Multiple sequence alignment - TraesCS7D01G512300

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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 TraesCS7D01G512300 chr7D 100.000 3233 0 0 1 3233 614057912 614061144 0.000000e+00 5971.0
1 TraesCS7D01G512300 chr7D 85.057 87 12 1 2628 2713 524442820 524442906 1.600000e-13 87.9
2 TraesCS7D01G512300 chr7D 74.093 193 44 3 1357 1549 614081406 614081220 1.240000e-09 75.0
3 TraesCS7D01G512300 chr7A 92.511 2417 150 7 848 3233 706137334 706139750 0.000000e+00 3432.0
4 TraesCS7D01G512300 chr7A 78.846 1196 197 29 1092 2270 706091989 706093145 0.000000e+00 756.0
5 TraesCS7D01G512300 chr7A 91.471 469 37 3 90 556 706136453 706136920 2.720000e-180 641.0
6 TraesCS7D01G512300 chr7A 94.444 216 7 1 548 758 706137075 706137290 8.650000e-86 327.0
7 TraesCS7D01G512300 chr7A 94.872 39 2 0 1515 1553 695934447 695934409 9.680000e-06 62.1
8 TraesCS7D01G512300 chr1D 78.117 754 138 15 2491 3223 480970723 480971470 1.370000e-123 453.0
9 TraesCS7D01G512300 chr5B 77.128 787 137 25 2446 3210 44459714 44460479 1.790000e-112 416.0
10 TraesCS7D01G512300 chr5B 76.385 343 72 9 2533 2871 101574481 101574144 3.310000e-40 176.0
11 TraesCS7D01G512300 chr5B 77.509 289 60 5 2857 3142 55544544 55544258 5.550000e-38 169.0
12 TraesCS7D01G512300 chr4B 76.156 692 131 18 2441 3112 377379412 377378735 1.860000e-87 333.0
13 TraesCS7D01G512300 chr4B 80.533 375 72 1 2488 2861 116956925 116956551 1.470000e-73 287.0
14 TraesCS7D01G512300 chr4B 75.478 575 102 22 2492 3045 163834516 163833960 8.960000e-61 244.0
15 TraesCS7D01G512300 chr4B 95.000 40 2 0 2788 2827 437852541 437852580 2.690000e-06 63.9
16 TraesCS7D01G512300 chr4A 85.547 256 29 8 188 438 631371665 631371413 8.900000e-66 261.0
17 TraesCS7D01G512300 chr3A 85.214 257 34 4 188 441 703404043 703404298 8.900000e-66 261.0
18 TraesCS7D01G512300 chr3A 84.980 253 33 5 188 437 111839848 111840098 5.350000e-63 252.0
19 TraesCS7D01G512300 chr3A 84.921 252 34 4 190 438 597887778 597888028 5.350000e-63 252.0
20 TraesCS7D01G512300 chr3A 72.553 470 107 8 2661 3111 1198021 1197555 2.020000e-27 134.0
21 TraesCS7D01G512300 chr1A 84.906 265 33 7 188 447 346468168 346467906 8.900000e-66 261.0
22 TraesCS7D01G512300 chr5A 85.944 249 24 11 188 429 576130985 576131229 4.140000e-64 255.0
23 TraesCS7D01G512300 chr5A 84.706 255 34 5 188 438 299295050 299294797 1.930000e-62 250.0
24 TraesCS7D01G512300 chr6A 84.706 255 34 5 188 438 547740502 547740755 1.930000e-62 250.0
25 TraesCS7D01G512300 chr2B 79.668 241 46 3 2857 3095 397010130 397010369 1.540000e-38 171.0
26 TraesCS7D01G512300 chr2B 100.000 28 0 0 3067 3094 3904781 3904754 6.000000e-03 52.8
27 TraesCS7D01G512300 chr2B 100.000 28 0 0 3067 3094 4183934 4183907 6.000000e-03 52.8
28 TraesCS7D01G512300 chr2A 73.846 455 94 12 2661 3095 71111173 71110724 1.200000e-34 158.0
29 TraesCS7D01G512300 chr2A 74.619 197 44 6 2932 3126 58906784 58906592 7.430000e-12 82.4
30 TraesCS7D01G512300 chrUn 77.821 257 50 5 2857 3109 8783864 8784117 5.590000e-33 152.0
31 TraesCS7D01G512300 chr2D 74.550 389 77 12 2743 3113 489939642 489939258 2.010000e-32 150.0
32 TraesCS7D01G512300 chr3D 85.057 87 12 1 2628 2713 472316108 472316022 1.600000e-13 87.9
33 TraesCS7D01G512300 chr3D 83.908 87 13 1 2628 2713 91977985 91977899 7.430000e-12 82.4
34 TraesCS7D01G512300 chr3B 81.034 116 16 5 2758 2871 257088271 257088160 1.600000e-13 87.9


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 TraesCS7D01G512300 chr7D 614057912 614061144 3232 False 5971.000000 5971 100.000000 1 3233 1 chr7D.!!$F2 3232
1 TraesCS7D01G512300 chr7A 706136453 706139750 3297 False 1466.666667 3432 92.808667 90 3233 3 chr7A.!!$F2 3143
2 TraesCS7D01G512300 chr7A 706091989 706093145 1156 False 756.000000 756 78.846000 1092 2270 1 chr7A.!!$F1 1178
3 TraesCS7D01G512300 chr1D 480970723 480971470 747 False 453.000000 453 78.117000 2491 3223 1 chr1D.!!$F1 732
4 TraesCS7D01G512300 chr5B 44459714 44460479 765 False 416.000000 416 77.128000 2446 3210 1 chr5B.!!$F1 764
5 TraesCS7D01G512300 chr4B 377378735 377379412 677 True 333.000000 333 76.156000 2441 3112 1 chr4B.!!$R3 671
6 TraesCS7D01G512300 chr4B 163833960 163834516 556 True 244.000000 244 75.478000 2492 3045 1 chr4B.!!$R2 553

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
806 986 0.247736 AGCTAGGAAGTCGCCACAAG 59.752 55.0 0.00 0.00 0.00 3.16 F
1795 1993 0.026803 GCCATTGACGATGTCGAAGC 59.973 55.0 9.67 0.38 43.02 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2112 0.109597 CTTCTTCCAACGCATGCACC 60.110 55.0 19.57 0.00 0.00 5.01 R
