Multiple sequence alignment - TraesCS6A01G363600

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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 TraesCS6A01G363600 chr6A 100.000 3020 0 0 1 3020 592598659 592601678 0.000000e+00 5578.0
1 TraesCS6A01G363600 chr6A 89.298 1710 168 9 714 2419 592469259 592467561 0.000000e+00 2130.0
2 TraesCS6A01G363600 chr6A 84.301 1637 236 16 804 2433 592458970 592457348 0.000000e+00 1580.0
3 TraesCS6A01G363600 chr6A 84.015 1614 242 11 812 2419 556038481 556036878 0.000000e+00 1537.0
4 TraesCS6A01G363600 chr6B 95.269 2325 79 14 714 3020 673764099 673766410 0.000000e+00 3655.0
5 TraesCS6A01G363600 chr6B 88.232 1691 173 13 739 2419 672499567 672497893 0.000000e+00 1997.0
6 TraesCS6A01G363600 chr6B 82.730 1714 274 16 806 2512 618670276 618668578 0.000000e+00 1506.0
7 TraesCS6A01G363600 chr6B 90.099 303 23 3 209 504 672500180 672499878 1.310000e-103 387.0
8 TraesCS6A01G363600 chr6B 85.906 298 26 4 209 498 673763526 673763815 1.360000e-78 303.0
9 TraesCS6A01G363600 chr6B 91.743 218 16 2 496 713 673763846 673764061 4.890000e-78 302.0
10 TraesCS6A01G363600 chr6B 89.450 218 21 2 496 713 22118397 22118182 1.070000e-69 274.0
11 TraesCS6A01G363600 chr6B 89.450 218 19 4 496 713 9112476 9112263 3.840000e-69 272.0
12 TraesCS6A01G363600 chr6B 88.991 218 22 2 496 713 9132055 9131840 4.960000e-68 268.0
13 TraesCS6A01G363600 chr6B 88.298 188 17 1 308 490 9132281 9132094 1.410000e-53 220.0
14 TraesCS6A01G363600 chr6B 86.634 202 21 2 308 504 9112701 9112501 5.070000e-53 219.0
15 TraesCS6A01G363600 chr6B 86.634 202 22 1 308 504 22118623 22118422 5.070000e-53 219.0
16 TraesCS6A01G363600 chr6B 93.878 49 3 0 219 267 672458246 672458198 1.160000e-09 75.0
17 TraesCS6A01G363600 chr6D 88.837 1711 168 15 714 2419 445793951 445792259 0.000000e+00 2080.0
18 TraesCS6A01G363600 chr6D 83.209 1745 265 22 795 2526 411470987 411469258 0.000000e+00 1574.0
19 TraesCS6A01G363600 chr6D 83.943 1613 250 9 810 2419 445788965 445787359 0.000000e+00 1535.0
20 TraesCS6A01G363600 chr6D 80.851 235 31 9 220 452 445963757 445963979 4.000000e-39 172.0
21 TraesCS6A01G363600 chr5B 89.908 218 20 2 496 713 667209047 667209262 2.290000e-71 279.0
22 TraesCS6A01G363600 chr5B 87.245 196 20 1 308 498 667208821 667209016 5.070000e-53 219.0
23 TraesCS6A01G363600 chr7A 89.815 216 20 2 496 711 714898571 714898358 2.970000e-70 276.0
24 TraesCS6A01G363600 chr7A 89.450 218 21 2 496 713 305165160 305164945 1.070000e-69 274.0
25 TraesCS6A01G363600 chr7A 88.596 228 18 4 714 940 305164904 305164684 1.380000e-68 270.0
26 TraesCS6A01G363600 chr4A 88.889 225 19 3 716 940 635618136 635618354 3.840000e-69 272.0
27 TraesCS6A01G363600 chr4A 85.393 89 12 1 2900 2987 626960584 626960496 1.150000e-14 91.6
28 TraesCS6A01G363600 chr1A 88.991 218 22 2 496 713 69141964 69142179 4.960000e-68 268.0
29 TraesCS6A01G363600 chr1A 88.991 218 22 2 496 713 412533260 412533475 4.960000e-68 268.0
30 TraesCS6A01G363600 chr1A 86.802 197 20 1 308 498 486125788 486125984 6.560000e-52 215.0
31 TraesCS6A01G363600 chr1A 83.529 85 13 1 2900 2983 9795651 9795567 8.980000e-11 78.7
32 TraesCS6A01G363600 chr1B 86.294 197 21 1 308 498 64109303 64109499 3.050000e-50 209.0
33 TraesCS6A01G363600 chr1B 86.224 196 22 1 308 498 614436627 614436822 1.100000e-49 207.0
34 TraesCS6A01G363600 chr1B 86.316 95 8 2 2895 2984 629488841 629488747 6.890000e-17 99.0
35 TraesCS6A01G363600 chr3D 92.308 91 6 1 2896 2985 411724433 411724343 8.790000e-26 128.0
36 TraesCS6A01G363600 chr7B 89.873 79 7 1 2894 2971 642676674 642676752 1.920000e-17 100.0
37 TraesCS6A01G363600 chr7B 84.615 91 11 3 2897 2984 40708171 40708081 1.490000e-13 87.9
38 TraesCS6A01G363600 chr3A 88.312 77 8 1 2908 2983 547198128 547198204 1.150000e-14 91.6
39 TraesCS6A01G363600 chr3B 84.444 90 9 4 2898 2984 775876842 775876755 1.930000e-12 84.2


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 TraesCS6A01G363600 chr6A 592598659 592601678 3019 False 5578.0 5578 100.000000 1 3020 1 chr6A.!!$F1 3019
1 TraesCS6A01G363600 chr6A 592467561 592469259 1698 True 2130.0 2130 89.298000 714 2419 1 chr6A.!!$R3 1705
2 TraesCS6A01G363600 chr6A 592457348 592458970 1622 True 1580.0 1580 84.301000 804 2433 1 chr6A.!!$R2 1629
