Multiple sequence alignment - TraesCS7A01G529100

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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 TraesCS7A01G529100 chr7A 100.000 3246 0 0 1 3246 709138910 709135665 0.000000e+00 5995.0
1 TraesCS7A01G529100 chr7A 91.707 205 15 2 287 491 708788969 708789171 1.910000e-72 283.0
2 TraesCS7A01G529100 chr2A 96.563 2968 86 5 287 3246 694744445 694741486 0.000000e+00 4902.0
3 TraesCS7A01G529100 chr2A 94.503 382 20 1 287 668 694745571 694745191 3.610000e-164 588.0
4 TraesCS7A01G529100 chr5A 95.724 2970 98 12 288 3246 262472483 262469532 0.000000e+00 4754.0
5 TraesCS7A01G529100 chr5A 97.895 285 6 0 847 1131 705868591 705868875 8.090000e-136 494.0
6 TraesCS7A01G529100 chr1A 95.682 2177 83 4 291 2459 446217430 446219603 0.000000e+00 3489.0
7 TraesCS7A01G529100 chr1A 98.246 285 5 0 847 1131 444168370 444168086 1.740000e-137 499.0
8 TraesCS7A01G529100 chr3B 95.216 2111 66 4 1165 3246 73032259 73034363 0.000000e+00 3306.0
9 TraesCS7A01G529100 chr3B 96.959 1085 33 0 1165 2249 452562180 452561096 0.000000e+00 1821.0
10 TraesCS7A01G529100 chr3B 98.246 285 5 0 847 1131 73031977 73032261 1.740000e-137 499.0
11 TraesCS7A01G529100 chr3B 93.171 205 14 0 291 495 765053455 765053251 5.260000e-78 302.0
12 TraesCS7A01G529100 chr1D 96.045 1694 59 3 1556 3246 97786081 97784393 0.000000e+00 2750.0
13 TraesCS7A01G529100 chr1D 95.322 342 16 0 609 950 117323607 117323266 7.920000e-151 544.0
14 TraesCS7A01G529100 chr5D 95.455 1694 48 6 1556 3246 309068879 309067212 0.000000e+00 2675.0
15 TraesCS7A01G529100 chr5D 95.906 342 14 0 609 950 309069215 309068874 3.660000e-154 555.0
16 TraesCS7A01G529100 chr4D 95.455 1694 48 6 1556 3246 77912520 77914187 0.000000e+00 2675.0
17 TraesCS7A01G529100 chr4D 95.601 341 15 0 610 950 77912185 77912525 6.120000e-152 547.0
18 TraesCS7A01G529100 chr6D 95.396 1694 49 6 1556 3246 56195689 56197356 0.000000e+00 2669.0
19 TraesCS7A01G529100 chr6D 95.280 1695 47 10 1556 3246 75302472 75300807 0.000000e+00 2656.0
20 TraesCS7A01G529100 chr6D 95.322 342 16 0 609 950 75302808 75302467 7.920000e-151 544.0
21 TraesCS7A01G529100 chr3D 95.269 1691 51 6 1559 3246 149698763 149697099 0.000000e+00 2652.0
22 TraesCS7A01G529100 chr3D 95.614 342 15 0 609 950 149699102 149698761 1.700000e-152 549.0
23 TraesCS7A01G529100 chr5B 94.946 1306 65 1 1556 2861 563525707 563524403 0.000000e+00 2045.0
24 TraesCS7A01G529100 chr5B 92.084 379 29 1 572 950 563526079 563525702 1.710000e-147 532.0
25 TraesCS7A01G529100 chr4B 96.774 1085 35 0 1165 2249 665901147 665902231 0.000000e+00 1810.0
26 TraesCS7A01G529100 chr4B 96.682 1085 36 0 1165 2249 629908303 629909387 0.000000e+00 1805.0
27 TraesCS7A01G529100 chr4B 96.140 285 11 0 847 1131 629908021 629908305 1.760000e-127 466.0
28 TraesCS7A01G529100 chr4A 97.880 283 6 0 849 1131 36003525 36003243 1.050000e-134 490.0
29 TraesCS7A01G529100 chr2B 96.491 285 10 0 847 1131 553880892 553881176 3.790000e-129 472.0
30 TraesCS7A01G529100 chr2B 94.146 205 12 0 291 495 71314348 71314144 2.430000e-81 313.0
31 TraesCS7A01G529100 chr2B 88.312 77 7 2 496 572 98678270 98678344 1.240000e-14 91.6
32 TraesCS7A01G529100 chr1B 94.146 205 12 0 291 495 307205960 307206164 2.430000e-81 313.0
33 TraesCS7A01G529100 chr6B 92.823 209 14 1 287 495 562540156 562539949 5.260000e-78 302.0


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 TraesCS7A01G529100 chr7A 709135665 709138910 3245 True 5995.0 5995 100.0000 1 3246 1 chr7A.!!$R1 3245
1 TraesCS7A01G529100 chr2A 694741486 694745571 4085 True 2745.0 4902 95.5330 287 3246 2 chr2A.!!$R1 2959
2 TraesCS7A01G529100 chr5A 262469532 262472483 2951 True 4754.0 4754 95.7240 288 3246 1 chr5A.!!$R1 2958
3 TraesCS7A01G529100 chr1A 446217430 446219603 2173 False 3489.0 3489 95.6820 291 2459 1 chr1A.!!$F1 2168
4 TraesCS7A01G529100 chr3B 73031977 73034363 2386 False 1902.5 3306 96.7310 847 3246 2 chr3B.!!$F1 2399
5 TraesCS7A01G529100 chr3B 452561096 452562180 1084 True 1821.0 1821 96.9590 1165 2249 1 chr3B.!!$R1 1084
6 TraesCS7A01G529100 chr1D 97784393 97786081 1688 True 2750.0 2750 96.0450 1556 3246 1 chr1D.!!$R1 1690
7 TraesCS7A01G529100 chr5D 309067212 309069215 2003 True 1615.0 2675 95.6805 609 3246 2 chr5D.!!$R1 2637
8 TraesCS7A01G529100 chr4D 77912185 77914187 2002 False 1611.0 2675 95.5280 610 3246 2 chr4D.!!$F1 2636
9 TraesCS7A01G529100 chr6D 56195689 56197356 1667 False 2669.0 2669 95.3960 1556 3246 1 chr6D.!!$F1 1690
10 TraesCS7A01G529100 chr6D 75300807 75302808 2001 True 1600.0 2656 95.3010 609 3246 2 chr6D.!!$R1 2637
11 TraesCS7A01G529100 chr3D 149697099 149699102 2003 True 1600.5 2652 95.4415 609 3246 2 chr3D.!!$R1 2637
12 TraesCS7A01G529100 chr5B 563524403 563526079 1676 True 1288.5 2045 93.5150 572 2861 2 chr5B.!!$R1 2289
