Multiple sequence alignment - TraesCS3D01G133600

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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 TraesCS3D01G133600 chr3D 100.000 2678 0 0 1 2678 92869848 92872525 0.000000e+00 4946.0
1 TraesCS3D01G133600 chr3D 82.332 549 75 16 1198 1736 92877175 92876639 8.740000e-125 457.0
2 TraesCS3D01G133600 chr3D 78.924 688 93 31 966 1632 92864771 92865427 1.150000e-113 420.0
3 TraesCS3D01G133600 chr3D 89.583 240 16 6 1066 1302 92890992 92891225 2.020000e-76 296.0
4 TraesCS3D01G133600 chr3D 97.959 49 1 0 2624 2672 261864723 261864675 4.750000e-13 86.1
5 TraesCS3D01G133600 chr3D 94.340 53 3 0 2624 2676 250060621 250060569 6.140000e-12 82.4
6 TraesCS3D01G133600 chr3D 94.340 53 3 0 2624 2676 311838279 311838331 6.140000e-12 82.4
7 TraesCS3D01G133600 chr3D 91.111 45 3 1 2289 2332 92872056 92872100 2.880000e-05 60.2
8 TraesCS3D01G133600 chr3D 91.111 45 3 1 2209 2253 92872136 92872179 2.880000e-05 60.2
9 TraesCS3D01G133600 chr3B 94.259 1951 58 10 1 1946 143571989 143570088 0.000000e+00 2933.0
10 TraesCS3D01G133600 chr3B 84.718 746 91 12 931 1667 143556758 143557489 0.000000e+00 725.0
11 TraesCS3D01G133600 chr3B 86.799 553 38 9 2090 2626 143569197 143568664 3.840000e-163 584.0
12 TraesCS3D01G133600 chr3B 81.992 522 83 10 1146 1662 143506017 143506532 1.470000e-117 433.0
13 TraesCS3D01G133600 chr3B 80.317 630 75 33 1003 1612 143585679 143585079 5.300000e-117 431.0
14 TraesCS3D01G133600 chr3B 86.713 286 34 4 257 540 143542857 143543140 5.570000e-82 315.0
15 TraesCS3D01G133600 chr3B 90.452 199 19 0 2428 2626 143605163 143604965 2.040000e-66 263.0
16 TraesCS3D01G133600 chr3B 89.873 158 16 0 1168 1325 143523222 143523065 1.260000e-48 204.0
17 TraesCS3D01G133600 chr3A 79.822 788 110 30 966 1736 547193948 547194703 1.830000e-146 529.0
18 TraesCS3D01G133600 chr3A 77.575 602 99 17 61 641 547189532 547190118 5.530000e-87 331.0
19 TraesCS3D01G133600 chr3A 94.340 53 3 0 2624 2676 334018413 334018465 6.140000e-12 82.4
20 TraesCS3D01G133600 chr1D 96.364 55 2 0 2624 2678 274458221 274458275 1.020000e-14 91.6
21 TraesCS3D01G133600 chr1D 94.545 55 3 0 2624 2678 194997890 194997944 4.750000e-13 86.1
22 TraesCS3D01G133600 chr1D 94.340 53 3 0 2624 2676 356531429 356531481 6.140000e-12 82.4
23 TraesCS3D01G133600 chr5D 96.296 54 2 0 2623 2676 377108994 377109047 3.670000e-14 89.8
24 TraesCS3D01G133600 chr4D 94.340 53 3 0 2624 2676 146058282 146058334 6.140000e-12 82.4


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 TraesCS3D01G133600 chr3D 92869848 92872525 2677 False 1688.8 4946 94.0740 1 2678 3 chr3D.!!$F4 2677
1 TraesCS3D01G133600 chr3D 92876639 92877175 536 True 457.0 457 82.3320 1198 1736 1 chr3D.!!$R1 538
2 TraesCS3D01G133600 chr3D 92864771 92865427 656 False 420.0 420 78.9240 966 1632 1 chr3D.!!$F1 666
3 TraesCS3D01G133600 chr3B 143568664 143571989 3325 True 1758.5 2933 90.5290 1 2626 2 chr3B.!!$R4 2625
4 TraesCS3D01G133600 chr3B 143556758 143557489 731 False 725.0 725 84.7180 931 1667 1 chr3B.!!$F3 736
5 TraesCS3D01G133600 chr3B 143506017 143506532 515 False 433.0 433 81.9920 1146 1662 1 chr3B.!!$F1 516
6 TraesCS3D01G133600 chr3B 143585079 143585679 600 True 431.0 431 80.3170 1003 1612 1 chr3B.!!$R2 609
7 TraesCS3D01G133600 chr3A 547189532 547194703 5171 False 430.0 529 78.6985 61 1736 2 chr3A.!!$F2 1675

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
380 390 0.108207 CCAGACATCAGCCTCCCATC 59.892 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 5472 0.178981 AGATTGGCCAGGCGCATAAT 60.179 50.0 10.83 0.0 40.31 1.28 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
132 136 4.767255 GTGAGACTGCCCGCCCAG 62.767 72.222 0.00 0.00 38.78 4.45
379 389 0.622738 ACCAGACATCAGCCTCCCAT 60.623 55.000 0.00 0.00 0.00 4.00
380 390 0.108207 CCAGACATCAGCCTCCCATC 59.892 60.000 0.00 0.00 0.00 3.51
382 392 1.070445 CAGACATCAGCCTCCCATCTC 59.930 57.143 0.00 0.00 0.00 2.75
385 395 0.249784 CATCAGCCTCCCATCTCGTG 60.250 60.000 0.00 0.00 0.00 4.35
441 451 3.777925 CGCGGTGAGGTTGAAGCG 61.778 66.667 0.00 0.00 41.56 4.68
443 453 2.664851 CGGTGAGGTTGAAGCGCA 60.665 61.111 11.47 0.00 0.00 6.09
444 454 2.250939 CGGTGAGGTTGAAGCGCAA 61.251 57.895 11.47 0.00 0.00 4.85
445 455 1.576421 GGTGAGGTTGAAGCGCAAG 59.424 57.895 11.47 0.00 37.12 4.01
636 676 8.672161 AGCGGGTATTTGGCTTTCTTGAAAAG 62.672 42.308 0.00 0.00 38.57 2.27
847 4366 8.521176 CAGATTTCAGACTCCAATTCAAATCTT 58.479 33.333 0.00 0.00 37.12 2.40
