Multiple sequence alignment - TraesCS7D01G347000

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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 TraesCS7D01G347000 chr7D 100.000 5234 0 0 1 5234 446433389 446428156 0.000000e+00 9666.0
1 TraesCS7D01G347000 chr7D 82.764 1346 197 27 2249 3572 446351778 446350446 0.000000e+00 1168.0
2 TraesCS7D01G347000 chr7D 86.721 369 39 5 3670 4038 446349707 446349349 8.160000e-108 401.0
3 TraesCS7D01G347000 chr7D 91.176 238 21 0 1094 1331 446354382 446354145 1.820000e-84 324.0
4 TraesCS7D01G347000 chr7D 87.361 269 19 5 4974 5228 469904966 469905233 1.430000e-75 294.0
5 TraesCS7D01G347000 chr7D 85.830 247 25 8 1096 1335 446315674 446315431 2.420000e-63 254.0
6 TraesCS7D01G347000 chr7D 93.878 49 3 0 4397 4445 453137147 453137195 2.020000e-09 75.0
7 TraesCS7D01G347000 chr7B 95.166 2503 111 9 2476 4973 463035560 463033063 0.000000e+00 3943.0
8 TraesCS7D01G347000 chr7B 92.213 1387 64 26 2 1360 463038962 463037592 0.000000e+00 1923.0
9 TraesCS7D01G347000 chr7B 81.886 1336 204 28 2264 3579 462864563 462863246 0.000000e+00 1092.0
10 TraesCS7D01G347000 chr7B 95.801 643 23 3 1808 2446 463036202 463035560 0.000000e+00 1035.0
11 TraesCS7D01G347000 chr7B 92.458 358 22 4 1351 1704 463037287 463036931 1.680000e-139 507.0
12 TraesCS7D01G347000 chr7B 86.181 398 39 10 204 590 46886501 46886109 2.920000e-112 416.0
13 TraesCS7D01G347000 chr7B 85.637 369 44 4 3670 4038 462862909 462862550 3.830000e-101 379.0
14 TraesCS7D01G347000 chr7B 89.496 238 23 2 1094 1331 462880296 462880061 3.060000e-77 300.0
15 TraesCS7D01G347000 chr7B 86.328 256 19 5 4973 5214 585313 585566 1.120000e-66 265.0
16 TraesCS7D01G347000 chr7B 85.425 247 26 8 1096 1335 462818867 462818624 1.130000e-61 248.0
17 TraesCS7D01G347000 chr7A 93.860 2622 122 18 2193 4809 497278500 497275913 0.000000e+00 3914.0
18 TraesCS7D01G347000 chr7A 93.065 1067 33 23 745 1797 497280245 497279206 0.000000e+00 1522.0
19 TraesCS7D01G347000 chr7A 93.818 275 9 6 1780 2050 497279191 497278921 1.750000e-109 407.0
20 TraesCS7D01G347000 chr7A 82.879 257 37 7 4973 5225 131412981 131412728 1.900000e-54 224.0
21 TraesCS7D01G347000 chr7A 93.960 149 8 1 597 744 497280425 497280277 1.900000e-54 224.0
22 TraesCS7D01G347000 chr7A 93.333 120 7 1 2042 2161 497278684 497278566 5.390000e-40 176.0
23 TraesCS7D01G347000 chr6B 89.357 2208 178 25 2193 4377 136451185 136449012 0.000000e+00 2723.0
24 TraesCS7D01G347000 chr6B 90.173 519 33 10 822 1331 136454398 136453889 0.000000e+00 660.0
25 TraesCS7D01G347000 chr6B 86.154 390 43 5 209 589 172736490 172736103 1.360000e-110 411.0
26 TraesCS7D01G347000 chr6B 87.912 273 19 4 4975 5234 41365480 41365751 5.090000e-80 309.0
27 TraesCS7D01G347000 chr6B 87.222 180 15 5 1802 1978 136451918 136451744 1.150000e-46 198.0
28 TraesCS7D01G347000 chr6A 88.899 2189 195 24 2209 4377 80516024 80513864 0.000000e+00 2652.0
29 TraesCS7D01G347000 chr6A 89.934 606 46 10 767 1360 80518030 80517428 0.000000e+00 767.0
30 TraesCS7D01G347000 chr6A 86.667 390 41 5 209 589 108945883 108945496 6.270000e-114 422.0
31 TraesCS7D01G347000 chr6A 81.250 480 58 21 1659 2125 80516937 80516477 4.980000e-95 359.0
32 TraesCS7D01G347000 chr6A 86.321 212 22 4 1403 1613 80517345 80517140 1.900000e-54 224.0
33 TraesCS7D01G347000 chr6A 97.222 36 1 0 2434 2469 80515741 80515706 1.570000e-05 62.1
34 TraesCS7D01G347000 chr6D 89.183 416 32 4 925 1328 62820386 62819972 1.680000e-139 507.0
35 TraesCS7D01G347000 chr6D 81.395 473 64 16 1662 2125 62819436 62818979 1.070000e-96 364.0
36 TraesCS7D01G347000 chr6D 89.606 279 15 4 4969 5234 267916203 267915926 5.020000e-90 342.0
37 TraesCS7D01G347000 chr6D 80.124 322 34 18 1326 1637 62819919 62819618 4.110000e-51 213.0
38 TraesCS7D01G347000 chr6D 89.820 167 16 1 770 936 62875693 62875528 4.110000e-51 213.0
39 TraesCS7D01G347000 chr2D 86.957 391 40 5 209 589 49888110 49887721 3.750000e-116 429.0
40 TraesCS7D01G347000 chr2D 90.741 270 12 3 4978 5234 541441579 541441848 1.080000e-91 348.0
41 TraesCS7D01G347000 chr2D 87.636 275 20 7 4973 5234 201365187 201364914 1.830000e-79 307.0
42 TraesCS7D01G347000 chr3A 86.181 398 41 8 200 587 611190475 611190868 8.110000e-113 418.0
43 TraesCS7D01G347000 chr3A 85.861 389 43 5 209 587 608139913 608140299 2.270000e-108 403.0
44 TraesCS7D01G347000 chr5A 86.340 388 42 5 209 587 667931031 667930646 3.770000e-111 412.0
45 TraesCS7D01G347000 chr5A 85.086 409 47 8 199 596 570173344 570172939 6.310000e-109 405.0
46 TraesCS7D01G347000 chr5A 87.786 262 26 5 4973 5228 484772857 484773118 8.520000e-78 302.0
47 TraesCS7D01G347000 chr5A 86.219 283 24 6 4965 5234 595940256 595940536 5.130000e-75 292.0
48 TraesCS7D01G347000 chr4A 87.410 278 21 4 4971 5234 114808319 114808596 1.830000e-79 307.0
49 TraesCS7D01G347000 chr1B 87.636 275 20 3 4974 5234 671266408 671266134 1.830000e-79 307.0
50 TraesCS7D01G347000 chr1B 90.244 82 3 3 2235 2312 20676190 20676270 9.270000e-18 102.0
51 TraesCS7D01G347000 chr1D 86.909 275 22 4 4974 5234 278817056 278817330 3.960000e-76 296.0
52 TraesCS7D01G347000 chr1D 93.750 64 3 1 2235 2298 14990154 14990216 1.550000e-15 95.3
53 TraesCS7D01G347000 chr1D 96.875 32 1 0 2098 2129 15004835 15004866 3.000000e-03 54.7
54 TraesCS7D01G347000 chr1D 96.875 32 1 0 2098 2129 15007694 15007725 3.000000e-03 54.7
