Multiple sequence alignment - TraesCS3B01G402800

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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 TraesCS3B01G402800 chr3B 100.000 4515 0 0 1 4515 637067624 637063110 0.000000e+00 8338
1 TraesCS3B01G402800 chr3D 86.378 1872 123 62 1 1804 477885080 477883273 0.000000e+00 1923
2 TraesCS3B01G402800 chr3D 82.071 898 83 28 2299 3132 477882827 477881944 0.000000e+00 695
3 TraesCS3B01G402800 chr3D 85.329 668 54 22 3375 4026 477881673 477881034 0.000000e+00 651
4 TraesCS3B01G402800 chr3D 89.941 338 17 8 4178 4515 477880892 477880572 1.940000e-113 420
5 TraesCS3B01G402800 chr3D 88.235 357 24 7 1845 2201 477883263 477882925 1.170000e-110 411
6 TraesCS3B01G402800 chr3D 90.909 55 5 0 3303 3357 477881770 477881716 1.740000e-09 75
7 TraesCS3B01G402800 chr3A 88.070 1601 105 37 638 2201 621221113 621219562 0.000000e+00 1820
8 TraesCS3B01G402800 chr3A 84.419 1688 145 43 2206 3801 621219515 621217854 0.000000e+00 1552
9 TraesCS3B01G402800 chr3A 85.821 402 27 17 4114 4515 621215479 621215108 2.530000e-107 399
10 TraesCS3B01G402800 chr3A 86.687 323 30 7 176 487 621221551 621221231 3.340000e-91 346
11 TraesCS3B01G402800 chr3A 94.884 215 11 0 3795 4009 621215697 621215483 2.010000e-88 337
12 TraesCS3B01G402800 chr5B 90.099 101 10 0 2074 2174 448106597 448106697 1.020000e-26 132


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 TraesCS3B01G402800 chr3B 637063110 637067624 4514 True 8338.000000 8338 100.000000 1 4515 1 chr3B.!!$R1 4514
1 TraesCS3B01G402800 chr3D 477880572 477885080 4508 True 695.833333 1923 87.143833 1 4515 6 chr3D.!!$R1 4514
2 TraesCS3B01G402800 chr3A 621215108 621221551 6443 True 890.800000 1820 87.976200 176 4515 5 chr3A.!!$R1 4339

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
603 658 0.036010 CTCCGTCCAGCCACAAGATT 60.036 55.0 0.0 0.0 0.0 2.40 F
1807 1927 0.035056 CCCGCCATTGACTCTCCTTT 60.035 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 2657 0.035881 TGGAGCTTCCTTGTGCAGAG 59.964 55.0 0.0 0.0 37.46 3.35 R
3680 3996 0.032678 CCAGACGACAGCACTCAACT 59.967 55.0 0.0 0.0 0.00 3.16 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
32 33 4.021807 TCGTCCTGTAATGTAAGCACTTGA 60.022 41.667 0.00 0.00 0.00 3.02
34 35 5.238583 GTCCTGTAATGTAAGCACTTGACT 58.761 41.667 0.00 0.00 0.00 3.41
35 36 5.701290 GTCCTGTAATGTAAGCACTTGACTT 59.299 40.000 0.00 0.00 0.00 3.01
36 37 5.700832 TCCTGTAATGTAAGCACTTGACTTG 59.299 40.000 0.00 0.00 0.00 3.16
37 38 5.106555 CCTGTAATGTAAGCACTTGACTTGG 60.107 44.000 0.00 0.00 0.00 3.61
38 39 3.923017 AATGTAAGCACTTGACTTGGC 57.077 42.857 0.00 0.00 0.00 4.52
39 40 2.340210 TGTAAGCACTTGACTTGGCA 57.660 45.000 0.00 0.00 0.00 4.92
40 41 2.221169 TGTAAGCACTTGACTTGGCAG 58.779 47.619 0.00 0.00 0.00 4.85
41 42 2.158827 TGTAAGCACTTGACTTGGCAGA 60.159 45.455 0.00 0.00 0.00 4.26
42 43 2.283145 AAGCACTTGACTTGGCAGAT 57.717 45.000 0.00 0.00 0.00 2.90
43 44 3.423539 AAGCACTTGACTTGGCAGATA 57.576 42.857 0.00 0.00 0.00 1.98
44 45 2.704572 AGCACTTGACTTGGCAGATAC 58.295 47.619 0.00 0.00 0.00 2.24
45 46 2.304180 AGCACTTGACTTGGCAGATACT 59.696 45.455 0.00 0.00 0.00 2.12
46 47 2.675348 GCACTTGACTTGGCAGATACTC 59.325 50.000 0.00 0.00 0.00 2.59
47 48 3.265791 CACTTGACTTGGCAGATACTCC 58.734 50.000 0.00 0.00 0.00 3.85
48 49 3.055530 CACTTGACTTGGCAGATACTCCT 60.056 47.826 0.00 0.00 0.00 3.69
49 50 4.160439 CACTTGACTTGGCAGATACTCCTA 59.840 45.833 0.00 0.00 0.00 2.94
50 51 4.160626 ACTTGACTTGGCAGATACTCCTAC 59.839 45.833 0.00 0.00 0.00 3.18
51 52 3.031736 TGACTTGGCAGATACTCCTACC 58.968 50.000 0.00 0.00 0.00 3.18
52 53 3.301274 GACTTGGCAGATACTCCTACCT 58.699 50.000 0.00 0.00 0.00 3.08
53 54 3.034635 ACTTGGCAGATACTCCTACCTG 58.965 50.000 0.00 0.00 0.00 4.00
54 55 3.300388 CTTGGCAGATACTCCTACCTGA 58.700 50.000 0.00 0.00 0.00 3.86
57 58 3.117131 TGGCAGATACTCCTACCTGATGA 60.117 47.826 0.00 0.00 0.00 2.92
63 64 5.538053 AGATACTCCTACCTGATGATGTGTG 59.462 44.000 0.00 0.00 0.00 3.82
64 65 2.169352 ACTCCTACCTGATGATGTGTGC 59.831 50.000 0.00 0.00 0.00 4.57
67 68 1.929169 CTACCTGATGATGTGTGCGTG 59.071 52.381 0.00 0.00 0.00 5.34
71 72 0.238025 TGATGATGTGTGCGTGCAAC 59.762 50.000 0.00 0.00 0.00 4.17
73 74 0.890542 ATGATGTGTGCGTGCAACCT 60.891 50.000 0.00 0.00 0.00 3.50
74 75 1.207593 GATGTGTGCGTGCAACCTC 59.792 57.895 0.00 0.00 0.00 3.85
76 77 0.819259 ATGTGTGCGTGCAACCTCTT 60.819 50.000 0.00 0.00 0.00 2.85
86 87 3.125316 CGTGCAACCTCTTATCCAGTTTC 59.875 47.826 0.00 0.00 0.00 2.78
89 90 3.270877 CAACCTCTTATCCAGTTTCCCG 58.729 50.000 0.00 0.00 0.00 5.14
95 97 4.030913 TCTTATCCAGTTTCCCGACAGAT 58.969 43.478 0.00 0.00 0.00 2.90
109 111 3.181517 CCGACAGATACACACATTTGCTG 60.182 47.826 0.00 0.00 0.00 4.41
116 118 0.810648 CACACATTTGCTGCCCGTAT 59.189 50.000 0.00 0.00 0.00 3.06
119 121 0.964860 ACATTTGCTGCCCGTATGCA 60.965 50.000 0.00 0.00 39.37 3.96
120 122 0.386476 CATTTGCTGCCCGTATGCAT 59.614 50.000 3.79 3.79 41.16 3.96
141 146 5.241064 GCATTTGCTTCATCATCATCCTACT 59.759 40.000 0.00 0.00 38.21 2.57
146 151 5.604231 TGCTTCATCATCATCCTACTAAGGT 59.396 40.000 0.00 0.00 44.09 3.50
