Multiple sequence alignment - TraesCS2D01G071500

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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 TraesCS2D01G071500 chr2D 100.000 9887 0 0 1 9887 30260991 30251105 0.000000e+00 18258.0
1 TraesCS2D01G071500 chr2D 85.426 892 96 18 2970 3843 25621626 25622501 0.000000e+00 896.0
2 TraesCS2D01G071500 chr2D 81.448 1008 114 36 1999 2963 25620556 25621533 0.000000e+00 758.0
3 TraesCS2D01G071500 chr2D 86.667 165 19 2 3839 4003 25622580 25622741 7.890000e-41 180.0
4 TraesCS2D01G071500 chr2D 94.118 102 4 2 5629 5729 14895366 14895266 4.780000e-33 154.0
5 TraesCS2D01G071500 chr2D 87.500 128 13 3 5628 5754 220975606 220975481 2.880000e-30 145.0
6 TraesCS2D01G071500 chr2D 96.721 61 2 0 9136 9196 513460406 513460346 1.760000e-17 102.0
7 TraesCS2D01G071500 chr2D 100.000 39 0 0 9069 9107 163251102 163251140 1.380000e-08 73.1
8 TraesCS2D01G071500 chr2D 90.385 52 3 2 9069 9120 35026527 35026478 6.410000e-07 67.6
9 TraesCS2D01G071500 chr2D 95.349 43 0 2 9069 9110 650582914 650582873 6.410000e-07 67.6
10 TraesCS2D01G071500 chr2A 96.860 5255 111 22 410 5636 32153254 32148026 0.000000e+00 8741.0
11 TraesCS2D01G071500 chr2A 96.272 3353 80 16 5716 9041 32148029 32144695 0.000000e+00 5457.0
12 TraesCS2D01G071500 chr2A 94.395 785 30 9 9098 9871 32144621 32143840 0.000000e+00 1194.0
13 TraesCS2D01G071500 chr2A 85.314 892 94 20 2970 3843 28020407 28019535 0.000000e+00 887.0
14 TraesCS2D01G071500 chr2A 80.735 1007 117 38 1999 2963 28021471 28020500 0.000000e+00 713.0
15 TraesCS2D01G071500 chr2A 94.712 416 21 1 1 416 32153762 32153348 0.000000e+00 645.0
16 TraesCS2D01G071500 chr2A 85.802 162 20 2 3842 4003 28019454 28019296 1.710000e-37 169.0
17 TraesCS2D01G071500 chr2A 89.474 76 7 1 9122 9196 157931593 157931518 2.940000e-15 95.3
18 TraesCS2D01G071500 chr2A 95.745 47 2 0 1516 1562 235331525 235331479 1.060000e-09 76.8
19 TraesCS2D01G071500 chr2B 96.633 3713 66 26 1944 5636 49086805 49090478 0.000000e+00 6109.0
20 TraesCS2D01G071500 chr2B 96.899 1580 45 4 5913 7488 49091090 49092669 0.000000e+00 2643.0
21 TraesCS2D01G071500 chr2B 95.412 959 33 7 693 1645 49085831 49086784 0.000000e+00 1517.0
22 TraesCS2D01G071500 chr2B 94.650 972 28 6 8122 9073 49098450 49099417 0.000000e+00 1485.0
23 TraesCS2D01G071500 chr2B 96.198 868 27 4 5859 6725 472413044 472412182 0.000000e+00 1415.0
24 TraesCS2D01G071500 chr2B 95.309 874 37 2 5859 6731 12748574 12747704 0.000000e+00 1384.0
25 TraesCS2D01G071500 chr2B 96.026 755 26 2 5978 6731 471716296 471715545 0.000000e+00 1225.0
26 TraesCS2D01G071500 chr2B 96.780 590 14 4 9143 9730 49099510 49100096 0.000000e+00 979.0
27 TraesCS2D01G071500 chr2B 93.874 653 25 4 7488 8125 49097752 49098404 0.000000e+00 970.0
28 TraesCS2D01G071500 chr2B 84.994 893 98 24 2970 3843 41199131 41198256 0.000000e+00 874.0
29 TraesCS2D01G071500 chr2B 81.629 1007 116 34 1999 2963 41200203 41199224 0.000000e+00 771.0
30 TraesCS2D01G071500 chr2B 94.919 433 19 2 533 963 49085399 49085830 0.000000e+00 675.0
31 TraesCS2D01G071500 chr2B 97.619 210 3 2 5716 5923 49090475 49090684 9.440000e-95 359.0
32 TraesCS2D01G071500 chr2B 86.420 162 19 2 3842 4003 41198174 41198016 3.670000e-39 174.0
33 TraesCS2D01G071500 chr2B 77.559 254 52 3 7191 7440 619946115 619946367 2.220000e-31 148.0
34 TraesCS2D01G071500 chr2B 94.186 86 5 0 1 86 49085317 49085402 2.240000e-26 132.0
35 TraesCS2D01G071500 chr2B 96.721 61 2 0 9136 9196 604998668 604998608 1.760000e-17 102.0
36 TraesCS2D01G071500 chr2B 87.931 58 7 0 5537 5594 716572050 716571993 1.780000e-07 69.4
37 TraesCS2D01G071500 chr2B 89.091 55 4 2 9069 9123 782178790 782178738 6.410000e-07 67.6
38 TraesCS2D01G071500 chr5B 96.339 874 28 2 5859 6731 110036673 110035803 0.000000e+00 1434.0
39 TraesCS2D01G071500 chr5B 94.700 868 23 3 5859 6725 429199238 429200083 0.000000e+00 1327.0
40 TraesCS2D01G071500 chr5B 82.418 273 39 6 7177 7440 606016444 606016716 7.720000e-56 230.0
41 TraesCS2D01G071500 chr4B 95.968 868 28 5 5865 6731 585448953 585448092 0.000000e+00 1402.0
42 TraesCS2D01G071500 chr4B 94.124 868 28 3 5859 6725 250312978 250313823 0.000000e+00 1299.0
43 TraesCS2D01G071500 chr4B 95.455 44 1 1 9066 9109 81308317 81308359 1.780000e-07 69.4
44 TraesCS2D01G071500 chr4B 100.000 28 0 0 7502 7529 43225778 43225805 1.800000e-02 52.8
45 TraesCS2D01G071500 chr3B 94.622 874 24 4 5859 6731 71106232 71105381 0.000000e+00 1332.0
46 TraesCS2D01G071500 chr3B 92.157 51 1 3 9069 9116 30405977 30405927 1.780000e-07 69.4
