Multiple sequence alignment - TraesCS6B01G089200

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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 TraesCS6B01G089200 chr6B 100.000 3182 0 0 1 3182 64690674 64687493 0.000000e+00 5877.0
1 TraesCS6B01G089200 chr6B 81.848 2121 372 13 1069 3182 2716441 2718555 0.000000e+00 1772.0
2 TraesCS6B01G089200 chr6B 81.837 947 162 8 1069 2010 2694530 2695471 0.000000e+00 787.0
3 TraesCS6B01G089200 chrUn 96.483 2445 58 9 748 3182 101626923 101629349 0.000000e+00 4013.0
4 TraesCS6B01G089200 chrUn 91.838 1752 128 7 1445 3182 94836791 94838541 0.000000e+00 2429.0
5 TraesCS6B01G089200 chrUn 95.722 187 7 1 476 661 101626738 101626924 1.860000e-77 300.0
6 TraesCS6B01G089200 chrUn 98.246 57 1 0 407 463 101626698 101626754 2.020000e-17 100.0
7 TraesCS6B01G089200 chrUn 85.263 95 13 1 536 629 94835824 94835918 2.610000e-16 97.1
8 TraesCS6B01G089200 chr5B 83.506 2219 353 10 971 3182 35548992 35546780 0.000000e+00 2058.0
9 TraesCS6B01G089200 chr5A 83.078 2216 353 11 974 3182 29711523 29709323 0.000000e+00 1995.0
10 TraesCS6B01G089200 chr3D 83.052 2189 355 14 1001 3182 26587036 26584857 0.000000e+00 1973.0
11 TraesCS6B01G089200 chr3D 92.935 184 13 0 224 407 90830752 90830569 5.230000e-68 268.0
12 TraesCS6B01G089200 chr3D 91.935 62 5 0 663 724 103823822 103823883 1.570000e-13 87.9
13 TraesCS6B01G089200 chr3D 80.342 117 8 9 656 761 126384956 126384844 1.220000e-09 75.0
14 TraesCS6B01G089200 chr4A 82.789 2173 359 15 1015 3179 657201004 657203169 0.000000e+00 1927.0
15 TraesCS6B01G089200 chr4A 82.265 2199 362 25 997 3182 657097102 657099285 0.000000e+00 1875.0
16 TraesCS6B01G089200 chr3A 82.527 2192 361 19 1001 3182 36662565 36660386 0.000000e+00 1906.0
17 TraesCS6B01G089200 chr7D 82.334 2168 360 15 1015 3176 9182434 9184584 0.000000e+00 1860.0
18 TraesCS6B01G089200 chr7D 90.099 404 35 3 9 408 563051320 563051722 1.310000e-143 520.0
19 TraesCS6B01G089200 chr3B 81.963 2190 377 17 1001 3182 44787487 44785308 0.000000e+00 1840.0
20 TraesCS6B01G089200 chr3B 87.923 414 43 3 1 408 235971532 235971944 6.170000e-132 481.0
21 TraesCS6B01G089200 chr3B 97.143 35 0 1 660 694 42678175 42678208 1.230000e-04 58.4
22 TraesCS6B01G089200 chr2B 82.176 2132 354 24 1066 3182 734396058 734398178 0.000000e+00 1808.0
23 TraesCS6B01G089200 chr2B 90.732 410 34 2 1 407 487238743 487238335 7.760000e-151 544.0
24 TraesCS6B01G089200 chr2B 86.165 412 33 7 1 408 646418290 646417899 1.060000e-114 424.0
25 TraesCS6B01G089200 chr2B 86.076 395 41 9 1 391 788996807 788997191 2.280000e-111 412.0
26 TraesCS6B01G089200 chr7A 82.136 2116 363 15 1075 3182 625913060 625910952 0.000000e+00 1799.0
27 TraesCS6B01G089200 chr6D 81.669 2133 342 29 1061 3182 424601 422507 0.000000e+00 1727.0
28 TraesCS6B01G089200 chr6D 83.344 1579 246 13 1602 3176 24750802 24749237 0.000000e+00 1443.0
29 TraesCS6B01G089200 chr6D 89.037 301 30 1 111 408 292863389 292863689 1.390000e-98 370.0
30 TraesCS6B01G089200 chr6D 97.436 39 0 1 656 694 296346028 296346065 7.370000e-07 65.8
31 TraesCS6B01G089200 chr1B 82.698 1653 262 14 1538 3182 2917427 2919063 0.000000e+00 1447.0
32 TraesCS6B01G089200 chr6A 83.207 1578 251 8 1602 3176 9014937 9013371 0.000000e+00 1434.0
33 TraesCS6B01G089200 chr6A 87.136 412 48 3 1 408 73787596 73787186 2.240000e-126 462.0
34 TraesCS6B01G089200 chr6A 97.297 37 0 1 658 694 363523470 363523505 9.530000e-06 62.1
35 TraesCS6B01G089200 chr1A 86.618 411 46 5 1 408 578244871 578245275 2.250000e-121 446.0
36 TraesCS6B01G089200 chr1A 79.808 104 12 3 659 754 53511197 53511095 2.050000e-07 67.6
37 TraesCS6B01G089200 chr1A 92.500 40 3 0 658 697 121746614 121746653 1.230000e-04 58.4
38 TraesCS6B01G089200 chr5D 89.049 347 34 2 65 408 41611567 41611222 8.160000e-116 427.0
39 TraesCS6B01G089200 chr5D 92.424 66 5 0 659 724 256747569 256747504 9.400000e-16 95.3
40 TraesCS6B01G089200 chr5D 83.333 66 11 0 659 724 344825435 344825500 9.530000e-06 62.1
41 TraesCS6B01G089200 chr2A 85.539 408 42 4 1 408 30237254 30237644 8.210000e-111 411.0
42 TraesCS6B01G089200 chr2A 100.000 29 0 0 724 752 535152475 535152447 2.000000e-03 54.7
43 TraesCS6B01G089200 chr4B 80.952 105 9 8 660 755 276714246 276714348 4.400000e-09 73.1


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 TraesCS6B01G089200 chr6B 64687493 64690674 3181 True 5877.00 5877 100.0000 1 3182 1 chr6B.!!$R1 3181
1 TraesCS6B01G089200 chr6B 2716441 2718555 2114 False 1772.00 1772 81.8480 1069 3182 1 chr6B.!!$F2 2113
2 TraesCS6B01G089200 chr6B 2694530 2695471 941 False 787.00 787 81.8370 1069 2010 1 chr6B.!!$F1 941
3 TraesCS6B01G089200 chrUn 101626698 101629349 2651 False 1471.00 4013 96.8170 407 3182 3 chrUn.!!$F2 2775
4 TraesCS6B01G089200 chrUn 94835824 94838541 2717 False 1263.05 2429 88.5505 536 3182 2 chrUn.!!$F1 2646
5 TraesCS6B01G089200 chr5B 35546780 35548992 2212 True 2058.00 2058 83.5060 971 3182 1 chr5B.!!$R1 2211
6 TraesCS6B01G089200 chr5A 29709323 29711523 2200 True 1995.00 1995 83.0780 974 3182 1 chr5A.!!$R1 2208
