Multiple sequence alignment - TraesCS3D01G137900

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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 TraesCS3D01G137900 chr3D 100.000 5377 0 0 1 5377 96400177 96394801 0.000000e+00 9930.0
1 TraesCS3D01G137900 chr3B 94.401 2661 85 15 2764 5377 147549461 147546818 0.000000e+00 4030.0
2 TraesCS3D01G137900 chr3B 90.720 1487 95 13 85 1555 147552239 147550780 0.000000e+00 1941.0
3 TraesCS3D01G137900 chr3B 91.591 1213 62 19 1575 2756 147550724 147549521 0.000000e+00 1639.0
4 TraesCS3D01G137900 chr3B 80.714 140 20 6 4769 4906 764524237 764524371 9.530000e-18 102.0
5 TraesCS3D01G137900 chr3B 100.000 37 0 0 58 94 147552650 147552614 9.660000e-08 69.4
6 TraesCS3D01G137900 chr3A 91.791 1547 90 18 1855 3366 114429326 114427782 0.000000e+00 2119.0
7 TraesCS3D01G137900 chr3A 87.891 1437 132 33 3362 4774 114427750 114426332 0.000000e+00 1652.0
8 TraesCS3D01G137900 chr3A 89.714 700 39 9 748 1435 114430571 114429893 0.000000e+00 863.0
9 TraesCS3D01G137900 chr3A 93.434 198 13 0 5180 5377 114426212 114426015 1.460000e-75 294.0
10 TraesCS3D01G137900 chr3A 91.351 185 15 1 1571 1754 114429731 114429547 8.940000e-63 252.0
11 TraesCS3D01G137900 chr5B 87.410 278 28 4 1217 1491 613107303 613107576 4.040000e-81 313.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G137900 chr3D 96394801 96400177 5376 True 9930.00 9930 100.0000 1 5377 1 chr3D.!!$R1 5376
1 TraesCS3D01G137900 chr3B 147546818 147552650 5832 True 1919.85 4030 94.1780 58 5377 4 chr3B.!!$R1 5319
2 TraesCS3D01G137900 chr3A 114426015 114430571 4556 True 1036.00 2119 90.8362 748 5377 5 chr3A.!!$R1 4629

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
305 692 0.469917 CCGGCCTGTCCATGTCTATT 59.530 55.000 0.00 0.00 34.01 1.73 F
1019 1422 0.389948 ATGTCCGAGACAGAAACGGC 60.390 55.000 11.50 0.00 46.04 5.68 F
1549 1984 0.035881 CTTGCTTCTCAGGGTGCTCA 59.964 55.000 0.00 0.00 0.00 4.26 F
1551 1986 0.251354 TGCTTCTCAGGGTGCTCATC 59.749 55.000 0.00 0.00 0.00 2.92 F
1575 2010 0.463295 CATTGAGCTCGTGGCAGGAT 60.463 55.000 10.69 0.00 44.79 3.24 F
2389 3012 1.466167 CAATCAAAGCCACTGGAGACG 59.534 52.381 0.00 0.00 0.00 4.18 F
3846 4593 2.095718 GGTCGACCATGAGCTCAAAAAC 60.096 50.000 29.75 12.57 35.64 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1845 0.107848 TAAAGCCTAAGGAGCGCCAC 60.108 55.000 9.88 0.0 36.29 5.01 R
1832 2427 0.764369 CCTACTGGCCTGGGAGCATA 60.764 60.000 14.82 0.0 0.00 3.14 R
3050 3733 2.420022 CAGGGCAACGGAGACATTAAAG 59.580 50.000 0.00 0.0 37.60 1.85 R
3247 3958 5.764686 TGCTGCCAAATCAAGACGATAATAT 59.235 36.000 0.00 0.0 32.51 1.28 R
3563 4310 6.590677 CACTGATCCACATCTGATAATAGCAG 59.409 42.308 0.00 0.0 33.29 4.24 R
4373 5143 0.861837 CCGCGCATTTCTCCATCTAC 59.138 55.000 8.75 0.0 0.00 2.59 R
5061 5861 0.610785 GGAAATGACTTTGGCCCGGA 60.611 55.000 0.73 0.0 0.00 5.14 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
20 21 3.085952 CAGCCTCATTTTACCTTCCCA 57.914 47.619 0.00 0.00 0.00 4.37
21 22 3.635591 CAGCCTCATTTTACCTTCCCAT 58.364 45.455 0.00 0.00 0.00 4.00
22 23 3.633986 CAGCCTCATTTTACCTTCCCATC 59.366 47.826 0.00 0.00 0.00 3.51
23 24 3.269381 AGCCTCATTTTACCTTCCCATCA 59.731 43.478 0.00 0.00 0.00 3.07
24 25 4.078980 AGCCTCATTTTACCTTCCCATCAT 60.079 41.667 0.00 0.00 0.00 2.45
25 26 4.038402 GCCTCATTTTACCTTCCCATCATG 59.962 45.833 0.00 0.00 0.00 3.07
26 27 4.038402 CCTCATTTTACCTTCCCATCATGC 59.962 45.833 0.00 0.00 0.00 4.06
27 28 4.608269 TCATTTTACCTTCCCATCATGCA 58.392 39.130 0.00 0.00 0.00 3.96
28 29 4.402155 TCATTTTACCTTCCCATCATGCAC 59.598 41.667 0.00 0.00 0.00 4.57
29 30 3.737559 TTTACCTTCCCATCATGCACT 57.262 42.857 0.00 0.00 0.00 4.40
30 31 4.853468 TTTACCTTCCCATCATGCACTA 57.147 40.909 0.00 0.00 0.00 2.74
31 32 4.853468 TTACCTTCCCATCATGCACTAA 57.147 40.909 0.00 0.00 0.00 2.24
32 33 3.959495 ACCTTCCCATCATGCACTAAT 57.041 42.857 0.00 0.00 0.00 1.73
33 34 4.255510 ACCTTCCCATCATGCACTAATT 57.744 40.909 0.00 0.00 0.00 1.40
34 35 3.956199 ACCTTCCCATCATGCACTAATTG 59.044 43.478 0.00 0.00 0.00 2.32
42 43 2.822255 GCACTAATTGCGGGCCGA 60.822 61.111 33.44 10.70 42.79 5.54
43 44 2.186826 GCACTAATTGCGGGCCGAT 61.187 57.895 33.44 13.02 42.79 4.18
44 45 1.941812 CACTAATTGCGGGCCGATC 59.058 57.895 33.44 14.10 0.00 3.69
