Multiple sequence alignment - TraesCS4A01G072400

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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 TraesCS4A01G072400 chr4A 100.000 4668 0 0 1 4668 70316011 70311344 0.000000e+00 8621.0
1 TraesCS4A01G072400 chr4A 85.222 203 25 5 4 201 519575481 519575683 2.200000e-48 204.0
2 TraesCS4A01G072400 chr4A 93.617 47 3 0 3011 3057 70312968 70312922 2.330000e-08 71.3
3 TraesCS4A01G072400 chr4A 93.617 47 3 0 3044 3090 70313001 70312955 2.330000e-08 71.3
4 TraesCS4A01G072400 chr4D 92.984 1411 67 15 3044 4432 388929541 388928141 0.000000e+00 2028.0
5 TraesCS4A01G072400 chr4D 90.708 1539 90 23 1548 3057 388931009 388929495 0.000000e+00 2001.0
6 TraesCS4A01G072400 chr4D 94.031 1089 56 8 414 1497 388932192 388931108 0.000000e+00 1642.0
7 TraesCS4A01G072400 chr4D 90.027 371 30 5 1 368 388939465 388939099 1.520000e-129 473.0
8 TraesCS4A01G072400 chr4D 88.949 371 29 10 1 368 388934195 388933834 9.210000e-122 448.0
9 TraesCS4A01G072400 chr4D 90.116 172 11 1 4497 4668 388928112 388927947 7.860000e-53 219.0
10 TraesCS4A01G072400 chr4B 94.658 1142 58 3 1917 3057 477229244 477228105 0.000000e+00 1768.0
11 TraesCS4A01G072400 chr4B 93.088 1085 59 8 417 1497 477230763 477229691 0.000000e+00 1574.0
12 TraesCS4A01G072400 chr4B 93.182 924 41 8 3044 3946 477228151 477227229 0.000000e+00 1338.0
13 TraesCS4A01G072400 chr4B 93.869 473 22 7 3962 4432 477227164 477226697 0.000000e+00 706.0
14 TraesCS4A01G072400 chr4B 93.976 166 9 1 4503 4668 477226663 477226499 2.790000e-62 250.0
15 TraesCS4A01G072400 chr4B 80.328 366 33 17 3 368 477232975 477232649 1.680000e-59 241.0
16 TraesCS4A01G072400 chr2D 89.011 182 15 4 9 185 22200977 22200796 2.190000e-53 220.0
17 TraesCS4A01G072400 chr7B 87.432 183 17 4 9 185 261985923 261986105 6.120000e-49 206.0
18 TraesCS4A01G072400 chr7D 85.938 192 24 3 10 199 75800853 75800663 7.920000e-48 202.0
19 TraesCS4A01G072400 chr5D 86.316 190 21 4 9 193 443898319 443898130 7.920000e-48 202.0
20 TraesCS4A01G072400 chr1A 84.286 210 26 6 3 208 404628963 404629169 1.020000e-46 198.0
21 TraesCS4A01G072400 chr2A 84.314 204 26 6 4 204 739854792 739854992 1.330000e-45 195.0


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 TraesCS4A01G072400 chr4A 70311344 70316011 4667 True 2921.2 8621 95.744667 1 4668 3 chr4A.!!$R1 4667
1 TraesCS4A01G072400 chr4D 388927947 388934195 6248 True 1267.6 2028 91.357600 1 4668 5 chr4D.!!$R2 4667
2 TraesCS4A01G072400 chr4B 477226499 477232975 6476 True 979.5 1768 91.516833 3 4668 6 chr4B.!!$R1 4665

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
660 2533 0.536687 CTCCGTGTAGAGGCCCGATA 60.537 60.0 0.00 0.00 0.00 2.92 F
1202 3076 0.318107 GATTTGGGAATCGCATGCGG 60.318 55.0 37.18 20.26 40.25 5.69 F
3054 5016 0.036388 GTCGACATTCCTCCTGCCAA 60.036 55.0 11.55 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 4590 0.453793 TTGTTGGACAGGTTGTTGCG 59.546 50.0 0.00 0.00 0.0 4.85 R
3068 5030 0.036388 TTGGCAGGAGGAATGTCGAC 60.036 55.0 9.11 9.11 0.0 4.20 R
4426 6496 0.027194 CATTCTCGTGCCGATTGCTG 59.973 55.0 0.00 0.00 42.0 4.41 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
64 65 8.236585 TGCCATAAGTATTGCACATCTAAATT 57.763 30.769 0.00 0.00 30.49 1.82
102 103 1.472552 CGCGGAGATTCATGTGGGTAA 60.473 52.381 0.00 0.00 0.00 2.85
103 104 1.940613 GCGGAGATTCATGTGGGTAAC 59.059 52.381 0.00 0.00 0.00 2.50
120 121 8.158132 TGTGGGTAACTTTTTCCTTTTCTTTTT 58.842 29.630 0.00 0.00 0.00 1.94
172 174 5.567037 TGCAATAACTAGGGCACATCTAT 57.433 39.130 0.00 0.00 0.00 1.98
195 197 5.581126 ATGTGCTCTAGAGAGACTCTTTG 57.419 43.478 24.24 0.55 44.74 2.77
196 198 4.402829 TGTGCTCTAGAGAGACTCTTTGT 58.597 43.478 24.24 0.00 44.74 2.83
269 271 8.780846 AAATATGAAGTTTCGTACCACACATA 57.219 30.769 0.00 0.00 31.98 2.29
271 273 4.562082 TGAAGTTTCGTACCACACATAGG 58.438 43.478 0.00 0.00 0.00 2.57
272 274 2.968675 AGTTTCGTACCACACATAGGC 58.031 47.619 0.00 0.00 0.00 3.93
274 276 3.007614 AGTTTCGTACCACACATAGGCTT 59.992 43.478 0.00 0.00 0.00 4.35
275 277 3.688694 TTCGTACCACACATAGGCTTT 57.311 42.857 0.00 0.00 0.00 3.51
276 278 3.688694 TCGTACCACACATAGGCTTTT 57.311 42.857 0.00 0.00 0.00 2.27
277 279 4.010667 TCGTACCACACATAGGCTTTTT 57.989 40.909 0.00 0.00 0.00 1.94
364 366 4.548451 TGGCAATTTTACCATGCATGAA 57.452 36.364 28.31 14.29 41.80 2.57
379 1288 8.632679 ACCATGCATGAATTTAACATAAGTAGG 58.367 33.333 28.31 6.86 0.00 3.18
380 1289 7.596248 CCATGCATGAATTTAACATAAGTAGGC 59.404 37.037 28.31 0.00 0.00 3.93
382 1291 7.706159 TGCATGAATTTAACATAAGTAGGCAG 58.294 34.615 0.00 0.00 0.00 4.85
384 1293 7.645340 GCATGAATTTAACATAAGTAGGCAGTG 59.355 37.037 0.00 0.00 0.00 3.66
385 1294 8.892723 CATGAATTTAACATAAGTAGGCAGTGA 58.107 33.333 0.00 0.00 0.00 3.41
387 1296 9.461312 TGAATTTAACATAAGTAGGCAGTGAAT 57.539 29.630 0.00 0.00 0.00 2.57