917 4438 7.360101 CGGTTCAGACTCGAATTTGTTTAATCT 60.360 37.037 0.00 0.00 0.00 2.40
946 4533 2.431057 CCTCCCTCCCATATATACGCAC 59.569 54.545 0.00 0.00 0.00 5.34
962 4549 3.081409 ACCGCCGCAGACCCTAAT 61.081 61.111 0.00 0.00 0.00 1.73
963 4550 2.189521 CCGCCGCAGACCCTAATT 59.810 61.111 0.00 0.00 0.00 1.40
964 4551 1.332144 ACCGCCGCAGACCCTAATTA 61.332 55.000 0.00 0.00 0.00 1.40
1024 4611 4.180057 GACAGTACTCATGGCAGAAGAAG 58.820 47.826 5.97 0.00 0.00 2.85
1045 4632 1.517913 GGCAACTACGGCGACTACC 60.518 63.158 16.62 3.04 0.00 3.18
1048 4635 0.241749 CAACTACGGCGACTACCACA 59.758 55.000 16.62 0.00 0.00 4.17
1071 4658 2.224867 CCTCACCATTGAACCTGAACCT 60.225 50.000 0.00 0.00 0.00 3.50
1072 4659 2.816087 CTCACCATTGAACCTGAACCTG 59.184 50.000 0.00 0.00 0.00 4.00
1073 4660 2.441375 TCACCATTGAACCTGAACCTGA 59.559 45.455 0.00 0.00 0.00 3.86
1074 4661 3.117701 TCACCATTGAACCTGAACCTGAA 60.118 43.478 0.00 0.00 0.00 3.02
1075 4662 3.004734 CACCATTGAACCTGAACCTGAAC 59.995 47.826 0.00 0.00 0.00 3.18
1076 4663 2.558359 CCATTGAACCTGAACCTGAACC 59.442 50.000 0.00 0.00 0.00 3.62
1152 4748 4.143333 CTGCTTGGCATGCTGGGC 62.143 66.667 23.54 18.03 38.13 5.36
1310 4930 0.808453 ACCGTCCACGTCAACAACAG 60.808 55.000 0.00 0.00 37.74 3.16
1314 4934 0.179032 TCCACGTCAACAACAGGCAT 60.179 50.000 0.00 0.00 0.00 4.40
1354 4974 0.033011 GGAGGAGAGCTACCTGGTCA 60.033 60.000 15.42 0.00 44.98 4.02
1356 4976 2.393646 GAGGAGAGCTACCTGGTCATT 58.606 52.381 15.42 0.00 44.98 2.57
1434 5054 2.878429 GCCTTCTGCGTCGAGAGA 59.122 61.111 0.00 0.00 38.16 3.10
1564 5184 1.813513 CGTTGAGATCAAGCCAACCT 58.186 50.000 0.00 0.00 37.47 3.50
1692 5318 9.463902 AGTGCGACATAAAGGAGTATAGTATAT 57.536 33.333 0.00 0.00 0.00 0.86
1738 5365 7.093552 GCACTCCTATCACCATAGATATTCAGT 60.094 40.741 0.00 0.00 34.82 3.41
1748 5375 9.464714 CACCATAGATATTCAGTTGTACTACAC 57.535 37.037 10.09 0.00 0.00 2.90
1797 5424 9.956720 ACTAAATGCAATATTATTCACTTCAGC 57.043 29.630 0.00 0.00 0.00 4.26
1844 5471 9.174166 ACTTCAGTCTATTTAGTGTTTTTGTGT 57.826 29.630 0.00 0.00 0.00 3.72
1853 5480 7.555639 TTTAGTGTTTTTGTGTATTATGCGC 57.444 32.000 0.00 0.00 0.00 6.09
1854 5481 4.481463 AGTGTTTTTGTGTATTATGCGCC 58.519 39.130 4.18 0.00 0.00 6.53
1855 5482 4.217550 AGTGTTTTTGTGTATTATGCGCCT 59.782 37.500 4.18 0.00 0.00 5.52
1856 5483 4.323336 GTGTTTTTGTGTATTATGCGCCTG 59.677 41.667 4.18 0.00 0.00 4.85
1857 5484 3.773860 TTTTGTGTATTATGCGCCTGG 57.226 42.857 4.18 0.00 0.00 4.45
1858 5485 1.021202 TTGTGTATTATGCGCCTGGC 58.979 50.000 9.11 9.11 43.96 4.85
1859 5486 0.817634 TGTGTATTATGCGCCTGGCC 60.818 55.000 14.12 6.66 42.61 5.36
1860 5487 0.817634 GTGTATTATGCGCCTGGCCA 60.818 55.000 14.12 4.71 42.61 5.36
1861 5488 0.106967 TGTATTATGCGCCTGGCCAA 60.107 50.000 14.12 1.12 42.61 4.52
1945 5572 4.006319 CCTTCTCAACTTGATTCCCACTC 58.994 47.826 0.00 0.00 0.00 3.51
1946 5573 4.263243 CCTTCTCAACTTGATTCCCACTCT 60.263 45.833 0.00 0.00 0.00 3.24
1947 5574 4.543590 TCTCAACTTGATTCCCACTCTC 57.456 45.455 0.00 0.00 0.00 3.20
1948 5575 3.903714 TCTCAACTTGATTCCCACTCTCA 59.096 43.478 0.00 0.00 0.00 3.27
1949 5576 4.533707 TCTCAACTTGATTCCCACTCTCAT 59.466 41.667 0.00 0.00 0.00 2.90
1950 5577 4.836825 TCAACTTGATTCCCACTCTCATC 58.163 43.478 0.00 0.00 0.00 2.92
1951 5578 4.286808 TCAACTTGATTCCCACTCTCATCA 59.713 41.667 0.00 0.00 0.00 3.07
1952 5579 4.916041 ACTTGATTCCCACTCTCATCAA 57.084 40.909 0.00 0.00 35.02 2.57
1953 5580 5.447778 ACTTGATTCCCACTCTCATCAAT 57.552 39.130 0.00 0.00 35.58 2.57
1954 5581 6.566079 ACTTGATTCCCACTCTCATCAATA 57.434 37.500 0.00 0.00 35.58 1.90
1959 5586 2.101415 TCCCACTCTCATCAATACGCTG 59.899 50.000 0.00 0.00 0.00 5.18
1987 5614 4.935205 GCATGTTTATATACAGGCGATCCA 59.065 41.667 15.34 0.00 44.45 3.41
1988 5615 5.163854 GCATGTTTATATACAGGCGATCCAC 60.164 44.000 15.34 0.00 44.45 4.02
1990 5617 5.779922 TGTTTATATACAGGCGATCCACTC 58.220 41.667 0.00 0.00 33.74 3.51
1991 5618 5.303333 TGTTTATATACAGGCGATCCACTCA 59.697 40.000 0.00 0.00 33.74 3.41
1992 5619 5.644977 TTATATACAGGCGATCCACTCAG 57.355 43.478 0.00 0.00 33.74 3.35
1993 5620 2.073252 ATACAGGCGATCCACTCAGA 57.927 50.000 0.00 0.00 33.74 3.27
1994 5621 1.847328 TACAGGCGATCCACTCAGAA 58.153 50.000 0.00 0.00 33.74 3.02
1996 5623 1.137872 ACAGGCGATCCACTCAGAATC 59.862 52.381 0.00 0.00 33.74 2.52
1997 5624 1.137675 CAGGCGATCCACTCAGAATCA 59.862 52.381 0.00 0.00 33.74 2.57
1998 5625 1.833630 AGGCGATCCACTCAGAATCAA 59.166 47.619 0.00 0.00 33.74 2.57
