Multiple sequence alignment - TraesCS1B01G198700

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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 TraesCS1B01G198700 chr1B 100.000 3080 0 0 1 3080 356870104 356873183 0.000000e+00 5688.0
1 TraesCS1B01G198700 chr1B 94.545 110 5 1 1 109 356848605 356848714 6.020000e-38 169.0
2 TraesCS1B01G198700 chr1B 92.727 110 5 2 1 109 207807966 207808073 4.690000e-34 156.0
3 TraesCS1B01G198700 chr1B 100.000 52 0 0 3458 3509 356873561 356873612 2.880000e-16 97.1
4 TraesCS1B01G198700 chr1D 93.875 2498 87 27 489 2949 256282602 256280134 0.000000e+00 3705.0
5 TraesCS1B01G198700 chr1D 95.614 114 5 0 360 473 256282771 256282658 2.150000e-42 183.0
6 TraesCS1B01G198700 chr1D 92.523 107 8 0 143 249 256283179 256283073 1.690000e-33 154.0
7 TraesCS1B01G198700 chr1D 84.672 137 17 3 210 344 256283078 256282944 2.200000e-27 134.0
8 TraesCS1B01G198700 chr1D 81.707 164 10 7 2659 2802 256278901 256278738 6.150000e-23 119.0
9 TraesCS1B01G198700 chr1A 94.233 2289 68 25 489 2742 329249160 329246901 0.000000e+00 3437.0
10 TraesCS1B01G198700 chr1A 92.637 747 40 4 1087 1827 549706931 549706194 0.000000e+00 1061.0
11 TraesCS1B01G198700 chr1A 86.992 369 21 7 130 473 329249582 329249216 1.180000e-104 390.0
12 TraesCS1B01G198700 chr1A 85.053 281 20 7 2659 2917 329240619 329240339 2.080000e-67 267.0
13 TraesCS1B01G198700 chr6D 91.733 750 53 3 1087 1827 78785316 78786065 0.000000e+00 1033.0
14 TraesCS1B01G198700 chr4B 77.406 1465 236 56 1049 2434 672309352 672307904 0.000000e+00 784.0
15 TraesCS1B01G198700 chr4B 78.297 1092 181 41 1374 2434 670113573 670114639 0.000000e+00 652.0
16 TraesCS1B01G198700 chrUn 78.926 1248 190 40 1067 2264 99863465 99864689 0.000000e+00 780.0
17 TraesCS1B01G198700 chr3B 94.132 409 23 1 1418 1825 47197604 47197196 3.850000e-174 621.0
18 TraesCS1B01G198700 chr3B 96.154 52 1 1 3458 3509 169949439 169949489 2.240000e-12 84.2
19 TraesCS1B01G198700 chr5D 87.059 510 58 6 1417 1921 380189669 380189163 1.410000e-158 569.0
20 TraesCS1B01G198700 chr2B 94.545 110 4 2 1 109 703269566 703269458 6.020000e-38 169.0
21 TraesCS1B01G198700 chr2B 93.636 110 5 2 1 109 703320423 703320315 2.800000e-36 163.0
22 TraesCS1B01G198700 chr2B 92.727 110 5 3 1 109 703321579 703321686 4.690000e-34 156.0
23 TraesCS1B01G198700 chr5B 94.393 107 4 2 1 106 564940670 564940565 2.800000e-36 163.0
24 TraesCS1B01G198700 chr5B 93.636 110 5 2 1 109 606167145 606167037 2.800000e-36 163.0
25 TraesCS1B01G198700 chr5B 92.035 113 7 2 1 112 42614796 42614685 1.300000e-34 158.0
26 TraesCS1B01G198700 chr5B 92.727 110 7 1 1 110 606038519 606038411 1.300000e-34 158.0


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 TraesCS1B01G198700 chr1B 356870104 356873612 3508 False 2892.55 5688 100.0000 1 3509 2 chr1B.!!$F3 3508
1 TraesCS1B01G198700 chr1D 256278738 256283179 4441 True 859.00 3705 89.6782 143 2949 5 chr1D.!!$R1 2806
2 TraesCS1B01G198700 chr1A 329246901 329249582 2681 True 1913.50 3437 90.6125 130 2742 2 chr1A.!!$R3 2612
3 TraesCS1B01G198700 chr1A 549706194 549706931 737 True 1061.00 1061 92.6370 1087 1827 1 chr1A.!!$R2 740
4 TraesCS1B01G198700 chr6D 78785316 78786065 749 False 1033.00 1033 91.7330 1087 1827 1 chr6D.!!$F1 740
5 TraesCS1B01G198700 chr4B 672307904 672309352 1448 True 784.00 784 77.4060 1049 2434 1 chr4B.!!$R1 1385
6 TraesCS1B01G198700 chr4B 670113573 670114639 1066 False 652.00 652 78.2970 1374 2434 1 chr4B.!!$F1 1060
7 TraesCS1B01G198700 chrUn 99863465 99864689 1224 False 780.00 780 78.9260 1067 2264 1 chrUn.!!$F1 1197
8 TraesCS1B01G198700 chr5D 380189163 380189669 506 True 569.00 569 87.0590 1417 1921 1 chr5D.!!$R1 504

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
40 41 0.109132 CTTGGATGTTTTGAGGGCGC 60.109 55.0 0.00 0.00 0.0 6.53 F
44 45 0.169009 GATGTTTTGAGGGCGCAGTC 59.831 55.0 10.83 5.36 0.0 3.51 F
105 106 0.248289 ACCCGTGGTCATTTACTCCG 59.752 55.0 0.00 0.00 0.0 4.63 F
875 1145 0.392461 CGACAACCCACCATCCGATT 60.392 55.0 0.00 0.00 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2190 1.379443 ACGCAGGTACCGATCCAGA 60.379 57.895 6.18 0.0 0.00 3.86 R
2025 2388 1.552792 TCGCACATGGTGAAGTGGATA 59.447 47.619 0.00 0.0 35.23 2.59 R
2385 2813 1.279271 AGCCCGTACAGCTTCTTGAAT 59.721 47.619 1.60 0.0 37.24 2.57 R
2957 3397 0.040425 ATGCAACGAAGAAACACGCC 60.040 50.000 0.00 0.0 0.00 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
17 18 4.479993 CAGGAGAAGGCGGCCCTG 62.480 72.222 17.02 15.64 41.90 4.45
27 28 4.473520 CGGCCCTGCGTCTTGGAT 62.474 66.667 0.00 0.00 0.00 3.41
28 29 2.825836 GGCCCTGCGTCTTGGATG 60.826 66.667 0.00 0.00 0.00 3.51
29 30 2.045926 GCCCTGCGTCTTGGATGT 60.046 61.111 0.00 0.00 0.00 3.06
30 31 1.675641 GCCCTGCGTCTTGGATGTT 60.676 57.895 0.00 0.00 0.00 2.71
31 32 1.244019 GCCCTGCGTCTTGGATGTTT 61.244 55.000 0.00 0.00 0.00 2.83
32 33 1.247567 CCCTGCGTCTTGGATGTTTT 58.752 50.000 0.00 0.00 0.00 2.43
33 34 1.068333 CCCTGCGTCTTGGATGTTTTG 60.068 52.381 0.00 0.00 0.00 2.44
34 35 1.879380 CCTGCGTCTTGGATGTTTTGA 59.121 47.619 0.00 0.00 0.00 2.69
35 36 2.095567 CCTGCGTCTTGGATGTTTTGAG 60.096 50.000 0.00 0.00 0.00 3.02
36 37 1.879380 TGCGTCTTGGATGTTTTGAGG 59.121 47.619 0.00 0.00 0.00 3.86
