Multiple sequence alignment - TraesCS7D01G011200

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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 TraesCS7D01G011200 chr7D 100.000 5880 0 0 1 5880 5084863 5078984 0.000000e+00 10859.0
1 TraesCS7D01G011200 chr7D 90.344 756 61 10 1662 2411 629558931 629559680 0.000000e+00 981.0
2 TraesCS7D01G011200 chr7D 98.060 464 9 0 5415 5878 5072676 5072213 0.000000e+00 808.0
3 TraesCS7D01G011200 chr7D 97.216 467 9 4 5415 5880 195614357 195613894 0.000000e+00 787.0
4 TraesCS7D01G011200 chr7D 95.833 432 17 1 4985 5415 6792157 6791726 0.000000e+00 697.0
5 TraesCS7D01G011200 chr7D 88.550 262 25 4 2159 2418 634273786 634274044 4.420000e-81 313.0
6 TraesCS7D01G011200 chr7D 81.553 206 38 0 38 243 102584891 102584686 2.820000e-38 171.0
7 TraesCS7D01G011200 chr7A 96.163 2580 83 11 2417 4983 6328061 6325485 0.000000e+00 4202.0
8 TraesCS7D01G011200 chr7A 92.196 1102 40 9 570 1665 6329114 6328053 0.000000e+00 1517.0
9 TraesCS7D01G011200 chr7A 87.854 247 29 1 2 248 6329664 6329419 7.460000e-74 289.0
10 TraesCS7D01G011200 chr7A 92.667 150 10 1 377 525 6329351 6329202 1.280000e-51 215.0
11 TraesCS7D01G011200 chr4A 95.701 2582 94 8 2417 4983 737538083 737535504 0.000000e+00 4137.0
12 TraesCS7D01G011200 chr4A 93.757 945 44 9 662 1603 737539028 737538096 0.000000e+00 1404.0
13 TraesCS7D01G011200 chr5D 91.081 897 69 9 4985 5878 537981177 537980289 0.000000e+00 1203.0
14 TraesCS7D01G011200 chr5D 97.228 469 11 2 5412 5880 45886799 45886333 0.000000e+00 793.0
15 TraesCS7D01G011200 chr5D 91.923 260 20 1 1863 2121 119459032 119458773 4.330000e-96 363.0
16 TraesCS7D01G011200 chr5D 81.604 212 39 0 32 243 486291621 486291832 6.060000e-40 176.0
17 TraesCS7D01G011200 chr5D 81.720 186 33 1 23 208 565183281 565183465 2.840000e-33 154.0
18 TraesCS7D01G011200 chr5D 81.250 176 32 1 31 205 494808581 494808756 2.210000e-29 141.0
19 TraesCS7D01G011200 chr6D 89.597 769 61 12 1661 2424 472534742 472533988 0.000000e+00 959.0
20 TraesCS7D01G011200 chr6D 97.419 465 11 1 5416 5880 174668973 174668510 0.000000e+00 791.0
21 TraesCS7D01G011200 chr6D 96.520 431 15 0 4985 5415 389921148 389920718 0.000000e+00 713.0
22 TraesCS7D01G011200 chr6D 84.669 711 73 24 1662 2368 307533838 307533160 0.000000e+00 676.0
23 TraesCS7D01G011200 chr6D 82.800 250 41 2 1 248 49224577 49224328 7.670000e-54 222.0
24 TraesCS7D01G011200 chr6D 76.233 223 50 2 22 243 470571447 470571227 1.340000e-21 115.0
25 TraesCS7D01G011200 chr1D 88.874 755 66 12 1669 2418 439568041 439567300 0.000000e+00 913.0
26 TraesCS7D01G011200 chr1D 88.624 756 62 18 1669 2418 439513556 439512819 0.000000e+00 898.0
27 TraesCS7D01G011200 chr1D 83.660 153 25 0 22 174 483132681 483132833 1.710000e-30 145.0
28 TraesCS7D01G011200 chr1D 81.765 170 29 2 2021 2190 314018468 314018301 2.210000e-29 141.0
29 TraesCS7D01G011200 chr1D 76.957 230 43 4 23 243 361519338 361519110 8.000000e-24 122.0
30 TraesCS7D01G011200 chr1D 82.308 130 23 0 114 243 419025847 419025718 4.820000e-21 113.0
31 TraesCS7D01G011200 chr3D 88.142 759 66 14 1665 2416 502712 503453 0.000000e+00 881.0
32 TraesCS7D01G011200 chr3D 96.984 431 13 0 4985 5415 37986530 37986960 0.000000e+00 725.0
33 TraesCS7D01G011200 chr3D 85.806 620 69 12 1662 2278 571605326 571604723 1.790000e-179 640.0
34 TraesCS7D01G011200 chr3D 81.897 116 18 3 2306 2419 19568753 19568867 1.740000e-15 95.3
35 TraesCS7D01G011200 chr4B 97.634 465 10 1 5416 5880 24533249 24532786 0.000000e+00 797.0
36 TraesCS7D01G011200 chr4B 96.065 432 16 1 4985 5415 580799577 580799146 0.000000e+00 702.0
37 TraesCS7D01G011200 chr4B 80.455 220 41 2 25 243 179316003 179316221 3.640000e-37 167.0
38 TraesCS7D01G011200 chr3B 97.634 465 9 2 5416 5880 454388339 454388801 0.000000e+00 797.0
39 TraesCS7D01G011200 chr3B 96.296 432 15 1 4985 5415 741435036 741435467 0.000000e+00 708.0
40 TraesCS7D01G011200 chr3B 82.805 221 37 1 23 243 644173853 644173634 4.650000e-46 196.0
41 TraesCS7D01G011200 chr3B 81.435 237 44 0 7 243 136100792 136100556 1.670000e-45 195.0
42 TraesCS7D01G011200 chr2D 97.228 469 11 2 5413 5880 359932066 359931599 0.000000e+00 793.0
43 TraesCS7D01G011200 chr2D 97.228 469 12 1 5412 5880 511663409 511663876 0.000000e+00 793.0
44 TraesCS7D01G011200 chr2D 97.229 433 12 0 4983 5415 632083930 632084362 0.000000e+00 734.0
45 TraesCS7D01G011200 chr2D 80.672 238 45 1 6 243 520511377 520511613 3.620000e-42 183.0
46 TraesCS7D01G011200 chr2D 80.861 209 39 1 34 242 72341486 72341693 4.710000e-36 163.0
47 TraesCS7D01G011200 chr1A 86.975 691 77 11 1666 2351 430199183 430198501 0.000000e+00 765.0
48 TraesCS7D01G011200 chr1A 86.783 575 60 13 1677 2244 1845146 1844581 1.390000e-175 627.0
49 TraesCS7D01G011200 chr1A 90.435 230 19 3 2190 2417 1844588 1844360 3.440000e-77 300.0
50 TraesCS7D01G011200 chr1A 81.538 130 21 3 1662 1789 449615988 449616116 2.900000e-18 104.0
