Multiple sequence alignment - TraesCS6D01G113500

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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 TraesCS6D01G113500 chr6D 100.000 2369 0 0 427 2795 80112056 80114424 0.000000e+00 4375.0
1 TraesCS6D01G113500 chr6D 97.328 262 6 1 1968 2229 388990621 388990881 7.100000e-121 444.0
2 TraesCS6D01G113500 chr6D 96.296 270 7 3 1965 2232 26354244 26353976 9.190000e-120 440.0
3 TraesCS6D01G113500 chr6D 87.037 270 31 4 434 701 80036436 80036703 4.520000e-78 302.0
4 TraesCS6D01G113500 chr6D 100.000 88 0 0 1 88 80111630 80111717 2.230000e-36 163.0
5 TraesCS6D01G113500 chr6B 91.761 1505 88 16 428 1909 153311396 153312887 0.000000e+00 2060.0
6 TraesCS6D01G113500 chr6B 86.479 355 46 2 2441 2795 153324377 153324729 3.380000e-104 388.0
7 TraesCS6D01G113500 chr6A 90.825 1188 60 24 684 1864 96813015 96814160 0.000000e+00 1544.0
8 TraesCS6D01G113500 chr6A 90.423 355 34 0 2441 2795 96815186 96815540 4.220000e-128 468.0
9 TraesCS6D01G113500 chr6A 89.416 274 29 0 428 701 96810063 96810336 2.060000e-91 346.0
10 TraesCS6D01G113500 chr6A 89.840 187 15 3 2253 2437 96814967 96815151 1.290000e-58 237.0
11 TraesCS6D01G113500 chr6A 96.552 58 2 0 1909 1966 96814788 96814845 2.290000e-16 97.1
12 TraesCS6D01G113500 chr2D 97.719 263 6 0 1971 2233 204112942 204112680 1.180000e-123 453.0
13 TraesCS6D01G113500 chr3D 96.981 265 8 0 1965 2229 83428532 83428796 1.980000e-121 446.0
14 TraesCS6D01G113500 chrUn 96.970 264 7 1 1968 2231 68758078 68758340 2.560000e-120 442.0
15 TraesCS6D01G113500 chrUn 96.269 268 10 0 1962 2229 108799230 108799497 9.190000e-120 440.0
16 TraesCS6D01G113500 chr2B 96.970 264 7 1 1966 2229 29981422 29981684 2.560000e-120 442.0
17 TraesCS6D01G113500 chr7A 96.617 266 8 1 1967 2232 252742737 252742473 9.190000e-120 440.0
18 TraesCS6D01G113500 chr5B 95.956 272 9 2 1958 2229 508186233 508186502 9.190000e-120 440.0
19 TraesCS6D01G113500 chr5D 77.913 575 97 19 1108 1670 213273430 213273986 5.770000e-87 331.0
20 TraesCS6D01G113500 chr5A 77.636 550 103 12 1128 1670 276332986 276332450 1.620000e-82 316.0
21 TraesCS6D01G113500 chr7D 72.779 529 114 23 2283 2792 119743243 119742726 4.820000e-33 152.0


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 TraesCS6D01G113500 chr6D 80111630 80114424 2794 False 2269.00 4375 100.0000 1 2795 2 chr6D.!!$F3 2794
1 TraesCS6D01G113500 chr6B 153311396 153312887 1491 False 2060.00 2060 91.7610 428 1909 1 chr6B.!!$F1 1481
2 TraesCS6D01G113500 chr6A 96810063 96815540 5477 False 538.42 1544 91.4112 428 2795 5 chr6A.!!$F1 2367
3 TraesCS6D01G113500 chr5D 213273430 213273986 556 False 331.00 331 77.9130 1108 1670 1 chr5D.!!$F1 562
4 TraesCS6D01G113500 chr5A 276332450 276332986 536 True 316.00 316 77.6360 1128 1670 1 chr5A.!!$R1 542

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
62 63 0.034198 TCACCCGTTGATTCTCGCAA 59.966 50.0 0.0 0.0 0.0 4.85 F
1037 3754 0.035458 CAACGAACCCTGCTTCTCCT 59.965 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 4223 0.033504 GTCCACCTCAAAGCTCACGA 59.966 55.0 0.0 0.0 0.00 4.35 R
2604 6041 0.459759 GTCCTTCCAACGACGGGATC 60.460 60.0 0.0 0.0 33.63 3.36 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
20 21 2.817396 GCTCCTCGCTCTGTTGCC 60.817 66.667 0.00 0.00 35.14 4.52
21 22 2.125350 CTCCTCGCTCTGTTGCCC 60.125 66.667 0.00 0.00 0.00 5.36
22 23 2.922503 TCCTCGCTCTGTTGCCCA 60.923 61.111 0.00 0.00 0.00 5.36
23 24 2.249413 CTCCTCGCTCTGTTGCCCAT 62.249 60.000 0.00 0.00 0.00 4.00
24 25 2.110967 CCTCGCTCTGTTGCCCATG 61.111 63.158 0.00 0.00 0.00 3.66
25 26 1.078918 CTCGCTCTGTTGCCCATGA 60.079 57.895 0.00 0.00 0.00 3.07
26 27 0.463295 CTCGCTCTGTTGCCCATGAT 60.463 55.000 0.00 0.00 0.00 2.45
27 28 0.745486 TCGCTCTGTTGCCCATGATG 60.745 55.000 0.00 0.00 0.00 3.07
28 29 0.745486 CGCTCTGTTGCCCATGATGA 60.745 55.000 0.00 0.00 0.00 2.92
29 30 1.466856 GCTCTGTTGCCCATGATGAA 58.533 50.000 0.00 0.00 0.00 2.57
30 31 1.133790 GCTCTGTTGCCCATGATGAAC 59.866 52.381 0.00 0.00 0.00 3.18
31 32 2.439409 CTCTGTTGCCCATGATGAACA 58.561 47.619 0.00 0.00 0.00 3.18
32 33 2.161855 TCTGTTGCCCATGATGAACAC 58.838 47.619 0.00 0.00 0.00 3.32
33 34 1.887854 CTGTTGCCCATGATGAACACA 59.112 47.619 0.00 0.00 0.00 3.72
34 35 2.494471 CTGTTGCCCATGATGAACACAT 59.506 45.455 0.00 0.00 0.00 3.21
35 36 2.492881 TGTTGCCCATGATGAACACATC 59.507 45.455 0.00 0.00 40.30 3.06
47 48 7.558161 TGATGAACACATCAATTATCTCACC 57.442 36.000 9.92 0.00 44.61 4.02
48 49 6.543465 TGATGAACACATCAATTATCTCACCC 59.457 38.462 9.92 0.00 44.61 4.61
49 50 4.875536 TGAACACATCAATTATCTCACCCG 59.124 41.667 0.00 0.00 34.30 5.28