45 46 0.532862 CACTAATTGCGGGCCGATCT 60.533 55.000 33.44 12.87 0.00 2.75
46 47 1.045407 ACTAATTGCGGGCCGATCTA 58.955 50.000 33.44 10.43 0.00 1.98
47 48 1.623811 ACTAATTGCGGGCCGATCTAT 59.376 47.619 33.44 12.52 0.00 1.98
48 49 2.038557 ACTAATTGCGGGCCGATCTATT 59.961 45.455 33.44 21.84 0.00 1.73
49 50 1.238439 AATTGCGGGCCGATCTATTG 58.762 50.000 33.44 0.00 0.00 1.90
50 51 1.237285 ATTGCGGGCCGATCTATTGC 61.237 55.000 33.44 9.78 0.00 3.56
51 52 2.280797 GCGGGCCGATCTATTGCA 60.281 61.111 33.44 0.00 0.00 4.08
52 53 1.672356 GCGGGCCGATCTATTGCAT 60.672 57.895 33.44 0.00 0.00 3.96
53 54 1.237285 GCGGGCCGATCTATTGCATT 61.237 55.000 33.44 0.00 0.00 3.56
54 55 1.943968 GCGGGCCGATCTATTGCATTA 60.944 52.381 33.44 0.00 0.00 1.90
55 56 2.632377 CGGGCCGATCTATTGCATTAT 58.368 47.619 24.41 0.00 0.00 1.28
56 57 2.352651 CGGGCCGATCTATTGCATTATG 59.647 50.000 24.41 0.00 0.00 1.90
94 95 4.721776 TGGAAGGTAAATGGATAGAGCACT 59.278 41.667 0.00 0.00 0.00 4.40
95 96 5.903010 TGGAAGGTAAATGGATAGAGCACTA 59.097 40.000 0.00 0.00 0.00 2.74
122 507 9.537848 CTATACATCCGACACTTTTTAAACAAC 57.462 33.333 0.00 0.00 0.00 3.32
164 550 6.478512 TCCAGCCATTTTTACTTTTGTTCT 57.521 33.333 0.00 0.00 0.00 3.01
166 552 8.012957 TCCAGCCATTTTTACTTTTGTTCTTA 57.987 30.769 0.00 0.00 0.00 2.10
178 564 6.739112 ACTTTTGTTCTTAAAGGCATCTCAC 58.261 36.000 0.00 0.00 37.01 3.51
188 574 2.459442 GCATCTCACGGTGCAGAGC 61.459 63.158 2.51 8.94 40.94 4.09
197 583 1.745087 ACGGTGCAGAGCAATTATTGG 59.255 47.619 7.08 0.00 41.47 3.16
267 654 5.843969 TGGATATTTGAGGTACATCTGCCTA 59.156 40.000 9.22 0.00 34.81 3.93
305 692 0.469917 CCGGCCTGTCCATGTCTATT 59.530 55.000 0.00 0.00 34.01 1.73
306 693 1.134098 CCGGCCTGTCCATGTCTATTT 60.134 52.381 0.00 0.00 34.01 1.40
307 694 2.104111 CCGGCCTGTCCATGTCTATTTA 59.896 50.000 0.00 0.00 34.01 1.40
308 695 3.244561 CCGGCCTGTCCATGTCTATTTAT 60.245 47.826 0.00 0.00 34.01 1.40
309 696 4.389374 CGGCCTGTCCATGTCTATTTATT 58.611 43.478 0.00 0.00 34.01 1.40
326 713 4.819105 TTATTGTTGACCTCGTCTCCAT 57.181 40.909 0.00 0.00 33.15 3.41
328 715 1.627864 TGTTGACCTCGTCTCCATCA 58.372 50.000 0.00 0.00 33.15 3.07
333 720 2.831526 TGACCTCGTCTCCATCAATGAA 59.168 45.455 0.00 0.00 33.15 2.57
336 723 4.848357 ACCTCGTCTCCATCAATGAAATT 58.152 39.130 0.00 0.00 36.63 1.82
352 739 2.295253 AATTGCGAACTCCTACGAGG 57.705 50.000 0.00 0.00 40.77 4.63
354 741 1.471119 TTGCGAACTCCTACGAGGAT 58.529 50.000 4.39 0.00 44.81 3.24
355 742 0.738975 TGCGAACTCCTACGAGGATG 59.261 55.000 4.39 2.83 44.81 3.51
370 757 4.191544 CGAGGATGAGTATGGCTTGAAAA 58.808 43.478 0.00 0.00 0.00 2.29
407 794 5.593010 GTGTCTTATGTGGGTCAGTCTATC 58.407 45.833 0.00 0.00 0.00 2.08
415 802 2.026169 TGGGTCAGTCTATCTCTCGTGT 60.026 50.000 0.00 0.00 0.00 4.49
431 818 2.411069 TCGTGTCTTACTCTTCTCGTCG 59.589 50.000 0.00 0.00 0.00 5.12
433 820 2.483491 GTGTCTTACTCTTCTCGTCGGT 59.517 50.000 0.00 0.00 0.00 4.69
461 856 0.603569 TCTTCACTCTTCGGGCTCAC 59.396 55.000 0.00 0.00 0.00 3.51
464 859 0.965866 TCACTCTTCGGGCTCACGAT 60.966 55.000 0.00 0.00 43.11 3.73
465 860 0.526524 CACTCTTCGGGCTCACGATC 60.527 60.000 0.00 0.00 43.11 3.69
472 867 1.215647 GGGCTCACGATCGTCAACT 59.784 57.895 19.84 0.00 0.00 3.16
473 868 1.078759 GGGCTCACGATCGTCAACTG 61.079 60.000 19.84 7.09 0.00 3.16
478 873 3.730963 GCTCACGATCGTCAACTGACATA 60.731 47.826 19.84 0.00 44.99 2.29
489 884 5.333339 CGTCAACTGACATAGGAACAACAAG 60.333 44.000 10.32 0.00 44.99 3.16
498 893 6.465084 ACATAGGAACAACAAGGACTTAGAC 58.535 40.000 0.00 0.00 0.00 2.59
499 894 6.042781 ACATAGGAACAACAAGGACTTAGACA 59.957 38.462 0.00 0.00 0.00 3.41
503 898 3.463944 ACAACAAGGACTTAGACAACGG 58.536 45.455 0.00 0.00 0.00 4.44
520 915 6.485313 AGACAACGGATGACAACAAAGATTTA 59.515 34.615 0.00 0.00 0.00 1.40
521 916 6.668323 ACAACGGATGACAACAAAGATTTAG 58.332 36.000 0.00 0.00 0.00 1.85
522 917 6.485313 ACAACGGATGACAACAAAGATTTAGA 59.515 34.615 0.00 0.00 0.00 2.10
523 918 6.481954 ACGGATGACAACAAAGATTTAGAC 57.518 37.500 0.00 0.00 0.00 2.59
524 919 6.231211 ACGGATGACAACAAAGATTTAGACT 58.769 36.000 0.00 0.00 0.00 3.24
525 920 7.383687 ACGGATGACAACAAAGATTTAGACTA 58.616 34.615 0.00 0.00 0.00 2.59
526 921 7.876068 ACGGATGACAACAAAGATTTAGACTAA 59.124 33.333 0.00 0.00 0.00 2.24
527 922 8.717821 CGGATGACAACAAAGATTTAGACTAAA 58.282 33.333 10.02 10.02 0.00 1.85
