Multiple sequence alignment - TraesCS5D01G282100

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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 TraesCS5D01G282100 chr5D 100.000 3758 0 0 503 4260 383743400 383747157 0.000000e+00 6940.0
1 TraesCS5D01G282100 chr5D 100.000 241 0 0 1 241 383742898 383743138 3.020000e-121 446.0
2 TraesCS5D01G282100 chr5A 92.852 1385 66 20 503 1857 484010280 484011661 0.000000e+00 1978.0
3 TraesCS5D01G282100 chr5A 92.950 1234 56 15 2186 3397 484011841 484013065 0.000000e+00 1768.0
4 TraesCS5D01G282100 chr5A 92.633 828 36 8 3432 4259 484013067 484013869 0.000000e+00 1168.0
5 TraesCS5D01G282100 chr5A 94.186 86 5 0 1662 1747 484011574 484011659 9.610000e-27 132.0
6 TraesCS5D01G282100 chr5A 94.643 56 3 0 186 241 484010114 484010169 2.110000e-13 87.9
7 TraesCS5D01G282100 chr5A 91.935 62 4 1 1655 1715 484011853 484011914 7.590000e-13 86.1
8 TraesCS5D01G282100 chr5B 90.757 1493 69 24 503 1944 460220766 460222240 0.000000e+00 1929.0
9 TraesCS5D01G282100 chr5B 93.156 1125 38 12 2186 3285 460222157 460223267 0.000000e+00 1615.0
10 TraesCS5D01G282100 chr5B 93.921 987 52 5 3278 4260 460223456 460224438 0.000000e+00 1483.0
11 TraesCS5D01G282100 chr5B 95.197 229 7 2 1746 1970 460221932 460222160 4.050000e-95 359.0
12 TraesCS5D01G282100 chr5B 95.890 219 8 1 1 218 460220070 460220288 1.880000e-93 353.0
13 TraesCS5D01G282100 chr5B 85.965 114 10 4 1854 1963 460221931 460222042 2.690000e-22 117.0
14 TraesCS5D01G282100 chr5B 94.366 71 4 0 1655 1725 460222169 460222239 4.500000e-20 110.0
15 TraesCS5D01G282100 chr4A 92.641 231 11 2 1965 2190 682738618 682738389 1.140000e-85 327.0
16 TraesCS5D01G282100 chr4A 91.416 233 14 2 1965 2192 682738922 682738691 8.890000e-82 315.0
17 TraesCS5D01G282100 chr1A 92.340 235 11 3 1961 2190 64694134 64694366 1.140000e-85 327.0
18 TraesCS5D01G282100 chr3B 92.920 226 10 2 1967 2187 817254649 817254873 1.480000e-84 324.0
19 TraesCS5D01G282100 chr3A 91.416 233 13 3 1967 2193 570310945 570310714 3.200000e-81 313.0
20 TraesCS5D01G282100 chr7B 91.630 227 13 2 1969 2190 482245635 482245860 4.140000e-80 309.0
21 TraesCS5D01G282100 chr4D 91.630 227 13 2 1969 2190 943019 943244 4.140000e-80 309.0
22 TraesCS5D01G282100 chr4B 91.892 222 11 3 1970 2186 640810015 640809796 1.920000e-78 303.0
23 TraesCS5D01G282100 chr2B 84.571 175 20 3 1969 2142 103922960 103922792 2.630000e-37 167.0


