Multiple sequence alignment - TraesCS7D01G079500

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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 TraesCS7D01G079500 chr7D 100.000 2720 0 0 1 2720 46854657 46851938 0.000000e+00 5024.0
1 TraesCS7D01G079500 chr7D 93.528 788 35 7 1 773 194789529 194790315 0.000000e+00 1158.0
2 TraesCS7D01G079500 chr7D 100.000 38 0 0 2679 2716 61979654 61979617 1.350000e-08 71.3
3 TraesCS7D01G079500 chr4A 93.491 1014 42 5 777 1775 660876893 660877897 0.000000e+00 1485.0
4 TraesCS7D01G079500 chr4A 84.448 688 74 15 1827 2496 660877902 660878574 0.000000e+00 647.0
5 TraesCS7D01G079500 chr4A 94.000 50 3 0 2671 2720 704495357 704495406 2.900000e-10 76.8
6 TraesCS7D01G079500 chr7A 88.934 1229 63 33 768 1955 49056913 49058109 0.000000e+00 1448.0
7 TraesCS7D01G079500 chr5D 94.839 775 25 7 1 770 345968684 345969448 0.000000e+00 1195.0
8 TraesCS7D01G079500 chr5D 92.583 782 37 6 1 777 409340545 409339780 0.000000e+00 1103.0
9 TraesCS7D01G079500 chr5D 92.318 781 42 7 1 776 549500808 549500041 0.000000e+00 1094.0
10 TraesCS7D01G079500 chr5D 100.000 38 0 0 2679 2716 356698275 356698238 1.350000e-08 71.3
11 TraesCS7D01G079500 chr5D 100.000 38 0 0 2679 2716 444478735 444478772 1.350000e-08 71.3
12 TraesCS7D01G079500 chr4D 93.325 794 32 10 1 775 308810822 308810031 0.000000e+00 1153.0
13 TraesCS7D01G079500 chr4D 92.967 782 47 7 1 776 505323613 505322834 0.000000e+00 1133.0
14 TraesCS7D01G079500 chr1D 92.308 793 46 9 1 779 450511409 450510618 0.000000e+00 1112.0
15 TraesCS7D01G079500 chr1D 91.026 780 55 6 1 776 259539001 259538233 0.000000e+00 1038.0
16 TraesCS7D01G079500 chr1D 88.513 679 44 21 102 775 22845208 22845857 0.000000e+00 791.0
17 TraesCS7D01G079500 chr6A 90.114 789 56 11 1 773 600311491 600310709 0.000000e+00 1005.0
18 TraesCS7D01G079500 chr6A 90.738 745 55 11 42 775 518605320 518604579 0.000000e+00 981.0
19 TraesCS7D01G079500 chr6A 90.566 53 5 0 2668 2720 317599388 317599440 1.350000e-08 71.3
20 TraesCS7D01G079500 chr3B 76.812 207 42 5 2151 2351 60735351 60735145 7.960000e-21 111.0
21 TraesCS7D01G079500 chr3B 88.889 45 3 2 2358 2402 361832861 361832903 1.000000e-03 54.7
22 TraesCS7D01G079500 chr2A 90.000 60 5 1 2662 2720 12151158 12151099 2.900000e-10 76.8
23 TraesCS7D01G079500 chr7B 95.652 46 1 1 2671 2716 642703081 642703125 3.760000e-09 73.1
24 TraesCS7D01G079500 chr1B 95.652 46 1 1 2671 2716 575150985 575150941 3.760000e-09 73.1
25 TraesCS7D01G079500 chr1A 93.478 46 1 2 2671 2716 535342018 535341975 1.750000e-07 67.6


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 TraesCS7D01G079500 chr7D 46851938 46854657 2719 True 5024 5024 100.0000 1 2720 1 chr7D.!!$R1 2719
1 TraesCS7D01G079500 chr7D 194789529 194790315 786 False 1158 1158 93.5280 1 773 1 chr7D.!!$F1 772
2 TraesCS7D01G079500 chr4A 660876893 660878574 1681 False 1066 1485 88.9695 777 2496 2 chr4A.!!$F2 1719
3 TraesCS7D01G079500 chr7A 49056913 49058109 1196 False 1448 1448 88.9340 768 1955 1 chr7A.!!$F1 1187
4 TraesCS7D01G079500 chr5D 345968684 345969448 764 False 1195 1195 94.8390 1 770 1 chr5D.!!$F1 769
5 TraesCS7D01G079500 chr5D 409339780 409340545 765 True 1103 1103 92.5830 1 777 1 chr5D.!!$R2 776
6 TraesCS7D01G079500 chr5D 549500041 549500808 767 True 1094 1094 92.3180 1 776 1 chr5D.!!$R3 775
7 TraesCS7D01G079500 chr4D 308810031 308810822 791 True 1153 1153 93.3250 1 775 1 chr4D.!!$R1 774
8 TraesCS7D01G079500 chr4D 505322834 505323613 779 True 1133 1133 92.9670 1 776 1 chr4D.!!$R2 775
9 TraesCS7D01G079500 chr1D 450510618 450511409 791 True 1112 1112 92.3080 1 779 1 chr1D.!!$R2 778
10 TraesCS7D01G079500 chr1D 259538233 259539001 768 True 1038 1038 91.0260 1 776 1 chr1D.!!$R1 775
11 TraesCS7D01G079500 chr1D 22845208 22845857 649 False 791 791 88.5130 102 775 1 chr1D.!!$F1 673
12 TraesCS7D01G079500 chr6A 600310709 600311491 782 True 1005 1005 90.1140 1 773 1 chr6A.!!$R2 772
13 TraesCS7D01G079500 chr6A 518604579 518605320 741 True 981 981 90.7380 42 775 1 chr6A.!!$R1 733

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
722 789 1.971167 TTTTTGCGCCGGCTCATCT 60.971 52.632 26.68 0.0 40.82 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 2702 0.103572 TAAACTCCGCCTATGGACGC 59.896 55.0 0.0 0.0 33.48 5.19 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
125 126 2.106074 GCCGGCATCGTCATCAACA 61.106 57.895 24.80 0.00 33.95 3.33
536 554 4.233635 CGACGGCGACTACTCCGG 62.234 72.222 16.62 0.00 46.93 5.14
722 789 1.971167 TTTTTGCGCCGGCTCATCT 60.971 52.632 26.68 0.00 40.82 2.90
1050 1146 2.939022 GACGGCGAGCATAATGGC 59.061 61.111 16.62 0.00 0.00 4.40
1052 1148 3.716006 CGGCGAGCATAATGGCGG 61.716 66.667 0.00 0.00 46.36 6.13
1053 1149 2.280797 GGCGAGCATAATGGCGGA 60.281 61.111 0.00 0.00 39.27 5.54