2923 3168 0.179137 GACTCCACATCGTCGATGCA 60.179 55.0 30.31 16.14 43.15 3.96 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
18 19 3.058115 CCACACATTGCCATGCATG 57.942 52.632 20.19 20.19 38.76 4.06
19 20 0.248012 CCACACATTGCCATGCATGT 59.752 50.000 24.58 4.09 38.76 3.21
20 21 1.635844 CACACATTGCCATGCATGTC 58.364 50.000 24.58 13.73 38.76 3.06
21 22 1.067495 CACACATTGCCATGCATGTCA 60.067 47.619 24.58 16.53 38.76 3.58
22 23 1.619332 ACACATTGCCATGCATGTCAA 59.381 42.857 23.87 23.87 38.76 3.18
23 24 2.037381 ACACATTGCCATGCATGTCAAA 59.963 40.909 25.19 15.93 38.76 2.69
24 25 3.266636 CACATTGCCATGCATGTCAAAT 58.733 40.909 25.19 17.30 38.76 2.32
25 26 3.308595 CACATTGCCATGCATGTCAAATC 59.691 43.478 25.19 8.00 38.76 2.17
26 27 3.055747 ACATTGCCATGCATGTCAAATCA 60.056 39.130 25.19 4.76 38.76 2.57
27 28 3.897141 TTGCCATGCATGTCAAATCAT 57.103 38.095 20.07 0.00 38.76 2.45
28 29 3.897141 TGCCATGCATGTCAAATCATT 57.103 38.095 24.58 0.00 31.71 2.57
29 30 3.526534 TGCCATGCATGTCAAATCATTG 58.473 40.909 24.58 6.89 33.77 2.82
30 31 2.286833 GCCATGCATGTCAAATCATTGC 59.713 45.455 24.58 12.87 36.45 3.56
31 32 3.792401 CCATGCATGTCAAATCATTGCT 58.208 40.909 24.58 0.00 36.45 3.91
32 33 3.802139 CCATGCATGTCAAATCATTGCTC 59.198 43.478 24.58 0.00 36.45 4.26
33 34 3.513680 TGCATGTCAAATCATTGCTCC 57.486 42.857 0.00 0.00 36.45 4.70
34 35 2.826725 TGCATGTCAAATCATTGCTCCA 59.173 40.909 0.00 0.00 36.45 3.86
35 36 3.184541 GCATGTCAAATCATTGCTCCAC 58.815 45.455 0.00 0.00 36.45 4.02
36 37 3.367600 GCATGTCAAATCATTGCTCCACA 60.368 43.478 0.00 0.00 36.45 4.17
37 38 4.679639 GCATGTCAAATCATTGCTCCACAT 60.680 41.667 0.00 0.00 36.45 3.21
38 39 4.443913 TGTCAAATCATTGCTCCACATG 57.556 40.909 0.00 0.00 36.45 3.21
39 40 3.184541 GTCAAATCATTGCTCCACATGC 58.815 45.455 0.00 0.00 36.45 4.06
40 41 2.159352 TCAAATCATTGCTCCACATGCG 60.159 45.455 0.00 0.00 36.45 4.73
41 42 1.753930 AATCATTGCTCCACATGCGA 58.246 45.000 0.00 0.00 0.00 5.10
42 43 1.753930 ATCATTGCTCCACATGCGAA 58.246 45.000 0.00 0.00 0.00 4.70
43 44 1.089112 TCATTGCTCCACATGCGAAG 58.911 50.000 0.00 0.00 0.00 3.79
44 45 1.089112 CATTGCTCCACATGCGAAGA 58.911 50.000 0.00 0.00 0.00 2.87
45 46 1.469703 CATTGCTCCACATGCGAAGAA 59.530 47.619 0.00 0.00 0.00 2.52
46 47 1.159285 TTGCTCCACATGCGAAGAAG 58.841 50.000 0.00 0.00 0.00 2.85
47 48 0.321346 TGCTCCACATGCGAAGAAGA 59.679 50.000 0.00 0.00 0.00 2.87
48 49 1.005340 GCTCCACATGCGAAGAAGAG 58.995 55.000 0.00 0.00 0.00 2.85
49 50 1.649664 CTCCACATGCGAAGAAGAGG 58.350 55.000 0.00 0.00 0.00 3.69
50 51 1.205655 CTCCACATGCGAAGAAGAGGA 59.794 52.381 0.00 0.00 0.00 3.71
51 52 1.205655 TCCACATGCGAAGAAGAGGAG 59.794 52.381 0.00 0.00 0.00 3.69
52 53 1.205655 CCACATGCGAAGAAGAGGAGA 59.794 52.381 0.00 0.00 0.00 3.71
53 54 2.158986 CCACATGCGAAGAAGAGGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
54 55 3.068732 CCACATGCGAAGAAGAGGAGATA 59.931 47.826 0.00 0.00 0.00 1.98
55 56 4.297510 CACATGCGAAGAAGAGGAGATAG 58.702 47.826 0.00 0.00 0.00 2.08
56 57 3.320541 ACATGCGAAGAAGAGGAGATAGG 59.679 47.826 0.00 0.00 0.00 2.57
57 58 1.683917 TGCGAAGAAGAGGAGATAGGC 59.316 52.381 0.00 0.00 0.00 3.93
58 59 1.960689 GCGAAGAAGAGGAGATAGGCT 59.039 52.381 0.00 0.00 0.00 4.58
59 60 2.364002 GCGAAGAAGAGGAGATAGGCTT 59.636 50.000 0.00 0.00 0.00 4.35
60 61 3.798548 GCGAAGAAGAGGAGATAGGCTTG 60.799 52.174 0.00 0.00 0.00 4.01
61 62 3.634448 CGAAGAAGAGGAGATAGGCTTGA 59.366 47.826 0.00 0.00 0.00 3.02
62 63 4.098654 CGAAGAAGAGGAGATAGGCTTGAA 59.901 45.833 0.00 0.00 0.00 2.69
63 64 5.221422 CGAAGAAGAGGAGATAGGCTTGAAT 60.221 44.000 0.00 0.00 0.00 2.57
64 65 5.806654 AGAAGAGGAGATAGGCTTGAATC 57.193 43.478 0.00 0.00 0.00 2.52
65 66 5.215069 AGAAGAGGAGATAGGCTTGAATCA 58.785 41.667 0.00 0.00 0.00 2.57
66 67 5.845614 AGAAGAGGAGATAGGCTTGAATCAT 59.154 40.000 0.00 0.00 0.00 2.45
67 68 5.486735 AGAGGAGATAGGCTTGAATCATG 57.513 43.478 0.00 0.00 0.00 3.07
68 69 4.906664 AGAGGAGATAGGCTTGAATCATGT 59.093 41.667 0.00 0.00 0.00 3.21
69 70 5.011943 AGAGGAGATAGGCTTGAATCATGTC 59.988 44.000 0.00 0.00 0.00 3.06
70 71 4.657504 AGGAGATAGGCTTGAATCATGTCA 59.342 41.667 3.61 0.00 0.00 3.58
71 72 4.754114 GGAGATAGGCTTGAATCATGTCAC 59.246 45.833 3.61 0.00 0.00 3.67
72 73 5.454471 GGAGATAGGCTTGAATCATGTCACT 60.454 44.000 3.61 0.37 0.00 3.41
73 74 5.609423 AGATAGGCTTGAATCATGTCACTC 58.391 41.667 3.61 0.18 0.00 3.51
74 75 2.996631 AGGCTTGAATCATGTCACTCC 58.003 47.619 3.61 0.00 0.00 3.85
75 76 2.019984 GGCTTGAATCATGTCACTCCC 58.980 52.381 0.00 0.00 0.00 4.30
