Multiple sequence alignment - TraesCS6A01G360000

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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 TraesCS6A01G360000 chr6A 100.000 5349 0 0 1 5349 591268746 591263398 0.000000e+00 9878.0
1 TraesCS6A01G360000 chr6A 86.000 100 14 0 1199 1298 181563849 181563948 2.040000e-19 108.0
2 TraesCS6A01G360000 chr6B 91.917 3489 166 56 1426 4838 667899558 667896110 0.000000e+00 4774.0
3 TraesCS6A01G360000 chr6B 89.922 645 26 21 815 1424 667900235 667899595 0.000000e+00 795.0
4 TraesCS6A01G360000 chr6B 90.661 257 22 1 4942 5198 667895844 667895590 1.850000e-89 340.0
5 TraesCS6A01G360000 chr6B 92.466 146 11 0 5202 5347 696012535 696012390 5.430000e-50 209.0
6 TraesCS6A01G360000 chr6B 97.297 111 3 0 671 781 667900444 667900334 7.070000e-44 189.0
7 TraesCS6A01G360000 chr6D 95.110 2556 77 21 2310 4838 441898300 441895766 0.000000e+00 3984.0
8 TraesCS6A01G360000 chr6D 86.498 911 68 24 1426 2314 441899256 441898379 0.000000e+00 950.0
9 TraesCS6A01G360000 chr6D 88.609 676 19 24 791 1424 441899959 441899300 0.000000e+00 769.0
10 TraesCS6A01G360000 chr6D 83.969 524 50 14 128 632 441900712 441900204 6.270000e-129 472.0
11 TraesCS6A01G360000 chr6D 88.142 253 16 6 4939 5185 441895434 441895190 6.780000e-74 289.0
12 TraesCS6A01G360000 chr6D 91.411 163 14 0 1 163 441900932 441900770 1.940000e-54 224.0
13 TraesCS6A01G360000 chr6D 91.946 149 9 2 635 781 441900158 441900011 7.020000e-49 206.0
14 TraesCS6A01G360000 chr6D 90.789 152 13 1 5196 5347 354544017 354543867 9.080000e-48 202.0
15 TraesCS6A01G360000 chr6D 86.000 100 14 0 1199 1298 138904815 138904914 2.040000e-19 108.0
16 TraesCS6A01G360000 chr6D 77.982 109 23 1 305 412 470517498 470517606 3.460000e-07 67.6
17 TraesCS6A01G360000 chr3B 95.588 408 14 2 2260 2664 242896005 242895599 0.000000e+00 651.0
18 TraesCS6A01G360000 chr3B 92.157 153 10 1 5195 5347 706775286 706775436 1.170000e-51 215.0
19 TraesCS6A01G360000 chr5A 92.949 156 6 4 5197 5349 19159065 19158912 6.970000e-54 222.0
20 TraesCS6A01G360000 chr5A 92.466 146 11 0 5202 5347 523613862 523613717 5.430000e-50 209.0
21 TraesCS6A01G360000 chr5A 92.466 146 11 0 5202 5347 595903250 595903395 5.430000e-50 209.0
22 TraesCS6A01G360000 chr5A 89.899 99 10 0 370 468 643370986 643370888 1.560000e-25 128.0
23 TraesCS6A01G360000 chr5A 85.827 127 8 5 5062 5186 471466388 471466506 5.620000e-25 126.0
24 TraesCS6A01G360000 chr4A 91.333 150 13 0 5198 5347 717962616 717962765 7.020000e-49 206.0
25 TraesCS6A01G360000 chr4A 89.899 99 10 0 370 468 575005144 575005242 1.560000e-25 128.0
26 TraesCS6A01G360000 chr4A 87.379 103 13 0 366 468 733536195 733536297 9.410000e-23 119.0
27 TraesCS6A01G360000 chr4B 91.781 146 12 0 5202 5347 137740680 137740535 2.530000e-48 204.0
28 TraesCS6A01G360000 chr1A 91.781 146 12 0 5202 5347 18354258 18354403 2.530000e-48 204.0
29 TraesCS6A01G360000 chr2A 82.353 170 23 5 305 467 207335785 207335616 2.010000e-29 141.0
30 TraesCS6A01G360000 chr2A 97.436 39 1 0 307 345 15030309 15030271 3.460000e-07 67.6
31 TraesCS6A01G360000 chr1B 90.909 99 9 0 370 468 22399131 22399033 3.360000e-27 134.0
32 TraesCS6A01G360000 chr1B 88.889 99 11 0 370 468 22607237 22607139 7.280000e-24 122.0
33 TraesCS6A01G360000 chrUn 80.328 183 29 6 293 468 229275570 229275752 1.210000e-26 132.0
34 TraesCS6A01G360000 chrUn 81.287 171 25 6 305 468 299751190 299751020 1.210000e-26 132.0
35 TraesCS6A01G360000 chr5D 81.609 174 18 8 5017 5186 369064879 369065042 1.210000e-26 132.0
36 TraesCS6A01G360000 chr2D 89.899 99 10 0 370 468 344312929 344313027 1.560000e-25 128.0
37 TraesCS6A01G360000 chr7A 87.736 106 13 0 1193 1298 567456848 567456743 2.020000e-24 124.0
38 TraesCS6A01G360000 chr7A 79.630 162 26 6 304 458 639268434 639268595 5.660000e-20 110.0
39 TraesCS6A01G360000 chr7A 83.200 125 16 3 366 487 654068276 654068154 5.660000e-20 110.0
40 TraesCS6A01G360000 chr7A 77.059 170 32 3 305 468 440347277 440347109 2.050000e-14 91.6
41 TraesCS6A01G360000 chr7A 76.879 173 29 7 304 468 610491415 610491584 2.650000e-13 87.9
42 TraesCS6A01G360000 chr1D 85.366 123 14 4 366 487 66266770 66266889 2.020000e-24 124.0
43 TraesCS6A01G360000 chr3D 91.111 90 8 0 1201 1290 363871932 363871843 7.280000e-24 122.0
44 TraesCS6A01G360000 chr3A 91.111 90 8 0 1201 1290 485014668 485014579 7.280000e-24 122.0
45 TraesCS6A01G360000 chr5B 80.108 186 18 12 5010 5186 437562439 437562614 2.620000e-23 121.0
46 TraesCS6A01G360000 chr7D 86.239 109 15 0 1193 1301 500974630 500974522 9.410000e-23 119.0
47 TraesCS6A01G360000 chr7B 86.792 106 14 0 1193 1298 529958354 529958249 9.410000e-23 119.0


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 TraesCS6A01G360000 chr6A 591263398 591268746 5348 True 9878.000000 9878 100.000000 1 5349 1 chr6A.!!$R1 5348
1 TraesCS6A01G360000 chr6B 667895590 667900444 4854 True 1524.500000 4774 92.449250 671 5198 4 chr6B.!!$R2 4527
2 TraesCS6A01G360000 chr6D 441895190 441900932 5742 True 984.857143 3984 89.383571 1 5185 7 chr6D.!!$R2 5184

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
402 512 0.240145 CGACGACTACAAGCACTGGA 59.760 55.0 0.00 0.0 0.00 3.86 F
1790 2112 0.107831 AACAAACAGCCAGTCGCCTA 59.892 50.0 0.00 0.0 38.78 3.93 F
1940 2264 0.737219 GATTGCTCCCATGTGTGCTC 59.263 55.0 3.95 0.0 0.00 4.26 F
