Multiple sequence alignment - TraesCS5B01G175300

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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 TraesCS5B01G175300 chr5B 100.000 2900 0 0 1 2900 321479089 321476190 0.000000e+00 5356
1 TraesCS5B01G175300 chr2D 88.235 1615 77 38 340 1933 85252345 85250823 0.000000e+00 1825
2 TraesCS5B01G175300 chr2D 91.732 1270 66 14 485 1746 84780779 84779541 0.000000e+00 1727
3 TraesCS5B01G175300 chr2D 92.180 1087 56 12 671 1756 85408973 85407915 0.000000e+00 1509
4 TraesCS5B01G175300 chr2D 90.583 1115 48 19 833 1933 85703786 85702715 0.000000e+00 1424
5 TraesCS5B01G175300 chr2D 86.133 1125 106 22 845 1933 83225228 83226338 0.000000e+00 1168
6 TraesCS5B01G175300 chr2D 94.611 167 9 0 2681 2847 85248929 85248763 2.870000e-65 259
7 TraesCS5B01G175300 chr2D 93.793 145 6 1 2703 2847 85701823 85701682 6.290000e-52 215
8 TraesCS5B01G175300 chr2D 83.929 224 34 2 10 231 155725222 155724999 2.260000e-51 213
9 TraesCS5B01G175300 chr2D 85.096 208 29 2 10 216 139257253 139257459 8.140000e-51 211
10 TraesCS5B01G175300 chr2D 84.579 214 11 10 340 542 84938324 84938122 2.950000e-45 193
11 TraesCS5B01G175300 chr2D 84.579 214 11 10 340 542 85409172 85408970 2.950000e-45 193
12 TraesCS5B01G175300 chr2B 92.247 1277 79 10 672 1933 137349499 137348228 0.000000e+00 1792
13 TraesCS5B01G175300 chr2B 91.949 1267 73 12 491 1756 136639342 136638104 0.000000e+00 1748
14 TraesCS5B01G175300 chr2B 92.093 1113 75 3 834 1933 137814501 137813389 0.000000e+00 1555
15 TraesCS5B01G175300 chr2B 91.736 1089 55 16 671 1756 137622677 137621621 0.000000e+00 1480
16 TraesCS5B01G175300 chr2B 87.811 1124 106 16 834 1933 135357980 135359096 0.000000e+00 1288
17 TraesCS5B01G175300 chr2B 85.179 1147 111 22 832 1933 135126705 135127837 0.000000e+00 1122
18 TraesCS5B01G175300 chr2B 95.808 167 7 0 2681 2847 137347330 137347164 1.320000e-68 270
19 TraesCS5B01G175300 chr2B 94.611 167 9 0 2681 2847 136635683 136635517 2.870000e-65 259
20 TraesCS5B01G175300 chr2B 84.038 213 13 11 340 542 136815512 136815311 4.930000e-43 185
21 TraesCS5B01G175300 chr2B 84.038 213 13 11 340 542 137015169 137014968 4.930000e-43 185
22 TraesCS5B01G175300 chr2B 77.447 235 30 11 84 295 582813006 582813240 5.080000e-23 119
23 TraesCS5B01G175300 chr5D 96.622 1036 25 3 904 1933 283110310 283109279 0.000000e+00 1711
24 TraesCS5B01G175300 chr5D 94.562 901 22 10 1947 2847 283109226 283108353 0.000000e+00 1367
25 TraesCS5B01G175300 chr5D 85.778 1118 100 23 845 1934 230369070 230370156 0.000000e+00 1129
26 TraesCS5B01G175300 chr5D 91.801 744 51 8 1947 2688 289420063 289419328 0.000000e+00 1027
27 TraesCS5B01G175300 chr5D 91.532 744 53 8 1947 2688 289354256 289353521 0.000000e+00 1016
28 TraesCS5B01G175300 chr5D 95.194 645 15 6 293 931 283110948 283110314 0.000000e+00 1005
29 TraesCS5B01G175300 chr5D 93.413 167 11 0 2681 2847 289353403 289353237 6.210000e-62 248
30 TraesCS5B01G175300 chr7A 90.973 1274 60 19 671 1933 618195514 618194285 0.000000e+00 1664
31 TraesCS5B01G175300 chr7A 92.318 729 46 8 1947 2673 627007695 627006975 0.000000e+00 1027
32 TraesCS5B01G175300 chr7A 91.801 744 51 8 1947 2688 628384897 628384162 0.000000e+00 1027
33 TraesCS5B01G175300 chr7A 90.674 193 6 4 354 542 618195695 618195511 2.230000e-61 246
34 TraesCS5B01G175300 chr7A 92.398 171 12 1 2681 2851 628384044 628383875 2.890000e-60 243
35 TraesCS5B01G175300 chr2A 89.540 1109 72 16 834 1933 84143642 84144715 0.000000e+00 1365
36 TraesCS5B01G175300 chr2A 87.245 1129 105 21 834 1933 83984996 83986114 0.000000e+00 1251
37 TraesCS5B01G175300 chr2A 91.951 733 46 12 1947 2673 84144768 84145493 0.000000e+00 1014
38 TraesCS5B01G175300 chr2A 84.136 353 18 22 340 690 85614038 85613722 1.010000e-79 307
39 TraesCS5B01G175300 chr2A 84.136 353 18 22 340 690 85811556 85811240 1.010000e-79 307
40 TraesCS5B01G175300 chr2A 83.853 353 19 22 340 690 85927463 85927147 4.700000e-78 302
41 TraesCS5B01G175300 chr5A 85.843 1109 97 24 854 1933 326437925 326436848 0.000000e+00 1123
42 TraesCS5B01G175300 chr5A 89.297 327 8 6 410 730 375377685 375377380 4.530000e-103 385
43 TraesCS5B01G175300 chr5A 82.759 232 34 4 1 231 675522120 675522346 4.900000e-48 202
44 TraesCS5B01G175300 chr7B 91.678 745 51 9 1947 2688 589695275 589694539 0.000000e+00 1022
45 TraesCS5B01G175300 chr7B 92.181 729 47 8 1947 2673 589736332 589737052 0.000000e+00 1022
46 TraesCS5B01G175300 chr7B 82.943 299 31 10 10 291 699171807 699171512 4.800000e-63 252
47 TraesCS5B01G175300 chr7B 84.753 223 33 1 10 231 126170586 126170364 3.760000e-54 222
48 TraesCS5B01G175300 chr7B 84.305 223 34 1 10 231 126207677 126207455 1.750000e-52 217
49 TraesCS5B01G175300 chr7B 83.333 234 33 4 1 231 63132940 63132710 8.140000e-51 211
50 TraesCS5B01G175300 chr7B 86.364 132 16 2 677 807 243910176 243910046 3.010000e-30 143
51 TraesCS5B01G175300 chr1B 91.667 744 52 8 1947 2688 133123133 133122398 0.000000e+00 1022
52 TraesCS5B01G175300 chr1B 91.398 744 54 8 1947 2688 426495938 426495203 0.000000e+00 1011
53 TraesCS5B01G175300 chr1B 92.814 167 10 1 2681 2847 133122286 133122122 1.040000e-59 241
