Multiple sequence alignment - TraesCS7B01G093500

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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 TraesCS7B01G093500 chr7B 100.000 5408 0 0 1 5408 107097015 107102422 0.000000e+00 9987.0
1 TraesCS7B01G093500 chr7B 77.165 508 59 26 3904 4390 634388937 634389408 5.410000e-60 243.0
2 TraesCS7B01G093500 chr7B 81.223 229 22 10 4159 4387 743206726 743206519 1.210000e-36 165.0
3 TraesCS7B01G093500 chr7B 93.333 45 3 0 4945 4989 107102010 107102054 3.500000e-07 67.6
4 TraesCS7B01G093500 chr7D 94.955 4440 140 30 570 4985 142686294 142690673 0.000000e+00 6881.0
5 TraesCS7B01G093500 chr7D 83.509 855 75 28 3902 4722 143713921 143714743 0.000000e+00 737.0
6 TraesCS7B01G093500 chr7D 91.942 484 28 5 6 486 142685634 142686109 0.000000e+00 667.0
7 TraesCS7B01G093500 chr7D 88.190 525 49 10 3902 4418 144334086 144333567 9.960000e-172 614.0
8 TraesCS7B01G093500 chr7D 86.444 568 47 12 4157 4722 143677367 143677906 3.610000e-166 595.0
9 TraesCS7B01G093500 chr7D 88.412 233 23 4 3902 4133 143677083 143677312 1.480000e-70 278.0
10 TraesCS7B01G093500 chr7D 84.211 266 18 9 4995 5243 142690632 142690890 2.520000e-58 237.0
11 TraesCS7B01G093500 chr7D 80.515 272 26 12 4995 5243 607204279 607204012 3.330000e-42 183.0
12 TraesCS7B01G093500 chr7A 94.438 3200 119 28 1810 4989 144659113 144662273 0.000000e+00 4868.0
13 TraesCS7B01G093500 chr7A 97.099 1034 26 2 774 1807 144657926 144658955 0.000000e+00 1740.0
14 TraesCS7B01G093500 chr7A 86.127 519 52 9 3902 4409 145459547 145460056 4.760000e-150 542.0
15 TraesCS7B01G093500 chr7A 84.518 394 46 11 2332 2721 116056673 116056291 5.110000e-100 375.0
16 TraesCS7B01G093500 chr7A 89.320 206 20 2 3171 3375 145397996 145398200 1.930000e-64 257.0
17 TraesCS7B01G093500 chr7A 83.459 266 22 9 4997 5243 548579446 548579708 1.520000e-55 228.0
18 TraesCS7B01G093500 chr7A 81.203 266 29 7 4996 5243 232333063 232332801 1.540000e-45 195.0
19 TraesCS7B01G093500 chr7A 97.059 34 1 0 750 783 144657739 144657772 2.100000e-04 58.4
20 TraesCS7B01G093500 chr5A 84.518 394 46 12 2332 2721 638639376 638639758 5.110000e-100 375.0
21 TraesCS7B01G093500 chr5A 79.182 269 32 16 4996 5243 426897134 426897399 1.210000e-36 165.0
22 TraesCS7B01G093500 chr5A 82.243 214 14 10 4995 5189 606814130 606813922 4.330000e-36 163.0
23 TraesCS7B01G093500 chr5B 84.416 385 46 10 2332 2713 523901071 523900698 3.080000e-97 366.0
24 TraesCS7B01G093500 chr5B 81.132 265 24 14 4996 5240 463219659 463219401 7.150000e-44 189.0
25 TraesCS7B01G093500 chr1B 84.496 387 43 13 2339 2721 18657174 18656801 3.080000e-97 366.0
26 TraesCS7B01G093500 chr1B 73.984 492 57 20 3910 4390 642535054 642534623 3.400000e-27 134.0
27 TraesCS7B01G093500 chr2A 83.461 393 46 14 2332 2720 533179969 533179592 1.110000e-91 348.0
28 TraesCS7B01G093500 chr2A 85.776 232 17 6 4156 4387 679008846 679009061 1.170000e-56 231.0
29 TraesCS7B01G093500 chr2A 78.868 265 26 13 4995 5231 30890323 30890061 9.380000e-33 152.0
30 TraesCS7B01G093500 chr2A 78.868 265 26 13 4995 5231 30909490 30909228 9.380000e-33 152.0
31 TraesCS7B01G093500 chr3A 86.755 302 37 3 3050 3349 38333339 38333639 3.120000e-87 333.0
32 TraesCS7B01G093500 chr3A 90.213 235 22 1 2555 2789 38333107 38333340 6.810000e-79 305.0
33 TraesCS7B01G093500 chr3A 79.406 471 54 22 3928 4390 38333868 38334303 5.300000e-75 292.0
34 TraesCS7B01G093500 chr3A 82.772 267 24 6 4995 5243 253767365 253767627 9.120000e-53 219.0
35 TraesCS7B01G093500 chr3A 83.784 222 22 3 4170 4391 462617337 462617130 1.190000e-46 198.0
36 TraesCS7B01G093500 chr3A 79.021 143 25 4 4848 4989 453306002 453305864 5.770000e-15 93.5
37 TraesCS7B01G093500 chr4A 86.000 300 39 3 3052 3349 53691026 53691324 8.740000e-83 318.0
38 TraesCS7B01G093500 chr6A 84.768 302 43 3 3050 3349 552050427 552050127 3.170000e-77 300.0
39 TraesCS7B01G093500 chr6A 89.362 235 24 1 2555 2789 552050659 552050426 1.470000e-75 294.0
40 TraesCS7B01G093500 chr1A 86.090 266 17 6 4996 5243 206137171 206136908 8.930000e-68 268.0
41 TraesCS7B01G093500 chr1A 83.955 268 22 6 4995 5243 557960731 557960996 2.520000e-58 237.0
42 TraesCS7B01G093500 chr1A 85.345 232 18 6 4156 4387 23298782 23298997 5.450000e-55 226.0
43 TraesCS7B01G093500 chr1A 83.186 226 24 3 4166 4391 578918996 578918785 1.540000e-45 195.0
44 TraesCS7B01G093500 chr6D 91.018 167 13 2 5241 5406 125402554 125402389 1.960000e-54 224.0
45 TraesCS7B01G093500 chr6D 81.716 268 26 14 4995 5243 63797536 63797799 9.180000e-48 202.0
