Multiple sequence alignment - TraesCS5D01G171700

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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 TraesCS5D01G171700 chr5D 100.000 3746 0 0 1 3746 268882842 268879097 0.000000e+00 6918.0
1 TraesCS5D01G171700 chr5D 83.287 359 51 8 1899 2254 486096006 486096358 4.670000e-84 322.0
2 TraesCS5D01G171700 chr5D 97.368 152 3 1 1455 1605 268881239 268881088 1.330000e-64 257.0
3 TraesCS5D01G171700 chr5D 97.368 152 3 1 1604 1755 268881388 268881238 1.330000e-64 257.0
4 TraesCS5D01G171700 chr5D 84.906 106 12 4 2345 2449 486096414 486096516 1.840000e-18 104.0
5 TraesCS5D01G171700 chr5B 93.932 1582 59 14 1604 3169 304604191 304602631 0.000000e+00 2355.0
6 TraesCS5D01G171700 chr5B 91.405 989 45 13 632 1605 304604999 304604036 0.000000e+00 1319.0
7 TraesCS5D01G171700 chr5B 83.784 629 57 23 3154 3746 304602614 304601995 4.230000e-154 555.0
8 TraesCS5D01G171700 chr5B 79.123 570 92 22 1899 2449 597099353 597099914 5.910000e-98 368.0
9 TraesCS5D01G171700 chr5B 94.416 197 8 1 3 196 304605530 304605334 2.190000e-77 300.0
10 TraesCS5D01G171700 chr5B 89.933 149 11 2 476 623 304605266 304605121 4.940000e-44 189.0
11 TraesCS5D01G171700 chr5B 90.769 130 11 1 3294 3423 455618944 455619072 4.970000e-39 172.0
12 TraesCS5D01G171700 chr5B 95.714 70 3 0 219 288 304605336 304605267 3.060000e-21 113.0
13 TraesCS5D01G171700 chr5B 83.871 93 12 3 3654 3745 322558391 322558481 6.670000e-13 86.1
14 TraesCS5D01G171700 chr5A 90.542 793 36 18 463 1216 356475653 356474861 0.000000e+00 1013.0
15 TraesCS5D01G171700 chr5A 91.781 584 40 7 2984 3562 356444160 356443580 0.000000e+00 806.0
16 TraesCS5D01G171700 chr5A 90.069 433 21 8 1 411 356476118 356475686 3.290000e-150 542.0
17 TraesCS5D01G171700 chr5A 92.169 166 9 2 2785 2950 356469424 356469263 8.090000e-57 231.0
18 TraesCS5D01G171700 chr5A 88.000 175 20 1 3572 3746 356443529 356443356 4.900000e-49 206.0
19 TraesCS5D01G171700 chr1D 75.977 1049 197 42 1780 2816 282939388 282938383 1.210000e-134 490.0
20 TraesCS5D01G171700 chr1D 75.158 475 88 23 725 1181 444867682 444867220 2.950000e-46 196.0
21 TraesCS5D01G171700 chr1B 79.892 557 80 19 1779 2329 384216087 384215557 2.730000e-101 379.0
22 TraesCS5D01G171700 chr1B 79.317 556 89 17 667 1207 384231214 384230670 2.130000e-97 366.0
23 TraesCS5D01G171700 chr1B 74.495 545 105 26 667 1188 605015340 605014807 4.900000e-49 206.0
24 TraesCS5D01G171700 chr1B 90.598 117 10 1 3298 3414 258435494 258435379 1.800000e-33 154.0
25 TraesCS5D01G171700 chr1B 88.679 106 10 2 1395 1498 384216317 384216212 1.090000e-25 128.0
26 TraesCS5D01G171700 chr1B 97.222 36 0 1 1378 1412 373689625 373689590 4.040000e-05 60.2
27 TraesCS5D01G171700 chr1B 97.222 36 0 1 1378 1412 472255860 472255895 4.040000e-05 60.2
28 TraesCS5D01G171700 chr7D 86.335 161 15 5 3586 3746 53255846 53255999 6.430000e-38 169.0
29 TraesCS5D01G171700 chr7D 78.824 170 29 6 3579 3746 168294151 168294315 1.420000e-19 108.0
30 TraesCS5D01G171700 chr4B 88.095 126 14 1 3298 3423 136484177 136484301 8.380000e-32 148.0
31 TraesCS5D01G171700 chr4B 84.354 147 15 5 3601 3746 671896094 671895955 1.810000e-28 137.0
32 TraesCS5D01G171700 chr2D 84.667 150 17 5 3572 3721 422095993 422096136 1.080000e-30 145.0
33 TraesCS5D01G171700 chr2D 92.593 54 4 0 3572 3625 343669333 343669280 1.120000e-10 78.7
34 TraesCS5D01G171700 chr3B 84.247 146 21 2 3601 3745 525377452 525377308 1.400000e-29 141.0
35 TraesCS5D01G171700 chr6B 83.562 146 20 4 3601 3746 127739759 127739618 2.350000e-27 134.0
36 TraesCS5D01G171700 chr6A 84.138 145 11 7 3601 3745 328527594 328527462 3.040000e-26 130.0
37 TraesCS5D01G171700 chr2A 89.216 102 11 0 1380 1481 683005726 683005827 1.090000e-25 128.0
38 TraesCS5D01G171700 chr2A 81.203 133 20 3 3615 3746 423142222 423142094 6.620000e-18 102.0
39 TraesCS5D01G171700 chr4A 90.909 55 4 1 173 226 643452467 643452521 5.190000e-09 73.1
40 TraesCS5D01G171700 chr4A 97.222 36 0 1 1378 1412 714763589 714763624 4.040000e-05 60.2
41 TraesCS5D01G171700 chr7A 97.222 36 0 1 1378 1412 103120454 103120419 4.040000e-05 60.2
42 TraesCS5D01G171700 chr1A 97.222 36 0 1 1378 1412 574284028 574284063 4.040000e-05 60.2
43 TraesCS5D01G171700 chr1A 97.222 36 0 1 1378 1412 592565396 592565431 4.040000e-05 60.2
44 TraesCS5D01G171700 chr3A 94.118 34 2 0 119 152 446672490 446672457 7.000000e-03 52.8


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 TraesCS5D01G171700 chr5D 268879097 268882842 3745 True 2477.333333 6918 98.245333 1 3746 3 chr5D.!!$R1 3745
