Multiple sequence alignment - TraesCS6B01G192300

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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 TraesCS6B01G192300 chr6B 100.000 2799 0 0 604 3402 226397690 226394892 0.000000e+00 5169.0
1 TraesCS6B01G192300 chr6B 100.000 256 0 0 1 256 226398293 226398038 1.100000e-129 473.0
2 TraesCS6B01G192300 chr6D 90.508 2813 117 60 615 3402 127381024 127378337 0.000000e+00 3578.0
3 TraesCS6B01G192300 chr6A 91.330 1511 67 23 1610 3081 150981547 150983032 0.000000e+00 2006.0
4 TraesCS6B01G192300 chr6A 88.389 956 59 24 615 1569 150980643 150981547 0.000000e+00 1103.0
5 TraesCS6B01G192300 chr6A 92.617 298 19 3 3108 3402 150983028 150983325 3.140000e-115 425.0
6 TraesCS6B01G192300 chr7B 76.080 648 133 15 1713 2349 544881944 544882580 5.480000e-83 318.0
7 TraesCS6B01G192300 chr7B 100.000 28 0 0 128 155 202367249 202367222 6.000000e-03 52.8
8 TraesCS6B01G192300 chr7D 75.814 645 140 12 1713 2349 515236912 515236276 2.550000e-81 313.0
9 TraesCS6B01G192300 chr7D 74.658 730 154 22 1634 2349 514093058 514093770 9.230000e-76 294.0
10 TraesCS6B01G192300 chr7D 75.309 648 138 15 1713 2349 515220706 515220070 1.190000e-74 291.0
11 TraesCS6B01G192300 chr7D 94.595 37 2 0 177 213 117674824 117674788 1.320000e-04 58.4
12 TraesCS6B01G192300 chr7A 74.863 728 160 16 1634 2349 588739729 588739013 3.300000e-80 309.0
13 TraesCS6B01G192300 chr7A 75.734 647 135 15 1713 2348 586692916 586692281 4.260000e-79 305.0
14 TraesCS6B01G192300 chr7A 74.828 727 158 16 1634 2349 587519182 587519894 4.260000e-79 305.0
15 TraesCS6B01G192300 chr2D 80.508 118 15 7 1769 1882 574346175 574346062 2.180000e-12 84.2
16 TraesCS6B01G192300 chr2B 79.661 118 16 7 1769 1882 690211224 690211111 1.010000e-10 78.7
17 TraesCS6B01G192300 chr4B 80.000 110 14 8 1774 1879 86465879 86465984 1.310000e-09 75.0
18 TraesCS6B01G192300 chr2A 78.992 119 17 7 1768 1882 712702425 712702311 1.310000e-09 75.0


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 TraesCS6B01G192300 chr6B 226394892 226398293 3401 True 2821 5169 100.000000 1 3402 2 chr6B.!!$R1 3401
1 TraesCS6B01G192300 chr6D 127378337 127381024 2687 True 3578 3578 90.508000 615 3402 1 chr6D.!!$R1 2787
2 TraesCS6B01G192300 chr6A 150980643 150983325 2682 False 1178 2006 90.778667 615 3402 3 chr6A.!!$F1 2787
3 TraesCS6B01G192300 chr7B 544881944 544882580 636 False 318 318 76.080000 1713 2349 1 chr7B.!!$F1 636
4 TraesCS6B01G192300 chr7D 515236276 515236912 636 True 313 313 75.814000 1713 2349 1 chr7D.!!$R3 636
5 TraesCS6B01G192300 chr7D 514093058 514093770 712 False 294 294 74.658000 1634 2349 1 chr7D.!!$F1 715
6 TraesCS6B01G192300 chr7D 515220070 515220706 636 True 291 291 75.309000 1713 2349 1 chr7D.!!$R2 636
7 TraesCS6B01G192300 chr7A 588739013 588739729 716 True 309 309 74.863000 1634 2349 1 chr7A.!!$R2 715
8 TraesCS6B01G192300 chr7A 586692281 586692916 635 True 305 305 75.734000 1713 2348 1 chr7A.!!$R1 635
9 TraesCS6B01G192300 chr7A 587519182 587519894 712 False 305 305 74.828000 1634 2349 1 chr7A.!!$F1 715

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
110 111 0.106469 TGGCTAGACGCTCCTCTGAT 60.106 55.0 0.00 0.0 39.13 2.90 F
1182 1191 0.107508 CCCTGGACATCGTGATGCTT 60.108 55.0 9.69 0.0 42.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2042 0.591741 CCTCGTACGACTTGATCCGC 60.592 60.0 15.28 0.0 0.0 5.54 R
2714 2763 0.035152 TGGGATGCTGCGATTGTTCT 60.035 50.0 0.00 0.0 0.0 3.01 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
22 23 5.878406 TTTGGGAAGGTTTTTATTGAGCA 57.122 34.783 0.00 0.00 0.00 4.26
23 24 6.432403 TTTGGGAAGGTTTTTATTGAGCAT 57.568 33.333 0.00 0.00 0.00 3.79
24 25 6.432403 TTGGGAAGGTTTTTATTGAGCATT 57.568 33.333 0.00 0.00 0.00 3.56
25 26 5.792741 TGGGAAGGTTTTTATTGAGCATTG 58.207 37.500 0.00 0.00 0.00 2.82
26 27 4.631377 GGGAAGGTTTTTATTGAGCATTGC 59.369 41.667 0.00 0.00 0.00 3.56
27 28 5.237048 GGAAGGTTTTTATTGAGCATTGCA 58.763 37.500 11.91 0.00 0.00 4.08
28 29 5.700373 GGAAGGTTTTTATTGAGCATTGCAA 59.300 36.000 11.91 0.00 0.00 4.08
29 30 6.372381 GGAAGGTTTTTATTGAGCATTGCAAT 59.628 34.615 11.91 5.99 39.20 3.56
30 31 7.548780 GGAAGGTTTTTATTGAGCATTGCAATA 59.451 33.333 12.53 4.49 37.22 1.90
31 32 8.483307 AAGGTTTTTATTGAGCATTGCAATAG 57.517 30.769 12.53 7.98 38.86 1.73
32 33 7.839907 AGGTTTTTATTGAGCATTGCAATAGA 58.160 30.769 12.53 0.15 38.86 1.98
33 34 7.977853 AGGTTTTTATTGAGCATTGCAATAGAG 59.022 33.333 12.53 0.81 38.86 2.43
34 35 7.761249 GGTTTTTATTGAGCATTGCAATAGAGT 59.239 33.333 12.53 0.00 38.86 3.24
35 36 8.801913 GTTTTTATTGAGCATTGCAATAGAGTC 58.198 33.333 12.53 7.04 38.86 3.36
36 37 7.870509 TTTATTGAGCATTGCAATAGAGTCT 57.129 32.000 12.53 0.00 38.86 3.24
37 38 8.962884 TTTATTGAGCATTGCAATAGAGTCTA 57.037 30.769 12.53 1.45 38.86 2.59
38 39 8.962884 TTATTGAGCATTGCAATAGAGTCTAA 57.037 30.769 12.53 4.38 38.86 2.10
