Multiple sequence alignment - TraesCS6D01G075300

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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 TraesCS6D01G075300 chr6D 100.000 4094 0 0 1 4094 38880499 38876406 0.000000e+00 7561.0
1 TraesCS6D01G075300 chr6D 83.660 306 46 4 3741 4044 38827833 38827530 6.700000e-73 285.0
2 TraesCS6D01G075300 chr6D 82.067 329 49 10 3729 4052 38706838 38706515 5.210000e-69 272.0
3 TraesCS6D01G075300 chr6D 92.763 152 4 3 2934 3083 38804753 38804607 3.210000e-51 213.0
4 TraesCS6D01G075300 chr6D 82.353 136 16 5 3468 3600 38637254 38637124 1.200000e-20 111.0
5 TraesCS6D01G075300 chr6D 87.879 66 8 0 1801 1866 127204526 127204461 1.220000e-10 78.7
6 TraesCS6D01G075300 chr6A 92.039 1859 114 17 1789 3634 51400251 51398414 0.000000e+00 2582.0
7 TraesCS6D01G075300 chr6A 90.732 1025 56 17 805 1802 51401279 51400267 0.000000e+00 1330.0
8 TraesCS6D01G075300 chr6A 92.727 385 27 1 3663 4046 51398351 51397967 4.620000e-154 555.0
9 TraesCS6D01G075300 chr6A 87.379 309 21 6 1 295 51402300 51401996 5.070000e-89 339.0
10 TraesCS6D01G075300 chr6B 90.346 1647 112 23 2415 4046 90102768 90101154 0.000000e+00 2117.0
11 TraesCS6D01G075300 chr6B 90.037 1626 97 30 788 2387 90104459 90102873 0.000000e+00 2045.0
12 TraesCS6D01G075300 chr6B 87.649 251 16 6 2 244 90106720 90106477 1.120000e-70 278.0
13 TraesCS6D01G075300 chr6B 91.111 45 3 1 2006 2049 517825544 517825588 4.420000e-05 60.2
14 TraesCS6D01G075300 chrUn 84.641 306 45 2 3741 4045 76975413 76975717 1.850000e-78 303.0
15 TraesCS6D01G075300 chrUn 84.641 306 45 2 3741 4045 261135552 261135856 1.850000e-78 303.0
16 TraesCS6D01G075300 chrUn 79.928 279 47 8 3741 4014 76981176 76981450 3.230000e-46 196.0
17 TraesCS6D01G075300 chrUn 79.928 279 47 8 3741 4014 261141315 261141589 3.230000e-46 196.0
18 TraesCS6D01G075300 chr1B 74.510 255 46 13 1800 2048 385642547 385642306 4.360000e-15 93.5
19 TraesCS6D01G075300 chr3A 88.060 67 7 1 1801 1866 534540193 534540259 1.220000e-10 78.7
20 TraesCS6D01G075300 chr5B 97.619 42 1 0 2008 2049 677786148 677786107 5.680000e-09 73.1
21 TraesCS6D01G075300 chr5B 97.619 42 1 0 2008 2049 677787126 677787085 5.680000e-09 73.1
22 TraesCS6D01G075300 chr5B 93.333 45 2 1 2006 2049 262818655 262818699 9.500000e-07 65.8
23 TraesCS6D01G075300 chr5B 93.333 45 2 1 2006 2049 654769511 654769555 9.500000e-07 65.8
24 TraesCS6D01G075300 chr3B 84.848 66 10 0 1801 1866 542127286 542127221 2.640000e-07 67.6
25 TraesCS6D01G075300 chr4B 91.304 46 3 1 2005 2049 558599954 558599909 1.230000e-05 62.1
26 TraesCS6D01G075300 chr4B 91.111 45 3 1 2006 2049 629777262 629777218 4.420000e-05 60.2


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 TraesCS6D01G075300 chr6D 38876406 38880499 4093 True 7561.0 7561 100.00000 1 4094 1 chr6D.!!$R5 4093
1 TraesCS6D01G075300 chr6A 51397967 51402300 4333 True 1201.5 2582 90.71925 1 4046 4 chr6A.!!$R1 4045
2 TraesCS6D01G075300 chr6B 90101154 90106720 5566 True 1480.0 2117 89.34400 2 4046 3 chr6B.!!$R1 4044

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
778 2043 0.039617 CACAAAATTCCGCTCCGCAA 60.040 50.000 0.00 0.0 0.00 4.85 F
845 2418 0.175760 CGTGGGTGCATGCTAGTAGT 59.824 55.000 20.33 0.0 0.00 2.73 F
1526 3122 1.005924 GGGGAATCTGGTGGACATTGT 59.994 52.381 0.00 0.0 0.00 2.71 F
2241 3875 1.068127 GGTACGACTGGATATGGCGTT 59.932 52.381 0.00 0.0 36.51 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 3294 1.167851 ATCACCAAGTCAACGGCATG 58.832 50.0 0.00 0.0 0.00 4.06 R
2715 4435 1.428869 AAGGCTGGTCTCAGTTCAGT 58.571 50.0 0.00 0.0 42.78 3.41 R
2964 4687 0.036577 CAGCAACAGCCTAGCTCAGT 60.037 55.0 0.00 0.0 36.40 3.41 R
4046 5808 0.036732 GCTGGTGACATGGAACAGGA 59.963 55.0 12.53 0.0 46.40 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 36 4.273235 TGTGATATGAAATTAGCGGCTGTG 59.727 41.667 13.86 0.00 0.00 3.66
33 37 4.273480 GTGATATGAAATTAGCGGCTGTGT 59.727 41.667 13.86 0.00 0.00 3.72
87 91 1.375396 CACGACGAAATGGCTCCCA 60.375 57.895 0.00 0.00 38.19 4.37
89 93 0.250553 ACGACGAAATGGCTCCCAAA 60.251 50.000 0.00 0.00 36.95 3.28
127 138 2.712087 TGGGGCTACCTTAGTGAAAACA 59.288 45.455 0.00 0.00 41.11 2.83
136 147 7.537649 GCTACCTTAGTGAAAACATTGTTTAGC 59.462 37.037 14.81 11.64 0.00 3.09
177 194 5.657826 TTTTGCTACCATGTGCATGTTAT 57.342 34.783 10.76 0.13 39.07 1.89
210 227 1.007580 TCTTTTGTGCGTGCGTGTAA 58.992 45.000 0.00 0.00 0.00 2.41
213 230 3.247886 TCTTTTGTGCGTGCGTGTAATTA 59.752 39.130 0.00 0.00 0.00 1.40
261 282 3.250744 CACACATAGGACACAACTACCG 58.749 50.000 0.00 0.00 0.00 4.02
262 283 2.268298 CACATAGGACACAACTACCGC 58.732 52.381 0.00 0.00 0.00 5.68
