Multiple sequence alignment - TraesCS3A01G120600

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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 TraesCS3A01G120600 chr3A 100.000 3449 0 0 1 3449 94256294 94252846 0.000000e+00 6370.0
1 TraesCS3A01G120600 chr3A 93.450 1603 79 17 812 2414 94859317 94857741 0.000000e+00 2355.0
2 TraesCS3A01G120600 chr3A 97.922 1203 19 4 2253 3449 94203078 94201876 0.000000e+00 2078.0
3 TraesCS3A01G120600 chr3A 88.321 1507 112 32 1216 2704 94384152 94382692 0.000000e+00 1749.0
4 TraesCS3A01G120600 chr3A 95.901 1049 29 7 2405 3449 94247070 94246032 0.000000e+00 1687.0
5 TraesCS3A01G120600 chr3A 87.487 983 115 6 1462 2440 95359243 95358265 0.000000e+00 1127.0
6 TraesCS3A01G120600 chr3A 86.806 432 24 13 798 1229 94385096 94384698 5.250000e-123 451.0
7 TraesCS3A01G120600 chr3A 84.941 425 58 1 996 1414 95127364 95126940 3.180000e-115 425.0
8 TraesCS3A01G120600 chr3A 81.761 159 15 6 2590 2746 94202528 94202382 1.680000e-23 121.0
9 TraesCS3A01G120600 chr3A 81.481 162 17 5 2590 2750 94253492 94253343 1.680000e-23 121.0
10 TraesCS3A01G120600 chr3A 81.481 162 17 5 2803 2952 94253705 94253545 1.680000e-23 121.0
11 TraesCS3A01G120600 chr3A 80.247 162 18 9 2803 2952 94246885 94246726 3.640000e-20 110.0
12 TraesCS3A01G120600 chr3A 96.721 61 1 1 2492 2551 94202580 94202520 2.190000e-17 100.0
13 TraesCS3A01G120600 chr3A 96.721 61 1 1 2751 2811 94202839 94202780 2.190000e-17 100.0
14 TraesCS3A01G120600 chr3A 96.721 61 1 1 2492 2551 94246725 94246665 2.190000e-17 100.0
15 TraesCS3A01G120600 chr3A 96.721 61 1 1 2492 2551 94253544 94253484 2.190000e-17 100.0
16 TraesCS3A01G120600 chr3A 96.721 61 1 1 2751 2811 94253803 94253744 2.190000e-17 100.0
17 TraesCS3A01G120600 chr3A 81.600 125 11 7 2804 2920 94382808 94382688 3.670000e-15 93.5
18 TraesCS3A01G120600 chr3B 93.724 1705 73 26 728 2414 126401074 126399386 0.000000e+00 2525.0
19 TraesCS3A01G120600 chr3B 88.690 1839 141 28 814 2643 126459186 126457406 0.000000e+00 2182.0
20 TraesCS3A01G120600 chr3B 87.487 983 115 6 1462 2440 126733158 126732180 0.000000e+00 1127.0
21 TraesCS3A01G120600 chr3B 90.351 456 30 5 292 742 126401541 126401095 1.380000e-163 586.0
22 TraesCS3A01G120600 chr3B 81.154 589 82 16 843 1414 126733746 126733170 2.440000e-121 446.0
23 TraesCS3A01G120600 chr3B 81.273 550 74 16 849 1381 126715200 126714663 5.320000e-113 418.0
24 TraesCS3A01G120600 chr3B 91.304 253 21 1 41 293 62389260 62389511 9.160000e-91 344.0
25 TraesCS3A01G120600 chr3B 84.190 253 27 6 296 541 126459697 126459451 2.070000e-57 233.0
26 TraesCS3A01G120600 chr3B 89.706 68 7 0 2633 2700 126399026 126398959 1.710000e-13 87.9
27 TraesCS3A01G120600 chr3D 94.573 1603 77 9 812 2414 80917671 80916079 0.000000e+00 2470.0
28 TraesCS3A01G120600 chr3D 93.302 1687 77 8 793 2473 80601547 80599891 0.000000e+00 2457.0
29 TraesCS3A01G120600 chr3D 87.998 1908 127 47 812 2704 80630627 80628807 0.000000e+00 2161.0
30 TraesCS3A01G120600 chr3D 90.672 729 39 10 2735 3449 80599911 80599198 0.000000e+00 942.0
31 TraesCS3A01G120600 chr3D 91.525 295 21 2 292 586 80602939 80602649 1.490000e-108 403.0
32 TraesCS3A01G120600 chr3D 81.407 398 48 18 2735 3115 80916058 80915670 5.590000e-78 302.0
33 TraesCS3A01G120600 chr3D 96.875 96 3 0 2492 2587 80916042 80915947 9.910000e-36 161.0
34 TraesCS3A01G120600 chr3D 83.439 157 10 6 2590 2746 80599838 80599698 7.770000e-27 132.0
35 TraesCS3A01G120600 chr3D 82.667 150 8 6 644 779 80601741 80601596 2.170000e-22 117.0
36 TraesCS3A01G120600 chr2B 92.742 248 17 1 46 293 436266089 436266335 1.180000e-94 357.0
37 TraesCS3A01G120600 chr2B 78.169 142 21 6 3255 3392 794907040 794906905 7.930000e-12 82.4
38 TraesCS3A01G120600 chr1D 92.369 249 18 1 45 293 384471189 384471436 1.520000e-93 353.0
39 TraesCS3A01G120600 chr6B 91.700 253 19 2 42 293 513140446 513140697 1.970000e-92 350.0
40 TraesCS3A01G120600 chr6B 91.667 252 20 1 42 293 75528021 75528271 7.080000e-92 348.0
41 TraesCS3A01G120600 chr6B 91.667 252 20 1 42 293 260601310 260601060 7.080000e-92 348.0
42 TraesCS3A01G120600 chr6B 82.857 105 10 7 3194 3294 437845790 437845890 1.710000e-13 87.9
43 TraesCS3A01G120600 chr5B 92.000 250 19 1 44 293 530709264 530709512 1.970000e-92 350.0
44 TraesCS3A01G120600 chr5B 82.772 267 32 9 3187 3449 509476316 509476572 3.460000e-55 226.0
45 TraesCS3A01G120600 chr2D 92.000 250 19 1 44 293 405281255 405281007 1.970000e-92 350.0
46 TraesCS3A01G120600 chr1B 91.968 249 19 1 45 293 68177215 68177462 7.080000e-92 348.0
47 TraesCS3A01G120600 chr2A 78.810 269 27 16 3187 3449 333732729 333732485 1.660000e-33 154.0
48 TraesCS3A01G120600 chr5D 78.378 222 34 9 3231 3449 448198740 448198950 7.770000e-27 132.0