1 TraesCS5D01G171700 chr5D 486096006 486096516 510 False 213.000000 322 84.096500 1899 2449 2 chr5D.!!$F1 550
2 TraesCS5D01G171700 chr5B 304601995 304605530 3535 True 805.166667 2355 91.530667 3 3746 6 chr5B.!!$R1 3743
3 TraesCS5D01G171700 chr5B 597099353 597099914 561 False 368.000000 368 79.123000 1899 2449 1 chr5B.!!$F3 550
4 TraesCS5D01G171700 chr5A 356474861 356476118 1257 True 777.500000 1013 90.305500 1 1216 2 chr5A.!!$R3 1215
5 TraesCS5D01G171700 chr5A 356443356 356444160 804 True 506.000000 806 89.890500 2984 3746 2 chr5A.!!$R2 762
6 TraesCS5D01G171700 chr1D 282938383 282939388 1005 True 490.000000 490 75.977000 1780 2816 1 chr1D.!!$R1 1036
7 TraesCS5D01G171700 chr1B 384230670 384231214 544 True 366.000000 366 79.317000 667 1207 1 chr1B.!!$R3 540
8 TraesCS5D01G171700 chr1B 384215557 384216317 760 True 253.500000 379 84.285500 1395 2329 2 chr1B.!!$R5 934
9 TraesCS5D01G171700 chr1B 605014807 605015340 533 True 206.000000 206 74.495000 667 1188 1 chr1B.!!$R4 521

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
680 835 0.036765 TCGATAAGCAGCCCACGTTT 60.037 50.000 0.00 0.00 0.00 3.60 F
723 878 0.392998 CCGGTGTAAGCTGGCTGATT 60.393 55.000 0.00 0.00 0.00 2.57 F
1264 1460 1.966762 CCATGCACCTTGGTTGACC 59.033 57.895 0.00 0.00 0.00 4.02 F
1616 1830 0.107456 CAGTGCAGGTCCTGTCACTT 59.893 55.000 30.51 19.96 41.88 3.16 F
1618 1832 0.179045 GTGCAGGTCCTGTCACTTGT 60.179 55.000 26.37 0.00 36.42 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1811 0.107456 AAGTGACAGGACCTGCACTG 59.893 55.0 33.38 12.65 42.85 3.66 R
1599 1813 0.179045 ACAAGTGACAGGACCTGCAC 60.179 55.0 27.82 27.82 38.12 4.57 R
2261 2481 0.250513 CAAGTCCCCACTAGGCAGAC 59.749 60.0 0.00 0.00 37.09 3.51 R
2468 2705 0.756294 TTGGCCTTCTTCGTCAGACA 59.244 50.0 3.32 0.00 0.00 3.41 R
3206 3492 1.024579 AGCGAATTACGTTGGCCTGG 61.025 55.0 3.32 0.00 41.89 4.45 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
67 68 6.257994 TCCTAGAATGATGGAAGCAGATTT 57.742 37.500 0.00 0.00 32.93 2.17
77 78 5.823209 TGGAAGCAGATTTCATACATGTG 57.177 39.130 9.11 0.00 0.00 3.21
109 110 6.541278 ACAAGTAAAAAGTCTAGTGACCAACC 59.459 38.462 0.00 0.00 43.91 3.77
148 155 2.669777 AAACCCAACGTCCGGTCTGG 62.670 60.000 0.00 0.00 40.09 3.86
275 293 1.854280 AGTCCCCTGTAAACCAAACCA 59.146 47.619 0.00 0.00 0.00 3.67
304 322 8.250332 AGTTGAAAAGCAATAAAGAAGAACACA 58.750 29.630 0.00 0.00 39.03 3.72
315 333 3.470567 GAACACAGGCTCGACGCG 61.471 66.667 3.53 3.53 40.44 6.01
353 376 2.182614 ATAACCGTGCGTGTTGCTGC 62.183 55.000 0.00 0.00 46.63 5.25
409 435 2.086869 CACGTCCAGCAAAGGATCAAT 58.913 47.619 0.00 0.00 40.42 2.57
410 436 2.489329 CACGTCCAGCAAAGGATCAATT 59.511 45.455 0.00 0.00 40.42 2.32
411 437 2.749621 ACGTCCAGCAAAGGATCAATTC 59.250 45.455 0.00 0.00 40.42 2.17
412 438 3.012518 CGTCCAGCAAAGGATCAATTCT 58.987 45.455 0.00 0.00 40.42 2.40
413 439 3.064545 CGTCCAGCAAAGGATCAATTCTC 59.935 47.826 0.00 0.00 40.42 2.87
414 440 4.012374 GTCCAGCAAAGGATCAATTCTCA 58.988 43.478 0.00 0.00 40.42 3.27
415 441 4.460382 GTCCAGCAAAGGATCAATTCTCAA 59.540 41.667 0.00 0.00 40.42 3.02
416 442 5.047802 GTCCAGCAAAGGATCAATTCTCAAA 60.048 40.000 0.00 0.00 40.42 2.69
417 443 5.539574 TCCAGCAAAGGATCAATTCTCAAAA 59.460 36.000 0.00 0.00 31.23 2.44
418 444 6.041865 TCCAGCAAAGGATCAATTCTCAAAAA 59.958 34.615 0.00 0.00 31.23 1.94
462 488 1.452833 GGATCAGGTGGCCAGCTTC 60.453 63.158 34.41 27.94 36.98 3.86
463 489 1.300963 GATCAGGTGGCCAGCTTCA 59.699 57.895 34.41 23.58 36.98 3.02
464 490 1.001641 ATCAGGTGGCCAGCTTCAC 60.002 57.895 34.41 7.57 36.98 3.18
515 553 1.129326 CAGTGAGTTGGTTCGTCGTC 58.871 55.000 0.00 0.00 0.00 4.20
643 798 8.944029 CAGAAATCTTCTCTCTAGCAATTTCAA 58.056 33.333 0.00 0.00 38.11 2.69
680 835 0.036765 TCGATAAGCAGCCCACGTTT 60.037 50.000 0.00 0.00 0.00 3.60
723 878 0.392998 CCGGTGTAAGCTGGCTGATT 60.393 55.000 0.00 0.00 0.00 2.57
847 1014 9.072375 CCATGATGAAGAGAGTGTACTTCTATA 57.928 37.037 0.00 0.00 41.79 1.31
1123 1317 4.055360 TGAGGTTGACTACAAATGTGTCG 58.945 43.478 0.00 0.00 39.30 4.35
1251 1447 3.691118 TCTTCACTGTAAATCTGCCATGC 59.309 43.478 0.00 0.00 0.00 4.06
1264 1460 1.966762 CCATGCACCTTGGTTGACC 59.033 57.895 0.00 0.00 0.00 4.02
1382 1578 9.771915 GTCGATATAACTTACTAGTAATCTGCC 57.228 37.037 15.57 2.63 33.17 4.85
1415 1613 6.473455 GTCAAGAAACAACACCTTTTCATCAG 59.527 38.462 0.00 0.00 34.68 2.90
1564 1778 4.696877 TGTCTTGCTCATTTGACCATACAG 59.303 41.667 0.00 0.00 0.00 2.74