55 TraesCS7D01G347000 chr4B 88.608 237 13 5 4974 5196 325028813 325029049 5.160000e-70 276.0
56 TraesCS7D01G347000 chr2A 79.208 404 65 8 4580 4967 157451036 157451436 4.020000e-66 263.0
57 TraesCS7D01G347000 chr3D 87.069 232 26 4 4973 5201 273976875 273977105 5.200000e-65 259.0
58 TraesCS7D01G347000 chr5D 94.737 133 7 0 5102 5234 397568879 397568747 1.910000e-49 207.0
59 TraesCS7D01G347000 chr1A 82.500 80 13 1 4393 4471 567316867 567316946 9.400000e-08 69.4


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 TraesCS7D01G347000 chr7D 446428156 446433389 5233 True 9666.000000 9666 100.000000 1 5234 1 chr7D.!!$R2 5233
1 TraesCS7D01G347000 chr7D 446349349 446354382 5033 True 631.000000 1168 86.887000 1094 4038 3 chr7D.!!$R3 2944
2 TraesCS7D01G347000 chr7B 463033063 463038962 5899 True 1852.000000 3943 93.909500 2 4973 4 chr7B.!!$R5 4971
3 TraesCS7D01G347000 chr7B 462862550 462864563 2013 True 735.500000 1092 83.761500 2264 4038 2 chr7B.!!$R4 1774
4 TraesCS7D01G347000 chr7A 497275913 497280425 4512 True 1248.600000 3914 93.607200 597 4809 5 chr7A.!!$R2 4212
5 TraesCS7D01G347000 chr6B 136449012 136454398 5386 True 1193.666667 2723 88.917333 822 4377 3 chr6B.!!$R2 3555
6 TraesCS7D01G347000 chr6A 80513864 80518030 4166 True 812.820000 2652 88.725200 767 4377 5 chr6A.!!$R2 3610
7 TraesCS7D01G347000 chr6D 62818979 62820386 1407 True 361.333333 507 83.567333 925 2125 3 chr6D.!!$R3 1200

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
169 170 0.742281 CTGTGAGATGGCAACCGAGG 60.742 60.000 0.00 0.00 0.00 4.63 F
513 515 0.821517 ATGAAGATGTACCCGTGCGA 59.178 50.000 0.00 0.00 0.00 5.10 F
793 831 0.911769 TGATCACAAAGGAGCCGGAT 59.088 50.000 5.05 0.00 0.00 4.18 F
1931 4907 0.167908 TTCATCCGTCGTGCATTTGC 59.832 50.000 0.00 0.00 42.50 3.68 F
2125 6601 0.820482 AACCACGGCCAAACAGTACC 60.820 55.000 2.24 0.00 0.00 3.34 F
2187 6665 1.455786 CCTTGTACAAAGTCTGCGACG 59.544 52.381 10.03 0.00 37.67 5.12 F
4126 9698 0.881159 TGTACCGCCGGTGAAAGTTG 60.881 55.000 21.20 0.02 36.19 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1061 0.179171 CTAGCGGTGTAGTGTGTCGG 60.179 60.000 0.00 0.00 0.00 4.79 R
1341 2749 0.310854 GAAAGTCAGTTGCCGGTTGG 59.689 55.000 1.90 0.00 38.77 3.77 R
2163 6641 2.602217 CGCAGACTTTGTACAAGGTTGC 60.602 50.000 28.00 28.00 34.50 4.17 R
3446 8356 2.762887 AGGTCGCTGAATGAGATCAAGA 59.237 45.455 0.00 0.00 0.00 3.02 R
4111 9683 3.361977 CCCAACTTTCACCGGCGG 61.362 66.667 27.06 27.06 0.00 6.13 R
4128 9700 3.444034 GCCTTTACCCATTTCAGAAGGAC 59.556 47.826 4.25 0.00 36.59 3.85 R
5121 10707 0.179145 CTAGTTGGCTACGTCGGTGG 60.179 60.000 0.00 0.00 0.00 4.61 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
28 29 2.887152 GCCCATGATTTGGTCTGGATAC 59.113 50.000 0.00 0.00 44.83 2.24
150 151 1.146358 GGCGACCGACTGTTAGATGC 61.146 60.000 0.00 0.00 0.00 3.91
166 167 1.028330 ATGCTGTGAGATGGCAACCG 61.028 55.000 0.00 0.00 39.46 4.44
169 170 0.742281 CTGTGAGATGGCAACCGAGG 60.742 60.000 0.00 0.00 0.00 4.63
234 235 1.655885 CTTGTGCACGCATGGGCATA 61.656 55.000 13.13 0.00 42.75 3.14
312 313 7.599630 AATCAAAAGAAAATTGCACGCATAT 57.400 28.000 0.00 0.00 0.00 1.78
313 314 6.392353 TCAAAAGAAAATTGCACGCATATG 57.608 33.333 0.00 0.00 0.00 1.78
499 501 6.544038 TGTTCACACACATAGAACATGAAG 57.456 37.500 0.00 0.00 44.60 3.02
500 502 6.287525 TGTTCACACACATAGAACATGAAGA 58.712 36.000 0.00 0.00 44.60 2.87
501 503 6.936335 TGTTCACACACATAGAACATGAAGAT 59.064 34.615 0.00 0.00 44.60 2.40
502 504 6.973229 TCACACACATAGAACATGAAGATG 57.027 37.500 0.00 0.00 35.49 2.90
507 509 6.258727 CACACATAGAACATGAAGATGTACCC 59.741 42.308 0.00 0.00 42.30 3.69
513 515 0.821517 ATGAAGATGTACCCGTGCGA 59.178 50.000 0.00 0.00 0.00 5.10
516 518 1.255667 AAGATGTACCCGTGCGACCT 61.256 55.000 0.00 0.00 0.00 3.85
576 579 5.291971 GGTTCATATGCACCCAAATTCATC 58.708 41.667 13.05 0.00 0.00 2.92
634 638 3.889815 TCCCACAGAATTAGCAGAATGG 58.110 45.455 0.00 0.00 35.86 3.16
706 710 1.015109 CGGCGACTTGCTCTAGTAGA 58.985 55.000 0.00 0.00 45.43 2.59
793 831 0.911769 TGATCACAAAGGAGCCGGAT 59.088 50.000 5.05 0.00 0.00 4.18
1007 1061 4.648626 TGCACCAGCCAGAGCCAC 62.649 66.667 0.00 0.00 41.25 5.01
1432 3282 3.954999 TGTTACGCTACTTTTGGTTTGC 58.045 40.909 0.00 0.00 0.00 3.68
1531 3387 6.222038 ACACCAAGATGAGAACATATACGT 57.778 37.500 0.00 0.00 36.82 3.57
1537 3393 8.830580 CCAAGATGAGAACATATACGTGAAATT 58.169 33.333 0.00 0.00 36.82 1.82
1648 3539 1.447838 GAAGCAAGCCGGTGATCGA 60.448 57.895 1.90 0.00 42.43 3.59
1931 4907 0.167908 TTCATCCGTCGTGCATTTGC 59.832 50.000 0.00 0.00 42.50 3.68
1975 6193 5.871396 TTTAATGCAAAACCAACTACCCA 57.129 34.783 0.00 0.00 0.00 4.51
2125 6601 0.820482 AACCACGGCCAAACAGTACC 60.820 55.000 2.24 0.00 0.00 3.34
2161 6639 9.701098 CATCCATATTAATTGTCAAGGATTTGG 57.299 33.333 0.00 4.17 32.61 3.28
2163 6641 8.694540 TCCATATTAATTGTCAAGGATTTGGTG 58.305 33.333 0.00 0.00 34.97 4.17
2187 6665 1.455786 CCTTGTACAAAGTCTGCGACG 59.544 52.381 10.03 0.00 37.67 5.12
2191 7040 2.729360 TGTACAAAGTCTGCGACGATTG 59.271 45.455 18.54 18.54 38.87 2.67
2313 7206 5.964168 GTCATTTTTCTTGATCGATCAGCTG 59.036 40.000 25.95 19.58 38.19 4.24
2920 7822 5.174398 TCGTGTTCATTTAGTTCTTCGACAC 59.826 40.000 0.00 0.00 33.46 3.67
2928 7830 5.652744 TTAGTTCTTCGACACTTTCAAGC 57.347 39.130 0.00 0.00 0.00 4.01