263 284 1.897133 ACATAGGACACAACTACCGCA 59.103 47.619 0.00 0.00 0.00 5.69
264 285 2.500098 ACATAGGACACAACTACCGCAT 59.500 45.455 0.00 0.00 0.00 4.73
265 286 2.665649 TAGGACACAACTACCGCATG 57.334 50.000 0.00 0.00 0.00 4.06
271 292 1.194547 CACAACTACCGCATGACACAC 59.805 52.381 0.00 0.00 0.00 3.82
272 293 1.202592 ACAACTACCGCATGACACACA 60.203 47.619 0.00 0.00 0.00 3.72
295 316 3.065786 TGGCGAGCAATCTCAAATCATTC 59.934 43.478 0.00 0.00 39.30 2.67
298 319 5.097529 GCGAGCAATCTCAAATCATTCAAA 58.902 37.500 0.00 0.00 39.30 2.69
299 320 5.574055 GCGAGCAATCTCAAATCATTCAAAA 59.426 36.000 0.00 0.00 39.30 2.44
300 321 6.089820 GCGAGCAATCTCAAATCATTCAAAAA 59.910 34.615 0.00 0.00 39.30 1.94
321 452 1.649390 AAAAAGACCACGCGCACACA 61.649 50.000 5.73 0.00 0.00 3.72
376 507 6.494893 TGTTACCTGATAGCACACATTTTC 57.505 37.500 0.00 0.00 0.00 2.29
384 515 3.996150 AGCACACATTTTCTCAACTGG 57.004 42.857 0.00 0.00 0.00 4.00
391 522 7.651808 CACACATTTTCTCAACTGGAATTACT 58.348 34.615 0.00 0.00 0.00 2.24
392 523 7.805071 CACACATTTTCTCAACTGGAATTACTC 59.195 37.037 0.00 0.00 0.00 2.59
393 524 7.040409 ACACATTTTCTCAACTGGAATTACTCC 60.040 37.037 0.00 0.00 45.64 3.85
395 526 8.383175 ACATTTTCTCAACTGGAATTACTCCTA 58.617 33.333 0.00 0.00 45.64 2.94
396 527 8.669243 CATTTTCTCAACTGGAATTACTCCTAC 58.331 37.037 0.00 0.00 45.64 3.18
397 528 5.934402 TCTCAACTGGAATTACTCCTACC 57.066 43.478 0.00 0.00 45.64 3.18
398 529 5.590818 TCTCAACTGGAATTACTCCTACCT 58.409 41.667 0.00 0.00 45.64 3.08
399 530 5.422331 TCTCAACTGGAATTACTCCTACCTG 59.578 44.000 0.00 0.00 45.64 4.00
400 531 5.091552 TCAACTGGAATTACTCCTACCTGT 58.908 41.667 0.00 0.00 45.64 4.00
401 532 5.187186 TCAACTGGAATTACTCCTACCTGTC 59.813 44.000 0.00 0.00 45.64 3.51
405 536 6.070710 ACTGGAATTACTCCTACCTGTCTTTC 60.071 42.308 0.00 0.00 45.64 2.62
406 537 5.783360 TGGAATTACTCCTACCTGTCTTTCA 59.217 40.000 0.00 0.00 45.64 2.69
419 550 5.243730 ACCTGTCTTTCAAAACACCCATATG 59.756 40.000 0.00 0.00 0.00 1.78
425 556 9.705290 GTCTTTCAAAACACCCATATGTTAATT 57.295 29.630 1.24 0.00 42.01 1.40
458 593 8.169977 AGGCATATAATCATTTGTTACACAGG 57.830 34.615 0.00 0.00 0.00 4.00
460 595 8.076178 GGCATATAATCATTTGTTACACAGGAC 58.924 37.037 0.00 0.00 0.00 3.85
461 596 7.798516 GCATATAATCATTTGTTACACAGGACG 59.201 37.037 0.00 0.00 0.00 4.79
463 598 7.681939 ATAATCATTTGTTACACAGGACGTT 57.318 32.000 0.00 0.00 0.00 3.99
466 601 5.358090 TCATTTGTTACACAGGACGTTACA 58.642 37.500 0.00 0.00 0.00 2.41
487 622 2.824041 GACGGCGCATCACCCATT 60.824 61.111 10.83 0.00 0.00 3.16
488 623 1.522806 GACGGCGCATCACCCATTA 60.523 57.895 10.83 0.00 0.00 1.90
498 1543 3.199727 GCATCACCCATTAAAAACCCCAT 59.800 43.478 0.00 0.00 0.00 4.00
547 1592 4.627611 GCAATCTTATGCGCCATCATAT 57.372 40.909 4.18 0.00 36.45 1.78
548 1593 4.990257 GCAATCTTATGCGCCATCATATT 58.010 39.130 4.18 0.00 36.45 1.28
549 1594 6.122850 GCAATCTTATGCGCCATCATATTA 57.877 37.500 4.18 0.00 36.45 0.98
550 1595 6.197276 GCAATCTTATGCGCCATCATATTAG 58.803 40.000 4.18 0.00 36.45 1.73
552 1597 6.915544 ATCTTATGCGCCATCATATTAGTG 57.084 37.500 4.18 0.00 0.00 2.74
553 1598 4.631377 TCTTATGCGCCATCATATTAGTGC 59.369 41.667 4.18 0.00 36.30 4.40
555 1600 0.804989 GCGCCATCATATTAGTGCCC 59.195 55.000 0.00 0.00 0.00 5.36
556 1601 1.453155 CGCCATCATATTAGTGCCCC 58.547 55.000 0.00 0.00 0.00 5.80
557 1602 1.839424 GCCATCATATTAGTGCCCCC 58.161 55.000 0.00 0.00 0.00 5.40
558 1603 1.355720 GCCATCATATTAGTGCCCCCT 59.644 52.381 0.00 0.00 0.00 4.79
559 1604 2.576191 GCCATCATATTAGTGCCCCCTA 59.424 50.000 0.00 0.00 0.00 3.53
562 1607 5.195940 CCATCATATTAGTGCCCCCTATTG 58.804 45.833 0.00 0.00 0.00 1.90
563 1608 5.044919 CCATCATATTAGTGCCCCCTATTGA 60.045 44.000 0.00 0.00 0.00 2.57
564 1609 5.499004 TCATATTAGTGCCCCCTATTGAC 57.501 43.478 0.00 0.00 0.00 3.18
565 1610 4.288626 TCATATTAGTGCCCCCTATTGACC 59.711 45.833 0.00 0.00 0.00 4.02
566 1611 0.834612 TTAGTGCCCCCTATTGACCG 59.165 55.000 0.00 0.00 0.00 4.79
567 1612 1.052124 TAGTGCCCCCTATTGACCGG 61.052 60.000 0.00 0.00 0.00 5.28
568 1613 3.093835 TGCCCCCTATTGACCGGG 61.094 66.667 6.32 0.00 40.29 5.73
570 1615 2.380285 GCCCCCTATTGACCGGGAA 61.380 63.158 6.32 0.00 43.44 3.97
571 1616 1.837090 CCCCCTATTGACCGGGAAG 59.163 63.158 6.32 0.00 43.44 3.46
572 1617 0.693092 CCCCCTATTGACCGGGAAGA 60.693 60.000 6.32 0.00 43.44 2.87
573 1618 1.209621 CCCCTATTGACCGGGAAGAA 58.790 55.000 6.32 0.00 43.44 2.52
574 1619 1.774856 CCCCTATTGACCGGGAAGAAT 59.225 52.381 6.32 0.33 43.44 2.40
575 1620 2.174854 CCCCTATTGACCGGGAAGAATT 59.825 50.000 6.32 0.00 43.44 2.17
576 1621 3.214328 CCCTATTGACCGGGAAGAATTG 58.786 50.000 6.32 0.00 43.44 2.32