1565 1779 4.095483 GTCTTGCTCATTTGACCATACAGG 59.905 45.833 0.00 0.00 45.67 4.00
1588 1802 7.304497 GGTCATAAATGTATAGACCCTCTGT 57.696 40.000 10.96 0.00 42.21 3.41
1589 1803 8.418597 GGTCATAAATGTATAGACCCTCTGTA 57.581 38.462 10.96 0.00 42.21 2.74
1590 1804 8.524487 GGTCATAAATGTATAGACCCTCTGTAG 58.476 40.741 10.96 0.00 42.21 2.74
1591 1805 9.298250 GTCATAAATGTATAGACCCTCTGTAGA 57.702 37.037 0.00 0.00 0.00 2.59
1592 1806 9.877222 TCATAAATGTATAGACCCTCTGTAGAA 57.123 33.333 0.00 0.00 0.00 2.10
1595 1809 7.973048 AATGTATAGACCCTCTGTAGAAACA 57.027 36.000 0.00 0.00 0.00 2.83
1605 1819 1.802960 CTGTAGAAACAGCAGTGCAGG 59.197 52.381 19.20 11.61 46.28 4.85
1606 1820 1.140852 TGTAGAAACAGCAGTGCAGGT 59.859 47.619 19.20 12.32 0.00 4.00
1607 1821 1.801178 GTAGAAACAGCAGTGCAGGTC 59.199 52.381 19.20 11.26 0.00 3.85
1608 1822 0.536006 AGAAACAGCAGTGCAGGTCC 60.536 55.000 19.20 10.30 0.00 4.46
1609 1823 0.536006 GAAACAGCAGTGCAGGTCCT 60.536 55.000 19.20 6.09 0.00 3.85
1610 1824 0.820891 AAACAGCAGTGCAGGTCCTG 60.821 55.000 19.20 15.15 34.12 3.86
1611 1825 1.987807 AACAGCAGTGCAGGTCCTGT 61.988 55.000 20.24 8.81 38.30 4.00
1612 1826 1.670406 CAGCAGTGCAGGTCCTGTC 60.670 63.158 20.24 12.69 33.43 3.51
1613 1827 2.142761 AGCAGTGCAGGTCCTGTCA 61.143 57.895 20.24 15.04 33.43 3.58
1614 1828 1.963338 GCAGTGCAGGTCCTGTCAC 60.963 63.158 26.35 26.35 38.12 3.67
1615 1829 1.750930 CAGTGCAGGTCCTGTCACT 59.249 57.895 28.78 28.78 43.69 3.41
1616 1830 0.107456 CAGTGCAGGTCCTGTCACTT 59.893 55.000 30.51 19.96 41.88 3.16
1617 1831 0.107456 AGTGCAGGTCCTGTCACTTG 59.893 55.000 28.78 4.93 41.88 3.16
1618 1832 0.179045 GTGCAGGTCCTGTCACTTGT 60.179 55.000 26.37 0.00 36.42 3.16
1619 1833 0.546122 TGCAGGTCCTGTCACTTGTT 59.454 50.000 20.24 0.00 33.43 2.83
1620 1834 1.064758 TGCAGGTCCTGTCACTTGTTT 60.065 47.619 20.24 0.00 33.43 2.83
1621 1835 2.171659 TGCAGGTCCTGTCACTTGTTTA 59.828 45.455 20.24 0.00 33.43 2.01
1622 1836 3.211045 GCAGGTCCTGTCACTTGTTTAA 58.789 45.455 20.24 0.00 33.43 1.52
1623 1837 3.821033 GCAGGTCCTGTCACTTGTTTAAT 59.179 43.478 20.24 0.00 33.43 1.40
1624 1838 4.083271 GCAGGTCCTGTCACTTGTTTAATC 60.083 45.833 20.24 0.00 33.43 1.75
1625 1839 5.308825 CAGGTCCTGTCACTTGTTTAATCT 58.691 41.667 11.09 0.00 0.00 2.40
1626 1840 5.180117 CAGGTCCTGTCACTTGTTTAATCTG 59.820 44.000 11.09 0.00 0.00 2.90
1627 1841 5.063880 GGTCCTGTCACTTGTTTAATCTGT 58.936 41.667 0.00 0.00 0.00 3.41
1628 1842 5.531287 GGTCCTGTCACTTGTTTAATCTGTT 59.469 40.000 0.00 0.00 0.00 3.16
1629 1843 6.039382 GGTCCTGTCACTTGTTTAATCTGTTT 59.961 38.462 0.00 0.00 0.00 2.83
1630 1844 7.132863 GTCCTGTCACTTGTTTAATCTGTTTC 58.867 38.462 0.00 0.00 0.00 2.78
1631 1845 7.012421 GTCCTGTCACTTGTTTAATCTGTTTCT 59.988 37.037 0.00 0.00 0.00 2.52
1632 1846 7.012327 TCCTGTCACTTGTTTAATCTGTTTCTG 59.988 37.037 0.00 0.00 0.00 3.02
1633 1847 7.201732 CCTGTCACTTGTTTAATCTGTTTCTGT 60.202 37.037 0.00 0.00 0.00 3.41
1634 1848 7.471721 TGTCACTTGTTTAATCTGTTTCTGTG 58.528 34.615 0.00 0.00 0.00 3.66
1635 1849 7.120579 TGTCACTTGTTTAATCTGTTTCTGTGT 59.879 33.333 0.00 0.00 0.00 3.72
1636 1850 8.609176 GTCACTTGTTTAATCTGTTTCTGTGTA 58.391 33.333 0.00 0.00 0.00 2.90
1637 1851 9.168451 TCACTTGTTTAATCTGTTTCTGTGTAA 57.832 29.630 0.00 0.00 0.00 2.41
1638 1852 9.781834 CACTTGTTTAATCTGTTTCTGTGTAAA 57.218 29.630 0.00 0.00 0.00 2.01
1642 1856 9.781834 TGTTTAATCTGTTTCTGTGTAAAGTTG 57.218 29.630 0.00 0.00 0.00 3.16
1643 1857 9.233232 GTTTAATCTGTTTCTGTGTAAAGTTGG 57.767 33.333 0.00 0.00 0.00 3.77
1644 1858 8.740123 TTAATCTGTTTCTGTGTAAAGTTGGA 57.260 30.769 0.00 0.00 0.00 3.53
1645 1859 7.823745 AATCTGTTTCTGTGTAAAGTTGGAT 57.176 32.000 0.00 0.00 0.00 3.41
1646 1860 7.823745 ATCTGTTTCTGTGTAAAGTTGGATT 57.176 32.000 0.00 0.00 0.00 3.01
1647 1861 8.918202 ATCTGTTTCTGTGTAAAGTTGGATTA 57.082 30.769 0.00 0.00 0.00 1.75
1648 1862 8.918202 TCTGTTTCTGTGTAAAGTTGGATTAT 57.082 30.769 0.00 0.00 0.00 1.28
1649 1863 9.349713 TCTGTTTCTGTGTAAAGTTGGATTATT 57.650 29.630 0.00 0.00 0.00 1.40
1650 1864 9.965824 CTGTTTCTGTGTAAAGTTGGATTATTT 57.034 29.630 0.00 0.00 0.00 1.40
1651 1865 9.743057 TGTTTCTGTGTAAAGTTGGATTATTTG 57.257 29.630 0.00 0.00 0.00 2.32
1652 1866 9.959749 GTTTCTGTGTAAAGTTGGATTATTTGA 57.040 29.630 0.00 0.00 0.00 2.69
1658 1872 9.573133 GTGTAAAGTTGGATTATTTGAATCAGG 57.427 33.333 0.17 0.00 0.00 3.86
1659 1873 9.527157 TGTAAAGTTGGATTATTTGAATCAGGA 57.473 29.630 0.17 0.00 0.00 3.86
1662 1876 8.655935 AAGTTGGATTATTTGAATCAGGAAGT 57.344 30.769 0.17 0.00 0.00 3.01
1663 1877 8.059798 AGTTGGATTATTTGAATCAGGAAGTG 57.940 34.615 0.17 0.00 0.00 3.16