1999 5626 2.158986 AGGCGATCCACTCAGAATCAAG 60.159 50.000 0.00 0.00 33.74 3.02
2000 5627 2.208431 GCGATCCACTCAGAATCAAGG 58.792 52.381 0.00 0.00 0.00 3.61
2001 5628 2.831333 CGATCCACTCAGAATCAAGGG 58.169 52.381 0.00 0.00 0.00 3.95
2002 5629 2.484417 CGATCCACTCAGAATCAAGGGG 60.484 54.545 0.00 0.00 37.42 4.79
2003 5630 2.044793 TCCACTCAGAATCAAGGGGT 57.955 50.000 4.25 0.00 37.35 4.95
2004 5631 2.348472 TCCACTCAGAATCAAGGGGTT 58.652 47.619 4.25 0.00 37.35 4.11
2005 5632 2.040278 TCCACTCAGAATCAAGGGGTTG 59.960 50.000 4.25 0.00 37.35 3.77
2006 5633 2.224867 CCACTCAGAATCAAGGGGTTGT 60.225 50.000 0.00 0.00 30.97 3.32
2007 5634 2.816087 CACTCAGAATCAAGGGGTTGTG 59.184 50.000 0.00 0.00 0.00 3.33
2008 5635 2.443255 ACTCAGAATCAAGGGGTTGTGT 59.557 45.455 0.00 0.00 0.00 3.72
2009 5636 3.650942 ACTCAGAATCAAGGGGTTGTGTA 59.349 43.478 0.00 0.00 0.00 2.90
2010 5637 4.289672 ACTCAGAATCAAGGGGTTGTGTAT 59.710 41.667 0.00 0.00 0.00 2.29
2011 5638 5.487488 ACTCAGAATCAAGGGGTTGTGTATA 59.513 40.000 0.00 0.00 0.00 1.47
2012 5639 5.741011 TCAGAATCAAGGGGTTGTGTATAC 58.259 41.667 0.00 0.00 0.00 1.47
2013 5640 5.487488 TCAGAATCAAGGGGTTGTGTATACT 59.513 40.000 4.17 0.00 0.00 2.12
2014 5641 6.670464 TCAGAATCAAGGGGTTGTGTATACTA 59.330 38.462 4.17 0.00 0.00 1.82
2015 5642 6.761714 CAGAATCAAGGGGTTGTGTATACTAC 59.238 42.308 4.17 1.85 32.75 2.73
2016 5643 6.672657 AGAATCAAGGGGTTGTGTATACTACT 59.327 38.462 4.17 0.00 33.80 2.57
2017 5644 7.842743 AGAATCAAGGGGTTGTGTATACTACTA 59.157 37.037 4.17 0.00 33.80 1.82
2018 5645 7.983166 ATCAAGGGGTTGTGTATACTACTAA 57.017 36.000 4.17 0.00 33.80 2.24
2019 5646 7.983166 TCAAGGGGTTGTGTATACTACTAAT 57.017 36.000 4.17 0.00 33.80 1.73
2020 5647 9.664777 ATCAAGGGGTTGTGTATACTACTAATA 57.335 33.333 4.17 0.00 33.80 0.98
2021 5648 9.664777 TCAAGGGGTTGTGTATACTACTAATAT 57.335 33.333 4.17 0.00 33.80 1.28
2036 5663 8.803397 ACTACTAATATATACAGTCCGATGCA 57.197 34.615 0.00 0.00 0.00 3.96
2037 5664 9.409918 ACTACTAATATATACAGTCCGATGCAT 57.590 33.333 0.00 0.00 0.00 3.96
2038 5665 9.885934 CTACTAATATATACAGTCCGATGCATC 57.114 37.037 17.10 17.10 0.00 3.91
2039 5666 8.526667 ACTAATATATACAGTCCGATGCATCT 57.473 34.615 23.73 7.10 0.00 2.90
2040 5667 8.972127 ACTAATATATACAGTCCGATGCATCTT 58.028 33.333 23.73 9.26 0.00 2.40
2041 5668 9.457110 CTAATATATACAGTCCGATGCATCTTC 57.543 37.037 23.73 13.42 0.00 2.87
2042 5669 5.728637 ATATACAGTCCGATGCATCTTCA 57.271 39.130 23.73 5.14 0.00 3.02
2043 5670 2.996249 ACAGTCCGATGCATCTTCAT 57.004 45.000 23.73 5.42 0.00 2.57
2044 5671 5.728637 ATACAGTCCGATGCATCTTCATA 57.271 39.130 23.73 9.37 0.00 2.15
2045 5672 3.722147 ACAGTCCGATGCATCTTCATAC 58.278 45.455 23.73 13.59 0.00 2.39
2046 5673 2.728318 CAGTCCGATGCATCTTCATACG 59.272 50.000 23.73 9.72 0.00 3.06
2047 5674 2.362397 AGTCCGATGCATCTTCATACGT 59.638 45.455 23.73 0.00 0.00 3.57
2048 5675 3.568430 AGTCCGATGCATCTTCATACGTA 59.432 43.478 23.73 0.00 0.00 3.57
2049 5676 4.037565 AGTCCGATGCATCTTCATACGTAA 59.962 41.667 23.73 0.00 0.00 3.18
2050 5677 4.743151 GTCCGATGCATCTTCATACGTAAA 59.257 41.667 23.73 0.00 0.00 2.01
2051 5678 4.743151 TCCGATGCATCTTCATACGTAAAC 59.257 41.667 23.73 0.00 0.00 2.01
2052 5679 4.084537 CCGATGCATCTTCATACGTAAACC 60.085 45.833 23.73 0.00 0.00 3.27
2053 5680 4.506288 CGATGCATCTTCATACGTAAACCA 59.494 41.667 23.73 0.00 0.00 3.67
2054 5681 5.556382 CGATGCATCTTCATACGTAAACCAC 60.556 44.000 23.73 0.00 0.00 4.16
2055 5682 3.936453 TGCATCTTCATACGTAAACCACC 59.064 43.478 0.00 0.00 0.00 4.61
2056 5683 4.189231 GCATCTTCATACGTAAACCACCT 58.811 43.478 0.00 0.00 0.00 4.00
2057 5684 4.270325 GCATCTTCATACGTAAACCACCTC 59.730 45.833 0.00 0.00 0.00 3.85
2058 5685 5.661458 CATCTTCATACGTAAACCACCTCT 58.339 41.667 0.00 0.00 0.00 3.69
2059 5686 5.068234 TCTTCATACGTAAACCACCTCTG 57.932 43.478 0.00 0.00 0.00 3.35
2060 5687 4.768448 TCTTCATACGTAAACCACCTCTGA 59.232 41.667 0.00 0.00 0.00 3.27
2061 5688 5.244402 TCTTCATACGTAAACCACCTCTGAA 59.756 40.000 0.00 0.85 0.00 3.02
2062 5689 5.068234 TCATACGTAAACCACCTCTGAAG 57.932 43.478 0.00 0.00 0.00 3.02
2063 5690 4.525487 TCATACGTAAACCACCTCTGAAGT 59.475 41.667 0.00 0.00 0.00 3.01
2064 5691 3.832615 ACGTAAACCACCTCTGAAGTT 57.167 42.857 0.00 0.00 0.00 2.66
2065 5692 4.146745 ACGTAAACCACCTCTGAAGTTT 57.853 40.909 0.00 0.00 36.47 2.66
2066 5693 4.124970 ACGTAAACCACCTCTGAAGTTTC 58.875 43.478 0.00 0.00 34.46 2.78
2067 5694 4.124238 CGTAAACCACCTCTGAAGTTTCA 58.876 43.478 0.00 0.00 34.46 2.69
2080 5707 3.251729 TGAAGTTTCAGTCATCAGCAAGC 59.748 43.478 0.00 0.00 32.50 4.01
