Multiple sequence alignment - TraesCS5A01G464700

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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 TraesCS5A01G464700 chr5A 100.000 6469 0 0 1 6469 644096724 644103192 0.000000e+00 11947.0
1 TraesCS5A01G464700 chr5A 100.000 2842 0 0 6933 9774 644103656 644106497 0.000000e+00 5249.0
2 TraesCS5A01G464700 chr7A 94.383 3507 148 17 2879 6341 712341214 712344715 0.000000e+00 5339.0
3 TraesCS5A01G464700 chr7A 92.204 667 45 4 2226 2891 712340481 712341141 0.000000e+00 937.0
4 TraesCS5A01G464700 chr7B 94.454 3498 138 26 2879 6332 732131021 732134506 0.000000e+00 5334.0
5 TraesCS5A01G464700 chr7B 94.313 3499 142 27 2879 6332 732179899 732183385 0.000000e+00 5306.0
6 TraesCS5A01G464700 chr7B 96.511 1605 45 2 2879 4473 237926561 237928164 0.000000e+00 2643.0
7 TraesCS5A01G464700 chr7B 93.142 627 40 2 5714 6340 394765962 394766585 0.000000e+00 917.0
8 TraesCS5A01G464700 chr7B 86.544 706 58 11 2219 2891 732179134 732179835 0.000000e+00 743.0
9 TraesCS5A01G464700 chr7B 89.610 231 23 1 2217 2447 394764745 394764974 9.600000e-75 292.0
10 TraesCS5A01G464700 chr7B 89.520 229 23 1 2219 2447 237925763 237925990 1.240000e-73 289.0
11 TraesCS5A01G464700 chr3B 94.200 3500 143 24 2879 6332 23788266 23791751 0.000000e+00 5284.0
12 TraesCS5A01G464700 chr3B 96.108 2749 84 12 2891 5627 444142463 444139726 0.000000e+00 4462.0
13 TraesCS5A01G464700 chr3B 95.687 1136 37 3 2879 4004 20816534 20815401 0.000000e+00 1816.0
14 TraesCS5A01G464700 chr3B 92.730 619 43 2 5714 6332 444139736 444139120 0.000000e+00 893.0
15 TraesCS5A01G464700 chr3B 89.002 491 31 5 2421 2891 23787706 23788193 3.930000e-163 586.0
16 TraesCS5A01G464700 chr3B 88.415 492 33 5 2421 2891 444143035 444142547 1.100000e-158 571.0
17 TraesCS5A01G464700 chr3B 88.223 484 41 8 2421 2891 20817087 20816607 1.840000e-156 564.0
18 TraesCS5A01G464700 chr4D 94.047 3494 135 22 2879 6325 8875294 8878761 0.000000e+00 5232.0
19 TraesCS5A01G464700 chr4D 89.858 493 24 7 2419 2889 8874731 8875219 2.330000e-170 610.0
20 TraesCS5A01G464700 chr4D 89.868 227 23 0 2221 2447 8874497 8874723 9.600000e-75 292.0
21 TraesCS5A01G464700 chr7D 93.063 3503 130 27 2879 6336 528806991 528810425 0.000000e+00 5018.0
22 TraesCS5A01G464700 chr7D 95.467 2603 97 9 2879 5466 614689338 614686742 0.000000e+00 4133.0
23 TraesCS5A01G464700 chr7D 86.553 937 83 31 5440 6339 156195903 156194973 0.000000e+00 992.0
24 TraesCS5A01G464700 chr7D 85.942 939 82 23 5440 6339 614686690 614685763 0.000000e+00 957.0
25 TraesCS5A01G464700 chr7D 85.394 938 89 22 5440 6339 614916440 614917367 0.000000e+00 929.0
26 TraesCS5A01G464700 chr7D 89.495 495 26 7 2419 2891 528806428 528806918 3.910000e-168 603.0
27 TraesCS5A01G464700 chr6D 92.377 3542 172 36 2879 6332 452943153 452939622 0.000000e+00 4955.0
28 TraesCS5A01G464700 chr5B 94.167 2846 118 19 6935 9774 648997713 649000516 0.000000e+00 4292.0
29 TraesCS5A01G464700 chr5B 90.581 1550 114 13 613 2149 648995948 648997478 0.000000e+00 2025.0
30 TraesCS5A01G464700 chr5B 86.121 562 49 17 1 533 648995383 648995944 6.580000e-161 579.0
31 TraesCS5A01G464700 chr5B 93.182 132 8 1 6338 6469 648997572 648997702 1.000000e-44 193.0
32 TraesCS5A01G464700 chr5B 82.407 108 15 2 724 827 648995186 648995293 3.760000e-14 91.6
33 TraesCS5A01G464700 chr5B 79.000 100 21 0 1802 1901 53527777 53527876 1.760000e-07 69.4
34 TraesCS5A01G464700 chr5D 93.593 2872 119 31 6934 9774 516638664 516641501 0.000000e+00 4224.0
35 TraesCS5A01G464700 chr5D 88.759 1539 123 24 629 2143 516636905 516638417 0.000000e+00 1838.0
36 TraesCS5A01G464700 chr5D 86.582 395 28 11 156 539 516636035 516636415 7.060000e-111 412.0
37 TraesCS5A01G464700 chr5D 86.095 338 28 11 1 319 516611556 516611893 7.270000e-91 346.0
38 TraesCS5A01G464700 chr5D 89.778 225 23 0 2226 2450 470508496 470508272 1.240000e-73 289.0
39 TraesCS5A01G464700 chr5D 81.714 175 15 7 1 160 516613372 516613544 7.970000e-26 130.0
40 TraesCS5A01G464700 chr5D 98.333 60 1 0 2161 2220 516638465 516638524 1.340000e-18 106.0
41 TraesCS5A01G464700 chrUn 95.368 734 23 2 2879 3602 402350940 402351672 0.000000e+00 1157.0
42 TraesCS5A01G464700 chr6B 92.652 626 44 2 5714 6339 703252914 703253537 0.000000e+00 900.0
43 TraesCS5A01G464700 chr6B 88.821 492 31 6 2421 2891 703249873 703250361 5.090000e-162 582.0
44 TraesCS5A01G464700 chr6B 76.159 302 65 7 7872 8169 9282675 9282377 1.700000e-32 152.0
45 TraesCS5A01G464700 chr4B 92.407 619 45 2 5714 6332 17052501 17051885 0.000000e+00 881.0
46 TraesCS5A01G464700 chr1B 93.211 383 22 2 2509 2891 58495292 58495670 2.380000e-155 560.0
47 TraesCS5A01G464700 chr1B 80.208 192 28 8 1112 1300 9899283 9899099 1.710000e-27 135.0
48 TraesCS5A01G464700 chr1B 78.894 199 36 5 1103 1300 9489987 9490180 7.970000e-26 130.0
49 TraesCS5A01G464700 chr2D 86.700 406 50 3 2226 2630 584774416 584774818 1.940000e-121 448.0
50 TraesCS5A01G464700 chr2D 72.917 864 215 16 7872 8724 25171462 25170607 2.080000e-71 281.0
51 TraesCS5A01G464700 chr4A 82.552 384 56 10 2250 2630 680585095 680584720 2.630000e-85 327.0
52 TraesCS5A01G464700 chr3D 89.823 226 22 1 2226 2450 13714533 13714308 1.240000e-73 289.0
