Multiple sequence alignment - TraesCS3A01G026300

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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 TraesCS3A01G026300 chr3A 100.000 2399 0 0 1 2399 13831169 13828771 0.000000e+00 4431.0
1 TraesCS3A01G026300 chr3A 97.959 147 2 1 215 361 667298751 667298606 1.100000e-63 254.0
2 TraesCS3A01G026300 chr3A 94.318 88 3 2 360 445 13824014 13823927 1.500000e-27 134.0
3 TraesCS3A01G026300 chr5A 98.085 2037 37 2 365 2399 693605924 693607960 0.000000e+00 3544.0
4 TraesCS3A01G026300 chr5A 86.561 759 83 10 1573 2324 345751852 345752598 0.000000e+00 819.0
5 TraesCS3A01G026300 chr5A 83.080 526 47 23 593 1094 669593436 669592929 7.870000e-120 440.0
6 TraesCS3A01G026300 chr2A 97.791 2037 43 2 365 2399 418808307 418810343 0.000000e+00 3511.0
7 TraesCS3A01G026300 chr2A 97.959 147 2 1 215 361 115422681 115422536 1.100000e-63 254.0
8 TraesCS3A01G026300 chr2A 79.902 204 14 13 366 543 762400137 762399935 9.000000e-25 124.0
9 TraesCS3A01G026300 chr6A 97.689 2034 45 2 368 2399 14150432 14148399 0.000000e+00 3494.0
10 TraesCS3A01G026300 chr6A 87.966 698 69 12 1699 2388 583032618 583033308 0.000000e+00 809.0
11 TraesCS3A01G026300 chr6A 97.959 147 2 1 215 361 583038136 583038281 1.100000e-63 254.0
12 TraesCS3A01G026300 chr5B 95.116 1597 66 3 812 2399 271155262 271156855 0.000000e+00 2507.0
13 TraesCS3A01G026300 chr6B 94.997 1599 66 4 812 2399 342808014 342806419 0.000000e+00 2497.0
14 TraesCS3A01G026300 chr6B 97.959 147 2 1 215 361 262412750 262412605 1.100000e-63 254.0
15 TraesCS3A01G026300 chr2B 94.856 836 41 2 665 1498 299000704 298999869 0.000000e+00 1304.0
16 TraesCS3A01G026300 chr2B 91.859 823 58 6 1577 2399 155140268 155139455 0.000000e+00 1140.0
17 TraesCS3A01G026300 chr2B 87.709 537 41 12 360 881 155156020 155155494 9.490000e-169 603.0
18 TraesCS3A01G026300 chr2B 83.112 527 46 24 592 1094 728615511 728616018 7.870000e-120 440.0
19 TraesCS3A01G026300 chr2B 87.755 294 27 6 1224 1517 155142153 155141869 3.820000e-88 335.0
20 TraesCS3A01G026300 chr2B 91.250 80 7 0 1510 1589 155140609 155140530 2.520000e-20 110.0
21 TraesCS3A01G026300 chr2B 95.455 44 2 0 1176 1219 728616012 728616055 1.190000e-08 71.3
22 TraesCS3A01G026300 chr1D 88.227 688 73 8 1705 2388 386796666 386795983 0.000000e+00 815.0
23 TraesCS3A01G026300 chr7B 83.302 527 45 24 592 1094 93325760 93325253 1.690000e-121 446.0
24 TraesCS3A01G026300 chr7B 83.080 526 47 23 593 1094 517843254 517843761 7.870000e-120 440.0
25 TraesCS3A01G026300 chr7B 82.890 526 48 23 593 1094 107641091 107640584 3.660000e-118 435.0
26 TraesCS3A01G026300 chr7B 97.959 147 2 1 215 361 193968650 193968795 1.100000e-63 254.0
27 TraesCS3A01G026300 chr7B 95.455 44 2 0 1176 1219 93325259 93325216 1.190000e-08 71.3
28 TraesCS3A01G026300 chr4B 82.510 526 50 25 593 1094 175557662 175557155 7.930000e-115 424.0
29 TraesCS3A01G026300 chr7A 99.315 146 1 0 215 360 688669816 688669961 5.090000e-67 265.0
30 TraesCS3A01G026300 chr7A 99.315 146 1 0 215 360 688676515 688676660 5.090000e-67 265.0
31 TraesCS3A01G026300 chr7A 96.094 128 5 0 360 487 688669907 688670034 2.420000e-50 209.0
32 TraesCS3A01G026300 chr7A 95.181 83 4 0 360 442 688676606 688676688 5.380000e-27 132.0
33 TraesCS3A01G026300 chr7A 96.226 53 2 0 489 541 688670059 688670111 1.180000e-13 87.9
34 TraesCS3A01G026300 chr1A 98.630 146 2 0 213 358 13743370 13743515 2.370000e-65 259.0
35 TraesCS3A01G026300 chrUn 97.973 148 2 1 214 361 34423257 34423403 3.060000e-64 255.0
36 TraesCS3A01G026300 chrUn 85.417 144 5 4 360 487 34423349 34423492 4.160000e-28 135.0
37 TraesCS3A01G026300 chr3D 82.018 228 9 12 13 213 6462427 6462649 5.310000e-37 165.0
38 TraesCS3A01G026300 chr3D 89.109 101 3 7 360 454 574281668 574281766 4.190000e-23 119.0
39 TraesCS3A01G026300 chr3D 88.000 100 6 6 360 454 135179995 135179897 1.950000e-21 113.0
40 TraesCS3A01G026300 chr3B 84.783 92 3 8 1129 1220 745725633 745725713 5.500000e-12 82.4
41 TraesCS3A01G026300 chr6D 89.062 64 2 3 424 487 408158311 408158369 9.200000e-10 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G026300 chr3A 13828771 13831169 2398 True 4431.000000 4431 100.0000 1 2399 1 chr3A.!!$R2 2398
1 TraesCS3A01G026300 chr5A 693605924 693607960 2036 False 3544.000000 3544 98.0850 365 2399 1 chr5A.!!$F2 2034
2 TraesCS3A01G026300 chr5A 345751852 345752598 746 False 819.000000 819 86.5610 1573 2324 1 chr5A.!!$F1 751
3 TraesCS3A01G026300 chr5A 669592929 669593436 507 True 440.000000 440 83.0800 593 1094 1 chr5A.!!$R1 501
4 TraesCS3A01G026300 chr2A 418808307 418810343 2036 False 3511.000000 3511 97.7910 365 2399 1 chr2A.!!$F1 2034
5 TraesCS3A01G026300 chr6A 14148399 14150432 2033 True 3494.000000 3494 97.6890 368 2399 1 chr6A.!!$R1 2031
6 TraesCS3A01G026300 chr6A 583032618 583033308 690 False 809.000000 809 87.9660 1699 2388 1 chr6A.!!$F1 689
7 TraesCS3A01G026300 chr5B 271155262 271156855 1593 False 2507.000000 2507 95.1160 812 2399 1 chr5B.!!$F1 1587
8 TraesCS3A01G026300 chr6B 342806419 342808014 1595 True 2497.000000 2497 94.9970 812 2399 1 chr6B.!!$R2 1587
9 TraesCS3A01G026300 chr2B 298999869 299000704 835 True 1304.000000 1304 94.8560 665 1498 1 chr2B.!!$R2 833
