Multiple sequence alignment - TraesCS3D01G215700

Loading Multiple Alignment...

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 TraesCS3D01G215700 chr3D 100.000 2559 0 0 1 2559 291977138 291974580 0.000000e+00 4726
1 TraesCS3D01G215700 chr3D 86.935 199 22 4 2032 2229 69796976 69796781 1.190000e-53 220
2 TraesCS3D01G215700 chr3A 91.398 2081 120 18 1 2036 384733278 384731212 0.000000e+00 2796
3 TraesCS3D01G215700 chr3B 93.713 1368 50 16 418 1764 385190412 385189060 0.000000e+00 2017
4 TraesCS3D01G215700 chr3B 93.089 463 11 4 1 463 385190880 385190439 0.000000e+00 658
5 TraesCS3D01G215700 chr3B 92.883 281 19 1 1750 2030 385186792 385186513 8.520000e-110 407
6 TraesCS3D01G215700 chr3B 82.528 269 30 7 2299 2554 385185855 385185591 1.190000e-53 220
7 TraesCS3D01G215700 chr2B 87.685 203 25 0 2028 2230 770183869 770184071 1.180000e-58 237
8 TraesCS3D01G215700 chr2A 87.379 206 25 1 2023 2228 240457859 240458063 4.260000e-58 235
9 TraesCS3D01G215700 chr2A 87.113 194 25 0 2033 2226 654689605 654689798 1.190000e-53 220
10 TraesCS3D01G215700 chr1B 87.692 195 24 0 2032 2226 53474614 53474808 7.120000e-56 228
11 TraesCS3D01G215700 chr1B 87.374 198 24 1 2032 2229 418041275 418041079 2.560000e-55 226
12 TraesCS3D01G215700 chr1B 86.765 204 25 2 2027 2230 448264539 448264338 2.560000e-55 226
13 TraesCS3D01G215700 chr5B 86.869 198 26 0 2032 2229 468893467 468893270 3.310000e-54 222
14 TraesCS3D01G215700 chr1A 86.364 198 27 0 2032 2229 50707477 50707280 1.540000e-52 217
15 TraesCS3D01G215700 chr6A 86.250 160 22 0 1871 2030 32904899 32905058 9.410000e-40 174
16 TraesCS3D01G215700 chr6B 81.333 225 29 9 1332 1553 23605252 23605038 1.220000e-38 171
17 TraesCS3D01G215700 chr6B 86.207 145 18 1 1173 1317 23605583 23605441 3.410000e-34 156
18 TraesCS3D01G215700 chr6D 78.469 209 37 5 192 400 13153160 13153360 2.070000e-26 130


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 TraesCS3D01G215700 chr3D 291974580 291977138 2558 True 4726.0 4726 100.00000 1 2559 1 chr3D.!!$R2 2558
1 TraesCS3D01G215700 chr3A 384731212 384733278 2066 True 2796.0 2796 91.39800 1 2036 1 chr3A.!!$R1 2035
2 TraesCS3D01G215700 chr3B 385185591 385190880 5289 True 825.5 2017 90.55325 1 2554 4 chr3B.!!$R1 2553

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
987 1091 0.036952 CCATCTTCACGCACCTCACT 60.037 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 5381 0.039074 ACGTCTCGAGGAGCAGTTTG 60.039 55.0 13.56 0.0 0.0 2.93 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
61 62 6.203915 TGTTTGCATCATGGTACGGTATATTC 59.796 38.462 0.00 0.00 0.00 1.75
166 167 6.993079 TGACCAGTGTATGTATAGGCTTATG 58.007 40.000 0.00 0.00 0.00 1.90
456 537 6.947464 TCAGGGAGAATTTCTTGTAGTAAGG 58.053 40.000 0.00 0.00 0.00 2.69
710 808 2.606308 GCTTGTTGATGTGTCCAGCTTG 60.606 50.000 0.00 0.00 0.00 4.01
711 809 1.608055 TGTTGATGTGTCCAGCTTGG 58.392 50.000 0.00 0.00 39.43 3.61
853 956 1.644786 CGCCCCAACCGATTCAGTTC 61.645 60.000 0.00 0.00 0.00 3.01
873 976 1.082117 CGTATTGTCCCGTGCACTCC 61.082 60.000 16.19 0.11 0.00 3.85
898 1001 2.239812 ATGCATGACGATGACGCGG 61.240 57.895 12.47 0.00 43.96 6.46
917 1020 1.366854 GCCGGTGAATCGAAGAACCC 61.367 60.000 1.90 0.00 43.58 4.11
918 1021 0.249398 CCGGTGAATCGAAGAACCCT 59.751 55.000 0.00 0.00 43.58 4.34
919 1022 1.641577 CGGTGAATCGAAGAACCCTC 58.358 55.000 7.86 0.00 43.58 4.30
950 1053 0.398318 ACCTTTCTTCTGCGAAGGCT 59.602 50.000 15.15 0.00 40.82 4.58
974 1078 0.833287 CACCCGTCCATCTCCATCTT 59.167 55.000 0.00 0.00 0.00 2.40
987 1091 0.036952 CCATCTTCACGCACCTCACT 60.037 55.000 0.00 0.00 0.00 3.41
1035 1142 2.125106 GCCAAGATCGCCGTCCTT 60.125 61.111 0.00 0.00 0.00 3.36
1093 1200 4.560492 ACCCCCAACCTCCCCCAA 62.560 66.667 0.00 0.00 0.00 4.12
1289 1396 2.046314 GCCACCAGGTGCGTATGT 60.046 61.111 14.98 0.00 37.19 2.29
1290 1397 1.219664 GCCACCAGGTGCGTATGTA 59.780 57.895 14.98 0.00 37.19 2.29
1291 1398 0.179056 GCCACCAGGTGCGTATGTAT 60.179 55.000 14.98 0.00 37.19 2.29
1305 1412 1.750193 ATGTATGCCACCGTCCAAAG 58.250 50.000 0.00 0.00 0.00 2.77
1309 1418 0.609131 ATGCCACCGTCCAAAGAAGG 60.609 55.000 0.00 0.00 46.21 3.46
1311 1420 0.955919 GCCACCGTCCAAAGAAGGAG 60.956 60.000 1.95 0.00 43.77 3.69
1335 1449 1.453148 GCGTTTTACTTGCTCGTACGT 59.547 47.619 16.05 0.00 0.00 3.57
1336 1450 2.656422 GCGTTTTACTTGCTCGTACGTA 59.344 45.455 16.05 0.00 0.00 3.57
1337 1451 3.478756 GCGTTTTACTTGCTCGTACGTAC 60.479 47.826 15.90 15.90 0.00 3.67
1417 1531 1.203162 TGTGGGACCAAATGCTTCCAT 60.203 47.619 0.00 0.00 0.00 3.41