1664 1878 7.671398 AGTTGGATTATTTGAATCAGGAAGTGT 59.329 33.333 0.17 0.00 0.00 3.55
1665 1879 7.630242 TGGATTATTTGAATCAGGAAGTGTC 57.370 36.000 0.17 0.00 0.00 3.67
1666 1880 7.405292 TGGATTATTTGAATCAGGAAGTGTCT 58.595 34.615 0.17 0.00 0.00 3.41
1667 1881 7.890127 TGGATTATTTGAATCAGGAAGTGTCTT 59.110 33.333 0.17 0.00 0.00 3.01
1668 1882 9.396022 GGATTATTTGAATCAGGAAGTGTCTTA 57.604 33.333 0.17 0.00 0.00 2.10
1672 1886 8.641498 ATTTGAATCAGGAAGTGTCTTAATGT 57.359 30.769 0.00 0.00 0.00 2.71
1673 1887 8.463930 TTTGAATCAGGAAGTGTCTTAATGTT 57.536 30.769 0.00 0.00 0.00 2.71
1674 1888 8.463930 TTGAATCAGGAAGTGTCTTAATGTTT 57.536 30.769 0.00 0.00 0.00 2.83
1675 1889 7.874940 TGAATCAGGAAGTGTCTTAATGTTTG 58.125 34.615 0.00 0.00 0.00 2.93
1676 1890 5.689383 TCAGGAAGTGTCTTAATGTTTGC 57.311 39.130 0.00 0.00 0.00 3.68
1677 1891 5.129634 TCAGGAAGTGTCTTAATGTTTGCA 58.870 37.500 0.00 0.00 0.00 4.08
1678 1892 5.592282 TCAGGAAGTGTCTTAATGTTTGCAA 59.408 36.000 0.00 0.00 0.00 4.08
1679 1893 5.916883 CAGGAAGTGTCTTAATGTTTGCAAG 59.083 40.000 0.00 0.00 0.00 4.01
1680 1894 5.594317 AGGAAGTGTCTTAATGTTTGCAAGT 59.406 36.000 0.00 0.00 0.00 3.16
1681 1895 6.096846 AGGAAGTGTCTTAATGTTTGCAAGTT 59.903 34.615 0.00 0.00 0.00 2.66
1682 1896 6.756542 GGAAGTGTCTTAATGTTTGCAAGTTT 59.243 34.615 0.00 0.00 0.00 2.66
1683 1897 7.277760 GGAAGTGTCTTAATGTTTGCAAGTTTT 59.722 33.333 0.00 0.00 0.00 2.43
1684 1898 9.296400 GAAGTGTCTTAATGTTTGCAAGTTTTA 57.704 29.630 0.00 0.00 0.00 1.52
1685 1899 8.856490 AGTGTCTTAATGTTTGCAAGTTTTAG 57.144 30.769 0.00 0.00 0.00 1.85
1686 1900 8.466798 AGTGTCTTAATGTTTGCAAGTTTTAGT 58.533 29.630 0.00 0.00 0.00 2.24
1687 1901 8.743099 GTGTCTTAATGTTTGCAAGTTTTAGTC 58.257 33.333 0.00 0.00 0.00 2.59
1688 1902 8.682710 TGTCTTAATGTTTGCAAGTTTTAGTCT 58.317 29.630 0.00 0.00 0.00 3.24
1689 1903 9.170584 GTCTTAATGTTTGCAAGTTTTAGTCTC 57.829 33.333 0.00 0.00 0.00 3.36
1690 1904 8.898761 TCTTAATGTTTGCAAGTTTTAGTCTCA 58.101 29.630 0.00 0.00 0.00 3.27
1691 1905 9.683069 CTTAATGTTTGCAAGTTTTAGTCTCAT 57.317 29.630 0.00 0.00 0.00 2.90
1692 1906 7.935338 AATGTTTGCAAGTTTTAGTCTCATG 57.065 32.000 0.00 0.00 0.00 3.07
1693 1907 6.449635 TGTTTGCAAGTTTTAGTCTCATGT 57.550 33.333 0.00 0.00 0.00 3.21
1694 1908 6.494842 TGTTTGCAAGTTTTAGTCTCATGTC 58.505 36.000 0.00 0.00 0.00 3.06
1695 1909 6.318648 TGTTTGCAAGTTTTAGTCTCATGTCT 59.681 34.615 0.00 0.00 0.00 3.41
1696 1910 6.942532 TTGCAAGTTTTAGTCTCATGTCTT 57.057 33.333 0.00 0.00 0.00 3.01
1697 1911 6.304356 TGCAAGTTTTAGTCTCATGTCTTG 57.696 37.500 0.00 0.00 35.59 3.02
1698 1912 5.149977 GCAAGTTTTAGTCTCATGTCTTGC 58.850 41.667 10.00 10.00 45.47 4.01
1699 1913 5.049129 GCAAGTTTTAGTCTCATGTCTTGCT 60.049 40.000 15.93 0.00 46.90 3.91
1700 1914 6.597614 CAAGTTTTAGTCTCATGTCTTGCTC 58.402 40.000 0.00 0.00 0.00 4.26
1701 1915 5.858381 AGTTTTAGTCTCATGTCTTGCTCA 58.142 37.500 0.00 0.00 0.00 4.26
1702 1916 6.471146 AGTTTTAGTCTCATGTCTTGCTCAT 58.529 36.000 0.00 0.00 0.00 2.90
1703 1917 6.939163 AGTTTTAGTCTCATGTCTTGCTCATT 59.061 34.615 0.00 0.00 0.00 2.57
1704 1918 7.446625 AGTTTTAGTCTCATGTCTTGCTCATTT 59.553 33.333 0.00 0.00 0.00 2.32
1705 1919 6.732531 TTAGTCTCATGTCTTGCTCATTTG 57.267 37.500 0.00 0.00 0.00 2.32
1706 1920 4.903054 AGTCTCATGTCTTGCTCATTTGA 58.097 39.130 0.00 0.00 0.00 2.69
1707 1921 4.694509 AGTCTCATGTCTTGCTCATTTGAC 59.305 41.667 0.00 0.00 0.00 3.18
1708 1922 4.005650 TCTCATGTCTTGCTCATTTGACC 58.994 43.478 0.00 0.00 0.00 4.02
1709 1923 3.753815 TCATGTCTTGCTCATTTGACCA 58.246 40.909 0.00 0.00 0.00 4.02
1765 1980 0.594602 GCAGTGCAGCAACAGAATGA 59.405 50.000 11.09 0.00 39.69 2.57
1805 2020 9.844257 TTTTGAAATGGTTTTGGTTTATCTGAT 57.156 25.926 0.00 0.00 0.00 2.90
1806 2021 8.830201 TTGAAATGGTTTTGGTTTATCTGATG 57.170 30.769 0.00 0.00 0.00 3.07
1807 2022 8.187913 TGAAATGGTTTTGGTTTATCTGATGA 57.812 30.769 0.00 0.00 0.00 2.92
1891 2111 7.214467 TGATTCTAATTGTTGTTCTGAACCC 57.786 36.000 17.26 8.85 0.00 4.11
2159 2379 4.437239 AGTGTTGAAGTCAGTCTTGTGAG 58.563 43.478 0.00 0.00 36.40 3.51
2261 2481 8.648097 GCATATGGTTGTTTATGATAGTAGTCG 58.352 37.037 4.56 0.00 0.00 4.18
2262 2482 9.692749 CATATGGTTGTTTATGATAGTAGTCGT 57.307 33.333 0.00 0.00 0.00 4.34
2263 2483 9.909644 ATATGGTTGTTTATGATAGTAGTCGTC 57.090 33.333 0.00 0.00 0.00 4.20
2329 2566 4.716784 TGGATCATAACCTGTTAGCTGTCT 59.283 41.667 0.00 0.00 0.00 3.41
2468 2705 6.249911 AGATGAAGATGAGGATGACATTGT 57.750 37.500 0.00 0.00 0.00 2.71
2485 2722 0.033504 TGTGTCTGACGAAGAAGGCC 59.966 55.000 0.00 0.00 36.40 5.19