54 TraesCS5B01G175300 chrUn 84.136 353 18 22 340 690 354326380 354326064 1.010000e-79 307
55 TraesCS5B01G175300 chr4A 84.136 353 18 22 340 690 349807091 349806775 1.010000e-79 307
56 TraesCS5B01G175300 chr4A 92.414 145 8 1 2703 2847 349804579 349804438 1.360000e-48 204
57 TraesCS5B01G175300 chr4B 83.056 301 41 6 1 291 449195388 449195688 6.160000e-67 265
58 TraesCS5B01G175300 chr4B 78.445 283 35 13 32 291 595302436 595302157 8.320000e-36 161
59 TraesCS5B01G175300 chr3B 83.333 288 40 7 4 287 502631610 502631327 2.870000e-65 259
60 TraesCS5B01G175300 chr3B 86.813 91 9 2 11 101 236494399 236494486 6.610000e-17 99
61 TraesCS5B01G175300 chr6A 84.444 225 32 3 10 231 108938849 108939073 4.870000e-53 219
62 TraesCS5B01G175300 chr3D 81.818 286 29 9 25 287 120104689 120104404 4.870000e-53 219
63 TraesCS5B01G175300 chr1D 83.857 223 35 1 10 231 351509987 351509765 8.140000e-51 211
64 TraesCS5B01G175300 chr6D 81.308 214 37 3 11 221 90121102 90120889 1.380000e-38 171
65 TraesCS5B01G175300 chr3A 88.636 132 13 2 677 807 564437957 564437827 2.990000e-35 159
66 TraesCS5B01G175300 chr6B 76.375 309 43 14 12 291 159697593 159697900 3.900000e-29 139


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 TraesCS5B01G175300 chr5B 321476190 321479089 2899 True 5356.0 5356 100.000000 1 2900 1 chr5B.!!$R1 2899
1 TraesCS5B01G175300 chr2D 84779541 84780779 1238 True 1727.0 1727 91.732000 485 1746 1 chr2D.!!$R1 1261
2 TraesCS5B01G175300 chr2D 83225228 83226338 1110 False 1168.0 1168 86.133000 845 1933 1 chr2D.!!$F1 1088
3 TraesCS5B01G175300 chr2D 85248763 85252345 3582 True 1042.0 1825 91.423000 340 2847 2 chr2D.!!$R4 2507
4 TraesCS5B01G175300 chr2D 85407915 85409172 1257 True 851.0 1509 88.379500 340 1756 2 chr2D.!!$R5 1416
5 TraesCS5B01G175300 chr2D 85701682 85703786 2104 True 819.5 1424 92.188000 833 2847 2 chr2D.!!$R6 2014
6 TraesCS5B01G175300 chr2B 137813389 137814501 1112 True 1555.0 1555 92.093000 834 1933 1 chr2B.!!$R4 1099
7 TraesCS5B01G175300 chr2B 137621621 137622677 1056 True 1480.0 1480 91.736000 671 1756 1 chr2B.!!$R3 1085
8 TraesCS5B01G175300 chr2B 135357980 135359096 1116 False 1288.0 1288 87.811000 834 1933 1 chr2B.!!$F2 1099
9 TraesCS5B01G175300 chr2B 135126705 135127837 1132 False 1122.0 1122 85.179000 832 1933 1 chr2B.!!$F1 1101
10 TraesCS5B01G175300 chr2B 137347164 137349499 2335 True 1031.0 1792 94.027500 672 2847 2 chr2B.!!$R6 2175
11 TraesCS5B01G175300 chr2B 136635517 136639342 3825 True 1003.5 1748 93.280000 491 2847 2 chr2B.!!$R5 2356
12 TraesCS5B01G175300 chr5D 283108353 283110948 2595 True 1361.0 1711 95.459333 293 2847 3 chr5D.!!$R2 2554
13 TraesCS5B01G175300 chr5D 230369070 230370156 1086 False 1129.0 1129 85.778000 845 1934 1 chr5D.!!$F1 1089
14 TraesCS5B01G175300 chr5D 289419328 289420063 735 True 1027.0 1027 91.801000 1947 2688 1 chr5D.!!$R1 741
15 TraesCS5B01G175300 chr5D 289353237 289354256 1019 True 632.0 1016 92.472500 1947 2847 2 chr5D.!!$R3 900
16 TraesCS5B01G175300 chr7A 627006975 627007695 720 True 1027.0 1027 92.318000 1947 2673 1 chr7A.!!$R1 726
17 TraesCS5B01G175300 chr7A 618194285 618195695 1410 True 955.0 1664 90.823500 354 1933 2 chr7A.!!$R2 1579
18 TraesCS5B01G175300 chr7A 628383875 628384897 1022 True 635.0 1027 92.099500 1947 2851 2 chr7A.!!$R3 904
19 TraesCS5B01G175300 chr2A 83984996 83986114 1118 False 1251.0 1251 87.245000 834 1933 1 chr2A.!!$F1 1099
20 TraesCS5B01G175300 chr2A 84143642 84145493 1851 False 1189.5 1365 90.745500 834 2673 2 chr2A.!!$F2 1839
21 TraesCS5B01G175300 chr5A 326436848 326437925 1077 True 1123.0 1123 85.843000 854 1933 1 chr5A.!!$R1 1079
22 TraesCS5B01G175300 chr7B 589694539 589695275 736 True 1022.0 1022 91.678000 1947 2688 1 chr7B.!!$R5 741
23 TraesCS5B01G175300 chr7B 589736332 589737052 720 False 1022.0 1022 92.181000 1947 2673 1 chr7B.!!$F1 726
24 TraesCS5B01G175300 chr1B 426495203 426495938 735 True 1011.0 1011 91.398000 1947 2688 1 chr1B.!!$R1 741
25 TraesCS5B01G175300 chr1B 133122122 133123133 1011 True 631.5 1022 92.240500 1947 2847 2 chr1B.!!$R2 900
26 TraesCS5B01G175300 chr4A 349804438 349807091 2653 True 255.5 307 88.275000 340 2847 2 chr4A.!!$R1 2507

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
185 186 0.031212 AAAATGGGCCGGGAATGGAT 60.031 50.0 2.18 0.0 0.0 3.41 F
186 187 0.469892 AAATGGGCCGGGAATGGATC 60.470 55.0 2.18 0.0 0.0 3.36 F
290 291 0.589223 CCGCGTTGGAGTTGCTTTTA 59.411 50.0 4.92 0.0 42.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1806 0.749454 CAGGCAATGGTGTAGAGCCC 60.749 60.000 0.00 0.0 46.35 5.19 R
1841 2171 3.772853 TTCCTTGGTGCTGCAGCGT 62.773 57.895 32.11 0.0 45.83 5.07 R
2281 2772 0.107945 CCCTAGGCAGCTCACAAGAC 60.108 60.000 2.05 0.0 0.00 3.01 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
26 27 4.167597 AAAAATGGGTGGCGACGT 57.832 50.000 0.00 0.00 0.00 4.34
27 28 1.953772 AAAAATGGGTGGCGACGTC 59.046 52.632 5.18 5.18 0.00 4.34
28 29 1.847890 AAAAATGGGTGGCGACGTCG 61.848 55.000 32.57 32.57 43.27 5.12
29 30 4.752879 AATGGGTGGCGACGTCGG 62.753 66.667 36.13 19.71 40.23 4.79
48 49 4.430765 GACGAAGAAGGCGGGCGA 62.431 66.667 0.00 0.00 0.00 5.54
