Multiple sequence alignment - TraesCS3D01G491400

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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 TraesCS3D01G491400 chr3D 100.000 3726 0 0 1 3726 585083630 585087355 0.000000e+00 6881.0
1 TraesCS3D01G491400 chr7D 97.497 1838 43 2 1260 3094 15782539 15780702 0.000000e+00 3136.0
2 TraesCS3D01G491400 chr7D 99.288 562 2 1 3167 3726 13613213 13612652 0.000000e+00 1014.0
3 TraesCS3D01G491400 chr7D 84.221 507 54 14 3167 3662 13661704 13661213 1.570000e-128 470.0
4 TraesCS3D01G491400 chr7D 80.069 291 27 16 2832 3094 15860639 15860926 1.770000e-43 187.0
5 TraesCS3D01G491400 chr7A 95.282 1950 74 14 1151 3094 56153920 56151983 0.000000e+00 3075.0
6 TraesCS3D01G491400 chr7A 94.425 1955 87 7 1146 3094 5200296 5202234 0.000000e+00 2987.0
7 TraesCS3D01G491400 chr7A 95.513 1471 57 7 1145 2607 5194466 5195935 0.000000e+00 2342.0
8 TraesCS3D01G491400 chr7A 92.055 579 34 7 2222 2795 14795807 14796378 0.000000e+00 804.0
9 TraesCS3D01G491400 chr7A 90.016 621 44 11 1145 1759 5222563 5223171 0.000000e+00 787.0
10 TraesCS3D01G491400 chr7A 93.186 499 28 2 3167 3663 13103796 13103302 0.000000e+00 728.0
11 TraesCS3D01G491400 chr7A 90.991 222 20 0 2734 2955 56117842 56117621 2.180000e-77 300.0
12 TraesCS3D01G491400 chr7A 81.203 399 33 15 2717 3078 5099484 5099091 2.190000e-72 283.0
13 TraesCS3D01G491400 chr7A 89.865 148 11 2 2951 3094 14796521 14796668 1.770000e-43 187.0
14 TraesCS3D01G491400 chr7A 94.958 119 6 0 2952 3070 56117594 56117476 1.770000e-43 187.0
15 TraesCS3D01G491400 chr7A 80.488 246 37 7 3167 3402 13116270 13116026 1.060000e-40 178.0
16 TraesCS3D01G491400 chr7A 76.871 294 38 24 87 370 5191405 5191678 5.020000e-29 139.0
17 TraesCS3D01G491400 chr7A 76.949 295 37 19 87 370 5193045 5193319 5.020000e-29 139.0
18 TraesCS3D01G491400 chr7A 88.430 121 7 4 2829 2949 14796376 14796489 5.020000e-29 139.0
19 TraesCS3D01G491400 chr7A 76.510 298 42 20 87 370 5189751 5190034 1.800000e-28 137.0
20 TraesCS3D01G491400 chr7A 94.595 74 4 0 3653 3726 82195722 82195649 8.460000e-22 115.0
21 TraesCS3D01G491400 chr7A 79.275 193 14 16 303 471 5221396 5221586 1.090000e-20 111.0
22 TraesCS3D01G491400 chr7A 90.698 86 4 4 303 385 5225443 5225527 1.090000e-20 111.0
23 TraesCS3D01G491400 chr4A 94.342 1944 90 10 1160 3094 719178162 719180094 0.000000e+00 2963.0
24 TraesCS3D01G491400 chr4A 95.126 595 29 0 2041 2635 719204667 719205261 0.000000e+00 939.0
25 TraesCS3D01G491400 chr4A 94.348 460 23 2 2627 3083 719205742 719206201 0.000000e+00 702.0
26 TraesCS3D01G491400 chr4A 91.079 482 36 3 3167 3646 722902406 722902882 0.000000e+00 645.0
27 TraesCS3D01G491400 chr4A 92.079 202 14 1 3447 3646 722884808 722885009 2.190000e-72 283.0
28 TraesCS3D01G491400 chr4A 82.520 246 32 7 3167 3402 722884480 722884724 4.880000e-49 206.0
29 TraesCS3D01G491400 chr4A 79.321 324 29 12 2792 3078 719094113 719093791 3.800000e-45 193.0
30 TraesCS3D01G491400 chr4A 92.958 71 3 2 212 280 719176954 719177024 6.580000e-18 102.0
31 TraesCS3D01G491400 chr3A 90.601 1713 116 21 1260 2942 725267974 725266277 0.000000e+00 2230.0
32 TraesCS3D01G491400 chr3B 94.014 1470 88 0 1272 2741 798166033 798164564 0.000000e+00 2228.0
33 TraesCS3D01G491400 chr3B 92.593 54 4 0 591 644 742324486 742324539 1.110000e-10 78.7
34 TraesCS3D01G491400 chrUn 87.638 995 96 7 1429 2408 51176104 51175122 0.000000e+00 1131.0
35 TraesCS3D01G491400 chr1A 86.207 232 26 6 1147 1377 420433565 420433791 2.870000e-61 246.0
36 TraesCS3D01G491400 chr6A 85.345 232 28 6 1147 1377 5159866 5160092 6.220000e-58 235.0
37 TraesCS3D01G491400 chr2A 82.967 182 25 6 1147 1327 656321369 656321545 3.850000e-35 159.0
38 TraesCS3D01G491400 chr4D 94.667 75 4 0 3652 3726 72678784 72678710 2.350000e-22 117.0
39 TraesCS3D01G491400 chr2D 97.015 67 2 0 3660 3726 360308232 360308298 3.040000e-21 113.0
40 TraesCS3D01G491400 chr7B 92.308 78 6 0 3649 3726 413721528 413721605 1.090000e-20 111.0
41 TraesCS3D01G491400 chr7B 92.308 78 3 2 3652 3726 607319048 607319125 1.420000e-19 108.0
42 TraesCS3D01G491400 chr7B 90.909 77 7 0 3650 3726 744290676 744290752 1.830000e-18 104.0
43 TraesCS3D01G491400 chr5D 93.333 75 5 0 3652 3726 338652420 338652494 1.090000e-20 111.0
44 TraesCS3D01G491400 chr5D 92.105 76 6 0 3651 3726 513514671 513514596 1.420000e-19 108.0
45 TraesCS3D01G491400 chr4B 98.000 50 1 0 3343 3392 660137778 660137827 1.840000e-13 87.9
46 TraesCS3D01G491400 chr2B 90.164 61 6 0 584 644 46976164 46976224 3.080000e-11 80.5
47 TraesCS3D01G491400 chr2B 90.566 53 5 0 589 641 340340337 340340285 1.860000e-08 71.3


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 TraesCS3D01G491400 chr3D 585083630 585087355 3725 False 6881.000000 6881 100.000000 1 3726 1 chr3D.!!$F1 3725
1 TraesCS3D01G491400 chr7D 15780702 15782539 1837 True 3136.000000 3136 97.497000 1260 3094 1 chr7D.!!$R3 1834
2 TraesCS3D01G491400 chr7D 13612652 13613213 561 True 1014.000000 1014 99.288000 3167 3726 1 chr7D.!!$R1 559
3 TraesCS3D01G491400 chr7A 56151983 56153920 1937 True 3075.000000 3075 95.282000 1151 3094 1 chr7A.!!$R4 1943
4 TraesCS3D01G491400 chr7A 5200296 5202234 1938 False 2987.000000 2987 94.425000 1146 3094 1 chr7A.!!$F1 1948
5 TraesCS3D01G491400 chr7A 5189751 5195935 6184 False 689.250000 2342 81.460750 87 2607 4 chr7A.!!$F2 2520