53 TraesCS5A01G464700 chr3D 89.778 225 23 0 2226 2450 394763003 394762779 1.240000e-73 289.0
54 TraesCS5A01G464700 chr2B 72.654 863 219 16 7872 8724 40905113 40904258 4.500000e-68 270.0
55 TraesCS5A01G464700 chr2A 72.500 840 218 12 7893 8724 27595069 27594235 9.740000e-65 259.0
56 TraesCS5A01G464700 chr2A 86.139 101 14 0 1083 1183 47309054 47309154 1.040000e-19 110.0
57 TraesCS5A01G464700 chr1D 79.798 198 36 3 1103 1300 7073664 7073857 3.680000e-29 141.0
58 TraesCS5A01G464700 chr1D 79.679 187 32 6 1112 1295 38726640 38726823 7.970000e-26 130.0
59 TraesCS5A01G464700 chr1A 79.397 199 35 5 1103 1300 8665096 8665289 1.710000e-27 135.0
60 TraesCS5A01G464700 chr1A 77.540 187 37 3 1112 1297 9236449 9236267 3.730000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G464700 chr5A 644096724 644106497 9773 False 8598.000000 11947 100.000000 1 9774 2 chr5A.!!$F1 9773
1 TraesCS5A01G464700 chr7A 712340481 712344715 4234 False 3138.000000 5339 93.293500 2226 6341 2 chr7A.!!$F1 4115
2 TraesCS5A01G464700 chr7B 732131021 732134506 3485 False 5334.000000 5334 94.454000 2879 6332 1 chr7B.!!$F1 3453
3 TraesCS5A01G464700 chr7B 732179134 732183385 4251 False 3024.500000 5306 90.428500 2219 6332 2 chr7B.!!$F4 4113
4 TraesCS5A01G464700 chr7B 237925763 237928164 2401 False 1466.000000 2643 93.015500 2219 4473 2 chr7B.!!$F2 2254
5 TraesCS5A01G464700 chr7B 394764745 394766585 1840 False 604.500000 917 91.376000 2217 6340 2 chr7B.!!$F3 4123
6 TraesCS5A01G464700 chr3B 23787706 23791751 4045 False 2935.000000 5284 91.601000 2421 6332 2 chr3B.!!$F1 3911
7 TraesCS5A01G464700 chr3B 444139120 444143035 3915 True 1975.333333 4462 92.417667 2421 6332 3 chr3B.!!$R2 3911
8 TraesCS5A01G464700 chr3B 20815401 20817087 1686 True 1190.000000 1816 91.955000 2421 4004 2 chr3B.!!$R1 1583
9 TraesCS5A01G464700 chr4D 8874497 8878761 4264 False 2044.666667 5232 91.257667 2221 6325 3 chr4D.!!$F1 4104
10 TraesCS5A01G464700 chr7D 528806428 528810425 3997 False 2810.500000 5018 91.279000 2419 6336 2 chr7D.!!$F2 3917
11 TraesCS5A01G464700 chr7D 614685763 614689338 3575 True 2545.000000 4133 90.704500 2879 6339 2 chr7D.!!$R2 3460
12 TraesCS5A01G464700 chr7D 156194973 156195903 930 True 992.000000 992 86.553000 5440 6339 1 chr7D.!!$R1 899
13 TraesCS5A01G464700 chr7D 614916440 614917367 927 False 929.000000 929 85.394000 5440 6339 1 chr7D.!!$F1 899
14 TraesCS5A01G464700 chr6D 452939622 452943153 3531 True 4955.000000 4955 92.377000 2879 6332 1 chr6D.!!$R1 3453
15 TraesCS5A01G464700 chr5B 648995186 649000516 5330 False 1436.120000 4292 89.291600 1 9774 5 chr5B.!!$F2 9773
16 TraesCS5A01G464700 chr5D 516636035 516641501 5466 False 1645.000000 4224 91.816750 156 9774 4 chr5D.!!$F2 9618
17 TraesCS5A01G464700 chr5D 516611556 516613544 1988 False 238.000000 346 83.904500 1 319 2 chr5D.!!$F1 318
18 TraesCS5A01G464700 chrUn 402350940 402351672 732 False 1157.000000 1157 95.368000 2879 3602 1 chrUn.!!$F1 723
19 TraesCS5A01G464700 chr6B 703249873 703253537 3664 False 741.000000 900 90.736500 2421 6339 2 chr6B.!!$F1 3918
20 TraesCS5A01G464700 chr4B 17051885 17052501 616 True 881.000000 881 92.407000 5714 6332 1 chr4B.!!$R1 618
21 TraesCS5A01G464700 chr2D 25170607 25171462 855 True 281.000000 281 72.917000 7872 8724 1 chr2D.!!$R1 852
22 TraesCS5A01G464700 chr2B 40904258 40905113 855 True 270.000000 270 72.654000 7872 8724 1 chr2B.!!$R1 852
23 TraesCS5A01G464700 chr2A 27594235 27595069 834 True 259.000000 259 72.500000 7893 8724 1 chr2A.!!$R1 831

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
90 294 0.036952 AATGTCTGCACCCACGAGAG 60.037 55.000 0.00 0.0 0.00 3.20 F
1316 2321 0.317603 CAAGTGAACGACTCCGACGT 60.318 55.000 0.00 0.0 45.89 4.34 F
1905 2910 0.035820 GCAACCCATACCTTGTCGGA 60.036 55.000 0.00 0.0 36.31 4.55 F
1945 2950 0.461693 GCACCACTCTGCATCTCTCC 60.462 60.000 0.00 0.0 37.11 3.71 F
2505 3580 0.546122 ATATCAAAGTGCCCTGGCGA 59.454 50.000 3.32 0.0 45.51 5.54 F
3347 4527 0.773644 AGCTTGTTGTCACCCTCCAT 59.226 50.000 0.00 0.0 0.00 3.41 F
4190 5896 1.002430 GATGTCAGGTTGTCCAGCTCA 59.998 52.381 0.00 0.0 35.89 4.26 F
4218 5924 1.165270 GGCCTTGTACATCGCACTTT 58.835 50.000 14.55 0.0 0.00 2.66 F
4813 6522 1.674057 CTGTCCGGCCAGTTCTTCT 59.326 57.895 3.79 0.0 0.00 2.85 F
6373 8341 0.036010 CCCGGAAGTTCACTGCTGAT 60.036 55.000 0.73 0.0 28.73 2.90 F
7819 9800 1.002544 AGGAGAAGAACGAAGGGCTTG 59.997 52.381 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 2593 0.249573 TTGGGGAACTCGAACACGAC 60.250 55.000 0.00 0.0 32.55 4.34 R
2146 3153 0.038744 CCCACAGTGGAAAGCCTGAT 59.961 55.000 22.37 0.0 40.96 2.90 R
3785 5102 0.548031 CCCCTATGCAGGAAGAGCAA 59.452 55.000 0.00 0.0 45.91 3.91 R
3922 5240 1.678627 GTATTGCAACACACACCACCA 59.321 47.619 0.00 0.0 0.00 4.17 R
4218 5924 0.836400 AAGGTCTTCTCGGGCAAGGA 60.836 55.000 0.00 0.0 0.00 3.36 R
4949 6658 1.293498 GTCCACACGGCTCTCACAT 59.707 57.895 0.00 0.0 0.00 3.21 R
6083 8049 0.035439 AACCCTACTGCCAATGTCCG 60.035 55.000 0.00 0.0 0.00 4.79 R
6117 8083 1.380785 CCTACCGCTAGGACACCCA 60.381 63.158 0.00 0.0 42.34 4.51 R
6417 8385 0.315251 GCTTTGCACCCAGGTTTCTC 59.685 55.000 0.00 0.0 0.00 2.87 R
8366 10347 0.467290 ACAACAAGCCCGGTGTGATT 60.467 50.000 0.00 0.0 0.00 2.57 R
