Multiple sequence alignment - TraesCS3A01G358800

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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 TraesCS3A01G358800 chr3A 100.000 3078 0 0 1 3078 606823097 606826174 0.000000e+00 5685
1 TraesCS3A01G358800 chr3B 89.047 2456 137 65 177 2579 617255428 617257804 0.000000e+00 2924
2 TraesCS3A01G358800 chr3B 86.177 463 35 12 2578 3014 617257834 617258293 9.990000e-130 473
3 TraesCS3A01G358800 chr3D 84.508 2711 192 101 202 2782 463804281 463806893 0.000000e+00 2470
4 TraesCS3A01G358800 chr6D 89.437 142 13 2 5 145 130197868 130197728 8.770000e-41 178
5 TraesCS3A01G358800 chr7A 86.713 143 18 1 2 143 518750464 518750606 1.140000e-34 158
6 TraesCS3A01G358800 chr7A 85.714 140 19 1 2 140 42976217 42976356 2.470000e-31 147
7 TraesCS3A01G358800 chr7A 83.099 142 21 3 7 146 131185599 131185739 3.220000e-25 126
8 TraesCS3A01G358800 chr4A 84.138 145 21 2 2 145 109423113 109423256 4.140000e-29 139
9 TraesCS3A01G358800 chr7D 85.185 135 18 2 2 135 540491448 540491581 1.490000e-28 137
10 TraesCS3A01G358800 chr6B 83.916 143 21 2 5 145 405057738 405057596 5.350000e-28 135
11 TraesCS3A01G358800 chr2A 84.028 144 16 4 5 143 7918868 7919009 6.930000e-27 132
12 TraesCS3A01G358800 chr2B 83.571 140 22 1 5 143 513699594 513699733 2.490000e-26 130


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 TraesCS3A01G358800 chr3A 606823097 606826174 3077 False 5685.0 5685 100.000 1 3078 1 chr3A.!!$F1 3077
1 TraesCS3A01G358800 chr3B 617255428 617258293 2865 False 1698.5 2924 87.612 177 3014 2 chr3B.!!$F1 2837
2 TraesCS3A01G358800 chr3D 463804281 463806893 2612 False 2470.0 2470 84.508 202 2782 1 chr3D.!!$F1 2580

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
142 143 0.036010 CGGTCCATTGGAGTTGCTCT 60.036 55.0 5.39 0.0 29.39 4.09 F
477 517 0.165944 CGGTTGATGTTTCGCCACTC 59.834 55.0 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1267 0.868406 GTGCACCAAGAAACGGAGAG 59.132 55.0 5.22 0.0 0.0 3.20 R
2179 2335 0.813610 CAAACCACTGACCTCGCACA 60.814 55.0 0.00 0.0 0.0 4.57 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 3.966215 CGCTGACATGAAACGGGT 58.034 55.556 0.00 0.00 0.00 5.28
18 19 1.787847 CGCTGACATGAAACGGGTC 59.212 57.895 0.00 0.00 0.00 4.46
19 20 1.787847 GCTGACATGAAACGGGTCG 59.212 57.895 0.00 0.00 34.32 4.79
20 21 1.635663 GCTGACATGAAACGGGTCGG 61.636 60.000 0.00 0.00 40.16 4.79
21 22 1.635663 CTGACATGAAACGGGTCGGC 61.636 60.000 0.00 0.00 34.32 5.54
22 23 2.736682 GACATGAAACGGGTCGGCG 61.737 63.158 0.00 0.00 0.00 6.46
23 24 4.160635 CATGAAACGGGTCGGCGC 62.161 66.667 0.00 0.00 0.00 6.53
41 42 2.672996 GTTGGGTGCACTGCCGAT 60.673 61.111 17.98 0.00 0.00 4.18
42 43 2.359850 TTGGGTGCACTGCCGATC 60.360 61.111 17.98 0.00 0.00 3.69
43 44 3.918253 TTGGGTGCACTGCCGATCC 62.918 63.158 17.98 7.97 0.00 3.36
44 45 4.408821 GGGTGCACTGCCGATCCA 62.409 66.667 17.98 0.00 0.00 3.41
45 46 2.359850 GGTGCACTGCCGATCCAA 60.360 61.111 17.98 0.00 0.00 3.53
46 47 1.971167 GGTGCACTGCCGATCCAAA 60.971 57.895 17.98 0.00 0.00 3.28
47 48 1.315257 GGTGCACTGCCGATCCAAAT 61.315 55.000 17.98 0.00 0.00 2.32
48 49 1.378531 GTGCACTGCCGATCCAAATA 58.621 50.000 10.32 0.00 0.00 1.40
49 50 1.064060 GTGCACTGCCGATCCAAATAC 59.936 52.381 10.32 0.00 0.00 1.89
50 51 1.339535 TGCACTGCCGATCCAAATACA 60.340 47.619 0.00 0.00 0.00 2.29
51 52 1.742831 GCACTGCCGATCCAAATACAA 59.257 47.619 0.00 0.00 0.00 2.41
52 53 2.163412 GCACTGCCGATCCAAATACAAA 59.837 45.455 0.00 0.00 0.00 2.83
53 54 3.366883 GCACTGCCGATCCAAATACAAAA 60.367 43.478 0.00 0.00 0.00 2.44
54 55 4.165779 CACTGCCGATCCAAATACAAAAC 58.834 43.478 0.00 0.00 0.00 2.43
55 56 4.079253 ACTGCCGATCCAAATACAAAACT 58.921 39.130 0.00 0.00 0.00 2.66
56 57 4.082787 ACTGCCGATCCAAATACAAAACTG 60.083 41.667 0.00 0.00 0.00 3.16
57 58 3.192422 TGCCGATCCAAATACAAAACTGG 59.808 43.478 0.00 0.00 0.00 4.00
58 59 3.442273 GCCGATCCAAATACAAAACTGGA 59.558 43.478 0.00 0.00 42.04 3.86
59 60 4.674362 GCCGATCCAAATACAAAACTGGAC 60.674 45.833 0.00 0.00 40.69 4.02
60 61 4.436852 CCGATCCAAATACAAAACTGGACG 60.437 45.833 0.00 0.00 40.69 4.79
61 62 4.436852 CGATCCAAATACAAAACTGGACGG 60.437 45.833 0.00 0.00 40.69 4.79
62 63 4.088056 TCCAAATACAAAACTGGACGGA 57.912 40.909 0.00 0.00 32.97 4.69
63 64 3.816523 TCCAAATACAAAACTGGACGGAC 59.183 43.478 0.00 0.00 32.97 4.79
64 65 3.364565 CCAAATACAAAACTGGACGGACG 60.365 47.826 0.00 0.00 0.00 4.79
65 66 1.435577 ATACAAAACTGGACGGACGC 58.564 50.000 0.00 0.00 0.00 5.19
66 67 0.600782 TACAAAACTGGACGGACGCC 60.601 55.000 0.00 0.00 0.00 5.68
88 89 3.059386 GGCGGCCGATCCAAACAA 61.059 61.111 33.48 0.00 34.01 2.83
89 90 2.631580 GGCGGCCGATCCAAACAAA 61.632 57.895 33.48 0.00 34.01 2.83
90 91 1.443702 GCGGCCGATCCAAACAAAC 60.444 57.895 33.48 1.41 34.01 2.93