10 TraesCS3A01G026300 chr2B 155155494 155156020 526 True 603.000000 603 87.7090 360 881 1 chr2B.!!$R1 521
11 TraesCS3A01G026300 chr2B 155139455 155142153 2698 True 528.333333 1140 90.2880 1224 2399 3 chr2B.!!$R3 1175
12 TraesCS3A01G026300 chr2B 728615511 728616055 544 False 255.650000 440 89.2835 592 1219 2 chr2B.!!$F1 627
13 TraesCS3A01G026300 chr1D 386795983 386796666 683 True 815.000000 815 88.2270 1705 2388 1 chr1D.!!$R1 683
14 TraesCS3A01G026300 chr7B 517843254 517843761 507 False 440.000000 440 83.0800 593 1094 1 chr7B.!!$F2 501
15 TraesCS3A01G026300 chr7B 107640584 107641091 507 True 435.000000 435 82.8900 593 1094 1 chr7B.!!$R1 501
16 TraesCS3A01G026300 chr7B 93325216 93325760 544 True 258.650000 446 89.3785 592 1219 2 chr7B.!!$R2 627
17 TraesCS3A01G026300 chr4B 175557155 175557662 507 True 424.000000 424 82.5100 593 1094 1 chr4B.!!$R1 501

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
274 275 0.036164 TGCTATGACGGTGCCACTTT 59.964 50.0 0.0 0.0 0.0 2.66 F
314 315 0.184211 AACCGCCTTGTAAACTGGGT 59.816 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1172 0.251121 TCGAAAAAGATGCAGGCCCA 60.251 50.0 0.0 0.0 0.0 5.36 R
1864 3468 6.365970 AAAGTGACAAGATGTAGACCTCAT 57.634 37.5 0.0 0.0 0.0 2.90 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
23 24 5.250200 AGAGAGTATAATGCTACCTCGAGG 58.750 45.833 30.11 30.11 42.17 4.63
24 25 3.759618 AGAGTATAATGCTACCTCGAGGC 59.240 47.826 31.56 17.82 39.32 4.70
25 26 3.759618 GAGTATAATGCTACCTCGAGGCT 59.240 47.826 31.56 19.89 39.32 4.58
26 27 3.759618 AGTATAATGCTACCTCGAGGCTC 59.240 47.826 31.56 19.66 39.32 4.70
27 28 2.366640 TAATGCTACCTCGAGGCTCT 57.633 50.000 31.56 14.91 39.32 4.09
28 29 1.490574 AATGCTACCTCGAGGCTCTT 58.509 50.000 31.56 14.52 39.32 2.85
29 30 1.490574 ATGCTACCTCGAGGCTCTTT 58.509 50.000 31.56 14.11 39.32 2.52
30 31 1.267121 TGCTACCTCGAGGCTCTTTT 58.733 50.000 31.56 13.33 39.32 2.27
31 32 1.204941 TGCTACCTCGAGGCTCTTTTC 59.795 52.381 31.56 13.41 39.32 2.29
32 33 1.478916 GCTACCTCGAGGCTCTTTTCT 59.521 52.381 31.56 11.77 39.32 2.52
33 34 2.688958 GCTACCTCGAGGCTCTTTTCTA 59.311 50.000 31.56 12.31 39.32 2.10
34 35 3.243267 GCTACCTCGAGGCTCTTTTCTAG 60.243 52.174 31.56 21.42 39.32 2.43
35 36 2.104170 ACCTCGAGGCTCTTTTCTAGG 58.896 52.381 31.56 11.17 39.32 3.02
36 37 2.104170 CCTCGAGGCTCTTTTCTAGGT 58.896 52.381 20.67 0.00 0.00 3.08
37 38 2.498078 CCTCGAGGCTCTTTTCTAGGTT 59.502 50.000 20.67 0.00 0.00 3.50
38 39 3.700038 CCTCGAGGCTCTTTTCTAGGTTA 59.300 47.826 20.67 0.00 0.00 2.85
39 40 4.342665 CCTCGAGGCTCTTTTCTAGGTTAT 59.657 45.833 20.67 0.00 0.00 1.89
40 41 5.163395 CCTCGAGGCTCTTTTCTAGGTTATT 60.163 44.000 20.67 0.00 0.00 1.40
41 42 6.295719 TCGAGGCTCTTTTCTAGGTTATTT 57.704 37.500 13.50 0.00 0.00 1.40
42 43 7.414222 TCGAGGCTCTTTTCTAGGTTATTTA 57.586 36.000 13.50 0.00 0.00 1.40
43 44 7.844009 TCGAGGCTCTTTTCTAGGTTATTTAA 58.156 34.615 13.50 0.00 0.00 1.52
44 45 8.483758 TCGAGGCTCTTTTCTAGGTTATTTAAT 58.516 33.333 13.50 0.00 0.00 1.40
45 46 9.110502 CGAGGCTCTTTTCTAGGTTATTTAATT 57.889 33.333 13.50 0.00 0.00 1.40
47 48 9.975218 AGGCTCTTTTCTAGGTTATTTAATTGA 57.025 29.630 0.00 0.00 0.00 2.57
56 57 9.793259 TCTAGGTTATTTAATTGATCCATCCAC 57.207 33.333 0.00 0.00 0.00 4.02
57 58 7.510549 AGGTTATTTAATTGATCCATCCACG 57.489 36.000 0.00 0.00 0.00 4.94
58 59 7.287061 AGGTTATTTAATTGATCCATCCACGA 58.713 34.615 0.00 0.00 0.00 4.35
59 60 7.777910 AGGTTATTTAATTGATCCATCCACGAA 59.222 33.333 0.00 0.00 0.00 3.85
60 61 8.576442 GGTTATTTAATTGATCCATCCACGAAT 58.424 33.333 0.00 0.00 0.00 3.34
61 62 9.965824 GTTATTTAATTGATCCATCCACGAATT 57.034 29.630 0.00 0.00 0.00 2.17
64 65 8.746052 TTTAATTGATCCATCCACGAATTAGT 57.254 30.769 0.00 0.00 0.00 2.24
65 66 6.867662 AATTGATCCATCCACGAATTAGTC 57.132 37.500 0.00 0.00 0.00 2.59
66 67 4.336889 TGATCCATCCACGAATTAGTCC 57.663 45.455 0.00 0.00 0.00 3.85
67 68 3.967326 TGATCCATCCACGAATTAGTCCT 59.033 43.478 0.00 0.00 0.00 3.85
68 69 5.144832 TGATCCATCCACGAATTAGTCCTA 58.855 41.667 0.00 0.00 0.00 2.94
69 70 5.243954 TGATCCATCCACGAATTAGTCCTAG 59.756 44.000 0.00 0.00 0.00 3.02
70 71 3.895656 TCCATCCACGAATTAGTCCTAGG 59.104 47.826 0.82 0.82 0.00 3.02
71 72 3.555168 CCATCCACGAATTAGTCCTAGGC 60.555 52.174 2.96 0.00 0.00 3.93
72 73 2.037144 TCCACGAATTAGTCCTAGGCC 58.963 52.381 2.96 0.00 0.00 5.19
73 74 1.070289 CCACGAATTAGTCCTAGGCCC 59.930 57.143 2.96 0.00 0.00 5.80
74 75 1.760613 CACGAATTAGTCCTAGGCCCA 59.239 52.381 2.96 0.00 0.00 5.36
75 76 2.040178 ACGAATTAGTCCTAGGCCCAG 58.960 52.381 2.96 0.00 0.00 4.45
76 77 2.317040 CGAATTAGTCCTAGGCCCAGA 58.683 52.381 2.96 0.00 0.00 3.86
77 78 2.698797 CGAATTAGTCCTAGGCCCAGAA 59.301 50.000 2.96 0.00 0.00 3.02
78 79 3.134081 CGAATTAGTCCTAGGCCCAGAAA 59.866 47.826 2.96 0.00 0.00 2.52
79 80 4.709250 GAATTAGTCCTAGGCCCAGAAAG 58.291 47.826 2.96 0.00 0.00 2.62
80 81 3.484953 TTAGTCCTAGGCCCAGAAAGA 57.515 47.619 2.96 0.00 0.00 2.52
81 82 1.872773 AGTCCTAGGCCCAGAAAGAG 58.127 55.000 2.96 0.00 0.00 2.85
82 83 0.179234 GTCCTAGGCCCAGAAAGAGC 59.821 60.000 2.96 0.00 0.00 4.09
83 84 0.043334 TCCTAGGCCCAGAAAGAGCT 59.957 55.000 2.96 0.00 0.00 4.09
84 85 0.467804 CCTAGGCCCAGAAAGAGCTC 59.532 60.000 5.27 5.27 0.00 4.09
85 86 0.467804 CTAGGCCCAGAAAGAGCTCC 59.532 60.000 10.93 0.00 0.00 4.70
