Multiple sequence alignment - TraesCS3D01G293700

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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 TraesCS3D01G293700 chr3D 100.000 6792 0 0 1 6792 404016073 404009282 0.000000e+00 12543
1 TraesCS3D01G293700 chr3A 93.652 3434 131 21 776 4133 526529301 526525879 0.000000e+00 5053
2 TraesCS3D01G293700 chr3A 92.978 2250 103 21 4167 6399 526525879 526523668 0.000000e+00 3229
3 TraesCS3D01G293700 chr3A 95.100 653 31 1 102 754 45123293 45122642 0.000000e+00 1027
4 TraesCS3D01G293700 chr3A 87.129 303 15 11 6504 6792 526521884 526521592 8.500000e-84 322
5 TraesCS3D01G293700 chr3A 97.101 69 1 1 6444 6512 526523669 526523602 1.550000e-21 115
6 TraesCS3D01G293700 chr3B 94.212 2419 88 15 790 3167 530268054 530265647 0.000000e+00 3644
7 TraesCS3D01G293700 chr3B 97.204 1824 47 4 3133 4953 530265647 530263825 0.000000e+00 3083
8 TraesCS3D01G293700 chr3B 95.224 1047 36 6 4945 5985 530258732 530257694 0.000000e+00 1644
9 TraesCS3D01G293700 chr3B 87.207 852 44 30 5985 6792 530257451 530256621 0.000000e+00 909
10 TraesCS3D01G293700 chr1A 95.412 1177 37 4 2008 3167 406445025 406443849 0.000000e+00 1858
11 TraesCS3D01G293700 chr1A 95.794 214 7 2 3133 3344 406443849 406443636 1.810000e-90 344
12 TraesCS3D01G293700 chr6A 95.327 1177 38 6 2008 3167 567284024 567285200 0.000000e+00 1853
13 TraesCS3D01G293700 chr6A 95.794 214 7 2 3133 3344 567285200 567285413 1.810000e-90 344
14 TraesCS3D01G293700 chr5B 95.246 1178 38 4 2008 3167 82200601 82199424 0.000000e+00 1849
15 TraesCS3D01G293700 chr5B 94.860 214 9 2 3133 3344 82199424 82199211 3.930000e-87 333
16 TraesCS3D01G293700 chr2B 95.242 1177 38 5 2008 3167 406626875 406628050 0.000000e+00 1847
17 TraesCS3D01G293700 chr2B 89.059 457 47 2 89 543 178316975 178316520 1.280000e-156 564
18 TraesCS3D01G293700 chr2B 95.794 214 7 2 3133 3344 406628050 406628263 1.810000e-90 344
19 TraesCS3D01G293700 chr2B 85.463 227 31 2 535 759 167896888 167896662 1.140000e-57 235
20 TraesCS3D01G293700 chr4B 95.157 1177 39 5 2008 3167 75056034 75054859 0.000000e+00 1842
21 TraesCS3D01G293700 chr4B 95.164 1034 33 7 2151 3167 433664892 433663859 0.000000e+00 1616
22 TraesCS3D01G293700 chr4B 95.794 214 7 2 3133 3344 98639338 98639125 1.810000e-90 344
23 TraesCS3D01G293700 chr4B 95.327 214 8 2 3133 3344 75054859 75054646 8.440000e-89 339
24 TraesCS3D01G293700 chr4B 88.789 223 9 6 2961 3167 389708145 389708367 6.760000e-65 259
25 TraesCS3D01G293700 chr2A 95.157 1177 40 4 2008 3167 449565791 449566967 0.000000e+00 1842
26 TraesCS3D01G293700 chr4A 95.072 1177 41 4 2008 3167 612152843 612154019 0.000000e+00 1836
27 TraesCS3D01G293700 chrUn 94.888 802 24 7 2383 3167 423031222 423030421 0.000000e+00 1238
28 TraesCS3D01G293700 chrUn 95.409 501 21 2 1 499 357663993 357663493 0.000000e+00 797
29 TraesCS3D01G293700 chrUn 93.235 340 20 2 1 338 147112355 147112017 1.320000e-136 497
30 TraesCS3D01G293700 chrUn 93.235 340 20 2 1 338 401084344 401084682 1.320000e-136 497
31 TraesCS3D01G293700 chrUn 93.235 340 20 2 1 338 410619954 410619616 1.320000e-136 497
32 TraesCS3D01G293700 chrUn 90.614 277 10 6 2907 3167 467279108 467278832 3.010000e-93 353
33 TraesCS3D01G293700 chrUn 89.558 249 10 6 2935 3167 471847993 471847745 1.110000e-77 302
34 TraesCS3D01G293700 chrUn 88.789 223 9 6 2961 3167 432417085 432417307 6.760000e-65 259
35 TraesCS3D01G293700 chrUn 88.636 220 9 6 2964 3167 469058681 469058462 3.140000e-63 254
36 TraesCS3D01G293700 chrUn 88.718 195 7 5 2988 3167 469944034 469943840 2.470000e-54 224
37 TraesCS3D01G293700 chr6D 95.658 760 31 2 1 759 47613207 47612449 0.000000e+00 1219
38 TraesCS3D01G293700 chr6D 84.685 222 30 4 529 747 406656457 406656237 1.150000e-52 219
39 TraesCS3D01G293700 chr7B 93.235 340 20 2 1 338 670958229 670957891 1.320000e-136 497
40 TraesCS3D01G293700 chr7B 95.327 214 8 2 3133 3344 133579600 133579387 8.440000e-89 339
41 TraesCS3D01G293700 chr7B 88.095 210 25 0 546 755 474466953 474467162 4.070000e-62 250
42 TraesCS3D01G293700 chr1D 93.215 339 21 2 1 338 104033493 104033156 1.320000e-136 497
43 TraesCS3D01G293700 chr1D 83.333 222 33 4 529 747 442409395 442409175 1.160000e-47 202
44 TraesCS3D01G293700 chr6B 85.680 419 33 12 128 543 215648172 215648566 3.790000e-112 416
45 TraesCS3D01G293700 chr6B 85.119 336 24 12 131 464 21120595 21120284 3.060000e-83 320
46 TraesCS3D01G293700 chr4D 85.000 220 28 5 529 744 6558392 6558610 1.150000e-52 219
47 TraesCS3D01G293700 chr7D 83.482 224 30 7 529 747 43661031 43660810 1.160000e-47 202
48 TraesCS3D01G293700 chr7D 83.036 224 31 7 529 747 43682385 43682164 5.370000e-46 196
49 TraesCS3D01G293700 chr7A 83.212 137 20 2 409 543 520507616 520507751 9.250000e-24 122


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 TraesCS3D01G293700 chr3D 404009282 404016073 6791 True 12543.00 12543 100.0000 1 6792 1 chr3D.!!$R1 6791
1 TraesCS3D01G293700 chr3A 526521592 526529301 7709 True 2179.75 5053 92.7150 776 6792 4 chr3A.!!$R2 6016