51 TraesCS7D01G011200 chr6B 87.939 655 56 9 1766 2416 6273681 6274316 0.000000e+00 750.0
52 TraesCS7D01G011200 chr6B 96.296 432 15 1 4985 5415 113678892 113678461 0.000000e+00 708.0
53 TraesCS7D01G011200 chr6B 80.189 212 39 3 33 243 695912796 695912587 7.890000e-34 156.0
54 TraesCS7D01G011200 chr6B 78.829 222 44 3 23 243 695906391 695906172 4.750000e-31 147.0
55 TraesCS7D01G011200 chr6A 84.820 751 77 23 1671 2414 444708374 444707654 0.000000e+00 721.0
56 TraesCS7D01G011200 chr6A 83.408 223 33 4 23 243 570385593 570385813 2.780000e-48 204.0
57 TraesCS7D01G011200 chr2B 82.730 857 101 37 4984 5818 49385869 49386700 0.000000e+00 719.0
58 TraesCS7D01G011200 chr2B 79.476 229 45 2 21 248 489364351 489364124 1.700000e-35 161.0
59 TraesCS7D01G011200 chr7B 89.944 358 29 6 2061 2416 854108 853756 6.950000e-124 455.0
60 TraesCS7D01G011200 chrUn 83.710 221 32 3 23 243 474691248 474691032 7.720000e-49 206.0
61 TraesCS7D01G011200 chrUn 81.651 109 17 3 113 219 27632909 27632802 2.920000e-13 87.9
62 TraesCS7D01G011200 chrUn 81.720 93 16 1 152 243 475313534 475313626 6.320000e-10 76.8
63 TraesCS7D01G011200 chr5A 82.949 217 31 5 31 243 590581726 590581940 2.160000e-44 191.0
64 TraesCS7D01G011200 chr4D 82.075 212 34 3 32 243 129756131 129755924 1.680000e-40 178.0
65 TraesCS7D01G011200 chr5B 81.183 186 34 1 23 208 708193547 708193363 1.320000e-31 148.0


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 TraesCS7D01G011200 chr7D 5078984 5084863 5879 True 10859.00 10859 100.000 1 5880 1 chr7D.!!$R2 5879
1 TraesCS7D01G011200 chr7D 629558931 629559680 749 False 981.00 981 90.344 1662 2411 1 chr7D.!!$F1 749
2 TraesCS7D01G011200 chr7A 6325485 6329664 4179 True 1555.75 4202 92.220 2 4983 4 chr7A.!!$R1 4981
3 TraesCS7D01G011200 chr4A 737535504 737539028 3524 True 2770.50 4137 94.729 662 4983 2 chr4A.!!$R1 4321
4 TraesCS7D01G011200 chr5D 537980289 537981177 888 True 1203.00 1203 91.081 4985 5878 1 chr5D.!!$R3 893
5 TraesCS7D01G011200 chr6D 472533988 472534742 754 True 959.00 959 89.597 1661 2424 1 chr6D.!!$R6 763
6 TraesCS7D01G011200 chr6D 307533160 307533838 678 True 676.00 676 84.669 1662 2368 1 chr6D.!!$R3 706
7 TraesCS7D01G011200 chr1D 439567300 439568041 741 True 913.00 913 88.874 1669 2418 1 chr1D.!!$R5 749
8 TraesCS7D01G011200 chr1D 439512819 439513556 737 True 898.00 898 88.624 1669 2418 1 chr1D.!!$R4 749
9 TraesCS7D01G011200 chr3D 502712 503453 741 False 881.00 881 88.142 1665 2416 1 chr3D.!!$F1 751
10 TraesCS7D01G011200 chr3D 571604723 571605326 603 True 640.00 640 85.806 1662 2278 1 chr3D.!!$R1 616
11 TraesCS7D01G011200 chr1A 430198501 430199183 682 True 765.00 765 86.975 1666 2351 1 chr1A.!!$R1 685
12 TraesCS7D01G011200 chr1A 1844360 1845146 786 True 463.50 627 88.609 1677 2417 2 chr1A.!!$R2 740
13 TraesCS7D01G011200 chr6B 6273681 6274316 635 False 750.00 750 87.939 1766 2416 1 chr6B.!!$F1 650
14 TraesCS7D01G011200 chr6A 444707654 444708374 720 True 721.00 721 84.820 1671 2414 1 chr6A.!!$R1 743
15 TraesCS7D01G011200 chr2B 49385869 49386700 831 False 719.00 719 82.730 4984 5818 1 chr2B.!!$F1 834

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
85 86 0.173708 GCTCCTCGAGTTCGTCCATT 59.826 55.000 12.31 0.00 40.80 3.16 F
255 256 0.386113 GTCCTTACAGGCGGCTCTAG 59.614 60.000 9.32 6.53 34.61 2.43 F
339 340 0.395311 CTACAGTAGGGGAGCGGTGA 60.395 60.000 0.00 0.00 0.00 4.02 F
640 685 0.521242 GATCAATGTGTTGACGGCGC 60.521 55.000 6.90 0.00 46.43 6.53 F
1939 2008 1.475280 CACATCATTGGAGCCCAACTG 59.525 52.381 8.59 9.14 46.95 3.16 F
2270 2394 1.492176 GAGGAATCTGATGGCAGGGAA 59.508 52.381 0.00 0.00 42.53 3.97 F
3126 3261 1.608025 GGCACTCCTGACATCGAACAA 60.608 52.381 0.00 0.00 0.00 2.83 F
4050 4185 0.888619 CACTAGTCCTCTCCGCACAA 59.111 55.000 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 1245 1.344763 GGACAAGCGCCCTACTATCAT 59.655 52.381 2.29 0.0 0.00 2.45 R
2200 2323 0.107831 TCACTTGGTTTAGCCGCACT 59.892 50.000 0.00 0.0 41.21 4.40 R
2270 2394 2.954989 TGAGAGCGATCTGTCAGCTAAT 59.045 45.455 8.50 0.0 41.84 1.73 R
2392 2519 4.157246 AGTGAATTCCAGTTTTTACCCCC 58.843 43.478 2.27 0.0 0.00 5.40 R
3653 3788 0.456653 GGCAGCTAACAACAATGCCG 60.457 55.000 0.00 0.0 46.19 5.69 R
3669 3804 2.035961 GTCCTCGCTACATATCTTGGCA 59.964 50.000 0.00 0.0 0.00 4.92 R
4621 4771 1.005630 GTGCTCCAACTCTGTCGCT 60.006 57.895 0.00 0.0 0.00 4.93 R
5131 5282 0.107459 GACTCTGACAATGGAGGGGC 60.107 60.000 0.00 0.0 34.22 5.80 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
19 20 0.176680 CTCTTAGGTGTGGCGCTCAT 59.823 55.000 7.64 0.00 0.00 2.90
41 42 0.244721 GGATGGCAGCGCTTTTTCTT 59.755 50.000 7.50 0.00 0.00 2.52
51 52 2.714480 GCGCTTTTTCTTCGAGTTTGTC 59.286 45.455 0.00 0.00 0.00 3.18
55 56 5.511729 CGCTTTTTCTTCGAGTTTGTCTTTT 59.488 36.000 0.00 0.00 0.00 2.27
58 59 4.893424 TTCTTCGAGTTTGTCTTTTGGG 57.107 40.909 0.00 0.00 0.00 4.12
66 67 1.533625 TTGTCTTTTGGGCTCCGATG 58.466 50.000 0.00 0.00 0.00 3.84
73 74 4.292178 GGGCTCCGATGCTCCTCG 62.292 72.222 0.00 0.00 38.37 4.63
