCGACGCAAAAAGGGA 59.484 37.500 0.00 0.78 0.00 4.20
51 52 2.478547 TTTTCGACGCAAAAAGGGAC 57.521 45.000 0.00 0.00 0.00 4.46
52 53 0.664224 TTTCGACGCAAAAAGGGACC 59.336 50.000 0.00 0.00 0.00 4.46
53 54 1.500512 TTCGACGCAAAAAGGGACCG 61.501 55.000 0.00 0.00 0.00 4.79
54 55 2.248835 CGACGCAAAAAGGGACCGT 61.249 57.895 0.00 0.00 34.52 4.83
55 56 0.945265 CGACGCAAAAAGGGACCGTA 60.945 55.000 0.00 0.00 31.65 4.02
56 57 1.228533 GACGCAAAAAGGGACCGTAA 58.771 50.000 0.00 0.00 31.65 3.18
57 58 1.603326 GACGCAAAAAGGGACCGTAAA 59.397 47.619 0.00 0.00 31.65 2.01
58 59 2.022934 ACGCAAAAAGGGACCGTAAAA 58.977 42.857 0.00 0.00 0.00 1.52
59 60 2.426381 ACGCAAAAAGGGACCGTAAAAA 59.574 40.909 0.00 0.00 0.00 1.94
273 274 3.003394 TCGTAAGATTACCTCGGGTGA 57.997 47.619 5.90 0.00 45.01 4.02
274 275 3.355378 TCGTAAGATTACCTCGGGTGAA 58.645 45.455 5.90 0.00 45.01 3.18
275 276 3.379372 TCGTAAGATTACCTCGGGTGAAG 59.621 47.826 5.90 0.00 45.01 3.02
276 277 3.379372 CGTAAGATTACCTCGGGTGAAGA 59.621 47.826 5.90 0.00 36.23 2.87
277 278 4.142315 CGTAAGATTACCTCGGGTGAAGAA 60.142 45.833 5.90 0.00 36.23 2.52
278 279 5.451520 CGTAAGATTACCTCGGGTGAAGAAT 60.452 44.000 5.90 0.00 36.23 2.40
279 280 6.238842 CGTAAGATTACCTCGGGTGAAGAATA 60.239 42.308 5.90 0.00 36.23 1.75
280 281 6.555463 AAGATTACCTCGGGTGAAGAATAA 57.445 37.500 5.90 0.00 36.19 1.40
281 282 5.915175 AGATTACCTCGGGTGAAGAATAAC 58.085 41.667 5.90 0.00 36.19 1.89
282 283 5.661759 AGATTACCTCGGGTGAAGAATAACT 59.338 40.000 5.90 0.00 36.19 2.24
283 284 5.750352 TTACCTCGGGTGAAGAATAACTT 57.250 39.130 5.90 0.00 38.14 2.66
284 285 6.855763 TTACCTCGGGTGAAGAATAACTTA 57.144 37.500 5.90 0.00 36.67 2.24
285 286 5.952347 ACCTCGGGTGAAGAATAACTTAT 57.048 39.130 0.00 0.00 39.13 1.73
286 287 6.309389 ACCTCGGGTGAAGAATAACTTATT 57.691 37.500 0.00 0.00 39.13 1.40
287 288 6.346896 ACCTCGGGTGAAGAATAACTTATTC 58.653 40.000 12.07 12.07 38.76 1.75
288 289 6.156429 ACCTCGGGTGAAGAATAACTTATTCT 59.844 38.462 15.62 15.62 44.74 2.40
289 290 7.848201 ACCTCGGGTGAAGAATAACTTATTCTG 60.848 40.741 20.22 10.00 43.39 3.02
297 298 5.757850 GAATAACTTATTCTGCACCCTGG 57.242 43.478 12.55 0.00 41.00 4.45
298 299 2.514458 AACTTATTCTGCACCCTGGG 57.486 50.000 12.28 12.28 0.00 4.45
299 300 1.372501 ACTTATTCTGCACCCTGGGT 58.627 50.000 14.05 14.05 35.62 4.51
300 301 7.850027 GAATAACTTATTCTGCACCCTGGGTG 61.850 46.154 36.31 36.31 46.08 4.61
301 302 9.907723 GAATAACTTATTCTGCACCCTGGGTGA 62.908 44.444 42.58 27.49 46.15 4.02
312 313 4.772886 ACCCTGGGTGATGAATAGTAAC 57.227 45.455 19.82 0.00 32.98 2.50
313 314 4.108570 ACCCTGGGTGATGAATAGTAACA 58.891 43.478 19.82 0.00 32.98 2.41
314 315 4.080526 ACCCTGGGTGATGAATAGTAACAC 60.081 45.833 19.82 0.00 32.98 3.32
315 316 4.164221 CCCTGGGTGATGAATAGTAACACT 59.836 45.833 3.97 0.00 0.00 3.55
316 317 5.365605 CCCTGGGTGATGAATAGTAACACTA 59.634 44.000 3.97 0.00 34.82 2.74
783 785 0.878961 GGTGACGGTTGGTGTGTCTC 60.879 60.000 0.00 0.00 33.81 3.36
838 840 1.002502 GGCGCAACCTAGGGTTTCT 60.003 57.895 14.81 0.00 44.33 2.52
844 846 2.289506 GCAACCTAGGGTTTCTTCGTCT 60.290 50.000 14.81 0.00 44.33 4.18
848 850 2.832733 CCTAGGGTTTCTTCGTCTTCCT 59.167 50.000 0.00 0.00 0.00 3.36
851 853 1.000618 GGGTTTCTTCGTCTTCCTCGT 59.999 52.381 0.00 0.00 0.00 4.18
854 856 1.612676 TTCTTCGTCTTCCTCGTCCA 58.387 50.000 0.00 0.00 0.00 4.02
855 857 1.166129 TCTTCGTCTTCCTCGTCCAG 58.834 55.000 0.00 0.00 0.00 3.86
858 860 0.036448 TCGTCTTCCTCGTCCAGAGT 59.964 55.000 0.00 0.00 45.44 3.24
865 867 0.818296 CCTCGTCCAGAGTTCGGATT 59.182 55.000 0.00 0.00 45.44 3.01
866 868 1.202313 CCTCGTCCAGAGTTCGGATTC 60.202 57.143 0.00 0.00 45.44 2.52
867 869 1.746220 CTCGTCCAGAGTTCGGATTCT 59.254 52.381 0.00 0.00 41.99 2.40
