Multiple sequence alignment - TraesCS3A01G236900

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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 TraesCS3A01G236900 chr3A 100.000 5823 0 0 1 5823 442767794 442773616 0.000000e+00 10754.0
1 TraesCS3A01G236900 chr3A 97.798 545 10 2 5279 5823 657463900 657463358 0.000000e+00 939.0
2 TraesCS3A01G236900 chr3A 98.718 78 1 0 1953 2030 136499772 136499849 7.870000e-29 139.0
3 TraesCS3A01G236900 chr3A 93.407 91 3 3 1953 2043 24625278 24625191 1.320000e-26 132.0
4 TraesCS3A01G236900 chr3A 97.403 77 0 2 1954 2030 724215936 724215862 4.740000e-26 130.0
5 TraesCS3A01G236900 chr3B 93.268 3283 128 26 2031 5280 421661913 421658691 0.000000e+00 4752.0
6 TraesCS3A01G236900 chr3B 94.318 1971 87 9 1 1950 421663866 421661900 0.000000e+00 2996.0
7 TraesCS3A01G236900 chr3B 92.308 52 3 1 5262 5312 739961355 739961304 8.090000e-09 73.1
8 TraesCS3A01G236900 chr3D 94.244 1772 67 8 2031 3774 328391144 328392908 0.000000e+00 2675.0
9 TraesCS3A01G236900 chr3D 94.930 1282 48 5 3880 5155 328393106 328394376 0.000000e+00 1991.0
10 TraesCS3A01G236900 chr3D 92.920 1356 49 6 1 1318 328389228 328390574 0.000000e+00 1929.0
11 TraesCS3A01G236900 chr3D 96.739 552 16 2 1399 1950 328390608 328391157 0.000000e+00 918.0
12 TraesCS3A01G236900 chr3D 98.347 121 2 0 3762 3882 328392938 328393058 4.570000e-51 213.0
13 TraesCS3A01G236900 chr1A 96.886 546 13 3 5279 5823 471475498 471474956 0.000000e+00 911.0
14 TraesCS3A01G236900 chr1A 92.443 397 10 4 5279 5656 568052221 568052616 3.070000e-152 549.0
15 TraesCS3A01G236900 chr4A 96.703 546 14 3 5279 5823 374500676 374500134 0.000000e+00 905.0
16 TraesCS3A01G236900 chr6A 93.705 556 18 5 5270 5823 322055232 322055772 0.000000e+00 817.0
17 TraesCS3A01G236900 chr6A 97.632 380 8 1 5444 5823 112265025 112264647 0.000000e+00 651.0
18 TraesCS3A01G236900 chr7A 91.993 562 9 7 5281 5823 689441197 689440653 0.000000e+00 756.0
19 TraesCS3A01G236900 chr7A 100.000 78 0 0 1953 2030 586345659 586345582 1.690000e-30 145.0
20 TraesCS3A01G236900 chr7A 94.048 84 3 2 1953 2036 66256978 66256897 6.130000e-25 126.0
21 TraesCS3A01G236900 chr7A 93.182 44 3 0 5355 5398 4753217 4753260 1.350000e-06 65.8
22 TraesCS3A01G236900 chr6B 91.115 574 15 10 5271 5823 139359259 139358701 0.000000e+00 745.0
23 TraesCS3A01G236900 chr5B 90.734 572 30 5 5270 5820 516024008 516024577 0.000000e+00 741.0
24 TraesCS3A01G236900 chr2A 88.772 570 40 9 5270 5817 18835356 18835923 0.000000e+00 676.0
25 TraesCS3A01G236900 chr2A 96.154 78 1 2 1953 2030 487789305 487789380 6.130000e-25 126.0
26 TraesCS3A01G236900 chr2A 93.750 80 3 2 1950 2029 642648564 642648641 1.030000e-22 119.0
27 TraesCS3A01G236900 chr5A 84.669 574 65 16 5270 5823 654093070 654092500 8.530000e-153 551.0
28 TraesCS3A01G236900 chr1D 96.203 79 2 1 1953 2031 423855963 423856040 1.700000e-25 128.0
29 TraesCS3A01G236900 chr4B 93.976 83 2 3 1953 2034 643334956 643335036 7.920000e-24 122.0
30 TraesCS3A01G236900 chr5D 90.000 60 3 3 5253 5312 399572890 399572834 2.250000e-09 75.0
31 TraesCS3A01G236900 chr2D 94.000 50 2 1 5264 5312 598653447 598653398 2.250000e-09 75.0
32 TraesCS3A01G236900 chr1B 89.474 57 3 3 5255 5310 540270173 540270227 1.050000e-07 69.4


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 TraesCS3A01G236900 chr3A 442767794 442773616 5822 False 10754.0 10754 100.000 1 5823 1 chr3A.!!$F2 5822
1 TraesCS3A01G236900 chr3A 657463358 657463900 542 True 939.0 939 97.798 5279 5823 1 chr3A.!!$R2 544
2 TraesCS3A01G236900 chr3B 421658691 421663866 5175 True 3874.0 4752 93.793 1 5280 2 chr3B.!!$R2 5279
3 TraesCS3A01G236900 chr3D 328389228 328394376 5148 False 1545.2 2675 95.436 1 5155 5 chr3D.!!$F1 5154
4 TraesCS3A01G236900 chr1A 471474956 471475498 542 True 911.0 911 96.886 5279 5823 1 chr1A.!!$R1 544
5 TraesCS3A01G236900 chr4A 374500134 374500676 542 True 905.0 905 96.703 5279 5823 1 chr4A.!!$R1 544
6 TraesCS3A01G236900 chr6A 322055232 322055772 540 False 817.0 817 93.705 5270 5823 1 chr6A.!!$F1 553
7 TraesCS3A01G236900 chr7A 689440653 689441197 544 True 756.0 756 91.993 5281 5823 1 chr7A.!!$R3 542
8 TraesCS3A01G236900 chr6B 139358701 139359259 558 True 745.0 745 91.115 5271 5823 1 chr6B.!!$R1 552
9 TraesCS3A01G236900 chr5B 516024008 516024577 569 False 741.0 741 90.734 5270 5820 1 chr5B.!!$F1 550
