Multiple sequence alignment - TraesCS1B01G157600

Loading Multiple Alignment...

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 TraesCS1B01G157600 chr1B 100.000 3491 0 0 1 3491 267964687 267968177 0.000000e+00 6447
1 TraesCS1B01G157600 chr1B 100.000 219 0 0 1 219 267957833 267958051 4.200000e-109 405
2 TraesCS1B01G157600 chr1B 96.522 230 7 1 1 230 587558496 587558724 2.540000e-101 379
3 TraesCS1B01G157600 chr1D 97.337 2666 57 6 836 3491 193357878 193360539 0.000000e+00 4518
4 TraesCS1B01G157600 chr1D 87.863 585 61 6 221 803 149689049 149688473 0.000000e+00 678
5 TraesCS1B01G157600 chr1D 87.267 589 59 8 221 804 128509750 128509173 0.000000e+00 658
6 TraesCS1B01G157600 chr1A 96.637 2617 62 11 894 3491 239099900 239102509 0.000000e+00 4322
7 TraesCS1B01G157600 chr1A 85.593 590 79 6 221 805 480627671 480627083 6.400000e-172 614
8 TraesCS1B01G157600 chr1A 98.630 219 3 0 1 219 380251847 380251629 4.230000e-104 388
9 TraesCS1B01G157600 chr1A 98.630 219 3 0 1 219 543858626 543858408 4.230000e-104 388
10 TraesCS1B01G157600 chr2B 87.352 593 51 11 221 804 794612835 794612258 0.000000e+00 658
11 TraesCS1B01G157600 chr2B 89.412 255 14 4 553 806 275251799 275251557 3.380000e-80 309
12 TraesCS1B01G157600 chr5A 86.838 585 65 9 221 803 619180427 619181001 0.000000e+00 643
13 TraesCS1B01G157600 chr5A 85.476 420 53 7 388 803 601996732 601996317 6.920000e-117 431
14 TraesCS1B01G157600 chr5A 98.636 220 3 0 1 220 369675005 369674786 1.170000e-104 390
15 TraesCS1B01G157600 chr5A 98.630 219 3 0 1 219 560017113 560017331 4.230000e-104 388
16 TraesCS1B01G157600 chr3B 85.943 562 71 8 221 779 228980343 228980899 8.340000e-166 593
17 TraesCS1B01G157600 chr7A 85.299 585 71 11 221 803 167182782 167182211 1.080000e-164 590
18 TraesCS1B01G157600 chr7B 87.967 482 40 8 221 701 69667650 69667186 1.420000e-153 553
19 TraesCS1B01G157600 chr7B 81.942 587 93 10 222 803 609814306 609814884 5.240000e-133 484
20 TraesCS1B01G157600 chr4B 99.087 219 2 0 1 219 422539392 422539174 9.080000e-106 394
21 TraesCS1B01G157600 chr4B 95.021 241 11 1 1 241 411561458 411561697 9.150000e-101 377
22 TraesCS1B01G157600 chr2A 98.636 220 3 0 1 220 508056781 508056562 1.170000e-104 390
23 TraesCS1B01G157600 chr6D 88.601 193 16 6 609 797 351407908 351408098 2.710000e-56 230


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 TraesCS1B01G157600 chr1B 267964687 267968177 3490 False 6447 6447 100.000 1 3491 1 chr1B.!!$F2 3490
1 TraesCS1B01G157600 chr1D 193357878 193360539 2661 False 4518 4518 97.337 836 3491 1 chr1D.!!$F1 2655
2 TraesCS1B01G157600 chr1D 149688473 149689049 576 True 678 678 87.863 221 803 1 chr1D.!!$R2 582
3 TraesCS1B01G157600 chr1D 128509173 128509750 577 True 658 658 87.267 221 804 1 chr1D.!!$R1 583
4 TraesCS1B01G157600 chr1A 239099900 239102509 2609 False 4322 4322 96.637 894 3491 1 chr1A.!!$F1 2597
5 TraesCS1B01G157600 chr1A 480627083 480627671 588 True 614 614 85.593 221 805 1 chr1A.!!$R2 584
6 TraesCS1B01G157600 chr2B 794612258 794612835 577 True 658 658 87.352 221 804 1 chr2B.!!$R2 583
7 TraesCS1B01G157600 chr5A 619180427 619181001 574 False 643 643 86.838 221 803 1 chr5A.!!$F2 582
8 TraesCS1B01G157600 chr3B 228980343 228980899 556 False 593 593 85.943 221 779 1 chr3B.!!$F1 558
9 TraesCS1B01G157600 chr7A 167182211 167182782 571 True 590 590 85.299 221 803 1 chr7A.!!$R1 582
10 TraesCS1B01G157600 chr7B 609814306 609814884 578 False 484 484 81.942 222 803 1 chr7B.!!$F1 581

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
42 43 0.030908 CCGTTCGGCACTAGGATCTC 59.969 60.000 0.0 0.00 0.00 2.75 F
44 45 0.030908 GTTCGGCACTAGGATCTCCG 59.969 60.000 0.0 0.00 42.08 4.63 F
92 93 0.036164 CATCACCCCCGTTCACTTGA 59.964 55.000 0.0 0.00 0.00 3.02 F
144 145 0.043940 AGATGCACTCTCCTTCCCCT 59.956 55.000 0.0 0.00 0.00 4.79 F
149 150 0.247736 CACTCTCCTTCCCCTCGTTG 59.752 60.000 0.0 0.00 0.00 4.10 F
993 1020 0.391228 GCTCTCCTCCTTCCGATTCC 59.609 60.000 0.0 0.00 0.00 3.01 F
1476 1509 1.606889 GGACGTGGTCTCCTGGAGT 60.607 63.158 22.5 3.58 32.47 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1317 0.032815 TGTGGACGAGTGAATTCGCA 59.967 50.000 20.55 0.0 44.15 5.10 R
1435 1468 2.046700 GGGCATCCGGTCGAACAA 60.047 61.111 0.00 0.0 0.00 2.83 R
1476 1509 2.186644 CACCCGTCGATCATGGCA 59.813 61.111 0.00 0.0 0.00 4.92 R
