Multiple sequence alignment - TraesCS7D01G526400

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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 TraesCS7D01G526400 chr7D 100.000 9150 0 0 1 9150 621810595 621819744 0.000000e+00 16897.0
1 TraesCS7D01G526400 chr7D 82.337 1104 168 20 1752 2844 621867814 621868901 0.000000e+00 933.0
2 TraesCS7D01G526400 chr7D 80.092 1090 177 21 1762 2835 3367127 3368192 0.000000e+00 774.0
3 TraesCS7D01G526400 chr7D 80.234 683 92 27 648 1319 621615273 621615923 2.990000e-129 473.0
4 TraesCS7D01G526400 chr7D 74.253 435 96 15 4897 5324 417912454 417912029 1.580000e-37 169.0
5 TraesCS7D01G526400 chr7D 93.827 81 5 0 2871 2951 621813545 621813465 1.250000e-23 122.0
6 TraesCS7D01G526400 chr7B 96.106 4520 149 8 4356 8862 717890830 717886325 0.000000e+00 7347.0
7 TraesCS7D01G526400 chr7B 97.185 2558 54 10 615 3158 717895263 717892710 0.000000e+00 4309.0
8 TraesCS7D01G526400 chr7B 91.215 2857 202 28 1 2822 718101418 718098576 0.000000e+00 3840.0
9 TraesCS7D01G526400 chr7B 96.147 571 22 0 3490 4060 717892378 717891808 0.000000e+00 933.0
10 TraesCS7D01G526400 chr7B 82.755 980 146 17 1770 2740 717659369 717658404 0.000000e+00 852.0
11 TraesCS7D01G526400 chr7B 79.648 1135 181 29 1790 2907 719431005 719432106 0.000000e+00 771.0
12 TraesCS7D01G526400 chr7B 89.146 562 54 6 7730 8286 718093922 718093363 0.000000e+00 693.0
13 TraesCS7D01G526400 chr7B 85.216 602 79 9 8099 8695 717657578 717656982 2.180000e-170 610.0
14 TraesCS7D01G526400 chr7B 95.090 387 17 2 1 385 717896631 717896245 7.860000e-170 608.0
15 TraesCS7D01G526400 chr7B 85.424 590 76 9 8099 8683 719628752 719629336 1.020000e-168 604.0
16 TraesCS7D01G526400 chr7B 82.788 581 80 11 8292 8862 717536695 717536125 1.370000e-137 501.0
17 TraesCS7D01G526400 chr7B 81.073 671 90 23 657 1316 718443818 718443174 1.370000e-137 501.0
18 TraesCS7D01G526400 chr7B 90.659 364 34 0 8345 8708 718093363 718093000 1.380000e-132 484.0
19 TraesCS7D01G526400 chr7B 92.283 311 15 6 3188 3494 717892710 717892405 5.070000e-117 433.0
20 TraesCS7D01G526400 chr7B 87.052 363 46 1 1735 2097 718442921 718442560 8.550000e-110 409.0
21 TraesCS7D01G526400 chr7B 97.156 211 5 1 413 623 717896251 717896042 1.130000e-93 355.0
22 TraesCS7D01G526400 chr7B 86.469 303 30 9 7199 7496 718094377 718094081 1.150000e-83 322.0
23 TraesCS7D01G526400 chr7B 95.181 166 7 1 8986 9150 717886327 717886162 2.530000e-65 261.0
24 TraesCS7D01G526400 chr7B 86.854 213 11 8 4053 4248 717891205 717890993 1.200000e-53 222.0
25 TraesCS7D01G526400 chr7B 89.571 163 15 2 8985 9147 717536128 717535968 1.200000e-48 206.0
26 TraesCS7D01G526400 chr7B 95.522 67 3 0 4308 4374 717890998 717890932 3.490000e-19 108.0
27 TraesCS7D01G526400 chr7B 90.123 81 8 0 2871 2951 717892917 717892997 1.260000e-18 106.0
28 TraesCS7D01G526400 chr7A 96.086 3168 62 6 1 3158 717370113 717373228 0.000000e+00 5107.0
29 TraesCS7D01G526400 chr7A 90.032 2498 204 25 4368 6851 717376083 717378549 0.000000e+00 3192.0
30 TraesCS7D01G526400 chr7A 95.159 1735 78 4 7132 8862 717378704 717380436 0.000000e+00 2734.0
31 TraesCS7D01G526400 chr7A 86.939 2205 251 29 632 2821 717252501 717254683 0.000000e+00 2442.0
32 TraesCS7D01G526400 chr7A 89.195 1814 151 30 7081 8862 717256178 717257978 0.000000e+00 2222.0
33 TraesCS7D01G526400 chr7A 86.103 1396 149 29 1457 2843 717582300 717583659 0.000000e+00 1461.0
34 TraesCS7D01G526400 chr7A 86.434 1290 128 25 1589 2843 717439395 717440672 0.000000e+00 1369.0
35 TraesCS7D01G526400 chr7A 92.793 777 37 5 3490 4248 717373560 717374335 0.000000e+00 1107.0
36 TraesCS7D01G526400 chr7A 84.448 598 72 7 8251 8847 717468447 717469024 3.710000e-158 569.0
37 TraesCS7D01G526400 chr7A 81.848 606 82 19 648 1244 717069556 717070142 1.380000e-132 484.0
38 TraesCS7D01G526400 chr7A 80.684 585 92 16 8286 8858 717394521 717395096 1.410000e-117 435.0
39 TraesCS7D01G526400 chr7A 91.401 314 18 6 3185 3494 717373225 717373533 1.100000e-113 422.0
40 TraesCS7D01G526400 chr7A 86.047 387 48 4 1735 2121 717070757 717071137 2.380000e-110 411.0
41 TraesCS7D01G526400 chr7A 79.470 604 88 16 8291 8862 717593348 717593947 6.660000e-106 396.0
42 TraesCS7D01G526400 chr7A 91.727 278 22 1 954 1230 717415061 717415338 1.440000e-102 385.0
43 TraesCS7D01G526400 chr7A 86.207 348 45 2 7694 8039 717466526 717466872 3.120000e-99 374.0
44 TraesCS7D01G526400 chr7A 88.088 319 23 9 6831 7142 717452146 717452456 1.880000e-96 364.0
45 TraesCS7D01G526400 chr7A 87.215 219 26 2 8054 8270 717467267 717467485 1.970000e-61 248.0
46 TraesCS7D01G526400 chr7A 96.575 146 5 0 6901 7046 717378564 717378709 9.180000e-60 243.0
47 TraesCS7D01G526400 chr7A 80.519 308 47 9 3053 3356 717440860 717441158 3.320000e-54 224.0
48 TraesCS7D01G526400 chr7A 89.222 167 15 3 8986 9150 717257976 717258141 1.200000e-48 206.0
49 TraesCS7D01G526400 chr7A 98.529 68 1 0 4308 4375 717374330 717374397 4.490000e-23 121.0
50 TraesCS7D01G526400 chr7A 91.358 81 7 0 2871 2951 717373031 717372951 2.700000e-20 111.0
51 TraesCS7D01G526400 chr7A 82.171 129 20 3 3491 3616 717584273 717584401 3.490000e-19 108.0
52 TraesCS7D01G526400 chr7A 81.928 83 13 2 5858 5939 693210717 693210798 1.650000e-07 69.4
53 TraesCS7D01G526400 chrUn 80.234 683 92 27 648 1319 314007956 314008606 2.990000e-129 473.0
54 TraesCS7D01G526400 chrUn 93.478 138 7 2 8855 8990 108731153 108731290 4.330000e-48 204.0
