Multiple sequence alignment - TraesCS2D01G150400

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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 TraesCS2D01G150400 chr2D 100.000 3844 0 0 1 3844 92922156 92918313 0.000000e+00 7099.0
1 TraesCS2D01G150400 chr2B 93.585 2307 92 26 758 3048 144434231 144431965 0.000000e+00 3389.0
2 TraesCS2D01G150400 chr2B 91.412 687 38 13 3166 3844 144431901 144431228 0.000000e+00 922.0
3 TraesCS2D01G150400 chr2B 93.258 89 5 1 3081 3168 399039179 399039267 3.120000e-26 130.0
4 TraesCS2D01G150400 chr2A 93.725 2231 103 19 698 2903 90597406 90595188 0.000000e+00 3310.0
5 TraesCS2D01G150400 chr2A 94.696 773 28 5 3079 3844 90594094 90593328 0.000000e+00 1188.0
6 TraesCS2D01G150400 chr2A 92.105 228 15 2 201 426 90598021 90597795 6.200000e-83 318.0
7 TraesCS2D01G150400 chr2A 95.429 175 5 3 2905 3078 90594405 90594233 3.780000e-70 276.0
8 TraesCS2D01G150400 chr2A 85.306 245 21 7 432 663 90597724 90597482 4.960000e-59 239.0
9 TraesCS2D01G150400 chr2A 92.308 104 8 0 100 203 90608549 90608446 8.600000e-32 148.0
10 TraesCS2D01G150400 chr2A 94.118 85 5 0 3081 3165 249493119 249493035 3.120000e-26 130.0
11 TraesCS2D01G150400 chr6B 79.666 359 61 11 1637 1989 200009040 200008688 8.250000e-62 248.0
12 TraesCS2D01G150400 chr6B 95.122 82 4 0 3082 3163 716460348 716460429 3.120000e-26 130.0
13 TraesCS2D01G150400 chr7D 72.684 637 117 46 1031 1631 593368960 593369575 3.970000e-35 159.0
14 TraesCS2D01G150400 chr1A 91.753 97 5 3 3081 3176 464775949 464775855 8.670000e-27 132.0
15 TraesCS2D01G150400 chr5A 94.118 85 5 0 3081 3165 115827443 115827527 3.120000e-26 130.0
16 TraesCS2D01G150400 chr7A 94.048 84 5 0 3082 3165 564635604 564635521 1.120000e-25 128.0
17 TraesCS2D01G150400 chr1D 94.048 84 5 0 3081 3164 155503243 155503326 1.120000e-25 128.0
18 TraesCS2D01G150400 chr3D 91.209 91 8 0 3081 3171 327741211 327741121 1.450000e-24 124.0
19 TraesCS2D01G150400 chr6A 84.524 84 11 2 2431 2514 492283683 492283602 8.850000e-12 82.4


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 TraesCS2D01G150400 chr2D 92918313 92922156 3843 True 7099.0 7099 100.0000 1 3844 1 chr2D.!!$R1 3843
1 TraesCS2D01G150400 chr2B 144431228 144434231 3003 True 2155.5 3389 92.4985 758 3844 2 chr2B.!!$R1 3086
2 TraesCS2D01G150400 chr2A 90593328 90598021 4693 True 1066.2 3310 92.2522 201 3844 5 chr2A.!!$R3 3643

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
755 876 0.179089 ATGCTGCTCGGCTAGACTTG 60.179 55.0 0.0 0.0 0.00 3.16 F
785 907 0.790814 CCGAGCTTTCTTCCACGAAC 59.209 55.0 0.0 0.0 0.00 3.95 F
2108 2262 0.320247 GCTATGGGATGACAGAGGCG 60.320 60.0 0.0 0.0 30.63 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2226 0.179018 AGCCCTGCTCAAACGAAGTT 60.179 50.0 0.00 0.00 46.24 2.66 R
2585 2739 0.390209 TAGCCGGCCGTTGTTAAGAC 60.390 55.0 26.15 3.21 0.00 3.01 R
3088 4173 0.960286 GGTAGGGTCATCGAGTAGCC 59.040 60.0 9.42 9.42 0.00 3.93 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
24 25 6.210287 AGCACTTACTACAGATGTACTTCC 57.790 41.667 5.19 0.00 0.00 3.46
25 26 5.952947 AGCACTTACTACAGATGTACTTCCT 59.047 40.000 5.19 0.00 0.00 3.36
26 27 6.095720 AGCACTTACTACAGATGTACTTCCTC 59.904 42.308 5.19 0.00 0.00 3.71
27 28 6.680872 GCACTTACTACAGATGTACTTCCTCC 60.681 46.154 5.19 0.00 0.00 4.30
28 29 6.377429 CACTTACTACAGATGTACTTCCTCCA 59.623 42.308 5.19 0.00 0.00 3.86
29 30 7.068839 CACTTACTACAGATGTACTTCCTCCAT 59.931 40.741 5.19 0.00 0.00 3.41
30 31 7.285858 ACTTACTACAGATGTACTTCCTCCATC 59.714 40.741 5.19 0.00 36.16 3.51
31 32 5.772004 ACTACAGATGTACTTCCTCCATCT 58.228 41.667 5.19 0.00 44.59 2.90
32 33 5.830991 ACTACAGATGTACTTCCTCCATCTC 59.169 44.000 5.19 0.00 42.50 2.75
33 34 4.614475 ACAGATGTACTTCCTCCATCTCA 58.386 43.478 5.19 0.00 42.50 3.27
34 35 5.215069 ACAGATGTACTTCCTCCATCTCAT 58.785 41.667 5.19 0.00 42.50 2.90
35 36 6.377080 ACAGATGTACTTCCTCCATCTCATA 58.623 40.000 5.19 0.00 42.50 2.15
36 37 7.015680 ACAGATGTACTTCCTCCATCTCATAT 58.984 38.462 5.19 0.00 42.50 1.78
37 38 7.512058 ACAGATGTACTTCCTCCATCTCATATT 59.488 37.037 5.19 0.00 42.50 1.28
38 39 8.373981 CAGATGTACTTCCTCCATCTCATATTT 58.626 37.037 5.19 0.00 42.50 1.40
39 40 9.607333 AGATGTACTTCCTCCATCTCATATTTA 57.393 33.333 5.19 0.00 40.95 1.40
42 43 9.213777 TGTACTTCCTCCATCTCATATTTAAGT 57.786 33.333 0.00 0.00 0.00 2.24
43 44 9.482627 GTACTTCCTCCATCTCATATTTAAGTG 57.517 37.037 0.00 0.00 0.00 3.16
44 45 8.095452 ACTTCCTCCATCTCATATTTAAGTGT 57.905 34.615 0.00 0.00 0.00 3.55
45 46 8.207545 ACTTCCTCCATCTCATATTTAAGTGTC 58.792 37.037 0.00 0.00 0.00 3.67
46 47 7.675161 TCCTCCATCTCATATTTAAGTGTCA 57.325 36.000 0.00 0.00 0.00 3.58
