Multiple sequence alignment - TraesCS5D01G228600

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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 TraesCS5D01G228600 chr5D 100.000 3633 0 0 1 3633 335878564 335874932 0.000000e+00 6709
1 TraesCS5D01G228600 chr5A 89.565 1447 87 24 2236 3633 437039502 437038071 0.000000e+00 1777
2 TraesCS5D01G228600 chr5A 96.712 517 17 0 1001 1517 437040883 437040367 0.000000e+00 861
3 TraesCS5D01G228600 chr5A 81.445 609 36 24 323 906 437041779 437041223 9.320000e-116 427
4 TraesCS5D01G228600 chr5A 89.231 260 17 4 1988 2236 437039788 437039529 7.570000e-82 315
5 TraesCS5D01G228600 chr5A 89.041 219 21 2 1626 1844 437040232 437040017 5.980000e-68 268
6 TraesCS5D01G228600 chr5B 87.779 1342 75 36 1988 3266 393844295 393842980 0.000000e+00 1487
7 TraesCS5D01G228600 chr5B 83.982 1592 86 63 1 1517 393846365 393844868 0.000000e+00 1371
8 TraesCS5D01G228600 chr5B 90.582 361 31 3 3266 3624 393839169 393838810 3.280000e-130 475
9 TraesCS5D01G228600 chr5B 87.927 381 32 9 1615 1988 393844701 393844328 1.550000e-118 436
10 TraesCS5D01G228600 chrUn 94.792 96 5 0 576 671 271164355 271164450 2.260000e-32 150


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 TraesCS5D01G228600 chr5D 335874932 335878564 3632 True 6709.00 6709 100.0000 1 3633 1 chr5D.!!$R1 3632
1 TraesCS5D01G228600 chr5A 437038071 437041779 3708 True 729.60 1777 89.1988 323 3633 5 chr5A.!!$R1 3310
2 TraesCS5D01G228600 chr5B 393838810 393846365 7555 True 942.25 1487 87.5675 1 3624 4 chr5B.!!$R1 3623

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
141 146 0.250553 CTACCAAACGCCACTTCCCA 60.251 55.0 0.0 0.0 0.00 4.37 F
263 268 0.317603 CGACCGATGTGATACCCGTC 60.318 60.0 0.0 0.0 0.00 4.79 F
264 269 0.317603 GACCGATGTGATACCCGTCG 60.318 60.0 0.0 0.0 40.21 5.12 F
565 609 0.537188 AACAGTAGCGTCCCCTGATG 59.463 55.0 0.0 0.0 0.00 3.07 F
1847 2295 0.877071 AATTGCTCCACTTGCTCACG 59.123 50.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2629 0.674895 AAGCGTTGAGATGGAGGTGC 60.675 55.000 0.00 0.0 0.00 5.01 R
2256 2794 4.090642 GCCATCGCAAATAGAATAGTCGAG 59.909 45.833 0.00 0.0 34.03 4.04 R
2266 2804 1.159713 TCAGCCGCCATCGCAAATAG 61.160 55.000 0.00 0.0 34.03 1.73 R
2479 3022 1.208614 CTTCCAGTTGCGCTTGAGC 59.791 57.895 9.73 0.0 37.78 4.26 R
2697 3240 0.782384 AAACACGACGACGAAGATGC 59.218 50.000 15.32 0.0 42.66 3.91 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
58 63 0.928451 GCGTGCCTTGTTGACGAAAC 60.928 55.000 0.00 0.00 39.41 2.78
65 70 2.164624 CCTTGTTGACGAAACCAAACCA 59.835 45.455 0.00 0.00 38.06 3.67
67 72 1.133407 TGTTGACGAAACCAAACCAGC 59.867 47.619 0.00 0.00 38.06 4.85
71 76 2.338620 GAAACCAAACCAGCCGCC 59.661 61.111 0.00 0.00 0.00 6.13
76 81 3.291383 CAAACCAGCCGCCGGAAA 61.291 61.111 7.68 0.00 0.00 3.13
77 82 2.983592 AAACCAGCCGCCGGAAAG 60.984 61.111 7.68 0.00 0.00 2.62
82 87 4.101448 AGCCGCCGGAAAGCAGAT 62.101 61.111 7.68 0.00 0.00 2.90
83 88 2.203015 GCCGCCGGAAAGCAGATA 60.203 61.111 7.68 0.00 0.00 1.98
84 89 2.247437 GCCGCCGGAAAGCAGATAG 61.247 63.158 7.68 0.00 0.00 2.08
85 90 2.247437 CCGCCGGAAAGCAGATAGC 61.247 63.158 5.05 0.00 46.19 2.97
101 106 2.765807 GCTAGCCAGCCAGAGGGA 60.766 66.667 2.29 0.00 42.37 4.20
102 107 2.370445 GCTAGCCAGCCAGAGGGAA 61.370 63.158 2.29 0.00 42.37 3.97
103 108 1.915078 GCTAGCCAGCCAGAGGGAAA 61.915 60.000 2.29 0.00 42.37 3.13
104 109 0.842635 CTAGCCAGCCAGAGGGAAAT 59.157 55.000 0.00 0.00 35.59 2.17
105 110 0.548031 TAGCCAGCCAGAGGGAAATG 59.452 55.000 0.00 0.00 35.59 2.32
106 111 1.210204 AGCCAGCCAGAGGGAAATGA 61.210 55.000 0.00 0.00 35.59 2.57
116 121 5.053145 CCAGAGGGAAATGAGAAATCGTAG 58.947 45.833 0.00 0.00 35.59 3.51
120 125 6.608002 AGAGGGAAATGAGAAATCGTAGTAGT 59.392 38.462 0.00 0.00 0.00 2.73
121 126 6.574350 AGGGAAATGAGAAATCGTAGTAGTG 58.426 40.000 0.00 0.00 0.00 2.74
141 146 0.250553 CTACCAAACGCCACTTCCCA 60.251 55.000 0.00 0.00 0.00 4.37