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 TraesCS5D01G282100 chr5D 383742898 383747157 4259 False 3693.000000 6940 100.000000 1 4260 2 chr5D.!!$F1 4259
1 TraesCS5D01G282100 chr5A 484010114 484013869 3755 False 870.000000 1978 93.199833 186 4259 6 chr5A.!!$F1 4073
2 TraesCS5D01G282100 chr5B 460220070 460224438 4368 False 852.285714 1929 92.750286 1 4260 7 chr5B.!!$F1 4259
3 TraesCS5D01G282100 chr4A 682738389 682738922 533 True 321.000000 327 92.028500 1965 2192 2 chr4A.!!$R1 227

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
628 981 0.028902 GACGCGGCATTAACAATCCC 59.971 55.0 7.34 0.0 0.00 3.85 F
811 1174 0.606096 TCAAAGGAGACGATCGCCAA 59.394 50.0 16.60 0.0 38.94 4.52 F
2150 2746 0.178876 TGGATGGACCTGGGAGTTGA 60.179 55.0 0.00 0.0 39.86 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2735 0.598065 CCGCTTTTTCAACTCCCAGG 59.402 55.0 0.0 0.0 0.00 4.45 R
2654 3262 0.109458 CCGTCCATCGTTTCAGTCGA 60.109 55.0 0.0 0.0 41.45 4.20 R
4026 4862 1.725641 TGCAGGATTACAACGCTGAG 58.274 50.0 0.0 0.0 0.00 3.35 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
44 45 4.981674 TGTTTGCTCCAAAATGATTCGAAC 59.018 37.500 0.00 0.00 35.03 3.95
90 92 6.811253 ATCTGCAAAAAGAAATACGTACCA 57.189 33.333 0.00 0.00 0.00 3.25
171 173 7.004086 AGATATCTGTGTTCTTCCCACAAAAA 58.996 34.615 3.89 0.00 41.91 1.94
178 180 4.051237 GTTCTTCCCACAAAAATCTGCAC 58.949 43.478 0.00 0.00 0.00 4.57
236 238 3.119245 GCTATTCCGTGTGACAACTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
628 981 0.028902 GACGCGGCATTAACAATCCC 59.971 55.000 7.34 0.00 0.00 3.85
636 989 3.751698 GGCATTAACAATCCCTCGATACC 59.248 47.826 0.00 0.00 0.00 2.73
710 1063 9.766754 AATCCCCTGCCATTTTTAATTAATTTT 57.233 25.926 5.91 0.00 0.00 1.82
711 1064 8.572855 TCCCCTGCCATTTTTAATTAATTTTG 57.427 30.769 5.91 0.00 0.00 2.44
712 1065 8.386264 TCCCCTGCCATTTTTAATTAATTTTGA 58.614 29.630 5.91 0.00 0.00 2.69
713 1066 8.676401 CCCCTGCCATTTTTAATTAATTTTGAG 58.324 33.333 5.91 0.00 0.00 3.02
745 1107 2.179267 TGAGCTAGCTCACACGCG 59.821 61.111 37.64 3.53 46.80 6.01
747 1109 3.691744 GAGCTAGCTCACACGCGCT 62.692 63.158 34.70 2.40 42.31 5.92
759 1122 1.076533 CACGCGCTCACGTAAATCCT 61.077 55.000 5.73 0.00 46.34 3.24
798 1161 2.890371 GCCATGGCAGCTCAAAGG 59.110 61.111 32.08 0.00 41.49 3.11
811 1174 0.606096 TCAAAGGAGACGATCGCCAA 59.394 50.000 16.60 0.00 38.94 4.52
1057 1421 1.589779 CGCCTCCGGTTTAAATACGAC 59.410 52.381 14.40 0.00 0.00 4.34
1126 1492 1.287503 GAGAGGCCGATCGATCCAC 59.712 63.158 18.66 15.13 0.00 4.02
