Multiple sequence alignment - TraesCS7D01G401000

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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 TraesCS7D01G401000 chr7D 100.000 3408 0 0 1 3408 518092224 518088817 0.000000e+00 6294.0
1 TraesCS7D01G401000 chr7D 93.240 1642 90 14 1000 2636 518573603 518575228 0.000000e+00 2398.0
2 TraesCS7D01G401000 chr7D 94.640 597 29 2 2040 2636 518602073 518602666 0.000000e+00 922.0
3 TraesCS7D01G401000 chr7D 94.683 583 28 1 2006 2588 518558394 518558973 0.000000e+00 902.0
4 TraesCS7D01G401000 chr7D 90.625 512 26 10 2879 3370 518092240 518092749 0.000000e+00 660.0
5 TraesCS7D01G401000 chr7D 100.000 209 0 0 3774 3982 518088451 518088243 1.740000e-103 387.0
6 TraesCS7D01G401000 chr7D 86.875 160 19 2 3781 3940 518093059 518093216 1.140000e-40 178.0
7 TraesCS7D01G401000 chr7D 97.561 41 1 0 3937 3977 518093243 518093283 1.990000e-08 71.3
8 TraesCS7D01G401000 chr7B 92.066 2483 130 35 171 2636 551538122 551540554 0.000000e+00 3432.0
9 TraesCS7D01G401000 chr7B 94.180 1615 76 14 1000 2604 551897191 551898797 0.000000e+00 2446.0
10 TraesCS7D01G401000 chr7B 93.939 495 25 4 2880 3370 551505357 551504864 0.000000e+00 743.0
11 TraesCS7D01G401000 chr7B 88.750 160 15 2 3781 3940 551504529 551504373 4.060000e-45 193.0
12 TraesCS7D01G401000 chr7B 84.146 82 9 3 2679 2759 551540737 551540815 4.270000e-10 76.8
13 TraesCS7D01G401000 chr7A 93.802 2146 96 22 638 2763 593016516 593014388 0.000000e+00 3192.0
14 TraesCS7D01G401000 chr7A 91.518 2299 122 36 549 2813 593375790 593378049 0.000000e+00 3097.0
15 TraesCS7D01G401000 chr7A 91.734 496 27 8 2879 3370 593373533 593373048 0.000000e+00 676.0
16 TraesCS7D01G401000 chr7A 83.146 267 23 9 132 380 593373605 593373867 1.440000e-54 224.0
17 TraesCS7D01G401000 chr7A 79.518 166 10 12 372 536 593375143 593375285 3.280000e-16 97.1
18 TraesCS7D01G401000 chr1D 80.688 901 160 10 1676 2569 10935927 10935034 0.000000e+00 688.0
19 TraesCS7D01G401000 chr3B 83.489 642 97 6 1935 2571 712559071 712559708 1.230000e-164 590.0
20 TraesCS7D01G401000 chr3A 79.724 434 73 10 1136 1559 673435182 673435610 2.330000e-77 300.0
21 TraesCS7D01G401000 chr4B 74.862 362 87 4 1166 1525 605398595 605398236 1.150000e-35 161.0
22 TraesCS7D01G401000 chr2D 84.746 118 17 1 1 117 475505505 475505622 2.510000e-22 117.0
23 TraesCS7D01G401000 chr2A 83.051 118 19 1 1 117 723831733 723831850 5.440000e-19 106.0
24 TraesCS7D01G401000 chr2A 100.000 30 0 0 3947 3976 692731112 692731083 5.560000e-04 56.5
25 TraesCS7D01G401000 chr4A 90.196 51 3 2 1341 1390 572506701 572506652 9.240000e-07 65.8
26 TraesCS7D01G401000 chr5D 100.000 33 0 0 3944 3976 118567238 118567206 1.190000e-05 62.1
27 TraesCS7D01G401000 chr4D 88.235 51 4 2 1341 1390 30518608 30518657 4.300000e-05 60.2


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 TraesCS7D01G401000 chr7D 518088243 518092224 3981 True 3340.500000 6294 100.000000 1 3982 2 chr7D.!!$R1 3981
1 TraesCS7D01G401000 chr7D 518573603 518575228 1625 False 2398.000000 2398 93.240000 1000 2636 1 chr7D.!!$F2 1636
2 TraesCS7D01G401000 chr7D 518602073 518602666 593 False 922.000000 922 94.640000 2040 2636 1 chr7D.!!$F3 596
3 TraesCS7D01G401000 chr7D 518558394 518558973 579 False 902.000000 902 94.683000 2006 2588 1 chr7D.!!$F1 582
4 TraesCS7D01G401000 chr7D 518092240 518093283 1043 False 303.100000 660 91.687000 2879 3977 3 chr7D.!!$F4 1098
5 TraesCS7D01G401000 chr7B 551897191 551898797 1606 False 2446.000000 2446 94.180000 1000 2604 1 chr7B.!!$F1 1604
6 TraesCS7D01G401000 chr7B 551538122 551540815 2693 False 1754.400000 3432 88.106000 171 2759 2 chr7B.!!$F2 2588
7 TraesCS7D01G401000 chr7B 551504373 551505357 984 True 468.000000 743 91.344500 2880 3940 2 chr7B.!!$R1 1060
8 TraesCS7D01G401000 chr7A 593014388 593016516 2128 True 3192.000000 3192 93.802000 638 2763 1 chr7A.!!$R1 2125
9 TraesCS7D01G401000 chr7A 593373605 593378049 4444 False 1139.366667 3097 84.727333 132 2813 3 chr7A.!!$F1 2681
10 TraesCS7D01G401000 chr1D 10935034 10935927 893 True 688.000000 688 80.688000 1676 2569 1 chr1D.!!$R1 893
11 TraesCS7D01G401000 chr3B 712559071 712559708 637 False 590.000000 590 83.489000 1935 2571 1 chr3B.!!$F1 636


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
87 88 0.033504 TTCTCCGCTCCGCATATTCC 59.966 55.0 0.00 0.00 0.00 3.01 F
437 1741 0.035317 TCATATGTCCCCTCATGCGC 59.965 55.0 0.00 0.00 0.00 6.09 F
1623 3476 0.318784 GTGTCCCTGTCACGTGAGAC 60.319 60.0 20.73 21.62 38.99 3.36 F