76 77 2.356535 GGCTTGAATCATGTCACTCCCT 60.357 50.000 0.00 0.00 0.00 4.20
77 78 3.118261 GGCTTGAATCATGTCACTCCCTA 60.118 47.826 0.00 0.00 0.00 3.53
78 79 4.125703 GCTTGAATCATGTCACTCCCTAG 58.874 47.826 0.00 0.00 0.00 3.02
79 80 4.141846 GCTTGAATCATGTCACTCCCTAGA 60.142 45.833 0.00 0.00 0.00 2.43
80 81 5.627735 GCTTGAATCATGTCACTCCCTAGAA 60.628 44.000 0.00 0.00 0.00 2.10
81 82 5.344743 TGAATCATGTCACTCCCTAGAAC 57.655 43.478 0.00 0.00 0.00 3.01
82 83 4.777366 TGAATCATGTCACTCCCTAGAACA 59.223 41.667 0.00 0.00 0.00 3.18
83 84 5.248248 TGAATCATGTCACTCCCTAGAACAA 59.752 40.000 0.00 0.00 0.00 2.83
84 85 4.808414 TCATGTCACTCCCTAGAACAAG 57.192 45.455 0.00 0.00 0.00 3.16
85 86 3.055819 TCATGTCACTCCCTAGAACAAGC 60.056 47.826 0.00 0.00 0.00 4.01
86 87 2.609747 TGTCACTCCCTAGAACAAGCT 58.390 47.619 0.00 0.00 0.00 3.74
87 88 2.300152 TGTCACTCCCTAGAACAAGCTG 59.700 50.000 0.00 0.00 0.00 4.24
88 89 2.300437 GTCACTCCCTAGAACAAGCTGT 59.700 50.000 0.00 0.00 0.00 4.40
147 148 4.540099 TGATGTATGTCCTTCCTTCCCTTT 59.460 41.667 0.00 0.00 0.00 3.11
154 155 4.909088 TGTCCTTCCTTCCCTTTTGTACTA 59.091 41.667 0.00 0.00 0.00 1.82
164 165 9.638176 CCTTCCCTTTTGTACTATCTACTAGTA 57.362 37.037 1.89 1.89 41.10 1.82
183 184 7.690256 ACTAGTAAAGGTCAATTTGATCTGGT 58.310 34.615 12.82 7.07 36.70 4.00
185 186 9.667107 CTAGTAAAGGTCAATTTGATCTGGTTA 57.333 33.333 12.82 6.37 36.70 2.85
202 204 2.889045 GGTTAAACCAGGGTTCAAGTCC 59.111 50.000 3.82 0.58 38.42 3.85
212 214 1.301716 TTCAAGTCCTGGTGCTCGC 60.302 57.895 0.00 0.00 0.00 5.03
249 251 9.099454 GATTTATTTTAGGATCTTCGGCGATAT 57.901 33.333 11.76 7.80 0.00 1.63
252 254 4.611310 TTAGGATCTTCGGCGATATACG 57.389 45.455 11.76 0.00 45.66 3.06
266 268 4.155462 GCGATATACGTTCAGTGGGAGATA 59.845 45.833 0.00 0.00 44.60 1.98
269 271 7.313646 CGATATACGTTCAGTGGGAGATATTT 58.686 38.462 0.00 0.00 37.22 1.40
271 273 6.732896 ATACGTTCAGTGGGAGATATTTCT 57.267 37.500 0.00 0.00 33.88 2.52
280 282 6.015856 CAGTGGGAGATATTTCTGTCGACTAT 60.016 42.308 17.92 5.53 30.30 2.12
295 297 2.856557 CGACTATGATGCGCCTATGATG 59.143 50.000 4.18 0.00 0.00 3.07
308 310 5.670097 CGCCTATGATGACTTCGTAAAATG 58.330 41.667 0.00 0.00 0.00 2.32
332 334 3.902881 AGATGATATCCCGGCTCAATC 57.097 47.619 0.00 0.00 0.00 2.67
338 340 1.467678 ATCCCGGCTCAATCTCTCGG 61.468 60.000 0.00 0.00 40.32 4.63
339 341 2.127869 CCCGGCTCAATCTCTCGGA 61.128 63.158 0.00 0.00 42.94 4.55
355 358 1.832912 GGAGGTGCTCATAGGGGTG 59.167 63.158 0.00 0.00 31.08 4.61
358 361 2.757124 GGTGCTCATAGGGGTGGGG 61.757 68.421 0.00 0.00 0.00 4.96
363 366 2.270874 CTCATAGGGGTGGGGTGTGC 62.271 65.000 0.00 0.00 0.00 4.57
378 381 1.722163 GTGCGTGTGTGCGTTCATG 60.722 57.895 0.00 0.00 37.81 3.07
379 382 1.884926 TGCGTGTGTGCGTTCATGA 60.885 52.632 0.00 0.00 37.81 3.07
393 396 4.388773 GCGTTCATGAAAGTGAGTGTATGA 59.611 41.667 20.26 0.00 0.00 2.15
394 397 5.445142 GCGTTCATGAAAGTGAGTGTATGAG 60.445 44.000 20.26 0.00 0.00 2.90
408 411 6.374333 TGAGTGTATGAGCGTATATATGAGCA 59.626 38.462 6.12 3.33 0.00 4.26
430 433 8.396272 AGCATTAGTGTCTTTACTGATGTTTT 57.604 30.769 10.87 0.00 43.02 2.43
458 461 7.485418 AAAATATTACGTACGCCATGATGAA 57.515 32.000 16.72 0.00 0.00 2.57
569 735 9.869757 ATAATAATACCTTTGCTTTTGTTCACC 57.130 29.630 0.00 0.00 0.00 4.02
640 811 2.738846 GTCCGTACACTCACTCGTAGAA 59.261 50.000 0.00 0.00 34.09 2.10
642 813 4.005650 TCCGTACACTCACTCGTAGAATT 58.994 43.478 0.00 0.00 34.09 2.17
758 929 1.829222 CAAACCCTAAGTCGCCTAGGA 59.171 52.381 14.75 0.00 32.87 2.94
760 931 0.333993 ACCCTAAGTCGCCTAGGACA 59.666 55.000 14.75 0.00 39.42 4.02
785 965 1.228657 GGCACGGAAACTGTGGAGAC 61.229 60.000 11.76 0.00 36.05 3.36
786 966 0.249911 GCACGGAAACTGTGGAGACT 60.250 55.000 11.76 0.00 36.05 3.24
787 967 1.000506 GCACGGAAACTGTGGAGACTA 59.999 52.381 11.76 0.00 36.05 2.59
789 969 1.272769 ACGGAAACTGTGGAGACTAGC 59.727 52.381 0.00 0.00 0.00 3.42
790 970 1.546476 CGGAAACTGTGGAGACTAGCT 59.454 52.381 0.00 0.00 0.00 3.32
791 971 2.753452 CGGAAACTGTGGAGACTAGCTA 59.247 50.000 0.00 0.00 0.00 3.32
792 972 3.181495 CGGAAACTGTGGAGACTAGCTAG 60.181 52.174 19.44 19.44 0.00 3.42
793 973 3.131400 GGAAACTGTGGAGACTAGCTAGG 59.869 52.174 24.35 6.76 0.00 3.02
794 974 3.741245 AACTGTGGAGACTAGCTAGGA 57.259 47.619 24.35 0.55 0.00 2.94
795 975 3.741245 ACTGTGGAGACTAGCTAGGAA 57.259 47.619 24.35 2.66 0.00 3.36
796 976 3.626930 ACTGTGGAGACTAGCTAGGAAG 58.373 50.000 24.35 12.25 0.00 3.46
797 977 3.010808 ACTGTGGAGACTAGCTAGGAAGT 59.989 47.826 24.35 6.10 0.00 3.01
798 978 3.622630 TGTGGAGACTAGCTAGGAAGTC 58.377 50.000 24.35 15.22 42.02 3.01
