Multiple sequence alignment - TraesCS2A01G150600

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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 TraesCS2A01G150600 chr2A 100.000 6413 0 0 1 6413 98144874 98138462 0.000000e+00 11843
1 TraesCS2A01G150600 chr2A 97.619 126 3 0 4227 4352 285626176 285626301 3.890000e-52 217
2 TraesCS2A01G150600 chr2D 90.165 4311 211 87 1 4228 99140337 99136157 0.000000e+00 5415
3 TraesCS2A01G150600 chr2D 93.950 1471 51 12 4356 5817 99136162 99134721 0.000000e+00 2189
4 TraesCS2A01G150600 chr2D 93.148 613 24 1 5819 6413 99134629 99134017 0.000000e+00 883
5 TraesCS2A01G150600 chr2B 92.751 2828 128 41 1435 4228 150716962 150714178 0.000000e+00 4015
6 TraesCS2A01G150600 chr2B 94.053 2102 79 12 4356 6413 150714183 150712084 0.000000e+00 3147
7 TraesCS2A01G150600 chr2B 87.344 1359 78 42 1 1340 150718373 150717090 0.000000e+00 1471
8 TraesCS2A01G150600 chr3B 98.485 132 2 0 4224 4355 332940699 332940568 3.870000e-57 233
9 TraesCS2A01G150600 chr5B 98.413 126 2 0 4230 4355 180041013 180041138 8.370000e-54 222
10 TraesCS2A01G150600 chr5B 96.899 129 4 0 4230 4358 269975457 269975329 3.890000e-52 217
11 TraesCS2A01G150600 chr4A 98.413 126 2 0 4230 4355 626311725 626311600 8.370000e-54 222
12 TraesCS2A01G150600 chr4A 98.413 126 2 0 4230 4355 626312942 626312817 8.370000e-54 222
13 TraesCS2A01G150600 chr6D 96.923 130 4 0 4226 4355 199649310 199649439 1.080000e-52 219
14 TraesCS2A01G150600 chr4B 96.923 130 4 0 4226 4355 271625287 271625158 1.080000e-52 219
15 TraesCS2A01G150600 chr4D 97.619 126 3 0 4230 4355 306398635 306398510 3.890000e-52 217


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 TraesCS2A01G150600 chr2A 98138462 98144874 6412 True 11843.000000 11843 100.000000 1 6413 1 chr2A.!!$R1 6412
1 TraesCS2A01G150600 chr2D 99134017 99140337 6320 True 2829.000000 5415 92.421000 1 6413 3 chr2D.!!$R1 6412
2 TraesCS2A01G150600 chr2B 150712084 150718373 6289 True 2877.666667 4015 91.382667 1 6413 3 chr2B.!!$R1 6412
3 TraesCS2A01G150600 chr4A 626311600 626312942 1342 True 222.000000 222 98.413000 4230 4355 2 chr4A.!!$R1 125

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
358 370 0.313987 ACACGATCAACAGTCGAGCA 59.686 50.0 2.28 0.0 41.40 4.26 F
1214 1269 0.175989 GATTTCTTCCGTCCCGCTCT 59.824 55.0 0.00 0.0 0.00 4.09 F
2176 2343 0.031994 CCAAACGGGTGCTCCAAAAG 59.968 55.0 7.20 0.0 34.36 2.27 F
3707 3890 0.881118 CCCACGCTAGCAAAATGTGT 59.119 50.0 16.45 0.0 0.00 3.72 F
4660 4871 0.242017 GTGTGGCTTCATTGCAGGAC 59.758 55.0 0.00 0.0 34.04 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2205 0.044702 TCCCCAGATCACACCCAGAT 59.955 55.000 0.00 0.00 0.00 2.90 R
2508 2678 0.035056 GAAGCCAAGGAGCAAGCCTA 60.035 55.000 0.00 0.00 37.26 3.93 R
3834 4019 0.613572 CAAGGCGGGTAATGGGGTTT 60.614 55.000 0.00 0.00 0.00 3.27 R
5293 6064 0.109272 CACAGCTGCAGCAAGAATGG 60.109 55.000 38.24 20.06 45.16 3.16 R
5899 6762 2.366266 TGTTTGTCCGTACCTTGCTAGT 59.634 45.455 0.00 0.00 0.00 2.57 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
53 56 2.691732 CCCCCTGGGCAATCATGT 59.308 61.111 7.39 0.00 35.35 3.21
87 90 0.396435 TTGGACTTGGACATCAGCGT 59.604 50.000 0.00 0.00 0.00 5.07
221 226 4.162131 ACAAAATGGTTGCATATTCTCCCC 59.838 41.667 0.00 0.00 0.00 4.81
234 239 4.697756 TCCCCGCGTGCTTTGGAG 62.698 66.667 4.92 0.00 0.00 3.86
236 241 3.121030 CCCGCGTGCTTTGGAGAG 61.121 66.667 4.92 0.00 0.00 3.20
255 261 0.594284 GGATAAACGGCCGTCGAGAG 60.594 60.000 34.29 0.00 42.43 3.20
331 343 4.399978 ACAAAGTGTCGAGAAACAAAACG 58.600 39.130 0.00 0.00 0.00 3.60
354 366 2.155732 CCAAAGACACGATCAACAGTCG 59.844 50.000 0.00 0.00 44.26 4.18
355 367 3.049912 CAAAGACACGATCAACAGTCGA 58.950 45.455 2.28 0.00 41.40 4.20
356 368 2.620779 AGACACGATCAACAGTCGAG 57.379 50.000 2.28 0.00 41.40 4.04
357 369 0.985549 GACACGATCAACAGTCGAGC 59.014 55.000 2.28 0.00 41.40 5.03
358 370 0.313987 ACACGATCAACAGTCGAGCA 59.686 50.000 2.28 0.00 41.40 4.26
360 372 0.881796 ACGATCAACAGTCGAGCAGA 59.118 50.000 2.28 0.00 41.40 4.26
385 406 2.059541 CCGAACTCCGACTTTTCTCAC 58.940 52.381 0.00 0.00 41.76 3.51
399 420 5.833131 ACTTTTCTCACCCAGCTTCAATTAA 59.167 36.000 0.00 0.00 0.00 1.40
400 421 6.494835 ACTTTTCTCACCCAGCTTCAATTAAT 59.505 34.615 0.00 0.00 0.00 1.40