594 989 4.901868 AGTGAATGTGTACCGGTACAAAT 58.098 39.130 41.27 38.13 46.33 2.32
624 1019 3.150767 TCCGGTTGGTTTAAATCCTGTG 58.849 45.455 0.00 0.00 36.30 3.66
661 1056 7.352719 ACAAATTCACGAACAGAAGATACTC 57.647 36.000 0.00 0.00 0.00 2.59
663 1058 7.116948 ACAAATTCACGAACAGAAGATACTCAG 59.883 37.037 0.00 0.00 0.00 3.35
665 1060 5.959618 TCACGAACAGAAGATACTCAGAA 57.040 39.130 0.00 0.00 0.00 3.02
712 1108 1.539827 CACCTCGATTCCCACCAAAAC 59.460 52.381 0.00 0.00 0.00 2.43
715 1111 2.084546 CTCGATTCCCACCAAAACCTC 58.915 52.381 0.00 0.00 0.00 3.85
716 1112 1.173913 CGATTCCCACCAAAACCTCC 58.826 55.000 0.00 0.00 0.00 4.30
720 1116 1.234529 CCCACCAAAACCTCCCCAA 59.765 57.895 0.00 0.00 0.00 4.12
787 1183 1.534697 GGACTTGGGTGGTGGAACA 59.465 57.895 0.00 0.00 39.98 3.18
1016 1419 1.079503 GCCATGTCCGAGACAGAAAC 58.920 55.000 11.50 0.32 46.04 2.78
1017 1420 1.350193 CCATGTCCGAGACAGAAACG 58.650 55.000 11.50 0.00 46.04 3.60
1018 1421 1.350193 CATGTCCGAGACAGAAACGG 58.650 55.000 11.50 0.00 46.04 4.44
1019 1422 0.389948 ATGTCCGAGACAGAAACGGC 60.390 55.000 11.50 0.00 46.04 5.68
1020 1423 2.087009 GTCCGAGACAGAAACGGCG 61.087 63.158 4.80 4.80 45.25 6.46
1021 1424 2.809601 CCGAGACAGAAACGGCGG 60.810 66.667 13.24 0.00 40.19 6.13
1204 1607 6.297276 TTCTCCAAGAAAAGGGTTACCCCC 62.297 50.000 18.15 4.23 40.73 5.40
1366 1772 2.256461 CCTGCCGCTTTTCTGTGC 59.744 61.111 0.00 0.00 0.00 4.57
1419 1826 1.081840 GTTGCTTCGCACTGGCTTC 60.082 57.895 0.00 0.00 38.71 3.86
1423 1830 1.373497 CTTCGCACTGGCTTCGTCT 60.373 57.895 0.00 0.00 38.10 4.18
1424 1831 1.621301 CTTCGCACTGGCTTCGTCTG 61.621 60.000 0.00 0.00 38.10 3.51
1426 1833 2.375766 CGCACTGGCTTCGTCTGTC 61.376 63.158 0.00 0.00 38.10 3.51
1435 1842 4.966005 TCGTCTGTCGAGGCTTTG 57.034 55.556 0.00 0.00 44.01 2.77
1436 1843 2.038690 TCGTCTGTCGAGGCTTTGT 58.961 52.632 0.00 0.00 44.01 2.83
1437 1844 0.387929 TCGTCTGTCGAGGCTTTGTT 59.612 50.000 0.00 0.00 44.01 2.83
1438 1845 0.508641 CGTCTGTCGAGGCTTTGTTG 59.491 55.000 0.00 0.00 42.86 3.33
1439 1846 1.583054 GTCTGTCGAGGCTTTGTTGT 58.417 50.000 0.00 0.00 0.00 3.32
1440 1847 1.261619 GTCTGTCGAGGCTTTGTTGTG 59.738 52.381 0.00 0.00 0.00 3.33
1441 1848 0.588252 CTGTCGAGGCTTTGTTGTGG 59.412 55.000 0.00 0.00 0.00 4.17
1442 1849 1.282875 GTCGAGGCTTTGTTGTGGC 59.717 57.895 0.00 0.00 0.00 5.01
1443 1850 2.250939 TCGAGGCTTTGTTGTGGCG 61.251 57.895 0.00 0.00 0.00 5.69
1444 1851 2.050077 GAGGCTTTGTTGTGGCGC 60.050 61.111 0.00 0.00 0.00 6.53
1445 1852 2.519302 AGGCTTTGTTGTGGCGCT 60.519 55.556 7.64 0.00 0.00 5.92
1446 1853 2.050077 GGCTTTGTTGTGGCGCTC 60.050 61.111 7.64 1.21 0.00 5.03
1447 1854 2.050077 GCTTTGTTGTGGCGCTCC 60.050 61.111 7.64 0.00 0.00 4.70
1448 1855 2.555547 GCTTTGTTGTGGCGCTCCT 61.556 57.895 7.64 0.00 0.00 3.69
1449 1856 2.032981 CTTTGTTGTGGCGCTCCTT 58.967 52.632 7.64 0.00 0.00 3.36
1499 1934 2.186826 GTTGGACACTGCCGCACTT 61.187 57.895 0.00 0.00 0.00 3.16
1543 1978 2.746362 GTGATGTTCTTGCTTCTCAGGG 59.254 50.000 0.00 0.00 0.00 4.45
1547 1982 0.767375 TTCTTGCTTCTCAGGGTGCT 59.233 50.000 0.00 0.00 0.00 4.40
1548 1983 0.322975 TCTTGCTTCTCAGGGTGCTC 59.677 55.000 0.00 0.00 0.00 4.26
1549 1984 0.035881 CTTGCTTCTCAGGGTGCTCA 59.964 55.000 0.00 0.00 0.00 4.26
1550 1985 0.694771 TTGCTTCTCAGGGTGCTCAT 59.305 50.000 0.00 0.00 0.00 2.90
1551 1986 0.251354 TGCTTCTCAGGGTGCTCATC 59.749 55.000 0.00 0.00 0.00 2.92
1552 1987 0.809241 GCTTCTCAGGGTGCTCATCG 60.809 60.000 0.00 0.00 0.00 3.84
1553 1988 0.820226 CTTCTCAGGGTGCTCATCGA 59.180 55.000 0.00 0.00 0.00 3.59
1554 1989 0.820226 TTCTCAGGGTGCTCATCGAG 59.180 55.000 0.00 0.00 0.00 4.04
1568 2003 0.529337 ATCGAGGCATTGAGCTCGTG 60.529 55.000 9.64 11.64 44.79 4.35
1571 2006 2.747460 GGCATTGAGCTCGTGGCA 60.747 61.111 28.84 4.46 44.79 4.92
1573 2008 2.758089 GCATTGAGCTCGTGGCAGG 61.758 63.158 17.47 0.00 44.79 4.85
1575 2010 0.463295 CATTGAGCTCGTGGCAGGAT 60.463 55.000 10.69 0.00 44.79 3.24
1700 2186 6.652900 TCGATACCACACAATGAATTTCTCAA 59.347 34.615 0.00 0.00 37.67 3.02
1711 2197 4.071423 TGAATTTCTCAACATTCGCCTCA 58.929 39.130 0.00 0.00 32.83 3.86
1719 2205 2.254546 ACATTCGCCTCACACAGAAA 57.745 45.000 0.00 0.00 0.00 2.52
1728 2214 3.428045 GCCTCACACAGAAATATTGGCAC 60.428 47.826 0.00 0.00 37.91 5.01
1731 2217 2.746904 CACACAGAAATATTGGCACCGA 59.253 45.455 0.00 0.00 0.00 4.69