37 38 1.200020 GCGTCTTGGATGTTTTGAGGG 59.800 52.381 0.00 0.00 0.00 4.30
38 39 1.200020 CGTCTTGGATGTTTTGAGGGC 59.800 52.381 0.00 0.00 0.00 5.19
39 40 1.200020 GTCTTGGATGTTTTGAGGGCG 59.800 52.381 0.00 0.00 0.00 6.13
40 41 0.109132 CTTGGATGTTTTGAGGGCGC 60.109 55.000 0.00 0.00 0.00 6.53
41 42 0.825425 TTGGATGTTTTGAGGGCGCA 60.825 50.000 10.83 0.00 0.00 6.09
42 43 1.243342 TGGATGTTTTGAGGGCGCAG 61.243 55.000 10.83 0.00 0.00 5.18
43 44 1.244019 GGATGTTTTGAGGGCGCAGT 61.244 55.000 10.83 0.00 0.00 4.40
44 45 0.169009 GATGTTTTGAGGGCGCAGTC 59.831 55.000 10.83 5.36 0.00 3.51
45 46 1.577328 ATGTTTTGAGGGCGCAGTCG 61.577 55.000 10.83 0.00 39.07 4.18
46 47 1.959226 GTTTTGAGGGCGCAGTCGA 60.959 57.895 10.83 1.19 38.10 4.20
47 48 1.959226 TTTTGAGGGCGCAGTCGAC 60.959 57.895 10.83 7.70 44.72 4.20
53 54 3.896133 GGCGCAGTCGACCCGATA 61.896 66.667 24.72 0.00 37.90 2.92
54 55 2.335369 GCGCAGTCGACCCGATAT 59.665 61.111 24.72 0.00 38.42 1.63
55 56 2.016704 GCGCAGTCGACCCGATATG 61.017 63.158 24.72 12.14 38.42 1.78
56 57 1.359117 CGCAGTCGACCCGATATGT 59.641 57.895 18.12 0.00 38.42 2.29
57 58 0.248907 CGCAGTCGACCCGATATGTT 60.249 55.000 18.12 0.00 38.42 2.71
58 59 1.801395 CGCAGTCGACCCGATATGTTT 60.801 52.381 18.12 0.00 38.42 2.83
59 60 2.277084 GCAGTCGACCCGATATGTTTT 58.723 47.619 13.01 0.00 38.42 2.43
60 61 2.030457 GCAGTCGACCCGATATGTTTTG 59.970 50.000 13.01 0.00 38.42 2.44
61 62 3.517602 CAGTCGACCCGATATGTTTTGA 58.482 45.455 13.01 0.00 38.42 2.69
62 63 3.930229 CAGTCGACCCGATATGTTTTGAA 59.070 43.478 13.01 0.00 38.42 2.69
63 64 4.032900 CAGTCGACCCGATATGTTTTGAAG 59.967 45.833 13.01 0.00 38.42 3.02
64 65 4.081862 AGTCGACCCGATATGTTTTGAAGA 60.082 41.667 13.01 0.00 38.42 2.87
65 66 4.628333 GTCGACCCGATATGTTTTGAAGAA 59.372 41.667 3.51 0.00 38.42 2.52
66 67 4.628333 TCGACCCGATATGTTTTGAAGAAC 59.372 41.667 0.00 0.00 0.00 3.01
67 68 4.201783 CGACCCGATATGTTTTGAAGAACC 60.202 45.833 0.00 0.00 0.00 3.62
68 69 4.658063 ACCCGATATGTTTTGAAGAACCA 58.342 39.130 0.00 0.00 0.00 3.67
69 70 4.700213 ACCCGATATGTTTTGAAGAACCAG 59.300 41.667 0.00 0.00 0.00 4.00
70 71 4.096382 CCCGATATGTTTTGAAGAACCAGG 59.904 45.833 0.00 0.00 0.00 4.45
71 72 4.096382 CCGATATGTTTTGAAGAACCAGGG 59.904 45.833 0.00 0.00 0.00 4.45
72 73 4.096382 CGATATGTTTTGAAGAACCAGGGG 59.904 45.833 0.00 0.00 0.00 4.79
73 74 2.080654 TGTTTTGAAGAACCAGGGGG 57.919 50.000 0.00 0.00 41.29 5.40
90 91 2.504519 GGCTGGTTAGGCTACCCG 59.495 66.667 3.48 0.14 45.44 5.28
91 92 2.364780 GGCTGGTTAGGCTACCCGT 61.365 63.158 3.48 0.00 45.44 5.28
92 93 1.153429 GCTGGTTAGGCTACCCGTG 60.153 63.158 3.48 0.52 37.39 4.94
93 94 1.520666 CTGGTTAGGCTACCCGTGG 59.479 63.158 3.48 0.00 37.39 4.94
94 95 1.229272 TGGTTAGGCTACCCGTGGT 60.229 57.895 3.48 1.14 40.16 4.16
95 96 1.259840 TGGTTAGGCTACCCGTGGTC 61.260 60.000 3.48 0.00 37.09 4.02
96 97 1.259840 GGTTAGGCTACCCGTGGTCA 61.260 60.000 0.00 0.00 37.09 4.02
97 98 0.828677 GTTAGGCTACCCGTGGTCAT 59.171 55.000 0.00 0.00 37.09 3.06
98 99 1.208776 GTTAGGCTACCCGTGGTCATT 59.791 52.381 0.00 0.00 37.09 2.57
99 100 1.575419 TAGGCTACCCGTGGTCATTT 58.425 50.000 0.00 0.00 37.09 2.32
100 101 1.575419 AGGCTACCCGTGGTCATTTA 58.425 50.000 0.00 0.00 37.09 1.40
101 102 1.208776 AGGCTACCCGTGGTCATTTAC 59.791 52.381 0.00 0.00 37.09 2.01
102 103 1.208776 GGCTACCCGTGGTCATTTACT 59.791 52.381 0.00 0.00 37.09 2.24
103 104 2.547826 GCTACCCGTGGTCATTTACTC 58.452 52.381 0.00 0.00 37.09 2.59
104 105 2.740904 GCTACCCGTGGTCATTTACTCC 60.741 54.545 0.00 0.00 37.09 3.85
105 106 0.248289 ACCCGTGGTCATTTACTCCG 59.752 55.000 0.00 0.00 0.00 4.63
106 107 0.533491 CCCGTGGTCATTTACTCCGA 59.467 55.000 0.00 0.00 0.00 4.55
107 108 1.636988 CCGTGGTCATTTACTCCGAC 58.363 55.000 0.00 0.00 0.00 4.79
108 109 1.067425 CCGTGGTCATTTACTCCGACA 60.067 52.381 0.00 0.00 0.00 4.35
109 110 2.610976 CCGTGGTCATTTACTCCGACAA 60.611 50.000 0.00 0.00 0.00 3.18
110 111 3.061322 CGTGGTCATTTACTCCGACAAA 58.939 45.455 0.00 0.00 0.00 2.83
111 112 3.682858 CGTGGTCATTTACTCCGACAAAT 59.317 43.478 0.00 0.00 0.00 2.32
112 113 4.865925 CGTGGTCATTTACTCCGACAAATA 59.134 41.667 0.00 0.00 0.00 1.40
113 114 5.005394 CGTGGTCATTTACTCCGACAAATAG 59.995 44.000 0.00 0.00 0.00 1.73
114 115 5.873164 GTGGTCATTTACTCCGACAAATAGT 59.127 40.000 0.00 0.00 0.00 2.12
115 116 7.037438 GTGGTCATTTACTCCGACAAATAGTA 58.963 38.462 0.00 0.00 0.00 1.82
116 117 7.546667 GTGGTCATTTACTCCGACAAATAGTAA 59.453 37.037 0.00 0.00 34.70 2.24
117 118 8.262227 TGGTCATTTACTCCGACAAATAGTAAT 58.738 33.333 0.00 0.00 36.05 1.89
118 119 9.754382 GGTCATTTACTCCGACAAATAGTAATA 57.246 33.333 0.00 0.00 36.05 0.98
120 121 9.976511 TCATTTACTCCGACAAATAGTAATAGG 57.023 33.333 0.00 0.00 36.05 2.57
121 122 9.204570 CATTTACTCCGACAAATAGTAATAGGG 57.795 37.037 0.00 0.00 36.05 3.53
122 123 5.803237 ACTCCGACAAATAGTAATAGGGG 57.197 43.478 0.00 0.00 0.00 4.79
123 124 4.040095 ACTCCGACAAATAGTAATAGGGGC 59.960 45.833 0.00 0.00 0.00 5.80
124 125 3.325716 TCCGACAAATAGTAATAGGGGCC 59.674 47.826 0.00 0.00 0.00 5.80
125 126 3.326880 CCGACAAATAGTAATAGGGGCCT 59.673 47.826 0.84 0.00 0.00 5.19
126 127 4.562963 CCGACAAATAGTAATAGGGGCCTC 60.563 50.000 0.84 0.00 0.00 4.70
127 128 4.562963 CGACAAATAGTAATAGGGGCCTCC 60.563 50.000 0.00 0.00 0.00 4.30
180 181 3.562973 AGAAACCATGCTGCTAATCATCG 59.437 43.478 0.00 0.00 0.00 3.84