1670 1802 3.482472 CGACGTCTATGCACACATACTTC 59.518 47.826 14.70 0.00 37.74 3.01
1680 1812 3.563808 GCACACATACTTCCAAGTGAACA 59.436 43.478 2.01 0.00 40.07 3.18
1721 1854 4.789807 ACAGTATAAGTAGAGCCCTCGAA 58.210 43.478 0.00 0.00 34.09 3.71
1725 1858 6.697892 CAGTATAAGTAGAGCCCTCGAAAAAG 59.302 42.308 0.00 0.00 34.09 2.27
1753 1886 5.709164 ACAGTATATGTAGACGGGGTATGAC 59.291 44.000 0.00 0.00 41.60 3.06
1756 1889 2.812836 TGTAGACGGGGTATGACTGA 57.187 50.000 0.00 0.00 0.00 3.41
1819 4242 4.759782 TCCATCAGCTCTAAGTAAACTGC 58.240 43.478 0.00 0.00 0.00 4.40
1832 4255 9.811995 TCTAAGTAAACTGCGTATAAATCATGT 57.188 29.630 0.00 0.00 0.00 3.21
1941 4364 3.894427 ACATGCCTCACCAAAACAATGTA 59.106 39.130 0.00 0.00 0.00 2.29
1942 4365 4.236935 CATGCCTCACCAAAACAATGTAC 58.763 43.478 0.00 0.00 0.00 2.90
1971 4394 6.677781 ACCCACAATTATGACGTTATCAAG 57.322 37.500 0.00 0.00 41.93 3.02
2028 4451 3.853831 CACACATTGCAAAGCCTGATA 57.146 42.857 1.71 0.00 0.00 2.15
2029 4452 4.177165 CACACATTGCAAAGCCTGATAA 57.823 40.909 1.71 0.00 0.00 1.75
2030 4453 4.751060 CACACATTGCAAAGCCTGATAAT 58.249 39.130 1.71 0.00 0.00 1.28
2031 4454 4.565166 CACACATTGCAAAGCCTGATAATG 59.435 41.667 1.71 0.00 37.26 1.90
2032 4455 3.554324 CACATTGCAAAGCCTGATAATGC 59.446 43.478 1.71 0.00 35.87 3.56
2033 4456 2.965572 TTGCAAAGCCTGATAATGCC 57.034 45.000 0.00 0.00 36.20 4.40
2034 4457 2.148446 TGCAAAGCCTGATAATGCCT 57.852 45.000 0.00 0.00 36.20 4.75
2035 4458 2.459644 TGCAAAGCCTGATAATGCCTT 58.540 42.857 0.00 0.00 36.20 4.35
2036 4459 2.166870 TGCAAAGCCTGATAATGCCTTG 59.833 45.455 0.00 0.00 36.20 3.61
2037 4460 2.167075 GCAAAGCCTGATAATGCCTTGT 59.833 45.455 0.00 0.00 32.73 3.16
2038 4461 3.381272 GCAAAGCCTGATAATGCCTTGTA 59.619 43.478 0.00 0.00 32.73 2.41
2039 4462 4.734695 GCAAAGCCTGATAATGCCTTGTAC 60.735 45.833 0.00 0.00 32.73 2.90
2040 4463 3.931907 AGCCTGATAATGCCTTGTACA 57.068 42.857 0.00 0.00 0.00 2.90
2041 4464 4.235079 AGCCTGATAATGCCTTGTACAA 57.765 40.909 8.28 8.28 0.00 2.41
2042 4465 4.796606 AGCCTGATAATGCCTTGTACAAT 58.203 39.130 9.13 0.00 0.00 2.71
2043 4466 4.581824 AGCCTGATAATGCCTTGTACAATG 59.418 41.667 9.13 7.68 0.00 2.82
2044 4467 4.339247 GCCTGATAATGCCTTGTACAATGT 59.661 41.667 9.13 0.00 0.00 2.71
2045 4468 5.530915 GCCTGATAATGCCTTGTACAATGTA 59.469 40.000 9.13 6.43 0.00 2.29
2046 4469 6.039270 GCCTGATAATGCCTTGTACAATGTAA 59.961 38.462 9.13 0.13 0.00 2.41
2047 4470 7.642669 CCTGATAATGCCTTGTACAATGTAAG 58.357 38.462 9.13 0.00 0.00 2.34
2048 4471 7.498900 CCTGATAATGCCTTGTACAATGTAAGA 59.501 37.037 9.13 0.00 0.00 2.10
2049 4472 8.978874 TGATAATGCCTTGTACAATGTAAGAT 57.021 30.769 9.13 4.06 0.00 2.40
2050 4473 8.839343 TGATAATGCCTTGTACAATGTAAGATG 58.161 33.333 9.13 0.00 0.00 2.90
2051 4474 4.963276 TGCCTTGTACAATGTAAGATGC 57.037 40.909 9.13 3.26 0.00 3.91
2052 4475 4.588899 TGCCTTGTACAATGTAAGATGCT 58.411 39.130 9.13 0.00 0.00 3.79
2053 4476 5.009631 TGCCTTGTACAATGTAAGATGCTT 58.990 37.500 9.13 0.00 0.00 3.91
2054 4477 6.176896 TGCCTTGTACAATGTAAGATGCTTA 58.823 36.000 9.13 0.00 0.00 3.09
2055 4478 6.316140 TGCCTTGTACAATGTAAGATGCTTAG 59.684 38.462 9.13 0.00 0.00 2.18
2056 4479 6.538742 GCCTTGTACAATGTAAGATGCTTAGA 59.461 38.462 9.13 0.00 0.00 2.10
2057 4480 7.254590 GCCTTGTACAATGTAAGATGCTTAGAG 60.255 40.741 9.13 0.00 0.00 2.43
2058 4481 7.981789 CCTTGTACAATGTAAGATGCTTAGAGA 59.018 37.037 9.13 0.00 0.00 3.10
2059 4482 9.371136 CTTGTACAATGTAAGATGCTTAGAGAA 57.629 33.333 9.13 0.00 0.00 2.87
2060 4483 8.932945 TGTACAATGTAAGATGCTTAGAGAAG 57.067 34.615 0.00 0.00 35.60 2.85
2061 4484 7.981789 TGTACAATGTAAGATGCTTAGAGAAGG 59.018 37.037 0.00 0.00 32.84 3.46
2062 4485 6.951971 ACAATGTAAGATGCTTAGAGAAGGT 58.048 36.000 0.00 0.00 32.84 3.50
2063 4486 6.820656 ACAATGTAAGATGCTTAGAGAAGGTG 59.179 38.462 0.00 0.00 32.84 4.00
2064 4487 4.759782 TGTAAGATGCTTAGAGAAGGTGC 58.240 43.478 0.00 0.00 32.84 5.01
2065 4488 4.467795 TGTAAGATGCTTAGAGAAGGTGCT 59.532 41.667 0.00 0.00 32.84 4.40
2066 4489 4.566426 AAGATGCTTAGAGAAGGTGCTT 57.434 40.909 0.00 0.00 32.84 3.91
2067 4490 5.683876 AAGATGCTTAGAGAAGGTGCTTA 57.316 39.130 0.00 0.00 32.84 3.09
2068 4491 5.275067 AGATGCTTAGAGAAGGTGCTTAG 57.725 43.478 0.00 0.00 32.84 2.18
2069 4492 4.959210 AGATGCTTAGAGAAGGTGCTTAGA 59.041 41.667 0.00 0.00 32.84 2.10
2070 4493 5.423610 AGATGCTTAGAGAAGGTGCTTAGAA 59.576 40.000 0.00 0.00 32.84 2.10
2071 4494 5.483685 TGCTTAGAGAAGGTGCTTAGAAA 57.516 39.130 0.00 0.00 32.84 2.52
2072 4495 5.865085 TGCTTAGAGAAGGTGCTTAGAAAA 58.135 37.500 0.00 0.00 32.84 2.29
2073 4496 6.296026 TGCTTAGAGAAGGTGCTTAGAAAAA 58.704 36.000 0.00 0.00 32.84 1.94