39 40 9.565090 TTATTGAGCATTGCAATAGAGTCTAAT 57.435 29.630 12.53 9.03 38.86 1.73
40 41 7.870509 TTGAGCATTGCAATAGAGTCTAATT 57.129 32.000 12.53 0.00 0.00 1.40
41 42 7.870509 TGAGCATTGCAATAGAGTCTAATTT 57.129 32.000 12.53 0.00 0.00 1.82
42 43 7.700505 TGAGCATTGCAATAGAGTCTAATTTG 58.299 34.615 12.53 6.55 0.00 2.32
43 44 7.035840 AGCATTGCAATAGAGTCTAATTTGG 57.964 36.000 12.53 0.00 0.00 3.28
44 45 6.604795 AGCATTGCAATAGAGTCTAATTTGGT 59.395 34.615 12.53 0.00 0.00 3.67
45 46 7.775093 AGCATTGCAATAGAGTCTAATTTGGTA 59.225 33.333 12.53 0.00 0.00 3.25
46 47 8.072567 GCATTGCAATAGAGTCTAATTTGGTAG 58.927 37.037 12.53 0.00 0.00 3.18
47 48 7.553881 TTGCAATAGAGTCTAATTTGGTAGC 57.446 36.000 3.45 0.00 0.00 3.58
48 49 6.889198 TGCAATAGAGTCTAATTTGGTAGCT 58.111 36.000 3.45 0.00 0.00 3.32
49 50 6.986817 TGCAATAGAGTCTAATTTGGTAGCTC 59.013 38.462 3.45 0.00 0.00 4.09
50 51 6.986817 GCAATAGAGTCTAATTTGGTAGCTCA 59.013 38.462 3.45 0.00 31.83 4.26
51 52 7.659390 GCAATAGAGTCTAATTTGGTAGCTCAT 59.341 37.037 3.45 0.00 31.83 2.90
52 53 8.986847 CAATAGAGTCTAATTTGGTAGCTCATG 58.013 37.037 3.45 0.00 31.83 3.07
53 54 6.552445 AGAGTCTAATTTGGTAGCTCATGT 57.448 37.500 0.00 0.00 31.83 3.21
54 55 6.344500 AGAGTCTAATTTGGTAGCTCATGTG 58.656 40.000 0.00 0.00 31.83 3.21
55 56 4.878397 AGTCTAATTTGGTAGCTCATGTGC 59.122 41.667 11.79 11.79 0.00 4.57
56 57 4.878397 GTCTAATTTGGTAGCTCATGTGCT 59.122 41.667 24.28 24.28 46.11 4.40
57 58 6.049149 GTCTAATTTGGTAGCTCATGTGCTA 58.951 40.000 22.27 22.27 43.74 3.49
58 59 6.201806 GTCTAATTTGGTAGCTCATGTGCTAG 59.798 42.308 25.61 15.24 44.93 3.42
70 71 3.558674 GTGCTAGCACATCAGGGTT 57.441 52.632 36.93 0.00 45.53 4.11
71 72 1.089920 GTGCTAGCACATCAGGGTTG 58.910 55.000 36.93 0.00 45.53 3.77
72 73 0.692476 TGCTAGCACATCAGGGTTGT 59.308 50.000 14.93 0.00 0.00 3.32
73 74 1.089920 GCTAGCACATCAGGGTTGTG 58.910 55.000 10.63 0.00 45.74 3.33
74 75 1.611673 GCTAGCACATCAGGGTTGTGT 60.612 52.381 10.63 0.00 44.96 3.72
75 76 2.783135 CTAGCACATCAGGGTTGTGTT 58.217 47.619 5.78 2.53 44.96 3.32
76 77 1.321474 AGCACATCAGGGTTGTGTTG 58.679 50.000 5.78 0.00 44.96 3.33
77 78 1.133823 AGCACATCAGGGTTGTGTTGA 60.134 47.619 5.78 0.00 44.96 3.18
78 79 1.888512 GCACATCAGGGTTGTGTTGAT 59.111 47.619 5.78 0.00 44.96 2.57
79 80 2.095059 GCACATCAGGGTTGTGTTGATC 60.095 50.000 5.78 0.00 44.96 2.92
80 81 2.489329 CACATCAGGGTTGTGTTGATCC 59.511 50.000 0.00 0.00 39.66 3.36
81 82 2.108075 ACATCAGGGTTGTGTTGATCCA 59.892 45.455 0.00 0.00 29.48 3.41
82 83 2.270352 TCAGGGTTGTGTTGATCCAC 57.730 50.000 0.00 0.00 35.86 4.02
83 84 1.202879 TCAGGGTTGTGTTGATCCACC 60.203 52.381 0.00 0.00 34.35 4.61
84 85 0.250727 AGGGTTGTGTTGATCCACCG 60.251 55.000 0.00 0.00 34.35 4.94
85 86 1.241315 GGGTTGTGTTGATCCACCGG 61.241 60.000 0.00 0.00 34.35 5.28
86 87 1.579429 GTTGTGTTGATCCACCGGC 59.421 57.895 0.00 0.00 34.35 6.13
87 88 1.963855 TTGTGTTGATCCACCGGCG 60.964 57.895 0.00 0.00 34.35 6.46
88 89 3.124921 GTGTTGATCCACCGGCGG 61.125 66.667 27.06 27.06 0.00 6.13
89 90 3.632080 TGTTGATCCACCGGCGGT 61.632 61.111 28.83 28.83 35.62 5.68
99 100 4.814294 CCGGCGGTGTGGCTAGAC 62.814 72.222 19.97 0.00 42.02 2.59
102 103 4.436998 GCGGTGTGGCTAGACGCT 62.437 66.667 11.18 0.00 46.02 5.07
103 104 2.202623 CGGTGTGGCTAGACGCTC 60.203 66.667 11.18 6.68 39.13 5.03
104 105 2.184579 GGTGTGGCTAGACGCTCC 59.815 66.667 14.22 14.22 39.13 4.70
105 106 2.352032 GGTGTGGCTAGACGCTCCT 61.352 63.158 20.71 0.00 39.13 3.69
106 107 1.139947 GTGTGGCTAGACGCTCCTC 59.860 63.158 11.18 0.00 39.13 3.71
107 108 1.000771 TGTGGCTAGACGCTCCTCT 60.001 57.895 11.18 0.00 39.13 3.69
108 109 1.315981 TGTGGCTAGACGCTCCTCTG 61.316 60.000 11.18 0.00 39.13 3.35
109 110 1.032657 GTGGCTAGACGCTCCTCTGA 61.033 60.000 0.54 0.00 39.13 3.27
110 111 0.106469 TGGCTAGACGCTCCTCTGAT 60.106 55.000 0.00 0.00 39.13 2.90
111 112 1.036707 GGCTAGACGCTCCTCTGATT 58.963 55.000 0.00 0.00 39.13 2.57
112 113 1.410882 GGCTAGACGCTCCTCTGATTT 59.589 52.381 0.00 0.00 39.13 2.17
113 114 2.159028 GGCTAGACGCTCCTCTGATTTT 60.159 50.000 0.00 0.00 39.13 1.82
114 115 3.068307 GGCTAGACGCTCCTCTGATTTTA 59.932 47.826 0.00 0.00 39.13 1.52
115 116 4.262249 GGCTAGACGCTCCTCTGATTTTAT 60.262 45.833 0.00 0.00 39.13 1.40
116 117 4.920927 GCTAGACGCTCCTCTGATTTTATC 59.079 45.833 0.00 0.00 35.14 1.75
117 118 5.278758 GCTAGACGCTCCTCTGATTTTATCT 60.279 44.000 0.00 0.00 35.14 1.98
118 119 5.195001 AGACGCTCCTCTGATTTTATCTC 57.805 43.478 0.00 0.00 0.00 2.75
119 120 4.892934 AGACGCTCCTCTGATTTTATCTCT 59.107 41.667 0.00 0.00 0.00 3.10
120 121 6.065374 AGACGCTCCTCTGATTTTATCTCTA 58.935 40.000 0.00 0.00 0.00 2.43
121 122 6.206634 AGACGCTCCTCTGATTTTATCTCTAG 59.793 42.308 0.00 0.00 0.00 2.43
122 123 5.160641 CGCTCCTCTGATTTTATCTCTAGC 58.839 45.833 0.00 0.00 0.00 3.42
123 124 5.048083 CGCTCCTCTGATTTTATCTCTAGCT 60.048 44.000 0.00 0.00 0.00 3.32