1614 1992 4.424061 ACATACACACATGAACATGCAC 57.576 40.909 13.71 0.00 42.39 4.57
1621 1999 2.022934 ACATGAACATGCACACACACA 58.977 42.857 13.71 0.00 42.39 3.72
1622 2000 2.223548 ACATGAACATGCACACACACAC 60.224 45.455 13.71 0.00 42.39 3.82
1688 2066 8.795842 TCCAATTTAGGATGTAATTTACGTGT 57.204 30.769 6.01 0.00 31.23 4.49
1689 2067 8.670135 TCCAATTTAGGATGTAATTTACGTGTG 58.330 33.333 6.01 0.00 31.23 3.82
1690 2068 8.455682 CCAATTTAGGATGTAATTTACGTGTGT 58.544 33.333 6.01 0.00 0.00 3.72
1691 2069 9.272901 CAATTTAGGATGTAATTTACGTGTGTG 57.727 33.333 6.01 0.00 0.00 3.82
1692 2070 8.780846 ATTTAGGATGTAATTTACGTGTGTGA 57.219 30.769 6.01 0.00 0.00 3.58
1693 2071 8.780846 TTTAGGATGTAATTTACGTGTGTGAT 57.219 30.769 6.01 0.00 0.00 3.06
1694 2072 6.662414 AGGATGTAATTTACGTGTGTGATG 57.338 37.500 6.01 0.00 0.00 3.07
1695 2073 6.170506 AGGATGTAATTTACGTGTGTGATGT 58.829 36.000 6.01 0.00 0.00 3.06
1696 2074 7.324935 AGGATGTAATTTACGTGTGTGATGTA 58.675 34.615 6.01 0.00 0.00 2.29
1697 2075 7.277098 AGGATGTAATTTACGTGTGTGATGTAC 59.723 37.037 6.01 0.00 0.00 2.90
1698 2076 7.063662 GGATGTAATTTACGTGTGTGATGTACA 59.936 37.037 6.01 0.00 36.82 2.90
1712 2090 5.871465 TGATGTACACAATTTACGCATGT 57.129 34.783 0.00 0.00 0.00 3.21
1714 2092 3.816091 TGTACACAATTTACGCATGTGC 58.184 40.909 6.08 0.00 46.42 4.57
1715 2093 3.500299 TGTACACAATTTACGCATGTGCT 59.500 39.130 6.08 0.00 46.42 4.40
1716 2094 2.932498 ACACAATTTACGCATGTGCTG 58.068 42.857 6.08 0.00 46.42 4.41
1717 2095 2.293122 ACACAATTTACGCATGTGCTGT 59.707 40.909 6.08 5.71 46.42 4.40
1718 2096 3.500299 ACACAATTTACGCATGTGCTGTA 59.500 39.130 6.08 4.81 46.42 2.74
1719 2097 3.845775 CACAATTTACGCATGTGCTGTAC 59.154 43.478 6.08 0.00 38.14 2.90
1720 2098 3.500299 ACAATTTACGCATGTGCTGTACA 59.500 39.130 6.08 0.00 44.87 2.90
1732 2110 3.689309 TGCTGTACACACACAAACATG 57.311 42.857 0.00 0.00 0.00 3.21
1733 2111 2.223456 TGCTGTACACACACAAACATGC 60.223 45.455 0.00 0.00 0.00 4.06
1734 2112 2.223456 GCTGTACACACACAAACATGCA 60.223 45.455 0.00 0.00 0.00 3.96
1735 2113 3.550639 GCTGTACACACACAAACATGCAT 60.551 43.478 0.00 0.00 0.00 3.96
1736 2114 4.320129 GCTGTACACACACAAACATGCATA 60.320 41.667 0.00 0.00 0.00 3.14
1737 2115 5.756849 CTGTACACACACAAACATGCATAA 58.243 37.500 0.00 0.00 0.00 1.90
1738 2116 6.324561 TGTACACACACAAACATGCATAAT 57.675 33.333 0.00 0.00 0.00 1.28
1739 2117 6.377780 TGTACACACACAAACATGCATAATC 58.622 36.000 0.00 0.00 0.00 1.75
