Multiple sequence alignment - TraesCS5D01G468500

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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 TraesCS5D01G468500 chr5D 100.000 5200 0 0 1 5200 509941173 509946372 0.000000e+00 9603.0
1 TraesCS5D01G468500 chr5D 95.508 1781 59 4 1792 3572 542243566 542245325 0.000000e+00 2826.0
2 TraesCS5D01G468500 chr5D 90.924 606 44 6 4595 5198 520631417 520630821 0.000000e+00 804.0
3 TraesCS5D01G468500 chr5D 95.813 406 17 0 1388 1793 542211004 542211409 0.000000e+00 656.0
4 TraesCS5D01G468500 chr5D 95.012 401 19 1 1384 1784 542245324 542245723 3.420000e-176 628.0
5 TraesCS5D01G468500 chr5D 89.299 271 27 2 4243 4513 520631683 520631415 6.450000e-89 339.0
6 TraesCS5D01G468500 chr7D 96.577 1782 59 2 1792 3572 74468356 74470136 0.000000e+00 2952.0
7 TraesCS5D01G468500 chr7D 93.438 1783 101 7 1792 3573 609646602 609648369 0.000000e+00 2630.0
8 TraesCS5D01G468500 chr7D 96.584 322 10 1 1388 1709 74452731 74453051 2.760000e-147 532.0
9 TraesCS5D01G468500 chr3D 95.689 1786 73 4 1792 3577 31007421 31005640 0.000000e+00 2868.0
10 TraesCS5D01G468500 chr3D 95.579 1787 74 5 1793 3577 31031796 31030013 0.000000e+00 2857.0
11 TraesCS5D01G468500 chr3D 96.250 400 15 0 1388 1787 31005638 31005239 0.000000e+00 656.0
12 TraesCS5D01G468500 chr3D 96.040 404 14 2 1388 1791 31055259 31054858 0.000000e+00 656.0
13 TraesCS5D01G468500 chr3D 96.000 400 16 0 1388 1787 31030011 31029612 0.000000e+00 651.0
14 TraesCS5D01G468500 chr3D 92.837 349 24 1 2949 3297 41708741 41709088 6.010000e-139 505.0
15 TraesCS5D01G468500 chr3D 90.909 231 20 1 3343 3572 41709085 41709315 5.060000e-80 309.0
16 TraesCS5D01G468500 chr3D 96.629 89 3 0 4509 4597 137515209 137515121 1.170000e-31 148.0
17 TraesCS5D01G468500 chr3D 81.159 138 21 3 1029 1165 44221487 44221620 7.120000e-19 106.0
18 TraesCS5D01G468500 chr2D 93.105 1784 97 14 1792 3572 15399733 15397973 0.000000e+00 2590.0
19 TraesCS5D01G468500 chr2D 95.833 96 3 1 4508 4603 564674113 564674207 2.510000e-33 154.0
20 TraesCS5D01G468500 chr2D 96.667 90 3 0 4508 4597 506785632 506785543 3.240000e-32 150.0
21 TraesCS5D01G468500 chr2B 92.803 1584 98 8 1792 3372 797774588 797773018 0.000000e+00 2279.0
22 TraesCS5D01G468500 chr2B 94.802 404 20 1 1390 1793 797772847 797772445 3.420000e-176 628.0
23 TraesCS5D01G468500 chr2B 94.500 400 18 1 1388 1787 797814151 797813756 9.570000e-172 614.0
24 TraesCS5D01G468500 chr2B 93.452 168 11 0 3406 3573 797773021 797772854 3.110000e-62 250.0
25 TraesCS5D01G468500 chr5A 94.863 584 25 3 3573 4151 637589786 637590369 0.000000e+00 907.0
26 TraesCS5D01G468500 chr5A 87.302 756 59 16 201 940 637588425 637589159 0.000000e+00 830.0
27 TraesCS5D01G468500 chr5A 95.745 423 11 1 972 1387 637589373 637589795 0.000000e+00 675.0
28 TraesCS5D01G468500 chr5A 95.588 204 7 2 1 204 637588198 637588399 5.020000e-85 326.0
29 TraesCS5D01G468500 chr2A 83.282 969 147 13 2266 3229 9112961 9113919 0.000000e+00 878.0
30 TraesCS5D01G468500 chr2A 89.934 606 53 6 4595 5200 425865489 425864892 0.000000e+00 774.0
31 TraesCS5D01G468500 chr2A 90.299 268 25 1 4247 4513 425865754 425865487 2.980000e-92 350.0
32 TraesCS5D01G468500 chr2A 92.079 101 7 1 4510 4609 385904528 385904628 1.950000e-29 141.0
33 TraesCS5D01G468500 chr2A 92.784 97 6 1 4504 4599 238533650 238533746 7.020000e-29 139.0
34 TraesCS5D01G468500 chr5B 89.419 671 47 13 3573 4231 640872963 640873621 0.000000e+00 824.0
35 TraesCS5D01G468500 chr5B 90.207 531 23 11 867 1387 640872461 640872972 0.000000e+00 665.0
36 TraesCS5D01G468500 chr5B 93.906 361 22 0 3212 3572 546723403 546723763 3.540000e-151 545.0
37 TraesCS5D01G468500 chr5B 87.179 234 6 3 2979 3209 546723104 546723316 1.450000e-60 244.0
38 TraesCS5D01G468500 chr5B 83.962 212 28 1 3361 3572 535199011 535198806 1.140000e-46 198.0
39 TraesCS5D01G468500 chr5B 95.699 93 3 1 4507 4598 705270925 705271017 1.170000e-31 148.0
40 TraesCS5D01G468500 chr5B 88.983 118 13 0 1 118 640869426 640869543 4.200000e-31 147.0
41 TraesCS5D01G468500 chr3A 91.060 604 49 3 4595 5198 728542073 728542671 0.000000e+00 811.0
42 TraesCS5D01G468500 chr3A 90.563 604 52 2 4595 5198 728572521 728573119 0.000000e+00 795.0
43 TraesCS5D01G468500 chr3A 90.563 604 52 2 4595 5198 728592949 728593547 0.000000e+00 795.0
44 TraesCS5D01G468500 chr3A 89.888 267 25 1 4244 4510 728541806 728542070 4.990000e-90 342.0
45 TraesCS5D01G468500 chr3A 89.513 267 26 1 4244 4510 728572254 728572518 2.320000e-88 337.0
46 TraesCS5D01G468500 chr3A 89.015 264 27 1 4244 4507 728592682 728592943 5.020000e-85 326.0
47 TraesCS5D01G468500 chr3A 80.220 273 48 4 1029 1300 56409218 56409485 3.180000e-47 200.0
48 TraesCS5D01G468500 chr3A 94.309 123 6 1 4905 5026 927810 927688 2.470000e-43 187.0
49 TraesCS5D01G468500 chr3A 96.667 90 3 0 4509 4598 437863467 437863556 3.240000e-32 150.0
50 TraesCS5D01G468500 chr3A 100.000 28 0 0 800 827 24053191 24053164 9.000000e-03 52.8
