Multiple sequence alignment - TraesCS1B01G392800

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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 TraesCS1B01G392800 chr1B 100.000 4037 0 0 1 4037 626070234 626066198 0.000000e+00 7456
1 TraesCS1B01G392800 chr1D 91.554 2818 174 23 218 3012 455653668 455650892 0.000000e+00 3827
2 TraesCS1B01G392800 chr1D 89.808 1040 66 9 3023 4037 455650848 455649824 0.000000e+00 1297
3 TraesCS1B01G392800 chr1D 92.941 85 6 0 1 85 474419922 474419838 1.520000e-24 124
4 TraesCS1B01G392800 chr1A 91.623 2459 159 25 573 3012 549288054 549285624 0.000000e+00 3356
5 TraesCS1B01G392800 chr1A 87.632 1043 79 24 3023 4037 549285573 549284553 0.000000e+00 1166
6 TraesCS1B01G392800 chr6A 94.118 85 5 0 1 85 508175951 508175867 3.270000e-26 130
7 TraesCS1B01G392800 chr2D 92.308 91 7 0 1 91 54126868 54126778 3.270000e-26 130
8 TraesCS1B01G392800 chr2D 91.304 92 7 1 1 91 609514062 609514153 1.520000e-24 124
9 TraesCS1B01G392800 chr7A 93.976 83 5 0 1 83 634707575 634707657 4.240000e-25 126
10 TraesCS1B01G392800 chr7B 92.941 85 6 0 1 85 135994060 135994144 1.520000e-24 124
11 TraesCS1B01G392800 chr2A 93.902 82 5 0 1 82 360945237 360945156 1.520000e-24 124
12 TraesCS1B01G392800 chr2A 93.902 82 4 1 1 82 175432948 175433028 5.480000e-24 122
13 TraesCS1B01G392800 chr3B 90.110 91 9 0 1 91 598910712 598910622 7.090000e-23 119


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 TraesCS1B01G392800 chr1B 626066198 626070234 4036 True 7456 7456 100.0000 1 4037 1 chr1B.!!$R1 4036
1 TraesCS1B01G392800 chr1D 455649824 455653668 3844 True 2562 3827 90.6810 218 4037 2 chr1D.!!$R2 3819
2 TraesCS1B01G392800 chr1A 549284553 549288054 3501 True 2261 3356 89.6275 573 4037 2 chr1A.!!$R1 3464

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
565 575 0.038166 GGTGGCTGGATGTTGGAGAA 59.962 55.0 0.0 0.0 0.0 2.87 F
646 656 0.040246 GCGTCCGTCTCTGCTATACC 60.040 60.0 0.0 0.0 0.0 2.73 F
1107 1126 0.322187 GGGACATGTTAACTGCCGGT 60.322 55.0 1.9 0.0 0.0 5.28 F
2060 2085 0.107459 GAGCAGGAAGGGGACATCAC 60.107 60.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1777 0.768622 TGGTGACCGAGTTGGGAATT 59.231 50.0 0.24 0.00 44.64 2.17 R
1755 1780 0.899720 GTATGGTGACCGAGTTGGGA 59.100 55.0 0.24 0.00 44.64 4.37 R
3019 3094 0.869880 CGTCAATGAGCGCGGTGATA 60.870 55.0 18.92 1.49 0.00 2.15 R
3354 3431 0.109597 GCCTTGTCAATCGTGCCAAG 60.110 55.0 0.00 0.00 0.00 3.61 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
48 49 3.878778 AGAATCGTTCTTGCCTATTGCT 58.121 40.909 0.00 0.00 36.36 3.91
49 50 5.023533 AGAATCGTTCTTGCCTATTGCTA 57.976 39.130 0.00 0.00 36.36 3.49
50 51 5.428253 AGAATCGTTCTTGCCTATTGCTAA 58.572 37.500 0.00 0.00 36.36 3.09
51 52 5.880332 AGAATCGTTCTTGCCTATTGCTAAA 59.120 36.000 0.00 0.00 36.36 1.85
52 53 6.374333 AGAATCGTTCTTGCCTATTGCTAAAA 59.626 34.615 0.00 0.00 36.36 1.52
53 54 6.699575 ATCGTTCTTGCCTATTGCTAAAAT 57.300 33.333 0.00 0.00 42.00 1.82
54 55 6.119144 TCGTTCTTGCCTATTGCTAAAATC 57.881 37.500 0.00 0.00 42.00 2.17
55 56 5.065988 TCGTTCTTGCCTATTGCTAAAATCC 59.934 40.000 0.00 0.00 42.00 3.01
56 57 5.273944 GTTCTTGCCTATTGCTAAAATCCG 58.726 41.667 0.00 0.00 42.00 4.18
57 58 4.776349 TCTTGCCTATTGCTAAAATCCGA 58.224 39.130 0.00 0.00 42.00 4.55
58 59 5.189928 TCTTGCCTATTGCTAAAATCCGAA 58.810 37.500 0.00 0.00 42.00 4.30
59 60 4.893424 TGCCTATTGCTAAAATCCGAAC 57.107 40.909 0.00 0.00 42.00 3.95
60 61 3.311322 TGCCTATTGCTAAAATCCGAACG 59.689 43.478 0.00 0.00 42.00 3.95
61 62 3.311596 GCCTATTGCTAAAATCCGAACGT 59.688 43.478 0.00 0.00 36.87 3.99
62 63 4.201881 GCCTATTGCTAAAATCCGAACGTT 60.202 41.667 0.00 0.00 36.87 3.99
63 64 5.006941 GCCTATTGCTAAAATCCGAACGTTA 59.993 40.000 0.00 0.00 36.87 3.18
64 65 6.646636 CCTATTGCTAAAATCCGAACGTTAG 58.353 40.000 0.00 0.00 0.00 2.34
65 66 4.932268 TTGCTAAAATCCGAACGTTAGG 57.068 40.909 20.25 20.25 0.00 2.69
66 67 3.929094 TGCTAAAATCCGAACGTTAGGT 58.071 40.909 24.27 11.14 0.00 3.08
67 68 5.070770 TGCTAAAATCCGAACGTTAGGTA 57.929 39.130 24.27 13.20 0.00 3.08
68 69 5.104374 TGCTAAAATCCGAACGTTAGGTAG 58.896 41.667 24.27 18.82 0.00 3.18
69 70 5.105063 GCTAAAATCCGAACGTTAGGTAGT 58.895 41.667 24.27 11.09 0.00 2.73
70 71 5.578336 GCTAAAATCCGAACGTTAGGTAGTT 59.422 40.000 24.27 17.93 0.00 2.24
71 72 6.751888 GCTAAAATCCGAACGTTAGGTAGTTA 59.248 38.462 24.27 18.06 0.00 2.24
72 73 7.436376 GCTAAAATCCGAACGTTAGGTAGTTAT 59.564 37.037 24.27 9.59 0.00 1.89
73 74 9.950680 CTAAAATCCGAACGTTAGGTAGTTATA 57.049 33.333 24.27 6.30 0.00 0.98
75 76 9.651913 AAAATCCGAACGTTAGGTAGTTATAAA 57.348 29.630 24.27 4.92 0.00 1.40
76 77 9.651913 AAATCCGAACGTTAGGTAGTTATAAAA 57.348 29.630 24.27 4.23 0.00 1.52
77 78 8.862550 ATCCGAACGTTAGGTAGTTATAAAAG 57.137 34.615 24.27 0.00 0.00 2.27
78 79 7.826690 TCCGAACGTTAGGTAGTTATAAAAGT 58.173 34.615 24.27 0.00 0.00 2.66
79 80 7.968405 TCCGAACGTTAGGTAGTTATAAAAGTC 59.032 37.037 24.27 0.00 0.00 3.01
80 81 7.220875 CCGAACGTTAGGTAGTTATAAAAGTCC 59.779 40.741 18.33 0.00 0.00 3.85
81 82 7.754924 CGAACGTTAGGTAGTTATAAAAGTCCA 59.245 37.037 0.00 0.00 0.00 4.02
82 83 9.423061 GAACGTTAGGTAGTTATAAAAGTCCAA 57.577 33.333 0.00 0.00 0.00 3.53
