Multiple sequence alignment - TraesCS5B01G424100

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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 TraesCS5B01G424100 chr5B 100.000 3458 0 0 1 3458 600339550 600336093 0.000000e+00 6386.0
1 TraesCS5B01G424100 chr5B 92.747 1103 66 7 912 2013 600135259 600134170 0.000000e+00 1581.0
2 TraesCS5B01G424100 chr5B 84.286 280 19 9 2181 2435 600133984 600133705 2.060000e-62 250.0
3 TraesCS5B01G424100 chr5B 81.871 171 25 2 105 270 499161396 499161565 4.650000e-29 139.0
4 TraesCS5B01G424100 chr5B 95.000 60 3 0 2010 2069 600134140 600134081 1.020000e-15 95.3
5 TraesCS5B01G424100 chr5B 84.706 85 13 0 2675 2759 490618479 490618395 6.150000e-13 86.1
6 TraesCS5B01G424100 chr5D 91.983 1185 92 2 885 2069 487836916 487835735 0.000000e+00 1659.0
7 TraesCS5B01G424100 chr5D 92.029 1104 73 9 912 2013 487599976 487598886 0.000000e+00 1537.0
8 TraesCS5B01G424100 chr5D 87.939 854 84 10 2617 3457 487833693 487832846 0.000000e+00 989.0
9 TraesCS5B01G424100 chr5D 83.974 755 74 21 104 833 487837668 487836936 0.000000e+00 680.0
10 TraesCS5B01G424100 chr5D 93.768 353 18 2 2258 2606 487834390 487834038 8.500000e-146 527.0
11 TraesCS5B01G424100 chr5D 86.100 259 15 1 2194 2431 487598692 487598434 3.420000e-65 259.0
12 TraesCS5B01G424100 chr5D 94.783 115 6 0 2149 2263 487835692 487835578 2.740000e-41 180.0
13 TraesCS5B01G424100 chr5D 90.541 74 4 1 1996 2069 487598870 487598800 1.020000e-15 95.3
14 TraesCS5B01G424100 chr5D 85.246 61 7 2 705 764 544792496 544792555 1.040000e-05 62.1
15 TraesCS5B01G424100 chr5A 91.716 1171 89 7 914 2080 608447796 608446630 0.000000e+00 1618.0
16 TraesCS5B01G424100 chr5A 91.938 1104 74 8 912 2013 608361852 608360762 0.000000e+00 1531.0
17 TraesCS5B01G424100 chr5A 84.111 793 121 5 2666 3457 608445200 608444412 0.000000e+00 761.0
18 TraesCS5B01G424100 chr5A 87.589 282 17 5 2260 2536 608446139 608445871 9.320000e-81 311.0
19 TraesCS5B01G424100 chr5A 84.444 270 20 2 2182 2429 608360578 608360309 2.670000e-61 246.0
20 TraesCS5B01G424100 chr5A 92.437 119 9 0 2145 2263 608446613 608446495 1.650000e-38 171.0
21 TraesCS5B01G424100 chr5A 75.910 357 58 20 1655 2000 42259926 42260265 1.280000e-34 158.0
22 TraesCS5B01G424100 chr5A 90.411 73 4 2 1997 2069 608360745 608360676 3.670000e-15 93.5
23 TraesCS5B01G424100 chr5A 81.818 99 18 0 2666 2764 519851695 519851597 2.210000e-12 84.2
24 TraesCS5B01G424100 chr7A 80.000 180 29 3 108 281 571257746 571257924 3.620000e-25 126.0
25 TraesCS5B01G424100 chr7A 82.895 76 11 2 721 794 82940617 82940542 2.230000e-07 67.6
26 TraesCS5B01G424100 chr7A 96.970 33 1 0 705 737 136464693 136464661 4.820000e-04 56.5
27 TraesCS5B01G424100 chr2B 79.213 178 32 4 108 281 140742268 140742444 6.060000e-23 119.0
28 TraesCS5B01G424100 chr4D 73.639 349 61 28 1167 1501 378450636 378450305 4.720000e-19 106.0
29 TraesCS5B01G424100 chr4A 72.905 358 69 26 1161 1501 86990196 86990542 7.900000e-17 99.0
30 TraesCS5B01G424100 chr4B 92.424 66 3 2 1167 1231 464955080 464955016 3.670000e-15 93.5
31 TraesCS5B01G424100 chr1B 93.333 45 2 1 694 737 419403943 419403899 8.010000e-07 65.8
32 TraesCS5B01G424100 chr1A 91.111 45 3 1 694 737 389130824 389130780 3.730000e-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 TraesCS5B01G424100 chr5B 600336093 600339550 3457 True 6386.000000 6386 100.000000 1 3458 1 chr5B.!!$R2 3457
1 TraesCS5B01G424100 chr5B 600133705 600135259 1554 True 642.100000 1581 90.677667 912 2435 3 chr5B.!!$R3 1523
2 TraesCS5B01G424100 chr5D 487832846 487837668 4822 True 807.000000 1659 90.489400 104 3457 5 chr5D.!!$R2 3353
3 TraesCS5B01G424100 chr5D 487598434 487599976 1542 True 630.433333 1537 89.556667 912 2431 3 chr5D.!!$R1 1519
4 TraesCS5B01G424100 chr5A 608444412 608447796 3384 True 715.250000 1618 88.963250 914 3457 4 chr5A.!!$R3 2543
5 TraesCS5B01G424100 chr5A 608360309 608361852 1543 True 623.500000 1531 88.931000 912 2429 3 chr5A.!!$R2 1517

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
76 77 0.176680 CCTGTTCCATGTCTCCCTCG 59.823 60.0 0.00 0.00 0.00 4.63 F
1666 1695 0.107081 TCCAGAAGGTTTTCGGCGAA 59.893 50.0 19.83 19.83 38.38 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2132 0.038526 CCGAGTTCAGGTGCGTTAGT 60.039 55.0 0.00 0.0 0.0 2.24 R
2914 5175 0.030235 CGGATGATGTCGACGCCTTA 59.970 55.0 11.62 0.0 0.0 2.69 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
27 28 2.026522 TTTTTGTTCGGGCTGACGG 58.973 52.632 0.00 0.00 0.00 4.79
28 29 2.065906 TTTTTGTTCGGGCTGACGGC 62.066 55.000 0.00 0.00 40.90 5.68
44 45 4.057428 GCCGCTGACTCGTGTCCT 62.057 66.667 14.57 0.00 42.28 3.85
