Multiple sequence alignment - TraesCS5D01G462000

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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 TraesCS5D01G462000 chr5D 100.000 3445 0 0 1 3445 505825235 505821791 0.000000e+00 6362.0
1 TraesCS5D01G462000 chr5D 82.570 1113 116 40 207 1301 505806060 505807112 0.000000e+00 909.0
2 TraesCS5D01G462000 chr5D 78.793 1193 143 46 1415 2536 505909465 505908312 0.000000e+00 701.0
3 TraesCS5D01G462000 chr5D 84.308 650 78 12 737 1366 505847497 505846852 6.320000e-172 614.0
4 TraesCS5D01G462000 chr5D 80.109 548 65 21 1425 1954 505807399 505807920 5.430000e-98 368.0
5 TraesCS5D01G462000 chr5D 78.418 607 84 27 837 1420 505910009 505909427 5.470000e-93 351.0
6 TraesCS5D01G462000 chr5D 77.725 633 68 40 2291 2895 505807936 505808523 1.540000e-83 320.0
7 TraesCS5D01G462000 chr5D 82.195 410 33 10 1425 1800 505846853 505846450 2.000000e-82 316.0
8 TraesCS5D01G462000 chr5D 83.796 216 15 8 1206 1420 505807231 505807427 1.630000e-43 187.0
9 TraesCS5D01G462000 chr5D 83.417 199 22 3 1437 1629 505924442 505924249 1.270000e-39 174.0
10 TraesCS5D01G462000 chr5D 82.803 157 18 4 777 924 505925266 505925110 7.760000e-27 132.0
11 TraesCS5D01G462000 chr5D 91.176 68 6 0 1974 2041 505846363 505846296 3.660000e-15 93.5
12 TraesCS5D01G462000 chr5D 84.706 85 11 2 1216 1299 514306731 514306648 2.200000e-12 84.2
13 TraesCS5D01G462000 chr5D 81.443 97 15 3 2900 2995 505907942 505907848 3.690000e-10 76.8
14 TraesCS5D01G462000 chr5D 100.000 29 0 0 1392 1420 505846853 505846825 2.000000e-03 54.7
15 TraesCS5D01G462000 chr5B 88.807 1492 71 37 1425 2871 635914415 635912975 0.000000e+00 1742.0
16 TraesCS5D01G462000 chr5B 89.083 687 41 10 650 1304 635915561 635914877 0.000000e+00 822.0
17 TraesCS5D01G462000 chr5B 84.823 705 67 18 737 1420 636284902 636284217 0.000000e+00 673.0
18 TraesCS5D01G462000 chr5B 88.889 549 33 5 803 1338 635800534 635801067 0.000000e+00 651.0
19 TraesCS5D01G462000 chr5B 84.322 708 47 27 734 1420 635904338 635903674 4.850000e-178 634.0
20 TraesCS5D01G462000 chr5B 79.853 953 112 37 1624 2536 636293031 636292119 1.050000e-174 623.0
21 TraesCS5D01G462000 chr5B 83.231 489 39 18 2291 2762 635902898 635902436 3.200000e-110 409.0
22 TraesCS5D01G462000 chr5B 81.020 490 62 9 961 1420 636293707 636293219 9.090000e-96 361.0
23 TraesCS5D01G462000 chr5B 80.040 501 67 19 1425 1896 635801310 635801806 1.180000e-89 340.0
24 TraesCS5D01G462000 chr5B 84.046 351 29 14 2842 3174 635900513 635900172 2.580000e-81 313.0
25 TraesCS5D01G462000 chr5B 81.124 445 37 10 1415 1817 636284255 636283816 2.580000e-81 313.0
26 TraesCS5D01G462000 chr5B 92.273 220 11 1 1425 1638 635903702 635903483 1.200000e-79 307.0
27 TraesCS5D01G462000 chr5B 80.976 410 36 18 1425 1801 635903443 635903043 1.560000e-73 287.0
28 TraesCS5D01G462000 chr5B 83.553 304 30 11 2291 2587 635801830 635802120 2.040000e-67 267.0
29 TraesCS5D01G462000 chr5B 84.878 205 12 7 1217 1420 635801152 635801338 4.540000e-44 189.0
30 TraesCS5D01G462000 chr5B 78.022 364 32 23 2253 2585 636283432 636283086 5.870000e-43 185.0
31 TraesCS5D01G462000 chr5B 98.947 95 1 0 3349 3443 635900106 635900012 1.640000e-38 171.0
32 TraesCS5D01G462000 chr5B 96.875 96 3 0 2763 2858 635902311 635902216 9.890000e-36 161.0
33 TraesCS5D01G462000 chr5B 88.889 117 7 5 3222 3333 635803832 635803947 4.640000e-29 139.0
34 TraesCS5D01G462000 chr5B 87.395 119 10 2 810 923 636342368 636342250 7.760000e-27 132.0
35 TraesCS5D01G462000 chr5B 93.750 64 4 0 1303 1366 635914477 635914414 2.830000e-16 97.1
36 TraesCS5D01G462000 chr5B 92.000 50 3 1 2648 2696 635802176 635802225 6.170000e-08 69.4
37 TraesCS5D01G462000 chr5B 75.484 155 23 8 2928 3069 636291758 636291606 1.030000e-05 62.1
38 TraesCS5D01G462000 chr5A 87.477 1597 75 42 1415 2929 633300781 633299228 0.000000e+00 1725.0
39 TraesCS5D01G462000 chr5A 94.110 730 18 9 711 1420 633301467 633300743 0.000000e+00 1086.0
40 TraesCS5D01G462000 chr5A 79.396 961 105 41 1624 2529 633530495 633529573 2.960000e-165 592.0
41 TraesCS5D01G462000 chr5A 82.820 617 78 18 737 1329 633457054 633456442 8.470000e-146 527.0
42 TraesCS5D01G462000 chr5A 84.916 537 54 13 734 1265 633275817 633275303 5.100000e-143 518.0
43 TraesCS5D01G462000 chr5A 82.059 641 71 17 742 1366 633329071 633328459 1.100000e-139 507.0
44 TraesCS5D01G462000 chr5A 90.435 345 20 7 2586 2929 633296063 633295731 3.160000e-120 442.0