9234 11243 0.385974 CTGCGCAGTTTAGTTGCCAC 60.386 55.000 29.24 0.0 38.31 5.01 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
28 230 8.128322 ACTGTTCTGAATAGTCATAGTTGTCT 57.872 34.615 13.23 0.00 31.85 3.41
30 232 9.429359 CTGTTCTGAATAGTCATAGTTGTCTTT 57.571 33.333 6.04 0.00 31.85 2.52
75 279 7.812690 ATGAATATGTGATGTGTGCTAATGT 57.187 32.000 0.00 0.00 0.00 2.71
76 280 7.250445 TGAATATGTGATGTGTGCTAATGTC 57.750 36.000 0.00 0.00 0.00 3.06
78 282 6.856135 ATATGTGATGTGTGCTAATGTCTG 57.144 37.500 0.00 0.00 0.00 3.51
86 290 0.673333 TGCTAATGTCTGCACCCACG 60.673 55.000 0.00 0.00 33.94 4.94
87 291 0.391130 GCTAATGTCTGCACCCACGA 60.391 55.000 0.00 0.00 0.00 4.35
89 293 1.204704 CTAATGTCTGCACCCACGAGA 59.795 52.381 0.00 0.00 0.00 4.04
90 294 0.036952 AATGTCTGCACCCACGAGAG 60.037 55.000 0.00 0.00 0.00 3.20
91 295 2.433318 GTCTGCACCCACGAGAGC 60.433 66.667 0.00 0.00 0.00 4.09
95 299 4.148825 GCACCCACGAGAGCGGAT 62.149 66.667 0.00 0.00 43.17 4.18
102 319 1.341531 CCACGAGAGCGGATATTCCTT 59.658 52.381 0.00 0.00 43.17 3.36
106 323 2.094649 CGAGAGCGGATATTCCTTACCC 60.095 54.545 0.00 0.00 33.30 3.69
126 343 3.519510 CCCTGAGGACAATAAACCAGAGA 59.480 47.826 0.00 0.00 33.47 3.10
127 344 4.383552 CCCTGAGGACAATAAACCAGAGAG 60.384 50.000 0.00 0.00 33.47 3.20
130 347 4.467795 TGAGGACAATAAACCAGAGAGAGG 59.532 45.833 0.00 0.00 0.00 3.69
131 348 4.430441 AGGACAATAAACCAGAGAGAGGT 58.570 43.478 0.00 0.00 42.34 3.85
132 349 5.590818 AGGACAATAAACCAGAGAGAGGTA 58.409 41.667 0.00 0.00 38.76 3.08
133 350 5.659079 AGGACAATAAACCAGAGAGAGGTAG 59.341 44.000 0.00 0.00 38.76 3.18
134 351 5.346181 ACAATAAACCAGAGAGAGGTAGC 57.654 43.478 0.00 0.00 38.76 3.58
205 426 1.228245 AGCCTTTTGCCGCTCTTGA 60.228 52.632 0.00 0.00 42.71 3.02
274 495 1.169661 TGTTTACAGCTGGTTGGGCG 61.170 55.000 19.93 0.00 34.52 6.13
275 496 1.602323 TTTACAGCTGGTTGGGCGG 60.602 57.895 19.93 0.00 34.52 6.13
283 504 1.302913 TGGTTGGGCGGTGTACATG 60.303 57.895 0.00 0.00 0.00 3.21
289 510 0.533491 GGGCGGTGTACATGTAGACA 59.467 55.000 28.33 15.17 31.67 3.41
291 512 1.997606 GGCGGTGTACATGTAGACAAC 59.002 52.381 28.33 18.44 31.67 3.32
306 527 2.017049 GACAACGAGCTGGCCAAATAT 58.983 47.619 7.01 0.00 0.00 1.28
313 534 4.256920 CGAGCTGGCCAAATATATAAGCT 58.743 43.478 7.01 8.70 41.96 3.74
336 559 6.399986 GCTGACGAATTTCCAAAATTAGTTGC 60.400 38.462 10.74 12.89 0.00 4.17
394 617 7.378966 TCCAGTGACTCAAAATTAGACACTAG 58.621 38.462 10.22 5.42 44.39 2.57
448 672 4.532834 AGTTTGGTTACATGACAAGTGGT 58.467 39.130 0.00 0.00 0.00 4.16
504 733 2.034179 CGTCCTCCTGCACATATTACGA 59.966 50.000 0.00 0.00 0.00 3.43
534 1031 6.246420 AGCTACTCTAAGCAAACAACAATG 57.754 37.500 0.00 0.00 45.30 2.82
544 1041 6.981762 AGCAAACAACAATGAAAACAATGA 57.018 29.167 0.00 0.00 0.00 2.57
545 1042 6.774084 AGCAAACAACAATGAAAACAATGAC 58.226 32.000 0.00 0.00 0.00 3.06
546 1043 6.370994 AGCAAACAACAATGAAAACAATGACA 59.629 30.769 0.00 0.00 0.00 3.58
547 1044 6.683708 GCAAACAACAATGAAAACAATGACAG 59.316 34.615 0.00 0.00 0.00 3.51
548 1045 7.412781 GCAAACAACAATGAAAACAATGACAGA 60.413 33.333 0.00 0.00 0.00 3.41
552 1049 5.280945 ACAATGAAAACAATGACAGAACGG 58.719 37.500 0.00 0.00 0.00 4.44
553 1050 5.067153 ACAATGAAAACAATGACAGAACGGA 59.933 36.000 0.00 0.00 0.00 4.69
563 1161 4.590850 TGACAGAACGGAGATGATATGG 57.409 45.455 0.00 0.00 0.00 2.74
596 1194 7.609760 TCTTTCATTACAAGTATCGCAATGT 57.390 32.000 0.00 0.00 0.00 2.71
598 1196 6.735678 TTCATTACAAGTATCGCAATGTGT 57.264 33.333 0.00 0.00 0.00 3.72
599 1197 6.735678 TCATTACAAGTATCGCAATGTGTT 57.264 33.333 0.00 0.00 0.00 3.32
601 1199 7.020602 TCATTACAAGTATCGCAATGTGTTTG 58.979 34.615 0.00 0.00 38.43 2.93
602 1200 4.159377 ACAAGTATCGCAATGTGTTTGG 57.841 40.909 0.00 0.00 35.75 3.28
604 1202 4.158384 CAAGTATCGCAATGTGTTTGGTC 58.842 43.478 0.00 0.00 35.75 4.02
650 1552 2.159170 GGAGATGGAGAACGAAGAGGTG 60.159 54.545 0.00 0.00 0.00 4.00
657 1559 4.192317 GGAGAACGAAGAGGTGCATAAAT 58.808 43.478 0.00 0.00 0.00 1.40
672 1574 6.096846 GGTGCATAAATGTAATCTGGTTTCCT 59.903 38.462 0.00 0.00 0.00 3.36
688 1590 1.913762 CCTCACGGGGAAGTGGAGT 60.914 63.158 0.00 0.00 42.10 3.85
709 1611 9.716531 TGGAGTGCTAATAATATTGAGAAGATG 57.283 33.333 0.00 0.00 0.00 2.90
721 1631 1.487976 GAGAAGATGGCTGTCATGGGA 59.512 52.381 0.00 0.00 35.97 4.37
727 1637 1.304282 GGCTGTCATGGGATGGTGT 59.696 57.895 0.00 0.00 0.00 4.16
735 1645 2.108075 TCATGGGATGGTGTGTTGAAGT 59.892 45.455 0.00 0.00 0.00 3.01
742 1652 1.400142 TGGTGTGTTGAAGTTTCTGCG 59.600 47.619 0.00 0.00 0.00 5.18
795 1705 8.562892 CAATAGCTGTGGAATGGTTAAGAATAG 58.437 37.037 0.00 0.00 0.00 1.73
835 1746 7.715657 TGATTAACTAATTAATTGCCCAGCAG 58.284 34.615 11.05 1.02 40.42 4.24
840 1751 5.716703 ACTAATTAATTGCCCAGCAGAGTTT 59.283 36.000 11.05 0.00 40.61 2.66
861 1774 0.834687 TTAAGGTGGTGAGGTCGGCT 60.835 55.000 0.00 0.00 0.00 5.52
895 1875 3.159213 TCCATGATGGAAGCAACTTGT 57.841 42.857 12.63 0.00 45.00 3.16
962 1946 1.293267 TACTTAAACGGCGGCAGTGC 61.293 55.000 13.24 6.55 0.00 4.40
987 1980 1.745087 CTTCCATGCGTGCCAAGTAAT 59.255 47.619 0.00 0.00 0.00 1.89
1015 2008 1.523154 AACAATGTCAACGGCCGCAT 61.523 50.000 28.58 17.92 0.00 4.73
1030 2023 1.727467 GCATTCTTATTGCCGGCGT 59.273 52.632 23.90 15.96 33.95 5.68
1067 2060 4.645921 GTTGGCAGCCACCGCAAC 62.646 66.667 15.89 5.37 37.52 4.17
