Multiple sequence alignment - TraesCS1A01G037200

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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 TraesCS1A01G037200 chr1A 100.000 1598 0 0 1 1598 20881041 20879444 0.000000e+00 2952.0
1 TraesCS1A01G037200 chr1A 100.000 476 0 0 2062 2537 20878980 20878505 0.000000e+00 880.0
2 TraesCS1A01G037200 chr1A 96.471 85 3 0 1 85 75739487 75739403 9.460000e-30 141.0
3 TraesCS1A01G037200 chr1D 88.448 1134 79 30 443 1551 18869185 18868079 0.000000e+00 1321.0
4 TraesCS1A01G037200 chr1D 88.372 258 19 9 2068 2323 18867992 18867744 1.480000e-77 300.0
5 TraesCS1A01G037200 chr1D 83.505 291 31 13 91 368 18869895 18869609 3.240000e-64 255.0
6 TraesCS1A01G037200 chr1D 83.333 120 20 0 368 487 364114956 364115075 7.420000e-21 111.0
7 TraesCS1A01G037200 chr1B 89.488 1075 70 22 536 1598 27355555 27354512 0.000000e+00 1319.0
8 TraesCS1A01G037200 chr1B 85.340 191 11 10 2068 2257 27354455 27354281 5.580000e-42 182.0
9 TraesCS1A01G037200 chr1B 83.333 162 25 2 89 248 27356483 27356322 5.650000e-32 148.0
10 TraesCS1A01G037200 chr5B 88.222 450 53 0 998 1447 710659516 710659965 2.870000e-149 538.0
11 TraesCS1A01G037200 chr5B 86.404 456 56 3 997 1449 710651566 710651114 6.310000e-136 494.0
12 TraesCS1A01G037200 chr4A 86.100 482 64 1 996 1474 604068514 604068995 1.350000e-142 516.0
13 TraesCS1A01G037200 chr4A 85.683 454 65 0 996 1449 604056046 604055593 1.770000e-131 479.0
14 TraesCS1A01G037200 chr4A 94.444 54 3 0 2305 2358 543368363 543368310 1.620000e-12 84.2
15 TraesCS1A01G037200 chr4A 94.444 54 2 1 2305 2358 742971430 742971482 5.820000e-12 82.4
16 TraesCS1A01G037200 chr5D 86.784 454 60 0 997 1450 560338201 560338654 8.100000e-140 507.0
17 TraesCS1A01G037200 chr5D 85.683 454 65 0 997 1450 560264140 560263687 1.770000e-131 479.0
18 TraesCS1A01G037200 chr5D 85.144 451 67 0 996 1446 560329745 560329295 1.780000e-126 462.0
19 TraesCS1A01G037200 chr5A 93.878 98 4 2 1 98 671874133 671874038 2.030000e-31 147.0
20 TraesCS1A01G037200 chr5A 96.471 85 3 0 1 85 547534742 547534826 9.460000e-30 141.0
21 TraesCS1A01G037200 chr5A 94.444 54 1 2 2305 2357 303399897 303399949 5.820000e-12 82.4
22 TraesCS1A01G037200 chr5A 94.340 53 3 0 2305 2357 341688338 341688286 5.820000e-12 82.4
23 TraesCS1A01G037200 chr6A 85.567 97 14 0 370 466 591771371 591771467 4.470000e-18 102.0
24 TraesCS1A01G037200 chr6A 97.727 44 1 0 1 44 83361797 83361840 2.710000e-10 76.8
25 TraesCS1A01G037200 chr2D 83.158 95 15 1 372 466 548886442 548886535 4.500000e-13 86.1
26 TraesCS1A01G037200 chr4D 94.444 54 3 0 2305 2358 53760068 53760121 1.620000e-12 84.2
27 TraesCS1A01G037200 chr3D 94.340 53 3 0 2305 2357 67481035 67480983 5.820000e-12 82.4
28 TraesCS1A01G037200 chr3D 89.231 65 5 2 2298 2362 389633084 389633022 2.090000e-11 80.5
29 TraesCS1A01G037200 chr7D 91.379 58 5 0 2305 2362 74596125 74596182 2.090000e-11 80.5
30 TraesCS1A01G037200 chr6D 87.879 66 4 4 2298 2362 356594144 356594206 9.730000e-10 75.0


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 TraesCS1A01G037200 chr1A 20878505 20881041 2536 True 1916.000000 2952 100.000000 1 2537 2 chr1A.!!$R2 2536
1 TraesCS1A01G037200 chr1D 18867744 18869895 2151 True 625.333333 1321 86.775000 91 2323 3 chr1D.!!$R1 2232
2 TraesCS1A01G037200 chr1B 27354281 27356483 2202 True 549.666667 1319 86.053667 89 2257 3 chr1B.!!$R1 2168

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
19 20 0.041839 GCTCGGCAAATCGCTATGTG 60.042 55.0 0.00 0.0 41.91 3.21 F
686 1495 0.096976 GAGCGCACGCACATGTAAAT 59.903 50.0 18.24 0.0 44.88 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 2207 0.535335 TGGGTGAAGGCGAGTATGAC 59.465 55.0 0.00 0.00 0.00 3.06 R
2065 2900 0.736636 TGCATACACGCTAGCTACGT 59.263 50.0 13.93 13.32 46.42 3.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.311294 GCTCGGCAAATCGCTATGT 58.689 52.632 0.00 0.00 41.91 2.29
19 20 0.041839 GCTCGGCAAATCGCTATGTG 60.042 55.000 0.00 0.00 41.91 3.21
20 21 0.583438 CTCGGCAAATCGCTATGTGG 59.417 55.000 0.00 0.00 41.91 4.17
21 22 0.176910 TCGGCAAATCGCTATGTGGA 59.823 50.000 0.00 0.00 41.91 4.02
22 23 0.583438 CGGCAAATCGCTATGTGGAG 59.417 55.000 0.00 0.00 41.91 3.86
23 24 1.668419 GGCAAATCGCTATGTGGAGT 58.332 50.000 0.00 0.00 41.91 3.85
24 25 2.801699 CGGCAAATCGCTATGTGGAGTA 60.802 50.000 0.00 0.00 41.91 2.59
