Multiple sequence alignment - TraesCS4B01G103500

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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 TraesCS4B01G103500 chr4B 100.000 3703 0 0 1 3703 109407775 109404073 0.000000e+00 6839
1 TraesCS4B01G103500 chr4B 97.895 95 2 0 2 96 19084084 19084178 8.230000e-37 165
2 TraesCS4B01G103500 chr7D 82.037 1915 241 45 542 2426 140864247 140862406 0.000000e+00 1535
3 TraesCS4B01G103500 chr7D 84.490 490 48 14 2470 2939 140862335 140861854 3.370000e-125 459
4 TraesCS4B01G103500 chr7D 97.938 97 2 0 3 99 342976068 342975972 6.360000e-38 169
5 TraesCS4B01G103500 chr4D 88.558 1241 85 30 2444 3653 77279959 77278745 0.000000e+00 1452
6 TraesCS4B01G103500 chr4D 91.631 932 55 6 475 1390 77289822 77288898 0.000000e+00 1267
7 TraesCS4B01G103500 chr4D 96.076 739 26 2 1709 2444 77280752 77280014 0.000000e+00 1201
8 TraesCS4B01G103500 chr4D 87.243 243 10 7 1381 1612 77288069 77287837 1.320000e-64 257
9 TraesCS4B01G103500 chr4D 95.876 97 3 1 3608 3703 77278760 77278664 4.950000e-34 156
10 TraesCS4B01G103500 chr4D 94.595 74 3 1 97 170 77904792 77904720 3.020000e-21 113
11 TraesCS4B01G103500 chr4D 96.825 63 1 1 97 159 77293399 77293338 1.820000e-18 104
12 TraesCS4B01G103500 chr7B 80.076 1837 239 58 311 2111 106139928 106138183 0.000000e+00 1247
13 TraesCS4B01G103500 chr7B 83.469 490 50 14 2470 2939 106137165 106136687 9.500000e-116 427
14 TraesCS4B01G103500 chr7B 86.755 302 31 2 2124 2425 106137530 106137238 9.920000e-86 327
15 TraesCS4B01G103500 chr4A 85.399 589 53 15 198 776 507965973 507966538 6.890000e-162 580
16 TraesCS4B01G103500 chr4A 94.828 174 9 0 1220 1393 507966540 507966713 4.710000e-69 272
17 TraesCS4B01G103500 chr7A 83.887 391 47 5 2040 2425 143082394 143082015 3.520000e-95 359
18 TraesCS4B01G103500 chr7A 90.000 200 17 3 2470 2668 143081942 143081745 4.750000e-64 255
19 TraesCS4B01G103500 chr7A 82.424 165 17 9 2613 2768 143095967 143095806 2.320000e-27 134
20 TraesCS4B01G103500 chr2B 97.917 96 2 0 1 96 783007959 783007864 2.290000e-37 167
21 TraesCS4B01G103500 chr6A 97.895 95 2 0 2 96 216183474 216183568 8.230000e-37 165
22 TraesCS4B01G103500 chr3D 97.895 95 2 0 3 97 185420007 185420101 8.230000e-37 165
23 TraesCS4B01G103500 chr2D 97.895 95 2 0 2 96 245407833 245407927 8.230000e-37 165
24 TraesCS4B01G103500 chr1B 97.895 95 2 0 2 96 443789167 443789261 8.230000e-37 165
25 TraesCS4B01G103500 chrUn 97.872 94 2 0 3 96 70911451 70911544 2.960000e-36 163
26 TraesCS4B01G103500 chrUn 97.872 94 2 0 3 96 70914840 70914933 2.960000e-36 163


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 TraesCS4B01G103500 chr4B 109404073 109407775 3702 True 6839.000000 6839 100.000000 1 3703 1 chr4B.!!$R1 3702
1 TraesCS4B01G103500 chr7D 140861854 140864247 2393 True 997.000000 1535 83.263500 542 2939 2 chr7D.!!$R2 2397
2 TraesCS4B01G103500 chr4D 77278664 77280752 2088 True 936.333333 1452 93.503333 1709 3703 3 chr4D.!!$R2 1994
3 TraesCS4B01G103500 chr4D 77287837 77293399 5562 True 542.666667 1267 91.899667 97 1612 3 chr4D.!!$R3 1515
4 TraesCS4B01G103500 chr7B 106136687 106139928 3241 True 667.000000 1247 83.433333 311 2939 3 chr7B.!!$R1 2628
5 TraesCS4B01G103500 chr4A 507965973 507966713 740 False 426.000000 580 90.113500 198 1393 2 chr4A.!!$F1 1195
6 TraesCS4B01G103500 chr7A 143081745 143082394 649 True 307.000000 359 86.943500 2040 2668 2 chr7A.!!$R2 628

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
39 40 0.104356 TAGTGGTGGGAAGGGGTTGA 60.104 55.0 0.00 0.00 0.00 3.18 F
254 3537 0.107945 GTGCTCTCCACCACTCCATC 60.108 60.0 0.00 0.00 38.55 3.51 F
1230 4586 0.169672 CGAGTGATTGCTGCAAAGGG 59.830 55.0 20.06 2.34 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 4631 1.016130 GGCCGCTATGGTCATCATCG 61.016 60.000 0.0 0.0 44.04 3.84 R
1900 6101 1.815408 GCCACACACCAGTCATTCAGT 60.815 52.381 0.0 0.0 0.00 3.41 R
2704 7614 0.802607 GACCAGACTTTAGCCTCGCG 60.803 60.000 0.0 0.0 0.00 5.87 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
17 18 4.131376 CCGCAGACTAAGGCATGG 57.869 61.111 0.00 0.00 0.00 3.66
18 19 2.182842 CCGCAGACTAAGGCATGGC 61.183 63.158 12.14 12.14 0.00 4.40
28 29 2.124151 GGCATGGCCTAGTGGTGG 60.124 66.667 8.35 0.00 46.69 4.61
29 30 2.124151 GCATGGCCTAGTGGTGGG 60.124 66.667 3.32 0.00 35.27 4.61
30 31 2.679342 GCATGGCCTAGTGGTGGGA 61.679 63.158 3.32 0.00 35.27 4.37
31 32 1.998530 CATGGCCTAGTGGTGGGAA 59.001 57.895 3.32 0.00 35.27 3.97
32 33 0.107017 CATGGCCTAGTGGTGGGAAG 60.107 60.000 3.32 0.00 35.27 3.46
33 34 1.281925 ATGGCCTAGTGGTGGGAAGG 61.282 60.000 3.32 0.00 35.27 3.46
