Multiple sequence alignment - TraesCS5A01G040700

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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 TraesCS5A01G040700 chr5A 100.000 2613 0 0 714 3326 36739882 36742494 0.000000e+00 4826.0
1 TraesCS5A01G040700 chr5A 100.000 378 0 0 1 378 36739169 36739546 0.000000e+00 699.0
2 TraesCS5A01G040700 chr5B 87.097 992 64 34 845 1824 45942914 45943853 0.000000e+00 1064.0
3 TraesCS5A01G040700 chr5B 90.597 787 68 3 2179 2960 393995055 393995840 0.000000e+00 1038.0
4 TraesCS5A01G040700 chr5B 93.033 244 10 2 1871 2107 45943963 45944206 1.900000e-92 350.0
5 TraesCS5A01G040700 chr5B 87.050 139 15 3 3184 3320 45977795 45977932 1.600000e-33 154.0
6 TraesCS5A01G040700 chr5B 78.367 245 24 9 2964 3187 45944310 45944546 7.490000e-27 132.0
7 TraesCS5A01G040700 chr5B 92.857 84 6 0 3243 3326 45976227 45976310 4.510000e-24 122.0
8 TraesCS5A01G040700 chrUn 87.642 793 75 13 2179 2961 43572230 43571451 0.000000e+00 900.0
9 TraesCS5A01G040700 chr7D 86.726 791 74 16 2179 2960 71228508 71227740 0.000000e+00 850.0
10 TraesCS5A01G040700 chr2D 86.301 803 81 16 2176 2960 623759239 623758448 0.000000e+00 846.0
11 TraesCS5A01G040700 chr2D 83.772 228 21 10 3 226 605726235 605726450 5.630000e-48 202.0
12 TraesCS5A01G040700 chr2D 84.615 104 16 0 757 860 27495908 27496011 1.630000e-18 104.0
13 TraesCS5A01G040700 chr2D 82.051 117 21 0 747 863 154109629 154109513 2.110000e-17 100.0
14 TraesCS5A01G040700 chr3A 85.876 793 79 16 2178 2960 23452890 23453659 0.000000e+00 813.0
15 TraesCS5A01G040700 chr3A 86.842 114 15 0 747 860 682006384 682006497 9.690000e-26 128.0
16 TraesCS5A01G040700 chr3A 83.333 114 19 0 747 860 60245943 60245830 4.540000e-19 106.0
17 TraesCS5A01G040700 chr3A 77.311 119 16 10 108 221 733870039 733870151 3.580000e-05 60.2
18 TraesCS5A01G040700 chr6B 84.005 794 76 21 2178 2960 664640566 664639813 0.000000e+00 715.0
19 TraesCS5A01G040700 chr6B 83.810 105 17 0 756 860 664091945 664092049 2.110000e-17 100.0
20 TraesCS5A01G040700 chr5D 85.115 739 57 25 730 1447 45953955 45953249 0.000000e+00 706.0
21 TraesCS5A01G040700 chr5D 92.857 378 21 2 1448 1825 45953133 45952762 8.120000e-151 544.0
22 TraesCS5A01G040700 chr5D 92.722 316 13 1 1871 2176 45952751 45952436 6.550000e-122 448.0
23 TraesCS5A01G040700 chr5D 77.957 372 37 13 2976 3312 45952426 45952065 1.220000e-44 191.0
24 TraesCS5A01G040700 chr5D 74.545 165 32 10 137 294 129879327 129879166 2.770000e-06 63.9
25 TraesCS5A01G040700 chr1A 88.434 562 48 10 2409 2960 475617337 475616783 0.000000e+00 662.0
26 TraesCS5A01G040700 chr1A 87.544 562 53 9 2409 2960 475711734 475711180 4.680000e-178 634.0
27 TraesCS5A01G040700 chr1A 85.455 110 15 1 747 855 22387573 22387464 2.710000e-21 113.0
28 TraesCS5A01G040700 chr2B 89.266 531 52 5 2178 2707 745670577 745670051 0.000000e+00 660.0
29 TraesCS5A01G040700 chr2A 86.612 605 57 12 2365 2960 753770304 753769715 0.000000e+00 647.0
30 TraesCS5A01G040700 chr2A 88.889 531 48 7 2178 2707 743065230 743064710 0.000000e+00 643.0
31 TraesCS5A01G040700 chr2A 85.577 104 15 0 757 860 724041333 724041436 3.510000e-20 110.0
32 TraesCS5A01G040700 chr2A 86.792 53 3 4 167 215 773068972 773069024 4.640000e-04 56.5
33 TraesCS5A01G040700 chr4B 84.211 114 18 0 747 860 433180631 433180744 9.750000e-21 111.0
34 TraesCS5A01G040700 chr3D 83.636 110 18 0 747 856 376270061 376270170 1.630000e-18 104.0
35 TraesCS5A01G040700 chr4D 83.529 85 10 4 134 215 473746348 473746431 3.560000e-10 76.8
36 TraesCS5A01G040700 chr4D 87.719 57 5 2 148 202 64619137 64619081 7.700000e-07 65.8
37 TraesCS5A01G040700 chr3B 81.000 100 15 3 122 218 3668559 3668461 3.560000e-10 76.8
38 TraesCS5A01G040700 chr6D 82.716 81 10 4 137 214 144095448 144095369 5.950000e-08 69.4


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 TraesCS5A01G040700 chr5A 36739169 36742494 3325 False 2762.500000 4826 100.000000 1 3326 2 chr5A.!!$F1 3325
1 TraesCS5A01G040700 chr5B 393995055 393995840 785 False 1038.000000 1038 90.597000 2179 2960 1 chr5B.!!$F1 781
2 TraesCS5A01G040700 chr5B 45942914 45944546 1632 False 515.333333 1064 86.165667 845 3187 3 chr5B.!!$F2 2342
3 TraesCS5A01G040700 chrUn 43571451 43572230 779 True 900.000000 900 87.642000 2179 2961 1 chrUn.!!$R1 782
4 TraesCS5A01G040700 chr7D 71227740 71228508 768 True 850.000000 850 86.726000 2179 2960 1 chr7D.!!$R1 781
5 TraesCS5A01G040700 chr2D 623758448 623759239 791 True 846.000000 846 86.301000 2176 2960 1 chr2D.!!$R2 784