402 423 5.178096 TCTCACCCAGCTTCAATTAATCA 57.822 39.130 0.00 0.00 0.00 2.57
403 424 5.569355 TCTCACCCAGCTTCAATTAATCAA 58.431 37.500 0.00 0.00 0.00 2.57
404 425 6.189859 TCTCACCCAGCTTCAATTAATCAAT 58.810 36.000 0.00 0.00 0.00 2.57
405 426 6.664816 TCTCACCCAGCTTCAATTAATCAATT 59.335 34.615 0.00 0.00 34.60 2.32
406 427 7.833682 TCTCACCCAGCTTCAATTAATCAATTA 59.166 33.333 0.00 0.00 32.96 1.40
407 428 8.537728 TCACCCAGCTTCAATTAATCAATTAT 57.462 30.769 0.00 0.00 32.96 1.28
408 429 8.415553 TCACCCAGCTTCAATTAATCAATTATG 58.584 33.333 0.00 0.00 32.96 1.90
409 430 7.170320 CACCCAGCTTCAATTAATCAATTATGC 59.830 37.037 0.00 0.00 32.96 3.14
410 431 7.147689 ACCCAGCTTCAATTAATCAATTATGCA 60.148 33.333 0.00 0.00 32.96 3.96
466 493 0.793861 GGATAAGACACGCACGCAAA 59.206 50.000 0.00 0.00 0.00 3.68
513 540 1.423161 CCTGATTCCCCCTGATTCCTC 59.577 57.143 0.00 0.00 0.00 3.71
514 541 1.423161 CTGATTCCCCCTGATTCCTCC 59.577 57.143 0.00 0.00 0.00 4.30
515 542 1.274943 TGATTCCCCCTGATTCCTCCA 60.275 52.381 0.00 0.00 0.00 3.86
517 544 1.766951 TTCCCCCTGATTCCTCCAAA 58.233 50.000 0.00 0.00 0.00 3.28
518 545 0.999712 TCCCCCTGATTCCTCCAAAC 59.000 55.000 0.00 0.00 0.00 2.93
519 546 0.704076 CCCCCTGATTCCTCCAAACA 59.296 55.000 0.00 0.00 0.00 2.83
520 547 1.288932 CCCCCTGATTCCTCCAAACAT 59.711 52.381 0.00 0.00 0.00 2.71
521 548 2.513738 CCCCCTGATTCCTCCAAACATA 59.486 50.000 0.00 0.00 0.00 2.29
526 553 6.398095 CCCTGATTCCTCCAAACATAAAAAC 58.602 40.000 0.00 0.00 0.00 2.43
527 554 6.014669 CCCTGATTCCTCCAAACATAAAAACA 60.015 38.462 0.00 0.00 0.00 2.83
528 555 7.310609 CCCTGATTCCTCCAAACATAAAAACAT 60.311 37.037 0.00 0.00 0.00 2.71
529 556 8.748412 CCTGATTCCTCCAAACATAAAAACATA 58.252 33.333 0.00 0.00 0.00 2.29
530 557 9.573133 CTGATTCCTCCAAACATAAAAACATAC 57.427 33.333 0.00 0.00 0.00 2.39
565 594 5.598416 AGAACTTTTCTTTTGGAACTGGG 57.402 39.130 0.00 0.00 36.36 4.45
602 631 4.836125 TGAAGTCAAATTGAGGTTGAGC 57.164 40.909 0.00 0.00 35.71 4.26
637 666 1.918957 CAGAAACCATTCCTCCTCCCT 59.081 52.381 0.00 0.00 36.12 4.20
667 697 4.767255 CTGGAGCACCCGAGGCAC 62.767 72.222 0.00 0.00 37.93 5.01
795 826 0.389757 TCTAGCTCGCTCTCGCTCTA 59.610 55.000 0.00 0.00 37.68 2.43
796 827 0.790207 CTAGCTCGCTCTCGCTCTAG 59.210 60.000 0.00 0.00 37.68 2.43
797 828 1.225376 TAGCTCGCTCTCGCTCTAGC 61.225 60.000 0.00 0.00 37.68 3.42
798 829 2.542907 GCTCGCTCTCGCTCTAGCT 61.543 63.158 0.00 0.00 39.32 3.32
799 830 1.569493 CTCGCTCTCGCTCTAGCTC 59.431 63.158 0.00 0.00 39.32 4.09
800 831 2.158058 CTCGCTCTCGCTCTAGCTCG 62.158 65.000 0.00 0.00 39.32 5.03
801 832 2.051345 GCTCTCGCTCTAGCTCGC 60.051 66.667 0.00 0.00 39.32 5.03
802 833 2.542907 GCTCTCGCTCTAGCTCGCT 61.543 63.158 0.00 0.00 39.32 4.93
803 834 1.569493 CTCTCGCTCTAGCTCGCTC 59.431 63.158 0.00 0.00 39.32 5.03
804 835 0.880278 CTCTCGCTCTAGCTCGCTCT 60.880 60.000 0.00 0.00 39.32 4.09
805 836 0.878523 TCTCGCTCTAGCTCGCTCTC 60.879 60.000 0.00 0.00 39.32 3.20
806 837 2.158058 CTCGCTCTAGCTCGCTCTCG 62.158 65.000 0.00 0.00 39.32 4.04
807 838 2.051345 GCTCTAGCTCGCTCTCGC 60.051 66.667 0.00 0.00 38.21 5.03
808 839 2.542907 GCTCTAGCTCGCTCTCGCT 61.543 63.158 0.00 0.00 40.15 4.93
809 840 1.569493 CTCTAGCTCGCTCTCGCTC 59.431 63.158 0.00 0.00 37.68 5.03
810 841 0.880278 CTCTAGCTCGCTCTCGCTCT 60.880 60.000 0.00 0.00 37.68 4.09
923 956 2.887889 CGCTCTCGAGTCCTAGCCG 61.888 68.421 13.13 6.78 38.10 5.52
935 968 0.895530 CCTAGCCGTCTTGACCTTCA 59.104 55.000 0.00 0.00 0.00 3.02
1056 1092 4.899239 GAGATGGGGCGGACGCTG 62.899 72.222 16.72 0.00 41.60 5.18
1203 1258 1.599542 CTCCGCCCAATCGATTTCTTC 59.400 52.381 8.21 0.00 0.00 2.87
1208 1263 1.940613 CCCAATCGATTTCTTCCGTCC 59.059 52.381 8.21 0.00 0.00 4.79
1209 1264 1.940613 CCAATCGATTTCTTCCGTCCC 59.059 52.381 8.21 0.00 0.00 4.46
1213 1268 1.146358 CGATTTCTTCCGTCCCGCTC 61.146 60.000 0.00 0.00 0.00 5.03
1214 1269 0.175989 GATTTCTTCCGTCCCGCTCT 59.824 55.000 0.00 0.00 0.00 4.09
1216 1271 0.320421 TTTCTTCCGTCCCGCTCTTG 60.320 55.000 0.00 0.00 0.00 3.02
1243 1302 3.660111 GGTGCTCACCGTGGTTGC 61.660 66.667 2.97 6.79 42.29 4.17
1244 1303 2.591715 GTGCTCACCGTGGTTGCT 60.592 61.111 12.91 0.00 0.00 3.91
1245 1304 2.186826 GTGCTCACCGTGGTTGCTT 61.187 57.895 12.91 0.00 0.00 3.91
1246 1305 2.186160 TGCTCACCGTGGTTGCTTG 61.186 57.895 12.91 0.00 0.00 4.01
