Multiple sequence alignment - TraesCS3A01G230200

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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 TraesCS3A01G230200 chr3A 100.000 3998 0 0 1 3998 430524679 430528676 0.000000e+00 7384.0
1 TraesCS3A01G230200 chr3A 82.857 140 22 2 2457 2595 19999515 19999653 1.510000e-24 124.0
2 TraesCS3A01G230200 chr3B 95.541 2198 70 18 1824 3998 417375116 417377308 0.000000e+00 3491.0
3 TraesCS3A01G230200 chr3B 91.638 873 37 14 885 1750 417374277 417375120 0.000000e+00 1175.0
4 TraesCS3A01G230200 chr3B 87.879 330 14 11 123 427 417371273 417371601 8.170000e-97 364.0
5 TraesCS3A01G230200 chr3B 95.946 222 9 0 501 722 417373202 417373423 1.060000e-95 361.0
6 TraesCS3A01G230200 chr3B 93.023 86 5 1 721 805 417374185 417374270 1.510000e-24 124.0
7 TraesCS3A01G230200 chr3B 83.206 131 20 2 2466 2595 24012376 24012247 7.020000e-23 119.0
8 TraesCS3A01G230200 chr3B 92.405 79 2 1 3128 3206 578594634 578594708 4.220000e-20 110.0
9 TraesCS3A01G230200 chr3B 100.000 35 0 0 443 477 417373134 417373168 9.270000e-07 65.8
10 TraesCS3A01G230200 chr3D 94.509 2149 67 24 1828 3948 304029752 304027627 0.000000e+00 3267.0
11 TraesCS3A01G230200 chr3D 90.315 857 40 17 906 1753 304030573 304029751 0.000000e+00 1083.0
12 TraesCS3A01G230200 chr3D 84.161 644 48 19 123 725 304031571 304030941 3.470000e-160 575.0
13 TraesCS3A01G230200 chr3D 96.429 56 2 0 3943 3998 304026255 304026200 4.250000e-15 93.5
14 TraesCS3A01G230200 chr5B 98.734 79 1 0 1749 1827 271145806 271145884 1.500000e-29 141.0
15 TraesCS3A01G230200 chr5B 96.386 83 0 2 1746 1828 315165356 315165277 2.510000e-27 134.0
16 TraesCS3A01G230200 chr5B 94.737 76 2 1 3133 3206 315165353 315165278 2.520000e-22 117.0
17 TraesCS3A01G230200 chr5B 92.405 79 4 2 3132 3208 315165275 315165353 1.170000e-20 111.0
18 TraesCS3A01G230200 chr5A 97.403 77 1 1 1752 1827 673554634 673554710 3.240000e-26 130.0
19 TraesCS3A01G230200 chr5A 93.671 79 1 3 3133 3208 659716002 659715925 9.080000e-22 115.0
20 TraesCS3A01G230200 chr4D 94.253 87 1 2 1745 1827 484149203 484149289 3.240000e-26 130.0
21 TraesCS3A01G230200 chr4A 94.118 85 5 0 1743 1827 542273923 542274007 3.240000e-26 130.0
22 TraesCS3A01G230200 chr5D 96.250 80 0 1 1751 1827 277244671 277244592 1.170000e-25 128.0
23 TraesCS3A01G230200 chr1D 97.368 76 1 1 1752 1827 408924568 408924494 1.170000e-25 128.0
24 TraesCS3A01G230200 chr2D 92.222 90 4 2 1749 1837 619666338 619666425 1.510000e-24 124.0
25 TraesCS3A01G230200 chr2D 90.426 94 4 4 1734 1825 261736133 261736223 7.020000e-23 119.0
26 TraesCS3A01G230200 chr6D 95.890 73 3 0 3134 3206 32062162 32062234 7.020000e-23 119.0
27 TraesCS3A01G230200 chr6D 92.500 80 3 2 3130 3209 139369338 139369262 1.170000e-20 111.0
28 TraesCS3A01G230200 chr4B 94.595 74 2 2 3135 3207 191210824 191210896 3.270000e-21 113.0
29 TraesCS3A01G230200 chr2B 94.595 74 3 1 3134 3207 738679249 738679177 3.270000e-21 113.0


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 TraesCS3A01G230200 chr3A 430524679 430528676 3997 False 7384.000000 7384 100.0000 1 3998 1 chr3A.!!$F2 3997
1 TraesCS3A01G230200 chr3B 417371273 417377308 6035 False 930.133333 3491 94.0045 123 3998 6 chr3B.!!$F2 3875
2 TraesCS3A01G230200 chr3D 304026200 304031571 5371 True 1254.625000 3267 91.3535 123 3998 4 chr3D.!!$R1 3875

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
40 41 0.030773 CTTAGCTGCATGCATGGCTG 59.969 55.0 33.08 23.36 45.94 4.85 F
492 2083 0.034896 TGGGTCGCCTGAAGAAAGTC 59.965 55.0 0.00 0.00 0.00 3.01 F
496 2087 0.034896 TCGCCTGAAGAAAGTCCACC 59.965 55.0 0.00 0.00 0.00 4.61 F
497 2088 0.035458 CGCCTGAAGAAAGTCCACCT 59.965 55.0 0.00 0.00 0.00 4.00 F
732 3086 0.110192 GAAGTGCAAGGTTACGCTGC 60.110 55.0 0.00 1.09 36.60 5.25 F
1483 4004 0.177373 GCCCCGAAAACGAGAGGTAT 59.823 55.0 0.00 0.00 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 3870 0.042188 CGCGGCGGACAATAATTCTG 60.042 55.000 15.84 0.00 0.00 3.02 R
2303 4843 0.744414 CGTGTATGGTCCCTGCCAAG 60.744 60.000 0.00 0.00 42.48 3.61 R
2306 4846 1.153429 GTCGTGTATGGTCCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85 R
2376 4917 1.758514 GATCCCCTCCGAGCTGTCA 60.759 63.158 0.00 0.00 0.00 3.58 R
2604 5145 1.219124 CATCGTCCTGGACACCCTG 59.781 63.158 25.42 12.75 32.09 4.45 R
3395 5943 0.616395 TGGGGATGAGTAACTGCCGA 60.616 55.000 0.00 0.00 0.00 5.54 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
25 26 8.173321 CAAATATTTGGTCGAAAAAGGCTTAG 57.827 34.615 18.72 0.00 34.59 2.18
26 27 3.636282 TTTGGTCGAAAAAGGCTTAGC 57.364 42.857 0.00 0.00 0.00 3.09
27 28 2.561478 TGGTCGAAAAAGGCTTAGCT 57.439 45.000 3.59 0.00 0.00 3.32
28 29 2.151202 TGGTCGAAAAAGGCTTAGCTG 58.849 47.619 3.59 0.00 0.00 4.24
29 30 1.135660 GGTCGAAAAAGGCTTAGCTGC 60.136 52.381 3.59 0.00 0.00 5.25
30 31 1.535462 GTCGAAAAAGGCTTAGCTGCA 59.465 47.619 3.59 0.00 34.04 4.41
31 32 2.162408 GTCGAAAAAGGCTTAGCTGCAT 59.838 45.455 3.59 0.00 34.04 3.96
32 33 2.162208 TCGAAAAAGGCTTAGCTGCATG 59.838 45.455 3.59 0.00 34.04 4.06
33 34 2.265683 GAAAAAGGCTTAGCTGCATGC 58.734 47.619 11.82 11.82 43.29 4.06