83 84 9.777297 AACGTTAGGTAGTTATAAAAGTCCAAA 57.223 29.630 0.00 0.00 0.00 3.28
84 85 9.777297 ACGTTAGGTAGTTATAAAAGTCCAAAA 57.223 29.630 0.00 0.00 0.00 2.44
99 100 6.456795 AGTCCAAAAGAATAAGGCAATAGC 57.543 37.500 0.00 0.00 41.10 2.97
114 115 5.223225 GCAATAGCCTACTTTGACAACTC 57.777 43.478 0.00 0.00 33.58 3.01
115 116 4.201724 GCAATAGCCTACTTTGACAACTCG 60.202 45.833 0.00 0.00 33.58 4.18
116 117 5.168569 CAATAGCCTACTTTGACAACTCGA 58.831 41.667 0.00 0.00 0.00 4.04
117 118 3.027974 AGCCTACTTTGACAACTCGAC 57.972 47.619 0.00 0.00 0.00 4.20
118 119 2.067013 GCCTACTTTGACAACTCGACC 58.933 52.381 0.00 0.00 0.00 4.79
119 120 2.547218 GCCTACTTTGACAACTCGACCA 60.547 50.000 0.00 0.00 0.00 4.02
120 121 3.318017 CCTACTTTGACAACTCGACCAG 58.682 50.000 0.00 0.00 0.00 4.00
121 122 2.981859 ACTTTGACAACTCGACCAGT 57.018 45.000 0.00 0.00 36.64 4.00
122 123 4.022589 CCTACTTTGACAACTCGACCAGTA 60.023 45.833 0.00 0.00 32.30 2.74
123 124 4.395959 ACTTTGACAACTCGACCAGTAA 57.604 40.909 0.00 0.00 32.30 2.24
124 125 4.117685 ACTTTGACAACTCGACCAGTAAC 58.882 43.478 0.00 0.00 32.30 2.50
125 126 3.804786 TTGACAACTCGACCAGTAACA 57.195 42.857 0.00 0.00 32.30 2.41
126 127 4.330944 TTGACAACTCGACCAGTAACAT 57.669 40.909 0.00 0.00 32.30 2.71
127 128 3.649073 TGACAACTCGACCAGTAACATG 58.351 45.455 0.00 0.00 32.30 3.21
128 129 2.412089 GACAACTCGACCAGTAACATGC 59.588 50.000 0.00 0.00 32.30 4.06
129 130 1.390123 CAACTCGACCAGTAACATGCG 59.610 52.381 0.00 0.00 32.30 4.73
130 131 0.601558 ACTCGACCAGTAACATGCGT 59.398 50.000 0.00 0.00 31.37 5.24
131 132 1.814394 ACTCGACCAGTAACATGCGTA 59.186 47.619 0.00 0.00 31.37 4.42
132 133 2.229543 ACTCGACCAGTAACATGCGTAA 59.770 45.455 0.00 0.00 31.37 3.18
133 134 3.247442 CTCGACCAGTAACATGCGTAAA 58.753 45.455 0.00 0.00 0.00 2.01
134 135 3.651206 TCGACCAGTAACATGCGTAAAA 58.349 40.909 0.00 0.00 0.00 1.52
135 136 4.247258 TCGACCAGTAACATGCGTAAAAT 58.753 39.130 0.00 0.00 0.00 1.82
136 137 5.409211 TCGACCAGTAACATGCGTAAAATA 58.591 37.500 0.00 0.00 0.00 1.40
137 138 6.044046 TCGACCAGTAACATGCGTAAAATAT 58.956 36.000 0.00 0.00 0.00 1.28
138 139 6.535865 TCGACCAGTAACATGCGTAAAATATT 59.464 34.615 0.00 0.00 0.00 1.28
139 140 6.627276 CGACCAGTAACATGCGTAAAATATTG 59.373 38.462 0.00 0.00 0.00 1.90
140 141 6.791303 ACCAGTAACATGCGTAAAATATTGG 58.209 36.000 0.00 0.00 0.00 3.16
141 142 5.685511 CCAGTAACATGCGTAAAATATTGGC 59.314 40.000 0.00 0.00 0.00 4.52
142 143 6.459573 CCAGTAACATGCGTAAAATATTGGCT 60.460 38.462 0.00 0.00 0.00 4.75
143 144 6.414694 CAGTAACATGCGTAAAATATTGGCTG 59.585 38.462 0.00 0.00 0.00 4.85
144 145 5.574891 AACATGCGTAAAATATTGGCTGA 57.425 34.783 0.00 0.00 0.00 4.26
145 146 4.920376 ACATGCGTAAAATATTGGCTGAC 58.080 39.130 0.00 0.00 0.00 3.51
146 147 4.397730 ACATGCGTAAAATATTGGCTGACA 59.602 37.500 0.00 0.00 0.00 3.58
147 148 5.105957 ACATGCGTAAAATATTGGCTGACAA 60.106 36.000 0.00 0.00 44.54 3.18
159 160 5.850557 TTGGCTGACAATATATTTGGGTG 57.149 39.130 0.00 0.00 33.18 4.61
160 161 3.636300 TGGCTGACAATATATTTGGGTGC 59.364 43.478 0.00 0.00 0.00 5.01
161 162 3.636300 GGCTGACAATATATTTGGGTGCA 59.364 43.478 0.00 0.00 0.00 4.57
162 163 4.281688 GGCTGACAATATATTTGGGTGCAT 59.718 41.667 0.00 0.00 0.00 3.96
163 164 5.476599 GGCTGACAATATATTTGGGTGCATA 59.523 40.000 0.00 0.00 0.00 3.14
164 165 6.153340 GGCTGACAATATATTTGGGTGCATAT 59.847 38.462 0.00 0.00 0.00 1.78
165 166 7.339212 GGCTGACAATATATTTGGGTGCATATA 59.661 37.037 0.00 0.00 0.00 0.86
166 167 8.739039 GCTGACAATATATTTGGGTGCATATAA 58.261 33.333 0.00 0.00 0.00 0.98
175 176 6.783708 TTTGGGTGCATATAAAGTAAAGGG 57.216 37.500 0.00 0.00 0.00 3.95
176 177 5.718801 TGGGTGCATATAAAGTAAAGGGA 57.281 39.130 0.00 0.00 0.00 4.20
177 178 6.080969 TGGGTGCATATAAAGTAAAGGGAA 57.919 37.500 0.00 0.00 0.00 3.97
178 179 6.126409 TGGGTGCATATAAAGTAAAGGGAAG 58.874 40.000 0.00 0.00 0.00 3.46
179 180 6.069323 TGGGTGCATATAAAGTAAAGGGAAGA 60.069 38.462 0.00 0.00 0.00 2.87
180 181 7.004691 GGGTGCATATAAAGTAAAGGGAAGAT 58.995 38.462 0.00 0.00 0.00 2.40
181 182 7.505923 GGGTGCATATAAAGTAAAGGGAAGATT 59.494 37.037 0.00 0.00 0.00 2.40
182 183 8.352942 GGTGCATATAAAGTAAAGGGAAGATTG 58.647 37.037 0.00 0.00 0.00 2.67
183 184 8.903820 GTGCATATAAAGTAAAGGGAAGATTGT 58.096 33.333 0.00 0.00 0.00 2.71
184 185 9.474313 TGCATATAAAGTAAAGGGAAGATTGTT 57.526 29.630 0.00 0.00 0.00 2.83
188 189 5.468540 AAGTAAAGGGAAGATTGTTTGGC 57.531 39.130 0.00 0.00 0.00 4.52
189 190 4.479158 AGTAAAGGGAAGATTGTTTGGCA 58.521 39.130 0.00 0.00 0.00 4.92
190 191 5.086621 AGTAAAGGGAAGATTGTTTGGCAT 58.913 37.500 0.00 0.00 0.00 4.40
191 192 3.967332 AAGGGAAGATTGTTTGGCATG 57.033 42.857 0.00 0.00 0.00 4.06
192 193 3.173953 AGGGAAGATTGTTTGGCATGA 57.826 42.857 0.00 0.00 0.00 3.07
193 194 2.827921 AGGGAAGATTGTTTGGCATGAC 59.172 45.455 0.00 0.00 0.00 3.06
194 195 2.094026 GGGAAGATTGTTTGGCATGACC 60.094 50.000 0.00 0.00 39.84 4.02
195 196 2.415893 GGAAGATTGTTTGGCATGACCG 60.416 50.000 0.00 0.00 43.94 4.79
196 197 2.198827 AGATTGTTTGGCATGACCGA 57.801 45.000 0.00 0.00 43.94 4.69
197 198 2.513753 AGATTGTTTGGCATGACCGAA 58.486 42.857 0.00 0.02 43.94 4.30
198 199 2.489329 AGATTGTTTGGCATGACCGAAG 59.511 45.455 0.00 0.00 42.91 3.79
