Multiple sequence alignment - TraesCS1A01G147300

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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 TraesCS1A01G147300 chr1A 100.000 3603 0 0 1 3603 254349419 254353021 0.000000e+00 6654.0
1 TraesCS1A01G147300 chr1A 84.722 648 82 10 1928 2560 253728763 253728118 1.830000e-177 632.0
2 TraesCS1A01G147300 chr1A 95.000 200 10 0 1 200 254347919 254347720 7.510000e-82 315.0
3 TraesCS1A01G147300 chr1A 75.820 579 112 26 2013 2580 381097054 381096493 5.930000e-68 268.0
4 TraesCS1A01G147300 chr1A 86.408 103 13 1 1238 1340 253729562 253729461 1.060000e-20 111.0
5 TraesCS1A01G147300 chr1B 95.647 1792 69 6 888 2675 288756645 288758431 0.000000e+00 2868.0
6 TraesCS1A01G147300 chr1B 88.323 668 69 9 201 866 288755997 288756657 0.000000e+00 793.0
7 TraesCS1A01G147300 chr1B 78.516 647 91 20 2852 3473 288798230 288798853 7.300000e-102 381.0
8 TraesCS1A01G147300 chr1B 95.500 200 9 0 1 200 170841219 170841418 1.610000e-83 320.0
9 TraesCS1A01G147300 chr1B 94.527 201 11 0 1 201 170839878 170839678 9.710000e-81 311.0
10 TraesCS1A01G147300 chr1B 74.797 615 121 29 1980 2580 411154702 411154108 2.780000e-61 246.0
11 TraesCS1A01G147300 chr1B 88.636 176 20 0 3036 3211 288797824 288797999 7.840000e-52 215.0
12 TraesCS1A01G147300 chr1D 97.147 736 17 3 887 1620 200868535 200869268 0.000000e+00 1240.0
13 TraesCS1A01G147300 chr1D 94.724 417 21 1 2274 2689 200869277 200869693 0.000000e+00 647.0
14 TraesCS1A01G147300 chr1D 87.751 449 52 3 201 648 200867932 200868378 4.120000e-144 521.0
15 TraesCS1A01G147300 chr1D 80.027 741 99 27 2692 3423 200869769 200870469 1.490000e-138 503.0
16 TraesCS1A01G147300 chr1D 82.520 492 79 7 201 690 434233231 434233717 3.320000e-115 425.0
17 TraesCS1A01G147300 chr1D 84.746 295 32 6 2313 2595 200464599 200464306 2.120000e-72 283.0
18 TraesCS1A01G147300 chr1D 75.244 614 120 30 1980 2580 303516910 303516316 2.760000e-66 263.0
19 TraesCS1A01G147300 chr1D 93.182 44 3 0 3459 3502 200870578 200870621 8.350000e-07 65.8
20 TraesCS1A01G147300 chr5A 79.666 659 111 16 1928 2570 676966726 676966075 1.530000e-123 453.0
21 TraesCS1A01G147300 chr5A 79.863 293 51 8 1051 1340 676968273 676967986 1.310000e-49 207.0
22 TraesCS1A01G147300 chr4B 80.795 604 92 14 1983 2570 637737810 637737215 5.490000e-123 451.0
23 TraesCS1A01G147300 chr4B 79.863 293 51 8 1051 1340 637739317 637739030 1.310000e-49 207.0
24 TraesCS1A01G147300 chr4D 79.091 660 113 16 1928 2570 497166938 497166287 7.150000e-117 431.0
25 TraesCS1A01G147300 chr4D 79.181 293 53 8 1051 1340 497168484 497168197 2.840000e-46 196.0
26 TraesCS1A01G147300 chr2A 96.000 200 8 0 1 200 29953451 29953252 3.470000e-85 326.0
27 TraesCS1A01G147300 chr2A 94.000 200 12 0 1 200 29954797 29954996 1.630000e-78 303.0
28 TraesCS1A01G147300 chr2A 77.899 276 37 16 2691 2958 4090870 4091129 2.240000e-32 150.0
29 TraesCS1A01G147300 chr5B 95.000 200 10 0 1 200 474045142 474044943 7.510000e-82 315.0
30 TraesCS1A01G147300 chr5B 92.500 200 13 2 1 200 474046486 474046683 5.890000e-73 285.0
31 TraesCS1A01G147300 chr3B 95.000 200 10 0 1 200 393249777 393249976 7.510000e-82 315.0
32 TraesCS1A01G147300 chr3B 93.035 201 14 0 1 201 393248434 393248234 9.780000e-76 294.0
33 TraesCS1A01G147300 chr3B 74.534 322 59 18 2745 3064 636268490 636268790 6.320000e-23 119.0
34 TraesCS1A01G147300 chr2B 77.778 297 45 18 2688 2975 5808750 5809034 2.880000e-36 163.0
35 TraesCS1A01G147300 chr2B 75.576 217 36 15 2771 2981 680065011 680064806 1.380000e-14 91.6
36 TraesCS1A01G147300 chr7B 76.452 310 50 14 2782 3087 716265534 716265824 2.900000e-31 147.0
37 TraesCS1A01G147300 chr7D 74.595 370 62 25 2696 3048 48362416 48362770 2.260000e-27 134.0
38 TraesCS1A01G147300 chr3A 75.664 226 38 10 2756 2981 620623544 620623752 2.960000e-16 97.1
39 TraesCS1A01G147300 chr7A 73.065 323 65 17 2772 3086 473673640 473673948 1.060000e-15 95.3
40 TraesCS1A01G147300 chr6B 73.490 298 59 16 2696 2981 15222226 15221937 1.060000e-15 95.3


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 TraesCS1A01G147300 chr1A 254349419 254353021 3602 False 6654.00 6654 100.0000 1 3603 1 chr1A.!!$F1 3602
1 TraesCS1A01G147300 chr1A 253728118 253729562 1444 True 371.50 632 85.5650 1238 2560 2 chr1A.!!$R3 1322
2 TraesCS1A01G147300 chr1A 381096493 381097054 561 True 268.00 268 75.8200 2013 2580 1 chr1A.!!$R2 567
3 TraesCS1A01G147300 chr1B 288755997 288758431 2434 False 1830.50 2868 91.9850 201 2675 2 chr1B.!!$F2 2474
4 TraesCS1A01G147300 chr1B 288797824 288798853 1029 False 298.00 381 83.5760 2852 3473 2 chr1B.!!$F3 621
5 TraesCS1A01G147300 chr1B 411154108 411154702 594 True 246.00 246 74.7970 1980 2580 1 chr1B.!!$R2 600
6 TraesCS1A01G147300 chr1D 200867932 200870621 2689 False 595.36 1240 90.5662 201 3502 5 chr1D.!!$F2 3301
7 TraesCS1A01G147300 chr1D 303516316 303516910 594 True 263.00 263 75.2440 1980 2580 1 chr1D.!!$R2 600