1425 1521 2.516589 CCACGACATGGTGATCGCG 61.517 63.158 0.00 0.00 44.46 5.87
1431 1527 0.032678 ACATGGTGATCGCGATCCTC 59.967 55.000 38.25 30.34 37.02 3.71
1775 1892 1.475751 CCCCAGTCCAATCGAATCCAG 60.476 57.143 0.00 0.00 0.00 3.86
1783 1900 2.486982 CCAATCGAATCCAGATCCATGC 59.513 50.000 0.00 0.00 0.00 4.06
1789 1906 3.364664 CGAATCCAGATCCATGCGATTTG 60.365 47.826 7.37 7.37 33.74 2.32
1791 1908 0.956633 CCAGATCCATGCGATTTGGG 59.043 55.000 18.41 9.08 45.53 4.12
1792 1909 1.477377 CCAGATCCATGCGATTTGGGA 60.477 52.381 18.41 0.00 45.53 4.37
1793 1910 2.511659 CAGATCCATGCGATTTGGGAT 58.488 47.619 0.00 0.00 42.66 3.85
1794 1911 2.889045 CAGATCCATGCGATTTGGGATT 59.111 45.455 0.00 0.00 40.15 3.01
1795 1912 3.319972 CAGATCCATGCGATTTGGGATTT 59.680 43.478 0.00 0.00 40.15 2.17
1796 1913 3.319972 AGATCCATGCGATTTGGGATTTG 59.680 43.478 0.00 0.00 40.15 2.32
1797 1914 1.755959 TCCATGCGATTTGGGATTTGG 59.244 47.619 0.00 0.00 34.85 3.28
1798 1915 1.202557 CCATGCGATTTGGGATTTGGG 60.203 52.381 0.00 0.00 0.00 4.12
1799 1916 1.481772 CATGCGATTTGGGATTTGGGT 59.518 47.619 0.00 0.00 0.00 4.51
1803 1920 1.204467 CGATTTGGGATTTGGGTGTGG 59.796 52.381 0.00 0.00 0.00 4.17
1805 1922 1.124477 TTTGGGATTTGGGTGTGGGC 61.124 55.000 0.00 0.00 0.00 5.36
1809 1926 0.831711 GGATTTGGGTGTGGGCACTT 60.832 55.000 0.00 0.00 44.65 3.16
1950 2068 2.812011 GGTGACGTGCCTTTAGTTTCAT 59.188 45.455 0.00 0.00 0.00 2.57
1962 2080 6.868339 GCCTTTAGTTTCATTAGCAAACATGT 59.132 34.615 0.00 0.00 36.38 3.21
1964 2082 8.299570 CCTTTAGTTTCATTAGCAAACATGTCT 58.700 33.333 0.00 0.00 36.38 3.41
1967 2085 6.441274 AGTTTCATTAGCAAACATGTCTGTG 58.559 36.000 0.00 0.00 36.38 3.66
1968 2086 4.424061 TCATTAGCAAACATGTCTGTGC 57.576 40.909 17.10 17.10 35.22 4.57
1969 2087 2.967459 TTAGCAAACATGTCTGTGCG 57.033 45.000 18.16 0.00 35.22 5.34
1970 2088 1.877637 TAGCAAACATGTCTGTGCGT 58.122 45.000 18.16 11.87 35.22 5.24
1971 2089 1.024271 AGCAAACATGTCTGTGCGTT 58.976 45.000 18.16 4.88 35.22 4.84
1972 2090 1.122849 GCAAACATGTCTGTGCGTTG 58.877 50.000 11.86 6.59 35.22 4.10
1973 2091 1.122849 CAAACATGTCTGTGCGTTGC 58.877 50.000 0.00 0.00 35.22 4.17
1974 2092 0.737804 AAACATGTCTGTGCGTTGCA 59.262 45.000 0.00 0.00 35.22 4.08
1975 2093 0.737804 AACATGTCTGTGCGTTGCAA 59.262 45.000 0.00 0.00 41.47 4.08
1976 2094 0.029300 ACATGTCTGTGCGTTGCAAC 59.971 50.000 19.89 19.89 41.47 4.17
1978 2096 0.308684 ATGTCTGTGCGTTGCAACAG 59.691 50.000 28.01 18.72 41.47 3.16
1979 2097 0.742635 TGTCTGTGCGTTGCAACAGA 60.743 50.000 28.01 20.65 41.47 3.41
1980 2098 0.376852 GTCTGTGCGTTGCAACAGAA 59.623 50.000 28.01 13.44 42.87 3.02
1981 2099 0.657312 TCTGTGCGTTGCAACAGAAG 59.343 50.000 28.01 18.38 41.47 2.85
1982 2100 0.317269 CTGTGCGTTGCAACAGAAGG 60.317 55.000 28.01 13.09 41.47 3.46
1983 2101 0.746204 TGTGCGTTGCAACAGAAGGA 60.746 50.000 28.01 11.07 41.47 3.36
1984 2102 0.380378 GTGCGTTGCAACAGAAGGAA 59.620 50.000 28.01 4.16 41.47 3.36
1985 2103 1.001378 GTGCGTTGCAACAGAAGGAAT 60.001 47.619 28.01 0.00 41.47 3.01
1986 2104 1.680735 TGCGTTGCAACAGAAGGAATT 59.319 42.857 28.01 0.00 34.76 2.17
1987 2105 2.100584 TGCGTTGCAACAGAAGGAATTT 59.899 40.909 28.01 0.00 34.76 1.82
2016 2134 6.538742 TCACAAGTTCCTAGCATAATAAGCAC 59.461 38.462 0.00 0.00 0.00 4.40
2020 2138 4.252971 TCCTAGCATAATAAGCACGACC 57.747 45.455 0.00 0.00 0.00 4.79
2021 2139 3.639561 TCCTAGCATAATAAGCACGACCA 59.360 43.478 0.00 0.00 0.00 4.02
2030 2148 0.759346 AAGCACGACCAAAGACTCCT 59.241 50.000 0.00 0.00 0.00 3.69
2036 2154 2.289694 ACGACCAAAGACTCCTCAATGG 60.290 50.000 0.00 0.00 37.10 3.16
2039 2157 3.753797 GACCAAAGACTCCTCAATGGTTC 59.246 47.826 0.00 0.00 41.04 3.62
2048 2166 5.440610 ACTCCTCAATGGTTCCATGTTATC 58.559 41.667 5.02 0.00 37.07 1.75
2056 2174 6.764308 ATGGTTCCATGTTATCTGTTTGAG 57.236 37.500 3.31 0.00 0.00 3.02
2065 2196 6.000891 TGTTATCTGTTTGAGCATGTTGTC 57.999 37.500 0.00 0.00 0.00 3.18
2066 2197 3.818961 ATCTGTTTGAGCATGTTGTCG 57.181 42.857 0.00 0.00 0.00 4.35
2070 2201 2.046313 GTTTGAGCATGTTGTCGCTTG 58.954 47.619 0.00 0.00 38.99 4.01
2077 2208 0.687354 ATGTTGTCGCTTGTCCTCCT 59.313 50.000 0.00 0.00 0.00 3.69
2083 2214 1.743252 CGCTTGTCCTCCTTCCTGC 60.743 63.158 0.00 0.00 0.00 4.85
2090 2221 0.618968 TCCTCCTTCCTGCCTTCCTC 60.619 60.000 0.00 0.00 0.00 3.71
2101 2232 1.899437 GCCTTCCTCGACCATGGTCA 61.899 60.000 37.42 25.18 44.77 4.02
2104 2235 0.459899 TTCCTCGACCATGGTCATCG 59.540 55.000 37.42 27.15 44.77 3.84
2121 2252 1.746615 CGGGTCCACCTGATTGCAG 60.747 63.158 0.00 0.00 45.36 4.41
2131 2262 2.829720 ACCTGATTGCAGTGCATTCAAT 59.170 40.909 31.46 23.41 44.47 2.57
2132 2263 3.186909 CCTGATTGCAGTGCATTCAATG 58.813 45.455 31.46 24.23 44.47 2.82
2135 2266 3.256136 TGATTGCAGTGCATTCAATGTGA 59.744 39.130 30.62 13.58 43.01 3.58
2140 2271 3.796717 GCAGTGCATTCAATGTGATCATG 59.203 43.478 11.09 0.00 40.17 3.07