2066 2411 0.752054 AGGCCATTTGGTGTTGTGTG 59.248 50.0 5.01 0.0 37.57 3.82 F
3984 4439 0.615331 TGGTCACTTCCAGCTGGATC 59.385 55.0 35.42 21.1 44.98 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2249 0.035630 AGAAGAGCACACATGGGAGC 60.036 55.000 9.62 9.62 0.00 4.70 R
3788 4240 1.371558 GAGTCCAGGACACCACCAC 59.628 63.158 22.31 0.61 34.60 4.16 R
3836 4291 1.207791 CAGGCTTCATAGGGGACACT 58.792 55.000 0.00 0.00 0.00 3.55 R
4041 4496 1.664649 CTTGCCGTGCGAGAAGTCA 60.665 57.895 7.20 0.00 42.27 3.41 R
5205 6030 0.107848 ACTTATTTGCGGACGGAGGG 60.108 55.000 0.00 0.00 0.00 4.30 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
21 22 1.206371 GCCCTATAACACACTCACGGT 59.794 52.381 0.00 0.00 0.00 4.83
31 32 4.056050 ACACACTCACGGTTAACTCATTC 58.944 43.478 5.42 0.00 0.00 2.67
50 51 1.281867 TCTTGGGTGGAATGTGCCTAG 59.718 52.381 0.00 0.00 0.00 3.02
60 61 2.113860 ATGTGCCTAGCATGTTCGTT 57.886 45.000 0.00 0.00 41.91 3.85
73 74 4.212636 GCATGTTCGTTACAGTACCTTGTT 59.787 41.667 0.00 0.00 40.83 2.83
75 76 6.073657 GCATGTTCGTTACAGTACCTTGTTAA 60.074 38.462 0.00 0.00 40.83 2.01
88 89 5.401531 ACCTTGTTAATAGCTCGTTCAGA 57.598 39.130 0.00 0.00 0.00 3.27
91 92 5.869888 CCTTGTTAATAGCTCGTTCAGAAGT 59.130 40.000 0.00 0.00 0.00 3.01
104 105 4.438797 CGTTCAGAAGTGAAAATGCAGTTG 59.561 41.667 0.00 0.00 44.44 3.16
107 108 4.036734 TCAGAAGTGAAAATGCAGTTGACC 59.963 41.667 0.00 0.00 31.86 4.02
109 110 3.996150 AGTGAAAATGCAGTTGACCTG 57.004 42.857 0.00 0.00 44.53 4.00
110 111 3.290710 AGTGAAAATGCAGTTGACCTGT 58.709 40.909 0.00 0.00 43.55 4.00
163 259 5.917541 ACCTTAGAAAATACACACACACG 57.082 39.130 0.00 0.00 0.00 4.49
176 272 3.602062 CACACACACGTTTGAGAAACAAC 59.398 43.478 9.03 0.00 41.44 3.32
186 282 7.486551 CACGTTTGAGAAACAACCATTTTTCTA 59.513 33.333 0.00 0.00 41.21 2.10
195 295 9.459640 GAAACAACCATTTTTCTAACCTTAGAC 57.540 33.333 0.00 0.00 39.36 2.59
199 299 9.410556 CAACCATTTTTCTAACCTTAGACAATG 57.589 33.333 13.62 13.62 39.36 2.82
221 329 3.547468 GCACACACACATTTGAGAAACAC 59.453 43.478 0.00 0.00 0.00 3.32
244 352 0.611618 GTTGGTGGATGGTCATGGCA 60.612 55.000 0.00 0.00 0.00 4.92
262 370 1.614317 GCAGTGGTACTTCAAGCCCAT 60.614 52.381 0.00 0.00 0.00 4.00
274 382 4.305539 TCAAGCCCATCAGAGATCAAAA 57.694 40.909 0.00 0.00 0.00 2.44
280 388 3.067742 CCCATCAGAGATCAAAACCATGC 59.932 47.826 0.00 0.00 0.00 4.06
289 398 1.266718 TCAAAACCATGCTTGACGCTC 59.733 47.619 0.22 0.00 40.11 5.03
295 404 1.400629 CCATGCTTGACGCTCTGTTTG 60.401 52.381 0.22 0.00 40.11 2.93
296 405 1.265095 CATGCTTGACGCTCTGTTTGT 59.735 47.619 0.00 0.00 40.11 2.83
300 409 3.375610 TGCTTGACGCTCTGTTTGTTTTA 59.624 39.130 0.00 0.00 40.11 1.52
301 410 4.142578 TGCTTGACGCTCTGTTTGTTTTAA 60.143 37.500 0.00 0.00 40.11 1.52
302 411 4.796312 GCTTGACGCTCTGTTTGTTTTAAA 59.204 37.500 0.00 0.00 35.14 1.52
304 413 6.183360 GCTTGACGCTCTGTTTGTTTTAAAAA 60.183 34.615 1.31 0.00 35.14 1.94
382 492 5.486735 TTTTGGATTCGTAGACCACCTAA 57.513 39.130 0.00 0.00 34.32 2.69
399 509 2.095364 CCTAACGACGACTACAAGCACT 60.095 50.000 0.00 0.00 0.00 4.40
402 512 0.240145 CGACGACTACAAGCACTGGA 59.760 55.000 0.00 0.00 0.00 3.86
403 513 1.729472 CGACGACTACAAGCACTGGAG 60.729 57.143 0.00 0.00 42.47 3.86
405 515 0.737715 CGACTACAAGCACTGGAGCC 60.738 60.000 0.00 0.00 40.05 4.70
418 528 4.704833 GAGCCAGCCGAAGCCACA 62.705 66.667 0.00 0.00 41.25 4.17
449 559 1.406860 GCCCCTCCCTCATCAGAGTC 61.407 65.000 0.00 0.00 40.40 3.36
461 571 3.055458 TCATCAGAGTCGGGCAAACATTA 60.055 43.478 0.00 0.00 0.00 1.90
467 577 4.876107 AGAGTCGGGCAAACATTATTGTAG 59.124 41.667 0.00 0.00 34.06 2.74
501 611 2.101582 AGTCGTCTATCTGCCAATGACC 59.898 50.000 0.00 0.00 0.00 4.02
513 623 1.399440 CCAATGACCATGAGCGTTCAG 59.601 52.381 8.26 0.00 36.61 3.02
514 624 2.079158 CAATGACCATGAGCGTTCAGT 58.921 47.619 8.26 0.60 36.61 3.41
529 639 1.559814 CAGTCGTCACTGCGTTGTG 59.440 57.895 4.02 4.02 43.77 3.33
530 640 1.591594 AGTCGTCACTGCGTTGTGG 60.592 57.895 9.37 0.00 38.40 4.17
534 644 0.318360 CGTCACTGCGTTGTGGTAGA 60.318 55.000 9.37 0.00 38.40 2.59
535 645 1.137513 GTCACTGCGTTGTGGTAGAC 58.862 55.000 9.37 0.00 38.40 2.59
536 646 0.747852 TCACTGCGTTGTGGTAGACA 59.252 50.000 9.37 0.00 38.40 3.41
537 647 1.343142 TCACTGCGTTGTGGTAGACAT 59.657 47.619 9.37 0.00 38.40 3.06
538 648 2.143122 CACTGCGTTGTGGTAGACATT 58.857 47.619 2.69 0.00 33.40 2.71
539 649 2.548057 CACTGCGTTGTGGTAGACATTT 59.452 45.455 2.69 0.00 33.40 2.32
540 650 3.003275 CACTGCGTTGTGGTAGACATTTT 59.997 43.478 2.69 0.00 33.40 1.82
578 688 5.428457 TGATCTATGAACCAAAGAGGCCTTA 59.572 40.000 6.77 0.00 43.14 2.69
589 699 5.893824 CCAAAGAGGCCTTAGGATTTATGTT 59.106 40.000 6.77 0.00 31.15 2.71
594 704 8.102484 AGAGGCCTTAGGATTTATGTTTCTAA 57.898 34.615 6.77 0.00 0.00 2.10
632 742 6.949352 ACAATCACTCAATTACATCCATCC 57.051 37.500 0.00 0.00 0.00 3.51
633 743 6.425735 ACAATCACTCAATTACATCCATCCA 58.574 36.000 0.00 0.00 0.00 3.41
634 744 7.064866 ACAATCACTCAATTACATCCATCCAT 58.935 34.615 0.00 0.00 0.00 3.41
635 745 7.230108 ACAATCACTCAATTACATCCATCCATC 59.770 37.037 0.00 0.00 0.00 3.51
636 746 5.299949 TCACTCAATTACATCCATCCATCG 58.700 41.667 0.00 0.00 0.00 3.84
637 747 4.067896 ACTCAATTACATCCATCCATCGC 58.932 43.478 0.00 0.00 0.00 4.58
643 753 3.788333 ACATCCATCCATCGCAAAAAG 57.212 42.857 0.00 0.00 0.00 2.27
645 755 3.379372 ACATCCATCCATCGCAAAAAGAG 59.621 43.478 0.00 0.00 0.00 2.85