91 92 1.953017 CGGCCGATCCAAACAAACA 59.047 52.632 24.07 0.00 34.01 2.83
92 93 0.312416 CGGCCGATCCAAACAAACAA 59.688 50.000 24.07 0.00 34.01 2.83
93 94 1.269309 CGGCCGATCCAAACAAACAAA 60.269 47.619 24.07 0.00 34.01 2.83
94 95 2.799917 CGGCCGATCCAAACAAACAAAA 60.800 45.455 24.07 0.00 34.01 2.44
95 96 3.198872 GGCCGATCCAAACAAACAAAAA 58.801 40.909 0.00 0.00 34.01 1.94
110 111 2.893671 AAAAACGGACAAATGCGCC 58.106 47.368 4.18 0.00 44.76 6.53
114 115 2.202298 CGGACAAATGCGCCGTTC 60.202 61.111 4.18 0.00 40.17 3.95
115 116 2.950673 GGACAAATGCGCCGTTCA 59.049 55.556 4.18 0.00 0.00 3.18
116 117 1.506262 GGACAAATGCGCCGTTCAT 59.494 52.632 4.18 0.00 0.00 2.57
117 118 0.109319 GGACAAATGCGCCGTTCATT 60.109 50.000 4.18 0.00 35.83 2.57
118 119 1.668628 GGACAAATGCGCCGTTCATTT 60.669 47.619 4.18 0.03 42.83 2.32
120 121 3.120627 AAATGCGCCGTTCATTTGG 57.879 47.368 4.18 0.00 41.15 3.28
121 122 0.600557 AAATGCGCCGTTCATTTGGA 59.399 45.000 4.18 0.00 41.15 3.53
122 123 0.817013 AATGCGCCGTTCATTTGGAT 59.183 45.000 4.18 0.00 30.60 3.41
123 124 0.381801 ATGCGCCGTTCATTTGGATC 59.618 50.000 4.18 0.00 0.00 3.36
124 125 1.297598 GCGCCGTTCATTTGGATCG 60.298 57.895 0.00 0.00 38.22 3.69
138 139 1.668419 GGATCGGTCCATTGGAGTTG 58.332 55.000 10.69 0.00 44.42 3.16
139 140 1.017387 GATCGGTCCATTGGAGTTGC 58.983 55.000 5.39 0.00 29.39 4.17
140 141 0.620556 ATCGGTCCATTGGAGTTGCT 59.379 50.000 5.39 0.00 29.39 3.91
141 142 0.036388 TCGGTCCATTGGAGTTGCTC 60.036 55.000 5.39 0.00 29.39 4.26
142 143 0.036010 CGGTCCATTGGAGTTGCTCT 60.036 55.000 5.39 0.00 29.39 4.09
143 144 1.207089 CGGTCCATTGGAGTTGCTCTA 59.793 52.381 5.39 0.00 29.39 2.43
144 145 2.354704 CGGTCCATTGGAGTTGCTCTAA 60.355 50.000 5.39 0.00 35.57 2.10
145 146 3.010420 GGTCCATTGGAGTTGCTCTAAC 58.990 50.000 5.39 0.00 34.03 2.34
146 147 3.559171 GGTCCATTGGAGTTGCTCTAACA 60.559 47.826 5.39 0.00 41.88 2.41
147 148 4.072131 GTCCATTGGAGTTGCTCTAACAA 58.928 43.478 5.39 0.00 41.88 2.83
148 149 4.154918 GTCCATTGGAGTTGCTCTAACAAG 59.845 45.833 5.39 0.00 41.88 3.16
149 150 4.074970 CCATTGGAGTTGCTCTAACAAGT 58.925 43.478 0.00 0.00 41.88 3.16
150 151 4.154918 CCATTGGAGTTGCTCTAACAAGTC 59.845 45.833 0.00 3.96 45.37 3.01
151 152 4.689612 TTGGAGTTGCTCTAACAAGTCT 57.310 40.909 10.85 0.00 45.40 3.24
152 153 4.258702 TGGAGTTGCTCTAACAAGTCTC 57.741 45.455 10.85 0.64 45.40 3.36
153 154 3.246619 GGAGTTGCTCTAACAAGTCTCG 58.753 50.000 10.85 0.00 45.40 4.04
154 155 3.246619 GAGTTGCTCTAACAAGTCTCGG 58.753 50.000 5.13 0.00 43.61 4.63
155 156 2.628657 AGTTGCTCTAACAAGTCTCGGT 59.371 45.455 0.00 0.00 41.88 4.69
156 157 2.987821 GTTGCTCTAACAAGTCTCGGTC 59.012 50.000 0.00 0.00 39.16 4.79
157 158 1.199327 TGCTCTAACAAGTCTCGGTCG 59.801 52.381 0.00 0.00 0.00 4.79
158 159 1.467734 GCTCTAACAAGTCTCGGTCGA 59.532 52.381 0.00 0.00 0.00 4.20
159 160 2.728535 GCTCTAACAAGTCTCGGTCGAC 60.729 54.545 7.13 7.13 0.00 4.20
160 161 2.743126 CTCTAACAAGTCTCGGTCGACT 59.257 50.000 16.46 0.00 45.73 4.18
168 169 4.879104 AGTCTCGGTCGACTTATACTTG 57.121 45.455 16.46 0.00 41.27 3.16
169 170 3.626670 AGTCTCGGTCGACTTATACTTGG 59.373 47.826 16.46 0.00 41.27 3.61
170 171 2.357009 TCTCGGTCGACTTATACTTGGC 59.643 50.000 16.46 0.00 0.00 4.52
171 172 2.093890 TCGGTCGACTTATACTTGGCA 58.906 47.619 16.46 0.00 0.00 4.92
172 173 2.098607 TCGGTCGACTTATACTTGGCAG 59.901 50.000 16.46 0.00 0.00 4.85
173 174 2.098607 CGGTCGACTTATACTTGGCAGA 59.901 50.000 16.46 0.00 0.00 4.26
174 175 3.445857 GGTCGACTTATACTTGGCAGAC 58.554 50.000 16.46 0.00 0.00 3.51
175 176 3.106672 GTCGACTTATACTTGGCAGACG 58.893 50.000 8.70 0.00 0.00 4.18
184 185 0.176680 CTTGGCAGACGGTAGATGCT 59.823 55.000 10.92 0.00 39.88 3.79
197 198 2.957491 AGATGCTAGTGACACTGCTC 57.043 50.000 18.58 15.71 0.00 4.26
200 201 1.807573 GCTAGTGACACTGCTCCGC 60.808 63.158 18.58 8.73 0.00 5.54
204 205 2.355837 TGACACTGCTCCGCGAAC 60.356 61.111 8.23 0.00 0.00 3.95
217 218 1.204312 GCGAACAGAGAAACGTGGC 59.796 57.895 0.00 0.00 0.00 5.01
307 308 3.737172 GGCACACCATGTCACGGC 61.737 66.667 0.00 0.00 35.26 5.68
395 435 4.899239 CGCGACCTCATCCTGCCC 62.899 72.222 0.00 0.00 0.00 5.36
396 436 4.899239 GCGACCTCATCCTGCCCG 62.899 72.222 0.00 0.00 0.00 6.13
397 437 4.899239 CGACCTCATCCTGCCCGC 62.899 72.222 0.00 0.00 0.00 6.13
398 438 4.554036 GACCTCATCCTGCCCGCC 62.554 72.222 0.00 0.00 0.00 6.13
465 505 4.096003 CCCGTCCAGCCGGTTGAT 62.096 66.667 21.18 0.00 46.66 2.57
477 517 0.165944 CGGTTGATGTTTCGCCACTC 59.834 55.000 0.00 0.00 0.00 3.51
478 518 0.165944 GGTTGATGTTTCGCCACTCG 59.834 55.000 0.00 0.00 40.15 4.18
479 519 0.452784 GTTGATGTTTCGCCACTCGC 60.453 55.000 0.00 0.00 38.27 5.03
480 520 1.573829 TTGATGTTTCGCCACTCGCC 61.574 55.000 0.00 0.00 38.27 5.54
540 583 1.126846 CACTAGAAACAAGAAGCCGCG 59.873 52.381 0.00 0.00 0.00 6.46
