Multiple sequence alignment - TraesCS6D01G151300

Loading Multiple Alignment...

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 TraesCS6D01G151300 chr6D 100.000 2660 0 0 1 2660 124610266 124607607 0.000000e+00 4913.0
1 TraesCS6D01G151300 chr6D 91.628 1087 42 13 675 1747 122979405 122980456 0.000000e+00 1458.0
2 TraesCS6D01G151300 chr6D 85.007 727 78 12 1 721 122988794 122989495 0.000000e+00 710.0
3 TraesCS6D01G151300 chr6D 89.811 530 31 10 1778 2288 122980455 122980980 0.000000e+00 658.0
4 TraesCS6D01G151300 chr6D 85.338 266 23 10 2410 2660 122982296 122982560 7.300000e-66 261.0
5 TraesCS6D01G151300 chr1B 84.487 1792 168 58 640 2362 398840682 398838932 0.000000e+00 1668.0
6 TraesCS6D01G151300 chr1B 88.814 742 77 2 968 1703 398962051 398962792 0.000000e+00 905.0
7 TraesCS6D01G151300 chr7D 85.752 1530 125 40 842 2362 545619909 545618464 0.000000e+00 1531.0
8 TraesCS6D01G151300 chr7D 88.132 910 71 19 880 1767 545647062 545647956 0.000000e+00 1048.0
9 TraesCS6D01G151300 chr7D 90.756 714 57 3 968 1675 518769000 518769710 0.000000e+00 944.0
10 TraesCS6D01G151300 chr7D 90.379 686 62 3 969 1650 545266879 545266194 0.000000e+00 898.0
11 TraesCS6D01G151300 chr7D 88.752 649 34 11 1726 2362 545621702 545621081 0.000000e+00 758.0
12 TraesCS6D01G151300 chr7D 88.281 640 49 16 1726 2359 545647969 545648588 0.000000e+00 743.0
13 TraesCS6D01G151300 chr7D 86.422 545 47 17 1836 2359 545651404 545651942 2.970000e-159 571.0
14 TraesCS6D01G151300 chr7D 87.597 258 24 5 2410 2660 545653402 545653658 2.590000e-75 292.0
15 TraesCS6D01G151300 chr7D 84.528 265 27 9 2410 2660 518775617 518775881 1.580000e-62 250.0
16 TraesCS6D01G151300 chr7D 82.836 134 12 7 717 848 545646941 545647065 2.800000e-20 110.0
17 TraesCS6D01G151300 chr5D 85.695 1503 113 36 880 2359 331837765 331839188 0.000000e+00 1491.0
18 TraesCS6D01G151300 chr6B 92.526 1057 44 15 683 1721 216631470 216632509 0.000000e+00 1482.0
19 TraesCS6D01G151300 chr6B 86.634 202 21 4 2410 2606 216633475 216633675 4.460000e-53 219.0
20 TraesCS6D01G151300 chr6A 91.166 1098 51 15 681 1767 158245725 158244663 0.000000e+00 1448.0
21 TraesCS6D01G151300 chr6A 86.000 900 103 13 878 1766 107264414 107265301 0.000000e+00 942.0
22 TraesCS6D01G151300 chr6A 86.466 266 20 10 2410 2660 158243718 158243454 7.250000e-71 278.0
23 TraesCS6D01G151300 chr6A 93.431 137 7 2 871 1006 158246057 158245922 4.490000e-48 202.0
24 TraesCS6D01G151300 chr6A 96.000 50 2 0 795 844 158246111 158246062 6.100000e-12 82.4
25 TraesCS6D01G151300 chr7A 88.276 1160 98 21 968 2094 626992528 626991374 0.000000e+00 1354.0
26 TraesCS6D01G151300 chr7A 88.844 735 70 8 943 1666 594434562 594435295 0.000000e+00 893.0
27 TraesCS6D01G151300 chr7A 89.564 642 35 10 1726 2362 628487207 628486593 0.000000e+00 785.0
28 TraesCS6D01G151300 chr7A 87.950 639 24 17 1726 2362 628491400 628490813 0.000000e+00 704.0
29 TraesCS6D01G151300 chr7A 86.115 677 58 21 1635 2307 628522236 628522880 0.000000e+00 697.0
30 TraesCS6D01G151300 chr7A 87.531 401 27 13 1972 2362 627230252 627229865 2.430000e-120 442.0
31 TraesCS6D01G151300 chr7A 85.536 401 49 6 459 853 628390402 628390005 6.850000e-111 411.0
32 TraesCS6D01G151300 chr7A 92.490 253 14 2 2108 2357 626990588 626990338 9.060000e-95 357.0
33 TraesCS6D01G151300 chr7A 86.905 252 26 4 2410 2654 628647830 628648081 2.610000e-70 276.0
34 TraesCS6D01G151300 chr7A 85.057 261 25 9 2410 2660 594450100 594450356 1.220000e-63 254.0
35 TraesCS6D01G151300 chr7A 83.459 266 28 10 2410 2660 169954957 169954693 1.590000e-57 233.0
36 TraesCS6D01G151300 chr2B 89.557 699 64 4 968 1657 182133679 182132981 0.000000e+00 878.0
37 TraesCS6D01G151300 chr7B 89.141 617 30 10 1751 2362 589699782 589699198 0.000000e+00 734.0
38 TraesCS6D01G151300 chr7B 86.422 545 47 17 1836 2359 589935889 589936427 2.970000e-159 571.0
39 TraesCS6D01G151300 chr7B 88.101 395 37 8 1969 2362 589737728 589738113 6.710000e-126 460.0
40 TraesCS6D01G151300 chr7B 81.059 623 64 23 1557 2157 589921599 589922189 5.220000e-122 448.0
41 TraesCS6D01G151300 chr7B 85.161 155 11 7 2387 2536 589937896 589938043 5.930000e-32 148.0
42 TraesCS6D01G151300 chr5A 85.171 263 36 3 374 635 69225970 69226230 1.570000e-67 267.0
43 TraesCS6D01G151300 chrUn 84.074 270 34 3 373 635 119815243 119814976 4.400000e-63 252.0
44 TraesCS6D01G151300 chr2A 82.213 253 44 1 384 635 692036395 692036143 1.600000e-52 217.0
45 TraesCS6D01G151300 chr3D 85.119 168 15 3 780 947 43727657 43727500 2.120000e-36 163.0
46 TraesCS6D01G151300 chr3A 85.333 150 10 7 798 947 55501495 55501358 7.670000e-31 145.0
47 TraesCS6D01G151300 chr1A 84.106 151 21 3 1 150 117894525 117894377 2.760000e-30 143.0


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 TraesCS6D01G151300 chr6D 124607607 124610266 2659 True 4913.000000 4913 100.000000 1 2660 1 chr6D.!!$R1 2659
1 TraesCS6D01G151300 chr6D 122979405 122982560 3155 False 792.333333 1458 88.925667 675 2660 3 chr6D.!!$F2 1985
2 TraesCS6D01G151300 chr6D 122988794 122989495 701 False 710.000000 710 85.007000 1 721 1 chr6D.!!$F1 720
3 TraesCS6D01G151300 chr1B 398838932 398840682 1750 True 1668.000000 1668 84.487000 640 2362 1 chr1B.!!$R1 1722