766 920 1.901085 CCCGTCCAAGAGAAGGAGG 59.099 63.158 0.00 0.00 46.30 4.30
829 1029 2.615869 CACACAACCAAACCAAACCAG 58.384 47.619 0.00 0.00 0.00 4.00
843 1067 0.603975 AACCAGACCGAAAGCAGAGC 60.604 55.000 0.00 0.00 0.00 4.09
897 1121 4.626081 CATAAGCGGAGGGGCGGG 62.626 72.222 0.00 0.00 38.18 6.13
937 1161 2.461110 CGTTGCGGAATTCGGAGGG 61.461 63.158 16.50 0.00 41.02 4.30
938 1162 2.437716 TTGCGGAATTCGGAGGGC 60.438 61.111 16.50 7.07 41.02 5.19
939 1163 3.987954 TTGCGGAATTCGGAGGGCC 62.988 63.158 16.50 0.00 41.02 5.80
943 1167 3.416880 GAATTCGGAGGGCCCCCA 61.417 66.667 21.43 4.89 38.92 4.96
1303 1548 0.813184 CAACATCATGTGGTCAGCCC 59.187 55.000 0.00 0.00 0.00 5.19
1304 1549 0.677731 AACATCATGTGGTCAGCCCG 60.678 55.000 0.00 0.00 35.15 6.13
1325 1583 4.825679 CCACCCCTCCCTCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
1326 1584 3.700350 CACCCCTCCCTCTCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
1331 1589 4.548513 CTCCCTCTCCCCTCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
1424 1689 5.052481 CGATATTCAGGTTCATCTTCTGCA 58.948 41.667 0.00 0.00 0.00 4.41
1482 1790 6.909357 CGTATTCCTCGTAATATTCCGTATCC 59.091 42.308 0.11 0.00 0.00 2.59
1601 1910 9.744468 GAATAAATAATGAATTAGGTGGCGTTT 57.256 29.630 0.00 0.00 0.00 3.60
1631 1940 0.108774 GATTGACCCGGGGAAGATCC 59.891 60.000 27.92 3.48 35.23 3.36
1633 1942 4.237207 GACCCGGGGAAGATCCGC 62.237 72.222 27.92 3.52 45.60 5.54
1635 1944 4.241555 CCCGGGGAAGATCCGCTG 62.242 72.222 14.71 5.13 46.22 5.18
1636 1945 4.241555 CCGGGGAAGATCCGCTGG 62.242 72.222 11.12 9.88 46.22 4.85
1637 1946 3.154473 CGGGGAAGATCCGCTGGA 61.154 66.667 11.12 0.00 46.22 3.86
1638 1947 2.511452 CGGGGAAGATCCGCTGGAT 61.511 63.158 9.42 9.42 46.22 3.41
1639 1948 1.185618 CGGGGAAGATCCGCTGGATA 61.186 60.000 9.60 0.00 46.22 2.59
1640 1949 1.056660 GGGGAAGATCCGCTGGATAA 58.943 55.000 9.60 0.00 43.27 1.75
1641 1950 1.270893 GGGGAAGATCCGCTGGATAAC 60.271 57.143 9.60 5.33 43.27 1.89
1643 1952 2.289133 GGGAAGATCCGCTGGATAACTC 60.289 54.545 9.60 7.08 43.27 3.01
1676 1998 9.166173 GAATAGCCTGCTTCCATTTTTATTTTT 57.834 29.630 0.00 0.00 0.00 1.94
1790 2112 0.107831 AACAAACAGCCAGTCGCCTA 59.892 50.000 0.00 0.00 38.78 3.93
1800 2122 2.419574 GCCAGTCGCCTACCTTTGATTA 60.420 50.000 0.00 0.00 0.00 1.75
1801 2123 3.744530 GCCAGTCGCCTACCTTTGATTAT 60.745 47.826 0.00 0.00 0.00 1.28
1807 2129 6.015603 AGTCGCCTACCTTTGATTATAGTACC 60.016 42.308 0.00 0.00 0.00 3.34
1813 2135 7.509659 CCTACCTTTGATTATAGTACCAGGTCT 59.490 40.741 0.00 0.00 35.06 3.85
1815 2137 6.901300 ACCTTTGATTATAGTACCAGGTCTGA 59.099 38.462 0.00 0.00 0.00 3.27
1914 2238 1.838715 AGGTTCTGCTCTGATGCTGAT 59.161 47.619 8.58 0.00 39.84 2.90
1916 2240 1.331138 GTTCTGCTCTGATGCTGATGC 59.669 52.381 8.58 0.00 39.84 3.91
1918 2242 2.037144 TCTGCTCTGATGCTGATGCTA 58.963 47.619 0.00 0.00 40.48 3.49
1919 2243 2.433239 TCTGCTCTGATGCTGATGCTAA 59.567 45.455 0.00 0.00 40.48 3.09
1921 2245 1.526041 GCTCTGATGCTGATGCTAACG 59.474 52.381 0.00 0.00 40.48 3.18
1922 2246 2.800985 GCTCTGATGCTGATGCTAACGA 60.801 50.000 0.00 0.00 40.48 3.85
1923 2247 3.651206 CTCTGATGCTGATGCTAACGAT 58.349 45.455 0.00 0.00 40.48 3.73
1925 2249 3.805971 TCTGATGCTGATGCTAACGATTG 59.194 43.478 0.00 0.00 40.48 2.67
1926 2250 2.288729 TGATGCTGATGCTAACGATTGC 59.711 45.455 0.00 0.00 40.48 3.56
1927 2251 2.028420 TGCTGATGCTAACGATTGCT 57.972 45.000 0.54 0.00 40.48 3.91
1929 2253 1.262683 GCTGATGCTAACGATTGCTCC 59.737 52.381 0.54 0.00 36.03 4.70
1930 2254 1.869767 CTGATGCTAACGATTGCTCCC 59.130 52.381 0.54 0.00 0.00 4.30
1931 2255 1.209261 TGATGCTAACGATTGCTCCCA 59.791 47.619 0.54 0.00 0.00 4.37
1932 2256 2.158769 TGATGCTAACGATTGCTCCCAT 60.159 45.455 0.54 0.00 0.00 4.00
1934 2258 1.065491 TGCTAACGATTGCTCCCATGT 60.065 47.619 0.54 0.00 0.00 3.21
1940 2264 0.737219 GATTGCTCCCATGTGTGCTC 59.263 55.000 3.95 0.00 0.00 4.26
1949 2273 1.609841 CCATGTGTGCTCTTCTGCTGA 60.610 52.381 0.00 0.00 0.00 4.26
1990 2335 2.501723 AGTCAGTTAGTGGCCATCGATT 59.498 45.455 9.72 0.00 0.00 3.34
1991 2336 2.866762 GTCAGTTAGTGGCCATCGATTC 59.133 50.000 9.72 0.00 0.00 2.52
1992 2337 2.499693 TCAGTTAGTGGCCATCGATTCA 59.500 45.455 9.72 0.00 0.00 2.57
2060 2405 2.028203 GCATTGTAAGGCCATTTGGTGT 60.028 45.455 5.01 0.00 37.57 4.16
2066 2411 0.752054 AGGCCATTTGGTGTTGTGTG 59.248 50.000 5.01 0.00 37.57 3.82
2075 2423 5.776173 TTTGGTGTTGTGTGTTATAAGGG 57.224 39.130 0.00 0.00 0.00 3.95
2085 2433 7.591421 TGTGTGTTATAAGGGATCGAAGATA 57.409 36.000 0.00 0.00 45.12 1.98
2104 2452 5.782047 AGATATGAGAGTGCTGAGTATTGC 58.218 41.667 0.00 0.00 0.00 3.56
2112 2463 4.611943 AGTGCTGAGTATTGCAGTATACG 58.388 43.478 0.00 0.00 40.57 3.06
2113 2464 3.736252 GTGCTGAGTATTGCAGTATACGG 59.264 47.826 0.00 0.00 40.06 4.02
2134 2485 0.820871 TGTTTCCTTGTGGTGGTTGC 59.179 50.000 0.00 0.00 34.23 4.17
2173 2527 1.830408 CGTTCCCTTTGGTGGGCAA 60.830 57.895 0.00 0.00 46.67 4.52
2214 2569 6.767524 TTTGCGTTTTCTATGGGATATTGT 57.232 33.333 0.00 0.00 0.00 2.71
2217 2572 5.295787 TGCGTTTTCTATGGGATATTGTCAC 59.704 40.000 0.00 0.00 0.00 3.67
2246 2601 3.648339 TTTGTGAGATTTCTTGCCTGC 57.352 42.857 0.00 0.00 0.00 4.85
2475 2913 9.877178 TCTACAGGAAAAGTAAGAATCTGAATC 57.123 33.333 0.00 0.00 0.00 2.52
2504 2942 5.684626 AGTAATTATAAGAACTCGAACGCGG 59.315 40.000 12.47 0.00 38.28 6.46
2595 3033 7.541162 TCTCAAATTTTGTGATCATGATGTCC 58.459 34.615 14.30 0.00 0.00 4.02