1740 2226 5.789643 AATATTGGCACCGATTTATGCTT 57.210 34.783 0.00 0.00 41.74 3.91
1749 2235 6.037830 GGCACCGATTTATGCTTAGTAGAAAA 59.962 38.462 0.00 0.00 41.74 2.29
1799 2394 3.063452 ACGCGGCACTAGAATATTTTGTG 59.937 43.478 12.47 10.23 0.00 3.33
1818 2413 1.702957 TGAAGGTACTGGGAAAGTGGG 59.297 52.381 0.00 0.00 40.86 4.61
1832 2427 4.508584 GGAAAGTGGGAAGTCCTGGTATTT 60.509 45.833 0.00 0.00 36.20 1.40
1903 2524 7.895759 AGTTGCTAATGGTTATTCAACAATGT 58.104 30.769 0.00 0.00 37.02 2.71
1912 2533 6.983307 TGGTTATTCAACAATGTGAAACCTTG 59.017 34.615 14.44 0.00 46.13 3.61
1933 2554 4.709250 TGGGCATATAATTTCGCACTACA 58.291 39.130 0.00 0.00 0.00 2.74
1959 2580 5.185828 GGTAATTCTGATGTTTCTGCCCTTT 59.814 40.000 0.00 0.00 0.00 3.11
1966 2587 4.837860 TGATGTTTCTGCCCTTTGGTAATT 59.162 37.500 0.00 0.00 0.00 1.40
1968 2589 5.622346 TGTTTCTGCCCTTTGGTAATTTT 57.378 34.783 0.00 0.00 0.00 1.82
2144 2765 5.709164 CCAAACATCTCAAGAAGTTCATCCT 59.291 40.000 5.50 0.00 35.25 3.24
2179 2800 2.258755 GTGCAAACTTCACACGCTTTT 58.741 42.857 0.00 0.00 34.73 2.27
2186 2807 4.468095 ACTTCACACGCTTTTATGTCAC 57.532 40.909 0.00 0.00 0.00 3.67
2253 2874 4.261614 GCTGGAAACGAAATTCTGTCCTTT 60.262 41.667 0.00 0.00 0.00 3.11
2271 2892 7.788026 TGTCCTTTGATATTCGTATGGTAAGT 58.212 34.615 0.00 0.00 0.00 2.24
2298 2921 5.128663 GCACCCACTTAATTTGTATTCCCAT 59.871 40.000 0.00 0.00 0.00 4.00
2317 2940 6.001460 TCCCATATCGAAGTTGTGACTTTTT 58.999 36.000 0.00 0.00 45.88 1.94
2331 2954 4.328712 GTGACTTTTTGCGTTGGTTTTCAT 59.671 37.500 0.00 0.00 0.00 2.57
2389 3012 1.466167 CAATCAAAGCCACTGGAGACG 59.534 52.381 0.00 0.00 0.00 4.18
2468 3091 8.996271 CCACTCCTTTTAGTCTTTTTATTACGT 58.004 33.333 0.00 0.00 0.00 3.57
2519 3142 9.907229 ATTTTCTCTTATTACTGGAACTTAGGG 57.093 33.333 0.00 0.00 0.00 3.53
2863 3539 8.568732 TGAAATAAGTTTTTACTTCTTTGGCG 57.431 30.769 6.25 0.00 29.88 5.69
2884 3567 8.725405 TGGCGTGATAAATTATTTCACTCTTA 57.275 30.769 7.79 0.00 38.06 2.10
2991 3674 9.654663 GTGTATCCTTATATGGTCTGGATAAAC 57.345 37.037 4.67 0.00 40.23 2.01
2994 3677 8.742125 ATCCTTATATGGTCTGGATAAACTCA 57.258 34.615 4.67 0.00 35.95 3.41
3022 3705 9.965824 ACCTTTTCATCAAATAACAGTGTTTAG 57.034 29.630 14.90 2.34 0.00 1.85
3059 3742 9.821662 GCGTATTATTATTCCCACTTTAATGTC 57.178 33.333 0.00 0.00 0.00 3.06
3563 4310 8.560374 AGTTGTAAGCTCTGTTATTTTTCACTC 58.440 33.333 0.00 0.00 0.00 3.51
3588 4335 6.461640 TGCTATTATCAGATGTGGATCAGTG 58.538 40.000 0.00 0.00 0.00 3.66
3846 4593 2.095718 GGTCGACCATGAGCTCAAAAAC 60.096 50.000 29.75 12.57 35.64 2.43
3961 4708 3.127030 GTGTGTAAGTCCCTTTATGCTGC 59.873 47.826 0.00 0.00 0.00 5.25
4045 4792 4.131596 CGTTTGGTGAGAAGGGAAAGTTA 58.868 43.478 0.00 0.00 0.00 2.24
4165 4912 9.727627 GATATTGATGTGAAGAAAAAGGTCATC 57.272 33.333 0.00 0.00 0.00 2.92
4188 4935 9.533253 CATCACTAGACCTTCAATTTTGTTTTT 57.467 29.630 0.00 0.00 0.00 1.94
4216 4967 7.944729 ATTGTCTTTTGATATGGCACTAACT 57.055 32.000 0.00 0.00 0.00 2.24
4218 4969 6.472016 TGTCTTTTGATATGGCACTAACTCA 58.528 36.000 0.00 0.00 0.00 3.41
4220 4971 7.611467 TGTCTTTTGATATGGCACTAACTCAAT 59.389 33.333 0.00 0.00 0.00 2.57
4371 5141 9.408648 CCAAGGTGGTCAAAGTATATAATTTCT 57.591 33.333 5.22 0.00 31.35 2.52
4462 5233 0.251922 ATCAGTGCCATGTTTGCCCT 60.252 50.000 0.00 0.00 0.00 5.19
4474 5245 1.140312 TTTGCCCTGACTCCTGTCTT 58.860 50.000 0.00 0.00 43.29 3.01
4532 5303 5.469760 TGGTGAAATGACAGTACATGACTTG 59.530 40.000 0.00 0.00 35.64 3.16
4642 5442 6.620678 ACATGTATATCTTTGTTGTGTTGGC 58.379 36.000 0.00 0.00 0.00 4.52
4783 5583 3.876309 TTCTTACAAAGGCCCAGTTCT 57.124 42.857 0.00 0.00 0.00 3.01
4815 5615 1.362584 TCTGGAGAATCTGGGGTCTGA 59.637 52.381 0.00 0.00 33.73 3.27
4842 5642 7.506296 AATCAACAAAACAAAAGAACTCGAC 57.494 32.000 0.00 0.00 0.00 4.20
4850 5650 4.909894 ACAAAAGAACTCGACTTTGCTTC 58.090 39.130 0.75 0.00 37.59 3.86
4854 5654 2.132762 GAACTCGACTTTGCTTCGGAA 58.867 47.619 0.00 0.00 37.09 4.30
4941 5741 3.943671 TTCTGGACAACTCCCTCAAAA 57.056 42.857 0.00 0.00 35.34 2.44
4956 5756 5.034797 CCCTCAAAAGAAAACGTTTCAGAC 58.965 41.667 15.01 6.67 0.00 3.51
4967 5767 4.866508 ACGTTTCAGACAGGAGAATACA 57.133 40.909 0.00 0.00 0.00 2.29
4973 5773 7.331791 GTTTCAGACAGGAGAATACACCTATT 58.668 38.462 0.00 0.00 35.44 1.73
4978 5778 7.989741 CAGACAGGAGAATACACCTATTGATTT 59.010 37.037 0.00 0.00 35.44 2.17