45 46 2.179517 CCGCTGACTCGTGTCCTC 59.820 66.667 14.57 5.80 42.28 3.71
46 47 2.179517 CGCTGACTCGTGTCCTCC 59.820 66.667 14.57 2.84 42.28 4.30
47 48 2.336478 CGCTGACTCGTGTCCTCCT 61.336 63.158 14.57 0.00 42.28 3.69
48 49 1.509004 GCTGACTCGTGTCCTCCTC 59.491 63.158 14.57 0.00 42.28 3.71
49 50 0.963355 GCTGACTCGTGTCCTCCTCT 60.963 60.000 14.57 0.00 42.28 3.69
50 51 1.540267 CTGACTCGTGTCCTCCTCTT 58.460 55.000 14.57 0.00 42.28 2.85
51 52 1.470890 CTGACTCGTGTCCTCCTCTTC 59.529 57.143 14.57 0.00 42.28 2.87
52 53 1.074084 TGACTCGTGTCCTCCTCTTCT 59.926 52.381 14.57 0.00 42.28 2.85
53 54 1.741145 GACTCGTGTCCTCCTCTTCTC 59.259 57.143 6.35 0.00 37.24 2.87
54 55 1.353022 ACTCGTGTCCTCCTCTTCTCT 59.647 52.381 0.00 0.00 0.00 3.10
55 56 1.742831 CTCGTGTCCTCCTCTTCTCTG 59.257 57.143 0.00 0.00 0.00 3.35
56 57 1.351350 TCGTGTCCTCCTCTTCTCTGA 59.649 52.381 0.00 0.00 0.00 3.27
57 58 1.470890 CGTGTCCTCCTCTTCTCTGAC 59.529 57.143 0.00 0.00 0.00 3.51
58 59 1.822371 GTGTCCTCCTCTTCTCTGACC 59.178 57.143 0.00 0.00 0.00 4.02
59 60 1.713647 TGTCCTCCTCTTCTCTGACCT 59.286 52.381 0.00 0.00 0.00 3.85
60 61 2.099405 GTCCTCCTCTTCTCTGACCTG 58.901 57.143 0.00 0.00 0.00 4.00
61 62 1.713647 TCCTCCTCTTCTCTGACCTGT 59.286 52.381 0.00 0.00 0.00 4.00
62 63 2.110899 TCCTCCTCTTCTCTGACCTGTT 59.889 50.000 0.00 0.00 0.00 3.16
63 64 2.495669 CCTCCTCTTCTCTGACCTGTTC 59.504 54.545 0.00 0.00 0.00 3.18
64 65 2.495669 CTCCTCTTCTCTGACCTGTTCC 59.504 54.545 0.00 0.00 0.00 3.62
65 66 2.158310 TCCTCTTCTCTGACCTGTTCCA 60.158 50.000 0.00 0.00 0.00 3.53
66 67 2.836981 CCTCTTCTCTGACCTGTTCCAT 59.163 50.000 0.00 0.00 0.00 3.41
67 68 3.369261 CCTCTTCTCTGACCTGTTCCATG 60.369 52.174 0.00 0.00 0.00 3.66
68 69 3.242867 TCTTCTCTGACCTGTTCCATGT 58.757 45.455 0.00 0.00 0.00 3.21
69 70 3.259374 TCTTCTCTGACCTGTTCCATGTC 59.741 47.826 0.00 0.00 31.39 3.06
70 71 2.894731 TCTCTGACCTGTTCCATGTCT 58.105 47.619 0.00 0.00 31.88 3.41
71 72 2.828520 TCTCTGACCTGTTCCATGTCTC 59.171 50.000 0.00 0.00 31.88 3.36
72 73 1.902508 TCTGACCTGTTCCATGTCTCC 59.097 52.381 0.00 0.00 31.88 3.71
73 74 0.984230 TGACCTGTTCCATGTCTCCC 59.016 55.000 0.00 0.00 31.88 4.30
74 75 1.280457 GACCTGTTCCATGTCTCCCT 58.720 55.000 0.00 0.00 0.00 4.20
75 76 1.208293 GACCTGTTCCATGTCTCCCTC 59.792 57.143 0.00 0.00 0.00 4.30
76 77 0.176680 CCTGTTCCATGTCTCCCTCG 59.823 60.000 0.00 0.00 0.00 4.63
77 78 1.186200 CTGTTCCATGTCTCCCTCGA 58.814 55.000 0.00 0.00 0.00 4.04
78 79 1.135915 CTGTTCCATGTCTCCCTCGAG 59.864 57.143 5.13 5.13 37.48 4.04
79 80 1.187087 GTTCCATGTCTCCCTCGAGT 58.813 55.000 12.31 0.00 37.40 4.18
80 81 1.550976 GTTCCATGTCTCCCTCGAGTT 59.449 52.381 12.31 0.00 37.40 3.01
81 82 1.186200 TCCATGTCTCCCTCGAGTTG 58.814 55.000 12.31 2.02 37.40 3.16
82 83 0.460987 CCATGTCTCCCTCGAGTTGC 60.461 60.000 12.31 0.00 37.40 4.17
83 84 0.247460 CATGTCTCCCTCGAGTTGCA 59.753 55.000 12.31 3.47 37.40 4.08
84 85 0.534412 ATGTCTCCCTCGAGTTGCAG 59.466 55.000 12.31 1.41 37.40 4.41
85 86 1.446966 GTCTCCCTCGAGTTGCAGC 60.447 63.158 12.31 0.00 37.40 5.25
86 87 2.507992 CTCCCTCGAGTTGCAGCG 60.508 66.667 12.31 0.00 0.00 5.18
87 88 2.989253 TCCCTCGAGTTGCAGCGA 60.989 61.111 12.31 7.90 35.01 4.93
88 89 2.185350 CCCTCGAGTTGCAGCGAT 59.815 61.111 12.31 0.00 35.81 4.58
89 90 2.169789 CCCTCGAGTTGCAGCGATG 61.170 63.158 12.31 0.00 35.81 3.84
90 91 2.169789 CCTCGAGTTGCAGCGATGG 61.170 63.158 12.31 8.51 35.81 3.51
91 92 2.806856 CTCGAGTTGCAGCGATGGC 61.807 63.158 3.62 0.00 35.81 4.40
92 93 3.869272 CGAGTTGCAGCGATGGCC 61.869 66.667 1.46 0.00 41.24 5.36
93 94 2.437359 GAGTTGCAGCGATGGCCT 60.437 61.111 3.32 0.00 41.24 5.19
94 95 2.437359 AGTTGCAGCGATGGCCTC 60.437 61.111 3.32 0.00 41.24 4.70
95 96 2.437359 GTTGCAGCGATGGCCTCT 60.437 61.111 3.32 0.00 41.24 3.69
96 97 2.437180 TTGCAGCGATGGCCTCTG 60.437 61.111 3.32 7.39 41.24 3.35
97 98 3.258228 TTGCAGCGATGGCCTCTGT 62.258 57.895 3.32 0.00 41.24 3.41
98 99 3.200593 GCAGCGATGGCCTCTGTG 61.201 66.667 3.32 0.00 41.24 3.66
99 100 2.580815 CAGCGATGGCCTCTGTGA 59.419 61.111 3.32 0.00 41.24 3.58
100 101 1.521010 CAGCGATGGCCTCTGTGAG 60.521 63.158 3.32 0.00 41.24 3.51
101 102 1.986757 AGCGATGGCCTCTGTGAGT 60.987 57.895 3.32 0.00 41.24 3.41
102 103 1.520342 GCGATGGCCTCTGTGAGTC 60.520 63.158 3.32 0.00 0.00 3.36
103 104 1.954362 GCGATGGCCTCTGTGAGTCT 61.954 60.000 3.32 0.00 0.00 3.24
104 105 1.393603 CGATGGCCTCTGTGAGTCTA 58.606 55.000 3.32 0.00 0.00 2.59
105 106 1.751351 CGATGGCCTCTGTGAGTCTAA 59.249 52.381 3.32 0.00 0.00 2.10
106 107 2.223688 CGATGGCCTCTGTGAGTCTAAG 60.224 54.545 3.32 0.00 0.00 2.18
107 108 2.604912 TGGCCTCTGTGAGTCTAAGA 57.395 50.000 3.32 0.00 0.00 2.10