4 TraesCS6D01G151300 chr1B 398962051 398962792 741 False 905.000000 905 88.814000 968 1703 1 chr1B.!!$F1 735
5 TraesCS6D01G151300 chr7D 545618464 545621702 3238 True 1144.500000 1531 87.252000 842 2362 2 chr7D.!!$R2 1520
6 TraesCS6D01G151300 chr7D 518769000 518769710 710 False 944.000000 944 90.756000 968 1675 1 chr7D.!!$F1 707
7 TraesCS6D01G151300 chr7D 545266194 545266879 685 True 898.000000 898 90.379000 969 1650 1 chr7D.!!$R1 681
8 TraesCS6D01G151300 chr7D 545646941 545653658 6717 False 552.800000 1048 86.653600 717 2660 5 chr7D.!!$F3 1943
9 TraesCS6D01G151300 chr5D 331837765 331839188 1423 False 1491.000000 1491 85.695000 880 2359 1 chr5D.!!$F1 1479
10 TraesCS6D01G151300 chr6B 216631470 216633675 2205 False 850.500000 1482 89.580000 683 2606 2 chr6B.!!$F1 1923
11 TraesCS6D01G151300 chr6A 107264414 107265301 887 False 942.000000 942 86.000000 878 1766 1 chr6A.!!$F1 888
12 TraesCS6D01G151300 chr6A 158243454 158246111 2657 True 502.600000 1448 91.765750 681 2660 4 chr6A.!!$R1 1979
13 TraesCS6D01G151300 chr7A 594434562 594435295 733 False 893.000000 893 88.844000 943 1666 1 chr7A.!!$F1 723
14 TraesCS6D01G151300 chr7A 626990338 626992528 2190 True 855.500000 1354 90.383000 968 2357 2 chr7A.!!$R4 1389
15 TraesCS6D01G151300 chr7A 628486593 628491400 4807 True 744.500000 785 88.757000 1726 2362 2 chr7A.!!$R5 636
16 TraesCS6D01G151300 chr7A 628522236 628522880 644 False 697.000000 697 86.115000 1635 2307 1 chr7A.!!$F3 672
17 TraesCS6D01G151300 chr2B 182132981 182133679 698 True 878.000000 878 89.557000 968 1657 1 chr2B.!!$R1 689
18 TraesCS6D01G151300 chr7B 589699198 589699782 584 True 734.000000 734 89.141000 1751 2362 1 chr7B.!!$R1 611
19 TraesCS6D01G151300 chr7B 589921599 589922189 590 False 448.000000 448 81.059000 1557 2157 1 chr7B.!!$F2 600
20 TraesCS6D01G151300 chr7B 589935889 589938043 2154 False 359.500000 571 85.791500 1836 2536 2 chr7B.!!$F3 700

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
420 421 0.039437 AGTACAACACGCAGACGAGG 60.039 55.0 0.00 0.0 43.93 4.63 F
450 451 0.108138 CCATCCTGACCTGTCGGAAC 60.108 60.0 7.69 0.0 38.21 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 6101 0.245539 GGGACTTGATCACGTCGGAA 59.754 55.0 21.91 0.0 31.18 4.30 R
2412 16114 0.930726 AGGGTACAGAGGAGGAGGAG 59.069 60.0 0.00 0.0 0.00 3.69 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
44 45 1.009829 CATAAGAGCACAAGGACCGC 58.990 55.000 0.00 0.00 0.00 5.68
45 46 0.107654 ATAAGAGCACAAGGACCGCC 60.108 55.000 0.00 0.00 0.00 6.13
47 48 3.050275 GAGCACAAGGACCGCCAC 61.050 66.667 0.00 0.00 36.29 5.01
49 50 2.167398 GAGCACAAGGACCGCCACTA 62.167 60.000 0.00 0.00 36.29 2.74
50 51 2.033194 GCACAAGGACCGCCACTAC 61.033 63.158 0.00 0.00 36.29 2.73
51 52 1.369692 CACAAGGACCGCCACTACA 59.630 57.895 0.00 0.00 36.29 2.74
52 53 0.949105 CACAAGGACCGCCACTACAC 60.949 60.000 0.00 0.00 36.29 2.90
54 55 2.939261 AAGGACCGCCACTACACCG 61.939 63.158 0.00 0.00 36.29 4.94
56 57 4.065281 GACCGCCACTACACCGCT 62.065 66.667 0.00 0.00 0.00 5.52
63 64 2.603473 ACTACACCGCTGCCTCCA 60.603 61.111 0.00 0.00 0.00 3.86
64 65 2.125512 CTACACCGCTGCCTCCAC 60.126 66.667 0.00 0.00 0.00 4.02
67 68 4.641645 CACCGCTGCCTCCACCAA 62.642 66.667 0.00 0.00 0.00 3.67
68 69 4.335647 ACCGCTGCCTCCACCAAG 62.336 66.667 0.00 0.00 0.00 3.61
72 73 4.020617 CTGCCTCCACCAAGCCGA 62.021 66.667 0.00 0.00 0.00 5.54
103 104 4.101448 ATGGCGGAGGACACCAGC 62.101 66.667 0.00 0.00 36.78 4.85
106 107 4.767255 GCGGAGGACACCAGCCAG 62.767 72.222 0.00 0.00 0.00 4.85
108 109 4.767255 GGAGGACACCAGCCAGCG 62.767 72.222 0.00 0.00 0.00 5.18
141 142 4.925861 GGCTCCAGGCGCCAGATC 62.926 72.222 31.54 19.65 46.77 2.75
143 144 2.108566 CTCCAGGCGCCAGATCTG 59.891 66.667 31.54 17.82 0.00 2.90
146 147 2.580815 CAGGCGCCAGATCTGACA 59.419 61.111 31.54 0.00 0.00 3.58
150 151 1.086634 GGCGCCAGATCTGACAGAAC 61.087 60.000 24.80 6.96 0.00 3.01
151 152 1.086634 GCGCCAGATCTGACAGAACC 61.087 60.000 24.62 4.74 0.00 3.62
152 153 0.803768 CGCCAGATCTGACAGAACCG 60.804 60.000 24.62 10.17 0.00 4.44
155 156 1.546029 CCAGATCTGACAGAACCGACA 59.454 52.381 24.62 0.00 0.00 4.35
157 158 3.443037 CAGATCTGACAGAACCGACATC 58.557 50.000 18.34 0.43 0.00 3.06
158 159 3.092301 AGATCTGACAGAACCGACATCA 58.908 45.455 9.70 0.00 0.00 3.07
159 160 3.130164 AGATCTGACAGAACCGACATCAG 59.870 47.826 9.70 0.00 38.51 2.90
160 161 1.067565 TCTGACAGAACCGACATCAGC 60.068 52.381 1.64 0.00 37.34 4.26
161 162 0.969149 TGACAGAACCGACATCAGCT 59.031 50.000 0.00 0.00 0.00 4.24
162 163 1.337167 TGACAGAACCGACATCAGCTG 60.337 52.381 7.63 7.63 0.00 4.24
163 164 0.681733 ACAGAACCGACATCAGCTGT 59.318 50.000 14.67 0.00 42.15 4.40
170 171 4.559835 ACATCAGCTGTCACGTCG 57.440 55.556 14.67 0.00 29.94 5.12
172 173 1.734117 CATCAGCTGTCACGTCGCA 60.734 57.895 14.67 0.00 0.00 5.10
174 175 3.406361 CAGCTGTCACGTCGCACC 61.406 66.667 5.25 0.00 0.00 5.01
200 201 3.443045 CCGCCACCTTCACCATGC 61.443 66.667 0.00 0.00 0.00 4.06
202 203 2.693762 CGCCACCTTCACCATGCAG 61.694 63.158 0.00 0.00 0.00 4.41
204 205 1.870055 GCCACCTTCACCATGCAGTG 61.870 60.000 0.00 0.00 39.20 3.66
207 208 1.672030 CCTTCACCATGCAGTGCGA 60.672 57.895 11.20 0.00 37.68 5.10
208 209 1.499056 CTTCACCATGCAGTGCGAC 59.501 57.895 11.20 0.00 37.68 5.19