45 TraesCS5D01G462000 chr5A 83.051 413 29 15 2291 2696 633274435 633274057 1.530000e-88 337.0
46 TraesCS5D01G462000 chr5A 84.615 338 44 4 1624 1954 633274787 633274451 2.560000e-86 329.0
47 TraesCS5D01G462000 chr5A 81.840 413 32 7 1425 1800 633456406 633456000 1.200000e-79 307.0
48 TraesCS5D01G462000 chr5A 81.598 413 33 8 1425 1800 633328460 633328054 5.590000e-78 302.0
49 TraesCS5D01G462000 chr5A 82.712 295 27 18 2253 2529 633455673 633455385 1.240000e-59 241.0
50 TraesCS5D01G462000 chr5A 85.714 203 13 8 1217 1418 633275169 633274982 2.100000e-47 200.0
51 TraesCS5D01G462000 chr5A 97.030 101 3 0 1320 1420 633530791 633530691 1.640000e-38 171.0
52 TraesCS5D01G462000 chr5A 80.000 235 41 2 1984 2218 633455897 633455669 5.910000e-38 169.0
53 TraesCS5D01G462000 chr5A 84.076 157 16 4 777 924 633630778 633630622 3.580000e-30 143.0
54 TraesCS5D01G462000 chr5A 81.333 150 21 4 3222 3368 633272096 633271951 7.810000e-22 115.0
55 TraesCS5D01G462000 chr5A 93.750 48 3 0 1984 2031 633327951 633327904 4.770000e-09 73.1
56 TraesCS5D01G462000 chr5A 90.244 41 2 2 2558 2597 633455327 633455288 6.000000e-03 52.8
57 TraesCS5D01G462000 chr6D 98.639 147 2 0 3297 3443 461858683 461858829 9.480000e-66 261.0


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 TraesCS5D01G462000 chr5D 505821791 505825235 3444 True 6362.000000 6362 100.000000 1 3445 1 chr5D.!!$R1 3444
1 TraesCS5D01G462000 chr5D 505806060 505808523 2463 False 446.000000 909 81.050000 207 2895 4 chr5D.!!$F1 2688
2 TraesCS5D01G462000 chr5D 505907848 505910009 2161 True 376.266667 701 79.551333 837 2995 3 chr5D.!!$R4 2158
3 TraesCS5D01G462000 chr5D 505846296 505847497 1201 True 269.550000 614 89.419750 737 2041 4 chr5D.!!$R3 1304
4 TraesCS5D01G462000 chr5B 635912975 635915561 2586 True 887.033333 1742 90.546667 650 2871 3 chr5B.!!$R3 2221
5 TraesCS5D01G462000 chr5B 636283086 636284902 1816 True 390.333333 673 81.323000 737 2585 3 chr5B.!!$R4 1848
6 TraesCS5D01G462000 chr5B 636291606 636293707 2101 True 348.700000 623 78.785667 961 3069 3 chr5B.!!$R5 2108
7 TraesCS5D01G462000 chr5B 635900012 635904338 4326 True 326.000000 634 88.667143 734 3443 7 chr5B.!!$R2 2709
8 TraesCS5D01G462000 chr5B 635800534 635803947 3413 False 275.900000 651 86.374833 803 3333 6 chr5B.!!$F1 2530
9 TraesCS5D01G462000 chr5A 633295731 633301467 5736 True 1084.333333 1725 90.674000 711 2929 3 chr5A.!!$R3 2218
10 TraesCS5D01G462000 chr5A 633529573 633530791 1218 True 381.500000 592 88.213000 1320 2529 2 chr5A.!!$R6 1209
11 TraesCS5D01G462000 chr5A 633271951 633275817 3866 True 299.800000 518 83.925800 734 3368 5 chr5A.!!$R2 2634
12 TraesCS5D01G462000 chr5A 633327904 633329071 1167 True 294.033333 507 85.802333 742 2031 3 chr5A.!!$R4 1289
13 TraesCS5D01G462000 chr5A 633455288 633457054 1766 True 259.360000 527 83.523200 737 2597 5 chr5A.!!$R5 1860

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
606 608 0.034670 AAGACATTCTGGCCTCCTGC 60.035 55.0 3.32 0.00 40.16 4.85 F
1407 2002 0.608582 GATGCCATCTCAGGGGATGC 60.609 60.0 3.55 0.92 41.04 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 3331 0.107831 AGAGGCGGTTGTAGCAAACA 59.892 50.0 0.00 0.0 35.88 2.83 R
3338 8532 0.757935 ATGGATTGGCCCATGCTGTC 60.758 55.0 9.79 0.0 44.77 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
24 25 5.799827 AGAAGCTTCTAGCCGATTATTCT 57.200 39.130 27.47 0.00 43.77 2.40
25 26 6.168270 AGAAGCTTCTAGCCGATTATTCTT 57.832 37.500 27.47 0.00 43.77 2.52
26 27 6.587273 AGAAGCTTCTAGCCGATTATTCTTT 58.413 36.000 27.47 0.00 43.77 2.52
27 28 7.051000 AGAAGCTTCTAGCCGATTATTCTTTT 58.949 34.615 27.47 0.00 43.77 2.27
28 29 7.554476 AGAAGCTTCTAGCCGATTATTCTTTTT 59.446 33.333 27.47 0.00 43.77 1.94
50 51 7.900782 TTTTTGGTTTTCATGACGGTTTTAA 57.099 28.000 0.00 0.00 0.00 1.52
51 52 8.494016 TTTTTGGTTTTCATGACGGTTTTAAT 57.506 26.923 0.00 0.00 0.00 1.40
52 53 8.494016 TTTTGGTTTTCATGACGGTTTTAATT 57.506 26.923 0.00 0.00 0.00 1.40
53 54 7.701809 TTGGTTTTCATGACGGTTTTAATTC 57.298 32.000 0.00 0.00 0.00 2.17
54 55 7.045126 TGGTTTTCATGACGGTTTTAATTCT 57.955 32.000 0.00 0.00 0.00 2.40
55 56 8.167605 TGGTTTTCATGACGGTTTTAATTCTA 57.832 30.769 0.00 0.00 0.00 2.10
56 57 8.798402 TGGTTTTCATGACGGTTTTAATTCTAT 58.202 29.630 0.00 0.00 0.00 1.98
57 58 9.634163 GGTTTTCATGACGGTTTTAATTCTATT 57.366 29.630 0.00 0.00 0.00 1.73
117 118 5.890424 TTTTTAAATGCCCGGACTTCTAG 57.110 39.130 0.73 0.00 0.00 2.43
118 119 2.614829 TAAATGCCCGGACTTCTAGC 57.385 50.000 0.73 0.00 0.00 3.42