124 125 6.516527 CGCTCCTCTGATTTTATCTCTAGCTT 60.517 42.308 0.00 0.00 0.00 3.74
125 126 7.216494 GCTCCTCTGATTTTATCTCTAGCTTT 58.784 38.462 0.00 0.00 0.00 3.51
126 127 7.714813 GCTCCTCTGATTTTATCTCTAGCTTTT 59.285 37.037 0.00 0.00 0.00 2.27
127 128 9.612066 CTCCTCTGATTTTATCTCTAGCTTTTT 57.388 33.333 0.00 0.00 0.00 1.94
131 132 9.890629 TCTGATTTTATCTCTAGCTTTTTAGCA 57.109 29.630 0.00 0.00 37.25 3.49
133 134 9.890629 TGATTTTATCTCTAGCTTTTTAGCAGA 57.109 29.630 0.00 0.69 37.25 4.26
135 136 7.757097 TTTATCTCTAGCTTTTTAGCAGACG 57.243 36.000 0.00 0.00 37.25 4.18
136 137 5.584253 ATCTCTAGCTTTTTAGCAGACGA 57.416 39.130 0.00 2.35 37.25 4.20
137 138 5.584253 TCTCTAGCTTTTTAGCAGACGAT 57.416 39.130 0.00 0.00 37.25 3.73
138 139 5.344066 TCTCTAGCTTTTTAGCAGACGATG 58.656 41.667 0.00 0.00 37.25 3.84
139 140 5.073311 TCTAGCTTTTTAGCAGACGATGT 57.927 39.130 0.00 0.00 37.25 3.06
140 141 6.095021 TCTCTAGCTTTTTAGCAGACGATGTA 59.905 38.462 0.00 0.00 37.25 2.29
141 142 6.627243 TCTAGCTTTTTAGCAGACGATGTAA 58.373 36.000 0.00 0.00 37.25 2.41
142 143 5.532025 AGCTTTTTAGCAGACGATGTAAC 57.468 39.130 0.00 0.00 37.25 2.50
143 144 5.238583 AGCTTTTTAGCAGACGATGTAACT 58.761 37.500 0.00 0.00 37.25 2.24
144 145 6.395629 AGCTTTTTAGCAGACGATGTAACTA 58.604 36.000 0.00 0.00 37.25 2.24
145 146 7.042335 AGCTTTTTAGCAGACGATGTAACTAT 58.958 34.615 0.00 0.00 37.25 2.12
146 147 7.549488 AGCTTTTTAGCAGACGATGTAACTATT 59.451 33.333 0.00 0.00 37.25 1.73
147 148 8.814235 GCTTTTTAGCAGACGATGTAACTATTA 58.186 33.333 0.00 0.00 34.41 0.98
154 155 8.982685 AGCAGACGATGTAACTATTATTTGATG 58.017 33.333 0.00 0.00 0.00 3.07
155 156 8.765219 GCAGACGATGTAACTATTATTTGATGT 58.235 33.333 0.00 0.00 0.00 3.06
157 158 9.817809 AGACGATGTAACTATTATTTGATGTGT 57.182 29.630 0.00 0.00 0.00 3.72
215 216 9.237846 GATGTTAATAAAACTAGCCATGAAAGC 57.762 33.333 0.00 0.00 0.00 3.51
216 217 7.543756 TGTTAATAAAACTAGCCATGAAAGCC 58.456 34.615 0.00 0.00 0.00 4.35
217 218 7.396055 TGTTAATAAAACTAGCCATGAAAGCCT 59.604 33.333 0.00 0.00 0.00 4.58
218 219 6.857437 AATAAAACTAGCCATGAAAGCCTT 57.143 33.333 0.00 0.00 0.00 4.35
219 220 6.857437 ATAAAACTAGCCATGAAAGCCTTT 57.143 33.333 0.00 0.00 0.00 3.11
220 221 7.954666 ATAAAACTAGCCATGAAAGCCTTTA 57.045 32.000 0.00 0.00 0.00 1.85
221 222 6.664428 AAAACTAGCCATGAAAGCCTTTAA 57.336 33.333 0.00 0.00 0.00 1.52
222 223 6.664428 AAACTAGCCATGAAAGCCTTTAAA 57.336 33.333 0.00 0.00 0.00 1.52
223 224 6.664428 AACTAGCCATGAAAGCCTTTAAAA 57.336 33.333 0.00 0.00 0.00 1.52
224 225 6.664428 ACTAGCCATGAAAGCCTTTAAAAA 57.336 33.333 0.00 0.00 0.00 1.94
243 244 5.873179 AAAAAGATTTGGCAGCATTCATG 57.127 34.783 0.00 0.00 0.00 3.07
244 245 4.811969 AAAGATTTGGCAGCATTCATGA 57.188 36.364 0.00 0.00 0.00 3.07
245 246 5.353394 AAAGATTTGGCAGCATTCATGAT 57.647 34.783 0.00 0.00 0.00 2.45
246 247 6.474140 AAAGATTTGGCAGCATTCATGATA 57.526 33.333 0.00 0.00 0.00 2.15
247 248 5.707242 AGATTTGGCAGCATTCATGATAG 57.293 39.130 0.00 0.00 0.00 2.08
248 249 5.138276 AGATTTGGCAGCATTCATGATAGT 58.862 37.500 0.00 0.00 0.00 2.12
249 250 6.301486 AGATTTGGCAGCATTCATGATAGTA 58.699 36.000 0.00 0.00 0.00 1.82
250 251 6.946583 AGATTTGGCAGCATTCATGATAGTAT 59.053 34.615 0.00 0.00 0.00 2.12
251 252 6.964807 TTTGGCAGCATTCATGATAGTATT 57.035 33.333 0.00 0.00 0.00 1.89
252 253 6.964807 TTGGCAGCATTCATGATAGTATTT 57.035 33.333 0.00 0.00 0.00 1.40
253 254 6.321848 TGGCAGCATTCATGATAGTATTTG 57.678 37.500 0.00 0.00 0.00 2.32
254 255 6.063404 TGGCAGCATTCATGATAGTATTTGA 58.937 36.000 0.00 0.00 0.00 2.69
255 256 6.717997 TGGCAGCATTCATGATAGTATTTGAT 59.282 34.615 0.00 0.00 0.00 2.57
626 627 2.423538 GAGAGAGAGAGAGTCAACCAGC 59.576 54.545 0.00 0.00 0.00 4.85
631 632 1.892474 GAGAGAGTCAACCAGCAGTCT 59.108 52.381 0.00 0.00 0.00 3.24
633 634 1.342819 GAGAGTCAACCAGCAGTCTGT 59.657 52.381 0.93 0.00 38.66 3.41
643 644 2.433838 CAGTCTGTGAGGCGCCAG 60.434 66.667 31.54 17.75 0.00 4.85
645 646 2.740055 GTCTGTGAGGCGCCAGTG 60.740 66.667 31.54 13.66 0.00 3.66
655 656 2.031919 CGCCAGTGGTGCCTACAA 59.968 61.111 10.38 0.00 0.00 2.41
656 657 2.325082 CGCCAGTGGTGCCTACAAC 61.325 63.158 10.38 0.00 0.00 3.32
657 658 1.971695 GCCAGTGGTGCCTACAACC 60.972 63.158 11.74 0.00 30.55 3.77
658 659 1.454104 CCAGTGGTGCCTACAACCA 59.546 57.895 0.00 0.00 30.55 3.67
665 666 1.339929 GGTGCCTACAACCAACCAAAG 59.660 52.381 0.00 0.00 0.00 2.77
670 671 2.031157 CCTACAACCAACCAAAGAAGCG 60.031 50.000 0.00 0.00 0.00 4.68
721 727 4.421479 CCTGGAGCGAGCGACGTT 62.421 66.667 0.00 0.00 44.60 3.99
722 728 3.175240 CTGGAGCGAGCGACGTTG 61.175 66.667 0.00 0.00 44.60 4.10
723 729 3.898627 CTGGAGCGAGCGACGTTGT 62.899 63.158 4.37 0.00 44.60 3.32
724 730 2.177531 GGAGCGAGCGACGTTGTA 59.822 61.111 4.37 0.00 44.60 2.41
725 731 1.868251 GGAGCGAGCGACGTTGTAG 60.868 63.158 4.37 0.00 44.60 2.74
726 732 1.134075 GAGCGAGCGACGTTGTAGA 59.866 57.895 4.37 0.00 44.60 2.59
727 733 1.126996 GAGCGAGCGACGTTGTAGAC 61.127 60.000 4.37 0.00 44.60 2.59