49 50 4.436998 ACGAAGAAGGCGGGCGAG 62.437 66.667 0.00 0.00 0.00 5.03
51 52 4.840005 GAAGAAGGCGGGCGAGGG 62.840 72.222 0.00 0.00 0.00 4.30
54 55 4.717313 GAAGGCGGGCGAGGGTTT 62.717 66.667 0.00 0.00 0.00 3.27
60 61 2.597510 GGGCGAGGGTTTGCTGTT 60.598 61.111 0.00 0.00 33.93 3.16
61 62 2.644992 GGCGAGGGTTTGCTGTTG 59.355 61.111 0.00 0.00 33.93 3.33
62 63 2.644992 GCGAGGGTTTGCTGTTGG 59.355 61.111 0.00 0.00 0.00 3.77
63 64 1.896660 GCGAGGGTTTGCTGTTGGA 60.897 57.895 0.00 0.00 0.00 3.53
64 65 1.452145 GCGAGGGTTTGCTGTTGGAA 61.452 55.000 0.00 0.00 0.00 3.53
65 66 1.247567 CGAGGGTTTGCTGTTGGAAT 58.752 50.000 0.00 0.00 0.00 3.01
66 67 1.068333 CGAGGGTTTGCTGTTGGAATG 60.068 52.381 0.00 0.00 0.00 2.67
67 68 1.273327 GAGGGTTTGCTGTTGGAATGG 59.727 52.381 0.00 0.00 0.00 3.16
68 69 0.321346 GGGTTTGCTGTTGGAATGGG 59.679 55.000 0.00 0.00 0.00 4.00
69 70 1.337118 GGTTTGCTGTTGGAATGGGA 58.663 50.000 0.00 0.00 0.00 4.37
70 71 1.273327 GGTTTGCTGTTGGAATGGGAG 59.727 52.381 0.00 0.00 0.00 4.30
71 72 2.238521 GTTTGCTGTTGGAATGGGAGA 58.761 47.619 0.00 0.00 0.00 3.71
72 73 2.205022 TTGCTGTTGGAATGGGAGAG 57.795 50.000 0.00 0.00 0.00 3.20
73 74 0.329261 TGCTGTTGGAATGGGAGAGG 59.671 55.000 0.00 0.00 0.00 3.69
74 75 0.620556 GCTGTTGGAATGGGAGAGGA 59.379 55.000 0.00 0.00 0.00 3.71
75 76 1.680249 GCTGTTGGAATGGGAGAGGAC 60.680 57.143 0.00 0.00 0.00 3.85
76 77 0.613260 TGTTGGAATGGGAGAGGACG 59.387 55.000 0.00 0.00 0.00 4.79
77 78 0.902531 GTTGGAATGGGAGAGGACGA 59.097 55.000 0.00 0.00 0.00 4.20
78 79 0.902531 TTGGAATGGGAGAGGACGAC 59.097 55.000 0.00 0.00 0.00 4.34
79 80 0.976073 TGGAATGGGAGAGGACGACC 60.976 60.000 0.00 0.00 0.00 4.79
80 81 0.976073 GGAATGGGAGAGGACGACCA 60.976 60.000 6.71 0.00 38.94 4.02
81 82 0.902531 GAATGGGAGAGGACGACCAA 59.097 55.000 6.71 0.00 36.44 3.67
82 83 1.486726 GAATGGGAGAGGACGACCAAT 59.513 52.381 6.71 0.00 36.44 3.16
83 84 0.833287 ATGGGAGAGGACGACCAATG 59.167 55.000 6.71 0.00 36.44 2.82
84 85 0.544357 TGGGAGAGGACGACCAATGT 60.544 55.000 6.71 0.00 38.94 2.71
85 86 0.108138 GGGAGAGGACGACCAATGTG 60.108 60.000 6.71 0.00 38.94 3.21
86 87 0.608640 GGAGAGGACGACCAATGTGT 59.391 55.000 6.71 0.00 38.94 3.72
87 88 1.404315 GGAGAGGACGACCAATGTGTC 60.404 57.143 6.71 0.00 38.94 3.67
88 89 1.272490 GAGAGGACGACCAATGTGTCA 59.728 52.381 6.71 0.00 38.94 3.58
89 90 1.000955 AGAGGACGACCAATGTGTCAC 59.999 52.381 6.71 0.00 38.94 3.67
90 91 0.034896 AGGACGACCAATGTGTCACC 59.965 55.000 6.71 5.39 38.94 4.02
91 92 1.289109 GGACGACCAATGTGTCACCG 61.289 60.000 0.00 0.00 34.88 4.94
92 93 0.319211 GACGACCAATGTGTCACCGA 60.319 55.000 0.00 0.00 34.88 4.69
93 94 0.599204 ACGACCAATGTGTCACCGAC 60.599 55.000 0.00 0.00 34.88 4.79
94 95 1.289109 CGACCAATGTGTCACCGACC 61.289 60.000 0.00 0.00 34.88 4.79
95 96 0.250124 GACCAATGTGTCACCGACCA 60.250 55.000 0.00 0.00 35.29 4.02
96 97 0.250295 ACCAATGTGTCACCGACCAG 60.250 55.000 0.00 0.00 0.00 4.00
97 98 1.577328 CCAATGTGTCACCGACCAGC 61.577 60.000 0.00 0.00 0.00 4.85
98 99 1.667830 AATGTGTCACCGACCAGCG 60.668 57.895 0.00 0.00 40.47 5.18
111 112 3.636231 CAGCGGGACAGGGGACAA 61.636 66.667 0.00 0.00 0.00 3.18
112 113 3.322466 AGCGGGACAGGGGACAAG 61.322 66.667 0.00 0.00 0.00 3.16
113 114 3.637273 GCGGGACAGGGGACAAGT 61.637 66.667 0.00 0.00 0.00 3.16
114 115 2.288025 GCGGGACAGGGGACAAGTA 61.288 63.158 0.00 0.00 0.00 2.24
115 116 1.898154 CGGGACAGGGGACAAGTAG 59.102 63.158 0.00 0.00 0.00 2.57
116 117 1.614241 CGGGACAGGGGACAAGTAGG 61.614 65.000 0.00 0.00 0.00 3.18
117 118 1.602771 GGACAGGGGACAAGTAGGC 59.397 63.158 0.00 0.00 0.00 3.93
118 119 1.218316 GACAGGGGACAAGTAGGCG 59.782 63.158 0.00 0.00 0.00 5.52
119 120 2.240162 GACAGGGGACAAGTAGGCGG 62.240 65.000 0.00 0.00 0.00 6.13
120 121 2.687566 AGGGGACAAGTAGGCGGG 60.688 66.667 0.00 0.00 0.00 6.13
121 122 3.793888 GGGGACAAGTAGGCGGGG 61.794 72.222 0.00 0.00 0.00 5.73
122 123 3.793888 GGGACAAGTAGGCGGGGG 61.794 72.222 0.00 0.00 0.00 5.40
123 124 4.484872 GGACAAGTAGGCGGGGGC 62.485 72.222 0.00 0.00 0.00 5.80
124 125 4.832608 GACAAGTAGGCGGGGGCG 62.833 72.222 0.00 0.00 0.00 6.13
142 143 4.678269 CGTGCGTCCGTCTCGTGT 62.678 66.667 0.00 0.00 0.00 4.49
143 144 2.799916 GTGCGTCCGTCTCGTGTC 60.800 66.667 0.00 0.00 0.00 3.67
144 145 4.034258 TGCGTCCGTCTCGTGTCC 62.034 66.667 0.00 0.00 0.00 4.02
147 148 4.034258 GTCCGTCTCGTGTCCGCA 62.034 66.667 0.00 0.00 0.00 5.69
148 149 4.034258 TCCGTCTCGTGTCCGCAC 62.034 66.667 0.00 0.00 41.97 5.34
149 150 4.039357 CCGTCTCGTGTCCGCACT 62.039 66.667 0.00 0.00 43.16 4.40
150 151 2.801162 CGTCTCGTGTCCGCACTG 60.801 66.667 0.00 0.00 43.16 3.66
151 152 2.643272 GTCTCGTGTCCGCACTGA 59.357 61.111 0.00 0.00 43.16 3.41
152 153 1.729838 GTCTCGTGTCCGCACTGAC 60.730 63.158 0.00 0.00 43.16 3.51
153 154 2.801162 CTCGTGTCCGCACTGACG 60.801 66.667 0.00 0.00 43.16 4.35
154 155 4.994201 TCGTGTCCGCACTGACGC 62.994 66.667 0.00 2.43 43.16 5.19
156 157 2.964925 GTGTCCGCACTGACGCAA 60.965 61.111 6.68 0.00 43.55 4.85
157 158 2.202946 TGTCCGCACTGACGCAAA 60.203 55.556 0.00 0.00 38.11 3.68
158 159 2.248431 GTCCGCACTGACGCAAAC 59.752 61.111 0.00 0.00 0.00 2.93
159 160 2.970324 TCCGCACTGACGCAAACC 60.970 61.111 0.00 0.00 0.00 3.27