389 1298 9.686683 AATTTAACATAAGTAGGCAGTGAATCT 57.313 29.630 0.00 0.00 0.00 2.40
390 1299 8.492673 TTTAACATAAGTAGGCAGTGAATCTG 57.507 34.615 0.00 0.00 46.12 2.90
391 1300 5.939764 ACATAAGTAGGCAGTGAATCTGA 57.060 39.130 0.00 0.00 46.27 3.27
392 1301 6.491714 ACATAAGTAGGCAGTGAATCTGAT 57.508 37.500 0.00 0.00 46.27 2.90
394 1303 8.023021 ACATAAGTAGGCAGTGAATCTGATAA 57.977 34.615 0.00 0.00 46.27 1.75
396 1305 9.499479 CATAAGTAGGCAGTGAATCTGATAATT 57.501 33.333 0.00 0.00 46.27 1.40
398 1307 8.814038 AAGTAGGCAGTGAATCTGATAATTTT 57.186 30.769 0.00 0.00 46.27 1.82
399 1308 9.905713 AAGTAGGCAGTGAATCTGATAATTTTA 57.094 29.630 0.00 0.00 46.27 1.52
400 1309 9.905713 AGTAGGCAGTGAATCTGATAATTTTAA 57.094 29.630 0.00 0.00 46.27 1.52
401 1310 9.937175 GTAGGCAGTGAATCTGATAATTTTAAC 57.063 33.333 0.00 0.00 46.27 2.01
402 1311 8.000780 AGGCAGTGAATCTGATAATTTTAACC 57.999 34.615 0.00 0.00 46.27 2.85
403 1312 7.615365 AGGCAGTGAATCTGATAATTTTAACCA 59.385 33.333 0.00 0.00 46.27 3.67
404 1313 8.416329 GGCAGTGAATCTGATAATTTTAACCAT 58.584 33.333 0.00 0.00 46.27 3.55
660 2533 0.536687 CTCCGTGTAGAGGCCCGATA 60.537 60.000 0.00 0.00 0.00 2.92
906 2779 1.003866 CCTCCCGCGAATCGAAATTTC 60.004 52.381 8.23 8.20 41.67 2.17
938 2812 2.766651 TCGATTAGGGCGGGCCTT 60.767 61.111 29.24 11.92 36.10 4.35
1155 3029 1.067060 GTGTTCTTGCCTGTTGGTTCC 59.933 52.381 0.00 0.00 35.27 3.62
1202 3076 0.318107 GATTTGGGAATCGCATGCGG 60.318 55.000 37.18 20.26 40.25 5.69
1267 3141 2.427506 CTGTTTCTGCTGACCTAACCC 58.572 52.381 0.00 0.00 0.00 4.11
1331 3205 7.254084 GCTTAAATTGGAAATAACCTGAATGCG 60.254 37.037 0.00 0.00 0.00 4.73
1340 3214 2.399396 ACCTGAATGCGAACAAAACG 57.601 45.000 0.00 0.00 0.00 3.60
1368 3242 0.449388 CAGATGCGCCTTCCAGTTTC 59.551 55.000 4.18 0.00 0.00 2.78
1378 3252 4.082787 CGCCTTCCAGTTTCATTGTTACAT 60.083 41.667 0.00 0.00 0.00 2.29
1394 3268 8.623903 CATTGTTACATGCCTACAGTATTTGAT 58.376 33.333 0.00 0.00 0.00 2.57
1395 3269 8.574251 TTGTTACATGCCTACAGTATTTGATT 57.426 30.769 0.00 0.00 0.00 2.57
1489 3363 9.274206 ACTAAATTCTCTGTGAAAAGTACTTCC 57.726 33.333 8.95 4.87 38.29 3.46
1490 3364 6.787085 AATTCTCTGTGAAAAGTACTTCCG 57.213 37.500 8.95 0.00 38.29 4.30
1491 3365 4.252971 TCTCTGTGAAAAGTACTTCCGG 57.747 45.455 8.95 0.00 0.00 5.14
1492 3366 3.893200 TCTCTGTGAAAAGTACTTCCGGA 59.107 43.478 8.95 0.00 0.00 5.14
1496 3401 4.817517 TGTGAAAAGTACTTCCGGAGATC 58.182 43.478 8.95 0.00 0.00 2.75
1520 3425 6.015856 TCCGTCCAAATTTAGCAATGAGAAAA 60.016 34.615 0.00 0.00 0.00 2.29
1521 3426 6.813152 CCGTCCAAATTTAGCAATGAGAAAAT 59.187 34.615 0.00 0.00 0.00 1.82
1522 3427 7.331687 CCGTCCAAATTTAGCAATGAGAAAATT 59.668 33.333 0.00 0.00 34.00 1.82
1542 3447 7.500629 AAATTCATATTTTCCTGGGCTTTCT 57.499 32.000 0.00 0.00 29.68 2.52
1543 3448 6.721704 ATTCATATTTTCCTGGGCTTTCTC 57.278 37.500 0.00 0.00 0.00 2.87
1544 3449 5.456921 TCATATTTTCCTGGGCTTTCTCT 57.543 39.130 0.00 0.00 0.00 3.10
1545 3450 5.831103 TCATATTTTCCTGGGCTTTCTCTT 58.169 37.500 0.00 0.00 0.00 2.85
1546 3451 5.653769 TCATATTTTCCTGGGCTTTCTCTTG 59.346 40.000 0.00 0.00 0.00 3.02
1555 3481 2.165234 GGGCTTTCTCTTGCTTGGATTC 59.835 50.000 0.00 0.00 0.00 2.52
1562 3488 2.678336 CTCTTGCTTGGATTCGGTTACC 59.322 50.000 0.00 0.00 0.00 2.85
1574 3500 3.420300 TCGGTTACCAGCACCAATTAA 57.580 42.857 1.13 0.00 33.36 1.40
1579 3505 1.627864 ACCAGCACCAATTAACCACC 58.372 50.000 0.00 0.00 0.00 4.61
1609 3535 3.313526 GTGCTCACTTTGTGATGTCACTT 59.686 43.478 13.71 0.00 46.55 3.16
1621 3547 4.997395 GTGATGTCACTTATGTGTGGTTCT 59.003 41.667 8.46 0.00 44.14 3.01
1629 3556 1.094785 ATGTGTGGTTCTATTGGCGC 58.905 50.000 0.00 0.00 0.00 6.53
1661 3588 5.437289 TGTCCTGTTTGCTATCTTGTTTG 57.563 39.130 0.00 0.00 0.00 2.93
1663 3590 5.359576 TGTCCTGTTTGCTATCTTGTTTGTT 59.640 36.000 0.00 0.00 0.00 2.83
1666 3593 7.277760 GTCCTGTTTGCTATCTTGTTTGTTTTT 59.722 33.333 0.00 0.00 0.00 1.94
1667 3594 7.277539 TCCTGTTTGCTATCTTGTTTGTTTTTG 59.722 33.333 0.00 0.00 0.00 2.44
1668 3595 7.064490 CCTGTTTGCTATCTTGTTTGTTTTTGT 59.936 33.333 0.00 0.00 0.00 2.83
1670 3597 8.439286 TGTTTGCTATCTTGTTTGTTTTTGTTC 58.561 29.630 0.00 0.00 0.00 3.18
1672 3599 8.715191 TTGCTATCTTGTTTGTTTTTGTTCAT 57.285 26.923 0.00 0.00 0.00 2.57
1673 3600 8.129161 TGCTATCTTGTTTGTTTTTGTTCATG 57.871 30.769 0.00 0.00 0.00 3.07
1674 3601 7.763528 TGCTATCTTGTTTGTTTTTGTTCATGT 59.236 29.630 0.00 0.00 0.00 3.21
1675 3602 8.057742 GCTATCTTGTTTGTTTTTGTTCATGTG 58.942 33.333 0.00 0.00 0.00 3.21
1676 3603 7.903995 ATCTTGTTTGTTTTTGTTCATGTGT 57.096 28.000 0.00 0.00 0.00 3.72
1677 3604 7.114882 TCTTGTTTGTTTTTGTTCATGTGTG 57.885 32.000 0.00 0.00 0.00 3.82
1687 3614 4.664150 TGTTCATGTGTGTGTAGTCTCA 57.336 40.909 0.00 0.00 0.00 3.27
1700 3627 5.069119 TGTGTAGTCTCACAATCTTGACACT 59.931 40.000 0.00 0.00 43.92 3.55