728 734 1.154263 GCGAGCGACGTTGTAGACT 60.154 57.895 4.37 0.00 44.60 3.24
729 735 1.126996 GCGAGCGACGTTGTAGACTC 61.127 60.000 4.37 1.58 44.60 3.36
730 736 0.443088 CGAGCGACGTTGTAGACTCT 59.557 55.000 4.37 0.00 37.22 3.24
731 737 1.657594 CGAGCGACGTTGTAGACTCTA 59.342 52.381 4.37 0.00 37.22 2.43
732 738 2.285141 CGAGCGACGTTGTAGACTCTAG 60.285 54.545 4.37 0.00 37.22 2.43
733 739 2.928757 GAGCGACGTTGTAGACTCTAGA 59.071 50.000 4.37 0.00 0.00 2.43
783 789 0.378962 GTCAGACGGAGATGAGACGG 59.621 60.000 0.00 0.00 0.00 4.79
867 873 4.038080 CGTTGGCGCCAAGAACCC 62.038 66.667 40.97 26.90 36.52 4.11
888 894 0.905839 CGTCGAAACGTACTAGCAGC 59.094 55.000 0.00 0.00 43.94 5.25
956 962 4.135153 CCACCTCTCGCCTCACCG 62.135 72.222 0.00 0.00 0.00 4.94
961 967 2.034532 TCTCGCCTCACCGTACCA 59.965 61.111 0.00 0.00 0.00 3.25
962 968 2.181021 CTCGCCTCACCGTACCAC 59.819 66.667 0.00 0.00 0.00 4.16
963 969 2.598099 TCGCCTCACCGTACCACA 60.598 61.111 0.00 0.00 0.00 4.17
964 970 2.431942 CGCCTCACCGTACCACAC 60.432 66.667 0.00 0.00 0.00 3.82
965 971 2.047560 GCCTCACCGTACCACACC 60.048 66.667 0.00 0.00 0.00 4.16
982 988 2.227036 CCCAGCCAGAGACCAAGGT 61.227 63.158 0.00 0.00 0.00 3.50
986 992 0.542232 AGCCAGAGACCAAGGTACGT 60.542 55.000 0.00 0.00 0.00 3.57
1005 1011 6.652481 GGTACGTAGCTACTATCAAGATGGTA 59.348 42.308 21.20 9.12 34.29 3.25
1030 1036 2.100991 GAAGAAGCAATGCCGCCG 59.899 61.111 0.00 0.00 0.00 6.46
1182 1191 0.107508 CCCTGGACATCGTGATGCTT 60.108 55.000 9.69 0.00 42.39 3.91
1486 1495 0.679505 CCTCGTGTGGGAGAAGAACA 59.320 55.000 0.00 0.00 36.08 3.18
1487 1496 1.276421 CCTCGTGTGGGAGAAGAACAT 59.724 52.381 0.00 0.00 36.08 2.71
1531 1540 1.064463 AGATCCTCCCCAACGTACGTA 60.064 52.381 23.12 4.28 0.00 3.57
1534 1543 0.967380 CCTCCCCAACGTACGTACCT 60.967 60.000 23.12 2.73 0.00 3.08
1590 1599 4.893524 ACCAAAACCAAAACCAAAACCAAA 59.106 33.333 0.00 0.00 0.00 3.28
1591 1600 5.362717 ACCAAAACCAAAACCAAAACCAAAA 59.637 32.000 0.00 0.00 0.00 2.44
1592 1601 5.692204 CCAAAACCAAAACCAAAACCAAAAC 59.308 36.000 0.00 0.00 0.00 2.43
1593 1602 5.455056 AAACCAAAACCAAAACCAAAACC 57.545 34.783 0.00 0.00 0.00 3.27
1594 1603 4.100279 ACCAAAACCAAAACCAAAACCA 57.900 36.364 0.00 0.00 0.00 3.67
1596 1605 4.893524 ACCAAAACCAAAACCAAAACCAAA 59.106 33.333 0.00 0.00 0.00 3.28
1597 1606 5.362717 ACCAAAACCAAAACCAAAACCAAAA 59.637 32.000 0.00 0.00 0.00 2.44
1598 1607 5.692204 CCAAAACCAAAACCAAAACCAAAAC 59.308 36.000 0.00 0.00 0.00 2.43
1601 1610 4.470602 ACCAAAACCAAAACCAAAACCAA 58.529 34.783 0.00 0.00 0.00 3.67
1602 1611 4.893524 ACCAAAACCAAAACCAAAACCAAA 59.106 33.333 0.00 0.00 0.00 3.28
1603 1612 5.540337 ACCAAAACCAAAACCAAAACCAAAT 59.460 32.000 0.00 0.00 0.00 2.32
1604 1613 6.096036 CCAAAACCAAAACCAAAACCAAATC 58.904 36.000 0.00 0.00 0.00 2.17
1605 1614 5.553290 AAACCAAAACCAAAACCAAATCG 57.447 34.783 0.00 0.00 0.00 3.34
1606 1615 4.209307 ACCAAAACCAAAACCAAATCGT 57.791 36.364 0.00 0.00 0.00 3.73
1607 1616 4.185394 ACCAAAACCAAAACCAAATCGTC 58.815 39.130 0.00 0.00 0.00 4.20
1608 1617 3.244111 CCAAAACCAAAACCAAATCGTCG 59.756 43.478 0.00 0.00 0.00 5.12
1609 1618 2.128367 AACCAAAACCAAATCGTCGC 57.872 45.000 0.00 0.00 0.00 5.19
1623 1632 3.362797 TCGCTTCGCTGACGGACT 61.363 61.111 0.00 0.00 40.63 3.85
1626 1635 2.089349 GCTTCGCTGACGGACTGAC 61.089 63.158 0.00 0.00 40.63 3.51
1628 1637 3.263503 TTCGCTGACGGACTGACGG 62.264 63.158 0.00 0.00 40.63 4.79
1629 1638 3.733960 CGCTGACGGACTGACGGA 61.734 66.667 0.00 0.00 38.39 4.69
1630 1639 2.179517 GCTGACGGACTGACGGAG 59.820 66.667 0.00 0.00 38.39 4.63
1631 1640 2.878429 CTGACGGACTGACGGAGG 59.122 66.667 0.00 0.00 38.39 4.30
1632 1641 3.343788 CTGACGGACTGACGGAGGC 62.344 68.421 0.00 0.00 38.39 4.70
1746 1756 3.879295 CTCAACCTCTTCAACTGCAAGAA 59.121 43.478 0.00 0.00 37.43 2.52
2066 2076 2.282958 AGGACTCCAAGTCGGCGA 60.283 61.111 4.99 4.99 45.96 5.54
2402 2430 1.069427 GAGCTCGCATGCCTCTGAT 59.931 57.895 13.15 0.00 0.00 2.90
2412 2444 2.655090 TGCCTCTGATTCAAACCACA 57.345 45.000 0.00 0.00 0.00 4.17
2416 2448 2.554032 CCTCTGATTCAAACCACACACC 59.446 50.000 0.00 0.00 0.00 4.16
2418 2450 2.092158 TCTGATTCAAACCACACACCCA 60.092 45.455 0.00 0.00 0.00 4.51
2420 2452 1.339929 GATTCAAACCACACACCCACC 59.660 52.381 0.00 0.00 0.00 4.61
2422 2454 1.380515 CAAACCACACACCCACCCA 60.381 57.895 0.00 0.00 0.00 4.51
2423 2455 1.380650 AAACCACACACCCACCCAC 60.381 57.895 0.00 0.00 0.00 4.61
2424 2456 2.864770 AAACCACACACCCACCCACC 62.865 60.000 0.00 0.00 0.00 4.61
2425 2457 4.596585 CCACACACCCACCCACCC 62.597 72.222 0.00 0.00 0.00 4.61
2426 2458 4.947147 CACACACCCACCCACCCG 62.947 72.222 0.00 0.00 0.00 5.28
2429 2461 4.995058 ACACCCACCCACCCGGAT 62.995 66.667 0.73 0.00 34.64 4.18
2576 2617 4.691860 ACTTGTCAATGATAGCAAGTGC 57.308 40.909 14.36 0.00 46.43 4.40
2594 2636 6.074142 GCAAGTGCCTGATTTTTGTTAAGAAG 60.074 38.462 0.00 0.00 34.31 2.85
