Multiple sequence alignment - TraesCS2D01G155700

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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 TraesCS2D01G155700 chr2D 100.000 6238 0 0 1 6238 99140363 99134126 0.000000e+00 11520
1 TraesCS2D01G155700 chr2B 92.887 4330 141 50 1426 5651 150716963 150712697 0.000000e+00 6135
2 TraesCS2D01G155700 chr2B 89.660 1354 76 31 1 1332 150718401 150717090 0.000000e+00 1666
3 TraesCS2D01G155700 chr2B 97.441 508 13 0 5731 6238 150712700 150712193 0.000000e+00 867
4 TraesCS2D01G155700 chr2A 90.185 4320 213 84 17 4207 98144884 98140647 0.000000e+00 5433
5 TraesCS2D01G155700 chr2A 93.950 1471 51 12 4202 5643 98140519 98139058 0.000000e+00 2189
6 TraesCS2D01G155700 chr2A 92.829 502 18 1 5735 6236 98139056 98138573 0.000000e+00 712
7 TraesCS2D01G155700 chr2A 91.818 110 5 4 5643 5751 712843626 712843520 3.900000e-32 150
8 TraesCS2D01G155700 chr7D 98.864 88 1 0 5648 5735 548668963 548669050 2.330000e-34 158
9 TraesCS2D01G155700 chr5D 94.175 103 4 2 5642 5743 57226052 57225951 8.370000e-34 156
10 TraesCS2D01G155700 chr1D 94.175 103 3 3 5647 5746 85191512 85191614 3.010000e-33 154
11 TraesCS2D01G155700 chr1D 94.845 97 5 0 5639 5735 494560270 494560366 1.080000e-32 152
12 TraesCS2D01G155700 chr6D 92.381 105 8 0 5633 5737 34808908 34809012 3.900000e-32 150
13 TraesCS2D01G155700 chr1B 93.204 103 6 1 5635 5736 250420249 250420351 3.900000e-32 150
14 TraesCS2D01G155700 chr7A 91.071 112 6 4 5647 5755 13666896 13666786 1.400000e-31 148
15 TraesCS2D01G155700 chr3A 89.076 119 6 7 5633 5745 711064812 711064929 2.340000e-29 141


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 TraesCS2D01G155700 chr2D 99134126 99140363 6237 True 11520.000000 11520 100.000000 1 6238 1 chr2D.!!$R1 6237
1 TraesCS2D01G155700 chr2B 150712193 150718401 6208 True 2889.333333 6135 93.329333 1 6238 3 chr2B.!!$R1 6237
2 TraesCS2D01G155700 chr2A 98138573 98144884 6311 True 2778.000000 5433 92.321333 17 6236 3 chr2A.!!$R2 6219

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
114 117 0.037326 GCTGGACTCGGACATCAACA 60.037 55.000 0.00 0.0 0.00 3.33 F
492 516 0.094730 GGATAAGACACGCACGCAAC 59.905 55.000 0.00 0.0 0.00 4.17 F
493 517 0.246757 GATAAGACACGCACGCAACG 60.247 55.000 0.00 0.0 0.00 4.10 F
845 902 0.322008 CTCCTGTGTCTTCTTGCCCC 60.322 60.000 0.00 0.0 0.00 5.80 F
2246 2431 0.524392 CGTTTGTGCGTTTCAGGCAA 60.524 50.000 0.00 0.0 40.93 4.52 F
2520 2733 0.901827 TGTTAGGCTTCCTGCGATCA 59.098 50.000 0.00 0.0 44.05 2.92 F
3723 3953 1.341209 CTGCGGCCATATCTCACAGTA 59.659 52.381 2.24 0.0 0.00 2.74 F
4067 4300 2.159338 GCACGATGGCATTCAAGACAAT 60.159 45.455 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1260 0.104304 ATCCGGGAAAGAATCGGTCG 59.896 55.000 0.00 0.0 43.75 4.79 R
1712 1875 0.321919 TCATTGTCTGTCTGGCTGGC 60.322 55.000 0.00 0.0 0.00 4.85 R
2249 2434 0.322816 GATGGCTTGCAGGACCAAGA 60.323 55.000 14.14 0.0 43.79 3.02 R
2349 2545 1.927174 CGTTTGGCACTTATCTCTCCG 59.073 52.381 0.00 0.0 0.00 4.63 R
3213 3431 0.105039 GGACATTCTCGGGCTACAGG 59.895 60.000 0.00 0.0 0.00 4.00 R
4067 4300 0.617935 TCATCTGGTTGATTGCGGGA 59.382 50.000 0.00 0.0 32.05 5.14 R
4911 5296 2.566833 TGCAGCAATGTCTAACAGGT 57.433 45.000 0.00 0.0 0.00 4.00 R
5830 6236 4.272261 GGTTTTGGTGTAGCAATTGTTTGG 59.728 41.667 7.40 0.0 33.22 3.28 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
31 34 3.459145 GGCTAACTCTACAAAGGCTAGC 58.541 50.000 6.04 6.04 33.96 3.42
60 63 1.502231 ACGAAGCACCATGATATCGC 58.498 50.000 0.00 0.00 33.88 4.58
61 64 0.792640 CGAAGCACCATGATATCGCC 59.207 55.000 0.00 0.00 0.00 5.54
62 65 1.160137 GAAGCACCATGATATCGCCC 58.840 55.000 0.00 0.00 0.00 6.13
96 99 1.942657 TCATGCCTTTGAATCTAGCGC 59.057 47.619 0.00 0.00 0.00 5.92
103 106 2.586258 TTGAATCTAGCGCTGGACTC 57.414 50.000 26.69 24.78 0.00 3.36
112 115 1.215382 CGCTGGACTCGGACATCAA 59.785 57.895 0.00 0.00 0.00 2.57
