Multiple sequence alignment - TraesCS4D01G305800

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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 TraesCS4D01G305800 chr4D 100.000 2941 0 0 1 2941 474379013 474376073 0.000000e+00 5432
1 TraesCS4D01G305800 chr4B 94.656 2208 71 18 753 2941 597742630 597740451 0.000000e+00 3380
2 TraesCS4D01G305800 chr4B 95.142 247 12 0 255 501 597743343 597743097 9.880000e-105 390
3 TraesCS4D01G305800 chr4B 86.822 258 8 3 1 257 597967553 597967321 6.250000e-67 265
4 TraesCS4D01G305800 chr4B 96.241 133 5 0 609 741 597742745 597742613 4.940000e-53 219
5 TraesCS4D01G305800 chr4A 90.865 1248 47 20 1415 2625 681790572 681791789 0.000000e+00 1611
6 TraesCS4D01G305800 chr4A 91.535 697 28 9 717 1411 681789861 681790528 0.000000e+00 931
7 TraesCS4D01G305800 chr4A 90.000 390 35 3 322 711 681788081 681788466 4.380000e-138 501
8 TraesCS4D01G305800 chr4A 96.262 214 8 0 2616 2829 681791936 681792149 4.660000e-93 351
9 TraesCS4D01G305800 chr2B 88.265 392 35 8 996 1381 443825230 443824844 2.670000e-125 459
10 TraesCS4D01G305800 chr2B 81.287 513 53 21 1452 1941 443824714 443824222 2.770000e-100 375
11 TraesCS4D01G305800 chrUn 88.114 387 40 4 996 1381 300432724 300432343 3.460000e-124 455
12 TraesCS4D01G305800 chrUn 81.481 513 52 24 1452 1941 300432217 300431725 5.950000e-102 381
13 TraesCS4D01G305800 chrUn 74.750 400 40 31 2514 2882 308098862 308099231 3.980000e-24 122
14 TraesCS4D01G305800 chr2D 87.080 387 44 4 996 1381 373903436 373903055 1.620000e-117 433
15 TraesCS4D01G305800 chr2D 81.836 512 51 22 1452 1941 373902929 373902438 2.750000e-105 392
16 TraesCS4D01G305800 chr2D 75.000 384 48 28 2514 2882 373901729 373901379 1.840000e-27 134


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 TraesCS4D01G305800 chr4D 474376073 474379013 2940 True 5432.000000 5432 100.000000 1 2941 1 chr4D.!!$R1 2940
1 TraesCS4D01G305800 chr4B 597740451 597743343 2892 True 1329.666667 3380 95.346333 255 2941 3 chr4B.!!$R2 2686
2 TraesCS4D01G305800 chr4A 681788081 681792149 4068 False 848.500000 1611 92.165500 322 2829 4 chr4A.!!$F1 2507
3 TraesCS4D01G305800 chr2B 443824222 443825230 1008 True 417.000000 459 84.776000 996 1941 2 chr2B.!!$R1 945
4 TraesCS4D01G305800 chrUn 300431725 300432724 999 True 418.000000 455 84.797500 996 1941 2 chrUn.!!$R1 945
5 TraesCS4D01G305800 chr2D 373901379 373903436 2057 True 319.666667 433 81.305333 996 2882 3 chr2D.!!$R1 1886

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
52 53 0.045623 TCTTTGCCCTCATCCCCCTA 59.954 55.0 0.0 0.0 0.0 3.53 F
250 251 0.110823 GTAGCAAACACGCCGAACAG 60.111 55.0 0.0 0.0 0.0 3.16 F
251 252 0.249531 TAGCAAACACGCCGAACAGA 60.250 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 3253 1.077663 AGGTTTGATGCCCACAGGAAT 59.922 47.619 0.0 0.0 31.86 3.01 R
1767 3567 1.213094 AACAGCACGAAGACGAACCG 61.213 55.000 0.0 0.0 42.66 4.44 R
2101 3944 3.090037 TCACAGGTTGACTAGTAGGAGC 58.910 50.000 0.0 0.0 0.00 4.70 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 2.859165 TCTCGCCCTCAAATTCAACT 57.141 45.000 0.00 0.00 0.00 3.16
21 22 2.426522 TCTCGCCCTCAAATTCAACTG 58.573 47.619 0.00 0.00 0.00 3.16
22 23 0.881118 TCGCCCTCAAATTCAACTGC 59.119 50.000 0.00 0.00 0.00 4.40
23 24 0.883833 CGCCCTCAAATTCAACTGCT 59.116 50.000 0.00 0.00 0.00 4.24
24 25 1.135575 CGCCCTCAAATTCAACTGCTC 60.136 52.381 0.00 0.00 0.00 4.26
25 26 2.165998 GCCCTCAAATTCAACTGCTCT 58.834 47.619 0.00 0.00 0.00 4.09
26 27 2.163211 GCCCTCAAATTCAACTGCTCTC 59.837 50.000 0.00 0.00 0.00 3.20
27 28 3.683802 CCCTCAAATTCAACTGCTCTCT 58.316 45.455 0.00 0.00 0.00 3.10
28 29 3.439476 CCCTCAAATTCAACTGCTCTCTG 59.561 47.826 0.00 0.00 0.00 3.35
29 30 4.070716 CCTCAAATTCAACTGCTCTCTGT 58.929 43.478 0.00 0.00 0.00 3.41
30 31 4.083431 CCTCAAATTCAACTGCTCTCTGTG 60.083 45.833 0.00 0.00 0.00 3.66
31 32 3.251729 TCAAATTCAACTGCTCTCTGTGC 59.748 43.478 0.00 0.00 0.00 4.57
32 33 2.556144 ATTCAACTGCTCTCTGTGCA 57.444 45.000 0.00 0.00 38.81 4.57
33 34 2.556144 TTCAACTGCTCTCTGTGCAT 57.444 45.000 0.00 0.00 39.86 3.96
34 35 2.090400 TCAACTGCTCTCTGTGCATC 57.910 50.000 0.00 0.00 39.86 3.91
35 36 1.622312 TCAACTGCTCTCTGTGCATCT 59.378 47.619 0.00 0.00 39.86 2.90
36 37 2.038164 TCAACTGCTCTCTGTGCATCTT 59.962 45.455 0.00 0.00 39.86 2.40
37 38 2.812591 CAACTGCTCTCTGTGCATCTTT 59.187 45.455 0.00 0.00 39.86 2.52
38 39 2.424557 ACTGCTCTCTGTGCATCTTTG 58.575 47.619 0.00 0.00 39.86 2.77
48 49 2.423388 GCATCTTTGCCCTCATCCC 58.577 57.895 0.00 0.00 43.38 3.85
49 50 1.111715 GCATCTTTGCCCTCATCCCC 61.112 60.000 0.00 0.00 43.38 4.81
50 51 0.468771 CATCTTTGCCCTCATCCCCC 60.469 60.000 0.00 0.00 0.00 5.40
51 52 0.628668 ATCTTTGCCCTCATCCCCCT 60.629 55.000 0.00 0.00 0.00 4.79
52 53 0.045623 TCTTTGCCCTCATCCCCCTA 59.954 55.000 0.00 0.00 0.00 3.53
53 54 1.152649 CTTTGCCCTCATCCCCCTAT 58.847 55.000 0.00 0.00 0.00 2.57
54 55 1.500736 CTTTGCCCTCATCCCCCTATT 59.499 52.381 0.00 0.00 0.00 1.73
55 56 1.619298 TTGCCCTCATCCCCCTATTT 58.381 50.000 0.00 0.00 0.00 1.40
56 57 0.852842 TGCCCTCATCCCCCTATTTG 59.147 55.000 0.00 0.00 0.00 2.32
57 58 1.149101 GCCCTCATCCCCCTATTTGA 58.851 55.000 0.00 0.00 0.00 2.69
58 59 1.499007 GCCCTCATCCCCCTATTTGAA 59.501 52.381 0.00 0.00 0.00 2.69