145 150 2.184167 AAACGCCACTTCCCACACG 61.184 57.895 0.00 0.00 0.00 4.49
167 172 2.358737 CTGGAACCTCGTGCCACC 60.359 66.667 0.00 0.00 36.10 4.61
170 175 1.966451 GGAACCTCGTGCCACCTTG 60.966 63.158 0.00 0.00 29.85 3.61
181 186 3.726517 CACCTTGGACGCGGCAAG 61.727 66.667 17.00 15.56 0.00 4.01
207 212 0.893727 ACAAGTCAAACCCGCCATCC 60.894 55.000 0.00 0.00 0.00 3.51
218 223 3.869272 GCCATCCGCTTCGTGCAG 61.869 66.667 0.00 0.00 43.06 4.41
220 225 3.120385 CATCCGCTTCGTGCAGCA 61.120 61.111 0.00 0.00 43.06 4.41
221 226 2.816958 ATCCGCTTCGTGCAGCAG 60.817 61.111 0.00 0.00 43.06 4.24
260 265 2.589798 TTTCGACCGATGTGATACCC 57.410 50.000 0.00 0.00 0.00 3.69
261 266 0.382873 TTCGACCGATGTGATACCCG 59.617 55.000 0.00 0.00 0.00 5.28
262 267 0.749091 TCGACCGATGTGATACCCGT 60.749 55.000 0.00 0.00 0.00 5.28
263 268 0.317603 CGACCGATGTGATACCCGTC 60.318 60.000 0.00 0.00 0.00 4.79
264 269 0.317603 GACCGATGTGATACCCGTCG 60.318 60.000 0.00 0.00 40.21 5.12
265 270 4.628160 CGATGTGATACCCGTCGG 57.372 61.111 3.60 3.60 37.62 4.79
282 287 1.068474 CGGGTTTTGCTCTCGTACTG 58.932 55.000 0.00 0.00 0.00 2.74
291 302 4.212143 TGCTCTCGTACTGGTACTAGAA 57.788 45.455 13.86 1.56 37.40 2.10
292 303 4.778579 TGCTCTCGTACTGGTACTAGAAT 58.221 43.478 13.86 0.00 37.40 2.40
319 330 4.357018 CAGAATGCAGTCGTCTGTAGTA 57.643 45.455 8.74 0.00 43.05 1.82
320 331 4.346970 CAGAATGCAGTCGTCTGTAGTAG 58.653 47.826 8.74 0.00 43.05 2.57
321 332 4.011023 AGAATGCAGTCGTCTGTAGTAGT 58.989 43.478 8.74 0.00 43.05 2.73
333 344 7.805071 GTCGTCTGTAGTAGTAGTAGATCTCTC 59.195 44.444 0.00 0.00 0.00 3.20
334 345 7.040478 TCGTCTGTAGTAGTAGTAGATCTCTCC 60.040 44.444 0.00 0.00 0.00 3.71
340 351 5.837979 AGTAGTAGTAGATCTCTCCGGTGTA 59.162 44.000 0.00 0.00 0.00 2.90
341 352 4.959723 AGTAGTAGATCTCTCCGGTGTAC 58.040 47.826 0.00 0.00 0.00 2.90
396 411 4.627447 ACGTGCGTGCGACGGTAA 62.627 61.111 16.74 0.00 42.82 2.85
397 412 3.176578 CGTGCGTGCGACGGTAAT 61.177 61.111 10.02 0.00 42.82 1.89
401 416 1.126479 GTGCGTGCGACGGTAATTTTA 59.874 47.619 10.02 0.00 42.82 1.52
402 417 1.390803 TGCGTGCGACGGTAATTTTAG 59.609 47.619 10.02 0.00 42.82 1.85
403 418 1.849348 GCGTGCGACGGTAATTTTAGC 60.849 52.381 10.02 0.00 42.82 3.09
404 419 1.390803 CGTGCGACGGTAATTTTAGCA 59.609 47.619 0.00 0.00 38.08 3.49
405 420 2.765918 GTGCGACGGTAATTTTAGCAC 58.234 47.619 0.00 1.93 44.85 4.40
406 421 1.733360 TGCGACGGTAATTTTAGCACC 59.267 47.619 0.00 0.00 0.00 5.01
488 532 1.006391 CACACACACTTCGTTGTCGTC 60.006 52.381 0.00 0.00 38.33 4.20
562 606 0.608640 AAGAACAGTAGCGTCCCCTG 59.391 55.000 0.00 0.00 0.00 4.45
565 609 0.537188 AACAGTAGCGTCCCCTGATG 59.463 55.000 0.00 0.00 0.00 3.07
573 617 1.379044 GTCCCCTGATGGCCACAAG 60.379 63.158 8.16 8.82 0.00 3.16
709 760 1.024579 AATAGTTTCCGTGCCCAGCG 61.025 55.000 0.00 0.00 0.00 5.18
712 763 2.975799 TTTCCGTGCCCAGCGAAC 60.976 61.111 0.00 0.00 0.00 3.95
751 813 4.697756 CACGCCCCTTTCCGCTCA 62.698 66.667 0.00 0.00 0.00 4.26
757 819 2.317609 CCCTTTCCGCTCACACACG 61.318 63.158 0.00 0.00 0.00 4.49
758 820 1.300620 CCTTTCCGCTCACACACGA 60.301 57.895 0.00 0.00 0.00 4.35
759 821 0.878523 CCTTTCCGCTCACACACGAA 60.879 55.000 0.00 0.00 0.00 3.85
760 822 0.934496 CTTTCCGCTCACACACGAAA 59.066 50.000 0.00 0.00 0.00 3.46
761 823 1.329292 CTTTCCGCTCACACACGAAAA 59.671 47.619 0.00 0.00 0.00 2.29
762 824 1.370609 TTCCGCTCACACACGAAAAA 58.629 45.000 0.00 0.00 0.00 1.94
763 825 0.934496 TCCGCTCACACACGAAAAAG 59.066 50.000 0.00 0.00 0.00 2.27
844 916 2.235402 ACACACCCCCTCTACAAATACG 59.765 50.000 0.00 0.00 0.00 3.06
866 943 1.451927 CCACCACCATCCCACATCG 60.452 63.158 0.00 0.00 0.00 3.84
933 1014 2.127003 CCTTTCGAAAACCGCCGC 60.127 61.111 12.41 0.00 38.37 6.53
934 1015 2.498887 CTTTCGAAAACCGCCGCG 60.499 61.111 12.41 5.59 38.37 6.46
935 1016 4.669874 TTTCGAAAACCGCCGCGC 62.670 61.111 8.44 0.00 38.37 6.86