10 TraesCS3A01G236900 chr2A 18835356 18835923 567 False 676.0 676 88.772 5270 5817 1 chr2A.!!$F1 547
11 TraesCS3A01G236900 chr5A 654092500 654093070 570 True 551.0 551 84.669 5270 5823 1 chr5A.!!$R1 553

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
705 744 0.833409 TCAGTCTGAGGCTGAAGGCA 60.833 55.0 15.33 0.0 44.01 4.75 F
1334 1386 0.028110 GCTAAAGAAGCCGCATTCCG 59.972 55.0 0.00 0.0 46.25 4.30 F
1371 1431 0.534877 TGGCGCTGATGTTTGTGTCT 60.535 50.0 7.64 0.0 0.00 3.41 F
2023 2083 0.677414 GGGTAAATGCCCGGTTCGAA 60.677 55.0 0.00 0.0 39.17 3.71 F
3637 3728 0.033366 AACGCCCTTGTTTTCATGGC 59.967 50.0 0.00 0.0 41.87 4.40 F
4485 4685 2.289002 CCATCTAGCAGACGCCAATTTC 59.711 50.0 0.00 0.0 39.83 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 2463 0.185901 ACAGTGTGATTGGCCCAAGT 59.814 50.000 1.16 0.00 0.00 3.16 R
2720 2808 0.627986 CCTGGGGAGCAAGGAAGAAT 59.372 55.000 0.00 0.00 35.40 2.40 R
2781 2869 3.181491 CCACAAAACGGTGATGTTTCAGT 60.181 43.478 0.00 0.00 41.01 3.41 R
3787 3920 0.251165 GTTGGTTCCAAGGCTGGCTA 60.251 55.000 3.41 0.00 43.17 3.93 R
4772 4972 0.108424 CTCTGCGGGGAGAGAGTTTG 60.108 60.000 11.31 0.00 41.95 2.93 R
5344 5553 8.239998 TGTATTTCGATGATGCAACAAAATGTA 58.760 29.630 12.71 2.77 0.00 2.29 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
79 80 5.610982 GCAAAAGAAATGTCGCAAACAGATG 60.611 40.000 0.00 0.00 42.37 2.90
148 178 2.092429 TGCCAAGGAAAATCGGAGCTAT 60.092 45.455 0.00 0.00 0.00 2.97
272 303 8.996988 TGTCGTTGAAGACATAAATTTTGTAC 57.003 30.769 0.00 0.00 45.18 2.90
295 326 3.684305 TCACAATACCTGAAGTTCGCATG 59.316 43.478 0.00 0.00 0.00 4.06
326 357 3.077359 AGTGAGCATAACAGCCACTTTC 58.923 45.455 0.00 0.00 40.60 2.62
343 374 8.759782 AGCCACTTTCTGTACTAATACTAACAT 58.240 33.333 0.00 0.00 32.00 2.71
365 396 4.868450 AAAATGACGACAACGAAACAGA 57.132 36.364 0.00 0.00 42.66 3.41
397 428 5.965922 TCAAAGCTGATTTAGATCGAGTGA 58.034 37.500 0.00 0.00 34.91 3.41
457 488 2.045926 AGAGGCCGTGTGGATTGC 60.046 61.111 0.00 0.00 37.49 3.56
493 524 4.127040 AGCTCTCAGTGCGGCTCG 62.127 66.667 0.00 0.00 35.28 5.03
643 677 5.644636 CGGAAAAATAGTTGGGTACTTAGCA 59.355 40.000 0.00 0.00 38.33 3.49
705 744 0.833409 TCAGTCTGAGGCTGAAGGCA 60.833 55.000 15.33 0.00 44.01 4.75
740 779 3.998156 GAAGCCCCTTCGGTTTCC 58.002 61.111 0.00 0.00 44.08 3.13
958 1004 1.607251 CGGTCATATTTCGGTAGGGGC 60.607 57.143 0.00 0.00 0.00 5.80
1014 1060 2.562298 GGAGAGGATGATACTGCTCCAG 59.438 54.545 14.51 0.00 41.14 3.86
1044 1090 2.962421 CAGGTTCCTACTCCAGATCCTC 59.038 54.545 0.00 0.00 0.00 3.71
1204 1252 0.778223 CGACGATGTGCGGTATCATG 59.222 55.000 0.00 0.00 46.49 3.07
1218 1266 3.118408 GGTATCATGTCCAGGTTAGTGCA 60.118 47.826 0.00 0.00 0.00 4.57
1222 1270 2.691409 TGTCCAGGTTAGTGCATAGC 57.309 50.000 0.00 0.00 0.00 2.97
1232 1280 1.504912 AGTGCATAGCATCCTCCTGT 58.495 50.000 0.00 0.00 41.91 4.00
1244 1292 3.808466 TCCTCCTGTCGAATCTGAATG 57.192 47.619 0.00 0.00 0.00 2.67
1254 1302 2.355756 CGAATCTGAATGCCCATTTCGT 59.644 45.455 0.00 0.00 32.12 3.85
1291 1340 5.714806 AGGTCATTTATTTTGTGTGTAGGGG 59.285 40.000 0.00 0.00 0.00 4.79
1334 1386 0.028110 GCTAAAGAAGCCGCATTCCG 59.972 55.000 0.00 0.00 46.25 4.30
1354 1414 6.702716 TCCGGCTTTATTTAAATTACCTGG 57.297 37.500 5.91 5.92 0.00 4.45
1371 1431 0.534877 TGGCGCTGATGTTTGTGTCT 60.535 50.000 7.64 0.00 0.00 3.41
1383 1443 8.365399 TGATGTTTGTGTCTTTAGTACTGAAG 57.635 34.615 18.82 18.82 0.00 3.02
1396 1456 5.031066 AGTACTGAAGTTTTGGTGTGCTA 57.969 39.130 0.00 0.00 0.00 3.49
1424 1484 4.023107 GGGTTTCTTTGCTGTCTAACTTCC 60.023 45.833 0.00 0.00 0.00 3.46
1489 1549 7.116805 GCAATTGCAAGCTGAAAGTAAAGTTAT 59.883 33.333 25.36 0.00 41.59 1.89
1512 1572 2.638480 TGCTAAACAGTGGAGTGCTT 57.362 45.000 0.00 0.00 0.00 3.91
1570 1630 6.976934 TGCTCTGTATACTGATGGACATTA 57.023 37.500 12.29 0.00 0.00 1.90
1602 1662 3.191162 TGCAGTTTTCAATGAGGAATCCG 59.809 43.478 0.00 0.00 0.00 4.18
1680 1740 2.759795 GGGCTTCCTCTTGGTGCT 59.240 61.111 0.00 0.00 35.50 4.40
1880 1940 7.151308 GGTGTCTATCTTAGATGTTCTCCATG 58.849 42.308 4.78 0.00 37.13 3.66
1898 1958 8.830915 TCTCCATGGGCAAAATAATACTTTTA 57.169 30.769 13.02 0.00 0.00 1.52
1956 2016 9.593565 TTTCACATGTAGATGTAGATATCTCCT 57.406 33.333 8.95 5.44 41.12 3.69
1957 2017 8.800370 TCACATGTAGATGTAGATATCTCCTC 57.200 38.462 8.95 4.88 41.12 3.71
1958 2018 7.831690 TCACATGTAGATGTAGATATCTCCTCC 59.168 40.741 8.95 0.00 41.12 4.30
1959 2019 7.833682 CACATGTAGATGTAGATATCTCCTCCT 59.166 40.741 8.95 5.78 41.12 3.69