13 TraesCS7A01G529100 chr4B 665901147 665902231 1084 False 1810.0 1810 96.7740 1165 2249 1 chr4B.!!$F1 1084
14 TraesCS7A01G529100 chr4B 629908021 629909387 1366 False 1135.5 1805 96.4110 847 2249 2 chr4B.!!$F2 1402

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
67 68 0.108585 TTGCTCTCAACCAGGGACAC 59.891 55.0 0.00 0.0 0.00 3.67 F
110 111 0.249657 CCGAGGTAGCATGAGCCTTC 60.250 60.0 0.00 0.0 43.56 3.46 F
111 112 0.461548 CGAGGTAGCATGAGCCTTCA 59.538 55.0 0.00 0.0 43.56 3.02 F
1751 2885 0.892814 TCGCCACCATGTTCATGCAA 60.893 50.0 7.21 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 2842 1.585651 AACACCCAACCCCAAGGACA 61.586 55.000 0.00 0.0 36.73 4.02 R
1780 2914 2.550277 TGCATGGTCTTCTCCTCCTA 57.450 50.000 0.00 0.0 0.00 2.94 R
1878 3012 7.890655 AGTCCTTTTGCTATCTCCTACAAATTT 59.109 33.333 0.00 0.0 32.50 1.82 R
2685 3869 1.554160 AGAGAATCACAGTGCCCTCAG 59.446 52.381 14.81 0.0 37.82 3.35 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
22 23 5.479716 AAAACTAGAAACACTGACCAACG 57.520 39.130 0.00 0.00 0.00 4.10
23 24 2.480845 ACTAGAAACACTGACCAACGC 58.519 47.619 0.00 0.00 0.00 4.84
24 25 2.159014 ACTAGAAACACTGACCAACGCA 60.159 45.455 0.00 0.00 0.00 5.24
25 26 1.967319 AGAAACACTGACCAACGCAT 58.033 45.000 0.00 0.00 0.00 4.73
26 27 2.297701 AGAAACACTGACCAACGCATT 58.702 42.857 0.00 0.00 0.00 3.56
27 28 2.687935 AGAAACACTGACCAACGCATTT 59.312 40.909 0.00 0.00 0.00 2.32
28 29 3.130340 AGAAACACTGACCAACGCATTTT 59.870 39.130 0.00 0.00 0.00 1.82
29 30 4.336993 AGAAACACTGACCAACGCATTTTA 59.663 37.500 0.00 0.00 0.00 1.52
30 31 3.896648 ACACTGACCAACGCATTTTAG 57.103 42.857 0.00 0.00 0.00 1.85
31 32 2.031157 ACACTGACCAACGCATTTTAGC 60.031 45.455 0.00 0.00 0.00 3.09
32 33 1.539827 ACTGACCAACGCATTTTAGCC 59.460 47.619 0.00 0.00 0.00 3.93
33 34 1.539388 CTGACCAACGCATTTTAGCCA 59.461 47.619 0.00 0.00 0.00 4.75
34 35 1.268352 TGACCAACGCATTTTAGCCAC 59.732 47.619 0.00 0.00 0.00 5.01
35 36 1.268352 GACCAACGCATTTTAGCCACA 59.732 47.619 0.00 0.00 0.00 4.17
36 37 1.892474 ACCAACGCATTTTAGCCACAT 59.108 42.857 0.00 0.00 0.00 3.21
37 38 3.085533 ACCAACGCATTTTAGCCACATA 58.914 40.909 0.00 0.00 0.00 2.29
38 39 3.699038 ACCAACGCATTTTAGCCACATAT 59.301 39.130 0.00 0.00 0.00 1.78
39 40 4.884744 ACCAACGCATTTTAGCCACATATA 59.115 37.500 0.00 0.00 0.00 0.86
40 41 5.358442 ACCAACGCATTTTAGCCACATATAA 59.642 36.000 0.00 0.00 0.00 0.98
41 42 6.127591 ACCAACGCATTTTAGCCACATATAAA 60.128 34.615 0.00 0.00 0.00 1.40
42 43 6.922957 CCAACGCATTTTAGCCACATATAAAT 59.077 34.615 0.00 0.00 0.00 1.40
43 44 7.096106 CCAACGCATTTTAGCCACATATAAATG 60.096 37.037 0.00 0.00 38.55 2.32
45 46 7.488322 ACGCATTTTAGCCACATATAAATGTT 58.512 30.769 0.00 0.00 44.07 2.71
46 47 7.647715 ACGCATTTTAGCCACATATAAATGTTC 59.352 33.333 0.00 0.00 44.07 3.18
47 48 7.862372 CGCATTTTAGCCACATATAAATGTTCT 59.138 33.333 0.00 0.00 44.07 3.01
48 49 9.533253 GCATTTTAGCCACATATAAATGTTCTT 57.467 29.630 0.00 0.00 44.07 2.52
51 52 8.925161 TTTAGCCACATATAAATGTTCTTTGC 57.075 30.769 0.00 0.00 44.07 3.68
52 53 6.780457 AGCCACATATAAATGTTCTTTGCT 57.220 33.333 0.00 0.00 44.07 3.91
53 54 6.799512 AGCCACATATAAATGTTCTTTGCTC 58.200 36.000 0.00 0.00 44.07 4.26
54 55 6.604795 AGCCACATATAAATGTTCTTTGCTCT 59.395 34.615 0.00 0.00 44.07 4.09
55 56 6.914757 GCCACATATAAATGTTCTTTGCTCTC 59.085 38.462 0.00 0.00 44.07 3.20
56 57 7.415541 GCCACATATAAATGTTCTTTGCTCTCA 60.416 37.037 0.00 0.00 44.07 3.27
57 58 8.461222 CCACATATAAATGTTCTTTGCTCTCAA 58.539 33.333 0.00 0.00 44.07 3.02
58 59 9.282247 CACATATAAATGTTCTTTGCTCTCAAC 57.718 33.333 0.00 0.00 44.07 3.18
59 60 8.462016 ACATATAAATGTTCTTTGCTCTCAACC 58.538 33.333 0.00 0.00 44.07 3.77
60 61 6.899393 ATAAATGTTCTTTGCTCTCAACCA 57.101 33.333 0.00 0.00 30.75 3.67
61 62 4.843220 AATGTTCTTTGCTCTCAACCAG 57.157 40.909 0.00 0.00 30.75 4.00
62 63 2.575532 TGTTCTTTGCTCTCAACCAGG 58.424 47.619 0.00 0.00 30.75 4.45
63 64 1.882623 GTTCTTTGCTCTCAACCAGGG 59.117 52.381 0.00 0.00 30.75 4.45
64 65 1.434188 TCTTTGCTCTCAACCAGGGA 58.566 50.000 0.00 0.00 30.75 4.20
65 66 1.072331 TCTTTGCTCTCAACCAGGGAC 59.928 52.381 0.00 0.00 30.75 4.46
66 67 0.843309 TTTGCTCTCAACCAGGGACA 59.157 50.000 0.00 0.00 30.75 4.02
67 68 0.108585 TTGCTCTCAACCAGGGACAC 59.891 55.000 0.00 0.00 0.00 3.67
68 69 1.053835 TGCTCTCAACCAGGGACACA 61.054 55.000 0.00 0.00 0.00 3.72
69 70 0.326264 GCTCTCAACCAGGGACACAT 59.674 55.000 0.00 0.00 0.00 3.21
70 71 1.677217 GCTCTCAACCAGGGACACATC 60.677 57.143 0.00 0.00 0.00 3.06
71 72 0.984230 TCTCAACCAGGGACACATCC 59.016 55.000 0.00 0.00 45.42 3.51
82 83 2.767505 GGACACATCCCCTTATAAGCG 58.232 52.381 6.99 0.00 39.39 4.68
83 84 2.367567 GGACACATCCCCTTATAAGCGA 59.632 50.000 6.99 5.11 39.39 4.93
84 85 3.555168 GGACACATCCCCTTATAAGCGAG 60.555 52.174 6.99 0.00 39.39 5.03
85 86 2.368875 ACACATCCCCTTATAAGCGAGG 59.631 50.000 6.99 8.56 0.00 4.63