980 1061 4.383602 CCAAGAAACCGCACGCCG 62.384 66.667 0.00 0.00 0.00 6.46
981 1062 3.342627 CAAGAAACCGCACGCCGA 61.343 61.111 0.00 0.00 40.02 5.54
1041 1367 1.301009 GATCGGGATCCTGAACGCC 60.301 63.158 27.03 12.61 34.70 5.68
1042 1368 2.028125 GATCGGGATCCTGAACGCCA 62.028 60.000 27.03 3.40 34.70 5.69
1065 1391 3.068691 TTCCTCCTCTCGGTGCCG 61.069 66.667 3.94 3.94 41.35 5.69
1185 1511 4.162690 GTCTCCATCGCGGGGCTT 62.163 66.667 6.13 0.00 33.78 4.35
1413 1739 4.169452 TGGAACAGGATCAGGGGG 57.831 61.111 0.00 0.00 0.00 5.40
1461 1787 2.419739 GCTCGAGGACAGGAGGGAC 61.420 68.421 15.58 0.00 0.00 4.46
1464 1790 2.701780 CGAGGACAGGAGGGACACG 61.702 68.421 0.00 0.00 0.00 4.49
1465 1791 2.283966 AGGACAGGAGGGACACGG 60.284 66.667 0.00 0.00 0.00 4.94
1539 1921 7.613585 TCATTTCATGCCTGACAATAACAAAT 58.386 30.769 0.00 0.00 0.00 2.32
1541 1923 5.581126 TCATGCCTGACAATAACAAATCC 57.419 39.130 0.00 0.00 0.00 3.01
1543 1925 4.782019 TGCCTGACAATAACAAATCCAC 57.218 40.909 0.00 0.00 0.00 4.02
1546 1928 3.440173 CCTGACAATAACAAATCCACGCT 59.560 43.478 0.00 0.00 0.00 5.07
1578 1960 6.381481 TTTGATCATCCGAGATGAATTTGG 57.619 37.500 16.96 0.00 0.00 3.28
1582 1964 7.053498 TGATCATCCGAGATGAATTTGGTTAA 58.947 34.615 16.96 0.00 0.00 2.01
1584 1966 7.083875 TCATCCGAGATGAATTTGGTTAAAC 57.916 36.000 12.41 0.00 0.00 2.01
1585 1967 6.884295 TCATCCGAGATGAATTTGGTTAAACT 59.116 34.615 12.41 0.00 0.00 2.66
1587 1969 7.843490 TCCGAGATGAATTTGGTTAAACTAG 57.157 36.000 0.00 0.00 0.00 2.57
1588 1970 7.391620 TCCGAGATGAATTTGGTTAAACTAGT 58.608 34.615 0.00 0.00 0.00 2.57
1589 1971 7.881232 TCCGAGATGAATTTGGTTAAACTAGTT 59.119 33.333 1.12 1.12 0.00 2.24
1613 2023 5.234752 AGTTTTTCCAACCTGTGTTTGAAC 58.765 37.500 0.00 0.00 36.26 3.18
1615 2025 5.476091 TTTTCCAACCTGTGTTTGAACTT 57.524 34.783 0.00 0.00 36.26 2.66
1616 2026 5.476091 TTTCCAACCTGTGTTTGAACTTT 57.524 34.783 0.00 0.00 36.26 2.66
1617 2027 4.448537 TCCAACCTGTGTTTGAACTTTG 57.551 40.909 0.00 0.00 30.42 2.77
1618 2028 4.082845 TCCAACCTGTGTTTGAACTTTGA 58.917 39.130 0.00 0.00 30.42 2.69
1619 2029 4.524714 TCCAACCTGTGTTTGAACTTTGAA 59.475 37.500 0.00 0.00 30.42 2.69
1620 2030 5.186797 TCCAACCTGTGTTTGAACTTTGAAT 59.813 36.000 0.00 0.00 30.42 2.57
1621 2031 5.519927 CCAACCTGTGTTTGAACTTTGAATC 59.480 40.000 0.00 0.00 30.42 2.52
1622 2032 5.913137 ACCTGTGTTTGAACTTTGAATCA 57.087 34.783 0.00 0.00 0.00 2.57
1623 2033 5.894807 ACCTGTGTTTGAACTTTGAATCAG 58.105 37.500 0.00 0.00 0.00 2.90
1628 2038 7.424803 TGTGTTTGAACTTTGAATCAGTATGG 58.575 34.615 0.00 0.00 36.16 2.74
1636 2046 9.346725 GAACTTTGAATCAGTATGGAAAATGAC 57.653 33.333 0.00 0.00 36.16 3.06
1659 2069 3.386486 TCTTTTTCACGTGTCTGCGTAT 58.614 40.909 16.51 0.00 43.83 3.06
1683 2093 2.287909 GCTCGCCGAGATATTTCTGACT 60.288 50.000 20.05 0.00 30.30 3.41
1685 2095 4.717991 CTCGCCGAGATATTTCTGACTAG 58.282 47.826 8.82 0.00 30.30 2.57
1689 2099 4.082463 GCCGAGATATTTCTGACTAGGGAG 60.082 50.000 0.00 0.00 30.30 4.30
1690 2100 4.461081 CCGAGATATTTCTGACTAGGGAGG 59.539 50.000 0.00 0.00 30.30 4.30
1699 2109 3.399644 TCTGACTAGGGAGGAGGATAAGG 59.600 52.174 0.00 0.00 0.00 2.69
1700 2110 2.158295 TGACTAGGGAGGAGGATAAGGC 60.158 54.545 0.00 0.00 0.00 4.35
1701 2111 1.866943 ACTAGGGAGGAGGATAAGGCA 59.133 52.381 0.00 0.00 0.00 4.75
1702 2112 2.158234 ACTAGGGAGGAGGATAAGGCAG 60.158 54.545 0.00 0.00 0.00 4.85
1708 2118 3.827876 GGAGGAGGATAAGGCAGTAGTAC 59.172 52.174 0.00 0.00 0.00 2.73
1712 2122 4.471548 GAGGATAAGGCAGTAGTACCTCA 58.528 47.826 0.00 0.00 41.28 3.86
1736 2146 2.545106 CCCAAAGTCAACAAATTGCAGC 59.455 45.455 0.00 0.00 35.63 5.25
1767 2177 6.974932 ATTGTAGTAGCACAACTTGATCTG 57.025 37.500 0.00 0.00 41.02 2.90
1832 2242 6.825213 TCATGTAGAGAGGGTCAATCAAATTG 59.175 38.462 0.00 0.00 41.57 2.32
1846 2294 2.294233 TCAAATTGCTCCACTTGCTCAC 59.706 45.455 0.00 0.00 0.00 3.51
1847 2295 0.877071 AATTGCTCCACTTGCTCACG 59.123 50.000 0.00 0.00 0.00 4.35