2074 4497 6.942576 TGCTTAGAGAAGGTGCTTAGAAAAAT 59.057 34.615 0.00 0.00 32.84 1.82
2075 4498 8.100791 TGCTTAGAGAAGGTGCTTAGAAAAATA 58.899 33.333 0.00 0.00 32.84 1.40
2076 4499 8.947115 GCTTAGAGAAGGTGCTTAGAAAAATAA 58.053 33.333 0.00 0.00 32.84 1.40
2080 4503 9.520515 AGAGAAGGTGCTTAGAAAAATAAATCA 57.479 29.630 0.00 0.00 0.00 2.57
2081 4504 9.780413 GAGAAGGTGCTTAGAAAAATAAATCAG 57.220 33.333 0.00 0.00 0.00 2.90
2082 4505 8.743714 AGAAGGTGCTTAGAAAAATAAATCAGG 58.256 33.333 0.00 0.00 0.00 3.86
2083 4506 8.422577 AAGGTGCTTAGAAAAATAAATCAGGT 57.577 30.769 0.00 0.00 0.00 4.00
2084 4507 8.422577 AGGTGCTTAGAAAAATAAATCAGGTT 57.577 30.769 0.00 0.00 0.00 3.50
2085 4508 8.870116 AGGTGCTTAGAAAAATAAATCAGGTTT 58.130 29.630 0.00 0.00 0.00 3.27
2086 4509 9.489084 GGTGCTTAGAAAAATAAATCAGGTTTT 57.511 29.630 0.00 0.00 0.00 2.43
2097 4520 9.489084 AAATAAATCAGGTTTTTCTTAAGCACC 57.511 29.630 0.00 1.55 0.00 5.01
2098 4521 4.766404 ATCAGGTTTTTCTTAAGCACCG 57.234 40.909 0.00 0.00 32.32 4.94
2099 4522 2.882137 TCAGGTTTTTCTTAAGCACCGG 59.118 45.455 0.00 0.00 32.32 5.28
2100 4523 2.621526 CAGGTTTTTCTTAAGCACCGGT 59.378 45.455 0.00 0.00 32.32 5.28
2101 4524 2.621526 AGGTTTTTCTTAAGCACCGGTG 59.378 45.455 30.66 30.66 32.32 4.94
2102 4525 2.359848 GGTTTTTCTTAAGCACCGGTGT 59.640 45.455 33.92 19.11 0.00 4.16
2103 4526 3.181484 GGTTTTTCTTAAGCACCGGTGTT 60.181 43.478 33.92 27.29 0.00 3.32
2104 4527 4.426416 GTTTTTCTTAAGCACCGGTGTTT 58.574 39.130 34.40 34.40 37.72 2.83
2105 4528 5.450274 GGTTTTTCTTAAGCACCGGTGTTTA 60.450 40.000 32.40 32.40 35.63 2.01
2106 4529 6.210796 GTTTTTCTTAAGCACCGGTGTTTAT 58.789 36.000 35.01 20.17 36.43 1.40
2107 4530 5.365403 TTTCTTAAGCACCGGTGTTTATG 57.635 39.130 35.01 33.93 36.43 1.90
2108 4531 4.010667 TCTTAAGCACCGGTGTTTATGT 57.989 40.909 34.91 21.56 36.43 2.29
2109 4532 3.749088 TCTTAAGCACCGGTGTTTATGTG 59.251 43.478 34.91 28.33 36.43 3.21
2110 4533 1.975660 AAGCACCGGTGTTTATGTGT 58.024 45.000 32.15 10.06 32.21 3.72
2111 4534 2.843401 AGCACCGGTGTTTATGTGTA 57.157 45.000 33.92 0.00 0.00 2.90
2112 4535 2.419667 AGCACCGGTGTTTATGTGTAC 58.580 47.619 33.92 14.30 0.00 2.90
2113 4536 2.144730 GCACCGGTGTTTATGTGTACA 58.855 47.619 33.92 0.00 0.00 2.90
2114 4537 2.158841 GCACCGGTGTTTATGTGTACAG 59.841 50.000 33.92 5.41 0.00 2.74
2115 4538 2.739913 CACCGGTGTTTATGTGTACAGG 59.260 50.000 26.95 0.00 35.04 4.00
2116 4539 2.633967 ACCGGTGTTTATGTGTACAGGA 59.366 45.455 6.12 0.00 33.46 3.86
2117 4540 3.262405 ACCGGTGTTTATGTGTACAGGAT 59.738 43.478 6.12 0.00 33.46 3.24
2118 4541 4.467082 ACCGGTGTTTATGTGTACAGGATA 59.533 41.667 6.12 0.00 33.46 2.59
2119 4542 5.047847 CCGGTGTTTATGTGTACAGGATAG 58.952 45.833 0.00 0.00 31.25 2.08
2120 4543 5.163488 CCGGTGTTTATGTGTACAGGATAGA 60.163 44.000 0.00 0.00 31.25 1.98
2121 4544 5.747197 CGGTGTTTATGTGTACAGGATAGAC 59.253 44.000 0.00 2.49 0.00 2.59
2122 4545 5.747197 GGTGTTTATGTGTACAGGATAGACG 59.253 44.000 0.00 0.00 0.00 4.18
2123 4546 5.231568 GTGTTTATGTGTACAGGATAGACGC 59.768 44.000 0.00 4.77 0.00 5.19
2124 4547 5.126545 TGTTTATGTGTACAGGATAGACGCT 59.873 40.000 0.00 0.00 0.00 5.07
2125 4548 5.847111 TTATGTGTACAGGATAGACGCTT 57.153 39.130 0.00 0.00 0.00 4.68
2126 4549 6.947644 TTATGTGTACAGGATAGACGCTTA 57.052 37.500 0.00 0.00 0.00 3.09
2127 4550 5.847111 ATGTGTACAGGATAGACGCTTAA 57.153 39.130 0.00 0.00 0.00 1.85
2128 4551 5.847111 TGTGTACAGGATAGACGCTTAAT 57.153 39.130 0.00 0.00 0.00 1.40
2129 4552 6.216801 TGTGTACAGGATAGACGCTTAATT 57.783 37.500 0.00 0.00 0.00 1.40
2130 4553 7.337480 TGTGTACAGGATAGACGCTTAATTA 57.663 36.000 0.00 0.00 0.00 1.40
2131 4554 7.423199 TGTGTACAGGATAGACGCTTAATTAG 58.577 38.462 0.00 0.00 0.00 1.73
2132 4555 6.862090 GTGTACAGGATAGACGCTTAATTAGG 59.138 42.308 0.00 0.00 0.00 2.69
2133 4556 4.884247 ACAGGATAGACGCTTAATTAGGC 58.116 43.478 9.43 9.43 0.00 3.93
2142 4565 3.707793 CGCTTAATTAGGCGTCTCTTCT 58.292 45.455 28.00 0.00 45.15 2.85
2143 4566 4.856664 CGCTTAATTAGGCGTCTCTTCTA 58.143 43.478 28.00 0.00 45.15 2.10
2144 4567 5.462405 CGCTTAATTAGGCGTCTCTTCTAT 58.538 41.667 28.00 0.00 45.15 1.98
2145 4568 6.609533 CGCTTAATTAGGCGTCTCTTCTATA 58.390 40.000 28.00 0.00 45.15 1.31
2146 4569 7.082602 CGCTTAATTAGGCGTCTCTTCTATAA 58.917 38.462 28.00 0.00 45.15 0.98
2147 4570 7.594015 CGCTTAATTAGGCGTCTCTTCTATAAA 59.406 37.037 28.00 0.00 45.15 1.40
2148 4571 9.257651 GCTTAATTAGGCGTCTCTTCTATAAAA 57.742 33.333 3.59 0.00 0.00 1.52
2154 4577 9.962783 TTAGGCGTCTCTTCTATAAAAATAGTC 57.037 33.333 0.00 0.00 0.00 2.59
2155 4578 8.008513 AGGCGTCTCTTCTATAAAAATAGTCA 57.991 34.615 0.00 0.00 0.00 3.41