1716 3643 4.203226 TGACACTTGCCATTTGAGTTGTA 58.797 39.130 0.00 0.00 0.00 2.41
1766 3696 3.126000 GTGGTCTATTTTGCTGTCTCTGC 59.874 47.826 0.00 0.00 0.00 4.26
1778 3708 3.867600 GCTGTCTCTGCTCTGGAATTTGA 60.868 47.826 0.00 0.00 0.00 2.69
1788 3718 7.448161 TCTGCTCTGGAATTTGATGTCTTAAAA 59.552 33.333 0.00 0.00 0.00 1.52
1790 3720 8.587608 TGCTCTGGAATTTGATGTCTTAAAATT 58.412 29.630 0.00 0.00 36.47 1.82
1791 3721 8.866956 GCTCTGGAATTTGATGTCTTAAAATTG 58.133 33.333 0.00 0.00 34.51 2.32
1793 3723 9.912634 TCTGGAATTTGATGTCTTAAAATTGAC 57.087 29.630 0.00 0.00 34.51 3.18
1800 3730 9.748708 TTTGATGTCTTAAAATTGACTTCCTTG 57.251 29.630 0.00 0.00 36.89 3.61
1801 3731 7.370383 TGATGTCTTAAAATTGACTTCCTTGC 58.630 34.615 0.00 0.00 36.89 4.01
1802 3732 6.707440 TGTCTTAAAATTGACTTCCTTGCA 57.293 33.333 0.00 0.00 34.57 4.08
1803 3733 6.738114 TGTCTTAAAATTGACTTCCTTGCAG 58.262 36.000 0.00 0.00 34.57 4.41
1804 3734 5.631096 GTCTTAAAATTGACTTCCTTGCAGC 59.369 40.000 0.00 0.00 0.00 5.25
1825 3755 5.752098 GCACAATTGCTATGTTTTCTGTC 57.248 39.130 5.05 0.00 46.17 3.51
1839 3770 3.827008 TTCTGTCAACTGTTCTCTGCT 57.173 42.857 0.00 0.00 0.00 4.24
1842 3773 1.942657 TGTCAACTGTTCTCTGCTTGC 59.057 47.619 0.00 0.00 0.00 4.01
1846 3781 3.809832 TCAACTGTTCTCTGCTTGCTAAC 59.190 43.478 0.00 0.00 0.00 2.34
1847 3782 3.475566 ACTGTTCTCTGCTTGCTAACA 57.524 42.857 0.00 0.00 0.00 2.41
1848 3783 3.134458 ACTGTTCTCTGCTTGCTAACAC 58.866 45.455 0.00 0.00 0.00 3.32
1863 3798 2.814280 AACACGTCTTCTGGGTAGTG 57.186 50.000 0.00 0.00 35.89 2.74
1864 3799 1.700955 ACACGTCTTCTGGGTAGTGT 58.299 50.000 0.00 0.00 37.91 3.55
1865 3800 1.612463 ACACGTCTTCTGGGTAGTGTC 59.388 52.381 0.00 0.00 38.26 3.67
1866 3801 1.611977 CACGTCTTCTGGGTAGTGTCA 59.388 52.381 0.00 0.00 0.00 3.58
1867 3802 2.231478 CACGTCTTCTGGGTAGTGTCAT 59.769 50.000 0.00 0.00 0.00 3.06
1868 3803 2.897969 ACGTCTTCTGGGTAGTGTCATT 59.102 45.455 0.00 0.00 0.00 2.57
1869 3804 4.082408 CACGTCTTCTGGGTAGTGTCATTA 60.082 45.833 0.00 0.00 0.00 1.90
1870 3805 4.158025 ACGTCTTCTGGGTAGTGTCATTAG 59.842 45.833 0.00 0.00 0.00 1.73
1880 3815 4.868734 GGTAGTGTCATTAGTAGTTGTGCC 59.131 45.833 0.00 0.00 0.00 5.01
1902 3837 5.521372 GCCAATTTTGATGTGCTCTAATTCC 59.479 40.000 0.00 0.00 0.00 3.01
1905 3840 7.820872 CCAATTTTGATGTGCTCTAATTCCTTT 59.179 33.333 0.00 0.00 0.00 3.11
1906 3841 8.653338 CAATTTTGATGTGCTCTAATTCCTTTG 58.347 33.333 0.00 0.00 0.00 2.77
1907 3842 7.523293 TTTTGATGTGCTCTAATTCCTTTGA 57.477 32.000 0.00 0.00 0.00 2.69
1908 3843 6.500684 TTGATGTGCTCTAATTCCTTTGAC 57.499 37.500 0.00 0.00 0.00 3.18
1909 3844 5.809001 TGATGTGCTCTAATTCCTTTGACT 58.191 37.500 0.00 0.00 0.00 3.41
1910 3845 5.877012 TGATGTGCTCTAATTCCTTTGACTC 59.123 40.000 0.00 0.00 0.00 3.36
1911 3846 5.489792 TGTGCTCTAATTCCTTTGACTCT 57.510 39.130 0.00 0.00 0.00 3.24
1912 3847 6.605471 TGTGCTCTAATTCCTTTGACTCTA 57.395 37.500 0.00 0.00 0.00 2.43
1913 3848 6.398918 TGTGCTCTAATTCCTTTGACTCTAC 58.601 40.000 0.00 0.00 0.00 2.59
1975 3934 9.762381 AGGGTACTGAATTATTATTTGTGGAAA 57.238 29.630 0.00 0.00 0.00 3.13
2037 3996 7.390440 ACTTCTGTGTTAGTGCTGCATTATTTA 59.610 33.333 5.27 0.00 0.00 1.40
2174 4133 0.481128 AGAAAGGGAAAGGGCCGAAA 59.519 50.000 0.00 0.00 0.00 3.46
2175 4134 1.133294 AGAAAGGGAAAGGGCCGAAAA 60.133 47.619 0.00 0.00 0.00 2.29
2176 4135 1.272490 GAAAGGGAAAGGGCCGAAAAG 59.728 52.381 0.00 0.00 0.00 2.27
2245 4207 5.099575 GGTGAGACAAAACATTCAAAACGT 58.900 37.500 0.00 0.00 0.00 3.99
2284 4246 2.746362 GCATGAAGATACCAGCATAGCC 59.254 50.000 0.00 0.00 0.00 3.93
2289 4251 1.831652 GATACCAGCATAGCCGGCCT 61.832 60.000 26.15 10.49 0.00 5.19
2316 4278 2.168313 CCAAAACTGCACCCAAAGAACT 59.832 45.455 0.00 0.00 0.00 3.01
2317 4279 3.383185 CCAAAACTGCACCCAAAGAACTA 59.617 43.478 0.00 0.00 0.00 2.24
2323 4285 5.079643 ACTGCACCCAAAGAACTATTTGAT 58.920 37.500 0.91 0.00 41.71 2.57
2362 4324 1.691434 CTCTCAGAAGAGTATGGGGCC 59.309 57.143 0.00 0.00 43.52 5.80
2434 4396 2.480419 CAGTAAGCGAAGAAAGGTGGTG 59.520 50.000 0.00 0.00 0.00 4.17
2476 4438 2.503895 AGAATGGTGAGGCTTTCAGG 57.496 50.000 0.00 0.00 36.21 3.86
2477 4439 0.813821 GAATGGTGAGGCTTTCAGGC 59.186 55.000 0.00 0.00 41.73 4.85
2499 4461 6.723977 AGGCCATATTTTTAGGTTTCTGTTGA 59.276 34.615 5.01 0.00 0.00 3.18
2557 4519 5.247507 TGAATTATGATTTTGCAGGGACG 57.752 39.130 0.00 0.00 0.00 4.79
2590 4552 8.997323 CGCATTAAGATAAAAAGAGATCAGGAT 58.003 33.333 0.00 0.00 0.00 3.24
2607 4569 1.453155 GATTCACCGTCAGCCATGTT 58.547 50.000 0.00 0.00 0.00 2.71
2628 4590 2.844348 TGGATGGTTCTAGGGTTCTTCC 59.156 50.000 0.00 0.00 0.00 3.46
2634 4596 1.344065 TCTAGGGTTCTTCCGCAACA 58.656 50.000 0.00 0.00 37.00 3.33
2729 4691 0.605589 GGTAAAGTCAGCTGCCGGTT 60.606 55.000 9.47 0.00 0.00 4.44
2796 4758 2.225496 TGGATGTAAAACCCCCTGCAAT 60.225 45.455 0.00 0.00 0.00 3.56
2869 4831 1.511850 CAACCACAGCGAAGATCACA 58.488 50.000 0.00 0.00 0.00 3.58