2081 5708 2.157738 AGTTTCAGTCATCAGCAAGCC 58.842 47.619 0.00 0.00 0.00 4.35
2082 5709 1.881973 GTTTCAGTCATCAGCAAGCCA 59.118 47.619 0.00 0.00 0.00 4.75
2083 5710 1.527034 TTCAGTCATCAGCAAGCCAC 58.473 50.000 0.00 0.00 0.00 5.01
2084 5711 0.397564 TCAGTCATCAGCAAGCCACA 59.602 50.000 0.00 0.00 0.00 4.17
2085 5712 1.003928 TCAGTCATCAGCAAGCCACAT 59.996 47.619 0.00 0.00 0.00 3.21
2086 5713 2.236893 TCAGTCATCAGCAAGCCACATA 59.763 45.455 0.00 0.00 0.00 2.29
2087 5714 2.353889 CAGTCATCAGCAAGCCACATAC 59.646 50.000 0.00 0.00 0.00 2.39
2088 5715 1.672881 GTCATCAGCAAGCCACATACC 59.327 52.381 0.00 0.00 0.00 2.73
2115 6499 3.904800 CAAAGGGTTTGGGTTTGAGTT 57.095 42.857 0.00 0.00 37.01 3.01
2128 6512 5.072600 TGGGTTTGAGTTAATGGACTAGTGT 59.927 40.000 0.00 0.00 0.00 3.55
2142 6526 3.987868 GACTAGTGTCACATTTCGCTCAA 59.012 43.478 0.00 0.00 42.48 3.02
2158 6542 5.833082 TCGCTCAATAGAGTTAATGGACTC 58.167 41.667 1.45 1.45 45.05 3.36
2255 6639 4.119442 TGGAGTATCTACAACCTTTCGC 57.881 45.455 0.00 0.00 33.73 4.70
2263 6647 1.981256 ACAACCTTTCGCCTTGTGAT 58.019 45.000 0.00 0.00 0.00 3.06
2264 6648 1.608590 ACAACCTTTCGCCTTGTGATG 59.391 47.619 0.00 0.00 0.00 3.07
2267 6651 0.109597 CCTTTCGCCTTGTGATGCAC 60.110 55.000 0.00 0.00 34.56 4.57
2270 6654 1.317613 TTCGCCTTGTGATGCACTTT 58.682 45.000 0.00 0.00 35.11 2.66
2271 6655 0.592637 TCGCCTTGTGATGCACTTTG 59.407 50.000 0.00 0.00 35.11 2.77
2288 6673 5.220567 GCACTTTGCTAGTTAATCTGAGCTC 60.221 44.000 6.82 6.82 40.96 4.09
2322 6707 7.655819 TTGGATCCTTTATTCATGGGGTATA 57.344 36.000 14.23 0.00 0.00 1.47
2329 6714 9.629649 TCCTTTATTCATGGGGTATATAGAACT 57.370 33.333 0.00 0.00 0.00 3.01
2378 6763 4.579869 AGAATCTACTTCAACCGCAACAT 58.420 39.130 0.00 0.00 36.24 2.71
2405 6790 4.973663 GCTAGAATCGCTTGAACTAGACTC 59.026 45.833 0.00 0.00 36.06 3.36
2412 6797 3.246619 GCTTGAACTAGACTCTTCACGG 58.753 50.000 0.00 0.00 0.00 4.94
2413 6798 3.305471 GCTTGAACTAGACTCTTCACGGT 60.305 47.826 0.00 0.00 0.00 4.83
2414 6799 3.917329 TGAACTAGACTCTTCACGGTG 57.083 47.619 0.56 0.56 0.00 4.94
2415 6800 3.483421 TGAACTAGACTCTTCACGGTGA 58.517 45.455 6.76 6.76 0.00 4.02
2416 6801 3.502595 TGAACTAGACTCTTCACGGTGAG 59.497 47.826 11.14 6.15 36.47 3.51
2417 6802 1.813786 ACTAGACTCTTCACGGTGAGC 59.186 52.381 11.14 0.70 33.92 4.26
2418 6803 1.813178 CTAGACTCTTCACGGTGAGCA 59.187 52.381 11.14 1.18 33.92 4.26
2419 6804 1.261480 AGACTCTTCACGGTGAGCAT 58.739 50.000 11.14 0.00 33.92 3.79
2420 6805 1.203523 AGACTCTTCACGGTGAGCATC 59.796 52.381 11.14 8.03 33.92 3.91
2422 6807 2.423892 GACTCTTCACGGTGAGCATCTA 59.576 50.000 11.14 0.00 34.92 1.98
2423 6808 2.425312 ACTCTTCACGGTGAGCATCTAG 59.575 50.000 11.14 5.01 34.92 2.43
2424 6809 2.685388 CTCTTCACGGTGAGCATCTAGA 59.315 50.000 11.14 9.04 34.92 2.43
2425 6810 3.291584 TCTTCACGGTGAGCATCTAGAT 58.708 45.455 11.14 0.00 34.92 1.98
2426 6811 4.461198 TCTTCACGGTGAGCATCTAGATA 58.539 43.478 11.14 0.00 34.92 1.98
2439 6839 4.560716 GCATCTAGATATTACGGCCACACA 60.561 45.833 4.54 0.00 0.00 3.72
2447 6847 0.970640 TACGGCCACACAGAAAGCTA 59.029 50.000 2.24 0.00 0.00 3.32
2449 6849 0.602638 CGGCCACACAGAAAGCTACA 60.603 55.000 2.24 0.00 0.00 2.74
2476 6876 1.227002 GTAGCTGCACTCTACCGGC 60.227 63.158 0.00 0.00 32.38 6.13
2480 6880 1.219124 CTGCACTCTACCGGCACAT 59.781 57.895 0.00 0.00 33.34 3.21
2515 6915 4.882842 TGCCTTGTCATCACAGTAGTTA 57.117 40.909 0.00 0.00 32.71 2.24
2524 6924 7.941919 TGTCATCACAGTAGTTATAGGTCATC 58.058 38.462 0.00 0.00 0.00 2.92
2533 6933 8.634444 CAGTAGTTATAGGTCATCTACTTGCTT 58.366 37.037 0.00 0.00 39.10 3.91
2549 6949 8.462811 TCTACTTGCTTTTGACATTTTTGTACA 58.537 29.630 0.00 0.00 0.00 2.90
2560 6960 3.708563 TTTTTGTACACTGCCTTCTGC 57.291 42.857 0.00 0.00 41.77 4.26
2593 6993 1.144093 TCCCGAAACTTGTTCCACCAT 59.856 47.619 0.00 0.00 0.00 3.55
2628 7028 3.379445 CGGCACACCTCCGGTACT 61.379 66.667 0.00 0.00 42.99 2.73
2629 7029 2.577593 GGCACACCTCCGGTACTC 59.422 66.667 0.00 0.00 32.11 2.59
2630 7030 2.280552 GGCACACCTCCGGTACTCA 61.281 63.158 0.00 0.00 32.11 3.41
2631 7031 1.669440 GCACACCTCCGGTACTCAA 59.331 57.895 0.00 0.00 32.11 3.02
2632 7032 0.249398 GCACACCTCCGGTACTCAAT 59.751 55.000 0.00 0.00 32.11 2.57
2633 7033 2.007049 GCACACCTCCGGTACTCAATG 61.007 57.143 0.00 0.00 32.11 2.82
2634 7034 1.275291 CACACCTCCGGTACTCAATGT 59.725 52.381 0.00 0.00 32.11 2.71
2635 7035 1.975680 ACACCTCCGGTACTCAATGTT 59.024 47.619 0.00 0.00 32.11 2.71
2636 7036 2.370849 ACACCTCCGGTACTCAATGTTT 59.629 45.455 0.00 0.00 32.11 2.83