119 120 0.107165 AAATGCCCGGACTTCTAGCC 60.107 55.000 0.73 0.00 0.00 3.93
120 121 0.983378 AATGCCCGGACTTCTAGCCT 60.983 55.000 0.73 0.00 0.00 4.58
121 122 1.690219 ATGCCCGGACTTCTAGCCTG 61.690 60.000 0.73 0.00 0.00 4.85
122 123 2.359967 GCCCGGACTTCTAGCCTGT 61.360 63.158 0.73 0.00 0.00 4.00
123 124 1.517832 CCCGGACTTCTAGCCTGTG 59.482 63.158 0.73 0.00 0.00 3.66
124 125 1.517832 CCGGACTTCTAGCCTGTGG 59.482 63.158 0.00 0.00 0.00 4.17
125 126 0.970937 CCGGACTTCTAGCCTGTGGA 60.971 60.000 0.00 0.00 0.00 4.02
126 127 0.895530 CGGACTTCTAGCCTGTGGAA 59.104 55.000 0.00 0.00 0.00 3.53
127 128 1.134965 CGGACTTCTAGCCTGTGGAAG 60.135 57.143 0.00 0.00 46.66 3.46
128 129 1.406205 GGACTTCTAGCCTGTGGAAGC 60.406 57.143 0.00 0.00 45.49 3.86
129 130 1.552792 GACTTCTAGCCTGTGGAAGCT 59.447 52.381 0.00 0.00 45.49 3.74
130 131 1.981495 ACTTCTAGCCTGTGGAAGCTT 59.019 47.619 0.00 0.00 45.49 3.74
131 132 2.027653 ACTTCTAGCCTGTGGAAGCTTC 60.028 50.000 18.54 18.54 45.49 3.86
132 133 1.944177 TCTAGCCTGTGGAAGCTTCT 58.056 50.000 25.05 6.87 40.56 2.85
133 134 3.101643 TCTAGCCTGTGGAAGCTTCTA 57.898 47.619 25.05 17.65 40.56 2.10
134 135 3.441101 TCTAGCCTGTGGAAGCTTCTAA 58.559 45.455 25.05 11.88 40.56 2.10
135 136 2.481289 AGCCTGTGGAAGCTTCTAAC 57.519 50.000 25.05 21.93 35.22 2.34
136 137 1.003696 AGCCTGTGGAAGCTTCTAACC 59.996 52.381 25.05 10.57 35.22 2.85
137 138 1.726853 CCTGTGGAAGCTTCTAACCG 58.273 55.000 25.05 18.17 0.00 4.44
138 139 1.002087 CCTGTGGAAGCTTCTAACCGT 59.998 52.381 25.05 0.00 0.00 4.83
139 140 2.550208 CCTGTGGAAGCTTCTAACCGTT 60.550 50.000 25.05 0.00 0.00 4.44
140 141 3.139077 CTGTGGAAGCTTCTAACCGTTT 58.861 45.455 25.05 0.00 0.00 3.60
141 142 3.547746 TGTGGAAGCTTCTAACCGTTTT 58.452 40.909 25.05 0.00 0.00 2.43
142 143 3.949113 TGTGGAAGCTTCTAACCGTTTTT 59.051 39.130 25.05 0.00 0.00 1.94
165 166 8.908172 TTTTTACGACGGTTTTTATTCTGTTT 57.092 26.923 0.00 0.00 0.00 2.83
166 167 8.908172 TTTTACGACGGTTTTTATTCTGTTTT 57.092 26.923 0.00 0.00 0.00 2.43
167 168 8.908172 TTTACGACGGTTTTTATTCTGTTTTT 57.092 26.923 0.00 0.00 0.00 1.94
168 169 6.799786 ACGACGGTTTTTATTCTGTTTTTG 57.200 33.333 0.00 0.00 0.00 2.44
169 170 6.324042 ACGACGGTTTTTATTCTGTTTTTGT 58.676 32.000 0.00 0.00 0.00 2.83
170 171 6.807720 ACGACGGTTTTTATTCTGTTTTTGTT 59.192 30.769 0.00 0.00 0.00 2.83
171 172 7.108005 CGACGGTTTTTATTCTGTTTTTGTTG 58.892 34.615 0.00 0.00 0.00 3.33
172 173 7.201367 CGACGGTTTTTATTCTGTTTTTGTTGT 60.201 33.333 0.00 0.00 0.00 3.32
173 174 8.312896 ACGGTTTTTATTCTGTTTTTGTTGTT 57.687 26.923 0.00 0.00 0.00 2.83
174 175 8.436970 ACGGTTTTTATTCTGTTTTTGTTGTTC 58.563 29.630 0.00 0.00 0.00 3.18
175 176 7.900864 CGGTTTTTATTCTGTTTTTGTTGTTCC 59.099 33.333 0.00 0.00 0.00 3.62
176 177 8.941977 GGTTTTTATTCTGTTTTTGTTGTTCCT 58.058 29.630 0.00 0.00 0.00 3.36
222 223 9.943163 TTTTTGAAACTTTTGAACTTTTTCTGG 57.057 25.926 0.00 0.00 32.36 3.86
227 228 9.371136 GAAACTTTTGAACTTTTTCTGGAATCT 57.629 29.630 0.00 0.00 32.36 2.40
231 232 5.850557 TGAACTTTTTCTGGAATCTGCAA 57.149 34.783 0.00 0.00 32.36 4.08
232 233 6.219417 TGAACTTTTTCTGGAATCTGCAAA 57.781 33.333 0.00 0.00 32.36 3.68
233 234 6.042143 TGAACTTTTTCTGGAATCTGCAAAC 58.958 36.000 0.00 0.00 32.36 2.93
270 271 8.033626 TGCATGTACATATTCAAATGCAGAAAA 58.966 29.630 8.32 0.00 43.86 2.29
294 295 7.624360 AAAATTCCAAGGACAAACTTTTTCC 57.376 32.000 0.00 0.00 0.00 3.13
296 297 3.714144 TCCAAGGACAAACTTTTTCCCA 58.286 40.909 3.46 0.00 0.00 4.37
298 299 4.532521 TCCAAGGACAAACTTTTTCCCAAA 59.467 37.500 3.46 0.00 0.00 3.28
299 300 5.190726 TCCAAGGACAAACTTTTTCCCAAAT 59.809 36.000 3.46 0.00 0.00 2.32
300 301 5.527214 CCAAGGACAAACTTTTTCCCAAATC 59.473 40.000 3.46 0.00 0.00 2.17
302 303 7.418483 CCAAGGACAAACTTTTTCCCAAATCTA 60.418 37.037 3.46 0.00 0.00 1.98
303 304 7.050970 AGGACAAACTTTTTCCCAAATCTAC 57.949 36.000 3.46 0.00 0.00 2.59
304 305 5.918576 GGACAAACTTTTTCCCAAATCTACG 59.081 40.000 0.00 0.00 0.00 3.51
305 306 6.238814 GGACAAACTTTTTCCCAAATCTACGA 60.239 38.462 0.00 0.00 0.00 3.43
306 307 7.102847 ACAAACTTTTTCCCAAATCTACGAA 57.897 32.000 0.00 0.00 0.00 3.85
307 308 6.976349 ACAAACTTTTTCCCAAATCTACGAAC 59.024 34.615 0.00 0.00 0.00 3.95
308 309 6.954487 AACTTTTTCCCAAATCTACGAACT 57.046 33.333 0.00 0.00 0.00 3.01
309 310 6.954487 ACTTTTTCCCAAATCTACGAACTT 57.046 33.333 0.00 0.00 0.00 2.66
310 311 7.342769 ACTTTTTCCCAAATCTACGAACTTT 57.657 32.000 0.00 0.00 0.00 2.66
364 365 5.312895 TCGATGAACTTTTCTCCAAATCCA 58.687 37.500 0.00 0.00 0.00 3.41
369 370 7.358770 TGAACTTTTCTCCAAATCCATGAAA 57.641 32.000 0.00 0.00 0.00 2.69