50 51 4.487714 ACACATCAATTATCTCACCCGT 57.512 40.909 0.00 0.00 0.00 5.28
51 52 4.843728 ACACATCAATTATCTCACCCGTT 58.156 39.130 0.00 0.00 0.00 4.44
52 53 4.635765 ACACATCAATTATCTCACCCGTTG 59.364 41.667 0.00 0.00 0.00 4.10
53 54 4.875536 CACATCAATTATCTCACCCGTTGA 59.124 41.667 0.00 0.00 0.00 3.18
54 55 5.528690 CACATCAATTATCTCACCCGTTGAT 59.471 40.000 0.00 0.00 36.91 2.57
55 56 6.038603 CACATCAATTATCTCACCCGTTGATT 59.961 38.462 0.00 0.00 34.96 2.57
56 57 6.260936 ACATCAATTATCTCACCCGTTGATTC 59.739 38.462 0.00 0.00 34.96 2.52
57 58 5.989477 TCAATTATCTCACCCGTTGATTCT 58.011 37.500 0.00 0.00 32.17 2.40
58 59 6.049149 TCAATTATCTCACCCGTTGATTCTC 58.951 40.000 0.00 0.00 32.17 2.87
59 60 2.586258 ATCTCACCCGTTGATTCTCG 57.414 50.000 0.00 0.00 32.17 4.04
60 61 0.108804 TCTCACCCGTTGATTCTCGC 60.109 55.000 0.00 0.00 32.17 5.03
61 62 0.389817 CTCACCCGTTGATTCTCGCA 60.390 55.000 0.00 0.00 32.17 5.10
62 63 0.034198 TCACCCGTTGATTCTCGCAA 59.966 50.000 0.00 0.00 0.00 4.85
63 64 0.871722 CACCCGTTGATTCTCGCAAA 59.128 50.000 0.00 0.00 0.00 3.68
64 65 1.265635 CACCCGTTGATTCTCGCAAAA 59.734 47.619 0.00 0.00 0.00 2.44
65 66 1.950909 ACCCGTTGATTCTCGCAAAAA 59.049 42.857 0.00 0.00 0.00 1.94
87 88 3.695830 AAAATCTCTCCCGTTGTAGCA 57.304 42.857 0.00 0.00 0.00 3.49
452 453 6.072112 TGTTTAAATTCTGGCTCTGTTCAC 57.928 37.500 0.00 0.00 0.00 3.18
454 455 1.813513 AATTCTGGCTCTGTTCACGG 58.186 50.000 0.00 0.00 0.00 4.94
468 469 0.608130 TCACGGAGGTCACCATCAAG 59.392 55.000 0.00 0.00 0.00 3.02
488 489 6.441274 TCAAGTACCTCGTGTAGTTTAGTTG 58.559 40.000 5.56 0.00 40.38 3.16
492 493 8.115490 AGTACCTCGTGTAGTTTAGTTGTAAT 57.885 34.615 0.00 0.00 28.20 1.89
510 511 9.442047 AGTTGTAATGTCAAATTTGGTTTCAAA 57.558 25.926 17.90 3.25 45.61 2.69
537 538 0.320421 ATTCCGTCCGTCTGGTTGTG 60.320 55.000 0.00 0.00 36.30 3.33
587 589 5.843673 TCATTTTTATGCCCGCTTCATTA 57.156 34.783 0.00 0.00 0.00 1.90
599 601 4.274950 CCCGCTTCATTATAAATTGGTCGT 59.725 41.667 0.00 0.00 0.00 4.34
601 603 6.148811 CCCGCTTCATTATAAATTGGTCGTAT 59.851 38.462 0.00 0.00 0.00 3.06
651 653 1.633774 CTAGCCCACTATCCACGGAT 58.366 55.000 3.62 3.62 38.54 4.18
671 673 5.360591 GGATGGATCTATTTGTTGTCGTCT 58.639 41.667 0.00 0.00 0.00 4.18
677 679 6.144724 GGATCTATTTGTTGTCGTCTATCTGC 59.855 42.308 0.00 0.00 0.00 4.26
714 3412 2.307768 TCTCTCACAGACTTCACGGTT 58.692 47.619 0.00 0.00 0.00 4.44
761 3462 1.290203 CTGGTGGTACATCGTCATGC 58.710 55.000 0.00 0.00 46.67 4.06
822 3526 0.249322 CGACGACTTGAACACCAGGT 60.249 55.000 0.00 0.00 37.84 4.00
836 3540 1.367471 CAGGTCAGTCGCCAAGTCA 59.633 57.895 0.00 0.00 0.00 3.41
877 3581 3.642755 CAGTTCACTGGCGTGTCC 58.357 61.111 0.00 2.67 41.89 4.02
901 3605 3.234386 GCGGTTTATGTTTGTTCTCTGC 58.766 45.455 0.00 0.00 0.00 4.26
1029 3746 1.599797 GACCCACCAACGAACCCTG 60.600 63.158 0.00 0.00 0.00 4.45
1032 3749 1.528309 CCACCAACGAACCCTGCTT 60.528 57.895 0.00 0.00 0.00 3.91
1037 3754 0.035458 CAACGAACCCTGCTTCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
1066 3787 2.734723 CCGCCATGTCCGATAGCG 60.735 66.667 0.00 0.00 46.04 4.26
1206 3927 3.923864 ACGCTCGCCAACCTCACA 61.924 61.111 0.00 0.00 0.00 3.58
1587 4314 1.651240 CGAGGATTTGGTGCTGGCTG 61.651 60.000 0.00 0.00 0.00 4.85
1595 4322 2.031163 GTGCTGGCTGACGGTTCT 59.969 61.111 0.00 0.00 0.00 3.01
1684 4411 2.154462 ACTGATGAAGTTTCTTGGGCG 58.846 47.619 0.00 0.00 34.57 6.13
1801 4528 6.183360 CGTATTGTTCGTGTGATGTGTATCAA 60.183 38.462 0.00 0.00 44.49 2.57
1854 4581 5.070714 TGAATATTGATTGCATTCTTGGGGG 59.929 40.000 9.81 0.00 31.37 5.40
1856 4583 3.464720 TTGATTGCATTCTTGGGGGTA 57.535 42.857 9.81 0.00 0.00 3.69
1865 4592 4.405358 GCATTCTTGGGGGTAAATTCATGA 59.595 41.667 0.00 0.00 0.00 3.07
1921 5231 7.478520 AATCAGTAGCGATAACCATGTTTAC 57.521 36.000 0.00 0.00 0.00 2.01
1951 5261 1.821216 AAACAGCCGATCGACCAAAT 58.179 45.000 18.66 0.00 0.00 2.32
1966 5276 4.863131 CGACCAAATCAGGAACTACTACAC 59.137 45.833 0.00 0.00 36.02 2.90
1967 5277 4.817517 ACCAAATCAGGAACTACTACACG 58.182 43.478 0.00 0.00 36.02 4.49
1968 5278 4.282703 ACCAAATCAGGAACTACTACACGT 59.717 41.667 0.00 0.00 36.02 4.49
1969 5279 5.221581 ACCAAATCAGGAACTACTACACGTT 60.222 40.000 0.00 0.00 36.02 3.99
1970 5280 5.347907 CCAAATCAGGAACTACTACACGTTC 59.652 44.000 0.00 0.00 36.02 3.95
1971 5281 5.979288 AATCAGGAACTACTACACGTTCT 57.021 39.130 0.00 0.00 39.47 3.01
1972 5282 5.564048 ATCAGGAACTACTACACGTTCTC 57.436 43.478 0.00 0.00 39.47 2.87
1973 5283 3.755378 TCAGGAACTACTACACGTTCTCC 59.245 47.826 0.00 0.00 39.47 3.71
1974 5284 3.087781 AGGAACTACTACACGTTCTCCC 58.912 50.000 0.00 0.00 39.47 4.30
1975 5285 3.087781 GGAACTACTACACGTTCTCCCT 58.912 50.000 0.00 0.00 39.47 4.20