2156 4579 7.921745 AGGCGTCTCTTCTATAAAAATAGTCAC 59.078 37.037 0.00 0.00 0.00 3.67
2157 4580 7.921745 GGCGTCTCTTCTATAAAAATAGTCACT 59.078 37.037 0.00 0.00 0.00 3.41
2158 4581 8.747666 GCGTCTCTTCTATAAAAATAGTCACTG 58.252 37.037 0.00 0.00 0.00 3.66
2177 4600 2.857483 TGATGCTTCAGAAAAACCCGA 58.143 42.857 0.00 0.00 0.00 5.14
2178 4601 3.420893 TGATGCTTCAGAAAAACCCGAT 58.579 40.909 0.00 0.00 0.00 4.18
2179 4602 3.826157 TGATGCTTCAGAAAAACCCGATT 59.174 39.130 0.00 0.00 0.00 3.34
2180 4603 4.280677 TGATGCTTCAGAAAAACCCGATTT 59.719 37.500 0.00 0.00 0.00 2.17
2181 4604 5.475220 TGATGCTTCAGAAAAACCCGATTTA 59.525 36.000 0.00 0.00 0.00 1.40
2182 4605 5.975693 TGCTTCAGAAAAACCCGATTTAT 57.024 34.783 0.00 0.00 0.00 1.40
2183 4606 6.339587 TGCTTCAGAAAAACCCGATTTATT 57.660 33.333 0.00 0.00 0.00 1.40
2184 4607 6.754193 TGCTTCAGAAAAACCCGATTTATTT 58.246 32.000 0.00 0.00 0.00 1.40
2185 4608 7.213678 TGCTTCAGAAAAACCCGATTTATTTT 58.786 30.769 0.00 0.00 0.00 1.82
2186 4609 7.713073 TGCTTCAGAAAAACCCGATTTATTTTT 59.287 29.630 0.00 0.00 38.03 1.94
2187 4610 8.221100 GCTTCAGAAAAACCCGATTTATTTTTC 58.779 33.333 11.59 11.59 45.95 2.29
2198 4621 9.067986 ACCCGATTTATTTTTCTAATCATCTCC 57.932 33.333 0.00 0.00 0.00 3.71
2199 4622 8.515414 CCCGATTTATTTTTCTAATCATCTCCC 58.485 37.037 0.00 0.00 0.00 4.30
2200 4623 9.289782 CCGATTTATTTTTCTAATCATCTCCCT 57.710 33.333 0.00 0.00 0.00 4.20
2207 4630 8.682936 TTTTTCTAATCATCTCCCTAAGCATC 57.317 34.615 0.00 0.00 0.00 3.91
2208 4631 7.623999 TTTCTAATCATCTCCCTAAGCATCT 57.376 36.000 0.00 0.00 0.00 2.90
2209 4632 8.727100 TTTCTAATCATCTCCCTAAGCATCTA 57.273 34.615 0.00 0.00 0.00 1.98
2210 4633 8.727100 TTCTAATCATCTCCCTAAGCATCTAA 57.273 34.615 0.00 0.00 0.00 2.10
2211 4634 8.128322 TCTAATCATCTCCCTAAGCATCTAAC 57.872 38.462 0.00 0.00 0.00 2.34
2212 4635 6.753913 AATCATCTCCCTAAGCATCTAACA 57.246 37.500 0.00 0.00 0.00 2.41
2213 4636 6.949117 ATCATCTCCCTAAGCATCTAACAT 57.051 37.500 0.00 0.00 0.00 2.71
2214 4637 6.753913 TCATCTCCCTAAGCATCTAACATT 57.246 37.500 0.00 0.00 0.00 2.71
2215 4638 6.528321 TCATCTCCCTAAGCATCTAACATTG 58.472 40.000 0.00 0.00 0.00 2.82
2216 4639 5.957771 TCTCCCTAAGCATCTAACATTGT 57.042 39.130 0.00 0.00 0.00 2.71
2217 4640 7.290014 TCATCTCCCTAAGCATCTAACATTGTA 59.710 37.037 0.00 0.00 0.00 2.41
2218 4641 6.817184 TCTCCCTAAGCATCTAACATTGTAC 58.183 40.000 0.00 0.00 0.00 2.90
2219 4642 6.382859 TCTCCCTAAGCATCTAACATTGTACA 59.617 38.462 0.00 0.00 0.00 2.90
2220 4643 6.953101 TCCCTAAGCATCTAACATTGTACAA 58.047 36.000 11.41 11.41 0.00 2.41
2221 4644 7.047891 TCCCTAAGCATCTAACATTGTACAAG 58.952 38.462 14.65 8.70 0.00 3.16
2222 4645 6.260936 CCCTAAGCATCTAACATTGTACAAGG 59.739 42.308 18.17 18.17 0.00 3.61
2223 4646 5.567138 AAGCATCTAACATTGTACAAGGC 57.433 39.130 19.55 5.11 0.00 4.35
2224 4647 3.947834 AGCATCTAACATTGTACAAGGCC 59.052 43.478 19.55 0.00 0.00 5.19
2225 4648 3.947834 GCATCTAACATTGTACAAGGCCT 59.052 43.478 19.55 0.00 0.00 5.19
2252 4675 7.129425 AGGTCTTTCCAGTGATCTAGTTCTAT 58.871 38.462 2.61 0.00 39.02 1.98
2272 5272 9.106070 GTTCTATATTAGGGAAATGTTTCACGT 57.894 33.333 7.69 0.00 45.12 4.49
2278 5278 1.136446 GGAAATGTTTCACGTCGACCG 60.136 52.381 10.58 7.90 38.92 4.79
2279 5279 1.788308 GAAATGTTTCACGTCGACCGA 59.212 47.619 10.58 3.92 40.70 4.69
2282 5282 1.299316 GTTTCACGTCGACCGACCA 60.299 57.895 15.74 0.00 41.76 4.02
2292 5302 1.070786 GACCGACCAGCCAAAGTCA 59.929 57.895 0.00 0.00 33.08 3.41
2294 5304 2.317609 CCGACCAGCCAAAGTCACG 61.318 63.158 0.00 0.00 33.08 4.35
2297 5307 1.557443 GACCAGCCAAAGTCACGTCG 61.557 60.000 0.00 0.00 33.08 5.12
2304 5314 1.056103 CAAAGTCACGTCGCTCTCAG 58.944 55.000 0.00 0.00 0.00 3.35
2305 5315 0.952280 AAAGTCACGTCGCTCTCAGA 59.048 50.000 0.00 0.00 0.00 3.27
2311 5321 2.255554 GTCGCTCTCAGACGCACA 59.744 61.111 0.00 0.00 0.00 4.57
2313 5323 2.256764 CGCTCTCAGACGCACAGT 59.743 61.111 0.00 0.00 0.00 3.55
2314 5324 2.085262 CGCTCTCAGACGCACAGTG 61.085 63.158 0.00 0.00 0.00 3.66
2383 5402 1.173444 AACTGCTCCTCGAGACGTGT 61.173 55.000 15.71 3.17 0.00 4.49
2386 5405 1.003331 CTGCTCCTCGAGACGTGTATC 60.003 57.143 15.71 0.00 0.00 2.24
2387 5406 0.042013 GCTCCTCGAGACGTGTATCG 60.042 60.000 15.71 10.53 44.69 2.92
2393 5412 3.314763 TCGAGACGTGTATCGATGTTC 57.685 47.619 14.92 0.00 46.54 3.18
2394 5413 2.031314 TCGAGACGTGTATCGATGTTCC 59.969 50.000 14.92 0.00 46.54 3.62
2395 5414 2.728922 GAGACGTGTATCGATGTTCCC 58.271 52.381 8.54 0.00 42.86 3.97
2396 5415 1.065102 AGACGTGTATCGATGTTCCCG 59.935 52.381 8.54 5.77 42.86 5.14
2397 5416 0.813184 ACGTGTATCGATGTTCCCGT 59.187 50.000 8.54 6.40 42.86 5.28
2398 5417 1.197055 CGTGTATCGATGTTCCCGTG 58.803 55.000 8.54 0.00 42.86 4.94