86 87 1.348036 ACATCCCCTTATAAGCGAGGC 59.652 52.381 6.99 0.00 0.00 4.70
87 88 1.625818 CATCCCCTTATAAGCGAGGCT 59.374 52.381 6.99 0.00 42.56 4.58
88 89 1.339097 TCCCCTTATAAGCGAGGCTC 58.661 55.000 3.87 3.87 38.25 4.70
89 90 0.321996 CCCCTTATAAGCGAGGCTCC 59.678 60.000 9.32 1.69 38.25 4.70
90 91 0.321996 CCCTTATAAGCGAGGCTCCC 59.678 60.000 9.32 0.00 38.25 4.30
91 92 0.321996 CCTTATAAGCGAGGCTCCCC 59.678 60.000 9.32 0.00 38.25 4.81
92 93 0.321996 CTTATAAGCGAGGCTCCCCC 59.678 60.000 9.32 0.00 38.25 5.40
93 94 1.469335 TTATAAGCGAGGCTCCCCCG 61.469 60.000 9.32 0.00 38.25 5.73
94 95 2.361865 TATAAGCGAGGCTCCCCCGA 62.362 60.000 9.32 0.00 38.25 5.14
98 99 4.517934 CGAGGCTCCCCCGAGGTA 62.518 72.222 9.32 0.00 39.21 3.08
99 100 2.522193 GAGGCTCCCCCGAGGTAG 60.522 72.222 2.15 0.00 39.21 3.18
100 101 4.862823 AGGCTCCCCCGAGGTAGC 62.863 72.222 0.00 0.00 39.21 3.58
102 103 2.844839 GCTCCCCCGAGGTAGCAT 60.845 66.667 0.00 0.00 38.17 3.79
103 104 3.142393 CTCCCCCGAGGTAGCATG 58.858 66.667 0.00 0.00 36.75 4.06
104 105 1.457643 CTCCCCCGAGGTAGCATGA 60.458 63.158 0.00 0.00 36.75 3.07
105 106 1.457643 TCCCCCGAGGTAGCATGAG 60.458 63.158 0.00 0.00 36.75 2.90
106 107 2.423446 CCCCGAGGTAGCATGAGC 59.577 66.667 0.00 0.00 42.56 4.26
107 108 2.423446 CCCGAGGTAGCATGAGCC 59.577 66.667 0.00 0.00 43.56 4.70
108 109 2.136878 CCCGAGGTAGCATGAGCCT 61.137 63.158 0.00 0.00 43.56 4.58
109 110 1.690219 CCCGAGGTAGCATGAGCCTT 61.690 60.000 0.00 0.00 43.56 4.35
110 111 0.249657 CCGAGGTAGCATGAGCCTTC 60.250 60.000 0.00 0.00 43.56 3.46
111 112 0.461548 CGAGGTAGCATGAGCCTTCA 59.538 55.000 0.00 0.00 43.56 3.02
112 113 1.134699 CGAGGTAGCATGAGCCTTCAA 60.135 52.381 0.00 0.00 43.56 2.69
113 114 2.677902 CGAGGTAGCATGAGCCTTCAAA 60.678 50.000 0.00 0.00 43.56 2.69
114 115 3.549794 GAGGTAGCATGAGCCTTCAAAT 58.450 45.455 0.00 0.00 43.56 2.32
115 116 3.549794 AGGTAGCATGAGCCTTCAAATC 58.450 45.455 0.00 0.00 43.56 2.17
116 117 2.289002 GGTAGCATGAGCCTTCAAATCG 59.711 50.000 0.00 0.00 43.56 3.34
117 118 2.408271 AGCATGAGCCTTCAAATCGA 57.592 45.000 0.00 0.00 43.56 3.59
118 119 2.286872 AGCATGAGCCTTCAAATCGAG 58.713 47.619 0.00 0.00 43.56 4.04
119 120 2.093288 AGCATGAGCCTTCAAATCGAGA 60.093 45.455 0.00 0.00 43.56 4.04
120 121 2.287373 GCATGAGCCTTCAAATCGAGAG 59.713 50.000 0.00 0.00 36.78 3.20
121 122 3.790091 CATGAGCCTTCAAATCGAGAGA 58.210 45.455 0.00 0.00 40.16 3.10
122 123 3.803231 CATGAGCCTTCAAATCGAGAGAG 59.197 47.826 0.00 0.00 39.50 3.20
123 124 3.740764 ATGAGCCTTCAAATCGAGAGAGC 60.741 47.826 0.00 0.00 39.50 4.09
124 125 5.956151 ATGAGCCTTCAAATCGAGAGAGCT 61.956 45.833 0.00 0.00 39.50 4.09
125 126 7.370024 ATGAGCCTTCAAATCGAGAGAGCTT 62.370 44.000 0.00 0.00 39.50 3.74
126 127 8.084926 ATGAGCCTTCAAATCGAGAGAGCTTA 62.085 42.308 0.00 0.00 39.50 3.09
127 128 9.763468 ATGAGCCTTCAAATCGAGAGAGCTTAG 62.763 44.444 0.00 0.00 39.50 2.18
138 139 7.899178 TCGAGAGAGCTTAGTATCTCAATAG 57.101 40.000 15.35 6.75 43.64 1.73
139 140 7.672240 TCGAGAGAGCTTAGTATCTCAATAGA 58.328 38.462 15.35 8.29 43.64 1.98
140 141 8.318412 TCGAGAGAGCTTAGTATCTCAATAGAT 58.682 37.037 15.35 0.00 43.64 1.98
141 142 8.390354 CGAGAGAGCTTAGTATCTCAATAGATG 58.610 40.741 15.35 0.00 43.64 2.90
142 143 8.579850 AGAGAGCTTAGTATCTCAATAGATGG 57.420 38.462 15.35 0.00 43.64 3.51
143 144 8.390143 AGAGAGCTTAGTATCTCAATAGATGGA 58.610 37.037 15.35 0.00 43.64 3.41
144 145 9.189156 GAGAGCTTAGTATCTCAATAGATGGAT 57.811 37.037 10.33 0.00 42.60 3.41
152 153 8.649591 AGTATCTCAATAGATGGATATCATGGC 58.350 37.037 4.83 0.00 42.60 4.40
153 154 6.879367 TCTCAATAGATGGATATCATGGCA 57.121 37.500 4.83 0.00 35.97 4.92
154 155 6.885922 TCTCAATAGATGGATATCATGGCAG 58.114 40.000 4.83 0.00 35.97 4.85
155 156 6.442885 TCTCAATAGATGGATATCATGGCAGT 59.557 38.462 4.83 0.00 35.97 4.40
156 157 6.647229 TCAATAGATGGATATCATGGCAGTC 58.353 40.000 4.83 0.00 35.97 3.51
157 158 6.442885 TCAATAGATGGATATCATGGCAGTCT 59.557 38.462 4.83 2.24 35.97 3.24
158 159 6.887886 ATAGATGGATATCATGGCAGTCTT 57.112 37.500 4.83 0.00 35.97 3.01
159 160 5.163281 AGATGGATATCATGGCAGTCTTC 57.837 43.478 4.83 0.00 35.97 2.87
160 161 4.596212 AGATGGATATCATGGCAGTCTTCA 59.404 41.667 4.83 0.00 35.97 3.02
161 162 4.776435 TGGATATCATGGCAGTCTTCAA 57.224 40.909 4.83 0.00 0.00 2.69
162 163 4.711399 TGGATATCATGGCAGTCTTCAAG 58.289 43.478 4.83 0.00 0.00 3.02
163 164 4.409901 TGGATATCATGGCAGTCTTCAAGA 59.590 41.667 4.83 0.00 0.00 3.02
164 165 4.754114 GGATATCATGGCAGTCTTCAAGAC 59.246 45.833 9.78 9.78 45.38 3.01
165 166 9.272581 ATGGATATCATGGCAGTCTTCAAGACA 62.273 40.741 19.89 0.00 40.07 3.41
174 175 3.026630 GTCTTCAAGACATGACCGACA 57.973 47.619 13.01 0.00 44.45 4.35
175 176 3.589988 GTCTTCAAGACATGACCGACAT 58.410 45.455 13.01 0.00 44.45 3.06
185 186 2.559698 TGACCGACATGGATTGTTGT 57.440 45.000 0.00 0.00 42.00 3.32
186 187 3.686916 TGACCGACATGGATTGTTGTA 57.313 42.857 0.00 0.00 42.00 2.41