183 184 2.216046 CCATGCTGCTAATCATCGTGT 58.784 47.619 0.00 0.00 0.00 4.49
235 236 5.509605 AAACAAGCTGTTTCGTTCAAAAC 57.490 34.783 8.03 0.00 46.61 2.43
240 269 5.761818 AGCTGTTTCGTTCAAAACAAAAG 57.238 34.783 4.04 0.00 45.67 2.27
243 272 6.307077 AGCTGTTTCGTTCAAAACAAAAGTAC 59.693 34.615 4.04 0.00 45.67 2.73
300 335 1.443872 GTACGCGTCCTGGTCAGTG 60.444 63.158 18.63 0.00 0.00 3.66
335 384 2.868899 CCCTTCCAAAAGAGCTTCTGT 58.131 47.619 0.00 0.00 34.14 3.41
344 393 1.202330 AGAGCTTCTGTGCCAGCTAT 58.798 50.000 0.00 0.00 46.72 2.97
423 634 1.111116 TGGATCGACCGTATCACCCC 61.111 60.000 0.00 0.00 42.61 4.95
424 635 1.664306 GATCGACCGTATCACCCCC 59.336 63.158 0.00 0.00 0.00 5.40
473 684 4.509616 CACCGTGTTGATTTGGGTATCTA 58.490 43.478 0.00 0.00 0.00 1.98
474 685 4.938832 CACCGTGTTGATTTGGGTATCTAA 59.061 41.667 0.00 0.00 0.00 2.10
477 688 6.661805 ACCGTGTTGATTTGGGTATCTAAATT 59.338 34.615 0.00 0.00 34.80 1.82
480 691 7.855904 CGTGTTGATTTGGGTATCTAAATTAGC 59.144 37.037 0.00 0.00 34.80 3.09
481 692 8.135529 GTGTTGATTTGGGTATCTAAATTAGCC 58.864 37.037 0.00 0.00 34.80 3.93
484 695 7.231467 TGATTTGGGTATCTAAATTAGCCCTC 58.769 38.462 13.08 5.76 34.80 4.30
485 696 4.884668 TGGGTATCTAAATTAGCCCTCG 57.115 45.455 13.08 0.00 37.09 4.63
486 697 4.485875 TGGGTATCTAAATTAGCCCTCGA 58.514 43.478 13.08 0.00 37.09 4.04
536 788 4.962995 AGGAGGAGATAAGAAACGGATGAA 59.037 41.667 0.00 0.00 0.00 2.57
606 861 1.622607 TACCTGCCCCAATCACCTCG 61.623 60.000 0.00 0.00 0.00 4.63
607 862 2.669133 CCTGCCCCAATCACCTCGA 61.669 63.158 0.00 0.00 0.00 4.04
685 940 3.242739 CGAACAGTTTCAAACCACCAGAG 60.243 47.826 0.00 0.00 0.00 3.35
869 1139 2.434331 CCCACGACAACCCACCAT 59.566 61.111 0.00 0.00 0.00 3.55
870 1140 1.674322 CCCACGACAACCCACCATC 60.674 63.158 0.00 0.00 0.00 3.51
871 1141 1.674322 CCACGACAACCCACCATCC 60.674 63.158 0.00 0.00 0.00 3.51
872 1142 2.032634 CACGACAACCCACCATCCG 61.033 63.158 0.00 0.00 0.00 4.18
873 1143 2.211410 ACGACAACCCACCATCCGA 61.211 57.895 0.00 0.00 0.00 4.55
874 1144 1.220749 CGACAACCCACCATCCGAT 59.779 57.895 0.00 0.00 0.00 4.18
875 1145 0.392461 CGACAACCCACCATCCGATT 60.392 55.000 0.00 0.00 0.00 3.34
889 1159 3.216187 TCCGATTTCCGATCTCTCTCT 57.784 47.619 0.00 0.00 41.76 3.10
982 1257 0.917333 AGACTCCTCCTCCTCCTCGT 60.917 60.000 0.00 0.00 0.00 4.18
1042 1317 4.778143 GGGCGGCGGTCATGTTCT 62.778 66.667 9.78 0.00 0.00 3.01
1860 2208 0.755698 ATCTGGATCGGTACCTGCGT 60.756 55.000 10.90 0.00 0.00 5.24
2025 2388 4.101448 GGGAGGCTGGACGTGCAT 62.101 66.667 11.16 0.00 0.00 3.96
2385 2813 4.508128 GACGCGCCGATGAGGGAA 62.508 66.667 5.73 0.00 41.48 3.97
2511 2939 1.108776 CCGAGAAGGACCGGTGATTA 58.891 55.000 14.63 0.00 45.00 1.75
2514 2942 3.123804 CGAGAAGGACCGGTGATTAATG 58.876 50.000 14.63 0.00 0.00 1.90
2517 2945 4.514401 AGAAGGACCGGTGATTAATGAAC 58.486 43.478 14.63 0.00 0.00 3.18
2518 2946 2.901249 AGGACCGGTGATTAATGAACG 58.099 47.619 14.63 5.28 0.00 3.95
2651 3084 4.882427 TGTAGTCTAGCTAGTGTAAGGCAG 59.118 45.833 20.10 0.00 0.00 4.85
2664 3097 1.999648 AAGGCAGTTGCAAAGGATGA 58.000 45.000 0.00 0.00 44.36 2.92
2747 3180 6.452494 TGTACATAGAAGAGAACTGGCTAC 57.548 41.667 0.00 0.00 0.00 3.58
2752 3185 8.941995 ACATAGAAGAGAACTGGCTACATATA 57.058 34.615 0.00 0.00 0.00 0.86
2782 3215 5.702865 CACAAATCCCAAATGTACAGAGTG 58.297 41.667 0.33 0.00 0.00 3.51
2786 3219 7.504238 ACAAATCCCAAATGTACAGAGTGTTAA 59.496 33.333 0.33 0.00 0.00 2.01
2798 3231 8.717821 TGTACAGAGTGTTAATATGCTTGTTTC 58.282 33.333 0.00 0.00 0.00 2.78
2801 3234 7.148573 ACAGAGTGTTAATATGCTTGTTTCGAG 60.149 37.037 0.00 0.00 0.00 4.04
2822 3256 7.112122 TCGAGGGTCTACTGTAATACTGTAAA 58.888 38.462 10.57 0.00 33.21 2.01
2826 3260 7.066766 AGGGTCTACTGTAATACTGTAAAGTCG 59.933 40.741 10.57 1.10 33.21 4.18
2831 3265 9.699985 CTACTGTAATACTGTAAAGTCGTGTAG 57.300 37.037 10.57 0.00 33.21 2.74
2832 3266 8.327941 ACTGTAATACTGTAAAGTCGTGTAGA 57.672 34.615 0.95 0.00 0.00 2.59
2834 3268 8.955061 TGTAATACTGTAAAGTCGTGTAGAAC 57.045 34.615 0.00 0.00 0.00 3.01
2836 3270 4.248691 ACTGTAAAGTCGTGTAGAACCC 57.751 45.455 0.00 0.00 0.00 4.11
2837 3271 3.893813 ACTGTAAAGTCGTGTAGAACCCT 59.106 43.478 0.00 0.00 0.00 4.34
2839 3273 5.713861 ACTGTAAAGTCGTGTAGAACCCTAT 59.286 40.000 0.00 0.00 0.00 2.57
2840 3274 6.886459 ACTGTAAAGTCGTGTAGAACCCTATA 59.114 38.462 0.00 0.00 0.00 1.31
2863 3303 3.119495 CGCCTTTCCTTTACATTCCAAGG 60.119 47.826 0.00 0.00 41.04 3.61
2889 3329 1.472480 CCTCGAAACCGCCATGAATTT 59.528 47.619 0.00 0.00 0.00 1.82
2921 3361 1.204146 GTTGCCCACCCTAGATCTCA 58.796 55.000 0.00 0.00 0.00 3.27
2923 3363 2.173569 GTTGCCCACCCTAGATCTCATT 59.826 50.000 0.00 0.00 0.00 2.57
2924 3364 1.770658 TGCCCACCCTAGATCTCATTG 59.229 52.381 0.00 0.00 0.00 2.82
2925 3365 1.771255 GCCCACCCTAGATCTCATTGT 59.229 52.381 0.00 0.00 0.00 2.71
2926 3366 2.173569 GCCCACCCTAGATCTCATTGTT 59.826 50.000 0.00 0.00 0.00 2.83
2930 3370 2.846206 ACCCTAGATCTCATTGTTGGCA 59.154 45.455 0.00 0.00 0.00 4.92
2933 3373 4.070716 CCTAGATCTCATTGTTGGCATCC 58.929 47.826 0.00 0.00 0.00 3.51
2935 3375 2.092753 AGATCTCATTGTTGGCATCCGT 60.093 45.455 0.00 0.00 0.00 4.69
2943 3383 0.960364 GTTGGCATCCGTCCACATGT 60.960 55.000 0.00 0.00 32.45 3.21
2959 3399 2.890945 ACATGTGGAAACAGTAAAGGGC 59.109 45.455 0.00 0.00 44.46 5.19