1247 1306 2.639286 CTCACCGTGGTTGCTTGC 59.361 61.111 0.00 0.00 0.00 4.01
1248 1307 1.893808 CTCACCGTGGTTGCTTGCT 60.894 57.895 0.00 0.00 0.00 3.91
1249 1308 1.447317 CTCACCGTGGTTGCTTGCTT 61.447 55.000 0.00 0.00 0.00 3.91
1250 1309 1.299316 CACCGTGGTTGCTTGCTTG 60.299 57.895 0.00 0.00 0.00 4.01
1251 1310 2.355009 CCGTGGTTGCTTGCTTGC 60.355 61.111 0.00 0.00 0.00 4.01
1252 1311 2.726912 CGTGGTTGCTTGCTTGCG 60.727 61.111 0.00 0.00 35.36 4.85
1253 1312 2.355009 GTGGTTGCTTGCTTGCGG 60.355 61.111 0.00 0.00 35.36 5.69
1254 1313 4.283403 TGGTTGCTTGCTTGCGGC 62.283 61.111 0.00 0.00 42.22 6.53
1341 1400 4.439968 CCTCTACGAGGTAAATTTCACCC 58.560 47.826 0.00 0.00 44.25 4.61
1360 1419 2.124570 CACCATCCCTCGCCCAAG 60.125 66.667 0.00 0.00 0.00 3.61
1436 1536 0.611896 AAATGTTCTTGGAGCCGGGG 60.612 55.000 2.18 0.00 0.00 5.73
1437 1537 1.789576 AATGTTCTTGGAGCCGGGGT 61.790 55.000 2.18 0.00 0.00 4.95
1439 1539 3.646715 TTCTTGGAGCCGGGGTGG 61.647 66.667 2.05 0.00 42.50 4.61
1531 1631 0.534203 GTTGCCGTCTGAACCTCCAA 60.534 55.000 0.00 0.00 0.00 3.53
1564 1664 6.695713 GCGGGTTCCAATTATTTTATCTCAAC 59.304 38.462 0.00 0.00 0.00 3.18
1565 1665 7.416326 GCGGGTTCCAATTATTTTATCTCAACT 60.416 37.037 0.00 0.00 0.00 3.16
1566 1666 8.466798 CGGGTTCCAATTATTTTATCTCAACTT 58.533 33.333 0.00 0.00 0.00 2.66
1625 1728 3.052082 CACCGAGCAACCCAGCAG 61.052 66.667 0.00 0.00 36.85 4.24
1626 1729 3.560251 ACCGAGCAACCCAGCAGT 61.560 61.111 0.00 0.00 36.85 4.40
1627 1730 2.743928 CCGAGCAACCCAGCAGTC 60.744 66.667 0.00 0.00 36.85 3.51
1674 1777 2.162008 GCGCGGTTAAAAATGGGTTCTA 59.838 45.455 8.83 0.00 0.00 2.10
1687 1798 6.857437 AATGGGTTCTATCCTTTTTCTTGG 57.143 37.500 0.00 0.00 0.00 3.61
1688 1799 5.333566 TGGGTTCTATCCTTTTTCTTGGT 57.666 39.130 0.00 0.00 0.00 3.67
1689 1800 5.076873 TGGGTTCTATCCTTTTTCTTGGTG 58.923 41.667 0.00 0.00 0.00 4.17
1708 1819 1.801771 TGGCGACATCGGTGTAAAAAG 59.198 47.619 0.00 0.00 39.09 2.27
1709 1820 1.129811 GGCGACATCGGTGTAAAAAGG 59.870 52.381 0.00 0.00 39.09 3.11
1711 1822 2.159747 GCGACATCGGTGTAAAAAGGAC 60.160 50.000 0.00 0.00 39.09 3.85
1712 1823 2.414138 CGACATCGGTGTAAAAAGGACC 59.586 50.000 0.00 0.00 39.09 4.46
1719 1830 1.069703 GTGTAAAAAGGACCGAACGCC 60.070 52.381 0.00 0.00 0.00 5.68
1720 1831 1.202675 TGTAAAAAGGACCGAACGCCT 60.203 47.619 0.00 0.00 35.61 5.52
1735 1860 1.888436 CGCCTGAGGTGACTAGCCAA 61.888 60.000 6.07 0.00 44.43 4.52
1754 1879 4.625311 GCCAAACAATGAATTTTCTACCCG 59.375 41.667 0.00 0.00 0.00 5.28
1831 1957 8.598075 CATTAATTTTCTGCCTTGCACTATTTC 58.402 33.333 0.00 0.00 33.79 2.17
1862 1988 3.396260 TTATACCAGGGCGAGCATTAC 57.604 47.619 0.00 0.00 0.00 1.89
1870 1996 2.084546 GGGCGAGCATTACTTTTCTGT 58.915 47.619 0.00 0.00 0.00 3.41
1948 2079 2.665537 TGCAGCAAGAAAACAAAACACG 59.334 40.909 0.00 0.00 0.00 4.49
2028 2183 1.593296 GCTAACCTGACCGGACGTCT 61.593 60.000 16.46 0.00 42.49 4.18
2049 2204 3.190849 CGCCATCTCAGCCGTGTG 61.191 66.667 0.00 0.00 0.00 3.82
2050 2205 2.265739 GCCATCTCAGCCGTGTGA 59.734 61.111 0.00 0.00 0.00 3.58
2051 2206 1.153289 GCCATCTCAGCCGTGTGAT 60.153 57.895 0.00 0.00 37.38 3.06
2052 2207 1.156645 GCCATCTCAGCCGTGTGATC 61.157 60.000 0.00 0.00 35.21 2.92
2053 2208 0.463204 CCATCTCAGCCGTGTGATCT 59.537 55.000 0.00 0.00 35.21 2.75
2054 2209 1.568606 CATCTCAGCCGTGTGATCTG 58.431 55.000 0.00 0.00 35.21 2.90
2055 2210 0.463204 ATCTCAGCCGTGTGATCTGG 59.537 55.000 0.00 0.00 32.55 3.86
2056 2211 1.153489 CTCAGCCGTGTGATCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
2057 2212 1.892819 CTCAGCCGTGTGATCTGGGT 61.893 60.000 0.00 0.00 0.00 4.51
2058 2213 1.742880 CAGCCGTGTGATCTGGGTG 60.743 63.158 10.19 10.19 43.90 4.61
2059 2214 2.217038 AGCCGTGTGATCTGGGTGT 61.217 57.895 0.00 0.00 31.06 4.16
2064 2219 1.205655 CGTGTGATCTGGGTGTGATCT 59.794 52.381 0.00 0.00 40.51 2.75
2075 2230 1.002921 TGTGATCTGGGGATCCGGT 59.997 57.895 5.45 0.00 45.62 5.28
2095 2250 3.822192 CCGACATCGCTCCACGGA 61.822 66.667 0.00 0.00 45.31 4.69
2126 2293 3.551259 AGGACGCCCTGTGTTAATG 57.449 52.632 0.00 0.00 42.42 1.90
2127 2294 0.690762 AGGACGCCCTGTGTTAATGT 59.309 50.000 0.00 0.00 42.42 2.71
2128 2295 1.073284 AGGACGCCCTGTGTTAATGTT 59.927 47.619 0.00 0.00 42.42 2.71
2129 2296 2.303600 AGGACGCCCTGTGTTAATGTTA 59.696 45.455 0.00 0.00 42.42 2.41
2130 2297 3.075884 GGACGCCCTGTGTTAATGTTAA 58.924 45.455 0.00 0.00 0.00 2.01