81 82 0.590230 CGATGCTCCTCGAGTTCGTC 60.590 60.000 12.31 9.36 41.12 4.20
85 86 0.173708 GCTCCTCGAGTTCGTCCATT 59.826 55.000 12.31 0.00 40.80 3.16
86 87 1.404391 GCTCCTCGAGTTCGTCCATTA 59.596 52.381 12.31 0.00 40.80 1.90
99 100 6.464311 GTTCGTCCATTAGAACGTAATTGAC 58.536 40.000 0.00 0.00 37.58 3.18
118 119 1.134560 ACGGAGCTCCAACGTAGATTC 59.865 52.381 31.67 0.74 39.30 2.52
121 122 2.957006 GGAGCTCCAACGTAGATTCCTA 59.043 50.000 28.43 0.00 35.64 2.94
122 123 3.243468 GGAGCTCCAACGTAGATTCCTAC 60.243 52.174 28.43 0.00 37.93 3.18
133 134 2.389715 AGATTCCTACCGTCTCCTTGG 58.610 52.381 0.00 0.00 0.00 3.61
134 135 1.413077 GATTCCTACCGTCTCCTTGGG 59.587 57.143 0.00 0.00 0.00 4.12
135 136 0.616679 TTCCTACCGTCTCCTTGGGG 60.617 60.000 0.00 0.00 0.00 4.96
137 138 1.987855 CTACCGTCTCCTTGGGGCA 60.988 63.158 0.00 0.00 0.00 5.36
138 139 1.961180 CTACCGTCTCCTTGGGGCAG 61.961 65.000 0.00 0.00 0.00 4.85
165 166 2.795175 AGTGTTTCTCGTCGTGTGAT 57.205 45.000 0.00 0.00 0.00 3.06
174 175 3.569250 TCGTCGTGTGATGAGATTTGA 57.431 42.857 0.00 0.00 35.21 2.69
219 220 2.494059 AGGGTTCAACAATGACGACTG 58.506 47.619 0.00 0.00 34.61 3.51
222 223 0.865111 TTCAACAATGACGACTGCGG 59.135 50.000 0.00 0.00 43.17 5.69
238 239 4.228567 GGCTCTAGGGCGCTGGTC 62.229 72.222 14.51 7.04 0.00 4.02
239 240 4.228567 GCTCTAGGGCGCTGGTCC 62.229 72.222 14.51 0.00 38.61 4.46
245 246 2.125106 GGGCGCTGGTCCTTACAG 60.125 66.667 7.64 0.00 38.95 2.74
246 247 2.125106 GGCGCTGGTCCTTACAGG 60.125 66.667 7.64 0.00 36.48 4.00
247 248 2.820037 GCGCTGGTCCTTACAGGC 60.820 66.667 0.00 0.00 34.61 4.85
248 249 2.509336 CGCTGGTCCTTACAGGCG 60.509 66.667 0.00 0.00 40.01 5.52
249 250 2.125106 GCTGGTCCTTACAGGCGG 60.125 66.667 0.00 0.00 34.61 6.13
250 251 2.125106 CTGGTCCTTACAGGCGGC 60.125 66.667 0.00 0.00 34.61 6.53
251 252 2.606519 TGGTCCTTACAGGCGGCT 60.607 61.111 5.25 5.25 34.61 5.52
252 253 2.187163 GGTCCTTACAGGCGGCTC 59.813 66.667 9.32 0.00 34.61 4.70
253 254 2.359967 GGTCCTTACAGGCGGCTCT 61.360 63.158 9.32 0.00 34.61 4.09
254 255 1.041447 GGTCCTTACAGGCGGCTCTA 61.041 60.000 9.32 0.00 34.61 2.43
255 256 0.386113 GTCCTTACAGGCGGCTCTAG 59.614 60.000 9.32 6.53 34.61 2.43
256 257 0.755698 TCCTTACAGGCGGCTCTAGG 60.756 60.000 9.32 15.83 34.61 3.02
257 258 1.742768 CTTACAGGCGGCTCTAGGG 59.257 63.158 9.32 0.00 0.00 3.53
258 259 2.370647 CTTACAGGCGGCTCTAGGGC 62.371 65.000 9.32 5.86 37.12 5.19
282 283 1.376683 TCCTTACGGGCACATGCAC 60.377 57.895 6.15 0.05 44.36 4.57
305 306 1.945354 GCCTTCCCGACTGTCATCGA 61.945 60.000 8.73 0.00 45.13 3.59
306 307 0.747255 CCTTCCCGACTGTCATCGAT 59.253 55.000 8.73 0.00 45.13 3.59
307 308 1.954382 CCTTCCCGACTGTCATCGATA 59.046 52.381 8.73 0.00 45.13 2.92
308 309 2.361119 CCTTCCCGACTGTCATCGATAA 59.639 50.000 8.73 0.00 45.13 1.75
309 310 3.005897 CCTTCCCGACTGTCATCGATAAT 59.994 47.826 8.73 0.00 45.13 1.28
333 334 2.499827 GCCGGCTACAGTAGGGGAG 61.500 68.421 22.15 0.00 0.00 4.30
335 336 2.846652 CGGCTACAGTAGGGGAGCG 61.847 68.421 9.74 0.00 35.71 5.03
336 337 2.499827 GGCTACAGTAGGGGAGCGG 61.500 68.421 9.74 0.00 35.71 5.52
337 338 1.757340 GCTACAGTAGGGGAGCGGT 60.757 63.158 9.74 0.00 0.00 5.68
339 340 0.395311 CTACAGTAGGGGAGCGGTGA 60.395 60.000 0.00 0.00 0.00 4.02
340 341 0.682209 TACAGTAGGGGAGCGGTGAC 60.682 60.000 0.00 0.00 0.00 3.67
343 344 3.075005 TAGGGGAGCGGTGACAGC 61.075 66.667 0.00 0.00 0.00 4.40
348 349 4.702081 GAGCGGTGACAGCGACGT 62.702 66.667 29.64 13.38 42.41 4.34
351 352 3.097728 CGGTGACAGCGACGTGTC 61.098 66.667 21.96 17.89 46.08 3.67
361 362 4.702081 GACGTGTCGGCAGCTCGT 62.702 66.667 3.66 3.66 38.50 4.18
362 363 4.280494 ACGTGTCGGCAGCTCGTT 62.280 61.111 0.00 0.00 33.19 3.85
363 364 3.470567 CGTGTCGGCAGCTCGTTC 61.471 66.667 0.00 0.00 0.00 3.95
364 365 2.049063 GTGTCGGCAGCTCGTTCT 60.049 61.111 0.00 0.00 0.00 3.01
365 366 2.049156 TGTCGGCAGCTCGTTCTG 60.049 61.111 0.00 3.01 37.15 3.02
366 367 2.258591 GTCGGCAGCTCGTTCTGA 59.741 61.111 10.08 0.00 36.19 3.27
367 368 2.089349 GTCGGCAGCTCGTTCTGAC 61.089 63.158 10.08 6.65 38.73 3.51
381 382 2.433491 TGACGGCGGAATTGGTCG 60.433 61.111 13.24 0.00 38.70 4.79
386 387 2.746803 GGCGGAATTGGTCGTTCGG 61.747 63.158 0.00 0.00 0.00 4.30
426 427 1.275856 GTGGGCAAGCCAAATGATTCA 59.724 47.619 13.87 0.00 37.98 2.57
493 495 8.462938 GTTGTTTCAATTTTGCGAAAATGATTG 58.537 29.630 16.22 10.23 40.05 2.67
498 500 8.936509 TCAATTTTGCGAAAATGATTGAAATG 57.063 26.923 12.33 3.69 40.05 2.32
518 520 9.241919 TGAAATGTATTATCAATGTTCACCAGT 57.758 29.630 0.00 0.00 0.00 4.00
577 622 2.818751 AACACCCTGTTGGACAAAGA 57.181 45.000 0.00 0.00 39.45 2.52
625 670 3.205338 CATATGTGGCCGTTCAAGATCA 58.795 45.455 0.00 0.00 0.00 2.92
626 671 2.198827 ATGTGGCCGTTCAAGATCAA 57.801 45.000 0.00 0.00 0.00 2.57
627 672 2.198827 TGTGGCCGTTCAAGATCAAT 57.801 45.000 0.00 0.00 0.00 2.57
628 673 1.811965 TGTGGCCGTTCAAGATCAATG 59.188 47.619 0.00 0.00 0.00 2.82
629 674 1.812571 GTGGCCGTTCAAGATCAATGT 59.187 47.619 0.00 0.00 0.00 2.71