34 35 2.680370 GGCCTAGTGGTGGGAAGGG 61.680 68.421 0.00 0.00 35.27 3.95
35 36 2.680370 GCCTAGTGGTGGGAAGGGG 61.680 68.421 0.00 0.00 35.27 4.79
36 37 1.229853 CCTAGTGGTGGGAAGGGGT 60.230 63.158 0.00 0.00 0.00 4.95
37 38 0.845102 CCTAGTGGTGGGAAGGGGTT 60.845 60.000 0.00 0.00 0.00 4.11
38 39 0.328258 CTAGTGGTGGGAAGGGGTTG 59.672 60.000 0.00 0.00 0.00 3.77
39 40 0.104356 TAGTGGTGGGAAGGGGTTGA 60.104 55.000 0.00 0.00 0.00 3.18
40 41 0.776080 AGTGGTGGGAAGGGGTTGAT 60.776 55.000 0.00 0.00 0.00 2.57
41 42 0.611896 GTGGTGGGAAGGGGTTGATG 60.612 60.000 0.00 0.00 0.00 3.07
42 43 1.682344 GGTGGGAAGGGGTTGATGC 60.682 63.158 0.00 0.00 0.00 3.91
43 44 1.682344 GTGGGAAGGGGTTGATGCC 60.682 63.158 0.00 0.00 0.00 4.40
44 45 1.856873 TGGGAAGGGGTTGATGCCT 60.857 57.895 0.00 0.00 0.00 4.75
45 46 1.388133 GGGAAGGGGTTGATGCCTT 59.612 57.895 0.00 0.00 0.00 4.35
46 47 0.684479 GGGAAGGGGTTGATGCCTTC 60.684 60.000 0.00 0.00 38.23 3.46
47 48 2.887790 GAAGGGGTTGATGCCTTCC 58.112 57.895 0.00 0.00 34.40 3.46
48 49 0.684479 GAAGGGGTTGATGCCTTCCC 60.684 60.000 0.00 0.00 39.22 3.97
49 50 1.442886 AAGGGGTTGATGCCTTCCCA 61.443 55.000 0.00 0.00 41.51 4.37
50 51 1.682344 GGGGTTGATGCCTTCCCAC 60.682 63.158 0.00 0.00 41.51 4.61
51 52 1.682344 GGGTTGATGCCTTCCCACC 60.682 63.158 0.00 0.00 39.68 4.61
52 53 1.682344 GGTTGATGCCTTCCCACCC 60.682 63.158 0.00 0.00 0.00 4.61
53 54 1.076549 GTTGATGCCTTCCCACCCA 59.923 57.895 0.00 0.00 0.00 4.51
54 55 1.076549 TTGATGCCTTCCCACCCAC 59.923 57.895 0.00 0.00 0.00 4.61
55 56 2.043953 GATGCCTTCCCACCCACC 60.044 66.667 0.00 0.00 0.00 4.61
56 57 3.662117 GATGCCTTCCCACCCACCC 62.662 68.421 0.00 0.00 0.00 4.61
58 59 4.366684 GCCTTCCCACCCACCCAG 62.367 72.222 0.00 0.00 0.00 4.45
59 60 3.661648 CCTTCCCACCCACCCAGG 61.662 72.222 0.00 0.00 37.03 4.45
60 61 2.858974 CTTCCCACCCACCCAGGT 60.859 66.667 0.00 0.00 42.40 4.00
61 62 2.370403 TTCCCACCCACCCAGGTT 60.370 61.111 0.00 0.00 38.39 3.50
62 63 2.426305 CTTCCCACCCACCCAGGTTC 62.426 65.000 0.00 0.00 38.39 3.62
63 64 3.182263 CCCACCCACCCAGGTTCA 61.182 66.667 0.00 0.00 38.39 3.18
64 65 2.773527 CCCACCCACCCAGGTTCAA 61.774 63.158 0.00 0.00 38.39 2.69
65 66 1.228552 CCACCCACCCAGGTTCAAG 60.229 63.158 0.00 0.00 38.39 3.02
66 67 1.228552 CACCCACCCAGGTTCAAGG 60.229 63.158 0.00 0.00 38.39 3.61
67 68 2.283173 CCCACCCAGGTTCAAGGC 60.283 66.667 0.00 0.00 34.66 4.35
68 69 2.520458 CCACCCAGGTTCAAGGCA 59.480 61.111 0.00 0.00 0.00 4.75
69 70 1.077265 CCACCCAGGTTCAAGGCAT 59.923 57.895 0.00 0.00 0.00 4.40
70 71 1.252904 CCACCCAGGTTCAAGGCATG 61.253 60.000 0.00 0.00 0.00 4.06
71 72 1.077265 ACCCAGGTTCAAGGCATGG 59.923 57.895 0.00 0.00 37.52 3.66
72 73 1.077265 CCCAGGTTCAAGGCATGGT 59.923 57.895 0.00 0.00 36.19 3.55
73 74 0.331278 CCCAGGTTCAAGGCATGGTA 59.669 55.000 0.00 0.00 36.19 3.25
74 75 1.463674 CCAGGTTCAAGGCATGGTAC 58.536 55.000 0.00 0.00 33.58 3.34
90 91 4.000331 TGGTACATGCAATTTGGGTTTG 58.000 40.909 0.00 0.00 0.00 2.93
91 92 3.389329 TGGTACATGCAATTTGGGTTTGT 59.611 39.130 0.00 0.00 0.00 2.83
92 93 4.141620 TGGTACATGCAATTTGGGTTTGTT 60.142 37.500 0.00 0.00 0.00 2.83
93 94 4.213059 GGTACATGCAATTTGGGTTTGTTG 59.787 41.667 0.00 0.00 0.00 3.33
94 95 2.617774 ACATGCAATTTGGGTTTGTTGC 59.382 40.909 0.00 2.25 45.27 4.17
138 139 5.650266 TGAAAGTAAGCTGTCAAAAACCAGA 59.350 36.000 0.00 0.00 36.11 3.86
169 170 8.630037 AGGTTAACCAAGAGAAGTTATTTTGTG 58.370 33.333 26.26 0.00 38.89 3.33
171 172 6.715347 AACCAAGAGAAGTTATTTTGTGCT 57.285 33.333 0.76 0.00 0.00 4.40
172 173 6.076981 ACCAAGAGAAGTTATTTTGTGCTG 57.923 37.500 0.76 0.00 0.00 4.41
175 2347 5.948992 AGAGAAGTTATTTTGTGCTGGAC 57.051 39.130 0.00 0.00 0.00 4.02
215 3498 3.176924 TCCAGTAGGTGAGCTTCTTCT 57.823 47.619 0.00 0.00 35.89 2.85
217 3500 3.511934 TCCAGTAGGTGAGCTTCTTCTTC 59.488 47.826 0.00 0.00 35.89 2.87
222 3505 2.094442 AGGTGAGCTTCTTCTTCGTAGC 60.094 50.000 0.00 0.00 0.00 3.58
244 3527 1.632589 TAACTGCTCTGTGCTCTCCA 58.367 50.000 3.20 0.00 43.37 3.86
246 3529 1.079266 CTGCTCTGTGCTCTCCACC 60.079 63.158 3.20 0.00 44.01 4.61
248 3531 1.375268 GCTCTGTGCTCTCCACCAC 60.375 63.158 0.00 0.00 44.01 4.16
249 3532 1.825281 GCTCTGTGCTCTCCACCACT 61.825 60.000 0.00 0.00 44.01 4.00
250 3533 0.246086 CTCTGTGCTCTCCACCACTC 59.754 60.000 0.00 0.00 44.01 3.51
251 3534 1.188219 TCTGTGCTCTCCACCACTCC 61.188 60.000 0.00 0.00 44.01 3.85
253 3536 0.837691 TGTGCTCTCCACCACTCCAT 60.838 55.000 0.00 0.00 44.01 3.41
254 3537 0.107945 GTGCTCTCCACCACTCCATC 60.108 60.000 0.00 0.00 38.55 3.51
255 3538 1.142748 GCTCTCCACCACTCCATCG 59.857 63.158 0.00 0.00 0.00 3.84
257 3540 1.305297 TCTCCACCACTCCATCGCT 60.305 57.895 0.00 0.00 0.00 4.93