2982 7884 2.508526 ACCATTCCTTCTCTTGTGCAC 58.491 47.619 10.75 10.75 0.00 4.57
3600 9170 6.149474 ACAAGCATTAACCTCTAACATGTCAC 59.851 38.462 0.00 0.00 0.00 3.67
4111 9683 6.625081 GCCTAACCATTCATCCAAACTTGTAC 60.625 42.308 0.00 0.00 0.00 2.90
4126 9698 0.881159 TGTACCGCCGGTGAAAGTTG 60.881 55.000 21.20 0.02 36.19 3.16
4128 9700 2.734948 TACCGCCGGTGAAAGTTGGG 62.735 60.000 21.20 0.00 36.19 4.12
4135 9707 1.202770 CGGTGAAAGTTGGGTCCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
4271 9847 6.348704 CCTCAATTTTTGGTGGATTGCAAATC 60.349 38.462 1.71 1.63 32.28 2.17
4310 9886 0.389025 GGTTGGGAACTTGCTGGTTG 59.611 55.000 0.02 0.00 0.00 3.77
4395 9977 5.483685 TTCACACTGTTGTAGATTAGGCT 57.516 39.130 0.00 0.00 33.30 4.58
4419 10001 4.098055 AGACGACACATCTATCACACAC 57.902 45.455 0.00 0.00 0.00 3.82
4438 10020 3.135225 CACCATTCGACCAAACTGTGTA 58.865 45.455 0.00 0.00 0.00 2.90
4487 10069 2.844122 AAACTCGTGTGCCAGAAAAC 57.156 45.000 0.00 0.00 0.00 2.43
4488 10070 1.745232 AACTCGTGTGCCAGAAAACA 58.255 45.000 0.00 0.00 0.00 2.83
4500 10082 3.175929 CCAGAAAACAAAACGGTGTGAC 58.824 45.455 0.00 0.00 0.00 3.67
4531 10113 4.261994 CCATGGGGCACGATTTTATTAAGG 60.262 45.833 2.85 0.00 0.00 2.69
4532 10114 2.691011 TGGGGCACGATTTTATTAAGGC 59.309 45.455 0.00 0.00 0.00 4.35
4533 10115 2.956333 GGGGCACGATTTTATTAAGGCT 59.044 45.455 0.00 0.00 0.00 4.58
4582 10167 3.393800 GGTTCTACTGCATGTGCGATAT 58.606 45.455 0.01 0.00 45.83 1.63
4636 10221 0.030504 TGTGTGCGTTCATTGGCAAG 59.969 50.000 5.96 0.00 41.46 4.01
4673 10258 4.385447 CGAAATGTTTGCGATGGTTTGAAT 59.615 37.500 0.00 0.00 0.00 2.57
4717 10302 4.304110 TGAATACTCGTGTGTGAAGGTTC 58.696 43.478 0.00 0.00 0.00 3.62
4777 10362 4.064491 GCTCGTGACAGCGCACAC 62.064 66.667 11.47 15.64 38.69 3.82
4826 10411 9.415544 CCTCCTTTTCTAAGTTTTTCATCAATG 57.584 33.333 0.00 0.00 0.00 2.82
4842 10427 3.669536 TCAATGGCGTTATCTGAACACA 58.330 40.909 0.00 0.00 0.00 3.72
4843 10428 4.260985 TCAATGGCGTTATCTGAACACAT 58.739 39.130 0.00 0.00 0.00 3.21
4846 10431 3.872696 TGGCGTTATCTGAACACATCAT 58.127 40.909 0.00 0.00 37.44 2.45
4861 10446 2.290641 ACATCATTGTTTCCCGCCAGTA 60.291 45.455 0.00 0.00 29.55 2.74
4869 10454 0.325296 TTCCCGCCAGTACTCCATCT 60.325 55.000 0.00 0.00 0.00 2.90
4931 10517 1.221466 CGGCCACACACCATATAGCG 61.221 60.000 2.24 0.00 0.00 4.26
4933 10519 1.831389 GCCACACACCATATAGCGCG 61.831 60.000 0.00 0.00 0.00 6.86
4973 10559 3.571401 GCTTATACCATTCCAAGCATGCT 59.429 43.478 16.30 16.30 42.31 3.79
4974 10560 4.558095 GCTTATACCATTCCAAGCATGCTG 60.558 45.833 23.48 15.04 42.31 4.41
4975 10561 2.804986 TACCATTCCAAGCATGCTGA 57.195 45.000 23.48 12.69 0.00 4.26
4976 10562 2.154567 ACCATTCCAAGCATGCTGAT 57.845 45.000 23.48 10.44 0.00 2.90
4977 10563 1.754803 ACCATTCCAAGCATGCTGATG 59.245 47.619 23.48 20.55 0.00 3.07
4978 10564 1.068588 CCATTCCAAGCATGCTGATGG 59.931 52.381 26.31 26.31 0.00 3.51
4979 10565 1.754803 CATTCCAAGCATGCTGATGGT 59.245 47.619 29.19 14.70 42.24 3.55
4980 10566 1.179152 TTCCAAGCATGCTGATGGTG 58.821 50.000 29.19 20.13 39.45 4.17
4981 10567 0.038599 TCCAAGCATGCTGATGGTGT 59.961 50.000 29.19 8.92 39.45 4.16
4982 10568 0.454600 CCAAGCATGCTGATGGTGTC 59.545 55.000 24.64 0.00 39.45 3.67
4983 10569 0.454600 CAAGCATGCTGATGGTGTCC 59.545 55.000 23.48 0.00 39.45 4.02
4984 10570 0.330604 AAGCATGCTGATGGTGTCCT 59.669 50.000 23.48 0.00 39.45 3.85
4985 10571 0.393944 AGCATGCTGATGGTGTCCTG 60.394 55.000 21.98 0.00 38.90 3.86
4986 10572 0.393402 GCATGCTGATGGTGTCCTGA 60.393 55.000 11.37 0.00 0.00 3.86
4987 10573 1.951895 GCATGCTGATGGTGTCCTGAA 60.952 52.381 11.37 0.00 0.00 3.02
4988 10574 1.741706 CATGCTGATGGTGTCCTGAAC 59.258 52.381 0.00 0.00 0.00 3.18
4989 10575 1.059098 TGCTGATGGTGTCCTGAACT 58.941 50.000 0.00 0.00 0.00 3.01
4990 10576 2.256306 TGCTGATGGTGTCCTGAACTA 58.744 47.619 0.00 0.00 0.00 2.24
4991 10577 2.234661 TGCTGATGGTGTCCTGAACTAG 59.765 50.000 0.00 0.00 0.00 2.57
5001 10587 2.544844 CCTGAACTAGGGGGTACTCA 57.455 55.000 0.00 0.00 43.33 3.41
5002 10588 2.108970 CCTGAACTAGGGGGTACTCAC 58.891 57.143 0.00 0.00 43.33 3.51
5003 10589 2.108970 CTGAACTAGGGGGTACTCACC 58.891 57.143 0.00 0.00 44.96 4.02
5004 10590 5.746498 CCTGAACTAGGGGGTACTCACCA 62.746 56.522 0.00 0.00 42.82 4.17
5011 10597 4.855596 GGTACTCACCACGTCGTC 57.144 61.111 0.00 0.00 45.04 4.20
5012 10598 2.251600 GGTACTCACCACGTCGTCT 58.748 57.895 0.00 0.00 45.04 4.18
5013 10599 0.595095 GGTACTCACCACGTCGTCTT 59.405 55.000 0.00 0.00 45.04 3.01
5014 10600 1.400759 GGTACTCACCACGTCGTCTTC 60.401 57.143 0.00 0.00 45.04 2.87
5015 10601 0.877071 TACTCACCACGTCGTCTTCC 59.123 55.000 0.00 0.00 0.00 3.46
5016 10602 1.442184 CTCACCACGTCGTCTTCCG 60.442 63.158 0.00 0.00 38.13 4.30
5017 10603 1.848932 CTCACCACGTCGTCTTCCGA 61.849 60.000 0.00 0.00 45.00 4.55
5024 10610 3.362262 TCGTCTTCCGACCAGTGG 58.638 61.111 7.91 7.91 41.60 4.00
5025 10611 2.261671 CGTCTTCCGACCAGTGGG 59.738 66.667 15.21 0.00 39.56 4.61
5050 10636 3.728373 GAGGACCCCATGGCGGTT 61.728 66.667 21.61 10.34 32.27 4.44
5051 10637 3.699134 GAGGACCCCATGGCGGTTC 62.699 68.421 21.61 20.06 32.27 3.62
5052 10638 4.041762 GGACCCCATGGCGGTTCA 62.042 66.667 21.61 0.00 32.27 3.18
5053 10639 2.275418 GACCCCATGGCGGTTCAT 59.725 61.111 21.61 3.67 32.27 2.57
5054 10640 1.529796 GACCCCATGGCGGTTCATA 59.470 57.895 21.61 0.00 32.27 2.15