55 TraesCS7D01G526400 chr5D 75.843 534 107 14 4794 5324 526097590 526097076 1.530000e-62 252.0
56 TraesCS7D01G526400 chr5D 95.420 131 6 0 8858 8988 269087738 269087868 9.310000e-50 209.0
57 TraesCS7D01G526400 chr5D 88.462 78 8 1 1322 1399 367588028 367588104 9.780000e-15 93.5
58 TraesCS7D01G526400 chr3D 96.992 133 4 0 8859 8991 32145449 32145581 3.320000e-54 224.0
59 TraesCS7D01G526400 chr3B 96.094 128 5 0 8861 8988 262424981 262425108 9.310000e-50 209.0
60 TraesCS7D01G526400 chr2D 93.571 140 7 1 8853 8992 136461724 136461861 3.350000e-49 207.0
61 TraesCS7D01G526400 chr2D 90.667 75 7 0 4236 4310 95638668 95638742 5.850000e-17 100.0
62 TraesCS7D01G526400 chr1D 94.776 134 6 1 8856 8988 462888630 462888497 3.350000e-49 207.0
63 TraesCS7D01G526400 chr1D 94.776 134 6 1 8856 8988 462925592 462925459 3.350000e-49 207.0
64 TraesCS7D01G526400 chr1D 94.776 134 6 1 8856 8988 462930182 462930049 3.350000e-49 207.0
65 TraesCS7D01G526400 chr2B 93.893 131 8 0 8858 8988 709138584 709138714 2.020000e-46 198.0
66 TraesCS7D01G526400 chr3A 97.101 69 2 0 4242 4310 691376579 691376647 5.800000e-22 117.0
67 TraesCS7D01G526400 chr2A 88.095 84 9 1 2868 2951 235675358 235675440 2.100000e-16 99.0
68 TraesCS7D01G526400 chr2A 88.889 81 8 1 2871 2951 235675440 235675361 2.100000e-16 99.0
69 TraesCS7D01G526400 chr6A 87.805 82 9 1 2864 2945 8621055 8620975 2.720000e-15 95.3
70 TraesCS7D01G526400 chr6A 91.304 69 5 1 2874 2942 8620972 8621039 9.780000e-15 93.5
71 TraesCS7D01G526400 chr6B 91.935 62 3 2 5262 5322 620871407 620871467 1.640000e-12 86.1
72 TraesCS7D01G526400 chr4A 96.774 31 1 0 5912 5942 437498891 437498861 1.700000e-02 52.8


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 TraesCS7D01G526400 chr7D 621810595 621819744 9149 False 16897.000000 16897 100.000000 1 9150 1 chr7D.!!$F3 9149
1 TraesCS7D01G526400 chr7D 621867814 621868901 1087 False 933.000000 933 82.337000 1752 2844 1 chr7D.!!$F4 1092
2 TraesCS7D01G526400 chr7D 3367127 3368192 1065 False 774.000000 774 80.092000 1762 2835 1 chr7D.!!$F1 1073
3 TraesCS7D01G526400 chr7D 621615273 621615923 650 False 473.000000 473 80.234000 648 1319 1 chr7D.!!$F2 671
4 TraesCS7D01G526400 chr7B 718098576 718101418 2842 True 3840.000000 3840 91.215000 1 2822 1 chr7B.!!$R1 2821
5 TraesCS7D01G526400 chr7B 717886162 717896631 10469 True 1619.555556 7347 94.613778 1 9150 9 chr7B.!!$R4 9149
6 TraesCS7D01G526400 chr7B 719431005 719432106 1101 False 771.000000 771 79.648000 1790 2907 1 chr7B.!!$F2 1117
7 TraesCS7D01G526400 chr7B 717656982 717659369 2387 True 731.000000 852 83.985500 1770 8695 2 chr7B.!!$R3 6925
8 TraesCS7D01G526400 chr7B 719628752 719629336 584 False 604.000000 604 85.424000 8099 8683 1 chr7B.!!$F3 584
9 TraesCS7D01G526400 chr7B 718093000 718094377 1377 True 499.666667 693 88.758000 7199 8708 3 chr7B.!!$R5 1509
10 TraesCS7D01G526400 chr7B 718442560 718443818 1258 True 455.000000 501 84.062500 657 2097 2 chr7B.!!$R6 1440
11 TraesCS7D01G526400 chr7B 717535968 717536695 727 True 353.500000 501 86.179500 8292 9147 2 chr7B.!!$R2 855
12 TraesCS7D01G526400 chr7A 717370113 717380436 10323 False 1846.571429 5107 94.367857 1 8862 7 chr7A.!!$F8 8861
13 TraesCS7D01G526400 chr7A 717252501 717258141 5640 False 1623.333333 2442 88.452000 632 9150 3 chr7A.!!$F7 8518
14 TraesCS7D01G526400 chr7A 717439395 717441158 1763 False 796.500000 1369 83.476500 1589 3356 2 chr7A.!!$F9 1767
15 TraesCS7D01G526400 chr7A 717582300 717584401 2101 False 784.500000 1461 84.137000 1457 3616 2 chr7A.!!$F11 2159
16 TraesCS7D01G526400 chr7A 717069556 717071137 1581 False 447.500000 484 83.947500 648 2121 2 chr7A.!!$F6 1473
17 TraesCS7D01G526400 chr7A 717394521 717395096 575 False 435.000000 435 80.684000 8286 8858 1 chr7A.!!$F2 572
18 TraesCS7D01G526400 chr7A 717466526 717469024 2498 False 397.000000 569 85.956667 7694 8847 3 chr7A.!!$F10 1153
19 TraesCS7D01G526400 chr7A 717593348 717593947 599 False 396.000000 396 79.470000 8291 8862 1 chr7A.!!$F5 571
20 TraesCS7D01G526400 chrUn 314007956 314008606 650 False 473.000000 473 80.234000 648 1319 1 chrUn.!!$F2 671
21 TraesCS7D01G526400 chr5D 526097076 526097590 514 True 252.000000 252 75.843000 4794 5324 1 chr5D.!!$R1 530

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
668 1460 1.064003 TGTACATGACCTGCCTTGGT 58.936 50.000 0.0 0.0 44.10 3.67 F
2484 3678 3.748048 CGATGAGAAGTCACAAACCATGT 59.252 43.478 0.0 0.0 45.34 3.21 F
3818 5296 0.388520 GGTTGTGAAAATGCGAGGGC 60.389 55.000 0.0 0.0 40.52 5.19 F
4714 9202 0.039256 CACGAGGCACCCAAAACATG 60.039 55.000 0.0 0.0 0.00 3.21 F
5233 9727 0.546122 ACAACAAGGGCACTGACTCA 59.454 50.000 0.0 0.0 0.00 3.41 F
6254 10759 0.673644 CACCACCCCTCGACATTGAC 60.674 60.000 0.0 0.0 0.00 3.18 F
6308 10813 0.319083 ATCGCAACGGTCAGGTAACA 59.681 50.000 0.0 0.0 41.41 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 3686 2.826128 AGCTTACAGTGATCCAAGACGA 59.174 45.455 0.00 0.00 0.00 4.20 R
4388 8876 0.259065 ATGACCGGCCTCTAGACTCA 59.741 55.000 0.00 0.00 0.00 3.41 R
5475 9976 0.179018 GTGGTGCCTTGGTGTCTTCT 60.179 55.000 0.00 0.00 0.00 2.85 R
5960 10462 0.695803 AGGGTGCTTCCTATGGAGGG 60.696 60.000 0.00 0.00 43.94 4.30 R
6263 10768 0.740868 CGATTGAGGTGCGTCCACAT 60.741 55.000 0.75 0.00 43.88 3.21 R
7988 12516 0.905357 AAGGGAGCATACGAGCTTGT 59.095 50.000 12.27 12.27 46.75 3.16 R
8203 13114 1.228894 ACTCGGTGAGGGAGCTTCA 60.229 57.895 0.00 0.00 34.87 3.02 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