558 601 4.800355 GTGGATCCACGTACGTCC 57.200 61.111 28.52 17.05 37.19 4.79
559 602 1.226491 GTGGATCCACGTACGTCCG 60.226 63.158 28.52 11.82 37.19 4.79
563 606 2.931713 GATCCACGTACGTCCGCCAG 62.932 65.000 19.94 6.03 0.00 4.85
639 699 4.056125 CCGTCCAGCGCTCTCACA 62.056 66.667 7.13 0.00 39.71 3.58
663 723 1.371635 ATTTTTGCTCCGTGCGTGC 60.372 52.632 0.00 0.00 46.63 5.34
664 724 3.798639 TTTTTGCTCCGTGCGTGCG 62.799 57.895 0.00 0.00 46.63 5.34
772 846 4.678743 GGGGTGGAGTGGTTGGCC 62.679 72.222 0.00 0.00 0.00 5.36
794 868 2.126502 GTTTTGTGCCCATCGCCG 60.127 61.111 0.00 0.00 36.24 6.46
859 935 3.026879 CGCAGCGCAGGATAGTCG 61.027 66.667 11.47 0.00 0.00 4.18
901 988 1.767289 CGCGTCGCCTTGTTATATCT 58.233 50.000 12.44 0.00 0.00 1.98
903 990 3.499048 CGCGTCGCCTTGTTATATCTAT 58.501 45.455 12.44 0.00 0.00 1.98
906 993 4.617530 GCGTCGCCTTGTTATATCTATCCA 60.618 45.833 5.75 0.00 0.00 3.41
907 994 4.857588 CGTCGCCTTGTTATATCTATCCAC 59.142 45.833 0.00 0.00 0.00 4.02
909 996 4.222145 TCGCCTTGTTATATCTATCCACCC 59.778 45.833 0.00 0.00 0.00 4.61
910 997 4.223032 CGCCTTGTTATATCTATCCACCCT 59.777 45.833 0.00 0.00 0.00 4.34
915 1003 4.286032 TGTTATATCTATCCACCCTGCACC 59.714 45.833 0.00 0.00 0.00 5.01
928 1016 4.570663 GCACCGGTCCGATCCTCG 62.571 72.222 14.39 0.00 40.07 4.63
960 1048 4.367023 CGCGGTCGGGAGGTTTGA 62.367 66.667 0.00 0.00 0.00 2.69
994 1093 4.993945 GTGCGTGCGTGCGTGAAG 62.994 66.667 3.11 0.00 37.81 3.02
1121 1245 2.181021 GCTGTACGTGACCCCTCG 59.819 66.667 0.00 0.00 35.62 4.63
1136 1260 2.011349 CTCGCCGATCGACAATCCG 61.011 63.158 18.66 9.01 43.16 4.18
1143 1267 0.931005 GATCGACAATCCGTTCCTGC 59.069 55.000 0.00 0.00 0.00 4.85
1154 1278 0.038159 CGTTCCTGCTCTCCGTTTCT 60.038 55.000 0.00 0.00 0.00 2.52
1160 1290 0.884704 TGCTCTCCGTTTCTTGGTGC 60.885 55.000 0.00 0.00 0.00 5.01
1183 1313 0.324943 GTTGCTCTGCCAAGGTCCTA 59.675 55.000 0.00 0.00 0.00 2.94
1198 1328 1.478916 GTCCTAACAGAGAGAGTGGCC 59.521 57.143 0.00 0.00 0.00 5.36
1344 1474 0.104934 ACACCAGGTGACCTTCTCCT 60.105 55.000 27.39 0.00 40.71 3.69
1380 1510 2.024871 CACCGGATCGACGCTCTC 59.975 66.667 9.46 0.00 0.00 3.20
1388 1518 1.263217 GATCGACGCTCTCCTCTTCTC 59.737 57.143 0.00 0.00 0.00 2.87
1392 1522 0.623723 ACGCTCTCCTCTTCTCCTCT 59.376 55.000 0.00 0.00 0.00 3.69
1412 1542 3.895025 CCGTCGTCTAACTCGGGA 58.105 61.111 0.00 0.00 39.41 5.14
1552 1683 1.900545 GAGTTCCAGAAGGACCGGGG 61.901 65.000 6.32 0.00 45.73 5.73
1593 1724 1.416813 CTTCCAGCACATCGACGAGC 61.417 60.000 3.01 1.12 0.00 5.03
1625 1756 6.070710 TCGATCTCGATCTTCTCCTATTCCTA 60.071 42.308 0.00 0.00 44.22 2.94
1653 1784 8.380644 ACACGTAATTCATTCTTATTCAGTTCG 58.619 33.333 0.00 0.00 0.00 3.95
1659 1790 7.843490 TTCATTCTTATTCAGTTCGTTAGGG 57.157 36.000 0.00 0.00 0.00 3.53
1681 1812 7.436933 AGGGTGAAAATTTTCTGATGTTCTTC 58.563 34.615 26.73 2.37 38.02 2.87
1689 1820 6.824305 TTTTCTGATGTTCTTCTGGGATTC 57.176 37.500 0.00 0.00 0.00 2.52
1690 1821 5.768980 TTCTGATGTTCTTCTGGGATTCT 57.231 39.130 0.00 0.00 0.00 2.40
1694 1825 1.066143 TGTTCTTCTGGGATTCTCGGC 60.066 52.381 0.00 0.00 0.00 5.54
1845 1976 0.888285 AGCTTCAACCTCAGCAGCAC 60.888 55.000 0.00 0.00 38.61 4.40
1995 2126 4.457496 CATGTGCGAGGAGGCGGT 62.457 66.667 0.00 0.00 35.06 5.68
2109 2240 3.532155 GAGGGATGAGCGCCGTCT 61.532 66.667 2.29 0.00 37.34 4.18
2110 2241 3.077556 AGGGATGAGCGCCGTCTT 61.078 61.111 2.29 0.00 0.00 3.01
2172 2328 8.187913 TCTGAATCTGAAGAAGAAGAAGAAGA 57.812 34.615 0.00 0.00 38.79 2.87
2173 2329 8.646004 TCTGAATCTGAAGAAGAAGAAGAAGAA 58.354 33.333 0.00 0.00 38.79 2.52
2174 2330 8.830201 TGAATCTGAAGAAGAAGAAGAAGAAG 57.170 34.615 0.00 0.00 38.79 2.85
2175 2331 8.646004 TGAATCTGAAGAAGAAGAAGAAGAAGA 58.354 33.333 0.00 0.00 38.79 2.87
2176 2332 9.143631 GAATCTGAAGAAGAAGAAGAAGAAGAG 57.856 37.037 0.00 0.00 38.79 2.85
2177 2333 6.454795 TCTGAAGAAGAAGAAGAAGAAGAGC 58.545 40.000 0.00 0.00 29.54 4.09
2178 2334 5.226396 TGAAGAAGAAGAAGAAGAAGAGCG 58.774 41.667 0.00 0.00 0.00 5.03
2179 2335 4.864704 AGAAGAAGAAGAAGAAGAGCGT 57.135 40.909 0.00 0.00 0.00 5.07
2232 2394 7.094248 TGCTGAATGCTTAGCTAATTTTCTTCA 60.094 33.333 6.64 10.61 43.37 3.02
2264 2426 6.087820 GTGTCGTACTTGTACATTCTCTTGAC 59.912 42.308 10.91 0.68 0.00 3.18
2292 2462 0.939577 TCGAGCAACGTCTGAACTGC 60.940 55.000 0.00 0.00 43.13 4.40
2305 2475 2.875080 GAACTGCGTTCAAAGCGTAT 57.125 45.000 13.97 0.00 41.62 3.06
2308 2478 0.373716 CTGCGTTCAAAGCGTATCCC 59.626 55.000 0.00 0.00 37.44 3.85
2325 2495 1.694150 TCCCTCTGAACTGTGTTCCTG 59.306 52.381 7.81 2.23 0.00 3.86
2327 2497 2.158755 CCCTCTGAACTGTGTTCCTGTT 60.159 50.000 7.81 0.00 37.86 3.16
2356 2529 9.642312 CTGAATTTGATAGTACATGAATGAACG 57.358 33.333 0.00 0.00 0.00 3.95
2383 2556 3.142174 CAAGAACTTCTGAACCCAGGAC 58.858 50.000 0.00 0.00 40.76 3.85