187 188 3.331150 TGACCGACATGGATTGTTGTAC 58.669 45.455 0.00 0.00 42.00 2.90
188 189 3.007506 TGACCGACATGGATTGTTGTACT 59.992 43.478 0.00 0.00 42.00 2.73
189 190 3.596214 ACCGACATGGATTGTTGTACTC 58.404 45.455 0.00 0.00 42.00 2.59
190 191 3.260884 ACCGACATGGATTGTTGTACTCT 59.739 43.478 0.00 0.00 42.00 3.24
191 192 4.464951 ACCGACATGGATTGTTGTACTCTA 59.535 41.667 0.00 0.00 42.00 2.43
192 193 5.043903 CCGACATGGATTGTTGTACTCTAG 58.956 45.833 0.00 0.00 42.00 2.43
193 194 5.394224 CCGACATGGATTGTTGTACTCTAGT 60.394 44.000 0.00 0.00 42.00 2.57
194 195 6.183360 CCGACATGGATTGTTGTACTCTAGTA 60.183 42.308 0.00 0.00 42.00 1.82
195 196 7.255569 CGACATGGATTGTTGTACTCTAGTAA 58.744 38.462 0.00 0.00 39.18 2.24
196 197 7.921214 CGACATGGATTGTTGTACTCTAGTAAT 59.079 37.037 0.00 0.00 39.18 1.89
197 198 9.601217 GACATGGATTGTTGTACTCTAGTAATT 57.399 33.333 0.00 0.00 39.18 1.40
209 210 9.817809 TGTACTCTAGTAATTAATTTCCTGCAG 57.182 33.333 6.78 6.78 31.52 4.41
221 222 4.706842 TTTCCTGCAGAAACTAGAAGGT 57.293 40.909 17.39 0.00 39.60 3.50
222 223 5.818678 TTTCCTGCAGAAACTAGAAGGTA 57.181 39.130 17.39 0.00 39.60 3.08
223 224 5.818678 TTCCTGCAGAAACTAGAAGGTAA 57.181 39.130 17.39 0.00 0.00 2.85
224 225 5.148651 TCCTGCAGAAACTAGAAGGTAAC 57.851 43.478 17.39 0.00 0.00 2.50
225 226 6.183361 TTTCCTGCAGAAACTAGAAGGTAACT 60.183 38.462 17.39 0.00 44.96 2.24
226 227 7.015877 TTTCCTGCAGAAACTAGAAGGTAACTA 59.984 37.037 17.39 0.00 43.11 2.24
256 257 9.298774 CCAACTATTACTAAAGAACTAAGTCCG 57.701 37.037 0.00 0.00 0.00 4.79
257 258 8.805688 CAACTATTACTAAAGAACTAAGTCCGC 58.194 37.037 0.00 0.00 0.00 5.54
258 259 7.192232 ACTATTACTAAAGAACTAAGTCCGCG 58.808 38.462 0.00 0.00 0.00 6.46
259 260 5.627499 TTACTAAAGAACTAAGTCCGCGA 57.373 39.130 8.23 0.00 0.00 5.87
260 261 3.831112 ACTAAAGAACTAAGTCCGCGAC 58.169 45.455 8.23 3.80 0.00 5.19
261 262 2.806608 AAAGAACTAAGTCCGCGACA 57.193 45.000 8.23 0.00 34.60 4.35
262 263 2.061740 AAGAACTAAGTCCGCGACAC 57.938 50.000 8.23 3.36 34.60 3.67
263 264 1.245732 AGAACTAAGTCCGCGACACT 58.754 50.000 8.23 6.22 34.60 3.55
264 265 1.612463 AGAACTAAGTCCGCGACACTT 59.388 47.619 21.99 21.99 37.80 3.16
265 266 2.816087 AGAACTAAGTCCGCGACACTTA 59.184 45.455 21.90 21.90 35.63 2.24
266 267 3.254166 AGAACTAAGTCCGCGACACTTAA 59.746 43.478 22.85 12.41 36.20 1.85
267 268 3.863142 ACTAAGTCCGCGACACTTAAT 57.137 42.857 22.85 15.33 36.20 1.40
268 269 4.970662 ACTAAGTCCGCGACACTTAATA 57.029 40.909 22.85 10.23 36.20 0.98
269 270 5.511234 ACTAAGTCCGCGACACTTAATAT 57.489 39.130 22.85 13.49 36.20 1.28
270 271 5.279384 ACTAAGTCCGCGACACTTAATATG 58.721 41.667 22.85 16.51 36.20 1.78
271 272 3.093717 AGTCCGCGACACTTAATATGG 57.906 47.619 8.23 0.00 34.60 2.74
272 273 2.691526 AGTCCGCGACACTTAATATGGA 59.308 45.455 8.23 0.00 34.60 3.41
273 274 3.321111 AGTCCGCGACACTTAATATGGAT 59.679 43.478 8.23 0.00 34.60 3.41
274 275 3.673809 GTCCGCGACACTTAATATGGATC 59.326 47.826 8.23 0.00 32.09 3.36
275 276 2.661675 CCGCGACACTTAATATGGATCG 59.338 50.000 8.23 0.00 0.00 3.69
276 277 3.561503 CGCGACACTTAATATGGATCGA 58.438 45.455 0.00 0.00 0.00 3.59
277 278 3.361053 CGCGACACTTAATATGGATCGAC 59.639 47.826 0.00 0.00 0.00 4.20
278 279 3.361053 GCGACACTTAATATGGATCGACG 59.639 47.826 0.00 0.00 0.00 5.12
279 280 4.779987 CGACACTTAATATGGATCGACGA 58.220 43.478 0.00 0.00 0.00 4.20
280 281 5.209977 CGACACTTAATATGGATCGACGAA 58.790 41.667 0.00 0.00 0.00 3.85
281 282 5.339875 CGACACTTAATATGGATCGACGAAG 59.660 44.000 0.00 0.00 0.00 3.79
321 322 4.466370 CCTAATGTCTCAGTTGGTAGGTCA 59.534 45.833 0.00 0.00 0.00 4.02
344 345 3.187022 CGTTCCGGGTTTAATTTTCGTCT 59.813 43.478 0.00 0.00 0.00 4.18
352 353 5.414765 GGGTTTAATTTTCGTCTCACCTCAT 59.585 40.000 0.00 0.00 0.00 2.90
394 395 2.127651 TGGTACTTCCTCCCACCTTT 57.872 50.000 0.00 0.00 37.07 3.11
406 407 3.249189 ACCTTTCCCTCAGCCGCA 61.249 61.111 0.00 0.00 0.00 5.69
444 445 2.579787 CGATCGAGTCCCGCACAC 60.580 66.667 10.26 0.00 38.37 3.82
514 515 3.891366 GGATCCCACCTATCATGGTTTTG 59.109 47.826 0.00 0.00 38.45 2.44
665 1791 1.992519 GATCAGCCCCACCTCATGCT 61.993 60.000 0.00 0.00 33.52 3.79
690 1816 1.920325 CCCACTGCTTCTCCCTCCA 60.920 63.158 0.00 0.00 0.00 3.86
763 1889 1.400142 CAGATCGTCTCGAGCAAGTCT 59.600 52.381 7.81 6.01 45.07 3.24
837 1963 1.794714 GGGAGAGGTAGATCAAGGCA 58.205 55.000 0.00 0.00 0.00 4.75
1401 2535 4.520492 CAGTTGCCTTTCACCAATAGAAGT 59.480 41.667 0.00 0.00 0.00 3.01
1403 2537 6.206634 CAGTTGCCTTTCACCAATAGAAGTTA 59.793 38.462 0.00 0.00 0.00 2.24
1475 2609 5.969423 ACTTCATTAATTGTGATGGCAAGG 58.031 37.500 0.00 0.00 0.00 3.61
1480 2614 3.947910 AATTGTGATGGCAAGGAACTG 57.052 42.857 0.00 0.00 40.86 3.16
1509 2643 2.669364 GGTATTATACACACGGGAGCG 58.331 52.381 4.67 0.00 0.00 5.03
1669 2803 1.524621 ACTGCAGTTGAAGCACGCT 60.525 52.632 15.25 0.00 37.02 5.07
1708 2842 1.391577 TGTGTGTTCTTGTGCTGCAT 58.608 45.000 5.27 0.00 0.00 3.96