1307 2312 2.337583 GCAGTGCTATCAAGTGAACGA 58.662 47.619 8.18 0.00 0.00 3.85
1316 2321 0.317603 CAAGTGAACGACTCCGACGT 60.318 55.000 0.00 0.00 45.89 4.34
1361 2366 1.149148 GACACGAGCTTCTTCAACCC 58.851 55.000 0.00 0.00 0.00 4.11
1372 2377 1.000506 TCTTCAACCCCGAGAAGAACG 59.999 52.381 2.65 0.00 45.13 3.95
1380 2385 3.117888 ACCCCGAGAAGAACGTACCTATA 60.118 47.826 0.00 0.00 0.00 1.31
1454 2459 1.227645 CCACCATCGGCATCGTGAT 60.228 57.895 0.00 0.00 37.69 3.06
1462 2467 0.460109 CGGCATCGTGATGACCTTCA 60.460 55.000 13.83 0.00 43.92 3.02
1465 2470 1.667724 GCATCGTGATGACCTTCAAGG 59.332 52.381 13.83 0.22 41.20 3.61
1518 2523 4.254709 TTCTGCCGCAGTGCCACT 62.255 61.111 19.77 0.00 32.61 4.00
1565 2570 2.182842 CCGGATGCTGCAAGGTAGC 61.183 63.158 6.36 0.00 41.49 3.58
1656 2661 1.414158 ACTACAGCCCATGCGACTAT 58.586 50.000 0.00 0.00 44.33 2.12
1806 2811 2.105128 GCGGCAGATCAGTACGCT 59.895 61.111 17.30 0.00 46.02 5.07
1905 2910 0.035820 GCAACCCATACCTTGTCGGA 60.036 55.000 0.00 0.00 36.31 4.55
1918 2923 2.517450 GTCGGAGAAAGCGGATGCG 61.517 63.158 0.65 0.65 43.52 4.73
1945 2950 0.461693 GCACCACTCTGCATCTCTCC 60.462 60.000 0.00 0.00 37.11 3.71
1949 2954 2.641815 ACCACTCTGCATCTCTCCTTTT 59.358 45.455 0.00 0.00 0.00 2.27
1985 2990 1.761784 CTCTCCTTACTGCTCTGCCAT 59.238 52.381 0.00 0.00 0.00 4.40
2027 3032 2.747686 CACCGCTACCCCAAGTGT 59.252 61.111 0.00 0.00 0.00 3.55
2046 3051 1.197036 GTAAACCGCAAGCTTGTCTCC 59.803 52.381 26.55 9.80 0.00 3.71
2067 3072 4.402528 TCCACCACCGCCGGATTG 62.403 66.667 11.71 2.99 0.00 2.67
2077 3082 2.514592 CCGGATTGGTCGCTGCAT 60.515 61.111 0.00 0.00 0.00 3.96
2083 3088 1.089481 ATTGGTCGCTGCATACCGTG 61.089 55.000 14.32 0.00 38.70 4.94
2126 3131 2.961424 CCCTTTCGGCCACTTCATT 58.039 52.632 2.24 0.00 0.00 2.57
2127 3132 1.256812 CCCTTTCGGCCACTTCATTT 58.743 50.000 2.24 0.00 0.00 2.32
2143 3150 5.184479 ACTTCATTTTAGAGCACATGCATGT 59.816 36.000 26.61 26.61 45.16 3.21
2278 3315 1.080354 AGGATCTGACCCCGGTTGA 59.920 57.895 0.00 0.00 0.00 3.18
2305 3342 6.745794 AAAAATCAGGATTTGACCCTTTCA 57.254 33.333 7.94 0.00 40.57 2.69
2336 3373 0.749049 GGTACTGGCGGTAGGGTTAG 59.251 60.000 6.39 0.00 0.00 2.34
2379 3417 2.044555 CGGTAGGGTGCGACAGAGA 61.045 63.158 0.00 0.00 0.00 3.10
2428 3503 2.314246 GTGGATAAGTACCCTACCGCT 58.686 52.381 0.00 0.00 0.00 5.52
2431 3506 3.087781 GGATAAGTACCCTACCGCTAGG 58.912 54.545 0.00 0.00 45.13 3.02
2505 3580 0.546122 ATATCAAAGTGCCCTGGCGA 59.454 50.000 3.32 0.00 45.51 5.54
2512 3587 1.819632 GTGCCCTGGCGATAGGTTG 60.820 63.158 3.32 0.00 45.51 3.77
2520 3616 1.954651 GCGATAGGTTGGCGGTAGC 60.955 63.158 0.00 0.00 44.18 3.58
2574 3670 6.861572 GCTGTAAGGTCCTGTGTTTTATTTTC 59.138 38.462 0.00 0.00 0.00 2.29
2641 3737 7.714377 AGGAAAATCACAGATAGATAAGCACAG 59.286 37.037 0.00 0.00 0.00 3.66
2771 3867 2.910319 AGGTAGCAATAACAGGACACCA 59.090 45.455 0.00 0.00 0.00 4.17
2861 3957 4.496336 GGCGGCATGCTCCTCCTT 62.496 66.667 18.92 0.00 45.43 3.36
2905 4085 2.431683 GCTGGGTTGGCTGAGTCA 59.568 61.111 0.00 0.00 0.00 3.41
3141 4321 2.616330 ATGCACGTCAACCAAGGCG 61.616 57.895 0.00 0.00 0.00 5.52
3235 4415 2.026262 TGACTTGGATCAGGTTTAGGGC 60.026 50.000 0.00 0.00 0.00 5.19
3347 4527 0.773644 AGCTTGTTGTCACCCTCCAT 59.226 50.000 0.00 0.00 0.00 3.41
3366 4546 2.409064 TGGTTCCAGGGTCAGAACTA 57.591 50.000 3.22 0.00 41.69 2.24
3596 4913 1.340308 CCTGAAGTGATGCCATGTCCA 60.340 52.381 0.00 0.00 0.00 4.02
3620 4937 1.826024 GTCCATCGTGGCCTCAGAT 59.174 57.895 3.32 5.33 37.47 2.90
3784 5101 6.773200 AGTCCAATATCGACTGAGAATACTGA 59.227 38.462 4.94 0.00 39.14 3.41
3785 5102 7.450014 AGTCCAATATCGACTGAGAATACTGAT 59.550 37.037 4.94 0.00 39.14 2.90
3922 5240 4.643387 GTGTCGTGGGGCCTTGCT 62.643 66.667 0.84 0.00 0.00 3.91
4082 5400 1.754803 CCCAAGCTCTATCGTGGTACA 59.245 52.381 0.00 0.00 34.42 2.90
4105 5811 5.885912 CAGCCACCAGTTAACCTATACAAAT 59.114 40.000 0.88 0.00 0.00 2.32
4190 5896 1.002430 GATGTCAGGTTGTCCAGCTCA 59.998 52.381 0.00 0.00 35.89 4.26
4218 5924 1.165270 GGCCTTGTACATCGCACTTT 58.835 50.000 14.55 0.00 0.00 2.66
4531 6240 4.697352 GTCTTACTGAACGGTAGAGGTACA 59.303 45.833 0.00 0.00 0.00 2.90
4586 6295 1.841556 AGTCGGCCAGGAAGTCCAA 60.842 57.895 2.24 0.00 38.89 3.53
4640 6349 2.104792 CAGGAAAGACCACCTCTGTGAA 59.895 50.000 0.00 0.00 45.76 3.18
4658 6367 6.043938 TCTGTGAAAAGAAACCATAGGTAGGT 59.956 38.462 0.00 0.00 42.34 3.08
4813 6522 1.674057 CTGTCCGGCCAGTTCTTCT 59.326 57.895 3.79 0.00 0.00 2.85
4920 6629 2.915604 ACATGGGAGATGGAAAGAGTGT 59.084 45.455 0.00 0.00 0.00 3.55
4949 6658 2.109387 CCAACGGTCCACCAACGA 59.891 61.111 0.00 0.00 35.14 3.85
4972 6681 2.280797 GAGCCGTGTGGACAAGCA 60.281 61.111 5.99 0.00 37.49 3.91
5036 6745 2.037772 CGGCTCTCCTGTAATATGGCTT 59.962 50.000 0.00 0.00 0.00 4.35
5258 6967 6.039270 GGGTCAAGCATAATGTAATTAGTGCA 59.961 38.462 12.58 0.00 42.97 4.57
5292 7002 2.840753 GGGGGCCTCCTGAAACACA 61.841 63.158 17.08 0.00 35.33 3.72
5518 7310 3.073678 TCATCTTCAAACCACATCACCG 58.926 45.455 0.00 0.00 0.00 4.94
5620 7550 5.315348 TCACCACATCAACTCATCAATCAA 58.685 37.500 0.00 0.00 0.00 2.57
5827 7792 2.816672 TCTTGTGCCAAATAATGCGTCA 59.183 40.909 0.00 0.00 0.00 4.35
5891 7856 4.868067 AGAGCTTACTTTTCTCGTTTCGA 58.132 39.130 0.00 0.00 32.42 3.71
6064 8030 4.832608 CCCTGCGGGCTTACGACC 62.833 72.222 5.85 0.00 35.35 4.79