159 164 2.755650 ACTAAGGTCTGAAGTTGTGCG 58.244 47.619 0.00 0.00 0.00 5.34
165 170 2.337583 GTCTGAAGTTGTGCGCAGATA 58.662 47.619 12.22 0.00 39.33 1.98
166 171 2.346847 GTCTGAAGTTGTGCGCAGATAG 59.653 50.000 12.22 3.65 39.33 2.08
168 173 2.995939 CTGAAGTTGTGCGCAGATAGAA 59.004 45.455 12.22 0.00 0.00 2.10
169 174 3.398406 TGAAGTTGTGCGCAGATAGAAA 58.602 40.909 12.22 0.00 0.00 2.52
170 175 3.186409 TGAAGTTGTGCGCAGATAGAAAC 59.814 43.478 12.22 3.84 0.00 2.78
171 176 1.726791 AGTTGTGCGCAGATAGAAACG 59.273 47.619 12.22 0.00 0.00 3.60
172 177 1.459592 GTTGTGCGCAGATAGAAACGT 59.540 47.619 12.22 0.00 0.00 3.99
173 178 1.067693 TGTGCGCAGATAGAAACGTG 58.932 50.000 12.22 0.00 0.00 4.49
174 179 1.068474 GTGCGCAGATAGAAACGTGT 58.932 50.000 12.22 0.00 0.00 4.49
175 180 1.459592 GTGCGCAGATAGAAACGTGTT 59.540 47.619 12.22 0.00 0.00 3.32
176 181 1.459209 TGCGCAGATAGAAACGTGTTG 59.541 47.619 5.66 0.00 0.00 3.33
177 182 1.786928 GCGCAGATAGAAACGTGTTGC 60.787 52.381 0.30 0.00 0.00 4.17
179 184 1.201921 GCAGATAGAAACGTGTTGCGG 60.202 52.381 0.00 0.00 46.52 5.69
181 186 1.001633 AGATAGAAACGTGTTGCGGGT 59.998 47.619 0.00 0.00 46.52 5.28
183 188 1.500512 TAGAAACGTGTTGCGGGTGC 61.501 55.000 0.00 0.00 46.52 5.01
201 219 1.191096 GCGCGTTAAATGGCTTGATG 58.809 50.000 8.43 0.00 0.00 3.07
227 247 7.095774 GGAAACGTGTGTGCTCGATATTATATT 60.096 37.037 0.00 0.00 35.78 1.28
228 248 7.709269 AACGTGTGTGCTCGATATTATATTT 57.291 32.000 0.00 0.00 35.78 1.40
249 269 6.734104 TTTTACTTTGTGCACTGCAATTTT 57.266 29.167 19.41 0.00 41.47 1.82
292 312 0.171455 CAGTACGTGGAGCTGACCTC 59.829 60.000 0.00 0.00 39.98 3.85
300 320 1.066143 TGGAGCTGACCTCGATTTTCC 60.066 52.381 0.00 0.00 41.71 3.13
355 377 0.727398 GGTCATAGCAAGTCGTTGGC 59.273 55.000 0.00 0.00 33.87 4.52
364 386 0.748729 AAGTCGTTGGCGGTTTTCCA 60.749 50.000 0.00 0.00 40.70 3.53
380 413 1.040893 TCCATGCGGTCGTATGAGGT 61.041 55.000 19.83 0.00 39.96 3.85
385 418 0.804933 GCGGTCGTATGAGGTTGGTC 60.805 60.000 0.00 0.00 0.00 4.02
403 436 4.899239 GGTGAGGCGCTGGATCCG 62.899 72.222 7.64 3.14 0.00 4.18
455 488 1.148157 GACACTCATGCGTGATCCCG 61.148 60.000 22.09 0.00 38.27 5.14
463 500 2.658593 CGTGATCCCGGCGACATC 60.659 66.667 9.30 9.84 0.00 3.06
474 511 1.468520 CGGCGACATCTTGGATTTTGT 59.531 47.619 0.00 0.00 0.00 2.83
494 541 0.607489 AGCCTAAGCCAGCACAGTTG 60.607 55.000 0.00 0.00 41.25 3.16
517 564 1.868251 GTACCGCGCTCGACAGAAG 60.868 63.158 5.56 0.00 38.10 2.85
518 565 2.036571 TACCGCGCTCGACAGAAGA 61.037 57.895 5.56 0.00 38.10 2.87
519 566 1.978712 TACCGCGCTCGACAGAAGAG 61.979 60.000 5.56 0.00 38.10 2.85
520 567 2.481009 CGCGCTCGACAGAAGAGA 59.519 61.111 5.56 0.00 37.93 3.10
523 570 1.419374 GCGCTCGACAGAAGAGAAAA 58.581 50.000 0.00 0.00 37.93 2.29
535 582 4.702131 CAGAAGAGAAAATTACCCCCACAG 59.298 45.833 0.00 0.00 0.00 3.66
536 583 3.087370 AGAGAAAATTACCCCCACAGC 57.913 47.619 0.00 0.00 0.00 4.40
537 584 2.100197 GAGAAAATTACCCCCACAGCC 58.900 52.381 0.00 0.00 0.00 4.85
538 585 1.431243 AGAAAATTACCCCCACAGCCA 59.569 47.619 0.00 0.00 0.00 4.75
539 586 1.548719 GAAAATTACCCCCACAGCCAC 59.451 52.381 0.00 0.00 0.00 5.01
540 587 0.485099 AAATTACCCCCACAGCCACA 59.515 50.000 0.00 0.00 0.00 4.17
541 588 0.485099 AATTACCCCCACAGCCACAA 59.515 50.000 0.00 0.00 0.00 3.33
542 589 0.039618 ATTACCCCCACAGCCACAAG 59.960 55.000 0.00 0.00 0.00 3.16
543 590 2.075355 TTACCCCCACAGCCACAAGG 62.075 60.000 0.00 0.00 38.23 3.61
559 606 4.342951 CCACAAGGCCACATCATCATAAAT 59.657 41.667 5.01 0.00 0.00 1.40
603 658 0.036010 CTCCGTCCAGCCACAAGATT 60.036 55.000 0.00 0.00 0.00 2.40
615 670 2.546373 CCACAAGATTGTTTGCCCACAG 60.546 50.000 0.00 0.00 39.91 3.66
616 671 1.069049 ACAAGATTGTTTGCCCACAGC 59.931 47.619 0.00 0.00 38.47 4.40
617 672 3.538565 ACAAGATTGTTTGCCCACAGCA 61.539 45.455 0.00 0.00 44.47 4.41
618 673 5.358492 ACAAGATTGTTTGCCCACAGCAG 62.358 47.826 0.00 0.00 42.60 4.24
798 879 0.320771 GCCTCCTCGCAGAAAGACAA 60.321 55.000 0.00 0.00 34.09 3.18
801 882 0.681733 TCCTCGCAGAAAGACAAGCT 59.318 50.000 0.00 0.00 34.09 3.74
802 883 1.074752 CCTCGCAGAAAGACAAGCTC 58.925 55.000 0.00 0.00 34.09 4.09
1010 1100 1.198408 CGTCCACTTCAGTAGCACGTA 59.802 52.381 0.00 0.00 0.00 3.57
1039 1129 2.513204 TCGGGTAGCTCTCGTCCG 60.513 66.667 0.00 0.00 41.36 4.79
1111 1202 2.969806 CTGGTGTGTGCATGCCGAC 61.970 63.158 16.68 12.12 0.00 4.79
1112 1203 3.737172 GGTGTGTGCATGCCGACC 61.737 66.667 16.68 11.66 0.00 4.79
1113 1204 4.088762 GTGTGTGCATGCCGACCG 62.089 66.667 16.68 0.00 0.00 4.79
1114 1205 4.306967 TGTGTGCATGCCGACCGA 62.307 61.111 16.68 0.00 0.00 4.69
1316 1415 2.648724 GCCATTGATTCGCGCGTG 60.649 61.111 30.98 19.03 0.00 5.34
1327 1426 3.335534 GCGCGTGTCGTTCAGGTT 61.336 61.111 8.43 0.00 41.07 3.50
1441 1540 4.087892 TTCTGCGGCAGCCTCTCC 62.088 66.667 24.78 0.00 44.33 3.71
1486 1591 2.519780 GACGAGGAGGAGCGGGAT 60.520 66.667 0.00 0.00 0.00 3.85
1493 1598 2.688666 AGGAGCGGGATGAGCCAA 60.689 61.111 0.00 0.00 38.95 4.52
1501 1606 2.510238 GATGAGCCAAGCGACGCT 60.510 61.111 18.46 18.46 42.56 5.07
1504 1609 2.126071 GAGCCAAGCGACGCTACA 60.126 61.111 24.77 0.00 38.25 2.74
1506 1611 3.854459 GCCAAGCGACGCTACAGC 61.854 66.667 24.77 21.20 38.25 4.40