2164 2295 2.357637 ACAAACCTGACATTGAACCACG 59.642 45.455 0.00 0.00 0.00 4.94
2173 2304 1.240641 ATTGAACCACGCCATCGCAA 61.241 50.000 0.00 0.00 39.84 4.85
2180 2311 1.596752 ACGCCATCGCAAGTCAACA 60.597 52.632 0.00 0.00 39.84 3.33
2181 2312 1.154413 CGCCATCGCAAGTCAACAC 60.154 57.895 0.00 0.00 39.48 3.32
2188 2319 4.634004 CCATCGCAAGTCAACACCTAATAA 59.366 41.667 0.00 0.00 39.48 1.40
2235 2368 1.959226 TGACGCTGCCTTTTCCGAC 60.959 57.895 0.00 0.00 0.00 4.79
2251 2384 2.228822 TCCGACCTCAACCTACGTTTAC 59.771 50.000 0.00 0.00 0.00 2.01
2252 2385 2.599659 CGACCTCAACCTACGTTTACC 58.400 52.381 0.00 0.00 0.00 2.85
2262 2395 2.481795 CCTACGTTTACCCCATACACCG 60.482 54.545 0.00 0.00 0.00 4.94
2269 2402 1.223487 CCCCATACACCGTCCCTTG 59.777 63.158 0.00 0.00 0.00 3.61
2286 2419 3.139077 CCTTGTACACCCACTCACTTTC 58.861 50.000 0.00 0.00 0.00 2.62
2295 2428 5.067283 ACACCCACTCACTTTCAAATTGTAC 59.933 40.000 0.00 0.00 0.00 2.90
2343 2476 9.203421 CAACCTTCTTTTAAAACACAAAGACTT 57.797 29.630 0.00 0.00 38.47 3.01
2422 2557 8.176814 ACAAAACAATTCTAAATGCATGATCG 57.823 30.769 0.00 0.00 0.00 3.69
2423 2558 6.817270 AAACAATTCTAAATGCATGATCGC 57.183 33.333 0.00 0.00 0.00 4.58
2424 2559 5.762825 ACAATTCTAAATGCATGATCGCT 57.237 34.783 0.00 0.00 0.00 4.93
2430 2565 9.585099 AATTCTAAATGCATGATCGCTTTTTAA 57.415 25.926 0.00 7.37 39.27 1.52
2492 2628 8.522178 AAACACGTGAACACTTTTTATGAAAA 57.478 26.923 25.01 0.00 33.86 2.29
2496 2632 6.252655 ACGTGAACACTTTTTATGAAAACTGC 59.747 34.615 3.51 0.00 31.72 4.40
2497 2633 6.252441 CGTGAACACTTTTTATGAAAACTGCA 59.748 34.615 3.51 0.00 31.72 4.41
2498 2634 7.391016 GTGAACACTTTTTATGAAAACTGCAC 58.609 34.615 0.00 0.00 31.72 4.57
2499 2635 6.252441 TGAACACTTTTTATGAAAACTGCACG 59.748 34.615 0.00 0.00 31.72 5.34
2500 2636 5.646606 ACACTTTTTATGAAAACTGCACGT 58.353 33.333 0.00 0.00 31.72 4.49
2501 2637 5.514914 ACACTTTTTATGAAAACTGCACGTG 59.485 36.000 12.28 12.28 33.34 4.49
2502 2638 5.514914 CACTTTTTATGAAAACTGCACGTGT 59.485 36.000 18.38 0.00 31.72 4.49
2503 2639 6.034470 CACTTTTTATGAAAACTGCACGTGTT 59.966 34.615 18.38 2.29 31.72 3.32
2504 2640 7.219154 CACTTTTTATGAAAACTGCACGTGTTA 59.781 33.333 18.38 5.94 31.72 2.41
2505 2641 7.755822 ACTTTTTATGAAAACTGCACGTGTTAA 59.244 29.630 18.38 2.41 31.72 2.01
2506 2642 8.635877 TTTTTATGAAAACTGCACGTGTTAAT 57.364 26.923 18.38 4.25 30.07 1.40
2507 2643 7.845617 TTTATGAAAACTGCACGTGTTAATC 57.154 32.000 18.38 9.01 0.00 1.75
2508 2644 5.689383 ATGAAAACTGCACGTGTTAATCT 57.311 34.783 18.38 0.00 0.00 2.40
2509 2645 4.843147 TGAAAACTGCACGTGTTAATCTG 58.157 39.130 18.38 6.45 0.00 2.90
2510 2646 4.572795 TGAAAACTGCACGTGTTAATCTGA 59.427 37.500 18.38 0.00 0.00 3.27
2511 2647 5.238432 TGAAAACTGCACGTGTTAATCTGAT 59.762 36.000 18.38 0.00 0.00 2.90
2512 2648 5.689383 AAACTGCACGTGTTAATCTGATT 57.311 34.783 18.38 8.14 0.00 2.57
2513 2649 5.689383 AACTGCACGTGTTAATCTGATTT 57.311 34.783 18.38 0.00 0.00 2.17
2514 2650 6.795098 AACTGCACGTGTTAATCTGATTTA 57.205 33.333 18.38 0.00 0.00 1.40
2515 2651 6.408858 ACTGCACGTGTTAATCTGATTTAG 57.591 37.500 18.38 0.00 0.00 1.85
2516 2652 5.932303 ACTGCACGTGTTAATCTGATTTAGT 59.068 36.000 18.38 0.07 0.00 2.24
2517 2653 6.128553 ACTGCACGTGTTAATCTGATTTAGTG 60.129 38.462 18.38 11.88 0.00 2.74
2518 2654 5.699001 TGCACGTGTTAATCTGATTTAGTGT 59.301 36.000 18.38 0.00 0.00 3.55
2519 2655 6.869388 TGCACGTGTTAATCTGATTTAGTGTA 59.131 34.615 18.38 8.55 0.00 2.90
2520 2656 7.062956 TGCACGTGTTAATCTGATTTAGTGTAG 59.937 37.037 18.38 0.00 0.00 2.74
2521 2657 7.391786 CACGTGTTAATCTGATTTAGTGTAGC 58.608 38.462 7.58 0.00 0.00 3.58
2522 2658 7.062956 CACGTGTTAATCTGATTTAGTGTAGCA 59.937 37.037 7.58 0.00 0.00 3.49
2523 2659 7.601130 ACGTGTTAATCTGATTTAGTGTAGCAA 59.399 33.333 8.38 0.00 0.00 3.91
2524 2660 8.110612 CGTGTTAATCTGATTTAGTGTAGCAAG 58.889 37.037 8.38 0.00 0.00 4.01
2525 2661 8.936864 GTGTTAATCTGATTTAGTGTAGCAAGT 58.063 33.333 8.38 0.00 0.00 3.16
2526 2662 8.935844 TGTTAATCTGATTTAGTGTAGCAAGTG 58.064 33.333 8.38 0.00 0.00 3.16
2527 2663 9.151471 GTTAATCTGATTTAGTGTAGCAAGTGA 57.849 33.333 8.38 0.00 0.00 3.41
2528 2664 9.890629 TTAATCTGATTTAGTGTAGCAAGTGAT 57.109 29.630 8.38 0.00 0.00 3.06
2529 2665 8.430801 AATCTGATTTAGTGTAGCAAGTGATC 57.569 34.615 0.00 0.00 0.00 2.92
2530 2666 6.935167 TCTGATTTAGTGTAGCAAGTGATCA 58.065 36.000 0.00 0.00 0.00 2.92
2531 2667 7.559486 TCTGATTTAGTGTAGCAAGTGATCAT 58.441 34.615 0.00 0.00 0.00 2.45
2532 2668 8.043113 TCTGATTTAGTGTAGCAAGTGATCATT 58.957 33.333 0.00 0.00 0.00 2.57
2533 2669 8.201554 TGATTTAGTGTAGCAAGTGATCATTC 57.798 34.615 0.00 0.00 0.00 2.67
2534 2670 6.985188 TTTAGTGTAGCAAGTGATCATTCC 57.015 37.500 0.00 0.00 0.00 3.01
2535 2671 3.878778 AGTGTAGCAAGTGATCATTCCC 58.121 45.455 0.00 0.00 0.00 3.97