2961 3401 1.134037 TGTGGAAACAGTAAAGGGCGT 60.134 47.619 0.00 0.00 44.46 5.68
2962 3402 1.265905 GTGGAAACAGTAAAGGGCGTG 59.734 52.381 0.00 0.00 44.46 5.34
2963 3403 1.134037 TGGAAACAGTAAAGGGCGTGT 60.134 47.619 0.00 0.00 35.01 4.49
2964 3404 1.951602 GGAAACAGTAAAGGGCGTGTT 59.048 47.619 0.00 0.00 34.60 3.32
2966 3406 3.624900 GAAACAGTAAAGGGCGTGTTTC 58.375 45.455 10.15 10.15 46.75 2.78
2967 3407 2.632987 ACAGTAAAGGGCGTGTTTCT 57.367 45.000 0.00 0.00 0.00 2.52
2969 3409 2.876550 ACAGTAAAGGGCGTGTTTCTTC 59.123 45.455 0.00 0.00 0.00 2.87
2970 3410 2.096417 CAGTAAAGGGCGTGTTTCTTCG 60.096 50.000 0.00 0.00 0.00 3.79
2971 3411 1.869132 GTAAAGGGCGTGTTTCTTCGT 59.131 47.619 0.00 0.00 0.00 3.85
2972 3412 1.385528 AAAGGGCGTGTTTCTTCGTT 58.614 45.000 0.00 0.00 0.00 3.85
2973 3413 0.661020 AAGGGCGTGTTTCTTCGTTG 59.339 50.000 0.00 0.00 0.00 4.10
2974 3414 1.370051 GGGCGTGTTTCTTCGTTGC 60.370 57.895 0.00 0.00 0.00 4.17
2975 3415 1.353804 GGCGTGTTTCTTCGTTGCA 59.646 52.632 0.00 0.00 0.00 4.08
2977 3417 1.318251 GCGTGTTTCTTCGTTGCATC 58.682 50.000 0.00 0.00 0.00 3.91
2978 3418 1.580439 CGTGTTTCTTCGTTGCATCG 58.420 50.000 10.93 10.93 0.00 3.84
2979 3419 1.318251 GTGTTTCTTCGTTGCATCGC 58.682 50.000 12.30 0.00 0.00 4.58
2980 3420 0.237235 TGTTTCTTCGTTGCATCGCC 59.763 50.000 12.30 0.00 0.00 5.54
2981 3421 0.517316 GTTTCTTCGTTGCATCGCCT 59.483 50.000 12.30 0.00 0.00 5.52
2982 3422 0.516877 TTTCTTCGTTGCATCGCCTG 59.483 50.000 12.30 5.18 0.00 4.85
2990 3430 3.524606 GCATCGCCTGCCTTGCAT 61.525 61.111 6.18 0.00 45.66 3.96
2992 3432 2.044650 ATCGCCTGCCTTGCATGT 60.045 55.556 0.00 0.00 38.13 3.21
2994 3434 1.097547 ATCGCCTGCCTTGCATGTAC 61.098 55.000 0.00 0.00 38.13 2.90
2998 3438 0.729116 CCTGCCTTGCATGTACTTCG 59.271 55.000 0.00 0.00 38.13 3.79
2999 3439 1.675714 CCTGCCTTGCATGTACTTCGA 60.676 52.381 0.00 0.00 38.13 3.71
3000 3440 1.394917 CTGCCTTGCATGTACTTCGAC 59.605 52.381 0.00 0.00 38.13 4.20
3001 3441 1.001974 TGCCTTGCATGTACTTCGACT 59.998 47.619 0.00 0.00 31.71 4.18
3004 3444 3.682858 GCCTTGCATGTACTTCGACTAAA 59.317 43.478 0.00 0.00 0.00 1.85
3005 3445 4.153475 GCCTTGCATGTACTTCGACTAAAA 59.847 41.667 0.00 0.00 0.00 1.52
3007 3447 6.077838 CCTTGCATGTACTTCGACTAAAAAC 58.922 40.000 0.00 0.00 0.00 2.43
3009 3449 4.983538 TGCATGTACTTCGACTAAAAACGA 59.016 37.500 0.00 0.00 36.75 3.85
3010 3450 5.636121 TGCATGTACTTCGACTAAAAACGAT 59.364 36.000 0.00 0.00 38.30 3.73
3012 3452 5.980324 TGTACTTCGACTAAAAACGATCG 57.020 39.130 14.88 14.88 38.30 3.69
3013 3453 5.451908 TGTACTTCGACTAAAAACGATCGT 58.548 37.500 16.60 16.60 38.30 3.73
3014 3454 5.565259 TGTACTTCGACTAAAAACGATCGTC 59.435 40.000 22.98 5.98 38.30 4.20
3015 3455 4.791974 ACTTCGACTAAAAACGATCGTCT 58.208 39.130 22.98 4.15 38.30 4.18
3016 3456 5.931532 ACTTCGACTAAAAACGATCGTCTA 58.068 37.500 22.98 12.20 38.30 2.59
3017 3457 5.792468 ACTTCGACTAAAAACGATCGTCTAC 59.208 40.000 22.98 8.11 38.30 2.59
3019 3459 5.082059 TCGACTAAAAACGATCGTCTACAC 58.918 41.667 22.98 9.11 36.03 2.90
3020 3460 4.847757 CGACTAAAAACGATCGTCTACACA 59.152 41.667 22.98 4.26 0.00 3.72
3021 3461 5.510674 CGACTAAAAACGATCGTCTACACAT 59.489 40.000 22.98 0.00 0.00 3.21
3022 3462 6.684131 CGACTAAAAACGATCGTCTACACATA 59.316 38.462 22.98 7.33 0.00 2.29
3023 3463 7.097530 CGACTAAAAACGATCGTCTACACATAG 60.098 40.741 22.98 17.25 0.00 2.23
3024 3464 7.533426 ACTAAAAACGATCGTCTACACATAGT 58.467 34.615 22.98 17.81 0.00 2.12
3025 3465 8.025445 ACTAAAAACGATCGTCTACACATAGTT 58.975 33.333 22.98 4.88 0.00 2.24
3027 3467 6.627690 AAACGATCGTCTACACATAGTTTG 57.372 37.500 22.98 0.00 0.00 2.93
3028 3468 5.556355 ACGATCGTCTACACATAGTTTGA 57.444 39.130 16.60 0.00 0.00 2.69
3029 3469 6.132791 ACGATCGTCTACACATAGTTTGAT 57.867 37.500 16.60 0.00 0.00 2.57
3030 3470 6.561614 ACGATCGTCTACACATAGTTTGATT 58.438 36.000 16.60 0.00 0.00 2.57
3031 3471 6.472486 ACGATCGTCTACACATAGTTTGATTG 59.528 38.462 16.60 0.00 0.00 2.67
3033 3473 7.009265 CGATCGTCTACACATAGTTTGATTGTT 59.991 37.037 7.03 0.00 0.00 2.83
3034 3474 7.576750 TCGTCTACACATAGTTTGATTGTTC 57.423 36.000 0.00 0.00 0.00 3.18
3035 3475 6.307077 TCGTCTACACATAGTTTGATTGTTCG 59.693 38.462 0.00 0.00 0.00 3.95
3036 3476 6.089016 CGTCTACACATAGTTTGATTGTTCGT 59.911 38.462 0.00 0.00 0.00 3.85
3037 3477 7.227461 GTCTACACATAGTTTGATTGTTCGTG 58.773 38.462 0.00 0.00 0.00 4.35
3038 3478 6.926826 TCTACACATAGTTTGATTGTTCGTGT 59.073 34.615 0.00 0.00 38.51 4.49
3039 3479 6.371809 ACACATAGTTTGATTGTTCGTGTT 57.628 33.333 0.00 0.00 31.39 3.32
3040 3480 6.791303 ACACATAGTTTGATTGTTCGTGTTT 58.209 32.000 0.00 0.00 31.39 2.83
3041 3481 7.921787 ACACATAGTTTGATTGTTCGTGTTTA 58.078 30.769 0.00 0.00 31.39 2.01
3042 3482 8.067784 ACACATAGTTTGATTGTTCGTGTTTAG 58.932 33.333 0.00 0.00 31.39 1.85
3043 3483 8.279800 CACATAGTTTGATTGTTCGTGTTTAGA 58.720 33.333 0.00 0.00 0.00 2.10
3044 3484 8.280497 ACATAGTTTGATTGTTCGTGTTTAGAC 58.720 33.333 0.00 0.00 0.00 2.59
3045 3485 6.920569 AGTTTGATTGTTCGTGTTTAGACT 57.079 33.333 0.00 0.00 0.00 3.24
3046 3486 6.715464 AGTTTGATTGTTCGTGTTTAGACTG 58.285 36.000 0.00 0.00 0.00 3.51
3047 3487 6.537301 AGTTTGATTGTTCGTGTTTAGACTGA 59.463 34.615 0.00 0.00 0.00 3.41
3048 3488 5.900339 TGATTGTTCGTGTTTAGACTGAC 57.100 39.130 0.00 0.00 0.00 3.51
3049 3489 5.597806 TGATTGTTCGTGTTTAGACTGACT 58.402 37.500 0.00 0.00 0.00 3.41