6 TraesCS3D01G491400 chr7A 14795807 14796668 861 False 376.666667 804 90.116667 2222 3094 3 chr7A.!!$F4 872
7 TraesCS3D01G491400 chr7A 5221396 5225527 4131 False 336.333333 787 86.663000 303 1759 3 chr7A.!!$F3 1456
8 TraesCS3D01G491400 chr4A 719176954 719180094 3140 False 1532.500000 2963 93.650000 212 3094 2 chr4A.!!$F2 2882
9 TraesCS3D01G491400 chr4A 719204667 719206201 1534 False 820.500000 939 94.737000 2041 3083 2 chr4A.!!$F3 1042
10 TraesCS3D01G491400 chr4A 722884480 722885009 529 False 244.500000 283 87.299500 3167 3646 2 chr4A.!!$F4 479
11 TraesCS3D01G491400 chr3A 725266277 725267974 1697 True 2230.000000 2230 90.601000 1260 2942 1 chr3A.!!$R1 1682
12 TraesCS3D01G491400 chr3B 798164564 798166033 1469 True 2228.000000 2228 94.014000 1272 2741 1 chr3B.!!$R1 1469
13 TraesCS3D01G491400 chrUn 51175122 51176104 982 True 1131.000000 1131 87.638000 1429 2408 1 chrUn.!!$R1 979

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
798 4212 0.034863 GTAGTCGAATTTGGCCCCCA 60.035 55.0 0.0 0.0 0.0 4.96 F
1051 4487 0.040058 TGCTGGATGGTGATTGCCTT 59.960 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 6000 1.052124 TCACCCTTGTTCCACTCGGT 61.052 55.000 0.0 0.0 0.00 4.69 R
2936 7761 2.041485 TCAGAATGGCAATGTCTTCCCA 59.959 45.455 0.0 0.0 36.16 4.37 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 0.549469 AGACCTTTTTGGGGTGACGT 59.451 50.000 0.00 0.00 41.11 4.34
22 23 0.466739 ACCTTTTTGGGGTGACGTCC 60.467 55.000 14.12 4.20 41.11 4.79
23 24 0.179001 CCTTTTTGGGGTGACGTCCT 60.179 55.000 14.12 0.00 0.00 3.85
24 25 0.951558 CTTTTTGGGGTGACGTCCTG 59.048 55.000 14.12 0.00 0.00 3.86
25 26 1.104577 TTTTTGGGGTGACGTCCTGC 61.105 55.000 14.12 3.15 0.00 4.85
28 29 3.311110 GGGGTGACGTCCTGCTGA 61.311 66.667 14.12 0.00 0.00 4.26
31 32 2.433318 GTGACGTCCTGCTGAGGC 60.433 66.667 14.12 0.00 39.57 4.70
41 42 2.187424 GCTGAGGCAGAGCAGAGG 59.813 66.667 0.00 0.00 36.40 3.69
46 47 2.438075 GGCAGAGCAGAGGCCAAG 60.438 66.667 5.01 0.00 46.92 3.61
47 48 2.350514 GCAGAGCAGAGGCCAAGT 59.649 61.111 5.01 0.00 42.56 3.16
48 49 1.744741 GCAGAGCAGAGGCCAAGTC 60.745 63.158 5.01 0.00 42.56 3.01
49 50 1.447489 CAGAGCAGAGGCCAAGTCG 60.447 63.158 5.01 0.00 42.56 4.18
50 51 2.125350 GAGCAGAGGCCAAGTCGG 60.125 66.667 5.01 0.00 42.56 4.79
51 52 2.604686 AGCAGAGGCCAAGTCGGA 60.605 61.111 5.01 0.00 42.56 4.55
58 59 3.998672 GCCAAGTCGGACCCGTGA 61.999 66.667 8.42 0.00 40.74 4.35
61 62 2.915659 AAGTCGGACCCGTGAGCA 60.916 61.111 8.42 0.00 40.74 4.26
62 63 2.932234 AAGTCGGACCCGTGAGCAG 61.932 63.158 8.42 0.00 40.74 4.24
63 64 3.371063 GTCGGACCCGTGAGCAGA 61.371 66.667 8.42 0.00 40.74 4.26
64 65 3.062466 TCGGACCCGTGAGCAGAG 61.062 66.667 8.42 0.00 40.74 3.35
65 66 4.803426 CGGACCCGTGAGCAGAGC 62.803 72.222 0.00 0.00 34.35 4.09
66 67 4.803426 GGACCCGTGAGCAGAGCG 62.803 72.222 0.00 0.00 0.00 5.03
87 88 3.715097 GGCACAGGCTGCTCCTCT 61.715 66.667 15.89 0.00 45.52 3.69
88 89 2.350514 GCACAGGCTGCTCCTCTT 59.649 61.111 15.89 0.00 45.52 2.85
89 90 1.303155 GCACAGGCTGCTCCTCTTT 60.303 57.895 15.89 0.00 45.52 2.52
90 91 1.584380 GCACAGGCTGCTCCTCTTTG 61.584 60.000 15.89 3.63 45.52 2.77
91 92 0.250640 CACAGGCTGCTCCTCTTTGT 60.251 55.000 15.89 0.00 45.52 2.83
107 1676 3.138283 TCTTTGTTTCCCACTCACCAGAT 59.862 43.478 0.00 0.00 0.00 2.90
109 1678 1.774254 TGTTTCCCACTCACCAGATGT 59.226 47.619 0.00 0.00 0.00 3.06
118 1687 4.760047 ACCAGATGTCGCGTGGGC 62.760 66.667 16.05 1.17 35.48 5.36
132 1701 3.319198 GGGCCAGGGTTGACGAGA 61.319 66.667 4.39 0.00 0.00 4.04
133 1702 2.266055 GGCCAGGGTTGACGAGAG 59.734 66.667 0.00 0.00 0.00 3.20
134 1703 2.283529 GGCCAGGGTTGACGAGAGA 61.284 63.158 0.00 0.00 0.00 3.10
135 1704 1.079750 GCCAGGGTTGACGAGAGAC 60.080 63.158 0.00 0.00 0.00 3.36
136 1705 1.592223 CCAGGGTTGACGAGAGACC 59.408 63.158 0.00 0.00 0.00 3.85
137 1706 1.213013 CAGGGTTGACGAGAGACCG 59.787 63.158 0.00 0.00 34.22 4.79
138 1707 1.977544 AGGGTTGACGAGAGACCGG 60.978 63.158 0.00 0.00 34.22 5.28
139 1708 2.572284 GGTTGACGAGAGACCGGG 59.428 66.667 6.32 0.00 0.00 5.73
140 1709 2.126031 GTTGACGAGAGACCGGGC 60.126 66.667 6.32 0.52 0.00 6.13
158 1727 4.415150 CCCAGCCGTCAGCCACAT 62.415 66.667 0.00 0.00 45.47 3.21
159 1728 2.821366 CCAGCCGTCAGCCACATC 60.821 66.667 0.00 0.00 45.47 3.06
160 1729 2.821366 CAGCCGTCAGCCACATCC 60.821 66.667 0.00 0.00 45.47 3.51
161 1730 4.457496 AGCCGTCAGCCACATCCG 62.457 66.667 0.00 0.00 45.47 4.18
162 1731 4.760047 GCCGTCAGCCACATCCGT 62.760 66.667 0.00 0.00 34.35 4.69
165 1734 2.509336 GTCAGCCACATCCGTCCG 60.509 66.667 0.00 0.00 0.00 4.79
166 1735 3.770040 TCAGCCACATCCGTCCGG 61.770 66.667 0.00 0.00 0.00 5.14
198 1767 4.344865 CCTCCACCAACCCACCCG 62.345 72.222 0.00 0.00 0.00 5.28
278 1849 3.116531 CGACGAAAGAACGGGGGC 61.117 66.667 0.00 0.00 37.61 5.80
280 1851 4.692475 ACGAAAGAACGGGGGCGG 62.692 66.667 0.00 0.00 37.61 6.13
282 1853 4.717313 GAAAGAACGGGGGCGGCT 62.717 66.667 9.56 0.00 0.00 5.52
284 1855 2.604299 GAAAGAACGGGGGCGGCTAT 62.604 60.000 9.56 0.00 0.00 2.97
285 1856 2.604299 AAAGAACGGGGGCGGCTATC 62.604 60.000 9.56 0.47 0.00 2.08
286 1857 3.547513 GAACGGGGGCGGCTATCT 61.548 66.667 9.56 0.00 0.00 1.98
296 1873 2.027751 GGCTATCTCCACGGACGC 59.972 66.667 0.00 0.00 0.00 5.19
372 1974 4.178214 CCGCATCGCACCGCAATT 62.178 61.111 0.00 0.00 0.00 2.32
376 1978 1.796151 CATCGCACCGCAATTGTCT 59.204 52.632 7.40 0.00 0.00 3.41