2131 2298 3.120095 GGACGCCCTGTGTTAATGTTAAC 60.120 47.826 8.36 8.36 42.51 2.01
2132 2299 2.481185 ACGCCCTGTGTTAATGTTAACG 59.519 45.455 10.16 0.00 44.52 3.18
2139 2306 7.461107 CCCTGTGTTAATGTTAACGATAACTG 58.539 38.462 23.01 16.36 44.52 3.16
2176 2343 0.031994 CCAAACGGGTGCTCCAAAAG 59.968 55.000 7.20 0.00 34.36 2.27
2243 2410 2.394563 GCGTTTCAGGCAGCTCCTC 61.395 63.158 2.11 0.00 45.52 3.71
2326 2496 6.019748 AGAGAGAGAGGATAAGAACCAAACA 58.980 40.000 0.00 0.00 0.00 2.83
2381 2551 1.156736 CCAAACGGGCTAGACAACAG 58.843 55.000 0.00 0.00 0.00 3.16
2391 2561 5.519206 CGGGCTAGACAACAGTAGTAATTTC 59.481 44.000 0.00 0.00 0.00 2.17
2505 2675 5.456921 AACTCCAACTCCATCCATGTTAT 57.543 39.130 0.00 0.00 0.00 1.89
2506 2676 4.785301 ACTCCAACTCCATCCATGTTATG 58.215 43.478 0.00 0.00 0.00 1.90
2507 2677 4.228210 ACTCCAACTCCATCCATGTTATGT 59.772 41.667 0.00 0.00 0.00 2.29
2508 2678 5.191727 TCCAACTCCATCCATGTTATGTT 57.808 39.130 0.00 0.00 0.00 2.71
2509 2679 6.069673 ACTCCAACTCCATCCATGTTATGTTA 60.070 38.462 0.00 0.00 0.00 2.41
2664 2834 5.288712 CAGTAACGACGAAACTGCAATCTAT 59.711 40.000 16.99 0.00 34.73 1.98
2665 2837 4.842139 AACGACGAAACTGCAATCTATC 57.158 40.909 0.00 0.00 0.00 2.08
2731 2904 5.870978 CCATTGAAAATGTGATTCCCTGAAC 59.129 40.000 0.00 0.00 0.00 3.18
2732 2905 6.457355 CATTGAAAATGTGATTCCCTGAACA 58.543 36.000 0.00 0.00 0.00 3.18
2872 3053 5.768164 TGTTACAATTTCACCCCTTCTTCTC 59.232 40.000 0.00 0.00 0.00 2.87
3018 3201 3.494048 GCATCCATCTCTAACACTCCCTG 60.494 52.174 0.00 0.00 0.00 4.45
3171 3354 5.066593 ACTGAGAGTTTCCACCTTTTGATC 58.933 41.667 0.00 0.00 0.00 2.92
3192 3375 2.291465 CCCGAACTACGAATGGATACGA 59.709 50.000 0.00 0.00 45.77 3.43
3320 3503 4.338118 CAGCATCAACGGGTATGGTATTTT 59.662 41.667 0.00 0.00 32.80 1.82
3357 3540 2.025981 TGAATCATTCCCCTGGTGTCTG 60.026 50.000 0.00 0.00 0.00 3.51
3453 3636 7.857456 TGAGGTAAGGACTAAGCATTATTTCA 58.143 34.615 0.00 0.00 0.00 2.69
3469 3652 2.775911 TTCATCTGGCTCTGAACCTG 57.224 50.000 0.00 0.00 0.00 4.00
3505 3688 6.586344 TGATTCTTCTGCTTACTCCATAAGG 58.414 40.000 0.00 0.00 40.74 2.69
3523 3706 6.433404 CCATAAGGAGGATGGAATTTCTGATG 59.567 42.308 0.00 0.00 45.89 3.07
3594 3777 1.486310 TCAGATGTATGGTCCTGTGGC 59.514 52.381 0.00 0.00 0.00 5.01
3663 3846 8.343168 ACGAAAATATGGTTGTCCTTTATCAA 57.657 30.769 0.00 0.00 34.23 2.57
3707 3890 0.881118 CCCACGCTAGCAAAATGTGT 59.119 50.000 16.45 0.00 0.00 3.72
3711 3894 3.482786 CACGCTAGCAAAATGTGTTCTC 58.517 45.455 16.45 0.00 0.00 2.87
3762 3947 9.593565 ACAGTGTGATATTATCCTCAGATTCTA 57.406 33.333 0.00 0.00 33.67 2.10
3834 4019 0.690192 TGCGAAAACTCCTGGATCCA 59.310 50.000 15.27 15.27 0.00 3.41
3873 4058 0.539986 GCATGGACGGACTAAGGGAA 59.460 55.000 0.00 0.00 0.00 3.97
3951 4136 6.537301 ACGATAATTACGTTGGTGATGACAAT 59.463 34.615 0.00 0.00 41.18 2.71
3988 4173 5.179522 AGGTAGCCTATGTGATGTGCACTA 61.180 45.833 19.41 4.84 39.28 2.74
4006 4191 8.391859 TGTGCACTAATATTTGTTGTATAACCG 58.608 33.333 19.41 0.00 35.92 4.44
4053 4238 5.525378 GTGACAAAGACTGAACTTCATCTGT 59.475 40.000 0.00 0.00 34.64 3.41
4200 4385 9.727627 GTCCAATATTTGTTTCTTCATCTCATC 57.272 33.333 0.00 0.00 0.00 2.92
4213 4398 8.298729 TCTTCATCTCATCTGTTAGTGTATGT 57.701 34.615 0.00 0.00 0.00 2.29
4222 4407 7.553760 TCATCTGTTAGTGTATGTTCATGCATT 59.446 33.333 0.00 5.68 0.00 3.56
4223 4408 7.686438 TCTGTTAGTGTATGTTCATGCATTT 57.314 32.000 0.00 2.66 0.00 2.32
4224 4409 8.109705 TCTGTTAGTGTATGTTCATGCATTTT 57.890 30.769 0.00 0.65 0.00 1.82
4225 4410 9.225436 TCTGTTAGTGTATGTTCATGCATTTTA 57.775 29.630 0.00 0.00 0.00 1.52
4226 4411 9.277565 CTGTTAGTGTATGTTCATGCATTTTAC 57.722 33.333 0.00 0.00 0.00 2.01
4227 4412 9.008965 TGTTAGTGTATGTTCATGCATTTTACT 57.991 29.630 0.00 2.64 0.00 2.24
4336 4521 6.607019 AGACTAATAAGGACTCCTAGACCAG 58.393 44.000 0.00 0.00 32.35 4.00
4416 4627 6.306987 AGATACAATCCAAACCCATACATCC 58.693 40.000 0.00 0.00 0.00 3.51
4437 4648 4.844085 TCCAACAGGATCTAACTTGGAAGA 59.156 41.667 10.42 0.00 37.93 2.87
4448 4659 3.160585 TGGAAGAGCCACACCTGG 58.839 61.111 0.00 0.00 43.33 4.45
4476 4687 4.403015 AAGCACAGCAAACAACAAAAAC 57.597 36.364 0.00 0.00 0.00 2.43
4489 4700 4.564769 ACAACAAAAACGTTAGGCAATGTG 59.435 37.500 0.00 0.00 34.07 3.21
4496 4707 4.483476 ACGTTAGGCAATGTGAGAAAAC 57.517 40.909 0.00 0.00 32.53 2.43