868 870 2.164624 CTCGTCCAGAGTTCGGATTCTT 59.835 50.000 0.00 0.00 41.99 2.52
871 873 3.858238 CGTCCAGAGTTCGGATTCTTTAC 59.142 47.826 0.00 0.00 34.32 2.01
872 874 3.858238 GTCCAGAGTTCGGATTCTTTACG 59.142 47.826 0.00 0.00 34.32 3.18
873 875 3.760151 TCCAGAGTTCGGATTCTTTACGA 59.240 43.478 0.00 0.00 34.47 3.43
879 881 4.220163 AGTTCGGATTCTTTACGAGTTCCT 59.780 41.667 0.00 0.00 37.95 3.36
882 884 3.546670 CGGATTCTTTACGAGTTCCTTCG 59.453 47.826 0.00 0.00 45.70 3.79
884 886 3.308438 TTCTTTACGAGTTCCTTCGGG 57.692 47.619 0.00 0.00 44.57 5.14
885 887 2.242043 TCTTTACGAGTTCCTTCGGGT 58.758 47.619 0.00 0.00 44.57 5.28
886 888 2.629617 TCTTTACGAGTTCCTTCGGGTT 59.370 45.455 0.00 0.00 44.57 4.11
934 936 0.895530 CTTCTGCGTGTTCCCCTAGA 59.104 55.000 0.00 0.00 0.00 2.43
955 957 0.160182 CGCGTGGTCGTAAAACACTC 59.840 55.000 0.00 0.00 39.49 3.51
968 971 5.510179 CGTAAAACACTCAAACCCTAGGAGA 60.510 44.000 11.48 1.65 33.00 3.71
969 972 5.584551 AAAACACTCAAACCCTAGGAGAT 57.415 39.130 11.48 0.00 33.00 2.75
972 985 4.684724 ACACTCAAACCCTAGGAGATGTA 58.315 43.478 11.48 0.00 33.00 2.29
980 993 1.220750 CCTAGGAGATGTAGGGGGTGT 59.779 57.143 1.05 0.00 34.42 4.16
985 998 0.326618 AGATGTAGGGGGTGTGGAGG 60.327 60.000 0.00 0.00 0.00 4.30
987 1000 3.782443 GTAGGGGGTGTGGAGGCG 61.782 72.222 0.00 0.00 0.00 5.52
1052 1065 2.167281 TGAAGCTTTCGGATGAGGAGAG 59.833 50.000 0.00 0.00 0.00 3.20
1061 1074 1.047801 GATGAGGAGAGGAAGGGAGC 58.952 60.000 0.00 0.00 0.00 4.70
1095 1108 1.205460 CGGGGAAGGAGAAGGGGAAA 61.205 60.000 0.00 0.00 0.00 3.13
1097 1110 0.033991 GGGAAGGAGAAGGGGAAAGC 60.034 60.000 0.00 0.00 0.00 3.51
1272 1285 2.188207 GGGAAGAGGAAGGCGCTC 59.812 66.667 7.64 0.00 0.00 5.03
1302 1315 1.676014 CCCTGGATGTTCGACAAGGAC 60.676 57.143 0.00 0.00 27.50 3.85
1436 1450 5.591877 GGAATCTGCTGAAGACATTGGTAAT 59.408 40.000 0.00 0.00 37.88 1.89
1437 1451 6.096001 GGAATCTGCTGAAGACATTGGTAATT 59.904 38.462 0.00 0.00 37.88 1.40
1443 1457 8.347004 TGCTGAAGACATTGGTAATTTAATCA 57.653 30.769 0.00 0.00 0.00 2.57
1532 1546 2.219903 TCGTATGCGCATTGATAAACCG 59.780 45.455 30.42 16.39 38.14 4.44
1557 1571 2.123589 TGAGGGGTTTCACTCTGAACA 58.876 47.619 0.00 0.00 35.89 3.18
1615 1629 0.262285 GTAGCTGTAGGAGGGGAGGT 59.738 60.000 0.00 0.00 0.00 3.85
1628 1642 0.325272 GGGAGGTGGAGGTTGAGAAC 59.675 60.000 0.00 0.00 0.00 3.01
1631 1645 1.671379 GGTGGAGGTTGAGAACGGC 60.671 63.158 0.00 0.00 0.00 5.68
1632 1646 1.070786 GTGGAGGTTGAGAACGGCA 59.929 57.895 0.00 0.00 0.00 5.69
1665 1679 7.316393 AGATTTGAATATGAATACCTCCCGA 57.684 36.000 0.00 0.00 0.00 5.14
1679 1693 3.326880 ACCTCCCGAATTTCTGTTACACT 59.673 43.478 0.00 0.00 0.00 3.55
1682 1696 3.500680 TCCCGAATTTCTGTTACACTTGC 59.499 43.478 0.00 0.00 0.00 4.01
1685 1699 2.989422 ATTTCTGTTACACTTGCGGC 57.011 45.000 0.00 0.00 0.00 6.53
1740 1754 0.678048 GCTGGCGAAGGGAGAACAAT 60.678 55.000 0.00 0.00 0.00 2.71
1743 1757 3.343617 CTGGCGAAGGGAGAACAATAAA 58.656 45.455 0.00 0.00 0.00 1.40
1749 1763 5.048991 GCGAAGGGAGAACAATAAAAGTTCA 60.049 40.000 8.54 0.00 45.93 3.18
1788 1802 4.232905 TGGGACAGAGAAGGGGTG 57.767 61.111 0.00 0.00 0.00 4.61
1792 1806 1.280457 GGACAGAGAAGGGGTGATGT 58.720 55.000 0.00 0.00 0.00 3.06
1794 1808 2.168728 GGACAGAGAAGGGGTGATGTAC 59.831 54.545 0.00 0.00 0.00 2.90
1802 1816 2.775418 AGGGGTGATGTACATGATGGA 58.225 47.619 14.43 0.00 0.00 3.41
1827 1841 1.133853 GGAGGAGGAGTAGCCGAAGTA 60.134 57.143 0.00 0.00 43.43 2.24
1874 1889 1.556373 TAGGTCAGGAGGTCGGTCGA 61.556 60.000 0.00 0.00 0.00 4.20
1876 1891 2.750637 TCAGGAGGTCGGTCGAGC 60.751 66.667 13.75 13.75 42.36 5.03
1897 1912 1.063806 GCGGCAGTGATAGCTTATCG 58.936 55.000 0.00 0.00 38.02 2.92