136 137 5.190992 TGGAGTGCATGCATAAATTCATC 57.809 39.130 25.64 7.38 0.00 2.92
138 139 5.127356 TGGAGTGCATGCATAAATTCATCAA 59.873 36.000 25.64 3.21 0.00 2.57
155 156 5.244755 TCATCAAGAAATCACATTGACGGA 58.755 37.500 0.00 0.00 35.89 4.69
170 171 1.196127 GACGGAAGGCGTGGTAAAAAG 59.804 52.381 0.00 0.00 0.00 2.27
171 172 0.519961 CGGAAGGCGTGGTAAAAAGG 59.480 55.000 0.00 0.00 0.00 3.11
183 184 5.465056 CGTGGTAAAAAGGCAAAATCAATGT 59.535 36.000 0.00 0.00 0.00 2.71
186 187 7.011857 GTGGTAAAAAGGCAAAATCAATGTTCA 59.988 33.333 0.00 0.00 0.00 3.18
192 193 6.849588 AGGCAAAATCAATGTTCAGAAAAC 57.150 33.333 0.00 0.00 0.00 2.43
193 194 5.463061 AGGCAAAATCAATGTTCAGAAAACG 59.537 36.000 0.00 0.00 0.00 3.60
207 208 9.360093 TGTTCAGAAAACGTAAATTTCAAACAT 57.640 25.926 18.37 0.00 38.43 2.71
234 235 5.261040 TGGAGTTCTGATTTTCTTCCCAT 57.739 39.130 0.00 0.00 0.00 4.00
242 243 4.996793 TGATTTTCTTCCCATGACTTCCA 58.003 39.130 0.00 0.00 0.00 3.53
361 367 7.337938 TCATTACCTGATGAAGTAATTGAGCA 58.662 34.615 0.00 0.00 37.12 4.26
362 368 7.828717 TCATTACCTGATGAAGTAATTGAGCAA 59.171 33.333 0.00 0.00 37.12 3.91
391 397 5.043732 AGAGATATATTCCCTCCGTCTGGAT 60.044 44.000 0.00 0.00 45.33 3.41
396 402 4.625607 ATTCCCTCCGTCTGGATTTATC 57.374 45.455 0.00 0.00 45.33 1.75
412 418 9.640952 CTGGATTTATCAGACCCCTTTATTTTA 57.359 33.333 0.00 0.00 34.36 1.52
474 499 4.105486 GCGGAAAGCTCAAATACAAATCC 58.895 43.478 0.00 0.00 44.04 3.01
483 508 8.902540 AGCTCAAATACAAATCCGACAATATA 57.097 30.769 0.00 0.00 0.00 0.86
484 509 9.507329 AGCTCAAATACAAATCCGACAATATAT 57.493 29.630 0.00 0.00 0.00 0.86
485 510 9.546909 GCTCAAATACAAATCCGACAATATATG 57.453 33.333 0.00 0.00 0.00 1.78
492 517 8.287439 ACAAATCCGACAATATATGTTTTGGA 57.713 30.769 7.81 6.10 44.12 3.53
493 518 8.405531 ACAAATCCGACAATATATGTTTTGGAG 58.594 33.333 7.81 0.00 44.12 3.86
494 519 6.560253 ATCCGACAATATATGTTTTGGAGC 57.440 37.500 0.00 0.00 44.12 4.70
495 520 5.432645 TCCGACAATATATGTTTTGGAGCA 58.567 37.500 0.00 0.00 44.12 4.26
496 521 6.061441 TCCGACAATATATGTTTTGGAGCAT 58.939 36.000 0.00 0.00 44.12 3.79
497 522 7.220740 TCCGACAATATATGTTTTGGAGCATA 58.779 34.615 0.00 0.00 44.12 3.14
498 523 7.882791 TCCGACAATATATGTTTTGGAGCATAT 59.117 33.333 0.00 0.00 44.12 1.78
555 583 4.930696 AGTTGGACCTAAAATACAAGGGG 58.069 43.478 0.00 0.00 37.18 4.79
556 584 3.375647 TGGACCTAAAATACAAGGGGC 57.624 47.619 0.00 0.00 37.18 5.80
557 585 2.923629 TGGACCTAAAATACAAGGGGCT 59.076 45.455 0.00 0.00 37.18 5.19
596 624 6.998673 CGGGGAGAGTATAAATCAAATTCCTT 59.001 38.462 0.00 0.00 0.00 3.36
715 744 5.664294 AGACTTTTATGCATGGCAAATCA 57.336 34.783 10.16 0.00 43.62 2.57
723 752 5.968528 ATGCATGGCAAATCAAATGTTTT 57.031 30.435 0.00 0.00 43.62 2.43
754 783 6.349611 GCAATTTATATTGGCACGAGGATGAT 60.350 38.462 7.83 0.00 41.21 2.45
772 801 9.294030 GAGGATGATAATTTAGTTTGCAAACAG 57.706 33.333 36.46 0.00 41.30 3.16
773 802 9.023962 AGGATGATAATTTAGTTTGCAAACAGA 57.976 29.630 36.46 24.31 41.30 3.41
785 814 6.873076 AGTTTGCAAACAGAACAATTTTCAGA 59.127 30.769 36.46 0.00 41.30 3.27
786 815 7.387397 AGTTTGCAAACAGAACAATTTTCAGAA 59.613 29.630 36.46 0.00 41.30 3.02
787 816 7.664082 TTGCAAACAGAACAATTTTCAGAAA 57.336 28.000 0.00 0.00 0.00 2.52
788 817 7.664082 TGCAAACAGAACAATTTTCAGAAAA 57.336 28.000 10.80 10.80 34.41 2.29
789 818 8.092521 TGCAAACAGAACAATTTTCAGAAAAA 57.907 26.923 12.38 0.00 38.66 1.94
828 857 9.810231 CATTTTACCATGCTTTGTCAATTAAAC 57.190 29.630 0.00 0.00 0.00 2.01
833 862 6.701400 ACCATGCTTTGTCAATTAAACTTGTC 59.299 34.615 0.00 0.00 0.00 3.18
835 864 7.385752 CCATGCTTTGTCAATTAAACTTGTCAT 59.614 33.333 0.00 0.00 0.00 3.06
838 867 6.922957 GCTTTGTCAATTAAACTTGTCATCCA 59.077 34.615 0.00 0.00 0.00 3.41
839 868 7.599998 GCTTTGTCAATTAAACTTGTCATCCAT 59.400 33.333 0.00 0.00 0.00 3.41
855 884 9.531942 TTGTCATCCATAATACATTTGATTTGC 57.468 29.630 0.00 0.00 0.00 3.68
856 885 8.143193 TGTCATCCATAATACATTTGATTTGCC 58.857 33.333 0.00 0.00 0.00 4.52
876 905 9.902684 ATTTGCCATAAAAATCAAATGTATGGA 57.097 25.926 11.31 0.00 42.54 3.41
877 906 8.945481 TTGCCATAAAAATCAAATGTATGGAG 57.055 30.769 11.31 0.00 42.54 3.86
878 907 7.499292 TGCCATAAAAATCAAATGTATGGAGG 58.501 34.615 11.31 0.00 42.54 4.30
879 908 7.344093 TGCCATAAAAATCAAATGTATGGAGGA 59.656 33.333 11.31 0.00 42.54 3.71
880 909 7.869429 GCCATAAAAATCAAATGTATGGAGGAG 59.131 37.037 11.31 0.00 42.54 3.69
881 910 8.917088 CCATAAAAATCAAATGTATGGAGGAGT 58.083 33.333 2.46 0.00 42.54 3.85
885 914 9.533831 AAAAATCAAATGTATGGAGGAGTAGTT 57.466 29.630 0.00 0.00 0.00 2.24
886 915 8.511604 AAATCAAATGTATGGAGGAGTAGTTG 57.488 34.615 0.00 0.00 0.00 3.16
887 916 6.620877 TCAAATGTATGGAGGAGTAGTTGT 57.379 37.500 0.00 0.00 0.00 3.32