7 TraesCS6B01G089200 chr3D 26584857 26587036 2179 True 1973.00 1973 83.0520 1001 3182 1 chr3D.!!$R1 2181
8 TraesCS6B01G089200 chr4A 657201004 657203169 2165 False 1927.00 1927 82.7890 1015 3179 1 chr4A.!!$F2 2164
9 TraesCS6B01G089200 chr4A 657097102 657099285 2183 False 1875.00 1875 82.2650 997 3182 1 chr4A.!!$F1 2185
10 TraesCS6B01G089200 chr3A 36660386 36662565 2179 True 1906.00 1906 82.5270 1001 3182 1 chr3A.!!$R1 2181
11 TraesCS6B01G089200 chr7D 9182434 9184584 2150 False 1860.00 1860 82.3340 1015 3176 1 chr7D.!!$F1 2161
12 TraesCS6B01G089200 chr3B 44785308 44787487 2179 True 1840.00 1840 81.9630 1001 3182 1 chr3B.!!$R1 2181
13 TraesCS6B01G089200 chr2B 734396058 734398178 2120 False 1808.00 1808 82.1760 1066 3182 1 chr2B.!!$F1 2116
14 TraesCS6B01G089200 chr7A 625910952 625913060 2108 True 1799.00 1799 82.1360 1075 3182 1 chr7A.!!$R1 2107
15 TraesCS6B01G089200 chr6D 422507 424601 2094 True 1727.00 1727 81.6690 1061 3182 1 chr6D.!!$R1 2121
16 TraesCS6B01G089200 chr6D 24749237 24750802 1565 True 1443.00 1443 83.3440 1602 3176 1 chr6D.!!$R2 1574
17 TraesCS6B01G089200 chr1B 2917427 2919063 1636 False 1447.00 1447 82.6980 1538 3182 1 chr1B.!!$F1 1644
18 TraesCS6B01G089200 chr6A 9013371 9014937 1566 True 1434.00 1434 83.2070 1602 3176 1 chr6A.!!$R1 1574

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
73 74 0.033306 GAGGAACCCTAGGACCGTCT 60.033 60.0 11.48 0.64 31.76 4.18 F
74 75 0.033306 AGGAACCCTAGGACCGTCTC 60.033 60.0 11.48 1.07 28.47 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1773 2.336809 CGAGATCGCTACCAGGGC 59.663 66.667 0.00 0.0 0.00 5.19 R
2184 2476 6.591834 GGAATCACTCCGGATATCAAAGTATG 59.408 42.308 3.57 0.0 33.37 2.39 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
20 21 3.601443 ACTCCGACCAGATCAAGAAAG 57.399 47.619 0.00 0.00 0.00 2.62
21 22 3.165875 ACTCCGACCAGATCAAGAAAGA 58.834 45.455 0.00 0.00 0.00 2.52
22 23 3.056465 ACTCCGACCAGATCAAGAAAGAC 60.056 47.826 0.00 0.00 0.00 3.01
23 24 2.897326 TCCGACCAGATCAAGAAAGACA 59.103 45.455 0.00 0.00 0.00 3.41
24 25 3.056536 TCCGACCAGATCAAGAAAGACAG 60.057 47.826 0.00 0.00 0.00 3.51
25 26 3.257393 CGACCAGATCAAGAAAGACAGG 58.743 50.000 0.00 0.00 0.00 4.00
26 27 3.006247 GACCAGATCAAGAAAGACAGGC 58.994 50.000 0.00 0.00 0.00 4.85
27 28 2.005451 CCAGATCAAGAAAGACAGGCG 58.995 52.381 0.00 0.00 0.00 5.52
28 29 2.613977 CCAGATCAAGAAAGACAGGCGT 60.614 50.000 0.00 0.00 0.00 5.68
29 30 2.670414 CAGATCAAGAAAGACAGGCGTC 59.330 50.000 0.00 1.99 42.95 5.19
30 31 2.300152 AGATCAAGAAAGACAGGCGTCA 59.700 45.455 11.04 0.00 45.23 4.35
31 32 2.154854 TCAAGAAAGACAGGCGTCAG 57.845 50.000 11.04 0.00 45.23 3.51
32 33 1.151668 CAAGAAAGACAGGCGTCAGG 58.848 55.000 11.04 0.00 45.23 3.86
33 34 0.603975 AAGAAAGACAGGCGTCAGGC 60.604 55.000 11.04 0.00 45.23 4.85
34 35 1.301716 GAAAGACAGGCGTCAGGCA 60.302 57.895 11.04 0.00 45.23 4.75
35 36 1.294659 GAAAGACAGGCGTCAGGCAG 61.295 60.000 11.04 0.00 45.23 4.85
36 37 1.758440 AAAGACAGGCGTCAGGCAGA 61.758 55.000 11.04 0.00 45.23 4.26
37 38 1.548357 AAGACAGGCGTCAGGCAGAT 61.548 55.000 11.04 0.00 45.23 2.90
38 39 1.520342 GACAGGCGTCAGGCAGATC 60.520 63.158 0.00 0.00 46.16 2.75
39 40 1.954362 GACAGGCGTCAGGCAGATCT 61.954 60.000 0.00 0.00 46.16 2.75
40 41 1.220206 CAGGCGTCAGGCAGATCTT 59.780 57.895 0.00 0.00 46.16 2.40
41 42 0.809241 CAGGCGTCAGGCAGATCTTC 60.809 60.000 0.00 0.00 46.16 2.87
42 43 1.219124 GGCGTCAGGCAGATCTTCA 59.781 57.895 0.00 0.00 46.16 3.02
43 44 0.179062 GGCGTCAGGCAGATCTTCAT 60.179 55.000 0.00 0.00 46.16 2.57
44 45 1.216122 GCGTCAGGCAGATCTTCATC 58.784 55.000 0.00 0.00 42.87 2.92
45 46 1.202510 GCGTCAGGCAGATCTTCATCT 60.203 52.381 0.00 0.00 40.32 2.90
46 47 2.741228 GCGTCAGGCAGATCTTCATCTT 60.741 50.000 0.00 0.00 37.25 2.40
47 48 2.864946 CGTCAGGCAGATCTTCATCTTG 59.135 50.000 0.00 0.00 37.25 3.02
48 49 3.678252 CGTCAGGCAGATCTTCATCTTGT 60.678 47.826 0.00 0.00 37.25 3.16
49 50 3.870419 GTCAGGCAGATCTTCATCTTGTC 59.130 47.826 0.00 0.00 37.25 3.18
50 51 3.516700 TCAGGCAGATCTTCATCTTGTCA 59.483 43.478 0.00 0.00 37.25 3.58
51 52 3.622163 CAGGCAGATCTTCATCTTGTCAC 59.378 47.826 0.00 0.00 37.25 3.67
52 53 3.518705 AGGCAGATCTTCATCTTGTCACT 59.481 43.478 0.00 0.00 37.25 3.41
53 54 4.019501 AGGCAGATCTTCATCTTGTCACTT 60.020 41.667 0.00 0.00 37.25 3.16
54 55 4.094590 GGCAGATCTTCATCTTGTCACTTG 59.905 45.833 0.00 0.00 37.25 3.16
55 56 4.934001 GCAGATCTTCATCTTGTCACTTGA 59.066 41.667 0.00 0.00 37.25 3.02
56 57 5.063691 GCAGATCTTCATCTTGTCACTTGAG 59.936 44.000 0.00 0.00 37.25 3.02
57 58 5.581479 CAGATCTTCATCTTGTCACTTGAGG 59.419 44.000 0.00 0.00 37.25 3.86
58 59 5.483231 AGATCTTCATCTTGTCACTTGAGGA 59.517 40.000 0.00 0.00 35.67 3.71
59 60 5.551305 TCTTCATCTTGTCACTTGAGGAA 57.449 39.130 0.00 0.00 0.00 3.36
60 61 5.300752 TCTTCATCTTGTCACTTGAGGAAC 58.699 41.667 0.00 0.00 0.00 3.62
61 62 4.008074 TCATCTTGTCACTTGAGGAACC 57.992 45.455 0.00 0.00 0.00 3.62
62 63 2.930826 TCTTGTCACTTGAGGAACCC 57.069 50.000 0.00 0.00 0.00 4.11
63 64 2.408565 TCTTGTCACTTGAGGAACCCT 58.591 47.619 0.00 0.00 36.03 4.34
64 65 3.583228 TCTTGTCACTTGAGGAACCCTA 58.417 45.455 0.00 0.00 31.76 3.53