2417 2590 4.918810 ACTTGACAAATGAACAGGTTCC 57.081 40.909 9.49 0.00 38.77 3.62
2421 2595 3.068024 TGACAAATGAACAGGTTCCAAGC 59.932 43.478 9.49 0.00 38.77 4.01
2442 2616 3.435566 CACGTCATGCAATCTACTACGT 58.564 45.455 0.00 0.00 42.22 3.57
2443 2617 4.594136 CACGTCATGCAATCTACTACGTA 58.406 43.478 3.55 0.00 39.79 3.57
2484 2658 3.181478 CGTAGAAGATAGGTGGGTGGAAC 60.181 52.174 0.00 0.00 0.00 3.62
2535 2709 2.991250 ACTGCGAATTATGTGCTTCCT 58.009 42.857 0.00 0.00 0.00 3.36
2536 2710 3.347216 ACTGCGAATTATGTGCTTCCTT 58.653 40.909 0.00 0.00 0.00 3.36
2537 2711 3.375299 ACTGCGAATTATGTGCTTCCTTC 59.625 43.478 0.00 0.00 0.00 3.46
2538 2712 2.682856 TGCGAATTATGTGCTTCCTTCC 59.317 45.455 0.00 0.00 0.00 3.46
2579 2753 2.048603 GCAAGGCTTACCCCAGCAG 61.049 63.158 0.00 0.00 42.10 4.24
2580 2754 1.685224 CAAGGCTTACCCCAGCAGA 59.315 57.895 0.00 0.00 42.10 4.26
2581 2755 0.393537 CAAGGCTTACCCCAGCAGAG 60.394 60.000 0.00 0.00 42.10 3.35
2582 2756 1.566298 AAGGCTTACCCCAGCAGAGG 61.566 60.000 0.00 0.00 42.10 3.69
2584 2758 1.562672 GGCTTACCCCAGCAGAGGAA 61.563 60.000 0.00 0.00 42.10 3.36
2625 2838 0.868406 GTTCCACGCCAGTTTCTCTG 59.132 55.000 0.00 0.00 43.27 3.35
2628 2841 1.272490 TCCACGCCAGTTTCTCTGTAG 59.728 52.381 0.00 0.00 42.19 2.74
2739 2953 3.812262 TCATGCCAATGGTAGTCATCAG 58.188 45.455 0.00 0.00 34.44 2.90
2759 2973 1.467374 GCACATCACATGGTTTACGGC 60.467 52.381 0.00 0.00 33.60 5.68
2768 2982 0.390603 TGGTTTACGGCCATGACTCG 60.391 55.000 2.24 0.00 0.00 4.18
2772 2986 1.934589 TTACGGCCATGACTCGAATG 58.065 50.000 2.24 0.00 0.00 2.67
2774 2988 1.143838 CGGCCATGACTCGAATGGA 59.856 57.895 17.07 0.00 46.44 3.41
2829 3043 7.223058 CAATAGTTGCTACACTTGCTAGTAC 57.777 40.000 0.00 0.00 31.96 2.73
2830 3044 6.777213 ATAGTTGCTACACTTGCTAGTACT 57.223 37.500 0.00 0.00 31.96 2.73
2838 3064 5.148651 ACACTTGCTAGTACTGGTAAAGG 57.851 43.478 20.11 13.68 31.96 3.11
2878 3113 2.817901 CTGCCCAAGAAAATGCATAGC 58.182 47.619 0.00 0.00 32.53 2.97
2879 3114 2.166870 CTGCCCAAGAAAATGCATAGCA 59.833 45.455 0.00 0.00 44.86 3.49
2880 3115 2.094078 TGCCCAAGAAAATGCATAGCAC 60.094 45.455 0.00 0.00 43.04 4.40
2881 3116 2.801063 CCCAAGAAAATGCATAGCACG 58.199 47.619 0.00 0.00 43.04 5.34
2882 3117 2.480073 CCCAAGAAAATGCATAGCACGG 60.480 50.000 0.00 0.00 43.04 4.94
2899 3137 3.734597 GCACGGCAAAGATCAATATGCAA 60.735 43.478 12.15 0.00 40.51 4.08
2901 3139 4.501559 CACGGCAAAGATCAATATGCAAAG 59.498 41.667 12.15 6.94 40.51 2.77
2929 3167 5.509501 ATGTTCAGCATTACCAACTGTTTGG 60.510 40.000 1.73 1.73 45.92 3.28
2969 3207 2.257676 GCTCTGCCAACAAGCTGC 59.742 61.111 0.00 0.00 33.23 5.25
2983 3222 3.118665 ACAAGCTGCCAAATTTCAGTGTT 60.119 39.130 8.27 1.63 33.09 3.32
3009 3248 1.819928 ACGTGGCTGCATACAAATCA 58.180 45.000 0.50 0.00 0.00 2.57
3014 3253 5.105957 ACGTGGCTGCATACAAATCAAAATA 60.106 36.000 0.50 0.00 0.00 1.40
3015 3254 5.229887 CGTGGCTGCATACAAATCAAAATAC 59.770 40.000 0.50 0.00 0.00 1.89
3016 3255 6.332630 GTGGCTGCATACAAATCAAAATACT 58.667 36.000 0.50 0.00 0.00 2.12
3017 3256 6.813152 GTGGCTGCATACAAATCAAAATACTT 59.187 34.615 0.50 0.00 0.00 2.24
3018 3257 7.331687 GTGGCTGCATACAAATCAAAATACTTT 59.668 33.333 0.50 0.00 0.00 2.66
3019 3258 7.331440 TGGCTGCATACAAATCAAAATACTTTG 59.669 33.333 0.50 0.00 42.88 2.77
3020 3259 7.201548 GGCTGCATACAAATCAAAATACTTTGG 60.202 37.037 0.50 0.00 41.98 3.28
3021 3260 7.593875 TGCATACAAATCAAAATACTTTGGC 57.406 32.000 0.00 0.00 41.98 4.52
3022 3261 7.157347 TGCATACAAATCAAAATACTTTGGCA 58.843 30.769 0.00 0.00 41.98 4.92
3023 3262 7.658982 TGCATACAAATCAAAATACTTTGGCAA 59.341 29.630 0.00 0.00 41.98 4.52
3024 3263 8.667463 GCATACAAATCAAAATACTTTGGCAAT 58.333 29.630 0.00 0.00 41.98 3.56
3025 3264 9.976255 CATACAAATCAAAATACTTTGGCAATG 57.024 29.630 11.20 11.20 41.98 2.82
3026 3265 6.901265 ACAAATCAAAATACTTTGGCAATGC 58.099 32.000 12.54 0.00 41.98 3.56
3042 3281 6.391227 GGCAATGCCTACTTTATGTTATGT 57.609 37.500 18.47 0.00 46.69 2.29
3043 3282 7.504924 GGCAATGCCTACTTTATGTTATGTA 57.495 36.000 18.47 0.00 46.69 2.29
3044 3283 7.936584 GGCAATGCCTACTTTATGTTATGTAA 58.063 34.615 18.47 0.00 46.69 2.41
3045 3284 8.076178 GGCAATGCCTACTTTATGTTATGTAAG 58.924 37.037 18.47 0.00 46.69 2.34
3046 3285 8.621286 GCAATGCCTACTTTATGTTATGTAAGT 58.379 33.333 0.00 0.00 35.25 2.24
3058 3297 9.926158 TTATGTTATGTAAGTACAAGTTTCCGA 57.074 29.630 0.00 0.00 39.99 4.55
3059 3298 7.642071 TGTTATGTAAGTACAAGTTTCCGAC 57.358 36.000 0.00 0.00 39.99 4.79
3060 3299 7.208777 TGTTATGTAAGTACAAGTTTCCGACA 58.791 34.615 0.00 0.00 39.99 4.35
3061 3300 7.383029 TGTTATGTAAGTACAAGTTTCCGACAG 59.617 37.037 0.00 0.00 39.99 3.51
3062 3301 5.266733 TGTAAGTACAAGTTTCCGACAGT 57.733 39.130 0.00 0.00 32.40 3.55
3063 3302 5.663456 TGTAAGTACAAGTTTCCGACAGTT 58.337 37.500 0.00 0.00 32.40 3.16