1711 1831 1.598601 CGGAGCTACGTCTACTTCCTC 59.401 57.143 11.15 0.00 0.00 3.71
1807 1927 0.035056 CCCGCCATTGACTCTCCTTT 60.035 55.000 0.00 0.00 0.00 3.11
1816 1936 1.068472 TGACTCTCCTTTTCGTCTCGC 60.068 52.381 0.00 0.00 0.00 5.03
1842 1962 7.909267 TCGTAGATGAGCAATTAAACATTGAG 58.091 34.615 0.00 0.00 0.00 3.02
1866 1986 3.512329 TCTGCAATGCCATTCTTGTCAAT 59.488 39.130 1.53 0.00 0.00 2.57
1867 1987 4.020928 TCTGCAATGCCATTCTTGTCAATT 60.021 37.500 1.53 0.00 0.00 2.32
1869 1989 5.170021 TGCAATGCCATTCTTGTCAATTAC 58.830 37.500 1.53 0.00 0.00 1.89
1870 1990 5.047164 TGCAATGCCATTCTTGTCAATTACT 60.047 36.000 1.53 0.00 0.00 2.24
1871 1991 6.152492 TGCAATGCCATTCTTGTCAATTACTA 59.848 34.615 1.53 0.00 0.00 1.82
1894 2014 2.826428 TGACACTCTGCACTTCTGTTC 58.174 47.619 0.00 0.00 0.00 3.18
2134 2254 0.037790 GATCGAGCAGTATGAGGCCC 60.038 60.000 0.00 0.00 39.69 5.80
2178 2298 3.120649 GGGAGAAGAAATTCAACGACACG 60.121 47.826 0.00 0.00 0.00 4.49
2182 2302 0.452122 GAAATTCAACGACACGCGGG 60.452 55.000 6.92 6.92 46.49 6.13
2201 2321 2.403987 CTCACCGAGCGAGGTACG 59.596 66.667 5.84 0.00 43.89 3.67
2202 2322 2.359107 TCACCGAGCGAGGTACGT 60.359 61.111 5.84 0.00 43.89 3.57
2203 2323 1.079197 TCACCGAGCGAGGTACGTA 60.079 57.895 5.84 0.00 43.89 3.57
2214 2375 2.222640 CGAGGTACGTATTTTGGCAACG 60.223 50.000 0.00 3.19 42.17 4.10
2220 2381 3.484683 ACGTATTTTGGCAACGAATTCG 58.515 40.909 25.64 25.64 40.49 3.34
2236 2397 4.144731 CGAATTCGTTTGCTCTGTCAAAAC 59.855 41.667 19.67 0.00 37.65 2.43
2251 2415 0.865769 AAAACACGGCAGAGTTAGCG 59.134 50.000 0.00 0.00 31.08 4.26
2261 2425 2.286294 GCAGAGTTAGCGTCATGAATGG 59.714 50.000 0.00 0.00 0.00 3.16
2270 2434 0.813184 GTCATGAATGGTGTGGCCTG 59.187 55.000 3.32 0.00 38.35 4.85
2271 2435 0.405198 TCATGAATGGTGTGGCCTGT 59.595 50.000 3.32 0.00 38.35 4.00
2272 2436 1.632920 TCATGAATGGTGTGGCCTGTA 59.367 47.619 3.32 0.00 38.35 2.74
2273 2437 2.241941 TCATGAATGGTGTGGCCTGTAT 59.758 45.455 3.32 0.00 38.35 2.29
2274 2438 2.127271 TGAATGGTGTGGCCTGTATG 57.873 50.000 3.32 0.00 38.35 2.39
2277 2441 2.603075 ATGGTGTGGCCTGTATGTTT 57.397 45.000 3.32 0.00 38.35 2.83
2278 2442 2.373335 TGGTGTGGCCTGTATGTTTT 57.627 45.000 3.32 0.00 38.35 2.43
2357 2521 3.605634 TCTTACACCGATTTGACCCATG 58.394 45.455 0.00 0.00 0.00 3.66
2358 2522 2.411628 TACACCGATTTGACCCATGG 57.588 50.000 4.14 4.14 0.00 3.66
2412 2576 1.337167 GCAGATTGCCAGTTCCAAACC 60.337 52.381 0.00 0.00 37.42 3.27
2445 2612 1.807142 GAAAAGCTCCTCGTTTCCAGG 59.193 52.381 0.00 0.00 37.25 4.45
2446 2613 1.056660 AAAGCTCCTCGTTTCCAGGA 58.943 50.000 0.00 0.00 37.75 3.86
2448 2615 1.446272 GCTCCTCGTTTCCAGGACG 60.446 63.158 0.00 0.00 41.62 4.79
2450 2617 2.154798 CTCCTCGTTTCCAGGACGCA 62.155 60.000 0.00 0.00 40.16 5.24
2481 2648 1.021390 CAGAAGAAATGGCGCGGACT 61.021 55.000 8.83 0.00 0.00 3.85
2493 2660 2.977178 CGGACTGCTGCCTTCTCT 59.023 61.111 0.00 0.00 0.00 3.10
2540 2707 1.856265 GCCACAAGACGAAGCCAAGG 61.856 60.000 0.00 0.00 0.00 3.61
2541 2708 1.237285 CCACAAGACGAAGCCAAGGG 61.237 60.000 0.00 0.00 0.00 3.95
2550 2726 1.228862 AAGCCAAGGGGACGCAAAT 60.229 52.632 0.00 0.00 35.59 2.32
2589 2765 1.800315 CTACACCAACTCCGCGTCG 60.800 63.158 4.92 0.00 0.00 5.12
2627 2803 2.650813 ATCAAGGCGCCATCGGAGTC 62.651 60.000 31.54 0.00 35.95 3.36
2628 2804 4.514577 AAGGCGCCATCGGAGTCG 62.515 66.667 31.54 0.00 30.97 4.18
2673 2849 3.102107 CTCGGACTGGAGCTCGTCG 62.102 68.421 7.83 7.01 0.00 5.12
2682 2858 4.135153 AGCTCGTCGCGCTTCCAT 62.135 61.111 3.37 0.00 45.59 3.41
2685 2861 1.589993 CTCGTCGCGCTTCCATGAT 60.590 57.895 5.56 0.00 0.00 2.45
2700 2876 0.179111 ATGATCACGCCGACGACAAT 60.179 50.000 0.00 0.00 43.93 2.71
2886 3086 1.200716 TCGTACAGGGATGAACACGTC 59.799 52.381 0.00 0.00 0.00 4.34
2937 3137 3.160047 CTCCCAGCGCCAGAGGAT 61.160 66.667 2.29 0.00 0.00 3.24
2960 3160 3.168773 ATGGTTACCATGACCGTGC 57.831 52.632 17.01 0.00 43.39 5.34
2964 3164 1.519408 GTTACCATGACCGTGCAAGT 58.481 50.000 0.00 0.00 0.00 3.16
2981 3181 4.966123 TGCAAACTGTTGGACCGA 57.034 50.000 0.00 0.00 35.10 4.69
2982 3182 3.412722 TGCAAACTGTTGGACCGAT 57.587 47.368 0.00 0.00 35.10 4.18
2984 3184 0.240945 GCAAACTGTTGGACCGATGG 59.759 55.000 0.00 0.00 35.10 3.51
2985 3185 0.881118 CAAACTGTTGGACCGATGGG 59.119 55.000 0.00 0.00 40.11 4.00
3012 3212 3.552384 ACGGCACCCACGGAGAAA 61.552 61.111 0.00 0.00 35.23 2.52
3126 3356 2.178521 CCGACAGACTCGTTCCCG 59.821 66.667 0.00 0.00 41.18 5.14
3178 3408 4.521062 ACGATGCAGAGCTCGGGC 62.521 66.667 21.84 21.84 39.16 6.13
3191 3421 0.250234 CTCGGGCTGATTGAGGTTGA 59.750 55.000 0.00 0.00 0.00 3.18
3239 3469 1.203162 TGATGATGGTGCTGGGGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
3241 3471 1.917872 TGATGGTGCTGGGGTTTTAC 58.082 50.000 0.00 0.00 0.00 2.01
3285 3533 0.737715 CTTCTGGTAGGTGCAGCGTC 60.738 60.000 10.78 7.50 0.00 5.19
3353 3622 0.338120 CTGAGGAAGGGAGGAGGTCT 59.662 60.000 0.00 0.00 0.00 3.85
3366 3635 0.603569 GAGGTCTTCTTGGAGACGCA 59.396 55.000 3.27 0.00 45.53 5.24
3381 3677 1.464997 GACGCAGACCTGTTCATTTCC 59.535 52.381 0.00 0.00 0.00 3.13
3389 3685 4.339247 AGACCTGTTCATTTCCAACAAGTG 59.661 41.667 0.00 0.00 33.36 3.16