59 60 2.110721 GCCCTCATCCCCCTATTTGAAT 59.889 50.000 0.00 0.00 0.00 2.57
60 61 3.438520 GCCCTCATCCCCCTATTTGAATT 60.439 47.826 0.00 0.00 0.00 2.17
61 62 4.819610 CCCTCATCCCCCTATTTGAATTT 58.180 43.478 0.00 0.00 0.00 1.82
62 63 4.835056 CCCTCATCCCCCTATTTGAATTTC 59.165 45.833 0.00 0.00 0.00 2.17
63 64 5.457686 CCTCATCCCCCTATTTGAATTTCA 58.542 41.667 0.00 0.00 0.00 2.69
64 65 5.898972 CCTCATCCCCCTATTTGAATTTCAA 59.101 40.000 7.74 7.74 34.03 2.69
65 66 6.556116 CCTCATCCCCCTATTTGAATTTCAAT 59.444 38.462 12.39 6.11 36.11 2.57
66 67 7.256083 CCTCATCCCCCTATTTGAATTTCAATC 60.256 40.741 12.39 0.00 36.11 2.67
67 68 7.364627 TCATCCCCCTATTTGAATTTCAATCT 58.635 34.615 12.39 6.36 36.11 2.40
68 69 7.506938 TCATCCCCCTATTTGAATTTCAATCTC 59.493 37.037 12.39 0.00 36.11 2.75
69 70 6.740693 TCCCCCTATTTGAATTTCAATCTCA 58.259 36.000 12.39 0.00 36.11 3.27
70 71 7.188381 TCCCCCTATTTGAATTTCAATCTCAA 58.812 34.615 12.39 0.00 36.11 3.02
71 72 7.845800 TCCCCCTATTTGAATTTCAATCTCAAT 59.154 33.333 12.39 5.74 36.11 2.57
72 73 8.488668 CCCCCTATTTGAATTTCAATCTCAATT 58.511 33.333 12.39 0.00 36.11 2.32
73 74 9.895138 CCCCTATTTGAATTTCAATCTCAATTT 57.105 29.630 12.39 0.00 36.11 1.82
79 80 9.526713 TTTGAATTTCAATCTCAATTTCGTTGA 57.473 25.926 12.39 0.00 39.12 3.18
80 81 9.695526 TTGAATTTCAATCTCAATTTCGTTGAT 57.304 25.926 7.74 0.00 37.55 2.57
81 82 9.695526 TGAATTTCAATCTCAATTTCGTTGATT 57.304 25.926 0.00 0.00 45.36 2.57
83 84 9.918630 AATTTCAATCTCAATTTCGTTGATTCT 57.081 25.926 0.00 0.00 45.36 2.40
84 85 9.918630 ATTTCAATCTCAATTTCGTTGATTCTT 57.081 25.926 0.00 0.00 45.36 2.52
85 86 9.748708 TTTCAATCTCAATTTCGTTGATTCTTT 57.251 25.926 0.00 0.00 45.36 2.52
86 87 9.748708 TTCAATCTCAATTTCGTTGATTCTTTT 57.251 25.926 0.00 0.00 45.36 2.27
87 88 9.398170 TCAATCTCAATTTCGTTGATTCTTTTC 57.602 29.630 0.00 0.00 45.36 2.29
88 89 9.403110 CAATCTCAATTTCGTTGATTCTTTTCT 57.597 29.630 0.00 0.00 45.36 2.52
89 90 9.617975 AATCTCAATTTCGTTGATTCTTTTCTC 57.382 29.630 0.00 0.00 45.36 2.87
90 91 7.584987 TCTCAATTTCGTTGATTCTTTTCTCC 58.415 34.615 0.00 0.00 45.36 3.71
91 92 7.228507 TCTCAATTTCGTTGATTCTTTTCTCCA 59.771 33.333 0.00 0.00 45.36 3.86
92 93 7.362662 TCAATTTCGTTGATTCTTTTCTCCAG 58.637 34.615 0.00 0.00 41.79 3.86
93 94 6.884280 ATTTCGTTGATTCTTTTCTCCAGT 57.116 33.333 0.00 0.00 0.00 4.00
94 95 6.693315 TTTCGTTGATTCTTTTCTCCAGTT 57.307 33.333 0.00 0.00 0.00 3.16
95 96 6.693315 TTCGTTGATTCTTTTCTCCAGTTT 57.307 33.333 0.00 0.00 0.00 2.66
96 97 6.060028 TCGTTGATTCTTTTCTCCAGTTTG 57.940 37.500 0.00 0.00 0.00 2.93
97 98 5.588648 TCGTTGATTCTTTTCTCCAGTTTGT 59.411 36.000 0.00 0.00 0.00 2.83
98 99 6.094881 TCGTTGATTCTTTTCTCCAGTTTGTT 59.905 34.615 0.00 0.00 0.00 2.83
99 100 6.197096 CGTTGATTCTTTTCTCCAGTTTGTTG 59.803 38.462 0.00 0.00 0.00 3.33
100 101 6.773976 TGATTCTTTTCTCCAGTTTGTTGT 57.226 33.333 0.00 0.00 0.00 3.32
101 102 7.169158 TGATTCTTTTCTCCAGTTTGTTGTT 57.831 32.000 0.00 0.00 0.00 2.83
102 103 7.257722 TGATTCTTTTCTCCAGTTTGTTGTTC 58.742 34.615 0.00 0.00 0.00 3.18
103 104 6.834168 TTCTTTTCTCCAGTTTGTTGTTCT 57.166 33.333 0.00 0.00 0.00 3.01
104 105 6.834168 TCTTTTCTCCAGTTTGTTGTTCTT 57.166 33.333 0.00 0.00 0.00 2.52
105 106 6.852664 TCTTTTCTCCAGTTTGTTGTTCTTC 58.147 36.000 0.00 0.00 0.00 2.87
106 107 6.659242 TCTTTTCTCCAGTTTGTTGTTCTTCT 59.341 34.615 0.00 0.00 0.00 2.85
107 108 6.834168 TTTCTCCAGTTTGTTGTTCTTCTT 57.166 33.333 0.00 0.00 0.00 2.52
108 109 6.834168 TTCTCCAGTTTGTTGTTCTTCTTT 57.166 33.333 0.00 0.00 0.00 2.52
109 110 6.194796 TCTCCAGTTTGTTGTTCTTCTTTG 57.805 37.500 0.00 0.00 0.00 2.77
110 111 4.743493 TCCAGTTTGTTGTTCTTCTTTGC 58.257 39.130 0.00 0.00 0.00 3.68
111 112 4.219507 TCCAGTTTGTTGTTCTTCTTTGCA 59.780 37.500 0.00 0.00 0.00 4.08
112 113 4.928615 CCAGTTTGTTGTTCTTCTTTGCAA 59.071 37.500 0.00 0.00 0.00 4.08
113 114 5.163963 CCAGTTTGTTGTTCTTCTTTGCAAC 60.164 40.000 0.00 0.00 40.89 4.17
114 115 5.404968 CAGTTTGTTGTTCTTCTTTGCAACA 59.595 36.000 0.00 5.05 46.09 3.33
115 116 6.091169 CAGTTTGTTGTTCTTCTTTGCAACAT 59.909 34.615 0.00 0.00 46.67 2.71
116 117 6.311200 AGTTTGTTGTTCTTCTTTGCAACATC 59.689 34.615 0.00 6.76 46.67 3.06
117 118 5.321959 TGTTGTTCTTCTTTGCAACATCA 57.678 34.783 0.00 0.00 43.92 3.07
118 119 5.101628 TGTTGTTCTTCTTTGCAACATCAC 58.898 37.500 0.00 0.00 43.92 3.06
119 120 3.951306 TGTTCTTCTTTGCAACATCACG 58.049 40.909 0.00 0.00 0.00 4.35
120 121 3.625313 TGTTCTTCTTTGCAACATCACGA 59.375 39.130 0.00 0.00 0.00 4.35
121 122 4.095632 TGTTCTTCTTTGCAACATCACGAA 59.904 37.500 0.00 0.00 0.00 3.85
122 123 5.215160 GTTCTTCTTTGCAACATCACGAAT 58.785 37.500 0.00 0.00 0.00 3.34
123 124 4.786507 TCTTCTTTGCAACATCACGAATG 58.213 39.130 0.00 0.00 41.48 2.67
124 125 4.514816 TCTTCTTTGCAACATCACGAATGA 59.485 37.500 0.00 0.00 38.83 2.57
125 126 4.145876 TCTTTGCAACATCACGAATGAC 57.854 40.909 0.00 0.85 37.79 3.06
126 127 3.563390 TCTTTGCAACATCACGAATGACA 59.437 39.130 0.00 2.92 37.79 3.58
127 128 4.216042 TCTTTGCAACATCACGAATGACAT 59.784 37.500 0.00 0.00 37.79 3.06
128 129 3.745332 TGCAACATCACGAATGACATC 57.255 42.857 9.06 0.00 37.79 3.06
129 130 3.337358 TGCAACATCACGAATGACATCT 58.663 40.909 9.06 0.00 37.79 2.90
130 131 3.752747 TGCAACATCACGAATGACATCTT 59.247 39.130 9.06 0.00 37.79 2.40