5055 10641 0.106918 GACCCCATGGCGGTTCATAA 60.107 55.000 21.61 0.00 32.27 1.90
5056 10642 0.555769 ACCCCATGGCGGTTCATAAT 59.444 50.000 16.72 0.00 33.59 1.28
5057 10643 0.961019 CCCCATGGCGGTTCATAATG 59.039 55.000 6.09 0.00 0.00 1.90
5058 10644 0.961019 CCCATGGCGGTTCATAATGG 59.039 55.000 6.09 0.00 38.01 3.16
5059 10645 0.961019 CCATGGCGGTTCATAATGGG 59.039 55.000 0.00 0.00 35.22 4.00
5060 10646 0.314935 CATGGCGGTTCATAATGGGC 59.685 55.000 0.00 0.00 0.00 5.36
5061 10647 0.827507 ATGGCGGTTCATAATGGGCC 60.828 55.000 0.00 0.00 40.88 5.80
5062 10648 1.454847 GGCGGTTCATAATGGGCCA 60.455 57.895 9.61 9.61 40.24 5.36
5063 10649 1.733526 GCGGTTCATAATGGGCCAC 59.266 57.895 9.28 0.00 0.00 5.01
5064 10650 0.751643 GCGGTTCATAATGGGCCACT 60.752 55.000 9.28 0.00 0.00 4.00
5065 10651 1.762708 CGGTTCATAATGGGCCACTT 58.237 50.000 9.28 7.43 0.00 3.16
5066 10652 1.676006 CGGTTCATAATGGGCCACTTC 59.324 52.381 9.28 0.00 0.00 3.01
5067 10653 1.676006 GGTTCATAATGGGCCACTTCG 59.324 52.381 9.28 0.00 0.00 3.79
5068 10654 1.676006 GTTCATAATGGGCCACTTCGG 59.324 52.381 9.28 0.00 38.11 4.30
5077 10663 4.431131 CCACTTCGGCCAGCCCAT 62.431 66.667 2.24 0.00 0.00 4.00
5078 10664 3.136123 CACTTCGGCCAGCCCATG 61.136 66.667 2.24 0.00 0.00 3.66
5079 10665 3.329889 ACTTCGGCCAGCCCATGA 61.330 61.111 2.24 0.00 0.00 3.07
5080 10666 2.825836 CTTCGGCCAGCCCATGAC 60.826 66.667 2.24 0.00 0.00 3.06
5081 10667 3.626996 CTTCGGCCAGCCCATGACA 62.627 63.158 2.24 0.00 0.00 3.58
5082 10668 2.898920 CTTCGGCCAGCCCATGACAT 62.899 60.000 2.24 0.00 0.00 3.06
5083 10669 1.631071 TTCGGCCAGCCCATGACATA 61.631 55.000 2.24 0.00 0.00 2.29
5084 10670 1.073722 CGGCCAGCCCATGACATAT 59.926 57.895 2.24 0.00 0.00 1.78
5085 10671 0.324614 CGGCCAGCCCATGACATATA 59.675 55.000 2.24 0.00 0.00 0.86
5086 10672 1.826385 GGCCAGCCCATGACATATAC 58.174 55.000 0.00 0.00 0.00 1.47
5087 10673 1.442769 GCCAGCCCATGACATATACG 58.557 55.000 0.00 0.00 0.00 3.06
5088 10674 1.001974 GCCAGCCCATGACATATACGA 59.998 52.381 0.00 0.00 0.00 3.43
5089 10675 2.932622 GCCAGCCCATGACATATACGAG 60.933 54.545 0.00 0.00 0.00 4.18
5090 10676 2.354103 CCAGCCCATGACATATACGAGG 60.354 54.545 0.00 0.00 0.00 4.63
5091 10677 2.562738 CAGCCCATGACATATACGAGGA 59.437 50.000 0.00 0.00 0.00 3.71
5092 10678 3.006859 CAGCCCATGACATATACGAGGAA 59.993 47.826 0.00 0.00 0.00 3.36
5093 10679 3.259374 AGCCCATGACATATACGAGGAAG 59.741 47.826 0.00 0.00 0.00 3.46
5094 10680 3.258372 GCCCATGACATATACGAGGAAGA 59.742 47.826 0.00 0.00 0.00 2.87
5095 10681 4.081420 GCCCATGACATATACGAGGAAGAT 60.081 45.833 0.00 0.00 0.00 2.40
5096 10682 5.569630 GCCCATGACATATACGAGGAAGATT 60.570 44.000 0.00 0.00 0.00 2.40
5097 10683 6.102663 CCCATGACATATACGAGGAAGATTC 58.897 44.000 0.00 0.00 0.00 2.52
5111 10697 5.557891 GGAAGATTCCACATCAAGACAAG 57.442 43.478 6.74 0.00 46.76 3.16
5112 10698 4.397417 GGAAGATTCCACATCAAGACAAGG 59.603 45.833 6.74 0.00 46.76 3.61
5113 10699 4.916041 AGATTCCACATCAAGACAAGGA 57.084 40.909 0.00 0.00 0.00 3.36
5114 10700 4.583871 AGATTCCACATCAAGACAAGGAC 58.416 43.478 0.00 0.00 0.00 3.85
5115 10701 4.288105 AGATTCCACATCAAGACAAGGACT 59.712 41.667 0.00 0.00 0.00 3.85
5116 10702 3.685139 TCCACATCAAGACAAGGACTC 57.315 47.619 0.00 0.00 0.00 3.36
5117 10703 2.303022 TCCACATCAAGACAAGGACTCC 59.697 50.000 0.00 0.00 0.00 3.85
5118 10704 2.304180 CCACATCAAGACAAGGACTCCT 59.696 50.000 0.00 0.00 33.87 3.69
5119 10705 3.594134 CACATCAAGACAAGGACTCCTC 58.406 50.000 0.00 0.00 30.89 3.71
5120 10706 3.260380 CACATCAAGACAAGGACTCCTCT 59.740 47.826 0.00 0.00 30.89 3.69
5121 10707 3.513515 ACATCAAGACAAGGACTCCTCTC 59.486 47.826 0.00 0.00 30.89 3.20
5122 10708 2.530701 TCAAGACAAGGACTCCTCTCC 58.469 52.381 0.00 0.00 30.89 3.71
5123 10709 2.158310 TCAAGACAAGGACTCCTCTCCA 60.158 50.000 0.00 0.00 30.89 3.86
5124 10710 1.931635 AGACAAGGACTCCTCTCCAC 58.068 55.000 0.00 0.00 30.89 4.02
5125 10711 0.899019 GACAAGGACTCCTCTCCACC 59.101 60.000 0.00 0.00 30.89 4.61
5126 10712 0.900647 ACAAGGACTCCTCTCCACCG 60.901 60.000 0.00 0.00 30.89 4.94
5127 10713 0.612174 CAAGGACTCCTCTCCACCGA 60.612 60.000 0.00 0.00 30.89 4.69
5128 10714 0.612453 AAGGACTCCTCTCCACCGAC 60.612 60.000 0.00 0.00 30.89 4.79
5129 10715 2.408241 GGACTCCTCTCCACCGACG 61.408 68.421 0.00 0.00 0.00 5.12
5130 10716 1.674980 GACTCCTCTCCACCGACGT 60.675 63.158 0.00 0.00 0.00 4.34
5131 10717 0.392193 GACTCCTCTCCACCGACGTA 60.392 60.000 0.00 0.00 0.00 3.57
5132 10718 0.392729 ACTCCTCTCCACCGACGTAG 60.393 60.000 0.00 0.00 0.00 3.51
5133 10719 1.716826 CTCCTCTCCACCGACGTAGC 61.717 65.000 0.00 0.00 0.00 3.58
5134 10720 2.772691 CCTCTCCACCGACGTAGCC 61.773 68.421 0.00 0.00 0.00 3.93
5135 10721 2.034532 TCTCCACCGACGTAGCCA 59.965 61.111 0.00 0.00 0.00 4.75
5136 10722 1.592400 CTCTCCACCGACGTAGCCAA 61.592 60.000 0.00 0.00 0.00 4.52
5137 10723 1.445582 CTCCACCGACGTAGCCAAC 60.446 63.158 0.00 0.00 0.00 3.77
5138 10724 1.874345 CTCCACCGACGTAGCCAACT 61.874 60.000 0.00 0.00 0.00 3.16
5139 10725 0.608856 TCCACCGACGTAGCCAACTA 60.609 55.000 0.00 0.00 0.00 2.24
5140 10726 0.179145 CCACCGACGTAGCCAACTAG 60.179 60.000 0.00 0.00 0.00 2.57
5141 10727 0.179145 CACCGACGTAGCCAACTAGG 60.179 60.000 0.00 0.00 39.62 3.02
5142 10728 0.322816 ACCGACGTAGCCAACTAGGA 60.323 55.000 0.00 0.00 41.22 2.94
5143 10729 0.813184 CCGACGTAGCCAACTAGGAA 59.187 55.000 0.00 0.00 41.22 3.36
5144 10730 1.407979 CCGACGTAGCCAACTAGGAAT 59.592 52.381 0.00 0.00 41.22 3.01