3 TraesCS6A01G363600 chr6A 556036878 556038481 1603 True 1537.0 1537 84.015000 812 2419 1 chr6A.!!$R1 1607
4 TraesCS6A01G363600 chr6B 618668578 618670276 1698 True 1506.0 1506 82.730000 806 2512 1 chr6B.!!$R1 1706
5 TraesCS6A01G363600 chr6B 673763526 673766410 2884 False 1420.0 3655 90.972667 209 3020 3 chr6B.!!$F1 2811
6 TraesCS6A01G363600 chr6B 672497893 672500180 2287 True 1192.0 1997 89.165500 209 2419 2 chr6B.!!$R6 2210
7 TraesCS6A01G363600 chr6D 445787359 445793951 6592 True 1807.5 2080 86.390000 714 2419 2 chr6D.!!$R2 1705
8 TraesCS6A01G363600 chr6D 411469258 411470987 1729 True 1574.0 1574 83.209000 795 2526 1 chr6D.!!$R1 1731

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
31 32 0.032267 GTATGCGCTAGGTCTGGTCC 59.968 60.0 9.73 0.0 0.00 4.46 F
983 1083 0.032540 CTTGAGGTTGCCCAAGTTGC 59.967 55.0 0.00 0.0 36.08 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 6920 1.140452 CATCAGTCAGTGCTGCCCTAT 59.860 52.381 9.02 0.0 36.49 2.57 R
2557 7560 0.788391 GAGTTAACGGTGGCTGTTCG 59.212 55.000 0.00 0.0 34.54 3.95 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
23 24 2.699251 TCACGTATGTATGCGCTAGG 57.301 50.000 9.73 0.00 39.55 3.02
24 25 1.951602 TCACGTATGTATGCGCTAGGT 59.048 47.619 9.73 0.55 39.55 3.08
25 26 2.031420 TCACGTATGTATGCGCTAGGTC 60.031 50.000 9.73 0.00 39.55 3.85
26 27 2.031069 CACGTATGTATGCGCTAGGTCT 60.031 50.000 9.73 0.00 39.55 3.85
27 28 2.031069 ACGTATGTATGCGCTAGGTCTG 60.031 50.000 9.73 0.00 39.55 3.51
28 29 2.668556 CGTATGTATGCGCTAGGTCTGG 60.669 54.545 9.73 0.00 0.00 3.86
29 30 1.414158 ATGTATGCGCTAGGTCTGGT 58.586 50.000 9.73 0.00 0.00 4.00
30 31 0.744874 TGTATGCGCTAGGTCTGGTC 59.255 55.000 9.73 0.00 0.00 4.02
31 32 0.032267 GTATGCGCTAGGTCTGGTCC 59.968 60.000 9.73 0.00 0.00 4.46
32 33 0.396556 TATGCGCTAGGTCTGGTCCA 60.397 55.000 9.73 0.00 0.00 4.02
33 34 1.961180 ATGCGCTAGGTCTGGTCCAC 61.961 60.000 9.73 0.00 0.00 4.02
34 35 2.646175 GCGCTAGGTCTGGTCCACA 61.646 63.158 0.00 0.00 0.00 4.17
35 36 1.215647 CGCTAGGTCTGGTCCACAC 59.784 63.158 0.00 0.00 0.00 3.82
36 37 1.251527 CGCTAGGTCTGGTCCACACT 61.252 60.000 0.00 0.00 0.00 3.55
37 38 0.533032 GCTAGGTCTGGTCCACACTC 59.467 60.000 0.00 0.00 0.00 3.51
38 39 0.811915 CTAGGTCTGGTCCACACTCG 59.188 60.000 0.00 0.00 0.00 4.18
39 40 1.248785 TAGGTCTGGTCCACACTCGC 61.249 60.000 0.00 0.00 0.00 5.03
40 41 2.734591 GTCTGGTCCACACTCGCA 59.265 61.111 0.00 0.00 0.00 5.10
41 42 1.373497 GTCTGGTCCACACTCGCAG 60.373 63.158 0.00 0.00 0.00 5.18
42 43 1.832608 TCTGGTCCACACTCGCAGT 60.833 57.895 0.00 0.00 0.00 4.40
50 51 4.767255 CACTCGCAGTGGGGCTCC 62.767 72.222 7.42 0.00 42.35 4.70
59 60 2.682136 TGGGGCTCCACGATCGAA 60.682 61.111 24.34 5.77 38.32 3.71
60 61 2.287274 TGGGGCTCCACGATCGAAA 61.287 57.895 24.34 5.39 38.32 3.46
61 62 1.078708 GGGGCTCCACGATCGAAAA 60.079 57.895 24.34 5.01 0.00 2.29
62 63 0.463833 GGGGCTCCACGATCGAAAAT 60.464 55.000 24.34 0.00 0.00 1.82
63 64 0.657840 GGGCTCCACGATCGAAAATG 59.342 55.000 24.34 9.42 0.00 2.32
64 65 0.657840 GGCTCCACGATCGAAAATGG 59.342 55.000 24.34 18.71 0.00 3.16
65 66 0.657840 GCTCCACGATCGAAAATGGG 59.342 55.000 24.34 13.12 32.73 4.00
66 67 0.657840 CTCCACGATCGAAAATGGGC 59.342 55.000 24.34 0.00 32.73 5.36
67 68 0.746563 TCCACGATCGAAAATGGGCC 60.747 55.000 24.34 0.00 32.73 5.80
68 69 1.351707 CACGATCGAAAATGGGCCG 59.648 57.895 24.34 0.00 0.00 6.13
69 70 2.327940 CGATCGAAAATGGGCCGC 59.672 61.111 10.26 0.00 0.00 6.53
70 71 2.468670 CGATCGAAAATGGGCCGCA 61.469 57.895 10.26 0.00 0.00 5.69
71 72 1.785041 CGATCGAAAATGGGCCGCAT 61.785 55.000 10.26 0.00 0.00 4.73
72 73 0.040067 GATCGAAAATGGGCCGCATC 60.040 55.000 7.12 0.00 0.00 3.91
73 74 0.751277 ATCGAAAATGGGCCGCATCA 60.751 50.000 7.12 0.00 0.00 3.07
74 75 1.226660 CGAAAATGGGCCGCATCAC 60.227 57.895 7.12 2.60 0.00 3.06
75 76 1.656818 CGAAAATGGGCCGCATCACT 61.657 55.000 7.12 0.00 0.00 3.41
76 77 1.388547 GAAAATGGGCCGCATCACTA 58.611 50.000 7.12 0.00 0.00 2.74
77 78 1.334869 GAAAATGGGCCGCATCACTAG 59.665 52.381 7.12 0.00 0.00 2.57
78 79 0.466189 AAATGGGCCGCATCACTAGG 60.466 55.000 7.12 0.00 0.00 3.02
82 83 4.175337 GCCGCATCACTAGGCCCA 62.175 66.667 0.00 0.00 44.80 5.36
83 84 2.589540 CCGCATCACTAGGCCCAA 59.410 61.111 0.00 0.00 0.00 4.12