1976 5286 3.128415 GGAACTACTACACGTTCTCCCTC 59.872 52.174 0.00 0.00 39.47 4.30
1977 5287 2.720915 ACTACTACACGTTCTCCCTCC 58.279 52.381 0.00 0.00 0.00 4.30
1978 5288 1.669779 CTACTACACGTTCTCCCTCCG 59.330 57.143 0.00 0.00 0.00 4.63
1979 5289 0.251077 ACTACACGTTCTCCCTCCGT 60.251 55.000 0.00 0.00 34.71 4.69
1980 5290 0.886563 CTACACGTTCTCCCTCCGTT 59.113 55.000 0.00 0.00 31.46 4.44
1981 5291 1.271656 CTACACGTTCTCCCTCCGTTT 59.728 52.381 0.00 0.00 31.46 3.60
1982 5292 0.033090 ACACGTTCTCCCTCCGTTTC 59.967 55.000 0.00 0.00 31.46 2.78
1983 5293 0.317479 CACGTTCTCCCTCCGTTTCT 59.683 55.000 0.00 0.00 31.46 2.52
1984 5294 1.046204 ACGTTCTCCCTCCGTTTCTT 58.954 50.000 0.00 0.00 0.00 2.52
1985 5295 1.415289 ACGTTCTCCCTCCGTTTCTTT 59.585 47.619 0.00 0.00 0.00 2.52
1986 5296 2.158856 ACGTTCTCCCTCCGTTTCTTTT 60.159 45.455 0.00 0.00 0.00 2.27
1987 5297 2.876550 CGTTCTCCCTCCGTTTCTTTTT 59.123 45.455 0.00 0.00 0.00 1.94
1988 5298 4.060205 CGTTCTCCCTCCGTTTCTTTTTA 58.940 43.478 0.00 0.00 0.00 1.52
1989 5299 4.151867 CGTTCTCCCTCCGTTTCTTTTTAG 59.848 45.833 0.00 0.00 0.00 1.85
1990 5300 4.968971 TCTCCCTCCGTTTCTTTTTAGT 57.031 40.909 0.00 0.00 0.00 2.24
1991 5301 4.891260 TCTCCCTCCGTTTCTTTTTAGTC 58.109 43.478 0.00 0.00 0.00 2.59
1992 5302 4.001652 CTCCCTCCGTTTCTTTTTAGTCC 58.998 47.826 0.00 0.00 0.00 3.85
1993 5303 2.740447 CCCTCCGTTTCTTTTTAGTCCG 59.260 50.000 0.00 0.00 0.00 4.79
1994 5304 2.159037 CCTCCGTTTCTTTTTAGTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
1995 5305 1.794116 TCCGTTTCTTTTTAGTCCGCG 59.206 47.619 0.00 0.00 0.00 6.46
1996 5306 1.528161 CCGTTTCTTTTTAGTCCGCGT 59.472 47.619 4.92 0.00 0.00 6.01
1997 5307 2.730928 CCGTTTCTTTTTAGTCCGCGTA 59.269 45.455 4.92 0.00 0.00 4.42
1998 5308 3.368843 CCGTTTCTTTTTAGTCCGCGTAT 59.631 43.478 4.92 0.00 0.00 3.06
1999 5309 4.562394 CCGTTTCTTTTTAGTCCGCGTATA 59.438 41.667 4.92 0.00 0.00 1.47
2000 5310 5.062058 CCGTTTCTTTTTAGTCCGCGTATAA 59.938 40.000 4.92 0.00 0.00 0.98
2001 5311 6.173724 CGTTTCTTTTTAGTCCGCGTATAAG 58.826 40.000 4.92 0.00 0.00 1.73
2002 5312 6.472680 GTTTCTTTTTAGTCCGCGTATAAGG 58.527 40.000 4.92 0.00 0.00 2.69
2003 5313 5.329035 TCTTTTTAGTCCGCGTATAAGGT 57.671 39.130 4.92 0.00 0.00 3.50
2004 5314 5.723295 TCTTTTTAGTCCGCGTATAAGGTT 58.277 37.500 4.92 0.00 0.00 3.50
2005 5315 6.165577 TCTTTTTAGTCCGCGTATAAGGTTT 58.834 36.000 4.92 0.00 0.00 3.27
2006 5316 5.783100 TTTTAGTCCGCGTATAAGGTTTG 57.217 39.130 4.92 0.00 0.00 2.93
2007 5317 2.304751 AGTCCGCGTATAAGGTTTGG 57.695 50.000 4.92 0.00 0.00 3.28
2008 5318 1.551883 AGTCCGCGTATAAGGTTTGGT 59.448 47.619 4.92 0.00 0.00 3.67
2009 5319 1.929169 GTCCGCGTATAAGGTTTGGTC 59.071 52.381 4.92 0.00 0.00 4.02
2010 5320 1.549620 TCCGCGTATAAGGTTTGGTCA 59.450 47.619 4.92 0.00 0.00 4.02
2011 5321 2.028294 TCCGCGTATAAGGTTTGGTCAA 60.028 45.455 4.92 0.00 0.00 3.18
2012 5322 2.743126 CCGCGTATAAGGTTTGGTCAAA 59.257 45.455 4.92 0.00 0.00 2.69
2013 5323 3.181514 CCGCGTATAAGGTTTGGTCAAAG 60.182 47.826 4.92 0.00 0.00 2.77
2014 5324 3.434299 CGCGTATAAGGTTTGGTCAAAGT 59.566 43.478 0.00 0.00 0.00 2.66
2015 5325 4.435121 CGCGTATAAGGTTTGGTCAAAGTC 60.435 45.833 0.00 0.00 0.00 3.01
2016 5326 4.453136 GCGTATAAGGTTTGGTCAAAGTCA 59.547 41.667 0.00 0.00 0.00 3.41
2017 5327 5.049267 GCGTATAAGGTTTGGTCAAAGTCAA 60.049 40.000 0.00 0.00 0.00 3.18
2018 5328 6.349033 GCGTATAAGGTTTGGTCAAAGTCAAT 60.349 38.462 0.00 0.00 0.00 2.57
2019 5329 7.241376 CGTATAAGGTTTGGTCAAAGTCAATC 58.759 38.462 0.00 0.00 0.00 2.67
2020 5330 7.119262 CGTATAAGGTTTGGTCAAAGTCAATCT 59.881 37.037 0.00 0.00 0.00 2.40
2021 5331 7.839680 ATAAGGTTTGGTCAAAGTCAATCTT 57.160 32.000 0.00 0.00 38.10 2.40
2022 5332 6.544928 AAGGTTTGGTCAAAGTCAATCTTT 57.455 33.333 0.00 0.00 45.96 2.52
2040 5350 9.832445 TCAATCTTTGTAGAGTTTGACTAACTT 57.168 29.630 3.78 0.00 47.00 2.66
2094 5404 7.275888 TGAAATCAATATTACCAGATGCACC 57.724 36.000 0.00 0.00 0.00 5.01
2095 5405 6.832900 TGAAATCAATATTACCAGATGCACCA 59.167 34.615 0.00 0.00 0.00 4.17
2096 5406 7.506599 TGAAATCAATATTACCAGATGCACCAT 59.493 33.333 0.00 0.00 0.00 3.55
2097 5407 6.829229 ATCAATATTACCAGATGCACCATG 57.171 37.500 0.00 0.00 0.00 3.66
2098 5408 5.939447 TCAATATTACCAGATGCACCATGA 58.061 37.500 0.00 0.00 0.00 3.07
2099 5409 6.363882 TCAATATTACCAGATGCACCATGAA 58.636 36.000 0.00 0.00 0.00 2.57
2100 5410 6.832900 TCAATATTACCAGATGCACCATGAAA 59.167 34.615 0.00 0.00 0.00 2.69
2101 5411 4.989279 ATTACCAGATGCACCATGAAAC 57.011 40.909 0.00 0.00 0.00 2.78
2102 5412 1.167851 ACCAGATGCACCATGAAACG 58.832 50.000 0.00 0.00 0.00 3.60
2103 5413 1.167851 CCAGATGCACCATGAAACGT 58.832 50.000 0.00 0.00 0.00 3.99