8 TraesCS1A01G147300 chr5A 676966075 676968273 2198 True 330.00 453 79.7645 1051 2570 2 chr5A.!!$R1 1519
9 TraesCS1A01G147300 chr4B 637737215 637739317 2102 True 329.00 451 80.3290 1051 2570 2 chr4B.!!$R1 1519
10 TraesCS1A01G147300 chr4D 497166287 497168484 2197 True 313.50 431 79.1360 1051 2570 2 chr4D.!!$R1 1519

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
192 193 0.107831 CCAGGTGGTCCTTTTCGACA 59.892 55.0 0.0 0.0 43.07 4.35 F
1595 2530 0.036388 GACTTCATGTCCGCCTTCCA 60.036 55.0 0.0 0.0 39.69 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2861 0.238553 GCACGAGGAAAAACAGAGCC 59.761 55.0 0.00 0.00 0.0 4.70 R
3551 4778 0.036388 CGTGTTGTGTGATAGGGCCT 60.036 55.0 12.58 12.58 0.0 5.19 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
24 25 3.414700 CACCGCTGCCGTTCTGTC 61.415 66.667 0.00 0.00 0.00 3.51
29 30 3.114616 CTGCCGTTCTGTCGCCAG 61.115 66.667 0.00 0.00 40.25 4.85
47 48 3.751246 CGCCGACTCCCGTTGGTA 61.751 66.667 1.08 0.00 45.15 3.25
48 49 2.125793 GCCGACTCCCGTTGGTAC 60.126 66.667 1.08 0.00 45.15 3.34
49 50 2.934570 GCCGACTCCCGTTGGTACA 61.935 63.158 0.00 0.00 45.15 2.90
50 51 1.214589 CCGACTCCCGTTGGTACAG 59.785 63.158 0.00 0.00 39.49 2.74
51 52 1.530013 CCGACTCCCGTTGGTACAGT 61.530 60.000 0.00 0.00 39.49 3.55
52 53 0.388134 CGACTCCCGTTGGTACAGTG 60.388 60.000 0.00 0.00 42.39 3.66
53 54 0.677842 GACTCCCGTTGGTACAGTGT 59.322 55.000 0.00 0.00 42.39 3.55
54 55 1.069668 GACTCCCGTTGGTACAGTGTT 59.930 52.381 0.00 0.00 42.39 3.32
55 56 1.202604 ACTCCCGTTGGTACAGTGTTG 60.203 52.381 0.00 0.00 42.39 3.33
56 57 0.533308 TCCCGTTGGTACAGTGTTGC 60.533 55.000 0.00 0.00 42.39 4.17
57 58 1.512156 CCCGTTGGTACAGTGTTGCC 61.512 60.000 0.00 5.31 42.39 4.52
58 59 1.567537 CGTTGGTACAGTGTTGCCG 59.432 57.895 0.00 0.00 42.39 5.69
60 61 1.894756 TTGGTACAGTGTTGCCGCC 60.895 57.895 0.00 0.00 42.39 6.13
61 62 2.032071 GGTACAGTGTTGCCGCCT 59.968 61.111 0.00 0.00 0.00 5.52
63 64 1.574428 GTACAGTGTTGCCGCCTTG 59.426 57.895 0.00 0.00 0.00 3.61
64 65 2.258013 TACAGTGTTGCCGCCTTGC 61.258 57.895 0.00 0.00 0.00 4.01
65 66 2.674563 TACAGTGTTGCCGCCTTGCT 62.675 55.000 0.00 0.00 0.00 3.91
66 67 3.289834 AGTGTTGCCGCCTTGCTG 61.290 61.111 0.00 0.00 0.00 4.41
67 68 3.595758 GTGTTGCCGCCTTGCTGT 61.596 61.111 0.00 0.00 0.00 4.40
68 69 3.594775 TGTTGCCGCCTTGCTGTG 61.595 61.111 0.00 0.00 0.00 3.66
69 70 3.595758 GTTGCCGCCTTGCTGTGT 61.596 61.111 0.00 0.00 0.00 3.72
70 71 3.594775 TTGCCGCCTTGCTGTGTG 61.595 61.111 0.00 0.00 0.00 3.82
135 136 4.922471 CGAAGGGGTCCTTTTTGTTAAA 57.078 40.909 0.34 0.00 44.82 1.52
136 137 5.462530 CGAAGGGGTCCTTTTTGTTAAAT 57.537 39.130 0.34 0.00 44.82 1.40
138 139 6.285224 CGAAGGGGTCCTTTTTGTTAAATTT 58.715 36.000 0.34 0.00 44.82 1.82
139 140 7.435305 CGAAGGGGTCCTTTTTGTTAAATTTA 58.565 34.615 0.34 0.00 44.82 1.40
140 141 8.092068 CGAAGGGGTCCTTTTTGTTAAATTTAT 58.908 33.333 0.00 0.00 44.82 1.40
141 142 9.431887 GAAGGGGTCCTTTTTGTTAAATTTATC 57.568 33.333 0.00 0.00 44.82 1.75
142 143 7.608153 AGGGGTCCTTTTTGTTAAATTTATCG 58.392 34.615 0.00 0.00 0.00 2.92
143 144 6.814644 GGGGTCCTTTTTGTTAAATTTATCGG 59.185 38.462 0.00 0.00 0.00 4.18
144 145 6.311935 GGGTCCTTTTTGTTAAATTTATCGGC 59.688 38.462 0.00 0.00 0.00 5.54
146 147 7.062956 GGTCCTTTTTGTTAAATTTATCGGCAG 59.937 37.037 0.00 0.00 0.00 4.85
147 148 7.062956 GTCCTTTTTGTTAAATTTATCGGCAGG 59.937 37.037 0.00 3.75 0.00 4.85
148 149 6.871492 CCTTTTTGTTAAATTTATCGGCAGGT 59.129 34.615 0.00 0.00 0.00 4.00
149 150 7.148656 CCTTTTTGTTAAATTTATCGGCAGGTG 60.149 37.037 0.00 0.00 0.00 4.00
150 151 4.974368 TGTTAAATTTATCGGCAGGTGG 57.026 40.909 0.00 0.00 0.00 4.61
151 152 4.337145 TGTTAAATTTATCGGCAGGTGGT 58.663 39.130 0.00 0.00 0.00 4.16
153 154 3.366052 AAATTTATCGGCAGGTGGTCT 57.634 42.857 0.00 0.00 0.00 3.85
155 156 2.871096 TTTATCGGCAGGTGGTCTTT 57.129 45.000 0.00 0.00 0.00 2.52
156 157 2.871096 TTATCGGCAGGTGGTCTTTT 57.129 45.000 0.00 0.00 0.00 2.27
157 158 2.871096 TATCGGCAGGTGGTCTTTTT 57.129 45.000 0.00 0.00 0.00 1.94
175 176 4.327982 TTTTTGTCAATTCATTCGCCCA 57.672 36.364 0.00 0.00 0.00 5.36
176 177 3.574284 TTTGTCAATTCATTCGCCCAG 57.426 42.857 0.00 0.00 0.00 4.45
177 178 1.462616 TGTCAATTCATTCGCCCAGG 58.537 50.000 0.00 0.00 0.00 4.45
178 179 1.271871 TGTCAATTCATTCGCCCAGGT 60.272 47.619 0.00 0.00 0.00 4.00
179 180 1.133025 GTCAATTCATTCGCCCAGGTG 59.867 52.381 0.00 0.00 0.00 4.00
180 181 0.457035 CAATTCATTCGCCCAGGTGG 59.543 55.000 0.00 0.00 37.09 4.61
182 183 0.394352 ATTCATTCGCCCAGGTGGTC 60.394 55.000 0.00 0.00 36.04 4.02
183 184 2.438434 CATTCGCCCAGGTGGTCC 60.438 66.667 0.00 0.00 36.04 4.46
188 189 1.971695 CGCCCAGGTGGTCCTTTTC 60.972 63.158 0.00 0.00 43.07 2.29
189 190 1.971695 GCCCAGGTGGTCCTTTTCG 60.972 63.158 0.00 0.00 43.07 3.46
190 191 1.758592 CCCAGGTGGTCCTTTTCGA 59.241 57.895 0.00 0.00 43.07 3.71
191 192 0.605589 CCCAGGTGGTCCTTTTCGAC 60.606 60.000 0.00 0.00 43.07 4.20
192 193 0.107831 CCAGGTGGTCCTTTTCGACA 59.892 55.000 0.00 0.00 43.07 4.35