114 117 0.037326 GCTGGACTCGGACATCAACA 60.037 55.000 0.00 0.00 0.00 3.33
134 137 1.703438 CGCCTGCTGATTGAGAGCAC 61.703 60.000 0.00 0.00 41.56 4.40
144 147 0.176910 TTGAGAGCACGACACCAACA 59.823 50.000 0.00 0.00 0.00 3.33
204 208 6.022958 ACATAGCTGTTCCCCCTTTATTTTT 58.977 36.000 0.00 0.00 28.70 1.94
211 215 7.632898 GCTGTTCCCCCTTTATTTTTATTCCTC 60.633 40.741 0.00 0.00 0.00 3.71
235 240 0.169009 GAAGGAGACGCACAAATGGC 59.831 55.000 0.00 0.00 0.00 4.40
271 278 4.295051 GCGTGCTTTGGAAAAGATAAACA 58.705 39.130 3.95 0.00 0.00 2.83
353 365 6.295039 GACAAAGTGTCGGAGAAATAAACA 57.705 37.500 0.00 0.00 39.69 2.83
355 367 7.272037 ACAAAGTGTCGGAGAAATAAACAAT 57.728 32.000 0.00 0.00 39.69 2.71
363 375 7.094805 TGTCGGAGAAATAAACAATCCAAAGAG 60.095 37.037 0.00 0.00 39.69 2.85
366 378 7.094805 CGGAGAAATAAACAATCCAAAGAGACA 60.095 37.037 0.00 0.00 0.00 3.41
374 386 6.713762 ACAATCCAAAGAGACAATCAACAA 57.286 33.333 0.00 0.00 0.00 2.83
380 392 8.690203 TCCAAAGAGACAATCAACAATCTTTA 57.310 30.769 0.00 0.00 35.75 1.85
389 401 4.977741 TCAACAATCTTTACGGTCGAAC 57.022 40.909 0.00 0.00 0.00 3.95
492 516 0.094730 GGATAAGACACGCACGCAAC 59.905 55.000 0.00 0.00 0.00 4.17
493 517 0.246757 GATAAGACACGCACGCAACG 60.247 55.000 0.00 0.00 0.00 4.10
494 518 2.222953 ATAAGACACGCACGCAACGC 62.223 55.000 0.00 0.00 0.00 4.84
536 561 0.552848 GCCTGATTCCCCCTGATTCA 59.447 55.000 0.00 0.00 33.51 2.57
549 575 6.073314 CCCCCTGATTCATTGAGACATAAAT 58.927 40.000 0.00 0.00 0.00 1.40
551 577 7.892241 CCCCCTGATTCATTGAGACATAAATAT 59.108 37.037 0.00 0.00 0.00 1.28
586 614 7.227049 ACAAGAACTTTCCTTTTGAAACTGA 57.773 32.000 0.00 0.00 38.04 3.41
587 615 7.315890 ACAAGAACTTTCCTTTTGAAACTGAG 58.684 34.615 0.00 0.00 38.04 3.35
588 616 7.176690 ACAAGAACTTTCCTTTTGAAACTGAGA 59.823 33.333 0.00 0.00 38.04 3.27
812 869 0.880278 CTAGCTCGCTCTCGCTCTCT 60.880 60.000 0.00 0.00 37.68 3.10
813 870 0.878523 TAGCTCGCTCTCGCTCTCTC 60.879 60.000 0.00 0.00 37.68 3.20
815 872 2.881266 CTCGCTCTCGCTCTCTCGG 61.881 68.421 0.00 0.00 35.26 4.63
816 873 3.947841 CGCTCTCGCTCTCTCGGG 61.948 72.222 0.00 0.00 0.00 5.14
818 875 3.591835 CTCTCGCTCTCTCGGGCC 61.592 72.222 0.00 0.00 0.00 5.80
842 899 1.155042 CTGCTCCTGTGTCTTCTTGC 58.845 55.000 0.00 0.00 0.00 4.01
845 902 0.322008 CTCCTGTGTCTTCTTGCCCC 60.322 60.000 0.00 0.00 0.00 5.80
850 907 0.955919 GTGTCTTCTTGCCCCTTCCG 60.956 60.000 0.00 0.00 0.00 4.30
913 972 2.637025 GCTCTAGCTCGCTCTCGG 59.363 66.667 0.00 0.00 38.21 4.63
935 994 1.825474 TCCTAGCCTTCTTGACCTTCG 59.175 52.381 0.00 0.00 0.00 3.79
1197 1260 2.031163 CCCTCCGCCCAATCGATC 59.969 66.667 0.00 0.00 0.00 3.69
1198 1261 2.356313 CCTCCGCCCAATCGATCG 60.356 66.667 9.36 9.36 0.00 3.69
1199 1262 2.728180 CTCCGCCCAATCGATCGA 59.272 61.111 21.86 21.86 0.00 3.59
1200 1263 1.661821 CTCCGCCCAATCGATCGAC 60.662 63.158 22.06 6.26 0.00 4.20
1201 1264 2.661866 CCGCCCAATCGATCGACC 60.662 66.667 22.06 5.78 0.00 4.79
1212 1275 1.066605 TCGATCGACCGATTCTTTCCC 59.933 52.381 15.15 0.00 34.60 3.97
1232 1295 2.159653 CCGGATTCTTTCGTCTTGCTTG 60.160 50.000 0.00 0.00 0.00 4.01
1233 1296 2.726066 CGGATTCTTTCGTCTTGCTTGC 60.726 50.000 0.00 0.00 0.00 4.01
1235 1298 3.057946 GGATTCTTTCGTCTTGCTTGCTT 60.058 43.478 0.00 0.00 0.00 3.91
1236 1299 4.154195 GGATTCTTTCGTCTTGCTTGCTTA 59.846 41.667 0.00 0.00 0.00 3.09
1238 1301 5.689383 TTCTTTCGTCTTGCTTGCTTATT 57.311 34.783 0.00 0.00 0.00 1.40
1239 1302 5.283060 TCTTTCGTCTTGCTTGCTTATTC 57.717 39.130 0.00 0.00 0.00 1.75
1240 1303 3.722555 TTCGTCTTGCTTGCTTATTCG 57.277 42.857 0.00 0.00 0.00 3.34
1242 1305 2.411748 TCGTCTTGCTTGCTTATTCGTG 59.588 45.455 0.00 0.00 0.00 4.35
1243 1306 2.474526 CGTCTTGCTTGCTTATTCGTGG 60.475 50.000 0.00 0.00 0.00 4.94
1244 1307 2.484264 GTCTTGCTTGCTTATTCGTGGT 59.516 45.455 0.00 0.00 0.00 4.16
1245 1308 2.742053 TCTTGCTTGCTTATTCGTGGTC 59.258 45.455 0.00 0.00 0.00 4.02