888 917 6.640518 TCAAATGTATGGAGGAGTAGTTGTC 58.359 40.000 0.00 0.00 0.00 3.18
889 918 6.212589 TCAAATGTATGGAGGAGTAGTTGTCA 59.787 38.462 0.00 0.00 0.00 3.58
890 919 6.814954 AATGTATGGAGGAGTAGTTGTCAT 57.185 37.500 0.00 0.00 0.00 3.06
891 920 7.914427 AATGTATGGAGGAGTAGTTGTCATA 57.086 36.000 0.00 0.00 0.00 2.15
892 921 7.914427 ATGTATGGAGGAGTAGTTGTCATAA 57.086 36.000 0.00 0.00 0.00 1.90
893 922 7.727578 TGTATGGAGGAGTAGTTGTCATAAA 57.272 36.000 0.00 0.00 0.00 1.40
931 960 1.267121 ATTACTGGTGTGCGGTCTCT 58.733 50.000 0.00 0.00 0.00 3.10
1070 1099 3.640000 GCGCACACAGCAGAACGT 61.640 61.111 0.30 0.00 46.13 3.99
1189 1218 3.511934 ACAAGCTCACCTACGAGATCTTT 59.488 43.478 0.00 0.00 34.79 2.52
1213 1242 1.178276 TCCTCGAGAGCAAGTTCCTC 58.822 55.000 15.71 0.00 0.00 3.71
1244 1273 1.906574 ACGACCCCAAGCTTCTATTCA 59.093 47.619 0.00 0.00 0.00 2.57
1666 1695 0.107081 TCCAGAAGGTTTTCGGCGAA 59.893 50.000 19.83 19.83 38.38 4.70
1726 1755 4.720902 TACGACCTCGCCACGGGA 62.721 66.667 0.00 0.00 44.43 5.14
1854 1883 4.309950 GGTGGAGGTGCGGTCGTT 62.310 66.667 0.00 0.00 0.00 3.85
1950 1979 2.427410 GCTCAACAACAAGCGCGG 60.427 61.111 8.83 0.00 0.00 6.46
1990 2019 1.747355 GTGGAGGATTTGCTGGTCATG 59.253 52.381 0.00 0.00 0.00 3.07
2033 2095 0.382515 CTCCACTTCCGAGATCGTCC 59.617 60.000 1.09 0.00 37.74 4.79
2069 2131 0.109643 CGTGTCCGACATGGTACGAA 60.110 55.000 12.29 0.00 45.57 3.85
2070 2132 1.666599 CGTGTCCGACATGGTACGAAA 60.667 52.381 12.29 0.00 45.57 3.46
2071 2133 1.723003 GTGTCCGACATGGTACGAAAC 59.277 52.381 4.13 8.42 39.52 2.78
2072 2134 1.614903 TGTCCGACATGGTACGAAACT 59.385 47.619 0.00 0.00 39.52 2.66
2076 2138 2.595536 CCGACATGGTACGAAACTAACG 59.404 50.000 9.95 0.00 0.00 3.18
2078 2140 2.988493 GACATGGTACGAAACTAACGCA 59.012 45.455 0.00 0.00 0.00 5.24
2079 2141 2.733026 ACATGGTACGAAACTAACGCAC 59.267 45.455 0.00 0.00 0.00 5.34
2080 2142 1.782044 TGGTACGAAACTAACGCACC 58.218 50.000 0.00 0.00 44.43 5.01
2081 2143 1.340889 TGGTACGAAACTAACGCACCT 59.659 47.619 0.00 0.00 44.46 4.00
2083 2145 2.607771 GGTACGAAACTAACGCACCTGA 60.608 50.000 0.00 0.00 41.97 3.86
2087 2149 2.155155 CGAAACTAACGCACCTGAACTC 59.845 50.000 0.00 0.00 0.00 3.01
2089 2151 0.038526 ACTAACGCACCTGAACTCGG 60.039 55.000 0.00 0.00 0.00 4.63
2090 2152 0.038526 CTAACGCACCTGAACTCGGT 60.039 55.000 0.00 0.00 34.38 4.69
2100 2162 2.135933 CTGAACTCGGTTTCAGTCCAC 58.864 52.381 15.12 0.00 45.12 4.02
2104 2166 0.107831 CTCGGTTTCAGTCCACCCAA 59.892 55.000 0.00 0.00 0.00 4.12
2108 2170 1.029681 GTTTCAGTCCACCCAACCAC 58.970 55.000 0.00 0.00 0.00 4.16
2111 2173 1.228245 CAGTCCACCCAACCACCAG 60.228 63.158 0.00 0.00 0.00 4.00
2112 2174 2.597510 GTCCACCCAACCACCAGC 60.598 66.667 0.00 0.00 0.00 4.85
2113 2175 3.099841 TCCACCCAACCACCAGCA 61.100 61.111 0.00 0.00 0.00 4.41
2114 2176 2.118076 CCACCCAACCACCAGCAT 59.882 61.111 0.00 0.00 0.00 3.79
2115 2177 1.533753 CCACCCAACCACCAGCATT 60.534 57.895 0.00 0.00 0.00 3.56
2116 2178 1.120795 CCACCCAACCACCAGCATTT 61.121 55.000 0.00 0.00 0.00 2.32
2119 2181 1.341080 CCCAACCACCAGCATTTCTT 58.659 50.000 0.00 0.00 0.00 2.52
2122 2184 2.564062 CCAACCACCAGCATTTCTTGAT 59.436 45.455 0.00 0.00 0.00 2.57
2127 2189 4.590222 ACCACCAGCATTTCTTGATTTCTT 59.410 37.500 0.00 0.00 0.00 2.52
2128 2190 4.927425 CCACCAGCATTTCTTGATTTCTTG 59.073 41.667 0.00 0.00 0.00 3.02
2130 2192 6.395629 CACCAGCATTTCTTGATTTCTTGAT 58.604 36.000 0.00 0.00 0.00 2.57
2135 2197 7.488471 CAGCATTTCTTGATTTCTTGATCTTCC 59.512 37.037 0.00 0.00 0.00 3.46
2141 2203 3.691118 TGATTTCTTGATCTTCCCTTGCG 59.309 43.478 0.00 0.00 0.00 4.85
2153 2215 2.811317 CTTGCGAGCGTGGTCCTC 60.811 66.667 0.00 0.00 0.00 3.71
2155 2217 2.771763 CTTGCGAGCGTGGTCCTCTT 62.772 60.000 0.00 0.00 0.00 2.85
2239 2320 1.673626 GGCGTTCGGACATAACAGGAA 60.674 52.381 0.00 0.00 0.00 3.36
2264 3897 0.976073 ACTACACCCGCATACAGGCT 60.976 55.000 0.00 0.00 0.00 4.58
2270 3903 1.480212 CCCGCATACAGGCTATGGGA 61.480 60.000 14.03 0.00 39.36 4.37
2276 3909 0.471022 TACAGGCTATGGGATCGCCA 60.471 55.000 7.38 6.35 46.14 5.69
2527 4209 3.580022 TGACATCATAGGGCCACTGATAG 59.420 47.826 17.33 14.31 0.00 2.08
2530 4212 5.155161 ACATCATAGGGCCACTGATAGTTA 58.845 41.667 17.33 0.00 0.00 2.24
2634 4873 8.434733 AATTTCTTCTAATAGACCCTTAACGC 57.565 34.615 0.00 0.00 0.00 4.84
2683 4943 0.533755 CTCCGCCATCCCATCTTCAC 60.534 60.000 0.00 0.00 0.00 3.18
2720 4980 2.203538 CTTGCCAAGCCCACCTGT 60.204 61.111 0.00 0.00 0.00 4.00
2721 4981 1.833934 CTTGCCAAGCCCACCTGTT 60.834 57.895 0.00 0.00 0.00 3.16
2724 4984 2.133641 GCCAAGCCCACCTGTTGTT 61.134 57.895 0.00 0.00 0.00 2.83
2743 5003 4.903010 ACACCACCACGACGCCAC 62.903 66.667 0.00 0.00 0.00 5.01