2871 4833 0.320771 ACCACAGCGAAGATCACACC 60.321 55.000 0.00 0.00 0.00 4.16
2882 4844 5.050499 GCGAAGATCACACCAAAGATAGATG 60.050 44.000 0.00 0.00 0.00 2.90
2918 4880 7.921214 CAGCAAAGATCATGCAAAAGATAGATT 59.079 33.333 21.14 0.00 46.22 2.40
2921 4883 8.630917 CAAAGATCATGCAAAAGATAGATTCCT 58.369 33.333 0.00 0.00 0.00 3.36
2929 4891 1.439543 AGATAGATTCCTGGGTGCCC 58.560 55.000 0.00 0.00 0.00 5.36
3043 5005 0.969149 TGGCACAGAGAGTCGACATT 59.031 50.000 19.50 4.76 0.00 2.71
3044 5006 1.067565 TGGCACAGAGAGTCGACATTC 60.068 52.381 19.50 14.24 0.00 2.67
3045 5007 1.634702 GCACAGAGAGTCGACATTCC 58.365 55.000 19.50 3.78 0.00 3.01
3046 5008 1.203523 GCACAGAGAGTCGACATTCCT 59.796 52.381 19.50 8.82 0.00 3.36
3047 5009 2.733858 GCACAGAGAGTCGACATTCCTC 60.734 54.545 19.50 16.72 0.00 3.71
3048 5010 2.096248 ACAGAGAGTCGACATTCCTCC 58.904 52.381 19.50 0.79 0.00 4.30
3049 5011 2.291282 ACAGAGAGTCGACATTCCTCCT 60.291 50.000 19.50 3.04 0.00 3.69
3050 5012 2.098934 CAGAGAGTCGACATTCCTCCTG 59.901 54.545 19.50 11.01 0.00 3.86
3051 5013 0.820871 AGAGTCGACATTCCTCCTGC 59.179 55.000 19.50 0.00 0.00 4.85
3052 5014 0.179097 GAGTCGACATTCCTCCTGCC 60.179 60.000 19.50 0.00 0.00 4.85
3053 5015 0.904865 AGTCGACATTCCTCCTGCCA 60.905 55.000 19.50 0.00 0.00 4.92
3054 5016 0.036388 GTCGACATTCCTCCTGCCAA 60.036 55.000 11.55 0.00 0.00 4.52
3055 5017 0.250234 TCGACATTCCTCCTGCCAAG 59.750 55.000 0.00 0.00 0.00 3.61
3056 5018 0.745845 CGACATTCCTCCTGCCAAGG 60.746 60.000 0.00 0.00 46.06 3.61
3057 5019 1.000396 ACATTCCTCCTGCCAAGGC 60.000 57.895 3.61 3.61 44.11 4.35
3058 5020 2.117156 CATTCCTCCTGCCAAGGCG 61.117 63.158 6.60 1.46 44.11 5.52
3068 5030 2.435586 CCAAGGCGGCACAGAGAG 60.436 66.667 13.08 0.00 0.00 3.20
3069 5031 2.345244 CAAGGCGGCACAGAGAGT 59.655 61.111 13.08 0.00 0.00 3.24
3070 5032 1.739562 CAAGGCGGCACAGAGAGTC 60.740 63.158 13.08 0.00 0.00 3.36
3071 5033 3.288308 AAGGCGGCACAGAGAGTCG 62.288 63.158 13.08 0.00 0.00 4.18
3072 5034 3.749064 GGCGGCACAGAGAGTCGA 61.749 66.667 3.07 0.00 0.00 4.20
3073 5035 2.505118 GCGGCACAGAGAGTCGAC 60.505 66.667 7.70 7.70 0.00 4.20
3074 5036 2.954611 CGGCACAGAGAGTCGACA 59.045 61.111 19.50 0.00 0.00 4.35
3075 5037 1.508545 CGGCACAGAGAGTCGACAT 59.491 57.895 19.50 5.56 0.00 3.06
3116 5078 2.048603 ATTCCTCCTGCAAAGGCGC 61.049 57.895 0.00 0.00 45.35 6.53
3184 5146 0.689623 CTCCTCCACAGAGTTTGCCT 59.310 55.000 0.00 0.00 38.58 4.75
3192 5154 0.031178 CAGAGTTTGCCTGTGTTGCC 59.969 55.000 0.00 0.00 29.96 4.52
3262 5224 2.637025 CCCGTTCTGCACAAACCG 59.363 61.111 2.46 0.00 0.00 4.44
3433 5404 6.556874 AGAAGGAAGAGAAGAAAGAGAGGAAA 59.443 38.462 0.00 0.00 0.00 3.13
3445 5416 5.948742 AAGAGAGGAAATTCCGAGATCTT 57.051 39.130 6.35 11.24 42.75 2.40
3476 5447 1.064389 GGAATCCACCTTCCTTGGAGG 60.064 57.143 0.00 0.00 46.46 4.30
3587 5558 3.451894 GTTTGGCGCCCATGGAGG 61.452 66.667 26.77 5.38 31.53 4.30
3620 5591 1.683385 GGCAACCAAGGGCTATTCATC 59.317 52.381 0.00 0.00 0.00 2.92
4007 6076 2.952714 AGGCACACTGAAAGGCATC 58.047 52.632 0.00 0.00 39.30 3.91
4054 6123 4.234550 TCTCTGTGGGTGGCATATCTATT 58.765 43.478 0.00 0.00 0.00 1.73
4200 6270 3.012518 CAAAGGTCAATCGAAGCTGGAT 58.987 45.455 0.00 0.00 0.00 3.41
4398 6468 2.400158 CGTCGCGTCCTCTTCTCCT 61.400 63.158 5.77 0.00 0.00 3.69
4413 6483 3.840124 TCTCCTCGTAGTATGCTCAGA 57.160 47.619 0.00 0.00 0.00 3.27
4420 6490 3.632145 TCGTAGTATGCTCAGAATCTGCA 59.368 43.478 5.18 1.12 41.13 4.41
4423 6493 4.212143 AGTATGCTCAGAATCTGCAACA 57.788 40.909 5.18 3.90 40.24 3.33
4424 6494 3.937706 AGTATGCTCAGAATCTGCAACAC 59.062 43.478 5.18 4.35 40.24 3.32
4425 6495 2.259266 TGCTCAGAATCTGCAACACA 57.741 45.000 5.18 0.00 33.48 3.72
4426 6496 1.875514 TGCTCAGAATCTGCAACACAC 59.124 47.619 5.18 0.00 33.48 3.82
4427 6497 1.875514 GCTCAGAATCTGCAACACACA 59.124 47.619 5.18 0.00 0.00 3.72
4428 6498 2.095869 GCTCAGAATCTGCAACACACAG 60.096 50.000 5.18 0.00 36.44 3.66
4432 6502 2.889045 AGAATCTGCAACACACAGCAAT 59.111 40.909 0.00 0.00 40.73 3.56
4434 6504 0.587768 TCTGCAACACACAGCAATCG 59.412 50.000 0.00 0.00 40.73 3.34
4435 6505 0.386352 CTGCAACACACAGCAATCGG 60.386 55.000 0.00 0.00 40.73 4.18
4436 6506 1.730547 GCAACACACAGCAATCGGC 60.731 57.895 0.00 0.00 45.30 5.54
4474 6544 7.502120 TTTTTCCTCTTCTGAAGATGAAGTG 57.498 36.000 26.13 13.67 41.19 3.16
4475 6545 4.199432 TCCTCTTCTGAAGATGAAGTGC 57.801 45.455 19.61 0.00 41.04 4.40
4476 6546 3.055530 TCCTCTTCTGAAGATGAAGTGCC 60.056 47.826 19.61 0.00 41.04 5.01
4477 6547 3.055240 CCTCTTCTGAAGATGAAGTGCCT 60.055 47.826 19.61 0.00 41.04 4.75
4478 6548 3.933955 CTCTTCTGAAGATGAAGTGCCTG 59.066 47.826 19.61 1.61 41.04 4.85
4479 6549 2.105006 TCTGAAGATGAAGTGCCTGC 57.895 50.000 0.00 0.00 0.00 4.85
4480 6550 1.627329 TCTGAAGATGAAGTGCCTGCT 59.373 47.619 0.00 0.00 0.00 4.24
4481 6551 2.833943 TCTGAAGATGAAGTGCCTGCTA 59.166 45.455 0.00 0.00 0.00 3.49