2637 7037 2.742053 CACCTCCGGTACTCAATGTTTG 59.258 50.000 0.00 0.00 32.11 2.93
2638 7038 2.370849 ACCTCCGGTACTCAATGTTTGT 59.629 45.455 0.00 0.00 32.11 2.83
2639 7039 2.742053 CCTCCGGTACTCAATGTTTGTG 59.258 50.000 0.00 0.00 0.00 3.33
2640 7040 3.399330 CTCCGGTACTCAATGTTTGTGT 58.601 45.455 0.00 1.27 40.19 3.72
2641 7041 3.395639 TCCGGTACTCAATGTTTGTGTC 58.604 45.455 0.00 0.00 38.26 3.67
2642 7042 2.482721 CCGGTACTCAATGTTTGTGTCC 59.517 50.000 0.00 1.46 38.26 4.02
2643 7043 3.135225 CGGTACTCAATGTTTGTGTCCA 58.865 45.455 0.00 0.00 38.26 4.02
2644 7044 3.562141 CGGTACTCAATGTTTGTGTCCAA 59.438 43.478 0.00 0.00 38.26 3.53
2645 7045 4.319477 CGGTACTCAATGTTTGTGTCCAAG 60.319 45.833 0.00 0.00 38.26 3.61
2646 7046 3.715628 ACTCAATGTTTGTGTCCAAGC 57.284 42.857 0.00 0.00 32.40 4.01
2647 7047 2.362077 ACTCAATGTTTGTGTCCAAGCC 59.638 45.455 0.00 0.00 32.40 4.35
2648 7048 1.336440 TCAATGTTTGTGTCCAAGCCG 59.664 47.619 0.00 0.00 31.38 5.52
2649 7049 1.066908 CAATGTTTGTGTCCAAGCCGT 59.933 47.619 0.00 0.00 31.38 5.68
2650 7050 0.667993 ATGTTTGTGTCCAAGCCGTG 59.332 50.000 0.00 0.00 31.38 4.94
2651 7051 0.393132 TGTTTGTGTCCAAGCCGTGA 60.393 50.000 0.00 0.00 31.38 4.35
2652 7052 0.028902 GTTTGTGTCCAAGCCGTGAC 59.971 55.000 0.00 0.00 0.00 3.67
2653 7053 0.393132 TTTGTGTCCAAGCCGTGACA 60.393 50.000 0.00 0.00 39.08 3.58
2655 7055 2.110213 TGTCCAAGCCGTGACACC 59.890 61.111 0.00 0.00 36.62 4.16
2656 7056 2.110213 GTCCAAGCCGTGACACCA 59.890 61.111 0.00 0.00 0.00 4.17
2657 7057 1.525077 GTCCAAGCCGTGACACCAA 60.525 57.895 0.00 0.00 0.00 3.67
2658 7058 0.889186 GTCCAAGCCGTGACACCAAT 60.889 55.000 0.00 0.00 0.00 3.16
2659 7059 0.687920 TCCAAGCCGTGACACCAATA 59.312 50.000 0.00 0.00 0.00 1.90
2660 7060 1.280710 TCCAAGCCGTGACACCAATAT 59.719 47.619 0.00 0.00 0.00 1.28
2661 7061 1.401552 CCAAGCCGTGACACCAATATG 59.598 52.381 0.00 0.00 0.00 1.78
2662 7062 2.083774 CAAGCCGTGACACCAATATGT 58.916 47.619 0.00 0.00 34.78 2.29
2663 7063 2.487762 CAAGCCGTGACACCAATATGTT 59.512 45.455 0.00 0.00 31.24 2.71
2664 7064 2.790433 AGCCGTGACACCAATATGTTT 58.210 42.857 0.00 0.00 31.24 2.83
2665 7065 3.945346 AGCCGTGACACCAATATGTTTA 58.055 40.909 0.00 0.00 31.24 2.01
2666 7066 4.328536 AGCCGTGACACCAATATGTTTAA 58.671 39.130 0.00 0.00 31.24 1.52
2667 7067 4.762765 AGCCGTGACACCAATATGTTTAAA 59.237 37.500 0.00 0.00 31.24 1.52
2668 7068 5.241949 AGCCGTGACACCAATATGTTTAAAA 59.758 36.000 0.00 0.00 31.24 1.52
2669 7069 5.921408 GCCGTGACACCAATATGTTTAAAAA 59.079 36.000 0.00 0.00 31.24 1.94
2670 7070 6.588373 GCCGTGACACCAATATGTTTAAAAAT 59.412 34.615 0.00 0.00 31.24 1.82
2671 7071 7.117092 GCCGTGACACCAATATGTTTAAAAATT 59.883 33.333 0.00 0.00 31.24 1.82
2672 7072 8.983724 CCGTGACACCAATATGTTTAAAAATTT 58.016 29.630 0.00 0.00 31.24 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.736252 CCAAGAATGTGATCGATCGGTAC 59.264 47.826 20.03 13.26 0.00 3.34
48 49 8.091449 CAGAGACTAGTGATACAAGGTTCTTTT 58.909 37.037 0.00 0.00 0.00 2.27
132 136 2.749839 TATGGTGCAAGGCCACGC 60.750 61.111 5.01 7.63 39.03 5.34
301 311 2.079158 ACATGCCTGAAGAACATGACG 58.921 47.619 15.78 0.00 43.04 4.35
364 374 0.033228 CGAGATGGGAGGCTGATGTC 59.967 60.000 0.00 0.00 0.00 3.06
379 389 1.134694 CGAGATGTGCGTCACGAGA 59.865 57.895 0.00 0.00 37.14 4.04
380 390 2.500442 GCGAGATGTGCGTCACGAG 61.500 63.158 0.00 0.00 37.14 4.18
457 467 4.415332 TTCCAGACTCCGCGCGAC 62.415 66.667 34.63 18.79 0.00 5.19
458 468 4.116328 CTTCCAGACTCCGCGCGA 62.116 66.667 34.63 16.66 0.00 5.87
460 470 4.443266 AGCTTCCAGACTCCGCGC 62.443 66.667 0.00 0.00 0.00 6.86
461 471 2.507992 CAGCTTCCAGACTCCGCG 60.508 66.667 0.00 0.00 0.00 6.46
847 4366 1.141019 GCGACCGGACTGCAGATTA 59.859 57.895 23.35 0.00 0.00 1.75
917 4438 2.059756 ATGGGAGGGAGGACTTTGAA 57.940 50.000 0.00 0.00 0.00 2.69
946 4533 0.179067 TTAATTAGGGTCTGCGGCGG 60.179 55.000 9.78 1.35 0.00 6.13
962 4549 3.947834 GCAGATCTAAAGGCCAAGCTTAA 59.052 43.478 5.01 0.00 0.00 1.85
963 4550 3.545703 GCAGATCTAAAGGCCAAGCTTA 58.454 45.455 5.01 0.00 0.00 3.09
964 4551 2.373224 GCAGATCTAAAGGCCAAGCTT 58.627 47.619 5.01 0.00 0.00 3.74
1024 4611 2.552585 TAGTCGCCGTAGTTGCCTGC 62.553 60.000 0.00 0.00 0.00 4.85
1045 4632 2.751259 CAGGTTCAATGGTGAGGATGTG 59.249 50.000 0.00 0.00 34.49 3.21
1048 4635 3.562176 GGTTCAGGTTCAATGGTGAGGAT 60.562 47.826 0.00 0.00 34.49 3.24
1071 4658 1.300963 GGCAGGCTGATCTGGTTCA 59.699 57.895 20.86 0.00 35.43 3.18
1072 4659 1.817099 CGGCAGGCTGATCTGGTTC 60.817 63.158 20.86 0.00 35.43 3.62
