Multiple sequence alignment - TraesCS5B01G365400

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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 TraesCS5B01G365400 chr5B 100.000 4437 0 0 1 4437 544325672 544330108 0.000000e+00 8194.0
1 TraesCS5B01G365400 chr5B 93.939 99 4 2 3967 4063 650023919 650023821 9.940000e-32 148.0
2 TraesCS5B01G365400 chr5B 94.792 96 4 1 3962 4057 658145688 658145782 9.940000e-32 148.0
3 TraesCS5B01G365400 chr5D 93.408 3216 131 31 223 3408 446397358 446400522 0.000000e+00 4689.0
4 TraesCS5B01G365400 chr5D 85.143 700 47 36 3766 4434 446400522 446401195 0.000000e+00 664.0
5 TraesCS5B01G365400 chr5D 96.629 89 2 1 3967 4054 522112056 522112144 3.580000e-31 147.0
6 TraesCS5B01G365400 chr5A 92.827 2370 124 26 1509 3863 564072360 564074698 0.000000e+00 3393.0
7 TraesCS5B01G365400 chr5A 91.853 1522 81 21 223 1714 564070849 564072357 0.000000e+00 2084.0
8 TraesCS5B01G365400 chr5A 86.458 480 42 14 3966 4434 564075033 564075500 5.120000e-139 505.0
9 TraesCS5B01G365400 chr5A 91.667 48 4 0 1496 1543 564072317 564072364 2.860000e-07 67.6
10 TraesCS5B01G365400 chr3A 85.256 156 17 5 37 189 521573991 521573839 5.940000e-34 156.0
11 TraesCS5B01G365400 chr3A 84.112 107 13 4 91 194 631713118 631713013 2.820000e-17 100.0
12 TraesCS5B01G365400 chr2A 85.161 155 19 3 34 186 16067468 16067620 5.940000e-34 156.0
13 TraesCS5B01G365400 chr7D 94.000 100 2 2 3968 4067 535550405 535550310 9.940000e-32 148.0
14 TraesCS5B01G365400 chr7D 95.604 91 4 0 3964 4054 599463144 599463234 3.580000e-31 147.0
15 TraesCS5B01G365400 chr1D 96.629 89 2 1 3967 4054 342187344 342187432 3.580000e-31 147.0
16 TraesCS5B01G365400 chr7B 98.780 82 0 1 3974 4054 678291170 678291251 1.290000e-30 145.0
17 TraesCS5B01G365400 chr4B 84.507 142 18 3 34 173 545148055 545148194 2.150000e-28 137.0
18 TraesCS5B01G365400 chr2D 89.423 104 9 2 89 190 558190084 558189981 3.600000e-26 130.0
19 TraesCS5B01G365400 chr1A 84.762 105 14 2 34 137 486600129 486600026 2.180000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G365400 chr5B 544325672 544330108 4436 False 8194.0 8194 100.00000 1 4437 1 chr5B.!!$F1 4436
1 TraesCS5B01G365400 chr5D 446397358 446401195 3837 False 2676.5 4689 89.27550 223 4434 2 chr5D.!!$F2 4211
2 TraesCS5B01G365400 chr5A 564070849 564075500 4651 False 1512.4 3393 90.70125 223 4434 4 chr5A.!!$F1 4211

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
595 596 0.174845 TGTTAAGCCGAGGATCCGTG 59.825 55.0 5.98 2.41 0.00 4.94 F
806 815 0.175760 TAGCACGAATCCCAGACAGC 59.824 55.0 0.00 0.00 0.00 4.40 F
1317 1344 0.542333 GGTAGGTCCTTCCCTGCTTC 59.458 60.0 3.05 0.00 37.38 3.86 F
3132 3400 0.031178 ACACCGTCACGTCTTACACC 59.969 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2660 0.176680 CTCGATGGCCAGCACTAAGT 59.823 55.000 22.95 0.0 0.00 2.24 R
2488 2740 2.740714 GCGTGATCGACAGGGTTGC 61.741 63.158 0.00 0.0 39.71 4.17 R
3137 3405 0.485543 TCGGGTATATCTGCAGGGGA 59.514 55.000 15.13 0.0 0.00 4.81 R
4123 4647 1.627864 CCCGTTTTGAAGGTCCCATT 58.372 50.000 0.00 0.0 0.00 3.16 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
39 40 6.873076 TGAAATACATTGACATTTTTGGAGGC 59.127 34.615 0.00 0.00 0.00 4.70
40 41 3.683365 ACATTGACATTTTTGGAGGCC 57.317 42.857 0.00 0.00 0.00 5.19
41 42 3.242011 ACATTGACATTTTTGGAGGCCT 58.758 40.909 3.86 3.86 0.00 5.19
42 43 3.259123 ACATTGACATTTTTGGAGGCCTC 59.741 43.478 25.59 25.59 0.00 4.70
55 56 3.339253 GAGGCCTCCAAATGCAAAATT 57.661 42.857 23.19 0.00 0.00 1.82
56 57 3.264947 GAGGCCTCCAAATGCAAAATTC 58.735 45.455 23.19 0.00 0.00 2.17
57 58 2.638855 AGGCCTCCAAATGCAAAATTCA 59.361 40.909 0.00 0.00 0.00 2.57
58 59 3.072768 AGGCCTCCAAATGCAAAATTCAA 59.927 39.130 0.00 0.00 0.00 2.69
59 60 3.819902 GGCCTCCAAATGCAAAATTCAAA 59.180 39.130 0.00 0.00 0.00 2.69
60 61 4.277921 GGCCTCCAAATGCAAAATTCAAAA 59.722 37.500 0.00 0.00 0.00 2.44
61 62 5.047872 GGCCTCCAAATGCAAAATTCAAAAT 60.048 36.000 0.00 0.00 0.00 1.82
62 63 6.448852 GCCTCCAAATGCAAAATTCAAAATT 58.551 32.000 0.00 0.00 0.00 1.82
63 64 6.583427 GCCTCCAAATGCAAAATTCAAAATTC 59.417 34.615 0.00 0.00 0.00 2.17
64 65 7.649973 CCTCCAAATGCAAAATTCAAAATTCA 58.350 30.769 0.00 0.00 0.00 2.57
65 66 8.301002 CCTCCAAATGCAAAATTCAAAATTCAT 58.699 29.630 0.00 0.00 0.00 2.57
66 67 9.123709 CTCCAAATGCAAAATTCAAAATTCATG 57.876 29.630 0.00 0.00 0.00 3.07
67 68 8.847196 TCCAAATGCAAAATTCAAAATTCATGA 58.153 25.926 0.00 0.00 0.00 3.07
68 69 9.464714 CCAAATGCAAAATTCAAAATTCATGAA 57.535 25.926 11.26 11.26 40.76 2.57
88 89 8.906867 TCATGAAAATTCTCATCCTTACAATCC 58.093 33.333 0.00 0.00 33.66 3.01
89 90 8.689061 CATGAAAATTCTCATCCTTACAATCCA 58.311 33.333 0.00 0.00 33.66 3.41
90 91 8.648698 TGAAAATTCTCATCCTTACAATCCAA 57.351 30.769 0.00 0.00 0.00 3.53
91 92 9.087871 TGAAAATTCTCATCCTTACAATCCAAA 57.912 29.630 0.00 0.00 0.00 3.28
92 93 9.927668 GAAAATTCTCATCCTTACAATCCAAAA 57.072 29.630 0.00 0.00 0.00 2.44