1941 1956 3.318922 AAGAGGGAGGACGGGAGGG 62.319 68.421 0.00 0.00 0.00 4.30
1942 1957 4.862823 GAGGGAGGACGGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
1963 1978 1.900545 CGGACAAAGGGGAGGAGGTC 61.901 65.000 0.00 0.00 0.00 3.85
1969 1984 0.325765 AAGGGGAGGAGGTCACTAGC 60.326 60.000 0.00 0.00 0.00 3.42
1978 1993 2.393646 GAGGTCACTAGCCCTCAGAAT 58.606 52.381 15.39 0.00 45.47 2.40
1984 2002 2.766263 CACTAGCCCTCAGAATACCACA 59.234 50.000 0.00 0.00 0.00 4.17
1993 2011 2.237143 TCAGAATACCACAGCCCTGAAG 59.763 50.000 1.69 0.00 0.00 3.02
1996 2014 3.054802 AGAATACCACAGCCCTGAAGAAG 60.055 47.826 1.69 0.00 0.00 2.85
2015 2033 0.988063 GGGAGGAAGGCTGAAGAAGT 59.012 55.000 0.00 0.00 0.00 3.01
2032 2050 4.601084 AGAAGTTAGATCTTCACGAGGGA 58.399 43.478 0.00 0.00 44.18 4.20
2038 2056 2.092103 AGATCTTCACGAGGGAGCTACT 60.092 50.000 0.00 0.00 0.00 2.57
2039 2057 1.464734 TCTTCACGAGGGAGCTACTG 58.535 55.000 0.00 0.00 0.00 2.74
2044 2062 1.478510 CACGAGGGAGCTACTGTTCAT 59.521 52.381 0.00 0.00 0.00 2.57
2048 2066 3.381908 CGAGGGAGCTACTGTTCATAAGT 59.618 47.826 0.00 0.00 0.00 2.24
2053 2071 5.396884 GGGAGCTACTGTTCATAAGTTGGAT 60.397 44.000 0.00 0.00 0.00 3.41
2068 2086 1.382695 GGATGAGACGGGGAAGGGA 60.383 63.158 0.00 0.00 0.00 4.20
2069 2087 0.764752 GGATGAGACGGGGAAGGGAT 60.765 60.000 0.00 0.00 0.00 3.85
2082 2100 2.439156 GGGATGTGGCTCTGGTGC 60.439 66.667 0.00 0.00 0.00 5.01
2089 2107 3.077907 GGCTCTGGTGCCCTACAA 58.922 61.111 2.60 0.00 46.82 2.41
2090 2108 1.378762 GGCTCTGGTGCCCTACAAA 59.621 57.895 2.60 0.00 46.82 2.83
2093 2111 1.278127 GCTCTGGTGCCCTACAAACTA 59.722 52.381 0.00 0.00 0.00 2.24
2094 2112 2.092914 GCTCTGGTGCCCTACAAACTAT 60.093 50.000 0.00 0.00 0.00 2.12
2095 2113 3.622455 GCTCTGGTGCCCTACAAACTATT 60.622 47.826 0.00 0.00 0.00 1.73
2096 2114 3.941483 CTCTGGTGCCCTACAAACTATTG 59.059 47.826 0.00 0.00 42.46 1.90
2118 2136 6.995511 TGTTACCAGTGATAATACCTTTGC 57.004 37.500 0.00 0.00 0.00 3.68
2119 2137 6.477253 TGTTACCAGTGATAATACCTTTGCA 58.523 36.000 0.00 0.00 0.00 4.08
2124 2142 6.151144 ACCAGTGATAATACCTTTGCACTTTC 59.849 38.462 0.00 0.00 34.66 2.62
2125 2143 6.375455 CCAGTGATAATACCTTTGCACTTTCT 59.625 38.462 0.00 0.00 34.66 2.52
2126 2144 7.246311 CAGTGATAATACCTTTGCACTTTCTG 58.754 38.462 0.00 0.00 34.66 3.02
2134 2152 4.500265 GCACTTTCTGGGCAGGAA 57.500 55.556 0.00 0.00 46.29 3.36
2135 2153 1.959848 GCACTTTCTGGGCAGGAAC 59.040 57.895 0.00 0.00 46.29 3.62
2136 2154 0.823356 GCACTTTCTGGGCAGGAACA 60.823 55.000 0.00 0.00 46.29 3.18
2138 2156 1.140312 ACTTTCTGGGCAGGAACAGA 58.860 50.000 0.00 0.00 41.63 3.41
2139 2157 1.707427 ACTTTCTGGGCAGGAACAGAT 59.293 47.619 0.00 0.00 42.73 2.90
2144 2162 1.281867 CTGGGCAGGAACAGATTGGTA 59.718 52.381 0.00 0.00 36.86 3.25
2149 2167 3.378427 GGCAGGAACAGATTGGTAATGTC 59.622 47.826 0.00 0.00 0.00 3.06
2150 2168 4.265073 GCAGGAACAGATTGGTAATGTCT 58.735 43.478 0.00 0.00 0.00 3.41
2152 2170 5.392380 GCAGGAACAGATTGGTAATGTCTTG 60.392 44.000 0.00 0.00 0.00 3.02
2155 2173 5.355350 GGAACAGATTGGTAATGTCTTGGAG 59.645 44.000 0.00 0.00 0.00 3.86
2161 2179 1.490910 GGTAATGTCTTGGAGGGGGAG 59.509 57.143 0.00 0.00 0.00 4.30
2164 2182 3.412408 GTCTTGGAGGGGGAGGGC 61.412 72.222 0.00 0.00 0.00 5.19
2179 2197 2.892425 GGCGGCAAGACTGATCCG 60.892 66.667 3.07 6.07 44.29 4.18
2182 2200 1.519455 CGGCAAGACTGATCCGTCC 60.519 63.158 13.06 0.00 37.33 4.79
2183 2201 1.596934 GGCAAGACTGATCCGTCCA 59.403 57.895 13.06 0.00 34.46 4.02
2184 2202 0.036388 GGCAAGACTGATCCGTCCAA 60.036 55.000 13.06 0.00 34.46 3.53
2187 2205 2.677902 GCAAGACTGATCCGTCCAATGA 60.678 50.000 13.06 0.00 34.46 2.57
2188 2206 2.932614 CAAGACTGATCCGTCCAATGAC 59.067 50.000 13.06 0.00 38.18 3.06