49 TraesCS3A01G120600 chr6A 80.741 135 22 4 3189 3319 1733372 1733506 6.090000e-18 102.0


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 TraesCS3A01G120600 chr3A 94252846 94256294 3448 True 1362.400000 6370 91.280800 1 3449 5 chr3A.!!$R6 3448
1 TraesCS3A01G120600 chr3A 94857741 94859317 1576 True 2355.000000 2355 93.450000 812 2414 1 chr3A.!!$R1 1602
2 TraesCS3A01G120600 chr3A 95358265 95359243 978 True 1127.000000 1127 87.487000 1462 2440 1 chr3A.!!$R3 978
3 TraesCS3A01G120600 chr3A 94382688 94385096 2408 True 764.500000 1749 85.575667 798 2920 3 chr3A.!!$R7 2122
4 TraesCS3A01G120600 chr3A 94246032 94247070 1038 True 632.333333 1687 90.956333 2405 3449 3 chr3A.!!$R5 1044
5 TraesCS3A01G120600 chr3A 94201876 94203078 1202 True 599.750000 2078 93.281250 2253 3449 4 chr3A.!!$R4 1196
6 TraesCS3A01G120600 chr3B 126457406 126459697 2291 True 1207.500000 2182 86.440000 296 2643 2 chr3B.!!$R3 2347
7 TraesCS3A01G120600 chr3B 126398959 126401541 2582 True 1066.300000 2525 91.260333 292 2700 3 chr3B.!!$R2 2408
8 TraesCS3A01G120600 chr3B 126732180 126733746 1566 True 786.500000 1127 84.320500 843 2440 2 chr3B.!!$R4 1597
9 TraesCS3A01G120600 chr3B 126714663 126715200 537 True 418.000000 418 81.273000 849 1381 1 chr3B.!!$R1 532
10 TraesCS3A01G120600 chr3D 80628807 80630627 1820 True 2161.000000 2161 87.998000 812 2704 1 chr3D.!!$R1 1892
11 TraesCS3A01G120600 chr3D 80915670 80917671 2001 True 977.666667 2470 90.951667 812 3115 3 chr3D.!!$R3 2303
12 TraesCS3A01G120600 chr3D 80599198 80602939 3741 True 810.200000 2457 88.321000 292 3449 5 chr3D.!!$R2 3157

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
167 168 0.320421 GGCGACTACCAGCACTGAAA 60.320 55.0 0.0 0.0 34.54 2.69 F
245 246 0.391130 GCTGTAGCACACAATCGGGA 60.391 55.0 0.0 0.0 41.59 5.14 F
265 266 0.392060 AATCGTCGTGTTAAGGCCCC 60.392 55.0 0.0 0.0 0.00 5.80 F
269 270 0.459063 GTCGTGTTAAGGCCCCGTAG 60.459 60.0 0.0 0.0 0.00 3.51 F
983 1976 0.674895 AGCAATCCCGCAGTTGAGTC 60.675 55.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 3510 0.467384 CTTCAGATGGGATCAGCGGT 59.533 55.000 0.0 0.0 33.94 5.68 R
2046 3642 2.095252 GTCCAGAAGCTCGTTCGCC 61.095 63.158 0.0 0.0 40.49 5.54 R
2075 3671 3.151022 CCCTCCGGGTCAGCTCTC 61.151 72.222 0.0 0.0 38.25 3.20 R
2316 3918 1.474879 TGCGCGATATTCCCGATGATA 59.525 47.619 12.1 0.0 0.00 2.15 R
2958 4788 6.324042 TGCAATGTGTACATCATGTTTCATC 58.676 36.000 0.0 0.0 35.10 2.92 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
19 20 2.211353 GAGGTTCGCTAGCTTACCTG 57.789 55.000 30.86 9.97 40.97 4.00
20 21 1.749634 GAGGTTCGCTAGCTTACCTGA 59.250 52.381 30.86 11.99 40.97 3.86
21 22 2.165845 GAGGTTCGCTAGCTTACCTGAA 59.834 50.000 30.86 16.54 40.97 3.02
22 23 2.565834 AGGTTCGCTAGCTTACCTGAAA 59.434 45.455 27.30 3.61 39.47 2.69
23 24 2.930682 GGTTCGCTAGCTTACCTGAAAG 59.069 50.000 21.45 1.10 0.00 2.62
24 25 3.586892 GTTCGCTAGCTTACCTGAAAGT 58.413 45.455 13.93 0.00 0.00 2.66
25 26 4.381292 GGTTCGCTAGCTTACCTGAAAGTA 60.381 45.833 21.45 0.00 0.00 2.24
26 27 5.166398 GTTCGCTAGCTTACCTGAAAGTAA 58.834 41.667 13.93 0.00 0.00 2.24
28 29 4.113354 CGCTAGCTTACCTGAAAGTAAGG 58.887 47.826 13.93 0.00 46.16 2.69
29 30 4.142227 CGCTAGCTTACCTGAAAGTAAGGA 60.142 45.833 13.93 0.00 46.16 3.36
30 31 5.452077 CGCTAGCTTACCTGAAAGTAAGGAT 60.452 44.000 13.93 0.00 46.16 3.24
31 32 5.986741 GCTAGCTTACCTGAAAGTAAGGATC 59.013 44.000 7.70 0.00 46.16 3.36
32 33 5.012328 AGCTTACCTGAAAGTAAGGATCG 57.988 43.478 12.08 0.00 46.16 3.69
33 34 4.710375 AGCTTACCTGAAAGTAAGGATCGA 59.290 41.667 12.08 0.00 46.16 3.59
34 35 5.187186 AGCTTACCTGAAAGTAAGGATCGAA 59.813 40.000 12.08 0.00 46.16 3.71
35 36 5.291371 GCTTACCTGAAAGTAAGGATCGAAC 59.709 44.000 12.08 0.00 46.16 3.95
36 37 6.600882 TTACCTGAAAGTAAGGATCGAACT 57.399 37.500 0.00 0.00 38.27 3.01
37 38 7.630082 GCTTACCTGAAAGTAAGGATCGAACTA 60.630 40.741 12.08 0.00 46.16 2.24
38 39 5.963594 ACCTGAAAGTAAGGATCGAACTAC 58.036 41.667 0.00 0.00 38.27 2.73
39 40 5.715753 ACCTGAAAGTAAGGATCGAACTACT 59.284 40.000 0.00 0.00 38.27 2.57
40 41 6.037098 CCTGAAAGTAAGGATCGAACTACTG 58.963 44.000 0.00 0.00 36.91 2.74
41 42 6.350277 CCTGAAAGTAAGGATCGAACTACTGT 60.350 42.308 0.00 0.00 36.91 3.55
42 43 6.989659 TGAAAGTAAGGATCGAACTACTGTT 58.010 36.000 0.00 0.00 39.42 3.16
43 44 7.439381 TGAAAGTAAGGATCGAACTACTGTTT 58.561 34.615 0.00 0.00 36.39 2.83
44 45 7.929785 TGAAAGTAAGGATCGAACTACTGTTTT 59.070 33.333 0.00 0.00 36.39 2.43
45 46 8.672823 AAAGTAAGGATCGAACTACTGTTTTT 57.327 30.769 0.00 0.00 36.39 1.94
68 69 3.992260 TTTTTGCGAGAAAATTCCCGA 57.008 38.095 1.04 0.00 29.21 5.14
69 70 4.513198 TTTTTGCGAGAAAATTCCCGAT 57.487 36.364 1.04 0.00 29.21 4.18
70 71 3.757745 TTTGCGAGAAAATTCCCGATC 57.242 42.857 1.04 0.00 29.21 3.69