47 TraesCS2D01G071500 chr3B 93.617 47 1 2 9067 9112 478996889 478996934 1.780000e-07 69.4
48 TraesCS2D01G071500 chr1B 93.936 874 30 3 5859 6731 605793452 605792601 0.000000e+00 1299.0
49 TraesCS2D01G071500 chr1B 83.399 253 32 7 7188 7433 542136621 542136870 9.990000e-55 226.0
50 TraesCS2D01G071500 chr1B 100.000 39 0 0 9069 9107 252969842 252969804 1.380000e-08 73.1
51 TraesCS2D01G071500 chr1D 83.382 343 47 4 81 416 414252413 414252752 9.640000e-80 309.0
52 TraesCS2D01G071500 chr1D 85.657 251 28 5 7188 7431 403274880 403275129 3.540000e-64 257.0
53 TraesCS2D01G071500 chr1D 77.528 267 49 7 7188 7447 22850856 22850594 6.190000e-32 150.0
54 TraesCS2D01G071500 chr1D 86.957 92 7 4 9128 9214 465974336 465974427 2.270000e-16 99.0
55 TraesCS2D01G071500 chr1D 88.889 54 4 2 7488 7541 420648999 420648948 2.300000e-06 65.8
56 TraesCS2D01G071500 chr5D 84.871 271 34 4 7177 7440 491433531 491433801 5.890000e-67 267.0
57 TraesCS2D01G071500 chr5D 91.304 46 4 0 9069 9114 60072210 60072165 8.290000e-06 63.9
58 TraesCS2D01G071500 chr5D 83.582 67 4 3 7468 7528 12985417 12985482 1.000000e-03 56.5
59 TraesCS2D01G071500 chr4A 88.889 180 15 5 1821 1996 639181930 639182108 6.010000e-52 217.0
60 TraesCS2D01G071500 chr4A 87.222 180 18 5 1822 2000 47732416 47732241 6.060000e-47 200.0
61 TraesCS2D01G071500 chr4A 87.151 179 18 5 1822 1999 563450442 563450616 2.180000e-46 198.0
62 TraesCS2D01G071500 chr1A 88.701 177 15 5 1822 1997 135964618 135964446 2.800000e-50 211.0
63 TraesCS2D01G071500 chr1A 84.158 202 29 3 1796 1996 591960053 591960252 1.010000e-44 193.0
64 TraesCS2D01G071500 chr1A 91.367 139 9 3 410 547 21212304 21212440 4.710000e-43 187.0
65 TraesCS2D01G071500 chr1A 95.455 44 1 1 9069 9112 58483386 58483344 1.780000e-07 69.4
66 TraesCS2D01G071500 chr5A 87.363 182 17 6 1821 1999 688666651 688666473 4.680000e-48 204.0
67 TraesCS2D01G071500 chr5A 92.308 104 7 1 5626 5729 215479493 215479595 8.000000e-31 147.0
68 TraesCS2D01G071500 chr5A 91.667 48 1 3 9069 9114 362781638 362781592 8.290000e-06 63.9
69 TraesCS2D01G071500 chr5A 85.075 67 3 4 7468 7528 9849514 9849449 2.980000e-05 62.1
70 TraesCS2D01G071500 chr5A 83.582 67 4 3 7468 7528 9849450 9849515 1.000000e-03 56.5
71 TraesCS2D01G071500 chr3A 87.640 178 16 6 1821 1995 102846122 102845948 1.680000e-47 202.0
72 TraesCS2D01G071500 chr3A 86.667 75 6 4 7462 7533 74232182 74232109 8.230000e-11 80.5
73 TraesCS2D01G071500 chr7D 86.957 184 15 7 1821 1997 452980828 452980647 2.180000e-46 198.0
74 TraesCS2D01G071500 chr7D 84.211 190 27 2 7254 7441 628763657 628763469 2.190000e-41 182.0
75 TraesCS2D01G071500 chr7D 95.000 100 3 2 5623 5720 426558885 426558984 1.330000e-33 156.0
76 TraesCS2D01G071500 chr7D 93.204 103 5 2 5618 5719 454088744 454088643 6.190000e-32 150.0
77 TraesCS2D01G071500 chr7D 93.137 102 5 2 5620 5720 519264531 519264631 2.220000e-31 148.0
78 TraesCS2D01G071500 chr7D 92.647 68 5 0 9126 9193 16920795 16920862 2.270000e-16 99.0
79 TraesCS2D01G071500 chr6D 97.849 93 1 1 5629 5721 309072593 309072502 1.030000e-34 159.0
80 TraesCS2D01G071500 chr6D 96.667 90 3 0 5631 5720 78083167 78083078 6.190000e-32 150.0
81 TraesCS2D01G071500 chr6D 89.583 48 3 2 9069 9116 100520403 100520358 1.070000e-04 60.2
82 TraesCS2D01G071500 chr4D 97.802 91 2 0 5630 5720 492239223 492239313 3.700000e-34 158.0
83 TraesCS2D01G071500 chr4D 91.549 71 4 2 9127 9196 291740452 291740521 8.170000e-16 97.1
84 TraesCS2D01G071500 chr4D 84.058 69 7 2 7468 7536 379148830 379148766 8.290000e-06 63.9
85 TraesCS2D01G071500 chrUn 92.105 76 6 0 3928 4003 479220814 479220739 3.780000e-19 108.0
86 TraesCS2D01G071500 chr7A 92.754 69 5 0 9128 9196 593450693 593450761 6.320000e-17 100.0
87 TraesCS2D01G071500 chr7A 94.872 39 2 0 7490 7528 167261641 167261679 2.980000e-05 62.1
88 TraesCS2D01G071500 chr7B 94.595 37 2 0 7492 7528 129535816 129535852 3.860000e-04 58.4
89 TraesCS2D01G071500 chr7B 82.192 73 7 4 7474 7541 687246354 687246283 3.860000e-04 58.4
90 TraesCS2D01G071500 chr6A 89.130 46 5 0 7494 7539 33013724 33013679 3.860000e-04 58.4


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 TraesCS2D01G071500 chr2D 30251105 30260991 9886 True 18258.000000 18258 100.000000 1 9887 1 chr2D.!!$R2 9886
1 TraesCS2D01G071500 chr2D 25620556 25622741 2185 False 611.333333 896 84.513667 1999 4003 3 chr2D.!!$F2 2004
2 TraesCS2D01G071500 chr2A 32143840 32153762 9922 True 4009.250000 8741 95.559750 1 9871 4 chr2A.!!$R4 9870