86 87 0.252696 TAGGCCCAGAAAGAGCTCCA 60.253 55.000 10.93 0.00 0.00 3.86
87 88 1.077858 GGCCCAGAAAGAGCTCCAG 60.078 63.158 10.93 0.00 0.00 3.86
88 89 1.077858 GCCCAGAAAGAGCTCCAGG 60.078 63.158 10.93 5.35 0.00 4.45
89 90 1.557269 GCCCAGAAAGAGCTCCAGGA 61.557 60.000 10.93 0.00 0.00 3.86
90 91 0.987294 CCCAGAAAGAGCTCCAGGAA 59.013 55.000 10.93 0.00 0.00 3.36
91 92 1.352352 CCCAGAAAGAGCTCCAGGAAA 59.648 52.381 10.93 0.00 0.00 3.13
92 93 2.617532 CCCAGAAAGAGCTCCAGGAAAG 60.618 54.545 10.93 0.00 0.00 2.62
93 94 2.039613 CCAGAAAGAGCTCCAGGAAAGT 59.960 50.000 10.93 0.00 0.00 2.66
94 95 3.333804 CAGAAAGAGCTCCAGGAAAGTC 58.666 50.000 10.93 0.00 0.00 3.01
95 96 3.007831 CAGAAAGAGCTCCAGGAAAGTCT 59.992 47.826 10.93 0.00 0.00 3.24
96 97 4.221703 CAGAAAGAGCTCCAGGAAAGTCTA 59.778 45.833 10.93 0.00 0.00 2.59
97 98 4.221924 AGAAAGAGCTCCAGGAAAGTCTAC 59.778 45.833 10.93 0.00 0.00 2.59
98 99 2.096248 AGAGCTCCAGGAAAGTCTACG 58.904 52.381 10.93 0.00 0.00 3.51
99 100 1.135333 GAGCTCCAGGAAAGTCTACGG 59.865 57.143 0.87 0.00 0.00 4.02
100 101 0.175989 GCTCCAGGAAAGTCTACGGG 59.824 60.000 0.00 0.00 0.00 5.28
101 102 0.175989 CTCCAGGAAAGTCTACGGGC 59.824 60.000 0.00 0.00 0.00 6.13
102 103 0.543410 TCCAGGAAAGTCTACGGGCA 60.543 55.000 0.00 0.00 0.00 5.36
103 104 0.323629 CCAGGAAAGTCTACGGGCAA 59.676 55.000 0.00 0.00 0.00 4.52
104 105 1.676014 CCAGGAAAGTCTACGGGCAAG 60.676 57.143 0.00 0.00 0.00 4.01
105 106 0.036294 AGGAAAGTCTACGGGCAAGC 60.036 55.000 0.00 0.00 0.00 4.01
106 107 0.321298 GGAAAGTCTACGGGCAAGCA 60.321 55.000 0.00 0.00 0.00 3.91
107 108 1.079503 GAAAGTCTACGGGCAAGCAG 58.920 55.000 0.00 0.00 0.00 4.24
108 109 0.685097 AAAGTCTACGGGCAAGCAGA 59.315 50.000 0.00 0.00 0.00 4.26
109 110 0.247736 AAGTCTACGGGCAAGCAGAG 59.752 55.000 0.00 0.00 0.00 3.35
110 111 0.612174 AGTCTACGGGCAAGCAGAGA 60.612 55.000 0.00 0.00 0.00 3.10
111 112 0.458716 GTCTACGGGCAAGCAGAGAC 60.459 60.000 0.00 0.00 0.00 3.36
112 113 1.517257 CTACGGGCAAGCAGAGACG 60.517 63.158 0.00 0.00 0.00 4.18
113 114 2.214181 CTACGGGCAAGCAGAGACGT 62.214 60.000 0.00 0.00 38.23 4.34
114 115 2.209064 TACGGGCAAGCAGAGACGTC 62.209 60.000 7.70 7.70 35.97 4.34
115 116 2.435059 GGGCAAGCAGAGACGTCC 60.435 66.667 13.01 3.77 0.00 4.79
116 117 2.343758 GGCAAGCAGAGACGTCCA 59.656 61.111 13.01 0.00 0.00 4.02
117 118 1.078848 GGCAAGCAGAGACGTCCAT 60.079 57.895 13.01 0.00 0.00 3.41
118 119 0.175760 GGCAAGCAGAGACGTCCATA 59.824 55.000 13.01 0.00 0.00 2.74
119 120 1.202580 GGCAAGCAGAGACGTCCATAT 60.203 52.381 13.01 0.00 0.00 1.78
120 121 2.131183 GCAAGCAGAGACGTCCATATC 58.869 52.381 13.01 2.86 0.00 1.63
121 122 2.389059 CAAGCAGAGACGTCCATATCG 58.611 52.381 13.01 1.51 0.00 2.92
122 123 1.968704 AGCAGAGACGTCCATATCGA 58.031 50.000 13.01 0.00 0.00 3.59
123 124 1.604755 AGCAGAGACGTCCATATCGAC 59.395 52.381 13.01 1.18 0.00 4.20
124 125 1.335142 GCAGAGACGTCCATATCGACC 60.335 57.143 13.01 0.00 0.00 4.79
125 126 1.947456 CAGAGACGTCCATATCGACCA 59.053 52.381 13.01 0.00 0.00 4.02
126 127 2.031595 CAGAGACGTCCATATCGACCAG 60.032 54.545 13.01 0.00 0.00 4.00
127 128 0.669077 AGACGTCCATATCGACCAGC 59.331 55.000 13.01 0.00 0.00 4.85
128 129 0.669077 GACGTCCATATCGACCAGCT 59.331 55.000 3.51 0.00 0.00 4.24
129 130 0.385751 ACGTCCATATCGACCAGCTG 59.614 55.000 6.78 6.78 0.00 4.24
130 131 0.941463 CGTCCATATCGACCAGCTGC 60.941 60.000 8.66 0.00 0.00 5.25
131 132 0.390860 GTCCATATCGACCAGCTGCT 59.609 55.000 8.66 0.00 0.00 4.24
132 133 1.613925 GTCCATATCGACCAGCTGCTA 59.386 52.381 8.66 0.00 0.00 3.49
133 134 2.232452 GTCCATATCGACCAGCTGCTAT 59.768 50.000 8.66 0.91 0.00 2.97
134 135 2.493675 TCCATATCGACCAGCTGCTATC 59.506 50.000 8.66 4.47 0.00 2.08
135 136 2.232208 CCATATCGACCAGCTGCTATCA 59.768 50.000 8.66 0.00 0.00 2.15
136 137 3.306294 CCATATCGACCAGCTGCTATCAA 60.306 47.826 8.66 0.00 0.00 2.57
137 138 4.502016 CATATCGACCAGCTGCTATCAAT 58.498 43.478 8.66 0.00 0.00 2.57
138 139 2.515926 TCGACCAGCTGCTATCAATC 57.484 50.000 8.66 0.00 0.00 2.67
139 140 1.135046 CGACCAGCTGCTATCAATCG 58.865 55.000 8.66 3.93 0.00 3.34
140 141 1.269257 CGACCAGCTGCTATCAATCGA 60.269 52.381 8.66 0.00 0.00 3.59
141 142 2.799562 CGACCAGCTGCTATCAATCGAA 60.800 50.000 8.66 0.00 0.00 3.71
142 143 3.397482 GACCAGCTGCTATCAATCGAAT 58.603 45.455 8.66 0.00 0.00 3.34
143 144 3.397482 ACCAGCTGCTATCAATCGAATC 58.603 45.455 8.66 0.00 0.00 2.52
144 145 3.181462 ACCAGCTGCTATCAATCGAATCA 60.181 43.478 8.66 0.00 0.00 2.57
145 146 4.001652 CCAGCTGCTATCAATCGAATCAT 58.998 43.478 8.66 0.00 0.00 2.45
146 147 4.093115 CCAGCTGCTATCAATCGAATCATC 59.907 45.833 8.66 0.00 0.00 2.92
147 148 4.093115 CAGCTGCTATCAATCGAATCATCC 59.907 45.833 0.00 0.00 0.00 3.51
148 149 3.999001 GCTGCTATCAATCGAATCATCCA 59.001 43.478 0.00 0.00 0.00 3.41
149 150 4.634883 GCTGCTATCAATCGAATCATCCAT 59.365 41.667 0.00 0.00 0.00 3.41
150 151 5.123502 GCTGCTATCAATCGAATCATCCATT 59.876 40.000 0.00 0.00 0.00 3.16
151 152 6.349115 GCTGCTATCAATCGAATCATCCATTT 60.349 38.462 0.00 0.00 0.00 2.32
152 153 6.905578 TGCTATCAATCGAATCATCCATTTG 58.094 36.000 0.00 0.00 0.00 2.32
153 154 5.798934 GCTATCAATCGAATCATCCATTTGC 59.201 40.000 0.00 0.00 0.00 3.68
154 155 5.777850 ATCAATCGAATCATCCATTTGCA 57.222 34.783 0.00 0.00 0.00 4.08
155 156 5.579564 TCAATCGAATCATCCATTTGCAA 57.420 34.783 0.00 0.00 0.00 4.08