378 1980 0.447801 ATCGCACCGCAATTGTCTTC 59.552 50.000 7.40 0.00 0.00 2.87
381 1983 0.598065 GCACCGCAATTGTCTTCCTT 59.402 50.000 7.40 0.00 0.00 3.36
389 1991 2.656560 ATTGTCTTCCTTCCTCGACG 57.343 50.000 0.00 0.00 0.00 5.12
390 1992 0.601558 TTGTCTTCCTTCCTCGACGG 59.398 55.000 0.00 0.00 0.00 4.79
391 1993 0.251033 TGTCTTCCTTCCTCGACGGA 60.251 55.000 0.00 0.11 41.06 4.69
396 1998 2.504244 CTTCCTCGACGGACGCAC 60.504 66.667 3.44 0.00 42.97 5.34
397 1999 4.394078 TTCCTCGACGGACGCACG 62.394 66.667 3.44 5.77 42.97 5.34
408 2016 4.724602 ACGCACGCACGCAGATCT 62.725 61.111 0.00 0.00 36.19 2.75
429 2050 4.335647 CCAAGGCAGGCAGGTCGT 62.336 66.667 0.00 0.00 0.00 4.34
430 2051 2.743928 CAAGGCAGGCAGGTCGTC 60.744 66.667 0.00 0.00 0.00 4.20
431 2052 2.925170 AAGGCAGGCAGGTCGTCT 60.925 61.111 0.00 0.00 0.00 4.18
432 2053 2.948720 AAGGCAGGCAGGTCGTCTC 61.949 63.158 0.00 0.00 0.00 3.36
433 2054 3.386237 GGCAGGCAGGTCGTCTCT 61.386 66.667 0.00 0.00 0.00 3.10
434 2055 2.183046 GCAGGCAGGTCGTCTCTC 59.817 66.667 0.00 0.00 0.00 3.20
443 2073 2.617538 TCGTCTCTCCCCCTCCCT 60.618 66.667 0.00 0.00 0.00 4.20
445 2075 2.695970 CGTCTCTCCCCCTCCCTCT 61.696 68.421 0.00 0.00 0.00 3.69
449 2079 4.179599 CTCCCCCTCCCTCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
465 2095 3.234730 CCCCCGAATCTCCTCCCG 61.235 72.222 0.00 0.00 0.00 5.14
578 3908 2.421619 GCAGGCAGTGGCTAGATATTC 58.578 52.381 20.14 0.00 40.87 1.75
579 3909 2.038295 GCAGGCAGTGGCTAGATATTCT 59.962 50.000 20.14 0.00 40.87 2.40
580 3910 3.259374 GCAGGCAGTGGCTAGATATTCTA 59.741 47.826 20.14 0.00 40.87 2.10
581 3911 4.081198 GCAGGCAGTGGCTAGATATTCTAT 60.081 45.833 20.14 0.00 40.87 1.98
582 3912 5.570439 GCAGGCAGTGGCTAGATATTCTATT 60.570 44.000 20.14 0.00 40.87 1.73
583 3913 6.105333 CAGGCAGTGGCTAGATATTCTATTC 58.895 44.000 20.14 0.00 40.87 1.75
584 3914 6.022315 AGGCAGTGGCTAGATATTCTATTCT 58.978 40.000 19.12 0.00 40.87 2.40
585 3915 7.123397 CAGGCAGTGGCTAGATATTCTATTCTA 59.877 40.741 20.14 0.00 40.87 2.10
586 3916 7.123547 AGGCAGTGGCTAGATATTCTATTCTAC 59.876 40.741 19.12 0.00 40.87 2.59
589 3919 8.465999 CAGTGGCTAGATATTCTATTCTACCTG 58.534 40.741 0.00 0.00 0.00 4.00
592 3922 6.183360 GGCTAGATATTCTATTCTACCTGGGC 60.183 46.154 0.00 0.00 0.00 5.36
618 3957 2.187946 CGCCGGATTTCCTGCTCT 59.812 61.111 5.05 0.00 43.05 4.09
619 3958 1.884926 CGCCGGATTTCCTGCTCTC 60.885 63.158 5.05 0.00 43.05 3.20
623 3962 1.147153 GGATTTCCTGCTCTCCGGG 59.853 63.158 0.00 0.00 41.74 5.73
624 3963 1.524849 GATTTCCTGCTCTCCGGGC 60.525 63.158 0.00 0.00 40.05 6.13
645 3984 2.898840 CGCTGCGCATTCCCAGAT 60.899 61.111 12.24 0.00 0.00 2.90
661 4000 3.246301 CCAGATAGTCAGATCCATGGGT 58.754 50.000 13.02 3.70 0.00 4.51
666 4005 1.308128 TCAGATCCATGGGTGGGCT 60.308 57.895 13.02 0.00 46.06 5.19
677 4016 4.284550 GTGGGCTGGGGCTTGTGA 62.285 66.667 0.00 0.00 38.73 3.58
678 4017 3.506743 TGGGCTGGGGCTTGTGAA 61.507 61.111 0.00 0.00 38.73 3.18
699 4077 1.437986 GAGGGCGCGATAGTTGACT 59.562 57.895 12.10 0.00 39.35 3.41
700 4078 0.595310 GAGGGCGCGATAGTTGACTC 60.595 60.000 12.10 0.51 39.35 3.36
702 4080 1.146358 GGGCGCGATAGTTGACTCAC 61.146 60.000 12.10 0.00 39.35 3.51
707 4085 3.039405 CGCGATAGTTGACTCACTCATC 58.961 50.000 0.00 0.00 39.35 2.92
708 4086 3.487544 CGCGATAGTTGACTCACTCATCA 60.488 47.826 0.00 0.00 39.35 3.07
709 4087 4.615949 GCGATAGTTGACTCACTCATCAT 58.384 43.478 0.00 0.00 39.35 2.45
710 4088 4.443725 GCGATAGTTGACTCACTCATCATG 59.556 45.833 0.00 0.00 39.35 3.07
711 4089 4.443725 CGATAGTTGACTCACTCATCATGC 59.556 45.833 0.00 0.00 0.00 4.06
712 4090 2.983229 AGTTGACTCACTCATCATGCC 58.017 47.619 0.00 0.00 0.00 4.40
713 4091 2.303890 AGTTGACTCACTCATCATGCCA 59.696 45.455 0.00 0.00 0.00 4.92
714 4092 3.054582 AGTTGACTCACTCATCATGCCAT 60.055 43.478 0.00 0.00 0.00 4.40
715 4093 2.914059 TGACTCACTCATCATGCCATG 58.086 47.619 0.00 0.00 0.00 3.66
716 4094 1.602851 GACTCACTCATCATGCCATGC 59.397 52.381 0.00 0.00 0.00 4.06
718 4096 0.256464 TCACTCATCATGCCATGCCA 59.744 50.000 0.00 0.00 0.00 4.92
720 4098 0.754217 ACTCATCATGCCATGCCACC 60.754 55.000 0.00 0.00 0.00 4.61
721 4099 1.792118 CTCATCATGCCATGCCACCG 61.792 60.000 0.00 0.00 0.00 4.94
722 4100 1.824760 CATCATGCCATGCCACCGA 60.825 57.895 0.00 0.00 0.00 4.69
741 4155 4.189188 CGACTACTGGACGGGCCG 62.189 72.222 27.06 27.06 40.66 6.13
753 4167 4.506255 GGGCCGGCCAAGCTACAT 62.506 66.667 44.46 0.00 37.98 2.29
754 4168 2.508928 GGCCGGCCAAGCTACATA 59.491 61.111 40.73 0.00 35.81 2.29
755 4169 1.073199 GGCCGGCCAAGCTACATAT 59.927 57.895 40.73 0.00 35.81 1.78
756 4170 0.323629 GGCCGGCCAAGCTACATATA 59.676 55.000 40.73 0.00 35.81 0.86
757 4171 1.439679 GCCGGCCAAGCTACATATAC 58.560 55.000 18.11 0.00 0.00 1.47
758 4172 1.002087 GCCGGCCAAGCTACATATACT 59.998 52.381 18.11 0.00 0.00 2.12
759 4173 2.232941 GCCGGCCAAGCTACATATACTA 59.767 50.000 18.11 0.00 0.00 1.82
760 4174 3.676324 GCCGGCCAAGCTACATATACTAG 60.676 52.174 18.11 0.00 0.00 2.57
761 4175 3.762288 CCGGCCAAGCTACATATACTAGA 59.238 47.826 2.24 0.00 0.00 2.43
762 4176 4.402793 CCGGCCAAGCTACATATACTAGAT 59.597 45.833 2.24 0.00 0.00 1.98
763 4177 5.105310 CCGGCCAAGCTACATATACTAGATT 60.105 44.000 2.24 0.00 0.00 2.40
764 4178 6.096423 CCGGCCAAGCTACATATACTAGATTA 59.904 42.308 2.24 0.00 0.00 1.75
765 4179 7.201920 CCGGCCAAGCTACATATACTAGATTAT 60.202 40.741 2.24 0.00 0.00 1.28