210 211 3.165498 CCGAAGGCGAAACCGAAG 58.835 61.111 0.00 0.00 46.14 3.79
237 238 6.062095 ACATATATACAAGGGACAAACTGCC 58.938 40.000 0.00 0.00 0.00 4.85
239 240 2.561478 TACAAGGGACAAACTGCCTC 57.439 50.000 0.00 0.00 40.68 4.70
335 338 2.503331 TGCCAGCATATTATTGGTCCG 58.497 47.619 0.00 0.00 34.43 4.79
375 378 4.439305 TTGCATCTGCCAAAGAACATAC 57.561 40.909 0.00 0.00 38.79 2.39
376 379 3.419943 TGCATCTGCCAAAGAACATACA 58.580 40.909 0.00 0.00 38.79 2.29
377 380 4.018490 TGCATCTGCCAAAGAACATACAT 58.982 39.130 0.00 0.00 38.79 2.29
378 381 5.192176 TGCATCTGCCAAAGAACATACATA 58.808 37.500 0.00 0.00 38.79 2.29
391 394 6.341316 AGAACATACATATCGTTTCTGCAGT 58.659 36.000 14.67 0.00 0.00 4.40
400 403 1.334419 CGTTTCTGCAGTTGAGCAAGG 60.334 52.381 14.67 1.06 45.13 3.61
404 407 0.313043 CTGCAGTTGAGCAAGGTTGG 59.687 55.000 5.25 0.00 45.13 3.77
414 417 3.084786 GAGCAAGGTTGGAACTTATGCT 58.915 45.455 13.33 13.33 41.23 3.79
450 457 0.647410 GTCAGCAACATCCGATCACG 59.353 55.000 0.00 0.00 39.43 4.35
488 495 2.098934 GCATACCGAAATCACAATGCCA 59.901 45.455 0.00 0.00 34.95 4.92
505 512 4.046286 TGCCAGTAATTCTTGGTCCAAT 57.954 40.909 4.34 0.00 0.00 3.16
506 513 4.415596 TGCCAGTAATTCTTGGTCCAATT 58.584 39.130 4.34 0.00 0.00 2.32
507 514 4.462483 TGCCAGTAATTCTTGGTCCAATTC 59.538 41.667 4.34 0.00 0.00 2.17
508 515 4.462483 GCCAGTAATTCTTGGTCCAATTCA 59.538 41.667 4.34 0.00 0.00 2.57
509 516 5.047377 GCCAGTAATTCTTGGTCCAATTCAA 60.047 40.000 4.34 0.00 0.00 2.69
510 517 6.624423 CCAGTAATTCTTGGTCCAATTCAAG 58.376 40.000 4.34 0.00 41.06 3.02
511 518 6.095377 CAGTAATTCTTGGTCCAATTCAAGC 58.905 40.000 4.34 0.00 39.92 4.01
512 519 5.774690 AGTAATTCTTGGTCCAATTCAAGCA 59.225 36.000 4.34 0.00 39.92 3.91
513 520 5.750352 AATTCTTGGTCCAATTCAAGCAT 57.250 34.783 4.34 0.00 39.92 3.79
565 575 0.038166 GGTGGCTGGATGTTGGAGAA 59.962 55.000 0.00 0.00 0.00 2.87
568 578 2.827921 GTGGCTGGATGTTGGAGAAAAT 59.172 45.455 0.00 0.00 0.00 1.82
569 579 3.259123 GTGGCTGGATGTTGGAGAAAATT 59.741 43.478 0.00 0.00 0.00 1.82
581 591 1.758862 GAGAAAATTGGGAGCCATGGG 59.241 52.381 15.13 0.00 31.53 4.00
583 593 2.022722 AGAAAATTGGGAGCCATGGGAT 60.023 45.455 15.13 0.00 31.53 3.85
608 618 2.052237 CGACGGTGCACAGCAAAC 60.052 61.111 20.43 6.59 41.47 2.93
619 629 3.337619 AGCAAACGCTCTGTGCTG 58.662 55.556 0.00 0.00 46.58 4.41
643 653 1.730487 CTGCGTCCGTCTCTGCTAT 59.270 57.895 0.00 0.00 0.00 2.97
646 656 0.040246 GCGTCCGTCTCTGCTATACC 60.040 60.000 0.00 0.00 0.00 2.73
647 657 1.306148 CGTCCGTCTCTGCTATACCA 58.694 55.000 0.00 0.00 0.00 3.25
648 658 1.880675 CGTCCGTCTCTGCTATACCAT 59.119 52.381 0.00 0.00 0.00 3.55
649 659 2.293677 CGTCCGTCTCTGCTATACCATT 59.706 50.000 0.00 0.00 0.00 3.16
650 660 3.501062 CGTCCGTCTCTGCTATACCATTA 59.499 47.826 0.00 0.00 0.00 1.90
651 661 4.613167 CGTCCGTCTCTGCTATACCATTAC 60.613 50.000 0.00 0.00 0.00 1.89
652 662 4.277672 GTCCGTCTCTGCTATACCATTACA 59.722 45.833 0.00 0.00 0.00 2.41
653 663 4.277672 TCCGTCTCTGCTATACCATTACAC 59.722 45.833 0.00 0.00 0.00 2.90
654 664 4.278669 CCGTCTCTGCTATACCATTACACT 59.721 45.833 0.00 0.00 0.00 3.55
655 665 5.221263 CCGTCTCTGCTATACCATTACACTT 60.221 44.000 0.00 0.00 0.00 3.16
656 666 5.915758 CGTCTCTGCTATACCATTACACTTC 59.084 44.000 0.00 0.00 0.00 3.01
657 667 6.238786 CGTCTCTGCTATACCATTACACTTCT 60.239 42.308 0.00 0.00 0.00 2.85
658 668 7.142680 GTCTCTGCTATACCATTACACTTCTC 58.857 42.308 0.00 0.00 0.00 2.87
659 669 7.013846 GTCTCTGCTATACCATTACACTTCTCT 59.986 40.741 0.00 0.00 0.00 3.10
660 670 7.229707 TCTCTGCTATACCATTACACTTCTCTC 59.770 40.741 0.00 0.00 0.00 3.20
661 671 7.063593 TCTGCTATACCATTACACTTCTCTCT 58.936 38.462 0.00 0.00 0.00 3.10
662 672 7.229707 TCTGCTATACCATTACACTTCTCTCTC 59.770 40.741 0.00 0.00 0.00 3.20
663 673 7.063593 TGCTATACCATTACACTTCTCTCTCT 58.936 38.462 0.00 0.00 0.00 3.10
664 674 7.229707 TGCTATACCATTACACTTCTCTCTCTC 59.770 40.741 0.00 0.00 0.00 3.20
665 675 7.447238 GCTATACCATTACACTTCTCTCTCTCT 59.553 40.741 0.00 0.00 0.00 3.10
666 676 7.817418 ATACCATTACACTTCTCTCTCTCTC 57.183 40.000 0.00 0.00 0.00 3.20
667 677 5.826643 ACCATTACACTTCTCTCTCTCTCT 58.173 41.667 0.00 0.00 0.00 3.10
668 678 5.885912 ACCATTACACTTCTCTCTCTCTCTC 59.114 44.000 0.00 0.00 0.00 3.20
669 679 6.122277 CCATTACACTTCTCTCTCTCTCTCT 58.878 44.000 0.00 0.00 0.00 3.10
670 680 6.260936 CCATTACACTTCTCTCTCTCTCTCTC 59.739 46.154 0.00 0.00 0.00 3.20
683 693 1.134521 TCTCTCTCTCTCTCTGTCCGC 60.135 57.143 0.00 0.00 0.00 5.54
1005 1024 1.134694 GCTGTTCGACGAAATGCCC 59.865 57.895 12.67 0.00 0.00 5.36
1044 1063 4.552365 ACCTCCATGATGCGGGCG 62.552 66.667 0.00 0.00 0.00 6.13
1103 1122 3.146066 TGTTCAGGGACATGTTAACTGC 58.854 45.455 16.13 7.72 0.00 4.40
1107 1126 0.322187 GGGACATGTTAACTGCCGGT 60.322 55.000 1.90 0.00 0.00 5.28
1155 1174 4.052229 CTTGTCGTCGCCCTCCGT 62.052 66.667 0.00 0.00 38.35 4.69
1182 1201 3.071206 GAGCTCGAGGACCTGGCA 61.071 66.667 15.58 0.00 0.00 4.92
1185 1204 2.948720 GCTCGAGGACCTGGCACTT 61.949 63.158 15.58 0.00 0.00 3.16
1208 1227 2.740055 CTCCCTGCACGCTGTCAC 60.740 66.667 0.00 0.00 0.00 3.67
1272 1291 1.513373 GCTCGTCGACATGTACGCA 60.513 57.895 17.16 5.14 38.94 5.24