6 TraesCS5A01G040700 chr3A 23452890 23453659 769 False 813.000000 813 85.876000 2178 2960 1 chr3A.!!$F1 782
7 TraesCS5A01G040700 chr6B 664639813 664640566 753 True 715.000000 715 84.005000 2178 2960 1 chr6B.!!$R1 782
8 TraesCS5A01G040700 chr5D 45952065 45953955 1890 True 472.250000 706 87.162750 730 3312 4 chr5D.!!$R2 2582
9 TraesCS5A01G040700 chr1A 475616783 475617337 554 True 662.000000 662 88.434000 2409 2960 1 chr1A.!!$R2 551
10 TraesCS5A01G040700 chr1A 475711180 475711734 554 True 634.000000 634 87.544000 2409 2960 1 chr1A.!!$R3 551
11 TraesCS5A01G040700 chr2B 745670051 745670577 526 True 660.000000 660 89.266000 2178 2707 1 chr2B.!!$R1 529
12 TraesCS5A01G040700 chr2A 753769715 753770304 589 True 647.000000 647 86.612000 2365 2960 1 chr2A.!!$R2 595
13 TraesCS5A01G040700 chr2A 743064710 743065230 520 True 643.000000 643 88.889000 2178 2707 1 chr2A.!!$R1 529

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
775 776 1.193874 GTATAATTTTCGCTCCCGCCG 59.806 52.381 0.0 0.0 0.00 6.46 F
1442 1474 0.040067 GCACTCCGCTTTCCTTTGTG 60.040 55.000 0.0 0.0 37.77 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2511 0.107703 TCCCCGAACATGATGTGAGC 60.108 55.0 0.0 0.0 0.0 4.26 R
2963 3272 0.178975 AGAGCCTCCCTATCGGTGAG 60.179 60.0 0.0 0.0 0.0 3.51 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
25 26 4.763594 TTTTGAAACCGCGAACATTTTC 57.236 36.364 8.23 8.74 0.00 2.29
26 27 3.701532 TTGAAACCGCGAACATTTTCT 57.298 38.095 8.23 0.00 0.00 2.52
27 28 2.993545 TGAAACCGCGAACATTTTCTG 58.006 42.857 8.23 0.00 0.00 3.02
28 29 2.614520 TGAAACCGCGAACATTTTCTGA 59.385 40.909 8.23 0.00 0.00 3.27
29 30 3.065510 TGAAACCGCGAACATTTTCTGAA 59.934 39.130 8.23 0.00 0.00 3.02
30 31 3.701532 AACCGCGAACATTTTCTGAAA 57.298 38.095 8.23 0.00 0.00 2.69
31 32 3.915437 ACCGCGAACATTTTCTGAAAT 57.085 38.095 8.23 0.00 35.90 2.17
32 33 3.821841 ACCGCGAACATTTTCTGAAATC 58.178 40.909 8.23 0.00 33.25 2.17
33 34 3.252215 ACCGCGAACATTTTCTGAAATCA 59.748 39.130 8.23 0.00 33.25 2.57
34 35 4.082787 ACCGCGAACATTTTCTGAAATCAT 60.083 37.500 8.23 0.00 33.25 2.45
35 36 4.263677 CCGCGAACATTTTCTGAAATCATG 59.736 41.667 8.23 8.24 33.25 3.07
36 37 5.088068 CGCGAACATTTTCTGAAATCATGA 58.912 37.500 17.33 0.00 33.25 3.07
37 38 5.568677 CGCGAACATTTTCTGAAATCATGAA 59.431 36.000 17.33 0.00 33.25 2.57
38 39 6.451571 CGCGAACATTTTCTGAAATCATGAAC 60.452 38.462 17.33 11.09 33.25 3.18
39 40 6.183360 GCGAACATTTTCTGAAATCATGAACC 60.183 38.462 17.33 7.98 33.25 3.62
40 41 6.862608 CGAACATTTTCTGAAATCATGAACCA 59.137 34.615 17.33 0.00 33.25 3.67
41 42 7.543172 CGAACATTTTCTGAAATCATGAACCAT 59.457 33.333 17.33 0.00 33.25 3.55
42 43 9.211485 GAACATTTTCTGAAATCATGAACCATT 57.789 29.630 17.33 5.17 33.25 3.16
43 44 9.563748 AACATTTTCTGAAATCATGAACCATTT 57.436 25.926 17.33 0.00 33.25 2.32
44 45 9.563748 ACATTTTCTGAAATCATGAACCATTTT 57.436 25.926 17.33 0.00 33.25 1.82
119 120 5.379732 TTTTGAAACCGTGAACACTTTCT 57.620 34.783 15.39 0.00 31.04 2.52
120 121 4.349663 TTGAAACCGTGAACACTTTCTG 57.650 40.909 15.39 0.00 31.04 3.02
121 122 3.601435 TGAAACCGTGAACACTTTCTGA 58.399 40.909 15.39 1.24 31.04 3.27
122 123 4.004314 TGAAACCGTGAACACTTTCTGAA 58.996 39.130 15.39 0.00 31.04 3.02
123 124 4.456222 TGAAACCGTGAACACTTTCTGAAA 59.544 37.500 15.39 2.44 31.04 2.69
124 125 5.124776 TGAAACCGTGAACACTTTCTGAAAT 59.875 36.000 2.88 0.00 31.04 2.17
125 126 4.813296 ACCGTGAACACTTTCTGAAATC 57.187 40.909 2.88 0.00 32.36 2.17
126 127 4.196193 ACCGTGAACACTTTCTGAAATCA 58.804 39.130 2.88 1.90 32.36 2.57
127 128 4.821805 ACCGTGAACACTTTCTGAAATCAT 59.178 37.500 2.88 0.00 32.36 2.45
128 129 5.149273 CCGTGAACACTTTCTGAAATCATG 58.851 41.667 13.14 13.14 32.36 3.07
129 130 5.049474 CCGTGAACACTTTCTGAAATCATGA 60.049 40.000 18.42 0.00 32.36 3.07
130 131 6.429624 CGTGAACACTTTCTGAAATCATGAA 58.570 36.000 14.24 0.00 32.36 2.57
131 132 6.358030 CGTGAACACTTTCTGAAATCATGAAC 59.642 38.462 14.24 0.00 32.36 3.18
132 133 6.638468 GTGAACACTTTCTGAAATCATGAACC 59.362 38.462 0.00 0.00 32.36 3.62
133 134 6.547141 TGAACACTTTCTGAAATCATGAACCT 59.453 34.615 0.00 0.00 32.36 3.50
134 135 6.966534 ACACTTTCTGAAATCATGAACCTT 57.033 33.333 0.00 0.00 0.00 3.50
135 136 7.352079 ACACTTTCTGAAATCATGAACCTTT 57.648 32.000 0.00 0.00 0.00 3.11
136 137 7.785033 ACACTTTCTGAAATCATGAACCTTTT 58.215 30.769 0.00 0.00 0.00 2.27
137 138 8.260114 ACACTTTCTGAAATCATGAACCTTTTT 58.740 29.630 0.00 0.00 0.00 1.94
175 176 5.553692 TTTTTGAAATCGCGAACATGTTC 57.446 34.783 25.68 25.68 36.29 3.18