3064 3303 6.804677 TGTAAGTACAAGTTTCCGACAGTTA 58.195 36.000 0.00 0.00 32.40 2.24
3065 3304 7.264221 TGTAAGTACAAGTTTCCGACAGTTAA 58.736 34.615 0.00 0.00 32.40 2.01
3066 3305 7.763528 TGTAAGTACAAGTTTCCGACAGTTAAA 59.236 33.333 0.00 0.00 32.40 1.52
3067 3306 6.594284 AGTACAAGTTTCCGACAGTTAAAC 57.406 37.500 0.00 0.00 34.13 2.01
3068 3307 6.108015 AGTACAAGTTTCCGACAGTTAAACA 58.892 36.000 0.00 0.00 35.93 2.83
3069 3308 6.764560 AGTACAAGTTTCCGACAGTTAAACAT 59.235 34.615 0.00 0.00 35.93 2.71
3070 3309 7.927629 AGTACAAGTTTCCGACAGTTAAACATA 59.072 33.333 0.00 0.00 35.93 2.29
3071 3310 7.556733 ACAAGTTTCCGACAGTTAAACATAA 57.443 32.000 0.00 0.00 35.93 1.90
3072 3311 7.987649 ACAAGTTTCCGACAGTTAAACATAAA 58.012 30.769 0.00 0.00 35.93 1.40
3073 3312 8.460428 ACAAGTTTCCGACAGTTAAACATAAAA 58.540 29.630 0.00 0.00 35.93 1.52
3074 3313 9.291664 CAAGTTTCCGACAGTTAAACATAAAAA 57.708 29.630 0.00 0.00 35.93 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.787847 GACCCGTTTCATGTCAGCG 59.212 57.895 0.00 0.00 0.00 5.18
1 2 1.635663 CCGACCCGTTTCATGTCAGC 61.636 60.000 0.00 0.00 0.00 4.26
2 3 1.635663 GCCGACCCGTTTCATGTCAG 61.636 60.000 0.00 0.00 0.00 3.51
3 4 1.669760 GCCGACCCGTTTCATGTCA 60.670 57.895 0.00 0.00 0.00 3.58
4 5 2.736682 CGCCGACCCGTTTCATGTC 61.737 63.158 0.00 0.00 0.00 3.06
5 6 2.740826 CGCCGACCCGTTTCATGT 60.741 61.111 0.00 0.00 0.00 3.21
6 7 4.160635 GCGCCGACCCGTTTCATG 62.161 66.667 0.00 0.00 0.00 3.07
24 25 2.672996 ATCGGCAGTGCACCCAAC 60.673 61.111 18.61 0.00 0.00 3.77
25 26 2.359850 GATCGGCAGTGCACCCAA 60.360 61.111 18.61 0.00 0.00 4.12
26 27 4.408821 GGATCGGCAGTGCACCCA 62.409 66.667 18.61 0.22 0.00 4.51
27 28 3.918253 TTGGATCGGCAGTGCACCC 62.918 63.158 18.61 7.72 0.00 4.61
28 29 1.315257 ATTTGGATCGGCAGTGCACC 61.315 55.000 18.61 14.14 0.00 5.01
29 30 1.064060 GTATTTGGATCGGCAGTGCAC 59.936 52.381 18.61 9.40 0.00 4.57
30 31 1.339535 TGTATTTGGATCGGCAGTGCA 60.340 47.619 18.61 0.00 0.00 4.57
31 32 1.378531 TGTATTTGGATCGGCAGTGC 58.621 50.000 6.55 6.55 0.00 4.40
32 33 4.082787 AGTTTTGTATTTGGATCGGCAGTG 60.083 41.667 0.00 0.00 0.00 3.66
33 34 4.079253 AGTTTTGTATTTGGATCGGCAGT 58.921 39.130 0.00 0.00 0.00 4.40
34 35 4.414852 CAGTTTTGTATTTGGATCGGCAG 58.585 43.478 0.00 0.00 0.00 4.85
35 36 3.192422 CCAGTTTTGTATTTGGATCGGCA 59.808 43.478 0.00 0.00 32.34 5.69
36 37 3.442273 TCCAGTTTTGTATTTGGATCGGC 59.558 43.478 0.00 0.00 34.90 5.54
37 38 4.436852 CGTCCAGTTTTGTATTTGGATCGG 60.437 45.833 0.00 0.00 41.41 4.18
38 39 4.436852 CCGTCCAGTTTTGTATTTGGATCG 60.437 45.833 0.00 2.36 41.41 3.69
39 40 4.698304 TCCGTCCAGTTTTGTATTTGGATC 59.302 41.667 0.00 0.00 41.41 3.36
40 41 4.457949 GTCCGTCCAGTTTTGTATTTGGAT 59.542 41.667 0.00 0.00 41.41 3.41
41 42 3.816523 GTCCGTCCAGTTTTGTATTTGGA 59.183 43.478 0.00 0.00 37.38 3.53
42 43 3.364565 CGTCCGTCCAGTTTTGTATTTGG 60.365 47.826 0.00 0.00 0.00 3.28
43 44 3.805823 CGTCCGTCCAGTTTTGTATTTG 58.194 45.455 0.00 0.00 0.00 2.32
44 45 2.224784 GCGTCCGTCCAGTTTTGTATTT 59.775 45.455 0.00 0.00 0.00 1.40
45 46 1.802365 GCGTCCGTCCAGTTTTGTATT 59.198 47.619 0.00 0.00 0.00 1.89
46 47 1.435577 GCGTCCGTCCAGTTTTGTAT 58.564 50.000 0.00 0.00 0.00 2.29
47 48 0.600782 GGCGTCCGTCCAGTTTTGTA 60.601 55.000 0.00 0.00 0.00 2.41
48 49 1.890510 GGCGTCCGTCCAGTTTTGT 60.891 57.895 0.00 0.00 0.00 2.83
49 50 2.943653 GGCGTCCGTCCAGTTTTG 59.056 61.111 0.00 0.00 0.00 2.44
50 51 2.663852 CGGCGTCCGTCCAGTTTT 60.664 61.111 9.69 0.00 42.73 2.43
71 72 2.631580 TTTGTTTGGATCGGCCGCC 61.632 57.895 23.51 18.27 40.66 6.13
72 73 1.443702 GTTTGTTTGGATCGGCCGC 60.444 57.895 23.51 7.37 40.66 6.53
73 74 0.312416 TTGTTTGTTTGGATCGGCCG 59.688 50.000 22.12 22.12 40.66 6.13
74 75 2.517650 TTTGTTTGTTTGGATCGGCC 57.482 45.000 0.00 0.00 37.10 6.13
92 93 0.937231 CGGCGCATTTGTCCGTTTTT 60.937 50.000 10.83 0.00 38.47 1.94
93 94 1.371145 CGGCGCATTTGTCCGTTTT 60.371 52.632 10.83 0.00 38.47 2.43
94 95 2.254051 CGGCGCATTTGTCCGTTT 59.746 55.556 10.83 0.00 38.47 3.60
98 99 0.109319 AATGAACGGCGCATTTGTCC 60.109 50.000 10.83 0.00 32.33 4.02
99 100 1.696988 AAATGAACGGCGCATTTGTC 58.303 45.000 19.79 0.00 42.54 3.18
100 101 3.883997 AAATGAACGGCGCATTTGT 57.116 42.105 19.79 0.00 42.54 2.83
102 103 0.600557 TCCAAATGAACGGCGCATTT 59.399 45.000 16.34 16.34 44.35 2.32
103 104 0.817013 ATCCAAATGAACGGCGCATT 59.183 45.000 10.83 6.89 37.56 3.56
104 105 0.381801 GATCCAAATGAACGGCGCAT 59.618 50.000 10.83 0.00 0.00 4.73
105 106 1.800032 GATCCAAATGAACGGCGCA 59.200 52.632 10.83 0.00 0.00 6.09
106 107 1.297598 CGATCCAAATGAACGGCGC 60.298 57.895 6.90 0.00 35.79 6.53
107 108 4.974468 CGATCCAAATGAACGGCG 57.026 55.556 4.80 4.80 35.79 6.46
119 120 1.668419 CAACTCCAATGGACCGATCC 58.332 55.000 0.00 0.00 46.48 3.36