3 TraesCS2D01G071500 chr2A 28019296 28021471 2175 True 589.666667 887 83.950333 1999 4003 3 chr2A.!!$R3 2004
4 TraesCS2D01G071500 chr2B 49085317 49092669 7352 False 1905.833333 6109 95.944667 1 7488 6 chr2B.!!$F2 7487
5 TraesCS2D01G071500 chr2B 472412182 472413044 862 True 1415.000000 1415 96.198000 5859 6725 1 chr2B.!!$R3 866
6 TraesCS2D01G071500 chr2B 12747704 12748574 870 True 1384.000000 1384 95.309000 5859 6731 1 chr2B.!!$R1 872
7 TraesCS2D01G071500 chr2B 471715545 471716296 751 True 1225.000000 1225 96.026000 5978 6731 1 chr2B.!!$R2 753
8 TraesCS2D01G071500 chr2B 49097752 49100096 2344 False 1144.666667 1485 95.101333 7488 9730 3 chr2B.!!$F3 2242
9 TraesCS2D01G071500 chr2B 41198016 41200203 2187 True 606.333333 874 84.347667 1999 4003 3 chr2B.!!$R7 2004
10 TraesCS2D01G071500 chr5B 110035803 110036673 870 True 1434.000000 1434 96.339000 5859 6731 1 chr5B.!!$R1 872
11 TraesCS2D01G071500 chr5B 429199238 429200083 845 False 1327.000000 1327 94.700000 5859 6725 1 chr5B.!!$F1 866
12 TraesCS2D01G071500 chr4B 585448092 585448953 861 True 1402.000000 1402 95.968000 5865 6731 1 chr4B.!!$R1 866
13 TraesCS2D01G071500 chr4B 250312978 250313823 845 False 1299.000000 1299 94.124000 5859 6725 1 chr4B.!!$F3 866
14 TraesCS2D01G071500 chr3B 71105381 71106232 851 True 1332.000000 1332 94.622000 5859 6731 1 chr3B.!!$R2 872
15 TraesCS2D01G071500 chr1B 605792601 605793452 851 True 1299.000000 1299 93.936000 5859 6731 1 chr1B.!!$R2 872

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
259 260 0.721718 CACGGAATCCTCAGAAACGC 59.278 55.000 0.00 0.00 0.00 4.84 F
536 637 1.079503 CTTCAGAACACGCCCTAAGC 58.920 55.000 0.00 0.00 38.52 3.09 F
1860 2248 1.348250 CATGGCATCCGTTTCGACG 59.652 57.895 0.00 0.00 0.00 5.12 F
2685 3118 3.385433 TGCCCTCTAAAATTCCATGCATG 59.615 43.478 20.19 20.19 0.00 4.06 F
3615 4153 1.347062 TGGTGATGCTGTGGTCAGTA 58.653 50.000 0.00 0.00 43.05 2.74 F
4605 5233 2.632996 TCTTGACCAAGAGACGTGGATT 59.367 45.455 8.27 0.00 42.06 3.01 F
5649 6278 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37 F
5650 6279 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00 F
5651 6280 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74 F
5652 6281 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90 F
6665 7753 2.089980 CAAGAGCCATCCTGTTCTTGG 58.910 52.381 9.04 0.00 41.61 3.61 F
7216 8307 3.003897 TCCGTTTCTTTTTACTGCGCATT 59.996 39.130 12.24 8.40 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 1654 0.893447 GCAGGTACCACTAACTCGGT 59.107 55.000 15.94 0.0 39.41 4.69 R
1865 2253 1.210155 GGAAACACACTGCATCCGC 59.790 57.895 0.00 0.0 39.24 5.54 R
3465 4000 2.381725 ACAACGGAAGCTTAGTAGGC 57.618 50.000 0.00 0.0 0.00 3.93 R
4180 4804 1.317613 TCAGGCACAATGGTGTTGTC 58.682 50.000 1.31 0.0 46.95 3.18 R
4867 5495 1.559149 CCAAGCACAATGGTTTGCGC 61.559 55.000 0.00 0.0 43.87 6.09 R
5704 6333 0.106116 ACATCTACTCCCTCCGTCCC 60.106 60.000 0.00 0.0 0.00 4.46 R
6924 8015 2.054799 TGCCAGTCAAGAGTTACCCTT 58.945 47.619 0.00 0.0 0.00 3.95 R
7098 8189 2.240667 CTGGTCCATTCCAACTCTCCAT 59.759 50.000 0.00 0.0 37.01 3.41 R
7103 8194 3.634397 TCATCTGGTCCATTCCAACTC 57.366 47.619 0.00 0.0 37.01 3.01 R
7210 8301 5.393962 ACTTCAGACAAATCTTAAATGCGC 58.606 37.500 0.00 0.0 30.42 6.09 R
8573 9748 3.445008 TCTTTGCCTGAGGACTACTGAT 58.555 45.455 0.65 0.0 0.00 2.90 R
9080 10268 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.0 0.00 2.71 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
92 93 5.820947 CCAATAAGATACTTTAAGGGCGTGT 59.179 40.000 0.00 0.00 0.00 4.49
145 146 2.626455 CGCGCGAGAAATTAGGCC 59.374 61.111 28.94 0.00 0.00 5.19
166 167 2.347731 GAACGGTCTTAAGCTTCCTGG 58.652 52.381 0.00 0.00 0.00 4.45
167 168 1.640917 ACGGTCTTAAGCTTCCTGGA 58.359 50.000 0.00 0.00 0.00 3.86
241 242 4.569279 TGGGTTTTCGCAGCTTCA 57.431 50.000 0.00 0.00 37.83 3.02
242 243 2.029743 TGGGTTTTCGCAGCTTCAC 58.970 52.632 0.00 0.00 37.83 3.18
259 260 0.721718 CACGGAATCCTCAGAAACGC 59.278 55.000 0.00 0.00 0.00 4.84
319 320 4.060038 CCCGTACCGGTTCGTGCT 62.060 66.667 28.34 0.00 46.80 4.40
321 322 2.564975 CGTACCGGTTCGTGCTCT 59.435 61.111 23.71 0.00 0.00 4.09
335 336 2.731451 CGTGCTCTCGATTCTTTTGTCA 59.269 45.455 0.00 0.00 0.00 3.58
338 339 2.473049 GCTCTCGATTCTTTTGTCACGC 60.473 50.000 0.00 0.00 0.00 5.34
380 381 1.960417 TTGGCAACGTGAAGACATCA 58.040 45.000 0.00 0.00 42.51 3.07
385 386 2.480037 GCAACGTGAAGACATCATGACA 59.520 45.455 6.89 0.00 46.22 3.58
390 391 3.611549 CGTGAAGACATCATGACACTCAG 59.388 47.826 0.00 0.00 46.22 3.35
392 393 4.863689 GTGAAGACATCATGACACTCAGAG 59.136 45.833 0.00 0.00 40.97 3.35