176 177 4.481930 TTTGAAATCGCGAACATGTTCT 57.518 36.364 30.45 14.91 37.44 3.01
177 178 3.454042 TGAAATCGCGAACATGTTCTG 57.546 42.857 30.45 24.50 37.44 3.02
178 179 3.063485 TGAAATCGCGAACATGTTCTGA 58.937 40.909 30.45 26.92 37.44 3.27
179 180 3.496507 TGAAATCGCGAACATGTTCTGAA 59.503 39.130 30.45 18.10 37.44 3.02
180 181 4.024472 TGAAATCGCGAACATGTTCTGAAA 60.024 37.500 30.45 16.57 37.44 2.69
181 182 4.685169 AATCGCGAACATGTTCTGAAAT 57.315 36.364 30.45 19.23 37.44 2.17
182 183 3.722555 TCGCGAACATGTTCTGAAATC 57.277 42.857 30.45 14.31 37.44 2.17
183 184 3.063485 TCGCGAACATGTTCTGAAATCA 58.937 40.909 30.45 9.34 37.44 2.57
184 185 3.684305 TCGCGAACATGTTCTGAAATCAT 59.316 39.130 30.45 0.00 37.44 2.45
185 186 3.782369 CGCGAACATGTTCTGAAATCATG 59.218 43.478 30.45 15.90 42.86 3.07
186 187 4.435917 CGCGAACATGTTCTGAAATCATGA 60.436 41.667 30.45 0.00 40.64 3.07
187 188 5.393124 GCGAACATGTTCTGAAATCATGAA 58.607 37.500 30.45 0.00 40.64 2.57
188 189 5.284660 GCGAACATGTTCTGAAATCATGAAC 59.715 40.000 30.45 14.59 40.64 3.18
224 225 9.757227 AATTCACGAACATTTTTAAATTCCTGA 57.243 25.926 0.00 0.00 0.00 3.86
225 226 9.757227 ATTCACGAACATTTTTAAATTCCTGAA 57.243 25.926 12.17 12.17 0.00 3.02
226 227 8.568732 TCACGAACATTTTTAAATTCCTGAAC 57.431 30.769 0.00 0.00 0.00 3.18
227 228 7.377397 TCACGAACATTTTTAAATTCCTGAACG 59.623 33.333 0.00 0.00 0.00 3.95
228 229 7.166804 CACGAACATTTTTAAATTCCTGAACGT 59.833 33.333 0.00 0.00 0.00 3.99
229 230 7.703197 ACGAACATTTTTAAATTCCTGAACGTT 59.297 29.630 0.00 0.00 0.00 3.99
230 231 8.205297 CGAACATTTTTAAATTCCTGAACGTTC 58.795 33.333 21.42 21.42 0.00 3.95
231 232 8.934507 AACATTTTTAAATTCCTGAACGTTCA 57.065 26.923 28.07 28.07 35.57 3.18
232 233 8.347729 ACATTTTTAAATTCCTGAACGTTCAC 57.652 30.769 26.53 3.20 32.90 3.18
233 234 8.194769 ACATTTTTAAATTCCTGAACGTTCACT 58.805 29.630 26.53 9.19 32.90 3.41
234 235 9.030301 CATTTTTAAATTCCTGAACGTTCACTT 57.970 29.630 26.53 15.75 32.90 3.16
235 236 7.979115 TTTTAAATTCCTGAACGTTCACTTG 57.021 32.000 26.53 16.78 32.90 3.16
236 237 6.928979 TTAAATTCCTGAACGTTCACTTGA 57.071 33.333 26.53 18.99 32.90 3.02
237 238 5.828299 AAATTCCTGAACGTTCACTTGAA 57.172 34.783 26.53 25.00 32.90 2.69
282 283 9.618890 TCCCAAACATTTTTAAATTCATCAACA 57.381 25.926 0.00 0.00 0.00 3.33
283 284 9.881529 CCCAAACATTTTTAAATTCATCAACAG 57.118 29.630 0.00 0.00 0.00 3.16
739 740 5.354234 CACAATATAGTATTGGGCCCGATTC 59.646 44.000 30.23 24.15 33.56 2.52
769 770 8.181573 TCAAATTCAGTGGTATAATTTTCGCTC 58.818 33.333 0.00 0.00 32.05 5.03
771 772 4.448210 TCAGTGGTATAATTTTCGCTCCC 58.552 43.478 0.00 0.00 0.00 4.30
772 773 3.247648 CAGTGGTATAATTTTCGCTCCCG 59.752 47.826 0.00 0.00 0.00 5.14
773 774 2.032290 GTGGTATAATTTTCGCTCCCGC 60.032 50.000 0.00 0.00 0.00 6.13
775 776 1.193874 GTATAATTTTCGCTCCCGCCG 59.806 52.381 0.00 0.00 0.00 6.46
776 777 1.782028 ATAATTTTCGCTCCCGCCGC 61.782 55.000 0.00 0.00 0.00 6.53
803 804 6.627671 GTCGATCTCGTTGGTTAAATTTATGC 59.372 38.462 0.00 0.00 40.80 3.14
827 828 6.411203 GCTTAAATTTAGATCTCGGAAAACGC 59.589 38.462 0.00 0.00 43.86 4.84
830 831 2.579207 TAGATCTCGGAAAACGCAGG 57.421 50.000 0.00 0.00 43.86 4.85
836 837 4.700365 GGAAAACGCAGGCGCACC 62.700 66.667 14.32 8.24 44.19 5.01
838 839 3.879351 GAAAACGCAGGCGCACCAG 62.879 63.158 14.32 0.00 44.19 4.00
864 865 6.078456 TGTGAAATGGAGGGACTATCAAAT 57.922 37.500 0.00 0.00 41.55 2.32
914 926 4.461992 AATACAAAACACAACCGACTCG 57.538 40.909 0.00 0.00 0.00 4.18
968 980 4.961438 ATTGACAAGAACAGCCCAAATT 57.039 36.364 0.00 0.00 0.00 1.82
1003 1017 2.203209 GCCGGGGCGATCTCATTT 60.203 61.111 2.18 0.00 0.00 2.32
1033 1047 2.892305 GATCCGATCGACCAAGCTG 58.108 57.895 18.66 0.00 0.00 4.24
1035 1049 1.680522 ATCCGATCGACCAAGCTGCT 61.681 55.000 18.66 0.00 0.00 4.24
1037 1051 1.153765 CGATCGACCAAGCTGCTCA 60.154 57.895 10.26 0.00 0.00 4.26
1038 1052 0.529337 CGATCGACCAAGCTGCTCAT 60.529 55.000 10.26 0.00 0.00 2.90
1136 1150 2.749044 CCAGCAGCAGGTTCGCAT 60.749 61.111 0.00 0.00 0.00 4.73
1146 1160 4.814294 GTTCGCATCTCCCGCCGT 62.814 66.667 0.00 0.00 0.00 5.68
1162 1181 2.059541 GCCGTTTCCTCGCATACTATC 58.940 52.381 0.00 0.00 0.00 2.08
1168 1187 1.000607 TCCTCGCATACTATCGGTTGC 60.001 52.381 0.00 0.00 0.00 4.17
1209 1234 0.109781 CACGGGGAGAAACAAATGCG 60.110 55.000 0.00 0.00 0.00 4.73
1231 1261 4.500837 CGTATATCCGCTTATGCTAGCTTG 59.499 45.833 17.23 4.51 39.03 4.01
1242 1272 6.609237 TTATGCTAGCTTGAACATGATGAC 57.391 37.500 17.23 0.00 0.00 3.06
1253 1283 7.012138 GCTTGAACATGATGACATATTCTGACT 59.988 37.037 0.00 0.00 39.70 3.41