5145 10731 2.543238 CCGACGTAGCCAACTAGGAATC 60.543 54.545 0.00 0.00 41.22 2.52
5146 10732 2.358267 CGACGTAGCCAACTAGGAATCT 59.642 50.000 0.00 0.00 41.22 2.40
5147 10733 3.181489 CGACGTAGCCAACTAGGAATCTT 60.181 47.826 0.00 0.00 41.22 2.40
5148 10734 4.113354 GACGTAGCCAACTAGGAATCTTG 58.887 47.826 0.00 0.00 41.22 3.02
5149 10735 3.514309 ACGTAGCCAACTAGGAATCTTGT 59.486 43.478 0.00 0.00 41.22 3.16
5150 10736 4.020485 ACGTAGCCAACTAGGAATCTTGTT 60.020 41.667 0.00 0.00 41.22 2.83
5151 10737 5.186409 ACGTAGCCAACTAGGAATCTTGTTA 59.814 40.000 0.00 0.00 41.22 2.41
5152 10738 6.127140 ACGTAGCCAACTAGGAATCTTGTTAT 60.127 38.462 0.00 0.00 41.22 1.89
5153 10739 6.421202 CGTAGCCAACTAGGAATCTTGTTATC 59.579 42.308 0.00 0.00 41.22 1.75
5154 10740 5.685728 AGCCAACTAGGAATCTTGTTATCC 58.314 41.667 0.00 0.00 41.22 2.59
5155 10741 5.430089 AGCCAACTAGGAATCTTGTTATCCT 59.570 40.000 0.00 0.00 45.39 3.24
5156 10742 6.615726 AGCCAACTAGGAATCTTGTTATCCTA 59.384 38.462 0.00 0.00 43.28 2.94
5160 10746 4.984146 AGGAATCTTGTTATCCTAGGCC 57.016 45.455 2.96 0.00 41.74 5.19
5161 10747 4.571951 AGGAATCTTGTTATCCTAGGCCT 58.428 43.478 11.78 11.78 41.74 5.19
5162 10748 4.595350 AGGAATCTTGTTATCCTAGGCCTC 59.405 45.833 9.68 0.00 41.74 4.70
5163 10749 4.263112 GGAATCTTGTTATCCTAGGCCTCC 60.263 50.000 9.68 0.00 0.00 4.30
5164 10750 2.317040 TCTTGTTATCCTAGGCCTCCG 58.683 52.381 9.68 0.62 0.00 4.63
5165 10751 1.344763 CTTGTTATCCTAGGCCTCCGG 59.655 57.143 9.68 12.23 0.00 5.14
5166 10752 0.263765 TGTTATCCTAGGCCTCCGGT 59.736 55.000 9.68 0.00 0.00 5.28
5167 10753 1.500303 TGTTATCCTAGGCCTCCGGTA 59.500 52.381 9.68 0.00 0.00 4.02
5168 10754 1.891811 GTTATCCTAGGCCTCCGGTAC 59.108 57.143 9.68 8.04 0.00 3.34
5169 10755 1.151760 TATCCTAGGCCTCCGGTACA 58.848 55.000 9.68 0.00 0.00 2.90
5170 10756 0.487772 ATCCTAGGCCTCCGGTACAT 59.512 55.000 9.68 0.00 0.00 2.29
5171 10757 0.263765 TCCTAGGCCTCCGGTACATT 59.736 55.000 9.68 0.00 0.00 2.71
5172 10758 1.500303 TCCTAGGCCTCCGGTACATTA 59.500 52.381 9.68 0.00 0.00 1.90
5173 10759 2.111255 TCCTAGGCCTCCGGTACATTAT 59.889 50.000 9.68 0.00 0.00 1.28
5174 10760 3.334581 TCCTAGGCCTCCGGTACATTATA 59.665 47.826 9.68 0.00 0.00 0.98
5175 10761 4.016851 TCCTAGGCCTCCGGTACATTATAT 60.017 45.833 9.68 0.00 0.00 0.86
5176 10762 5.194334 TCCTAGGCCTCCGGTACATTATATA 59.806 44.000 9.68 0.00 0.00 0.86
5177 10763 5.895534 CCTAGGCCTCCGGTACATTATATAA 59.104 44.000 9.68 0.00 0.00 0.98
5178 10764 5.934402 AGGCCTCCGGTACATTATATAAG 57.066 43.478 0.00 0.00 0.00 1.73
5179 10765 4.161754 AGGCCTCCGGTACATTATATAAGC 59.838 45.833 0.00 0.00 0.00 3.09
5180 10766 4.439968 GCCTCCGGTACATTATATAAGCC 58.560 47.826 0.00 0.80 0.00 4.35
5181 10767 4.679662 CCTCCGGTACATTATATAAGCCG 58.320 47.826 16.76 16.76 37.72 5.52
5182 10768 4.400251 CCTCCGGTACATTATATAAGCCGA 59.600 45.833 21.58 12.53 40.04 5.54
5183 10769 5.450137 CCTCCGGTACATTATATAAGCCGAG 60.450 48.000 21.58 17.47 40.04 4.63
5184 10770 4.400251 TCCGGTACATTATATAAGCCGAGG 59.600 45.833 21.58 12.43 40.04 4.63
5185 10771 4.110482 CGGTACATTATATAAGCCGAGGC 58.890 47.826 17.94 5.89 40.04 4.70
5186 10772 4.439968 GGTACATTATATAAGCCGAGGCC 58.560 47.826 10.95 0.00 43.17 5.19
5187 10773 4.081309 GGTACATTATATAAGCCGAGGCCA 60.081 45.833 10.95 0.00 43.17 5.36
5188 10774 4.207891 ACATTATATAAGCCGAGGCCAG 57.792 45.455 10.95 0.00 43.17 4.85
5189 10775 3.055094 ACATTATATAAGCCGAGGCCAGG 60.055 47.826 10.95 9.58 43.17 4.45
5200 10786 2.423446 GGCCAGGCTGGTCGATAG 59.577 66.667 32.80 7.84 40.46 2.08
5201 10787 2.134287 GGCCAGGCTGGTCGATAGA 61.134 63.158 32.80 0.00 40.46 1.98
5228 10814 9.685276 TTATTATGACATTCATCATCATACCCC 57.315 33.333 0.00 0.00 39.97 4.95
5229 10815 5.855338 ATGACATTCATCATCATACCCCT 57.145 39.130 0.00 0.00 33.99 4.79
5230 10816 6.957853 ATGACATTCATCATCATACCCCTA 57.042 37.500 0.00 0.00 33.99 3.53
5231 10817 6.364568 TGACATTCATCATCATACCCCTAG 57.635 41.667 0.00 0.00 0.00 3.02
5232 10818 5.249163 TGACATTCATCATCATACCCCTAGG 59.751 44.000 0.06 0.06 40.04 3.02
5233 10819 8.957842 ATGACATTCATCATCATACCCCTAGGG 61.958 44.444 22.25 22.25 41.20 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.966451 GTTTGACAGGCACCCCTCG 60.966 63.158 0.00 0.00 40.33 4.63
60 61 1.063190 ACAGATGGACCCTCATACCGA 60.063 52.381 0.00 0.00 0.00 4.69
124 125 4.324991 AGTCGGTCGCCCCAAACC 62.325 66.667 0.00 0.00 0.00 3.27
131 132 1.146358 GCATCTAACAGTCGGTCGCC 61.146 60.000 0.00 0.00 0.00 5.54
142 143 2.910199 TGCCATCTCACAGCATCTAAC 58.090 47.619 0.00 0.00 0.00 2.34
143 144 3.273434 GTTGCCATCTCACAGCATCTAA 58.727 45.455 0.00 0.00 36.20 2.10
150 151 0.742281 CCTCGGTTGCCATCTCACAG 60.742 60.000 0.00 0.00 0.00 3.66
185 186 1.402852 CGAGGAACGAGAGCACATTCA 60.403 52.381 0.00 0.00 45.77 2.57
217 218 1.453562 ATATGCCCATGCGTGCACA 60.454 52.632 18.64 0.00 40.88 4.57
288 289 5.927954 ATGCGTGCAATTTTCTTTTGATT 57.072 30.435 0.00 0.00 0.00 2.57
289 290 6.591062 ACATATGCGTGCAATTTTCTTTTGAT 59.409 30.769 1.58 0.00 0.00 2.57
312 313 1.796982 GCACACACATTTGCGAACACA 60.797 47.619 0.00 0.00 0.00 3.72
313 314 0.845768 GCACACACATTTGCGAACAC 59.154 50.000 0.00 0.00 0.00 3.32
390 392 9.677567 GTGAAACACTATTTAGAAGCATTGAAA 57.322 29.630 0.00 0.00 36.32 2.69
456 458 8.105742 GTGAACAAAGTTTCACGGAAAAATAAC 58.894 33.333 0.52 0.00 44.41 1.89
499 501 0.390735 AAAGGTCGCACGGGTACATC 60.391 55.000 0.00 0.00 0.00 3.06