1352 1445 2.438434 CACCATCCCTCGCCCAAC 60.438 66.667 0.00 0.00 0.00 3.77
1552 1686 4.557895 CGGCGGGTTCCAATTATTTTATCC 60.558 45.833 0.00 0.00 0.00 2.59
1557 1696 7.331791 CGGGTTCCAATTATTTTATCCCAAAA 58.668 34.615 0.00 0.00 33.33 2.44
1558 1697 7.279090 CGGGTTCCAATTATTTTATCCCAAAAC 59.721 37.037 0.00 0.00 33.33 2.43
1559 1698 7.554835 GGGTTCCAATTATTTTATCCCAAAACC 59.445 37.037 0.00 0.00 33.33 3.27
1560 1699 8.325787 GGTTCCAATTATTTTATCCCAAAACCT 58.674 33.333 0.00 0.00 0.00 3.50
1569 1708 6.538945 TTTATCCCAAAACCTATTTCTGCC 57.461 37.500 0.00 0.00 0.00 4.85
1610 1749 1.374758 GACTCACCGAGCAACCCAG 60.375 63.158 0.00 0.00 32.04 4.45
1611 1750 2.100879 GACTCACCGAGCAACCCAGT 62.101 60.000 0.00 0.00 32.04 4.00
1612 1751 0.830444 ACTCACCGAGCAACCCAGTA 60.830 55.000 0.00 0.00 32.04 2.74
1622 1764 2.955881 AACCCAGTAGCAGTCCGCC 61.956 63.158 0.00 0.00 44.04 6.13
1707 1870 0.803740 GAACGCTCGAGGTGACTAGT 59.196 55.000 15.58 0.00 44.43 2.57
1708 1871 2.005451 GAACGCTCGAGGTGACTAGTA 58.995 52.381 15.58 0.00 44.43 1.82
1709 1872 1.367659 ACGCTCGAGGTGACTAGTAC 58.632 55.000 15.58 0.00 44.43 2.73
1710 1873 1.066286 ACGCTCGAGGTGACTAGTACT 60.066 52.381 15.58 0.00 44.43 2.73
1711 1874 2.167281 ACGCTCGAGGTGACTAGTACTA 59.833 50.000 15.58 1.89 44.43 1.82
1712 1875 2.796031 CGCTCGAGGTGACTAGTACTAG 59.204 54.545 25.30 25.30 44.43 2.57
1713 1876 2.545106 GCTCGAGGTGACTAGTACTAGC 59.455 54.545 26.54 19.57 44.43 3.42
1714 1877 3.132925 CTCGAGGTGACTAGTACTAGCC 58.867 54.545 26.54 18.27 44.43 3.93
1715 1878 2.502947 TCGAGGTGACTAGTACTAGCCA 59.497 50.000 26.54 20.63 44.43 4.75
1716 1879 2.873472 CGAGGTGACTAGTACTAGCCAG 59.127 54.545 26.54 14.82 44.43 4.85
1721 1884 2.241430 TGACTAGTACTAGCCAGCCAGA 59.759 50.000 26.54 0.00 36.66 3.86
1745 1908 6.542821 ACAGACAATGAATTTTCTACCCAGA 58.457 36.000 0.00 0.00 0.00 3.86
1822 1986 4.519540 TTTCTGCCTTGCACTATTTTCC 57.480 40.909 0.00 0.00 33.79 3.13
1869 2033 4.582701 TTATTTTTCTGCCCTGTGTGTG 57.417 40.909 0.00 0.00 0.00 3.82
1870 2034 2.136298 TTTTTCTGCCCTGTGTGTGA 57.864 45.000 0.00 0.00 0.00 3.58
1878 2042 4.959839 TCTGCCCTGTGTGTGATATACTAA 59.040 41.667 0.00 0.00 0.00 2.24
1883 2047 4.686091 CCTGTGTGTGATATACTAATGCGG 59.314 45.833 0.00 0.00 0.00 5.69
1939 2106 4.149747 CGTGCAACAAGAAAACAAAACACT 59.850 37.500 0.00 0.00 35.74 3.55
1940 2107 5.373262 GTGCAACAAGAAAACAAAACACTG 58.627 37.500 0.00 0.00 36.32 3.66
1941 2108 5.050431 GTGCAACAAGAAAACAAAACACTGT 60.050 36.000 0.00 0.00 36.32 3.55
1942 2109 5.176590 TGCAACAAGAAAACAAAACACTGTC 59.823 36.000 0.00 0.00 0.00 3.51
1943 2110 5.389411 GCAACAAGAAAACAAAACACTGTCC 60.389 40.000 0.00 0.00 0.00 4.02
1944 2111 4.816392 ACAAGAAAACAAAACACTGTCCC 58.184 39.130 0.00 0.00 0.00 4.46
1945 2112 4.526650 ACAAGAAAACAAAACACTGTCCCT 59.473 37.500 0.00 0.00 0.00 4.20
1946 2113 5.712917 ACAAGAAAACAAAACACTGTCCCTA 59.287 36.000 0.00 0.00 0.00 3.53
1947 2114 6.209788 ACAAGAAAACAAAACACTGTCCCTAA 59.790 34.615 0.00 0.00 0.00 2.69
1948 2115 6.844097 AGAAAACAAAACACTGTCCCTAAA 57.156 33.333 0.00 0.00 0.00 1.85
1949 2116 7.234661 AGAAAACAAAACACTGTCCCTAAAA 57.765 32.000 0.00 0.00 0.00 1.52
1950 2117 7.672240 AGAAAACAAAACACTGTCCCTAAAAA 58.328 30.769 0.00 0.00 0.00 1.94
2004 2172 5.273833 TGGTCCATTGGGCATTATGATAT 57.726 39.130 9.97 0.00 0.00 1.63
2005 2173 5.018149 TGGTCCATTGGGCATTATGATATG 58.982 41.667 9.97 0.00 0.00 1.78
2006 2174 4.403432 GGTCCATTGGGCATTATGATATGG 59.597 45.833 9.97 3.11 33.91 2.74
2007 2175 5.018809 GTCCATTGGGCATTATGATATGGT 58.981 41.667 1.41 0.00 34.21 3.55
2008 2176 5.126061 GTCCATTGGGCATTATGATATGGTC 59.874 44.000 1.41 0.00 34.21 4.02
2126 2305 2.340443 GGCGATCGGATCAGGACC 59.660 66.667 18.30 9.16 0.00 4.46
2127 2306 2.340443 GCGATCGGATCAGGACCC 59.660 66.667 18.30 0.00 0.00 4.46
2211 2396 1.565759 CACAATCATTGAGGGAGGGGA 59.434 52.381 3.79 0.00 0.00 4.81
2246 2431 0.524392 CGTTTGTGCGTTTCAGGCAA 60.524 50.000 0.00 0.00 40.93 4.52