577 1622 2.618709 CCTATTGACCGGGAAGAATTGC 59.381 50.000 6.32 0.00 34.72 3.56
578 1623 2.514458 ATTGACCGGGAAGAATTGCT 57.486 45.000 6.32 0.00 36.31 3.91
580 1625 2.396590 TGACCGGGAAGAATTGCTAC 57.603 50.000 6.32 0.00 36.31 3.58
581 1626 1.626321 TGACCGGGAAGAATTGCTACA 59.374 47.619 6.32 0.00 36.31 2.74
582 1627 2.280628 GACCGGGAAGAATTGCTACAG 58.719 52.381 6.32 0.00 36.31 2.74
583 1628 1.906574 ACCGGGAAGAATTGCTACAGA 59.093 47.619 6.32 0.00 36.31 3.41
584 1629 2.304761 ACCGGGAAGAATTGCTACAGAA 59.695 45.455 6.32 0.00 36.31 3.02
585 1630 2.939103 CCGGGAAGAATTGCTACAGAAG 59.061 50.000 0.00 0.00 36.31 2.85
586 1631 2.939103 CGGGAAGAATTGCTACAGAAGG 59.061 50.000 0.00 0.00 36.31 3.46
587 1632 2.685388 GGGAAGAATTGCTACAGAAGGC 59.315 50.000 0.00 0.00 36.31 4.35
588 1633 2.352960 GGAAGAATTGCTACAGAAGGCG 59.647 50.000 0.00 0.00 31.69 5.52
589 1634 2.029838 AGAATTGCTACAGAAGGCGG 57.970 50.000 0.00 0.00 0.00 6.13
590 1635 1.555075 AGAATTGCTACAGAAGGCGGA 59.445 47.619 0.00 0.00 0.00 5.54
591 1636 2.171448 AGAATTGCTACAGAAGGCGGAT 59.829 45.455 0.00 0.00 0.00 4.18
592 1637 1.959042 ATTGCTACAGAAGGCGGATG 58.041 50.000 0.00 0.00 0.00 3.51
593 1638 0.107703 TTGCTACAGAAGGCGGATGG 60.108 55.000 0.00 0.00 0.00 3.51
594 1639 1.889573 GCTACAGAAGGCGGATGGC 60.890 63.158 0.00 0.00 42.51 4.40
603 1648 2.907407 GCGGATGGCCCCTTTAGC 60.907 66.667 0.00 0.00 34.80 3.09
633 1795 1.941294 CAAGTCCATGAGAGCTGATGC 59.059 52.381 0.00 0.00 40.05 3.91
636 1798 0.103755 TCCATGAGAGCTGATGCGTC 59.896 55.000 0.00 0.00 45.42 5.19
644 1806 0.249238 AGCTGATGCGTCGAGGATTC 60.249 55.000 9.75 5.14 45.42 2.52
649 1811 0.319040 ATGCGTCGAGGATTCCATCG 60.319 55.000 9.75 14.59 40.26 3.84
668 1830 5.584649 CCATCGGCTAAATAGTTCTTCACAA 59.415 40.000 0.00 0.00 0.00 3.33
669 1831 6.093495 CCATCGGCTAAATAGTTCTTCACAAA 59.907 38.462 0.00 0.00 0.00 2.83
670 1832 7.361713 CCATCGGCTAAATAGTTCTTCACAAAA 60.362 37.037 0.00 0.00 0.00 2.44
671 1833 7.499321 TCGGCTAAATAGTTCTTCACAAAAA 57.501 32.000 0.00 0.00 0.00 1.94
672 1834 7.581476 TCGGCTAAATAGTTCTTCACAAAAAG 58.419 34.615 0.00 0.00 0.00 2.27
674 1836 6.586463 GGCTAAATAGTTCTTCACAAAAAGGC 59.414 38.462 0.00 0.00 0.00 4.35
676 1838 7.327032 GCTAAATAGTTCTTCACAAAAAGGCAG 59.673 37.037 0.00 0.00 0.00 4.85
677 1839 6.715347 AATAGTTCTTCACAAAAAGGCAGT 57.285 33.333 0.00 0.00 0.00 4.40
679 1841 5.405935 AGTTCTTCACAAAAAGGCAGTTT 57.594 34.783 0.00 0.00 0.00 2.66
680 1842 5.793817 AGTTCTTCACAAAAAGGCAGTTTT 58.206 33.333 0.00 0.00 40.26 2.43
710 1975 4.633565 GGATCAGGCAGTTTGTTTCTAGAG 59.366 45.833 0.00 0.00 0.00 2.43
748 2013 3.444029 AGCCAAAGCAATATGGAAACCT 58.556 40.909 0.00 0.00 43.56 3.50
749 2014 4.609301 AGCCAAAGCAATATGGAAACCTA 58.391 39.130 0.00 0.00 43.56 3.08
773 2038 0.994263 GCATGCACAAAATTCCGCTC 59.006 50.000 14.21 0.00 0.00 5.03
775 2040 0.171007 ATGCACAAAATTCCGCTCCG 59.829 50.000 0.00 0.00 0.00 4.63
776 2041 1.801512 GCACAAAATTCCGCTCCGC 60.802 57.895 0.00 0.00 0.00 5.54
778 2043 0.039617 CACAAAATTCCGCTCCGCAA 60.040 50.000 0.00 0.00 0.00 4.85
801 2327 4.439305 AAAAATGTGATGATCGTGGGTG 57.561 40.909 0.00 0.00 0.00 4.61
802 2328 1.382522 AATGTGATGATCGTGGGTGC 58.617 50.000 0.00 0.00 0.00 5.01
803 2329 0.252761 ATGTGATGATCGTGGGTGCA 59.747 50.000 0.00 0.00 0.00 4.57
840 2413 0.179076 CTGATCGTGGGTGCATGCTA 60.179 55.000 20.33 2.15 0.00 3.49
841 2414 0.179076 TGATCGTGGGTGCATGCTAG 60.179 55.000 20.33 3.95 0.00 3.42
842 2415 0.179073 GATCGTGGGTGCATGCTAGT 60.179 55.000 20.33 0.00 0.00 2.57
843 2416 1.068588 GATCGTGGGTGCATGCTAGTA 59.931 52.381 20.33 0.00 0.00 1.82
844 2417 0.459899 TCGTGGGTGCATGCTAGTAG 59.540 55.000 20.33 6.29 0.00 2.57
845 2418 0.175760 CGTGGGTGCATGCTAGTAGT 59.824 55.000 20.33 0.00 0.00 2.73
846 2419 1.407618 CGTGGGTGCATGCTAGTAGTA 59.592 52.381 20.33 0.00 0.00 1.82
847 2420 2.543861 CGTGGGTGCATGCTAGTAGTAG 60.544 54.545 20.33 0.00 0.00 2.57
848 2421 2.693591 GTGGGTGCATGCTAGTAGTAGA 59.306 50.000 20.33 0.00 0.00 2.59
897 2473 3.279434 AGCTCTCAAAACAAAACGGACT 58.721 40.909 0.00 0.00 0.00 3.85
1114 2706 4.741239 TCCTCTCCCCAGCCCCAC 62.741 72.222 0.00 0.00 0.00 4.61
1526 3122 1.005924 GGGGAATCTGGTGGACATTGT 59.994 52.381 0.00 0.00 0.00 2.71
1527 3123 2.369394 GGGAATCTGGTGGACATTGTC 58.631 52.381 8.34 8.34 0.00 3.18
1572 3168 3.806949 TTTAGGGGGATGCCATGATAC 57.193 47.619 5.30 0.00 0.00 2.24
1678 3277 3.441222 TGCTCTGTAAATGTTGGATGCAG 59.559 43.478 0.00 0.00 0.00 4.41
1695 3294 2.224018 TGCAGTTTTCAGGTTTGCCATC 60.224 45.455 0.00 0.00 37.19 3.51
1698 3297 3.991773 CAGTTTTCAGGTTTGCCATCATG 59.008 43.478 0.00 0.00 37.19 3.07
1735 3334 9.313118 GGTGATTTTAACTGAACTGAAATTGTT 57.687 29.630 0.00 0.00 0.00 2.83