500 502 0.035739 AAAAGGTCGCACGGGTACAT 59.964 50.000 0.00 0.00 0.00 2.29
501 503 0.179051 AAAAAGGTCGCACGGGTACA 60.179 50.000 0.00 0.00 0.00 2.90
502 504 0.514255 GAAAAAGGTCGCACGGGTAC 59.486 55.000 0.00 0.00 0.00 3.34
507 509 2.969443 AATCTGAAAAAGGTCGCACG 57.031 45.000 0.00 0.00 0.00 5.34
541 544 7.895759 GGTGCATATGAACCCACAATATATTT 58.104 34.615 21.16 0.00 37.82 1.40
568 571 3.716431 AGGGAAGTGCATGGATGAATTT 58.284 40.909 0.00 0.00 0.00 1.82
570 573 3.294214 GAAGGGAAGTGCATGGATGAAT 58.706 45.455 0.00 0.00 0.00 2.57
576 579 0.804989 GAACGAAGGGAAGTGCATGG 59.195 55.000 0.00 0.00 0.00 3.66
634 638 6.934048 ATGCAGAGGAGCTTTAAAATCTAC 57.066 37.500 0.00 0.00 34.99 2.59
706 710 1.893808 CAAACAGTGCGGCCAGACT 60.894 57.895 2.24 0.00 0.00 3.24
793 831 3.759618 CGTAAAATTGTAGGAGGCCCAAA 59.240 43.478 0.00 0.00 33.88 3.28
881 921 8.446599 TCATCATCATCATGCATATATGGTTC 57.553 34.615 14.51 0.00 0.00 3.62
937 986 1.003118 AGGCATGGAGAAAAGTACGCA 59.997 47.619 0.00 0.00 0.00 5.24
1007 1061 0.179171 CTAGCGGTGTAGTGTGTCGG 60.179 60.000 0.00 0.00 0.00 4.79
1047 1129 5.759963 CTTGGCTCCGTAGTACTACTTATG 58.240 45.833 26.36 15.99 34.04 1.90
1341 2749 0.310854 GAAAGTCAGTTGCCGGTTGG 59.689 55.000 1.90 0.00 38.77 3.77
1408 3174 3.865224 ACCAAAAGTAGCGTAACAACG 57.135 42.857 0.00 0.00 0.00 4.10
1432 3282 0.313987 CATAGGTGCTGCATGCCATG 59.686 55.000 16.68 0.00 42.00 3.66
1531 3387 8.691661 AAGTTAGCCTTCAACTAGAAATTTCA 57.308 30.769 19.99 5.68 35.19 2.69
1537 3393 7.988599 TGTTGTAAAGTTAGCCTTCAACTAGAA 59.011 33.333 0.00 0.00 38.11 2.10
1931 4907 6.890979 AATGGAGAAGGAGACAAAGAAAAG 57.109 37.500 0.00 0.00 0.00 2.27
1975 6193 7.596248 GTGAACTGCAAATTAATGTTGACAGAT 59.404 33.333 22.47 17.30 35.51 2.90
2125 6601 5.786121 ATTAATATGGATGGGAGGGAGTG 57.214 43.478 0.00 0.00 0.00 3.51
2161 6639 3.792124 GCAGACTTTGTACAAGGTTGCAC 60.792 47.826 30.21 18.79 36.04 4.57
2163 6641 2.602217 CGCAGACTTTGTACAAGGTTGC 60.602 50.000 28.00 28.00 34.50 4.17
2313 7206 4.856509 AGTTCCTTAATTCCCAACCTAGC 58.143 43.478 0.00 0.00 0.00 3.42
2920 7822 6.151648 TGAGGGAAATATGTGAAGCTTGAAAG 59.848 38.462 2.10 0.00 0.00 2.62
2928 7830 7.452880 TTGAGTTTGAGGGAAATATGTGAAG 57.547 36.000 0.00 0.00 0.00 3.02
2982 7884 8.299570 TGTAACCGACTAAAGGAAACTACTTAG 58.700 37.037 0.00 0.00 42.68 2.18
3055 7964 8.330466 TGTTGAAACTTTGTCAAGAGAAGTAA 57.670 30.769 0.00 0.00 35.71 2.24
3303 8213 4.012374 GGCTCACATTCTCTTGATCCAAA 58.988 43.478 0.00 0.00 29.87 3.28
3446 8356 2.762887 AGGTCGCTGAATGAGATCAAGA 59.237 45.455 0.00 0.00 0.00 3.02
3600 9170 7.624360 TTTGCCTGTAGTATTGTAAGATTGG 57.376 36.000 0.00 0.00 0.00 3.16
3796 9367 6.617371 ACCTCCTTGAAATCTATATGACAGGT 59.383 38.462 0.00 0.00 0.00 4.00
3809 9380 3.585732 TCCTTCGGTTACCTCCTTGAAAT 59.414 43.478 0.00 0.00 0.00 2.17
4111 9683 3.361977 CCCAACTTTCACCGGCGG 61.362 66.667 27.06 27.06 0.00 6.13
4126 9698 3.732048 TTACCCATTTCAGAAGGACCC 57.268 47.619 0.00 0.00 0.00 4.46
4128 9700 3.444034 GCCTTTACCCATTTCAGAAGGAC 59.556 47.826 4.25 0.00 36.59 3.85
4135 9707 3.850173 ACCTCTAGCCTTTACCCATTTCA 59.150 43.478 0.00 0.00 0.00 2.69
4184 9756 5.459107 CGGAGATACATTTTTGAGACTACCG 59.541 44.000 0.00 0.00 0.00 4.02
4220 9792 5.485620 CAGACGATGTCCCATGAATATCAT 58.514 41.667 0.00 0.00 33.21 2.45
4310 9886 1.867233 CATGCTAATGGACGGTGCTAC 59.133 52.381 0.31 0.00 0.00 3.58
4391 9973 4.645136 TGATAGATGTGTCGTCTTAAGCCT 59.355 41.667 0.00 0.00 31.62 4.58
4395 9977 6.090783 GTGTGTGATAGATGTGTCGTCTTAA 58.909 40.000 0.00 0.00 31.62 1.85
4419 10001 2.156891 CGTACACAGTTTGGTCGAATGG 59.843 50.000 0.00 0.00 0.00 3.16
4487 10069 2.330041 GGCCGTCACACCGTTTTG 59.670 61.111 0.00 0.00 0.00 2.44
4488 10070 2.903350 GGGCCGTCACACCGTTTT 60.903 61.111 0.00 0.00 0.00 2.43
4531 10113 0.253044 TGCCCCTTATCACACTCAGC 59.747 55.000 0.00 0.00 0.00 4.26
4532 10114 1.278985 TGTGCCCCTTATCACACTCAG 59.721 52.381 0.00 0.00 38.18 3.35
4533 10115 1.357137 TGTGCCCCTTATCACACTCA 58.643 50.000 0.00 0.00 38.18 3.41
4582 10167 1.276820 CCGTGCGCGTTACAACTACA 61.277 55.000 19.61 0.00 36.15 2.74
4636 10221 3.551551 ACATTTCGTTCTTGTTAAGCGC 58.448 40.909 0.00 0.00 0.00 5.92
4717 10302 7.042725 CCTCCAACTATGTGTGTGTAAATATCG 60.043 40.741 0.00 0.00 0.00 2.92
4777 10362 0.111530 CGCGAGCTAGCATAAAAGCG 60.112 55.000 18.83 18.45 43.63 4.68
4826 10411 4.094887 ACAATGATGTGTTCAGATAACGCC 59.905 41.667 0.00 0.00 38.69 5.68
4842 10427 2.026262 AGTACTGGCGGGAAACAATGAT 60.026 45.455 0.00 0.00 0.00 2.45
4843 10428 1.349688 AGTACTGGCGGGAAACAATGA 59.650 47.619 0.00 0.00 0.00 2.57
4846 10431 0.035739 GGAGTACTGGCGGGAAACAA 59.964 55.000 0.00 0.00 0.00 2.83
4880 10465 9.736023 GCTTTTATTTATCACCACTCTTATTGG 57.264 33.333 0.00 0.00 40.32 3.16
4881 10466 9.736023 GGCTTTTATTTATCACCACTCTTATTG 57.264 33.333 0.00 0.00 0.00 1.90
4882 10467 9.700831 AGGCTTTTATTTATCACCACTCTTATT 57.299 29.630 0.00 0.00 0.00 1.40
4885 10470 9.125026 CATAGGCTTTTATTTATCACCACTCTT 57.875 33.333 0.00 0.00 0.00 2.85
4887 10472 7.363431 GCATAGGCTTTTATTTATCACCACTC 58.637 38.462 0.00 0.00 36.96 3.51
4888 10473 6.017109 CGCATAGGCTTTTATTTATCACCACT 60.017 38.462 0.00 0.00 38.10 4.00
4931 10517 2.953824 CGCTAGCTCTGTCTGCGC 60.954 66.667 13.93 0.00 40.15 6.09
4933 10519 1.877617 CTGCGCTAGCTCTGTCTGC 60.878 63.158 13.93 7.36 45.42 4.26
4959 10545 1.754803 ACCATCAGCATGCTTGGAATG 59.245 47.619 34.76 25.15 40.28 2.67