34 35 1.259609 AAAAGGCTTAGCTGCATGCA 58.740 45.000 21.29 21.29 45.94 3.96
35 36 1.481871 AAAGGCTTAGCTGCATGCAT 58.518 45.000 22.97 10.26 45.94 3.96
36 37 0.744874 AAGGCTTAGCTGCATGCATG 59.255 50.000 22.97 22.70 45.94 4.06
37 38 1.107538 AGGCTTAGCTGCATGCATGG 61.108 55.000 27.34 12.00 45.94 3.66
38 39 1.299926 GCTTAGCTGCATGCATGGC 60.300 57.895 27.34 21.81 45.94 4.40
39 40 1.735376 GCTTAGCTGCATGCATGGCT 61.735 55.000 30.08 30.08 45.94 4.75
40 41 0.030773 CTTAGCTGCATGCATGGCTG 59.969 55.000 33.08 23.36 45.94 4.85
41 42 0.681887 TTAGCTGCATGCATGGCTGT 60.682 50.000 33.08 17.91 45.94 4.40
42 43 0.681887 TAGCTGCATGCATGGCTGTT 60.682 50.000 33.08 22.52 45.94 3.16
43 44 1.809619 GCTGCATGCATGGCTGTTG 60.810 57.895 27.34 7.95 42.31 3.33
44 45 1.809619 CTGCATGCATGGCTGTTGC 60.810 57.895 27.34 13.78 40.55 4.17
45 46 2.225791 CTGCATGCATGGCTGTTGCT 62.226 55.000 27.34 0.00 40.77 3.91
46 47 1.809619 GCATGCATGGCTGTTGCTG 60.810 57.895 27.34 0.13 40.77 4.41
47 48 1.589630 CATGCATGGCTGTTGCTGT 59.410 52.632 19.40 0.00 40.77 4.40
48 49 0.735978 CATGCATGGCTGTTGCTGTG 60.736 55.000 19.40 0.00 40.77 3.66
49 50 1.884075 ATGCATGGCTGTTGCTGTGG 61.884 55.000 0.00 0.00 40.77 4.17
50 51 2.567497 GCATGGCTGTTGCTGTGGT 61.567 57.895 0.00 0.00 39.59 4.16
51 52 2.043625 CATGGCTGTTGCTGTGGTT 58.956 52.632 0.00 0.00 39.59 3.67
52 53 0.319211 CATGGCTGTTGCTGTGGTTG 60.319 55.000 0.00 0.00 39.59 3.77
53 54 2.028043 GGCTGTTGCTGTGGTTGC 59.972 61.111 0.00 0.00 39.59 4.17
54 55 2.784356 GGCTGTTGCTGTGGTTGCA 61.784 57.895 0.00 0.00 39.59 4.08
55 56 1.364901 GCTGTTGCTGTGGTTGCAT 59.635 52.632 0.00 0.00 40.34 3.96
56 57 0.249573 GCTGTTGCTGTGGTTGCATT 60.250 50.000 0.00 0.00 40.34 3.56
57 58 1.774639 CTGTTGCTGTGGTTGCATTC 58.225 50.000 0.00 0.00 40.34 2.67
58 59 0.388659 TGTTGCTGTGGTTGCATTCC 59.611 50.000 0.00 0.00 40.34 3.01
59 60 0.664166 GTTGCTGTGGTTGCATTCCG 60.664 55.000 0.00 0.00 40.34 4.30
60 61 1.106351 TTGCTGTGGTTGCATTCCGT 61.106 50.000 0.00 0.00 40.34 4.69
61 62 1.081242 GCTGTGGTTGCATTCCGTG 60.081 57.895 0.00 0.00 0.00 4.94
62 63 1.795170 GCTGTGGTTGCATTCCGTGT 61.795 55.000 0.00 0.00 0.00 4.49
63 64 0.040157 CTGTGGTTGCATTCCGTGTG 60.040 55.000 0.00 0.00 0.00 3.82
64 65 0.464554 TGTGGTTGCATTCCGTGTGA 60.465 50.000 0.00 0.00 0.00 3.58
65 66 0.238289 GTGGTTGCATTCCGTGTGAG 59.762 55.000 0.00 0.00 0.00 3.51
66 67 0.179032 TGGTTGCATTCCGTGTGAGT 60.179 50.000 0.00 0.00 0.00 3.41
67 68 0.517316 GGTTGCATTCCGTGTGAGTC 59.483 55.000 0.00 0.00 0.00 3.36
68 69 0.517316 GTTGCATTCCGTGTGAGTCC 59.483 55.000 0.00 0.00 0.00 3.85
69 70 0.396435 TTGCATTCCGTGTGAGTCCT 59.604 50.000 0.00 0.00 0.00 3.85
70 71 0.396435 TGCATTCCGTGTGAGTCCTT 59.604 50.000 0.00 0.00 0.00 3.36
71 72 1.202758 TGCATTCCGTGTGAGTCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
72 73 1.197721 GCATTCCGTGTGAGTCCTTTG 59.802 52.381 0.00 0.00 0.00 2.77
73 74 1.806542 CATTCCGTGTGAGTCCTTTGG 59.193 52.381 0.00 0.00 0.00 3.28
74 75 0.107831 TTCCGTGTGAGTCCTTTGGG 59.892 55.000 0.00 0.00 0.00 4.12
75 76 1.052124 TCCGTGTGAGTCCTTTGGGT 61.052 55.000 0.00 0.00 0.00 4.51
76 77 0.682852 CCGTGTGAGTCCTTTGGGTA 59.317 55.000 0.00 0.00 0.00 3.69
77 78 1.607251 CCGTGTGAGTCCTTTGGGTAC 60.607 57.143 0.00 0.00 0.00 3.34
93 94 4.886496 GGGTACCGCCTAGATAGATTTT 57.114 45.455 5.65 0.00 40.86 1.82
94 95 5.990120 GGGTACCGCCTAGATAGATTTTA 57.010 43.478 5.65 0.00 40.86 1.52
95 96 5.963594 GGGTACCGCCTAGATAGATTTTAG 58.036 45.833 5.65 0.00 40.86 1.85
96 97 5.479724 GGGTACCGCCTAGATAGATTTTAGT 59.520 44.000 5.65 0.00 40.86 2.24
97 98 6.660949 GGGTACCGCCTAGATAGATTTTAGTA 59.339 42.308 5.65 0.00 40.86 1.82
98 99 7.362487 GGGTACCGCCTAGATAGATTTTAGTAC 60.362 44.444 5.65 0.00 40.86 2.73
99 100 7.175641 GGTACCGCCTAGATAGATTTTAGTACA 59.824 40.741 0.00 0.00 0.00 2.90
100 101 7.216973 ACCGCCTAGATAGATTTTAGTACAG 57.783 40.000 0.00 0.00 0.00 2.74
101 102 6.776603 ACCGCCTAGATAGATTTTAGTACAGT 59.223 38.462 0.00 0.00 0.00 3.55
102 103 7.941238 ACCGCCTAGATAGATTTTAGTACAGTA 59.059 37.037 0.00 0.00 0.00 2.74
103 104 8.235905 CCGCCTAGATAGATTTTAGTACAGTAC 58.764 40.741 2.05 2.05 0.00 2.73
104 105 8.781196 CGCCTAGATAGATTTTAGTACAGTACA 58.219 37.037 13.37 0.00 0.00 2.90
113 114 8.532819 AGATTTTAGTACAGTACAGAAGGAAGG 58.467 37.037 13.37 0.00 0.00 3.46
114 115 7.607615 TTTTAGTACAGTACAGAAGGAAGGT 57.392 36.000 13.37 0.00 0.00 3.50
115 116 8.710749 TTTTAGTACAGTACAGAAGGAAGGTA 57.289 34.615 13.37 0.00 0.00 3.08
116 117 8.710749 TTTAGTACAGTACAGAAGGAAGGTAA 57.289 34.615 13.37 0.00 0.00 2.85
117 118 6.837471 AGTACAGTACAGAAGGAAGGTAAG 57.163 41.667 13.37 0.00 0.00 2.34
118 119 5.715753 AGTACAGTACAGAAGGAAGGTAAGG 59.284 44.000 13.37 0.00 0.00 2.69
119 120 3.261137 ACAGTACAGAAGGAAGGTAAGGC 59.739 47.826 0.00 0.00 0.00 4.35
120 121 3.515901 CAGTACAGAAGGAAGGTAAGGCT 59.484 47.826 0.00 0.00 0.00 4.58
121 122 4.710375 CAGTACAGAAGGAAGGTAAGGCTA 59.290 45.833 0.00 0.00 0.00 3.93
146 147 1.152881 GATTTGGAGGATGGCGCCT 60.153 57.895 29.70 13.55 42.17 5.52
167 168 5.555017 CCTAAGGAGATAATGACCCATGTG 58.445 45.833 0.00 0.00 0.00 3.21
177 178 5.964958 AATGACCCATGTGTTTTCTAGTG 57.035 39.130 0.00 0.00 0.00 2.74