3411 3707 1.374560 TGCTGTAACGTGTGTTTGCT 58.625 45.000 0.00 0.00 39.54 3.91
3413 3709 1.741993 CTGTAACGTGTGTTTGCTGC 58.258 50.000 0.00 0.00 39.54 5.25
3424 3724 3.499537 TGTGTTTGCTGCTGATTGTCTAG 59.500 43.478 0.00 0.00 0.00 2.43
3427 3727 3.969287 TTGCTGCTGATTGTCTAGAGT 57.031 42.857 0.00 0.00 0.00 3.24
3437 3737 2.526304 TGTCTAGAGTGTGTGTTGGC 57.474 50.000 0.00 0.00 0.00 4.52
3439 3739 1.070134 GTCTAGAGTGTGTGTTGGCCA 59.930 52.381 0.00 0.00 0.00 5.36
3458 3758 0.537371 AGCTTTTTCCTGTGGTCCGG 60.537 55.000 0.00 0.00 0.00 5.14
3460 3760 1.687563 CTTTTTCCTGTGGTCCGGTT 58.312 50.000 0.00 0.00 0.00 4.44
3503 3814 2.712539 CGGCGTTGTCAAGCACAA 59.287 55.556 0.00 0.00 43.12 3.33
3555 3867 3.760684 GGAGATGAGATGCCTTTGTTTGT 59.239 43.478 0.00 0.00 0.00 2.83
3559 3871 4.057406 TGAGATGCCTTTGTTTGTTTGG 57.943 40.909 0.00 0.00 0.00 3.28
3569 3881 2.298610 TGTTTGTTTGGTATCCGTGCA 58.701 42.857 0.00 0.00 0.00 4.57
3583 3895 3.294493 TGCAAACCTCGCCCAAGC 61.294 61.111 0.00 0.00 0.00 4.01
3584 3896 4.056125 GCAAACCTCGCCCAAGCC 62.056 66.667 0.00 0.00 34.57 4.35
3585 3897 3.373565 CAAACCTCGCCCAAGCCC 61.374 66.667 0.00 0.00 34.57 5.19
3586 3898 3.897122 AAACCTCGCCCAAGCCCA 61.897 61.111 0.00 0.00 34.57 5.36
3587 3899 3.444818 AAACCTCGCCCAAGCCCAA 62.445 57.895 0.00 0.00 34.57 4.12
3588 3900 3.868200 AACCTCGCCCAAGCCCAAG 62.868 63.158 0.00 0.00 34.57 3.61
3608 3920 1.408702 GGCAAGACAGGAAAAGTTGCA 59.591 47.619 7.58 0.00 44.29 4.08
3610 3922 3.054878 GCAAGACAGGAAAAGTTGCATG 58.945 45.455 0.00 0.00 42.48 4.06
3680 3996 3.206150 GACTGAAACTCAAACAGCTCCA 58.794 45.455 0.00 0.00 35.38 3.86
3718 4034 4.379243 CGGTCTTCTGTGCGGCCT 62.379 66.667 0.00 0.00 0.00 5.19
3720 4036 2.031163 GTCTTCTGTGCGGCCTGT 59.969 61.111 0.00 0.00 0.00 4.00
3722 4038 1.148273 TCTTCTGTGCGGCCTGTTT 59.852 52.632 0.00 0.00 0.00 2.83
3723 4039 1.165907 TCTTCTGTGCGGCCTGTTTG 61.166 55.000 0.00 0.00 0.00 2.93
3724 4040 2.133742 CTTCTGTGCGGCCTGTTTGG 62.134 60.000 0.00 0.00 39.35 3.28
3725 4041 2.594303 CTGTGCGGCCTGTTTGGA 60.594 61.111 0.00 0.00 38.35 3.53
3726 4042 2.904866 TGTGCGGCCTGTTTGGAC 60.905 61.111 0.00 0.00 41.70 4.02
3733 4049 1.227853 GCCTGTTTGGACGGTCTGT 60.228 57.895 8.23 0.00 38.35 3.41
3734 4050 1.507141 GCCTGTTTGGACGGTCTGTG 61.507 60.000 8.23 0.00 38.35 3.66
3736 4052 1.831389 CTGTTTGGACGGTCTGTGCG 61.831 60.000 8.23 0.00 42.78 5.34
3737 4053 2.280524 TTTGGACGGTCTGTGCGG 60.281 61.111 8.23 0.00 42.78 5.69
3767 4086 4.101448 CTCCACCTCCGGCCCTTG 62.101 72.222 0.00 0.00 0.00 3.61
3770 4089 3.966543 CACCTCCGGCCCTTGGTT 61.967 66.667 0.00 0.00 0.00 3.67
3771 4090 3.966543 ACCTCCGGCCCTTGGTTG 61.967 66.667 0.00 0.00 0.00 3.77
3823 6304 2.485426 CCCACAACACTCATGATGACAC 59.515 50.000 0.00 0.00 33.05 3.67
3824 6305 2.485426 CCACAACACTCATGATGACACC 59.515 50.000 0.00 0.00 33.05 4.16
3928 6409 1.102809 TGTGTTGCCTCCAGTTGCAG 61.103 55.000 0.00 0.00 38.95 4.41
3996 6481 1.078567 CAGCTGCCCTTCCAGTCTC 60.079 63.158 0.00 0.00 35.28 3.36
3999 6484 1.920325 CTGCCCTTCCAGTCTCCCA 60.920 63.158 0.00 0.00 0.00 4.37
4009 6494 0.250234 CAGTCTCCCATCGCTGGAAA 59.750 55.000 6.92 0.00 46.37 3.13
4010 6495 0.984230 AGTCTCCCATCGCTGGAAAA 59.016 50.000 6.92 0.00 46.37 2.29
4011 6496 1.087501 GTCTCCCATCGCTGGAAAAC 58.912 55.000 6.92 0.00 46.37 2.43
4014 6499 2.162681 CTCCCATCGCTGGAAAACTTT 58.837 47.619 6.92 0.00 46.37 2.66
4015 6500 2.558359 CTCCCATCGCTGGAAAACTTTT 59.442 45.455 6.92 0.00 46.37 2.27
4016 6501 2.295909 TCCCATCGCTGGAAAACTTTTG 59.704 45.455 6.92 0.00 46.37 2.44
4017 6502 2.061028 CCATCGCTGGAAAACTTTTGC 58.939 47.619 0.00 0.00 46.37 3.68
4020 6505 3.238108 TCGCTGGAAAACTTTTGCAAA 57.762 38.095 8.05 8.05 0.00 3.68
4021 6506 3.589988 TCGCTGGAAAACTTTTGCAAAA 58.410 36.364 22.61 22.61 0.00 2.44
4025 6510 4.631377 GCTGGAAAACTTTTGCAAAACTCT 59.369 37.500 20.46 5.72 0.00 3.24
4029 6545 5.064707 GGAAAACTTTTGCAAAACTCTTCCC 59.935 40.000 26.21 18.04 0.00 3.97
4067 6583 0.749649 CTAGGCAGCCTACCAGACAG 59.250 60.000 18.06 3.72 34.61 3.51
4097 6613 4.340381 GCTGAGATTAAGGATGCAAATGGT 59.660 41.667 0.00 0.00 0.00 3.55
4098 6614 5.735354 GCTGAGATTAAGGATGCAAATGGTG 60.735 44.000 0.00 0.00 0.00 4.17
4099 6615 4.646040 TGAGATTAAGGATGCAAATGGTGG 59.354 41.667 0.00 0.00 0.00 4.61
4100 6616 4.613437 AGATTAAGGATGCAAATGGTGGT 58.387 39.130 0.00 0.00 0.00 4.16
4101 6617 5.765510 AGATTAAGGATGCAAATGGTGGTA 58.234 37.500 0.00 0.00 0.00 3.25
4102 6618 5.594317 AGATTAAGGATGCAAATGGTGGTAC 59.406 40.000 0.00 0.00 0.00 3.34
4103 6619 2.143876 AGGATGCAAATGGTGGTACC 57.856 50.000 4.43 4.43 39.22 3.34
4104 6620 1.111277 GGATGCAAATGGTGGTACCC 58.889 55.000 10.07 0.11 37.50 3.69
4105 6621 1.618345 GGATGCAAATGGTGGTACCCA 60.618 52.381 10.07 0.63 37.50 4.51
4115 6631 3.300032 TGGTACCCACTGCCTCTAG 57.700 57.895 10.07 0.00 0.00 2.43
4116 6632 0.325296 TGGTACCCACTGCCTCTAGG 60.325 60.000 10.07 0.00 38.53 3.02
4136 6652 3.197983 AGGGTATTCTCCGAACCTCTTTG 59.802 47.826 0.00 0.00 33.59 2.77
4172 6688 8.871686 ATGAACTAAAATTTCCAAAGTCACAC 57.128 30.769 0.00 0.00 0.00 3.82
4224 6740 1.036707 CGTGGGGGTCACAAATTTGT 58.963 50.000 18.13 18.13 46.36 2.83
4227 6743 3.257127 CGTGGGGGTCACAAATTTGTATT 59.743 43.478 22.87 0.00 46.36 1.89