1287 1306 2.978824 GCAAGGTGCCTCGACCTA 59.021 61.111 0.00 0.00 46.29 3.08
1288 1307 1.522569 GCAAGGTGCCTCGACCTAT 59.477 57.895 0.00 0.00 46.29 2.57
1409 1428 1.229209 TGGACCTTCTCGCCTCCTT 60.229 57.895 0.00 0.00 0.00 3.36
1413 1435 0.832135 ACCTTCTCGCCTCCTTGTCA 60.832 55.000 0.00 0.00 0.00 3.58
1428 1450 2.957402 TGTCATTGCTGAAAGAGGGT 57.043 45.000 0.00 0.00 34.07 4.34
1564 1589 1.115467 CCTATTGTCCTCGACAGGCT 58.885 55.000 0.00 0.00 43.69 4.58
1590 1615 1.675641 GTTGAACGCCCTGCTGGAT 60.676 57.895 11.88 0.00 35.39 3.41
1638 1663 3.616721 ACGCTCAGGCTGTTCCGT 61.617 61.111 15.27 17.29 40.77 4.69
1680 1705 1.667830 CACGTGGAGCACCGTCATT 60.668 57.895 7.95 0.00 39.42 2.57
1752 1777 3.962530 AATGAGGGAGGCCGGGGAA 62.963 63.158 2.18 0.00 0.00 3.97
1754 1779 3.097162 GAGGGAGGCCGGGGAAAT 61.097 66.667 2.18 0.00 0.00 2.17
1755 1780 2.617215 AGGGAGGCCGGGGAAATT 60.617 61.111 2.18 0.00 0.00 1.82
1984 2009 2.502947 CTCACCTGGAACTCCATGATCA 59.497 50.000 0.00 0.00 46.46 2.92
2008 2033 3.719646 CTGGGGATGAATGGCCGCA 62.720 63.158 0.00 0.00 43.74 5.69
2029 2054 4.899239 GTGATGCCCTCGCCCTCG 62.899 72.222 0.00 0.00 0.00 4.63
2060 2085 0.107459 GAGCAGGAAGGGGACATCAC 60.107 60.000 0.00 0.00 0.00 3.06
2067 2092 1.910580 AAGGGGACATCACGCCGAAT 61.911 55.000 0.00 0.00 45.58 3.34
2127 2152 2.122954 GGTCTGGTGGAGGAGGGT 59.877 66.667 0.00 0.00 0.00 4.34
2211 2236 1.873572 CATCGTCGACATGCTCGCA 60.874 57.895 17.16 0.00 42.62 5.10
2247 2272 3.489513 GGGGCCGCTAGGGTCATT 61.490 66.667 13.57 0.00 44.60 2.57
2267 2292 2.964209 TGAGGAGAGGATATCCACCAC 58.036 52.381 23.81 19.48 39.47 4.16
2331 2356 2.091112 CCACAGCAGCGACTCGAAG 61.091 63.158 1.63 0.00 0.00 3.79
2334 2359 1.803519 CAGCAGCGACTCGAAGGTC 60.804 63.158 1.63 0.00 0.00 3.85
2341 2366 2.360350 ACTCGAAGGTCGGCCGTA 60.360 61.111 27.15 9.34 40.88 4.02
2355 2380 2.819595 CGTAATGCTGCCTGCCGT 60.820 61.111 0.00 0.00 42.00 5.68
2532 2557 0.320771 ACAGCTTCATGTCGTGGGAC 60.321 55.000 0.00 0.00 43.71 4.46
2619 2644 2.173569 GCCTACTCCTCCACATCCAAAT 59.826 50.000 0.00 0.00 0.00 2.32
2671 2696 5.012664 ACACCAGTGTCATGATTAAGGTACA 59.987 40.000 0.00 0.00 40.24 2.90
2672 2697 6.115446 CACCAGTGTCATGATTAAGGTACAT 58.885 40.000 0.00 0.00 0.00 2.29
2698 2723 5.386060 ACGAAGTCCTCACCATCATCTATA 58.614 41.667 0.00 0.00 29.74 1.31
2712 2737 9.035890 ACCATCATCTATATTTATCAACTCGGA 57.964 33.333 0.00 0.00 0.00 4.55
2770 2795 5.176590 GCCGAATTTTGTAGTGCATTTTGAA 59.823 36.000 0.00 0.00 0.00 2.69
2772 2797 7.062839 GCCGAATTTTGTAGTGCATTTTGAATA 59.937 33.333 0.00 0.00 0.00 1.75
2790 2815 6.418057 TGAATACCTGCTTTGGATTTGTTT 57.582 33.333 0.00 0.00 0.00 2.83
2791 2816 6.222389 TGAATACCTGCTTTGGATTTGTTTG 58.778 36.000 0.00 0.00 0.00 2.93
2820 2845 7.148188 TGCAATTCTCAGTATGGTTCTTTCATC 60.148 37.037 0.00 0.00 36.16 2.92
2825 2850 6.667848 TCTCAGTATGGTTCTTTCATCACCTA 59.332 38.462 0.00 0.00 36.16 3.08
2842 2877 0.319555 CTATGGATGGTGGGTACGCG 60.320 60.000 3.53 3.53 0.00 6.01
2952 2987 4.009675 ACCGATGATGCTGTGTTTACATT 58.990 39.130 0.00 0.00 35.97 2.71
3001 3036 1.043816 CCGGCTCCATGAGATACTGT 58.956 55.000 0.00 0.00 0.00 3.55
3012 3047 4.487714 TGAGATACTGTGGAATGGGTTC 57.512 45.455 0.00 0.00 0.00 3.62
3013 3048 3.843619 TGAGATACTGTGGAATGGGTTCA 59.156 43.478 0.00 0.00 36.01 3.18
3019 3094 4.030216 ACTGTGGAATGGGTTCAAACTTT 58.970 39.130 0.00 0.00 36.01 2.66
3021 3096 5.838521 ACTGTGGAATGGGTTCAAACTTTAT 59.161 36.000 0.00 0.00 36.01 1.40
3092 3167 1.083706 ATCCTCTCCACCAGCCCTT 59.916 57.895 0.00 0.00 0.00 3.95
3100 3175 2.123897 ACCAGCCCTTTGCAACGT 60.124 55.556 0.00 0.00 44.83 3.99
3130 3205 1.718757 GGACCGTTGCCATCATGAGC 61.719 60.000 0.09 0.09 0.00 4.26
3151 3226 2.042259 CATCAGCTTGCCGGCTTCA 61.042 57.895 29.70 10.82 41.00 3.02
3163 3238 1.453928 GGCTTCATACCTGGCCCAC 60.454 63.158 0.00 0.00 38.77 4.61
3164 3239 1.302949 GCTTCATACCTGGCCCACA 59.697 57.895 0.00 0.00 0.00 4.17
3169 3244 1.916273 ATACCTGGCCCACACGACA 60.916 57.895 0.00 0.00 0.00 4.35
3264 3339 2.758089 GGAGCATGCCGAAGCTGTG 61.758 63.158 15.66 0.00 42.04 3.66
3312 3387 2.046314 CATCCAAACCTCCGGCGT 60.046 61.111 6.01 0.00 0.00 5.68
3354 3431 2.583593 GCGGGACAGAGATGCGTC 60.584 66.667 0.00 0.00 0.00 5.19
3356 3433 1.513158 CGGGACAGAGATGCGTCTT 59.487 57.895 10.42 0.00 33.97 3.01
3369 3446 1.565156 GCGTCTTGGCACGATTGACA 61.565 55.000 0.00 0.00 42.69 3.58
3389 3466 3.042560 GCTTGCGAGGCCAAAGTT 58.957 55.556 5.01 0.00 0.00 2.66
3539 3623 0.519961 GTGTCATTACCGGTGGCAAC 59.480 55.000 19.93 11.05 32.28 4.17
3560 3644 0.874175 GGTTGGTCTGCGTTTTTGGC 60.874 55.000 0.00 0.00 0.00 4.52
3602 3686 5.825593 TCCTGTCATCTTCTGGTTTACTT 57.174 39.130 0.00 0.00 0.00 2.24
3816 3924 6.582295 GGTATGTTATCAAGTTGTTTGTGCTG 59.418 38.462 2.11 0.00 38.01 4.41
3837 3953 1.558756 CCAGCTGGATGAGTCCTCTTT 59.441 52.381 29.88 0.00 45.32 2.52
3838 3954 2.768527 CCAGCTGGATGAGTCCTCTTTA 59.231 50.000 29.88 0.00 45.32 1.85
3839 3955 3.198635 CCAGCTGGATGAGTCCTCTTTAA 59.801 47.826 29.88 0.00 45.32 1.52
3840 3956 4.141528 CCAGCTGGATGAGTCCTCTTTAAT 60.142 45.833 29.88 0.00 45.32 1.40
3841 3957 4.815308 CAGCTGGATGAGTCCTCTTTAATG 59.185 45.833 5.57 0.00 45.32 1.90
3842 3958 3.563390 GCTGGATGAGTCCTCTTTAATGC 59.437 47.826 0.00 0.00 45.32 3.56