131 132 4.216042 TGCAACATCACGAATGACATCTTT 59.784 37.500 9.06 0.00 37.79 2.52
132 133 5.156355 GCAACATCACGAATGACATCTTTT 58.844 37.500 9.06 0.00 37.79 2.27
133 134 5.060077 GCAACATCACGAATGACATCTTTTG 59.940 40.000 9.06 3.65 37.79 2.44
134 135 4.726416 ACATCACGAATGACATCTTTTGC 58.274 39.130 9.06 0.00 37.79 3.68
135 136 3.829886 TCACGAATGACATCTTTTGCC 57.170 42.857 0.00 0.00 0.00 4.52
136 137 2.487762 TCACGAATGACATCTTTTGCCC 59.512 45.455 0.00 0.00 0.00 5.36
137 138 2.489329 CACGAATGACATCTTTTGCCCT 59.511 45.455 0.00 0.00 0.00 5.19
138 139 3.689161 CACGAATGACATCTTTTGCCCTA 59.311 43.478 0.00 0.00 0.00 3.53
139 140 3.689649 ACGAATGACATCTTTTGCCCTAC 59.310 43.478 0.00 0.00 0.00 3.18
140 141 3.065371 CGAATGACATCTTTTGCCCTACC 59.935 47.826 0.00 0.00 0.00 3.18
141 142 4.273318 GAATGACATCTTTTGCCCTACCT 58.727 43.478 0.00 0.00 0.00 3.08
142 143 3.806949 TGACATCTTTTGCCCTACCTT 57.193 42.857 0.00 0.00 0.00 3.50
143 144 3.686016 TGACATCTTTTGCCCTACCTTC 58.314 45.455 0.00 0.00 0.00 3.46
144 145 3.017442 GACATCTTTTGCCCTACCTTCC 58.983 50.000 0.00 0.00 0.00 3.46
145 146 2.291605 ACATCTTTTGCCCTACCTTCCC 60.292 50.000 0.00 0.00 0.00 3.97
146 147 1.451449 TCTTTTGCCCTACCTTCCCA 58.549 50.000 0.00 0.00 0.00 4.37
147 148 2.000048 TCTTTTGCCCTACCTTCCCAT 59.000 47.619 0.00 0.00 0.00 4.00
148 149 2.381961 TCTTTTGCCCTACCTTCCCATT 59.618 45.455 0.00 0.00 0.00 3.16
149 150 2.525105 TTTGCCCTACCTTCCCATTC 57.475 50.000 0.00 0.00 0.00 2.67
150 151 1.377690 TTGCCCTACCTTCCCATTCA 58.622 50.000 0.00 0.00 0.00 2.57
151 152 1.607225 TGCCCTACCTTCCCATTCAT 58.393 50.000 0.00 0.00 0.00 2.57
152 153 1.929494 TGCCCTACCTTCCCATTCATT 59.071 47.619 0.00 0.00 0.00 2.57
153 154 2.310538 GCCCTACCTTCCCATTCATTG 58.689 52.381 0.00 0.00 0.00 2.82
154 155 2.358195 GCCCTACCTTCCCATTCATTGT 60.358 50.000 0.00 0.00 0.00 2.71
155 156 3.555966 CCCTACCTTCCCATTCATTGTC 58.444 50.000 0.00 0.00 0.00 3.18
156 157 3.053693 CCCTACCTTCCCATTCATTGTCA 60.054 47.826 0.00 0.00 0.00 3.58
157 158 4.569653 CCCTACCTTCCCATTCATTGTCAA 60.570 45.833 0.00 0.00 0.00 3.18
158 159 5.203528 CCTACCTTCCCATTCATTGTCAAT 58.796 41.667 0.00 0.00 0.00 2.57
159 160 5.300286 CCTACCTTCCCATTCATTGTCAATC 59.700 44.000 0.00 0.00 0.00 2.67
160 161 4.026052 ACCTTCCCATTCATTGTCAATCC 58.974 43.478 0.00 0.00 0.00 3.01
161 162 4.025360 CCTTCCCATTCATTGTCAATCCA 58.975 43.478 0.00 0.00 0.00 3.41
162 163 4.142093 CCTTCCCATTCATTGTCAATCCAC 60.142 45.833 0.00 0.00 0.00 4.02
163 164 4.320546 TCCCATTCATTGTCAATCCACT 57.679 40.909 0.00 0.00 0.00 4.00
164 165 4.676109 TCCCATTCATTGTCAATCCACTT 58.324 39.130 0.00 0.00 0.00 3.16
165 166 5.085920 TCCCATTCATTGTCAATCCACTTT 58.914 37.500 0.00 0.00 0.00 2.66
166 167 5.543405 TCCCATTCATTGTCAATCCACTTTT 59.457 36.000 0.00 0.00 0.00 2.27
167 168 5.870978 CCCATTCATTGTCAATCCACTTTTC 59.129 40.000 0.00 0.00 0.00 2.29
168 169 6.457355 CCATTCATTGTCAATCCACTTTTCA 58.543 36.000 0.00 0.00 0.00 2.69
169 170 7.101054 CCATTCATTGTCAATCCACTTTTCAT 58.899 34.615 0.00 0.00 0.00 2.57
170 171 8.252417 CCATTCATTGTCAATCCACTTTTCATA 58.748 33.333 0.00 0.00 0.00 2.15
171 172 9.811995 CATTCATTGTCAATCCACTTTTCATAT 57.188 29.630 0.00 0.00 0.00 1.78
173 174 9.859427 TTCATTGTCAATCCACTTTTCATATTC 57.141 29.630 0.00 0.00 0.00 1.75
174 175 9.022884 TCATTGTCAATCCACTTTTCATATTCA 57.977 29.630 0.00 0.00 0.00 2.57
175 176 9.079833 CATTGTCAATCCACTTTTCATATTCAC 57.920 33.333 0.00 0.00 0.00 3.18
176 177 7.757941 TGTCAATCCACTTTTCATATTCACA 57.242 32.000 0.00 0.00 0.00 3.58
177 178 8.175925 TGTCAATCCACTTTTCATATTCACAA 57.824 30.769 0.00 0.00 0.00 3.33
178 179 8.298854 TGTCAATCCACTTTTCATATTCACAAG 58.701 33.333 0.00 0.00 0.00 3.16
179 180 7.274250 GTCAATCCACTTTTCATATTCACAAGC 59.726 37.037 0.00 0.00 0.00 4.01
180 181 7.177216 TCAATCCACTTTTCATATTCACAAGCT 59.823 33.333 0.00 0.00 0.00 3.74
181 182 8.461222 CAATCCACTTTTCATATTCACAAGCTA 58.539 33.333 0.00 0.00 0.00 3.32
182 183 8.757982 ATCCACTTTTCATATTCACAAGCTAT 57.242 30.769 0.00 0.00 0.00 2.97
183 184 9.851686 ATCCACTTTTCATATTCACAAGCTATA 57.148 29.630 0.00 0.00 0.00 1.31
184 185 9.679661 TCCACTTTTCATATTCACAAGCTATAA 57.320 29.630 0.00 0.00 0.00 0.98
190 191 9.474313 TTTCATATTCACAAGCTATAAAACCCT 57.526 29.630 0.00 0.00 0.00 4.34
191 192 9.474313 TTCATATTCACAAGCTATAAAACCCTT 57.526 29.630 0.00 0.00 0.00 3.95
192 193 9.120538 TCATATTCACAAGCTATAAAACCCTTC 57.879 33.333 0.00 0.00 0.00 3.46
193 194 8.902806 CATATTCACAAGCTATAAAACCCTTCA 58.097 33.333 0.00 0.00 0.00 3.02
194 195 7.775053 ATTCACAAGCTATAAAACCCTTCAA 57.225 32.000 0.00 0.00 0.00 2.69
195 196 7.589958 TTCACAAGCTATAAAACCCTTCAAA 57.410 32.000 0.00 0.00 0.00 2.69
196 197 7.775053 TCACAAGCTATAAAACCCTTCAAAT 57.225 32.000 0.00 0.00 0.00 2.32
197 198 7.601856 TCACAAGCTATAAAACCCTTCAAATG 58.398 34.615 0.00 0.00 0.00 2.32
198 199 7.450014 TCACAAGCTATAAAACCCTTCAAATGA 59.550 33.333 0.00 0.00 0.00 2.57
199 200 8.087750 CACAAGCTATAAAACCCTTCAAATGAA 58.912 33.333 0.00 0.00 0.00 2.57
200 201 8.646900 ACAAGCTATAAAACCCTTCAAATGAAA 58.353 29.630 0.00 0.00 33.07 2.69
201 202 9.487790 CAAGCTATAAAACCCTTCAAATGAAAA 57.512 29.630 0.00 0.00 33.07 2.29
202 203 9.489084 AAGCTATAAAACCCTTCAAATGAAAAC 57.511 29.630 0.00 0.00 33.07 2.43
203 204 8.094548 AGCTATAAAACCCTTCAAATGAAAACC 58.905 33.333 0.00 0.00 33.07 3.27