84 85 1.077787 CCGCATCACTAGGCCCAAA 60.078 57.895 0.00 0.00 0.00 3.28
85 86 1.097547 CCGCATCACTAGGCCCAAAG 61.098 60.000 0.00 0.00 0.00 2.77
86 87 0.392998 CGCATCACTAGGCCCAAAGT 60.393 55.000 0.00 0.00 0.00 2.66
87 88 1.098050 GCATCACTAGGCCCAAAGTG 58.902 55.000 19.59 19.59 43.63 3.16
88 89 1.614317 GCATCACTAGGCCCAAAGTGT 60.614 52.381 22.86 12.31 42.96 3.55
89 90 2.355716 GCATCACTAGGCCCAAAGTGTA 60.356 50.000 22.86 13.95 42.96 2.90
90 91 3.872240 GCATCACTAGGCCCAAAGTGTAA 60.872 47.826 22.86 10.79 42.96 2.41
91 92 3.695830 TCACTAGGCCCAAAGTGTAAG 57.304 47.619 22.86 5.25 42.96 2.34
92 93 2.084546 CACTAGGCCCAAAGTGTAAGC 58.915 52.381 18.08 0.00 38.62 3.09
93 94 1.004394 ACTAGGCCCAAAGTGTAAGCC 59.996 52.381 0.00 0.00 44.20 4.35
94 95 1.004277 CTAGGCCCAAAGTGTAAGCCA 59.996 52.381 0.00 0.00 46.35 4.75
95 96 0.409484 AGGCCCAAAGTGTAAGCCAT 59.591 50.000 0.00 0.00 46.35 4.40
96 97 0.817654 GGCCCAAAGTGTAAGCCATC 59.182 55.000 0.00 0.00 43.32 3.51
97 98 1.616994 GGCCCAAAGTGTAAGCCATCT 60.617 52.381 0.00 0.00 43.32 2.90
98 99 2.171003 GCCCAAAGTGTAAGCCATCTT 58.829 47.619 0.00 0.00 36.35 2.40
99 100 2.562738 GCCCAAAGTGTAAGCCATCTTT 59.437 45.455 0.00 0.00 33.85 2.52
100 101 3.614870 GCCCAAAGTGTAAGCCATCTTTG 60.615 47.826 8.82 8.82 43.30 2.77
101 102 3.578688 CCAAAGTGTAAGCCATCTTTGC 58.421 45.455 9.92 0.00 42.73 3.68
102 103 3.256631 CCAAAGTGTAAGCCATCTTTGCT 59.743 43.478 9.92 0.00 42.73 3.91
104 105 4.773323 AAGTGTAAGCCATCTTTGCTTC 57.227 40.909 0.10 0.00 45.58 3.86
105 106 4.026356 AGTGTAAGCCATCTTTGCTTCT 57.974 40.909 0.10 0.00 45.58 2.85
106 107 3.755378 AGTGTAAGCCATCTTTGCTTCTG 59.245 43.478 0.10 0.00 45.58 3.02
107 108 2.489329 TGTAAGCCATCTTTGCTTCTGC 59.511 45.455 0.10 0.00 45.58 4.26
108 109 1.920610 AAGCCATCTTTGCTTCTGCT 58.079 45.000 0.00 0.00 45.58 4.24
109 110 1.174783 AGCCATCTTTGCTTCTGCTG 58.825 50.000 0.00 0.00 40.48 4.41
110 111 1.171308 GCCATCTTTGCTTCTGCTGA 58.829 50.000 0.00 0.00 40.48 4.26
111 112 1.542915 GCCATCTTTGCTTCTGCTGAA 59.457 47.619 5.85 5.85 40.48 3.02
112 113 2.165845 GCCATCTTTGCTTCTGCTGAAT 59.834 45.455 6.48 0.00 40.48 2.57
113 114 3.734293 GCCATCTTTGCTTCTGCTGAATC 60.734 47.826 6.48 3.38 40.48 2.52
114 115 3.487042 CCATCTTTGCTTCTGCTGAATCG 60.487 47.826 6.48 0.00 40.48 3.34
115 116 3.044235 TCTTTGCTTCTGCTGAATCGA 57.956 42.857 6.48 0.00 40.48 3.59
116 117 2.998670 TCTTTGCTTCTGCTGAATCGAG 59.001 45.455 6.48 5.50 40.48 4.04
117 118 1.081892 TTGCTTCTGCTGAATCGAGC 58.918 50.000 6.48 7.22 40.48 5.03
118 119 0.248565 TGCTTCTGCTGAATCGAGCT 59.751 50.000 13.89 0.00 39.90 4.09
119 120 0.651551 GCTTCTGCTGAATCGAGCTG 59.348 55.000 6.48 0.00 39.90 4.24
120 121 0.651551 CTTCTGCTGAATCGAGCTGC 59.348 55.000 6.48 11.38 39.90 5.25
121 122 0.742281 TTCTGCTGAATCGAGCTGCC 60.742 55.000 14.37 0.00 39.90 4.85
122 123 2.510012 TGCTGAATCGAGCTGCCG 60.510 61.111 14.37 0.00 39.90 5.69
123 124 3.267860 GCTGAATCGAGCTGCCGG 61.268 66.667 0.00 0.00 35.95 6.13
124 125 2.496341 CTGAATCGAGCTGCCGGA 59.504 61.111 5.05 2.13 0.00 5.14
125 126 1.591059 CTGAATCGAGCTGCCGGAG 60.591 63.158 5.05 0.10 0.00 4.63
126 127 2.290122 CTGAATCGAGCTGCCGGAGT 62.290 60.000 5.05 0.97 0.00 3.85
127 128 1.035385 TGAATCGAGCTGCCGGAGTA 61.035 55.000 5.05 0.00 0.00 2.59
128 129 0.102481 GAATCGAGCTGCCGGAGTAA 59.898 55.000 5.05 0.00 0.00 2.24
129 130 0.535335 AATCGAGCTGCCGGAGTAAA 59.465 50.000 5.05 0.00 0.00 2.01
130 131 0.535335 ATCGAGCTGCCGGAGTAAAA 59.465 50.000 5.05 0.00 0.00 1.52
131 132 0.319083 TCGAGCTGCCGGAGTAAAAA 59.681 50.000 5.05 0.00 0.00 1.94
132 133 0.721718 CGAGCTGCCGGAGTAAAAAG 59.278 55.000 5.05 0.00 0.00 2.27
133 134 1.087501 GAGCTGCCGGAGTAAAAAGG 58.912 55.000 5.05 0.00 0.00 3.11
134 135 0.400594 AGCTGCCGGAGTAAAAAGGT 59.599 50.000 5.05 0.00 0.00 3.50
135 136 0.521735 GCTGCCGGAGTAAAAAGGTG 59.478 55.000 5.05 0.00 0.00 4.00
136 137 1.165270 CTGCCGGAGTAAAAAGGTGG 58.835 55.000 5.05 0.00 0.00 4.61
137 138 0.250989 TGCCGGAGTAAAAAGGTGGG 60.251 55.000 5.05 0.00 0.00 4.61
138 139 0.037160 GCCGGAGTAAAAAGGTGGGA 59.963 55.000 5.05 0.00 0.00 4.37
139 140 1.817357 CCGGAGTAAAAAGGTGGGAC 58.183 55.000 0.00 0.00 0.00 4.46
140 141 1.612462 CCGGAGTAAAAAGGTGGGACC 60.612 57.143 0.00 0.00 38.99 4.46