71 72 2.691409 TGCGAGAAAATTCCCGATCT 57.309 45.000 1.04 0.00 29.21 2.75
72 73 3.812156 TGCGAGAAAATTCCCGATCTA 57.188 42.857 1.04 0.00 29.21 1.98
73 74 4.336889 TGCGAGAAAATTCCCGATCTAT 57.663 40.909 1.04 0.00 29.21 1.98
74 75 4.703897 TGCGAGAAAATTCCCGATCTATT 58.296 39.130 1.04 0.00 29.21 1.73
75 76 4.750098 TGCGAGAAAATTCCCGATCTATTC 59.250 41.667 1.04 0.00 29.21 1.75
76 77 4.750098 GCGAGAAAATTCCCGATCTATTCA 59.250 41.667 1.04 0.00 29.21 2.57
77 78 5.409826 GCGAGAAAATTCCCGATCTATTCAT 59.590 40.000 1.04 0.00 29.21 2.57
78 79 6.073003 GCGAGAAAATTCCCGATCTATTCATT 60.073 38.462 1.04 0.00 29.21 2.57
79 80 7.520614 GCGAGAAAATTCCCGATCTATTCATTT 60.521 37.037 1.04 0.00 29.21 2.32
80 81 8.345565 CGAGAAAATTCCCGATCTATTCATTTT 58.654 33.333 0.00 0.00 29.21 1.82
82 83 9.807649 AGAAAATTCCCGATCTATTCATTTTTG 57.192 29.630 0.00 0.00 0.00 2.44
83 84 9.801873 GAAAATTCCCGATCTATTCATTTTTGA 57.198 29.630 0.00 0.00 0.00 2.69
85 86 9.971922 AAATTCCCGATCTATTCATTTTTGATC 57.028 29.630 0.00 0.00 0.00 2.92
86 87 8.696043 ATTCCCGATCTATTCATTTTTGATCA 57.304 30.769 0.00 0.00 34.80 2.92
87 88 8.696043 TTCCCGATCTATTCATTTTTGATCAT 57.304 30.769 0.00 0.00 34.80 2.45
88 89 8.102800 TCCCGATCTATTCATTTTTGATCATG 57.897 34.615 0.00 0.00 34.80 3.07
89 90 7.938490 TCCCGATCTATTCATTTTTGATCATGA 59.062 33.333 0.00 0.00 34.80 3.07
90 91 8.019669 CCCGATCTATTCATTTTTGATCATGAC 58.980 37.037 0.00 0.00 34.80 3.06
91 92 8.562052 CCGATCTATTCATTTTTGATCATGACA 58.438 33.333 0.00 0.00 34.80 3.58
92 93 9.595357 CGATCTATTCATTTTTGATCATGACAG 57.405 33.333 0.00 0.00 34.80 3.51
98 99 9.630098 ATTCATTTTTGATCATGACAGTACAAC 57.370 29.630 0.00 0.00 0.00 3.32
99 100 7.297391 TCATTTTTGATCATGACAGTACAACG 58.703 34.615 0.00 0.00 0.00 4.10
100 101 6.852858 TTTTTGATCATGACAGTACAACGA 57.147 33.333 0.00 0.00 0.00 3.85
101 102 6.852858 TTTTGATCATGACAGTACAACGAA 57.147 33.333 0.00 0.00 0.00 3.85
102 103 7.433708 TTTTGATCATGACAGTACAACGAAT 57.566 32.000 0.00 0.00 0.00 3.34
103 104 8.541133 TTTTGATCATGACAGTACAACGAATA 57.459 30.769 0.00 0.00 0.00 1.75
104 105 8.716646 TTTGATCATGACAGTACAACGAATAT 57.283 30.769 0.00 0.00 0.00 1.28
105 106 7.930513 TGATCATGACAGTACAACGAATATC 57.069 36.000 0.00 0.00 0.00 1.63
106 107 7.488322 TGATCATGACAGTACAACGAATATCA 58.512 34.615 0.00 0.00 0.00 2.15
107 108 7.649306 TGATCATGACAGTACAACGAATATCAG 59.351 37.037 0.00 0.00 0.00 2.90
108 109 7.095695 TCATGACAGTACAACGAATATCAGA 57.904 36.000 0.00 0.00 0.00 3.27
109 110 7.543756 TCATGACAGTACAACGAATATCAGAA 58.456 34.615 0.00 0.00 0.00 3.02
110 111 8.032451 TCATGACAGTACAACGAATATCAGAAA 58.968 33.333 0.00 0.00 0.00 2.52
111 112 8.820933 CATGACAGTACAACGAATATCAGAAAT 58.179 33.333 0.00 0.00 0.00 2.17
113 114 9.863845 TGACAGTACAACGAATATCAGAAATAA 57.136 29.630 0.00 0.00 0.00 1.40
139 140 9.915629 ATAGAAATTACATCAAGATCCGTAGAC 57.084 33.333 0.00 0.00 0.00 2.59
140 141 7.210873 AGAAATTACATCAAGATCCGTAGACC 58.789 38.462 0.00 0.00 0.00 3.85
141 142 6.479972 AATTACATCAAGATCCGTAGACCA 57.520 37.500 0.00 0.00 0.00 4.02
142 143 3.802948 ACATCAAGATCCGTAGACCAC 57.197 47.619 0.00 0.00 0.00 4.16
143 144 2.431057 ACATCAAGATCCGTAGACCACC 59.569 50.000 0.00 0.00 0.00 4.61
144 145 2.526888 TCAAGATCCGTAGACCACCT 57.473 50.000 0.00 0.00 0.00 4.00
145 146 3.657398 TCAAGATCCGTAGACCACCTA 57.343 47.619 0.00 0.00 0.00 3.08
146 147 3.552875 TCAAGATCCGTAGACCACCTAG 58.447 50.000 0.00 0.00 0.00 3.02
147 148 1.984066 AGATCCGTAGACCACCTAGC 58.016 55.000 0.00 0.00 0.00 3.42
148 149 0.592148 GATCCGTAGACCACCTAGCG 59.408 60.000 0.00 0.00 0.00 4.26
149 150 0.822532 ATCCGTAGACCACCTAGCGG 60.823 60.000 0.00 0.00 40.32 5.52
150 151 2.412112 CGTAGACCACCTAGCGGC 59.588 66.667 0.00 0.00 0.00 6.53
151 152 2.412112 GTAGACCACCTAGCGGCG 59.588 66.667 0.51 0.51 0.00 6.46
152 153 2.117156 GTAGACCACCTAGCGGCGA 61.117 63.158 12.98 0.00 0.00 5.54
153 154 2.117156 TAGACCACCTAGCGGCGAC 61.117 63.158 12.98 1.23 0.00 5.19
154 155 2.547640 TAGACCACCTAGCGGCGACT 62.548 60.000 12.98 10.32 0.00 4.18
155 156 2.044650 ACCACCTAGCGGCGACTA 60.045 61.111 12.98 10.99 0.00 2.59
156 157 2.333706 GACCACCTAGCGGCGACTAC 62.334 65.000 12.98 0.00 0.00 2.73
157 158 2.412112 CACCTAGCGGCGACTACC 59.588 66.667 12.98 0.00 0.00 3.18
158 159 2.044650 ACCTAGCGGCGACTACCA 60.045 61.111 12.98 0.00 0.00 3.25
159 160 2.119655 ACCTAGCGGCGACTACCAG 61.120 63.158 12.98 1.90 0.00 4.00
160 161 2.026301 CTAGCGGCGACTACCAGC 59.974 66.667 12.98 0.00 0.00 4.85
161 162 2.752640 TAGCGGCGACTACCAGCA 60.753 61.111 12.98 0.00 33.49 4.41
162 163 2.938539 CTAGCGGCGACTACCAGCAC 62.939 65.000 12.98 0.00 33.49 4.40
163 164 4.436998 GCGGCGACTACCAGCACT 62.437 66.667 12.98 0.00 34.54 4.40
164 165 2.507102 CGGCGACTACCAGCACTG 60.507 66.667 0.00 0.00 34.54 3.66
165 166 2.970639 GGCGACTACCAGCACTGA 59.029 61.111 0.00 0.00 34.54 3.41