194 195 2.294074 CAGGTGGTCCTTTTCGACAAA 58.706 47.619 0.00 0.00 43.07 2.83
195 196 2.685897 CAGGTGGTCCTTTTCGACAAAA 59.314 45.455 0.00 0.00 43.07 2.44
257 258 2.034053 GTCCCATGCGTTCAAAAACTCA 59.966 45.455 0.00 0.00 34.79 3.41
273 274 7.976734 TCAAAAACTCATGTATTCCGTTGTTTT 59.023 29.630 0.00 0.00 37.78 2.43
316 318 2.078849 ATGATCAACGTGTCGAAGCA 57.921 45.000 0.00 0.00 0.00 3.91
323 325 0.171455 ACGTGTCGAAGCATCTCCTC 59.829 55.000 0.00 0.00 0.00 3.71
340 343 4.141274 TCTCCTCTGTTTTGTTGGGATTGA 60.141 41.667 0.00 0.00 0.00 2.57
363 367 0.911769 CTAGCCTCCAACCACCATGA 59.088 55.000 0.00 0.00 0.00 3.07
384 388 3.826729 GAGGTAAAGGTGGCACTTTGAAT 59.173 43.478 16.16 3.09 40.64 2.57
418 422 1.070134 CCGACTCCAACTCTGGTGAAA 59.930 52.381 0.47 0.00 43.97 2.69
419 423 2.135933 CGACTCCAACTCTGGTGAAAC 58.864 52.381 0.47 0.00 43.97 2.78
426 430 6.042781 ACTCCAACTCTGGTGAAACATAAGTA 59.957 38.462 0.47 0.00 43.97 2.24
427 431 7.016153 TCCAACTCTGGTGAAACATAAGTAT 57.984 36.000 0.00 0.00 43.97 2.12
435 439 7.936847 TCTGGTGAAACATAAGTATCACACTTT 59.063 33.333 7.03 0.00 41.54 2.66
461 466 2.795681 GCATACCCACAACGCATCAATG 60.796 50.000 0.00 0.00 0.00 2.82
490 495 4.405680 TCCACAGTGTCTTTCTCTTGAAGA 59.594 41.667 0.00 0.00 33.28 2.87
506 511 5.928839 TCTTGAAGACAGAGATAGCAAACAC 59.071 40.000 0.00 0.00 0.00 3.32
516 521 4.995124 AGATAGCAAACACTCGTATCGTT 58.005 39.130 0.00 0.00 0.00 3.85
573 578 3.003275 CACAACATATATTGGACCGCCAC 59.997 47.826 0.00 0.00 45.94 5.01
579 584 2.830186 TATTGGACCGCCACCCAAGC 62.830 60.000 0.00 0.00 45.94 4.01
648 653 2.842496 ACATTGGAGATCTCTTGAGCCA 59.158 45.455 21.81 8.52 0.00 4.75
686 691 4.854924 CCGATCGGGCCATGCACA 62.855 66.667 26.95 0.00 0.00 4.57
700 705 2.327343 GCACATTCCTGACGCAGCA 61.327 57.895 0.00 0.00 0.00 4.41
722 727 1.227943 GGCCAGGCGAATGCATCTA 60.228 57.895 5.00 0.00 45.35 1.98
723 728 1.233285 GGCCAGGCGAATGCATCTAG 61.233 60.000 5.00 0.00 45.35 2.43
724 729 0.533755 GCCAGGCGAATGCATCTAGT 60.534 55.000 0.00 0.00 45.35 2.57
725 730 1.270305 GCCAGGCGAATGCATCTAGTA 60.270 52.381 0.00 0.00 45.35 1.82
752 757 5.049680 TCCTTGCACGAACTAGTTCAAAATC 60.050 40.000 29.95 16.29 39.46 2.17
756 761 5.700832 TGCACGAACTAGTTCAAAATCTGAT 59.299 36.000 29.95 5.71 39.46 2.90
765 770 6.174451 AGTTCAAAATCTGATGTGACATCG 57.826 37.500 19.53 14.27 32.78 3.84
782 787 2.132996 CGGCCCTGCTCTGAGATCT 61.133 63.158 9.28 0.00 0.00 2.75
872 878 3.827505 AAAAACTGGAGCTCCTGCA 57.172 47.368 32.88 14.63 42.74 4.41
873 879 2.071778 AAAAACTGGAGCTCCTGCAA 57.928 45.000 32.88 14.27 42.74 4.08
874 880 2.071778 AAAACTGGAGCTCCTGCAAA 57.928 45.000 32.88 13.91 42.74 3.68
875 881 2.071778 AAACTGGAGCTCCTGCAAAA 57.928 45.000 32.88 13.19 42.74 2.44
876 882 2.071778 AACTGGAGCTCCTGCAAAAA 57.928 45.000 32.88 12.48 42.74 1.94
1371 2265 2.429610 CGTCCGATCCCCTTCTTTCTTA 59.570 50.000 0.00 0.00 0.00 2.10
1452 2387 3.009115 CGGTGGGTGGTGGAGGAT 61.009 66.667 0.00 0.00 0.00 3.24
1493 2428 0.391130 GCCTACACTGACCAATGCGA 60.391 55.000 0.00 0.00 0.00 5.10
1585 2520 1.618837 AGTGCTACACCGACTTCATGT 59.381 47.619 0.00 0.00 34.49 3.21
1586 2521 1.993370 GTGCTACACCGACTTCATGTC 59.007 52.381 0.00 0.00 42.06 3.06
1595 2530 0.036388 GACTTCATGTCCGCCTTCCA 60.036 55.000 0.00 0.00 39.69 3.53
1655 2590 3.350219 AAGTCCCACGCACTTGATTAT 57.650 42.857 0.00 0.00 32.65 1.28
1656 2591 4.481368 AAGTCCCACGCACTTGATTATA 57.519 40.909 0.00 0.00 32.65 0.98
1679 2614 1.686587 TCTCTGTTTTCTCTGTCGCCA 59.313 47.619 0.00 0.00 0.00 5.69
1684 2619 2.290367 TGTTTTCTCTGTCGCCATTGTG 59.710 45.455 0.00 0.00 0.00 3.33
1693 2646 3.304721 GCCATTGTGCTGGTGCCA 61.305 61.111 0.00 0.00 38.63 4.92
1779 2732 2.513204 TCGTACCCGGAGAGCGAG 60.513 66.667 0.73 0.00 33.95 5.03
1833 2786 3.119245 TCCAATGCTACGACAAGGTACTC 60.119 47.826 0.00 0.00 38.49 2.59
1894 2861 9.107367 GTATCTCGAAAGTTTCTTGACATTTTG 57.893 33.333 13.56 0.00 0.00 2.44
2596 3647 2.434884 ACACGGATGAGCCAAGCG 60.435 61.111 0.00 0.00 35.94 4.68
2597 3648 2.125552 CACGGATGAGCCAAGCGA 60.126 61.111 0.00 0.00 35.94 4.93
2599 3650 2.587194 CGGATGAGCCAAGCGAGG 60.587 66.667 0.00 0.00 35.94 4.63
2808 3936 3.428198 TGATAATTGTTTTGCGTGCTTGC 59.572 39.130 0.00 0.00 0.00 4.01
2818 3946 1.811965 TGCGTGCTTGCAATAGTTCAT 59.188 42.857 0.00 0.00 43.02 2.57
2819 3947 3.006247 TGCGTGCTTGCAATAGTTCATA 58.994 40.909 0.00 0.00 43.02 2.15
2820 3948 3.627123 TGCGTGCTTGCAATAGTTCATAT 59.373 39.130 0.00 0.00 43.02 1.78
2821 3949 4.813697 TGCGTGCTTGCAATAGTTCATATA 59.186 37.500 0.00 0.00 43.02 0.86
2824 3952 6.358030 GCGTGCTTGCAATAGTTCATATAAAG 59.642 38.462 0.00 0.00 34.15 1.85
2825 3953 7.630026 CGTGCTTGCAATAGTTCATATAAAGA 58.370 34.615 0.00 0.00 0.00 2.52
2827 3955 8.830580 GTGCTTGCAATAGTTCATATAAAGAGA 58.169 33.333 0.00 0.00 0.00 3.10
2828 3956 8.830580 TGCTTGCAATAGTTCATATAAAGAGAC 58.169 33.333 0.00 0.00 0.00 3.36
2829 3957 8.830580 GCTTGCAATAGTTCATATAAAGAGACA 58.169 33.333 0.00 0.00 0.00 3.41
2842 3970 9.655769 CATATAAAGAGACATTTGTGGAAATCG 57.344 33.333 0.00 0.00 28.65 3.34