2782 4799 1.071314 TCCTTCTGGCAAAAGGGGGA 61.071 55.0 19.18 0.00 42.99 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 3509 1.595328 CACGACGTCCAAACAACATCA 59.405 47.619 10.58 0.00 0.00 3.07 R
2328 4196 1.507630 CGATGTACGTCCGGGACAA 59.492 57.895 25.80 11.24 37.22 3.18 R
2824 4841 0.178876 TGTTGATCCACTCCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86 R
3847 5930 2.126071 TGCGCTTCTGACTACCGC 60.126 61.111 9.73 0.00 44.39 5.68 R


All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.930935 ACCACTCCACTCCACAACT 58.069 52.632 0.00 0.00 0.00 3.16
19 20 0.759346 ACCACTCCACTCCACAACTC 59.241 55.000 0.00 0.00 0.00 3.01
20 21 1.051812 CCACTCCACTCCACAACTCT 58.948 55.000 0.00 0.00 0.00 3.24
21 22 1.270518 CCACTCCACTCCACAACTCTG 60.271 57.143 0.00 0.00 0.00 3.35
22 23 1.051812 ACTCCACTCCACAACTCTGG 58.948 55.000 0.00 0.00 0.00 3.86
23 24 0.322975 CTCCACTCCACAACTCTGGG 59.677 60.000 0.00 0.00 31.41 4.45
24 25 0.105194 TCCACTCCACAACTCTGGGA 60.105 55.000 0.00 0.00 31.41 4.37
27 28 1.079543 CTCCACAACTCTGGGAGCG 60.080 63.158 0.00 0.00 41.53 5.03
28 29 2.046892 CCACAACTCTGGGAGCGG 60.047 66.667 0.00 0.00 32.04 5.52
29 30 2.583441 CCACAACTCTGGGAGCGGA 61.583 63.158 0.00 0.00 32.04 5.54
30 31 1.079543 CACAACTCTGGGAGCGGAG 60.080 63.158 0.00 0.00 32.04 4.63
31 32 1.534235 ACAACTCTGGGAGCGGAGT 60.534 57.895 0.00 0.00 43.60 3.85
32 33 4.217112 AACTCTGGGAGCGGAGTT 57.783 55.556 0.00 0.00 44.72 3.01
33 34 1.674057 AACTCTGGGAGCGGAGTTG 59.326 57.895 0.00 0.00 46.76 3.16
34 35 1.831652 AACTCTGGGAGCGGAGTTGG 61.832 60.000 0.00 0.00 46.76 3.77
35 36 3.672295 CTCTGGGAGCGGAGTTGGC 62.672 68.421 0.00 0.00 0.00 4.52
36 37 4.020617 CTGGGAGCGGAGTTGGCA 62.021 66.667 0.00 0.00 0.00 4.92
37 38 3.965539 CTGGGAGCGGAGTTGGCAG 62.966 68.421 0.00 0.00 0.00 4.85
38 39 3.706373 GGGAGCGGAGTTGGCAGA 61.706 66.667 0.00 0.00 0.00 4.26
39 40 2.125350 GGAGCGGAGTTGGCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
40 41 2.817396 GAGCGGAGTTGGCAGAGC 60.817 66.667 0.00 0.00 0.00 4.09
41 42 3.308014 GAGCGGAGTTGGCAGAGCT 62.308 63.158 0.00 0.00 37.69 4.09
42 43 3.123620 GCGGAGTTGGCAGAGCTG 61.124 66.667 0.00 0.00 0.00 4.24
55 56 3.549299 CAGAGCTGCAGTGTAAAAAGG 57.451 47.619 16.64 0.00 0.00 3.11
56 57 3.141398 CAGAGCTGCAGTGTAAAAAGGA 58.859 45.455 16.64 0.00 0.00 3.36
57 58 3.188048 CAGAGCTGCAGTGTAAAAAGGAG 59.812 47.826 16.64 0.00 0.00 3.69
58 59 2.485814 GAGCTGCAGTGTAAAAAGGAGG 59.514 50.000 16.64 0.00 0.00 4.30
59 60 2.106511 AGCTGCAGTGTAAAAAGGAGGA 59.893 45.455 16.64 0.00 0.00 3.71
60 61 2.485814 GCTGCAGTGTAAAAAGGAGGAG 59.514 50.000 16.64 0.00 0.00 3.69
61 62 3.744660 CTGCAGTGTAAAAAGGAGGAGT 58.255 45.455 5.25 0.00 0.00 3.85
62 63 4.137543 CTGCAGTGTAAAAAGGAGGAGTT 58.862 43.478 5.25 0.00 0.00 3.01
63 64 3.882888 TGCAGTGTAAAAAGGAGGAGTTG 59.117 43.478 0.00 0.00 0.00 3.16
64 65 3.304726 GCAGTGTAAAAAGGAGGAGTTGC 60.305 47.826 0.00 0.00 0.00 4.17
65 66 3.882888 CAGTGTAAAAAGGAGGAGTTGCA 59.117 43.478 0.00 0.00 0.00 4.08
66 67 4.023707 CAGTGTAAAAAGGAGGAGTTGCAG 60.024 45.833 0.00 0.00 0.00 4.41
67 68 3.883489 GTGTAAAAAGGAGGAGTTGCAGT 59.117 43.478 0.00 0.00 0.00 4.40
68 69 4.338400 GTGTAAAAAGGAGGAGTTGCAGTT 59.662 41.667 0.00 0.00 0.00 3.16
69 70 4.953579 TGTAAAAAGGAGGAGTTGCAGTTT 59.046 37.500 0.00 0.00 0.00 2.66
70 71 4.655762 AAAAAGGAGGAGTTGCAGTTTC 57.344 40.909 0.00 0.00 0.00 2.78
71 72 3.584733 AAAGGAGGAGTTGCAGTTTCT 57.415 42.857 0.00 0.00 0.00 2.52
72 73 2.849294 AGGAGGAGTTGCAGTTTCTC 57.151 50.000 0.32 0.32 0.00 2.87
73 74 1.349357 AGGAGGAGTTGCAGTTTCTCC 59.651 52.381 15.73 15.73 45.56 3.71
75 76 1.869690 GGAGTTGCAGTTTCTCCGC 59.130 57.895 11.49 0.00 38.37 5.54
76 77 0.603975 GGAGTTGCAGTTTCTCCGCT 60.604 55.000 11.49 0.00 38.37 5.52
77 78 0.793250 GAGTTGCAGTTTCTCCGCTC 59.207 55.000 0.00 0.00 0.00 5.03
78 79 0.603975 AGTTGCAGTTTCTCCGCTCC 60.604 55.000 0.00 0.00 0.00 4.70
79 80 1.667830 TTGCAGTTTCTCCGCTCCG 60.668 57.895 0.00 0.00 0.00 4.63
80 81 3.491652 GCAGTTTCTCCGCTCCGC 61.492 66.667 0.00 0.00 0.00 5.54
81 82 2.048222 CAGTTTCTCCGCTCCGCA 60.048 61.111 0.00 0.00 0.00 5.69
82 83 1.448540 CAGTTTCTCCGCTCCGCAT 60.449 57.895 0.00 0.00 0.00 4.73
83 84 0.179111 CAGTTTCTCCGCTCCGCATA 60.179 55.000 0.00 0.00 0.00 3.14
84 85 0.753262 AGTTTCTCCGCTCCGCATAT 59.247 50.000 0.00 0.00 0.00 1.78
85 86 1.139058 AGTTTCTCCGCTCCGCATATT 59.861 47.619 0.00 0.00 0.00 1.28
86 87 1.527311 GTTTCTCCGCTCCGCATATTC 59.473 52.381 0.00 0.00 0.00 1.75
87 88 0.033504 TTCTCCGCTCCGCATATTCC 59.966 55.000 0.00 0.00 0.00 3.01
88 89 1.734477 CTCCGCTCCGCATATTCCG 60.734 63.158 0.00 0.00 0.00 4.30
89 90 2.142357 CTCCGCTCCGCATATTCCGA 62.142 60.000 0.00 0.00 0.00 4.55