156 157 5.342433 TCAATCGAATCATCCATTTGCAAC 58.658 37.500 0.00 0.00 0.00 4.17
157 158 5.125900 TCAATCGAATCATCCATTTGCAACT 59.874 36.000 0.00 0.00 0.00 3.16
158 159 4.621068 TCGAATCATCCATTTGCAACTC 57.379 40.909 0.00 0.00 0.00 3.01
159 160 4.264253 TCGAATCATCCATTTGCAACTCT 58.736 39.130 0.00 0.00 0.00 3.24
160 161 4.333649 TCGAATCATCCATTTGCAACTCTC 59.666 41.667 0.00 0.00 0.00 3.20
161 162 4.095334 CGAATCATCCATTTGCAACTCTCA 59.905 41.667 0.00 0.00 0.00 3.27
162 163 5.220989 CGAATCATCCATTTGCAACTCTCAT 60.221 40.000 0.00 0.00 0.00 2.90
163 164 6.017687 CGAATCATCCATTTGCAACTCTCATA 60.018 38.462 0.00 0.00 0.00 2.15
164 165 7.308408 CGAATCATCCATTTGCAACTCTCATAT 60.308 37.037 0.00 0.00 0.00 1.78
165 166 6.872628 TCATCCATTTGCAACTCTCATATC 57.127 37.500 0.00 0.00 0.00 1.63
166 167 5.766670 TCATCCATTTGCAACTCTCATATCC 59.233 40.000 0.00 0.00 0.00 2.59
167 168 5.114764 TCCATTTGCAACTCTCATATCCA 57.885 39.130 0.00 0.00 0.00 3.41
168 169 4.883585 TCCATTTGCAACTCTCATATCCAC 59.116 41.667 0.00 0.00 0.00 4.02
169 170 4.885907 CCATTTGCAACTCTCATATCCACT 59.114 41.667 0.00 0.00 0.00 4.00
170 171 5.359009 CCATTTGCAACTCTCATATCCACTT 59.641 40.000 0.00 0.00 0.00 3.16
171 172 5.885230 TTTGCAACTCTCATATCCACTTG 57.115 39.130 0.00 0.00 0.00 3.16
172 173 4.824479 TGCAACTCTCATATCCACTTGA 57.176 40.909 0.00 0.00 0.00 3.02
173 174 5.164620 TGCAACTCTCATATCCACTTGAA 57.835 39.130 0.00 0.00 0.00 2.69
174 175 4.937620 TGCAACTCTCATATCCACTTGAAC 59.062 41.667 0.00 0.00 0.00 3.18
175 176 4.937620 GCAACTCTCATATCCACTTGAACA 59.062 41.667 0.00 0.00 0.00 3.18
176 177 5.163814 GCAACTCTCATATCCACTTGAACAC 60.164 44.000 0.00 0.00 0.00 3.32
177 178 5.091261 ACTCTCATATCCACTTGAACACC 57.909 43.478 0.00 0.00 0.00 4.16
178 179 4.780021 ACTCTCATATCCACTTGAACACCT 59.220 41.667 0.00 0.00 0.00 4.00
179 180 5.105146 ACTCTCATATCCACTTGAACACCTC 60.105 44.000 0.00 0.00 0.00 3.85
180 181 5.026121 TCTCATATCCACTTGAACACCTCT 58.974 41.667 0.00 0.00 0.00 3.69
181 182 5.089970 TCATATCCACTTGAACACCTCTG 57.910 43.478 0.00 0.00 0.00 3.35
182 183 4.777366 TCATATCCACTTGAACACCTCTGA 59.223 41.667 0.00 0.00 0.00 3.27
183 184 2.910688 TCCACTTGAACACCTCTGAC 57.089 50.000 0.00 0.00 0.00 3.51
184 185 1.068588 TCCACTTGAACACCTCTGACG 59.931 52.381 0.00 0.00 0.00 4.35
185 186 1.068588 CCACTTGAACACCTCTGACGA 59.931 52.381 0.00 0.00 0.00 4.20
186 187 2.289072 CCACTTGAACACCTCTGACGAT 60.289 50.000 0.00 0.00 0.00 3.73
187 188 2.733552 CACTTGAACACCTCTGACGATG 59.266 50.000 0.00 0.00 0.00 3.84
188 189 2.628178 ACTTGAACACCTCTGACGATGA 59.372 45.455 0.00 0.00 0.00 2.92
189 190 3.259374 ACTTGAACACCTCTGACGATGAT 59.741 43.478 0.00 0.00 0.00 2.45
190 191 3.510388 TGAACACCTCTGACGATGATC 57.490 47.619 0.00 0.00 0.00 2.92
191 192 2.159379 TGAACACCTCTGACGATGATCG 60.159 50.000 14.01 14.01 46.93 3.69
192 193 1.751437 ACACCTCTGACGATGATCGA 58.249 50.000 22.88 0.00 43.74 3.59
193 194 2.302260 ACACCTCTGACGATGATCGAT 58.698 47.619 22.88 0.00 43.74 3.59
194 195 2.292016 ACACCTCTGACGATGATCGATC 59.708 50.000 22.88 18.72 43.74 3.69
195 196 2.291741 CACCTCTGACGATGATCGATCA 59.708 50.000 29.09 29.09 43.74 2.92
196 197 2.292016 ACCTCTGACGATGATCGATCAC 59.708 50.000 29.49 20.60 43.74 3.06
197 198 2.291741 CCTCTGACGATGATCGATCACA 59.708 50.000 29.49 20.62 43.74 3.58
198 199 3.057666 CCTCTGACGATGATCGATCACAT 60.058 47.826 29.49 15.66 43.74 3.21
199 200 3.893720 TCTGACGATGATCGATCACATG 58.106 45.455 29.49 22.34 43.74 3.21
200 201 2.985139 CTGACGATGATCGATCACATGG 59.015 50.000 29.49 18.08 43.74 3.66
201 202 2.362077 TGACGATGATCGATCACATGGT 59.638 45.455 29.49 21.03 43.74 3.55
202 203 2.728318 GACGATGATCGATCACATGGTG 59.272 50.000 29.49 16.89 43.74 4.17
203 204 2.101415 ACGATGATCGATCACATGGTGT 59.899 45.455 29.49 17.47 43.74 4.16
204 205 2.473984 CGATGATCGATCACATGGTGTG 59.526 50.000 29.49 9.82 45.40 3.82
215 216 2.771089 ACATGGTGTGAGTAAGTGCTG 58.229 47.619 0.00 0.00 0.00 4.41
216 217 2.104792 ACATGGTGTGAGTAAGTGCTGT 59.895 45.455 0.00 0.00 0.00 4.40
217 218 3.141398 CATGGTGTGAGTAAGTGCTGTT 58.859 45.455 0.00 0.00 0.00 3.16
218 219 4.202315 ACATGGTGTGAGTAAGTGCTGTTA 60.202 41.667 0.00 0.00 0.00 2.41
219 220 3.990092 TGGTGTGAGTAAGTGCTGTTAG 58.010 45.455 0.00 0.00 0.00 2.34
220 221 3.244078 TGGTGTGAGTAAGTGCTGTTAGG 60.244 47.826 0.00 0.00 0.00 2.69
221 222 3.006537 GGTGTGAGTAAGTGCTGTTAGGA 59.993 47.826 0.00 0.00 0.00 2.94
222 223 4.502604 GGTGTGAGTAAGTGCTGTTAGGAA 60.503 45.833 0.00 0.00 0.00 3.36
223 224 5.238583 GTGTGAGTAAGTGCTGTTAGGAAT 58.761 41.667 0.00 0.00 0.00 3.01
224 225 5.701290 GTGTGAGTAAGTGCTGTTAGGAATT 59.299 40.000 0.00 0.00 0.00 2.17
225 226 6.872020 GTGTGAGTAAGTGCTGTTAGGAATTA 59.128 38.462 0.00 0.00 0.00 1.40
226 227 7.386848 GTGTGAGTAAGTGCTGTTAGGAATTAA 59.613 37.037 0.00 0.00 28.56 1.40
227 228 8.100791 TGTGAGTAAGTGCTGTTAGGAATTAAT 58.899 33.333 0.00 0.00 28.56 1.40
228 229 8.947115 GTGAGTAAGTGCTGTTAGGAATTAATT 58.053 33.333 0.00 0.00 28.56 1.40
265 266 8.812147 TTAACTATTAATCACTGCTATGACGG 57.188 34.615 0.00 0.00 0.00 4.79
266 267 6.406692 ACTATTAATCACTGCTATGACGGT 57.593 37.500 0.00 0.00 0.00 4.83
267 268 6.216569 ACTATTAATCACTGCTATGACGGTG 58.783 40.000 0.00 3.06 46.37 4.94
268 269 1.656652 AATCACTGCTATGACGGTGC 58.343 50.000 4.34 0.00 44.94 5.01
269 270 0.179073 ATCACTGCTATGACGGTGCC 60.179 55.000 4.34 0.00 44.94 5.01