3843 3959 4.685575 GCTGGATGAGTCCTCTTTAATGCT 60.686 45.833 0.00 0.00 45.32 3.79
3844 3960 5.435291 CTGGATGAGTCCTCTTTAATGCTT 58.565 41.667 0.00 0.00 45.32 3.91
3861 3977 1.332375 GCTTGTCCACTTGTTACGCAA 59.668 47.619 0.00 0.00 35.50 4.85
3931 4047 6.588204 TGTTATATTAGCACTCCCGTTTCAT 58.412 36.000 0.00 0.00 0.00 2.57
3942 4059 1.497278 CGTTTCATGGCGTCTGTGG 59.503 57.895 0.00 0.00 0.00 4.17
3975 4092 8.496707 AATCCATTTGATTGGTTTTTATCAGC 57.503 30.769 0.00 0.00 42.18 4.26
3978 4095 8.102047 TCCATTTGATTGGTTTTTATCAGCAAT 58.898 29.630 0.00 0.00 43.40 3.56
4004 4121 9.638239 TTTGATTTGTCTTGTATAATCTTTGCC 57.362 29.630 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.311596 ACGTTCGGATTTTAGCAATAGGC 59.688 43.478 0.00 0.00 45.30 3.93
40 41 5.479716 AACGTTCGGATTTTAGCAATAGG 57.520 39.130 0.00 0.00 0.00 2.57
41 42 6.257193 ACCTAACGTTCGGATTTTAGCAATAG 59.743 38.462 24.30 1.44 0.00 1.73
42 43 6.108015 ACCTAACGTTCGGATTTTAGCAATA 58.892 36.000 24.30 0.00 0.00 1.90
43 44 4.939439 ACCTAACGTTCGGATTTTAGCAAT 59.061 37.500 24.30 0.00 0.00 3.56
44 45 4.317488 ACCTAACGTTCGGATTTTAGCAA 58.683 39.130 24.30 0.00 0.00 3.91
45 46 3.929094 ACCTAACGTTCGGATTTTAGCA 58.071 40.909 24.30 0.00 0.00 3.49
46 47 5.105063 ACTACCTAACGTTCGGATTTTAGC 58.895 41.667 24.30 0.00 0.00 3.09
47 48 8.862550 ATAACTACCTAACGTTCGGATTTTAG 57.137 34.615 24.30 16.55 0.00 1.85
49 50 9.651913 TTTATAACTACCTAACGTTCGGATTTT 57.348 29.630 24.30 14.76 0.00 1.82
50 51 9.651913 TTTTATAACTACCTAACGTTCGGATTT 57.348 29.630 24.30 15.06 0.00 2.17
51 52 9.305925 CTTTTATAACTACCTAACGTTCGGATT 57.694 33.333 24.30 16.30 0.00 3.01
52 53 8.470002 ACTTTTATAACTACCTAACGTTCGGAT 58.530 33.333 24.30 9.99 0.00 4.18
53 54 7.826690 ACTTTTATAACTACCTAACGTTCGGA 58.173 34.615 24.30 8.08 0.00 4.55
54 55 7.220875 GGACTTTTATAACTACCTAACGTTCGG 59.779 40.741 16.75 16.75 0.00 4.30
55 56 7.754924 TGGACTTTTATAACTACCTAACGTTCG 59.245 37.037 2.82 0.00 0.00 3.95
56 57 8.986477 TGGACTTTTATAACTACCTAACGTTC 57.014 34.615 2.82 0.00 0.00 3.95
57 58 9.777297 TTTGGACTTTTATAACTACCTAACGTT 57.223 29.630 5.88 5.88 0.00 3.99
58 59 9.777297 TTTTGGACTTTTATAACTACCTAACGT 57.223 29.630 0.00 0.00 0.00 3.99
73 74 7.819415 GCTATTGCCTTATTCTTTTGGACTTTT 59.181 33.333 0.00 0.00 0.00 2.27
74 75 7.323420 GCTATTGCCTTATTCTTTTGGACTTT 58.677 34.615 0.00 0.00 0.00 2.66
75 76 6.867550 GCTATTGCCTTATTCTTTTGGACTT 58.132 36.000 0.00 0.00 0.00 3.01
76 77 6.456795 GCTATTGCCTTATTCTTTTGGACT 57.543 37.500 0.00 0.00 0.00 3.85
92 93 4.201724 CGAGTTGTCAAAGTAGGCTATTGC 60.202 45.833 0.00 0.00 38.76 3.56
93 94 5.062308 GTCGAGTTGTCAAAGTAGGCTATTG 59.938 44.000 0.00 0.00 0.00 1.90
94 95 5.169295 GTCGAGTTGTCAAAGTAGGCTATT 58.831 41.667 0.00 0.00 0.00 1.73
95 96 4.381718 GGTCGAGTTGTCAAAGTAGGCTAT 60.382 45.833 0.00 0.00 0.00 2.97
96 97 3.057033 GGTCGAGTTGTCAAAGTAGGCTA 60.057 47.826 0.00 0.00 0.00 3.93
97 98 2.288886 GGTCGAGTTGTCAAAGTAGGCT 60.289 50.000 0.00 0.00 0.00 4.58
98 99 2.067013 GGTCGAGTTGTCAAAGTAGGC 58.933 52.381 0.00 0.00 0.00 3.93
99 100 3.243771 ACTGGTCGAGTTGTCAAAGTAGG 60.244 47.826 0.00 0.00 0.00 3.18
100 101 3.978687 ACTGGTCGAGTTGTCAAAGTAG 58.021 45.455 0.00 0.00 0.00 2.57
101 102 5.163530 TGTTACTGGTCGAGTTGTCAAAGTA 60.164 40.000 0.00 0.00 35.96 2.24
102 103 2.981859 ACTGGTCGAGTTGTCAAAGT 57.018 45.000 0.00 0.00 0.00 2.66
103 104 4.116961 TGTTACTGGTCGAGTTGTCAAAG 58.883 43.478 0.00 0.00 35.96 2.77
104 105 4.126208 TGTTACTGGTCGAGTTGTCAAA 57.874 40.909 0.00 0.00 35.96 2.69
105 106 3.804786 TGTTACTGGTCGAGTTGTCAA 57.195 42.857 0.00 0.00 35.96 3.18
106 107 3.649073 CATGTTACTGGTCGAGTTGTCA 58.351 45.455 0.00 0.00 35.96 3.58
107 108 2.412089 GCATGTTACTGGTCGAGTTGTC 59.588 50.000 0.00 0.00 35.96 3.18
108 109 2.413837 GCATGTTACTGGTCGAGTTGT 58.586 47.619 0.00 0.00 35.96 3.32
109 110 1.390123 CGCATGTTACTGGTCGAGTTG 59.610 52.381 0.00 0.00 35.96 3.16
110 111 1.000506 ACGCATGTTACTGGTCGAGTT 59.999 47.619 0.00 0.00 35.96 3.01
111 112 0.601558 ACGCATGTTACTGGTCGAGT 59.398 50.000 0.00 0.00 38.88 4.18
112 113 2.554806 TACGCATGTTACTGGTCGAG 57.445 50.000 0.00 0.00 0.00 4.04
113 114 3.300852 TTTACGCATGTTACTGGTCGA 57.699 42.857 0.00 0.00 0.00 4.20
114 115 4.593597 ATTTTACGCATGTTACTGGTCG 57.406 40.909 0.00 0.00 0.00 4.79
115 116 6.910433 CCAATATTTTACGCATGTTACTGGTC 59.090 38.462 0.00 0.00 0.00 4.02
116 117 6.679392 GCCAATATTTTACGCATGTTACTGGT 60.679 38.462 0.00 0.00 0.00 4.00
117 118 5.685511 GCCAATATTTTACGCATGTTACTGG 59.314 40.000 0.00 0.00 0.00 4.00
118 119 6.414694 CAGCCAATATTTTACGCATGTTACTG 59.585 38.462 0.00 0.00 0.00 2.74
119 120 6.317642 TCAGCCAATATTTTACGCATGTTACT 59.682 34.615 0.00 0.00 0.00 2.24
120 121 6.413818 GTCAGCCAATATTTTACGCATGTTAC 59.586 38.462 0.00 0.00 0.00 2.50
121 122 6.094186 TGTCAGCCAATATTTTACGCATGTTA 59.906 34.615 0.00 0.00 0.00 2.41
122 123 5.105957 TGTCAGCCAATATTTTACGCATGTT 60.106 36.000 0.00 0.00 0.00 2.71
123 124 4.397730 TGTCAGCCAATATTTTACGCATGT 59.602 37.500 0.00 0.00 0.00 3.21
124 125 4.919206 TGTCAGCCAATATTTTACGCATG 58.081 39.130 0.00 0.00 0.00 4.06
125 126 5.574891 TTGTCAGCCAATATTTTACGCAT 57.425 34.783 0.00 0.00 0.00 4.73