141 142 1.612462 CGGAGTAAAAAGGTGGGACCC 60.612 57.143 2.45 2.45 39.75 4.46
142 143 1.272313 GGAGTAAAAAGGTGGGACCCC 60.272 57.143 8.45 2.69 39.75 4.95
143 144 1.709115 GAGTAAAAAGGTGGGACCCCT 59.291 52.381 8.45 0.00 39.75 4.79
144 145 2.914941 GAGTAAAAAGGTGGGACCCCTA 59.085 50.000 8.45 0.00 39.75 3.53
145 146 3.331591 GAGTAAAAAGGTGGGACCCCTAA 59.668 47.826 8.45 0.00 39.75 2.69
146 147 3.728456 AGTAAAAAGGTGGGACCCCTAAA 59.272 43.478 8.45 0.00 39.75 1.85
147 148 3.710086 AAAAAGGTGGGACCCCTAAAA 57.290 42.857 8.45 0.00 39.75 1.52
148 149 3.710086 AAAAGGTGGGACCCCTAAAAA 57.290 42.857 8.45 0.00 39.75 1.94
196 197 5.468540 AAAAAGTAAAGGAGGCCATTCAC 57.531 39.130 5.01 0.00 0.00 3.18
197 198 2.403252 AGTAAAGGAGGCCATTCACG 57.597 50.000 5.01 0.00 0.00 4.35
198 199 0.733150 GTAAAGGAGGCCATTCACGC 59.267 55.000 5.01 0.00 0.00 5.34
204 205 4.481112 GGCCATTCACGCCGCAAG 62.481 66.667 0.00 0.00 36.47 4.01
231 233 1.863880 CGAGAGTTTCGCCGTCGAG 60.864 63.158 0.00 0.00 46.34 4.04
268 270 4.060667 CGCCCAATCCACCCCCTT 62.061 66.667 0.00 0.00 0.00 3.95
276 278 2.244769 CAATCCACCCCCTTAATCACCT 59.755 50.000 0.00 0.00 0.00 4.00
277 279 2.974285 TCCACCCCCTTAATCACCTA 57.026 50.000 0.00 0.00 0.00 3.08
278 280 3.223940 TCCACCCCCTTAATCACCTAA 57.776 47.619 0.00 0.00 0.00 2.69
298 300 1.990060 TTTCCTCCCAGCTCTCCCG 60.990 63.158 0.00 0.00 0.00 5.14
350 359 0.822944 GGCTCCTCCTAGGTACGGAC 60.823 65.000 9.08 8.14 36.53 4.79
370 379 2.450886 ACTTGGGTCCATTCCTTTTCCT 59.549 45.455 0.00 0.00 0.00 3.36
384 393 2.169832 TTTCCTTCTCGAGCAACCTG 57.830 50.000 7.81 0.00 0.00 4.00
388 397 0.390472 CTTCTCGAGCAACCTGGGTC 60.390 60.000 7.81 0.00 0.00 4.46
445 454 0.738975 TGGTCGATTCCGCTCTGTAG 59.261 55.000 0.00 0.00 35.37 2.74
469 478 2.579787 CGTAGCCTCGGTTCTGCG 60.580 66.667 0.00 0.00 32.71 5.18
482 491 0.390340 TTCTGCGCCTGCTCTGTTAG 60.390 55.000 4.18 0.00 43.34 2.34
491 500 3.683847 GCCTGCTCTGTTAGTTCCATCAT 60.684 47.826 0.00 0.00 0.00 2.45
498 507 6.605471 TCTGTTAGTTCCATCATGTACTGT 57.395 37.500 0.00 0.00 0.00 3.55
529 571 3.022287 CCGCTGTTGTGTGTGGAC 58.978 61.111 0.00 0.00 36.02 4.02
589 631 8.974060 TGGTTTAGTCAGTAAAATCTGTTCTT 57.026 30.769 0.00 0.00 36.85 2.52
606 648 4.202040 TGTTCTTGAGTGTGCAGAAATTGG 60.202 41.667 0.00 0.00 0.00 3.16
614 656 5.186198 AGTGTGCAGAAATTGGTATACTCC 58.814 41.667 2.25 0.00 0.00 3.85
639 681 5.242838 GTCTGATTTGTTGGGTGGTATTTCA 59.757 40.000 0.00 0.00 0.00 2.69
643 685 7.607250 TGATTTGTTGGGTGGTATTTCAATAC 58.393 34.615 1.58 1.58 40.37 1.89
660 702 0.669619 TACACGAGTTCAGTTCGGCA 59.330 50.000 0.00 0.00 42.12 5.69
684 726 6.271585 AGGGGAATGTTCAGATATCATGTT 57.728 37.500 5.32 0.00 0.00 2.71
690 732 8.902806 GGAATGTTCAGATATCATGTTGGTTTA 58.097 33.333 5.32 0.00 0.00 2.01
691 733 9.941664 GAATGTTCAGATATCATGTTGGTTTAG 57.058 33.333 5.32 0.00 0.00 1.85
719 806 6.591935 TCAGATTGGTATATTTCTGGGTGTC 58.408 40.000 0.00 0.00 36.95 3.67
736 823 9.527157 TCTGGGTGTCATTTTTATCTGAAATTA 57.473 29.630 0.00 0.00 0.00 1.40
767 854 4.154195 CACTTCTTTGTTCTACGGAATGGG 59.846 45.833 0.00 0.00 33.71 4.00
786 873 1.336125 GGTGCAAATAGGATGCTGCTC 59.664 52.381 0.00 0.00 44.14 4.26
839 933 4.837050 GCACATAAAACTTTCGACACGTAC 59.163 41.667 0.00 0.00 0.00 3.67
863 958 7.041721 ACAAGAAAACCTTCAAAGTTTCATCC 58.958 34.615 7.95 0.00 36.44 3.51
881 977 5.491070 TCATCCATGTTTCCTTCTACAGTG 58.509 41.667 0.00 0.00 0.00 3.66
983 1083 0.032540 CTTGAGGTTGCCCAAGTTGC 59.967 55.000 0.00 0.00 36.08 4.17
1039 1139 2.479275 CCACTGCTTGCAGATATCATCG 59.521 50.000 26.71 0.77 0.00 3.84
1097 1197 0.109272 CTCGTGTCAAAGCGGCTCTA 60.109 55.000 1.45 0.00 0.00 2.43
1261 1361 0.467290 GGACCAGGTGAACAGCCAAA 60.467 55.000 0.00 0.00 0.00 3.28
1337 1437 3.677190 TCTGTGCACACATTGATGATGA 58.323 40.909 17.42 4.61 41.01 2.92
1341 1441 2.100087 TGCACACATTGATGATGATGGC 59.900 45.455 0.00 0.00 39.15 4.40
1354 1454 7.615403 TGATGATGATGGCCTTAGTTATCTAC 58.385 38.462 3.32 0.00 0.00 2.59
1456 1556 4.550076 AGTTGCTGCTATCTCTCTGTTT 57.450 40.909 0.00 0.00 0.00 2.83
1514 1614 0.474854 TGGCTGGAGTACCTTGGGAA 60.475 55.000 0.00 0.00 37.04 3.97
1568 1668 0.745486 TGCGATGGAATCAGCCAGTG 60.745 55.000 0.00 0.00 45.97 3.66
1590 1690 3.762288 GTGACCTCCTAAAATTTGGTCCC 59.238 47.826 17.46 6.73 44.60 4.46
1647 1747 5.106277 GGTTAATGGAACTTACTGGTTGAGC 60.106 44.000 0.00 0.00 38.21 4.26