132 133 9.918630 AAACAAATATAGATGAAGGCATAATGC 57.081 29.630 0.00 0.00 44.08 3.56
171 172 7.123160 TTCATGATGAAATACGTTGAAACGA 57.877 32.000 21.38 6.42 43.16 3.85
172 173 7.233689 TTCATGATGAAATACGTTGAAACGAG 58.766 34.615 21.38 0.00 43.16 4.18
173 174 7.623297 TTCATGATGAAATACGTTGAAACGAGG 60.623 37.037 21.38 0.00 43.16 4.63
182 183 3.907894 GTTGAAACGAGGGTTATGCAA 57.092 42.857 0.00 0.00 34.62 4.08
183 184 4.231718 GTTGAAACGAGGGTTATGCAAA 57.768 40.909 0.00 0.00 34.62 3.68
184 185 4.612943 GTTGAAACGAGGGTTATGCAAAA 58.387 39.130 0.00 0.00 34.62 2.44
185 186 4.920640 TGAAACGAGGGTTATGCAAAAA 57.079 36.364 0.00 0.00 34.62 1.94
186 187 4.865776 TGAAACGAGGGTTATGCAAAAAG 58.134 39.130 0.00 0.00 34.62 2.27
187 188 4.580995 TGAAACGAGGGTTATGCAAAAAGA 59.419 37.500 0.00 0.00 34.62 2.52
188 189 5.067936 TGAAACGAGGGTTATGCAAAAAGAA 59.932 36.000 0.00 0.00 34.62 2.52
189 190 5.523438 AACGAGGGTTATGCAAAAAGAAA 57.477 34.783 0.00 0.00 33.72 2.52
190 191 5.722021 ACGAGGGTTATGCAAAAAGAAAT 57.278 34.783 0.00 0.00 0.00 2.17
191 192 6.827586 ACGAGGGTTATGCAAAAAGAAATA 57.172 33.333 0.00 0.00 0.00 1.40
192 193 7.404671 ACGAGGGTTATGCAAAAAGAAATAT 57.595 32.000 0.00 0.00 0.00 1.28
193 194 7.257722 ACGAGGGTTATGCAAAAAGAAATATG 58.742 34.615 0.00 0.00 0.00 1.78
194 195 7.122055 ACGAGGGTTATGCAAAAAGAAATATGA 59.878 33.333 0.00 0.00 0.00 2.15
195 196 8.137437 CGAGGGTTATGCAAAAAGAAATATGAT 58.863 33.333 0.00 0.00 0.00 2.45
198 199 9.696917 GGGTTATGCAAAAAGAAATATGATAGG 57.303 33.333 0.00 0.00 0.00 2.57
204 205 9.905713 TGCAAAAAGAAATATGATAGGAGTACT 57.094 29.630 0.00 0.00 0.00 2.73
215 216 9.875708 ATATGATAGGAGTACTATTCATCCCTC 57.124 37.037 0.00 0.00 42.43 4.30
216 217 6.494952 TGATAGGAGTACTATTCATCCCTCC 58.505 44.000 0.00 0.00 42.43 4.30
217 218 4.834406 AGGAGTACTATTCATCCCTCCA 57.166 45.455 0.00 0.00 40.74 3.86
218 219 4.746466 AGGAGTACTATTCATCCCTCCAG 58.254 47.826 0.00 0.00 40.74 3.86
219 220 4.420552 AGGAGTACTATTCATCCCTCCAGA 59.579 45.833 0.00 0.00 40.74 3.86
220 221 4.525100 GGAGTACTATTCATCCCTCCAGAC 59.475 50.000 0.00 0.00 38.65 3.51
221 222 4.484912 AGTACTATTCATCCCTCCAGACC 58.515 47.826 0.00 0.00 0.00 3.85
300 301 4.985044 TTCTTTCCATTTTCGTCGTCTC 57.015 40.909 0.00 0.00 0.00 3.36
301 302 3.985008 TCTTTCCATTTTCGTCGTCTCA 58.015 40.909 0.00 0.00 0.00 3.27
302 303 3.987868 TCTTTCCATTTTCGTCGTCTCAG 59.012 43.478 0.00 0.00 0.00 3.35
303 304 3.653539 TTCCATTTTCGTCGTCTCAGA 57.346 42.857 0.00 0.00 0.00 3.27
304 305 3.653539 TCCATTTTCGTCGTCTCAGAA 57.346 42.857 0.00 0.00 0.00 3.02
305 306 3.985008 TCCATTTTCGTCGTCTCAGAAA 58.015 40.909 0.00 0.00 32.76 2.52
334 335 0.806241 GGAAAAATTACGAGCCGCCA 59.194 50.000 0.00 0.00 0.00 5.69
379 380 4.452733 CCCGACGACTTCCTGGCC 62.453 72.222 0.00 0.00 0.00 5.36
380 381 4.796231 CCGACGACTTCCTGGCCG 62.796 72.222 0.00 0.00 0.00 6.13
456 457 4.084147 CCTCCACCCCTCCCCGTA 62.084 72.222 0.00 0.00 0.00 4.02
506 507 1.513586 CGTCCTCGTAACACGCTCC 60.514 63.158 0.00 0.00 42.21 4.70
580 581 0.739462 CCTGAATGCGCGACCTGTTA 60.739 55.000 12.10 0.00 0.00 2.41
595 596 0.174845 TGTTAAGCCGAGGATCCGTG 59.825 55.000 5.98 2.41 0.00 4.94
604 605 3.399181 GGATCCGTGGCCCAGACA 61.399 66.667 0.00 0.00 0.00 3.41
609 610 2.124983 CGTGGCCCAGACATGAGG 60.125 66.667 0.00 0.00 26.80 3.86
715 716 4.553330 AATCGTTGGGTTAGTCTGTCAT 57.447 40.909 0.00 0.00 0.00 3.06
723 724 4.042809 TGGGTTAGTCTGTCATCCATTGTT 59.957 41.667 0.00 0.00 0.00 2.83
729 730 5.006386 AGTCTGTCATCCATTGTTTTCCTC 58.994 41.667 0.00 0.00 0.00 3.71
733 734 3.091545 TCATCCATTGTTTTCCTCTGGC 58.908 45.455 0.00 0.00 0.00 4.85
735 736 2.238521 TCCATTGTTTTCCTCTGGCAC 58.761 47.619 0.00 0.00 0.00 5.01
740 746 3.569194 TGTTTTCCTCTGGCACTACAA 57.431 42.857 0.00 0.00 0.00 2.41
741 747 3.211045 TGTTTTCCTCTGGCACTACAAC 58.789 45.455 0.00 0.00 0.00 3.32
750 759 3.510360 TCTGGCACTACAACTTAGGTCTC 59.490 47.826 0.00 0.00 0.00 3.36
766 775 3.446873 AGGTCTCTATCTGTGTTGAGCAG 59.553 47.826 0.00 0.00 35.43 4.24
787 796 1.490574 GGGGCTGTCTACACTCTGAT 58.509 55.000 0.00 0.00 0.00 2.90
792 801 3.490078 GGCTGTCTACACTCTGATAGCAC 60.490 52.174 12.28 1.11 45.20 4.40
803 812 2.362397 TCTGATAGCACGAATCCCAGAC 59.638 50.000 0.00 0.00 0.00 3.51
806 815 0.175760 TAGCACGAATCCCAGACAGC 59.824 55.000 0.00 0.00 0.00 4.40
813 822 1.277557 GAATCCCAGACAGCAGAGTGT 59.722 52.381 0.00 0.00 0.00 3.55
822 831 0.664761 CAGCAGAGTGTTGGTTGGTG 59.335 55.000 0.00 0.00 33.46 4.17
846 855 5.594926 CTGTCTGGAATTTGCTGTCTTTTT 58.405 37.500 0.00 0.00 0.00 1.94
860 869 7.028962 TGCTGTCTTTTTGGATTATCAAATCG 58.971 34.615 0.00 0.00 42.16 3.34
863 872 8.292444 TGTCTTTTTGGATTATCAAATCGGAT 57.708 30.769 0.00 0.00 42.16 4.18
879 888 9.502091 TCAAATCGGATAAATATGGTCCTTAAG 57.498 33.333 0.00 0.00 0.00 1.85
910 922 7.554476 AGCTTATTTTTACTTCTGATGGAGGAC 59.446 37.037 0.00 0.00 0.00 3.85
918 930 0.618680 CTGATGGAGGACCCCAGACA 60.619 60.000 7.63 8.72 39.97 3.41