2104 5414 2.290008 ACCAGATGCACCATGAAACGTA 60.290 45.455 0.00 0.00 0.00 3.57
2105 5415 2.945008 CCAGATGCACCATGAAACGTAT 59.055 45.455 0.00 0.00 0.00 3.06
2106 5416 3.378112 CCAGATGCACCATGAAACGTATT 59.622 43.478 0.00 0.00 0.00 1.89
2107 5417 4.142403 CCAGATGCACCATGAAACGTATTT 60.142 41.667 0.00 0.00 0.00 1.40
2108 5418 5.401550 CAGATGCACCATGAAACGTATTTT 58.598 37.500 0.00 0.00 0.00 1.82
2109 5419 5.512788 CAGATGCACCATGAAACGTATTTTC 59.487 40.000 0.00 0.00 43.63 2.29
2180 5490 8.840833 AAATTTGGTCAAACTTTGTGTAGTTT 57.159 26.923 1.44 0.00 46.42 2.66
2190 5500 6.190954 ACTTTGTGTAGTTTGACTTTGACC 57.809 37.500 0.00 0.00 0.00 4.02
2191 5501 5.708230 ACTTTGTGTAGTTTGACTTTGACCA 59.292 36.000 0.00 0.00 0.00 4.02
2192 5502 6.207810 ACTTTGTGTAGTTTGACTTTGACCAA 59.792 34.615 0.00 0.00 0.00 3.67
2193 5503 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
2194 5504 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
2195 5505 6.791303 TGTGTAGTTTGACTTTGACCAAATC 58.209 36.000 0.00 0.00 35.14 2.17
2196 5506 6.601613 TGTGTAGTTTGACTTTGACCAAATCT 59.398 34.615 0.00 0.00 35.14 2.40
2197 5507 7.122055 TGTGTAGTTTGACTTTGACCAAATCTT 59.878 33.333 0.00 0.00 35.14 2.40
2198 5508 8.617809 GTGTAGTTTGACTTTGACCAAATCTTA 58.382 33.333 0.00 0.00 35.14 2.10
2199 5509 9.349713 TGTAGTTTGACTTTGACCAAATCTTAT 57.650 29.630 0.00 0.00 35.14 1.73
2203 5513 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
2204 5514 7.015226 TGACTTTGACCAAATCTTATATGCG 57.985 36.000 0.00 0.00 0.00 4.73
2205 5515 6.038161 TGACTTTGACCAAATCTTATATGCGG 59.962 38.462 0.00 0.00 0.00 5.69
2206 5516 6.119536 ACTTTGACCAAATCTTATATGCGGA 58.880 36.000 0.00 0.00 0.00 5.54
2207 5517 6.260936 ACTTTGACCAAATCTTATATGCGGAG 59.739 38.462 0.00 0.00 0.00 4.63
2208 5518 5.290493 TGACCAAATCTTATATGCGGAGT 57.710 39.130 0.00 0.00 0.00 3.85
2209 5519 6.413783 TGACCAAATCTTATATGCGGAGTA 57.586 37.500 0.00 0.00 0.00 2.59
2210 5520 6.822442 TGACCAAATCTTATATGCGGAGTAA 58.178 36.000 0.00 0.00 0.00 2.24
2211 5521 7.276658 TGACCAAATCTTATATGCGGAGTAAA 58.723 34.615 0.00 0.00 0.00 2.01
2212 5522 7.771361 TGACCAAATCTTATATGCGGAGTAAAA 59.229 33.333 0.00 0.00 0.00 1.52
2213 5523 8.514330 ACCAAATCTTATATGCGGAGTAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
2214 5524 8.621286 ACCAAATCTTATATGCGGAGTAAAAAG 58.379 33.333 0.00 0.00 0.00 2.27
2215 5525 8.836413 CCAAATCTTATATGCGGAGTAAAAAGA 58.164 33.333 0.00 0.00 0.00 2.52
2219 5529 7.902032 TCTTATATGCGGAGTAAAAAGAAACG 58.098 34.615 0.00 0.00 0.00 3.60
2220 5530 3.824414 ATGCGGAGTAAAAAGAAACGG 57.176 42.857 0.00 0.00 0.00 4.44
2221 5531 2.836262 TGCGGAGTAAAAAGAAACGGA 58.164 42.857 0.00 0.00 0.00 4.69
2222 5532 2.803956 TGCGGAGTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
2223 5533 2.159037 GCGGAGTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
2224 5534 2.740447 CGGAGTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
2225 5535 3.555586 CGGAGTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
2239 5549 2.167281 CGGAGGGAGTATATGCATCTGG 59.833 54.545 0.19 0.00 33.24 3.86
2330 5736 4.083565 AGGCGTTAGAGGAGGATAGATTC 58.916 47.826 0.00 0.00 0.00 2.52
2337 5743 7.650104 CGTTAGAGGAGGATAGATTCTGTTTTC 59.350 40.741 0.00 0.00 0.00 2.29
2375 5781 0.040646 ACCGGATCCCTATCGCCATA 59.959 55.000 9.46 0.00 32.44 2.74
2378 5784 2.100197 CGGATCCCTATCGCCATAAGA 58.900 52.381 6.06 0.00 32.44 2.10
2393 5799 6.208599 TCGCCATAAGAAAGAGGACAATTTTT 59.791 34.615 0.00 0.00 0.00 1.94
2399 5805 9.807921 ATAAGAAAGAGGACAATTTTTACTCCA 57.192 29.630 0.00 0.00 0.00 3.86
2400 5806 7.751768 AGAAAGAGGACAATTTTTACTCCAG 57.248 36.000 0.00 0.00 0.00 3.86
2403 5809 5.810095 AGAGGACAATTTTTACTCCAGAGG 58.190 41.667 0.00 0.00 0.00 3.69
2406 5812 3.751518 ACAATTTTTACTCCAGAGGCGT 58.248 40.909 0.00 0.00 0.00 5.68
2427 5833 4.610905 CGTCCCGACTCTCAAATATACTCG 60.611 50.000 0.00 0.00 0.00 4.18
2428 5834 3.819337 TCCCGACTCTCAAATATACTCGG 59.181 47.826 0.00 0.00 39.13 4.63
2430 5836 3.253677 CCGACTCTCAAATATACTCGGCT 59.746 47.826 0.00 0.00 33.42 5.52
2437 5843 1.424638 AATATACTCGGCTGCCCACT 58.575 50.000 14.12 0.00 0.00 4.00
2459 5896 3.276846 GCGACGTTGCCAACCTGT 61.277 61.111 17.43 0.00 0.00 4.00
2461 5898 2.177580 CGACGTTGCCAACCTGTGT 61.178 57.895 1.21 0.00 0.00 3.72
2463 5900 2.101209 GACGTTGCCAACCTGTGTCG 62.101 60.000 1.21 0.00 0.00 4.35
2464 5901 2.331451 GTTGCCAACCTGTGTCGC 59.669 61.111 0.00 0.00 0.00 5.19
2472 5909 0.388649 AACCTGTGTCGCGTCATCTC 60.389 55.000 9.67 0.00 0.00 2.75
2479 5916 2.586079 CGCGTCATCTCCGGCATT 60.586 61.111 0.00 0.00 0.00 3.56
2491 5928 2.100991 GGCATTGCTTTCGGCGAG 59.899 61.111 10.46 0.00 45.43 5.03