2 TraesCS3D01G293700 chr3A 45122642 45123293 651 True 1027.00 1027 95.1000 102 754 1 chr3A.!!$R1 652
3 TraesCS3D01G293700 chr3B 530263825 530268054 4229 True 3363.50 3644 95.7080 790 4953 2 chr3B.!!$R2 4163
4 TraesCS3D01G293700 chr3B 530256621 530258732 2111 True 1276.50 1644 91.2155 4945 6792 2 chr3B.!!$R1 1847
5 TraesCS3D01G293700 chr1A 406443636 406445025 1389 True 1101.00 1858 95.6030 2008 3344 2 chr1A.!!$R1 1336
6 TraesCS3D01G293700 chr6A 567284024 567285413 1389 False 1098.50 1853 95.5605 2008 3344 2 chr6A.!!$F1 1336
7 TraesCS3D01G293700 chr5B 82199211 82200601 1390 True 1091.00 1849 95.0530 2008 3344 2 chr5B.!!$R1 1336
8 TraesCS3D01G293700 chr2B 406626875 406628263 1388 False 1095.50 1847 95.5180 2008 3344 2 chr2B.!!$F1 1336
9 TraesCS3D01G293700 chr4B 433663859 433664892 1033 True 1616.00 1616 95.1640 2151 3167 1 chr4B.!!$R2 1016
10 TraesCS3D01G293700 chr4B 75054646 75056034 1388 True 1090.50 1842 95.2420 2008 3344 2 chr4B.!!$R3 1336
11 TraesCS3D01G293700 chr2A 449565791 449566967 1176 False 1842.00 1842 95.1570 2008 3167 1 chr2A.!!$F1 1159
12 TraesCS3D01G293700 chr4A 612152843 612154019 1176 False 1836.00 1836 95.0720 2008 3167 1 chr4A.!!$F1 1159
13 TraesCS3D01G293700 chrUn 423030421 423031222 801 True 1238.00 1238 94.8880 2383 3167 1 chrUn.!!$R4 784
14 TraesCS3D01G293700 chrUn 357663493 357663993 500 True 797.00 797 95.4090 1 499 1 chrUn.!!$R2 498
15 TraesCS3D01G293700 chr6D 47612449 47613207 758 True 1219.00 1219 95.6580 1 759 1 chr6D.!!$R1 758

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
65 67 0.179065 GCTACTACCGGCGGGATTTT 60.179 55.000 31.78 11.45 36.97 1.82 F
651 653 0.185901 AGGCTTTGACCTCCAAGCAA 59.814 50.000 11.92 0.00 33.62 3.91 F
709 711 0.249573 TCGAACGACTGGGGTTTGAC 60.250 55.000 0.00 0.00 33.86 3.18 F
722 724 0.382873 GTTTGACCGGCCGAAACTTT 59.617 50.000 30.73 2.44 0.00 2.66 F
723 725 0.664224 TTTGACCGGCCGAAACTTTC 59.336 50.000 30.73 12.86 0.00 2.62 F
2199 2233 1.067565 TGGTCTAGCTCTGCAAACTCG 60.068 52.381 0.00 0.00 0.00 4.18 F
2257 2291 1.470494 GCTCTTGCCCTAGCTTTGTTC 59.530 52.381 0.00 0.00 40.80 3.18 F
3235 3324 3.026694 AGCCCTAAACAGCATTCCATTC 58.973 45.455 0.00 0.00 0.00 2.67 F
5616 6015 0.246635 AGGACGCGCACACTTCTAAT 59.753 50.000 5.73 0.00 0.00 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1593 2.119801 ATGAAGGGTGCTAAGTGCTG 57.880 50.000 0.00 0.00 43.37 4.41 R
2199 2233 1.501582 AGGCAGTAATCCTGAGGACC 58.498 55.000 1.77 0.00 44.49 4.46 R
2699 2733 3.774766 TCTGCTTCATTGTAGGCTAAGGA 59.225 43.478 0.00 0.00 0.00 3.36 R
2849 2886 0.173481 CGACTCGGTCACCATCACAT 59.827 55.000 0.00 0.00 32.09 3.21 R
3235 3324 1.529226 TTACATCCAAACGGGTGCTG 58.471 50.000 0.00 0.00 38.11 4.41 R
3668 3758 2.912956 TCCCATTAGAGCTCACAACCTT 59.087 45.455 17.77 0.00 0.00 3.50 R
4690 5083 3.027974 ACCGACTGCTGTACTTCTTTC 57.972 47.619 0.00 0.00 0.00 2.62 R
5668 6067 0.036010 TAGGCTTGCTTGCAGAGTCC 60.036 55.000 0.00 3.76 34.04 3.85 R
6673 9097 1.078497 ACGGATCGCTGAAATGCCA 60.078 52.632 0.00 0.00 0.00 4.92 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
39 41 4.376146 GCTTTTTGTTGCAACCATCCTAA 58.624 39.130 26.14 10.22 0.00 2.69
40 42 4.448732 GCTTTTTGTTGCAACCATCCTAAG 59.551 41.667 26.14 18.91 0.00 2.18
41 43 5.738783 GCTTTTTGTTGCAACCATCCTAAGA 60.739 40.000 26.14 5.73 0.00 2.10
42 44 6.418057 TTTTTGTTGCAACCATCCTAAGAT 57.582 33.333 26.14 0.00 0.00 2.40
43 45 6.418057 TTTTGTTGCAACCATCCTAAGATT 57.582 33.333 26.14 0.00 0.00 2.40
44 46 6.418057 TTTGTTGCAACCATCCTAAGATTT 57.582 33.333 26.14 0.00 0.00 2.17
45 47 6.418057 TTGTTGCAACCATCCTAAGATTTT 57.582 33.333 26.14 0.00 0.00 1.82
46 48 5.782047 TGTTGCAACCATCCTAAGATTTTG 58.218 37.500 26.14 0.00 0.00 2.44
47 49 4.454728 TGCAACCATCCTAAGATTTTGC 57.545 40.909 9.25 9.25 43.39 3.68
48 50 4.088634 TGCAACCATCCTAAGATTTTGCT 58.911 39.130 14.39 0.00 43.44 3.91
49 51 5.260424 TGCAACCATCCTAAGATTTTGCTA 58.740 37.500 14.39 3.85 43.44 3.49
50 52 5.125417 TGCAACCATCCTAAGATTTTGCTAC 59.875 40.000 14.39 0.00 43.44 3.58
51 53 5.358160 GCAACCATCCTAAGATTTTGCTACT 59.642 40.000 9.03 0.00 41.60 2.57
52 54 6.542370 GCAACCATCCTAAGATTTTGCTACTA 59.458 38.462 9.03 0.00 41.60 1.82
53 55 7.467403 GCAACCATCCTAAGATTTTGCTACTAC 60.467 40.741 9.03 0.00 41.60 2.73
54 56 6.592870 ACCATCCTAAGATTTTGCTACTACC 58.407 40.000 0.00 0.00 0.00 3.18
55 57 5.696724 CCATCCTAAGATTTTGCTACTACCG 59.303 44.000 0.00 0.00 0.00 4.02
56 58 5.272283 TCCTAAGATTTTGCTACTACCGG 57.728 43.478 0.00 0.00 0.00 5.28
57 59 3.808174 CCTAAGATTTTGCTACTACCGGC 59.192 47.826 0.00 0.00 0.00 6.13
58 60 1.935933 AGATTTTGCTACTACCGGCG 58.064 50.000 0.00 0.00 0.00 6.46
59 61 0.935196 GATTTTGCTACTACCGGCGG 59.065 55.000 27.06 27.06 0.00 6.13
60 62 0.463116 ATTTTGCTACTACCGGCGGG 60.463 55.000 31.78 16.15 40.11 6.13
61 63 1.543065 TTTTGCTACTACCGGCGGGA 61.543 55.000 31.78 23.16 36.97 5.14
62 64 1.332144 TTTGCTACTACCGGCGGGAT 61.332 55.000 31.78 17.21 36.97 3.85
63 65 1.332144 TTGCTACTACCGGCGGGATT 61.332 55.000 31.78 19.68 36.97 3.01