936 948 4.336433 CAGACAGCACGAATCCCATTTTAT 59.664 41.667 0.00 0.00 0.00 1.40
942 954 5.043248 GCACGAATCCCATTTTATTTCTGG 58.957 41.667 0.00 0.00 0.00 3.86
943 955 5.043248 CACGAATCCCATTTTATTTCTGGC 58.957 41.667 0.00 0.00 0.00 4.85
946 958 2.451490 TCCCATTTTATTTCTGGCGCA 58.549 42.857 10.83 0.00 0.00 6.09
947 959 2.828520 TCCCATTTTATTTCTGGCGCAA 59.171 40.909 10.83 0.00 0.00 4.85
948 960 3.259374 TCCCATTTTATTTCTGGCGCAAA 59.741 39.130 10.83 0.85 0.00 3.68
949 961 3.999663 CCCATTTTATTTCTGGCGCAAAA 59.000 39.130 10.83 5.83 0.00 2.44
958 985 2.297701 TCTGGCGCAAAAAGACTTCTT 58.702 42.857 10.83 0.00 37.91 2.52
992 1019 4.562394 GCATGATAACAAACATGAAACCGG 59.438 41.667 0.00 0.00 44.28 5.28
1086 1113 1.178534 CGCTTGTGTCCATGGGGTTT 61.179 55.000 13.02 0.00 34.93 3.27
1254 1281 6.586082 GTGTTGTATTTTTAGGGATGCTTGTG 59.414 38.462 0.00 0.00 0.00 3.33
1266 1293 2.101700 GCTTGTGGGAGCATACTGC 58.898 57.895 0.00 0.00 45.46 4.40
1290 1317 3.370209 GGGGCTTAGTTTCGGACAACTAT 60.370 47.826 11.10 0.00 38.71 2.12
1317 1344 0.542333 GGTAGGTCCTTCCCTGCTTC 59.458 60.000 3.05 0.00 37.38 3.86
1591 1836 2.000447 GGCGCGATAACTCTCAAGTTT 59.000 47.619 12.10 0.00 43.28 2.66
1598 1843 5.680151 GCGATAACTCTCAAGTTTAGAGCCT 60.680 44.000 13.00 4.70 43.28 4.58
1635 1887 2.777692 TGGGATGTAGGTTGGGAATCTC 59.222 50.000 0.00 0.00 0.00 2.75
1653 1905 6.550108 GGAATCTCCATACCAGACTAGTTACA 59.450 42.308 0.00 0.00 36.28 2.41
2138 2390 5.156355 GCACAATAGATCAAACCACACAAG 58.844 41.667 0.00 0.00 0.00 3.16
2408 2660 0.624254 TAGCTCTCCCTTCTGGACGA 59.376 55.000 0.00 0.00 38.61 4.20
2453 2705 2.997899 CCACGAGATGGCAGATTCC 58.002 57.895 0.00 0.00 43.24 3.01
2488 2740 4.557496 GCAGTTGGTTTCAGCTAGGAAAAG 60.557 45.833 1.09 0.00 38.41 2.27
2692 2944 2.615869 CTCAGAAGGAGCAGTAACAGC 58.384 52.381 0.00 0.00 36.69 4.40
2787 3039 5.163374 GCTTTCTCCTATGGCCAATCATTTT 60.163 40.000 10.96 0.00 0.00 1.82
2788 3040 6.631088 GCTTTCTCCTATGGCCAATCATTTTT 60.631 38.462 10.96 0.00 0.00 1.94
2789 3041 6.469782 TTCTCCTATGGCCAATCATTTTTC 57.530 37.500 10.96 0.00 0.00 2.29
2790 3042 4.895297 TCTCCTATGGCCAATCATTTTTCC 59.105 41.667 10.96 0.00 0.00 3.13
2791 3043 4.882559 TCCTATGGCCAATCATTTTTCCT 58.117 39.130 10.96 0.00 0.00 3.36
2792 3044 5.279685 TCCTATGGCCAATCATTTTTCCTT 58.720 37.500 10.96 0.00 0.00 3.36
2793 3045 5.725822 TCCTATGGCCAATCATTTTTCCTTT 59.274 36.000 10.96 0.00 0.00 3.11
2794 3046 6.900186 TCCTATGGCCAATCATTTTTCCTTTA 59.100 34.615 10.96 0.00 0.00 1.85
2795 3047 7.401493 TCCTATGGCCAATCATTTTTCCTTTAA 59.599 33.333 10.96 0.00 0.00 1.52
2796 3048 7.495606 CCTATGGCCAATCATTTTTCCTTTAAC 59.504 37.037 10.96 0.00 0.00 2.01
2797 3049 5.555966 TGGCCAATCATTTTTCCTTTAACC 58.444 37.500 0.61 0.00 0.00 2.85
2798 3050 5.309282 TGGCCAATCATTTTTCCTTTAACCT 59.691 36.000 0.61 0.00 0.00 3.50
2799 3051 6.498651 TGGCCAATCATTTTTCCTTTAACCTA 59.501 34.615 0.61 0.00 0.00 3.08
2800 3052 7.181845 TGGCCAATCATTTTTCCTTTAACCTAT 59.818 33.333 0.61 0.00 0.00 2.57
2801 3053 7.710907 GGCCAATCATTTTTCCTTTAACCTATC 59.289 37.037 0.00 0.00 0.00 2.08
2802 3054 7.710907 GCCAATCATTTTTCCTTTAACCTATCC 59.289 37.037 0.00 0.00 0.00 2.59
2827 3095 5.471424 TCCCAGAGTATCCTTCTCATTCAT 58.529 41.667 0.00 0.00 33.66 2.57
2828 3096 6.624297 TCCCAGAGTATCCTTCTCATTCATA 58.376 40.000 0.00 0.00 33.66 2.15
2905 3173 1.372997 GTTCGGACGCAAGCTCTCA 60.373 57.895 0.00 0.00 45.62 3.27
2981 3249 1.601419 GACGGAATCCCTGACGACCA 61.601 60.000 0.00 0.00 0.00 4.02
2992 3260 2.289694 CCTGACGACCATCTTCCTGTTT 60.290 50.000 0.00 0.00 0.00 2.83
3028 3296 2.125552 TCCGCCAGCTTCATCGTG 60.126 61.111 0.00 0.00 0.00 4.35
3056 3324 2.459202 CTACGCCCCCGAGGTTTGTT 62.459 60.000 0.00 0.00 38.26 2.83
3065 3333 1.135315 CCGAGGTTTGTTCATGCCATG 60.135 52.381 0.00 0.00 0.00 3.66
3067 3335 1.895131 GAGGTTTGTTCATGCCATGGT 59.105 47.619 14.67 0.00 0.00 3.55
3072 3340 4.096382 GGTTTGTTCATGCCATGGTAGTAG 59.904 45.833 14.67 3.47 0.00 2.57
3073 3341 4.568072 TTGTTCATGCCATGGTAGTAGT 57.432 40.909 14.67 0.00 0.00 2.73
3074 3342 3.872696 TGTTCATGCCATGGTAGTAGTG 58.127 45.455 14.67 4.09 0.00 2.74
3075 3343 2.614057 GTTCATGCCATGGTAGTAGTGC 59.386 50.000 14.67 0.00 0.00 4.40
3076 3344 1.140852 TCATGCCATGGTAGTAGTGCC 59.859 52.381 14.67 0.00 0.00 5.01
3077 3345 0.474184 ATGCCATGGTAGTAGTGCCC 59.526 55.000 14.67 0.00 0.00 5.36
3078 3346 0.620410 TGCCATGGTAGTAGTGCCCT 60.620 55.000 14.67 0.00 0.00 5.19
3079 3347 0.106894 GCCATGGTAGTAGTGCCCTC 59.893 60.000 14.67 0.00 0.00 4.30
3080 3348 1.794714 CCATGGTAGTAGTGCCCTCT 58.205 55.000 2.57 0.00 0.00 3.69
3081 3349 2.958818 CCATGGTAGTAGTGCCCTCTA 58.041 52.381 2.57 0.00 0.00 2.43
3082 3350 3.305720 CCATGGTAGTAGTGCCCTCTAA 58.694 50.000 2.57 0.00 0.00 2.10
3083 3351 3.069729 CCATGGTAGTAGTGCCCTCTAAC 59.930 52.174 2.57 0.00 0.00 2.34
3088 3356 3.459710 AGTAGTGCCCTCTAACTCTGT 57.540 47.619 0.00 0.00 0.00 3.41
3093 3361 4.895961 AGTGCCCTCTAACTCTGTTAAAC 58.104 43.478 0.00 0.00 0.00 2.01