418 519 1.303317 CCAAACTGGGCCTAGCGTT 60.303 57.895 17.38 7.97 32.67 4.84
431 532 1.949847 TAGCGTTGAGAGGAGCTGGC 61.950 60.000 0.00 0.00 40.51 4.85
460 561 3.165160 AACGGTGCTGGCTTCTCGT 62.165 57.895 0.00 0.00 0.00 4.18
462 563 1.961277 CGGTGCTGGCTTCTCGTTT 60.961 57.895 0.00 0.00 0.00 3.60
504 605 2.674747 GCTGAGAAGCTCTGGAGTTGAG 60.675 54.545 0.00 0.00 31.52 3.02
536 637 1.079503 CTTCAGAACACGCCCTAAGC 58.920 55.000 0.00 0.00 38.52 3.09
554 655 6.912591 CCCTAAGCGAAATACATTTGTTGATC 59.087 38.462 0.00 0.00 0.00 2.92
578 679 5.469421 CCTTAATTTTTGTGCAAGCCAATGA 59.531 36.000 0.00 0.00 0.00 2.57
1486 1872 1.396996 GCGTACCCAAGCAATGTAGTG 59.603 52.381 0.00 0.00 0.00 2.74
1514 1900 5.850557 TTTTCAAGAAAATGCAGAGGACA 57.149 34.783 3.98 0.00 35.57 4.02
1659 2047 5.447818 GGATCCTCATGTCACAAAACGATTC 60.448 44.000 3.84 0.00 0.00 2.52
1671 2059 4.514577 CGATTCGGCCAGGCGACT 62.515 66.667 16.40 11.14 46.44 4.18
1762 2150 3.198635 AGAGCTGGCTTTTAGACTATGCA 59.801 43.478 0.00 0.00 0.00 3.96
1860 2248 1.348250 CATGGCATCCGTTTCGACG 59.652 57.895 0.00 0.00 0.00 5.12
2192 2599 5.747342 TGTGTACTGTACTCCTTTGGTTTT 58.253 37.500 17.98 0.00 0.00 2.43
2627 3060 3.794971 TGGGTTTATGGGGCCTTATAAGT 59.205 43.478 11.50 0.00 0.00 2.24
2685 3118 3.385433 TGCCCTCTAAAATTCCATGCATG 59.615 43.478 20.19 20.19 0.00 4.06
3371 3906 4.080919 TGGGAACATAAGTCCTGATGACAG 60.081 45.833 0.00 0.00 40.54 3.51
3465 4000 4.494764 GTCTCTAATACTGTTACACGCACG 59.505 45.833 0.00 0.00 0.00 5.34
3615 4153 1.347062 TGGTGATGCTGTGGTCAGTA 58.653 50.000 0.00 0.00 43.05 2.74
3627 4165 5.163519 GCTGTGGTCAGTATTGGCAAATATT 60.164 40.000 3.01 0.00 43.05 1.28
3939 4563 8.635124 CCATGTTAATTGCGTAAAAGTAAGTTG 58.365 33.333 0.00 0.00 0.00 3.16
4090 4714 4.196971 ACTTTGCTGAAGTTTACGGAAGT 58.803 39.130 0.94 0.00 46.34 3.01
4180 4804 5.928839 ACGAGCAACAGCTTATAGGATAATG 59.071 40.000 0.00 0.00 39.10 1.90
4605 5233 2.632996 TCTTGACCAAGAGACGTGGATT 59.367 45.455 8.27 0.00 42.06 3.01
5026 5655 3.799432 TGCCACACTTTACTAACCCAT 57.201 42.857 0.00 0.00 0.00 4.00
5648 6277 1.273759 AAAAGTACTCCCTCCGTCCC 58.726 55.000 0.00 0.00 0.00 4.46
5649 6278 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
5650 6279 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
5651 6280 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
5652 6281 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
5653 6282 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
5654 6283 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
5655 6284 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5656 6285 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5657 6286 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5658 6287 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5659 6288 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5660 6289 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5661 6290 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5662 6291 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5663 6292 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5664 6293 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5665 6294 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5666 6295 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5667 6296 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5709 6338 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5710 6339 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5711 6340 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5712 6341 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5713 6342 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5714 6343 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5949 6996 3.020274 TGTGCTGCCACACTTCTTTTTA 58.980 40.909 7.61 0.00 46.51 1.52
6283 7332 3.056607 GTCTTGATTTGTTGGTGGGATGG 60.057 47.826 0.00 0.00 0.00 3.51
6514 7602 4.669206 AGAGCCTGATTCATGTACTCTG 57.331 45.455 0.00 0.00 32.06 3.35
6518 7606 4.343526 AGCCTGATTCATGTACTCTGGTAG 59.656 45.833 14.35 0.00 32.36 3.18
6569 7657 7.426929 AGGCAATAGATTTATTTCGCTACAG 57.573 36.000 0.00 0.00 0.00 2.74
6665 7753 2.089980 CAAGAGCCATCCTGTTCTTGG 58.910 52.381 9.04 0.00 41.61 3.61
6770 7858 7.672983 TCCTTGAAGTATCTGTGATTTTGAC 57.327 36.000 0.00 0.00 0.00 3.18
6897 7987 9.906660 GATAGAGTTACTCAGGTATGATTTCTG 57.093 37.037 15.23 0.00 34.12 3.02
6977 8068 9.190858 TGTTTTATGTACTTGCATGAATTTCAC 57.809 29.630 6.60 0.00 0.00 3.18
6993 8084 9.956720 ATGAATTTCACTTCTTACAAGTTTCTG 57.043 29.630 0.15 0.00 0.00 3.02