65 66 3.578716 TCTTGTCACTTGAGGAACCCTAG 59.421 47.826 0.00 0.00 31.76 3.02
66 67 2.257207 TGTCACTTGAGGAACCCTAGG 58.743 52.381 0.06 0.06 31.76 3.02
67 68 2.158219 TGTCACTTGAGGAACCCTAGGA 60.158 50.000 11.48 0.00 31.76 2.94
68 69 2.234168 GTCACTTGAGGAACCCTAGGAC 59.766 54.545 11.48 0.96 31.76 3.85
69 70 1.555533 CACTTGAGGAACCCTAGGACC 59.444 57.143 11.48 10.76 31.76 4.46
70 71 0.824759 CTTGAGGAACCCTAGGACCG 59.175 60.000 11.48 0.00 31.76 4.79
71 72 0.115745 TTGAGGAACCCTAGGACCGT 59.884 55.000 11.48 0.00 31.76 4.83
72 73 0.324091 TGAGGAACCCTAGGACCGTC 60.324 60.000 11.48 10.07 31.76 4.79
73 74 0.033306 GAGGAACCCTAGGACCGTCT 60.033 60.000 11.48 0.64 31.76 4.18
74 75 0.033306 AGGAACCCTAGGACCGTCTC 60.033 60.000 11.48 1.07 28.47 3.36
75 76 1.042003 GGAACCCTAGGACCGTCTCC 61.042 65.000 11.48 6.29 39.81 3.71
85 86 3.180891 GGACCGTCTCCTTAAATCAGG 57.819 52.381 0.00 0.00 35.89 3.86
86 87 2.552031 GACCGTCTCCTTAAATCAGGC 58.448 52.381 0.00 0.00 33.35 4.85
87 88 1.209747 ACCGTCTCCTTAAATCAGGCC 59.790 52.381 0.00 0.00 33.35 5.19
88 89 1.571919 CGTCTCCTTAAATCAGGCCG 58.428 55.000 0.00 0.00 33.35 6.13
89 90 1.136305 CGTCTCCTTAAATCAGGCCGA 59.864 52.381 0.00 0.00 33.35 5.54
90 91 2.799917 CGTCTCCTTAAATCAGGCCGAG 60.800 54.545 0.00 0.00 33.35 4.63
91 92 1.139058 TCTCCTTAAATCAGGCCGAGC 59.861 52.381 0.00 0.00 33.35 5.03
129 130 4.592192 CGGCACCGCGGATCAGAT 62.592 66.667 35.90 4.54 0.00 2.90
130 131 2.663188 GGCACCGCGGATCAGATC 60.663 66.667 35.90 11.45 0.00 2.75
131 132 3.032609 GCACCGCGGATCAGATCG 61.033 66.667 35.90 9.98 0.00 3.69
132 133 2.355126 CACCGCGGATCAGATCGG 60.355 66.667 35.90 12.61 46.61 4.18
133 134 3.606662 ACCGCGGATCAGATCGGG 61.607 66.667 35.90 13.84 45.58 5.14
137 138 4.363990 CGGATCAGATCGGGGCGG 62.364 72.222 9.65 0.00 0.00 6.13
138 139 3.234730 GGATCAGATCGGGGCGGT 61.235 66.667 4.23 0.00 0.00 5.68
139 140 2.029666 GATCAGATCGGGGCGGTG 59.970 66.667 0.00 0.00 0.00 4.94
140 141 4.241555 ATCAGATCGGGGCGGTGC 62.242 66.667 0.00 0.00 0.00 5.01
160 161 3.957535 GGATCTGGCGCCGCATTG 61.958 66.667 23.90 9.35 0.00 2.82
161 162 3.957535 GATCTGGCGCCGCATTGG 61.958 66.667 23.90 7.45 42.50 3.16
170 171 3.063704 CCGCATTGGGAGCAGCAA 61.064 61.111 1.69 0.00 0.00 3.91
171 172 2.488355 CGCATTGGGAGCAGCAAG 59.512 61.111 0.00 0.00 0.00 4.01
172 173 2.890371 GCATTGGGAGCAGCAAGG 59.110 61.111 0.00 0.00 0.00 3.61
173 174 2.718073 GCATTGGGAGCAGCAAGGG 61.718 63.158 0.00 0.00 0.00 3.95
174 175 1.304713 CATTGGGAGCAGCAAGGGT 60.305 57.895 0.00 0.00 0.00 4.34
175 176 1.304713 ATTGGGAGCAGCAAGGGTG 60.305 57.895 0.00 0.00 0.00 4.61
184 185 3.373565 GCAAGGGTGCCGGGAAAG 61.374 66.667 2.18 0.00 45.68 2.62
185 186 2.676471 CAAGGGTGCCGGGAAAGG 60.676 66.667 2.18 0.00 0.00 3.11
186 187 3.979497 AAGGGTGCCGGGAAAGGG 61.979 66.667 2.18 0.00 0.00 3.95
205 206 4.547367 GCCTCGCGGGTAGCCAAT 62.547 66.667 12.31 0.00 44.76 3.16
206 207 3.134879 CCTCGCGGGTAGCCAATA 58.865 61.111 12.31 0.00 44.76 1.90
207 208 1.006102 CCTCGCGGGTAGCCAATAG 60.006 63.158 12.31 4.22 44.76 1.73
208 209 1.664965 CTCGCGGGTAGCCAATAGC 60.665 63.158 12.31 5.11 44.76 2.97
238 239 4.349503 ATGGAGCAGGCCACGCAA 62.350 61.111 18.34 0.00 41.56 4.85
239 240 3.866379 ATGGAGCAGGCCACGCAAA 62.866 57.895 18.34 4.73 41.56 3.68
240 241 4.043200 GGAGCAGGCCACGCAAAC 62.043 66.667 18.34 9.44 0.00 2.93
271 272 2.439156 GCTGCCTCGGCCTTGAAT 60.439 61.111 0.00 0.00 41.09 2.57
272 273 2.476320 GCTGCCTCGGCCTTGAATC 61.476 63.158 0.00 0.00 41.09 2.52
273 274 1.222936 CTGCCTCGGCCTTGAATCT 59.777 57.895 0.00 0.00 41.09 2.40
274 275 1.078214 TGCCTCGGCCTTGAATCTG 60.078 57.895 0.00 0.00 41.09 2.90
275 276 1.221840 GCCTCGGCCTTGAATCTGA 59.778 57.895 0.00 0.00 34.56 3.27
276 277 0.813210 GCCTCGGCCTTGAATCTGAG 60.813 60.000 0.00 0.00 35.90 3.35
277 278 0.179062 CCTCGGCCTTGAATCTGAGG 60.179 60.000 0.00 2.53 46.05 3.86
278 279 0.539051 CTCGGCCTTGAATCTGAGGT 59.461 55.000 0.00 0.00 35.42 3.85
279 280 0.250234 TCGGCCTTGAATCTGAGGTG 59.750 55.000 0.00 0.44 35.42 4.00
280 281 0.250234 CGGCCTTGAATCTGAGGTGA 59.750 55.000 0.00 0.00 35.42 4.02
281 282 1.339055 CGGCCTTGAATCTGAGGTGAA 60.339 52.381 0.00 0.00 35.42 3.18
282 283 2.795329 GGCCTTGAATCTGAGGTGAAA 58.205 47.619 0.00 0.00 35.42 2.69
283 284 3.157087 GGCCTTGAATCTGAGGTGAAAA 58.843 45.455 0.00 0.00 35.42 2.29
284 285 3.057245 GGCCTTGAATCTGAGGTGAAAAC 60.057 47.826 0.00 0.00 35.42 2.43
285 286 3.365364 GCCTTGAATCTGAGGTGAAAACG 60.365 47.826 5.43 0.00 35.42 3.60
286 287 3.365364 CCTTGAATCTGAGGTGAAAACGC 60.365 47.826 0.00 0.00 0.00 4.84
287 288 2.151202 TGAATCTGAGGTGAAAACGCC 58.849 47.619 0.00 0.00 0.00 5.68
288 289 1.128692 GAATCTGAGGTGAAAACGCCG 59.871 52.381 0.00 0.00 0.00 6.46
289 290 1.298859 ATCTGAGGTGAAAACGCCGC 61.299 55.000 0.00 0.00 0.00 6.53
290 291 3.295228 CTGAGGTGAAAACGCCGCG 62.295 63.158 12.14 12.14 0.00 6.46
291 292 4.736631 GAGGTGAAAACGCCGCGC 62.737 66.667 13.88 0.00 0.00 6.86
306 307 4.605967 CGCCGCGAGAGAGAGCTC 62.606 72.222 8.23 5.27 41.62 4.09
312 313 3.591835 GAGAGAGAGCTCGCCCCG 61.592 72.222 14.35 0.00 45.98 5.73