1740 2118 5.710513 ACACACACAAACATGCATAATCT 57.289 34.783 0.00 0.00 0.00 2.40
1741 2119 5.463286 ACACACACAAACATGCATAATCTG 58.537 37.500 0.00 0.00 0.00 2.90
1742 2120 5.009911 ACACACACAAACATGCATAATCTGT 59.990 36.000 0.00 0.00 0.00 3.41
1743 2121 5.921976 CACACACAAACATGCATAATCTGTT 59.078 36.000 0.00 0.00 34.71 3.16
1744 2122 6.088483 CACACACAAACATGCATAATCTGTTC 59.912 38.462 0.00 0.00 32.18 3.18
1745 2123 6.016024 ACACACAAACATGCATAATCTGTTCT 60.016 34.615 0.00 0.00 32.18 3.01
1753 2131 8.922058 ACATGCATAATCTGTTCTTCAAATTC 57.078 30.769 0.00 0.00 0.00 2.17
1989 2580 2.357517 CCTGTTCGGCAAGCGTCT 60.358 61.111 0.00 0.00 0.00 4.18
2119 2715 1.375013 GGAAAAGTGCCGCTCCGTA 60.375 57.895 0.00 0.00 0.00 4.02
2136 2732 0.872021 GTACGCTCCGCTTCTGGATG 60.872 60.000 0.00 0.00 37.41 3.51
2139 2735 1.522580 GCTCCGCTTCTGGATGGAC 60.523 63.158 0.00 0.00 37.41 4.02
2150 2746 0.178876 TGGATGGACCTGGGAGTTGA 60.179 55.000 0.00 0.00 39.86 3.18
2151 2747 0.991920 GGATGGACCTGGGAGTTGAA 59.008 55.000 0.00 0.00 35.41 2.69
2158 2754 0.598065 CCTGGGAGTTGAAAAAGCGG 59.402 55.000 0.00 0.00 0.00 5.52
2263 2866 4.000325 ACAATTTACGCATGTGCTCTACA 59.000 39.130 6.08 0.00 44.87 2.74
2654 3262 2.420129 CCACTTATTAGCTGCTCCCGTT 60.420 50.000 4.91 0.00 0.00 4.44
2843 3451 5.827797 TGTGTTTTCTAGCTGGTTGATTTCT 59.172 36.000 0.00 0.00 0.00 2.52
2930 3542 8.956533 ATAGCAGGTTTGTTTGTGTTTATTTT 57.043 26.923 0.00 0.00 0.00 1.82
2932 3544 6.876257 AGCAGGTTTGTTTGTGTTTATTTTGA 59.124 30.769 0.00 0.00 0.00 2.69
2939 3551 7.979115 TGTTTGTGTTTATTTTGAGCTACAC 57.021 32.000 5.39 5.39 37.11 2.90
3064 3696 3.708563 AATTGGTTGTGAGTTTGTCGG 57.291 42.857 0.00 0.00 0.00 4.79
3082 3714 0.872388 GGATTGAAAGTGACGCGGTT 59.128 50.000 12.47 0.00 0.00 4.44
3210 3842 8.518702 GGAAATTTAAGATCTAGGCAATCCATC 58.481 37.037 0.00 0.00 33.74 3.51
3290 4120 6.159988 AGTAGTGCATTAGTGAAGTTGAGAC 58.840 40.000 0.00 0.00 0.00 3.36
3356 4188 6.171921 TGAATTTTTGGTTTGCCTGATATGG 58.828 36.000 0.00 0.00 35.27 2.74
3378 4210 5.012046 TGGGATATAGCACTCATCAAACGAT 59.988 40.000 0.00 0.00 0.00 3.73
3386 4218 4.457810 CACTCATCAAACGATGACACAAC 58.542 43.478 1.05 0.00 43.45 3.32
3403 4235 6.545666 TGACACAACACTGAAGGTATTCAAAT 59.454 34.615 0.00 0.00 44.68 2.32
3406 4238 8.730680 ACACAACACTGAAGGTATTCAAATATC 58.269 33.333 0.00 0.00 44.68 1.63
3410 4242 7.327975 ACACTGAAGGTATTCAAATATCGTGA 58.672 34.615 10.75 0.00 44.68 4.35
3493 4325 5.380900 TCAGTTTATGGTGTTGGATGTTCA 58.619 37.500 0.00 0.00 0.00 3.18