4979 5779 8.552296 AGACAGGAGAATACACCTATTGATTTT 58.448 33.333 0.00 0.00 35.44 1.82
4980 5780 8.738645 ACAGGAGAATACACCTATTGATTTTC 57.261 34.615 0.00 0.00 35.44 2.29
4981 5781 8.328758 ACAGGAGAATACACCTATTGATTTTCA 58.671 33.333 0.00 0.00 35.44 2.69
4982 5782 8.834465 CAGGAGAATACACCTATTGATTTTCAG 58.166 37.037 0.00 0.00 35.44 3.02
4983 5783 8.552296 AGGAGAATACACCTATTGATTTTCAGT 58.448 33.333 0.00 0.00 35.44 3.41
4984 5784 9.178758 GGAGAATACACCTATTGATTTTCAGTT 57.821 33.333 0.00 0.00 0.00 3.16
5001 5801 9.807921 ATTTTCAGTTTTTCACTAGGATCCTAA 57.192 29.630 21.93 6.76 32.76 2.69
5015 5815 4.657504 AGGATCCTAATGCAGATTCTGTGA 59.342 41.667 14.27 3.10 33.43 3.58
5022 5822 1.008329 GCAGATTCTGTGAGCAGCTC 58.992 55.000 16.21 16.21 42.29 4.09
5054 5854 1.745087 GATTCTGGAAAATCCTGCGCA 59.255 47.619 10.98 10.98 37.46 6.09
5061 5861 3.006752 TGGAAAATCCTGCGCAAAAAGAT 59.993 39.130 13.05 8.80 37.46 2.40
5063 5863 2.947448 AATCCTGCGCAAAAAGATCC 57.053 45.000 13.05 0.00 0.00 3.36
5073 5873 1.618343 CAAAAAGATCCGGGCCAAAGT 59.382 47.619 4.39 0.00 0.00 2.66
5105 5905 5.277779 CCAAACGTTGTGATTGTGATACAGT 60.278 40.000 0.00 0.00 0.00 3.55
5192 6004 6.042777 TCACTAATTACTGTCACATAGCAGC 58.957 40.000 0.00 0.00 36.26 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.085952 TGGGAAGGTAAAATGAGGCTG 57.914 47.619 0.00 0.00 0.00 4.85
1 2 3.269381 TGATGGGAAGGTAAAATGAGGCT 59.731 43.478 0.00 0.00 0.00 4.58
2 3 3.631250 TGATGGGAAGGTAAAATGAGGC 58.369 45.455 0.00 0.00 0.00 4.70
3 4 4.038402 GCATGATGGGAAGGTAAAATGAGG 59.962 45.833 0.00 0.00 0.00 3.86
4 5 4.646040 TGCATGATGGGAAGGTAAAATGAG 59.354 41.667 0.00 0.00 0.00 2.90
5 6 4.402155 GTGCATGATGGGAAGGTAAAATGA 59.598 41.667 0.00 0.00 0.00 2.57
6 7 4.403432 AGTGCATGATGGGAAGGTAAAATG 59.597 41.667 0.00 0.00 0.00 2.32
7 8 4.613437 AGTGCATGATGGGAAGGTAAAAT 58.387 39.130 0.00 0.00 0.00 1.82
8 9 4.046286 AGTGCATGATGGGAAGGTAAAA 57.954 40.909 0.00 0.00 0.00 1.52
9 10 3.737559 AGTGCATGATGGGAAGGTAAA 57.262 42.857 0.00 0.00 0.00 2.01
10 11 4.853468 TTAGTGCATGATGGGAAGGTAA 57.147 40.909 0.00 0.00 0.00 2.85
11 12 5.132502 CAATTAGTGCATGATGGGAAGGTA 58.867 41.667 0.00 0.00 0.00 3.08
12 13 3.956199 CAATTAGTGCATGATGGGAAGGT 59.044 43.478 0.00 0.00 0.00 3.50
13 14 4.579454 CAATTAGTGCATGATGGGAAGG 57.421 45.455 0.00 0.00 0.00 3.46
26 27 0.532862 AGATCGGCCCGCAATTAGTG 60.533 55.000 0.00 0.00 0.00 2.74
27 28 1.045407 TAGATCGGCCCGCAATTAGT 58.955 50.000 0.00 0.00 0.00 2.24
28 29 2.386661 ATAGATCGGCCCGCAATTAG 57.613 50.000 0.00 0.00 0.00 1.73
29 30 2.422597 CAATAGATCGGCCCGCAATTA 58.577 47.619 0.00 0.00 0.00 1.40
30 31 1.238439 CAATAGATCGGCCCGCAATT 58.762 50.000 0.00 0.00 0.00 2.32
31 32 1.237285 GCAATAGATCGGCCCGCAAT 61.237 55.000 0.00 0.00 0.00 3.56
32 33 1.891919 GCAATAGATCGGCCCGCAA 60.892 57.895 0.00 0.00 0.00 4.85
33 34 2.280797 GCAATAGATCGGCCCGCA 60.281 61.111 0.00 0.00 0.00 5.69
34 35 1.237285 AATGCAATAGATCGGCCCGC 61.237 55.000 0.00 0.00 0.00 6.13
35 36 2.093306 TAATGCAATAGATCGGCCCG 57.907 50.000 0.00 0.00 0.00 6.13
36 37 2.684881 CCATAATGCAATAGATCGGCCC 59.315 50.000 0.00 0.00 0.00 5.80
37 38 2.684881 CCCATAATGCAATAGATCGGCC 59.315 50.000 0.00 0.00 0.00 6.13
38 39 2.098117 GCCCATAATGCAATAGATCGGC 59.902 50.000 0.00 0.00 0.00 5.54
39 40 3.614092 AGCCCATAATGCAATAGATCGG 58.386 45.455 0.00 0.00 0.00 4.18
40 41 6.595326 TCTTTAGCCCATAATGCAATAGATCG 59.405 38.462 0.00 0.00 0.00 3.69
41 42 7.928307 TCTTTAGCCCATAATGCAATAGATC 57.072 36.000 0.00 0.00 0.00 2.75
42 43 8.111545 TGATCTTTAGCCCATAATGCAATAGAT 58.888 33.333 0.00 0.00 0.00 1.98
43 44 7.460910 TGATCTTTAGCCCATAATGCAATAGA 58.539 34.615 0.00 0.00 0.00 1.98
44 45 7.692460 TGATCTTTAGCCCATAATGCAATAG 57.308 36.000 0.00 0.00 0.00 1.73
45 46 7.725397 AGTTGATCTTTAGCCCATAATGCAATA 59.275 33.333 0.00 0.00 0.00 1.90
46 47 6.552350 AGTTGATCTTTAGCCCATAATGCAAT 59.448 34.615 0.00 0.00 0.00 3.56
47 48 5.893255 AGTTGATCTTTAGCCCATAATGCAA 59.107 36.000 0.00 0.00 0.00 4.08
48 49 5.300034 CAGTTGATCTTTAGCCCATAATGCA 59.700 40.000 0.00 0.00 0.00 3.96
49 50 5.278660 CCAGTTGATCTTTAGCCCATAATGC 60.279 44.000 0.00 0.00 0.00 3.56
50 51 6.064060 TCCAGTTGATCTTTAGCCCATAATG 58.936 40.000 0.00 0.00 0.00 1.90
51 52 6.266131 TCCAGTTGATCTTTAGCCCATAAT 57.734 37.500 0.00 0.00 0.00 1.28