1919 6920 5.610398 TCTGCACTGTGAAGATTTTGAGTA 58.390 37.500 14.56 0.00 0.00 2.59
1924 6925 6.037610 GCACTGTGAAGATTTTGAGTATAGGG 59.962 42.308 12.86 0.00 0.00 3.53
2134 7135 0.904865 TGACGAGGGGATGAAGTGCT 60.905 55.000 0.00 0.00 0.00 4.40
2142 7143 2.172293 GGGGATGAAGTGCTTCTCATCT 59.828 50.000 16.69 0.00 40.14 2.90
2311 7312 3.181465 ACGTTCACAGAAGTTGGACTCAT 60.181 43.478 0.00 0.00 0.00 2.90
2424 7425 3.696051 ACAGCCTAAAAGGTATGTGCATG 59.304 43.478 0.00 0.00 36.51 4.06
2448 7449 3.185246 AGGAATGGACGCAAGACATAG 57.815 47.619 0.00 0.00 43.62 2.23
2519 7522 4.194640 TGCAGCTATCATTTTCCTCTGAC 58.805 43.478 0.00 0.00 0.00 3.51
2521 7524 4.774124 CAGCTATCATTTTCCTCTGACCA 58.226 43.478 0.00 0.00 0.00 4.02
2557 7560 9.928236 CTCTAGGTGTTAACTCTTACGTATTAC 57.072 37.037 7.22 0.00 0.00 1.89
2572 7575 2.747396 ATTACGAACAGCCACCGTTA 57.253 45.000 0.00 0.00 37.69 3.18
2573 7576 2.522836 TTACGAACAGCCACCGTTAA 57.477 45.000 0.00 0.00 37.69 2.01
2574 7577 1.782044 TACGAACAGCCACCGTTAAC 58.218 50.000 0.00 0.00 37.69 2.01
2575 7578 0.105408 ACGAACAGCCACCGTTAACT 59.895 50.000 3.71 0.00 32.03 2.24
2576 7579 0.788391 CGAACAGCCACCGTTAACTC 59.212 55.000 3.71 0.00 0.00 3.01
2580 7583 3.036075 ACAGCCACCGTTAACTCTTAC 57.964 47.619 3.71 0.00 0.00 2.34
2625 7637 1.202879 TCCTTGCATTCCGAACTTGGT 60.203 47.619 0.00 0.00 0.00 3.67
2727 7739 2.434702 GGTTCTGTATCCCGATTCAGGT 59.565 50.000 10.35 0.00 37.00 4.00
2793 7805 1.084289 GTAATCGGGGACTTGTGTGC 58.916 55.000 0.00 0.00 0.00 4.57
2874 7892 9.472361 GGTAGGTTTGTTTATCCTTTCTTTTTC 57.528 33.333 0.00 0.00 33.34 2.29
2876 7894 7.207383 AGGTTTGTTTATCCTTTCTTTTTCGG 58.793 34.615 0.00 0.00 0.00 4.30
2877 7895 6.422701 GGTTTGTTTATCCTTTCTTTTTCGGG 59.577 38.462 0.00 0.00 0.00 5.14
2891 7909 4.467198 TTTTCGGGAGTCTTGGATAGTC 57.533 45.455 0.00 0.00 0.00 2.59
2937 7955 7.273381 CCCATAATTTAAGAGCGTTTTTGACAG 59.727 37.037 0.00 0.00 0.00 3.51
2958 7976 5.087397 CAGTAGTGTAGTGTTAAGACGCTC 58.913 45.833 0.00 0.00 45.06 5.03
2959 7977 4.758674 AGTAGTGTAGTGTTAAGACGCTCA 59.241 41.667 0.00 0.00 45.06 4.26
2972 7990 4.408182 AGACGCTCATATATTATGGGGC 57.592 45.455 0.00 1.51 0.00 5.80
2992 8010 1.409427 CGGAGGGAGTAGCTTCGATTT 59.591 52.381 0.00 0.00 0.00 2.17
3001 8019 6.987404 GGGAGTAGCTTCGATTTTATCTCTTT 59.013 38.462 0.00 0.00 0.00 2.52
3004 8022 6.818644 AGTAGCTTCGATTTTATCTCTTTGCA 59.181 34.615 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.158494 CCTAGCGCATACATACGTGATTTA 58.842 41.667 11.47 0.00 0.00 1.40
1 2 3.987868 CCTAGCGCATACATACGTGATTT 59.012 43.478 11.47 0.00 0.00 2.17
2 3 3.005472 ACCTAGCGCATACATACGTGATT 59.995 43.478 11.47 0.00 0.00 2.57
4 5 1.951602 ACCTAGCGCATACATACGTGA 59.048 47.619 11.47 0.00 0.00 4.35
5 6 2.031069 AGACCTAGCGCATACATACGTG 60.031 50.000 11.47 0.00 0.00 4.49
6 7 2.031069 CAGACCTAGCGCATACATACGT 60.031 50.000 11.47 0.00 0.00 3.57
7 8 2.585845 CAGACCTAGCGCATACATACG 58.414 52.381 11.47 0.00 0.00 3.06
8 9 2.296471 ACCAGACCTAGCGCATACATAC 59.704 50.000 11.47 0.00 0.00 2.39
9 10 2.557056 GACCAGACCTAGCGCATACATA 59.443 50.000 11.47 0.00 0.00 2.29
10 11 1.341531 GACCAGACCTAGCGCATACAT 59.658 52.381 11.47 0.00 0.00 2.29
11 12 0.744874 GACCAGACCTAGCGCATACA 59.255 55.000 11.47 0.00 0.00 2.29
12 13 0.032267 GGACCAGACCTAGCGCATAC 59.968 60.000 11.47 0.00 0.00 2.39
13 14 0.396556 TGGACCAGACCTAGCGCATA 60.397 55.000 11.47 0.00 0.00 3.14
14 15 1.685765 TGGACCAGACCTAGCGCAT 60.686 57.895 11.47 0.00 0.00 4.73
15 16 2.283604 TGGACCAGACCTAGCGCA 60.284 61.111 11.47 0.00 0.00 6.09
16 17 2.184579 GTGGACCAGACCTAGCGC 59.815 66.667 0.00 0.00 0.00 5.92
17 18 1.215647 GTGTGGACCAGACCTAGCG 59.784 63.158 10.71 0.00 0.00 4.26
18 19 0.533032 GAGTGTGGACCAGACCTAGC 59.467 60.000 17.77 2.40 0.00 3.42
19 20 0.811915 CGAGTGTGGACCAGACCTAG 59.188 60.000 17.77 6.28 0.00 3.02
20 21 1.248785 GCGAGTGTGGACCAGACCTA 61.249 60.000 17.77 0.00 0.00 3.08
21 22 2.574955 GCGAGTGTGGACCAGACCT 61.575 63.158 17.77 5.86 0.00 3.85
22 23 2.048127 GCGAGTGTGGACCAGACC 60.048 66.667 17.77 8.83 0.00 3.85
23 24 1.373497 CTGCGAGTGTGGACCAGAC 60.373 63.158 13.87 13.87 0.00 3.51
24 25 1.832608 ACTGCGAGTGTGGACCAGA 60.833 57.895 0.00 0.00 0.00 3.86
25 26 1.665916 CACTGCGAGTGTGGACCAG 60.666 63.158 0.00 0.00 41.19 4.00