2536 2672 3.521126 AGTGTAGCAAGTGATCATTCCCT 59.479 43.478 0.00 0.00 0.00 4.20
2537 2673 3.873952 GTGTAGCAAGTGATCATTCCCTC 59.126 47.826 0.00 0.00 0.00 4.30
2538 2674 2.725221 AGCAAGTGATCATTCCCTCC 57.275 50.000 0.00 0.00 0.00 4.30
2539 2675 1.134280 AGCAAGTGATCATTCCCTCCG 60.134 52.381 0.00 0.00 0.00 4.63
2540 2676 1.959042 CAAGTGATCATTCCCTCCGG 58.041 55.000 0.00 0.00 0.00 5.14
2541 2677 1.210478 CAAGTGATCATTCCCTCCGGT 59.790 52.381 0.00 0.00 0.00 5.28
2542 2678 2.434336 CAAGTGATCATTCCCTCCGGTA 59.566 50.000 0.00 0.00 0.00 4.02
2543 2679 2.320781 AGTGATCATTCCCTCCGGTAG 58.679 52.381 0.00 0.00 0.00 3.18
2544 2680 2.040178 GTGATCATTCCCTCCGGTAGT 58.960 52.381 0.00 0.00 0.00 2.73
2545 2681 2.434702 GTGATCATTCCCTCCGGTAGTT 59.565 50.000 0.00 0.00 0.00 2.24
2546 2682 3.112263 TGATCATTCCCTCCGGTAGTTT 58.888 45.455 0.00 0.00 0.00 2.66
2547 2683 3.134081 TGATCATTCCCTCCGGTAGTTTC 59.866 47.826 0.00 0.00 0.00 2.78
2548 2684 2.829023 TCATTCCCTCCGGTAGTTTCT 58.171 47.619 0.00 0.00 0.00 2.52
2549 2685 2.500098 TCATTCCCTCCGGTAGTTTCTG 59.500 50.000 0.00 0.00 0.00 3.02
2550 2686 1.272807 TTCCCTCCGGTAGTTTCTGG 58.727 55.000 0.00 0.00 35.33 3.86
2551 2687 1.221021 CCCTCCGGTAGTTTCTGGC 59.779 63.158 0.00 0.00 34.12 4.85
2552 2688 1.153628 CCTCCGGTAGTTTCTGGCG 60.154 63.158 0.00 0.00 34.12 5.69
2553 2689 1.601419 CCTCCGGTAGTTTCTGGCGA 61.601 60.000 0.00 0.00 34.12 5.54
2554 2690 0.245539 CTCCGGTAGTTTCTGGCGAA 59.754 55.000 0.00 0.00 34.12 4.70
2555 2691 0.680618 TCCGGTAGTTTCTGGCGAAA 59.319 50.000 0.00 1.37 36.82 3.46
2556 2692 1.276989 TCCGGTAGTTTCTGGCGAAAT 59.723 47.619 0.00 1.98 40.91 2.17
2557 2693 1.664151 CCGGTAGTTTCTGGCGAAATC 59.336 52.381 0.00 3.45 40.91 2.17
2558 2694 2.618053 CGGTAGTTTCTGGCGAAATCT 58.382 47.619 7.54 8.78 40.91 2.40
2559 2695 3.000727 CGGTAGTTTCTGGCGAAATCTT 58.999 45.455 7.54 1.85 40.91 2.40
2560 2696 3.435671 CGGTAGTTTCTGGCGAAATCTTT 59.564 43.478 7.54 0.00 40.91 2.52
2561 2697 4.083484 CGGTAGTTTCTGGCGAAATCTTTT 60.083 41.667 7.54 0.00 40.91 2.27
2562 2698 5.121142 CGGTAGTTTCTGGCGAAATCTTTTA 59.879 40.000 7.54 0.00 40.91 1.52
2563 2699 6.312487 GGTAGTTTCTGGCGAAATCTTTTAC 58.688 40.000 7.54 6.43 40.91 2.01
2564 2700 6.148976 GGTAGTTTCTGGCGAAATCTTTTACT 59.851 38.462 7.54 0.00 40.91 2.24
2565 2701 6.242508 AGTTTCTGGCGAAATCTTTTACTC 57.757 37.500 7.54 0.00 40.91 2.59
2566 2702 4.921470 TTCTGGCGAAATCTTTTACTCG 57.079 40.909 0.00 0.00 0.00 4.18
2569 2705 2.782198 GCGAAATCTTTTACTCGCGT 57.218 45.000 5.77 0.00 46.00 6.01
2570 2706 2.679792 GCGAAATCTTTTACTCGCGTC 58.320 47.619 5.77 0.00 46.00 5.19
2571 2707 2.534347 GCGAAATCTTTTACTCGCGTCC 60.534 50.000 5.77 0.00 46.00 4.79
2572 2708 2.664568 CGAAATCTTTTACTCGCGTCCA 59.335 45.455 5.77 0.00 0.00 4.02
2573 2709 3.306166 CGAAATCTTTTACTCGCGTCCAT 59.694 43.478 5.77 0.00 0.00 3.41
2574 2710 4.501559 CGAAATCTTTTACTCGCGTCCATA 59.498 41.667 5.77 0.00 0.00 2.74
2575 2711 5.331607 CGAAATCTTTTACTCGCGTCCATAG 60.332 44.000 5.77 0.00 0.00 2.23
2576 2712 3.431922 TCTTTTACTCGCGTCCATAGG 57.568 47.619 5.77 0.00 0.00 2.57
2577 2713 1.859080 CTTTTACTCGCGTCCATAGGC 59.141 52.381 5.77 0.00 0.00 3.93
2583 2719 2.499685 GCGTCCATAGGCGGAGTT 59.500 61.111 0.00 0.00 35.10 3.01
2584 2720 1.153429 GCGTCCATAGGCGGAGTTT 60.153 57.895 0.00 0.00 35.10 2.66
2585 2721 0.103572 GCGTCCATAGGCGGAGTTTA 59.896 55.000 0.00 0.00 35.10 2.01
2586 2722 1.270147 GCGTCCATAGGCGGAGTTTAT 60.270 52.381 0.00 0.00 35.10 1.40
2587 2723 2.805657 GCGTCCATAGGCGGAGTTTATT 60.806 50.000 0.00 0.00 35.10 1.40
2588 2724 3.463944 CGTCCATAGGCGGAGTTTATTT 58.536 45.455 0.00 0.00 35.10 1.40
2589 2725 3.493503 CGTCCATAGGCGGAGTTTATTTC 59.506 47.826 0.00 0.00 35.10 2.17
2590 2726 3.813724 GTCCATAGGCGGAGTTTATTTCC 59.186 47.826 0.00 0.00 35.10 3.13
2591 2727 3.714798 TCCATAGGCGGAGTTTATTTCCT 59.285 43.478 0.00 0.00 32.34 3.36
2598 2734 4.217767 GGCGGAGTTTATTTCCTTGTTTCT 59.782 41.667 0.00 0.00 32.34 2.52
2603 2739 9.738832 CGGAGTTTATTTCCTTGTTTCTTTTAA 57.261 29.630 0.00 0.00 32.34 1.52
2606 2742 9.542462 AGTTTATTTCCTTGTTTCTTTTAAGCC 57.458 29.630 0.00 0.00 0.00 4.35
2607 2743 8.770828 GTTTATTTCCTTGTTTCTTTTAAGCCC 58.229 33.333 0.00 0.00 0.00 5.19
2608 2744 5.941555 TTTCCTTGTTTCTTTTAAGCCCA 57.058 34.783 0.00 0.00 0.00 5.36
2609 2745 5.529581 TTCCTTGTTTCTTTTAAGCCCAG 57.470 39.130 0.00 0.00 0.00 4.45
2610 2746 3.320826 TCCTTGTTTCTTTTAAGCCCAGC 59.679 43.478 0.00 0.00 0.00 4.85
2611 2747 3.321968 CCTTGTTTCTTTTAAGCCCAGCT 59.678 43.478 0.00 0.00 42.56 4.24
2612 2748 4.550422 CTTGTTTCTTTTAAGCCCAGCTC 58.450 43.478 0.00 0.00 38.25 4.09
2613 2749 3.832527 TGTTTCTTTTAAGCCCAGCTCT 58.167 40.909 0.00 0.00 38.25 4.09
2614 2750 3.821033 TGTTTCTTTTAAGCCCAGCTCTC 59.179 43.478 0.00 0.00 38.25 3.20
2615 2751 2.789409 TCTTTTAAGCCCAGCTCTCC 57.211 50.000 0.00 0.00 38.25 3.71