224 231 1.713937 ATGGCGTGTGTGTGTGTGTG 61.714 55.000 0.00 0.00 0.00 3.82
227 234 0.109964 GCGTGTGTGTGTGTGTGTTT 60.110 50.000 0.00 0.00 0.00 2.83
228 235 1.664588 GCGTGTGTGTGTGTGTGTTTT 60.665 47.619 0.00 0.00 0.00 2.43
229 236 1.975362 CGTGTGTGTGTGTGTGTTTTG 59.025 47.619 0.00 0.00 0.00 2.44
230 237 2.349912 CGTGTGTGTGTGTGTGTTTTGA 60.350 45.455 0.00 0.00 0.00 2.69
231 238 3.669290 CGTGTGTGTGTGTGTGTTTTGAT 60.669 43.478 0.00 0.00 0.00 2.57
235 242 3.256879 TGTGTGTGTGTGTTTTGATGGTT 59.743 39.130 0.00 0.00 0.00 3.67
266 294 4.289672 TCAGGCTACCATTCTCTTTTTCCT 59.710 41.667 0.00 0.00 0.00 3.36
278 306 8.599774 CATTCTCTTTTTCCTCTCTCGATAAAC 58.400 37.037 0.00 0.00 0.00 2.01
290 318 7.043059 CCTCTCTCGATAAACTGCTTTAACATC 60.043 40.741 0.00 0.00 0.00 3.06
292 320 6.403049 TCTCGATAAACTGCTTTAACATCCA 58.597 36.000 0.00 0.00 0.00 3.41
318 346 2.218759 CAGTTTATACGCTGATGACGCC 59.781 50.000 0.00 0.00 34.87 5.68
360 388 1.348696 TGGTCTGCAAATGAGCTCAGA 59.651 47.619 22.96 9.76 33.64 3.27
427 483 3.828921 AGCGGTTCTTAAGGAGGTTTTT 58.171 40.909 1.85 0.00 0.00 1.94
477 2050 0.801574 TCCCCCTTACCTACTTGGGT 59.198 55.000 0.00 0.00 42.86 4.51
491 2082 0.472471 TTGGGTCGCCTGAAGAAAGT 59.528 50.000 0.00 0.00 0.00 2.66
492 2083 0.034896 TGGGTCGCCTGAAGAAAGTC 59.965 55.000 0.00 0.00 0.00 3.01
493 2084 0.673956 GGGTCGCCTGAAGAAAGTCC 60.674 60.000 0.00 0.00 0.00 3.85
494 2085 0.034896 GGTCGCCTGAAGAAAGTCCA 59.965 55.000 0.00 0.00 0.00 4.02
495 2086 1.149148 GTCGCCTGAAGAAAGTCCAC 58.851 55.000 0.00 0.00 0.00 4.02
496 2087 0.034896 TCGCCTGAAGAAAGTCCACC 59.965 55.000 0.00 0.00 0.00 4.61
497 2088 0.035458 CGCCTGAAGAAAGTCCACCT 59.965 55.000 0.00 0.00 0.00 4.00
498 2089 1.814793 GCCTGAAGAAAGTCCACCTC 58.185 55.000 0.00 0.00 0.00 3.85
499 2090 1.611936 GCCTGAAGAAAGTCCACCTCC 60.612 57.143 0.00 0.00 0.00 4.30
603 2194 1.354040 GTTCTGTCCTCTGCACGATG 58.646 55.000 0.00 0.00 0.00 3.84
702 2293 3.958860 GCACAGGAGGGCCACAGT 61.959 66.667 6.18 0.00 36.29 3.55
732 3086 0.110192 GAAGTGCAAGGTTACGCTGC 60.110 55.000 0.00 1.09 36.60 5.25
734 3088 2.112087 TGCAAGGTTACGCTGCCA 59.888 55.556 5.13 0.00 35.13 4.92
757 3111 3.978723 CTGTCCTCGTCAGCGCCAG 62.979 68.421 2.29 0.00 38.14 4.85
805 3160 3.006217 CCATGCGATCAGAAGGACAGATA 59.994 47.826 0.00 0.00 0.00 1.98
806 3161 3.998099 TGCGATCAGAAGGACAGATAG 57.002 47.619 0.00 0.00 0.00 2.08
807 3162 3.555966 TGCGATCAGAAGGACAGATAGA 58.444 45.455 0.00 0.00 0.00 1.98
808 3163 3.567585 TGCGATCAGAAGGACAGATAGAG 59.432 47.826 0.00 0.00 0.00 2.43
809 3164 3.818210 GCGATCAGAAGGACAGATAGAGA 59.182 47.826 0.00 0.00 0.00 3.10
810 3165 4.320202 GCGATCAGAAGGACAGATAGAGAC 60.320 50.000 0.00 0.00 0.00 3.36
811 3166 4.215399 CGATCAGAAGGACAGATAGAGACC 59.785 50.000 0.00 0.00 0.00 3.85
812 3167 4.871871 TCAGAAGGACAGATAGAGACCT 57.128 45.455 0.00 0.00 0.00 3.85
813 3168 5.977821 TCAGAAGGACAGATAGAGACCTA 57.022 43.478 0.00 0.00 0.00 3.08
814 3169 6.523035 TCAGAAGGACAGATAGAGACCTAT 57.477 41.667 0.00 0.00 38.26 2.57
818 3173 5.799827 AGGACAGATAGAGACCTATTTGC 57.200 43.478 0.00 0.00 39.68 3.68
820 3175 4.551388 GACAGATAGAGACCTATTTGCCG 58.449 47.826 0.00 0.00 39.68 5.69
825 3180 0.462759 GAGACCTATTTGCCGCTGCT 60.463 55.000 0.70 0.00 38.71 4.24
828 3183 0.463833 ACCTATTTGCCGCTGCTACC 60.464 55.000 0.70 0.00 38.71 3.18
831 3186 0.746563 TATTTGCCGCTGCTACCACC 60.747 55.000 0.70 0.00 38.71 4.61
839 3194 1.375908 CTGCTACCACCGTGCACAT 60.376 57.895 18.64 0.34 32.91 3.21
841 3196 2.452813 GCTACCACCGTGCACATCG 61.453 63.158 18.64 5.82 0.00 3.84
859 3214 4.052519 GAAACGGCGTTTCTGGGA 57.947 55.556 42.13 0.00 45.65 4.37
860 3215 1.866925 GAAACGGCGTTTCTGGGAG 59.133 57.895 42.13 2.78 45.65 4.30
861 3216 0.883370 GAAACGGCGTTTCTGGGAGT 60.883 55.000 42.13 21.15 45.65 3.85
884 3239 3.555586 CCAGCTGGATTTGGTTCTTTTGG 60.556 47.826 29.88 0.00 37.39 3.28
885 3240 2.634453 AGCTGGATTTGGTTCTTTTGGG 59.366 45.455 0.00 0.00 0.00 4.12
886 3241 2.368548 GCTGGATTTGGTTCTTTTGGGT 59.631 45.455 0.00 0.00 0.00 4.51
888 3243 4.685848 GCTGGATTTGGTTCTTTTGGGTTT 60.686 41.667 0.00 0.00 0.00 3.27
889 3244 5.436175 CTGGATTTGGTTCTTTTGGGTTTT 58.564 37.500 0.00 0.00 0.00 2.43
890 3245 5.189180 TGGATTTGGTTCTTTTGGGTTTTG 58.811 37.500 0.00 0.00 0.00 2.44
891 3246 4.578516 GGATTTGGTTCTTTTGGGTTTTGG 59.421 41.667 0.00 0.00 0.00 3.28
892 3247 4.642466 TTTGGTTCTTTTGGGTTTTGGT 57.358 36.364 0.00 0.00 0.00 3.67
893 3248 4.642466 TTGGTTCTTTTGGGTTTTGGTT 57.358 36.364 0.00 0.00 0.00 3.67
894 3249 4.209307 TGGTTCTTTTGGGTTTTGGTTC 57.791 40.909 0.00 0.00 0.00 3.62
895 3250 3.841255 TGGTTCTTTTGGGTTTTGGTTCT 59.159 39.130 0.00 0.00 0.00 3.01
896 3251 4.287326 TGGTTCTTTTGGGTTTTGGTTCTT 59.713 37.500 0.00 0.00 0.00 2.52
897 3252 5.221945 TGGTTCTTTTGGGTTTTGGTTCTTT 60.222 36.000 0.00 0.00 0.00 2.52
898 3253 5.708230 GGTTCTTTTGGGTTTTGGTTCTTTT 59.292 36.000 0.00 0.00 0.00 2.27
899 3254 6.348950 GGTTCTTTTGGGTTTTGGTTCTTTTG 60.349 38.462 0.00 0.00 0.00 2.44
900 3255 4.697828 TCTTTTGGGTTTTGGTTCTTTTGC 59.302 37.500 0.00 0.00 0.00 3.68
902 3257 1.134670 TGGGTTTTGGTTCTTTTGCCG 60.135 47.619 0.00 0.00 0.00 5.69