1073 4660 2.270205 CGGCAGGCTGATCTGGTT 59.730 61.111 20.86 0.00 35.43 3.67
1074 4661 3.005539 ACGGCAGGCTGATCTGGT 61.006 61.111 20.86 4.61 35.43 4.00
1075 4662 2.202987 GACGGCAGGCTGATCTGG 60.203 66.667 20.86 3.94 35.43 3.86
1076 4663 2.584418 CGACGGCAGGCTGATCTG 60.584 66.667 20.86 9.11 37.79 2.90
1105 4692 2.789203 GATCGTCGTCGTTGCTGCC 61.789 63.158 1.33 0.00 38.33 4.85
1314 4934 1.444383 GCAGACTCGTCGCATGTGA 60.444 57.895 4.45 4.45 34.09 3.58
1354 4974 3.286576 CGCTCGATTCGTCGTAGTAAAT 58.713 45.455 5.89 0.00 0.00 1.40
1356 4976 1.004610 CCGCTCGATTCGTCGTAGTAA 60.005 52.381 17.01 0.00 0.00 2.24
1428 5048 1.729470 CCCTGGTCGACCATCTCTCG 61.729 65.000 36.21 22.91 46.46 4.04
1434 5054 1.109920 CGAGATCCCTGGTCGACCAT 61.110 60.000 36.21 22.62 46.46 3.55
1692 5318 3.006940 GCGTTGTTGATGATCCCTGTAA 58.993 45.455 0.00 0.00 0.00 2.41
1709 5335 3.296854 TCTATGGTGATAGGAGTGCGTT 58.703 45.455 0.00 0.00 33.48 4.84
1797 5424 7.275341 TGAAGTTTTGTACATGCTTTGTCAAAG 59.725 33.333 19.20 19.20 39.87 2.77
1835 5462 3.857093 CCAGGCGCATAATACACAAAAAC 59.143 43.478 10.83 0.00 0.00 2.43
1844 5471 1.073763 AGATTGGCCAGGCGCATAATA 59.926 47.619 10.83 0.00 40.31 0.98
1845 5472 0.178981 AGATTGGCCAGGCGCATAAT 60.179 50.000 10.83 0.00 40.31 1.28
1846 5473 0.395586 AAGATTGGCCAGGCGCATAA 60.396 50.000 10.83 0.00 40.31 1.90
1847 5474 0.395586 AAAGATTGGCCAGGCGCATA 60.396 50.000 10.83 0.00 40.31 3.14
1848 5475 1.259840 AAAAGATTGGCCAGGCGCAT 61.260 50.000 10.83 0.00 40.31 4.73
1849 5476 1.470996 AAAAAGATTGGCCAGGCGCA 61.471 50.000 10.83 1.44 40.31 6.09
1850 5477 0.737367 GAAAAAGATTGGCCAGGCGC 60.737 55.000 5.11 0.00 0.00 6.53
1851 5478 0.890683 AGAAAAAGATTGGCCAGGCG 59.109 50.000 5.11 0.00 0.00 5.52
1852 5479 1.673923 GCAGAAAAAGATTGGCCAGGC 60.674 52.381 5.11 1.26 0.00 4.85
1853 5480 1.897802 AGCAGAAAAAGATTGGCCAGG 59.102 47.619 5.11 0.00 0.00 4.45
1854 5481 3.672767 AAGCAGAAAAAGATTGGCCAG 57.327 42.857 5.11 0.00 0.00 4.85
1855 5482 3.387374 TGAAAGCAGAAAAAGATTGGCCA 59.613 39.130 0.00 0.00 0.00 5.36
1856 5483 3.993920 TGAAAGCAGAAAAAGATTGGCC 58.006 40.909 0.00 0.00 0.00 5.36
1857 5484 5.121298 GGATTGAAAGCAGAAAAAGATTGGC 59.879 40.000 0.00 0.00 0.00 4.52
1858 5485 6.225318 TGGATTGAAAGCAGAAAAAGATTGG 58.775 36.000 0.00 0.00 0.00 3.16
1859 5486 7.900782 ATGGATTGAAAGCAGAAAAAGATTG 57.099 32.000 0.00 0.00 0.00 2.67
1860 5487 7.389607 CCAATGGATTGAAAGCAGAAAAAGATT 59.610 33.333 0.00 0.00 40.14 2.40
1861 5488 6.877322 CCAATGGATTGAAAGCAGAAAAAGAT 59.123 34.615 0.00 0.00 40.14 2.40
1919 5546 3.009584 GGGAATCAAGTTGAGAAGGAGGT 59.990 47.826 11.91 0.00 0.00 3.85
1920 5547 3.009473 TGGGAATCAAGTTGAGAAGGAGG 59.991 47.826 11.91 0.00 0.00 4.30
1945 5572 3.582444 GCTTCACAGCGTATTGATGAG 57.418 47.619 0.00 0.00 37.44 2.90
1959 5586 5.465390 TCGCCTGTATATAAACATGCTTCAC 59.535 40.000 0.00 0.00 38.43 3.18
1981 5608 2.484417 CCCCTTGATTCTGAGTGGATCG 60.484 54.545 0.00 0.00 0.00 3.69
1982 5609 2.507471 ACCCCTTGATTCTGAGTGGATC 59.493 50.000 0.00 0.00 0.00 3.36
1983 5610 2.566746 ACCCCTTGATTCTGAGTGGAT 58.433 47.619 0.00 0.00 0.00 3.41
1984 5611 2.040278 CAACCCCTTGATTCTGAGTGGA 59.960 50.000 0.00 0.00 0.00 4.02
1985 5612 2.224867 ACAACCCCTTGATTCTGAGTGG 60.225 50.000 0.00 0.00 0.00 4.00
1987 5614 2.443255 ACACAACCCCTTGATTCTGAGT 59.557 45.455 0.00 0.00 0.00 3.41
1988 5615 3.146104 ACACAACCCCTTGATTCTGAG 57.854 47.619 0.00 0.00 0.00 3.35
1990 5617 5.745227 AGTATACACAACCCCTTGATTCTG 58.255 41.667 5.50 0.00 0.00 3.02
1991 5618 6.672657 AGTAGTATACACAACCCCTTGATTCT 59.327 38.462 5.50 0.00 46.26 2.40
1992 5619 6.885922 AGTAGTATACACAACCCCTTGATTC 58.114 40.000 5.50 0.00 46.26 2.52
1993 5620 6.886178 AGTAGTATACACAACCCCTTGATT 57.114 37.500 5.50 0.00 46.26 2.57
1994 5621 7.983166 TTAGTAGTATACACAACCCCTTGAT 57.017 36.000 5.50 0.00 46.26 2.57
2010 5637 9.895138 TGCATCGGACTGTATATATTAGTAGTA 57.105 33.333 0.00 0.00 0.00 1.82
2011 5638 8.803397 TGCATCGGACTGTATATATTAGTAGT 57.197 34.615 0.00 0.00 0.00 2.73
2012 5639 9.885934 GATGCATCGGACTGTATATATTAGTAG 57.114 37.037 11.68 0.00 0.00 2.57
2013 5640 9.628500 AGATGCATCGGACTGTATATATTAGTA 57.372 33.333 20.67 0.00 0.00 1.82
2014 5641 8.526667 AGATGCATCGGACTGTATATATTAGT 57.473 34.615 20.67 0.00 0.00 2.24
2015 5642 9.457110 GAAGATGCATCGGACTGTATATATTAG 57.543 37.037 20.67 0.00 0.00 1.73
2016 5643 8.966868 TGAAGATGCATCGGACTGTATATATTA 58.033 33.333 20.67 0.00 0.00 0.98
2017 5644 7.840931 TGAAGATGCATCGGACTGTATATATT 58.159 34.615 20.67 4.95 0.00 1.28