2616 2752 1.282157 TCTTTTAAGCCCAGCTCTCCC 59.718 52.381 0.00 0.00 38.25 4.30
2617 2753 1.283321 CTTTTAAGCCCAGCTCTCCCT 59.717 52.381 0.00 0.00 38.25 4.20
2618 2754 1.372501 TTTAAGCCCAGCTCTCCCTT 58.627 50.000 0.00 0.00 38.25 3.95
2619 2755 1.372501 TTAAGCCCAGCTCTCCCTTT 58.627 50.000 0.00 0.00 38.25 3.11
2620 2756 2.263895 TAAGCCCAGCTCTCCCTTTA 57.736 50.000 0.00 0.00 38.25 1.85
2621 2757 1.601248 AAGCCCAGCTCTCCCTTTAT 58.399 50.000 0.00 0.00 38.25 1.40
2622 2758 1.601248 AGCCCAGCTCTCCCTTTATT 58.399 50.000 0.00 0.00 30.62 1.40
2623 2759 1.925959 AGCCCAGCTCTCCCTTTATTT 59.074 47.619 0.00 0.00 30.62 1.40
2624 2760 3.123273 AGCCCAGCTCTCCCTTTATTTA 58.877 45.455 0.00 0.00 30.62 1.40
2625 2761 3.724209 AGCCCAGCTCTCCCTTTATTTAT 59.276 43.478 0.00 0.00 30.62 1.40
2626 2762 4.168871 AGCCCAGCTCTCCCTTTATTTATT 59.831 41.667 0.00 0.00 30.62 1.40
2627 2763 4.895889 GCCCAGCTCTCCCTTTATTTATTT 59.104 41.667 0.00 0.00 0.00 1.40
2628 2764 5.363868 GCCCAGCTCTCCCTTTATTTATTTT 59.636 40.000 0.00 0.00 0.00 1.82
2629 2765 6.127054 GCCCAGCTCTCCCTTTATTTATTTTT 60.127 38.462 0.00 0.00 0.00 1.94
2630 2766 7.267857 CCCAGCTCTCCCTTTATTTATTTTTG 58.732 38.462 0.00 0.00 0.00 2.44
2631 2767 6.758416 CCAGCTCTCCCTTTATTTATTTTTGC 59.242 38.462 0.00 0.00 0.00 3.68
2632 2768 6.758416 CAGCTCTCCCTTTATTTATTTTTGCC 59.242 38.462 0.00 0.00 0.00 4.52
2633 2769 6.669591 AGCTCTCCCTTTATTTATTTTTGCCT 59.330 34.615 0.00 0.00 0.00 4.75
2634 2770 7.180946 AGCTCTCCCTTTATTTATTTTTGCCTT 59.819 33.333 0.00 0.00 0.00 4.35
2635 2771 7.278646 GCTCTCCCTTTATTTATTTTTGCCTTG 59.721 37.037 0.00 0.00 0.00 3.61
2636 2772 7.619965 TCTCCCTTTATTTATTTTTGCCTTGG 58.380 34.615 0.00 0.00 0.00 3.61
2637 2773 6.176896 TCCCTTTATTTATTTTTGCCTTGGC 58.823 36.000 4.43 4.43 0.00 4.52
2638 2774 6.012945 TCCCTTTATTTATTTTTGCCTTGGCT 60.013 34.615 13.18 0.00 0.00 4.75
2639 2775 6.658816 CCCTTTATTTATTTTTGCCTTGGCTT 59.341 34.615 13.18 0.00 0.00 4.35
2640 2776 7.361971 CCCTTTATTTATTTTTGCCTTGGCTTG 60.362 37.037 13.18 0.00 0.00 4.01
2641 2777 7.174772 CCTTTATTTATTTTTGCCTTGGCTTGT 59.825 33.333 13.18 0.00 0.00 3.16
2642 2778 8.457238 TTTATTTATTTTTGCCTTGGCTTGTT 57.543 26.923 13.18 0.00 0.00 2.83
2643 2779 6.957920 ATTTATTTTTGCCTTGGCTTGTTT 57.042 29.167 13.18 0.00 0.00 2.83
2644 2780 9.561069 TTATTTATTTTTGCCTTGGCTTGTTTA 57.439 25.926 13.18 0.00 0.00 2.01
2645 2781 8.634335 ATTTATTTTTGCCTTGGCTTGTTTAT 57.366 26.923 13.18 2.39 0.00 1.40
2646 2782 7.665561 TTATTTTTGCCTTGGCTTGTTTATC 57.334 32.000 13.18 0.00 0.00 1.75
2647 2783 3.296322 TTTGCCTTGGCTTGTTTATCG 57.704 42.857 13.18 0.00 0.00 2.92
2648 2784 1.904287 TGCCTTGGCTTGTTTATCGT 58.096 45.000 13.18 0.00 0.00 3.73
2649 2785 1.810151 TGCCTTGGCTTGTTTATCGTC 59.190 47.619 13.18 0.00 0.00 4.20
2650 2786 1.202031 GCCTTGGCTTGTTTATCGTCG 60.202 52.381 4.11 0.00 0.00 5.12
2651 2787 1.202031 CCTTGGCTTGTTTATCGTCGC 60.202 52.381 0.00 0.00 0.00 5.19
2652 2788 1.463056 CTTGGCTTGTTTATCGTCGCA 59.537 47.619 0.00 0.00 0.00 5.10
2653 2789 1.514003 TGGCTTGTTTATCGTCGCAA 58.486 45.000 0.00 0.00 0.00 4.85
2654 2790 1.874231 TGGCTTGTTTATCGTCGCAAA 59.126 42.857 0.00 0.00 0.00 3.68
2655 2791 2.486203 TGGCTTGTTTATCGTCGCAAAT 59.514 40.909 0.00 0.00 0.00 2.32
2656 2792 3.098636 GGCTTGTTTATCGTCGCAAATC 58.901 45.455 0.00 0.00 0.00 2.17
2657 2793 3.425625 GGCTTGTTTATCGTCGCAAATCA 60.426 43.478 0.00 0.00 0.00 2.57
2658 2794 4.342772 GCTTGTTTATCGTCGCAAATCAT 58.657 39.130 0.00 0.00 0.00 2.45
2659 2795 4.202959 GCTTGTTTATCGTCGCAAATCATG 59.797 41.667 0.00 0.00 0.00 3.07
2660 2796 4.937696 TGTTTATCGTCGCAAATCATGT 57.062 36.364 0.00 0.00 0.00 3.21
2661 2797 6.410243 TTGTTTATCGTCGCAAATCATGTA 57.590 33.333 0.00 0.00 0.00 2.29
2662 2798 6.597262 TGTTTATCGTCGCAAATCATGTAT 57.403 33.333 0.00 0.00 0.00 2.29
2663 2799 7.701809 TGTTTATCGTCGCAAATCATGTATA 57.298 32.000 0.00 0.00 0.00 1.47
2664 2800 8.305441 TGTTTATCGTCGCAAATCATGTATAT 57.695 30.769 0.00 0.00 0.00 0.86
2665 2801 9.413048 TGTTTATCGTCGCAAATCATGTATATA 57.587 29.630 0.00 0.00 0.00 0.86
2671 2807 9.083080 TCGTCGCAAATCATGTATATATAAAGG 57.917 33.333 0.00 0.00 0.00 3.11
2672 2808 7.846107 CGTCGCAAATCATGTATATATAAAGGC 59.154 37.037 0.00 0.00 0.00 4.35
2673 2809 7.846107 GTCGCAAATCATGTATATATAAAGGCG 59.154 37.037 0.00 0.00 38.68 5.52
2674 2810 7.762159 TCGCAAATCATGTATATATAAAGGCGA 59.238 33.333 0.00 0.00 43.06 5.54
2675 2811 7.846107 CGCAAATCATGTATATATAAAGGCGAC 59.154 37.037 0.00 0.00 39.57 5.19
2683 2819 8.218338 TGTATATATAAAGGCGACTACTAGGC 57.782 38.462 0.00 0.00 42.68 3.93
2689 2825 4.625781 CGACTACTAGGCGCCGGC 62.626 72.222 23.20 19.07 41.27 6.13
2690 2826 4.625781 GACTACTAGGCGCCGGCG 62.626 72.222 43.13 43.13 41.24 6.46
2716 2852 3.353836 CAACAGTTGGGCCGGTCG 61.354 66.667 1.90 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 176 2.436824 GGCTCCGTCTTGGGCTTC 60.437 66.667 0.00 0.00 38.76 3.86