940 3451 3.055891 GGGGAGCACATGTAAATTTTGCT 60.056 43.478 12.88 12.88 46.12 3.91
941 3452 4.159506 GGGGAGCACATGTAAATTTTGCTA 59.840 41.667 12.97 0.00 43.53 3.49
942 3453 5.343249 GGGAGCACATGTAAATTTTGCTAG 58.657 41.667 12.97 0.00 43.53 3.42
943 3454 5.125417 GGGAGCACATGTAAATTTTGCTAGA 59.875 40.000 12.97 0.00 43.53 2.43
944 3455 6.261118 GGAGCACATGTAAATTTTGCTAGAG 58.739 40.000 12.97 0.00 43.53 2.43
968 3479 5.688220 ACTCCCTTCAAGGATAGGATCTA 57.312 43.478 4.43 0.00 37.67 1.98
1009 3527 2.646799 AATTAACTCCATGCGCGCGC 62.647 55.000 45.02 45.02 42.35 6.86
1096 3615 1.000521 CTGCCTCCCATTTCCTGCA 60.001 57.895 0.00 0.00 0.00 4.41
1349 3870 3.964875 CACCACCAAGCACACGGC 61.965 66.667 0.00 0.00 45.30 5.68
1409 3930 2.287915 CACATCCAACATTAGCTACGGC 59.712 50.000 0.00 0.00 39.06 5.68
1483 4004 0.177373 GCCCCGAAAACGAGAGGTAT 59.823 55.000 0.00 0.00 0.00 2.73
1512 4034 0.379669 CGCATGCAGGTTGGAGATTC 59.620 55.000 19.57 0.00 0.00 2.52
1581 4103 1.148273 GTATTGGAGGATGGCGCCA 59.852 57.895 34.80 34.80 0.00 5.69
1699 4224 2.094649 GTCTCCCAGTTCAAGAGGTACG 60.095 54.545 0.00 0.00 0.00 3.67
1702 4227 3.087031 TCCCAGTTCAAGAGGTACGTAG 58.913 50.000 0.00 0.00 0.00 3.51
1741 4266 8.217778 GCTCAGCATTAATAATCTCTACGTTTC 58.782 37.037 0.00 0.00 0.00 2.78
1754 4279 8.977267 ATCTCTACGTTTCCTTAGTATGTACT 57.023 34.615 0.00 0.00 40.24 2.73
1755 4280 8.430801 TCTCTACGTTTCCTTAGTATGTACTC 57.569 38.462 0.00 0.00 37.73 2.59
1756 4281 7.497249 TCTCTACGTTTCCTTAGTATGTACTCC 59.503 40.741 0.00 0.00 37.73 3.85
1757 4282 5.588958 ACGTTTCCTTAGTATGTACTCCC 57.411 43.478 0.00 0.00 37.73 4.30
1758 4283 5.267587 ACGTTTCCTTAGTATGTACTCCCT 58.732 41.667 0.00 0.00 37.73 4.20
1759 4284 5.359292 ACGTTTCCTTAGTATGTACTCCCTC 59.641 44.000 0.00 0.00 37.73 4.30
1760 4285 5.593502 CGTTTCCTTAGTATGTACTCCCTCT 59.406 44.000 0.00 0.00 37.73 3.69
1761 4286 6.459848 CGTTTCCTTAGTATGTACTCCCTCTG 60.460 46.154 0.00 0.00 37.73 3.35
1762 4287 5.728937 TCCTTAGTATGTACTCCCTCTGT 57.271 43.478 0.00 0.00 37.73 3.41
1763 4288 6.836714 TCCTTAGTATGTACTCCCTCTGTA 57.163 41.667 0.00 0.00 37.73 2.74
1764 4289 7.217028 TCCTTAGTATGTACTCCCTCTGTAA 57.783 40.000 0.00 0.00 37.73 2.41
1765 4290 7.645942 TCCTTAGTATGTACTCCCTCTGTAAA 58.354 38.462 0.00 0.00 37.73 2.01
1766 4291 7.559170 TCCTTAGTATGTACTCCCTCTGTAAAC 59.441 40.741 0.00 0.00 37.73 2.01
1767 4292 7.560626 CCTTAGTATGTACTCCCTCTGTAAACT 59.439 40.741 0.00 0.00 37.73 2.66
1768 4293 9.624373 CTTAGTATGTACTCCCTCTGTAAACTA 57.376 37.037 0.00 0.00 37.73 2.24
1769 4294 9.979897 TTAGTATGTACTCCCTCTGTAAACTAA 57.020 33.333 0.00 0.00 37.73 2.24
1778 4303 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1779 4304 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1780 4305 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
1781 4306 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
1782 4307 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1821 4346 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
1822 4347 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
1823 4348 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
1824 4349 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
1825 4350 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2014 4540 1.649664 CTGGTTCATGAAGCTCCTCG 58.350 55.000 31.37 14.90 39.38 4.63
2246 4772 1.670811 CTGCCACGATTGGGTAATCAC 59.329 52.381 0.00 0.00 44.15 3.06
2249 4775 2.033299 GCCACGATTGGGTAATCACATG 59.967 50.000 0.00 0.00 44.15 3.21
2303 4843 9.860898 ATTTTACTGGAGTAATTCTGAATTTGC 57.139 29.630 19.68 13.23 39.89 3.68
2306 4846 6.917533 ACTGGAGTAATTCTGAATTTGCTTG 58.082 36.000 19.68 13.63 32.38 4.01
2511 5052 1.884926 CATCCTCGCCTTCTTCGCC 60.885 63.158 0.00 0.00 0.00 5.54
2553 5094 3.775654 CCGGTCCTCCTCCAGCAC 61.776 72.222 0.00 0.00 0.00 4.40
2624 5165 0.544357 AGGGTGTCCAGGACGATGAA 60.544 55.000 15.24 0.00 34.95 2.57
2646 5187 5.016051 ACTACATCGAGCACATGAAGAAT 57.984 39.130 0.00 0.00 0.00 2.40
2770 5311 2.915659 TCCCCTTCAGCGACGTGT 60.916 61.111 0.00 0.00 0.00 4.49
2855 5396 2.838225 GGGGATCTCGCTCCGGAA 60.838 66.667 5.23 0.00 36.05 4.30
2877 5418 4.107051 GTGGCCATGCACGACTGC 62.107 66.667 9.72 0.00 44.52 4.40
3210 5757 3.354467 AGTTTACAGAGGGAGTACTCGG 58.646 50.000 16.56 6.25 42.31 4.63
3240 5787 5.221641 ACAAGTGGAGTAGCACAATGACTAA 60.222 40.000 0.00 0.00 0.00 2.24
3252 5799 6.815641 AGCACAATGACTAATCTACTTGACAG 59.184 38.462 0.00 0.00 0.00 3.51
3341 5889 3.673746 CCGAGAACAACGTACGGTATA 57.326 47.619 21.06 0.00 38.97 1.47
3361 5909 7.425882 CGGTATAAGTCGATCGTATGATTTCTC 59.574 40.741 15.94 0.00 34.09 2.87
3395 5943 7.945033 AATGCAAAATTTACATGAAGAACGT 57.055 28.000 0.00 0.00 0.00 3.99
3527 6091 1.071471 AAGGAAGGACAGCCACACG 59.929 57.895 0.00 0.00 36.29 4.49
3676 6240 3.208594 CGATGATGAGGCAAGAAATGGA 58.791 45.455 0.00 0.00 0.00 3.41
3683 6247 2.422832 GAGGCAAGAAATGGAAGAGCAG 59.577 50.000 0.00 0.00 0.00 4.24
3735 6299 2.354259 CTGATCAAGGAACAGGCTGAC 58.646 52.381 23.66 14.16 30.45 3.51
3796 6360 2.362503 AGACGGCGGATCTCACCA 60.363 61.111 13.24 0.00 0.00 4.17
3865 6429 1.290203 CGTACCTGACATGACATGCC 58.710 55.000 15.49 4.95 0.00 4.40