3121 3389 2.462889 GTCAAACGTCTTACACCGTCA 58.537 47.619 0.00 0.00 36.04 4.35
3123 3391 1.188573 CAAACGTCTTACACCGTCACG 59.811 52.381 0.00 0.00 36.04 4.35
3127 3395 1.334419 CGTCTTACACCGTCACGTCTT 60.334 52.381 0.00 0.00 0.00 3.01
3128 3396 2.096268 CGTCTTACACCGTCACGTCTTA 60.096 50.000 0.00 0.00 0.00 2.10
3129 3397 3.229552 GTCTTACACCGTCACGTCTTAC 58.770 50.000 0.00 0.00 0.00 2.34
3130 3398 2.877786 TCTTACACCGTCACGTCTTACA 59.122 45.455 0.00 0.00 0.00 2.41
3131 3399 2.686558 TACACCGTCACGTCTTACAC 57.313 50.000 0.00 0.00 0.00 2.90
3132 3400 0.031178 ACACCGTCACGTCTTACACC 59.969 55.000 0.00 0.00 0.00 4.16
3133 3401 1.000233 CACCGTCACGTCTTACACCG 61.000 60.000 0.00 0.00 0.00 4.94
3134 3402 1.283793 CCGTCACGTCTTACACCGT 59.716 57.895 0.00 0.00 37.90 4.83
3135 3403 0.727122 CCGTCACGTCTTACACCGTC 60.727 60.000 0.00 0.00 34.59 4.79
3136 3404 1.056464 CGTCACGTCTTACACCGTCG 61.056 60.000 0.00 0.00 34.59 5.12
3137 3405 0.040958 GTCACGTCTTACACCGTCGT 60.041 55.000 0.00 0.00 34.59 4.34
3138 3406 0.235665 TCACGTCTTACACCGTCGTC 59.764 55.000 0.00 0.00 34.59 4.20
3139 3407 0.727122 CACGTCTTACACCGTCGTCC 60.727 60.000 0.00 0.00 34.59 4.79
3140 3408 1.154150 CGTCTTACACCGTCGTCCC 60.154 63.158 0.00 0.00 0.00 4.46
3141 3409 1.213799 GTCTTACACCGTCGTCCCC 59.786 63.158 0.00 0.00 0.00 4.81
3399 3667 1.203052 CCACCTGACAATGACATTGCC 59.797 52.381 24.85 16.59 43.98 4.52
3408 3676 3.437795 GACATTGCCGCAGCTGCT 61.438 61.111 34.22 15.66 40.80 4.24
3414 3685 4.261781 GCCGCAGCTGCTATTGCC 62.262 66.667 34.22 13.16 39.32 4.52
3420 3691 2.711924 GCTGCTATTGCCGCTGTC 59.288 61.111 8.19 0.00 44.32 3.51
3421 3692 3.009140 CTGCTATTGCCGCTGTCG 58.991 61.111 0.00 0.00 38.71 4.35
3433 3704 0.872021 CGCTGTCGGCATTAGACTCC 60.872 60.000 4.16 0.00 41.91 3.85
3434 3705 0.461961 GCTGTCGGCATTAGACTCCT 59.538 55.000 0.00 0.00 41.35 3.69
3435 3706 1.804372 GCTGTCGGCATTAGACTCCTG 60.804 57.143 0.00 0.00 41.35 3.86
3463 3734 2.744243 GGATCCTGCAGAGCTGGCT 61.744 63.158 17.39 0.00 45.32 4.75
3471 3742 2.071262 CAGAGCTGGCTCCAGGGAT 61.071 63.158 17.60 0.00 43.70 3.85
3489 3760 1.468914 GATGGAAGCCGTTGAGTTTCC 59.531 52.381 0.70 0.70 39.59 3.13
3496 3767 2.370849 AGCCGTTGAGTTTCCTTCCTTA 59.629 45.455 0.00 0.00 0.00 2.69
3565 3836 7.680739 AGAGAATAGAAAGGGAAGGAGTAAAGT 59.319 37.037 0.00 0.00 0.00 2.66
3574 3845 5.012768 AGGGAAGGAGTAAAGTTGATTTCGA 59.987 40.000 0.00 0.00 32.01 3.71
3587 3859 5.180117 AGTTGATTTCGAGTTCTGGATGTTG 59.820 40.000 0.00 0.00 0.00 3.33
3592 3864 3.130633 TCGAGTTCTGGATGTTGTTGTG 58.869 45.455 0.00 0.00 0.00 3.33
3600 3872 5.380900 TCTGGATGTTGTTGTGGAATTACA 58.619 37.500 0.00 0.00 0.00 2.41
3608 3880 5.508200 TGTTGTGGAATTACACTGGTTTC 57.492 39.130 21.32 6.47 41.84 2.78
3609 3881 4.950475 TGTTGTGGAATTACACTGGTTTCA 59.050 37.500 21.32 8.66 41.84 2.69
3610 3882 5.067153 TGTTGTGGAATTACACTGGTTTCAG 59.933 40.000 21.32 0.00 46.10 3.02
3625 3902 7.859613 CTGGTTTCAGTAGATGATATGTACG 57.140 40.000 0.00 0.00 37.89 3.67
3641 3918 9.981114 TGATATGTACGATGATATTGTGACTTT 57.019 29.630 0.00 0.00 0.00 2.66
3651 3928 3.502123 ATTGTGACTTTTTCGAGGGGA 57.498 42.857 0.00 0.00 0.00 4.81
3653 3930 3.284793 TGTGACTTTTTCGAGGGGAAA 57.715 42.857 0.00 0.00 42.75 3.13
3667 3944 4.448210 GAGGGGAAAATACAACGCTGATA 58.552 43.478 0.00 0.00 0.00 2.15
3670 3947 5.531287 AGGGGAAAATACAACGCTGATAATC 59.469 40.000 0.00 0.00 0.00 1.75
3673 3950 6.260050 GGGAAAATACAACGCTGATAATCTGA 59.740 38.462 0.00 0.00 0.00 3.27
3677 3954 9.507280 AAAATACAACGCTGATAATCTGAAATG 57.493 29.630 0.00 0.00 0.00 2.32
3686 3963 7.029563 GCTGATAATCTGAAATGTCCGTTTTT 58.970 34.615 0.00 0.00 0.00 1.94
3687 3964 7.008628 GCTGATAATCTGAAATGTCCGTTTTTG 59.991 37.037 0.00 0.00 0.00 2.44
3689 3966 4.582701 ATCTGAAATGTCCGTTTTTGCA 57.417 36.364 0.00 0.00 0.00 4.08
3690 3967 3.701241 TCTGAAATGTCCGTTTTTGCAC 58.299 40.909 0.00 0.00 0.00 4.57
3691 3968 2.455032 TGAAATGTCCGTTTTTGCACG 58.545 42.857 0.00 0.00 40.02 5.34
3692 3969 1.189227 GAAATGTCCGTTTTTGCACGC 59.811 47.619 0.00 0.00 38.93 5.34
3693 3970 0.932585 AATGTCCGTTTTTGCACGCG 60.933 50.000 3.53 3.53 38.93 6.01
3694 3971 2.724358 GTCCGTTTTTGCACGCGG 60.724 61.111 12.47 10.12 44.95 6.46
3695 3972 3.203412 TCCGTTTTTGCACGCGGT 61.203 55.556 12.47 0.00 44.07 5.68
3705 3982 2.945984 CACGCGGTCTGCATTTGT 59.054 55.556 12.47 0.00 46.97 2.83
3752 4029 6.983307 TGCTTCATCTAGCAGAGAAATTAGTC 59.017 38.462 0.00 0.00 45.72 2.59
3774 4052 5.125097 GTCTCTGCATTTTGTCCATCAATCT 59.875 40.000 0.00 0.00 35.84 2.40
3775 4053 5.124936 TCTCTGCATTTTGTCCATCAATCTG 59.875 40.000 0.00 0.00 35.84 2.90
3778 4056 3.615496 GCATTTTGTCCATCAATCTGTGC 59.385 43.478 0.00 0.00 35.84 4.57
3799 4077 8.114331 TGTGCATTCCTCCATTATCATAATTC 57.886 34.615 0.00 0.00 0.00 2.17
3810 4088 7.389884 TCCATTATCATAATTCTTGCTCTCAGC 59.610 37.037 0.00 0.00 42.82 4.26
3851 4129 1.342374 TGCTCTCTGACTCCTGCCATA 60.342 52.381 0.00 0.00 0.00 2.74
3866 4144 4.141756 CCTGCCATATGATGTATCTCTCCC 60.142 50.000 3.65 0.00 0.00 4.30