196 203 3.692406 GGCTCCGTCTTCACCGGT 61.692 66.667 0.00 0.00 45.63 5.28
265 275 2.264480 CATTCCAGGGTCGCGTCA 59.736 61.111 5.77 0.00 0.00 4.35
422 433 2.876879 CGTCGCCAACGCAAACTGA 61.877 57.895 0.00 0.00 45.76 3.41
722 789 1.817941 GCCTAAAATCGCCGCCTGA 60.818 57.895 0.00 0.00 0.00 3.86
955 1042 1.072806 AGAAACAGCAGCATCAGGTGA 59.927 47.619 0.00 0.00 45.95 4.02
995 1082 3.315140 TGGCGTTGGACATCGGGA 61.315 61.111 5.12 0.00 0.00 5.14
1212 1308 3.626924 ACCACCAGGAGCACCGAC 61.627 66.667 0.00 0.00 41.83 4.79
1221 1317 4.275508 AGCACCAGCACCACCAGG 62.276 66.667 0.00 0.00 45.49 4.45
1376 1472 2.202864 GCTCCAGCTCCGAGAAGC 60.203 66.667 10.87 0.00 42.82 3.86
1775 1892 3.553508 CCAAATCCCAAATCGCATGGATC 60.554 47.826 0.00 0.00 40.56 3.36
1783 1900 1.204467 CCACACCCAAATCCCAAATCG 59.796 52.381 0.00 0.00 0.00 3.34
1789 1906 2.119391 TGCCCACACCCAAATCCC 59.881 61.111 0.00 0.00 0.00 3.85
1790 1907 3.376546 GTGCCCACACCCAAATCC 58.623 61.111 0.00 0.00 41.21 3.01
1799 1916 2.229792 GTTCTTGATCAAGTGCCCACA 58.770 47.619 29.80 10.49 39.38 4.17
1803 1920 3.565482 TGTCTTGTTCTTGATCAAGTGCC 59.435 43.478 29.80 20.00 40.97 5.01
1805 1922 4.320057 GGCTGTCTTGTTCTTGATCAAGTG 60.320 45.833 29.80 17.48 40.97 3.16
1809 1926 3.141398 GTGGCTGTCTTGTTCTTGATCA 58.859 45.455 0.00 0.00 0.00 2.92
1950 2068 2.217750 ACGCACAGACATGTTTGCTAA 58.782 42.857 15.86 0.00 37.65 3.09
1962 2080 0.657312 CTTCTGTTGCAACGCACAGA 59.343 50.000 23.79 18.52 41.23 3.41
1964 2082 0.746204 TCCTTCTGTTGCAACGCACA 60.746 50.000 23.79 6.94 38.71 4.57
1967 2085 2.422276 AATTCCTTCTGTTGCAACGC 57.578 45.000 23.79 2.38 0.00 4.84
1993 2111 5.523916 CGTGCTTATTATGCTAGGAACTTGT 59.476 40.000 0.00 0.00 41.75 3.16
1996 2114 5.290386 GTCGTGCTTATTATGCTAGGAACT 58.710 41.667 0.00 0.00 46.37 3.01
2000 2118 3.990092 TGGTCGTGCTTATTATGCTAGG 58.010 45.455 3.56 0.00 0.00 3.02
2016 2134 2.289694 ACCATTGAGGAGTCTTTGGTCG 60.290 50.000 0.00 0.00 41.22 4.79
2020 2138 3.754965 TGGAACCATTGAGGAGTCTTTG 58.245 45.455 0.00 0.00 41.22 2.77
2021 2139 4.202609 ACATGGAACCATTGAGGAGTCTTT 60.203 41.667 3.35 0.00 41.22 2.52
2030 2148 6.718912 TCAAACAGATAACATGGAACCATTGA 59.281 34.615 3.35 0.15 33.90 2.57
2036 2154 5.627499 TGCTCAAACAGATAACATGGAAC 57.373 39.130 0.00 0.00 0.00 3.62
2039 2157 5.571784 ACATGCTCAAACAGATAACATGG 57.428 39.130 0.00 0.00 36.78 3.66
2048 2166 1.265095 AGCGACAACATGCTCAAACAG 59.735 47.619 0.00 0.00 36.53 3.16
2056 2174 0.166814 GAGGACAAGCGACAACATGC 59.833 55.000 0.00 0.00 0.00 4.06
2065 2196 1.743252 GCAGGAAGGAGGACAAGCG 60.743 63.158 0.00 0.00 0.00 4.68
2066 2197 1.377856 GGCAGGAAGGAGGACAAGC 60.378 63.158 0.00 0.00 0.00 4.01
2070 2201 0.912006 AGGAAGGCAGGAAGGAGGAC 60.912 60.000 0.00 0.00 0.00 3.85
2077 2208 0.909610 ATGGTCGAGGAAGGCAGGAA 60.910 55.000 0.00 0.00 0.00 3.36
2090 2221 2.644555 GGACCCGATGACCATGGTCG 62.645 65.000 34.01 24.90 46.60 4.79
2101 2232 1.224592 GCAATCAGGTGGACCCGAT 59.775 57.895 0.00 0.00 38.74 4.18
2104 2235 0.962356 CACTGCAATCAGGTGGACCC 60.962 60.000 0.00 0.00 44.54 4.46
2117 2248 2.820787 TGATCACATTGAATGCACTGCA 59.179 40.909 6.09 6.09 44.86 4.41
2121 2252 3.382227 TCCCATGATCACATTGAATGCAC 59.618 43.478 4.84 0.00 34.15 4.57
2131 2262 2.374839 TCAGGTTTGTCCCATGATCACA 59.625 45.455 0.00 0.00 36.75 3.58
2132 2263 2.749621 GTCAGGTTTGTCCCATGATCAC 59.250 50.000 0.00 0.00 36.75 3.06
2135 2266 3.744940 ATGTCAGGTTTGTCCCATGAT 57.255 42.857 0.00 0.00 36.75 2.45
2140 2271 2.296190 GGTTCAATGTCAGGTTTGTCCC 59.704 50.000 0.00 0.00 36.75 4.46
2146 2277 0.951558 GCGTGGTTCAATGTCAGGTT 59.048 50.000 0.00 0.00 0.00 3.50
2148 2279 0.888736 TGGCGTGGTTCAATGTCAGG 60.889 55.000 0.00 0.00 0.00 3.86
2149 2280 1.131126 GATGGCGTGGTTCAATGTCAG 59.869 52.381 0.00 0.00 0.00 3.51
2164 2295 1.210155 GGTGTTGACTTGCGATGGC 59.790 57.895 0.00 0.00 40.52 4.40
2202 2334 2.228103 AGCGTCACAACTATCTCAACGA 59.772 45.455 0.00 0.00 0.00 3.85
2210 2342 2.185004 AAAGGCAGCGTCACAACTAT 57.815 45.000 0.00 0.00 0.00 2.12
2212 2344 0.663153 GAAAAGGCAGCGTCACAACT 59.337 50.000 0.00 0.00 0.00 3.16
2214 2346 1.781025 CGGAAAAGGCAGCGTCACAA 61.781 55.000 0.00 0.00 0.00 3.33
2215 2347 2.250939 CGGAAAAGGCAGCGTCACA 61.251 57.895 0.00 0.00 0.00 3.58
2235 2368 1.624813 TGGGGTAAACGTAGGTTGAGG 59.375 52.381 0.79 0.00 36.25 3.86
2251 2384 1.223487 CAAGGGACGGTGTATGGGG 59.777 63.158 0.00 0.00 0.00 4.96
2252 2385 1.134610 GTACAAGGGACGGTGTATGGG 60.135 57.143 0.00 0.00 36.45 4.00
2262 2395 1.053424 TGAGTGGGTGTACAAGGGAC 58.947 55.000 0.00 0.00 0.00 4.46
2269 2402 5.067283 ACAATTTGAAAGTGAGTGGGTGTAC 59.933 40.000 12.62 0.00 0.00 2.90
2295 2428 8.638565 GGTTGATTCATTTCGAAAAACACTATG 58.361 33.333 15.66 6.86 36.59 2.23
2314 2447 9.936759 TCTTTGTGTTTTAAAAGAAGGTTGATT 57.063 25.926 0.00 0.00 38.98 2.57