2400 5419 0.533032 TGTATCGATGTTCCCGTGCA 59.467 50.000 8.54 0.00 0.00 4.57
2401 5420 1.066787 TGTATCGATGTTCCCGTGCAA 60.067 47.619 8.54 0.00 0.00 4.08
2402 5421 1.326548 GTATCGATGTTCCCGTGCAAC 59.673 52.381 8.54 0.00 0.00 4.17
2403 5422 0.321210 ATCGATGTTCCCGTGCAACA 60.321 50.000 0.00 0.00 38.12 3.33
2443 5466 5.106157 CCCCTTAATTATCGCTTGCCTTATG 60.106 44.000 0.00 0.00 0.00 1.90
2447 5470 7.041098 CCTTAATTATCGCTTGCCTTATGTCTT 60.041 37.037 0.00 0.00 0.00 3.01
2448 5471 8.896320 TTAATTATCGCTTGCCTTATGTCTTA 57.104 30.769 0.00 0.00 0.00 2.10
2449 5472 7.426929 AATTATCGCTTGCCTTATGTCTTAG 57.573 36.000 0.00 0.00 0.00 2.18
2454 5477 4.441634 CGCTTGCCTTATGTCTTAGTACCT 60.442 45.833 0.00 0.00 0.00 3.08
2457 5480 6.037281 GCTTGCCTTATGTCTTAGTACCTTTC 59.963 42.308 0.00 0.00 0.00 2.62
2473 5496 0.323629 TTTCTTGTACCTCCAGCCCG 59.676 55.000 0.00 0.00 0.00 6.13
2476 5499 2.463589 CTTGTACCTCCAGCCCGCAA 62.464 60.000 0.00 0.00 0.00 4.85
2487 5510 0.974383 AGCCCGCAACAAGTACTACT 59.026 50.000 0.00 0.00 0.00 2.57
2489 5512 2.005560 GCCCGCAACAAGTACTACTCC 61.006 57.143 0.00 0.00 0.00 3.85
2491 5514 2.607187 CCGCAACAAGTACTACTCCTG 58.393 52.381 0.00 0.00 0.00 3.86
2495 5518 4.440250 CGCAACAAGTACTACTCCTGCTAT 60.440 45.833 0.00 0.00 29.85 2.97
2507 5530 5.235305 ACTCCTGCTATAAAAATGTTGCG 57.765 39.130 0.00 0.00 0.00 4.85
2510 5533 4.095782 TCCTGCTATAAAAATGTTGCGTCC 59.904 41.667 0.00 0.00 0.00 4.79
2512 5535 3.181505 TGCTATAAAAATGTTGCGTCCGG 60.182 43.478 0.00 0.00 0.00 5.14
2518 5541 1.644786 AATGTTGCGTCCGGCTAAGC 61.645 55.000 0.00 0.00 44.05 3.09
2525 5548 1.562575 CGTCCGGCTAAGCAAAACGT 61.563 55.000 0.00 0.00 0.00 3.99
2527 5550 0.589223 TCCGGCTAAGCAAAACGTTG 59.411 50.000 0.00 0.00 37.83 4.10
2554 5577 4.440839 AATGAATCGAAAAGCTGGAACC 57.559 40.909 0.00 0.00 0.00 3.62
2555 5578 1.804151 TGAATCGAAAAGCTGGAACCG 59.196 47.619 0.00 0.00 0.00 4.44
2556 5579 2.073816 GAATCGAAAAGCTGGAACCGA 58.926 47.619 0.00 0.00 0.00 4.69
2557 5580 2.403252 ATCGAAAAGCTGGAACCGAT 57.597 45.000 0.00 0.00 32.74 4.18
2558 5581 1.438651 TCGAAAAGCTGGAACCGATG 58.561 50.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 4.095610 CCAATCCGAAGCACGTAAAATTC 58.904 43.478 0.00 0.00 40.78 2.17
853 956 1.079405 AGTGCACGGGACAATACGG 60.079 57.895 12.01 0.00 0.00 4.02
873 976 1.871039 TCATCGTCATGCATGCAGATG 59.129 47.619 34.02 34.02 39.94 2.90
898 1001 1.366854 GGGTTCTTCGATTCACCGGC 61.367 60.000 0.00 0.00 0.00 6.13
903 1006 5.693769 AAATAGGAGGGTTCTTCGATTCA 57.306 39.130 0.00 0.00 0.00 2.57
917 1020 7.442666 GCAGAAGAAAGGTGGTATAAATAGGAG 59.557 40.741 0.00 0.00 0.00 3.69
918 1021 7.280356 GCAGAAGAAAGGTGGTATAAATAGGA 58.720 38.462 0.00 0.00 0.00 2.94
919 1022 6.202954 CGCAGAAGAAAGGTGGTATAAATAGG 59.797 42.308 0.00 0.00 0.00 2.57
950 1053 2.927856 AGATGGACGGGTGTGGCA 60.928 61.111 0.00 0.00 0.00 4.92
974 1078 0.881796 CTAGTGAGTGAGGTGCGTGA 59.118 55.000 0.00 0.00 0.00 4.35
987 1091 2.111384 GAGACCATGCTTCCCTAGTGA 58.889 52.381 0.00 0.00 0.00 3.41
1093 1200 1.616159 CACTGGGTTTCATTTCCGGT 58.384 50.000 0.00 0.00 40.50 5.28
1286 1393 1.280710 TCTTTGGACGGTGGCATACAT 59.719 47.619 0.00 0.00 0.00 2.29
1289 1396 1.339631 CCTTCTTTGGACGGTGGCATA 60.340 52.381 0.00 0.00 0.00 3.14
1290 1397 0.609131 CCTTCTTTGGACGGTGGCAT 60.609 55.000 0.00 0.00 0.00 4.40
1291 1398 1.228124 CCTTCTTTGGACGGTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
1305 1412 3.492313 CAAGTAAAACGCATGCTCCTTC 58.508 45.455 17.13 2.03 0.00 3.46
1309 1418 2.619013 AGCAAGTAAAACGCATGCTC 57.381 45.000 17.13 0.00 43.43 4.26
1311 1420 1.250476 CGAGCAAGTAAAACGCATGC 58.750 50.000 7.91 7.91 37.28 4.06
1335 1449 5.302059 GGAGAGTCATGCTGGTTATGTAGTA 59.698 44.000 0.00 0.00 0.00 1.82
1336 1450 4.100189 GGAGAGTCATGCTGGTTATGTAGT 59.900 45.833 0.00 0.00 0.00 2.73
1337 1451 4.502259 GGGAGAGTCATGCTGGTTATGTAG 60.502 50.000 0.00 0.00 0.00 2.74
1486 1618 2.041265 ATGGGCTTCGGAGGTCCT 59.959 61.111 12.26 0.00 0.00 3.85
1670 1802 4.979815 TGTATATATCGCGTGTTCACTTGG 59.020 41.667 5.77 0.00 0.00 3.61
1680 1812 3.972403 TGTTGTGCTGTATATATCGCGT 58.028 40.909 5.77 0.00 0.00 6.01
1721 1854 7.551617 CCCCGTCTACATATACTGTTTTCTTTT 59.448 37.037 0.00 0.00 39.39 2.27
1725 1858 5.910614 ACCCCGTCTACATATACTGTTTTC 58.089 41.667 0.00 0.00 39.39 2.29
1743 1876 5.830000 TCGATATTATCAGTCATACCCCG 57.170 43.478 4.63 0.00 0.00 5.73
1851 4274 7.173907 CACAAGGAATCAACTTCTAACATCAGT 59.826 37.037 0.00 0.00 34.08 3.41
1941 4364 3.275999 GTCATAATTGTGGGTTAGCCGT 58.724 45.455 2.06 0.00 34.97 5.68
1942 4365 2.286833 CGTCATAATTGTGGGTTAGCCG 59.713 50.000 2.06 0.00 34.97 5.52