630 675 1.811965 TGGCCGTTCAAGATCAATGTG 59.188 47.619 0.00 0.00 0.00 3.21
631 676 1.812571 GGCCGTTCAAGATCAATGTGT 59.187 47.619 0.00 0.00 0.00 3.72
632 677 2.228822 GGCCGTTCAAGATCAATGTGTT 59.771 45.455 0.00 0.00 0.00 3.32
633 678 3.236816 GCCGTTCAAGATCAATGTGTTG 58.763 45.455 0.00 0.00 36.65 3.33
635 680 4.466828 CCGTTCAAGATCAATGTGTTGAC 58.533 43.478 0.00 0.00 46.43 3.18
636 681 4.143835 CGTTCAAGATCAATGTGTTGACG 58.856 43.478 0.00 0.00 46.43 4.35
637 682 4.466828 GTTCAAGATCAATGTGTTGACGG 58.533 43.478 0.00 0.00 46.43 4.79
638 683 2.483877 TCAAGATCAATGTGTTGACGGC 59.516 45.455 0.00 0.00 46.43 5.68
639 684 1.078709 AGATCAATGTGTTGACGGCG 58.921 50.000 4.80 4.80 46.43 6.46
640 685 0.521242 GATCAATGTGTTGACGGCGC 60.521 55.000 6.90 0.00 46.43 6.53
641 686 1.922135 ATCAATGTGTTGACGGCGCC 61.922 55.000 19.07 19.07 46.43 6.53
642 687 3.361977 AATGTGTTGACGGCGCCC 61.362 61.111 23.46 8.57 0.00 6.13
643 688 4.634703 ATGTGTTGACGGCGCCCA 62.635 61.111 23.46 11.71 0.00 5.36
666 711 4.163552 CGATCCATGCATGCATTTGTATC 58.836 43.478 30.32 24.31 33.90 2.24
820 865 3.249559 GCAACAAGCAGTATGGAGATAGC 59.750 47.826 0.00 0.00 44.79 2.97
960 1007 2.282958 ACCTCCCAGCTCGACGAA 60.283 61.111 0.00 0.00 0.00 3.85
1210 1261 7.986085 ATGAATGTTTGTATGATAGTAGGGC 57.014 36.000 0.00 0.00 0.00 5.19
1495 1547 3.770263 ATGCCGAAGTGTGATTTCATG 57.230 42.857 0.00 0.00 0.00 3.07
1498 1550 2.744202 GCCGAAGTGTGATTTCATGTCT 59.256 45.455 0.00 0.00 0.00 3.41
1503 1555 5.615544 CGAAGTGTGATTTCATGTCTGTTCC 60.616 44.000 0.00 0.00 0.00 3.62
1557 1609 7.561021 TTGTGAATTATTCGGCAAGCTTATA 57.439 32.000 0.00 0.00 0.00 0.98
1565 1617 4.137116 TCGGCAAGCTTATAAGACATGT 57.863 40.909 16.85 0.00 0.00 3.21
1573 1627 8.889717 GCAAGCTTATAAGACATGTACCTTTTA 58.110 33.333 16.85 0.00 0.00 1.52
1651 1705 7.531857 TGCTTTTTATTGGGTGAGTGAATTA 57.468 32.000 0.00 0.00 0.00 1.40
1652 1706 7.375053 TGCTTTTTATTGGGTGAGTGAATTAC 58.625 34.615 0.00 0.00 0.00 1.89
1656 1710 7.931578 TTTATTGGGTGAGTGAATTACGAAT 57.068 32.000 0.00 0.00 0.00 3.34
1657 1711 9.451002 TTTTATTGGGTGAGTGAATTACGAATA 57.549 29.630 0.00 0.00 0.00 1.75
1658 1712 9.451002 TTTATTGGGTGAGTGAATTACGAATAA 57.549 29.630 0.00 0.00 0.00 1.40
1659 1713 9.621629 TTATTGGGTGAGTGAATTACGAATAAT 57.378 29.630 0.00 0.00 32.01 1.28
1660 1714 7.548196 TTGGGTGAGTGAATTACGAATAATC 57.452 36.000 0.00 0.00 30.27 1.75
1707 1764 9.536510 TTACCCCTAATTTAGCATTTTTACACT 57.463 29.630 0.00 0.00 0.00 3.55
1709 1766 9.185680 ACCCCTAATTTAGCATTTTTACACTAG 57.814 33.333 0.00 0.00 0.00 2.57
1710 1767 9.185680 CCCCTAATTTAGCATTTTTACACTAGT 57.814 33.333 0.00 0.00 0.00 2.57
1721 1779 7.543756 CATTTTTACACTAGTTACCCCCATTG 58.456 38.462 0.00 0.00 0.00 2.82
1727 1785 5.222254 ACACTAGTTACCCCCATTGAACAAT 60.222 40.000 0.00 0.00 0.00 2.71
1809 1869 7.524717 TTTTATAAGAGCCTTCTTGCAAAGT 57.475 32.000 0.00 0.00 46.34 2.66
1829 1890 4.618965 AGTTCGTGTTTTACTGAGAGTCC 58.381 43.478 0.00 0.00 0.00 3.85
1897 1963 8.038944 TCCGATCCTATTATGTTAATAACTGGC 58.961 37.037 4.67 0.00 31.07 4.85
1939 2008 1.475280 CACATCATTGGAGCCCAACTG 59.525 52.381 8.59 9.14 46.95 3.16
1966 2035 6.875948 AACACATGTTTGACAATAGCACTA 57.124 33.333 0.00 0.00 33.93 2.74
2033 2103 6.212388 TCCCAAAGCCTAAAATAAATGCTTCA 59.788 34.615 0.00 0.00 41.12 3.02
2115 2185 5.008811 CACAACCCACAATGCAAAATTGAAT 59.991 36.000 5.55 0.00 33.51 2.57
2122 2192 7.041235 CCCACAATGCAAAATTGAATGTACTTT 60.041 33.333 5.55 0.00 33.51 2.66
2154 2224 5.245531 AGATAATTGTTCGTCTTTCCTGCA 58.754 37.500 0.00 0.00 0.00 4.41
2270 2394 1.492176 GAGGAATCTGATGGCAGGGAA 59.508 52.381 0.00 0.00 42.53 3.97
2278 2402 1.845791 TGATGGCAGGGAATTAGCTGA 59.154 47.619 0.00 0.00 0.00 4.26
2340 2467 6.779115 CAAACTTTTGCTAAATGGGGTAAC 57.221 37.500 0.00 0.00 0.00 2.50
2443 2570 7.131907 TCTTAATGCCAGTATAGGTAGCAAA 57.868 36.000 0.00 0.00 36.95 3.68
2450 2577 8.582657 TGCCAGTATAGGTAGCAAAATTTTAA 57.417 30.769 2.44 0.00 0.00 1.52
2482 2609 4.141801 TGTGTAATCATACGGAGAAAGGGG 60.142 45.833 0.00 0.00 34.60 4.79
2495 2622 4.309933 GAGAAAGGGGCATTTTCTTTGTG 58.690 43.478 14.18 0.00 43.07 3.33
2503 2630 4.627035 GGGCATTTTCTTTGTGCAGATTAC 59.373 41.667 0.00 0.00 40.53 1.89
2648 2776 5.623169 TCTCCGGTTTATTACACCAAGTTT 58.377 37.500 0.00 0.00 33.36 2.66
2674 2805 5.677319 TTTTGTGGGTTTATGACACCAAA 57.323 34.783 0.00 0.00 35.80 3.28
2997 3130 8.870160 TTATCATTTGGAAGTTGTTCTGTTTG 57.130 30.769 0.00 0.00 32.72 2.93
3002 3135 4.523083 TGGAAGTTGTTCTGTTTGTAGCT 58.477 39.130 0.00 0.00 32.72 3.32
3017 3152 7.192913 TGTTTGTAGCTTATGTTTGACTTGTG 58.807 34.615 0.00 0.00 0.00 3.33
3126 3261 1.608025 GGCACTCCTGACATCGAACAA 60.608 52.381 0.00 0.00 0.00 2.83
3213 3348 5.132502 TCTCTTCAGGAAACATTTGCTTCA 58.867 37.500 0.00 0.00 36.67 3.02
3237 3372 4.441695 CGCGCTCTTCTCAGCCCA 62.442 66.667 5.56 0.00 35.84 5.36
3519 3654 2.091111 TGCAGATCATCTGGAGGAGGTA 60.091 50.000 16.70 0.00 44.43 3.08
3598 3733 2.484889 GCGTTGGTCAGAAAGAAGTCT 58.515 47.619 0.00 0.00 0.00 3.24