6995 8086 7.881775 ATTTCACTTCTTACAAGTTTCTGGT 57.118 32.000 0.00 0.00 0.00 4.00
7098 8189 9.352784 CAAATCTTAGAAAATTACCGCAAATCA 57.647 29.630 0.00 0.00 0.00 2.57
7103 8194 5.894807 AGAAAATTACCGCAAATCATGGAG 58.105 37.500 0.00 0.00 0.00 3.86
7210 8301 7.486802 TTACTCCTTCCGTTTCTTTTTACTG 57.513 36.000 0.00 0.00 0.00 2.74
7216 8307 3.003897 TCCGTTTCTTTTTACTGCGCATT 59.996 39.130 12.24 8.40 0.00 3.56
7528 8620 5.245526 ACGTCTTACATTTAGGAACAGAGGT 59.754 40.000 0.00 0.00 0.00 3.85
7638 8730 7.643123 ACATCTTAACTCATTTATTGACCCCT 58.357 34.615 0.00 0.00 0.00 4.79
7668 8760 5.293560 CGTCCTTTATTCTCCTGGAATCTC 58.706 45.833 0.00 0.00 42.96 2.75
7835 8946 4.119862 TCTGCAAGCGATATTCAGGTAAC 58.880 43.478 0.00 0.00 0.00 2.50
8162 9330 8.023021 TGATGATAGCGCCTCCTTATTTATAT 57.977 34.615 2.29 0.00 0.00 0.86
8548 9723 7.205515 AGTCCAGATATTCCATTCCCATATC 57.794 40.000 0.00 0.00 32.22 1.63
8573 9748 6.313411 CACAGAAGCATTTTCAAAGTTGGAAA 59.687 34.615 0.99 0.99 39.78 3.13
8645 9820 4.159506 GCTACACTTATGCCATTTTTCCCA 59.840 41.667 0.00 0.00 0.00 4.37
8882 10070 1.003223 GTTCGGGACAAAAGTTGACGG 60.003 52.381 0.00 0.00 0.00 4.79
9020 10208 8.860088 AGGTATAATTTGGATTCATACCTTTGC 58.140 33.333 7.68 0.00 45.87 3.68
9022 10210 4.654091 ATTTGGATTCATACCTTTGCGG 57.346 40.909 0.00 0.00 39.35 5.69
9041 10229 1.333619 GGCTTGTTTGCTTTCTCACGA 59.666 47.619 0.00 0.00 0.00 4.35
9054 10242 5.422666 TTTCTCACGACGTAGACAACTAA 57.577 39.130 0.00 0.00 0.00 2.24
9095 10283 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
9098 10286 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
9099 10287 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
9173 10400 8.359642 TCCCAAAATTCTTGTCTTAGATTTGTG 58.640 33.333 0.00 0.00 28.79 3.33
9368 10596 2.128535 TGGTTTTCCACACCTGACCTA 58.871 47.619 0.00 0.00 46.22 3.08
9426 10654 2.667171 GCCGCGTTTCATCTTTTGCTTA 60.667 45.455 4.92 0.00 0.00 3.09
9533 10761 0.602638 AGACATTTTCGGCAGCACGA 60.603 50.000 0.00 0.00 41.76 4.35
9591 10819 8.076178 GTGCAGTGTGTTATTAATTGGATATCC 58.924 37.037 15.39 15.39 0.00 2.59
9596 10824 9.337396 GTGTGTTATTAATTGGATATCCTGTCA 57.663 33.333 22.35 4.80 36.82 3.58
9608 10836 2.242572 CCTGTCATCGATGCAGCCG 61.243 63.158 29.10 19.46 33.55 5.52
9734 10962 5.486063 GGTTATTTTACAGGAATTTGGGGGT 59.514 40.000 0.00 0.00 0.00 4.95
9738 10966 7.634526 ATTTTACAGGAATTTGGGGGTTTAA 57.365 32.000 0.00 0.00 0.00 1.52
9739 10967 6.673839 TTTACAGGAATTTGGGGGTTTAAG 57.326 37.500 0.00 0.00 0.00 1.85
9751 10979 1.671556 GGGTTTAAGCGTGCCCATTTG 60.672 52.381 0.00 0.00 40.76 2.32
9757 10985 5.899120 TTAAGCGTGCCCATTTGTTATTA 57.101 34.783 0.00 0.00 0.00 0.98
9758 10986 6.458232 TTAAGCGTGCCCATTTGTTATTAT 57.542 33.333 0.00 0.00 0.00 1.28
9760 10988 6.458232 AAGCGTGCCCATTTGTTATTATTA 57.542 33.333 0.00 0.00 0.00 0.98
9761 10989 6.648879 AGCGTGCCCATTTGTTATTATTAT 57.351 33.333 0.00 0.00 0.00 1.28
9763 10991 7.145323 AGCGTGCCCATTTGTTATTATTATTC 58.855 34.615 0.00 0.00 0.00 1.75
9764 10992 7.014230 AGCGTGCCCATTTGTTATTATTATTCT 59.986 33.333 0.00 0.00 0.00 2.40
9765 10993 7.651704 GCGTGCCCATTTGTTATTATTATTCTT 59.348 33.333 0.00 0.00 0.00 2.52
9821 11056 9.733556 TTCTGTAAGCCTGAAAGATTATTAACA 57.266 29.630 0.00 0.00 34.07 2.41
9822 11057 9.905713 TCTGTAAGCCTGAAAGATTATTAACAT 57.094 29.630 0.00 0.00 34.07 2.71
9823 11058 9.941664 CTGTAAGCCTGAAAGATTATTAACATG 57.058 33.333 0.00 0.00 34.07 3.21
9825 11060 6.396829 AGCCTGAAAGATTATTAACATGGC 57.603 37.500 0.00 0.00 34.07 4.40
9826 11061 5.009010 AGCCTGAAAGATTATTAACATGGCG 59.991 40.000 0.00 0.00 40.23 5.69
9827 11062 5.008613 GCCTGAAAGATTATTAACATGGCGA 59.991 40.000 0.00 0.00 34.07 5.54
9828 11063 6.294176 GCCTGAAAGATTATTAACATGGCGAT 60.294 38.462 0.00 0.00 34.07 4.58
9829 11064 7.301054 CCTGAAAGATTATTAACATGGCGATC 58.699 38.462 0.00 0.00 34.07 3.69
9848 11085 6.657541 GGCGATCTTTTATATGGGTGGAAATA 59.342 38.462 0.00 0.00 0.00 1.40
9858 11095 9.995003 TTATATGGGTGGAAATATGAAATTTGC 57.005 29.630 0.00 0.00 0.00 3.68
9875 11112 9.698309 TGAAATTTGCGGTAAAAATATTCTTGA 57.302 25.926 0.00 0.00 0.00 3.02
9882 11119 9.781834 TGCGGTAAAAATATTCTTGAATAGTTG 57.218 29.630 14.16 5.59 0.00 3.16
9883 11120 9.233232 GCGGTAAAAATATTCTTGAATAGTTGG 57.767 33.333 14.16 5.99 0.00 3.77
9884 11121 9.233232 CGGTAAAAATATTCTTGAATAGTTGGC 57.767 33.333 14.16 8.96 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.353423 AGTATATTGAGAAGCCAACAAAATGT 57.647 30.769 0.00 0.00 0.00 2.71
128 129 2.626455 GGCCTAATTTCTCGCGCG 59.374 61.111 26.76 26.76 0.00 6.86