1751 2885 0.892814 TCGCCACCATGTTCATGCAA 60.893 50.000 7.21 0.00 0.00 4.08
1780 2914 6.183360 CGAATTGGACTGAGAAATGCTAACAT 60.183 38.462 0.00 0.00 38.49 2.71
1878 3012 7.597743 GCTGCAGTGTAGTAGTACTCTTTAAAA 59.402 37.037 16.64 0.00 31.89 1.52
1905 3039 6.374417 TTGTAGGAGATAGCAAAAGGACTT 57.626 37.500 0.00 0.00 0.00 3.01
2026 3160 3.967332 AAAGGAAAATGCCCACAGATG 57.033 42.857 0.00 0.00 0.00 2.90
2220 3376 0.680280 ACCTGCATAGACCGTCTCGT 60.680 55.000 3.74 0.00 0.00 4.18
2304 3486 1.600916 GGGACACACAACTCCCAGC 60.601 63.158 0.00 0.00 45.22 4.85
2612 3794 0.824109 TACCTGATGCCTTCACTCCG 59.176 55.000 0.00 0.00 0.00 4.63
2654 3836 5.585445 ACATTTTGCTTTTTGATTCAGTGCA 59.415 32.000 0.00 0.00 0.00 4.57
2685 3869 6.590234 ATGGGGAGAACATAAAACTTCAAC 57.410 37.500 0.00 0.00 0.00 3.18
2739 3923 4.951254 TCATGTAAGTGACGTCTTTCCAA 58.049 39.130 17.92 0.00 0.00 3.53
2744 3928 6.053005 TGTAAGTGACGTCTTTCCAAGAATT 58.947 36.000 17.92 1.69 39.67 2.17
2752 3936 9.667107 TGACGTCTTTCCAAGAATTTTCTATAT 57.333 29.630 17.92 0.00 39.67 0.86
2874 4058 1.067283 CACTTGCATCGACCTCTCACT 60.067 52.381 0.00 0.00 0.00 3.41
2964 4148 4.462133 CTCGACTCATAGTTCCCTTCCTA 58.538 47.826 0.00 0.00 0.00 2.94
3171 4356 6.649141 TCTGACTACGTACTTGCATGAATTTT 59.351 34.615 6.60 0.00 0.00 1.82
3184 4369 6.245408 TGCATGAATTTTAGACCCTACTTGT 58.755 36.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.311596 GCGTTGGTCAGTGTTTCTAGTTT 59.688 43.478 0.00 0.00 0.00 2.66
3 4 2.159014 TGCGTTGGTCAGTGTTTCTAGT 60.159 45.455 0.00 0.00 0.00 2.57
5 6 2.605837 TGCGTTGGTCAGTGTTTCTA 57.394 45.000 0.00 0.00 0.00 2.10
6 7 1.967319 ATGCGTTGGTCAGTGTTTCT 58.033 45.000 0.00 0.00 0.00 2.52
7 8 2.774439 AATGCGTTGGTCAGTGTTTC 57.226 45.000 0.00 0.00 0.00 2.78
8 9 3.518634 AAAATGCGTTGGTCAGTGTTT 57.481 38.095 0.00 0.00 0.00 2.83
9 10 3.550030 GCTAAAATGCGTTGGTCAGTGTT 60.550 43.478 0.00 0.00 0.00 3.32
10 11 2.031157 GCTAAAATGCGTTGGTCAGTGT 60.031 45.455 0.00 0.00 0.00 3.55
11 12 2.584791 GCTAAAATGCGTTGGTCAGTG 58.415 47.619 0.00 0.00 0.00 3.66
12 13 1.539827 GGCTAAAATGCGTTGGTCAGT 59.460 47.619 0.00 0.00 0.00 3.41
13 14 1.539388 TGGCTAAAATGCGTTGGTCAG 59.461 47.619 0.00 0.00 0.00 3.51
14 15 1.268352 GTGGCTAAAATGCGTTGGTCA 59.732 47.619 0.00 0.00 0.00 4.02
15 16 1.268352 TGTGGCTAAAATGCGTTGGTC 59.732 47.619 0.00 0.00 0.00 4.02
16 17 1.323412 TGTGGCTAAAATGCGTTGGT 58.677 45.000 0.00 0.00 0.00 3.67
17 18 2.652941 ATGTGGCTAAAATGCGTTGG 57.347 45.000 0.00 0.00 0.00 3.77
18 19 7.434897 ACATTTATATGTGGCTAAAATGCGTTG 59.565 33.333 0.00 0.00 43.29 4.10
19 20 7.488322 ACATTTATATGTGGCTAAAATGCGTT 58.512 30.769 0.00 0.00 43.29 4.84
20 21 7.038154 ACATTTATATGTGGCTAAAATGCGT 57.962 32.000 0.00 0.00 43.29 5.24
21 22 7.862372 AGAACATTTATATGTGGCTAAAATGCG 59.138 33.333 0.00 0.00 44.14 4.73
22 23 9.533253 AAGAACATTTATATGTGGCTAAAATGC 57.467 29.630 0.00 0.00 44.14 3.56
25 26 9.364989 GCAAAGAACATTTATATGTGGCTAAAA 57.635 29.630 0.00 0.00 44.14 1.52
26 27 8.748412 AGCAAAGAACATTTATATGTGGCTAAA 58.252 29.630 0.00 0.00 44.14 1.85
27 28 8.292444 AGCAAAGAACATTTATATGTGGCTAA 57.708 30.769 0.00 0.00 44.14 3.09
28 29 7.775093 AGAGCAAAGAACATTTATATGTGGCTA 59.225 33.333 0.00 0.00 44.14 3.93
29 30 6.604795 AGAGCAAAGAACATTTATATGTGGCT 59.395 34.615 0.00 4.93 44.14 4.75
30 31 6.799512 AGAGCAAAGAACATTTATATGTGGC 58.200 36.000 0.00 0.73 44.14 5.01
31 32 7.988737 TGAGAGCAAAGAACATTTATATGTGG 58.011 34.615 0.00 0.00 44.14 4.17
32 33 9.282247 GTTGAGAGCAAAGAACATTTATATGTG 57.718 33.333 0.00 0.00 39.20 3.21
33 34 8.462016 GGTTGAGAGCAAAGAACATTTATATGT 58.538 33.333 0.00 0.00 40.15 2.29
34 35 8.461222 TGGTTGAGAGCAAAGAACATTTATATG 58.539 33.333 0.00 0.00 35.42 1.78
35 36 8.579850 TGGTTGAGAGCAAAGAACATTTATAT 57.420 30.769 0.00 0.00 35.42 0.86
36 37 7.121168 CCTGGTTGAGAGCAAAGAACATTTATA 59.879 37.037 0.00 0.00 35.42 0.98
37 38 6.071728 CCTGGTTGAGAGCAAAGAACATTTAT 60.072 38.462 0.00 0.00 35.42 1.40
38 39 5.241506 CCTGGTTGAGAGCAAAGAACATTTA 59.758 40.000 0.00 0.00 35.42 1.40
39 40 4.038402 CCTGGTTGAGAGCAAAGAACATTT 59.962 41.667 0.00 0.00 35.42 2.32
40 41 3.571401 CCTGGTTGAGAGCAAAGAACATT 59.429 43.478 0.00 0.00 35.42 2.71
41 42 3.152341 CCTGGTTGAGAGCAAAGAACAT 58.848 45.455 0.00 0.00 35.42 2.71
42 43 2.575532 CCTGGTTGAGAGCAAAGAACA 58.424 47.619 0.00 0.00 35.42 3.18
43 44 1.882623 CCCTGGTTGAGAGCAAAGAAC 59.117 52.381 0.00 0.00 35.42 3.01
44 45 1.774254 TCCCTGGTTGAGAGCAAAGAA 59.226 47.619 0.00 0.00 35.42 2.52
45 46 1.072331 GTCCCTGGTTGAGAGCAAAGA 59.928 52.381 0.00 0.00 35.42 2.52
46 47 1.202806 TGTCCCTGGTTGAGAGCAAAG 60.203 52.381 0.00 0.00 35.42 2.77
47 48 0.843309 TGTCCCTGGTTGAGAGCAAA 59.157 50.000 0.00 0.00 35.42 3.68
48 49 0.108585 GTGTCCCTGGTTGAGAGCAA 59.891 55.000 0.00 0.00 31.98 3.91
49 50 1.053835 TGTGTCCCTGGTTGAGAGCA 61.054 55.000 0.00 0.00 0.00 4.26
50 51 0.326264 ATGTGTCCCTGGTTGAGAGC 59.674 55.000 0.00 0.00 0.00 4.09