204 205 8.094548 GCTATAAAACCCTTCAAATGAAAACCT 58.905 33.333 0.00 0.00 33.07 3.50
207 208 7.669089 AAAACCCTTCAAATGAAAACCTAGA 57.331 32.000 0.00 0.00 33.07 2.43
208 209 7.669089 AAACCCTTCAAATGAAAACCTAGAA 57.331 32.000 0.00 0.00 33.07 2.10
209 210 7.669089 AACCCTTCAAATGAAAACCTAGAAA 57.331 32.000 0.00 0.00 33.07 2.52
210 211 7.050970 ACCCTTCAAATGAAAACCTAGAAAC 57.949 36.000 0.00 0.00 33.07 2.78
211 212 6.041637 ACCCTTCAAATGAAAACCTAGAAACC 59.958 38.462 0.00 0.00 33.07 3.27
212 213 6.267699 CCCTTCAAATGAAAACCTAGAAACCT 59.732 38.462 0.00 0.00 33.07 3.50
213 214 7.371159 CCTTCAAATGAAAACCTAGAAACCTC 58.629 38.462 0.00 0.00 33.07 3.85
214 215 7.231519 CCTTCAAATGAAAACCTAGAAACCTCT 59.768 37.037 0.00 0.00 33.07 3.69
215 216 8.533569 TTCAAATGAAAACCTAGAAACCTCTT 57.466 30.769 0.00 0.00 32.70 2.85
216 217 8.166422 TCAAATGAAAACCTAGAAACCTCTTC 57.834 34.615 0.00 0.00 32.70 2.87
217 218 7.230712 TCAAATGAAAACCTAGAAACCTCTTCC 59.769 37.037 0.00 0.00 32.70 3.46
218 219 5.906772 TGAAAACCTAGAAACCTCTTCCT 57.093 39.130 0.00 0.00 32.70 3.36
219 220 7.569599 ATGAAAACCTAGAAACCTCTTCCTA 57.430 36.000 0.00 0.00 32.70 2.94
220 221 7.005709 TGAAAACCTAGAAACCTCTTCCTAG 57.994 40.000 0.00 0.00 32.70 3.02
221 222 6.557633 TGAAAACCTAGAAACCTCTTCCTAGT 59.442 38.462 0.00 0.00 32.70 2.57
222 223 7.072076 TGAAAACCTAGAAACCTCTTCCTAGTT 59.928 37.037 0.00 0.00 32.70 2.24
223 224 6.361768 AACCTAGAAACCTCTTCCTAGTTG 57.638 41.667 0.00 0.00 32.70 3.16
224 225 4.223255 ACCTAGAAACCTCTTCCTAGTTGC 59.777 45.833 0.00 0.00 32.70 4.17
225 226 4.468153 CCTAGAAACCTCTTCCTAGTTGCT 59.532 45.833 0.00 0.00 33.82 3.91
226 227 4.545208 AGAAACCTCTTCCTAGTTGCTC 57.455 45.455 0.00 0.00 0.00 4.26
227 228 3.262151 AGAAACCTCTTCCTAGTTGCTCC 59.738 47.826 0.00 0.00 0.00 4.70
228 229 1.187087 ACCTCTTCCTAGTTGCTCCG 58.813 55.000 0.00 0.00 0.00 4.63
229 230 1.187087 CCTCTTCCTAGTTGCTCCGT 58.813 55.000 0.00 0.00 0.00 4.69
230 231 1.135333 CCTCTTCCTAGTTGCTCCGTC 59.865 57.143 0.00 0.00 0.00 4.79
231 232 0.809385 TCTTCCTAGTTGCTCCGTCG 59.191 55.000 0.00 0.00 0.00 5.12
232 233 0.526662 CTTCCTAGTTGCTCCGTCGT 59.473 55.000 0.00 0.00 0.00 4.34
233 234 1.741706 CTTCCTAGTTGCTCCGTCGTA 59.258 52.381 0.00 0.00 0.00 3.43
234 235 1.376543 TCCTAGTTGCTCCGTCGTAG 58.623 55.000 0.00 0.00 0.00 3.51
235 236 0.248539 CCTAGTTGCTCCGTCGTAGC 60.249 60.000 2.38 2.38 40.50 3.58
239 240 4.255126 TGCTCCGTCGTAGCAAAC 57.745 55.556 10.34 0.00 46.57 2.93
240 241 1.364536 TGCTCCGTCGTAGCAAACA 59.635 52.632 10.34 0.00 46.57 2.83
241 242 0.942410 TGCTCCGTCGTAGCAAACAC 60.942 55.000 10.34 0.00 46.57 3.32
242 243 1.941476 GCTCCGTCGTAGCAAACACG 61.941 60.000 4.77 0.00 39.83 4.49
243 244 1.941476 CTCCGTCGTAGCAAACACGC 61.941 60.000 0.00 0.00 39.23 5.34
244 245 2.468532 CGTCGTAGCAAACACGCC 59.531 61.111 0.00 0.00 39.23 5.68
245 246 2.468532 GTCGTAGCAAACACGCCG 59.531 61.111 0.00 0.00 39.23 6.46
246 247 2.017783 GTCGTAGCAAACACGCCGA 61.018 57.895 0.00 0.00 39.23 5.54
247 248 1.300003 TCGTAGCAAACACGCCGAA 60.300 52.632 0.00 0.00 39.23 4.30
248 249 1.154727 CGTAGCAAACACGCCGAAC 60.155 57.895 0.00 0.00 31.94 3.95
249 250 1.823260 CGTAGCAAACACGCCGAACA 61.823 55.000 0.00 0.00 31.94 3.18
250 251 0.110823 GTAGCAAACACGCCGAACAG 60.111 55.000 0.00 0.00 0.00 3.16
251 252 0.249531 TAGCAAACACGCCGAACAGA 60.250 50.000 0.00 0.00 0.00 3.41
252 253 1.082756 GCAAACACGCCGAACAGAG 60.083 57.895 0.00 0.00 0.00 3.35
253 254 1.082756 CAAACACGCCGAACAGAGC 60.083 57.895 0.00 0.00 0.00 4.09
422 423 2.271800 GTTACCTTGGCTCATGACTCG 58.728 52.381 0.00 0.00 0.00 4.18
473 474 1.209019 AGCTTCCTTGATGTCGCTGAT 59.791 47.619 0.00 0.00 0.00 2.90
497 498 0.392461 TCATTGCCGCCAAGGTAGAC 60.392 55.000 0.00 0.00 43.70 2.59
504 505 1.258445 CGCCAAGGTAGACTGGAGGT 61.258 60.000 0.00 0.00 0.00 3.85
505 506 0.250513 GCCAAGGTAGACTGGAGGTG 59.749 60.000 0.00 0.00 0.00 4.00
506 507 0.905357 CCAAGGTAGACTGGAGGTGG 59.095 60.000 0.00 0.00 0.00 4.61
507 508 0.905357 CAAGGTAGACTGGAGGTGGG 59.095 60.000 0.00 0.00 0.00 4.61
514 515 2.276740 CTGGAGGTGGGGAATGGC 59.723 66.667 0.00 0.00 0.00 4.40
543 544 3.877344 TTGATTGGTGGTGGCGGGG 62.877 63.158 0.00 0.00 0.00 5.73
567 568 1.372251 CGGTGCTAGCTATGAGGCG 60.372 63.158 17.23 0.00 37.29 5.52
607 880 2.270527 GGAGAGGCAGCTTGGGTC 59.729 66.667 0.00 0.00 0.00 4.46
608 881 2.125350 GAGAGGCAGCTTGGGTCG 60.125 66.667 0.00 0.00 0.00 4.79
700 973 0.944311 GAGGAAAGTTCTCGCGTGCA 60.944 55.000 5.77 0.00 0.00 4.57
741 2403 2.760650 GGGATTGGGAGGTAAAGCTTTG 59.239 50.000 22.02 0.00 0.00 2.77
746 2408 1.464734 GGAGGTAAAGCTTTGCTCCC 58.535 55.000 23.82 20.07 38.25 4.30
752 2414 6.013639 GGAGGTAAAGCTTTGCTCCCTATATA 60.014 42.308 23.82 0.00 38.25 0.86
766 2428 4.047883 CCCTATATATTGGGAGGGGAAGG 58.952 52.174 23.59 5.31 44.34 3.46
767 2429 3.459969 CCTATATATTGGGAGGGGAAGGC 59.540 52.174 5.37 0.00 0.00 4.35
768 2430 2.835696 TATATTGGGAGGGGAAGGCT 57.164 50.000 0.00 0.00 0.00 4.58
769 2431 1.152649 ATATTGGGAGGGGAAGGCTG 58.847 55.000 0.00 0.00 0.00 4.85
849 2512 6.976934 AAGGTTCTCTAGGAATGAGAGATC 57.023 41.667 3.34 3.28 46.77 2.75
850 2513 5.070001 AGGTTCTCTAGGAATGAGAGATCG 58.930 45.833 3.34 0.00 46.77 3.69
851 2514 5.067273 GGTTCTCTAGGAATGAGAGATCGA 58.933 45.833 3.34 0.00 46.77 3.59