4300 6816 2.376109 AGACCATACACCTACACTCCG 58.624 52.381 0.00 0.00 0.00 4.63
4337 6853 7.930865 AGAATATTGTATGCAAAGAGACCTCTC 59.069 37.037 0.00 0.00 39.39 3.20
4398 6914 6.518493 TGTAAATATAAGCCTAACAGGTCGG 58.482 40.000 0.00 0.00 37.80 4.79
4405 6921 0.964358 CCTAACAGGTCGGTCGGAGT 60.964 60.000 0.00 0.00 0.00 3.85
4406 6922 0.450983 CTAACAGGTCGGTCGGAGTC 59.549 60.000 0.00 0.00 0.00 3.36
4430 6946 3.070018 CAGGCTTAGTTCAGACCACTTG 58.930 50.000 0.00 0.00 0.00 3.16
4495 7012 5.659849 ATAGGAAGAGCAAAATCCCTCAT 57.340 39.130 0.00 0.00 33.55 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.683832 AGTGCTTACATTACAGGACGATC 58.316 43.478 0.00 0.00 36.52 3.69
32 33 3.034635 CAGGTAGGAGTATCTGCCAAGT 58.965 50.000 0.00 0.00 41.21 3.16
34 35 3.398318 TCAGGTAGGAGTATCTGCCAA 57.602 47.619 0.00 0.00 41.21 4.52
35 36 3.117131 TCATCAGGTAGGAGTATCTGCCA 60.117 47.826 0.00 0.00 41.21 4.92
36 37 3.501349 TCATCAGGTAGGAGTATCTGCC 58.499 50.000 0.00 0.00 37.31 4.85
37 38 4.526262 ACATCATCAGGTAGGAGTATCTGC 59.474 45.833 0.00 0.00 37.31 4.26
38 39 5.538053 ACACATCATCAGGTAGGAGTATCTG 59.462 44.000 0.00 0.00 38.59 2.90
39 40 5.538053 CACACATCATCAGGTAGGAGTATCT 59.462 44.000 0.00 0.00 33.73 1.98
40 41 5.777802 CACACATCATCAGGTAGGAGTATC 58.222 45.833 0.00 0.00 0.00 2.24
41 42 4.039730 GCACACATCATCAGGTAGGAGTAT 59.960 45.833 0.00 0.00 0.00 2.12
42 43 3.384789 GCACACATCATCAGGTAGGAGTA 59.615 47.826 0.00 0.00 0.00 2.59
43 44 2.169352 GCACACATCATCAGGTAGGAGT 59.831 50.000 0.00 0.00 0.00 3.85
44 45 2.800985 CGCACACATCATCAGGTAGGAG 60.801 54.545 0.00 0.00 0.00 3.69
45 46 1.136891 CGCACACATCATCAGGTAGGA 59.863 52.381 0.00 0.00 0.00 2.94
46 47 1.134699 ACGCACACATCATCAGGTAGG 60.135 52.381 0.00 0.00 0.00 3.18
47 48 1.929169 CACGCACACATCATCAGGTAG 59.071 52.381 0.00 0.00 0.00 3.18
48 49 2.006552 GCACGCACACATCATCAGGTA 61.007 52.381 0.00 0.00 0.00 3.08
49 50 1.300971 GCACGCACACATCATCAGGT 61.301 55.000 0.00 0.00 0.00 4.00
50 51 1.300266 TGCACGCACACATCATCAGG 61.300 55.000 0.00 0.00 0.00 3.86
51 52 0.518195 TTGCACGCACACATCATCAG 59.482 50.000 0.00 0.00 0.00 2.90
52 53 0.238025 GTTGCACGCACACATCATCA 59.762 50.000 0.00 0.00 0.00 3.07
53 54 0.454957 GGTTGCACGCACACATCATC 60.455 55.000 0.00 0.00 0.00 2.92
54 55 0.890542 AGGTTGCACGCACACATCAT 60.891 50.000 0.00 0.00 0.00 2.45
57 58 0.819259 AAGAGGTTGCACGCACACAT 60.819 50.000 0.00 0.00 0.00 3.21
63 64 1.009829 CTGGATAAGAGGTTGCACGC 58.990 55.000 0.00 0.00 0.00 5.34
64 65 2.386661 ACTGGATAAGAGGTTGCACG 57.613 50.000 0.00 0.00 0.00 5.34
67 68 3.017442 GGGAAACTGGATAAGAGGTTGC 58.983 50.000 0.00 0.00 0.00 4.17
71 72 2.500098 TGTCGGGAAACTGGATAAGAGG 59.500 50.000 0.00 0.00 37.31 3.69
73 74 3.437213 TCTGTCGGGAAACTGGATAAGA 58.563 45.455 0.00 0.00 37.31 2.10
74 75 3.887621 TCTGTCGGGAAACTGGATAAG 57.112 47.619 0.00 0.00 37.31 1.73
76 77 4.098960 GTGTATCTGTCGGGAAACTGGATA 59.901 45.833 0.00 0.00 37.31 2.59
86 87 2.095853 GCAAATGTGTGTATCTGTCGGG 59.904 50.000 0.00 0.00 0.00 5.14
89 90 3.426695 GGCAGCAAATGTGTGTATCTGTC 60.427 47.826 0.00 0.00 0.00 3.51
95 97 0.536233 ACGGGCAGCAAATGTGTGTA 60.536 50.000 0.00 0.00 0.00 2.90
109 111 0.455410 TGAAGCAAATGCATACGGGC 59.545 50.000 8.28 1.37 45.16 6.13
116 118 3.958147 AGGATGATGATGAAGCAAATGCA 59.042 39.130 8.28 0.00 45.16 3.96
119 121 7.664731 CCTTAGTAGGATGATGATGAAGCAAAT 59.335 37.037 0.00 0.00 45.05 2.32
120 122 6.994496 CCTTAGTAGGATGATGATGAAGCAAA 59.006 38.462 0.00 0.00 45.05 3.68
141 146 1.202592 TGCGCACAACTTCAGACCTTA 60.203 47.619 5.66 0.00 0.00 2.69
146 151 2.231235 TCTATCTGCGCACAACTTCAGA 59.769 45.455 5.66 0.00 39.54 3.27
159 164 1.201921 CCGCAACACGTTTCTATCTGC 60.202 52.381 0.00 0.00 41.42 4.26
165 170 2.830285 GCACCCGCAACACGTTTCT 61.830 57.895 0.00 0.00 41.42 2.52
166 171 2.353030 GCACCCGCAACACGTTTC 60.353 61.111 0.00 0.00 41.42 2.78
177 182 2.099446 CCATTTAACGCGCACCCG 59.901 61.111 5.73 0.00 37.57 5.28
179 184 1.070471 CAAGCCATTTAACGCGCACC 61.070 55.000 5.73 0.00 0.00 5.01
181 186 0.808125 ATCAAGCCATTTAACGCGCA 59.192 45.000 5.73 0.00 0.00 6.09
183 188 1.400142 TCCATCAAGCCATTTAACGCG 59.600 47.619 3.53 3.53 0.00 6.01
184 189 3.502191 TTCCATCAAGCCATTTAACGC 57.498 42.857 0.00 0.00 0.00 4.84
185 190 3.851403 CGTTTCCATCAAGCCATTTAACG 59.149 43.478 0.00 0.00 0.00 3.18
186 191 4.621034 CACGTTTCCATCAAGCCATTTAAC 59.379 41.667 0.00 0.00 0.00 2.01
201 219 1.705256 TATCGAGCACACACGTTTCC 58.295 50.000 0.00 0.00 0.00 3.13
227 247 5.005203 CGAAAATTGCAGTGCACAAAGTAAA 59.995 36.000 19.58 0.00 38.71 2.01
228 248 4.502282 CGAAAATTGCAGTGCACAAAGTAA 59.498 37.500 19.58 14.02 38.71 2.24
233 253 2.159324 TGACGAAAATTGCAGTGCACAA 60.159 40.909 19.58 4.24 38.71 3.33
234 254 1.403323 TGACGAAAATTGCAGTGCACA 59.597 42.857 19.58 9.87 38.71 4.57
249 269 1.879380 CAAACAAAGAGGCCATGACGA 59.121 47.619 5.01 0.00 0.00 4.20
300 320 3.434637 CTCACCGTTTCCAACAACAAAG 58.565 45.455 0.00 0.00 0.00 2.77
355 377 1.015085 TACGACCGCATGGAAAACCG 61.015 55.000 0.00 0.00 39.21 4.44
364 386 0.179084 CCAACCTCATACGACCGCAT 60.179 55.000 0.00 0.00 0.00 4.73
380 413 4.680237 CAGCGCCTCACCGACCAA 62.680 66.667 2.29 0.00 0.00 3.67