51 52 1.065854 GGATGTGTCCCTGGTTGAGAG 60.066 57.143 0.00 0.00 38.69 3.20
52 53 0.984230 GGATGTGTCCCTGGTTGAGA 59.016 55.000 0.00 0.00 38.69 3.27
53 54 3.558674 GGATGTGTCCCTGGTTGAG 57.441 57.895 0.00 0.00 38.69 3.02
62 63 2.367567 TCGCTTATAAGGGGATGTGTCC 59.632 50.000 24.56 0.55 44.29 4.02
63 64 3.555168 CCTCGCTTATAAGGGGATGTGTC 60.555 52.174 24.56 1.20 39.25 3.67
64 65 2.368875 CCTCGCTTATAAGGGGATGTGT 59.631 50.000 24.56 0.00 39.25 3.72
65 66 2.872038 GCCTCGCTTATAAGGGGATGTG 60.872 54.545 24.56 12.48 39.25 3.21
66 67 1.348036 GCCTCGCTTATAAGGGGATGT 59.652 52.381 24.56 0.00 39.25 3.06
67 68 1.625818 AGCCTCGCTTATAAGGGGATG 59.374 52.381 24.56 15.79 33.89 3.51
68 69 1.903183 GAGCCTCGCTTATAAGGGGAT 59.097 52.381 24.56 11.79 39.88 3.85
69 70 1.339097 GAGCCTCGCTTATAAGGGGA 58.661 55.000 24.56 13.17 39.88 4.81
70 71 0.321996 GGAGCCTCGCTTATAAGGGG 59.678 60.000 24.56 16.52 39.88 4.79
71 72 0.321996 GGGAGCCTCGCTTATAAGGG 59.678 60.000 20.54 20.54 39.88 3.95
72 73 0.321996 GGGGAGCCTCGCTTATAAGG 59.678 60.000 14.28 4.84 39.88 2.69
73 74 0.321996 GGGGGAGCCTCGCTTATAAG 59.678 60.000 8.20 8.20 39.88 1.73
74 75 1.469335 CGGGGGAGCCTCGCTTATAA 61.469 60.000 8.80 0.00 41.95 0.98
75 76 1.906824 CGGGGGAGCCTCGCTTATA 60.907 63.158 8.80 0.00 41.95 0.98
76 77 3.234730 CGGGGGAGCCTCGCTTAT 61.235 66.667 8.80 0.00 41.95 1.73
82 83 2.522193 CTACCTCGGGGGAGCCTC 60.522 72.222 0.00 0.00 36.65 4.70
86 87 1.457643 TCATGCTACCTCGGGGGAG 60.458 63.158 10.15 10.15 46.37 4.30
87 88 1.457643 CTCATGCTACCTCGGGGGA 60.458 63.158 6.13 0.00 38.76 4.81
88 89 3.142393 CTCATGCTACCTCGGGGG 58.858 66.667 6.13 0.00 41.89 5.40
89 90 2.423446 GCTCATGCTACCTCGGGG 59.577 66.667 0.00 0.00 36.03 5.73
90 91 1.690219 AAGGCTCATGCTACCTCGGG 61.690 60.000 2.02 0.00 39.59 5.14
91 92 0.249657 GAAGGCTCATGCTACCTCGG 60.250 60.000 2.02 0.00 39.59 4.63
92 93 0.461548 TGAAGGCTCATGCTACCTCG 59.538 55.000 2.02 0.00 39.59 4.63
93 94 2.698855 TTGAAGGCTCATGCTACCTC 57.301 50.000 2.02 0.00 39.59 3.85
94 95 3.549794 GATTTGAAGGCTCATGCTACCT 58.450 45.455 0.00 0.00 39.59 3.08
95 96 2.289002 CGATTTGAAGGCTCATGCTACC 59.711 50.000 0.00 0.00 39.59 3.18
96 97 3.198068 TCGATTTGAAGGCTCATGCTAC 58.802 45.455 0.00 0.00 39.59 3.58
97 98 3.132824 TCTCGATTTGAAGGCTCATGCTA 59.867 43.478 0.00 0.00 39.59 3.49
98 99 2.093288 TCTCGATTTGAAGGCTCATGCT 60.093 45.455 0.00 0.00 39.59 3.79
99 100 2.283298 TCTCGATTTGAAGGCTCATGC 58.717 47.619 0.00 0.00 38.76 4.06
100 101 3.790091 TCTCTCGATTTGAAGGCTCATG 58.210 45.455 0.00 0.00 0.00 3.07
101 102 3.740764 GCTCTCTCGATTTGAAGGCTCAT 60.741 47.826 0.00 0.00 0.00 2.90
102 103 2.417924 GCTCTCTCGATTTGAAGGCTCA 60.418 50.000 0.00 0.00 0.00 4.26
103 104 2.159114 AGCTCTCTCGATTTGAAGGCTC 60.159 50.000 0.00 0.00 0.00 4.70
104 105 1.830477 AGCTCTCTCGATTTGAAGGCT 59.170 47.619 0.00 0.00 0.00 4.58
105 106 2.307934 AGCTCTCTCGATTTGAAGGC 57.692 50.000 0.00 0.00 0.00 4.35
106 107 5.004922 ACTAAGCTCTCTCGATTTGAAGG 57.995 43.478 0.00 0.00 0.00 3.46
107 108 7.648142 AGATACTAAGCTCTCTCGATTTGAAG 58.352 38.462 0.00 0.00 0.00 3.02
108 109 7.283354 TGAGATACTAAGCTCTCTCGATTTGAA 59.717 37.037 0.00 0.00 38.98 2.69
109 110 6.768381 TGAGATACTAAGCTCTCTCGATTTGA 59.232 38.462 0.00 0.00 38.98 2.69
110 111 6.964908 TGAGATACTAAGCTCTCTCGATTTG 58.035 40.000 0.00 0.00 38.98 2.32
111 112 7.575414 TTGAGATACTAAGCTCTCTCGATTT 57.425 36.000 0.00 0.00 38.98 2.17
112 113 7.759489 ATTGAGATACTAAGCTCTCTCGATT 57.241 36.000 0.00 0.00 38.98 3.34
113 114 8.318412 TCTATTGAGATACTAAGCTCTCTCGAT 58.682 37.037 13.23 13.23 38.98 3.59
114 115 7.672240 TCTATTGAGATACTAAGCTCTCTCGA 58.328 38.462 0.00 0.00 38.98 4.04
115 116 7.899178 TCTATTGAGATACTAAGCTCTCTCG 57.101 40.000 0.00 0.00 38.98 4.04
116 117 8.677300 CCATCTATTGAGATACTAAGCTCTCTC 58.323 40.741 0.00 0.00 40.68 3.20
117 118 8.390143 TCCATCTATTGAGATACTAAGCTCTCT 58.610 37.037 0.00 0.00 40.68 3.10
118 119 8.574251 TCCATCTATTGAGATACTAAGCTCTC 57.426 38.462 0.00 0.00 40.68 3.20
126 127 8.649591 GCCATGATATCCATCTATTGAGATACT 58.350 37.037 0.00 0.00 40.68 2.12
127 128 8.427276 TGCCATGATATCCATCTATTGAGATAC 58.573 37.037 0.00 0.00 40.68 2.24
128 129 8.557304 TGCCATGATATCCATCTATTGAGATA 57.443 34.615 0.00 0.00 40.68 1.98
129 130 7.127493 ACTGCCATGATATCCATCTATTGAGAT 59.873 37.037 0.00 0.00 43.63 2.75
130 131 6.442885 ACTGCCATGATATCCATCTATTGAGA 59.557 38.462 0.00 0.00 35.71 3.27
131 132 6.651086 ACTGCCATGATATCCATCTATTGAG 58.349 40.000 0.00 0.00 31.94 3.02
132 133 6.442885 AGACTGCCATGATATCCATCTATTGA 59.557 38.462 0.00 0.00 31.94 2.57
133 134 6.651086 AGACTGCCATGATATCCATCTATTG 58.349 40.000 0.00 0.00 31.94 1.90
134 135 6.887886 AGACTGCCATGATATCCATCTATT 57.112 37.500 0.00 0.00 31.94 1.73
135 136 6.442885 TGAAGACTGCCATGATATCCATCTAT 59.557 38.462 0.00 0.00 31.94 1.98
136 137 5.781818 TGAAGACTGCCATGATATCCATCTA 59.218 40.000 0.00 0.00 31.94 1.98