46 TraesCS7B01G093500 chr3B 82.397 267 24 9 4995 5243 661813807 661813546 1.530000e-50 211.0
47 TraesCS7B01G093500 chr3B 82.949 217 23 8 4166 4382 16264249 16264451 3.330000e-42 183.0
48 TraesCS7B01G093500 chr3D 82.156 269 23 12 4996 5243 179234748 179235012 1.970000e-49 207.0
49 TraesCS7B01G093500 chr3D 82.251 231 19 6 5033 5243 612800671 612800899 4.300000e-41 180.0
50 TraesCS7B01G093500 chr2B 82.022 267 26 7 4995 5243 708319670 708319932 1.970000e-49 207.0
51 TraesCS7B01G093500 chrUn 78.868 265 26 13 4995 5231 342017663 342017401 9.380000e-33 152.0
52 TraesCS7B01G093500 chrUn 96.667 60 1 1 3963 4022 11851747 11851805 1.240000e-16 99.0


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 TraesCS7B01G093500 chr7B 107097015 107102422 5407 False 5027.300000 9987 96.666500 1 5408 2 chr7B.!!$F2 5407
1 TraesCS7B01G093500 chr7D 142685634 142690890 5256 False 2595.000000 6881 90.369333 6 5243 3 chr7D.!!$F2 5237
2 TraesCS7B01G093500 chr7D 143713921 143714743 822 False 737.000000 737 83.509000 3902 4722 1 chr7D.!!$F1 820
3 TraesCS7B01G093500 chr7D 144333567 144334086 519 True 614.000000 614 88.190000 3902 4418 1 chr7D.!!$R1 516
4 TraesCS7B01G093500 chr7D 143677083 143677906 823 False 436.500000 595 87.428000 3902 4722 2 chr7D.!!$F3 820
5 TraesCS7B01G093500 chr7A 144657739 144662273 4534 False 2222.133333 4868 96.198667 750 4989 3 chr7A.!!$F4 4239
6 TraesCS7B01G093500 chr7A 145459547 145460056 509 False 542.000000 542 86.127000 3902 4409 1 chr7A.!!$F2 507
7 TraesCS7B01G093500 chr3A 38333107 38334303 1196 False 310.000000 333 85.458000 2555 4390 3 chr3A.!!$F2 1835
8 TraesCS7B01G093500 chr6A 552050127 552050659 532 True 297.000000 300 87.065000 2555 3349 2 chr6A.!!$R1 794

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
245 247 0.040067 CTGTTTTCTGCTGCCGGTTC 60.040 55.0 1.9 0.0 0.00 3.62 F
454 458 0.458889 TCCGTCCCGAATTAGTTGCG 60.459 55.0 0.0 0.0 0.00 4.85 F
1128 1393 0.519519 TCCAACAAAATAGCACGGCG 59.480 50.0 4.8 4.8 0.00 6.46 F
2988 3411 0.038744 AGCAGCATACCACAAGGCTT 59.961 50.0 0.0 0.0 39.06 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1327 1.066858 AGCGGGCTATCCAATATCACG 60.067 52.381 0.0 0.0 31.46 4.35 R
2070 2492 3.934068 AGCCTGCCATCAAAAGAAAATG 58.066 40.909 0.0 0.0 0.00 2.32 R
3012 3435 0.664166 CCCACGCACAAAGCATGTTC 60.664 55.000 0.0 0.0 46.13 3.18 R
4729 5256 0.035056 TCTTGCTAAAGCTGGCCCTC 60.035 55.000 0.0 0.0 42.66 4.30 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
20 21 3.492421 GGCATCTGCAATTTCTTTCGA 57.508 42.857 4.33 0.00 44.36 3.71
61 62 0.533951 GGCTTCTTGATTGGCCCTTG 59.466 55.000 0.00 0.00 38.77 3.61
62 63 0.108472 GCTTCTTGATTGGCCCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
63 64 1.553706 CTTCTTGATTGGCCCTTGCT 58.446 50.000 0.00 0.00 37.74 3.91
64 65 1.897802 CTTCTTGATTGGCCCTTGCTT 59.102 47.619 0.00 0.00 37.74 3.91
71 72 5.337578 TGATTGGCCCTTGCTTAATTTAC 57.662 39.130 0.00 0.00 37.74 2.01
75 76 2.526077 GCCCTTGCTTAATTTACGTGC 58.474 47.619 0.00 0.00 33.53 5.34
91 92 0.525029 GTGCCGCGTCTACTACTTCC 60.525 60.000 4.92 0.00 0.00 3.46
96 97 2.516923 CGCGTCTACTACTTCCAACTG 58.483 52.381 0.00 0.00 0.00 3.16
105 106 9.708092 GTCTACTACTTCCAACTGTTTTCTAAT 57.292 33.333 0.00 0.00 0.00 1.73
109 110 8.211629 ACTACTTCCAACTGTTTTCTAATCAGT 58.788 33.333 0.00 0.00 43.04 3.41
111 112 8.974060 ACTTCCAACTGTTTTCTAATCAGTTA 57.026 30.769 12.82 0.92 46.27 2.24
135 136 3.334583 TTGGAGCTAGCTAGTGTTTGG 57.665 47.619 19.38 0.00 0.00 3.28
153 154 1.008995 GCGCAGTTCCTTTTTCGCA 60.009 52.632 0.30 0.00 41.84 5.10
154 155 0.387239 GCGCAGTTCCTTTTTCGCAT 60.387 50.000 0.30 0.00 41.84 4.73
227 229 1.518903 GGCAGCCTCGTTTTGAAGCT 61.519 55.000 3.29 0.00 45.36 3.74
245 247 0.040067 CTGTTTTCTGCTGCCGGTTC 60.040 55.000 1.90 0.00 0.00 3.62
282 284 5.937540 CCCCCTTTTGAAAGCGAATAATTTT 59.062 36.000 0.00 0.00 34.69 1.82
332 334 7.739498 TTCAGATACGGGCTATTTAAATTCC 57.261 36.000 5.91 8.13 0.00 3.01
383 387 3.296709 CTAGTCGGTTGGCGGCACT 62.297 63.158 12.92 7.83 0.00 4.40
402 406 2.559668 ACTGTGACATGAAGGCAAATGG 59.440 45.455 0.00 0.00 36.65 3.16
437 441 9.208022 GCCATTTTAAAATGCTATATTTCCTCC 57.792 33.333 28.17 5.64 43.38 4.30
442 446 3.983044 ATGCTATATTTCCTCCGTCCC 57.017 47.619 0.00 0.00 0.00 4.46
453 457 1.287425 CTCCGTCCCGAATTAGTTGC 58.713 55.000 0.00 0.00 0.00 4.17
454 458 0.458889 TCCGTCCCGAATTAGTTGCG 60.459 55.000 0.00 0.00 0.00 4.85
472 476 1.806623 GCGGCTCAAACGGATGTATCT 60.807 52.381 0.00 0.00 0.00 1.98