799 979 2.614983 GTGGAGACTAGCTAGGAAGTCG 59.385 54.545 24.35 0.00 45.47 4.18
800 980 1.605232 GGAGACTAGCTAGGAAGTCGC 59.395 57.143 24.35 16.15 45.47 5.19
801 981 1.605232 GAGACTAGCTAGGAAGTCGCC 59.395 57.143 24.35 9.29 45.47 5.54
802 982 1.064611 AGACTAGCTAGGAAGTCGCCA 60.065 52.381 24.35 0.00 45.47 5.69
803 983 1.065851 GACTAGCTAGGAAGTCGCCAC 59.934 57.143 24.35 0.20 33.38 5.01
804 984 1.103803 CTAGCTAGGAAGTCGCCACA 58.896 55.000 13.32 0.00 0.00 4.17
805 985 1.476891 CTAGCTAGGAAGTCGCCACAA 59.523 52.381 13.32 0.00 0.00 3.33
806 986 0.247736 AGCTAGGAAGTCGCCACAAG 59.752 55.000 0.00 0.00 0.00 3.16
807 987 1.362406 GCTAGGAAGTCGCCACAAGC 61.362 60.000 0.00 0.00 38.52 4.01
808 988 0.741221 CTAGGAAGTCGCCACAAGCC 60.741 60.000 0.00 0.00 38.78 4.35
809 989 2.180159 TAGGAAGTCGCCACAAGCCC 62.180 60.000 0.00 0.00 38.78 5.19
810 990 2.281484 GAAGTCGCCACAAGCCCA 60.281 61.111 0.00 0.00 38.78 5.36
811 991 2.594592 AAGTCGCCACAAGCCCAC 60.595 61.111 0.00 0.00 38.78 4.61
812 992 4.988598 AGTCGCCACAAGCCCACG 62.989 66.667 0.00 0.00 38.78 4.94
813 993 4.980805 GTCGCCACAAGCCCACGA 62.981 66.667 0.00 0.00 38.78 4.35
814 994 4.015406 TCGCCACAAGCCCACGAT 62.015 61.111 0.00 0.00 38.78 3.73
815 995 3.803082 CGCCACAAGCCCACGATG 61.803 66.667 0.00 0.00 38.78 3.84
816 996 4.120331 GCCACAAGCCCACGATGC 62.120 66.667 0.00 0.00 34.35 3.91
817 997 3.803082 CCACAAGCCCACGATGCG 61.803 66.667 0.00 0.00 0.00 4.73
818 998 3.049674 CACAAGCCCACGATGCGT 61.050 61.111 0.00 0.00 42.36 5.24
837 1017 2.916423 CGTGTGCGCTGATCGATC 59.084 61.111 18.72 18.72 41.67 3.69
838 1018 1.873572 CGTGTGCGCTGATCGATCA 60.874 57.895 25.80 25.80 41.67 2.92
839 1019 1.633171 GTGTGCGCTGATCGATCAC 59.367 57.895 23.99 18.25 41.67 3.06
840 1020 1.873572 TGTGCGCTGATCGATCACG 60.874 57.895 29.54 29.54 41.67 4.35
841 1021 1.874019 GTGCGCTGATCGATCACGT 60.874 57.895 31.55 4.04 41.67 4.49
842 1022 1.873572 TGCGCTGATCGATCACGTG 60.874 57.895 31.55 27.43 41.67 4.49
843 1023 1.586303 GCGCTGATCGATCACGTGA 60.586 57.895 31.55 22.48 41.67 4.35
844 1024 1.802300 GCGCTGATCGATCACGTGAC 61.802 60.000 31.55 21.73 41.67 3.67
845 1025 0.523335 CGCTGATCGATCACGTGACA 60.523 55.000 27.42 12.93 41.67 3.58
846 1026 1.629013 GCTGATCGATCACGTGACAA 58.371 50.000 23.99 9.67 40.69 3.18
864 1044 5.009811 GTGACAAGTTATAGTAGAGGCCGAT 59.990 44.000 0.00 0.00 0.00 4.18
867 1047 6.885922 ACAAGTTATAGTAGAGGCCGATTTT 58.114 36.000 0.00 0.00 0.00 1.82
879 1059 2.100749 GGCCGATTTTATCCTGGTTTGG 59.899 50.000 0.00 0.00 0.00 3.28
900 1080 2.634982 TACCTACGTACGCCACTTTG 57.365 50.000 16.72 0.00 0.00 2.77
959 1139 3.021177 TCCGGCCGGATATATCACATA 57.979 47.619 42.66 16.84 39.76 2.29
1012 1200 2.558359 CCAACCAGCAGAAACCCTAAAG 59.442 50.000 0.00 0.00 0.00 1.85
1017 1205 3.367703 CCAGCAGAAACCCTAAAGCAATG 60.368 47.826 0.00 0.00 0.00 2.82
1031 1219 2.111384 AGCAATGGGACGTATGTCTCT 58.889 47.619 15.92 0.00 46.35 3.10
1034 1222 2.430694 CAATGGGACGTATGTCTCTCCA 59.569 50.000 15.92 13.92 46.35 3.86
1039 1230 0.753262 ACGTATGTCTCTCCATGGCC 59.247 55.000 6.96 0.00 0.00 5.36
1075 1266 2.888534 GACGCCGCCTAAATCGCA 60.889 61.111 0.00 0.00 0.00 5.10
1078 1269 2.551270 GCCGCCTAAATCGCATCG 59.449 61.111 0.00 0.00 0.00 3.84
1155 1346 3.362399 CTCCAGACGCCTGCACGAT 62.362 63.158 3.48 0.00 39.07 3.73
1245 1440 4.760047 CCTCCCGTGTTCCTGCCG 62.760 72.222 0.00 0.00 0.00 5.69
1309 1504 3.909732 CACTCCTCTATCAAGTCCTCCT 58.090 50.000 0.00 0.00 0.00 3.69
1348 1543 1.300931 ATCCATGTCGCGAATCCGG 60.301 57.895 12.06 9.74 36.06 5.14
1349 1544 2.028125 ATCCATGTCGCGAATCCGGT 62.028 55.000 12.06 0.00 36.06 5.28
1350 1545 2.525248 CCATGTCGCGAATCCGGTG 61.525 63.158 12.06 3.52 36.06 4.94
1360 1555 0.179045 GAATCCGGTGGGTCCATCAG 60.179 60.000 0.00 0.00 35.57 2.90
1362 1557 4.489771 CCGGTGGGTCCATCAGCC 62.490 72.222 0.00 0.00 43.86 4.85
1382 1577 1.662044 CAAGGAACTGGCTTGCCAC 59.338 57.895 10.65 1.16 40.86 5.01
1444 1639 0.972983 ACCAGGACTCATGGACCTCG 60.973 60.000 16.68 0.00 40.51 4.63
1463 1658 2.930019 CACTGGAGCCTGGACCCA 60.930 66.667 0.00 2.31 0.00 4.51
1487 1682 1.203758 ACCAGCATACGATGACGACAA 59.796 47.619 0.00 0.00 42.66 3.18
1488 1683 1.854743 CCAGCATACGATGACGACAAG 59.145 52.381 0.00 0.00 42.66 3.16
1489 1684 2.530177 CAGCATACGATGACGACAAGT 58.470 47.619 0.00 0.00 42.66 3.16
1500 1695 1.956170 CGACAAGTCGCCACAGCTT 60.956 57.895 9.85 0.00 46.50 3.74
1518 1713 2.666526 GAGAATCCCCGCGGCATC 60.667 66.667 22.85 14.33 0.00 3.91
1563 1758 2.094894 CCTCTACGACTCTAAACGCGAA 59.905 50.000 15.93 0.00 0.00 4.70