210 211 3.434319 CACCATGCAGTGCGACCC 61.434 66.667 11.20 0.00 0.00 4.46
213 214 4.720902 CATGCAGTGCGACCCCCA 62.721 66.667 11.20 0.00 0.00 4.96
214 215 3.965258 ATGCAGTGCGACCCCCAA 61.965 61.111 11.20 0.00 0.00 4.12
215 216 4.947147 TGCAGTGCGACCCCCAAC 62.947 66.667 11.20 0.00 0.00 3.77
218 219 2.203877 AGTGCGACCCCCAACCTA 60.204 61.111 0.00 0.00 0.00 3.08
220 221 2.120940 TGCGACCCCCAACCTAGA 59.879 61.111 0.00 0.00 0.00 2.43
221 222 1.987855 TGCGACCCCCAACCTAGAG 60.988 63.158 0.00 0.00 0.00 2.43
225 226 2.258748 GACCCCCAACCTAGAGCAGC 62.259 65.000 0.00 0.00 0.00 5.25
229 230 1.296715 CCAACCTAGAGCAGCCGTT 59.703 57.895 0.00 0.00 0.00 4.44
230 231 0.741221 CCAACCTAGAGCAGCCGTTC 60.741 60.000 0.00 0.00 0.00 3.95
231 232 1.078759 CAACCTAGAGCAGCCGTTCG 61.079 60.000 0.00 0.00 0.00 3.95
232 233 2.583593 CCTAGAGCAGCCGTTCGC 60.584 66.667 0.00 0.00 37.98 4.70
261 262 1.064946 CGAGAGGCATCGGAGACAC 59.935 63.158 4.41 0.00 42.51 3.67
262 263 1.439644 GAGAGGCATCGGAGACACC 59.560 63.158 0.00 0.00 42.51 4.16
279 280 2.024871 CGACTGGACGGATCGAGC 59.975 66.667 0.00 0.00 38.10 5.03
280 281 2.761195 CGACTGGACGGATCGAGCA 61.761 63.158 1.84 0.00 38.10 4.26
281 282 1.226717 GACTGGACGGATCGAGCAC 60.227 63.158 1.84 0.00 34.15 4.40
282 283 2.105128 CTGGACGGATCGAGCACC 59.895 66.667 1.84 3.36 0.00 5.01
285 286 1.218316 GGACGGATCGAGCACCTTT 59.782 57.895 1.84 0.00 0.00 3.11
286 287 1.084370 GGACGGATCGAGCACCTTTG 61.084 60.000 1.84 0.00 0.00 2.77
287 288 0.108804 GACGGATCGAGCACCTTTGA 60.109 55.000 1.84 0.00 0.00 2.69
288 289 0.320374 ACGGATCGAGCACCTTTGAA 59.680 50.000 1.84 0.00 0.00 2.69
300 301 3.566130 CTTTGAAGGAGGGAGCAGG 57.434 57.895 0.00 0.00 0.00 4.85
301 302 0.679321 CTTTGAAGGAGGGAGCAGGC 60.679 60.000 0.00 0.00 0.00 4.85
302 303 2.142292 TTTGAAGGAGGGAGCAGGCC 62.142 60.000 0.00 0.00 0.00 5.19
303 304 3.011517 GAAGGAGGGAGCAGGCCA 61.012 66.667 5.01 0.00 0.00 5.36
304 305 3.013932 AAGGAGGGAGCAGGCCAG 61.014 66.667 5.01 0.00 0.00 4.85
311 312 4.039092 GAGCAGGCCAGCCCTTGA 62.039 66.667 17.68 0.00 43.06 3.02
314 315 2.421399 GCAGGCCAGCCCTTGATTC 61.421 63.158 9.39 0.00 43.06 2.52
316 317 1.000396 AGGCCAGCCCTTGATTCAC 60.000 57.895 5.01 0.00 43.06 3.18
317 318 2.054453 GGCCAGCCCTTGATTCACC 61.054 63.158 0.00 0.00 0.00 4.02
319 320 1.750399 CCAGCCCTTGATTCACCCG 60.750 63.158 0.00 0.00 0.00 5.28
320 321 1.299648 CAGCCCTTGATTCACCCGA 59.700 57.895 0.00 0.00 0.00 5.14
321 322 0.745845 CAGCCCTTGATTCACCCGAG 60.746 60.000 0.00 0.00 0.00 4.63
322 323 2.115291 GCCCTTGATTCACCCGAGC 61.115 63.158 0.00 0.00 0.00 5.03
337 338 4.496336 AGCGGGCAAGGCTGGATC 62.496 66.667 4.54 0.00 39.77 3.36
340 341 3.001514 GGGCAAGGCTGGATCTGA 58.998 61.111 0.00 0.00 0.00 3.27
341 342 1.452833 GGGCAAGGCTGGATCTGAC 60.453 63.158 0.00 0.00 0.00 3.51
342 343 1.817099 GGCAAGGCTGGATCTGACG 60.817 63.158 0.00 0.00 0.00 4.35
343 344 2.467826 GCAAGGCTGGATCTGACGC 61.468 63.158 0.00 0.00 0.00 5.19
345 346 2.293318 AAGGCTGGATCTGACGCCA 61.293 57.895 14.32 6.44 44.85 5.69
348 349 2.109126 GCTGGATCTGACGCCAACC 61.109 63.158 3.13 0.00 32.95 3.77
349 350 1.599047 CTGGATCTGACGCCAACCT 59.401 57.895 3.13 0.00 32.95 3.50
351 352 1.519455 GGATCTGACGCCAACCTCG 60.519 63.158 0.00 0.00 0.00 4.63
353 354 3.665675 ATCTGACGCCAACCTCGCC 62.666 63.158 0.00 0.00 0.00 5.54
371 372 2.833227 GCACACCACCACCACCTA 59.167 61.111 0.00 0.00 0.00 3.08
372 373 1.302511 GCACACCACCACCACCTAG 60.303 63.158 0.00 0.00 0.00 3.02
373 374 1.302511 CACACCACCACCACCTAGC 60.303 63.158 0.00 0.00 0.00 3.42
375 376 1.302511 CACCACCACCACCTAGCAC 60.303 63.158 0.00 0.00 0.00 4.40
376 377 1.768482 ACCACCACCACCTAGCACA 60.768 57.895 0.00 0.00 0.00 4.57
377 378 1.302511 CCACCACCACCTAGCACAC 60.303 63.158 0.00 0.00 0.00 3.82
378 379 1.302511 CACCACCACCTAGCACACC 60.303 63.158 0.00 0.00 0.00 4.16
380 381 1.003355 CCACCACCTAGCACACCAG 60.003 63.158 0.00 0.00 0.00 4.00
381 382 1.672356 CACCACCTAGCACACCAGC 60.672 63.158 0.00 0.00 0.00 4.85
382 383 2.434884 CCACCTAGCACACCAGCG 60.435 66.667 0.00 0.00 40.15 5.18
404 405 3.108343 GCTCGAGCGGCAGTAGTA 58.892 61.111 23.61 0.00 0.00 1.82
406 407 1.989966 GCTCGAGCGGCAGTAGTACA 61.990 60.000 23.61 0.00 0.00 2.90
408 409 0.169672 TCGAGCGGCAGTAGTACAAC 59.830 55.000 1.45 0.00 0.00 3.32
410 411 1.347320 GAGCGGCAGTAGTACAACAC 58.653 55.000 1.45 0.00 0.00 3.32
411 412 0.388134 AGCGGCAGTAGTACAACACG 60.388 55.000 1.45 3.04 0.00 4.49
412 413 1.952266 GCGGCAGTAGTACAACACGC 61.952 60.000 13.18 13.18 38.94 5.34
413 414 0.665068 CGGCAGTAGTACAACACGCA 60.665 55.000 2.52 0.00 0.00 5.24
414 415 1.068474 GGCAGTAGTACAACACGCAG 58.932 55.000 2.52 0.00 0.00 5.18
415 416 1.336517 GGCAGTAGTACAACACGCAGA 60.337 52.381 2.52 0.00 0.00 4.26
416 417 1.719780 GCAGTAGTACAACACGCAGAC 59.280 52.381 2.52 0.00 0.00 3.51
418 419 1.875514 AGTAGTACAACACGCAGACGA 59.124 47.619 2.52 0.00 43.93 4.20
419 420 2.095869 AGTAGTACAACACGCAGACGAG 60.096 50.000 2.52 0.00 43.93 4.18
420 421 0.039437 AGTACAACACGCAGACGAGG 60.039 55.000 0.00 0.00 43.93 4.63
422 423 0.240145 TACAACACGCAGACGAGGAG 59.760 55.000 0.00 0.00 43.93 3.69
423 424 1.734477 CAACACGCAGACGAGGAGG 60.734 63.158 0.00 0.00 43.93 4.30
427 428 4.504916 CGCAGACGAGGAGGCAGG 62.505 72.222 0.00 0.00 43.93 4.85