3502 4334 5.105797 TGGTGTTGGATGTTCAGCATATTTC 60.106 40.000 0.00 0.00 38.06 2.17
3562 4394 2.939103 CACTACTGCCCATAGTTGCTTC 59.061 50.000 0.00 0.00 30.22 3.86
3580 4412 3.124297 GCTTCGAGAACCTCAGAAATGTG 59.876 47.826 0.00 0.00 0.00 3.21
3596 4428 4.849813 AATGTGATGTCCTGATGGAGAA 57.150 40.909 0.00 0.00 44.16 2.87
3652 4484 3.947910 TTTAGTCGGACTTCGGTTGAT 57.052 42.857 16.95 0.00 39.77 2.57
3668 4500 8.545229 TTCGGTTGATCAAATTATGCATTTTT 57.455 26.923 10.35 2.82 32.24 1.94
3829 4665 8.908903 TGATTCAGTACTCTCCTAATCTCTTTC 58.091 37.037 0.00 0.00 0.00 2.62
3878 4714 7.148239 CCTCCTTAACAACTACATTCATGGTTC 60.148 40.741 0.00 0.00 0.00 3.62
3947 4783 4.614946 CTTCTTTTGGTTTGCAAGAGAGG 58.385 43.478 0.00 0.00 0.00 3.69
3995 4831 4.519213 TCTCTACACCTCAGAGTAAGCTC 58.481 47.826 0.00 0.00 40.41 4.09
4215 5051 5.482163 TGTATCCGATGATCATTTGGCTA 57.518 39.130 18.47 12.76 32.18 3.93
4239 5075 9.591792 CTAGCTATGATCGATATTTTGGATTGA 57.408 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.336755 GCAAACACATTGGAACCTCGT 59.663 47.619 0.00 0.00 39.54 4.18
171 173 3.479489 TGTGATTTGAGTGTGTGCAGAT 58.521 40.909 0.00 0.00 0.00 2.90
178 180 5.909054 GTGTTGTGTATGTGATTTGAGTGTG 59.091 40.000 0.00 0.00 0.00 3.82
628 981 0.387367 CAAGATCCGCGGGTATCGAG 60.387 60.000 27.83 14.98 42.43 4.04
636 989 4.845580 AGCTGGCAAGATCCGCGG 62.846 66.667 22.12 22.12 33.22 6.46
739 1093 1.349259 GGATTTACGTGAGCGCGTGT 61.349 55.000 18.13 1.53 45.33 4.49
745 1107 3.746045 TGGGATAGGATTTACGTGAGC 57.254 47.619 0.00 0.00 0.00 4.26
747 1109 4.262292 CGGATTGGGATAGGATTTACGTGA 60.262 45.833 0.00 0.00 0.00 4.35
759 1122 1.148027 AGAGGAGAGCGGATTGGGATA 59.852 52.381 0.00 0.00 0.00 2.59
798 1161 1.858091 ATCATGTTGGCGATCGTCTC 58.142 50.000 21.85 14.07 0.00 3.36
811 1174 1.340889 GTGGGTTGCACACAATCATGT 59.659 47.619 1.31 0.00 38.76 3.21
1426 1804 6.877611 AATGTAGTAAAATGATTAGGCCGG 57.122 37.500 0.00 0.00 0.00 6.13
1485 1863 4.489493 GCAACACATACGCACGTAAATTAC 59.511 41.667 7.02 0.00 33.99 1.89
1614 1992 2.355197 TGAAGAACAGGTGTGTGTGTG 58.645 47.619 0.00 0.00 36.84 3.82
1621 1999 6.772716 ACATACTGAATTTGAAGAACAGGTGT 59.227 34.615 0.00 0.00 33.57 4.16
1622 2000 7.206981 ACATACTGAATTTGAAGAACAGGTG 57.793 36.000 0.00 0.00 33.57 4.00
1663 2041 8.670135 CACACGTAAATTACATCCTAAATTGGA 58.330 33.333 3.91 0.00 40.82 3.53
1664 2042 8.455682 ACACACGTAAATTACATCCTAAATTGG 58.544 33.333 3.91 0.00 0.00 3.16