265 3564 2.415010 CTCCATCGCTCCACTCCG 59.585 66.667 0.00 0.00 0.00 4.63
286 3597 0.246086 CTCGTCCTTGAGCTGAGCTT 59.754 55.000 9.00 0.00 39.88 3.74
290 3601 2.413453 CGTCCTTGAGCTGAGCTTAAAC 59.587 50.000 9.00 6.07 39.88 2.01
320 3631 1.069090 ACGCGCTTTGTCTTCTCCA 59.931 52.632 5.73 0.00 0.00 3.86
325 3636 2.426522 CGCTTTGTCTTCTCCATTGGA 58.573 47.619 5.05 5.05 0.00 3.53
338 3649 2.017049 CCATTGGAGTTGGACGATTCC 58.983 52.381 0.00 0.00 43.19 3.01
349 3660 1.943340 GGACGATTCCTTCCTTGCATC 59.057 52.381 0.00 0.00 39.13 3.91
394 3705 2.508891 CGGCGACTGAAGCTAAGCG 61.509 63.158 0.00 0.00 34.52 4.68
399 3710 1.414527 GACTGAAGCTAAGCGTCGGC 61.415 60.000 0.00 0.00 44.81 5.54
400 3711 1.446099 CTGAAGCTAAGCGTCGGCA 60.446 57.895 0.00 0.00 39.73 5.69
420 3731 0.896226 AGGTAAGCTCGTCTTCCACC 59.104 55.000 0.00 4.87 34.86 4.61
429 3740 0.584876 CGTCTTCCACCCGTGTTTTC 59.415 55.000 0.00 0.00 0.00 2.29
430 3741 0.949397 GTCTTCCACCCGTGTTTTCC 59.051 55.000 0.00 0.00 0.00 3.13
467 3781 6.964908 TGCTTCATTTCGTCATTGTTTTCTA 58.035 32.000 0.00 0.00 0.00 2.10
468 3782 6.855914 TGCTTCATTTCGTCATTGTTTTCTAC 59.144 34.615 0.00 0.00 0.00 2.59
469 3783 7.078228 GCTTCATTTCGTCATTGTTTTCTACT 58.922 34.615 0.00 0.00 0.00 2.57
470 3784 7.591426 GCTTCATTTCGTCATTGTTTTCTACTT 59.409 33.333 0.00 0.00 0.00 2.24
471 3785 9.450807 CTTCATTTCGTCATTGTTTTCTACTTT 57.549 29.630 0.00 0.00 0.00 2.66
472 3786 9.796120 TTCATTTCGTCATTGTTTTCTACTTTT 57.204 25.926 0.00 0.00 0.00 2.27
473 3787 9.445786 TCATTTCGTCATTGTTTTCTACTTTTC 57.554 29.630 0.00 0.00 0.00 2.29
474 3788 9.450807 CATTTCGTCATTGTTTTCTACTTTTCT 57.549 29.630 0.00 0.00 0.00 2.52
476 3790 9.849166 TTTCGTCATTGTTTTCTACTTTTCTTT 57.151 25.926 0.00 0.00 0.00 2.52
477 3791 9.849166 TTCGTCATTGTTTTCTACTTTTCTTTT 57.151 25.926 0.00 0.00 0.00 2.27
478 3792 9.498307 TCGTCATTGTTTTCTACTTTTCTTTTC 57.502 29.630 0.00 0.00 0.00 2.29
479 3793 9.503427 CGTCATTGTTTTCTACTTTTCTTTTCT 57.497 29.630 0.00 0.00 0.00 2.52
520 3834 2.342279 GCGGTGGTGCTCACTACA 59.658 61.111 16.38 0.00 43.51 2.74
531 3845 1.402456 GCTCACTACATGTTCGACGGT 60.402 52.381 2.30 0.00 0.00 4.83
532 3846 2.251040 CTCACTACATGTTCGACGGTG 58.749 52.381 2.30 4.76 0.00 4.94
533 3847 1.068125 TCACTACATGTTCGACGGTGG 60.068 52.381 2.30 0.00 0.00 4.61
534 3848 0.389426 ACTACATGTTCGACGGTGGC 60.389 55.000 2.30 0.00 0.00 5.01
535 3849 0.389296 CTACATGTTCGACGGTGGCA 60.389 55.000 2.30 0.00 0.00 4.92
692 4026 1.455773 AGATCCATCCGTCGCCTGA 60.456 57.895 0.00 0.00 0.00 3.86
693 4027 1.300233 GATCCATCCGTCGCCTGAC 60.300 63.158 0.00 0.00 41.91 3.51
706 4040 1.383799 CCTGACCATCAGCCCCAAA 59.616 57.895 0.02 0.00 42.98 3.28
807 4147 3.777556 GGCCAGGTTGGACTTTGG 58.222 61.111 0.00 0.00 44.12 3.28
812 4152 1.228154 AGGTTGGACTTTGGCGGAC 60.228 57.895 0.00 0.00 0.00 4.79
817 4157 1.228154 GGACTTTGGCGGACTGGTT 60.228 57.895 0.00 0.00 0.00 3.67
836 4176 3.612371 GAGGAAGACGACGCGCACT 62.612 63.158 5.73 0.00 0.00 4.40
885 4225 3.123620 CCAAGCTCAGGCGCTCAC 61.124 66.667 7.64 0.00 44.37 3.51
922 4265 1.553651 GGAAACCCTCCTCTGGTCTCT 60.554 57.143 0.00 0.00 41.61 3.10
934 4277 0.250234 TGGTCTCTCGGCATTTGAGG 59.750 55.000 0.00 0.00 34.19 3.86
936 4279 1.472376 GGTCTCTCGGCATTTGAGGAG 60.472 57.143 0.00 0.00 34.19 3.69
1108 4464 1.270907 CCGGCCTAGGATAGCAATCT 58.729 55.000 14.75 0.00 37.37 2.40
1131 4487 2.508887 CTCGTCTGGCTGCTGCTC 60.509 66.667 15.64 6.34 39.59 4.26
1185 4541 3.004024 AGCATGCTTTCACTGAAAACG 57.996 42.857 16.30 0.00 30.84 3.60
1230 4586 0.169672 CGAGTGATTGCTGCAAAGGG 59.830 55.000 20.06 2.34 0.00 3.95
1239 4595 1.685224 CTGCAAAGGGGGTGAGCTA 59.315 57.895 0.00 0.00 0.00 3.32
1315 4671 2.669569 GCGTGCTTCTTGGAGGCA 60.670 61.111 0.30 0.30 45.18 4.75
1364 4720 1.498865 GCTCACGCCGGAATGGTATG 61.499 60.000 5.05 0.00 41.21 2.39
1396 4752 5.394773 GGAACTCCCATCTTTACTCTCAGTC 60.395 48.000 0.00 0.00 34.14 3.51
1397 4753 4.941713 ACTCCCATCTTTACTCTCAGTCT 58.058 43.478 0.00 0.00 0.00 3.24
1398 4754 4.953579 ACTCCCATCTTTACTCTCAGTCTC 59.046 45.833 0.00 0.00 0.00 3.36
1399 4755 4.282496 TCCCATCTTTACTCTCAGTCTCC 58.718 47.826 0.00 0.00 0.00 3.71
1400 4756 4.017037 TCCCATCTTTACTCTCAGTCTCCT 60.017 45.833 0.00 0.00 0.00 3.69
1401 4757 5.193930 TCCCATCTTTACTCTCAGTCTCCTA 59.806 44.000 0.00 0.00 0.00 2.94
1402 4758 5.300792 CCCATCTTTACTCTCAGTCTCCTAC 59.699 48.000 0.00 0.00 0.00 3.18
1404 4760 6.378564 CCATCTTTACTCTCAGTCTCCTACAA 59.621 42.308 0.00 0.00 0.00 2.41
1413 5601 5.706369 TCTCAGTCTCCTACAACTACAAGTC 59.294 44.000 0.00 0.00 0.00 3.01
1431 5619 5.946377 ACAAGTCTTGTTTTCTTTCACTCCT 59.054 36.000 12.62 0.00 42.22 3.69