766 4180 8.847196 CGGCCAAGCTACATATACTAGATTATA 58.153 37.037 2.24 0.00 0.00 0.98
775 4189 7.942990 ACATATACTAGATTATAGAAGCGGCC 58.057 38.462 0.00 0.00 0.00 6.13
777 4191 4.522722 ACTAGATTATAGAAGCGGCCAC 57.477 45.455 2.24 0.00 0.00 5.01
790 4204 0.738412 CGGCCACGGTAGTCGAATTT 60.738 55.000 2.24 0.00 42.43 1.82
792 4206 0.725117 GCCACGGTAGTCGAATTTGG 59.275 55.000 0.00 0.00 42.43 3.28
795 4209 0.392060 ACGGTAGTCGAATTTGGCCC 60.392 55.000 0.00 0.00 42.43 5.80
798 4212 0.034863 GTAGTCGAATTTGGCCCCCA 60.035 55.000 0.00 0.00 0.00 4.96
801 4215 0.898326 GTCGAATTTGGCCCCCAAGT 60.898 55.000 0.00 0.00 44.84 3.16
830 4244 2.447244 GGCTGATCCGATTCGATTCT 57.553 50.000 7.83 0.00 0.00 2.40
831 4245 2.760374 GGCTGATCCGATTCGATTCTT 58.240 47.619 7.83 0.00 0.00 2.52
837 4251 0.529773 CCGATTCGATTCTTGCCGGA 60.530 55.000 5.05 0.00 37.87 5.14
838 4252 0.577269 CGATTCGATTCTTGCCGGAC 59.423 55.000 5.05 0.00 0.00 4.79
839 4253 1.802880 CGATTCGATTCTTGCCGGACT 60.803 52.381 5.05 0.00 0.00 3.85
842 4256 0.108804 TCGATTCTTGCCGGACTGAC 60.109 55.000 5.05 0.00 0.00 3.51
843 4257 0.389817 CGATTCTTGCCGGACTGACA 60.390 55.000 5.05 0.00 0.00 3.58
844 4258 1.079503 GATTCTTGCCGGACTGACAC 58.920 55.000 5.05 0.00 0.00 3.67
846 4260 0.531974 TTCTTGCCGGACTGACACAC 60.532 55.000 5.05 0.00 0.00 3.82
847 4261 1.227527 CTTGCCGGACTGACACACA 60.228 57.895 5.05 0.00 0.00 3.72
855 4269 2.633657 CTGACACACAGCCAACGC 59.366 61.111 0.00 0.00 39.86 4.84
856 4270 2.896801 CTGACACACAGCCAACGCC 61.897 63.158 0.00 0.00 39.86 5.68
858 4272 4.539083 ACACACAGCCAACGCCGA 62.539 61.111 0.00 0.00 34.57 5.54
859 4273 4.012895 CACACAGCCAACGCCGAC 62.013 66.667 0.00 0.00 34.57 4.79
866 4280 4.619227 CCAACGCCGACCACCTGT 62.619 66.667 0.00 0.00 0.00 4.00
868 4282 4.309950 AACGCCGACCACCTGTCC 62.310 66.667 0.00 0.00 41.18 4.02
870 4284 4.742201 CGCCGACCACCTGTCCTG 62.742 72.222 0.00 0.00 41.18 3.86
872 4286 4.742201 CCGACCACCTGTCCTGCG 62.742 72.222 0.00 0.00 41.18 5.18
874 4288 4.314440 GACCACCTGTCCTGCGCA 62.314 66.667 10.98 10.98 38.09 6.09
875 4289 4.320456 ACCACCTGTCCTGCGCAG 62.320 66.667 30.52 30.52 0.00 5.18
891 4305 2.659016 AGCTGCGCTTCTGCTGTA 59.341 55.556 9.73 0.00 46.37 2.74
892 4306 1.220206 AGCTGCGCTTCTGCTGTAT 59.780 52.632 9.73 0.00 46.37 2.29
893 4307 0.392193 AGCTGCGCTTCTGCTGTATT 60.392 50.000 9.73 0.00 46.37 1.89
894 4308 0.247974 GCTGCGCTTCTGCTGTATTG 60.248 55.000 9.73 0.00 36.79 1.90
895 4309 1.081892 CTGCGCTTCTGCTGTATTGT 58.918 50.000 9.73 0.00 36.97 2.71
896 4310 1.466167 CTGCGCTTCTGCTGTATTGTT 59.534 47.619 9.73 0.00 36.97 2.83
901 4315 4.024556 GCGCTTCTGCTGTATTGTTATCAT 60.025 41.667 0.00 0.00 36.97 2.45
903 4317 5.333645 CGCTTCTGCTGTATTGTTATCATCC 60.334 44.000 0.00 0.00 36.97 3.51
904 4318 5.762218 GCTTCTGCTGTATTGTTATCATCCT 59.238 40.000 0.00 0.00 36.03 3.24
909 4323 6.653020 TGCTGTATTGTTATCATCCTCTGTT 58.347 36.000 0.00 0.00 0.00 3.16
911 4325 7.066163 TGCTGTATTGTTATCATCCTCTGTTTG 59.934 37.037 0.00 0.00 0.00 2.93
913 4327 6.883756 TGTATTGTTATCATCCTCTGTTTGCA 59.116 34.615 0.00 0.00 0.00 4.08
922 4336 2.072298 CCTCTGTTTGCAGTGCTACTC 58.928 52.381 17.60 5.42 43.05 2.59
923 4337 1.723542 CTCTGTTTGCAGTGCTACTCG 59.276 52.381 17.60 9.75 43.05 4.18
924 4338 0.164647 CTGTTTGCAGTGCTACTCGC 59.835 55.000 17.60 1.57 37.92 5.03
943 4357 1.738700 GCAGCAGCTCTAGTCCAAGAC 60.739 57.143 0.00 0.00 37.91 3.01
958 4388 4.021925 GACGCAGGGTGGCCTCTT 62.022 66.667 3.32 0.00 0.00 2.85
960 4390 4.020617 CGCAGGGTGGCCTCTTCA 62.021 66.667 3.32 0.00 0.00 3.02
968 4398 2.708325 GGGTGGCCTCTTCATCTATCTT 59.292 50.000 3.32 0.00 0.00 2.40
991 4421 9.981114 TCTTCTTTTCTGTTTGTTTTTCTTTCT 57.019 25.926 0.00 0.00 0.00 2.52
1007 4437 9.878667 TTTTTCTTTCTATACATACATGGTCGA 57.121 29.630 0.00 0.00 0.00 4.20
1016 4446 2.602257 TACATGGTCGATGAAGCTGG 57.398 50.000 1.37 0.00 35.80 4.85
1039 4475 0.534427 CATGCCGTCTGATGCTGGAT 60.534 55.000 4.20 0.00 0.00 3.41
1041 4477 1.890979 GCCGTCTGATGCTGGATGG 60.891 63.158 0.00 0.00 40.51 3.51
1044 4480 0.176449 CGTCTGATGCTGGATGGTGA 59.824 55.000 0.00 0.00 0.00 4.02
1045 4481 1.202615 CGTCTGATGCTGGATGGTGAT 60.203 52.381 0.00 0.00 0.00 3.06
1050 4486 0.260816 ATGCTGGATGGTGATTGCCT 59.739 50.000 0.00 0.00 0.00 4.75
1051 4487 0.040058 TGCTGGATGGTGATTGCCTT 59.960 50.000 0.00 0.00 0.00 4.35
1053 4489 1.134907 GCTGGATGGTGATTGCCTTTG 60.135 52.381 0.00 0.00 0.00 2.77
1054 4490 2.173519 CTGGATGGTGATTGCCTTTGT 58.826 47.619 0.00 0.00 0.00 2.83
1055 4491 1.894466 TGGATGGTGATTGCCTTTGTG 59.106 47.619 0.00 0.00 0.00 3.33
1056 4492 1.895131 GGATGGTGATTGCCTTTGTGT 59.105 47.619 0.00 0.00 0.00 3.72
1057 4493 2.299867 GGATGGTGATTGCCTTTGTGTT 59.700 45.455 0.00 0.00 0.00 3.32
1058 4494 3.578688 GATGGTGATTGCCTTTGTGTTC 58.421 45.455 0.00 0.00 0.00 3.18
1059 4495 1.686052 TGGTGATTGCCTTTGTGTTCC 59.314 47.619 0.00 0.00 0.00 3.62
1063 4499 2.361757 TGATTGCCTTTGTGTTCCTGTG 59.638 45.455 0.00 0.00 0.00 3.66
1064 4500 0.459489 TTGCCTTTGTGTTCCTGTGC 59.541 50.000 0.00 0.00 0.00 4.57
1065 4501 0.682532 TGCCTTTGTGTTCCTGTGCA 60.683 50.000 0.00 0.00 0.00 4.57
1066 4502 0.675633 GCCTTTGTGTTCCTGTGCAT 59.324 50.000 0.00 0.00 0.00 3.96
1067 4503 1.603678 GCCTTTGTGTTCCTGTGCATG 60.604 52.381 0.00 0.00 0.00 4.06
1068 4504 1.682854 CCTTTGTGTTCCTGTGCATGT 59.317 47.619 0.00 0.00 0.00 3.21
1105 4549 2.035632 ACTATGGTCCTGAGCAGCTAC 58.964 52.381 0.00 0.00 42.52 3.58