160 161 4.368808 CCGCACTGACGCAAACCG 62.369 66.667 0.00 0.00 44.21 4.44
161 162 4.368808 CGCACTGACGCAAACCGG 62.369 66.667 0.00 0.00 42.52 5.28
168 169 3.849619 GACGCAAACCGGCTTAAAA 57.150 47.368 0.00 0.00 43.29 1.52
169 170 2.122563 GACGCAAACCGGCTTAAAAA 57.877 45.000 0.00 0.00 43.29 1.94
170 171 2.668250 GACGCAAACCGGCTTAAAAAT 58.332 42.857 0.00 0.00 43.29 1.82
171 172 2.399448 ACGCAAACCGGCTTAAAAATG 58.601 42.857 0.00 0.00 42.52 2.32
172 173 1.724082 CGCAAACCGGCTTAAAAATGG 59.276 47.619 0.00 0.00 0.00 3.16
173 174 2.073056 GCAAACCGGCTTAAAAATGGG 58.927 47.619 0.00 0.00 0.00 4.00
174 175 2.073056 CAAACCGGCTTAAAAATGGGC 58.927 47.619 0.00 0.00 0.00 5.36
175 176 0.611200 AACCGGCTTAAAAATGGGCC 59.389 50.000 0.00 0.00 41.02 5.80
178 179 1.520192 GGCTTAAAAATGGGCCGGG 59.480 57.895 2.18 0.00 35.08 5.73
179 180 0.973496 GGCTTAAAAATGGGCCGGGA 60.973 55.000 2.18 0.00 35.08 5.14
180 181 0.899019 GCTTAAAAATGGGCCGGGAA 59.101 50.000 2.18 0.00 0.00 3.97
181 182 1.484653 GCTTAAAAATGGGCCGGGAAT 59.515 47.619 2.18 0.00 0.00 3.01
182 183 2.741553 GCTTAAAAATGGGCCGGGAATG 60.742 50.000 2.18 0.00 0.00 2.67
183 184 1.490574 TAAAAATGGGCCGGGAATGG 58.509 50.000 2.18 0.00 0.00 3.16
184 185 0.252467 AAAAATGGGCCGGGAATGGA 60.252 50.000 2.18 0.00 0.00 3.41
185 186 0.031212 AAAATGGGCCGGGAATGGAT 60.031 50.000 2.18 0.00 0.00 3.41
186 187 0.469892 AAATGGGCCGGGAATGGATC 60.470 55.000 2.18 0.00 0.00 3.36
187 188 2.697147 AATGGGCCGGGAATGGATCG 62.697 60.000 2.18 0.00 0.00 3.69
188 189 4.643387 GGGCCGGGAATGGATCGG 62.643 72.222 2.18 0.00 45.84 4.18
191 192 2.281070 CCGGGAATGGATCGGCAG 60.281 66.667 0.00 0.00 37.25 4.85
192 193 2.281070 CGGGAATGGATCGGCAGG 60.281 66.667 0.00 0.00 0.00 4.85
193 194 2.595754 GGGAATGGATCGGCAGGC 60.596 66.667 0.00 0.00 0.00 4.85
194 195 2.974698 GGAATGGATCGGCAGGCG 60.975 66.667 10.80 10.80 0.00 5.52
195 196 3.654020 GAATGGATCGGCAGGCGC 61.654 66.667 12.43 0.00 37.44 6.53
196 197 4.488136 AATGGATCGGCAGGCGCA 62.488 61.111 12.43 4.41 41.24 6.09
203 204 4.741781 CGGCAGGCGCACGAAAAG 62.742 66.667 10.83 0.00 41.24 2.27
221 222 3.698463 CGGACGCGCGTCTGTTTT 61.698 61.111 46.84 23.67 44.19 2.43
223 224 2.127758 GACGCGCGTCTGTTTTGG 60.128 61.111 45.56 12.76 41.57 3.28
224 225 2.877974 GACGCGCGTCTGTTTTGGT 61.878 57.895 45.56 18.67 41.57 3.67
225 226 2.127758 CGCGCGTCTGTTTTGGTC 60.128 61.111 24.19 0.00 0.00 4.02
226 227 2.127758 GCGCGTCTGTTTTGGTCG 60.128 61.111 8.43 0.00 0.00 4.79
227 228 2.591311 GCGCGTCTGTTTTGGTCGA 61.591 57.895 8.43 0.00 0.00 4.20
228 229 1.200839 CGCGTCTGTTTTGGTCGAC 59.799 57.895 7.13 7.13 0.00 4.20
230 231 1.200839 CGTCTGTTTTGGTCGACGC 59.799 57.895 9.92 3.20 41.97 5.19
231 232 1.568025 GTCTGTTTTGGTCGACGCC 59.432 57.895 9.92 0.00 0.00 5.68
232 233 1.144276 TCTGTTTTGGTCGACGCCA 59.856 52.632 9.92 0.00 36.62 5.69
233 234 1.155424 TCTGTTTTGGTCGACGCCAC 61.155 55.000 9.92 4.27 38.42 5.01
234 235 1.433053 CTGTTTTGGTCGACGCCACA 61.433 55.000 9.92 8.66 38.42 4.17
235 236 1.010462 GTTTTGGTCGACGCCACAC 60.010 57.895 9.92 7.12 38.42 3.82
236 237 2.181521 TTTTGGTCGACGCCACACC 61.182 57.895 9.92 3.75 38.42 4.16
237 238 4.953868 TTGGTCGACGCCACACCG 62.954 66.667 9.92 0.00 38.42 4.94
243 244 4.612412 GACGCCACACCGACCCAA 62.612 66.667 0.00 0.00 0.00 4.12
244 245 4.178169 ACGCCACACCGACCCAAA 62.178 61.111 0.00 0.00 0.00 3.28
245 246 2.671619 CGCCACACCGACCCAAAT 60.672 61.111 0.00 0.00 0.00 2.32
246 247 2.961768 GCCACACCGACCCAAATG 59.038 61.111 0.00 0.00 0.00 2.32
247 248 2.635443 GCCACACCGACCCAAATGG 61.635 63.158 0.00 0.00 41.37 3.16
248 249 1.074072 CCACACCGACCCAAATGGA 59.926 57.895 0.00 0.00 37.39 3.41
249 250 1.241315 CCACACCGACCCAAATGGAC 61.241 60.000 0.00 0.00 37.39 4.02
253 254 4.160635 CGACCCAAATGGACGCGC 62.161 66.667 5.73 0.00 44.79 6.86
254 255 2.746277 GACCCAAATGGACGCGCT 60.746 61.111 5.73 0.00 37.39 5.92
255 256 2.746277 ACCCAAATGGACGCGCTC 60.746 61.111 5.73 2.64 37.39 5.03
256 257 3.864686 CCCAAATGGACGCGCTCG 61.865 66.667 5.73 0.00 42.43 5.03
257 258 2.813474 CCAAATGGACGCGCTCGA 60.813 61.111 5.73 0.29 39.41 4.04
258 259 2.387445 CCAAATGGACGCGCTCGAA 61.387 57.895 5.73 0.00 39.41 3.71
259 260 1.225745 CAAATGGACGCGCTCGAAC 60.226 57.895 5.73 0.00 39.41 3.95
260 261 2.726691 AAATGGACGCGCTCGAACG 61.727 57.895 5.73 3.34 39.41 3.95
261 262 3.620300 AATGGACGCGCTCGAACGA 62.620 57.895 13.23 0.00 39.41 3.85
262 263 3.620300 ATGGACGCGCTCGAACGAA 62.620 57.895 13.23 0.00 39.41 3.85
263 264 3.101428 GGACGCGCTCGAACGAAA 61.101 61.111 13.23 0.00 39.41 3.46
264 265 2.442188 GGACGCGCTCGAACGAAAT 61.442 57.895 13.23 0.00 39.41 2.17
265 266 1.295220 GACGCGCTCGAACGAAATG 60.295 57.895 13.23 0.69 39.41 2.32
266 267 2.020016 CGCGCTCGAACGAAATGG 59.980 61.111 13.23 0.00 38.10 3.16
267 268 2.399611 GCGCTCGAACGAAATGGG 59.600 61.111 13.23 0.00 34.06 4.00
268 269 2.388232 GCGCTCGAACGAAATGGGT 61.388 57.895 13.23 0.00 34.06 4.51
269 270 1.708027 CGCTCGAACGAAATGGGTC 59.292 57.895 1.02 0.00 34.06 4.46
270 271 1.708027 GCTCGAACGAAATGGGTCG 59.292 57.895 0.00 0.00 46.54 4.79
271 272 1.708027 CTCGAACGAAATGGGTCGC 59.292 57.895 0.00 0.00 45.00 5.19
272 273 1.693083 CTCGAACGAAATGGGTCGCC 61.693 60.000 0.00 0.00 45.00 5.54