126 127 5.574891 ATTGTCAGCCAATATTTTACGCA 57.425 34.783 0.00 0.00 42.03 5.24
136 137 5.221501 GCACCCAAATATATTGTCAGCCAAT 60.222 40.000 0.00 0.00 45.68 3.16
137 138 4.099266 GCACCCAAATATATTGTCAGCCAA 59.901 41.667 0.00 0.00 37.49 4.52
138 139 3.636300 GCACCCAAATATATTGTCAGCCA 59.364 43.478 0.00 0.00 0.00 4.75
139 140 3.636300 TGCACCCAAATATATTGTCAGCC 59.364 43.478 0.00 0.00 0.00 4.85
140 141 4.916983 TGCACCCAAATATATTGTCAGC 57.083 40.909 0.00 1.61 0.00 4.26
149 150 9.088987 CCCTTTACTTTATATGCACCCAAATAT 57.911 33.333 0.00 0.00 0.00 1.28
150 151 8.282982 TCCCTTTACTTTATATGCACCCAAATA 58.717 33.333 0.00 0.00 0.00 1.40
151 152 7.129425 TCCCTTTACTTTATATGCACCCAAAT 58.871 34.615 0.00 0.00 0.00 2.32
152 153 6.494952 TCCCTTTACTTTATATGCACCCAAA 58.505 36.000 0.00 0.00 0.00 3.28
153 154 6.080969 TCCCTTTACTTTATATGCACCCAA 57.919 37.500 0.00 0.00 0.00 4.12
154 155 5.718801 TCCCTTTACTTTATATGCACCCA 57.281 39.130 0.00 0.00 0.00 4.51
155 156 6.362248 TCTTCCCTTTACTTTATATGCACCC 58.638 40.000 0.00 0.00 0.00 4.61
156 157 8.352942 CAATCTTCCCTTTACTTTATATGCACC 58.647 37.037 0.00 0.00 0.00 5.01
157 158 8.903820 ACAATCTTCCCTTTACTTTATATGCAC 58.096 33.333 0.00 0.00 0.00 4.57
158 159 9.474313 AACAATCTTCCCTTTACTTTATATGCA 57.526 29.630 0.00 0.00 0.00 3.96
162 163 8.745590 GCCAAACAATCTTCCCTTTACTTTATA 58.254 33.333 0.00 0.00 0.00 0.98
163 164 7.234577 TGCCAAACAATCTTCCCTTTACTTTAT 59.765 33.333 0.00 0.00 0.00 1.40
164 165 6.551601 TGCCAAACAATCTTCCCTTTACTTTA 59.448 34.615 0.00 0.00 0.00 1.85
165 166 5.365314 TGCCAAACAATCTTCCCTTTACTTT 59.635 36.000 0.00 0.00 0.00 2.66
166 167 4.898861 TGCCAAACAATCTTCCCTTTACTT 59.101 37.500 0.00 0.00 0.00 2.24
167 168 4.479158 TGCCAAACAATCTTCCCTTTACT 58.521 39.130 0.00 0.00 0.00 2.24
168 169 4.864704 TGCCAAACAATCTTCCCTTTAC 57.135 40.909 0.00 0.00 0.00 2.01
169 170 5.047377 GTCATGCCAAACAATCTTCCCTTTA 60.047 40.000 0.00 0.00 0.00 1.85
170 171 3.903090 TCATGCCAAACAATCTTCCCTTT 59.097 39.130 0.00 0.00 0.00 3.11
171 172 3.259123 GTCATGCCAAACAATCTTCCCTT 59.741 43.478 0.00 0.00 0.00 3.95
172 173 2.827921 GTCATGCCAAACAATCTTCCCT 59.172 45.455 0.00 0.00 0.00 4.20
173 174 2.094026 GGTCATGCCAAACAATCTTCCC 60.094 50.000 1.78 0.00 37.17 3.97
174 175 2.415893 CGGTCATGCCAAACAATCTTCC 60.416 50.000 6.92 0.00 36.97 3.46
175 176 2.487762 TCGGTCATGCCAAACAATCTTC 59.512 45.455 6.92 0.00 36.97 2.87
176 177 2.513753 TCGGTCATGCCAAACAATCTT 58.486 42.857 6.92 0.00 36.97 2.40
177 178 2.198827 TCGGTCATGCCAAACAATCT 57.801 45.000 6.92 0.00 36.97 2.40
178 179 2.415893 CCTTCGGTCATGCCAAACAATC 60.416 50.000 6.92 0.00 36.97 2.67
179 180 1.545582 CCTTCGGTCATGCCAAACAAT 59.454 47.619 6.92 0.00 36.97 2.71
180 181 0.958091 CCTTCGGTCATGCCAAACAA 59.042 50.000 6.92 0.00 36.97 2.83
181 182 1.523154 GCCTTCGGTCATGCCAAACA 61.523 55.000 6.92 0.00 36.97 2.83
182 183 1.212751 GCCTTCGGTCATGCCAAAC 59.787 57.895 6.92 0.00 36.97 2.93
183 184 2.331893 CGCCTTCGGTCATGCCAAA 61.332 57.895 6.92 0.00 36.97 3.28
184 185 2.739849 TTCGCCTTCGGTCATGCCAA 62.740 55.000 6.92 0.95 36.97 4.52
185 186 2.739849 TTTCGCCTTCGGTCATGCCA 62.740 55.000 6.92 0.00 36.97 4.92
186 187 2.038269 TTTCGCCTTCGGTCATGCC 61.038 57.895 0.00 0.00 36.13 4.40
187 188 1.134694 GTTTCGCCTTCGGTCATGC 59.865 57.895 0.00 0.00 36.13 4.06
188 189 1.794222 GGTTTCGCCTTCGGTCATG 59.206 57.895 0.00 0.00 36.13 3.07
189 190 1.740296 CGGTTTCGCCTTCGGTCAT 60.740 57.895 0.00 0.00 36.13 3.06
190 191 2.356553 CGGTTTCGCCTTCGGTCA 60.357 61.111 0.00 0.00 36.13 4.02
191 192 1.623973 CTTCGGTTTCGCCTTCGGTC 61.624 60.000 0.00 0.00 36.13 4.79
192 193 1.666872 CTTCGGTTTCGCCTTCGGT 60.667 57.895 0.00 0.00 36.13 4.69
193 194 2.388232 CCTTCGGTTTCGCCTTCGG 61.388 63.158 0.00 0.00 36.13 4.30
194 195 0.388907 TACCTTCGGTTTCGCCTTCG 60.389 55.000 0.00 0.00 37.09 3.79
195 196 1.073964 GTACCTTCGGTTTCGCCTTC 58.926 55.000 0.00 0.00 37.09 3.46
196 197 0.393820 TGTACCTTCGGTTTCGCCTT 59.606 50.000 0.00 0.00 37.09 4.35
197 198 0.611714 ATGTACCTTCGGTTTCGCCT 59.388 50.000 0.00 0.00 37.09 5.52
198 199 2.298411 TATGTACCTTCGGTTTCGCC 57.702 50.000 0.00 0.00 37.09 5.54
199 200 6.151691 TGTATATATGTACCTTCGGTTTCGC 58.848 40.000 7.12 0.00 37.09 4.70
200 201 7.327761 CCTTGTATATATGTACCTTCGGTTTCG 59.672 40.741 7.12 0.00 37.09 3.46
201 202 7.601508 CCCTTGTATATATGTACCTTCGGTTTC 59.398 40.741 7.12 0.00 37.09 2.78
202 203 7.290714 TCCCTTGTATATATGTACCTTCGGTTT 59.709 37.037 7.12 0.00 37.09 3.27
203 204 6.783977 TCCCTTGTATATATGTACCTTCGGTT 59.216 38.462 7.12 0.00 37.09 4.44
204 205 6.210185 GTCCCTTGTATATATGTACCTTCGGT 59.790 42.308 7.12 0.00 40.16 4.69
205 206 6.209986 TGTCCCTTGTATATATGTACCTTCGG 59.790 42.308 7.12 2.57 0.00 4.30
206 207 7.223260 TGTCCCTTGTATATATGTACCTTCG 57.777 40.000 7.12 0.00 0.00 3.79
207 208 9.269453 GTTTGTCCCTTGTATATATGTACCTTC 57.731 37.037 7.12 0.00 0.00 3.46
208 209 8.999895 AGTTTGTCCCTTGTATATATGTACCTT 58.000 33.333 7.12 0.00 0.00 3.50
209 210 8.429641 CAGTTTGTCCCTTGTATATATGTACCT 58.570 37.037 7.12 0.00 0.00 3.08
210 211 7.172703 GCAGTTTGTCCCTTGTATATATGTACC 59.827 40.741 7.12 0.00 0.00 3.34
211 212 7.172703 GGCAGTTTGTCCCTTGTATATATGTAC 59.827 40.741 2.82 2.82 0.00 2.90