90 91 1.734477 CCGCTCCGCATATTCCGAG 60.734 63.158 0.00 0.00 0.00 4.63
91 92 1.285950 CGCTCCGCATATTCCGAGA 59.714 57.895 0.00 0.00 0.00 4.04
92 93 0.730834 CGCTCCGCATATTCCGAGAG 60.731 60.000 0.00 2.33 0.00 3.20
93 94 1.011451 GCTCCGCATATTCCGAGAGC 61.011 60.000 14.37 14.37 39.69 4.09
112 113 2.776659 GGTGATTACCGAACAGGGC 58.223 57.895 0.00 0.00 46.96 5.19
113 114 0.746923 GGTGATTACCGAACAGGGCC 60.747 60.000 0.00 0.00 46.96 5.80
114 115 0.252197 GTGATTACCGAACAGGGCCT 59.748 55.000 0.00 0.00 46.96 5.19
115 116 1.483415 GTGATTACCGAACAGGGCCTA 59.517 52.381 5.28 0.00 46.96 3.93
116 117 2.093341 GTGATTACCGAACAGGGCCTAA 60.093 50.000 5.28 0.00 46.96 2.69
117 118 2.093341 TGATTACCGAACAGGGCCTAAC 60.093 50.000 5.28 0.00 46.96 2.34
118 119 1.648116 TTACCGAACAGGGCCTAACT 58.352 50.000 5.28 0.00 46.96 2.24
119 120 2.530460 TACCGAACAGGGCCTAACTA 57.470 50.000 5.28 0.00 46.96 2.24
120 121 1.192428 ACCGAACAGGGCCTAACTAG 58.808 55.000 5.28 0.00 46.96 2.57
121 122 1.272872 ACCGAACAGGGCCTAACTAGA 60.273 52.381 5.28 0.00 46.96 2.43
122 123 1.409427 CCGAACAGGGCCTAACTAGAG 59.591 57.143 5.28 0.00 35.97 2.43
123 124 2.376109 CGAACAGGGCCTAACTAGAGA 58.624 52.381 5.28 0.00 0.00 3.10
124 125 2.758979 CGAACAGGGCCTAACTAGAGAA 59.241 50.000 5.28 0.00 0.00 2.87
125 126 3.385111 CGAACAGGGCCTAACTAGAGAAT 59.615 47.826 5.28 0.00 0.00 2.40
126 127 4.500035 CGAACAGGGCCTAACTAGAGAATC 60.500 50.000 5.28 0.00 0.00 2.52
127 128 3.310193 ACAGGGCCTAACTAGAGAATCC 58.690 50.000 5.28 0.00 33.66 3.01
128 129 3.309296 CAGGGCCTAACTAGAGAATCCA 58.691 50.000 5.28 0.00 33.66 3.41
129 130 3.323403 CAGGGCCTAACTAGAGAATCCAG 59.677 52.174 5.28 0.00 33.66 3.86
130 131 2.635427 GGGCCTAACTAGAGAATCCAGG 59.365 54.545 0.84 0.00 33.66 4.45
140 141 2.244510 AGAGAATCCAGGCTCTCTCTCA 59.755 50.000 12.95 0.00 44.04 3.27
144 145 4.288105 AGAATCCAGGCTCTCTCTCAAAAA 59.712 41.667 0.00 0.00 0.00 1.94
171 174 8.658840 AAAACTAGAGAGTCTAGGTGATCTTT 57.341 34.615 14.09 3.51 45.71 2.52
187 190 0.100325 CTTTCCGTGTGTTGCTGCAA 59.900 50.000 11.69 11.69 0.00 4.08
242 246 8.398491 TGTACGAAGAAATTACCTAAATCGAC 57.602 34.615 0.00 0.00 0.00 4.20
253 257 9.978044 AATTACCTAAATCGACTGAGTAATACC 57.022 33.333 9.00 0.00 30.83 2.73
271 275 3.366052 ACCAGTATTTCTCCCGCAAAT 57.634 42.857 0.00 0.00 0.00 2.32
272 276 3.697166 ACCAGTATTTCTCCCGCAAATT 58.303 40.909 0.00 0.00 0.00 1.82
273 277 4.086457 ACCAGTATTTCTCCCGCAAATTT 58.914 39.130 0.00 0.00 0.00 1.82
274 278 4.526650 ACCAGTATTTCTCCCGCAAATTTT 59.473 37.500 0.00 0.00 0.00 1.82
275 279 5.011635 ACCAGTATTTCTCCCGCAAATTTTT 59.988 36.000 0.00 0.00 0.00 1.94
341 360 7.892778 TTGTACAATTATCTAAACACGAGCA 57.107 32.000 3.59 0.00 0.00 4.26
344 363 6.648725 ACAATTATCTAAACACGAGCACTC 57.351 37.500 0.00 0.00 0.00 3.51
437 1741 0.035317 TCATATGTCCCCTCATGCGC 59.965 55.000 0.00 0.00 0.00 6.09
445 1749 2.610694 CCCTCATGCGCGCCATTAG 61.611 63.158 30.77 20.34 29.71 1.73
446 1750 1.889105 CCTCATGCGCGCCATTAGT 60.889 57.895 30.77 4.40 29.71 2.24
448 1752 2.150809 CTCATGCGCGCCATTAGTCG 62.151 60.000 30.77 9.65 29.71 4.18
449 1753 2.106131 ATGCGCGCCATTAGTCGA 59.894 55.556 30.77 6.52 0.00 4.20
450 1754 1.951130 ATGCGCGCCATTAGTCGAG 60.951 57.895 30.77 0.00 0.00 4.04
451 1755 3.989595 GCGCGCCATTAGTCGAGC 61.990 66.667 23.24 0.00 43.28 5.03
452 1756 3.330853 CGCGCCATTAGTCGAGCC 61.331 66.667 0.00 0.00 0.00 4.70
453 1757 3.330853 GCGCCATTAGTCGAGCCG 61.331 66.667 0.00 0.00 0.00 5.52
454 1758 2.658593 CGCCATTAGTCGAGCCGG 60.659 66.667 0.00 0.00 0.00 6.13
455 1759 2.967615 GCCATTAGTCGAGCCGGC 60.968 66.667 21.89 21.89 0.00 6.13
456 1760 2.499205 CCATTAGTCGAGCCGGCA 59.501 61.111 31.54 4.59 32.13 5.69
457 1761 1.069765 CCATTAGTCGAGCCGGCAT 59.930 57.895 31.54 14.28 32.13 4.40
458 1762 0.532862 CCATTAGTCGAGCCGGCATT 60.533 55.000 31.54 9.09 32.13 3.56
459 1763 1.299541 CATTAGTCGAGCCGGCATTT 58.700 50.000 31.54 8.11 32.13 2.32
460 1764 2.479837 CATTAGTCGAGCCGGCATTTA 58.520 47.619 31.54 10.57 32.13 1.40
461 1765 2.902705 TTAGTCGAGCCGGCATTTAT 57.097 45.000 31.54 14.04 32.13 1.40
462 1766 4.242475 CATTAGTCGAGCCGGCATTTATA 58.758 43.478 31.54 12.91 32.13 0.98
463 1767 2.150397 AGTCGAGCCGGCATTTATAC 57.850 50.000 31.54 16.83 32.13 1.47
464 1768 0.782384 GTCGAGCCGGCATTTATACG 59.218 55.000 31.54 20.03 0.00 3.06
465 1769 0.386476 TCGAGCCGGCATTTATACGT 59.614 50.000 31.54 3.33 0.00 3.57
466 1770 1.608109 TCGAGCCGGCATTTATACGTA 59.392 47.619 31.54 0.00 0.00 3.57
494 1798 5.587388 ATGATTTGATTTGATTGACGGCT 57.413 34.783 0.00 0.00 0.00 5.52
571 2367 0.875059 CGGTCAAAAAGGCTCTCACC 59.125 55.000 0.00 0.00 0.00 4.02