428 429 3.386237 GCAGACGAGGAGGCAGGT 61.386 66.667 0.00 0.00 0.00 4.00
431 432 1.979693 AGACGAGGAGGCAGGTCAC 60.980 63.158 0.00 0.00 31.93 3.67
432 433 2.997897 ACGAGGAGGCAGGTCACC 60.998 66.667 0.00 0.00 0.00 4.02
433 434 2.997315 CGAGGAGGCAGGTCACCA 60.997 66.667 0.00 0.00 0.00 4.17
434 435 2.362369 CGAGGAGGCAGGTCACCAT 61.362 63.158 0.00 0.00 0.00 3.55
435 436 1.524482 GAGGAGGCAGGTCACCATC 59.476 63.158 0.00 0.00 0.00 3.51
436 437 1.977293 GAGGAGGCAGGTCACCATCC 61.977 65.000 0.00 0.00 0.00 3.51
437 438 1.997874 GGAGGCAGGTCACCATCCT 60.998 63.158 6.61 6.61 35.45 3.24
445 446 3.842869 GTCACCATCCTGACCTGTC 57.157 57.895 0.00 0.00 35.44 3.51
446 447 0.108615 GTCACCATCCTGACCTGTCG 60.109 60.000 0.00 0.00 35.44 4.35
447 448 1.219124 CACCATCCTGACCTGTCGG 59.781 63.158 0.00 0.00 35.77 4.79
448 449 1.078528 ACCATCCTGACCTGTCGGA 59.921 57.895 7.69 9.85 38.21 4.55
449 450 0.544357 ACCATCCTGACCTGTCGGAA 60.544 55.000 7.69 0.00 38.21 4.30
450 451 0.108138 CCATCCTGACCTGTCGGAAC 60.108 60.000 7.69 0.00 38.21 3.62
452 453 1.605058 ATCCTGACCTGTCGGAACCG 61.605 60.000 7.69 6.94 38.21 4.44
453 454 2.273179 CCTGACCTGTCGGAACCGA 61.273 63.158 12.04 12.04 46.87 4.69
461 462 4.373116 TCGGAACCGAGCAGCCAC 62.373 66.667 12.04 0.00 44.01 5.01
465 466 3.842925 GAACCGAGCAGCCACCCAA 62.843 63.158 0.00 0.00 0.00 4.12
467 468 2.597217 CCGAGCAGCCACCCAAAA 60.597 61.111 0.00 0.00 0.00 2.44
468 469 2.644992 CGAGCAGCCACCCAAAAC 59.355 61.111 0.00 0.00 0.00 2.43
469 470 2.192861 CGAGCAGCCACCCAAAACA 61.193 57.895 0.00 0.00 0.00 2.83
470 471 1.526575 CGAGCAGCCACCCAAAACAT 61.527 55.000 0.00 0.00 0.00 2.71
471 472 0.244721 GAGCAGCCACCCAAAACATC 59.755 55.000 0.00 0.00 0.00 3.06
472 473 0.469705 AGCAGCCACCCAAAACATCA 60.470 50.000 0.00 0.00 0.00 3.07
473 474 0.319813 GCAGCCACCCAAAACATCAC 60.320 55.000 0.00 0.00 0.00 3.06
474 475 0.318120 CAGCCACCCAAAACATCACC 59.682 55.000 0.00 0.00 0.00 4.02
475 476 1.178534 AGCCACCCAAAACATCACCG 61.179 55.000 0.00 0.00 0.00 4.94
476 477 1.288752 CCACCCAAAACATCACCGC 59.711 57.895 0.00 0.00 0.00 5.68
477 478 1.288752 CACCCAAAACATCACCGCC 59.711 57.895 0.00 0.00 0.00 6.13
478 479 1.906333 ACCCAAAACATCACCGCCC 60.906 57.895 0.00 0.00 0.00 6.13
479 480 2.645192 CCCAAAACATCACCGCCCC 61.645 63.158 0.00 0.00 0.00 5.80
480 481 2.566010 CAAAACATCACCGCCCCG 59.434 61.111 0.00 0.00 0.00 5.73
481 482 3.370231 AAAACATCACCGCCCCGC 61.370 61.111 0.00 0.00 0.00 6.13
500 501 4.516195 GGCGCCGAGGGAGACTTC 62.516 72.222 12.58 0.00 0.00 3.01
506 507 2.182030 GAGGGAGACTTCGCCGTG 59.818 66.667 0.00 0.00 36.62 4.94
507 508 3.991536 GAGGGAGACTTCGCCGTGC 62.992 68.421 0.00 0.00 36.62 5.34
510 511 4.373116 GAGACTTCGCCGTGCCCA 62.373 66.667 0.00 0.00 0.00 5.36
512 513 3.423154 GACTTCGCCGTGCCCAAG 61.423 66.667 0.00 0.00 0.00 3.61
514 515 4.697756 CTTCGCCGTGCCCAAGGA 62.698 66.667 4.39 0.00 31.21 3.36
521 522 4.678743 GTGCCCAAGGACACCCCC 62.679 72.222 0.00 0.00 34.66 5.40
523 524 4.678743 GCCCAAGGACACCCCCAC 62.679 72.222 0.00 0.00 34.66 4.61
525 526 2.773527 CCCAAGGACACCCCCACAA 61.774 63.158 0.00 0.00 34.66 3.33
526 527 1.530655 CCAAGGACACCCCCACAAC 60.531 63.158 0.00 0.00 34.66 3.32
527 528 1.896660 CAAGGACACCCCCACAACG 60.897 63.158 0.00 0.00 34.66 4.10
530 531 4.612412 GACACCCCCACAACGCGA 62.612 66.667 15.93 0.00 0.00 5.87
531 532 4.619227 ACACCCCCACAACGCGAG 62.619 66.667 15.93 7.57 0.00 5.03
535 536 3.726517 CCCCACAACGCGAGCAAG 61.727 66.667 15.93 0.00 0.00 4.01
536 537 3.726517 CCCACAACGCGAGCAAGG 61.727 66.667 15.93 7.79 0.00 3.61
537 538 2.972505 CCACAACGCGAGCAAGGT 60.973 61.111 15.93 0.00 0.00 3.50
538 539 2.551270 CACAACGCGAGCAAGGTC 59.449 61.111 15.93 0.00 0.00 3.85
539 540 2.665185 ACAACGCGAGCAAGGTCC 60.665 61.111 15.93 0.00 0.00 4.46
541 542 3.626924 AACGCGAGCAAGGTCCCT 61.627 61.111 15.93 0.00 0.00 4.20
542 543 3.883744 AACGCGAGCAAGGTCCCTG 62.884 63.158 15.93 0.00 0.00 4.45
583 584 4.648626 TTCGCCCTGCAGCTTGCT 62.649 61.111 8.66 0.00 45.31 3.91
588 589 3.441290 CCTGCAGCTTGCTCCAGC 61.441 66.667 8.66 2.61 45.31 4.85
592 593 3.429141 CAGCTTGCTCCAGCGGTG 61.429 66.667 7.86 7.86 45.24 4.94
593 594 4.711949 AGCTTGCTCCAGCGGTGG 62.712 66.667 27.73 27.73 45.24 4.61
611 612 2.284699 CGGAGAGGAGGGGTGGTT 60.285 66.667 0.00 0.00 0.00 3.67
614 615 0.778083 GGAGAGGAGGGGTGGTTTTT 59.222 55.000 0.00 0.00 0.00 1.94
773 804 3.521560 TGGAAAGATAGCGTCATCACAC 58.478 45.455 2.00 0.00 0.00 3.82
779 810 7.652105 GGAAAGATAGCGTCATCACACTAAATA 59.348 37.037 2.00 0.00 0.00 1.40
854 1807 1.675310 CCTGATTGCCGCCAGTTCA 60.675 57.895 0.00 0.00 0.00 3.18
954 1912 1.347050 CTGATCGGCATCCTCATCCTT 59.653 52.381 0.00 0.00 0.00 3.36
1263 2285 1.629043 TCAAGCTTCCGTGTCCTAGT 58.371 50.000 0.00 0.00 0.00 2.57
1304 5752 3.324108 GACGTGCCCCCACCCTTA 61.324 66.667 0.00 0.00 38.79 2.69
1685 6377 2.528797 GACGTGTGGTCAAGCGATT 58.471 52.632 0.00 0.00 45.36 3.34
1712 6411 5.356470 AGCAGAGGAAGAAATCATAAGCAAC 59.644 40.000 0.00 0.00 0.00 4.17
1767 10612 1.805345 CAAAGCAGAGGAAGCAGAGTG 59.195 52.381 0.00 0.00 0.00 3.51
1768 10613 0.321475 AAGCAGAGGAAGCAGAGTGC 60.321 55.000 0.00 0.00 45.46 4.40
2087 12413 5.693769 TTTCCCGGAGAAGAACAGATATT 57.306 39.130 0.73 0.00 35.40 1.28