4981 10567 5.492211 GGTGAGTACCCCCTAGTTCAGGA 62.492 56.522 0.00 0.00 43.42 3.86
4982 10568 2.108970 GTGAGTACCCCCTAGTTCAGG 58.891 57.143 0.00 0.00 45.07 3.86
4983 10569 2.108970 GGTGAGTACCCCCTAGTTCAG 58.891 57.143 0.00 0.00 41.36 3.02
4984 10570 1.433985 TGGTGAGTACCCCCTAGTTCA 59.566 52.381 0.00 0.00 46.96 3.18
4985 10571 1.829849 GTGGTGAGTACCCCCTAGTTC 59.170 57.143 0.00 0.00 46.96 3.01
4986 10572 1.894093 CGTGGTGAGTACCCCCTAGTT 60.894 57.143 0.00 0.00 46.96 2.24
4987 10573 0.324091 CGTGGTGAGTACCCCCTAGT 60.324 60.000 0.00 0.00 46.96 2.57
4988 10574 0.324091 ACGTGGTGAGTACCCCCTAG 60.324 60.000 0.00 0.00 46.96 3.02
4989 10575 0.323725 GACGTGGTGAGTACCCCCTA 60.324 60.000 0.00 0.00 46.96 3.53
4990 10576 1.608627 GACGTGGTGAGTACCCCCT 60.609 63.158 0.00 0.00 46.96 4.79
4991 10577 2.976356 GACGTGGTGAGTACCCCC 59.024 66.667 0.00 0.00 46.96 5.40
4992 10578 2.205243 GACGACGTGGTGAGTACCCC 62.205 65.000 8.32 0.00 46.96 4.95
4993 10579 1.211190 GACGACGTGGTGAGTACCC 59.789 63.158 8.32 0.00 46.96 3.69
4995 10581 1.400759 GGAAGACGACGTGGTGAGTAC 60.401 57.143 8.32 0.00 0.00 2.73
4996 10582 0.877071 GGAAGACGACGTGGTGAGTA 59.123 55.000 8.32 0.00 0.00 2.59
4997 10583 1.658673 GGAAGACGACGTGGTGAGT 59.341 57.895 8.32 0.00 0.00 3.41
4998 10584 4.554163 GGAAGACGACGTGGTGAG 57.446 61.111 8.32 0.00 0.00 3.51
5038 10624 0.961019 CATTATGAACCGCCATGGGG 59.039 55.000 21.60 21.60 44.64 4.96
5039 10625 0.961019 CCATTATGAACCGCCATGGG 59.039 55.000 15.13 3.37 44.64 4.00
5040 10626 0.961019 CCCATTATGAACCGCCATGG 59.039 55.000 7.63 7.63 46.41 3.66
5041 10627 0.314935 GCCCATTATGAACCGCCATG 59.685 55.000 0.00 0.00 0.00 3.66
5042 10628 0.827507 GGCCCATTATGAACCGCCAT 60.828 55.000 0.00 0.00 36.38 4.40
5043 10629 1.454847 GGCCCATTATGAACCGCCA 60.455 57.895 0.00 0.00 36.38 5.69
5044 10630 1.454847 TGGCCCATTATGAACCGCC 60.455 57.895 0.00 0.00 36.91 6.13
5045 10631 0.751643 AGTGGCCCATTATGAACCGC 60.752 55.000 0.00 8.36 0.00 5.68
5046 10632 1.676006 GAAGTGGCCCATTATGAACCG 59.324 52.381 0.00 0.00 0.00 4.44
5047 10633 1.676006 CGAAGTGGCCCATTATGAACC 59.324 52.381 0.00 0.00 0.00 3.62
5048 10634 1.676006 CCGAAGTGGCCCATTATGAAC 59.324 52.381 0.00 0.00 0.00 3.18
5049 10635 2.051334 CCGAAGTGGCCCATTATGAA 57.949 50.000 0.00 0.00 0.00 2.57
5050 10636 3.798794 CCGAAGTGGCCCATTATGA 57.201 52.632 0.00 0.00 0.00 2.15
5060 10646 4.431131 ATGGGCTGGCCGAAGTGG 62.431 66.667 16.08 0.00 42.50 4.00
5061 10647 3.136123 CATGGGCTGGCCGAAGTG 61.136 66.667 16.08 7.92 36.85 3.16
5062 10648 3.329889 TCATGGGCTGGCCGAAGT 61.330 61.111 16.08 0.00 36.85 3.01
5063 10649 2.825836 GTCATGGGCTGGCCGAAG 60.826 66.667 16.08 7.85 36.85 3.79
5064 10650 1.631071 TATGTCATGGGCTGGCCGAA 61.631 55.000 16.08 0.00 36.85 4.30
5065 10651 1.418097 ATATGTCATGGGCTGGCCGA 61.418 55.000 16.08 4.71 36.85 5.54
5066 10652 0.324614 TATATGTCATGGGCTGGCCG 59.675 55.000 16.08 2.08 36.85 6.13
5067 10653 1.826385 GTATATGTCATGGGCTGGCC 58.174 55.000 14.23 14.23 0.00 5.36
5068 10654 1.001974 TCGTATATGTCATGGGCTGGC 59.998 52.381 0.00 0.00 0.00 4.85
5069 10655 2.354103 CCTCGTATATGTCATGGGCTGG 60.354 54.545 0.00 0.00 0.00 4.85
5070 10656 2.562738 TCCTCGTATATGTCATGGGCTG 59.437 50.000 0.00 0.00 0.00 4.85
5071 10657 2.889512 TCCTCGTATATGTCATGGGCT 58.110 47.619 0.00 0.00 0.00 5.19
5072 10658 3.258372 TCTTCCTCGTATATGTCATGGGC 59.742 47.826 0.00 0.00 0.00 5.36
5073 10659 5.667539 ATCTTCCTCGTATATGTCATGGG 57.332 43.478 0.00 0.00 0.00 4.00
5074 10660 6.102663 GGAATCTTCCTCGTATATGTCATGG 58.897 44.000 1.57 0.00 44.11 3.66
5090 10676 5.123027 GTCCTTGTCTTGATGTGGAATCTTC 59.877 44.000 0.00 0.00 0.00 2.87
5091 10677 5.006386 GTCCTTGTCTTGATGTGGAATCTT 58.994 41.667 0.00 0.00 0.00 2.40
5092 10678 4.288105 AGTCCTTGTCTTGATGTGGAATCT 59.712 41.667 0.00 0.00 0.00 2.40
5093 10679 4.583871 AGTCCTTGTCTTGATGTGGAATC 58.416 43.478 0.00 0.00 0.00 2.52
5094 10680 4.566488 GGAGTCCTTGTCTTGATGTGGAAT 60.566 45.833 0.41 0.00 0.00 3.01
5095 10681 3.244561 GGAGTCCTTGTCTTGATGTGGAA 60.245 47.826 0.41 0.00 0.00 3.53
5096 10682 2.303022 GGAGTCCTTGTCTTGATGTGGA 59.697 50.000 0.41 0.00 0.00 4.02
5097 10683 2.304180 AGGAGTCCTTGTCTTGATGTGG 59.696 50.000 5.62 0.00 0.00 4.17
5098 10684 3.260380 AGAGGAGTCCTTGTCTTGATGTG 59.740 47.826 14.41 0.00 31.76 3.21
5099 10685 3.513515 GAGAGGAGTCCTTGTCTTGATGT 59.486 47.826 14.41 0.00 31.76 3.06
5100 10686 3.118811 GGAGAGGAGTCCTTGTCTTGATG 60.119 52.174 14.41 0.00 31.76 3.07
5101 10687 3.103742 GGAGAGGAGTCCTTGTCTTGAT 58.896 50.000 14.41 0.00 31.76 2.57
5102 10688 2.158310 TGGAGAGGAGTCCTTGTCTTGA 60.158 50.000 14.41 0.15 37.52 3.02
5103 10689 2.028567 GTGGAGAGGAGTCCTTGTCTTG 60.029 54.545 14.41 0.00 37.52 3.02
5104 10690 2.252714 GTGGAGAGGAGTCCTTGTCTT 58.747 52.381 14.41 0.00 37.52 3.01
5105 10691 1.551329 GGTGGAGAGGAGTCCTTGTCT 60.551 57.143 14.41 6.09 37.52 3.41
5106 10692 0.899019 GGTGGAGAGGAGTCCTTGTC 59.101 60.000 14.41 13.10 37.52 3.18
5107 10693 0.900647 CGGTGGAGAGGAGTCCTTGT 60.901 60.000 14.41 3.63 37.52 3.16
5108 10694 0.612174 TCGGTGGAGAGGAGTCCTTG 60.612 60.000 14.41 0.00 37.52 3.61
5109 10695 0.612453 GTCGGTGGAGAGGAGTCCTT 60.612 60.000 14.41 3.20 37.52 3.36
5110 10696 1.000646 GTCGGTGGAGAGGAGTCCT 60.001 63.158 12.85 12.85 37.52 3.85
5111 10697 2.408241 CGTCGGTGGAGAGGAGTCC 61.408 68.421 0.00 0.00 37.10 3.85