1852 3481 3.876589 TTCCGCCACAAGTCCGCTC 62.877 63.158 0.00 0.00 0.00 5.03
1867 3496 2.278857 CTCCGCCGACAATCCTCG 60.279 66.667 0.00 0.00 0.00 4.63
1974 3608 1.460273 ATGTTGGTGGACGTTTGGGC 61.460 55.000 0.00 0.00 0.00 5.36
1978 3612 1.597578 GGTGGACGTTTGGGCGTTA 60.598 57.895 0.00 0.00 45.79 3.18
2241 3875 1.068127 GGTACGACTGGATATGGCGTT 59.932 52.381 0.00 0.00 36.51 4.84
2522 4233 6.806739 TCGTATATATGTGCTTGCATCTACAC 59.193 38.462 0.00 0.00 0.00 2.90
2523 4234 6.586082 CGTATATATGTGCTTGCATCTACACA 59.414 38.462 12.19 12.19 46.16 3.72
2531 4242 4.460034 TGCTTGCATCTACACATTTCACAT 59.540 37.500 0.00 0.00 0.00 3.21
2620 4340 8.459394 AGTCATAAATCATAATCCCCCAAAGAT 58.541 33.333 0.00 0.00 0.00 2.40
2621 4341 9.753674 GTCATAAATCATAATCCCCCAAAGATA 57.246 33.333 0.00 0.00 0.00 1.98
2642 4362 8.723942 AGATACAGAGGTTGCTAAAACAATAG 57.276 34.615 0.00 0.00 0.00 1.73
2666 4386 6.383147 AGCTACCTAGTACATACATGGTGTTT 59.617 38.462 10.68 4.18 36.20 2.83
2672 4392 4.700213 AGTACATACATGGTGTTTGCCTTC 59.300 41.667 10.68 0.00 33.51 3.46
2690 4410 3.763360 CCTTCCCTGTCATGTTTTATGCA 59.237 43.478 0.00 0.00 0.00 3.96
2715 4435 5.008613 GCTCCACATTCTTCAGTTGTTACAA 59.991 40.000 0.00 0.00 0.00 2.41
2716 4436 6.371809 TCCACATTCTTCAGTTGTTACAAC 57.628 37.500 19.35 19.35 0.00 3.32
2717 4437 6.119536 TCCACATTCTTCAGTTGTTACAACT 58.880 36.000 23.25 23.25 0.00 3.16
2718 4438 6.038161 TCCACATTCTTCAGTTGTTACAACTG 59.962 38.462 37.86 37.86 46.67 3.16
2737 4457 3.584848 ACTGAACTGAGACCAGCCTTATT 59.415 43.478 5.95 0.00 44.16 1.40
2752 4472 6.462500 CAGCCTTATTGTCTAGCTACATGAT 58.538 40.000 0.00 0.00 31.23 2.45
2895 4615 2.821991 ACTTTGAGAGGTGGAGTTCG 57.178 50.000 0.00 0.00 0.00 3.95
2902 4622 3.243636 TGAGAGGTGGAGTTCGTTGTTAC 60.244 47.826 0.00 0.00 0.00 2.50
2913 4633 4.807304 AGTTCGTTGTTACTGTGTGGTAAG 59.193 41.667 0.00 0.00 33.12 2.34
2922 4642 2.373836 ACTGTGTGGTAAGGGCACATAA 59.626 45.455 0.00 0.00 41.49 1.90
2963 4686 0.752054 GCAGGAGATGAGTCCCAGAG 59.248 60.000 0.00 0.00 37.31 3.35
2964 4687 1.687682 GCAGGAGATGAGTCCCAGAGA 60.688 57.143 0.00 0.00 37.31 3.10
2965 4688 2.031120 CAGGAGATGAGTCCCAGAGAC 58.969 57.143 0.00 0.00 46.71 3.36
2998 4721 5.631096 GCTGTTGCTGTAAAAGAATTTCTCC 59.369 40.000 0.00 0.00 34.62 3.71
3112 4837 1.279271 ACATTAGTCACCTGGCTGTCC 59.721 52.381 0.00 0.00 0.00 4.02
3162 4887 2.418746 GCCCTGTACAGTGTACATGGAG 60.419 54.545 40.02 29.15 35.93 3.86
3270 4995 6.621613 TCAGTTATGTATCATAGGATGTCGC 58.378 40.000 0.00 0.00 34.89 5.19
3301 5026 3.491639 TCGAGTAAAATGTGTGGTCGTTG 59.508 43.478 0.00 0.00 0.00 4.10
3405 5130 2.025131 TCATGCACCCTCAATTGGATCA 60.025 45.455 5.42 0.00 0.00 2.92
3498 5223 0.749649 TGGATGCACCCAACACAAAC 59.250 50.000 0.00 0.00 38.00 2.93
3499 5224 1.039856 GGATGCACCCAACACAAACT 58.960 50.000 0.00 0.00 0.00 2.66
3500 5225 1.412343 GGATGCACCCAACACAAACTT 59.588 47.619 0.00 0.00 0.00 2.66
3634 5359 8.404000 ACACATTTAGAATAGTAGTGGTAGACG 58.596 37.037 0.00 0.00 0.00 4.18
3638 5366 7.545362 TTAGAATAGTAGTGGTAGACGACAC 57.455 40.000 0.00 0.00 37.86 3.67
3727 5489 4.353777 ACCATAGGTCTAGAACTCAAGCA 58.646 43.478 15.16 0.00 0.00 3.91
3766 5528 3.951775 GAGAGAAGCTCCTTGAGAACA 57.048 47.619 0.00 0.00 37.69 3.18
3798 5560 4.272489 CAGGTCCTGATTATTTGCTCCAA 58.728 43.478 14.26 0.00 32.44 3.53
3799 5561 4.337555 CAGGTCCTGATTATTTGCTCCAAG 59.662 45.833 14.26 0.00 32.44 3.61
3817 5579 2.257353 GCCATCAGCGGTGAAAACT 58.743 52.632 22.64 1.34 35.88 2.66
3818 5580 1.448985 GCCATCAGCGGTGAAAACTA 58.551 50.000 22.64 0.00 35.88 2.24
3823 5585 3.120321 TCAGCGGTGAAAACTATGTGT 57.880 42.857 16.20 0.00 0.00 3.72
3834 5596 7.358023 GGTGAAAACTATGTGTAAATTTGTGCG 60.358 37.037 0.00 0.00 0.00 5.34
3844 5606 5.513495 GTGTAAATTTGTGCGAGTTTTGACA 59.487 36.000 0.00 0.00 0.00 3.58
3859 5621 4.370364 TTTGACAAACTCCAAGCAAGAC 57.630 40.909 0.00 0.00 0.00 3.01
3861 5623 3.206150 TGACAAACTCCAAGCAAGACTC 58.794 45.455 0.00 0.00 0.00 3.36
3980 5742 4.018050 ACTTGAGCCTTTGGAGACCATATT 60.018 41.667 0.00 0.00 31.53 1.28
4024 5786 3.151912 AGCAGCCAGTCTTCTTTCATT 57.848 42.857 0.00 0.00 0.00 2.57
4025 5787 3.080319 AGCAGCCAGTCTTCTTTCATTC 58.920 45.455 0.00 0.00 0.00 2.67
4030 5792 4.018597 AGCCAGTCTTCTTTCATTCCATCT 60.019 41.667 0.00 0.00 0.00 2.90
4038 5800 7.605691 GTCTTCTTTCATTCCATCTTCTTCTGA 59.394 37.037 0.00 0.00 0.00 3.27
4046 5808 6.556974 TTCCATCTTCTTCTGAGTCATCAT 57.443 37.500 0.00 0.00 34.12 2.45
4047 5809 6.159299 TCCATCTTCTTCTGAGTCATCATC 57.841 41.667 0.00 0.00 34.12 2.92
4048 5810 5.070180 TCCATCTTCTTCTGAGTCATCATCC 59.930 44.000 0.00 0.00 34.12 3.51
4049 5811 5.070714 CCATCTTCTTCTGAGTCATCATCCT 59.929 44.000 0.00 0.00 34.12 3.24