1574 1769 4.690719 ACGCGAATCGGCCCACAA 62.691 61.111 15.93 0.00 43.86 3.33
1650 1845 4.075682 TGAAAACCACGCTGGATTATTCA 58.924 39.130 10.46 10.64 40.96 2.57
1695 1890 4.547905 ACGGCGGCGTATCACGAG 62.548 66.667 36.78 3.91 46.05 4.18
1713 1911 2.048603 GGGCAAGATCCTGGTGTGC 61.049 63.158 0.00 0.00 34.42 4.57
1728 1926 2.429571 TGCGCGGACGTGAACTAC 60.430 61.111 8.83 0.00 42.83 2.73
1768 1966 1.065701 ACGATCATAGCGTCACTCACC 59.934 52.381 0.00 0.00 37.42 4.02
1795 1993 0.026803 GCCATTGACGATGTCGAAGC 59.973 55.000 9.67 0.38 43.02 3.86
1838 2036 5.596772 AGAGAAATAGCTACTTCCTGGAGTC 59.403 44.000 11.17 1.96 0.00 3.36
1842 2040 3.176924 AGCTACTTCCTGGAGTCTCAA 57.823 47.619 1.47 0.00 0.00 3.02
1864 2062 0.916086 TCAACTGTTGTGGGTGTCCT 59.084 50.000 19.12 0.00 0.00 3.85
1884 2082 6.069673 TGTCCTTCATGGTCAAATACAGGTAT 60.070 38.462 0.00 0.00 37.07 2.73
1934 2135 0.109597 GTGCATGCGTTGGAAGAAGG 60.110 55.000 14.09 0.00 0.00 3.46
1940 2141 0.238553 GCGTTGGAAGAAGGCAAGAC 59.761 55.000 0.00 0.00 0.00 3.01
2067 2268 4.035208 GGGTGTGCCTATTTCATCTTTACG 59.965 45.833 0.00 0.00 34.45 3.18
2076 2277 6.419710 CCTATTTCATCTTTACGCACGATGTA 59.580 38.462 0.00 0.00 36.72 2.29
2116 2317 1.235281 CGGTGAGGTCAGTCTCGTGA 61.235 60.000 0.00 0.00 36.61 4.35
2234 2441 3.300009 GGCTTCAACAAGAACATTGACG 58.700 45.455 0.00 0.00 34.61 4.35
2331 2538 4.371855 TTTACCACGTGCAACATTTTCA 57.628 36.364 10.91 0.00 35.74 2.69
2334 2541 2.946329 ACCACGTGCAACATTTTCACTA 59.054 40.909 10.91 0.00 35.74 2.74
2417 2639 2.439338 GTGTGTGTGTGGTGGCCA 60.439 61.111 0.00 0.00 0.00 5.36
2667 2895 2.760650 ACACGATGCTAGATGAGGTTCA 59.239 45.455 0.00 0.00 0.00 3.18
2838 3067 3.747854 TGATCAGATGACATCAGAGCC 57.252 47.619 19.53 12.48 31.24 4.70
2884 3129 3.221222 GCATAGGCACGAGGGACT 58.779 61.111 0.00 0.00 40.98 3.85
2912 3157 1.374758 CTTCTGCGGTGGAGTGGTC 60.375 63.158 0.00 0.00 0.00 4.02
2923 3168 0.608640 GGAGTGGTCGTTCCTGTGAT 59.391 55.000 1.80 0.00 37.07 3.06
2946 3191 0.390735 TCGACGATGTGGAGTCTCGA 60.391 55.000 6.52 0.88 36.32 4.04
2967 3212 2.672651 CATGGCGTTGCAGGGTCA 60.673 61.111 0.00 0.00 0.00 4.02
3046 3292 2.978010 CGTCAACGCCAGGCCTTT 60.978 61.111 0.00 0.00 0.00 3.11
3050 3296 0.955905 TCAACGCCAGGCCTTTTAAC 59.044 50.000 0.00 0.00 0.00 2.01
3057 3303 2.942306 GCCAGGCCTTTTAACGTGGATA 60.942 50.000 0.00 0.00 43.01 2.59
3149 3405 3.021695 TGACCACTAAGAGTATGTCGGG 58.978 50.000 0.00 0.00 34.04 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.258676 TGACATGCATGGCAATGTGT 58.741 45.000 32.92 9.12 44.23 3.72
8 9 3.526534 CAATGATTTGACATGCATGGCA 58.473 40.909 31.52 31.52 45.84 4.92
9 10 2.286833 GCAATGATTTGACATGCATGGC 59.713 45.455 29.41 27.98 34.60 4.40
10 11 3.792401 AGCAATGATTTGACATGCATGG 58.208 40.909 29.41 12.50 34.60 3.66
11 12 3.802139 GGAGCAATGATTTGACATGCATG 59.198 43.478 25.09 25.09 34.60 4.06
12 13 3.449377 TGGAGCAATGATTTGACATGCAT 59.551 39.130 0.00 0.00 34.60 3.96
13 14 2.826725 TGGAGCAATGATTTGACATGCA 59.173 40.909 0.00 0.00 34.60 3.96
14 15 3.184541 GTGGAGCAATGATTTGACATGC 58.815 45.455 0.00 0.00 34.60 4.06
15 16 4.443913 TGTGGAGCAATGATTTGACATG 57.556 40.909 0.00 0.00 34.60 3.21
16 17 4.679639 GCATGTGGAGCAATGATTTGACAT 60.680 41.667 0.00 0.00 34.60 3.06
17 18 3.367600 GCATGTGGAGCAATGATTTGACA 60.368 43.478 0.00 0.00 34.60 3.58
18 19 3.184541 GCATGTGGAGCAATGATTTGAC 58.815 45.455 0.00 0.00 34.60 3.18
19 20 2.159352 CGCATGTGGAGCAATGATTTGA 60.159 45.455 0.00 0.00 34.60 2.69
20 21 2.159352 TCGCATGTGGAGCAATGATTTG 60.159 45.455 6.39 0.00 35.85 2.32
21 22 2.093890 TCGCATGTGGAGCAATGATTT 58.906 42.857 6.39 0.00 0.00 2.17
22 23 1.753930 TCGCATGTGGAGCAATGATT 58.246 45.000 6.39 0.00 0.00 2.57
23 24 1.674441 CTTCGCATGTGGAGCAATGAT 59.326 47.619 6.39 0.00 0.00 2.45
24 25 1.089112 CTTCGCATGTGGAGCAATGA 58.911 50.000 6.39 0.00 0.00 2.57
25 26 1.089112 TCTTCGCATGTGGAGCAATG 58.911 50.000 9.90 0.00 0.00 2.82
26 27 1.741706 CTTCTTCGCATGTGGAGCAAT 59.258 47.619 9.90 0.00 0.00 3.56
27 28 1.159285 CTTCTTCGCATGTGGAGCAA 58.841 50.000 9.90 4.76 0.00 3.91
28 29 0.321346 TCTTCTTCGCATGTGGAGCA 59.679 50.000 9.90 0.00 0.00 4.26
29 30 1.005340 CTCTTCTTCGCATGTGGAGC 58.995 55.000 9.90 0.00 0.00 4.70
30 31 1.205655 TCCTCTTCTTCGCATGTGGAG 59.794 52.381 8.38 8.38 0.00 3.86
31 32 1.205655 CTCCTCTTCTTCGCATGTGGA 59.794 52.381 6.39 0.00 0.00 4.02
32 33 1.205655 TCTCCTCTTCTTCGCATGTGG 59.794 52.381 6.39 0.00 0.00 4.17
33 34 2.662006 TCTCCTCTTCTTCGCATGTG 57.338 50.000 0.00 0.00 0.00 3.21
34 35 3.320541 CCTATCTCCTCTTCTTCGCATGT 59.679 47.826 0.00 0.00 0.00 3.21