2498 5935 2.668212 CTTTCGGCGAGCACCCAA 60.668 61.111 10.46 0.00 0.00 4.12
2500 5937 3.758973 TTTCGGCGAGCACCCAACA 62.759 57.895 10.46 0.00 0.00 3.33
2507 5944 1.968540 GAGCACCCAACACCTCTGC 60.969 63.158 0.00 0.00 0.00 4.26
2547 5984 2.930019 CCCTCCTGCCACACTCCA 60.930 66.667 0.00 0.00 0.00 3.86
2551 5988 1.407437 CCTCCTGCCACACTCCAATAC 60.407 57.143 0.00 0.00 0.00 1.89
2557 5994 0.245539 CCACACTCCAATACGGTCGT 59.754 55.000 0.69 0.69 35.57 4.34
2560 5997 1.342174 ACACTCCAATACGGTCGTTGT 59.658 47.619 0.16 0.00 35.57 3.32
2562 5999 1.265568 CTCCAATACGGTCGTTGTCG 58.734 55.000 0.16 0.00 35.57 4.35
2565 6002 0.986992 CAATACGGTCGTTGTCGTCC 59.013 55.000 0.16 0.00 40.31 4.79
2568 6005 3.677648 CGGTCGTTGTCGTCCCCT 61.678 66.667 0.00 0.00 40.93 4.79
2576 6013 1.100510 TTGTCGTCCCCTGTATCGAG 58.899 55.000 0.00 0.00 33.09 4.04
2593 6030 4.708968 GCTCTATCCTCGCCGCCG 62.709 72.222 0.00 0.00 0.00 6.46
2641 6078 2.511403 GGGCCGGATCTTCTTCCC 59.489 66.667 5.05 0.00 31.61 3.97
2664 6101 1.079057 GCCTCTCCGTCCACTTTCC 60.079 63.158 0.00 0.00 0.00 3.13
2691 6128 4.335647 AAGCCCTGCCGACCACTG 62.336 66.667 0.00 0.00 0.00 3.66
2701 6138 1.592400 CCGACCACTGGTAGCTTCGA 61.592 60.000 0.00 0.00 35.25 3.71
2716 6153 1.325640 CTTCGACATCGGCTCAACATG 59.674 52.381 0.73 0.00 40.29 3.21
2723 6160 3.499737 GGCTCAACATGGCCGACG 61.500 66.667 0.00 0.00 38.91 5.12
2766 6203 3.304659 CCTTCAAGTGTTCGATGGTTTGG 60.305 47.826 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.125350 GGGCAACAGAGCGAGGAG 60.125 66.667 0.00 0.00 39.74 3.69
8 9 0.745486 CATCATGGGCAACAGAGCGA 60.745 55.000 0.00 0.00 39.74 4.93
9 10 0.745486 TCATCATGGGCAACAGAGCG 60.745 55.000 0.00 0.00 39.74 5.03
10 11 1.133790 GTTCATCATGGGCAACAGAGC 59.866 52.381 0.00 0.00 39.74 4.09
11 12 2.163010 GTGTTCATCATGGGCAACAGAG 59.837 50.000 0.00 0.00 39.74 3.35
12 13 2.161855 GTGTTCATCATGGGCAACAGA 58.838 47.619 0.00 0.00 39.74 3.41
13 14 1.887854 TGTGTTCATCATGGGCAACAG 59.112 47.619 0.00 0.00 39.74 3.16
14 15 1.992538 TGTGTTCATCATGGGCAACA 58.007 45.000 0.00 0.00 39.74 3.33
15 16 3.155093 GATGTGTTCATCATGGGCAAC 57.845 47.619 0.00 0.00 46.78 4.17
25 26 5.528690 CGGGTGAGATAATTGATGTGTTCAT 59.471 40.000 0.00 0.00 33.34 2.57
26 27 4.875536 CGGGTGAGATAATTGATGTGTTCA 59.124 41.667 0.00 0.00 0.00 3.18
27 28 4.876107 ACGGGTGAGATAATTGATGTGTTC 59.124 41.667 0.00 0.00 0.00 3.18
28 29 4.843728 ACGGGTGAGATAATTGATGTGTT 58.156 39.130 0.00 0.00 0.00 3.32
29 30 4.487714 ACGGGTGAGATAATTGATGTGT 57.512 40.909 0.00 0.00 0.00 3.72
30 31 4.875536 TCAACGGGTGAGATAATTGATGTG 59.124 41.667 0.00 0.00 0.00 3.21
31 32 5.097742 TCAACGGGTGAGATAATTGATGT 57.902 39.130 0.00 0.00 0.00 3.06
32 33 6.484643 AGAATCAACGGGTGAGATAATTGATG 59.515 38.462 0.82 0.00 40.43 3.07
33 34 6.595682 AGAATCAACGGGTGAGATAATTGAT 58.404 36.000 0.82 0.00 40.43 2.57
34 35 5.989477 AGAATCAACGGGTGAGATAATTGA 58.011 37.500 0.82 0.00 40.43 2.57
35 36 5.050769 CGAGAATCAACGGGTGAGATAATTG 60.051 44.000 0.82 0.00 40.43 2.32
36 37 5.050490 CGAGAATCAACGGGTGAGATAATT 58.950 41.667 0.82 0.00 40.43 1.40
37 38 4.621991 CGAGAATCAACGGGTGAGATAAT 58.378 43.478 0.82 0.00 40.43 1.28
38 39 3.737047 GCGAGAATCAACGGGTGAGATAA 60.737 47.826 0.82 0.00 40.43 1.75
39 40 2.223735 GCGAGAATCAACGGGTGAGATA 60.224 50.000 0.82 0.00 40.43 1.98
40 41 1.471676 GCGAGAATCAACGGGTGAGAT 60.472 52.381 0.82 0.00 40.43 2.75
41 42 0.108804 GCGAGAATCAACGGGTGAGA 60.109 55.000 0.82 0.00 40.43 3.27
42 43 0.389817 TGCGAGAATCAACGGGTGAG 60.390 55.000 0.82 0.00 40.43 3.51
43 44 0.034198 TTGCGAGAATCAACGGGTGA 59.966 50.000 0.00 0.00 41.67 4.02
44 45 0.871722 TTTGCGAGAATCAACGGGTG 59.128 50.000 0.00 0.00 33.17 4.61
45 46 1.600023 TTTTGCGAGAATCAACGGGT 58.400 45.000 0.00 0.00 33.17 5.28
46 47 2.697431 TTTTTGCGAGAATCAACGGG 57.303 45.000 0.00 0.00 33.17 5.28
66 67 4.015872 TGCTACAACGGGAGAGATTTTT 57.984 40.909 0.00 0.00 0.00 1.94
67 68 3.695830 TGCTACAACGGGAGAGATTTT 57.304 42.857 0.00 0.00 0.00 1.82
426 427 7.750903 GTGAACAGAGCCAGAATTTAAACATAC 59.249 37.037 0.00 0.00 0.00 2.39
452 453 1.134788 GGTACTTGATGGTGACCTCCG 60.135 57.143 2.11 0.00 0.00 4.63
454 455 3.528597 GAGGTACTTGATGGTGACCTC 57.471 52.381 2.11 3.76 46.89 3.85
468 469 7.809806 ACATTACAACTAAACTACACGAGGTAC 59.190 37.037 0.00 0.00 0.00 3.34
502 503 7.756272 ACGGACGGAATTTAATTATTTGAAACC 59.244 33.333 0.00 0.00 0.00 3.27
510 511 5.677567 ACCAGACGGACGGAATTTAATTAT 58.322 37.500 0.00 0.00 35.59 1.28
553 555 7.661027 CGGGCATAAAAATGAATGGGATTTAAT 59.339 33.333 0.00 0.00 0.00 1.40
587 589 9.179909 TGAACACCAAATATACGACCAATTTAT 57.820 29.630 0.00 0.00 0.00 1.40