385 418 4.899239 GGATCCAGCGCCTCACCG 62.899 72.222 6.95 0.00 0.00 4.94
403 436 3.511146 TGGAATCTTTTTGTGCCTGGATC 59.489 43.478 0.00 0.00 0.00 3.36
455 488 3.487544 GCTACAAAATCCAAGATGTCGCC 60.488 47.826 0.00 0.00 30.77 5.54
463 500 4.016444 TGGCTTAGGCTACAAAATCCAAG 58.984 43.478 7.43 0.00 38.73 3.61
474 511 0.984230 AACTGTGCTGGCTTAGGCTA 59.016 50.000 7.43 0.00 38.73 3.93
517 564 2.100197 GGCTGTGGGGGTAATTTTCTC 58.900 52.381 0.00 0.00 0.00 2.87
518 565 1.431243 TGGCTGTGGGGGTAATTTTCT 59.569 47.619 0.00 0.00 0.00 2.52
519 566 1.548719 GTGGCTGTGGGGGTAATTTTC 59.451 52.381 0.00 0.00 0.00 2.29
520 567 1.133009 TGTGGCTGTGGGGGTAATTTT 60.133 47.619 0.00 0.00 0.00 1.82
523 570 0.039618 CTTGTGGCTGTGGGGGTAAT 59.960 55.000 0.00 0.00 0.00 1.89
536 583 1.771565 ATGATGATGTGGCCTTGTGG 58.228 50.000 3.32 0.00 0.00 4.17
537 584 4.987408 TTTATGATGATGTGGCCTTGTG 57.013 40.909 3.32 0.00 0.00 3.33
538 585 6.238731 CGTTATTTATGATGATGTGGCCTTGT 60.239 38.462 3.32 0.00 0.00 3.16
539 586 6.144854 CGTTATTTATGATGATGTGGCCTTG 58.855 40.000 3.32 0.00 0.00 3.61
540 587 5.241506 CCGTTATTTATGATGATGTGGCCTT 59.758 40.000 3.32 0.00 0.00 4.35
541 588 4.761739 CCGTTATTTATGATGATGTGGCCT 59.238 41.667 3.32 0.00 0.00 5.19
542 589 4.759693 TCCGTTATTTATGATGATGTGGCC 59.240 41.667 0.00 0.00 0.00 5.36
543 590 5.334879 GGTCCGTTATTTATGATGATGTGGC 60.335 44.000 0.00 0.00 0.00 5.01
544 591 5.181245 GGGTCCGTTATTTATGATGATGTGG 59.819 44.000 0.00 0.00 0.00 4.17
545 592 5.181245 GGGGTCCGTTATTTATGATGATGTG 59.819 44.000 0.00 0.00 0.00 3.21
546 593 5.313712 GGGGTCCGTTATTTATGATGATGT 58.686 41.667 0.00 0.00 0.00 3.06
547 594 4.391830 CGGGGTCCGTTATTTATGATGATG 59.608 45.833 0.00 0.00 42.73 3.07
548 595 4.575885 CGGGGTCCGTTATTTATGATGAT 58.424 43.478 0.00 0.00 42.73 2.45
549 596 3.997762 CGGGGTCCGTTATTTATGATGA 58.002 45.455 0.00 0.00 42.73 2.92
597 652 1.787012 GCTGTGGGCAAACAATCTTG 58.213 50.000 0.00 0.00 41.35 3.02
615 670 4.687215 TCCTGTGCCGTGCTCTGC 62.687 66.667 0.00 0.00 0.00 4.26
616 671 2.740055 GTCCTGTGCCGTGCTCTG 60.740 66.667 0.00 0.00 0.00 3.35
617 672 4.008933 GGTCCTGTGCCGTGCTCT 62.009 66.667 0.00 0.00 0.00 4.09
660 715 2.700773 GCCTGTTCCATCGGCCAAC 61.701 63.158 2.24 0.00 37.86 3.77
663 718 2.825836 CTGCCTGTTCCATCGGCC 60.826 66.667 0.00 0.00 43.12 6.13
669 734 1.220749 GGTATCGCTGCCTGTTCCA 59.779 57.895 0.00 0.00 0.00 3.53
705 770 3.170672 CGAGGGCCATGGGATCCA 61.171 66.667 15.13 0.00 38.19 3.41
818 899 0.315220 GCTCGTGCTCGTACGTAGAG 60.315 60.000 16.05 16.64 44.06 2.43
819 900 1.712081 GCTCGTGCTCGTACGTAGA 59.288 57.895 16.05 7.76 44.06 2.59
820 901 1.647577 CGCTCGTGCTCGTACGTAG 60.648 63.158 16.05 12.17 44.06 3.51
838 919 0.110644 CTTGGTTTTCTCGTGCTCGC 60.111 55.000 2.69 0.00 36.96 5.03
984 1074 1.870055 TACTGAAGTGGACGTCCGGC 61.870 60.000 28.70 22.87 39.43 6.13
985 1075 0.170561 CTACTGAAGTGGACGTCCGG 59.829 60.000 28.70 15.84 39.43 5.14
990 1080 0.039437 ACGTGCTACTGAAGTGGACG 60.039 55.000 18.00 18.00 41.95 4.79
1010 1100 1.654954 CTACCCGAGCTGCACGTACT 61.655 60.000 17.58 2.92 0.00 2.73
1111 1202 2.556287 GCACGCTCAAAACCTCGG 59.444 61.111 0.00 0.00 0.00 4.63
1112 1203 2.170985 CGCACGCTCAAAACCTCG 59.829 61.111 0.00 0.00 0.00 4.63
1113 1204 2.127232 GCGCACGCTCAAAACCTC 60.127 61.111 7.96 0.00 38.26 3.85
1114 1205 4.012895 CGCGCACGCTCAAAACCT 62.013 61.111 13.70 0.00 39.32 3.50
1155 1246 3.716539 ATGGTCATCGGTGCCGTCG 62.717 63.158 10.60 3.40 40.74 5.12
1156 1247 1.883084 GATGGTCATCGGTGCCGTC 60.883 63.158 13.29 13.29 40.74 4.79
1157 1248 2.186903 GATGGTCATCGGTGCCGT 59.813 61.111 10.60 3.86 40.74 5.68
1165 1256 1.269309 CGGAGGAAGTCGATGGTCATC 60.269 57.143 1.08 1.08 34.56 2.92
1282 1373 3.005898 CGCCGACATTGACATCCG 58.994 61.111 0.00 0.00 0.00 4.18
1316 1415 2.668280 GCTCCGCAACCTGAACGAC 61.668 63.158 0.00 0.00 0.00 4.34
1486 1591 2.126071 GTAGCGTCGCTTGGCTCA 60.126 61.111 26.96 2.45 40.44 4.26
1493 1598 4.436998 GGTGGCTGTAGCGTCGCT 62.437 66.667 25.08 25.08 43.26 4.93
1538 1643 2.948720 GCTCCTGTCCCTGCTCGTT 61.949 63.158 0.00 0.00 0.00 3.85
1539 1644 3.386237 GCTCCTGTCCCTGCTCGT 61.386 66.667 0.00 0.00 0.00 4.18
1544 1649 4.463879 CGGCTGCTCCTGTCCCTG 62.464 72.222 0.00 0.00 0.00 4.45
1566 1683 3.775654 CCTCCGCTTCGCCCTTCT 61.776 66.667 0.00 0.00 0.00 2.85
1807 1927 1.593469 CTCATCTACGAGCGAGACGAA 59.407 52.381 0.00 0.00 34.70 3.85
1816 1936 7.909267 TCAATGTTTAATTGCTCATCTACGAG 58.091 34.615 0.00 0.00 36.02 4.18
1842 1962 1.203994 ACAAGAATGGCATTGCAGAGC 59.796 47.619 19.07 1.54 0.00 4.09
1866 1986 6.646653 CAGAAGTGCAGAGTGTCAAATAGTAA 59.353 38.462 0.00 0.00 0.00 2.24
1867 1987 6.159293 CAGAAGTGCAGAGTGTCAAATAGTA 58.841 40.000 0.00 0.00 0.00 1.82
1869 1989 4.993584 ACAGAAGTGCAGAGTGTCAAATAG 59.006 41.667 0.00 0.00 0.00 1.73
1870 1990 4.960938 ACAGAAGTGCAGAGTGTCAAATA 58.039 39.130 0.00 0.00 0.00 1.40
1871 1991 3.813443 ACAGAAGTGCAGAGTGTCAAAT 58.187 40.909 0.00 0.00 0.00 2.32
1880 2000 1.413812 TGAGCAGAACAGAAGTGCAGA 59.586 47.619 0.00 0.00 39.80 4.26
1923 2043 4.477975 CGACTCTCCGCGACCACC 62.478 72.222 8.23 0.00 0.00 4.61
2120 2240 1.003442 TCCTGGGCCTCATACTGCT 59.997 57.895 4.53 0.00 0.00 4.24