47 48 8.267620 TCCTCCATCTCATATTTAAGTGTCAT 57.732 34.615 0.00 0.00 0.00 3.06
48 49 8.717717 TCCTCCATCTCATATTTAAGTGTCATT 58.282 33.333 0.00 0.00 0.00 2.57
49 50 8.997323 CCTCCATCTCATATTTAAGTGTCATTC 58.003 37.037 0.00 0.00 0.00 2.67
50 51 9.551734 CTCCATCTCATATTTAAGTGTCATTCA 57.448 33.333 0.00 0.00 0.00 2.57
51 52 9.904198 TCCATCTCATATTTAAGTGTCATTCAA 57.096 29.630 0.00 0.00 0.00 2.69
55 56 8.664798 TCTCATATTTAAGTGTCATTCAAACGG 58.335 33.333 0.00 0.00 0.00 4.44
56 57 8.554835 TCATATTTAAGTGTCATTCAAACGGA 57.445 30.769 0.00 0.00 0.00 4.69
57 58 9.173021 TCATATTTAAGTGTCATTCAAACGGAT 57.827 29.630 0.00 0.00 0.00 4.18
58 59 9.225201 CATATTTAAGTGTCATTCAAACGGATG 57.775 33.333 0.00 0.00 0.00 3.51
59 60 6.627395 TTTAAGTGTCATTCAAACGGATGT 57.373 33.333 0.00 0.00 0.00 3.06
60 61 7.731882 TTTAAGTGTCATTCAAACGGATGTA 57.268 32.000 0.00 0.00 0.00 2.29
61 62 7.915293 TTAAGTGTCATTCAAACGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
62 63 6.817765 AAGTGTCATTCAAACGGATGTATT 57.182 33.333 0.00 0.00 0.00 1.89
63 64 6.817765 AGTGTCATTCAAACGGATGTATTT 57.182 33.333 0.00 0.00 0.00 1.40
64 65 6.842163 AGTGTCATTCAAACGGATGTATTTC 58.158 36.000 0.00 0.00 0.00 2.17
65 66 5.732647 GTGTCATTCAAACGGATGTATTTCG 59.267 40.000 0.00 0.00 0.00 3.46
66 67 5.410132 TGTCATTCAAACGGATGTATTTCGT 59.590 36.000 0.00 0.00 38.89 3.85
67 68 6.072948 TGTCATTCAAACGGATGTATTTCGTT 60.073 34.615 0.00 0.00 47.00 3.85
68 69 6.248420 GTCATTCAAACGGATGTATTTCGTTG 59.752 38.462 0.00 0.00 44.75 4.10
69 70 5.676532 TTCAAACGGATGTATTTCGTTGT 57.323 34.783 0.00 0.00 44.75 3.32
70 71 6.782298 TTCAAACGGATGTATTTCGTTGTA 57.218 33.333 0.00 0.00 44.75 2.41
71 72 6.971527 TCAAACGGATGTATTTCGTTGTAT 57.028 33.333 0.00 0.00 44.75 2.29
72 73 8.476657 TTCAAACGGATGTATTTCGTTGTATA 57.523 30.769 0.00 0.00 44.75 1.47
73 74 8.122306 TCAAACGGATGTATTTCGTTGTATAG 57.878 34.615 0.00 0.00 44.75 1.31
74 75 7.975058 TCAAACGGATGTATTTCGTTGTATAGA 59.025 33.333 0.00 0.00 44.75 1.98
75 76 8.761497 CAAACGGATGTATTTCGTTGTATAGAT 58.239 33.333 0.00 0.00 44.75 1.98
76 77 7.869016 ACGGATGTATTTCGTTGTATAGATG 57.131 36.000 0.00 0.00 32.95 2.90
77 78 6.365247 ACGGATGTATTTCGTTGTATAGATGC 59.635 38.462 0.00 0.00 32.95 3.91
78 79 6.586463 CGGATGTATTTCGTTGTATAGATGCT 59.414 38.462 0.00 0.00 0.00 3.79
79 80 7.116376 CGGATGTATTTCGTTGTATAGATGCTT 59.884 37.037 0.00 0.00 0.00 3.91
80 81 9.419297 GGATGTATTTCGTTGTATAGATGCTTA 57.581 33.333 0.00 0.00 0.00 3.09
88 89 9.594478 TTCGTTGTATAGATGCTTAATTCAAGA 57.406 29.630 0.00 0.00 36.22 3.02
89 90 9.249457 TCGTTGTATAGATGCTTAATTCAAGAG 57.751 33.333 0.00 0.00 36.22 2.85
90 91 9.249457 CGTTGTATAGATGCTTAATTCAAGAGA 57.751 33.333 0.00 0.00 36.22 3.10
97 98 8.401490 AGATGCTTAATTCAAGAGAAAACAGT 57.599 30.769 0.00 0.00 37.29 3.55
98 99 8.295288 AGATGCTTAATTCAAGAGAAAACAGTG 58.705 33.333 0.00 0.00 37.29 3.66
99 100 7.566760 TGCTTAATTCAAGAGAAAACAGTGA 57.433 32.000 0.00 0.00 37.29 3.41
100 101 7.642669 TGCTTAATTCAAGAGAAAACAGTGAG 58.357 34.615 0.00 0.00 37.29 3.51
101 102 7.283127 TGCTTAATTCAAGAGAAAACAGTGAGT 59.717 33.333 0.00 0.00 37.29 3.41
102 103 8.131731 GCTTAATTCAAGAGAAAACAGTGAGTT 58.868 33.333 0.00 0.00 38.12 3.01
111 112 2.959507 AACAGTGAGTTTGTTTGGGC 57.040 45.000 0.00 0.00 37.03 5.36
112 113 0.738389 ACAGTGAGTTTGTTTGGGCG 59.262 50.000 0.00 0.00 0.00 6.13
113 114 1.021202 CAGTGAGTTTGTTTGGGCGA 58.979 50.000 0.00 0.00 0.00 5.54
114 115 1.403679 CAGTGAGTTTGTTTGGGCGAA 59.596 47.619 0.00 0.00 0.00 4.70
115 116 1.676006 AGTGAGTTTGTTTGGGCGAAG 59.324 47.619 0.00 0.00 0.00 3.79
135 136 3.307379 GATTGTATCGAGGGGGCAC 57.693 57.895 0.00 0.00 0.00 5.01
136 137 0.468226 GATTGTATCGAGGGGGCACA 59.532 55.000 0.00 0.00 0.00 4.57
137 138 0.916086 ATTGTATCGAGGGGGCACAA 59.084 50.000 0.00 0.00 33.96 3.33
138 139 0.693622 TTGTATCGAGGGGGCACAAA 59.306 50.000 0.00 0.00 0.00 2.83
139 140 0.251916 TGTATCGAGGGGGCACAAAG 59.748 55.000 0.00 0.00 0.00 2.77
140 141 1.095807 GTATCGAGGGGGCACAAAGC 61.096 60.000 0.00 0.00 44.65 3.51
141 142 1.271840 TATCGAGGGGGCACAAAGCT 61.272 55.000 0.00 0.00 44.79 3.74
142 143 1.271840 ATCGAGGGGGCACAAAGCTA 61.272 55.000 0.00 0.00 44.79 3.32
143 144 1.224592 CGAGGGGGCACAAAGCTAT 59.775 57.895 0.00 0.00 44.79 2.97
144 145 0.468226 CGAGGGGGCACAAAGCTATA 59.532 55.000 0.00 0.00 44.79 1.31
145 146 1.134220 CGAGGGGGCACAAAGCTATAA 60.134 52.381 0.00 0.00 44.79 0.98
146 147 2.487265 CGAGGGGGCACAAAGCTATAAT 60.487 50.000 0.00 0.00 44.79 1.28
147 148 2.887152 GAGGGGGCACAAAGCTATAATG 59.113 50.000 0.00 0.00 44.79 1.90
148 149 2.513738 AGGGGGCACAAAGCTATAATGA 59.486 45.455 0.00 0.00 44.79 2.57
149 150 3.140895 AGGGGGCACAAAGCTATAATGAT 59.859 43.478 0.00 0.00 44.79 2.45