270 271 1.079197 CACTGCTATGACGGTGCCA 60.079 57.895 0.00 0.00 39.90 4.92
271 272 1.079127 ACTGCTATGACGGTGCCAC 60.079 57.895 0.00 0.00 0.00 5.01
272 273 1.219124 CTGCTATGACGGTGCCACT 59.781 57.895 0.00 0.00 0.00 4.00
273 274 0.391661 CTGCTATGACGGTGCCACTT 60.392 55.000 0.00 0.00 0.00 3.16
274 275 0.036164 TGCTATGACGGTGCCACTTT 59.964 50.000 0.00 0.00 0.00 2.66
275 276 1.165270 GCTATGACGGTGCCACTTTT 58.835 50.000 0.00 0.00 0.00 2.27
276 277 1.135689 GCTATGACGGTGCCACTTTTG 60.136 52.381 0.00 0.00 0.00 2.44
297 298 3.013276 GCAACTGCCTCCTTTTGTAAC 57.987 47.619 0.00 0.00 34.31 2.50
298 299 2.288213 GCAACTGCCTCCTTTTGTAACC 60.288 50.000 0.00 0.00 34.31 2.85
299 300 1.892209 ACTGCCTCCTTTTGTAACCG 58.108 50.000 0.00 0.00 0.00 4.44
300 301 0.521735 CTGCCTCCTTTTGTAACCGC 59.478 55.000 0.00 0.00 0.00 5.68
301 302 0.891904 TGCCTCCTTTTGTAACCGCC 60.892 55.000 0.00 0.00 0.00 6.13
302 303 0.608308 GCCTCCTTTTGTAACCGCCT 60.608 55.000 0.00 0.00 0.00 5.52
303 304 1.905637 CCTCCTTTTGTAACCGCCTT 58.094 50.000 0.00 0.00 0.00 4.35
304 305 1.539827 CCTCCTTTTGTAACCGCCTTG 59.460 52.381 0.00 0.00 0.00 3.61
305 306 2.227194 CTCCTTTTGTAACCGCCTTGT 58.773 47.619 0.00 0.00 0.00 3.16
306 307 3.404899 CTCCTTTTGTAACCGCCTTGTA 58.595 45.455 0.00 0.00 0.00 2.41
307 308 3.816523 CTCCTTTTGTAACCGCCTTGTAA 59.183 43.478 0.00 0.00 0.00 2.41
308 309 4.205587 TCCTTTTGTAACCGCCTTGTAAA 58.794 39.130 0.00 0.00 0.00 2.01
309 310 4.036616 TCCTTTTGTAACCGCCTTGTAAAC 59.963 41.667 0.00 0.00 0.00 2.01
310 311 4.037089 CCTTTTGTAACCGCCTTGTAAACT 59.963 41.667 0.00 0.00 0.00 2.66
311 312 4.555348 TTTGTAACCGCCTTGTAAACTG 57.445 40.909 0.00 0.00 0.00 3.16
312 313 2.496111 TGTAACCGCCTTGTAAACTGG 58.504 47.619 0.00 0.00 0.00 4.00
313 314 1.808343 GTAACCGCCTTGTAAACTGGG 59.192 52.381 0.00 0.00 0.00 4.45
314 315 0.184211 AACCGCCTTGTAAACTGGGT 59.816 50.000 0.00 0.00 0.00 4.51
315 316 1.058284 ACCGCCTTGTAAACTGGGTA 58.942 50.000 0.00 0.00 0.00 3.69
316 317 1.631898 ACCGCCTTGTAAACTGGGTAT 59.368 47.619 0.00 0.00 0.00 2.73
317 318 2.839425 ACCGCCTTGTAAACTGGGTATA 59.161 45.455 0.00 0.00 0.00 1.47
318 319 3.263937 ACCGCCTTGTAAACTGGGTATAA 59.736 43.478 0.00 0.00 0.00 0.98
319 320 4.263418 ACCGCCTTGTAAACTGGGTATAAA 60.263 41.667 0.00 0.00 0.00 1.40
320 321 4.885325 CCGCCTTGTAAACTGGGTATAAAT 59.115 41.667 0.00 0.00 0.00 1.40
321 322 6.056884 CCGCCTTGTAAACTGGGTATAAATA 58.943 40.000 0.00 0.00 0.00 1.40
322 323 6.017687 CCGCCTTGTAAACTGGGTATAAATAC 60.018 42.308 0.00 0.00 0.00 1.89
337 338 8.934023 GGTATAAATACCCCAATCTTCAATCA 57.066 34.615 7.80 0.00 45.62 2.57
338 339 9.362151 GGTATAAATACCCCAATCTTCAATCAA 57.638 33.333 7.80 0.00 45.62 2.57
343 344 9.713684 AAATACCCCAATCTTCAATCAATAGAA 57.286 29.630 0.00 0.00 0.00 2.10
344 345 9.887862 AATACCCCAATCTTCAATCAATAGAAT 57.112 29.630 0.00 0.00 0.00 2.40
347 348 9.136323 ACCCCAATCTTCAATCAATAGAATAAC 57.864 33.333 0.00 0.00 0.00 1.89
348 349 9.359653 CCCCAATCTTCAATCAATAGAATAACT 57.640 33.333 0.00 0.00 0.00 2.24
1129 1172 2.685017 TGGCGGAGGATGCACTCT 60.685 61.111 4.51 0.00 37.63 3.24
2023 3629 9.049523 CACTATTACTGTAAGGTCTACATCGTA 57.950 37.037 6.40 0.00 39.30 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.250200 CCTCGAGGTAGCATTATACTCTCT 58.750 45.833 24.04 0.00 0.00 3.10
1 2 4.142556 GCCTCGAGGTAGCATTATACTCTC 60.143 50.000 31.43 6.09 37.57 3.20
2 3 3.759618 GCCTCGAGGTAGCATTATACTCT 59.240 47.826 31.43 0.00 37.57 3.24
3 4 3.759618 AGCCTCGAGGTAGCATTATACTC 59.240 47.826 31.43 10.77 37.57 2.59
4 5 3.759618 GAGCCTCGAGGTAGCATTATACT 59.240 47.826 31.43 16.09 37.57 2.12
5 6 3.759618 AGAGCCTCGAGGTAGCATTATAC 59.240 47.826 31.43 11.49 37.57 1.47
6 7 4.035612 AGAGCCTCGAGGTAGCATTATA 57.964 45.455 31.43 0.00 37.57 0.98
7 8 2.883026 AGAGCCTCGAGGTAGCATTAT 58.117 47.619 31.43 8.55 37.57 1.28
8 9 2.366640 AGAGCCTCGAGGTAGCATTA 57.633 50.000 31.43 0.00 37.57 1.90
9 10 1.490574 AAGAGCCTCGAGGTAGCATT 58.509 50.000 31.43 16.54 37.57 3.56
10 11 1.490574 AAAGAGCCTCGAGGTAGCAT 58.509 50.000 31.43 13.63 37.57 3.79
11 12 1.204941 GAAAAGAGCCTCGAGGTAGCA 59.795 52.381 31.43 0.00 37.57 3.49
12 13 1.478916 AGAAAAGAGCCTCGAGGTAGC 59.521 52.381 31.43 20.31 37.57 3.58
13 14 3.316868 CCTAGAAAAGAGCCTCGAGGTAG 59.683 52.174 31.43 20.72 37.57 3.18
14 15 3.288964 CCTAGAAAAGAGCCTCGAGGTA 58.711 50.000 31.43 12.98 37.57 3.08
15 16 2.104170 CCTAGAAAAGAGCCTCGAGGT 58.896 52.381 31.43 18.69 37.57 3.85
16 17 2.104170 ACCTAGAAAAGAGCCTCGAGG 58.896 52.381 27.83 27.83 39.58 4.63
17 18 3.878160 AACCTAGAAAAGAGCCTCGAG 57.122 47.619 5.13 5.13 0.00 4.04
18 19 5.934402 AATAACCTAGAAAAGAGCCTCGA 57.066 39.130 0.00 0.00 0.00 4.04
19 20 8.664211 ATTAAATAACCTAGAAAAGAGCCTCG 57.336 34.615 0.00 0.00 0.00 4.63
21 22 9.975218 TCAATTAAATAACCTAGAAAAGAGCCT 57.025 29.630 0.00 0.00 0.00 4.58
30 31 9.793259 GTGGATGGATCAATTAAATAACCTAGA 57.207 33.333 0.00 0.00 0.00 2.43
31 32 8.721478 CGTGGATGGATCAATTAAATAACCTAG 58.279 37.037 0.00 0.00 0.00 3.02
32 33 8.433599 TCGTGGATGGATCAATTAAATAACCTA 58.566 33.333 0.00 0.00 0.00 3.08
33 34 7.287061 TCGTGGATGGATCAATTAAATAACCT 58.713 34.615 0.00 0.00 0.00 3.50
34 35 7.504924 TCGTGGATGGATCAATTAAATAACC 57.495 36.000 0.00 0.00 0.00 2.85
35 36 9.965824 AATTCGTGGATGGATCAATTAAATAAC 57.034 29.630 0.00 0.00 0.00 1.89