3050 3490 5.462068 TGATTGTTCGTGTTTAGACTGACTG 59.538 40.000 0.00 0.00 0.00 3.51
3051 3491 3.120792 TGTTCGTGTTTAGACTGACTGC 58.879 45.455 0.00 0.00 0.00 4.40
3052 3492 3.120792 GTTCGTGTTTAGACTGACTGCA 58.879 45.455 0.00 0.00 0.00 4.41
3054 3494 1.452025 CGTGTTTAGACTGACTGCACG 59.548 52.381 14.34 14.34 40.61 5.34
3055 3495 2.739292 GTGTTTAGACTGACTGCACGA 58.261 47.619 0.00 0.00 0.00 4.35
3056 3496 3.120792 GTGTTTAGACTGACTGCACGAA 58.879 45.455 0.00 0.00 0.00 3.85
3057 3497 3.182572 GTGTTTAGACTGACTGCACGAAG 59.817 47.826 0.00 0.00 0.00 3.79
3058 3498 3.067601 TGTTTAGACTGACTGCACGAAGA 59.932 43.478 0.00 0.00 0.00 2.87
3060 3500 2.890808 AGACTGACTGCACGAAGAAA 57.109 45.000 0.00 0.00 0.00 2.52
3061 3501 2.474816 AGACTGACTGCACGAAGAAAC 58.525 47.619 0.00 0.00 0.00 2.78
3062 3502 2.101582 AGACTGACTGCACGAAGAAACT 59.898 45.455 0.00 0.00 0.00 2.66
3065 3505 4.632153 ACTGACTGCACGAAGAAACTAAT 58.368 39.130 0.00 0.00 0.00 1.73
3066 3506 5.057149 ACTGACTGCACGAAGAAACTAATT 58.943 37.500 0.00 0.00 0.00 1.40
3067 3507 5.527582 ACTGACTGCACGAAGAAACTAATTT 59.472 36.000 0.00 0.00 0.00 1.82
3068 3508 6.038271 ACTGACTGCACGAAGAAACTAATTTT 59.962 34.615 0.00 0.00 0.00 1.82
3069 3509 6.198687 TGACTGCACGAAGAAACTAATTTTG 58.801 36.000 0.00 0.00 0.00 2.44
3070 3510 6.037720 TGACTGCACGAAGAAACTAATTTTGA 59.962 34.615 0.00 0.00 0.00 2.69
3075 3515 6.795593 GCACGAAGAAACTAATTTTGACCTAC 59.204 38.462 0.00 0.00 0.00 3.18
3077 3517 8.009974 CACGAAGAAACTAATTTTGACCTACAG 58.990 37.037 0.00 0.00 0.00 2.74
3078 3518 7.713942 ACGAAGAAACTAATTTTGACCTACAGT 59.286 33.333 0.00 0.00 0.00 3.55
3079 3519 8.557029 CGAAGAAACTAATTTTGACCTACAGTT 58.443 33.333 0.00 0.00 0.00 3.16
3481 3921 2.103771 GAGTCCTCCATGCTGCTATGAA 59.896 50.000 11.82 0.00 0.00 2.57
3482 3922 2.507058 AGTCCTCCATGCTGCTATGAAA 59.493 45.455 11.82 2.24 0.00 2.69
3483 3923 3.054139 AGTCCTCCATGCTGCTATGAAAA 60.054 43.478 11.82 0.42 0.00 2.29
3484 3924 3.887716 GTCCTCCATGCTGCTATGAAAAT 59.112 43.478 11.82 0.00 0.00 1.82
3485 3925 5.065914 GTCCTCCATGCTGCTATGAAAATA 58.934 41.667 11.82 0.00 0.00 1.40
3486 3926 5.709164 GTCCTCCATGCTGCTATGAAAATAT 59.291 40.000 11.82 0.00 0.00 1.28
3488 3928 5.475909 CCTCCATGCTGCTATGAAAATATGT 59.524 40.000 11.82 0.00 0.00 2.29
3489 3929 6.656270 CCTCCATGCTGCTATGAAAATATGTA 59.344 38.462 11.82 0.00 0.00 2.29
3491 3931 8.640063 TCCATGCTGCTATGAAAATATGTATT 57.360 30.769 11.82 0.00 0.00 1.89
3492 3932 8.517056 TCCATGCTGCTATGAAAATATGTATTG 58.483 33.333 11.82 0.00 0.00 1.90
3494 3934 6.372981 TGCTGCTATGAAAATATGTATTGCG 58.627 36.000 0.00 0.00 0.00 4.85
3495 3935 6.204495 TGCTGCTATGAAAATATGTATTGCGA 59.796 34.615 0.00 0.00 0.00 5.10
3496 3936 7.077605 GCTGCTATGAAAATATGTATTGCGAA 58.922 34.615 0.00 0.00 0.00 4.70
3497 3937 7.591057 GCTGCTATGAAAATATGTATTGCGAAA 59.409 33.333 0.00 0.00 0.00 3.46
3499 3939 9.794685 TGCTATGAAAATATGTATTGCGAAAAA 57.205 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.479993 CAGGGCCGCCTTCTCCTG 62.480 72.222 9.86 3.73 40.46 3.86
10 11 4.473520 ATCCAAGACGCAGGGCCG 62.474 66.667 0.00 0.00 0.00 6.13
11 12 2.825836 CATCCAAGACGCAGGGCC 60.826 66.667 0.00 0.00 0.00 5.80
12 13 1.244019 AAACATCCAAGACGCAGGGC 61.244 55.000 0.00 0.00 0.00 5.19
13 14 1.068333 CAAAACATCCAAGACGCAGGG 60.068 52.381 0.00 0.00 0.00 4.45
14 15 1.879380 TCAAAACATCCAAGACGCAGG 59.121 47.619 0.00 0.00 0.00 4.85
15 16 2.095567 CCTCAAAACATCCAAGACGCAG 60.096 50.000 0.00 0.00 0.00 5.18
16 17 1.879380 CCTCAAAACATCCAAGACGCA 59.121 47.619 0.00 0.00 0.00 5.24
17 18 1.200020 CCCTCAAAACATCCAAGACGC 59.800 52.381 0.00 0.00 0.00 5.19
18 19 1.200020 GCCCTCAAAACATCCAAGACG 59.800 52.381 0.00 0.00 0.00 4.18
19 20 1.200020 CGCCCTCAAAACATCCAAGAC 59.800 52.381 0.00 0.00 0.00 3.01
20 21 1.533625 CGCCCTCAAAACATCCAAGA 58.466 50.000 0.00 0.00 0.00 3.02
21 22 0.109132 GCGCCCTCAAAACATCCAAG 60.109 55.000 0.00 0.00 0.00 3.61
22 23 0.825425 TGCGCCCTCAAAACATCCAA 60.825 50.000 4.18 0.00 0.00 3.53
23 24 1.228398 TGCGCCCTCAAAACATCCA 60.228 52.632 4.18 0.00 0.00 3.41
24 25 1.244019 ACTGCGCCCTCAAAACATCC 61.244 55.000 4.18 0.00 0.00 3.51
25 26 0.169009 GACTGCGCCCTCAAAACATC 59.831 55.000 4.18 0.00 0.00 3.06
26 27 1.577328 CGACTGCGCCCTCAAAACAT 61.577 55.000 4.18 0.00 0.00 2.71
27 28 2.250939 CGACTGCGCCCTCAAAACA 61.251 57.895 4.18 0.00 0.00 2.83
28 29 1.959226 TCGACTGCGCCCTCAAAAC 60.959 57.895 4.18 0.00 37.46 2.43
29 30 1.959226 GTCGACTGCGCCCTCAAAA 60.959 57.895 8.70 0.00 37.46 2.44
30 31 2.357034 GTCGACTGCGCCCTCAAA 60.357 61.111 8.70 0.00 37.46 2.69
31 32 4.373116 GGTCGACTGCGCCCTCAA 62.373 66.667 16.46 0.00 31.69 3.02
36 37 3.208884 ATATCGGGTCGACTGCGCC 62.209 63.158 16.46 7.02 39.18 6.53
37 38 2.016704 CATATCGGGTCGACTGCGC 61.017 63.158 16.46 0.00 39.18 6.09
38 39 0.248907 AACATATCGGGTCGACTGCG 60.249 55.000 16.46 0.18 39.18 5.18
39 40 1.935933 AAACATATCGGGTCGACTGC 58.064 50.000 16.46 0.00 39.18 4.40
40 41 3.517602 TCAAAACATATCGGGTCGACTG 58.482 45.455 16.46 8.74 39.18 3.51
41 42 3.880047 TCAAAACATATCGGGTCGACT 57.120 42.857 16.46 0.00 39.18 4.18
42 43 4.178540 TCTTCAAAACATATCGGGTCGAC 58.821 43.478 7.13 7.13 39.18 4.20
43 44 4.459390 TCTTCAAAACATATCGGGTCGA 57.541 40.909 0.00 0.00 41.13 4.20
44 45 4.201783 GGTTCTTCAAAACATATCGGGTCG 60.202 45.833 0.00 0.00 0.00 4.79