35 36 3.860378 GCCTATCTCCTCTTCTTCGCATG 60.860 52.174 0.00 0.00 0.00 4.06
36 37 2.298729 GCCTATCTCCTCTTCTTCGCAT 59.701 50.000 0.00 0.00 0.00 4.73
37 38 1.683917 GCCTATCTCCTCTTCTTCGCA 59.316 52.381 0.00 0.00 0.00 5.10
38 39 1.960689 AGCCTATCTCCTCTTCTTCGC 59.039 52.381 0.00 0.00 0.00 4.70
39 40 3.634448 TCAAGCCTATCTCCTCTTCTTCG 59.366 47.826 0.00 0.00 0.00 3.79
40 41 5.606348 TTCAAGCCTATCTCCTCTTCTTC 57.394 43.478 0.00 0.00 0.00 2.87
41 42 5.664908 TGATTCAAGCCTATCTCCTCTTCTT 59.335 40.000 0.00 0.00 0.00 2.52
42 43 5.215069 TGATTCAAGCCTATCTCCTCTTCT 58.785 41.667 0.00 0.00 0.00 2.85
43 44 5.543507 TGATTCAAGCCTATCTCCTCTTC 57.456 43.478 0.00 0.00 0.00 2.87
44 45 5.369110 ACATGATTCAAGCCTATCTCCTCTT 59.631 40.000 0.00 0.00 0.00 2.85
45 46 4.906664 ACATGATTCAAGCCTATCTCCTCT 59.093 41.667 0.00 0.00 0.00 3.69
46 47 5.221601 TGACATGATTCAAGCCTATCTCCTC 60.222 44.000 0.00 0.00 0.00 3.71
47 48 4.657504 TGACATGATTCAAGCCTATCTCCT 59.342 41.667 0.00 0.00 0.00 3.69
48 49 4.754114 GTGACATGATTCAAGCCTATCTCC 59.246 45.833 0.00 0.00 0.00 3.71
49 50 5.609423 AGTGACATGATTCAAGCCTATCTC 58.391 41.667 0.00 0.00 0.00 2.75
50 51 5.454471 GGAGTGACATGATTCAAGCCTATCT 60.454 44.000 0.00 0.00 0.00 1.98
51 52 4.754114 GGAGTGACATGATTCAAGCCTATC 59.246 45.833 0.00 0.00 0.00 2.08
52 53 4.445448 GGGAGTGACATGATTCAAGCCTAT 60.445 45.833 0.00 0.00 0.00 2.57
53 54 3.118261 GGGAGTGACATGATTCAAGCCTA 60.118 47.826 0.00 0.00 0.00 3.93
54 55 2.356535 GGGAGTGACATGATTCAAGCCT 60.357 50.000 0.00 0.00 0.00 4.58
55 56 2.019984 GGGAGTGACATGATTCAAGCC 58.980 52.381 0.00 0.00 0.00 4.35
56 57 2.996631 AGGGAGTGACATGATTCAAGC 58.003 47.619 0.00 0.00 0.00 4.01
57 58 5.604758 TCTAGGGAGTGACATGATTCAAG 57.395 43.478 0.00 0.00 0.00 3.02
58 59 5.248248 TGTTCTAGGGAGTGACATGATTCAA 59.752 40.000 0.00 0.00 0.00 2.69
59 60 4.777366 TGTTCTAGGGAGTGACATGATTCA 59.223 41.667 0.00 0.00 0.00 2.57
60 61 5.344743 TGTTCTAGGGAGTGACATGATTC 57.655 43.478 0.00 0.00 0.00 2.52
61 62 5.738909 CTTGTTCTAGGGAGTGACATGATT 58.261 41.667 0.00 0.00 0.00 2.57
62 63 4.383552 GCTTGTTCTAGGGAGTGACATGAT 60.384 45.833 0.00 0.00 0.00 2.45
63 64 3.055819 GCTTGTTCTAGGGAGTGACATGA 60.056 47.826 0.00 0.00 0.00 3.07
64 65 3.055530 AGCTTGTTCTAGGGAGTGACATG 60.056 47.826 0.00 0.00 0.00 3.21
65 66 3.055530 CAGCTTGTTCTAGGGAGTGACAT 60.056 47.826 0.00 0.00 0.00 3.06
66 67 2.300152 CAGCTTGTTCTAGGGAGTGACA 59.700 50.000 0.00 0.00 0.00 3.58
67 68 2.300437 ACAGCTTGTTCTAGGGAGTGAC 59.700 50.000 0.00 0.00 0.00 3.67
68 69 2.609747 ACAGCTTGTTCTAGGGAGTGA 58.390 47.619 0.00 0.00 0.00 3.41
69 70 3.070018 CAACAGCTTGTTCTAGGGAGTG 58.930 50.000 0.00 0.00 38.77 3.51
70 71 2.551071 GCAACAGCTTGTTCTAGGGAGT 60.551 50.000 0.00 0.00 38.77 3.85
71 72 2.079925 GCAACAGCTTGTTCTAGGGAG 58.920 52.381 0.00 0.00 38.77 4.30
72 73 1.608025 CGCAACAGCTTGTTCTAGGGA 60.608 52.381 0.00 0.00 38.77 4.20
73 74 0.798776 CGCAACAGCTTGTTCTAGGG 59.201 55.000 0.00 0.00 38.77 3.53
74 75 1.195448 CACGCAACAGCTTGTTCTAGG 59.805 52.381 0.00 0.00 38.77 3.02
75 76 1.398960 GCACGCAACAGCTTGTTCTAG 60.399 52.381 0.00 0.00 38.77 2.43
76 77 0.586319 GCACGCAACAGCTTGTTCTA 59.414 50.000 0.00 0.00 38.77 2.10
77 78 1.356624 GCACGCAACAGCTTGTTCT 59.643 52.632 0.00 0.00 38.77 3.01
78 79 0.931662 CTGCACGCAACAGCTTGTTC 60.932 55.000 0.00 0.00 38.77 3.18
79 80 1.064621 CTGCACGCAACAGCTTGTT 59.935 52.632 0.00 0.00 42.08 2.83
80 81 2.717485 CTGCACGCAACAGCTTGT 59.283 55.556 0.00 0.00 30.90 3.16
85 86 0.728129 CAATCAGCTGCACGCAACAG 60.728 55.000 9.47 0.00 42.61 3.16
86 87 1.283487 CAATCAGCTGCACGCAACA 59.717 52.632 9.47 0.00 42.61 3.33
87 88 0.318107 AACAATCAGCTGCACGCAAC 60.318 50.000 9.47 0.00 42.61 4.17
88 89 0.385029 AAACAATCAGCTGCACGCAA 59.615 45.000 9.47 0.00 42.61 4.85
164 165 7.070571 TGGTTTAACCAGATCAAATTGACCTTT 59.929 33.333 13.44 0.00 44.79 3.11
167 168 6.339587 TGGTTTAACCAGATCAAATTGACC 57.660 37.500 13.44 0.00 44.79 4.02
181 182 2.889045 GGACTTGAACCCTGGTTTAACC 59.111 50.000 7.27 7.27 38.60 2.85
183 184 3.827722 CAGGACTTGAACCCTGGTTTAA 58.172 45.455 2.55 4.61 44.68 1.52
185 186 2.364972 CAGGACTTGAACCCTGGTTT 57.635 50.000 2.55 0.00 44.68 3.27
202 204 1.600957 CAGGATAAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
249 251 5.421056 ACAGAAATATCTCCCACTGAACGTA 59.579 40.000 0.00 0.00 32.03 3.57
252 254 4.806247 CGACAGAAATATCTCCCACTGAAC 59.194 45.833 0.00 0.00 32.03 3.18
266 268 2.797156 GCGCATCATAGTCGACAGAAAT 59.203 45.455 19.50 3.01 0.00 2.17
269 271 0.030773 GGCGCATCATAGTCGACAGA 59.969 55.000 19.50 12.79 0.00 3.41