1107 4551 1.341156 ATGGTCCTGAGCAGCTACCC 61.341 60.000 9.26 0.00 42.52 3.69
1108 4552 1.990060 GGTCCTGAGCAGCTACCCA 60.990 63.158 0.00 0.00 30.91 4.51
1129 4573 2.836981 AGCATAGGATAGGATCTGTGCC 59.163 50.000 8.11 0.00 45.24 5.01
1130 4574 2.836981 GCATAGGATAGGATCTGTGCCT 59.163 50.000 0.00 0.00 40.62 4.75
1131 4575 3.369261 GCATAGGATAGGATCTGTGCCTG 60.369 52.174 0.00 0.00 40.62 4.85
1132 4576 1.055040 AGGATAGGATCTGTGCCTGC 58.945 55.000 0.00 0.00 36.96 4.85
1133 4577 0.320247 GGATAGGATCTGTGCCTGCG 60.320 60.000 0.00 0.00 36.96 5.18
1134 4578 0.948141 GATAGGATCTGTGCCTGCGC 60.948 60.000 0.00 0.00 36.96 6.09
1135 4579 2.388890 ATAGGATCTGTGCCTGCGCC 62.389 60.000 4.18 0.00 36.96 6.53
1137 4581 3.200593 GATCTGTGCCTGCGCCTG 61.201 66.667 4.18 0.00 0.00 4.85
1139 4583 4.994471 TCTGTGCCTGCGCCTGTG 62.994 66.667 4.18 0.00 0.00 3.66
1148 4966 3.797546 GCGCCTGTGCTCTGCTTC 61.798 66.667 0.00 0.00 34.43 3.86
1155 4973 2.492012 CTGTGCTCTGCTTCTTCTTGT 58.508 47.619 0.00 0.00 0.00 3.16
1193 5187 8.534496 AGCATGATTATTTGTTCTTTAAAGGCT 58.466 29.630 15.13 7.54 0.00 4.58
1209 5203 4.771114 AAGGCTGGCTTTTAACCTTTTT 57.229 36.364 11.07 0.00 37.45 1.94
1269 5272 5.851720 TGTACATGACATTTTTGGTGCATT 58.148 33.333 0.00 0.00 31.20 3.56
1270 5273 5.925397 TGTACATGACATTTTTGGTGCATTC 59.075 36.000 0.00 0.00 31.20 2.67
1274 5278 4.630111 TGACATTTTTGGTGCATTCCTTC 58.370 39.130 0.00 0.00 0.00 3.46
1498 5502 0.674895 ACTCCATTCAGAAGCCACGC 60.675 55.000 0.00 0.00 0.00 5.34
1952 6000 0.466007 TGAGCTGCAGCAGGTTTTCA 60.466 50.000 38.24 27.93 42.53 2.69
2762 7565 1.450312 CCAAGAGACGGCCCATCAC 60.450 63.158 0.00 0.00 0.00 3.06
2844 7657 6.750501 GGAGGAACCGCTGTTTAATTTTTATC 59.249 38.462 0.00 0.00 33.97 1.75
2923 7748 4.780021 AGTCTCCACTACTTCCATGTGATT 59.220 41.667 0.00 0.00 33.95 2.57
2924 7749 4.872691 GTCTCCACTACTTCCATGTGATTG 59.127 45.833 0.00 0.00 33.95 2.67
2925 7750 4.777366 TCTCCACTACTTCCATGTGATTGA 59.223 41.667 0.00 0.00 33.95 2.57
2926 7751 5.426509 TCTCCACTACTTCCATGTGATTGAT 59.573 40.000 0.00 0.00 33.95 2.57
2927 7752 5.430886 TCCACTACTTCCATGTGATTGATG 58.569 41.667 0.00 0.00 33.95 3.07
2936 7761 3.359033 CATGTGATTGATGAACCCTGGT 58.641 45.455 0.00 0.00 0.00 4.00
3104 9239 7.538303 CAAAAATTTGTTGCACTTTAGTCCT 57.462 32.000 0.00 0.00 33.59 3.85
3105 9240 7.973601 CAAAAATTTGTTGCACTTTAGTCCTT 58.026 30.769 0.00 0.00 33.59 3.36
3106 9241 8.450180 CAAAAATTTGTTGCACTTTAGTCCTTT 58.550 29.630 0.00 0.00 33.59 3.11
3107 9242 8.560355 AAAATTTGTTGCACTTTAGTCCTTTT 57.440 26.923 0.00 0.00 0.00 2.27
3108 9243 8.560355 AAATTTGTTGCACTTTAGTCCTTTTT 57.440 26.923 0.00 0.00 0.00 1.94
3140 9275 7.538303 CAAAAATTTGTTGCACTTTAGTCCT 57.462 32.000 0.00 0.00 33.59 3.85
3141 9276 7.973601 CAAAAATTTGTTGCACTTTAGTCCTT 58.026 30.769 0.00 0.00 33.59 3.36
3142 9277 8.450180 CAAAAATTTGTTGCACTTTAGTCCTTT 58.550 29.630 0.00 0.00 33.59 3.11
3143 9278 8.560355 AAAATTTGTTGCACTTTAGTCCTTTT 57.440 26.923 0.00 0.00 0.00 2.27
3144 9279 8.560355 AAATTTGTTGCACTTTAGTCCTTTTT 57.440 26.923 0.00 0.00 0.00 1.94
3165 9300 6.448207 TTTTGTTGTGTCATGATTCTCACA 57.552 33.333 11.64 11.64 38.71 3.58
3300 9444 3.773119 ACCGTATATTGAAGGACAGGTGT 59.227 43.478 0.00 0.00 0.00 4.16
3493 9676 2.559668 ACCAGGATGCAGTTTCAACATG 59.440 45.455 0.00 0.00 31.97 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.235724 CGTCACCCCAAAAAGGTCTC 58.764 55.000 0.00 0.00 34.56 3.36
1 2 0.549469 ACGTCACCCCAAAAAGGTCT 59.451 50.000 0.00 0.00 34.56 3.85
2 3 0.949397 GACGTCACCCCAAAAAGGTC 59.051 55.000 11.55 0.00 34.56 3.85
3 4 0.466739 GGACGTCACCCCAAAAAGGT 60.467 55.000 18.91 0.00 38.48 3.50
4 5 0.179001 AGGACGTCACCCCAAAAAGG 60.179 55.000 18.91 0.00 37.03 3.11
5 6 0.951558 CAGGACGTCACCCCAAAAAG 59.048 55.000 18.91 0.00 0.00 2.27
8 9 2.112297 GCAGGACGTCACCCCAAA 59.888 61.111 18.91 0.00 0.00 3.28
9 10 2.847234 AGCAGGACGTCACCCCAA 60.847 61.111 18.91 0.00 0.00 4.12
10 11 3.625897 CAGCAGGACGTCACCCCA 61.626 66.667 18.91 0.00 0.00 4.96
11 12 3.302347 CTCAGCAGGACGTCACCCC 62.302 68.421 18.91 0.00 0.00 4.95
12 13 2.262915 CTCAGCAGGACGTCACCC 59.737 66.667 18.91 0.00 0.00 4.61
13 14 2.262915 CCTCAGCAGGACGTCACC 59.737 66.667 18.91 0.62 43.65 4.02
14 15 2.433318 GCCTCAGCAGGACGTCAC 60.433 66.667 18.91 6.91 43.65 3.67
15 16 2.917227 TGCCTCAGCAGGACGTCA 60.917 61.111 18.91 0.00 46.52 4.35
24 25 2.187424 CCTCTGCTCTGCCTCAGC 59.813 66.667 0.00 0.00 40.48 4.26
25 26 2.187424 GCCTCTGCTCTGCCTCAG 59.813 66.667 0.00 0.00 33.53 3.35
28 29 2.932194 TTGGCCTCTGCTCTGCCT 60.932 61.111 3.32 0.00 45.56 4.75
31 32 1.447489 CGACTTGGCCTCTGCTCTG 60.447 63.158 3.32 0.00 37.74 3.35
32 33 2.654079 CCGACTTGGCCTCTGCTCT 61.654 63.158 3.32 0.00 37.74 4.09
33 34 2.125350 CCGACTTGGCCTCTGCTC 60.125 66.667 3.32 0.00 37.74 4.26
37 38 3.003763 GGGTCCGACTTGGCCTCT 61.004 66.667 3.32 0.00 37.80 3.69
38 39 4.452733 CGGGTCCGACTTGGCCTC 62.453 72.222 3.32 0.00 42.83 4.70
41 42 3.934391 CTCACGGGTCCGACTTGGC 62.934 68.421 16.90 0.00 42.83 4.52
43 44 2.432628 GCTCACGGGTCCGACTTG 60.433 66.667 16.90 4.34 42.83 3.16
44 45 2.915659 TGCTCACGGGTCCGACTT 60.916 61.111 16.90 0.00 42.83 3.01
45 46 3.374402 CTGCTCACGGGTCCGACT 61.374 66.667 16.90 0.00 42.83 4.18
46 47 3.343788 CTCTGCTCACGGGTCCGAC 62.344 68.421 16.90 3.36 42.83 4.79
47 48 3.062466 CTCTGCTCACGGGTCCGA 61.062 66.667 16.90 0.00 42.83 4.55