361 362 4.176851 GTCGCCTCCTCCGACGAC 62.177 72.222 0.00 0.00 46.64 4.34
375 376 4.129737 CGACGGCGTGTGGAGGAT 62.130 66.667 21.19 0.00 0.00 3.24
376 377 2.509336 GACGGCGTGTGGAGGATG 60.509 66.667 21.19 0.00 0.00 3.51
377 378 4.082523 ACGGCGTGTGGAGGATGG 62.083 66.667 13.76 0.00 0.00 3.51
378 379 3.770040 CGGCGTGTGGAGGATGGA 61.770 66.667 0.00 0.00 0.00 3.41
379 380 2.187946 GGCGTGTGGAGGATGGAG 59.812 66.667 0.00 0.00 0.00 3.86
380 381 2.187946 GCGTGTGGAGGATGGAGG 59.812 66.667 0.00 0.00 0.00 4.30
381 382 2.903357 CGTGTGGAGGATGGAGGG 59.097 66.667 0.00 0.00 0.00 4.30
382 383 2.735772 CGTGTGGAGGATGGAGGGG 61.736 68.421 0.00 0.00 0.00 4.79
383 384 1.306997 GTGTGGAGGATGGAGGGGA 60.307 63.158 0.00 0.00 0.00 4.81
384 385 1.003442 TGTGGAGGATGGAGGGGAG 59.997 63.158 0.00 0.00 0.00 4.30
385 386 1.768077 GTGGAGGATGGAGGGGAGG 60.768 68.421 0.00 0.00 0.00 4.30
386 387 2.122189 GGAGGATGGAGGGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
387 388 2.122189 GAGGATGGAGGGGAGGGG 60.122 72.222 0.00 0.00 0.00 4.79
388 389 4.523282 AGGATGGAGGGGAGGGGC 62.523 72.222 0.00 0.00 0.00 5.80
389 390 4.523282 GGATGGAGGGGAGGGGCT 62.523 72.222 0.00 0.00 0.00 5.19
390 391 2.368878 GATGGAGGGGAGGGGCTT 60.369 66.667 0.00 0.00 0.00 4.35
391 392 2.697644 ATGGAGGGGAGGGGCTTG 60.698 66.667 0.00 0.00 0.00 4.01
392 393 3.287954 ATGGAGGGGAGGGGCTTGA 62.288 63.158 0.00 0.00 0.00 3.02
393 394 3.093172 GGAGGGGAGGGGCTTGAG 61.093 72.222 0.00 0.00 0.00 3.02
394 395 3.093172 GAGGGGAGGGGCTTGAGG 61.093 72.222 0.00 0.00 0.00 3.86
395 396 3.952799 GAGGGGAGGGGCTTGAGGT 62.953 68.421 0.00 0.00 0.00 3.85
396 397 3.732849 GGGGAGGGGCTTGAGGTG 61.733 72.222 0.00 0.00 0.00 4.00
397 398 3.732849 GGGAGGGGCTTGAGGTGG 61.733 72.222 0.00 0.00 0.00 4.61
398 399 4.432741 GGAGGGGCTTGAGGTGGC 62.433 72.222 0.00 0.00 0.00 5.01
446 447 5.674525 TGCAAATCCCTCTACTCATTACTG 58.325 41.667 0.00 0.00 0.00 2.74
447 448 5.425217 TGCAAATCCCTCTACTCATTACTGA 59.575 40.000 0.00 0.00 0.00 3.41
448 449 6.070251 TGCAAATCCCTCTACTCATTACTGAA 60.070 38.462 0.00 0.00 0.00 3.02
449 450 6.995091 GCAAATCCCTCTACTCATTACTGAAT 59.005 38.462 0.00 0.00 0.00 2.57
450 451 7.041508 GCAAATCCCTCTACTCATTACTGAATG 60.042 40.741 0.00 0.00 43.39 2.67
451 452 7.682787 AATCCCTCTACTCATTACTGAATGT 57.317 36.000 0.00 0.00 42.71 2.71
452 453 8.783660 AATCCCTCTACTCATTACTGAATGTA 57.216 34.615 0.00 0.00 42.71 2.29
453 454 8.783660 ATCCCTCTACTCATTACTGAATGTAA 57.216 34.615 0.00 0.00 42.71 2.41
454 455 8.008513 TCCCTCTACTCATTACTGAATGTAAC 57.991 38.462 0.00 0.00 43.08 2.50
455 456 7.839705 TCCCTCTACTCATTACTGAATGTAACT 59.160 37.037 0.00 0.00 43.08 2.24
456 457 9.132923 CCCTCTACTCATTACTGAATGTAACTA 57.867 37.037 0.00 0.00 43.08 2.24
462 463 9.448438 ACTCATTACTGAATGTAACTATTGCAA 57.552 29.630 0.00 0.00 43.08 4.08
463 464 9.926751 CTCATTACTGAATGTAACTATTGCAAG 57.073 33.333 4.94 0.00 43.08 4.01
464 465 9.448438 TCATTACTGAATGTAACTATTGCAAGT 57.552 29.630 4.94 0.00 43.08 3.16
465 466 9.708222 CATTACTGAATGTAACTATTGCAAGTC 57.292 33.333 4.94 0.00 43.08 3.01
466 467 9.672673 ATTACTGAATGTAACTATTGCAAGTCT 57.327 29.630 4.94 0.00 43.08 3.24
467 468 7.602517 ACTGAATGTAACTATTGCAAGTCTC 57.397 36.000 4.94 0.00 0.00 3.36
468 469 7.161404 ACTGAATGTAACTATTGCAAGTCTCA 58.839 34.615 4.94 2.06 0.00 3.27
469 470 7.661437 ACTGAATGTAACTATTGCAAGTCTCAA 59.339 33.333 4.94 0.00 0.00 3.02
470 471 8.389779 TGAATGTAACTATTGCAAGTCTCAAA 57.610 30.769 4.94 0.00 0.00 2.69
471 472 8.845227 TGAATGTAACTATTGCAAGTCTCAAAA 58.155 29.630 4.94 0.00 0.00 2.44
472 473 9.677567 GAATGTAACTATTGCAAGTCTCAAAAA 57.322 29.630 4.94 0.00 0.00 1.94
539 540 7.121315 ACCGATCGATATACATTCAGAGATTCA 59.879 37.037 18.66 0.00 0.00 2.57
593 595 5.722021 GAGATCCCTCTTCTGATTACTCC 57.278 47.826 0.00 0.00 36.50 3.85
668 837 9.930693 CTTGATTACTAACATAATACTCCCTCC 57.069 37.037 0.00 0.00 0.00 4.30
669 838 9.442062 TTGATTACTAACATAATACTCCCTCCA 57.558 33.333 0.00 0.00 0.00 3.86
670 839 9.615660 TGATTACTAACATAATACTCCCTCCAT 57.384 33.333 0.00 0.00 0.00 3.41
672 841 9.615660 ATTACTAACATAATACTCCCTCCATCA 57.384 33.333 0.00 0.00 0.00 3.07
673 842 7.304497 ACTAACATAATACTCCCTCCATCAC 57.696 40.000 0.00 0.00 0.00 3.06
674 843 6.844388 ACTAACATAATACTCCCTCCATCACA 59.156 38.462 0.00 0.00 0.00 3.58
675 844 6.575244 AACATAATACTCCCTCCATCACAA 57.425 37.500 0.00 0.00 0.00 3.33
676 845 6.575244 ACATAATACTCCCTCCATCACAAA 57.425 37.500 0.00 0.00 0.00 2.83
677 846 6.969043 ACATAATACTCCCTCCATCACAAAA 58.031 36.000 0.00 0.00 0.00 2.44
678 847 7.586349 ACATAATACTCCCTCCATCACAAAAT 58.414 34.615 0.00 0.00 0.00 1.82
679 848 8.723365 ACATAATACTCCCTCCATCACAAAATA 58.277 33.333 0.00 0.00 0.00 1.40
680 849 9.573166 CATAATACTCCCTCCATCACAAAATAA 57.427 33.333 0.00 0.00 0.00 1.40
681 850 9.799106 ATAATACTCCCTCCATCACAAAATAAG 57.201 33.333 0.00 0.00 0.00 1.73
682 851 5.520748 ACTCCCTCCATCACAAAATAAGT 57.479 39.130 0.00 0.00 0.00 2.24
683 852 5.256474 ACTCCCTCCATCACAAAATAAGTG 58.744 41.667 0.00 0.00 38.32 3.16
684 853 5.222130 ACTCCCTCCATCACAAAATAAGTGT 60.222 40.000 0.00 0.00 38.16 3.55
685 854 5.253330 TCCCTCCATCACAAAATAAGTGTC 58.747 41.667 0.00 0.00 38.16 3.67