4513 4724 5.376625 AGAAAACAATAGCAGACAGGAACA 58.623 37.500 0.00 0.00 0.00 3.18
4537 4748 4.065088 GTGACTGACAAAGCCACTGATTA 58.935 43.478 0.00 0.00 36.42 1.75
4565 4776 7.931407 TGTCATAATTATGTACATGTCCTCACC 59.069 37.037 21.89 2.06 35.26 4.02
4566 4777 7.387948 GTCATAATTATGTACATGTCCTCACCC 59.612 40.741 21.89 0.00 35.26 4.61
4592 4803 5.591472 GCATCTGCTATGCCAATATTATGGA 59.409 40.000 12.07 0.00 39.37 3.41
4646 4857 4.248859 CTCCACTAAACTCAGATGTGTGG 58.751 47.826 0.00 0.00 43.22 4.17
4660 4871 0.242017 GTGTGGCTTCATTGCAGGAC 59.758 55.000 0.00 0.00 34.04 3.85
4696 4907 7.653311 AGAAAAACCAGATTTGCATCAAACTAC 59.347 33.333 0.00 0.00 36.13 2.73
4817 5181 5.751028 GTCTATGGACTAAGAACTGCATCAC 59.249 44.000 1.27 0.00 39.24 3.06
4829 5193 4.468095 ACTGCATCACGTTAAAACTCAC 57.532 40.909 0.00 0.00 0.00 3.51
4831 5195 4.024893 ACTGCATCACGTTAAAACTCACAG 60.025 41.667 0.00 0.00 0.00 3.66
4998 5370 9.952030 TGAGGTACTTTTATCATATTGTCACAA 57.048 29.630 0.00 0.00 41.55 3.33
5039 5806 6.721571 TGCAAAAGAAGAAGTAACTATCCG 57.278 37.500 0.00 0.00 0.00 4.18
5084 5854 6.371548 GTGCAATCTGTTCCTGTTAGACATTA 59.628 38.462 0.00 0.00 0.00 1.90
5104 5874 8.792830 ACATTACTGCATCTTAACATAGTTGT 57.207 30.769 0.00 0.00 37.82 3.32
5106 5876 8.668353 CATTACTGCATCTTAACATAGTTGTGT 58.332 33.333 0.00 0.00 35.83 3.72
5197 5967 3.158676 GCTCCCTATACAGACAGGTAGG 58.841 54.545 0.00 0.00 34.74 3.18
5231 6001 6.967199 CCTTGCTGAGTCCGTTTTAAATAATC 59.033 38.462 0.00 0.00 0.00 1.75
5275 6046 3.243839 GGTCACAGCACAACATCCAAATT 60.244 43.478 0.00 0.00 0.00 1.82
5461 6232 5.212745 AGCAAGAGAGCCTACTAGGTAAAT 58.787 41.667 3.95 0.00 37.80 1.40
5554 6325 9.983804 GTAAAACCAAGTTGTAGATATACAAGC 57.016 33.333 13.06 8.50 40.21 4.01
5669 6440 6.347240 GCAGATTTGCTACTGACTATGTATGC 60.347 42.308 0.00 0.00 46.95 3.14
5694 6465 8.798153 GCAATATTATGTAAACAGTTGAAGTGC 58.202 33.333 0.00 0.00 0.00 4.40
5727 6498 2.082140 ACCTGTTCTTTGTTTCCCCC 57.918 50.000 0.00 0.00 0.00 5.40
5788 6561 6.596888 TGTCAATCCTTCAGCTTCTAAATGAG 59.403 38.462 0.00 0.00 0.00 2.90
5854 6717 7.468141 TCTTCTAGTGCAGTTCTTTCAGATA 57.532 36.000 0.00 0.00 0.00 1.98
5906 6769 8.999431 CAACCTTAAACTTCAGATTACTAGCAA 58.001 33.333 0.00 0.00 0.00 3.91
5925 6788 3.855524 GCAAGGTACGGACAAACAATTGG 60.856 47.826 10.83 0.00 41.01 3.16
6028 6891 4.056092 GGAAACGATTCCGGTCTCTAAT 57.944 45.455 8.86 0.00 45.44 1.73
6143 7024 2.060370 CCCAAAAGCAATGGCCAGT 58.940 52.632 13.05 5.37 42.56 4.00
6173 7054 3.790416 TTCAGCCAGTGCCCGCTTT 62.790 57.895 0.00 0.00 38.69 3.51
6215 7096 3.853831 TGCAATACCAAGCTTGTCATG 57.146 42.857 24.35 17.26 0.00 3.07
6302 7183 1.541588 CTCGGATGCGATCTATCACCA 59.458 52.381 10.57 0.00 0.00 4.17
6305 7186 2.415224 CGGATGCGATCTATCACCAGAG 60.415 54.545 0.00 0.00 0.00 3.35
6383 7264 4.020218 TGAATGTTCTCCCTCTTGATCGTT 60.020 41.667 0.00 0.00 0.00 3.85
6410 7291 1.398692 TTTCTGCAACACCTTCCCAC 58.601 50.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.996788 AGATTCAAAGACATGATTGCCC 57.003 40.909 0.00 0.00 0.00 5.36
53 56 4.537135 AGTCCAACGCTAGATTCAAAGA 57.463 40.909 0.00 0.00 0.00 2.52
87 90 1.681076 TGCTCTCAATCAGCAGGCA 59.319 52.632 0.00 0.00 42.09 4.75
221 226 0.179111 TATCCTCTCCAAAGCACGCG 60.179 55.000 3.53 3.53 0.00 6.01
234 239 0.594284 CTCGACGGCCGTTTATCCTC 60.594 60.000 34.65 16.77 39.75 3.71
236 241 0.594284 CTCTCGACGGCCGTTTATCC 60.594 60.000 34.65 18.39 39.75 2.59
255 261 0.038618 AAATGGAACGCCTTTTCGCC 60.039 50.000 0.00 0.00 37.02 5.54
285 291 9.378551 TGTCAAATTATTAGAAAGCTGTATCGT 57.621 29.630 0.00 0.00 0.00 3.73
331 343 1.197721 CTGTTGATCGTGTCTTTGGGC 59.802 52.381 0.00 0.00 0.00 5.36
354 366 1.153997 GAGTTCGGTCCGTCTGCTC 60.154 63.158 11.88 10.56 0.00 4.26
355 367 2.637383 GGAGTTCGGTCCGTCTGCT 61.637 63.158 11.88 5.34 0.00 4.24
356 368 2.126031 GGAGTTCGGTCCGTCTGC 60.126 66.667 11.88 12.28 0.00 4.26
367 388 2.224209 TGGGTGAGAAAAGTCGGAGTTC 60.224 50.000 0.00 0.00 0.00 3.01
385 406 7.211573 TGCATAATTGATTAATTGAAGCTGGG 58.788 34.615 5.75 0.00 37.12 4.45
406 427 9.590451 AGATCATTCGAATTAATTTGTTTGCAT 57.410 25.926 8.21 8.87 0.00 3.96
407 428 8.862074 CAGATCATTCGAATTAATTTGTTTGCA 58.138 29.630 8.21 0.00 0.00 4.08
408 429 7.842721 GCAGATCATTCGAATTAATTTGTTTGC 59.157 33.333 8.21 8.43 0.00 3.68