1665 2043 9.272901 CACACACGTAAATTACATCCTAAATTG 57.727 33.333 3.91 0.00 0.00 2.32
1666 2044 9.221933 TCACACACGTAAATTACATCCTAAATT 57.778 29.630 3.91 0.00 0.00 1.82
1667 2045 8.780846 TCACACACGTAAATTACATCCTAAAT 57.219 30.769 3.91 0.00 0.00 1.40
1668 2046 8.661257 CATCACACACGTAAATTACATCCTAAA 58.339 33.333 3.91 0.00 0.00 1.85
1669 2047 7.820386 ACATCACACACGTAAATTACATCCTAA 59.180 33.333 3.91 0.00 0.00 2.69
1670 2048 7.324935 ACATCACACACGTAAATTACATCCTA 58.675 34.615 3.91 0.00 0.00 2.94
1671 2049 6.170506 ACATCACACACGTAAATTACATCCT 58.829 36.000 3.91 0.00 0.00 3.24
1672 2050 6.417191 ACATCACACACGTAAATTACATCC 57.583 37.500 3.91 0.00 0.00 3.51
1673 2051 7.955502 TGTACATCACACACGTAAATTACATC 58.044 34.615 3.91 0.00 30.04 3.06
1674 2052 7.892778 TGTACATCACACACGTAAATTACAT 57.107 32.000 3.91 0.00 30.04 2.29
1689 2067 5.507876 CACATGCGTAAATTGTGTACATCAC 59.492 40.000 0.00 0.00 46.31 3.06
1690 2068 5.626211 CACATGCGTAAATTGTGTACATCA 58.374 37.500 0.00 0.00 36.77 3.07
1691 2069 4.495472 GCACATGCGTAAATTGTGTACATC 59.505 41.667 0.00 0.00 42.11 3.06
1692 2070 4.411327 GCACATGCGTAAATTGTGTACAT 58.589 39.130 0.00 0.00 42.11 2.29
1693 2071 3.816091 GCACATGCGTAAATTGTGTACA 58.184 40.909 7.42 0.00 42.11 2.90
1695 2073 9.611627 GTGTACAGCACATGCGTAAATTGTGTA 62.612 40.741 0.00 3.24 46.91 2.90
1696 2074 8.896917 GTGTACAGCACATGCGTAAATTGTGT 62.897 42.308 0.00 4.03 46.91 3.72
1697 2075 6.613411 GTGTACAGCACATGCGTAAATTGTG 61.613 44.000 0.00 1.85 46.91 3.33
1698 2076 4.612712 GTGTACAGCACATGCGTAAATTGT 60.613 41.667 0.00 5.19 46.91 2.71
1699 2077 3.845775 GTGTACAGCACATGCGTAAATTG 59.154 43.478 0.00 0.00 46.91 2.32
1700 2078 4.078363 GTGTACAGCACATGCGTAAATT 57.922 40.909 0.00 0.00 46.91 1.82
1701 2079 3.740044 GTGTACAGCACATGCGTAAAT 57.260 42.857 0.00 0.00 46.91 1.40
1712 2090 2.223456 GCATGTTTGTGTGTGTACAGCA 60.223 45.455 0.00 0.00 37.52 4.41
1713 2091 2.223456 TGCATGTTTGTGTGTGTACAGC 60.223 45.455 0.00 0.00 37.52 4.40
1714 2092 3.689309 TGCATGTTTGTGTGTGTACAG 57.311 42.857 0.00 0.00 37.52 2.74
1715 2093 5.757850 TTATGCATGTTTGTGTGTGTACA 57.242 34.783 10.16 0.00 0.00 2.90
1716 2094 6.524239 CAGATTATGCATGTTTGTGTGTGTAC 59.476 38.462 10.16 0.00 0.00 2.90
1717 2095 6.206438 ACAGATTATGCATGTTTGTGTGTGTA 59.794 34.615 10.16 0.00 0.00 2.90
1718 2096 5.009911 ACAGATTATGCATGTTTGTGTGTGT 59.990 36.000 10.16 0.00 0.00 3.72
1719 2097 5.463286 ACAGATTATGCATGTTTGTGTGTG 58.537 37.500 10.16 0.00 0.00 3.82
1720 2098 5.710513 ACAGATTATGCATGTTTGTGTGT 57.289 34.783 10.16 2.85 0.00 3.72