3966 4468 7.615403 AGAGAATGTTGCATTTCTACAGTAGA 58.385 34.615 6.15 6.15 34.15 2.59
4058 4578 2.169352 ACCTAGACTACGACGGAGCTTA 59.831 50.000 7.09 0.00 0.00 3.09
4064 4584 3.966154 ACTACGACGGAGCTTATTGATG 58.034 45.455 7.09 0.00 0.00 3.07
4065 4585 2.225068 ACGACGGAGCTTATTGATGG 57.775 50.000 0.00 0.00 0.00 3.51
4073 4593 5.070446 ACGGAGCTTATTGATGGTAATCTGA 59.930 40.000 0.00 0.00 33.61 3.27
4075 4595 6.517362 CGGAGCTTATTGATGGTAATCTGAGA 60.517 42.308 0.00 0.00 33.61 3.27
4082 4602 9.716531 TTATTGATGGTAATCTGAGATAGCTTG 57.283 33.333 0.00 0.00 33.61 4.01
4084 4604 6.753180 TGATGGTAATCTGAGATAGCTTGTC 58.247 40.000 0.00 0.00 33.61 3.18
4099 4619 3.197766 AGCTTGTCTATCGATTGGACCAA 59.802 43.478 20.70 9.92 0.00 3.67
4141 4669 2.029380 GGAAATGGGACCTTCAAAACGG 60.029 50.000 0.00 0.00 0.00 4.44
4223 4754 3.104512 CCCTCCCAATTTTAGAAACCCC 58.895 50.000 0.00 0.00 0.00 4.95
4238 4769 2.442643 CCCCATCCACATGCCCAC 60.443 66.667 0.00 0.00 0.00 4.61
4239 4770 2.359797 CCCATCCACATGCCCACA 59.640 61.111 0.00 0.00 0.00 4.17
4251 4801 4.135153 CCCACACGCGAGAGGAGG 62.135 72.222 20.45 10.92 0.00 4.30
4276 4826 4.765970 TCCTCCTGCATGCCCCCT 62.766 66.667 16.68 0.00 0.00 4.79
4303 4853 4.148825 CCCTCCCTCGCTTGGTCG 62.149 72.222 0.00 0.00 0.00 4.79
4304 4854 3.382832 CCTCCCTCGCTTGGTCGT 61.383 66.667 0.00 0.00 0.00 4.34
4305 4855 2.182030 CTCCCTCGCTTGGTCGTC 59.818 66.667 0.00 0.00 0.00 4.20
4434 4984 1.719117 GACGGTGAGCGAGAGAGAG 59.281 63.158 12.27 0.00 0.00 3.20
4435 4985 0.741574 GACGGTGAGCGAGAGAGAGA 60.742 60.000 12.27 0.00 0.00 3.10
4436 4986 0.107410 ACGGTGAGCGAGAGAGAGAT 60.107 55.000 12.27 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.550196 GCCTCCAAAAATGTCAATGTATTTCAT 59.450 33.333 0.00 0.00 38.57 2.57
14 15 6.873076 GCCTCCAAAAATGTCAATGTATTTCA 59.127 34.615 0.00 0.00 0.00 2.69
15 16 6.313658 GGCCTCCAAAAATGTCAATGTATTTC 59.686 38.462 0.00 0.00 0.00 2.17
16 17 6.013466 AGGCCTCCAAAAATGTCAATGTATTT 60.013 34.615 0.00 0.00 0.00 1.40
17 18 5.484998 AGGCCTCCAAAAATGTCAATGTATT 59.515 36.000 0.00 0.00 0.00 1.89
18 19 5.025453 AGGCCTCCAAAAATGTCAATGTAT 58.975 37.500 0.00 0.00 0.00 2.29
19 20 4.415596 AGGCCTCCAAAAATGTCAATGTA 58.584 39.130 0.00 0.00 0.00 2.29
20 21 3.242011 AGGCCTCCAAAAATGTCAATGT 58.758 40.909 0.00 0.00 0.00 2.71
21 22 3.853475 GAGGCCTCCAAAAATGTCAATG 58.147 45.455 23.19 0.00 0.00 2.82
35 36 3.264947 GAATTTTGCATTTGGAGGCCTC 58.735 45.455 25.59 25.59 0.00 4.70
36 37 2.638855 TGAATTTTGCATTTGGAGGCCT 59.361 40.909 3.86 3.86 0.00 5.19
37 38 3.056588 TGAATTTTGCATTTGGAGGCC 57.943 42.857 0.00 0.00 0.00 5.19
38 39 5.435820 TTTTGAATTTTGCATTTGGAGGC 57.564 34.783 0.00 0.00 0.00 4.70
39 40 7.649973 TGAATTTTGAATTTTGCATTTGGAGG 58.350 30.769 0.00 0.00 0.00 4.30
40 41 9.123709 CATGAATTTTGAATTTTGCATTTGGAG 57.876 29.630 0.00 0.00 0.00 3.86
41 42 8.847196 TCATGAATTTTGAATTTTGCATTTGGA 58.153 25.926 0.00 0.00 0.00 3.53
42 43 9.464714 TTCATGAATTTTGAATTTTGCATTTGG 57.535 25.926 3.38 0.00 0.00 3.28
62 63 8.906867 GGATTGTAAGGATGAGAATTTTCATGA 58.093 33.333 15.67 0.00 37.90 3.07
63 64 8.689061 TGGATTGTAAGGATGAGAATTTTCATG 58.311 33.333 15.67 0.00 37.90 3.07
64 65 8.827832 TGGATTGTAAGGATGAGAATTTTCAT 57.172 30.769 11.05 11.05 40.40 2.57
65 66 8.648698 TTGGATTGTAAGGATGAGAATTTTCA 57.351 30.769 0.54 0.54 0.00 2.69
66 67 9.927668 TTTTGGATTGTAAGGATGAGAATTTTC 57.072 29.630 0.00 0.00 0.00 2.29
106 107 9.918630 GCATTATGCCTTCATCTATATTTGTTT 57.081 29.630 5.80 0.00 37.42 2.83
107 108 9.081204 TGCATTATGCCTTCATCTATATTTGTT 57.919 29.630 15.06 0.00 44.23 2.83
108 109 8.517878 GTGCATTATGCCTTCATCTATATTTGT 58.482 33.333 15.06 0.00 44.23 2.83
109 110 8.517056 TGTGCATTATGCCTTCATCTATATTTG 58.483 33.333 15.06 0.00 44.23 2.32
110 111 8.640063 TGTGCATTATGCCTTCATCTATATTT 57.360 30.769 15.06 0.00 44.23 1.40
111 112 8.640063 TTGTGCATTATGCCTTCATCTATATT 57.360 30.769 15.06 0.00 44.23 1.28
112 113 8.640063 TTTGTGCATTATGCCTTCATCTATAT 57.360 30.769 15.06 0.00 44.23 0.86
113 114 8.517056 CATTTGTGCATTATGCCTTCATCTATA 58.483 33.333 15.06 0.00 44.23 1.31
114 115 6.964807 TTTGTGCATTATGCCTTCATCTAT 57.035 33.333 15.06 0.00 44.23 1.98
115 116 6.321945 ACATTTGTGCATTATGCCTTCATCTA 59.678 34.615 15.06 0.00 44.23 1.98
116 117 5.128171 ACATTTGTGCATTATGCCTTCATCT 59.872 36.000 15.06 0.37 44.23 2.90
117 118 5.233476 CACATTTGTGCATTATGCCTTCATC 59.767 40.000 15.06 0.00 44.23 2.92
118 119 5.113383 CACATTTGTGCATTATGCCTTCAT 58.887 37.500 15.06 0.00 44.23 2.57
119 120 4.496360 CACATTTGTGCATTATGCCTTCA 58.504 39.130 15.06 8.49 44.23 3.02
131 132 8.710551 TTCATCATGAAATTTACACATTTGTGC 58.289 29.630 10.52 0.00 40.41 4.57
146 147 7.774224 CGTTTCAACGTATTTCATCATGAAA 57.226 32.000 15.23 15.23 46.46 2.69
162 163 3.907894 TTGCATAACCCTCGTTTCAAC 57.092 42.857 0.00 0.00 33.17 3.18
163 164 4.920640 TTTTGCATAACCCTCGTTTCAA 57.079 36.364 0.00 0.00 33.17 2.69
164 165 4.580995 TCTTTTTGCATAACCCTCGTTTCA 59.419 37.500 0.00 0.00 33.17 2.69