185 187 3.154710 TGTAGTCTTCTTCTTCCTCGCA 58.845 45.455 0.00 0.00 0.00 5.10
423 429 5.308237 AGAGTCCCACAACTAACTTGATTCT 59.692 40.000 0.00 0.00 33.59 2.40
668 1460 1.064003 TGTACATGACCTGCCTTGGT 58.936 50.000 0.00 0.00 44.10 3.67
2201 3383 5.645497 AGTGAGATAGACTGGAAAACAATGC 59.355 40.000 0.00 0.00 0.00 3.56
2280 3471 4.854173 TGGCTCAATGCTACTTTTCCATA 58.146 39.130 0.00 0.00 42.39 2.74
2484 3678 3.748048 CGATGAGAAGTCACAAACCATGT 59.252 43.478 0.00 0.00 45.34 3.21
3068 4446 7.039882 AGAAATTGAATGGCTCTAAGCATTTG 58.960 34.615 0.86 0.00 44.75 2.32
3146 4554 5.751028 GGACTCTCTAAATCATGTGCAGTAC 59.249 44.000 0.00 0.00 0.00 2.73
3165 4575 6.875195 GCAGTACACCACACTAGGTTATTTTA 59.125 38.462 0.00 0.00 40.77 1.52
3186 4596 6.585695 TTAATGTAACATTGGCGGGTTTAA 57.414 33.333 0.00 0.00 0.00 1.52
3399 4844 3.813166 ACGACCATACAAAACCTTGACAG 59.187 43.478 0.00 0.00 36.33 3.51
3424 4869 2.983898 AGACAAACCCCCTAGCTAAACA 59.016 45.455 0.00 0.00 0.00 2.83
3435 4880 2.674796 AGCTAAACAAGGCTAGGACG 57.325 50.000 0.00 0.00 37.00 4.79
3436 4881 2.176889 AGCTAAACAAGGCTAGGACGA 58.823 47.619 0.00 0.00 37.00 4.20
3437 4882 2.094130 AGCTAAACAAGGCTAGGACGAC 60.094 50.000 0.00 0.00 37.00 4.34
3438 4883 2.094130 GCTAAACAAGGCTAGGACGACT 60.094 50.000 0.00 0.00 0.00 4.18
3439 4884 2.457366 AAACAAGGCTAGGACGACTG 57.543 50.000 0.00 0.00 0.00 3.51
3441 4886 0.889306 ACAAGGCTAGGACGACTGTC 59.111 55.000 0.00 0.00 44.72 3.51
3613 5091 4.325119 TGCACAATTTTGCTGGCATTAAT 58.675 34.783 16.97 0.00 43.41 1.40
3656 5134 1.442886 TTGGGGAGGGTCTTGCCAAT 61.443 55.000 0.00 0.00 39.65 3.16
3665 5143 4.218312 AGGGTCTTGCCAATCCAAATATC 58.782 43.478 2.19 0.00 39.65 1.63
3684 5162 9.123902 CAAATATCCATGTTTACCTCAAGATCA 57.876 33.333 0.00 0.00 0.00 2.92
3812 5290 2.393764 CCAAGACGGTTGTGAAAATGC 58.606 47.619 0.00 0.00 0.00 3.56
3818 5296 0.388520 GGTTGTGAAAATGCGAGGGC 60.389 55.000 0.00 0.00 40.52 5.19
3900 5378 3.317711 GTCCACACATTGATGGTGTTTCA 59.682 43.478 10.26 0.00 46.75 2.69
4044 6155 6.594937 CCATTGAATTTTAATCACTTGTGGGG 59.405 38.462 0.64 0.00 0.00 4.96
4095 6816 2.808543 GCCCGGAAGTGATGTATGAATC 59.191 50.000 0.73 0.00 0.00 2.52
4097 6818 3.059884 CCGGAAGTGATGTATGAATCCG 58.940 50.000 0.00 4.42 45.83 4.18
4103 6824 6.862090 GGAAGTGATGTATGAATCCGTAGTAC 59.138 42.308 0.00 0.00 0.00 2.73
4135 6873 4.024048 CCAGTGCAGTTTGGTAAGTGTTAG 60.024 45.833 0.00 0.00 37.10 2.34
4214 7008 4.272489 TGGAGGCATGGATTCTAAACAAG 58.728 43.478 0.00 0.00 0.00 3.16
4250 7045 9.893305 AGAATTAGTTTTTCATCTACGGTTTTG 57.107 29.630 0.00 0.00 0.00 2.44
4251 7046 8.515473 AATTAGTTTTTCATCTACGGTTTTGC 57.485 30.769 0.00 0.00 0.00 3.68
4252 7047 5.767816 AGTTTTTCATCTACGGTTTTGCT 57.232 34.783 0.00 0.00 0.00 3.91
4253 7048 6.870971 AGTTTTTCATCTACGGTTTTGCTA 57.129 33.333 0.00 0.00 0.00 3.49
4254 7049 6.899114 AGTTTTTCATCTACGGTTTTGCTAG 58.101 36.000 0.00 0.00 0.00 3.42
4255 7050 6.708949 AGTTTTTCATCTACGGTTTTGCTAGA 59.291 34.615 0.00 0.00 0.00 2.43
4256 7051 7.227910 AGTTTTTCATCTACGGTTTTGCTAGAA 59.772 33.333 0.00 0.00 0.00 2.10
4257 7052 6.476243 TTTCATCTACGGTTTTGCTAGAAC 57.524 37.500 0.00 0.00 0.00 3.01
4258 7053 5.401531 TCATCTACGGTTTTGCTAGAACT 57.598 39.130 0.00 0.00 0.00 3.01
4259 7054 5.408356 TCATCTACGGTTTTGCTAGAACTC 58.592 41.667 0.00 0.00 0.00 3.01
4260 7055 4.859304 TCTACGGTTTTGCTAGAACTCA 57.141 40.909 0.00 0.00 0.00 3.41
4261 7056 5.401531 TCTACGGTTTTGCTAGAACTCAT 57.598 39.130 0.00 0.00 0.00 2.90
4262 7057 5.408356 TCTACGGTTTTGCTAGAACTCATC 58.592 41.667 0.00 0.00 0.00 2.92
4263 7058 4.273148 ACGGTTTTGCTAGAACTCATCT 57.727 40.909 0.00 0.00 42.48 2.90
4264 7059 4.246458 ACGGTTTTGCTAGAACTCATCTC 58.754 43.478 0.00 0.00 39.71 2.75
4265 7060 3.304559 CGGTTTTGCTAGAACTCATCTCG 59.695 47.826 0.00 0.00 39.71 4.04
4266 7061 3.062774 GGTTTTGCTAGAACTCATCTCGC 59.937 47.826 0.00 0.00 44.84 5.03
4267 7062 3.876274 TTTGCTAGAACTCATCTCGCT 57.124 42.857 0.00 0.00 44.86 4.93
4268 7063 2.859526 TGCTAGAACTCATCTCGCTG 57.140 50.000 0.00 0.00 44.86 5.18
4269 7064 2.369394 TGCTAGAACTCATCTCGCTGA 58.631 47.619 0.00 0.00 44.86 4.26
4270 7065 2.357323 TGCTAGAACTCATCTCGCTGAG 59.643 50.000 0.00 7.62 44.86 3.35
4278 7073 4.630894 CTCATCTCGCTGAGTTCTAGTT 57.369 45.455 5.66 0.00 38.27 2.24
4279 7074 5.743026 CTCATCTCGCTGAGTTCTAGTTA 57.257 43.478 5.66 0.00 38.27 2.24
4280 7075 6.312399 CTCATCTCGCTGAGTTCTAGTTAT 57.688 41.667 5.66 0.00 38.27 1.89
4281 7076 6.066054 TCATCTCGCTGAGTTCTAGTTATG 57.934 41.667 5.66 0.00 0.00 1.90
4282 7077 5.590663 TCATCTCGCTGAGTTCTAGTTATGT 59.409 40.000 5.66 0.00 0.00 2.29
4283 7078 5.487153 TCTCGCTGAGTTCTAGTTATGTC 57.513 43.478 5.66 0.00 0.00 3.06
4284 7079 5.186942 TCTCGCTGAGTTCTAGTTATGTCT 58.813 41.667 5.66 0.00 0.00 3.41
4285 7080 5.294799 TCTCGCTGAGTTCTAGTTATGTCTC 59.705 44.000 5.66 0.00 0.00 3.36
4286 7081 4.941873 TCGCTGAGTTCTAGTTATGTCTCA 59.058 41.667 0.00 0.00 0.00 3.27
4287 7082 5.590663 TCGCTGAGTTCTAGTTATGTCTCAT 59.409 40.000 0.00 0.00 32.73 2.90
4288 7083 6.095580 TCGCTGAGTTCTAGTTATGTCTCATT 59.904 38.462 0.00 0.00 32.73 2.57
4289 7084 6.416455 CGCTGAGTTCTAGTTATGTCTCATTC 59.584 42.308 0.00 0.00 32.73 2.67
4290 7085 7.261325 GCTGAGTTCTAGTTATGTCTCATTCA 58.739 38.462 0.00 0.00 32.73 2.57
4291 7086 7.221838 GCTGAGTTCTAGTTATGTCTCATTCAC 59.778 40.741 0.00 0.00 32.73 3.18
4292 7087 8.354711 TGAGTTCTAGTTATGTCTCATTCACT 57.645 34.615 0.00 0.00 0.00 3.41
4293 7088 8.807118 TGAGTTCTAGTTATGTCTCATTCACTT 58.193 33.333 0.00 0.00 0.00 3.16