409 430 8.046132 CGCAGATCATTCGAATTAATTTGTTTG 58.954 33.333 8.21 12.36 0.00 2.93
410 431 7.967854 TCGCAGATCATTCGAATTAATTTGTTT 59.032 29.630 8.21 2.19 0.00 2.83
440 467 1.222115 GCGTGTCTTATCCGGATGGC 61.222 60.000 27.55 13.35 34.14 4.40
466 493 1.591158 CGCACGTTAAAGAGTGTGTGT 59.409 47.619 10.54 0.00 42.11 3.72
602 631 1.264749 TTCTGATGACCCGACCCAGG 61.265 60.000 0.00 0.00 0.00 4.45
637 666 3.561313 GGTGCTCCAGGGAGTTTTTATGA 60.561 47.826 16.31 0.00 43.70 2.15
678 708 1.025041 CTTTTATCGGAGCTTGGCCC 58.975 55.000 0.00 0.00 0.00 5.80
714 744 1.600638 GGAGAACGTTAGGTGGGGG 59.399 63.158 0.00 0.00 0.00 5.40
801 832 0.882927 CTAGGACCCGAGAGCGAGAG 60.883 65.000 0.00 0.00 40.82 3.20
802 833 1.146485 CTAGGACCCGAGAGCGAGA 59.854 63.158 0.00 0.00 40.82 4.04
803 834 2.548295 GCTAGGACCCGAGAGCGAG 61.548 68.421 0.15 0.00 40.82 5.03
804 835 2.516460 GCTAGGACCCGAGAGCGA 60.516 66.667 0.15 0.00 40.82 4.93
805 836 2.517402 AGCTAGGACCCGAGAGCG 60.517 66.667 0.15 0.00 39.96 5.03
806 837 3.124686 CAGCTAGGACCCGAGAGC 58.875 66.667 0.15 2.04 35.07 4.09
807 838 1.452145 GAGCAGCTAGGACCCGAGAG 61.452 65.000 0.00 0.00 0.00 3.20
808 839 1.454111 GAGCAGCTAGGACCCGAGA 60.454 63.158 0.00 0.00 0.00 4.04
809 840 2.494530 GGAGCAGCTAGGACCCGAG 61.495 68.421 0.00 0.00 0.00 4.63
810 841 2.442272 GGAGCAGCTAGGACCCGA 60.442 66.667 0.00 0.00 0.00 5.14
923 956 1.003718 CGGGGGTGAAGGTCAAGAC 60.004 63.158 0.00 0.00 0.00 3.01
1230 1289 1.447317 AAGCAAGCAACCACGGTGAG 61.447 55.000 10.28 2.33 0.00 3.51
1231 1290 1.453015 AAGCAAGCAACCACGGTGA 60.453 52.632 10.28 0.00 0.00 4.02
1232 1291 1.299316 CAAGCAAGCAACCACGGTG 60.299 57.895 0.00 0.00 0.00 4.94
1233 1292 3.119193 CAAGCAAGCAACCACGGT 58.881 55.556 0.00 0.00 0.00 4.83
1234 1293 2.355009 GCAAGCAAGCAACCACGG 60.355 61.111 0.00 0.00 0.00 4.94
1235 1294 2.726912 CGCAAGCAAGCAACCACG 60.727 61.111 1.32 0.00 0.00 4.94
1236 1295 2.355009 CCGCAAGCAAGCAACCAC 60.355 61.111 1.32 0.00 0.00 4.16
1237 1296 4.283403 GCCGCAAGCAAGCAACCA 62.283 61.111 1.32 0.00 42.97 3.67
1254 1313 1.153449 TCTTTATCTGCGTGGGCCG 60.153 57.895 0.00 0.00 38.85 6.13
1255 1314 1.429148 CGTCTTTATCTGCGTGGGCC 61.429 60.000 0.00 0.00 38.85 5.80
1256 1315 1.429148 CCGTCTTTATCTGCGTGGGC 61.429 60.000 0.00 0.00 40.52 5.36
1257 1316 0.174845 TCCGTCTTTATCTGCGTGGG 59.825 55.000 0.00 0.00 0.00 4.61
1258 1317 1.134367 TCTCCGTCTTTATCTGCGTGG 59.866 52.381 0.00 0.00 0.00 4.94
1259 1318 2.561733 TCTCCGTCTTTATCTGCGTG 57.438 50.000 0.00 0.00 0.00 5.34
1260 1319 2.287069 CGATCTCCGTCTTTATCTGCGT 60.287 50.000 0.00 0.00 0.00 5.24
1360 1419 0.318762 AACTCTCTCGACTTGTGGGC 59.681 55.000 0.00 0.00 0.00 5.36
1436 1536 2.841881 TCATTTACTCCTACCCACCCAC 59.158 50.000 0.00 0.00 0.00 4.61
1437 1537 3.112263 CTCATTTACTCCTACCCACCCA 58.888 50.000 0.00 0.00 0.00 4.51
1439 1539 2.483188 CGCTCATTTACTCCTACCCACC 60.483 54.545 0.00 0.00 0.00 4.61
1440 1540 2.822764 CGCTCATTTACTCCTACCCAC 58.177 52.381 0.00 0.00 0.00 4.61
1564 1664 5.054390 TCCGCAGCCAAAATAAGTTTAAG 57.946 39.130 0.00 0.00 0.00 1.85
1565 1665 4.762765 TCTCCGCAGCCAAAATAAGTTTAA 59.237 37.500 0.00 0.00 0.00 1.52
1566 1666 4.155280 GTCTCCGCAGCCAAAATAAGTTTA 59.845 41.667 0.00 0.00 0.00 2.01
1596 1696 1.270826 TGCTCGGTGAGTCTTCTTCTG 59.729 52.381 0.00 0.00 31.39 3.02
1625 1728 1.060122 CGGTTATTCAAAGCGGACGAC 59.940 52.381 0.00 0.00 37.48 4.34
1626 1729 1.352114 CGGTTATTCAAAGCGGACGA 58.648 50.000 0.00 0.00 37.48 4.20
1627 1730 0.247537 GCGGTTATTCAAAGCGGACG 60.248 55.000 10.78 0.00 40.96 4.79
1674 1777 1.886542 GTCGCCACCAAGAAAAAGGAT 59.113 47.619 0.00 0.00 0.00 3.24
1685 1796 1.817911 TTACACCGATGTCGCCACCA 61.818 55.000 0.00 0.00 40.48 4.17
1687 1798 1.149987 TTTTACACCGATGTCGCCAC 58.850 50.000 0.00 0.00 40.48 5.01
1688 1799 1.801771 CTTTTTACACCGATGTCGCCA 59.198 47.619 0.00 0.00 40.48 5.69
1689 1800 1.129811 CCTTTTTACACCGATGTCGCC 59.870 52.381 0.00 0.00 40.48 5.54
1708 1819 3.692406 ACCTCAGGCGTTCGGTCC 61.692 66.667 0.00 0.00 0.00 4.46
1709 1820 2.432628 CACCTCAGGCGTTCGGTC 60.433 66.667 0.00 0.00 0.00 4.79
1711 1822 1.592400 TAGTCACCTCAGGCGTTCGG 61.592 60.000 0.00 0.00 0.00 4.30
1712 1823 0.179161 CTAGTCACCTCAGGCGTTCG 60.179 60.000 0.00 0.00 0.00 3.95
1719 1830 2.839486 TGTTTGGCTAGTCACCTCAG 57.161 50.000 0.00 0.00 0.00 3.35
1720 1831 3.072330 TCATTGTTTGGCTAGTCACCTCA 59.928 43.478 0.00 0.00 0.00 3.86