165 166 5.116069 TCTTTTTGCATAACCCTCGTTTC 57.884 39.130 0.00 0.00 33.17 2.78
166 167 5.523438 TTCTTTTTGCATAACCCTCGTTT 57.477 34.783 0.00 0.00 33.17 3.60
167 168 5.523438 TTTCTTTTTGCATAACCCTCGTT 57.477 34.783 0.00 0.00 35.90 3.85
168 169 5.722021 ATTTCTTTTTGCATAACCCTCGT 57.278 34.783 0.00 0.00 0.00 4.18
169 170 7.479980 TCATATTTCTTTTTGCATAACCCTCG 58.520 34.615 0.00 0.00 0.00 4.63
172 173 9.696917 CCTATCATATTTCTTTTTGCATAACCC 57.303 33.333 0.00 0.00 0.00 4.11
178 179 9.905713 AGTACTCCTATCATATTTCTTTTTGCA 57.094 29.630 0.00 0.00 0.00 4.08
189 190 9.875708 GAGGGATGAATAGTACTCCTATCATAT 57.124 37.037 0.00 0.00 35.22 1.78
190 191 8.282982 GGAGGGATGAATAGTACTCCTATCATA 58.717 40.741 0.00 0.00 40.93 2.15
191 192 7.129425 GGAGGGATGAATAGTACTCCTATCAT 58.871 42.308 0.00 5.53 40.93 2.45
192 193 6.046762 TGGAGGGATGAATAGTACTCCTATCA 59.953 42.308 0.00 0.29 43.70 2.15
193 194 6.494952 TGGAGGGATGAATAGTACTCCTATC 58.505 44.000 0.00 0.00 43.70 2.08
194 195 6.278239 TCTGGAGGGATGAATAGTACTCCTAT 59.722 42.308 0.00 0.00 43.70 2.57
195 196 5.615692 TCTGGAGGGATGAATAGTACTCCTA 59.384 44.000 0.00 0.00 43.70 2.94
196 197 4.420552 TCTGGAGGGATGAATAGTACTCCT 59.579 45.833 0.00 0.00 43.70 3.69
197 198 4.525100 GTCTGGAGGGATGAATAGTACTCC 59.475 50.000 0.00 0.00 43.63 3.85
198 199 4.525100 GGTCTGGAGGGATGAATAGTACTC 59.475 50.000 0.00 0.00 0.00 2.59
199 200 4.078571 TGGTCTGGAGGGATGAATAGTACT 60.079 45.833 0.00 0.00 0.00 2.73
200 201 4.223953 TGGTCTGGAGGGATGAATAGTAC 58.776 47.826 0.00 0.00 0.00 2.73
201 202 4.552883 TGGTCTGGAGGGATGAATAGTA 57.447 45.455 0.00 0.00 0.00 1.82
202 203 3.421394 TGGTCTGGAGGGATGAATAGT 57.579 47.619 0.00 0.00 0.00 2.12
203 204 3.262915 GGATGGTCTGGAGGGATGAATAG 59.737 52.174 0.00 0.00 0.00 1.73
204 205 3.116199 AGGATGGTCTGGAGGGATGAATA 60.116 47.826 0.00 0.00 0.00 1.75
205 206 2.061061 GGATGGTCTGGAGGGATGAAT 58.939 52.381 0.00 0.00 0.00 2.57
206 207 1.010046 AGGATGGTCTGGAGGGATGAA 59.990 52.381 0.00 0.00 0.00 2.57
207 208 0.644380 AGGATGGTCTGGAGGGATGA 59.356 55.000 0.00 0.00 0.00 2.92
208 209 1.516110 AAGGATGGTCTGGAGGGATG 58.484 55.000 0.00 0.00 0.00 3.51
209 210 2.428484 CCTAAGGATGGTCTGGAGGGAT 60.428 54.545 0.00 0.00 0.00 3.85
210 211 1.062121 CCTAAGGATGGTCTGGAGGGA 60.062 57.143 0.00 0.00 0.00 4.20
211 212 1.428869 CCTAAGGATGGTCTGGAGGG 58.571 60.000 0.00 0.00 0.00 4.30
212 213 0.761802 GCCTAAGGATGGTCTGGAGG 59.238 60.000 0.00 0.00 0.00 4.30
213 214 0.390860 CGCCTAAGGATGGTCTGGAG 59.609 60.000 0.00 0.00 0.00 3.86
214 215 0.325296 ACGCCTAAGGATGGTCTGGA 60.325 55.000 0.00 0.00 0.00 3.86
215 216 1.410004 TACGCCTAAGGATGGTCTGG 58.590 55.000 0.00 0.00 0.00 3.86
216 217 3.458189 CTTTACGCCTAAGGATGGTCTG 58.542 50.000 0.00 0.00 0.00 3.51
217 218 2.158943 GCTTTACGCCTAAGGATGGTCT 60.159 50.000 0.00 0.00 0.00 3.85
218 219 2.210961 GCTTTACGCCTAAGGATGGTC 58.789 52.381 0.00 0.00 0.00 4.02
219 220 1.557832 TGCTTTACGCCTAAGGATGGT 59.442 47.619 0.00 0.00 38.05 3.55
220 221 1.940613 GTGCTTTACGCCTAAGGATGG 59.059 52.381 0.00 0.00 38.05 3.51
221 222 2.351726 GTGTGCTTTACGCCTAAGGATG 59.648 50.000 0.00 0.00 38.05 3.51
312 313 1.063616 GCGGCTCGTAATTTTTCCCTC 59.936 52.381 0.00 0.00 0.00 4.30
314 315 0.099968 GGCGGCTCGTAATTTTTCCC 59.900 55.000 0.00 0.00 0.00 3.97
323 324 4.382320 GGGTGTTGGCGGCTCGTA 62.382 66.667 11.43 0.00 0.00 3.43
396 397 1.925888 GTCGGGGTAGGTAGGAGGA 59.074 63.158 0.00 0.00 0.00 3.71
444 445 3.370277 TGGGATACGGGGAGGGGT 61.370 66.667 0.00 0.00 37.60 4.95
456 457 2.444895 GGGCGGAGAGAGTGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
575 576 0.460311 ACGGATCCTCGGCTTAACAG 59.540 55.000 10.75 0.00 0.00 3.16
580 581 4.162690 GCCACGGATCCTCGGCTT 62.163 66.667 26.32 0.00 41.50 4.35
600 601 0.543749 GCAACCTAGGCCTCATGTCT 59.456 55.000 9.68 0.00 0.00 3.41
715 716 2.158475 AGTGCCAGAGGAAAACAATGGA 60.158 45.455 0.00 0.00 32.55 3.41
723 724 3.857157 AAGTTGTAGTGCCAGAGGAAA 57.143 42.857 0.00 0.00 0.00 3.13
729 730 3.511934 AGAGACCTAAGTTGTAGTGCCAG 59.488 47.826 0.00 0.00 0.00 4.85
733 734 7.121463 ACACAGATAGAGACCTAAGTTGTAGTG 59.879 40.741 0.00 0.00 0.00 2.74
735 736 7.633193 ACACAGATAGAGACCTAAGTTGTAG 57.367 40.000 0.00 0.00 0.00 2.74
740 746 5.126384 GCTCAACACAGATAGAGACCTAAGT 59.874 44.000 0.00 0.00 0.00 2.24
741 747 5.126222 TGCTCAACACAGATAGAGACCTAAG 59.874 44.000 0.00 0.00 0.00 2.18
750 759 1.134280 CCCCCTGCTCAACACAGATAG 60.134 57.143 0.00 0.00 37.32 2.08
787 796 0.175760 GCTGTCTGGGATTCGTGCTA 59.824 55.000 0.00 0.00 0.00 3.49
792 801 0.534412 ACTCTGCTGTCTGGGATTCG 59.466 55.000 0.00 0.00 0.00 3.34
803 812 0.664761 CACCAACCAACACTCTGCTG 59.335 55.000 0.00 0.00 0.00 4.41
806 815 0.664761 CAGCACCAACCAACACTCTG 59.335 55.000 0.00 0.00 0.00 3.35
813 822 0.257328 TTCCAGACAGCACCAACCAA 59.743 50.000 0.00 0.00 0.00 3.67
822 831 2.157738 AGACAGCAAATTCCAGACAGC 58.842 47.619 0.00 0.00 0.00 4.40