51 TraesCS5D01G468500 chr3A 100.000 28 0 0 801 828 547129672 547129699 9.000000e-03 52.8
52 TraesCS5D01G468500 chr4B 90.759 606 47 6 4595 5198 442585511 442584913 0.000000e+00 800.0
53 TraesCS5D01G468500 chr4B 91.176 272 23 1 4243 4513 442585780 442585509 8.230000e-98 368.0
54 TraesCS5D01G468500 chr6B 88.595 605 59 5 4595 5198 694658620 694658025 0.000000e+00 726.0
55 TraesCS5D01G468500 chr6B 88.603 272 22 3 4244 4513 694658882 694658618 6.500000e-84 322.0
56 TraesCS5D01G468500 chr1A 89.894 564 34 5 3010 3572 549491576 549492117 0.000000e+00 704.0
57 TraesCS5D01G468500 chr1A 94.710 397 21 0 1388 1784 549490830 549491226 7.400000e-173 617.0
58 TraesCS5D01G468500 chr1A 83.182 220 21 11 3356 3572 13881988 13882194 2.470000e-43 187.0
59 TraesCS5D01G468500 chr4D 89.091 385 16 3 4814 5198 482345510 482345868 6.140000e-124 455.0
60 TraesCS5D01G468500 chr4D 91.882 271 21 1 4244 4513 482345119 482345389 1.370000e-100 377.0
61 TraesCS5D01G468500 chr4D 93.496 123 8 0 4595 4717 482345387 482345509 3.200000e-42 183.0
62 TraesCS5D01G468500 chr1B 88.672 256 26 2 4258 4513 426502701 426502953 5.060000e-80 309.0
63 TraesCS5D01G468500 chr6A 83.986 281 43 2 1031 1310 15375300 15375579 8.580000e-68 268.0
64 TraesCS5D01G468500 chr6A 97.368 38 1 0 382 419 8131220 8131183 1.210000e-06 65.8
65 TraesCS5D01G468500 chr3B 81.818 242 42 2 1066 1306 69620583 69620823 8.830000e-48 202.0
66 TraesCS5D01G468500 chr3B 94.792 96 5 0 4511 4606 492773283 492773188 3.240000e-32 150.0
67 TraesCS5D01G468500 chr6D 95.652 92 4 0 4508 4599 413410129 413410038 1.170000e-31 148.0
68 TraesCS5D01G468500 chr6D 89.091 110 12 0 1060 1169 14019719 14019828 2.530000e-28 137.0
69 TraesCS5D01G468500 chr6D 97.059 34 1 0 792 825 46062980 46062947 2.020000e-04 58.4
70 TraesCS5D01G468500 chrUn 83.898 118 18 1 5079 5195 291741770 291741653 1.530000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G468500 chr5D 509941173 509946372 5199 False 9603.000000 9603 100.000000 1 5200 1 chr5D.!!$F1 5199
1 TraesCS5D01G468500 chr5D 542243566 542245723 2157 False 1727.000000 2826 95.260000 1384 3572 2 chr5D.!!$F3 2188
2 TraesCS5D01G468500 chr5D 520630821 520631683 862 True 571.500000 804 90.111500 4243 5198 2 chr5D.!!$R1 955
3 TraesCS5D01G468500 chr7D 74468356 74470136 1780 False 2952.000000 2952 96.577000 1792 3572 1 chr7D.!!$F2 1780
4 TraesCS5D01G468500 chr7D 609646602 609648369 1767 False 2630.000000 2630 93.438000 1792 3573 1 chr7D.!!$F3 1781
5 TraesCS5D01G468500 chr3D 31005239 31007421 2182 True 1762.000000 2868 95.969500 1388 3577 2 chr3D.!!$R3 2189
6 TraesCS5D01G468500 chr3D 31029612 31031796 2184 True 1754.000000 2857 95.789500 1388 3577 2 chr3D.!!$R4 2189
7 TraesCS5D01G468500 chr3D 41708741 41709315 574 False 407.000000 505 91.873000 2949 3572 2 chr3D.!!$F2 623
8 TraesCS5D01G468500 chr2D 15397973 15399733 1760 True 2590.000000 2590 93.105000 1792 3572 1 chr2D.!!$R1 1780
9 TraesCS5D01G468500 chr2B 797772445 797774588 2143 True 1052.333333 2279 93.685667 1390 3573 3 chr2B.!!$R2 2183
10 TraesCS5D01G468500 chr5A 637588198 637590369 2171 False 684.500000 907 93.374500 1 4151 4 chr5A.!!$F1 4150
11 TraesCS5D01G468500 chr2A 9112961 9113919 958 False 878.000000 878 83.282000 2266 3229 1 chr2A.!!$F1 963
12 TraesCS5D01G468500 chr2A 425864892 425865754 862 True 562.000000 774 90.116500 4247 5200 2 chr2A.!!$R1 953
13 TraesCS5D01G468500 chr5B 640869426 640873621 4195 False 545.333333 824 89.536333 1 4231 3 chr5B.!!$F3 4230
14 TraesCS5D01G468500 chr5B 546723104 546723763 659 False 394.500000 545 90.542500 2979 3572 2 chr5B.!!$F2 593
15 TraesCS5D01G468500 chr3A 728541806 728542671 865 False 576.500000 811 90.474000 4244 5198 2 chr3A.!!$F4 954
16 TraesCS5D01G468500 chr3A 728572254 728573119 865 False 566.000000 795 90.038000 4244 5198 2 chr3A.!!$F5 954
17 TraesCS5D01G468500 chr3A 728592682 728593547 865 False 560.500000 795 89.789000 4244 5198 2 chr3A.!!$F6 954
18 TraesCS5D01G468500 chr4B 442584913 442585780 867 True 584.000000 800 90.967500 4243 5198 2 chr4B.!!$R1 955
19 TraesCS5D01G468500 chr6B 694658025 694658882 857 True 524.000000 726 88.599000 4244 5198 2 chr6B.!!$R1 954
20 TraesCS5D01G468500 chr1A 549490830 549492117 1287 False 660.500000 704 92.302000 1388 3572 2 chr1A.!!$F2 2184
21 TraesCS5D01G468500 chr4D 482345119 482345868 749 False 338.333333 455 91.489667 4244 5198 3 chr4D.!!$F1 954

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
542 2389 0.109272 GGCGTCTGTGATGACTTCGA 60.109 55.0 0.00 0.00 35.00 3.71 F
1385 3826 0.107017 TTCTACCCCTACTCGGACCG 60.107 60.0 7.84 7.84 33.16 4.79 F
1535 3976 0.666577 GTCGCCCGTGATATGCCTAC 60.667 60.0 0.00 0.00 0.00 3.18 F
1536 3977 0.826256 TCGCCCGTGATATGCCTACT 60.826 55.0 0.00 0.00 0.00 2.57 F
1625 4066 0.944386 TGACAAAGGTCTTTCTGCGC 59.056 50.0 0.00 0.00 44.61 6.09 F
3389 6105 1.049289 GCAAGGGGTCGGGTAGAGAT 61.049 60.0 0.00 0.00 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 4225 0.106519 CAGAATGGATTTCCCCGGCT 60.107 55.0 0.00 0.0 34.67 5.52 R