4294 7089 9.646427 GAGTTCTAGTTATGTCTCATTCACTTT 57.354 33.333 0.00 0.00 0.00 2.66
4306 7101 9.330063 TGTCTCATTCACTTTTATAGCTATTGG 57.670 33.333 12.39 2.86 0.00 3.16
4307 7102 9.547753 GTCTCATTCACTTTTATAGCTATTGGA 57.452 33.333 12.39 0.00 0.00 3.53
4310 7105 9.288576 TCATTCACTTTTATAGCTATTGGATGG 57.711 33.333 17.80 5.28 0.00 3.51
4311 7106 9.071276 CATTCACTTTTATAGCTATTGGATGGT 57.929 33.333 12.39 1.76 0.00 3.55
4312 7107 9.646522 ATTCACTTTTATAGCTATTGGATGGTT 57.353 29.630 12.39 0.00 0.00 3.67
4329 7124 6.127758 TGGATGGTTGCACAAAGTTGATATAC 60.128 38.462 0.00 0.00 0.00 1.47
4388 8876 0.603707 CACGTGAATGTGGTCTGCCT 60.604 55.000 10.90 0.00 36.20 4.75
4404 8892 1.076632 CCTGAGTCTAGAGGCCGGT 60.077 63.158 1.90 0.00 0.00 5.28
4435 8923 2.093306 TGCCGAGTTTGAGTGGTATG 57.907 50.000 0.00 0.00 0.00 2.39
4441 8929 3.146066 GAGTTTGAGTGGTATGGTTGCA 58.854 45.455 0.00 0.00 0.00 4.08
4452 8940 1.180029 ATGGTTGCAGATCAGGTTGC 58.820 50.000 0.00 0.00 40.67 4.17
4467 8955 8.307483 AGATCAGGTTGCTGTGTATATATGTAC 58.693 37.037 2.82 2.82 0.00 2.90
4468 8956 6.755206 TCAGGTTGCTGTGTATATATGTACC 58.245 40.000 7.12 0.00 0.00 3.34
4475 8963 9.597170 TTGCTGTGTATATATGTACCGTAAAAA 57.403 29.630 7.12 0.00 0.00 1.94
4487 8975 7.422465 TGTACCGTAAAAATCCCTAGTACAT 57.578 36.000 0.00 0.00 35.25 2.29
4503 8991 5.994887 AGTACATCTAAGCTCTACGACAG 57.005 43.478 0.00 0.00 0.00 3.51
4536 9024 1.295792 GAGAACGGTGCAAAGTGTCA 58.704 50.000 0.00 0.00 0.00 3.58
4568 9056 1.884235 CCGAAGTGGGCAAGGATATC 58.116 55.000 0.00 0.00 0.00 1.63
4633 9121 0.839946 AAGAAGATAGCGGCACCCAT 59.160 50.000 1.45 0.00 0.00 4.00
4714 9202 0.039256 CACGAGGCACCCAAAACATG 60.039 55.000 0.00 0.00 0.00 3.21
4821 9310 1.134367 CTCGCCATCTAGACGACCAAA 59.866 52.381 0.00 0.00 0.00 3.28
4895 9384 2.754375 CAAACCGCCACCTAGGGT 59.246 61.111 14.81 0.00 38.09 4.34
5048 9538 3.878237 TCCATAGTAGGAGGTGTCGAT 57.122 47.619 0.00 0.00 32.77 3.59
5050 9540 2.558795 CCATAGTAGGAGGTGTCGATGG 59.441 54.545 0.00 0.00 0.00 3.51
5233 9727 0.546122 ACAACAAGGGCACTGACTCA 59.454 50.000 0.00 0.00 0.00 3.41
5380 9876 3.361786 AGCAACAACCCAACAAAGTACT 58.638 40.909 0.00 0.00 0.00 2.73
5694 10196 1.692519 AGAAACTCGCCTACACCAAGT 59.307 47.619 0.00 0.00 0.00 3.16
5757 10259 2.050350 CCCTTGCTGCCCACATGAG 61.050 63.158 0.00 0.00 0.00 2.90
5769 10271 2.082231 CCACATGAGCAAGAGGTGAAG 58.918 52.381 0.00 0.00 0.00 3.02
5797 10299 1.302949 GCCACCATGAAGCCTACCA 59.697 57.895 0.00 0.00 0.00 3.25
6002 10507 2.037847 GCATCCCCAGCCACCTTT 59.962 61.111 0.00 0.00 0.00 3.11
6037 10542 5.301298 GGAATACAACCTAGTCACTACCGAT 59.699 44.000 0.00 0.00 0.00 4.18
6108 10613 2.821991 AGTTCCCAGAGAGTGAAACG 57.178 50.000 0.00 0.00 45.86 3.60
6254 10759 0.673644 CACCACCCCTCGACATTGAC 60.674 60.000 0.00 0.00 0.00 3.18
6262 10767 1.428448 CTCGACATTGACGCCAGAAA 58.572 50.000 3.63 0.00 0.00 2.52
6263 10768 1.798223 CTCGACATTGACGCCAGAAAA 59.202 47.619 3.63 0.00 0.00 2.29
6308 10813 0.319083 ATCGCAACGGTCAGGTAACA 59.681 50.000 0.00 0.00 41.41 2.41
6365 10870 1.354040 CGAAGACTGCCACATCAGAC 58.646 55.000 0.00 0.00 37.51 3.51
6421 10928 4.437239 AGGCAGTCATTCAGATTCTAACG 58.563 43.478 0.00 0.00 0.00 3.18
6487 10994 4.683334 GTTCGGCAGCGGCACAAC 62.683 66.667 11.88 8.69 43.71 3.32
6505 11012 3.136626 ACAACATAGCCTTATCCTCCCAC 59.863 47.826 0.00 0.00 0.00 4.61
7042 11554 2.884894 ATACGAACCAACCGGATCTC 57.115 50.000 9.46 0.00 31.94 2.75
7155 11667 4.625607 AGCCTCCACCATTAGCTATTAC 57.374 45.455 0.00 0.00 30.46 1.89
7256 11777 0.964358 AGAGCAAGCAATCAGGGCAC 60.964 55.000 0.00 0.00 0.00 5.01
7267 11788 0.955428 TCAGGGCACGATGAAACTGC 60.955 55.000 0.00 0.00 0.00 4.40
7316 11837 1.670811 AGTTGGTGTCTTTGTTCTGCG 59.329 47.619 0.00 0.00 0.00 5.18
7547 12073 7.851822 ACATGTAAAGAAAGTAATTTGCACG 57.148 32.000 0.00 0.00 34.55 5.34
7660 12186 5.163622 GGAATCAATACCCACACATTCACTG 60.164 44.000 0.00 0.00 0.00 3.66
7988 12516 8.134202 TGTCTCTCAATATAAGTTTGGACAGA 57.866 34.615 0.00 0.00 0.00 3.41
8097 13005 4.007644 CAGTCCAGCCAGCCACGA 62.008 66.667 0.00 0.00 0.00 4.35
8445 14340 0.653636 TTGCCTTCAACGTCGAACAC 59.346 50.000 0.00 0.00 0.00 3.32
8625 14526 5.892160 CCATTGAGGATATGGCTACAATG 57.108 43.478 0.00 0.00 41.97 2.82
8865 14824 6.529463 TTTACTTACGCTTTGTTGTACTCC 57.471 37.500 0.00 0.00 0.00 3.85
8866 14825 3.396560 ACTTACGCTTTGTTGTACTCCC 58.603 45.455 0.00 0.00 0.00 4.30
8867 14826 3.070590 ACTTACGCTTTGTTGTACTCCCT 59.929 43.478 0.00 0.00 0.00 4.20
8868 14827 2.165319 ACGCTTTGTTGTACTCCCTC 57.835 50.000 0.00 0.00 0.00 4.30
8869 14828 1.270678 ACGCTTTGTTGTACTCCCTCC 60.271 52.381 0.00 0.00 0.00 4.30
8870 14829 1.439679 GCTTTGTTGTACTCCCTCCG 58.560 55.000 0.00 0.00 0.00 4.63
8871 14830 1.270678 GCTTTGTTGTACTCCCTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
8872 14831 2.809299 GCTTTGTTGTACTCCCTCCGTT 60.809 50.000 0.00 0.00 0.00 4.44
8873 14832 2.825861 TTGTTGTACTCCCTCCGTTC 57.174 50.000 0.00 0.00 0.00 3.95
8874 14833 0.971386 TGTTGTACTCCCTCCGTTCC 59.029 55.000 0.00 0.00 0.00 3.62
8875 14834 0.971386 GTTGTACTCCCTCCGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
8876 14835 0.971386 TTGTACTCCCTCCGTTCCAC 59.029 55.000 0.00 0.00 0.00 4.02
8877 14836 0.178955 TGTACTCCCTCCGTTCCACA 60.179 55.000 0.00 0.00 0.00 4.17
8878 14837 0.971386 GTACTCCCTCCGTTCCACAA 59.029 55.000 0.00 0.00 0.00 3.33
8879 14838 1.553704 GTACTCCCTCCGTTCCACAAT 59.446 52.381 0.00 0.00 0.00 2.71