599 601 6.323482 CCATCCAACCATGAACACCAAATATA 59.677 38.462 0.00 0.00 0.00 0.86
601 603 4.465660 CCATCCAACCATGAACACCAAATA 59.534 41.667 0.00 0.00 0.00 1.40
610 612 1.838112 GTCAGCCATCCAACCATGAA 58.162 50.000 0.00 0.00 0.00 2.57
611 613 0.392863 CGTCAGCCATCCAACCATGA 60.393 55.000 0.00 0.00 0.00 3.07
651 653 7.203218 CAGATAGACGACAACAAATAGATCCA 58.797 38.462 0.00 0.00 0.00 3.41
677 679 0.037605 AGAACCTCCAACGCGGTTAG 60.038 55.000 12.47 3.22 43.23 2.34
694 697 1.982660 ACCGTGAAGTCTGTGAGAGA 58.017 50.000 0.00 0.00 0.00 3.10
696 699 2.307768 AGAACCGTGAAGTCTGTGAGA 58.692 47.619 0.00 0.00 0.00 3.27
714 3412 1.150827 CAGTGAAGTGCGATGCAAGA 58.849 50.000 0.00 0.00 41.47 3.02
822 3526 0.171231 CGAGATGACTTGGCGACTGA 59.829 55.000 0.00 0.00 0.00 3.41
854 3558 0.106708 ACGCCAGTGAACTGTGACAT 59.893 50.000 9.49 0.00 42.27 3.06
877 3581 3.059188 AGAGAACAAACATAAACCGCGTG 60.059 43.478 4.92 0.00 0.00 5.34
901 3605 1.564622 CGTGTGTTGTCGGAAGCAG 59.435 57.895 0.00 0.00 0.00 4.24
1024 3741 3.394836 GCGGAGGAGAAGCAGGGT 61.395 66.667 0.00 0.00 0.00 4.34
1025 3742 4.168291 GGCGGAGGAGAAGCAGGG 62.168 72.222 0.00 0.00 0.00 4.45
1046 3764 3.883744 CTATCGGACATGGCGGGCC 62.884 68.421 6.24 1.86 0.00 5.80
1066 3787 3.202706 GGATTTCTCGCGGTGGGC 61.203 66.667 6.13 0.00 38.69 5.36
1491 4218 1.738099 CTCAAAGCTCACGACCCCG 60.738 63.158 0.00 0.00 42.50 5.73
1496 4223 0.033504 GTCCACCTCAAAGCTCACGA 59.966 55.000 0.00 0.00 0.00 4.35
1587 4314 2.027625 CGGCTTGACCAGAACCGTC 61.028 63.158 0.00 0.00 39.05 4.79
1595 4322 3.636231 CACCCTCCGGCTTGACCA 61.636 66.667 0.00 0.00 39.03 4.02
1684 4411 0.972883 ACTGCCAGAGTCAGAGAACC 59.027 55.000 0.00 0.00 35.61 3.62
1801 4528 9.167311 GATAGTCAAACAATCCTACAGAAATGT 57.833 33.333 0.00 0.00 31.83 2.71
1854 4581 7.171508 TCGCCAGATACATTCTCATGAATTTAC 59.828 37.037 0.00 0.00 40.61 2.01
1856 4583 6.017605 GTCGCCAGATACATTCTCATGAATTT 60.018 38.462 0.00 0.00 40.61 1.82
1865 4592 3.495100 GGAATGGTCGCCAGATACATTCT 60.495 47.826 18.75 0.00 44.23 2.40
1901 4629 5.114081 GTGGTAAACATGGTTATCGCTACT 58.886 41.667 18.15 0.00 0.00 2.57
1921 5231 1.879380 TCGGCTGTTTTTCATCTGTGG 59.121 47.619 0.00 0.00 0.00 4.17
1951 5261 3.755378 GGAGAACGTGTAGTAGTTCCTGA 59.245 47.826 4.91 0.00 45.60 3.86
1966 5276 2.165319 AAAGAAACGGAGGGAGAACG 57.835 50.000 0.00 0.00 0.00 3.95
1967 5277 5.061853 ACTAAAAAGAAACGGAGGGAGAAC 58.938 41.667 0.00 0.00 0.00 3.01
1968 5278 5.300411 ACTAAAAAGAAACGGAGGGAGAA 57.700 39.130 0.00 0.00 0.00 2.87
1969 5279 4.262765 GGACTAAAAAGAAACGGAGGGAGA 60.263 45.833 0.00 0.00 0.00 3.71
1970 5280 4.001652 GGACTAAAAAGAAACGGAGGGAG 58.998 47.826 0.00 0.00 0.00 4.30
1971 5281 3.555586 CGGACTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
1972 5282 2.740447 CGGACTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
1973 5283 2.159037 GCGGACTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
1974 5284 2.159881 CGCGGACTAAAAAGAAACGGAG 60.160 50.000 0.00 0.00 0.00 4.63
1975 5285 1.794116 CGCGGACTAAAAAGAAACGGA 59.206 47.619 0.00 0.00 0.00 4.69
1976 5286 1.528161 ACGCGGACTAAAAAGAAACGG 59.472 47.619 12.47 0.00 0.00 4.44
1977 5287 2.936050 ACGCGGACTAAAAAGAAACG 57.064 45.000 12.47 0.00 0.00 3.60
1978 5288 6.091305 ACCTTATACGCGGACTAAAAAGAAAC 59.909 38.462 12.47 0.00 0.00 2.78
1979 5289 6.165577 ACCTTATACGCGGACTAAAAAGAAA 58.834 36.000 12.47 0.00 0.00 2.52
1980 5290 5.723295 ACCTTATACGCGGACTAAAAAGAA 58.277 37.500 12.47 0.00 0.00 2.52
1981 5291 5.329035 ACCTTATACGCGGACTAAAAAGA 57.671 39.130 12.47 0.00 0.00 2.52
1982 5292 6.245724 CAAACCTTATACGCGGACTAAAAAG 58.754 40.000 12.47 1.60 0.00 2.27
1983 5293 5.122082 CCAAACCTTATACGCGGACTAAAAA 59.878 40.000 12.47 0.00 0.00 1.94
1984 5294 4.630940 CCAAACCTTATACGCGGACTAAAA 59.369 41.667 12.47 0.00 0.00 1.52
1985 5295 4.183101 CCAAACCTTATACGCGGACTAAA 58.817 43.478 12.47 0.00 0.00 1.85
1986 5296 3.195396 ACCAAACCTTATACGCGGACTAA 59.805 43.478 12.47 4.07 0.00 2.24
1987 5297 2.760092 ACCAAACCTTATACGCGGACTA 59.240 45.455 12.47 0.00 0.00 2.59
1988 5298 1.551883 ACCAAACCTTATACGCGGACT 59.448 47.619 12.47 0.00 0.00 3.85
1989 5299 1.929169 GACCAAACCTTATACGCGGAC 59.071 52.381 12.47 0.00 0.00 4.79
1990 5300 1.549620 TGACCAAACCTTATACGCGGA 59.450 47.619 12.47 0.00 0.00 5.54
1991 5301 2.012937 TGACCAAACCTTATACGCGG 57.987 50.000 12.47 0.00 0.00 6.46
1992 5302 3.434299 ACTTTGACCAAACCTTATACGCG 59.566 43.478 3.53 3.53 0.00 6.01
1993 5303 4.453136 TGACTTTGACCAAACCTTATACGC 59.547 41.667 0.00 0.00 0.00 4.42
1994 5304 6.548441 TTGACTTTGACCAAACCTTATACG 57.452 37.500 0.00 0.00 0.00 3.06
1995 5305 8.336801 AGATTGACTTTGACCAAACCTTATAC 57.663 34.615 0.00 0.00 0.00 1.47