26 27 2.421314 CACTGCGAGTGTGGACCA 59.579 61.111 7.80 0.00 41.19 4.02
31 32 4.320456 AGCCCCACTGCGAGTGTG 62.320 66.667 13.06 5.41 44.50 3.82
32 33 4.008933 GAGCCCCACTGCGAGTGT 62.009 66.667 13.06 0.00 44.50 3.55
33 34 4.767255 GGAGCCCCACTGCGAGTG 62.767 72.222 8.73 8.73 45.53 3.51
42 43 1.832719 TTTTCGATCGTGGAGCCCCA 61.833 55.000 15.94 0.00 40.95 4.96
43 44 0.463833 ATTTTCGATCGTGGAGCCCC 60.464 55.000 15.94 0.00 0.00 5.80
44 45 0.657840 CATTTTCGATCGTGGAGCCC 59.342 55.000 15.94 0.00 0.00 5.19
45 46 0.657840 CCATTTTCGATCGTGGAGCC 59.342 55.000 15.94 0.00 33.53 4.70
46 47 0.657840 CCCATTTTCGATCGTGGAGC 59.342 55.000 20.64 0.00 33.53 4.70
47 48 0.657840 GCCCATTTTCGATCGTGGAG 59.342 55.000 20.64 12.95 33.53 3.86
48 49 0.746563 GGCCCATTTTCGATCGTGGA 60.747 55.000 20.64 6.76 33.53 4.02
49 50 1.727467 GGCCCATTTTCGATCGTGG 59.273 57.895 15.94 14.80 0.00 4.94
50 51 1.351707 CGGCCCATTTTCGATCGTG 59.648 57.895 15.94 5.71 0.00 4.35
51 52 2.469516 GCGGCCCATTTTCGATCGT 61.470 57.895 15.94 0.00 0.00 3.73
52 53 1.785041 ATGCGGCCCATTTTCGATCG 61.785 55.000 9.36 9.36 0.00 3.69
53 54 0.040067 GATGCGGCCCATTTTCGATC 60.040 55.000 7.97 0.00 33.29 3.69
54 55 0.751277 TGATGCGGCCCATTTTCGAT 60.751 50.000 7.97 0.00 33.29 3.59
55 56 1.377856 TGATGCGGCCCATTTTCGA 60.378 52.632 7.97 0.00 33.29 3.71
56 57 1.226660 GTGATGCGGCCCATTTTCG 60.227 57.895 7.97 0.00 33.29 3.46
57 58 1.334869 CTAGTGATGCGGCCCATTTTC 59.665 52.381 7.97 0.00 33.29 2.29
58 59 1.392589 CTAGTGATGCGGCCCATTTT 58.607 50.000 7.97 1.42 33.29 1.82
59 60 0.466189 CCTAGTGATGCGGCCCATTT 60.466 55.000 7.97 1.70 33.29 2.32
60 61 1.149174 CCTAGTGATGCGGCCCATT 59.851 57.895 7.97 0.00 33.29 3.16
61 62 2.831770 CCTAGTGATGCGGCCCAT 59.168 61.111 6.43 6.43 36.70 4.00
62 63 4.175337 GCCTAGTGATGCGGCCCA 62.175 66.667 0.00 0.00 37.86 5.36
65 66 3.697439 TTGGGCCTAGTGATGCGGC 62.697 63.158 4.53 0.00 43.03 6.53
66 67 1.077787 TTTGGGCCTAGTGATGCGG 60.078 57.895 4.53 0.00 0.00 5.69
67 68 0.392998 ACTTTGGGCCTAGTGATGCG 60.393 55.000 4.53 0.00 0.00 4.73
68 69 1.098050 CACTTTGGGCCTAGTGATGC 58.902 55.000 25.59 0.00 43.45 3.91
69 70 2.496899 ACACTTTGGGCCTAGTGATG 57.503 50.000 32.05 15.67 43.45 3.07
70 71 3.622455 GCTTACACTTTGGGCCTAGTGAT 60.622 47.826 32.05 22.32 43.45 3.06
71 72 2.290071 GCTTACACTTTGGGCCTAGTGA 60.290 50.000 32.05 19.32 43.45 3.41
72 73 2.084546 GCTTACACTTTGGGCCTAGTG 58.915 52.381 27.01 27.01 45.61 2.74
73 74 1.004394 GGCTTACACTTTGGGCCTAGT 59.996 52.381 4.53 5.50 39.68 2.57
74 75 1.004277 TGGCTTACACTTTGGGCCTAG 59.996 52.381 4.53 4.77 42.84 3.02
75 76 1.068948 TGGCTTACACTTTGGGCCTA 58.931 50.000 4.53 0.00 42.84 3.93
76 77 0.409484 ATGGCTTACACTTTGGGCCT 59.591 50.000 4.53 0.00 42.84 5.19
77 78 0.817654 GATGGCTTACACTTTGGGCC 59.182 55.000 0.00 0.00 42.73 5.80
78 79 1.839424 AGATGGCTTACACTTTGGGC 58.161 50.000 0.00 0.00 0.00 5.36
79 80 3.614870 GCAAAGATGGCTTACACTTTGGG 60.615 47.826 16.39 0.00 42.23 4.12
80 81 3.256631 AGCAAAGATGGCTTACACTTTGG 59.743 43.478 16.39 3.48 42.23 3.28
81 82 4.510038 AGCAAAGATGGCTTACACTTTG 57.490 40.909 0.00 0.00 43.36 2.77
90 91 1.174783 CAGCAGAAGCAAAGATGGCT 58.825 50.000 0.00 0.00 45.49 4.75
91 92 1.171308 TCAGCAGAAGCAAAGATGGC 58.829 50.000 0.00 0.00 45.49 4.40
92 93 3.487042 CGATTCAGCAGAAGCAAAGATGG 60.487 47.826 7.88 0.00 45.49 3.51
93 94 3.373130 TCGATTCAGCAGAAGCAAAGATG 59.627 43.478 7.88 0.00 45.49 2.90
94 95 3.603532 TCGATTCAGCAGAAGCAAAGAT 58.396 40.909 7.88 0.00 45.49 2.40
95 96 2.998670 CTCGATTCAGCAGAAGCAAAGA 59.001 45.455 7.88 0.00 45.49 2.52
96 97 2.475852 GCTCGATTCAGCAGAAGCAAAG 60.476 50.000 7.88 5.24 45.49 2.77
97 98 1.466167 GCTCGATTCAGCAGAAGCAAA 59.534 47.619 7.88 0.00 45.49 3.68
98 99 1.081892 GCTCGATTCAGCAGAAGCAA 58.918 50.000 7.88 0.00 45.49 3.91
99 100 0.248565 AGCTCGATTCAGCAGAAGCA 59.751 50.000 7.88 0.00 45.49 3.91
100 101 0.651551 CAGCTCGATTCAGCAGAAGC 59.348 55.000 0.00 0.00 42.40 3.86
101 102 0.651551 GCAGCTCGATTCAGCAGAAG 59.348 55.000 0.00 0.00 42.40 2.85
102 103 0.742281 GGCAGCTCGATTCAGCAGAA 60.742 55.000 0.00 0.00 42.40 3.02
103 104 1.153489 GGCAGCTCGATTCAGCAGA 60.153 57.895 9.67 0.00 42.40 4.26
104 105 2.523507 CGGCAGCTCGATTCAGCAG 61.524 63.158 9.67 4.36 42.40 4.24
105 106 2.510012 CGGCAGCTCGATTCAGCA 60.510 61.111 9.67 0.00 42.40 4.41