1432 5620 7.110155 ACAAGTCTTGTTTTCTTTCACTCCTA 58.890 34.615 12.62 0.00 42.22 2.94
1433 5621 7.281100 ACAAGTCTTGTTTTCTTTCACTCCTAG 59.719 37.037 12.62 0.00 42.22 3.02
1438 5626 5.238583 TGTTTTCTTTCACTCCTAGCTAGC 58.761 41.667 15.74 6.62 0.00 3.42
1496 5684 4.843984 CGGCGACTTTTTAACACTTGTATG 59.156 41.667 0.00 0.00 0.00 2.39
1535 5723 7.387397 CAGAAGATAGGCTTAGGCTTCTAAATG 59.613 40.741 14.80 11.27 42.28 2.32
1686 5885 9.577110 AATGTATAGAAACAAACATGCTGAATG 57.423 29.630 2.54 0.00 36.21 2.67
1764 5965 6.245408 AGGTGTGACTTTTCAAATGCCTATA 58.755 36.000 0.00 0.00 31.90 1.31
1776 5977 3.662247 ATGCCTATACGAACCTGCTAC 57.338 47.619 0.00 0.00 0.00 3.58
1791 5992 0.790814 GCTACGCACTTCACTTCCAC 59.209 55.000 0.00 0.00 0.00 4.02
1821 6022 8.099364 TCATCACTTTAAGCCTAAAACTTGAG 57.901 34.615 0.00 0.00 0.00 3.02
2059 6260 6.509656 AGTTACCATGCATAATTGATTGCTG 58.490 36.000 0.00 6.77 39.60 4.41
2273 7121 5.761234 TGCAATATCCGAACACCTTAATACC 59.239 40.000 0.00 0.00 0.00 2.73
2371 7219 5.120674 TCACGCAGATTAACATCAAACTGAG 59.879 40.000 0.00 0.00 0.00 3.35
2425 7273 5.287035 GCAGCACATATTTTTGTACTTCTGC 59.713 40.000 0.00 0.00 34.25 4.26
2441 7289 1.521450 CTGCTGTTCTTGTGGCCAGG 61.521 60.000 5.11 0.00 0.00 4.45
2449 7352 2.189191 CTTGTGGCCAGGCAGCTAGA 62.189 60.000 15.19 0.00 0.00 2.43
2467 7370 6.989169 CAGCTAGAAAAGTAGGCATTATGTCT 59.011 38.462 4.29 4.29 35.80 3.41
2468 7371 7.170658 CAGCTAGAAAAGTAGGCATTATGTCTC 59.829 40.741 1.32 0.00 32.64 3.36
2478 7381 4.139786 GGCATTATGTCTCATGTGGTCAT 58.860 43.478 0.00 2.60 34.21 3.06
2515 7418 2.998316 TCACATATCCACGGCATTGA 57.002 45.000 0.00 0.00 0.00 2.57
2519 7422 4.036616 TCACATATCCACGGCATTGAAATG 59.963 41.667 0.00 0.00 39.40 2.32
2704 7614 8.922676 GGCAAATGATGATGATTATTCATGAAC 58.077 33.333 11.07 0.00 42.73 3.18
2820 7736 4.667668 GCACAACTTGTTTGAGCTATCTCG 60.668 45.833 0.00 0.00 45.47 4.04
2823 7739 1.936547 CTTGTTTGAGCTATCTCGGCC 59.063 52.381 0.00 0.00 42.26 6.13
2849 7766 5.353394 TGGACCTGGTTTATCATAGTGAC 57.647 43.478 0.00 0.00 0.00 3.67
2852 7769 4.755411 ACCTGGTTTATCATAGTGACGTG 58.245 43.478 0.00 0.00 0.00 4.49
2853 7770 4.119862 CCTGGTTTATCATAGTGACGTGG 58.880 47.826 0.00 0.00 0.00 4.94
2868 7787 0.316689 CGTGGGTCGTGTTCTTTTGC 60.317 55.000 0.00 0.00 34.52 3.68
2905 7836 2.143122 TGCTGTCTGCCTTTACTTTCG 58.857 47.619 0.00 0.00 42.00 3.46
2939 7870 6.409234 CCTTAGCCCAAGAACAGGTTATATCA 60.409 42.308 0.00 0.00 36.22 2.15
2946 7877 7.280205 CCCAAGAACAGGTTATATCACTGTAAC 59.720 40.741 7.14 5.76 44.08 2.50
2948 7879 6.040878 AGAACAGGTTATATCACTGTAACGC 58.959 40.000 7.14 0.68 44.08 4.84
2949 7880 5.333299 ACAGGTTATATCACTGTAACGCA 57.667 39.130 5.38 0.00 43.13 5.24
2952 7883 5.117135 CAGGTTATATCACTGTAACGCATCG 59.883 44.000 0.00 0.00 31.65 3.84
3009 7940 7.805163 AGATTTATCATGTACCATGTTCCTCA 58.195 34.615 4.30 0.00 0.00 3.86
3013 7944 5.698741 TCATGTACCATGTTCCTCAAGAT 57.301 39.130 4.30 0.00 0.00 2.40
3016 7947 6.947733 TCATGTACCATGTTCCTCAAGATTTT 59.052 34.615 4.30 0.00 0.00 1.82
3056 7994 1.434513 TTGATTCAGGCCCAGTGGGT 61.435 55.000 29.23 8.40 46.51 4.51
3073 8011 5.949354 CAGTGGGTTTATGGAAGGATTTACA 59.051 40.000 0.00 0.00 0.00 2.41
3118 8056 7.968014 AGGAATTTTAGAGCATTTGAATCCT 57.032 32.000 0.00 0.00 0.00 3.24
3158 8103 8.603898 TTTAGCCCTATCGATTCCTATGATTA 57.396 34.615 1.71 0.00 0.00 1.75
3164 8109 8.642432 CCCTATCGATTCCTATGATTAGCATAA 58.358 37.037 1.71 0.00 38.92 1.90
3174 8119 9.653287 TCCTATGATTAGCATAACTAAATTCCG 57.347 33.333 0.00 0.00 43.99 4.30
3175 8120 8.391106 CCTATGATTAGCATAACTAAATTCCGC 58.609 37.037 0.00 0.00 43.99 5.54
3176 8121 7.986085 ATGATTAGCATAACTAAATTCCGCT 57.014 32.000 0.00 0.00 43.99 5.52
3178 8123 9.672673 ATGATTAGCATAACTAAATTCCGCTAT 57.327 29.630 0.00 0.00 43.99 2.97
3179 8124 9.151471 TGATTAGCATAACTAAATTCCGCTATC 57.849 33.333 0.00 0.00 43.99 2.08
3180 8125 7.900782 TTAGCATAACTAAATTCCGCTATCC 57.099 36.000 0.00 0.00 37.93 2.59
3181 8126 5.246307 AGCATAACTAAATTCCGCTATCCC 58.754 41.667 0.00 0.00 0.00 3.85
3182 8127 5.013183 AGCATAACTAAATTCCGCTATCCCT 59.987 40.000 0.00 0.00 0.00 4.20
3183 8128 6.212791 AGCATAACTAAATTCCGCTATCCCTA 59.787 38.462 0.00 0.00 0.00 3.53
3184 8129 6.877322 GCATAACTAAATTCCGCTATCCCTAA 59.123 38.462 0.00 0.00 0.00 2.69
3185 8130 7.389607 GCATAACTAAATTCCGCTATCCCTAAA 59.610 37.037 0.00 0.00 0.00 1.85
3186 8131 9.280174 CATAACTAAATTCCGCTATCCCTAAAA 57.720 33.333 0.00 0.00 0.00 1.52
3187 8132 9.856162 ATAACTAAATTCCGCTATCCCTAAAAA 57.144 29.630 0.00 0.00 0.00 1.94
3231 8176 6.650120 TCTATTCCTACACCTTTCATTCCAC 58.350 40.000 0.00 0.00 0.00 4.02
3232 8177 4.715534 TTCCTACACCTTTCATTCCACA 57.284 40.909 0.00 0.00 0.00 4.17