2744 5004 4.602259 CACCACCACGACGCCACT 62.602 66.667 0.00 0.00 0.00 4.00
2747 5007 2.734723 CACCACGACGCCACTCAG 60.735 66.667 0.00 0.00 0.00 3.35
2797 5057 2.024871 CGATCGCCGAGACTCCAC 59.975 66.667 0.26 0.00 41.76 4.02
2798 5058 2.473760 CGATCGCCGAGACTCCACT 61.474 63.158 0.26 0.00 41.76 4.00
2807 5067 1.806461 GAGACTCCACTGTGCCACGA 61.806 60.000 1.29 0.00 0.00 4.35
2817 5077 3.601685 TGCCACGACGCTGAGACA 61.602 61.111 0.00 0.00 0.00 3.41
2822 5083 0.240145 CACGACGCTGAGACACCTTA 59.760 55.000 0.00 0.00 0.00 2.69
2836 5097 0.248907 ACCTTATCGTCGATGCGGTG 60.249 55.000 22.01 9.03 29.39 4.94
2844 5105 1.815003 TCGATGCGGTGGATGCAAG 60.815 57.895 0.00 0.00 46.87 4.01
2914 5175 2.113243 GAAGAGGGACAACGGCACCT 62.113 60.000 0.00 0.00 35.67 4.00
2938 5199 0.310854 CGTCGACATCATCCGATCCA 59.689 55.000 17.16 0.00 37.14 3.41
2939 5200 1.772182 GTCGACATCATCCGATCCAC 58.228 55.000 11.55 0.00 37.14 4.02
2940 5201 1.067060 GTCGACATCATCCGATCCACA 59.933 52.381 11.55 0.00 37.14 4.17
2989 5250 3.052082 CCTGAGCAAGGTGGCACG 61.052 66.667 12.17 0.00 41.74 5.34
3014 5276 1.128507 GCAACGATGATGCTCGACAAA 59.871 47.619 0.00 0.00 41.12 2.83
3046 5308 1.830279 AAGACGACACCATAGTCCGA 58.170 50.000 0.00 0.00 33.63 4.55
3059 5321 4.261867 CCATAGTCCGACATGACCGAATTA 60.262 45.833 0.00 0.00 35.83 1.40
3070 5332 2.675844 TGACCGAATTAGGCACGATTTG 59.324 45.455 4.26 0.00 33.69 2.32
3115 5377 2.689471 CTCTGCAGCTGACTAGATCTGT 59.311 50.000 20.43 1.20 0.00 3.41
3157 5419 2.360350 CACAGCCACCGGAATGCT 60.360 61.111 9.46 10.17 35.25 3.79
3185 5447 0.846693 ACTTTGAACTGCCCCTCACT 59.153 50.000 0.00 0.00 0.00 3.41
3197 5459 0.995024 CCCTCACTGACCCCTTCATT 59.005 55.000 0.00 0.00 32.17 2.57
3244 5506 2.595754 GGCGGATCTGAATGGGGC 60.596 66.667 5.48 0.00 0.00 5.80
3248 5510 0.399454 CGGATCTGAATGGGGCTCAT 59.601 55.000 0.00 0.00 37.79 2.90
3256 5518 2.513317 TGAATGGGGCTCATATCCACAA 59.487 45.455 0.00 0.00 40.93 3.33
3259 5521 0.550914 GGGGCTCATATCCACAACCA 59.449 55.000 0.00 0.00 0.00 3.67
3261 5523 1.212935 GGGCTCATATCCACAACCACT 59.787 52.381 0.00 0.00 0.00 4.00
3270 5532 1.735360 CACAACCACTGCCACCAAG 59.265 57.895 0.00 0.00 0.00 3.61
3275 5537 0.760189 ACCACTGCCACCAAGCATTT 60.760 50.000 0.00 0.00 43.09 2.32
3286 5548 3.698040 CACCAAGCATTTCCTAAGAGCAT 59.302 43.478 0.00 0.00 0.00 3.79
3297 5559 0.975556 TAAGAGCATGCCGGAGACCA 60.976 55.000 15.66 0.00 0.00 4.02
3457 5719 1.271926 CCATCGGGTATTTGATCCCCC 60.272 57.143 0.00 0.00 40.54 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.026522 CCGTCAGCCCGAACAAAAA 58.973 52.632 0.00 0.00 0.00 1.94
10 11 2.548295 GCCGTCAGCCCGAACAAAA 61.548 57.895 0.00 0.00 34.35 2.44
11 12 2.975799 GCCGTCAGCCCGAACAAA 60.976 61.111 0.00 0.00 34.35 2.83
27 28 3.973267 GAGGACACGAGTCAGCGGC 62.973 68.421 14.98 0.00 46.80 6.53
28 29 2.179517 GAGGACACGAGTCAGCGG 59.820 66.667 14.98 0.00 46.80 5.52
29 30 2.179517 GGAGGACACGAGTCAGCG 59.820 66.667 14.98 0.00 46.80 5.18
30 31 0.963355 AGAGGAGGACACGAGTCAGC 60.963 60.000 14.98 5.66 46.80 4.26
31 32 1.470890 GAAGAGGAGGACACGAGTCAG 59.529 57.143 14.98 0.00 46.80 3.51
32 33 1.074084 AGAAGAGGAGGACACGAGTCA 59.926 52.381 14.98 0.00 46.80 3.41
33 34 1.741145 GAGAAGAGGAGGACACGAGTC 59.259 57.143 4.21 4.21 44.21 3.36
34 35 1.353022 AGAGAAGAGGAGGACACGAGT 59.647 52.381 0.00 0.00 0.00 4.18
35 36 1.742831 CAGAGAAGAGGAGGACACGAG 59.257 57.143 0.00 0.00 0.00 4.18
36 37 1.351350 TCAGAGAAGAGGAGGACACGA 59.649 52.381 0.00 0.00 0.00 4.35
37 38 1.470890 GTCAGAGAAGAGGAGGACACG 59.529 57.143 0.00 0.00 0.00 4.49
38 39 1.822371 GGTCAGAGAAGAGGAGGACAC 59.178 57.143 0.00 0.00 0.00 3.67
39 40 1.713647 AGGTCAGAGAAGAGGAGGACA 59.286 52.381 0.00 0.00 0.00 4.02
40 41 2.099405 CAGGTCAGAGAAGAGGAGGAC 58.901 57.143 0.00 0.00 0.00 3.85
41 42 1.713647 ACAGGTCAGAGAAGAGGAGGA 59.286 52.381 0.00 0.00 0.00 3.71
42 43 2.230130 ACAGGTCAGAGAAGAGGAGG 57.770 55.000 0.00 0.00 0.00 4.30
43 44 2.495669 GGAACAGGTCAGAGAAGAGGAG 59.504 54.545 0.00 0.00 0.00 3.69
44 45 2.158310 TGGAACAGGTCAGAGAAGAGGA 60.158 50.000 0.00 0.00 0.00 3.71
45 46 2.251818 TGGAACAGGTCAGAGAAGAGG 58.748 52.381 0.00 0.00 0.00 3.69
58 59 1.135915 CTCGAGGGAGACATGGAACAG 59.864 57.143 3.91 0.00 42.72 3.16
59 60 1.186200 CTCGAGGGAGACATGGAACA 58.814 55.000 3.91 0.00 43.42 3.18
60 61 1.187087 ACTCGAGGGAGACATGGAAC 58.813 55.000 18.41 0.00 43.27 3.62
61 62 1.550524 CAACTCGAGGGAGACATGGAA 59.449 52.381 18.41 0.00 43.27 3.53
62 63 1.186200 CAACTCGAGGGAGACATGGA 58.814 55.000 18.41 0.00 43.27 3.41
63 64 0.460987 GCAACTCGAGGGAGACATGG 60.461 60.000 18.41 0.00 43.27 3.66
64 65 0.247460 TGCAACTCGAGGGAGACATG 59.753 55.000 18.41 5.09 43.27 3.21