1960 2020 7.833682 ACATGTAGATGTAGATATCTCCTCCTG 59.166 40.741 8.95 0.12 41.27 3.86
1961 2021 7.336475 TGTAGATGTAGATATCTCCTCCTGT 57.664 40.000 8.95 0.00 38.35 4.00
1962 2022 7.760607 TGTAGATGTAGATATCTCCTCCTGTT 58.239 38.462 8.95 0.00 38.35 3.16
1963 2023 8.891501 TGTAGATGTAGATATCTCCTCCTGTTA 58.108 37.037 8.95 0.00 38.35 2.41
1964 2024 9.914834 GTAGATGTAGATATCTCCTCCTGTTAT 57.085 37.037 8.95 0.00 38.35 1.89
1966 2026 8.845793 AGATGTAGATATCTCCTCCTGTTATCT 58.154 37.037 8.95 0.00 31.97 1.98
1967 2027 9.474313 GATGTAGATATCTCCTCCTGTTATCTT 57.526 37.037 8.95 0.00 33.09 2.40
1968 2028 8.642935 TGTAGATATCTCCTCCTGTTATCTTG 57.357 38.462 8.95 0.00 33.09 3.02
1969 2029 8.448816 TGTAGATATCTCCTCCTGTTATCTTGA 58.551 37.037 8.95 0.00 33.09 3.02
1970 2030 9.303116 GTAGATATCTCCTCCTGTTATCTTGAA 57.697 37.037 8.95 0.00 33.09 2.69
1971 2031 8.189119 AGATATCTCCTCCTGTTATCTTGAAC 57.811 38.462 0.00 0.00 0.00 3.18
1972 2032 8.010105 AGATATCTCCTCCTGTTATCTTGAACT 58.990 37.037 0.00 0.00 0.00 3.01
1973 2033 5.667539 TCTCCTCCTGTTATCTTGAACTG 57.332 43.478 0.00 0.00 0.00 3.16
1974 2034 4.467795 TCTCCTCCTGTTATCTTGAACTGG 59.532 45.833 6.00 6.00 45.21 4.00
1975 2035 4.168101 TCCTCCTGTTATCTTGAACTGGT 58.832 43.478 10.73 0.00 44.55 4.00
1976 2036 4.597507 TCCTCCTGTTATCTTGAACTGGTT 59.402 41.667 10.73 0.00 44.55 3.67
1977 2037 5.073144 TCCTCCTGTTATCTTGAACTGGTTT 59.927 40.000 10.73 0.00 44.55 3.27
1978 2038 5.182001 CCTCCTGTTATCTTGAACTGGTTTG 59.818 44.000 10.73 4.79 44.55 2.93
1979 2039 5.690865 TCCTGTTATCTTGAACTGGTTTGT 58.309 37.500 10.73 0.00 44.55 2.83
1980 2040 6.833041 TCCTGTTATCTTGAACTGGTTTGTA 58.167 36.000 10.73 0.00 44.55 2.41
1981 2041 7.458397 TCCTGTTATCTTGAACTGGTTTGTAT 58.542 34.615 10.73 0.00 44.55 2.29
1982 2042 7.942341 TCCTGTTATCTTGAACTGGTTTGTATT 59.058 33.333 10.73 0.00 44.55 1.89
1983 2043 8.576442 CCTGTTATCTTGAACTGGTTTGTATTT 58.424 33.333 4.54 0.00 41.25 1.40
1984 2044 9.612620 CTGTTATCTTGAACTGGTTTGTATTTC 57.387 33.333 0.00 0.00 0.00 2.17
1985 2045 8.573035 TGTTATCTTGAACTGGTTTGTATTTCC 58.427 33.333 0.00 0.00 0.00 3.13
1986 2046 5.682943 TCTTGAACTGGTTTGTATTTCCG 57.317 39.130 0.00 0.00 0.00 4.30
1987 2047 5.127491 TCTTGAACTGGTTTGTATTTCCGT 58.873 37.500 0.00 0.00 0.00 4.69
1988 2048 5.591067 TCTTGAACTGGTTTGTATTTCCGTT 59.409 36.000 0.00 0.00 0.00 4.44
1989 2049 5.427036 TGAACTGGTTTGTATTTCCGTTC 57.573 39.130 0.00 0.00 36.43 3.95
1990 2050 5.127491 TGAACTGGTTTGTATTTCCGTTCT 58.873 37.500 0.01 0.00 36.62 3.01
1991 2051 5.591067 TGAACTGGTTTGTATTTCCGTTCTT 59.409 36.000 0.01 0.00 36.62 2.52
1992 2052 6.766944 TGAACTGGTTTGTATTTCCGTTCTTA 59.233 34.615 0.01 0.00 36.62 2.10
1993 2053 6.796705 ACTGGTTTGTATTTCCGTTCTTAG 57.203 37.500 0.00 0.00 0.00 2.18
1994 2054 6.293698 ACTGGTTTGTATTTCCGTTCTTAGT 58.706 36.000 0.00 0.00 0.00 2.24
1995 2055 7.444299 ACTGGTTTGTATTTCCGTTCTTAGTA 58.556 34.615 0.00 0.00 0.00 1.82
1996 2056 7.933033 ACTGGTTTGTATTTCCGTTCTTAGTAA 59.067 33.333 0.00 0.00 0.00 2.24
1997 2057 8.851541 TGGTTTGTATTTCCGTTCTTAGTAAT 57.148 30.769 0.00 0.00 0.00 1.89
1998 2058 8.723311 TGGTTTGTATTTCCGTTCTTAGTAATG 58.277 33.333 0.00 0.00 0.00 1.90
1999 2059 8.179615 GGTTTGTATTTCCGTTCTTAGTAATGG 58.820 37.037 0.00 0.00 36.94 3.16
2000 2060 8.938906 GTTTGTATTTCCGTTCTTAGTAATGGA 58.061 33.333 0.00 0.00 41.72 3.41
2005 2065 5.093849 TCCGTTCTTAGTAATGGAAAGGG 57.906 43.478 13.31 7.78 40.74 3.95
2006 2066 4.080751 TCCGTTCTTAGTAATGGAAAGGGG 60.081 45.833 13.31 5.11 40.74 4.79
2007 2067 4.324022 CCGTTCTTAGTAATGGAAAGGGGT 60.324 45.833 8.22 0.00 37.68 4.95
2008 2068 5.104817 CCGTTCTTAGTAATGGAAAGGGGTA 60.105 44.000 8.22 0.00 37.68 3.69
2009 2069 6.408869 CGTTCTTAGTAATGGAAAGGGGTAA 58.591 40.000 0.00 0.00 0.00 2.85
2010 2070 6.880529 CGTTCTTAGTAATGGAAAGGGGTAAA 59.119 38.462 0.00 0.00 0.00 2.01
2011 2071 7.555195 CGTTCTTAGTAATGGAAAGGGGTAAAT 59.445 37.037 0.00 0.00 0.00 1.40
2012 2072 8.683615 GTTCTTAGTAATGGAAAGGGGTAAATG 58.316 37.037 0.00 0.00 0.00 2.32
2013 2073 6.831868 TCTTAGTAATGGAAAGGGGTAAATGC 59.168 38.462 0.00 0.00 0.00 3.56
2014 2074 4.286707 AGTAATGGAAAGGGGTAAATGCC 58.713 43.478 0.00 0.00 0.00 4.40
2021 2081 3.504927 GGGTAAATGCCCGGTTCG 58.495 61.111 0.00 0.00 39.17 3.95
2022 2082 1.078285 GGGTAAATGCCCGGTTCGA 60.078 57.895 0.00 0.00 39.17 3.71
2023 2083 0.677414 GGGTAAATGCCCGGTTCGAA 60.677 55.000 0.00 0.00 39.17 3.71