2298 2331 2.540101 GACATCAATCTCGCTAAACCCG 59.460 50.000 0.00 0.0 0.00 5.28 R
2337 2370 3.825143 GCCTTGTCATGGGCAATAAAT 57.175 42.857 11.15 0.0 46.84 1.40 R
2461 2494 2.428171 CCATTAAGCACCCATTGTCCTG 59.572 50.000 0.00 0.0 0.00 3.86 R
2804 2844 3.869912 GCAGAAGCCATAGGTGAAACAGA 60.870 47.826 0.00 0.0 33.93 3.41 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
17 18 2.502093 TGTGTTGAACGCGGAGGT 59.498 55.556 12.47 0.00 0.00 3.85
18 19 1.885388 TGTGTTGAACGCGGAGGTG 60.885 57.895 12.47 0.00 0.00 4.00
19 20 2.970324 TGTTGAACGCGGAGGTGC 60.970 61.111 12.47 0.00 0.00 5.01
20 21 3.723348 GTTGAACGCGGAGGTGCC 61.723 66.667 12.47 0.00 0.00 5.01
36 37 2.202570 CCGTCCGTTCGGCACTAG 60.203 66.667 6.35 0.00 43.96 2.57
37 38 2.202570 CGTCCGTTCGGCACTAGG 60.203 66.667 6.35 0.00 0.00 3.02
38 39 2.693762 CGTCCGTTCGGCACTAGGA 61.694 63.158 6.35 0.00 0.00 2.94
39 40 1.814527 GTCCGTTCGGCACTAGGAT 59.185 57.895 6.35 0.00 33.15 3.24
40 41 0.248949 GTCCGTTCGGCACTAGGATC 60.249 60.000 6.35 0.00 33.15 3.36
41 42 0.395311 TCCGTTCGGCACTAGGATCT 60.395 55.000 6.35 0.00 0.00 2.75
42 43 0.030908 CCGTTCGGCACTAGGATCTC 59.969 60.000 0.00 0.00 0.00 2.75
43 44 0.030908 CGTTCGGCACTAGGATCTCC 59.969 60.000 0.00 0.00 0.00 3.71
44 45 0.030908 GTTCGGCACTAGGATCTCCG 59.969 60.000 0.00 0.00 42.08 4.63
45 46 1.107538 TTCGGCACTAGGATCTCCGG 61.108 60.000 0.00 0.00 42.08 5.14
46 47 1.828660 CGGCACTAGGATCTCCGGT 60.829 63.158 0.00 0.00 42.08 5.28
47 48 1.742768 GGCACTAGGATCTCCGGTG 59.257 63.158 0.00 15.88 42.73 4.94
48 49 0.755698 GGCACTAGGATCTCCGGTGA 60.756 60.000 21.08 8.96 42.60 4.02
49 50 1.333177 GCACTAGGATCTCCGGTGAT 58.667 55.000 18.63 18.63 42.60 3.06
50 51 1.689273 GCACTAGGATCTCCGGTGATT 59.311 52.381 19.47 8.05 42.60 2.57
51 52 2.103263 GCACTAGGATCTCCGGTGATTT 59.897 50.000 19.47 13.39 42.60 2.17
52 53 3.722147 CACTAGGATCTCCGGTGATTTG 58.278 50.000 19.47 12.17 42.60 2.32
53 54 2.700897 ACTAGGATCTCCGGTGATTTGG 59.299 50.000 19.47 14.63 42.08 3.28
54 55 1.879575 AGGATCTCCGGTGATTTGGA 58.120 50.000 19.47 0.40 42.08 3.53
55 56 2.412591 AGGATCTCCGGTGATTTGGAT 58.587 47.619 19.47 0.00 42.08 3.41
56 57 2.370189 AGGATCTCCGGTGATTTGGATC 59.630 50.000 19.47 7.17 42.08 3.36
57 58 2.104792 GGATCTCCGGTGATTTGGATCA 59.895 50.000 19.47 0.00 39.92 2.92
67 68 3.766151 TGATTTGGATCACGACGAGTAC 58.234 45.455 0.00 0.00 37.37 2.73
68 69 2.251869 TTTGGATCACGACGAGTACG 57.748 50.000 0.00 0.00 45.75 3.67
69 70 1.441738 TTGGATCACGACGAGTACGA 58.558 50.000 0.00 0.00 42.66 3.43
70 71 0.723414 TGGATCACGACGAGTACGAC 59.277 55.000 0.00 0.00 42.66 4.34
71 72 1.005340 GGATCACGACGAGTACGACT 58.995 55.000 0.00 0.00 42.66 4.18
72 73 1.005137 GGATCACGACGAGTACGACTC 60.005 57.143 0.00 0.00 41.71 3.36
73 74 1.005137 GATCACGACGAGTACGACTCC 60.005 57.143 0.00 0.00 42.12 3.85
74 75 0.319813 TCACGACGAGTACGACTCCA 60.320 55.000 0.00 0.00 42.12 3.86
75 76 0.725686 CACGACGAGTACGACTCCAT 59.274 55.000 0.00 0.00 42.12 3.41
76 77 1.005340 ACGACGAGTACGACTCCATC 58.995 55.000 0.00 6.63 42.12 3.51
77 78 1.004595 CGACGAGTACGACTCCATCA 58.995 55.000 8.73 0.00 42.12 3.07
78 79 1.267433 CGACGAGTACGACTCCATCAC 60.267 57.143 8.73 0.00 42.12 3.06
79 80 1.063764 GACGAGTACGACTCCATCACC 59.936 57.143 8.73 0.00 42.12 4.02
80 81 0.381089 CGAGTACGACTCCATCACCC 59.619 60.000 8.73 0.00 42.12 4.61
81 82 0.745468 GAGTACGACTCCATCACCCC 59.255 60.000 0.00 0.00 39.28 4.95
82 83 0.686769 AGTACGACTCCATCACCCCC 60.687 60.000 0.00 0.00 0.00 5.40
83 84 1.755395 TACGACTCCATCACCCCCG 60.755 63.158 0.00 0.00 0.00 5.73
84 85 2.503846 TACGACTCCATCACCCCCGT 62.504 60.000 0.00 0.00 0.00 5.28
85 86 2.656069 CGACTCCATCACCCCCGTT 61.656 63.158 0.00 0.00 0.00 4.44
86 87 1.221021 GACTCCATCACCCCCGTTC 59.779 63.158 0.00 0.00 0.00 3.95
87 88 1.537889 ACTCCATCACCCCCGTTCA 60.538 57.895 0.00 0.00 0.00 3.18
88 89 1.078426 CTCCATCACCCCCGTTCAC 60.078 63.158 0.00 0.00 0.00 3.18
89 90 1.537889 TCCATCACCCCCGTTCACT 60.538 57.895 0.00 0.00 0.00 3.41
90 91 1.131303 TCCATCACCCCCGTTCACTT 61.131 55.000 0.00 0.00 0.00 3.16
91 92 0.960364 CCATCACCCCCGTTCACTTG 60.960 60.000 0.00 0.00 0.00 3.16
92 93 0.036164 CATCACCCCCGTTCACTTGA 59.964 55.000 0.00 0.00 0.00 3.02
93 94 0.768622 ATCACCCCCGTTCACTTGAA 59.231 50.000 0.00 0.00 0.00 2.69
101 102 3.729004 GTTCACTTGAACGCTTCCG 57.271 52.632 6.36 0.00 43.97 4.30
102 103 0.384353 GTTCACTTGAACGCTTCCGC 60.384 55.000 6.36 0.00 43.97 5.54