64 66 1.332144 TGCTACTACCGGCGGGATTT 61.332 55.000 31.78 14.50 36.97 2.17
65 67 0.179065 GCTACTACCGGCGGGATTTT 60.179 55.000 31.78 11.45 36.97 1.82
66 68 1.744798 GCTACTACCGGCGGGATTTTT 60.745 52.381 31.78 10.61 36.97 1.94
67 69 1.937899 CTACTACCGGCGGGATTTTTG 59.062 52.381 31.78 12.29 36.97 2.44
68 70 1.310216 ACTACCGGCGGGATTTTTGC 61.310 55.000 31.78 0.00 36.97 3.68
69 71 1.001887 TACCGGCGGGATTTTTGCT 60.002 52.632 31.78 8.11 36.97 3.91
70 72 0.252479 TACCGGCGGGATTTTTGCTA 59.748 50.000 31.78 6.97 36.97 3.49
71 73 1.310216 ACCGGCGGGATTTTTGCTAC 61.310 55.000 31.78 0.00 36.97 3.58
72 74 1.309499 CCGGCGGGATTTTTGCTACA 61.309 55.000 20.56 0.00 34.06 2.74
73 75 0.738389 CGGCGGGATTTTTGCTACAT 59.262 50.000 0.00 0.00 0.00 2.29
74 76 1.268539 CGGCGGGATTTTTGCTACATC 60.269 52.381 0.00 0.00 0.00 3.06
75 77 1.067060 GGCGGGATTTTTGCTACATCC 59.933 52.381 0.00 0.00 36.48 3.51
76 78 1.748493 GCGGGATTTTTGCTACATCCA 59.252 47.619 7.56 0.00 38.66 3.41
77 79 2.362077 GCGGGATTTTTGCTACATCCAT 59.638 45.455 7.56 0.00 38.66 3.41
78 80 3.550842 GCGGGATTTTTGCTACATCCATC 60.551 47.826 7.56 0.00 38.66 3.51
79 81 3.631686 CGGGATTTTTGCTACATCCATCA 59.368 43.478 7.56 0.00 38.66 3.07
80 82 4.279169 CGGGATTTTTGCTACATCCATCAT 59.721 41.667 7.56 0.00 38.66 2.45
81 83 5.473162 CGGGATTTTTGCTACATCCATCATA 59.527 40.000 7.56 0.00 38.66 2.15
82 84 6.151648 CGGGATTTTTGCTACATCCATCATAT 59.848 38.462 7.56 0.00 38.66 1.78
83 85 7.318141 GGGATTTTTGCTACATCCATCATATG 58.682 38.462 0.00 0.00 38.66 1.78
84 86 7.039504 GGGATTTTTGCTACATCCATCATATGT 60.040 37.037 1.90 0.00 38.66 2.29
85 87 7.811236 GGATTTTTGCTACATCCATCATATGTG 59.189 37.037 1.90 0.77 38.05 3.21
86 88 6.638096 TTTTGCTACATCCATCATATGTGG 57.362 37.500 14.65 14.65 38.05 4.17
87 89 4.290711 TGCTACATCCATCATATGTGGG 57.709 45.455 18.44 13.90 38.05 4.61
88 90 3.009363 TGCTACATCCATCATATGTGGGG 59.991 47.826 18.44 14.69 38.05 4.96
89 91 3.623203 GCTACATCCATCATATGTGGGGG 60.623 52.174 18.44 14.45 38.05 5.40
181 183 6.072508 CGGCCTAGTATAAGTTACAACCGATA 60.073 42.308 0.00 0.00 38.00 2.92
182 184 7.522073 CGGCCTAGTATAAGTTACAACCGATAA 60.522 40.741 0.00 0.00 38.00 1.75
214 216 5.652014 ACCTTCAACAGACATGACAGAAAAA 59.348 36.000 0.00 0.00 0.00 1.94
322 324 1.779025 TATGACGGCGAGGCTACGAC 61.779 60.000 16.62 7.33 38.00 4.34
382 384 1.180456 TACCAAACGACAGCGGAGGA 61.180 55.000 0.00 0.00 43.17 3.71
418 420 1.015085 CGCCATGTTGCAACCAATGG 61.015 55.000 30.84 30.84 35.26 3.16
443 445 4.639171 GGCCGCAAAACACCCACG 62.639 66.667 0.00 0.00 0.00 4.94
451 453 1.069022 CAAAACACCCACGAGATGCAG 60.069 52.381 0.00 0.00 0.00 4.41
459 461 1.150827 CACGAGATGCAGCTTCAACA 58.849 50.000 5.67 0.00 0.00 3.33
489 491 1.155424 GGTTGCCAACAAGTCGACGA 61.155 55.000 10.46 0.00 36.16 4.20
490 492 0.232303 GTTGCCAACAAGTCGACGAG 59.768 55.000 10.46 9.31 36.16 4.18
563 565 3.299190 TTTTTCGCAAGGGCCGGG 61.299 61.111 2.18 0.00 36.38 5.73
590 592 4.864334 GAGGCGCCATGGTGGAGG 62.864 72.222 31.54 6.03 40.96 4.30
651 653 0.185901 AGGCTTTGACCTCCAAGCAA 59.814 50.000 11.92 0.00 33.62 3.91
652 654 0.600057 GGCTTTGACCTCCAAGCAAG 59.400 55.000 11.92 0.00 35.94 4.01
653 655 0.600057 GCTTTGACCTCCAAGCAAGG 59.400 55.000 6.30 0.00 39.96 3.61
654 656 1.251251 CTTTGACCTCCAAGCAAGGG 58.749 55.000 0.00 0.00 38.29 3.95
655 657 0.850100 TTTGACCTCCAAGCAAGGGA 59.150 50.000 0.00 0.00 38.29 4.20
662 664 2.795231 TCCAAGCAAGGGAGAAGATG 57.205 50.000 0.00 0.00 0.00 2.90
663 665 1.101331 CCAAGCAAGGGAGAAGATGC 58.899 55.000 0.00 0.00 39.06 3.91
664 666 1.615116 CCAAGCAAGGGAGAAGATGCA 60.615 52.381 0.00 0.00 41.18 3.96
665 667 2.165167 CAAGCAAGGGAGAAGATGCAA 58.835 47.619 0.00 0.00 41.18 4.08
666 668 2.758979 CAAGCAAGGGAGAAGATGCAAT 59.241 45.455 0.00 0.00 41.18 3.56
667 669 2.652590 AGCAAGGGAGAAGATGCAATC 58.347 47.619 0.00 0.00 46.04 2.67
684 686 6.993786 TGCAATCTGAACGGTTATTATTCA 57.006 33.333 0.00 0.00 0.00 2.57
686 688 6.597672 TGCAATCTGAACGGTTATTATTCAGT 59.402 34.615 11.75 0.00 46.20 3.41
687 689 7.766738 TGCAATCTGAACGGTTATTATTCAGTA 59.233 33.333 11.75 1.94 46.20 2.74
688 690 8.609176 GCAATCTGAACGGTTATTATTCAGTAA 58.391 33.333 11.75 0.00 46.20 2.24
692 694 9.027129 TCTGAACGGTTATTATTCAGTAAATCG 57.973 33.333 11.75 0.00 46.20 3.34
693 695 8.929827 TGAACGGTTATTATTCAGTAAATCGA 57.070 30.769 0.00 0.00 0.00 3.59
694 696 9.368674 TGAACGGTTATTATTCAGTAAATCGAA 57.631 29.630 0.00 0.00 0.00 3.71
695 697 9.628983 GAACGGTTATTATTCAGTAAATCGAAC 57.371 33.333 0.00 0.00 0.00 3.95
696 698 7.834529 ACGGTTATTATTCAGTAAATCGAACG 58.165 34.615 0.00 0.00 0.00 3.95
697 699 7.701924 ACGGTTATTATTCAGTAAATCGAACGA 59.298 33.333 0.00 0.00 0.00 3.85
698 700 7.994894 CGGTTATTATTCAGTAAATCGAACGAC 59.005 37.037 0.00 0.00 0.00 4.34
699 701 9.028185 GGTTATTATTCAGTAAATCGAACGACT 57.972 33.333 0.00 0.00 0.00 4.18
700 702 9.831054 GTTATTATTCAGTAAATCGAACGACTG 57.169 33.333 14.53 14.53 40.56 3.51
701 703 6.880822 TTATTCAGTAAATCGAACGACTGG 57.119 37.500 18.40 5.93 39.81 4.00
702 704 3.226346 TCAGTAAATCGAACGACTGGG 57.774 47.619 18.40 1.38 39.81 4.45