2486 2723 0.033504 GTGTCTGACGAAGAAGGCCA 59.966 55.000 5.01 0.00 36.40 5.36
2590 2830 1.001268 TGAGTGAGACTCTGTGCGAAC 60.001 52.381 3.68 0.00 45.27 3.95
2664 2904 2.016318 CCGCTGCATGGTGAATTCTTA 58.984 47.619 7.05 0.00 0.00 2.10
2684 2924 3.884037 AACAAGATTGGGTGTCCTTCT 57.116 42.857 0.00 0.00 0.00 2.85
2763 3003 6.260050 GTGAGTGAGTGTTTGTATTTTCCTGA 59.740 38.462 0.00 0.00 0.00 3.86
2787 3028 7.766278 TGAGTTTCTATGCTTATTCTCTTGGTC 59.234 37.037 0.00 0.00 0.00 4.02
2802 3043 1.705256 TGGTCGAACGCTGATGTAAC 58.295 50.000 0.00 0.00 0.00 2.50
2866 3107 4.154918 GCAGTAAGAATTGTGGTCTTCTGG 59.845 45.833 11.80 0.00 36.69 3.86
2874 3115 1.276622 GTGGTCTTCTGGCTCCCTTA 58.723 55.000 0.00 0.00 0.00 2.69
2875 3116 1.208293 GTGGTCTTCTGGCTCCCTTAG 59.792 57.143 0.00 0.00 0.00 2.18
2898 3139 7.591006 AGCAGCAATGAATGTAATTTTCTTG 57.409 32.000 0.00 0.00 36.07 3.02
2899 3140 6.091713 AGCAGCAATGAATGTAATTTTCTTGC 59.908 34.615 0.00 12.61 36.07 4.01
2900 3141 6.128499 GCAGCAATGAATGTAATTTTCTTGCA 60.128 34.615 17.77 0.00 36.07 4.08
2901 3142 7.413657 GCAGCAATGAATGTAATTTTCTTGCAT 60.414 33.333 17.77 6.29 36.07 3.96
2902 3143 9.089601 CAGCAATGAATGTAATTTTCTTGCATA 57.910 29.630 17.77 0.00 36.07 3.14
2903 3144 9.656040 AGCAATGAATGTAATTTTCTTGCATAA 57.344 25.926 17.77 0.00 36.07 1.90
2917 3158 9.709495 TTTTCTTGCATAAATTTTAGACTGCAT 57.291 25.926 13.73 0.00 39.16 3.96
3011 3263 6.743575 ATTGTGTAATAGAGTTGCAGGTTC 57.256 37.500 0.00 0.00 0.00 3.62
3072 3324 6.271488 TGTTTGGATAGGAAGATTTTGCTG 57.729 37.500 0.00 0.00 35.58 4.41
3106 3358 6.374588 TCCCTAAATGTGTCTTGGGTTAAAA 58.625 36.000 0.00 0.00 36.23 1.52
3107 3359 6.265876 TCCCTAAATGTGTCTTGGGTTAAAAC 59.734 38.462 0.00 0.00 36.23 2.43
3145 3397 4.404715 TGAAGCTATACAGAGGTTACCCAC 59.595 45.833 0.00 0.00 37.29 4.61
3206 3492 2.774007 CGTCATGGAAATTTCTGCGTC 58.226 47.619 17.42 1.61 0.00 5.19
3218 3504 3.583276 CTGCGTCCAGGCCAACGTA 62.583 63.158 21.43 17.59 40.87 3.57
3220 3506 1.743995 GCGTCCAGGCCAACGTAAT 60.744 57.895 21.43 0.00 40.87 1.89
3222 3508 0.725117 CGTCCAGGCCAACGTAATTC 59.275 55.000 5.01 0.00 34.30 2.17
3230 3516 2.505866 GCCAACGTAATTCGCTTCAAG 58.494 47.619 0.00 0.00 44.19 3.02
3356 3644 2.177394 TGTTTGATGAGCCTGCGTAA 57.823 45.000 0.00 0.00 0.00 3.18
3423 3711 5.428253 TCTTAGCTGGTATTGTTGGATGAC 58.572 41.667 0.00 0.00 0.00 3.06
3437 3725 0.888619 GATGACCGGACTGAGACACA 59.111 55.000 9.46 0.00 0.00 3.72
3443 3731 2.048127 GACTGAGACACACCCGGC 60.048 66.667 0.00 0.00 0.00 6.13
3516 3807 5.820947 TCTCAGATGGTCATGATCACATTTG 59.179 40.000 11.75 14.58 34.15 2.32
3536 3828 4.717233 TGGTGCATCATTGAAATACACC 57.283 40.909 17.25 17.25 44.98 4.16
3548 3840 8.946085 TCATTGAAATACACCATTACTCTCAAC 58.054 33.333 0.00 0.00 0.00 3.18
3562 3854 9.087424 CATTACTCTCAACTTCGTGAAATCATA 57.913 33.333 0.00 0.00 0.00 2.15
3565 3857 8.378172 ACTCTCAACTTCGTGAAATCATAAAA 57.622 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 155 8.830580 TCATATACTAGTTGGACACGTACTAAC 58.169 37.037 0.00 11.23 0.00 2.34
275 293 7.259290 TCTTCTTTATTGCTTTTCAACTCGT 57.741 32.000 0.00 0.00 37.53 4.18
330 348 1.680668 CAACACGCACGGTTATTTGG 58.319 50.000 0.00 0.00 0.00 3.28
353 376 1.472376 GCACTAGCACTTCTAGCAGGG 60.472 57.143 0.00 0.00 46.93 4.45
380 406 2.902705 TGCTGGACGTGAAAAGTACT 57.097 45.000 0.00 0.00 27.15 2.73
386 412 2.151202 GATCCTTTGCTGGACGTGAAA 58.849 47.619 0.00 0.00 39.17 2.69
434 460 3.774766 GGCCACCTGATCCCTAAATTTTT 59.225 43.478 0.00 0.00 0.00 1.94
435 461 3.245948 TGGCCACCTGATCCCTAAATTTT 60.246 43.478 0.00 0.00 0.00 1.82
436 462 2.314549 TGGCCACCTGATCCCTAAATTT 59.685 45.455 0.00 0.00 0.00 1.82
437 463 1.929494 TGGCCACCTGATCCCTAAATT 59.071 47.619 0.00 0.00 0.00 1.82
438 464 1.496429 CTGGCCACCTGATCCCTAAAT 59.504 52.381 0.00 0.00 0.00 1.40
439 465 0.918983 CTGGCCACCTGATCCCTAAA 59.081 55.000 0.00 0.00 0.00 1.85
462 488 2.661537 TGCTTGTGCGTCGAGGTG 60.662 61.111 7.01 0.00 43.34 4.00
463 489 2.644555 AAGTGCTTGTGCGTCGAGGT 62.645 55.000 7.01 0.00 43.34 3.85
464 490 1.891060 GAAGTGCTTGTGCGTCGAGG 61.891 60.000 0.00 0.00 43.34 4.63
465 491 1.488957 GAAGTGCTTGTGCGTCGAG 59.511 57.895 0.00 0.00 43.34 4.04
466 492 2.300066 CGAAGTGCTTGTGCGTCGA 61.300 57.895 0.00 0.00 40.56 4.20
467 493 2.168621 CGAAGTGCTTGTGCGTCG 59.831 61.111 0.00 0.00 43.34 5.12
515 553 1.047739 GACGACAACAACTACCGACG 58.952 55.000 0.00 0.00 0.00 5.12
559 600 0.290840 CGTTCGATCGTGTGTTAGCG 59.709 55.000 15.94 4.52 0.00 4.26
560 601 1.609932 TCGTTCGATCGTGTGTTAGC 58.390 50.000 15.94 0.00 0.00 3.09