846 855 9.973661 ACCATATTTATCCGATTTGATAATCCA 57.026 29.630 0.00 0.00 37.14 3.41
860 869 8.731605 GCTTAAGCTTAAGGACCATATTTATCC 58.268 37.037 35.64 17.38 40.31 2.59
879 888 9.508567 CCATCAGAAGTAAAAATAAGCTTAAGC 57.491 33.333 20.09 20.09 42.49 3.09
910 922 1.450312 GGATTCGTGCTGTCTGGGG 60.450 63.158 0.00 0.00 0.00 4.96
918 930 5.163519 CCAGAAATAAAATGGGATTCGTGCT 60.164 40.000 0.00 0.00 0.00 4.40
936 948 2.687935 AGAAGTCTTTTTGCGCCAGAAA 59.312 40.909 4.18 0.10 0.00 2.52
942 954 2.910987 GCAAAGAAGTCTTTTTGCGC 57.089 45.000 19.82 0.00 46.41 6.09
970 997 5.708948 ACCGGTTTCATGTTTGTTATCATG 58.291 37.500 0.00 0.00 41.64 3.07
992 1019 4.127171 ACAGCCACGATACATGGATTAAC 58.873 43.478 0.00 0.00 39.87 2.01
1266 1293 0.323629 TGTCCGAAACTAAGCCCCAG 59.676 55.000 0.00 0.00 0.00 4.45
1309 1336 5.665916 AAATAAACAATGGAGAAGCAGGG 57.334 39.130 0.00 0.00 0.00 4.45
1591 1836 3.664551 TGTAGCAACCTCTAGGCTCTA 57.335 47.619 0.00 0.00 39.01 2.43
1598 1843 5.155161 ACATCCCATATGTAGCAACCTCTA 58.845 41.667 1.24 0.00 0.00 2.43
1635 1887 8.424918 AGATTCAATGTAACTAGTCTGGTATGG 58.575 37.037 0.00 0.00 0.00 2.74
1653 1905 6.491714 ACTAGTCTGGTATGCAGATTCAAT 57.508 37.500 0.00 0.00 0.00 2.57
1693 1945 1.273495 TGCCTCTCCCAGAAGACATCT 60.273 52.381 0.00 0.00 39.68 2.90
1996 2248 5.178096 TGGTCCAAAATGCTGAGAAGATA 57.822 39.130 0.00 0.00 0.00 1.98
2138 2390 8.936864 AGTACAGTTACAAATTAGAGTGAATGC 58.063 33.333 0.00 0.00 0.00 3.56
2408 2660 0.176680 CTCGATGGCCAGCACTAAGT 59.823 55.000 22.95 0.00 0.00 2.24
2488 2740 2.740714 GCGTGATCGACAGGGTTGC 61.741 63.158 0.00 0.00 39.71 4.17
2692 2944 3.278574 TCAGTTGAGTGGGTTGTTTCAG 58.721 45.455 0.00 0.00 0.00 3.02
2787 3039 5.355711 TCTGGGAAGGATAGGTTAAAGGAA 58.644 41.667 0.00 0.00 0.00 3.36
2788 3040 4.967871 TCTGGGAAGGATAGGTTAAAGGA 58.032 43.478 0.00 0.00 0.00 3.36
2789 3041 4.722279 ACTCTGGGAAGGATAGGTTAAAGG 59.278 45.833 0.00 0.00 0.00 3.11
2790 3042 5.959583 ACTCTGGGAAGGATAGGTTAAAG 57.040 43.478 0.00 0.00 0.00 1.85
2791 3043 6.557633 GGATACTCTGGGAAGGATAGGTTAAA 59.442 42.308 0.00 0.00 0.00 1.52
2792 3044 6.082707 GGATACTCTGGGAAGGATAGGTTAA 58.917 44.000 0.00 0.00 0.00 2.01
2793 3045 5.652324 GGATACTCTGGGAAGGATAGGTTA 58.348 45.833 0.00 0.00 0.00 2.85
2794 3046 4.494591 GGATACTCTGGGAAGGATAGGTT 58.505 47.826 0.00 0.00 0.00 3.50
2795 3047 4.134933 GGATACTCTGGGAAGGATAGGT 57.865 50.000 0.00 0.00 0.00 3.08
2827 3095 3.550842 CCTCTGCGTCGATCAACATGATA 60.551 47.826 0.00 0.00 37.20 2.15
2828 3096 2.467838 CTCTGCGTCGATCAACATGAT 58.532 47.619 0.00 0.00 40.34 2.45
2905 3173 3.187700 GACGTAAAGCATCGAGGACATT 58.812 45.455 0.00 0.00 0.00 2.71
2992 3260 4.843719 ATGCAGATGCGCGCTCCA 62.844 61.111 33.29 20.35 45.83 3.86
3028 3296 2.897350 GGGGCGTAGATGTGCAGC 60.897 66.667 0.00 0.00 0.00 5.25
3056 3324 1.140852 GGCACTACTACCATGGCATGA 59.859 52.381 28.43 8.88 38.69 3.07
3065 3333 3.633065 CAGAGTTAGAGGGCACTACTACC 59.367 52.174 0.00 0.00 0.00 3.18
3067 3335 4.587976 ACAGAGTTAGAGGGCACTACTA 57.412 45.455 0.00 0.00 0.00 1.82
3072 3340 4.001652 GGTTTAACAGAGTTAGAGGGCAC 58.998 47.826 0.00 0.00 0.00 5.01
3073 3341 3.908103 AGGTTTAACAGAGTTAGAGGGCA 59.092 43.478 0.00 0.00 0.00 5.36
3074 3342 4.223255 AGAGGTTTAACAGAGTTAGAGGGC 59.777 45.833 0.00 0.00 0.00 5.19
3075 3343 6.361768 AAGAGGTTTAACAGAGTTAGAGGG 57.638 41.667 0.00 0.00 0.00 4.30
3076 3344 6.651225 CCAAAGAGGTTTAACAGAGTTAGAGG 59.349 42.308 0.00 0.00 0.00 3.69
3077 3345 7.659652 CCAAAGAGGTTTAACAGAGTTAGAG 57.340 40.000 0.00 0.00 0.00 2.43
3093 3361 4.025145 GTGTAAGACGTTTGACCAAAGAGG 60.025 45.833 0.00 0.00 45.67 3.69
3112 3380 1.266718 GGTGTAAGACGTGACGGTGTA 59.733 52.381 10.66 0.00 0.00 2.90
3123 3391 1.213799 GGGGACGACGGTGTAAGAC 59.786 63.158 0.00 0.00 0.00 3.01
3127 3395 3.376078 GCAGGGGACGACGGTGTA 61.376 66.667 0.00 0.00 0.00 2.90
3129 3397 4.742201 CTGCAGGGGACGACGGTG 62.742 72.222 5.57 0.00 0.00 4.94
3130 3398 2.849096 TATCTGCAGGGGACGACGGT 62.849 60.000 15.13 0.00 0.00 4.83
3131 3399 1.464376 ATATCTGCAGGGGACGACGG 61.464 60.000 15.13 0.00 0.00 4.79
3132 3400 1.068472 GTATATCTGCAGGGGACGACG 60.068 57.143 15.13 0.00 0.00 5.12
3133 3401 1.272769 GGTATATCTGCAGGGGACGAC 59.727 57.143 15.13 4.97 0.00 4.34
3134 3402 1.629043 GGTATATCTGCAGGGGACGA 58.371 55.000 15.13 0.00 0.00 4.20
3135 3403 0.608640 GGGTATATCTGCAGGGGACG 59.391 60.000 15.13 0.00 0.00 4.79
3136 3404 0.608640 CGGGTATATCTGCAGGGGAC 59.391 60.000 15.13 7.12 0.00 4.46
3137 3405 0.485543 TCGGGTATATCTGCAGGGGA 59.514 55.000 15.13 0.00 0.00 4.81
3138 3406 0.608640 GTCGGGTATATCTGCAGGGG 59.391 60.000 15.13 0.00 0.00 4.79
3139 3407 1.273606 CTGTCGGGTATATCTGCAGGG 59.726 57.143 15.13 0.00 0.00 4.45
3140 3408 1.337260 GCTGTCGGGTATATCTGCAGG 60.337 57.143 15.13 0.00 0.00 4.85
3141 3409 1.337260 GGCTGTCGGGTATATCTGCAG 60.337 57.143 7.63 7.63 0.00 4.41
3191 3459 4.830765 CCGAAGCGGGCGATGGAA 62.831 66.667 0.00 0.00 44.15 3.53
3376 3644 0.677731 ATGTCATTGTCAGGTGGCCG 60.678 55.000 0.00 0.00 0.00 6.13