2789 5321 0.253894 TGCATGCACCTACAGCTCAT 59.746 50.0 18.46 0.0 0.00 2.90 R
2916 5449 0.532862 CTTTAGTGCGCCCGATCCAT 60.533 55.0 4.18 0.0 0.00 3.41 R
3404 6120 0.676782 GGTAACAGCTCCACCGCATT 60.677 55.0 0.00 0.0 0.00 3.56 R
3433 6149 2.557056 CAGACTTCTGTCACGGTTCCTA 59.443 50.0 0.00 0.0 45.20 2.94 R
4597 7526 0.107831 ACGGGTGAAAGCTTGCTGTA 59.892 50.0 5.89 0.0 0.00 2.74 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
120 121 0.668535 GATTTTACCCAGCGATGGCC 59.331 55.000 15.97 0.00 41.24 5.36
142 143 0.395312 TTCCACCTCCACTTCGGAAC 59.605 55.000 0.00 0.00 45.75 3.62
186 187 4.224433 CAGCTGCACAAGAAACAACTATG 58.776 43.478 0.00 0.00 0.00 2.23
232 2060 4.592192 GCGATGCAGCGAGGCCTA 62.592 66.667 30.90 0.00 0.00 3.93
242 2070 1.227380 CGAGGCCTATGTCTGGTGC 60.227 63.158 4.42 0.00 0.00 5.01
243 2071 1.907739 GAGGCCTATGTCTGGTGCA 59.092 57.895 4.42 0.00 0.00 4.57
244 2072 0.179062 GAGGCCTATGTCTGGTGCAG 60.179 60.000 4.42 0.00 0.00 4.41
245 2073 1.821332 GGCCTATGTCTGGTGCAGC 60.821 63.158 9.47 9.47 0.00 5.25
246 2074 2.176273 GCCTATGTCTGGTGCAGCG 61.176 63.158 11.91 6.42 0.00 5.18
251 2085 3.181967 GTCTGGTGCAGCGCTACG 61.182 66.667 10.99 0.00 0.00 3.51
254 2088 3.350909 CTGGTGCAGCGCTACGGTA 62.351 63.158 10.99 0.00 35.27 4.02
256 2094 2.181021 GTGCAGCGCTACGGTAGT 59.819 61.111 10.99 0.00 35.27 2.73
259 2097 1.586564 GCAGCGCTACGGTAGTGAG 60.587 63.158 27.89 20.17 38.55 3.51
261 2099 1.077930 AGCGCTACGGTAGTGAGGA 60.078 57.895 27.89 0.00 38.55 3.71
276 2114 2.094234 GTGAGGAAGGAGAGAGAAGTGC 60.094 54.545 0.00 0.00 0.00 4.40
280 2118 0.612744 AAGGAGAGAGAAGTGCAGCC 59.387 55.000 0.00 0.00 0.00 4.85
333 2176 5.337571 CCATGGGCTAGCTCGAGATATTTTA 60.338 44.000 18.75 1.97 0.00 1.52
382 2225 2.823154 AGGAGTGAACTGAGTGTAGCTC 59.177 50.000 0.00 0.00 44.36 4.09
397 2240 2.173126 AGCTCAGATGGCTAGGTTCT 57.827 50.000 0.00 0.00 38.36 3.01
400 2243 4.033709 AGCTCAGATGGCTAGGTTCTTTA 58.966 43.478 0.00 0.00 38.36 1.85
406 2249 4.721776 AGATGGCTAGGTTCTTTATGGTGA 59.278 41.667 0.00 0.00 0.00 4.02
453 2299 2.074547 TACTTGGTACTCGTGCTTGC 57.925 50.000 0.00 0.00 0.00 4.01
494 2341 1.880027 AGCTTCCGGATGTTTGTTCAC 59.120 47.619 17.82 0.00 0.00 3.18
496 2343 3.071479 GCTTCCGGATGTTTGTTCACTA 58.929 45.455 17.82 0.00 0.00 2.74
506 2353 3.964688 TGTTTGTTCACTAGGAGGAGACA 59.035 43.478 0.00 0.00 0.00 3.41
515 2362 1.938585 AGGAGGAGACATTTCCGTCA 58.061 50.000 0.00 0.00 42.29 4.35
542 2389 0.109272 GGCGTCTGTGATGACTTCGA 60.109 55.000 0.00 0.00 35.00 3.71
606 2477 5.715070 CTCGTAGGGATAGGATGAATGAAC 58.285 45.833 0.00 0.00 0.00 3.18
611 2482 7.066645 CGTAGGGATAGGATGAATGAACGTATA 59.933 40.741 0.00 0.00 0.00 1.47
614 2485 7.619698 AGGGATAGGATGAATGAACGTATATGA 59.380 37.037 0.00 0.00 0.00 2.15
686 2571 5.587043 TCGGTAAAAGATATTTTCGGCATGT 59.413 36.000 0.41 0.00 0.00 3.21
690 2575 8.068380 GGTAAAAGATATTTTCGGCATGTAGAC 58.932 37.037 0.41 0.00 0.00 2.59
800 2938 9.834628 ATTCATCAAACAAATCATCAAAAATGC 57.165 25.926 0.00 0.00 0.00 3.56
802 2940 9.058174 TCATCAAACAAATCATCAAAAATGCTT 57.942 25.926 0.00 0.00 0.00 3.91
822 2960 7.959658 TGCTTTTATATTATGGGATGGATGG 57.040 36.000 0.00 0.00 0.00 3.51
824 2962 7.835682 TGCTTTTATATTATGGGATGGATGGAG 59.164 37.037 0.00 0.00 0.00 3.86
834 2972 2.224305 GGATGGATGGAGTAGGAAACCG 60.224 54.545 0.00 0.00 0.00 4.44
837 2975 3.918566 TGGATGGAGTAGGAAACCGATA 58.081 45.455 0.00 0.00 0.00 2.92
925 3175 6.309737 GGAACACAATCGTACCGGATAATATC 59.690 42.308 9.46 0.00 0.00 1.63
944 3195 6.737254 ATATCCCGTTCCATTTTAATAGCG 57.263 37.500 0.00 0.00 0.00 4.26
1314 3748 2.762745 GACGCCAACCTGAAGAAACTA 58.237 47.619 0.00 0.00 0.00 2.24
1320 3754 2.993899 CAACCTGAAGAAACTACGCGAT 59.006 45.455 15.93 0.00 0.00 4.58
1377 3818 2.097825 TGCGAGTTCTTCTACCCCTAC 58.902 52.381 0.00 0.00 0.00 3.18
1378 3819 2.291411 TGCGAGTTCTTCTACCCCTACT 60.291 50.000 0.00 0.00 0.00 2.57
1379 3820 2.358582 GCGAGTTCTTCTACCCCTACTC 59.641 54.545 0.00 0.00 0.00 2.59
1380 3821 2.613133 CGAGTTCTTCTACCCCTACTCG 59.387 54.545 0.00 0.00 45.67 4.18
1381 3822 2.950975 GAGTTCTTCTACCCCTACTCGG 59.049 54.545 0.00 0.00 0.00 4.63
1382 3823 2.579860 AGTTCTTCTACCCCTACTCGGA 59.420 50.000 0.00 0.00 33.16 4.55
1383 3824 2.687425 GTTCTTCTACCCCTACTCGGAC 59.313 54.545 0.00 0.00 33.16 4.79
1384 3825 1.213926 TCTTCTACCCCTACTCGGACC 59.786 57.143 0.00 0.00 33.16 4.46
1385 3826 0.107017 TTCTACCCCTACTCGGACCG 60.107 60.000 7.84 7.84 33.16 4.79
1386 3827 2.124151 TACCCCTACTCGGACCGC 60.124 66.667 9.66 0.00 33.16 5.68
1403 3844 6.790285 GGACCGCCGAAAATATAAAATAGA 57.210 37.500 0.00 0.00 0.00 1.98
1480 3921 1.134189 AGCCTTTACCGTAAGATGGCC 60.134 52.381 19.53 0.00 39.68 5.36
1481 3922 1.407712 GCCTTTACCGTAAGATGGCCA 60.408 52.381 8.56 8.56 43.02 5.36
1535 3976 0.666577 GTCGCCCGTGATATGCCTAC 60.667 60.000 0.00 0.00 0.00 3.18
1536 3977 0.826256 TCGCCCGTGATATGCCTACT 60.826 55.000 0.00 0.00 0.00 2.57
1544 3985 4.321974 CCGTGATATGCCTACTTCATAGCA 60.322 45.833 0.00 0.00 39.56 3.49
1576 4017 6.161855 TGTTCAGCTAGAGAAAAGTTCAGA 57.838 37.500 0.00 0.00 0.00 3.27