1996 5306 8.934023 AAGATTGACTTTGACCAAACCTTATA 57.066 30.769 0.00 0.00 34.94 0.98
1997 5307 7.839680 AAGATTGACTTTGACCAAACCTTAT 57.160 32.000 0.00 0.00 34.94 1.73
1998 5308 7.654022 AAAGATTGACTTTGACCAAACCTTA 57.346 32.000 0.00 0.00 45.66 2.69
1999 5309 6.544928 AAAGATTGACTTTGACCAAACCTT 57.455 33.333 0.00 0.00 45.66 3.50
2013 5323 9.262358 AGTTAGTCAAACTCTACAAAGATTGAC 57.738 33.333 15.20 15.20 45.64 3.18
2068 5378 9.013229 GGTGCATCTGGTAATATTGATTTCATA 57.987 33.333 0.00 0.00 0.00 2.15
2069 5379 7.506599 TGGTGCATCTGGTAATATTGATTTCAT 59.493 33.333 0.00 0.00 0.00 2.57
2070 5380 6.832900 TGGTGCATCTGGTAATATTGATTTCA 59.167 34.615 0.00 0.00 0.00 2.69
2071 5381 7.275888 TGGTGCATCTGGTAATATTGATTTC 57.724 36.000 0.00 0.00 0.00 2.17
2072 5382 7.506599 TCATGGTGCATCTGGTAATATTGATTT 59.493 33.333 0.00 0.00 0.00 2.17
2073 5383 7.005902 TCATGGTGCATCTGGTAATATTGATT 58.994 34.615 0.00 0.00 0.00 2.57
2074 5384 6.545567 TCATGGTGCATCTGGTAATATTGAT 58.454 36.000 0.00 0.00 0.00 2.57
2075 5385 5.939447 TCATGGTGCATCTGGTAATATTGA 58.061 37.500 0.00 0.00 0.00 2.57
2076 5386 6.638096 TTCATGGTGCATCTGGTAATATTG 57.362 37.500 0.00 0.00 0.00 1.90
2077 5387 6.238731 CGTTTCATGGTGCATCTGGTAATATT 60.239 38.462 0.00 0.00 0.00 1.28
2078 5388 5.239306 CGTTTCATGGTGCATCTGGTAATAT 59.761 40.000 0.00 0.00 0.00 1.28
2079 5389 4.574421 CGTTTCATGGTGCATCTGGTAATA 59.426 41.667 0.00 0.00 0.00 0.98
2080 5390 3.378112 CGTTTCATGGTGCATCTGGTAAT 59.622 43.478 0.00 0.00 0.00 1.89
2081 5391 2.746904 CGTTTCATGGTGCATCTGGTAA 59.253 45.455 0.00 0.00 0.00 2.85
2082 5392 2.290008 ACGTTTCATGGTGCATCTGGTA 60.290 45.455 0.00 0.00 0.00 3.25
2083 5393 1.167851 CGTTTCATGGTGCATCTGGT 58.832 50.000 0.00 0.00 0.00 4.00
2084 5394 1.167851 ACGTTTCATGGTGCATCTGG 58.832 50.000 0.00 0.00 0.00 3.86
2085 5395 4.621068 AATACGTTTCATGGTGCATCTG 57.379 40.909 0.00 0.00 0.00 2.90
2086 5396 5.640732 GAAAATACGTTTCATGGTGCATCT 58.359 37.500 0.00 0.00 44.42 2.90
2087 5397 5.932021 GAAAATACGTTTCATGGTGCATC 57.068 39.130 0.00 0.00 44.42 3.91
2154 5464 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
2155 5465 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
2166 5476 6.207810 TGGTCAAAGTCAAACTACACAAAGTT 59.792 34.615 0.00 0.00 41.46 2.66
2167 5477 5.708230 TGGTCAAAGTCAAACTACACAAAGT 59.292 36.000 0.00 0.00 0.00 2.66
2168 5478 6.189677 TGGTCAAAGTCAAACTACACAAAG 57.810 37.500 0.00 0.00 0.00 2.77
2169 5479 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
2170 5480 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
2171 5481 6.601613 AGATTTGGTCAAAGTCAAACTACACA 59.398 34.615 2.55 0.00 35.97 3.72
2172 5482 7.027778 AGATTTGGTCAAAGTCAAACTACAC 57.972 36.000 2.55 0.00 35.97 2.90
2173 5483 7.639113 AAGATTTGGTCAAAGTCAAACTACA 57.361 32.000 2.55 0.00 35.97 2.74
2177 5487 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
2178 5488 7.967854 CGCATATAAGATTTGGTCAAAGTCAAA 59.032 33.333 2.55 0.00 37.29 2.69
2179 5489 7.415095 CCGCATATAAGATTTGGTCAAAGTCAA 60.415 37.037 2.55 0.00 33.32 3.18
2180 5490 6.038161 CCGCATATAAGATTTGGTCAAAGTCA 59.962 38.462 2.55 0.00 33.32 3.41
2181 5491 6.260050 TCCGCATATAAGATTTGGTCAAAGTC 59.740 38.462 2.55 1.51 33.32 3.01
2182 5492 6.119536 TCCGCATATAAGATTTGGTCAAAGT 58.880 36.000 2.55 0.00 33.32 2.66
2183 5493 6.260936 ACTCCGCATATAAGATTTGGTCAAAG 59.739 38.462 2.55 0.00 33.32 2.77
2184 5494 6.119536 ACTCCGCATATAAGATTTGGTCAAA 58.880 36.000 0.00 0.00 34.46 2.69
2185 5495 5.680619 ACTCCGCATATAAGATTTGGTCAA 58.319 37.500 0.00 0.00 0.00 3.18
2186 5496 5.290493 ACTCCGCATATAAGATTTGGTCA 57.710 39.130 0.00 0.00 0.00 4.02
2187 5497 7.724305 TTTACTCCGCATATAAGATTTGGTC 57.276 36.000 0.00 0.00 0.00 4.02
2188 5498 8.514330 TTTTTACTCCGCATATAAGATTTGGT 57.486 30.769 0.00 0.00 0.00 3.67
2189 5499 8.836413 TCTTTTTACTCCGCATATAAGATTTGG 58.164 33.333 0.00 0.00 0.00 3.28
2193 5503 8.548721 CGTTTCTTTTTACTCCGCATATAAGAT 58.451 33.333 0.00 0.00 0.00 2.40
2194 5504 7.010738 CCGTTTCTTTTTACTCCGCATATAAGA 59.989 37.037 0.00 0.00 0.00 2.10
2195 5505 7.010738 TCCGTTTCTTTTTACTCCGCATATAAG 59.989 37.037 0.00 0.00 0.00 1.73
2196 5506 6.817641 TCCGTTTCTTTTTACTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
2197 5507 6.339730 TCCGTTTCTTTTTACTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
2198 5508 5.180271 TCCGTTTCTTTTTACTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
2199 5509 4.567971 TCCGTTTCTTTTTACTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
2200 5510 3.404899 TCCGTTTCTTTTTACTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
2201 5511 2.803956 CTCCGTTTCTTTTTACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