2613 2655 0.894141 GTGGCCCATGCATGTTAACA 59.106 50.000 24.58 11.41 40.13 2.41
2624 2666 2.892373 ATGTTAACAACGTGATGCCG 57.108 45.000 13.23 0.00 0.00 5.69
2665 2711 1.742308 ACCACCCACCACAATCTACT 58.258 50.000 0.00 0.00 0.00 2.57
2667 2713 2.039879 ACCACCCACCACAATCTACTTC 59.960 50.000 0.00 0.00 0.00 3.01
2668 2714 2.039746 CCACCCACCACAATCTACTTCA 59.960 50.000 0.00 0.00 0.00 3.02
2669 2715 3.338249 CACCCACCACAATCTACTTCAG 58.662 50.000 0.00 0.00 0.00 3.02
2670 2716 3.007940 CACCCACCACAATCTACTTCAGA 59.992 47.826 0.00 0.00 37.79 3.27
2671 2717 3.650942 ACCCACCACAATCTACTTCAGAA 59.349 43.478 0.00 0.00 36.67 3.02
2687 2736 1.070309 CAGAACGTTGCTCTTGCTCAC 60.070 52.381 5.00 0.00 40.48 3.51
2688 2737 0.937304 GAACGTTGCTCTTGCTCACA 59.063 50.000 5.00 0.00 40.48 3.58
2714 2763 6.043411 CCGAAACCCAACAAAATTTACTTCA 58.957 36.000 0.00 0.00 0.00 3.02
2726 2775 7.379529 ACAAAATTTACTTCAGAACAATCGCAG 59.620 33.333 0.00 0.00 0.00 5.18
2731 2780 1.372582 TCAGAACAATCGCAGCATCC 58.627 50.000 0.00 0.00 0.00 3.51
2930 3006 4.467769 AGATACATGGCAGCTTGCTAAAT 58.532 39.130 0.00 0.00 44.28 1.40
2967 3043 7.776933 TTATTCCAAGAACTGAAGATCATCG 57.223 36.000 0.00 0.00 0.00 3.84
3082 3162 9.052759 TCAAGATCACACATCATATCATCTTTG 57.947 33.333 0.00 0.00 28.74 2.77
3142 3222 5.257082 TCAAGACCGATAATGTTCGATGA 57.743 39.130 0.00 0.00 41.62 2.92
3143 3223 5.041287 TCAAGACCGATAATGTTCGATGAC 58.959 41.667 0.00 0.00 41.62 3.06
3144 3224 4.649088 AGACCGATAATGTTCGATGACA 57.351 40.909 0.00 0.00 41.62 3.58
3145 3225 5.006153 AGACCGATAATGTTCGATGACAA 57.994 39.130 0.00 0.00 41.62 3.18
3146 3226 4.804139 AGACCGATAATGTTCGATGACAAC 59.196 41.667 0.00 0.00 41.62 3.32
3157 3237 7.026631 TGTTCGATGACAACAAAGAAAAGAT 57.973 32.000 0.00 0.00 30.67 2.40
3158 3238 6.912051 TGTTCGATGACAACAAAGAAAAGATG 59.088 34.615 0.00 0.00 30.67 2.90
3166 3254 6.564328 ACAACAAAGAAAAGATGAGTTCACC 58.436 36.000 0.00 0.00 0.00 4.02
3228 3316 0.528684 GGAGGAACTTGCGGATCGAG 60.529 60.000 0.00 0.00 41.55 4.04
3314 3402 0.756294 TCCTGAAACAAGGCGAGTCA 59.244 50.000 0.00 0.00 37.24 3.41
3323 3411 2.146342 CAAGGCGAGTCATTCAGTGTT 58.854 47.619 0.00 0.00 0.00 3.32
3333 3421 5.610398 AGTCATTCAGTGTTGATGTGTACA 58.390 37.500 0.00 0.00 32.27 2.90
3336 3424 5.466393 TCATTCAGTGTTGATGTGTACAGTG 59.534 40.000 0.00 0.00 43.70 3.66
3342 3430 5.822519 AGTGTTGATGTGTACAGTGATTTGT 59.177 36.000 0.00 0.00 35.09 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.878406 TGCTCAATAAAAACCTTCCCAAA 57.122 34.783 0.00 0.00 0.00 3.28
1 2 6.229733 CAATGCTCAATAAAAACCTTCCCAA 58.770 36.000 0.00 0.00 0.00 4.12
2 3 5.792741 CAATGCTCAATAAAAACCTTCCCA 58.207 37.500 0.00 0.00 0.00 4.37
3 4 4.631377 GCAATGCTCAATAAAAACCTTCCC 59.369 41.667 0.00 0.00 0.00 3.97
4 5 5.237048 TGCAATGCTCAATAAAAACCTTCC 58.763 37.500 6.82 0.00 0.00 3.46
5 6 6.783892 TTGCAATGCTCAATAAAAACCTTC 57.216 33.333 6.82 0.00 0.00 3.46
6 7 8.313292 TCTATTGCAATGCTCAATAAAAACCTT 58.687 29.630 22.27 0.00 36.37 3.50
7 8 7.839907 TCTATTGCAATGCTCAATAAAAACCT 58.160 30.769 22.27 0.00 36.37 3.50
8 9 7.761249 ACTCTATTGCAATGCTCAATAAAAACC 59.239 33.333 22.27 0.00 36.37 3.27
9 10 8.693542 ACTCTATTGCAATGCTCAATAAAAAC 57.306 30.769 22.27 0.00 36.37 2.43
10 11 8.742777 AGACTCTATTGCAATGCTCAATAAAAA 58.257 29.630 22.27 0.00 36.37 1.94
11 12 8.284945 AGACTCTATTGCAATGCTCAATAAAA 57.715 30.769 22.27 0.00 36.37 1.52
12 13 7.870509 AGACTCTATTGCAATGCTCAATAAA 57.129 32.000 22.27 0.00 36.37 1.40
13 14 8.962884 TTAGACTCTATTGCAATGCTCAATAA 57.037 30.769 22.27 11.01 36.37 1.40
14 15 9.565090 AATTAGACTCTATTGCAATGCTCAATA 57.435 29.630 22.27 2.38 35.87 1.90
15 16 8.461249 AATTAGACTCTATTGCAATGCTCAAT 57.539 30.769 22.27 8.86 37.79 2.57
16 17 7.870509 AATTAGACTCTATTGCAATGCTCAA 57.129 32.000 22.27 7.05 0.00 3.02
17 18 7.201758 CCAAATTAGACTCTATTGCAATGCTCA 60.202 37.037 22.27 0.44 0.00 4.26
18 19 7.137426 CCAAATTAGACTCTATTGCAATGCTC 58.863 38.462 22.27 10.14 0.00 4.26
19 20 6.604795 ACCAAATTAGACTCTATTGCAATGCT 59.395 34.615 22.27 12.56 0.00 3.79
20 21 6.799512 ACCAAATTAGACTCTATTGCAATGC 58.200 36.000 22.27 0.00 0.00 3.56
21 22 8.072567 GCTACCAAATTAGACTCTATTGCAATG 58.927 37.037 22.27 11.73 0.00 2.82
22 23 7.995488 AGCTACCAAATTAGACTCTATTGCAAT 59.005 33.333 17.56 17.56 0.00 3.56
23 24 7.338710 AGCTACCAAATTAGACTCTATTGCAA 58.661 34.615 0.00 0.00 0.00 4.08
24 25 6.889198 AGCTACCAAATTAGACTCTATTGCA 58.111 36.000 0.00 0.00 0.00 4.08
25 26 6.986817 TGAGCTACCAAATTAGACTCTATTGC 59.013 38.462 0.00 0.00 0.00 3.56
26 27 8.986847 CATGAGCTACCAAATTAGACTCTATTG 58.013 37.037 0.00 0.00 0.00 1.90
27 28 8.709308 ACATGAGCTACCAAATTAGACTCTATT 58.291 33.333 0.00 0.00 0.00 1.73
28 29 8.147058 CACATGAGCTACCAAATTAGACTCTAT 58.853 37.037 0.00 0.00 0.00 1.98
29 30 7.492524 CACATGAGCTACCAAATTAGACTCTA 58.507 38.462 0.00 0.00 0.00 2.43
30 31 6.344500 CACATGAGCTACCAAATTAGACTCT 58.656 40.000 0.00 0.00 0.00 3.24