1616 4057 3.047877 CGGCCCGTGACAAAGGTC 61.048 66.667 0.00 0.00 44.57 3.85
1618 4059 1.228154 GGCCCGTGACAAAGGTCTT 60.228 57.895 0.00 0.00 44.61 3.01
1625 4066 0.944386 TGACAAAGGTCTTTCTGCGC 59.056 50.000 0.00 0.00 44.61 6.09
1641 4082 2.363925 GCCCCCACTCGTACCTCT 60.364 66.667 0.00 0.00 0.00 3.69
1658 4099 4.277552 TAGGAGCATGCTAGGCGT 57.722 55.556 22.74 12.57 38.32 5.68
1680 4121 1.308746 GGGAGGGGGATCCAAGGAA 60.309 63.158 15.23 0.00 41.52 3.36
1681 4122 1.356494 GGGAGGGGGATCCAAGGAAG 61.356 65.000 15.23 0.00 41.52 3.46
1909 4438 7.491372 GTCTATGAAATCGTGTGAATTCCACTA 59.509 37.037 18.73 12.05 45.86 2.74
1977 4506 5.543714 TGACAAACATACTGACGTACCATT 58.456 37.500 0.00 0.00 0.00 3.16
2070 4599 8.815565 TTTGTCATTCTTGCCCTGTATAATTA 57.184 30.769 0.00 0.00 0.00 1.40
2081 4610 5.178809 GCCCTGTATAATTATTCCACGACAC 59.821 44.000 2.68 0.00 0.00 3.67
2152 4681 6.518208 TTAATGGGAAAAGAATTACCACGG 57.482 37.500 0.00 0.00 33.42 4.94
2231 4760 2.158827 TGTTAACTCTGCTTCTGCCACA 60.159 45.455 7.22 0.00 38.71 4.17
2319 4848 2.522436 TCGGTTCCGACCACTGGT 60.522 61.111 10.00 0.00 46.91 4.00
2789 5321 9.996554 ATCATCACGTACATCTGGATTAAAATA 57.003 29.630 0.00 0.00 0.00 1.40
2801 5333 8.034313 TCTGGATTAAAATATGAGCTGTAGGT 57.966 34.615 0.00 0.00 0.00 3.08
2894 5426 7.824779 AGATCAAAAGTTTAGGAGGACATACAC 59.175 37.037 0.00 0.00 0.00 2.90
2916 5449 4.868171 ACGAGCTCAAATACTGCGATTTTA 59.132 37.500 15.40 0.00 0.00 1.52
2925 5458 2.494059 ACTGCGATTTTATGGATCGGG 58.506 47.619 8.35 0.00 44.80 5.14
3102 5638 3.939939 TGCTCCGGCTCAGCAACA 61.940 61.111 13.53 0.00 44.02 3.33
3389 6105 1.049289 GCAAGGGGTCGGGTAGAGAT 61.049 60.000 0.00 0.00 0.00 2.75
3433 6149 1.674962 GAGCTGTTACCCTACGACGAT 59.325 52.381 0.00 0.00 0.00 3.73
3504 6220 3.838271 GCGGTGGGCATCTCGAGA 61.838 66.667 19.19 19.19 42.87 4.04
3512 6228 0.179124 GGCATCTCGAGAGAAAGCGT 60.179 55.000 21.52 0.00 41.36 5.07
3597 6314 4.410400 GCTGGGAGGTCAACCCCG 62.410 72.222 0.00 0.00 46.21 5.73
3632 6349 4.280494 ACGCACGCACTCTCGGTT 62.280 61.111 0.00 0.00 0.00 4.44
3810 6527 0.878086 GCTACTGCGCCTCAATCTCC 60.878 60.000 4.18 0.00 0.00 3.71
3837 6554 1.437772 CGACCTCTATGGAGACGCGT 61.438 60.000 13.85 13.85 41.86 6.01
3893 6610 1.080501 CTGCCGCACCGATATCGAT 60.081 57.895 26.32 6.38 43.02 3.59
3905 6622 3.382865 CCGATATCGATGATGACTGGGAT 59.617 47.826 26.32 0.00 43.02 3.85
3963 6680 1.883732 CCGAGACTCCGCTTTCTGA 59.116 57.895 0.00 0.00 0.00 3.27
3998 6715 9.939802 AATAACTACGATAAGAAACAGTTCCTT 57.060 29.630 0.00 0.00 33.92 3.36
4028 6745 2.749800 GCCTTGGTTGACAAAGGAGAGT 60.750 50.000 19.29 0.00 38.91 3.24
4128 6850 2.001812 TGTTTGCAACACAACGCATT 57.998 40.000 0.00 0.00 38.23 3.56
4152 6874 4.419522 ACGCTGCGATTTGAAGTTTATT 57.580 36.364 30.47 0.00 0.00 1.40
4154 6876 6.119144 ACGCTGCGATTTGAAGTTTATTAT 57.881 33.333 30.47 0.00 0.00 1.28
4155 6877 6.192360 ACGCTGCGATTTGAAGTTTATTATC 58.808 36.000 30.47 0.00 0.00 1.75
4156 6878 6.183360 ACGCTGCGATTTGAAGTTTATTATCA 60.183 34.615 30.47 0.00 0.00 2.15
4157 6879 6.139169 CGCTGCGATTTGAAGTTTATTATCAC 59.861 38.462 18.66 0.00 0.00 3.06
4158 6880 6.139169 GCTGCGATTTGAAGTTTATTATCACG 59.861 38.462 0.00 0.00 0.00 4.35
4159 6881 5.963004 TGCGATTTGAAGTTTATTATCACGC 59.037 36.000 0.00 0.00 36.93 5.34
4161 6883 5.907391 CGATTTGAAGTTTATTATCACGCCC 59.093 40.000 0.00 0.00 0.00 6.13
4162 6884 4.868450 TTGAAGTTTATTATCACGCCCG 57.132 40.909 0.00 0.00 0.00 6.13
4165 6887 5.417811 TGAAGTTTATTATCACGCCCGTTA 58.582 37.500 0.00 0.00 0.00 3.18
4166 6888 5.521010 TGAAGTTTATTATCACGCCCGTTAG 59.479 40.000 0.00 0.00 0.00 2.34
4168 6890 5.045872 AGTTTATTATCACGCCCGTTAGTC 58.954 41.667 0.00 0.00 0.00 2.59
4169 6891 4.924305 TTATTATCACGCCCGTTAGTCT 57.076 40.909 0.00 0.00 0.00 3.24
4170 6892 2.857592 TTATCACGCCCGTTAGTCTC 57.142 50.000 0.00 0.00 0.00 3.36
4172 6894 1.183549 ATCACGCCCGTTAGTCTCTT 58.816 50.000 0.00 0.00 0.00 2.85
4181 6906 5.577945 CGCCCGTTAGTCTCTTATTTTGTAA 59.422 40.000 0.00 0.00 0.00 2.41
4182 6907 6.257193 CGCCCGTTAGTCTCTTATTTTGTAAT 59.743 38.462 0.00 0.00 0.00 1.89
4206 6931 4.073293 ACACTTGTTCTAGTTCTGGTGG 57.927 45.455 0.00 0.00 0.00 4.61
4214 6939 3.280295 TCTAGTTCTGGTGGACGAGATC 58.720 50.000 0.00 0.00 30.87 2.75
4218 6943 0.532573 TCTGGTGGACGAGATCAAGC 59.467 55.000 0.00 0.00 0.00 4.01
4231 6956 5.692204 ACGAGATCAAGCCGTTTTATCTATG 59.308 40.000 0.00 0.00 32.03 2.23
4232 6957 5.119279 CGAGATCAAGCCGTTTTATCTATGG 59.881 44.000 0.00 0.00 0.00 2.74
4236 6961 2.851195 AGCCGTTTTATCTATGGGCAG 58.149 47.619 2.45 0.00 42.89 4.85
4237 6962 2.172717 AGCCGTTTTATCTATGGGCAGT 59.827 45.455 2.45 0.00 42.89 4.40
4239 6964 3.804036 CCGTTTTATCTATGGGCAGTGA 58.196 45.455 0.00 0.00 0.00 3.41
4241 6966 4.452455 CCGTTTTATCTATGGGCAGTGATC 59.548 45.833 0.00 0.00 0.00 2.92
4303 7028 1.372582 GATGCAGCGAGATTCAACCA 58.627 50.000 0.00 0.00 0.00 3.67
4346 7185 5.719173 ACTTTCTCATCTTCTTCTTCCTCG 58.281 41.667 0.00 0.00 0.00 4.63
4428 7353 0.787084 CCCCTCATCTAGGCCTCCTA 59.213 60.000 9.68 0.00 45.03 2.94