580 2376 1.484038 AGGCTCTCACCACTGATCTC 58.516 55.000 0.00 0.00 0.00 2.75
764 2568 1.333931 TGATCACGCACGAGATCTACC 59.666 52.381 24.02 6.13 40.94 3.18
772 2576 2.144730 CACGAGATCTACCGGAGTAGG 58.855 57.143 9.46 0.00 45.24 3.18
905 2719 2.030562 CCCACCACACGACCACTC 59.969 66.667 0.00 0.00 0.00 3.51
912 2726 1.205655 CCACACGACCACTCATCTCAT 59.794 52.381 0.00 0.00 0.00 2.90
913 2727 2.265683 CACACGACCACTCATCTCATG 58.734 52.381 0.00 0.00 0.00 3.07
914 2728 1.284657 CACGACCACTCATCTCATGC 58.715 55.000 0.00 0.00 0.00 4.06
915 2729 0.897621 ACGACCACTCATCTCATGCA 59.102 50.000 0.00 0.00 0.00 3.96
937 2751 4.143333 CCGTCCACCTACTGGCCG 62.143 72.222 0.00 0.00 41.32 6.13
996 2810 1.250840 GGCACCAACCCCAACATCTC 61.251 60.000 0.00 0.00 0.00 2.75
1127 2962 1.169661 TCTAGCTAGCTGCCTCGCTC 61.170 60.000 27.68 0.00 39.15 5.03
1598 3448 4.735873 GCTCTACATCCAGGTACGTAAACC 60.736 50.000 0.00 0.00 40.06 3.27
1623 3476 0.318784 GTGTCCCTGTCACGTGAGAC 60.319 60.000 20.73 21.62 38.99 3.36
1643 3496 3.463944 ACCGATTCACGAGTTGTTTCTT 58.536 40.909 0.00 0.00 45.77 2.52
1647 3500 4.898488 CGATTCACGAGTTGTTTCTTTGTC 59.102 41.667 0.00 0.00 45.77 3.18
1656 3509 7.751793 ACGAGTTGTTTCTTTGTCGTTTTTAAT 59.248 29.630 0.00 0.00 37.36 1.40
1667 3520 9.407514 CTTTGTCGTTTTTAATGATGTTGTTTG 57.592 29.630 0.00 0.00 0.00 2.93
1967 3832 3.404773 CCCTTCTTCTTCGGGCCT 58.595 61.111 0.84 0.00 0.00 5.19
1970 3835 1.592223 CTTCTTCTTCGGGCCTCGT 59.408 57.895 0.84 0.00 40.32 4.18
2573 4441 4.899239 GGCCTCACCGCCGAGATG 62.899 72.222 0.00 0.00 39.64 2.90
2575 4443 2.782222 GCCTCACCGCCGAGATGTA 61.782 63.158 1.19 0.00 34.79 2.29
2646 4526 3.125316 GCCGCATATACAAAACGTCCTA 58.875 45.455 0.00 0.00 0.00 2.94
2760 4777 9.137459 CTGGATCTACTAGTAAGGAATGAAAGA 57.863 37.037 3.76 0.00 0.00 2.52
2771 4788 4.853007 AGGAATGAAAGATGTCCTTCTGG 58.147 43.478 0.00 0.00 37.17 3.86
2782 4799 1.071314 TCCTTCTGGCAAAAGGGGGA 61.071 55.000 19.18 0.00 42.99 4.81
2786 4803 1.715785 TCTGGCAAAAGGGGGAAAAG 58.284 50.000 0.00 0.00 0.00 2.27
2790 4807 1.347707 GGCAAAAGGGGGAAAAGGAAG 59.652 52.381 0.00 0.00 0.00 3.46
2805 4822 3.146104 AGGAAGGATGAAAGGTGTGTG 57.854 47.619 0.00 0.00 0.00 3.82
2806 4823 1.541588 GGAAGGATGAAAGGTGTGTGC 59.458 52.381 0.00 0.00 0.00 4.57
2807 4824 2.508526 GAAGGATGAAAGGTGTGTGCT 58.491 47.619 0.00 0.00 0.00 4.40
2808 4825 3.559171 GGAAGGATGAAAGGTGTGTGCTA 60.559 47.826 0.00 0.00 0.00 3.49
2809 4826 3.059352 AGGATGAAAGGTGTGTGCTAC 57.941 47.619 0.00 0.00 0.00 3.58
2810 4827 2.639839 AGGATGAAAGGTGTGTGCTACT 59.360 45.455 0.00 0.00 0.00 2.57
2811 4828 3.838317 AGGATGAAAGGTGTGTGCTACTA 59.162 43.478 0.00 0.00 0.00 1.82
2812 4829 3.933332 GGATGAAAGGTGTGTGCTACTAC 59.067 47.826 0.00 0.00 0.00 2.73
2813 4830 4.562757 GGATGAAAGGTGTGTGCTACTACA 60.563 45.833 0.00 0.00 0.00 2.74
2814 4831 4.409718 TGAAAGGTGTGTGCTACTACAA 57.590 40.909 0.00 0.00 31.36 2.41
2815 4832 4.968259 TGAAAGGTGTGTGCTACTACAAT 58.032 39.130 0.00 0.00 31.36 2.71
2816 4833 6.104146 TGAAAGGTGTGTGCTACTACAATA 57.896 37.500 0.00 0.00 31.36 1.90
2817 4834 6.707290 TGAAAGGTGTGTGCTACTACAATAT 58.293 36.000 0.00 0.00 31.36 1.28
2818 4835 6.816640 TGAAAGGTGTGTGCTACTACAATATC 59.183 38.462 0.00 0.00 31.36 1.63
2819 4836 6.546428 AAGGTGTGTGCTACTACAATATCT 57.454 37.500 0.00 0.00 31.36 1.98
2820 4837 7.655521 AAGGTGTGTGCTACTACAATATCTA 57.344 36.000 0.00 0.00 31.36 1.98
2821 4838 7.040473 AGGTGTGTGCTACTACAATATCTAC 57.960 40.000 0.00 0.00 31.36 2.59
2822 4839 6.834451 AGGTGTGTGCTACTACAATATCTACT 59.166 38.462 0.00 0.00 31.36 2.57
2823 4840 7.342284 AGGTGTGTGCTACTACAATATCTACTT 59.658 37.037 0.00 0.00 31.36 2.24
2824 4841 7.980099 GGTGTGTGCTACTACAATATCTACTTT 59.020 37.037 0.00 0.00 31.36 2.66
2825 4842 8.808529 GTGTGTGCTACTACAATATCTACTTTG 58.191 37.037 0.00 0.00 31.36 2.77
2826 4843 8.745590 TGTGTGCTACTACAATATCTACTTTGA 58.254 33.333 0.00 0.00 31.36 2.69
2827 4844 9.239002 GTGTGCTACTACAATATCTACTTTGAG 57.761 37.037 0.00 0.00 31.36 3.02
2828 4845 8.414003 TGTGCTACTACAATATCTACTTTGAGG 58.586 37.037 0.00 0.00 0.00 3.86
2829 4846 7.868415 GTGCTACTACAATATCTACTTTGAGGG 59.132 40.741 0.00 0.00 0.00 4.30
2830 4847 7.015292 TGCTACTACAATATCTACTTTGAGGGG 59.985 40.741 0.00 0.00 0.00 4.79
2831 4848 6.749036 ACTACAATATCTACTTTGAGGGGG 57.251 41.667 0.00 0.00 0.00 5.40
2832 4849 6.449956 ACTACAATATCTACTTTGAGGGGGA 58.550 40.000 0.00 0.00 0.00 4.81
2833 4850 5.896073 ACAATATCTACTTTGAGGGGGAG 57.104 43.478 0.00 0.00 0.00 4.30
2834 4851 5.289510 ACAATATCTACTTTGAGGGGGAGT 58.710 41.667 0.00 0.00 0.00 3.85
2835 4852 5.131142 ACAATATCTACTTTGAGGGGGAGTG 59.869 44.000 0.00 0.00 0.00 3.51