4482 6552 2.935201 CTGAAGATGAAGTGCCTGCTAC 59.065 50.000 0.00 0.00 0.00 3.58
4483 6553 2.568956 TGAAGATGAAGTGCCTGCTACT 59.431 45.455 0.00 0.00 0.00 2.57
4484 6554 2.977772 AGATGAAGTGCCTGCTACTC 57.022 50.000 0.00 0.00 0.00 2.59
4485 6555 2.182827 AGATGAAGTGCCTGCTACTCA 58.817 47.619 0.00 0.00 0.00 3.41
4486 6556 2.168106 AGATGAAGTGCCTGCTACTCAG 59.832 50.000 0.00 0.00 42.49 3.35
4487 6557 1.632589 TGAAGTGCCTGCTACTCAGA 58.367 50.000 0.00 0.00 45.72 3.27
4488 6558 2.182827 TGAAGTGCCTGCTACTCAGAT 58.817 47.619 0.00 0.00 45.72 2.90
4489 6559 3.365472 TGAAGTGCCTGCTACTCAGATA 58.635 45.455 0.00 0.00 45.72 1.98
4490 6560 3.382865 TGAAGTGCCTGCTACTCAGATAG 59.617 47.826 0.00 0.00 45.72 2.08
4491 6561 3.304911 AGTGCCTGCTACTCAGATAGA 57.695 47.619 0.00 0.00 45.72 1.98
4536 6606 2.757868 TCTGAAGAAGAGCCTGCTACTC 59.242 50.000 0.00 0.00 0.00 2.59
4537 6607 2.495270 CTGAAGAAGAGCCTGCTACTCA 59.505 50.000 0.00 0.00 36.58 3.41
4538 6608 2.232452 TGAAGAAGAGCCTGCTACTCAC 59.768 50.000 0.00 0.00 36.58 3.51
4539 6609 2.230130 AGAAGAGCCTGCTACTCACT 57.770 50.000 0.00 1.39 36.58 3.41
4540 6610 3.374042 AGAAGAGCCTGCTACTCACTA 57.626 47.619 0.00 0.00 36.58 2.74
4541 6611 3.702792 AGAAGAGCCTGCTACTCACTAA 58.297 45.455 0.00 0.00 36.58 2.24
4575 6651 1.982395 CTGCGATATCGGGGGCCTA 60.982 63.158 25.51 0.00 40.23 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.277423 TCCGCGTAAGATCAATGACATAGA 59.723 41.667 4.92 0.00 43.02 1.98
127 129 5.172232 CACATCTAAGTGACTAAATCGAGCG 59.828 44.000 0.00 0.00 42.05 5.03
131 133 6.647212 TTGCACATCTAAGTGACTAAATCG 57.353 37.500 0.00 0.00 42.05 3.34
172 174 6.184068 ACAAAGAGTCTCTCTAGAGCACATA 58.816 40.000 15.35 0.00 40.28 2.29
364 366 9.113838 CAGATTCACTGCCTACTTATGTTAAAT 57.886 33.333 0.00 0.00 39.86 1.40
379 1288 9.455847 GATGGTTAAAATTATCAGATTCACTGC 57.544 33.333 0.00 0.00 45.38 4.40
446 2319 1.367195 GAAACGTGTTCGCGTGGTG 60.367 57.895 11.96 0.00 45.00 4.17
447 2320 2.862776 CGAAACGTGTTCGCGTGGT 61.863 57.895 11.96 3.93 45.00 4.16
625 2498 2.754658 AGTCGCTGACGGGTAGGG 60.755 66.667 3.62 0.00 40.63 3.53
628 2501 3.129502 CGGAGTCGCTGACGGGTA 61.130 66.667 3.62 0.00 40.63 3.69
710 2583 2.789491 GGCGGTATATATAGCCGGAC 57.211 55.000 23.38 9.97 45.02 4.79
886 2759 1.003866 GAAATTTCGATTCGCGGGAGG 60.004 52.381 6.13 0.00 41.33 4.30
887 2760 1.003866 GGAAATTTCGATTCGCGGGAG 60.004 52.381 6.13 0.00 41.33 4.30
938 2812 3.932580 AATCAAGAGCGCGACGGCA 62.933 57.895 12.10 0.00 39.92 5.69
947 2821 1.657822 GAACCCTCGGAATCAAGAGC 58.342 55.000 0.43 0.00 33.39 4.09
1073 2947 2.404995 ACCTTAGCGGTCGTCTCCG 61.405 63.158 10.81 10.81 44.93 4.63
1155 3029 2.274437 CACACCCAACAGATCTGATCG 58.726 52.381 29.27 15.32 0.00 3.69
1331 3205 2.933906 TCTGACAGACCACGTTTTGTTC 59.066 45.455 0.00 0.00 0.00 3.18
1340 3214 2.103042 GGCGCATCTGACAGACCAC 61.103 63.158 10.83 0.00 0.00 4.16
1368 3242 7.984391 TCAAATACTGTAGGCATGTAACAATG 58.016 34.615 0.00 0.00 0.00 2.82
1378 3252 8.523915 AATCAATCAATCAAATACTGTAGGCA 57.476 30.769 0.00 0.00 0.00 4.75
1490 3364 3.541632 TGCTAAATTTGGACGGATCTCC 58.458 45.455 5.63 0.00 0.00 3.71
1491 3365 5.296780 TCATTGCTAAATTTGGACGGATCTC 59.703 40.000 5.63 0.00 0.00 2.75
1492 3366 5.192927 TCATTGCTAAATTTGGACGGATCT 58.807 37.500 5.63 0.00 0.00 2.75
1496 3401 4.963276 TCTCATTGCTAAATTTGGACGG 57.037 40.909 5.63 0.00 0.00 4.79
1498 3403 9.206870 TGAATTTTCTCATTGCTAAATTTGGAC 57.793 29.630 5.63 0.00 32.14 4.02
1520 3425 6.438620 AGAGAAAGCCCAGGAAAATATGAAT 58.561 36.000 0.00 0.00 0.00 2.57
1521 3426 5.831103 AGAGAAAGCCCAGGAAAATATGAA 58.169 37.500 0.00 0.00 0.00 2.57
1522 3427 5.456921 AGAGAAAGCCCAGGAAAATATGA 57.543 39.130 0.00 0.00 0.00 2.15
1527 3432 1.963515 GCAAGAGAAAGCCCAGGAAAA 59.036 47.619 0.00 0.00 0.00 2.29
1536 3441 2.159462 CCGAATCCAAGCAAGAGAAAGC 60.159 50.000 0.00 0.00 0.00 3.51
1537 3442 3.077359 ACCGAATCCAAGCAAGAGAAAG 58.923 45.455 0.00 0.00 0.00 2.62
1539 3444 2.859165 ACCGAATCCAAGCAAGAGAA 57.141 45.000 0.00 0.00 0.00 2.87
1540 3445 2.859165 AACCGAATCCAAGCAAGAGA 57.141 45.000 0.00 0.00 0.00 3.10
1541 3446 2.678336 GGTAACCGAATCCAAGCAAGAG 59.322 50.000 0.00 0.00 0.00 2.85
1542 3447 2.039216 TGGTAACCGAATCCAAGCAAGA 59.961 45.455 0.00 0.00 0.00 3.02
1543 3448 2.420022 CTGGTAACCGAATCCAAGCAAG 59.580 50.000 0.00 0.00 0.00 4.01
1544 3449 2.432444 CTGGTAACCGAATCCAAGCAA 58.568 47.619 0.00 0.00 0.00 3.91
1545 3450 1.948611 GCTGGTAACCGAATCCAAGCA 60.949 52.381 0.00 0.00 0.00 3.91
1546 3451 0.733150 GCTGGTAACCGAATCCAAGC 59.267 55.000 0.00 0.00 0.00 4.01
1555 3481 2.162809 GGTTAATTGGTGCTGGTAACCG 59.837 50.000 0.00 0.00 40.86 4.44
1562 3488 3.959535 ATTGGTGGTTAATTGGTGCTG 57.040 42.857 0.00 0.00 0.00 4.41
1609 3535 2.093181 AGCGCCAATAGAACCACACATA 60.093 45.455 2.29 0.00 0.00 2.29
1629 3556 2.030805 GCAAACAGGACAAGGCAAGTAG 60.031 50.000 0.00 0.00 0.00 2.57