4429 7354 1.364328 CCCCTCATCTAGGCCTCCTAT 59.636 57.143 9.68 0.00 45.03 2.57
4443 7370 1.536418 CCTATCCTCCGCCATCCCA 60.536 63.158 0.00 0.00 0.00 4.37
4513 7442 4.744570 TGTTTCTCGTCAGATCCATGTAC 58.255 43.478 0.00 0.00 0.00 2.90
4514 7443 4.462834 TGTTTCTCGTCAGATCCATGTACT 59.537 41.667 0.00 0.00 0.00 2.73
4515 7444 4.902443 TTCTCGTCAGATCCATGTACTC 57.098 45.455 0.00 0.00 0.00 2.59
4516 7445 3.215151 TCTCGTCAGATCCATGTACTCC 58.785 50.000 0.00 0.00 0.00 3.85
4517 7446 2.294791 CTCGTCAGATCCATGTACTCCC 59.705 54.545 0.00 0.00 0.00 4.30
4518 7447 2.091830 TCGTCAGATCCATGTACTCCCT 60.092 50.000 0.00 0.00 0.00 4.20
4519 7448 2.294791 CGTCAGATCCATGTACTCCCTC 59.705 54.545 0.00 0.00 0.00 4.30
4520 7449 3.571590 GTCAGATCCATGTACTCCCTCT 58.428 50.000 0.00 0.00 0.00 3.69
4521 7450 3.320541 GTCAGATCCATGTACTCCCTCTG 59.679 52.174 0.00 1.08 0.00 3.35
4522 7451 3.052566 TCAGATCCATGTACTCCCTCTGT 60.053 47.826 0.00 0.00 32.49 3.41
4523 7452 3.708631 CAGATCCATGTACTCCCTCTGTT 59.291 47.826 0.00 0.00 0.00 3.16
4524 7453 3.964031 AGATCCATGTACTCCCTCTGTTC 59.036 47.826 0.00 0.00 0.00 3.18
4525 7454 3.474798 TCCATGTACTCCCTCTGTTCT 57.525 47.619 0.00 0.00 0.00 3.01
4526 7455 4.603094 TCCATGTACTCCCTCTGTTCTA 57.397 45.455 0.00 0.00 0.00 2.10
4527 7456 4.942944 TCCATGTACTCCCTCTGTTCTAA 58.057 43.478 0.00 0.00 0.00 2.10
4528 7457 5.338632 TCCATGTACTCCCTCTGTTCTAAA 58.661 41.667 0.00 0.00 0.00 1.85
4529 7458 5.964477 TCCATGTACTCCCTCTGTTCTAAAT 59.036 40.000 0.00 0.00 0.00 1.40
4530 7459 6.443849 TCCATGTACTCCCTCTGTTCTAAATT 59.556 38.462 0.00 0.00 0.00 1.82
4531 7460 7.622081 TCCATGTACTCCCTCTGTTCTAAATTA 59.378 37.037 0.00 0.00 0.00 1.40
4532 7461 7.711339 CCATGTACTCCCTCTGTTCTAAATTAC 59.289 40.741 0.00 0.00 0.00 1.89
4533 7462 8.478877 CATGTACTCCCTCTGTTCTAAATTACT 58.521 37.037 0.00 0.00 0.00 2.24
4534 7463 8.431910 TGTACTCCCTCTGTTCTAAATTACTT 57.568 34.615 0.00 0.00 0.00 2.24
4535 7464 8.311836 TGTACTCCCTCTGTTCTAAATTACTTG 58.688 37.037 0.00 0.00 0.00 3.16
4536 7465 7.317722 ACTCCCTCTGTTCTAAATTACTTGT 57.682 36.000 0.00 0.00 0.00 3.16
4537 7466 7.387643 ACTCCCTCTGTTCTAAATTACTTGTC 58.612 38.462 0.00 0.00 0.00 3.18
4538 7467 7.016268 ACTCCCTCTGTTCTAAATTACTTGTCA 59.984 37.037 0.00 0.00 0.00 3.58
4539 7468 7.918076 TCCCTCTGTTCTAAATTACTTGTCAT 58.082 34.615 0.00 0.00 0.00 3.06
4540 7469 7.824289 TCCCTCTGTTCTAAATTACTTGTCATG 59.176 37.037 0.00 0.00 0.00 3.07
4541 7470 7.066284 CCCTCTGTTCTAAATTACTTGTCATGG 59.934 40.741 0.00 0.00 0.00 3.66
4542 7471 7.607991 CCTCTGTTCTAAATTACTTGTCATGGT 59.392 37.037 0.00 0.00 0.00 3.55
4543 7472 8.918202 TCTGTTCTAAATTACTTGTCATGGTT 57.082 30.769 0.00 0.00 0.00 3.67
4544 7473 9.349713 TCTGTTCTAAATTACTTGTCATGGTTT 57.650 29.630 0.00 0.00 0.00 3.27
4545 7474 9.965824 CTGTTCTAAATTACTTGTCATGGTTTT 57.034 29.630 0.00 0.00 0.00 2.43
4557 7486 9.097257 ACTTGTCATGGTTTTAGTTCAAATTTG 57.903 29.630 12.15 12.15 0.00 2.32
4558 7487 9.311916 CTTGTCATGGTTTTAGTTCAAATTTGA 57.688 29.630 16.91 16.91 34.92 2.69
4559 7488 9.658799 TTGTCATGGTTTTAGTTCAAATTTGAA 57.341 25.926 26.01 26.01 44.31 2.69
4572 7501 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
4573 7502 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
4574 7503 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4575 7504 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4576 7505 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4577 7506 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4578 7507 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4579 7508 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
4580 7509 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
4581 7510 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
4582 7511 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
4583 7512 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
4584 7513 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
4585 7514 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
4586 7515 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
4587 7516 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
4588 7517 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
4589 7518 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
4590 7519 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4591 7520 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4592 7521 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4593 7522 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4594 7523 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4595 7524 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4596 7525 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
4597 7526 4.720273 AGTAATTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
4598 7527 5.901276 AGTAATTTGGAACGGAGGGAGTATA 59.099 40.000 0.00 0.00 0.00 1.47
4631 7560 2.281761 CGTGGGTTGCAGCTCCTT 60.282 61.111 0.00 0.00 0.00 3.36
4677 7606 2.805546 CGGCCGCAGCTTCTAGTA 59.194 61.111 14.67 0.00 39.73 1.82