65 66 0.534412 CTGCAACTCGAGGGAGACAT 59.466 55.000 18.41 0.00 43.27 3.06
66 67 1.967535 CTGCAACTCGAGGGAGACA 59.032 57.895 18.41 6.55 43.27 3.41
67 68 1.446966 GCTGCAACTCGAGGGAGAC 60.447 63.158 18.41 1.84 43.27 3.36
68 69 2.973899 GCTGCAACTCGAGGGAGA 59.026 61.111 18.41 0.00 43.27 3.71
69 70 2.290122 ATCGCTGCAACTCGAGGGAG 62.290 60.000 18.41 11.42 46.13 4.30
70 71 2.351244 ATCGCTGCAACTCGAGGGA 61.351 57.895 18.41 3.20 38.17 4.20
71 72 2.169789 CATCGCTGCAACTCGAGGG 61.170 63.158 18.41 9.72 38.17 4.30
72 73 2.169789 CCATCGCTGCAACTCGAGG 61.170 63.158 18.41 9.90 38.17 4.63
73 74 2.806856 GCCATCGCTGCAACTCGAG 61.807 63.158 11.84 11.84 38.17 4.04
74 75 2.815211 GCCATCGCTGCAACTCGA 60.815 61.111 0.00 7.64 39.17 4.04
75 76 3.869272 GGCCATCGCTGCAACTCG 61.869 66.667 0.00 0.00 34.44 4.18
76 77 2.437359 AGGCCATCGCTGCAACTC 60.437 61.111 5.01 0.00 34.44 3.01
77 78 2.437359 GAGGCCATCGCTGCAACT 60.437 61.111 5.01 0.00 34.44 3.16
78 79 2.437359 AGAGGCCATCGCTGCAAC 60.437 61.111 5.01 0.00 34.44 4.17
79 80 2.437180 CAGAGGCCATCGCTGCAA 60.437 61.111 5.01 0.00 36.54 4.08
80 81 3.709633 ACAGAGGCCATCGCTGCA 61.710 61.111 5.01 0.00 45.44 4.41
81 82 3.200593 CACAGAGGCCATCGCTGC 61.201 66.667 5.01 0.00 45.44 5.25
82 83 1.521010 CTCACAGAGGCCATCGCTG 60.521 63.158 5.01 9.47 46.67 5.18
83 84 1.954362 GACTCACAGAGGCCATCGCT 61.954 60.000 5.01 0.00 30.04 4.93
84 85 1.520342 GACTCACAGAGGCCATCGC 60.520 63.158 5.01 0.00 30.04 4.58
85 86 1.393603 TAGACTCACAGAGGCCATCG 58.606 55.000 5.01 0.00 38.74 3.84
86 87 3.027412 TCTTAGACTCACAGAGGCCATC 58.973 50.000 5.01 0.00 38.74 3.51
87 88 3.107402 TCTTAGACTCACAGAGGCCAT 57.893 47.619 5.01 0.00 38.74 4.40
88 89 2.604912 TCTTAGACTCACAGAGGCCA 57.395 50.000 5.01 0.00 38.74 5.36
89 90 3.963428 TTTCTTAGACTCACAGAGGCC 57.037 47.619 0.00 0.00 38.74 5.19
90 91 4.826556 ACATTTCTTAGACTCACAGAGGC 58.173 43.478 0.00 0.00 38.12 4.70
91 92 6.148480 CCAAACATTTCTTAGACTCACAGAGG 59.852 42.308 0.00 0.00 33.35 3.69
92 93 6.931281 TCCAAACATTTCTTAGACTCACAGAG 59.069 38.462 0.00 0.00 35.52 3.35
93 94 6.826668 TCCAAACATTTCTTAGACTCACAGA 58.173 36.000 0.00 0.00 0.00 3.41
94 95 6.708054 ACTCCAAACATTTCTTAGACTCACAG 59.292 38.462 0.00 0.00 0.00 3.66
95 96 6.483307 CACTCCAAACATTTCTTAGACTCACA 59.517 38.462 0.00 0.00 0.00 3.58
96 97 6.566753 GCACTCCAAACATTTCTTAGACTCAC 60.567 42.308 0.00 0.00 0.00 3.51
97 98 5.470098 GCACTCCAAACATTTCTTAGACTCA 59.530 40.000 0.00 0.00 0.00 3.41
98 99 5.470098 TGCACTCCAAACATTTCTTAGACTC 59.530 40.000 0.00 0.00 0.00 3.36
99 100 5.376625 TGCACTCCAAACATTTCTTAGACT 58.623 37.500 0.00 0.00 0.00 3.24
100 101 5.689383 TGCACTCCAAACATTTCTTAGAC 57.311 39.130 0.00 0.00 0.00 2.59
101 102 5.335897 GCATGCACTCCAAACATTTCTTAGA 60.336 40.000 14.21 0.00 0.00 2.10
102 103 4.860907 GCATGCACTCCAAACATTTCTTAG 59.139 41.667 14.21 0.00 0.00 2.18
103 104 4.280425 TGCATGCACTCCAAACATTTCTTA 59.720 37.500 18.46 0.00 0.00 2.10
104 105 3.069872 TGCATGCACTCCAAACATTTCTT 59.930 39.130 18.46 0.00 0.00 2.52
105 106 2.629137 TGCATGCACTCCAAACATTTCT 59.371 40.909 18.46 0.00 0.00 2.52
106 107 3.029320 TGCATGCACTCCAAACATTTC 57.971 42.857 18.46 0.00 0.00 2.17
107 108 3.688694 ATGCATGCACTCCAAACATTT 57.311 38.095 25.37 0.00 0.00 2.32
136 137 4.726416 CCTTCCGTCAATGTGATTTCTTG 58.274 43.478 0.00 0.00 0.00 3.02
138 139 2.749621 GCCTTCCGTCAATGTGATTTCT 59.250 45.455 0.00 0.00 0.00 2.52
152 153 0.519961 CCTTTTTACCACGCCTTCCG 59.480 55.000 0.00 0.00 44.21 4.30
155 156 1.404843 TTGCCTTTTTACCACGCCTT 58.595 45.000 0.00 0.00 0.00 4.35
160 161 6.859420 ACATTGATTTTGCCTTTTTACCAC 57.141 33.333 0.00 0.00 0.00 4.16
170 171 5.234116 ACGTTTTCTGAACATTGATTTTGCC 59.766 36.000 0.00 0.00 0.00 4.52
171 172 6.272698 ACGTTTTCTGAACATTGATTTTGC 57.727 33.333 0.00 0.00 0.00 3.68
207 208 7.728083 TGGGAAGAAAATCAGAACTCCAAAATA 59.272 33.333 0.00 0.00 0.00 1.40
213 214 5.124617 GTCATGGGAAGAAAATCAGAACTCC 59.875 44.000 0.00 0.00 0.00 3.85
227 228 2.584835 TTGGTGGAAGTCATGGGAAG 57.415 50.000 0.00 0.00 0.00 3.46
228 229 2.109834 ACATTGGTGGAAGTCATGGGAA 59.890 45.455 0.00 0.00 0.00 3.97
234 235 3.501828 CGAAATCACATTGGTGGAAGTCA 59.498 43.478 0.00 0.00 45.32 3.41
242 243 3.364460 TCATCCCGAAATCACATTGGT 57.636 42.857 0.00 0.00 0.00 3.67
336 338 7.337938 TGCTCAATTACTTCATCAGGTAATGA 58.662 34.615 0.00 0.00 43.70 2.57
338 340 8.579850 TTTGCTCAATTACTTCATCAGGTAAT 57.420 30.769 0.00 0.00 39.41 1.89
362 368 9.581289 CAGACGGAGGGAATATATCTCTATATT 57.419 37.037 0.00 0.00 39.70 1.28
391 397 7.896496 TGGCTTAAAATAAAGGGGTCTGATAAA 59.104 33.333 0.00 0.00 0.00 1.40
396 402 5.480422 AGTTGGCTTAAAATAAAGGGGTCTG 59.520 40.000 0.00 0.00 0.00 3.51
432 457 7.671495 TCCGCGATGTAATTAGTGTATAGTA 57.329 36.000 8.23 0.00 0.00 1.82