2202 5512 2.159037 CCTCCGTTTCTTTTTACTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
2203 5513 2.740447 CCCTCCGTTTCTTTTTACTCCG 59.260 50.000 0.00 0.00 0.00 4.63
2204 5514 4.001652 CTCCCTCCGTTTCTTTTTACTCC 58.998 47.826 0.00 0.00 0.00 3.85
2205 5515 4.639334 ACTCCCTCCGTTTCTTTTTACTC 58.361 43.478 0.00 0.00 0.00 2.59
2206 5516 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
2207 5517 7.254692 GCATATACTCCCTCCGTTTCTTTTTAC 60.255 40.741 0.00 0.00 0.00 2.01
2208 5518 6.764560 GCATATACTCCCTCCGTTTCTTTTTA 59.235 38.462 0.00 0.00 0.00 1.52
2209 5519 5.589050 GCATATACTCCCTCCGTTTCTTTTT 59.411 40.000 0.00 0.00 0.00 1.94
2210 5520 5.123936 GCATATACTCCCTCCGTTTCTTTT 58.876 41.667 0.00 0.00 0.00 2.27
2211 5521 4.163458 TGCATATACTCCCTCCGTTTCTTT 59.837 41.667 0.00 0.00 0.00 2.52
2212 5522 3.709653 TGCATATACTCCCTCCGTTTCTT 59.290 43.478 0.00 0.00 0.00 2.52
2213 5523 3.305720 TGCATATACTCCCTCCGTTTCT 58.694 45.455 0.00 0.00 0.00 2.52
2214 5524 3.746045 TGCATATACTCCCTCCGTTTC 57.254 47.619 0.00 0.00 0.00 2.78
2215 5525 3.904339 AGATGCATATACTCCCTCCGTTT 59.096 43.478 0.00 0.00 0.00 3.60
2216 5526 3.259374 CAGATGCATATACTCCCTCCGTT 59.741 47.826 0.00 0.00 0.00 4.44
2217 5527 2.828520 CAGATGCATATACTCCCTCCGT 59.171 50.000 0.00 0.00 0.00 4.69
2218 5528 2.167281 CCAGATGCATATACTCCCTCCG 59.833 54.545 0.00 0.00 0.00 4.63
2219 5529 3.055530 CACCAGATGCATATACTCCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
2220 5530 3.055530 CCACCAGATGCATATACTCCCTC 60.056 52.174 0.00 0.00 0.00 4.30
2221 5531 2.909006 CCACCAGATGCATATACTCCCT 59.091 50.000 0.00 0.00 0.00 4.20
2222 5532 2.616510 GCCACCAGATGCATATACTCCC 60.617 54.545 0.00 0.00 0.00 4.30
2223 5533 2.304180 AGCCACCAGATGCATATACTCC 59.696 50.000 0.00 0.00 0.00 3.85
2224 5534 3.692257 AGCCACCAGATGCATATACTC 57.308 47.619 0.00 0.00 0.00 2.59
2225 5535 3.392285 TGAAGCCACCAGATGCATATACT 59.608 43.478 0.00 0.00 0.00 2.12
2255 5565 9.793259 AAGGTGTTACTTCATTCTATCAAAAGA 57.207 29.630 0.00 0.00 0.00 2.52
2262 5572 8.079211 TGCTCTAAGGTGTTACTTCATTCTAT 57.921 34.615 0.00 0.00 32.02 1.98
2263 5573 7.476540 TGCTCTAAGGTGTTACTTCATTCTA 57.523 36.000 0.00 0.00 32.02 2.10
2265 5575 8.894768 ATATGCTCTAAGGTGTTACTTCATTC 57.105 34.615 0.00 0.00 32.02 2.67
2272 5678 6.862090 CGGTTAGATATGCTCTAAGGTGTTAC 59.138 42.308 0.00 0.00 45.07 2.50
2347 5753 2.754254 GGATCCGGTTTGGTGCCC 60.754 66.667 0.00 0.00 39.52 5.36
2351 5757 0.756903 CGATAGGGATCCGGTTTGGT 59.243 55.000 5.45 0.00 39.52 3.67
2358 5764 2.100197 TCTTATGGCGATAGGGATCCG 58.900 52.381 5.45 0.00 0.00 4.18
2375 5781 7.998964 TCTGGAGTAAAAATTGTCCTCTTTCTT 59.001 33.333 0.00 0.00 0.00 2.52
2378 5784 6.717084 CCTCTGGAGTAAAAATTGTCCTCTTT 59.283 38.462 0.00 0.00 0.00 2.52
2454 5891 1.213013 GAGATGACGCGACACAGGT 59.787 57.895 15.93 0.00 0.00 4.00
2459 5896 4.492160 GCCGGAGATGACGCGACA 62.492 66.667 15.93 15.16 0.00 4.35
2461 5898 3.076258 AATGCCGGAGATGACGCGA 62.076 57.895 15.93 0.00 0.00 5.87
2463 5900 3.017323 CAATGCCGGAGATGACGC 58.983 61.111 5.05 0.00 0.00 5.19
2464 5901 1.091771 AAGCAATGCCGGAGATGACG 61.092 55.000 5.05 0.00 0.00 4.35
2472 5909 4.834892 CGCCGAAAGCAATGCCGG 62.835 66.667 15.33 15.33 44.04 6.13
2491 5928 2.985847 GGCAGAGGTGTTGGGTGC 60.986 66.667 0.00 0.00 0.00 5.01
2547 5984 3.406682 GGACGACAACGACCGTATT 57.593 52.632 0.00 0.00 43.02 1.89
2557 5994 1.100510 CTCGATACAGGGGACGACAA 58.899 55.000 0.00 0.00 0.00 3.18
2560 5997 0.818445 GAGCTCGATACAGGGGACGA 60.818 60.000 0.00 0.00 0.00 4.20
2562 5999 2.273538 TAGAGCTCGATACAGGGGAC 57.726 55.000 8.37 0.00 0.00 4.46
2565 6002 3.013921 GAGGATAGAGCTCGATACAGGG 58.986 54.545 19.86 0.00 0.00 4.45
2568 6005 2.077627 GCGAGGATAGAGCTCGATACA 58.922 52.381 19.86 0.15 42.46 2.29
2576 6013 4.708968 CGGCGGCGAGGATAGAGC 62.709 72.222 29.19 0.00 0.00 4.09
2604 6041 0.459759 GTCCTTCCAACGACGGGATC 60.460 60.000 0.00 0.00 33.63 3.36
2610 6047 2.741211 GCCCGTCCTTCCAACGAC 60.741 66.667 0.00 0.00 42.62 4.34
2624 6061 2.511403 GGGAAGAAGATCCGGCCC 59.489 66.667 0.00 0.00 40.62 5.80
2626 6063 2.511403 GGGGGAAGAAGATCCGGC 59.489 66.667 0.00 0.00 40.62 6.13
2657 6094 1.002366 CTTCGAGATGGCGGAAAGTG 58.998 55.000 0.00 0.00 0.00 3.16
2664 6101 2.587194 CAGGGCTTCGAGATGGCG 60.587 66.667 6.49 0.00 32.83 5.69
2691 6128 0.595310 GAGCCGATGTCGAAGCTACC 60.595 60.000 3.62 0.00 43.02 3.18
2701 6138 1.750399 GGCCATGTTGAGCCGATGT 60.750 57.895 0.00 0.00 39.87 3.06
2720 6157 4.736896 GAGGTGTCACGGCCCGTC 62.737 72.222 5.41 0.00 38.32 4.79
2723 6160 3.626924 ACAGAGGTGTCACGGCCC 61.627 66.667 0.00 0.00 26.76 5.80


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

AutoCloner maintained by Alex Coulton.