8880 14839 1.946984 ACTCCCTCCGTTCCACAATA 58.053 50.000 0.00 0.00 0.00 1.90
8881 14840 1.553704 ACTCCCTCCGTTCCACAATAC 59.446 52.381 0.00 0.00 0.00 1.89
8882 14841 1.553248 CTCCCTCCGTTCCACAATACA 59.447 52.381 0.00 0.00 0.00 2.29
8883 14842 2.170607 CTCCCTCCGTTCCACAATACAT 59.829 50.000 0.00 0.00 0.00 2.29
8884 14843 2.093181 TCCCTCCGTTCCACAATACATG 60.093 50.000 0.00 0.00 0.00 3.21
8885 14844 1.670811 CCTCCGTTCCACAATACATGC 59.329 52.381 0.00 0.00 0.00 4.06
8886 14845 1.670811 CTCCGTTCCACAATACATGCC 59.329 52.381 0.00 0.00 0.00 4.40
8887 14846 1.280710 TCCGTTCCACAATACATGCCT 59.719 47.619 0.00 0.00 0.00 4.75
8888 14847 2.091541 CCGTTCCACAATACATGCCTT 58.908 47.619 0.00 0.00 0.00 4.35
8889 14848 2.491693 CCGTTCCACAATACATGCCTTT 59.508 45.455 0.00 0.00 0.00 3.11
8890 14849 3.427503 CCGTTCCACAATACATGCCTTTC 60.428 47.826 0.00 0.00 0.00 2.62
8891 14850 3.190327 CGTTCCACAATACATGCCTTTCA 59.810 43.478 0.00 0.00 0.00 2.69
8892 14851 4.142403 CGTTCCACAATACATGCCTTTCAT 60.142 41.667 0.00 0.00 35.31 2.57
8893 14852 5.622007 CGTTCCACAATACATGCCTTTCATT 60.622 40.000 0.00 0.00 31.79 2.57
8894 14853 5.999205 TCCACAATACATGCCTTTCATTT 57.001 34.783 0.00 0.00 31.79 2.32
8895 14854 7.319646 GTTCCACAATACATGCCTTTCATTTA 58.680 34.615 0.00 0.00 31.79 1.40
8896 14855 7.658525 TCCACAATACATGCCTTTCATTTAT 57.341 32.000 0.00 0.00 31.28 1.40
8897 14856 7.715657 TCCACAATACATGCCTTTCATTTATC 58.284 34.615 0.00 0.00 29.29 1.75
8898 14857 7.341512 TCCACAATACATGCCTTTCATTTATCA 59.658 33.333 0.00 0.00 29.29 2.15
8899 14858 7.980662 CCACAATACATGCCTTTCATTTATCAA 59.019 33.333 0.00 0.00 29.29 2.57
8900 14859 9.368674 CACAATACATGCCTTTCATTTATCAAA 57.631 29.630 0.00 0.00 29.29 2.69
8901 14860 9.941325 ACAATACATGCCTTTCATTTATCAAAA 57.059 25.926 0.00 0.00 29.29 2.44
8953 14912 9.787435 GTATATAGGTACATCCATTTTTGGACA 57.213 33.333 0.00 0.00 41.33 4.02
8955 14914 9.707957 ATATAGGTACATCCATTTTTGGACAAA 57.292 29.630 0.00 0.00 41.33 2.83
8956 14915 6.933514 AGGTACATCCATTTTTGGACAAAT 57.066 33.333 0.00 0.00 41.33 2.32
8957 14916 6.700352 AGGTACATCCATTTTTGGACAAATG 58.300 36.000 0.00 0.04 41.33 2.32
8958 14917 6.496565 AGGTACATCCATTTTTGGACAAATGA 59.503 34.615 7.56 0.00 43.99 2.57
8959 14918 7.016072 AGGTACATCCATTTTTGGACAAATGAA 59.984 33.333 7.56 0.00 43.99 2.57
8960 14919 7.659390 GGTACATCCATTTTTGGACAAATGAAA 59.341 33.333 7.56 0.00 43.99 2.69
8961 14920 7.733402 ACATCCATTTTTGGACAAATGAAAG 57.267 32.000 7.56 0.85 43.99 2.62
8962 14921 6.205270 ACATCCATTTTTGGACAAATGAAAGC 59.795 34.615 7.56 0.00 43.99 3.51
8963 14922 5.062528 TCCATTTTTGGACAAATGAAAGCC 58.937 37.500 7.56 0.00 43.99 4.35
8964 14923 4.820716 CCATTTTTGGACAAATGAAAGCCA 59.179 37.500 7.56 0.00 43.99 4.75
8965 14924 5.298777 CCATTTTTGGACAAATGAAAGCCAA 59.701 36.000 7.56 0.00 43.99 4.52
8966 14925 6.432107 CATTTTTGGACAAATGAAAGCCAAG 58.568 36.000 0.00 0.00 43.99 3.61
8967 14926 4.751767 TTTGGACAAATGAAAGCCAAGT 57.248 36.364 0.00 0.00 39.52 3.16
8968 14927 5.860941 TTTGGACAAATGAAAGCCAAGTA 57.139 34.783 0.00 0.00 39.52 2.24
8969 14928 6.418057 TTTGGACAAATGAAAGCCAAGTAT 57.582 33.333 0.00 0.00 39.52 2.12
8970 14929 6.418057 TTGGACAAATGAAAGCCAAGTATT 57.582 33.333 0.00 0.00 33.96 1.89
8971 14930 6.418057 TGGACAAATGAAAGCCAAGTATTT 57.582 33.333 0.00 0.00 0.00 1.40
8972 14931 6.825610 TGGACAAATGAAAGCCAAGTATTTT 58.174 32.000 0.00 0.00 0.00 1.82
8973 14932 6.705381 TGGACAAATGAAAGCCAAGTATTTTG 59.295 34.615 0.00 0.00 0.00 2.44
8974 14933 6.147656 GGACAAATGAAAGCCAAGTATTTTGG 59.852 38.462 1.59 1.59 42.37 3.28
8975 14934 6.825610 ACAAATGAAAGCCAAGTATTTTGGA 58.174 32.000 9.99 0.00 42.06 3.53
8976 14935 7.278875 ACAAATGAAAGCCAAGTATTTTGGAA 58.721 30.769 9.99 0.00 42.06 3.53
8977 14936 7.226523 ACAAATGAAAGCCAAGTATTTTGGAAC 59.773 33.333 9.99 0.00 42.06 3.62
8978 14937 4.865776 TGAAAGCCAAGTATTTTGGAACG 58.134 39.130 9.99 0.00 42.06 3.95
8979 14938 3.934457 AAGCCAAGTATTTTGGAACGG 57.066 42.857 9.99 0.00 42.06 4.44
8980 14939 3.149005 AGCCAAGTATTTTGGAACGGA 57.851 42.857 9.99 0.00 42.06 4.69
8981 14940 3.081804 AGCCAAGTATTTTGGAACGGAG 58.918 45.455 9.99 0.00 42.06 4.63
8982 14941 2.163613 GCCAAGTATTTTGGAACGGAGG 59.836 50.000 9.99 0.00 42.06 4.30
8983 14942 2.752903 CCAAGTATTTTGGAACGGAGGG 59.247 50.000 0.00 0.00 42.06 4.30
8984 14943 3.560453 CCAAGTATTTTGGAACGGAGGGA 60.560 47.826 0.00 0.00 42.06 4.20
8985 14944 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
8986 14945 2.910977 AGTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
8987 14946 4.098894 AGTATTTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
9055 15014 8.296000 TCGCTTTCTTCAACAAATAAATGATCA 58.704 29.630 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 187 2.283676 AGGTGGATCGACGGGTGT 60.284 61.111 1.47 0.00 0.00 4.16
246 248 2.125147 CAGGGCAAGGCGATCGAA 60.125 61.111 21.57 0.00 0.00 3.71
619 626 5.848406 AGCTCCAAAATCCTCTAGAATACG 58.152 41.667 0.00 0.00 0.00 3.06
955 1757 9.056005 GCAATCAATTTCACACTATCCACTATA 57.944 33.333 0.00 0.00 0.00 1.31
1623 2734 4.199310 ACCATACGCACATGCTAAGAAAT 58.801 39.130 1.82 0.00 39.32 2.17
2280 3471 5.134725 AGTCCCCTTAATTCATCTGCATT 57.865 39.130 0.00 0.00 0.00 3.56
2484 3678 3.069586 AGTGATCCAAGACGAACTTCACA 59.930 43.478 14.09 0.00 36.61 3.58
2492 3686 2.826128 AGCTTACAGTGATCCAAGACGA 59.174 45.455 0.00 0.00 0.00 4.20
3165 4575 4.767928 TCTTAAACCCGCCAATGTTACATT 59.232 37.500 4.56 4.56 0.00 2.71
3186 4596 2.039879 AGAAACCTGCGTGGGTATTTCT 59.960 45.455 8.84 8.84 38.87 2.52