2197 2215 3.154589 GTCCAATGACGGGAAGGAC 57.845 57.895 0.00 0.00 41.59 3.85
2200 2218 1.003118 TCCAATGACGGGAAGGACAAG 59.997 52.381 0.00 0.00 0.00 3.16
2202 2220 2.356125 CCAATGACGGGAAGGACAAGAT 60.356 50.000 0.00 0.00 0.00 2.40
2212 2230 3.013682 GGACAAGATCCCAGAGGGT 57.986 57.895 1.36 0.00 44.74 4.34
2218 2236 3.012959 ACAAGATCCCAGAGGGTAAGAGA 59.987 47.826 1.36 0.00 44.74 3.10
2221 2239 5.005628 AGATCCCAGAGGGTAAGAGATAC 57.994 47.826 1.36 0.00 44.74 2.24
2230 2248 7.417342 CCAGAGGGTAAGAGATACAAGAAGAAG 60.417 44.444 0.00 0.00 36.14 2.85
2234 2252 4.495690 AAGAGATACAAGAAGAAGGGGC 57.504 45.455 0.00 0.00 0.00 5.80
2249 2267 2.266055 GGCGAGACAAGGTGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
2250 2268 2.435059 GCGAGACAAGGTGAGGGC 60.435 66.667 0.00 0.00 0.00 5.19
2255 2273 1.201429 AGACAAGGTGAGGGCGGATT 61.201 55.000 0.00 0.00 0.00 3.01
2257 2275 1.002134 CAAGGTGAGGGCGGATTGT 60.002 57.895 0.00 0.00 0.00 2.71
2290 2308 1.072505 GGCGGTCCTTGGTCAGAAA 59.927 57.895 0.00 0.00 0.00 2.52
2294 2314 1.882352 CGGTCCTTGGTCAGAAAAGGG 60.882 57.143 11.62 0.00 42.77 3.95
2316 2336 1.002274 GCAGAAGGGGAGGAGGAGA 59.998 63.158 0.00 0.00 0.00 3.71
2320 2340 1.062505 AGAAGGGGAGGAGGAGATCAC 60.063 57.143 0.00 0.00 0.00 3.06
2322 2342 0.264359 AGGGGAGGAGGAGATCACTG 59.736 60.000 0.00 0.00 0.00 3.66
2323 2343 0.263172 GGGGAGGAGGAGATCACTGA 59.737 60.000 0.00 0.00 0.00 3.41
2329 2349 3.885297 GAGGAGGAGATCACTGAGAAGAG 59.115 52.174 0.00 0.00 0.00 2.85
2330 2350 3.527253 AGGAGGAGATCACTGAGAAGAGA 59.473 47.826 0.00 0.00 0.00 3.10
2331 2351 4.017591 AGGAGGAGATCACTGAGAAGAGAA 60.018 45.833 0.00 0.00 0.00 2.87
2342 2362 5.475220 CACTGAGAAGAGAAGTAGAGTGGAA 59.525 44.000 0.00 0.00 0.00 3.53
2348 2368 3.028130 GAGAAGTAGAGTGGAAGGAGGG 58.972 54.545 0.00 0.00 0.00 4.30
2349 2369 2.384029 AGAAGTAGAGTGGAAGGAGGGT 59.616 50.000 0.00 0.00 0.00 4.34
2350 2370 3.174779 GAAGTAGAGTGGAAGGAGGGTT 58.825 50.000 0.00 0.00 0.00 4.11
2354 2374 0.542333 GAGTGGAAGGAGGGTTAGGC 59.458 60.000 0.00 0.00 0.00 3.93
2355 2375 1.221021 GTGGAAGGAGGGTTAGGCG 59.779 63.158 0.00 0.00 0.00 5.52
2359 2379 1.538135 AAGGAGGGTTAGGCGTGGT 60.538 57.895 0.00 0.00 0.00 4.16
2366 2386 2.120940 TTAGGCGTGGTGGGAGGA 59.879 61.111 0.00 0.00 0.00 3.71
2367 2387 1.306654 TTAGGCGTGGTGGGAGGAT 60.307 57.895 0.00 0.00 0.00 3.24
2373 2393 0.673644 CGTGGTGGGAGGATGTCAAC 60.674 60.000 0.00 0.00 0.00 3.18
2377 2397 1.098050 GTGGGAGGATGTCAACATGC 58.902 55.000 6.53 6.53 43.83 4.06
2384 2404 2.983229 GGATGTCAACATGCTCAGAGT 58.017 47.619 7.32 0.00 40.86 3.24
2387 2407 3.036075 TGTCAACATGCTCAGAGTGAG 57.964 47.619 0.00 0.00 46.90 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.063630 TCGAAAATAAGACAAAACTTACGGAAC 58.936 33.333 0.00 0.00 35.60 3.62
13 14 8.063630 GTCGAAAATAAGACAAAACTTACGGAA 58.936 33.333 0.00 0.00 35.60 4.30
14 15 7.566709 GTCGAAAATAAGACAAAACTTACGGA 58.433 34.615 0.00 0.00 35.60 4.69
15 16 6.513991 CGTCGAAAATAAGACAAAACTTACGG 59.486 38.462 0.00 0.00 37.23 4.02
16 17 6.029668 GCGTCGAAAATAAGACAAAACTTACG 59.970 38.462 0.00 0.00 37.23 3.18
17 18 6.847289 TGCGTCGAAAATAAGACAAAACTTAC 59.153 34.615 0.00 0.00 37.23 2.34
18 19 6.946165 TGCGTCGAAAATAAGACAAAACTTA 58.054 32.000 0.00 0.00 37.23 2.24
19 20 5.812652 TGCGTCGAAAATAAGACAAAACTT 58.187 33.333 0.00 0.00 37.23 2.66
20 21 5.412526 TGCGTCGAAAATAAGACAAAACT 57.587 34.783 0.00 0.00 37.23 2.66
21 22 6.485253 TTTGCGTCGAAAATAAGACAAAAC 57.515 33.333 0.00 0.00 37.23 2.43
22 23 7.253817 CCTTTTTGCGTCGAAAATAAGACAAAA 60.254 33.333 16.07 8.79 37.23 2.44
23 24 6.197468 CCTTTTTGCGTCGAAAATAAGACAAA 59.803 34.615 16.07 4.36 37.23 2.83
24 25 5.683743 CCTTTTTGCGTCGAAAATAAGACAA 59.316 36.000 16.07 1.81 37.23 3.18