474 478 3.050619 CGGCTCAAACGGATGTATCTAC 58.949 50.000 0.00 0.00 0.00 2.59
491 554 5.654603 ATCTACGTCATTGTGGACAAGTA 57.345 39.130 0.00 0.00 39.47 2.24
507 570 5.007136 GGACAAGTAGATGATGCTAGTTTGC 59.993 44.000 0.00 0.00 33.00 3.68
509 572 4.760530 AGTAGATGATGCTAGTTTGCCA 57.239 40.909 0.00 0.00 0.00 4.92
537 600 6.485830 AGATCGATTCTGAAATCCCACTTA 57.514 37.500 0.00 0.00 38.46 2.24
547 610 8.934023 TCTGAAATCCCACTTACAAATACTTT 57.066 30.769 0.00 0.00 0.00 2.66
549 612 9.626045 CTGAAATCCCACTTACAAATACTTTTC 57.374 33.333 0.00 0.00 0.00 2.29
551 614 9.626045 GAAATCCCACTTACAAATACTTTTCTG 57.374 33.333 0.00 0.00 0.00 3.02
574 679 7.176515 TCTGTAATCATGTTGTTGTTTATGCCT 59.823 33.333 0.00 0.00 0.00 4.75
589 694 7.835822 TGTTTATGCCTTAGTATTTGCAACAT 58.164 30.769 0.00 0.00 37.27 2.71
592 697 3.119173 TGCCTTAGTATTTGCAACATGGC 60.119 43.478 0.00 7.19 37.38 4.40
610 715 0.607489 GCTGTGCACATCCTCCAACT 60.607 55.000 22.00 0.00 0.00 3.16
633 738 2.228103 CTCTGTAGCTGTGTTACGTGGA 59.772 50.000 0.00 0.00 0.00 4.02
681 786 4.050553 GTGCGGTTGTTAAGTACTGTACA 58.949 43.478 19.27 0.76 36.59 2.90
791 1056 3.312146 TGTGTGCTGATGCGGTTATAATG 59.688 43.478 0.00 0.00 43.34 1.90
881 1146 2.161211 GCAGTTCAGCAGGAATTGACTC 59.839 50.000 14.84 0.00 43.72 3.36
937 1202 6.345096 TGAGATTCTATGGATGCGTGATAA 57.655 37.500 0.00 0.00 0.00 1.75
951 1216 5.879237 TGCGTGATAATTTAGGCTGAAAAG 58.121 37.500 0.00 0.00 0.00 2.27
961 1226 8.409358 AATTTAGGCTGAAAAGTACAGTGAAT 57.591 30.769 0.00 0.00 37.64 2.57
1128 1393 0.519519 TCCAACAAAATAGCACGGCG 59.480 50.000 4.80 4.80 0.00 6.46
1194 1459 4.327982 TCCACAGAACTTCTCTCAAGTG 57.672 45.455 0.00 0.00 29.07 3.16
1308 1573 4.078630 AGGGACCTTGTAAATAATGCCCAT 60.079 41.667 0.00 0.00 35.50 4.00
1419 1684 5.243507 TGTTTCATTCAATGGTAGCACACAT 59.756 36.000 0.00 0.00 0.00 3.21
1481 1746 6.456988 CGAAGAATGAATGTTACAAGGGTAGC 60.457 42.308 0.00 0.00 0.00 3.58
1677 1942 7.278868 GGTGATAAACTTACAGAAGATCCTGTG 59.721 40.741 13.15 1.16 46.00 3.66
1899 2320 9.023962 TGGTTCTGTAATCAGCAAATTTTATCT 57.976 29.630 0.00 0.00 41.10 1.98
1912 2333 7.451566 AGCAAATTTTATCTACCTTGTTGGAGT 59.548 33.333 0.00 0.00 39.71 3.85
1953 2374 9.431887 CTGTATGTACCACCATAAATATGTACC 57.568 37.037 0.00 0.00 31.82 3.34
1966 2387 9.917129 CATAAATATGTACCGTGTTGAGGTATA 57.083 33.333 0.00 0.00 44.96 1.47
1969 2390 8.827177 AATATGTACCGTGTTGAGGTATATTG 57.173 34.615 9.33 0.00 44.96 1.90
2070 2492 5.652994 TTGGGTCTTGGTAAACAATATGC 57.347 39.130 0.00 0.00 38.65 3.14
2182 2604 1.145738 AGCCCACAAACAGATCTTGGT 59.854 47.619 9.11 0.00 0.00 3.67
2230 2652 3.640967 AGCATGCAACCTACAAGGAAAAA 59.359 39.130 21.98 0.00 37.67 1.94
2231 2653 3.989817 GCATGCAACCTACAAGGAAAAAG 59.010 43.478 14.21 0.00 37.67 2.27
2386 2808 7.955864 GGTGAGTTGTGTATAAGAAATTCGTTC 59.044 37.037 0.00 0.00 36.38 3.95
2484 2906 6.998074 TGATGGTCTGTGAAAGTTATTGTTCT 59.002 34.615 0.00 0.00 0.00 3.01
2485 2907 7.502226 TGATGGTCTGTGAAAGTTATTGTTCTT 59.498 33.333 0.00 0.00 0.00 2.52
2486 2908 8.918202 ATGGTCTGTGAAAGTTATTGTTCTTA 57.082 30.769 0.00 0.00 0.00 2.10
2487 2909 8.918202 TGGTCTGTGAAAGTTATTGTTCTTAT 57.082 30.769 0.00 0.00 0.00 1.73
2706 3128 4.147135 GGCTCCACCTGTCCCTAA 57.853 61.111 0.00 0.00 34.51 2.69
2785 3207 0.446616 GAATGGCGGTTCGAAGAACC 59.553 55.000 19.03 19.03 45.90 3.62
2824 3246 1.374758 CCGCTCAGGAAAAGTCGCT 60.375 57.895 0.00 0.00 45.00 4.93
2988 3411 0.038744 AGCAGCATACCACAAGGCTT 59.961 50.000 0.00 0.00 39.06 4.35
3012 3435 5.976534 TCATTCATGTTTTTCCTCACAAACG 59.023 36.000 0.00 0.00 35.93 3.60
3082 3516 3.222173 TGTGCAGTGACCACCTTATTT 57.778 42.857 0.00 0.00 32.30 1.40
3089 3523 5.006746 GCAGTGACCACCTTATTTAAGATCG 59.993 44.000 0.00 0.00 35.33 3.69
3116 3551 3.120923 CCTTTGTTGATTGCATTTGCGTC 60.121 43.478 0.00 0.00 45.83 5.19
3251 3695 2.916934 ACTCATGTACCCCTTTGGCTTA 59.083 45.455 0.00 0.00 37.83 3.09
3284 3732 6.343716 AGCATAAAAATGATGTGGTGAACA 57.656 33.333 0.00 0.00 44.79 3.18
3570 4018 0.788391 AAACCGACGATGACGCTTTC 59.212 50.000 0.00 0.00 43.96 2.62
3706 4154 6.812160 GTGGTACATAACTTCAGAGGTAACAG 59.188 42.308 0.00 0.00 44.52 3.16
3829 4277 6.573664 CAATGATGGAAACTTCACCACTAA 57.426 37.500 0.00 0.00 45.94 2.24
3851 4299 1.068816 GTGTTTTGGACGGCCATGTAC 60.069 52.381 13.08 10.68 45.46 2.90
3865 4313 4.279169 GGCCATGTACATTGTGCATTATCT 59.721 41.667 16.48 0.00 36.79 1.98
4109 4597 6.017933 CAGTTGCTTCAATCTGAAACGATAC 58.982 40.000 0.00 0.00 35.73 2.24
4246 4767 5.823312 TGGGAATATGGATCAATGAGATGG 58.177 41.667 0.00 0.00 37.00 3.51