1382 1414 9.652114 ATGGCTTGATTCCTTTAATTCTTCTAT 57.348 29.630 0.00 0.00 0.00 1.98
1383 1415 9.125026 TGGCTTGATTCCTTTAATTCTTCTATC 57.875 33.333 0.00 0.00 0.00 2.08
1384 1416 9.348476 GGCTTGATTCCTTTAATTCTTCTATCT 57.652 33.333 0.00 0.00 0.00 1.98
1442 1474 0.040067 GCACTCCGCTTTCCTTTGTG 60.040 55.000 0.00 0.00 37.77 3.33
1446 1593 0.889186 TCCGCTTTCCTTTGTGCTCC 60.889 55.000 0.00 0.00 0.00 4.70
1470 1617 0.320374 CACGCCACTTCCTCCAAGTA 59.680 55.000 0.00 0.00 44.14 2.24
1475 1622 1.339151 CCACTTCCTCCAAGTACTGCC 60.339 57.143 0.00 0.00 44.14 4.85
1476 1623 1.347707 CACTTCCTCCAAGTACTGCCA 59.652 52.381 0.00 0.00 44.14 4.92
1479 1626 1.267121 TCCTCCAAGTACTGCCACTC 58.733 55.000 0.00 0.00 0.00 3.51
1492 1639 0.179054 GCCACTCCTCCGGTAATTCC 60.179 60.000 0.00 0.00 0.00 3.01
1500 1647 6.041751 CACTCCTCCGGTAATTCCTACTAATT 59.958 42.308 0.00 0.00 33.69 1.40
1501 1648 6.267242 ACTCCTCCGGTAATTCCTACTAATTC 59.733 42.308 0.00 0.00 31.63 2.17
1502 1649 6.138263 TCCTCCGGTAATTCCTACTAATTCA 58.862 40.000 0.00 0.00 31.63 2.57
1554 1701 7.013274 TCCAAGTTCAAGAATTTGTTCAGTAGG 59.987 37.037 14.33 0.83 36.62 3.18
1619 1766 1.081892 CACGAAGATGGAGCCACAAG 58.918 55.000 0.00 0.00 0.00 3.16
1629 1776 2.113986 GCCACAAGGGTGCTCTGT 59.886 61.111 0.00 0.00 43.88 3.41
1686 1833 3.615496 ACGATGTGTATTACCGCAACTTC 59.385 43.478 0.00 0.00 0.00 3.01
1709 1856 1.825474 CTGGTGGATGACGGTAGAAGT 59.175 52.381 0.00 0.00 0.00 3.01
1745 1892 2.397413 AAACTGGTGAGAGCCGTGGG 62.397 60.000 0.00 0.00 0.00 4.61
1797 1944 1.672356 CGGAGTTGGCAAGGTGAGG 60.672 63.158 0.00 0.00 0.00 3.86
1800 1947 0.606673 GAGTTGGCAAGGTGAGGGAC 60.607 60.000 0.00 0.00 0.00 4.46
1814 1961 4.158209 GGTGAGGGACTACAGTTTAGTCTC 59.842 50.000 14.54 11.52 43.55 3.36
1833 2053 6.678547 AGTCTCTGATTTATACTCCCTCTGT 58.321 40.000 0.00 0.00 0.00 3.41
1836 2056 8.915036 GTCTCTGATTTATACTCCCTCTGTAAA 58.085 37.037 0.00 0.00 0.00 2.01
1837 2057 9.488762 TCTCTGATTTATACTCCCTCTGTAAAA 57.511 33.333 0.00 0.00 0.00 1.52
1896 2118 7.976734 AGTAGTTTATTTCGACAGAAGATGAGG 59.023 37.037 0.00 0.00 37.70 3.86
1907 2129 3.631686 CAGAAGATGAGGTGAGATCTCGT 59.368 47.826 17.76 5.04 34.19 4.18
1913 2135 3.017442 TGAGGTGAGATCTCGTAACAGG 58.983 50.000 17.76 0.00 34.19 4.00
2168 2444 4.404654 GGCTCGCCGGTTTTGCTG 62.405 66.667 1.90 0.00 0.00 4.41
2170 2446 2.556287 CTCGCCGGTTTTGCTGTC 59.444 61.111 1.90 0.00 0.00 3.51
2194 2470 1.164411 CCGCAGTAATGTTGCTTGGA 58.836 50.000 0.00 0.00 39.38 3.53
2202 2478 1.269012 ATGTTGCTTGGAACCATGGG 58.731 50.000 18.09 0.00 0.00 4.00
2249 2526 2.283298 ACATCGGCTCACATCATGTTC 58.717 47.619 0.00 0.00 0.00 3.18
2273 2554 2.294074 GATTTGTGCCTAACGCCCATA 58.706 47.619 0.00 0.00 36.24 2.74
2284 2565 6.943146 TGCCTAACGCCCATAATATTTTATGA 59.057 34.615 15.15 0.00 41.04 2.15
2343 2624 6.069905 TGTTCCTAATAAACCTACTGCATGGA 60.070 38.462 7.42 0.00 0.00 3.41
2354 2635 1.561076 ACTGCATGGAGAGTGCCATAA 59.439 47.619 22.24 0.00 46.70 1.90
2433 2723 6.479660 CACTGTTCAACATTTTGTATTGCCTT 59.520 34.615 0.00 0.00 34.02 4.35
2672 2967 7.754069 AAAAATAACATGAACACACACACAG 57.246 32.000 0.00 0.00 0.00 3.66
2777 3073 2.045536 CAGGAGGGGAAGCAGCAC 60.046 66.667 0.00 0.00 0.00 4.40
2809 3106 2.949963 GCTTGGGCCCACATAGATTCAA 60.950 50.000 28.70 4.25 0.00 2.69
2813 3110 3.513515 TGGGCCCACATAGATTCAAAAAC 59.486 43.478 24.45 0.00 0.00 2.43
2821 3118 6.294508 CCACATAGATTCAAAAACGAAAGGGT 60.295 38.462 0.00 0.00 0.00 4.34
2835 3132 2.285442 GGGTGTAGGCCTGGTCCT 60.285 66.667 17.99 13.10 40.21 3.85
2879 3184 4.973168 TGAAGTTTGAGTGATAAGCTGGT 58.027 39.130 0.00 0.00 0.00 4.00
2880 3185 4.756642 TGAAGTTTGAGTGATAAGCTGGTG 59.243 41.667 0.00 0.00 0.00 4.17
2961 3270 0.394488 TCCTGAATCTCGCCTCTCGT 60.394 55.000 0.00 0.00 39.67 4.18
2962 3271 0.030101 CCTGAATCTCGCCTCTCGTC 59.970 60.000 0.00 0.00 39.67 4.20
2963 3272 0.030101 CTGAATCTCGCCTCTCGTCC 59.970 60.000 0.00 0.00 39.67 4.79
2964 3273 0.394488 TGAATCTCGCCTCTCGTCCT 60.394 55.000 0.00 0.00 39.67 3.85
2965 3274 0.309612 GAATCTCGCCTCTCGTCCTC 59.690 60.000 0.00 0.00 39.67 3.71
2966 3275 0.394488 AATCTCGCCTCTCGTCCTCA 60.394 55.000 0.00 0.00 39.67 3.86
2967 3276 1.098712 ATCTCGCCTCTCGTCCTCAC 61.099 60.000 0.00 0.00 39.67 3.51
2968 3277 2.750637 TCGCCTCTCGTCCTCACC 60.751 66.667 0.00 0.00 39.67 4.02
2995 3307 2.680352 GCTCTCCACTCGGGGACA 60.680 66.667 0.00 0.00 36.60 4.02
3002 3314 1.422024 TCCACTCGGGGACAAATTTCA 59.578 47.619 0.00 0.00 37.22 2.69
3063 3392 0.322546 CCCCACCTTGTAACCTGCTC 60.323 60.000 0.00 0.00 0.00 4.26
3064 3393 0.400213 CCCACCTTGTAACCTGCTCA 59.600 55.000 0.00 0.00 0.00 4.26