1884 2335 7.923414 AATCAACTAGTCCCAACTTCATTAC 57.077 36.000 0.00 0.00 36.92 1.89
1885 2336 5.801380 TCAACTAGTCCCAACTTCATTACC 58.199 41.667 0.00 0.00 36.92 2.85
1892 2349 4.013728 TCCCAACTTCATTACCATTTCCG 58.986 43.478 0.00 0.00 0.00 4.30
1893 2350 3.428862 CCCAACTTCATTACCATTTCCGC 60.429 47.826 0.00 0.00 0.00 5.54
1943 2409 7.750229 AGTAAAGAAATCATCAAGTGCAGAA 57.250 32.000 0.00 0.00 0.00 3.02
1944 2410 7.814642 AGTAAAGAAATCATCAAGTGCAGAAG 58.185 34.615 0.00 0.00 0.00 2.85
1958 2424 5.990408 AGTGCAGAAGAACGTTTTGAATAG 58.010 37.500 0.46 0.00 0.00 1.73
1959 2425 4.613031 GTGCAGAAGAACGTTTTGAATAGC 59.387 41.667 0.46 2.32 0.00 2.97
1974 2440 9.090692 GTTTTGAATAGCAGCAATGTTTGATAT 57.909 29.630 0.00 0.00 0.00 1.63
1980 2446 4.280174 AGCAGCAATGTTTGATATGATCCC 59.720 41.667 0.00 0.00 0.00 3.85
2009 2508 2.749621 GTCAACGGATTGCTCCTGATTT 59.250 45.455 0.00 0.00 39.65 2.17
2010 2509 3.191371 GTCAACGGATTGCTCCTGATTTT 59.809 43.478 0.00 0.00 39.65 1.82
2048 2547 2.282462 AAAGCAACCCTCAGGCCG 60.282 61.111 0.00 0.00 36.11 6.13
2191 2701 1.804151 GGTCGCACAATTCAACTGCTA 59.196 47.619 0.00 0.00 0.00 3.49
2216 2726 8.649973 ACGTGACCAAATTATCTCTTTCTATC 57.350 34.615 0.00 0.00 0.00 2.08
2217 2727 8.478877 ACGTGACCAAATTATCTCTTTCTATCT 58.521 33.333 0.00 0.00 0.00 1.98
2256 2794 8.727910 ACGAGGGTCAGAAAAGAAATAATTTAC 58.272 33.333 0.00 0.00 0.00 2.01
2279 2822 3.987868 TCGACTATTCTATTTGCGATGGC 59.012 43.478 0.00 0.00 40.52 4.40
2303 2846 4.142513 GGCTGACTGACCATTTCATCTTTC 60.143 45.833 0.00 0.00 32.17 2.62
2309 2852 2.428530 GACCATTTCATCTTTCCCTGCC 59.571 50.000 0.00 0.00 0.00 4.85
2681 3224 2.189594 TGGATTGGATGGATGCGATC 57.810 50.000 0.73 0.73 38.05 3.69
2682 3225 1.081892 GGATTGGATGGATGCGATCG 58.918 55.000 11.69 11.69 39.23 3.69
2683 3226 1.609061 GGATTGGATGGATGCGATCGT 60.609 52.381 17.81 0.00 39.23 3.73
2684 3227 1.728971 GATTGGATGGATGCGATCGTC 59.271 52.381 17.81 7.09 30.85 4.20
2685 3228 0.752658 TTGGATGGATGCGATCGTCT 59.247 50.000 17.81 3.95 0.00 4.18
2697 3240 1.457738 GATCGTCTCGTCGTGTCATG 58.542 55.000 0.00 0.00 0.00 3.07
2699 3242 1.442017 CGTCTCGTCGTGTCATGCA 60.442 57.895 0.00 0.00 0.00 3.96
2700 3243 0.798389 CGTCTCGTCGTGTCATGCAT 60.798 55.000 0.00 0.00 0.00 3.96
2701 3244 0.917259 GTCTCGTCGTGTCATGCATC 59.083 55.000 0.00 0.00 0.00 3.91
2705 3248 0.295763 CGTCGTGTCATGCATCTTCG 59.704 55.000 0.00 0.00 0.00 3.79
2714 3257 0.109272 ATGCATCTTCGTCGTCGTGT 60.109 50.000 1.33 0.00 38.33 4.49
2806 3361 1.685765 CCGTGGTCATGAGGAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
2974 3536 7.865706 ACTCACAAAGTCACAAGTTTATTCT 57.134 32.000 0.00 0.00 30.02 2.40
2975 3537 8.958119 ACTCACAAAGTCACAAGTTTATTCTA 57.042 30.769 0.00 0.00 30.02 2.10
2999 3561 2.539346 TTCGCTCGTGAAGTAGTAGC 57.461 50.000 0.00 0.00 0.00 3.58
3019 3585 7.310664 AGTAGCATTCATTTTGACATCAAGTG 58.689 34.615 0.00 0.00 37.15 3.16
3049 3618 0.251787 GAAAAGTCACCAGGGGGCAT 60.252 55.000 0.00 0.00 37.90 4.40
3057 3627 0.614697 ACCAGGGGGCATAAAACTGC 60.615 55.000 0.00 0.00 41.53 4.40
3092 3662 7.512297 CATCAAGTGTTTTAAATGGTTGATGC 58.488 34.615 19.45 0.00 41.46 3.91
3252 3838 3.998672 TTCTCCGGCGTGTCACCC 61.999 66.667 6.01 0.00 0.00 4.61
3257 3843 2.668212 CGGCGTGTCACCCACATT 60.668 61.111 0.00 0.00 44.78 2.71
3317 7722 2.692024 TCACCTAATTACCGCCCCATA 58.308 47.619 0.00 0.00 0.00 2.74
3395 7801 1.452108 CCATCCTTCCCACCGAAGC 60.452 63.158 0.00 0.00 45.83 3.86
3409 7815 3.309954 CACCGAAGCATTACTAGAAAGGC 59.690 47.826 0.00 0.00 36.44 4.35
3430 7836 3.937706 GCAAGCTATGAAGACAGATGTGT 59.062 43.478 0.00 0.00 40.71 3.72
3475 7881 3.099841 TCCAGCCCACCACAACCA 61.100 61.111 0.00 0.00 0.00 3.67
3476 7882 2.123511 CCAGCCCACCACAACCAA 60.124 61.111 0.00 0.00 0.00 3.67
3477 7883 2.202395 CCAGCCCACCACAACCAAG 61.202 63.158 0.00 0.00 0.00 3.61
3481 7888 1.463553 GCCCACCACAACCAAGAAGG 61.464 60.000 0.00 0.00 45.67 3.46
3505 7912 2.101917 TCCTCCTCGTTTCACTTTCGTT 59.898 45.455 0.00 0.00 0.00 3.85