166 167 1.292223 GGCGACTACCAGCACTGAA 59.708 57.895 0.00 0.00 34.54 3.02
167 168 0.320421 GGCGACTACCAGCACTGAAA 60.320 55.000 0.00 0.00 34.54 2.69
168 169 1.071605 GCGACTACCAGCACTGAAAG 58.928 55.000 0.00 0.00 42.29 2.62
169 170 1.071605 CGACTACCAGCACTGAAAGC 58.928 55.000 0.00 0.00 37.60 3.51
170 171 1.071605 GACTACCAGCACTGAAAGCG 58.928 55.000 0.00 0.00 37.60 4.68
171 172 0.679505 ACTACCAGCACTGAAAGCGA 59.320 50.000 0.00 0.00 37.60 4.93
172 173 1.337260 ACTACCAGCACTGAAAGCGAG 60.337 52.381 0.00 0.00 37.60 5.03
173 174 0.670546 TACCAGCACTGAAAGCGAGC 60.671 55.000 0.00 0.00 37.60 5.03
174 175 2.684843 CCAGCACTGAAAGCGAGCC 61.685 63.158 0.00 0.00 37.60 4.70
175 176 2.740055 AGCACTGAAAGCGAGCCG 60.740 61.111 0.00 0.00 37.60 5.52
176 177 2.738521 GCACTGAAAGCGAGCCGA 60.739 61.111 0.00 0.00 37.60 5.54
177 178 2.317609 GCACTGAAAGCGAGCCGAA 61.318 57.895 0.00 0.00 37.60 4.30
178 179 1.784062 CACTGAAAGCGAGCCGAAG 59.216 57.895 0.00 0.00 37.60 3.79
201 202 4.530857 CCACCGTCATCGCCCCTC 62.531 72.222 0.00 0.00 35.54 4.30
202 203 4.530857 CACCGTCATCGCCCCTCC 62.531 72.222 0.00 0.00 35.54 4.30
204 205 3.550431 CCGTCATCGCCCCTCCAT 61.550 66.667 0.00 0.00 35.54 3.41
205 206 2.029666 CGTCATCGCCCCTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
206 207 2.796193 CGTCATCGCCCCTCCATCA 61.796 63.158 0.00 0.00 0.00 3.07
207 208 1.227674 GTCATCGCCCCTCCATCAC 60.228 63.158 0.00 0.00 0.00 3.06
208 209 2.111878 CATCGCCCCTCCATCACC 59.888 66.667 0.00 0.00 0.00 4.02
209 210 3.550431 ATCGCCCCTCCATCACCG 61.550 66.667 0.00 0.00 0.00 4.94
212 213 4.864334 GCCCCTCCATCACCGCAG 62.864 72.222 0.00 0.00 0.00 5.18
213 214 3.402681 CCCCTCCATCACCGCAGT 61.403 66.667 0.00 0.00 0.00 4.40
214 215 2.187946 CCCTCCATCACCGCAGTC 59.812 66.667 0.00 0.00 0.00 3.51
215 216 2.202797 CCTCCATCACCGCAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
225 226 2.972505 CGCAGTCGGGCACAACTT 60.973 61.111 0.00 0.00 0.00 2.66
226 227 2.639286 GCAGTCGGGCACAACTTG 59.361 61.111 0.00 0.00 0.00 3.16
244 245 2.089854 GCTGTAGCACACAATCGGG 58.910 57.895 0.00 0.00 41.59 5.14
245 246 0.391130 GCTGTAGCACACAATCGGGA 60.391 55.000 0.00 0.00 41.59 5.14
246 247 1.943968 GCTGTAGCACACAATCGGGAA 60.944 52.381 0.00 0.00 41.59 3.97
247 248 2.422597 CTGTAGCACACAATCGGGAAA 58.577 47.619 0.00 0.00 36.48 3.13
248 249 3.009723 CTGTAGCACACAATCGGGAAAT 58.990 45.455 0.00 0.00 36.48 2.17
249 250 3.006940 TGTAGCACACAATCGGGAAATC 58.993 45.455 0.00 0.00 32.95 2.17
250 251 1.086696 AGCACACAATCGGGAAATCG 58.913 50.000 0.00 0.00 0.00 3.34
251 252 0.802494 GCACACAATCGGGAAATCGT 59.198 50.000 0.00 0.00 0.00 3.73
252 253 1.202031 GCACACAATCGGGAAATCGTC 60.202 52.381 0.00 0.00 0.00 4.20
253 254 1.060553 CACACAATCGGGAAATCGTCG 59.939 52.381 0.00 0.00 0.00 5.12
254 255 1.337447 ACACAATCGGGAAATCGTCGT 60.337 47.619 0.00 0.00 0.00 4.34
255 256 1.060553 CACAATCGGGAAATCGTCGTG 59.939 52.381 0.00 0.00 0.00 4.35
256 257 1.337447 ACAATCGGGAAATCGTCGTGT 60.337 47.619 0.00 0.00 0.00 4.49
257 258 1.730064 CAATCGGGAAATCGTCGTGTT 59.270 47.619 0.00 0.00 0.00 3.32
258 259 2.924926 CAATCGGGAAATCGTCGTGTTA 59.075 45.455 0.00 0.00 0.00 2.41
259 260 2.721274 TCGGGAAATCGTCGTGTTAA 57.279 45.000 0.00 0.00 0.00 2.01
260 261 2.598589 TCGGGAAATCGTCGTGTTAAG 58.401 47.619 0.00 0.00 0.00 1.85
261 262 1.657094 CGGGAAATCGTCGTGTTAAGG 59.343 52.381 0.00 0.00 0.00 2.69
262 263 1.395954 GGGAAATCGTCGTGTTAAGGC 59.604 52.381 0.00 0.00 0.00 4.35
263 264 1.395954 GGAAATCGTCGTGTTAAGGCC 59.604 52.381 0.00 0.00 0.00 5.19
264 265 1.395954 GAAATCGTCGTGTTAAGGCCC 59.604 52.381 0.00 0.00 0.00 5.80
265 266 0.392060 AATCGTCGTGTTAAGGCCCC 60.392 55.000 0.00 0.00 0.00 5.80
266 267 2.567564 ATCGTCGTGTTAAGGCCCCG 62.568 60.000 0.00 0.00 0.00 5.73
267 268 2.344872 GTCGTGTTAAGGCCCCGT 59.655 61.111 0.00 0.00 0.00 5.28
268 269 1.591183 GTCGTGTTAAGGCCCCGTA 59.409 57.895 0.00 0.00 0.00 4.02
269 270 0.459063 GTCGTGTTAAGGCCCCGTAG 60.459 60.000 0.00 0.00 0.00 3.51
282 283 4.063967 CGTAGGACCAGCGCACCA 62.064 66.667 11.47 0.00 0.00 4.17
283 284 2.125512 GTAGGACCAGCGCACCAG 60.126 66.667 11.47 0.00 0.00 4.00
284 285 2.283604 TAGGACCAGCGCACCAGA 60.284 61.111 11.47 0.00 0.00 3.86
285 286 1.911269 TAGGACCAGCGCACCAGAA 60.911 57.895 11.47 0.00 0.00 3.02
286 287 2.167398 TAGGACCAGCGCACCAGAAC 62.167 60.000 11.47 0.00 0.00 3.01
287 288 2.280797 GACCAGCGCACCAGAACA 60.281 61.111 11.47 0.00 0.00 3.18
288 289 2.281070 ACCAGCGCACCAGAACAG 60.281 61.111 11.47 0.00 0.00 3.16
289 290 3.730761 CCAGCGCACCAGAACAGC 61.731 66.667 11.47 0.00 0.00 4.40
290 291 2.974148 CAGCGCACCAGAACAGCA 60.974 61.111 11.47 0.00 0.00 4.41
291 292 2.203195 AGCGCACCAGAACAGCAA 60.203 55.556 11.47 0.00 0.00 3.91
292 293 2.050985 GCGCACCAGAACAGCAAC 60.051 61.111 0.30 0.00 0.00 4.17