52 53 5.708736 TCCAGTTGATCTTTAGCCCATAA 57.291 39.130 0.00 0.00 0.00 1.90
53 54 5.397899 CCTTCCAGTTGATCTTTAGCCCATA 60.398 44.000 0.00 0.00 0.00 2.74
54 55 4.530875 CTTCCAGTTGATCTTTAGCCCAT 58.469 43.478 0.00 0.00 0.00 4.00
55 56 3.308402 CCTTCCAGTTGATCTTTAGCCCA 60.308 47.826 0.00 0.00 0.00 5.36
56 57 3.282885 CCTTCCAGTTGATCTTTAGCCC 58.717 50.000 0.00 0.00 0.00 5.19
94 95 9.926158 TGTTTAAAAAGTGTCGGATGTATAGTA 57.074 29.630 0.00 0.00 0.00 1.82
95 96 8.836268 TGTTTAAAAAGTGTCGGATGTATAGT 57.164 30.769 0.00 0.00 0.00 2.12
103 488 5.038033 GCATGTTGTTTAAAAAGTGTCGGA 58.962 37.500 0.00 0.00 0.00 4.55
178 564 1.534595 GCCAATAATTGCTCTGCACCG 60.535 52.381 0.00 0.00 38.71 4.94
188 574 3.009723 ACTGACGTCCAGCCAATAATTG 58.990 45.455 14.12 0.00 46.81 2.32
197 583 2.280119 TGTGCACTGACGTCCAGC 60.280 61.111 19.41 14.44 46.81 4.85
251 638 0.744874 GCGTAGGCAGATGTACCTCA 59.255 55.000 1.75 0.00 37.50 3.86
298 685 6.931838 AGACGAGGTCAACAATAAATAGACA 58.068 36.000 0.00 0.00 34.60 3.41
305 692 4.221924 TGATGGAGACGAGGTCAACAATAA 59.778 41.667 0.00 0.00 34.60 1.40
306 693 3.767131 TGATGGAGACGAGGTCAACAATA 59.233 43.478 0.00 0.00 34.60 1.90
307 694 2.567169 TGATGGAGACGAGGTCAACAAT 59.433 45.455 0.00 0.00 34.60 2.71
308 695 1.967779 TGATGGAGACGAGGTCAACAA 59.032 47.619 0.00 0.00 34.60 2.83
309 696 1.627864 TGATGGAGACGAGGTCAACA 58.372 50.000 0.00 0.00 34.60 3.33
326 713 4.092821 CGTAGGAGTTCGCAATTTCATTGA 59.907 41.667 0.49 0.00 42.83 2.57
328 715 4.250464 TCGTAGGAGTTCGCAATTTCATT 58.750 39.130 0.00 0.00 0.00 2.57
333 720 1.822990 TCCTCGTAGGAGTTCGCAATT 59.177 47.619 11.31 0.00 40.06 2.32
336 723 4.728409 TCCTCGTAGGAGTTCGCA 57.272 55.556 11.31 0.00 40.06 5.10
379 766 3.096852 TGACCCACATAAGACACGAGAT 58.903 45.455 0.00 0.00 0.00 2.75
390 777 4.141459 ACGAGAGATAGACTGACCCACATA 60.141 45.833 0.00 0.00 0.00 2.29
407 794 3.680937 ACGAGAAGAGTAAGACACGAGAG 59.319 47.826 0.00 0.00 0.00 3.20
415 802 3.686726 GGTTACCGACGAGAAGAGTAAGA 59.313 47.826 0.00 0.00 0.00 2.10
431 818 5.290386 CGAAGAGTGAAGATATGGGTTACC 58.710 45.833 0.00 0.00 37.24 2.85
433 820 4.344102 CCCGAAGAGTGAAGATATGGGTTA 59.656 45.833 0.00 0.00 0.00 2.85
472 867 4.974645 AGTCCTTGTTGTTCCTATGTCA 57.025 40.909 0.00 0.00 0.00 3.58
473 868 6.590677 GTCTAAGTCCTTGTTGTTCCTATGTC 59.409 42.308 0.00 0.00 0.00 3.06
478 873 5.123936 GTTGTCTAAGTCCTTGTTGTTCCT 58.876 41.667 0.00 0.00 0.00 3.36
489 884 3.587797 TGTCATCCGTTGTCTAAGTCC 57.412 47.619 0.00 0.00 0.00 3.85
498 893 6.797033 GTCTAAATCTTTGTTGTCATCCGTTG 59.203 38.462 0.00 0.00 0.00 4.10
499 894 6.710744 AGTCTAAATCTTTGTTGTCATCCGTT 59.289 34.615 0.00 0.00 0.00 4.44
520 915 7.923414 AAGCATCCGAAAGTTAATTTAGTCT 57.077 32.000 0.00 0.00 0.00 3.24
561 956 7.285788 CGGTACACATTCACTACACTTTTAAC 58.714 38.462 0.00 0.00 0.00 2.01
577 972 6.431543 TGATTTTCATTTGTACCGGTACACAT 59.568 34.615 40.21 35.59 44.81 3.21
594 989 6.406692 TTTAAACCAACCGGATGATTTTCA 57.593 33.333 9.63 0.00 35.59 2.69
661 1056 6.089249 ACTTGCAAGGGTTTTAATCTTCTG 57.911 37.500 29.18 0.12 0.00 3.02
663 1058 8.880878 TTTAACTTGCAAGGGTTTTAATCTTC 57.119 30.769 29.18 0.00 0.00 2.87
665 1060 9.489084 GATTTTAACTTGCAAGGGTTTTAATCT 57.511 29.630 29.18 13.93 30.49 2.40
712 1108 0.842635 CTTGAGGAGGATTGGGGAGG 59.157 60.000 0.00 0.00 0.00 4.30
715 1111 1.767681 CTCTCTTGAGGAGGATTGGGG 59.232 57.143 0.00 0.00 42.10 4.96
787 1183 3.764466 CGTCCCGGAGCTGCTTCT 61.764 66.667 0.73 0.00 0.00 2.85
835 1231 4.389077 CCTCGCTCGTTTATTTCAGAAAGT 59.611 41.667 1.28 0.00 0.00 2.66
1158 1561 1.139308 CAGAGGCTCAGAGCGAGTG 59.861 63.158 18.26 8.97 43.62 3.51
1204 1607 2.892425 GACGCGAGGCCATGGAAG 60.892 66.667 18.40 3.75 0.00 3.46
1419 1826 0.508641 CAACAAAGCCTCGACAGACG 59.491 55.000 0.00 0.00 44.09 4.18
1423 1830 1.444119 GCCACAACAAAGCCTCGACA 61.444 55.000 0.00 0.00 0.00 4.35
1424 1831 1.282875 GCCACAACAAAGCCTCGAC 59.717 57.895 0.00 0.00 0.00 4.20
1426 1833 2.252260 CGCCACAACAAAGCCTCG 59.748 61.111 0.00 0.00 0.00 4.63
1428 1835 2.519302 AGCGCCACAACAAAGCCT 60.519 55.556 2.29 0.00 0.00 4.58
1429 1836 2.050077 GAGCGCCACAACAAAGCC 60.050 61.111 2.29 0.00 0.00 4.35
1430 1837 2.050077 GGAGCGCCACAACAAAGC 60.050 61.111 2.29 0.00 0.00 3.51
1431 1838 1.197721 CTAAGGAGCGCCACAACAAAG 59.802 52.381 9.88 0.00 36.29 2.77
1432 1839 1.234821 CTAAGGAGCGCCACAACAAA 58.765 50.000 9.88 0.00 36.29 2.83