2134 2254 0.967887 TCCGTCTGAGCCTTCTCCTG 60.968 60.000 0.00 0.00 38.58 3.86
2190 2310 1.591619 GCCAAAATACGTACCTCGCTC 59.408 52.381 0.00 0.00 44.19 5.03
2192 2312 1.361793 TGCCAAAATACGTACCTCGC 58.638 50.000 0.00 0.00 44.19 5.03
2194 2314 2.995258 TCGTTGCCAAAATACGTACCTC 59.005 45.455 0.00 0.00 36.70 3.85
2214 2375 5.034152 TGTTTTGACAGAGCAAACGAATTC 58.966 37.500 0.00 0.00 37.48 2.17
2220 2381 2.450160 CCGTGTTTTGACAGAGCAAAC 58.550 47.619 0.00 0.00 37.48 2.93
2225 2386 1.528586 CTCTGCCGTGTTTTGACAGAG 59.471 52.381 4.13 4.13 45.85 3.35
2236 2397 0.458543 ATGACGCTAACTCTGCCGTG 60.459 55.000 0.00 0.00 0.00 4.94
2251 2415 0.813184 CAGGCCACACCATTCATGAC 59.187 55.000 5.01 0.00 43.14 3.06
2357 2521 3.006247 TGCAGTTTGGAAAGCAAAAACC 58.994 40.909 0.00 0.00 34.96 3.27
2358 2522 3.063861 CCTGCAGTTTGGAAAGCAAAAAC 59.936 43.478 13.81 0.00 36.44 2.43
2406 2570 2.315176 TCACCACCTGATTTGGTTTGG 58.685 47.619 0.00 0.00 45.62 3.28
2409 2573 3.181466 GCTTTTCACCACCTGATTTGGTT 60.181 43.478 0.00 0.00 45.62 3.67
2412 2576 3.305608 GGAGCTTTTCACCACCTGATTTG 60.306 47.826 0.00 0.00 0.00 2.32
2430 2597 1.446272 CGTCCTGGAAACGAGGAGC 60.446 63.158 0.00 0.00 42.62 4.70
2445 2612 0.179240 CTGATGCGTTCTTGTGCGTC 60.179 55.000 0.00 0.00 45.23 5.19
2446 2613 0.599991 TCTGATGCGTTCTTGTGCGT 60.600 50.000 0.00 0.00 0.00 5.24
2448 2615 1.800586 TCTTCTGATGCGTTCTTGTGC 59.199 47.619 0.00 0.00 0.00 4.57
2450 2617 4.083110 CCATTTCTTCTGATGCGTTCTTGT 60.083 41.667 0.00 0.00 0.00 3.16
2481 2648 0.887836 CTTGTGCAGAGAAGGCAGCA 60.888 55.000 0.00 0.00 42.85 4.41
2488 2655 1.271054 GGAGCTTCCTTGTGCAGAGAA 60.271 52.381 0.00 0.00 32.53 2.87
2490 2657 0.035881 TGGAGCTTCCTTGTGCAGAG 59.964 55.000 0.00 0.00 37.46 3.35
2493 2660 1.601759 GCTGGAGCTTCCTTGTGCA 60.602 57.895 0.00 0.00 37.46 4.57
2540 2707 1.794222 CCGTCTGAATTTGCGTCCC 59.206 57.895 0.00 0.00 0.00 4.46
2541 2708 1.134694 GCCGTCTGAATTTGCGTCC 59.865 57.895 0.00 0.00 0.00 4.79
2550 2726 2.568612 CTCGAGCAGCCGTCTGAA 59.431 61.111 0.00 0.00 42.95 3.02
2570 2746 1.288127 GACGCGGAGTTGGTGTAGT 59.712 57.895 12.47 0.00 0.00 2.73
2571 2747 1.800315 CGACGCGGAGTTGGTGTAG 60.800 63.158 12.47 0.00 0.00 2.74
2605 2781 2.514592 CGATGGCGCCTTGATGGT 60.515 61.111 29.70 4.43 38.35 3.55
2608 2784 2.109799 CTCCGATGGCGCCTTGAT 59.890 61.111 29.70 13.50 35.83 2.57
2673 2849 2.325857 GCGTGATCATGGAAGCGC 59.674 61.111 16.59 13.08 38.15 5.92
2682 2858 0.800683 GATTGTCGTCGGCGTGATCA 60.801 55.000 10.18 2.17 39.49 2.92
2685 2861 1.731613 GTGATTGTCGTCGGCGTGA 60.732 57.895 10.18 3.31 39.49 4.35
2700 2876 2.337170 ACGTCGATGTTGCCGTGA 59.663 55.556 3.92 0.00 31.43 4.35
2865 3065 1.201647 ACGTGTTCATCCCTGTACGAG 59.798 52.381 0.00 0.00 35.69 4.18
2960 3160 1.533756 CGGTCCAACAGTTTGCACTTG 60.534 52.381 0.00 0.00 0.00 3.16
2964 3164 0.950836 CATCGGTCCAACAGTTTGCA 59.049 50.000 0.00 0.00 0.00 4.08
2994 3194 3.818121 TTTCTCCGTGGGTGCCGTG 62.818 63.158 0.00 0.00 0.00 4.94
2997 3197 2.671963 GGTTTCTCCGTGGGTGCC 60.672 66.667 0.00 0.00 0.00 5.01
3065 3274 0.179134 GACAGGGATCTTCACGTCGG 60.179 60.000 0.00 0.00 0.00 4.79
3120 3350 1.511768 CGTCTCCTCCTTCGGGAAC 59.488 63.158 0.00 0.00 44.53 3.62
3126 3356 2.185608 GGCAGCGTCTCCTCCTTC 59.814 66.667 0.00 0.00 0.00 3.46
3132 3362 0.744414 TAATTGCTGGCAGCGTCTCC 60.744 55.000 32.12 7.78 46.26 3.71
3178 3408 1.093159 GCAGCCTCAACCTCAATCAG 58.907 55.000 0.00 0.00 0.00 2.90
3179 3409 0.694771 AGCAGCCTCAACCTCAATCA 59.305 50.000 0.00 0.00 0.00 2.57
3191 3421 3.295273 TGTCGTGTCGAGCAGCCT 61.295 61.111 0.00 0.00 36.23 4.58
3239 3469 3.704566 AGGATCATACAACTGCTTCGGTA 59.295 43.478 0.00 0.00 0.00 4.02
3241 3471 3.126831 GAGGATCATACAACTGCTTCGG 58.873 50.000 0.00 0.00 33.17 4.30
3297 3545 1.414866 GGATCCCAGAGAGGAAGCCC 61.415 65.000 0.00 0.00 40.04 5.19
3353 3622 0.318441 CAGGTCTGCGTCTCCAAGAA 59.682 55.000 0.00 0.00 0.00 2.52
3366 3635 4.339247 CACTTGTTGGAAATGAACAGGTCT 59.661 41.667 0.00 0.00 40.50 3.85
3381 3677 2.548057 ACGTTACAGCATCCACTTGTTG 59.452 45.455 0.00 0.00 34.39 3.33
3389 3685 2.916111 CAAACACACGTTACAGCATCC 58.084 47.619 0.00 0.00 33.99 3.51
3399 3695 1.024271 AATCAGCAGCAAACACACGT 58.976 45.000 0.00 0.00 0.00 4.49
3411 3707 3.321968 ACACACACTCTAGACAATCAGCA 59.678 43.478 0.00 0.00 0.00 4.41
3413 3709 4.687948 CCAACACACACTCTAGACAATCAG 59.312 45.833 0.00 0.00 0.00 2.90
3424 3724 1.103398 AAGCTGGCCAACACACACTC 61.103 55.000 7.01 0.00 0.00 3.51
3427 3727 0.901124 AAAAAGCTGGCCAACACACA 59.099 45.000 7.01 0.00 0.00 3.72
3437 3737 0.961753 GGACCACAGGAAAAAGCTGG 59.038 55.000 0.00 0.00 0.00 4.85
3439 3739 0.537371 CCGGACCACAGGAAAAAGCT 60.537 55.000 0.00 0.00 33.26 3.74
3477 3781 3.372676 GACAACGCCGCAGAGCATG 62.373 63.158 0.00 0.00 0.00 4.06
3503 3814 4.583073 GGTGATTCCTGTAAACAAACTGGT 59.417 41.667 0.00 0.00 39.01 4.00
3514 3825 2.678786 ACTGCCGGTGATTCCTGTA 58.321 52.632 1.90 0.00 0.00 2.74
3539 3851 4.058721 ACCAAACAAACAAAGGCATCTC 57.941 40.909 0.00 0.00 0.00 2.75
3555 3867 2.156098 GAGGTTTGCACGGATACCAAA 58.844 47.619 1.42 0.00 33.02 3.28
3559 3871 1.702491 GGCGAGGTTTGCACGGATAC 61.702 60.000 0.00 0.00 0.00 2.24
3569 3881 3.444818 TTGGGCTTGGGCGAGGTTT 62.445 57.895 0.00 0.00 39.81 3.27