4269 4790 2.957402 AGGAAGGCTTTGATGTCACA 57.043 45.000 0.00 0.00 0.00 3.58
4411 4938 0.517316 CTGTTGCAACGAGTAAGGGC 59.483 55.000 23.79 0.00 0.00 5.19
4439 4966 6.092092 CGATCTTCTATGTTCTGATGGCTAG 58.908 44.000 0.00 0.00 0.00 3.42
4464 4991 1.723870 CTGGCATCTAACGGCAAGC 59.276 57.895 0.00 0.00 38.61 4.01
4476 5003 0.449388 CGGCAAGCTTGAGAACATCC 59.551 55.000 30.39 17.43 0.00 3.51
4477 5004 1.538047 GGCAAGCTTGAGAACATCCA 58.462 50.000 30.39 0.00 0.00 3.41
4478 5005 2.097825 GGCAAGCTTGAGAACATCCAT 58.902 47.619 30.39 0.00 0.00 3.41
4496 5023 2.573369 CATCATGAAAGAGGAGCCAGG 58.427 52.381 0.00 0.00 0.00 4.45
4666 5193 1.691482 GCCATAGGTAGGGAGGTGTGA 60.691 57.143 0.00 0.00 0.00 3.58
4691 5218 5.692204 GCTGCTTGTAACATATCATACGAGT 59.308 40.000 11.01 0.00 36.37 4.18
4723 5250 6.184789 GGTCACATTTTTAGGATAGTTGGGA 58.815 40.000 0.00 0.00 0.00 4.37
4724 5251 6.095021 GGTCACATTTTTAGGATAGTTGGGAC 59.905 42.308 0.00 0.00 35.75 4.46
4725 5252 6.884836 GTCACATTTTTAGGATAGTTGGGACT 59.115 38.462 0.00 0.00 39.97 3.85
4726 5253 7.393515 GTCACATTTTTAGGATAGTTGGGACTT 59.606 37.037 0.00 0.00 37.33 3.01
4727 5254 7.393234 TCACATTTTTAGGATAGTTGGGACTTG 59.607 37.037 0.00 0.00 37.33 3.16
4728 5255 6.663523 ACATTTTTAGGATAGTTGGGACTTGG 59.336 38.462 0.00 0.00 37.33 3.61
4729 5256 4.855298 TTTAGGATAGTTGGGACTTGGG 57.145 45.455 0.00 0.00 37.33 4.12
4764 5292 5.464030 AGCAAGAAAAATCAGTGAATGCT 57.536 34.783 0.00 2.45 36.83 3.79
4798 5326 4.329256 GTGTAAAGCTATTCGAGAACCACC 59.671 45.833 0.00 0.00 0.00 4.61
4816 5344 6.097915 ACCACCTGTATAATTGATAGTCCG 57.902 41.667 0.00 0.00 0.00 4.79
4853 5381 1.903183 GAGCAACTCTAGGGGAAGTGT 59.097 52.381 0.00 0.00 0.00 3.55
4871 5399 4.168101 AGTGTATGGATGAACCCGGATAT 58.832 43.478 0.73 0.00 38.00 1.63
4879 5407 6.884832 TGGATGAACCCGGATATATATGAAC 58.115 40.000 0.73 0.00 38.00 3.18
4880 5408 6.672218 TGGATGAACCCGGATATATATGAACT 59.328 38.462 0.73 0.00 38.00 3.01
4883 5411 7.733773 TGAACCCGGATATATATGAACTCAT 57.266 36.000 0.73 0.00 40.22 2.90
4888 5416 7.829211 ACCCGGATATATATGAACTCATTTTGG 59.171 37.037 0.73 0.00 37.76 3.28
4943 5471 5.540911 CAAAAAGTTGCATGGGTATGTCTT 58.459 37.500 0.00 0.00 36.65 3.01
4944 5472 5.391312 AAAAGTTGCATGGGTATGTCTTC 57.609 39.130 0.00 0.00 36.65 2.87
4945 5473 3.719268 AGTTGCATGGGTATGTCTTCA 57.281 42.857 0.00 0.00 36.65 3.02
4946 5474 4.240881 AGTTGCATGGGTATGTCTTCAT 57.759 40.909 0.00 0.00 36.65 2.57
4947 5475 3.949754 AGTTGCATGGGTATGTCTTCATG 59.050 43.478 0.00 0.00 39.74 3.07
4948 5476 3.650281 TGCATGGGTATGTCTTCATGT 57.350 42.857 0.00 0.00 39.17 3.21
4949 5477 4.769345 TGCATGGGTATGTCTTCATGTA 57.231 40.909 0.00 0.00 39.17 2.29
4950 5478 4.450976 TGCATGGGTATGTCTTCATGTAC 58.549 43.478 0.00 0.00 39.17 2.90
4951 5479 4.164030 TGCATGGGTATGTCTTCATGTACT 59.836 41.667 0.00 0.00 39.17 2.73
4952 5480 5.365314 TGCATGGGTATGTCTTCATGTACTA 59.635 40.000 0.00 0.00 39.17 1.82
4953 5481 6.043127 TGCATGGGTATGTCTTCATGTACTAT 59.957 38.462 0.00 0.00 39.17 2.12
4954 5482 6.369890 GCATGGGTATGTCTTCATGTACTATG 59.630 42.308 0.00 0.00 39.17 2.23
4955 5483 7.445121 CATGGGTATGTCTTCATGTACTATGT 58.555 38.462 0.00 0.00 35.70 2.29
4956 5484 8.585018 CATGGGTATGTCTTCATGTACTATGTA 58.415 37.037 0.00 0.00 35.70 2.29
4957 5485 7.948357 TGGGTATGTCTTCATGTACTATGTAC 58.052 38.462 0.00 1.33 35.70 2.90
4958 5486 7.082602 GGGTATGTCTTCATGTACTATGTACG 58.917 42.308 0.00 0.00 35.70 3.67
4959 5487 7.255381 GGGTATGTCTTCATGTACTATGTACGT 60.255 40.741 0.00 0.00 35.70 3.57
4960 5488 7.590322 GGTATGTCTTCATGTACTATGTACGTG 59.410 40.741 18.62 18.62 35.70 4.49
4961 5489 5.337554 TGTCTTCATGTACTATGTACGTGC 58.662 41.667 19.45 0.00 35.15 5.34
4962 5490 5.106078 TGTCTTCATGTACTATGTACGTGCA 60.106 40.000 19.45 9.28 35.15 4.57
4963 5491 5.977725 GTCTTCATGTACTATGTACGTGCAT 59.022 40.000 22.72 22.72 38.05 3.96
4964 5492 7.136772 GTCTTCATGTACTATGTACGTGCATA 58.863 38.462 22.52 22.52 35.89 3.14
4965 5493 7.646526 GTCTTCATGTACTATGTACGTGCATAA 59.353 37.037 23.72 11.95 35.89 1.90
4966 5494 8.192110 TCTTCATGTACTATGTACGTGCATAAA 58.808 33.333 23.72 14.01 35.89 1.40
4967 5495 7.924103 TCATGTACTATGTACGTGCATAAAG 57.076 36.000 23.72 18.27 35.89 1.85
4968 5496 7.485810 TCATGTACTATGTACGTGCATAAAGT 58.514 34.615 23.72 22.19 35.89 2.66
4969 5497 7.977293 TCATGTACTATGTACGTGCATAAAGTT 59.023 33.333 23.72 12.71 35.89 2.66
4970 5498 8.600625 CATGTACTATGTACGTGCATAAAGTTT 58.399 33.333 23.72 9.25 35.89 2.66
4971 5499 8.176814 TGTACTATGTACGTGCATAAAGTTTC 57.823 34.615 23.72 17.12 31.76 2.78
4972 5500 7.813627 TGTACTATGTACGTGCATAAAGTTTCA 59.186 33.333 23.72 18.85 31.76 2.69