3100 3438 5.412904 GCCTAACATTATGTATGCCTCTTCC 59.587 44.000 0.00 0.00 37.81 3.46
3106 3444 2.113860 TGTATGCCTCTTCCAGTTGC 57.886 50.000 0.00 0.00 0.00 4.17
3137 3475 3.017581 GGTGGGGAGCCTGTGGAT 61.018 66.667 0.00 0.00 0.00 3.41
3204 3554 9.678260 ACATATAAAATGAAAGACTCTTGAGCT 57.322 29.630 0.00 0.00 0.00 4.09
3209 3559 8.457238 AAAATGAAAGACTCTTGAGCTAAACT 57.543 30.769 0.00 0.00 0.00 2.66
3210 3560 8.457238 AAATGAAAGACTCTTGAGCTAAACTT 57.543 30.769 0.00 0.00 0.00 2.66
3211 3561 8.457238 AATGAAAGACTCTTGAGCTAAACTTT 57.543 30.769 0.00 0.00 0.00 2.66
3212 3562 7.865706 TGAAAGACTCTTGAGCTAAACTTTT 57.134 32.000 0.00 0.00 0.00 2.27
3213 3563 7.920738 TGAAAGACTCTTGAGCTAAACTTTTC 58.079 34.615 0.00 0.00 0.00 2.29
3214 3564 7.552687 TGAAAGACTCTTGAGCTAAACTTTTCA 59.447 33.333 0.00 0.00 0.00 2.69
3215 3565 7.489574 AAGACTCTTGAGCTAAACTTTTCAG 57.510 36.000 0.00 0.00 0.00 3.02
3271 3621 4.640789 TTTTTGAAGGCAGCGAAAGTAA 57.359 36.364 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.865365 AGAAAATGTTCGCGGTTTCAAAAA 59.135 33.333 6.13 0.00 38.90 1.94
4 5 4.266502 CAGAAAATGTTCGCGGTTTCAAAA 59.733 37.500 6.13 0.00 38.90 2.44
5 6 3.794028 CAGAAAATGTTCGCGGTTTCAAA 59.206 39.130 6.13 0.00 38.90 2.69
6 7 3.065510 TCAGAAAATGTTCGCGGTTTCAA 59.934 39.130 6.13 0.00 38.90 2.69
7 8 2.614520 TCAGAAAATGTTCGCGGTTTCA 59.385 40.909 6.13 0.75 38.90 2.69
8 9 3.262135 TCAGAAAATGTTCGCGGTTTC 57.738 42.857 6.13 8.89 38.90 2.78
9 10 3.701532 TTCAGAAAATGTTCGCGGTTT 57.298 38.095 6.13 0.00 38.90 3.27
10 11 3.701532 TTTCAGAAAATGTTCGCGGTT 57.298 38.095 6.13 0.00 38.90 4.44
11 12 3.252215 TGATTTCAGAAAATGTTCGCGGT 59.748 39.130 6.13 0.00 38.90 5.68
12 13 3.820689 TGATTTCAGAAAATGTTCGCGG 58.179 40.909 6.13 0.00 38.90 6.46
13 14 5.088068 TCATGATTTCAGAAAATGTTCGCG 58.912 37.500 0.00 0.00 38.90 5.87
14 15 6.183360 GGTTCATGATTTCAGAAAATGTTCGC 60.183 38.462 0.00 0.00 38.90 4.70
15 16 6.862608 TGGTTCATGATTTCAGAAAATGTTCG 59.137 34.615 0.00 0.00 38.90 3.95
16 17 8.767478 ATGGTTCATGATTTCAGAAAATGTTC 57.233 30.769 0.00 0.00 35.21 3.18
17 18 9.563748 AAATGGTTCATGATTTCAGAAAATGTT 57.436 25.926 0.00 0.00 35.21 2.71
18 19 9.563748 AAAATGGTTCATGATTTCAGAAAATGT 57.436 25.926 0.00 0.00 35.21 2.71
96 97 5.631512 CAGAAAGTGTTCACGGTTTCAAAAA 59.368 36.000 15.07 0.00 36.09 1.94
97 98 5.048643 TCAGAAAGTGTTCACGGTTTCAAAA 60.049 36.000 15.07 3.47 36.09 2.44
98 99 4.456222 TCAGAAAGTGTTCACGGTTTCAAA 59.544 37.500 15.07 5.11 36.09 2.69
99 100 4.004314 TCAGAAAGTGTTCACGGTTTCAA 58.996 39.130 15.07 5.34 36.09 2.69
100 101 3.601435 TCAGAAAGTGTTCACGGTTTCA 58.399 40.909 15.07 0.24 36.09 2.69
101 102 4.609691 TTCAGAAAGTGTTCACGGTTTC 57.390 40.909 8.58 8.58 36.09 2.78
102 103 5.124776 TGATTTCAGAAAGTGTTCACGGTTT 59.875 36.000 1.28 0.00 36.09 3.27
103 104 4.638421 TGATTTCAGAAAGTGTTCACGGTT 59.362 37.500 1.28 0.00 36.09 4.44
104 105 4.196193 TGATTTCAGAAAGTGTTCACGGT 58.804 39.130 1.28 0.00 36.09 4.83
105 106 4.811555 TGATTTCAGAAAGTGTTCACGG 57.188 40.909 1.28 0.00 36.09 4.94
106 107 5.989249 TCATGATTTCAGAAAGTGTTCACG 58.011 37.500 1.28 0.00 36.09 4.35
107 108 6.638468 GGTTCATGATTTCAGAAAGTGTTCAC 59.362 38.462 0.00 0.00 36.09 3.18
108 109 6.547141 AGGTTCATGATTTCAGAAAGTGTTCA 59.453 34.615 0.00 0.80 36.09 3.18
109 110 6.974965 AGGTTCATGATTTCAGAAAGTGTTC 58.025 36.000 0.00 0.00 0.00 3.18
110 111 6.966534 AGGTTCATGATTTCAGAAAGTGTT 57.033 33.333 0.00 0.00 0.00 3.32
111 112 6.966534 AAGGTTCATGATTTCAGAAAGTGT 57.033 33.333 0.00 0.00 0.00 3.55
112 113 8.652810 AAAAAGGTTCATGATTTCAGAAAGTG 57.347 30.769 0.00 1.23 0.00 3.16
153 154 5.172951 CAGAACATGTTCGCGATTTCAAAAA 59.827 36.000 28.18 0.00 43.97 1.94
154 155 4.674662 CAGAACATGTTCGCGATTTCAAAA 59.325 37.500 28.18 0.00 43.97 2.44
155 156 4.024472 TCAGAACATGTTCGCGATTTCAAA 60.024 37.500 28.18 7.39 43.97 2.69
156 157 3.496507 TCAGAACATGTTCGCGATTTCAA 59.503 39.130 28.18 7.99 43.97 2.69
157 158 3.063485 TCAGAACATGTTCGCGATTTCA 58.937 40.909 28.18 10.66 43.97 2.69
158 159 3.722555 TCAGAACATGTTCGCGATTTC 57.277 42.857 28.18 8.13 43.97 2.17
159 160 4.481930 TTTCAGAACATGTTCGCGATTT 57.518 36.364 28.18 10.90 43.97 2.17
160 161 4.154015 TGATTTCAGAACATGTTCGCGATT 59.846 37.500 28.18 19.13 43.97 3.34
161 162 3.684305 TGATTTCAGAACATGTTCGCGAT 59.316 39.130 28.18 20.84 43.97 4.58
162 163 3.063485 TGATTTCAGAACATGTTCGCGA 58.937 40.909 28.18 24.99 43.97 5.87
163 164 3.454042 TGATTTCAGAACATGTTCGCG 57.546 42.857 28.18 23.42 43.97 5.87
164 165 4.973396 TCATGATTTCAGAACATGTTCGC 58.027 39.130 28.18 16.45 43.97 4.70