25 26 2.802816 GGCAAATCGCTATGTGGAGTAG 59.197 50.000 0.00 0.00 41.91 2.57
26 27 3.492656 GGCAAATCGCTATGTGGAGTAGA 60.493 47.826 0.00 0.00 41.91 2.59
27 28 4.119862 GCAAATCGCTATGTGGAGTAGAA 58.880 43.478 0.00 0.00 37.77 2.10
28 29 4.210120 GCAAATCGCTATGTGGAGTAGAAG 59.790 45.833 0.00 0.00 37.77 2.85
29 30 3.651803 ATCGCTATGTGGAGTAGAAGC 57.348 47.619 0.00 0.00 0.00 3.86
30 31 2.656002 TCGCTATGTGGAGTAGAAGCT 58.344 47.619 0.00 0.00 0.00 3.74
31 32 3.816994 TCGCTATGTGGAGTAGAAGCTA 58.183 45.455 0.00 0.00 0.00 3.32
32 33 3.815962 TCGCTATGTGGAGTAGAAGCTAG 59.184 47.826 0.00 0.00 0.00 3.42
33 34 3.566322 CGCTATGTGGAGTAGAAGCTAGT 59.434 47.826 0.00 0.00 0.00 2.57
34 35 4.036971 CGCTATGTGGAGTAGAAGCTAGTT 59.963 45.833 0.00 0.00 0.00 2.24
35 36 5.450688 CGCTATGTGGAGTAGAAGCTAGTTT 60.451 44.000 0.00 0.00 0.00 2.66
36 37 5.980715 GCTATGTGGAGTAGAAGCTAGTTTC 59.019 44.000 11.09 11.09 0.00 2.78
37 38 6.405953 GCTATGTGGAGTAGAAGCTAGTTTCA 60.406 42.308 19.87 5.02 0.00 2.69
38 39 5.392767 TGTGGAGTAGAAGCTAGTTTCAG 57.607 43.478 19.87 0.00 0.00 3.02
39 40 4.220821 TGTGGAGTAGAAGCTAGTTTCAGG 59.779 45.833 19.87 0.00 0.00 3.86
40 41 4.463186 GTGGAGTAGAAGCTAGTTTCAGGA 59.537 45.833 19.87 3.74 0.00 3.86
41 42 5.047235 GTGGAGTAGAAGCTAGTTTCAGGAA 60.047 44.000 19.87 1.68 0.00 3.36
42 43 5.186021 TGGAGTAGAAGCTAGTTTCAGGAAG 59.814 44.000 19.87 0.00 0.00 3.46
43 44 5.079689 AGTAGAAGCTAGTTTCAGGAAGC 57.920 43.478 19.87 4.90 35.16 3.86
44 45 4.775253 AGTAGAAGCTAGTTTCAGGAAGCT 59.225 41.667 19.87 3.88 46.96 3.74
45 46 3.936564 AGAAGCTAGTTTCAGGAAGCTG 58.063 45.455 19.87 0.00 44.30 4.24
46 47 3.580458 AGAAGCTAGTTTCAGGAAGCTGA 59.420 43.478 19.87 0.00 44.30 4.26
47 48 4.224818 AGAAGCTAGTTTCAGGAAGCTGAT 59.775 41.667 19.87 0.00 44.30 2.90
48 49 4.566426 AGCTAGTTTCAGGAAGCTGATT 57.434 40.909 8.42 0.00 43.46 2.57
49 50 4.916183 AGCTAGTTTCAGGAAGCTGATTT 58.084 39.130 8.42 0.00 43.46 2.17
50 51 5.320277 AGCTAGTTTCAGGAAGCTGATTTT 58.680 37.500 8.42 0.00 43.46 1.82
51 52 5.182760 AGCTAGTTTCAGGAAGCTGATTTTG 59.817 40.000 8.42 0.00 43.46 2.44
52 53 5.182001 GCTAGTTTCAGGAAGCTGATTTTGA 59.818 40.000 8.42 0.00 33.82 2.69
53 54 5.702349 AGTTTCAGGAAGCTGATTTTGAG 57.298 39.130 0.00 0.00 32.91 3.02
54 55 4.522022 AGTTTCAGGAAGCTGATTTTGAGG 59.478 41.667 0.00 0.00 32.91 3.86
55 56 4.371624 TTCAGGAAGCTGATTTTGAGGA 57.628 40.909 0.00 0.00 32.91 3.71
56 57 3.947868 TCAGGAAGCTGATTTTGAGGAG 58.052 45.455 0.00 0.00 0.00 3.69
57 58 3.328931 TCAGGAAGCTGATTTTGAGGAGT 59.671 43.478 0.00 0.00 0.00 3.85
58 59 4.077822 CAGGAAGCTGATTTTGAGGAGTT 58.922 43.478 0.00 0.00 0.00 3.01
59 60 4.522022 CAGGAAGCTGATTTTGAGGAGTTT 59.478 41.667 0.00 0.00 0.00 2.66
60 61 5.010415 CAGGAAGCTGATTTTGAGGAGTTTT 59.990 40.000 0.00 0.00 0.00 2.43
61 62 5.010415 AGGAAGCTGATTTTGAGGAGTTTTG 59.990 40.000 0.00 0.00 0.00 2.44
62 63 5.010012 GGAAGCTGATTTTGAGGAGTTTTGA 59.990 40.000 0.00 0.00 0.00 2.69
63 64 6.461509 GGAAGCTGATTTTGAGGAGTTTTGAA 60.462 38.462 0.00 0.00 0.00 2.69
64 65 6.469782 AGCTGATTTTGAGGAGTTTTGAAA 57.530 33.333 0.00 0.00 0.00 2.69
65 66 6.510536 AGCTGATTTTGAGGAGTTTTGAAAG 58.489 36.000 0.00 0.00 0.00 2.62
66 67 6.097412 AGCTGATTTTGAGGAGTTTTGAAAGT 59.903 34.615 0.00 0.00 0.00 2.66
67 68 6.758416 GCTGATTTTGAGGAGTTTTGAAAGTT 59.242 34.615 0.00 0.00 0.00 2.66
68 69 7.278646 GCTGATTTTGAGGAGTTTTGAAAGTTT 59.721 33.333 0.00 0.00 0.00 2.66
69 70 8.477984 TGATTTTGAGGAGTTTTGAAAGTTTG 57.522 30.769 0.00 0.00 0.00 2.93
70 71 7.548780 TGATTTTGAGGAGTTTTGAAAGTTTGG 59.451 33.333 0.00 0.00 0.00 3.28
71 72 6.597832 TTTGAGGAGTTTTGAAAGTTTGGA 57.402 33.333 0.00 0.00 0.00 3.53
72 73 5.835113 TGAGGAGTTTTGAAAGTTTGGAG 57.165 39.130 0.00 0.00 0.00 3.86
73 74 5.505780 TGAGGAGTTTTGAAAGTTTGGAGA 58.494 37.500 0.00 0.00 0.00 3.71
74 75 5.590259 TGAGGAGTTTTGAAAGTTTGGAGAG 59.410 40.000 0.00 0.00 0.00 3.20
75 76 4.889995 AGGAGTTTTGAAAGTTTGGAGAGG 59.110 41.667 0.00 0.00 0.00 3.69
76 77 4.887655 GGAGTTTTGAAAGTTTGGAGAGGA 59.112 41.667 0.00 0.00 0.00 3.71
77 78 5.536538 GGAGTTTTGAAAGTTTGGAGAGGAT 59.463 40.000 0.00 0.00 0.00 3.24
78 79 6.294231 GGAGTTTTGAAAGTTTGGAGAGGATC 60.294 42.308 0.00 0.00 0.00 3.36
79 80 6.129179 AGTTTTGAAAGTTTGGAGAGGATCA 58.871 36.000 0.00 0.00 37.82 2.92
80 81 6.264067 AGTTTTGAAAGTTTGGAGAGGATCAG 59.736 38.462 0.00 0.00 37.82 2.90
81 82 5.567037 TTGAAAGTTTGGAGAGGATCAGA 57.433 39.130 0.00 0.00 37.82 3.27
82 83 5.567037 TGAAAGTTTGGAGAGGATCAGAA 57.433 39.130 0.00 0.00 37.82 3.02