273 274 2.782615 GAACGAAATGGGTCGCCG 59.217 61.111 0.00 0.00 45.00 6.46
274 275 3.376914 GAACGAAATGGGTCGCCGC 62.377 63.158 0.00 0.00 45.00 6.53
277 278 3.428282 GAAATGGGTCGCCGCGTT 61.428 61.111 13.39 0.00 34.50 4.84
278 279 3.661025 GAAATGGGTCGCCGCGTTG 62.661 63.158 13.39 0.00 33.46 4.10
284 285 4.072088 GTCGCCGCGTTGGAGTTG 62.072 66.667 13.39 0.00 42.00 3.16
287 288 3.660111 GCCGCGTTGGAGTTGCTT 61.660 61.111 4.92 0.00 42.00 3.91
288 289 3.030652 CCGCGTTGGAGTTGCTTT 58.969 55.556 4.92 0.00 42.00 3.51
289 290 1.358759 CCGCGTTGGAGTTGCTTTT 59.641 52.632 4.92 0.00 42.00 2.27
290 291 0.589223 CCGCGTTGGAGTTGCTTTTA 59.411 50.000 4.92 0.00 42.00 1.52
291 292 1.662026 CCGCGTTGGAGTTGCTTTTAC 60.662 52.381 4.92 0.00 42.00 2.01
307 308 9.601971 GTTGCTTTTACGAGTGTGATATTTTTA 57.398 29.630 0.00 0.00 0.00 1.52
308 309 9.601971 TTGCTTTTACGAGTGTGATATTTTTAC 57.398 29.630 0.00 0.00 0.00 2.01
463 478 3.496870 GGAGCCAAGAAAAGGAACAGAGA 60.497 47.826 0.00 0.00 0.00 3.10
464 479 4.137543 GAGCCAAGAAAAGGAACAGAGAA 58.862 43.478 0.00 0.00 0.00 2.87
465 480 4.536765 AGCCAAGAAAAGGAACAGAGAAA 58.463 39.130 0.00 0.00 0.00 2.52
466 481 4.582240 AGCCAAGAAAAGGAACAGAGAAAG 59.418 41.667 0.00 0.00 0.00 2.62
467 482 4.580580 GCCAAGAAAAGGAACAGAGAAAGA 59.419 41.667 0.00 0.00 0.00 2.52
468 483 5.067805 GCCAAGAAAAGGAACAGAGAAAGAA 59.932 40.000 0.00 0.00 0.00 2.52
469 484 6.733145 CCAAGAAAAGGAACAGAGAAAGAAG 58.267 40.000 0.00 0.00 0.00 2.85
470 485 6.238869 CCAAGAAAAGGAACAGAGAAAGAAGG 60.239 42.308 0.00 0.00 0.00 3.46
471 486 4.824537 AGAAAAGGAACAGAGAAAGAAGGC 59.175 41.667 0.00 0.00 0.00 4.35
583 605 4.115199 GGGAGGGATGCAGCCGTT 62.115 66.667 18.48 7.03 0.00 4.44
661 683 1.211212 CACCTGAAGATCTCCATGGCA 59.789 52.381 6.96 0.00 0.00 4.92
1182 1260 2.526873 AAGGCCACCGGTGAGTCT 60.527 61.111 36.07 27.21 0.00 3.24
1349 1427 1.819226 GCATCTGATGTCGCTGCTCG 61.819 60.000 18.19 0.00 40.15 5.03
1485 1563 0.668706 CCTCTGATATTGCCTCCGCG 60.669 60.000 0.00 0.00 38.08 6.46
1536 1614 4.341783 GCTGCTGGTGCTGACCCT 62.342 66.667 0.00 0.00 42.34 4.34
1685 1778 1.807742 CGTGAAGAAGGTCTCTCGTCT 59.192 52.381 0.00 0.00 31.02 4.18
1713 1806 2.358737 AAGGCCCGCTCTTTCGTG 60.359 61.111 0.00 0.00 0.00 4.35
1841 2171 0.378962 CCGAAGCAAAACCGTGTCAA 59.621 50.000 0.00 0.00 0.00 3.18
1907 2352 3.412237 ACGCCCTTGCTAGTCTTTTAA 57.588 42.857 0.00 0.00 34.43 1.52
1934 2382 6.774673 TCCTAAACCATTCACACATGAGTAA 58.225 36.000 0.00 0.00 35.83 2.24
1935 2383 7.227873 TCCTAAACCATTCACACATGAGTAAA 58.772 34.615 0.00 0.00 35.83 2.01
1936 2384 7.888021 TCCTAAACCATTCACACATGAGTAAAT 59.112 33.333 0.00 0.00 35.83 1.40
1937 2385 7.970061 CCTAAACCATTCACACATGAGTAAATG 59.030 37.037 11.14 11.14 35.83 2.32
1938 2386 7.523293 AAACCATTCACACATGAGTAAATGA 57.477 32.000 17.80 0.00 35.83 2.57
1939 2387 7.523293 AACCATTCACACATGAGTAAATGAA 57.477 32.000 17.80 8.17 35.83 2.57
1941 2389 7.370383 ACCATTCACACATGAGTAAATGAAAC 58.630 34.615 17.80 0.00 35.83 2.78
1944 2392 7.800155 TTCACACATGAGTAAATGAAACTCA 57.200 32.000 8.25 8.25 35.83 3.41
2137 2627 3.347216 TCAAAGTAAAGCAGATGAGCCC 58.653 45.455 0.00 0.00 34.23 5.19
2138 2628 2.424956 CAAAGTAAAGCAGATGAGCCCC 59.575 50.000 0.00 0.00 34.23 5.80
2281 2772 4.469552 TGAACTTGTCGATACACACGTAG 58.530 43.478 0.00 0.00 34.61 3.51
2314 2805 2.772515 GCCTAGGGTTTGGAGACTATGT 59.227 50.000 11.72 0.00 0.00 2.29
2422 2915 7.148787 CGAGTAACATTGGTTAGTGAACTCTTC 60.149 40.741 0.03 0.00 41.95 2.87
2594 3088 2.040278 TGTATGCTTCTGTGGCTCCTTT 59.960 45.455 0.00 0.00 0.00 3.11
2638 4053 3.412386 GGAAAAGTGTGTACTGAGGCAT 58.588 45.455 0.00 0.00 37.19 4.40
2640 4055 5.186198 GGAAAAGTGTGTACTGAGGCATAT 58.814 41.667 0.00 0.00 37.19 1.78
2711 4352 1.468506 TTCGGCTCTACACCACTGCA 61.469 55.000 0.00 0.00 0.00 4.41
2847 4488 0.318107 CTGCACCAAAGAAGCAACCG 60.318 55.000 0.00 0.00 37.89 4.44
2848 4489 0.749818 TGCACCAAAGAAGCAACCGA 60.750 50.000 0.00 0.00 34.97 4.69
2849 4490 0.040067 GCACCAAAGAAGCAACCGAG 60.040 55.000 0.00 0.00 0.00 4.63
2850 4491 1.308998 CACCAAAGAAGCAACCGAGT 58.691 50.000 0.00 0.00 0.00 4.18
2851 4492 2.489971 CACCAAAGAAGCAACCGAGTA 58.510 47.619 0.00 0.00 0.00 2.59
2852 4493 2.875933 CACCAAAGAAGCAACCGAGTAA 59.124 45.455 0.00 0.00 0.00 2.24
2853 4494 2.876550 ACCAAAGAAGCAACCGAGTAAC 59.123 45.455 0.00 0.00 0.00 2.50
2854 4495 2.875933 CCAAAGAAGCAACCGAGTAACA 59.124 45.455 0.00 0.00 0.00 2.41
2855 4496 3.058914 CCAAAGAAGCAACCGAGTAACAG 60.059 47.826 0.00 0.00 0.00 3.16
2856 4497 3.746045 AAGAAGCAACCGAGTAACAGA 57.254 42.857 0.00 0.00 0.00 3.41
2857 4498 3.305398 AGAAGCAACCGAGTAACAGAG 57.695 47.619 0.00 0.00 0.00 3.35
2858 4499 2.628657 AGAAGCAACCGAGTAACAGAGT 59.371 45.455 0.00 0.00 0.00 3.24
2859 4500 2.726832 AGCAACCGAGTAACAGAGTC 57.273 50.000 0.00 0.00 0.00 3.36
2860 4501 1.961394 AGCAACCGAGTAACAGAGTCA 59.039 47.619 0.00 0.00 0.00 3.41
2861 4502 2.563179 AGCAACCGAGTAACAGAGTCAT 59.437 45.455 0.00 0.00 0.00 3.06
2862 4503 2.668457 GCAACCGAGTAACAGAGTCATG 59.332 50.000 0.00 0.00 0.00 3.07
2863 4504 3.861131 GCAACCGAGTAACAGAGTCATGT 60.861 47.826 0.00 0.00 33.96 3.21
2864 4505 4.307432 CAACCGAGTAACAGAGTCATGTT 58.693 43.478 11.17 11.17 45.19 2.71