2024 2084 1.166989 GGTAAATGCCCGGTTCGAAA 58.833 50.000 0.00 0.00 0.00 3.46
2025 2085 1.540707 GGTAAATGCCCGGTTCGAAAA 59.459 47.619 0.00 0.00 0.00 2.29
2026 2086 2.030096 GGTAAATGCCCGGTTCGAAAAA 60.030 45.455 0.00 0.00 0.00 1.94
2101 2161 9.803315 CAGATATGTACTGTATTACACACTTGT 57.197 33.333 0.00 0.00 40.02 3.16
2168 2229 6.533367 GGAAGCAGTTTTATTTTTGTGTGTGA 59.467 34.615 0.00 0.00 0.00 3.58
2187 2248 4.222588 TGTGAAAATGCCTAAATGGAAGGG 59.777 41.667 0.00 0.00 38.35 3.95
2214 2275 6.127281 TGTGGAACTCGCCTTAGTTAATATGA 60.127 38.462 0.00 0.00 39.78 2.15
2258 2319 3.076621 TGTTTGCAGGAGCTCAGTAATG 58.923 45.455 17.19 6.88 42.74 1.90
2265 2326 2.503356 AGGAGCTCAGTAATGGGTTCTG 59.497 50.000 17.19 0.00 0.00 3.02
2288 2349 9.163894 TCTGGATATCAATTCTATCTTTCCACT 57.836 33.333 4.83 0.00 0.00 4.00
2325 2386 6.654793 TTGCATTTTTAAGTTTGTGGTGTC 57.345 33.333 0.00 0.00 0.00 3.67
2340 2425 1.532868 GGTGTCATAATGATGCCGAGC 59.467 52.381 0.00 0.00 32.62 5.03
2350 2435 2.384828 TGATGCCGAGCCTCTTTACTA 58.615 47.619 0.00 0.00 0.00 1.82
2351 2436 2.362397 TGATGCCGAGCCTCTTTACTAG 59.638 50.000 0.00 0.00 0.00 2.57
2373 2458 9.313118 ACTAGTTTTTCATTGTTGGTGATTTTC 57.687 29.630 0.00 0.00 0.00 2.29
2374 2459 7.552458 AGTTTTTCATTGTTGGTGATTTTCC 57.448 32.000 0.00 0.00 0.00 3.13
2378 2463 4.399219 TCATTGTTGGTGATTTTCCCGTA 58.601 39.130 0.00 0.00 0.00 4.02
2443 2531 0.841289 TCGGAACAAGGGAGTTGGTT 59.159 50.000 0.00 0.00 35.62 3.67
2524 2612 6.981762 ATTTTGTCTAGTTCATGCTCTCAG 57.018 37.500 0.00 0.00 0.00 3.35
2720 2808 4.545208 TGTTCACCGTCCTAATGAATCA 57.455 40.909 0.00 0.00 34.98 2.57
2781 2869 9.159254 AGACATCTCAAATCTGGGTATATTACA 57.841 33.333 0.00 0.00 0.00 2.41
2891 2980 7.932335 TGTGTATTTGATTTTTAGTGTCGGTT 58.068 30.769 0.00 0.00 0.00 4.44
2892 2981 8.071368 TGTGTATTTGATTTTTAGTGTCGGTTC 58.929 33.333 0.00 0.00 0.00 3.62
2893 2982 7.267600 GTGTATTTGATTTTTAGTGTCGGTTCG 59.732 37.037 0.00 0.00 0.00 3.95
3033 3124 6.569610 CGTTTTTGCAGGTATTATGGACACTT 60.570 38.462 0.00 0.00 0.00 3.16
3063 3154 4.637483 TGTGGCTTCAGTTTCTTCTTTG 57.363 40.909 0.00 0.00 0.00 2.77
3084 3175 9.177608 TCTTTGGACCTTTTATGTTCATCTATG 57.822 33.333 0.00 0.00 0.00 2.23
3135 3226 9.791820 CACTGCTGTCATTTTATGATTAATGAA 57.208 29.630 0.00 0.00 41.10 2.57
3232 3323 3.313690 CCGTTTGGTAAGCCACAATTTC 58.686 45.455 0.00 0.00 46.01 2.17
3432 3523 9.620660 GTTACTTTTGGTAATGTGTATTTCTGG 57.379 33.333 0.00 0.00 41.68 3.86
3622 3713 3.528532 AGCTACCATGTAAAGGTAACGC 58.471 45.455 0.00 0.00 40.87 4.84
3637 3728 0.033366 AACGCCCTTGTTTTCATGGC 59.967 50.000 0.00 0.00 41.87 4.40
3758 3849 9.908152 ACATTTTACAAGTAGGAAAATACAAGC 57.092 29.630 0.00 0.00 32.79 4.01
3787 3920 7.833285 TTTCTGATTTAAGCTAGTTTGGGTT 57.167 32.000 1.54 0.00 0.00 4.11
3951 4134 3.198068 ACTGCTGCTATTTGGTGTATCG 58.802 45.455 0.00 0.00 0.00 2.92
4025 4208 9.262358 GTCTCTGATCCAGGTAAATATAAACAC 57.738 37.037 0.00 0.00 31.51 3.32
4111 4294 7.640597 AGTTTGCTAGGTTTAGTCAAAACTT 57.359 32.000 0.00 0.00 45.70 2.66
4113 4296 7.338449 AGTTTGCTAGGTTTAGTCAAAACTTCA 59.662 33.333 0.00 0.00 45.70 3.02
4154 4338 6.005823 TCGGCCTGTATAGTTATAGTAGCAA 58.994 40.000 0.00 0.00 0.00 3.91
4417 4617 8.632906 AGGATGATGATCTTCCAATTGTTATC 57.367 34.615 24.09 2.17 41.64 1.75
4444 4644 4.440839 AAGCTTTAAAAGGCGAGAATGG 57.559 40.909 0.00 0.00 0.00 3.16
4485 4685 2.289002 CCATCTAGCAGACGCCAATTTC 59.711 50.000 0.00 0.00 39.83 2.17
4510 4710 7.817478 TCGAAAAGCACATTGAGAGTTAGATTA 59.183 33.333 0.00 0.00 0.00 1.75
4511 4711 7.900352 CGAAAAGCACATTGAGAGTTAGATTAC 59.100 37.037 0.00 0.00 0.00 1.89
4512 4712 6.893958 AAGCACATTGAGAGTTAGATTACG 57.106 37.500 0.00 0.00 0.00 3.18
4513 4713 5.967088 AGCACATTGAGAGTTAGATTACGT 58.033 37.500 0.00 0.00 0.00 3.57
4514 4714 5.807520 AGCACATTGAGAGTTAGATTACGTG 59.192 40.000 0.00 0.00 0.00 4.49
4515 4715 5.005779 GCACATTGAGAGTTAGATTACGTGG 59.994 44.000 0.00 0.00 0.00 4.94
4516 4716 6.100004 CACATTGAGAGTTAGATTACGTGGT 58.900 40.000 0.00 0.00 0.00 4.16
4517 4717 7.255569 CACATTGAGAGTTAGATTACGTGGTA 58.744 38.462 0.00 0.00 0.00 3.25
4518 4718 7.921214 CACATTGAGAGTTAGATTACGTGGTAT 59.079 37.037 0.00 0.00 0.00 2.73
4519 4719 7.921214 ACATTGAGAGTTAGATTACGTGGTATG 59.079 37.037 0.00 0.00 0.00 2.39
4604 4804 5.702670 CGCTATGGAATTATGTCTTGATGGT 59.297 40.000 0.00 0.00 0.00 3.55
4734 4934 6.761242 ACCAAACTTGTATTTGAAAAGAAGGC 59.239 34.615 0.00 0.00 41.28 4.35
4737 4937 5.519722 ACTTGTATTTGAAAAGAAGGCACG 58.480 37.500 0.00 0.00 0.00 5.34