293 294 2.546494 GCGCACCAGAACAGCAACT 61.546 57.895 0.30 0.00 0.00 3.16
294 295 1.280746 CGCACCAGAACAGCAACTG 59.719 57.895 0.00 0.00 37.52 3.16
356 358 5.942325 AAAGTTTACGTTTCATGTTGCAC 57.058 34.783 0.00 0.00 0.00 4.57
359 361 5.587289 AGTTTACGTTTCATGTTGCACAAT 58.413 33.333 0.00 0.00 0.00 2.71
364 366 8.581057 TTACGTTTCATGTTGCACAATAAAAT 57.419 26.923 0.00 0.00 0.00 1.82
408 414 9.624697 TGTGATTTTCTCAAATAACAAGCATAC 57.375 29.630 0.00 0.00 39.81 2.39
469 477 1.344438 TCAAGCTCACCATCACGTTCT 59.656 47.619 0.00 0.00 0.00 3.01
546 555 0.752658 CGGGTGGAGCAGATGTATGA 59.247 55.000 0.00 0.00 0.00 2.15
634 645 1.223187 AGTTCCGGTTTGTGTTAGCG 58.777 50.000 0.00 0.00 36.35 4.26
657 1520 5.509972 CGTCGTGAAGTGAAAACAATTGAAA 59.490 36.000 13.59 0.00 0.00 2.69
687 1550 5.798125 TCTGTTCCAAAACATTGCCATTA 57.202 34.783 0.00 0.00 44.18 1.90
755 1656 4.640771 AAACAGCTGAAATCTGGGAGTA 57.359 40.909 23.35 0.00 35.94 2.59
756 1657 3.902881 ACAGCTGAAATCTGGGAGTAG 57.097 47.619 23.35 0.00 35.94 2.57
757 1658 2.093235 ACAGCTGAAATCTGGGAGTAGC 60.093 50.000 23.35 0.00 35.94 3.58
787 1735 4.473643 CCAAGAAGTGCGTGGGAA 57.526 55.556 0.00 0.00 41.78 3.97
789 1737 2.107950 CCAAGAAGTGCGTGGGAATA 57.892 50.000 0.00 0.00 41.78 1.75
790 1738 2.432444 CCAAGAAGTGCGTGGGAATAA 58.568 47.619 0.00 0.00 41.78 1.40
791 1739 2.161609 CCAAGAAGTGCGTGGGAATAAC 59.838 50.000 0.00 0.00 41.78 1.89
793 1741 4.250464 CAAGAAGTGCGTGGGAATAACTA 58.750 43.478 0.00 0.00 0.00 2.24
794 1742 4.124851 AGAAGTGCGTGGGAATAACTAG 57.875 45.455 0.00 0.00 0.00 2.57
795 1743 2.311124 AGTGCGTGGGAATAACTAGC 57.689 50.000 0.00 0.00 0.00 3.42
796 1744 1.553248 AGTGCGTGGGAATAACTAGCA 59.447 47.619 0.00 0.00 0.00 3.49
800 1748 3.196039 TGCGTGGGAATAACTAGCAAGTA 59.804 43.478 0.00 0.00 33.75 2.24
802 1750 3.795101 CGTGGGAATAACTAGCAAGTACG 59.205 47.826 0.00 0.00 33.75 3.67
818 1784 6.750963 AGCAAGTACGTATAACTAGCAAGAAC 59.249 38.462 0.00 0.00 0.00 3.01
983 1976 0.674895 AGCAATCCCGCAGTTGAGTC 60.675 55.000 0.00 0.00 0.00 3.36
990 1983 0.882042 CCGCAGTTGAGTCAGCAGTT 60.882 55.000 9.82 0.00 0.00 3.16
1017 2010 3.310860 AATGCCTGGGACGACGACC 62.311 63.158 7.89 7.89 0.00 4.79
1382 2942 0.677098 ATCTGGCTCAACTGCAGCAG 60.677 55.000 21.54 21.54 38.77 4.24
1416 2976 4.874977 GGTCTCGCGGCAGCCTAC 62.875 72.222 10.54 0.00 41.18 3.18
1425 2985 4.489771 GCAGCCTACCACGCCCAT 62.490 66.667 0.00 0.00 0.00 4.00
2059 3655 1.077089 GTACCTGGCGAACGAGCTTC 61.077 60.000 0.00 0.00 37.29 3.86
2316 3918 0.896019 AGCAGTCTACGCCTGTGTCT 60.896 55.000 0.00 0.00 32.41 3.41
2456 4064 5.521010 GCTCTCTGCATATCTAATCAGCATC 59.479 44.000 0.00 0.00 42.31 3.91
2691 4499 7.016072 TGGTTCCAAGGTGAATCATAATGTTTT 59.984 33.333 0.00 0.00 30.58 2.43
2822 4639 7.565323 AGAAATGAGATTCATGCTACCTTTC 57.435 36.000 0.00 0.00 37.15 2.62
2823 4640 7.344913 AGAAATGAGATTCATGCTACCTTTCT 58.655 34.615 0.00 0.00 37.15 2.52
2824 4641 7.833183 AGAAATGAGATTCATGCTACCTTTCTT 59.167 33.333 0.00 0.00 37.15 2.52
2825 4642 7.951347 AATGAGATTCATGCTACCTTTCTTT 57.049 32.000 0.00 0.00 37.15 2.52
2981 4811 5.453266 CGATGAAACATGATGTACACATTGC 59.547 40.000 0.00 0.00 36.57 3.56
3170 5010 1.004440 AGTCGAAGCTTGCCCACTC 60.004 57.895 2.10 0.00 0.00 3.51
3222 5062 0.475044 AACAGCCGGGTAAACCTCAA 59.525 50.000 5.47 0.00 36.97 3.02
3298 5138 4.262292 GCGGAGTAAAATTTTGTTTCCCCT 60.262 41.667 13.76 0.00 0.00 4.79
3303 5143 9.470399 GGAGTAAAATTTTGTTTCCCCTAGATA 57.530 33.333 13.76 0.00 0.00 1.98
3412 5252 2.058798 CGCGCAGTTCACGGATATTAT 58.941 47.619 8.75 0.00 0.00 1.28
3419 5259 6.299604 GCAGTTCACGGATATTATGAATTCG 58.700 40.000 0.04 0.00 34.98 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.749634 TCAGGTAAGCTAGCGAACCTC 59.250 52.381 30.20 13.26 40.39 3.85
1 2 1.848652 TCAGGTAAGCTAGCGAACCT 58.151 50.000 28.41 28.41 43.15 3.50
2 3 2.667473 TTCAGGTAAGCTAGCGAACC 57.333 50.000 25.63 25.63 0.00 3.62
5 6 4.142227 CCTTACTTTCAGGTAAGCTAGCGA 60.142 45.833 9.55 0.00 44.11 4.93
6 7 4.113354 CCTTACTTTCAGGTAAGCTAGCG 58.887 47.826 9.55 0.00 44.11 4.26
7 8 5.340439 TCCTTACTTTCAGGTAAGCTAGC 57.660 43.478 6.62 6.62 44.11 3.42
8 9 6.039493 TCGATCCTTACTTTCAGGTAAGCTAG 59.961 42.308 8.38 0.00 44.11 3.42
9 10 5.889853 TCGATCCTTACTTTCAGGTAAGCTA 59.110 40.000 8.38 1.33 44.11 3.32
10 11 4.710375 TCGATCCTTACTTTCAGGTAAGCT 59.290 41.667 8.38 0.00 44.11 3.74
11 12 5.007385 TCGATCCTTACTTTCAGGTAAGC 57.993 43.478 8.38 0.00 44.11 3.09
12 13 6.631962 AGTTCGATCCTTACTTTCAGGTAAG 58.368 40.000 7.24 7.24 44.69 2.34
13 14 6.600882 AGTTCGATCCTTACTTTCAGGTAA 57.399 37.500 0.00 0.00 32.59 2.85
14 15 6.888632 AGTAGTTCGATCCTTACTTTCAGGTA 59.111 38.462 0.00 0.00 32.59 3.08
15 16 5.715753 AGTAGTTCGATCCTTACTTTCAGGT 59.284 40.000 0.00 0.00 32.59 4.00