2152 13262 2.652382 TTTGTCGCGTCAGGAAGGCA 62.652 55.000 5.77 0.00 38.71 4.75
2164 13274 2.562298 CAGGAAGGCACCAAAAAGCATA 59.438 45.455 3.78 0.00 0.00 3.14
2320 14565 5.122396 GCAGAGAAAATCAATACTTGACGGT 59.878 40.000 0.00 0.00 43.48 4.83
2332 14578 7.825270 TCAATACTTGACGGTAATGGTGTTTAT 59.175 33.333 0.00 0.00 34.08 1.40
2333 14579 9.100554 CAATACTTGACGGTAATGGTGTTTATA 57.899 33.333 0.00 0.00 0.00 0.98
2334 14580 6.973229 ACTTGACGGTAATGGTGTTTATAC 57.027 37.500 0.00 0.00 0.00 1.47
2335 14581 6.704310 ACTTGACGGTAATGGTGTTTATACT 58.296 36.000 0.00 0.00 0.00 2.12
2338 14584 7.167924 TGACGGTAATGGTGTTTATACTACA 57.832 36.000 0.00 0.00 0.00 2.74
2340 14586 8.259411 TGACGGTAATGGTGTTTATACTACATT 58.741 33.333 9.53 9.53 36.25 2.71
2341 14587 9.101655 GACGGTAATGGTGTTTATACTACATTT 57.898 33.333 9.75 0.00 35.00 2.32
2382 16079 6.015603 TGGCAACATCAAGTCAATTACAATGA 60.016 34.615 0.00 0.00 46.17 2.57
2390 16087 8.634335 TCAAGTCAATTACAATGAGAAATCCA 57.366 30.769 0.00 0.00 0.00 3.41
2391 16088 8.514594 TCAAGTCAATTACAATGAGAAATCCAC 58.485 33.333 0.00 0.00 0.00 4.02
2392 16089 8.298854 CAAGTCAATTACAATGAGAAATCCACA 58.701 33.333 0.00 0.00 0.00 4.17
2393 16090 8.048534 AGTCAATTACAATGAGAAATCCACAG 57.951 34.615 0.00 0.00 0.00 3.66
2394 16091 7.121759 AGTCAATTACAATGAGAAATCCACAGG 59.878 37.037 0.00 0.00 0.00 4.00
2395 16092 6.947733 TCAATTACAATGAGAAATCCACAGGT 59.052 34.615 0.00 0.00 0.00 4.00
2396 16093 8.106462 TCAATTACAATGAGAAATCCACAGGTA 58.894 33.333 0.00 0.00 0.00 3.08
2397 16094 8.906867 CAATTACAATGAGAAATCCACAGGTAT 58.093 33.333 0.00 0.00 0.00 2.73
2399 16096 6.764308 ACAATGAGAAATCCACAGGTATTG 57.236 37.500 0.00 0.00 0.00 1.90
2400 16097 6.248433 ACAATGAGAAATCCACAGGTATTGT 58.752 36.000 0.00 0.00 41.94 2.71
2405 16107 7.103641 TGAGAAATCCACAGGTATTGTAGTTC 58.896 38.462 0.00 0.00 38.16 3.01
2407 16109 7.690256 AGAAATCCACAGGTATTGTAGTTCTT 58.310 34.615 0.00 0.00 38.16 2.52
2408 16110 7.824779 AGAAATCCACAGGTATTGTAGTTCTTC 59.175 37.037 0.00 0.00 38.16 2.87
2412 16114 5.875359 CCACAGGTATTGTAGTTCTTCTTCC 59.125 44.000 0.00 0.00 38.16 3.46
2418 16120 5.685520 ATTGTAGTTCTTCTTCCTCCTCC 57.314 43.478 0.00 0.00 0.00 4.30
2426 16128 1.388174 TCTTCCTCCTCCTCCTCTGT 58.612 55.000 0.00 0.00 0.00 3.41
2430 16132 0.105913 CCTCCTCCTCCTCTGTACCC 60.106 65.000 0.00 0.00 0.00 3.69
2434 16136 1.219213 CCTCCTCCTCTGTACCCTCAT 59.781 57.143 0.00 0.00 0.00 2.90
2435 16137 2.593026 CTCCTCCTCTGTACCCTCATC 58.407 57.143 0.00 0.00 0.00 2.92
2452 16156 0.176680 ATCGTCATCCGCAGCTTCTT 59.823 50.000 0.00 0.00 36.19 2.52
2455 16159 0.674895 GTCATCCGCAGCTTCTTGGT 60.675 55.000 0.00 0.00 0.00 3.67
2465 16173 2.057922 AGCTTCTTGGTTTCCTCCTGA 58.942 47.619 0.00 0.00 0.00 3.86
2474 16182 5.324832 TGGTTTCCTCCTGAAGAGAAATT 57.675 39.130 0.00 0.00 46.50 1.82
2482 16190 6.293004 CTCCTGAAGAGAAATTAGGAGTGT 57.707 41.667 9.24 0.00 46.50 3.55
2483 16191 7.411486 CTCCTGAAGAGAAATTAGGAGTGTA 57.589 40.000 9.24 0.00 46.50 2.90
2557 16265 5.760743 ACTTCAAAGTAGCAAAGAGGAGAAC 59.239 40.000 0.00 0.00 37.52 3.01
2565 16273 5.640189 AGCAAAGAGGAGAACAATCAATG 57.360 39.130 0.00 0.00 0.00 2.82
2609 16317 7.354751 GGCTTACCCATGGTTTTTATCAATA 57.645 36.000 11.73 0.00 37.09 1.90
2610 16318 7.207383 GGCTTACCCATGGTTTTTATCAATAC 58.793 38.462 11.73 0.00 37.09 1.89
2611 16319 7.069455 GGCTTACCCATGGTTTTTATCAATACT 59.931 37.037 11.73 0.00 37.09 2.12
2612 16320 8.474831 GCTTACCCATGGTTTTTATCAATACTT 58.525 33.333 11.73 0.00 37.09 2.24
2614 16322 9.535170 TTACCCATGGTTTTTATCAATACTTCA 57.465 29.630 11.73 0.00 37.09 3.02
2615 16323 8.429237 ACCCATGGTTTTTATCAATACTTCAA 57.571 30.769 11.73 0.00 27.29 2.69
2634 16352 8.117813 ACTTCAAAGTACTTCAAAACTTCCAA 57.882 30.769 8.95 0.00 37.52 3.53
2635 16353 8.581578 ACTTCAAAGTACTTCAAAACTTCCAAA 58.418 29.630 8.95 0.00 37.52 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.961019 ATGGCATCACAGCAACGTTT 59.039 45.000 0.00 0.00 35.83 3.60
17 18 2.785540 TGTGCTCTTATGGCATCACA 57.214 45.000 13.14 13.14 41.86 3.58
21 22 2.648059 GTCCTTGTGCTCTTATGGCAT 58.352 47.619 4.88 4.88 41.86 4.40
44 45 2.125512 GAGGCAGCGGTGTAGTGG 60.126 66.667 17.07 0.00 0.00 4.00
45 46 2.125512 GGAGGCAGCGGTGTAGTG 60.126 66.667 17.07 0.00 0.00 2.74
47 48 2.125512 GTGGAGGCAGCGGTGTAG 60.126 66.667 17.07 0.00 0.00 2.74
50 51 4.641645 TTGGTGGAGGCAGCGGTG 62.642 66.667 10.98 10.98 0.00 4.94
51 52 4.335647 CTTGGTGGAGGCAGCGGT 62.336 66.667 0.00 0.00 0.00 5.68
56 57 4.329545 GTCGGCTTGGTGGAGGCA 62.330 66.667 0.00 0.00 41.92 4.75
90 91 4.767255 GCTGGCTGGTGTCCTCCG 62.767 72.222 0.00 0.00 0.00 4.63
91 92 4.767255 CGCTGGCTGGTGTCCTCC 62.767 72.222 0.00 0.00 0.00 4.30
126 127 2.108566 CAGATCTGGCGCCTGGAG 59.891 66.667 30.13 18.89 0.00 3.86
130 131 1.260538 TTCTGTCAGATCTGGCGCCT 61.261 55.000 29.70 7.33 38.19 5.52
131 132 1.086634 GTTCTGTCAGATCTGGCGCC 61.087 60.000 22.73 22.73 38.19 6.53
132 133 1.086634 GGTTCTGTCAGATCTGGCGC 61.087 60.000 21.79 13.03 38.19 6.53
133 134 0.803768 CGGTTCTGTCAGATCTGGCG 60.804 60.000 21.79 16.08 38.19 5.69
134 135 0.532573 TCGGTTCTGTCAGATCTGGC 59.467 55.000 20.65 20.65 35.37 4.85
136 137 3.119352 TGATGTCGGTTCTGTCAGATCTG 60.119 47.826 17.07 17.07 0.00 2.90
137 138 3.092301 TGATGTCGGTTCTGTCAGATCT 58.908 45.455 2.68 0.00 0.00 2.75