150 151 3.256631 GGGGGCACAAAGCTATAATGATG 59.743 47.826 0.00 0.00 44.79 3.07
151 152 3.891366 GGGGCACAAAGCTATAATGATGT 59.109 43.478 0.00 0.00 44.79 3.06
152 153 4.342092 GGGGCACAAAGCTATAATGATGTT 59.658 41.667 0.00 0.00 44.79 2.71
153 154 5.534654 GGGGCACAAAGCTATAATGATGTTA 59.465 40.000 0.00 0.00 44.79 2.41
154 155 6.040391 GGGGCACAAAGCTATAATGATGTTAA 59.960 38.462 0.00 0.00 44.79 2.01
155 156 7.255942 GGGGCACAAAGCTATAATGATGTTAAT 60.256 37.037 0.00 0.00 44.79 1.40
156 157 8.143835 GGGCACAAAGCTATAATGATGTTAATT 58.856 33.333 0.00 0.00 44.79 1.40
157 158 8.971321 GGCACAAAGCTATAATGATGTTAATTG 58.029 33.333 0.00 0.00 44.79 2.32
158 159 9.734620 GCACAAAGCTATAATGATGTTAATTGA 57.265 29.630 0.00 0.00 41.15 2.57
182 183 9.277783 TGACTAGAAAGAAGAGAAAGAAATTGG 57.722 33.333 0.00 0.00 0.00 3.16
183 184 8.105097 ACTAGAAAGAAGAGAAAGAAATTGGC 57.895 34.615 0.00 0.00 0.00 4.52
184 185 7.941790 ACTAGAAAGAAGAGAAAGAAATTGGCT 59.058 33.333 0.00 0.00 0.00 4.75
185 186 7.213216 AGAAAGAAGAGAAAGAAATTGGCTC 57.787 36.000 0.00 0.00 0.00 4.70
186 187 7.003482 AGAAAGAAGAGAAAGAAATTGGCTCT 58.997 34.615 0.00 0.00 37.53 4.09
187 188 7.505248 AGAAAGAAGAGAAAGAAATTGGCTCTT 59.495 33.333 0.00 0.00 45.61 2.85
188 189 8.697507 AAAGAAGAGAAAGAAATTGGCTCTTA 57.302 30.769 0.00 0.00 43.68 2.10
189 190 7.680442 AGAAGAGAAAGAAATTGGCTCTTAC 57.320 36.000 0.00 0.00 43.68 2.34
190 191 7.227156 AGAAGAGAAAGAAATTGGCTCTTACA 58.773 34.615 0.00 0.00 43.68 2.41
191 192 6.809630 AGAGAAAGAAATTGGCTCTTACAC 57.190 37.500 0.00 0.00 32.35 2.90
192 193 5.409826 AGAGAAAGAAATTGGCTCTTACACG 59.590 40.000 0.00 0.00 32.35 4.49
193 194 4.455877 AGAAAGAAATTGGCTCTTACACGG 59.544 41.667 0.00 0.00 32.77 4.94
194 195 3.695830 AGAAATTGGCTCTTACACGGA 57.304 42.857 0.00 0.00 0.00 4.69
195 196 3.335579 AGAAATTGGCTCTTACACGGAC 58.664 45.455 0.00 0.00 0.00 4.79
196 197 2.851263 AATTGGCTCTTACACGGACA 57.149 45.000 0.00 0.00 0.00 4.02
197 198 2.386661 ATTGGCTCTTACACGGACAG 57.613 50.000 0.00 0.00 0.00 3.51
198 199 1.045407 TTGGCTCTTACACGGACAGT 58.955 50.000 0.00 0.00 0.00 3.55
214 215 0.884514 CAGTGAGACTCGAAGCTCCA 59.115 55.000 10.62 0.00 0.00 3.86
215 216 1.270826 CAGTGAGACTCGAAGCTCCAA 59.729 52.381 10.62 0.00 0.00 3.53
230 231 3.391296 AGCTCCAACCTTTAGTGAGTTCA 59.609 43.478 0.00 0.00 0.00 3.18
263 264 6.664515 TGTTTCTGTAGCTGTAATTTTTCCG 58.335 36.000 0.00 0.00 0.00 4.30
306 309 3.702548 ATGTATGGCACATGCATTGACTT 59.297 39.130 13.55 10.57 46.41 3.01
309 312 6.041182 ATGTATGGCACATGCATTGACTTTAT 59.959 34.615 13.55 4.62 46.41 1.40
336 339 8.832487 TGTCGTCGTAGAATTTAAGAACTATC 57.168 34.615 0.00 0.00 39.69 2.08
338 341 9.282247 GTCGTCGTAGAATTTAAGAACTATCAA 57.718 33.333 0.00 0.00 39.69 2.57
363 366 1.614903 CTCTTTCTTTGCACATGCCCA 59.385 47.619 0.49 0.00 41.18 5.36
372 375 1.477700 TGCACATGCCCAGAAAATAGC 59.522 47.619 0.49 0.00 41.18 2.97
455 522 1.612442 GGGGGTAGTGCTCACTCCA 60.612 63.158 5.72 0.00 42.54 3.86
456 523 0.983378 GGGGGTAGTGCTCACTCCAT 60.983 60.000 5.72 0.00 42.54 3.41
457 524 0.912486 GGGGTAGTGCTCACTCCATT 59.088 55.000 5.72 0.00 42.54 3.16
484 551 4.819630 TGTTTACTCCGCATATTGGATTCC 59.180 41.667 0.00 0.00 34.32 3.01
490 564 4.728772 TCCGCATATTGGATTCCTCAAAT 58.271 39.130 3.95 0.00 0.00 2.32
642 722 1.552792 GGCTCCAGACAAAGCTAGTCT 59.447 52.381 14.20 14.20 46.72 3.24
654 734 4.576330 AAGCTAGTCTGGGCAGTAAATT 57.424 40.909 0.00 0.00 0.00 1.82
663 743 8.366359 AGTCTGGGCAGTAAATTAAAATGAAT 57.634 30.769 0.00 0.00 0.00 2.57
665 745 8.250332 GTCTGGGCAGTAAATTAAAATGAATGA 58.750 33.333 0.00 0.00 0.00 2.57
667 747 9.090692 CTGGGCAGTAAATTAAAATGAATGAAG 57.909 33.333 0.00 0.00 0.00 3.02
668 748 8.040132 TGGGCAGTAAATTAAAATGAATGAAGG 58.960 33.333 0.00 0.00 0.00 3.46
670 750 9.305925 GGCAGTAAATTAAAATGAATGAAGGAG 57.694 33.333 0.00 0.00 0.00 3.69
671 751 9.860898 GCAGTAAATTAAAATGAATGAAGGAGT 57.139 29.630 0.00 0.00 0.00 3.85
695 775 9.627395 AGTATATTTTATCATACAGTCAGACGC 57.373 33.333 0.00 0.00 31.33 5.19
696 776 9.627395 GTATATTTTATCATACAGTCAGACGCT 57.373 33.333 0.00 0.00 0.00 5.07
734 855 1.069022 GCACGTGTGAAATGCATGTCT 60.069 47.619 17.76 0.00 39.23 3.41
752 873 1.338337 TCTTATGCTGCTCGGCTAGAC 59.662 52.381 0.00 0.00 0.00 2.59
755 876 0.179089 ATGCTGCTCGGCTAGACTTG 60.179 55.000 0.00 0.00 0.00 3.16
785 907 0.790814 CCGAGCTTTCTTCCACGAAC 59.209 55.000 0.00 0.00 0.00 3.95
883 1011 5.711036 CCTCCGCTATCTATAAGTACCACTT 59.289 44.000 0.00 0.00 41.97 3.16
966 1111 1.915141 CTCCACCAACCAATTCAGCT 58.085 50.000 0.00 0.00 0.00 4.24
967 1112 1.815003 CTCCACCAACCAATTCAGCTC 59.185 52.381 0.00 0.00 0.00 4.09
968 1113 1.144708 TCCACCAACCAATTCAGCTCA 59.855 47.619 0.00 0.00 0.00 4.26