2836 4853 1.952621 TCTACTTTGAGGGGGAGTGG 58.047 55.000 0.00 0.00 0.00 4.00
2837 4854 1.435563 TCTACTTTGAGGGGGAGTGGA 59.564 52.381 0.00 0.00 0.00 4.02
2838 4855 2.045885 TCTACTTTGAGGGGGAGTGGAT 59.954 50.000 0.00 0.00 0.00 3.41
2839 4856 1.290134 ACTTTGAGGGGGAGTGGATC 58.710 55.000 0.00 0.00 0.00 3.36
2840 4857 1.289160 CTTTGAGGGGGAGTGGATCA 58.711 55.000 0.00 0.00 0.00 2.92
2841 4858 1.635487 CTTTGAGGGGGAGTGGATCAA 59.365 52.381 0.00 0.00 0.00 2.57
2842 4859 0.991920 TTGAGGGGGAGTGGATCAAC 59.008 55.000 0.00 0.00 0.00 3.18
2843 4860 0.178876 TGAGGGGGAGTGGATCAACA 60.179 55.000 2.34 0.00 0.00 3.33
2844 4861 0.543749 GAGGGGGAGTGGATCAACAG 59.456 60.000 2.34 0.00 0.00 3.16
2845 4862 1.077429 GGGGGAGTGGATCAACAGC 60.077 63.158 2.34 0.00 0.00 4.40
2846 4863 1.566298 GGGGGAGTGGATCAACAGCT 61.566 60.000 2.34 0.00 0.00 4.24
2847 4864 1.204146 GGGGAGTGGATCAACAGCTA 58.796 55.000 2.34 0.00 0.00 3.32
2848 4865 1.134371 GGGGAGTGGATCAACAGCTAC 60.134 57.143 2.34 0.00 0.00 3.58
2849 4866 1.555075 GGGAGTGGATCAACAGCTACA 59.445 52.381 2.34 0.00 0.00 2.74
2850 4867 2.419297 GGGAGTGGATCAACAGCTACAG 60.419 54.545 2.34 0.00 0.00 2.74
2851 4868 2.234908 GGAGTGGATCAACAGCTACAGT 59.765 50.000 2.34 0.00 0.00 3.55
2852 4869 3.307059 GGAGTGGATCAACAGCTACAGTT 60.307 47.826 2.34 0.00 0.00 3.16
2853 4870 3.929610 GAGTGGATCAACAGCTACAGTTC 59.070 47.826 2.34 0.00 0.00 3.01
2854 4871 3.324846 AGTGGATCAACAGCTACAGTTCA 59.675 43.478 2.34 0.00 0.00 3.18
2855 4872 3.433615 GTGGATCAACAGCTACAGTTCAC 59.566 47.826 0.00 0.00 0.00 3.18
2856 4873 3.070878 TGGATCAACAGCTACAGTTCACA 59.929 43.478 0.00 0.00 0.00 3.58
2857 4874 4.065088 GGATCAACAGCTACAGTTCACAA 58.935 43.478 0.00 0.00 0.00 3.33
2858 4875 4.515191 GGATCAACAGCTACAGTTCACAAA 59.485 41.667 0.00 0.00 0.00 2.83
2859 4876 5.008613 GGATCAACAGCTACAGTTCACAAAA 59.991 40.000 0.00 0.00 0.00 2.44
2860 4877 5.888691 TCAACAGCTACAGTTCACAAAAA 57.111 34.783 0.00 0.00 0.00 1.94
2905 4922 2.023673 CACTCCAACTTCTTGCCACAA 58.976 47.619 0.00 0.00 0.00 3.33
2910 4927 2.689983 CCAACTTCTTGCCACAAACTCT 59.310 45.455 0.00 0.00 0.00 3.24
2920 4937 2.551071 GCCACAAACTCTACTGGCTTCT 60.551 50.000 0.12 0.00 44.99 2.85
3050 5068 9.167311 ACTCAAGAAATAAGTGATGAATGTACC 57.833 33.333 0.00 0.00 0.00 3.34
3052 5070 9.739276 TCAAGAAATAAGTGATGAATGTACCTT 57.261 29.630 0.00 0.00 0.00 3.50
3159 5178 8.665685 ACGGTGACATAAATATCAAAGAAGAAC 58.334 33.333 0.00 0.00 0.00 3.01
3193 5212 1.009829 GATAACTTGAGCCGCCACTG 58.990 55.000 0.00 0.00 0.00 3.66
3271 5291 1.922447 AGAACAGGCCCCAATGTATGA 59.078 47.619 0.00 0.00 0.00 2.15
3321 5357 1.404477 CTTGCGCACCTTAAAAACCG 58.596 50.000 11.12 0.00 0.00 4.44
3360 5398 4.655963 AGTGTTAATCAGTGGAAGCACAT 58.344 39.130 8.91 0.00 0.00 3.21
3394 5476 1.972872 ATTCCATGCGAGGATTCCAC 58.027 50.000 5.29 0.00 37.56 4.02
3400 5482 2.859165 TGCGAGGATTCCACTTCTTT 57.141 45.000 5.29 0.00 0.00 2.52
3402 5484 3.486383 TGCGAGGATTCCACTTCTTTTT 58.514 40.909 5.29 0.00 0.00 1.94
3403 5485 3.502211 TGCGAGGATTCCACTTCTTTTTC 59.498 43.478 5.29 0.00 0.00 2.29
3407 5489 6.072673 GCGAGGATTCCACTTCTTTTTCTTTA 60.073 38.462 5.29 0.00 0.00 1.85
3820 5903 2.742372 GAGCGGCGACCAACATGT 60.742 61.111 12.98 0.00 0.00 3.21
3840 5923 3.516300 TGTGGCCCTACGAAGAAGATAAA 59.484 43.478 0.00 0.00 0.00 1.40
3843 5926 3.121544 GCCCTACGAAGAAGATAAACGG 58.878 50.000 0.00 0.00 0.00 4.44
3847 5930 0.044161 CGAAGAAGATAAACGGCGCG 60.044 55.000 6.90 0.00 0.00 6.86
3854 5937 3.704908 ATAAACGGCGCGCGGTAGT 62.705 57.895 38.71 30.71 0.00 2.73
3942 6054 2.100749 CTGCGGAAAAACAAGGAAAGGT 59.899 45.455 0.00 0.00 0.00 3.50
3977 6089 5.064198 ACCATTTTATTACATGTCGTCCACG 59.936 40.000 0.00 0.00 41.45 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.759346 GAGTTGTGGAGTGGAGTGGT 59.241 55.000 0.00 0.00 0.00 4.16
2 3 1.270518 CCAGAGTTGTGGAGTGGAGTG 60.271 57.143 0.00 0.00 40.44 3.51
4 5 0.322975 CCCAGAGTTGTGGAGTGGAG 59.677 60.000 0.00 0.00 40.44 3.86
5 6 0.105194 TCCCAGAGTTGTGGAGTGGA 60.105 55.000 0.00 0.00 40.44 4.02
6 7 0.322975 CTCCCAGAGTTGTGGAGTGG 59.677 60.000 0.00 0.00 40.44 4.00
7 8 0.321122 GCTCCCAGAGTTGTGGAGTG 60.321 60.000 6.64 0.00 40.78 3.51
8 9 1.821061 CGCTCCCAGAGTTGTGGAGT 61.821 60.000 6.64 0.00 40.78 3.85
9 10 1.079543 CGCTCCCAGAGTTGTGGAG 60.080 63.158 0.00 0.00 40.44 3.86
10 11 2.583441 CCGCTCCCAGAGTTGTGGA 61.583 63.158 0.00 0.00 40.44 4.02
11 12 2.046892 CCGCTCCCAGAGTTGTGG 60.047 66.667 0.00 0.00 37.34 4.17
12 13 1.079543 CTCCGCTCCCAGAGTTGTG 60.080 63.158 0.00 0.00 31.39 3.33
13 14 1.534235 ACTCCGCTCCCAGAGTTGT 60.534 57.895 0.00 0.00 40.43 3.32