4818 7751 2.355009 AAAAAGCTTGCAGCCGCG 60.355 55.556 0.00 0.00 43.77 6.46
4841 7774 3.007070 GCCGTCGCCGTTGTTGTAG 62.007 63.158 0.00 0.00 0.00 2.74
4842 7775 1.662446 CCGTCGCCGTTGTTGTAGT 60.662 57.895 0.00 0.00 0.00 2.73
4843 7776 0.387112 CCGTCGCCGTTGTTGTAGTA 60.387 55.000 0.00 0.00 0.00 1.82
4844 7777 0.979811 CGTCGCCGTTGTTGTAGTAG 59.020 55.000 0.00 0.00 0.00 2.57
4845 7778 1.664016 CGTCGCCGTTGTTGTAGTAGT 60.664 52.381 0.00 0.00 0.00 2.73
4882 7815 1.956802 CTTCCTTGGTTGCCGGTTC 59.043 57.895 1.90 0.00 0.00 3.62
4885 7818 1.830408 CCTTGGTTGCCGGTTCCAA 60.830 57.895 19.94 19.94 38.65 3.53
4913 7846 9.723601 AAACAATTGATATGGTTGTAGCAAAAT 57.276 25.926 13.59 0.00 34.13 1.82
5001 7936 3.374220 TCTTCATGGTTTGCAGCAAAG 57.626 42.857 21.21 9.50 33.82 2.77
5033 7969 0.452987 CCCATCGTTGAGGTTGCATG 59.547 55.000 0.00 0.00 0.00 4.06
5075 8011 0.236449 GAAAAATGTCGTCGCCGGTT 59.764 50.000 1.90 0.00 33.95 4.44
5076 8012 0.664224 AAAAATGTCGTCGCCGGTTT 59.336 45.000 1.90 0.00 33.95 3.27
5077 8013 0.664224 AAAATGTCGTCGCCGGTTTT 59.336 45.000 1.90 0.00 33.95 2.43
5179 8115 9.956640 ATTTGGTTCCAGCAAAAATAATTATCA 57.043 25.926 5.29 0.00 46.75 2.15
5183 8119 9.087424 GGTTCCAGCAAAAATAATTATCAGTTC 57.913 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 1.296715 CGAAGTGGAGGTGGAAGGG 59.703 63.158 0.00 0.00 0.00 3.95
142 143 2.390599 CGGTGGTGTGATCGGCTTG 61.391 63.158 0.00 0.00 0.00 4.01
153 154 3.807538 GCAGCTGCATCGGTGGTG 61.808 66.667 33.36 2.87 41.59 4.17
232 2060 1.448540 GTAGCGCTGCACCAGACAT 60.449 57.895 22.90 0.00 32.44 3.06
242 2070 1.064296 CCTCACTACCGTAGCGCTG 59.936 63.158 22.90 5.81 0.00 5.18
243 2071 0.679002 TTCCTCACTACCGTAGCGCT 60.679 55.000 17.26 17.26 0.00 5.92
244 2072 0.248539 CTTCCTCACTACCGTAGCGC 60.249 60.000 0.00 0.00 0.00 5.92
245 2073 0.381089 CCTTCCTCACTACCGTAGCG 59.619 60.000 5.42 0.00 0.00 4.26
246 2074 1.677052 CTCCTTCCTCACTACCGTAGC 59.323 57.143 5.42 0.00 0.00 3.58
251 2085 3.655615 TCTCTCTCCTTCCTCACTACC 57.344 52.381 0.00 0.00 0.00 3.18
254 2088 3.430453 CACTTCTCTCTCCTTCCTCACT 58.570 50.000 0.00 0.00 0.00 3.41
256 2094 2.175202 GCACTTCTCTCTCCTTCCTCA 58.825 52.381 0.00 0.00 0.00 3.86
259 2097 1.405391 GCTGCACTTCTCTCTCCTTCC 60.405 57.143 0.00 0.00 0.00 3.46
261 2099 0.612744 GGCTGCACTTCTCTCTCCTT 59.387 55.000 0.50 0.00 0.00 3.36
362 2205 3.224884 GAGCTACACTCAGTTCACTCC 57.775 52.381 0.00 0.00 45.49 3.85
382 2225 4.818546 CACCATAAAGAACCTAGCCATCTG 59.181 45.833 0.00 0.00 0.00 2.90
406 2249 7.839680 AACTTGAATCTTGATAGGTTGGTTT 57.160 32.000 0.00 0.00 0.00 3.27
474 2320 1.880027 GTGAACAAACATCCGGAAGCT 59.120 47.619 9.01 0.00 0.00 3.74
480 2326 3.056107 TCCTCCTAGTGAACAAACATCCG 60.056 47.826 0.00 0.00 0.00 4.18
494 2341 3.024547 TGACGGAAATGTCTCCTCCTAG 58.975 50.000 0.00 0.00 39.64 3.02
496 2343 1.938585 TGACGGAAATGTCTCCTCCT 58.061 50.000 0.00 0.00 39.64 3.69
506 2353 2.006888 CGCCATGTAGTTGACGGAAAT 58.993 47.619 0.00 0.00 0.00 2.17
515 2362 2.233676 TCATCACAGACGCCATGTAGTT 59.766 45.455 0.00 0.00 0.00 2.24
542 2389 4.321718 CCGGCATCATATCTTGAGATTGT 58.678 43.478 0.00 0.00 37.89 2.71
798 2936 7.707648 TCCATCCATCCCATAATATAAAAGCA 58.292 34.615 0.00 0.00 0.00 3.91
799 2937 7.836183 ACTCCATCCATCCCATAATATAAAAGC 59.164 37.037 0.00 0.00 0.00 3.51
802 2940 9.003145 CCTACTCCATCCATCCCATAATATAAA 57.997 37.037 0.00 0.00 0.00 1.40
805 2943 6.766795 TCCTACTCCATCCATCCCATAATAT 58.233 40.000 0.00 0.00 0.00 1.28
807 2945 5.041695 TCCTACTCCATCCATCCCATAAT 57.958 43.478 0.00 0.00 0.00 1.28
809 2947 4.502036 TTCCTACTCCATCCATCCCATA 57.498 45.455 0.00 0.00 0.00 2.74
810 2948 3.367280 TTCCTACTCCATCCATCCCAT 57.633 47.619 0.00 0.00 0.00 4.00
811 2949 2.777692 GTTTCCTACTCCATCCATCCCA 59.222 50.000 0.00 0.00 0.00 4.37
812 2950 2.106684 GGTTTCCTACTCCATCCATCCC 59.893 54.545 0.00 0.00 0.00 3.85
925 3175 4.625972 AACGCTATTAAAATGGAACGGG 57.374 40.909 0.00 0.00 0.00 5.28
944 3195 2.710220 TGCTGACATGCATGACAAAC 57.290 45.000 32.75 24.22 38.12 2.93
1176 3610 3.839353 GATGGCGGGGGCTGATCTG 62.839 68.421 0.00 0.00 0.00 2.90
1380 3821 6.790285 TCTATTTTATATTTTCGGCGGTCC 57.210 37.500 7.21 0.00 0.00 4.46
1381 3822 7.632721 TGTTCTATTTTATATTTTCGGCGGTC 58.367 34.615 7.21 0.00 0.00 4.79
1382 3823 7.556733 TGTTCTATTTTATATTTTCGGCGGT 57.443 32.000 7.21 0.00 0.00 5.68
1383 3824 6.577427 GCTGTTCTATTTTATATTTTCGGCGG 59.423 38.462 7.21 0.00 0.00 6.13
1384 3825 7.321271 CAGCTGTTCTATTTTATATTTTCGGCG 59.679 37.037 5.25 0.00 0.00 6.46
1385 3826 7.113544 GCAGCTGTTCTATTTTATATTTTCGGC 59.886 37.037 16.64 0.00 0.00 5.54
1386 3827 8.128582 TGCAGCTGTTCTATTTTATATTTTCGG 58.871 33.333 16.64 0.00 0.00 4.30
1480 3921 1.813753 CCGATGTAACCGTGGCCTG 60.814 63.158 3.32 0.00 0.00 4.85
1481 3922 2.582436 CCGATGTAACCGTGGCCT 59.418 61.111 3.32 0.00 0.00 5.19
1535 3976 6.161855 TGAACAGTACCCTATGCTATGAAG 57.838 41.667 0.00 0.00 0.00 3.02
1536 3977 5.453339 GCTGAACAGTACCCTATGCTATGAA 60.453 44.000 3.77 0.00 0.00 2.57
1544 3985 5.390087 TCTCTAGCTGAACAGTACCCTAT 57.610 43.478 0.00 0.00 0.00 2.57