3275 8221 5.397142 AATTCCTTTGAGAAGTCCAATGC 57.603 39.130 0.00 0.00 0.00 3.56
3279 8225 3.190118 CCTTTGAGAAGTCCAATGCACTC 59.810 47.826 0.00 0.00 0.00 3.51
3304 8252 4.646945 TCACTATTTCTCTCTACCCTGCAG 59.353 45.833 6.78 6.78 0.00 4.41
3320 8269 1.079197 CAGTGTCATGTGGCGGCTA 60.079 57.895 11.43 0.00 0.00 3.93
3382 8331 3.818787 CCGGCCTTGCAGCATCAC 61.819 66.667 0.00 0.00 0.00 3.06
3388 8337 1.374343 CCTTGCAGCATCACGCATCT 61.374 55.000 0.00 0.00 46.13 2.90
3390 8339 0.674269 TTGCAGCATCACGCATCTGA 60.674 50.000 0.00 0.00 46.13 3.27
3403 8352 1.605710 GCATCTGACTTGCAACAGTGT 59.394 47.619 14.65 3.12 39.90 3.55
3405 8354 2.689553 TCTGACTTGCAACAGTGTCA 57.310 45.000 15.85 15.85 37.76 3.58
3406 8355 2.279741 TCTGACTTGCAACAGTGTCAC 58.720 47.619 13.51 0.00 35.83 3.67
3448 8397 2.140717 GTGGCTAGCTTTGTAACACGT 58.859 47.619 15.72 0.00 0.00 4.49
3462 8411 2.192861 CACGTTGGCCAGGCTTTGA 61.193 57.895 12.43 0.00 0.00 2.69
3478 8427 4.766969 CTTTGAAGCAGCAAAAGACAAC 57.233 40.909 8.77 0.00 37.32 3.32
3481 8430 0.249031 AAGCAGCAAAAGACAACGGC 60.249 50.000 0.00 0.00 0.00 5.68
3504 8453 0.030504 TGGCTTTGCAACATCACACG 59.969 50.000 0.00 0.00 0.00 4.49
3507 8456 1.002468 GCTTTGCAACATCACACGTCT 60.002 47.619 0.00 0.00 0.00 4.18
3517 8466 1.674359 TCACACGTCTGGTTTGCAAT 58.326 45.000 0.00 0.00 0.00 3.56
3535 8484 3.134127 GAGCGACCCAATGGCACC 61.134 66.667 0.00 0.00 33.70 5.01
3587 8538 7.121759 AGCACACTCTATAAAGATTGCATGTTT 59.878 33.333 0.00 0.00 36.19 2.83
3588 8539 7.430502 GCACACTCTATAAAGATTGCATGTTTC 59.569 37.037 0.00 0.00 36.19 2.78
3603 8556 6.003326 TGCATGTTTCTGGTTCATAGAAGAA 58.997 36.000 0.00 0.00 35.74 2.52
3604 8557 6.149973 TGCATGTTTCTGGTTCATAGAAGAAG 59.850 38.462 0.00 0.00 35.74 2.85
3655 8642 8.801882 TTTCGGGAAATACATTCTTTAGACAT 57.198 30.769 0.00 0.00 38.18 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.182842 GCCATGCCTTAGTCTGCGG 61.183 63.158 0.00 0.00 0.00 5.69
1 2 2.182842 GGCCATGCCTTAGTCTGCG 61.183 63.158 0.00 0.00 46.69 5.18
2 3 3.833304 GGCCATGCCTTAGTCTGC 58.167 61.111 0.00 0.00 46.69 4.26
12 13 2.124151 CCCACCACTAGGCCATGC 60.124 66.667 5.01 0.00 39.06 4.06
13 14 0.107017 CTTCCCACCACTAGGCCATG 60.107 60.000 5.01 0.00 39.06 3.66
14 15 1.281925 CCTTCCCACCACTAGGCCAT 61.282 60.000 5.01 0.00 39.06 4.40
15 16 1.923395 CCTTCCCACCACTAGGCCA 60.923 63.158 5.01 0.00 39.06 5.36
16 17 2.680370 CCCTTCCCACCACTAGGCC 61.680 68.421 0.00 0.00 39.06 5.19
17 18 2.680370 CCCCTTCCCACCACTAGGC 61.680 68.421 0.00 0.00 39.06 3.93
18 19 0.845102 AACCCCTTCCCACCACTAGG 60.845 60.000 0.00 0.00 42.21 3.02
19 20 0.328258 CAACCCCTTCCCACCACTAG 59.672 60.000 0.00 0.00 0.00 2.57
20 21 0.104356 TCAACCCCTTCCCACCACTA 60.104 55.000 0.00 0.00 0.00 2.74
21 22 0.776080 ATCAACCCCTTCCCACCACT 60.776 55.000 0.00 0.00 0.00 4.00
22 23 0.611896 CATCAACCCCTTCCCACCAC 60.612 60.000 0.00 0.00 0.00 4.16
23 24 1.773635 CATCAACCCCTTCCCACCA 59.226 57.895 0.00 0.00 0.00 4.17
24 25 1.682344 GCATCAACCCCTTCCCACC 60.682 63.158 0.00 0.00 0.00 4.61
25 26 1.682344 GGCATCAACCCCTTCCCAC 60.682 63.158 0.00 0.00 0.00 4.61
26 27 1.442886 AAGGCATCAACCCCTTCCCA 61.443 55.000 0.00 0.00 36.78 4.37
27 28 1.388133 AAGGCATCAACCCCTTCCC 59.612 57.895 0.00 0.00 36.78 3.97
30 31 1.388133 GGGAAGGCATCAACCCCTT 59.612 57.895 0.00 0.00 43.87 3.95
31 32 1.856873 TGGGAAGGCATCAACCCCT 60.857 57.895 0.00 0.00 41.44 4.79
32 33 1.682344 GTGGGAAGGCATCAACCCC 60.682 63.158 0.00 0.00 41.44 4.95
33 34 1.682344 GGTGGGAAGGCATCAACCC 60.682 63.158 0.00 0.00 42.37 4.11
34 35 1.682344 GGGTGGGAAGGCATCAACC 60.682 63.158 5.53 5.53 36.20 3.77
35 36 1.076549 TGGGTGGGAAGGCATCAAC 59.923 57.895 0.00 0.00 0.00 3.18
36 37 1.076549 GTGGGTGGGAAGGCATCAA 59.923 57.895 0.00 0.00 0.00 2.57
37 38 2.763215 GTGGGTGGGAAGGCATCA 59.237 61.111 0.00 0.00 0.00 3.07
38 39 2.043953 GGTGGGTGGGAAGGCATC 60.044 66.667 0.00 0.00 0.00 3.91
39 40 3.672503 GGGTGGGTGGGAAGGCAT 61.673 66.667 0.00 0.00 0.00 4.40
41 42 4.366684 CTGGGTGGGTGGGAAGGC 62.367 72.222 0.00 0.00 0.00 4.35
42 43 3.661648 CCTGGGTGGGTGGGAAGG 61.662 72.222 0.00 0.00 0.00 3.46
43 44 2.426305 GAACCTGGGTGGGTGGGAAG 62.426 65.000 0.00 0.00 39.85 3.46
44 45 2.370403 AACCTGGGTGGGTGGGAA 60.370 61.111 0.00 0.00 39.85 3.97
45 46 2.856988 GAACCTGGGTGGGTGGGA 60.857 66.667 0.00 0.00 39.85 4.37
46 47 2.713531 CTTGAACCTGGGTGGGTGGG 62.714 65.000 0.00 0.00 39.85 4.61
47 48 1.228552 CTTGAACCTGGGTGGGTGG 60.229 63.158 0.00 0.00 39.85 4.61
48 49 1.228552 CCTTGAACCTGGGTGGGTG 60.229 63.158 0.00 0.00 39.85 4.61
49 50 3.146828 GCCTTGAACCTGGGTGGGT 62.147 63.158 0.00 0.00 42.05 4.51
50 51 2.283173 GCCTTGAACCTGGGTGGG 60.283 66.667 0.00 0.00 41.11 4.61