448 473 2.351418 TGTATTTGAGCTTTCCGCGATG 59.649 45.455 8.23 0.00 45.59 3.84
452 477 4.105486 GGATTTGTATTTGAGCTTTCCGC 58.895 43.478 0.00 0.00 39.57 5.54
453 478 4.094294 TCGGATTTGTATTTGAGCTTTCCG 59.906 41.667 0.00 0.00 43.64 4.30
474 499 9.973246 GTATATGCTCCAAAACATATATTGTCG 57.027 33.333 6.12 0.00 41.40 4.35
518 543 9.542462 TTAGGTCCAACTTTAATGATCTATTCG 57.458 33.333 0.00 0.00 0.00 3.34
585 613 9.959721 AGTACATACAGTAACAAGGAATTTGAT 57.040 29.630 0.00 0.00 40.14 2.57
685 713 6.321945 TGCCATGCATAAAAGTCTAACATCAT 59.678 34.615 0.00 0.00 31.71 2.45
689 718 5.973899 TTGCCATGCATAAAAGTCTAACA 57.026 34.783 0.00 0.00 38.76 2.41
697 726 7.450124 AACATTTGATTTGCCATGCATAAAA 57.550 28.000 0.00 1.15 38.76 1.52
723 752 7.043961 TCGTGCCAATATAAATTGCCATAAA 57.956 32.000 0.00 0.00 41.06 1.40
742 771 5.909610 GCAAACTAAATTATCATCCTCGTGC 59.090 40.000 0.00 0.00 0.00 5.34
744 773 7.624360 TTGCAAACTAAATTATCATCCTCGT 57.376 32.000 0.00 0.00 0.00 4.18
802 831 9.810231 GTTTAATTGACAAAGCATGGTAAAATG 57.190 29.630 0.00 0.00 0.00 2.32
811 840 7.599998 GGATGACAAGTTTAATTGACAAAGCAT 59.400 33.333 0.00 0.00 38.12 3.79
851 880 9.381033 CTCCATACATTTGATTTTTATGGCAAA 57.619 29.630 0.00 0.00 39.32 3.68
855 884 8.917088 ACTCCTCCATACATTTGATTTTTATGG 58.083 33.333 0.00 0.00 40.37 2.74
860 889 8.960591 CAACTACTCCTCCATACATTTGATTTT 58.039 33.333 0.00 0.00 0.00 1.82
861 890 8.109634 ACAACTACTCCTCCATACATTTGATTT 58.890 33.333 0.00 0.00 0.00 2.17
862 891 7.633789 ACAACTACTCCTCCATACATTTGATT 58.366 34.615 0.00 0.00 0.00 2.57
863 892 7.092891 TGACAACTACTCCTCCATACATTTGAT 60.093 37.037 0.00 0.00 0.00 2.57
864 893 6.212589 TGACAACTACTCCTCCATACATTTGA 59.787 38.462 0.00 0.00 0.00 2.69
865 894 6.406370 TGACAACTACTCCTCCATACATTTG 58.594 40.000 0.00 0.00 0.00 2.32
866 895 6.620877 TGACAACTACTCCTCCATACATTT 57.379 37.500 0.00 0.00 0.00 2.32
867 896 6.814954 ATGACAACTACTCCTCCATACATT 57.185 37.500 0.00 0.00 0.00 2.71
868 897 7.914427 TTATGACAACTACTCCTCCATACAT 57.086 36.000 0.00 0.00 0.00 2.29
869 898 7.727578 TTTATGACAACTACTCCTCCATACA 57.272 36.000 0.00 0.00 0.00 2.29
893 922 7.405769 CAGTAATTGGCAAATCAAACGTTTTT 58.594 30.769 11.66 0.93 0.00 1.94
984 1013 6.497624 TTTTATAGTGGCGGGAAGGTATAA 57.502 37.500 0.00 0.00 0.00 0.98
985 1014 6.497624 TTTTTATAGTGGCGGGAAGGTATA 57.502 37.500 0.00 0.00 0.00 1.47
986 1015 5.374071 CTTTTTATAGTGGCGGGAAGGTAT 58.626 41.667 0.00 0.00 0.00 2.73
1070 1099 1.011595 AGCTGAGAGGAGGGGTTCTA 58.988 55.000 0.00 0.00 0.00 2.10
1150 1179 2.284625 TCCACGTCCATGGAGGCT 60.285 61.111 29.84 16.59 44.14 4.58
1189 1218 1.561643 ACTTGCTCTCGAGGATGGAA 58.438 50.000 13.56 9.73 0.00 3.53
1213 1242 2.101770 GGGTCGTCGTAGCCGAAG 59.898 66.667 0.00 0.00 41.80 3.79
1280 1309 3.728373 GGTCACCTTCCCGGCCAT 61.728 66.667 2.24 0.00 35.61 4.40
1384 1413 3.325753 GCCTCCAGCCTCACCAGT 61.326 66.667 0.00 0.00 34.35 4.00
1438 1467 1.347817 CGTCGAAGAAGTCTGCCAGC 61.348 60.000 0.00 0.00 39.69 4.85
1650 1679 1.202604 TCAGTTCGCCGAAAACCTTCT 60.203 47.619 0.00 0.00 0.00 2.85
1651 1680 1.070108 GTCAGTTCGCCGAAAACCTTC 60.070 52.381 0.00 0.00 0.00 3.46
1666 1695 2.049985 GTGTCTCGCAGCGTCAGT 60.050 61.111 15.93 0.00 0.00 3.41
1726 1755 1.990614 GGAGAAGAGGAACGGGCCT 60.991 63.158 0.84 0.00 42.17 5.19
1728 1757 2.585153 GGGAGAAGAGGAACGGGC 59.415 66.667 0.00 0.00 0.00 6.13
1962 1991 2.589157 AAATCCTCCACGCCGGACA 61.589 57.895 5.05 0.00 39.64 4.02
1978 2007 1.452110 CGATGGACATGACCAGCAAA 58.548 50.000 27.39 3.66 45.28 3.68
1979 2008 0.392863 CCGATGGACATGACCAGCAA 60.393 55.000 27.39 4.02 45.28 3.91
2006 2035 4.785453 GGAAGTGGAGGCGCCCTG 62.785 72.222 26.15 0.00 31.76 4.45
2069 2131 1.604693 CCGAGTTCAGGTGCGTTAGTT 60.605 52.381 0.00 0.00 0.00 2.24
2070 2132 0.038526 CCGAGTTCAGGTGCGTTAGT 60.039 55.000 0.00 0.00 0.00 2.24
2071 2133 0.038526 ACCGAGTTCAGGTGCGTTAG 60.039 55.000 0.00 0.00 41.10 2.34
2072 2134 0.390124 AACCGAGTTCAGGTGCGTTA 59.610 50.000 0.00 0.00 41.95 3.18
2076 2138 3.000815 TGAAACCGAGTTCAGGTGC 57.999 52.632 0.00 0.00 41.95 5.01
2081 2143 1.202604 GGTGGACTGAAACCGAGTTCA 60.203 52.381 1.53 1.53 36.15 3.18
2083 2145 0.108019 GGGTGGACTGAAACCGAGTT 59.892 55.000 0.00 0.00 37.33 3.01
2087 2149 1.170290 GGTTGGGTGGACTGAAACCG 61.170 60.000 0.00 0.00 37.33 4.44
2089 2151 1.029681 GTGGTTGGGTGGACTGAAAC 58.970 55.000 0.00 0.00 0.00 2.78
2090 2152 0.106419 GGTGGTTGGGTGGACTGAAA 60.106 55.000 0.00 0.00 0.00 2.69
2100 2162 1.001181 CAAGAAATGCTGGTGGTTGGG 59.999 52.381 0.00 0.00 0.00 4.12
2104 2166 4.154942 AGAAATCAAGAAATGCTGGTGGT 58.845 39.130 0.00 0.00 0.00 4.16
2108 2170 6.864342 AGATCAAGAAATCAAGAAATGCTGG 58.136 36.000 0.00 0.00 0.00 4.85