3889 6454 6.127619 CCATTGGGAAGAACAGAGGTTATTTC 60.128 42.308 0.00 0.00 38.47 2.17
3892 6457 4.270834 GGAAGAACAGAGGTTATTTCCCC 58.729 47.826 10.12 0.00 40.99 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.201435 GCTAAGCCTTTTTCGACCAAATATTTG 60.201 37.037 19.40 19.40 37.90 2.32
1 2 6.811665 GCTAAGCCTTTTTCGACCAAATATTT 59.188 34.615 0.00 0.00 0.00 1.40
2 3 6.152831 AGCTAAGCCTTTTTCGACCAAATATT 59.847 34.615 0.00 0.00 0.00 1.28
3 4 5.652452 AGCTAAGCCTTTTTCGACCAAATAT 59.348 36.000 0.00 0.00 0.00 1.28
4 5 5.007682 AGCTAAGCCTTTTTCGACCAAATA 58.992 37.500 0.00 0.00 0.00 1.40
5 6 3.826729 AGCTAAGCCTTTTTCGACCAAAT 59.173 39.130 0.00 0.00 0.00 2.32
6 7 3.004315 CAGCTAAGCCTTTTTCGACCAAA 59.996 43.478 0.00 0.00 0.00 3.28
7 8 2.552315 CAGCTAAGCCTTTTTCGACCAA 59.448 45.455 0.00 0.00 0.00 3.67
8 9 2.151202 CAGCTAAGCCTTTTTCGACCA 58.849 47.619 0.00 0.00 0.00 4.02
9 10 1.135660 GCAGCTAAGCCTTTTTCGACC 60.136 52.381 0.00 0.00 0.00 4.79
10 11 1.535462 TGCAGCTAAGCCTTTTTCGAC 59.465 47.619 0.00 0.00 0.00 4.20
11 12 1.890876 TGCAGCTAAGCCTTTTTCGA 58.109 45.000 0.00 0.00 0.00 3.71
12 13 2.523015 CATGCAGCTAAGCCTTTTTCG 58.477 47.619 0.00 0.00 0.00 3.46
13 14 2.265683 GCATGCAGCTAAGCCTTTTTC 58.734 47.619 14.21 0.00 41.15 2.29
14 15 1.619827 TGCATGCAGCTAAGCCTTTTT 59.380 42.857 18.46 0.00 45.94 1.94
15 16 1.259609 TGCATGCAGCTAAGCCTTTT 58.740 45.000 18.46 0.00 45.94 2.27
16 17 1.136305 CATGCATGCAGCTAAGCCTTT 59.864 47.619 26.69 1.43 45.94 3.11
17 18 0.744874 CATGCATGCAGCTAAGCCTT 59.255 50.000 26.69 2.26 45.94 4.35
18 19 1.107538 CCATGCATGCAGCTAAGCCT 61.108 55.000 26.69 3.09 45.94 4.58
19 20 1.362717 CCATGCATGCAGCTAAGCC 59.637 57.895 26.69 0.00 45.94 4.35
20 21 1.299926 GCCATGCATGCAGCTAAGC 60.300 57.895 26.69 18.49 45.94 3.09
21 22 0.030773 CAGCCATGCATGCAGCTAAG 59.969 55.000 27.95 16.47 45.94 2.18
22 23 0.681887 ACAGCCATGCATGCAGCTAA 60.682 50.000 27.95 5.63 45.94 3.09
23 24 0.681887 AACAGCCATGCATGCAGCTA 60.682 50.000 27.95 6.01 45.94 3.32
24 25 1.982395 AACAGCCATGCATGCAGCT 60.982 52.632 26.69 25.40 45.94 4.24
25 26 1.809619 CAACAGCCATGCATGCAGC 60.810 57.895 26.69 23.56 45.96 5.25
26 27 1.809619 GCAACAGCCATGCATGCAG 60.810 57.895 26.69 14.50 43.29 4.41
27 28 2.263227 GCAACAGCCATGCATGCA 59.737 55.556 25.04 25.04 43.29 3.96
28 29 1.809619 CAGCAACAGCCATGCATGC 60.810 57.895 21.69 11.82 46.22 4.06
29 30 0.735978 CACAGCAACAGCCATGCATG 60.736 55.000 20.19 20.19 46.22 4.06
30 31 1.589630 CACAGCAACAGCCATGCAT 59.410 52.632 8.45 0.00 46.22 3.96
31 32 2.566570 CCACAGCAACAGCCATGCA 61.567 57.895 8.45 0.00 46.22 3.96
32 33 2.091102 AACCACAGCAACAGCCATGC 62.091 55.000 0.00 0.00 44.15 4.06
33 34 0.319211 CAACCACAGCAACAGCCATG 60.319 55.000 0.00 0.00 0.00 3.66
34 35 2.043625 CAACCACAGCAACAGCCAT 58.956 52.632 0.00 0.00 0.00 4.40
35 36 2.784356 GCAACCACAGCAACAGCCA 61.784 57.895 0.00 0.00 0.00 4.75
36 37 2.028043 GCAACCACAGCAACAGCC 59.972 61.111 0.00 0.00 0.00 4.85
37 38 0.249573 AATGCAACCACAGCAACAGC 60.250 50.000 0.00 0.00 46.27 4.40
38 39 1.603678 GGAATGCAACCACAGCAACAG 60.604 52.381 8.18 0.00 46.27 3.16
39 40 0.388659 GGAATGCAACCACAGCAACA 59.611 50.000 8.18 0.00 46.27 3.33
40 41 0.664166 CGGAATGCAACCACAGCAAC 60.664 55.000 12.59 0.00 46.27 4.17
41 42 1.106351 ACGGAATGCAACCACAGCAA 61.106 50.000 12.59 0.00 46.27 3.91
43 44 1.081242 CACGGAATGCAACCACAGC 60.081 57.895 12.59 0.00 0.00 4.40
44 45 0.040157 CACACGGAATGCAACCACAG 60.040 55.000 12.59 5.10 0.00 3.66
45 46 0.464554 TCACACGGAATGCAACCACA 60.465 50.000 12.59 0.00 0.00 4.17
46 47 0.238289 CTCACACGGAATGCAACCAC 59.762 55.000 12.59 0.00 0.00 4.16
47 48 0.179032 ACTCACACGGAATGCAACCA 60.179 50.000 12.59 0.00 0.00 3.67
48 49 0.517316 GACTCACACGGAATGCAACC 59.483 55.000 0.00 0.00 0.00 3.77
49 50 0.517316 GGACTCACACGGAATGCAAC 59.483 55.000 0.00 0.00 0.00 4.17
50 51 0.396435 AGGACTCACACGGAATGCAA 59.604 50.000 0.00 0.00 0.00 4.08
51 52 0.396435 AAGGACTCACACGGAATGCA 59.604 50.000 0.00 0.00 0.00 3.96
52 53 1.197721 CAAAGGACTCACACGGAATGC 59.802 52.381 0.00 0.00 0.00 3.56
53 54 1.806542 CCAAAGGACTCACACGGAATG 59.193 52.381 0.00 0.00 0.00 2.67
54 55 1.271379 CCCAAAGGACTCACACGGAAT 60.271 52.381 0.00 0.00 33.47 3.01
55 56 0.107831 CCCAAAGGACTCACACGGAA 59.892 55.000 0.00 0.00 33.47 4.30
56 57 1.052124 ACCCAAAGGACTCACACGGA 61.052 55.000 0.00 0.00 36.73 4.69
57 58 0.682852 TACCCAAAGGACTCACACGG 59.317 55.000 0.00 0.00 36.73 4.94
58 59 1.607251 GGTACCCAAAGGACTCACACG 60.607 57.143 0.00 0.00 36.73 4.49
59 60 1.607251 CGGTACCCAAAGGACTCACAC 60.607 57.143 6.25 0.00 36.73 3.82
60 61 0.682852 CGGTACCCAAAGGACTCACA 59.317 55.000 6.25 0.00 36.73 3.58
61 62 0.672711 GCGGTACCCAAAGGACTCAC 60.673 60.000 6.25 0.00 36.73 3.51
62 63 1.675219 GCGGTACCCAAAGGACTCA 59.325 57.895 6.25 0.00 36.73 3.41
63 64 1.078637 GGCGGTACCCAAAGGACTC 60.079 63.158 6.25 0.00 36.73 3.36
64 65 0.252375 TAGGCGGTACCCAAAGGACT 60.252 55.000 6.25 1.36 40.58 3.85
65 66 0.177373 CTAGGCGGTACCCAAAGGAC 59.823 60.000 6.25 0.00 40.58 3.85
66 67 0.041535 TCTAGGCGGTACCCAAAGGA 59.958 55.000 6.25 0.00 40.58 3.36