3511 7918 3.822996 TCGTTTCACTTTCGTTTGCAAA 58.177 36.364 8.05 8.05 0.00 3.68
3512 7919 3.604627 TCGTTTCACTTTCGTTTGCAAAC 59.395 39.130 28.61 28.61 35.59 2.93
3514 7921 4.488573 CGTTTCACTTTCGTTTGCAAACAG 60.489 41.667 34.59 27.31 38.81 3.16
3545 7952 3.127533 GCATCGCACCGCCTTCTT 61.128 61.111 0.00 0.00 0.00 2.52
3571 7978 0.859232 GTTTCTGCGCGACTCTTTCA 59.141 50.000 12.10 0.00 0.00 2.69
3580 7987 1.464997 GCGACTCTTTCATGTTGGACC 59.535 52.381 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 53 1.535226 GGCTGGTTTGGTTTCGTCAAC 60.535 52.381 0.00 0.00 34.18 3.18
65 70 2.650813 CTATCTGCTTTCCGGCGGCT 62.651 60.000 23.83 0.31 38.38 5.52
67 72 2.247437 GCTATCTGCTTTCCGGCGG 61.247 63.158 22.51 22.51 39.72 6.13
85 90 0.842635 ATTTCCCTCTGGCTGGCTAG 59.157 55.000 2.00 0.00 0.00 3.42
86 91 0.548031 CATTTCCCTCTGGCTGGCTA 59.452 55.000 2.00 0.00 0.00 3.93
87 92 1.210204 TCATTTCCCTCTGGCTGGCT 61.210 55.000 2.00 0.00 0.00 4.75
88 93 0.750911 CTCATTTCCCTCTGGCTGGC 60.751 60.000 0.00 0.00 0.00 4.85
89 94 0.914644 TCTCATTTCCCTCTGGCTGG 59.085 55.000 0.00 0.00 0.00 4.85
90 95 2.795231 TTCTCATTTCCCTCTGGCTG 57.205 50.000 0.00 0.00 0.00 4.85
91 96 3.683847 CGATTTCTCATTTCCCTCTGGCT 60.684 47.826 0.00 0.00 0.00 4.75
92 97 2.615912 CGATTTCTCATTTCCCTCTGGC 59.384 50.000 0.00 0.00 0.00 4.85
93 98 3.878778 ACGATTTCTCATTTCCCTCTGG 58.121 45.455 0.00 0.00 0.00 3.86
94 99 5.665459 ACTACGATTTCTCATTTCCCTCTG 58.335 41.667 0.00 0.00 0.00 3.35
95 100 5.941555 ACTACGATTTCTCATTTCCCTCT 57.058 39.130 0.00 0.00 0.00 3.69
96 101 6.697892 CACTACTACGATTTCTCATTTCCCTC 59.302 42.308 0.00 0.00 0.00 4.30
97 102 6.574350 CACTACTACGATTTCTCATTTCCCT 58.426 40.000 0.00 0.00 0.00 4.20
98 103 5.234543 GCACTACTACGATTTCTCATTTCCC 59.765 44.000 0.00 0.00 0.00 3.97
99 104 6.043411 AGCACTACTACGATTTCTCATTTCC 58.957 40.000 0.00 0.00 0.00 3.13
100 105 8.052313 GTAGCACTACTACGATTTCTCATTTC 57.948 38.462 0.45 0.00 41.88 2.17
101 106 7.988904 GTAGCACTACTACGATTTCTCATTT 57.011 36.000 0.45 0.00 41.88 2.32
116 121 0.794473 GTGGCGTTTGGTAGCACTAC 59.206 55.000 0.00 0.00 35.40 2.73
120 125 0.887387 GGAAGTGGCGTTTGGTAGCA 60.887 55.000 0.00 0.00 34.54 3.49
121 126 1.583495 GGGAAGTGGCGTTTGGTAGC 61.583 60.000 0.00 0.00 0.00 3.58
141 146 4.235762 AGGTTCCAGTGCGCGTGT 62.236 61.111 8.43 0.00 0.00 4.49
145 150 3.414700 CACGAGGTTCCAGTGCGC 61.415 66.667 0.00 0.00 0.00 6.09
153 158 1.966451 CCAAGGTGGCACGAGGTTC 60.966 63.158 12.17 0.00 0.00 3.62
181 186 1.282875 GGTTTGACTTGTCTGCGCC 59.717 57.895 4.18 0.00 0.00 6.53
183 188 1.569493 CGGGTTTGACTTGTCTGCG 59.431 57.895 2.35 0.00 0.00 5.18
225 230 3.729698 AAAAAGGTACCGCGGCGC 61.730 61.111 28.58 24.21 0.00 6.53
259 264 2.380410 CGAGAGCAAAACCCGACGG 61.380 63.158 6.99 6.99 0.00 4.79
260 265 0.387622 TACGAGAGCAAAACCCGACG 60.388 55.000 0.00 0.00 0.00 5.12
261 266 1.066136 GTACGAGAGCAAAACCCGAC 58.934 55.000 0.00 0.00 0.00 4.79
262 267 0.963962 AGTACGAGAGCAAAACCCGA 59.036 50.000 0.00 0.00 0.00 5.14
263 268 1.068474 CAGTACGAGAGCAAAACCCG 58.932 55.000 0.00 0.00 0.00 5.28
264 269 1.270678 ACCAGTACGAGAGCAAAACCC 60.271 52.381 0.00 0.00 0.00 4.11
265 270 2.165319 ACCAGTACGAGAGCAAAACC 57.835 50.000 0.00 0.00 0.00 3.27
282 287 4.025647 GCATTCTGCGTCAATTCTAGTACC 60.026 45.833 0.00 0.00 31.71 3.34
313 324 5.837979 ACCGGAGAGATCTACTACTACTACA 59.162 44.000 9.46 0.00 0.00 2.74
319 330 4.408270 TGTACACCGGAGAGATCTACTACT 59.592 45.833 9.46 0.00 0.00 2.57
320 331 4.701765 TGTACACCGGAGAGATCTACTAC 58.298 47.826 9.46 0.00 0.00 2.73
321 332 5.363562 TTGTACACCGGAGAGATCTACTA 57.636 43.478 9.46 0.00 0.00 1.82
333 344 3.002451 TCGTTTCACATTTTGTACACCGG 59.998 43.478 0.00 0.00 0.00 5.28
334 345 4.025563 TCTCGTTTCACATTTTGTACACCG 60.026 41.667 0.00 0.00 0.00 4.94
340 351 9.581099 AAGTATTTTTCTCGTTTCACATTTTGT 57.419 25.926 0.00 0.00 0.00 2.83
395 410 4.328983 CACGTATGAGTCGGTGCTAAAATT 59.671 41.667 0.00 0.00 0.00 1.82