2843 3971 7.687941 ATAAAGAGACATTTGTGGAAATCGT 57.312 32.000 0.00 0.00 28.65 3.73
2844 3972 5.362556 AAGAGACATTTGTGGAAATCGTG 57.637 39.130 0.00 0.00 28.65 4.35
2845 3973 4.641396 AGAGACATTTGTGGAAATCGTGA 58.359 39.130 0.00 0.00 28.65 4.35
2851 3979 6.102663 ACATTTGTGGAAATCGTGACAAAAA 58.897 32.000 0.00 0.00 40.61 1.94
2875 4003 6.470557 AAACAAATCAATGCTCCGAAAATG 57.529 33.333 0.00 0.00 0.00 2.32
2876 4004 5.389859 ACAAATCAATGCTCCGAAAATGA 57.610 34.783 0.00 0.00 0.00 2.57
2878 4006 5.808540 ACAAATCAATGCTCCGAAAATGATG 59.191 36.000 0.00 0.00 0.00 3.07
2882 4010 5.401550 TCAATGCTCCGAAAATGATGTTTC 58.598 37.500 0.00 0.00 34.71 2.78
2884 4012 4.424061 TGCTCCGAAAATGATGTTTCTG 57.576 40.909 0.00 0.00 35.70 3.02
2893 4021 7.083858 CGAAAATGATGTTTCTGAAAGCCTTA 58.916 34.615 2.48 0.00 35.70 2.69
2894 4022 7.594758 CGAAAATGATGTTTCTGAAAGCCTTAA 59.405 33.333 2.48 0.00 35.70 1.85
2901 4029 7.448748 TGTTTCTGAAAGCCTTAAGGAATAC 57.551 36.000 26.21 12.92 37.39 1.89
2941 4070 4.712763 GTGACTTCCACGAATGTCATTTC 58.287 43.478 0.00 0.00 40.78 2.17
3005 4136 7.722795 TTATCACACAAAGATTTCAGAACGA 57.277 32.000 0.00 0.00 0.00 3.85
3007 4138 6.228273 TCACACAAAGATTTCAGAACGATC 57.772 37.500 0.00 0.00 0.00 3.69
3009 4140 6.146184 TCACACAAAGATTTCAGAACGATCTC 59.854 38.462 0.00 0.00 32.03 2.75
3011 4142 6.483307 ACACAAAGATTTCAGAACGATCTCAA 59.517 34.615 0.00 0.00 32.03 3.02
3014 4145 8.571336 ACAAAGATTTCAGAACGATCTCAATTT 58.429 29.630 0.00 0.00 32.03 1.82
3015 4146 9.403110 CAAAGATTTCAGAACGATCTCAATTTT 57.597 29.630 0.00 0.00 32.03 1.82
3018 4149 9.442047 AGATTTCAGAACGATCTCAATTTTACT 57.558 29.630 0.00 0.00 32.03 2.24
3063 4194 2.315925 TCATCCCGAGCTCATTTGAC 57.684 50.000 15.40 0.00 0.00 3.18
3072 4203 1.092345 GCTCATTTGACCTCGGGAGC 61.092 60.000 0.00 0.00 40.63 4.70
3073 4204 0.807667 CTCATTTGACCTCGGGAGCG 60.808 60.000 0.00 0.00 0.00 5.03
3096 4227 4.636206 GGAAGAGTACTTTCGCCATTTCAT 59.364 41.667 0.00 0.00 36.39 2.57
3121 4252 6.119536 TCTCTATCTTCTCTTCTCACACCTC 58.880 44.000 0.00 0.00 0.00 3.85
3126 4257 1.615883 TCTCTTCTCACACCTCTGTGC 59.384 52.381 0.00 0.00 46.59 4.57
3129 4260 2.170397 TCTTCTCACACCTCTGTGCAAA 59.830 45.455 0.00 0.00 46.59 3.68
3175 4306 7.871973 CACTATAGTCTAGTAGTACGACATGGT 59.128 40.741 1.26 0.00 30.37 3.55
3203 4357 6.127535 ACACTATAGCTTGCCTAGTTTTACGA 60.128 38.462 0.00 0.00 0.00 3.43
3219 4373 3.767900 CGACATGATCGTCTTTGCG 57.232 52.632 0.00 0.00 46.25 4.85
3228 4382 2.114670 CGTCTTTGCGCCCCATGAT 61.115 57.895 4.18 0.00 0.00 2.45
3229 4383 1.729881 GTCTTTGCGCCCCATGATC 59.270 57.895 4.18 0.00 0.00 2.92
3232 4386 2.345880 CTTTGCGCCCCATGATCAGC 62.346 60.000 4.18 0.00 0.00 4.26
3259 4413 1.236616 TTGTGGCGGTCAAGATGCAG 61.237 55.000 0.00 0.00 0.00 4.41
3266 4420 1.138859 CGGTCAAGATGCAGGTGGATA 59.861 52.381 0.00 0.00 0.00 2.59
3275 4429 0.107017 GCAGGTGGATAGGCACATGT 60.107 55.000 0.00 0.00 35.78 3.21
3281 4435 1.409064 TGGATAGGCACATGTCTCGTC 59.591 52.381 0.00 0.00 0.00 4.20
3282 4436 1.683917 GGATAGGCACATGTCTCGTCT 59.316 52.381 0.00 0.00 0.00 4.18
3286 4440 0.814457 GGCACATGTCTCGTCTCTCT 59.186 55.000 0.00 0.00 0.00 3.10
3287 4441 2.017782 GGCACATGTCTCGTCTCTCTA 58.982 52.381 0.00 0.00 0.00 2.43
3288 4442 2.032799 GGCACATGTCTCGTCTCTCTAG 59.967 54.545 0.00 0.00 0.00 2.43
3293 4447 2.475155 TGTCTCGTCTCTCTAGGGGTA 58.525 52.381 0.00 0.00 0.00 3.69
3295 4449 4.229639 TGTCTCGTCTCTCTAGGGGTATA 58.770 47.826 0.00 0.00 0.00 1.47
3336 4490 4.034975 GCACAATTGTCTTCTCTCTATGCC 59.965 45.833 8.48 0.00 0.00 4.40
3347 4501 3.058450 CTCTCTATGCCAAAGATGAGCG 58.942 50.000 0.00 0.00 0.00 5.03
3355 4509 0.723414 CAAAGATGAGCGATGCACGT 59.277 50.000 9.76 0.00 44.60 4.49
3369 4523 4.988598 ACGTGAGCGGTGCAAGGG 62.989 66.667 0.00 0.00 43.45 3.95
3371 4525 2.281484 GTGAGCGGTGCAAGGGAA 60.281 61.111 0.00 0.00 0.00 3.97
3377 4531 1.073199 CGGTGCAAGGGAAGGAAGT 59.927 57.895 0.00 0.00 0.00 3.01
3427 4603 4.856801 GATGGCCATCCACCGCGT 62.857 66.667 32.15 1.12 46.92 6.01
3430 4606 4.856801 GGCCATCCACCGCGTCAT 62.857 66.667 4.92 0.00 0.00 3.06
3455 4632 2.680352 ACTCCGTCATGCCCTCGT 60.680 61.111 0.00 0.00 0.00 4.18
3502 4729 1.588824 CGCCTCTTTGCAGCATCCAA 61.589 55.000 0.00 0.00 0.00 3.53
3503 4730 0.172803 GCCTCTTTGCAGCATCCAAG 59.827 55.000 0.00 0.00 0.00 3.61
3504 4731 1.542492 CCTCTTTGCAGCATCCAAGT 58.458 50.000 0.00 0.00 0.00 3.16
3505 4732 1.201647 CCTCTTTGCAGCATCCAAGTG 59.798 52.381 0.00 0.00 0.00 3.16
3506 4733 0.599558 TCTTTGCAGCATCCAAGTGC 59.400 50.000 0.00 0.00 45.38 4.40
3507 4734 0.389426 CTTTGCAGCATCCAAGTGCC 60.389 55.000 0.00 0.00 46.19 5.01
3508 4735 1.818959 TTTGCAGCATCCAAGTGCCC 61.819 55.000 0.00 0.00 46.19 5.36
3509 4736 3.455469 GCAGCATCCAAGTGCCCC 61.455 66.667 0.00 0.00 46.19 5.80
3510 4737 2.757099 CAGCATCCAAGTGCCCCC 60.757 66.667 0.00 0.00 46.19 5.40
3542 4769 3.136123 CCGCTCCCCGACGACTAA 61.136 66.667 0.00 0.00 40.02 2.24
3543 4770 2.101770 CGCTCCCCGACGACTAAC 59.898 66.667 0.00 0.00 40.02 2.34