138 139 3.443037 CTGATGTCGGTTCTGTCAGATC 58.557 50.000 2.68 2.70 38.81 2.75
141 142 1.067283 AGCTGATGTCGGTTCTGTCAG 60.067 52.381 0.00 0.00 39.35 3.51
143 144 1.337260 ACAGCTGATGTCGGTTCTGTC 60.337 52.381 23.35 0.00 37.75 3.51
155 156 1.734477 GTGCGACGTGACAGCTGAT 60.734 57.895 23.35 4.35 0.00 2.90
157 158 3.406361 GGTGCGACGTGACAGCTG 61.406 66.667 13.48 13.48 0.00 4.24
181 182 4.047125 ATGGTGAAGGTGGCGGGG 62.047 66.667 0.00 0.00 0.00 5.73
184 185 2.672651 TGCATGGTGAAGGTGGCG 60.673 61.111 0.00 0.00 0.00 5.69
185 186 1.604593 ACTGCATGGTGAAGGTGGC 60.605 57.895 0.00 0.00 0.00 5.01
186 187 1.870055 GCACTGCATGGTGAAGGTGG 61.870 60.000 10.09 0.00 39.34 4.61
187 188 1.582968 GCACTGCATGGTGAAGGTG 59.417 57.895 10.09 2.39 39.34 4.00
188 189 1.968017 CGCACTGCATGGTGAAGGT 60.968 57.895 10.09 0.00 39.34 3.50
191 192 1.965930 GGTCGCACTGCATGGTGAA 60.966 57.895 10.09 0.00 39.34 3.18
194 195 4.722700 GGGGTCGCACTGCATGGT 62.723 66.667 1.11 0.00 0.00 3.55
196 197 4.720902 TGGGGGTCGCACTGCATG 62.721 66.667 1.11 0.00 0.00 4.06
197 198 3.965258 TTGGGGGTCGCACTGCAT 61.965 61.111 1.11 0.00 0.00 3.96
200 201 2.521958 CTAGGTTGGGGGTCGCACTG 62.522 65.000 0.00 0.00 0.00 3.66
202 203 2.240162 CTCTAGGTTGGGGGTCGCAC 62.240 65.000 0.00 0.00 0.00 5.34
204 205 2.901042 CTCTAGGTTGGGGGTCGC 59.099 66.667 0.00 0.00 0.00 5.19
207 208 2.301738 GCTGCTCTAGGTTGGGGGT 61.302 63.158 0.00 0.00 0.00 4.95
208 209 2.592308 GCTGCTCTAGGTTGGGGG 59.408 66.667 0.00 0.00 0.00 5.40
210 211 2.185310 AACGGCTGCTCTAGGTTGGG 62.185 60.000 0.00 0.00 0.00 4.12
213 214 1.215647 CGAACGGCTGCTCTAGGTT 59.784 57.895 0.00 0.00 0.00 3.50
214 215 2.885861 CGAACGGCTGCTCTAGGT 59.114 61.111 0.00 0.00 0.00 3.08
215 216 2.583593 GCGAACGGCTGCTCTAGG 60.584 66.667 0.00 0.00 39.11 3.02
231 232 4.577246 CTCTCGGCGGCTACCAGC 62.577 72.222 7.21 0.00 41.46 4.85
232 233 3.905678 CCTCTCGGCGGCTACCAG 61.906 72.222 7.21 0.00 0.00 4.00
254 255 2.567049 CGTCCAGTCGGTGTCTCC 59.433 66.667 0.00 0.00 0.00 3.71
255 256 2.567049 CCGTCCAGTCGGTGTCTC 59.433 66.667 0.00 0.00 44.77 3.36
262 263 2.024871 GCTCGATCCGTCCAGTCG 59.975 66.667 0.00 0.00 36.75 4.18
263 264 1.226717 GTGCTCGATCCGTCCAGTC 60.227 63.158 0.00 0.00 0.00 3.51
264 265 2.711922 GGTGCTCGATCCGTCCAGT 61.712 63.158 0.00 0.00 0.00 4.00
266 267 1.541310 AAAGGTGCTCGATCCGTCCA 61.541 55.000 0.00 0.00 0.00 4.02
267 268 1.084370 CAAAGGTGCTCGATCCGTCC 61.084 60.000 0.00 0.00 0.00 4.79
269 270 0.320374 TTCAAAGGTGCTCGATCCGT 59.680 50.000 0.00 0.00 0.00 4.69
274 275 0.321671 CCTCCTTCAAAGGTGCTCGA 59.678 55.000 8.60 0.00 46.54 4.04
275 276 0.674895 CCCTCCTTCAAAGGTGCTCG 60.675 60.000 8.60 0.00 46.54 5.03
277 278 0.695347 CTCCCTCCTTCAAAGGTGCT 59.305 55.000 8.60 0.00 46.54 4.40
278 279 0.962855 GCTCCCTCCTTCAAAGGTGC 60.963 60.000 8.60 3.97 46.54 5.01
279 280 0.401738 TGCTCCCTCCTTCAAAGGTG 59.598 55.000 8.60 6.31 46.54 4.00
280 281 0.695347 CTGCTCCCTCCTTCAAAGGT 59.305 55.000 8.60 0.00 46.54 3.50
282 283 0.679321 GCCTGCTCCCTCCTTCAAAG 60.679 60.000 0.00 0.00 0.00 2.77
285 286 3.011517 GGCCTGCTCCCTCCTTCA 61.012 66.667 0.00 0.00 0.00 3.02
286 287 3.011517 TGGCCTGCTCCCTCCTTC 61.012 66.667 3.32 0.00 0.00 3.46
287 288 3.013932 CTGGCCTGCTCCCTCCTT 61.014 66.667 3.32 0.00 0.00 3.36
294 295 2.850828 AATCAAGGGCTGGCCTGCTC 62.851 60.000 30.65 28.54 36.10 4.26
295 296 2.850828 GAATCAAGGGCTGGCCTGCT 62.851 60.000 30.65 12.35 36.10 4.24
300 301 2.054453 GGGTGAATCAAGGGCTGGC 61.054 63.158 0.00 0.00 0.00 4.85
301 302 1.750399 CGGGTGAATCAAGGGCTGG 60.750 63.158 0.00 0.00 0.00 4.85
302 303 0.745845 CTCGGGTGAATCAAGGGCTG 60.746 60.000 0.00 0.00 0.00 4.85
303 304 1.604378 CTCGGGTGAATCAAGGGCT 59.396 57.895 0.00 0.00 0.00 5.19
304 305 2.115291 GCTCGGGTGAATCAAGGGC 61.115 63.158 0.00 0.00 0.00 5.19
306 307 1.815421 CCGCTCGGGTGAATCAAGG 60.815 63.158 0.00 0.00 0.00 3.61
307 308 3.799753 CCGCTCGGGTGAATCAAG 58.200 61.111 0.00 0.00 0.00 3.02
319 320 4.496336 ATCCAGCCTTGCCCGCTC 62.496 66.667 0.00 0.00 33.17 5.03
320 321 4.496336 GATCCAGCCTTGCCCGCT 62.496 66.667 0.00 0.00 36.91 5.52
321 322 4.496336 AGATCCAGCCTTGCCCGC 62.496 66.667 0.00 0.00 0.00 6.13
322 323 2.515523 CAGATCCAGCCTTGCCCG 60.516 66.667 0.00 0.00 0.00 6.13
325 326 2.467826 GCGTCAGATCCAGCCTTGC 61.468 63.158 0.00 0.00 0.00 4.01
326 327 1.817099 GGCGTCAGATCCAGCCTTG 60.817 63.158 10.06 0.00 45.67 3.61
330 331 2.109126 GGTTGGCGTCAGATCCAGC 61.109 63.158 0.00 1.39 33.32 4.85
331 332 0.460987 GAGGTTGGCGTCAGATCCAG 60.461 60.000 9.82 0.00 33.32 3.86
353 354 3.171828 TAGGTGGTGGTGGTGTGCG 62.172 63.158 0.00 0.00 0.00 5.34
354 355 1.302511 CTAGGTGGTGGTGGTGTGC 60.303 63.158 0.00 0.00 0.00 4.57
355 356 1.302511 GCTAGGTGGTGGTGGTGTG 60.303 63.158 0.00 0.00 0.00 3.82
358 359 1.768482 TGTGCTAGGTGGTGGTGGT 60.768 57.895 0.00 0.00 0.00 4.16
359 360 1.302511 GTGTGCTAGGTGGTGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
360 361 1.302511 GGTGTGCTAGGTGGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
361 362 1.768482 TGGTGTGCTAGGTGGTGGT 60.768 57.895 0.00 0.00 0.00 4.16
388 389 0.450583 TTGTACTACTGCCGCTCGAG 59.549 55.000 8.45 8.45 0.00 4.04
392 393 0.388134 CGTGTTGTACTACTGCCGCT 60.388 55.000 8.88 0.00 0.00 5.52
394 395 0.665068 TGCGTGTTGTACTACTGCCG 60.665 55.000 17.21 13.21 0.00 5.69