405 406 7.960738 AGTCGTGAATTTTGGTTTACATAATCG 59.039 33.333 0.00 0.00 30.82 3.34
408 409 8.733128 CGTGAATTTTGGTTTACATAATCGATG 58.267 33.333 0.00 0.00 41.79 3.84
503 505 8.926715 GTTGTAAACTTCTTTTCAAATCCACT 57.073 30.769 0.00 0.00 45.32 4.00
554 556 9.743057 TTTTTGAAGTCATGATTTATGTTTCGT 57.257 25.926 3.10 0.00 38.01 3.85
555 557 9.743057 TTTTGAAGTCATGATTTATGTTTCGTT 57.257 25.926 3.10 0.00 38.01 3.85
556 558 9.743057 TTTGAAGTCATGATTTATGTTTCGTTT 57.257 25.926 3.10 0.00 38.01 3.60
557 559 9.743057 TTGAAGTCATGATTTATGTTTCGTTTT 57.257 25.926 3.10 0.00 38.01 2.43
558 560 9.393249 TGAAGTCATGATTTATGTTTCGTTTTC 57.607 29.630 3.10 0.00 38.01 2.29
559 561 8.742554 AAGTCATGATTTATGTTTCGTTTTCC 57.257 30.769 0.93 0.00 38.01 3.13
560 562 7.312899 AGTCATGATTTATGTTTCGTTTTCCC 58.687 34.615 0.00 0.00 38.01 3.97
561 563 6.250527 GTCATGATTTATGTTTCGTTTTCCCG 59.749 38.462 0.00 0.00 38.01 5.14
562 564 5.943706 TGATTTATGTTTCGTTTTCCCGA 57.056 34.783 0.00 0.00 34.52 5.14
563 565 5.691815 TGATTTATGTTTCGTTTTCCCGAC 58.308 37.500 0.00 0.00 36.42 4.79
564 566 4.486574 TTTATGTTTCGTTTTCCCGACC 57.513 40.909 0.00 0.00 36.42 4.79
565 567 2.265589 ATGTTTCGTTTTCCCGACCT 57.734 45.000 0.00 0.00 36.42 3.85
566 568 2.041251 TGTTTCGTTTTCCCGACCTT 57.959 45.000 0.00 0.00 36.42 3.50
567 569 2.367486 TGTTTCGTTTTCCCGACCTTT 58.633 42.857 0.00 0.00 36.42 3.11
568 570 2.754002 TGTTTCGTTTTCCCGACCTTTT 59.246 40.909 0.00 0.00 36.42 2.27
569 571 3.193056 TGTTTCGTTTTCCCGACCTTTTT 59.807 39.130 0.00 0.00 36.42 1.94
575 577 4.626172 CGTTTTCCCGACCTTTTTGAAAAA 59.374 37.500 2.83 2.83 36.87 1.94
599 601 5.397142 AATCTTCCAAAAGACATTCTGGC 57.603 39.130 0.00 0.00 44.13 4.85
600 602 3.157087 TCTTCCAAAAGACATTCTGGCC 58.843 45.455 0.00 0.00 36.59 5.36
601 603 2.978156 TCCAAAAGACATTCTGGCCT 57.022 45.000 3.32 0.00 0.00 5.19
603 605 1.821136 CCAAAAGACATTCTGGCCTCC 59.179 52.381 3.32 0.00 0.00 4.30
604 606 2.556114 CCAAAAGACATTCTGGCCTCCT 60.556 50.000 3.32 0.00 0.00 3.69
605 607 2.490903 CAAAAGACATTCTGGCCTCCTG 59.509 50.000 3.32 0.00 0.00 3.86
606 608 0.034670 AAGACATTCTGGCCTCCTGC 60.035 55.000 3.32 0.00 40.16 4.85
615 617 2.045926 GCCTCCTGCCACGTCATT 60.046 61.111 0.00 0.00 0.00 2.57
616 618 2.109126 GCCTCCTGCCACGTCATTC 61.109 63.158 0.00 0.00 0.00 2.67
617 619 1.811266 CCTCCTGCCACGTCATTCG 60.811 63.158 0.00 0.00 46.00 3.34
618 620 1.811266 CTCCTGCCACGTCATTCGG 60.811 63.158 0.00 0.00 44.69 4.30
622 624 3.799755 GCCACGTCATTCGGCACC 61.800 66.667 8.85 0.00 44.69 5.01
623 625 3.124921 CCACGTCATTCGGCACCC 61.125 66.667 0.00 0.00 44.69 4.61
624 626 3.124921 CACGTCATTCGGCACCCC 61.125 66.667 0.00 0.00 44.69 4.95
674 676 1.219664 CCAGGTCGCCCGTTTGATA 59.780 57.895 0.00 0.00 35.12 2.15
693 695 0.676782 AGGCCGGCAAATGACTACAC 60.677 55.000 30.85 5.70 0.00 2.90
699 701 0.719465 GCAAATGACTACACGGACGG 59.281 55.000 0.00 0.00 0.00 4.79
700 702 1.355971 CAAATGACTACACGGACGGG 58.644 55.000 0.00 0.00 0.00 5.28
892 934 2.039480 ACCGTCGTCTATATAGCCTCCA 59.961 50.000 4.75 0.00 0.00 3.86
1367 1962 4.844420 GGATTCTCCCAGTCGCAG 57.156 61.111 0.00 0.00 0.00 5.18
1368 1963 1.522580 GGATTCTCCCAGTCGCAGC 60.523 63.158 0.00 0.00 0.00 5.25
1369 1964 1.522580 GATTCTCCCAGTCGCAGCC 60.523 63.158 0.00 0.00 0.00 4.85
1374 1969 4.529219 CCCAGTCGCAGCCGCATA 62.529 66.667 0.00 0.00 38.40 3.14
1375 1970 2.963854 CCAGTCGCAGCCGCATAG 60.964 66.667 0.00 0.00 38.40 2.23
1376 1971 2.963854 CAGTCGCAGCCGCATAGG 60.964 66.667 0.00 0.00 44.97 2.57
1377 1972 3.147595 AGTCGCAGCCGCATAGGA 61.148 61.111 0.00 0.00 45.00 2.94
1378 1973 2.659897 GTCGCAGCCGCATAGGAG 60.660 66.667 0.00 0.00 45.00 3.69
1379 1974 3.916544 TCGCAGCCGCATAGGAGG 61.917 66.667 0.00 0.00 45.00 4.30
1380 1975 4.976925 CGCAGCCGCATAGGAGGG 62.977 72.222 0.00 0.00 45.00 4.30
1388 1983 4.976925 CATAGGAGGGCGCCGCAG 62.977 72.222 22.54 1.52 0.00 5.18
1398 1993 3.344215 CGCCGCAGATGCCATCTC 61.344 66.667 3.68 0.00 37.58 2.75
1399 1994 2.203112 GCCGCAGATGCCATCTCA 60.203 61.111 3.68 0.00 37.58 3.27
1400 1995 2.252346 GCCGCAGATGCCATCTCAG 61.252 63.158 3.68 1.65 37.58 3.35
1401 1996 1.597302 CCGCAGATGCCATCTCAGG 60.597 63.158 3.68 7.37 37.58 3.86
1402 1997 1.597302 CGCAGATGCCATCTCAGGG 60.597 63.158 3.68 0.00 37.58 4.45
1403 1998 1.228184 GCAGATGCCATCTCAGGGG 60.228 63.158 3.68 0.00 37.58 4.79
1404 1999 1.703014 GCAGATGCCATCTCAGGGGA 61.703 60.000 3.68 0.00 37.58 4.81
1405 2000 1.065647 CAGATGCCATCTCAGGGGAT 58.934 55.000 3.68 0.00 39.39 3.85