4973 5501 7.661127 ACTATGTACGTGCATAAAGTTTCAA 57.339 32.000 23.72 4.14 31.76 2.69
4974 5502 7.739295 ACTATGTACGTGCATAAAGTTTCAAG 58.261 34.615 23.72 14.54 31.76 3.02
4975 5503 6.795098 ATGTACGTGCATAAAGTTTCAAGA 57.205 33.333 18.03 0.00 0.00 3.02
4976 5504 6.606234 TGTACGTGCATAAAGTTTCAAGAA 57.394 33.333 0.82 0.00 0.00 2.52
4977 5505 7.017498 TGTACGTGCATAAAGTTTCAAGAAA 57.983 32.000 0.82 0.00 0.00 2.52
4978 5506 7.473366 TGTACGTGCATAAAGTTTCAAGAAAA 58.527 30.769 0.82 0.00 31.33 2.29
4979 5507 7.968956 TGTACGTGCATAAAGTTTCAAGAAAAA 59.031 29.630 0.82 0.00 31.33 1.94
5024 5552 3.699779 TGTGCGTGCATAAAGTTTCAA 57.300 38.095 0.00 0.00 0.00 2.69
5128 5671 8.769891 GGAGACAAAACAAAAAGAACTTTTTCA 58.230 29.630 18.40 0.00 46.30 2.69
5129 5672 9.580916 GAGACAAAACAAAAAGAACTTTTTCAC 57.419 29.630 18.40 5.33 46.30 3.18
5130 5673 9.103861 AGACAAAACAAAAAGAACTTTTTCACA 57.896 25.926 18.40 0.00 46.30 3.58
5140 5683 9.179552 AAAAGAACTTTTTCACAAAATTTGTGC 57.820 25.926 28.35 14.87 45.23 4.57
5176 5719 8.570488 ACATTTGTGAATATGAATGCGTGATAT 58.430 29.630 0.00 0.00 33.84 1.63
5189 5732 9.502145 TGAATGCGTGATATATTTTCTTTCAAC 57.498 29.630 0.00 0.00 0.00 3.18
5244 5787 3.467374 TTTTGAAAAGTGGGTGCATCC 57.533 42.857 9.82 9.82 0.00 3.51
5253 5796 3.083997 GGTGCATCCCGTCTCCCT 61.084 66.667 0.00 0.00 0.00 4.20
5254 5797 2.501610 GTGCATCCCGTCTCCCTC 59.498 66.667 0.00 0.00 0.00 4.30
5255 5798 2.764128 TGCATCCCGTCTCCCTCC 60.764 66.667 0.00 0.00 0.00 4.30
5256 5799 2.444895 GCATCCCGTCTCCCTCCT 60.445 66.667 0.00 0.00 0.00 3.69
5257 5800 2.801631 GCATCCCGTCTCCCTCCTG 61.802 68.421 0.00 0.00 0.00 3.86
5258 5801 2.136878 CATCCCGTCTCCCTCCTGG 61.137 68.421 0.00 0.00 0.00 4.45
5268 5811 3.905678 CCTCCTGGGTAGCTCGCG 61.906 72.222 0.00 0.00 0.00 5.87
5269 5812 4.577246 CTCCTGGGTAGCTCGCGC 62.577 72.222 0.00 0.00 0.00 6.86
5272 5815 4.914420 CTGGGTAGCTCGCGCGAG 62.914 72.222 46.00 46.00 44.56 5.03
5296 5839 3.395630 GGGAGGCACCGAAACCTA 58.604 61.111 0.00 0.00 40.11 3.08
5297 5840 1.681076 GGGAGGCACCGAAACCTAA 59.319 57.895 0.00 0.00 40.11 2.69
5298 5841 0.037160 GGGAGGCACCGAAACCTAAA 59.963 55.000 0.00 0.00 40.11 1.85
5299 5842 1.162698 GGAGGCACCGAAACCTAAAC 58.837 55.000 0.00 0.00 36.05 2.01
5300 5843 1.162698 GAGGCACCGAAACCTAAACC 58.837 55.000 0.00 0.00 36.05 3.27
5301 5844 0.475044 AGGCACCGAAACCTAAACCA 59.525 50.000 0.00 0.00 33.38 3.67
5302 5845 0.879090 GGCACCGAAACCTAAACCAG 59.121 55.000 0.00 0.00 0.00 4.00
5303 5846 1.543871 GGCACCGAAACCTAAACCAGA 60.544 52.381 0.00 0.00 0.00 3.86
5304 5847 2.223745 GCACCGAAACCTAAACCAGAA 58.776 47.619 0.00 0.00 0.00 3.02
5305 5848 2.225727 GCACCGAAACCTAAACCAGAAG 59.774 50.000 0.00 0.00 0.00 2.85
5306 5849 3.735591 CACCGAAACCTAAACCAGAAGA 58.264 45.455 0.00 0.00 0.00 2.87
5307 5850 3.746492 CACCGAAACCTAAACCAGAAGAG 59.254 47.826 0.00 0.00 0.00 2.85
5308 5851 2.742589 CCGAAACCTAAACCAGAAGAGC 59.257 50.000 0.00 0.00 0.00 4.09
5309 5852 2.742589 CGAAACCTAAACCAGAAGAGCC 59.257 50.000 0.00 0.00 0.00 4.70
5310 5853 2.881111 AACCTAAACCAGAAGAGCCC 57.119 50.000 0.00 0.00 0.00 5.19
5311 5854 0.992695 ACCTAAACCAGAAGAGCCCC 59.007 55.000 0.00 0.00 0.00 5.80
5312 5855 0.256177 CCTAAACCAGAAGAGCCCCC 59.744 60.000 0.00 0.00 0.00 5.40
5313 5856 0.107654 CTAAACCAGAAGAGCCCCCG 60.108 60.000 0.00 0.00 0.00 5.73
5314 5857 0.838987 TAAACCAGAAGAGCCCCCGT 60.839 55.000 0.00 0.00 0.00 5.28
5315 5858 2.125766 AAACCAGAAGAGCCCCCGTC 62.126 60.000 0.00 0.00 0.00 4.79
5316 5859 3.787001 CCAGAAGAGCCCCCGTCC 61.787 72.222 0.00 0.00 0.00 4.79
5317 5860 3.003173 CAGAAGAGCCCCCGTCCA 61.003 66.667 0.00 0.00 0.00 4.02
5318 5861 3.003763 AGAAGAGCCCCCGTCCAC 61.004 66.667 0.00 0.00 0.00 4.02
5319 5862 3.003763 GAAGAGCCCCCGTCCACT 61.004 66.667 0.00 0.00 0.00 4.00
5320 5863 3.316573 GAAGAGCCCCCGTCCACTG 62.317 68.421 0.00 0.00 0.00 3.66
5326 5869 4.394712 CCCCGTCCACTGGTGCTC 62.395 72.222 0.00 0.00 0.00 4.26
5327 5870 4.742201 CCCGTCCACTGGTGCTCG 62.742 72.222 0.00 2.75 0.00 5.03
5330 5873 4.008933 GTCCACTGGTGCTCGCCT 62.009 66.667 0.86 0.00 0.00 5.52
5331 5874 4.007644 TCCACTGGTGCTCGCCTG 62.008 66.667 5.04 5.04 0.00 4.85
5396 5939 3.508840 GAAGCGGCGGGTTGGATG 61.509 66.667 13.81 0.00 33.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.119708 AGTCGAAAGAAATTGCAGATGCC 60.120 43.478 1.72 0.00 45.01 4.40
1 2 4.088823 AGTCGAAAGAAATTGCAGATGC 57.911 40.909 0.00 0.00 45.01 3.91
2 3 6.998258 AAAAGTCGAAAGAAATTGCAGATG 57.002 33.333 0.00 0.00 45.01 2.90