852 2515 5.710099 GGTTCTCTAGGAATGAGAGATCGAT 59.290 44.000 0.00 0.00 46.77 3.59
900 2563 5.427378 TGTTGCACAGCTATAAATAGAGCA 58.573 37.500 9.48 4.64 42.66 4.26
961 2624 3.075134 AGTTCCTCATTCCTCAAGGCTTT 59.925 43.478 0.00 0.00 34.44 3.51
990 2653 1.646189 GTGCTTCTACTACCAGCAGC 58.354 55.000 0.00 0.00 44.15 5.25
1482 3253 1.702401 TCTGGTGACCCATTAGTTGCA 59.298 47.619 0.00 0.00 40.90 4.08
1488 3259 3.129287 GTGACCCATTAGTTGCATTCCTG 59.871 47.826 0.00 0.00 0.00 3.86
1505 3276 1.331214 CTGTGGGCATCAAACCTGTT 58.669 50.000 0.00 0.00 0.00 3.16
1632 3410 2.092968 TGATATTCCTGGCACCACTGAC 60.093 50.000 0.00 0.00 0.00 3.51
1657 3456 1.266989 CTTTCGGTCAGTGCCCTTTTC 59.733 52.381 0.00 0.00 0.00 2.29
1661 3460 1.814793 GGTCAGTGCCCTTTTCTCTC 58.185 55.000 0.00 0.00 0.00 3.20
1767 3567 2.120909 CCCACCATCGGCATTCACC 61.121 63.158 0.00 0.00 0.00 4.02
1972 3808 3.455910 TGCTACAAGCCTATGGATCAAGT 59.544 43.478 0.00 0.00 41.51 3.16
2058 3897 2.032178 GTCTTGTGTCCACTGTTTCTGC 59.968 50.000 0.00 0.00 0.00 4.26
2101 3944 8.169268 CAGCTCTTCGGTTAGTTTAATTAGTTG 58.831 37.037 0.00 0.00 0.00 3.16
2355 4292 9.673454 GTTTTGAACCTCGTACTATTTTCATTT 57.327 29.630 0.00 0.00 0.00 2.32
2830 5021 4.081322 ACAAGTAGTTTCAACGGATGGT 57.919 40.909 0.00 0.00 0.00 3.55
2926 5117 4.459330 TGTTCTCACATGGTCATTCACAA 58.541 39.130 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.813754 CAGTTGAATTTGAGGGCGAGAA 59.186 45.455 0.00 0.00 0.00 2.87
1 2 2.426522 CAGTTGAATTTGAGGGCGAGA 58.573 47.619 0.00 0.00 0.00 4.04
2 3 1.135575 GCAGTTGAATTTGAGGGCGAG 60.136 52.381 0.00 0.00 0.00 5.03
3 4 0.881118 GCAGTTGAATTTGAGGGCGA 59.119 50.000 0.00 0.00 0.00 5.54
4 5 0.883833 AGCAGTTGAATTTGAGGGCG 59.116 50.000 0.00 0.00 0.00 6.13
5 6 2.163211 GAGAGCAGTTGAATTTGAGGGC 59.837 50.000 0.00 0.00 0.00 5.19
6 7 3.439476 CAGAGAGCAGTTGAATTTGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
7 8 4.070716 ACAGAGAGCAGTTGAATTTGAGG 58.929 43.478 0.00 0.00 0.00 3.86
8 9 4.613167 GCACAGAGAGCAGTTGAATTTGAG 60.613 45.833 0.00 0.00 0.00 3.02
9 10 3.251729 GCACAGAGAGCAGTTGAATTTGA 59.748 43.478 0.00 0.00 0.00 2.69
10 11 3.004002 TGCACAGAGAGCAGTTGAATTTG 59.996 43.478 0.00 0.00 37.02 2.32
11 12 3.216800 TGCACAGAGAGCAGTTGAATTT 58.783 40.909 0.00 0.00 37.02 1.82
12 13 2.854963 TGCACAGAGAGCAGTTGAATT 58.145 42.857 0.00 0.00 37.02 2.17
13 14 2.556144 TGCACAGAGAGCAGTTGAAT 57.444 45.000 0.00 0.00 37.02 2.57
14 15 2.038164 AGATGCACAGAGAGCAGTTGAA 59.962 45.455 0.00 0.00 46.36 2.69
15 16 1.622312 AGATGCACAGAGAGCAGTTGA 59.378 47.619 0.00 0.00 46.36 3.18
16 17 2.096220 AGATGCACAGAGAGCAGTTG 57.904 50.000 0.00 0.00 46.36 3.16
17 18 2.812591 CAAAGATGCACAGAGAGCAGTT 59.187 45.455 0.00 0.00 46.36 3.16
18 19 2.424557 CAAAGATGCACAGAGAGCAGT 58.575 47.619 0.00 0.00 46.36 4.40
31 32 0.468771 GGGGGATGAGGGCAAAGATG 60.469 60.000 0.00 0.00 0.00 2.90
32 33 0.628668 AGGGGGATGAGGGCAAAGAT 60.629 55.000 0.00 0.00 0.00 2.40
33 34 0.045623 TAGGGGGATGAGGGCAAAGA 59.954 55.000 0.00 0.00 0.00 2.52
34 35 1.152649 ATAGGGGGATGAGGGCAAAG 58.847 55.000 0.00 0.00 0.00 2.77
35 36 1.619298 AATAGGGGGATGAGGGCAAA 58.381 50.000 0.00 0.00 0.00 3.68
36 37 1.217689 CAAATAGGGGGATGAGGGCAA 59.782 52.381 0.00 0.00 0.00 4.52
37 38 0.852842 CAAATAGGGGGATGAGGGCA 59.147 55.000 0.00 0.00 0.00 5.36
38 39 1.149101 TCAAATAGGGGGATGAGGGC 58.851 55.000 0.00 0.00 0.00 5.19
39 40 4.475919 AATTCAAATAGGGGGATGAGGG 57.524 45.455 0.00 0.00 0.00 4.30
40 41 5.457686 TGAAATTCAAATAGGGGGATGAGG 58.542 41.667 0.00 0.00 0.00 3.86
41 42 7.508296 AGATTGAAATTCAAATAGGGGGATGAG 59.492 37.037 12.75 0.00 40.12 2.90
42 43 7.364627 AGATTGAAATTCAAATAGGGGGATGA 58.635 34.615 12.75 0.00 40.12 2.92
43 44 7.288389 TGAGATTGAAATTCAAATAGGGGGATG 59.712 37.037 12.75 0.00 40.12 3.51
44 45 7.364627 TGAGATTGAAATTCAAATAGGGGGAT 58.635 34.615 12.75 0.00 40.12 3.85
45 46 6.740693 TGAGATTGAAATTCAAATAGGGGGA 58.259 36.000 12.75 0.00 40.12 4.81
46 47 7.422465 TTGAGATTGAAATTCAAATAGGGGG 57.578 36.000 12.75 0.00 40.12 5.40
47 48 9.895138 AAATTGAGATTGAAATTCAAATAGGGG 57.105 29.630 12.75 0.00 40.12 4.79
53 54 9.526713 TCAACGAAATTGAGATTGAAATTCAAA 57.473 25.926 12.75 0.00 42.62 2.69
68 69 7.141363 ACTGGAGAAAAGAATCAACGAAATTG 58.859 34.615 0.00 0.00 39.94 2.32
69 70 7.277174 ACTGGAGAAAAGAATCAACGAAATT 57.723 32.000 0.00 0.00 0.00 1.82
70 71 6.884280 ACTGGAGAAAAGAATCAACGAAAT 57.116 33.333 0.00 0.00 0.00 2.17
71 72 6.693315 AACTGGAGAAAAGAATCAACGAAA 57.307 33.333 0.00 0.00 0.00 3.46
72 73 6.094881 ACAAACTGGAGAAAAGAATCAACGAA 59.905 34.615 0.00 0.00 0.00 3.85
73 74 5.588648 ACAAACTGGAGAAAAGAATCAACGA 59.411 36.000 0.00 0.00 0.00 3.85
74 75 5.821204 ACAAACTGGAGAAAAGAATCAACG 58.179 37.500 0.00 0.00 0.00 4.10
75 76 7.035612 ACAACAAACTGGAGAAAAGAATCAAC 58.964 34.615 0.00 0.00 0.00 3.18
76 77 7.169158 ACAACAAACTGGAGAAAAGAATCAA 57.831 32.000 0.00 0.00 0.00 2.57
77 78 6.773976 ACAACAAACTGGAGAAAAGAATCA 57.226 33.333 0.00 0.00 0.00 2.57
78 79 7.484140 AGAACAACAAACTGGAGAAAAGAATC 58.516 34.615 0.00 0.00 0.00 2.52
79 80 7.410120 AGAACAACAAACTGGAGAAAAGAAT 57.590 32.000 0.00 0.00 0.00 2.40
80 81 6.834168 AGAACAACAAACTGGAGAAAAGAA 57.166 33.333 0.00 0.00 0.00 2.52
81 82 6.659242 AGAAGAACAACAAACTGGAGAAAAGA 59.341 34.615 0.00 0.00 0.00 2.52