1640 3567 5.438761 ACAAACAAGATAGCAAACAGGAC 57.561 39.130 0.00 0.00 0.00 3.85
1661 3588 6.551736 AGACTACACACACATGAACAAAAAC 58.448 36.000 0.00 0.00 0.00 2.43
1663 3590 5.877564 TGAGACTACACACACATGAACAAAA 59.122 36.000 0.00 0.00 0.00 2.44
1666 3593 4.142049 TGTGAGACTACACACACATGAACA 60.142 41.667 0.00 0.00 44.29 3.18
1667 3594 4.368315 TGTGAGACTACACACACATGAAC 58.632 43.478 0.00 0.00 44.29 3.18
1668 3595 4.664150 TGTGAGACTACACACACATGAA 57.336 40.909 0.00 0.00 44.29 2.57
1674 3601 9.245281 AGTGTCAAGATTGTGAGACTACACACA 62.245 40.741 3.41 0.00 46.94 3.72
1675 3602 6.956755 AGTGTCAAGATTGTGAGACTACACAC 60.957 42.308 3.41 7.04 46.94 3.82
1676 3603 5.069119 AGTGTCAAGATTGTGAGACTACACA 59.931 40.000 3.41 0.00 46.94 3.72
1677 3604 5.533482 AGTGTCAAGATTGTGAGACTACAC 58.467 41.667 3.41 0.00 46.94 2.90
1687 3614 4.341806 TCAAATGGCAAGTGTCAAGATTGT 59.658 37.500 0.00 0.00 31.21 2.71
1700 3627 6.832520 ATACATGTACAACTCAAATGGCAA 57.167 33.333 7.96 0.00 0.00 4.52
1739 3666 5.376625 AGACAGCAAAATAGACCACAAAGA 58.623 37.500 0.00 0.00 0.00 2.52
1743 3670 4.318332 CAGAGACAGCAAAATAGACCACA 58.682 43.478 0.00 0.00 0.00 4.17
1778 3708 7.288810 TGCAAGGAAGTCAATTTTAAGACAT 57.711 32.000 0.00 0.00 37.23 3.06
1788 3718 1.985473 TGTGCTGCAAGGAAGTCAAT 58.015 45.000 2.77 0.00 34.45 2.57
1790 3720 1.985473 ATTGTGCTGCAAGGAAGTCA 58.015 45.000 2.77 0.00 40.86 3.41
1791 3721 2.669364 CAATTGTGCTGCAAGGAAGTC 58.331 47.619 2.77 0.00 40.86 3.01
1792 3722 2.806608 CAATTGTGCTGCAAGGAAGT 57.193 45.000 2.77 0.00 40.86 3.01
1804 3734 6.919662 AGTTGACAGAAAACATAGCAATTGTG 59.080 34.615 7.40 0.00 0.00 3.33
1821 3751 2.032204 GCAAGCAGAGAACAGTTGACAG 60.032 50.000 0.00 0.00 0.00 3.51
1825 3755 3.561310 TGTTAGCAAGCAGAGAACAGTTG 59.439 43.478 0.00 0.00 0.00 3.16
1839 3770 1.414919 ACCCAGAAGACGTGTTAGCAA 59.585 47.619 0.00 0.00 0.00 3.91
1842 3773 3.255149 ACACTACCCAGAAGACGTGTTAG 59.745 47.826 0.00 0.00 32.23 2.34
1846 3781 1.611977 TGACACTACCCAGAAGACGTG 59.388 52.381 0.00 0.00 0.00 4.49
1847 3782 1.991121 TGACACTACCCAGAAGACGT 58.009 50.000 0.00 0.00 0.00 4.34
1848 3783 3.594603 AATGACACTACCCAGAAGACG 57.405 47.619 0.00 0.00 0.00 4.18
1880 3815 8.653338 CAAAGGAATTAGAGCACATCAAAATTG 58.347 33.333 0.00 0.00 30.29 2.32
1992 3951 7.145985 CAGAAGTGCTACAAGTTACAGTTAGA 58.854 38.462 0.00 0.00 0.00 2.10
2037 3996 4.397730 TCAAACTTACACAAGCACACACAT 59.602 37.500 0.00 0.00 34.94 3.21
2174 4133 8.525290 TTGTCATTCCTTTTCTCTTTCTTCTT 57.475 30.769 0.00 0.00 0.00 2.52
2175 4134 7.995488 TCTTGTCATTCCTTTTCTCTTTCTTCT 59.005 33.333 0.00 0.00 0.00 2.85
2176 4135 8.159344 TCTTGTCATTCCTTTTCTCTTTCTTC 57.841 34.615 0.00 0.00 0.00 2.87
2245 4207 6.239217 TCATGCTTTCTCTTCTTATGGCTA 57.761 37.500 0.00 0.00 0.00 3.93
2284 4246 1.073199 AGTTTTGGACTCCAGGCCG 59.927 57.895 0.00 0.00 33.81 6.13
2289 4251 0.467290 GGGTGCAGTTTTGGACTCCA 60.467 55.000 0.00 0.00 44.27 3.86
2305 4267 6.209391 CCAACTGATCAAATAGTTCTTTGGGT 59.791 38.462 0.00 0.00 36.87 4.51
2306 4268 6.434028 TCCAACTGATCAAATAGTTCTTTGGG 59.566 38.462 0.00 0.00 36.87 4.12
2316 4278 6.213397 TCCACTCTTCTCCAACTGATCAAATA 59.787 38.462 0.00 0.00 0.00 1.40
2317 4279 5.013495 TCCACTCTTCTCCAACTGATCAAAT 59.987 40.000 0.00 0.00 0.00 2.32
2323 4285 2.894126 GAGTCCACTCTTCTCCAACTGA 59.106 50.000 0.00 0.00 39.81 3.41
2362 4324 5.551233 TGTACTGTCTGAATGAAAGAAGGG 58.449 41.667 0.00 0.00 34.16 3.95
2434 4396 1.562672 TTTGACTAGGGCCTGGGAGC 61.563 60.000 21.86 10.44 0.00 4.70
2476 4438 9.435688 AAATCAACAGAAACCTAAAAATATGGC 57.564 29.630 0.00 0.00 0.00 4.40
2509 4471 7.175797 TGGTCAGTAACTCTAGAAGAGAATGA 58.824 38.462 10.80 1.98 45.07 2.57
2518 4480 9.421399 TCATAATTCATGGTCAGTAACTCTAGA 57.579 33.333 0.00 0.00 35.16 2.43
2527 4489 7.172868 TGCAAAATCATAATTCATGGTCAGT 57.827 32.000 0.00 0.00 35.16 3.41
2557 4519 9.095065 TCTCTTTTTATCTTAATGCGAAGTACC 57.905 33.333 0.00 0.00 0.00 3.34
2590 4552 0.888736 CCAACATGGCTGACGGTGAA 60.889 55.000 0.00 0.00 0.00 3.18
2593 4555 0.677731 CATCCAACATGGCTGACGGT 60.678 55.000 0.00 0.00 35.77 4.83
2607 4569 2.844348 GGAAGAACCCTAGAACCATCCA 59.156 50.000 0.00 0.00 0.00 3.41
2628 4590 0.453793 TTGTTGGACAGGTTGTTGCG 59.546 50.000 0.00 0.00 0.00 4.85
2729 4691 2.165167 CCTCTTGATGCTTTGCTGGAA 58.835 47.619 0.00 0.00 0.00 3.53
2755 4717 3.499157 CCATTTGTTTTGGCACAGATTGG 59.501 43.478 0.00 0.00 42.39 3.16
2796 4758 4.074970 GGAAGGAACTCTTTGCAAGATCA 58.925 43.478 0.00 0.00 38.49 2.92
2855 4817 2.146342 CTTTGGTGTGATCTTCGCTGT 58.854 47.619 0.00 0.00 0.00 4.40
2869 4831 2.358195 GGTTGGGGCATCTATCTTTGGT 60.358 50.000 0.00 0.00 0.00 3.67
2871 4833 3.217626 GAGGTTGGGGCATCTATCTTTG 58.782 50.000 0.00 0.00 0.00 2.77
2882 4844 0.613012 ATCTTTGCTGAGGTTGGGGC 60.613 55.000 0.00 0.00 0.00 5.80
2929 4891 4.260375 GCAGATGAAGGTGTAGCATTAACG 60.260 45.833 0.00 0.00 0.00 3.18