25 26 5.209240 CCTTTTTGCGTCGAAAATAAGACA 58.791 37.500 16.07 0.00 37.23 3.41
26 27 4.615541 CCCTTTTTGCGTCGAAAATAAGAC 59.384 41.667 16.07 0.00 0.00 3.01
27 28 4.515944 TCCCTTTTTGCGTCGAAAATAAGA 59.484 37.500 16.07 4.34 0.00 2.10
28 29 4.615541 GTCCCTTTTTGCGTCGAAAATAAG 59.384 41.667 0.00 6.46 0.00 1.73
29 30 4.538917 GTCCCTTTTTGCGTCGAAAATAA 58.461 39.130 0.00 0.00 0.00 1.40
30 31 3.058085 GGTCCCTTTTTGCGTCGAAAATA 60.058 43.478 0.00 0.00 0.00 1.40
31 32 2.287970 GGTCCCTTTTTGCGTCGAAAAT 60.288 45.455 0.00 0.00 0.00 1.82
32 33 1.065851 GGTCCCTTTTTGCGTCGAAAA 59.934 47.619 0.00 0.00 0.00 2.29
33 34 0.664224 GGTCCCTTTTTGCGTCGAAA 59.336 50.000 0.00 0.00 0.00 3.46
34 35 1.500512 CGGTCCCTTTTTGCGTCGAA 61.501 55.000 0.00 0.00 0.00 3.71
35 36 1.957186 CGGTCCCTTTTTGCGTCGA 60.957 57.895 0.00 0.00 0.00 4.20
36 37 0.945265 TACGGTCCCTTTTTGCGTCG 60.945 55.000 0.00 0.00 0.00 5.12
37 38 1.228533 TTACGGTCCCTTTTTGCGTC 58.771 50.000 0.00 0.00 0.00 5.19
38 39 1.677942 TTTACGGTCCCTTTTTGCGT 58.322 45.000 0.00 0.00 0.00 5.24
39 40 2.778187 TTTTACGGTCCCTTTTTGCG 57.222 45.000 0.00 0.00 0.00 4.85
242 243 9.406828 CGAGGTAATCTTACGATCATTTCATAA 57.593 33.333 0.00 0.00 34.50 1.90
243 244 8.027189 CCGAGGTAATCTTACGATCATTTCATA 58.973 37.037 0.00 0.00 34.50 2.15
244 245 6.868864 CCGAGGTAATCTTACGATCATTTCAT 59.131 38.462 0.00 0.00 34.50 2.57
245 246 6.213677 CCGAGGTAATCTTACGATCATTTCA 58.786 40.000 0.00 0.00 34.50 2.69
246 247 5.634020 CCCGAGGTAATCTTACGATCATTTC 59.366 44.000 0.00 0.00 34.50 2.17
247 248 5.070047 ACCCGAGGTAATCTTACGATCATTT 59.930 40.000 0.00 0.00 32.11 2.32
248 249 4.587684 ACCCGAGGTAATCTTACGATCATT 59.412 41.667 0.00 0.00 32.11 2.57
249 250 4.022242 CACCCGAGGTAATCTTACGATCAT 60.022 45.833 0.00 0.00 32.11 2.45
250 251 3.317149 CACCCGAGGTAATCTTACGATCA 59.683 47.826 0.00 0.00 32.11 2.92
251 252 3.567164 TCACCCGAGGTAATCTTACGATC 59.433 47.826 0.00 0.00 32.11 3.69
252 253 3.559069 TCACCCGAGGTAATCTTACGAT 58.441 45.455 0.00 0.00 32.11 3.73
253 254 3.003394 TCACCCGAGGTAATCTTACGA 57.997 47.619 0.00 0.00 32.11 3.43
254 255 3.379372 TCTTCACCCGAGGTAATCTTACG 59.621 47.826 0.00 0.00 32.11 3.18
255 256 4.996788 TCTTCACCCGAGGTAATCTTAC 57.003 45.455 0.00 0.00 32.11 2.34
256 257 7.343833 AGTTATTCTTCACCCGAGGTAATCTTA 59.656 37.037 0.00 0.00 32.11 2.10
257 258 6.156429 AGTTATTCTTCACCCGAGGTAATCTT 59.844 38.462 0.00 0.00 32.11 2.40
258 259 5.661759 AGTTATTCTTCACCCGAGGTAATCT 59.338 40.000 0.00 0.00 32.11 2.40
259 260 5.915175 AGTTATTCTTCACCCGAGGTAATC 58.085 41.667 0.00 0.00 32.11 1.75
260 261 5.952347 AGTTATTCTTCACCCGAGGTAAT 57.048 39.130 0.00 0.00 32.11 1.89
261 262 5.750352 AAGTTATTCTTCACCCGAGGTAA 57.250 39.130 0.00 0.00 32.11 2.85
262 263 7.427989 AATAAGTTATTCTTCACCCGAGGTA 57.572 36.000 2.10 0.00 37.56 3.08
263 264 5.952347 ATAAGTTATTCTTCACCCGAGGT 57.048 39.130 0.00 0.00 37.56 3.85
264 265 6.846325 GAATAAGTTATTCTTCACCCGAGG 57.154 41.667 22.93 0.00 41.00 4.63
273 274 9.397480 ACCCAGGGTGCAGAATAAGTTATTCTT 62.397 40.741 28.07 14.74 42.47 2.52
274 275 8.008283 ACCCAGGGTGCAGAATAAGTTATTCT 62.008 42.308 25.91 25.91 44.21 2.40
275 276 4.580580 CCCAGGGTGCAGAATAAGTTATTC 59.419 45.833 22.80 22.80 43.77 1.75
276 277 4.017499 ACCCAGGGTGCAGAATAAGTTATT 60.017 41.667 11.70 7.87 32.98 1.40
277 278 3.527665 ACCCAGGGTGCAGAATAAGTTAT 59.472 43.478 11.70 0.00 32.98 1.89
278 279 2.916934 ACCCAGGGTGCAGAATAAGTTA 59.083 45.455 11.70 0.00 32.98 2.24
279 280 1.710809 ACCCAGGGTGCAGAATAAGTT 59.289 47.619 11.70 0.00 32.98 2.66
280 281 1.372501 ACCCAGGGTGCAGAATAAGT 58.627 50.000 11.70 0.00 32.98 2.24
291 292 4.080526 GTGTTACTATTCATCACCCAGGGT 60.081 45.833 4.76 4.76 35.62 4.34