1433 1840 0.605319 CCTAAGGAGCGCCACAACAA 60.605 55.000 9.88 0.00 36.29 2.83
1434 1841 1.003839 CCTAAGGAGCGCCACAACA 60.004 57.895 9.88 0.00 36.29 3.33
1435 1842 2.399356 GCCTAAGGAGCGCCACAAC 61.399 63.158 9.88 0.00 36.29 3.32
1436 1843 2.046314 GCCTAAGGAGCGCCACAA 60.046 61.111 9.88 0.00 36.29 3.33
1437 1844 2.124507 AAAGCCTAAGGAGCGCCACA 62.125 55.000 9.88 0.00 36.29 4.17
1438 1845 0.107848 TAAAGCCTAAGGAGCGCCAC 60.108 55.000 9.88 0.00 36.29 5.01
1439 1846 0.178068 CTAAAGCCTAAGGAGCGCCA 59.822 55.000 9.88 0.00 36.29 5.69
1440 1847 1.160946 GCTAAAGCCTAAGGAGCGCC 61.161 60.000 2.29 0.00 34.64 6.53
1441 1848 0.462047 TGCTAAAGCCTAAGGAGCGC 60.462 55.000 0.00 0.00 41.18 5.92
1442 1849 1.576356 CTGCTAAAGCCTAAGGAGCG 58.424 55.000 0.00 0.00 41.18 5.03
1443 1850 1.475930 CCCTGCTAAAGCCTAAGGAGC 60.476 57.143 8.09 0.00 41.18 4.70
1444 1851 2.103941 CTCCCTGCTAAAGCCTAAGGAG 59.896 54.545 8.09 9.38 41.18 3.69
1445 1852 2.119495 CTCCCTGCTAAAGCCTAAGGA 58.881 52.381 8.09 4.42 41.18 3.36
1446 1853 1.475930 GCTCCCTGCTAAAGCCTAAGG 60.476 57.143 0.00 0.00 41.18 2.69
1447 1854 1.808133 CGCTCCCTGCTAAAGCCTAAG 60.808 57.143 0.00 0.00 41.18 2.18
1448 1855 0.178068 CGCTCCCTGCTAAAGCCTAA 59.822 55.000 0.00 0.00 41.18 2.69
1449 1856 1.686325 CCGCTCCCTGCTAAAGCCTA 61.686 60.000 0.00 0.00 41.18 3.93
1543 1978 0.935898 CTCAATGCCTCGATGAGCAC 59.064 55.000 7.03 0.00 42.84 4.40
1547 1982 0.249197 CGAGCTCAATGCCTCGATGA 60.249 55.000 15.40 0.00 44.23 2.92
1548 1983 0.529337 ACGAGCTCAATGCCTCGATG 60.529 55.000 22.73 0.00 44.23 3.84
1549 1984 0.529337 CACGAGCTCAATGCCTCGAT 60.529 55.000 22.73 9.73 44.23 3.59
1550 1985 1.153765 CACGAGCTCAATGCCTCGA 60.154 57.895 22.73 0.00 44.23 4.04
1551 1986 2.169789 CCACGAGCTCAATGCCTCG 61.170 63.158 15.40 17.11 44.23 4.63
1552 1987 2.467826 GCCACGAGCTCAATGCCTC 61.468 63.158 15.40 0.29 44.23 4.70
1553 1988 2.437359 GCCACGAGCTCAATGCCT 60.437 61.111 15.40 0.00 44.23 4.75
1554 1989 2.747460 TGCCACGAGCTCAATGCC 60.747 61.111 15.40 1.55 44.23 4.40
1571 2006 1.822990 CTTCACAAGGCATTGCATCCT 59.177 47.619 11.69 0.00 40.27 3.24
1573 2008 3.441572 ACTACTTCACAAGGCATTGCATC 59.558 43.478 11.69 0.00 40.27 3.91
1575 2010 2.553602 CACTACTTCACAAGGCATTGCA 59.446 45.455 11.69 0.00 40.27 4.08
1577 2012 2.095059 GGCACTACTTCACAAGGCATTG 60.095 50.000 10.01 10.01 42.46 2.82
1578 2013 2.162681 GGCACTACTTCACAAGGCATT 58.837 47.619 0.00 0.00 0.00 3.56
1579 2014 1.073763 TGGCACTACTTCACAAGGCAT 59.926 47.619 0.00 0.00 0.00 4.40
1580 2015 0.472044 TGGCACTACTTCACAAGGCA 59.528 50.000 0.00 0.00 0.00 4.75
1581 2016 1.160137 CTGGCACTACTTCACAAGGC 58.840 55.000 0.00 0.00 0.00 4.35
1649 2135 5.125356 TGAAATGCCACCATGTACTCATAG 58.875 41.667 0.00 0.00 32.47 2.23
1662 2148 3.006940 TGGTATCGAACTGAAATGCCAC 58.993 45.455 0.00 0.00 31.32 5.01
1700 2186 2.254546 TTTCTGTGTGAGGCGAATGT 57.745 45.000 0.00 0.00 0.00 2.71
1711 2197 3.066291 TCGGTGCCAATATTTCTGTGT 57.934 42.857 0.00 0.00 0.00 3.72
1719 2205 6.003950 ACTAAGCATAAATCGGTGCCAATAT 58.996 36.000 0.00 0.00 42.20 1.28
1749 2235 8.584157 CCATTTCTCATCTCAGCTTACTAGTAT 58.416 37.037 2.79 0.00 0.00 2.12
1754 2240 4.080695 TGCCATTTCTCATCTCAGCTTACT 60.081 41.667 0.00 0.00 0.00 2.24
1799 2394 1.982958 TCCCACTTTCCCAGTACCTTC 59.017 52.381 0.00 0.00 32.76 3.46
1818 2413 4.141482 TGGGAGCATAAATACCAGGACTTC 60.141 45.833 0.00 0.00 0.00 3.01
1832 2427 0.764369 CCTACTGGCCTGGGAGCATA 60.764 60.000 14.82 0.00 0.00 3.14
1900 2521 7.436320 AAATTATATGCCCAAGGTTTCACAT 57.564 32.000 0.00 0.00 0.00 3.21
1903 2524 5.451242 GCGAAATTATATGCCCAAGGTTTCA 60.451 40.000 0.00 0.00 0.00 2.69
1912 2533 5.391950 CCATGTAGTGCGAAATTATATGCCC 60.392 44.000 0.00 0.00 0.00 5.36
1933 2554 4.646492 GGGCAGAAACATCAGAATTACCAT 59.354 41.667 0.00 0.00 0.00 3.55
2174 2795 8.816144 TCAAATGAAAACAAGTGACATAAAAGC 58.184 29.630 0.00 0.00 0.00 3.51
2179 2800 9.513906 TCCTATCAAATGAAAACAAGTGACATA 57.486 29.630 0.00 0.00 0.00 2.29
2224 2845 5.882557 ACAGAATTTCGTTTCCAGCTGATAT 59.117 36.000 17.39 0.00 0.00 1.63
2229 2850 2.814336 GGACAGAATTTCGTTTCCAGCT 59.186 45.455 8.35 0.00 0.00 4.24
2238 2859 7.005062 ACGAATATCAAAGGACAGAATTTCG 57.995 36.000 0.00 0.00 37.78 3.46
2245 2866 7.926555 ACTTACCATACGAATATCAAAGGACAG 59.073 37.037 0.00 0.00 0.00 3.51