2962 4924 1.615384 GGCAAAGGATCAGCACTTCCT 60.615 52.381 0.00 0.00 44.35 3.36
3024 4986 0.969149 AATGTCGACTCTCTGTGCCA 59.031 50.000 17.92 0.00 0.00 4.92
3051 5013 2.435586 CTCTCTGTGCCGCCTTGG 60.436 66.667 0.00 0.00 42.50 3.61
3052 5014 1.739562 GACTCTCTGTGCCGCCTTG 60.740 63.158 0.00 0.00 0.00 3.61
3053 5015 2.659610 GACTCTCTGTGCCGCCTT 59.340 61.111 0.00 0.00 0.00 4.35
3054 5016 3.753434 CGACTCTCTGTGCCGCCT 61.753 66.667 0.00 0.00 0.00 5.52
3055 5017 3.749064 TCGACTCTCTGTGCCGCC 61.749 66.667 0.00 0.00 0.00 6.13
3056 5018 2.505118 GTCGACTCTCTGTGCCGC 60.505 66.667 8.70 0.00 0.00 6.53
3057 5019 0.109086 AATGTCGACTCTCTGTGCCG 60.109 55.000 17.92 0.00 0.00 5.69
3058 5020 1.634702 GAATGTCGACTCTCTGTGCC 58.365 55.000 17.92 0.00 0.00 5.01
3059 5021 1.203523 AGGAATGTCGACTCTCTGTGC 59.796 52.381 17.92 1.05 0.00 4.57
3060 5022 2.159310 GGAGGAATGTCGACTCTCTGTG 60.159 54.545 17.92 0.00 0.00 3.66
3061 5023 2.096248 GGAGGAATGTCGACTCTCTGT 58.904 52.381 17.92 5.09 0.00 3.41
3062 5024 2.098934 CAGGAGGAATGTCGACTCTCTG 59.901 54.545 17.92 10.49 0.00 3.35
3063 5025 2.374184 CAGGAGGAATGTCGACTCTCT 58.626 52.381 17.92 8.86 0.00 3.10
3064 5026 1.202359 GCAGGAGGAATGTCGACTCTC 60.202 57.143 17.92 16.26 0.00 3.20
3065 5027 0.820871 GCAGGAGGAATGTCGACTCT 59.179 55.000 17.92 8.87 0.00 3.24
3066 5028 0.179097 GGCAGGAGGAATGTCGACTC 60.179 60.000 17.92 6.69 0.00 3.36
3067 5029 0.904865 TGGCAGGAGGAATGTCGACT 60.905 55.000 17.92 0.00 0.00 4.18
3068 5030 0.036388 TTGGCAGGAGGAATGTCGAC 60.036 55.000 9.11 9.11 0.00 4.20
3069 5031 0.250234 CTTGGCAGGAGGAATGTCGA 59.750 55.000 0.00 0.00 0.00 4.20
3070 5032 0.745845 CCTTGGCAGGAGGAATGTCG 60.746 60.000 0.00 0.00 44.19 4.35
3071 5033 0.329596 ACCTTGGCAGGAGGAATGTC 59.670 55.000 12.14 0.00 44.19 3.06
3072 5034 0.779997 AACCTTGGCAGGAGGAATGT 59.220 50.000 12.14 0.00 44.19 2.71
3073 5035 2.806945 TAACCTTGGCAGGAGGAATG 57.193 50.000 12.14 0.00 44.19 2.67
3074 5036 3.269381 TCAATAACCTTGGCAGGAGGAAT 59.731 43.478 12.14 2.74 44.19 3.01
3075 5037 2.647299 TCAATAACCTTGGCAGGAGGAA 59.353 45.455 12.14 0.49 44.19 3.36
3184 5146 1.464734 TTGTTTCCTTCGGCAACACA 58.535 45.000 0.00 0.00 30.12 3.72
3192 5154 6.918022 AGAAGCAACTTTTATTGTTTCCTTCG 59.082 34.615 10.31 0.00 45.67 3.79
3262 5224 1.478916 GGAGAGACTACAGGCACCTTC 59.521 57.143 0.00 0.00 0.00 3.46
3356 5321 5.013183 ACTTTGACTGCTTAACCTCTGGTAT 59.987 40.000 0.00 0.00 33.12 2.73
3433 5404 5.648092 CCAGGTAACAAAAAGATCTCGGAAT 59.352 40.000 0.00 0.00 41.41 3.01
3445 5416 4.463050 AGGTGGATTCCAGGTAACAAAA 57.537 40.909 5.39 0.00 41.41 2.44
3476 5447 1.137282 GAGATTCCCGGTCTCCTCAAC 59.863 57.143 8.98 0.00 36.87 3.18
3587 5558 1.686052 TGGTTGCCATGAAAACTCCAC 59.314 47.619 0.00 0.00 0.00 4.02
3620 5591 5.219343 TGATACATATGAAGGTCAGGCAG 57.781 43.478 10.38 0.00 0.00 4.85
3895 5885 9.769093 GGTAACAAGATTGTCATACAACATTAC 57.231 33.333 0.00 1.40 41.40 1.89
3896 5886 8.952278 GGGTAACAAGATTGTCATACAACATTA 58.048 33.333 0.00 0.00 41.31 1.90
3897 5887 7.093945 GGGGTAACAAGATTGTCATACAACATT 60.094 37.037 0.00 0.00 41.31 2.71
3898 5888 6.377146 GGGGTAACAAGATTGTCATACAACAT 59.623 38.462 0.00 0.00 41.31 2.71
3899 5889 5.708230 GGGGTAACAAGATTGTCATACAACA 59.292 40.000 0.00 0.00 41.31 3.33
3900 5890 5.944007 AGGGGTAACAAGATTGTCATACAAC 59.056 40.000 0.00 0.00 41.31 3.32
3901 5891 5.943416 CAGGGGTAACAAGATTGTCATACAA 59.057 40.000 0.00 0.00 41.31 2.41
3902 5892 5.249622 TCAGGGGTAACAAGATTGTCATACA 59.750 40.000 0.00 0.00 41.31 2.29
3903 5893 5.741011 TCAGGGGTAACAAGATTGTCATAC 58.259 41.667 0.00 0.00 41.31 2.39
3904 5894 6.381498 TTCAGGGGTAACAAGATTGTCATA 57.619 37.500 0.00 0.00 41.31 2.15
3905 5895 4.927267 TCAGGGGTAACAAGATTGTCAT 57.073 40.909 0.00 0.00 41.31 3.06
3906 5896 4.715534 TTCAGGGGTAACAAGATTGTCA 57.284 40.909 0.00 0.00 41.31 3.58
3907 5897 5.710099 TCATTTCAGGGGTAACAAGATTGTC 59.290 40.000 0.00 0.00 41.31 3.18
3908 5898 5.640147 TCATTTCAGGGGTAACAAGATTGT 58.360 37.500 0.00 0.00 44.72 2.71
3909 5899 6.588719 TTCATTTCAGGGGTAACAAGATTG 57.411 37.500 0.00 0.00 39.74 2.67
3910 5900 7.893302 TGTATTCATTTCAGGGGTAACAAGATT 59.107 33.333 0.00 0.00 39.74 2.40
3911 5901 7.410174 TGTATTCATTTCAGGGGTAACAAGAT 58.590 34.615 0.00 0.00 39.74 2.40
3912 5902 6.785076 TGTATTCATTTCAGGGGTAACAAGA 58.215 36.000 0.00 0.00 39.74 3.02
3913 5903 7.339212 TGATGTATTCATTTCAGGGGTAACAAG 59.661 37.037 0.00 0.00 34.06 3.16
3948 5960 1.270907 AGCCACGATTCCTCTCAGTT 58.729 50.000 0.00 0.00 0.00 3.16
3949 5961 1.270907 AAGCCACGATTCCTCTCAGT 58.729 50.000 0.00 0.00 0.00 3.41
3950 5962 2.005451 CAAAGCCACGATTCCTCTCAG 58.995 52.381 0.00 0.00 0.00 3.35
3951 5963 1.347707 ACAAAGCCACGATTCCTCTCA 59.652 47.619 0.00 0.00 0.00 3.27
3956 5984 0.521735 GGACACAAAGCCACGATTCC 59.478 55.000 0.00 0.00 0.00 3.01
4007 6076 6.415798 AAAACAAAGTGAAAAATGGAACGG 57.584 33.333 0.00 0.00 0.00 4.44