981 1126 1.089920 CAGCTCAAAACGATCCAGGG 58.910 55.000 0.00 0.00 0.00 4.45
1104 1256 1.136984 CTACGTCTTCGAGCGCCTT 59.863 57.895 2.29 0.00 40.62 4.35
1656 1808 2.983592 GGCGACAACCCCAACCTG 60.984 66.667 0.00 0.00 0.00 4.00
1785 1937 3.000080 GAAGCGCTTCGACACGGTG 62.000 63.158 32.36 6.58 40.32 4.94
1971 2123 3.365265 CACGCCAAGCTCCCCAAC 61.365 66.667 0.00 0.00 0.00 3.77
1994 2146 1.533338 CGTGCTCGGACAGGTACATAC 60.533 57.143 0.00 0.00 0.00 2.39
2033 2185 2.560981 TCGTGCTTTGACCATGACTAGA 59.439 45.455 0.00 0.00 0.00 2.43
2035 2187 2.668457 GTGCTTTGACCATGACTAGACG 59.332 50.000 0.00 0.00 0.00 4.18
2037 2189 2.924290 GCTTTGACCATGACTAGACGAC 59.076 50.000 0.00 0.00 0.00 4.34
2038 2190 2.913777 TTGACCATGACTAGACGACG 57.086 50.000 0.00 0.00 0.00 5.12
2039 2191 2.103537 TGACCATGACTAGACGACGA 57.896 50.000 0.00 0.00 0.00 4.20
2040 2192 1.736126 TGACCATGACTAGACGACGAC 59.264 52.381 0.00 0.00 0.00 4.34
2041 2193 1.063764 GACCATGACTAGACGACGACC 59.936 57.143 0.00 0.00 0.00 4.79
2042 2194 1.092348 CCATGACTAGACGACGACCA 58.908 55.000 0.00 0.00 0.00 4.02
2043 2195 1.676529 CCATGACTAGACGACGACCAT 59.323 52.381 0.00 0.00 0.00 3.55
2044 2196 2.541794 CCATGACTAGACGACGACCATG 60.542 54.545 0.00 4.70 0.00 3.66
2072 2226 8.511321 CATGCCAGTTAAACTTATCTGTTTGTA 58.489 33.333 0.00 0.00 40.00 2.41
2074 2228 8.347035 TGCCAGTTAAACTTATCTGTTTGTAAC 58.653 33.333 0.00 0.00 40.00 2.50
2108 2262 0.320247 GCTATGGGATGACAGAGGCG 60.320 60.000 0.00 0.00 30.63 5.52
2305 2459 2.125793 GTACCTCGACAACCCGGC 60.126 66.667 0.00 0.00 0.00 6.13
2306 2460 3.384532 TACCTCGACAACCCGGCC 61.385 66.667 0.00 0.00 0.00 6.13
2438 2592 3.590574 AAGGGGTTCCAGGTGGCC 61.591 66.667 0.00 0.00 34.83 5.36
2585 2739 8.496751 CATTGAGCTGTAAGAGTTATGATGATG 58.503 37.037 0.00 0.00 34.07 3.07
2604 2758 0.390209 GTCTTAACAACGGCCGGCTA 60.390 55.000 31.76 11.80 0.00 3.93
2605 2759 0.538118 TCTTAACAACGGCCGGCTAT 59.462 50.000 31.76 15.38 0.00 2.97
2606 2760 0.935196 CTTAACAACGGCCGGCTATC 59.065 55.000 31.76 9.02 0.00 2.08
2607 2761 0.538118 TTAACAACGGCCGGCTATCT 59.462 50.000 31.76 10.97 0.00 1.98
2608 2762 0.538118 TAACAACGGCCGGCTATCTT 59.462 50.000 31.76 10.75 0.00 2.40
2609 2763 1.024579 AACAACGGCCGGCTATCTTG 61.025 55.000 31.76 24.39 0.00 3.02
2714 2868 2.292016 CGAGGACGAGATCAAGCAGTAT 59.708 50.000 0.00 0.00 42.66 2.12
2822 2976 1.677552 GAAGGACCTGAGGGCGAAA 59.322 57.895 2.38 0.00 35.63 3.46
2846 3000 2.969238 GCCGGATCGTGCTGATGG 60.969 66.667 5.05 0.00 37.47 3.51
2865 3020 5.476254 TGATGGTGCTTGATTATTTGTGTGA 59.524 36.000 0.00 0.00 0.00 3.58
2886 3043 6.209986 TGTGAGAAATATATACCCGGTTCGAT 59.790 38.462 0.00 0.00 0.00 3.59
2942 3881 2.533916 AGAGAGTGTGAGCAAGGATCA 58.466 47.619 0.00 0.00 0.00 2.92
2963 3902 0.321475 TCAGTCGCCAATGTGCATGA 60.321 50.000 0.00 0.00 0.00 3.07
3088 4173 7.372451 TGGAAGTACCATTGAAAGTTTATCG 57.628 36.000 0.00 0.00 44.64 2.92
3097 4182 4.707030 TGAAAGTTTATCGGCTACTCGA 57.293 40.909 0.00 0.00 43.61 4.04
3107 4192 0.960286 GGCTACTCGATGACCCTACC 59.040 60.000 0.00 0.00 0.00 3.18
3109 4194 2.029623 GCTACTCGATGACCCTACCAA 58.970 52.381 0.00 0.00 0.00 3.67
3133 4218 3.054361 AGGGATGAATCGGCAAGTTAACT 60.054 43.478 1.12 1.12 0.00 2.24
3134 4219 4.163458 AGGGATGAATCGGCAAGTTAACTA 59.837 41.667 8.92 0.00 0.00 2.24
3249 4337 2.891191 AAAATCCCTAGTTTCCCGCA 57.109 45.000 0.00 0.00 0.00 5.69
3286 4374 7.524717 AGTTAAAATTGTACCATCTGCAACT 57.475 32.000 0.00 0.00 0.00 3.16
3290 4378 2.093306 TGTACCATCTGCAACTTCGG 57.907 50.000 0.00 0.00 0.00 4.30
3291 4379 1.346395 TGTACCATCTGCAACTTCGGT 59.654 47.619 0.00 0.00 0.00 4.69
3292 4380 2.563620 TGTACCATCTGCAACTTCGGTA 59.436 45.455 0.00 0.00 0.00 4.02
3293 4381 3.196901 TGTACCATCTGCAACTTCGGTAT 59.803 43.478 0.00 0.00 32.01 2.73
3294 4382 3.350219 ACCATCTGCAACTTCGGTATT 57.650 42.857 0.00 0.00 0.00 1.89
3499 4597 5.532779 AGAAGATGAGAACCACAAAGGAAAC 59.467 40.000 0.00 0.00 41.22 2.78
3568 4666 9.305925 GAATAAAAACCAAATCTTCTAGGCATG 57.694 33.333 0.00 0.00 0.00 4.06
3664 4762 2.242043 CCTGGCCAAACAGAACAATCT 58.758 47.619 7.01 0.00 40.97 2.40
3696 4795 4.382040 CGCAGGAAGAAAGATGGTAGAGAA 60.382 45.833 0.00 0.00 0.00 2.87
3717 4819 6.871844 AGAAGTTATTACGAAGTAGGTTCCC 58.128 40.000 0.00 0.00 46.93 3.97
3755 4857 2.484889 ACAAGTTTCTCGTGAGCTTCC 58.515 47.619 0.00 0.00 0.00 3.46
3776 4878 3.247173 CCTCGAATGTCTTGCAGAATAGC 59.753 47.826 0.00 0.00 0.00 2.97
3804 4906 0.249868 TGTTGCTCCAACCTGAGACG 60.250 55.000 5.72 0.00 42.96 4.18
3814 4916 3.623060 CCAACCTGAGACGGTGAATAATG 59.377 47.826 0.00 0.00 37.36 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.117397 AGGAAGTACATCTGTAGTAAGTGCTA 58.883 38.462 0.00 0.00 33.33 3.49