4742 4942 4.398549 TTTGAAAAGAAGGCACGTATCG 57.601 40.909 0.00 0.00 0.00 2.92
4747 4947 5.640357 TGAAAAGAAGGCACGTATCGTATTT 59.360 36.000 0.00 0.00 38.32 1.40
4784 4984 4.543590 TCACTGATTCAAACTCTCTCCC 57.456 45.455 0.00 0.00 0.00 4.30
4893 5097 3.244457 GGGTGCTACTGGTAGAACACTTT 60.244 47.826 17.58 0.00 41.08 2.66
4894 5098 3.746492 GGTGCTACTGGTAGAACACTTTG 59.254 47.826 17.58 0.00 42.34 2.77
4898 5102 5.526111 TGCTACTGGTAGAACACTTTGTTTC 59.474 40.000 11.44 0.00 41.28 2.78
4915 5119 5.934935 TGTTTCAACTTCCGGTAAGATTC 57.065 39.130 17.18 5.49 38.67 2.52
4959 5163 3.646715 GCACCCTACTGTGGCCCA 61.647 66.667 0.00 0.00 36.73 5.36
5064 5268 5.220605 GGTCTTTGTAAATCTCGGTGCATAC 60.221 44.000 0.00 0.00 0.00 2.39
5087 5291 2.419673 TCCTGACGCTATTTTGCACATG 59.580 45.455 0.00 0.00 0.00 3.21
5129 5335 1.254026 TAGAGTACGCAGCAGGTTGT 58.746 50.000 0.00 0.00 0.00 3.32
5155 5361 8.767085 TGTACCATAGTTTTGTAGAAGAAAACG 58.233 33.333 6.73 0.00 44.51 3.60
5159 5365 8.221766 CCATAGTTTTGTAGAAGAAAACGAGTC 58.778 37.037 6.73 0.00 44.51 3.36
5168 5374 6.541111 AGAAGAAAACGAGTCCATTTACAC 57.459 37.500 0.00 0.00 0.00 2.90
5181 5387 4.074970 CCATTTACACAAGGAAGAGCACT 58.925 43.478 0.00 0.00 0.00 4.40
5190 5396 7.649057 ACACAAGGAAGAGCACTAAATTAAAC 58.351 34.615 0.00 0.00 0.00 2.01
5204 5410 9.944663 CACTAAATTAAACAAGAAACAGCACTA 57.055 29.630 0.00 0.00 0.00 2.74
5210 5417 8.726870 TTAAACAAGAAACAGCACTAACTACT 57.273 30.769 0.00 0.00 0.00 2.57
5243 5451 0.770557 AACCCCTACCACTCTGCCAA 60.771 55.000 0.00 0.00 0.00 4.52
5244 5452 0.550147 ACCCCTACCACTCTGCCAAT 60.550 55.000 0.00 0.00 0.00 3.16
5246 5454 0.620556 CCCTACCACTCTGCCAATGT 59.379 55.000 0.00 0.00 0.00 2.71
5267 5475 6.417191 TGTCCGTAGCTTTATTTCATCAAC 57.583 37.500 0.00 0.00 0.00 3.18
5268 5476 6.170506 TGTCCGTAGCTTTATTTCATCAACT 58.829 36.000 0.00 0.00 0.00 3.16
5343 5552 4.806892 TCATAATCTTCAATGGCCATGGT 58.193 39.130 21.63 0.16 0.00 3.55
5344 5553 5.210430 TCATAATCTTCAATGGCCATGGTT 58.790 37.500 21.63 11.80 0.00 3.67
5387 5596 9.653287 TCGAAATACACTATCACTCTCAATTTT 57.347 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 5.772521 ACATTAACCAAGTCAAGTCATTGC 58.227 37.500 0.00 0.00 36.30 3.56
148 178 4.933505 TCTCATTTGTGCAAATTCCACA 57.066 36.364 7.36 7.56 38.84 4.17
175 205 6.294508 GCCCTTGAAGTTTTTATAACTCTGCA 60.295 38.462 0.00 0.00 0.00 4.41
197 228 5.179533 GCTAGGTATGCTTTATCTTAGCCC 58.820 45.833 0.00 0.00 37.85 5.19
270 301 4.021807 TGCGAACTTCAGGTATTGTGAGTA 60.022 41.667 0.00 0.00 0.00 2.59
272 303 3.325870 TGCGAACTTCAGGTATTGTGAG 58.674 45.455 0.00 0.00 0.00 3.51
295 326 3.694072 TGTTATGCTCACTTATTGTGCCC 59.306 43.478 0.00 0.00 45.81 5.36
310 341 4.003648 AGTACAGAAAGTGGCTGTTATGC 58.996 43.478 0.00 0.00 43.67 3.14
343 374 5.970140 TCTGTTTCGTTGTCGTCATTTTA 57.030 34.783 0.00 0.00 38.33 1.52
397 428 3.335484 TCCCCAGCTAAACTTACCCAATT 59.665 43.478 0.00 0.00 0.00 2.32
457 488 0.970937 TCCGTCTCCTGCTGGTAAGG 60.971 60.000 9.73 10.64 36.02 2.69
558 592 0.530650 TCCGCTCTCAAATGATCGGC 60.531 55.000 11.55 4.19 37.06 5.54
559 593 1.067669 TCTCCGCTCTCAAATGATCGG 59.932 52.381 10.64 10.64 38.34 4.18
560 594 2.498807 TCTCCGCTCTCAAATGATCG 57.501 50.000 0.00 0.00 0.00 3.69
568 602 2.973899 GGTGCTTCTCCGCTCTCA 59.026 61.111 0.00 0.00 0.00 3.27
610 644 8.229253 ACCCAACTATTTTTCCGGAATAATAC 57.771 34.615 26.64 0.00 0.00 1.89
619 653 5.644636 TGCTAAGTACCCAACTATTTTTCCG 59.355 40.000 0.00 0.00 37.50 4.30
643 677 1.653115 GATGTAGATCCGACGGCGT 59.347 57.895 14.65 14.65 35.23 5.68
705 744 4.176271 GCTTCTTTGCAAAAACTGTCTGT 58.824 39.130 13.84 0.00 0.00 3.41
740 779 1.926511 GAGCGGAGGTGCAAATGTGG 61.927 60.000 0.00 0.00 39.88 4.17
978 1024 2.492567 CCTCTCCTATCCCTTCTCCTGG 60.493 59.091 0.00 0.00 0.00 4.45
1014 1060 0.837940 GTAGGAACCTGGATGGGGAC 59.162 60.000 0.00 0.00 41.11 4.46
1044 1090 0.179100 ACCTGACGATGCGATCCTTG 60.179 55.000 0.00 0.00 0.00 3.61
1054 1100 0.249073 GCAGCGACATACCTGACGAT 60.249 55.000 0.00 0.00 41.98 3.73
1204 1252 2.691409 TGCTATGCACTAACCTGGAC 57.309 50.000 0.00 0.00 31.71 4.02
1218 1266 3.257873 CAGATTCGACAGGAGGATGCTAT 59.742 47.826 0.00 0.00 29.87 2.97
1222 1270 3.808466 TTCAGATTCGACAGGAGGATG 57.192 47.619 0.00 0.00 0.00 3.51
1232 1280 2.613595 CGAAATGGGCATTCAGATTCGA 59.386 45.455 13.82 0.00 39.80 3.71
1244 1292 1.000274 AGACAGCAAAACGAAATGGGC 60.000 47.619 0.00 0.00 0.00 5.36