120 121 1.017387 GCAACTCCAATGGACCGATC 58.983 55.000 0.00 0.00 0.00 3.69
121 122 0.620556 AGCAACTCCAATGGACCGAT 59.379 50.000 0.00 0.00 0.00 4.18
122 123 0.036388 GAGCAACTCCAATGGACCGA 60.036 55.000 0.00 0.00 0.00 4.69
123 124 0.036010 AGAGCAACTCCAATGGACCG 60.036 55.000 0.00 0.00 0.00 4.79
124 125 3.010420 GTTAGAGCAACTCCAATGGACC 58.990 50.000 0.00 0.00 34.06 4.46
125 126 3.674997 TGTTAGAGCAACTCCAATGGAC 58.325 45.455 0.00 0.00 38.05 4.02
126 127 4.202461 ACTTGTTAGAGCAACTCCAATGGA 60.202 41.667 0.48 0.48 38.05 3.41
127 128 4.074970 ACTTGTTAGAGCAACTCCAATGG 58.925 43.478 0.00 0.00 38.05 3.16
128 129 4.999950 AGACTTGTTAGAGCAACTCCAATG 59.000 41.667 0.00 0.00 38.05 2.82
129 130 5.234466 AGACTTGTTAGAGCAACTCCAAT 57.766 39.130 0.00 0.00 38.05 3.16
130 131 4.632153 GAGACTTGTTAGAGCAACTCCAA 58.368 43.478 0.00 0.00 38.05 3.53
131 132 3.305403 CGAGACTTGTTAGAGCAACTCCA 60.305 47.826 0.00 0.00 38.05 3.86
132 133 3.246619 CGAGACTTGTTAGAGCAACTCC 58.753 50.000 0.00 0.00 38.05 3.85
133 134 3.246619 CCGAGACTTGTTAGAGCAACTC 58.753 50.000 0.00 0.00 38.05 3.01
134 135 2.628657 ACCGAGACTTGTTAGAGCAACT 59.371 45.455 0.00 0.00 38.05 3.16
135 136 2.987821 GACCGAGACTTGTTAGAGCAAC 59.012 50.000 0.00 0.00 37.67 4.17
136 137 2.351447 CGACCGAGACTTGTTAGAGCAA 60.351 50.000 0.00 0.00 0.00 3.91
137 138 1.199327 CGACCGAGACTTGTTAGAGCA 59.801 52.381 0.00 0.00 0.00 4.26
138 139 1.467734 TCGACCGAGACTTGTTAGAGC 59.532 52.381 0.00 0.00 0.00 4.09
139 140 3.120182 GTCGACCGAGACTTGTTAGAG 57.880 52.381 3.51 0.00 38.09 2.43
148 149 3.791455 GCCAAGTATAAGTCGACCGAGAC 60.791 52.174 13.01 7.94 41.23 3.36
149 150 2.357009 GCCAAGTATAAGTCGACCGAGA 59.643 50.000 13.01 0.00 0.00 4.04
150 151 2.098607 TGCCAAGTATAAGTCGACCGAG 59.901 50.000 13.01 0.00 0.00 4.63
151 152 2.093890 TGCCAAGTATAAGTCGACCGA 58.906 47.619 13.01 0.00 0.00 4.69
152 153 2.098607 TCTGCCAAGTATAAGTCGACCG 59.901 50.000 13.01 0.00 0.00 4.79
153 154 3.445857 GTCTGCCAAGTATAAGTCGACC 58.554 50.000 13.01 0.00 0.00 4.79
154 155 3.106672 CGTCTGCCAAGTATAAGTCGAC 58.893 50.000 7.70 7.70 0.00 4.20
155 156 2.098607 CCGTCTGCCAAGTATAAGTCGA 59.901 50.000 0.00 0.00 0.00 4.20
156 157 2.159282 ACCGTCTGCCAAGTATAAGTCG 60.159 50.000 0.00 0.00 0.00 4.18
157 158 3.521947 ACCGTCTGCCAAGTATAAGTC 57.478 47.619 0.00 0.00 0.00 3.01
158 159 4.275810 TCTACCGTCTGCCAAGTATAAGT 58.724 43.478 0.00 0.00 0.00 2.24
159 160 4.913335 TCTACCGTCTGCCAAGTATAAG 57.087 45.455 0.00 0.00 0.00 1.73
160 161 4.500887 GCATCTACCGTCTGCCAAGTATAA 60.501 45.833 0.00 0.00 0.00 0.98
161 162 3.005472 GCATCTACCGTCTGCCAAGTATA 59.995 47.826 0.00 0.00 0.00 1.47
162 163 2.224066 GCATCTACCGTCTGCCAAGTAT 60.224 50.000 0.00 0.00 0.00 2.12
163 164 1.136305 GCATCTACCGTCTGCCAAGTA 59.864 52.381 0.00 0.00 0.00 2.24
164 165 0.108138 GCATCTACCGTCTGCCAAGT 60.108 55.000 0.00 0.00 0.00 3.16
165 166 0.176680 AGCATCTACCGTCTGCCAAG 59.823 55.000 0.00 0.00 36.56 3.61
166 167 1.409064 CTAGCATCTACCGTCTGCCAA 59.591 52.381 0.00 0.00 36.56 4.52
167 168 1.032794 CTAGCATCTACCGTCTGCCA 58.967 55.000 0.00 0.00 36.56 4.92
168 169 1.033574 ACTAGCATCTACCGTCTGCC 58.966 55.000 0.00 0.00 36.56 4.85
169 170 1.676529 TCACTAGCATCTACCGTCTGC 59.323 52.381 0.00 0.00 36.15 4.26
170 171 2.683362 TGTCACTAGCATCTACCGTCTG 59.317 50.000 0.00 0.00 0.00 3.51
171 172 2.683867 GTGTCACTAGCATCTACCGTCT 59.316 50.000 0.00 0.00 0.00 4.18
172 173 2.683867 AGTGTCACTAGCATCTACCGTC 59.316 50.000 2.87 0.00 0.00 4.79
173 174 2.423892 CAGTGTCACTAGCATCTACCGT 59.576 50.000 4.85 0.00 0.00 4.83
174 175 2.796383 GCAGTGTCACTAGCATCTACCG 60.796 54.545 17.31 0.44 0.00 4.02
175 176 2.428890 AGCAGTGTCACTAGCATCTACC 59.571 50.000 21.60 0.47 0.00 3.18
197 198 1.487231 CACGTTTCTCTGTTCGCGG 59.513 57.895 6.13 0.00 0.00 6.46
200 201 0.937699 TCGCCACGTTTCTCTGTTCG 60.938 55.000 0.00 0.00 0.00 3.95
204 205 3.147294 CGTCGCCACGTTTCTCTG 58.853 61.111 0.00 0.00 41.42 3.35
217 218 1.057847 GAGATGAGAACAAACGCGTCG 59.942 52.381 14.44 10.01 32.47 5.12
292 293 4.088762 GCGCCGTGACATGGTGTG 62.089 66.667 24.63 12.29 37.12 3.82
307 308 1.320555 GTGCCTATATTATGCGTCGCG 59.679 52.381 13.38 0.00 0.00 5.87
380 393 4.899239 GCGGGCAGGATGAGGTCG 62.899 72.222 0.00 0.00 39.69 4.79
410 450 0.871722 TTTGAATTCCGTGGTGCGAG 59.128 50.000 2.27 0.00 44.77 5.03
456 496 2.178273 GGCGAAACATCAACCGGC 59.822 61.111 0.00 0.00 40.15 6.13
540 583 1.140375 GGACGTACGTGGATCCACC 59.860 63.158 34.05 21.39 43.49 4.61
639 699 2.687370 GCACGGAGCAAAAATGGATTT 58.313 42.857 0.00 0.00 44.79 2.17
671 731 3.764466 CCTCTTCCGAGCGCCAGT 61.764 66.667 2.29 0.00 35.90 4.00
673 733 3.452786 CTCCTCTTCCGAGCGCCA 61.453 66.667 2.29 0.00 35.90 5.69
772 846 1.080569 GATGGGCACAAAACCAGCG 60.081 57.895 0.00 0.00 40.67 5.18
842 918 3.026879 CGACTATCCTGCGCTGCG 61.027 66.667 19.17 19.17 0.00 5.18