3556 4783 2.588286 ACTAACGTAGTCCAGGCCC 58.412 57.895 0.00 0.00 45.00 5.80
3557 4784 0.040794 ACTAACGTAGTCCAGGCCCT 59.959 55.000 0.00 0.00 45.00 5.19
3558 4785 1.285962 ACTAACGTAGTCCAGGCCCTA 59.714 52.381 0.00 0.00 45.00 3.53
3559 4786 2.091444 ACTAACGTAGTCCAGGCCCTAT 60.091 50.000 0.00 0.00 45.00 2.57
3560 4787 1.411041 AACGTAGTCCAGGCCCTATC 58.589 55.000 0.00 0.00 45.00 2.08
3561 4788 0.260816 ACGTAGTCCAGGCCCTATCA 59.739 55.000 0.00 0.00 29.74 2.15
3562 4789 0.674534 CGTAGTCCAGGCCCTATCAC 59.325 60.000 0.00 0.00 0.00 3.06
3563 4790 1.789523 GTAGTCCAGGCCCTATCACA 58.210 55.000 0.00 0.00 0.00 3.58
3564 4791 1.413077 GTAGTCCAGGCCCTATCACAC 59.587 57.143 0.00 0.00 0.00 3.82
3565 4792 0.252696 AGTCCAGGCCCTATCACACA 60.253 55.000 0.00 0.00 0.00 3.72
3566 4793 0.618458 GTCCAGGCCCTATCACACAA 59.382 55.000 0.00 0.00 0.00 3.33
3567 4794 0.618458 TCCAGGCCCTATCACACAAC 59.382 55.000 0.00 0.00 0.00 3.32
3568 4795 0.327924 CCAGGCCCTATCACACAACA 59.672 55.000 0.00 0.00 0.00 3.33
3569 4796 1.453155 CAGGCCCTATCACACAACAC 58.547 55.000 0.00 0.00 0.00 3.32
3570 4797 0.036388 AGGCCCTATCACACAACACG 60.036 55.000 0.00 0.00 0.00 4.49
3571 4798 0.036765 GGCCCTATCACACAACACGA 60.037 55.000 0.00 0.00 0.00 4.35
3572 4799 1.359848 GCCCTATCACACAACACGAG 58.640 55.000 0.00 0.00 0.00 4.18
3573 4800 2.007049 GCCCTATCACACAACACGAGG 61.007 57.143 0.00 0.00 0.00 4.63
3574 4801 1.359848 CCTATCACACAACACGAGGC 58.640 55.000 0.00 0.00 0.00 4.70
3575 4802 1.066858 CCTATCACACAACACGAGGCT 60.067 52.381 0.00 0.00 0.00 4.58
3576 4803 2.263077 CTATCACACAACACGAGGCTC 58.737 52.381 3.87 3.87 0.00 4.70
3577 4804 0.320771 ATCACACAACACGAGGCTCC 60.321 55.000 9.32 0.00 0.00 4.70
3578 4805 2.029073 ACACAACACGAGGCTCCG 59.971 61.111 9.32 6.86 0.00 4.63
3579 4806 2.029073 CACAACACGAGGCTCCGT 59.971 61.111 9.32 7.54 44.43 4.69
3580 4807 2.022129 CACAACACGAGGCTCCGTC 61.022 63.158 9.32 0.00 41.29 4.79
3581 4808 2.432628 CAACACGAGGCTCCGTCC 60.433 66.667 9.32 0.00 41.29 4.79
3582 4809 3.692406 AACACGAGGCTCCGTCCC 61.692 66.667 9.32 0.00 41.29 4.46
3583 4810 4.988716 ACACGAGGCTCCGTCCCA 62.989 66.667 9.32 0.00 41.29 4.37
3584 4811 4.135153 CACGAGGCTCCGTCCCAG 62.135 72.222 9.32 0.00 41.29 4.45
3587 4814 3.775654 GAGGCTCCGTCCCAGGTG 61.776 72.222 2.15 0.00 0.00 4.00
3591 4818 4.087892 CTCCGTCCCAGGTGCCAG 62.088 72.222 0.00 0.00 0.00 4.85
3595 4822 4.284550 GTCCCAGGTGCCAGCCAA 62.285 66.667 0.00 0.00 0.00 4.52
3596 4823 3.970410 TCCCAGGTGCCAGCCAAG 61.970 66.667 0.00 0.00 0.00 3.61
3597 4824 3.970410 CCCAGGTGCCAGCCAAGA 61.970 66.667 0.00 0.00 0.00 3.02
3598 4825 2.360852 CCAGGTGCCAGCCAAGAG 60.361 66.667 0.00 0.00 0.00 2.85
3599 4826 3.060615 CAGGTGCCAGCCAAGAGC 61.061 66.667 0.00 0.00 44.25 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.414700 GACAGAACGGCAGCGGTG 61.415 66.667 10.98 10.98 0.00 4.94
31 32 2.125793 GTACCAACGGGAGTCGGC 60.126 66.667 0.00 0.00 41.90 5.54
32 33 1.214589 CTGTACCAACGGGAGTCGG 59.785 63.158 0.00 0.00 46.69 4.79
33 34 0.388134 CACTGTACCAACGGGAGTCG 60.388 60.000 0.00 0.00 46.69 4.18
36 37 1.508632 CAACACTGTACCAACGGGAG 58.491 55.000 0.00 0.00 36.19 4.30
37 38 0.533308 GCAACACTGTACCAACGGGA 60.533 55.000 0.00 0.00 36.19 5.14
38 39 1.512156 GGCAACACTGTACCAACGGG 61.512 60.000 0.00 0.00 36.19 5.28
39 40 1.837538 CGGCAACACTGTACCAACGG 61.838 60.000 0.00 0.00 38.04 4.44
40 41 1.567537 CGGCAACACTGTACCAACG 59.432 57.895 0.00 0.00 0.00 4.10
41 42 1.281656 GCGGCAACACTGTACCAAC 59.718 57.895 0.00 0.00 0.00 3.77
42 43 1.894756 GGCGGCAACACTGTACCAA 60.895 57.895 3.07 0.00 0.00 3.67
43 44 2.281208 GGCGGCAACACTGTACCA 60.281 61.111 3.07 0.00 0.00 3.25
45 46 1.574428 CAAGGCGGCAACACTGTAC 59.426 57.895 13.08 0.00 0.00 2.90
46 47 2.258013 GCAAGGCGGCAACACTGTA 61.258 57.895 13.08 0.00 0.00 2.74
47 48 3.595758 GCAAGGCGGCAACACTGT 61.596 61.111 13.08 0.00 0.00 3.55
48 49 3.289834 AGCAAGGCGGCAACACTG 61.290 61.111 13.08 1.10 35.83 3.66
49 50 3.289834 CAGCAAGGCGGCAACACT 61.290 61.111 13.08 0.00 35.83 3.55
50 51 3.595758 ACAGCAAGGCGGCAACAC 61.596 61.111 13.08 0.00 35.83 3.32
51 52 3.594775 CACAGCAAGGCGGCAACA 61.595 61.111 13.08 0.00 35.83 3.33
52 53 3.595758 ACACAGCAAGGCGGCAAC 61.596 61.111 13.08 0.00 35.83 4.17
53 54 3.594775 CACACAGCAAGGCGGCAA 61.595 61.111 13.08 0.00 35.83 4.52
60 61 4.034258 CTGCCGCCACACAGCAAG 62.034 66.667 0.00 0.00 35.79 4.01
107 108 4.410400 GGACCCCTTCGGCTGTGG 62.410 72.222 0.00 0.00 33.26 4.17
108 109 2.411765 AAAGGACCCCTTCGGCTGTG 62.412 60.000 0.00 0.00 43.92 3.66
112 113 0.826256 ACAAAAAGGACCCCTTCGGC 60.826 55.000 0.00 0.00 43.92 5.54
115 116 9.431887 GATAAATTTAACAAAAAGGACCCCTTC 57.568 33.333 1.21 0.00 43.92 3.46
117 118 7.310175 CCGATAAATTTAACAAAAAGGACCCCT 60.310 37.037 1.21 0.00 33.87 4.79
118 119 6.814644 CCGATAAATTTAACAAAAAGGACCCC 59.185 38.462 1.21 0.00 0.00 4.95
119 120 6.311935 GCCGATAAATTTAACAAAAAGGACCC 59.688 38.462 1.21 0.00 0.00 4.46
120 121 6.869388 TGCCGATAAATTTAACAAAAAGGACC 59.131 34.615 1.21 0.00 0.00 4.46