75 76 1.471684 AGTTGGAAGTAGTAGACGCGG 59.528 52.381 12.47 0.00 0.00 6.46
105 106 7.287927 ACACTAGCTAGCTCCAATTATAACTGA 59.712 37.037 23.26 0.00 0.00 3.41
109 110 7.715249 CCAAACACTAGCTAGCTCCAATTATAA 59.285 37.037 23.26 0.00 0.00 0.98
110 111 7.217200 CCAAACACTAGCTAGCTCCAATTATA 58.783 38.462 23.26 0.00 0.00 0.98
111 112 6.058183 CCAAACACTAGCTAGCTCCAATTAT 58.942 40.000 23.26 0.42 0.00 1.28
120 121 1.019278 TGCGCCAAACACTAGCTAGC 61.019 55.000 20.91 6.62 0.00 3.42
135 136 0.387239 ATGCGAAAAAGGAACTGCGC 60.387 50.000 0.00 0.00 40.86 6.09
175 177 1.771255 CCGAGGGAATTCAGGGAAGAT 59.229 52.381 7.93 0.00 0.00 2.40
179 181 2.257391 TTACCGAGGGAATTCAGGGA 57.743 50.000 7.93 0.00 0.00 4.20
186 188 4.221924 CCAAACCATTTTTACCGAGGGAAT 59.778 41.667 0.00 0.00 0.00 3.01
189 191 2.353307 GCCAAACCATTTTTACCGAGGG 60.353 50.000 0.00 0.00 0.00 4.30
227 229 1.781025 CGAACCGGCAGCAGAAAACA 61.781 55.000 0.00 0.00 0.00 2.83
267 269 8.737648 GCTGATCTAACAAAATTATTCGCTTTC 58.262 33.333 0.00 0.00 0.00 2.62
332 334 6.035005 CCTCGCCATAATATGATTACGAACTG 59.965 42.308 1.10 0.00 0.00 3.16
346 348 0.693049 GGACATCCCCTCGCCATAAT 59.307 55.000 0.00 0.00 0.00 1.28
348 350 0.485543 TAGGACATCCCCTCGCCATA 59.514 55.000 0.00 0.00 37.74 2.74
383 387 1.273048 GCCATTTGCCTTCATGTCACA 59.727 47.619 0.00 0.00 0.00 3.58
442 446 2.505866 GTTTGAGCCGCAACTAATTCG 58.494 47.619 0.00 0.00 35.91 3.34
453 457 2.225068 AGATACATCCGTTTGAGCCG 57.775 50.000 0.00 0.00 0.00 5.52
454 458 3.050619 CGTAGATACATCCGTTTGAGCC 58.949 50.000 0.00 0.00 0.00 4.70
472 476 5.184287 TCATCTACTTGTCCACAATGACGTA 59.816 40.000 0.00 0.00 38.11 3.57
474 478 4.494484 TCATCTACTTGTCCACAATGACG 58.506 43.478 0.00 0.00 38.11 4.35
491 554 3.881688 GACATGGCAAACTAGCATCATCT 59.118 43.478 0.00 0.00 35.83 2.90
529 592 9.802039 ATTACAGAAAAGTATTTGTAAGTGGGA 57.198 29.630 2.90 0.00 39.02 4.37
547 610 7.812191 GGCATAAACAACAACATGATTACAGAA 59.188 33.333 0.00 0.00 0.00 3.02
549 612 7.315142 AGGCATAAACAACAACATGATTACAG 58.685 34.615 0.00 0.00 0.00 2.74
551 614 9.289303 CTAAGGCATAAACAACAACATGATTAC 57.711 33.333 0.00 0.00 0.00 1.89
556 619 9.638239 AAATACTAAGGCATAAACAACAACATG 57.362 29.630 0.00 0.00 0.00 3.21
557 620 9.638239 CAAATACTAAGGCATAAACAACAACAT 57.362 29.630 0.00 0.00 0.00 2.71
558 621 7.596995 GCAAATACTAAGGCATAAACAACAACA 59.403 33.333 0.00 0.00 0.00 3.33
559 622 7.596995 TGCAAATACTAAGGCATAAACAACAAC 59.403 33.333 0.00 0.00 0.00 3.32
560 623 7.661968 TGCAAATACTAAGGCATAAACAACAA 58.338 30.769 0.00 0.00 0.00 2.83
562 625 7.596995 TGTTGCAAATACTAAGGCATAAACAAC 59.403 33.333 0.00 0.00 35.98 3.32
563 626 7.661968 TGTTGCAAATACTAAGGCATAAACAA 58.338 30.769 0.00 0.00 35.98 2.83
564 627 7.220741 TGTTGCAAATACTAAGGCATAAACA 57.779 32.000 0.00 0.00 35.98 2.83
565 628 7.222611 CCATGTTGCAAATACTAAGGCATAAAC 59.777 37.037 0.00 0.00 35.98 2.01
566 629 7.264221 CCATGTTGCAAATACTAAGGCATAAA 58.736 34.615 0.00 0.00 35.98 1.40
567 630 6.682611 GCCATGTTGCAAATACTAAGGCATAA 60.683 38.462 0.00 0.00 38.27 1.90
568 631 5.221224 GCCATGTTGCAAATACTAAGGCATA 60.221 40.000 0.00 0.00 38.27 3.14
574 679 4.617995 GCACAGCCATGTTGCAAATACTAA 60.618 41.667 0.00 0.00 37.65 2.24
592 697 2.027745 AGTAGTTGGAGGATGTGCACAG 60.028 50.000 25.84 0.00 0.00 3.66
610 715 3.189910 CCACGTAACACAGCTACAGAGTA 59.810 47.826 0.00 0.00 0.00 2.59
633 738 1.612950 TGTGAATTGCATCAAAGGCGT 59.387 42.857 0.00 0.00 0.00 5.68
791 1056 4.133078 CCCAGAGGTATGATGAAAGCTTC 58.867 47.826 0.00 0.00 0.00 3.86
881 1146 0.742281 CCATCCAAGTCAGCCAGTCG 60.742 60.000 0.00 0.00 0.00 4.18
937 1202 7.448469 ACATTCACTGTACTTTTCAGCCTAAAT 59.552 33.333 0.00 0.00 35.91 1.40
951 1216 3.678056 TGAGGGTCACATTCACTGTAC 57.322 47.619 0.00 0.00 35.91 2.90
961 1226 2.708861 ACAAGTTGGTATGAGGGTCACA 59.291 45.455 7.96 0.00 0.00 3.58
1062 1327 1.066858 AGCGGGCTATCCAATATCACG 60.067 52.381 0.00 0.00 31.46 4.35
1128 1393 3.252974 ACATCTAACCAGTGTAGCTGC 57.747 47.619 0.00 0.00 43.71 5.25
1194 1459 8.213518 TGGAAGCTAACAATTCAGTTGATATC 57.786 34.615 0.00 0.00 40.37 1.63
1263 1528 5.450137 CCTCAGATGATTCCAAGAATGCAAC 60.450 44.000 0.00 0.00 0.00 4.17
1308 1573 4.225942 GCATCCAATCCATCTGGTAGGATA 59.774 45.833 14.75 0.00 43.67 2.59
1419 1684 5.124457 GCATTGCTTCTCTTTGTCCTTATGA 59.876 40.000 0.16 0.00 0.00 2.15
1899 2320 7.325694 GCAAGTAACTATACTCCAACAAGGTA 58.674 38.462 0.00 0.00 41.57 3.08
1912 2333 6.268387 GGTACATACAGGGGCAAGTAACTATA 59.732 42.308 0.00 0.00 0.00 1.31
1967 2388 9.579932 AGACAGACATAGTGATATCAGATACAA 57.420 33.333 5.42 0.00 0.00 2.41