103 104 0.531974 TTCACTTGAACGCTTCCGCT 60.532 50.000 0.00 0.00 38.22 5.52
104 105 0.531974 TCACTTGAACGCTTCCGCTT 60.532 50.000 0.00 0.00 38.22 4.68
105 106 1.144969 CACTTGAACGCTTCCGCTTA 58.855 50.000 0.00 0.00 38.22 3.09
106 107 1.126846 CACTTGAACGCTTCCGCTTAG 59.873 52.381 0.00 0.00 38.22 2.18
107 108 0.095417 CTTGAACGCTTCCGCTTAGC 59.905 55.000 0.00 0.00 38.22 3.09
120 121 2.892784 GCTTAGCGATCTACAAGGGT 57.107 50.000 0.00 0.00 0.00 4.34
122 123 4.522722 GCTTAGCGATCTACAAGGGTAT 57.477 45.455 0.00 0.00 0.00 2.73
123 124 4.238514 GCTTAGCGATCTACAAGGGTATG 58.761 47.826 0.00 0.00 0.00 2.39
124 125 4.262079 GCTTAGCGATCTACAAGGGTATGT 60.262 45.833 0.00 0.00 37.32 2.29
125 126 5.048224 GCTTAGCGATCTACAAGGGTATGTA 60.048 44.000 0.00 0.00 34.75 2.29
134 135 4.408182 ACAAGGGTATGTAGATGCACTC 57.592 45.455 0.00 0.00 25.83 3.51
135 136 4.033709 ACAAGGGTATGTAGATGCACTCT 58.966 43.478 0.00 0.00 38.06 3.24
136 137 4.100189 ACAAGGGTATGTAGATGCACTCTC 59.900 45.833 0.00 0.00 35.28 3.20
137 138 3.235200 AGGGTATGTAGATGCACTCTCC 58.765 50.000 0.00 0.00 35.28 3.71
138 139 3.116939 AGGGTATGTAGATGCACTCTCCT 60.117 47.826 0.00 0.00 35.28 3.69
139 140 3.643792 GGGTATGTAGATGCACTCTCCTT 59.356 47.826 0.00 0.00 35.28 3.36
140 141 4.262249 GGGTATGTAGATGCACTCTCCTTC 60.262 50.000 0.00 0.00 35.28 3.46
141 142 4.262249 GGTATGTAGATGCACTCTCCTTCC 60.262 50.000 0.00 0.00 35.28 3.46
142 143 2.111384 TGTAGATGCACTCTCCTTCCC 58.889 52.381 0.00 0.00 35.28 3.97
143 144 1.414550 GTAGATGCACTCTCCTTCCCC 59.585 57.143 0.00 0.00 35.28 4.81
144 145 0.043940 AGATGCACTCTCCTTCCCCT 59.956 55.000 0.00 0.00 0.00 4.79
145 146 0.467804 GATGCACTCTCCTTCCCCTC 59.532 60.000 0.00 0.00 0.00 4.30
146 147 1.333636 ATGCACTCTCCTTCCCCTCG 61.334 60.000 0.00 0.00 0.00 4.63
147 148 1.985116 GCACTCTCCTTCCCCTCGT 60.985 63.158 0.00 0.00 0.00 4.18
148 149 1.545706 GCACTCTCCTTCCCCTCGTT 61.546 60.000 0.00 0.00 0.00 3.85
149 150 0.247736 CACTCTCCTTCCCCTCGTTG 59.752 60.000 0.00 0.00 0.00 4.10
150 151 1.219393 CTCTCCTTCCCCTCGTTGC 59.781 63.158 0.00 0.00 0.00 4.17
151 152 1.229209 TCTCCTTCCCCTCGTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
152 153 1.078848 CTCCTTCCCCTCGTTGCTG 60.079 63.158 0.00 0.00 0.00 4.41
153 154 2.045926 CCTTCCCCTCGTTGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
154 155 2.750350 CTTCCCCTCGTTGCTGGT 59.250 61.111 0.00 0.00 0.00 4.00
155 156 1.376037 CTTCCCCTCGTTGCTGGTC 60.376 63.158 0.00 0.00 0.00 4.02
156 157 1.831652 CTTCCCCTCGTTGCTGGTCT 61.832 60.000 0.00 0.00 0.00 3.85
157 158 1.827399 TTCCCCTCGTTGCTGGTCTC 61.827 60.000 0.00 0.00 0.00 3.36
158 159 2.286523 CCCCTCGTTGCTGGTCTCT 61.287 63.158 0.00 0.00 0.00 3.10
159 160 1.216710 CCCTCGTTGCTGGTCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
160 161 1.216710 CCTCGTTGCTGGTCTCTCC 59.783 63.158 0.00 0.00 0.00 3.71
161 162 1.536073 CCTCGTTGCTGGTCTCTCCA 61.536 60.000 0.00 0.00 45.01 3.86
162 163 0.534412 CTCGTTGCTGGTCTCTCCAT 59.466 55.000 0.00 0.00 46.12 3.41
163 164 1.751351 CTCGTTGCTGGTCTCTCCATA 59.249 52.381 0.00 0.00 46.12 2.74
164 165 1.751351 TCGTTGCTGGTCTCTCCATAG 59.249 52.381 0.00 0.00 46.12 2.23
165 166 1.751351 CGTTGCTGGTCTCTCCATAGA 59.249 52.381 0.00 0.00 46.12 1.98
166 167 2.363680 CGTTGCTGGTCTCTCCATAGAT 59.636 50.000 0.00 0.00 46.12 1.98
167 168 3.570125 CGTTGCTGGTCTCTCCATAGATA 59.430 47.826 0.00 0.00 46.12 1.98
168 169 4.320861 CGTTGCTGGTCTCTCCATAGATAG 60.321 50.000 0.00 0.00 46.12 2.08
169 170 4.731313 TGCTGGTCTCTCCATAGATAGA 57.269 45.455 0.00 0.00 46.12 1.98
170 171 5.268131 TGCTGGTCTCTCCATAGATAGAT 57.732 43.478 0.00 0.00 46.12 1.98
171 172 5.260424 TGCTGGTCTCTCCATAGATAGATC 58.740 45.833 0.00 0.00 46.12 2.75
172 173 5.015072 TGCTGGTCTCTCCATAGATAGATCT 59.985 44.000 0.00 0.00 46.12 2.75
173 174 5.951747 GCTGGTCTCTCCATAGATAGATCTT 59.048 44.000 0.00 0.00 46.12 2.40
174 175 6.127647 GCTGGTCTCTCCATAGATAGATCTTG 60.128 46.154 0.00 0.00 46.12 3.02
175 176 6.252233 TGGTCTCTCCATAGATAGATCTTGG 58.748 44.000 0.00 1.69 41.93 3.61
176 177 6.183361 TGGTCTCTCCATAGATAGATCTTGGT 60.183 42.308 0.00 0.00 41.93 3.67
177 178 6.152661 GGTCTCTCCATAGATAGATCTTGGTG 59.847 46.154 0.00 3.27 36.89 4.17
178 179 6.945435 GTCTCTCCATAGATAGATCTTGGTGA 59.055 42.308 0.00 7.70 38.32 4.02
179 180 7.615365 GTCTCTCCATAGATAGATCTTGGTGAT 59.385 40.741 13.06 0.00 37.20 3.06