686 855 5.014123 TCCCTCCATCACAAAATAAGTGTCT 59.986 40.000 0.00 0.00 38.16 3.41
687 856 5.355350 CCCTCCATCACAAAATAAGTGTCTC 59.645 44.000 0.00 0.00 38.16 3.36
688 857 5.939883 CCTCCATCACAAAATAAGTGTCTCA 59.060 40.000 0.00 0.00 38.16 3.27
689 858 6.430925 CCTCCATCACAAAATAAGTGTCTCAA 59.569 38.462 0.00 0.00 38.16 3.02
690 859 7.121759 CCTCCATCACAAAATAAGTGTCTCAAT 59.878 37.037 0.00 0.00 38.16 2.57
691 860 8.044060 TCCATCACAAAATAAGTGTCTCAATC 57.956 34.615 0.00 0.00 38.16 2.67
692 861 7.884877 TCCATCACAAAATAAGTGTCTCAATCT 59.115 33.333 0.00 0.00 38.16 2.40
693 862 8.517878 CCATCACAAAATAAGTGTCTCAATCTT 58.482 33.333 0.00 0.00 38.16 2.40
698 867 9.846248 ACAAAATAAGTGTCTCAATCTTAATGC 57.154 29.630 0.00 0.00 0.00 3.56
699 868 9.844790 CAAAATAAGTGTCTCAATCTTAATGCA 57.155 29.630 0.00 0.00 0.00 3.96
701 870 9.846248 AAATAAGTGTCTCAATCTTAATGCAAC 57.154 29.630 0.00 0.00 0.00 4.17
702 871 8.798859 ATAAGTGTCTCAATCTTAATGCAACT 57.201 30.769 0.00 0.00 0.00 3.16
703 872 7.516198 AAGTGTCTCAATCTTAATGCAACTT 57.484 32.000 0.00 0.00 0.00 2.66
704 873 7.516198 AGTGTCTCAATCTTAATGCAACTTT 57.484 32.000 0.00 0.00 0.00 2.66
705 874 7.365741 AGTGTCTCAATCTTAATGCAACTTTG 58.634 34.615 0.00 0.00 0.00 2.77
706 875 7.013655 AGTGTCTCAATCTTAATGCAACTTTGT 59.986 33.333 0.00 0.00 0.00 2.83
707 876 8.289618 GTGTCTCAATCTTAATGCAACTTTGTA 58.710 33.333 0.00 0.00 0.00 2.41
708 877 8.289618 TGTCTCAATCTTAATGCAACTTTGTAC 58.710 33.333 0.00 0.00 0.00 2.90
709 878 8.507249 GTCTCAATCTTAATGCAACTTTGTACT 58.493 33.333 0.00 0.00 0.00 2.73
710 879 9.719355 TCTCAATCTTAATGCAACTTTGTACTA 57.281 29.630 0.00 0.00 0.00 1.82
739 908 9.849166 ATTAGTACAAACATTTATTTTGGGACG 57.151 29.630 0.00 0.00 38.12 4.79
740 909 7.513371 AGTACAAACATTTATTTTGGGACGA 57.487 32.000 0.00 0.00 38.12 4.20
741 910 7.942990 AGTACAAACATTTATTTTGGGACGAA 58.057 30.769 0.00 0.00 38.12 3.85
742 911 8.079809 AGTACAAACATTTATTTTGGGACGAAG 58.920 33.333 0.00 0.00 38.12 3.79
743 912 6.220201 ACAAACATTTATTTTGGGACGAAGG 58.780 36.000 0.00 0.00 38.12 3.46
744 913 5.400066 AACATTTATTTTGGGACGAAGGG 57.600 39.130 0.00 0.00 0.00 3.95
745 914 4.668636 ACATTTATTTTGGGACGAAGGGA 58.331 39.130 0.00 0.00 0.00 4.20
746 915 4.705023 ACATTTATTTTGGGACGAAGGGAG 59.295 41.667 0.00 0.00 0.00 4.30
857 1125 2.036387 TGAGGTCTCCAAGTCGTCAAA 58.964 47.619 0.00 0.00 28.47 2.69
946 1214 0.035534 TTAGCAATCAAGCGAGCCCA 60.036 50.000 0.00 0.00 40.15 5.36
966 1234 4.558178 CCAGAAGCATATACAGAGCAGAG 58.442 47.826 0.00 0.00 0.00 3.35
967 1235 3.989167 CAGAAGCATATACAGAGCAGAGC 59.011 47.826 0.00 0.00 0.00 4.09
968 1236 3.640498 AGAAGCATATACAGAGCAGAGCA 59.360 43.478 0.00 0.00 0.00 4.26
969 1237 3.663995 AGCATATACAGAGCAGAGCAG 57.336 47.619 0.00 0.00 0.00 4.24
1281 1565 2.651361 CTCACGTTCCTGCGGACT 59.349 61.111 0.00 0.00 35.98 3.85
1449 1733 2.038033 GGGACTGTACAACACCAAGCTA 59.962 50.000 12.51 0.00 0.00 3.32
2184 2476 4.434520 GTCTGGAAGTACTTGGATAGCAC 58.565 47.826 14.14 0.00 33.76 4.40
2242 2536 2.371910 AAGCTAGAGAACTTGGTCGC 57.628 50.000 0.00 0.00 0.00 5.19
2346 2640 1.080638 TTATGGCAACTTGGAGGGGT 58.919 50.000 0.00 0.00 37.61 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.257393 CCTGTCTTTCTTGATCTGGTCG 58.743 50.000 0.00 0.00 0.00 4.79
5 6 3.006247 GCCTGTCTTTCTTGATCTGGTC 58.994 50.000 0.00 0.00 0.00 4.02
6 7 2.613977 CGCCTGTCTTTCTTGATCTGGT 60.614 50.000 0.00 0.00 0.00 4.00
7 8 2.005451 CGCCTGTCTTTCTTGATCTGG 58.995 52.381 0.00 0.00 0.00 3.86
8 9 2.670414 GACGCCTGTCTTTCTTGATCTG 59.330 50.000 0.00 0.00 42.08 2.90
9 10 2.300152 TGACGCCTGTCTTTCTTGATCT 59.700 45.455 0.00 0.00 45.70 2.75
10 11 2.670414 CTGACGCCTGTCTTTCTTGATC 59.330 50.000 0.00 0.00 45.70 2.92
11 12 2.613977 CCTGACGCCTGTCTTTCTTGAT 60.614 50.000 0.00 0.00 45.70 2.57
12 13 1.270305 CCTGACGCCTGTCTTTCTTGA 60.270 52.381 0.00 0.00 45.70 3.02
13 14 1.151668 CCTGACGCCTGTCTTTCTTG 58.848 55.000 0.00 0.00 45.70 3.02
14 15 0.603975 GCCTGACGCCTGTCTTTCTT 60.604 55.000 0.00 0.00 45.70 2.52
15 16 1.004440 GCCTGACGCCTGTCTTTCT 60.004 57.895 0.00 0.00 45.70 2.52
16 17 1.294659 CTGCCTGACGCCTGTCTTTC 61.295 60.000 0.00 0.00 45.70 2.62
17 18 1.302033 CTGCCTGACGCCTGTCTTT 60.302 57.895 0.00 0.00 45.70 2.52
18 19 1.548357 ATCTGCCTGACGCCTGTCTT 61.548 55.000 0.00 0.00 45.70 3.01
19 20 1.954362 GATCTGCCTGACGCCTGTCT 61.954 60.000 0.00 0.00 45.70 3.41
20 21 1.520342 GATCTGCCTGACGCCTGTC 60.520 63.158 0.00 0.00 45.71 3.51
21 22 1.548357 AAGATCTGCCTGACGCCTGT 61.548 55.000 0.00 0.00 36.24 4.00
22 23 0.809241 GAAGATCTGCCTGACGCCTG 60.809 60.000 0.00 0.00 36.24 4.85
23 24 1.260538 TGAAGATCTGCCTGACGCCT 61.261 55.000 0.00 0.00 36.24 5.52
24 25 0.179062 ATGAAGATCTGCCTGACGCC 60.179 55.000 0.00 0.00 36.24 5.68
25 26 1.202510 AGATGAAGATCTGCCTGACGC 60.203 52.381 0.00 0.00 37.56 5.19
26 27 2.864946 CAAGATGAAGATCTGCCTGACG 59.135 50.000 0.00 0.00 39.04 4.35
27 28 3.870419 GACAAGATGAAGATCTGCCTGAC 59.130 47.826 0.00 0.00 39.04 3.51
28 29 3.516700 TGACAAGATGAAGATCTGCCTGA 59.483 43.478 0.00 0.00 39.04 3.86
29 30 3.622163 GTGACAAGATGAAGATCTGCCTG 59.378 47.826 0.00 0.00 39.04 4.85