4054 6123 0.327480 ACCCAGGGACATGATAGCCA 60.327 55.000 14.54 0.00 0.00 4.75
4175 6245 4.082571 CCAGCTTCGATTGACCTTTGATTT 60.083 41.667 0.00 0.00 0.00 2.17
4178 6248 2.038426 TCCAGCTTCGATTGACCTTTGA 59.962 45.455 0.00 0.00 0.00 2.69
4179 6249 2.426522 TCCAGCTTCGATTGACCTTTG 58.573 47.619 0.00 0.00 0.00 2.77
4200 6270 2.815211 GAACGCTGCAGCCGATCA 60.815 61.111 32.07 0.00 37.91 2.92
4398 6468 3.632145 TGCAGATTCTGAGCATACTACGA 59.368 43.478 17.87 0.00 32.44 3.43
4413 6483 2.351060 CGATTGCTGTGTGTTGCAGATT 60.351 45.455 0.00 0.00 40.46 2.40
4420 6490 1.654220 GTGCCGATTGCTGTGTGTT 59.346 52.632 0.00 0.00 42.00 3.32
4423 6493 2.029288 CTCGTGCCGATTGCTGTGT 61.029 57.895 0.00 0.00 42.00 3.72
4424 6494 1.291184 TTCTCGTGCCGATTGCTGTG 61.291 55.000 0.00 0.00 42.00 3.66
4425 6495 0.391661 ATTCTCGTGCCGATTGCTGT 60.392 50.000 0.00 0.00 42.00 4.40
4426 6496 0.027194 CATTCTCGTGCCGATTGCTG 59.973 55.000 0.00 0.00 42.00 4.41
4427 6497 0.391661 ACATTCTCGTGCCGATTGCT 60.392 50.000 0.00 0.00 42.00 3.91
4428 6498 0.447801 AACATTCTCGTGCCGATTGC 59.552 50.000 0.00 0.00 41.77 3.56
4454 6524 3.055530 GGCACTTCATCTTCAGAAGAGGA 60.056 47.826 21.10 21.10 45.56 3.71
4455 6525 3.055240 AGGCACTTCATCTTCAGAAGAGG 60.055 47.826 17.24 17.24 44.00 3.69
4456 6526 3.933955 CAGGCACTTCATCTTCAGAAGAG 59.066 47.826 17.91 10.30 44.00 2.85
4457 6527 3.867600 GCAGGCACTTCATCTTCAGAAGA 60.868 47.826 15.44 15.44 44.00 2.87
4458 6528 2.419324 GCAGGCACTTCATCTTCAGAAG 59.581 50.000 3.45 3.45 46.08 2.85
4459 6529 2.039480 AGCAGGCACTTCATCTTCAGAA 59.961 45.455 0.00 0.00 34.60 3.02
4460 6530 1.627329 AGCAGGCACTTCATCTTCAGA 59.373 47.619 0.00 0.00 34.60 3.27
4461 6531 2.110901 AGCAGGCACTTCATCTTCAG 57.889 50.000 0.00 0.00 34.60 3.02
4462 6532 2.568956 AGTAGCAGGCACTTCATCTTCA 59.431 45.455 0.00 0.00 34.60 3.02
4463 6533 3.194062 GAGTAGCAGGCACTTCATCTTC 58.806 50.000 0.00 0.00 34.60 2.87
4464 6534 2.568956 TGAGTAGCAGGCACTTCATCTT 59.431 45.455 0.00 0.00 34.60 2.40
4465 6535 2.168106 CTGAGTAGCAGGCACTTCATCT 59.832 50.000 0.00 0.00 41.07 2.90
4466 6536 2.167281 TCTGAGTAGCAGGCACTTCATC 59.833 50.000 0.00 0.00 44.98 2.92
4467 6537 2.182827 TCTGAGTAGCAGGCACTTCAT 58.817 47.619 0.00 0.00 44.98 2.57
4468 6538 1.632589 TCTGAGTAGCAGGCACTTCA 58.367 50.000 0.00 0.00 44.98 3.02
4469 6539 2.977772 ATCTGAGTAGCAGGCACTTC 57.022 50.000 0.00 0.00 44.98 3.01
4470 6540 3.636300 CTCTATCTGAGTAGCAGGCACTT 59.364 47.826 0.00 0.00 44.98 3.16
4471 6541 3.117701 TCTCTATCTGAGTAGCAGGCACT 60.118 47.826 0.00 0.00 44.98 4.40
4472 6542 3.218453 TCTCTATCTGAGTAGCAGGCAC 58.782 50.000 0.00 0.00 44.98 5.01
4473 6543 3.137360 TCTCTCTATCTGAGTAGCAGGCA 59.863 47.826 0.00 0.00 44.98 4.75
4474 6544 3.750371 TCTCTCTATCTGAGTAGCAGGC 58.250 50.000 0.00 0.00 44.98 4.85
4475 6545 4.997395 GTCTCTCTCTATCTGAGTAGCAGG 59.003 50.000 0.00 0.00 44.98 4.85
4476 6546 4.686091 CGTCTCTCTCTATCTGAGTAGCAG 59.314 50.000 0.00 0.00 46.31 4.24
4477 6547 4.100344 ACGTCTCTCTCTATCTGAGTAGCA 59.900 45.833 0.00 0.00 43.13 3.49
4478 6548 4.628074 ACGTCTCTCTCTATCTGAGTAGC 58.372 47.826 0.00 0.00 43.13 3.58
4479 6549 8.827177 AAATACGTCTCTCTCTATCTGAGTAG 57.173 38.462 0.00 0.00 43.13 2.57
4480 6550 9.263538 GAAAATACGTCTCTCTCTATCTGAGTA 57.736 37.037 0.00 0.00 43.13 2.59
4481 6551 7.227910 GGAAAATACGTCTCTCTCTATCTGAGT 59.772 40.741 0.00 0.00 43.13 3.41
4482 6552 7.308348 GGGAAAATACGTCTCTCTCTATCTGAG 60.308 44.444 0.00 0.00 43.96 3.35
4483 6553 6.487331 GGGAAAATACGTCTCTCTCTATCTGA 59.513 42.308 0.00 0.00 0.00 3.27
4484 6554 6.488683 AGGGAAAATACGTCTCTCTCTATCTG 59.511 42.308 0.00 0.00 0.00 2.90
4485 6555 6.607019 AGGGAAAATACGTCTCTCTCTATCT 58.393 40.000 0.00 0.00 0.00 1.98
4486 6556 6.887626 AGGGAAAATACGTCTCTCTCTATC 57.112 41.667 0.00 0.00 0.00 2.08
4487 6557 6.887626 GAGGGAAAATACGTCTCTCTCTAT 57.112 41.667 0.00 0.00 39.21 1.98
4492 6562 5.585820 AGAAGAGGGAAAATACGTCTCTC 57.414 43.478 0.00 0.00 42.12 3.20
4493 6563 5.717654 AGAAGAAGAGGGAAAATACGTCTCT 59.282 40.000 0.00 0.00 36.49 3.10
4494 6564 5.808030 CAGAAGAAGAGGGAAAATACGTCTC 59.192 44.000 0.00 0.00 32.44 3.36
4495 6565 5.480772 TCAGAAGAAGAGGGAAAATACGTCT 59.519 40.000 0.00 0.00 34.83 4.18
4536 6606 4.635765 CAGGTCAGTCTCTCTCTCTTAGTG 59.364 50.000 0.00 0.00 0.00 2.74
4537 6607 4.843728 CAGGTCAGTCTCTCTCTCTTAGT 58.156 47.826 0.00 0.00 0.00 2.24
4538 6608 3.627577 GCAGGTCAGTCTCTCTCTCTTAG 59.372 52.174 0.00 0.00 0.00 2.18
4539 6609 3.616219 GCAGGTCAGTCTCTCTCTCTTA 58.384 50.000 0.00 0.00 0.00 2.10
4540 6610 2.446435 GCAGGTCAGTCTCTCTCTCTT 58.554 52.381 0.00 0.00 0.00 2.85
4541 6611 1.678728 CGCAGGTCAGTCTCTCTCTCT 60.679 57.143 0.00 0.00 0.00 3.10
4553 6629 2.207229 CCCCCGATATCGCAGGTCA 61.207 63.158 19.78 0.00 38.18 4.02


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

AutoCloner maintained by Alex Coulton.