2023 4446 8.437360 TCTTACATTGTACAAGGCATTATCAG 57.563 34.615 19.55 1.89 0.00 2.90
2028 4451 5.653769 AGCATCTTACATTGTACAAGGCATT 59.346 36.000 19.55 3.76 0.00 3.56
2029 4452 5.195940 AGCATCTTACATTGTACAAGGCAT 58.804 37.500 19.55 4.48 0.00 4.40
2030 4453 4.588899 AGCATCTTACATTGTACAAGGCA 58.411 39.130 19.55 4.48 0.00 4.75
2031 4454 5.567138 AAGCATCTTACATTGTACAAGGC 57.433 39.130 19.55 5.11 0.00 4.35
2032 4455 7.981789 TCTCTAAGCATCTTACATTGTACAAGG 59.018 37.037 18.17 18.17 0.00 3.61
2033 4456 8.932945 TCTCTAAGCATCTTACATTGTACAAG 57.067 34.615 14.65 8.70 0.00 3.16
2034 4457 9.371136 CTTCTCTAAGCATCTTACATTGTACAA 57.629 33.333 11.41 11.41 0.00 2.41
2035 4458 7.981789 CCTTCTCTAAGCATCTTACATTGTACA 59.018 37.037 0.00 0.00 0.00 2.90
2036 4459 7.982354 ACCTTCTCTAAGCATCTTACATTGTAC 59.018 37.037 0.00 0.00 0.00 2.90
2037 4460 7.981789 CACCTTCTCTAAGCATCTTACATTGTA 59.018 37.037 0.00 0.00 0.00 2.41
2038 4461 6.820656 CACCTTCTCTAAGCATCTTACATTGT 59.179 38.462 0.00 0.00 0.00 2.71
2039 4462 6.238320 GCACCTTCTCTAAGCATCTTACATTG 60.238 42.308 0.00 0.00 0.00 2.82
2040 4463 5.819901 GCACCTTCTCTAAGCATCTTACATT 59.180 40.000 0.00 0.00 0.00 2.71
2041 4464 5.130145 AGCACCTTCTCTAAGCATCTTACAT 59.870 40.000 0.00 0.00 0.00 2.29
2042 4465 4.467795 AGCACCTTCTCTAAGCATCTTACA 59.532 41.667 0.00 0.00 0.00 2.41
2043 4466 5.017294 AGCACCTTCTCTAAGCATCTTAC 57.983 43.478 0.00 0.00 0.00 2.34
2044 4467 5.683876 AAGCACCTTCTCTAAGCATCTTA 57.316 39.130 0.00 0.00 0.00 2.10
2045 4468 4.566426 AAGCACCTTCTCTAAGCATCTT 57.434 40.909 0.00 0.00 0.00 2.40
2046 4469 4.959210 TCTAAGCACCTTCTCTAAGCATCT 59.041 41.667 0.00 0.00 0.00 2.90
2047 4470 5.269505 TCTAAGCACCTTCTCTAAGCATC 57.730 43.478 0.00 0.00 0.00 3.91
2048 4471 5.683876 TTCTAAGCACCTTCTCTAAGCAT 57.316 39.130 0.00 0.00 0.00 3.79
2049 4472 5.483685 TTTCTAAGCACCTTCTCTAAGCA 57.516 39.130 0.00 0.00 0.00 3.91
2050 4473 6.803154 TTTTTCTAAGCACCTTCTCTAAGC 57.197 37.500 0.00 0.00 0.00 3.09
2054 4477 9.520515 TGATTTATTTTTCTAAGCACCTTCTCT 57.479 29.630 0.00 0.00 0.00 3.10
2055 4478 9.780413 CTGATTTATTTTTCTAAGCACCTTCTC 57.220 33.333 0.00 0.00 0.00 2.87
2056 4479 8.743714 CCTGATTTATTTTTCTAAGCACCTTCT 58.256 33.333 0.00 0.00 0.00 2.85
2057 4480 8.523658 ACCTGATTTATTTTTCTAAGCACCTTC 58.476 33.333 0.00 0.00 0.00 3.46
2058 4481 8.422577 ACCTGATTTATTTTTCTAAGCACCTT 57.577 30.769 0.00 0.00 0.00 3.50
2059 4482 8.422577 AACCTGATTTATTTTTCTAAGCACCT 57.577 30.769 0.00 0.00 0.00 4.00
2060 4483 9.489084 AAAACCTGATTTATTTTTCTAAGCACC 57.511 29.630 0.00 0.00 0.00 5.01
2071 4494 9.489084 GGTGCTTAAGAAAAACCTGATTTATTT 57.511 29.630 6.67 0.00 0.00 1.40
2072 4495 7.812669 CGGTGCTTAAGAAAAACCTGATTTATT 59.187 33.333 6.67 0.00 0.00 1.40
2073 4496 7.312899 CGGTGCTTAAGAAAAACCTGATTTAT 58.687 34.615 6.67 0.00 0.00 1.40
2074 4497 6.294286 CCGGTGCTTAAGAAAAACCTGATTTA 60.294 38.462 6.67 0.00 0.00 1.40
2075 4498 5.508994 CCGGTGCTTAAGAAAAACCTGATTT 60.509 40.000 6.67 0.00 0.00 2.17
2076 4499 4.022329 CCGGTGCTTAAGAAAAACCTGATT 60.022 41.667 6.67 0.00 0.00 2.57
2077 4500 3.506067 CCGGTGCTTAAGAAAAACCTGAT 59.494 43.478 6.67 0.00 0.00 2.90
2078 4501 2.882137 CCGGTGCTTAAGAAAAACCTGA 59.118 45.455 6.67 0.00 0.00 3.86
2079 4502 2.621526 ACCGGTGCTTAAGAAAAACCTG 59.378 45.455 6.12 6.78 0.00 4.00
2080 4503 2.621526 CACCGGTGCTTAAGAAAAACCT 59.378 45.455 24.02 0.00 0.00 3.50
2081 4504 2.359848 ACACCGGTGCTTAAGAAAAACC 59.640 45.455 34.26 6.81 0.00 3.27
2082 4505 3.703286 ACACCGGTGCTTAAGAAAAAC 57.297 42.857 34.26 0.00 0.00 2.43
2083 4506 4.722361 AAACACCGGTGCTTAAGAAAAA 57.278 36.364 34.26 0.00 0.00 1.94
2084 4507 5.299782 ACATAAACACCGGTGCTTAAGAAAA 59.700 36.000 34.26 12.62 0.00 2.29
2085 4508 4.822896 ACATAAACACCGGTGCTTAAGAAA 59.177 37.500 34.26 13.38 0.00 2.52
2086 4509 4.214545 CACATAAACACCGGTGCTTAAGAA 59.785 41.667 34.26 13.77 0.00 2.52
2087 4510 3.749088 CACATAAACACCGGTGCTTAAGA 59.251 43.478 34.26 14.15 0.00 2.10
2088 4511 3.500680 ACACATAAACACCGGTGCTTAAG 59.499 43.478 34.26 28.37 34.69 1.85
2089 4512 3.478509 ACACATAAACACCGGTGCTTAA 58.521 40.909 34.26 17.52 34.69 1.85
2090 4513 3.128852 ACACATAAACACCGGTGCTTA 57.871 42.857 34.26 30.62 34.69 3.09
2091 4514 1.975660 ACACATAAACACCGGTGCTT 58.024 45.000 34.26 29.48 34.69 3.91
2092 4515 2.224329 TGTACACATAAACACCGGTGCT 60.224 45.455 34.26 20.93 34.69 4.40
2093 4516 2.144730 TGTACACATAAACACCGGTGC 58.855 47.619 34.26 14.11 34.69 5.01
2094 4517 2.739913 CCTGTACACATAAACACCGGTG 59.260 50.000 32.83 32.83 37.29 4.94
2095 4518 2.633967 TCCTGTACACATAAACACCGGT 59.366 45.455 0.00 0.00 0.00 5.28