31 32 5.007136 GCACATGAGCTACCAAATTAGACTC 59.993 44.000 7.97 0.00 0.00 3.36
32 33 4.878397 GCACATGAGCTACCAAATTAGACT 59.122 41.667 7.97 0.00 0.00 3.24
33 34 4.878397 AGCACATGAGCTACCAAATTAGAC 59.122 41.667 16.52 0.00 44.50 2.59
34 35 5.102953 AGCACATGAGCTACCAAATTAGA 57.897 39.130 16.52 0.00 44.50 2.10
35 36 5.049818 GCTAGCACATGAGCTACCAAATTAG 60.050 44.000 19.33 10.98 44.50 1.73
36 37 4.816385 GCTAGCACATGAGCTACCAAATTA 59.184 41.667 19.33 0.70 44.50 1.40
37 38 3.629398 GCTAGCACATGAGCTACCAAATT 59.371 43.478 19.33 0.00 44.50 1.82
38 39 3.209410 GCTAGCACATGAGCTACCAAAT 58.791 45.455 19.33 0.00 44.50 2.32
39 40 2.027285 TGCTAGCACATGAGCTACCAAA 60.027 45.455 19.33 2.81 44.50 3.28
40 41 1.554617 TGCTAGCACATGAGCTACCAA 59.445 47.619 19.33 6.66 44.50 3.67
41 42 1.134699 GTGCTAGCACATGAGCTACCA 60.135 52.381 36.93 16.48 44.50 3.25
42 43 1.576356 GTGCTAGCACATGAGCTACC 58.424 55.000 36.93 14.24 44.50 3.18
52 53 1.089920 CAACCCTGATGTGCTAGCAC 58.910 55.000 35.76 35.76 46.33 4.40
53 54 0.692476 ACAACCCTGATGTGCTAGCA 59.308 50.000 14.93 14.93 0.00 3.49
54 55 1.089920 CACAACCCTGATGTGCTAGC 58.910 55.000 8.10 8.10 41.42 3.42
60 61 2.108075 TGGATCAACACAACCCTGATGT 59.892 45.455 0.00 0.00 29.97 3.06
61 62 2.489329 GTGGATCAACACAACCCTGATG 59.511 50.000 0.00 0.00 40.99 3.07
62 63 2.555227 GGTGGATCAACACAACCCTGAT 60.555 50.000 1.86 0.00 43.08 2.90
63 64 1.202879 GGTGGATCAACACAACCCTGA 60.203 52.381 1.86 0.00 43.08 3.86
64 65 1.247567 GGTGGATCAACACAACCCTG 58.752 55.000 1.86 0.00 43.08 4.45
65 66 0.250727 CGGTGGATCAACACAACCCT 60.251 55.000 1.86 0.00 43.08 4.34
66 67 1.241315 CCGGTGGATCAACACAACCC 61.241 60.000 1.86 0.00 43.08 4.11
67 68 1.862602 GCCGGTGGATCAACACAACC 61.863 60.000 1.90 0.00 43.08 3.77
68 69 1.579429 GCCGGTGGATCAACACAAC 59.421 57.895 1.90 0.00 43.08 3.32
69 70 1.963855 CGCCGGTGGATCAACACAA 60.964 57.895 7.26 0.00 43.08 3.33
70 71 2.358125 CGCCGGTGGATCAACACA 60.358 61.111 7.26 0.00 43.08 3.72
71 72 3.124921 CCGCCGGTGGATCAACAC 61.125 66.667 30.98 0.00 40.60 3.32
72 73 3.632080 ACCGCCGGTGGATCAACA 61.632 61.111 40.02 0.00 32.98 3.33
82 83 4.814294 GTCTAGCCACACCGCCGG 62.814 72.222 0.00 0.00 0.00 6.13
94 95 6.206634 AGAGATAAAATCAGAGGAGCGTCTAG 59.793 42.308 0.00 0.00 0.00 2.43
95 96 6.065374 AGAGATAAAATCAGAGGAGCGTCTA 58.935 40.000 0.00 0.00 0.00 2.59
96 97 4.892934 AGAGATAAAATCAGAGGAGCGTCT 59.107 41.667 0.00 0.00 0.00 4.18
97 98 5.195001 AGAGATAAAATCAGAGGAGCGTC 57.805 43.478 0.00 0.00 0.00 5.19
98 99 5.278758 GCTAGAGATAAAATCAGAGGAGCGT 60.279 44.000 0.00 0.00 0.00 5.07
99 100 5.048083 AGCTAGAGATAAAATCAGAGGAGCG 60.048 44.000 0.00 0.00 0.00 5.03
100 101 6.345096 AGCTAGAGATAAAATCAGAGGAGC 57.655 41.667 0.00 0.00 0.00 4.70
101 102 9.612066 AAAAAGCTAGAGATAAAATCAGAGGAG 57.388 33.333 0.00 0.00 0.00 3.69
105 106 9.890629 TGCTAAAAAGCTAGAGATAAAATCAGA 57.109 29.630 0.00 0.00 35.49 3.27
107 108 9.890629 TCTGCTAAAAAGCTAGAGATAAAATCA 57.109 29.630 0.00 0.00 35.49 2.57
109 110 8.821894 CGTCTGCTAAAAAGCTAGAGATAAAAT 58.178 33.333 0.00 0.00 35.49 1.82
110 111 8.033038 TCGTCTGCTAAAAAGCTAGAGATAAAA 58.967 33.333 0.00 0.00 35.49 1.52
111 112 7.544622 TCGTCTGCTAAAAAGCTAGAGATAAA 58.455 34.615 0.00 0.00 35.49 1.40
112 113 7.096884 TCGTCTGCTAAAAAGCTAGAGATAA 57.903 36.000 0.00 0.00 35.49 1.75
113 114 6.694877 TCGTCTGCTAAAAAGCTAGAGATA 57.305 37.500 0.00 0.00 35.49 1.98
114 115 5.584253 TCGTCTGCTAAAAAGCTAGAGAT 57.416 39.130 0.00 0.00 35.49 2.75
115 116 5.105716 ACATCGTCTGCTAAAAAGCTAGAGA 60.106 40.000 0.00 0.00 35.49 3.10
116 117 5.105752 ACATCGTCTGCTAAAAAGCTAGAG 58.894 41.667 0.00 0.00 35.49 2.43
117 118 5.073311 ACATCGTCTGCTAAAAAGCTAGA 57.927 39.130 0.00 0.00 35.49 2.43
118 119 6.531948 AGTTACATCGTCTGCTAAAAAGCTAG 59.468 38.462 0.00 0.00 35.49 3.42
119 120 6.395629 AGTTACATCGTCTGCTAAAAAGCTA 58.604 36.000 0.00 0.00 35.49 3.32
120 121 5.238583 AGTTACATCGTCTGCTAAAAAGCT 58.761 37.500 0.00 0.00 35.49 3.74
121 122 5.532025 AGTTACATCGTCTGCTAAAAAGC 57.468 39.130 0.00 0.00 0.00 3.51
128 129 8.982685 CATCAAATAATAGTTACATCGTCTGCT 58.017 33.333 0.00 0.00 0.00 4.24
129 130 8.765219 ACATCAAATAATAGTTACATCGTCTGC 58.235 33.333 0.00 0.00 0.00 4.26
131 132 9.817809 ACACATCAAATAATAGTTACATCGTCT 57.182 29.630 0.00 0.00 0.00 4.18
189 190 9.237846 GCTTTCATGGCTAGTTTTATTAACATC 57.762 33.333 0.00 0.00 0.00 3.06
190 191 8.197439 GGCTTTCATGGCTAGTTTTATTAACAT 58.803 33.333 0.00 0.00 0.00 2.71
191 192 7.396055 AGGCTTTCATGGCTAGTTTTATTAACA 59.604 33.333 0.00 0.00 41.20 2.41
192 193 7.772166 AGGCTTTCATGGCTAGTTTTATTAAC 58.228 34.615 0.00 0.00 41.20 2.01
193 194 7.954666 AGGCTTTCATGGCTAGTTTTATTAA 57.045 32.000 0.00 0.00 41.20 1.40
194 195 7.954666 AAGGCTTTCATGGCTAGTTTTATTA 57.045 32.000 0.00 0.00 42.20 0.98
195 196 6.857437 AAGGCTTTCATGGCTAGTTTTATT 57.143 33.333 0.00 0.00 42.20 1.40