2309 2504 3.908643 AATGCAATGCAGAGAGAGAGA 57.091 42.857 14.98 0.00 43.65 3.10
2329 2525 4.094476 AGAGAGGATAAGAACCAAACCGA 58.906 43.478 0.00 0.00 0.00 4.69
2349 2545 3.486108 CGACTACACGATAGGATTGCAAC 59.514 47.826 0.00 0.00 43.77 4.17
2384 2580 2.095263 CCAAACGGGCTAGACAACAATG 60.095 50.000 0.00 0.00 0.00 2.82
2426 2622 1.664956 AAAGGGAGGCTTGTTGGGGT 61.665 55.000 0.00 0.00 0.00 4.95
2429 2625 1.303643 GGAGGCTTGTTGGGGTGAG 60.304 63.158 0.00 0.00 0.00 3.51
2432 2628 1.603739 GGCTTGTTGGGGTGAGACC 60.604 63.158 0.00 0.00 37.60 3.85
2476 2672 2.162921 CTCACCGACTGCTTGCGTTG 62.163 60.000 0.00 0.00 0.00 4.10
2520 2733 0.901827 TGTTAGGCTTCCTGCGATCA 59.098 50.000 0.00 0.00 44.05 2.92
2648 2861 5.505165 TTAACGACGAAACTGCAATCTAC 57.495 39.130 0.00 0.00 0.00 2.59
2649 2862 3.021269 ACGACGAAACTGCAATCTACA 57.979 42.857 0.00 0.00 0.00 2.74
2650 2863 2.729882 ACGACGAAACTGCAATCTACAC 59.270 45.455 0.00 0.00 0.00 2.90
2709 2924 7.438160 CCATCATCTCCATTGAAAATGTGATTG 59.562 37.037 0.00 1.05 0.00 2.67
2717 2932 6.347888 CCATTGAAAATGTGATTGCCTGAAAC 60.348 38.462 0.00 0.00 0.00 2.78
2733 2948 4.858692 CCTGAAACATAAAATTGCACGGAG 59.141 41.667 0.00 0.00 0.00 4.63
2752 2968 6.094048 CACGGAGAAACAGAAATCATACCAAT 59.906 38.462 0.00 0.00 0.00 3.16
2803 3019 5.186409 AGCAATCAGGCATTTCTGTAACAAT 59.814 36.000 0.00 0.00 36.25 2.71
2850 3066 3.189287 CCAGCCTGAGTGTGTTACAATTC 59.811 47.826 0.00 0.00 0.00 2.17
2853 3069 3.568007 GCCTGAGTGTGTTACAATTCCAA 59.432 43.478 0.00 0.00 0.00 3.53
2876 3092 2.956799 TTCTTCTGCAGGTTGCCGCA 62.957 55.000 15.13 0.00 44.23 5.69
3015 3233 4.302455 CATCTCTAACACTCCCTAATGCG 58.698 47.826 0.00 0.00 0.00 4.73
3048 3266 1.356124 AGGGCAAGCTCTCAGAGAAA 58.644 50.000 5.62 0.00 0.00 2.52
3213 3431 1.363744 CTGACATTCTTCCGCACCTC 58.636 55.000 0.00 0.00 0.00 3.85
3243 3461 2.715046 GAGAATGTCCTGGTTGATGCA 58.285 47.619 0.00 0.00 0.00 3.96
3246 3464 3.508793 AGAATGTCCTGGTTGATGCAAAG 59.491 43.478 0.00 0.00 0.00 2.77
3465 3684 3.243569 CCTCTGGCTCTGAACCTAATACG 60.244 52.174 0.00 0.00 0.00 3.06
3555 3780 4.922206 TCAACAAAGGTTATGATGGCTCT 58.078 39.130 0.00 0.00 34.87 4.09
3723 3953 1.341209 CTGCGGCCATATCTCACAGTA 59.659 52.381 2.24 0.00 0.00 2.74
3847 4077 2.361104 GCCTTGGCATGGACGGAA 60.361 61.111 22.50 0.00 0.00 4.30
4067 4300 2.159338 GCACGATGGCATTCAAGACAAT 60.159 45.455 0.00 0.00 0.00 2.71
4188 4421 7.362662 TGTTTCTTCATCTCATTTGTTAGTGC 58.637 34.615 0.00 0.00 0.00 4.40
4311 4677 3.804325 CCACACCTCAGATAATAAGCACG 59.196 47.826 0.00 0.00 0.00 5.34
4312 4678 4.433615 CACACCTCAGATAATAAGCACGT 58.566 43.478 0.00 0.00 0.00 4.49
4367 4733 5.700402 ATAATAGCAGACAGGAACCAGTT 57.300 39.130 0.00 0.00 0.00 3.16
4369 4735 5.700402 AATAGCAGACAGGAACCAGTTAT 57.300 39.130 0.00 0.00 0.00 1.89
4396 4762 5.048504 ACAAAGCCACTGATTGTTGTCATAG 60.049 40.000 0.00 0.00 33.73 2.23
4481 4858 2.840651 ACCCTCCACTAAACTCAGATGG 59.159 50.000 0.00 0.00 0.00 3.51
4505 4882 2.606725 GACTTCATTGCAGGATGTCTCG 59.393 50.000 20.08 4.46 39.31 4.04
4665 5042 8.165239 ACTAAGAACTGCATCATGTTAAAACA 57.835 30.769 0.00 0.00 44.06 2.83
4703 5081 7.757624 TGGATTGTGTACAAACTTTGTTTTCTC 59.242 33.333 12.35 6.07 42.22 2.87
4718 5096 4.816385 TGTTTTCTCCAGTCAGTGATGTTC 59.184 41.667 0.00 0.00 0.00 3.18
4911 5296 4.453177 CCATTTCATGGTGCAATGTGTA 57.547 40.909 0.00 0.00 45.54 2.90
5060 5449 1.743252 CTTCCCTTGCTGAGTCCGC 60.743 63.158 0.00 0.00 0.00 5.54
5073 5462 6.919721 TGCTGAGTCCGCTTTAAATAATTTT 58.080 32.000 8.09 0.00 0.00 1.82
5074 5463 7.375053 TGCTGAGTCCGCTTTAAATAATTTTT 58.625 30.769 8.09 0.00 0.00 1.94
5198 5603 4.996122 CAGCAACTTCTGAAGAATGACTCT 59.004 41.667 23.36 11.00 36.19 3.24
5663 6069 8.896722 AATATATGATACTCCCTCCGTAAACT 57.103 34.615 0.00 0.00 0.00 2.66
5664 6070 9.986157 AATATATGATACTCCCTCCGTAAACTA 57.014 33.333 0.00 0.00 0.00 2.24
5665 6071 9.986157 ATATATGATACTCCCTCCGTAAACTAA 57.014 33.333 0.00 0.00 0.00 2.24