271 273 1.314730 TAGGCGCATCATAGTCGACA 58.685 50.000 19.50 4.13 32.86 4.35
280 282 2.759191 GAAGTCATCATAGGCGCATCA 58.241 47.619 10.83 0.00 0.00 3.07
308 310 4.537135 TGAGCCGGGATATCATCTTAAC 57.463 45.455 2.18 0.00 0.00 2.01
321 323 2.081425 CTCCGAGAGATTGAGCCGGG 62.081 65.000 2.18 0.00 40.48 5.73
332 334 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
338 340 1.700042 CCCACCCCTATGAGCACCTC 61.700 65.000 0.00 0.00 0.00 3.85
339 341 1.694169 CCCACCCCTATGAGCACCT 60.694 63.158 0.00 0.00 0.00 4.00
358 361 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
363 366 1.003972 ACTTTCATGAACGCACACACG 60.004 47.619 7.89 0.00 39.50 4.49
372 375 5.445142 CGCTCATACACTCACTTTCATGAAC 60.445 44.000 7.89 0.00 0.00 3.18
378 381 9.066939 CATATATACGCTCATACACTCACTTTC 57.933 37.037 0.00 0.00 0.00 2.62
379 382 8.793592 TCATATATACGCTCATACACTCACTTT 58.206 33.333 0.00 0.00 0.00 2.66
393 396 7.397892 AGACACTAATGCTCATATATACGCT 57.602 36.000 6.88 0.00 0.00 5.07
394 397 8.467402 AAAGACACTAATGCTCATATATACGC 57.533 34.615 0.00 0.00 0.00 4.42
440 443 3.586892 TGTTTCATCATGGCGTACGTAA 58.413 40.909 17.90 5.78 0.00 3.18
443 446 2.415168 ACTTGTTTCATCATGGCGTACG 59.585 45.455 11.84 11.84 0.00 3.67
561 727 3.071479 GCTAACTTGATCCGGTGAACAA 58.929 45.455 0.00 3.43 32.96 2.83
569 735 2.936498 ACAATTCCGCTAACTTGATCCG 59.064 45.455 0.00 0.00 0.00 4.18
616 782 1.677576 ACGAGTGAGTGTACGGACAAA 59.322 47.619 0.00 0.00 37.31 2.83
640 811 1.315257 GCCCATCAACCGAGCACAAT 61.315 55.000 0.00 0.00 0.00 2.71
642 813 2.359850 GCCCATCAACCGAGCACA 60.360 61.111 0.00 0.00 0.00 4.57
723 894 0.730494 GTTTGCGCTTCATGGAGCAC 60.730 55.000 25.59 16.88 42.83 4.40
758 929 1.300697 GTTTCCGTGCCGACTCTGT 60.301 57.895 0.00 0.00 0.00 3.41
760 931 1.006102 CAGTTTCCGTGCCGACTCT 60.006 57.895 0.00 0.00 0.00 3.24
785 965 1.103803 TGTGGCGACTTCCTAGCTAG 58.896 55.000 14.20 14.20 0.00 3.42
786 966 1.476891 CTTGTGGCGACTTCCTAGCTA 59.523 52.381 0.00 0.00 0.00 3.32
787 967 0.247736 CTTGTGGCGACTTCCTAGCT 59.752 55.000 0.00 0.00 0.00 3.32
789 969 0.741221 GGCTTGTGGCGACTTCCTAG 60.741 60.000 0.00 0.00 42.94 3.02
790 970 1.295423 GGCTTGTGGCGACTTCCTA 59.705 57.895 0.00 0.00 42.94 2.94
791 971 2.032681 GGCTTGTGGCGACTTCCT 59.967 61.111 0.00 0.00 42.94 3.36
792 972 3.056328 GGGCTTGTGGCGACTTCC 61.056 66.667 0.00 0.00 42.94 3.46
793 973 2.281484 TGGGCTTGTGGCGACTTC 60.281 61.111 0.00 0.00 42.94 3.01
794 974 2.594592 GTGGGCTTGTGGCGACTT 60.595 61.111 0.00 0.00 42.52 3.01
795 975 4.988598 CGTGGGCTTGTGGCGACT 62.989 66.667 0.00 0.00 43.35 4.18
796 976 4.980805 TCGTGGGCTTGTGGCGAC 62.981 66.667 0.00 0.00 42.41 5.19
797 977 4.015406 ATCGTGGGCTTGTGGCGA 62.015 61.111 0.00 0.00 42.94 5.54
798 978 3.803082 CATCGTGGGCTTGTGGCG 61.803 66.667 0.00 0.00 42.94 5.69
799 979 4.120331 GCATCGTGGGCTTGTGGC 62.120 66.667 0.00 0.00 40.90 5.01
800 980 3.803082 CGCATCGTGGGCTTGTGG 61.803 66.667 0.00 0.00 0.00 4.17
801 981 3.049674 ACGCATCGTGGGCTTGTG 61.050 61.111 0.00 0.00 39.18 3.33
820 1000 1.873572 TGATCGATCAGCGCACACG 60.874 57.895 23.99 10.08 44.07 4.49
821 1001 1.633171 GTGATCGATCAGCGCACAC 59.367 57.895 27.95 11.55 40.61 3.82
822 1002 1.873572 CGTGATCGATCAGCGCACA 60.874 57.895 27.95 2.20 40.61 4.57
823 1003 1.874019 ACGTGATCGATCAGCGCAC 60.874 57.895 31.63 20.60 40.61 5.34
824 1004 1.873572 CACGTGATCGATCAGCGCA 60.874 57.895 31.63 13.06 40.61 6.09
825 1005 1.586303 TCACGTGATCGATCAGCGC 60.586 57.895 31.63 20.74 40.61 5.92
826 1006 0.523335 TGTCACGTGATCGATCAGCG 60.523 55.000 30.81 30.81 37.51 5.18
827 1007 1.585668 CTTGTCACGTGATCGATCAGC 59.414 52.381 27.95 19.92 37.51 4.26
828 1008 2.868662 ACTTGTCACGTGATCGATCAG 58.131 47.619 27.95 21.89 37.51 2.90
829 1009 3.297830 AACTTGTCACGTGATCGATCA 57.702 42.857 23.99 23.99 40.62 2.92
830 1010 6.200100 ACTATAACTTGTCACGTGATCGATC 58.800 40.000 23.12 18.72 40.62 3.69
831 1011 6.132791 ACTATAACTTGTCACGTGATCGAT 57.867 37.500 23.12 11.65 40.62 3.59
832 1012 5.556355 ACTATAACTTGTCACGTGATCGA 57.444 39.130 23.12 13.68 40.62 3.59
833 1013 6.712549 TCTACTATAACTTGTCACGTGATCG 58.287 40.000 23.12 14.91 43.34 3.69
834 1014 7.133513 CCTCTACTATAACTTGTCACGTGATC 58.866 42.308 23.12 15.44 0.00 2.92
835 1015 6.459848 GCCTCTACTATAACTTGTCACGTGAT 60.460 42.308 23.12 7.75 0.00 3.06
836 1016 5.163683 GCCTCTACTATAACTTGTCACGTGA 60.164 44.000 15.76 15.76 0.00 4.35
837 1017 5.035443 GCCTCTACTATAACTTGTCACGTG 58.965 45.833 9.94 9.94 0.00 4.49
838 1018 4.097589 GGCCTCTACTATAACTTGTCACGT 59.902 45.833 0.00 0.00 0.00 4.49
839 1019 4.608951 GGCCTCTACTATAACTTGTCACG 58.391 47.826 0.00 0.00 0.00 4.35