38 39 9.354673 ACTAATTCGTGGATGGATCAATTAAAT 57.645 29.630 0.00 0.00 0.00 1.40
39 40 8.746052 ACTAATTCGTGGATGGATCAATTAAA 57.254 30.769 0.00 0.00 0.00 1.52
40 41 7.444183 GGACTAATTCGTGGATGGATCAATTAA 59.556 37.037 0.00 0.00 0.00 1.40
41 42 6.934645 GGACTAATTCGTGGATGGATCAATTA 59.065 38.462 0.00 0.00 0.00 1.40
42 43 5.765182 GGACTAATTCGTGGATGGATCAATT 59.235 40.000 0.00 0.00 0.00 2.32
43 44 5.072329 AGGACTAATTCGTGGATGGATCAAT 59.928 40.000 0.00 0.00 0.00 2.57
44 45 4.408921 AGGACTAATTCGTGGATGGATCAA 59.591 41.667 0.00 0.00 0.00 2.57
45 46 3.967326 AGGACTAATTCGTGGATGGATCA 59.033 43.478 0.00 0.00 0.00 2.92
46 47 4.608948 AGGACTAATTCGTGGATGGATC 57.391 45.455 0.00 0.00 0.00 3.36
47 48 4.528596 CCTAGGACTAATTCGTGGATGGAT 59.471 45.833 1.05 0.00 0.00 3.41
48 49 3.895656 CCTAGGACTAATTCGTGGATGGA 59.104 47.826 1.05 0.00 0.00 3.41
49 50 3.555168 GCCTAGGACTAATTCGTGGATGG 60.555 52.174 14.75 0.00 0.00 3.51
50 51 3.555168 GGCCTAGGACTAATTCGTGGATG 60.555 52.174 14.75 0.00 0.00 3.51
51 52 2.633481 GGCCTAGGACTAATTCGTGGAT 59.367 50.000 14.75 0.00 0.00 3.41
52 53 2.037144 GGCCTAGGACTAATTCGTGGA 58.963 52.381 14.75 0.00 0.00 4.02
53 54 1.070289 GGGCCTAGGACTAATTCGTGG 59.930 57.143 16.16 0.00 0.00 4.94
54 55 1.760613 TGGGCCTAGGACTAATTCGTG 59.239 52.381 16.16 0.00 0.00 4.35
55 56 2.040178 CTGGGCCTAGGACTAATTCGT 58.960 52.381 16.16 0.00 0.00 3.85
56 57 2.317040 TCTGGGCCTAGGACTAATTCG 58.683 52.381 16.16 0.00 0.00 3.34
57 58 4.409247 TCTTTCTGGGCCTAGGACTAATTC 59.591 45.833 16.16 0.00 0.00 2.17
58 59 4.371681 TCTTTCTGGGCCTAGGACTAATT 58.628 43.478 16.16 0.00 0.00 1.40
59 60 3.970640 CTCTTTCTGGGCCTAGGACTAAT 59.029 47.826 16.16 0.00 0.00 1.73
60 61 3.375699 CTCTTTCTGGGCCTAGGACTAA 58.624 50.000 16.16 3.93 0.00 2.24
61 62 2.955461 GCTCTTTCTGGGCCTAGGACTA 60.955 54.545 16.16 7.79 0.00 2.59
62 63 1.872773 CTCTTTCTGGGCCTAGGACT 58.127 55.000 16.16 0.00 0.00 3.85
63 64 0.179234 GCTCTTTCTGGGCCTAGGAC 59.821 60.000 17.16 10.52 0.00 3.85
64 65 0.043334 AGCTCTTTCTGGGCCTAGGA 59.957 55.000 17.16 4.07 0.00 2.94
65 66 0.467804 GAGCTCTTTCTGGGCCTAGG 59.532 60.000 17.16 3.67 0.00 3.02
66 67 0.467804 GGAGCTCTTTCTGGGCCTAG 59.532 60.000 14.64 10.47 0.00 3.02
67 68 0.252696 TGGAGCTCTTTCTGGGCCTA 60.253 55.000 14.64 0.00 0.00 3.93
68 69 1.539869 TGGAGCTCTTTCTGGGCCT 60.540 57.895 14.64 0.00 0.00 5.19
69 70 1.077858 CTGGAGCTCTTTCTGGGCC 60.078 63.158 14.64 0.00 0.00 5.80
70 71 1.077858 CCTGGAGCTCTTTCTGGGC 60.078 63.158 14.64 0.00 0.00 5.36
71 72 0.987294 TTCCTGGAGCTCTTTCTGGG 59.013 55.000 14.64 7.17 0.00 4.45
72 73 2.039613 ACTTTCCTGGAGCTCTTTCTGG 59.960 50.000 14.64 10.53 0.00 3.86
73 74 3.007831 AGACTTTCCTGGAGCTCTTTCTG 59.992 47.826 14.64 1.06 0.00 3.02
74 75 3.247162 AGACTTTCCTGGAGCTCTTTCT 58.753 45.455 14.64 1.47 0.00 2.52
75 76 3.694043 AGACTTTCCTGGAGCTCTTTC 57.306 47.619 14.64 0.00 0.00 2.62
76 77 3.056465 CGTAGACTTTCCTGGAGCTCTTT 60.056 47.826 14.64 0.00 0.00 2.52
77 78 2.494073 CGTAGACTTTCCTGGAGCTCTT 59.506 50.000 14.64 0.00 0.00 2.85
78 79 2.096248 CGTAGACTTTCCTGGAGCTCT 58.904 52.381 14.64 1.10 0.00 4.09
79 80 1.135333 CCGTAGACTTTCCTGGAGCTC 59.865 57.143 4.71 4.71 0.00 4.09
80 81 1.187087 CCGTAGACTTTCCTGGAGCT 58.813 55.000 0.00 0.00 0.00 4.09
81 82 0.175989 CCCGTAGACTTTCCTGGAGC 59.824 60.000 0.00 0.00 0.00 4.70
82 83 0.175989 GCCCGTAGACTTTCCTGGAG 59.824 60.000 0.00 0.00 0.00 3.86
83 84 0.543410 TGCCCGTAGACTTTCCTGGA 60.543 55.000 0.00 0.00 0.00 3.86
84 85 0.323629 TTGCCCGTAGACTTTCCTGG 59.676 55.000 0.00 0.00 0.00 4.45
85 86 1.726853 CTTGCCCGTAGACTTTCCTG 58.273 55.000 0.00 0.00 0.00 3.86
86 87 0.036294 GCTTGCCCGTAGACTTTCCT 60.036 55.000 0.00 0.00 0.00 3.36
87 88 0.321298 TGCTTGCCCGTAGACTTTCC 60.321 55.000 0.00 0.00 0.00 3.13
88 89 1.079503 CTGCTTGCCCGTAGACTTTC 58.920 55.000 0.00 0.00 0.00 2.62
89 90 0.685097 TCTGCTTGCCCGTAGACTTT 59.315 50.000 0.00 0.00 0.00 2.66
90 91 0.247736 CTCTGCTTGCCCGTAGACTT 59.752 55.000 0.00 0.00 0.00 3.01
91 92 0.612174 TCTCTGCTTGCCCGTAGACT 60.612 55.000 0.00 0.00 0.00 3.24
92 93 0.458716 GTCTCTGCTTGCCCGTAGAC 60.459 60.000 0.00 0.00 0.00 2.59
93 94 1.890894 GTCTCTGCTTGCCCGTAGA 59.109 57.895 0.00 0.00 0.00 2.59
94 95 1.517257 CGTCTCTGCTTGCCCGTAG 60.517 63.158 0.00 0.00 0.00 3.51
95 96 2.209064 GACGTCTCTGCTTGCCCGTA 62.209 60.000 8.70 0.00 0.00 4.02
96 97 3.575351 GACGTCTCTGCTTGCCCGT 62.575 63.158 8.70 0.00 0.00 5.28
97 98 2.811317 GACGTCTCTGCTTGCCCG 60.811 66.667 8.70 0.00 0.00 6.13
98 99 2.435059 GGACGTCTCTGCTTGCCC 60.435 66.667 16.46 0.00 0.00 5.36
99 100 0.175760 TATGGACGTCTCTGCTTGCC 59.824 55.000 16.46 0.00 0.00 4.52
100 101 2.131183 GATATGGACGTCTCTGCTTGC 58.869 52.381 16.46 0.00 0.00 4.01
101 102 2.033424 TCGATATGGACGTCTCTGCTTG 59.967 50.000 16.46 0.87 0.00 4.01
102 103 2.033550 GTCGATATGGACGTCTCTGCTT 59.966 50.000 16.46 0.00 0.00 3.91
103 104 1.604755 GTCGATATGGACGTCTCTGCT 59.395 52.381 16.46 0.00 0.00 4.24
104 105 1.335142 GGTCGATATGGACGTCTCTGC 60.335 57.143 16.46 0.00 37.82 4.26
105 106 1.947456 TGGTCGATATGGACGTCTCTG 59.053 52.381 16.46 2.32 37.82 3.35
106 107 2.222886 CTGGTCGATATGGACGTCTCT 58.777 52.381 16.46 5.59 37.82 3.10
107 108 1.335142 GCTGGTCGATATGGACGTCTC 60.335 57.143 16.46 6.30 37.82 3.36
108 109 0.669077 GCTGGTCGATATGGACGTCT 59.331 55.000 16.46 0.00 37.82 4.18