83 84 5.308825 TGAAAGTTTGGAGAGGATCAGAAC 58.691 41.667 0.00 0.00 37.82 3.01
84 85 4.982241 AAGTTTGGAGAGGATCAGAACA 57.018 40.909 0.00 0.00 37.82 3.18
85 86 4.982241 AGTTTGGAGAGGATCAGAACAA 57.018 40.909 0.00 0.00 37.82 2.83
86 87 5.310409 AGTTTGGAGAGGATCAGAACAAA 57.690 39.130 0.00 0.00 37.82 2.83
87 88 5.066593 AGTTTGGAGAGGATCAGAACAAAC 58.933 41.667 17.23 17.23 41.84 2.93
149 152 0.902531 CCTCCTTGGTCGCCTTCTTA 59.097 55.000 0.00 0.00 0.00 2.10
197 202 1.519455 CTCGGCTTCGGTGGACATC 60.519 63.158 0.00 0.00 34.13 3.06
200 205 1.514087 GGCTTCGGTGGACATCGTA 59.486 57.895 4.77 0.00 36.14 3.43
206 211 1.819903 TCGGTGGACATCGTAATGACA 59.180 47.619 4.77 0.00 36.14 3.58
211 216 4.495422 GTGGACATCGTAATGACAGAAGT 58.505 43.478 0.00 0.00 36.67 3.01
217 222 1.317611 CGTAATGACAGAAGTGACGCG 59.682 52.381 3.53 3.53 0.00 6.01
218 223 2.592194 GTAATGACAGAAGTGACGCGA 58.408 47.619 15.93 0.00 0.00 5.87
220 225 2.370281 ATGACAGAAGTGACGCGAAT 57.630 45.000 15.93 0.00 0.00 3.34
233 238 1.128507 ACGCGAATGTAGACGACGTAA 59.871 47.619 15.93 0.00 39.07 3.18
248 253 3.123804 GACGTAATGGATGCAGACGAAT 58.876 45.455 24.69 8.77 37.00 3.34
251 268 3.555547 CGTAATGGATGCAGACGAATTCA 59.444 43.478 16.37 0.00 35.59 2.57
281 298 6.139679 AGACAGTCCCCAAAAATCTAATCA 57.860 37.500 0.00 0.00 0.00 2.57
283 300 4.700213 ACAGTCCCCAAAAATCTAATCACG 59.300 41.667 0.00 0.00 0.00 4.35
311 574 1.001268 TGTCTCGGATTCATAGAGCGC 60.001 52.381 0.00 0.00 32.42 5.92
319 613 4.319177 GGATTCATAGAGCGCCTGTTAAT 58.681 43.478 2.29 2.85 0.00 1.40
321 615 3.013276 TCATAGAGCGCCTGTTAATCG 57.987 47.619 2.29 0.00 0.00 3.34
337 631 1.407936 ATCGCACAGGTATGAGCTCT 58.592 50.000 16.19 3.04 40.46 4.09
364 658 0.108377 TCATTCCCACGTCCACATCG 60.108 55.000 0.00 0.00 0.00 3.84
406 730 5.885230 TCTCAAACTTCAATAGCATGTGG 57.115 39.130 0.00 0.00 0.00 4.17
409 733 6.489700 TCTCAAACTTCAATAGCATGTGGAAA 59.510 34.615 0.00 0.00 0.00 3.13
417 741 5.360714 TCAATAGCATGTGGAAAAGAATCCC 59.639 40.000 0.00 0.00 38.82 3.85
441 765 7.724506 CCCTTATAAAAAGGTCTAATTCCTCCC 59.275 40.741 3.27 0.00 35.65 4.30
445 1094 6.927691 AAAAAGGTCTAATTCCTCCCCTAT 57.072 37.500 0.00 0.00 33.76 2.57
449 1098 5.095097 AGGTCTAATTCCTCCCCTATTAGC 58.905 45.833 0.00 0.00 33.77 3.09
468 1123 1.946283 GCAGGGTGAGACTAAACTGCC 60.946 57.143 0.00 0.00 43.94 4.85
471 1126 1.282157 GGGTGAGACTAAACTGCCCAT 59.718 52.381 0.00 0.00 34.21 4.00
472 1127 2.290960 GGGTGAGACTAAACTGCCCATT 60.291 50.000 0.00 0.00 34.21 3.16
487 1147 3.074412 GCCCATTATATCCCTTGACACG 58.926 50.000 0.00 0.00 0.00 4.49
492 1152 6.285224 CCATTATATCCCTTGACACGTACAA 58.715 40.000 7.06 7.06 0.00 2.41
493 1153 6.764085 CCATTATATCCCTTGACACGTACAAA 59.236 38.462 8.32 0.00 0.00 2.83
518 1309 3.134081 CGCTTAGAGATTTTCCCACCCTA 59.866 47.826 0.00 0.00 0.00 3.53
559 1368 2.222953 CCGCTAGAAATGGTTTACGCAC 60.223 50.000 0.00 0.00 0.00 5.34
638 1447 4.598257 CGGACTGAAGCAACCGAT 57.402 55.556 0.00 0.00 46.94 4.18
642 1451 0.924090 GACTGAAGCAACCGATAGCG 59.076 55.000 0.00 0.00 35.48 4.26
643 1452 1.084370 ACTGAAGCAACCGATAGCGC 61.084 55.000 0.00 0.00 35.83 5.92
645 1454 1.083806 TGAAGCAACCGATAGCGCAG 61.084 55.000 11.47 0.00 35.83 5.18
646 1455 1.766143 GAAGCAACCGATAGCGCAGG 61.766 60.000 11.47 10.07 35.83 4.85
647 1456 3.272334 GCAACCGATAGCGCAGGG 61.272 66.667 11.47 7.39 35.83 4.45
648 1457 2.186903 CAACCGATAGCGCAGGGT 59.813 61.111 11.47 8.12 35.83 4.34
650 1459 0.597637 CAACCGATAGCGCAGGGTAG 60.598 60.000 11.47 0.00 35.83 3.18
651 1460 1.041447 AACCGATAGCGCAGGGTAGT 61.041 55.000 11.47 0.00 35.83 2.73
653 1462 1.734137 CGATAGCGCAGGGTAGTGT 59.266 57.895 11.47 0.00 0.00 3.55
656 1465 0.976073 ATAGCGCAGGGTAGTGTGGT 60.976 55.000 11.47 0.00 41.38 4.16
657 1466 0.323633 TAGCGCAGGGTAGTGTGGTA 60.324 55.000 11.47 0.00 39.33 3.25
658 1467 1.189524 AGCGCAGGGTAGTGTGGTAA 61.190 55.000 11.47 0.00 36.91 2.85
659 1468 0.320946 GCGCAGGGTAGTGTGGTAAA 60.321 55.000 0.30 0.00 0.00 2.01
660 1469 1.677820 GCGCAGGGTAGTGTGGTAAAT 60.678 52.381 0.30 0.00 0.00 1.40
661 1470 2.006888 CGCAGGGTAGTGTGGTAAATG 58.993 52.381 0.00 0.00 0.00 2.32
669 1478 0.802494 GTGTGGTAAATGGGCACGAG 59.198 55.000 0.00 0.00 0.00 4.18
685 1494 1.495509 GAGCGCACGCACATGTAAA 59.504 52.632 18.24 0.00 44.88 2.01
686 1495 0.096976 GAGCGCACGCACATGTAAAT 59.903 50.000 18.24 0.00 44.88 1.40
687 1496 0.179192 AGCGCACGCACATGTAAATG 60.179 50.000 18.24 0.00 44.88 2.32