1576 4017 2.056223 CCCCCGTGTCCGATAGTGT 61.056 63.158 0.00 0.00 35.63 3.55
1616 4057 2.747855 GAGTGGGGGCGCAGAAAG 60.748 66.667 10.83 0.00 0.00 2.62
1625 4066 0.467659 CCTAGAGGTACGAGTGGGGG 60.468 65.000 0.00 0.00 0.00 5.40
1641 4082 1.796190 CGACGCCTAGCATGCTCCTA 61.796 60.000 26.57 5.88 0.00 2.94
1671 4112 0.924823 ATGCTCTGCCTTCCTTGGAT 59.075 50.000 0.00 0.00 0.00 3.41
1680 4121 1.949547 GCTTCAGTTCATGCTCTGCCT 60.950 52.381 10.65 0.00 0.00 4.75
1681 4122 0.450983 GCTTCAGTTCATGCTCTGCC 59.549 55.000 10.65 1.56 0.00 4.85
1723 4164 1.280421 GACTCCTCTTTCACCAGCCAT 59.720 52.381 0.00 0.00 0.00 4.40
1784 4225 0.106519 CAGAATGGATTTCCCCGGCT 60.107 55.000 0.00 0.00 34.67 5.52
1785 4226 1.738346 GCAGAATGGATTTCCCCGGC 61.738 60.000 0.00 0.00 35.86 6.13
1787 4228 1.312815 GAGCAGAATGGATTTCCCCG 58.687 55.000 0.00 0.00 35.86 5.73
1789 4230 2.027385 GTGGAGCAGAATGGATTTCCC 58.973 52.381 0.00 0.00 35.86 3.97
1909 4438 3.689649 GGTTGGATACGATGCAAAACTCT 59.310 43.478 0.00 0.00 42.30 3.24
1977 4506 1.473257 GCTGCGTACCAAGGATCATGA 60.473 52.381 0.00 0.00 0.00 3.07
2081 4610 1.300620 TGTCTGACCCGCTTTCACG 60.301 57.895 5.17 0.00 0.00 4.35
2152 4681 4.446385 TCAATGCGCGGTATGTAATAACTC 59.554 41.667 8.83 0.00 33.20 3.01
2202 4731 6.321717 CAGAAGCAGAGTTAACACAAACAAA 58.678 36.000 8.61 0.00 0.00 2.83
2231 4760 1.813753 CACGGATTCGGCATTCGGT 60.814 57.895 0.00 0.00 38.35 4.69
2319 4848 3.685139 AGAGGCAGTGAAATCTTCGAA 57.315 42.857 0.00 0.00 0.00 3.71
2789 5321 0.253894 TGCATGCACCTACAGCTCAT 59.746 50.000 18.46 0.00 0.00 2.90
2894 5426 3.933155 AAATCGCAGTATTTGAGCTCG 57.067 42.857 9.64 0.00 0.00 5.03
2916 5449 0.532862 CTTTAGTGCGCCCGATCCAT 60.533 55.000 4.18 0.00 0.00 3.41
2925 5458 5.485662 AAGTTTATCCATCTTTAGTGCGC 57.514 39.130 0.00 0.00 0.00 6.09
3098 5634 3.728385 ATCCCCTCTCCTTCTTTGTTG 57.272 47.619 0.00 0.00 0.00 3.33
3102 5638 3.808189 TCTGAATCCCCTCTCCTTCTTT 58.192 45.455 0.00 0.00 0.00 2.52
3180 5738 7.399191 TCAAGACTGGATACTGGTGTACTAATT 59.601 37.037 0.00 0.00 40.36 1.40
3404 6120 0.676782 GGTAACAGCTCCACCGCATT 60.677 55.000 0.00 0.00 0.00 3.56
3433 6149 2.557056 CAGACTTCTGTCACGGTTCCTA 59.443 50.000 0.00 0.00 45.20 2.94
3810 6527 1.148157 CCATAGAGGTCGCAACGCTG 61.148 60.000 0.00 0.00 0.00 5.18
3837 6554 2.411701 CAGCGAGGGCGATACGAA 59.588 61.111 0.00 0.00 46.35 3.85
3893 6610 0.543277 GTCCTGCATCCCAGTCATCA 59.457 55.000 0.00 0.00 40.06 3.07
3905 6622 2.050836 TTTTCTCGCCTGGTCCTGCA 62.051 55.000 0.00 0.00 0.00 4.41
3941 6658 3.916392 AAAGCGGAGTCTCGGCGTG 62.916 63.158 22.36 4.24 45.79 5.34
3998 6715 2.040145 TGTCAACCAAGGCATCATCTCA 59.960 45.455 0.00 0.00 0.00 3.27
4028 6745 5.105567 ACCATTCATTTGTATACCGGACA 57.894 39.130 9.46 0.00 0.00 4.02
4128 6850 1.790755 ACTTCAAATCGCAGCGTACA 58.209 45.000 15.93 0.00 0.00 2.90
4152 6874 2.048444 AGAGACTAACGGGCGTGATA 57.952 50.000 0.00 0.00 0.00 2.15
4154 6876 1.825090 TAAGAGACTAACGGGCGTGA 58.175 50.000 0.00 0.00 0.00 4.35
4155 6877 2.865343 ATAAGAGACTAACGGGCGTG 57.135 50.000 0.00 0.00 0.00 5.34
4156 6878 3.881937 AAATAAGAGACTAACGGGCGT 57.118 42.857 0.00 0.00 0.00 5.68
4157 6879 3.930848 ACAAAATAAGAGACTAACGGGCG 59.069 43.478 0.00 0.00 0.00 6.13
4158 6880 6.973229 TTACAAAATAAGAGACTAACGGGC 57.027 37.500 0.00 0.00 0.00 6.13
4159 6881 8.712285 TGATTACAAAATAAGAGACTAACGGG 57.288 34.615 0.00 0.00 0.00 5.28
4181 6906 5.760253 CACCAGAACTAGAACAAGTGTTGAT 59.240 40.000 0.42 0.00 38.56 2.57
4182 6907 5.116180 CACCAGAACTAGAACAAGTGTTGA 58.884 41.667 0.42 0.00 38.56 3.18
4195 6920 3.081710 TGATCTCGTCCACCAGAACTA 57.918 47.619 0.00 0.00 0.00 2.24
4206 6931 4.113354 AGATAAAACGGCTTGATCTCGTC 58.887 43.478 0.00 0.00 36.01 4.20
4214 6939 2.948979 TGCCCATAGATAAAACGGCTTG 59.051 45.455 0.00 0.00 37.29 4.01
4218 6943 3.804036 TCACTGCCCATAGATAAAACGG 58.196 45.455 0.00 0.00 0.00 4.44
4303 7028 1.146930 AACGCATGCAGGATCGGAT 59.853 52.632 19.57 0.00 0.00 4.18
4359 7198 2.530151 AGAAGGGGGCAGCACTCA 60.530 61.111 0.00 0.00 0.00 3.41
4406 7331 0.487772 GAGGCCTAGATGAGGGGGTA 59.512 60.000 4.42 0.00 46.81 3.69
4428 7353 3.164479 CATGGGATGGCGGAGGAT 58.836 61.111 0.00 0.00 0.00 3.24
4429 7354 3.877450 GCATGGGATGGCGGAGGA 61.877 66.667 0.00 0.00 0.00 3.71
4477 7404 1.887198 AGAAACATGAGAGACGACGGT 59.113 47.619 0.00 0.00 0.00 4.83
4513 7442 7.386851 TGACAAGTAATTTAGAACAGAGGGAG 58.613 38.462 0.00 0.00 0.00 4.30
4514 7443 7.311092 TGACAAGTAATTTAGAACAGAGGGA 57.689 36.000 0.00 0.00 0.00 4.20
4515 7444 7.066284 CCATGACAAGTAATTTAGAACAGAGGG 59.934 40.741 0.00 0.00 0.00 4.30
4516 7445 7.607991 ACCATGACAAGTAATTTAGAACAGAGG 59.392 37.037 0.00 0.00 0.00 3.69
4517 7446 8.553459 ACCATGACAAGTAATTTAGAACAGAG 57.447 34.615 0.00 0.00 0.00 3.35
4518 7447 8.918202 AACCATGACAAGTAATTTAGAACAGA 57.082 30.769 0.00 0.00 0.00 3.41
4519 7448 9.965824 AAAACCATGACAAGTAATTTAGAACAG 57.034 29.630 0.00 0.00 0.00 3.16
4531 7460 9.097257 CAAATTTGAACTAAAACCATGACAAGT 57.903 29.630 13.08 0.00 0.00 3.16
4532 7461 9.311916 TCAAATTTGAACTAAAACCATGACAAG 57.688 29.630 18.45 0.00 33.55 3.16