2015 2437 5.072600 TGTTCAACAGGTCTTAAGGGTACAT 59.927 40.000 1.85 0.00 0.00 2.29
2070 2492 3.934068 AGCCTGCCATCAAAAGAAAATG 58.066 40.909 0.00 0.00 0.00 2.32
2459 2881 6.998074 AGAACAATAACTTTCACAGACCATCA 59.002 34.615 0.00 0.00 0.00 3.07
2785 3207 1.215244 CAGCATCGTACTGCATCCAG 58.785 55.000 9.50 0.00 44.77 3.86
2824 3246 0.741915 GGCCAACAAAGAACCGAACA 59.258 50.000 0.00 0.00 0.00 3.18
2904 3327 9.653287 ACACATATTGCATATATGTAGGTACAC 57.347 33.333 22.72 0.00 41.69 2.90
2937 3360 6.649155 TGCAGCTCTACACCTATTATTTGAA 58.351 36.000 0.00 0.00 0.00 2.69
2988 3411 5.976534 CGTTTGTGAGGAAAAACATGAATGA 59.023 36.000 0.00 0.00 36.31 2.57
3012 3435 0.664166 CCCACGCACAAAGCATGTTC 60.664 55.000 0.00 0.00 46.13 3.18
3061 3495 2.949177 ATAAGGTGGTCACTGCACAA 57.051 45.000 0.93 0.00 0.00 3.33
3082 3516 6.128282 GCAATCAACAAAGGAGAACGATCTTA 60.128 38.462 0.00 0.00 35.54 2.10
3089 3523 5.333568 GCAAATGCAATCAACAAAGGAGAAC 60.334 40.000 0.00 0.00 41.59 3.01
3116 3551 2.423577 GGGTAAGCAAGTACACAGTGG 58.576 52.381 5.31 0.00 0.00 4.00
3274 3722 1.131638 AGAGCTCCTTGTTCACCACA 58.868 50.000 10.93 0.00 0.00 4.17
3284 3732 0.036858 GCTTCGTTCCAGAGCTCCTT 60.037 55.000 10.93 0.00 0.00 3.36
3391 3839 7.893124 TCTCCCGAAAAAGTAGATACATACT 57.107 36.000 0.00 0.00 37.61 2.12
3409 3857 7.587757 CGCAAAGAAATTAAAGATATTCTCCCG 59.412 37.037 0.00 0.00 31.20 5.14
3418 3866 7.881775 ATCTACCCGCAAAGAAATTAAAGAT 57.118 32.000 0.00 0.00 0.00 2.40
3570 4018 5.392874 CGAAAGTATCTCATCTACACGAACG 59.607 44.000 0.00 0.00 0.00 3.95
3829 4277 4.589046 TGGCCGTCCAAAACACAT 57.411 50.000 0.00 0.00 39.99 3.21
4109 4597 4.516698 TGTTTTCTCTTAAGCTGCCTTCAG 59.483 41.667 0.00 0.00 43.16 3.02
4149 4663 2.263741 GCACCACAGCAGGGACAAG 61.264 63.158 0.00 0.00 0.00 3.16
4246 4767 3.438434 GTGACATCAAAGCCTTCCTTCTC 59.562 47.826 0.00 0.00 31.99 2.87
4269 4790 1.843368 TCCTTCCGTCGTTCTGGTAT 58.157 50.000 0.00 0.00 0.00 2.73
4411 4938 5.400782 CCATCAGAACATAGAAGATCGTTCG 59.599 44.000 0.00 0.00 42.01 3.95
4464 4991 6.038382 CCTCTTTCATGATGGATGTTCTCAAG 59.962 42.308 0.00 0.00 33.29 3.02
4476 5003 2.573369 CCTGGCTCCTCTTTCATGATG 58.427 52.381 0.00 0.00 0.00 3.07
4477 5004 1.493871 CCCTGGCTCCTCTTTCATGAT 59.506 52.381 0.00 0.00 0.00 2.45
4478 5005 0.914644 CCCTGGCTCCTCTTTCATGA 59.085 55.000 0.00 0.00 0.00 3.07
4666 5193 5.842907 TCGTATGATATGTTACAAGCAGCT 58.157 37.500 0.00 0.00 0.00 4.24
4691 5218 4.776837 TCCTAAAAATGTGACCCCTACGTA 59.223 41.667 0.00 0.00 0.00 3.57
4700 5227 6.884836 AGTCCCAACTATCCTAAAAATGTGAC 59.115 38.462 0.00 0.00 32.59 3.67
4702 5229 7.362920 CCAAGTCCCAACTATCCTAAAAATGTG 60.363 40.741 0.00 0.00 33.48 3.21
4723 5250 1.140134 TAAAGCTGGCCCTCCCAAGT 61.140 55.000 0.00 0.00 44.81 3.16
4724 5251 0.394899 CTAAAGCTGGCCCTCCCAAG 60.395 60.000 0.00 0.00 44.81 3.61
4725 5252 1.691219 CTAAAGCTGGCCCTCCCAA 59.309 57.895 0.00 0.00 44.81 4.12
4726 5253 2.983879 GCTAAAGCTGGCCCTCCCA 61.984 63.158 0.00 0.00 42.79 4.37
4727 5254 2.124109 GCTAAAGCTGGCCCTCCC 60.124 66.667 0.00 0.00 38.21 4.30
4728 5255 1.000896 TTGCTAAAGCTGGCCCTCC 60.001 57.895 0.00 0.00 42.66 4.30
4729 5256 0.035056 TCTTGCTAAAGCTGGCCCTC 60.035 55.000 0.00 0.00 42.66 4.30
4764 5292 5.637006 ATAGCTTTACACGGATGCAAAAA 57.363 34.783 0.00 0.00 0.00 1.94
4798 5326 6.701841 ACACAAGCGGACTATCAATTATACAG 59.298 38.462 0.00 0.00 0.00 2.74
4816 5344 1.740025 GCTCCAATACCAGACACAAGC 59.260 52.381 0.00 0.00 0.00 4.01
4853 5381 8.647796 GTTCATATATATCCGGGTTCATCCATA 58.352 37.037 0.00 0.00 38.11 2.74
4932 5460 7.255346 CGTACATAGTACATGAAGACATACCCA 60.255 40.741 0.00 0.00 35.09 4.51
4943 5471 7.485810 ACTTTATGCACGTACATAGTACATGA 58.514 34.615 8.44 0.00 34.15 3.07
4944 5472 7.694388 ACTTTATGCACGTACATAGTACATG 57.306 36.000 8.44 3.87 34.15 3.21
4945 5473 8.712285 AAACTTTATGCACGTACATAGTACAT 57.288 30.769 8.44 0.00 34.15 2.29
4946 5474 7.813627 TGAAACTTTATGCACGTACATAGTACA 59.186 33.333 8.44 7.61 34.15 2.90
4947 5475 8.176814 TGAAACTTTATGCACGTACATAGTAC 57.823 34.615 8.44 5.59 34.15 2.73
4948 5476 8.760103 TTGAAACTTTATGCACGTACATAGTA 57.240 30.769 8.44 1.57 34.15 1.82
4949 5477 7.601130 TCTTGAAACTTTATGCACGTACATAGT 59.399 33.333 8.44 3.77 34.15 2.12
4950 5478 7.959733 TCTTGAAACTTTATGCACGTACATAG 58.040 34.615 8.44 3.16 34.15 2.23
4951 5479 7.892778 TCTTGAAACTTTATGCACGTACATA 57.107 32.000 4.31 4.31 0.00 2.29
4952 5480 6.795098 TCTTGAAACTTTATGCACGTACAT 57.205 33.333 6.50 6.50 0.00 2.29
4953 5481 6.606234 TTCTTGAAACTTTATGCACGTACA 57.394 33.333 0.00 0.00 0.00 2.90
4954 5482 7.901874 TTTTCTTGAAACTTTATGCACGTAC 57.098 32.000 0.00 0.00 0.00 3.67