2865 4506 3.914312 ACCGAGTAACAGAGTCATGTTG 58.086 45.455 14.48 0.00 43.14 3.33
2866 4507 3.321111 ACCGAGTAACAGAGTCATGTTGT 59.679 43.478 14.48 0.00 43.14 3.32
2867 4508 4.521639 ACCGAGTAACAGAGTCATGTTGTA 59.478 41.667 14.48 0.00 43.14 2.41
2868 4509 5.010314 ACCGAGTAACAGAGTCATGTTGTAA 59.990 40.000 14.48 0.00 43.14 2.41
2869 4510 5.924254 CCGAGTAACAGAGTCATGTTGTAAA 59.076 40.000 14.48 0.00 43.14 2.01
2870 4511 6.422701 CCGAGTAACAGAGTCATGTTGTAAAA 59.577 38.462 14.48 0.00 43.14 1.52
2871 4512 7.042321 CCGAGTAACAGAGTCATGTTGTAAAAA 60.042 37.037 14.48 0.00 43.14 1.94
2899 4540 8.483307 ACAGATATGAATGAAAAATTGTTGGC 57.517 30.769 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.847890 CGACGTCGCCACCCATTTTT 61.848 55.000 26.59 0.00 0.00 1.94
10 11 2.322081 CGACGTCGCCACCCATTTT 61.322 57.895 26.59 0.00 0.00 1.82
11 12 2.740826 CGACGTCGCCACCCATTT 60.741 61.111 26.59 0.00 0.00 2.32
12 13 4.752879 CCGACGTCGCCACCCATT 62.753 66.667 31.73 0.00 38.18 3.16
25 26 3.179939 GCCTTCTTCGTCGCCGAC 61.180 66.667 7.29 7.29 44.13 4.79
26 27 4.771356 CGCCTTCTTCGTCGCCGA 62.771 66.667 0.00 0.00 42.41 5.54
31 32 4.430765 TCGCCCGCCTTCTTCGTC 62.431 66.667 0.00 0.00 0.00 4.20
32 33 4.436998 CTCGCCCGCCTTCTTCGT 62.437 66.667 0.00 0.00 0.00 3.85
34 35 4.840005 CCCTCGCCCGCCTTCTTC 62.840 72.222 0.00 0.00 0.00 2.87
37 38 4.717313 AAACCCTCGCCCGCCTTC 62.717 66.667 0.00 0.00 0.00 3.46
43 44 2.597510 AACAGCAAACCCTCGCCC 60.598 61.111 0.00 0.00 0.00 6.13
44 45 2.644992 CAACAGCAAACCCTCGCC 59.355 61.111 0.00 0.00 0.00 5.54
45 46 1.452145 TTCCAACAGCAAACCCTCGC 61.452 55.000 0.00 0.00 0.00 5.03
46 47 1.068333 CATTCCAACAGCAAACCCTCG 60.068 52.381 0.00 0.00 0.00 4.63
47 48 1.273327 CCATTCCAACAGCAAACCCTC 59.727 52.381 0.00 0.00 0.00 4.30
48 49 1.341080 CCATTCCAACAGCAAACCCT 58.659 50.000 0.00 0.00 0.00 4.34
49 50 0.321346 CCCATTCCAACAGCAAACCC 59.679 55.000 0.00 0.00 0.00 4.11
50 51 1.273327 CTCCCATTCCAACAGCAAACC 59.727 52.381 0.00 0.00 0.00 3.27
51 52 2.229784 CTCTCCCATTCCAACAGCAAAC 59.770 50.000 0.00 0.00 0.00 2.93
52 53 2.517959 CTCTCCCATTCCAACAGCAAA 58.482 47.619 0.00 0.00 0.00 3.68
53 54 1.272092 CCTCTCCCATTCCAACAGCAA 60.272 52.381 0.00 0.00 0.00 3.91
54 55 0.329261 CCTCTCCCATTCCAACAGCA 59.671 55.000 0.00 0.00 0.00 4.41
55 56 0.620556 TCCTCTCCCATTCCAACAGC 59.379 55.000 0.00 0.00 0.00 4.40
56 57 1.406069 CGTCCTCTCCCATTCCAACAG 60.406 57.143 0.00 0.00 0.00 3.16
57 58 0.613260 CGTCCTCTCCCATTCCAACA 59.387 55.000 0.00 0.00 0.00 3.33
58 59 0.902531 TCGTCCTCTCCCATTCCAAC 59.097 55.000 0.00 0.00 0.00 3.77
59 60 0.902531 GTCGTCCTCTCCCATTCCAA 59.097 55.000 0.00 0.00 0.00 3.53
60 61 0.976073 GGTCGTCCTCTCCCATTCCA 60.976 60.000 0.00 0.00 0.00 3.53
61 62 0.976073 TGGTCGTCCTCTCCCATTCC 60.976 60.000 0.00 0.00 34.23 3.01
62 63 0.902531 TTGGTCGTCCTCTCCCATTC 59.097 55.000 0.00 0.00 34.23 2.67
63 64 1.210478 CATTGGTCGTCCTCTCCCATT 59.790 52.381 0.00 0.00 34.23 3.16
64 65 0.833287 CATTGGTCGTCCTCTCCCAT 59.167 55.000 0.00 0.00 34.23 4.00
65 66 0.544357 ACATTGGTCGTCCTCTCCCA 60.544 55.000 0.00 0.00 34.23 4.37
66 67 0.108138 CACATTGGTCGTCCTCTCCC 60.108 60.000 0.00 0.00 34.23 4.30
67 68 0.608640 ACACATTGGTCGTCCTCTCC 59.391 55.000 0.00 0.00 34.23 3.71
68 69 1.272490 TGACACATTGGTCGTCCTCTC 59.728 52.381 0.00 0.00 40.72 3.20
69 70 1.000955 GTGACACATTGGTCGTCCTCT 59.999 52.381 0.00 0.00 40.72 3.69
70 71 1.429463 GTGACACATTGGTCGTCCTC 58.571 55.000 0.00 0.00 40.72 3.71
71 72 0.034896 GGTGACACATTGGTCGTCCT 59.965 55.000 8.08 0.00 40.72 3.85
72 73 1.289109 CGGTGACACATTGGTCGTCC 61.289 60.000 8.08 0.00 40.72 4.79
73 74 0.319211 TCGGTGACACATTGGTCGTC 60.319 55.000 8.08 0.00 40.72 4.20
74 75 0.599204 GTCGGTGACACATTGGTCGT 60.599 55.000 8.08 0.00 40.72 4.34
75 76 1.289109 GGTCGGTGACACATTGGTCG 61.289 60.000 8.08 0.55 40.72 4.79
76 77 0.250124 TGGTCGGTGACACATTGGTC 60.250 55.000 8.08 0.00 38.29 4.02
77 78 0.250295 CTGGTCGGTGACACATTGGT 60.250 55.000 8.08 0.00 33.68 3.67
78 79 1.577328 GCTGGTCGGTGACACATTGG 61.577 60.000 8.08 0.00 33.68 3.16
79 80 1.868997 GCTGGTCGGTGACACATTG 59.131 57.895 8.08 0.00 33.68 2.82
80 81 1.667830 CGCTGGTCGGTGACACATT 60.668 57.895 8.08 0.00 33.68 2.71
81 82 2.048222 CGCTGGTCGGTGACACAT 60.048 61.111 8.08 0.00 33.68 3.21
94 95 3.612247 CTTGTCCCCTGTCCCGCTG 62.612 68.421 0.00 0.00 0.00 5.18
95 96 2.741878 TACTTGTCCCCTGTCCCGCT 62.742 60.000 0.00 0.00 0.00 5.52
96 97 2.240162 CTACTTGTCCCCTGTCCCGC 62.240 65.000 0.00 0.00 0.00 6.13
97 98 1.614241 CCTACTTGTCCCCTGTCCCG 61.614 65.000 0.00 0.00 0.00 5.14
98 99 1.911702 GCCTACTTGTCCCCTGTCCC 61.912 65.000 0.00 0.00 0.00 4.46
99 100 1.602771 GCCTACTTGTCCCCTGTCC 59.397 63.158 0.00 0.00 0.00 4.02
100 101 1.218316 CGCCTACTTGTCCCCTGTC 59.782 63.158 0.00 0.00 0.00 3.51
101 102 2.291043 CCGCCTACTTGTCCCCTGT 61.291 63.158 0.00 0.00 0.00 4.00
102 103 2.584608 CCGCCTACTTGTCCCCTG 59.415 66.667 0.00 0.00 0.00 4.45
103 104 2.687566 CCCGCCTACTTGTCCCCT 60.688 66.667 0.00 0.00 0.00 4.79
104 105 3.793888 CCCCGCCTACTTGTCCCC 61.794 72.222 0.00 0.00 0.00 4.81
105 106 3.793888 CCCCCGCCTACTTGTCCC 61.794 72.222 0.00 0.00 0.00 4.46
106 107 4.484872 GCCCCCGCCTACTTGTCC 62.485 72.222 0.00 0.00 0.00 4.02
107 108 4.832608 CGCCCCCGCCTACTTGTC 62.833 72.222 0.00 0.00 0.00 3.18