180 181 8.840751 TCTCTCCATAGATAGATCTTGGTGATA 58.159 37.037 13.06 6.19 37.20 2.15
181 182 8.815565 TCTCCATAGATAGATCTTGGTGATAC 57.184 38.462 0.00 0.00 38.32 2.24
182 183 7.554476 TCTCCATAGATAGATCTTGGTGATACG 59.446 40.741 0.00 0.00 38.32 3.06
183 184 7.175797 TCCATAGATAGATCTTGGTGATACGT 58.824 38.462 0.00 0.00 38.32 3.57
184 185 8.326529 TCCATAGATAGATCTTGGTGATACGTA 58.673 37.037 0.00 0.00 38.32 3.57
185 186 8.616942 CCATAGATAGATCTTGGTGATACGTAG 58.383 40.741 0.00 0.00 38.32 3.51
186 187 8.616942 CATAGATAGATCTTGGTGATACGTAGG 58.383 40.741 0.00 0.00 38.32 3.18
187 188 6.780901 AGATAGATCTTGGTGATACGTAGGA 58.219 40.000 0.00 0.00 35.14 2.94
188 189 7.232188 AGATAGATCTTGGTGATACGTAGGAA 58.768 38.462 0.00 0.00 35.14 3.36
189 190 7.724506 AGATAGATCTTGGTGATACGTAGGAAA 59.275 37.037 0.00 0.00 35.14 3.13
190 191 6.540438 AGATCTTGGTGATACGTAGGAAAA 57.460 37.500 0.08 0.00 35.14 2.29
191 192 7.125792 AGATCTTGGTGATACGTAGGAAAAT 57.874 36.000 0.08 0.00 35.14 1.82
192 193 7.565680 AGATCTTGGTGATACGTAGGAAAATT 58.434 34.615 0.08 0.00 35.14 1.82
193 194 8.047310 AGATCTTGGTGATACGTAGGAAAATTT 58.953 33.333 0.08 0.00 35.14 1.82
194 195 7.989416 TCTTGGTGATACGTAGGAAAATTTT 57.011 32.000 2.28 2.28 0.00 1.82
195 196 7.812648 TCTTGGTGATACGTAGGAAAATTTTG 58.187 34.615 8.47 0.00 0.00 2.44
196 197 7.662258 TCTTGGTGATACGTAGGAAAATTTTGA 59.338 33.333 8.47 0.00 0.00 2.69
197 198 7.747155 TGGTGATACGTAGGAAAATTTTGAA 57.253 32.000 8.47 0.00 0.00 2.69
198 199 8.343168 TGGTGATACGTAGGAAAATTTTGAAT 57.657 30.769 8.47 0.00 0.00 2.57
199 200 8.798402 TGGTGATACGTAGGAAAATTTTGAATT 58.202 29.630 8.47 0.00 0.00 2.17
200 201 9.634163 GGTGATACGTAGGAAAATTTTGAATTT 57.366 29.630 8.47 0.00 0.00 1.82
204 205 7.637709 ACGTAGGAAAATTTTGAATTTCTGC 57.362 32.000 8.47 0.00 36.15 4.26
205 206 7.433680 ACGTAGGAAAATTTTGAATTTCTGCT 58.566 30.769 8.47 0.00 36.15 4.24
206 207 8.573035 ACGTAGGAAAATTTTGAATTTCTGCTA 58.427 29.630 8.47 0.00 36.15 3.49
207 208 8.850452 CGTAGGAAAATTTTGAATTTCTGCTAC 58.150 33.333 8.47 6.07 36.15 3.58
208 209 7.873739 AGGAAAATTTTGAATTTCTGCTACG 57.126 32.000 8.47 0.00 36.15 3.51
209 210 7.433680 AGGAAAATTTTGAATTTCTGCTACGT 58.566 30.769 8.47 0.00 36.15 3.57
210 211 7.926018 AGGAAAATTTTGAATTTCTGCTACGTT 59.074 29.630 8.47 0.00 36.15 3.99
211 212 8.214472 GGAAAATTTTGAATTTCTGCTACGTTC 58.786 33.333 8.47 0.00 36.15 3.95
212 213 7.637709 AAATTTTGAATTTCTGCTACGTTCC 57.362 32.000 0.00 0.00 0.00 3.62
213 214 4.759516 TTTGAATTTCTGCTACGTTCCC 57.240 40.909 0.00 0.00 0.00 3.97
214 215 2.706890 TGAATTTCTGCTACGTTCCCC 58.293 47.619 0.00 0.00 0.00 4.81
215 216 2.039216 TGAATTTCTGCTACGTTCCCCA 59.961 45.455 0.00 0.00 0.00 4.96
216 217 2.871096 ATTTCTGCTACGTTCCCCAA 57.129 45.000 0.00 0.00 0.00 4.12
217 218 1.886886 TTTCTGCTACGTTCCCCAAC 58.113 50.000 0.00 0.00 0.00 3.77
218 219 0.759959 TTCTGCTACGTTCCCCAACA 59.240 50.000 0.00 0.00 32.14 3.33
219 220 0.981183 TCTGCTACGTTCCCCAACAT 59.019 50.000 0.00 0.00 32.14 2.71
237 238 3.256704 ACATCCAGTTCCTTTGGTCCTA 58.743 45.455 0.00 0.00 37.02 2.94
292 295 0.895530 CCAACTTCCCTGACTCGCTA 59.104 55.000 0.00 0.00 0.00 4.26
296 299 0.749649 CTTCCCTGACTCGCTAGCAT 59.250 55.000 16.45 0.00 0.00 3.79
311 314 3.766591 GCTAGCATAGATTCAGGCCTCTA 59.233 47.826 10.63 1.16 42.77 2.43
386 389 2.125269 GGACCGTGCGCAATAGGT 60.125 61.111 26.73 26.73 40.11 3.08
454 458 7.768120 TCTTTAAAATGTGTGGTTTCTTGCAAT 59.232 29.630 0.00 0.00 0.00 3.56
464 468 1.177895 TTCTTGCAATTCTGGCGGCA 61.178 50.000 12.58 12.58 0.00 5.69
467 471 4.842091 GCAATTCTGGCGGCAGCG 62.842 66.667 32.43 20.58 46.35 5.18
594 600 2.105128 CGTCCTGATGTCTCCGGC 59.895 66.667 0.00 0.00 0.00 6.13
601 607 3.047718 GATGTCTCCGGCGTGTCGA 62.048 63.158 6.01 0.00 0.00 4.20
656 671 2.023673 CTTGTTGAGTTGTGCCCTCAA 58.976 47.619 0.00 0.00 44.44 3.02
675 690 6.478129 CCTCAACATTAACCTTGGTACCTTA 58.522 40.000 14.36 0.00 0.00 2.69
686 701 4.454504 CCTTGGTACCTTATGTTGTGTGTC 59.545 45.833 14.36 0.00 0.00 3.67
732 752 3.357079 GGGCGTGTTGTGGCTGAG 61.357 66.667 0.00 0.00 0.00 3.35
765 786 3.223589 GTGGCTTGGGCGGTTTGT 61.224 61.111 0.00 0.00 39.81 2.83
805 826 2.968655 CGAAAGCCTTTTTCGGTAAACG 59.031 45.455 12.72 0.00 45.17 3.60
833 854 9.174166 TGGTAAAGATAGAAATTTTCTACAGGC 57.826 33.333 18.65 10.17 44.43 4.85
834 855 9.174166 GGTAAAGATAGAAATTTTCTACAGGCA 57.826 33.333 18.65 0.90 44.43 4.75
853 874 8.986477 ACAGGCAATGTTTTTATACTTCATTC 57.014 30.769 0.00 0.00 39.96 2.67