51 52 1.077265 ATGCCTTGAACCTGGGTGG 59.923 57.895 0.00 0.00 42.93 4.61
52 53 1.252904 CCATGCCTTGAACCTGGGTG 61.253 60.000 0.00 0.00 0.00 4.61
53 54 1.077265 CCATGCCTTGAACCTGGGT 59.923 57.895 0.00 0.00 0.00 4.51
54 55 0.331278 TACCATGCCTTGAACCTGGG 59.669 55.000 0.00 0.00 0.00 4.45
55 56 1.271871 TGTACCATGCCTTGAACCTGG 60.272 52.381 0.00 0.00 0.00 4.45
56 57 2.198827 TGTACCATGCCTTGAACCTG 57.801 50.000 0.00 0.00 0.00 4.00
57 58 2.726821 CATGTACCATGCCTTGAACCT 58.273 47.619 0.00 0.00 0.00 3.50
58 59 1.134946 GCATGTACCATGCCTTGAACC 59.865 52.381 16.40 0.00 39.01 3.62
59 60 1.818060 TGCATGTACCATGCCTTGAAC 59.182 47.619 22.42 0.00 43.94 3.18
60 61 2.212812 TGCATGTACCATGCCTTGAA 57.787 45.000 22.42 4.73 43.94 2.69
61 62 2.212812 TTGCATGTACCATGCCTTGA 57.787 45.000 22.42 5.06 43.94 3.02
62 63 3.530265 AATTGCATGTACCATGCCTTG 57.470 42.857 22.42 0.00 43.94 3.61
63 64 3.369681 CCAAATTGCATGTACCATGCCTT 60.370 43.478 22.42 14.62 43.94 4.35
64 65 2.168936 CCAAATTGCATGTACCATGCCT 59.831 45.455 22.42 10.19 43.94 4.75
65 66 2.553086 CCAAATTGCATGTACCATGCC 58.447 47.619 22.42 8.62 43.94 4.40
66 67 2.093553 ACCCAAATTGCATGTACCATGC 60.094 45.455 19.53 19.53 44.76 4.06
67 68 3.891422 ACCCAAATTGCATGTACCATG 57.109 42.857 0.00 0.00 0.00 3.66
68 69 4.041444 ACAAACCCAAATTGCATGTACCAT 59.959 37.500 0.00 0.00 0.00 3.55
69 70 3.389329 ACAAACCCAAATTGCATGTACCA 59.611 39.130 0.00 0.00 0.00 3.25
70 71 4.001618 ACAAACCCAAATTGCATGTACC 57.998 40.909 0.00 0.00 0.00 3.34
71 72 4.319405 GCAACAAACCCAAATTGCATGTAC 60.319 41.667 3.06 0.00 45.38 2.90
72 73 3.812053 GCAACAAACCCAAATTGCATGTA 59.188 39.130 3.06 0.00 45.38 2.29
73 74 2.617774 GCAACAAACCCAAATTGCATGT 59.382 40.909 3.06 0.00 45.38 3.21
74 75 3.270962 GCAACAAACCCAAATTGCATG 57.729 42.857 3.06 0.00 45.38 4.06
77 78 3.986442 AATGCAACAAACCCAAATTGC 57.014 38.095 0.00 0.94 46.08 3.56
78 79 4.818546 TGGTAATGCAACAAACCCAAATTG 59.181 37.500 0.00 0.00 0.00 2.32
79 80 4.819088 GTGGTAATGCAACAAACCCAAATT 59.181 37.500 0.00 0.00 0.00 1.82
80 81 4.384940 GTGGTAATGCAACAAACCCAAAT 58.615 39.130 0.00 0.00 0.00 2.32
81 82 3.738281 CGTGGTAATGCAACAAACCCAAA 60.738 43.478 0.00 0.00 0.00 3.28
82 83 2.223829 CGTGGTAATGCAACAAACCCAA 60.224 45.455 0.00 0.00 0.00 4.12
83 84 1.338337 CGTGGTAATGCAACAAACCCA 59.662 47.619 0.00 0.00 0.00 4.51
84 85 1.338655 ACGTGGTAATGCAACAAACCC 59.661 47.619 0.00 0.00 0.00 4.11
85 86 2.785713 ACGTGGTAATGCAACAAACC 57.214 45.000 0.00 0.00 0.00 3.27
86 87 3.047093 GGAACGTGGTAATGCAACAAAC 58.953 45.455 0.00 0.00 0.00 2.93
87 88 2.688446 TGGAACGTGGTAATGCAACAAA 59.312 40.909 0.00 0.00 0.00 2.83
88 89 2.298610 TGGAACGTGGTAATGCAACAA 58.701 42.857 0.00 0.00 0.00 2.83
89 90 1.968704 TGGAACGTGGTAATGCAACA 58.031 45.000 0.00 0.00 0.00 3.33
90 91 3.569250 AATGGAACGTGGTAATGCAAC 57.431 42.857 0.00 0.00 0.00 4.17
91 92 5.906113 AATAATGGAACGTGGTAATGCAA 57.094 34.783 0.00 0.00 0.00 4.08
92 93 5.416013 TCAAATAATGGAACGTGGTAATGCA 59.584 36.000 0.00 0.00 0.00 3.96
93 94 5.885881 TCAAATAATGGAACGTGGTAATGC 58.114 37.500 0.00 0.00 0.00 3.56
94 95 8.026607 ACTTTCAAATAATGGAACGTGGTAATG 58.973 33.333 0.00 0.00 0.00 1.90
95 96 8.117813 ACTTTCAAATAATGGAACGTGGTAAT 57.882 30.769 0.00 0.00 0.00 1.89
156 157 5.453567 AAGGTCCAGCACAAAATAACTTC 57.546 39.130 0.00 0.00 0.00 3.01
186 2358 3.030291 CTCACCTACTGGATGCTTCTCT 58.970 50.000 0.00 0.00 37.04 3.10
189 2361 1.484240 AGCTCACCTACTGGATGCTTC 59.516 52.381 0.00 0.00 34.95 3.86
192 2364 1.484240 AGAAGCTCACCTACTGGATGC 59.516 52.381 0.00 0.00 37.04 3.91
193 2365 3.450457 AGAAGAAGCTCACCTACTGGATG 59.550 47.826 0.00 0.00 37.04 3.51
195 2367 3.176924 AGAAGAAGCTCACCTACTGGA 57.823 47.619 0.00 0.00 37.04 3.86
240 3523 1.142748 GAGCGATGGAGTGGTGGAG 59.857 63.158 0.00 0.00 0.00 3.86
241 3524 2.359169 GGAGCGATGGAGTGGTGGA 61.359 63.158 0.00 0.00 0.00 4.02
244 3527 1.608717 GAGTGGAGCGATGGAGTGGT 61.609 60.000 0.00 0.00 0.00 4.16
246 3529 1.142748 GGAGTGGAGCGATGGAGTG 59.857 63.158 0.00 0.00 0.00 3.51
248 3531 2.415010 CGGAGTGGAGCGATGGAG 59.585 66.667 0.00 0.00 0.00 3.86
249 3532 2.362503 ACGGAGTGGAGCGATGGA 60.363 61.111 0.00 0.00 42.51 3.41
265 3564 0.457681 GCTCAGCTCAAGGACGAGAC 60.458 60.000 0.00 0.00 34.79 3.36
286 3597 1.135660 CGCGTGAGAGCTCTCTGTTTA 60.136 52.381 36.78 19.08 43.25 2.01
338 3649 2.796651 GGCGCAGATGCAAGGAAG 59.203 61.111 10.83 0.00 42.21 3.46
382 3693 1.014044 TTGCCGACGCTTAGCTTCAG 61.014 55.000 11.16 0.59 35.36 3.02
394 3705 1.077089 GACGAGCTTACCTTGCCGAC 61.077 60.000 0.00 0.00 0.00 4.79
399 3710 2.338500 GTGGAAGACGAGCTTACCTTG 58.662 52.381 0.00 0.00 36.55 3.61