2463 2599 4.776795 AAAAGTGTTCACGTGTTTTCCT 57.223 36.364 16.51 3.71 0.00 3.36
2471 2607 7.734538 CAGTTTTCATAAAAAGTGTTCACGT 57.265 32.000 1.22 0.00 45.01 4.49
2480 2616 6.567769 AACACGTGCAGTTTTCATAAAAAG 57.432 33.333 17.22 0.00 35.10 2.27
2492 2628 5.932303 ACTAAATCAGATTAACACGTGCAGT 59.068 36.000 17.22 3.62 0.00 4.40
2496 2632 7.062956 TGCTACACTAAATCAGATTAACACGTG 59.937 37.037 15.48 15.48 0.00 4.49
2497 2633 7.094631 TGCTACACTAAATCAGATTAACACGT 58.905 34.615 0.00 0.00 0.00 4.49
2498 2634 7.520119 TGCTACACTAAATCAGATTAACACG 57.480 36.000 0.00 0.00 0.00 4.49
2499 2635 8.936864 ACTTGCTACACTAAATCAGATTAACAC 58.063 33.333 0.00 0.00 0.00 3.32
2500 2636 8.935844 CACTTGCTACACTAAATCAGATTAACA 58.064 33.333 0.00 0.00 0.00 2.41
2501 2637 9.151471 TCACTTGCTACACTAAATCAGATTAAC 57.849 33.333 0.00 0.00 0.00 2.01
2502 2638 9.890629 ATCACTTGCTACACTAAATCAGATTAA 57.109 29.630 0.00 0.00 0.00 1.40
2503 2639 9.534565 GATCACTTGCTACACTAAATCAGATTA 57.465 33.333 0.00 0.00 0.00 1.75
2504 2640 8.043113 TGATCACTTGCTACACTAAATCAGATT 58.957 33.333 0.00 0.00 0.00 2.40
2505 2641 7.559486 TGATCACTTGCTACACTAAATCAGAT 58.441 34.615 0.00 0.00 0.00 2.90
2506 2642 6.935167 TGATCACTTGCTACACTAAATCAGA 58.065 36.000 0.00 0.00 0.00 3.27
2507 2643 7.783090 ATGATCACTTGCTACACTAAATCAG 57.217 36.000 0.00 0.00 0.00 2.90
2508 2644 7.280876 GGAATGATCACTTGCTACACTAAATCA 59.719 37.037 0.00 0.00 0.00 2.57
2509 2645 7.254932 GGGAATGATCACTTGCTACACTAAATC 60.255 40.741 0.00 0.00 0.00 2.17
2510 2646 6.543831 GGGAATGATCACTTGCTACACTAAAT 59.456 38.462 0.00 0.00 0.00 1.40
2511 2647 5.880332 GGGAATGATCACTTGCTACACTAAA 59.120 40.000 0.00 0.00 0.00 1.85
2512 2648 5.189736 AGGGAATGATCACTTGCTACACTAA 59.810 40.000 0.00 0.00 35.03 2.24
2513 2649 4.716784 AGGGAATGATCACTTGCTACACTA 59.283 41.667 0.00 0.00 35.03 2.74
2514 2650 3.521126 AGGGAATGATCACTTGCTACACT 59.479 43.478 0.00 0.00 35.03 3.55
2515 2651 3.873952 GAGGGAATGATCACTTGCTACAC 59.126 47.826 0.00 0.00 40.23 2.90
2516 2652 3.118261 GGAGGGAATGATCACTTGCTACA 60.118 47.826 0.00 0.00 40.23 2.74
2517 2653 3.471680 GGAGGGAATGATCACTTGCTAC 58.528 50.000 0.00 0.00 40.23 3.58
2518 2654 2.103094 CGGAGGGAATGATCACTTGCTA 59.897 50.000 0.00 0.00 40.23 3.49
2519 2655 1.134280 CGGAGGGAATGATCACTTGCT 60.134 52.381 0.00 0.00 40.23 3.91
2520 2656 1.303309 CGGAGGGAATGATCACTTGC 58.697 55.000 0.00 0.00 40.23 4.01
2534 2670 3.101221 TTCGCCAGAAACTACCGGAGG 62.101 57.143 9.46 2.01 44.17 4.30
2535 2671 0.245539 TTCGCCAGAAACTACCGGAG 59.754 55.000 9.46 3.52 32.65 4.63
2536 2672 0.680618 TTTCGCCAGAAACTACCGGA 59.319 50.000 9.46 0.00 41.06 5.14
2537 2673 3.220447 TTTCGCCAGAAACTACCGG 57.780 52.632 0.00 0.00 41.06 5.28
2545 2681 4.921470 CGAGTAAAAGATTTCGCCAGAA 57.079 40.909 0.00 0.00 33.98 3.02
2566 2702 0.103572 TAAACTCCGCCTATGGACGC 59.896 55.000 0.00 0.00 33.48 5.19
2567 2703 2.814280 ATAAACTCCGCCTATGGACG 57.186 50.000 0.00 0.00 33.48 4.79
2568 2704 3.813724 GGAAATAAACTCCGCCTATGGAC 59.186 47.826 0.00 0.00 33.48 4.02
2569 2705 3.714798 AGGAAATAAACTCCGCCTATGGA 59.285 43.478 0.00 0.00 38.08 3.41
2570 2706 4.086706 AGGAAATAAACTCCGCCTATGG 57.913 45.455 0.00 0.00 38.08 2.74
2571 2707 4.881850 ACAAGGAAATAAACTCCGCCTATG 59.118 41.667 0.00 0.00 38.08 2.23
2572 2708 5.112129 ACAAGGAAATAAACTCCGCCTAT 57.888 39.130 0.00 0.00 38.08 2.57
2573 2709 4.563140 ACAAGGAAATAAACTCCGCCTA 57.437 40.909 0.00 0.00 38.08 3.93
2574 2710 3.434940 ACAAGGAAATAAACTCCGCCT 57.565 42.857 0.00 0.00 38.08 5.52
2575 2711 4.217767 AGAAACAAGGAAATAAACTCCGCC 59.782 41.667 0.00 0.00 38.08 6.13
2576 2712 5.372547 AGAAACAAGGAAATAAACTCCGC 57.627 39.130 0.00 0.00 38.08 5.54
2577 2713 9.738832 TTAAAAGAAACAAGGAAATAAACTCCG 57.261 29.630 0.00 0.00 38.08 4.63
2580 2716 9.542462 GGCTTAAAAGAAACAAGGAAATAAACT 57.458 29.630 0.00 0.00 0.00 2.66
2581 2717 8.770828 GGGCTTAAAAGAAACAAGGAAATAAAC 58.229 33.333 0.00 0.00 0.00 2.01
2582 2718 8.487028 TGGGCTTAAAAGAAACAAGGAAATAAA 58.513 29.630 0.00 0.00 0.00 1.40
2583 2719 8.024145 TGGGCTTAAAAGAAACAAGGAAATAA 57.976 30.769 0.00 0.00 0.00 1.40
2584 2720 7.604657 TGGGCTTAAAAGAAACAAGGAAATA 57.395 32.000 0.00 0.00 0.00 1.40
2585 2721 6.493189 TGGGCTTAAAAGAAACAAGGAAAT 57.507 33.333 0.00 0.00 0.00 2.17
2586 2722 5.683770 GCTGGGCTTAAAAGAAACAAGGAAA 60.684 40.000 0.00 0.00 0.00 3.13
2587 2723 4.202212 GCTGGGCTTAAAAGAAACAAGGAA 60.202 41.667 0.00 0.00 0.00 3.36
2588 2724 3.320826 GCTGGGCTTAAAAGAAACAAGGA 59.679 43.478 0.00 0.00 0.00 3.36
2589 2725 3.321968 AGCTGGGCTTAAAAGAAACAAGG 59.678 43.478 0.00 0.00 33.89 3.61
2590 2726 4.279420 AGAGCTGGGCTTAAAAGAAACAAG 59.721 41.667 0.00 0.00 39.88 3.16
2591 2727 4.215109 AGAGCTGGGCTTAAAAGAAACAA 58.785 39.130 0.00 0.00 39.88 2.83
2598 2734 1.372501 AGGGAGAGCTGGGCTTAAAA 58.627 50.000 0.00 0.00 39.88 1.52