1 2 5.952947 AGGAAGTACATCTGTAGTAAGTGCT 59.047 40.000 0.00 0.00 33.33 4.40
2 3 6.210287 AGGAAGTACATCTGTAGTAAGTGC 57.790 41.667 0.00 0.00 33.33 4.40
3 4 6.377429 TGGAGGAAGTACATCTGTAGTAAGTG 59.623 42.308 0.00 0.00 33.33 3.16
4 5 6.491383 TGGAGGAAGTACATCTGTAGTAAGT 58.509 40.000 0.00 0.00 33.33 2.24
5 6 7.504238 AGATGGAGGAAGTACATCTGTAGTAAG 59.496 40.741 5.68 0.00 46.85 2.34
6 7 7.355101 AGATGGAGGAAGTACATCTGTAGTAA 58.645 38.462 5.68 0.00 46.85 2.24
7 8 6.912426 AGATGGAGGAAGTACATCTGTAGTA 58.088 40.000 5.68 0.00 46.85 1.82
8 9 5.772004 AGATGGAGGAAGTACATCTGTAGT 58.228 41.667 5.68 0.00 46.85 2.73
16 17 9.213777 ACTTAAATATGAGATGGAGGAAGTACA 57.786 33.333 0.00 0.00 0.00 2.90
17 18 9.482627 CACTTAAATATGAGATGGAGGAAGTAC 57.517 37.037 0.00 0.00 0.00 2.73
18 19 9.213777 ACACTTAAATATGAGATGGAGGAAGTA 57.786 33.333 0.00 0.00 0.00 2.24
19 20 8.095452 ACACTTAAATATGAGATGGAGGAAGT 57.905 34.615 0.00 0.00 0.00 3.01
20 21 8.206867 TGACACTTAAATATGAGATGGAGGAAG 58.793 37.037 0.00 0.00 0.00 3.46
21 22 8.089625 TGACACTTAAATATGAGATGGAGGAA 57.910 34.615 0.00 0.00 0.00 3.36
22 23 7.675161 TGACACTTAAATATGAGATGGAGGA 57.325 36.000 0.00 0.00 0.00 3.71
23 24 8.915057 AATGACACTTAAATATGAGATGGAGG 57.085 34.615 0.00 0.00 0.00 4.30
24 25 9.551734 TGAATGACACTTAAATATGAGATGGAG 57.448 33.333 0.00 0.00 0.00 3.86
25 26 9.904198 TTGAATGACACTTAAATATGAGATGGA 57.096 29.630 0.00 0.00 0.00 3.41
29 30 8.664798 CCGTTTGAATGACACTTAAATATGAGA 58.335 33.333 0.00 0.00 0.00 3.27
30 31 8.664798 TCCGTTTGAATGACACTTAAATATGAG 58.335 33.333 0.00 0.00 0.00 2.90
31 32 8.554835 TCCGTTTGAATGACACTTAAATATGA 57.445 30.769 0.00 0.00 0.00 2.15
32 33 9.225201 CATCCGTTTGAATGACACTTAAATATG 57.775 33.333 0.00 0.00 0.00 1.78
33 34 8.956426 ACATCCGTTTGAATGACACTTAAATAT 58.044 29.630 0.00 0.00 0.00 1.28
34 35 8.330466 ACATCCGTTTGAATGACACTTAAATA 57.670 30.769 0.00 0.00 0.00 1.40
35 36 7.214467 ACATCCGTTTGAATGACACTTAAAT 57.786 32.000 0.00 0.00 0.00 1.40
36 37 6.627395 ACATCCGTTTGAATGACACTTAAA 57.373 33.333 0.00 0.00 0.00 1.52
37 38 7.915293 ATACATCCGTTTGAATGACACTTAA 57.085 32.000 0.00 0.00 0.00 1.85
38 39 7.915293 AATACATCCGTTTGAATGACACTTA 57.085 32.000 0.00 0.00 0.00 2.24
39 40 6.817765 AATACATCCGTTTGAATGACACTT 57.182 33.333 0.00 0.00 0.00 3.16
40 41 6.402118 CGAAATACATCCGTTTGAATGACACT 60.402 38.462 0.00 0.00 0.00 3.55
41 42 5.732647 CGAAATACATCCGTTTGAATGACAC 59.267 40.000 0.00 0.00 0.00 3.67
42 43 5.410132 ACGAAATACATCCGTTTGAATGACA 59.590 36.000 0.00 0.00 32.03 3.58
43 44 5.864986 ACGAAATACATCCGTTTGAATGAC 58.135 37.500 0.00 0.00 32.03 3.06
44 45 6.072948 ACAACGAAATACATCCGTTTGAATGA 60.073 34.615 0.00 0.00 43.51 2.57
45 46 6.083630 ACAACGAAATACATCCGTTTGAATG 58.916 36.000 0.00 0.00 43.51 2.67
46 47 6.249035 ACAACGAAATACATCCGTTTGAAT 57.751 33.333 0.00 0.00 43.51 2.57
47 48 5.676532 ACAACGAAATACATCCGTTTGAA 57.323 34.783 0.00 0.00 43.51 2.69
48 49 6.971527 ATACAACGAAATACATCCGTTTGA 57.028 33.333 0.00 0.00 43.51 2.69
49 50 8.122306 TCTATACAACGAAATACATCCGTTTG 57.878 34.615 0.00 0.00 43.51 2.93
50 51 8.761497 CATCTATACAACGAAATACATCCGTTT 58.239 33.333 0.00 0.00 43.51 3.60
51 52 7.095774 GCATCTATACAACGAAATACATCCGTT 60.096 37.037 0.00 0.00 45.82 4.44
52 53 6.365247 GCATCTATACAACGAAATACATCCGT 59.635 38.462 0.00 0.00 38.24 4.69
53 54 6.586463 AGCATCTATACAACGAAATACATCCG 59.414 38.462 0.00 0.00 0.00 4.18
54 55 7.891183 AGCATCTATACAACGAAATACATCC 57.109 36.000 0.00 0.00 0.00 3.51
62 63 9.594478 TCTTGAATTAAGCATCTATACAACGAA 57.406 29.630 0.00 0.00 36.31 3.85
63 64 9.249457 CTCTTGAATTAAGCATCTATACAACGA 57.751 33.333 0.00 0.00 36.31 3.85
64 65 9.249457 TCTCTTGAATTAAGCATCTATACAACG 57.751 33.333 0.00 0.00 36.31 4.10
71 72 9.507329 ACTGTTTTCTCTTGAATTAAGCATCTA 57.493 29.630 0.00 0.00 36.31 1.98
72 73 8.295288 CACTGTTTTCTCTTGAATTAAGCATCT 58.705 33.333 0.00 0.00 36.31 2.90
73 74 8.292448 TCACTGTTTTCTCTTGAATTAAGCATC 58.708 33.333 0.00 0.00 36.31 3.91
74 75 8.169977 TCACTGTTTTCTCTTGAATTAAGCAT 57.830 30.769 0.00 0.00 36.31 3.79
75 76 7.283127 ACTCACTGTTTTCTCTTGAATTAAGCA 59.717 33.333 0.00 0.00 36.31 3.91
76 77 7.643579 ACTCACTGTTTTCTCTTGAATTAAGC 58.356 34.615 0.00 0.00 36.31 3.09
78 79 9.787532 CAAACTCACTGTTTTCTCTTGAATTAA 57.212 29.630 0.00 0.00 45.69 1.40
79 80 8.956426 ACAAACTCACTGTTTTCTCTTGAATTA 58.044 29.630 0.00 0.00 45.69 1.40
80 81 7.830739 ACAAACTCACTGTTTTCTCTTGAATT 58.169 30.769 0.00 0.00 45.69 2.17
81 82 7.396540 ACAAACTCACTGTTTTCTCTTGAAT 57.603 32.000 0.00 0.00 45.69 2.57
82 83 6.817765 ACAAACTCACTGTTTTCTCTTGAA 57.182 33.333 0.00 0.00 45.69 2.69
83 84 6.817765 AACAAACTCACTGTTTTCTCTTGA 57.182 33.333 0.00 0.00 45.69 3.02