1735 1860 3.194755 GGCCGGGTAGAAAATTCATTGTT 59.805 43.478 2.18 0.00 0.00 2.83
1754 1879 4.803908 CCCTTTCCTGCTCCGGCC 62.804 72.222 0.00 0.00 37.74 6.13
1831 1957 4.265073 GCCCTGGTATAATAATGCTGAGG 58.735 47.826 0.00 0.00 0.00 3.86
1870 1996 5.240183 GGTCGCACTAGTATAATACACAGGA 59.760 44.000 0.00 0.00 0.00 3.86
1948 2079 1.661341 GTCATCAGATGTGACAGCCC 58.339 55.000 10.34 0.00 44.13 5.19
2048 2203 1.206878 CCCAGATCACACCCAGATCA 58.793 55.000 6.03 0.00 43.35 2.92
2049 2204 0.471617 CCCCAGATCACACCCAGATC 59.528 60.000 0.00 0.00 41.68 2.75
2050 2205 0.044702 TCCCCAGATCACACCCAGAT 59.955 55.000 0.00 0.00 0.00 2.90
2051 2206 0.044702 ATCCCCAGATCACACCCAGA 59.955 55.000 0.00 0.00 0.00 3.86
2052 2207 2.625252 ATCCCCAGATCACACCCAG 58.375 57.895 0.00 0.00 0.00 4.45
2053 2208 4.940571 ATCCCCAGATCACACCCA 57.059 55.556 0.00 0.00 0.00 4.51
2075 2230 4.451150 GTGGAGCGATGTCGGCCA 62.451 66.667 2.24 0.00 40.23 5.36
2081 2236 4.148825 GCCTCCGTGGAGCGATGT 62.149 66.667 10.53 0.00 44.77 3.06
2087 2242 4.271816 CCGATCGCCTCCGTGGAG 62.272 72.222 10.32 9.02 41.63 3.86
2093 2248 1.903890 TCCTGATCCGATCGCCTCC 60.904 63.158 10.32 0.00 0.00 4.30
2095 2250 2.556459 CGTCCTGATCCGATCGCCT 61.556 63.158 10.32 0.00 0.00 5.52
2124 2291 5.123344 GGGTTGCTTCAGTTATCGTTAACAT 59.877 40.000 16.54 1.49 40.20 2.71
2125 2292 4.453136 GGGTTGCTTCAGTTATCGTTAACA 59.547 41.667 16.54 0.00 40.20 2.41
2126 2293 4.435121 CGGGTTGCTTCAGTTATCGTTAAC 60.435 45.833 8.09 8.09 38.39 2.01
2127 2294 3.680937 CGGGTTGCTTCAGTTATCGTTAA 59.319 43.478 0.00 0.00 0.00 2.01
2128 2295 3.255725 CGGGTTGCTTCAGTTATCGTTA 58.744 45.455 0.00 0.00 0.00 3.18
2129 2296 2.073816 CGGGTTGCTTCAGTTATCGTT 58.926 47.619 0.00 0.00 0.00 3.85
2130 2297 1.674817 CCGGGTTGCTTCAGTTATCGT 60.675 52.381 0.00 0.00 0.00 3.73
2131 2298 1.006832 CCGGGTTGCTTCAGTTATCG 58.993 55.000 0.00 0.00 0.00 2.92
2132 2299 2.396590 TCCGGGTTGCTTCAGTTATC 57.603 50.000 0.00 0.00 0.00 1.75
2139 2306 2.282180 TGGCTTCCGGGTTGCTTC 60.282 61.111 0.00 0.00 0.00 3.86
2172 2339 4.549458 CTCAATGATTGTGTTCCGCTTTT 58.451 39.130 4.93 0.00 0.00 2.27
2176 2343 1.133025 CCCTCAATGATTGTGTTCCGC 59.867 52.381 4.93 0.00 0.00 5.54
2243 2410 2.879907 CAATGCCTTGCAGGACCG 59.120 61.111 0.00 0.00 43.65 4.79
2263 2430 1.022982 ACTGTGATGTGATGCTGGCG 61.023 55.000 0.00 0.00 0.00 5.69
2265 2432 2.934553 CAGTACTGTGATGTGATGCTGG 59.065 50.000 15.06 0.00 0.00 4.85
2268 2435 2.349590 TGCAGTACTGTGATGTGATGC 58.650 47.619 23.44 7.07 35.05 3.91
2326 2496 2.039418 TGCAATCCTATCGTGTAGCCT 58.961 47.619 0.00 0.00 0.00 4.58
2381 2551 9.457436 TTTCCAGGTTATCCTTGAAATTACTAC 57.543 33.333 12.79 0.00 44.86 2.73
2391 2561 4.273318 CTCCCTTTTCCAGGTTATCCTTG 58.727 47.826 0.00 0.00 43.07 3.61
2505 2675 0.609131 GCCAAGGAGCAAGCCTAACA 60.609 55.000 0.00 0.00 37.26 2.41
2506 2676 0.322906 AGCCAAGGAGCAAGCCTAAC 60.323 55.000 0.00 0.00 37.26 2.34
2507 2677 0.405585 AAGCCAAGGAGCAAGCCTAA 59.594 50.000 0.00 0.00 37.26 2.69
2508 2678 0.035056 GAAGCCAAGGAGCAAGCCTA 60.035 55.000 0.00 0.00 37.26 3.93
2509 2679 1.303970 GAAGCCAAGGAGCAAGCCT 60.304 57.895 0.00 0.00 40.93 4.58
2639 2809 2.212869 TGCAGTTTCGTCGTTACTGT 57.787 45.000 21.58 0.00 40.99 3.55
2642 2812 5.552104 CGATAGATTGCAGTTTCGTCGTTAC 60.552 44.000 0.00 0.00 39.76 2.50
2777 2951 3.766545 TGCCTGATTGCTTAACCTCTTT 58.233 40.909 0.00 0.00 0.00 2.52
2908 3089 1.530646 CCTCCGTTTACGTACTCGAGC 60.531 57.143 13.61 0.00 40.62 5.03
3018 3201 1.066605 CTTTAGTGCCTGGCATGCATC 59.933 52.381 26.22 11.53 41.91 3.91
3093 3276 2.037772 CCCTCTCGTGGCAATAGCTTAT 59.962 50.000 0.00 0.00 41.70 1.73
3171 3354 2.291465 TCGTATCCATTCGTAGTTCGGG 59.709 50.000 0.00 0.00 40.32 5.14
3192 3375 5.665459 CGGAAGAATGTCAGGTCTTAATCT 58.335 41.667 2.35 0.00 34.23 2.40
3320 3503 7.339466 GGAATGATTCAGCTACCTAAAAGGAAA 59.661 37.037 7.56 0.00 37.67 3.13
3357 3540 4.335400 TCTGAAAATGGGGCTTTGTTTC 57.665 40.909 0.00 0.00 0.00 2.78
3453 3636 3.387374 CAGTATCAGGTTCAGAGCCAGAT 59.613 47.826 14.49 14.49 36.44 2.90
3469 3652 6.054295 AGCAGAAGAATCATGAACCAGTATC 58.946 40.000 0.00 0.00 0.00 2.24
3505 3688 3.887716 CCACCATCAGAAATTCCATCCTC 59.112 47.826 0.00 0.00 0.00 3.71
3523 3706 3.965347 AGGACCTACATACATACACCACC 59.035 47.826 0.00 0.00 0.00 4.61