840 1020 4.337555 TCGGCCTCTACTATAACTTGTCAC 59.662 45.833 0.00 0.00 0.00 3.67
841 1021 4.529897 TCGGCCTCTACTATAACTTGTCA 58.470 43.478 0.00 0.00 0.00 3.58
842 1022 5.708877 ATCGGCCTCTACTATAACTTGTC 57.291 43.478 0.00 0.00 0.00 3.18
843 1023 6.481434 AAATCGGCCTCTACTATAACTTGT 57.519 37.500 0.00 0.00 0.00 3.16
844 1024 9.141400 GATAAAATCGGCCTCTACTATAACTTG 57.859 37.037 0.00 0.00 0.00 3.16
845 1025 8.312564 GGATAAAATCGGCCTCTACTATAACTT 58.687 37.037 0.00 0.00 0.00 2.66
846 1026 7.674772 AGGATAAAATCGGCCTCTACTATAACT 59.325 37.037 0.00 0.00 0.00 2.24
867 1047 4.549668 ACGTAGGTATCCAAACCAGGATA 58.450 43.478 0.00 0.00 46.41 2.59
879 1059 3.111098 CAAAGTGGCGTACGTAGGTATC 58.889 50.000 17.90 7.55 0.00 2.24
956 1136 7.962918 GCGGCAAGAACCAATTATATTAGTATG 59.037 37.037 0.00 0.00 0.00 2.39
959 1139 5.240844 GGCGGCAAGAACCAATTATATTAGT 59.759 40.000 3.07 0.00 0.00 2.24
1012 1200 2.474816 GAGAGACATACGTCCCATTGC 58.525 52.381 0.00 0.00 43.73 3.56
1017 1205 1.341531 CCATGGAGAGACATACGTCCC 59.658 57.143 5.56 0.00 43.73 4.46
1059 1250 2.203015 ATGCGATTTAGGCGGCGT 60.203 55.556 9.37 0.00 0.00 5.68
1155 1346 3.418913 CGCGTGAAATCGGTGGCA 61.419 61.111 0.00 0.00 0.00 4.92
1235 1430 4.329545 GGAGCCACGGCAGGAACA 62.330 66.667 11.35 0.00 44.88 3.18
1245 1440 4.626081 ACCGTGCACAGGAGCCAC 62.626 66.667 27.07 0.00 0.00 5.01
1348 1543 3.918253 TTGCGGCTGATGGACCCAC 62.918 63.158 0.00 0.00 0.00 4.61
1349 1544 3.626996 CTTGCGGCTGATGGACCCA 62.627 63.158 0.00 0.00 0.00 4.51
1350 1545 2.825836 CTTGCGGCTGATGGACCC 60.826 66.667 0.00 0.00 0.00 4.46
1360 1555 2.985847 AAGCCAGTTCCTTGCGGC 60.986 61.111 0.00 0.00 45.23 6.53
1364 1559 4.179361 TGGCAAGCCAGTTCCTTG 57.821 55.556 10.24 0.00 41.89 3.61
1444 1639 2.665603 GGTCCAGGCTCCAGTGAC 59.334 66.667 0.00 0.00 0.00 3.67
1463 1658 1.001268 CGTCATCGTATGCTGGTAGCT 60.001 52.381 2.24 0.00 42.97 3.32
1487 1682 0.322975 ATTCTCAAGCTGTGGCGACT 59.677 50.000 0.00 0.00 44.37 4.18
1488 1683 0.723981 GATTCTCAAGCTGTGGCGAC 59.276 55.000 0.00 0.00 44.37 5.19
1489 1684 0.391661 GGATTCTCAAGCTGTGGCGA 60.392 55.000 0.00 0.00 44.37 5.54
1490 1685 1.372087 GGGATTCTCAAGCTGTGGCG 61.372 60.000 0.00 0.00 44.37 5.69
1493 1688 1.372087 GCGGGGATTCTCAAGCTGTG 61.372 60.000 0.00 0.00 0.00 3.66
1494 1689 1.078143 GCGGGGATTCTCAAGCTGT 60.078 57.895 0.00 0.00 0.00 4.40
1500 1695 3.460672 GATGCCGCGGGGATTCTCA 62.461 63.158 29.38 14.92 32.75 3.27
1695 1890 2.048603 GCACACCAGGATCTTGCCC 61.049 63.158 0.00 0.00 0.00 5.36
1713 1911 1.800315 CCAGTAGTTCACGTCCGCG 60.800 63.158 0.00 0.00 44.93 6.46
1728 1926 2.821366 GGCGTGAGGATGCACCAG 60.821 66.667 7.86 0.00 42.04 4.00
1795 1993 0.327924 TGGCACCACCCTCTGTAATG 59.672 55.000 0.00 0.00 37.83 1.90
1838 2036 1.949525 CCCACAACAGTTGACCTTGAG 59.050 52.381 20.56 0.00 0.00 3.02
1842 2040 0.623723 ACACCCACAACAGTTGACCT 59.376 50.000 20.56 0.00 0.00 3.85
1864 2062 7.572814 TCATCATACCTGTATTTGACCATGAA 58.427 34.615 0.00 0.00 0.00 2.57
1884 2082 2.275134 ACATGTGTGTTGGCTCATCA 57.725 45.000 0.00 0.00 34.01 3.07
1914 2112 0.109597 CTTCTTCCAACGCATGCACC 60.110 55.000 19.57 0.00 0.00 5.01
1974 2175 2.575805 CAAGGAAGAGAACTTGGCCT 57.424 50.000 3.32 0.00 40.20 5.19
2076 2277 4.812626 CCGTCAACAAAGTTGTACCTAAGT 59.187 41.667 9.43 0.00 41.31 2.24
2116 2317 2.753168 GCCAGTCTGGAGGAAGGTTTTT 60.753 50.000 23.77 0.00 40.96 1.94
2305 2512 4.782019 ATGTTGCACGTGGTAAATCAAT 57.218 36.364 18.88 0.00 0.00 2.57
2331 2538 8.766994 AATATTTGCCACATTAGGATTGTAGT 57.233 30.769 0.00 0.00 0.00 2.73
2334 2541 7.765360 CACAAATATTTGCCACATTAGGATTGT 59.235 33.333 24.82 0.79 41.79 2.71
2429 2651 4.711949 CCTGCAGCCTTCACCGCT 62.712 66.667 8.66 0.00 36.91 5.52
2529 2752 3.341629 CCACCAGGCCCTCCATGT 61.342 66.667 0.00 0.00 33.74 3.21
2667 2895 2.088104 TTCACCCGGATCTGCTCTAT 57.912 50.000 0.73 0.00 0.00 1.98
2757 2986 3.354131 GAGCTTCTCCACGGTGATC 57.646 57.895 10.28 0.00 0.00 2.92
2785 3014 0.252558 TTCCCTGGGAGGTAGTGGAC 60.253 60.000 16.38 0.00 31.93 4.02
2818 3047 2.367894 GGGCTCTGATGTCATCTGATCA 59.632 50.000 19.27 0.00 36.78 2.92
2884 3129 1.185618 ACCGCAGAAGCAGTCCACTA 61.186 55.000 0.00 0.00 42.27 2.74
2912 3157 0.647410 GTCGATGCATCACAGGAACG 59.353 55.000 25.70 10.40 0.00 3.95
2923 3168 0.179137 GACTCCACATCGTCGATGCA 60.179 55.000 30.31 16.14 43.15 3.96
2967 3212 3.445518 ATCACGCATCCGTCGCCAT 62.446 57.895 0.00 0.00 46.39 4.40
3037 3283 1.834188 ATCCACGTTAAAAGGCCTGG 58.166 50.000 5.69 0.31 0.00 4.45
3133 3389 2.032620 CCAGCCCGACATACTCTTAGT 58.967 52.381 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.