3379 3647 1.203052 GGCAATGTCATTGTCAGGTGG 59.797 52.381 22.42 0.00 44.04 4.61
3420 3691 3.570125 TGTATCTCAGGAGTCTAATGCCG 59.430 47.826 0.00 0.00 0.00 5.69
3421 3692 4.342378 TGTGTATCTCAGGAGTCTAATGCC 59.658 45.833 0.00 0.00 0.00 4.40
3433 3704 2.697229 TGCAGGATCCTGTGTATCTCAG 59.303 50.000 36.32 13.03 45.24 3.35
3434 3705 2.697229 CTGCAGGATCCTGTGTATCTCA 59.303 50.000 36.32 24.26 45.24 3.27
3435 3706 2.961741 TCTGCAGGATCCTGTGTATCTC 59.038 50.000 36.32 21.39 45.24 2.75
3447 3718 2.744243 GGAGCCAGCTCTGCAGGAT 61.744 63.158 18.54 0.00 42.38 3.24
3449 3720 3.683966 CTGGAGCCAGCTCTGCAGG 62.684 68.421 18.54 5.82 45.24 4.85
3452 3723 4.486503 CCCTGGAGCCAGCTCTGC 62.487 72.222 18.54 4.46 42.35 4.26
3471 3742 0.472471 AGGAAACTCAACGGCTTCCA 59.528 50.000 2.78 0.00 39.91 3.53
3482 3753 5.949952 TGGCCTAAAATAAGGAAGGAAACTC 59.050 40.000 3.32 0.00 39.15 3.01
3489 3760 7.041721 GGAAACAATGGCCTAAAATAAGGAAG 58.958 38.462 3.32 0.00 39.15 3.46
3496 3767 4.467438 CAGAGGGAAACAATGGCCTAAAAT 59.533 41.667 3.32 0.00 0.00 1.82
3538 3809 7.663043 TTACTCCTTCCCTTTCTATTCTCTC 57.337 40.000 0.00 0.00 0.00 3.20
3545 3816 7.569599 ATCAACTTTACTCCTTCCCTTTCTA 57.430 36.000 0.00 0.00 0.00 2.10
3565 3836 5.063204 ACAACATCCAGAACTCGAAATCAA 58.937 37.500 0.00 0.00 0.00 2.57
3574 3845 3.576078 TCCACAACAACATCCAGAACT 57.424 42.857 0.00 0.00 0.00 3.01
3587 3859 5.067283 ACTGAAACCAGTGTAATTCCACAAC 59.933 40.000 3.83 0.00 42.84 3.32
3592 3864 7.103641 TCATCTACTGAAACCAGTGTAATTCC 58.896 38.462 8.21 0.00 44.07 3.01
3600 3872 7.284716 TCGTACATATCATCTACTGAAACCAGT 59.715 37.037 3.47 3.47 45.94 4.00
3612 3884 9.794685 GTCACAATATCATCGTACATATCATCT 57.205 33.333 0.00 0.00 0.00 2.90
3613 3885 9.794685 AGTCACAATATCATCGTACATATCATC 57.205 33.333 0.00 0.00 0.00 2.92
3615 3887 9.981114 AAAGTCACAATATCATCGTACATATCA 57.019 29.630 0.00 0.00 0.00 2.15
3625 3902 6.238484 CCCCTCGAAAAAGTCACAATATCATC 60.238 42.308 0.00 0.00 0.00 2.92
3641 3918 2.485038 GCGTTGTATTTTCCCCTCGAAA 59.515 45.455 0.00 0.00 38.74 3.46
3651 3928 9.507280 CATTTCAGATTATCAGCGTTGTATTTT 57.493 29.630 0.00 0.00 0.00 1.82
3653 3930 8.213518 ACATTTCAGATTATCAGCGTTGTATT 57.786 30.769 0.00 0.00 0.00 1.89
3660 3937 3.804325 ACGGACATTTCAGATTATCAGCG 59.196 43.478 0.00 0.00 0.00 5.18
3667 3944 4.744631 GTGCAAAAACGGACATTTCAGATT 59.255 37.500 0.00 0.00 0.00 2.40
3670 3947 2.467305 CGTGCAAAAACGGACATTTCAG 59.533 45.455 0.00 0.00 39.89 3.02
3673 3950 1.204792 GCGTGCAAAAACGGACATTT 58.795 45.000 0.00 0.00 43.75 2.32
3687 3964 2.502510 CAAATGCAGACCGCGTGC 60.503 61.111 12.75 12.75 46.97 5.34
3689 3966 0.383949 AAAACAAATGCAGACCGCGT 59.616 45.000 4.92 0.00 46.97 6.01
3690 3967 1.486439 AAAAACAAATGCAGACCGCG 58.514 45.000 0.00 0.00 46.97 6.46
3710 3987 6.508030 TGAAGCAGGTGGTATATTTGGATA 57.492 37.500 0.00 0.00 0.00 2.59
3711 3988 5.387113 TGAAGCAGGTGGTATATTTGGAT 57.613 39.130 0.00 0.00 0.00 3.41
3712 3989 4.853468 TGAAGCAGGTGGTATATTTGGA 57.147 40.909 0.00 0.00 0.00 3.53
3714 3991 6.148480 GCTAGATGAAGCAGGTGGTATATTTG 59.852 42.308 0.00 0.00 42.30 2.32
3717 3994 5.413309 GCTAGATGAAGCAGGTGGTATAT 57.587 43.478 0.00 0.00 42.30 0.86
3718 3995 4.873746 GCTAGATGAAGCAGGTGGTATA 57.126 45.455 0.00 0.00 42.30 1.47
3719 3996 3.760580 GCTAGATGAAGCAGGTGGTAT 57.239 47.619 0.00 0.00 42.30 2.73
3752 4029 5.105877 ACAGATTGATGGACAAAATGCAGAG 60.106 40.000 0.00 0.00 42.03 3.35
3774 4052 7.946219 AGAATTATGATAATGGAGGAATGCACA 59.054 33.333 0.00 0.00 0.00 4.57
3775 4053 8.345724 AGAATTATGATAATGGAGGAATGCAC 57.654 34.615 0.00 0.00 0.00 4.57
3778 4056 9.021807 AGCAAGAATTATGATAATGGAGGAATG 57.978 33.333 0.00 0.00 0.00 2.67
3799 4077 4.573607 TGCACATATTAAGCTGAGAGCAAG 59.426 41.667 0.00 0.00 45.56 4.01
3810 4088 6.366644 GCATATTTGCGTGCACATATTAAG 57.633 37.500 18.64 0.00 39.49 1.85
3846 4124 5.896678 AGTAGGGAGAGATACATCATATGGC 59.103 44.000 2.13 0.00 33.60 4.40
3851 4129 5.150715 TGCAAGTAGGGAGAGATACATCAT 58.849 41.667 0.00 0.00 0.00 2.45
3926 4428 9.474249 GCAACATTCTCTAATTACGTTCTTTAC 57.526 33.333 0.00 0.00 0.00 2.01
3927 4429 9.210329 TGCAACATTCTCTAATTACGTTCTTTA 57.790 29.630 0.00 0.00 0.00 1.85
3931 4433 8.895932 AAATGCAACATTCTCTAATTACGTTC 57.104 30.769 0.00 0.00 0.00 3.95
4058 4578 7.743749 ACAAGCTATCTCAGATTACCATCAAT 58.256 34.615 0.00 0.00 29.80 2.57
4084 4604 2.487934 CTGCCTTGGTCCAATCGATAG 58.512 52.381 4.34 0.00 0.00 2.08
4123 4647 1.627864 CCCGTTTTGAAGGTCCCATT 58.372 50.000 0.00 0.00 0.00 3.16
4181 4709 4.499116 CGGGAGGAGGGTGGGGAT 62.499 72.222 0.00 0.00 0.00 3.85
4223 4754 2.409055 CGTGTGGGCATGTGGATGG 61.409 63.158 0.00 0.00 0.00 3.51
4238 4769 4.135153 CACCCCTCCTCTCGCGTG 62.135 72.222 5.77 3.13 0.00 5.34
4239 4770 4.361971 TCACCCCTCCTCTCGCGT 62.362 66.667 5.77 0.00 0.00 6.01
4251 4801 1.997874 ATGCAGGAGGAGGTCACCC 60.998 63.158 0.00 0.00 0.00 4.61
4276 4826 4.316823 AGGGAGGGAGGCGTGTCA 62.317 66.667 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.