703 705 2.094390 TCAGTAAATCGAACGACTGGGG 60.094 50.000 18.40 0.83 39.81 4.96
704 706 1.897802 AGTAAATCGAACGACTGGGGT 59.102 47.619 0.00 0.00 0.00 4.95
705 707 2.301009 AGTAAATCGAACGACTGGGGTT 59.699 45.455 0.00 0.00 0.00 4.11
706 708 2.265589 AAATCGAACGACTGGGGTTT 57.734 45.000 0.00 0.00 0.00 3.27
707 709 1.519408 AATCGAACGACTGGGGTTTG 58.481 50.000 0.00 0.00 0.00 2.93
708 710 0.682852 ATCGAACGACTGGGGTTTGA 59.317 50.000 0.00 5.77 40.90 2.69
709 711 0.249573 TCGAACGACTGGGGTTTGAC 60.250 55.000 0.00 0.00 33.86 3.18
710 712 1.226030 CGAACGACTGGGGTTTGACC 61.226 60.000 0.00 0.00 37.60 4.02
711 713 1.226030 GAACGACTGGGGTTTGACCG 61.226 60.000 0.00 0.00 39.83 4.79
712 714 2.358247 CGACTGGGGTTTGACCGG 60.358 66.667 0.00 0.00 39.83 5.28
713 715 2.671963 GACTGGGGTTTGACCGGC 60.672 66.667 0.00 0.00 39.83 6.13
714 716 4.280019 ACTGGGGTTTGACCGGCC 62.280 66.667 0.00 0.00 39.83 6.13
717 719 4.646877 GGGGTTTGACCGGCCGAA 62.647 66.667 30.73 10.83 39.83 4.30
718 720 2.595172 GGGTTTGACCGGCCGAAA 60.595 61.111 30.73 17.14 39.83 3.46
719 721 2.640989 GGTTTGACCGGCCGAAAC 59.359 61.111 30.73 27.14 0.00 2.78
720 722 1.895231 GGTTTGACCGGCCGAAACT 60.895 57.895 29.04 11.52 31.54 2.66
721 723 1.449726 GGTTTGACCGGCCGAAACTT 61.450 55.000 29.04 10.89 31.54 2.66
722 724 0.382873 GTTTGACCGGCCGAAACTTT 59.617 50.000 30.73 2.44 0.00 2.66
723 725 0.664224 TTTGACCGGCCGAAACTTTC 59.336 50.000 30.73 12.86 0.00 2.62
732 734 4.753877 GAAACTTTCGGCCGGCGC 62.754 66.667 27.83 12.82 0.00 6.53
765 767 7.639113 CCAGTACTGGCCTTTATATTTTTGA 57.361 36.000 28.48 0.00 44.73 2.69
766 768 7.707104 CCAGTACTGGCCTTTATATTTTTGAG 58.293 38.462 28.48 0.00 44.73 3.02
767 769 7.201821 CCAGTACTGGCCTTTATATTTTTGAGG 60.202 40.741 28.48 0.00 44.73 3.86
768 770 6.833933 AGTACTGGCCTTTATATTTTTGAGGG 59.166 38.462 3.32 0.00 0.00 4.30
769 771 5.837829 ACTGGCCTTTATATTTTTGAGGGA 58.162 37.500 3.32 0.00 0.00 4.20
770 772 6.443832 ACTGGCCTTTATATTTTTGAGGGAT 58.556 36.000 3.32 0.00 0.00 3.85
771 773 6.551227 ACTGGCCTTTATATTTTTGAGGGATC 59.449 38.462 3.32 0.00 0.00 3.36
772 774 6.439487 TGGCCTTTATATTTTTGAGGGATCA 58.561 36.000 3.32 0.00 0.00 2.92
773 775 6.550854 TGGCCTTTATATTTTTGAGGGATCAG 59.449 38.462 3.32 0.00 0.00 2.90
774 776 6.777580 GGCCTTTATATTTTTGAGGGATCAGA 59.222 38.462 0.00 0.00 0.00 3.27
775 777 7.452813 GGCCTTTATATTTTTGAGGGATCAGAT 59.547 37.037 0.00 0.00 0.00 2.90
776 778 9.520515 GCCTTTATATTTTTGAGGGATCAGATA 57.479 33.333 0.00 0.00 0.00 1.98
784 786 9.620259 ATTTTTGAGGGATCAGATAGTTACTTC 57.380 33.333 0.00 0.00 0.00 3.01
785 787 6.732896 TTGAGGGATCAGATAGTTACTTCC 57.267 41.667 0.00 0.00 0.00 3.46
786 788 5.777449 TGAGGGATCAGATAGTTACTTCCA 58.223 41.667 0.00 0.00 0.00 3.53
787 789 6.385443 TGAGGGATCAGATAGTTACTTCCAT 58.615 40.000 0.00 0.00 0.00 3.41
788 790 6.846505 TGAGGGATCAGATAGTTACTTCCATT 59.153 38.462 0.00 0.00 0.00 3.16
918 921 2.351244 AATCTCGAGCCCGCAGTCA 61.351 57.895 7.81 0.00 35.37 3.41
1086 1095 3.519930 GAGACGGAGGCGGAGGAC 61.520 72.222 0.00 0.00 0.00 3.85
1170 1179 2.110226 CTTTCGACGTCGCCTCTTATC 58.890 52.381 32.19 0.00 39.60 1.75
1254 1263 2.325082 GGTTAGCGCAGGTGGTGTG 61.325 63.158 11.47 0.00 40.22 3.82
1416 1449 1.526917 CCCCGTCATTGATGCCTCC 60.527 63.158 0.00 0.00 0.00 4.30
1496 1529 8.192774 TGACAAGATAGTTAAACAGGTATACCG 58.807 37.037 16.31 13.22 42.08 4.02
1560 1593 5.740099 GCTGAGTATCGTGTTCTCTTTAGTC 59.260 44.000 0.00 0.00 38.61 2.59
1590 1623 9.998752 ACTTAGCACCCTTCATATAGATATACT 57.001 33.333 0.00 0.00 0.00 2.12
1622 1655 6.335471 TCCTCTTATAGTTCGTGTCACAAA 57.665 37.500 3.42 0.00 0.00 2.83
1627 1660 7.726079 TCTTATAGTTCGTGTCACAAAAATCG 58.274 34.615 3.42 0.00 0.00 3.34
1655 1688 3.505680 TCCTGTATTCGTGCAAGCAAATT 59.494 39.130 0.00 0.00 0.00 1.82
1678 1711 5.909621 ATATTCTGAATGCTGTGCTTGTT 57.090 34.783 13.01 0.00 0.00 2.83
1679 1712 8.504812 TTATATTCTGAATGCTGTGCTTGTTA 57.495 30.769 13.01 0.00 0.00 2.41
1680 1713 4.488126 TTCTGAATGCTGTGCTTGTTAC 57.512 40.909 0.00 0.00 0.00 2.50
1819 1852 1.826385 AGTAGTGTGCCATTGCCTTC 58.174 50.000 0.00 0.00 36.33 3.46
1920 1953 6.698008 TTGTTTATGAGACAATAGGCATGG 57.302 37.500 0.00 0.00 32.44 3.66
1954 1987 6.321181 TGAACTATTCTGGCTGTTTTCAACTT 59.679 34.615 0.00 0.00 0.00 2.66
2121 2154 8.565896 TCAGCAGTACATATTCAATTTGAAGT 57.434 30.769 16.34 11.50 40.05 3.01
2170 2204 4.897140 ACATTTTTGCATGCCTACACATT 58.103 34.783 16.68 0.00 0.00 2.71
2199 2233 1.067565 TGGTCTAGCTCTGCAAACTCG 60.068 52.381 0.00 0.00 0.00 4.18
2257 2291 1.470494 GCTCTTGCCCTAGCTTTGTTC 59.530 52.381 0.00 0.00 40.80 3.18
2394 2428 8.435931 AGGCCTCTGTGAATATTACATATACA 57.564 34.615 0.00 0.00 0.00 2.29
2441 2475 4.517285 TCAAACAAGTAGAGATCATGGGC 58.483 43.478 0.00 0.00 0.00 5.36
2658 2692 6.126652 ACCATGGTAGCTCTGTCAAGATTATT 60.127 38.462 18.10 0.00 0.00 1.40
3037 3077 5.561679 AGGACTGAACCAAATAGTTCCTTC 58.438 41.667 2.24 0.00 44.55 3.46
3235 3324 3.026694 AGCCCTAAACAGCATTCCATTC 58.973 45.455 0.00 0.00 0.00 2.67
3392 3482 6.045072 AGATGTGCATCATGGTTTGATTTT 57.955 33.333 13.79 0.00 42.62 1.82