5666 6072 8.896722 ATATGATACTCCCTCCGTAAACTAAT 57.103 34.615 0.00 0.00 0.00 1.73
5667 6073 9.986157 ATATGATACTCCCTCCGTAAACTAATA 57.014 33.333 0.00 0.00 0.00 0.98
5668 6074 8.896722 ATGATACTCCCTCCGTAAACTAATAT 57.103 34.615 0.00 0.00 0.00 1.28
5669 6075 9.986157 ATGATACTCCCTCCGTAAACTAATATA 57.014 33.333 0.00 0.00 0.00 0.86
5670 6076 9.812347 TGATACTCCCTCCGTAAACTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
5673 6079 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5674 6080 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5675 6081 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5676 6082 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5677 6083 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5678 6084 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5679 6085 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5680 6086 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
5681 6087 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
5693 6099 7.870588 AAGAGCGTTTAGAACACTACTTTAG 57.129 36.000 0.00 0.00 0.00 1.85
5694 6100 6.979465 AGAGCGTTTAGAACACTACTTTAGT 58.021 36.000 0.00 0.00 40.28 2.24
5695 6101 8.103948 AGAGCGTTTAGAACACTACTTTAGTA 57.896 34.615 0.00 0.00 37.23 1.82
5696 6102 8.571336 AGAGCGTTTAGAACACTACTTTAGTAA 58.429 33.333 0.00 0.00 37.23 2.24
5697 6103 9.351570 GAGCGTTTAGAACACTACTTTAGTAAT 57.648 33.333 0.00 0.00 37.23 1.89
5698 6104 9.351570 AGCGTTTAGAACACTACTTTAGTAATC 57.648 33.333 0.00 0.00 37.23 1.75
5699 6105 9.351570 GCGTTTAGAACACTACTTTAGTAATCT 57.648 33.333 5.76 5.76 37.23 2.40
5830 6236 0.880718 GAATGCTAGCAGGGTACGGC 60.881 60.000 23.89 2.25 38.13 5.68
5853 6259 4.272261 CCAAACAATTGCTACACCAAAACC 59.728 41.667 5.05 0.00 35.10 3.27
5864 6270 5.243060 GCTACACCAAAACCTTTTCTGGTAT 59.757 40.000 0.00 0.00 39.83 2.73
5913 6319 0.330604 ACATGAGCACTGCCCTTCAT 59.669 50.000 0.00 0.00 0.00 2.57
6113 6519 0.179000 CCAGTGCCCGCTTCTTAGAT 59.821 55.000 0.00 0.00 0.00 1.98
6128 6534 7.412781 CGCTTCTTAGATTGCTCATCAATATCC 60.413 40.741 6.27 0.00 44.95 2.59
6193 6599 1.590932 CGGCCAATCATCTCTTCCAG 58.409 55.000 2.24 0.00 0.00 3.86
6197 6603 2.553172 GCCAATCATCTCTTCCAGCATC 59.447 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.945938 TCTAGCTAGCCTTTGTAGAGTTAG 57.054 41.667 16.35 2.02 0.00 2.34
14 15 6.607004 TTTCTAGCTAGCCTTTGTAGAGTT 57.393 37.500 16.35 0.00 0.00 3.01
15 16 5.394773 GCTTTCTAGCTAGCCTTTGTAGAGT 60.395 44.000 16.35 0.00 44.27 3.24
31 34 2.143122 TGGTGCTTCGTTGCTTTCTAG 58.857 47.619 4.36 0.00 0.00 2.43
73 76 3.608707 CGCTAGATTCAAAGGCATGATGC 60.609 47.826 9.33 9.33 44.08 3.91
74 77 3.608707 GCGCTAGATTCAAAGGCATGATG 60.609 47.826 0.00 0.00 0.00 3.07
96 99 1.714794 GTGTTGATGTCCGAGTCCAG 58.285 55.000 0.00 0.00 0.00 3.86
103 106 3.027170 GCAGGCGTGTTGATGTCCG 62.027 63.158 8.40 0.00 0.00 4.79
112 115 0.390866 CTCTCAATCAGCAGGCGTGT 60.391 55.000 8.40 0.00 0.00 4.49
114 117 1.449246 GCTCTCAATCAGCAGGCGT 60.449 57.895 0.00 0.00 36.82 5.68
134 137 0.792640 GAGCTCATGTGTTGGTGTCG 59.207 55.000 9.40 0.00 0.00 4.35
204 208 3.381908 GCGTCTCCTTCAGAAGAGGAATA 59.618 47.826 12.14 0.00 32.58 1.75
211 215 2.154854 TTGTGCGTCTCCTTCAGAAG 57.845 50.000 2.78 2.78 33.93 2.85
221 225 1.246056 ATGCAGCCATTTGTGCGTCT 61.246 50.000 0.00 0.00 42.96 4.18
235 240 1.835483 GCACGCGGGAGAATATGCAG 61.835 60.000 15.48 0.00 33.27 4.41
348 360 8.231692 TGTTGATTGTCTCTTTGGATTGTTTA 57.768 30.769 0.00 0.00 0.00 2.01
352 364 7.600065 AGATTGTTGATTGTCTCTTTGGATTG 58.400 34.615 0.00 0.00 0.00 2.67
353 365 7.771927 AGATTGTTGATTGTCTCTTTGGATT 57.228 32.000 0.00 0.00 0.00 3.01
355 367 7.587037 AAAGATTGTTGATTGTCTCTTTGGA 57.413 32.000 0.00 0.00 33.11 3.53
363 375 5.119588 TCGACCGTAAAGATTGTTGATTGTC 59.880 40.000 0.00 0.00 0.00 3.18
366 378 5.467399 TGTTCGACCGTAAAGATTGTTGATT 59.533 36.000 0.00 0.00 0.00 2.57