212 213 7.071950 AGGCAGTTTGTCCCTTGTATATATGTA 59.928 37.037 0.00 0.00 0.00 2.29
213 214 6.062095 GGCAGTTTGTCCCTTGTATATATGT 58.938 40.000 0.00 0.00 0.00 2.29
214 215 6.299141 AGGCAGTTTGTCCCTTGTATATATG 58.701 40.000 0.00 0.00 0.00 1.78
215 216 6.465894 GGAGGCAGTTTGTCCCTTGTATATAT 60.466 42.308 0.00 0.00 0.00 0.86
216 217 5.163237 GGAGGCAGTTTGTCCCTTGTATATA 60.163 44.000 0.00 0.00 0.00 0.86
237 238 3.738282 GCTATCGCATAAGTTGTCAGGAG 59.262 47.826 0.00 0.00 35.78 3.69
239 240 3.457234 TGCTATCGCATAAGTTGTCAGG 58.543 45.455 0.00 0.00 42.25 3.86
274 275 9.997482 TGTAAACGGAAATTATTTTAGATGCTC 57.003 29.630 0.00 0.00 0.00 4.26
286 287 7.630944 GCCCATTTGGTATGTAAACGGAAATTA 60.631 37.037 0.00 0.00 36.04 1.40
291 292 3.018149 GCCCATTTGGTATGTAAACGGA 58.982 45.455 0.00 0.00 36.04 4.69
335 338 3.841643 CAAATCTGTCCATGCTTGAACC 58.158 45.455 0.22 0.00 0.00 3.62
375 378 3.371898 TGCTCAACTGCAGAAACGATATG 59.628 43.478 23.35 6.03 38.12 1.78
376 379 3.599343 TGCTCAACTGCAGAAACGATAT 58.401 40.909 23.35 0.00 38.12 1.63
377 380 3.038788 TGCTCAACTGCAGAAACGATA 57.961 42.857 23.35 0.00 38.12 2.92
378 381 1.882912 TGCTCAACTGCAGAAACGAT 58.117 45.000 23.35 0.00 38.12 3.73
391 394 3.255642 GCATAAGTTCCAACCTTGCTCAA 59.744 43.478 0.00 0.00 0.00 3.02
450 457 6.367422 TCGGTATGCAAACAAAATTCATTTCC 59.633 34.615 0.00 0.00 0.00 3.13
488 495 5.774690 TGCTTGAATTGGACCAAGAATTACT 59.225 36.000 13.43 0.00 41.56 2.24
556 566 2.247358 GGCTCCCAATTTTCTCCAACA 58.753 47.619 0.00 0.00 0.00 3.33
565 575 2.121129 CAATCCCATGGCTCCCAATTT 58.879 47.619 6.09 0.00 36.95 1.82
568 578 0.259647 CTCAATCCCATGGCTCCCAA 59.740 55.000 6.09 0.00 36.95 4.12
569 579 0.624206 TCTCAATCCCATGGCTCCCA 60.624 55.000 6.09 0.00 38.19 4.37
581 591 0.179111 TGCACCGTCGGATCTCAATC 60.179 55.000 20.51 0.00 0.00 2.67
583 593 1.080093 GTGCACCGTCGGATCTCAA 60.080 57.895 20.51 0.00 0.00 3.02
643 653 6.964464 AGAGAGAGAGAGAAGTGTAATGGTA 58.036 40.000 0.00 0.00 0.00 3.25
646 656 7.050377 AGAGAGAGAGAGAGAGAAGTGTAATG 58.950 42.308 0.00 0.00 0.00 1.90
647 657 7.126421 AGAGAGAGAGAGAGAGAGAAGTGTAAT 59.874 40.741 0.00 0.00 0.00 1.89
648 658 6.440647 AGAGAGAGAGAGAGAGAGAAGTGTAA 59.559 42.308 0.00 0.00 0.00 2.41
649 659 5.958380 AGAGAGAGAGAGAGAGAGAAGTGTA 59.042 44.000 0.00 0.00 0.00 2.90
650 660 4.780021 AGAGAGAGAGAGAGAGAGAAGTGT 59.220 45.833 0.00 0.00 0.00 3.55
651 661 5.128499 AGAGAGAGAGAGAGAGAGAGAAGTG 59.872 48.000 0.00 0.00 0.00 3.16
652 662 5.276440 AGAGAGAGAGAGAGAGAGAGAAGT 58.724 45.833 0.00 0.00 0.00 3.01
653 663 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
654 664 5.362143 CAGAGAGAGAGAGAGAGAGAGAGAA 59.638 48.000 0.00 0.00 0.00 2.87
655 665 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
656 666 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
657 667 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
658 668 4.202202 GGACAGAGAGAGAGAGAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
659 669 3.706594 GGACAGAGAGAGAGAGAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
660 670 3.491619 CGGACAGAGAGAGAGAGAGAGAG 60.492 56.522 0.00 0.00 0.00 3.20
661 671 2.430694 CGGACAGAGAGAGAGAGAGAGA 59.569 54.545 0.00 0.00 0.00 3.10
662 672 2.826428 CGGACAGAGAGAGAGAGAGAG 58.174 57.143 0.00 0.00 0.00 3.20
663 673 1.134521 GCGGACAGAGAGAGAGAGAGA 60.135 57.143 0.00 0.00 0.00 3.10
664 674 1.299541 GCGGACAGAGAGAGAGAGAG 58.700 60.000 0.00 0.00 0.00 3.20
665 675 0.107410 GGCGGACAGAGAGAGAGAGA 60.107 60.000 0.00 0.00 0.00 3.10
666 676 1.436195 CGGCGGACAGAGAGAGAGAG 61.436 65.000 0.00 0.00 0.00 3.20
667 677 1.450491 CGGCGGACAGAGAGAGAGA 60.450 63.158 0.00 0.00 0.00 3.10
668 678 2.477176 CCGGCGGACAGAGAGAGAG 61.477 68.421 24.41 0.00 0.00 3.20
669 679 2.438614 CCGGCGGACAGAGAGAGA 60.439 66.667 24.41 0.00 0.00 3.10
670 680 1.388065 ATTCCGGCGGACAGAGAGAG 61.388 60.000 31.23 0.00 0.00 3.20
1065 1084 3.267233 ATGCACAGGGCCTGGGAA 61.267 61.111 39.33 31.37 43.89 3.97
1182 1201 2.530151 TGCAGGGAGGCTCCAAGT 60.530 61.111 33.27 15.62 38.64 3.16
1272 1291 0.617820 ACCATAGGTCGAGGCACCTT 60.618 55.000 0.00 0.00 45.24 3.50
1288 1307 3.636231 CACCTTCCTGGCGGACCA 61.636 66.667 8.58 0.00 46.51 4.02
1392 1411 1.219393 CAAGGAGGCGAGAAGGTCC 59.781 63.158 0.00 0.00 0.00 4.46
1409 1428 2.106338 TCACCCTCTTTCAGCAATGACA 59.894 45.455 0.00 0.00 0.00 3.58
1413 1435 2.957402 TGTCACCCTCTTTCAGCAAT 57.043 45.000 0.00 0.00 0.00 3.56
1564 1589 1.896660 GGGCGTTCAACAGAGGCAA 60.897 57.895 0.00 0.00 0.00 4.52
1638 1663 3.008517 TTCCTCTCGGGCATGCCA 61.009 61.111 36.56 17.75 37.98 4.92
1734 1759 3.962530 TTCCCCGGCCTCCCTCATT 62.963 63.158 0.00 0.00 0.00 2.57
1752 1777 0.768622 TGGTGACCGAGTTGGGAATT 59.231 50.000 0.24 0.00 44.64 2.17
1754 1779 1.276989 GTATGGTGACCGAGTTGGGAA 59.723 52.381 0.24 0.00 44.64 3.97
1755 1780 0.899720 GTATGGTGACCGAGTTGGGA 59.100 55.000 0.24 0.00 44.64 4.37
1928 1953 1.452110 CATCGCATTGAACACCCTCA 58.548 50.000 0.00 0.00 0.00 3.86
1984 2009 4.181010 ATTCATCCCCAGCGCGCT 62.181 61.111 31.32 31.32 0.00 5.92
2008 2033 4.760047 GGCGAGGGCATCACGTGT 62.760 66.667 16.51 0.00 42.47 4.49
2029 2054 1.142748 CCTGCTCCATCCTGTCGAC 59.857 63.158 9.11 9.11 0.00 4.20