124 125 7.148656 CCACCTGCCGATAAATTTAACAAAAAG 60.149 37.037 1.21 0.00 0.00 2.27
125 126 6.647067 CCACCTGCCGATAAATTTAACAAAAA 59.353 34.615 1.21 0.00 0.00 1.94
126 127 6.159988 CCACCTGCCGATAAATTTAACAAAA 58.840 36.000 1.21 0.00 0.00 2.44
128 129 4.767928 ACCACCTGCCGATAAATTTAACAA 59.232 37.500 1.21 0.00 0.00 2.83
129 130 4.337145 ACCACCTGCCGATAAATTTAACA 58.663 39.130 1.21 0.00 0.00 2.41
130 131 4.638865 AGACCACCTGCCGATAAATTTAAC 59.361 41.667 1.21 0.00 0.00 2.01
131 132 4.850680 AGACCACCTGCCGATAAATTTAA 58.149 39.130 1.21 0.00 0.00 1.52
132 133 4.497291 AGACCACCTGCCGATAAATTTA 57.503 40.909 0.00 0.00 0.00 1.40
133 134 3.366052 AGACCACCTGCCGATAAATTT 57.634 42.857 0.00 0.00 0.00 1.82
134 135 3.366052 AAGACCACCTGCCGATAAATT 57.634 42.857 0.00 0.00 0.00 1.82
135 136 3.366052 AAAGACCACCTGCCGATAAAT 57.634 42.857 0.00 0.00 0.00 1.40
136 137 2.871096 AAAGACCACCTGCCGATAAA 57.129 45.000 0.00 0.00 0.00 1.40
138 139 2.871096 AAAAAGACCACCTGCCGATA 57.129 45.000 0.00 0.00 0.00 2.92
139 140 3.745723 AAAAAGACCACCTGCCGAT 57.254 47.368 0.00 0.00 0.00 4.18
155 156 3.305950 CCTGGGCGAATGAATTGACAAAA 60.306 43.478 0.00 0.00 0.00 2.44
156 157 2.230992 CCTGGGCGAATGAATTGACAAA 59.769 45.455 0.00 0.00 0.00 2.83
157 158 1.818060 CCTGGGCGAATGAATTGACAA 59.182 47.619 0.00 0.00 0.00 3.18
159 160 1.133025 CACCTGGGCGAATGAATTGAC 59.867 52.381 0.00 0.00 0.00 3.18
160 161 1.462616 CACCTGGGCGAATGAATTGA 58.537 50.000 0.00 0.00 0.00 2.57
161 162 0.457035 CCACCTGGGCGAATGAATTG 59.543 55.000 0.00 0.00 0.00 2.32
162 163 0.039618 ACCACCTGGGCGAATGAATT 59.960 50.000 0.00 0.00 42.05 2.17
163 164 0.394352 GACCACCTGGGCGAATGAAT 60.394 55.000 0.00 0.00 42.05 2.57
165 166 2.668632 GACCACCTGGGCGAATGA 59.331 61.111 0.00 0.00 42.05 2.57
167 168 1.789576 AAAGGACCACCTGGGCGAAT 61.790 55.000 0.00 0.00 47.00 3.34
168 169 2.002018 AAAAGGACCACCTGGGCGAA 62.002 55.000 0.00 0.00 47.00 4.70
169 170 2.406002 GAAAAGGACCACCTGGGCGA 62.406 60.000 0.00 0.00 47.00 5.54
170 171 1.971695 GAAAAGGACCACCTGGGCG 60.972 63.158 0.00 0.00 47.00 6.13
176 177 3.786516 TTTTTGTCGAAAAGGACCACC 57.213 42.857 0.00 0.00 36.07 4.61
194 195 5.332743 TCTTGGTTGGCCAGATTAGATTTT 58.667 37.500 5.11 0.00 46.91 1.82
195 196 4.934356 TCTTGGTTGGCCAGATTAGATTT 58.066 39.130 5.11 0.00 46.91 2.17
197 198 3.782523 TCTCTTGGTTGGCCAGATTAGAT 59.217 43.478 5.11 0.00 46.91 1.98
198 199 3.181329 TCTCTTGGTTGGCCAGATTAGA 58.819 45.455 5.11 7.50 46.91 2.10
199 200 3.634397 TCTCTTGGTTGGCCAGATTAG 57.366 47.619 5.11 2.98 46.91 1.73
280 281 7.522236 CGTTGATCATAGTCATAGCTTGGTCTA 60.522 40.741 0.00 0.00 0.00 2.59
282 283 5.403766 CGTTGATCATAGTCATAGCTTGGTC 59.596 44.000 0.00 0.00 0.00 4.02
284 285 5.176406 CACGTTGATCATAGTCATAGCTTGG 59.824 44.000 0.00 0.00 0.00 3.61
301 303 1.668919 GGAGATGCTTCGACACGTTGA 60.669 52.381 0.00 0.00 0.00 3.18
316 318 4.664688 ATCCCAACAAAACAGAGGAGAT 57.335 40.909 0.00 0.00 0.00 2.75
340 343 0.919710 GGTGGTTGGAGGCTAGGAAT 59.080 55.000 0.00 0.00 0.00 3.01
363 367 3.306472 TTCAAAGTGCCACCTTTACCT 57.694 42.857 0.00 0.00 33.00 3.08
366 370 2.817258 CCGATTCAAAGTGCCACCTTTA 59.183 45.455 0.00 0.00 33.00 1.85
435 439 2.505405 TGCGTTGTGGGTATGCTAAAA 58.495 42.857 0.00 0.00 0.00 1.52
447 452 4.097714 GGATAACACATTGATGCGTTGTG 58.902 43.478 7.52 7.52 44.85 3.33
448 453 3.755905 TGGATAACACATTGATGCGTTGT 59.244 39.130 7.45 1.62 34.33 3.32
449 454 4.354071 TGGATAACACATTGATGCGTTG 57.646 40.909 7.45 0.00 34.33 4.10
465 470 6.267699 TCTTCAAGAGAAAGACACTGTGGATA 59.732 38.462 13.09 0.00 32.35 2.59
490 495 3.944055 ACGAGTGTTTGCTATCTCTGT 57.056 42.857 0.00 0.00 0.00 3.41
506 511 1.132453 TGGACTGCAGAACGATACGAG 59.868 52.381 23.35 0.00 0.00 4.18
536 541 1.134521 GTTGTGGACATCGGATAGGCA 60.135 52.381 0.00 0.00 0.00 4.75
573 578 2.660189 ATGCAAAATCTTCGCTTGGG 57.340 45.000 0.00 0.00 0.00 4.12
579 584 7.412853 AGCTATACTCAAATGCAAAATCTTCG 58.587 34.615 0.00 0.00 0.00 3.79
663 668 0.606096 CATGGCCCGATCGGTGTATA 59.394 55.000 31.22 13.85 0.00 1.47
686 691 0.957395 CCTTGTGCTGCGTCAGGAAT 60.957 55.000 5.16 0.00 32.80 3.01
700 705 3.064324 GCATTCGCCTGGCCTTGT 61.064 61.111 14.12 0.00 0.00 3.16
722 727 4.017808 ACTAGTTCGTGCAAGGATCTACT 58.982 43.478 0.00 0.00 33.35 2.57
723 728 4.373348 ACTAGTTCGTGCAAGGATCTAC 57.627 45.455 0.00 0.00 33.35 2.59
724 729 4.461431 TGAACTAGTTCGTGCAAGGATCTA 59.539 41.667 26.35 5.41 42.28 1.98
725 730 3.258372 TGAACTAGTTCGTGCAAGGATCT 59.742 43.478 26.35 2.64 42.28 2.75
752 757 0.812811 CAGGGCCGATGTCACATCAG 60.813 60.000 18.05 7.64 0.00 2.90
756 761 3.315142 GAGCAGGGCCGATGTCACA 62.315 63.158 8.26 0.00 0.00 3.58
765 770 1.336632 ACAGATCTCAGAGCAGGGCC 61.337 60.000 0.00 0.00 0.00 5.80
782 787 2.425592 CCTCCTCACCGTTGCACA 59.574 61.111 0.00 0.00 0.00 4.57
1113 1121 0.251165 CCATGGTCTTCCGGTGGTTT 60.251 55.000 2.57 0.00 37.35 3.27
1371 2265 1.063488 GTCACAAACGCCGCAAAGT 59.937 52.632 0.00 0.00 0.00 2.66
1452 2387 2.838202 GAGGTCCTGGTCTTTGTCCATA 59.162 50.000 0.00 0.00 34.26 2.74