292 293 4.164221 AGTGTTACTATTCATCACCCAGGG 59.836 45.833 2.85 2.85 0.00 4.45
293 294 5.359194 AGTGTTACTATTCATCACCCAGG 57.641 43.478 0.00 0.00 0.00 4.45
744 745 4.282449 CACCACGTGGGATGGACTATATAA 59.718 45.833 36.47 0.00 39.87 0.98
745 746 3.830178 CACCACGTGGGATGGACTATATA 59.170 47.826 36.47 0.00 39.87 0.86
746 747 2.632996 CACCACGTGGGATGGACTATAT 59.367 50.000 36.47 9.86 39.87 0.86
747 748 2.036387 CACCACGTGGGATGGACTATA 58.964 52.381 36.47 0.00 39.87 1.31
748 749 0.830648 CACCACGTGGGATGGACTAT 59.169 55.000 36.47 11.21 39.87 2.12
749 750 0.251877 TCACCACGTGGGATGGACTA 60.252 55.000 36.47 9.63 39.87 2.59
750 751 1.535444 TCACCACGTGGGATGGACT 60.535 57.895 36.47 12.80 39.87 3.85
838 840 1.166129 CTCTGGACGAGGAAGACGAA 58.834 55.000 0.00 0.00 36.06 3.85
844 846 0.251033 TCCGAACTCTGGACGAGGAA 60.251 55.000 0.00 0.00 44.33 3.36
848 850 1.835494 AGAATCCGAACTCTGGACGA 58.165 50.000 0.00 0.00 38.60 4.20
851 853 3.760151 TCGTAAAGAATCCGAACTCTGGA 59.240 43.478 0.00 0.00 40.46 3.86
854 856 5.388408 AACTCGTAAAGAATCCGAACTCT 57.612 39.130 0.00 0.00 0.00 3.24
855 857 4.562000 GGAACTCGTAAAGAATCCGAACTC 59.438 45.833 0.00 0.00 0.00 3.01
858 860 4.796038 AGGAACTCGTAAAGAATCCGAA 57.204 40.909 0.00 0.00 38.64 4.30
890 892 0.419865 TGGTGGATGGGTAGGGAGAA 59.580 55.000 0.00 0.00 0.00 2.87
934 936 1.592131 TGTTTTACGACCACGCGCT 60.592 52.632 5.73 0.00 43.96 5.92
955 957 2.706190 CCCCTACATCTCCTAGGGTTTG 59.294 54.545 9.46 6.57 46.73 2.93
968 971 2.001269 GCCTCCACACCCCCTACAT 61.001 63.158 0.00 0.00 0.00 2.29
969 972 2.609610 GCCTCCACACCCCCTACA 60.610 66.667 0.00 0.00 0.00 2.74
980 993 4.465446 CTCCTCCCTCCGCCTCCA 62.465 72.222 0.00 0.00 0.00 3.86
985 998 2.801631 CCATCACTCCTCCCTCCGC 61.802 68.421 0.00 0.00 0.00 5.54
987 1000 1.127343 CTTCCATCACTCCTCCCTCC 58.873 60.000 0.00 0.00 0.00 4.30
988 1001 1.127343 CCTTCCATCACTCCTCCCTC 58.873 60.000 0.00 0.00 0.00 4.30
989 1002 0.327000 CCCTTCCATCACTCCTCCCT 60.327 60.000 0.00 0.00 0.00 4.20
990 1003 1.348775 CCCCTTCCATCACTCCTCCC 61.349 65.000 0.00 0.00 0.00 4.30
993 1006 1.972207 GCTACCCCTTCCATCACTCCT 60.972 57.143 0.00 0.00 0.00 3.69
1052 1065 1.704007 CCTGATCCTGGCTCCCTTCC 61.704 65.000 0.00 0.00 0.00 3.46
1061 1074 1.190833 CCCCGAGATCCTGATCCTGG 61.191 65.000 3.55 6.02 38.58 4.45
1116 1129 0.904865 TCTCCGACATCACCTTGCCT 60.905 55.000 0.00 0.00 0.00 4.75
1119 1132 0.898320 ACCTCTCCGACATCACCTTG 59.102 55.000 0.00 0.00 0.00 3.61
1272 1285 0.401738 ACATCCAGGGGCCATTATCG 59.598 55.000 4.39 0.00 0.00 2.92
1302 1315 6.425210 TCATAATCTTCTATCACCACCAGG 57.575 41.667 0.00 0.00 42.21 4.45
1314 1327 8.379331 GGCCTTTTACTAGGATCATAATCTTCT 58.621 37.037 0.00 0.00 37.50 2.85
1397 1411 5.072736 AGCAGATTCCTCATTCATCATACCA 59.927 40.000 0.00 0.00 0.00 3.25
1436 1450 4.320935 GCCTCTTCAAAACGGCTGATTAAA 60.321 41.667 0.00 0.00 39.42 1.52
1437 1451 3.190535 GCCTCTTCAAAACGGCTGATTAA 59.809 43.478 0.00 0.00 39.42 1.40
1443 1457 0.108585 TCTGCCTCTTCAAAACGGCT 59.891 50.000 0.00 0.00 42.90 5.52
1490 1504 9.838339 ATACGAACTTTGATCCTCAGATATTTT 57.162 29.630 0.00 0.00 30.90 1.82
1532 1546 3.198635 TCAGAGTGAAACCCCTCATGATC 59.801 47.826 0.00 0.00 37.80 2.92
1557 1571 1.215679 TCCTCTCCCTCCGACTCCTT 61.216 60.000 0.00 0.00 0.00 3.36
1615 1629 1.371183 CTGCCGTTCTCAACCTCCA 59.629 57.895 0.00 0.00 0.00 3.86
1628 1642 1.086696 CAAATCTACACCACCTGCCG 58.913 55.000 0.00 0.00 0.00 5.69
1631 1645 7.864108 TTCATATTCAAATCTACACCACCTG 57.136 36.000 0.00 0.00 0.00 4.00
1632 1646 9.561069 GTATTCATATTCAAATCTACACCACCT 57.439 33.333 0.00 0.00 0.00 4.00
1665 1679 2.350388 CGCCGCAAGTGTAACAGAAATT 60.350 45.455 0.00 0.00 41.43 1.82
1679 1693 1.673993 ATGACCAATGACGCCGCAA 60.674 52.632 0.00 0.00 0.00 4.85