48 49 4.803426 GCTCTGCTCACGGGTCCG 62.803 72.222 7.97 7.97 46.03 4.79
49 50 4.803426 CGCTCTGCTCACGGGTCC 62.803 72.222 0.00 0.00 0.00 4.46
76 77 0.884514 GGAAACAAAGAGGAGCAGCC 59.115 55.000 0.00 0.00 0.00 4.85
77 78 0.884514 GGGAAACAAAGAGGAGCAGC 59.115 55.000 0.00 0.00 0.00 5.25
79 80 1.494721 AGTGGGAAACAAAGAGGAGCA 59.505 47.619 0.00 0.00 0.00 4.26
80 81 2.155279 GAGTGGGAAACAAAGAGGAGC 58.845 52.381 0.00 0.00 0.00 4.70
82 83 2.158667 GGTGAGTGGGAAACAAAGAGGA 60.159 50.000 0.00 0.00 0.00 3.71
83 84 2.230660 GGTGAGTGGGAAACAAAGAGG 58.769 52.381 0.00 0.00 0.00 3.69
85 86 2.507886 TCTGGTGAGTGGGAAACAAAGA 59.492 45.455 0.00 0.00 0.00 2.52
87 88 3.221771 CATCTGGTGAGTGGGAAACAAA 58.778 45.455 0.00 0.00 0.00 2.83
88 89 2.174639 ACATCTGGTGAGTGGGAAACAA 59.825 45.455 0.00 0.00 0.00 2.83
89 90 1.774254 ACATCTGGTGAGTGGGAAACA 59.226 47.619 0.00 0.00 0.00 2.83
90 91 2.427506 GACATCTGGTGAGTGGGAAAC 58.572 52.381 0.00 0.00 0.00 2.78
91 92 1.001974 CGACATCTGGTGAGTGGGAAA 59.998 52.381 0.00 0.00 0.00 3.13
118 1687 1.592223 GGTCTCTCGTCAACCCTGG 59.408 63.158 0.00 0.00 0.00 4.45
122 1691 2.572284 CCCGGTCTCTCGTCAACC 59.428 66.667 0.00 0.00 0.00 3.77
123 1692 2.126031 GCCCGGTCTCTCGTCAAC 60.126 66.667 0.00 0.00 0.00 3.18
146 1715 2.509336 GACGGATGTGGCTGACGG 60.509 66.667 0.00 0.00 0.00 4.79
173 1742 3.182263 TTGGTGGAGGGTGGGTGG 61.182 66.667 0.00 0.00 0.00 4.61
174 1743 2.115266 GTTGGTGGAGGGTGGGTG 59.885 66.667 0.00 0.00 0.00 4.61
175 1744 3.182996 GGTTGGTGGAGGGTGGGT 61.183 66.667 0.00 0.00 0.00 4.51
181 1750 4.344865 CGGGTGGGTTGGTGGAGG 62.345 72.222 0.00 0.00 0.00 4.30
274 1843 4.301027 CGTGGAGATAGCCGCCCC 62.301 72.222 0.00 0.00 34.97 5.80
278 1849 2.331805 CGTCCGTGGAGATAGCCG 59.668 66.667 0.00 0.00 0.00 5.52
280 1851 0.882474 ATAGCGTCCGTGGAGATAGC 59.118 55.000 0.00 0.00 0.00 2.97
281 1852 2.814919 AGAATAGCGTCCGTGGAGATAG 59.185 50.000 0.00 0.00 0.00 2.08
282 1853 2.860009 AGAATAGCGTCCGTGGAGATA 58.140 47.619 0.00 0.00 0.00 1.98
284 1855 2.336945 TAGAATAGCGTCCGTGGAGA 57.663 50.000 0.00 0.00 0.00 3.71
285 1856 3.644884 AATAGAATAGCGTCCGTGGAG 57.355 47.619 0.00 0.00 0.00 3.86
286 1857 5.284079 GTTAAATAGAATAGCGTCCGTGGA 58.716 41.667 0.00 0.00 0.00 4.02
296 1873 2.410730 CGCGCCCGGTTAAATAGAATAG 59.589 50.000 0.00 0.00 0.00 1.73
372 1974 2.264124 CCGTCGAGGAAGGAAGACA 58.736 57.895 6.70 0.00 45.00 3.41
390 1992 4.196826 GATCTGCGTGCGTGCGTC 62.197 66.667 3.11 0.00 37.81 5.19
391 1993 4.724602 AGATCTGCGTGCGTGCGT 62.725 61.111 0.00 0.00 37.81 5.24
396 1998 0.807275 TTGGATGAGATCTGCGTGCG 60.807 55.000 0.00 0.00 0.00 5.34
397 1999 0.935898 CTTGGATGAGATCTGCGTGC 59.064 55.000 0.00 0.00 0.00 5.34
398 2000 1.579698 CCTTGGATGAGATCTGCGTG 58.420 55.000 0.00 0.00 0.00 5.34
399 2001 0.179062 GCCTTGGATGAGATCTGCGT 60.179 55.000 0.00 0.00 0.00 5.24
400 2002 0.179065 TGCCTTGGATGAGATCTGCG 60.179 55.000 0.00 0.00 0.00 5.18
403 2005 0.473326 GCCTGCCTTGGATGAGATCT 59.527 55.000 0.00 0.00 0.00 2.75
408 2016 2.202236 GACCTGCCTGCCTTGGATGA 62.202 60.000 0.00 0.00 0.00 2.92
429 2050 2.015726 GGAGAGGGAGGGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
430 2051 2.612251 GGAGAGGGAGGGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
431 2052 3.036959 GGGAGAGGGAGGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
432 2053 4.179599 GGGGAGAGGGAGGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
449 2079 2.444140 ACGGGAGGAGATTCGGGG 60.444 66.667 0.00 0.00 0.00 5.73
567 3897 6.183360 GCCCAGGTAGAATAGAATATCTAGCC 60.183 46.154 8.02 2.35 44.03 3.93
576 3906 1.420430 CCCGCCCAGGTAGAATAGAA 58.580 55.000 0.00 0.00 38.74 2.10
578 3908 1.371558 GCCCGCCCAGGTAGAATAG 59.628 63.158 0.00 0.00 38.74 1.73
579 3909 2.504274 CGCCCGCCCAGGTAGAATA 61.504 63.158 0.00 0.00 38.74 1.75
580 3910 3.861797 CGCCCGCCCAGGTAGAAT 61.862 66.667 0.00 0.00 38.74 2.40
631 3970 0.829990 TGACTATCTGGGAATGCGCA 59.170 50.000 14.96 14.96 35.49 6.09
632 3971 1.069204 TCTGACTATCTGGGAATGCGC 59.931 52.381 0.00 0.00 0.00 6.09
633 3972 3.583806 GATCTGACTATCTGGGAATGCG 58.416 50.000 0.00 0.00 0.00 4.73
634 3973 3.326006 TGGATCTGACTATCTGGGAATGC 59.674 47.826 0.00 0.00 0.00 3.56
635 3974 5.489249 CATGGATCTGACTATCTGGGAATG 58.511 45.833 0.00 0.00 0.00 2.67
636 3975 4.535294 CCATGGATCTGACTATCTGGGAAT 59.465 45.833 5.56 0.00 0.00 3.01
638 3977 3.514539 CCATGGATCTGACTATCTGGGA 58.485 50.000 5.56 0.00 0.00 4.37
640 3979 3.007723 CACCCATGGATCTGACTATCTGG 59.992 52.174 15.22 0.00 0.00 3.86
641 3980 4.268797 CACCCATGGATCTGACTATCTG 57.731 50.000 15.22 0.00 0.00 2.90
661 4000 3.506743 TTCACAAGCCCCAGCCCA 61.507 61.111 0.00 0.00 41.25 5.36
666 4005 2.538141 CCTCCCTTCACAAGCCCCA 61.538 63.158 0.00 0.00 0.00 4.96
672 4011 4.697756 CGCGCCCTCCCTTCACAA 62.698 66.667 0.00 0.00 0.00 3.33
675 4014 2.443203 TATCGCGCCCTCCCTTCA 60.443 61.111 0.00 0.00 0.00 3.02
676 4015 2.029307 AACTATCGCGCCCTCCCTTC 62.029 60.000 0.00 0.00 0.00 3.46
677 4016 2.064581 AACTATCGCGCCCTCCCTT 61.065 57.895 0.00 0.00 0.00 3.95
678 4017 2.444140 AACTATCGCGCCCTCCCT 60.444 61.111 0.00 0.00 0.00 4.20
699 4077 0.256464 TGGCATGGCATGATGAGTGA 59.744 50.000 30.69 2.83 0.00 3.41
700 4078 0.384309 GTGGCATGGCATGATGAGTG 59.616 55.000 30.69 4.50 0.00 3.51
702 4080 1.792118 CGGTGGCATGGCATGATGAG 61.792 60.000 30.69 12.89 0.00 2.90
707 4085 3.520862 GGTCGGTGGCATGGCATG 61.521 66.667 26.07 22.99 0.00 4.06