1493 2428 2.693762 TACTCGTAGCTGCGGCGTT 61.694 57.895 24.11 8.46 44.37 4.84
1519 2454 2.809174 CATGTCGTCGCAGCCGAA 60.809 61.111 0.00 0.00 41.80 4.30
1585 2520 3.998672 GTGGTCGTGGAAGGCGGA 61.999 66.667 0.00 0.00 0.00 5.54
1586 2521 3.530910 AAGTGGTCGTGGAAGGCGG 62.531 63.158 0.00 0.00 0.00 6.13
1655 2590 4.929808 GGCGACAGAGAAAACAGAGAAATA 59.070 41.667 0.00 0.00 0.00 1.40
1656 2591 3.748568 GGCGACAGAGAAAACAGAGAAAT 59.251 43.478 0.00 0.00 0.00 2.17
1679 2614 1.878948 GCAAATTGGCACCAGCACAAT 60.879 47.619 0.00 0.00 44.61 2.71
1684 2619 0.952010 CAAGGCAAATTGGCACCAGC 60.952 55.000 21.49 0.00 46.46 4.85
1833 2786 1.470098 CTTGAATTCAACCGGAGCTGG 59.530 52.381 16.91 0.61 0.00 4.85
1894 2861 0.238553 GCACGAGGAAAAACAGAGCC 59.761 55.000 0.00 0.00 0.00 4.70
2571 3622 1.202371 GGCTCATCCGTGTCACGAATA 60.202 52.381 26.53 11.71 46.05 1.75
2599 3650 1.451747 AGCGACCGAGGAGGACTAC 60.452 63.158 0.00 0.00 45.00 2.73
2675 3726 4.098654 CAGATACTCTACACCCCACTCAAG 59.901 50.000 0.00 0.00 0.00 3.02
2677 3728 3.632333 CAGATACTCTACACCCCACTCA 58.368 50.000 0.00 0.00 0.00 3.41
2678 3729 2.362717 GCAGATACTCTACACCCCACTC 59.637 54.545 0.00 0.00 0.00 3.51
2679 3730 2.023888 AGCAGATACTCTACACCCCACT 60.024 50.000 0.00 0.00 0.00 4.00
2680 3731 2.362717 GAGCAGATACTCTACACCCCAC 59.637 54.545 0.00 0.00 33.69 4.61
2681 3732 2.667470 GAGCAGATACTCTACACCCCA 58.333 52.381 0.00 0.00 33.69 4.96
2686 3737 2.852449 CTCGGGAGCAGATACTCTACA 58.148 52.381 0.00 0.00 36.87 2.74
2708 3833 5.051891 ACTGTTAATCAAAGAGCATGTGC 57.948 39.130 0.00 0.00 42.49 4.57
2709 3834 9.462174 TTTTTACTGTTAATCAAAGAGCATGTG 57.538 29.630 0.00 0.00 31.63 3.21
2778 3906 9.540431 GCACGCAAAACAATTATCAAAATTTAT 57.460 25.926 0.00 0.00 0.00 1.40
2783 3911 6.417327 CAAGCACGCAAAACAATTATCAAAA 58.583 32.000 0.00 0.00 0.00 2.44
2791 3919 3.359194 TGCAAGCACGCAAAACAAT 57.641 42.105 0.00 0.00 39.45 2.71
2800 3928 7.630026 TCTTTATATGAACTATTGCAAGCACG 58.370 34.615 4.94 0.00 0.00 5.34
2816 3944 9.655769 CGATTTCCACAAATGTCTCTTTATATG 57.344 33.333 0.00 0.00 31.94 1.78
2818 3946 8.664798 CACGATTTCCACAAATGTCTCTTTATA 58.335 33.333 0.00 0.00 31.94 0.98
2819 3947 7.390440 TCACGATTTCCACAAATGTCTCTTTAT 59.610 33.333 0.00 0.00 31.94 1.40
2820 3948 6.708502 TCACGATTTCCACAAATGTCTCTTTA 59.291 34.615 0.00 0.00 31.94 1.85
2821 3949 5.530915 TCACGATTTCCACAAATGTCTCTTT 59.469 36.000 0.00 0.00 31.94 2.52
2824 3952 4.213270 TGTCACGATTTCCACAAATGTCTC 59.787 41.667 0.00 0.00 31.94 3.36
2825 3953 4.133820 TGTCACGATTTCCACAAATGTCT 58.866 39.130 0.00 0.00 31.94 3.41
2827 3955 4.909696 TTGTCACGATTTCCACAAATGT 57.090 36.364 0.00 0.00 31.94 2.71
2828 3956 6.580963 TTTTTGTCACGATTTCCACAAATG 57.419 33.333 0.00 0.00 38.27 2.32
2851 3979 6.705381 TCATTTTCGGAGCATTGATTTGTTTT 59.295 30.769 0.00 0.00 0.00 2.43
2852 3980 6.222389 TCATTTTCGGAGCATTGATTTGTTT 58.778 32.000 0.00 0.00 0.00 2.83
2853 3981 5.782047 TCATTTTCGGAGCATTGATTTGTT 58.218 33.333 0.00 0.00 0.00 2.83
2854 3982 5.389859 TCATTTTCGGAGCATTGATTTGT 57.610 34.783 0.00 0.00 0.00 2.83
2855 3983 5.808540 ACATCATTTTCGGAGCATTGATTTG 59.191 36.000 0.00 0.00 0.00 2.32
2867 3995 4.622740 GGCTTTCAGAAACATCATTTTCGG 59.377 41.667 0.00 0.00 39.96 4.30
2869 3997 8.816640 TTAAGGCTTTCAGAAACATCATTTTC 57.183 30.769 4.45 0.00 35.97 2.29
2875 4003 6.575162 TTCCTTAAGGCTTTCAGAAACATC 57.425 37.500 17.32 0.00 34.44 3.06
2876 4004 7.890655 AGTATTCCTTAAGGCTTTCAGAAACAT 59.109 33.333 17.32 0.00 34.44 2.71
2878 4006 7.390718 TCAGTATTCCTTAAGGCTTTCAGAAAC 59.609 37.037 17.32 7.32 34.44 2.78
2882 4010 7.872113 AATCAGTATTCCTTAAGGCTTTCAG 57.128 36.000 17.32 1.83 34.44 3.02
3033 4164 5.296780 TGAGCTCGGGATGAACAATAAAATC 59.703 40.000 9.64 0.00 0.00 2.17
3040 4171 2.749076 CAAATGAGCTCGGGATGAACAA 59.251 45.455 9.64 0.00 0.00 2.83
3063 4194 1.453379 TACTCTTCCGCTCCCGAGG 60.453 63.158 0.00 0.00 36.29 4.63
3072 4203 2.295253 ATGGCGAAAGTACTCTTCCG 57.705 50.000 0.00 0.00 34.63 4.30
3073 4204 4.000988 TGAAATGGCGAAAGTACTCTTCC 58.999 43.478 0.00 0.00 32.90 3.46
3087 4218 7.933033 AGAAGAGAAGATAGAGAATGAAATGGC 59.067 37.037 0.00 0.00 0.00 4.40
3096 4227 6.489603 AGGTGTGAGAAGAGAAGATAGAGAA 58.510 40.000 0.00 0.00 0.00 2.87
3121 4252 8.377681 GTGTCATATCATCAAAATTTTGCACAG 58.622 33.333 23.36 13.49 38.05 3.66
3126 4257 8.036575 AGTGGGTGTCATATCATCAAAATTTTG 58.963 33.333 22.40 22.40 39.48 2.44
3175 4306 6.540438 AAACTAGGCAAGCTATAGTGTGTA 57.460 37.500 0.84 0.00 30.35 2.90
3184 4315 4.524316 TGTCGTAAAACTAGGCAAGCTA 57.476 40.909 0.00 0.00 0.00 3.32
3188 4319 4.565166 CGATCATGTCGTAAAACTAGGCAA 59.435 41.667 8.84 0.00 45.19 4.52
3203 4357 1.369091 GGGCGCAAAGACGATCATGT 61.369 55.000 10.83 0.00 34.06 3.21
3212 4366 0.749091 CTGATCATGGGGCGCAAAGA 60.749 55.000 10.83 10.36 0.00 2.52
3214 4368 2.417257 GCTGATCATGGGGCGCAAA 61.417 57.895 10.83 0.00 0.00 3.68
3219 4373 2.281345 CTCGGCTGATCATGGGGC 60.281 66.667 0.00 0.00 0.00 5.80
3228 4382 1.301716 GCCACAAGAACTCGGCTGA 60.302 57.895 0.00 0.00 41.50 4.26