374 386 4.450080 GTCCTTTTGTTCGACCGTAAAGAT 59.550 41.667 8.35 0.00 0.00 2.40
380 392 2.996444 GGTCCTTTTGTTCGACCGT 58.004 52.632 0.00 0.00 36.97 4.83
389 401 2.572290 AGTCGGAGTTTGGTCCTTTTG 58.428 47.619 0.00 0.00 34.00 2.44
492 516 1.495951 GCACGTTAAAGAGGGTGCG 59.504 57.895 0.00 0.00 45.13 5.34
494 518 1.908066 GCCGCACGTTAAAGAGGGTG 61.908 60.000 0.00 0.00 0.00 4.61
495 519 1.670083 GCCGCACGTTAAAGAGGGT 60.670 57.895 0.00 0.00 0.00 4.34
496 520 2.396157 GGCCGCACGTTAAAGAGGG 61.396 63.158 0.00 0.00 0.00 4.30
700 736 1.499688 GCGGGCTTTTATCGGAGCTC 61.500 60.000 4.71 4.71 38.89 4.09
818 875 2.125753 GACACAGGAGCAGCGAGG 60.126 66.667 0.00 0.00 0.00 4.63
819 876 0.735632 GAAGACACAGGAGCAGCGAG 60.736 60.000 0.00 0.00 0.00 5.03
820 877 1.181741 AGAAGACACAGGAGCAGCGA 61.182 55.000 0.00 0.00 0.00 4.93
821 878 0.320247 AAGAAGACACAGGAGCAGCG 60.320 55.000 0.00 0.00 0.00 5.18
830 887 0.110486 GGAAGGGGCAAGAAGACACA 59.890 55.000 0.00 0.00 0.00 3.72
832 889 1.374947 CGGAAGGGGCAAGAAGACA 59.625 57.895 0.00 0.00 0.00 3.41
913 972 1.574263 AGGTCAAGAAGGCTAGGACC 58.426 55.000 15.11 15.11 43.67 4.46
1197 1260 0.104304 ATCCGGGAAAGAATCGGTCG 59.896 55.000 0.00 0.00 43.75 4.79
1198 1261 2.158943 AGAATCCGGGAAAGAATCGGTC 60.159 50.000 0.00 0.00 43.75 4.79
1199 1262 1.838077 AGAATCCGGGAAAGAATCGGT 59.162 47.619 0.00 0.00 43.75 4.69
1200 1263 2.622064 AGAATCCGGGAAAGAATCGG 57.378 50.000 0.00 0.00 44.59 4.18
1201 1264 3.001330 CGAAAGAATCCGGGAAAGAATCG 59.999 47.826 0.00 5.70 0.00 3.34
1206 1269 2.973945 AGACGAAAGAATCCGGGAAAG 58.026 47.619 0.00 0.00 0.00 2.62
1212 1275 2.726066 GCAAGCAAGACGAAAGAATCCG 60.726 50.000 0.00 0.00 0.00 4.18
1232 1295 0.719465 CACCACGACCACGAATAAGC 59.281 55.000 0.00 0.00 42.66 3.09
1233 1296 1.355971 CCACCACGACCACGAATAAG 58.644 55.000 0.00 0.00 42.66 1.73
1235 1298 1.079681 GCCACCACGACCACGAATA 60.080 57.895 0.00 0.00 42.66 1.75
1236 1299 2.358247 GCCACCACGACCACGAAT 60.358 61.111 0.00 0.00 42.66 3.34
1242 1305 2.845752 TTATCTGCGCCACCACGACC 62.846 60.000 4.18 0.00 34.06 4.79
1243 1306 1.017177 TTTATCTGCGCCACCACGAC 61.017 55.000 4.18 0.00 34.06 4.34
1244 1307 0.739462 CTTTATCTGCGCCACCACGA 60.739 55.000 4.18 0.00 34.06 4.35
1245 1308 0.739462 TCTTTATCTGCGCCACCACG 60.739 55.000 4.18 0.00 0.00 4.94
1333 1426 4.731853 TGGGCGAGGGATGGTGGA 62.732 66.667 0.00 0.00 0.00 4.02
1352 1445 0.969894 AACTCTCTCGACTTGTGGGG 59.030 55.000 0.00 0.00 0.00 4.96
1552 1686 1.467374 CGCGGCAGAAATAGGTTTTGG 60.467 52.381 0.00 0.00 0.00 3.28
1557 1696 1.144057 CTCCGCGGCAGAAATAGGT 59.856 57.895 23.51 0.00 0.00 3.08
1558 1697 0.876342 GTCTCCGCGGCAGAAATAGG 60.876 60.000 23.51 1.60 0.00 2.57
1559 1698 1.209275 CGTCTCCGCGGCAGAAATAG 61.209 60.000 23.51 11.25 0.00 1.73
1560 1699 1.226859 CGTCTCCGCGGCAGAAATA 60.227 57.895 23.51 0.00 0.00 1.40
1561 1700 2.298158 ATCGTCTCCGCGGCAGAAAT 62.298 55.000 23.51 16.60 0.00 2.17
1565 1704 2.050895 CTATCGTCTCCGCGGCAG 60.051 66.667 23.51 18.77 0.00 4.85
1566 1705 2.946172 TACCTATCGTCTCCGCGGCA 62.946 60.000 23.51 6.36 0.00 5.69
1567 1706 2.185103 CTACCTATCGTCTCCGCGGC 62.185 65.000 23.51 5.56 0.00 6.53
1568 1707 0.602106 TCTACCTATCGTCTCCGCGG 60.602 60.000 22.12 22.12 0.00 6.46
1569 1708 1.194997 CTTCTACCTATCGTCTCCGCG 59.805 57.143 0.00 0.00 0.00 6.46
1610 1749 2.596904 TATTCAAGGCGGACTGCTAC 57.403 50.000 6.16 0.00 45.43 3.58
1611 1750 2.419574 GGTTATTCAAGGCGGACTGCTA 60.420 50.000 6.16 0.00 45.43 3.49
1612 1751 1.679032 GGTTATTCAAGGCGGACTGCT 60.679 52.381 6.16 0.00 45.43 4.24
1622 1764 1.202290 GCATGTGGGCGGTTATTCAAG 60.202 52.381 0.00 0.00 0.00 3.02
1683 1846 0.391597 TCACCTCGAGCGTTCCTTTT 59.608 50.000 6.99 0.00 0.00 2.27
1707 1870 1.272480 TGTCTGTCTGGCTGGCTAGTA 60.272 52.381 2.00 0.00 0.00 1.82
1708 1871 0.542938 TGTCTGTCTGGCTGGCTAGT 60.543 55.000 2.00 0.00 0.00 2.57
1709 1872 0.610174 TTGTCTGTCTGGCTGGCTAG 59.390 55.000 2.00 0.00 0.00 3.42