2018 5645 7.410120 TGAAGATGCATCGGACTGTATATAT 57.590 36.000 20.67 0.00 0.00 0.86
2019 5646 6.834168 TGAAGATGCATCGGACTGTATATA 57.166 37.500 20.67 0.00 0.00 0.86
2020 5647 5.728637 TGAAGATGCATCGGACTGTATAT 57.271 39.130 20.67 0.00 0.00 0.86
2021 5648 5.728637 ATGAAGATGCATCGGACTGTATA 57.271 39.130 20.67 2.37 0.00 1.47
2022 5649 4.613925 ATGAAGATGCATCGGACTGTAT 57.386 40.909 20.67 7.29 0.00 2.29
2023 5650 4.556699 CGTATGAAGATGCATCGGACTGTA 60.557 45.833 20.67 8.00 0.00 2.74
2024 5651 2.996249 ATGAAGATGCATCGGACTGT 57.004 45.000 20.67 0.00 0.00 3.55
2025 5652 2.728318 CGTATGAAGATGCATCGGACTG 59.272 50.000 20.67 5.65 0.00 3.51
2026 5653 2.362397 ACGTATGAAGATGCATCGGACT 59.638 45.455 20.67 10.04 0.00 3.85
2027 5654 2.743938 ACGTATGAAGATGCATCGGAC 58.256 47.619 20.67 15.49 0.00 4.79
2028 5655 4.577834 TTACGTATGAAGATGCATCGGA 57.422 40.909 20.67 9.21 0.00 4.55
2029 5656 4.084537 GGTTTACGTATGAAGATGCATCGG 60.085 45.833 20.67 8.01 0.00 4.18
2030 5657 4.506288 TGGTTTACGTATGAAGATGCATCG 59.494 41.667 20.67 10.38 0.00 3.84
2031 5658 5.277345 GGTGGTTTACGTATGAAGATGCATC 60.277 44.000 19.37 19.37 0.00 3.91
2032 5659 4.574828 GGTGGTTTACGTATGAAGATGCAT 59.425 41.667 0.00 0.00 0.00 3.96
2033 5660 3.936453 GGTGGTTTACGTATGAAGATGCA 59.064 43.478 0.00 0.00 0.00 3.96
2034 5661 4.189231 AGGTGGTTTACGTATGAAGATGC 58.811 43.478 0.00 0.00 0.00 3.91
2035 5662 5.520288 CAGAGGTGGTTTACGTATGAAGATG 59.480 44.000 0.00 0.00 38.33 2.90
2036 5663 5.421056 TCAGAGGTGGTTTACGTATGAAGAT 59.579 40.000 0.00 0.00 41.00 2.40
2037 5664 4.768448 TCAGAGGTGGTTTACGTATGAAGA 59.232 41.667 0.00 0.00 41.00 2.87
2038 5665 5.068234 TCAGAGGTGGTTTACGTATGAAG 57.932 43.478 0.00 0.00 41.00 3.02
2039 5666 5.011329 ACTTCAGAGGTGGTTTACGTATGAA 59.989 40.000 0.00 8.76 46.78 2.57
2040 5667 4.525487 ACTTCAGAGGTGGTTTACGTATGA 59.475 41.667 0.00 0.00 41.87 2.15
2041 5668 4.817517 ACTTCAGAGGTGGTTTACGTATG 58.182 43.478 0.00 0.00 37.64 2.39
2042 5669 5.479124 AACTTCAGAGGTGGTTTACGTAT 57.521 39.130 0.00 0.00 0.00 3.06
2043 5670 4.942761 AACTTCAGAGGTGGTTTACGTA 57.057 40.909 0.00 0.00 0.00 3.57
2044 5671 3.832615 AACTTCAGAGGTGGTTTACGT 57.167 42.857 0.00 0.00 0.00 3.57
2045 5672 4.124238 TGAAACTTCAGAGGTGGTTTACG 58.876 43.478 0.00 0.00 32.95 3.18
2058 5685 3.251729 GCTTGCTGATGACTGAAACTTCA 59.748 43.478 0.00 0.00 35.57 3.02
2059 5686 3.365767 GGCTTGCTGATGACTGAAACTTC 60.366 47.826 0.00 0.00 0.00 3.01
2060 5687 2.555757 GGCTTGCTGATGACTGAAACTT 59.444 45.455 0.00 0.00 0.00 2.66
2061 5688 2.157738 GGCTTGCTGATGACTGAAACT 58.842 47.619 0.00 0.00 0.00 2.66
2062 5689 1.881973 TGGCTTGCTGATGACTGAAAC 59.118 47.619 0.00 0.00 0.00 2.78
2063 5690 1.881973 GTGGCTTGCTGATGACTGAAA 59.118 47.619 0.00 0.00 0.00 2.69
2064 5691 1.202794 TGTGGCTTGCTGATGACTGAA 60.203 47.619 0.00 0.00 0.00 3.02
2065 5692 0.397564 TGTGGCTTGCTGATGACTGA 59.602 50.000 0.00 0.00 0.00 3.41
2066 5693 1.460504 ATGTGGCTTGCTGATGACTG 58.539 50.000 0.00 0.00 0.00 3.51
2067 5694 2.636830 GTATGTGGCTTGCTGATGACT 58.363 47.619 0.00 0.00 0.00 3.41
2068 5695 1.672881 GGTATGTGGCTTGCTGATGAC 59.327 52.381 0.00 0.00 0.00 3.06
2069 5696 1.281577 TGGTATGTGGCTTGCTGATGA 59.718 47.619 0.00 0.00 0.00 2.92
2070 5697 1.753930 TGGTATGTGGCTTGCTGATG 58.246 50.000 0.00 0.00 0.00 3.07
2071 5698 2.512692 TTGGTATGTGGCTTGCTGAT 57.487 45.000 0.00 0.00 0.00 2.90
2072 5699 2.093890 CATTGGTATGTGGCTTGCTGA 58.906 47.619 0.00 0.00 0.00 4.26
2073 5700 1.135527 CCATTGGTATGTGGCTTGCTG 59.864 52.381 0.00 0.00 0.00 4.41
2074 5701 1.477553 CCATTGGTATGTGGCTTGCT 58.522 50.000 0.00 0.00 0.00 3.91
2080 5707 1.481772 CCTTTGGCCATTGGTATGTGG 59.518 52.381 6.09 0.00 38.55 4.17
2081 5708 1.481772 CCCTTTGGCCATTGGTATGTG 59.518 52.381 6.09 0.00 0.00 3.21
2082 5709 1.078656 ACCCTTTGGCCATTGGTATGT 59.921 47.619 17.23 8.72 33.59 2.29
2083 5710 1.864669 ACCCTTTGGCCATTGGTATG 58.135 50.000 17.23 8.18 33.59 2.39
2084 5711 2.571202 CAAACCCTTTGGCCATTGGTAT 59.429 45.455 18.59 7.11 37.01 2.73
2085 5712 1.974236 CAAACCCTTTGGCCATTGGTA 59.026 47.619 18.59 0.00 37.01 3.25
2086 5713 0.764271 CAAACCCTTTGGCCATTGGT 59.236 50.000 6.09 11.21 37.01 3.67
2087 5714 3.629548 CAAACCCTTTGGCCATTGG 57.370 52.632 6.09 12.22 37.01 3.16
2115 6499 4.868171 GCGAAATGTGACACTAGTCCATTA 59.132 41.667 7.20 0.00 44.33 1.90
2128 6512 7.011389 CCATTAACTCTATTGAGCGAAATGTGA 59.989 37.037 17.24 0.00 43.85 3.58
2142 6526 4.497674 GCGTCACGAGTCCATTAACTCTAT 60.498 45.833 0.00 0.00 42.90 1.98
2216 6600 9.525826 GATACTCCATGAATAAAGGATCCAATT 57.474 33.333 15.82 11.15 0.00 2.32