396 411 3.863424 CACGTATGAGTCGGTGCTAAAAT 59.137 43.478 0.00 0.00 0.00 1.82
397 412 3.247442 CACGTATGAGTCGGTGCTAAAA 58.753 45.455 0.00 0.00 0.00 1.52
401 416 1.248785 ACCACGTATGAGTCGGTGCT 61.249 55.000 0.00 0.00 0.00 4.40
402 417 1.076533 CACCACGTATGAGTCGGTGC 61.077 60.000 6.09 0.00 36.91 5.01
403 418 1.076533 GCACCACGTATGAGTCGGTG 61.077 60.000 13.13 13.13 41.65 4.94
404 419 1.214589 GCACCACGTATGAGTCGGT 59.785 57.895 3.25 0.00 0.00 4.69
405 420 1.872234 CGCACCACGTATGAGTCGG 60.872 63.158 3.25 0.00 36.87 4.79
406 421 3.675485 CGCACCACGTATGAGTCG 58.325 61.111 3.25 0.00 36.87 4.18
488 532 1.889530 GAGGACCCCGAGACTTGGTG 61.890 65.000 8.01 0.00 30.97 4.17
573 617 4.195416 TCAAAAATCAAAAGGTTGTGGGC 58.805 39.130 0.00 0.00 36.07 5.36
575 619 5.065859 GGGTTCAAAAATCAAAAGGTTGTGG 59.934 40.000 0.00 0.00 36.07 4.17
576 620 5.879777 AGGGTTCAAAAATCAAAAGGTTGTG 59.120 36.000 0.00 0.00 36.07 3.33
577 621 6.061022 AGGGTTCAAAAATCAAAAGGTTGT 57.939 33.333 0.00 0.00 36.07 3.32
578 622 6.238076 CGAAGGGTTCAAAAATCAAAAGGTTG 60.238 38.462 0.00 0.00 35.95 3.77
579 623 5.815222 CGAAGGGTTCAAAAATCAAAAGGTT 59.185 36.000 0.00 0.00 0.00 3.50
580 624 5.105106 ACGAAGGGTTCAAAAATCAAAAGGT 60.105 36.000 0.00 0.00 0.00 3.50
581 625 5.356426 ACGAAGGGTTCAAAAATCAAAAGG 58.644 37.500 0.00 0.00 0.00 3.11
582 626 5.173131 CGACGAAGGGTTCAAAAATCAAAAG 59.827 40.000 0.00 0.00 0.00 2.27
709 760 2.245159 TGCTGATGGATGGATCGTTC 57.755 50.000 0.00 0.00 0.00 3.95
712 763 1.233019 GGTTGCTGATGGATGGATCG 58.767 55.000 0.00 0.00 0.00 3.69
751 813 2.159156 GGGCTTTTCCTTTTTCGTGTGT 60.159 45.455 0.00 0.00 34.39 3.72
757 819 5.023533 AGTTCTTGGGCTTTTCCTTTTTC 57.976 39.130 0.00 0.00 34.39 2.29
758 820 5.435686 AAGTTCTTGGGCTTTTCCTTTTT 57.564 34.783 0.00 0.00 34.39 1.94
759 821 5.428253 GAAAGTTCTTGGGCTTTTCCTTTT 58.572 37.500 0.00 0.00 35.35 2.27
760 822 4.141711 GGAAAGTTCTTGGGCTTTTCCTTT 60.142 41.667 6.97 0.00 35.35 3.11
761 823 3.388024 GGAAAGTTCTTGGGCTTTTCCTT 59.612 43.478 6.97 0.00 35.35 3.36
762 824 2.965831 GGAAAGTTCTTGGGCTTTTCCT 59.034 45.455 6.97 0.00 35.35 3.36
763 825 2.965831 AGGAAAGTTCTTGGGCTTTTCC 59.034 45.455 6.25 6.25 35.35 3.13
798 860 2.278738 GATTGGATTGGGCCGGGT 59.721 61.111 2.18 0.00 0.00 5.28
866 943 1.880027 GTGGTCTGGGAATTGTGTGAC 59.120 52.381 0.00 0.00 0.00 3.67
955 1036 2.675423 GGTTTCTTGGACGGGGGC 60.675 66.667 0.00 0.00 0.00 5.80
956 1037 2.359478 CGGTTTCTTGGACGGGGG 60.359 66.667 0.00 0.00 0.00 5.40
1140 1466 1.522569 GAAGACCCCCAGGACGATG 59.477 63.158 0.00 0.00 36.73 3.84
1209 1535 1.008938 AGGTAGAACCAGAGGAGGCAT 59.991 52.381 0.00 0.00 41.95 4.40
1413 1739 4.329545 TTGGCGTCCTGGAGGCAC 62.330 66.667 34.25 25.33 44.00 5.01
1461 1787 1.531149 GACATGAACTGTTGGACCGTG 59.469 52.381 0.00 0.00 38.54 4.94
1464 1790 2.427506 GAGGACATGAACTGTTGGACC 58.572 52.381 0.00 0.00 38.54 4.46
1465 1791 2.427506 GGAGGACATGAACTGTTGGAC 58.572 52.381 0.00 0.00 38.54 4.02
1468 1794 2.455674 TCGGAGGACATGAACTGTTG 57.544 50.000 0.00 0.00 38.54 3.33
1470 1796 2.428890 GAGATCGGAGGACATGAACTGT 59.571 50.000 0.00 0.00 42.15 3.55
1539 1921 8.946085 GGATGATCAAATATATTTTAGCGTGGA 58.054 33.333 8.01 1.85 0.00 4.02
1541 1923 8.655970 TCGGATGATCAAATATATTTTAGCGTG 58.344 33.333 8.01 0.00 0.00 5.34
1543 1925 9.087424 TCTCGGATGATCAAATATATTTTAGCG 57.913 33.333 8.01 0.00 0.00 4.26
1561 1943 7.088589 AGTTTAACCAAATTCATCTCGGATG 57.911 36.000 7.36 7.36 0.00 3.51
1582 1964 7.395206 AACACAGGTTGGAAAAACTAACTAGTT 59.605 33.333 13.68 13.68 40.99 2.24
1584 1966 6.937436 ACACAGGTTGGAAAAACTAACTAG 57.063 37.500 0.00 0.00 39.42 2.57
1585 1967 7.393796 TCAAACACAGGTTGGAAAAACTAACTA 59.606 33.333 0.00 0.00 39.42 2.24
1587 1969 6.391537 TCAAACACAGGTTGGAAAAACTAAC 58.608 36.000 0.00 0.00 33.99 2.34
1588 1970 6.591750 TCAAACACAGGTTGGAAAAACTAA 57.408 33.333 0.00 0.00 33.99 2.24
1589 1971 6.209788 AGTTCAAACACAGGTTGGAAAAACTA 59.790 34.615 0.00 0.00 45.95 2.24