3229 4383 2.671177 CGCCACAAGAACTCGGCTG 61.671 63.158 0.00 0.00 42.59 4.85
3232 4386 2.027625 GACCGCCACAAGAACTCGG 61.028 63.158 0.00 0.00 45.04 4.63
3247 4401 2.486191 CCTATCCACCTGCATCTTGACC 60.486 54.545 0.00 0.00 0.00 4.02
3259 4413 1.539065 CGAGACATGTGCCTATCCACC 60.539 57.143 1.15 0.00 34.85 4.61
3266 4420 0.814457 GAGAGACGAGACATGTGCCT 59.186 55.000 1.15 0.00 0.00 4.75
3275 4429 3.261390 GCTATACCCCTAGAGAGACGAGA 59.739 52.174 0.00 0.00 0.00 4.04
3281 4435 4.929479 ACTGATGCTATACCCCTAGAGAG 58.071 47.826 0.00 0.00 0.00 3.20
3282 4436 5.080337 CAACTGATGCTATACCCCTAGAGA 58.920 45.833 0.00 0.00 0.00 3.10
3306 4460 4.022589 AGAGAAGACAATTGTGCAATGTGG 60.023 41.667 17.58 0.00 0.00 4.17
3336 4490 0.723414 ACGTGCATCGCTCATCTTTG 59.277 50.000 8.31 0.00 44.19 2.77
3347 4501 4.152625 GCACCGCTCACGTGCATC 62.153 66.667 11.67 0.91 42.21 3.91
3355 4509 2.032528 CTTCCCTTGCACCGCTCA 59.967 61.111 0.00 0.00 0.00 4.26
3369 4523 6.032717 GGTCGTGTTATAGTACACTTCCTTC 58.967 44.000 6.22 0.00 44.85 3.46
3371 4525 4.400567 GGGTCGTGTTATAGTACACTTCCT 59.599 45.833 6.22 0.00 44.85 3.36
3377 4531 3.385433 CCATGGGGTCGTGTTATAGTACA 59.615 47.826 2.85 0.00 0.00 2.90
3393 4547 2.423373 CCATCTGAAGGTTACCCATGGG 60.423 54.545 30.23 30.23 42.03 4.00
3401 4555 2.204463 TGGATGGCCATCTGAAGGTTA 58.796 47.619 37.94 15.95 39.92 2.85
3402 4556 1.002069 TGGATGGCCATCTGAAGGTT 58.998 50.000 37.94 7.62 39.92 3.50
3413 4567 4.856801 ATGACGCGGTGGATGGCC 62.857 66.667 12.47 0.00 0.00 5.36
3415 4569 2.588877 GGATGACGCGGTGGATGG 60.589 66.667 12.47 0.00 0.00 3.51
3427 4603 2.994995 ACGGAGTGCGTGGGATGA 60.995 61.111 9.56 0.00 42.51 2.92
3525 4752 3.136123 TTAGTCGTCGGGGAGCGG 61.136 66.667 0.00 0.00 0.00 5.52
3526 4753 2.101770 GTTAGTCGTCGGGGAGCG 59.898 66.667 0.00 0.00 0.00 5.03
3527 4754 2.101770 CGTTAGTCGTCGGGGAGC 59.898 66.667 0.00 0.00 34.52 4.70
3538 4765 0.040794 AGGGCCTGGACTACGTTAGT 59.959 55.000 4.50 0.00 42.86 2.24
3539 4766 2.062971 TAGGGCCTGGACTACGTTAG 57.937 55.000 18.53 0.00 0.00 2.34
3540 4767 2.091720 TGATAGGGCCTGGACTACGTTA 60.092 50.000 18.53 0.00 0.00 3.18
3541 4768 1.342674 TGATAGGGCCTGGACTACGTT 60.343 52.381 18.53 0.00 0.00 3.99
3542 4769 0.260816 TGATAGGGCCTGGACTACGT 59.739 55.000 18.53 0.00 0.00 3.57
3543 4770 0.674534 GTGATAGGGCCTGGACTACG 59.325 60.000 18.53 0.00 0.00 3.51
3544 4771 1.413077 GTGTGATAGGGCCTGGACTAC 59.587 57.143 18.53 8.67 0.00 2.73
3545 4772 1.007842 TGTGTGATAGGGCCTGGACTA 59.992 52.381 18.53 0.00 0.00 2.59
3546 4773 0.252696 TGTGTGATAGGGCCTGGACT 60.253 55.000 18.53 0.00 0.00 3.85
3547 4774 0.618458 TTGTGTGATAGGGCCTGGAC 59.382 55.000 18.53 10.33 0.00 4.02
3548 4775 0.618458 GTTGTGTGATAGGGCCTGGA 59.382 55.000 18.53 0.00 0.00 3.86
3549 4776 0.327924 TGTTGTGTGATAGGGCCTGG 59.672 55.000 18.53 0.00 0.00 4.45
3550 4777 1.453155 GTGTTGTGTGATAGGGCCTG 58.547 55.000 18.53 0.00 0.00 4.85
3551 4778 0.036388 CGTGTTGTGTGATAGGGCCT 60.036 55.000 12.58 12.58 0.00 5.19
3552 4779 0.036765 TCGTGTTGTGTGATAGGGCC 60.037 55.000 0.00 0.00 0.00 5.80
3553 4780 1.359848 CTCGTGTTGTGTGATAGGGC 58.640 55.000 0.00 0.00 0.00 5.19
3554 4781 2.007049 GCCTCGTGTTGTGTGATAGGG 61.007 57.143 0.00 0.00 0.00 3.53
3555 4782 1.066858 AGCCTCGTGTTGTGTGATAGG 60.067 52.381 0.00 0.00 0.00 2.57
3556 4783 2.263077 GAGCCTCGTGTTGTGTGATAG 58.737 52.381 0.00 0.00 0.00 2.08
3557 4784 1.067142 GGAGCCTCGTGTTGTGTGATA 60.067 52.381 0.00 0.00 0.00 2.15
3558 4785 0.320771 GGAGCCTCGTGTTGTGTGAT 60.321 55.000 0.00 0.00 0.00 3.06
3559 4786 1.069090 GGAGCCTCGTGTTGTGTGA 59.931 57.895 0.00 0.00 0.00 3.58
3560 4787 2.310233 CGGAGCCTCGTGTTGTGTG 61.310 63.158 0.00 0.00 0.00 3.82
3561 4788 2.029073 CGGAGCCTCGTGTTGTGT 59.971 61.111 0.00 0.00 0.00 3.72
3562 4789 2.022129 GACGGAGCCTCGTGTTGTG 61.022 63.158 6.67 0.00 43.96 3.33
3563 4790 2.338984 GACGGAGCCTCGTGTTGT 59.661 61.111 6.67 0.00 43.96 3.32
3564 4791 2.432628 GGACGGAGCCTCGTGTTG 60.433 66.667 6.67 0.00 43.96 3.33
3565 4792 3.692406 GGGACGGAGCCTCGTGTT 61.692 66.667 6.67 0.00 43.96 3.32
3566 4793 4.988716 TGGGACGGAGCCTCGTGT 62.989 66.667 6.67 0.00 43.96 4.49
3567 4794 4.135153 CTGGGACGGAGCCTCGTG 62.135 72.222 6.67 0.00 43.96 4.35
3570 4797 3.775654 CACCTGGGACGGAGCCTC 61.776 72.222 0.00 0.00 36.31 4.70
3574 4801 4.087892 CTGGCACCTGGGACGGAG 62.088 72.222 0.00 0.00 36.31 4.63
3578 4805 4.284550 TTGGCTGGCACCTGGGAC 62.285 66.667 2.29 0.00 0.00 4.46
3579 4806 3.970410 CTTGGCTGGCACCTGGGA 61.970 66.667 2.29 0.00 0.00 4.37
3580 4807 3.933048 CTCTTGGCTGGCACCTGGG 62.933 68.421 2.29 0.00 0.00 4.45
3581 4808 2.360852 CTCTTGGCTGGCACCTGG 60.361 66.667 2.29 0.00 0.00 4.45
3582 4809 3.060615 GCTCTTGGCTGGCACCTG 61.061 66.667 2.29 0.00 38.06 4.00
3583 4810 3.564345 CTGCTCTTGGCTGGCACCT 62.564 63.158 2.29 0.00 42.39 4.00
3584 4811 3.060615 CTGCTCTTGGCTGGCACC 61.061 66.667 2.29 0.00 42.39 5.01


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

AutoCloner maintained by Alex Coulton.