3653 3788 5.183904 AGCATGAGAACCCAAAAGATACAAC 59.816 40.000 0.00 0.00 0.00 3.32
3669 3804 2.704725 CAACGGCATTGTTGTTAGCT 57.295 45.000 7.35 0.00 43.28 3.32
3984 4119 2.161211 GCTGAGATGTGCCAAAGAGTTC 59.839 50.000 0.00 0.00 0.00 3.01
3985 4120 3.405831 CTGAGATGTGCCAAAGAGTTCA 58.594 45.455 0.00 0.00 0.00 3.18
4050 4185 0.888619 CACTAGTCCTCTCCGCACAA 59.111 55.000 0.00 0.00 0.00 3.33
4144 4279 3.777522 ACTGCTCAGGATAAAGGCTAAGT 59.222 43.478 1.66 0.00 0.00 2.24
4400 4544 4.072131 GGTCTTGCAAATCTGTACTCCAA 58.928 43.478 0.00 0.00 0.00 3.53
4517 4661 1.886542 GGTTCATGTCACCAAACCCTC 59.113 52.381 10.83 0.00 36.06 4.30
4519 4663 2.955660 GTTCATGTCACCAAACCCTCAA 59.044 45.455 0.00 0.00 0.00 3.02
4523 4667 4.099266 TCATGTCACCAAACCCTCAAAAAG 59.901 41.667 0.00 0.00 0.00 2.27
4532 4677 3.108847 ACCCTCAAAAAGTTTCACCCA 57.891 42.857 0.00 0.00 0.00 4.51
4535 4680 4.473196 ACCCTCAAAAAGTTTCACCCAATT 59.527 37.500 0.00 0.00 0.00 2.32
4621 4771 2.260434 GCCTACGTGAACGCCTCA 59.740 61.111 0.00 0.00 44.43 3.86
4798 4948 1.066587 CAAGCTCGACGGGAGGATC 59.933 63.158 0.00 0.00 43.36 3.36
4799 4949 2.482333 AAGCTCGACGGGAGGATCG 61.482 63.158 0.00 0.00 43.36 3.69
4890 5040 4.869215 ACGCTCTCATGAGATTATCACAG 58.131 43.478 25.30 12.25 41.91 3.66
4983 5133 7.359595 TGTTGTAGTTCAATGCATGTAAAGTC 58.640 34.615 0.00 0.00 38.38 3.01
5044 5195 3.404224 TGGCAGTACAACGAATACCAA 57.596 42.857 0.00 0.00 0.00 3.67
5046 5197 4.135306 TGGCAGTACAACGAATACCAAAA 58.865 39.130 0.00 0.00 0.00 2.44
5047 5198 4.579340 TGGCAGTACAACGAATACCAAAAA 59.421 37.500 0.00 0.00 0.00 1.94
5048 5199 5.241949 TGGCAGTACAACGAATACCAAAAAT 59.758 36.000 0.00 0.00 0.00 1.82
5087 5238 0.182061 TCCGTAGACCACCTAGCGAT 59.818 55.000 0.00 0.00 0.00 4.58
5131 5282 2.663630 AAGGATCGCCGTCGTCATCG 62.664 60.000 0.00 0.00 39.96 3.84
5141 5292 2.063979 TCGTCATCGCCCCTCCATT 61.064 57.895 0.00 0.00 36.96 3.16
5143 5294 1.224592 GTCATCGCCCCTCCATTGT 59.775 57.895 0.00 0.00 0.00 2.71
5145 5296 1.224315 CATCGCCCCTCCATTGTCA 59.776 57.895 0.00 0.00 0.00 3.58
5200 5351 1.533469 AAGTCGTCGTGCTAAGGCCT 61.533 55.000 0.00 0.00 37.74 5.19
5228 5379 1.601759 AGCGCACCAGAACAGCAAT 60.602 52.632 11.47 0.00 0.00 3.56
5232 5383 1.855213 GCACCAGAACAGCAATCGCA 61.855 55.000 0.00 0.00 42.27 5.10
5235 5386 1.579964 CCAGAACAGCAATCGCAGCA 61.580 55.000 0.00 0.00 42.27 4.41
5249 5400 3.860641 TCGCAGCAGATGAAGAATAACA 58.139 40.909 0.00 0.00 0.00 2.41
5296 5447 1.445731 CACACGAACGTAGACGAACAC 59.554 52.381 9.41 0.00 43.02 3.32
5298 5449 0.662619 ACGAACGTAGACGAACACCA 59.337 50.000 9.41 0.00 43.02 4.17
5443 5598 5.508320 GGGGAACGTAGCAGAAATTCAAAAA 60.508 40.000 0.00 0.00 0.00 1.94
5479 5636 7.055667 TCACCAAGATCAATCTATGGAGTAC 57.944 40.000 19.34 0.00 37.92 2.73
5491 5653 5.057819 TCTATGGAGTACTCTAGCAACGAG 58.942 45.833 21.88 10.63 34.70 4.18
5501 5663 2.465010 TAGCAACGAGGGGAAGGGGA 62.465 60.000 0.00 0.00 0.00 4.81
5505 5667 3.083997 CGAGGGGAAGGGGAGTGG 61.084 72.222 0.00 0.00 0.00 4.00
5559 5724 1.136252 CGTTGCAAGAACGTGGATGAG 60.136 52.381 0.00 0.00 38.69 2.90
5576 5741 1.552337 TGAGGGAGTCGTACTCGTAGT 59.448 52.381 8.33 0.00 45.96 2.73
5614 5779 0.173481 TTCCGATCTGAGCACCGAAG 59.827 55.000 0.00 0.00 0.00 3.79
5615 5780 0.679960 TCCGATCTGAGCACCGAAGA 60.680 55.000 0.00 0.00 0.00 2.87
5708 5884 0.193574 AGAGGTTGGGGAAGACTCCA 59.806 55.000 0.00 0.00 46.10 3.86
5725 5901 1.818363 CATCCAGCAGCAGCACGAT 60.818 57.895 3.17 0.23 45.49 3.73
5754 5930 2.268920 GATGGAGGAGCGTGGCAA 59.731 61.111 0.00 0.00 0.00 4.52
5758 5934 2.514824 GAGGAGCGTGGCAATCCC 60.515 66.667 10.19 0.60 33.30 3.85
5828 6011 2.448705 GCTGCGCCGAAAGAGAGAC 61.449 63.158 4.18 0.00 0.00 3.36
5846 6029 3.108521 CGTTCTCGTGTCTCTTGGG 57.891 57.895 0.00 0.00 0.00 4.12
5847 6030 1.009389 CGTTCTCGTGTCTCTTGGGC 61.009 60.000 0.00 0.00 0.00 5.36
5848 6031 0.033504 GTTCTCGTGTCTCTTGGGCA 59.966 55.000 0.00 0.00 0.00 5.36
5849 6032 0.318441 TTCTCGTGTCTCTTGGGCAG 59.682 55.000 0.00 0.00 0.00 4.85
5852 6035 2.360475 GTGTCTCTTGGGCAGCCC 60.360 66.667 25.54 25.54 45.71 5.19
5862 6045 2.574018 GGGCAGCCCAAACCTCAAC 61.574 63.158 27.33 0.00 44.65 3.18
5871 6054 6.940298 GCAGCCCAAACCTCAACTATATATAA 59.060 38.462 0.00 0.00 0.00 0.98
5875 6058 7.402862 CCCAAACCTCAACTATATATAAGGGG 58.597 42.308 11.31 7.99 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.405105 GAAAAAGCGCTGCCATCCATA 59.595 47.619 12.58 0.00 0.00 2.74
41 42 2.218603 GAGCCCAAAAGACAAACTCGA 58.781 47.619 0.00 0.00 0.00 4.04
51 52 1.379642 GGAGCATCGGAGCCCAAAAG 61.380 60.000 0.00 0.00 34.37 2.27
55 56 3.157252 GAGGAGCATCGGAGCCCA 61.157 66.667 9.03 0.00 34.37 5.36
58 59 2.010582 AACTCGAGGAGCATCGGAGC 62.011 60.000 18.41 0.00 42.93 4.70
66 67 0.173708 AATGGACGAACTCGAGGAGC 59.826 55.000 18.41 4.38 43.02 4.70
73 74 6.529125 TCAATTACGTTCTAATGGACGAACTC 59.471 38.462 3.76 0.00 37.85 3.01
99 100 1.536284 GGAATCTACGTTGGAGCTCCG 60.536 57.143 27.43 17.83 39.43 4.63
103 104 2.543238 CGGTAGGAATCTACGTTGGAGC 60.543 54.545 0.00 0.00 45.10 4.70