3928 4315 5.588648 GGCAAGTATGTTAGCTGGACATTTA 59.411 40.000 18.78 3.90 38.58 1.40
3944 4331 7.620880 TGGACATTTATAGTAGTCTGTGCTTT 58.379 34.615 0.00 0.00 0.00 3.51
4213 4600 9.916397 GTTCTTGATTTTATACCTGTCAATACG 57.084 33.333 0.00 0.00 0.00 3.06
4239 4627 7.232118 AGCTCTGCACATTTTTATTAACCTT 57.768 32.000 0.00 0.00 0.00 3.50
4487 4880 7.039993 TCGGTGCTAATTGAAGAGCTATACATA 60.040 37.037 3.90 0.00 39.54 2.29
4690 5083 1.164041 ACAACGAGGGCCAGTTTTCG 61.164 55.000 13.61 11.95 38.88 3.46
4810 5203 7.364522 TGAGGTCTGAATTTTTCGATACTTG 57.635 36.000 0.00 0.00 0.00 3.16
4826 5219 5.985530 CGATACTTGTTCCATTCATGCTCTA 59.014 40.000 0.00 0.00 0.00 2.43
4943 5336 3.498927 GCACATGCTGCAAACTAGAAT 57.501 42.857 6.36 0.00 46.29 2.40
4976 5369 9.809096 TGTATAGTTTCAGAAGAAAGCTGATAG 57.191 33.333 0.00 0.00 43.95 2.08
4977 5370 9.810545 GTATAGTTTCAGAAGAAAGCTGATAGT 57.189 33.333 0.00 0.00 43.95 2.12
4978 5371 8.715191 ATAGTTTCAGAAGAAAGCTGATAGTG 57.285 34.615 0.00 0.00 43.95 2.74
4979 5372 6.763355 AGTTTCAGAAGAAAGCTGATAGTGA 58.237 36.000 0.00 0.00 43.95 3.41
4980 5373 7.393216 AGTTTCAGAAGAAAGCTGATAGTGAT 58.607 34.615 0.00 0.00 43.95 3.06
4985 5378 5.663106 AGAAGAAAGCTGATAGTGATACCCA 59.337 40.000 0.00 0.00 0.00 4.51
5053 5446 2.325082 CGGTGGTCGAAAAGGCAGG 61.325 63.158 0.00 0.00 42.43 4.85
5061 5454 3.335579 GTCGAAAAGGCAGGTACAGAAT 58.664 45.455 0.00 0.00 0.00 2.40
5113 5506 5.562506 TTCTACTCAATCGTCACCTACTG 57.437 43.478 0.00 0.00 0.00 2.74
5209 5602 8.684386 TGAACACATAACTTGAGTTTATTCCA 57.316 30.769 1.20 0.00 38.95 3.53
5397 5791 4.941873 AGGATTAACGTGGGAATTTCTGTC 59.058 41.667 0.00 0.00 0.00 3.51
5417 5811 4.638421 TGTCGGGCTTAAATTTGTGGATAG 59.362 41.667 0.00 0.00 0.00 2.08
5506 5900 6.040278 TGCACATTCTTGATAACCAAACAGAA 59.960 34.615 0.00 0.00 33.76 3.02
5616 6015 0.246635 AGGACGCGCACACTTCTAAT 59.753 50.000 5.73 0.00 0.00 1.73
5668 6067 2.674420 TCCCCTACTATTCCTGGTTCG 58.326 52.381 0.00 0.00 0.00 3.95
5679 6078 0.671781 CCTGGTTCGGACTCTGCAAG 60.672 60.000 0.00 0.00 0.00 4.01
5745 6144 0.623723 ACAATGGGGCGTGGTAGATT 59.376 50.000 0.00 0.00 0.00 2.40
5758 6157 2.642311 TGGTAGATTGCTTCCACTTCCA 59.358 45.455 0.00 0.00 36.75 3.53
5759 6158 3.274288 GGTAGATTGCTTCCACTTCCAG 58.726 50.000 0.00 0.00 32.27 3.86
5797 6196 6.296145 CCCAGAAGACTGAGGAATAGAACTTT 60.296 42.308 0.00 0.00 46.03 2.66
5798 6197 7.093289 CCCAGAAGACTGAGGAATAGAACTTTA 60.093 40.741 0.00 0.00 46.03 1.85
5817 6216 8.459911 AACTTTATATACAAATGGGTAGTGCC 57.540 34.615 0.00 0.00 0.00 5.01
5902 6301 1.587066 TGTATACGGAAAAGCCCCCT 58.413 50.000 0.00 0.00 0.00 4.79
6046 6688 1.955663 CCAAAGCTTTGCCGGTTGC 60.956 57.895 29.93 2.43 36.86 4.17
6079 6741 3.347216 GCTTGGAAATGTCTGCTTAGGA 58.653 45.455 0.00 0.00 0.00 2.94
6080 6742 3.376546 GCTTGGAAATGTCTGCTTAGGAG 59.623 47.826 0.00 0.00 0.00 3.69
6082 6744 4.207891 TGGAAATGTCTGCTTAGGAGAC 57.792 45.455 23.91 23.91 40.34 3.36
6083 6745 3.055094 TGGAAATGTCTGCTTAGGAGACC 60.055 47.826 26.66 14.27 39.36 3.85
6084 6746 3.055094 GGAAATGTCTGCTTAGGAGACCA 60.055 47.826 26.66 16.84 39.36 4.02
6085 6747 4.565652 GGAAATGTCTGCTTAGGAGACCAA 60.566 45.833 26.66 12.88 39.36 3.67
6086 6748 3.902881 ATGTCTGCTTAGGAGACCAAG 57.097 47.619 26.66 0.00 39.36 3.61
6118 6780 6.238566 CGATCTGGTTGTGCATATTTGAATCT 60.239 38.462 0.00 0.00 0.00 2.40
6145 6817 5.780958 AAGGAGAGCAAGTTATTAAGGGT 57.219 39.130 0.00 0.00 0.00 4.34
6187 6866 5.664294 ATTGTTGCTGCTGATTGGATAAA 57.336 34.783 0.00 0.00 0.00 1.40
6231 6910 2.890311 GGAGATCGAGATCACATCCTGT 59.110 50.000 14.64 0.00 40.22 4.00
6536 8946 5.707242 AAAAAGGAATCTTCGGAGTTTCC 57.293 39.130 21.61 21.61 45.85 3.13
6565 8986 3.118223 GGAAGATCCATCTTTTCCGACCT 60.118 47.826 3.31 0.00 46.47 3.85
6568 8989 4.290942 AGATCCATCTTTTCCGACCTACT 58.709 43.478 0.00 0.00 31.97 2.57
6579 9000 6.446781 TTTCCGACCTACTAGTATGAAGTG 57.553 41.667 11.63 0.00 0.00 3.16
6581 9002 3.004524 CCGACCTACTAGTATGAAGTGGC 59.995 52.174 11.63 1.56 0.00 5.01
6582 9003 3.630769 CGACCTACTAGTATGAAGTGGCA 59.369 47.826 11.63 0.00 0.00 4.92
6649 9073 2.187163 GGTCAGCTTACCGGAGCC 59.813 66.667 9.46 0.00 43.74 4.70
6685 9109 1.398390 GTAGAAGGTGGCATTTCAGCG 59.602 52.381 14.49 0.00 39.81 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 1.472728 CCGCCGGTAGTAGCAAAATCT 60.473 52.381 1.90 0.00 0.00 2.40
40 42 0.935196 CCGCCGGTAGTAGCAAAATC 59.065 55.000 1.90 0.00 0.00 2.17
41 43 0.463116 CCCGCCGGTAGTAGCAAAAT 60.463 55.000 1.90 0.00 0.00 1.82
42 44 1.078988 CCCGCCGGTAGTAGCAAAA 60.079 57.895 1.90 0.00 0.00 2.44
43 45 1.332144 ATCCCGCCGGTAGTAGCAAA 61.332 55.000 1.90 0.00 0.00 3.68
44 46 1.332144 AATCCCGCCGGTAGTAGCAA 61.332 55.000 1.90 0.00 0.00 3.91
45 47 1.332144 AAATCCCGCCGGTAGTAGCA 61.332 55.000 1.90 0.00 0.00 3.49
46 48 0.179065 AAAATCCCGCCGGTAGTAGC 60.179 55.000 1.90 0.00 0.00 3.58
47 49 1.937899 CAAAAATCCCGCCGGTAGTAG 59.062 52.381 1.90 0.00 0.00 2.57
48 50 2.013058 GCAAAAATCCCGCCGGTAGTA 61.013 52.381 1.90 0.00 0.00 1.82
49 51 1.310216 GCAAAAATCCCGCCGGTAGT 61.310 55.000 1.90 0.00 0.00 2.73