400 3711 1.275573 GGTGGAAGACGAGCTTACCTT 59.724 52.381 0.00 0.00 36.55 3.50
467 3781 5.863935 GCTGTTGTGACAAGAAAAGAAAAGT 59.136 36.000 0.00 0.00 34.85 2.66
468 3782 5.863397 TGCTGTTGTGACAAGAAAAGAAAAG 59.137 36.000 0.00 0.00 34.85 2.27
469 3783 5.777802 TGCTGTTGTGACAAGAAAAGAAAA 58.222 33.333 0.00 0.00 34.85 2.29
470 3784 5.384063 TGCTGTTGTGACAAGAAAAGAAA 57.616 34.783 0.00 0.00 34.85 2.52
471 3785 5.581126 ATGCTGTTGTGACAAGAAAAGAA 57.419 34.783 0.00 0.00 34.85 2.52
472 3786 4.260743 CGATGCTGTTGTGACAAGAAAAGA 60.261 41.667 0.00 0.00 34.85 2.52
473 3787 3.970610 CGATGCTGTTGTGACAAGAAAAG 59.029 43.478 0.00 0.00 34.85 2.27
474 3788 3.625313 TCGATGCTGTTGTGACAAGAAAA 59.375 39.130 0.00 0.00 34.85 2.29
475 3789 3.202097 TCGATGCTGTTGTGACAAGAAA 58.798 40.909 0.00 0.00 34.85 2.52
476 3790 2.832563 TCGATGCTGTTGTGACAAGAA 58.167 42.857 0.00 0.00 34.85 2.52
477 3791 2.524569 TCGATGCTGTTGTGACAAGA 57.475 45.000 0.00 0.00 34.85 3.02
478 3792 2.094894 GGATCGATGCTGTTGTGACAAG 59.905 50.000 9.99 0.00 34.85 3.16
479 3793 2.076100 GGATCGATGCTGTTGTGACAA 58.924 47.619 9.99 0.00 34.85 3.18
520 3834 0.319083 TACTTGCCACCGTCGAACAT 59.681 50.000 0.00 0.00 0.00 2.71
692 4026 1.002134 CGTCTTTGGGGCTGATGGT 60.002 57.895 0.00 0.00 0.00 3.55
693 4027 1.750399 CCGTCTTTGGGGCTGATGG 60.750 63.158 0.00 0.00 0.00 3.51
706 4040 2.446036 GGCCTATCCCACCCGTCT 60.446 66.667 0.00 0.00 0.00 4.18
718 4052 2.193127 TCCTTGAGATTTTCGGGCCTA 58.807 47.619 0.84 0.00 0.00 3.93
795 4135 1.228154 AGTCCGCCAAAGTCCAACC 60.228 57.895 0.00 0.00 0.00 3.77
797 4137 1.228124 CCAGTCCGCCAAAGTCCAA 60.228 57.895 0.00 0.00 0.00 3.53
805 4145 2.111999 CTTCCTCAACCAGTCCGCCA 62.112 60.000 0.00 0.00 0.00 5.69
807 4147 0.670854 GTCTTCCTCAACCAGTCCGC 60.671 60.000 0.00 0.00 0.00 5.54
812 4152 1.009389 GCGTCGTCTTCCTCAACCAG 61.009 60.000 0.00 0.00 0.00 4.00
817 4157 3.666253 TGCGCGTCGTCTTCCTCA 61.666 61.111 8.43 0.00 0.00 3.86
922 4265 0.250234 CCAGTCTCCTCAAATGCCGA 59.750 55.000 0.00 0.00 0.00 5.54
1034 4390 2.741092 GCTTCACCGACTGGGACA 59.259 61.111 0.00 0.00 40.75 4.02
1143 4499 1.950909 CCAAGCAAAGGAACGTTACCA 59.049 47.619 6.97 0.00 0.00 3.25
1172 4528 2.490115 ACAAGTGCCGTTTTCAGTGAAA 59.510 40.909 14.35 14.35 0.00 2.69
1200 4556 1.863454 CAATCACTCGAGTATGCTGCC 59.137 52.381 19.57 0.00 0.00 4.85
1230 4586 2.586792 CACTGCCCTAGCTCACCC 59.413 66.667 0.00 0.00 40.80 4.61
1239 4595 4.655647 CTGCCACAGCACTGCCCT 62.656 66.667 0.00 0.00 46.52 5.19
1275 4631 1.016130 GGCCGCTATGGTCATCATCG 61.016 60.000 0.00 0.00 44.04 3.84
1315 4671 2.559668 CCAAATTCACAGCAGTGGACAT 59.440 45.455 9.58 0.00 45.91 3.06
1353 4709 3.804036 TCCAAGTAAGCATACCATTCCG 58.196 45.455 0.00 0.00 32.08 4.30
1396 4752 7.711339 AGAAAACAAGACTTGTAGTTGTAGGAG 59.289 37.037 20.85 0.00 44.59 3.69
1397 4753 7.562135 AGAAAACAAGACTTGTAGTTGTAGGA 58.438 34.615 20.85 0.00 44.59 2.94
1398 4754 7.787725 AGAAAACAAGACTTGTAGTTGTAGG 57.212 36.000 20.85 0.00 44.59 3.18
1399 4755 9.704098 GAAAGAAAACAAGACTTGTAGTTGTAG 57.296 33.333 20.85 0.00 44.59 2.74
1400 4756 9.221933 TGAAAGAAAACAAGACTTGTAGTTGTA 57.778 29.630 20.85 2.31 44.59 2.41
1401 4757 8.021396 GTGAAAGAAAACAAGACTTGTAGTTGT 58.979 33.333 20.85 13.38 44.59 3.32
1402 4758 8.237267 AGTGAAAGAAAACAAGACTTGTAGTTG 58.763 33.333 20.85 0.00 44.59 3.16
1404 4760 7.065923 GGAGTGAAAGAAAACAAGACTTGTAGT 59.934 37.037 20.85 11.78 44.59 2.73
1413 5601 6.128418 GCTAGCTAGGAGTGAAAGAAAACAAG 60.128 42.308 22.10 0.00 0.00 3.16
1431 5619 6.936900 ACAGAATCTTCAAAACAAGCTAGCTA 59.063 34.615 19.70 0.00 0.00 3.32
1432 5620 5.767168 ACAGAATCTTCAAAACAAGCTAGCT 59.233 36.000 12.68 12.68 0.00 3.32
1433 5621 6.006759 ACAGAATCTTCAAAACAAGCTAGC 57.993 37.500 6.62 6.62 0.00 3.42
1496 5684 4.999950 CCTATCTTCTGGCAATCCATGTAC 59.000 45.833 0.00 0.00 42.51 2.90
1548 5736 2.443887 AATTCACATGTGCCAACAGC 57.556 45.000 21.38 0.00 40.39 4.40
1549 5737 4.771590 ACTAATTCACATGTGCCAACAG 57.228 40.909 21.38 14.91 40.39 3.16
1550 5738 4.261952 CCAACTAATTCACATGTGCCAACA 60.262 41.667 21.38 0.00 41.58 3.33
1660 5859 9.577110 CATTCAGCATGTTTGTTTCTATACATT 57.423 29.630 0.00 0.00 37.40 2.71
1661 5860 8.742777 ACATTCAGCATGTTTGTTTCTATACAT 58.257 29.630 0.00 0.00 44.40 2.29
1663 5862 9.708222 CTACATTCAGCATGTTTGTTTCTATAC 57.292 33.333 0.00 0.00 44.40 1.47
1666 5865 6.206438 TGCTACATTCAGCATGTTTGTTTCTA 59.794 34.615 0.00 0.00 44.40 2.10
1667 5866 5.009911 TGCTACATTCAGCATGTTTGTTTCT 59.990 36.000 0.00 0.00 44.40 2.52
1668 5867 5.221880 TGCTACATTCAGCATGTTTGTTTC 58.778 37.500 0.00 0.00 44.40 2.78
1669 5868 5.199024 TGCTACATTCAGCATGTTTGTTT 57.801 34.783 0.00 0.00 44.40 2.83