16 17 6.037098 CAGTAGTTCGATCCTTACTTTCAGG 58.963 44.000 0.00 0.00 0.00 3.86
17 18 6.622549 ACAGTAGTTCGATCCTTACTTTCAG 58.377 40.000 0.00 0.00 0.00 3.02
18 19 6.585695 ACAGTAGTTCGATCCTTACTTTCA 57.414 37.500 0.00 0.00 0.00 2.69
19 20 7.886405 AAACAGTAGTTCGATCCTTACTTTC 57.114 36.000 0.00 0.00 36.84 2.62
20 21 8.672823 AAAAACAGTAGTTCGATCCTTACTTT 57.327 30.769 0.00 0.00 36.84 2.66
56 57 9.807649 CAAAAATGAATAGATCGGGAATTTTCT 57.192 29.630 8.56 0.00 0.00 2.52
57 58 9.801873 TCAAAAATGAATAGATCGGGAATTTTC 57.198 29.630 8.56 0.00 0.00 2.29
59 60 9.971922 GATCAAAAATGAATAGATCGGGAATTT 57.028 29.630 0.00 0.00 0.00 1.82
60 61 9.135189 TGATCAAAAATGAATAGATCGGGAATT 57.865 29.630 0.00 0.00 38.28 2.17
61 62 8.696043 TGATCAAAAATGAATAGATCGGGAAT 57.304 30.769 0.00 0.00 38.28 3.01
62 63 8.570488 CATGATCAAAAATGAATAGATCGGGAA 58.430 33.333 0.00 0.00 38.28 3.97
63 64 7.938490 TCATGATCAAAAATGAATAGATCGGGA 59.062 33.333 0.00 0.00 38.28 5.14
64 65 8.019669 GTCATGATCAAAAATGAATAGATCGGG 58.980 37.037 0.00 0.00 38.28 5.14
65 66 8.562052 TGTCATGATCAAAAATGAATAGATCGG 58.438 33.333 0.00 0.00 38.28 4.18
66 67 9.595357 CTGTCATGATCAAAAATGAATAGATCG 57.405 33.333 0.00 0.00 38.28 3.69
72 73 9.630098 GTTGTACTGTCATGATCAAAAATGAAT 57.370 29.630 0.00 0.00 34.70 2.57
73 74 7.802720 CGTTGTACTGTCATGATCAAAAATGAA 59.197 33.333 0.00 0.00 34.70 2.57
74 75 7.172361 TCGTTGTACTGTCATGATCAAAAATGA 59.828 33.333 0.00 0.00 0.00 2.57
75 76 7.297391 TCGTTGTACTGTCATGATCAAAAATG 58.703 34.615 0.00 0.00 0.00 2.32
76 77 7.433708 TCGTTGTACTGTCATGATCAAAAAT 57.566 32.000 0.00 0.00 0.00 1.82
77 78 6.852858 TCGTTGTACTGTCATGATCAAAAA 57.147 33.333 0.00 0.00 0.00 1.94
78 79 6.852858 TTCGTTGTACTGTCATGATCAAAA 57.147 33.333 0.00 0.00 0.00 2.44
79 80 8.716646 ATATTCGTTGTACTGTCATGATCAAA 57.283 30.769 0.00 0.00 0.00 2.69
80 81 7.978975 TGATATTCGTTGTACTGTCATGATCAA 59.021 33.333 0.00 0.00 0.00 2.57
81 82 7.488322 TGATATTCGTTGTACTGTCATGATCA 58.512 34.615 0.00 0.00 0.00 2.92
82 83 7.862873 TCTGATATTCGTTGTACTGTCATGATC 59.137 37.037 0.00 0.00 0.00 2.92
83 84 7.716612 TCTGATATTCGTTGTACTGTCATGAT 58.283 34.615 0.00 0.00 0.00 2.45
84 85 7.095695 TCTGATATTCGTTGTACTGTCATGA 57.904 36.000 0.00 0.00 0.00 3.07
85 86 7.755582 TTCTGATATTCGTTGTACTGTCATG 57.244 36.000 0.00 0.00 0.00 3.07
86 87 8.948631 ATTTCTGATATTCGTTGTACTGTCAT 57.051 30.769 0.00 0.00 0.00 3.06
87 88 9.863845 TTATTTCTGATATTCGTTGTACTGTCA 57.136 29.630 0.00 0.00 0.00 3.58
113 114 9.915629 GTCTACGGATCTTGATGTAATTTCTAT 57.084 33.333 0.00 0.00 0.00 1.98
114 115 8.358148 GGTCTACGGATCTTGATGTAATTTCTA 58.642 37.037 0.00 0.00 0.00 2.10
115 116 7.147724 TGGTCTACGGATCTTGATGTAATTTCT 60.148 37.037 0.00 0.00 0.00 2.52
116 117 6.984474 TGGTCTACGGATCTTGATGTAATTTC 59.016 38.462 0.00 0.00 0.00 2.17
117 118 6.761714 GTGGTCTACGGATCTTGATGTAATTT 59.238 38.462 0.00 0.00 0.00 1.82
118 119 6.281405 GTGGTCTACGGATCTTGATGTAATT 58.719 40.000 0.00 0.00 0.00 1.40
119 120 5.221461 GGTGGTCTACGGATCTTGATGTAAT 60.221 44.000 0.00 0.00 0.00 1.89
120 121 4.098960 GGTGGTCTACGGATCTTGATGTAA 59.901 45.833 0.00 0.00 0.00 2.41
121 122 3.635373 GGTGGTCTACGGATCTTGATGTA 59.365 47.826 0.00 0.00 0.00 2.29
122 123 2.431057 GGTGGTCTACGGATCTTGATGT 59.569 50.000 0.00 0.00 0.00 3.06
123 124 2.695666 AGGTGGTCTACGGATCTTGATG 59.304 50.000 0.00 0.00 0.00 3.07
124 125 3.033659 AGGTGGTCTACGGATCTTGAT 57.966 47.619 0.00 0.00 0.00 2.57
125 126 2.526888 AGGTGGTCTACGGATCTTGA 57.473 50.000 0.00 0.00 0.00 3.02
126 127 2.034812 GCTAGGTGGTCTACGGATCTTG 59.965 54.545 0.00 0.00 0.00 3.02
127 128 2.308690 GCTAGGTGGTCTACGGATCTT 58.691 52.381 0.00 0.00 0.00 2.40
128 129 1.814634 CGCTAGGTGGTCTACGGATCT 60.815 57.143 0.00 0.00 0.00 2.75
129 130 0.592148 CGCTAGGTGGTCTACGGATC 59.408 60.000 0.00 0.00 0.00 3.36
130 131 0.822532 CCGCTAGGTGGTCTACGGAT 60.823 60.000 0.00 0.00 41.13 4.18
131 132 1.452651 CCGCTAGGTGGTCTACGGA 60.453 63.158 0.00 0.00 41.13 4.69
132 133 3.117372 CCGCTAGGTGGTCTACGG 58.883 66.667 0.00 0.00 36.81 4.02
133 134 2.412112 GCCGCTAGGTGGTCTACG 59.588 66.667 0.00 0.00 40.50 3.51
134 135 2.412112 CGCCGCTAGGTGGTCTAC 59.588 66.667 0.00 0.00 44.11 2.59
141 142 2.044650 TGGTAGTCGCCGCTAGGT 60.045 61.111 0.00 0.00 40.50 3.08
142 143 2.722487 CTGGTAGTCGCCGCTAGG 59.278 66.667 0.00 0.00 41.62 3.02
143 144 2.026301 GCTGGTAGTCGCCGCTAG 59.974 66.667 0.00 0.00 0.00 3.42
144 145 2.752640 TGCTGGTAGTCGCCGCTA 60.753 61.111 0.00 0.00 0.00 4.26
145 146 4.436998 GTGCTGGTAGTCGCCGCT 62.437 66.667 0.00 0.00 0.00 5.52
146 147 4.436998 AGTGCTGGTAGTCGCCGC 62.437 66.667 0.00 0.00 0.00 6.53
147 148 2.486636 TTCAGTGCTGGTAGTCGCCG 62.487 60.000 0.00 0.00 0.00 6.46
148 149 0.320421 TTTCAGTGCTGGTAGTCGCC 60.320 55.000 0.00 0.00 0.00 5.54
149 150 1.071605 CTTTCAGTGCTGGTAGTCGC 58.928 55.000 0.00 0.00 0.00 5.19