688 1497 1.133363 GCGCACGCACATGTAAATGG 61.133 55.000 10.65 0.00 41.49 3.16
689 1498 0.523125 CGCACGCACATGTAAATGGG 60.523 55.000 0.00 1.52 35.06 4.00
731 1545 2.501610 GGCCGGGAGCTGAGTTAG 59.498 66.667 2.18 0.00 43.05 2.34
732 1546 2.501610 GCCGGGAGCTGAGTTAGG 59.498 66.667 2.18 0.00 38.99 2.69
733 1547 2.058595 GCCGGGAGCTGAGTTAGGA 61.059 63.158 2.18 0.00 38.99 2.94
734 1548 2.022240 GCCGGGAGCTGAGTTAGGAG 62.022 65.000 2.18 0.00 38.99 3.69
735 1549 0.684805 CCGGGAGCTGAGTTAGGAGT 60.685 60.000 0.00 0.00 0.00 3.85
851 1665 1.289109 CGTCCAACACCTGTAAGCCG 61.289 60.000 0.00 0.00 0.00 5.52
854 1668 2.358247 AACACCTGTAAGCCGCGG 60.358 61.111 24.05 24.05 0.00 6.46
872 1686 1.296715 GATCACACCTGTCCCGCTT 59.703 57.895 0.00 0.00 0.00 4.68
876 1690 2.125912 CACCTGTCCCGCTTCTCG 60.126 66.667 0.00 0.00 38.08 4.04
925 1739 2.025981 TCCAGATCAAATCACCCACAGG 60.026 50.000 0.00 0.00 40.04 4.00
926 1740 1.747355 CAGATCAAATCACCCACAGGC 59.253 52.381 0.00 0.00 36.11 4.85
927 1741 1.106285 GATCAAATCACCCACAGGCC 58.894 55.000 0.00 0.00 36.11 5.19
928 1742 0.409092 ATCAAATCACCCACAGGCCA 59.591 50.000 5.01 0.00 36.11 5.36
929 1743 0.539438 TCAAATCACCCACAGGCCAC 60.539 55.000 5.01 0.00 36.11 5.01
930 1744 0.827089 CAAATCACCCACAGGCCACA 60.827 55.000 5.01 0.00 36.11 4.17
931 1745 0.540365 AAATCACCCACAGGCCACAG 60.540 55.000 5.01 0.00 36.11 3.66
963 1790 0.738975 TCTTCCATCCAGCGACGTAG 59.261 55.000 0.00 0.00 0.00 3.51
982 1809 3.398954 AGTGTACGTGCAAACAAGTTG 57.601 42.857 8.25 0.00 39.36 3.16
995 1826 2.227194 ACAAGTTGGACGAAACCATCC 58.773 47.619 7.96 0.00 39.82 3.51
997 1828 2.185004 AGTTGGACGAAACCATCCAG 57.815 50.000 0.00 0.00 45.66 3.86
1074 1906 0.379316 TGTACATCGTCGTCATCGGG 59.621 55.000 0.00 0.00 37.69 5.14
1375 2207 1.880340 GTGCTCGAGGCCTTCATCG 60.880 63.158 15.58 6.18 40.92 3.84
1455 2287 4.988598 CAGTTCGGTGGCGCAGGT 62.989 66.667 10.83 0.00 0.00 4.00
1558 2393 6.527423 TGACCGTCTTGAGGTTTAATTACTT 58.473 36.000 0.00 0.00 43.01 2.24
1559 2394 7.669427 TGACCGTCTTGAGGTTTAATTACTTA 58.331 34.615 0.00 0.00 43.01 2.24
1560 2395 8.316214 TGACCGTCTTGAGGTTTAATTACTTAT 58.684 33.333 0.00 0.00 43.01 1.73
1561 2396 9.159364 GACCGTCTTGAGGTTTAATTACTTATT 57.841 33.333 0.00 0.00 43.01 1.40
1562 2397 9.511272 ACCGTCTTGAGGTTTAATTACTTATTT 57.489 29.630 0.00 0.00 39.29 1.40
2148 2988 6.070767 AGGACTGTAGGTACACGTACTAGTTA 60.071 42.308 0.00 0.00 37.89 2.24
2157 2997 4.338879 ACACGTACTAGTTATGGTCCTGT 58.661 43.478 0.00 0.00 0.00 4.00
2158 2998 4.768968 ACACGTACTAGTTATGGTCCTGTT 59.231 41.667 0.00 0.00 0.00 3.16
2159 2999 5.105997 ACACGTACTAGTTATGGTCCTGTTC 60.106 44.000 0.00 0.00 0.00 3.18
2160 3000 5.012239 ACGTACTAGTTATGGTCCTGTTCA 58.988 41.667 0.00 0.00 0.00 3.18
2161 3001 5.477984 ACGTACTAGTTATGGTCCTGTTCAA 59.522 40.000 0.00 0.00 0.00 2.69
2162 3002 6.154021 ACGTACTAGTTATGGTCCTGTTCAAT 59.846 38.462 0.00 0.00 0.00 2.57
2163 3003 7.039882 CGTACTAGTTATGGTCCTGTTCAATT 58.960 38.462 0.00 0.00 0.00 2.32
2164 3004 7.548075 CGTACTAGTTATGGTCCTGTTCAATTT 59.452 37.037 0.00 0.00 0.00 1.82
2165 3005 7.923414 ACTAGTTATGGTCCTGTTCAATTTC 57.077 36.000 0.00 0.00 0.00 2.17
2166 3006 6.884836 ACTAGTTATGGTCCTGTTCAATTTCC 59.115 38.462 0.00 0.00 0.00 3.13
2167 3007 5.640147 AGTTATGGTCCTGTTCAATTTCCA 58.360 37.500 0.00 0.00 0.00 3.53
2168 3008 6.256053 AGTTATGGTCCTGTTCAATTTCCAT 58.744 36.000 0.00 0.00 37.80 3.41
2169 3009 6.378280 AGTTATGGTCCTGTTCAATTTCCATC 59.622 38.462 0.00 0.00 36.01 3.51
2170 3010 4.387026 TGGTCCTGTTCAATTTCCATCT 57.613 40.909 0.00 0.00 0.00 2.90
2171 3011 5.512942 TGGTCCTGTTCAATTTCCATCTA 57.487 39.130 0.00 0.00 0.00 1.98
2172 3012 5.253330 TGGTCCTGTTCAATTTCCATCTAC 58.747 41.667 0.00 0.00 0.00 2.59
2173 3013 4.332819 GGTCCTGTTCAATTTCCATCTACG 59.667 45.833 0.00 0.00 0.00 3.51
2174 3014 4.935808 GTCCTGTTCAATTTCCATCTACGT 59.064 41.667 0.00 0.00 0.00 3.57
2175 3015 6.103997 GTCCTGTTCAATTTCCATCTACGTA 58.896 40.000 0.00 0.00 0.00 3.57
2176 3016 6.255887 GTCCTGTTCAATTTCCATCTACGTAG 59.744 42.308 16.73 16.73 0.00 3.51
2261 3114 4.763793 ACTGTACGTACATGTACTTCTGGT 59.236 41.667 27.50 21.33 44.01 4.00
2277 3130 5.770162 ACTTCTGGTCCTGTTTAATTTCCAG 59.230 40.000 0.00 0.00 41.30 3.86
2314 3167 5.414454 CCCTCCGTTTCAAATCATTTCAGTA 59.586 40.000 0.00 0.00 0.00 2.74
2317 3170 6.898041 TCCGTTTCAAATCATTTCAGTACAG 58.102 36.000 0.00 0.00 0.00 2.74