858 879 8.431593 GCAATGTTTTTATACTTCATTCGCAAA 58.568 29.630 0.00 0.00 0.00 3.68
989 1016 1.608717 GCTTGCTCTCCTCCTTCCGA 61.609 60.000 0.00 0.00 0.00 4.55
993 1020 0.391228 GCTCTCCTCCTTCCGATTCC 59.609 60.000 0.00 0.00 0.00 3.01
994 1021 2.032151 GCTCTCCTCCTTCCGATTCCT 61.032 57.143 0.00 0.00 0.00 3.36
1135 1168 1.717077 ACCACTCCTTCTCCCTCTACA 59.283 52.381 0.00 0.00 0.00 2.74
1284 1317 2.412591 CTCCCCTGGGACATCTATGTT 58.587 52.381 16.20 0.00 41.95 2.71
1359 1392 2.544277 CCGCCTATTCGACGAAATACCA 60.544 50.000 15.22 0.00 0.00 3.25
1476 1509 1.606889 GGACGTGGTCTCCTGGAGT 60.607 63.158 22.50 3.58 32.47 3.85
2298 2331 3.521531 AGAGAGGAGTGAAAAAGATCCCC 59.478 47.826 0.00 0.00 31.86 4.81
2544 2578 2.706339 CCTGTCTGAATCAGGGGAAG 57.294 55.000 10.71 3.38 46.03 3.46
2580 2614 3.950397 TGGTTCTGGTTACTTATGCAGG 58.050 45.455 0.00 0.00 0.00 4.85
2804 2844 7.726033 ACCAGAGAGTAAACATCTTCAGTAT 57.274 36.000 0.00 0.00 0.00 2.12
2897 2941 3.071602 AGACCGCTGACTATTTATGCCAT 59.928 43.478 0.00 0.00 0.00 4.40
3215 3260 3.334583 TCCGGAGCATGCTATATTTCC 57.665 47.619 22.74 15.62 0.00 3.13
3276 3321 8.258007 TCCTGAAAGTCATATGGTACTTTACTG 58.742 37.037 17.81 14.70 43.97 2.74
3355 3400 3.888930 TGACCTGTGAATCCACCTTTTTC 59.111 43.478 0.00 0.00 42.53 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.885388 CACCTCCGCGTTCAACACA 60.885 57.895 4.92 0.00 0.00 3.72
1 2 2.935955 CACCTCCGCGTTCAACAC 59.064 61.111 4.92 0.00 0.00 3.32
2 3 2.970324 GCACCTCCGCGTTCAACA 60.970 61.111 4.92 0.00 0.00 3.33
3 4 3.723348 GGCACCTCCGCGTTCAAC 61.723 66.667 4.92 0.00 0.00 3.18
20 21 2.001361 ATCCTAGTGCCGAACGGACG 62.001 60.000 17.63 0.00 37.50 4.79
21 22 0.248949 GATCCTAGTGCCGAACGGAC 60.249 60.000 17.63 11.59 37.50 4.79
22 23 0.395311 AGATCCTAGTGCCGAACGGA 60.395 55.000 17.63 0.00 37.50 4.69
23 24 0.030908 GAGATCCTAGTGCCGAACGG 59.969 60.000 9.00 9.00 38.57 4.44
24 25 0.030908 GGAGATCCTAGTGCCGAACG 59.969 60.000 0.00 0.00 0.00 3.95
25 26 0.030908 CGGAGATCCTAGTGCCGAAC 59.969 60.000 0.00 0.00 44.43 3.95
26 27 1.107538 CCGGAGATCCTAGTGCCGAA 61.108 60.000 0.00 0.00 44.43 4.30
27 28 1.528542 CCGGAGATCCTAGTGCCGA 60.529 63.158 0.00 0.00 44.43 5.54
28 29 1.828660 ACCGGAGATCCTAGTGCCG 60.829 63.158 9.46 0.00 41.53 5.69
29 30 0.755698 TCACCGGAGATCCTAGTGCC 60.756 60.000 9.46 0.00 0.00 5.01
30 31 1.333177 ATCACCGGAGATCCTAGTGC 58.667 55.000 9.46 0.00 0.00 4.40
31 32 3.493350 CCAAATCACCGGAGATCCTAGTG 60.493 52.174 15.13 10.95 0.00 2.74
32 33 2.700897 CCAAATCACCGGAGATCCTAGT 59.299 50.000 15.13 0.00 0.00 2.57
33 34 2.965831 TCCAAATCACCGGAGATCCTAG 59.034 50.000 15.13 5.05 0.00 3.02
34 35 3.040655 TCCAAATCACCGGAGATCCTA 57.959 47.619 15.13 0.00 0.00 2.94
35 36 1.879575 TCCAAATCACCGGAGATCCT 58.120 50.000 15.13 2.86 0.00 3.24
36 37 2.104792 TGATCCAAATCACCGGAGATCC 59.895 50.000 15.13 2.03 36.98 3.36
37 38 3.475566 TGATCCAAATCACCGGAGATC 57.524 47.619 15.13 10.62 36.98 2.75
45 46 7.861595 TCGTACTCGTCGTGATCCAAATCAC 62.862 48.000 8.20 8.20 45.52 3.06
46 47 3.729762 CGTACTCGTCGTGATCCAAATCA 60.730 47.826 0.56 0.00 39.63 2.57
47 48 2.782192 CGTACTCGTCGTGATCCAAATC 59.218 50.000 0.56 0.00 0.00 2.17
48 49 2.421073 TCGTACTCGTCGTGATCCAAAT 59.579 45.455 0.56 0.00 38.33 2.32
49 50 1.805943 TCGTACTCGTCGTGATCCAAA 59.194 47.619 0.56 0.00 38.33 3.28
50 51 1.129251 GTCGTACTCGTCGTGATCCAA 59.871 52.381 0.56 0.00 38.33 3.53
51 52 0.723414 GTCGTACTCGTCGTGATCCA 59.277 55.000 0.56 0.00 38.33 3.41
52 53 1.005137 GAGTCGTACTCGTCGTGATCC 60.005 57.143 0.56 0.00 35.28 3.36
53 54 1.005137 GGAGTCGTACTCGTCGTGATC 60.005 57.143 0.56 0.00 45.96 2.92
54 55 1.005340 GGAGTCGTACTCGTCGTGAT 58.995 55.000 0.56 0.00 45.96 3.06
55 56 0.319813 TGGAGTCGTACTCGTCGTGA 60.320 55.000 0.56 0.00 45.96 4.35
56 57 0.725686 ATGGAGTCGTACTCGTCGTG 59.274 55.000 8.33 0.00 45.96 4.35
57 58 1.005340 GATGGAGTCGTACTCGTCGT 58.995 55.000 8.33 0.00 45.96 4.34
58 59 1.004595 TGATGGAGTCGTACTCGTCG 58.995 55.000 8.33 0.00 45.96 5.12
59 60 1.063764 GGTGATGGAGTCGTACTCGTC 59.936 57.143 8.33 9.13 45.96 4.20
60 61 1.093159 GGTGATGGAGTCGTACTCGT 58.907 55.000 8.33 1.85 45.96 4.18
61 62 0.381089 GGGTGATGGAGTCGTACTCG 59.619 60.000 8.33 0.00 45.96 4.18
62 63 0.745468 GGGGTGATGGAGTCGTACTC 59.255 60.000 6.50 6.50 44.32 2.59
63 64 0.686769 GGGGGTGATGGAGTCGTACT 60.687 60.000 0.00 0.00 0.00 2.73