1710 1873 1.065926 CATTGTCTGTCTGGCTGGCTA 60.066 52.381 2.00 0.00 0.00 3.93
1711 1874 0.322277 CATTGTCTGTCTGGCTGGCT 60.322 55.000 2.00 0.00 0.00 4.75
1712 1875 0.321919 TCATTGTCTGTCTGGCTGGC 60.322 55.000 0.00 0.00 0.00 4.85
1713 1876 2.189594 TTCATTGTCTGTCTGGCTGG 57.810 50.000 0.00 0.00 0.00 4.85
1714 1877 4.778534 AAATTCATTGTCTGTCTGGCTG 57.221 40.909 0.00 0.00 0.00 4.85
1715 1878 5.075493 AGAAAATTCATTGTCTGTCTGGCT 58.925 37.500 0.00 0.00 33.20 4.75
1716 1879 5.382618 AGAAAATTCATTGTCTGTCTGGC 57.617 39.130 0.00 0.00 33.20 4.85
1721 1884 6.431234 GTCTGGGTAGAAAATTCATTGTCTGT 59.569 38.462 2.84 0.00 35.24 3.41
1745 1908 2.754664 CTTGCCCTTTCCTGCTCCGT 62.755 60.000 0.00 0.00 0.00 4.69
1822 1986 3.009723 CGCCCTGGTATAATAATGCTGG 58.990 50.000 0.00 0.00 0.00 4.85
1869 2033 5.419542 TCTCAATGGCCGCATTAGTATATC 58.580 41.667 0.00 0.00 0.00 1.63
1870 2034 5.420725 TCTCAATGGCCGCATTAGTATAT 57.579 39.130 0.00 0.00 0.00 0.86
1878 2042 2.422303 CCAATCTCAATGGCCGCAT 58.578 52.632 0.00 0.00 0.00 4.73
1922 2089 4.526650 AGGGACAGTGTTTTGTTTTCTTGT 59.473 37.500 0.00 0.00 0.00 3.16
1949 2116 3.067180 CAGATGTGACAGCCAGTGTTTTT 59.933 43.478 0.00 0.00 40.56 1.94
1950 2117 2.620115 CAGATGTGACAGCCAGTGTTTT 59.380 45.455 0.00 0.00 40.56 2.43
1951 2118 2.158769 TCAGATGTGACAGCCAGTGTTT 60.159 45.455 0.00 0.00 40.56 2.83
1952 2119 1.417517 TCAGATGTGACAGCCAGTGTT 59.582 47.619 0.00 0.00 40.56 3.32
1953 2120 1.051008 TCAGATGTGACAGCCAGTGT 58.949 50.000 0.00 0.00 44.49 3.55
2004 2172 3.378512 AGCATGATCTTGACTAGGACCA 58.621 45.455 12.54 0.00 0.00 4.02
2005 2173 5.293560 GTTAGCATGATCTTGACTAGGACC 58.706 45.833 12.54 0.00 0.00 4.46
2006 2174 5.069781 AGGTTAGCATGATCTTGACTAGGAC 59.930 44.000 12.54 8.66 0.00 3.85
2007 2175 5.069648 CAGGTTAGCATGATCTTGACTAGGA 59.930 44.000 12.54 0.00 0.00 2.94
2008 2176 5.069648 TCAGGTTAGCATGATCTTGACTAGG 59.930 44.000 12.54 5.39 29.72 3.02
2126 2305 1.400494 GTTATTGCTAACACAGGGCGG 59.600 52.381 0.00 0.00 37.70 6.13
2127 2306 2.356135 AGTTATTGCTAACACAGGGCG 58.644 47.619 0.00 0.00 39.81 6.13
2211 2396 4.387862 CACAAACGATAAACTAGACGGCTT 59.612 41.667 0.00 0.00 0.00 4.35
2246 2431 0.538287 GGCTTGCAGGACCAAGAAGT 60.538 55.000 0.00 0.00 43.79 3.01
2249 2434 0.322816 GATGGCTTGCAGGACCAAGA 60.323 55.000 14.14 0.00 43.79 3.02
2309 2504 3.838903 AGTCGGTTTGGTTCTTATCCTCT 59.161 43.478 0.00 0.00 0.00 3.69
2329 2525 3.444916 CGTTGCAATCCTATCGTGTAGT 58.555 45.455 0.59 0.00 0.00 2.73
2349 2545 1.927174 CGTTTGGCACTTATCTCTCCG 59.073 52.381 0.00 0.00 0.00 4.63
2426 2622 3.118555 TCAAAAGAAACGGTCTGGTCTCA 60.119 43.478 0.00 0.00 36.40 3.27
2429 2625 3.002348 CACTCAAAAGAAACGGTCTGGTC 59.998 47.826 0.00 0.00 36.40 4.02
2432 2628 4.588278 GAACACTCAAAAGAAACGGTCTG 58.412 43.478 0.00 0.00 36.40 3.51
2491 2687 2.225467 GAAGCCTAACATGGATGGAGC 58.775 52.381 0.00 0.00 0.00 4.70
2520 2733 4.969484 TCGCTTTCCTAACCTTTCTTTCT 58.031 39.130 0.00 0.00 0.00 2.52
2554 2767 6.523840 ACCAAATTTCTAATGCTTTGCTTCA 58.476 32.000 0.00 0.00 0.00 3.02
2648 2861 2.306341 CTGGTACTGCATCTCCAGTG 57.694 55.000 17.51 0.00 45.17 3.66
2709 2924 3.367630 CCGTGCAATTTTATGTTTCAGGC 59.632 43.478 0.00 0.00 0.00 4.85
2717 2932 5.698832 TCTGTTTCTCCGTGCAATTTTATG 58.301 37.500 0.00 0.00 0.00 1.90
2763 2979 8.466798 GCCTGATTGCTTAACCTCTTTAATTAA 58.533 33.333 0.00 0.00 0.00 1.40
2764 2980 7.613801 TGCCTGATTGCTTAACCTCTTTAATTA 59.386 33.333 0.00 0.00 0.00 1.40
2765 2981 6.437162 TGCCTGATTGCTTAACCTCTTTAATT 59.563 34.615 0.00 0.00 0.00 1.40
2766 2982 5.951747 TGCCTGATTGCTTAACCTCTTTAAT 59.048 36.000 0.00 0.00 0.00 1.40
2767 2983 5.321102 TGCCTGATTGCTTAACCTCTTTAA 58.679 37.500 0.00 0.00 0.00 1.52
2768 2984 4.917385 TGCCTGATTGCTTAACCTCTTTA 58.083 39.130 0.00 0.00 0.00 1.85
2769 2985 3.766545 TGCCTGATTGCTTAACCTCTTT 58.233 40.909 0.00 0.00 0.00 2.52
2803 3019 2.775384 AGGATAAAGTGGGCGTGGATAA 59.225 45.455 0.00 0.00 0.00 1.75