137 138 4.596212 TGAAGACTGCCATGATATCCATCT 59.404 41.667 0.00 0.00 31.94 2.90
138 139 4.903054 TGAAGACTGCCATGATATCCATC 58.097 43.478 0.00 0.00 31.94 3.51
139 140 4.987963 TGAAGACTGCCATGATATCCAT 57.012 40.909 0.00 0.00 35.44 3.41
140 141 4.409901 TCTTGAAGACTGCCATGATATCCA 59.590 41.667 0.00 0.00 0.00 3.41
141 142 4.754114 GTCTTGAAGACTGCCATGATATCC 59.246 45.833 17.61 0.00 41.88 2.59
142 143 5.363101 TGTCTTGAAGACTGCCATGATATC 58.637 41.667 24.09 0.00 45.27 1.63
143 144 5.363562 TGTCTTGAAGACTGCCATGATAT 57.636 39.130 24.09 0.00 45.27 1.63
144 145 4.824479 TGTCTTGAAGACTGCCATGATA 57.176 40.909 24.09 0.00 45.27 2.15
145 146 3.708403 TGTCTTGAAGACTGCCATGAT 57.292 42.857 24.09 0.00 45.27 2.45
146 147 3.008266 TCATGTCTTGAAGACTGCCATGA 59.992 43.478 24.09 20.24 45.27 3.07
147 148 3.126514 GTCATGTCTTGAAGACTGCCATG 59.873 47.826 24.09 18.55 45.27 3.66
148 149 3.341823 GTCATGTCTTGAAGACTGCCAT 58.658 45.455 24.09 8.34 45.27 4.40
149 150 2.550855 GGTCATGTCTTGAAGACTGCCA 60.551 50.000 24.09 6.31 45.27 4.92
150 151 2.079925 GGTCATGTCTTGAAGACTGCC 58.920 52.381 24.09 18.42 45.27 4.85
151 152 1.728971 CGGTCATGTCTTGAAGACTGC 59.271 52.381 24.09 14.77 45.27 4.40
152 153 2.989840 GTCGGTCATGTCTTGAAGACTG 59.010 50.000 24.09 18.69 45.27 3.51
153 154 2.628178 TGTCGGTCATGTCTTGAAGACT 59.372 45.455 24.09 8.84 45.27 3.24
154 155 3.026630 TGTCGGTCATGTCTTGAAGAC 57.973 47.619 18.01 18.01 45.26 3.01
155 156 3.588955 CATGTCGGTCATGTCTTGAAGA 58.411 45.455 7.00 0.00 46.18 2.87
165 166 3.071874 ACAACAATCCATGTCGGTCAT 57.928 42.857 0.00 0.00 42.99 3.06
166 167 2.559698 ACAACAATCCATGTCGGTCA 57.440 45.000 0.00 0.00 42.99 4.02
167 168 3.596214 AGTACAACAATCCATGTCGGTC 58.404 45.455 0.00 0.00 42.99 4.79
168 169 3.260884 AGAGTACAACAATCCATGTCGGT 59.739 43.478 0.00 0.00 42.99 4.69
169 170 3.861840 AGAGTACAACAATCCATGTCGG 58.138 45.455 0.00 0.00 42.99 4.79
170 171 5.651530 ACTAGAGTACAACAATCCATGTCG 58.348 41.667 0.00 0.00 42.99 4.35
171 172 9.601217 AATTACTAGAGTACAACAATCCATGTC 57.399 33.333 0.00 0.00 42.99 3.06
183 184 9.817809 CTGCAGGAAATTAATTACTAGAGTACA 57.182 33.333 5.57 0.00 28.19 2.90
186 187 9.959721 TTTCTGCAGGAAATTAATTACTAGAGT 57.040 29.630 15.13 0.00 38.81 3.24
188 189 9.959721 AGTTTCTGCAGGAAATTAATTACTAGA 57.040 29.630 9.61 2.05 44.46 2.43
191 192 9.959721 TCTAGTTTCTGCAGGAAATTAATTACT 57.040 29.630 13.81 4.98 44.46 2.24
194 195 8.743714 CCTTCTAGTTTCTGCAGGAAATTAATT 58.256 33.333 13.81 0.00 44.46 1.40
195 196 7.890655 ACCTTCTAGTTTCTGCAGGAAATTAAT 59.109 33.333 13.81 0.00 44.46 1.40
196 197 7.231467 ACCTTCTAGTTTCTGCAGGAAATTAA 58.769 34.615 13.81 7.63 44.46 1.40
197 198 6.779860 ACCTTCTAGTTTCTGCAGGAAATTA 58.220 36.000 13.81 11.89 44.46 1.40
198 199 5.635120 ACCTTCTAGTTTCTGCAGGAAATT 58.365 37.500 13.81 11.43 44.46 1.82
199 200 5.248380 ACCTTCTAGTTTCTGCAGGAAAT 57.752 39.130 13.08 13.08 44.46 2.17
200 201 4.706842 ACCTTCTAGTTTCTGCAGGAAA 57.293 40.909 9.61 8.05 41.11 3.13
201 202 5.307196 AGTTACCTTCTAGTTTCTGCAGGAA 59.693 40.000 15.13 9.08 0.00 3.36
202 203 4.838986 AGTTACCTTCTAGTTTCTGCAGGA 59.161 41.667 15.13 0.46 0.00 3.86
203 204 5.153950 AGTTACCTTCTAGTTTCTGCAGG 57.846 43.478 15.13 0.00 0.00 4.85
204 205 8.779354 AATTAGTTACCTTCTAGTTTCTGCAG 57.221 34.615 7.63 7.63 0.00 4.41
205 206 7.822822 GGAATTAGTTACCTTCTAGTTTCTGCA 59.177 37.037 0.00 0.00 0.00 4.41
206 207 7.822822 TGGAATTAGTTACCTTCTAGTTTCTGC 59.177 37.037 0.00 0.00 0.00 4.26
207 208 9.720769 TTGGAATTAGTTACCTTCTAGTTTCTG 57.279 33.333 0.00 0.00 0.00 3.02
208 209 9.722184 GTTGGAATTAGTTACCTTCTAGTTTCT 57.278 33.333 0.00 0.00 0.00 2.52
209 210 9.722184 AGTTGGAATTAGTTACCTTCTAGTTTC 57.278 33.333 0.00 0.00 0.00 2.78
230 231 9.298774 CGGACTTAGTTCTTTAGTAATAGTTGG 57.701 37.037 0.00 0.00 0.00 3.77
231 232 8.805688 GCGGACTTAGTTCTTTAGTAATAGTTG 58.194 37.037 0.00 0.00 0.00 3.16
232 233 7.699812 CGCGGACTTAGTTCTTTAGTAATAGTT 59.300 37.037 0.00 0.00 0.00 2.24
233 234 7.066284 TCGCGGACTTAGTTCTTTAGTAATAGT 59.934 37.037 6.13 0.00 0.00 2.12
234 235 7.375544 GTCGCGGACTTAGTTCTTTAGTAATAG 59.624 40.741 6.13 0.00 0.00 1.73
235 236 7.148255 TGTCGCGGACTTAGTTCTTTAGTAATA 60.148 37.037 6.13 0.00 33.15 0.98
236 237 6.032717 GTCGCGGACTTAGTTCTTTAGTAAT 58.967 40.000 6.13 0.00 0.00 1.89
237 238 5.048782 TGTCGCGGACTTAGTTCTTTAGTAA 60.049 40.000 6.13 0.00 33.15 2.24
238 239 4.455533 TGTCGCGGACTTAGTTCTTTAGTA 59.544 41.667 6.13 0.00 33.15 1.82
239 240 3.254166 TGTCGCGGACTTAGTTCTTTAGT 59.746 43.478 6.13 0.00 33.15 2.24
240 241 3.607209 GTGTCGCGGACTTAGTTCTTTAG 59.393 47.826 6.13 0.00 33.15 1.85
241 242 3.254166 AGTGTCGCGGACTTAGTTCTTTA 59.746 43.478 6.13 0.00 33.15 1.85
242 243 2.035576 AGTGTCGCGGACTTAGTTCTTT 59.964 45.455 6.13 0.00 33.15 2.52
243 244 1.612463 AGTGTCGCGGACTTAGTTCTT 59.388 47.619 6.13 0.00 33.15 2.52