30 31 3.518705 AGTGACAAGATGAAGATCTGCCT 59.481 43.478 0.00 0.00 39.04 4.75
31 32 3.871485 AGTGACAAGATGAAGATCTGCC 58.129 45.455 0.00 0.00 39.04 4.85
32 33 4.934001 TCAAGTGACAAGATGAAGATCTGC 59.066 41.667 0.00 0.00 39.04 4.26
33 34 5.581479 CCTCAAGTGACAAGATGAAGATCTG 59.419 44.000 0.00 0.00 39.04 2.90
34 35 5.483231 TCCTCAAGTGACAAGATGAAGATCT 59.517 40.000 0.00 0.00 41.00 2.75
35 36 5.728471 TCCTCAAGTGACAAGATGAAGATC 58.272 41.667 0.00 0.00 0.00 2.75
36 37 5.752036 TCCTCAAGTGACAAGATGAAGAT 57.248 39.130 0.00 0.00 0.00 2.40
37 38 5.300752 GTTCCTCAAGTGACAAGATGAAGA 58.699 41.667 0.00 0.00 0.00 2.87
38 39 4.453819 GGTTCCTCAAGTGACAAGATGAAG 59.546 45.833 0.00 0.00 0.00 3.02
39 40 4.389374 GGTTCCTCAAGTGACAAGATGAA 58.611 43.478 0.00 0.00 0.00 2.57
40 41 3.244561 GGGTTCCTCAAGTGACAAGATGA 60.245 47.826 0.00 0.00 0.00 2.92
41 42 3.077359 GGGTTCCTCAAGTGACAAGATG 58.923 50.000 0.00 0.00 0.00 2.90
42 43 2.982488 AGGGTTCCTCAAGTGACAAGAT 59.018 45.455 0.00 0.00 0.00 2.40
43 44 2.408565 AGGGTTCCTCAAGTGACAAGA 58.591 47.619 0.00 0.00 0.00 3.02
44 45 2.938956 AGGGTTCCTCAAGTGACAAG 57.061 50.000 0.00 0.00 0.00 3.16
45 46 2.637872 CCTAGGGTTCCTCAAGTGACAA 59.362 50.000 0.00 0.00 34.61 3.18
46 47 2.158219 TCCTAGGGTTCCTCAAGTGACA 60.158 50.000 9.46 0.00 34.61 3.58
47 48 2.234168 GTCCTAGGGTTCCTCAAGTGAC 59.766 54.545 9.46 0.00 34.61 3.67
48 49 2.537143 GTCCTAGGGTTCCTCAAGTGA 58.463 52.381 9.46 0.00 34.61 3.41
49 50 1.555533 GGTCCTAGGGTTCCTCAAGTG 59.444 57.143 9.46 0.00 34.61 3.16
50 51 1.895866 CGGTCCTAGGGTTCCTCAAGT 60.896 57.143 9.46 0.00 34.61 3.16
51 52 0.824759 CGGTCCTAGGGTTCCTCAAG 59.175 60.000 9.46 0.00 34.61 3.02
52 53 0.115745 ACGGTCCTAGGGTTCCTCAA 59.884 55.000 9.46 0.00 34.61 3.02
53 54 0.324091 GACGGTCCTAGGGTTCCTCA 60.324 60.000 9.46 0.00 34.61 3.86
54 55 0.033306 AGACGGTCCTAGGGTTCCTC 60.033 60.000 9.46 8.76 34.61 3.71
55 56 0.033306 GAGACGGTCCTAGGGTTCCT 60.033 60.000 9.46 0.07 37.71 3.36
56 57 1.042003 GGAGACGGTCCTAGGGTTCC 61.042 65.000 9.46 8.57 42.99 3.62
57 58 2.502633 GGAGACGGTCCTAGGGTTC 58.497 63.158 9.46 0.38 42.99 3.62
58 59 4.781264 GGAGACGGTCCTAGGGTT 57.219 61.111 9.46 0.00 42.99 4.11
66 67 2.552031 GCCTGATTTAAGGAGACGGTC 58.448 52.381 0.00 0.00 40.02 4.79
67 68 1.209747 GGCCTGATTTAAGGAGACGGT 59.790 52.381 0.00 0.00 40.02 4.83
68 69 1.806623 CGGCCTGATTTAAGGAGACGG 60.807 57.143 0.00 0.00 40.02 4.79
69 70 1.136305 TCGGCCTGATTTAAGGAGACG 59.864 52.381 0.00 0.00 40.02 4.18
70 71 2.827652 CTCGGCCTGATTTAAGGAGAC 58.172 52.381 0.00 0.00 40.02 3.36
71 72 1.139058 GCTCGGCCTGATTTAAGGAGA 59.861 52.381 0.00 0.00 40.02 3.71
72 73 1.587547 GCTCGGCCTGATTTAAGGAG 58.412 55.000 0.00 0.00 40.02 3.69
73 74 0.180406 GGCTCGGCCTGATTTAAGGA 59.820 55.000 0.00 0.00 46.69 3.36
74 75 2.707902 GGCTCGGCCTGATTTAAGG 58.292 57.895 0.00 0.00 46.69 2.69
112 113 4.592192 ATCTGATCCGCGGTGCCG 62.592 66.667 27.15 14.45 43.09 5.69
113 114 2.663188 GATCTGATCCGCGGTGCC 60.663 66.667 27.15 15.56 0.00 5.01
114 115 3.032609 CGATCTGATCCGCGGTGC 61.033 66.667 27.15 18.53 0.00 5.01
115 116 2.355126 CCGATCTGATCCGCGGTG 60.355 66.667 27.15 13.92 38.99 4.94
116 117 3.606662 CCCGATCTGATCCGCGGT 61.607 66.667 27.15 12.96 42.08 5.68
117 118 4.363990 CCCCGATCTGATCCGCGG 62.364 72.222 22.12 22.12 43.20 6.46
120 121 4.363990 CCGCCCCGATCTGATCCG 62.364 72.222 11.84 9.11 0.00 4.18
121 122 3.234730 ACCGCCCCGATCTGATCC 61.235 66.667 11.84 0.00 0.00 3.36
122 123 2.029666 CACCGCCCCGATCTGATC 59.970 66.667 7.60 7.60 0.00 2.92
123 124 4.241555 GCACCGCCCCGATCTGAT 62.242 66.667 0.00 0.00 0.00 2.90
143 144 3.957535 CAATGCGGCGCCAGATCC 61.958 66.667 30.82 9.14 0.00 3.36
144 145 3.957535 CCAATGCGGCGCCAGATC 61.958 66.667 30.82 12.57 0.00 2.75
153 154 3.060020 CTTGCTGCTCCCAATGCGG 62.060 63.158 0.00 0.00 39.61 5.69
154 155 2.488355 CTTGCTGCTCCCAATGCG 59.512 61.111 0.00 0.00 0.00 4.73
155 156 2.718073 CCCTTGCTGCTCCCAATGC 61.718 63.158 0.00 0.00 0.00 3.56
156 157 1.304713 ACCCTTGCTGCTCCCAATG 60.305 57.895 0.00 0.00 0.00 2.82
157 158 1.304713 CACCCTTGCTGCTCCCAAT 60.305 57.895 0.00 0.00 0.00 3.16
158 159 2.115910 CACCCTTGCTGCTCCCAA 59.884 61.111 0.00 0.00 0.00 4.12
159 160 4.666253 GCACCCTTGCTGCTCCCA 62.666 66.667 0.00 0.00 46.17 4.37
168 169 2.676471 CCTTTCCCGGCACCCTTG 60.676 66.667 0.00 0.00 0.00 3.61
169 170 3.979497 CCCTTTCCCGGCACCCTT 61.979 66.667 0.00 0.00 0.00 3.95
190 191 1.664965 GCTATTGGCTACCCGCGAG 60.665 63.158 8.23 0.00 40.44 5.03
191 192 2.420043 GCTATTGGCTACCCGCGA 59.580 61.111 8.23 0.00 40.44 5.87
192 193 3.036084 CGCTATTGGCTACCCGCG 61.036 66.667 0.00 0.00 40.44 6.46
193 194 3.346606 GCGCTATTGGCTACCCGC 61.347 66.667 0.00 0.00 39.13 6.13
194 195 3.036084 CGCGCTATTGGCTACCCG 61.036 66.667 5.56 0.00 39.13 5.28
195 196 1.954651 GACGCGCTATTGGCTACCC 60.955 63.158 5.73 0.00 39.13 3.69
196 197 2.300787 CGACGCGCTATTGGCTACC 61.301 63.158 5.73 0.00 39.13 3.18
197 198 3.221956 CGACGCGCTATTGGCTAC 58.778 61.111 5.73 0.00 39.13 3.58
221 222 3.866379 TTTGCGTGGCCTGCTCCAT 62.866 57.895 19.16 0.00 38.57 3.41
222 223 4.577677 TTTGCGTGGCCTGCTCCA 62.578 61.111 19.16 3.51 0.00 3.86