3583 3895 1.615392 CTTTTCCTGTCTTGCCTTGGG 59.385 52.381 0.00 0.00 0.00 4.12
3584 3896 2.310538 ACTTTTCCTGTCTTGCCTTGG 58.689 47.619 0.00 0.00 0.00 3.61
3585 3897 3.709987 CAACTTTTCCTGTCTTGCCTTG 58.290 45.455 0.00 0.00 0.00 3.61
3586 3898 2.101415 GCAACTTTTCCTGTCTTGCCTT 59.899 45.455 0.00 0.00 32.71 4.35
3587 3899 1.683385 GCAACTTTTCCTGTCTTGCCT 59.317 47.619 0.00 0.00 32.71 4.75
3588 3900 1.408702 TGCAACTTTTCCTGTCTTGCC 59.591 47.619 0.00 0.00 37.09 4.52
3632 3944 1.450312 GCTGCAGGGTCGCACTAAT 60.450 57.895 17.12 0.00 36.86 1.73
3680 3996 0.032678 CCAGACGACAGCACTCAACT 59.967 55.000 0.00 0.00 0.00 3.16
3717 4033 1.831389 CGCACAGACCGTCCAAACAG 61.831 60.000 0.00 0.00 0.00 3.16
3718 4034 1.885388 CGCACAGACCGTCCAAACA 60.885 57.895 0.00 0.00 0.00 2.83
3720 4036 2.280524 CCGCACAGACCGTCCAAA 60.281 61.111 0.00 0.00 0.00 3.28
3767 4086 1.529309 GAGAGAGGATGGGCCAACC 59.471 63.158 24.37 24.37 40.02 3.77
3768 4087 1.144936 CGAGAGAGGATGGGCCAAC 59.855 63.158 11.89 8.12 40.02 3.77
3769 4088 2.066393 CCGAGAGAGGATGGGCCAA 61.066 63.158 11.89 0.00 40.02 4.52
3770 4089 2.444706 CCGAGAGAGGATGGGCCA 60.445 66.667 9.61 9.61 40.02 5.36
3771 4090 3.934962 GCCGAGAGAGGATGGGCC 61.935 72.222 0.00 0.00 35.68 5.80
3802 6283 2.485426 GTGTCATCATGAGTGTTGTGGG 59.515 50.000 0.09 0.00 0.00 4.61
3823 6304 2.591429 TCACGCACTTGGCTGTGG 60.591 61.111 11.75 6.00 42.90 4.17
3824 6305 2.633657 GTCACGCACTTGGCTGTG 59.366 61.111 6.80 6.80 43.54 3.66
3996 6481 2.676076 CAAAAGTTTTCCAGCGATGGG 58.324 47.619 21.53 0.72 0.00 4.00
3999 6484 3.451141 TTGCAAAAGTTTTCCAGCGAT 57.549 38.095 0.00 0.00 0.00 4.58
4009 6494 4.817318 TGGGAAGAGTTTTGCAAAAGTT 57.183 36.364 28.22 19.69 32.00 2.66
4010 6495 4.758688 CTTGGGAAGAGTTTTGCAAAAGT 58.241 39.130 28.01 28.01 34.41 2.66
4011 6496 3.557185 GCTTGGGAAGAGTTTTGCAAAAG 59.443 43.478 24.46 10.00 0.00 2.27
4014 6499 2.362077 GAGCTTGGGAAGAGTTTTGCAA 59.638 45.455 0.00 0.00 0.00 4.08
4015 6500 1.956477 GAGCTTGGGAAGAGTTTTGCA 59.044 47.619 0.00 0.00 0.00 4.08
4016 6501 1.068954 CGAGCTTGGGAAGAGTTTTGC 60.069 52.381 0.00 0.00 0.00 3.68
4017 6502 1.537202 CCGAGCTTGGGAAGAGTTTTG 59.463 52.381 12.81 0.00 0.00 2.44
4020 6505 1.003233 GCCGAGCTTGGGAAGAGTT 60.003 57.895 22.06 0.00 0.00 3.01
4021 6506 2.665603 GCCGAGCTTGGGAAGAGT 59.334 61.111 22.06 0.00 0.00 3.24
4025 6510 4.735132 CGTCGCCGAGCTTGGGAA 62.735 66.667 22.06 0.00 35.63 3.97
4046 6562 1.075226 TCTGGTAGGCTGCCTAGGG 60.075 63.158 28.02 19.29 36.71 3.53
4051 6567 1.965754 CTCCTGTCTGGTAGGCTGCC 61.966 65.000 15.45 15.45 35.23 4.85
4067 6583 1.765314 TCCTTAATCTCAGCAGGCTCC 59.235 52.381 0.00 0.00 0.00 4.70
4076 6592 4.646040 CCACCATTTGCATCCTTAATCTCA 59.354 41.667 0.00 0.00 0.00 3.27
4077 6593 4.646492 ACCACCATTTGCATCCTTAATCTC 59.354 41.667 0.00 0.00 0.00 2.75
4078 6594 4.613437 ACCACCATTTGCATCCTTAATCT 58.387 39.130 0.00 0.00 0.00 2.40
4079 6595 5.221244 GGTACCACCATTTGCATCCTTAATC 60.221 44.000 7.15 0.00 38.42 1.75
4099 6615 2.517609 CCCTAGAGGCAGTGGGTAC 58.482 63.158 0.00 0.00 35.13 3.34
4102 6618 1.694696 GAATACCCTAGAGGCAGTGGG 59.305 57.143 0.00 0.00 44.89 4.61
4103 6619 2.630580 GAGAATACCCTAGAGGCAGTGG 59.369 54.545 0.00 0.00 40.58 4.00
4104 6620 2.630580 GGAGAATACCCTAGAGGCAGTG 59.369 54.545 0.00 0.00 40.58 3.66
4105 6621 2.753507 CGGAGAATACCCTAGAGGCAGT 60.754 54.545 0.00 0.00 40.58 4.40
4106 6622 1.889829 CGGAGAATACCCTAGAGGCAG 59.110 57.143 0.00 0.00 40.58 4.85
4107 6623 1.497716 TCGGAGAATACCCTAGAGGCA 59.502 52.381 0.00 0.00 40.58 4.75
4108 6624 2.289592 TCGGAGAATACCCTAGAGGC 57.710 55.000 0.00 0.00 40.58 4.70
4109 6625 2.892215 GGTTCGGAGAATACCCTAGAGG 59.108 54.545 0.00 0.00 45.90 3.69
4110 6626 3.822167 GAGGTTCGGAGAATACCCTAGAG 59.178 52.174 0.00 0.00 45.90 2.43
4111 6627 3.462579 AGAGGTTCGGAGAATACCCTAGA 59.537 47.826 0.00 0.00 45.90 2.43
4112 6628 3.834938 AGAGGTTCGGAGAATACCCTAG 58.165 50.000 0.00 0.00 45.90 3.02
4113 6629 3.967467 AGAGGTTCGGAGAATACCCTA 57.033 47.619 0.00 0.00 45.90 3.53
4114 6630 2.850695 AGAGGTTCGGAGAATACCCT 57.149 50.000 0.00 0.00 45.90 4.34
4115 6631 3.532542 CAAAGAGGTTCGGAGAATACCC 58.467 50.000 0.00 0.00 45.90 3.69
4116 6632 3.532542 CCAAAGAGGTTCGGAGAATACC 58.467 50.000 0.00 0.00 45.90 2.73
4157 6673 6.696411 TCAAAAGTTGTGTGACTTTGGAAAT 58.304 32.000 5.37 0.00 46.23 2.17
4224 6740 7.419518 CCTTTTCCAATCTCTCAGCTAGGAATA 60.420 40.741 0.00 0.00 34.06 1.75
4227 6743 4.163078 CCTTTTCCAATCTCTCAGCTAGGA 59.837 45.833 0.00 0.00 0.00 2.94
4300 6816 9.571810 TTGCATACAATATTCTGTGTTGAATTC 57.428 29.630 0.00 0.00 37.73 2.17
4337 6853 4.580167 TGACTTCCAACTTGGTCAAATCAG 59.420 41.667 7.72 0.00 39.03 2.90
4338 6854 4.531854 TGACTTCCAACTTGGTCAAATCA 58.468 39.130 7.72 0.00 39.03 2.57
4391 6907 3.450115 GGGACTCCGACCGACCTG 61.450 72.222 0.00 0.00 0.00 4.00
4398 6914 1.677637 CTAAGCCTGGGGACTCCGAC 61.678 65.000 0.00 0.00 38.76 4.79
4405 6921 1.276622 GTCTGAACTAAGCCTGGGGA 58.723 55.000 0.00 0.00 0.00 4.81
4406 6922 0.253327 GGTCTGAACTAAGCCTGGGG 59.747 60.000 0.00 0.00 0.00 4.96
4430 6946 4.441792 TGATATGTATATGTGGATGCGGC 58.558 43.478 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.