395 396 1.068474 CTGCGTGTTGTACTACTGCC 58.932 55.000 17.21 4.63 0.00 4.85
396 397 1.719780 GTCTGCGTGTTGTACTACTGC 59.280 52.381 14.60 14.60 0.00 4.40
397 398 1.976728 CGTCTGCGTGTTGTACTACTG 59.023 52.381 8.88 3.01 0.00 2.74
398 399 1.875514 TCGTCTGCGTGTTGTACTACT 59.124 47.619 8.88 0.00 39.49 2.57
399 400 2.240040 CTCGTCTGCGTGTTGTACTAC 58.760 52.381 0.05 0.05 39.49 2.73
400 401 1.198408 CCTCGTCTGCGTGTTGTACTA 59.802 52.381 0.00 0.00 39.49 1.82
401 402 0.039437 CCTCGTCTGCGTGTTGTACT 60.039 55.000 0.00 0.00 39.49 2.73
403 404 0.240145 CTCCTCGTCTGCGTGTTGTA 59.760 55.000 0.00 0.00 39.49 2.41
404 405 1.007271 CTCCTCGTCTGCGTGTTGT 60.007 57.895 0.00 0.00 39.49 3.32
406 407 2.651361 CCTCCTCGTCTGCGTGTT 59.349 61.111 0.00 0.00 39.49 3.32
408 409 3.978723 CTGCCTCCTCGTCTGCGTG 62.979 68.421 0.00 0.00 39.49 5.34
410 411 4.504916 CCTGCCTCCTCGTCTGCG 62.505 72.222 0.00 0.00 39.92 5.18
411 412 3.363844 GACCTGCCTCCTCGTCTGC 62.364 68.421 0.00 0.00 0.00 4.26
412 413 1.979155 TGACCTGCCTCCTCGTCTG 60.979 63.158 0.00 0.00 0.00 3.51
413 414 1.979693 GTGACCTGCCTCCTCGTCT 60.980 63.158 0.00 0.00 0.00 4.18
414 415 2.574399 GTGACCTGCCTCCTCGTC 59.426 66.667 0.00 0.00 0.00 4.20
415 416 2.997897 GGTGACCTGCCTCCTCGT 60.998 66.667 0.00 0.00 0.00 4.18
416 417 2.303549 GATGGTGACCTGCCTCCTCG 62.304 65.000 2.11 0.00 0.00 4.63
417 418 1.524482 GATGGTGACCTGCCTCCTC 59.476 63.158 2.11 0.00 0.00 3.71
418 419 1.997874 GGATGGTGACCTGCCTCCT 60.998 63.158 2.11 0.00 0.00 3.69
419 420 1.997874 AGGATGGTGACCTGCCTCC 60.998 63.158 9.55 7.34 36.30 4.30
420 421 1.222936 CAGGATGGTGACCTGCCTC 59.777 63.158 11.96 0.20 46.30 4.70
427 428 0.108615 CGACAGGTCAGGATGGTGAC 60.109 60.000 0.00 0.00 45.30 3.67
428 429 1.257750 CCGACAGGTCAGGATGGTGA 61.258 60.000 0.00 0.00 36.16 4.02
431 432 0.108138 GTTCCGACAGGTCAGGATGG 60.108 60.000 11.74 0.37 39.05 3.51
432 433 0.108138 GGTTCCGACAGGTCAGGATG 60.108 60.000 11.74 0.00 39.05 3.51
433 434 1.605058 CGGTTCCGACAGGTCAGGAT 61.605 60.000 5.19 0.00 39.05 3.24
434 435 2.273179 CGGTTCCGACAGGTCAGGA 61.273 63.158 5.19 8.31 39.05 3.86
435 436 2.214181 CTCGGTTCCGACAGGTCAGG 62.214 65.000 10.00 2.61 39.05 3.86
436 437 1.213013 CTCGGTTCCGACAGGTCAG 59.787 63.158 10.00 0.00 39.05 3.51
437 438 2.927580 GCTCGGTTCCGACAGGTCA 61.928 63.158 10.00 0.00 39.05 4.02
438 439 2.126031 GCTCGGTTCCGACAGGTC 60.126 66.667 10.00 0.00 39.05 3.85
439 440 2.915659 TGCTCGGTTCCGACAGGT 60.916 61.111 10.00 0.00 39.05 4.00
440 441 2.125912 CTGCTCGGTTCCGACAGG 60.126 66.667 22.96 12.47 35.79 4.00
441 442 2.811317 GCTGCTCGGTTCCGACAG 60.811 66.667 24.69 24.69 38.86 3.51
444 445 4.373116 GTGGCTGCTCGGTTCCGA 62.373 66.667 13.34 13.34 36.95 4.55
447 448 3.842925 TTGGGTGGCTGCTCGGTTC 62.843 63.158 0.00 0.00 0.00 3.62
448 449 2.920076 TTTTGGGTGGCTGCTCGGTT 62.920 55.000 0.00 0.00 0.00 4.44
449 450 3.429372 TTTTGGGTGGCTGCTCGGT 62.429 57.895 0.00 0.00 0.00 4.69
450 451 2.597217 TTTTGGGTGGCTGCTCGG 60.597 61.111 0.00 0.00 0.00 4.63
452 453 0.244721 GATGTTTTGGGTGGCTGCTC 59.755 55.000 0.00 0.00 0.00 4.26
453 454 0.469705 TGATGTTTTGGGTGGCTGCT 60.470 50.000 0.00 0.00 0.00 4.24
455 456 0.318120 GGTGATGTTTTGGGTGGCTG 59.682 55.000 0.00 0.00 0.00 4.85
458 459 1.288752 GCGGTGATGTTTTGGGTGG 59.711 57.895 0.00 0.00 0.00 4.61
459 460 1.288752 GGCGGTGATGTTTTGGGTG 59.711 57.895 0.00 0.00 0.00 4.61
460 461 1.906333 GGGCGGTGATGTTTTGGGT 60.906 57.895 0.00 0.00 0.00 4.51
461 462 2.645192 GGGGCGGTGATGTTTTGGG 61.645 63.158 0.00 0.00 0.00 4.12
462 463 2.969827 GGGGCGGTGATGTTTTGG 59.030 61.111 0.00 0.00 0.00 3.28
465 466 4.344865 AGCGGGGCGGTGATGTTT 62.345 61.111 0.00 0.00 35.85 2.83
483 484 4.516195 GAAGTCTCCCTCGGCGCC 62.516 72.222 19.07 19.07 0.00 6.53
486 487 4.516195 GGCGAAGTCTCCCTCGGC 62.516 72.222 3.56 3.56 43.24 5.54
487 488 4.194720 CGGCGAAGTCTCCCTCGG 62.195 72.222 0.00 0.00 0.00 4.63
489 490 2.182030 CACGGCGAAGTCTCCCTC 59.818 66.667 16.62 0.00 0.00 4.30
490 491 4.070552 GCACGGCGAAGTCTCCCT 62.071 66.667 16.62 0.00 0.00 4.20
494 495 3.883744 CTTGGGCACGGCGAAGTCT 62.884 63.158 16.62 0.00 0.00 3.24
495 496 3.423154 CTTGGGCACGGCGAAGTC 61.423 66.667 16.62 7.08 0.00 3.01
497 498 4.697756 TCCTTGGGCACGGCGAAG 62.698 66.667 16.62 6.05 0.00 3.79
504 505 4.678743 GGGGGTGTCCTTGGGCAC 62.679 72.222 15.37 15.37 35.33 5.01
506 507 4.678743 GTGGGGGTGTCCTTGGGC 62.679 72.222 0.00 0.00 35.33 5.36
507 508 2.773527 TTGTGGGGGTGTCCTTGGG 61.774 63.158 0.00 0.00 35.33 4.12
508 509 1.530655 GTTGTGGGGGTGTCCTTGG 60.531 63.158 0.00 0.00 35.33 3.61
509 510 1.896660 CGTTGTGGGGGTGTCCTTG 60.897 63.158 0.00 0.00 35.33 3.61
510 511 2.513895 CGTTGTGGGGGTGTCCTT 59.486 61.111 0.00 0.00 35.33 3.36
513 514 4.612412 TCGCGTTGTGGGGGTGTC 62.612 66.667 5.77 0.00 0.00 3.67
514 515 4.619227 CTCGCGTTGTGGGGGTGT 62.619 66.667 5.77 0.00 0.00 4.16
518 519 3.726517 CTTGCTCGCGTTGTGGGG 61.727 66.667 5.77 0.00 0.00 4.96
520 521 2.954753 GACCTTGCTCGCGTTGTGG 61.955 63.158 5.77 6.19 0.00 4.17
521 522 2.551270 GACCTTGCTCGCGTTGTG 59.449 61.111 5.77 0.00 0.00 3.33
523 524 3.423154 GGGACCTTGCTCGCGTTG 61.423 66.667 5.77 1.17 0.00 4.10
525 526 4.379243 CAGGGACCTTGCTCGCGT 62.379 66.667 5.77 0.00 0.00 6.01
565 566 4.112341 GCAAGCTGCAGGGCGAAG 62.112 66.667 17.12 0.00 44.26 3.79