1406 2001 1.065647 AGATGCCATCTCAGGGGATG 58.934 55.000 0.08 2.05 41.77 3.51
1407 2002 0.608582 GATGCCATCTCAGGGGATGC 60.609 60.000 3.55 0.92 41.04 3.91
1408 2003 1.066585 ATGCCATCTCAGGGGATGCT 61.067 55.000 3.55 0.00 41.04 3.79
1409 2004 1.072852 GCCATCTCAGGGGATGCTC 59.927 63.158 3.55 0.00 41.04 4.26
1410 2005 1.759881 CCATCTCAGGGGATGCTCC 59.240 63.158 3.55 0.00 41.04 4.70
1413 2008 4.247380 CTCAGGGGATGCTCCGGC 62.247 72.222 0.00 0.00 37.43 6.13
1434 2029 2.252346 CCGCAGATGCCATCTCAGC 61.252 63.158 3.68 5.59 37.58 4.26
1728 2637 2.396590 TCGTTATTTGGGCTGTCCTC 57.603 50.000 0.00 0.00 36.20 3.71
2242 3429 2.443390 GGTCCCCAGCTACGCCTA 60.443 66.667 0.00 0.00 0.00 3.93
2243 3430 2.794028 GGTCCCCAGCTACGCCTAC 61.794 68.421 0.00 0.00 0.00 3.18
2245 3432 4.587189 CCCCAGCTACGCCTACGC 62.587 72.222 0.00 0.00 45.53 4.42
2317 3505 2.583472 CCATTGGGCCTTCTTCCAC 58.417 57.895 4.53 0.00 32.00 4.02
2536 3763 3.953612 TGGCTCTGTTTTGACAAAGATGT 59.046 39.130 0.10 0.00 44.25 3.06
2552 3779 4.214980 AGATGTTTGCTCTGTTTTGACG 57.785 40.909 0.00 0.00 0.00 4.35
2640 3971 7.066163 TGTCAGTGCTCTCACATTATAAAATGG 59.934 37.037 0.00 0.00 45.72 3.16
2684 4015 3.076621 TGTCAGTGTGCAATCTGATTCC 58.923 45.455 20.02 11.29 41.67 3.01
2698 4049 8.854117 GCAATCTGATTCCTAATCTTTGGTAAT 58.146 33.333 0.00 0.00 38.72 1.89
2784 4268 4.381505 GGAGTACTTGAGAGCTTCTTCCTG 60.382 50.000 0.00 0.00 0.00 3.86
2911 6534 3.881220 TCATTCGGTGGTTATTTCCCTC 58.119 45.455 0.00 0.00 0.00 4.30
2912 6535 2.793288 TTCGGTGGTTATTTCCCTCC 57.207 50.000 0.00 0.00 33.23 4.30
2916 6539 3.851458 GGTGGTTATTTCCCTCCGTAT 57.149 47.619 0.00 0.00 0.00 3.06
2940 6647 1.229428 TTGCTCTTCCTGACGCTTTG 58.771 50.000 0.00 0.00 0.00 2.77
2951 6659 1.152963 ACGCTTTGGTGTTGCCTCT 60.153 52.632 0.00 0.00 38.35 3.69
2959 6667 3.971245 TGGTGTTGCCTCTTTTGTTTT 57.029 38.095 0.00 0.00 38.35 2.43
2983 6691 7.857734 TGACTGATTCAGTTTCTGTTAAACA 57.142 32.000 19.88 7.02 45.44 2.83
3086 8267 9.796180 TCTAGGTTTACCATTTTTAAGCAAGTA 57.204 29.630 1.13 0.00 38.89 2.24
3120 8304 2.938451 TCTCGCGATGATTTCTGCAATT 59.062 40.909 10.36 0.00 0.00 2.32
3150 8334 7.588497 AAAGTTCTGCAAAACCTTCTCTAAT 57.412 32.000 0.00 0.00 0.00 1.73
3151 8335 8.691661 AAAGTTCTGCAAAACCTTCTCTAATA 57.308 30.769 0.00 0.00 0.00 0.98
3152 8336 7.674471 AGTTCTGCAAAACCTTCTCTAATAC 57.326 36.000 0.00 0.00 0.00 1.89
3153 8337 7.454225 AGTTCTGCAAAACCTTCTCTAATACT 58.546 34.615 0.00 0.00 0.00 2.12
3154 8338 7.389053 AGTTCTGCAAAACCTTCTCTAATACTG 59.611 37.037 0.00 0.00 0.00 2.74
3155 8339 6.769512 TCTGCAAAACCTTCTCTAATACTGT 58.230 36.000 0.00 0.00 0.00 3.55
3156 8340 7.903145 TCTGCAAAACCTTCTCTAATACTGTA 58.097 34.615 0.00 0.00 0.00 2.74
3157 8341 8.372459 TCTGCAAAACCTTCTCTAATACTGTAA 58.628 33.333 0.00 0.00 0.00 2.41
3158 8342 9.167311 CTGCAAAACCTTCTCTAATACTGTAAT 57.833 33.333 0.00 0.00 0.00 1.89
3159 8343 8.946085 TGCAAAACCTTCTCTAATACTGTAATG 58.054 33.333 0.00 0.00 0.00 1.90
3160 8344 7.910683 GCAAAACCTTCTCTAATACTGTAATGC 59.089 37.037 0.00 0.00 0.00 3.56
3161 8345 9.167311 CAAAACCTTCTCTAATACTGTAATGCT 57.833 33.333 0.00 0.00 0.00 3.79
3192 8376 9.529325 TGATGTACTAATGTACTAATGTTCTGC 57.471 33.333 7.67 0.00 46.70 4.26
3193 8377 9.529325 GATGTACTAATGTACTAATGTTCTGCA 57.471 33.333 7.67 0.00 46.70 4.41
3194 8378 9.884636 ATGTACTAATGTACTAATGTTCTGCAA 57.115 29.630 7.67 0.00 46.70 4.08
3195 8379 9.713713 TGTACTAATGTACTAATGTTCTGCAAA 57.286 29.630 7.67 0.00 46.70 3.68
3198 8382 8.512138 ACTAATGTACTAATGTTCTGCAAAACC 58.488 33.333 0.00 0.00 0.00 3.27
3199 8383 7.524717 AATGTACTAATGTTCTGCAAAACCT 57.475 32.000 0.00 0.00 0.00 3.50
3200 8384 6.952773 TGTACTAATGTTCTGCAAAACCTT 57.047 33.333 0.00 0.00 0.00 3.50
3201 8385 6.966021 TGTACTAATGTTCTGCAAAACCTTC 58.034 36.000 0.00 0.00 0.00 3.46
3202 8386 6.770785 TGTACTAATGTTCTGCAAAACCTTCT 59.229 34.615 0.00 0.00 0.00 2.85
3203 8387 7.934665 TGTACTAATGTTCTGCAAAACCTTCTA 59.065 33.333 0.00 0.00 0.00 2.10
3204 8388 8.947115 GTACTAATGTTCTGCAAAACCTTCTAT 58.053 33.333 0.00 0.00 0.00 1.98
3206 8390 9.515226 ACTAATGTTCTGCAAAACCTTCTATAA 57.485 29.630 0.00 0.00 0.00 0.98
3210 8394 9.686683 ATGTTCTGCAAAACCTTCTATAATACT 57.313 29.630 0.00 0.00 0.00 2.12
3211 8395 8.946085 TGTTCTGCAAAACCTTCTATAATACTG 58.054 33.333 0.00 0.00 0.00 2.74
3212 8396 8.947115 GTTCTGCAAAACCTTCTATAATACTGT 58.053 33.333 0.00 0.00 0.00 3.55
3217 8401 9.665264 GCAAAACCTTCTATAATACTGTAATGC 57.335 33.333 0.00 0.00 0.00 3.56
3218 8402 9.864034 CAAAACCTTCTATAATACTGTAATGCG 57.136 33.333 0.00 0.00 0.00 4.73