108 109 2.948315 GGAGACGGTAGGAATCTACGTT 59.052 50.000 0.00 0.00 45.10 3.99
118 119 2.732619 GCCCCAAGGAGACGGTAGG 61.733 68.421 0.00 0.00 33.47 3.18
121 122 3.322466 CTGCCCCAAGGAGACGGT 61.322 66.667 0.00 0.00 33.47 4.83
122 123 3.322466 ACTGCCCCAAGGAGACGG 61.322 66.667 0.00 0.00 33.47 4.79
133 134 3.477530 AGAAACACTAAACTCACTGCCC 58.522 45.455 0.00 0.00 0.00 5.36
134 135 3.184581 CGAGAAACACTAAACTCACTGCC 59.815 47.826 0.00 0.00 0.00 4.85
135 136 3.802685 ACGAGAAACACTAAACTCACTGC 59.197 43.478 0.00 0.00 0.00 4.40
137 138 4.201990 ACGACGAGAAACACTAAACTCACT 60.202 41.667 0.00 0.00 0.00 3.41
138 139 4.040376 ACGACGAGAAACACTAAACTCAC 58.960 43.478 0.00 0.00 0.00 3.51
165 166 3.708403 AGCACCTGACATCAAATCTCA 57.292 42.857 0.00 0.00 0.00 3.27
174 175 5.129980 TCAATAGATCTGAAGCACCTGACAT 59.870 40.000 5.18 0.00 0.00 3.06
209 210 0.101399 CTAGAGCCGCAGTCGTCATT 59.899 55.000 0.00 0.00 0.00 2.57
210 211 1.729470 CCTAGAGCCGCAGTCGTCAT 61.729 60.000 0.00 0.00 0.00 3.06
222 223 4.228567 GGACCAGCGCCCTAGAGC 62.229 72.222 2.29 0.00 39.42 4.09
239 240 1.742768 CCCTAGAGCCGCCTGTAAG 59.257 63.158 0.00 0.00 0.00 2.34
240 241 2.432300 GCCCTAGAGCCGCCTGTAA 61.432 63.158 0.00 0.00 0.00 2.41
241 242 2.838225 GCCCTAGAGCCGCCTGTA 60.838 66.667 0.00 0.00 0.00 2.74
247 248 3.718210 GACCAACGCCCTAGAGCCG 62.718 68.421 0.00 0.00 0.00 5.52
248 249 2.187163 GACCAACGCCCTAGAGCC 59.813 66.667 0.00 0.00 0.00 4.70
249 250 1.900545 AAGGACCAACGCCCTAGAGC 61.901 60.000 0.00 0.00 31.36 4.09
250 251 1.136500 GTAAGGACCAACGCCCTAGAG 59.864 57.143 0.00 0.00 31.36 2.43
251 252 1.188863 GTAAGGACCAACGCCCTAGA 58.811 55.000 0.00 0.00 31.36 2.43
252 253 0.179119 CGTAAGGACCAACGCCCTAG 60.179 60.000 6.48 0.00 31.66 3.02
253 254 1.892338 CGTAAGGACCAACGCCCTA 59.108 57.895 6.48 0.00 31.66 3.53
254 255 2.660802 CGTAAGGACCAACGCCCT 59.339 61.111 6.48 0.00 31.66 5.19
282 283 1.446272 GACAGTCGGGAAGGCTTCG 60.446 63.158 20.26 11.32 28.06 3.79
287 288 0.747255 ATCGATGACAGTCGGGAAGG 59.253 55.000 0.00 0.00 41.74 3.46
305 306 2.170607 ACTGTAGCCGGCTTGACATTAT 59.829 45.455 37.74 18.16 0.00 1.28
306 307 1.553248 ACTGTAGCCGGCTTGACATTA 59.447 47.619 37.74 12.41 0.00 1.90
307 308 0.324943 ACTGTAGCCGGCTTGACATT 59.675 50.000 37.74 24.32 0.00 2.71
308 309 1.137086 CTACTGTAGCCGGCTTGACAT 59.863 52.381 37.74 22.75 0.00 3.06
309 310 0.530744 CTACTGTAGCCGGCTTGACA 59.469 55.000 37.74 31.03 0.00 3.58
335 336 3.097728 CGACACGTCGCTGTCACC 61.098 66.667 20.29 3.41 46.50 4.02
344 345 4.702081 ACGAGCTGCCGACACGTC 62.702 66.667 15.53 0.00 31.69 4.34
345 346 4.280494 AACGAGCTGCCGACACGT 62.280 61.111 15.53 8.56 38.81 4.49
346 347 3.470567 GAACGAGCTGCCGACACG 61.471 66.667 15.53 8.01 0.00 4.49
347 348 2.049063 AGAACGAGCTGCCGACAC 60.049 61.111 15.53 7.51 0.00 3.67
348 349 2.049156 CAGAACGAGCTGCCGACA 60.049 61.111 15.53 0.00 0.00 4.35
349 350 2.089349 GTCAGAACGAGCTGCCGAC 61.089 63.158 15.53 9.67 35.86 4.79
350 351 2.258591 GTCAGAACGAGCTGCCGA 59.741 61.111 15.53 0.00 35.86 5.54
360 361 0.953960 ACCAATTCCGCCGTCAGAAC 60.954 55.000 0.00 0.00 0.00 3.01
361 362 0.672401 GACCAATTCCGCCGTCAGAA 60.672 55.000 0.00 0.00 0.00 3.02
362 363 1.079405 GACCAATTCCGCCGTCAGA 60.079 57.895 0.00 0.00 0.00 3.27
363 364 2.452813 CGACCAATTCCGCCGTCAG 61.453 63.158 0.00 0.00 0.00 3.51
364 365 2.433491 CGACCAATTCCGCCGTCA 60.433 61.111 0.00 0.00 0.00 4.35
365 366 1.963190 GAACGACCAATTCCGCCGTC 61.963 60.000 0.00 0.00 32.64 4.79
366 367 2.030958 GAACGACCAATTCCGCCGT 61.031 57.895 0.00 0.00 34.74 5.68
367 368 2.782615 GAACGACCAATTCCGCCG 59.217 61.111 0.00 0.00 0.00 6.46
368 369 2.746803 CCGAACGACCAATTCCGCC 61.747 63.158 0.00 0.00 0.00 6.13
369 370 2.030958 ACCGAACGACCAATTCCGC 61.031 57.895 0.00 0.00 0.00 5.54
370 371 1.632046 CCACCGAACGACCAATTCCG 61.632 60.000 0.00 0.00 0.00 4.30
371 372 0.604511 ACCACCGAACGACCAATTCC 60.605 55.000 0.00 0.00 0.00 3.01
372 373 0.515564 CACCACCGAACGACCAATTC 59.484 55.000 0.00 0.00 0.00 2.17
373 374 0.107081 TCACCACCGAACGACCAATT 59.893 50.000 0.00 0.00 0.00 2.32
374 375 0.107081 TTCACCACCGAACGACCAAT 59.893 50.000 0.00 0.00 0.00 3.16
375 376 0.531090 CTTCACCACCGAACGACCAA 60.531 55.000 0.00 0.00 0.00 3.67
381 382 2.027625 CGCCTCTTCACCACCGAAC 61.028 63.158 0.00 0.00 0.00 3.95
386 387 3.307379 AAGAACGCCTCTTCACCAC 57.693 52.632 0.00 0.00 40.61 4.16
405 406 0.247185 AATCATTTGGCTTGCCCACG 59.753 50.000 9.35 0.00 45.34 4.94
455 456 5.590530 ATTGAAACAACAAGGTGCTGTAA 57.409 34.783 0.00 0.00 33.22 2.41
456 457 5.590530 AATTGAAACAACAAGGTGCTGTA 57.409 34.783 0.00 0.00 33.22 2.74
458 459 5.561993 CAAAATTGAAACAACAAGGTGCTG 58.438 37.500 0.00 0.00 33.22 4.41
558 585 2.818751 TCTTTGTCCAACAGGGTGTT 57.181 45.000 0.00 0.00 42.08 3.32
577 622 6.127168 TGACCAAGATGTGATCGTAACCTATT 60.127 38.462 0.00 0.00 0.00 1.73
625 670 3.361977 GGGCGCCGTCAACACATT 61.362 61.111 22.54 0.00 0.00 2.71
626 671 4.634703 TGGGCGCCGTCAACACAT 62.635 61.111 22.54 0.00 0.00 3.21