575 576 3.429141 CACCGCTGGAGCAAGCTG 61.429 66.667 0.00 1.16 41.24 4.24
576 577 4.711949 CCACCGCTGGAGCAAGCT 62.712 66.667 0.00 0.00 40.55 3.74
595 596 0.778083 AAAAACCACCCCTCCTCTCC 59.222 55.000 0.00 0.00 0.00 3.71
625 626 1.814169 GGAAGGAAACCTAGCGCCG 60.814 63.158 2.29 0.00 31.13 6.46
626 627 1.814169 CGGAAGGAAACCTAGCGCC 60.814 63.158 2.29 0.00 31.13 6.53
627 628 0.390735 TTCGGAAGGAAACCTAGCGC 60.391 55.000 0.00 0.00 31.13 5.92
628 629 1.933853 CATTCGGAAGGAAACCTAGCG 59.066 52.381 0.00 0.00 38.36 4.26
629 630 2.987232 ACATTCGGAAGGAAACCTAGC 58.013 47.619 9.64 0.00 38.36 3.42
632 633 9.117183 GTTATAATTACATTCGGAAGGAAACCT 57.883 33.333 9.64 0.00 38.36 3.50
635 636 7.496591 AGCGTTATAATTACATTCGGAAGGAAA 59.503 33.333 9.64 0.00 38.36 3.13
637 638 6.422701 CAGCGTTATAATTACATTCGGAAGGA 59.577 38.462 9.64 0.00 0.00 3.36
638 639 6.422701 TCAGCGTTATAATTACATTCGGAAGG 59.577 38.462 0.11 0.11 0.00 3.46
773 804 4.911390 AGAGCGGGGATTTGGATATTTAG 58.089 43.478 0.00 0.00 0.00 1.85
779 810 1.747206 CGAAAGAGCGGGGATTTGGAT 60.747 52.381 0.00 0.00 0.00 3.41
876 1829 0.244178 AGAAAGAAGAGACGCGGGAC 59.756 55.000 12.47 0.00 0.00 4.46
1232 2248 3.730061 CGGAAGCTTGATGTTCTTGATGC 60.730 47.826 2.10 0.00 0.00 3.91
1304 5752 0.613777 GACCTGGTTCTTGATCCCGT 59.386 55.000 0.00 0.00 0.00 5.28
1545 6101 0.245539 GGGACTTGATCACGTCGGAA 59.754 55.000 21.91 0.00 31.18 4.30
1685 6377 5.587844 GCTTATGATTTCTTCCTCTGCTTCA 59.412 40.000 0.00 0.00 0.00 3.02
1712 6411 1.577328 CTACCACCAACAAGGCTGCG 61.577 60.000 0.00 0.00 43.14 5.18
1767 10612 2.417719 CAACCAAGACTACCACTGAGC 58.582 52.381 0.00 0.00 0.00 4.26
1768 10613 2.224281 TGCAACCAAGACTACCACTGAG 60.224 50.000 0.00 0.00 0.00 3.35
1769 10614 1.765904 TGCAACCAAGACTACCACTGA 59.234 47.619 0.00 0.00 0.00 3.41
2087 12413 3.746045 ACTTTTCTAGACGGAGCACAA 57.254 42.857 0.00 0.00 0.00 3.33
2152 13262 8.584157 TGTACTGAATGAAATATGCTTTTTGGT 58.416 29.630 0.00 0.00 0.00 3.67
2346 15953 6.938507 ACTTGATGTTGCCAATGAATATGTT 58.061 32.000 0.00 0.00 0.00 2.71
2359 15966 7.307694 TCTCATTGTAATTGACTTGATGTTGC 58.692 34.615 0.00 0.00 0.00 4.17
2363 15970 9.512435 GGATTTCTCATTGTAATTGACTTGATG 57.488 33.333 0.00 0.00 0.00 3.07
2365 15972 8.514594 GTGGATTTCTCATTGTAATTGACTTGA 58.485 33.333 0.00 0.00 0.00 3.02
2367 15974 8.408043 TGTGGATTTCTCATTGTAATTGACTT 57.592 30.769 0.00 0.00 0.00 3.01
2368 15975 7.121759 CCTGTGGATTTCTCATTGTAATTGACT 59.878 37.037 0.00 0.00 0.00 3.41
2369 15976 7.094205 ACCTGTGGATTTCTCATTGTAATTGAC 60.094 37.037 0.00 0.00 0.00 3.18
2382 16079 7.259088 AGAACTACAATACCTGTGGATTTCT 57.741 36.000 0.00 0.00 38.78 2.52
2388 16085 5.875359 GGAAGAAGAACTACAATACCTGTGG 59.125 44.000 0.00 0.00 42.08 4.17
2390 16087 6.070710 GGAGGAAGAAGAACTACAATACCTGT 60.071 42.308 0.00 0.00 42.47 4.00
2391 16088 6.155393 AGGAGGAAGAAGAACTACAATACCTG 59.845 42.308 0.00 0.00 0.00 4.00
2392 16089 6.265304 AGGAGGAAGAAGAACTACAATACCT 58.735 40.000 0.00 0.00 0.00 3.08
2393 16090 6.407187 GGAGGAGGAAGAAGAACTACAATACC 60.407 46.154 0.00 0.00 0.00 2.73
2394 16091 6.381707 AGGAGGAGGAAGAAGAACTACAATAC 59.618 42.308 0.00 0.00 0.00 1.89
2395 16092 6.503944 AGGAGGAGGAAGAAGAACTACAATA 58.496 40.000 0.00 0.00 0.00 1.90
2396 16093 5.346270 AGGAGGAGGAAGAAGAACTACAAT 58.654 41.667 0.00 0.00 0.00 2.71
2397 16094 4.753186 AGGAGGAGGAAGAAGAACTACAA 58.247 43.478 0.00 0.00 0.00 2.41
2399 16096 3.702548 GGAGGAGGAGGAAGAAGAACTAC 59.297 52.174 0.00 0.00 0.00 2.73
2400 16097 3.598782 AGGAGGAGGAGGAAGAAGAACTA 59.401 47.826 0.00 0.00 0.00 2.24
2405 16107 2.292192 ACAGAGGAGGAGGAGGAAGAAG 60.292 54.545 0.00 0.00 0.00 2.85
2407 16109 1.388174 ACAGAGGAGGAGGAGGAAGA 58.612 55.000 0.00 0.00 0.00 2.87
2408 16110 2.661718 GTACAGAGGAGGAGGAGGAAG 58.338 57.143 0.00 0.00 0.00 3.46
2412 16114 0.930726 AGGGTACAGAGGAGGAGGAG 59.069 60.000 0.00 0.00 0.00 3.69
2418 16120 1.950909 GACGATGAGGGTACAGAGGAG 59.049 57.143 0.00 0.00 0.00 3.69
2452 16156 5.324832 AATTTCTCTTCAGGAGGAAACCA 57.675 39.130 0.00 0.00 42.29 3.67
2455 16159 6.951971 CTCCTAATTTCTCTTCAGGAGGAAA 58.048 40.000 9.49 0.00 45.77 3.13
2465 16173 9.793259 TCAAAATGTACACTCCTAATTTCTCTT 57.207 29.630 0.00 0.00 0.00 2.85
2474 16182 5.643348 CAGCATGTCAAAATGTACACTCCTA 59.357 40.000 0.00 0.00 0.00 2.94
2482 16190 5.479724 TCATTTCCCAGCATGTCAAAATGTA 59.520 36.000 14.72 5.79 37.96 2.29
2483 16191 4.283978 TCATTTCCCAGCATGTCAAAATGT 59.716 37.500 14.72 0.00 37.96 2.71
2565 16273 3.804325 GCCCTTTCTCTTTTGTTTCAAGC 59.196 43.478 0.00 0.00 0.00 4.01
2609 16317 7.696992 TGGAAGTTTTGAAGTACTTTGAAGT 57.303 32.000 10.02 5.49 42.91 3.01
2610 16318 8.980143 TTTGGAAGTTTTGAAGTACTTTGAAG 57.020 30.769 10.02 0.00 34.88 3.02
2611 16319 9.765795 TTTTTGGAAGTTTTGAAGTACTTTGAA 57.234 25.926 10.02 5.12 34.88 2.69
2612 16320 9.418045 CTTTTTGGAAGTTTTGAAGTACTTTGA 57.582 29.630 10.02 0.00 34.88 2.69
2613 16321 9.418045 TCTTTTTGGAAGTTTTGAAGTACTTTG 57.582 29.630 10.02 0.00 34.88 2.77
2614 16322 9.419297 GTCTTTTTGGAAGTTTTGAAGTACTTT 57.581 29.630 10.02 0.00 34.88 2.66
2615 16323 8.581578 TGTCTTTTTGGAAGTTTTGAAGTACTT 58.418 29.630 8.13 8.13 37.31 2.24
2634 16352 8.443953 GATGGCTAGTATTCTGAATGTCTTTT 57.556 34.615 13.01 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.