1291 1340 6.706716 GCTCAGATTTGTTCCTACTATTACCC 59.293 42.308 0.00 0.00 0.00 3.69
1334 1386 4.743151 GCGCCAGGTAATTTAAATAAAGCC 59.257 41.667 0.01 2.20 0.00 4.35
1354 1414 2.405892 AAAGACACAAACATCAGCGC 57.594 45.000 0.00 0.00 0.00 5.92
1371 1431 5.883673 AGCACACCAAAACTTCAGTACTAAA 59.116 36.000 0.00 0.00 0.00 1.85
1383 1443 1.336755 CCCACACTAGCACACCAAAAC 59.663 52.381 0.00 0.00 0.00 2.43
1396 1456 2.024414 GACAGCAAAGAAACCCACACT 58.976 47.619 0.00 0.00 0.00 3.55
1424 1484 9.060347 ACAGCATTGTCAGGATTTACATAATAG 57.940 33.333 0.00 0.00 29.46 1.73
1443 1503 2.288030 GCAGTGCTTGAAGAACAGCATT 60.288 45.455 14.96 0.00 36.40 3.56
1489 1549 4.651778 AGCACTCCACTGTTTAGCAAATA 58.348 39.130 0.00 0.00 0.00 1.40
1570 1630 5.357878 TCATTGAAAACTGCAACAGAAGTCT 59.642 36.000 0.78 0.00 35.18 3.24
1602 1662 4.130118 CCACTGATAGCACCATTACCTTC 58.870 47.826 0.00 0.00 0.00 3.46
1657 1717 0.830648 CCAAGAGGAAGCCCGTCATA 59.169 55.000 0.00 0.00 36.89 2.15
1659 1719 1.841556 ACCAAGAGGAAGCCCGTCA 60.842 57.895 0.00 0.00 38.69 4.35
1680 1740 4.286297 AGCCGCCTTTATAGCATCAATA 57.714 40.909 0.00 0.00 0.00 1.90
1880 1940 7.817478 ACTTGCACTAAAAGTATTATTTTGCCC 59.183 33.333 0.00 0.00 36.11 5.36
1898 1958 2.362077 GTTTCCAACCATCACTTGCACT 59.638 45.455 0.00 0.00 0.00 4.40
1921 1981 9.376075 CTACATCTACATGTGAAAAGATGAACT 57.624 33.333 30.04 17.35 45.29 3.01
1950 2010 5.130145 CCAGTTCAAGATAACAGGAGGAGAT 59.870 44.000 0.00 0.00 38.04 2.75
1951 2011 4.467795 CCAGTTCAAGATAACAGGAGGAGA 59.532 45.833 0.00 0.00 38.04 3.71
1952 2012 4.223923 ACCAGTTCAAGATAACAGGAGGAG 59.776 45.833 5.33 0.00 38.04 3.69
1953 2013 4.168101 ACCAGTTCAAGATAACAGGAGGA 58.832 43.478 5.33 0.00 38.04 3.71
1954 2014 4.559862 ACCAGTTCAAGATAACAGGAGG 57.440 45.455 5.33 0.00 38.04 4.30
1955 2015 5.765182 ACAAACCAGTTCAAGATAACAGGAG 59.235 40.000 5.33 0.00 38.04 3.69
1956 2016 5.690865 ACAAACCAGTTCAAGATAACAGGA 58.309 37.500 5.33 0.00 38.04 3.86
1957 2017 7.687941 ATACAAACCAGTTCAAGATAACAGG 57.312 36.000 0.00 0.00 40.74 4.00
1958 2018 9.612620 GAAATACAAACCAGTTCAAGATAACAG 57.387 33.333 0.00 0.00 0.00 3.16
1959 2019 8.573035 GGAAATACAAACCAGTTCAAGATAACA 58.427 33.333 0.00 0.00 0.00 2.41
1960 2020 7.749126 CGGAAATACAAACCAGTTCAAGATAAC 59.251 37.037 0.00 0.00 0.00 1.89
1961 2021 7.446013 ACGGAAATACAAACCAGTTCAAGATAA 59.554 33.333 0.00 0.00 0.00 1.75
1962 2022 6.938030 ACGGAAATACAAACCAGTTCAAGATA 59.062 34.615 0.00 0.00 0.00 1.98
1963 2023 5.768164 ACGGAAATACAAACCAGTTCAAGAT 59.232 36.000 0.00 0.00 0.00 2.40
1964 2024 5.127491 ACGGAAATACAAACCAGTTCAAGA 58.873 37.500 0.00 0.00 0.00 3.02
1965 2025 5.432885 ACGGAAATACAAACCAGTTCAAG 57.567 39.130 0.00 0.00 0.00 3.02
1966 2026 5.591067 AGAACGGAAATACAAACCAGTTCAA 59.409 36.000 4.32 0.00 38.40 2.69
1967 2027 5.127491 AGAACGGAAATACAAACCAGTTCA 58.873 37.500 4.32 0.00 38.40 3.18
1968 2028 5.684550 AGAACGGAAATACAAACCAGTTC 57.315 39.130 0.00 0.00 37.41 3.01
1969 2029 6.769341 ACTAAGAACGGAAATACAAACCAGTT 59.231 34.615 0.00 0.00 0.00 3.16
1970 2030 6.293698 ACTAAGAACGGAAATACAAACCAGT 58.706 36.000 0.00 0.00 0.00 4.00
1971 2031 6.796705 ACTAAGAACGGAAATACAAACCAG 57.203 37.500 0.00 0.00 0.00 4.00
1972 2032 8.723311 CATTACTAAGAACGGAAATACAAACCA 58.277 33.333 0.00 0.00 0.00 3.67
1973 2033 8.179615 CCATTACTAAGAACGGAAATACAAACC 58.820 37.037 0.00 0.00 0.00 3.27
1974 2034 8.938906 TCCATTACTAAGAACGGAAATACAAAC 58.061 33.333 0.00 0.00 0.00 2.93
1975 2035 9.504708 TTCCATTACTAAGAACGGAAATACAAA 57.495 29.630 0.00 0.00 29.82 2.83
1976 2036 9.504708 TTTCCATTACTAAGAACGGAAATACAA 57.495 29.630 0.00 0.00 37.54 2.41
1977 2037 9.158233 CTTTCCATTACTAAGAACGGAAATACA 57.842 33.333 0.00 0.00 40.64 2.29
1978 2038 8.610035 CCTTTCCATTACTAAGAACGGAAATAC 58.390 37.037 0.00 0.00 40.64 1.89
1979 2039 7.771826 CCCTTTCCATTACTAAGAACGGAAATA 59.228 37.037 0.00 0.00 40.64 1.40
1980 2040 6.602009 CCCTTTCCATTACTAAGAACGGAAAT 59.398 38.462 0.00 0.00 40.64 2.17
1981 2041 5.941647 CCCTTTCCATTACTAAGAACGGAAA 59.058 40.000 0.00 0.00 39.54 3.13
1982 2042 5.493809 CCCTTTCCATTACTAAGAACGGAA 58.506 41.667 0.00 0.00 32.21 4.30
1983 2043 4.080751 CCCCTTTCCATTACTAAGAACGGA 60.081 45.833 0.00 0.00 32.21 4.69
1984 2044 4.196971 CCCCTTTCCATTACTAAGAACGG 58.803 47.826 0.00 0.00 0.00 4.44
1985 2045 4.840271 ACCCCTTTCCATTACTAAGAACG 58.160 43.478 0.00 0.00 0.00 3.95
1986 2046 8.683615 CATTTACCCCTTTCCATTACTAAGAAC 58.316 37.037 0.00 0.00 0.00 3.01