84 85 6.308766 CCAAACAAACTCACTGTTTTCTCTTG 59.691 38.462 0.00 0.00 45.69 3.02
85 86 6.389906 CCAAACAAACTCACTGTTTTCTCTT 58.610 36.000 0.00 0.00 45.69 2.85
86 87 5.105756 CCCAAACAAACTCACTGTTTTCTCT 60.106 40.000 0.00 0.00 45.69 3.10
87 88 5.102313 CCCAAACAAACTCACTGTTTTCTC 58.898 41.667 0.00 0.00 45.69 2.87
88 89 4.620567 GCCCAAACAAACTCACTGTTTTCT 60.621 41.667 0.00 0.00 45.69 2.52
89 90 3.616821 GCCCAAACAAACTCACTGTTTTC 59.383 43.478 0.00 0.00 45.69 2.29
90 91 3.595173 GCCCAAACAAACTCACTGTTTT 58.405 40.909 0.00 0.00 45.69 2.43
92 93 1.134175 CGCCCAAACAAACTCACTGTT 59.866 47.619 0.00 0.00 41.29 3.16
93 94 0.738389 CGCCCAAACAAACTCACTGT 59.262 50.000 0.00 0.00 0.00 3.55
94 95 1.021202 TCGCCCAAACAAACTCACTG 58.979 50.000 0.00 0.00 0.00 3.66
95 96 1.676006 CTTCGCCCAAACAAACTCACT 59.324 47.619 0.00 0.00 0.00 3.41
96 97 1.864029 GCTTCGCCCAAACAAACTCAC 60.864 52.381 0.00 0.00 0.00 3.51
97 98 0.383949 GCTTCGCCCAAACAAACTCA 59.616 50.000 0.00 0.00 0.00 3.41
98 99 0.660300 CGCTTCGCCCAAACAAACTC 60.660 55.000 0.00 0.00 0.00 3.01
99 100 1.098712 TCGCTTCGCCCAAACAAACT 61.099 50.000 0.00 0.00 0.00 2.66
100 101 0.039527 ATCGCTTCGCCCAAACAAAC 60.040 50.000 0.00 0.00 0.00 2.93
101 102 0.671251 AATCGCTTCGCCCAAACAAA 59.329 45.000 0.00 0.00 0.00 2.83
102 103 0.039617 CAATCGCTTCGCCCAAACAA 60.040 50.000 0.00 0.00 0.00 2.83
103 104 1.169661 ACAATCGCTTCGCCCAAACA 61.170 50.000 0.00 0.00 0.00 2.83
104 105 0.800012 TACAATCGCTTCGCCCAAAC 59.200 50.000 0.00 0.00 0.00 2.93
105 106 1.668751 GATACAATCGCTTCGCCCAAA 59.331 47.619 0.00 0.00 0.00 3.28
106 107 1.295792 GATACAATCGCTTCGCCCAA 58.704 50.000 0.00 0.00 0.00 4.12
107 108 0.874175 CGATACAATCGCTTCGCCCA 60.874 55.000 0.00 0.00 46.55 5.36
108 109 1.853319 CGATACAATCGCTTCGCCC 59.147 57.895 0.00 0.00 46.55 6.13
117 118 0.468226 TGTGCCCCCTCGATACAATC 59.532 55.000 0.00 0.00 0.00 2.67
118 119 0.916086 TTGTGCCCCCTCGATACAAT 59.084 50.000 0.00 0.00 0.00 2.71
119 120 0.693622 TTTGTGCCCCCTCGATACAA 59.306 50.000 0.00 0.00 0.00 2.41
120 121 0.251916 CTTTGTGCCCCCTCGATACA 59.748 55.000 0.00 0.00 0.00 2.29
121 122 1.095807 GCTTTGTGCCCCCTCGATAC 61.096 60.000 0.00 0.00 35.15 2.24
122 123 1.223487 GCTTTGTGCCCCCTCGATA 59.777 57.895 0.00 0.00 35.15 2.92
123 124 1.271840 TAGCTTTGTGCCCCCTCGAT 61.272 55.000 0.00 0.00 44.23 3.59
124 125 1.271840 ATAGCTTTGTGCCCCCTCGA 61.272 55.000 0.00 0.00 44.23 4.04
125 126 0.468226 TATAGCTTTGTGCCCCCTCG 59.532 55.000 0.00 0.00 44.23 4.63
126 127 2.729028 TTATAGCTTTGTGCCCCCTC 57.271 50.000 0.00 0.00 44.23 4.30
127 128 2.513738 TCATTATAGCTTTGTGCCCCCT 59.486 45.455 0.00 0.00 44.23 4.79
128 129 2.944129 TCATTATAGCTTTGTGCCCCC 58.056 47.619 0.00 0.00 44.23 5.40
129 130 3.891366 ACATCATTATAGCTTTGTGCCCC 59.109 43.478 0.00 0.00 44.23 5.80
130 131 5.520376 AACATCATTATAGCTTTGTGCCC 57.480 39.130 0.00 0.00 44.23 5.36
131 132 8.971321 CAATTAACATCATTATAGCTTTGTGCC 58.029 33.333 0.00 0.00 44.23 5.01
132 133 9.734620 TCAATTAACATCATTATAGCTTTGTGC 57.265 29.630 0.00 0.00 43.29 4.57
156 157 9.277783 CCAATTTCTTTCTCTTCTTTCTAGTCA 57.722 33.333 0.00 0.00 0.00 3.41
157 158 8.233868 GCCAATTTCTTTCTCTTCTTTCTAGTC 58.766 37.037 0.00 0.00 0.00 2.59
158 159 7.941790 AGCCAATTTCTTTCTCTTCTTTCTAGT 59.058 33.333 0.00 0.00 0.00 2.57
159 160 8.334263 AGCCAATTTCTTTCTCTTCTTTCTAG 57.666 34.615 0.00 0.00 0.00 2.43
160 161 8.160106 AGAGCCAATTTCTTTCTCTTCTTTCTA 58.840 33.333 0.00 0.00 30.63 2.10
161 162 7.003482 AGAGCCAATTTCTTTCTCTTCTTTCT 58.997 34.615 0.00 0.00 30.63 2.52
162 163 7.213216 AGAGCCAATTTCTTTCTCTTCTTTC 57.787 36.000 0.00 0.00 30.63 2.62
163 164 7.594351 AAGAGCCAATTTCTTTCTCTTCTTT 57.406 32.000 0.00 0.00 39.18 2.52
164 165 7.721399 TGTAAGAGCCAATTTCTTTCTCTTCTT 59.279 33.333 6.13 0.00 41.56 2.52
165 166 7.174080 GTGTAAGAGCCAATTTCTTTCTCTTCT 59.826 37.037 6.13 0.00 41.56 2.85
166 167 7.301789 GTGTAAGAGCCAATTTCTTTCTCTTC 58.698 38.462 6.13 1.23 41.56 2.87
167 168 6.073003 CGTGTAAGAGCCAATTTCTTTCTCTT 60.073 38.462 7.76 7.76 43.84 2.85
168 169 5.409826 CGTGTAAGAGCCAATTTCTTTCTCT 59.590 40.000 0.00 0.00 36.38 3.10
169 170 5.390991 CCGTGTAAGAGCCAATTTCTTTCTC 60.391 44.000 0.00 0.00 36.38 2.87
170 171 4.455877 CCGTGTAAGAGCCAATTTCTTTCT 59.544 41.667 0.00 0.00 36.38 2.52
171 172 4.454504 TCCGTGTAAGAGCCAATTTCTTTC 59.545 41.667 0.00 0.00 36.38 2.62
172 173 4.215613 GTCCGTGTAAGAGCCAATTTCTTT 59.784 41.667 0.00 0.00 36.38 2.52
173 174 3.751698 GTCCGTGTAAGAGCCAATTTCTT 59.248 43.478 0.00 0.00 38.40 2.52
174 175 3.244422 TGTCCGTGTAAGAGCCAATTTCT 60.244 43.478 0.00 0.00 0.00 2.52
175 176 3.071479 TGTCCGTGTAAGAGCCAATTTC 58.929 45.455 0.00 0.00 0.00 2.17
176 177 3.074412 CTGTCCGTGTAAGAGCCAATTT 58.926 45.455 0.00 0.00 0.00 1.82