711 4089 2.717044 TAGTCGGTCGGTGGCATGG 61.717 63.158 0.00 0.00 0.00 3.66
712 4090 1.518572 GTAGTCGGTCGGTGGCATG 60.519 63.158 0.00 0.00 0.00 4.06
713 4091 1.681327 AGTAGTCGGTCGGTGGCAT 60.681 57.895 0.00 0.00 0.00 4.40
714 4092 2.282674 AGTAGTCGGTCGGTGGCA 60.283 61.111 0.00 0.00 0.00 4.92
715 4093 2.181021 CAGTAGTCGGTCGGTGGC 59.819 66.667 0.00 0.00 0.00 5.01
716 4094 1.676635 TCCAGTAGTCGGTCGGTGG 60.677 63.158 0.00 0.00 0.00 4.61
718 4096 2.037136 CGTCCAGTAGTCGGTCGGT 61.037 63.158 0.00 0.00 32.43 4.69
720 4098 2.758089 CCCGTCCAGTAGTCGGTCG 61.758 68.421 0.00 0.00 42.30 4.79
721 4099 3.061260 GCCCGTCCAGTAGTCGGTC 62.061 68.421 0.00 0.00 42.30 4.79
722 4100 3.066814 GCCCGTCCAGTAGTCGGT 61.067 66.667 0.00 0.00 42.30 4.69
750 4164 7.560262 TGGCCGCTTCTATAATCTAGTATATGT 59.440 37.037 0.00 0.00 0.00 2.29
751 4165 7.863375 GTGGCCGCTTCTATAATCTAGTATATG 59.137 40.741 9.68 0.00 0.00 1.78
752 4166 7.255173 CGTGGCCGCTTCTATAATCTAGTATAT 60.255 40.741 15.69 0.00 0.00 0.86
753 4167 6.037940 CGTGGCCGCTTCTATAATCTAGTATA 59.962 42.308 15.69 0.00 0.00 1.47
754 4168 5.163642 CGTGGCCGCTTCTATAATCTAGTAT 60.164 44.000 15.69 0.00 0.00 2.12
755 4169 4.155462 CGTGGCCGCTTCTATAATCTAGTA 59.845 45.833 15.69 0.00 0.00 1.82
756 4170 3.057456 CGTGGCCGCTTCTATAATCTAGT 60.057 47.826 15.69 0.00 0.00 2.57
757 4171 3.502920 CGTGGCCGCTTCTATAATCTAG 58.497 50.000 15.69 0.00 0.00 2.43
758 4172 2.230508 CCGTGGCCGCTTCTATAATCTA 59.769 50.000 15.69 0.00 0.00 1.98
759 4173 1.000955 CCGTGGCCGCTTCTATAATCT 59.999 52.381 15.69 0.00 0.00 2.40
760 4174 1.270147 ACCGTGGCCGCTTCTATAATC 60.270 52.381 15.69 0.00 0.00 1.75
761 4175 0.756903 ACCGTGGCCGCTTCTATAAT 59.243 50.000 15.69 0.00 0.00 1.28
762 4176 1.338973 CTACCGTGGCCGCTTCTATAA 59.661 52.381 15.69 0.00 0.00 0.98
763 4177 0.956633 CTACCGTGGCCGCTTCTATA 59.043 55.000 15.69 0.00 0.00 1.31
764 4178 1.041447 ACTACCGTGGCCGCTTCTAT 61.041 55.000 15.69 0.00 0.00 1.98
765 4179 1.660560 GACTACCGTGGCCGCTTCTA 61.661 60.000 15.69 0.00 0.00 2.10
766 4180 2.995574 ACTACCGTGGCCGCTTCT 60.996 61.111 15.69 0.00 0.00 2.85
770 4184 3.711541 ATTCGACTACCGTGGCCGC 62.712 63.158 6.11 6.11 39.75 6.53
775 4189 0.725117 GGCCAAATTCGACTACCGTG 59.275 55.000 0.00 0.00 39.75 4.94
777 4191 1.093496 GGGGCCAAATTCGACTACCG 61.093 60.000 4.39 0.00 40.25 4.02
784 4198 0.815095 GTACTTGGGGGCCAAATTCG 59.185 55.000 4.39 0.00 43.44 3.34
817 4231 0.529773 CCGGCAAGAATCGAATCGGA 60.530 55.000 1.76 0.00 38.42 4.55
819 4233 0.577269 GTCCGGCAAGAATCGAATCG 59.423 55.000 0.00 0.00 0.00 3.34
821 4235 1.207089 TCAGTCCGGCAAGAATCGAAT 59.793 47.619 0.00 0.00 0.00 3.34
823 4237 0.108804 GTCAGTCCGGCAAGAATCGA 60.109 55.000 0.00 0.00 0.00 3.59
824 4238 0.389817 TGTCAGTCCGGCAAGAATCG 60.390 55.000 0.00 0.00 0.00 3.34
827 4241 0.531974 GTGTGTCAGTCCGGCAAGAA 60.532 55.000 0.00 0.00 0.00 2.52
828 4242 1.069090 GTGTGTCAGTCCGGCAAGA 59.931 57.895 0.00 0.00 0.00 3.02
829 4243 1.224069 CTGTGTGTCAGTCCGGCAAG 61.224 60.000 0.00 0.00 39.17 4.01
830 4244 1.227527 CTGTGTGTCAGTCCGGCAA 60.228 57.895 0.00 0.00 39.17 4.52
831 4245 2.421314 CTGTGTGTCAGTCCGGCA 59.579 61.111 0.00 0.00 39.17 5.69
837 4251 2.180204 GCGTTGGCTGTGTGTCAGT 61.180 57.895 0.00 0.00 45.23 3.41
838 4252 2.633657 GCGTTGGCTGTGTGTCAG 59.366 61.111 0.00 0.00 46.12 3.51
839 4253 2.899838 GGCGTTGGCTGTGTGTCA 60.900 61.111 0.00 0.00 39.81 3.58
842 4256 4.012895 GTCGGCGTTGGCTGTGTG 62.013 66.667 6.85 0.00 46.03 3.82
849 4263 4.619227 ACAGGTGGTCGGCGTTGG 62.619 66.667 6.85 0.00 0.00 3.77
858 4272 4.320456 CTGCGCAGGACAGGTGGT 62.320 66.667 29.88 0.00 0.00 4.16
860 4274 4.694233 AGCTGCGCAGGACAGGTG 62.694 66.667 36.47 12.15 43.82 4.00
861 4275 4.694233 CAGCTGCGCAGGACAGGT 62.694 66.667 36.47 15.97 46.27 4.00
880 4294 5.762218 AGGATGATAACAATACAGCAGAAGC 59.238 40.000 0.00 0.00 42.56 3.86
881 4295 7.171167 CAGAGGATGATAACAATACAGCAGAAG 59.829 40.741 0.00 0.00 0.00 2.85
882 4296 6.988580 CAGAGGATGATAACAATACAGCAGAA 59.011 38.462 0.00 0.00 0.00 3.02
883 4297 6.098838 ACAGAGGATGATAACAATACAGCAGA 59.901 38.462 0.00 0.00 0.00 4.26
884 4298 6.286758 ACAGAGGATGATAACAATACAGCAG 58.713 40.000 0.00 0.00 0.00 4.24
885 4299 6.239217 ACAGAGGATGATAACAATACAGCA 57.761 37.500 0.00 0.00 0.00 4.41
886 4300 7.412853 CAAACAGAGGATGATAACAATACAGC 58.587 38.462 0.00 0.00 0.00 4.40
887 4301 7.066163 TGCAAACAGAGGATGATAACAATACAG 59.934 37.037 0.00 0.00 0.00 2.74
888 4302 6.883756 TGCAAACAGAGGATGATAACAATACA 59.116 34.615 0.00 0.00 0.00 2.29
889 4303 7.320443 TGCAAACAGAGGATGATAACAATAC 57.680 36.000 0.00 0.00 0.00 1.89
903 4317 4.049339 GCGAGTAGCACTGCAAACAGAG 62.049 54.545 3.30 0.00 45.98 3.35
904 4318 2.200858 GCGAGTAGCACTGCAAACAGA 61.201 52.381 3.30 0.00 45.98 3.41
922 4336 0.805322 CTTGGACTAGAGCTGCTGCG 60.805 60.000 7.01 0.00 45.42 5.18
923 4337 0.534412 TCTTGGACTAGAGCTGCTGC 59.466 55.000 7.01 7.62 40.05 5.25
924 4338 1.468908 CGTCTTGGACTAGAGCTGCTG 60.469 57.143 7.01 0.00 0.00 4.41
943 4357 3.335356 ATGAAGAGGCCACCCTGCG 62.335 63.158 5.01 0.00 43.12 5.18
989 4419 6.434340 AGCTTCATCGACCATGTATGTATAGA 59.566 38.462 0.00 0.00 33.66 1.98
991 4421 6.389906 CAGCTTCATCGACCATGTATGTATA 58.610 40.000 0.00 0.00 33.66 1.47
992 4422 5.233225 CAGCTTCATCGACCATGTATGTAT 58.767 41.667 0.00 0.00 33.66 2.29
993 4423 4.501400 CCAGCTTCATCGACCATGTATGTA 60.501 45.833 0.00 0.00 33.66 2.29