165 166 6.372981 TGTTCATGATTTCAGAACATGTTCG 58.627 36.000 28.18 22.80 44.60 3.95
198 199 9.757227 TCAGGAATTTAAAAATGTTCGTGAATT 57.243 25.926 16.47 0.00 32.01 2.17
199 200 9.757227 TTCAGGAATTTAAAAATGTTCGTGAAT 57.243 25.926 21.74 0.00 36.33 2.57
200 201 9.026074 GTTCAGGAATTTAAAAATGTTCGTGAA 57.974 29.630 21.74 21.74 37.51 3.18
201 202 7.377397 CGTTCAGGAATTTAAAAATGTTCGTGA 59.623 33.333 15.49 15.49 32.58 4.35
202 203 7.166804 ACGTTCAGGAATTTAAAAATGTTCGTG 59.833 33.333 12.51 12.51 0.00 4.35
203 204 7.197703 ACGTTCAGGAATTTAAAAATGTTCGT 58.802 30.769 0.00 2.98 0.00 3.85
204 205 7.617533 ACGTTCAGGAATTTAAAAATGTTCG 57.382 32.000 0.00 2.47 0.00 3.95
205 206 9.026074 TGAACGTTCAGGAATTTAAAAATGTTC 57.974 29.630 26.53 18.06 40.48 3.18
206 207 8.813282 GTGAACGTTCAGGAATTTAAAAATGTT 58.187 29.630 30.38 5.68 37.98 2.71
207 208 8.194769 AGTGAACGTTCAGGAATTTAAAAATGT 58.805 29.630 30.38 0.00 37.98 2.71
208 209 8.574196 AGTGAACGTTCAGGAATTTAAAAATG 57.426 30.769 30.38 0.00 37.98 2.32
209 210 9.030301 CAAGTGAACGTTCAGGAATTTAAAAAT 57.970 29.630 30.38 1.02 37.98 1.82
210 211 8.244802 TCAAGTGAACGTTCAGGAATTTAAAAA 58.755 29.630 30.38 1.43 37.98 1.94
211 212 7.763356 TCAAGTGAACGTTCAGGAATTTAAAA 58.237 30.769 30.38 1.65 37.98 1.52
212 213 7.323049 TCAAGTGAACGTTCAGGAATTTAAA 57.677 32.000 30.38 2.21 37.98 1.52
213 214 6.928979 TCAAGTGAACGTTCAGGAATTTAA 57.071 33.333 30.38 10.89 37.98 1.52
214 215 6.721321 GTTCAAGTGAACGTTCAGGAATTTA 58.279 36.000 30.38 12.03 43.97 1.40
215 216 5.578776 GTTCAAGTGAACGTTCAGGAATTT 58.421 37.500 30.38 16.26 43.97 1.82
216 217 5.169836 GTTCAAGTGAACGTTCAGGAATT 57.830 39.130 30.38 18.90 43.97 2.17
217 218 4.813296 GTTCAAGTGAACGTTCAGGAAT 57.187 40.909 30.38 14.32 43.97 3.01
256 257 9.618890 TGTTGATGAATTTAAAAATGTTTGGGA 57.381 25.926 0.00 0.00 0.00 4.37
257 258 9.881529 CTGTTGATGAATTTAAAAATGTTTGGG 57.118 29.630 0.00 0.00 0.00 4.12
290 291 7.894847 GTTCAAGTGAACGTTCATGAATTTTT 58.105 30.769 33.26 18.75 43.97 1.94
291 292 7.449934 GTTCAAGTGAACGTTCATGAATTTT 57.550 32.000 33.26 20.00 43.97 1.82
714 715 3.008594 TCGGGCCCAATACTATATTGTGG 59.991 47.826 24.92 0.00 0.00 4.17
715 716 4.280436 TCGGGCCCAATACTATATTGTG 57.720 45.455 24.92 0.00 0.00 3.33
716 717 5.497474 GAATCGGGCCCAATACTATATTGT 58.503 41.667 24.92 0.00 0.00 2.71
717 718 4.881850 GGAATCGGGCCCAATACTATATTG 59.118 45.833 24.92 0.00 0.00 1.90
718 719 4.538490 TGGAATCGGGCCCAATACTATATT 59.462 41.667 24.92 7.40 0.00 1.28
719 720 4.108570 TGGAATCGGGCCCAATACTATAT 58.891 43.478 24.92 0.00 0.00 0.86
720 721 3.522759 TGGAATCGGGCCCAATACTATA 58.477 45.455 24.92 0.00 0.00 1.31
721 722 2.344592 TGGAATCGGGCCCAATACTAT 58.655 47.619 24.92 1.50 0.00 2.12
722 723 1.809133 TGGAATCGGGCCCAATACTA 58.191 50.000 24.92 5.23 0.00 1.82
723 724 1.149101 ATGGAATCGGGCCCAATACT 58.851 50.000 24.92 0.00 35.85 2.12
724 725 1.886542 GAATGGAATCGGGCCCAATAC 59.113 52.381 24.92 8.30 35.85 1.89
725 726 1.496857 TGAATGGAATCGGGCCCAATA 59.503 47.619 24.92 6.78 35.85 1.90
726 727 0.261402 TGAATGGAATCGGGCCCAAT 59.739 50.000 24.92 5.75 35.85 3.16
727 728 0.040351 TTGAATGGAATCGGGCCCAA 59.960 50.000 24.92 2.23 35.85 4.12
728 729 0.040351 TTTGAATGGAATCGGGCCCA 59.960 50.000 24.92 9.77 36.79 5.36
732 733 4.440525 CCACTGAATTTGAATGGAATCGGG 60.441 45.833 0.00 0.00 31.69 5.14
769 770 4.933064 GAGATCGACTGCGGCGGG 62.933 72.222 14.26 2.36 38.28 6.13
771 772 4.538283 ACGAGATCGACTGCGGCG 62.538 66.667 9.58 0.51 43.02 6.46
772 773 2.202623 AACGAGATCGACTGCGGC 60.203 61.111 9.58 0.00 43.02 6.53
773 774 1.874019 CCAACGAGATCGACTGCGG 60.874 63.158 9.58 0.00 43.02 5.69
775 776 2.273370 TAACCAACGAGATCGACTGC 57.727 50.000 9.58 0.00 43.02 4.40
776 777 5.779806 AATTTAACCAACGAGATCGACTG 57.220 39.130 9.58 5.77 43.02 3.51
803 804 7.461107 TGCGTTTTCCGAGATCTAAATTTAAG 58.539 34.615 0.00 0.00 39.56 1.85
809 810 3.259064 CCTGCGTTTTCCGAGATCTAAA 58.741 45.455 0.00 0.00 39.56 1.85
827 828 1.236616 TTCACAATCTGGTGCGCCTG 61.237 55.000 18.96 17.66 38.66 4.85
830 831 1.621107 CATTTCACAATCTGGTGCGC 58.379 50.000 0.00 0.00 38.66 6.09
836 837 3.960571 AGTCCCTCCATTTCACAATCTG 58.039 45.455 0.00 0.00 0.00 2.90
838 839 5.684704 TGATAGTCCCTCCATTTCACAATC 58.315 41.667 0.00 0.00 0.00 2.67
864 865 2.809119 CACGGTGGTGCAAACAGTTATA 59.191 45.455 0.00 0.00 37.35 0.98
914 926 3.324207 GGGGGCCGATTTCAGATAC 57.676 57.895 0.00 0.00 0.00 2.24
933 945 8.603181 TGTTCTTGTCAATATGATATGACGTTG 58.397 33.333 0.00 0.00 46.99 4.10
934 946 8.716646 TGTTCTTGTCAATATGATATGACGTT 57.283 30.769 0.00 0.00 46.99 3.99