109 110 0.669077 AGCTGGTCGATATGGACGTC 59.331 55.000 7.13 7.13 37.82 4.34
110 111 0.385751 CAGCTGGTCGATATGGACGT 59.614 55.000 5.57 0.00 37.82 4.34
111 112 0.941463 GCAGCTGGTCGATATGGACG 60.941 60.000 17.12 0.86 37.82 4.79
112 113 0.390860 AGCAGCTGGTCGATATGGAC 59.609 55.000 13.85 9.23 36.18 4.02
113 114 1.995376 TAGCAGCTGGTCGATATGGA 58.005 50.000 23.94 0.00 0.00 3.41
114 115 2.232208 TGATAGCAGCTGGTCGATATGG 59.768 50.000 23.94 0.00 0.00 2.74
115 116 3.582714 TGATAGCAGCTGGTCGATATG 57.417 47.619 23.94 0.00 0.00 1.78
116 117 4.676459 CGATTGATAGCAGCTGGTCGATAT 60.676 45.833 23.94 10.41 0.00 1.63
117 118 3.366374 CGATTGATAGCAGCTGGTCGATA 60.366 47.826 23.94 4.90 0.00 2.92
118 119 2.608998 CGATTGATAGCAGCTGGTCGAT 60.609 50.000 23.94 14.13 0.00 3.59
119 120 1.269257 CGATTGATAGCAGCTGGTCGA 60.269 52.381 23.94 9.44 0.00 4.20
120 121 1.135046 CGATTGATAGCAGCTGGTCG 58.865 55.000 23.94 14.73 0.00 4.79
121 122 2.515926 TCGATTGATAGCAGCTGGTC 57.484 50.000 23.94 9.84 0.00 4.02
122 123 2.988010 TTCGATTGATAGCAGCTGGT 57.012 45.000 23.72 23.72 0.00 4.00
123 124 3.396560 TGATTCGATTGATAGCAGCTGG 58.603 45.455 17.12 0.00 0.00 4.85
124 125 4.093115 GGATGATTCGATTGATAGCAGCTG 59.907 45.833 10.11 10.11 0.00 4.24
125 126 4.252073 GGATGATTCGATTGATAGCAGCT 58.748 43.478 0.00 0.00 0.00 4.24
126 127 3.999001 TGGATGATTCGATTGATAGCAGC 59.001 43.478 0.00 0.00 0.00 5.25
127 128 6.738832 AATGGATGATTCGATTGATAGCAG 57.261 37.500 0.00 0.00 30.13 4.24
128 129 6.569035 GCAAATGGATGATTCGATTGATAGCA 60.569 38.462 0.00 0.00 31.52 3.49
129 130 5.798934 GCAAATGGATGATTCGATTGATAGC 59.201 40.000 0.00 0.00 31.52 2.97
130 131 6.905578 TGCAAATGGATGATTCGATTGATAG 58.094 36.000 0.00 0.00 31.52 2.08
131 132 6.880942 TGCAAATGGATGATTCGATTGATA 57.119 33.333 0.00 0.00 31.52 2.15
132 133 5.777850 TGCAAATGGATGATTCGATTGAT 57.222 34.783 0.00 0.00 31.52 2.57
133 134 5.125900 AGTTGCAAATGGATGATTCGATTGA 59.874 36.000 0.00 0.00 31.52 2.57
134 135 5.345702 AGTTGCAAATGGATGATTCGATTG 58.654 37.500 0.00 0.00 31.52 2.67
135 136 5.359009 AGAGTTGCAAATGGATGATTCGATT 59.641 36.000 3.09 0.00 32.33 3.34
136 137 4.885907 AGAGTTGCAAATGGATGATTCGAT 59.114 37.500 3.09 0.00 0.00 3.59
137 138 4.264253 AGAGTTGCAAATGGATGATTCGA 58.736 39.130 3.09 0.00 0.00 3.71
138 139 4.095334 TGAGAGTTGCAAATGGATGATTCG 59.905 41.667 3.09 0.00 0.00 3.34
139 140 5.571784 TGAGAGTTGCAAATGGATGATTC 57.428 39.130 3.09 0.00 0.00 2.52
140 141 7.039923 GGATATGAGAGTTGCAAATGGATGATT 60.040 37.037 3.09 0.00 0.00 2.57
141 142 6.433404 GGATATGAGAGTTGCAAATGGATGAT 59.567 38.462 3.09 0.00 0.00 2.45
142 143 5.766670 GGATATGAGAGTTGCAAATGGATGA 59.233 40.000 3.09 0.00 0.00 2.92
143 144 5.533528 TGGATATGAGAGTTGCAAATGGATG 59.466 40.000 3.09 0.00 0.00 3.51
144 145 5.533903 GTGGATATGAGAGTTGCAAATGGAT 59.466 40.000 3.09 0.00 0.00 3.41
145 146 4.883585 GTGGATATGAGAGTTGCAAATGGA 59.116 41.667 3.09 0.00 0.00 3.41
146 147 4.885907 AGTGGATATGAGAGTTGCAAATGG 59.114 41.667 3.09 0.00 0.00 3.16
147 148 6.094464 TCAAGTGGATATGAGAGTTGCAAATG 59.906 38.462 3.09 0.00 0.00 2.32
148 149 6.182627 TCAAGTGGATATGAGAGTTGCAAAT 58.817 36.000 0.00 0.00 0.00 2.32
149 150 5.559770 TCAAGTGGATATGAGAGTTGCAAA 58.440 37.500 0.00 0.00 0.00 3.68
150 151 5.164620 TCAAGTGGATATGAGAGTTGCAA 57.835 39.130 0.00 0.00 0.00 4.08
151 152 4.824479 TCAAGTGGATATGAGAGTTGCA 57.176 40.909 0.00 0.00 0.00 4.08
152 153 4.937620 TGTTCAAGTGGATATGAGAGTTGC 59.062 41.667 0.00 0.00 0.00 4.17
153 154 5.352569 GGTGTTCAAGTGGATATGAGAGTTG 59.647 44.000 0.00 0.00 0.00 3.16
154 155 5.249393 AGGTGTTCAAGTGGATATGAGAGTT 59.751 40.000 0.00 0.00 0.00 3.01
155 156 4.780021 AGGTGTTCAAGTGGATATGAGAGT 59.220 41.667 0.00 0.00 0.00 3.24
156 157 5.128499 AGAGGTGTTCAAGTGGATATGAGAG 59.872 44.000 0.00 0.00 0.00 3.20
157 158 5.026121 AGAGGTGTTCAAGTGGATATGAGA 58.974 41.667 0.00 0.00 0.00 3.27
158 159 5.105187 TCAGAGGTGTTCAAGTGGATATGAG 60.105 44.000 0.00 0.00 0.00 2.90
159 160 4.777366 TCAGAGGTGTTCAAGTGGATATGA 59.223 41.667 0.00 0.00 0.00 2.15
160 161 4.872691 GTCAGAGGTGTTCAAGTGGATATG 59.127 45.833 0.00 0.00 0.00 1.78
161 162 4.382040 CGTCAGAGGTGTTCAAGTGGATAT 60.382 45.833 0.00 0.00 0.00 1.63
162 163 3.056821 CGTCAGAGGTGTTCAAGTGGATA 60.057 47.826 0.00 0.00 0.00 2.59
163 164 2.289072 CGTCAGAGGTGTTCAAGTGGAT 60.289 50.000 0.00 0.00 0.00 3.41
164 165 1.068588 CGTCAGAGGTGTTCAAGTGGA 59.931 52.381 0.00 0.00 0.00 4.02
165 166 1.068588 TCGTCAGAGGTGTTCAAGTGG 59.931 52.381 0.00 0.00 0.00 4.00
166 167 2.509052 TCGTCAGAGGTGTTCAAGTG 57.491 50.000 0.00 0.00 0.00 3.16
167 168 2.628178 TCATCGTCAGAGGTGTTCAAGT 59.372 45.455 0.00 0.00 0.00 3.16
168 169 3.303881 TCATCGTCAGAGGTGTTCAAG 57.696 47.619 0.00 0.00 0.00 3.02
169 170 3.673323 CGATCATCGTCAGAGGTGTTCAA 60.673 47.826 0.00 0.00 34.72 2.69
170 171 2.159379 CGATCATCGTCAGAGGTGTTCA 60.159 50.000 0.00 0.00 34.72 3.18
171 172 2.097629 TCGATCATCGTCAGAGGTGTTC 59.902 50.000 7.00 0.00 41.35 3.18
172 173 2.092323 TCGATCATCGTCAGAGGTGTT 58.908 47.619 7.00 0.00 41.35 3.32
173 174 1.751437 TCGATCATCGTCAGAGGTGT 58.249 50.000 7.00 0.00 41.35 4.16
174 175 2.291741 TGATCGATCATCGTCAGAGGTG 59.708 50.000 23.99 0.00 41.35 4.00
175 176 2.292016 GTGATCGATCATCGTCAGAGGT 59.708 50.000 29.53 0.00 41.35 3.85