64 65 1.821258 GGGGGTGATGGAGTCGTAC 59.179 63.158 0.00 0.00 0.00 3.67
65 66 1.755395 CGGGGGTGATGGAGTCGTA 60.755 63.158 0.00 0.00 0.00 3.43
66 67 3.075005 CGGGGGTGATGGAGTCGT 61.075 66.667 0.00 0.00 0.00 4.34
67 68 2.573609 GAACGGGGGTGATGGAGTCG 62.574 65.000 0.00 0.00 0.00 4.18
68 69 1.221021 GAACGGGGGTGATGGAGTC 59.779 63.158 0.00 0.00 0.00 3.36
69 70 1.537889 TGAACGGGGGTGATGGAGT 60.538 57.895 0.00 0.00 0.00 3.85
70 71 1.078426 GTGAACGGGGGTGATGGAG 60.078 63.158 0.00 0.00 0.00 3.86
71 72 1.131303 AAGTGAACGGGGGTGATGGA 61.131 55.000 0.00 0.00 0.00 3.41
72 73 0.960364 CAAGTGAACGGGGGTGATGG 60.960 60.000 0.00 0.00 0.00 3.51
73 74 0.036164 TCAAGTGAACGGGGGTGATG 59.964 55.000 0.00 0.00 0.00 3.07
74 75 0.768622 TTCAAGTGAACGGGGGTGAT 59.231 50.000 0.00 0.00 0.00 3.06
75 76 0.179040 GTTCAAGTGAACGGGGGTGA 60.179 55.000 8.34 0.00 43.97 4.02
76 77 2.327228 GTTCAAGTGAACGGGGGTG 58.673 57.895 8.34 0.00 43.97 4.61
77 78 4.892002 GTTCAAGTGAACGGGGGT 57.108 55.556 8.34 0.00 43.97 4.95
101 102 2.892784 ACCCTTGTAGATCGCTAAGC 57.107 50.000 0.00 0.00 0.00 3.09
102 103 5.455056 ACATACCCTTGTAGATCGCTAAG 57.545 43.478 0.00 0.00 0.00 2.18
111 112 5.303078 AGAGTGCATCTACATACCCTTGTAG 59.697 44.000 5.47 5.47 46.85 2.74
112 113 5.208890 AGAGTGCATCTACATACCCTTGTA 58.791 41.667 0.00 0.00 36.10 2.41
113 114 4.033709 AGAGTGCATCTACATACCCTTGT 58.966 43.478 0.00 0.00 36.10 3.16
114 115 4.502259 GGAGAGTGCATCTACATACCCTTG 60.502 50.000 0.00 0.00 38.94 3.61
115 116 3.643792 GGAGAGTGCATCTACATACCCTT 59.356 47.826 0.00 0.00 38.94 3.95
116 117 3.116939 AGGAGAGTGCATCTACATACCCT 60.117 47.826 9.98 4.47 42.01 4.34
117 118 3.235200 AGGAGAGTGCATCTACATACCC 58.765 50.000 9.98 2.71 42.01 3.69
118 119 4.262249 GGAAGGAGAGTGCATCTACATACC 60.262 50.000 9.98 6.83 42.01 2.73
119 120 4.262249 GGGAAGGAGAGTGCATCTACATAC 60.262 50.000 9.98 0.82 42.01 2.39
120 121 3.898123 GGGAAGGAGAGTGCATCTACATA 59.102 47.826 9.98 0.00 42.01 2.29
121 122 2.703007 GGGAAGGAGAGTGCATCTACAT 59.297 50.000 9.98 0.00 42.01 2.29
122 123 2.111384 GGGAAGGAGAGTGCATCTACA 58.889 52.381 9.98 0.00 42.01 2.74
123 124 1.414550 GGGGAAGGAGAGTGCATCTAC 59.585 57.143 0.00 0.00 38.84 2.59
124 125 1.292242 AGGGGAAGGAGAGTGCATCTA 59.708 52.381 0.00 0.00 38.84 1.98
125 126 0.043940 AGGGGAAGGAGAGTGCATCT 59.956 55.000 0.00 0.00 42.61 2.90
126 127 0.467804 GAGGGGAAGGAGAGTGCATC 59.532 60.000 0.00 0.00 0.00 3.91
127 128 1.333636 CGAGGGGAAGGAGAGTGCAT 61.334 60.000 0.00 0.00 0.00 3.96
128 129 1.984570 CGAGGGGAAGGAGAGTGCA 60.985 63.158 0.00 0.00 0.00 4.57
129 130 1.545706 AACGAGGGGAAGGAGAGTGC 61.546 60.000 0.00 0.00 0.00 4.40
130 131 0.247736 CAACGAGGGGAAGGAGAGTG 59.752 60.000 0.00 0.00 0.00 3.51
131 132 1.545706 GCAACGAGGGGAAGGAGAGT 61.546 60.000 0.00 0.00 0.00 3.24
132 133 1.219393 GCAACGAGGGGAAGGAGAG 59.781 63.158 0.00 0.00 0.00 3.20
133 134 1.229209 AGCAACGAGGGGAAGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
134 135 1.078848 CAGCAACGAGGGGAAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
135 136 2.592993 CCAGCAACGAGGGGAAGGA 61.593 63.158 0.00 0.00 0.00 3.36
136 137 2.045926 CCAGCAACGAGGGGAAGG 60.046 66.667 0.00 0.00 0.00 3.46
137 138 1.376037 GACCAGCAACGAGGGGAAG 60.376 63.158 0.00 0.00 0.00 3.46
138 139 1.827399 GAGACCAGCAACGAGGGGAA 61.827 60.000 0.00 0.00 0.00 3.97
139 140 2.203788 AGACCAGCAACGAGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
140 141 2.232298 GAGAGACCAGCAACGAGGGG 62.232 65.000 0.00 0.00 0.00 4.79
141 142 1.216710 GAGAGACCAGCAACGAGGG 59.783 63.158 0.00 0.00 0.00 4.30
142 143 1.216710 GGAGAGACCAGCAACGAGG 59.783 63.158 0.00 0.00 38.79 4.63
143 144 1.967535 TGGAGAGACCAGCAACGAG 59.032 57.895 0.00 0.00 44.64 4.18
144 145 4.191243 TGGAGAGACCAGCAACGA 57.809 55.556 0.00 0.00 44.64 3.85
147 148 7.915671 AAGATCTATCTATGGAGAGACCAGCAA 60.916 40.741 5.47 0.00 43.76 3.91
148 149 6.468505 AAGATCTATCTATGGAGAGACCAGCA 60.469 42.308 5.47 0.00 43.76 4.41
149 150 5.951747 AAGATCTATCTATGGAGAGACCAGC 59.048 44.000 5.47 0.00 43.76 4.85
150 151 6.377996 CCAAGATCTATCTATGGAGAGACCAG 59.622 46.154 5.47 0.00 43.76 4.00
151 152 6.183361 ACCAAGATCTATCTATGGAGAGACCA 60.183 42.308 15.80 0.00 41.74 4.02
152 153 6.152661 CACCAAGATCTATCTATGGAGAGACC 59.847 46.154 15.80 0.00 41.74 3.85
153 154 6.945435 TCACCAAGATCTATCTATGGAGAGAC 59.055 42.308 15.80 1.08 41.74 3.36
154 155 7.096402 TCACCAAGATCTATCTATGGAGAGA 57.904 40.000 15.80 5.84 42.87 3.10