2324 3177 9.725019 TTCAAATCATTTCAGTACAGATGTAGT 57.275 29.630 0.00 0.00 34.69 2.73
2325 3178 9.725019 TCAAATCATTTCAGTACAGATGTAGTT 57.275 29.630 0.00 0.00 32.19 2.24
2326 3179 9.979270 CAAATCATTTCAGTACAGATGTAGTTC 57.021 33.333 0.00 0.00 32.19 3.01
2327 3180 9.725019 AAATCATTTCAGTACAGATGTAGTTCA 57.275 29.630 0.00 0.00 32.19 3.18
2328 3181 9.896645 AATCATTTCAGTACAGATGTAGTTCAT 57.103 29.630 0.00 0.00 39.77 2.57
2444 3297 9.743057 ATTCACGAACATTTTCTAAAATTGTGA 57.257 25.926 13.06 13.06 36.52 3.58
2445 3298 9.743057 TTCACGAACATTTTCTAAAATTGTGAT 57.257 25.926 15.53 0.00 36.52 3.06
2464 3317 9.689976 ATTGTGATATTTTTGAATTCACGAACA 57.310 25.926 7.89 2.24 39.58 3.18
2465 3318 9.689976 TTGTGATATTTTTGAATTCACGAACAT 57.310 25.926 7.89 2.42 39.58 2.71
2466 3319 9.689976 TGTGATATTTTTGAATTCACGAACATT 57.310 25.926 7.89 0.00 39.58 2.71
2473 3326 8.870160 TTTTGAATTCACGAACATTTGAATCT 57.130 26.923 7.89 0.00 40.77 2.40
2474 3327 7.856492 TTGAATTCACGAACATTTGAATCTG 57.144 32.000 7.89 0.00 40.77 2.90
2475 3328 6.969366 TGAATTCACGAACATTTGAATCTGT 58.031 32.000 3.38 0.00 40.77 3.41
2476 3329 6.857451 TGAATTCACGAACATTTGAATCTGTG 59.143 34.615 3.38 0.00 40.77 3.66
2477 3330 6.558771 ATTCACGAACATTTGAATCTGTGA 57.441 33.333 0.00 0.00 37.85 3.58
2478 3331 5.596268 TCACGAACATTTGAATCTGTGAG 57.404 39.130 0.00 0.00 31.99 3.51
2479 3332 4.083855 TCACGAACATTTGAATCTGTGAGC 60.084 41.667 0.00 0.00 31.99 4.26
2480 3333 3.814842 ACGAACATTTGAATCTGTGAGCA 59.185 39.130 0.00 0.00 0.00 4.26
2481 3334 4.456911 ACGAACATTTGAATCTGTGAGCAT 59.543 37.500 0.00 0.00 0.00 3.79
2482 3335 5.048504 ACGAACATTTGAATCTGTGAGCATT 60.049 36.000 0.00 0.00 0.00 3.56
2483 3336 5.860182 CGAACATTTGAATCTGTGAGCATTT 59.140 36.000 0.00 0.00 0.00 2.32
2484 3337 6.364165 CGAACATTTGAATCTGTGAGCATTTT 59.636 34.615 0.00 0.00 0.00 1.82
2485 3338 7.095940 CGAACATTTGAATCTGTGAGCATTTTT 60.096 33.333 0.00 0.00 0.00 1.94
2486 3339 9.195411 GAACATTTGAATCTGTGAGCATTTTTA 57.805 29.630 0.00 0.00 0.00 1.52
2487 3340 9.545105 AACATTTGAATCTGTGAGCATTTTTAA 57.455 25.926 0.00 0.00 0.00 1.52
2488 3341 9.545105 ACATTTGAATCTGTGAGCATTTTTAAA 57.455 25.926 0.00 0.00 0.00 1.52
2533 3386 9.799106 AATTTATGATATGTTTCGAATCCTCCT 57.201 29.630 0.00 0.00 0.00 3.69
2535 3388 9.929180 TTTATGATATGTTTCGAATCCTCCTAG 57.071 33.333 0.00 0.00 0.00 3.02
2536 3389 7.782897 ATGATATGTTTCGAATCCTCCTAGA 57.217 36.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.717707 TCTACTCCACATAGCGATTTGC 58.282 45.455 0.00 0.00 46.98 3.68
6 7 4.210120 GCTTCTACTCCACATAGCGATTTG 59.790 45.833 0.00 0.00 0.00 2.32
7 8 4.100189 AGCTTCTACTCCACATAGCGATTT 59.900 41.667 0.00 0.00 34.01 2.17
8 9 3.639094 AGCTTCTACTCCACATAGCGATT 59.361 43.478 0.00 0.00 34.01 3.34
9 10 3.226777 AGCTTCTACTCCACATAGCGAT 58.773 45.455 0.00 0.00 34.01 4.58
10 11 2.656002 AGCTTCTACTCCACATAGCGA 58.344 47.619 0.00 0.00 34.01 4.93
11 12 3.566322 ACTAGCTTCTACTCCACATAGCG 59.434 47.826 0.00 0.00 34.01 4.26
12 13 5.523438 AACTAGCTTCTACTCCACATAGC 57.477 43.478 0.00 0.00 0.00 2.97
13 14 7.101652 TGAAACTAGCTTCTACTCCACATAG 57.898 40.000 7.37 0.00 0.00 2.23
14 15 6.096987 CCTGAAACTAGCTTCTACTCCACATA 59.903 42.308 7.37 0.00 0.00 2.29
15 16 5.105146 CCTGAAACTAGCTTCTACTCCACAT 60.105 44.000 7.37 0.00 0.00 3.21
16 17 4.220821 CCTGAAACTAGCTTCTACTCCACA 59.779 45.833 7.37 0.00 0.00 4.17
17 18 4.463186 TCCTGAAACTAGCTTCTACTCCAC 59.537 45.833 7.37 0.00 0.00 4.02
18 19 4.673968 TCCTGAAACTAGCTTCTACTCCA 58.326 43.478 7.37 0.00 0.00 3.86
19 20 5.656480 CTTCCTGAAACTAGCTTCTACTCC 58.344 45.833 7.37 0.00 0.00 3.85
20 21 5.105513 AGCTTCCTGAAACTAGCTTCTACTC 60.106 44.000 7.37 0.00 40.91 2.59
21 22 4.775253 AGCTTCCTGAAACTAGCTTCTACT 59.225 41.667 7.37 0.00 40.91 2.57
22 23 4.867608 CAGCTTCCTGAAACTAGCTTCTAC 59.132 45.833 7.37 0.00 41.76 2.59
23 24 4.772624 TCAGCTTCCTGAAACTAGCTTCTA 59.227 41.667 7.37 0.00 44.79 2.10
24 25 3.580458 TCAGCTTCCTGAAACTAGCTTCT 59.420 43.478 7.37 0.00 44.79 2.85
25 26 3.931578 TCAGCTTCCTGAAACTAGCTTC 58.068 45.455 0.00 0.00 44.79 3.86
36 37 3.683802 ACTCCTCAAAATCAGCTTCCTG 58.316 45.455 0.00 0.00 40.54 3.86
37 38 4.379302 AACTCCTCAAAATCAGCTTCCT 57.621 40.909 0.00 0.00 0.00 3.36
38 39 5.010012 TCAAAACTCCTCAAAATCAGCTTCC 59.990 40.000 0.00 0.00 0.00 3.46
39 40 6.076981 TCAAAACTCCTCAAAATCAGCTTC 57.923 37.500 0.00 0.00 0.00 3.86
40 41 6.469782 TTCAAAACTCCTCAAAATCAGCTT 57.530 33.333 0.00 0.00 0.00 3.74