2096 4519 3.322211 TCCTGTACACATAAACACCGG 57.678 47.619 0.00 0.00 0.00 5.28
2097 4520 5.747197 GTCTATCCTGTACACATAAACACCG 59.253 44.000 0.00 0.00 0.00 4.94
2098 4521 5.747197 CGTCTATCCTGTACACATAAACACC 59.253 44.000 0.00 0.00 0.00 4.16
2099 4522 5.231568 GCGTCTATCCTGTACACATAAACAC 59.768 44.000 0.00 0.00 0.00 3.32
2100 4523 5.126545 AGCGTCTATCCTGTACACATAAACA 59.873 40.000 0.00 0.00 0.00 2.83
2101 4524 5.589192 AGCGTCTATCCTGTACACATAAAC 58.411 41.667 0.00 0.00 0.00 2.01
2102 4525 5.847111 AGCGTCTATCCTGTACACATAAA 57.153 39.130 0.00 0.00 0.00 1.40
2103 4526 5.847111 AAGCGTCTATCCTGTACACATAA 57.153 39.130 0.00 0.00 0.00 1.90
2104 4527 6.947644 TTAAGCGTCTATCCTGTACACATA 57.052 37.500 0.00 0.00 0.00 2.29
2105 4528 5.847111 TTAAGCGTCTATCCTGTACACAT 57.153 39.130 0.00 0.00 0.00 3.21
2106 4529 5.847111 ATTAAGCGTCTATCCTGTACACA 57.153 39.130 0.00 0.00 0.00 3.72
2107 4530 6.862090 CCTAATTAAGCGTCTATCCTGTACAC 59.138 42.308 0.00 0.00 0.00 2.90
2108 4531 6.516194 GCCTAATTAAGCGTCTATCCTGTACA 60.516 42.308 0.00 0.00 0.00 2.90
2109 4532 5.862860 GCCTAATTAAGCGTCTATCCTGTAC 59.137 44.000 0.00 0.00 0.00 2.90
2110 4533 6.022163 GCCTAATTAAGCGTCTATCCTGTA 57.978 41.667 0.00 0.00 0.00 2.74
2111 4534 4.884247 GCCTAATTAAGCGTCTATCCTGT 58.116 43.478 0.00 0.00 0.00 4.00
2122 4545 8.813643 TTTATAGAAGAGACGCCTAATTAAGC 57.186 34.615 0.00 0.00 0.00 3.09
2128 4551 9.962783 GACTATTTTTATAGAAGAGACGCCTAA 57.037 33.333 0.00 0.00 0.00 2.69
2129 4552 9.128404 TGACTATTTTTATAGAAGAGACGCCTA 57.872 33.333 0.00 0.00 0.00 3.93
2130 4553 7.921745 GTGACTATTTTTATAGAAGAGACGCCT 59.078 37.037 0.00 0.00 0.00 5.52
2131 4554 7.921745 AGTGACTATTTTTATAGAAGAGACGCC 59.078 37.037 0.00 0.00 0.00 5.68
2132 4555 8.747666 CAGTGACTATTTTTATAGAAGAGACGC 58.252 37.037 0.00 2.00 0.00 5.19
2157 4580 2.857483 TCGGGTTTTTCTGAAGCATCA 58.143 42.857 0.00 0.00 0.00 3.07
2158 4581 4.440839 AATCGGGTTTTTCTGAAGCATC 57.559 40.909 0.00 0.00 0.00 3.91
2159 4582 4.871933 AAATCGGGTTTTTCTGAAGCAT 57.128 36.364 0.00 0.00 0.00 3.79
2160 4583 5.975693 ATAAATCGGGTTTTTCTGAAGCA 57.024 34.783 0.00 0.00 0.00 3.91
2161 4584 7.652300 AAAATAAATCGGGTTTTTCTGAAGC 57.348 32.000 0.00 0.00 0.00 3.86
2172 4595 9.067986 GGAGATGATTAGAAAAATAAATCGGGT 57.932 33.333 0.00 0.00 33.28 5.28
2173 4596 8.515414 GGGAGATGATTAGAAAAATAAATCGGG 58.485 37.037 0.00 0.00 33.28 5.14
2174 4597 9.289782 AGGGAGATGATTAGAAAAATAAATCGG 57.710 33.333 0.00 0.00 33.28 4.18
2181 4604 9.294614 GATGCTTAGGGAGATGATTAGAAAAAT 57.705 33.333 0.00 0.00 0.00 1.82
2182 4605 8.497745 AGATGCTTAGGGAGATGATTAGAAAAA 58.502 33.333 0.00 0.00 0.00 1.94
2183 4606 8.038862 AGATGCTTAGGGAGATGATTAGAAAA 57.961 34.615 0.00 0.00 0.00 2.29
2184 4607 7.623999 AGATGCTTAGGGAGATGATTAGAAA 57.376 36.000 0.00 0.00 0.00 2.52
2185 4608 8.589338 GTTAGATGCTTAGGGAGATGATTAGAA 58.411 37.037 0.00 0.00 0.00 2.10
2186 4609 7.730332 TGTTAGATGCTTAGGGAGATGATTAGA 59.270 37.037 0.00 0.00 0.00 2.10
2187 4610 7.901029 TGTTAGATGCTTAGGGAGATGATTAG 58.099 38.462 0.00 0.00 0.00 1.73
2188 4611 7.855784 TGTTAGATGCTTAGGGAGATGATTA 57.144 36.000 0.00 0.00 0.00 1.75
2189 4612 6.753913 TGTTAGATGCTTAGGGAGATGATT 57.246 37.500 0.00 0.00 0.00 2.57
2190 4613 6.949117 ATGTTAGATGCTTAGGGAGATGAT 57.051 37.500 0.00 0.00 0.00 2.45
2191 4614 6.100279 ACAATGTTAGATGCTTAGGGAGATGA 59.900 38.462 0.00 0.00 0.00 2.92
2192 4615 6.294473 ACAATGTTAGATGCTTAGGGAGATG 58.706 40.000 0.00 0.00 0.00 2.90
2193 4616 6.506538 ACAATGTTAGATGCTTAGGGAGAT 57.493 37.500 0.00 0.00 0.00 2.75
2194 4617 5.957771 ACAATGTTAGATGCTTAGGGAGA 57.042 39.130 0.00 0.00 0.00 3.71
2195 4618 6.582636 TGTACAATGTTAGATGCTTAGGGAG 58.417 40.000 0.00 0.00 0.00 4.30
2196 4619 6.553953 TGTACAATGTTAGATGCTTAGGGA 57.446 37.500 0.00 0.00 0.00 4.20
2197 4620 6.260936 CCTTGTACAATGTTAGATGCTTAGGG 59.739 42.308 9.13 0.00 0.00 3.53
2198 4621 6.238484 GCCTTGTACAATGTTAGATGCTTAGG 60.238 42.308 9.13 2.44 0.00 2.69
2199 4622 6.238484 GGCCTTGTACAATGTTAGATGCTTAG 60.238 42.308 9.13 0.00 0.00 2.18
2200 4623 5.588648 GGCCTTGTACAATGTTAGATGCTTA 59.411 40.000 9.13 0.00 0.00 3.09
2201 4624 4.399303 GGCCTTGTACAATGTTAGATGCTT 59.601 41.667 9.13 0.00 0.00 3.91
2202 4625 3.947834 GGCCTTGTACAATGTTAGATGCT 59.052 43.478 9.13 0.00 0.00 3.79
2203 4626 3.947834 AGGCCTTGTACAATGTTAGATGC 59.052 43.478 9.13 2.54 0.00 3.91
2204 4627 6.260936 CCTTAGGCCTTGTACAATGTTAGATG 59.739 42.308 12.58 0.00 0.00 2.90
2205 4628 6.069615 ACCTTAGGCCTTGTACAATGTTAGAT 60.070 38.462 12.58 0.00 0.00 1.98
2206 4629 5.249852 ACCTTAGGCCTTGTACAATGTTAGA 59.750 40.000 12.58 0.00 0.00 2.10