638 683 2.592574 ATGCATGGATCGTGGGCG 60.593 61.111 0.00 0.00 39.92 6.13
639 684 3.036577 CATGCATGGATCGTGGGC 58.963 61.111 19.40 0.00 0.00 5.36
640 685 1.176619 ATGCATGCATGGATCGTGGG 61.177 55.000 31.74 0.00 33.26 4.61
641 686 0.671796 AATGCATGCATGGATCGTGG 59.328 50.000 32.79 3.05 37.91 4.94
642 687 2.124122 CAAATGCATGCATGGATCGTG 58.876 47.619 32.79 25.72 37.91 4.35
643 688 1.752498 ACAAATGCATGCATGGATCGT 59.248 42.857 32.79 26.05 37.91 3.73
644 689 2.502213 ACAAATGCATGCATGGATCG 57.498 45.000 32.79 25.48 37.91 3.69
645 690 4.163552 CGATACAAATGCATGCATGGATC 58.836 43.478 32.79 29.19 37.91 3.36
666 711 4.592485 AATAGATTGTCTAGCTCCACCG 57.408 45.455 0.00 0.00 31.67 4.94
714 759 7.500992 TCCAGAAAATTCGAGCTAATGATAGT 58.499 34.615 0.00 0.00 0.00 2.12
811 856 5.047590 CGACTACTCTCTCTAGCTATCTCCA 60.048 48.000 0.00 0.00 0.00 3.86
812 857 5.408356 CGACTACTCTCTCTAGCTATCTCC 58.592 50.000 0.00 0.00 0.00 3.71
820 865 5.353123 AGTCTTTTGCGACTACTCTCTCTAG 59.647 44.000 0.00 0.00 42.19 2.43
856 901 7.114388 CGTACCTTTTTCCACTAATTTTTCTGC 59.886 37.037 0.00 0.00 0.00 4.26
1198 1245 1.344763 GGACAAGCGCCCTACTATCAT 59.655 52.381 2.29 0.00 0.00 2.45
1207 1258 4.796038 TTATACTATAGGACAAGCGCCC 57.204 45.455 2.29 0.00 0.00 6.13
1210 1261 5.289675 GCAGCATTATACTATAGGACAAGCG 59.710 44.000 4.43 0.00 0.00 4.68
1221 1272 6.345096 TCACAGCATAGCAGCATTATACTA 57.655 37.500 0.00 0.00 36.85 1.82
1222 1273 5.219343 TCACAGCATAGCAGCATTATACT 57.781 39.130 0.00 0.00 36.85 2.12
1223 1274 5.468072 AGTTCACAGCATAGCAGCATTATAC 59.532 40.000 0.00 0.00 36.85 1.47
1495 1547 5.642063 TCAATGAAATAGAACCGGAACAGAC 59.358 40.000 9.46 0.00 0.00 3.51
1498 1550 6.127758 CCAATCAATGAAATAGAACCGGAACA 60.128 38.462 9.46 0.00 0.00 3.18
1503 1555 9.450807 GATAAACCAATCAATGAAATAGAACCG 57.549 33.333 0.00 0.00 0.00 4.44
1573 1627 9.308000 TCACTCACCCAAATATTTAAAGAACAT 57.692 29.630 0.00 0.00 0.00 2.71
1651 1705 7.438459 CCGGAATTCACTCTTAAGATTATTCGT 59.562 37.037 5.44 0.00 0.00 3.85
1652 1706 7.438459 ACCGGAATTCACTCTTAAGATTATTCG 59.562 37.037 9.46 8.73 0.00 3.34
1656 1710 8.857694 AAAACCGGAATTCACTCTTAAGATTA 57.142 30.769 9.46 0.00 0.00 1.75
1657 1711 7.761038 AAAACCGGAATTCACTCTTAAGATT 57.239 32.000 9.46 0.00 0.00 2.40
1658 1712 7.761038 AAAAACCGGAATTCACTCTTAAGAT 57.239 32.000 9.46 0.00 0.00 2.40
1659 1713 7.173735 GGTAAAAACCGGAATTCACTCTTAAGA 59.826 37.037 9.46 4.81 0.00 2.10
1660 1714 7.303261 GGTAAAAACCGGAATTCACTCTTAAG 58.697 38.462 9.46 0.00 0.00 1.85
1703 1759 3.653836 TGTTCAATGGGGGTAACTAGTGT 59.346 43.478 0.00 0.00 0.00 3.55
1707 1764 7.290248 TGAAAAATTGTTCAATGGGGGTAACTA 59.710 33.333 8.67 0.00 34.59 2.24
1708 1765 6.100424 TGAAAAATTGTTCAATGGGGGTAACT 59.900 34.615 8.67 0.00 34.59 2.24
1709 1766 6.292150 TGAAAAATTGTTCAATGGGGGTAAC 58.708 36.000 8.67 0.00 34.59 2.50
1710 1767 6.500589 TGAAAAATTGTTCAATGGGGGTAA 57.499 33.333 8.67 0.00 34.59 2.85
1711 1768 6.296145 GGATGAAAAATTGTTCAATGGGGGTA 60.296 38.462 14.95 0.00 40.76 3.69
1712 1769 5.514659 GGATGAAAAATTGTTCAATGGGGGT 60.515 40.000 14.95 0.00 40.76 4.95
1713 1770 4.943093 GGATGAAAAATTGTTCAATGGGGG 59.057 41.667 14.95 0.00 40.76 5.40
1721 1779 7.041721 GGGGTAATCTGGATGAAAAATTGTTC 58.958 38.462 1.01 1.01 0.00 3.18
1727 1785 5.269554 AGTGGGGTAATCTGGATGAAAAA 57.730 39.130 0.00 0.00 0.00 1.94
1789 1849 4.154918 CGAACTTTGCAAGAAGGCTCTTAT 59.845 41.667 0.00 0.00 40.05 1.73
1790 1850 3.498397 CGAACTTTGCAAGAAGGCTCTTA 59.502 43.478 0.00 0.00 40.05 2.10
1809 1869 4.340097 TCTGGACTCTCAGTAAAACACGAA 59.660 41.667 0.00 0.00 36.25 3.85
1829 1890 3.631453 TGCTTGGGCACTTAGTCTG 57.369 52.632 0.00 0.00 44.28 3.51
1874 1940 9.726438 ACTGCCAGTTATTAACATAATAGGATC 57.274 33.333 9.15 0.00 0.00 3.36
1939 2008 7.222611 AGTGCTATTGTCAAACATGTGTTTTTC 59.777 33.333 8.32 5.83 45.07 2.29
1953 2022 5.921962 ACAGATCTGTAGTGCTATTGTCA 57.078 39.130 26.87 0.00 42.90 3.58
1966 2035 9.896645 ACATCACATTCTATTTTACAGATCTGT 57.103 29.630 30.11 30.11 46.87 3.41
2115 2185 7.101054 ACAATTATCTTGAGCGGTAAAGTACA 58.899 34.615 11.45 0.00 0.00 2.90
2122 2192 4.751060 ACGAACAATTATCTTGAGCGGTA 58.249 39.130 0.00 0.00 0.00 4.02
2196 2315 0.533308 TTGGTTTAGCCGCACTCGTT 60.533 50.000 0.00 0.00 41.21 3.85
2197 2316 0.949105 CTTGGTTTAGCCGCACTCGT 60.949 55.000 0.00 0.00 41.21 4.18
2200 2323 0.107831 TCACTTGGTTTAGCCGCACT 59.892 50.000 0.00 0.00 41.21 4.40
2270 2394 2.954989 TGAGAGCGATCTGTCAGCTAAT 59.045 45.455 8.50 0.00 41.84 1.73
2278 2402 6.312426 CAGTAATTCTTTTGAGAGCGATCTGT 59.688 38.462 8.50 0.00 0.00 3.41
2340 2467 9.325248 ACCCCATTAAATATATTTTCATCCTGG 57.675 33.333 15.64 12.32 0.00 4.45
2392 2519 4.157246 AGTGAATTCCAGTTTTTACCCCC 58.843 43.478 2.27 0.00 0.00 5.40
2450 2577 8.638873 TCTCCGTATGATTACACATTATTCAGT 58.361 33.333 0.00 0.00 0.00 3.41
2482 2609 5.153513 TCGTAATCTGCACAAAGAAAATGC 58.846 37.500 0.00 0.00 39.88 3.56
2495 2622 7.881643 ATATGATCAGTTCTTCGTAATCTGC 57.118 36.000 0.09 0.00 0.00 4.26
2503 2630 8.930760 GGGAATAGAAATATGATCAGTTCTTCG 58.069 37.037 18.80 0.00 32.69 3.79