45 46 4.698304 TGGTTCTTCAAAACATATCGGGTC 59.302 41.667 0.00 0.00 0.00 4.46
46 47 4.658063 TGGTTCTTCAAAACATATCGGGT 58.342 39.130 0.00 0.00 0.00 5.28
47 48 4.096382 CCTGGTTCTTCAAAACATATCGGG 59.904 45.833 0.00 0.00 0.00 5.14
48 49 4.096382 CCCTGGTTCTTCAAAACATATCGG 59.904 45.833 0.00 0.00 0.00 4.18
49 50 4.096382 CCCCTGGTTCTTCAAAACATATCG 59.904 45.833 0.00 0.00 0.00 2.92
50 51 4.402474 CCCCCTGGTTCTTCAAAACATATC 59.598 45.833 0.00 0.00 0.00 1.63
51 52 4.352893 CCCCCTGGTTCTTCAAAACATAT 58.647 43.478 0.00 0.00 0.00 1.78
52 53 3.773560 CCCCCTGGTTCTTCAAAACATA 58.226 45.455 0.00 0.00 0.00 2.29
53 54 2.608623 CCCCCTGGTTCTTCAAAACAT 58.391 47.619 0.00 0.00 0.00 2.71
54 55 2.080654 CCCCCTGGTTCTTCAAAACA 57.919 50.000 0.00 0.00 0.00 2.83
70 71 2.753884 GGTAGCCTAACCAGCCCCC 61.754 68.421 0.00 0.00 39.50 5.40
71 72 2.753884 GGGTAGCCTAACCAGCCCC 61.754 68.421 0.00 0.00 41.67 5.80
72 73 2.916661 GGGTAGCCTAACCAGCCC 59.083 66.667 0.00 0.00 41.67 5.19
73 74 2.364780 ACGGGTAGCCTAACCAGCC 61.365 63.158 6.63 0.00 41.67 4.85
74 75 1.153429 CACGGGTAGCCTAACCAGC 60.153 63.158 6.63 0.00 41.67 4.85
75 76 1.262640 ACCACGGGTAGCCTAACCAG 61.263 60.000 6.63 1.43 41.67 4.00
76 77 1.229272 ACCACGGGTAGCCTAACCA 60.229 57.895 6.63 0.00 41.67 3.67
77 78 1.259840 TGACCACGGGTAGCCTAACC 61.260 60.000 9.73 0.00 35.25 2.85
78 79 0.828677 ATGACCACGGGTAGCCTAAC 59.171 55.000 9.73 0.00 35.25 2.34
79 80 1.575419 AATGACCACGGGTAGCCTAA 58.425 50.000 9.73 0.00 35.25 2.69
80 81 1.575419 AAATGACCACGGGTAGCCTA 58.425 50.000 9.73 0.00 35.25 3.93
81 82 1.208776 GTAAATGACCACGGGTAGCCT 59.791 52.381 9.73 0.00 35.25 4.58
82 83 1.208776 AGTAAATGACCACGGGTAGCC 59.791 52.381 0.00 0.00 35.25 3.93
83 84 2.547826 GAGTAAATGACCACGGGTAGC 58.452 52.381 0.00 0.00 35.25 3.58
84 85 2.480759 CGGAGTAAATGACCACGGGTAG 60.481 54.545 0.00 0.00 35.25 3.18
85 86 1.477700 CGGAGTAAATGACCACGGGTA 59.522 52.381 0.00 0.00 35.25 3.69
86 87 0.248289 CGGAGTAAATGACCACGGGT 59.752 55.000 0.00 0.00 39.44 5.28
87 88 0.533491 TCGGAGTAAATGACCACGGG 59.467 55.000 0.00 0.00 0.00 5.28
88 89 1.067425 TGTCGGAGTAAATGACCACGG 60.067 52.381 0.00 0.00 0.00 4.94
89 90 2.357327 TGTCGGAGTAAATGACCACG 57.643 50.000 0.00 0.00 0.00 4.94
90 91 5.873164 ACTATTTGTCGGAGTAAATGACCAC 59.127 40.000 9.29 0.00 30.96 4.16
91 92 6.045072 ACTATTTGTCGGAGTAAATGACCA 57.955 37.500 9.29 0.00 30.96 4.02
92 93 8.658499 ATTACTATTTGTCGGAGTAAATGACC 57.342 34.615 9.29 0.00 30.96 4.02
94 95 9.976511 CCTATTACTATTTGTCGGAGTAAATGA 57.023 33.333 9.29 0.00 30.96 2.57
95 96 9.204570 CCCTATTACTATTTGTCGGAGTAAATG 57.795 37.037 9.29 4.30 30.96 2.32
96 97 8.373220 CCCCTATTACTATTTGTCGGAGTAAAT 58.627 37.037 0.00 5.73 32.47 1.40
97 98 7.687592 GCCCCTATTACTATTTGTCGGAGTAAA 60.688 40.741 0.00 0.00 0.00 2.01
98 99 6.239402 GCCCCTATTACTATTTGTCGGAGTAA 60.239 42.308 0.00 0.00 0.00 2.24
99 100 5.244626 GCCCCTATTACTATTTGTCGGAGTA 59.755 44.000 0.00 0.00 0.00 2.59
100 101 4.040095 GCCCCTATTACTATTTGTCGGAGT 59.960 45.833 0.00 0.00 0.00 3.85
101 102 4.562963 GGCCCCTATTACTATTTGTCGGAG 60.563 50.000 0.00 0.00 0.00 4.63
102 103 3.325716 GGCCCCTATTACTATTTGTCGGA 59.674 47.826 0.00 0.00 0.00 4.55
103 104 3.326880 AGGCCCCTATTACTATTTGTCGG 59.673 47.826 0.00 0.00 0.00 4.79
104 105 4.562963 GGAGGCCCCTATTACTATTTGTCG 60.563 50.000 0.00 0.00 0.00 4.35
105 106 4.597940 AGGAGGCCCCTATTACTATTTGTC 59.402 45.833 10.79 0.00 45.48 3.18
106 107 4.578128 AGGAGGCCCCTATTACTATTTGT 58.422 43.478 10.79 0.00 45.48 2.83
119 120 4.432741 GCCAGTGAAGGAGGCCCC 62.433 72.222 0.00 0.00 42.58 5.80
123 124 0.107312 CAGATGGCCAGTGAAGGAGG 60.107 60.000 13.05 0.00 0.00 4.30
124 125 0.617413 ACAGATGGCCAGTGAAGGAG 59.383 55.000 21.83 4.38 0.00 3.69
125 126 1.003580 GAACAGATGGCCAGTGAAGGA 59.996 52.381 21.83 0.00 0.00 3.36
126 127 1.271543 TGAACAGATGGCCAGTGAAGG 60.272 52.381 21.83 6.50 0.00 3.46
127 128 2.189594 TGAACAGATGGCCAGTGAAG 57.810 50.000 21.83 8.17 0.00 3.02
128 129 2.885135 ATGAACAGATGGCCAGTGAA 57.115 45.000 21.83 9.24 0.00 3.18
180 181 1.302192 TTGTCGCCTGGCCTAACAC 60.302 57.895 14.12 2.93 0.00 3.32
183 184 0.905809 TAGGTTGTCGCCTGGCCTAA 60.906 55.000 14.12 2.87 39.60 2.69
240 269 6.687105 GCGTCCATCTTGTTTCATTTATGTAC 59.313 38.462 0.00 0.00 0.00 2.90
243 272 5.883661 AGCGTCCATCTTGTTTCATTTATG 58.116 37.500 0.00 0.00 0.00 1.90
335 384 2.507058 AGAGAATGTTCCATAGCTGGCA 59.493 45.455 0.00 0.00 42.80 4.92
344 393 6.822170 CAGATGAAGATGAAGAGAATGTTCCA 59.178 38.462 0.00 0.00 37.63 3.53
356 405 3.507233 GGCAACAACCAGATGAAGATGAA 59.493 43.478 0.00 0.00 0.00 2.57
448 659 1.288752 CCAAATCAACACGGTGCCC 59.711 57.895 8.30 0.00 0.00 5.36
473 684 4.580580 GGATGTGAATTCGAGGGCTAATTT 59.419 41.667 0.04 0.00 0.00 1.82
474 685 4.137543 GGATGTGAATTCGAGGGCTAATT 58.862 43.478 0.04 0.00 0.00 1.40
477 688 1.416401 GGGATGTGAATTCGAGGGCTA 59.584 52.381 0.04 0.00 0.00 3.93
480 691 0.464036 TCGGGATGTGAATTCGAGGG 59.536 55.000 0.04 0.00 0.00 4.30
481 692 1.571919 GTCGGGATGTGAATTCGAGG 58.428 55.000 0.04 0.00 0.00 4.63
484 695 1.588404 CTTCGTCGGGATGTGAATTCG 59.412 52.381 0.04 0.00 0.00 3.34
485 696 2.860735 CTCTTCGTCGGGATGTGAATTC 59.139 50.000 0.00 0.00 0.00 2.17
486 697 2.893637 CTCTTCGTCGGGATGTGAATT 58.106 47.619 0.00 0.00 0.00 2.17