155 156 7.959658 ATCACCAAGATCTATCTATGGAGAG 57.040 40.000 15.80 6.64 37.68 3.20
156 157 7.554476 CGTATCACCAAGATCTATCTATGGAGA 59.446 40.741 15.80 13.49 38.10 3.71
157 158 7.338196 ACGTATCACCAAGATCTATCTATGGAG 59.662 40.741 15.80 8.98 37.92 3.86
158 159 7.175797 ACGTATCACCAAGATCTATCTATGGA 58.824 38.462 15.80 0.00 37.92 3.41
159 160 7.397892 ACGTATCACCAAGATCTATCTATGG 57.602 40.000 8.57 8.57 39.18 2.74
160 161 8.616942 CCTACGTATCACCAAGATCTATCTATG 58.383 40.741 0.00 0.00 38.19 2.23
161 162 8.549731 TCCTACGTATCACCAAGATCTATCTAT 58.450 37.037 0.00 0.00 38.19 1.98
162 163 7.914859 TCCTACGTATCACCAAGATCTATCTA 58.085 38.462 0.00 0.00 38.19 1.98
163 164 6.780901 TCCTACGTATCACCAAGATCTATCT 58.219 40.000 0.00 0.00 38.19 1.98
164 165 7.450124 TTCCTACGTATCACCAAGATCTATC 57.550 40.000 0.00 0.00 38.19 2.08
165 166 7.834881 TTTCCTACGTATCACCAAGATCTAT 57.165 36.000 0.00 0.00 38.19 1.98
166 167 7.649533 TTTTCCTACGTATCACCAAGATCTA 57.350 36.000 0.00 0.00 38.19 1.98
167 168 6.540438 TTTTCCTACGTATCACCAAGATCT 57.460 37.500 0.00 0.00 38.19 2.75
168 169 7.787725 AATTTTCCTACGTATCACCAAGATC 57.212 36.000 0.00 0.00 38.19 2.75
169 170 8.458843 CAAAATTTTCCTACGTATCACCAAGAT 58.541 33.333 0.00 0.00 40.86 2.40
170 171 7.662258 TCAAAATTTTCCTACGTATCACCAAGA 59.338 33.333 0.00 0.00 0.00 3.02
171 172 7.812648 TCAAAATTTTCCTACGTATCACCAAG 58.187 34.615 0.00 0.00 0.00 3.61
172 173 7.747155 TCAAAATTTTCCTACGTATCACCAA 57.253 32.000 0.00 0.00 0.00 3.67
173 174 7.747155 TTCAAAATTTTCCTACGTATCACCA 57.253 32.000 0.00 0.00 0.00 4.17
174 175 9.634163 AAATTCAAAATTTTCCTACGTATCACC 57.366 29.630 0.00 0.00 0.00 4.02
178 179 9.353999 GCAGAAATTCAAAATTTTCCTACGTAT 57.646 29.630 0.00 0.00 33.30 3.06
179 180 8.573035 AGCAGAAATTCAAAATTTTCCTACGTA 58.427 29.630 0.00 0.00 33.30 3.57
180 181 7.433680 AGCAGAAATTCAAAATTTTCCTACGT 58.566 30.769 0.00 0.00 33.30 3.57
181 182 7.873739 AGCAGAAATTCAAAATTTTCCTACG 57.126 32.000 0.00 0.00 33.30 3.51
182 183 8.850452 CGTAGCAGAAATTCAAAATTTTCCTAC 58.150 33.333 0.00 13.60 33.30 3.18
183 184 8.573035 ACGTAGCAGAAATTCAAAATTTTCCTA 58.427 29.630 0.00 0.00 33.30 2.94
184 185 7.433680 ACGTAGCAGAAATTCAAAATTTTCCT 58.566 30.769 0.00 0.86 33.30 3.36
185 186 7.637709 ACGTAGCAGAAATTCAAAATTTTCC 57.362 32.000 0.00 0.00 33.30 3.13
186 187 8.214472 GGAACGTAGCAGAAATTCAAAATTTTC 58.786 33.333 0.00 0.00 33.08 2.29
187 188 7.170828 GGGAACGTAGCAGAAATTCAAAATTTT 59.829 33.333 0.00 0.00 0.00 1.82
188 189 6.645003 GGGAACGTAGCAGAAATTCAAAATTT 59.355 34.615 0.00 0.00 0.00 1.82
189 190 6.156519 GGGAACGTAGCAGAAATTCAAAATT 58.843 36.000 0.00 0.00 0.00 1.82
190 191 5.336451 GGGGAACGTAGCAGAAATTCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
191 192 4.022676 GGGGAACGTAGCAGAAATTCAAAA 60.023 41.667 0.00 0.00 0.00 2.44
192 193 3.504520 GGGGAACGTAGCAGAAATTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
193 194 3.078837 GGGGAACGTAGCAGAAATTCAA 58.921 45.455 0.00 0.00 0.00 2.69
194 195 2.039216 TGGGGAACGTAGCAGAAATTCA 59.961 45.455 0.00 0.00 0.00 2.57
195 196 2.706890 TGGGGAACGTAGCAGAAATTC 58.293 47.619 0.00 0.00 0.00 2.17
196 197 2.817844 GTTGGGGAACGTAGCAGAAATT 59.182 45.455 0.00 0.00 0.00 1.82
197 198 2.224670 TGTTGGGGAACGTAGCAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
198 199 1.141254 TGTTGGGGAACGTAGCAGAAA 59.859 47.619 0.00 0.00 0.00 2.52
199 200 0.759959 TGTTGGGGAACGTAGCAGAA 59.240 50.000 0.00 0.00 0.00 3.02
200 201 0.981183 ATGTTGGGGAACGTAGCAGA 59.019 50.000 0.00 0.00 0.00 4.26
201 202 1.369625 GATGTTGGGGAACGTAGCAG 58.630 55.000 0.00 0.00 0.00 4.24
202 203 0.035820 GGATGTTGGGGAACGTAGCA 60.036 55.000 0.00 0.00 0.00 3.49
203 204 0.035820 TGGATGTTGGGGAACGTAGC 60.036 55.000 0.00 0.00 0.00 3.58
204 205 1.278127 ACTGGATGTTGGGGAACGTAG 59.722 52.381 0.00 0.00 0.00 3.51
205 206 1.354101 ACTGGATGTTGGGGAACGTA 58.646 50.000 0.00 0.00 0.00 3.57
206 207 0.476771 AACTGGATGTTGGGGAACGT 59.523 50.000 0.00 0.00 37.52 3.99
207 208 1.165270 GAACTGGATGTTGGGGAACG 58.835 55.000 0.00 0.00 39.30 3.95
208 209 1.075536 AGGAACTGGATGTTGGGGAAC 59.924 52.381 0.00 0.00 39.30 3.62
209 210 1.455822 AGGAACTGGATGTTGGGGAA 58.544 50.000 0.00 0.00 39.30 3.97
210 211 1.455822 AAGGAACTGGATGTTGGGGA 58.544 50.000 0.00 0.00 40.86 4.81
211 212 1.895131 CAAAGGAACTGGATGTTGGGG 59.105 52.381 0.00 0.00 40.86 4.96
212 213 1.895131 CCAAAGGAACTGGATGTTGGG 59.105 52.381 0.00 0.00 40.86 4.12