2651 3092 7.701539 TTACTGACAACTATTGGATTGCATT 57.298 32.000 0.00 0.00 34.12 3.56
2745 3186 9.025041 AGCAAATAATAATTATTAGCCACTCCC 57.975 33.333 19.81 6.35 34.88 4.30
2934 3375 0.755327 GACCAACAGCCCCAACACTT 60.755 55.000 0.00 0.00 0.00 3.16
2978 3419 2.397044 ACCTTCCTTTGGCCAATCAA 57.603 45.000 21.26 11.25 0.00 2.57
3023 3466 6.430925 GCTTGTTCCCATATGCAATACATAGA 59.569 38.462 0.00 0.00 44.40 1.98
3024 3467 7.121759 GCTTGTTCCCATATGCAATACATAGAT 59.878 37.037 0.00 0.00 44.40 1.98
3062 3505 4.985538 ACACTTACATGGGAGACAATTGT 58.014 39.130 11.78 11.78 0.00 2.71
3063 3506 5.385198 ACACTTACATGGGAGACAATTGTT 58.615 37.500 13.36 2.74 0.00 2.83
3070 3513 7.630242 ACATGGGAGACAATTGTTGTTATAG 57.370 36.000 13.36 4.44 45.52 1.31
3112 3555 6.825213 AGACATGTTCATGTGTATGCACTTAT 59.175 34.615 20.83 0.00 45.44 1.73
3113 3556 7.986889 AGACATGTTCATGTGTATGCACTTATA 59.013 33.333 20.83 0.00 45.44 0.98
3114 3557 8.681486 ACATGTTCATGTGTATGCACTTATAT 57.319 30.769 16.19 0.00 45.44 0.86
3115 3558 9.777297 ACATGTTCATGTGTATGCACTTATATA 57.223 29.630 16.19 0.00 45.44 0.86
3247 3693 4.128643 ACTACGACATAGAGGCTGTCTAC 58.871 47.826 0.00 0.00 40.76 2.59
3445 3891 7.942341 ACACTTTGGTTTGATATCTTCAAGGTA 59.058 33.333 3.98 0.00 44.90 3.08
3446 3892 8.792633 CACTTTGGTTTGATATCTTCAAGGTAA 58.207 33.333 3.98 0.00 44.90 2.85
3447 3893 9.014297 ACTTTGGTTTGATATCTTCAAGGTAAG 57.986 33.333 3.98 1.91 44.90 2.34
3448 3894 8.934023 TTTGGTTTGATATCTTCAAGGTAAGT 57.066 30.769 3.98 0.00 44.90 2.24
3449 3895 8.561738 TTGGTTTGATATCTTCAAGGTAAGTC 57.438 34.615 3.98 0.00 44.90 3.01
3450 3896 7.918076 TGGTTTGATATCTTCAAGGTAAGTCT 58.082 34.615 3.98 0.00 44.90 3.24
3451 3897 7.824289 TGGTTTGATATCTTCAAGGTAAGTCTG 59.176 37.037 3.98 0.00 44.90 3.51
3452 3898 7.281100 GGTTTGATATCTTCAAGGTAAGTCTGG 59.719 40.741 3.98 0.00 44.90 3.86
3533 3979 1.621317 TCATCACCTTACTGCCAACGA 59.379 47.619 0.00 0.00 0.00 3.85
3700 4146 6.325596 GGAACTGCTATGATTTTGTTCCTTC 58.674 40.000 13.45 0.00 45.67 3.46
3788 4240 1.110442 TTGCCACCACAAGAACTTGG 58.890 50.000 17.05 5.44 44.45 3.61
3836 4291 5.465390 GCATATGGACAGTCTGCGTTTATTA 59.535 40.000 4.56 0.00 0.00 0.98
3982 4437 1.951209 TATGGTCACTTCCAGCTGGA 58.049 50.000 32.00 32.00 43.73 3.86
3984 4439 0.615331 TGGTCACTTCCAGCTGGATC 59.385 55.000 35.42 21.10 44.98 3.36
3989 4444 1.471684 CACTTCCAGCTGGATCTTTGC 59.528 52.381 35.42 0.00 44.98 3.68
4001 4456 3.265221 TGGATCTTTGCTTGATCTGGACT 59.735 43.478 11.69 0.00 39.95 3.85
4016 4471 4.401022 TCTGGACTTTGCTGAATCACATT 58.599 39.130 0.00 0.00 0.00 2.71
4110 4565 2.113139 CCGCTGTGGGTCAAAGGT 59.887 61.111 0.00 0.00 0.00 3.50
4113 4568 1.152756 GCTGTGGGTCAAAGGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
4286 4741 5.163269 TGAGATTTGGGAAGTGATCGATGAT 60.163 40.000 0.54 0.00 0.00 2.45
4298 4757 3.389002 TGATCGATGATCCTTGACCATGT 59.611 43.478 0.54 0.00 38.20 3.21
4301 4760 3.389002 TCGATGATCCTTGACCATGTCAT 59.611 43.478 0.00 0.00 42.40 3.06
4349 4808 5.391416 CGCGTATAGACACTGATGATCTGAT 60.391 44.000 6.32 0.00 0.00 2.90
4415 4881 0.108851 TCCGATGACATGACACCGTG 60.109 55.000 10.97 3.08 35.46 4.94
4609 5088 1.747444 TGGGGCTCTCTCCTTTTTCT 58.253 50.000 0.00 0.00 0.00 2.52
4658 5138 2.929641 TGTGCAAAGAAGTGTCCATCA 58.070 42.857 0.00 0.00 0.00 3.07
4735 5218 6.712095 TGTCTGCTTCATAGTTTCAGTTTCAT 59.288 34.615 0.00 0.00 0.00 2.57
4737 5220 7.748241 GTCTGCTTCATAGTTTCAGTTTCATTC 59.252 37.037 0.00 0.00 0.00 2.67
4790 5279 1.130054 AGCAGAGCCAAACAGGAGGA 61.130 55.000 0.00 0.00 41.22 3.71
4791 5280 0.676151 GCAGAGCCAAACAGGAGGAG 60.676 60.000 0.00 0.00 41.22 3.69
4793 5282 1.377856 GAGCCAAACAGGAGGAGGC 60.378 63.158 0.00 0.00 45.54 4.70
4794 5283 2.436109 GCCAAACAGGAGGAGGCA 59.564 61.111 0.00 0.00 44.59 4.75
4796 5285 1.001641 CCAAACAGGAGGAGGCAGG 60.002 63.158 0.00 0.00 41.22 4.85
4797 5286 1.001641 CAAACAGGAGGAGGCAGGG 60.002 63.158 0.00 0.00 0.00 4.45
4798 5287 2.234296 AAACAGGAGGAGGCAGGGG 61.234 63.158 0.00 0.00 0.00 4.79
4801 5290 4.361429 AGGAGGAGGCAGGGGCTT 62.361 66.667 0.00 0.00 38.98 4.35
4802 5291 2.366972 GGAGGAGGCAGGGGCTTA 60.367 66.667 0.00 0.00 38.98 3.09
4803 5292 2.001269 GGAGGAGGCAGGGGCTTAA 61.001 63.158 0.00 0.00 38.98 1.85
4823 5312 6.015688 GCTTAAACTTAACCTTAACCTGCCTT 60.016 38.462 0.00 0.00 0.00 4.35
4824 5313 7.514784 TTAAACTTAACCTTAACCTGCCTTC 57.485 36.000 0.00 0.00 0.00 3.46
4825 5314 4.717279 ACTTAACCTTAACCTGCCTTCA 57.283 40.909 0.00 0.00 0.00 3.02
4826 5315 4.395625 ACTTAACCTTAACCTGCCTTCAC 58.604 43.478 0.00 0.00 0.00 3.18
4827 5316 1.892209 AACCTTAACCTGCCTTCACG 58.108 50.000 0.00 0.00 0.00 4.35
4828 5317 1.053424 ACCTTAACCTGCCTTCACGA 58.947 50.000 0.00 0.00 0.00 4.35
4829 5318 1.270678 ACCTTAACCTGCCTTCACGAC 60.271 52.381 0.00 0.00 0.00 4.34
4830 5319 1.439679 CTTAACCTGCCTTCACGACC 58.560 55.000 0.00 0.00 0.00 4.79
4831 5320 0.759959 TTAACCTGCCTTCACGACCA 59.240 50.000 0.00 0.00 0.00 4.02
4832 5321 0.759959 TAACCTGCCTTCACGACCAA 59.240 50.000 0.00 0.00 0.00 3.67
4833 5322 0.110486 AACCTGCCTTCACGACCAAT 59.890 50.000 0.00 0.00 0.00 3.16
4834 5323 0.110486 ACCTGCCTTCACGACCAATT 59.890 50.000 0.00 0.00 0.00 2.32
4835 5324 0.804989 CCTGCCTTCACGACCAATTC 59.195 55.000 0.00 0.00 0.00 2.17
4836 5325 1.611673 CCTGCCTTCACGACCAATTCT 60.612 52.381 0.00 0.00 0.00 2.40
4837 5326 2.154462 CTGCCTTCACGACCAATTCTT 58.846 47.619 0.00 0.00 0.00 2.52
4838 5327 2.554032 CTGCCTTCACGACCAATTCTTT 59.446 45.455 0.00 0.00 0.00 2.52