67 68 1.129058 ATCTAGGCGGTACCCAAAGG 58.871 55.000 6.25 0.00 40.58 3.11
68 69 3.228453 TCTATCTAGGCGGTACCCAAAG 58.772 50.000 6.25 0.00 40.58 2.77
69 70 3.317455 TCTATCTAGGCGGTACCCAAA 57.683 47.619 6.25 0.00 40.58 3.28
70 71 3.537795 ATCTATCTAGGCGGTACCCAA 57.462 47.619 6.25 0.00 40.58 4.12
71 72 3.537795 AATCTATCTAGGCGGTACCCA 57.462 47.619 6.25 0.00 40.58 4.51
72 73 4.886496 AAAATCTATCTAGGCGGTACCC 57.114 45.455 6.25 0.00 40.58 3.69
73 74 6.587206 ACTAAAATCTATCTAGGCGGTACC 57.413 41.667 0.16 0.16 39.61 3.34
74 75 8.103948 TGTACTAAAATCTATCTAGGCGGTAC 57.896 38.462 0.00 0.00 0.00 3.34
75 76 7.941238 ACTGTACTAAAATCTATCTAGGCGGTA 59.059 37.037 0.00 0.00 0.00 4.02
76 77 6.776603 ACTGTACTAAAATCTATCTAGGCGGT 59.223 38.462 0.00 0.00 0.00 5.68
77 78 7.216973 ACTGTACTAAAATCTATCTAGGCGG 57.783 40.000 0.00 0.00 0.00 6.13
78 79 8.781196 TGTACTGTACTAAAATCTATCTAGGCG 58.219 37.037 17.98 0.00 0.00 5.52
87 88 8.532819 CCTTCCTTCTGTACTGTACTAAAATCT 58.467 37.037 17.98 0.00 0.00 2.40
88 89 8.312564 ACCTTCCTTCTGTACTGTACTAAAATC 58.687 37.037 17.98 0.00 0.00 2.17
89 90 8.203681 ACCTTCCTTCTGTACTGTACTAAAAT 57.796 34.615 17.98 0.00 0.00 1.82
90 91 7.607615 ACCTTCCTTCTGTACTGTACTAAAA 57.392 36.000 17.98 9.06 0.00 1.52
91 92 8.710749 TTACCTTCCTTCTGTACTGTACTAAA 57.289 34.615 17.98 11.15 0.00 1.85
92 93 7.395489 CCTTACCTTCCTTCTGTACTGTACTAA 59.605 40.741 17.98 11.45 0.00 2.24
93 94 6.888632 CCTTACCTTCCTTCTGTACTGTACTA 59.111 42.308 17.98 4.75 0.00 1.82
94 95 5.715753 CCTTACCTTCCTTCTGTACTGTACT 59.284 44.000 17.98 0.00 0.00 2.73
95 96 5.624052 GCCTTACCTTCCTTCTGTACTGTAC 60.624 48.000 10.98 10.98 0.00 2.90
96 97 4.465305 GCCTTACCTTCCTTCTGTACTGTA 59.535 45.833 0.00 0.00 0.00 2.74
97 98 3.261137 GCCTTACCTTCCTTCTGTACTGT 59.739 47.826 0.00 0.00 0.00 3.55
98 99 3.515901 AGCCTTACCTTCCTTCTGTACTG 59.484 47.826 0.00 0.00 0.00 2.74
99 100 3.792515 AGCCTTACCTTCCTTCTGTACT 58.207 45.455 0.00 0.00 0.00 2.73
100 101 4.710865 ACTAGCCTTACCTTCCTTCTGTAC 59.289 45.833 0.00 0.00 0.00 2.90
101 102 4.944177 ACTAGCCTTACCTTCCTTCTGTA 58.056 43.478 0.00 0.00 0.00 2.74
102 103 3.792515 ACTAGCCTTACCTTCCTTCTGT 58.207 45.455 0.00 0.00 0.00 3.41
103 104 6.284459 CAATACTAGCCTTACCTTCCTTCTG 58.716 44.000 0.00 0.00 0.00 3.02
104 105 5.367060 CCAATACTAGCCTTACCTTCCTTCT 59.633 44.000 0.00 0.00 0.00 2.85
105 106 5.365895 TCCAATACTAGCCTTACCTTCCTTC 59.634 44.000 0.00 0.00 0.00 3.46
106 107 5.286221 TCCAATACTAGCCTTACCTTCCTT 58.714 41.667 0.00 0.00 0.00 3.36
107 108 4.892198 TCCAATACTAGCCTTACCTTCCT 58.108 43.478 0.00 0.00 0.00 3.36
108 109 5.827326 ATCCAATACTAGCCTTACCTTCC 57.173 43.478 0.00 0.00 0.00 3.46
109 110 6.486993 CCAAATCCAATACTAGCCTTACCTTC 59.513 42.308 0.00 0.00 0.00 3.46
110 111 6.159751 TCCAAATCCAATACTAGCCTTACCTT 59.840 38.462 0.00 0.00 0.00 3.50
111 112 5.670361 TCCAAATCCAATACTAGCCTTACCT 59.330 40.000 0.00 0.00 0.00 3.08
112 113 5.937111 TCCAAATCCAATACTAGCCTTACC 58.063 41.667 0.00 0.00 0.00 2.85
113 114 5.998363 CCTCCAAATCCAATACTAGCCTTAC 59.002 44.000 0.00 0.00 0.00 2.34
114 115 5.908831 TCCTCCAAATCCAATACTAGCCTTA 59.091 40.000 0.00 0.00 0.00 2.69
115 116 4.726825 TCCTCCAAATCCAATACTAGCCTT 59.273 41.667 0.00 0.00 0.00 4.35
116 117 4.307259 TCCTCCAAATCCAATACTAGCCT 58.693 43.478 0.00 0.00 0.00 4.58
117 118 4.706842 TCCTCCAAATCCAATACTAGCC 57.293 45.455 0.00 0.00 0.00 3.93
118 119 5.006386 CCATCCTCCAAATCCAATACTAGC 58.994 45.833 0.00 0.00 0.00 3.42
119 120 5.006386 GCCATCCTCCAAATCCAATACTAG 58.994 45.833 0.00 0.00 0.00 2.57
120 121 4.504864 CGCCATCCTCCAAATCCAATACTA 60.505 45.833 0.00 0.00 0.00 1.82
121 122 3.748668 CGCCATCCTCCAAATCCAATACT 60.749 47.826 0.00 0.00 0.00 2.12
146 147 6.575244 AACACATGGGTCATTATCTCCTTA 57.425 37.500 0.00 0.00 0.00 2.69
167 168 2.861147 AGGGACAGGCACTAGAAAAC 57.139 50.000 0.00 0.00 36.02 2.43
177 178 4.576463 CACATTAAGATTGTAGGGACAGGC 59.424 45.833 0.00 0.00 36.76 4.85
227 234 8.664992 TGGTAGCCTGATTATATAAACCATCAA 58.335 33.333 8.29 0.00 29.85 2.57
228 235 8.213489 TGGTAGCCTGATTATATAAACCATCA 57.787 34.615 8.29 3.48 29.85 3.07
229 236 9.686683 AATGGTAGCCTGATTATATAAACCATC 57.313 33.333 19.12 6.55 42.74 3.51
230 237 9.686683 GAATGGTAGCCTGATTATATAAACCAT 57.313 33.333 15.44 15.44 44.82 3.55
231 238 8.890472 AGAATGGTAGCCTGATTATATAAACCA 58.110 33.333 12.92 12.92 38.72 3.67
243 271 4.289672 AGGAAAAAGAGAATGGTAGCCTGA 59.710 41.667 0.00 0.00 0.00 3.86
244 272 4.593956 AGGAAAAAGAGAATGGTAGCCTG 58.406 43.478 0.00 0.00 0.00 4.85
278 306 4.067896 ACTGACACTGGATGTTAAAGCAG 58.932 43.478 0.00 0.00 43.56 4.24
290 318 3.845178 TCAGCGTATAAACTGACACTGG 58.155 45.455 2.55 0.00 37.99 4.00
292 320 5.103000 GTCATCAGCGTATAAACTGACACT 58.897 41.667 7.85 0.00 45.19 3.55
318 346 1.548269 ACGCCCCACCAAACAATTATG 59.452 47.619 0.00 0.00 0.00 1.90
360 388 2.596346 TGGGTGCAACAGATGATTTGT 58.404 42.857 3.06 0.00 39.98 2.83
427 483 0.398696 TTGCCCGCAGACTCCTTAAA 59.601 50.000 0.00 0.00 0.00 1.52
428 484 0.398696 TTTGCCCGCAGACTCCTTAA 59.601 50.000 0.00 0.00 0.00 1.85
429 485 0.618458 ATTTGCCCGCAGACTCCTTA 59.382 50.000 0.00 0.00 0.00 2.69
432 488 1.017387 CTAATTTGCCCGCAGACTCC 58.983 55.000 0.00 0.00 0.00 3.85