82 83 6.856895 AGAAGAACAACAAACTGGAGAAAAG 58.143 36.000 0.00 0.00 0.00 2.27
83 84 6.834168 AGAAGAACAACAAACTGGAGAAAA 57.166 33.333 0.00 0.00 0.00 2.29
84 85 6.834168 AAGAAGAACAACAAACTGGAGAAA 57.166 33.333 0.00 0.00 0.00 2.52
85 86 6.620678 CAAAGAAGAACAACAAACTGGAGAA 58.379 36.000 0.00 0.00 0.00 2.87
86 87 5.393027 GCAAAGAAGAACAACAAACTGGAGA 60.393 40.000 0.00 0.00 0.00 3.71
87 88 4.800471 GCAAAGAAGAACAACAAACTGGAG 59.200 41.667 0.00 0.00 0.00 3.86
88 89 4.219507 TGCAAAGAAGAACAACAAACTGGA 59.780 37.500 0.00 0.00 0.00 3.86
89 90 4.493547 TGCAAAGAAGAACAACAAACTGG 58.506 39.130 0.00 0.00 0.00 4.00
90 91 5.404968 TGTTGCAAAGAAGAACAACAAACTG 59.595 36.000 0.00 0.00 46.72 3.16
91 92 5.537188 TGTTGCAAAGAAGAACAACAAACT 58.463 33.333 0.00 0.00 46.72 2.66
92 93 5.837586 TGTTGCAAAGAAGAACAACAAAC 57.162 34.783 0.00 0.00 46.72 2.93
96 97 4.204978 CGTGATGTTGCAAAGAAGAACAAC 59.795 41.667 0.00 0.00 42.10 3.32
97 98 4.095632 TCGTGATGTTGCAAAGAAGAACAA 59.904 37.500 0.00 0.00 33.50 2.83
98 99 3.625313 TCGTGATGTTGCAAAGAAGAACA 59.375 39.130 0.00 0.00 34.25 3.18
99 100 4.209452 TCGTGATGTTGCAAAGAAGAAC 57.791 40.909 0.00 0.00 0.00 3.01
100 101 4.891627 TTCGTGATGTTGCAAAGAAGAA 57.108 36.364 0.00 0.00 0.00 2.52
101 102 4.514816 TCATTCGTGATGTTGCAAAGAAGA 59.485 37.500 0.00 0.00 37.06 2.87
102 103 4.614284 GTCATTCGTGATGTTGCAAAGAAG 59.386 41.667 0.00 0.00 37.06 2.85
103 104 4.036144 TGTCATTCGTGATGTTGCAAAGAA 59.964 37.500 0.00 1.12 37.06 2.52
104 105 3.563390 TGTCATTCGTGATGTTGCAAAGA 59.437 39.130 0.00 0.00 37.06 2.52
105 106 3.887741 TGTCATTCGTGATGTTGCAAAG 58.112 40.909 0.00 0.00 37.06 2.77
106 107 3.978718 TGTCATTCGTGATGTTGCAAA 57.021 38.095 0.00 0.00 37.06 3.68
107 108 3.752747 AGATGTCATTCGTGATGTTGCAA 59.247 39.130 0.00 0.00 37.06 4.08
108 109 3.337358 AGATGTCATTCGTGATGTTGCA 58.663 40.909 0.00 0.00 37.06 4.08
109 110 4.346734 AAGATGTCATTCGTGATGTTGC 57.653 40.909 0.00 0.00 37.06 4.17
110 111 5.060077 GCAAAAGATGTCATTCGTGATGTTG 59.940 40.000 0.00 0.00 37.06 3.33
111 112 5.156355 GCAAAAGATGTCATTCGTGATGTT 58.844 37.500 0.00 0.00 37.06 2.71
112 113 4.379813 GGCAAAAGATGTCATTCGTGATGT 60.380 41.667 0.00 0.00 37.06 3.06
113 114 4.100529 GGCAAAAGATGTCATTCGTGATG 58.899 43.478 0.00 0.00 37.08 3.07
114 115 3.129287 GGGCAAAAGATGTCATTCGTGAT 59.871 43.478 0.00 0.00 34.42 3.06
115 116 2.487762 GGGCAAAAGATGTCATTCGTGA 59.512 45.455 0.00 0.00 34.42 4.35
116 117 2.489329 AGGGCAAAAGATGTCATTCGTG 59.511 45.455 0.00 0.00 34.42 4.35
117 118 2.795329 AGGGCAAAAGATGTCATTCGT 58.205 42.857 0.00 0.00 34.42 3.85
118 119 3.065371 GGTAGGGCAAAAGATGTCATTCG 59.935 47.826 0.00 0.00 34.42 3.34
119 120 4.273318 AGGTAGGGCAAAAGATGTCATTC 58.727 43.478 0.00 0.00 34.42 2.67
120 121 4.322057 AGGTAGGGCAAAAGATGTCATT 57.678 40.909 0.00 0.00 34.42 2.57
121 122 4.273318 GAAGGTAGGGCAAAAGATGTCAT 58.727 43.478 0.00 0.00 34.42 3.06
122 123 3.561313 GGAAGGTAGGGCAAAAGATGTCA 60.561 47.826 0.00 0.00 34.42 3.58
123 124 3.017442 GGAAGGTAGGGCAAAAGATGTC 58.983 50.000 0.00 0.00 0.00 3.06
124 125 2.291605 GGGAAGGTAGGGCAAAAGATGT 60.292 50.000 0.00 0.00 0.00 3.06
125 126 2.291540 TGGGAAGGTAGGGCAAAAGATG 60.292 50.000 0.00 0.00 0.00 2.90
126 127 2.000048 TGGGAAGGTAGGGCAAAAGAT 59.000 47.619 0.00 0.00 0.00 2.40
127 128 1.451449 TGGGAAGGTAGGGCAAAAGA 58.549 50.000 0.00 0.00 0.00 2.52
128 129 2.532250 ATGGGAAGGTAGGGCAAAAG 57.468 50.000 0.00 0.00 0.00 2.27
129 130 2.110899 TGAATGGGAAGGTAGGGCAAAA 59.889 45.455 0.00 0.00 0.00 2.44
130 131 1.713647 TGAATGGGAAGGTAGGGCAAA 59.286 47.619 0.00 0.00 0.00 3.68
131 132 1.377690 TGAATGGGAAGGTAGGGCAA 58.622 50.000 0.00 0.00 0.00 4.52
132 133 1.607225 ATGAATGGGAAGGTAGGGCA 58.393 50.000 0.00 0.00 0.00 5.36
133 134 2.310538 CAATGAATGGGAAGGTAGGGC 58.689 52.381 0.00 0.00 0.00 5.19
134 135 3.053693 TGACAATGAATGGGAAGGTAGGG 60.054 47.826 0.00 0.00 0.00 3.53
135 136 4.235079 TGACAATGAATGGGAAGGTAGG 57.765 45.455 0.00 0.00 0.00 3.18
136 137 5.300286 GGATTGACAATGAATGGGAAGGTAG 59.700 44.000 5.14 0.00 0.00 3.18
137 138 5.200483 GGATTGACAATGAATGGGAAGGTA 58.800 41.667 5.14 0.00 0.00 3.08
138 139 4.026052 GGATTGACAATGAATGGGAAGGT 58.974 43.478 5.14 0.00 0.00 3.50
139 140 4.025360 TGGATTGACAATGAATGGGAAGG 58.975 43.478 5.14 0.00 0.00 3.46
140 141 4.708421 AGTGGATTGACAATGAATGGGAAG 59.292 41.667 5.14 0.00 0.00 3.46
141 142 4.676109 AGTGGATTGACAATGAATGGGAA 58.324 39.130 5.14 0.00 0.00 3.97
142 143 4.320546 AGTGGATTGACAATGAATGGGA 57.679 40.909 5.14 0.00 0.00 4.37
143 144 5.410355 AAAGTGGATTGACAATGAATGGG 57.590 39.130 5.14 0.00 0.00 4.00
144 145 6.457355 TGAAAAGTGGATTGACAATGAATGG 58.543 36.000 5.14 0.00 0.00 3.16
145 146 9.811995 ATATGAAAAGTGGATTGACAATGAATG 57.188 29.630 5.14 0.00 0.00 2.67
147 148 9.859427 GAATATGAAAAGTGGATTGACAATGAA 57.141 29.630 5.14 0.00 0.00 2.57
148 149 9.022884 TGAATATGAAAAGTGGATTGACAATGA 57.977 29.630 5.14 0.00 0.00 2.57
149 150 9.079833 GTGAATATGAAAAGTGGATTGACAATG 57.920 33.333 5.14 0.00 0.00 2.82
150 151 8.805175 TGTGAATATGAAAAGTGGATTGACAAT 58.195 29.630 0.00 0.00 0.00 2.71
151 152 8.175925 TGTGAATATGAAAAGTGGATTGACAA 57.824 30.769 0.00 0.00 0.00 3.18
152 153 7.757941 TGTGAATATGAAAAGTGGATTGACA 57.242 32.000 0.00 0.00 0.00 3.58
153 154 7.274250 GCTTGTGAATATGAAAAGTGGATTGAC 59.726 37.037 0.00 0.00 0.00 3.18