213 214 2.558359 GACCAAAGGAACTGGATGTTGG 59.442 50.000 0.00 0.00 40.86 3.77
214 215 2.558359 GGACCAAAGGAACTGGATGTTG 59.442 50.000 0.00 0.00 40.86 3.33
215 216 2.447047 AGGACCAAAGGAACTGGATGTT 59.553 45.455 0.00 0.00 40.86 2.71
216 217 2.065799 AGGACCAAAGGAACTGGATGT 58.934 47.619 0.00 0.00 40.86 3.06
217 218 2.887151 AGGACCAAAGGAACTGGATG 57.113 50.000 0.00 0.00 40.86 3.51
218 219 3.532102 AGTAGGACCAAAGGAACTGGAT 58.468 45.455 0.00 0.00 40.86 3.41
219 220 2.986050 AGTAGGACCAAAGGAACTGGA 58.014 47.619 0.00 0.00 40.86 3.86
237 238 2.660552 CAACCACGTCGCGGAAGT 60.661 61.111 6.13 0.48 0.00 3.01
292 295 2.903135 GGTAGAGGCCTGAATCTATGCT 59.097 50.000 12.00 0.00 31.05 3.79
296 299 1.132817 GGGGGTAGAGGCCTGAATCTA 60.133 57.143 12.00 1.76 0.00 1.98
337 340 0.385751 CGAGCATCCCGACACATAGT 59.614 55.000 0.00 0.00 0.00 2.12
350 353 3.612247 AAAGCGTCCAGGCGAGCAT 62.612 57.895 7.39 0.00 38.18 3.79
386 389 0.608035 GGGGAACGCTGGATGACAAA 60.608 55.000 0.00 0.00 38.67 2.83
467 471 0.882042 CTGGTCATGGATGCGGCTAC 60.882 60.000 0.00 0.00 0.00 3.58
480 484 0.107643 TGTTGATGGCGTTCTGGTCA 59.892 50.000 0.00 0.00 0.00 4.02
547 552 2.600173 CTGGGGAGGCGGCAAAAA 60.600 61.111 13.08 0.00 0.00 1.94
601 607 3.804490 AAAAATGGGCCGGCACAT 58.196 50.000 38.42 38.42 42.67 3.21
624 639 4.123497 ACTCAACAAGCCCAAAGAAAAC 57.877 40.909 0.00 0.00 0.00 2.43
625 640 4.020662 ACAACTCAACAAGCCCAAAGAAAA 60.021 37.500 0.00 0.00 0.00 2.29
656 671 7.175990 CACAACATAAGGTACCAAGGTTAATGT 59.824 37.037 15.94 8.14 0.00 2.71
675 690 0.657312 CGCACACAGACACACAACAT 59.343 50.000 0.00 0.00 0.00 2.71
686 701 2.534019 GGTCCACACACGCACACAG 61.534 63.158 0.00 0.00 0.00 3.66
732 752 0.592247 CCACAAACAAGCACACGAGC 60.592 55.000 0.00 0.00 0.00 5.03
765 786 6.348704 GCTTTCGCCCCGCTTTATATATAAAA 60.349 38.462 16.69 4.08 32.39 1.52
807 828 9.174166 GCCTGTAGAAAATTTCTATCTTTACCA 57.826 33.333 17.26 8.69 43.59 3.25
808 829 9.174166 TGCCTGTAGAAAATTTCTATCTTTACC 57.826 33.333 17.26 4.89 43.59 2.85
812 833 9.247861 ACATTGCCTGTAGAAAATTTCTATCTT 57.752 29.630 17.26 0.00 43.59 2.40
813 834 8.814038 ACATTGCCTGTAGAAAATTTCTATCT 57.186 30.769 17.26 0.00 43.59 1.98
814 835 9.860898 AAACATTGCCTGTAGAAAATTTCTATC 57.139 29.630 17.26 11.80 43.59 2.08
817 838 8.962884 AAAAACATTGCCTGTAGAAAATTTCT 57.037 26.923 13.20 13.20 43.72 2.52
824 845 9.290988 TGAAGTATAAAAACATTGCCTGTAGAA 57.709 29.630 0.00 0.00 36.98 2.10
825 846 8.856153 TGAAGTATAAAAACATTGCCTGTAGA 57.144 30.769 0.00 0.00 36.98 2.59
828 849 7.754924 CGAATGAAGTATAAAAACATTGCCTGT 59.245 33.333 0.00 0.00 40.84 4.00
829 850 7.253750 GCGAATGAAGTATAAAAACATTGCCTG 60.254 37.037 0.00 0.00 32.50 4.85
830 851 6.751888 GCGAATGAAGTATAAAAACATTGCCT 59.248 34.615 0.00 0.00 32.50 4.75
831 852 6.529829 TGCGAATGAAGTATAAAAACATTGCC 59.470 34.615 0.00 0.00 32.50 4.52
832 853 7.504922 TGCGAATGAAGTATAAAAACATTGC 57.495 32.000 0.00 0.00 32.50 3.56
989 1016 1.819632 GGCCGCATTCGTCAGGAAT 60.820 57.895 0.00 0.00 46.29 3.01
993 1020 2.892425 GGAGGCCGCATTCGTCAG 60.892 66.667 9.31 0.00 0.00 3.51
994 1021 4.812476 CGGAGGCCGCATTCGTCA 62.812 66.667 9.31 0.00 41.17 4.35
1135 1168 2.200092 GGAGCGGAGGAGGAGGAT 59.800 66.667 0.00 0.00 0.00 3.24
1284 1317 0.032815 TGTGGACGAGTGAATTCGCA 59.967 50.000 20.55 0.00 44.15 5.10
1359 1392 2.342648 GAGACAAGGTTCGGCCGT 59.657 61.111 27.15 2.66 43.70 5.68
1435 1468 2.046700 GGGCATCCGGTCGAACAA 60.047 61.111 0.00 0.00 0.00 2.83
1476 1509 2.186644 CACCCGTCGATCATGGCA 59.813 61.111 0.00 0.00 0.00 4.92
2298 2331 2.540101 GACATCAATCTCGCTAAACCCG 59.460 50.000 0.00 0.00 0.00 5.28
2337 2370 3.825143 GCCTTGTCATGGGCAATAAAT 57.175 42.857 11.15 0.00 46.84 1.40
2461 2494 2.428171 CCATTAAGCACCCATTGTCCTG 59.572 50.000 0.00 0.00 0.00 3.86
2544 2578 4.154918 CCAGAACCAAGAGCTACAATGAAC 59.845 45.833 0.00 0.00 0.00 3.18
2580 2614 6.020984 GTCAAATTTTCAACACAAACCAAGC 58.979 36.000 0.00 0.00 0.00 4.01
2781 2818 7.920151 CAGATACTGAAGATGTTTACTCTCTGG 59.080 40.741 0.00 0.00 32.44 3.86
2804 2844 3.869912 GCAGAAGCCATAGGTGAAACAGA 60.870 47.826 0.00 0.00 33.93 3.41
3215 3260 7.116805 TCACTATTCATAGCACAAATCGCATAG 59.883 37.037 0.00 0.00 33.68 2.23
3302 3347 4.703897 TGCTAACTGCTCTTTGTGTACTT 58.296 39.130 0.00 0.00 43.37 2.24
3450 3496 9.592196 AGAATTTGCCTGTGTATATCCATAAAT 57.408 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.