5112 10698 0.392193 TACGTCGGTGGAGAGGAGTC 60.392 60.000 0.00 0.00 0.00 3.36
5113 10699 0.392729 CTACGTCGGTGGAGAGGAGT 60.393 60.000 0.00 0.00 0.00 3.85
5114 10700 1.716826 GCTACGTCGGTGGAGAGGAG 61.717 65.000 0.00 0.00 0.00 3.69
5115 10701 1.748122 GCTACGTCGGTGGAGAGGA 60.748 63.158 0.00 0.00 0.00 3.71
5116 10702 2.772691 GGCTACGTCGGTGGAGAGG 61.773 68.421 0.00 0.00 0.00 3.69
5117 10703 1.592400 TTGGCTACGTCGGTGGAGAG 61.592 60.000 0.00 0.00 0.00 3.20
5118 10704 1.604308 TTGGCTACGTCGGTGGAGA 60.604 57.895 0.00 0.00 0.00 3.71
5119 10705 1.445582 GTTGGCTACGTCGGTGGAG 60.446 63.158 0.00 0.00 0.00 3.86
5120 10706 0.608856 TAGTTGGCTACGTCGGTGGA 60.609 55.000 0.00 0.00 0.00 4.02
5121 10707 0.179145 CTAGTTGGCTACGTCGGTGG 60.179 60.000 0.00 0.00 0.00 4.61
5122 10708 0.179145 CCTAGTTGGCTACGTCGGTG 60.179 60.000 0.00 0.00 0.00 4.94
5123 10709 0.322816 TCCTAGTTGGCTACGTCGGT 60.323 55.000 0.00 0.00 35.26 4.69
5124 10710 0.813184 TTCCTAGTTGGCTACGTCGG 59.187 55.000 0.00 0.00 35.26 4.79
5125 10711 2.358267 AGATTCCTAGTTGGCTACGTCG 59.642 50.000 0.00 0.00 35.26 5.12
5126 10712 4.113354 CAAGATTCCTAGTTGGCTACGTC 58.887 47.826 0.00 0.00 35.26 4.34
5127 10713 3.514309 ACAAGATTCCTAGTTGGCTACGT 59.486 43.478 0.00 0.00 35.26 3.57
5128 10714 4.124851 ACAAGATTCCTAGTTGGCTACG 57.875 45.455 0.00 0.00 35.26 3.51
5129 10715 6.706716 GGATAACAAGATTCCTAGTTGGCTAC 59.293 42.308 0.00 0.00 35.26 3.58
5130 10716 6.615726 AGGATAACAAGATTCCTAGTTGGCTA 59.384 38.462 0.00 0.00 38.11 3.93
5131 10717 5.430089 AGGATAACAAGATTCCTAGTTGGCT 59.570 40.000 0.00 0.00 38.11 4.75
5132 10718 5.685728 AGGATAACAAGATTCCTAGTTGGC 58.314 41.667 0.00 0.00 38.11 4.52
5138 10724 5.727630 AGGCCTAGGATAACAAGATTCCTA 58.272 41.667 14.75 0.00 40.37 2.94
5139 10725 4.571951 AGGCCTAGGATAACAAGATTCCT 58.428 43.478 14.75 1.21 42.49 3.36
5140 10726 4.263112 GGAGGCCTAGGATAACAAGATTCC 60.263 50.000 14.75 0.00 0.00 3.01
5141 10727 4.561734 CGGAGGCCTAGGATAACAAGATTC 60.562 50.000 14.75 0.00 0.00 2.52
5142 10728 3.325135 CGGAGGCCTAGGATAACAAGATT 59.675 47.826 14.75 0.00 0.00 2.40
5143 10729 2.900546 CGGAGGCCTAGGATAACAAGAT 59.099 50.000 14.75 0.00 0.00 2.40
5144 10730 2.317040 CGGAGGCCTAGGATAACAAGA 58.683 52.381 14.75 0.00 0.00 3.02
5145 10731 1.344763 CCGGAGGCCTAGGATAACAAG 59.655 57.143 19.36 0.00 46.14 3.16
5146 10732 1.420430 CCGGAGGCCTAGGATAACAA 58.580 55.000 19.36 0.00 46.14 2.83
5147 10733 3.143010 CCGGAGGCCTAGGATAACA 57.857 57.895 19.36 0.00 46.14 2.41
5160 10746 5.450137 CCTCGGCTTATATAATGTACCGGAG 60.450 48.000 9.46 15.16 39.59 4.63
5161 10747 4.400251 CCTCGGCTTATATAATGTACCGGA 59.600 45.833 9.46 0.00 39.59 5.14
5162 10748 4.679662 CCTCGGCTTATATAATGTACCGG 58.320 47.826 18.48 0.00 39.59 5.28
5163 10749 4.110482 GCCTCGGCTTATATAATGTACCG 58.890 47.826 15.09 15.09 40.47 4.02
5164 10750 4.081309 TGGCCTCGGCTTATATAATGTACC 60.081 45.833 3.32 0.00 41.60 3.34
5165 10751 5.080969 TGGCCTCGGCTTATATAATGTAC 57.919 43.478 3.32 0.00 41.60 2.90
5166 10752 4.161565 CCTGGCCTCGGCTTATATAATGTA 59.838 45.833 3.32 0.00 41.60 2.29
5167 10753 3.055094 CCTGGCCTCGGCTTATATAATGT 60.055 47.826 3.32 0.00 41.60 2.71
5168 10754 3.535561 CCTGGCCTCGGCTTATATAATG 58.464 50.000 3.32 0.00 41.60 1.90
5169 10755 2.092914 GCCTGGCCTCGGCTTATATAAT 60.093 50.000 24.05 0.00 44.17 1.28
5170 10756 1.278127 GCCTGGCCTCGGCTTATATAA 59.722 52.381 24.05 0.00 44.17 0.98
5171 10757 0.902531 GCCTGGCCTCGGCTTATATA 59.097 55.000 24.05 0.00 44.17 0.86
5172 10758 1.679898 GCCTGGCCTCGGCTTATAT 59.320 57.895 24.05 0.00 44.17 0.86
5173 10759 3.148084 GCCTGGCCTCGGCTTATA 58.852 61.111 24.05 0.00 44.17 0.98
5181 10767 2.093537 CTATCGACCAGCCTGGCCTC 62.094 65.000 16.57 6.80 42.67 4.70
5182 10768 2.041922 TATCGACCAGCCTGGCCT 60.042 61.111 16.57 0.00 42.67 5.19
5183 10769 1.476007 ATCTATCGACCAGCCTGGCC 61.476 60.000 16.57 0.00 42.67 5.36
5184 10770 0.394565 AATCTATCGACCAGCCTGGC 59.605 55.000 11.63 11.65 42.67 4.85
5185 10771 4.543590 AATAATCTATCGACCAGCCTGG 57.456 45.455 9.83 9.83 45.02 4.45
5186 10772 6.754209 GTCATAATAATCTATCGACCAGCCTG 59.246 42.308 0.00 0.00 0.00 4.85
5187 10773 6.437477 TGTCATAATAATCTATCGACCAGCCT 59.563 38.462 0.00 0.00 0.00 4.58
5188 10774 6.631016 TGTCATAATAATCTATCGACCAGCC 58.369 40.000 0.00 0.00 0.00 4.85
5189 10775 8.709386 AATGTCATAATAATCTATCGACCAGC 57.291 34.615 0.00 0.00 0.00 4.85
5190 10776 9.860898 TGAATGTCATAATAATCTATCGACCAG 57.139 33.333 0.00 0.00 0.00 4.00
5202 10788 9.685276 GGGGTATGATGATGAATGTCATAATAA 57.315 33.333 0.00 0.00 37.20 1.40
5203 10789 9.061252 AGGGGTATGATGATGAATGTCATAATA 57.939 33.333 0.00 0.00 37.20 0.98
5204 10790 7.936497 AGGGGTATGATGATGAATGTCATAAT 58.064 34.615 0.00 0.00 37.20 1.28
5205 10791 7.333779 AGGGGTATGATGATGAATGTCATAA 57.666 36.000 0.00 0.00 37.20 1.90
5206 10792 6.957853 AGGGGTATGATGATGAATGTCATA 57.042 37.500 0.00 0.00 37.20 2.15
5207 10793 5.855338 AGGGGTATGATGATGAATGTCAT 57.145 39.130 0.00 0.00 40.34 3.06
5208 10794 5.249163 CCTAGGGGTATGATGATGAATGTCA 59.751 44.000 0.00 0.00 0.00 3.58
5209 10795 5.338708 CCCTAGGGGTATGATGATGAATGTC 60.339 48.000 21.44 0.00 38.25 3.06
5210 10796 4.537688 CCCTAGGGGTATGATGATGAATGT 59.462 45.833 21.44 0.00 38.25 2.71
5211 10797 5.108187 CCCTAGGGGTATGATGATGAATG 57.892 47.826 21.44 0.00 38.25 2.67


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

AutoCloner maintained by Alex Coulton.