154 155 7.177216 AGCTTGTGAATATGAAAAGTGGATTGA 59.823 33.333 0.00 0.00 0.00 2.57
155 156 7.318141 AGCTTGTGAATATGAAAAGTGGATTG 58.682 34.615 0.00 0.00 0.00 2.67
156 157 7.472334 AGCTTGTGAATATGAAAAGTGGATT 57.528 32.000 0.00 0.00 0.00 3.01
157 158 8.757982 ATAGCTTGTGAATATGAAAAGTGGAT 57.242 30.769 0.00 0.00 0.00 3.41
158 159 9.679661 TTATAGCTTGTGAATATGAAAAGTGGA 57.320 29.630 0.00 0.00 0.00 4.02
164 165 9.474313 AGGGTTTTATAGCTTGTGAATATGAAA 57.526 29.630 0.00 0.00 0.00 2.69
165 166 9.474313 AAGGGTTTTATAGCTTGTGAATATGAA 57.526 29.630 0.00 0.00 0.00 2.57
166 167 9.120538 GAAGGGTTTTATAGCTTGTGAATATGA 57.879 33.333 0.00 0.00 0.00 2.15
167 168 8.902806 TGAAGGGTTTTATAGCTTGTGAATATG 58.097 33.333 0.00 0.00 0.00 1.78
168 169 9.474313 TTGAAGGGTTTTATAGCTTGTGAATAT 57.526 29.630 0.00 0.00 0.00 1.28
169 170 8.871629 TTGAAGGGTTTTATAGCTTGTGAATA 57.128 30.769 0.00 0.00 0.00 1.75
170 171 7.775053 TTGAAGGGTTTTATAGCTTGTGAAT 57.225 32.000 0.00 0.00 0.00 2.57
171 172 7.589958 TTTGAAGGGTTTTATAGCTTGTGAA 57.410 32.000 0.00 0.00 0.00 3.18
172 173 7.450014 TCATTTGAAGGGTTTTATAGCTTGTGA 59.550 33.333 0.00 0.00 0.00 3.58
173 174 7.601856 TCATTTGAAGGGTTTTATAGCTTGTG 58.398 34.615 0.00 0.00 0.00 3.33
174 175 7.775053 TCATTTGAAGGGTTTTATAGCTTGT 57.225 32.000 0.00 0.00 0.00 3.16
175 176 9.487790 TTTTCATTTGAAGGGTTTTATAGCTTG 57.512 29.630 0.00 0.00 35.21 4.01
176 177 9.489084 GTTTTCATTTGAAGGGTTTTATAGCTT 57.511 29.630 0.00 0.00 35.21 3.74
177 178 8.094548 GGTTTTCATTTGAAGGGTTTTATAGCT 58.905 33.333 0.00 0.00 35.21 3.32
178 179 8.094548 AGGTTTTCATTTGAAGGGTTTTATAGC 58.905 33.333 0.00 0.00 35.21 2.97
181 182 9.374711 TCTAGGTTTTCATTTGAAGGGTTTTAT 57.625 29.630 0.00 0.00 35.21 1.40
182 183 8.770010 TCTAGGTTTTCATTTGAAGGGTTTTA 57.230 30.769 0.00 0.00 35.21 1.52
183 184 7.669089 TCTAGGTTTTCATTTGAAGGGTTTT 57.331 32.000 0.00 0.00 35.21 2.43
184 185 7.669089 TTCTAGGTTTTCATTTGAAGGGTTT 57.331 32.000 0.00 0.00 35.21 3.27
185 186 7.418597 GGTTTCTAGGTTTTCATTTGAAGGGTT 60.419 37.037 0.00 0.00 35.21 4.11
186 187 6.041637 GGTTTCTAGGTTTTCATTTGAAGGGT 59.958 38.462 0.00 0.00 35.21 4.34
187 188 6.267699 AGGTTTCTAGGTTTTCATTTGAAGGG 59.732 38.462 0.00 0.00 35.21 3.95
188 189 7.231519 AGAGGTTTCTAGGTTTTCATTTGAAGG 59.768 37.037 0.00 0.00 35.21 3.46
189 190 8.171164 AGAGGTTTCTAGGTTTTCATTTGAAG 57.829 34.615 0.00 0.00 35.21 3.02
190 191 8.533569 AAGAGGTTTCTAGGTTTTCATTTGAA 57.466 30.769 0.00 0.00 31.96 2.69
191 192 7.230712 GGAAGAGGTTTCTAGGTTTTCATTTGA 59.769 37.037 0.00 0.00 31.96 2.69
192 193 7.231519 AGGAAGAGGTTTCTAGGTTTTCATTTG 59.768 37.037 0.00 0.00 31.96 2.32
193 194 7.298374 AGGAAGAGGTTTCTAGGTTTTCATTT 58.702 34.615 0.00 0.00 31.96 2.32
194 195 6.853490 AGGAAGAGGTTTCTAGGTTTTCATT 58.147 36.000 0.00 0.00 31.96 2.57
195 196 6.455690 AGGAAGAGGTTTCTAGGTTTTCAT 57.544 37.500 0.00 0.00 31.96 2.57
196 197 5.906772 AGGAAGAGGTTTCTAGGTTTTCA 57.093 39.130 0.00 0.00 31.96 2.69
197 198 7.006865 ACTAGGAAGAGGTTTCTAGGTTTTC 57.993 40.000 5.62 0.00 43.88 2.29
198 199 7.225011 CAACTAGGAAGAGGTTTCTAGGTTTT 58.775 38.462 5.62 0.00 38.51 2.43
199 200 6.744622 GCAACTAGGAAGAGGTTTCTAGGTTT 60.745 42.308 5.62 0.00 38.51 3.27
200 201 5.280062 GCAACTAGGAAGAGGTTTCTAGGTT 60.280 44.000 5.62 0.00 38.51 3.50
201 202 4.223255 GCAACTAGGAAGAGGTTTCTAGGT 59.777 45.833 5.62 0.00 41.94 3.08
202 203 4.468153 AGCAACTAGGAAGAGGTTTCTAGG 59.532 45.833 5.62 0.00 43.88 3.02
203 204 5.394773 GGAGCAACTAGGAAGAGGTTTCTAG 60.395 48.000 0.00 0.00 44.79 2.43
204 205 4.466726 GGAGCAACTAGGAAGAGGTTTCTA 59.533 45.833 0.00 0.00 31.96 2.10
205 206 3.262151 GGAGCAACTAGGAAGAGGTTTCT 59.738 47.826 0.00 0.00 34.29 2.52
206 207 3.601435 GGAGCAACTAGGAAGAGGTTTC 58.399 50.000 0.00 0.00 0.00 2.78
207 208 2.028020 CGGAGCAACTAGGAAGAGGTTT 60.028 50.000 0.00 0.00 0.00 3.27
208 209 1.550976 CGGAGCAACTAGGAAGAGGTT 59.449 52.381 0.00 0.00 0.00 3.50
209 210 1.187087 CGGAGCAACTAGGAAGAGGT 58.813 55.000 0.00 0.00 0.00 3.85
210 211 1.135333 GACGGAGCAACTAGGAAGAGG 59.865 57.143 0.00 0.00 0.00 3.69
211 212 1.202200 CGACGGAGCAACTAGGAAGAG 60.202 57.143 0.00 0.00 0.00 2.85
212 213 0.809385 CGACGGAGCAACTAGGAAGA 59.191 55.000 0.00 0.00 0.00 2.87
213 214 0.526662 ACGACGGAGCAACTAGGAAG 59.473 55.000 0.00 0.00 0.00 3.46
214 215 1.741706 CTACGACGGAGCAACTAGGAA 59.258 52.381 0.00 0.00 0.00 3.36
215 216 1.376543 CTACGACGGAGCAACTAGGA 58.623 55.000 0.00 0.00 0.00 2.94
216 217 0.248539 GCTACGACGGAGCAACTAGG 60.249 60.000 27.04 0.00 39.84 3.02
217 218 0.450583 TGCTACGACGGAGCAACTAG 59.549 55.000 31.87 7.15 46.71 2.57
218 219 2.558617 TGCTACGACGGAGCAACTA 58.441 52.632 31.87 9.19 46.71 2.24
219 220 3.362262 TGCTACGACGGAGCAACT 58.638 55.556 31.87 0.00 46.71 3.16
223 224 1.779683 GTGTTTGCTACGACGGAGC 59.220 57.895 25.40 25.40 40.53 4.70
224 225 1.941476 GCGTGTTTGCTACGACGGAG 61.941 60.000 1.58 1.58 43.82 4.63
225 226 2.017783 GCGTGTTTGCTACGACGGA 61.018 57.895 0.00 0.00 43.82 4.69
226 227 2.468532 GCGTGTTTGCTACGACGG 59.531 61.111 0.00 0.00 43.82 4.79
227 228 2.468532 GGCGTGTTTGCTACGACG 59.531 61.111 1.32 0.00 43.82 5.12
228 229 1.550659 TTCGGCGTGTTTGCTACGAC 61.551 55.000 6.85 0.00 45.73 4.34
229 230 1.300003 TTCGGCGTGTTTGCTACGA 60.300 52.632 6.85 0.00 43.82 3.43