843 919 3.333969 GCGACTATCCTGCGCTGC 61.334 66.667 9.73 0.00 46.53 5.25
848 924 2.336809 CTCCCGCGACTATCCTGC 59.663 66.667 8.23 0.00 0.00 4.85
849 925 1.101635 TCACTCCCGCGACTATCCTG 61.102 60.000 8.23 0.00 0.00 3.86
850 926 1.102222 GTCACTCCCGCGACTATCCT 61.102 60.000 8.23 0.00 0.00 3.24
851 927 1.359475 GTCACTCCCGCGACTATCC 59.641 63.158 8.23 0.00 0.00 2.59
852 928 1.009900 CGTCACTCCCGCGACTATC 60.010 63.158 8.23 0.00 0.00 2.08
853 929 1.748122 ACGTCACTCCCGCGACTAT 60.748 57.895 8.23 0.00 0.00 2.12
854 930 2.359107 ACGTCACTCCCGCGACTA 60.359 61.111 8.23 0.00 0.00 2.59
855 931 4.039357 CACGTCACTCCCGCGACT 62.039 66.667 8.23 0.00 0.00 4.18
856 932 4.034258 TCACGTCACTCCCGCGAC 62.034 66.667 8.23 0.00 0.00 5.19
857 933 4.034258 GTCACGTCACTCCCGCGA 62.034 66.667 8.23 0.00 0.00 5.87
858 934 4.337060 TGTCACGTCACTCCCGCG 62.337 66.667 0.00 0.00 0.00 6.46
859 935 2.733593 GTGTCACGTCACTCCCGC 60.734 66.667 0.00 0.00 35.68 6.13
860 936 2.049433 GGTGTCACGTCACTCCCG 60.049 66.667 0.00 0.00 38.28 5.14
861 937 1.300697 GTGGTGTCACGTCACTCCC 60.301 63.158 8.25 0.05 38.28 4.30
862 938 4.338327 GTGGTGTCACGTCACTCC 57.662 61.111 3.47 3.47 38.28 3.85
901 988 2.285069 ACCGGTGCAGGGTGGATA 60.285 61.111 6.12 0.00 36.14 2.59
907 994 4.530857 GATCGGACCGGTGCAGGG 62.531 72.222 26.61 10.07 35.02 4.45
909 996 3.432051 GAGGATCGGACCGGTGCAG 62.432 68.421 26.61 17.97 28.76 4.41
910 997 3.458163 GAGGATCGGACCGGTGCA 61.458 66.667 26.61 13.45 28.76 4.57
950 1038 0.624254 CCCTTACCCTCAAACCTCCC 59.376 60.000 0.00 0.00 0.00 4.30
951 1039 0.624254 CCCCTTACCCTCAAACCTCC 59.376 60.000 0.00 0.00 0.00 4.30
952 1040 1.665137 TCCCCTTACCCTCAAACCTC 58.335 55.000 0.00 0.00 0.00 3.85
953 1041 2.143231 TTCCCCTTACCCTCAAACCT 57.857 50.000 0.00 0.00 0.00 3.50
954 1042 3.468071 AATTCCCCTTACCCTCAAACC 57.532 47.619 0.00 0.00 0.00 3.27
955 1043 3.442625 CGAAATTCCCCTTACCCTCAAAC 59.557 47.826 0.00 0.00 0.00 2.93
956 1044 3.074836 ACGAAATTCCCCTTACCCTCAAA 59.925 43.478 0.00 0.00 0.00 2.69
957 1045 2.645797 ACGAAATTCCCCTTACCCTCAA 59.354 45.455 0.00 0.00 0.00 3.02
958 1046 2.026636 CACGAAATTCCCCTTACCCTCA 60.027 50.000 0.00 0.00 0.00 3.86
959 1047 2.640184 CACGAAATTCCCCTTACCCTC 58.360 52.381 0.00 0.00 0.00 4.30
960 1048 1.340697 GCACGAAATTCCCCTTACCCT 60.341 52.381 0.00 0.00 0.00 4.34
1121 1245 1.488261 GGAACGGATTGTCGATCGGC 61.488 60.000 13.98 13.98 38.33 5.54
1136 1260 1.801178 CAAGAAACGGAGAGCAGGAAC 59.199 52.381 0.00 0.00 0.00 3.62
1143 1267 0.868406 GTGCACCAAGAAACGGAGAG 59.132 55.000 5.22 0.00 0.00 3.20
1160 1290 2.620112 CCTTGGCAGAGCAACGGTG 61.620 63.158 0.00 0.00 0.00 4.94
1183 1313 2.659610 GCGGCCACTCTCTCTGTT 59.340 61.111 2.24 0.00 0.00 3.16
1198 1328 3.274586 CGTCATCCTGCATGGGCG 61.275 66.667 0.00 0.00 45.35 6.13
1344 1474 2.052690 CGGCGAAGGAGAGGGAGAA 61.053 63.158 0.00 0.00 0.00 2.87
1380 1510 1.671901 GACGGGCAGAGGAGAAGAGG 61.672 65.000 0.00 0.00 0.00 3.69
1388 1518 1.139095 GTTAGACGACGGGCAGAGG 59.861 63.158 0.00 0.00 0.00 3.69
1392 1522 2.693762 CCGAGTTAGACGACGGGCA 61.694 63.158 0.00 0.00 38.48 5.36
1572 1703 2.456119 CGTCGATGTGCTGGAAGGC 61.456 63.158 0.00 0.00 0.00 4.35
1619 1750 9.832445 ATAAGAATGAATTACGTGTGTAGGAAT 57.168 29.630 0.00 0.00 0.00 3.01
1625 1756 8.547967 ACTGAATAAGAATGAATTACGTGTGT 57.452 30.769 0.00 0.00 0.00 3.72
1653 1784 8.360390 AGAACATCAGAAAATTTTCACCCTAAC 58.640 33.333 28.00 15.79 39.61 2.34
1659 1790 7.383300 CCCAGAAGAACATCAGAAAATTTTCAC 59.617 37.037 28.00 7.50 39.61 3.18
1681 1812 2.587194 CTGCGCCGAGAATCCCAG 60.587 66.667 4.18 0.00 0.00 4.45
1689 1820 3.642755 AGTTGAAACTGCGCCGAG 58.357 55.556 4.18 0.00 37.98 4.63
1966 2097 3.402681 CACATGCTCCCCGGGTCT 61.403 66.667 21.85 0.00 0.00 3.85
1973 2104 2.202987 CTCCTCGCACATGCTCCC 60.203 66.667 1.82 0.00 39.32 4.30
1979 2110 4.457496 CACCGCCTCCTCGCACAT 62.457 66.667 0.00 0.00 0.00 3.21
1995 2126 3.640407 GGTGGTGCAGCTCCTCCA 61.640 66.667 25.68 8.51 38.19 3.86
2172 2328 2.049063 GACCTCGCACACGCTCTT 60.049 61.111 0.00 0.00 39.84 2.85
2173 2329 3.274455 CTGACCTCGCACACGCTCT 62.274 63.158 0.00 0.00 39.84 4.09
2174 2330 2.807045 CTGACCTCGCACACGCTC 60.807 66.667 0.00 0.00 39.84 5.03
2175 2331 3.606662 ACTGACCTCGCACACGCT 61.607 61.111 0.00 0.00 39.84 5.07
2176 2332 3.406361 CACTGACCTCGCACACGC 61.406 66.667 0.00 0.00 39.84 5.34
2177 2333 2.734723 CCACTGACCTCGCACACG 60.735 66.667 0.00 0.00 42.01 4.49
2178 2334 0.814010 AAACCACTGACCTCGCACAC 60.814 55.000 0.00 0.00 0.00 3.82
2179 2335 0.813610 CAAACCACTGACCTCGCACA 60.814 55.000 0.00 0.00 0.00 4.57
2232 2394 3.999001 TGTACAAGTACGACACGAGAGAT 59.001 43.478 0.00 0.00 38.85 2.75
2264 2426 2.434359 GTTGCTCGAGGAACGGGG 60.434 66.667 30.05 0.00 43.48 5.73