944 956 5.389859 TTTGGGCTGTTCTTGTCAATATG 57.610 39.130 0.00 0.00 0.00 1.78
945 957 6.351286 GGAATTTGGGCTGTTCTTGTCAATAT 60.351 38.462 0.00 0.00 0.00 1.28
946 958 5.047377 GGAATTTGGGCTGTTCTTGTCAATA 60.047 40.000 0.00 0.00 0.00 1.90
947 959 4.262592 GGAATTTGGGCTGTTCTTGTCAAT 60.263 41.667 0.00 0.00 0.00 2.57
948 960 3.069443 GGAATTTGGGCTGTTCTTGTCAA 59.931 43.478 0.00 0.00 0.00 3.18
949 961 2.627699 GGAATTTGGGCTGTTCTTGTCA 59.372 45.455 0.00 0.00 0.00 3.58
950 962 2.029020 GGGAATTTGGGCTGTTCTTGTC 60.029 50.000 0.00 0.00 0.00 3.18
968 980 4.715130 CCTGGGTGGAGACGGGGA 62.715 72.222 0.00 0.00 38.35 4.81
988 1002 2.484264 GGATTAAAATGAGATCGCCCCG 59.516 50.000 0.00 0.00 0.00 5.73
989 1003 2.820197 GGGATTAAAATGAGATCGCCCC 59.180 50.000 0.00 0.00 0.00 5.80
990 1004 3.253432 GTGGGATTAAAATGAGATCGCCC 59.747 47.826 0.00 0.00 33.34 6.13
991 1005 3.058914 CGTGGGATTAAAATGAGATCGCC 60.059 47.826 0.00 0.00 33.34 5.54
992 1006 3.607078 GCGTGGGATTAAAATGAGATCGC 60.607 47.826 0.00 0.00 34.46 4.58
993 1007 3.362986 CGCGTGGGATTAAAATGAGATCG 60.363 47.826 0.00 0.00 0.00 3.69
994 1008 3.807622 TCGCGTGGGATTAAAATGAGATC 59.192 43.478 5.77 0.00 0.00 2.75
999 1013 2.349438 CGGATCGCGTGGGATTAAAATG 60.349 50.000 5.77 0.00 0.00 2.32
1003 1017 0.677288 ATCGGATCGCGTGGGATTAA 59.323 50.000 5.77 0.00 0.00 1.40
1033 1047 2.096713 GCGATTCCGTATGTTCATGAGC 60.097 50.000 2.05 2.05 38.24 4.26
1035 1049 2.479837 GGCGATTCCGTATGTTCATGA 58.520 47.619 0.00 0.00 38.24 3.07
1067 1081 3.499737 GGTTGGCCATGAGACGCG 61.500 66.667 6.09 3.53 34.09 6.01
1068 1082 2.359850 TGGTTGGCCATGAGACGC 60.360 61.111 6.09 0.00 40.46 5.19
1136 1150 3.755628 CGAGGAAACGGCGGGAGA 61.756 66.667 13.24 0.00 0.00 3.71
1146 1160 3.713288 CAACCGATAGTATGCGAGGAAA 58.287 45.455 0.00 0.00 0.00 3.13
1162 1181 1.237285 CCTGGGAGTGAAAGCAACCG 61.237 60.000 0.00 0.00 0.00 4.44
1168 1187 2.728007 GGAAATCCCTGGGAGTGAAAG 58.272 52.381 21.99 0.00 34.05 2.62
1231 1261 7.496920 TGGAAGTCAGAATATGTCATCATGTTC 59.503 37.037 8.79 8.79 45.83 3.18
1242 1272 8.195436 AGATGCAAAATTGGAAGTCAGAATATG 58.805 33.333 0.00 0.00 30.51 1.78
1253 1283 4.317488 GGCTGAAAGATGCAAAATTGGAA 58.683 39.130 0.00 0.00 34.07 3.53
1351 1381 9.075678 AGAATTAAAGGAATCAAGCCATATCTG 57.924 33.333 0.00 0.00 0.00 2.90
1387 1419 9.191995 CGCACAAATATCATATCAGTAGTACAA 57.808 33.333 2.52 0.00 0.00 2.41
1388 1420 7.328493 GCGCACAAATATCATATCAGTAGTACA 59.672 37.037 0.30 0.00 0.00 2.90
1389 1421 7.461546 CGCGCACAAATATCATATCAGTAGTAC 60.462 40.741 8.75 0.00 0.00 2.73
1390 1422 6.526674 CGCGCACAAATATCATATCAGTAGTA 59.473 38.462 8.75 0.00 0.00 1.82
1391 1423 5.346011 CGCGCACAAATATCATATCAGTAGT 59.654 40.000 8.75 0.00 0.00 2.73
1392 1424 5.722321 GCGCGCACAAATATCATATCAGTAG 60.722 44.000 29.10 0.00 0.00 2.57
1393 1425 4.091365 GCGCGCACAAATATCATATCAGTA 59.909 41.667 29.10 0.00 0.00 2.74
1395 1427 3.124128 AGCGCGCACAAATATCATATCAG 59.876 43.478 35.10 0.00 0.00 2.90
1396 1428 3.066380 AGCGCGCACAAATATCATATCA 58.934 40.909 35.10 0.00 0.00 2.15
1397 1429 3.410850 CAGCGCGCACAAATATCATATC 58.589 45.455 35.10 0.00 0.00 1.63
1398 1430 2.413239 GCAGCGCGCACAAATATCATAT 60.413 45.455 35.10 3.94 41.79 1.78
1399 1431 1.069973 GCAGCGCGCACAAATATCATA 60.070 47.619 35.10 0.00 41.79 2.15
1400 1432 0.317269 GCAGCGCGCACAAATATCAT 60.317 50.000 35.10 4.83 41.79 2.45
1401 1433 1.062365 GCAGCGCGCACAAATATCA 59.938 52.632 35.10 0.00 41.79 2.15
1402 1434 3.893803 GCAGCGCGCACAAATATC 58.106 55.556 35.10 8.44 41.79 1.63
1442 1474 1.004918 AAGTGGCGTGTAGTGGAGC 60.005 57.895 0.00 0.00 0.00 4.70
1446 1593 0.389948 GGAGGAAGTGGCGTGTAGTG 60.390 60.000 0.00 0.00 0.00 2.74
1492 1639 5.187967 ACAAGAGGAGGTGGTGAATTAGTAG 59.812 44.000 0.00 0.00 0.00 2.57
1500 1647 2.103153 AGAACAAGAGGAGGTGGTGA 57.897 50.000 0.00 0.00 0.00 4.02
1501 1648 2.938956 AAGAACAAGAGGAGGTGGTG 57.061 50.000 0.00 0.00 0.00 4.17
1502 1649 2.777692 TGAAAGAACAAGAGGAGGTGGT 59.222 45.455 0.00 0.00 0.00 4.16
1554 1701 2.631418 TCGTCGGTGAGAAACTGATC 57.369 50.000 0.00 0.00 45.96 2.92
1619 1766 1.966451 CGGGTCAAACAGAGCACCC 60.966 63.158 0.00 0.00 46.51 4.61
1629 1776 1.067821 GGTGAAAACATGCGGGTCAAA 59.932 47.619 0.00 0.00 0.00 2.69
1686 1833 0.179100 CTACCGTCATCCACCAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
1709 1856 1.746322 TTTACCACCGTGTCTCCGCA 61.746 55.000 0.00 0.00 0.00 5.69
1777 1924 2.672996 CACCTTGCCAACTCCGGG 60.673 66.667 0.00 0.00 0.00 5.73
1860 2080 9.013229 TGTCGAAATAAACTACTACTCCAGTAA 57.987 33.333 0.00 0.00 39.28 2.24