177 178 2.038557 ACTGTCCGTGTAAGAGCCAATT 59.961 45.455 0.00 0.00 0.00 2.32
178 179 1.623811 ACTGTCCGTGTAAGAGCCAAT 59.376 47.619 0.00 0.00 0.00 3.16
179 180 1.045407 ACTGTCCGTGTAAGAGCCAA 58.955 50.000 0.00 0.00 0.00 4.52
180 181 0.317160 CACTGTCCGTGTAAGAGCCA 59.683 55.000 0.00 0.00 38.84 4.75
181 182 0.601558 TCACTGTCCGTGTAAGAGCC 59.398 55.000 0.00 0.00 44.16 4.70
182 183 1.540267 TCTCACTGTCCGTGTAAGAGC 59.460 52.381 0.00 0.00 44.16 4.09
183 184 2.814919 AGTCTCACTGTCCGTGTAAGAG 59.185 50.000 0.00 0.00 44.16 2.85
184 185 2.812591 GAGTCTCACTGTCCGTGTAAGA 59.187 50.000 0.00 0.00 44.16 2.10
185 186 2.412977 CGAGTCTCACTGTCCGTGTAAG 60.413 54.545 0.00 0.00 44.16 2.34
186 187 1.534163 CGAGTCTCACTGTCCGTGTAA 59.466 52.381 0.00 0.00 44.16 2.41
187 188 1.154197 CGAGTCTCACTGTCCGTGTA 58.846 55.000 0.00 0.00 44.16 2.90
188 189 0.534427 TCGAGTCTCACTGTCCGTGT 60.534 55.000 0.00 0.00 44.16 4.49
189 190 0.591659 TTCGAGTCTCACTGTCCGTG 59.408 55.000 0.00 0.00 45.18 4.94
190 191 0.875728 CTTCGAGTCTCACTGTCCGT 59.124 55.000 0.00 0.00 0.00 4.69
191 192 0.455295 GCTTCGAGTCTCACTGTCCG 60.455 60.000 0.00 0.00 0.00 4.79
192 193 0.885196 AGCTTCGAGTCTCACTGTCC 59.115 55.000 0.00 0.00 0.00 4.02
193 194 1.135517 GGAGCTTCGAGTCTCACTGTC 60.136 57.143 15.04 0.00 0.00 3.51
194 195 0.885196 GGAGCTTCGAGTCTCACTGT 59.115 55.000 15.04 0.00 0.00 3.55
195 196 0.884514 TGGAGCTTCGAGTCTCACTG 59.115 55.000 15.04 0.00 0.00 3.66
196 197 1.271102 GTTGGAGCTTCGAGTCTCACT 59.729 52.381 15.04 0.00 0.00 3.41
197 198 1.670380 GGTTGGAGCTTCGAGTCTCAC 60.670 57.143 15.04 7.67 0.00 3.51
198 199 0.603569 GGTTGGAGCTTCGAGTCTCA 59.396 55.000 15.04 2.74 0.00 3.27
199 200 0.892063 AGGTTGGAGCTTCGAGTCTC 59.108 55.000 7.29 7.29 0.00 3.36
214 215 7.009179 TCATCAGATGAACTCACTAAAGGTT 57.991 36.000 10.93 0.00 36.11 3.50
215 216 6.611613 TCATCAGATGAACTCACTAAAGGT 57.388 37.500 10.93 0.00 36.11 3.50
230 231 5.987098 ACAGCTACAGAAACATCATCAGAT 58.013 37.500 0.00 0.00 33.87 2.90
244 245 5.106712 TGCTTCGGAAAAATTACAGCTACAG 60.107 40.000 0.00 0.00 0.00 2.74
263 264 3.944422 TGTCTCAAGTCGTTTTGCTTC 57.056 42.857 0.00 0.00 0.00 3.86
335 338 6.728200 CATGTGCAAAGAAAGAGTAAGTTGA 58.272 36.000 0.00 0.00 0.00 3.18
336 339 5.400485 GCATGTGCAAAGAAAGAGTAAGTTG 59.600 40.000 0.00 0.00 41.59 3.16
338 341 4.022849 GGCATGTGCAAAGAAAGAGTAAGT 60.023 41.667 7.36 0.00 44.36 2.24
351 354 2.094078 GCTATTTTCTGGGCATGTGCAA 60.094 45.455 7.36 0.00 44.36 4.08
363 366 7.928706 ACACATCTAGCTTTATCGCTATTTTCT 59.071 33.333 0.00 0.00 41.31 2.52
426 429 1.213926 CACTACCCCCTCCGTAGTACT 59.786 57.143 0.00 0.00 43.54 2.73
427 430 1.685148 CACTACCCCCTCCGTAGTAC 58.315 60.000 0.61 0.00 43.54 2.73
428 431 0.106519 GCACTACCCCCTCCGTAGTA 60.107 60.000 0.61 0.00 43.54 1.82
429 432 1.380920 GCACTACCCCCTCCGTAGT 60.381 63.158 0.00 0.00 45.70 2.73
430 433 1.076192 AGCACTACCCCCTCCGTAG 60.076 63.158 0.00 0.00 39.32 3.51
432 435 2.363925 GAGCACTACCCCCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
433 436 2.363795 TGAGCACTACCCCCTCCG 60.364 66.667 0.00 0.00 0.00 4.63
434 437 1.306226 AGTGAGCACTACCCCCTCC 60.306 63.158 0.41 0.00 40.43 4.30
435 438 1.331399 GGAGTGAGCACTACCCCCTC 61.331 65.000 2.65 0.00 42.66 4.30
436 439 1.306226 GGAGTGAGCACTACCCCCT 60.306 63.158 2.65 0.00 42.66 4.79
437 440 0.983378 ATGGAGTGAGCACTACCCCC 60.983 60.000 10.20 4.99 41.64 5.40
457 524 6.576662 TCCAATATGCGGAGTAAACAAAAA 57.423 33.333 0.00 0.00 0.00 1.94
462 529 5.063880 AGGAATCCAATATGCGGAGTAAAC 58.936 41.667 0.61 0.00 35.56 2.01
467 534 3.407424 TGAGGAATCCAATATGCGGAG 57.593 47.619 0.61 0.00 35.56 4.63
478 545 9.717892 GTCGAACTTATAAAATTTGAGGAATCC 57.282 33.333 0.00 0.00 0.00 3.01
577 656 9.862371 TCAAGTTTGTAGAAAAATTACTTGCAA 57.138 25.926 0.00 0.00 40.26 4.08
614 694 3.317993 GCTTTGTCTGGAGCCAAACTTTA 59.682 43.478 0.00 0.00 32.80 1.85
642 722 8.040132 CCTTCATTCATTTTAATTTACTGCCCA 58.960 33.333 0.00 0.00 0.00 5.36
644 724 9.305925 CTCCTTCATTCATTTTAATTTACTGCC 57.694 33.333 0.00 0.00 0.00 4.85
670 750 9.627395 AGCGTCTGACTGTATGATAAAATATAC 57.373 33.333 6.21 0.00 0.00 1.47
671 751 9.626045 CAGCGTCTGACTGTATGATAAAATATA 57.374 33.333 6.21 0.00 32.44 0.86
672 752 7.600375 CCAGCGTCTGACTGTATGATAAAATAT 59.400 37.037 6.21 0.00 32.44 1.28
676 756 4.401202 TCCAGCGTCTGACTGTATGATAAA 59.599 41.667 6.21 0.00 32.44 1.40
678 758 3.551846 TCCAGCGTCTGACTGTATGATA 58.448 45.455 6.21 0.00 32.44 2.15
679 759 2.360483 CTCCAGCGTCTGACTGTATGAT 59.640 50.000 6.21 0.00 32.44 2.45
680 760 1.745653 CTCCAGCGTCTGACTGTATGA 59.254 52.381 6.21 0.00 32.44 2.15
681 761 1.202348 CCTCCAGCGTCTGACTGTATG 60.202 57.143 6.21 0.00 32.44 2.39