106 107 3.267860 CCGGCAGCTCGATTCAGC 61.268 66.667 4.99 0.00 39.99 4.26
107 108 1.591059 CTCCGGCAGCTCGATTCAG 60.591 63.158 0.00 0.00 0.00 3.02
108 109 1.035385 TACTCCGGCAGCTCGATTCA 61.035 55.000 0.00 0.00 0.00 2.57
109 110 0.102481 TTACTCCGGCAGCTCGATTC 59.898 55.000 0.00 0.00 0.00 2.52
110 111 0.535335 TTTACTCCGGCAGCTCGATT 59.465 50.000 0.00 0.00 0.00 3.34
111 112 0.535335 TTTTACTCCGGCAGCTCGAT 59.465 50.000 0.00 0.00 0.00 3.59
112 113 0.319083 TTTTTACTCCGGCAGCTCGA 59.681 50.000 0.00 0.00 0.00 4.04
113 114 0.721718 CTTTTTACTCCGGCAGCTCG 59.278 55.000 0.00 0.00 0.00 5.03
114 115 1.087501 CCTTTTTACTCCGGCAGCTC 58.912 55.000 0.00 0.00 0.00 4.09
115 116 0.400594 ACCTTTTTACTCCGGCAGCT 59.599 50.000 0.00 0.00 0.00 4.24
116 117 0.521735 CACCTTTTTACTCCGGCAGC 59.478 55.000 0.00 0.00 0.00 5.25
117 118 1.165270 CCACCTTTTTACTCCGGCAG 58.835 55.000 0.00 0.00 0.00 4.85
118 119 0.250989 CCCACCTTTTTACTCCGGCA 60.251 55.000 0.00 0.00 0.00 5.69
119 120 0.037160 TCCCACCTTTTTACTCCGGC 59.963 55.000 0.00 0.00 0.00 6.13
120 121 1.612462 GGTCCCACCTTTTTACTCCGG 60.612 57.143 0.00 0.00 34.73 5.14
121 122 1.612462 GGGTCCCACCTTTTTACTCCG 60.612 57.143 1.78 0.00 38.64 4.63
122 123 1.272313 GGGGTCCCACCTTTTTACTCC 60.272 57.143 10.98 0.00 38.64 3.85
123 124 1.709115 AGGGGTCCCACCTTTTTACTC 59.291 52.381 10.98 0.00 38.64 2.59
124 125 1.842699 AGGGGTCCCACCTTTTTACT 58.157 50.000 10.98 0.00 38.64 2.24
125 126 3.812611 TTAGGGGTCCCACCTTTTTAC 57.187 47.619 10.98 0.00 38.64 2.01
126 127 4.828875 TTTTAGGGGTCCCACCTTTTTA 57.171 40.909 10.98 0.00 38.64 1.52
127 128 3.710086 TTTTAGGGGTCCCACCTTTTT 57.290 42.857 10.98 0.00 38.64 1.94
128 129 3.710086 TTTTTAGGGGTCCCACCTTTT 57.290 42.857 10.98 0.00 38.64 2.27
145 146 4.772624 GGGATGCCTCCTTTACTTCTTTTT 59.227 41.667 8.03 0.00 41.74 1.94
146 147 4.044698 AGGGATGCCTCCTTTACTTCTTTT 59.955 41.667 0.00 0.00 41.74 2.27
147 148 3.593780 AGGGATGCCTCCTTTACTTCTTT 59.406 43.478 0.00 0.00 41.74 2.52
148 149 3.193782 AGGGATGCCTCCTTTACTTCTT 58.806 45.455 0.00 0.00 41.74 2.52
149 150 2.774809 GAGGGATGCCTCCTTTACTTCT 59.225 50.000 22.16 0.00 41.74 2.85
150 151 2.505819 TGAGGGATGCCTCCTTTACTTC 59.494 50.000 28.47 3.65 41.74 3.01
151 152 2.562296 TGAGGGATGCCTCCTTTACTT 58.438 47.619 28.47 0.00 41.74 2.24
152 153 2.270434 TGAGGGATGCCTCCTTTACT 57.730 50.000 28.47 0.00 41.74 2.24
153 154 3.366052 TTTGAGGGATGCCTCCTTTAC 57.634 47.619 28.47 5.62 41.74 2.01
154 155 4.396357 TTTTTGAGGGATGCCTCCTTTA 57.604 40.909 28.47 8.86 41.74 1.85
155 156 2.999185 TTTTGAGGGATGCCTCCTTT 57.001 45.000 28.47 0.00 41.74 3.11
156 157 2.999185 TTTTTGAGGGATGCCTCCTT 57.001 45.000 28.47 0.00 41.74 3.36
174 175 4.022329 CGTGAATGGCCTCCTTTACTTTTT 60.022 41.667 3.32 0.00 0.00 1.94
175 176 3.506067 CGTGAATGGCCTCCTTTACTTTT 59.494 43.478 3.32 0.00 0.00 2.27
176 177 3.081804 CGTGAATGGCCTCCTTTACTTT 58.918 45.455 3.32 0.00 0.00 2.66
177 178 2.711542 CGTGAATGGCCTCCTTTACTT 58.288 47.619 3.32 0.00 0.00 2.24
178 179 1.679032 GCGTGAATGGCCTCCTTTACT 60.679 52.381 3.32 0.00 0.00 2.24
179 180 0.733150 GCGTGAATGGCCTCCTTTAC 59.267 55.000 3.32 1.30 0.00 2.01
180 181 3.168773 GCGTGAATGGCCTCCTTTA 57.831 52.632 3.32 0.00 0.00 1.85
181 182 4.002797 GCGTGAATGGCCTCCTTT 57.997 55.556 3.32 0.00 0.00 3.11
188 189 4.481112 CCTTGCGGCGTGAATGGC 62.481 66.667 9.37 0.00 0.00 4.40
189 190 3.814268 CCCTTGCGGCGTGAATGG 61.814 66.667 9.37 4.79 0.00 3.16
190 191 2.745884 TCCCTTGCGGCGTGAATG 60.746 61.111 9.37 0.00 0.00 2.67
191 192 2.436646 CTCCCTTGCGGCGTGAAT 60.437 61.111 9.37 0.00 0.00 2.57
192 193 4.697756 CCTCCCTTGCGGCGTGAA 62.698 66.667 9.37 0.54 0.00 3.18
201 202 3.474570 CTCTCGCCCCCTCCCTTG 61.475 72.222 0.00 0.00 0.00 3.61
202 203 3.564347 AACTCTCGCCCCCTCCCTT 62.564 63.158 0.00 0.00 0.00 3.95
203 204 3.564347 AAACTCTCGCCCCCTCCCT 62.564 63.158 0.00 0.00 0.00 4.20
204 205 3.009714 AAACTCTCGCCCCCTCCC 61.010 66.667 0.00 0.00 0.00 4.30
205 206 2.585153 GAAACTCTCGCCCCCTCC 59.415 66.667 0.00 0.00 0.00 4.30
206 207 2.184579 CGAAACTCTCGCCCCCTC 59.815 66.667 0.00 0.00 41.49 4.30
242 244 1.303282 GGATTGGGCGGAGAAACCT 59.697 57.895 0.00 0.00 36.31 3.50
268 270 4.080526 GCTGGGAGGAAACTTAGGTGATTA 60.081 45.833 0.00 0.00 44.43 1.75