3198 4608 4.020128 TCTCTAGGAGGAAAAGAAACCTGC 60.020 45.833 0.00 0.00 43.35 4.85
3264 4709 3.006967 TGCCTACTCTCTTGAAGTTGTCC 59.993 47.826 0.00 0.00 0.00 4.02
3369 4814 8.723311 CAAGGTTTTGTATGGTCGTTCTTTATA 58.277 33.333 0.00 0.00 0.00 0.98
3370 4815 7.446013 TCAAGGTTTTGTATGGTCGTTCTTTAT 59.554 33.333 0.00 0.00 35.73 1.40
3376 4821 4.200874 TGTCAAGGTTTTGTATGGTCGTT 58.799 39.130 0.00 0.00 35.73 3.85
3399 4844 0.542333 GCTAGGGGGTTTGTCTCTCC 59.458 60.000 0.00 0.00 0.00 3.71
3424 4869 1.751924 GATGACAGTCGTCCTAGCCTT 59.248 52.381 11.33 0.00 41.85 4.35
3434 4879 8.110612 GTGTTTGTATATTTCAGATGACAGTCG 58.889 37.037 0.00 0.00 0.00 4.18
3435 4880 9.155975 AGTGTTTGTATATTTCAGATGACAGTC 57.844 33.333 0.00 0.00 0.00 3.51
3438 4883 9.098355 GCTAGTGTTTGTATATTTCAGATGACA 57.902 33.333 0.00 0.00 0.00 3.58
3439 4884 9.098355 TGCTAGTGTTTGTATATTTCAGATGAC 57.902 33.333 0.00 0.00 0.00 3.06
3441 4886 9.708222 GTTGCTAGTGTTTGTATATTTCAGATG 57.292 33.333 0.00 0.00 0.00 2.90
3442 4887 8.893727 GGTTGCTAGTGTTTGTATATTTCAGAT 58.106 33.333 0.00 0.00 0.00 2.90
3443 4888 7.335924 GGGTTGCTAGTGTTTGTATATTTCAGA 59.664 37.037 0.00 0.00 0.00 3.27
3444 4889 7.120579 TGGGTTGCTAGTGTTTGTATATTTCAG 59.879 37.037 0.00 0.00 0.00 3.02
3445 4890 6.943146 TGGGTTGCTAGTGTTTGTATATTTCA 59.057 34.615 0.00 0.00 0.00 2.69
3446 4891 7.120726 ACTGGGTTGCTAGTGTTTGTATATTTC 59.879 37.037 0.00 0.00 0.00 2.17
3448 4893 6.374333 CACTGGGTTGCTAGTGTTTGTATATT 59.626 38.462 0.00 0.00 39.48 1.28
3449 4894 5.880332 CACTGGGTTGCTAGTGTTTGTATAT 59.120 40.000 0.00 0.00 39.48 0.86
3450 4895 5.242434 CACTGGGTTGCTAGTGTTTGTATA 58.758 41.667 0.00 0.00 39.48 1.47
3613 5091 2.047655 GCGGGTGGTCATGTTCGA 60.048 61.111 0.00 0.00 0.00 3.71
3656 5134 7.638444 TCTTGAGGTAAACATGGATATTTGGA 58.362 34.615 0.00 0.00 0.00 3.53
3665 5143 5.491070 TGTCTGATCTTGAGGTAAACATGG 58.509 41.667 0.00 0.00 0.00 3.66
3684 5162 5.238624 CATATCCCATGTTGGAGATGTCT 57.761 43.478 14.22 0.00 45.09 3.41
3812 5290 4.778415 CGTCACCGTCAGCCCTCG 62.778 72.222 0.00 0.00 0.00 4.63
3818 5296 1.446099 CCACCATCGTCACCGTCAG 60.446 63.158 0.00 0.00 35.01 3.51
3878 5356 3.317711 TGAAACACCATCAATGTGTGGAC 59.682 43.478 12.75 7.00 38.86 4.02
4044 6155 1.280066 CGCCACTAATGCATTTTGCC 58.720 50.000 18.75 4.52 44.23 4.52
4095 6816 4.497674 GCACTGGAGATAACTGTACTACGG 60.498 50.000 0.00 0.00 0.00 4.02
4097 6818 5.125739 ACTGCACTGGAGATAACTGTACTAC 59.874 44.000 4.30 0.00 0.00 2.73
4103 6824 3.438087 CCAAACTGCACTGGAGATAACTG 59.562 47.826 4.30 0.00 34.35 3.16
4135 6873 6.927381 TGCTAGAACTCAAACACTAACTTACC 59.073 38.462 0.00 0.00 0.00 2.85
4258 7053 5.590663 ACATAACTAGAACTCAGCGAGATGA 59.409 40.000 11.64 0.00 33.32 2.92
4259 7054 5.826586 ACATAACTAGAACTCAGCGAGATG 58.173 41.667 11.64 5.68 33.32 2.90
4260 7055 5.825679 AGACATAACTAGAACTCAGCGAGAT 59.174 40.000 11.64 0.93 33.32 2.75
4261 7056 5.186942 AGACATAACTAGAACTCAGCGAGA 58.813 41.667 11.64 0.00 33.32 4.04
4262 7057 5.065346 TGAGACATAACTAGAACTCAGCGAG 59.935 44.000 0.00 4.36 35.52 5.03
4263 7058 4.941873 TGAGACATAACTAGAACTCAGCGA 59.058 41.667 0.00 0.00 32.04 4.93
4264 7059 5.236655 TGAGACATAACTAGAACTCAGCG 57.763 43.478 0.00 0.00 32.04 5.18
4265 7060 7.221838 GTGAATGAGACATAACTAGAACTCAGC 59.778 40.741 0.00 0.00 37.70 4.26
4266 7061 8.465999 AGTGAATGAGACATAACTAGAACTCAG 58.534 37.037 0.00 0.00 37.70 3.35
4267 7062 8.354711 AGTGAATGAGACATAACTAGAACTCA 57.645 34.615 0.00 0.00 38.44 3.41
4268 7063 9.646427 AAAGTGAATGAGACATAACTAGAACTC 57.354 33.333 0.00 0.00 0.00 3.01
4280 7075 9.330063 CCAATAGCTATAAAAGTGAATGAGACA 57.670 33.333 6.68 0.00 0.00 3.41
4281 7076 9.547753 TCCAATAGCTATAAAAGTGAATGAGAC 57.452 33.333 6.68 0.00 0.00 3.36
4284 7079 9.288576 CCATCCAATAGCTATAAAAGTGAATGA 57.711 33.333 6.68 0.00 0.00 2.57
4285 7080 9.071276 ACCATCCAATAGCTATAAAAGTGAATG 57.929 33.333 6.68 0.73 0.00 2.67
4286 7081 9.646522 AACCATCCAATAGCTATAAAAGTGAAT 57.353 29.630 6.68 0.00 0.00 2.57
4287 7082 8.902806 CAACCATCCAATAGCTATAAAAGTGAA 58.097 33.333 6.68 0.00 0.00 3.18
4288 7083 7.013274 GCAACCATCCAATAGCTATAAAAGTGA 59.987 37.037 6.68 0.00 0.00 3.41
4289 7084 7.141363 GCAACCATCCAATAGCTATAAAAGTG 58.859 38.462 6.68 0.85 0.00 3.16
4290 7085 6.833416 TGCAACCATCCAATAGCTATAAAAGT 59.167 34.615 6.68 0.00 0.00 2.66
4291 7086 7.141363 GTGCAACCATCCAATAGCTATAAAAG 58.859 38.462 6.68 0.00 0.00 2.27
4292 7087 6.605194 TGTGCAACCATCCAATAGCTATAAAA 59.395 34.615 6.68 0.00 34.36 1.52
4293 7088 6.125719 TGTGCAACCATCCAATAGCTATAAA 58.874 36.000 6.68 0.00 34.36 1.40
4294 7089 5.689835 TGTGCAACCATCCAATAGCTATAA 58.310 37.500 6.68 0.00 34.36 0.98
4295 7090 5.303259 TGTGCAACCATCCAATAGCTATA 57.697 39.130 6.68 0.00 34.36 1.31
4296 7091 4.169059 TGTGCAACCATCCAATAGCTAT 57.831 40.909 0.00 0.00 34.36 2.97
4297 7092 3.643199 TGTGCAACCATCCAATAGCTA 57.357 42.857 0.00 0.00 34.36 3.32
4298 7093 2.512692 TGTGCAACCATCCAATAGCT 57.487 45.000 0.00 0.00 34.36 3.32
4299 7094 3.056607 ACTTTGTGCAACCATCCAATAGC 60.057 43.478 0.00 0.00 34.36 2.97
4300 7095 4.789012 ACTTTGTGCAACCATCCAATAG 57.211 40.909 0.00 0.00 34.36 1.73
4301 7096 4.586421 TCAACTTTGTGCAACCATCCAATA 59.414 37.500 0.00 0.00 34.36 1.90
4302 7097 3.387374 TCAACTTTGTGCAACCATCCAAT 59.613 39.130 0.00 0.00 34.36 3.16
4303 7098 2.762887 TCAACTTTGTGCAACCATCCAA 59.237 40.909 0.00 0.00 34.36 3.53
4304 7099 2.382882 TCAACTTTGTGCAACCATCCA 58.617 42.857 0.00 0.00 34.36 3.41
4305 7100 3.665745 ATCAACTTTGTGCAACCATCC 57.334 42.857 0.00 0.00 34.36 3.51