2603 2739 1.601248 AATAAAGGGAGAGCTGGGCT 58.399 50.000 0.00 0.00 43.88 5.19
2604 2740 2.443958 AAATAAAGGGAGAGCTGGGC 57.556 50.000 0.00 0.00 0.00 5.36
2605 2741 7.267857 CAAAAATAAATAAAGGGAGAGCTGGG 58.732 38.462 0.00 0.00 0.00 4.45
2606 2742 6.758416 GCAAAAATAAATAAAGGGAGAGCTGG 59.242 38.462 0.00 0.00 0.00 4.85
2607 2743 6.758416 GGCAAAAATAAATAAAGGGAGAGCTG 59.242 38.462 0.00 0.00 0.00 4.24
2608 2744 6.669591 AGGCAAAAATAAATAAAGGGAGAGCT 59.330 34.615 0.00 0.00 0.00 4.09
2609 2745 6.878317 AGGCAAAAATAAATAAAGGGAGAGC 58.122 36.000 0.00 0.00 0.00 4.09
2610 2746 7.765819 CCAAGGCAAAAATAAATAAAGGGAGAG 59.234 37.037 0.00 0.00 0.00 3.20
2611 2747 7.619965 CCAAGGCAAAAATAAATAAAGGGAGA 58.380 34.615 0.00 0.00 0.00 3.71
2612 2748 6.316140 GCCAAGGCAAAAATAAATAAAGGGAG 59.684 38.462 6.14 0.00 41.49 4.30
2613 2749 6.012945 AGCCAAGGCAAAAATAAATAAAGGGA 60.013 34.615 14.40 0.00 44.88 4.20
2614 2750 6.179756 AGCCAAGGCAAAAATAAATAAAGGG 58.820 36.000 14.40 0.00 44.88 3.95
2615 2751 7.174772 ACAAGCCAAGGCAAAAATAAATAAAGG 59.825 33.333 14.40 0.00 44.88 3.11
2616 2752 8.098220 ACAAGCCAAGGCAAAAATAAATAAAG 57.902 30.769 14.40 0.00 44.88 1.85
2617 2753 8.457238 AACAAGCCAAGGCAAAAATAAATAAA 57.543 26.923 14.40 0.00 44.88 1.40
2618 2754 8.457238 AAACAAGCCAAGGCAAAAATAAATAA 57.543 26.923 14.40 0.00 44.88 1.40
2619 2755 9.732130 ATAAACAAGCCAAGGCAAAAATAAATA 57.268 25.926 14.40 0.00 44.88 1.40
2620 2756 6.957920 AAACAAGCCAAGGCAAAAATAAAT 57.042 29.167 14.40 0.00 44.88 1.40
2621 2757 7.095439 CGATAAACAAGCCAAGGCAAAAATAAA 60.095 33.333 14.40 0.00 44.88 1.40
2622 2758 6.367422 CGATAAACAAGCCAAGGCAAAAATAA 59.633 34.615 14.40 0.00 44.88 1.40
2623 2759 5.866633 CGATAAACAAGCCAAGGCAAAAATA 59.133 36.000 14.40 1.45 44.88 1.40
2624 2760 4.690280 CGATAAACAAGCCAAGGCAAAAAT 59.310 37.500 14.40 0.00 44.88 1.82
2625 2761 4.054671 CGATAAACAAGCCAAGGCAAAAA 58.945 39.130 14.40 0.00 44.88 1.94
2626 2762 3.068873 ACGATAAACAAGCCAAGGCAAAA 59.931 39.130 14.40 0.00 44.88 2.44
2627 2763 2.625790 ACGATAAACAAGCCAAGGCAAA 59.374 40.909 14.40 0.00 44.88 3.68
2628 2764 2.227865 GACGATAAACAAGCCAAGGCAA 59.772 45.455 14.40 0.00 44.88 4.52
2629 2765 1.810151 GACGATAAACAAGCCAAGGCA 59.190 47.619 14.40 0.00 44.88 4.75
2630 2766 1.202031 CGACGATAAACAAGCCAAGGC 60.202 52.381 2.02 2.02 42.33 4.35
2631 2767 1.202031 GCGACGATAAACAAGCCAAGG 60.202 52.381 0.00 0.00 0.00 3.61
2632 2768 1.463056 TGCGACGATAAACAAGCCAAG 59.537 47.619 0.00 0.00 0.00 3.61
2633 2769 1.514003 TGCGACGATAAACAAGCCAA 58.486 45.000 0.00 0.00 0.00 4.52
2634 2770 1.514003 TTGCGACGATAAACAAGCCA 58.486 45.000 0.00 0.00 0.00 4.75
2635 2771 2.604969 TTTGCGACGATAAACAAGCC 57.395 45.000 0.00 0.00 0.00 4.35
2636 2772 3.742786 TGATTTGCGACGATAAACAAGC 58.257 40.909 0.00 0.00 0.00 4.01
2637 2773 5.323900 ACATGATTTGCGACGATAAACAAG 58.676 37.500 0.00 0.00 0.00 3.16
2638 2774 5.289917 ACATGATTTGCGACGATAAACAA 57.710 34.783 0.00 0.00 0.00 2.83
2639 2775 4.937696 ACATGATTTGCGACGATAAACA 57.062 36.364 0.00 0.00 0.00 2.83
2645 2781 9.083080 CCTTTATATATACATGATTTGCGACGA 57.917 33.333 0.00 0.00 0.00 4.20
2646 2782 7.846107 GCCTTTATATATACATGATTTGCGACG 59.154 37.037 0.00 0.00 0.00 5.12
2647 2783 7.846107 CGCCTTTATATATACATGATTTGCGAC 59.154 37.037 0.00 0.00 37.16 5.19
2648 2784 7.762159 TCGCCTTTATATATACATGATTTGCGA 59.238 33.333 0.00 0.00 41.00 5.10
2649 2785 7.846107 GTCGCCTTTATATATACATGATTTGCG 59.154 37.037 0.00 0.00 36.42 4.85
2650 2786 8.883731 AGTCGCCTTTATATATACATGATTTGC 58.116 33.333 0.00 0.00 0.00 3.68
2657 2793 8.848182 GCCTAGTAGTCGCCTTTATATATACAT 58.152 37.037 0.00 0.00 0.00 2.29
2658 2794 7.011763 CGCCTAGTAGTCGCCTTTATATATACA 59.988 40.741 0.00 0.00 0.00 2.29
2659 2795 7.351223 CGCCTAGTAGTCGCCTTTATATATAC 58.649 42.308 0.00 0.00 0.00 1.47
2660 2796 6.017605 GCGCCTAGTAGTCGCCTTTATATATA 60.018 42.308 14.42 0.00 42.71 0.86
2661 2797 5.221009 GCGCCTAGTAGTCGCCTTTATATAT 60.221 44.000 14.42 0.00 42.71 0.86
2662 2798 4.095483 GCGCCTAGTAGTCGCCTTTATATA 59.905 45.833 14.42 0.00 42.71 0.86
2663 2799 3.119566 GCGCCTAGTAGTCGCCTTTATAT 60.120 47.826 14.42 0.00 42.71 0.86
2664 2800 2.227388 GCGCCTAGTAGTCGCCTTTATA 59.773 50.000 14.42 0.00 42.71 0.98
2665 2801 1.000496 GCGCCTAGTAGTCGCCTTTAT 60.000 52.381 14.42 0.00 42.71 1.40
2666 2802 0.383231 GCGCCTAGTAGTCGCCTTTA 59.617 55.000 14.42 0.00 42.71 1.85
2667 2803 1.141234 GCGCCTAGTAGTCGCCTTT 59.859 57.895 14.42 0.00 42.71 3.11
2668 2804 2.806237 GCGCCTAGTAGTCGCCTT 59.194 61.111 14.42 0.00 42.71 4.35
2672 2808 4.625781 GCCGGCGCCTAGTAGTCG 62.626 72.222 26.68 8.26 0.00 4.18
2673 2809 4.625781 CGCCGGCGCCTAGTAGTC 62.626 72.222 38.48 0.00 0.00 2.59
2699 2835 3.353836 CGACCGGCCCAACTGTTG 61.354 66.667 13.50 13.50 0.00 3.33


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

AutoCloner maintained by Alex Coulton.