3594 3777 6.447162 TGTAAGCATCACATAGAGGATAACG 58.553 40.000 0.00 0.00 0.00 3.18
3663 3846 5.355350 CCTCGATTCTTTGCTTCATACCTTT 59.645 40.000 0.00 0.00 0.00 3.11
3731 3916 7.727634 TCTGAGGATAATATCACACTGTGAGAT 59.272 37.037 21.32 21.32 46.04 2.75
3732 3917 7.062957 TCTGAGGATAATATCACACTGTGAGA 58.937 38.462 15.86 13.02 46.04 3.27
3751 3936 6.876257 CGATAATCCCCTTTTAGAATCTGAGG 59.124 42.308 0.00 0.00 0.00 3.86
3762 3947 9.297037 CATTTAGGAATACGATAATCCCCTTTT 57.703 33.333 0.00 0.00 33.55 2.27
3834 4019 0.613572 CAAGGCGGGTAATGGGGTTT 60.614 55.000 0.00 0.00 0.00 3.27
3951 4136 1.004277 GCTACCTTGGTCATGTGGGAA 59.996 52.381 0.00 0.00 0.00 3.97
3988 4173 7.341445 ACCATGCGGTTATACAACAAATATT 57.659 32.000 0.00 0.00 46.31 1.28
4004 4189 7.383843 ACTCAGTTAAAATTTAAAACCATGCGG 59.616 33.333 0.00 0.00 38.77 5.69
4006 4191 9.255304 TCACTCAGTTAAAATTTAAAACCATGC 57.745 29.630 0.00 0.00 0.00 4.06
4062 4247 5.068855 TGTCTTGAATGCCATTGTTCTTCAA 59.931 36.000 0.00 0.00 40.53 2.69
4063 4248 4.583907 TGTCTTGAATGCCATTGTTCTTCA 59.416 37.500 0.00 0.00 0.00 3.02
4068 4253 3.244181 GGGTTGTCTTGAATGCCATTGTT 60.244 43.478 0.00 0.00 0.00 2.83
4200 4385 9.277565 GTAAAATGCATGAACATACACTAACAG 57.722 33.333 0.00 0.00 0.00 3.16
4213 4398 8.965819 TGCTTTCCTAATAGTAAAATGCATGAA 58.034 29.630 0.00 0.00 0.00 2.57
4245 4430 2.559705 CCCCTTGGGCCTTCAATAAAGT 60.560 50.000 4.53 0.00 35.35 2.66
4416 4627 4.633565 GCTCTTCCAAGTTAGATCCTGTTG 59.366 45.833 0.00 0.00 0.00 3.33
4437 4648 2.158608 GCTTATTATCCCAGGTGTGGCT 60.159 50.000 0.00 0.00 43.44 4.75
4448 4659 5.708948 TGTTGTTTGCTGTGCTTATTATCC 58.291 37.500 0.00 0.00 0.00 2.59
4476 4687 4.481930 TGTTTTCTCACATTGCCTAACG 57.518 40.909 0.00 0.00 0.00 3.18
4489 4700 5.470098 TGTTCCTGTCTGCTATTGTTTTCTC 59.530 40.000 0.00 0.00 0.00 2.87
4496 4707 4.153117 GTCACTTGTTCCTGTCTGCTATTG 59.847 45.833 0.00 0.00 0.00 1.90
4607 4818 3.104512 TGGAGGGTCACTACTACAATGG 58.895 50.000 0.00 0.00 0.00 3.16
4646 4857 0.723981 GAGACGTCCTGCAATGAAGC 59.276 55.000 13.01 0.00 0.00 3.86
4660 4871 5.931441 ATCTGGTTTTTCTTTCTGAGACG 57.069 39.130 0.00 0.00 33.02 4.18
4817 5181 6.055231 TCCATTGAACTGTGAGTTTTAACG 57.945 37.500 0.00 0.00 38.80 3.18
4829 5193 6.738114 AGTTTGTACACAATCCATTGAACTG 58.262 36.000 6.29 0.00 40.14 3.16
4831 5195 7.491048 ACAAAGTTTGTACACAATCCATTGAAC 59.509 33.333 19.59 0.00 43.27 3.18
5066 5833 5.237815 TGCAGTAATGTCTAACAGGAACAG 58.762 41.667 0.00 0.00 0.00 3.16
5084 5854 6.486657 ACAACACAACTATGTTAAGATGCAGT 59.513 34.615 0.00 0.00 40.89 4.40
5104 5874 3.625853 TCAAACACCTGGAATCACAACA 58.374 40.909 0.00 0.00 0.00 3.33
5106 5876 4.163441 TCTCAAACACCTGGAATCACAA 57.837 40.909 0.00 0.00 0.00 3.33
5197 5967 2.615747 GGACTCAGCAAGGGAAGTAACC 60.616 54.545 0.00 0.00 0.00 2.85
5231 6001 8.236586 TGACCGAAATGATCAAGAAATAAACAG 58.763 33.333 0.00 0.00 0.00 3.16
5293 6064 0.109272 CACAGCTGCAGCAAGAATGG 60.109 55.000 38.24 20.06 45.16 3.16
5669 6440 8.998989 CGCACTTCAACTGTTTACATAATATTG 58.001 33.333 0.00 0.00 0.00 1.90
5694 6465 8.612619 ACAAAGAACAGGTAATTCTTATATGCG 58.387 33.333 0.69 0.00 43.91 4.73
5727 6498 9.319143 CCTTCCAGTATACATCAAACTTAAGAG 57.681 37.037 10.09 0.00 0.00 2.85
5788 6561 6.927294 ATATTCTTCCGAAAGTCATGGAAC 57.073 37.500 0.00 0.00 36.87 3.62
5854 6717 9.868277 GCTAGATATTCTTATACTTGAGCATGT 57.132 33.333 0.00 0.00 0.00 3.21
5897 6760 4.039004 TGTTTGTCCGTACCTTGCTAGTAA 59.961 41.667 0.00 0.00 0.00 2.24
5899 6762 2.366266 TGTTTGTCCGTACCTTGCTAGT 59.634 45.455 0.00 0.00 0.00 2.57
5906 6769 3.217681 ACCAATTGTTTGTCCGTACCT 57.782 42.857 4.43 0.00 0.00 3.08
5933 6796 7.544622 AGAACCTTTTGTACCAGAAAAAGTTC 58.455 34.615 16.31 16.31 40.30 3.01
6028 6891 5.919755 TGGTATATGGTCGCAAGTTGATTA 58.080 37.500 7.16 0.00 39.48 1.75
6143 7024 2.760634 TGGCTGAACATAGCGAGAAA 57.239 45.000 0.00 0.00 44.60 2.52
6173 7054 7.049754 TGCAAGATATTGATGAGCAGTCTAAA 58.950 34.615 3.77 0.00 0.00 1.85
6215 7096 4.576330 AATACAAGCAGGATATAGGCCC 57.424 45.455 0.00 0.00 0.00 5.80
6302 7183 5.028549 ACACAGTTCATGAGTTTGTCTCT 57.971 39.130 0.00 0.00 43.13 3.10
6305 7186 5.277538 GGAGAACACAGTTCATGAGTTTGTC 60.278 44.000 11.92 0.00 41.97 3.18
6314 7195 3.007940 TCGAATGGGAGAACACAGTTCAT 59.992 43.478 11.92 0.00 30.90 2.57
6383 7264 5.451798 GGAAGGTGTTGCAGAAATGAGAAAA 60.452 40.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.