4050 5812 5.595257 TCTTCTTCTGAGTCATCATCCTG 57.405 43.478 0.00 0.00 34.12 3.86
4051 5813 5.022122 TCTTCTTCTGAGTCATCATCCTGT 58.978 41.667 0.00 0.00 34.12 4.00
4052 5814 5.483231 TCTTCTTCTGAGTCATCATCCTGTT 59.517 40.000 0.00 0.00 34.12 3.16
4053 5815 5.336150 TCTTCTGAGTCATCATCCTGTTC 57.664 43.478 0.00 0.00 34.12 3.18
4054 5816 4.161189 TCTTCTGAGTCATCATCCTGTTCC 59.839 45.833 0.00 0.00 34.12 3.62
4055 5817 3.444029 TCTGAGTCATCATCCTGTTCCA 58.556 45.455 0.00 0.00 34.12 3.53
4056 5818 4.035814 TCTGAGTCATCATCCTGTTCCAT 58.964 43.478 0.00 0.00 34.12 3.41
4057 5819 4.127907 CTGAGTCATCATCCTGTTCCATG 58.872 47.826 0.00 0.00 34.12 3.66
4058 5820 3.520721 TGAGTCATCATCCTGTTCCATGT 59.479 43.478 0.00 0.00 0.00 3.21
4059 5821 4.125703 GAGTCATCATCCTGTTCCATGTC 58.874 47.826 0.00 0.00 0.00 3.06
4060 5822 3.520721 AGTCATCATCCTGTTCCATGTCA 59.479 43.478 0.00 0.00 0.00 3.58
4061 5823 3.624861 GTCATCATCCTGTTCCATGTCAC 59.375 47.826 0.00 0.00 0.00 3.67
4062 5824 2.787473 TCATCCTGTTCCATGTCACC 57.213 50.000 0.00 0.00 0.00 4.02
4063 5825 1.984424 TCATCCTGTTCCATGTCACCA 59.016 47.619 0.00 0.00 0.00 4.17
4064 5826 2.026915 TCATCCTGTTCCATGTCACCAG 60.027 50.000 0.00 0.00 0.00 4.00
4065 5827 0.036732 TCCTGTTCCATGTCACCAGC 59.963 55.000 0.00 0.00 0.00 4.85
4066 5828 0.962356 CCTGTTCCATGTCACCAGCC 60.962 60.000 0.00 0.00 0.00 4.85
4067 5829 0.037303 CTGTTCCATGTCACCAGCCT 59.963 55.000 0.00 0.00 0.00 4.58
4068 5830 0.036732 TGTTCCATGTCACCAGCCTC 59.963 55.000 0.00 0.00 0.00 4.70
4069 5831 0.036732 GTTCCATGTCACCAGCCTCA 59.963 55.000 0.00 0.00 0.00 3.86
4070 5832 0.994247 TTCCATGTCACCAGCCTCAT 59.006 50.000 0.00 0.00 0.00 2.90
4071 5833 0.543277 TCCATGTCACCAGCCTCATC 59.457 55.000 0.00 0.00 0.00 2.92
4072 5834 0.812811 CCATGTCACCAGCCTCATCG 60.813 60.000 0.00 0.00 0.00 3.84
4073 5835 0.107993 CATGTCACCAGCCTCATCGT 60.108 55.000 0.00 0.00 0.00 3.73
4074 5836 0.176680 ATGTCACCAGCCTCATCGTC 59.823 55.000 0.00 0.00 0.00 4.20
4075 5837 1.184970 TGTCACCAGCCTCATCGTCA 61.185 55.000 0.00 0.00 0.00 4.35
4076 5838 0.176680 GTCACCAGCCTCATCGTCAT 59.823 55.000 0.00 0.00 0.00 3.06
4077 5839 0.461548 TCACCAGCCTCATCGTCATC 59.538 55.000 0.00 0.00 0.00 2.92
4078 5840 0.873312 CACCAGCCTCATCGTCATCG 60.873 60.000 0.00 0.00 38.55 3.84
4079 5841 1.323271 ACCAGCCTCATCGTCATCGT 61.323 55.000 0.00 0.00 38.33 3.73
4080 5842 0.596083 CCAGCCTCATCGTCATCGTC 60.596 60.000 0.00 0.00 38.33 4.20
4081 5843 0.101219 CAGCCTCATCGTCATCGTCA 59.899 55.000 0.00 0.00 38.33 4.35
4082 5844 1.035923 AGCCTCATCGTCATCGTCAT 58.964 50.000 0.00 0.00 38.33 3.06
4083 5845 1.135046 GCCTCATCGTCATCGTCATG 58.865 55.000 0.00 0.00 38.33 3.07
4084 5846 1.135046 CCTCATCGTCATCGTCATGC 58.865 55.000 0.00 0.00 38.33 4.06
4085 5847 1.269465 CCTCATCGTCATCGTCATGCT 60.269 52.381 0.00 0.00 38.33 3.79
4086 5848 2.049959 CTCATCGTCATCGTCATGCTC 58.950 52.381 0.00 0.00 38.33 4.26
4087 5849 0.774685 CATCGTCATCGTCATGCTCG 59.225 55.000 4.24 4.24 38.33 5.03
4088 5850 0.663153 ATCGTCATCGTCATGCTCGA 59.337 50.000 13.30 13.30 38.99 4.04
4089 5851 0.450184 TCGTCATCGTCATGCTCGAA 59.550 50.000 14.51 0.26 40.61 3.71
4090 5852 1.065551 TCGTCATCGTCATGCTCGAAT 59.934 47.619 14.51 4.11 40.61 3.34
4091 5853 1.854743 CGTCATCGTCATGCTCGAATT 59.145 47.619 14.51 0.26 40.61 2.17
4092 5854 2.097685 CGTCATCGTCATGCTCGAATTC 60.098 50.000 14.51 0.00 40.61 2.17
4093 5855 2.860136 GTCATCGTCATGCTCGAATTCA 59.140 45.455 14.51 0.00 40.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 36 2.064581 AGGACGGAGGTGCCCATAC 61.065 63.158 0.00 0.00 34.61 2.39
33 37 2.063979 CAGGACGGAGGTGCCCATA 61.064 63.158 0.00 0.00 34.61 2.74
51 55 5.610982 CGTCGTGCCGGTCAATATAATTAAC 60.611 44.000 1.90 0.00 0.00 2.01
73 77 0.603065 GCTTTTGGGAGCCATTTCGT 59.397 50.000 0.00 0.00 36.66 3.85
177 194 6.018669 ACGCACAAAAGAAAGAAAAACACAAA 60.019 30.769 0.00 0.00 0.00 2.83
263 284 0.606130 TTGCTCGCCATGTGTGTCAT 60.606 50.000 0.00 0.00 37.22 3.06
264 285 0.606130 ATTGCTCGCCATGTGTGTCA 60.606 50.000 0.00 0.00 0.00 3.58
265 286 0.097674 GATTGCTCGCCATGTGTGTC 59.902 55.000 0.00 0.00 0.00 3.67
271 292 2.356695 TGATTTGAGATTGCTCGCCATG 59.643 45.455 0.00 0.00 44.33 3.66
272 293 2.646930 TGATTTGAGATTGCTCGCCAT 58.353 42.857 0.00 0.00 44.33 4.40
302 323 1.063488 GTGTGCGCGTGGTCTTTTT 59.937 52.632 8.43 0.00 0.00 1.94
303 324 1.444119 ATGTGTGCGCGTGGTCTTTT 61.444 50.000 8.43 0.00 0.00 2.27
305 326 2.280797 ATGTGTGCGCGTGGTCTT 60.281 55.556 8.43 0.00 0.00 3.01
306 327 2.987282 TTCATGTGTGCGCGTGGTCT 62.987 55.000 8.43 0.00 0.00 3.85
309 330 1.066656 CATTTCATGTGTGCGCGTGG 61.067 55.000 8.43 0.00 0.00 4.94