3219 8403 9.826574 AAAACCTTCTATAATACTGTAATGCGA 57.173 29.630 0.00 0.00 0.00 5.10
3220 8404 9.477484 AAACCTTCTATAATACTGTAATGCGAG 57.523 33.333 0.00 0.00 0.00 5.03
3309 8501 4.018779 ACCTATTTGGCCTGTAGTTTGCTA 60.019 41.667 3.32 0.00 40.22 3.49
3336 8530 3.118645 CGATACATGTCAAGAATCGCTCG 59.881 47.826 13.34 0.00 33.84 5.03
3338 8532 0.043566 CATGTCAAGAATCGCTCGCG 60.044 55.000 0.00 0.00 41.35 5.87
3421 8621 3.007614 TCTTCCTCCGGTTTAGGAACTTG 59.992 47.826 17.05 9.58 45.97 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.902771 AGAATAATCGGCTAGAAGCTTCTA 57.097 37.500 29.65 29.65 41.99 2.10
2 3 5.799827 AGAATAATCGGCTAGAAGCTTCT 57.200 39.130 30.63 30.63 41.99 2.85
3 4 6.852858 AAAGAATAATCGGCTAGAAGCTTC 57.147 37.500 19.11 19.11 41.99 3.86
4 5 7.631717 AAAAAGAATAATCGGCTAGAAGCTT 57.368 32.000 0.00 0.00 41.99 3.74
26 27 7.900782 TTAAAACCGTCATGAAAACCAAAAA 57.099 28.000 0.00 0.00 0.00 1.94
27 28 8.494016 AATTAAAACCGTCATGAAAACCAAAA 57.506 26.923 0.00 0.00 0.00 2.44
28 29 7.982354 AGAATTAAAACCGTCATGAAAACCAAA 59.018 29.630 0.00 0.00 0.00 3.28
29 30 7.493367 AGAATTAAAACCGTCATGAAAACCAA 58.507 30.769 0.00 0.00 0.00 3.67
30 31 7.045126 AGAATTAAAACCGTCATGAAAACCA 57.955 32.000 0.00 0.00 0.00 3.67
31 32 9.634163 AATAGAATTAAAACCGTCATGAAAACC 57.366 29.630 0.00 0.00 0.00 3.27
95 96 4.157105 GCTAGAAGTCCGGGCATTTAAAAA 59.843 41.667 9.71 0.00 0.00 1.94
96 97 3.692593 GCTAGAAGTCCGGGCATTTAAAA 59.307 43.478 9.71 0.00 0.00 1.52
97 98 3.275999 GCTAGAAGTCCGGGCATTTAAA 58.724 45.455 9.71 0.00 0.00 1.52
98 99 2.420967 GGCTAGAAGTCCGGGCATTTAA 60.421 50.000 9.71 0.00 0.00 1.52
99 100 1.140252 GGCTAGAAGTCCGGGCATTTA 59.860 52.381 9.71 0.00 0.00 1.40
100 101 0.107165 GGCTAGAAGTCCGGGCATTT 60.107 55.000 9.71 0.00 0.00 2.32
101 102 0.983378 AGGCTAGAAGTCCGGGCATT 60.983 55.000 9.71 0.00 0.00 3.56
102 103 1.383248 AGGCTAGAAGTCCGGGCAT 60.383 57.895 9.71 0.00 0.00 4.40
103 104 2.038975 AGGCTAGAAGTCCGGGCA 59.961 61.111 9.71 0.00 0.00 5.36
104 105 2.359967 ACAGGCTAGAAGTCCGGGC 61.360 63.158 0.00 0.00 0.00 6.13
105 106 1.517832 CACAGGCTAGAAGTCCGGG 59.482 63.158 0.00 0.00 0.00 5.73
106 107 0.970937 TCCACAGGCTAGAAGTCCGG 60.971 60.000 0.00 0.00 0.00 5.14
107 108 0.895530 TTCCACAGGCTAGAAGTCCG 59.104 55.000 0.00 0.00 0.00 4.79
108 109 1.406205 GCTTCCACAGGCTAGAAGTCC 60.406 57.143 17.38 4.10 39.36 3.85
109 110 1.552792 AGCTTCCACAGGCTAGAAGTC 59.447 52.381 17.38 11.96 39.36 3.01
110 111 1.650528 AGCTTCCACAGGCTAGAAGT 58.349 50.000 17.38 0.00 39.36 3.01
111 112 2.235898 AGAAGCTTCCACAGGCTAGAAG 59.764 50.000 22.81 13.81 39.99 2.85
112 113 2.260822 AGAAGCTTCCACAGGCTAGAA 58.739 47.619 22.81 0.00 37.87 2.10
113 114 1.944177 AGAAGCTTCCACAGGCTAGA 58.056 50.000 22.81 0.00 37.87 2.43
114 115 3.526534 GTTAGAAGCTTCCACAGGCTAG 58.473 50.000 22.81 0.00 37.87 3.42
115 116 2.236395 GGTTAGAAGCTTCCACAGGCTA 59.764 50.000 22.81 4.08 37.87 3.93
116 117 1.003696 GGTTAGAAGCTTCCACAGGCT 59.996 52.381 22.81 5.11 40.85 4.58
117 118 1.454201 GGTTAGAAGCTTCCACAGGC 58.546 55.000 22.81 7.53 0.00 4.85
118 119 1.002087 ACGGTTAGAAGCTTCCACAGG 59.998 52.381 22.81 16.05 0.00 4.00
119 120 2.457366 ACGGTTAGAAGCTTCCACAG 57.543 50.000 22.81 20.47 0.00 3.66
120 121 2.922740 AACGGTTAGAAGCTTCCACA 57.077 45.000 22.81 5.88 0.00 4.17
121 122 4.563337 AAAAACGGTTAGAAGCTTCCAC 57.437 40.909 22.81 18.51 0.00 4.02
140 141 8.908172 AAACAGAATAAAAACCGTCGTAAAAA 57.092 26.923 0.00 0.00 0.00 1.94
141 142 8.908172 AAAACAGAATAAAAACCGTCGTAAAA 57.092 26.923 0.00 0.00 0.00 1.52
142 143 8.796278 CAAAAACAGAATAAAAACCGTCGTAAA 58.204 29.630 0.00 0.00 0.00 2.01
143 144 7.967303 ACAAAAACAGAATAAAAACCGTCGTAA 59.033 29.630 0.00 0.00 0.00 3.18
144 145 7.470900 ACAAAAACAGAATAAAAACCGTCGTA 58.529 30.769 0.00 0.00 0.00 3.43
145 146 6.324042 ACAAAAACAGAATAAAAACCGTCGT 58.676 32.000 0.00 0.00 0.00 4.34
146 147 6.799786 ACAAAAACAGAATAAAAACCGTCG 57.200 33.333 0.00 0.00 0.00 5.12
147 148 7.955502 ACAACAAAAACAGAATAAAAACCGTC 58.044 30.769 0.00 0.00 0.00 4.79
148 149 7.892778 ACAACAAAAACAGAATAAAAACCGT 57.107 28.000 0.00 0.00 0.00 4.83
149 150 7.900864 GGAACAACAAAAACAGAATAAAAACCG 59.099 33.333 0.00 0.00 0.00 4.44
150 151 8.941977 AGGAACAACAAAAACAGAATAAAAACC 58.058 29.630 0.00 0.00 0.00 3.27
196 197 9.943163 CCAGAAAAAGTTCAAAAGTTTCAAAAA 57.057 25.926 0.00 0.00 36.09 1.94
197 198 9.331282 TCCAGAAAAAGTTCAAAAGTTTCAAAA 57.669 25.926 0.00 0.00 36.09 2.44
198 199 8.894768 TCCAGAAAAAGTTCAAAAGTTTCAAA 57.105 26.923 0.00 0.00 36.09 2.69