4306 7101 5.965334 CGTATATCAACTTTGTGCAACCATC 59.035 40.000 0.00 0.00 34.36 3.51
4307 7102 5.676079 GCGTATATCAACTTTGTGCAACCAT 60.676 40.000 0.00 0.00 34.36 3.55
4308 7103 4.378978 GCGTATATCAACTTTGTGCAACCA 60.379 41.667 0.00 0.00 34.36 3.67
4309 7104 4.095610 GCGTATATCAACTTTGTGCAACC 58.904 43.478 0.00 0.00 34.36 3.77
4310 7105 4.095610 GGCGTATATCAACTTTGTGCAAC 58.904 43.478 0.00 0.00 37.35 4.17
4311 7106 3.127895 GGGCGTATATCAACTTTGTGCAA 59.872 43.478 0.00 0.00 0.00 4.08
4312 7107 2.680841 GGGCGTATATCAACTTTGTGCA 59.319 45.455 0.00 0.00 0.00 4.57
4329 7124 1.464608 CTACAAACAGACACATGGGCG 59.535 52.381 0.00 0.00 0.00 6.13
4388 8876 0.259065 ATGACCGGCCTCTAGACTCA 59.741 55.000 0.00 0.00 0.00 3.41
4404 8892 4.576873 TCAAACTCGGCAAACTAAACATGA 59.423 37.500 0.00 0.00 0.00 3.07
4435 8923 0.524862 CAGCAACCTGATCTGCAACC 59.475 55.000 7.34 0.00 41.77 3.77
4441 8929 7.308450 ACATATATACACAGCAACCTGATCT 57.692 36.000 0.00 0.00 41.77 2.75
4467 8955 7.384387 GCTTAGATGTACTAGGGATTTTTACGG 59.616 40.741 0.00 0.00 32.30 4.02
4468 8956 8.142551 AGCTTAGATGTACTAGGGATTTTTACG 58.857 37.037 0.00 0.00 32.30 3.18
4475 8963 6.013553 TCGTAGAGCTTAGATGTACTAGGGAT 60.014 42.308 3.46 0.00 32.30 3.85
4487 8975 1.743958 GGTGCTGTCGTAGAGCTTAGA 59.256 52.381 0.00 0.00 36.95 2.10
4568 9056 0.107017 CATGCTAGGGTTCTGGGTGG 60.107 60.000 0.00 0.00 0.00 4.61
4714 9202 3.050275 GGCCTGGTCTTGTCGCAC 61.050 66.667 0.00 0.00 0.00 5.34
4821 9310 0.698238 TGGACTGGTGGCTATGCTTT 59.302 50.000 0.00 0.00 0.00 3.51
5048 9538 2.749584 CCTAGCTGGGATGCAGCCA 61.750 63.158 24.75 8.17 46.14 4.75
5050 9540 2.594013 GCCTAGCTGGGATGCAGC 60.594 66.667 22.15 0.00 45.38 5.25
5116 9607 1.963515 GAACAGTGTTGGGCCTTGATT 59.036 47.619 14.57 0.00 0.00 2.57
5233 9727 2.434884 CCATTGCGGCGTCAGTCT 60.435 61.111 9.37 0.00 0.00 3.24
5315 9810 2.605366 GCCTATTTCGAGAGAGTGCAAC 59.395 50.000 0.00 0.00 43.69 4.17
5380 9876 3.788708 TCCCCACCATATTGTATTGGTCA 59.211 43.478 0.00 0.00 44.38 4.02
5475 9976 0.179018 GTGGTGCCTTGGTGTCTTCT 60.179 55.000 0.00 0.00 0.00 2.85
5648 10150 3.568007 TGAAAGCTTTGCATTCCTAACGT 59.432 39.130 18.30 0.00 35.72 3.99
5651 10153 5.789643 AAGTGAAAGCTTTGCATTCCTAA 57.210 34.783 18.30 0.00 35.72 2.69
5652 10154 6.237901 TCTAAGTGAAAGCTTTGCATTCCTA 58.762 36.000 18.30 1.99 35.72 2.94
5694 10196 1.433985 TGGTAGTGGTTGGGACTCCTA 59.566 52.381 0.00 0.00 0.00 2.94
5698 10200 1.513858 TTGTGGTAGTGGTTGGGACT 58.486 50.000 0.00 0.00 0.00 3.85
5757 10259 3.673599 GTGGCCTTCACCTCTTGC 58.326 61.111 3.32 0.00 40.39 4.01
5797 10299 2.620627 CGGGCTCTAGGGTTGGATTTTT 60.621 50.000 0.00 0.00 0.00 1.94
5960 10462 0.695803 AGGGTGCTTCCTATGGAGGG 60.696 60.000 0.00 0.00 43.94 4.30
6002 10507 1.276989 GTTGTATTCCCTCGACCCACA 59.723 52.381 0.00 0.00 0.00 4.17
6087 10592 3.368531 GCGTTTCACTCTCTGGGAACTAT 60.369 47.826 0.00 0.00 37.89 2.12
6108 10613 1.210155 GTTTGTGGCATCGGTCTGC 59.790 57.895 0.00 0.00 41.53 4.26
6254 10759 1.154225 GCGTCCACATTTTCTGGCG 60.154 57.895 0.00 0.00 33.86 5.69
6262 10767 1.453155 GATTGAGGTGCGTCCACATT 58.547 50.000 0.75 0.00 43.88 2.71
6263 10768 0.740868 CGATTGAGGTGCGTCCACAT 60.741 55.000 0.75 0.00 43.88 3.21
6308 10813 3.850098 CTTGGAGTTGGCCGGCTGT 62.850 63.158 28.56 8.37 0.00 4.40
6333 10838 3.382832 CTTCGCTCCTCCCGGTGT 61.383 66.667 0.00 0.00 0.00 4.16
6347 10852 1.002430 TGGTCTGATGTGGCAGTCTTC 59.998 52.381 0.00 0.00 37.20 2.87
6365 10870 9.672673 CCCAGTATATGAATATAAAAGGTCTGG 57.327 37.037 11.76 11.76 34.76 3.86
6487 10994 1.338200 GCGTGGGAGGATAAGGCTATG 60.338 57.143 0.00 0.00 0.00 2.23
6505 11012 2.978010 GGTGGTGAGTTGGGTGCG 60.978 66.667 0.00 0.00 0.00 5.34
6698 11205 2.697761 GCATGGTGGAGCTGCACAG 61.698 63.158 34.97 25.12 35.96 3.66
7042 11554 3.054878 GTGATGGTTGCTCTTTTTGCTG 58.945 45.455 0.00 0.00 0.00 4.41
7098 11610 4.514585 GTGGTGGTGGTGGTGGCA 62.515 66.667 0.00 0.00 0.00 4.92
7256 11777 1.154225 GGTTGCCGCAGTTTCATCG 60.154 57.895 0.00 0.00 0.00 3.84
7267 11788 1.429148 GATACGCCTGAAGGTTGCCG 61.429 60.000 0.00 0.00 37.57 5.69
7316 11837 3.940209 TTTGAAACCATGATGGCTGAC 57.060 42.857 12.25 1.62 42.67 3.51
7660 12186 2.021931 GCTCGCACGTTAGCATGC 59.978 61.111 10.51 10.51 38.63 4.06
7935 12463 3.524095 TTGACCCATTGACACATTCCT 57.476 42.857 0.00 0.00 0.00 3.36
7988 12516 0.905357 AAGGGAGCATACGAGCTTGT 59.095 50.000 12.27 12.27 46.75 3.16
8097 13005 4.031129 CAGAGCCCAGGCAGCTGT 62.031 66.667 16.64 3.35 41.75 4.40
8203 13114 1.228894 ACTCGGTGAGGGAGCTTCA 60.229 57.895 0.00 0.00 34.87 3.02
8211 13122 3.775654 GGAGCCCACTCGGTGAGG 61.776 72.222 5.71 6.45 44.48 3.86
8445 14340 4.186926 CACAGTATGACAGAGGGTTCATG 58.813 47.826 0.00 0.00 39.69 3.07
8625 14526 5.897377 TGGCTGCCTCTTTAATAAACTTC 57.103 39.130 21.03 0.00 0.00 3.01
8683 14584 3.866066 GCTTCTTGTGGCTCACTGATGTA 60.866 47.826 6.83 0.00 35.11 2.29
8862 14821 1.553248 TGTATTGTGGAACGGAGGGAG 59.447 52.381 0.00 0.00 42.39 4.30
8863 14822 1.646912 TGTATTGTGGAACGGAGGGA 58.353 50.000 0.00 0.00 42.39 4.20
8864 14823 2.288666 CATGTATTGTGGAACGGAGGG 58.711 52.381 0.00 0.00 42.39 4.30
8865 14824 1.670811 GCATGTATTGTGGAACGGAGG 59.329 52.381 0.00 0.00 42.39 4.30
8866 14825 1.670811 GGCATGTATTGTGGAACGGAG 59.329 52.381 0.00 0.00 42.39 4.63
8867 14826 1.280710 AGGCATGTATTGTGGAACGGA 59.719 47.619 0.00 0.00 42.39 4.69
8868 14827 1.750193 AGGCATGTATTGTGGAACGG 58.250 50.000 0.00 0.00 42.39 4.44
8869 14828 3.190327 TGAAAGGCATGTATTGTGGAACG 59.810 43.478 0.00 0.00 42.39 3.95