1861 2081 8.565896 TGTCGAAATAAACTACTACTCCAGTA 57.434 34.615 0.00 0.00 38.80 2.74
1862 2082 7.392673 TCTGTCGAAATAAACTACTACTCCAGT 59.607 37.037 0.00 0.00 41.62 4.00
1863 2083 7.759465 TCTGTCGAAATAAACTACTACTCCAG 58.241 38.462 0.00 0.00 0.00 3.86
1864 2084 7.692460 TCTGTCGAAATAAACTACTACTCCA 57.308 36.000 0.00 0.00 0.00 3.86
1865 2085 8.457261 TCTTCTGTCGAAATAAACTACTACTCC 58.543 37.037 0.00 0.00 0.00 3.85
1867 2087 9.790389 CATCTTCTGTCGAAATAAACTACTACT 57.210 33.333 0.00 0.00 0.00 2.57
1868 2088 9.784680 TCATCTTCTGTCGAAATAAACTACTAC 57.215 33.333 0.00 0.00 0.00 2.73
1882 2102 3.631686 AGATCTCACCTCATCTTCTGTCG 59.368 47.826 0.00 0.00 0.00 4.35
1896 2118 1.409427 CCCCCTGTTACGAGATCTCAC 59.591 57.143 22.31 13.27 0.00 3.51
1907 2129 4.231890 AGGCTGATTAATTTCCCCCTGTTA 59.768 41.667 0.00 0.00 0.00 2.41
1913 2135 5.804639 ACAAAAAGGCTGATTAATTTCCCC 58.195 37.500 0.00 0.00 0.00 4.81
2168 2444 1.732259 CAACATTACTGCGGTGAGGAC 59.268 52.381 8.92 0.00 0.00 3.85
2170 2446 0.447801 GCAACATTACTGCGGTGAGG 59.552 55.000 8.92 4.13 0.00 3.86
2194 2470 3.965258 TGCGGCTGACCCATGGTT 61.965 61.111 11.73 0.00 35.25 3.67
2202 2478 0.317938 CGAGTATAGGTGCGGCTGAC 60.318 60.000 0.00 0.00 0.00 3.51
2235 2511 0.107703 TCCCCGAACATGATGTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
2249 2526 1.988834 GCGTTAGGCACAAATCCCCG 61.989 60.000 0.00 0.00 42.87 5.73
2343 2624 9.920946 TTTCTATTTTATTCCTTATGGCACTCT 57.079 29.630 0.00 0.00 0.00 3.24
2379 2663 4.456911 CACATGGAGAAAACTACATGCACT 59.543 41.667 18.60 1.45 46.76 4.40
2547 2837 6.995091 GCTTTCACATAACCATCTCTATCCTT 59.005 38.462 0.00 0.00 0.00 3.36
2596 2887 5.747951 AGAAGAAAAGAACTCTTGTGCTG 57.252 39.130 0.00 0.00 36.12 4.41
2749 3045 0.623324 CCCCTCCTGGTTGTCCCATA 60.623 60.000 0.00 0.00 44.15 2.74
2786 3083 0.184451 ATCTATGTGGGCCCAAGCAG 59.816 55.000 30.64 22.71 42.56 4.24
2809 3106 1.144298 AGGCCTACACCCTTTCGTTTT 59.856 47.619 1.29 0.00 0.00 2.43
2813 3110 1.078426 CCAGGCCTACACCCTTTCG 60.078 63.158 3.98 0.00 0.00 3.46
2821 3118 2.043939 TCTAGAAAGGACCAGGCCTACA 59.956 50.000 3.98 0.00 37.26 2.74
2879 3184 3.719268 ACTGCTTTCATGGGATACACA 57.281 42.857 0.00 0.00 39.74 3.72
2880 3185 7.801716 TTAATACTGCTTTCATGGGATACAC 57.198 36.000 0.00 0.00 39.74 2.90
2961 3270 1.152525 GCCTCCCTATCGGTGAGGA 60.153 63.158 19.03 0.00 44.31 3.71
2962 3271 1.152440 AGCCTCCCTATCGGTGAGG 60.152 63.158 13.41 13.41 44.35 3.86
2963 3272 0.178975 AGAGCCTCCCTATCGGTGAG 60.179 60.000 0.00 0.00 0.00 3.51
2964 3273 0.178987 GAGAGCCTCCCTATCGGTGA 60.179 60.000 0.00 0.00 0.00 4.02
2965 3274 1.182385 GGAGAGCCTCCCTATCGGTG 61.182 65.000 9.46 0.00 44.36 4.94
2966 3275 1.154221 GGAGAGCCTCCCTATCGGT 59.846 63.158 9.46 0.00 44.36 4.69
2967 3276 4.105388 GGAGAGCCTCCCTATCGG 57.895 66.667 9.46 0.00 44.36 4.18
2989 3301 5.356426 CGGGAAATTATGAAATTTGTCCCC 58.644 41.667 12.08 10.04 43.51 4.81
2990 3302 4.808895 GCGGGAAATTATGAAATTTGTCCC 59.191 41.667 0.00 9.27 43.69 4.46
2995 3307 6.280643 GCTTAGGCGGGAAATTATGAAATTT 58.719 36.000 0.00 0.00 45.78 1.82
3122 3460 1.607225 ATTTATCCACAGGCTCCCCA 58.393 50.000 0.00 0.00 0.00 4.96
3124 3462 3.131046 CACAAATTTATCCACAGGCTCCC 59.869 47.826 0.00 0.00 0.00 4.30
3137 3475 9.081997 CACTTTCAAAGTAACAGCACAAATTTA 57.918 29.630 1.43 0.00 40.46 1.40
3191 3541 7.051000 ACTGAAAAGTTTAGCTCAAGAGTCTT 58.949 34.615 0.00 0.00 0.00 3.01
3199 3549 7.566760 TGATGAAACTGAAAAGTTTAGCTCA 57.433 32.000 3.95 5.29 41.49 4.26
3204 3554 8.188139 GTGACCTTGATGAAACTGAAAAGTTTA 58.812 33.333 3.95 0.00 41.49 2.01
3205 3555 7.035612 GTGACCTTGATGAAACTGAAAAGTTT 58.964 34.615 3.61 3.61 43.77 2.66
3206 3556 6.152661 TGTGACCTTGATGAAACTGAAAAGTT 59.847 34.615 0.00 0.00 0.00 2.66
3207 3557 5.652014 TGTGACCTTGATGAAACTGAAAAGT 59.348 36.000 0.00 0.00 0.00 2.66
3208 3558 5.973565 GTGTGACCTTGATGAAACTGAAAAG 59.026 40.000 0.00 0.00 0.00 2.27
3209 3559 5.417266 TGTGTGACCTTGATGAAACTGAAAA 59.583 36.000 0.00 0.00 0.00 2.29
3210 3560 4.946772 TGTGTGACCTTGATGAAACTGAAA 59.053 37.500 0.00 0.00 0.00 2.69
3211 3561 4.522114 TGTGTGACCTTGATGAAACTGAA 58.478 39.130 0.00 0.00 0.00 3.02
3212 3562 4.149511 TGTGTGACCTTGATGAAACTGA 57.850 40.909 0.00 0.00 0.00 3.41
3213 3563 4.898829 TTGTGTGACCTTGATGAAACTG 57.101 40.909 0.00 0.00 0.00 3.16
3214 3564 5.192927 TCTTTGTGTGACCTTGATGAAACT 58.807 37.500 0.00 0.00 0.00 2.66
3215 3565 5.499139 TCTTTGTGTGACCTTGATGAAAC 57.501 39.130 0.00 0.00 0.00 2.78
3255 3605 5.993106 ATATCTTTACTTTCGCTGCCTTC 57.007 39.130 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.