50 52 1.029947 AGCAAAAATCCCGCCGGTAG 61.030 55.000 1.90 0.00 0.00 3.18
51 53 0.252479 TAGCAAAAATCCCGCCGGTA 59.748 50.000 1.90 0.00 0.00 4.02
52 54 1.001887 TAGCAAAAATCCCGCCGGT 60.002 52.632 1.90 0.00 0.00 5.28
53 55 1.309499 TGTAGCAAAAATCCCGCCGG 61.309 55.000 0.00 0.00 0.00 6.13
54 56 0.738389 ATGTAGCAAAAATCCCGCCG 59.262 50.000 0.00 0.00 0.00 6.46
55 57 1.067060 GGATGTAGCAAAAATCCCGCC 59.933 52.381 0.00 0.00 34.89 6.13
56 58 1.748493 TGGATGTAGCAAAAATCCCGC 59.252 47.619 5.96 0.00 39.36 6.13
57 59 3.631686 TGATGGATGTAGCAAAAATCCCG 59.368 43.478 5.96 0.00 39.36 5.14
58 60 5.796424 ATGATGGATGTAGCAAAAATCCC 57.204 39.130 5.96 0.00 39.36 3.85
59 61 7.811236 CACATATGATGGATGTAGCAAAAATCC 59.189 37.037 10.38 2.04 40.34 3.01
60 62 7.811236 CCACATATGATGGATGTAGCAAAAATC 59.189 37.037 10.38 0.00 39.87 2.17
61 63 7.256048 CCCACATATGATGGATGTAGCAAAAAT 60.256 37.037 19.79 0.00 39.87 1.82
62 64 6.040729 CCCACATATGATGGATGTAGCAAAAA 59.959 38.462 19.79 0.00 39.87 1.94
63 65 5.535783 CCCACATATGATGGATGTAGCAAAA 59.464 40.000 19.79 0.00 39.87 2.44
64 66 5.072055 CCCACATATGATGGATGTAGCAAA 58.928 41.667 19.79 0.00 39.87 3.68
65 67 4.507157 CCCCACATATGATGGATGTAGCAA 60.507 45.833 19.79 0.00 39.87 3.91
66 68 3.009363 CCCCACATATGATGGATGTAGCA 59.991 47.826 19.79 0.00 39.87 3.49
67 69 3.614092 CCCCACATATGATGGATGTAGC 58.386 50.000 19.79 0.00 39.87 3.58
68 70 4.226427 CCCCCACATATGATGGATGTAG 57.774 50.000 19.79 7.69 39.87 2.74
114 116 3.565910 TTTGCACCAATTCGCCGCC 62.566 57.895 0.00 0.00 0.00 6.13
119 121 0.309302 TGTCCGTTTGCACCAATTCG 59.691 50.000 0.00 0.00 0.00 3.34
191 193 5.756195 TTTTCTGTCATGTCTGTTGAAGG 57.244 39.130 0.00 0.00 0.00 3.46
214 216 2.893489 GCTTTTCCATGAGGGTTGAAGT 59.107 45.455 0.00 0.00 38.11 3.01
322 324 4.675029 AACCTCGCCGTCAACCCG 62.675 66.667 0.00 0.00 0.00 5.28
382 384 2.667318 CGTTGCTTCGTGGTCGCAT 61.667 57.895 0.00 0.00 36.96 4.73
468 470 0.028902 GTCGACTTGTTGGCAACCAC 59.971 55.000 26.31 13.78 30.78 4.16
478 480 2.963371 GCCTCCTCGTCGACTTGT 59.037 61.111 14.70 0.00 0.00 3.16
481 483 2.820479 CTCGCCTCCTCGTCGACT 60.820 66.667 14.70 0.00 0.00 4.18
552 554 2.124695 CTCTTACCCGGCCCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
554 556 0.618981 CTTTCTCTTACCCGGCCCTT 59.381 55.000 0.00 0.00 0.00 3.95
556 558 0.178301 CTCTTTCTCTTACCCGGCCC 59.822 60.000 0.00 0.00 0.00 5.80
563 565 1.936547 CATGGCGCCTCTTTCTCTTAC 59.063 52.381 29.70 0.00 0.00 2.34
590 592 2.276058 GCTCGACGCAAACGCATC 60.276 61.111 0.00 0.00 45.53 3.91
647 649 2.241685 AGATTGCATCTTCTCCCTTGCT 59.758 45.455 0.00 0.00 35.76 3.91
651 653 3.681034 CGTTCAGATTGCATCTTCTCCCT 60.681 47.826 0.00 0.00 37.58 4.20
652 654 2.611292 CGTTCAGATTGCATCTTCTCCC 59.389 50.000 0.00 0.00 37.58 4.30
653 655 2.611292 CCGTTCAGATTGCATCTTCTCC 59.389 50.000 0.00 0.00 37.58 3.71
654 656 3.265791 ACCGTTCAGATTGCATCTTCTC 58.734 45.455 0.00 0.00 37.58 2.87
655 657 3.340814 ACCGTTCAGATTGCATCTTCT 57.659 42.857 0.00 0.00 37.58 2.85
656 658 5.741388 ATAACCGTTCAGATTGCATCTTC 57.259 39.130 0.00 0.00 37.58 2.87
657 659 7.807977 ATAATAACCGTTCAGATTGCATCTT 57.192 32.000 0.00 0.00 37.58 2.40
658 660 7.498900 TGAATAATAACCGTTCAGATTGCATCT 59.501 33.333 0.00 0.00 41.15 2.90
659 661 7.639039 TGAATAATAACCGTTCAGATTGCATC 58.361 34.615 0.00 0.00 0.00 3.91
660 662 7.566760 TGAATAATAACCGTTCAGATTGCAT 57.433 32.000 0.00 0.00 0.00 3.96
661 663 6.993786 TGAATAATAACCGTTCAGATTGCA 57.006 33.333 0.00 0.00 0.00 4.08
668 670 8.929827 TCGATTTACTGAATAATAACCGTTCA 57.070 30.769 0.00 0.00 0.00 3.18
669 671 9.628983 GTTCGATTTACTGAATAATAACCGTTC 57.371 33.333 0.00 0.00 0.00 3.95
670 672 8.323140 CGTTCGATTTACTGAATAATAACCGTT 58.677 33.333 0.00 0.00 0.00 4.44
671 673 7.701924 TCGTTCGATTTACTGAATAATAACCGT 59.298 33.333 0.00 0.00 0.00 4.83
672 674 7.994894 GTCGTTCGATTTACTGAATAATAACCG 59.005 37.037 0.00 0.00 0.00 4.44
673 675 9.028185 AGTCGTTCGATTTACTGAATAATAACC 57.972 33.333 0.00 0.00 0.00 2.85
674 676 9.831054 CAGTCGTTCGATTTACTGAATAATAAC 57.169 33.333 13.43 0.00 41.47 1.89
675 677 9.027129 CCAGTCGTTCGATTTACTGAATAATAA 57.973 33.333 18.07 0.00 41.47 1.40
676 678 7.650504 CCCAGTCGTTCGATTTACTGAATAATA 59.349 37.037 18.07 0.00 41.47 0.98
677 679 6.479001 CCCAGTCGTTCGATTTACTGAATAAT 59.521 38.462 18.07 0.00 41.47 1.28
678 680 5.808540 CCCAGTCGTTCGATTTACTGAATAA 59.191 40.000 18.07 0.00 41.47 1.40
679 681 5.345702 CCCAGTCGTTCGATTTACTGAATA 58.654 41.667 18.07 0.00 41.47 1.75
680 682 4.181578 CCCAGTCGTTCGATTTACTGAAT 58.818 43.478 18.07 0.74 41.47 2.57
681 683 3.581755 CCCAGTCGTTCGATTTACTGAA 58.418 45.455 18.07 0.00 41.47 3.02
682 684 2.094390 CCCCAGTCGTTCGATTTACTGA 60.094 50.000 18.07 1.21 41.47 3.41
683 685 2.268298 CCCCAGTCGTTCGATTTACTG 58.732 52.381 12.27 12.27 39.22 2.74
684 686 1.897802 ACCCCAGTCGTTCGATTTACT 59.102 47.619 0.00 0.00 0.00 2.24
685 687 2.375173 ACCCCAGTCGTTCGATTTAC 57.625 50.000 0.00 0.00 0.00 2.01
686 688 3.068560 CAAACCCCAGTCGTTCGATTTA 58.931 45.455 0.00 0.00 0.00 1.40
687 689 1.877443 CAAACCCCAGTCGTTCGATTT 59.123 47.619 0.00 0.00 0.00 2.17