2217 6601 8.898728 AGATACTCCATGAATAAAGGATCCAAT 58.101 33.333 15.82 4.38 30.64 3.16
2264 6648 4.633565 AGCTCAGATTAACTAGCAAAGTGC 59.366 41.667 0.00 0.00 45.46 4.40
2298 6683 4.898014 ACCCCATGAATAAAGGATCCAA 57.102 40.909 15.82 0.00 0.00 3.53
2322 6707 9.892130 CTCTTCCCAAACTGTATAAAGTTCTAT 57.108 33.333 8.79 0.00 39.48 1.98
2329 6714 8.662255 TCTAAACCTCTTCCCAAACTGTATAAA 58.338 33.333 0.00 0.00 0.00 1.40
2332 6717 6.697641 TCTAAACCTCTTCCCAAACTGTAT 57.302 37.500 0.00 0.00 0.00 2.29
2346 6731 7.275999 CGGTTGAAGTAGATTCTTCTAAACCTC 59.724 40.741 22.08 8.22 42.21 3.85
2378 6763 6.918569 GTCTAGTTCAAGCGATTCTAGCAATA 59.081 38.462 3.46 0.00 37.01 1.90
2392 6777 4.023107 TCACCGTGAAGAGTCTAGTTCAAG 60.023 45.833 0.00 0.00 34.52 3.02
2405 6790 3.724508 ATCTAGATGCTCACCGTGAAG 57.275 47.619 3.89 0.00 0.00 3.02
2412 6797 4.082190 TGGCCGTAATATCTAGATGCTCAC 60.082 45.833 15.79 6.94 0.00 3.51
2413 6798 4.082190 GTGGCCGTAATATCTAGATGCTCA 60.082 45.833 15.79 6.54 0.00 4.26
2414 6799 4.082190 TGTGGCCGTAATATCTAGATGCTC 60.082 45.833 15.79 7.20 0.00 4.26
2415 6800 3.832490 TGTGGCCGTAATATCTAGATGCT 59.168 43.478 15.79 4.69 0.00 3.79
2416 6801 3.927142 GTGTGGCCGTAATATCTAGATGC 59.073 47.826 15.79 8.57 0.00 3.91
2417 6802 5.048013 TCTGTGTGGCCGTAATATCTAGATG 60.048 44.000 15.79 0.00 0.00 2.90
2418 6803 5.077564 TCTGTGTGGCCGTAATATCTAGAT 58.922 41.667 10.73 10.73 0.00 1.98
2419 6804 4.466827 TCTGTGTGGCCGTAATATCTAGA 58.533 43.478 0.00 0.00 0.00 2.43
2420 6805 4.848562 TCTGTGTGGCCGTAATATCTAG 57.151 45.455 0.00 0.00 0.00 2.43
2422 6807 4.442706 CTTTCTGTGTGGCCGTAATATCT 58.557 43.478 0.00 0.00 0.00 1.98
2423 6808 3.002348 GCTTTCTGTGTGGCCGTAATATC 59.998 47.826 0.00 0.00 0.00 1.63
2424 6809 2.943033 GCTTTCTGTGTGGCCGTAATAT 59.057 45.455 0.00 0.00 0.00 1.28
2425 6810 2.027561 AGCTTTCTGTGTGGCCGTAATA 60.028 45.455 0.00 0.00 0.00 0.98
2426 6811 1.165270 GCTTTCTGTGTGGCCGTAAT 58.835 50.000 0.00 0.00 0.00 1.89
2447 6847 4.058817 GAGTGCAGCTACAACTAACTTGT 58.941 43.478 0.00 0.00 45.57 3.16
2449 6849 4.608948 AGAGTGCAGCTACAACTAACTT 57.391 40.909 0.00 0.00 0.00 2.66
2460 6860 2.997315 TGCCGGTAGAGTGCAGCT 60.997 61.111 1.90 0.00 0.00 4.24
2476 6876 2.288395 GGCAAGGTTCAACTTCCATGTG 60.288 50.000 0.00 0.00 0.00 3.21
2480 6880 2.031120 CAAGGCAAGGTTCAACTTCCA 58.969 47.619 0.00 0.00 0.00 3.53
2515 6915 6.711277 TGTCAAAAGCAAGTAGATGACCTAT 58.289 36.000 0.00 0.00 37.07 2.57
2524 6924 8.531530 GTGTACAAAAATGTCAAAAGCAAGTAG 58.468 33.333 0.00 0.00 0.00 2.57
2533 6933 5.590530 AGGCAGTGTACAAAAATGTCAAA 57.409 34.783 0.00 0.00 0.00 2.69
2569 6969 2.048601 TGGAACAAGTTTCGGGACCTA 58.951 47.619 0.00 0.00 31.92 3.08
2577 6977 4.022329 CCAACCTATGGTGGAACAAGTTTC 60.022 45.833 0.00 0.00 44.16 2.78
2602 7002 0.743345 GAGGTGTGCCGTATGGTTCC 60.743 60.000 2.17 0.84 40.50 3.62
2605 7005 2.987125 GGAGGTGTGCCGTATGGT 59.013 61.111 2.17 0.00 40.50 3.55
2626 7026 2.362077 GGCTTGGACACAAACATTGAGT 59.638 45.455 0.00 0.00 37.18 3.41
2627 7027 2.605338 CGGCTTGGACACAAACATTGAG 60.605 50.000 0.00 0.00 35.89 3.02
2628 7028 1.336440 CGGCTTGGACACAAACATTGA 59.664 47.619 0.00 0.00 35.89 2.57
2629 7029 1.066908 ACGGCTTGGACACAAACATTG 59.933 47.619 0.00 0.00 35.89 2.82
2630 7030 1.066908 CACGGCTTGGACACAAACATT 59.933 47.619 0.00 0.00 35.89 2.71
2631 7031 0.667993 CACGGCTTGGACACAAACAT 59.332 50.000 0.00 0.00 35.89 2.71
2632 7032 0.393132 TCACGGCTTGGACACAAACA 60.393 50.000 0.00 0.00 35.89 2.83
2633 7033 0.028902 GTCACGGCTTGGACACAAAC 59.971 55.000 0.00 0.00 35.89 2.93
2634 7034 0.393132 TGTCACGGCTTGGACACAAA 60.393 50.000 0.00 0.00 39.00 2.83
2635 7035 1.222113 TGTCACGGCTTGGACACAA 59.778 52.632 0.00 0.00 39.00 3.33
2636 7036 2.904131 TGTCACGGCTTGGACACA 59.096 55.556 0.00 0.00 39.00 3.72
2638 7038 2.110213 GGTGTCACGGCTTGGACA 59.890 61.111 0.00 0.00 41.44 4.02
2639 7039 0.889186 ATTGGTGTCACGGCTTGGAC 60.889 55.000 0.00 0.00 34.63 4.02
2640 7040 0.687920 TATTGGTGTCACGGCTTGGA 59.312 50.000 0.00 0.00 0.00 3.53
2641 7041 1.401552 CATATTGGTGTCACGGCTTGG 59.598 52.381 0.00 0.00 0.00 3.61
2642 7042 2.083774 ACATATTGGTGTCACGGCTTG 58.916 47.619 0.00 0.00 0.00 4.01
2643 7043 2.489938 ACATATTGGTGTCACGGCTT 57.510 45.000 0.00 0.00 0.00 4.35
2644 7044 2.489938 AACATATTGGTGTCACGGCT 57.510 45.000 0.00 0.00 0.00 5.52
2645 7045 4.688511 TTAAACATATTGGTGTCACGGC 57.311 40.909 0.00 0.00 0.00 5.68
2646 7046 8.527567 AATTTTTAAACATATTGGTGTCACGG 57.472 30.769 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.