6117 8083 2.032071 GTTGCACACCCTACCGCT 59.968 61.111 0.00 0.00 0.00 5.52
6146 8112 3.524606 CGGTAGGGTCGACGGCAT 61.525 66.667 9.92 0.00 0.00 4.40
6175 8141 1.227823 CCGTTTGGTGAGGCTGACA 60.228 57.895 6.41 0.00 0.00 3.58
6186 8153 4.502259 GGTGAGGCTGACATGGATAAGTAG 60.502 50.000 6.41 0.00 0.00 2.57
6200 8167 4.237207 GTAGCCTACCGCCAGGGC 62.237 72.222 0.00 0.00 45.57 5.19
6259 8227 2.638855 TCTGGCGGTAAGAAAAAGGGTA 59.361 45.455 0.00 0.00 0.00 3.69
6340 8308 1.600023 AACACGAAATTCGGCCTCAA 58.400 45.000 19.95 0.00 45.59 3.02
6341 8309 0.872388 ACACGAAATTCGGCCTCAAC 59.128 50.000 19.95 0.00 45.59 3.18
6342 8310 0.168128 CACGAAATTCGGCCTCAACC 59.832 55.000 19.95 0.00 45.59 3.77
6343 8311 0.250553 ACGAAATTCGGCCTCAACCA 60.251 50.000 19.95 0.00 45.59 3.67
6344 8312 0.447801 CGAAATTCGGCCTCAACCAG 59.552 55.000 7.61 0.00 36.00 4.00
6345 8313 1.821216 GAAATTCGGCCTCAACCAGA 58.179 50.000 0.00 0.00 0.00 3.86
6355 8323 0.954452 CTCAACCAGACACCTTTGCC 59.046 55.000 0.00 0.00 0.00 4.52
6373 8341 0.036010 CCCGGAAGTTCACTGCTGAT 60.036 55.000 0.73 0.00 28.73 2.90
6399 8367 2.046892 CTGGCGCTACCTGCACTT 60.047 61.111 7.64 0.00 43.06 3.16
6417 8385 4.025061 GCACTTGATCCTCAATTCGATCTG 60.025 45.833 7.74 0.00 35.59 2.90
6422 8390 6.225981 TGATCCTCAATTCGATCTGAGAAA 57.774 37.500 20.38 11.51 41.38 2.52
6981 8959 7.648142 TCCAAAAAGAACAGTCATTACATCAC 58.352 34.615 0.00 0.00 0.00 3.06
7031 9009 8.139989 GCTAGTGCAATGGATCAAAAGAATATT 58.860 33.333 0.20 0.00 39.41 1.28
7053 9031 1.999648 AAAAGATGCCACTGGAGCAA 58.000 45.000 0.00 0.00 44.83 3.91
7056 9034 1.760192 AGATGCCACTGGAGCAATTC 58.240 50.000 0.00 0.00 44.83 2.17
7064 9042 4.580167 GCCACTGGAGCAATTCACAATATA 59.420 41.667 0.00 0.00 0.00 0.86
7088 9066 5.686397 AGCGTAAATTCTGCGATAACTAGTC 59.314 40.000 0.00 0.00 34.69 2.59
7097 9075 3.181507 TGCGATAACTAGTCGTGTACACC 60.182 47.826 20.11 7.27 40.98 4.16
7144 9122 3.742385 TCCGCAGATATCAATGAATGCA 58.258 40.909 5.32 0.00 33.33 3.96
7151 9129 6.312487 CAGATATCAATGAATGCAACGATCC 58.688 40.000 5.32 0.00 0.00 3.36
7180 9158 3.437795 CTTGCTTGCAGCCGGGAG 61.438 66.667 2.18 0.00 41.51 4.30
7213 9191 3.460857 ACGAAGGATCTTATGACTGCC 57.539 47.619 0.00 0.00 0.00 4.85
7404 9382 6.488683 TGTTGTGTTTAACTGGAATAAGGGAG 59.511 38.462 0.00 0.00 0.00 4.30
7417 9395 9.853177 CTGGAATAAGGGAGTTATTTTCACTAT 57.147 33.333 0.00 0.00 40.77 2.12
7518 9497 5.551760 AGAAATCAATAGTTTCAGTGCGG 57.448 39.130 0.00 0.00 37.89 5.69
7670 9651 7.282224 TGCCTGTCCACTTTGTATTATCAATAC 59.718 37.037 2.73 2.73 43.19 1.89
7782 9763 8.821147 TTATTACTTGTTGCTCTACTTTCGAA 57.179 30.769 0.00 0.00 0.00 3.71
7789 9770 5.182570 TGTTGCTCTACTTTCGAAGCTACTA 59.817 40.000 16.23 4.76 0.00 1.82
7819 9800 1.002544 AGGAGAAGAACGAAGGGCTTG 59.997 52.381 0.00 0.00 0.00 4.01
8041 10022 5.321927 GAGGAATTTACCAAGGAAGTGGAA 58.678 41.667 0.00 0.00 41.65 3.53
8344 10325 1.480789 TCTCGGATTTCGGGACATCA 58.519 50.000 0.00 0.00 44.46 3.07
8366 10347 9.364989 CATCAAAGTTTCTTACAAAGGACAAAA 57.635 29.630 0.00 0.00 0.00 2.44
8533 10514 6.291377 TGGAAATCATAGGCTCATAGTTGAC 58.709 40.000 0.00 0.00 0.00 3.18
8654 10638 4.204012 ACTGGCTGTAAAGTGTTTAGCAA 58.796 39.130 0.00 0.00 0.00 3.91
8724 10708 3.181461 GCCATGCTTAGAAGAGCTAGGAA 60.181 47.826 10.73 0.00 43.11 3.36
8727 10711 5.295540 CCATGCTTAGAAGAGCTAGGAAAAC 59.704 44.000 0.00 0.00 43.11 2.43
8803 10788 3.065510 CCTGAGCATTGCTTCTGAGATTG 59.934 47.826 13.35 0.00 39.88 2.67
8804 10789 3.939592 CTGAGCATTGCTTCTGAGATTGA 59.060 43.478 13.35 0.00 39.88 2.57
8805 10790 4.329392 TGAGCATTGCTTCTGAGATTGAA 58.671 39.130 13.35 0.00 39.88 2.69
8806 10791 4.395231 TGAGCATTGCTTCTGAGATTGAAG 59.605 41.667 13.35 0.00 39.88 3.02
8807 10792 4.586884 AGCATTGCTTCTGAGATTGAAGA 58.413 39.130 5.03 0.00 42.37 2.87
8808 10793 5.194432 AGCATTGCTTCTGAGATTGAAGAT 58.806 37.500 5.03 0.00 42.37 2.40
8809 10794 5.652891 AGCATTGCTTCTGAGATTGAAGATT 59.347 36.000 5.03 0.00 42.37 2.40
9019 11005 4.183865 TGACAACATTGAGATCGACATCC 58.816 43.478 0.00 0.00 0.00 3.51
9087 11073 8.783660 TGTGATATTCAGTACCTTAGAATCCT 57.216 34.615 4.38 0.00 34.19 3.24
9091 11077 9.413048 GATATTCAGTACCTTAGAATCCTTTCG 57.587 37.037 4.38 0.00 36.93 3.46
9118 11104 6.369065 GGATTGTAGATTAACCGATGTCCATC 59.631 42.308 0.00 0.00 34.56 3.51
9234 11243 1.817357 TGGAGCACTTGAAGATGCAG 58.183 50.000 17.46 0.00 44.59 4.41
9306 11315 6.398095 TGGTGCTACAATATATCAGGAATCG 58.602 40.000 0.00 0.00 0.00 3.34
9311 11320 6.983307 GCTACAATATATCAGGAATCGCAGAT 59.017 38.462 0.00 0.00 45.12 2.90
9320 11329 9.896645 ATATCAGGAATCGCAGATAATAACATT 57.103 29.630 0.00 0.00 45.12 2.71
9387 11396 9.102757 GAGACTACTGAATGCTAAAATGAATCA 57.897 33.333 0.00 0.00 0.00 2.57
9427 11436 4.508047 CCATCCTCTATTCTCAATTGGGGG 60.508 50.000 5.25 0.00 35.32 5.40
9445 11454 4.790765 GGGGGAAGTTTCAGAAATTGAG 57.209 45.455 0.00 0.00 37.07 3.02
9449 11458 5.465051 GGGAAGTTTCAGAAATTGAGAAGC 58.535 41.667 0.00 0.00 37.07 3.86
9681 11690 1.403647 CGTCAGCGTTTACCTGATGGA 60.404 52.381 10.34 0.00 41.01 3.41
9753 11766 1.588139 CAGTTATCGGACGGACGGC 60.588 63.158 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 279 4.056125 CGCTCTCGTGGGTGCAGA 62.056 66.667 0.00 0.00 0.00 4.26
78 282 2.088674 ATATCCGCTCTCGTGGGTGC 62.089 60.000 0.00 0.00 41.26 5.01