562 603 3.370276 TGTTTCGTTCGATCGTGTGTTA 58.630 40.909 15.94 0.00 0.00 2.41
643 798 1.760192 GATTTGCTGCTGGGTCTGAT 58.240 50.000 0.00 0.00 0.00 2.90
680 835 2.591429 CCACGCACCAGCTCAACA 60.591 61.111 0.00 0.00 39.10 3.33
723 878 3.735514 GCCTTAACTTTTTCCGTGTGCAA 60.736 43.478 0.00 0.00 0.00 4.08
847 1014 4.282703 AGTCTACGGTTGTGACCTGTTAAT 59.717 41.667 0.00 0.00 44.20 1.40
854 1021 1.617357 AGGAAGTCTACGGTTGTGACC 59.383 52.381 0.00 0.00 42.87 4.02
985 1171 0.449388 GCCATATTAGCCGCATCAGC 59.551 55.000 0.00 0.00 37.42 4.26
1123 1317 3.314553 TCCTTTCACGATCGAACAGAAC 58.685 45.455 24.34 0.00 0.00 3.01
1251 1447 3.486383 ACATAACTGGTCAACCAAGGTG 58.514 45.455 3.03 3.27 46.97 4.00
1302 1498 9.337396 CCTGCTAACACTATAATGTTCCAATTA 57.663 33.333 2.26 0.00 41.89 1.40
1303 1499 7.834181 ACCTGCTAACACTATAATGTTCCAATT 59.166 33.333 2.26 0.00 41.89 2.32
1304 1500 7.346471 ACCTGCTAACACTATAATGTTCCAAT 58.654 34.615 2.26 0.00 41.89 3.16
1305 1501 6.717289 ACCTGCTAACACTATAATGTTCCAA 58.283 36.000 2.26 0.00 41.89 3.53
1321 1517 2.749076 GCACATGATGACAACCTGCTAA 59.251 45.455 0.00 0.00 0.00 3.09
1325 1521 4.449131 AGATAGCACATGATGACAACCTG 58.551 43.478 0.00 0.00 0.00 4.00
1365 1561 8.376270 ACAAGAAAAGGCAGATTACTAGTAAGT 58.624 33.333 19.58 7.80 39.91 2.24
1415 1613 4.283467 ACAGAAAATAAAAGGGGGCAGAAC 59.717 41.667 0.00 0.00 0.00 3.01
1512 1715 8.129211 AGACTAAACTTGCAAACATTAAGACAC 58.871 33.333 0.00 0.00 0.00 3.67
1564 1778 7.304497 ACAGAGGGTCTATACATTTATGACC 57.696 40.000 0.00 0.00 44.51 4.02
1565 1779 9.298250 TCTACAGAGGGTCTATACATTTATGAC 57.702 37.037 0.00 0.00 0.00 3.06
1566 1780 9.877222 TTCTACAGAGGGTCTATACATTTATGA 57.123 33.333 0.00 0.00 0.00 2.15
1569 1783 9.483489 TGTTTCTACAGAGGGTCTATACATTTA 57.517 33.333 0.00 0.00 0.00 1.40
1570 1784 8.375493 TGTTTCTACAGAGGGTCTATACATTT 57.625 34.615 0.00 0.00 0.00 2.32
1571 1785 7.973048 TGTTTCTACAGAGGGTCTATACATT 57.027 36.000 0.00 0.00 0.00 2.71
1586 1800 1.140852 ACCTGCACTGCTGTTTCTACA 59.859 47.619 1.98 0.00 0.00 2.74
1587 1801 1.801178 GACCTGCACTGCTGTTTCTAC 59.199 52.381 1.98 0.00 0.00 2.59
1588 1802 1.270839 GGACCTGCACTGCTGTTTCTA 60.271 52.381 1.98 0.00 0.00 2.10
1589 1803 0.536006 GGACCTGCACTGCTGTTTCT 60.536 55.000 1.98 0.00 0.00 2.52
1590 1804 0.536006 AGGACCTGCACTGCTGTTTC 60.536 55.000 1.98 1.06 0.00 2.78
1591 1805 0.820891 CAGGACCTGCACTGCTGTTT 60.821 55.000 8.99 0.00 0.00 2.83
1592 1806 1.228063 CAGGACCTGCACTGCTGTT 60.228 57.895 8.99 0.00 0.00 3.16
1593 1807 2.388890 GACAGGACCTGCACTGCTGT 62.389 60.000 21.95 12.20 38.25 4.40
1594 1808 1.670406 GACAGGACCTGCACTGCTG 60.670 63.158 21.95 6.61 38.25 4.41
1595 1809 2.142761 TGACAGGACCTGCACTGCT 61.143 57.895 21.95 0.00 38.25 4.24
1596 1810 1.963338 GTGACAGGACCTGCACTGC 60.963 63.158 27.80 13.67 38.25 4.40
1597 1811 0.107456 AAGTGACAGGACCTGCACTG 59.893 55.000 33.38 12.65 42.85 3.66
1598 1812 0.107456 CAAGTGACAGGACCTGCACT 59.893 55.000 30.20 30.20 44.23 4.40
1599 1813 0.179045 ACAAGTGACAGGACCTGCAC 60.179 55.000 27.82 27.82 38.12 4.57
1600 1814 0.546122 AACAAGTGACAGGACCTGCA 59.454 50.000 21.95 16.72 34.37 4.41
1601 1815 1.680338 AAACAAGTGACAGGACCTGC 58.320 50.000 21.95 14.33 34.37 4.85
1602 1816 5.180117 CAGATTAAACAAGTGACAGGACCTG 59.820 44.000 20.45 20.45 37.52 4.00
1603 1817 5.163195 ACAGATTAAACAAGTGACAGGACCT 60.163 40.000 0.00 0.00 0.00 3.85
1604 1818 5.063880 ACAGATTAAACAAGTGACAGGACC 58.936 41.667 0.00 0.00 0.00 4.46
1605 1819 6.619801 AACAGATTAAACAAGTGACAGGAC 57.380 37.500 0.00 0.00 0.00 3.85
1606 1820 7.012327 CAGAAACAGATTAAACAAGTGACAGGA 59.988 37.037 0.00 0.00 0.00 3.86
1607 1821 7.134815 CAGAAACAGATTAAACAAGTGACAGG 58.865 38.462 0.00 0.00 0.00 4.00
1608 1822 7.641411 CACAGAAACAGATTAAACAAGTGACAG 59.359 37.037 0.00 0.00 0.00 3.51
1609 1823 7.120579 ACACAGAAACAGATTAAACAAGTGACA 59.879 33.333 0.00 0.00 0.00 3.58
1610 1824 7.472543 ACACAGAAACAGATTAAACAAGTGAC 58.527 34.615 0.00 0.00 0.00 3.67
1611 1825 7.624360 ACACAGAAACAGATTAAACAAGTGA 57.376 32.000 0.00 0.00 0.00 3.41
1612 1826 9.781834 TTTACACAGAAACAGATTAAACAAGTG 57.218 29.630 0.00 0.00 0.00 3.16
1616 1830 9.781834 CAACTTTACACAGAAACAGATTAAACA 57.218 29.630 0.00 0.00 0.00 2.83
1617 1831 9.233232 CCAACTTTACACAGAAACAGATTAAAC 57.767 33.333 0.00 0.00 0.00 2.01
1618 1832 9.179909 TCCAACTTTACACAGAAACAGATTAAA 57.820 29.630 0.00 0.00 0.00 1.52
1619 1833 8.740123 TCCAACTTTACACAGAAACAGATTAA 57.260 30.769 0.00 0.00 0.00 1.40
1620 1834 8.918202 ATCCAACTTTACACAGAAACAGATTA 57.082 30.769 0.00 0.00 0.00 1.75
1621 1835 7.823745 ATCCAACTTTACACAGAAACAGATT 57.176 32.000 0.00 0.00 0.00 2.40