1682 1696 2.472059 CCCATGACCAATGACGCCG 61.472 63.158 0.00 0.00 38.72 6.46
1685 1699 0.541392 TCTCCCCATGACCAATGACG 59.459 55.000 0.00 0.00 38.72 4.35
1740 1754 2.708861 TGAGCCACCTCCTGAACTTTTA 59.291 45.455 0.00 0.00 37.29 1.52
1743 1757 1.140312 TTGAGCCACCTCCTGAACTT 58.860 50.000 0.00 0.00 37.29 2.66
1749 1763 2.348998 CGCTTTGAGCCACCTCCT 59.651 61.111 0.00 0.00 38.18 3.69
1788 1802 4.375272 CTCCACACTCCATCATGTACATC 58.625 47.826 5.07 0.00 0.00 3.06
1792 1806 3.033909 CTCCTCCACACTCCATCATGTA 58.966 50.000 0.00 0.00 0.00 2.29
1794 1808 1.140452 CCTCCTCCACACTCCATCATG 59.860 57.143 0.00 0.00 0.00 3.07
1802 1816 0.324830 GGCTACTCCTCCTCCACACT 60.325 60.000 0.00 0.00 0.00 3.55
1843 1858 1.702957 CCTGACCTACTGGACCCAAAA 59.297 52.381 0.00 0.00 39.52 2.44
1849 1864 1.476477 GACCTCCTGACCTACTGGAC 58.524 60.000 0.00 0.00 40.77 4.02
1874 1889 2.202987 GCTATCACTGCCGCTGCT 60.203 61.111 0.70 0.00 38.71 4.24
1876 1891 2.064762 GATAAGCTATCACTGCCGCTG 58.935 52.381 0.00 0.00 35.28 5.18
1897 1912 0.520404 TCGAGTCACTCTTACGCCAC 59.480 55.000 2.61 0.00 0.00 5.01
1941 1956 1.900545 CTCCTCCCCTTTGTCCGTCC 61.901 65.000 0.00 0.00 0.00 4.79
1942 1957 1.597461 CTCCTCCCCTTTGTCCGTC 59.403 63.158 0.00 0.00 0.00 4.79
1963 1978 2.766263 TGTGGTATTCTGAGGGCTAGTG 59.234 50.000 0.00 0.00 0.00 2.74
1969 1984 0.181350 GGGCTGTGGTATTCTGAGGG 59.819 60.000 0.00 0.00 0.00 4.30
1975 1990 3.274288 CTTCTTCAGGGCTGTGGTATTC 58.726 50.000 0.00 0.00 0.00 1.75
1978 1993 0.984230 CCTTCTTCAGGGCTGTGGTA 59.016 55.000 0.00 0.00 39.39 3.25
1993 2011 1.280457 TCTTCAGCCTTCCTCCCTTC 58.720 55.000 0.00 0.00 0.00 3.46
1996 2014 0.988063 ACTTCTTCAGCCTTCCTCCC 59.012 55.000 0.00 0.00 0.00 4.30
2015 2033 3.019799 AGCTCCCTCGTGAAGATCTAA 57.980 47.619 0.00 0.00 0.00 2.10
2026 2044 3.381908 ACTTATGAACAGTAGCTCCCTCG 59.618 47.826 0.00 0.00 0.00 4.63
2032 2050 6.155221 TCTCATCCAACTTATGAACAGTAGCT 59.845 38.462 0.00 0.00 33.13 3.32
2038 2056 4.503910 CCGTCTCATCCAACTTATGAACA 58.496 43.478 0.00 0.00 33.13 3.18
2039 2057 3.871594 CCCGTCTCATCCAACTTATGAAC 59.128 47.826 0.00 0.00 33.13 3.18
2044 2062 2.241281 TCCCCGTCTCATCCAACTTA 57.759 50.000 0.00 0.00 0.00 2.24
2048 2066 1.271840 CCCTTCCCCGTCTCATCCAA 61.272 60.000 0.00 0.00 0.00 3.53
2053 2071 1.080354 ACATCCCTTCCCCGTCTCA 59.920 57.895 0.00 0.00 0.00 3.27
2096 2114 6.598064 AGTGCAAAGGTATTATCACTGGTAAC 59.402 38.462 0.00 0.00 32.89 2.50
2097 2115 6.717289 AGTGCAAAGGTATTATCACTGGTAA 58.283 36.000 0.00 0.00 32.89 2.85
2100 2118 6.375455 AGAAAGTGCAAAGGTATTATCACTGG 59.625 38.462 0.00 0.00 33.81 4.00
2101 2119 7.246311 CAGAAAGTGCAAAGGTATTATCACTG 58.754 38.462 0.00 0.00 33.81 3.66
2103 2121 6.404734 CCCAGAAAGTGCAAAGGTATTATCAC 60.405 42.308 0.00 0.00 0.00 3.06
2107 2125 3.761752 GCCCAGAAAGTGCAAAGGTATTA 59.238 43.478 0.00 0.00 0.00 0.98
2108 2126 2.562738 GCCCAGAAAGTGCAAAGGTATT 59.437 45.455 0.00 0.00 0.00 1.89
2109 2127 2.171003 GCCCAGAAAGTGCAAAGGTAT 58.829 47.619 0.00 0.00 0.00 2.73
2111 2129 0.396974 TGCCCAGAAAGTGCAAAGGT 60.397 50.000 0.00 0.00 30.85 3.50
2114 2132 0.106268 TCCTGCCCAGAAAGTGCAAA 60.106 50.000 0.00 0.00 34.06 3.68
2118 2136 1.202806 TCTGTTCCTGCCCAGAAAGTG 60.203 52.381 0.00 0.00 34.88 3.16
2119 2137 1.140312 TCTGTTCCTGCCCAGAAAGT 58.860 50.000 0.00 0.00 34.88 2.66
2124 2142 0.038744 ACCAATCTGTTCCTGCCCAG 59.961 55.000 0.00 0.00 0.00 4.45
2125 2143 1.367346 TACCAATCTGTTCCTGCCCA 58.633 50.000 0.00 0.00 0.00 5.36
2126 2144 2.507407 TTACCAATCTGTTCCTGCCC 57.493 50.000 0.00 0.00 0.00 5.36
2129 2147 5.124457 CCAAGACATTACCAATCTGTTCCTG 59.876 44.000 0.00 0.00 0.00 3.86
2133 2151 5.256474 CCTCCAAGACATTACCAATCTGTT 58.744 41.667 0.00 0.00 0.00 3.16