434 490 2.420129 CCTACTAATTTGCCCGCAGACT 60.420 50.000 0.00 0.00 0.00 3.24
436 492 1.745827 GCCTACTAATTTGCCCGCAGA 60.746 52.381 0.00 0.00 0.00 4.26
437 493 0.663153 GCCTACTAATTTGCCCGCAG 59.337 55.000 0.00 0.00 0.00 5.18
438 494 0.254747 AGCCTACTAATTTGCCCGCA 59.745 50.000 0.00 0.00 0.00 5.69
439 495 1.333931 GAAGCCTACTAATTTGCCCGC 59.666 52.381 0.00 0.00 0.00 6.13
440 496 1.947456 GGAAGCCTACTAATTTGCCCG 59.053 52.381 0.00 0.00 0.00 6.13
441 497 2.307768 GGGAAGCCTACTAATTTGCCC 58.692 52.381 0.00 0.00 0.00 5.36
477 2050 0.034896 GGTGGACTTTCTTCAGGCGA 59.965 55.000 0.00 0.00 0.00 5.54
491 2082 0.834612 AAACACGAACTGGAGGTGGA 59.165 50.000 0.00 0.00 36.02 4.02
492 2083 0.944386 CAAACACGAACTGGAGGTGG 59.056 55.000 0.00 0.00 36.02 4.61
493 2084 1.948104 TCAAACACGAACTGGAGGTG 58.052 50.000 0.00 0.00 37.67 4.00
494 2085 2.767505 GATCAAACACGAACTGGAGGT 58.232 47.619 0.00 0.00 0.00 3.85
495 2086 1.726791 CGATCAAACACGAACTGGAGG 59.273 52.381 0.00 0.00 0.00 4.30
496 2087 1.126846 GCGATCAAACACGAACTGGAG 59.873 52.381 0.00 0.00 0.00 3.86
497 2088 1.144969 GCGATCAAACACGAACTGGA 58.855 50.000 0.00 0.00 0.00 3.86
498 2089 0.865111 TGCGATCAAACACGAACTGG 59.135 50.000 0.00 0.00 0.00 4.00
499 2090 2.157474 TGATGCGATCAAACACGAACTG 59.843 45.455 0.00 0.00 36.11 3.16
702 2293 0.257328 TTGCACTTCCCACCTGTCAA 59.743 50.000 0.00 0.00 0.00 3.18
732 3086 0.742281 CTGACGAGGACAGCCATTGG 60.742 60.000 0.00 0.00 36.29 3.16
764 3118 5.337491 GCATGGAAGTTCATAACCAAACCAT 60.337 40.000 5.01 0.00 36.00 3.55
765 3119 4.021544 GCATGGAAGTTCATAACCAAACCA 60.022 41.667 5.01 0.00 36.00 3.67
766 3120 4.494484 GCATGGAAGTTCATAACCAAACC 58.506 43.478 5.01 0.00 36.00 3.27
805 3160 0.462759 GCAGCGGCAAATAGGTCTCT 60.463 55.000 3.18 0.00 40.72 3.10
806 3161 0.462759 AGCAGCGGCAAATAGGTCTC 60.463 55.000 12.44 0.00 44.61 3.36
807 3162 0.830648 TAGCAGCGGCAAATAGGTCT 59.169 50.000 12.44 0.00 44.61 3.85
808 3163 0.938008 GTAGCAGCGGCAAATAGGTC 59.062 55.000 12.44 0.00 44.61 3.85
809 3164 0.463833 GGTAGCAGCGGCAAATAGGT 60.464 55.000 12.44 0.00 44.61 3.08
810 3165 0.463654 TGGTAGCAGCGGCAAATAGG 60.464 55.000 12.44 0.00 44.61 2.57
811 3166 0.657840 GTGGTAGCAGCGGCAAATAG 59.342 55.000 12.44 0.00 44.61 1.73
812 3167 0.746563 GGTGGTAGCAGCGGCAAATA 60.747 55.000 12.44 0.00 44.61 1.40
813 3168 2.046285 GGTGGTAGCAGCGGCAAAT 61.046 57.895 12.44 0.00 44.61 2.32
814 3169 2.671619 GGTGGTAGCAGCGGCAAA 60.672 61.111 12.44 0.00 44.61 3.68
820 3175 3.423154 GTGCACGGTGGTAGCAGC 61.423 66.667 13.98 13.98 39.21 5.25
825 3180 2.263227 CCGATGTGCACGGTGGTA 59.737 61.111 13.13 0.00 44.57 3.25
831 3186 2.474266 CCGTTTCCGATGTGCACG 59.526 61.111 13.13 0.00 35.63 5.34
833 3188 3.418913 CGCCGTTTCCGATGTGCA 61.419 61.111 0.00 0.00 35.63 4.57
836 3191 1.864176 GAAACGCCGTTTCCGATGT 59.136 52.632 27.66 0.00 44.04 3.06
843 3198 0.883370 GACTCCCAGAAACGCCGTTT 60.883 55.000 16.07 16.07 38.54 3.60
846 3201 2.434359 GGACTCCCAGAAACGCCG 60.434 66.667 0.00 0.00 0.00 6.46
884 3239 0.934496 GCGGCAAAAGAACCAAAACC 59.066 50.000 0.00 0.00 0.00 3.27
885 3240 0.934496 GGCGGCAAAAGAACCAAAAC 59.066 50.000 3.07 0.00 0.00 2.43
886 3241 0.179070 GGGCGGCAAAAGAACCAAAA 60.179 50.000 12.47 0.00 0.00 2.44
888 3243 2.503382 GGGGCGGCAAAAGAACCAA 61.503 57.895 12.47 0.00 0.00 3.67
889 3244 2.915137 GGGGCGGCAAAAGAACCA 60.915 61.111 12.47 0.00 0.00 3.67
890 3245 2.600470 AGGGGCGGCAAAAGAACC 60.600 61.111 12.47 0.00 0.00 3.62
891 3246 1.587043 GAGAGGGGCGGCAAAAGAAC 61.587 60.000 12.47 0.00 0.00 3.01
892 3247 1.303317 GAGAGGGGCGGCAAAAGAA 60.303 57.895 12.47 0.00 0.00 2.52
893 3248 2.351276 GAGAGGGGCGGCAAAAGA 59.649 61.111 12.47 0.00 0.00 2.52
894 3249 2.751837 GGAGAGGGGCGGCAAAAG 60.752 66.667 12.47 0.00 0.00 2.27
895 3250 4.360405 GGGAGAGGGGCGGCAAAA 62.360 66.667 12.47 0.00 0.00 2.44
940 3451 5.675421 TCCTATCCTTGAAGGGAGTACTCTA 59.325 44.000 21.88 2.35 38.92 2.43
941 3452 4.482772 TCCTATCCTTGAAGGGAGTACTCT 59.517 45.833 21.88 2.62 38.92 3.24
942 3453 4.805744 TCCTATCCTTGAAGGGAGTACTC 58.194 47.826 14.87 14.87 38.92 2.59
943 3454 4.901785 TCCTATCCTTGAAGGGAGTACT 57.098 45.455 11.99 0.00 38.92 2.73
944 3455 5.399113 AGATCCTATCCTTGAAGGGAGTAC 58.601 45.833 11.99 3.60 38.92 2.73
988 3505 1.656429 CGCGCGCATGGAGTTAATTAC 60.656 52.381 32.61 0.00 0.00 1.89
1009 3527 0.639756 GCATGCCAATTACAAACGCG 59.360 50.000 6.36 3.53 0.00 6.01
1010 3528 1.655099 CTGCATGCCAATTACAAACGC 59.345 47.619 16.68 0.00 0.00 4.84
1011 3529 3.214697 TCTGCATGCCAATTACAAACG 57.785 42.857 16.68 0.00 0.00 3.60
1012 3530 6.308675 CAAAATCTGCATGCCAATTACAAAC 58.691 36.000 16.68 0.00 0.00 2.93
1349 3870 0.042188 CGCGGCGGACAATAATTCTG 60.042 55.000 15.84 0.00 0.00 3.02
1353 3874 2.244651 GCTCGCGGCGGACAATAAT 61.245 57.895 23.46 0.00 0.00 1.28
1354 3875 2.888534 GCTCGCGGCGGACAATAA 60.889 61.111 23.46 0.00 0.00 1.40
1388 3909 2.287915 GCCGTAGCTAATGTTGGATGTG 59.712 50.000 0.00 0.00 35.50 3.21
1389 3910 2.561569 GCCGTAGCTAATGTTGGATGT 58.438 47.619 0.00 0.00 35.50 3.06
1390 3911 1.526887 CGCCGTAGCTAATGTTGGATG 59.473 52.381 0.00 0.00 36.60 3.51
1467 3988 3.103738 CGTACATACCTCTCGTTTTCGG 58.896 50.000 0.00 0.00 44.25 4.30