1622 1836 7.823745 AATCCAACTTTACACAGAAACAGAT 57.176 32.000 0.00 0.00 0.00 2.90
1623 1837 8.918202 ATAATCCAACTTTACACAGAAACAGA 57.082 30.769 0.00 0.00 0.00 3.41
1624 1838 9.965824 AAATAATCCAACTTTACACAGAAACAG 57.034 29.630 0.00 0.00 0.00 3.16
1625 1839 9.743057 CAAATAATCCAACTTTACACAGAAACA 57.257 29.630 0.00 0.00 0.00 2.83
1626 1840 9.959749 TCAAATAATCCAACTTTACACAGAAAC 57.040 29.630 0.00 0.00 0.00 2.78
1632 1846 9.573133 CCTGATTCAAATAATCCAACTTTACAC 57.427 33.333 0.00 0.00 0.00 2.90
1633 1847 9.527157 TCCTGATTCAAATAATCCAACTTTACA 57.473 29.630 0.00 0.00 0.00 2.41
1636 1850 9.093458 ACTTCCTGATTCAAATAATCCAACTTT 57.907 29.630 0.00 0.00 0.00 2.66
1637 1851 8.526147 CACTTCCTGATTCAAATAATCCAACTT 58.474 33.333 0.00 0.00 0.00 2.66
1638 1852 7.671398 ACACTTCCTGATTCAAATAATCCAACT 59.329 33.333 0.00 0.00 0.00 3.16
1639 1853 7.830739 ACACTTCCTGATTCAAATAATCCAAC 58.169 34.615 0.00 0.00 0.00 3.77
1640 1854 7.890127 AGACACTTCCTGATTCAAATAATCCAA 59.110 33.333 0.00 0.00 0.00 3.53
1641 1855 7.405292 AGACACTTCCTGATTCAAATAATCCA 58.595 34.615 0.00 0.00 0.00 3.41
1642 1856 7.872113 AGACACTTCCTGATTCAAATAATCC 57.128 36.000 0.00 0.00 0.00 3.01
1646 1860 9.739276 ACATTAAGACACTTCCTGATTCAAATA 57.261 29.630 0.00 0.00 0.00 1.40
1647 1861 8.641498 ACATTAAGACACTTCCTGATTCAAAT 57.359 30.769 0.00 0.00 0.00 2.32
1648 1862 8.463930 AACATTAAGACACTTCCTGATTCAAA 57.536 30.769 0.00 0.00 0.00 2.69
1649 1863 8.352201 CAAACATTAAGACACTTCCTGATTCAA 58.648 33.333 0.00 0.00 0.00 2.69
1650 1864 7.522073 GCAAACATTAAGACACTTCCTGATTCA 60.522 37.037 0.00 0.00 0.00 2.57
1651 1865 6.803807 GCAAACATTAAGACACTTCCTGATTC 59.196 38.462 0.00 0.00 0.00 2.52
1652 1866 6.265196 TGCAAACATTAAGACACTTCCTGATT 59.735 34.615 0.00 0.00 0.00 2.57
1653 1867 5.769662 TGCAAACATTAAGACACTTCCTGAT 59.230 36.000 0.00 0.00 0.00 2.90
1654 1868 5.129634 TGCAAACATTAAGACACTTCCTGA 58.870 37.500 0.00 0.00 0.00 3.86
1655 1869 5.437289 TGCAAACATTAAGACACTTCCTG 57.563 39.130 0.00 0.00 0.00 3.86
1656 1870 5.594317 ACTTGCAAACATTAAGACACTTCCT 59.406 36.000 0.00 0.00 0.00 3.36
1657 1871 5.831997 ACTTGCAAACATTAAGACACTTCC 58.168 37.500 0.00 0.00 0.00 3.46
1658 1872 7.755582 AAACTTGCAAACATTAAGACACTTC 57.244 32.000 0.00 0.00 0.00 3.01
1659 1873 9.301153 CTAAAACTTGCAAACATTAAGACACTT 57.699 29.630 0.00 0.00 0.00 3.16
1660 1874 8.466798 ACTAAAACTTGCAAACATTAAGACACT 58.533 29.630 0.00 0.00 0.00 3.55
1661 1875 8.628882 ACTAAAACTTGCAAACATTAAGACAC 57.371 30.769 0.00 0.00 0.00 3.67
1662 1876 8.682710 AGACTAAAACTTGCAAACATTAAGACA 58.317 29.630 0.00 0.00 0.00 3.41
1663 1877 9.170584 GAGACTAAAACTTGCAAACATTAAGAC 57.829 33.333 0.00 0.00 0.00 3.01
1664 1878 8.898761 TGAGACTAAAACTTGCAAACATTAAGA 58.101 29.630 0.00 0.00 0.00 2.10
1665 1879 9.683069 ATGAGACTAAAACTTGCAAACATTAAG 57.317 29.630 0.00 0.00 0.00 1.85
1666 1880 9.462174 CATGAGACTAAAACTTGCAAACATTAA 57.538 29.630 0.00 0.00 0.00 1.40
1667 1881 8.629158 ACATGAGACTAAAACTTGCAAACATTA 58.371 29.630 0.00 0.00 0.00 1.90
1668 1882 7.491682 ACATGAGACTAAAACTTGCAAACATT 58.508 30.769 0.00 0.00 0.00 2.71
1669 1883 7.013655 AGACATGAGACTAAAACTTGCAAACAT 59.986 33.333 0.00 0.00 0.00 2.71
1670 1884 6.318648 AGACATGAGACTAAAACTTGCAAACA 59.681 34.615 0.00 0.00 0.00 2.83
1671 1885 6.729187 AGACATGAGACTAAAACTTGCAAAC 58.271 36.000 0.00 0.00 0.00 2.93
1672 1886 6.942532 AGACATGAGACTAAAACTTGCAAA 57.057 33.333 0.00 0.00 0.00 3.68
1673 1887 6.728200 CAAGACATGAGACTAAAACTTGCAA 58.272 36.000 0.00 0.00 0.00 4.08
1674 1888 6.304356 CAAGACATGAGACTAAAACTTGCA 57.696 37.500 0.00 0.00 0.00 4.08
1675 1889 5.149977 GCAAGACATGAGACTAAAACTTGC 58.850 41.667 0.00 0.00 46.88 4.01
1676 1890 6.203530 TGAGCAAGACATGAGACTAAAACTTG 59.796 38.462 0.00 0.00 37.24 3.16
1677 1891 6.291377 TGAGCAAGACATGAGACTAAAACTT 58.709 36.000 0.00 0.00 0.00 2.66
1678 1892 5.858381 TGAGCAAGACATGAGACTAAAACT 58.142 37.500 0.00 0.00 0.00 2.66
1679 1893 6.734104 ATGAGCAAGACATGAGACTAAAAC 57.266 37.500 0.00 0.00 0.00 2.43
1680 1894 7.445096 TCAAATGAGCAAGACATGAGACTAAAA 59.555 33.333 0.00 0.00 0.00 1.52
1681 1895 6.936335 TCAAATGAGCAAGACATGAGACTAAA 59.064 34.615 0.00 0.00 0.00 1.85
1682 1896 6.369890 GTCAAATGAGCAAGACATGAGACTAA 59.630 38.462 0.00 0.00 33.61 2.24
1683 1897 5.871524 GTCAAATGAGCAAGACATGAGACTA 59.128 40.000 0.00 0.00 33.61 2.59
1684 1898 4.694509 GTCAAATGAGCAAGACATGAGACT 59.305 41.667 0.00 0.00 33.61 3.24
1685 1899 4.142730 GGTCAAATGAGCAAGACATGAGAC 60.143 45.833 0.00 0.00 41.81 3.36
1686 1900 4.005650 GGTCAAATGAGCAAGACATGAGA 58.994 43.478 0.00 0.00 41.81 3.27