125 126 4.678269 ACACGAGACGGACGCACG 62.678 66.667 0.00 0.00 40.31 5.34
126 127 2.799916 GACACGAGACGGACGCAC 60.800 66.667 0.00 0.00 0.00 5.34
127 128 4.034258 GGACACGAGACGGACGCA 62.034 66.667 0.00 0.00 0.00 5.24
130 131 4.034258 TGCGGACACGAGACGGAC 62.034 66.667 0.00 0.00 44.60 4.79
131 132 4.034258 GTGCGGACACGAGACGGA 62.034 66.667 0.63 0.00 44.60 4.69
140 141 2.202946 TTTGCGTCAGTGCGGACA 60.203 55.556 10.52 0.00 37.66 4.02
141 142 2.248431 GTTTGCGTCAGTGCGGAC 59.752 61.111 0.00 0.00 37.81 4.79
142 143 2.970324 GGTTTGCGTCAGTGCGGA 60.970 61.111 8.63 3.53 37.81 5.54
143 144 4.368808 CGGTTTGCGTCAGTGCGG 62.369 66.667 8.63 0.00 37.81 5.69
144 145 4.368808 CCGGTTTGCGTCAGTGCG 62.369 66.667 0.00 3.07 37.81 5.34
145 146 4.683334 GCCGGTTTGCGTCAGTGC 62.683 66.667 1.90 0.00 0.00 4.40
146 147 1.225376 TAAGCCGGTTTGCGTCAGTG 61.225 55.000 14.54 0.00 36.02 3.66
147 148 0.533308 TTAAGCCGGTTTGCGTCAGT 60.533 50.000 14.54 0.00 36.02 3.41
148 149 0.589223 TTTAAGCCGGTTTGCGTCAG 59.411 50.000 14.54 0.00 36.02 3.51
149 150 1.022735 TTTTAAGCCGGTTTGCGTCA 58.977 45.000 14.54 0.00 36.02 4.35
150 151 2.122563 TTTTTAAGCCGGTTTGCGTC 57.877 45.000 14.54 0.00 36.02 5.19
151 152 2.399448 CATTTTTAAGCCGGTTTGCGT 58.601 42.857 14.54 0.00 36.02 5.24
152 153 1.724082 CCATTTTTAAGCCGGTTTGCG 59.276 47.619 14.54 0.00 36.02 4.85
153 154 2.073056 CCCATTTTTAAGCCGGTTTGC 58.927 47.619 14.54 0.00 0.00 3.68
154 155 2.073056 GCCCATTTTTAAGCCGGTTTG 58.927 47.619 14.54 0.00 0.00 2.93
155 156 1.002659 GGCCCATTTTTAAGCCGGTTT 59.997 47.619 9.08 9.08 35.30 3.27
156 157 0.611200 GGCCCATTTTTAAGCCGGTT 59.389 50.000 1.90 0.00 35.30 4.44
157 158 2.282827 GGCCCATTTTTAAGCCGGT 58.717 52.632 1.90 0.00 35.30 5.28
160 161 0.973496 TCCCGGCCCATTTTTAAGCC 60.973 55.000 0.00 0.00 42.18 4.35
161 162 0.899019 TTCCCGGCCCATTTTTAAGC 59.101 50.000 0.00 0.00 0.00 3.09
162 163 2.158971 CCATTCCCGGCCCATTTTTAAG 60.159 50.000 0.00 0.00 0.00 1.85
163 164 1.834263 CCATTCCCGGCCCATTTTTAA 59.166 47.619 0.00 0.00 0.00 1.52
164 165 1.007238 TCCATTCCCGGCCCATTTTTA 59.993 47.619 0.00 0.00 0.00 1.52
165 166 0.252467 TCCATTCCCGGCCCATTTTT 60.252 50.000 0.00 0.00 0.00 1.94
166 167 0.031212 ATCCATTCCCGGCCCATTTT 60.031 50.000 0.00 0.00 0.00 1.82
167 168 0.469892 GATCCATTCCCGGCCCATTT 60.470 55.000 0.00 0.00 0.00 2.32
168 169 1.153756 GATCCATTCCCGGCCCATT 59.846 57.895 0.00 0.00 0.00 3.16
169 170 2.846532 GATCCATTCCCGGCCCAT 59.153 61.111 0.00 0.00 0.00 4.00
170 171 3.872603 CGATCCATTCCCGGCCCA 61.873 66.667 0.00 0.00 0.00 5.36
171 172 4.643387 CCGATCCATTCCCGGCCC 62.643 72.222 0.00 0.00 36.62 5.80
174 175 2.281070 CTGCCGATCCATTCCCGG 60.281 66.667 0.00 0.00 45.51 5.73
175 176 2.281070 CCTGCCGATCCATTCCCG 60.281 66.667 0.00 0.00 0.00 5.14
176 177 2.595754 GCCTGCCGATCCATTCCC 60.596 66.667 0.00 0.00 0.00 3.97
177 178 2.974698 CGCCTGCCGATCCATTCC 60.975 66.667 0.00 0.00 40.02 3.01
178 179 3.654020 GCGCCTGCCGATCCATTC 61.654 66.667 0.00 0.00 40.02 2.67
179 180 4.488136 TGCGCCTGCCGATCCATT 62.488 61.111 4.18 0.00 41.78 3.16
186 187 4.741781 CTTTTCGTGCGCCTGCCG 62.742 66.667 4.18 1.74 41.78 5.69
206 207 2.127758 CCAAAACAGACGCGCGTC 60.128 61.111 46.21 46.21 44.86 5.19
207 208 2.877974 GACCAAAACAGACGCGCGT 61.878 57.895 38.52 38.52 0.00 6.01
208 209 2.127758 GACCAAAACAGACGCGCG 60.128 61.111 30.96 30.96 0.00 6.86
209 210 2.127758 CGACCAAAACAGACGCGC 60.128 61.111 5.73 0.00 0.00 6.86
210 211 1.200839 GTCGACCAAAACAGACGCG 59.799 57.895 3.53 3.53 0.00 6.01
213 214 1.155424 TGGCGTCGACCAAAACAGAC 61.155 55.000 10.58 0.00 36.55 3.51
214 215 1.144276 TGGCGTCGACCAAAACAGA 59.856 52.632 10.58 0.00 36.55 3.41
215 216 1.278637 GTGGCGTCGACCAAAACAG 59.721 57.895 10.58 0.00 42.70 3.16
216 217 1.449778 TGTGGCGTCGACCAAAACA 60.450 52.632 10.58 6.93 42.70 2.83
217 218 1.010462 GTGTGGCGTCGACCAAAAC 60.010 57.895 10.58 4.27 42.70 2.43
218 219 2.181521 GGTGTGGCGTCGACCAAAA 61.182 57.895 10.58 0.00 42.70 2.44
219 220 2.589442 GGTGTGGCGTCGACCAAA 60.589 61.111 10.58 0.00 42.70 3.28
220 221 4.953868 CGGTGTGGCGTCGACCAA 62.954 66.667 10.58 0.00 42.70 3.67
226 227 4.612412 TTGGGTCGGTGTGGCGTC 62.612 66.667 0.00 0.00 0.00 5.19
227 228 3.485346 ATTTGGGTCGGTGTGGCGT 62.485 57.895 0.00 0.00 0.00 5.68
228 229 2.671619 ATTTGGGTCGGTGTGGCG 60.672 61.111 0.00 0.00 0.00 5.69
229 230 2.635443 CCATTTGGGTCGGTGTGGC 61.635 63.158 0.00 0.00 0.00 5.01
230 231 1.074072 TCCATTTGGGTCGGTGTGG 59.926 57.895 0.00 0.00 38.11 4.17
231 232 1.573829 CGTCCATTTGGGTCGGTGTG 61.574 60.000 0.00 0.00 43.28 3.82
232 233 1.302192 CGTCCATTTGGGTCGGTGT 60.302 57.895 0.00 0.00 43.28 4.16
233 234 2.686816 GCGTCCATTTGGGTCGGTG 61.687 63.158 13.59 0.00 46.41 4.94
234 235 2.359478 GCGTCCATTTGGGTCGGT 60.359 61.111 13.59 0.00 46.41 4.69
235 236 3.496131 CGCGTCCATTTGGGTCGG 61.496 66.667 0.00 0.00 46.41 4.79
237 238 2.746277 AGCGCGTCCATTTGGGTC 60.746 61.111 8.43 0.00 38.11 4.46
238 239 2.746277 GAGCGCGTCCATTTGGGT 60.746 61.111 8.43 0.00 38.11 4.51
239 240 3.864686 CGAGCGCGTCCATTTGGG 61.865 66.667 8.43 0.00 35.41 4.12
240 241 2.387445 TTCGAGCGCGTCCATTTGG 61.387 57.895 10.30 0.00 38.98 3.28