14 15 3.382111 ACTCCGCTCCCAGAGTTG 58.618 61.111 0.00 0.00 40.43 3.16
15 16 4.217112 AACTCCGCTCCCAGAGTT 57.783 55.556 0.00 0.00 46.05 3.01
16 17 2.286523 CCAACTCCGCTCCCAGAGT 61.287 63.158 0.00 0.00 45.18 3.24
17 18 2.581354 CCAACTCCGCTCCCAGAG 59.419 66.667 0.00 0.00 36.16 3.35
18 19 3.706373 GCCAACTCCGCTCCCAGA 61.706 66.667 0.00 0.00 0.00 3.86
19 20 3.965539 CTGCCAACTCCGCTCCCAG 62.966 68.421 0.00 0.00 0.00 4.45
20 21 4.020617 CTGCCAACTCCGCTCCCA 62.021 66.667 0.00 0.00 0.00 4.37
21 22 3.672295 CTCTGCCAACTCCGCTCCC 62.672 68.421 0.00 0.00 0.00 4.30
22 23 2.125350 CTCTGCCAACTCCGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
23 24 2.817396 GCTCTGCCAACTCCGCTC 60.817 66.667 0.00 0.00 0.00 5.03
24 25 3.317571 AGCTCTGCCAACTCCGCT 61.318 61.111 0.00 0.00 0.00 5.52
25 26 3.123620 CAGCTCTGCCAACTCCGC 61.124 66.667 0.00 0.00 0.00 5.54
35 36 3.141398 TCCTTTTTACACTGCAGCTCTG 58.859 45.455 15.27 7.51 0.00 3.35
36 37 3.406764 CTCCTTTTTACACTGCAGCTCT 58.593 45.455 15.27 0.00 0.00 4.09
37 38 2.485814 CCTCCTTTTTACACTGCAGCTC 59.514 50.000 15.27 0.00 0.00 4.09
38 39 2.106511 TCCTCCTTTTTACACTGCAGCT 59.893 45.455 15.27 0.98 0.00 4.24
39 40 2.485814 CTCCTCCTTTTTACACTGCAGC 59.514 50.000 15.27 0.00 0.00 5.25
40 41 3.744660 ACTCCTCCTTTTTACACTGCAG 58.255 45.455 13.48 13.48 0.00 4.41
41 42 3.857157 ACTCCTCCTTTTTACACTGCA 57.143 42.857 0.00 0.00 0.00 4.41
42 43 3.304726 GCAACTCCTCCTTTTTACACTGC 60.305 47.826 0.00 0.00 0.00 4.40
43 44 3.882888 TGCAACTCCTCCTTTTTACACTG 59.117 43.478 0.00 0.00 0.00 3.66
44 45 4.137543 CTGCAACTCCTCCTTTTTACACT 58.862 43.478 0.00 0.00 0.00 3.55
45 46 3.883489 ACTGCAACTCCTCCTTTTTACAC 59.117 43.478 0.00 0.00 0.00 2.90
46 47 4.164843 ACTGCAACTCCTCCTTTTTACA 57.835 40.909 0.00 0.00 0.00 2.41
47 48 5.299531 AGAAACTGCAACTCCTCCTTTTTAC 59.700 40.000 0.00 0.00 0.00 2.01
48 49 5.445964 AGAAACTGCAACTCCTCCTTTTTA 58.554 37.500 0.00 0.00 0.00 1.52
49 50 4.281657 AGAAACTGCAACTCCTCCTTTTT 58.718 39.130 0.00 0.00 0.00 1.94
50 51 3.885901 GAGAAACTGCAACTCCTCCTTTT 59.114 43.478 0.00 0.00 0.00 2.27
51 52 3.481453 GAGAAACTGCAACTCCTCCTTT 58.519 45.455 0.00 0.00 0.00 3.11
52 53 2.224646 GGAGAAACTGCAACTCCTCCTT 60.225 50.000 16.48 0.00 44.54 3.36
53 54 1.349357 GGAGAAACTGCAACTCCTCCT 59.651 52.381 16.48 0.00 44.54 3.69
54 55 1.814793 GGAGAAACTGCAACTCCTCC 58.185 55.000 16.48 12.78 44.54 4.30
55 56 1.433534 CGGAGAAACTGCAACTCCTC 58.566 55.000 19.37 10.59 45.40 3.71
56 57 3.614399 CGGAGAAACTGCAACTCCT 57.386 52.632 19.37 3.52 45.40 3.69
75 76 0.730834 CGCTCTCGGAATATGCGGAG 60.731 60.000 11.30 11.30 42.46 4.63
76 77 1.285950 CGCTCTCGGAATATGCGGA 59.714 57.895 0.00 0.00 42.46 5.54
77 78 3.848142 CGCTCTCGGAATATGCGG 58.152 61.111 0.00 0.00 42.46 5.69
94 95 0.746923 GGCCCTGTTCGGTAATCACC 60.747 60.000 0.00 0.00 41.93 4.02
95 96 0.252197 AGGCCCTGTTCGGTAATCAC 59.748 55.000 0.00 0.00 0.00 3.06
96 97 1.868713 TAGGCCCTGTTCGGTAATCA 58.131 50.000 0.00 0.00 0.00 2.57
97 98 2.169978 AGTTAGGCCCTGTTCGGTAATC 59.830 50.000 0.00 0.00 0.00 1.75
98 99 2.193993 AGTTAGGCCCTGTTCGGTAAT 58.806 47.619 0.00 0.00 0.00 1.89
99 100 1.648116 AGTTAGGCCCTGTTCGGTAA 58.352 50.000 0.00 0.00 0.00 2.85
100 101 2.025037 TCTAGTTAGGCCCTGTTCGGTA 60.025 50.000 0.00 0.00 0.00 4.02
101 102 1.192428 CTAGTTAGGCCCTGTTCGGT 58.808 55.000 0.00 0.00 0.00 4.69
102 103 1.409427 CTCTAGTTAGGCCCTGTTCGG 59.591 57.143 0.00 0.00 0.00 4.30
103 104 2.376109 TCTCTAGTTAGGCCCTGTTCG 58.624 52.381 0.00 0.00 0.00 3.95
104 105 4.202274 GGATTCTCTAGTTAGGCCCTGTTC 60.202 50.000 0.00 0.00 0.00 3.18
105 106 3.712218 GGATTCTCTAGTTAGGCCCTGTT 59.288 47.826 0.00 0.00 0.00 3.16
106 107 3.310193 GGATTCTCTAGTTAGGCCCTGT 58.690 50.000 0.00 0.00 0.00 4.00
107 108 3.309296 TGGATTCTCTAGTTAGGCCCTG 58.691 50.000 0.00 0.00 0.00 4.45
108 109 3.582164 CTGGATTCTCTAGTTAGGCCCT 58.418 50.000 0.00 0.00 0.00 5.19
109 110 2.635427 CCTGGATTCTCTAGTTAGGCCC 59.365 54.545 0.00 0.00 0.00 5.80
110 111 2.037902 GCCTGGATTCTCTAGTTAGGCC 59.962 54.545 0.00 0.00 42.49 5.19
111 112 3.394674 GCCTGGATTCTCTAGTTAGGC 57.605 52.381 0.00 0.00 41.92 3.93
112 113 4.479158 AGAGCCTGGATTCTCTAGTTAGG 58.521 47.826 0.00 0.00 37.86 2.69
113 114 5.385198 AGAGAGCCTGGATTCTCTAGTTAG 58.615 45.833 22.20 0.00 46.21 2.34
114 115 5.396057 AGAGAGCCTGGATTCTCTAGTTA 57.604 43.478 22.20 0.00 46.21 2.24
115 116 4.264373 AGAGAGCCTGGATTCTCTAGTT 57.736 45.455 22.20 6.06 46.21 2.24
116 117 3.971468 AGAGAGCCTGGATTCTCTAGT 57.029 47.619 22.20 6.33 46.21 2.57
120 121 2.665165 TGAGAGAGAGCCTGGATTCTC 58.335 52.381 16.47 16.47 40.07 2.87
121 122 2.844654 TGAGAGAGAGCCTGGATTCT 57.155 50.000 0.00 0.00 0.00 2.40