536 788 2.787473 TCTGATTCGGTTGCTGGATT 57.213 45.000 0.00 0.00 0.00 3.01
606 861 4.927782 TGGCGTGCTGGTGTGGTC 62.928 66.667 0.00 0.00 0.00 4.02
607 862 4.935495 CTGGCGTGCTGGTGTGGT 62.935 66.667 0.00 0.00 0.00 4.16
713 969 2.408050 GAGTCGCGGATATGAATGCTT 58.592 47.619 6.13 0.00 0.00 3.91
714 970 1.667177 CGAGTCGCGGATATGAATGCT 60.667 52.381 6.13 0.00 36.03 3.79
715 971 0.710567 CGAGTCGCGGATATGAATGC 59.289 55.000 6.13 0.00 36.03 3.56
869 1139 3.142951 GAGAGAGAGATCGGAAATCGGA 58.857 50.000 0.00 0.00 39.77 4.55
870 1140 3.146066 AGAGAGAGAGATCGGAAATCGG 58.854 50.000 0.00 0.00 39.77 4.18
871 1141 4.065088 AGAGAGAGAGAGATCGGAAATCG 58.935 47.826 0.00 0.00 40.90 3.34
872 1142 5.308825 AGAGAGAGAGAGAGATCGGAAATC 58.691 45.833 0.00 0.00 0.00 2.17
873 1143 5.308825 GAGAGAGAGAGAGAGATCGGAAAT 58.691 45.833 0.00 0.00 0.00 2.17
874 1144 4.444306 GGAGAGAGAGAGAGAGATCGGAAA 60.444 50.000 0.00 0.00 0.00 3.13
875 1145 3.071023 GGAGAGAGAGAGAGAGATCGGAA 59.929 52.174 0.00 0.00 0.00 4.30
889 1159 1.134037 GCGAGAAGGGTAGGAGAGAGA 60.134 57.143 0.00 0.00 0.00 3.10
963 1238 0.917333 ACGAGGAGGAGGAGGAGTCT 60.917 60.000 0.00 0.00 0.00 3.24
1842 2190 1.379443 ACGCAGGTACCGATCCAGA 60.379 57.895 6.18 0.00 0.00 3.86
1845 2193 2.106332 CCACGCAGGTACCGATCC 59.894 66.667 6.18 0.00 0.00 3.36
1903 2266 2.354729 CCCGTCCATGAAGCCCAA 59.645 61.111 0.00 0.00 0.00 4.12
1962 2325 4.838152 TCCTTGCCGCCGCTCATC 62.838 66.667 0.00 0.00 35.36 2.92
2025 2388 1.552792 TCGCACATGGTGAAGTGGATA 59.447 47.619 0.00 0.00 35.23 2.59
2385 2813 1.279271 AGCCCGTACAGCTTCTTGAAT 59.721 47.619 1.60 0.00 37.24 2.57
2532 2965 3.066621 TGTGAAAGACGCAGAAAGCAAAT 59.933 39.130 0.00 0.00 46.13 2.32
2591 3024 7.865385 CCCAAATTACAATCGAGAACAGAAAAA 59.135 33.333 0.00 0.00 0.00 1.94
2651 3084 4.293415 CAACTTGAGTCATCCTTTGCAAC 58.707 43.478 0.00 0.00 0.00 4.17
2664 3097 2.017049 GAGTGCACAACCAACTTGAGT 58.983 47.619 21.04 0.00 33.59 3.41
2716 3149 7.816995 CAGTTCTCTTCTATGTACAGCTTCTTT 59.183 37.037 0.33 0.00 0.00 2.52
2747 3180 6.638096 TTGGGATTTGTGCACTGATATATG 57.362 37.500 19.41 0.00 0.00 1.78
2752 3185 3.579586 ACATTTGGGATTTGTGCACTGAT 59.420 39.130 19.41 11.66 0.00 2.90
2782 3215 5.585047 AGACCCTCGAAACAAGCATATTAAC 59.415 40.000 0.00 0.00 0.00 2.01
2786 3219 3.914426 AGACCCTCGAAACAAGCATAT 57.086 42.857 0.00 0.00 0.00 1.78
2798 3231 6.932356 TTACAGTATTACAGTAGACCCTCG 57.068 41.667 0.00 0.00 0.00 4.63
2801 3234 7.148171 ACGACTTTACAGTATTACAGTAGACCC 60.148 40.741 0.00 0.00 31.22 4.46
2822 3256 2.615912 GCGTATAGGGTTCTACACGACT 59.384 50.000 8.18 0.00 46.01 4.18
2826 3260 4.366586 GAAAGGCGTATAGGGTTCTACAC 58.633 47.826 0.00 0.00 0.00 2.90
2831 3265 3.555527 AAGGAAAGGCGTATAGGGTTC 57.444 47.619 0.00 0.00 0.00 3.62
2832 3266 4.225717 TGTAAAGGAAAGGCGTATAGGGTT 59.774 41.667 0.00 0.00 0.00 4.11
2834 3268 4.411256 TGTAAAGGAAAGGCGTATAGGG 57.589 45.455 0.00 0.00 0.00 3.53
2836 3270 6.053005 TGGAATGTAAAGGAAAGGCGTATAG 58.947 40.000 0.00 0.00 0.00 1.31
2837 3271 5.991861 TGGAATGTAAAGGAAAGGCGTATA 58.008 37.500 0.00 0.00 0.00 1.47
2839 3273 4.289238 TGGAATGTAAAGGAAAGGCGTA 57.711 40.909 0.00 0.00 0.00 4.42
2840 3274 3.149005 TGGAATGTAAAGGAAAGGCGT 57.851 42.857 0.00 0.00 0.00 5.68
2863 3303 0.672401 TGGCGGTTTCGAGGTCATTC 60.672 55.000 0.00 0.00 39.00 2.67
2872 3312 2.346099 ACAAATTCATGGCGGTTTCG 57.654 45.000 0.00 0.00 39.81 3.46
2889 3329 2.662070 GGCAACCTACCCGGCTACA 61.662 63.158 0.00 0.00 35.61 2.74
2921 3361 0.251121 TGTGGACGGATGCCAACAAT 60.251 50.000 0.00 0.00 37.12 2.71
2923 3363 0.959867 CATGTGGACGGATGCCAACA 60.960 55.000 0.00 0.00 37.12 3.33
2924 3364 0.960364 ACATGTGGACGGATGCCAAC 60.960 55.000 0.00 0.00 37.12 3.77
2925 3365 0.959867 CACATGTGGACGGATGCCAA 60.960 55.000 18.51 0.00 37.12 4.52
2926 3366 1.377072 CACATGTGGACGGATGCCA 60.377 57.895 18.51 0.00 0.00 4.92
2943 3383 1.134037 ACACGCCCTTTACTGTTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
2949 3389 2.096417 CGAAGAAACACGCCCTTTACTG 60.096 50.000 0.00 0.00 0.00 2.74
2950 3390 2.140717 CGAAGAAACACGCCCTTTACT 58.859 47.619 0.00 0.00 0.00 2.24
2951 3391 1.869132 ACGAAGAAACACGCCCTTTAC 59.131 47.619 0.00 0.00 0.00 2.01
2952 3392 2.243602 ACGAAGAAACACGCCCTTTA 57.756 45.000 0.00 0.00 0.00 1.85
2953 3393 1.064952 CAACGAAGAAACACGCCCTTT 59.935 47.619 0.00 0.00 0.00 3.11
2955 3395 1.782028 GCAACGAAGAAACACGCCCT 61.782 55.000 0.00 0.00 0.00 5.19
2957 3397 0.040425 ATGCAACGAAGAAACACGCC 60.040 50.000 0.00 0.00 0.00 5.68
2959 3399 1.580439 CGATGCAACGAAGAAACACG 58.420 50.000 11.36 0.00 35.09 4.49
2961 3401 0.237235 GGCGATGCAACGAAGAAACA 59.763 50.000 21.39 0.00 35.09 2.83
2962 3402 0.517316 AGGCGATGCAACGAAGAAAC 59.483 50.000 21.39 0.49 35.09 2.78
2963 3403 0.516877 CAGGCGATGCAACGAAGAAA 59.483 50.000 21.39 0.00 35.09 2.52
2964 3404 2.161831 CAGGCGATGCAACGAAGAA 58.838 52.632 21.39 0.00 35.09 2.52
2974 3414 1.096967 TACATGCAAGGCAGGCGATG 61.097 55.000 2.46 0.00 44.57 3.84
2975 3415 1.097547 GTACATGCAAGGCAGGCGAT 61.098 55.000 2.46 0.00 44.57 4.58
2977 3417 1.308069 AAGTACATGCAAGGCAGGCG 61.308 55.000 2.46 0.00 44.57 5.52
2978 3418 0.453390 GAAGTACATGCAAGGCAGGC 59.547 55.000 2.46 0.00 44.57 4.85
2979 3419 0.729116 CGAAGTACATGCAAGGCAGG 59.271 55.000 0.87 0.87 46.22 4.85
2980 3420 1.394917 GTCGAAGTACATGCAAGGCAG 59.605 52.381 0.00 0.00 43.65 4.85