150 151 1.071605 GCTTTCAGTGCTGGTAGTCG 58.928 55.000 0.00 0.00 0.00 4.18
151 152 1.071605 CGCTTTCAGTGCTGGTAGTC 58.928 55.000 0.00 0.00 0.00 2.59
152 153 0.679505 TCGCTTTCAGTGCTGGTAGT 59.320 50.000 0.00 0.00 0.00 2.73
153 154 1.354040 CTCGCTTTCAGTGCTGGTAG 58.646 55.000 0.00 0.00 0.00 3.18
154 155 0.670546 GCTCGCTTTCAGTGCTGGTA 60.671 55.000 0.00 0.00 0.00 3.25
155 156 1.963338 GCTCGCTTTCAGTGCTGGT 60.963 57.895 0.00 0.00 0.00 4.00
156 157 2.684843 GGCTCGCTTTCAGTGCTGG 61.685 63.158 0.00 0.00 0.00 4.85
157 158 2.866028 GGCTCGCTTTCAGTGCTG 59.134 61.111 0.00 0.00 0.00 4.41
158 159 2.715532 TTCGGCTCGCTTTCAGTGCT 62.716 55.000 0.00 0.00 0.00 4.40
159 160 2.233007 CTTCGGCTCGCTTTCAGTGC 62.233 60.000 0.00 0.00 0.00 4.40
160 161 1.630244 CCTTCGGCTCGCTTTCAGTG 61.630 60.000 0.00 0.00 0.00 3.66
161 162 1.374758 CCTTCGGCTCGCTTTCAGT 60.375 57.895 0.00 0.00 0.00 3.41
162 163 2.744768 GCCTTCGGCTCGCTTTCAG 61.745 63.158 0.00 0.00 46.69 3.02
163 164 2.742372 GCCTTCGGCTCGCTTTCA 60.742 61.111 0.00 0.00 46.69 2.69
184 185 4.530857 GAGGGGCGATGACGGTGG 62.531 72.222 0.00 0.00 40.15 4.61
185 186 4.530857 GGAGGGGCGATGACGGTG 62.531 72.222 0.00 0.00 40.15 4.94
187 188 3.521529 GATGGAGGGGCGATGACGG 62.522 68.421 0.00 0.00 40.15 4.79
188 189 2.029666 GATGGAGGGGCGATGACG 59.970 66.667 0.00 0.00 42.93 4.35
189 190 1.227674 GTGATGGAGGGGCGATGAC 60.228 63.158 0.00 0.00 0.00 3.06
190 191 2.443394 GGTGATGGAGGGGCGATGA 61.443 63.158 0.00 0.00 0.00 2.92
191 192 2.111878 GGTGATGGAGGGGCGATG 59.888 66.667 0.00 0.00 0.00 3.84
192 193 3.550431 CGGTGATGGAGGGGCGAT 61.550 66.667 0.00 0.00 0.00 4.58
195 196 4.864334 CTGCGGTGATGGAGGGGC 62.864 72.222 0.00 0.00 0.00 5.80
196 197 3.391665 GACTGCGGTGATGGAGGGG 62.392 68.421 0.80 0.00 0.00 4.79
197 198 2.187946 GACTGCGGTGATGGAGGG 59.812 66.667 0.80 0.00 0.00 4.30
198 199 2.202797 CGACTGCGGTGATGGAGG 60.203 66.667 0.80 0.00 0.00 4.30
208 209 2.972505 AAGTTGTGCCCGACTGCG 60.973 61.111 0.00 0.00 35.40 5.18
209 210 2.639286 CAAGTTGTGCCCGACTGC 59.361 61.111 0.00 0.00 35.40 4.40
226 227 0.391130 TCCCGATTGTGTGCTACAGC 60.391 55.000 0.00 0.00 41.10 4.40
227 228 2.093306 TTCCCGATTGTGTGCTACAG 57.907 50.000 0.00 0.00 41.10 2.74
228 229 2.552599 TTTCCCGATTGTGTGCTACA 57.447 45.000 0.00 0.00 37.56 2.74
229 230 2.030457 CGATTTCCCGATTGTGTGCTAC 59.970 50.000 0.00 0.00 0.00 3.58
230 231 2.276201 CGATTTCCCGATTGTGTGCTA 58.724 47.619 0.00 0.00 0.00 3.49
231 232 1.086696 CGATTTCCCGATTGTGTGCT 58.913 50.000 0.00 0.00 0.00 4.40
232 233 0.802494 ACGATTTCCCGATTGTGTGC 59.198 50.000 0.00 0.00 0.00 4.57
233 234 1.060553 CGACGATTTCCCGATTGTGTG 59.939 52.381 0.00 0.00 0.00 3.82
234 235 1.337447 ACGACGATTTCCCGATTGTGT 60.337 47.619 0.00 0.00 0.00 3.72
235 236 1.060553 CACGACGATTTCCCGATTGTG 59.939 52.381 0.00 0.00 0.00 3.33
236 237 1.337447 ACACGACGATTTCCCGATTGT 60.337 47.619 0.00 0.00 0.00 2.71
237 238 1.355971 ACACGACGATTTCCCGATTG 58.644 50.000 0.00 0.00 0.00 2.67
238 239 2.088950 AACACGACGATTTCCCGATT 57.911 45.000 0.00 0.00 0.00 3.34
239 240 2.945447 TAACACGACGATTTCCCGAT 57.055 45.000 0.00 0.00 0.00 4.18
240 241 2.598589 CTTAACACGACGATTTCCCGA 58.401 47.619 0.00 0.00 0.00 5.14
241 242 1.657094 CCTTAACACGACGATTTCCCG 59.343 52.381 0.00 0.00 0.00 5.14
242 243 1.395954 GCCTTAACACGACGATTTCCC 59.604 52.381 0.00 0.00 0.00 3.97
243 244 1.395954 GGCCTTAACACGACGATTTCC 59.604 52.381 0.00 0.00 0.00 3.13
244 245 1.395954 GGGCCTTAACACGACGATTTC 59.604 52.381 0.84 0.00 0.00 2.17
245 246 1.445871 GGGCCTTAACACGACGATTT 58.554 50.000 0.84 0.00 0.00 2.17
246 247 0.392060 GGGGCCTTAACACGACGATT 60.392 55.000 0.84 0.00 0.00 3.34
247 248 1.219935 GGGGCCTTAACACGACGAT 59.780 57.895 0.84 0.00 0.00 3.73
248 249 2.658422 GGGGCCTTAACACGACGA 59.342 61.111 0.84 0.00 0.00 4.20
249 250 2.211619 TACGGGGCCTTAACACGACG 62.212 60.000 0.84 0.00 0.00 5.12
250 251 0.459063 CTACGGGGCCTTAACACGAC 60.459 60.000 0.84 0.00 0.00 4.34
251 252 1.606885 CCTACGGGGCCTTAACACGA 61.607 60.000 0.84 0.00 0.00 4.35
252 253 1.153509 CCTACGGGGCCTTAACACG 60.154 63.158 0.84 0.00 0.00 4.49
253 254 0.107993 GTCCTACGGGGCCTTAACAC 60.108 60.000 0.84 0.00 34.39 3.32
254 255 2.289840 GTCCTACGGGGCCTTAACA 58.710 57.895 0.84 0.00 34.39 2.41
263 264 4.814294 GTGCGCTGGTCCTACGGG 62.814 72.222 9.73 0.00 0.00 5.28
264 265 4.814294 GGTGCGCTGGTCCTACGG 62.814 72.222 9.73 0.00 0.00 4.02
265 266 3.989698 CTGGTGCGCTGGTCCTACG 62.990 68.421 9.73 0.30 0.00 3.51
266 267 2.125512 CTGGTGCGCTGGTCCTAC 60.126 66.667 9.73 0.00 0.00 3.18
267 268 1.911269 TTCTGGTGCGCTGGTCCTA 60.911 57.895 9.73 0.00 0.00 2.94
268 269 3.241530 TTCTGGTGCGCTGGTCCT 61.242 61.111 9.73 0.00 0.00 3.85
269 270 3.050275 GTTCTGGTGCGCTGGTCC 61.050 66.667 9.73 6.75 0.00 4.46
270 271 2.280797 TGTTCTGGTGCGCTGGTC 60.281 61.111 9.73 0.00 0.00 4.02