2060 2085 1.809619 ATCGTGACACCATTCGGCG 60.810 57.895 0.00 0.00 34.57 6.46
2067 2092 2.358615 GCCAGCATCGTGACACCA 60.359 61.111 0.00 0.00 0.00 4.17
2127 2152 2.659016 CTCTCGAAGCAGGCCACA 59.341 61.111 5.01 0.00 0.00 4.17
2211 2236 2.847234 TCAAGGTCCCCTGCACGT 60.847 61.111 0.00 0.00 32.13 4.49
2247 2272 2.426414 GGTGGTGGATATCCTCTCCTCA 60.426 54.545 22.35 9.41 36.82 3.86
2267 2292 4.031129 AGGCTGCTGGACTGCTGG 62.031 66.667 0.00 1.80 42.51 4.85
2331 2356 3.573491 GCAGCATTACGGCCGACC 61.573 66.667 35.90 14.32 32.71 4.79
2355 2380 2.583441 CGGCTCCAACTCCAGGACA 61.583 63.158 0.00 0.00 0.00 4.02
2437 2462 2.437180 CCTCATCAGCTGCCGCAA 60.437 61.111 9.47 0.00 39.10 4.85
2442 2467 1.446791 CCTCTCCCTCATCAGCTGC 59.553 63.158 9.47 0.00 0.00 5.25
2506 2531 1.326852 CGACATGAAGCTGTGAGCATC 59.673 52.381 0.00 0.00 45.56 3.91
2532 2557 2.124983 CTGTCAGGGTGGCATCCG 60.125 66.667 11.96 6.72 28.30 4.18
2619 2644 9.948964 CATGATAATAAGGTAAGATGATGGTGA 57.051 33.333 0.00 0.00 0.00 4.02
2671 2696 6.013379 AGATGATGGTGAGGACTTCGTATAT 58.987 40.000 0.00 0.00 0.00 0.86
2672 2697 5.386060 AGATGATGGTGAGGACTTCGTATA 58.614 41.667 0.00 0.00 0.00 1.47
2748 2773 8.372521 GGTATTCAAAATGCACTACAAAATTCG 58.627 33.333 0.00 0.00 0.00 3.34
2754 2779 5.476599 AGCAGGTATTCAAAATGCACTACAA 59.523 36.000 0.00 0.00 39.34 2.41
2770 2795 5.539955 ACTCAAACAAATCCAAAGCAGGTAT 59.460 36.000 0.00 0.00 0.00 2.73
2772 2797 3.706086 ACTCAAACAAATCCAAAGCAGGT 59.294 39.130 0.00 0.00 0.00 4.00
2790 2815 4.558226 ACCATACTGAGAATTGCACTCA 57.442 40.909 5.49 5.49 41.26 3.41
2791 2816 5.181748 AGAACCATACTGAGAATTGCACTC 58.818 41.667 0.00 0.00 35.26 3.51
2825 2850 1.044231 TACGCGTACCCACCATCCAT 61.044 55.000 16.41 0.00 0.00 3.41
2842 2877 5.192327 CAATCCTGCATTTCCTTCCATAC 57.808 43.478 0.00 0.00 0.00 2.39
2952 2987 2.405805 CGGATGGCAATGGCGAACA 61.406 57.895 1.51 0.00 42.47 3.18
3001 3036 5.245075 GGTGATAAAGTTTGAACCCATTCCA 59.755 40.000 0.00 0.00 33.49 3.53
3012 3047 1.463056 TGAGCGCGGTGATAAAGTTTG 59.537 47.619 18.92 0.00 0.00 2.93
3013 3048 1.803334 TGAGCGCGGTGATAAAGTTT 58.197 45.000 18.92 0.00 0.00 2.66
3019 3094 0.869880 CGTCAATGAGCGCGGTGATA 60.870 55.000 18.92 1.49 0.00 2.15
3021 3096 2.809174 CGTCAATGAGCGCGGTGA 60.809 61.111 18.92 8.19 0.00 4.02
3061 3136 1.555075 GAGAGGATGTGCAAGGTGGTA 59.445 52.381 0.00 0.00 0.00 3.25
3092 3167 1.840630 CGCCATGACTCACGTTGCAA 61.841 55.000 0.00 0.00 0.00 4.08
3100 3175 2.579657 AACGGTCCGCCATGACTCA 61.580 57.895 12.28 0.00 35.54 3.41
3130 3205 3.207669 GCCGGCAAGCTGATGGAG 61.208 66.667 24.80 0.00 0.00 3.86
3141 3216 2.589540 CCAGGTATGAAGCCGGCA 59.410 61.111 31.54 8.70 0.00 5.69
3151 3226 1.485294 TTGTCGTGTGGGCCAGGTAT 61.485 55.000 6.40 0.00 0.00 2.73
3163 3238 4.811206 TGGTTCCCCATTGTCGTG 57.189 55.556 0.00 0.00 35.17 4.35
3264 3339 0.673644 CACCGGGAAGTGTGATGTCC 60.674 60.000 6.32 0.00 34.37 4.02
3278 3353 0.465705 ATGGAGCTACACATCACCGG 59.534 55.000 0.00 0.00 0.00 5.28
3312 3387 2.357760 GCACTTTCGGGTACGCCA 60.358 61.111 4.09 0.00 40.69 5.69
3315 3390 3.484547 GCGGCACTTTCGGGTACG 61.485 66.667 0.00 0.00 42.74 3.67
3354 3431 0.109597 GCCTTGTCAATCGTGCCAAG 60.110 55.000 0.00 0.00 0.00 3.61
3356 3433 0.537143 AAGCCTTGTCAATCGTGCCA 60.537 50.000 0.00 0.00 0.00 4.92
3363 3440 1.589716 GCCTCGCAAGCCTTGTCAAT 61.590 55.000 6.28 0.00 37.18 2.57
3539 3623 0.593773 CAAAAACGCAGACCAACCGG 60.594 55.000 0.00 0.00 38.77 5.28
3560 3644 4.999950 AGGAACAACACTGCTATTCTCTTG 59.000 41.667 0.00 0.00 0.00 3.02
3658 3743 6.436532 ACAGAAAATCTCCATCAGAGCAAAAT 59.563 34.615 0.00 0.00 42.90 1.82
3664 3749 7.174599 ACTTTGAACAGAAAATCTCCATCAGAG 59.825 37.037 0.00 0.00 44.75 3.35
3668 3753 5.860716 GCACTTTGAACAGAAAATCTCCATC 59.139 40.000 0.00 0.00 0.00 3.51
3671 3756 5.186996 TGCACTTTGAACAGAAAATCTCC 57.813 39.130 0.00 0.00 0.00 3.71
3781 3889 3.653164 TGATAACATACCAGCCTCCAGA 58.347 45.455 0.00 0.00 0.00 3.86
3837 3953 3.187637 GCGTAACAAGTGGACAAGCATTA 59.812 43.478 0.00 0.00 0.00 1.90
3838 3954 2.031157 GCGTAACAAGTGGACAAGCATT 60.031 45.455 0.00 0.00 0.00 3.56
3839 3955 1.535462 GCGTAACAAGTGGACAAGCAT 59.465 47.619 0.00 0.00 0.00 3.79
3840 3956 0.941542 GCGTAACAAGTGGACAAGCA 59.058 50.000 0.00 0.00 0.00 3.91
3841 3957 0.941542 TGCGTAACAAGTGGACAAGC 59.058 50.000 0.00 0.00 0.00 4.01
3842 3958 2.612212 AGTTGCGTAACAAGTGGACAAG 59.388 45.455 18.75 0.00 40.53 3.16
3843 3959 2.634600 AGTTGCGTAACAAGTGGACAA 58.365 42.857 18.75 0.00 40.53 3.18
3844 3960 2.319136 AGTTGCGTAACAAGTGGACA 57.681 45.000 18.75 0.00 40.53 4.02
3861 3977 3.513515 TCAGGGCACAAAAAGAAACAAGT 59.486 39.130 0.00 0.00 0.00 3.16
3903 4019 4.755123 ACGGGAGTGCTAATATAACATTGC 59.245 41.667 0.00 0.00 44.82 3.56
3922 4038 1.671054 ACAGACGCCATGAAACGGG 60.671 57.895 0.00 0.00 0.00 5.28
3931 4047 1.783071 TATGGATACCACAGACGCCA 58.217 50.000 0.00 0.00 35.80 5.69
3978 4095 9.638239 GGCAAAGATTATACAAGACAAATCAAA 57.362 29.630 0.00 0.00 32.04 2.69
3985 4102 5.355071 CAGCAGGCAAAGATTATACAAGACA 59.645 40.000 0.00 0.00 0.00 3.41
3999 4116 1.344114 GGAAATGAACCAGCAGGCAAA 59.656 47.619 0.00 0.00 39.06 3.68
4004 4121 6.949352 ACATATTAGGAAATGAACCAGCAG 57.051 37.500 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.