4982 5510 7.602265 GCACATAAAACATGGGTATGAAAAGTT 59.398 33.333 15.46 0.00 37.73 2.66
4983 5511 7.096551 GCACATAAAACATGGGTATGAAAAGT 58.903 34.615 15.46 0.00 37.73 2.66
4984 5512 6.253298 CGCACATAAAACATGGGTATGAAAAG 59.747 38.462 15.46 6.92 37.73 2.27
4985 5513 6.096036 CGCACATAAAACATGGGTATGAAAA 58.904 36.000 15.46 0.00 37.73 2.29
4986 5514 5.184096 ACGCACATAAAACATGGGTATGAAA 59.816 36.000 15.46 0.00 37.70 2.69
4987 5515 4.702612 ACGCACATAAAACATGGGTATGAA 59.297 37.500 15.46 0.00 37.70 2.57
4988 5516 4.095632 CACGCACATAAAACATGGGTATGA 59.904 41.667 15.46 0.00 37.41 2.15
4989 5517 4.350346 CACGCACATAAAACATGGGTATG 58.650 43.478 0.00 4.47 37.41 2.39
4990 5518 3.181491 GCACGCACATAAAACATGGGTAT 60.181 43.478 0.00 0.00 37.41 2.73
4991 5519 2.162608 GCACGCACATAAAACATGGGTA 59.837 45.455 0.00 0.00 37.41 3.69
4992 5520 1.067915 GCACGCACATAAAACATGGGT 60.068 47.619 0.00 0.00 39.82 4.51
4993 5521 1.067985 TGCACGCACATAAAACATGGG 60.068 47.619 0.00 0.00 0.00 4.00
5001 5529 5.363979 TGAAACTTTATGCACGCACATAA 57.636 34.783 6.61 6.61 40.00 1.90
5082 5610 7.124298 TGTCTCCATAGTGCTTCTAAATAGTGT 59.876 37.037 0.00 0.00 31.94 3.55
5100 5628 8.846943 AAAAGTTCTTTTTGTTTTGTCTCCAT 57.153 26.923 4.91 0.00 37.59 3.41
5128 5671 1.065701 TGTACGCGGCACAAATTTTGT 59.934 42.857 12.47 8.97 46.75 2.83
5129 5672 1.450161 GTGTACGCGGCACAAATTTTG 59.550 47.619 24.34 7.59 36.88 2.44
5130 5673 1.065701 TGTGTACGCGGCACAAATTTT 59.934 42.857 27.88 0.32 42.96 1.82
5134 5677 1.160946 ATGTGTGTACGCGGCACAAA 61.161 50.000 30.30 27.23 46.65 2.83
5135 5678 1.160946 AATGTGTGTACGCGGCACAA 61.161 50.000 30.30 22.51 46.65 3.33
5137 5680 0.724453 CAAATGTGTGTACGCGGCAC 60.724 55.000 23.12 23.12 37.37 5.01
5176 5719 8.696410 AAGCGTCAAAAAGTTGAAAGAAAATA 57.304 26.923 0.00 0.00 45.29 1.40
5177 5720 7.595311 AAGCGTCAAAAAGTTGAAAGAAAAT 57.405 28.000 0.00 0.00 45.29 1.82
5182 5725 7.418521 CGTTTTAAAGCGTCAAAAAGTTGAAAG 59.581 33.333 15.35 0.00 45.29 2.62
5186 5729 5.943573 CACGTTTTAAAGCGTCAAAAAGTTG 59.056 36.000 24.53 8.87 43.95 3.16
5189 5732 4.264380 AGCACGTTTTAAAGCGTCAAAAAG 59.736 37.500 24.53 14.57 43.95 2.27
5251 5794 3.905678 CGCGAGCTACCCAGGAGG 61.906 72.222 0.00 0.00 43.78 4.30
5279 5822 0.037160 TTTAGGTTTCGGTGCCTCCC 59.963 55.000 0.00 0.00 36.38 4.30
5280 5823 1.162698 GTTTAGGTTTCGGTGCCTCC 58.837 55.000 0.00 0.00 36.38 4.30
5281 5824 1.162698 GGTTTAGGTTTCGGTGCCTC 58.837 55.000 0.00 0.00 36.38 4.70
5282 5825 0.475044 TGGTTTAGGTTTCGGTGCCT 59.525 50.000 0.00 0.00 38.81 4.75
5283 5826 0.879090 CTGGTTTAGGTTTCGGTGCC 59.121 55.000 0.00 0.00 0.00 5.01
5284 5827 1.886886 TCTGGTTTAGGTTTCGGTGC 58.113 50.000 0.00 0.00 0.00 5.01
5285 5828 3.735591 TCTTCTGGTTTAGGTTTCGGTG 58.264 45.455 0.00 0.00 0.00 4.94
5286 5829 3.806157 GCTCTTCTGGTTTAGGTTTCGGT 60.806 47.826 0.00 0.00 0.00 4.69
5287 5830 2.742589 GCTCTTCTGGTTTAGGTTTCGG 59.257 50.000 0.00 0.00 0.00 4.30
5288 5831 2.742589 GGCTCTTCTGGTTTAGGTTTCG 59.257 50.000 0.00 0.00 0.00 3.46
5289 5832 3.082548 GGGCTCTTCTGGTTTAGGTTTC 58.917 50.000 0.00 0.00 0.00 2.78
5290 5833 2.225041 GGGGCTCTTCTGGTTTAGGTTT 60.225 50.000 0.00 0.00 0.00 3.27
5291 5834 1.354705 GGGGCTCTTCTGGTTTAGGTT 59.645 52.381 0.00 0.00 0.00 3.50
5292 5835 0.992695 GGGGCTCTTCTGGTTTAGGT 59.007 55.000 0.00 0.00 0.00 3.08
5293 5836 0.256177 GGGGGCTCTTCTGGTTTAGG 59.744 60.000 0.00 0.00 0.00 2.69
5294 5837 0.107654 CGGGGGCTCTTCTGGTTTAG 60.108 60.000 0.00 0.00 0.00 1.85
5295 5838 0.838987 ACGGGGGCTCTTCTGGTTTA 60.839 55.000 0.00 0.00 0.00 2.01
5296 5839 2.125766 GACGGGGGCTCTTCTGGTTT 62.126 60.000 0.00 0.00 0.00 3.27
5297 5840 2.529389 ACGGGGGCTCTTCTGGTT 60.529 61.111 0.00 0.00 0.00 3.67
5298 5841 3.003763 GACGGGGGCTCTTCTGGT 61.004 66.667 0.00 0.00 0.00 4.00
5299 5842 3.787001 GGACGGGGGCTCTTCTGG 61.787 72.222 0.00 0.00 0.00 3.86
5300 5843 3.003173 TGGACGGGGGCTCTTCTG 61.003 66.667 0.00 0.00 0.00 3.02
5301 5844 3.003763 GTGGACGGGGGCTCTTCT 61.004 66.667 0.00 0.00 0.00 2.85
5302 5845 3.003763 AGTGGACGGGGGCTCTTC 61.004 66.667 0.00 0.00 0.00 2.87
5303 5846 3.322466 CAGTGGACGGGGGCTCTT 61.322 66.667 0.00 0.00 0.00 2.85
5309 5852 4.394712 GAGCACCAGTGGACGGGG 62.395 72.222 18.40 0.65 35.41 5.73
5310 5853 4.742201 CGAGCACCAGTGGACGGG 62.742 72.222 18.40 3.31 37.23 5.28
5313 5856 4.008933 AGGCGAGCACCAGTGGAC 62.009 66.667 18.40 7.56 0.00 4.02
5314 5857 4.007644 CAGGCGAGCACCAGTGGA 62.008 66.667 18.40 0.00 0.00 4.02
5379 5922 3.508840 CATCCAACCCGCCGCTTC 61.509 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.