244 245 1.245732 AGTGTCGCGGACTTAGTTCT 58.754 50.000 6.13 0.00 33.15 3.01
245 246 2.061740 AAGTGTCGCGGACTTAGTTC 57.938 50.000 18.96 0.00 31.72 3.01
246 247 3.648339 TTAAGTGTCGCGGACTTAGTT 57.352 42.857 22.38 10.94 37.25 2.24
247 248 3.863142 ATTAAGTGTCGCGGACTTAGT 57.137 42.857 22.38 19.24 37.25 2.24
248 249 4.680110 CCATATTAAGTGTCGCGGACTTAG 59.320 45.833 22.38 15.01 37.25 2.18
249 250 4.338964 TCCATATTAAGTGTCGCGGACTTA 59.661 41.667 20.77 20.77 35.30 2.24
250 251 3.131577 TCCATATTAAGTGTCGCGGACTT 59.868 43.478 22.38 22.38 37.43 3.01
251 252 2.691526 TCCATATTAAGTGTCGCGGACT 59.308 45.455 6.13 6.02 33.15 3.85
252 253 3.088194 TCCATATTAAGTGTCGCGGAC 57.912 47.619 6.13 3.28 0.00 4.79
253 254 3.610821 CGATCCATATTAAGTGTCGCGGA 60.611 47.826 6.13 0.00 0.00 5.54
254 255 2.661675 CGATCCATATTAAGTGTCGCGG 59.338 50.000 6.13 0.00 0.00 6.46
255 256 3.361053 GTCGATCCATATTAAGTGTCGCG 59.639 47.826 0.00 0.00 0.00 5.87
256 257 3.361053 CGTCGATCCATATTAAGTGTCGC 59.639 47.826 0.00 0.00 0.00 5.19
257 258 4.779987 TCGTCGATCCATATTAAGTGTCG 58.220 43.478 0.00 0.00 0.00 4.35
258 259 6.207213 ACTTCGTCGATCCATATTAAGTGTC 58.793 40.000 0.00 0.00 0.00 3.67
259 260 6.145338 ACTTCGTCGATCCATATTAAGTGT 57.855 37.500 0.00 0.00 0.00 3.55
260 261 7.361127 AGTACTTCGTCGATCCATATTAAGTG 58.639 38.462 0.00 0.00 0.00 3.16
261 262 7.507733 AGTACTTCGTCGATCCATATTAAGT 57.492 36.000 0.00 0.00 0.00 2.24
264 265 9.881649 ACTATAGTACTTCGTCGATCCATATTA 57.118 33.333 2.75 0.00 0.00 0.98
265 266 8.789825 ACTATAGTACTTCGTCGATCCATATT 57.210 34.615 2.75 0.00 0.00 1.28
266 267 8.259411 AGACTATAGTACTTCGTCGATCCATAT 58.741 37.037 5.09 0.00 0.00 1.78
267 268 7.609960 AGACTATAGTACTTCGTCGATCCATA 58.390 38.462 5.09 0.00 0.00 2.74
268 269 6.465948 AGACTATAGTACTTCGTCGATCCAT 58.534 40.000 5.09 0.00 0.00 3.41
269 270 5.851720 AGACTATAGTACTTCGTCGATCCA 58.148 41.667 5.09 0.00 0.00 3.41
270 271 6.158598 AGAGACTATAGTACTTCGTCGATCC 58.841 44.000 5.09 0.00 0.00 3.36
271 272 8.915871 ATAGAGACTATAGTACTTCGTCGATC 57.084 38.462 5.09 1.19 0.00 3.69
272 273 9.357652 GAATAGAGACTATAGTACTTCGTCGAT 57.642 37.037 5.09 3.10 0.00 3.59
273 274 7.812191 GGAATAGAGACTATAGTACTTCGTCGA 59.188 40.741 5.09 0.00 0.00 4.20
274 275 7.814107 AGGAATAGAGACTATAGTACTTCGTCG 59.186 40.741 5.09 0.00 0.00 5.12
286 287 9.875708 AACTGAGACATTAGGAATAGAGACTAT 57.124 33.333 0.00 0.00 0.00 2.12
296 297 5.091552 ACCTACCAACTGAGACATTAGGAA 58.908 41.667 8.30 0.00 0.00 3.36
417 418 0.915227 GACTCGATCGCGGAGTTTTC 59.085 55.000 16.01 2.55 38.28 2.29
453 454 3.619929 CCTTTCAGTTAATAACGACGGGG 59.380 47.826 0.00 0.00 36.23 5.73
534 1660 2.554893 GTGGGACGAAATAAAACCAGCA 59.445 45.455 0.00 0.00 0.00 4.41
665 1791 2.116983 GAGAAGCAGTGGGTGGAGCA 62.117 60.000 0.00 0.00 0.00 4.26
1226 2360 2.216046 CCTATGAGCGCATCACATGTT 58.784 47.619 11.47 0.00 41.91 2.71
1354 2488 3.199071 TGACCCTAACCGCAATTCTACAT 59.801 43.478 0.00 0.00 0.00 2.29
1475 2609 6.636044 GTGTATAATACCGACTGCTACAGTTC 59.364 42.308 1.15 0.00 45.44 3.01
1480 2614 4.908156 CGTGTGTATAATACCGACTGCTAC 59.092 45.833 0.00 0.00 0.00 3.58
1509 2643 4.464008 TCCATCCCAATACAGAATTGAGC 58.536 43.478 0.00 0.00 46.81 4.26
1669 2803 3.727726 CAACATACATGGTGGCGAGATA 58.272 45.455 0.00 0.00 41.71 1.98
1708 2842 1.585651 AACACCCAACCCCAAGGACA 61.586 55.000 0.00 0.00 36.73 4.02
1751 2885 2.839486 TTCTCAGTCCAATTCGTGCT 57.161 45.000 0.00 0.00 0.00 4.40
1780 2914 2.550277 TGCATGGTCTTCTCCTCCTA 57.450 50.000 0.00 0.00 0.00 2.94
1878 3012 7.890655 AGTCCTTTTGCTATCTCCTACAAATTT 59.109 33.333 0.00 0.00 32.50 1.82
1905 3039 9.874205 GTTTTTAAATCAATGGATCCTTCATCA 57.126 29.630 14.23 0.00 32.33 3.07
2220 3376 2.092212 GGGAGCATCTCTTCATTCCCAA 60.092 50.000 2.57 0.00 43.04 4.12
2304 3486 8.553459 ACGAGCCAAGATAAAGAATATTATGG 57.447 34.615 0.00 0.00 0.00 2.74
2612 3794 6.575162 AAATGTCAGACAAACAGATTACCC 57.425 37.500 7.50 0.00 0.00 3.69
2654 3836 8.116026 AGTTTTATGTTCTCCCCATTAGTGATT 58.884 33.333 0.00 0.00 0.00 2.57
2685 3869 1.554160 AGAGAATCACAGTGCCCTCAG 59.446 52.381 14.81 0.00 37.82 3.35
2752 3936 8.630091 TCTAAGGGCCTGAGAGGTTATATAATA 58.370 37.037 17.28 0.00 37.80 0.98
2874 4058 3.558314 ATCCTCGGGATGGTGATCA 57.442 52.632 4.81 0.00 41.43 2.92
2964 4148 2.637025 GCAACGTTGCGTGGACAT 59.363 55.556 34.84 0.00 45.11 3.06
2982 4166 9.624697 GATGAATTAACAACTTAGCAACAATGA 57.375 29.630 0.00 0.00 0.00 2.57
3155 4339 6.759497 AGGGTCTAAAATTCATGCAAGTAC 57.241 37.500 0.00 0.00 0.00 2.73
3156 4340 7.630082 AGTAGGGTCTAAAATTCATGCAAGTA 58.370 34.615 0.00 0.00 0.00 2.24
3157 4341 6.485171 AGTAGGGTCTAAAATTCATGCAAGT 58.515 36.000 0.00 0.00 0.00 3.16
3158 4342 7.094205 ACAAGTAGGGTCTAAAATTCATGCAAG 60.094 37.037 0.00 0.00 0.00 4.01
3171 4356 4.413760 AGCAACTGTACAAGTAGGGTCTA 58.586 43.478 0.00 0.00 38.56 2.59
3184 4369 4.383850 ACACAAAATGCAAGCAACTGTA 57.616 36.364 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.