2292 2462 1.927174 CAGAGGGATACGCTTTGAACG 59.073 52.381 0.00 0.00 31.87 3.95
2300 2470 1.204941 ACACAGTTCAGAGGGATACGC 59.795 52.381 0.00 0.00 37.60 4.42
2301 2471 3.512680 GAACACAGTTCAGAGGGATACG 58.487 50.000 5.09 0.00 37.60 3.06
2304 2474 2.304180 CAGGAACACAGTTCAGAGGGAT 59.696 50.000 11.51 0.00 0.00 3.85
2305 2475 1.694150 CAGGAACACAGTTCAGAGGGA 59.306 52.381 11.51 0.00 0.00 4.20
2308 2478 3.535561 ACAACAGGAACACAGTTCAGAG 58.464 45.455 11.51 3.78 0.00 3.35
2327 2497 9.889128 TCATTCATGTACTATCAAATTCAGACA 57.111 29.630 0.00 0.00 0.00 3.41
2356 2529 2.031944 GGTTCAGAAGTTCTTGTTCCGC 60.032 50.000 1.56 0.00 0.00 5.54
2421 2595 3.435566 ACGTAGTAGATTGCATGACGTG 58.564 45.455 0.00 0.00 41.94 4.49
2484 2658 5.994054 TCAGTGAACTTCTGAGAATCTTTGG 59.006 40.000 0.00 0.00 37.07 3.28
2535 2709 4.974645 TTTTCCTCTGCTAGAACTGGAA 57.025 40.909 0.00 0.00 28.02 3.53
2536 2710 4.532126 TGATTTTCCTCTGCTAGAACTGGA 59.468 41.667 0.00 0.00 0.00 3.86
2537 2711 4.836825 TGATTTTCCTCTGCTAGAACTGG 58.163 43.478 0.00 0.00 0.00 4.00
2538 2712 4.874966 CCTGATTTTCCTCTGCTAGAACTG 59.125 45.833 0.00 0.00 0.00 3.16
2579 2753 4.527509 TCTGTGTTCTGTGATCTTCCTC 57.472 45.455 0.00 0.00 0.00 3.71
2580 2754 5.486526 GAATCTGTGTTCTGTGATCTTCCT 58.513 41.667 0.00 0.00 0.00 3.36
2581 2755 4.328440 CGAATCTGTGTTCTGTGATCTTCC 59.672 45.833 0.00 0.00 0.00 3.46
2582 2756 4.926238 ACGAATCTGTGTTCTGTGATCTTC 59.074 41.667 0.00 0.00 0.00 2.87
2584 2758 4.240888 CACGAATCTGTGTTCTGTGATCT 58.759 43.478 0.00 0.00 36.07 2.75
2625 2838 2.857186 TTTACACCGGGGGTTTCTAC 57.143 50.000 7.51 0.00 31.02 2.59
2628 2841 3.575256 AGAAATTTTACACCGGGGGTTTC 59.425 43.478 7.51 4.81 31.02 2.78
2695 2908 3.537793 AAAGAAGAAGGCTTTTACGCG 57.462 42.857 3.53 3.53 33.61 6.01
2698 2911 6.584184 GCATGAGAAAAGAAGAAGGCTTTTAC 59.416 38.462 0.00 0.00 43.45 2.01
2739 2953 1.467374 GCCGTAAACCATGTGATGTGC 60.467 52.381 0.00 0.00 0.00 4.57
2759 2973 4.201950 GGTTGAAATCCATTCGAGTCATGG 60.202 45.833 8.11 8.11 42.51 3.66
2768 2982 6.659242 TGGAAAGAGTAGGTTGAAATCCATTC 59.341 38.462 0.00 0.00 38.60 2.67
2772 2986 7.110155 TGTATGGAAAGAGTAGGTTGAAATCC 58.890 38.462 0.00 0.00 0.00 3.01
2774 2988 6.599638 GCTGTATGGAAAGAGTAGGTTGAAAT 59.400 38.462 0.00 0.00 0.00 2.17
2829 3043 0.036388 TTGGCGCTCTCCTTTACCAG 60.036 55.000 7.64 0.00 0.00 4.00
2830 3044 0.398696 TTTGGCGCTCTCCTTTACCA 59.601 50.000 7.64 0.00 0.00 3.25
2838 3064 0.449388 CAGGTTCATTTGGCGCTCTC 59.551 55.000 7.64 0.00 0.00 3.20
2878 3113 3.696281 TGCATATTGATCTTTGCCGTG 57.304 42.857 0.00 0.00 34.20 4.94
2879 3114 4.675510 CTTTGCATATTGATCTTTGCCGT 58.324 39.130 0.00 0.00 34.20 5.68
2880 3115 3.488310 GCTTTGCATATTGATCTTTGCCG 59.512 43.478 0.00 0.00 34.20 5.69
2881 3116 4.435425 TGCTTTGCATATTGATCTTTGCC 58.565 39.130 0.00 0.00 31.71 4.52
2882 3117 6.411630 TTTGCTTTGCATATTGATCTTTGC 57.588 33.333 0.00 0.00 38.76 3.68
2964 3202 2.694628 TGAACACTGAAATTTGGCAGCT 59.305 40.909 0.00 0.00 35.57 4.24
2968 3206 6.200097 ACGTATTTTGAACACTGAAATTTGGC 59.800 34.615 0.00 0.00 0.00 4.52
2969 3207 7.306515 CCACGTATTTTGAACACTGAAATTTGG 60.307 37.037 0.00 0.00 0.00 3.28
2983 3222 3.339141 TGTATGCAGCCACGTATTTTGA 58.661 40.909 0.00 0.00 0.00 2.69
3020 3259 8.621286 ACTTACATAACATAAAGTAGGCATTGC 58.379 33.333 0.00 0.00 30.62 3.56
3032 3271 9.926158 TCGGAAACTTGTACTTACATAACATAA 57.074 29.630 0.00 0.00 35.89 1.90
3033 3272 9.357652 GTCGGAAACTTGTACTTACATAACATA 57.642 33.333 0.00 0.00 35.89 2.29
3034 3273 7.874016 TGTCGGAAACTTGTACTTACATAACAT 59.126 33.333 0.00 0.00 35.89 2.71
3035 3274 7.208777 TGTCGGAAACTTGTACTTACATAACA 58.791 34.615 0.00 0.00 35.89 2.41
3036 3275 7.383300 ACTGTCGGAAACTTGTACTTACATAAC 59.617 37.037 0.00 0.00 35.89 1.89
3037 3276 7.436118 ACTGTCGGAAACTTGTACTTACATAA 58.564 34.615 0.00 0.00 35.89 1.90
3038 3277 6.985117 ACTGTCGGAAACTTGTACTTACATA 58.015 36.000 0.00 0.00 35.89 2.29
3039 3278 5.850614 ACTGTCGGAAACTTGTACTTACAT 58.149 37.500 0.00 0.00 35.89 2.29
3040 3279 5.266733 ACTGTCGGAAACTTGTACTTACA 57.733 39.130 0.00 0.00 0.00 2.41
3041 3280 7.698836 TTAACTGTCGGAAACTTGTACTTAC 57.301 36.000 0.00 0.00 0.00 2.34
3042 3281 7.763528 TGTTTAACTGTCGGAAACTTGTACTTA 59.236 33.333 11.67 0.00 34.77 2.24
3043 3282 6.594937 TGTTTAACTGTCGGAAACTTGTACTT 59.405 34.615 11.67 0.00 34.77 2.24
3044 3283 6.108015 TGTTTAACTGTCGGAAACTTGTACT 58.892 36.000 11.67 0.00 34.77 2.73
3045 3284 6.348621 TGTTTAACTGTCGGAAACTTGTAC 57.651 37.500 11.67 0.00 34.77 2.90
3046 3285 8.659925 TTATGTTTAACTGTCGGAAACTTGTA 57.340 30.769 11.67 3.74 34.77 2.41
3047 3286 7.556733 TTATGTTTAACTGTCGGAAACTTGT 57.443 32.000 11.67 4.36 34.77 3.16
3048 3287 8.844441 TTTTATGTTTAACTGTCGGAAACTTG 57.156 30.769 11.67 0.00 34.77 3.16


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

AutoCloner maintained by Alex Coulton.