346 477 8.397575 TGTGTGCTATCAGGTAACAAAAATTA 57.602 30.769 0.00 0.00 41.41 1.40
351 482 6.892658 AAATGTGTGCTATCAGGTAACAAA 57.107 33.333 0.00 0.00 41.41 2.83
384 515 8.504815 GTTTTGAAAGACAGGTAGGAGTAATTC 58.495 37.037 0.00 0.00 0.00 2.17
391 522 4.457466 GGTGTTTTGAAAGACAGGTAGGA 58.543 43.478 6.17 0.00 34.18 2.94
392 523 3.568430 GGGTGTTTTGAAAGACAGGTAGG 59.432 47.826 6.17 0.00 34.18 3.18
393 524 4.204012 TGGGTGTTTTGAAAGACAGGTAG 58.796 43.478 6.17 0.00 34.18 3.18
395 526 3.094484 TGGGTGTTTTGAAAGACAGGT 57.906 42.857 6.17 0.00 34.18 4.00
396 527 5.243730 ACATATGGGTGTTTTGAAAGACAGG 59.756 40.000 7.80 0.00 34.18 4.00
397 528 6.331369 ACATATGGGTGTTTTGAAAGACAG 57.669 37.500 7.80 0.00 34.18 3.51
398 529 6.723298 AACATATGGGTGTTTTGAAAGACA 57.277 33.333 7.80 0.00 39.15 3.41
399 530 9.705290 AATTAACATATGGGTGTTTTGAAAGAC 57.295 29.630 7.80 0.00 42.08 3.01
443 574 7.124823 TGTGTAACGTCCTGTGTAACAAATGA 61.125 38.462 0.00 0.00 45.59 2.57
444 575 5.006844 TGTGTAACGTCCTGTGTAACAAATG 59.993 40.000 0.00 0.00 45.59 2.32
446 577 4.329528 GTGTGTAACGTCCTGTGTAACAAA 59.670 41.667 0.00 0.00 45.59 2.83
448 579 3.446799 GTGTGTAACGTCCTGTGTAACA 58.553 45.455 0.00 0.00 44.18 2.41
461 596 2.274834 GATGCGCCGTCGTGTGTAAC 62.275 60.000 4.18 0.00 38.14 2.50
463 598 2.505337 GATGCGCCGTCGTGTGTA 60.505 61.111 4.18 0.00 38.14 2.90
472 607 0.453793 TTTTAATGGGTGATGCGCCG 59.546 50.000 4.18 0.00 34.37 6.46
476 611 2.569404 TGGGGTTTTTAATGGGTGATGC 59.431 45.455 0.00 0.00 0.00 3.91
525 1570 1.677942 TGATGGCGCATAAGATTGCA 58.322 45.000 10.83 0.00 42.91 4.08
526 1571 4.627611 ATATGATGGCGCATAAGATTGC 57.372 40.909 10.83 0.00 39.29 3.56
527 1572 7.184779 CACTAATATGATGGCGCATAAGATTG 58.815 38.462 10.83 2.21 34.67 2.67
529 1574 5.295292 GCACTAATATGATGGCGCATAAGAT 59.705 40.000 10.83 0.00 34.67 2.40
531 1576 4.201851 GGCACTAATATGATGGCGCATAAG 60.202 45.833 10.83 0.00 34.67 1.73
532 1577 3.689161 GGCACTAATATGATGGCGCATAA 59.311 43.478 10.83 0.00 34.67 1.90
534 1579 2.086869 GGCACTAATATGATGGCGCAT 58.913 47.619 10.83 0.00 0.00 4.73
536 1581 0.804989 GGGCACTAATATGATGGCGC 59.195 55.000 0.00 0.00 39.68 6.53
537 1582 1.453155 GGGGCACTAATATGATGGCG 58.547 55.000 0.00 0.00 39.68 5.69
538 1583 1.355720 AGGGGGCACTAATATGATGGC 59.644 52.381 0.00 0.00 38.14 4.40
539 1584 5.044919 TCAATAGGGGGCACTAATATGATGG 60.045 44.000 0.00 0.00 0.00 3.51
540 1585 5.882557 GTCAATAGGGGGCACTAATATGATG 59.117 44.000 0.00 0.00 0.00 3.07
541 1586 5.044846 GGTCAATAGGGGGCACTAATATGAT 60.045 44.000 0.00 0.00 0.00 2.45
543 1588 4.589908 GGTCAATAGGGGGCACTAATATG 58.410 47.826 0.00 0.00 0.00 1.78
544 1589 3.263425 CGGTCAATAGGGGGCACTAATAT 59.737 47.826 0.00 0.00 0.00 1.28
545 1590 2.635915 CGGTCAATAGGGGGCACTAATA 59.364 50.000 0.00 0.00 0.00 0.98
546 1591 1.420138 CGGTCAATAGGGGGCACTAAT 59.580 52.381 0.00 0.00 0.00 1.73
547 1592 0.834612 CGGTCAATAGGGGGCACTAA 59.165 55.000 0.00 0.00 0.00 2.24
548 1593 1.052124 CCGGTCAATAGGGGGCACTA 61.052 60.000 0.00 0.00 0.00 2.74
549 1594 2.375345 CCGGTCAATAGGGGGCACT 61.375 63.158 0.00 0.00 0.00 4.40
550 1595 2.192175 CCGGTCAATAGGGGGCAC 59.808 66.667 0.00 0.00 0.00 5.01
556 1601 2.618709 GCAATTCTTCCCGGTCAATAGG 59.381 50.000 0.00 0.00 0.00 2.57
557 1602 3.545703 AGCAATTCTTCCCGGTCAATAG 58.454 45.455 0.00 0.00 0.00 1.73
558 1603 3.644966 AGCAATTCTTCCCGGTCAATA 57.355 42.857 0.00 0.00 0.00 1.90
559 1604 2.514458 AGCAATTCTTCCCGGTCAAT 57.486 45.000 0.00 0.00 0.00 2.57
562 1607 2.093658 TCTGTAGCAATTCTTCCCGGTC 60.094 50.000 0.00 0.00 0.00 4.79
563 1608 1.906574 TCTGTAGCAATTCTTCCCGGT 59.093 47.619 0.00 0.00 0.00 5.28
564 1609 2.691409 TCTGTAGCAATTCTTCCCGG 57.309 50.000 0.00 0.00 0.00 5.73
565 1610 2.939103 CCTTCTGTAGCAATTCTTCCCG 59.061 50.000 0.00 0.00 0.00 5.14
566 1611 2.685388 GCCTTCTGTAGCAATTCTTCCC 59.315 50.000 0.00 0.00 0.00 3.97
567 1612 2.352960 CGCCTTCTGTAGCAATTCTTCC 59.647 50.000 0.00 0.00 0.00 3.46
568 1613 2.352960 CCGCCTTCTGTAGCAATTCTTC 59.647 50.000 0.00 0.00 0.00 2.87
570 1615 1.555075 TCCGCCTTCTGTAGCAATTCT 59.445 47.619 0.00 0.00 0.00 2.40
571 1616 2.024176 TCCGCCTTCTGTAGCAATTC 57.976 50.000 0.00 0.00 0.00 2.17
572 1617 2.292267 CATCCGCCTTCTGTAGCAATT 58.708 47.619 0.00 0.00 0.00 2.32
573 1618 1.475751 CCATCCGCCTTCTGTAGCAAT 60.476 52.381 0.00 0.00 0.00 3.56
574 1619 0.107703 CCATCCGCCTTCTGTAGCAA 60.108 55.000 0.00 0.00 0.00 3.91
575 1620 1.522092 CCATCCGCCTTCTGTAGCA 59.478 57.895 0.00 0.00 0.00 3.49
576 1621 1.889573 GCCATCCGCCTTCTGTAGC 60.890 63.158 0.00 0.00 0.00 3.58
577 1622 4.445699 GCCATCCGCCTTCTGTAG 57.554 61.111 0.00 0.00 0.00 2.74
586 1631 2.907407 GCTAAAGGGGCCATCCGC 60.907 66.667 4.39 0.00 44.97 5.54