223 224 4.043200 GTTTGCGTGGCCTGCTCC 62.043 66.667 19.16 5.75 0.00 4.70
224 225 4.389576 CGTTTGCGTGGCCTGCTC 62.390 66.667 19.16 10.14 0.00 4.26
254 255 2.439156 ATTCAAGGCCGAGGCAGC 60.439 61.111 16.65 0.00 44.11 5.25
255 256 1.094073 CAGATTCAAGGCCGAGGCAG 61.094 60.000 16.65 5.35 44.11 4.85
256 257 1.078214 CAGATTCAAGGCCGAGGCA 60.078 57.895 16.65 0.00 44.11 4.75
257 258 0.813210 CTCAGATTCAAGGCCGAGGC 60.813 60.000 5.37 5.37 41.06 4.70
258 259 0.179062 CCTCAGATTCAAGGCCGAGG 60.179 60.000 0.00 0.07 34.54 4.63
259 260 0.539051 ACCTCAGATTCAAGGCCGAG 59.461 55.000 0.00 0.00 36.01 4.63
260 261 0.250234 CACCTCAGATTCAAGGCCGA 59.750 55.000 0.00 0.00 36.01 5.54
261 262 0.250234 TCACCTCAGATTCAAGGCCG 59.750 55.000 0.00 0.00 36.01 6.13
262 263 2.496899 TTCACCTCAGATTCAAGGCC 57.503 50.000 0.00 0.00 36.01 5.19
263 264 3.365364 CGTTTTCACCTCAGATTCAAGGC 60.365 47.826 5.31 0.00 36.01 4.35
264 265 3.365364 GCGTTTTCACCTCAGATTCAAGG 60.365 47.826 4.12 4.12 38.70 3.61
265 266 3.365364 GGCGTTTTCACCTCAGATTCAAG 60.365 47.826 0.00 0.00 0.00 3.02
266 267 2.552315 GGCGTTTTCACCTCAGATTCAA 59.448 45.455 0.00 0.00 0.00 2.69
267 268 2.151202 GGCGTTTTCACCTCAGATTCA 58.849 47.619 0.00 0.00 0.00 2.57
268 269 1.128692 CGGCGTTTTCACCTCAGATTC 59.871 52.381 0.00 0.00 0.00 2.52
269 270 1.156736 CGGCGTTTTCACCTCAGATT 58.843 50.000 0.00 0.00 0.00 2.40
270 271 1.298859 GCGGCGTTTTCACCTCAGAT 61.299 55.000 9.37 0.00 0.00 2.90
271 272 1.959226 GCGGCGTTTTCACCTCAGA 60.959 57.895 9.37 0.00 0.00 3.27
272 273 2.556287 GCGGCGTTTTCACCTCAG 59.444 61.111 9.37 0.00 0.00 3.35
273 274 3.342627 CGCGGCGTTTTCACCTCA 61.343 61.111 15.36 0.00 0.00 3.86
274 275 4.736631 GCGCGGCGTTTTCACCTC 62.737 66.667 24.46 0.00 0.00 3.85
289 290 4.605967 GAGCTCTCTCTCGCGGCG 62.606 72.222 17.70 17.70 36.42 6.46
295 296 3.591835 CGGGGCGAGCTCTCTCTC 61.592 72.222 12.85 0.34 37.19 3.20
358 359 4.129737 ATCCTCCACACGCCGTCG 62.130 66.667 0.00 0.00 42.43 5.12
359 360 2.509336 CATCCTCCACACGCCGTC 60.509 66.667 0.00 0.00 0.00 4.79
360 361 4.082523 CCATCCTCCACACGCCGT 62.083 66.667 0.00 0.00 0.00 5.68
361 362 3.723235 CTCCATCCTCCACACGCCG 62.723 68.421 0.00 0.00 0.00 6.46
362 363 2.187946 CTCCATCCTCCACACGCC 59.812 66.667 0.00 0.00 0.00 5.68
363 364 2.187946 CCTCCATCCTCCACACGC 59.812 66.667 0.00 0.00 0.00 5.34
364 365 2.735772 CCCCTCCATCCTCCACACG 61.736 68.421 0.00 0.00 0.00 4.49
365 366 1.306997 TCCCCTCCATCCTCCACAC 60.307 63.158 0.00 0.00 0.00 3.82
366 367 1.003442 CTCCCCTCCATCCTCCACA 59.997 63.158 0.00 0.00 0.00 4.17
367 368 1.768077 CCTCCCCTCCATCCTCCAC 60.768 68.421 0.00 0.00 0.00 4.02
368 369 2.705410 CCTCCCCTCCATCCTCCA 59.295 66.667 0.00 0.00 0.00 3.86
369 370 2.122189 CCCTCCCCTCCATCCTCC 60.122 72.222 0.00 0.00 0.00 4.30
370 371 2.122189 CCCCTCCCCTCCATCCTC 60.122 72.222 0.00 0.00 0.00 3.71
371 372 4.523282 GCCCCTCCCCTCCATCCT 62.523 72.222 0.00 0.00 0.00 3.24
372 373 4.523282 AGCCCCTCCCCTCCATCC 62.523 72.222 0.00 0.00 0.00 3.51
373 374 2.368878 AAGCCCCTCCCCTCCATC 60.369 66.667 0.00 0.00 0.00 3.51
374 375 2.697644 CAAGCCCCTCCCCTCCAT 60.698 66.667 0.00 0.00 0.00 3.41
375 376 3.950861 CTCAAGCCCCTCCCCTCCA 62.951 68.421 0.00 0.00 0.00 3.86
376 377 3.093172 CTCAAGCCCCTCCCCTCC 61.093 72.222 0.00 0.00 0.00 4.30
377 378 3.093172 CCTCAAGCCCCTCCCCTC 61.093 72.222 0.00 0.00 0.00 4.30
378 379 3.960313 ACCTCAAGCCCCTCCCCT 61.960 66.667 0.00 0.00 0.00 4.79
379 380 3.732849 CACCTCAAGCCCCTCCCC 61.733 72.222 0.00 0.00 0.00 4.81
380 381 3.732849 CCACCTCAAGCCCCTCCC 61.733 72.222 0.00 0.00 0.00 4.30
381 382 4.432741 GCCACCTCAAGCCCCTCC 62.433 72.222 0.00 0.00 0.00 4.30
382 383 4.432741 GGCCACCTCAAGCCCCTC 62.433 72.222 0.00 0.00 43.76 4.30
398 399 0.526096 CATTTCATTTCAGCCGCCGG 60.526 55.000 0.00 0.00 0.00 6.13
399 400 0.451383 TCATTTCATTTCAGCCGCCG 59.549 50.000 0.00 0.00 0.00 6.46
400 401 2.652941 TTCATTTCATTTCAGCCGCC 57.347 45.000 0.00 0.00 0.00 6.13
401 402 3.772932 TCATTCATTTCATTTCAGCCGC 58.227 40.909 0.00 0.00 0.00 6.53
402 403 4.208460 GCATCATTCATTTCATTTCAGCCG 59.792 41.667 0.00 0.00 0.00 5.52
403 404 5.113383 TGCATCATTCATTTCATTTCAGCC 58.887 37.500 0.00 0.00 0.00 4.85
404 405 6.656314 TTGCATCATTCATTTCATTTCAGC 57.344 33.333 0.00 0.00 0.00 4.26
405 406 8.335356 GGATTTGCATCATTCATTTCATTTCAG 58.665 33.333 0.00 0.00 0.00 3.02
446 447 9.677567 TTTTTGAGACTTGCAATAGTTACATTC 57.322 29.630 0.00 0.00 0.00 2.67
474 475 9.683069 CTGCTGTTTTTGAAATAGTTACATTCT 57.317 29.630 0.00 0.00 0.00 2.40
539 540 6.041296 AGTTTCCAAATCAAATTGCTCTCACT 59.959 34.615 0.00 0.00 0.00 3.41
624 627 8.988934 GTAATCAAGAGTGATGTTGTCTTTGTA 58.011 33.333 0.00 0.00 44.02 2.41
659 828 6.012858 ACACTTATTTTGTGATGGAGGGAGTA 60.013 38.462 0.00 0.00 38.65 2.59
660 829 5.222130 ACACTTATTTTGTGATGGAGGGAGT 60.222 40.000 0.00 0.00 38.65 3.85
661 830 5.256474 ACACTTATTTTGTGATGGAGGGAG 58.744 41.667 0.00 0.00 38.65 4.30
662 831 5.014123 AGACACTTATTTTGTGATGGAGGGA 59.986 40.000 0.00 0.00 38.65 4.20
663 832 5.256474 AGACACTTATTTTGTGATGGAGGG 58.744 41.667 0.00 0.00 38.65 4.30
664 833 5.939883 TGAGACACTTATTTTGTGATGGAGG 59.060 40.000 0.00 0.00 38.65 4.30