1591 1973 5.234752 AGTTCAAACACAGGTTGGAAAAAC 58.765 37.500 0.00 0.00 45.95 2.43
1592 1974 5.476091 AGTTCAAACACAGGTTGGAAAAA 57.524 34.783 0.00 0.00 45.95 1.94
1594 1976 5.011125 TCAAAGTTCAAACACAGGTTGGAAA 59.989 36.000 0.00 0.00 45.95 3.13
1596 1978 4.082845 TCAAAGTTCAAACACAGGTTGGA 58.917 39.130 0.00 0.00 37.30 3.53
1597 1979 4.448537 TCAAAGTTCAAACACAGGTTGG 57.551 40.909 0.00 0.00 37.30 3.77
1598 1980 6.098679 TGATTCAAAGTTCAAACACAGGTTG 58.901 36.000 0.00 0.00 37.30 3.77
1599 1981 6.071391 ACTGATTCAAAGTTCAAACACAGGTT 60.071 34.615 0.00 0.00 39.43 3.50
1613 2023 9.565213 GAAGTCATTTTCCATACTGATTCAAAG 57.435 33.333 0.00 0.00 0.00 2.77
1615 2025 8.868522 AGAAGTCATTTTCCATACTGATTCAA 57.131 30.769 0.00 0.00 0.00 2.69
1616 2026 8.868522 AAGAAGTCATTTTCCATACTGATTCA 57.131 30.769 0.00 0.00 0.00 2.57
1620 2030 9.130661 TGAAAAAGAAGTCATTTTCCATACTGA 57.869 29.630 15.41 0.00 40.68 3.41
1621 2031 9.185192 GTGAAAAAGAAGTCATTTTCCATACTG 57.815 33.333 15.41 0.00 40.68 2.74
1622 2032 8.076178 CGTGAAAAAGAAGTCATTTTCCATACT 58.924 33.333 15.41 0.00 40.68 2.12
1623 2033 7.860872 ACGTGAAAAAGAAGTCATTTTCCATAC 59.139 33.333 15.41 8.82 40.68 2.39
1628 2038 6.967199 AGACACGTGAAAAAGAAGTCATTTTC 59.033 34.615 25.01 12.55 41.33 2.29
1636 2046 2.030457 ACGCAGACACGTGAAAAAGAAG 59.970 45.455 25.01 7.87 46.28 2.85
1659 2069 1.409064 AGAAATATCTCGGCGAGCACA 59.591 47.619 31.01 18.19 0.00 4.57
1683 2093 1.866943 ACTGCCTTATCCTCCTCCCTA 59.133 52.381 0.00 0.00 0.00 3.53
1685 2095 2.252714 CTACTGCCTTATCCTCCTCCC 58.747 57.143 0.00 0.00 0.00 4.30
1689 2099 3.827876 GAGGTACTACTGCCTTATCCTCC 59.172 52.174 0.00 0.00 41.55 4.30
1690 2100 4.471548 TGAGGTACTACTGCCTTATCCTC 58.528 47.826 0.00 0.00 41.55 3.71
1699 2109 0.830648 TGGGCATGAGGTACTACTGC 59.169 55.000 0.00 0.00 41.55 4.40
1700 2110 3.055094 ACTTTGGGCATGAGGTACTACTG 60.055 47.826 0.00 0.00 41.55 2.74
1701 2111 3.182152 ACTTTGGGCATGAGGTACTACT 58.818 45.455 0.00 0.00 41.55 2.57
1702 2112 3.055385 TGACTTTGGGCATGAGGTACTAC 60.055 47.826 0.00 0.00 41.55 2.73
1708 2118 1.619654 TGTTGACTTTGGGCATGAGG 58.380 50.000 0.00 0.00 0.00 3.86
1712 2122 3.140623 GCAATTTGTTGACTTTGGGCAT 58.859 40.909 0.00 0.00 0.00 4.40
1736 2146 7.426929 AGTTGTGCTACTACAATTTCTCAAG 57.573 36.000 0.00 0.00 42.02 3.02
1767 2177 2.409378 CCGTACACGTAAACATCACACC 59.591 50.000 0.58 0.00 37.74 4.16
1832 2242 3.867771 CTCGTGAGCAAGTGGAGC 58.132 61.111 0.00 0.00 0.00 4.70
1846 2294 2.604914 AGTTGATTATTGTCTGCGCTCG 59.395 45.455 9.73 0.00 0.00 5.03
1847 2295 4.806247 ACTAGTTGATTATTGTCTGCGCTC 59.194 41.667 9.73 0.00 0.00 5.03
1884 2335 2.358582 TGCAACTATCATGCGGAAATGG 59.641 45.455 0.00 0.00 46.76 3.16
1885 2336 3.696281 TGCAACTATCATGCGGAAATG 57.304 42.857 0.00 0.00 46.76 2.32
1893 2350 1.672363 ACCACGCATGCAACTATCATG 59.328 47.619 19.57 0.00 43.02 3.07
1943 2409 4.829064 TTGCTGCTATTCAAAACGTTCT 57.171 36.364 0.00 0.00 0.00 3.01
1944 2410 4.917415 ACATTGCTGCTATTCAAAACGTTC 59.083 37.500 0.00 0.00 0.00 3.95
1958 2424 4.553323 GGGATCATATCAAACATTGCTGC 58.447 43.478 0.00 0.00 0.00 5.25
1959 2425 4.021719 GGGGGATCATATCAAACATTGCTG 60.022 45.833 0.00 0.00 0.00 4.41
1980 2446 0.732571 CAATCCGTTGACAATCGGGG 59.267 55.000 21.22 9.25 45.79 5.73
2009 2508 6.945938 TTGGGTCGAAGAAAAATCACTAAA 57.054 33.333 0.00 0.00 39.69 1.85
2010 2509 6.514376 GCTTTGGGTCGAAGAAAAATCACTAA 60.514 38.462 0.00 0.00 39.69 2.24
2048 2547 6.799926 TTGGAAAGAATTTAATGCAAAGCC 57.200 33.333 0.00 0.00 39.27 4.35
2106 2616 2.980233 GGTGCCACTGCCACACTC 60.980 66.667 0.00 0.00 36.33 3.51
2119 2629 0.674895 AAGCGTTGAGATGGAGGTGC 60.675 55.000 0.00 0.00 0.00 5.01
2191 2701 8.478877 AGATAGAAAGAGATAATTTGGTCACGT 58.521 33.333 0.00 0.00 0.00 4.49
2228 2739 7.761038 ATTATTTCTTTTCTGACCCTCGTTT 57.239 32.000 0.00 0.00 0.00 3.60
2256 2794 4.090642 GCCATCGCAAATAGAATAGTCGAG 59.909 45.833 0.00 0.00 34.03 4.04