621 1783 1.431036 CTCGACGCATCAGCTCTCA 59.569 57.895 0.00 0.00 39.10 3.27
633 1795 1.661821 GCCGATGGAATCCTCGACG 60.662 63.158 18.14 10.43 41.39 5.12
636 1798 2.526304 TTTAGCCGATGGAATCCTCG 57.474 50.000 12.15 12.15 41.39 4.63
644 1806 5.116180 TGTGAAGAACTATTTAGCCGATGG 58.884 41.667 0.00 0.00 0.00 3.51
649 1811 6.586463 GCCTTTTTGTGAAGAACTATTTAGCC 59.414 38.462 0.00 0.00 0.00 3.93
683 1845 5.385198 AGAAACAAACTGCCTGATCCTAAA 58.615 37.500 0.00 0.00 0.00 1.85
685 1847 4.640771 AGAAACAAACTGCCTGATCCTA 57.359 40.909 0.00 0.00 0.00 2.94
687 1849 4.579869 TCTAGAAACAAACTGCCTGATCC 58.420 43.478 0.00 0.00 0.00 3.36
688 1850 5.121454 CACTCTAGAAACAAACTGCCTGATC 59.879 44.000 0.00 0.00 0.00 2.92
690 1852 4.100963 TCACTCTAGAAACAAACTGCCTGA 59.899 41.667 0.00 0.00 0.00 3.86
691 1853 4.380531 TCACTCTAGAAACAAACTGCCTG 58.619 43.478 0.00 0.00 0.00 4.85
699 1964 2.912956 AGCCCCATCACTCTAGAAACAA 59.087 45.455 0.00 0.00 0.00 2.83
748 2013 3.613671 CGGAATTTTGTGCATGCCTTGTA 60.614 43.478 16.68 0.00 0.00 2.41
749 2014 2.769893 GGAATTTTGTGCATGCCTTGT 58.230 42.857 16.68 0.00 0.00 3.16
784 2310 0.252761 TGCACCCACGATCATCACAT 59.747 50.000 0.00 0.00 0.00 3.21
785 2311 0.252761 ATGCACCCACGATCATCACA 59.747 50.000 0.00 0.00 0.00 3.58
786 2312 1.382522 AATGCACCCACGATCATCAC 58.617 50.000 0.00 0.00 0.00 3.06
815 2388 1.278985 TGCACCCACGATCAGATTTCT 59.721 47.619 0.00 0.00 0.00 2.52
820 2393 1.450134 GCATGCACCCACGATCAGA 60.450 57.895 14.21 0.00 0.00 3.27
821 2394 0.179076 TAGCATGCACCCACGATCAG 60.179 55.000 21.98 0.00 0.00 2.90
840 2413 1.205055 GGCCTGGCCTTTCTACTACT 58.795 55.000 30.42 0.00 46.69 2.57
841 2414 3.782632 GGCCTGGCCTTTCTACTAC 57.217 57.895 30.42 0.00 46.69 2.73
897 2473 1.035923 TTTGTGCTGGCGAAATGGAA 58.964 45.000 0.00 0.00 0.00 3.53
1007 2583 1.143969 CGCGTCCGAGTTGGTTATCC 61.144 60.000 0.00 0.00 39.52 2.59
1526 3122 7.591421 TTCAAATACCTATGATGTCTACGGA 57.409 36.000 0.00 0.00 0.00 4.69
1527 3123 8.833231 ATTTCAAATACCTATGATGTCTACGG 57.167 34.615 0.00 0.00 0.00 4.02
1534 3130 8.806146 CCCCCTAAATTTCAAATACCTATGATG 58.194 37.037 0.00 0.00 0.00 3.07
1538 3134 7.454694 GCATCCCCCTAAATTTCAAATACCTAT 59.545 37.037 0.00 0.00 0.00 2.57
1572 3168 6.709643 CCACAATGCTTCTTAACTCTTATCG 58.290 40.000 0.00 0.00 0.00 2.92
1651 3250 3.826157 TCCAACATTTACAGAGCAAAGGG 59.174 43.478 0.00 0.00 0.00 3.95
1678 3277 2.738314 GCATGATGGCAAACCTGAAAAC 59.262 45.455 0.00 0.00 36.63 2.43
1695 3294 1.167851 ATCACCAAGTCAACGGCATG 58.832 50.000 0.00 0.00 0.00 4.06
1698 3297 2.793278 AAAATCACCAAGTCAACGGC 57.207 45.000 0.00 0.00 0.00 5.68
1735 3334 2.096442 CGCTCAGCATCACGCAAGA 61.096 57.895 0.00 0.00 46.13 3.02
1852 3481 2.125673 AACGAGGATTGTCGGCGG 60.126 61.111 7.21 0.00 44.53 6.13
1867 3496 1.981256 TTGCCTCTTTCACCCTCAAC 58.019 50.000 0.00 0.00 0.00 3.18
2019 3653 2.543635 AGGCCAAAGATTTGCCTCATT 58.456 42.857 5.01 0.00 39.06 2.57
2522 4233 9.926751 GTAGATGATCTGTTACAATGTGAAATG 57.073 33.333 4.96 0.00 0.00 2.32
2523 4234 9.671279 TGTAGATGATCTGTTACAATGTGAAAT 57.329 29.630 4.96 0.00 0.00 2.17
2531 4242 6.037062 CCGCAAATGTAGATGATCTGTTACAA 59.963 38.462 4.96 0.00 30.64 2.41
2563 4282 2.386661 AATAAGAGGAGCACACGTGG 57.613 50.000 21.57 10.05 0.00 4.94
2567 4286 7.604545 AGTTCTTTCTAAATAAGAGGAGCACAC 59.395 37.037 0.00 0.00 35.05 3.82
2620 4340 6.472887 AGCTATTGTTTTAGCAACCTCTGTA 58.527 36.000 6.28 0.00 45.72 2.74
2621 4341 5.316987 AGCTATTGTTTTAGCAACCTCTGT 58.683 37.500 6.28 0.00 45.72 3.41
2642 4362 5.786264 ACACCATGTATGTACTAGGTAGC 57.214 43.478 0.00 0.00 34.13 3.58
2666 4386 2.380064 AAAACATGACAGGGAAGGCA 57.620 45.000 0.00 0.00 0.00 4.75
2672 4392 2.756760 AGCTGCATAAAACATGACAGGG 59.243 45.455 0.00 0.00 0.00 4.45
2690 4410 3.498774 ACAACTGAAGAATGTGGAGCT 57.501 42.857 0.00 0.00 0.00 4.09
2715 4435 1.428869 AAGGCTGGTCTCAGTTCAGT 58.571 50.000 0.00 0.00 42.78 3.41
2716 4436 3.902881 ATAAGGCTGGTCTCAGTTCAG 57.097 47.619 0.00 0.00 42.78 3.02
2717 4437 3.327757 ACAATAAGGCTGGTCTCAGTTCA 59.672 43.478 0.00 0.00 42.78 3.18
2718 4438 3.935828 GACAATAAGGCTGGTCTCAGTTC 59.064 47.826 0.00 0.00 42.78 3.01
2719 4439 3.584848 AGACAATAAGGCTGGTCTCAGTT 59.415 43.478 5.80 0.00 42.78 3.16
2720 4440 3.177228 AGACAATAAGGCTGGTCTCAGT 58.823 45.455 5.80 0.00 42.78 3.41
2721 4441 3.902881 AGACAATAAGGCTGGTCTCAG 57.097 47.619 5.80 0.00 43.64 3.35
2722 4442 3.133003 GCTAGACAATAAGGCTGGTCTCA 59.867 47.826 12.68 3.06 40.76 3.27
2727 4447 4.672587 TGTAGCTAGACAATAAGGCTGG 57.327 45.455 0.00 0.00 35.25 4.85
2737 4457 7.877612 TCAAGTTTCAAATCATGTAGCTAGACA 59.122 33.333 0.00 0.00 0.00 3.41
2752 4472 6.091441 CACCAAACGGAAAATCAAGTTTCAAA 59.909 34.615 5.44 0.00 38.93 2.69