41 42 6.097412 ACTTTCAAAACTCCTCAAAATCAGCT 59.903 34.615 0.00 0.00 0.00 4.24
42 43 6.276091 ACTTTCAAAACTCCTCAAAATCAGC 58.724 36.000 0.00 0.00 0.00 4.26
43 44 8.598075 CAAACTTTCAAAACTCCTCAAAATCAG 58.402 33.333 0.00 0.00 0.00 2.90
44 45 7.548780 CCAAACTTTCAAAACTCCTCAAAATCA 59.451 33.333 0.00 0.00 0.00 2.57
45 46 7.763985 TCCAAACTTTCAAAACTCCTCAAAATC 59.236 33.333 0.00 0.00 0.00 2.17
46 47 7.619965 TCCAAACTTTCAAAACTCCTCAAAAT 58.380 30.769 0.00 0.00 0.00 1.82
47 48 6.998802 TCCAAACTTTCAAAACTCCTCAAAA 58.001 32.000 0.00 0.00 0.00 2.44
48 49 6.435904 TCTCCAAACTTTCAAAACTCCTCAAA 59.564 34.615 0.00 0.00 0.00 2.69
49 50 5.949354 TCTCCAAACTTTCAAAACTCCTCAA 59.051 36.000 0.00 0.00 0.00 3.02
50 51 5.505780 TCTCCAAACTTTCAAAACTCCTCA 58.494 37.500 0.00 0.00 0.00 3.86
51 52 5.009110 CCTCTCCAAACTTTCAAAACTCCTC 59.991 44.000 0.00 0.00 0.00 3.71
52 53 4.889995 CCTCTCCAAACTTTCAAAACTCCT 59.110 41.667 0.00 0.00 0.00 3.69
53 54 4.887655 TCCTCTCCAAACTTTCAAAACTCC 59.112 41.667 0.00 0.00 0.00 3.85
54 55 6.263168 TGATCCTCTCCAAACTTTCAAAACTC 59.737 38.462 0.00 0.00 0.00 3.01
55 56 6.129179 TGATCCTCTCCAAACTTTCAAAACT 58.871 36.000 0.00 0.00 0.00 2.66
56 57 6.263168 TCTGATCCTCTCCAAACTTTCAAAAC 59.737 38.462 0.00 0.00 0.00 2.43
57 58 6.364701 TCTGATCCTCTCCAAACTTTCAAAA 58.635 36.000 0.00 0.00 0.00 2.44
58 59 5.940617 TCTGATCCTCTCCAAACTTTCAAA 58.059 37.500 0.00 0.00 0.00 2.69
59 60 5.567037 TCTGATCCTCTCCAAACTTTCAA 57.433 39.130 0.00 0.00 0.00 2.69
60 61 5.163205 TGTTCTGATCCTCTCCAAACTTTCA 60.163 40.000 0.00 0.00 0.00 2.69
61 62 5.308825 TGTTCTGATCCTCTCCAAACTTTC 58.691 41.667 0.00 0.00 0.00 2.62
62 63 5.310409 TGTTCTGATCCTCTCCAAACTTT 57.690 39.130 0.00 0.00 0.00 2.66
63 64 4.982241 TGTTCTGATCCTCTCCAAACTT 57.018 40.909 0.00 0.00 0.00 2.66
64 65 4.982241 TTGTTCTGATCCTCTCCAAACT 57.018 40.909 0.00 0.00 0.00 2.66
65 66 4.216472 GGTTTGTTCTGATCCTCTCCAAAC 59.784 45.833 12.77 12.77 39.41 2.93
66 67 4.398319 GGTTTGTTCTGATCCTCTCCAAA 58.602 43.478 0.00 0.00 0.00 3.28
67 68 3.244911 GGGTTTGTTCTGATCCTCTCCAA 60.245 47.826 0.00 0.00 0.00 3.53
68 69 2.305927 GGGTTTGTTCTGATCCTCTCCA 59.694 50.000 0.00 0.00 0.00 3.86
69 70 2.573915 AGGGTTTGTTCTGATCCTCTCC 59.426 50.000 0.00 0.00 0.00 3.71
70 71 3.990959 AGGGTTTGTTCTGATCCTCTC 57.009 47.619 0.00 0.00 0.00 3.20
71 72 4.597507 TGTAAGGGTTTGTTCTGATCCTCT 59.402 41.667 0.00 0.00 0.00 3.69
72 73 4.906618 TGTAAGGGTTTGTTCTGATCCTC 58.093 43.478 0.00 0.00 0.00 3.71
73 74 4.351111 ACTGTAAGGGTTTGTTCTGATCCT 59.649 41.667 0.00 0.00 39.30 3.24
74 75 4.652822 ACTGTAAGGGTTTGTTCTGATCC 58.347 43.478 0.00 0.00 39.30 3.36
75 76 5.875359 CCTACTGTAAGGGTTTGTTCTGATC 59.125 44.000 0.00 0.00 39.30 2.92
76 77 5.803470 GCCTACTGTAAGGGTTTGTTCTGAT 60.803 44.000 5.76 0.00 39.30 2.90
77 78 4.504340 GCCTACTGTAAGGGTTTGTTCTGA 60.504 45.833 5.76 0.00 39.30 3.27
78 79 3.751698 GCCTACTGTAAGGGTTTGTTCTG 59.248 47.826 5.76 0.00 39.30 3.02
79 80 3.244805 GGCCTACTGTAAGGGTTTGTTCT 60.245 47.826 0.00 0.00 39.30 3.01
80 81 3.079578 GGCCTACTGTAAGGGTTTGTTC 58.920 50.000 0.00 0.00 39.30 3.18
81 82 2.444010 TGGCCTACTGTAAGGGTTTGTT 59.556 45.455 3.32 0.00 39.30 2.83
82 83 2.059490 TGGCCTACTGTAAGGGTTTGT 58.941 47.619 3.32 0.00 39.30 2.83
83 84 2.871096 TGGCCTACTGTAAGGGTTTG 57.129 50.000 3.32 0.00 39.30 2.93
84 85 4.086457 CAATTGGCCTACTGTAAGGGTTT 58.914 43.478 3.32 0.00 39.30 3.27
85 86 3.563479 CCAATTGGCCTACTGTAAGGGTT 60.563 47.826 12.53 0.00 39.30 4.11
86 87 2.025321 CCAATTGGCCTACTGTAAGGGT 60.025 50.000 12.53 0.00 39.30 4.34
87 88 2.654863 CCAATTGGCCTACTGTAAGGG 58.345 52.381 12.53 0.00 39.30 3.95
149 152 1.153409 CGAGAAGGCTGCTGCTGAT 60.153 57.895 15.64 1.92 39.59 2.90
197 202 1.317611 CGCGTCACTTCTGTCATTACG 59.682 52.381 0.00 0.00 0.00 3.18
200 205 2.148916 TTCGCGTCACTTCTGTCATT 57.851 45.000 5.77 0.00 0.00 2.57
206 211 2.728225 CGTCTACATTCGCGTCACTTCT 60.728 50.000 5.77 0.00 0.00 2.85
211 216 0.519792 CGTCGTCTACATTCGCGTCA 60.520 55.000 5.77 0.00 0.00 4.35
217 222 4.148348 GCATCCATTACGTCGTCTACATTC 59.852 45.833 0.00 0.00 0.00 2.67
218 223 4.049186 GCATCCATTACGTCGTCTACATT 58.951 43.478 0.00 0.00 0.00 2.71
220 225 2.424246 TGCATCCATTACGTCGTCTACA 59.576 45.455 0.00 0.00 0.00 2.74
233 238 3.548770 ACATGAATTCGTCTGCATCCAT 58.451 40.909 0.00 0.00 0.00 3.41
248 253 2.225522 TGGGGACTGTCTCCTACATGAA 60.226 50.000 26.18 2.32 38.07 2.57
251 268 2.642171 TTGGGGACTGTCTCCTACAT 57.358 50.000 26.18 0.00 38.07 2.29