271 272 2.281070 CTGTTCTGGTGCGCTGGT 60.281 61.111 9.73 0.00 0.00 4.00
272 273 3.730761 GCTGTTCTGGTGCGCTGG 61.731 66.667 9.73 0.00 0.00 4.85
273 274 2.545596 TTGCTGTTCTGGTGCGCTG 61.546 57.895 9.73 0.00 0.00 5.18
274 275 2.203195 TTGCTGTTCTGGTGCGCT 60.203 55.556 9.73 0.00 0.00 5.92
275 276 2.050985 GTTGCTGTTCTGGTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
276 277 1.280746 CAGTTGCTGTTCTGGTGCG 59.719 57.895 0.00 0.00 0.00 5.34
277 278 1.656441 CCAGTTGCTGTTCTGGTGC 59.344 57.895 3.38 0.00 44.19 5.01
281 282 4.630894 TGTAAAACCAGTTGCTGTTCTG 57.369 40.909 0.00 0.00 0.00 3.02
282 283 4.887071 TCATGTAAAACCAGTTGCTGTTCT 59.113 37.500 0.00 0.00 0.00 3.01
283 284 5.181690 TCATGTAAAACCAGTTGCTGTTC 57.818 39.130 0.00 0.00 0.00 3.18
284 285 5.359576 TCTTCATGTAAAACCAGTTGCTGTT 59.640 36.000 0.00 0.00 0.00 3.16
285 286 4.887071 TCTTCATGTAAAACCAGTTGCTGT 59.113 37.500 0.00 0.00 0.00 4.40
286 287 5.437289 TCTTCATGTAAAACCAGTTGCTG 57.563 39.130 0.00 0.00 0.00 4.41
287 288 6.655078 ATTCTTCATGTAAAACCAGTTGCT 57.345 33.333 0.00 0.00 0.00 3.91
288 289 7.713764 AAATTCTTCATGTAAAACCAGTTGC 57.286 32.000 0.00 0.00 0.00 4.17
332 333 6.689241 TGTGCAACATGAAACGTAAACTTTAG 59.311 34.615 0.00 0.00 45.67 1.85
333 334 6.552629 TGTGCAACATGAAACGTAAACTTTA 58.447 32.000 0.00 0.00 45.67 1.85
334 335 5.403246 TGTGCAACATGAAACGTAAACTTT 58.597 33.333 0.00 0.00 45.67 2.66
364 366 8.472007 AAATCACAATACTTGACTACCCAAAA 57.528 30.769 0.00 0.00 0.00 2.44
408 414 3.062786 GCGCAATGCAATACTAGCG 57.937 52.632 5.91 11.57 46.99 4.26
469 477 1.257743 CACCTCGAAGACCTTCCTGA 58.742 55.000 4.36 0.00 36.27 3.86
530 539 6.644592 GTCTATTTCTCATACATCTGCTCCAC 59.355 42.308 0.00 0.00 0.00 4.02
546 555 1.202582 AGCAGCGTCACGTCTATTTCT 59.797 47.619 0.00 0.00 0.00 2.52
613 624 2.601266 CGCTAACACAAACCGGAACTTG 60.601 50.000 9.46 11.30 0.00 3.16
614 625 1.600485 CGCTAACACAAACCGGAACTT 59.400 47.619 9.46 0.00 0.00 2.66
615 626 1.223187 CGCTAACACAAACCGGAACT 58.777 50.000 9.46 0.00 0.00 3.01
616 627 0.939419 ACGCTAACACAAACCGGAAC 59.061 50.000 9.46 0.00 0.00 3.62
617 628 1.219646 GACGCTAACACAAACCGGAA 58.780 50.000 9.46 0.00 0.00 4.30
634 645 6.504180 CGTTTCAATTGTTTTCACTTCACGAC 60.504 38.462 5.13 0.00 0.00 4.34
719 1582 7.176285 TCAGCTGTTTTAACATTGAAAATGC 57.824 32.000 14.67 0.00 38.41 3.56
726 1589 6.366877 CCCAGATTTCAGCTGTTTTAACATTG 59.633 38.462 14.67 2.52 38.41 2.82
755 1656 4.284234 ACTTCTTGGGCAATATTTTGTGCT 59.716 37.500 0.00 0.00 40.70 4.40
756 1657 4.389687 CACTTCTTGGGCAATATTTTGTGC 59.610 41.667 0.00 0.00 40.14 4.57
757 1658 4.389687 GCACTTCTTGGGCAATATTTTGTG 59.610 41.667 0.00 0.00 46.29 3.33
787 1735 9.060347 TGCTAGTTATACGTACTTGCTAGTTAT 57.940 33.333 19.24 1.44 42.34 1.89
789 1737 7.325660 TGCTAGTTATACGTACTTGCTAGTT 57.674 36.000 19.24 0.00 42.34 2.24
790 1738 6.932356 TGCTAGTTATACGTACTTGCTAGT 57.068 37.500 19.24 6.00 42.34 2.57
791 1739 7.637229 TCTTGCTAGTTATACGTACTTGCTAG 58.363 38.462 19.99 19.99 42.97 3.42
793 1741 6.446781 TCTTGCTAGTTATACGTACTTGCT 57.553 37.500 19.24 9.44 42.34 3.91
794 1742 6.020041 GGTTCTTGCTAGTTATACGTACTTGC 60.020 42.308 14.03 14.03 42.25 4.01
795 1743 7.220300 CAGGTTCTTGCTAGTTATACGTACTTG 59.780 40.741 0.00 0.00 0.00 3.16
796 1744 7.256286 CAGGTTCTTGCTAGTTATACGTACTT 58.744 38.462 0.00 0.00 0.00 2.24
800 1748 4.679905 GCCAGGTTCTTGCTAGTTATACGT 60.680 45.833 0.00 0.00 0.00 3.57
802 1750 4.811557 CAGCCAGGTTCTTGCTAGTTATAC 59.188 45.833 0.00 0.00 30.53 1.47
818 1784 2.831742 ATTGCGCCATCAGCCAGG 60.832 61.111 4.18 0.00 38.78 4.45
948 1933 1.697284 TGCTTTGCCAATGGTGTGTA 58.303 45.000 0.00 0.00 0.00 2.90
983 1976 2.046283 CATTGTGTGCTGAACTGCTG 57.954 50.000 5.42 0.00 0.00 4.41
1060 2053 1.492319 TACGCCGTGCACAAGAACAC 61.492 55.000 18.64 0.00 0.00 3.32
1410 2970 4.489771 GCATGGGCGTGGTAGGCT 62.490 66.667 0.00 0.00 36.85 4.58
1914 3510 0.467384 CTTCAGATGGGATCAGCGGT 59.533 55.000 0.00 0.00 33.94 5.68
2046 3642 2.095252 GTCCAGAAGCTCGTTCGCC 61.095 63.158 0.00 0.00 40.49 5.54
2075 3671 3.151022 CCCTCCGGGTCAGCTCTC 61.151 72.222 0.00 0.00 38.25 3.20
2316 3918 1.474879 TGCGCGATATTCCCGATGATA 59.525 47.619 12.10 0.00 0.00 2.15
2456 4064 6.381801 CCTTGTCTAAAAATGCCAACTAGTG 58.618 40.000 0.00 0.00 0.00 2.74
2822 4639 9.053135 CATGACAAATTTTGACAACAACAAAAG 57.947 29.630 15.81 0.00 45.74 2.27
2823 4640 8.562892 ACATGACAAATTTTGACAACAACAAAA 58.437 25.926 15.81 0.00 46.29 2.44
2824 4641 8.092521 ACATGACAAATTTTGACAACAACAAA 57.907 26.923 15.81 0.00 38.68 2.83
2825 4642 7.664082 ACATGACAAATTTTGACAACAACAA 57.336 28.000 15.81 0.00 38.68 2.83
2958 4788 6.324042 TGCAATGTGTACATCATGTTTCATC 58.676 36.000 0.00 0.00 35.10 2.92


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

AutoCloner maintained by Alex Coulton.