8870 14829 4.782019 TGAAAGGCATGTATTGTGGAAC 57.218 40.909 0.00 0.00 37.35 3.62
8871 14830 5.999205 AATGAAAGGCATGTATTGTGGAA 57.001 34.783 0.00 0.00 37.28 3.53
8872 14831 5.999205 AAATGAAAGGCATGTATTGTGGA 57.001 34.783 0.00 0.00 37.28 4.02
8873 14832 7.490840 TGATAAATGAAAGGCATGTATTGTGG 58.509 34.615 0.00 0.00 37.50 4.17
8874 14833 8.929827 TTGATAAATGAAAGGCATGTATTGTG 57.070 30.769 0.00 0.00 37.50 3.33
8875 14834 9.941325 TTTTGATAAATGAAAGGCATGTATTGT 57.059 25.926 0.00 0.00 37.50 2.71
8927 14886 9.787435 TGTCCAAAAATGGATGTACCTATATAC 57.213 33.333 0.19 0.00 40.51 1.47
8929 14888 9.707957 TTTGTCCAAAAATGGATGTACCTATAT 57.292 29.630 0.19 0.00 40.51 0.86
8930 14889 9.707957 ATTTGTCCAAAAATGGATGTACCTATA 57.292 29.630 0.19 0.00 40.51 1.31
8931 14890 8.477256 CATTTGTCCAAAAATGGATGTACCTAT 58.523 33.333 0.19 0.00 41.71 2.57
8932 14891 7.671819 TCATTTGTCCAAAAATGGATGTACCTA 59.328 33.333 9.17 0.00 44.28 3.08
8933 14892 6.496565 TCATTTGTCCAAAAATGGATGTACCT 59.503 34.615 9.17 0.00 44.28 3.08
8934 14893 6.696411 TCATTTGTCCAAAAATGGATGTACC 58.304 36.000 9.17 0.00 44.28 3.34
8935 14894 8.600449 TTTCATTTGTCCAAAAATGGATGTAC 57.400 30.769 9.17 0.00 44.28 2.90
8936 14895 7.387397 GCTTTCATTTGTCCAAAAATGGATGTA 59.613 33.333 9.17 0.00 44.28 2.29
8937 14896 6.205270 GCTTTCATTTGTCCAAAAATGGATGT 59.795 34.615 9.17 0.00 44.28 3.06
8938 14897 6.348704 GGCTTTCATTTGTCCAAAAATGGATG 60.349 38.462 9.17 5.11 44.28 3.51
8939 14898 5.706833 GGCTTTCATTTGTCCAAAAATGGAT 59.293 36.000 9.17 0.00 44.28 3.41
8940 14899 5.062528 GGCTTTCATTTGTCCAAAAATGGA 58.937 37.500 9.17 0.00 44.28 3.41
8941 14900 4.820716 TGGCTTTCATTTGTCCAAAAATGG 59.179 37.500 9.17 0.00 44.28 3.16
8942 14901 6.038492 ACTTGGCTTTCATTTGTCCAAAAATG 59.962 34.615 3.76 3.76 45.10 2.32
8943 14902 6.121590 ACTTGGCTTTCATTTGTCCAAAAAT 58.878 32.000 0.00 0.00 36.49 1.82
8944 14903 5.495640 ACTTGGCTTTCATTTGTCCAAAAA 58.504 33.333 0.00 0.00 36.49 1.94
8945 14904 5.096443 ACTTGGCTTTCATTTGTCCAAAA 57.904 34.783 0.00 0.00 36.49 2.44
8946 14905 4.751767 ACTTGGCTTTCATTTGTCCAAA 57.248 36.364 0.00 0.00 36.49 3.28
8947 14906 6.418057 AATACTTGGCTTTCATTTGTCCAA 57.582 33.333 0.00 0.00 35.70 3.53
8948 14907 6.418057 AAATACTTGGCTTTCATTTGTCCA 57.582 33.333 0.00 0.00 0.00 4.02
8949 14908 6.147656 CCAAAATACTTGGCTTTCATTTGTCC 59.852 38.462 0.00 0.00 32.18 4.02
8950 14909 6.928492 TCCAAAATACTTGGCTTTCATTTGTC 59.072 34.615 0.00 0.00 39.38 3.18
8951 14910 6.825610 TCCAAAATACTTGGCTTTCATTTGT 58.174 32.000 0.00 0.00 39.38 2.83
8952 14911 7.569226 CGTTCCAAAATACTTGGCTTTCATTTG 60.569 37.037 0.00 0.00 39.38 2.32
8953 14912 6.423604 CGTTCCAAAATACTTGGCTTTCATTT 59.576 34.615 0.00 0.00 39.38 2.32
8954 14913 5.925969 CGTTCCAAAATACTTGGCTTTCATT 59.074 36.000 0.00 0.00 39.38 2.57
8955 14914 5.469479 CGTTCCAAAATACTTGGCTTTCAT 58.531 37.500 0.00 0.00 39.38 2.57
8956 14915 4.261825 CCGTTCCAAAATACTTGGCTTTCA 60.262 41.667 0.00 0.00 39.38 2.69
8957 14916 4.022676 TCCGTTCCAAAATACTTGGCTTTC 60.023 41.667 0.00 0.00 39.38 2.62
8958 14917 3.892588 TCCGTTCCAAAATACTTGGCTTT 59.107 39.130 0.00 0.00 39.38 3.51
8959 14918 3.492337 TCCGTTCCAAAATACTTGGCTT 58.508 40.909 0.00 0.00 39.38 4.35
8960 14919 3.081804 CTCCGTTCCAAAATACTTGGCT 58.918 45.455 0.00 0.00 39.38 4.75
8961 14920 2.163613 CCTCCGTTCCAAAATACTTGGC 59.836 50.000 0.00 0.00 39.38 4.52
8962 14921 2.752903 CCCTCCGTTCCAAAATACTTGG 59.247 50.000 0.00 0.00 40.87 3.61
8963 14922 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
8964 14923 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
8965 14924 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
8966 14925 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
8967 14926 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
8968 14927 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
8969 14928 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
8970 14929 2.301009 GTTCTACTCCCTCCGTTCCAAA 59.699 50.000 0.00 0.00 0.00 3.28
8971 14930 1.897802 GTTCTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
8972 14931 1.076677 AGTTCTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 0.00 3.53
8973 14932 1.477295 CAGTTCTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
8974 14933 2.444421 TCAGTTCTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
8975 14934 2.561858 GTTCAGTTCTACTCCCTCCGTT 59.438 50.000 0.00 0.00 0.00 4.44
8976 14935 2.169330 GTTCAGTTCTACTCCCTCCGT 58.831 52.381 0.00 0.00 0.00 4.69
8977 14936 2.448453 AGTTCAGTTCTACTCCCTCCG 58.552 52.381 0.00 0.00 0.00 4.63
8978 14937 4.893829 AAAGTTCAGTTCTACTCCCTCC 57.106 45.455 0.00 0.00 0.00 4.30
8979 14938 5.470437 CCAAAAAGTTCAGTTCTACTCCCTC 59.530 44.000 0.00 0.00 0.00 4.30
8980 14939 5.104067 ACCAAAAAGTTCAGTTCTACTCCCT 60.104 40.000 0.00 0.00 0.00 4.20
8981 14940 5.131067 ACCAAAAAGTTCAGTTCTACTCCC 58.869 41.667 0.00 0.00 0.00 4.30
8982 14941 6.694877 AACCAAAAAGTTCAGTTCTACTCC 57.305 37.500 0.00 0.00 0.00 3.85
8983 14942 8.027189 ACAAAACCAAAAAGTTCAGTTCTACTC 58.973 33.333 0.00 0.00 0.00 2.59
8984 14943 7.812669 CACAAAACCAAAAAGTTCAGTTCTACT 59.187 33.333 0.00 0.00 0.00 2.57
8985 14944 7.810759 TCACAAAACCAAAAAGTTCAGTTCTAC 59.189 33.333 0.00 0.00 0.00 2.59
8986 14945 7.887381 TCACAAAACCAAAAAGTTCAGTTCTA 58.113 30.769 0.00 0.00 0.00 2.10
8987 14946 6.754193 TCACAAAACCAAAAAGTTCAGTTCT 58.246 32.000 0.00 0.00 0.00 3.01
9050 15009 7.537596 AAAATGTATTTGTTCTGGGTGATCA 57.462 32.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.