4839 5328 3.745799 TGCCTTCACGACCAATTCTTTA 58.254 40.909 0.00 0.00 0.00 1.85
4840 5329 4.331968 TGCCTTCACGACCAATTCTTTAT 58.668 39.130 0.00 0.00 0.00 1.40
4841 5330 4.764823 TGCCTTCACGACCAATTCTTTATT 59.235 37.500 0.00 0.00 0.00 1.40
4842 5331 5.242838 TGCCTTCACGACCAATTCTTTATTT 59.757 36.000 0.00 0.00 0.00 1.40
4843 5332 6.156519 GCCTTCACGACCAATTCTTTATTTT 58.843 36.000 0.00 0.00 0.00 1.82
4844 5333 6.645003 GCCTTCACGACCAATTCTTTATTTTT 59.355 34.615 0.00 0.00 0.00 1.94
4890 5379 4.537135 TCTTGGTCTAGGACAATGTGAC 57.463 45.455 0.00 0.00 33.68 3.67
4934 5453 5.239306 CACATGAGAAGCTTGGTCAGTAAAA 59.761 40.000 2.10 0.00 0.00 1.52
4945 5764 6.417930 GCTTGGTCAGTAAAACAAATGTCTTC 59.582 38.462 0.00 0.00 0.00 2.87
5085 5904 0.899019 GGAGGTCCCTGAGAGTTGTC 59.101 60.000 0.00 0.00 0.00 3.18
5147 5972 3.129638 TGGAGAAAAACAGGTCAAAACGG 59.870 43.478 0.00 0.00 0.00 4.44
5150 5975 2.863401 AAAACAGGTCAAAACGGAGC 57.137 45.000 0.00 0.00 35.57 4.70
5167 5992 3.678252 CGGAGCACATCAATCTGAACTCT 60.678 47.826 0.00 0.00 0.00 3.24
5186 6011 4.757149 ACTCTGTATTGTTCAGAAGCAACC 59.243 41.667 0.00 0.00 40.68 3.77
5191 6016 8.264347 TCTGTATTGTTCAGAAGCAACCATATA 58.736 33.333 0.00 0.00 38.71 0.86
5198 6023 8.892723 TGTTCAGAAGCAACCATATATTGTAAG 58.107 33.333 0.00 0.00 0.00 2.34
5199 6024 7.496529 TCAGAAGCAACCATATATTGTAAGC 57.503 36.000 6.31 6.31 0.00 3.09
5200 6025 6.486657 TCAGAAGCAACCATATATTGTAAGCC 59.513 38.462 9.38 0.00 0.00 4.35
5201 6026 6.488006 CAGAAGCAACCATATATTGTAAGCCT 59.512 38.462 9.38 0.20 0.00 4.58
5202 6027 7.661437 CAGAAGCAACCATATATTGTAAGCCTA 59.339 37.037 9.38 0.00 0.00 3.93
5203 6028 7.661847 AGAAGCAACCATATATTGTAAGCCTAC 59.338 37.037 9.38 0.00 0.00 3.18
5204 6029 7.079451 AGCAACCATATATTGTAAGCCTACT 57.921 36.000 9.38 0.00 0.00 2.57
5205 6030 7.162082 AGCAACCATATATTGTAAGCCTACTC 58.838 38.462 9.38 0.00 0.00 2.59
5206 6031 6.371825 GCAACCATATATTGTAAGCCTACTCC 59.628 42.308 0.00 0.00 0.00 3.85
5207 6032 6.622427 ACCATATATTGTAAGCCTACTCCC 57.378 41.667 0.00 0.00 0.00 4.30
5208 6033 6.331846 ACCATATATTGTAAGCCTACTCCCT 58.668 40.000 0.00 0.00 0.00 4.20
5209 6034 6.440965 ACCATATATTGTAAGCCTACTCCCTC 59.559 42.308 0.00 0.00 0.00 4.30
5210 6035 6.127026 CCATATATTGTAAGCCTACTCCCTCC 60.127 46.154 0.00 0.00 0.00 4.30
5211 6036 1.481871 TTGTAAGCCTACTCCCTCCG 58.518 55.000 0.00 0.00 0.00 4.63
5212 6037 0.333993 TGTAAGCCTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
5213 6038 1.031235 GTAAGCCTACTCCCTCCGTC 58.969 60.000 0.00 0.00 0.00 4.79
5214 6039 0.106318 TAAGCCTACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
5215 6040 3.217743 GCCTACTCCCTCCGTCCG 61.218 72.222 0.00 0.00 0.00 4.79
5216 6041 3.217743 CCTACTCCCTCCGTCCGC 61.218 72.222 0.00 0.00 0.00 5.54
5217 6042 2.439701 CTACTCCCTCCGTCCGCA 60.440 66.667 0.00 0.00 0.00 5.69
5218 6043 2.036098 TACTCCCTCCGTCCGCAA 59.964 61.111 0.00 0.00 0.00 4.85
5219 6044 1.601419 CTACTCCCTCCGTCCGCAAA 61.601 60.000 0.00 0.00 0.00 3.68
5220 6045 0.974010 TACTCCCTCCGTCCGCAAAT 60.974 55.000 0.00 0.00 0.00 2.32
5221 6046 0.974010 ACTCCCTCCGTCCGCAAATA 60.974 55.000 0.00 0.00 0.00 1.40
5222 6047 0.177141 CTCCCTCCGTCCGCAAATAA 59.823 55.000 0.00 0.00 0.00 1.40
5223 6048 0.177141 TCCCTCCGTCCGCAAATAAG 59.823 55.000 0.00 0.00 0.00 1.73
5224 6049 0.107848 CCCTCCGTCCGCAAATAAGT 60.108 55.000 0.00 0.00 0.00 2.24
5225 6050 1.006832 CCTCCGTCCGCAAATAAGTG 58.993 55.000 0.00 0.00 0.00 3.16
5226 6051 1.674817 CCTCCGTCCGCAAATAAGTGT 60.675 52.381 0.00 0.00 0.00 3.55
5227 6052 2.417651 CCTCCGTCCGCAAATAAGTGTA 60.418 50.000 0.00 0.00 0.00 2.90
5228 6053 2.601763 CTCCGTCCGCAAATAAGTGTAC 59.398 50.000 0.00 0.00 0.00 2.90
5229 6054 2.231964 TCCGTCCGCAAATAAGTGTACT 59.768 45.455 0.00 0.00 0.00 2.73
5230 6055 2.997986 CCGTCCGCAAATAAGTGTACTT 59.002 45.455 2.51 2.51 39.85 2.24
5231 6056 3.061697 CCGTCCGCAAATAAGTGTACTTC 59.938 47.826 0.00 0.00 37.40 3.01
5232 6057 3.924686 CGTCCGCAAATAAGTGTACTTCT 59.075 43.478 0.00 0.00 37.40 2.85
5233 6058 5.097529 CGTCCGCAAATAAGTGTACTTCTA 58.902 41.667 0.00 0.00 37.40 2.10
5234 6059 5.574055 CGTCCGCAAATAAGTGTACTTCTAA 59.426 40.000 0.00 0.00 37.40 2.10
5235 6060 6.453396 CGTCCGCAAATAAGTGTACTTCTAAC 60.453 42.308 0.00 0.00 37.40 2.34
5236 6061 6.589139 GTCCGCAAATAAGTGTACTTCTAACT 59.411 38.462 0.00 0.00 37.40 2.24
5237 6062 7.117379 GTCCGCAAATAAGTGTACTTCTAACTT 59.883 37.037 0.00 0.00 37.40 2.66
5238 6063 7.330208 TCCGCAAATAAGTGTACTTCTAACTTC 59.670 37.037 0.00 0.00 37.40 3.01
5239 6064 7.331193 CCGCAAATAAGTGTACTTCTAACTTCT 59.669 37.037 0.00 0.00 37.40 2.85
5240 6065 9.350357 CGCAAATAAGTGTACTTCTAACTTCTA 57.650 33.333 0.00 0.00 37.40 2.10
5348 6173 8.904099 AAGTATAATTCAAAACGGATCTAGGG 57.096 34.615 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.408634 CACCCAAGAATGAGTTAACCGT 58.591 45.455 0.88 0.00 0.00 4.83
31 32 1.755179 CTAGGCACATTCCACCCAAG 58.245 55.000 0.00 0.00 0.00 3.61
50 51 3.744426 ACAAGGTACTGTAACGAACATGC 59.256 43.478 0.00 0.00 40.86 4.06
60 61 6.764308 ACGAGCTATTAACAAGGTACTGTA 57.236 37.500 0.00 0.00 40.86 2.74
73 74 7.413000 GCATTTTCACTTCTGAACGAGCTATTA 60.413 37.037 0.00 0.00 36.06 0.98
75 76 5.163814 GCATTTTCACTTCTGAACGAGCTAT 60.164 40.000 0.00 0.00 36.06 2.97
88 89 4.311816 CAGGTCAACTGCATTTTCACTT 57.688 40.909 0.00 0.00 40.97 3.16
107 108 6.884280 AGAAGAAAGGAAACAACCATACAG 57.116 37.500 0.00 0.00 0.00 2.74