2981 3421 1.001974 AGTCGAAGTACATGCAAGGCA 59.998 47.619 0.00 0.00 44.86 4.75
2982 3422 1.726853 AGTCGAAGTACATGCAAGGC 58.273 50.000 0.00 0.00 0.00 4.35
2983 3423 5.856126 TTTTAGTCGAAGTACATGCAAGG 57.144 39.130 0.00 0.00 0.00 3.61
2986 3426 4.983538 TCGTTTTTAGTCGAAGTACATGCA 59.016 37.500 0.00 0.00 33.13 3.96
2987 3427 5.505165 TCGTTTTTAGTCGAAGTACATGC 57.495 39.130 0.00 0.00 33.13 4.06
2988 3428 6.033196 ACGATCGTTTTTAGTCGAAGTACATG 59.967 38.462 16.60 0.00 39.45 3.21
2990 3430 5.451908 ACGATCGTTTTTAGTCGAAGTACA 58.548 37.500 16.60 0.00 39.45 2.90
2992 3432 5.931532 AGACGATCGTTTTTAGTCGAAGTA 58.068 37.500 23.63 0.00 39.45 2.24
2994 3434 5.791974 TGTAGACGATCGTTTTTAGTCGAAG 59.208 40.000 23.63 0.00 39.45 3.79
2998 3438 6.866179 ATGTGTAGACGATCGTTTTTAGTC 57.134 37.500 23.63 7.50 0.00 2.59
2999 3439 7.533426 ACTATGTGTAGACGATCGTTTTTAGT 58.467 34.615 23.63 17.32 0.00 2.24
3000 3440 7.966157 ACTATGTGTAGACGATCGTTTTTAG 57.034 36.000 23.63 16.77 0.00 1.85
3001 3441 8.641155 CAAACTATGTGTAGACGATCGTTTTTA 58.359 33.333 23.63 12.47 0.00 1.52
3004 3444 6.384224 TCAAACTATGTGTAGACGATCGTTT 58.616 36.000 23.63 19.61 0.00 3.60
3005 3445 5.946298 TCAAACTATGTGTAGACGATCGTT 58.054 37.500 23.63 14.33 0.00 3.85
3007 3447 6.472486 ACAATCAAACTATGTGTAGACGATCG 59.528 38.462 14.88 14.88 0.00 3.69
3009 3449 7.009265 CGAACAATCAAACTATGTGTAGACGAT 59.991 37.037 0.00 0.00 0.00 3.73
3010 3450 6.307077 CGAACAATCAAACTATGTGTAGACGA 59.693 38.462 0.00 0.00 0.00 4.20
3012 3452 7.095774 ACACGAACAATCAAACTATGTGTAGAC 60.096 37.037 0.00 0.00 36.38 2.59
3013 3453 6.926826 ACACGAACAATCAAACTATGTGTAGA 59.073 34.615 0.00 0.00 36.38 2.59
3014 3454 7.117241 ACACGAACAATCAAACTATGTGTAG 57.883 36.000 0.00 0.00 36.38 2.74
3015 3455 7.485418 AACACGAACAATCAAACTATGTGTA 57.515 32.000 0.00 0.00 37.07 2.90
3016 3456 6.371809 AACACGAACAATCAAACTATGTGT 57.628 33.333 0.00 0.00 39.49 3.72
3017 3457 8.279800 TCTAAACACGAACAATCAAACTATGTG 58.720 33.333 0.00 0.00 0.00 3.21
3019 3459 8.495949 AGTCTAAACACGAACAATCAAACTATG 58.504 33.333 0.00 0.00 0.00 2.23
3020 3460 8.495949 CAGTCTAAACACGAACAATCAAACTAT 58.504 33.333 0.00 0.00 0.00 2.12
3021 3461 7.707464 TCAGTCTAAACACGAACAATCAAACTA 59.293 33.333 0.00 0.00 0.00 2.24
3022 3462 6.537301 TCAGTCTAAACACGAACAATCAAACT 59.463 34.615 0.00 0.00 0.00 2.66
3023 3463 6.627671 GTCAGTCTAAACACGAACAATCAAAC 59.372 38.462 0.00 0.00 0.00 2.93
3024 3464 6.537301 AGTCAGTCTAAACACGAACAATCAAA 59.463 34.615 0.00 0.00 0.00 2.69
3025 3465 6.019075 CAGTCAGTCTAAACACGAACAATCAA 60.019 38.462 0.00 0.00 0.00 2.57
3027 3467 5.612709 GCAGTCAGTCTAAACACGAACAATC 60.613 44.000 0.00 0.00 0.00 2.67
3028 3468 4.211374 GCAGTCAGTCTAAACACGAACAAT 59.789 41.667 0.00 0.00 0.00 2.71
3029 3469 3.554324 GCAGTCAGTCTAAACACGAACAA 59.446 43.478 0.00 0.00 0.00 2.83
3030 3470 3.120792 GCAGTCAGTCTAAACACGAACA 58.879 45.455 0.00 0.00 0.00 3.18
3031 3471 3.060473 GTGCAGTCAGTCTAAACACGAAC 60.060 47.826 0.00 0.00 0.00 3.95
3033 3473 2.739292 GTGCAGTCAGTCTAAACACGA 58.261 47.619 0.00 0.00 0.00 4.35
3034 3474 1.452025 CGTGCAGTCAGTCTAAACACG 59.548 52.381 0.00 0.00 39.15 4.49
3035 3475 2.739292 TCGTGCAGTCAGTCTAAACAC 58.261 47.619 0.00 0.00 0.00 3.32
3036 3476 3.067601 TCTTCGTGCAGTCAGTCTAAACA 59.932 43.478 0.00 0.00 0.00 2.83
3037 3477 3.639538 TCTTCGTGCAGTCAGTCTAAAC 58.360 45.455 0.00 0.00 0.00 2.01
3038 3478 4.316205 TTCTTCGTGCAGTCAGTCTAAA 57.684 40.909 0.00 0.00 0.00 1.85
3039 3479 4.049186 GTTTCTTCGTGCAGTCAGTCTAA 58.951 43.478 0.00 0.00 0.00 2.10
3040 3480 3.318275 AGTTTCTTCGTGCAGTCAGTCTA 59.682 43.478 0.00 0.00 0.00 2.59
3041 3481 2.101582 AGTTTCTTCGTGCAGTCAGTCT 59.898 45.455 0.00 0.00 0.00 3.24
3042 3482 2.474816 AGTTTCTTCGTGCAGTCAGTC 58.525 47.619 0.00 0.00 0.00 3.51
3043 3483 2.604046 AGTTTCTTCGTGCAGTCAGT 57.396 45.000 0.00 0.00 0.00 3.41
3044 3484 5.597813 AATTAGTTTCTTCGTGCAGTCAG 57.402 39.130 0.00 0.00 0.00 3.51
3045 3485 6.037720 TCAAAATTAGTTTCTTCGTGCAGTCA 59.962 34.615 0.00 0.00 0.00 3.41
3046 3486 6.357240 GTCAAAATTAGTTTCTTCGTGCAGTC 59.643 38.462 0.00 0.00 0.00 3.51
3047 3487 6.199393 GTCAAAATTAGTTTCTTCGTGCAGT 58.801 36.000 0.00 0.00 0.00 4.40
3048 3488 5.625311 GGTCAAAATTAGTTTCTTCGTGCAG 59.375 40.000 0.00 0.00 0.00 4.41
3049 3489 5.298276 AGGTCAAAATTAGTTTCTTCGTGCA 59.702 36.000 0.00 0.00 0.00 4.57
3050 3490 5.758924 AGGTCAAAATTAGTTTCTTCGTGC 58.241 37.500 0.00 0.00 0.00 5.34
3051 3491 7.857569 TGTAGGTCAAAATTAGTTTCTTCGTG 58.142 34.615 0.00 0.00 0.00 4.35
3052 3492 7.713942 ACTGTAGGTCAAAATTAGTTTCTTCGT 59.286 33.333 0.00 0.00 0.00 3.85
3461 3901 1.798626 TCATAGCAGCATGGAGGACT 58.201 50.000 0.00 0.00 35.86 3.85
3462 3902 2.627515 TTCATAGCAGCATGGAGGAC 57.372 50.000 0.00 0.00 35.86 3.85
3463 3903 3.650281 TTTTCATAGCAGCATGGAGGA 57.350 42.857 0.00 0.00 35.86 3.71
3468 3908 7.007995 CGCAATACATATTTTCATAGCAGCATG 59.992 37.037 0.00 0.00 40.87 4.06
3470 3910 6.204495 TCGCAATACATATTTTCATAGCAGCA 59.796 34.615 0.00 0.00 0.00 4.41
3471 3911 6.602179 TCGCAATACATATTTTCATAGCAGC 58.398 36.000 0.00 0.00 0.00 5.25
3472 3912 9.449550 TTTTCGCAATACATATTTTCATAGCAG 57.550 29.630 0.00 0.00 0.00 4.24
3473 3913 9.794685 TTTTTCGCAATACATATTTTCATAGCA 57.205 25.926 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.