1987 2047 7.340999 GCATTTACCCCTTTCCATTACTAAGAA 59.659 37.037 0.00 0.00 0.00 2.52
1988 2048 6.831868 GCATTTACCCCTTTCCATTACTAAGA 59.168 38.462 0.00 0.00 0.00 2.10
1989 2049 6.040504 GGCATTTACCCCTTTCCATTACTAAG 59.959 42.308 0.00 0.00 0.00 2.18
1990 2050 5.894964 GGCATTTACCCCTTTCCATTACTAA 59.105 40.000 0.00 0.00 0.00 2.24
1991 2051 5.451354 GGCATTTACCCCTTTCCATTACTA 58.549 41.667 0.00 0.00 0.00 1.82
1992 2052 4.286707 GGCATTTACCCCTTTCCATTACT 58.713 43.478 0.00 0.00 0.00 2.24
1993 2053 3.386726 GGGCATTTACCCCTTTCCATTAC 59.613 47.826 0.00 0.00 45.00 1.89
1994 2054 3.648739 GGGCATTTACCCCTTTCCATTA 58.351 45.455 0.00 0.00 45.00 1.90
1995 2055 2.477245 GGGCATTTACCCCTTTCCATT 58.523 47.619 0.00 0.00 45.00 3.16
1996 2056 2.174685 GGGCATTTACCCCTTTCCAT 57.825 50.000 0.00 0.00 45.00 3.41
1997 2057 3.701800 GGGCATTTACCCCTTTCCA 57.298 52.632 0.00 0.00 45.00 3.53
2005 2065 1.166989 TTTCGAACCGGGCATTTACC 58.833 50.000 6.32 0.00 0.00 2.85
2006 2066 2.993449 TTTTCGAACCGGGCATTTAC 57.007 45.000 6.32 0.00 0.00 2.01
2026 2086 8.331931 TCCAGGGTATCTACATCTACATTTTT 57.668 34.615 0.00 0.00 0.00 1.94
2027 2087 7.569111 ACTCCAGGGTATCTACATCTACATTTT 59.431 37.037 0.00 0.00 0.00 1.82
2028 2088 7.076446 ACTCCAGGGTATCTACATCTACATTT 58.924 38.462 0.00 0.00 0.00 2.32
2029 2089 6.625267 ACTCCAGGGTATCTACATCTACATT 58.375 40.000 0.00 0.00 0.00 2.71
2030 2090 6.220881 ACTCCAGGGTATCTACATCTACAT 57.779 41.667 0.00 0.00 0.00 2.29
2031 2091 5.664815 ACTCCAGGGTATCTACATCTACA 57.335 43.478 0.00 0.00 0.00 2.74
2032 2092 6.980416 AAACTCCAGGGTATCTACATCTAC 57.020 41.667 0.00 0.00 0.00 2.59
2034 2094 9.845214 ATTATAAACTCCAGGGTATCTACATCT 57.155 33.333 0.00 0.00 0.00 2.90
2036 2096 9.845214 AGATTATAAACTCCAGGGTATCTACAT 57.155 33.333 0.00 0.00 0.00 2.29
2037 2097 9.670442 AAGATTATAAACTCCAGGGTATCTACA 57.330 33.333 0.00 0.00 0.00 2.74
2039 2099 9.892444 TGAAGATTATAAACTCCAGGGTATCTA 57.108 33.333 0.00 0.00 0.00 1.98
2040 2100 8.798975 TGAAGATTATAAACTCCAGGGTATCT 57.201 34.615 0.00 0.00 0.00 1.98
2041 2101 8.871125 TCTGAAGATTATAAACTCCAGGGTATC 58.129 37.037 8.74 0.00 0.00 2.24
2042 2102 8.798975 TCTGAAGATTATAAACTCCAGGGTAT 57.201 34.615 8.74 0.00 0.00 2.73
2043 2103 8.618240 TTCTGAAGATTATAAACTCCAGGGTA 57.382 34.615 8.74 0.00 0.00 3.69
2044 2104 7.510675 TTCTGAAGATTATAAACTCCAGGGT 57.489 36.000 8.74 0.00 0.00 4.34
2101 2161 2.144078 TGTCCGAGTCCTGGGCAAA 61.144 57.895 0.00 0.00 38.38 3.68
2168 2229 5.032170 ACATCCCTTCCATTTAGGCATTTT 58.968 37.500 0.00 0.00 37.29 1.82
2187 2248 2.674796 ACTAAGGCGAGTTCCACATC 57.325 50.000 0.00 0.00 0.00 3.06
2232 2293 2.360165 CTGAGCTCCTGCAAACAAAACT 59.640 45.455 12.15 0.00 42.74 2.66
2235 2296 2.057137 ACTGAGCTCCTGCAAACAAA 57.943 45.000 12.15 0.00 42.74 2.83
2258 2319 9.225436 GAAAGATAGAATTGATATCCAGAACCC 57.775 37.037 0.00 0.00 31.22 4.11
2265 2326 9.784531 TTCAGTGGAAAGATAGAATTGATATCC 57.215 33.333 0.00 0.00 31.22 2.59
2288 2349 8.939201 TTAAAAATGCAAATGAGTTGACTTCA 57.061 26.923 0.00 0.00 39.87 3.02
2325 2386 2.469274 AGAGGCTCGGCATCATTATG 57.531 50.000 9.22 0.00 42.11 1.90
2340 2425 8.630037 ACCAACAATGAAAAACTAGTAAAGAGG 58.370 33.333 0.00 0.00 0.00 3.69
2350 2435 6.542005 GGGAAAATCACCAACAATGAAAAACT 59.458 34.615 0.00 0.00 0.00 2.66
2351 2436 6.510960 CGGGAAAATCACCAACAATGAAAAAC 60.511 38.462 0.00 0.00 0.00 2.43
2374 2459 0.322098 TGTGATTGGCCCAAGTACGG 60.322 55.000 1.16 0.00 0.00 4.02
2378 2463 0.185901 ACAGTGTGATTGGCCCAAGT 59.814 50.000 1.16 0.00 0.00 3.16
2524 2612 6.759497 AGGTAGTTAGATGGCAATTTCAAC 57.241 37.500 0.00 0.00 0.00 3.18
2720 2808 0.627986 CCTGGGGAGCAAGGAAGAAT 59.372 55.000 0.00 0.00 35.40 2.40
2781 2869 3.181491 CCACAAAACGGTGATGTTTCAGT 60.181 43.478 0.00 0.00 41.01 3.41
2887 2975 4.565166 TGCAGAAGATACAATTACGAACCG 59.435 41.667 0.00 0.00 0.00 4.44
2891 2980 8.978539 GTGAATATGCAGAAGATACAATTACGA 58.021 33.333 0.00 0.00 0.00 3.43
2892 2981 8.982685 AGTGAATATGCAGAAGATACAATTACG 58.017 33.333 0.00 0.00 0.00 3.18
3033 3124 6.003950 AGAAACTGAAGCCACAAAAGCTATA 58.996 36.000 0.00 0.00 40.49 1.31
3063 3154 9.832445 TCTAACATAGATGAACATAAAAGGTCC 57.168 33.333 0.00 0.00 0.00 4.46
3135 3226 7.394016 TCATGAATCTGGTACGGCAAATATAT 58.606 34.615 0.00 0.00 32.53 0.86
3144 3235 4.503910 TCAAACTCATGAATCTGGTACGG 58.496 43.478 0.00 0.00 0.00 4.02
3150 3241 7.541091 CACCAAATCTTCAAACTCATGAATCTG 59.459 37.037 0.00 0.00 38.55 2.90
3255 3346 8.201242 ACACATAACCATCCCAAATTTTAAGT 57.799 30.769 0.00 0.00 0.00 2.24