196 197 6.857437 AAAGGCTTTCATGGCTAGTTTTAT 57.143 33.333 6.68 0.00 42.20 1.40
197 198 7.768807 TTAAAGGCTTTCATGGCTAGTTTTA 57.231 32.000 17.13 0.00 42.20 1.52
198 199 6.664428 TTAAAGGCTTTCATGGCTAGTTTT 57.336 33.333 17.13 0.00 42.20 2.43
199 200 6.664428 TTTAAAGGCTTTCATGGCTAGTTT 57.336 33.333 17.13 0.00 42.20 2.66
200 201 6.664428 TTTTAAAGGCTTTCATGGCTAGTT 57.336 33.333 17.13 0.00 42.20 2.24
201 202 6.664428 TTTTTAAAGGCTTTCATGGCTAGT 57.336 33.333 17.13 0.00 42.20 2.57
221 222 5.553123 TCATGAATGCTGCCAAATCTTTTT 58.447 33.333 0.00 0.00 0.00 1.94
222 223 5.155278 TCATGAATGCTGCCAAATCTTTT 57.845 34.783 0.00 0.00 0.00 2.27
223 224 4.811969 TCATGAATGCTGCCAAATCTTT 57.188 36.364 0.00 0.00 0.00 2.52
224 225 5.597182 ACTATCATGAATGCTGCCAAATCTT 59.403 36.000 0.00 0.00 0.00 2.40
225 226 5.138276 ACTATCATGAATGCTGCCAAATCT 58.862 37.500 0.00 0.00 0.00 2.40
226 227 5.449107 ACTATCATGAATGCTGCCAAATC 57.551 39.130 0.00 0.00 0.00 2.17
227 228 7.534723 AATACTATCATGAATGCTGCCAAAT 57.465 32.000 0.00 0.00 0.00 2.32
228 229 6.964807 AATACTATCATGAATGCTGCCAAA 57.035 33.333 0.00 0.00 0.00 3.28
229 230 6.546772 TCAAATACTATCATGAATGCTGCCAA 59.453 34.615 0.00 0.00 0.00 4.52
230 231 6.063404 TCAAATACTATCATGAATGCTGCCA 58.937 36.000 0.00 0.00 0.00 4.92
231 232 6.564709 TCAAATACTATCATGAATGCTGCC 57.435 37.500 0.00 0.00 0.00 4.85
603 604 3.941483 CTGGTTGACTCTCTCTCTCTCTC 59.059 52.174 0.00 0.00 0.00 3.20
604 605 3.873801 GCTGGTTGACTCTCTCTCTCTCT 60.874 52.174 0.00 0.00 0.00 3.10
605 606 2.423538 GCTGGTTGACTCTCTCTCTCTC 59.576 54.545 0.00 0.00 0.00 3.20
606 607 2.224992 TGCTGGTTGACTCTCTCTCTCT 60.225 50.000 0.00 0.00 0.00 3.10
607 608 2.164219 CTGCTGGTTGACTCTCTCTCTC 59.836 54.545 0.00 0.00 0.00 3.20
608 609 2.170166 CTGCTGGTTGACTCTCTCTCT 58.830 52.381 0.00 0.00 0.00 3.10
609 610 1.892474 ACTGCTGGTTGACTCTCTCTC 59.108 52.381 0.00 0.00 0.00 3.20
610 611 1.892474 GACTGCTGGTTGACTCTCTCT 59.108 52.381 0.00 0.00 0.00 3.10
611 612 1.892474 AGACTGCTGGTTGACTCTCTC 59.108 52.381 0.00 0.00 0.00 3.20
612 613 1.617850 CAGACTGCTGGTTGACTCTCT 59.382 52.381 0.00 0.00 38.51 3.10
613 614 1.342819 ACAGACTGCTGGTTGACTCTC 59.657 52.381 1.25 0.00 46.60 3.20
626 627 2.433838 CTGGCGCCTCACAGACTG 60.434 66.667 29.70 0.00 36.86 3.51
631 632 4.624364 CACCACTGGCGCCTCACA 62.624 66.667 29.70 5.90 0.00 3.58
643 644 0.466555 TGGTTGGTTGTAGGCACCAC 60.467 55.000 0.00 0.00 32.38 4.16
645 646 1.339929 CTTTGGTTGGTTGTAGGCACC 59.660 52.381 0.00 0.00 0.00 5.01
654 655 1.040339 TGGCGCTTCTTTGGTTGGTT 61.040 50.000 7.64 0.00 0.00 3.67
655 656 1.454847 TGGCGCTTCTTTGGTTGGT 60.455 52.632 7.64 0.00 0.00 3.67
656 657 1.007387 GTGGCGCTTCTTTGGTTGG 60.007 57.895 7.64 0.00 0.00 3.77
657 658 1.007387 GGTGGCGCTTCTTTGGTTG 60.007 57.895 7.64 0.00 0.00 3.77
658 659 1.152756 AGGTGGCGCTTCTTTGGTT 60.153 52.632 7.64 0.00 0.00 3.67
665 666 1.285950 GGAAAACAGGTGGCGCTTC 59.714 57.895 7.64 0.00 0.00 3.86
670 671 0.890683 CAGGATGGAAAACAGGTGGC 59.109 55.000 0.00 0.00 0.00 5.01
707 713 1.868251 CTACAACGTCGCTCGCTCC 60.868 63.158 0.00 0.00 44.19 4.70
708 714 1.126996 GTCTACAACGTCGCTCGCTC 61.127 60.000 0.00 0.00 44.19 5.03
714 720 2.030701 CCTCTAGAGTCTACAACGTCGC 59.969 54.545 18.42 0.00 0.00 5.19
715 721 2.608546 CCCTCTAGAGTCTACAACGTCG 59.391 54.545 18.42 0.00 0.00 5.12
716 722 3.622612 GTCCCTCTAGAGTCTACAACGTC 59.377 52.174 18.42 0.00 0.00 4.34
717 723 3.608796 GTCCCTCTAGAGTCTACAACGT 58.391 50.000 18.42 0.00 0.00 3.99
718 724 2.608546 CGTCCCTCTAGAGTCTACAACG 59.391 54.545 18.42 13.21 0.00 4.10
719 725 2.355444 GCGTCCCTCTAGAGTCTACAAC 59.645 54.545 18.42 6.25 0.00 3.32
720 726 2.641305 GCGTCCCTCTAGAGTCTACAA 58.359 52.381 18.42 0.00 0.00 2.41
721 727 1.472904 CGCGTCCCTCTAGAGTCTACA 60.473 57.143 18.42 0.00 0.00 2.74
722 728 1.219646 CGCGTCCCTCTAGAGTCTAC 58.780 60.000 18.42 11.60 0.00 2.59
723 729 0.532417 GCGCGTCCCTCTAGAGTCTA 60.532 60.000 18.42 0.00 0.00 2.59
724 730 1.820481 GCGCGTCCCTCTAGAGTCT 60.820 63.158 18.42 0.00 0.00 3.24
725 731 2.716864 GCGCGTCCCTCTAGAGTC 59.283 66.667 18.42 7.69 0.00 3.36
726 732 3.203412 CGCGCGTCCCTCTAGAGT 61.203 66.667 24.19 0.00 0.00 3.24
727 733 3.203412 ACGCGCGTCCCTCTAGAG 61.203 66.667 32.73 13.18 0.00 2.43
728 734 3.506096 CACGCGCGTCCCTCTAGA 61.506 66.667 35.61 0.00 0.00 2.43
776 782 2.287274 TTTCCCCGATGCCGTCTCA 61.287 57.895 0.00 0.00 0.00 3.27
783 789 3.202706 GCTCCGTTTCCCCGATGC 61.203 66.667 0.00 0.00 0.00 3.91
862 868 1.729131 TACGTTTCGACGCGGGTTC 60.729 57.895 12.47 0.00 36.44 3.62
863 869 2.016165 GTACGTTTCGACGCGGGTT 61.016 57.895 12.47 0.00 36.44 4.11
867 873 0.790495 TGCTAGTACGTTTCGACGCG 60.790 55.000 3.53 3.53 36.44 6.01
956 962 1.192146 TCTCTGGCTGGGTGTGGTAC 61.192 60.000 0.00 0.00 0.00 3.34
961 967 1.770110 TTGGTCTCTGGCTGGGTGT 60.770 57.895 0.00 0.00 0.00 4.16
962 968 1.002868 CTTGGTCTCTGGCTGGGTG 60.003 63.158 0.00 0.00 0.00 4.61