1721 2099 6.384224 AGAACAGATTATGCATGTTTGTGTG 58.616 36.000 10.16 2.24 37.29 3.82
1722 2100 6.579666 AGAACAGATTATGCATGTTTGTGT 57.420 33.333 10.16 5.93 37.29 3.72
1723 2101 7.085746 TGAAGAACAGATTATGCATGTTTGTG 58.914 34.615 10.16 5.29 37.29 3.33
1724 2102 7.218228 TGAAGAACAGATTATGCATGTTTGT 57.782 32.000 10.16 6.85 37.29 2.83
1725 2103 8.523523 TTTGAAGAACAGATTATGCATGTTTG 57.476 30.769 10.16 6.20 37.29 2.93
1726 2104 9.715121 AATTTGAAGAACAGATTATGCATGTTT 57.285 25.926 10.16 0.00 37.29 2.83
1727 2105 9.362539 GAATTTGAAGAACAGATTATGCATGTT 57.637 29.630 10.16 5.82 39.76 2.71
1728 2106 8.525316 TGAATTTGAAGAACAGATTATGCATGT 58.475 29.630 10.16 0.00 34.23 3.21
1729 2107 8.920509 TGAATTTGAAGAACAGATTATGCATG 57.079 30.769 10.16 0.00 34.23 4.06
1730 2108 8.746530 ACTGAATTTGAAGAACAGATTATGCAT 58.253 29.630 3.79 3.79 34.23 3.96
1731 2109 8.114331 ACTGAATTTGAAGAACAGATTATGCA 57.886 30.769 0.00 0.00 34.23 3.96
1736 2114 9.288576 TCACATACTGAATTTGAAGAACAGATT 57.711 29.630 0.00 0.00 36.28 2.40
1737 2115 8.853077 TCACATACTGAATTTGAAGAACAGAT 57.147 30.769 0.00 0.00 33.53 2.90
1738 2116 8.853077 ATCACATACTGAATTTGAAGAACAGA 57.147 30.769 0.00 0.00 28.37 3.41
1739 2117 9.903682 AAATCACATACTGAATTTGAAGAACAG 57.096 29.630 0.00 0.00 28.37 3.16
1919 2302 1.424403 TGTACAGCACATGCGTACAC 58.576 50.000 24.48 12.65 45.81 2.90
2088 2684 3.796717 GCACTTTTCCAACTCCGAAAAAG 59.203 43.478 5.21 5.21 41.96 2.27
2094 2690 1.574428 CGGCACTTTTCCAACTCCG 59.426 57.895 0.00 0.00 0.00 4.63
2127 2723 0.835941 CTCCCAGGTCCATCCAGAAG 59.164 60.000 0.00 0.00 39.02 2.85
2136 2732 1.613925 GCTTTTTCAACTCCCAGGTCC 59.386 52.381 0.00 0.00 0.00 4.46
2139 2735 0.598065 CCGCTTTTTCAACTCCCAGG 59.402 55.000 0.00 0.00 0.00 4.45
2150 2746 1.599797 CGTCCACTCCCCGCTTTTT 60.600 57.895 0.00 0.00 0.00 1.94
2151 2747 2.032071 CGTCCACTCCCCGCTTTT 59.968 61.111 0.00 0.00 0.00 2.27
2175 2771 4.351874 TGCATATACTAAGGCCCTGTTC 57.648 45.455 0.00 0.00 0.00 3.18
2240 2837 5.815222 ATGTAGAGCACATGCGTAAATTGTA 59.185 36.000 0.00 0.00 46.41 2.41
2372 2980 2.027325 CCATGCATGGTGGTGATCG 58.973 57.895 33.68 8.38 43.05 3.69
2654 3262 0.109458 CCGTCCATCGTTTCAGTCGA 60.109 55.000 0.00 0.00 41.45 4.20
2794 3402 9.371136 CATGATATACGGCTATTACTCAACAAT 57.629 33.333 0.00 0.00 0.00 2.71
2795 3403 8.364894 ACATGATATACGGCTATTACTCAACAA 58.635 33.333 0.00 0.00 0.00 2.83
2796 3404 7.812669 CACATGATATACGGCTATTACTCAACA 59.187 37.037 0.00 0.00 0.00 3.33