281 298 2.559922 ATCCGAGACAGGAGAGGCGT 62.560 60.000 0.00 0.00 44.55 5.68
283 300 0.387565 GAATCCGAGACAGGAGAGGC 59.612 60.000 0.00 0.00 44.55 4.70
319 613 1.135139 GAAGAGCTCATACCTGTGCGA 59.865 52.381 17.77 0.00 44.59 5.10
321 615 2.797792 CGAGAAGAGCTCATACCTGTGC 60.798 54.545 17.77 0.00 44.15 4.57
337 631 1.218047 CGTGGGAATGAGCCGAGAA 59.782 57.895 0.00 0.00 0.00 2.87
364 658 1.534729 AGAGAAATGGTTCCCGCAAC 58.465 50.000 0.00 0.00 33.92 4.17
390 714 6.899393 TTCTTTTCCACATGCTATTGAAGT 57.101 33.333 0.00 0.00 0.00 3.01
417 741 8.503573 AGGGGAGGAATTAGACCTTTTTATAAG 58.496 37.037 0.00 0.00 37.93 1.73
441 765 5.364157 AGTTTAGTCTCACCCTGCTAATAGG 59.636 44.000 0.00 0.00 37.59 2.57
445 1094 3.306780 GCAGTTTAGTCTCACCCTGCTAA 60.307 47.826 0.00 0.00 41.48 3.09
449 1098 1.339151 GGGCAGTTTAGTCTCACCCTG 60.339 57.143 0.00 0.00 31.62 4.45
459 1114 6.431234 GTCAAGGGATATAATGGGCAGTTTAG 59.569 42.308 0.00 0.00 0.00 1.85
468 1123 5.849510 TGTACGTGTCAAGGGATATAATGG 58.150 41.667 0.00 0.00 0.00 3.16
471 1126 6.342906 CCTTTGTACGTGTCAAGGGATATAA 58.657 40.000 22.35 2.82 42.21 0.98
472 1127 5.682990 GCCTTTGTACGTGTCAAGGGATATA 60.683 44.000 27.31 6.90 42.21 0.86
487 1147 5.447413 GGAAAATCTCTAAGCGCCTTTGTAC 60.447 44.000 2.29 0.00 0.00 2.90
492 1152 2.026262 TGGGAAAATCTCTAAGCGCCTT 60.026 45.455 2.29 0.00 0.00 4.35
493 1153 1.559682 TGGGAAAATCTCTAAGCGCCT 59.440 47.619 2.29 0.00 0.00 5.52
559 1368 5.893824 AGCTTCTTAATTCTGGGGTTTATGG 59.106 40.000 0.00 0.00 0.00 2.74
637 1446 0.976073 ACCACACTACCCTGCGCTAT 60.976 55.000 9.73 0.00 0.00 2.97
638 1447 0.323633 TACCACACTACCCTGCGCTA 60.324 55.000 9.73 0.00 0.00 4.26
642 1451 2.365582 CCATTTACCACACTACCCTGC 58.634 52.381 0.00 0.00 0.00 4.85
643 1452 2.944094 GCCCATTTACCACACTACCCTG 60.944 54.545 0.00 0.00 0.00 4.45
645 1454 1.004979 TGCCCATTTACCACACTACCC 59.995 52.381 0.00 0.00 0.00 3.69
646 1455 2.089201 GTGCCCATTTACCACACTACC 58.911 52.381 0.00 0.00 0.00 3.18
647 1456 1.735571 CGTGCCCATTTACCACACTAC 59.264 52.381 0.00 0.00 0.00 2.73
648 1457 1.624312 TCGTGCCCATTTACCACACTA 59.376 47.619 0.00 0.00 0.00 2.74
650 1459 0.802494 CTCGTGCCCATTTACCACAC 59.198 55.000 0.00 0.00 0.00 3.82
651 1460 0.958382 GCTCGTGCCCATTTACCACA 60.958 55.000 0.00 0.00 0.00 4.17
653 1462 1.743623 CGCTCGTGCCCATTTACCA 60.744 57.895 3.52 0.00 35.36 3.25
656 1465 2.046796 TGCGCTCGTGCCCATTTA 60.047 55.556 9.73 0.00 35.36 1.40
657 1466 3.737172 GTGCGCTCGTGCCCATTT 61.737 61.111 9.73 0.00 35.36 2.32
669 1478 1.133363 CCATTTACATGTGCGTGCGC 61.133 55.000 9.11 9.85 42.35 6.09
685 1494 4.760047 GCTGACGGTCGTGCCCAT 62.760 66.667 12.84 0.00 0.00 4.00
729 1543 2.196749 CGCTTCTCGTACGTACTCCTA 58.803 52.381 22.55 5.61 0.00 2.94
730 1544 1.005340 CGCTTCTCGTACGTACTCCT 58.995 55.000 22.55 0.00 0.00 3.69
731 1545 0.588482 GCGCTTCTCGTACGTACTCC 60.588 60.000 22.55 0.00 41.07 3.85
732 1546 0.373024 AGCGCTTCTCGTACGTACTC 59.627 55.000 22.55 0.00 41.07 2.59
733 1547 0.096628 CAGCGCTTCTCGTACGTACT 59.903 55.000 22.55 0.00 41.07 2.73
734 1548 0.860618 CCAGCGCTTCTCGTACGTAC 60.861 60.000 15.90 15.90 41.07 3.67
735 1549 1.020861 TCCAGCGCTTCTCGTACGTA 61.021 55.000 16.05 1.79 41.07 3.57
788 1602 1.197721 CTTTACACCAAGCTGCTTCCG 59.802 52.381 12.82 8.14 0.00 4.30
851 1665 2.125106 GGGACAGGTGTGATCCGC 60.125 66.667 0.00 0.00 32.90 5.54
854 1668 0.741221 GAAGCGGGACAGGTGTGATC 60.741 60.000 0.00 0.00 0.00 2.92
872 1686 7.069578 GTGGGATAAAATATATAGGGAGCGAGA 59.930 40.741 0.00 0.00 0.00 4.04
876 1690 8.989131 TGTAGTGGGATAAAATATATAGGGAGC 58.011 37.037 0.00 0.00 0.00 4.70
925 1739 1.403323 GAATGGAAGCTTAGCTGTGGC 59.597 52.381 7.77 0.00 39.62 5.01
926 1740 2.996631 AGAATGGAAGCTTAGCTGTGG 58.003 47.619 7.77 0.00 39.62 4.17
927 1741 3.376546 GGAAGAATGGAAGCTTAGCTGTG 59.623 47.826 7.77 0.00 39.62 3.66
928 1742 3.009473 TGGAAGAATGGAAGCTTAGCTGT 59.991 43.478 7.77 0.00 39.62 4.40
929 1743 3.614092 TGGAAGAATGGAAGCTTAGCTG 58.386 45.455 7.77 0.00 39.62 4.24
930 1744 4.459330 GATGGAAGAATGGAAGCTTAGCT 58.541 43.478 0.00 0.00 42.56 3.32
931 1745 3.567585 GGATGGAAGAATGGAAGCTTAGC 59.432 47.826 0.00 0.00 0.00 3.09
963 1790 2.096174 TCCAACTTGTTTGCACGTACAC 59.904 45.455 0.00 0.00 33.34 2.90
964 1791 2.096174 GTCCAACTTGTTTGCACGTACA 59.904 45.455 0.00 0.00 33.34 2.90
982 1809 1.133025 CATTGCTGGATGGTTTCGTCC 59.867 52.381 0.00 0.00 46.74 4.79
1074 1906 4.400961 AGGTTCCAGCTGGCGAGC 62.401 66.667 28.91 25.26 46.64 5.03