2806 4526 7.256286 GGTCATGAAAAAGAAGAATGGATGAG 58.744 38.462 0.00 0.00 0.00 2.90
2884 4604 2.433239 ACAGTAACAACGAACTCCACCT 59.567 45.455 0.00 0.00 0.00 4.00
2895 4615 2.551032 GCCCTTACCACACAGTAACAAC 59.449 50.000 0.00 0.00 0.00 3.32
2902 4622 2.779755 TATGTGCCCTTACCACACAG 57.220 50.000 0.00 0.00 46.55 3.66
2922 4642 5.046304 TGCCTTAAGCTAATTCTGAGACACT 60.046 40.000 0.00 0.00 44.23 3.55
2934 4657 4.033709 ACTCATCTCCTGCCTTAAGCTAA 58.966 43.478 0.00 0.00 44.23 3.09
2963 4686 0.248843 AGCAACAGCCTAGCTCAGTC 59.751 55.000 0.00 0.00 36.40 3.51
2964 4687 0.036577 CAGCAACAGCCTAGCTCAGT 60.037 55.000 0.00 0.00 36.40 3.41
2965 4688 0.036577 ACAGCAACAGCCTAGCTCAG 60.037 55.000 0.00 0.00 36.40 3.35
2966 4689 1.266178 TACAGCAACAGCCTAGCTCA 58.734 50.000 0.00 0.00 36.40 4.26
3081 4806 4.595781 AGGTGACTAATGTGTAGGAACCAA 59.404 41.667 8.54 0.00 40.61 3.67
3112 4837 3.783111 TCGATACGAGTAGCATGTACG 57.217 47.619 0.00 0.00 0.00 3.67
3162 4887 4.060900 CTGACAGTACCATATCCATGCAC 58.939 47.826 0.00 0.00 0.00 4.57
3260 4985 3.824443 TCGAGATAATTGGCGACATCCTA 59.176 43.478 0.00 0.00 42.32 2.94
3270 4995 7.065803 ACCACACATTTTACTCGAGATAATTGG 59.934 37.037 21.68 18.42 0.00 3.16
3405 5130 1.137872 CGTTAGCATGCTCCCTTCTCT 59.862 52.381 26.57 0.00 0.00 3.10
3727 5489 4.473444 TCTCCAAGTTTGCTTCCTGAATT 58.527 39.130 0.00 0.00 31.49 2.17
3766 5528 4.345286 AGGACCTGCAGCCCCTCT 62.345 66.667 16.57 3.97 0.00 3.69
3798 5560 0.250901 AGTTTTCACCGCTGATGGCT 60.251 50.000 0.00 0.00 39.13 4.75
3799 5561 1.448985 TAGTTTTCACCGCTGATGGC 58.551 50.000 0.00 0.00 37.64 4.40
3808 5570 7.358023 CGCACAAATTTACACATAGTTTTCACC 60.358 37.037 0.00 0.00 0.00 4.02
3817 5579 7.377397 GTCAAAACTCGCACAAATTTACACATA 59.623 33.333 0.00 0.00 0.00 2.29
3818 5580 6.198216 GTCAAAACTCGCACAAATTTACACAT 59.802 34.615 0.00 0.00 0.00 3.21
3823 5585 6.983910 GTTTGTCAAAACTCGCACAAATTTA 58.016 32.000 0.00 0.00 42.09 1.40
3844 5606 3.117888 TGAAGGAGTCTTGCTTGGAGTTT 60.118 43.478 0.00 0.00 34.85 2.66
3859 5621 0.689623 AGTGCCTCTGGTTGAAGGAG 59.310 55.000 0.00 0.00 0.00 3.69
3861 5623 2.938354 CAGTGCCTCTGGTTGAAGG 58.062 57.895 0.00 0.00 40.23 3.46
3878 5640 4.680237 CGTGGCTGAGCGGAACCA 62.680 66.667 0.00 0.00 0.00 3.67
3980 5742 1.610522 GCTCCTTGAAGCTGCAGAAAA 59.389 47.619 20.43 4.28 39.27 2.29
4024 5786 5.070180 GGATGATGACTCAGAAGAAGATGGA 59.930 44.000 0.00 0.00 34.12 3.41
4025 5787 5.070714 AGGATGATGACTCAGAAGAAGATGG 59.929 44.000 0.00 0.00 34.12 3.51
4030 5792 5.337894 GGAACAGGATGATGACTCAGAAGAA 60.338 44.000 0.00 0.00 39.69 2.52
4038 5800 3.520721 TGACATGGAACAGGATGATGACT 59.479 43.478 0.00 0.00 46.40 3.41
4046 5808 0.036732 GCTGGTGACATGGAACAGGA 59.963 55.000 12.53 0.00 46.40 3.86
4050 5812 0.036732 TGAGGCTGGTGACATGGAAC 59.963 55.000 0.00 0.00 41.51 3.62
4051 5813 0.994247 ATGAGGCTGGTGACATGGAA 59.006 50.000 0.00 0.00 41.51 3.53
4052 5814 0.543277 GATGAGGCTGGTGACATGGA 59.457 55.000 0.00 0.00 41.51 3.41
4053 5815 0.812811 CGATGAGGCTGGTGACATGG 60.813 60.000 0.00 0.00 41.51 3.66
4054 5816 0.107993 ACGATGAGGCTGGTGACATG 60.108 55.000 0.00 0.00 41.51 3.21
4055 5817 0.176680 GACGATGAGGCTGGTGACAT 59.823 55.000 0.00 0.00 41.51 3.06
4056 5818 1.184970 TGACGATGAGGCTGGTGACA 61.185 55.000 0.00 0.00 39.59 3.58
4057 5819 0.176680 ATGACGATGAGGCTGGTGAC 59.823 55.000 0.00 0.00 0.00 3.67
4058 5820 0.461548 GATGACGATGAGGCTGGTGA 59.538 55.000 0.00 0.00 0.00 4.02
4059 5821 0.873312 CGATGACGATGAGGCTGGTG 60.873 60.000 0.00 0.00 42.66 4.17
4060 5822 1.323271 ACGATGACGATGAGGCTGGT 61.323 55.000 0.00 0.00 42.66 4.00
4061 5823 0.596083 GACGATGACGATGAGGCTGG 60.596 60.000 0.00 0.00 42.66 4.85
4062 5824 0.101219 TGACGATGACGATGAGGCTG 59.899 55.000 0.00 0.00 42.66 4.85
4063 5825 1.035923 ATGACGATGACGATGAGGCT 58.964 50.000 0.00 0.00 42.66 4.58
4064 5826 1.135046 CATGACGATGACGATGAGGC 58.865 55.000 0.00 0.00 42.66 4.70
4065 5827 1.135046 GCATGACGATGACGATGAGG 58.865 55.000 0.00 0.00 42.66 3.86
4066 5828 2.049959 GAGCATGACGATGACGATGAG 58.950 52.381 0.00 0.00 42.66 2.90
4067 5829 1.597937 CGAGCATGACGATGACGATGA 60.598 52.381 0.00 0.00 42.66 2.92
4068 5830 0.774685 CGAGCATGACGATGACGATG 59.225 55.000 0.00 0.00 42.66 3.84
4069 5831 0.663153 TCGAGCATGACGATGACGAT 59.337 50.000 10.48 0.00 42.66 3.73
4070 5832 0.450184 TTCGAGCATGACGATGACGA 59.550 50.000 14.17 0.00 42.66 4.20
4071 5833 1.481240 ATTCGAGCATGACGATGACG 58.519 50.000 14.17 0.00 45.75 4.35
4072 5834 2.860136 TGAATTCGAGCATGACGATGAC 59.140 45.455 14.17 9.78 39.45 3.06
4073 5835 3.163630 TGAATTCGAGCATGACGATGA 57.836 42.857 14.17 3.69 39.45 2.92


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

AutoCloner maintained by Alex Coulton.