2850 3066 0.111253 ACCTGCAGAAGAAGGGTTGG 59.889 55.000 17.39 0.00 45.98 3.77
2853 3069 0.538287 GCAACCTGCAGAAGAAGGGT 60.538 55.000 17.39 0.00 43.46 4.34
2952 3168 1.262417 TCACAGTGGGAGCGTATGAA 58.738 50.000 0.00 0.00 0.00 2.57
3072 3290 5.471456 GCAATAGCTTACAGCATCCATTAGT 59.529 40.000 0.00 0.00 45.56 2.24
3183 3401 6.051717 CGGAAGAATGTCAGGTCTTAATCAT 58.948 40.000 2.35 0.00 34.23 2.45
3213 3431 0.105039 GGACATTCTCGGGCTACAGG 59.895 60.000 0.00 0.00 0.00 4.00
3243 3461 4.601857 TCAGAGACCTTTATGTTCCCCTTT 59.398 41.667 0.00 0.00 0.00 3.11
3246 3464 4.779993 ATCAGAGACCTTTATGTTCCCC 57.220 45.455 0.00 0.00 0.00 4.81
3465 3684 5.189180 AGTAAGCAGAAGAATCATGAACCC 58.811 41.667 0.00 0.00 0.00 4.11
3555 3780 4.344968 CCACAGGACCATACATCTGACATA 59.655 45.833 0.00 0.00 0.00 2.29
3847 4077 2.238646 TGAACCAATCGTGCTCCCTTAT 59.761 45.455 0.00 0.00 0.00 1.73
4008 4238 4.112634 TGAAGTTCAGTCTTTGTCACTCG 58.887 43.478 0.08 0.00 0.00 4.18
4050 4283 2.033801 CGGGATTGTCTTGAATGCCATC 59.966 50.000 0.00 0.00 42.47 3.51
4067 4300 0.617935 TCATCTGGTTGATTGCGGGA 59.382 50.000 0.00 0.00 32.05 5.14
4297 4663 6.598525 TGTTGTTTGACGTGCTTATTATCTG 58.401 36.000 0.00 0.00 0.00 2.90
4311 4677 6.654793 TGCCTAACATTTTTGTTGTTTGAC 57.345 33.333 1.76 0.00 38.26 3.18
4312 4678 7.335422 ACATTGCCTAACATTTTTGTTGTTTGA 59.665 29.630 1.76 0.00 38.26 2.69
4367 4733 5.301551 ACAACAATCAGTGGCTTTGTCAATA 59.698 36.000 7.25 0.00 32.66 1.90
4369 4735 3.446873 ACAACAATCAGTGGCTTTGTCAA 59.553 39.130 7.25 0.00 32.66 3.18
4396 4762 3.551890 CGCAGTGAGGACATGTACATAAC 59.448 47.826 11.55 5.29 0.00 1.89
4456 4833 1.975680 TGAGTTTAGTGGAGGGTCACC 59.024 52.381 0.00 0.00 38.34 4.02
4481 4858 2.421424 GACATCCTGCAATGAAGTCACC 59.579 50.000 13.43 0.00 31.05 4.02
4505 4882 5.990996 TGATGCAAATCTGGTTTTTCTTTCC 59.009 36.000 0.00 0.00 0.00 3.13
4665 5042 7.048629 TGTACACAATCCATTGAAACAATGT 57.951 32.000 18.69 2.04 40.14 2.71
4718 5096 8.867935 GCTGTAGAACATGATAATATAGCTGTG 58.132 37.037 0.00 0.00 30.61 3.66
4871 5256 7.283127 TGAAATGGAAGCTGTATTGGATAGTTC 59.717 37.037 0.00 0.00 0.00 3.01
4911 5296 2.566833 TGCAGCAATGTCTAACAGGT 57.433 45.000 0.00 0.00 0.00 4.00
5073 5462 9.405587 GTGACCGAAATGATCAAGAAATAAAAA 57.594 29.630 0.00 0.00 0.00 1.94
5074 5463 8.572185 TGTGACCGAAATGATCAAGAAATAAAA 58.428 29.630 0.00 0.00 0.00 1.52
5424 5829 7.405292 ACTATCATGAACCATCCAAGAGAAAA 58.595 34.615 0.00 0.00 0.00 2.29
5651 6057 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5652 6058 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5653 6059 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5654 6060 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5655 6061 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5673 6079 9.351570 AGATTACTAAAGTAGTGTTCTAAACGC 57.648 33.333 0.00 0.00 39.81 4.84
5715 6121 8.780003 TCTTCTATAGTACTCCCTCTGTAAACT 58.220 37.037 0.00 0.00 0.00 2.66
5716 6122 8.977267 TCTTCTATAGTACTCCCTCTGTAAAC 57.023 38.462 0.00 0.00 0.00 2.01
5718 6124 9.575868 CAATCTTCTATAGTACTCCCTCTGTAA 57.424 37.037 0.00 0.00 0.00 2.41
5719 6125 8.725256 ACAATCTTCTATAGTACTCCCTCTGTA 58.275 37.037 0.00 0.00 0.00 2.74
5720 6126 7.588169 ACAATCTTCTATAGTACTCCCTCTGT 58.412 38.462 0.00 0.00 0.00 3.41
5721 6127 8.472007 AACAATCTTCTATAGTACTCCCTCTG 57.528 38.462 0.00 0.00 0.00 3.35
5722 6128 8.507761 AGAACAATCTTCTATAGTACTCCCTCT 58.492 37.037 0.00 0.00 29.15 3.69
5723 6129 8.700439 AGAACAATCTTCTATAGTACTCCCTC 57.300 38.462 0.00 0.00 29.15 4.30
5830 6236 4.272261 GGTTTTGGTGTAGCAATTGTTTGG 59.728 41.667 7.40 0.00 33.22 3.28
6113 6519 5.474532 GGTATTGCAGGATATTGATGAGCAA 59.525 40.000 0.00 0.00 43.50 3.91
6128 6534 4.171005 CAATGACAAGCTTGGTATTGCAG 58.829 43.478 28.93 16.13 32.78 4.41
6193 6599 5.011943 AGGATTGAGGAGATCTACAAGATGC 59.988 44.000 7.93 3.02 34.53 3.91
6197 6603 4.022416 CCGAGGATTGAGGAGATCTACAAG 60.022 50.000 7.93 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.