2134 2152 4.324563 CCCTCCAAGACATTACCAATCTGT 60.325 45.833 0.00 0.00 0.00 3.41
2135 2153 4.202441 CCCTCCAAGACATTACCAATCTG 58.798 47.826 0.00 0.00 0.00 2.90
2136 2154 3.203040 CCCCTCCAAGACATTACCAATCT 59.797 47.826 0.00 0.00 0.00 2.40
2138 2156 2.244769 CCCCCTCCAAGACATTACCAAT 59.755 50.000 0.00 0.00 0.00 3.16
2139 2157 1.638589 CCCCCTCCAAGACATTACCAA 59.361 52.381 0.00 0.00 0.00 3.67
2144 2162 0.921256 CCCTCCCCCTCCAAGACATT 60.921 60.000 0.00 0.00 0.00 2.71
2161 2179 2.514824 GGATCAGTCTTGCCGCCC 60.515 66.667 0.00 0.00 0.00 6.13
2167 2185 2.932614 GTCATTGGACGGATCAGTCTTG 59.067 50.000 22.65 17.45 40.76 3.02
2179 2197 0.323629 TGTCCTTCCCGTCATTGGAC 59.676 55.000 0.00 0.00 45.22 4.02
2182 2200 2.472695 TCTTGTCCTTCCCGTCATTG 57.527 50.000 0.00 0.00 0.00 2.82
2183 2201 2.092914 GGATCTTGTCCTTCCCGTCATT 60.093 50.000 0.00 0.00 44.16 2.57
2184 2202 1.486726 GGATCTTGTCCTTCCCGTCAT 59.513 52.381 0.00 0.00 44.16 3.06
2187 2205 2.297937 GGGATCTTGTCCTTCCCGT 58.702 57.895 0.00 0.00 46.91 5.28
2206 2224 6.609616 CCTTCTTCTTGTATCTCTTACCCTCT 59.390 42.308 0.00 0.00 0.00 3.69
2209 2227 5.163290 CCCCTTCTTCTTGTATCTCTTACCC 60.163 48.000 0.00 0.00 0.00 3.69
2212 2230 4.099573 CGCCCCTTCTTCTTGTATCTCTTA 59.900 45.833 0.00 0.00 0.00 2.10
2218 2236 2.168728 GTCTCGCCCCTTCTTCTTGTAT 59.831 50.000 0.00 0.00 0.00 2.29
2221 2239 0.321671 TGTCTCGCCCCTTCTTCTTG 59.678 55.000 0.00 0.00 0.00 3.02
2230 2248 2.266055 CTCACCTTGTCTCGCCCC 59.734 66.667 0.00 0.00 0.00 5.80
2234 2252 2.125912 CGCCCTCACCTTGTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
2255 2273 1.686325 GCCTCCCTCGCAGGATTACA 61.686 60.000 4.00 0.00 37.67 2.41
2257 2275 2.498941 CGCCTCCCTCGCAGGATTA 61.499 63.158 4.00 0.00 37.67 1.75
2278 2296 3.363787 CCCCCTTTTCTGACCAAGG 57.636 57.895 7.56 7.56 39.58 3.61
2294 2314 4.760220 TCCTCCCCTTCTGCCCCC 62.760 72.222 0.00 0.00 0.00 5.40
2299 2319 1.062581 TGATCTCCTCCTCCCCTTCTG 60.063 57.143 0.00 0.00 0.00 3.02
2303 2323 0.264359 CAGTGATCTCCTCCTCCCCT 59.736 60.000 0.00 0.00 0.00 4.79
2306 2326 2.746279 TCTCAGTGATCTCCTCCTCC 57.254 55.000 0.00 0.00 0.00 4.30
2310 2330 4.949856 ACTTCTCTTCTCAGTGATCTCCTC 59.050 45.833 0.00 0.00 0.00 3.71
2316 2336 5.652014 CCACTCTACTTCTCTTCTCAGTGAT 59.348 44.000 0.00 0.00 33.30 3.06
2320 2340 5.125417 CCTTCCACTCTACTTCTCTTCTCAG 59.875 48.000 0.00 0.00 0.00 3.35
2322 2342 5.258051 TCCTTCCACTCTACTTCTCTTCTC 58.742 45.833 0.00 0.00 0.00 2.87
2323 2343 5.261216 CTCCTTCCACTCTACTTCTCTTCT 58.739 45.833 0.00 0.00 0.00 2.85
2329 2349 2.822697 ACCCTCCTTCCACTCTACTTC 58.177 52.381 0.00 0.00 0.00 3.01
2330 2350 3.277416 AACCCTCCTTCCACTCTACTT 57.723 47.619 0.00 0.00 0.00 2.24
2331 2351 3.309994 CCTAACCCTCCTTCCACTCTACT 60.310 52.174 0.00 0.00 0.00 2.57
2342 2362 2.122056 ACCACGCCTAACCCTCCT 59.878 61.111 0.00 0.00 0.00 3.69
2348 2368 1.623542 ATCCTCCCACCACGCCTAAC 61.624 60.000 0.00 0.00 0.00 2.34
2349 2369 1.306654 ATCCTCCCACCACGCCTAA 60.307 57.895 0.00 0.00 0.00 2.69
2350 2370 2.063979 CATCCTCCCACCACGCCTA 61.064 63.158 0.00 0.00 0.00 3.93
2354 2374 0.673644 GTTGACATCCTCCCACCACG 60.674 60.000 0.00 0.00 0.00 4.94
2355 2375 0.400213 TGTTGACATCCTCCCACCAC 59.600 55.000 0.00 0.00 0.00 4.16
2359 2379 0.994247 AGCATGTTGACATCCTCCCA 59.006 50.000 0.00 0.00 33.61 4.37
2366 2386 3.597255 CTCACTCTGAGCATGTTGACAT 58.403 45.455 4.19 0.00 37.72 3.06
2367 2387 2.289257 CCTCACTCTGAGCATGTTGACA 60.289 50.000 4.19 0.00 42.98 3.58
2373 2393 1.274447 TGTGTCCTCACTCTGAGCATG 59.726 52.381 4.19 0.00 42.98 4.06
2377 2397 7.102346 AGAATTATTTGTGTCCTCACTCTGAG 58.898 38.462 2.45 2.45 43.91 3.35


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

AutoCloner maintained by Alex Coulton.