199 200 8.894768 TTCCAGAAAAAGTTCAAAAGTTTCAA 57.105 26.923 0.00 0.00 36.09 2.69
200 201 9.150348 GATTCCAGAAAAAGTTCAAAAGTTTCA 57.850 29.630 0.00 0.00 36.09 2.69
201 202 9.371136 AGATTCCAGAAAAAGTTCAAAAGTTTC 57.629 29.630 0.00 0.00 36.09 2.78
202 203 9.154847 CAGATTCCAGAAAAAGTTCAAAAGTTT 57.845 29.630 0.00 0.00 36.09 2.66
203 204 7.278646 GCAGATTCCAGAAAAAGTTCAAAAGTT 59.721 33.333 0.00 0.00 36.09 2.66
204 205 6.758416 GCAGATTCCAGAAAAAGTTCAAAAGT 59.242 34.615 0.00 0.00 36.09 2.66
205 206 6.757947 TGCAGATTCCAGAAAAAGTTCAAAAG 59.242 34.615 0.00 0.00 36.09 2.27
210 211 6.276091 AGTTTGCAGATTCCAGAAAAAGTTC 58.724 36.000 0.00 0.00 0.00 3.01
270 271 6.601613 GGGAAAAAGTTTGTCCTTGGAATTTT 59.398 34.615 21.77 0.00 0.00 1.82
272 273 5.190726 TGGGAAAAAGTTTGTCCTTGGAATT 59.809 36.000 21.77 0.00 0.00 2.17
273 274 4.719273 TGGGAAAAAGTTTGTCCTTGGAAT 59.281 37.500 21.77 0.00 0.00 3.01
280 281 5.918576 CGTAGATTTGGGAAAAAGTTTGTCC 59.081 40.000 15.63 15.63 0.00 4.02
284 285 7.342769 AGTTCGTAGATTTGGGAAAAAGTTT 57.657 32.000 0.00 0.00 35.04 2.66
344 345 7.543359 TTCATGGATTTGGAGAAAAGTTCAT 57.457 32.000 0.00 0.00 0.00 2.57
383 384 9.781834 TCATCGATTATGTAAACCAAAATTCAC 57.218 29.630 0.00 0.00 36.89 3.18
478 480 8.926715 AGTGGATTTGAAAAGAAGTTTACAAC 57.073 30.769 0.00 0.00 0.00 3.32
497 499 9.698309 CACGAGTTCATAAAATAGATAGTGGAT 57.302 33.333 0.00 0.00 0.00 3.41
498 500 8.909923 TCACGAGTTCATAAAATAGATAGTGGA 58.090 33.333 0.00 0.00 0.00 4.02
499 501 9.529325 TTCACGAGTTCATAAAATAGATAGTGG 57.471 33.333 0.00 0.00 0.00 4.00
536 538 6.250527 CGGGAAAACGAAACATAAATCATGAC 59.749 38.462 0.00 0.00 35.47 3.06
537 539 6.149640 TCGGGAAAACGAAACATAAATCATGA 59.850 34.615 0.00 0.00 40.34 3.07
546 548 2.265589 AGGTCGGGAAAACGAAACAT 57.734 45.000 0.00 0.00 45.38 2.71
548 550 3.425577 AAAAGGTCGGGAAAACGAAAC 57.574 42.857 0.00 0.00 45.38 2.78
575 577 6.226052 GCCAGAATGTCTTTTGGAAGATTTT 58.774 36.000 0.00 0.00 43.41 1.82
578 580 3.766051 GGCCAGAATGTCTTTTGGAAGAT 59.234 43.478 0.00 0.00 43.41 2.40
598 600 2.045926 AATGACGTGGCAGGAGGC 60.046 61.111 14.98 0.00 43.74 4.70
599 601 1.811266 CGAATGACGTGGCAGGAGG 60.811 63.158 14.98 0.00 37.22 4.30
600 602 1.811266 CCGAATGACGTGGCAGGAG 60.811 63.158 14.98 0.00 40.78 3.69
601 603 2.264480 CCGAATGACGTGGCAGGA 59.736 61.111 14.98 0.00 40.78 3.86
606 608 3.124921 GGGTGCCGAATGACGTGG 61.125 66.667 0.00 0.00 40.78 4.94
607 609 3.124921 GGGGTGCCGAATGACGTG 61.125 66.667 0.00 0.00 40.78 4.49
608 610 4.752879 CGGGGTGCCGAATGACGT 62.753 66.667 0.00 0.00 40.78 4.34
610 612 4.090588 TCCGGGGTGCCGAATGAC 62.091 66.667 0.00 0.00 34.88 3.06
611 613 3.781307 CTCCGGGGTGCCGAATGA 61.781 66.667 0.00 0.00 34.88 2.57
623 625 3.706373 CACCCACTCCACCTCCGG 61.706 72.222 0.00 0.00 0.00 5.14
624 626 4.394712 GCACCCACTCCACCTCCG 62.395 72.222 0.00 0.00 0.00 4.63
625 627 4.394712 CGCACCCACTCCACCTCC 62.395 72.222 0.00 0.00 0.00 4.30
674 676 0.676782 GTGTAGTCATTTGCCGGCCT 60.677 55.000 26.77 15.18 0.00 5.19
693 695 2.439701 TACTCAGCTCCCCGTCCG 60.440 66.667 0.00 0.00 0.00 4.79
699 701 4.697102 AGCTCCTACTCAGCTCCC 57.303 61.111 0.00 0.00 44.25 4.30
892 934 3.234730 GGGAGGACGGCGATGGAT 61.235 66.667 16.62 0.00 0.00 3.41
958 1015 1.069973 CGCAAGAACGCACAGATGAAA 60.070 47.619 0.00 0.00 43.02 2.69
1371 1966 4.976925 CTGCGGCGCCCTCCTATG 62.977 72.222 30.82 5.76 0.00 2.23
1381 1976 3.344215 GAGATGGCATCTGCGGCG 61.344 66.667 33.30 0.51 40.38 6.46
1382 1977 2.203112 TGAGATGGCATCTGCGGC 60.203 61.111 33.30 19.14 40.38 6.53
1383 1978 1.597302 CCTGAGATGGCATCTGCGG 60.597 63.158 33.30 26.02 40.38 5.69
1384 1979 1.597302 CCCTGAGATGGCATCTGCG 60.597 63.158 33.30 21.80 40.38 5.18
1385 1980 1.228184 CCCCTGAGATGGCATCTGC 60.228 63.158 33.30 22.94 40.38 4.26
1386 1981 1.065647 ATCCCCTGAGATGGCATCTG 58.934 55.000 33.30 19.63 40.38 2.90
1387 1982 1.065647 CATCCCCTGAGATGGCATCT 58.934 55.000 29.19 29.19 43.70 2.90
1388 1983 0.608582 GCATCCCCTGAGATGGCATC 60.609 60.000 19.78 19.78 43.26 3.91
1389 1984 1.066585 AGCATCCCCTGAGATGGCAT 61.067 55.000 0.00 0.00 43.26 4.40
1390 1985 1.695239 AGCATCCCCTGAGATGGCA 60.695 57.895 3.89 0.00 43.26 4.92
1391 1986 1.072852 GAGCATCCCCTGAGATGGC 59.927 63.158 3.89 0.00 43.26 4.40
1413 2008 4.923942 AGATGGCATCTGCGGCGG 62.924 66.667 28.33 1.35 43.26 6.13
1728 2637 1.683943 ATCAATGAGTTCATGGCGGG 58.316 50.000 0.00 0.00 36.56 6.13
1961 3094 3.958147 ATTGGCGGTGGTCGAGCTG 62.958 63.158 16.64 6.92 42.43 4.24
1962 3095 3.706373 ATTGGCGGTGGTCGAGCT 61.706 61.111 16.64 0.00 42.43 4.09