963 969 2.227036 CCTTGGTCTCTGGCTGGGT 61.227 63.158 0.00 0.00 0.00 4.51
964 970 0.909610 TACCTTGGTCTCTGGCTGGG 60.910 60.000 0.00 0.00 0.00 4.45
965 971 0.250513 GTACCTTGGTCTCTGGCTGG 59.749 60.000 0.00 0.00 0.00 4.85
982 988 7.095481 CGTTACCATCTTGATAGTAGCTACGTA 60.095 40.741 17.99 11.08 0.00 3.57
986 992 5.048224 GCCGTTACCATCTTGATAGTAGCTA 60.048 44.000 0.00 0.00 0.00 3.32
1005 1011 1.303317 ATTGCTTCTTCCCGCCGTT 60.303 52.632 0.00 0.00 0.00 4.44
1161 1170 1.524621 CATCACGATGTCCAGGGGC 60.525 63.158 0.00 0.00 34.23 5.80
1531 1540 0.984995 GCAAGAGTGGGTAGGAAGGT 59.015 55.000 0.00 0.00 0.00 3.50
1534 1543 2.879756 GCAATGCAAGAGTGGGTAGGAA 60.880 50.000 0.00 0.00 0.00 3.36
1590 1599 1.679153 AGCGACGATTTGGTTTTGGTT 59.321 42.857 0.00 0.00 0.00 3.67
1591 1600 1.314730 AGCGACGATTTGGTTTTGGT 58.685 45.000 0.00 0.00 0.00 3.67
1592 1601 2.315901 GAAGCGACGATTTGGTTTTGG 58.684 47.619 0.00 0.00 0.00 3.28
1593 1602 1.969256 CGAAGCGACGATTTGGTTTTG 59.031 47.619 5.15 0.00 35.09 2.44
1594 1603 2.309898 CGAAGCGACGATTTGGTTTT 57.690 45.000 5.15 0.00 35.09 2.43
1609 1618 1.797933 CGTCAGTCCGTCAGCGAAG 60.798 63.158 0.00 0.00 41.33 3.79
1623 1632 4.471908 ATGCATGCGCCTCCGTCA 62.472 61.111 14.09 0.00 37.32 4.35
1746 1756 2.029073 CGTTCTCCACCAGCACGT 59.971 61.111 0.00 0.00 37.04 4.49
2032 2042 0.591741 CCTCGTACGACTTGATCCGC 60.592 60.000 15.28 0.00 0.00 5.54
2066 2076 4.115199 GAAGCGGGTGGCCCTGAT 62.115 66.667 0.00 0.00 42.67 2.90
2402 2430 0.684805 GGGTGGGTGTGTGGTTTGAA 60.685 55.000 0.00 0.00 0.00 2.69
2412 2444 4.995058 ATCCGGGTGGGTGGGTGT 62.995 66.667 0.00 0.00 37.00 4.16
2425 2457 3.798202 AGAAAGAAAGAATCCGGATCCG 58.202 45.455 27.65 27.65 39.44 4.18
2426 2458 6.071896 ACAAAAGAAAGAAAGAATCCGGATCC 60.072 38.462 19.43 4.43 0.00 3.36
2427 2459 6.914259 ACAAAAGAAAGAAAGAATCCGGATC 58.086 36.000 19.43 11.42 0.00 3.36
2428 2460 6.901081 ACAAAAGAAAGAAAGAATCCGGAT 57.099 33.333 12.38 12.38 0.00 4.18
2429 2461 6.709018 AACAAAAGAAAGAAAGAATCCGGA 57.291 33.333 6.61 6.61 0.00 5.14
2529 2570 1.532868 GTCAGCTGCTTACACCAGTTG 59.467 52.381 9.47 0.00 41.21 3.16
2530 2571 1.140852 TGTCAGCTGCTTACACCAGTT 59.859 47.619 12.35 0.00 32.93 3.16
2531 2572 0.758734 TGTCAGCTGCTTACACCAGT 59.241 50.000 12.35 0.00 32.93 4.00
2576 2617 5.230182 GGCCACTTCTTAACAAAAATCAGG 58.770 41.667 0.00 0.00 0.00 3.86
2594 2636 0.894141 TGTTAACATGCATGGGCCAC 59.106 50.000 29.41 19.35 40.13 5.01
2622 2664 1.910580 AACTATCACCAGGGCCACGG 61.911 60.000 6.18 8.62 0.00 4.94
2624 2666 1.475213 GCTAACTATCACCAGGGCCAC 60.475 57.143 6.18 0.00 0.00 5.01
2665 2711 1.867233 GAGCAAGAGCAACGTTCTGAA 59.133 47.619 0.00 0.00 45.49 3.02
2667 2713 1.070309 GTGAGCAAGAGCAACGTTCTG 60.070 52.381 0.00 0.00 45.49 3.02
2668 2714 1.221414 GTGAGCAAGAGCAACGTTCT 58.779 50.000 0.00 0.00 45.49 3.01
2669 2715 0.937304 TGTGAGCAAGAGCAACGTTC 59.063 50.000 0.00 0.00 45.49 3.95
2670 2716 0.940126 CTGTGAGCAAGAGCAACGTT 59.060 50.000 0.00 0.00 45.49 3.99
2671 2717 1.502163 GCTGTGAGCAAGAGCAACGT 61.502 55.000 3.99 0.00 45.49 3.99
2687 2736 2.524569 ATTTTGTTGGGTTTCGGCTG 57.475 45.000 0.00 0.00 0.00 4.85
2688 2737 3.552132 AAATTTTGTTGGGTTTCGGCT 57.448 38.095 0.00 0.00 0.00 5.52
2714 2763 0.035152 TGGGATGCTGCGATTGTTCT 60.035 50.000 0.00 0.00 0.00 3.01
2726 2775 2.281345 CGCAGGAGGATGGGATGC 60.281 66.667 0.00 0.00 35.25 3.91
2930 3006 3.712016 TGGAATAAAGCAGGCAGTGTA 57.288 42.857 0.00 0.00 0.00 2.90
2967 3043 2.768492 CGCTTCCATGAGCCAAGGC 61.768 63.158 2.02 2.02 39.51 4.35
3113 3193 8.937884 TCGAACATTATCGGTCTTGAAAATTTA 58.062 29.630 0.00 0.00 42.92 1.40
3136 3216 6.483307 ACTCATCTTTTCTTTGTTGTCATCGA 59.517 34.615 0.00 0.00 0.00 3.59
3142 3222 6.564328 GGTGAACTCATCTTTTCTTTGTTGT 58.436 36.000 0.00 0.00 0.00 3.32
3143 3223 5.682862 CGGTGAACTCATCTTTTCTTTGTTG 59.317 40.000 0.00 0.00 0.00 3.33
3144 3224 5.588648 TCGGTGAACTCATCTTTTCTTTGTT 59.411 36.000 0.00 0.00 0.00 2.83
3145 3225 5.123227 TCGGTGAACTCATCTTTTCTTTGT 58.877 37.500 0.00 0.00 0.00 2.83
3146 3226 5.673337 TCGGTGAACTCATCTTTTCTTTG 57.327 39.130 0.00 0.00 0.00 2.77
3157 3237 0.179234 TGCAAGGTTCGGTGAACTCA 59.821 50.000 9.32 1.47 41.70 3.41
3158 3238 1.002792 GTTGCAAGGTTCGGTGAACTC 60.003 52.381 0.00 0.94 41.70 3.01
3166 3254 1.283793 CAGCCTGTTGCAAGGTTCG 59.716 57.895 0.00 0.00 44.83 3.95
3201 3289 1.339055 CGCAAGTTCCTCCAAGATGGA 60.339 52.381 0.00 0.00 45.98 3.41
3228 3316 3.388350 AGAAGGAGATATCGGTTGGGAAC 59.612 47.826 0.00 0.00 0.00 3.62
3314 3402 5.610398 TCACTGTACACATCAACACTGAAT 58.390 37.500 0.00 0.00 34.49 2.57
3323 3411 7.334171 CCAATCTACAAATCACTGTACACATCA 59.666 37.037 0.00 0.00 0.00 3.07
3333 3421 6.015180 ACAAACATGCCAATCTACAAATCACT 60.015 34.615 0.00 0.00 0.00 3.41
3336 3424 8.028938 AGTTACAAACATGCCAATCTACAAATC 58.971 33.333 0.00 0.00 0.00 2.17
3342 3430 8.978874 ATATGAGTTACAAACATGCCAATCTA 57.021 30.769 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.