1670 5869 4.852134 TGCTACATTCAGCATGTTTGTT 57.148 36.364 0.00 0.00 44.40 2.83
1686 5885 8.738199 TATACTTCGTATAAAGCACATGCTAC 57.262 34.615 6.84 0.55 38.92 3.58
1717 5916 8.609483 ACCTTGAGAATGTAATGCAGGATATAT 58.391 33.333 0.00 0.00 0.00 0.86
1776 5977 3.289128 TCAGTGGAAGTGAAGTGCG 57.711 52.632 0.00 0.00 44.79 5.34
1791 5992 8.734386 AGTTTTAGGCTTAAAGTGATGATTCAG 58.266 33.333 5.58 0.00 30.85 3.02
1821 6022 5.557891 AAGCTGATGAAAGTATGAACAGC 57.442 39.130 0.00 0.00 46.02 4.40
1900 6101 1.815408 GCCACACACCAGTCATTCAGT 60.815 52.381 0.00 0.00 0.00 3.41
2059 6260 5.801947 CACCTGCAAACTTATATTCAACAGC 59.198 40.000 0.00 0.00 0.00 4.40
2273 7121 8.084684 TCAATATCTCTACATCTGATTTCCACG 58.915 37.037 0.00 0.00 0.00 4.94
2371 7219 1.081906 CATGTGGACAGTTGCGCAC 60.082 57.895 11.12 5.61 36.27 5.34
2425 7273 1.521450 CTGCCTGGCCACAAGAACAG 61.521 60.000 17.53 0.03 0.00 3.16
2441 7289 5.529060 ACATAATGCCTACTTTTCTAGCTGC 59.471 40.000 0.00 0.00 0.00 5.25
2449 7352 6.319658 CCACATGAGACATAATGCCTACTTTT 59.680 38.462 0.00 0.00 0.00 2.27
2467 7370 6.096705 AGACAAAACTTTGAATGACCACATGA 59.903 34.615 9.12 0.00 40.55 3.07
2468 7371 6.275335 AGACAAAACTTTGAATGACCACATG 58.725 36.000 9.12 0.00 40.55 3.21
2478 7381 9.897744 GATATGTGATTGAGACAAAACTTTGAA 57.102 29.630 9.12 0.00 40.55 2.69
2519 7422 9.713740 GCATAATATGTGCAGCTTAATCTAATC 57.286 33.333 1.92 0.00 42.08 1.75
2704 7614 0.802607 GACCAGACTTTAGCCTCGCG 60.803 60.000 0.00 0.00 0.00 5.87
2823 7739 5.586243 CACTATGATAAACCAGGTCCAACTG 59.414 44.000 0.00 0.00 38.21 3.16
2852 7769 1.804748 CTAGGCAAAAGAACACGACCC 59.195 52.381 0.00 0.00 0.00 4.46
2853 7770 2.762745 TCTAGGCAAAAGAACACGACC 58.237 47.619 0.00 0.00 0.00 4.79
2868 7787 4.639334 ACAGCAGAACATATGCATCTAGG 58.361 43.478 0.19 0.00 46.31 3.02
2905 7836 2.570302 TCTTGGGCTAAGGAACTACACC 59.430 50.000 10.91 0.00 38.49 4.16
2939 7870 2.380084 AACATCCGATGCGTTACAGT 57.620 45.000 8.36 0.00 0.00 3.55
3016 7947 4.360964 GCATGGCTGGCGCACAAA 62.361 61.111 10.83 0.00 38.10 2.83
3022 7960 2.011741 ATCAACATGCATGGCTGGCG 62.012 55.000 29.41 11.41 0.00 5.69
3024 7962 1.478916 TGAATCAACATGCATGGCTGG 59.521 47.619 29.41 15.58 0.00 4.85
3056 7994 8.058847 ACAATAGGCTGTAAATCCTTCCATAAA 58.941 33.333 0.00 0.00 34.02 1.40
3092 8030 9.652114 AGGATTCAAATGCTCTAAAATTCCTAT 57.348 29.630 0.00 0.00 30.72 2.57
3136 8079 5.069781 GCTAATCATAGGAATCGATAGGGCT 59.930 44.000 0.00 0.00 0.00 5.19
3137 8080 5.163405 TGCTAATCATAGGAATCGATAGGGC 60.163 44.000 0.00 0.00 0.00 5.19
3153 8098 9.151471 GATAGCGGAATTTAGTTATGCTAATCA 57.849 33.333 0.00 0.00 39.23 2.57
3158 8103 5.013183 AGGGATAGCGGAATTTAGTTATGCT 59.987 40.000 8.40 0.00 35.35 3.79
3214 8159 4.286297 TCCTGTGGAATGAAAGGTGTAG 57.714 45.455 0.00 0.00 0.00 2.74
3231 8176 4.811555 TGAGTTCACGTTGAAATTCCTG 57.188 40.909 0.00 0.00 38.22 3.86
3232 8177 5.828299 TTTGAGTTCACGTTGAAATTCCT 57.172 34.783 0.00 0.00 38.22 3.36
3267 8213 5.645497 AGAAATAGTGAAGAGTGCATTGGAC 59.355 40.000 0.00 0.00 0.00 4.02
3275 8221 6.605594 AGGGTAGAGAGAAATAGTGAAGAGTG 59.394 42.308 0.00 0.00 0.00 3.51
3279 8225 5.127845 TGCAGGGTAGAGAGAAATAGTGAAG 59.872 44.000 0.00 0.00 0.00 3.02
3304 8252 1.217882 GTATAGCCGCCACATGACAC 58.782 55.000 0.00 0.00 0.00 3.67
3320 8269 4.048504 GCCGCTGTTTCTTTTTGTTGTAT 58.951 39.130 0.00 0.00 0.00 2.29
3371 8320 0.674269 TCAGATGCGTGATGCTGCAA 60.674 50.000 6.36 0.00 45.45 4.08
3382 8331 0.870393 ACTGTTGCAAGTCAGATGCG 59.130 50.000 20.45 0.00 46.76 4.73
3388 8337 1.378531 GGTGACACTGTTGCAAGTCA 58.621 50.000 13.51 13.51 38.56 3.41
3390 8339 1.095228 CCGGTGACACTGTTGCAAGT 61.095 55.000 13.35 0.00 0.00 3.16
3423 8372 2.107950 TACAAAGCTAGCCACGCAAT 57.892 45.000 12.13 0.00 0.00 3.56
3448 8397 3.458653 GCTTCAAAGCCTGGCCAA 58.541 55.556 16.57 2.42 46.20 4.52
3462 8411 0.249031 GCCGTTGTCTTTTGCTGCTT 60.249 50.000 0.00 0.00 0.00 3.91
3477 8426 2.560119 TTGCAAAGCCATTCGCCGT 61.560 52.632 0.00 0.00 38.78 5.68
3478 8427 2.088178 GTTGCAAAGCCATTCGCCG 61.088 57.895 0.00 0.00 38.78 6.46
3481 8430 1.987770 GTGATGTTGCAAAGCCATTCG 59.012 47.619 0.00 0.00 0.00 3.34
3504 8453 0.874390 TCGCTCATTGCAAACCAGAC 59.126 50.000 1.71 0.00 43.06 3.51
3507 8456 1.523154 GGGTCGCTCATTGCAAACCA 61.523 55.000 15.69 0.00 44.42 3.67
3517 8466 2.359850 GTGCCATTGGGTCGCTCA 60.360 61.111 4.53 0.00 36.17 4.26
3541 8490 2.900167 CTGTGGTCGTCGTCGGTCA 61.900 63.158 1.55 0.00 37.69 4.02
3629 8616 8.624367 TGTCTAAAGAATGTATTTCCCGAAAA 57.376 30.769 0.00 0.00 34.67 2.29
3632 8619 7.201696 GCAATGTCTAAAGAATGTATTTCCCGA 60.202 37.037 0.00 0.00 34.67 5.14


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

AutoCloner maintained by Alex Coulton.