2111 2173 6.755607 GGGAAGATCAAGAAATCAAGAAATGC 59.244 38.462 0.00 0.00 0.00 3.56
2112 2174 8.064336 AGGGAAGATCAAGAAATCAAGAAATG 57.936 34.615 0.00 0.00 0.00 2.32
2113 2175 8.529476 CAAGGGAAGATCAAGAAATCAAGAAAT 58.471 33.333 0.00 0.00 0.00 2.17
2114 2176 7.524367 GCAAGGGAAGATCAAGAAATCAAGAAA 60.524 37.037 0.00 0.00 0.00 2.52
2115 2177 6.071728 GCAAGGGAAGATCAAGAAATCAAGAA 60.072 38.462 0.00 0.00 0.00 2.52
2116 2178 5.416952 GCAAGGGAAGATCAAGAAATCAAGA 59.583 40.000 0.00 0.00 0.00 3.02
2119 2181 3.691118 CGCAAGGGAAGATCAAGAAATCA 59.309 43.478 0.00 0.00 0.00 2.57
2122 2184 3.338249 CTCGCAAGGGAAGATCAAGAAA 58.662 45.455 0.00 0.00 44.69 2.52
2127 2189 1.153568 CGCTCGCAAGGGAAGATCA 60.154 57.895 0.00 0.00 44.69 2.92
2128 2190 1.153549 ACGCTCGCAAGGGAAGATC 60.154 57.895 0.00 0.00 44.69 2.75
2130 2192 2.048222 CACGCTCGCAAGGGAAGA 60.048 61.111 0.00 0.00 44.69 2.87
2135 2197 4.379243 AGGACCACGCTCGCAAGG 62.379 66.667 0.00 0.00 38.47 3.61
2141 2203 0.884704 TGCAAAAGAGGACCACGCTC 60.885 55.000 0.00 0.00 0.00 5.03
2239 2320 2.081462 GTATGCGGGTGTAGTTGCTTT 58.919 47.619 0.00 0.00 0.00 3.51
2486 4164 9.117183 TGATGTCAATCCTCTATTTTCTTCATG 57.883 33.333 0.00 0.00 31.15 3.07
2491 4169 8.381636 CCCTATGATGTCAATCCTCTATTTTCT 58.618 37.037 0.00 0.00 31.15 2.52
2495 4173 5.045286 GGCCCTATGATGTCAATCCTCTATT 60.045 44.000 0.00 0.00 31.15 1.73
2611 4336 6.038356 CGCGTTAAGGGTCTATTAGAAGAAA 58.962 40.000 0.00 0.00 0.00 2.52
2614 4339 3.734735 GCGCGTTAAGGGTCTATTAGAAG 59.265 47.826 8.43 0.00 34.93 2.85
2615 4340 3.130869 TGCGCGTTAAGGGTCTATTAGAA 59.869 43.478 8.43 0.00 34.93 2.10
2621 4860 1.216178 GGTGCGCGTTAAGGGTCTA 59.784 57.895 8.43 0.00 34.93 2.59
2683 4943 2.009774 GGTCAATGTGTTGATCCCTCG 58.990 52.381 0.00 0.00 45.46 4.63
2720 4980 1.084935 CGTCGTGGTGGTGTCAACAA 61.085 55.000 0.00 0.00 42.96 2.83
2721 4981 1.519676 CGTCGTGGTGGTGTCAACA 60.520 57.895 0.00 0.00 38.45 3.33
2724 4984 4.595538 GGCGTCGTGGTGGTGTCA 62.596 66.667 0.00 0.00 0.00 3.58
2743 5003 2.033141 CAGGGTGGTGGTGCTGAG 59.967 66.667 0.00 0.00 0.00 3.35
2744 5004 4.269523 GCAGGGTGGTGGTGCTGA 62.270 66.667 0.00 0.00 34.23 4.26
2797 5057 3.108289 CTCAGCGTCGTGGCACAG 61.108 66.667 19.09 10.60 41.80 3.66
2798 5058 3.601685 TCTCAGCGTCGTGGCACA 61.602 61.111 19.09 1.83 34.64 4.57
2807 5067 1.132643 GACGATAAGGTGTCTCAGCGT 59.867 52.381 0.00 0.00 36.92 5.07
2817 5077 0.248907 CACCGCATCGACGATAAGGT 60.249 55.000 22.94 22.94 33.49 3.50
2822 5083 1.300156 CATCCACCGCATCGACGAT 60.300 57.895 4.05 4.05 34.06 3.73
2844 5105 0.250513 AGGGAAGAGTTGATGCGGTC 59.749 55.000 0.00 0.00 0.00 4.79
2909 5170 1.146358 GATGTCGACGCCTTAGGTGC 61.146 60.000 12.27 4.07 36.54 5.01
2914 5175 0.030235 CGGATGATGTCGACGCCTTA 59.970 55.000 11.62 0.00 0.00 2.69
2938 5199 5.010282 GGAAACCCTAGATTTGTGTCATGT 58.990 41.667 0.00 0.00 0.00 3.21
2939 5200 5.567138 GGAAACCCTAGATTTGTGTCATG 57.433 43.478 0.00 0.00 0.00 3.07
2986 5247 0.371301 CATCATCGTTGCAGTCCGTG 59.629 55.000 0.00 0.00 0.00 4.94
2988 5249 1.086067 AGCATCATCGTTGCAGTCCG 61.086 55.000 0.00 0.00 42.62 4.79
2989 5250 0.654683 GAGCATCATCGTTGCAGTCC 59.345 55.000 0.00 0.00 42.62 3.85
3040 5302 2.100916 CCTAATTCGGTCATGTCGGACT 59.899 50.000 9.88 0.00 37.91 3.85
3046 5308 1.206132 TCGTGCCTAATTCGGTCATGT 59.794 47.619 0.00 0.00 0.00 3.21
3083 5345 1.938657 GCTGCAGAGTCGAGGTAGCA 61.939 60.000 20.43 6.87 39.60 3.49
3126 5388 1.591594 CTGTGTGCGTCTTCACGGT 60.592 57.895 0.00 0.00 46.80 4.83
3157 5419 2.038557 GGCAGTTCAAAGTCCTCTACCA 59.961 50.000 0.00 0.00 0.00 3.25
3185 5447 1.002624 GCGGTGAATGAAGGGGTCA 60.003 57.895 0.00 0.00 41.67 4.02
3210 5472 4.258206 CACTGTGTGGCCCTTTGT 57.742 55.556 0.00 0.00 0.00 2.83
3244 5506 2.292267 GGCAGTGGTTGTGGATATGAG 58.708 52.381 0.00 0.00 0.00 2.90
3248 5510 0.037590 GGTGGCAGTGGTTGTGGATA 59.962 55.000 0.00 0.00 0.00 2.59
3256 5518 0.760189 AAATGCTTGGTGGCAGTGGT 60.760 50.000 0.00 0.00 45.75 4.16
3259 5521 0.178953 AGGAAATGCTTGGTGGCAGT 60.179 50.000 0.00 0.00 45.75 4.40
3261 5523 2.170166 CTTAGGAAATGCTTGGTGGCA 58.830 47.619 0.00 0.00 46.63 4.92
3270 5532 1.002033 CGGCATGCTCTTAGGAAATGC 60.002 52.381 18.92 11.64 39.19 3.56
3275 5537 0.397114 TCTCCGGCATGCTCTTAGGA 60.397 55.000 18.92 16.30 0.00 2.94
3297 5559 1.308128 TGGAGGGTCATCATGGGCT 60.308 57.895 0.00 0.00 0.00 5.19
3341 5603 1.446272 GCGAAGTCCCTTGGTCGAG 60.446 63.158 0.00 0.00 35.54 4.04
3415 5677 0.692756 TAATGGGCCACCGATGAGGA 60.693 55.000 9.28 0.00 45.00 3.71
3420 5682 0.986019 TGGTCTAATGGGCCACCGAT 60.986 55.000 9.28 0.00 40.75 4.18


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

AutoCloner maintained by Alex Coulton.