2207 4630 5.497474 ACCTTAGGCCTTGTACAATGTTAG 58.503 41.667 12.58 0.00 0.00 2.34
2208 4631 5.249852 AGACCTTAGGCCTTGTACAATGTTA 59.750 40.000 12.58 1.57 0.00 2.41
2209 4632 4.042934 AGACCTTAGGCCTTGTACAATGTT 59.957 41.667 12.58 2.48 0.00 2.71
2210 4633 3.587506 AGACCTTAGGCCTTGTACAATGT 59.412 43.478 12.58 0.93 0.00 2.71
2211 4634 4.222124 AGACCTTAGGCCTTGTACAATG 57.778 45.455 12.58 7.68 0.00 2.82
2212 4635 4.929146 AAGACCTTAGGCCTTGTACAAT 57.071 40.909 12.58 0.00 0.00 2.71
2213 4636 4.506095 GGAAAGACCTTAGGCCTTGTACAA 60.506 45.833 12.58 8.28 35.41 2.41
2214 4637 3.008704 GGAAAGACCTTAGGCCTTGTACA 59.991 47.826 12.58 0.00 35.41 2.90
2215 4638 3.008704 TGGAAAGACCTTAGGCCTTGTAC 59.991 47.826 12.58 0.00 39.86 2.90
2216 4639 3.253220 TGGAAAGACCTTAGGCCTTGTA 58.747 45.455 12.58 0.00 39.86 2.41
2217 4640 2.040412 CTGGAAAGACCTTAGGCCTTGT 59.960 50.000 12.58 6.22 39.86 3.16
2218 4641 2.040412 ACTGGAAAGACCTTAGGCCTTG 59.960 50.000 12.58 4.20 39.86 3.61
2219 4642 2.040412 CACTGGAAAGACCTTAGGCCTT 59.960 50.000 12.58 0.00 39.86 4.35
2220 4643 1.630878 CACTGGAAAGACCTTAGGCCT 59.369 52.381 11.78 11.78 39.86 5.19
2221 4644 1.628846 TCACTGGAAAGACCTTAGGCC 59.371 52.381 0.00 0.00 39.86 5.19
2222 4645 3.198853 AGATCACTGGAAAGACCTTAGGC 59.801 47.826 0.00 0.00 39.86 3.93
2223 4646 5.659079 ACTAGATCACTGGAAAGACCTTAGG 59.341 44.000 0.00 0.00 39.86 2.69
2224 4647 6.783708 ACTAGATCACTGGAAAGACCTTAG 57.216 41.667 0.00 0.00 39.86 2.18
2225 4648 6.954684 AGAACTAGATCACTGGAAAGACCTTA 59.045 38.462 0.00 0.00 39.86 2.69
2252 4675 5.577945 GTCGACGTGAAACATTTCCCTAATA 59.422 40.000 0.00 0.00 35.74 0.98
2272 5272 2.342279 CTTTGGCTGGTCGGTCGA 59.658 61.111 0.00 0.00 0.00 4.20
2278 5278 1.557443 CGACGTGACTTTGGCTGGTC 61.557 60.000 0.00 0.00 0.00 4.02
2279 5279 1.594293 CGACGTGACTTTGGCTGGT 60.594 57.895 0.00 0.00 0.00 4.00
2282 5282 1.664965 GAGCGACGTGACTTTGGCT 60.665 57.895 0.00 0.00 0.00 4.75
2285 5285 1.056103 CTGAGAGCGACGTGACTTTG 58.944 55.000 0.00 0.00 0.00 2.77
2286 5286 0.952280 TCTGAGAGCGACGTGACTTT 59.048 50.000 0.00 0.00 0.00 2.66
2294 5304 1.799519 CTGTGCGTCTGAGAGCGAC 60.800 63.158 8.26 4.85 35.87 5.19
2297 5307 1.006805 ACACTGTGCGTCTGAGAGC 60.007 57.895 7.90 0.00 0.00 4.09
2362 5381 0.039074 ACGTCTCGAGGAGCAGTTTG 60.039 55.000 13.56 0.00 0.00 2.93
2373 5392 2.031314 GGAACATCGATACACGTCTCGA 59.969 50.000 14.46 14.46 46.71 4.04
2383 5402 1.066787 TGTTGCACGGGAACATCGATA 60.067 47.619 0.00 0.00 0.00 2.92
2386 5405 1.497278 CTGTTGCACGGGAACATCG 59.503 57.895 10.41 0.00 32.96 3.84
2387 5406 1.210155 GCTGTTGCACGGGAACATC 59.790 57.895 10.41 4.49 39.41 3.06
2389 5408 2.904866 GGCTGTTGCACGGGAACA 60.905 61.111 9.77 9.77 41.91 3.18
2396 5415 0.752658 AAAAAGGAGGGCTGTTGCAC 59.247 50.000 0.00 0.00 44.43 4.57
2397 5416 1.039856 GAAAAAGGAGGGCTGTTGCA 58.960 50.000 0.00 0.00 41.91 4.08
2398 5417 0.318441 GGAAAAAGGAGGGCTGTTGC 59.682 55.000 0.00 0.00 38.76 4.17
2400 5419 1.203063 GGAGGAAAAAGGAGGGCTGTT 60.203 52.381 0.00 0.00 0.00 3.16
2401 5420 0.405973 GGAGGAAAAAGGAGGGCTGT 59.594 55.000 0.00 0.00 0.00 4.40
2402 5421 0.323816 GGGAGGAAAAAGGAGGGCTG 60.324 60.000 0.00 0.00 0.00 4.85
2403 5422 1.510431 GGGGAGGAAAAAGGAGGGCT 61.510 60.000 0.00 0.00 0.00 5.19
2443 5466 6.210185 TGGAGGTACAAGAAAGGTACTAAGAC 59.790 42.308 0.00 0.00 38.49 3.01
2447 5470 4.465305 GCTGGAGGTACAAGAAAGGTACTA 59.535 45.833 0.00 0.00 38.49 1.82
2449 5472 3.597255 GCTGGAGGTACAAGAAAGGTAC 58.403 50.000 0.00 0.00 40.24 3.34
2454 5477 0.323629 CGGGCTGGAGGTACAAGAAA 59.676 55.000 0.00 0.00 0.00 2.52
2457 5480 2.125106 GCGGGCTGGAGGTACAAG 60.125 66.667 0.00 0.00 0.00 3.16
2473 5496 3.320673 AGCAGGAGTAGTACTTGTTGC 57.679 47.619 19.04 19.04 32.78 4.17
2476 5499 9.601217 CATTTTTATAGCAGGAGTAGTACTTGT 57.399 33.333 0.00 0.00 0.00 3.16
2487 5510 4.095782 GGACGCAACATTTTTATAGCAGGA 59.904 41.667 0.00 0.00 0.00 3.86
2489 5512 4.028383 CGGACGCAACATTTTTATAGCAG 58.972 43.478 0.00 0.00 0.00 4.24
2491 5514 3.359654 CCGGACGCAACATTTTTATAGC 58.640 45.455 0.00 0.00 0.00 2.97
2495 5518 1.240256 AGCCGGACGCAACATTTTTA 58.760 45.000 5.05 0.00 41.38 1.52
2507 5530 0.589708 AACGTTTTGCTTAGCCGGAC 59.410 50.000 5.05 0.00 0.00 4.79
2518 5541 5.623264 TCGATTCATTAGTTGCAACGTTTTG 59.377 36.000 23.21 18.16 35.62 2.44
2525 5548 5.858049 CAGCTTTTCGATTCATTAGTTGCAA 59.142 36.000 0.00 0.00 0.00 4.08
2527 5550 4.795278 CCAGCTTTTCGATTCATTAGTTGC 59.205 41.667 0.00 0.00 0.00 4.17
2531 5554 5.573146 GGTTCCAGCTTTTCGATTCATTAG 58.427 41.667 0.00 0.00 0.00 1.73
2533 5556 3.119849 CGGTTCCAGCTTTTCGATTCATT 60.120 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.