2797 3405 7.813148 ACACATGATATACGGCTATTACTCAAC 59.187 37.037 0.00 0.00 0.00 3.18
2996 3625 8.721479 CCTATCATGATATAAATGACCTCCCAT 58.279 37.037 15.71 0.00 36.89 4.00
3064 3696 3.124636 ACATAACCGCGTCACTTTCAATC 59.875 43.478 4.92 0.00 0.00 2.67
3082 3714 5.304101 AGAAACTCCAATGCACCAAAACATA 59.696 36.000 0.00 0.00 0.00 2.29
3137 3769 3.674997 TGCTTTATGTCTGGACTTGGTC 58.325 45.455 2.38 0.00 0.00 4.02
3290 4120 3.123959 CCAATCCTTTGCAAAAGCATTCG 59.876 43.478 13.84 0.00 0.00 3.34
3378 4210 5.029807 TGAATACCTTCAGTGTTGTGTCA 57.970 39.130 0.00 0.00 36.46 3.58
3386 4218 7.770801 TCACGATATTTGAATACCTTCAGTG 57.229 36.000 0.00 0.00 42.19 3.66
3403 4235 5.351948 TGAAACTCCCATTCATCACGATA 57.648 39.130 0.00 0.00 32.10 2.92
3406 4238 2.096496 GCTGAAACTCCCATTCATCACG 59.904 50.000 0.00 0.00 36.30 4.35
3410 4242 3.265221 TCTCTGCTGAAACTCCCATTCAT 59.735 43.478 0.00 0.00 36.30 2.57
3442 4274 3.912496 TGAGGCTGCTTTCTTGCTATA 57.088 42.857 0.00 0.00 0.00 1.31
3493 4325 8.942338 TTAGTGAGTGATAAACGAAATATGCT 57.058 30.769 0.00 0.00 0.00 3.79
3502 4334 5.416083 TGGTGGATTAGTGAGTGATAAACG 58.584 41.667 0.00 0.00 0.00 3.60
3562 4394 4.248859 ACATCACATTTCTGAGGTTCTCG 58.751 43.478 0.00 0.00 31.16 4.04
3580 4412 3.198635 TCTGGTTTCTCCATCAGGACATC 59.801 47.826 0.00 0.00 46.12 3.06
3596 4428 2.233271 CAGGTGCATTTGACTCTGGTT 58.767 47.619 0.00 0.00 0.00 3.67
3608 4440 4.511246 CATCGCCCCCAGGTGCAT 62.511 66.667 0.00 0.00 43.91 3.96
3668 4500 7.120051 ACTAAAGCTAAGTGGAGTCTCTATGA 58.880 38.462 0.00 0.00 0.00 2.15
3675 4507 4.221041 ACCTGACTAAAGCTAAGTGGAGTC 59.779 45.833 6.38 4.90 35.07 3.36
3730 4562 6.716628 CCCGTACTACTAGTACCATTATTGGA 59.283 42.308 17.29 0.00 46.27 3.53
3732 4564 6.571150 GCCCCGTACTACTAGTACCATTATTG 60.571 46.154 17.29 5.05 46.27 1.90
3743 4575 2.617774 GTCTTCTGCCCCGTACTACTAG 59.382 54.545 0.00 0.00 0.00 2.57
3829 4665 5.691754 GGTTTGGTGCTTTAGAAAATCACAG 59.308 40.000 8.19 0.00 0.00 3.66
3878 4714 4.058817 GAGAAGTTGGTGTGAAGTGTAGG 58.941 47.826 0.00 0.00 0.00 3.18
3924 4760 4.045636 TCTCTTGCAAACCAAAAGAAGC 57.954 40.909 0.00 0.00 27.82 3.86
4026 4862 1.725641 TGCAGGATTACAACGCTGAG 58.274 50.000 0.00 0.00 0.00 3.35
4106 4942 8.641499 TGTGGAATTTTGTAGTCAATTGTTTC 57.359 30.769 5.13 0.00 33.32 2.78
4112 4948 6.165577 GCCATTGTGGAATTTTGTAGTCAAT 58.834 36.000 0.00 0.00 40.96 2.57
4215 5051 8.853077 TTCAATCCAAAATATCGATCATAGCT 57.147 30.769 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.