1965 3125 3.632080 ACCATTGGCGGTGGTCGA 61.632 61.111 1.54 0.00 46.79 4.20
2144 3331 0.107831 AGAGGCGGTTGTAGCAAACA 59.892 50.000 0.00 0.00 35.88 2.83
2515 3742 4.574599 ACATCTTTGTCAAAACAGAGCC 57.425 40.909 0.00 0.00 37.50 4.70
2536 3763 4.335315 ACATCTTCGTCAAAACAGAGCAAA 59.665 37.500 0.00 0.00 0.00 3.68
2552 3779 2.660189 CCACATTTGGCCACATCTTC 57.340 50.000 3.88 0.00 35.56 2.87
2640 3971 5.073311 TCCACAGCAAGTATGAAGAGTAC 57.927 43.478 0.00 0.00 0.00 2.73
2684 4015 9.490379 AAGCGTAGGAATATTACCAAAGATTAG 57.510 33.333 0.00 0.00 0.00 1.73
2698 4049 4.947388 AGGCAAAATCAAAGCGTAGGAATA 59.053 37.500 0.00 0.00 0.00 1.75
2784 4268 5.305585 TCAACTCAAACTGAATCAGTACCC 58.694 41.667 17.04 0.00 44.62 3.69
2911 6534 4.034510 GTCAGGAAGAGCAAAATGATACGG 59.965 45.833 0.00 0.00 0.00 4.02
2912 6535 4.259970 CGTCAGGAAGAGCAAAATGATACG 60.260 45.833 0.00 0.00 0.00 3.06
2913 6536 4.494855 GCGTCAGGAAGAGCAAAATGATAC 60.495 45.833 0.00 0.00 0.00 2.24
2916 6539 1.806542 GCGTCAGGAAGAGCAAAATGA 59.193 47.619 0.00 0.00 0.00 2.57
2940 6647 3.616821 GTCAAAACAAAAGAGGCAACACC 59.383 43.478 0.00 0.00 41.41 4.16
2951 6659 8.087750 ACAGAAACTGAATCAGTCAAAACAAAA 58.912 29.630 17.02 0.00 44.62 2.44
2959 6667 7.857734 TGTTTAACAGAAACTGAATCAGTCA 57.142 32.000 17.02 3.31 44.62 3.41
3033 6747 4.483476 GGTGATGTTATATCGCCAAACC 57.517 45.455 15.15 0.00 45.46 3.27
3086 8267 2.376109 TCGCGAGACTCCCTCTAAATT 58.624 47.619 3.71 0.00 39.78 1.82
3120 8304 8.232913 AGAAGGTTTTGCAGAACTTTATGTAA 57.767 30.769 16.01 0.00 30.19 2.41
3172 8356 8.512138 GGTTTTGCAGAACATTAGTACATTAGT 58.488 33.333 20.43 0.00 0.00 2.24
3173 8357 8.730680 AGGTTTTGCAGAACATTAGTACATTAG 58.269 33.333 20.43 0.00 0.00 1.73
3174 8358 8.630054 AGGTTTTGCAGAACATTAGTACATTA 57.370 30.769 20.43 0.00 0.00 1.90
3175 8359 7.524717 AGGTTTTGCAGAACATTAGTACATT 57.475 32.000 20.43 0.00 0.00 2.71
3176 8360 7.448469 AGAAGGTTTTGCAGAACATTAGTACAT 59.552 33.333 18.42 0.00 34.11 2.29
3177 8361 6.770785 AGAAGGTTTTGCAGAACATTAGTACA 59.229 34.615 18.42 0.00 34.11 2.90
3178 8362 7.203255 AGAAGGTTTTGCAGAACATTAGTAC 57.797 36.000 18.42 7.69 34.11 2.73
3180 8364 9.515226 TTATAGAAGGTTTTGCAGAACATTAGT 57.485 29.630 18.42 12.04 34.11 2.24
3184 8368 9.686683 AGTATTATAGAAGGTTTTGCAGAACAT 57.313 29.630 20.43 11.83 0.00 2.71
3185 8369 8.946085 CAGTATTATAGAAGGTTTTGCAGAACA 58.054 33.333 20.43 1.27 0.00 3.18
3186 8370 8.947115 ACAGTATTATAGAAGGTTTTGCAGAAC 58.053 33.333 11.54 11.54 0.00 3.01
3191 8375 9.665264 GCATTACAGTATTATAGAAGGTTTTGC 57.335 33.333 0.00 0.00 0.00 3.68
3192 8376 9.864034 CGCATTACAGTATTATAGAAGGTTTTG 57.136 33.333 0.00 0.00 0.00 2.44
3193 8377 9.826574 TCGCATTACAGTATTATAGAAGGTTTT 57.173 29.630 0.00 0.00 0.00 2.43
3194 8378 9.477484 CTCGCATTACAGTATTATAGAAGGTTT 57.523 33.333 0.00 0.00 0.00 3.27
3195 8379 8.639761 ACTCGCATTACAGTATTATAGAAGGTT 58.360 33.333 0.00 0.00 0.00 3.50
3196 8380 8.179509 ACTCGCATTACAGTATTATAGAAGGT 57.820 34.615 0.00 0.00 0.00 3.50
3204 8388 9.135843 GTGCATAATACTCGCATTACAGTATTA 57.864 33.333 12.06 12.06 45.55 0.98
3205 8389 7.872993 AGTGCATAATACTCGCATTACAGTATT 59.127 33.333 9.18 9.18 44.45 1.89
3206 8390 7.378966 AGTGCATAATACTCGCATTACAGTAT 58.621 34.615 0.00 0.00 37.41 2.12
3207 8391 6.745116 AGTGCATAATACTCGCATTACAGTA 58.255 36.000 0.00 0.00 38.07 2.74
3208 8392 5.601662 AGTGCATAATACTCGCATTACAGT 58.398 37.500 0.00 0.00 38.07 3.55
3209 8393 7.637709 TTAGTGCATAATACTCGCATTACAG 57.362 36.000 0.00 0.00 38.07 2.74
3210 8394 7.870445 TCATTAGTGCATAATACTCGCATTACA 59.130 33.333 0.00 0.00 38.07 2.41
3211 8395 8.239681 TCATTAGTGCATAATACTCGCATTAC 57.760 34.615 0.00 0.00 38.07 1.89
3212 8396 8.872845 CATCATTAGTGCATAATACTCGCATTA 58.127 33.333 0.00 0.00 38.07 1.90
3213 8397 7.388776 ACATCATTAGTGCATAATACTCGCATT 59.611 33.333 0.00 0.00 38.07 3.56
3214 8398 6.875726 ACATCATTAGTGCATAATACTCGCAT 59.124 34.615 0.00 0.00 38.07 4.73
3215 8399 6.146021 CACATCATTAGTGCATAATACTCGCA 59.854 38.462 0.00 0.00 32.61 5.10
3216 8400 6.528826 CACATCATTAGTGCATAATACTCGC 58.471 40.000 0.00 0.00 32.61 5.03
3293 8483 2.491693 GCAATTAGCAAACTACAGGCCA 59.508 45.455 5.01 0.00 44.79 5.36
3309 8501 5.741425 CGATTCTTGACATGTATCGCAATT 58.259 37.500 13.34 0.00 32.82 2.32
3336 8530 3.129913 GATTGGCCCATGCTGTCGC 62.130 63.158 0.00 0.00 37.74 5.19
3338 8532 0.757935 ATGGATTGGCCCATGCTGTC 60.758 55.000 9.79 0.00 44.77 3.51
3421 8621 0.960861 CCCTTCCCAAAACCGAGCTC 60.961 60.000 2.73 2.73 0.00 4.09


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

AutoCloner maintained by Alex Coulton.