176 177 2.291741 TGTGATCGATCATCGTCAGAGG 59.708 50.000 29.53 0.00 41.35 3.69
177 178 3.615849 TGTGATCGATCATCGTCAGAG 57.384 47.619 29.53 0.00 41.35 3.35
178 179 3.304928 CCATGTGATCGATCATCGTCAGA 60.305 47.826 29.53 7.56 41.35 3.27
179 180 2.985139 CCATGTGATCGATCATCGTCAG 59.015 50.000 29.53 16.07 41.35 3.51
180 181 2.362077 ACCATGTGATCGATCATCGTCA 59.638 45.455 29.53 22.19 41.35 4.35
181 182 2.728318 CACCATGTGATCGATCATCGTC 59.272 50.000 29.53 17.50 39.30 4.20
182 183 2.101415 ACACCATGTGATCGATCATCGT 59.899 45.455 29.53 20.29 39.30 3.73
183 184 2.747436 ACACCATGTGATCGATCATCG 58.253 47.619 29.53 19.76 39.30 3.84
195 196 2.104792 ACAGCACTTACTCACACCATGT 59.895 45.455 0.00 0.00 0.00 3.21
196 197 2.771089 ACAGCACTTACTCACACCATG 58.229 47.619 0.00 0.00 0.00 3.66
197 198 3.492102 AACAGCACTTACTCACACCAT 57.508 42.857 0.00 0.00 0.00 3.55
198 199 3.244078 CCTAACAGCACTTACTCACACCA 60.244 47.826 0.00 0.00 0.00 4.17
199 200 3.006537 TCCTAACAGCACTTACTCACACC 59.993 47.826 0.00 0.00 0.00 4.16
200 201 4.252971 TCCTAACAGCACTTACTCACAC 57.747 45.455 0.00 0.00 0.00 3.82
201 202 4.948341 TTCCTAACAGCACTTACTCACA 57.052 40.909 0.00 0.00 0.00 3.58
202 203 7.900782 TTAATTCCTAACAGCACTTACTCAC 57.099 36.000 0.00 0.00 0.00 3.51
239 240 9.424319 CCGTCATAGCAGTGATTAATAGTTAAT 57.576 33.333 0.00 0.00 38.49 1.40
240 241 8.418662 ACCGTCATAGCAGTGATTAATAGTTAA 58.581 33.333 0.00 0.00 0.00 2.01
241 242 7.865889 CACCGTCATAGCAGTGATTAATAGTTA 59.134 37.037 0.00 0.00 31.79 2.24
242 243 6.701841 CACCGTCATAGCAGTGATTAATAGTT 59.298 38.462 0.00 0.00 31.79 2.24
243 244 6.216569 CACCGTCATAGCAGTGATTAATAGT 58.783 40.000 0.00 0.00 31.79 2.12
244 245 5.119279 GCACCGTCATAGCAGTGATTAATAG 59.881 44.000 0.00 0.00 31.79 1.73
245 246 4.988540 GCACCGTCATAGCAGTGATTAATA 59.011 41.667 0.00 0.00 31.79 0.98
246 247 3.809832 GCACCGTCATAGCAGTGATTAAT 59.190 43.478 0.00 0.00 31.79 1.40
247 248 3.194861 GCACCGTCATAGCAGTGATTAA 58.805 45.455 0.00 0.00 31.79 1.40
248 249 2.483013 GGCACCGTCATAGCAGTGATTA 60.483 50.000 0.00 0.00 31.79 1.75
249 250 1.656652 GCACCGTCATAGCAGTGATT 58.343 50.000 0.00 0.00 31.79 2.57
250 251 0.179073 GGCACCGTCATAGCAGTGAT 60.179 55.000 0.00 0.00 31.79 3.06
251 252 1.218047 GGCACCGTCATAGCAGTGA 59.782 57.895 0.00 0.00 31.79 3.41
252 253 1.079197 TGGCACCGTCATAGCAGTG 60.079 57.895 0.00 0.00 0.00 3.66
253 254 1.079127 GTGGCACCGTCATAGCAGT 60.079 57.895 6.29 0.00 0.00 4.40
254 255 0.391661 AAGTGGCACCGTCATAGCAG 60.392 55.000 15.27 0.00 0.00 4.24
255 256 0.036164 AAAGTGGCACCGTCATAGCA 59.964 50.000 15.27 0.00 0.00 3.49
256 257 1.135689 CAAAAGTGGCACCGTCATAGC 60.136 52.381 15.27 0.00 0.00 2.97
257 258 1.468520 CCAAAAGTGGCACCGTCATAG 59.531 52.381 15.27 0.00 38.35 2.23
258 259 1.529226 CCAAAAGTGGCACCGTCATA 58.471 50.000 15.27 0.00 38.35 2.15
259 260 2.340427 CCAAAAGTGGCACCGTCAT 58.660 52.632 15.27 0.00 38.35 3.06
260 261 3.834726 CCAAAAGTGGCACCGTCA 58.165 55.556 15.27 0.00 38.35 4.35
277 278 2.288213 GGTTACAAAAGGAGGCAGTTGC 60.288 50.000 0.00 0.00 41.14 4.17
278 279 2.031157 CGGTTACAAAAGGAGGCAGTTG 60.031 50.000 0.00 0.00 0.00 3.16
279 280 2.227194 CGGTTACAAAAGGAGGCAGTT 58.773 47.619 0.00 0.00 0.00 3.16
280 281 1.892209 CGGTTACAAAAGGAGGCAGT 58.108 50.000 0.00 0.00 0.00 4.40
281 282 0.521735 GCGGTTACAAAAGGAGGCAG 59.478 55.000 0.00 0.00 0.00 4.85
282 283 0.891904 GGCGGTTACAAAAGGAGGCA 60.892 55.000 0.00 0.00 0.00 4.75
283 284 0.608308 AGGCGGTTACAAAAGGAGGC 60.608 55.000 0.00 0.00 0.00 4.70
284 285 1.539827 CAAGGCGGTTACAAAAGGAGG 59.460 52.381 0.00 0.00 0.00 4.30
285 286 2.227194 ACAAGGCGGTTACAAAAGGAG 58.773 47.619 0.00 0.00 0.00 3.69
286 287 2.351706 ACAAGGCGGTTACAAAAGGA 57.648 45.000 0.00 0.00 0.00 3.36
287 288 4.037089 AGTTTACAAGGCGGTTACAAAAGG 59.963 41.667 0.00 0.00 0.00 3.11
288 289 4.973663 CAGTTTACAAGGCGGTTACAAAAG 59.026 41.667 0.00 0.00 0.00 2.27
289 290 4.202030 CCAGTTTACAAGGCGGTTACAAAA 60.202 41.667 0.00 0.00 0.00 2.44
290 291 3.315749 CCAGTTTACAAGGCGGTTACAAA 59.684 43.478 0.00 0.00 0.00 2.83
291 292 2.879646 CCAGTTTACAAGGCGGTTACAA 59.120 45.455 0.00 0.00 0.00 2.41
292 293 2.496111 CCAGTTTACAAGGCGGTTACA 58.504 47.619 0.00 0.00 0.00 2.41
293 294 1.808343 CCCAGTTTACAAGGCGGTTAC 59.192 52.381 0.00 0.00 0.00 2.50
294 295 1.420891 ACCCAGTTTACAAGGCGGTTA 59.579 47.619 0.00 0.00 0.00 2.85
295 296 0.184211 ACCCAGTTTACAAGGCGGTT 59.816 50.000 0.00 0.00 0.00 4.44
296 297 1.058284 TACCCAGTTTACAAGGCGGT 58.942 50.000 0.00 0.00 0.00 5.68
297 298 2.413310 ATACCCAGTTTACAAGGCGG 57.587 50.000 0.00 0.00 0.00 6.13
298 299 6.017687 GGTATTTATACCCAGTTTACAAGGCG 60.018 42.308 7.56 0.00 45.62 5.52
299 300 7.268199 GGTATTTATACCCAGTTTACAAGGC 57.732 40.000 7.56 0.00 45.62 4.35
317 318 9.713684 TTCTATTGATTGAAGATTGGGGTATTT 57.286 29.630 0.00 0.00 0.00 1.40
318 319 9.887862 ATTCTATTGATTGAAGATTGGGGTATT 57.112 29.630 0.00 0.00 0.00 1.89
321 322 9.136323 GTTATTCTATTGATTGAAGATTGGGGT 57.864 33.333 0.00 0.00 0.00 4.95
322 323 9.359653 AGTTATTCTATTGATTGAAGATTGGGG 57.640 33.333 0.00 0.00 0.00 4.96
398 401 5.556915 AGGAACGAATGGATTGAACAGTTA 58.443 37.500 0.00 0.00 0.00 2.24
1129 1172 0.251121 TCGAAAAAGATGCAGGCCCA 60.251 50.000 0.00 0.00 0.00 5.36
1864 3468 6.365970 AAAGTGACAAGATGTAGACCTCAT 57.634 37.500 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.