86 290 3.056465 CAGGGTAAGGAATATCCGCTCTC 60.056 52.174 0.00 0.00 42.75 3.20
87 291 2.900546 CAGGGTAAGGAATATCCGCTCT 59.099 50.000 0.00 0.00 42.75 4.09
89 293 2.900546 CTCAGGGTAAGGAATATCCGCT 59.099 50.000 0.00 0.00 42.75 5.52
90 294 2.028020 CCTCAGGGTAAGGAATATCCGC 60.028 54.545 0.00 0.00 42.75 5.54
91 295 3.258622 GTCCTCAGGGTAAGGAATATCCG 59.741 52.174 0.00 0.00 44.40 4.18
94 298 7.947782 TTATTGTCCTCAGGGTAAGGAATAT 57.052 36.000 0.00 0.00 44.40 1.28
95 299 7.366191 GGTTTATTGTCCTCAGGGTAAGGAATA 60.366 40.741 0.00 0.00 44.40 1.75
102 319 4.431378 TCTGGTTTATTGTCCTCAGGGTA 58.569 43.478 0.00 0.00 0.00 3.69
106 323 5.395103 CCTCTCTCTGGTTTATTGTCCTCAG 60.395 48.000 0.00 0.00 0.00 3.35
126 343 2.234908 CAACTGTAAGGCTGCTACCTCT 59.765 50.000 0.00 0.00 39.93 3.69
127 344 2.028020 ACAACTGTAAGGCTGCTACCTC 60.028 50.000 0.00 0.00 39.93 3.85
130 347 2.095718 GCAACAACTGTAAGGCTGCTAC 60.096 50.000 0.00 0.00 39.30 3.58
131 348 2.151202 GCAACAACTGTAAGGCTGCTA 58.849 47.619 0.00 0.00 39.30 3.49
132 349 0.954452 GCAACAACTGTAAGGCTGCT 59.046 50.000 0.00 0.00 39.30 4.24
133 350 0.954452 AGCAACAACTGTAAGGCTGC 59.046 50.000 0.00 0.00 39.30 5.25
134 351 3.403038 ACTAGCAACAACTGTAAGGCTG 58.597 45.455 11.60 6.48 39.30 4.85
205 426 9.173021 TCAATTGATCGTGGTTAACAAGATTAT 57.827 29.630 3.38 4.58 46.20 1.28
274 495 2.921754 GCTCGTTGTCTACATGTACACC 59.078 50.000 8.57 0.00 0.00 4.16
275 496 3.608506 CAGCTCGTTGTCTACATGTACAC 59.391 47.826 0.08 2.60 0.00 2.90
283 504 0.320421 TTGGCCAGCTCGTTGTCTAC 60.320 55.000 5.11 0.00 0.00 2.59
289 510 4.455877 GCTTATATATTTGGCCAGCTCGTT 59.544 41.667 5.11 0.00 0.00 3.85
291 512 4.093998 CAGCTTATATATTTGGCCAGCTCG 59.906 45.833 5.11 0.00 33.85 5.03
313 534 6.640499 CAGCAACTAATTTTGGAAATTCGTCA 59.360 34.615 2.21 0.00 0.00 4.35
336 559 2.069273 GGTCACAACGGAATGACTCAG 58.931 52.381 12.91 0.00 43.91 3.35
394 617 1.225855 TGACGTCCTGATTGCAACAC 58.774 50.000 14.12 0.00 0.00 3.32
490 719 5.463392 AGCTATGTGTTCGTAATATGTGCAG 59.537 40.000 0.00 0.00 0.00 4.41
504 733 6.464222 TGTTTGCTTAGAGTAGCTATGTGTT 58.536 36.000 0.00 0.00 41.76 3.32
534 1031 5.179368 TCATCTCCGTTCTGTCATTGTTTTC 59.821 40.000 0.00 0.00 0.00 2.29
544 1041 3.960755 TGACCATATCATCTCCGTTCTGT 59.039 43.478 0.00 0.00 29.99 3.41
545 1042 4.590850 TGACCATATCATCTCCGTTCTG 57.409 45.455 0.00 0.00 29.99 3.02
546 1043 5.614324 TTTGACCATATCATCTCCGTTCT 57.386 39.130 0.00 0.00 37.11 3.01
547 1044 6.867662 ATTTTGACCATATCATCTCCGTTC 57.132 37.500 0.00 0.00 37.11 3.95
548 1045 8.378565 AGATATTTTGACCATATCATCTCCGTT 58.621 33.333 3.41 0.00 37.11 4.44
580 1178 4.757657 ACCAAACACATTGCGATACTTGTA 59.242 37.500 0.00 0.00 37.73 2.41
582 1180 4.083324 AGACCAAACACATTGCGATACTTG 60.083 41.667 0.00 0.00 37.73 3.16
585 1183 5.321516 GTTAGACCAAACACATTGCGATAC 58.678 41.667 0.00 0.00 37.73 2.24
587 1185 3.190535 GGTTAGACCAAACACATTGCGAT 59.809 43.478 0.00 0.00 38.42 4.58
588 1186 2.550606 GGTTAGACCAAACACATTGCGA 59.449 45.455 0.00 0.00 38.42 5.10
589 1187 2.928694 GGTTAGACCAAACACATTGCG 58.071 47.619 0.00 0.00 38.42 4.85
601 1199 7.147707 ACCTTACATTCAGATAGTGGTTAGACC 60.148 40.741 0.00 0.00 39.22 3.85
602 1200 7.783042 ACCTTACATTCAGATAGTGGTTAGAC 58.217 38.462 0.00 0.00 0.00 2.59
604 1202 6.918569 CGACCTTACATTCAGATAGTGGTTAG 59.081 42.308 0.00 0.00 0.00 2.34
610 1511 5.446860 TCTCCGACCTTACATTCAGATAGT 58.553 41.667 0.00 0.00 0.00 2.12
611 1512 6.385843 CATCTCCGACCTTACATTCAGATAG 58.614 44.000 0.00 0.00 0.00 2.08
613 1514 4.039730 CCATCTCCGACCTTACATTCAGAT 59.960 45.833 0.00 0.00 0.00 2.90
614 1515 3.384789 CCATCTCCGACCTTACATTCAGA 59.615 47.826 0.00 0.00 0.00 3.27
615 1516 3.384789 TCCATCTCCGACCTTACATTCAG 59.615 47.826 0.00 0.00 0.00 3.02
617 1518 3.637229 TCTCCATCTCCGACCTTACATTC 59.363 47.826 0.00 0.00 0.00 2.67
650 1552 7.196331 GTGAGGAAACCAGATTACATTTATGC 58.804 38.462 0.00 0.00 0.00 3.14
672 1574 2.879233 GCACTCCACTTCCCCGTGA 61.879 63.158 0.00 0.00 37.06 4.35
688 1590 8.159447 ACAGCCATCTTCTCAATATTATTAGCA 58.841 33.333 0.00 0.00 0.00 3.49
709 1611 1.033746 CACACCATCCCATGACAGCC 61.034 60.000 0.00 0.00 0.00 4.85
721 1631 2.033299 CGCAGAAACTTCAACACACCAT 59.967 45.455 0.00 0.00 0.00 3.55
727 1637 3.554324 GTGTAGACGCAGAAACTTCAACA 59.446 43.478 0.00 0.00 0.00 3.33
742 1652 0.441533 TTCGCTCTCGTCGTGTAGAC 59.558 55.000 0.00 0.00 46.16 2.59
795 1705 4.096984 AGTTAATCAAGTTAGGCATGCTGC 59.903 41.667 18.92 1.03 44.08 5.25
827 1738 1.541588 CCTTAACAAACTCTGCTGGGC 59.458 52.381 0.00 0.00 0.00 5.36
835 1746 3.813724 GACCTCACCACCTTAACAAACTC 59.186 47.826 0.00 0.00 0.00 3.01
840 1751 0.682852 CCGACCTCACCACCTTAACA 59.317 55.000 0.00 0.00 0.00 2.41
945 1925 2.175811 GCACTGCCGCCGTTTAAG 59.824 61.111 0.00 0.00 0.00 1.85
962 1946 3.818787 GCACGCATGGAAGCCAGG 61.819 66.667 0.00 0.00 36.75 4.45
987 1980 4.024387 GCCGTTGACATTGTTGAAGAGTAA 60.024 41.667 0.00 0.00 0.00 2.24
1015 2008 0.958382 AGCAACGCCGGCAATAAGAA 60.958 50.000 28.98 0.00 0.00 2.52
1030 2023 1.812686 AACGACGGCAGTAGGAGCAA 61.813 55.000 0.00 0.00 0.00 3.91
1213 2218 1.374947 CCTGGATGGACGTGTTGGT 59.625 57.895 0.00 0.00 38.35 3.67
1307 2312 4.525912 ACCACTTTATTAACGTCGGAGT 57.474 40.909 0.00 0.00 0.00 3.85
1317 2322 9.549078 TCATTCATATTGCGTACCACTTTATTA 57.451 29.630 0.00 0.00 0.00 0.98