130 131 0.300789 GTTCGGCCTAATTTCTCGCG 59.699 55.000 0.00 0.00 0.00 5.87
145 146 1.993370 CAGGAAGCTTAAGACCGTTCG 59.007 52.381 6.67 0.00 0.00 3.95
154 155 2.260822 AGCTGACTCCAGGAAGCTTAA 58.739 47.619 8.19 0.00 43.33 1.85
241 242 0.736325 CGCGTTTCTGAGGATTCCGT 60.736 55.000 0.00 0.00 0.00 4.69
242 243 0.736325 ACGCGTTTCTGAGGATTCCG 60.736 55.000 5.58 0.00 0.00 4.30
259 260 3.239026 CACACGTAATTAGGCGAACTACG 59.761 47.826 17.39 17.39 45.66 3.51
277 278 2.981560 CTTGGCGGTGGCATCACAC 61.982 63.158 0.00 0.00 45.32 3.82
319 320 1.719246 CGCGTGACAAAAGAATCGAGA 59.281 47.619 0.00 0.00 0.00 4.04
321 322 0.162933 GCGCGTGACAAAAGAATCGA 59.837 50.000 8.43 0.00 0.00 3.59
335 336 3.114647 GATCGAGAGGACTGCGCGT 62.115 63.158 8.43 3.28 0.00 6.01
338 339 0.863538 CAACGATCGAGAGGACTGCG 60.864 60.000 24.34 0.00 0.00 5.18
380 381 1.203523 GAGGAACGCTCTGAGTGTCAT 59.796 52.381 22.77 14.14 38.11 3.06
385 386 1.048601 TTTGGAGGAACGCTCTGAGT 58.951 50.000 6.53 0.00 0.00 3.41
390 391 0.955919 CCCAGTTTGGAGGAACGCTC 60.956 60.000 0.00 0.00 40.96 5.03
392 393 2.626780 GCCCAGTTTGGAGGAACGC 61.627 63.158 0.00 0.00 40.96 4.84
418 519 4.074526 GTGCGCCAGCTCCTCTCA 62.075 66.667 4.18 0.00 45.42 3.27
440 541 2.357517 AGAAGCCAGCACCGTTCG 60.358 61.111 0.00 0.00 0.00 3.95
452 553 1.195674 GCTCCAACTCAAACGAGAAGC 59.804 52.381 0.00 0.00 34.41 3.86
460 561 0.250901 GCTCTGGGCTCCAACTCAAA 60.251 55.000 0.00 0.00 38.06 2.69
462 563 2.947532 CGCTCTGGGCTCCAACTCA 61.948 63.158 0.00 0.00 39.13 3.41
494 595 2.671177 CCGCGTTGCTCAACTCCAG 61.671 63.158 4.92 0.00 39.08 3.86
504 605 2.357034 TGAAGTCCTCCGCGTTGC 60.357 61.111 4.92 0.00 0.00 4.17
554 655 5.469421 TCATTGGCTTGCACAAAAATTAAGG 59.531 36.000 0.00 0.00 0.00 2.69
578 679 5.471556 TGGAACAGAATCATTGCATTTGT 57.528 34.783 0.00 0.00 0.00 2.83
773 1145 9.078990 ACCTTCATATTCTAGATGACGATAACA 57.921 33.333 0.00 0.00 33.06 2.41
814 1186 6.407202 ACACGATTTTAAGGTAGCTTCTGAT 58.593 36.000 11.11 3.55 0.00 2.90
815 1187 5.790593 ACACGATTTTAAGGTAGCTTCTGA 58.209 37.500 11.11 0.00 0.00 3.27
816 1188 7.591006 TTACACGATTTTAAGGTAGCTTCTG 57.409 36.000 11.11 0.49 0.00 3.02
817 1189 8.788325 AATTACACGATTTTAAGGTAGCTTCT 57.212 30.769 11.11 0.00 0.00 2.85
1272 1646 2.289444 ACCACTAACTCGGTGTGAATGG 60.289 50.000 0.00 0.00 33.05 3.16
1280 1654 0.893447 GCAGGTACCACTAACTCGGT 59.107 55.000 15.94 0.00 39.41 4.69
1282 1656 1.736032 GCTGCAGGTACCACTAACTCG 60.736 57.143 17.12 0.00 0.00 4.18
1504 1890 4.141620 ACTCTTTCTTTTCTGTCCTCTGCA 60.142 41.667 0.00 0.00 0.00 4.41
1514 1900 8.414003 GGATTGTAACCAAACTCTTTCTTTTCT 58.586 33.333 0.00 0.00 33.44 2.52
1659 2047 3.197790 CAATCAGTCGCCTGGCCG 61.198 66.667 14.12 8.64 39.31 6.13
1671 2059 5.128205 CAATCATCTACTGCCCTTCAATCA 58.872 41.667 0.00 0.00 0.00 2.57
1675 2063 2.923121 GCAATCATCTACTGCCCTTCA 58.077 47.619 0.00 0.00 0.00 3.02
1762 2150 4.789807 CAGGAGTCCAAAAGGATCATCAT 58.210 43.478 12.86 0.00 0.00 2.45
1781 2169 4.764823 TCCTATTACAAACCAAACAGCAGG 59.235 41.667 0.00 0.00 0.00 4.85
1863 2251 1.228245 AAACACACTGCATCCGCCT 60.228 52.632 0.00 0.00 37.32 5.52
1865 2253 1.210155 GGAAACACACTGCATCCGC 59.790 57.895 0.00 0.00 39.24 5.54
2155 2556 9.332502 AGTACAGTACACATCAAACAATTGTTA 57.667 29.630 23.53 10.14 37.25 2.41
2590 3018 7.147794 CCCATAAACCCAGCGTATATATGAGTA 60.148 40.741 6.12 0.00 0.00 2.59
2600 3028 1.225148 GCCCCATAAACCCAGCGTA 59.775 57.895 0.00 0.00 0.00 4.42
2601 3029 2.044352 GCCCCATAAACCCAGCGT 60.044 61.111 0.00 0.00 0.00 5.07
2602 3030 2.833121 GGCCCCATAAACCCAGCG 60.833 66.667 0.00 0.00 0.00 5.18
2627 3060 2.816411 CCCTGTTAGTGAGGGTAGTCA 58.184 52.381 0.00 0.00 44.85 3.41
2685 3118 7.770801 AAAAATACTGAACTTGGTTTTCTGC 57.229 32.000 0.00 0.00 0.00 4.26
2777 3210 9.690913 CACTGAATATACCAAATATCCATCCAT 57.309 33.333 0.00 0.00 0.00 3.41
2783 3216 9.950496 ATGACTCACTGAATATACCAAATATCC 57.050 33.333 0.00 0.00 0.00 2.59
2788 3221 9.817809 GACTAATGACTCACTGAATATACCAAA 57.182 33.333 0.00 0.00 0.00 3.28
2789 3222 9.201989 AGACTAATGACTCACTGAATATACCAA 57.798 33.333 0.00 0.00 0.00 3.67
2790 3223 8.633561 CAGACTAATGACTCACTGAATATACCA 58.366 37.037 0.00 0.00 0.00 3.25
2791 3224 8.634444 ACAGACTAATGACTCACTGAATATACC 58.366 37.037 0.00 0.00 0.00 2.73
2792 3225 9.457110 CACAGACTAATGACTCACTGAATATAC 57.543 37.037 0.00 0.00 0.00 1.47
2793 3226 8.633561 CCACAGACTAATGACTCACTGAATATA 58.366 37.037 0.00 0.00 0.00 0.86
2794 3227 7.418368 CCCACAGACTAATGACTCACTGAATAT 60.418 40.741 0.00 0.00 0.00 1.28
3246 3771 8.301002 GCACATTAAGGTTTAATTTGGTAGACA 58.699 33.333 8.79 0.00 0.00 3.41