2266 2804 1.159713 TCAGCCGCCATCGCAAATAG 61.160 55.000 0.00 0.00 34.03 1.73
2279 2822 1.667724 GATGAAATGGTCAGTCAGCCG 59.332 52.381 0.00 0.00 40.43 5.52
2410 2953 3.902086 TCGTCGTTGGACCACGCA 61.902 61.111 10.47 0.30 40.17 5.24
2479 3022 1.208614 CTTCCAGTTGCGCTTGAGC 59.791 57.895 9.73 0.00 37.78 4.26
2637 3180 1.011333 TAAATAACCGAGCCAAGCGC 58.989 50.000 0.00 0.00 37.98 5.92
2638 3181 3.617669 CAATAAATAACCGAGCCAAGCG 58.382 45.455 0.00 0.00 0.00 4.68
2639 3182 3.066760 AGCAATAAATAACCGAGCCAAGC 59.933 43.478 0.00 0.00 0.00 4.01
2640 3183 4.900635 AGCAATAAATAACCGAGCCAAG 57.099 40.909 0.00 0.00 0.00 3.61
2681 3224 0.798389 ATGCATGACACGACGAGACG 60.798 55.000 0.00 0.00 39.31 4.18
2682 3225 0.917259 GATGCATGACACGACGAGAC 59.083 55.000 2.46 0.00 0.00 3.36
2683 3226 0.811281 AGATGCATGACACGACGAGA 59.189 50.000 2.46 0.00 0.00 4.04
2684 3227 1.585668 GAAGATGCATGACACGACGAG 59.414 52.381 2.46 0.00 0.00 4.18
2685 3228 1.629013 GAAGATGCATGACACGACGA 58.371 50.000 2.46 0.00 0.00 4.20
2697 3240 0.782384 AAACACGACGACGAAGATGC 59.218 50.000 15.32 0.00 42.66 3.91
2699 3242 2.225963 AGAGAAACACGACGACGAAGAT 59.774 45.455 15.32 0.00 42.66 2.40
2700 3243 1.600957 AGAGAAACACGACGACGAAGA 59.399 47.619 15.32 0.00 42.66 2.87
2701 3244 2.033793 AGAGAAACACGACGACGAAG 57.966 50.000 15.32 8.51 42.66 3.79
2705 3248 3.549299 TCCTAAGAGAAACACGACGAC 57.451 47.619 0.00 0.00 0.00 4.34
2714 3257 4.302067 AGATCAGGCCATCCTAAGAGAAA 58.698 43.478 5.01 0.00 41.93 2.52
2842 3397 8.749354 TCTGTTACATATATAATGGTCTGCGAT 58.251 33.333 0.00 0.00 0.00 4.58
2843 3398 8.117813 TCTGTTACATATATAATGGTCTGCGA 57.882 34.615 0.00 0.00 0.00 5.10
2844 3399 8.932945 ATCTGTTACATATATAATGGTCTGCG 57.067 34.615 0.00 0.00 0.00 5.18
2900 3460 8.786898 TCAATTGAAAAAGATGGACAGAAGTAG 58.213 33.333 5.45 0.00 0.00 2.57
2906 3466 6.530534 GCAGATCAATTGAAAAAGATGGACAG 59.469 38.462 13.09 0.00 0.00 3.51
2914 3474 6.702723 TCAAAGGTGCAGATCAATTGAAAAAG 59.297 34.615 13.09 4.36 0.00 2.27
2968 3530 7.033791 ACTTCACGAGCGAATTTCTAGAATAA 58.966 34.615 5.89 0.00 0.00 1.40
2974 3536 5.306532 ACTACTTCACGAGCGAATTTCTA 57.693 39.130 0.00 0.00 0.00 2.10
2975 3537 4.175787 ACTACTTCACGAGCGAATTTCT 57.824 40.909 0.00 0.00 0.00 2.52
3027 3593 1.827245 GCCCCCTGGTGACTTTTCAAT 60.827 52.381 0.00 0.00 31.90 2.57
3049 3618 4.661222 TGATGTTCAGATGGGCAGTTTTA 58.339 39.130 0.00 0.00 0.00 1.52
3092 3662 5.283294 TGTCAAAACACTGAATGAGCAATG 58.717 37.500 0.00 0.00 0.00 2.82
3162 3734 5.127031 GCCATCTTGGAAAAATACAGCCTTA 59.873 40.000 0.00 0.00 40.96 2.69
3317 7722 1.004628 TGTCTGCCACCTTGTATGCAT 59.995 47.619 3.79 3.79 32.53 3.96
3395 7801 7.712639 TCTTCATAGCTTGCCTTTCTAGTAATG 59.287 37.037 0.00 0.00 0.00 1.90
3409 7815 5.163784 CCAACACATCTGTCTTCATAGCTTG 60.164 44.000 0.00 0.00 0.00 4.01
3475 7881 4.081586 GTGAAACGAGGAGGATACCTTCTT 60.082 45.833 0.00 0.00 40.10 2.52
3476 7882 3.447944 GTGAAACGAGGAGGATACCTTCT 59.552 47.826 0.00 0.00 43.32 2.85
3477 7883 3.447944 AGTGAAACGAGGAGGATACCTTC 59.552 47.826 0.00 0.00 45.86 3.46
3481 7888 3.858238 CGAAAGTGAAACGAGGAGGATAC 59.142 47.826 0.00 0.00 45.86 2.24
3511 7918 0.976641 TGCCTAGCTACAACTGCTGT 59.023 50.000 0.00 0.00 41.32 4.40
3512 7919 2.208431 GATGCCTAGCTACAACTGCTG 58.792 52.381 0.00 0.00 41.32 4.41
3514 7921 1.212616 CGATGCCTAGCTACAACTGC 58.787 55.000 0.00 0.00 0.00 4.40
3516 7923 0.824109 TGCGATGCCTAGCTACAACT 59.176 50.000 0.00 0.00 0.00 3.16
3520 7927 1.661821 CGGTGCGATGCCTAGCTAC 60.662 63.158 0.00 0.00 0.00 3.58
3544 7951 0.941936 TCGCGCAGAAACGACATCAA 60.942 50.000 8.75 0.00 32.45 2.57
3545 7952 1.372375 TCGCGCAGAAACGACATCA 60.372 52.632 8.75 0.00 32.45 3.07
3571 7978 1.282157 GAAGGGCTACTGGTCCAACAT 59.718 52.381 0.00 0.00 43.45 2.71
3580 7987 3.742640 GCCTATGTTCAGAAGGGCTACTG 60.743 52.174 8.37 0.00 36.96 2.74


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

AutoCloner maintained by Alex Coulton.