688 690 1.071071 TCAAACCCCAGTCGTTCGATT 59.929 47.619 0.00 0.00 0.00 3.34
689 691 0.682852 TCAAACCCCAGTCGTTCGAT 59.317 50.000 0.00 0.00 0.00 3.59
690 692 0.249573 GTCAAACCCCAGTCGTTCGA 60.250 55.000 0.00 0.00 0.00 3.71
691 693 1.226030 GGTCAAACCCCAGTCGTTCG 61.226 60.000 0.00 0.00 30.04 3.95
692 694 1.226030 CGGTCAAACCCCAGTCGTTC 61.226 60.000 0.00 0.00 33.75 3.95
693 695 1.227734 CGGTCAAACCCCAGTCGTT 60.228 57.895 0.00 0.00 33.75 3.85
694 696 2.424302 CGGTCAAACCCCAGTCGT 59.576 61.111 0.00 0.00 33.75 4.34
695 697 2.358247 CCGGTCAAACCCCAGTCG 60.358 66.667 0.00 0.00 33.75 4.18
696 698 2.671963 GCCGGTCAAACCCCAGTC 60.672 66.667 1.90 0.00 33.75 3.51
697 699 4.280019 GGCCGGTCAAACCCCAGT 62.280 66.667 0.00 0.00 33.75 4.00
700 702 4.646877 TTCGGCCGGTCAAACCCC 62.647 66.667 27.83 0.00 33.75 4.95
701 703 2.595172 TTTCGGCCGGTCAAACCC 60.595 61.111 27.83 0.00 33.75 4.11
702 704 1.449726 AAGTTTCGGCCGGTCAAACC 61.450 55.000 27.70 15.52 31.50 3.27
703 705 0.382873 AAAGTTTCGGCCGGTCAAAC 59.617 50.000 27.83 26.35 0.00 2.93
704 706 0.664224 GAAAGTTTCGGCCGGTCAAA 59.336 50.000 27.83 16.16 0.00 2.69
705 707 2.323213 GAAAGTTTCGGCCGGTCAA 58.677 52.632 27.83 13.35 0.00 3.18
706 708 4.052519 GAAAGTTTCGGCCGGTCA 57.947 55.556 27.83 6.94 0.00 4.02
715 717 4.753877 GCGCCGGCCGAAAGTTTC 62.754 66.667 30.73 5.47 40.02 2.78
742 744 7.201821 CCCTCAAAAATATAAAGGCCAGTACTG 60.202 40.741 16.34 16.34 0.00 2.74
743 745 6.833933 CCCTCAAAAATATAAAGGCCAGTACT 59.166 38.462 5.01 0.00 0.00 2.73
744 746 6.831868 TCCCTCAAAAATATAAAGGCCAGTAC 59.168 38.462 5.01 0.00 0.00 2.73
745 747 6.975949 TCCCTCAAAAATATAAAGGCCAGTA 58.024 36.000 5.01 0.00 0.00 2.74
746 748 5.837829 TCCCTCAAAAATATAAAGGCCAGT 58.162 37.500 5.01 0.00 0.00 4.00
747 749 6.550854 TGATCCCTCAAAAATATAAAGGCCAG 59.449 38.462 5.01 0.00 0.00 4.85
748 750 6.439487 TGATCCCTCAAAAATATAAAGGCCA 58.561 36.000 5.01 0.00 0.00 5.36
749 751 6.777580 TCTGATCCCTCAAAAATATAAAGGCC 59.222 38.462 0.00 0.00 0.00 5.19
750 752 7.823745 TCTGATCCCTCAAAAATATAAAGGC 57.176 36.000 0.00 0.00 0.00 4.35
758 760 9.620259 GAAGTAACTATCTGATCCCTCAAAAAT 57.380 33.333 0.00 0.00 0.00 1.82
759 761 8.047310 GGAAGTAACTATCTGATCCCTCAAAAA 58.953 37.037 0.00 0.00 0.00 1.94
760 762 7.182026 TGGAAGTAACTATCTGATCCCTCAAAA 59.818 37.037 0.00 0.00 0.00 2.44
761 763 6.672218 TGGAAGTAACTATCTGATCCCTCAAA 59.328 38.462 0.00 0.00 0.00 2.69
762 764 6.202331 TGGAAGTAACTATCTGATCCCTCAA 58.798 40.000 0.00 0.00 0.00 3.02
763 765 5.777449 TGGAAGTAACTATCTGATCCCTCA 58.223 41.667 0.00 0.00 0.00 3.86
764 766 6.926630 ATGGAAGTAACTATCTGATCCCTC 57.073 41.667 0.00 0.00 0.00 4.30
765 767 7.698163 AAATGGAAGTAACTATCTGATCCCT 57.302 36.000 0.00 0.00 0.00 4.20
766 768 8.753497 AAAAATGGAAGTAACTATCTGATCCC 57.247 34.615 0.00 0.00 0.00 3.85
799 801 9.279904 CAGAATGTTGTGTTCGTTTTACTTTTA 57.720 29.630 0.00 0.00 0.00 1.52
806 808 3.443976 GCCAGAATGTTGTGTTCGTTTT 58.556 40.909 0.00 0.00 0.00 2.43
1064 1073 3.827898 CCGCCTCCGTCTCCAGAC 61.828 72.222 0.00 0.00 41.47 3.51
1170 1179 4.452733 GGGTCGTCCTCCGCCTTG 62.453 72.222 0.00 0.00 36.19 3.61
1496 1529 5.425630 AGTATCAAAAACCGGACTACCATC 58.574 41.667 9.46 0.00 35.59 3.51
1560 1593 2.119801 ATGAAGGGTGCTAAGTGCTG 57.880 50.000 0.00 0.00 43.37 4.41
1589 1622 9.295214 CACGAACTATAAGAGGATGCATTATAG 57.705 37.037 19.08 19.08 41.82 1.31
1590 1623 8.803235 ACACGAACTATAAGAGGATGCATTATA 58.197 33.333 0.00 0.00 0.00 0.98
1591 1624 7.671302 ACACGAACTATAAGAGGATGCATTAT 58.329 34.615 0.00 0.00 0.00 1.28
1592 1625 7.050970 ACACGAACTATAAGAGGATGCATTA 57.949 36.000 0.00 0.00 0.00 1.90
1622 1655 6.926826 TGCACGAATACAGGATTATACGATTT 59.073 34.615 0.00 0.00 0.00 2.17
1627 1660 5.465390 TGCTTGCACGAATACAGGATTATAC 59.535 40.000 0.00 0.00 0.00 1.47
1655 1688 7.770433 AGTAACAAGCACAGCATTCAGAATATA 59.230 33.333 0.00 0.00 0.00 0.86
1700 1733 5.482526 TGAAGTAGTACTCCACCTGCAAATA 59.517 40.000 2.58 0.00 0.00 1.40
1819 1852 7.064609 AGAGTGTTTTCATTACATGTATGTCCG 59.935 37.037 6.36 0.00 41.97 4.79
1920 1953 6.096001 ACAGCCAGAATAGTTCATCCATTTTC 59.904 38.462 0.00 0.00 0.00 2.29
2121 2154 4.405358 ACAAAAACAGATGCCAAGAAAGGA 59.595 37.500 0.00 0.00 0.00 3.36
2127 2161 3.731652 TCCACAAAAACAGATGCCAAG 57.268 42.857 0.00 0.00 0.00 3.61
2170 2204 2.366590 CAGAGCTAGACCATGCACCATA 59.633 50.000 0.00 0.00 0.00 2.74
2199 2233 1.501582 AGGCAGTAATCCTGAGGACC 58.498 55.000 1.77 0.00 44.49 4.46
2220 2254 7.011723 GGCAAGAGCAAAACATCATGTTTACT 61.012 38.462 16.23 15.71 44.95 2.24
2257 2291 5.604758 TTCATCTCCATTCCACTAGACAG 57.395 43.478 0.00 0.00 0.00 3.51
2394 2428 9.118300 GAATAGAATGGAGTGAATCAGAACAAT 57.882 33.333 0.00 0.00 0.00 2.71
2441 2475 6.094048 CCCAATAGTTATTCCACAAGACACTG 59.906 42.308 0.00 0.00 0.00 3.66
2658 2692 6.339220 AGGTACATATCATATTCCTGGGGAA 58.661 40.000 1.29 1.29 46.39 3.97
2699 2733 3.774766 TCTGCTTCATTGTAGGCTAAGGA 59.225 43.478 0.00 0.00 0.00 3.36
2849 2886 0.173481 CGACTCGGTCACCATCACAT 59.827 55.000 0.00 0.00 32.09 3.21
3235 3324 1.529226 TTACATCCAAACGGGTGCTG 58.471 50.000 0.00 0.00 38.11 4.41