3262 3787 2.755103 GGAAAGGAGGTGCACATTAAGG 59.245 50.000 20.43 0.00 0.00 2.69
3371 3906 4.000988 ACCATGTTGTACGACAGGATTTC 58.999 43.478 25.77 0.00 33.41 2.17
3465 4000 2.381725 ACAACGGAAGCTTAGTAGGC 57.618 50.000 0.00 0.00 0.00 3.93
3853 4477 6.986904 ACCTTTTCTGTAGCAGCTATAAAC 57.013 37.500 5.14 0.00 0.00 2.01
3939 4563 8.738645 AGGACAAGAGGTGAAAATAATATCAC 57.261 34.615 0.00 0.00 44.07 3.06
4180 4804 1.317613 TCAGGCACAATGGTGTTGTC 58.682 50.000 1.31 0.00 46.95 3.18
4605 5233 3.181451 ACTCTTCAGGAACATCAACAGCA 60.181 43.478 0.00 0.00 0.00 4.41
4785 5413 5.530519 TTTCATTGCTTGTCGTAGATGTC 57.469 39.130 0.00 0.00 40.67 3.06
4867 5495 1.559149 CCAAGCACAATGGTTTGCGC 61.559 55.000 0.00 0.00 43.87 6.09
4957 5585 7.607250 TGGCAAGTTTTAGAAAGAAGAAACAA 58.393 30.769 0.00 0.00 35.13 2.83
5026 5655 5.076182 TGGATGAATTCTTTGCCACACTTA 58.924 37.500 7.05 0.00 0.00 2.24
5523 6152 2.033141 CCACAGCTCCACCACCAG 59.967 66.667 0.00 0.00 0.00 4.00
5633 6262 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
5634 6263 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
5635 6264 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5636 6265 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
5637 6266 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
5638 6267 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
5639 6268 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
5640 6269 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
5641 6270 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
5642 6271 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
5643 6272 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
5685 6314 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
5686 6315 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
5687 6316 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
5688 6317 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
5689 6318 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
5690 6319 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
5691 6320 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
5692 6321 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
5693 6322 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5694 6323 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5695 6324 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5696 6325 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5697 6326 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5698 6327 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
5699 6328 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
5700 6329 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
5701 6330 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
5702 6331 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
5703 6332 0.106167 CATCTACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
5704 6333 0.106116 ACATCTACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
5705 6334 1.133730 AGACATCTACTCCCTCCGTCC 60.134 57.143 0.00 0.00 0.00 4.79
5706 6335 1.950909 CAGACATCTACTCCCTCCGTC 59.049 57.143 0.00 0.00 0.00 4.79
5707 6336 2.024825 GCAGACATCTACTCCCTCCGT 61.025 57.143 0.00 0.00 0.00 4.69
5708 6337 0.671251 GCAGACATCTACTCCCTCCG 59.329 60.000 0.00 0.00 0.00 4.63
5709 6338 2.080654 AGCAGACATCTACTCCCTCC 57.919 55.000 0.00 0.00 0.00 4.30
5710 6339 5.303078 TCATTTAGCAGACATCTACTCCCTC 59.697 44.000 0.00 0.00 0.00 4.30
5711 6340 5.211973 TCATTTAGCAGACATCTACTCCCT 58.788 41.667 0.00 0.00 0.00 4.20
5712 6341 5.537300 TCATTTAGCAGACATCTACTCCC 57.463 43.478 0.00 0.00 0.00 4.30
5713 6342 6.578023 AGTTCATTTAGCAGACATCTACTCC 58.422 40.000 0.00 0.00 0.00 3.85
5714 6343 7.465245 GCAAGTTCATTTAGCAGACATCTACTC 60.465 40.741 0.00 0.00 0.00 2.59
5863 6494 5.648092 GGAAACTACTGGTGCATTGAAGTAT 59.352 40.000 0.00 0.00 0.00 2.12
5949 6996 8.663209 AGCAGTCCAGACTTCTTGATATATAT 57.337 34.615 0.00 0.00 40.20 0.86
6283 7332 3.449377 TGGTTTCCAGTTTTCCAAACCTC 59.551 43.478 12.40 0.00 45.50 3.85
6514 7602 3.609853 TCACCATCACATGAAAGCTACC 58.390 45.455 0.00 0.00 0.00 3.18
6518 7606 3.004106 GGCTATCACCATCACATGAAAGC 59.996 47.826 0.00 0.00 0.00 3.51
6665 7753 5.442391 TCCCTAAGTAAATATTGGGTGCAC 58.558 41.667 8.80 8.80 36.23 4.57
6793 7881 7.621991 ACTCGACGAATATCTGCAATTTAAAG 58.378 34.615 0.00 0.00 0.00 1.85
6794 7882 7.534085 ACTCGACGAATATCTGCAATTTAAA 57.466 32.000 0.00 0.00 0.00 1.52
6916 8007 4.224370 GTCAAGAGTTACCCTTACCCATGA 59.776 45.833 0.00 0.00 0.00 3.07