122 123 3.902881 TTTGAGAGAGAGCCTGGATTC 57.097 47.619 0.00 0.00 0.00 2.52
123 124 4.647564 TTTTTGAGAGAGAGCCTGGATT 57.352 40.909 0.00 0.00 0.00 3.01
158 161 3.162666 ACACACGGAAAGATCACCTAGA 58.837 45.455 0.00 0.00 0.00 2.43
171 174 0.100325 CTTTTGCAGCAACACACGGA 59.900 50.000 7.54 0.00 0.00 4.69
239 243 7.140048 GGAGAAATACTGGTATTACTCAGTCG 58.860 42.308 16.36 0.00 42.51 4.18
242 246 6.448006 CGGGAGAAATACTGGTATTACTCAG 58.552 44.000 6.44 9.45 34.90 3.35
418 1721 0.035317 GCGCATGAGGGGACATATGA 59.965 55.000 10.38 0.00 0.00 2.15
437 1741 2.658593 CCGGCTCGACTAATGGCG 60.659 66.667 10.09 10.09 46.76 5.69
445 1749 0.782384 CGTATAAATGCCGGCTCGAC 59.218 55.000 29.70 15.13 0.00 4.20
446 1750 0.386476 ACGTATAAATGCCGGCTCGA 59.614 50.000 29.70 7.94 0.00 4.04
448 1752 3.022607 ACTACGTATAAATGCCGGCTC 57.977 47.619 29.70 0.00 0.00 4.70
449 1753 3.571401 AGTACTACGTATAAATGCCGGCT 59.429 43.478 29.70 10.43 0.00 5.52
450 1754 3.905784 AGTACTACGTATAAATGCCGGC 58.094 45.455 22.73 22.73 0.00 6.13
451 1755 6.845302 TCATAGTACTACGTATAAATGCCGG 58.155 40.000 4.31 0.00 0.00 6.13
452 1756 8.906636 AATCATAGTACTACGTATAAATGCCG 57.093 34.615 4.31 0.00 0.00 5.69
466 1770 8.830580 CCGTCAATCAAATCAAATCATAGTACT 58.169 33.333 0.00 0.00 0.00 2.73
486 1790 4.947147 GTGCCACCCAGCCGTCAA 62.947 66.667 0.00 0.00 0.00 3.18
494 1798 1.563577 TTATTAGCCGGTGCCACCCA 61.564 55.000 8.62 0.00 38.69 4.51
571 2367 2.600731 GTTCAGACGTGGAGATCAGTG 58.399 52.381 0.00 0.00 0.00 3.66
764 2568 1.590238 CACGTACGTACTCCTACTCCG 59.410 57.143 22.34 9.24 0.00 4.63
772 2576 2.900122 TGGTAAGCACGTACGTACTC 57.100 50.000 22.34 12.99 0.00 2.59
832 2642 2.660552 AAAGACCCGACACGCACG 60.661 61.111 0.00 0.00 0.00 5.34
876 2686 0.255033 GTGGTGGGGGTTAGTGGATC 59.745 60.000 0.00 0.00 0.00 3.36
905 2719 2.141517 GGACGGAGAATGCATGAGATG 58.858 52.381 0.00 0.00 0.00 2.90
912 2726 0.535335 GTAGGTGGACGGAGAATGCA 59.465 55.000 0.00 0.00 0.00 3.96
913 2727 0.824759 AGTAGGTGGACGGAGAATGC 59.175 55.000 0.00 0.00 0.00 3.56
914 2728 2.586258 CAGTAGGTGGACGGAGAATG 57.414 55.000 0.00 0.00 0.00 2.67
947 2761 1.238625 GGCCATTTGGTCGTCGGAAA 61.239 55.000 0.00 0.00 37.57 3.13
996 2810 1.895231 GGCCGCGTTTTATAGGGGG 60.895 63.158 4.92 0.00 44.91 5.40
1127 2962 1.636340 GACAACGCCATCGATTCGG 59.364 57.895 17.68 9.14 39.41 4.30
1598 3448 1.956170 GTGACAGGGACACGTGCAG 60.956 63.158 17.22 3.57 35.97 4.41
1623 3476 4.211389 CAAAGAAACAACTCGTGAATCGG 58.789 43.478 0.00 0.00 40.32 4.18
1643 3496 7.759886 TCCAAACAACATCATTAAAAACGACAA 59.240 29.630 0.00 0.00 0.00 3.18
1647 3500 6.197468 ACGTCCAAACAACATCATTAAAAACG 59.803 34.615 0.00 0.00 0.00 3.60
1656 3509 1.595328 CACGACGTCCAAACAACATCA 59.405 47.619 10.58 0.00 0.00 3.07
1667 3520 2.733593 GTCACCTGCACGACGTCC 60.734 66.667 10.58 0.00 0.00 4.79
2328 4196 1.507630 CGATGTACGTCCGGGACAA 59.492 57.895 25.80 11.24 37.22 3.18
2606 4475 2.506438 GCACCAGGACGAGTACGC 60.506 66.667 0.00 0.00 43.96 4.42
2713 4730 8.542497 TCCAGTAAATCACATACAACAAGTAC 57.458 34.615 0.00 0.00 35.05 2.73
2717 4734 9.378551 GTAGATCCAGTAAATCACATACAACAA 57.621 33.333 0.00 0.00 0.00 2.83
2718 4735 8.758829 AGTAGATCCAGTAAATCACATACAACA 58.241 33.333 0.00 0.00 0.00 3.33
2760 4777 1.550869 CCCCTTTTGCCAGAAGGACAT 60.551 52.381 15.27 0.00 45.25 3.06
2767 4784 1.715785 CTTTTCCCCCTTTTGCCAGA 58.284 50.000 0.00 0.00 0.00 3.86
2771 4788 1.347707 CCTTCCTTTTCCCCCTTTTGC 59.652 52.381 0.00 0.00 0.00 3.68
2782 4799 4.342092 CACACACCTTTCATCCTTCCTTTT 59.658 41.667 0.00 0.00 0.00 2.27
2786 4803 1.541588 GCACACACCTTTCATCCTTCC 59.458 52.381 0.00 0.00 0.00 3.46
2790 4807 3.059352 AGTAGCACACACCTTTCATCC 57.941 47.619 0.00 0.00 0.00 3.51
2805 4822 7.379750 CCCCTCAAAGTAGATATTGTAGTAGC 58.620 42.308 0.00 0.00 0.00 3.58
2806 4823 7.728981 TCCCCCTCAAAGTAGATATTGTAGTAG 59.271 40.741 0.00 0.00 0.00 2.57
2807 4824 7.598248 TCCCCCTCAAAGTAGATATTGTAGTA 58.402 38.462 0.00 0.00 0.00 1.82
2808 4825 6.449956 TCCCCCTCAAAGTAGATATTGTAGT 58.550 40.000 0.00 0.00 0.00 2.73
2809 4826 6.555360 ACTCCCCCTCAAAGTAGATATTGTAG 59.445 42.308 0.00 0.00 0.00 2.74
2810 4827 6.326583 CACTCCCCCTCAAAGTAGATATTGTA 59.673 42.308 0.00 0.00 0.00 2.41
2811 4828 5.131142 CACTCCCCCTCAAAGTAGATATTGT 59.869 44.000 0.00 0.00 0.00 2.71
2812 4829 5.455326 CCACTCCCCCTCAAAGTAGATATTG 60.455 48.000 0.00 0.00 0.00 1.90
2813 4830 4.660771 CCACTCCCCCTCAAAGTAGATATT 59.339 45.833 0.00 0.00 0.00 1.28
2814 4831 4.077982 TCCACTCCCCCTCAAAGTAGATAT 60.078 45.833 0.00 0.00 0.00 1.63
2815 4832 3.273886 TCCACTCCCCCTCAAAGTAGATA 59.726 47.826 0.00 0.00 0.00 1.98