109 110 7.511959 AGAAGAAGAAAGGAAACAACCATAC 57.488 36.000 0.00 0.00 0.00 2.39
110 111 8.533569 AAAGAAGAAGAAAGGAAACAACCATA 57.466 30.769 0.00 0.00 0.00 2.74
163 259 8.600625 GGTTAGAAAAATGGTTGTTTCTCAAAC 58.399 33.333 2.12 3.46 41.89 2.93
176 272 7.542130 GTGCATTGTCTAAGGTTAGAAAAATGG 59.458 37.037 22.78 12.38 39.67 3.16
186 282 3.315191 GTGTGTGTGCATTGTCTAAGGTT 59.685 43.478 0.00 0.00 0.00 3.50
195 295 3.967401 TCTCAAATGTGTGTGTGCATTG 58.033 40.909 0.00 0.00 35.72 2.82
199 299 3.547468 GTGTTTCTCAAATGTGTGTGTGC 59.453 43.478 0.00 0.00 0.00 4.57
221 329 0.332632 ATGACCATCCACCAACTGGG 59.667 55.000 0.00 0.00 41.06 4.45
238 346 1.470098 GCTTGAAGTACCACTGCCATG 59.530 52.381 0.00 0.00 0.00 3.66
240 348 0.250727 GGCTTGAAGTACCACTGCCA 60.251 55.000 8.87 0.00 36.53 4.92
244 352 1.985159 TGATGGGCTTGAAGTACCACT 59.015 47.619 11.82 3.77 35.52 4.00
262 370 4.456911 GTCAAGCATGGTTTTGATCTCTGA 59.543 41.667 7.57 0.00 35.91 3.27
280 388 6.862944 TTTTAAAACAAACAGAGCGTCAAG 57.137 33.333 0.00 0.00 0.00 3.02
308 417 9.770503 CTTGACAGTTGATGAATAGATCAAAAG 57.229 33.333 0.00 0.00 42.58 2.27
309 418 9.506018 TCTTGACAGTTGATGAATAGATCAAAA 57.494 29.630 0.00 0.00 42.58 2.44
310 419 9.676861 ATCTTGACAGTTGATGAATAGATCAAA 57.323 29.630 0.00 0.00 42.58 2.69
364 474 2.684881 TCGTTAGGTGGTCTACGAATCC 59.315 50.000 0.00 0.00 32.69 3.01
366 476 2.096496 CGTCGTTAGGTGGTCTACGAAT 59.904 50.000 0.00 0.00 35.22 3.34
373 483 1.806542 TGTAGTCGTCGTTAGGTGGTC 59.193 52.381 0.00 0.00 0.00 4.02
382 492 0.039437 CCAGTGCTTGTAGTCGTCGT 60.039 55.000 0.00 0.00 0.00 4.34
414 524 4.101790 GCAATGACGGCGGTGTGG 62.102 66.667 13.24 0.00 0.00 4.17
438 548 1.338105 TGTTTGCCCGACTCTGATGAG 60.338 52.381 0.00 0.00 45.43 2.90
449 559 3.078594 GGCTACAATAATGTTTGCCCG 57.921 47.619 13.53 0.00 44.86 6.13
461 571 2.039879 ACTTCCCGAACAAGGCTACAAT 59.960 45.455 0.00 0.00 0.00 2.71
467 577 1.289800 GACGACTTCCCGAACAAGGC 61.290 60.000 0.00 0.00 0.00 4.35
501 611 0.710567 GTGACGACTGAACGCTCATG 59.289 55.000 0.00 0.00 36.70 3.07
513 623 0.595567 TACCACAACGCAGTGACGAC 60.596 55.000 12.77 0.00 45.00 4.34
514 624 0.318360 CTACCACAACGCAGTGACGA 60.318 55.000 12.77 0.00 45.00 4.20
540 650 9.396022 GGTTCATAGATCAAATTGTAGGAGAAA 57.604 33.333 0.00 0.00 0.00 2.52
543 653 8.737168 TTGGTTCATAGATCAAATTGTAGGAG 57.263 34.615 0.00 0.00 0.00 3.69
545 655 9.177608 TCTTTGGTTCATAGATCAAATTGTAGG 57.822 33.333 0.00 0.00 0.00 3.18
547 657 9.177608 CCTCTTTGGTTCATAGATCAAATTGTA 57.822 33.333 0.00 0.00 0.00 2.41
548 658 7.363268 GCCTCTTTGGTTCATAGATCAAATTGT 60.363 37.037 0.00 0.00 38.35 2.71
549 659 6.976925 GCCTCTTTGGTTCATAGATCAAATTG 59.023 38.462 0.00 0.00 38.35 2.32
550 660 6.097412 GGCCTCTTTGGTTCATAGATCAAATT 59.903 38.462 0.00 0.00 38.35 1.82
551 661 5.595952 GGCCTCTTTGGTTCATAGATCAAAT 59.404 40.000 0.00 0.00 38.35 2.32
552 662 4.949856 GGCCTCTTTGGTTCATAGATCAAA 59.050 41.667 0.00 0.00 38.35 2.69
553 663 4.228210 AGGCCTCTTTGGTTCATAGATCAA 59.772 41.667 0.00 0.00 38.35 2.57
554 664 3.782523 AGGCCTCTTTGGTTCATAGATCA 59.217 43.478 0.00 0.00 38.35 2.92
555 665 4.429854 AGGCCTCTTTGGTTCATAGATC 57.570 45.455 0.00 0.00 38.35 2.75
556 666 4.870021 AAGGCCTCTTTGGTTCATAGAT 57.130 40.909 5.23 0.00 38.35 1.98
594 704 9.743057 TTGAGTGATTGTATTTCGTTGAAATTT 57.257 25.926 9.77 0.00 41.64 1.82
599 709 8.994170 TGTAATTGAGTGATTGTATTTCGTTGA 58.006 29.630 0.00 0.00 0.00 3.18
616 726 4.067192 TGCGATGGATGGATGTAATTGAG 58.933 43.478 0.00 0.00 0.00 3.02
632 742 5.355350 AGAAATACCCTCTCTTTTTGCGATG 59.645 40.000 0.00 0.00 0.00 3.84
633 743 5.501156 AGAAATACCCTCTCTTTTTGCGAT 58.499 37.500 0.00 0.00 0.00 4.58
634 744 4.906618 AGAAATACCCTCTCTTTTTGCGA 58.093 39.130 0.00 0.00 0.00 5.10
635 745 5.220681 GCTAGAAATACCCTCTCTTTTTGCG 60.221 44.000 0.00 0.00 0.00 4.85
636 746 5.648092 TGCTAGAAATACCCTCTCTTTTTGC 59.352 40.000 0.00 0.00 0.00 3.68
637 747 7.872113 ATGCTAGAAATACCCTCTCTTTTTG 57.128 36.000 0.00 0.00 0.00 2.44
643 753 6.919721 CAGAGTATGCTAGAAATACCCTCTC 58.080 44.000 10.72 4.61 31.98 3.20
668 820 1.004185 CTGTACGGGAGTCGACGTATG 60.004 57.143 17.83 4.67 45.75 2.39
694 846 3.547746 AGACAACGAGAGATCCTACTCC 58.452 50.000 0.00 0.00 37.60 3.85
766 920 0.534203 TGGCAAGTCCACTTCCGTTC 60.534 55.000 0.00 0.00 40.72 3.95
781 935 2.142761 CGGAGGAGGATGGATGGCA 61.143 63.158 0.00 0.00 0.00 4.92
829 1029 1.807573 CCTCGCTCTGCTTTCGGTC 60.808 63.158 0.00 0.00 0.00 4.79
937 1161 2.195956 GCTATTCCTGGTGGGGGC 59.804 66.667 0.00 0.00 35.33 5.80
938 1162 1.999634 CTGGCTATTCCTGGTGGGGG 62.000 65.000 0.00 0.00 35.26 5.40
939 1163 1.533711 CTGGCTATTCCTGGTGGGG 59.466 63.158 0.00 0.00 35.26 4.96
940 1164 1.152881 GCTGGCTATTCCTGGTGGG 60.153 63.158 0.00 0.00 34.64 4.61
943 1167 1.918253 CTGGCTGGCTATTCCTGGT 59.082 57.895 2.00 0.00 34.64 4.00
1308 1553 4.825679 GGGGAGAGGGAGGGGTGG 62.826 77.778 0.00 0.00 0.00 4.61
1310 1555 3.369388 GAGGGGAGAGGGAGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
1482 1790 0.875059 GGAGCCAGAAAACAACTCCG 59.125 55.000 0.00 0.00 37.75 4.63
1623 1932 2.630580 AGAGTTATCCAGCGGATCTTCC 59.369 50.000 12.43 3.67 42.11 3.46
1631 1940 1.406898 TCAGCAGAGAGTTATCCAGCG 59.593 52.381 0.00 0.00 0.00 5.18
1679 2001 7.069331 ACCCAAATTGTGTCTGAATCAAACTTA 59.931 33.333 0.00 0.00 0.00 2.24
1790 2112 6.901300 TCAGACCTGGTACTATAATCAAAGGT 59.099 38.462 0.00 0.00 39.46 3.50