3622 3713 0.609662 CCAGGCCATGAAAACAAGGG 59.390 55.000 5.01 0.00 0.00 3.95
3637 3728 7.910162 CACGAACTTGATAAATATGAAACCAGG 59.090 37.037 0.00 0.00 0.00 4.45
3758 3849 7.809806 CCAAACTAGCTTAAATCAGAAAACCAG 59.190 37.037 0.00 0.00 0.00 4.00
3787 3920 0.251165 GTTGGTTCCAAGGCTGGCTA 60.251 55.000 3.41 0.00 43.17 3.93
3840 3973 8.776376 AGAAAAGTGTTTCACAAAATTGACAT 57.224 26.923 0.00 0.00 44.82 3.06
3906 4089 6.756299 TGAGTGCTTGCAATGTTATGATAA 57.244 33.333 0.00 0.00 0.00 1.75
3951 4134 3.427233 GCATGAATCCTTCAGAACACTGC 60.427 47.826 0.00 0.00 43.98 4.40
4025 4208 7.473027 AAAATGCTTTGATTCAGTGAAACAG 57.527 32.000 14.54 6.91 41.43 3.16
4074 4257 7.865706 ACCTAGCAAACTTATTGGATAACTG 57.134 36.000 0.00 0.00 0.00 3.16
4111 4294 5.355910 GGCCGAAAAGGTACTGAATAATTGA 59.644 40.000 0.00 0.00 40.86 2.57
4113 4296 5.357032 CAGGCCGAAAAGGTACTGAATAATT 59.643 40.000 0.00 0.00 44.44 1.40
4249 4433 4.948341 TGCAAACTCAGGTGAACTACTA 57.052 40.909 0.00 0.00 0.00 1.82
4296 4480 9.179552 CATGATTTTCAACATTTCAGTTCGTTA 57.820 29.630 0.00 0.00 0.00 3.18
4298 4482 7.424803 TCATGATTTTCAACATTTCAGTTCGT 58.575 30.769 0.00 0.00 0.00 3.85
4299 4483 7.804600 TCTCATGATTTTCAACATTTCAGTTCG 59.195 33.333 0.00 0.00 0.00 3.95
4300 4484 9.635520 ATCTCATGATTTTCAACATTTCAGTTC 57.364 29.630 0.00 0.00 0.00 3.01
4301 4485 9.991906 AATCTCATGATTTTCAACATTTCAGTT 57.008 25.926 0.00 0.00 39.68 3.16
4417 4617 4.387862 TCTCGCCTTTTAAAGCTTAAGTCG 59.612 41.667 0.00 1.57 0.00 4.18
4444 4644 5.467035 TGGGGACAATTCAAATTCAGTTC 57.533 39.130 0.00 0.00 37.44 3.01
4485 4685 5.845985 TCTAACTCTCAATGTGCTTTTCG 57.154 39.130 0.00 0.00 0.00 3.46
4510 4710 2.771943 ACATGATCCCTTCATACCACGT 59.228 45.455 0.00 0.00 43.40 4.49
4511 4711 3.475566 ACATGATCCCTTCATACCACG 57.524 47.619 0.00 0.00 43.40 4.94
4512 4712 6.998074 TCATTAACATGATCCCTTCATACCAC 59.002 38.462 0.00 0.00 43.40 4.16
4513 4713 7.147958 TCATTAACATGATCCCTTCATACCA 57.852 36.000 0.00 0.00 43.40 3.25
4514 4714 8.352942 GTTTCATTAACATGATCCCTTCATACC 58.647 37.037 0.00 0.00 43.40 2.73
4515 4715 8.902806 TGTTTCATTAACATGATCCCTTCATAC 58.097 33.333 0.00 0.00 43.40 2.39
4516 4716 9.473007 TTGTTTCATTAACATGATCCCTTCATA 57.527 29.630 0.00 0.00 45.72 2.15
4517 4717 7.959658 TGTTTCATTAACATGATCCCTTCAT 57.040 32.000 0.00 0.00 46.27 2.57
4518 4718 7.669304 TCTTGTTTCATTAACATGATCCCTTCA 59.331 33.333 0.00 0.00 45.72 3.02
4519 4719 8.055279 TCTTGTTTCATTAACATGATCCCTTC 57.945 34.615 0.00 0.00 45.72 3.46
4553 4753 7.504924 TTCATTTACGGGATATTCCATGTTC 57.495 36.000 0.00 0.00 38.64 3.18
4734 4934 4.263016 CACACATGCAAATACGATACGTG 58.737 43.478 0.00 0.00 41.39 4.49
4772 4972 0.108424 CTCTGCGGGGAGAGAGTTTG 60.108 60.000 11.31 0.00 41.95 2.93
4784 4984 2.789917 GTGCTTCATGCTCTGCGG 59.210 61.111 0.00 0.00 43.37 5.69
4893 5097 4.449743 CGAATCTTACCGGAAGTTGAAACA 59.550 41.667 9.46 0.00 36.45 2.83
4894 5098 4.954442 CGAATCTTACCGGAAGTTGAAAC 58.046 43.478 9.46 0.00 36.45 2.78
4959 5163 4.328712 GGAACAAACAAACAAACAAGCGAT 59.671 37.500 0.00 0.00 0.00 4.58
5005 5209 5.874810 CACCTATTCCTCAAGTCGAATTTCA 59.125 40.000 0.00 0.00 31.33 2.69
5104 5308 5.080969 ACCTGCTGCGTACTCTAATTTTA 57.919 39.130 0.00 0.00 0.00 1.52
5129 5335 8.767085 CGTTTTCTTCTACAAAACTATGGTACA 58.233 33.333 0.00 0.00 41.05 2.90
5155 5361 4.393371 GCTCTTCCTTGTGTAAATGGACTC 59.607 45.833 0.00 0.00 0.00 3.36
5159 5365 4.074970 AGTGCTCTTCCTTGTGTAAATGG 58.925 43.478 0.00 0.00 0.00 3.16
5168 5374 8.567948 TCTTGTTTAATTTAGTGCTCTTCCTTG 58.432 33.333 0.00 0.00 0.00 3.61
5190 5396 4.143305 GCGAGTAGTTAGTGCTGTTTCTTG 60.143 45.833 0.00 0.00 0.00 3.02
5204 5410 3.313012 TGCATTGTGTAGCGAGTAGTT 57.687 42.857 0.00 0.00 0.00 2.24
5210 5417 0.958382 GGGGTTGCATTGTGTAGCGA 60.958 55.000 0.00 0.00 0.00 4.93
5243 5451 6.823689 AGTTGATGAAATAAAGCTACGGACAT 59.176 34.615 0.00 0.00 0.00 3.06
5244 5452 6.170506 AGTTGATGAAATAAAGCTACGGACA 58.829 36.000 0.00 0.00 0.00 4.02
5246 5454 7.681939 AAAGTTGATGAAATAAAGCTACGGA 57.318 32.000 0.00 0.00 0.00 4.69
5267 5475 9.140286 GGGCTCTTTTGCTAGTTAAAATAAAAG 57.860 33.333 0.00 0.00 36.80 2.27
5268 5476 7.810759 CGGGCTCTTTTGCTAGTTAAAATAAAA 59.189 33.333 7.27 0.00 0.00 1.52
5343 5552 9.071221 GTATTTCGATGATGCAACAAAATGTAA 57.929 29.630 12.71 0.73 0.00 2.41
5344 5553 8.239998 TGTATTTCGATGATGCAACAAAATGTA 58.760 29.630 12.71 2.77 0.00 2.29


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

AutoCloner maintained by Alex Coulton.