665 834 7.439157 TTGAGACACTTATTTTGTGATGGAG 57.561 36.000 0.00 0.00 38.65 3.86
666 835 7.884877 AGATTGAGACACTTATTTTGTGATGGA 59.115 33.333 0.00 0.00 38.65 3.41
667 836 8.048534 AGATTGAGACACTTATTTTGTGATGG 57.951 34.615 0.00 0.00 38.65 3.51
672 841 9.846248 GCATTAAGATTGAGACACTTATTTTGT 57.154 29.630 0.00 0.00 0.00 2.83
673 842 9.844790 TGCATTAAGATTGAGACACTTATTTTG 57.155 29.630 0.00 0.00 0.00 2.44
675 844 9.846248 GTTGCATTAAGATTGAGACACTTATTT 57.154 29.630 0.00 0.00 0.00 1.40
676 845 9.236006 AGTTGCATTAAGATTGAGACACTTATT 57.764 29.630 0.00 0.00 0.00 1.40
677 846 8.798859 AGTTGCATTAAGATTGAGACACTTAT 57.201 30.769 0.00 0.00 0.00 1.73
678 847 8.621532 AAGTTGCATTAAGATTGAGACACTTA 57.378 30.769 0.00 0.00 0.00 2.24
679 848 7.516198 AAGTTGCATTAAGATTGAGACACTT 57.484 32.000 0.00 0.00 0.00 3.16
680 849 7.013655 ACAAAGTTGCATTAAGATTGAGACACT 59.986 33.333 0.00 0.00 0.00 3.55
681 850 7.141363 ACAAAGTTGCATTAAGATTGAGACAC 58.859 34.615 0.00 0.00 0.00 3.67
682 851 7.275888 ACAAAGTTGCATTAAGATTGAGACA 57.724 32.000 0.00 0.00 0.00 3.41
683 852 8.507249 AGTACAAAGTTGCATTAAGATTGAGAC 58.493 33.333 0.00 0.00 0.00 3.36
684 853 8.621532 AGTACAAAGTTGCATTAAGATTGAGA 57.378 30.769 0.00 0.00 0.00 3.27
713 882 9.849166 CGTCCCAAAATAAATGTTTGTACTAAT 57.151 29.630 0.00 0.00 34.75 1.73
714 883 9.064706 TCGTCCCAAAATAAATGTTTGTACTAA 57.935 29.630 0.00 0.00 34.75 2.24
715 884 8.618702 TCGTCCCAAAATAAATGTTTGTACTA 57.381 30.769 0.00 0.00 34.75 1.82
716 885 7.513371 TCGTCCCAAAATAAATGTTTGTACT 57.487 32.000 0.00 0.00 34.75 2.73
717 886 7.327518 CCTTCGTCCCAAAATAAATGTTTGTAC 59.672 37.037 0.00 0.00 34.75 2.90
718 887 7.371936 CCTTCGTCCCAAAATAAATGTTTGTA 58.628 34.615 0.00 0.00 34.75 2.41
719 888 6.220201 CCTTCGTCCCAAAATAAATGTTTGT 58.780 36.000 0.00 0.00 34.75 2.83
720 889 5.637387 CCCTTCGTCCCAAAATAAATGTTTG 59.363 40.000 0.00 0.00 36.03 2.93
721 890 5.540719 TCCCTTCGTCCCAAAATAAATGTTT 59.459 36.000 0.00 0.00 0.00 2.83
722 891 5.081032 TCCCTTCGTCCCAAAATAAATGTT 58.919 37.500 0.00 0.00 0.00 2.71
723 892 4.668636 TCCCTTCGTCCCAAAATAAATGT 58.331 39.130 0.00 0.00 0.00 2.71
724 893 4.705023 ACTCCCTTCGTCCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
725 894 4.930696 ACTCCCTTCGTCCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
726 895 4.376225 ACTCCCTTCGTCCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
727 896 5.703730 ATACTCCCTTCGTCCCAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
728 897 7.951806 TCTATATACTCCCTTCGTCCCAAAATA 59.048 37.037 0.00 0.00 0.00 1.40
729 898 5.906772 ATATACTCCCTTCGTCCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
730 899 6.138263 TCTATATACTCCCTTCGTCCCAAAA 58.862 40.000 0.00 0.00 0.00 2.44
731 900 5.708544 TCTATATACTCCCTTCGTCCCAAA 58.291 41.667 0.00 0.00 0.00 3.28
732 901 5.163012 ACTCTATATACTCCCTTCGTCCCAA 60.163 44.000 0.00 0.00 0.00 4.12
733 902 4.353191 ACTCTATATACTCCCTTCGTCCCA 59.647 45.833 0.00 0.00 0.00 4.37
734 903 4.920999 ACTCTATATACTCCCTTCGTCCC 58.079 47.826 0.00 0.00 0.00 4.46
735 904 6.002704 TCAACTCTATATACTCCCTTCGTCC 58.997 44.000 0.00 0.00 0.00 4.79
736 905 6.935771 TCTCAACTCTATATACTCCCTTCGTC 59.064 42.308 0.00 0.00 0.00 4.20
737 906 6.711645 GTCTCAACTCTATATACTCCCTTCGT 59.288 42.308 0.00 0.00 0.00 3.85
738 907 6.128499 CGTCTCAACTCTATATACTCCCTTCG 60.128 46.154 0.00 0.00 0.00 3.79
739 908 6.935771 TCGTCTCAACTCTATATACTCCCTTC 59.064 42.308 0.00 0.00 0.00 3.46
740 909 6.839454 TCGTCTCAACTCTATATACTCCCTT 58.161 40.000 0.00 0.00 0.00 3.95
741 910 6.436738 TCGTCTCAACTCTATATACTCCCT 57.563 41.667 0.00 0.00 0.00 4.20
742 911 7.390996 TCAATCGTCTCAACTCTATATACTCCC 59.609 40.741 0.00 0.00 0.00 4.30
743 912 8.231837 GTCAATCGTCTCAACTCTATATACTCC 58.768 40.741 0.00 0.00 0.00 3.85
744 913 8.775527 TGTCAATCGTCTCAACTCTATATACTC 58.224 37.037 0.00 0.00 0.00 2.59
745 914 8.678593 TGTCAATCGTCTCAACTCTATATACT 57.321 34.615 0.00 0.00 0.00 2.12
746 915 9.335891 CATGTCAATCGTCTCAACTCTATATAC 57.664 37.037 0.00 0.00 0.00 1.47
889 1157 2.575532 CAAGTTGCTCTCACTTCCCAA 58.424 47.619 0.00 0.00 0.00 4.12
921 1189 4.453819 GGCTCGCTTGATTGCTAATATTCT 59.546 41.667 0.00 0.00 0.00 2.40
946 1214 3.640498 TGCTCTGCTCTGTATATGCTTCT 59.360 43.478 0.00 0.00 0.00 2.85
966 1234 1.480954 TGGCAAGTAGTAGTAGCCTGC 59.519 52.381 0.00 3.36 45.42 4.85
967 1235 3.522553 GTTGGCAAGTAGTAGTAGCCTG 58.477 50.000 0.00 0.00 45.42 4.85
968 1236 2.500504 GGTTGGCAAGTAGTAGTAGCCT 59.499 50.000 0.00 0.00 45.42 4.58
969 1237 2.235402 TGGTTGGCAAGTAGTAGTAGCC 59.765 50.000 0.00 0.00 45.41 3.93
1281 1565 2.525629 TTGGTGCCCAGGTCGAGA 60.526 61.111 0.00 0.00 33.81 4.04
1489 1773 2.336809 CGAGATCGCTACCAGGGC 59.663 66.667 0.00 0.00 0.00 5.19
2184 2476 6.591834 GGAATCACTCCGGATATCAAAGTATG 59.408 42.308 3.57 0.00 33.37 2.39
2217 2509 3.193056 ACCAAGTTCTCTAGCTTACCGAC 59.807 47.826 0.00 0.00 0.00 4.79
2242 2536 5.665459 AGCTATTGTTGTACAAGCCTAGAG 58.335 41.667 8.98 3.51 41.94 2.43
2346 2640 1.678635 CCAGGCTTGCCGGAATTGA 60.679 57.895 5.05 0.00 0.00 2.57
2899 3201 8.465999 CACACAAATTAATATTCCCAGCAACTA 58.534 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.