1800 2122 8.849543 TTAATTAACCTCAGACCTGGTACTAT 57.150 34.615 0.00 0.00 35.17 2.12
1801 2123 8.849543 ATTAATTAACCTCAGACCTGGTACTA 57.150 34.615 0.00 0.00 35.17 1.82
1807 2129 5.057149 CCGGATTAATTAACCTCAGACCTG 58.943 45.833 0.00 0.00 0.00 4.00
1813 2135 4.300345 TCTCCCCGGATTAATTAACCTCA 58.700 43.478 0.73 0.00 0.00 3.86
1815 2137 4.973211 TCTTCTCCCCGGATTAATTAACCT 59.027 41.667 0.73 0.00 0.00 3.50
1914 2238 1.065491 ACATGGGAGCAATCGTTAGCA 60.065 47.619 0.00 0.00 0.00 3.49
1916 2240 2.352651 CACACATGGGAGCAATCGTTAG 59.647 50.000 0.00 0.00 0.00 2.34
1918 2242 1.167851 CACACATGGGAGCAATCGTT 58.832 50.000 0.00 0.00 0.00 3.85
1919 2243 1.308069 GCACACATGGGAGCAATCGT 61.308 55.000 12.88 0.00 0.00 3.73
1921 2245 0.737219 GAGCACACATGGGAGCAATC 59.263 55.000 19.83 5.53 0.00 2.67
1922 2246 0.330604 AGAGCACACATGGGAGCAAT 59.669 50.000 19.83 4.35 0.00 3.56
1923 2247 0.111061 AAGAGCACACATGGGAGCAA 59.889 50.000 19.83 0.00 0.00 3.91
1925 2249 0.035630 AGAAGAGCACACATGGGAGC 60.036 55.000 9.62 9.62 0.00 4.70
1926 2250 1.735386 CAGAAGAGCACACATGGGAG 58.265 55.000 0.00 0.00 0.00 4.30
1927 2251 0.321919 GCAGAAGAGCACACATGGGA 60.322 55.000 0.00 0.00 0.00 4.37
1929 2253 0.803117 CAGCAGAAGAGCACACATGG 59.197 55.000 0.00 0.00 36.85 3.66
1930 2254 1.804601 TCAGCAGAAGAGCACACATG 58.195 50.000 0.00 0.00 36.85 3.21
1931 2255 2.290134 ACATCAGCAGAAGAGCACACAT 60.290 45.455 0.00 0.00 36.85 3.21
1932 2256 1.071228 ACATCAGCAGAAGAGCACACA 59.929 47.619 0.00 0.00 36.85 3.72
1934 2258 2.148768 CAACATCAGCAGAAGAGCACA 58.851 47.619 0.00 0.00 36.85 4.57
1940 2264 3.822996 CTGAAAGCAACATCAGCAGAAG 58.177 45.455 0.00 0.00 36.92 2.85
1964 2288 1.765904 TGGCCACTAACTGACTGACAA 59.234 47.619 0.00 0.00 0.00 3.18
1990 2335 3.056179 TGAACGCTCATAGTCATTGGTGA 60.056 43.478 0.00 0.00 0.00 4.02
1991 2336 3.261580 TGAACGCTCATAGTCATTGGTG 58.738 45.455 0.00 0.00 0.00 4.17
1992 2337 3.195610 TCTGAACGCTCATAGTCATTGGT 59.804 43.478 0.00 0.00 0.00 3.67
2060 2405 6.288941 TCTTCGATCCCTTATAACACACAA 57.711 37.500 0.00 0.00 0.00 3.33
2066 2411 8.962679 ACTCTCATATCTTCGATCCCTTATAAC 58.037 37.037 0.00 0.00 0.00 1.89
2075 2423 5.048782 ACTCAGCACTCTCATATCTTCGATC 60.049 44.000 0.00 0.00 0.00 3.69
2085 2433 3.197333 ACTGCAATACTCAGCACTCTCAT 59.803 43.478 0.00 0.00 36.62 2.90
2104 2452 4.153475 CCACAAGGAAACAACCGTATACTG 59.847 45.833 0.56 0.00 36.89 2.74
2112 2463 1.480789 ACCACCACAAGGAAACAACC 58.519 50.000 0.00 0.00 38.69 3.77
2113 2464 2.887337 CAACCACCACAAGGAAACAAC 58.113 47.619 0.00 0.00 38.69 3.32
2173 2527 7.338800 ACGCAAATTTGAAGATCTATTGGAT 57.661 32.000 22.31 0.00 37.37 3.41
2228 2583 2.156917 CAGCAGGCAAGAAATCTCACA 58.843 47.619 0.00 0.00 0.00 3.58
2242 2597 2.681848 GACATCAACAAGATCCAGCAGG 59.318 50.000 0.00 0.00 33.72 4.85
2246 2601 4.569966 GCAGTAGACATCAACAAGATCCAG 59.430 45.833 0.00 0.00 33.72 3.86
2321 2759 3.640498 TCTGCAGTCCTATCAGATTCAGG 59.360 47.826 14.67 0.00 32.48 3.86
2333 2771 1.353694 AGGCAAGAAATCTGCAGTCCT 59.646 47.619 14.67 3.98 0.00 3.85
2475 2913 7.042925 CGTTCGAGTTCTTATAATTACTTGGGG 60.043 40.741 11.57 2.76 0.00 4.96
2504 2942 4.216257 TGCAGATTTAAGCAACAGGAGAAC 59.784 41.667 0.00 0.00 37.90 3.01
2545 2983 1.634960 TGTAGGAATGGGACGTGACA 58.365 50.000 0.00 0.00 0.00 3.58
2595 3033 4.890158 TGTGGCACTATCATATACAGGG 57.110 45.455 19.83 0.00 0.00 4.45
2651 3092 6.329986 TGATTATGAGAAAAGGATAGGGAGCA 59.670 38.462 0.00 0.00 0.00 4.26
2745 3186 7.572523 TTTATAGATGAGGCCAACAAAGATG 57.427 36.000 5.01 0.00 0.00 2.90
2934 3375 3.072915 TGAGTAGGGACCGATAACCGATA 59.927 47.826 0.00 0.00 41.76 2.92
3023 3466 8.046294 TGTAAGTGTACAACAGTTCACAAAAT 57.954 30.769 0.00 0.00 40.62 1.82
3024 3467 7.436430 TGTAAGTGTACAACAGTTCACAAAA 57.564 32.000 0.00 0.00 40.62 2.44
3113 3556 9.548631 AATGTACCACTCAGCTACCTAATATAT 57.451 33.333 0.00 0.00 0.00 0.86
3114 3557 8.951614 AATGTACCACTCAGCTACCTAATATA 57.048 34.615 0.00 0.00 0.00 0.86
3115 3558 7.857404 AATGTACCACTCAGCTACCTAATAT 57.143 36.000 0.00 0.00 0.00 1.28
3116 3559 7.670605 AAATGTACCACTCAGCTACCTAATA 57.329 36.000 0.00 0.00 0.00 0.98
3202 3648 2.135933 GTGTTATACTCCGATGGCTGC 58.864 52.381 0.00 0.00 0.00 5.25
3247 3693 5.334879 CCCATACTCCTTTTTCAAACAGTCG 60.335 44.000 0.00 0.00 0.00 4.18
3445 3891 4.159879 CGTATAACCCAGACTTCCAGACTT 59.840 45.833 0.00 0.00 0.00 3.01
3446 3892 3.700038 CGTATAACCCAGACTTCCAGACT 59.300 47.826 0.00 0.00 0.00 3.24
3447 3893 3.737355 GCGTATAACCCAGACTTCCAGAC 60.737 52.174 0.00 0.00 0.00 3.51
3448 3894 2.429610 GCGTATAACCCAGACTTCCAGA 59.570 50.000 0.00 0.00 0.00 3.86
3449 3895 2.483188 GGCGTATAACCCAGACTTCCAG 60.483 54.545 0.00 0.00 0.00 3.86
3450 3896 1.483415 GGCGTATAACCCAGACTTCCA 59.517 52.381 0.00 0.00 0.00 3.53
3451 3897 1.761198 AGGCGTATAACCCAGACTTCC 59.239 52.381 0.00 0.00 0.00 3.46
3452 3898 3.538634 AAGGCGTATAACCCAGACTTC 57.461 47.619 0.00 0.00 0.00 3.01
3533 3979 6.308766 GCTTTATTTTGTCGATGTTCTGCAAT 59.691 34.615 0.00 0.00 0.00 3.56
3682 4128 5.859205 ATGGGAAGGAACAAAATCATAGC 57.141 39.130 0.00 0.00 0.00 2.97
3771 4223 2.807247 ACCAAGTTCTTGTGGTGGC 58.193 52.632 10.93 0.00 46.53 5.01
3788 4240 1.371558 GAGTCCAGGACACCACCAC 59.628 63.158 22.31 0.61 34.60 4.16
3836 4291 1.207791 CAGGCTTCATAGGGGACACT 58.792 55.000 0.00 0.00 0.00 3.55
3902 4357 6.959671 TGAAACCACAAACATTTTGAACTC 57.040 33.333 5.67 0.00 0.00 3.01
3982 4437 4.082354 GCAAAGTCCAGATCAAGCAAAGAT 60.082 41.667 0.00 0.00 0.00 2.40