276 278 2.188817 GGAGAGCTGGGAGGAAACTTA 58.811 52.381 0.00 0.00 44.43 2.24
277 279 0.988063 GGAGAGCTGGGAGGAAACTT 59.012 55.000 0.00 0.00 44.43 2.66
350 359 3.175438 AGGAAAAGGAATGGACCCAAG 57.825 47.619 0.00 0.00 0.00 3.61
370 379 1.118965 TGACCCAGGTTGCTCGAGAA 61.119 55.000 18.75 1.15 0.00 2.87
445 454 2.202623 CCGAGGCTACGCAGACAC 60.203 66.667 0.00 0.00 28.86 3.67
469 478 2.284190 GATGGAACTAACAGAGCAGGC 58.716 52.381 0.00 0.00 0.00 4.85
482 491 3.941483 CCCTTGACAGTACATGATGGAAC 59.059 47.826 0.00 0.00 0.00 3.62
491 500 3.054655 GGCCTAATTCCCTTGACAGTACA 60.055 47.826 0.00 0.00 0.00 2.90
498 507 0.107214 CAGCGGCCTAATTCCCTTGA 60.107 55.000 0.00 0.00 0.00 3.02
529 571 1.471684 GCATTTCACAGAGCTTCCAGG 59.528 52.381 0.00 0.00 0.00 4.45
589 631 5.804639 AGTATACCAATTTCTGCACACTCA 58.195 37.500 0.00 0.00 0.00 3.41
614 656 1.604604 ACCACCCAACAAATCAGACG 58.395 50.000 0.00 0.00 0.00 4.18
639 681 2.288579 TGCCGAACTGAACTCGTGTATT 60.289 45.455 0.00 0.00 34.46 1.89
643 685 0.508641 CTTGCCGAACTGAACTCGTG 59.491 55.000 0.00 0.00 34.46 4.35
660 702 6.271585 ACATGATATCTGAACATTCCCCTT 57.728 37.500 0.00 0.00 0.00 3.95
684 726 9.747898 AAATATACCAATCTGAACACTAAACCA 57.252 29.630 0.00 0.00 0.00 3.67
690 732 7.056635 CCCAGAAATATACCAATCTGAACACT 58.943 38.462 3.34 0.00 41.38 3.55
691 733 6.828785 ACCCAGAAATATACCAATCTGAACAC 59.171 38.462 3.34 0.00 41.38 3.32
736 823 7.876068 TCCGTAGAACAAAGAAGTGATGTAAAT 59.124 33.333 0.00 0.00 0.00 1.40
741 828 6.402550 CCATTCCGTAGAACAAAGAAGTGATG 60.403 42.308 0.00 0.00 33.97 3.07
767 854 1.336125 GGAGCAGCATCCTATTTGCAC 59.664 52.381 0.00 0.00 42.62 4.57
786 873 7.863375 TCTTCACAACAAACGGTAAATTAATGG 59.137 33.333 0.00 0.00 0.00 3.16
839 933 7.041107 TGGATGAAACTTTGAAGGTTTTCTTG 58.959 34.615 6.87 0.00 35.74 3.02
863 958 5.633830 AATGCACTGTAGAAGGAAACATG 57.366 39.130 0.00 0.00 0.00 3.21
881 977 7.645340 CCAGATAACAGCTGTAACAAATAATGC 59.355 37.037 22.01 2.31 0.00 3.56
1039 1139 2.015587 ACTCGACACGGTAATCCTCTC 58.984 52.381 0.00 0.00 0.00 3.20
1120 1220 3.414700 GCCAACACGGAGAGCACG 61.415 66.667 0.00 0.00 36.56 5.34
1126 1226 2.111043 ACCACAGCCAACACGGAG 59.889 61.111 0.00 0.00 36.56 4.63
1256 1356 3.242870 CGATAGAACAAGGATGCTTTGGC 60.243 47.826 0.00 0.00 39.76 4.52
1261 1361 2.988010 TGCGATAGAACAAGGATGCT 57.012 45.000 0.00 0.00 39.76 3.79
1337 1437 6.239629 GCAGTAAGGTAGATAACTAAGGCCAT 60.240 42.308 5.01 0.00 0.00 4.40
1341 1441 9.444600 TTTTTGCAGTAAGGTAGATAACTAAGG 57.555 33.333 0.00 0.00 0.00 2.69
1354 1454 4.261614 GGACCTCAACTTTTTGCAGTAAGG 60.262 45.833 12.70 8.50 32.17 2.69
1456 1556 4.041075 TGCTATACAGTCAACAAGGTGGAA 59.959 41.667 0.00 0.00 0.00 3.53
1514 1614 5.192522 ACAAGTTCTCCCAATGATCCATACT 59.807 40.000 0.00 0.00 0.00 2.12
1919 6920 1.140452 CATCAGTCAGTGCTGCCCTAT 59.860 52.381 9.02 0.00 36.49 2.57
2311 7312 0.906066 TGGCAGCCTATAACGGTCAA 59.094 50.000 14.15 0.00 0.00 3.18
2424 7425 2.552315 TGTCTTGCGTCCATTCCTTTTC 59.448 45.455 0.00 0.00 0.00 2.29
2448 7449 0.940126 CTACACCCATGCTCGATTGC 59.060 55.000 0.00 0.00 0.00 3.56
2519 7522 3.679389 ACACCTAGAGCATTTGAACTGG 58.321 45.455 0.00 0.00 0.00 4.00
2521 7524 6.534634 AGTTAACACCTAGAGCATTTGAACT 58.465 36.000 8.61 0.00 0.00 3.01
2557 7560 0.788391 GAGTTAACGGTGGCTGTTCG 59.212 55.000 0.00 0.00 34.54 3.95
2580 7583 9.726034 GACACATTTAAAAATAGAAACAATGCG 57.274 29.630 0.00 0.00 0.00 4.73
2727 7739 2.631160 TCCGAAAAAGCAAGACCTCA 57.369 45.000 0.00 0.00 0.00 3.86
2793 7805 9.097257 CATTAAGCATAAATTACAAACAAGGGG 57.903 33.333 0.00 0.00 0.00 4.79
2874 7892 1.065701 CGTGACTATCCAAGACTCCCG 59.934 57.143 0.00 0.00 0.00 5.14
2876 7894 4.822896 ACTATCGTGACTATCCAAGACTCC 59.177 45.833 0.00 0.00 0.00 3.85
2877 7895 6.707161 AGTACTATCGTGACTATCCAAGACTC 59.293 42.308 0.00 0.00 0.00 3.36
2891 7909 1.872313 GACGGAGGGAGTACTATCGTG 59.128 57.143 0.00 0.00 32.98 4.35
2937 7955 5.039480 TGAGCGTCTTAACACTACACTAC 57.961 43.478 0.00 0.00 0.00 2.73
2958 7976 3.045634 TCCCTCCGCCCCATAATATATG 58.954 50.000 0.00 0.00 0.00 1.78
2959 7977 3.311402 ACTCCCTCCGCCCCATAATATAT 60.311 47.826 0.00 0.00 0.00 0.86
2972 7990 1.033574 AATCGAAGCTACTCCCTCCG 58.966 55.000 0.00 0.00 0.00 4.63
2992 8010 6.111382 CAGACAGGAGAATGCAAAGAGATAA 58.889 40.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.