230 231 1.154727 GTTCGGCGTGTTTGCTACG 60.155 57.895 6.85 0.00 43.93 3.51
231 232 0.110823 CTGTTCGGCGTGTTTGCTAC 60.111 55.000 6.85 0.00 34.52 3.58
232 233 0.249531 TCTGTTCGGCGTGTTTGCTA 60.250 50.000 6.85 0.00 34.52 3.49
233 234 1.498865 CTCTGTTCGGCGTGTTTGCT 61.499 55.000 6.85 0.00 34.52 3.91
234 235 1.082756 CTCTGTTCGGCGTGTTTGC 60.083 57.895 6.85 0.00 0.00 3.68
235 236 1.082756 GCTCTGTTCGGCGTGTTTG 60.083 57.895 6.85 0.00 0.00 2.93
236 237 0.884704 ATGCTCTGTTCGGCGTGTTT 60.885 50.000 6.85 0.00 0.00 2.83
237 238 0.037697 TATGCTCTGTTCGGCGTGTT 60.038 50.000 6.85 0.00 0.00 3.32
238 239 0.458543 CTATGCTCTGTTCGGCGTGT 60.459 55.000 6.85 0.00 0.00 4.49
239 240 1.148157 CCTATGCTCTGTTCGGCGTG 61.148 60.000 6.85 0.00 0.00 5.34
240 241 1.141881 CCTATGCTCTGTTCGGCGT 59.858 57.895 6.85 0.00 0.00 5.68
241 242 0.596083 CTCCTATGCTCTGTTCGGCG 60.596 60.000 0.00 0.00 0.00 6.46
242 243 0.747255 TCTCCTATGCTCTGTTCGGC 59.253 55.000 0.00 0.00 0.00 5.54
243 244 2.865670 GCATCTCCTATGCTCTGTTCGG 60.866 54.545 2.78 0.00 41.52 4.30
244 245 2.402305 GCATCTCCTATGCTCTGTTCG 58.598 52.381 2.78 0.00 41.52 3.95
245 246 2.549778 GGGCATCTCCTATGCTCTGTTC 60.550 54.545 9.60 0.00 42.03 3.18
246 247 1.419387 GGGCATCTCCTATGCTCTGTT 59.581 52.381 9.60 0.00 42.03 3.16
247 248 1.055040 GGGCATCTCCTATGCTCTGT 58.945 55.000 9.60 0.00 42.03 3.41
248 249 1.054231 TGGGCATCTCCTATGCTCTG 58.946 55.000 10.89 0.00 45.35 3.35
249 250 1.055040 GTGGGCATCTCCTATGCTCT 58.945 55.000 10.89 0.00 45.35 4.09
250 251 0.761187 TGTGGGCATCTCCTATGCTC 59.239 55.000 9.60 6.42 45.35 4.26
251 252 1.350351 GATGTGGGCATCTCCTATGCT 59.650 52.381 9.60 0.00 45.97 3.79
252 253 1.818642 GATGTGGGCATCTCCTATGC 58.181 55.000 1.33 1.33 45.97 3.14
306 307 3.821033 GGCTCCCGCAATTTGAATACTAT 59.179 43.478 0.00 0.00 38.10 2.12
437 438 3.622826 CTCGTTGGTCCCACCGGT 61.623 66.667 0.00 0.00 42.58 5.28
453 454 0.610174 TCAGCGACATCAAGGAAGCT 59.390 50.000 0.00 0.00 35.06 3.74
473 474 1.314534 CCTTGGCGGCAATGATGACA 61.315 55.000 25.71 0.00 32.33 3.58
497 498 2.276740 GCCATTCCCCACCTCCAG 59.723 66.667 0.00 0.00 0.00 3.86
514 515 2.176546 CAATCAACCAGCGTGCCG 59.823 61.111 0.00 0.00 0.00 5.69
520 521 1.966762 CCACCACCAATCAACCAGC 59.033 57.895 0.00 0.00 0.00 4.85
522 523 1.900981 CGCCACCACCAATCAACCA 60.901 57.895 0.00 0.00 0.00 3.67
523 524 2.635443 CCGCCACCACCAATCAACC 61.635 63.158 0.00 0.00 0.00 3.77
543 544 2.857744 ATAGCTAGCACCGTCGCCC 61.858 63.158 18.83 0.00 0.00 6.13
551 552 1.212616 CAACGCCTCATAGCTAGCAC 58.787 55.000 18.83 0.00 0.00 4.40
552 553 0.104855 CCAACGCCTCATAGCTAGCA 59.895 55.000 18.83 3.19 0.00 3.49
553 554 0.105039 ACCAACGCCTCATAGCTAGC 59.895 55.000 6.62 6.62 0.00 3.42
559 560 1.827394 GGCCTACCAACGCCTCATA 59.173 57.895 0.00 0.00 42.21 2.15
567 568 1.474330 CCCATTCAAGGCCTACCAAC 58.526 55.000 5.16 0.00 39.06 3.77
700 973 1.427753 CCTCCCCAAAACCCTAGTTGT 59.572 52.381 0.00 0.00 35.97 3.32
746 2408 4.164988 CAGCCTTCCCCTCCCAATATATAG 59.835 50.000 0.00 0.00 0.00 1.31
752 2414 1.149133 AACAGCCTTCCCCTCCCAAT 61.149 55.000 0.00 0.00 0.00 3.16
849 2512 0.179215 GGTCGAAGCACAGCAAATCG 60.179 55.000 0.00 0.00 34.52 3.34
850 2513 0.874390 TGGTCGAAGCACAGCAAATC 59.126 50.000 0.00 0.00 0.00 2.17
851 2514 0.877071 CTGGTCGAAGCACAGCAAAT 59.123 50.000 0.00 0.00 0.00 2.32
852 2515 0.179059 TCTGGTCGAAGCACAGCAAA 60.179 50.000 0.00 0.00 32.52 3.68
900 2563 0.389391 CGAGATTGGGTGGCGTAGAT 59.611 55.000 0.00 0.00 0.00 1.98
1068 2731 3.131396 GGTCACCGTCATATTCACCATC 58.869 50.000 0.00 0.00 0.00 3.51
1070 2733 2.184533 AGGTCACCGTCATATTCACCA 58.815 47.619 0.00 0.00 0.00 4.17
1158 2821 3.158648 CCGCCCGGGACCTGAATA 61.159 66.667 29.31 0.00 38.47 1.75
1261 2932 5.292765 CAATCATACTCGGTTATCAGCTGT 58.707 41.667 14.67 3.75 0.00 4.40
1482 3253 1.077663 AGGTTTGATGCCCACAGGAAT 59.922 47.619 0.00 0.00 31.86 3.01
1488 3259 2.514803 ACTAACAGGTTTGATGCCCAC 58.485 47.619 0.79 0.00 0.00 4.61
1632 3410 1.493311 GCACTGACCGAAAGAAGCG 59.507 57.895 0.00 0.00 0.00 4.68
1657 3456 7.284034 ACAAATTAAGGATGTAGCCAATGAGAG 59.716 37.037 0.00 0.00 0.00 3.20
1661 3460 7.198390 CAGACAAATTAAGGATGTAGCCAATG 58.802 38.462 0.00 0.00 0.00 2.82
1767 3567 1.213094 AACAGCACGAAGACGAACCG 61.213 55.000 0.00 0.00 42.66 4.44
1972 3808 6.698380 GCTAATACCAGTAGCTAAGCCATAA 58.302 40.000 0.00 0.00 40.71 1.90
2017 3853 6.715347 AGACCACAAGCAAACTCTTATTTT 57.285 33.333 0.00 0.00 0.00 1.82
2058 3897 4.947388 AGAGCTGAACAGTAGGAAGACTAG 59.053 45.833 0.00 0.00 30.77 2.57
2101 3944 3.090037 TCACAGGTTGACTAGTAGGAGC 58.910 50.000 0.00 0.00 0.00 4.70
2355 4292 5.104900 GCCTTAAAGATGAGGTCCTTACAGA 60.105 44.000 0.00 0.00 34.81 3.41
2411 4416 4.157105 CAGACAATCAAGATCAACCATGCA 59.843 41.667 0.00 0.00 0.00 3.96
2412 4417 4.397103 TCAGACAATCAAGATCAACCATGC 59.603 41.667 0.00 0.00 0.00 4.06
2413 4418 5.646793 ACTCAGACAATCAAGATCAACCATG 59.353 40.000 0.00 0.00 0.00 3.66
2414 4419 5.813383 ACTCAGACAATCAAGATCAACCAT 58.187 37.500 0.00 0.00 0.00 3.55
2830 5021 9.214957 CACTCCAATCTACTTTGTGTAATTGTA 57.785 33.333 0.00 0.00 33.24 2.41
2895 5086 5.239306 TGACCATGTGAGAACATTTGAACTC 59.761 40.000 0.00 0.00 0.00 3.01
2907 5098 3.559811 CCCTTGTGAATGACCATGTGAGA 60.560 47.826 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.