1318 2323 8.342634 GTCATTCATATTGCGTACCACTTTATT 58.657 33.333 0.00 0.00 0.00 1.40
1319 2324 7.497579 TGTCATTCATATTGCGTACCACTTTAT 59.502 33.333 0.00 0.00 0.00 1.40
1341 2346 1.540363 GGGTTGAAGAAGCTCGTGTCA 60.540 52.381 0.00 0.00 0.00 3.58
1361 2366 4.084641 CGTCTATAGGTACGTTCTTCTCGG 60.085 50.000 0.00 0.00 34.48 4.63
1372 2377 3.307242 CGGTATACGCCGTCTATAGGTAC 59.693 52.174 0.00 0.00 46.11 3.34
1454 2459 0.260230 TGTTTGGCCCTTGAAGGTCA 59.740 50.000 10.82 5.48 40.63 4.02
1551 2556 0.466922 GGATGGCTACCTTGCAGCAT 60.467 55.000 0.00 0.00 40.95 3.79
1565 2570 3.083349 TGACCTCCGGCTGGATGG 61.083 66.667 16.52 19.93 45.33 3.51
1588 2593 0.249573 TTGGGGAACTCGAACACGAC 60.250 55.000 0.00 0.00 32.55 4.34
1656 2661 3.270000 TCGTCGACGATGAAGGCA 58.730 55.556 34.97 12.17 44.22 4.75
1893 2898 1.134788 CCGCTTTCTCCGACAAGGTAT 60.135 52.381 0.00 0.00 41.99 2.73
1918 2923 1.741770 CAGAGTGGTGCTTACCGGC 60.742 63.158 0.00 0.00 0.00 6.13
1949 2954 2.537143 GAGAGGGTGGAGGAGTGTAAA 58.463 52.381 0.00 0.00 0.00 2.01
1960 2965 0.827368 GAGCAGTAAGGAGAGGGTGG 59.173 60.000 0.00 0.00 0.00 4.61
1961 2966 1.480137 CAGAGCAGTAAGGAGAGGGTG 59.520 57.143 0.00 0.00 0.00 4.61
1962 2967 1.859302 CAGAGCAGTAAGGAGAGGGT 58.141 55.000 0.00 0.00 0.00 4.34
1963 2968 0.463620 GCAGAGCAGTAAGGAGAGGG 59.536 60.000 0.00 0.00 0.00 4.30
1966 2971 1.759445 GATGGCAGAGCAGTAAGGAGA 59.241 52.381 0.00 0.00 0.00 3.71
1993 2998 0.546598 GTGGGTGGCTAAGCATAGGT 59.453 55.000 0.00 0.00 0.00 3.08
2027 3032 1.519408 GGAGACAAGCTTGCGGTTTA 58.481 50.000 26.27 0.00 0.00 2.01
2143 3150 1.067295 ACAGTGGAAAGCCTGATCCA 58.933 50.000 0.00 0.00 43.32 3.41
2144 3151 1.457346 CACAGTGGAAAGCCTGATCC 58.543 55.000 0.00 0.00 36.21 3.36
2145 3152 1.457346 CCACAGTGGAAAGCCTGATC 58.543 55.000 15.35 0.00 40.96 2.92
2146 3153 0.038744 CCCACAGTGGAAAGCCTGAT 59.961 55.000 22.37 0.00 40.96 2.90
2286 3323 4.664688 AGTGAAAGGGTCAAATCCTGAT 57.335 40.909 0.00 0.00 38.23 2.90
2289 3326 3.307480 CGGTAGTGAAAGGGTCAAATCCT 60.307 47.826 0.00 0.00 38.23 3.24
2305 3342 1.684734 CAGTACCCCTGGCGGTAGT 60.685 63.158 12.60 12.85 41.83 2.73
2336 3373 2.990479 CCCTGGTGGTAGGCTGTC 59.010 66.667 0.00 0.00 36.47 3.51
2354 3391 2.495409 CGCACCCTACCGCCAGATA 61.495 63.158 0.00 0.00 0.00 1.98
2355 3392 3.849951 CGCACCCTACCGCCAGAT 61.850 66.667 0.00 0.00 0.00 2.90
2428 3503 1.635487 ACCCTACCGTCAGTGTACCTA 59.365 52.381 0.00 0.00 0.00 3.08
2431 3506 0.108945 GCACCCTACCGTCAGTGTAC 60.109 60.000 0.00 0.00 32.75 2.90
2432 3507 1.588824 CGCACCCTACCGTCAGTGTA 61.589 60.000 0.00 0.00 32.75 2.90
2433 3508 2.927580 CGCACCCTACCGTCAGTGT 61.928 63.158 0.00 0.00 32.75 3.55
2435 3510 3.379445 CCGCACCCTACCGTCAGT 61.379 66.667 0.00 0.00 0.00 3.41
2505 3580 1.070758 CTCATGCTACCGCCAACCTAT 59.929 52.381 0.00 0.00 34.43 2.57
2512 3587 1.521681 GGTGTCTCATGCTACCGCC 60.522 63.158 0.00 0.00 34.43 6.13
2520 3616 1.144057 GGCGGTAGGGTGTCTCATG 59.856 63.158 0.00 0.00 0.00 3.07
2521 3617 1.305802 TGGCGGTAGGGTGTCTCAT 60.306 57.895 0.00 0.00 0.00 2.90
2524 3620 3.391382 GCTGGCGGTAGGGTGTCT 61.391 66.667 0.00 0.00 0.00 3.41
2527 3623 4.814294 GACGCTGGCGGTAGGGTG 62.814 72.222 18.99 0.00 42.96 4.61
2543 3639 1.229082 AGGACCTTACAGCCACGGA 60.229 57.895 0.00 0.00 0.00 4.69
2551 3647 6.265876 GGGAAAATAAAACACAGGACCTTACA 59.734 38.462 0.00 0.00 0.00 2.41
2555 3651 4.810345 TGGGAAAATAAAACACAGGACCT 58.190 39.130 0.00 0.00 0.00 3.85
2574 3670 1.035139 AGCAAGCAACTGAACTTGGG 58.965 50.000 5.04 0.00 42.82 4.12
2620 3716 5.922053 TGCTGTGCTTATCTATCTGTGATT 58.078 37.500 0.00 0.00 0.00 2.57
2861 3957 1.959226 GGCCGCTCGAAGACAAACA 60.959 57.895 0.00 0.00 0.00 2.83
2888 4068 1.673665 CTGACTCAGCCAACCCAGC 60.674 63.158 0.00 0.00 0.00 4.85
2905 4085 1.135139 CGACGATGATGGACCTCAACT 59.865 52.381 0.00 0.00 0.00 3.16
3235 4415 5.801947 GCCACATGTTCTTACTTATTTGCAG 59.198 40.000 0.00 0.00 0.00 4.41
3347 4527 2.409064 TAGTTCTGACCCTGGAACCA 57.591 50.000 0.00 0.00 41.69 3.67
3366 4546 3.188786 GACGGCTCGAATGCGCTT 61.189 61.111 9.73 0.00 37.46 4.68
3393 4573 0.745845 AGGCCGCAGAGCTAAACATG 60.746 55.000 0.00 0.00 0.00 3.21
3620 4937 0.874390 GGCATCAAGTTTCGTCTGCA 59.126 50.000 0.00 0.00 0.00 4.41
3784 5101 1.144503 CCCCTATGCAGGAAGAGCAAT 59.855 52.381 0.00 0.00 45.91 3.56
3785 5102 0.548031 CCCCTATGCAGGAAGAGCAA 59.452 55.000 0.00 0.00 45.91 3.91
3922 5240 1.678627 GTATTGCAACACACACCACCA 59.321 47.619 0.00 0.00 0.00 4.17
4082 5400 5.508280 TTTGTATAGGTTAACTGGTGGCT 57.492 39.130 5.42 0.00 0.00 4.75
4105 5811 7.675962 ATACTTTCACGGTTGCTAAACAATA 57.324 32.000 0.00 0.00 41.27 1.90
4148 5854 6.061022 TCTTTTCAGGTATACCAATGAGCA 57.939 37.500 23.87 7.64 38.89 4.26
4190 5896 2.969821 TGTACAAGGCCTTCACCAAT 57.030 45.000 17.29 0.00 0.00 3.16
4218 5924 0.836400 AAGGTCTTCTCGGGCAAGGA 60.836 55.000 0.00 0.00 0.00 3.36
4586 6295 2.102588 GACAACGCCCTATGGATGTACT 59.897 50.000 0.00 0.00 0.00 2.73
4813 6522 1.557371 TCTCATTGGGTGCGTGGATAA 59.443 47.619 0.00 0.00 0.00 1.75
4949 6658 1.293498 GTCCACACGGCTCTCACAT 59.707 57.895 0.00 0.00 0.00 3.21
5036 6745 1.608109 TGAACTACGACAACCGCTACA 59.392 47.619 0.00 0.00 43.32 2.74
5103 6812 3.494045 TTTTCGTGTGCACATTGACAA 57.506 38.095 24.69 18.98 0.00 3.18
5245 6954 2.548057 CCGGCGATTGCACTAATTACAT 59.452 45.455 9.30 0.00 45.35 2.29