1687 1901 4.352600 GGTCAAATGAGCAAGACATGAG 57.647 45.455 0.00 0.00 41.81 2.90
1707 1921 6.706270 GGTCTATACATTTGTGACCTGTATGG 59.294 42.308 10.06 8.83 42.63 2.74
1708 1922 6.706270 GGGTCTATACATTTGTGACCTGTATG 59.294 42.308 14.68 0.00 44.60 2.39
1709 1923 6.615726 AGGGTCTATACATTTGTGACCTGTAT 59.384 38.462 14.68 7.42 44.60 2.29
1794 2009 6.520272 AGCATGACTAGTCATCAGATAAACC 58.480 40.000 31.17 13.11 46.57 3.27
1805 2020 4.507710 GACATGGAAAGCATGACTAGTCA 58.492 43.478 27.07 27.07 44.59 3.41
1806 2021 3.873952 GGACATGGAAAGCATGACTAGTC 59.126 47.826 16.32 16.32 34.39 2.59
1807 2022 3.264193 TGGACATGGAAAGCATGACTAGT 59.736 43.478 0.00 0.00 34.39 2.57
1817 2032 7.396540 AGCTTATAAAGTTGGACATGGAAAG 57.603 36.000 0.00 0.00 0.00 2.62
1891 2111 5.121811 AGCTAACATATCCTTCTGCACAAG 58.878 41.667 0.00 0.00 0.00 3.16
2159 2379 3.243068 ACGATCACCAAGCTGTTGTTTTC 60.243 43.478 0.00 0.00 30.95 2.29
2218 2438 9.442047 AACCATATGCTGTCTATAATTTCTAGC 57.558 33.333 0.00 0.00 0.00 3.42
2261 2481 0.250513 CAAGTCCCCACTAGGCAGAC 59.749 60.000 0.00 0.00 37.09 3.51
2262 2482 0.909610 CCAAGTCCCCACTAGGCAGA 60.910 60.000 0.00 0.00 30.14 4.26
2263 2483 1.201429 ACCAAGTCCCCACTAGGCAG 61.201 60.000 0.00 0.00 30.14 4.85
2329 2566 1.704387 TTGTCTCGTATACGCCGCGA 61.704 55.000 21.79 10.62 39.60 5.87
2468 2705 0.756294 TTGGCCTTCTTCGTCAGACA 59.244 50.000 3.32 0.00 0.00 3.41
2485 2722 4.592942 TCCATTTCATCAGGTTCCTCTTG 58.407 43.478 0.00 0.00 0.00 3.02
2486 2723 4.934797 TCCATTTCATCAGGTTCCTCTT 57.065 40.909 0.00 0.00 0.00 2.85
2520 2757 1.749033 GTCGTCCCCATCATCCTCC 59.251 63.158 0.00 0.00 0.00 4.30
2546 2786 4.327680 AGGGTATTTGAGAGCAACAAGAC 58.672 43.478 0.00 0.00 32.79 3.01
2590 2830 2.435586 CAGCTTGAGGGAGCCGTG 60.436 66.667 0.00 0.00 43.74 4.94
2664 2904 3.884037 AGAAGGACACCCAATCTTGTT 57.116 42.857 0.00 0.00 29.79 2.83
2725 2965 4.818546 CACTCACTCACAGAAAGAACCATT 59.181 41.667 0.00 0.00 0.00 3.16
2763 3003 6.758886 CGACCAAGAGAATAAGCATAGAAACT 59.241 38.462 0.00 0.00 0.00 2.66
2787 3028 4.109766 TCCAATAGTTACATCAGCGTTCG 58.890 43.478 0.00 0.00 0.00 3.95
2802 3043 1.177256 GCTGCCATGCCCTCCAATAG 61.177 60.000 0.00 0.00 0.00 1.73
2874 3115 6.091713 GCAAGAAAATTACATTCATTGCTGCT 59.908 34.615 0.00 0.00 37.61 4.24
2875 3116 6.128499 TGCAAGAAAATTACATTCATTGCTGC 60.128 34.615 17.04 0.00 39.24 5.25
2876 3117 7.354025 TGCAAGAAAATTACATTCATTGCTG 57.646 32.000 17.04 0.00 39.24 4.41
2877 3118 9.656040 TTATGCAAGAAAATTACATTCATTGCT 57.344 25.926 17.04 10.67 39.24 3.91
2922 3163 8.268850 AGATCGTTGCACAAGATTTTACTAAT 57.731 30.769 0.00 0.00 0.00 1.73
2925 3166 7.667043 TTAGATCGTTGCACAAGATTTTACT 57.333 32.000 0.00 0.00 0.00 2.24
2988 3240 5.351465 CGAACCTGCAACTCTATTACACAAT 59.649 40.000 0.00 0.00 0.00 2.71
3005 3257 6.647067 AGAGAAGAGAAAAATGTACGAACCTG 59.353 38.462 0.00 0.00 0.00 4.00
3011 3263 7.385205 TGAGGAAAGAGAAGAGAAAAATGTACG 59.615 37.037 0.00 0.00 0.00 3.67
3072 3324 7.454260 AGACACATTTAGGGAAAGTTGATTC 57.546 36.000 0.00 0.00 0.00 2.52
3106 3358 1.344763 CTTCAGAGTCACCCGGAAAGT 59.655 52.381 0.73 0.00 0.00 2.66
3107 3359 1.941668 GCTTCAGAGTCACCCGGAAAG 60.942 57.143 0.73 0.00 0.00 2.62
3145 3397 3.952323 TGTATCCTCCTCTAAACGTCCAG 59.048 47.826 0.00 0.00 0.00 3.86
3206 3492 1.024579 AGCGAATTACGTTGGCCTGG 61.025 55.000 3.32 0.00 41.89 4.45
3218 3504 5.865552 CCAATTGATGAACTTGAAGCGAATT 59.134 36.000 7.12 0.00 0.00 2.17
3220 3506 4.518590 TCCAATTGATGAACTTGAAGCGAA 59.481 37.500 7.12 0.00 0.00 4.70
3222 3508 4.424061 TCCAATTGATGAACTTGAAGCG 57.576 40.909 7.12 0.00 0.00 4.68
3230 3516 4.565564 GCATTCTGCTTCCAATTGATGAAC 59.434 41.667 7.12 0.00 40.96 3.18
3260 3546 7.827819 TGAACGATGAACTTGAAGTAATAGG 57.172 36.000 0.00 0.00 0.00 2.57
3325 3613 5.060940 GGCTCATCAAACAACGCTTTTTATC 59.939 40.000 0.00 0.00 0.00 1.75
3328 3616 3.123050 GGCTCATCAAACAACGCTTTTT 58.877 40.909 0.00 0.00 0.00 1.94
3356 3644 9.054580 ACTTTACCTGACCAAATACCTAATACT 57.945 33.333 0.00 0.00 0.00 2.12
3423 3711 2.657237 GGGTGTGTCTCAGTCCGG 59.343 66.667 0.00 0.00 0.00 5.14
3437 3725 1.913778 AAATAAAGAAACGGCCGGGT 58.086 45.000 31.76 17.28 0.00 5.28
3486 3777 6.092396 GTGATCATGACCATCTGAGATTATGC 59.908 42.308 0.00 0.00 0.00 3.14
3496 3787 4.863548 ACCAAATGTGATCATGACCATCT 58.136 39.130 0.00 0.00 34.19 2.90
3536 3828 7.351414 TGATTTCACGAAGTTGAGAGTAATG 57.649 36.000 0.00 0.00 41.61 1.90
3690 4023 6.036246 TCATTGATTCTAGAAATGTTCGCG 57.964 37.500 9.71 0.00 33.84 5.87


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

AutoCloner maintained by Alex Coulton.