2253 2874 6.213677 GTGCTCACTTACCATACGAATATCA 58.786 40.000 0.00 0.00 0.00 2.15
2271 2892 5.417580 GGAATACAAATTAAGTGGGTGCTCA 59.582 40.000 0.00 0.00 0.00 4.26
2298 2921 4.271533 ACGCAAAAAGTCACAACTTCGATA 59.728 37.500 0.00 0.00 45.07 2.92
2317 2940 1.403814 TCCCAATGAAAACCAACGCA 58.596 45.000 0.00 0.00 0.00 5.24
2468 3091 5.009811 TCACAATCACAGCATCATTTCACAA 59.990 36.000 0.00 0.00 0.00 3.33
2884 3567 6.721318 TGTGAGAGGAATAGCCAAACTTATT 58.279 36.000 0.00 0.00 40.02 1.40
2894 3577 5.016051 TGACAATCTGTGAGAGGAATAGC 57.984 43.478 0.00 0.00 0.00 2.97
2991 3674 9.778993 CACTGTTATTTGATGAAAAGGTATGAG 57.221 33.333 0.00 0.00 0.00 2.90
3022 3705 9.454585 GGGAATAATAATACGCAAAACTAAACC 57.545 33.333 0.00 0.00 0.00 3.27
3027 3710 7.875327 AGTGGGAATAATAATACGCAAAACT 57.125 32.000 0.00 0.00 0.00 2.66
3050 3733 2.420022 CAGGGCAACGGAGACATTAAAG 59.580 50.000 0.00 0.00 37.60 1.85
3247 3958 5.764686 TGCTGCCAAATCAAGACGATAATAT 59.235 36.000 0.00 0.00 32.51 1.28
3563 4310 6.590677 CACTGATCCACATCTGATAATAGCAG 59.409 42.308 0.00 0.00 33.29 4.24
3588 4335 6.147164 TCCTGACATTCAACAGAAATACGTTC 59.853 38.462 0.00 0.00 36.38 3.95
3821 4568 3.083997 GCTCATGGTCGACCCCCT 61.084 66.667 31.19 13.59 34.29 4.79
3846 4593 1.565759 TCCCATCCCCAAGATCAGTTG 59.434 52.381 0.00 0.00 30.59 3.16
3961 4708 9.743057 CAGTGAGATAAGTAAGGAACATAGAAG 57.257 37.037 0.00 0.00 0.00 2.85
4045 4792 3.200483 GTCGTTACCACCTGAAACAAGT 58.800 45.455 0.00 0.00 0.00 3.16
4216 4967 9.899661 ATGGCATAGTAACTAACAAAGTATTGA 57.100 29.630 0.00 0.00 37.50 2.57
4220 4971 9.727859 TTCAATGGCATAGTAACTAACAAAGTA 57.272 29.630 0.00 0.00 37.50 2.24
4283 5053 4.320935 GCAGTACACAACCAATTTACCTGG 60.321 45.833 0.00 0.00 40.05 4.45
4371 5141 1.933181 CGCGCATTTCTCCATCTACAA 59.067 47.619 8.75 0.00 0.00 2.41
4372 5142 1.570813 CGCGCATTTCTCCATCTACA 58.429 50.000 8.75 0.00 0.00 2.74
4373 5143 0.861837 CCGCGCATTTCTCCATCTAC 59.138 55.000 8.75 0.00 0.00 2.59
4462 5233 6.173339 GGTTCATATGAAAAGACAGGAGTCA 58.827 40.000 19.55 0.00 40.42 3.41
4474 5245 2.760092 GCTGGCTTGGGTTCATATGAAA 59.240 45.455 19.55 1.88 35.58 2.69
4532 5303 0.322975 TGGTTTCTGCAGAGCCTCTC 59.677 55.000 28.23 14.22 0.00 3.20
4562 5362 5.924254 TCAGTACCACATAACTTTTGTCTCG 59.076 40.000 0.00 0.00 0.00 4.04
4740 5540 8.548721 AGAAACAACAGTTACAATTCTACGAAG 58.451 33.333 0.00 0.00 0.00 3.79
4815 5615 8.983724 TCGAGTTCTTTTGTTTTGTTGATTTTT 58.016 25.926 0.00 0.00 0.00 1.94
4836 5636 2.234300 TTTCCGAAGCAAAGTCGAGT 57.766 45.000 0.00 0.00 41.02 4.18
4842 5642 2.030007 TGCCAAGATTTCCGAAGCAAAG 60.030 45.455 0.00 0.00 0.00 2.77
4850 5650 3.181493 CCAGAATTCTGCCAAGATTTCCG 60.181 47.826 27.01 7.59 40.99 4.30
4854 5654 4.581309 TCTCCAGAATTCTGCCAAGATT 57.419 40.909 27.01 0.00 42.47 2.40
4941 5741 4.402056 TCTCCTGTCTGAAACGTTTTCT 57.598 40.909 15.89 0.00 0.00 2.52
4956 5756 8.737168 TGAAAATCAATAGGTGTATTCTCCTG 57.263 34.615 3.42 0.00 37.97 3.86
4973 5773 7.944554 AGGATCCTAGTGAAAAACTGAAAATCA 59.055 33.333 14.27 0.00 40.26 2.57
4978 5778 7.336931 GCATTAGGATCCTAGTGAAAAACTGAA 59.663 37.037 36.04 15.77 40.26 3.02
4979 5779 6.823689 GCATTAGGATCCTAGTGAAAAACTGA 59.176 38.462 36.04 14.43 40.26 3.41
4980 5780 6.599244 TGCATTAGGATCCTAGTGAAAAACTG 59.401 38.462 36.04 16.24 40.26 3.16
4981 5781 6.721318 TGCATTAGGATCCTAGTGAAAAACT 58.279 36.000 36.04 7.60 43.40 2.66
4982 5782 6.823689 TCTGCATTAGGATCCTAGTGAAAAAC 59.176 38.462 36.04 22.84 38.14 2.43
4983 5783 6.957631 TCTGCATTAGGATCCTAGTGAAAAA 58.042 36.000 36.04 20.34 38.14 1.94
4984 5784 6.560003 TCTGCATTAGGATCCTAGTGAAAA 57.440 37.500 36.04 18.97 38.14 2.29
4985 5785 6.753913 ATCTGCATTAGGATCCTAGTGAAA 57.246 37.500 36.04 25.07 38.14 2.69
4986 5786 6.556495 AGAATCTGCATTAGGATCCTAGTGAA 59.444 38.462 36.04 28.88 38.14 3.18
5015 5815 2.186243 TCAAGATTCTGGAGAGCTGCT 58.814 47.619 0.00 0.00 0.00 4.24
5043 5843 2.415893 CGGATCTTTTTGCGCAGGATTT 60.416 45.455 11.31 0.00 0.00 2.17
5054 5854 1.893137 GACTTTGGCCCGGATCTTTTT 59.107 47.619 0.73 0.00 0.00 1.94
5061 5861 0.610785 GGAAATGACTTTGGCCCGGA 60.611 55.000 0.73 0.00 0.00 5.14
5063 5863 1.604147 GGGGAAATGACTTTGGCCCG 61.604 60.000 0.00 0.00 34.85 6.13
5073 5873 2.656002 TCACAACGTTTGGGGAAATGA 58.344 42.857 0.00 0.00 33.95 2.57


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

AutoCloner maintained by Alex Coulton.