1305 2137 1.880340 GATCTCCTTGCACGCGAGG 60.880 63.158 15.93 17.94 46.58 4.63
1375 2207 0.535335 TGGGTGAAGGCGAGTATGAC 59.465 55.000 0.00 0.00 0.00 3.06
1558 2393 9.781834 CCATCACGAAATTAAGCAAAGTAAATA 57.218 29.630 0.00 0.00 0.00 1.40
1559 2394 7.759433 CCCATCACGAAATTAAGCAAAGTAAAT 59.241 33.333 0.00 0.00 0.00 1.40
1560 2395 7.087639 CCCATCACGAAATTAAGCAAAGTAAA 58.912 34.615 0.00 0.00 0.00 2.01
1561 2396 6.616947 CCCATCACGAAATTAAGCAAAGTAA 58.383 36.000 0.00 0.00 0.00 2.24
1562 2397 5.392595 GCCCATCACGAAATTAAGCAAAGTA 60.393 40.000 0.00 0.00 0.00 2.24
1563 2398 4.618227 GCCCATCACGAAATTAAGCAAAGT 60.618 41.667 0.00 0.00 0.00 2.66
1564 2399 3.859386 GCCCATCACGAAATTAAGCAAAG 59.141 43.478 0.00 0.00 0.00 2.77
1565 2400 3.671971 CGCCCATCACGAAATTAAGCAAA 60.672 43.478 0.00 0.00 0.00 3.68
2061 2896 3.608707 GCATACACGCTAGCTACGTACAT 60.609 47.826 13.93 11.90 42.96 2.29
2062 2897 2.286595 GCATACACGCTAGCTACGTACA 60.287 50.000 13.93 10.59 42.96 2.90
2063 2898 2.286595 TGCATACACGCTAGCTACGTAC 60.287 50.000 13.93 1.78 42.96 3.67
2064 2899 1.941975 TGCATACACGCTAGCTACGTA 59.058 47.619 13.93 11.20 42.96 3.57
2065 2900 0.736636 TGCATACACGCTAGCTACGT 59.263 50.000 13.93 13.32 46.42 3.57
2066 2901 2.051879 ATGCATACACGCTAGCTACG 57.948 50.000 13.93 12.26 0.00 3.51
2076 2911 5.094812 CACAAACACCATGTATGCATACAC 58.905 41.667 35.53 16.42 45.11 2.90
2148 2988 4.939255 AGATGGAAATTGAACAGGACCAT 58.061 39.130 0.00 0.00 39.00 3.55
2161 3001 9.675464 TGGAAATTAAACTACGTAGATGGAAAT 57.325 29.630 28.74 15.79 0.00 2.17
2162 3002 9.675464 ATGGAAATTAAACTACGTAGATGGAAA 57.325 29.630 28.74 14.40 0.00 3.13
2163 3003 9.321562 GATGGAAATTAAACTACGTAGATGGAA 57.678 33.333 28.74 14.77 0.00 3.53
2164 3004 8.701895 AGATGGAAATTAAACTACGTAGATGGA 58.298 33.333 28.74 11.93 0.00 3.41
2165 3005 8.888579 AGATGGAAATTAAACTACGTAGATGG 57.111 34.615 28.74 3.64 0.00 3.51
2167 3007 9.674824 CGTAGATGGAAATTAAACTACGTAGAT 57.325 33.333 28.74 14.92 44.04 1.98
2196 3036 3.244353 GCACATGCACAGGGAGTAGATAT 60.244 47.826 0.00 0.00 41.59 1.63
2261 3114 8.090788 AGATACTAGCTGGAAATTAAACAGGA 57.909 34.615 3.17 0.00 32.98 3.86
2277 3130 3.421919 ACGGAGGGAGTAGATACTAGC 57.578 52.381 0.00 0.00 36.50 3.42
2418 3271 9.743057 TCACAATTTTAGAAAATGTTCGTGAAT 57.257 25.926 14.06 0.00 38.53 2.57
2419 3272 9.743057 ATCACAATTTTAGAAAATGTTCGTGAA 57.257 25.926 17.31 0.00 38.53 3.18
2438 3291 9.689976 TGTTCGTGAATTCAAAAATATCACAAT 57.310 25.926 10.35 0.00 40.22 2.71
2439 3292 9.689976 ATGTTCGTGAATTCAAAAATATCACAA 57.310 25.926 10.35 0.00 40.22 3.33
2440 3293 9.689976 AATGTTCGTGAATTCAAAAATATCACA 57.310 25.926 10.35 5.49 40.22 3.58
2447 3300 9.311916 AGATTCAAATGTTCGTGAATTCAAAAA 57.688 25.926 10.35 4.71 42.98 1.94
2448 3301 8.754096 CAGATTCAAATGTTCGTGAATTCAAAA 58.246 29.630 10.35 5.08 42.98 2.44
2449 3302 7.920151 ACAGATTCAAATGTTCGTGAATTCAAA 59.080 29.630 10.35 0.00 42.98 2.69
2450 3303 7.379262 CACAGATTCAAATGTTCGTGAATTCAA 59.621 33.333 10.35 0.00 42.98 2.69
2451 3304 6.857451 CACAGATTCAAATGTTCGTGAATTCA 59.143 34.615 3.38 3.38 42.98 2.57
2452 3305 7.077605 TCACAGATTCAAATGTTCGTGAATTC 58.922 34.615 0.00 0.00 42.98 2.17
2453 3306 6.969366 TCACAGATTCAAATGTTCGTGAATT 58.031 32.000 0.82 0.00 42.98 2.17
2454 3307 6.558771 TCACAGATTCAAATGTTCGTGAAT 57.441 33.333 0.00 0.00 45.03 2.57
2455 3308 5.560760 GCTCACAGATTCAAATGTTCGTGAA 60.561 40.000 0.00 0.00 38.09 3.18
2456 3309 4.083855 GCTCACAGATTCAAATGTTCGTGA 60.084 41.667 0.00 0.00 0.00 4.35
2457 3310 4.153986 GCTCACAGATTCAAATGTTCGTG 58.846 43.478 0.00 0.00 0.00 4.35
2458 3311 3.814842 TGCTCACAGATTCAAATGTTCGT 59.185 39.130 0.00 0.00 0.00 3.85
2459 3312 4.408993 TGCTCACAGATTCAAATGTTCG 57.591 40.909 0.00 0.00 0.00 3.95
2460 3313 7.647907 AAAATGCTCACAGATTCAAATGTTC 57.352 32.000 0.00 0.00 0.00 3.18
2461 3314 9.545105 TTAAAAATGCTCACAGATTCAAATGTT 57.455 25.926 0.00 0.00 0.00 2.71
2462 3315 9.545105 TTTAAAAATGCTCACAGATTCAAATGT 57.455 25.926 0.00 0.00 0.00 2.71
2507 3360 9.799106 AGGAGGATTCGAAACATATCATAAATT 57.201 29.630 0.00 0.00 0.00 1.82
2509 3362 9.929180 CTAGGAGGATTCGAAACATATCATAAA 57.071 33.333 0.00 0.00 0.00 1.40
2510 3363 9.309224 TCTAGGAGGATTCGAAACATATCATAA 57.691 33.333 0.00 0.00 0.00 1.90
2511 3364 8.879427 TCTAGGAGGATTCGAAACATATCATA 57.121 34.615 0.00 0.86 0.00 2.15
2512 3365 7.782897 TCTAGGAGGATTCGAAACATATCAT 57.217 36.000 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.