994 4424 3.461061 CAGCTTCATCGACCATGTATGT 58.539 45.455 0.00 0.00 33.66 2.29
995 4425 2.804527 CCAGCTTCATCGACCATGTATG 59.195 50.000 0.00 0.00 33.66 2.39
996 4426 2.700371 TCCAGCTTCATCGACCATGTAT 59.300 45.455 0.00 0.00 33.66 2.29
997 4427 2.101415 CTCCAGCTTCATCGACCATGTA 59.899 50.000 0.00 0.00 33.66 2.29
998 4428 0.904649 TCCAGCTTCATCGACCATGT 59.095 50.000 0.00 0.00 33.66 3.21
1007 4437 1.455217 GGCATGGCTCCAGCTTCAT 60.455 57.895 12.86 0.00 41.70 2.57
1016 4446 2.541120 GCATCAGACGGCATGGCTC 61.541 63.158 18.09 13.24 0.00 4.70
1039 4475 1.686052 GGAACACAAAGGCAATCACCA 59.314 47.619 0.00 0.00 0.00 4.17
1041 4477 2.362077 ACAGGAACACAAAGGCAATCAC 59.638 45.455 0.00 0.00 0.00 3.06
1044 4480 1.069049 GCACAGGAACACAAAGGCAAT 59.931 47.619 0.00 0.00 0.00 3.56
1045 4481 0.459489 GCACAGGAACACAAAGGCAA 59.541 50.000 0.00 0.00 0.00 4.52
1050 4486 2.738000 GCAACATGCACAGGAACACAAA 60.738 45.455 0.00 0.00 44.26 2.83
1051 4487 1.202394 GCAACATGCACAGGAACACAA 60.202 47.619 0.00 0.00 44.26 3.33
1053 4489 3.184094 GCAACATGCACAGGAACAC 57.816 52.632 0.00 0.00 44.26 3.32
1084 4528 0.829333 AGCTGCTCAGGACCATAGTG 59.171 55.000 0.00 0.00 0.00 2.74
1091 4535 1.519719 CTGGGTAGCTGCTCAGGAC 59.480 63.158 22.93 0.00 33.48 3.85
1105 4549 3.197333 CACAGATCCTATCCTATGCTGGG 59.803 52.174 0.00 0.00 0.00 4.45
1107 4551 3.369261 GGCACAGATCCTATCCTATGCTG 60.369 52.174 0.00 0.00 34.30 4.41
1108 4552 2.836981 GGCACAGATCCTATCCTATGCT 59.163 50.000 0.00 0.00 34.30 3.79
1110 4554 3.369261 GCAGGCACAGATCCTATCCTATG 60.369 52.174 0.00 0.00 31.52 2.23
1111 4555 2.836981 GCAGGCACAGATCCTATCCTAT 59.163 50.000 0.00 0.00 31.52 2.57
1112 4556 2.251818 GCAGGCACAGATCCTATCCTA 58.748 52.381 0.00 0.00 31.52 2.94
1113 4557 1.055040 GCAGGCACAGATCCTATCCT 58.945 55.000 0.00 0.00 31.52 3.24
1115 4559 0.948141 GCGCAGGCACAGATCCTATC 60.948 60.000 0.30 0.00 39.62 2.08
1116 4560 1.070445 GCGCAGGCACAGATCCTAT 59.930 57.895 0.30 0.00 39.62 2.57
1133 4577 0.321475 AGAAGAAGCAGAGCACAGGC 60.321 55.000 0.00 0.00 41.61 4.85
1134 4578 1.805345 CAAGAAGAAGCAGAGCACAGG 59.195 52.381 0.00 0.00 0.00 4.00
1135 4579 2.223611 CACAAGAAGAAGCAGAGCACAG 59.776 50.000 0.00 0.00 0.00 3.66
1137 4581 2.216898 ACACAAGAAGAAGCAGAGCAC 58.783 47.619 0.00 0.00 0.00 4.40
1139 4583 2.765122 AGACACAAGAAGAAGCAGAGC 58.235 47.619 0.00 0.00 0.00 4.09
1140 4584 5.132897 ACTAGACACAAGAAGAAGCAGAG 57.867 43.478 0.00 0.00 0.00 3.35
1141 4585 5.069119 TGAACTAGACACAAGAAGAAGCAGA 59.931 40.000 0.00 0.00 0.00 4.26
1143 4587 5.276461 TGAACTAGACACAAGAAGAAGCA 57.724 39.130 0.00 0.00 0.00 3.91
1148 4966 7.038048 TCATGCTATGAACTAGACACAAGAAG 58.962 38.462 0.00 0.00 36.11 2.85
1155 4973 9.836864 ACAAATAATCATGCTATGAACTAGACA 57.163 29.630 0.00 0.00 43.50 3.41
1185 5179 5.880164 AAAGGTTAAAAGCCAGCCTTTAA 57.120 34.783 5.22 2.75 44.72 1.52
1193 5187 5.654650 TCTGACTGAAAAAGGTTAAAAGCCA 59.345 36.000 0.00 0.00 0.00 4.75
1256 5259 4.020839 CCTGAGAAGGAATGCACCAAAAAT 60.021 41.667 0.00 0.00 0.00 1.82
1258 5261 2.892852 CCTGAGAAGGAATGCACCAAAA 59.107 45.455 0.00 0.00 0.00 2.44
1269 5272 2.501723 GCCATCTTGTACCTGAGAAGGA 59.498 50.000 13.32 0.00 33.67 3.36
1270 5273 2.503356 AGCCATCTTGTACCTGAGAAGG 59.497 50.000 7.51 7.51 34.67 3.46
1274 5278 2.762887 TGAGAGCCATCTTGTACCTGAG 59.237 50.000 0.00 0.00 35.30 3.35
1447 5451 1.734163 CAGGGTCATGGAAACCGTAC 58.266 55.000 0.00 0.00 37.69 3.67
1498 5502 1.349234 TGACAAGCATGATGACGACG 58.651 50.000 0.00 0.00 0.00 5.12
1531 5535 1.296715 GGCGATGGTCTGGTCAACT 59.703 57.895 0.00 0.00 0.00 3.16
1952 6000 1.052124 TCACCCTTGTTCCACTCGGT 61.052 55.000 0.00 0.00 0.00 4.69
2762 7565 3.846360 AGGATACCAAGAAGACGAAACG 58.154 45.455 0.00 0.00 37.17 3.60
2844 7657 7.596749 AAATACAGGACTCGTTACTCAAATG 57.403 36.000 0.00 0.00 0.00 2.32
2936 7761 2.041485 TCAGAATGGCAATGTCTTCCCA 59.959 45.455 0.00 0.00 36.16 4.37
3114 9249 7.064490 AGGACTAAAGTGCAACAAATTTTTGTG 59.936 33.333 9.29 5.62 42.95 3.33
3115 9250 7.102993 AGGACTAAAGTGCAACAAATTTTTGT 58.897 30.769 4.39 2.88 42.30 2.83
3116 9251 7.538303 AGGACTAAAGTGCAACAAATTTTTG 57.462 32.000 4.39 1.56 41.43 2.44
3117 9252 8.560355 AAAGGACTAAAGTGCAACAAATTTTT 57.440 26.923 4.39 0.00 41.43 1.94
3118 9253 8.560355 AAAAGGACTAAAGTGCAACAAATTTT 57.440 26.923 4.39 0.00 41.43 1.82
3119 9254 8.560355 AAAAAGGACTAAAGTGCAACAAATTT 57.440 26.923 4.39 0.00 41.43 1.82
3156 9291 9.387123 GAACAGTTCATAAGTTTTGTGAGAATC 57.613 33.333 8.54 0.00 32.27 2.52
3157 9292 9.125026 AGAACAGTTCATAAGTTTTGTGAGAAT 57.875 29.630 15.85 0.00 32.27 2.40
3158 9293 8.397906 CAGAACAGTTCATAAGTTTTGTGAGAA 58.602 33.333 15.85 0.00 32.27 2.87
3159 9294 7.552687 ACAGAACAGTTCATAAGTTTTGTGAGA 59.447 33.333 15.85 0.00 38.60 3.27
3160 9295 7.697691 ACAGAACAGTTCATAAGTTTTGTGAG 58.302 34.615 15.85 0.00 38.60 3.51
3161 9296 7.201696 GGACAGAACAGTTCATAAGTTTTGTGA 60.202 37.037 15.85 0.00 39.65 3.58
3162 9297 6.912591 GGACAGAACAGTTCATAAGTTTTGTG 59.087 38.462 15.85 3.54 39.65 3.33
3163 9298 6.039382 GGGACAGAACAGTTCATAAGTTTTGT 59.961 38.462 15.85 8.00 41.43 2.83
3164 9299 6.039270 TGGGACAGAACAGTTCATAAGTTTTG 59.961 38.462 15.85 4.90 34.62 2.44
3165 9300 6.126409 TGGGACAGAACAGTTCATAAGTTTT 58.874 36.000 15.85 0.00 0.00 2.43
3300 9444 4.162320 CCTATCAGGCAAAGTAACAGGAGA 59.838 45.833 0.00 0.00 0.00 3.71
3493 9676 2.158813 TCTCCTCCCAAATATGCGGAAC 60.159 50.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.