241 242 1.225745 GTTCGAGCGCGTCCATTTG 60.226 57.895 10.30 0.00 38.98 2.32
242 243 2.726691 CGTTCGAGCGCGTCCATTT 61.727 57.895 9.17 0.00 38.98 2.32
243 244 3.179265 CGTTCGAGCGCGTCCATT 61.179 61.111 9.17 0.00 38.98 3.16
244 245 3.620300 TTCGTTCGAGCGCGTCCAT 62.620 57.895 17.42 0.00 38.98 3.41
245 246 3.827551 TTTCGTTCGAGCGCGTCCA 62.828 57.895 17.42 0.00 38.98 4.02
246 247 2.442188 ATTTCGTTCGAGCGCGTCC 61.442 57.895 17.42 0.42 38.98 4.79
247 248 1.295220 CATTTCGTTCGAGCGCGTC 60.295 57.895 17.42 3.06 38.98 5.19
248 249 2.726691 CCATTTCGTTCGAGCGCGT 61.727 57.895 17.42 2.19 38.98 6.01
249 250 2.020016 CCATTTCGTTCGAGCGCG 59.980 61.111 17.42 2.41 39.35 6.86
250 251 2.292802 GACCCATTTCGTTCGAGCGC 62.293 60.000 17.42 0.00 0.00 5.92
251 252 1.708027 GACCCATTTCGTTCGAGCG 59.292 57.895 16.09 16.09 0.00 5.03
252 253 1.708027 CGACCCATTTCGTTCGAGC 59.292 57.895 0.00 0.00 34.16 5.03
253 254 1.693083 GGCGACCCATTTCGTTCGAG 61.693 60.000 0.00 0.00 41.26 4.04
254 255 1.738830 GGCGACCCATTTCGTTCGA 60.739 57.895 0.00 0.00 41.26 3.71
255 256 2.782615 GGCGACCCATTTCGTTCG 59.217 61.111 0.00 0.00 41.26 3.95
256 257 2.782615 CGGCGACCCATTTCGTTC 59.217 61.111 0.00 0.00 41.26 3.95
257 258 3.428282 GCGGCGACCCATTTCGTT 61.428 61.111 12.98 0.00 41.26 3.85
260 261 3.428282 AACGCGGCGACCCATTTC 61.428 61.111 30.94 0.00 0.00 2.17
261 262 3.732892 CAACGCGGCGACCCATTT 61.733 61.111 30.94 8.75 0.00 2.32
267 268 4.072088 CAACTCCAACGCGGCGAC 62.072 66.667 30.94 0.11 33.14 5.19
270 271 2.677573 AAAAGCAACTCCAACGCGGC 62.678 55.000 12.47 0.36 33.14 6.53
271 272 0.589223 TAAAAGCAACTCCAACGCGG 59.411 50.000 12.47 0.00 0.00 6.46
272 273 1.670326 GTAAAAGCAACTCCAACGCG 58.330 50.000 3.53 3.53 0.00 6.01
273 274 1.262151 TCGTAAAAGCAACTCCAACGC 59.738 47.619 0.00 0.00 0.00 4.84
274 275 2.542595 ACTCGTAAAAGCAACTCCAACG 59.457 45.455 0.00 0.00 0.00 4.10
275 276 3.311596 ACACTCGTAAAAGCAACTCCAAC 59.688 43.478 0.00 0.00 0.00 3.77
276 277 3.311322 CACACTCGTAAAAGCAACTCCAA 59.689 43.478 0.00 0.00 0.00 3.53
277 278 2.869801 CACACTCGTAAAAGCAACTCCA 59.130 45.455 0.00 0.00 0.00 3.86
278 279 3.128349 TCACACTCGTAAAAGCAACTCC 58.872 45.455 0.00 0.00 0.00 3.85
279 280 4.992381 ATCACACTCGTAAAAGCAACTC 57.008 40.909 0.00 0.00 0.00 3.01
280 281 7.435068 AAATATCACACTCGTAAAAGCAACT 57.565 32.000 0.00 0.00 0.00 3.16
281 282 8.502161 AAAAATATCACACTCGTAAAAGCAAC 57.498 30.769 0.00 0.00 0.00 4.17
282 283 9.601971 GTAAAAATATCACACTCGTAAAAGCAA 57.398 29.630 0.00 0.00 0.00 3.91
283 284 8.995220 AGTAAAAATATCACACTCGTAAAAGCA 58.005 29.630 0.00 0.00 0.00 3.91
307 308 9.495382 ACTTCCAGAACTCCTATAAGAATTAGT 57.505 33.333 0.00 0.00 31.76 2.24
321 325 6.095580 GGAAATAATCCCAACTTCCAGAACTC 59.904 42.308 0.00 0.00 43.00 3.01
463 478 3.006967 TCTCGTAGCTTCTTGCCTTCTTT 59.993 43.478 0.00 0.00 44.23 2.52
464 479 2.563179 TCTCGTAGCTTCTTGCCTTCTT 59.437 45.455 0.00 0.00 44.23 2.52
465 480 2.171840 TCTCGTAGCTTCTTGCCTTCT 58.828 47.619 0.00 0.00 44.23 2.85
466 481 2.656560 TCTCGTAGCTTCTTGCCTTC 57.343 50.000 0.00 0.00 44.23 3.46
467 482 2.037251 TGTTCTCGTAGCTTCTTGCCTT 59.963 45.455 0.00 0.00 44.23 4.35
468 483 1.618837 TGTTCTCGTAGCTTCTTGCCT 59.381 47.619 0.00 0.00 44.23 4.75
469 484 1.996191 CTGTTCTCGTAGCTTCTTGCC 59.004 52.381 0.00 0.00 44.23 4.52
470 485 2.920490 CTCTGTTCTCGTAGCTTCTTGC 59.080 50.000 0.00 0.00 43.29 4.01
471 486 3.191581 TCCTCTGTTCTCGTAGCTTCTTG 59.808 47.826 0.00 0.00 0.00 3.02
608 630 1.204146 TTTCCCAGAGATCCCCGAAG 58.796 55.000 0.00 0.00 0.00 3.79
962 1039 1.461461 GGATCTGGGGATCGGGGAA 60.461 63.158 0.00 0.00 46.77 3.97
1393 1471 2.065899 CCCTTGAGGTGGTGAACAAA 57.934 50.000 0.00 0.00 0.00 2.83
1446 1524 2.746375 ATCGAAGGAGCCGGGCATT 61.746 57.895 23.09 12.74 0.00 3.56
1685 1778 4.388499 GGGCCTTGGAAGCGACGA 62.388 66.667 0.84 0.00 0.00 4.20
1713 1806 0.749454 CAGGCAATGGTGTAGAGCCC 60.749 60.000 0.00 0.00 46.35 5.19
1841 2171 3.772853 TTCCTTGGTGCTGCAGCGT 62.773 57.895 32.11 0.00 45.83 5.07
1907 2352 5.630121 TCATGTGTGAATGGTTTAGGAAGT 58.370 37.500 0.00 0.00 0.00 3.01
1934 2382 7.869429 GGATTCAAAGAACACATGAGTTTCATT 59.131 33.333 9.96 3.66 34.28 2.57
1935 2383 7.373493 GGATTCAAAGAACACATGAGTTTCAT 58.627 34.615 9.96 0.00 37.65 2.57
1936 2384 6.239008 GGGATTCAAAGAACACATGAGTTTCA 60.239 38.462 9.96 0.00 0.00 2.69
1937 2385 6.015940 AGGGATTCAAAGAACACATGAGTTTC 60.016 38.462 9.96 4.12 0.00 2.78
1938 2386 5.835280 AGGGATTCAAAGAACACATGAGTTT 59.165 36.000 9.96 0.00 0.00 2.66
1939 2387 5.388654 AGGGATTCAAAGAACACATGAGTT 58.611 37.500 8.34 8.34 0.00 3.01
1941 2389 5.972107 AAGGGATTCAAAGAACACATGAG 57.028 39.130 0.00 0.00 0.00 2.90
2281 2772 0.107945 CCCTAGGCAGCTCACAAGAC 60.108 60.000 2.05 0.00 0.00 3.01
2422 2915 1.806542 GCTTCACCCACACATACACAG 59.193 52.381 0.00 0.00 0.00 3.66
2516 3010 1.693062 TGCACAAATTCAGGCCAACAT 59.307 42.857 5.01 0.00 0.00 2.71
2594 3088 4.864806 CGACTAGAGCAGCAGAATGTTTTA 59.135 41.667 0.00 0.00 39.31 1.52
2640 4055 8.054572 TGAAAACAGAGATGAATCCATTGGATA 58.945 33.333 18.49 4.62 42.27 2.59
2873 4514 8.938906 GCCAACAATTTTTCATTCATATCTGTT 58.061 29.630 0.00 0.00 0.00 3.16
2874 4515 8.483307 GCCAACAATTTTTCATTCATATCTGT 57.517 30.769 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.