2577 2704 9.736023 CCATGTATAAGCTAAATTTGAACTTCC 57.264 33.333 0.00 0.00 0.00 3.46
2657 2788 4.145807 ACGAATTTGGTGTCATAAACCCA 58.854 39.130 0.00 0.00 36.83 4.51
2997 3130 6.539649 TGTCACAAGTCAAACATAAGCTAC 57.460 37.500 0.00 0.00 0.00 3.58
3213 3348 1.064803 CTGAGAAGAGCGCGTCTGTAT 59.935 52.381 11.03 0.00 34.84 2.29
3579 3714 3.983741 AGAGACTTCTTTCTGACCAACG 58.016 45.455 0.00 0.00 0.00 4.10
3598 3733 5.545723 AGGACTTCCTCAAGAAATTCAGAGA 59.454 40.000 14.32 0.78 44.77 3.10
3653 3788 0.456653 GGCAGCTAACAACAATGCCG 60.457 55.000 0.00 0.00 46.19 5.69
3661 3796 4.816385 GCTACATATCTTGGCAGCTAACAA 59.184 41.667 0.00 2.71 35.64 2.83
3669 3804 2.035961 GTCCTCGCTACATATCTTGGCA 59.964 50.000 0.00 0.00 0.00 4.92
3984 4119 3.487202 CCACCGGTTGCGTCGATG 61.487 66.667 2.97 0.00 0.00 3.84
3985 4120 3.642778 CTCCACCGGTTGCGTCGAT 62.643 63.158 2.97 0.00 0.00 3.59
4050 4185 4.021016 ACTTCTGCTTCGGAGTATCTTTGT 60.021 41.667 0.00 0.00 33.73 2.83
4144 4279 2.270923 CGATGATTGAGCGACCTTCAA 58.729 47.619 0.00 0.00 38.76 2.69
4246 4381 8.436046 TTTTGCTGCATTTGATTAAGAAAACT 57.564 26.923 1.84 0.00 0.00 2.66
4279 4423 7.656137 TGCCAAGAGAAAAATAGTATACGGATC 59.344 37.037 0.00 0.00 0.00 3.36
4400 4544 1.152247 TCCCTGCAGTGTGAGAGGT 60.152 57.895 13.81 0.00 0.00 3.85
4503 4647 3.436243 ACTTTTTGAGGGTTTGGTGACA 58.564 40.909 0.00 0.00 39.83 3.58
4517 4661 6.923928 ACATCAATTGGGTGAAACTTTTTG 57.076 33.333 15.61 0.00 36.74 2.44
4519 4663 6.039941 TCGTACATCAATTGGGTGAAACTTTT 59.960 34.615 15.61 0.00 36.74 2.27
4523 4667 5.560966 ATCGTACATCAATTGGGTGAAAC 57.439 39.130 15.61 12.13 0.00 2.78
4532 4677 5.733226 TTGCATCGAATCGTACATCAATT 57.267 34.783 1.52 0.00 0.00 2.32
4535 4680 3.059665 GCATTGCATCGAATCGTACATCA 60.060 43.478 3.15 0.00 0.00 3.07
4621 4771 1.005630 GTGCTCCAACTCTGTCGCT 60.006 57.895 0.00 0.00 0.00 4.93
4627 4777 1.007271 CGACACGTGCTCCAACTCT 60.007 57.895 17.22 0.00 0.00 3.24
4631 4781 2.028484 GGACGACACGTGCTCCAA 59.972 61.111 17.22 0.00 44.36 3.53
4914 5064 4.695606 AGAGGAGTAATGTGGAGGGTAAA 58.304 43.478 0.00 0.00 0.00 2.01
5004 5155 7.390996 ACTGCCATGATTGAAGATGAATAGATC 59.609 37.037 0.00 0.00 0.00 2.75
5087 5238 1.339929 TCGCTTCAGTGCTTGTAGTCA 59.660 47.619 0.00 0.00 0.00 3.41
5116 5267 4.925576 GGCGATGACGACGGCGAT 62.926 66.667 22.49 0.00 45.03 4.58
5131 5282 0.107459 GACTCTGACAATGGAGGGGC 60.107 60.000 0.00 0.00 34.22 5.80
5141 5292 1.069090 GTTGTGCCCGACTCTGACA 59.931 57.895 0.00 0.00 0.00 3.58
5143 5294 0.249868 CAAGTTGTGCCCGACTCTGA 60.250 55.000 0.00 0.00 34.00 3.27
5145 5296 0.180406 AACAAGTTGTGCCCGACTCT 59.820 50.000 9.79 0.00 34.00 3.24
5200 5351 1.960040 CTGGTGCGCTGGTCCTATGA 61.960 60.000 9.73 0.00 0.00 2.15
5228 5379 3.860641 TGTTATTCTTCATCTGCTGCGA 58.139 40.909 0.00 0.00 0.00 5.10
5232 5383 7.039434 TCCGATCTATGTTATTCTTCATCTGCT 60.039 37.037 0.00 0.00 0.00 4.24
5235 5386 8.310382 CCTTCCGATCTATGTTATTCTTCATCT 58.690 37.037 0.00 0.00 0.00 2.90
5268 5419 0.943673 TACGTTCGTGTGTCTTCGGA 59.056 50.000 8.14 0.00 0.00 4.55
5296 5447 1.594862 GATTTGCTCGGATCTCGTTGG 59.405 52.381 0.00 0.00 40.32 3.77
5298 5449 1.207089 TGGATTTGCTCGGATCTCGTT 59.793 47.619 0.00 0.00 40.32 3.85
5412 5567 1.122632 TGCTACGTTCCCCAACAGGA 61.123 55.000 0.00 0.00 38.24 3.86
5413 5568 0.673644 CTGCTACGTTCCCCAACAGG 60.674 60.000 0.00 0.00 32.14 4.00
5414 5569 0.320374 TCTGCTACGTTCCCCAACAG 59.680 55.000 0.00 0.00 32.14 3.16
5415 5570 0.759959 TTCTGCTACGTTCCCCAACA 59.240 50.000 0.00 0.00 32.14 3.33
5443 5598 5.185454 TGATCTTGGTGATGCGTAGAAATT 58.815 37.500 0.00 0.00 35.14 1.82
5444 5599 4.769688 TGATCTTGGTGATGCGTAGAAAT 58.230 39.130 0.00 0.00 35.14 2.17
5479 5636 0.461961 CCTTCCCCTCGTTGCTAGAG 59.538 60.000 0.00 0.00 35.60 2.43
5491 5653 0.267960 TAGATCCACTCCCCTTCCCC 59.732 60.000 0.00 0.00 0.00 4.81
5559 5724 2.015736 TCACTACGAGTACGACTCCC 57.984 55.000 8.73 0.00 42.12 4.30
5576 5741 2.602257 ATCAACCGCGATCTGAATCA 57.398 45.000 8.23 0.00 31.76 2.57
5620 5795 2.970324 GTGTTGAACGCGGAGGCA 60.970 61.111 12.47 0.00 39.92 4.75
5708 5884 1.818363 CATCGTGCTGCTGCTGGAT 60.818 57.895 17.00 14.87 40.48 3.41
5725 5901 3.245346 TCCATCACCACCACGCCA 61.245 61.111 0.00 0.00 0.00 5.69
5778 5954 4.507916 TCCTCCTCCTCTCCCGCG 62.508 72.222 0.00 0.00 0.00 6.46
5782 5958 0.996762 TCTCCCTCCTCCTCCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
5828 6011 1.009389 GCCCAAGAGACACGAGAACG 61.009 60.000 0.00 0.00 45.75 3.95
5835 6018 2.360475 GGGCTGCCCAAGAGACAC 60.360 66.667 32.46 0.97 44.65 3.67
5845 6028 0.251165 TAGTTGAGGTTTGGGCTGCC 60.251 55.000 11.05 11.05 0.00 4.85
5846 6029 1.839424 ATAGTTGAGGTTTGGGCTGC 58.161 50.000 0.00 0.00 0.00 5.25
5847 6030 7.607991 CCTTATATATAGTTGAGGTTTGGGCTG 59.392 40.741 1.41 0.00 0.00 4.85
5848 6031 7.257053 CCCTTATATATAGTTGAGGTTTGGGCT 60.257 40.741 7.23 0.00 0.00 5.19
5849 6032 6.884836 CCCTTATATATAGTTGAGGTTTGGGC 59.115 42.308 7.23 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.