682 762 1.107114 CCTCCAGCGTCTGACTGTAT 58.893 55.000 6.21 0.00 32.44 2.29
683 763 0.251209 ACCTCCAGCGTCTGACTGTA 60.251 55.000 6.21 0.00 32.44 2.74
684 764 1.531840 ACCTCCAGCGTCTGACTGT 60.532 57.895 6.21 0.00 32.44 3.55
685 765 1.080230 CACCTCCAGCGTCTGACTG 60.080 63.158 6.21 0.00 32.44 3.51
686 766 1.531840 ACACCTCCAGCGTCTGACT 60.532 57.895 6.21 0.00 32.44 3.41
687 767 1.373497 CACACCTCCAGCGTCTGAC 60.373 63.158 8.20 0.00 32.44 3.51
688 768 2.574018 CCACACCTCCAGCGTCTGA 61.574 63.158 8.20 0.00 32.44 3.27
689 769 2.047844 CCACACCTCCAGCGTCTG 60.048 66.667 0.52 0.52 0.00 3.51
692 772 2.426023 GAACCACACCTCCAGCGT 59.574 61.111 0.00 0.00 0.00 5.07
693 773 2.358737 GGAACCACACCTCCAGCG 60.359 66.667 0.00 0.00 0.00 5.18
695 775 0.320771 CGAAGGAACCACACCTCCAG 60.321 60.000 0.00 0.00 36.67 3.86
696 776 1.752198 CGAAGGAACCACACCTCCA 59.248 57.895 0.00 0.00 36.67 3.86
734 855 1.403814 AGTCTAGCCGAGCAGCATAA 58.596 50.000 0.00 0.00 34.23 1.90
752 873 0.179189 GCTCGGTGCGAATTTCCAAG 60.179 55.000 0.00 0.00 34.74 3.61
805 933 1.812686 CGGTTGTTGTCCGGGAGAGA 61.813 60.000 0.00 0.00 43.68 3.10
883 1011 2.676822 AGTGGAAGGAGCTCGCGA 60.677 61.111 9.26 9.26 0.00 5.87
966 1111 0.690192 TCTGCCCTGGATCGTTTTGA 59.310 50.000 0.00 0.00 0.00 2.69
967 1112 0.804989 GTCTGCCCTGGATCGTTTTG 59.195 55.000 0.00 0.00 0.00 2.44
968 1113 0.673644 CGTCTGCCCTGGATCGTTTT 60.674 55.000 0.00 0.00 0.00 2.43
1236 1388 2.202987 GGGAGGAGCAGCATCACG 60.203 66.667 0.00 0.00 0.00 4.35
1785 1937 1.487976 TCCACCAGCTCCATCATCTTC 59.512 52.381 0.00 0.00 0.00 2.87
1994 2146 3.684788 CACGAGGAAGGAAATGTTAGGTG 59.315 47.826 0.00 0.00 0.00 4.00
2002 2154 2.814336 GTCAAAGCACGAGGAAGGAAAT 59.186 45.455 0.00 0.00 0.00 2.17
2033 2185 2.819595 GCATGGCATGGTCGTCGT 60.820 61.111 27.48 0.00 0.00 4.34
2035 2187 2.438254 TGGCATGGCATGGTCGTC 60.438 61.111 27.48 11.14 0.00 4.20
2037 2189 0.747644 TAACTGGCATGGCATGGTCG 60.748 55.000 27.48 13.00 0.00 4.79
2038 2190 1.473258 TTAACTGGCATGGCATGGTC 58.527 50.000 27.48 12.58 0.00 4.02
2039 2191 1.550072 GTTTAACTGGCATGGCATGGT 59.450 47.619 27.48 15.24 0.00 3.55
2040 2192 1.826720 AGTTTAACTGGCATGGCATGG 59.173 47.619 27.48 14.54 0.00 3.66
2041 2193 3.598019 AAGTTTAACTGGCATGGCATG 57.402 42.857 23.59 22.99 0.00 4.06
2042 2194 5.068198 CAGATAAGTTTAACTGGCATGGCAT 59.932 40.000 23.59 11.65 32.02 4.40
2043 2195 4.398988 CAGATAAGTTTAACTGGCATGGCA 59.601 41.667 21.97 21.97 32.02 4.92
2044 2196 4.399303 ACAGATAAGTTTAACTGGCATGGC 59.601 41.667 13.29 13.29 37.72 4.40
2072 2226 0.179018 AGCCCTGCTCAAACGAAGTT 60.179 50.000 0.00 0.00 46.24 2.66
2074 2228 1.667724 CATAGCCCTGCTCAAACGAAG 59.332 52.381 0.00 0.00 40.44 3.79
2108 2262 3.771160 ATCGACAGCACCGGACCC 61.771 66.667 9.46 0.00 0.00 4.46
2321 2475 2.032071 CACCCGTCCTTGTCCACC 59.968 66.667 0.00 0.00 0.00 4.61
2544 2698 2.621998 CTCAATGAGGACCCATGCATTC 59.378 50.000 1.53 0.00 0.00 2.67
2585 2739 0.390209 TAGCCGGCCGTTGTTAAGAC 60.390 55.000 26.15 3.21 0.00 3.01
2604 2758 6.329460 TCCTTCATCCTGATCAAGATCAAGAT 59.671 38.462 16.95 15.17 45.16 2.40
2605 2759 5.664457 TCCTTCATCCTGATCAAGATCAAGA 59.336 40.000 16.95 12.78 46.10 3.02
2606 2760 5.926663 TCCTTCATCCTGATCAAGATCAAG 58.073 41.667 10.19 10.19 46.10 3.02
2607 2761 5.963214 TCCTTCATCCTGATCAAGATCAA 57.037 39.130 13.25 0.00 46.10 2.57
2608 2762 5.605488 TCATCCTTCATCCTGATCAAGATCA 59.395 40.000 11.87 11.87 44.83 2.92
2609 2763 6.111669 TCATCCTTCATCCTGATCAAGATC 57.888 41.667 3.71 3.12 38.29 2.75
2714 2868 3.872603 ACCACCTGCTTCGCCACA 61.873 61.111 0.00 0.00 0.00 4.17
2846 3000 9.793252 ATATTTCTCACACAAATAATCAAGCAC 57.207 29.630 0.00 0.00 31.15 4.40
2865 3020 8.913487 AAAAATCGAACCGGGTATATATTTCT 57.087 30.769 6.32 0.00 0.00 2.52
2942 3881 1.133598 CATGCACATTGGCGACTGATT 59.866 47.619 0.00 0.00 36.28 2.57
3088 4173 0.960286 GGTAGGGTCATCGAGTAGCC 59.040 60.000 9.42 9.42 0.00 3.93
3107 4192 3.480470 ACTTGCCGATTCATCCCTATTG 58.520 45.455 0.00 0.00 0.00 1.90
3109 4194 3.864789 AACTTGCCGATTCATCCCTAT 57.135 42.857 0.00 0.00 0.00 2.57
3133 4218 9.098355 CTGTTCAAGAATTCATCCGATTAACTA 57.902 33.333 8.44 0.00 0.00 2.24
3134 4219 7.066284 CCTGTTCAAGAATTCATCCGATTAACT 59.934 37.037 8.44 0.00 0.00 2.24
3196 4284 1.963855 CGTTGAACCCGATGCCACA 60.964 57.895 0.00 0.00 0.00 4.17
3499 4597 9.880064 GATGTGATGATGTTAAGATTTCTGATG 57.120 33.333 0.00 0.00 0.00 3.07
3664 4762 3.513912 TCTTTCTTCCTGCGGTCTTATGA 59.486 43.478 0.00 0.00 0.00 2.15
3717 4819 6.787085 ACTTGTATTGACTTCTCTTTTCCG 57.213 37.500 0.00 0.00 0.00 4.30
3776 4878 1.000938 GTTGGAGCAACAAAGGCAGAG 60.001 52.381 0.00 0.00 43.09 3.35


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

AutoCloner maintained by Alex Coulton.