2816 4833 2.045885 TCCACTCCCCCTCAAAGTAGAT 59.954 50.000 0.00 0.00 0.00 1.98
2817 4834 1.435563 TCCACTCCCCCTCAAAGTAGA 59.564 52.381 0.00 0.00 0.00 2.59
2818 4835 1.952621 TCCACTCCCCCTCAAAGTAG 58.047 55.000 0.00 0.00 0.00 2.57
2819 4836 2.225779 TGATCCACTCCCCCTCAAAGTA 60.226 50.000 0.00 0.00 0.00 2.24
2820 4837 1.290134 GATCCACTCCCCCTCAAAGT 58.710 55.000 0.00 0.00 0.00 2.66
2821 4838 1.289160 TGATCCACTCCCCCTCAAAG 58.711 55.000 0.00 0.00 0.00 2.77
2822 4839 1.354368 GTTGATCCACTCCCCCTCAAA 59.646 52.381 0.00 0.00 0.00 2.69
2823 4840 0.991920 GTTGATCCACTCCCCCTCAA 59.008 55.000 0.00 0.00 0.00 3.02
2824 4841 0.178876 TGTTGATCCACTCCCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
2825 4842 0.543749 CTGTTGATCCACTCCCCCTC 59.456 60.000 0.00 0.00 0.00 4.30
2826 4843 1.566298 GCTGTTGATCCACTCCCCCT 61.566 60.000 0.00 0.00 0.00 4.79
2827 4844 1.077429 GCTGTTGATCCACTCCCCC 60.077 63.158 0.00 0.00 0.00 5.40
2828 4845 1.134371 GTAGCTGTTGATCCACTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
2829 4846 1.555075 TGTAGCTGTTGATCCACTCCC 59.445 52.381 0.00 0.00 0.00 4.30
2830 4847 2.234908 ACTGTAGCTGTTGATCCACTCC 59.765 50.000 0.00 0.00 0.00 3.85
2831 4848 3.601443 ACTGTAGCTGTTGATCCACTC 57.399 47.619 0.00 0.00 0.00 3.51
2832 4849 3.324846 TGAACTGTAGCTGTTGATCCACT 59.675 43.478 0.00 0.00 0.00 4.00
2833 4850 3.433615 GTGAACTGTAGCTGTTGATCCAC 59.566 47.826 0.00 0.00 0.00 4.02
2834 4851 3.070878 TGTGAACTGTAGCTGTTGATCCA 59.929 43.478 0.00 0.00 0.00 3.41
2835 4852 3.664107 TGTGAACTGTAGCTGTTGATCC 58.336 45.455 0.00 0.00 0.00 3.36
2836 4853 5.673337 TTTGTGAACTGTAGCTGTTGATC 57.327 39.130 0.00 0.00 0.00 2.92
2837 4854 6.449635 TTTTTGTGAACTGTAGCTGTTGAT 57.550 33.333 0.00 0.00 0.00 2.57
2838 4855 5.888691 TTTTTGTGAACTGTAGCTGTTGA 57.111 34.783 0.00 0.00 0.00 3.18
2858 4875 9.447040 GCTTACTTTAGTCGTTCATTTTCTTTT 57.553 29.630 0.00 0.00 0.00 2.27
2859 4876 8.074370 GGCTTACTTTAGTCGTTCATTTTCTTT 58.926 33.333 0.00 0.00 0.00 2.52
2860 4877 7.227910 TGGCTTACTTTAGTCGTTCATTTTCTT 59.772 33.333 0.00 0.00 0.00 2.52
2861 4878 6.708949 TGGCTTACTTTAGTCGTTCATTTTCT 59.291 34.615 0.00 0.00 0.00 2.52
2862 4879 6.795593 GTGGCTTACTTTAGTCGTTCATTTTC 59.204 38.462 0.00 0.00 0.00 2.29
2863 4880 6.485648 AGTGGCTTACTTTAGTCGTTCATTTT 59.514 34.615 0.00 0.00 35.67 1.82
2864 4881 5.995897 AGTGGCTTACTTTAGTCGTTCATTT 59.004 36.000 0.00 0.00 35.67 2.32
2865 4882 5.548406 AGTGGCTTACTTTAGTCGTTCATT 58.452 37.500 0.00 0.00 35.67 2.57
2866 4883 5.148651 AGTGGCTTACTTTAGTCGTTCAT 57.851 39.130 0.00 0.00 35.67 2.57
2867 4884 4.553323 GAGTGGCTTACTTTAGTCGTTCA 58.447 43.478 0.00 0.00 40.53 3.18
2868 4885 3.925299 GGAGTGGCTTACTTTAGTCGTTC 59.075 47.826 0.00 0.00 40.53 3.95
2869 4886 3.322828 TGGAGTGGCTTACTTTAGTCGTT 59.677 43.478 0.00 0.00 40.53 3.85
2870 4887 2.895404 TGGAGTGGCTTACTTTAGTCGT 59.105 45.455 0.00 0.00 40.53 4.34
2871 4888 3.587797 TGGAGTGGCTTACTTTAGTCG 57.412 47.619 0.00 0.00 40.53 4.18
2872 4889 4.895961 AGTTGGAGTGGCTTACTTTAGTC 58.104 43.478 0.00 0.00 40.53 2.59
2873 4890 4.976540 AGTTGGAGTGGCTTACTTTAGT 57.023 40.909 0.00 0.00 40.53 2.24
2874 4891 5.552178 AGAAGTTGGAGTGGCTTACTTTAG 58.448 41.667 0.00 0.00 40.53 1.85
2875 4892 5.562298 AGAAGTTGGAGTGGCTTACTTTA 57.438 39.130 0.00 0.00 40.53 1.85
2876 4893 4.439253 AGAAGTTGGAGTGGCTTACTTT 57.561 40.909 0.00 0.00 40.53 2.66
2877 4894 4.137543 CAAGAAGTTGGAGTGGCTTACTT 58.862 43.478 0.00 0.00 40.53 2.24
2905 4922 4.423625 ACACAAAGAAGCCAGTAGAGTT 57.576 40.909 0.00 0.00 0.00 3.01
2920 4937 0.466555 AGCGGTTGGGCTAACACAAA 60.467 50.000 15.85 0.00 42.62 2.83
3050 5068 0.246635 CGTGGGGGACTGTACAGAAG 59.753 60.000 29.30 4.31 0.00 2.85
3052 5070 0.405198 TACGTGGGGGACTGTACAGA 59.595 55.000 29.30 2.44 0.00 3.41
3203 5222 2.349297 ACAGTCGAGCTTAGTTTCGG 57.651 50.000 8.01 0.00 37.42 4.30
3255 5274 3.070015 GGATTTTCATACATTGGGGCCTG 59.930 47.826 0.84 0.00 0.00 4.85
3360 5398 2.886913 TGGAATTCCTTCAACCATGCA 58.113 42.857 24.73 0.00 36.82 3.96
3382 5455 3.753797 AGAAAAAGAAGTGGAATCCTCGC 59.246 43.478 0.00 0.00 0.00 5.03
3801 5884 4.063967 ATGTTGGTCGCCGCTCGA 62.064 61.111 0.00 0.00 46.29 4.04
3820 5903 3.429822 CGTTTATCTTCTTCGTAGGGCCA 60.430 47.826 6.18 0.00 0.00 5.36
3843 5926 3.248171 CTTCTGACTACCGCGCGC 61.248 66.667 27.36 23.91 0.00 6.86
3847 5930 2.126071 TGCGCTTCTGACTACCGC 60.126 61.111 9.73 0.00 44.39 5.68
3854 5937 3.617143 ATGCTGGCTGCGCTTCTGA 62.617 57.895 9.73 0.00 46.63 3.27
3942 6054 5.883115 TGTAATAAAATGGTGATTGAGCGGA 59.117 36.000 0.00 0.00 0.00 5.54



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

AutoCloner maintained by Alex Coulton.