5258 6967 2.124320 CCCATTGGTCCGGCGATT 60.124 61.111 9.30 0.00 0.00 3.34
5518 7310 2.104451 AGATGAGGTGATGAGGTGATGC 59.896 50.000 0.00 0.00 0.00 3.91
5790 7754 5.127682 GGCACAAGATGAACCCTATTTCATT 59.872 40.000 0.15 0.00 44.59 2.57
5827 7792 8.553696 TCGTTTTAGTTAAGAAGCTTTCGATTT 58.446 29.630 0.00 0.00 34.02 2.17
5891 7856 0.107703 TTTGCGGATCGAGATGGCTT 60.108 50.000 0.00 0.00 0.00 4.35
6061 8027 3.866356 GGTAAGTGCCGAACGGTC 58.134 61.111 14.63 7.73 37.65 4.79
6083 8049 0.035439 AACCCTACTGCCAATGTCCG 60.035 55.000 0.00 0.00 0.00 4.79
6117 8083 1.380785 CCTACCGCTAGGACACCCA 60.381 63.158 0.00 0.00 42.34 4.51
6175 8141 1.900486 GGCGGTAGGCTACTTATCCAT 59.100 52.381 23.01 0.00 42.94 3.41
6200 8167 2.526873 ATAGCCTACCGCCAGGGG 60.527 66.667 0.00 0.00 43.47 4.79
6275 8243 3.173151 GGGATTTGACCCCTGTTTGATT 58.827 45.455 0.00 0.00 43.81 2.57
6283 8251 2.919772 AAATTCGGGATTTGACCCCT 57.080 45.000 0.00 0.00 46.62 4.79
6340 8308 2.113139 CGGGCAAAGGTGTCTGGT 59.887 61.111 0.00 0.00 31.59 4.00
6342 8310 1.228124 TTCCGGGCAAAGGTGTCTG 60.228 57.895 0.00 0.00 35.33 3.51
6343 8311 1.073199 CTTCCGGGCAAAGGTGTCT 59.927 57.895 0.00 0.00 0.00 3.41
6344 8312 0.822121 AACTTCCGGGCAAAGGTGTC 60.822 55.000 0.00 0.00 0.00 3.67
6345 8313 0.822121 GAACTTCCGGGCAAAGGTGT 60.822 55.000 0.00 0.00 0.00 4.16
6355 8323 1.081892 CATCAGCAGTGAACTTCCGG 58.918 55.000 0.00 0.00 35.88 5.14
6373 8341 2.679996 TAGCGCCAGAGCAGGACA 60.680 61.111 2.29 0.00 39.83 4.02
6417 8385 0.315251 GCTTTGCACCCAGGTTTCTC 59.685 55.000 0.00 0.00 0.00 2.87
6422 8390 0.538287 GAGAAGCTTTGCACCCAGGT 60.538 55.000 0.00 0.00 0.00 4.00
6932 8908 1.899437 TTGAAGGCGCAGTAGGGGAG 61.899 60.000 10.83 0.00 0.00 4.30
6981 8959 6.480320 GCTGTCTTACTGTCCCAACAATATAG 59.520 42.308 0.00 0.00 34.24 1.31
7031 9009 3.495331 TGCTCCAGTGGCATCTTTTTAA 58.505 40.909 3.51 0.00 34.56 1.52
7041 9019 0.961019 TTGTGAATTGCTCCAGTGGC 59.039 50.000 3.51 0.00 0.00 5.01
7053 9031 7.170828 TCGCAGAATTTACGCTATATTGTGAAT 59.829 33.333 4.70 0.00 0.00 2.57
7056 9034 6.210396 TCGCAGAATTTACGCTATATTGTG 57.790 37.500 0.00 0.00 0.00 3.33
7064 9042 5.589192 ACTAGTTATCGCAGAATTTACGCT 58.411 37.500 0.00 0.00 43.58 5.07
7088 9066 6.525121 AATAAATGATCATCGGTGTACACG 57.475 37.500 19.41 14.40 0.00 4.49
7169 9147 2.046023 CACATTCTCCCGGCTGCA 60.046 61.111 0.50 0.00 0.00 4.41
7180 9158 1.529438 TCCTTCGTTGTTCGCACATTC 59.471 47.619 0.00 0.00 39.67 2.67
7345 9323 1.194218 TGCCACGAATGAGATCTCCA 58.806 50.000 20.03 8.63 0.00 3.86
7432 9410 4.578105 CAGGATATTCCTTTGGCAAGAGAC 59.422 45.833 0.00 0.00 46.91 3.36
7524 9503 8.031277 TGTGCTATATATGTGAACTGCATCTAG 58.969 37.037 0.00 0.00 0.00 2.43
7670 9651 2.238942 TTGGCCACATACATAGCGAG 57.761 50.000 3.88 0.00 0.00 5.03
7680 9661 4.283363 TGCATGTTAATTTTGGCCACAT 57.717 36.364 3.88 0.00 0.00 3.21
7782 9763 2.769095 CTCCTTTGGAGCCTTAGTAGCT 59.231 50.000 0.27 0.00 43.29 3.32
7819 9800 6.294564 GGACCAAACCTCCATTCTTCTTAAAC 60.295 42.308 0.00 0.00 0.00 2.01
8041 10022 3.520721 TGTGGATCATCTGTGACTGGATT 59.479 43.478 0.00 0.00 37.14 3.01
8344 10325 9.936759 TGATTTTTGTCCTTTGTAAGAAACTTT 57.063 25.926 0.00 0.00 0.00 2.66
8366 10347 0.467290 ACAACAAGCCCGGTGTGATT 60.467 50.000 0.00 0.00 0.00 2.57
8549 10530 3.885901 GCCTCTCCACTGTTTTCTTTCTT 59.114 43.478 0.00 0.00 0.00 2.52
8654 10638 5.419155 TCTCTGGACGATCTTCTACAACATT 59.581 40.000 0.00 0.00 0.00 2.71
8724 10708 6.315144 GCTTTTGTTGTTTATGTTCCCAGTTT 59.685 34.615 0.00 0.00 0.00 2.66
8727 10711 4.749598 GGCTTTTGTTGTTTATGTTCCCAG 59.250 41.667 0.00 0.00 0.00 4.45
8867 10853 9.743581 TGGCATGATACAATAGTCAATATTCAT 57.256 29.630 0.00 0.00 31.40 2.57
8888 10874 3.192001 CACTGCAACAGACTTTATGGCAT 59.808 43.478 4.88 4.88 35.18 4.40
9019 11005 5.765182 AGGAATTAATCATTTACTCCAGGCG 59.235 40.000 3.55 0.00 0.00 5.52
9087 11073 6.211587 TCGGTTAATCTACAATCCTCGAAA 57.788 37.500 0.00 0.00 0.00 3.46
9090 11076 5.529791 ACATCGGTTAATCTACAATCCTCG 58.470 41.667 0.00 0.00 0.00 4.63
9091 11077 5.927115 GGACATCGGTTAATCTACAATCCTC 59.073 44.000 0.00 0.00 0.00 3.71
9118 11104 3.535561 ACTCTGATATGCCCTGTTTTCG 58.464 45.455 0.00 0.00 0.00 3.46
9127 11113 9.875691 TGTCATATAACATAACTCTGATATGCC 57.124 33.333 0.00 0.00 34.75 4.40
9234 11243 0.385974 CTGCGCAGTTTAGTTGCCAC 60.386 55.000 29.24 0.00 38.31 5.01
9306 11315 8.633075 TTTTAGCAGCAAATGTTATTATCTGC 57.367 30.769 14.62 14.62 43.94 4.26
9333 11342 5.048224 CAGTGCTGTCTTCCATTGAATTTCT 60.048 40.000 0.00 0.00 0.00 2.52
9352 11361 1.257743 TCAGTAGTCTCCACCAGTGC 58.742 55.000 0.00 0.00 0.00 4.40
9403 11412 4.105377 CCCCAATTGAGAATAGAGGATGGT 59.895 45.833 7.12 0.00 0.00 3.55
9404 11413 4.508047 CCCCCAATTGAGAATAGAGGATGG 60.508 50.000 7.12 0.00 0.00 3.51
9427 11436 6.148264 CAGCTTCTCAATTTCTGAAACTTCC 58.852 40.000 4.73 0.00 32.17 3.46
9428 11437 6.016777 TCCAGCTTCTCAATTTCTGAAACTTC 60.017 38.462 4.73 0.00 32.17 3.01
9445 11454 2.386660 GCGTGAGTGCTCCAGCTTC 61.387 63.158 0.00 0.00 42.66 3.86
9449 11458 1.140589 CCTAGCGTGAGTGCTCCAG 59.859 63.158 0.00 0.00 45.87 3.86
9681 11690 7.011950 CACTTCTACAGTCGATCTTCAGATAGT 59.988 40.741 0.00 0.00 31.14 2.12
9753 11766 1.334243 GAAGTACCGGAGAGACGATGG 59.666 57.143 9.46 0.00 35.47 3.51


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

AutoCloner maintained by Alex Coulton.