6924 8015 2.054799 TGCCAGTCAAGAGTTACCCTT 58.945 47.619 0.00 0.00 0.00 3.95
6977 8068 8.836413 TGTCATTTACCAGAAACTTGTAAGAAG 58.164 33.333 0.00 0.00 0.00 2.85
6993 8084 7.562135 TGAACCTTATAGTCCTGTCATTTACC 58.438 38.462 0.00 0.00 0.00 2.85
6995 8086 8.141909 CGATGAACCTTATAGTCCTGTCATTTA 58.858 37.037 0.00 0.00 0.00 1.40
7098 8189 2.240667 CTGGTCCATTCCAACTCTCCAT 59.759 50.000 0.00 0.00 37.01 3.41
7103 8194 3.634397 TCATCTGGTCCATTCCAACTC 57.366 47.619 0.00 0.00 37.01 3.01
7210 8301 5.393962 ACTTCAGACAAATCTTAAATGCGC 58.606 37.500 0.00 0.00 30.42 6.09
7216 8307 9.787532 CAAAGTTTGACTTCAGACAAATCTTAA 57.212 29.630 10.19 0.00 37.47 1.85
7327 8419 9.385902 CGACATTCACAATACCAAATCAATATC 57.614 33.333 0.00 0.00 0.00 1.63
7638 8730 6.612456 TCCAGGAGAATAAAGGACGGTAAATA 59.388 38.462 0.00 0.00 0.00 1.40
7668 8760 8.073768 ACATAAATAAGTGAAAACACCTGAACG 58.926 33.333 0.00 0.00 0.00 3.95
8548 9723 5.350633 TCCAACTTTGAAAATGCTTCTGTG 58.649 37.500 0.00 0.00 0.00 3.66
8573 9748 3.445008 TCTTTGCCTGAGGACTACTGAT 58.555 45.455 0.65 0.00 0.00 2.90
8882 10070 6.823689 AGTTCCTAATGTACATGTCAATCACC 59.176 38.462 9.63 0.00 0.00 4.02
9020 10208 1.758783 GTGAGAAAGCAAACAAGCCG 58.241 50.000 0.00 0.00 34.23 5.52
9022 10210 2.376032 GTCGTGAGAAAGCAAACAAGC 58.624 47.619 0.00 0.00 45.01 4.01
9041 10229 9.314321 CATTGGAAGATATTTAGTTGTCTACGT 57.686 33.333 0.00 0.00 0.00 3.57
9073 10261 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
9075 10263 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
9076 10264 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
9077 10265 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
9079 10267 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
9080 10268 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
9081 10269 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
9082 10270 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
9083 10271 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
9085 10273 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
9088 10276 2.108970 ACTCAAATACTCCCTCCGTCC 58.891 52.381 0.00 0.00 0.00 4.79
9089 10277 3.056035 ACAACTCAAATACTCCCTCCGTC 60.056 47.826 0.00 0.00 0.00 4.79
9090 10278 2.904434 ACAACTCAAATACTCCCTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
9092 10280 4.430908 CGTACAACTCAAATACTCCCTCC 58.569 47.826 0.00 0.00 0.00 4.30
9093 10281 3.864003 GCGTACAACTCAAATACTCCCTC 59.136 47.826 0.00 0.00 0.00 4.30
9095 10283 3.592059 TGCGTACAACTCAAATACTCCC 58.408 45.455 0.00 0.00 0.00 4.30
9098 10286 6.259167 TCAAACTTGCGTACAACTCAAATACT 59.741 34.615 0.00 0.00 0.00 2.12
9099 10287 6.423862 TCAAACTTGCGTACAACTCAAATAC 58.576 36.000 0.00 0.00 0.00 1.89
9173 10400 7.645340 ACACGTGTTAGATACATCCGTATTTAC 59.355 37.037 17.22 0.00 37.36 2.01
9368 10596 1.202475 ACGGTGCAAAAATTTCGGCTT 60.202 42.857 13.23 0.00 0.00 4.35
9396 10624 1.226295 GAAACGCGGCCTAACATGC 60.226 57.895 12.47 0.00 0.00 4.06
9533 10761 2.760092 ACGCAATATGCAAAGAATGGGT 59.240 40.909 2.99 0.00 45.36 4.51
9557 10785 1.590610 AACACACTGCACCAAACGCA 61.591 50.000 0.00 0.00 37.88 5.24
9558 10786 0.378962 TAACACACTGCACCAAACGC 59.621 50.000 0.00 0.00 0.00 4.84
9591 10819 2.242572 CCGGCTGCATCGATGACAG 61.243 63.158 29.64 29.64 36.05 3.51
9596 10824 1.391933 TACACTCCGGCTGCATCGAT 61.392 55.000 10.58 0.00 0.00 3.59
9598 10826 0.941463 GATACACTCCGGCTGCATCG 60.941 60.000 0.50 0.00 0.00 3.84
9608 10836 5.046520 ACCTTACAGGAACAAGATACACTCC 60.047 44.000 0.00 0.00 37.67 3.85
9734 10962 4.792521 ATAACAAATGGGCACGCTTAAA 57.207 36.364 0.00 0.00 0.00 1.52
9738 10966 6.648879 ATAATAATAACAAATGGGCACGCT 57.351 33.333 0.00 0.00 0.00 5.07
9739 10967 7.145323 AGAATAATAATAACAAATGGGCACGC 58.855 34.615 0.00 0.00 0.00 5.34
9761 10989 9.778741 ACTCAAGAATTCTACATGTACAAAGAA 57.221 29.630 8.75 16.42 32.85 2.52
9800 11035 7.255104 CGCCATGTTAATAATCTTTCAGGCTTA 60.255 37.037 0.00 0.00 35.23 3.09
9820 11055 4.156556 CCACCCATATAAAAGATCGCCATG 59.843 45.833 0.00 0.00 0.00 3.66
9821 11056 4.042809 TCCACCCATATAAAAGATCGCCAT 59.957 41.667 0.00 0.00 0.00 4.40
9822 11057 3.392947 TCCACCCATATAAAAGATCGCCA 59.607 43.478 0.00 0.00 0.00 5.69
9823 11058 4.015872 TCCACCCATATAAAAGATCGCC 57.984 45.455 0.00 0.00 0.00 5.54
9825 11060 9.448438 TCATATTTCCACCCATATAAAAGATCG 57.552 33.333 0.00 0.00 0.00 3.69
9836 11073 5.358922 CGCAAATTTCATATTTCCACCCAT 58.641 37.500 0.00 0.00 0.00 4.00
9858 11095 9.233232 GCCAACTATTCAAGAATATTTTTACCG 57.767 33.333 3.20 0.00 33.29 4.02


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

AutoCloner maintained by Alex Coulton.