1483 4004 4.688966 TGCATGCGGGCACGTACA 62.689 61.111 11.45 0.00 43.45 2.90
1507 4029 5.365619 AGACAACACCGTTACTTTGAATCT 58.634 37.500 0.00 0.00 0.00 2.40
1512 4034 6.572254 CGAAAATAGACAACACCGTTACTTTG 59.428 38.462 0.00 0.00 0.00 2.77
1581 4103 1.755008 GTACCTCAGCGCCTCCTCT 60.755 63.158 2.29 0.00 0.00 3.69
1640 4162 3.551496 TACAGGTCGTCGGGGTCGT 62.551 63.158 0.00 0.00 37.69 4.34
1648 4170 4.112341 AGGCGCGTACAGGTCGTC 62.112 66.667 8.43 0.00 0.00 4.20
1649 4171 4.112341 GAGGCGCGTACAGGTCGT 62.112 66.667 8.43 0.00 0.00 4.34
1650 4172 3.736482 GAGAGGCGCGTACAGGTCG 62.736 68.421 8.43 0.00 0.00 4.79
1737 4262 6.380560 ACAGAGGGAGTACATACTAAGGAAAC 59.619 42.308 0.00 0.00 36.50 2.78
1741 4266 7.560626 AGTTTACAGAGGGAGTACATACTAAGG 59.439 40.741 0.00 0.00 36.50 2.69
1752 4277 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
1753 4278 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
1754 4279 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
1755 4280 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
1756 4281 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
1795 4320 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1796 4321 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
1797 4322 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
1798 4323 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1799 4324 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1809 4334 9.710818 ACTGAATTATACTCCCTCTGTAAACTA 57.289 33.333 0.00 0.00 0.00 2.24
1810 4335 8.478877 CACTGAATTATACTCCCTCTGTAAACT 58.521 37.037 0.00 0.00 0.00 2.66
1811 4336 8.475639 TCACTGAATTATACTCCCTCTGTAAAC 58.524 37.037 0.00 0.00 0.00 2.01
1812 4337 8.603898 TCACTGAATTATACTCCCTCTGTAAA 57.396 34.615 0.00 0.00 0.00 2.01
1813 4338 7.839705 ACTCACTGAATTATACTCCCTCTGTAA 59.160 37.037 0.00 0.00 0.00 2.41
1814 4339 7.285629 CACTCACTGAATTATACTCCCTCTGTA 59.714 40.741 0.00 0.00 0.00 2.74
1815 4340 6.097554 CACTCACTGAATTATACTCCCTCTGT 59.902 42.308 0.00 0.00 0.00 3.41
1816 4341 6.322456 TCACTCACTGAATTATACTCCCTCTG 59.678 42.308 0.00 0.00 0.00 3.35
1817 4342 6.322712 GTCACTCACTGAATTATACTCCCTCT 59.677 42.308 0.00 0.00 0.00 3.69
1818 4343 6.322712 AGTCACTCACTGAATTATACTCCCTC 59.677 42.308 0.00 0.00 32.26 4.30
1819 4344 6.198639 AGTCACTCACTGAATTATACTCCCT 58.801 40.000 0.00 0.00 32.26 4.20
1820 4345 6.472686 AGTCACTCACTGAATTATACTCCC 57.527 41.667 0.00 0.00 32.26 4.30
1821 4346 9.303537 GTTTAGTCACTCACTGAATTATACTCC 57.696 37.037 0.00 0.00 33.42 3.85
1822 4347 9.011407 CGTTTAGTCACTCACTGAATTATACTC 57.989 37.037 0.00 0.00 33.42 2.59
1823 4348 7.488471 GCGTTTAGTCACTCACTGAATTATACT 59.512 37.037 0.00 0.00 33.42 2.12
1824 4349 7.274904 TGCGTTTAGTCACTCACTGAATTATAC 59.725 37.037 0.00 0.00 33.42 1.47
1825 4350 7.317390 TGCGTTTAGTCACTCACTGAATTATA 58.683 34.615 0.00 0.00 33.42 0.98
1826 4351 6.163476 TGCGTTTAGTCACTCACTGAATTAT 58.837 36.000 0.00 0.00 33.42 1.28
2014 4540 2.185608 GAACGGCCTGCTCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
2246 4772 7.344441 TGCGATACGAAAATGTTAGAATCATG 58.656 34.615 0.00 0.00 0.00 3.07
2249 4775 6.934210 ACTGCGATACGAAAATGTTAGAATC 58.066 36.000 0.00 0.00 0.00 2.52
2303 4843 0.744414 CGTGTATGGTCCCTGCCAAG 60.744 60.000 0.00 0.00 42.48 3.61
2306 4846 1.153429 GTCGTGTATGGTCCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
2376 4917 1.758514 GATCCCCTCCGAGCTGTCA 60.759 63.158 0.00 0.00 0.00 3.58
2604 5145 1.219124 CATCGTCCTGGACACCCTG 59.781 63.158 25.42 12.75 32.09 4.45
2624 5165 4.456280 TTCTTCATGTGCTCGATGTAGT 57.544 40.909 0.00 0.00 0.00 2.73
2634 5175 3.944015 AGAACCTGCTATTCTTCATGTGC 59.056 43.478 0.00 0.00 32.32 4.57
2751 5292 3.382832 ACGTCGCTGAAGGGGAGG 61.383 66.667 0.00 0.00 44.63 4.30
2770 5311 2.214181 GAGAAGGCGCTCCAGTCGAA 62.214 60.000 7.64 0.00 33.74 3.71
2835 5376 4.292178 CGGAGCGAGATCCCCTGC 62.292 72.222 1.42 0.00 35.82 4.85
2877 5418 2.680913 CCTTTGGAGCCGCTTGACG 61.681 63.158 0.00 0.00 43.15 4.35
3177 5718 9.084533 CTCCCTCTGTAAACTAATATAAGAGCT 57.915 37.037 0.00 0.00 0.00 4.09
3210 5757 3.508793 TGTGCTACTCCACTTGTACTACC 59.491 47.826 0.00 0.00 36.68 3.18
3240 5787 8.854614 ATTAAGCTTTTCACTGTCAAGTAGAT 57.145 30.769 3.20 0.00 33.79 1.98
3341 5889 3.975670 GCGAGAAATCATACGATCGACTT 59.024 43.478 24.34 1.27 0.00 3.01
3395 5943 0.616395 TGGGGATGAGTAACTGCCGA 60.616 55.000 0.00 0.00 0.00 5.54
3527 6091 0.908198 ACAGGAAGATCACCAGCTCC 59.092 55.000 10.74 0.24 0.00 4.70
3605 6169 1.739338 ATCTCCTCATGTCGGCGTCC 61.739 60.000 6.85 0.00 0.00 4.79
3611 6175 0.668535 TGGCGTATCTCCTCATGTCG 59.331 55.000 0.00 0.00 0.00 4.35
3676 6240 1.446907 CCAACAATCGAGCTGCTCTT 58.553 50.000 25.59 12.62 0.00 2.85
3683 6247 1.573829 TTCACGCCCAACAATCGAGC 61.574 55.000 0.00 0.00 0.00 5.03
3735 6299 2.464865 GGAGCATGTCAAGCTACTACG 58.535 52.381 4.99 0.00 43.58 3.51
3859 6423 2.173519 CTGTTCTTCCCAATGGCATGT 58.826 47.619 0.00 0.00 0.00 3.21
3865 6429 6.127619 GGAAATAACCTCTGTTCTTCCCAATG 60.128 42.308 7.50 0.00 38.98 2.82
3892 6457 2.757314 GGCTTCTTTCATCTTCTTGGGG 59.243 50.000 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.