4533 7462 9.658799 TTCAAATTTGAACTAAAACCATGACAA 57.341 25.926 26.01 1.80 41.88 3.18
4548 7477 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
4549 7478 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
4550 7479 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
4551 7480 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
4552 7481 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4553 7482 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4554 7483 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4555 7484 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4556 7485 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4557 7486 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
4558 7487 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
4559 7488 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
4560 7489 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
4561 7490 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
4562 7491 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
4563 7492 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
4564 7493 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
4565 7494 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
4566 7495 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
4567 7496 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
4568 7497 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
4569 7498 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4570 7499 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4571 7500 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4572 7501 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4573 7502 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4574 7503 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4575 7504 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4576 7505 5.662208 TGTATACTCCCTCCGTTCCAAATTA 59.338 40.000 4.17 0.00 0.00 1.40
4577 7506 4.472108 TGTATACTCCCTCCGTTCCAAATT 59.528 41.667 4.17 0.00 0.00 1.82
4578 7507 4.035112 TGTATACTCCCTCCGTTCCAAAT 58.965 43.478 4.17 0.00 0.00 2.32
4579 7508 3.443052 TGTATACTCCCTCCGTTCCAAA 58.557 45.455 4.17 0.00 0.00 3.28
4580 7509 3.028850 CTGTATACTCCCTCCGTTCCAA 58.971 50.000 4.17 0.00 0.00 3.53
4581 7510 2.662866 CTGTATACTCCCTCCGTTCCA 58.337 52.381 4.17 0.00 0.00 3.53
4582 7511 1.340568 GCTGTATACTCCCTCCGTTCC 59.659 57.143 4.17 0.00 0.00 3.62
4583 7512 2.029623 TGCTGTATACTCCCTCCGTTC 58.970 52.381 4.17 0.00 0.00 3.95
4584 7513 2.154567 TGCTGTATACTCCCTCCGTT 57.845 50.000 4.17 0.00 0.00 4.44
4585 7514 2.032620 CTTGCTGTATACTCCCTCCGT 58.967 52.381 4.17 0.00 0.00 4.69
4586 7515 1.269831 GCTTGCTGTATACTCCCTCCG 60.270 57.143 4.17 0.00 0.00 4.63
4587 7516 2.043227 AGCTTGCTGTATACTCCCTCC 58.957 52.381 4.17 0.00 0.00 4.30
4588 7517 3.828875 AAGCTTGCTGTATACTCCCTC 57.171 47.619 0.00 0.00 0.00 4.30
4589 7518 3.519510 TGAAAGCTTGCTGTATACTCCCT 59.480 43.478 5.89 0.00 0.00 4.20
4590 7519 3.623510 GTGAAAGCTTGCTGTATACTCCC 59.376 47.826 5.89 0.00 0.00 4.30
4591 7520 3.623510 GGTGAAAGCTTGCTGTATACTCC 59.376 47.826 5.89 0.00 0.00 3.85
4592 7521 3.623510 GGGTGAAAGCTTGCTGTATACTC 59.376 47.826 5.89 0.00 0.00 2.59
4593 7522 3.610911 GGGTGAAAGCTTGCTGTATACT 58.389 45.455 5.89 0.00 0.00 2.12
4594 7523 2.351726 CGGGTGAAAGCTTGCTGTATAC 59.648 50.000 5.89 0.00 0.00 1.47
4595 7524 2.027561 ACGGGTGAAAGCTTGCTGTATA 60.028 45.455 5.89 0.00 0.00 1.47
4596 7525 1.271379 ACGGGTGAAAGCTTGCTGTAT 60.271 47.619 5.89 0.00 0.00 2.29
4597 7526 0.107831 ACGGGTGAAAGCTTGCTGTA 59.892 50.000 5.89 0.00 0.00 2.74
4598 7527 1.152963 ACGGGTGAAAGCTTGCTGT 60.153 52.632 5.89 0.00 0.00 4.40
4837 7770 5.945784 ACATCCGGTAAACAGTACTACTACA 59.054 40.000 0.00 0.00 0.00 2.74
4839 7772 6.260936 GCTACATCCGGTAAACAGTACTACTA 59.739 42.308 0.00 0.00 0.00 1.82
4841 7774 5.067023 AGCTACATCCGGTAAACAGTACTAC 59.933 44.000 0.00 0.00 0.00 2.73
4842 7775 5.195940 AGCTACATCCGGTAAACAGTACTA 58.804 41.667 0.00 0.00 0.00 1.82
4843 7776 4.021916 AGCTACATCCGGTAAACAGTACT 58.978 43.478 0.00 0.00 0.00 2.73
4844 7777 4.382345 AGCTACATCCGGTAAACAGTAC 57.618 45.455 0.00 0.00 0.00 2.73
4845 7778 4.142093 GGAAGCTACATCCGGTAAACAGTA 60.142 45.833 0.00 0.00 0.00 2.74
4882 7815 7.063308 GCTACAACCATATCAATTGTTTGTTGG 59.937 37.037 21.15 16.73 37.68 3.77
4885 7818 7.225784 TGCTACAACCATATCAATTGTTTGT 57.774 32.000 5.13 8.80 37.68 2.83
4913 7846 1.269309 CCGGCCGACATTTGTTTTTGA 60.269 47.619 30.73 0.00 0.00 2.69
5001 7936 1.895051 CGATGGGCGTCAACATTTTC 58.105 50.000 0.00 0.00 34.64 2.29
5033 7969 2.924290 GCTACACAGGTTCGTGAAGATC 59.076 50.000 0.00 0.00 39.34 2.75
5075 8011 2.030363 CGGCACCTTCATTTGCTACAAA 60.030 45.455 0.00 0.00 38.85 2.83
5076 8012 1.539388 CGGCACCTTCATTTGCTACAA 59.461 47.619 0.00 0.00 38.85 2.41
5077 8013 1.164411 CGGCACCTTCATTTGCTACA 58.836 50.000 0.00 0.00 38.85 2.74
5179 8115 1.207329 GTGGCGAGGGATGTTAGAACT 59.793 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.