3984 4439 3.255149 AGCAAAGTCCAGATCAAGCAAAG 59.745 43.478 0.00 0.00 0.00 2.77
3989 4444 4.698780 TGATTCAGCAAAGTCCAGATCAAG 59.301 41.667 0.00 0.00 0.00 3.02
4041 4496 1.664649 CTTGCCGTGCGAGAAGTCA 60.665 57.895 7.20 0.00 42.27 3.41
4113 4568 3.496309 CTCCAGGTTGCAGTGGCCA 62.496 63.158 0.00 0.00 40.13 5.36
4215 4670 4.849329 CTCGACGGCGGTACCTGC 62.849 72.222 12.58 17.13 38.28 4.85
4286 4741 2.428530 CGAGAGATGACATGGTCAAGGA 59.571 50.000 2.87 0.00 45.96 3.36
4298 4757 2.096013 CGACACAGTTAGCGAGAGATGA 59.904 50.000 0.00 0.00 0.00 2.92
4301 4760 1.520494 ACGACACAGTTAGCGAGAGA 58.480 50.000 0.00 0.00 0.00 3.10
4349 4808 1.125093 TGGCTTCTTCCGTTCCTCCA 61.125 55.000 0.00 0.00 0.00 3.86
4658 5138 4.708726 GCACTTGCAATCAATTAGGAGT 57.291 40.909 0.00 0.00 41.59 3.85
4735 5218 2.575532 CAACCCAGACAAGAAGCAGAA 58.424 47.619 0.00 0.00 0.00 3.02
4737 5220 0.595095 GCAACCCAGACAAGAAGCAG 59.405 55.000 0.00 0.00 0.00 4.24
4790 5279 2.556782 GGTTAAGTTTAAGCCCCTGCCT 60.557 50.000 3.11 0.00 38.69 4.75
4791 5280 1.822990 GGTTAAGTTTAAGCCCCTGCC 59.177 52.381 3.11 0.00 38.69 4.85
4793 5282 5.184479 GGTTAAGGTTAAGTTTAAGCCCCTG 59.816 44.000 9.50 0.00 40.90 4.45
4794 5283 5.075483 AGGTTAAGGTTAAGTTTAAGCCCCT 59.925 40.000 9.50 7.68 40.90 4.79
4796 5285 5.336213 GCAGGTTAAGGTTAAGTTTAAGCCC 60.336 44.000 9.50 5.02 40.90 5.19
4797 5286 5.336213 GGCAGGTTAAGGTTAAGTTTAAGCC 60.336 44.000 9.50 9.26 40.90 4.35
4798 5287 5.475909 AGGCAGGTTAAGGTTAAGTTTAAGC 59.524 40.000 5.85 5.85 40.45 3.09
4799 5288 7.229907 TGAAGGCAGGTTAAGGTTAAGTTTAAG 59.770 37.037 0.00 0.00 0.00 1.85
4800 5289 7.013559 GTGAAGGCAGGTTAAGGTTAAGTTTAA 59.986 37.037 0.00 0.00 0.00 1.52
4801 5290 6.487668 GTGAAGGCAGGTTAAGGTTAAGTTTA 59.512 38.462 0.00 0.00 0.00 2.01
4802 5291 5.301045 GTGAAGGCAGGTTAAGGTTAAGTTT 59.699 40.000 0.00 0.00 0.00 2.66
4803 5292 4.825634 GTGAAGGCAGGTTAAGGTTAAGTT 59.174 41.667 0.00 0.00 0.00 2.66
4842 5331 5.992829 TGGTCGTGCTGTTATTCTAGAAAAA 59.007 36.000 9.71 0.00 0.00 1.94
4843 5332 5.543714 TGGTCGTGCTGTTATTCTAGAAAA 58.456 37.500 9.71 2.88 0.00 2.29
4844 5333 5.142061 TGGTCGTGCTGTTATTCTAGAAA 57.858 39.130 9.71 0.00 0.00 2.52
4845 5334 4.794278 TGGTCGTGCTGTTATTCTAGAA 57.206 40.909 7.82 7.82 0.00 2.10
4846 5335 4.794278 TTGGTCGTGCTGTTATTCTAGA 57.206 40.909 0.00 0.00 0.00 2.43
4847 5336 5.812642 AGAATTGGTCGTGCTGTTATTCTAG 59.187 40.000 0.00 0.00 31.22 2.43
4848 5337 5.730550 AGAATTGGTCGTGCTGTTATTCTA 58.269 37.500 0.00 0.00 31.22 2.10
4849 5338 4.579869 AGAATTGGTCGTGCTGTTATTCT 58.420 39.130 0.00 0.00 0.00 2.40
4850 5339 4.946784 AGAATTGGTCGTGCTGTTATTC 57.053 40.909 0.00 0.00 0.00 1.75
4851 5340 5.046910 CAAGAATTGGTCGTGCTGTTATT 57.953 39.130 0.00 0.00 43.94 1.40
4852 5341 4.685169 CAAGAATTGGTCGTGCTGTTAT 57.315 40.909 0.00 0.00 43.94 1.89
4879 5368 4.924305 ATTATGCCATGTCACATTGTCC 57.076 40.909 0.00 0.00 0.00 4.02
4880 5369 6.697019 GGTTAATTATGCCATGTCACATTGTC 59.303 38.462 0.00 0.00 0.00 3.18
4908 5427 2.740981 CTGACCAAGCTTCTCATGTGAC 59.259 50.000 0.00 0.00 0.00 3.67
4934 5453 5.237815 TCGCTGTTCATAGAAGACATTTGT 58.762 37.500 0.00 0.00 0.00 2.83
4945 5764 5.739752 TGAAATGGATTCGCTGTTCATAG 57.260 39.130 0.00 0.00 41.18 2.23
4954 5773 8.935844 TGTGATACTTATATGAAATGGATTCGC 58.064 33.333 0.00 0.00 41.18 4.70
5104 5929 1.611936 GGGGAAGAAGAAGACTGCCAC 60.612 57.143 0.00 0.00 34.87 5.01
5147 5972 4.252073 ACAGAGTTCAGATTGATGTGCTC 58.748 43.478 0.00 0.00 0.00 4.26
5150 5975 7.606858 ACAATACAGAGTTCAGATTGATGTG 57.393 36.000 0.00 0.00 32.90 3.21
5167 5992 8.978874 ATATATGGTTGCTTCTGAACAATACA 57.021 30.769 8.07 9.94 0.00 2.29
5178 6003 6.884280 AGGCTTACAATATATGGTTGCTTC 57.116 37.500 13.92 3.55 0.00 3.86
5186 6011 6.405953 CGGAGGGAGTAGGCTTACAATATATG 60.406 46.154 8.86 0.00 31.96 1.78
5191 6016 2.040178 CGGAGGGAGTAGGCTTACAAT 58.960 52.381 8.86 0.00 31.96 2.71
5198 6023 3.217743 CGGACGGAGGGAGTAGGC 61.218 72.222 0.00 0.00 0.00 3.93
5199 6024 3.217743 GCGGACGGAGGGAGTAGG 61.218 72.222 0.00 0.00 0.00 3.18
5200 6025 1.601419 TTTGCGGACGGAGGGAGTAG 61.601 60.000 0.00 0.00 0.00 2.57
5201 6026 0.974010 ATTTGCGGACGGAGGGAGTA 60.974 55.000 0.00 0.00 0.00 2.59
5202 6027 0.974010 TATTTGCGGACGGAGGGAGT 60.974 55.000 0.00 0.00 0.00 3.85
5203 6028 0.177141 TTATTTGCGGACGGAGGGAG 59.823 55.000 0.00 0.00 0.00 4.30
5204 6029 0.177141 CTTATTTGCGGACGGAGGGA 59.823 55.000 0.00 0.00 0.00 4.20
5205 6030 0.107848 ACTTATTTGCGGACGGAGGG 60.108 55.000 0.00 0.00 0.00 4.30
5206 6031 1.006832 CACTTATTTGCGGACGGAGG 58.993 55.000 0.00 0.00 0.00 4.30
5207 6032 1.722011 ACACTTATTTGCGGACGGAG 58.278 50.000 0.00 0.00 0.00 4.63
5208 6033 2.231964 AGTACACTTATTTGCGGACGGA 59.768 45.455 0.00 0.00 0.00 4.69
5209 6034 2.613691 AGTACACTTATTTGCGGACGG 58.386 47.619 0.00 0.00 0.00 4.79
5210 6035 3.924686 AGAAGTACACTTATTTGCGGACG 59.075 43.478 0.00 0.00 36.11 4.79
5211 6036 6.589139 AGTTAGAAGTACACTTATTTGCGGAC 59.411 38.462 0.00 0.00 36.11 4.79
5212 6037 6.694447 AGTTAGAAGTACACTTATTTGCGGA 58.306 36.000 0.00 0.00 36.11 5.54
5213 6038 6.963049 AGTTAGAAGTACACTTATTTGCGG 57.037 37.500 0.00 0.00 36.11 5.69
5214 6039 8.240883 AGAAGTTAGAAGTACACTTATTTGCG 57.759 34.615 0.00 0.00 36.11 4.85
5322 6147 9.338622 CCCTAGATCCGTTTTGAATTATACTTT 57.661 33.333 0.00 0.00 0.00 2.66
5323 6148 8.904099 CCCTAGATCCGTTTTGAATTATACTT 57.096 34.615 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.