3392 3482 7.610865 TGACACACTACATGAGATGTTCATTA 58.389 34.615 0.00 0.00 44.14 1.90
3668 3758 2.912956 TCCCATTAGAGCTCACAACCTT 59.087 45.455 17.77 0.00 0.00 3.50
3803 4189 9.744468 TCTGAAAATGGTTTTAAGCTAAAAGTC 57.256 29.630 0.00 0.00 38.23 3.01
3811 4197 7.710907 AGTCCTTTTCTGAAAATGGTTTTAAGC 59.289 33.333 15.30 6.51 39.53 3.09
3928 4315 7.106239 ACTGCAATAAAAGCACAGACTACTAT 58.894 34.615 0.00 0.00 37.02 2.12
3944 4331 8.031864 CACACCATAAATTACCAACTGCAATAA 58.968 33.333 0.00 0.00 0.00 1.40
4213 4600 7.762382 AGGTTAATAAAAATGTGCAGAGCTAC 58.238 34.615 0.00 0.00 0.00 3.58
4690 5083 3.027974 ACCGACTGCTGTACTTCTTTC 57.972 47.619 0.00 0.00 0.00 2.62
4810 5203 5.753438 TCGTACAATAGAGCATGAATGGAAC 59.247 40.000 0.00 0.00 0.00 3.62
4826 5219 6.072673 GGAAACTGAACCTTCAATCGTACAAT 60.073 38.462 0.00 0.00 36.64 2.71
4975 5368 5.219739 AGATATGGACAACTGGGTATCACT 58.780 41.667 0.00 0.00 0.00 3.41
4976 5369 5.552870 AGATATGGACAACTGGGTATCAC 57.447 43.478 0.00 0.00 0.00 3.06
4977 5370 6.140377 TGTAGATATGGACAACTGGGTATCA 58.860 40.000 0.00 0.00 0.00 2.15
4978 5371 6.295349 CCTGTAGATATGGACAACTGGGTATC 60.295 46.154 0.00 0.00 0.00 2.24
4979 5372 5.544176 CCTGTAGATATGGACAACTGGGTAT 59.456 44.000 0.00 0.00 0.00 2.73
4980 5373 4.899457 CCTGTAGATATGGACAACTGGGTA 59.101 45.833 0.00 0.00 0.00 3.69
4985 5378 5.395768 GCACTTCCTGTAGATATGGACAACT 60.396 44.000 0.00 0.00 0.00 3.16
5053 5446 3.444034 GGCCTTTTCCTTGGATTCTGTAC 59.556 47.826 0.00 0.00 0.00 2.90
5061 5454 1.149101 ACTCAGGCCTTTTCCTTGGA 58.851 50.000 0.00 0.00 33.25 3.53
5113 5506 9.657419 ACAAACCATAATCAGATCCAAAATTTC 57.343 29.630 0.00 0.00 0.00 2.17
5209 5602 9.160496 CATCTAGCTTCTCTTAGTGTTGATTTT 57.840 33.333 0.00 0.00 0.00 1.82
5397 5791 5.449999 GGTTCTATCCACAAATTTAAGCCCG 60.450 44.000 0.00 0.00 0.00 6.13
5506 5900 2.203294 AGGTTTGCCTTCCGCGTT 60.203 55.556 4.92 0.00 44.18 4.84
5584 5978 1.171308 GCGTCCTGTACACTCCACTA 58.829 55.000 0.00 0.00 0.00 2.74
5585 5979 1.863662 CGCGTCCTGTACACTCCACT 61.864 60.000 0.00 0.00 0.00 4.00
5586 5980 1.443872 CGCGTCCTGTACACTCCAC 60.444 63.158 0.00 0.00 0.00 4.02
5587 5981 2.959372 CGCGTCCTGTACACTCCA 59.041 61.111 0.00 0.00 0.00 3.86
5588 5982 2.506438 GCGCGTCCTGTACACTCC 60.506 66.667 8.43 0.00 0.00 3.85
5593 5992 1.615107 GAAGTGTGCGCGTCCTGTAC 61.615 60.000 8.43 0.00 0.00 2.90
5616 6015 6.265196 GTGCCCTGATATGGATATTGAAAACA 59.735 38.462 0.00 0.00 0.00 2.83
5668 6067 0.036010 TAGGCTTGCTTGCAGAGTCC 60.036 55.000 0.00 3.76 34.04 3.85
5679 6078 1.017387 CGGTCCAGAAATAGGCTTGC 58.983 55.000 0.00 0.00 0.00 4.01
5758 6157 0.546267 TCTGGGCCTTCTCAGCTTCT 60.546 55.000 4.53 0.00 0.00 2.85
5759 6158 0.326264 TTCTGGGCCTTCTCAGCTTC 59.674 55.000 4.53 0.00 0.00 3.86
5764 6163 0.979665 CAGTCTTCTGGGCCTTCTCA 59.020 55.000 4.53 0.00 37.97 3.27
5797 6196 8.275758 TGAAAAGGCACTACCCATTTGTATATA 58.724 33.333 0.00 0.00 38.49 0.86
5798 6197 7.122715 TGAAAAGGCACTACCCATTTGTATAT 58.877 34.615 0.00 0.00 38.49 0.86
5817 6216 7.775120 ACATCCTTATAAAGTGGCATGAAAAG 58.225 34.615 0.00 0.00 0.00 2.27
6046 6688 3.891422 TTTCCAAGCCAAAGCATATGG 57.109 42.857 4.56 0.00 43.56 2.74
6079 6741 3.769844 ACCAGATCGACATAACTTGGTCT 59.230 43.478 0.00 0.00 31.88 3.85
6080 6742 4.124851 ACCAGATCGACATAACTTGGTC 57.875 45.455 0.00 0.00 0.00 4.02
6082 6744 4.093408 CACAACCAGATCGACATAACTTGG 59.907 45.833 0.00 0.00 0.00 3.61
6083 6745 4.436050 GCACAACCAGATCGACATAACTTG 60.436 45.833 0.00 0.00 0.00 3.16
6084 6746 3.684788 GCACAACCAGATCGACATAACTT 59.315 43.478 0.00 0.00 0.00 2.66
6085 6747 3.262420 GCACAACCAGATCGACATAACT 58.738 45.455 0.00 0.00 0.00 2.24
6086 6748 3.000041 TGCACAACCAGATCGACATAAC 59.000 45.455 0.00 0.00 0.00 1.89
6118 6780 7.176690 CCCTTAATAACTTGCTCTCCTTTTTGA 59.823 37.037 0.00 0.00 0.00 2.69
6131 6793 4.156008 AGCGCAAAGACCCTTAATAACTTG 59.844 41.667 11.47 0.00 0.00 3.16
6145 6817 1.962822 CAGCACCAGAGCGCAAAGA 60.963 57.895 11.47 0.00 40.15 2.52
6231 6910 4.522789 GCCCAAATCAAAGAAAGACCACTA 59.477 41.667 0.00 0.00 0.00 2.74
6306 6987 1.497278 CCAACGATGAGCAACACGG 59.503 57.895 0.00 0.00 0.00 4.94
6307 6988 1.497278 CCCAACGATGAGCAACACG 59.503 57.895 0.00 0.00 0.00 4.49
6448 7132 1.271379 CCGTAGTGTGACTACTTGGCA 59.729 52.381 11.18 0.00 46.68 4.92
6449 7133 1.271656 ACCGTAGTGTGACTACTTGGC 59.728 52.381 11.18 0.00 46.68 4.52
6450 7134 3.005050 TCAACCGTAGTGTGACTACTTGG 59.995 47.826 11.18 8.62 46.68 3.61
6555 8965 6.127535 CCACTTCATACTAGTAGGTCGGAAAA 60.128 42.308 13.85 0.02 0.00 2.29
6556 8966 5.359009 CCACTTCATACTAGTAGGTCGGAAA 59.641 44.000 13.85 0.68 0.00 3.13
6558 8968 4.458397 CCACTTCATACTAGTAGGTCGGA 58.542 47.826 13.85 1.55 0.00 4.55
6559 8969 3.004524 GCCACTTCATACTAGTAGGTCGG 59.995 52.174 13.85 10.86 0.00 4.79
6562 8972 7.290248 ACAATATGCCACTTCATACTAGTAGGT 59.710 37.037 13.85 4.95 32.36 3.08
6565 8986 8.360390 CAGACAATATGCCACTTCATACTAGTA 58.640 37.037 4.77 4.77 32.36 1.82
6568 8989 6.326323 TCCAGACAATATGCCACTTCATACTA 59.674 38.462 0.00 0.00 32.36 1.82
6673 9097 1.078497 ACGGATCGCTGAAATGCCA 60.078 52.632 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.