Multiple sequence alignment - TraesCS3D01G401500

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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 TraesCS3D01G401500 chr3D 100.000 3048 0 0 1 3048 516195253 516192206 0.000000e+00 5629.0
1 TraesCS3D01G401500 chr3D 80.601 1098 128 51 1546 2575 515819222 515820302 0.000000e+00 769.0
2 TraesCS3D01G401500 chr3D 82.114 492 47 21 1922 2378 515820931 515820446 1.710000e-102 383.0
3 TraesCS3D01G401500 chr3D 94.444 36 1 1 2970 3005 515824797 515824831 2.000000e-03 54.7
4 TraesCS3D01G401500 chr3A 92.851 1175 51 16 379 1525 651502939 651501770 0.000000e+00 1674.0
5 TraesCS3D01G401500 chr3A 88.030 919 66 10 1542 2423 651501785 651500874 0.000000e+00 1048.0
6 TraesCS3D01G401500 chr3A 81.232 1071 129 40 1546 2575 650195527 650196566 0.000000e+00 798.0
7 TraesCS3D01G401500 chr3A 89.780 499 24 13 2568 3039 651500793 651500295 5.590000e-172 614.0
8 TraesCS3D01G401500 chr3A 81.911 492 50 20 1922 2378 650197196 650196709 2.220000e-101 379.0
9 TraesCS3D01G401500 chr3A 86.458 192 26 0 1332 1523 650195340 650195531 8.560000e-51 211.0
10 TraesCS3D01G401500 chr3A 91.398 93 8 0 159 251 651503231 651503139 8.870000e-26 128.0
11 TraesCS3D01G401500 chr3A 90.625 64 5 1 20 82 671738888 671738951 1.950000e-12 84.2
12 TraesCS3D01G401500 chr3A 95.238 42 2 0 2420 2461 651500835 651500794 1.960000e-07 67.6
13 TraesCS3D01G401500 chr3A 100.000 29 0 0 2977 3005 650197388 650197416 2.000000e-03 54.7
14 TraesCS3D01G401500 chr3B 91.267 1042 60 16 498 1525 679624738 679623714 0.000000e+00 1391.0
15 TraesCS3D01G401500 chr3B 93.303 657 14 4 2420 3048 679622774 679622120 0.000000e+00 942.0
16 TraesCS3D01G401500 chr3B 90.964 664 54 4 1542 2200 679623729 679623067 0.000000e+00 889.0
17 TraesCS3D01G401500 chr3B 79.955 1342 156 59 1302 2570 678711031 678712332 0.000000e+00 883.0
18 TraesCS3D01G401500 chr3B 96.234 239 8 1 2185 2423 679623050 679622813 1.020000e-104 390.0
19 TraesCS3D01G401500 chr3B 81.673 502 52 23 1913 2378 678712977 678712480 6.170000e-102 381.0
20 TraesCS3D01G401500 chr3B 88.353 249 12 2 247 494 679625828 679625596 1.790000e-72 283.0
21 TraesCS3D01G401500 chr3B 82.119 302 47 6 573 871 46026028 46025731 5.040000e-63 252.0
22 TraesCS3D01G401500 chr3B 81.788 302 48 6 573 871 45962049 45961752 2.350000e-61 246.0
23 TraesCS3D01G401500 chr3B 81.788 302 48 6 573 871 46012037 46011740 2.350000e-61 246.0
24 TraesCS3D01G401500 chr3B 81.457 302 49 6 573 871 45782121 45781824 1.090000e-59 241.0
25 TraesCS3D01G401500 chr3B 81.457 302 49 6 573 871 45879411 45879114 1.090000e-59 241.0
26 TraesCS3D01G401500 chr3B 81.457 302 49 6 573 871 45945604 45945307 1.090000e-59 241.0
27 TraesCS3D01G401500 chr3B 81.126 302 50 6 573 871 45827850 45827553 5.080000e-58 235.0
28 TraesCS3D01G401500 chr3B 81.690 213 29 7 1253 1463 45758800 45759004 5.230000e-38 169.0
29 TraesCS3D01G401500 chr3B 81.690 213 29 7 1253 1463 45962790 45962994 5.230000e-38 169.0
30 TraesCS3D01G401500 chr3B 81.690 213 29 7 1253 1463 46012882 46013086 5.230000e-38 169.0
31 TraesCS3D01G401500 chr3B 81.818 209 28 7 1253 1459 45924039 45924239 1.880000e-37 167.0
32 TraesCS3D01G401500 chr3B 81.818 209 28 7 1253 1459 45974332 45974532 1.880000e-37 167.0
33 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45768529 45768406 3.210000e-20 110.0
34 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45838670 45838547 3.210000e-20 110.0
35 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45875951 45875828 3.210000e-20 110.0
36 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45890045 45889922 3.210000e-20 110.0
37 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45933757 45933634 3.210000e-20 110.0
38 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 45983727 45983604 3.210000e-20 110.0
39 TraesCS3D01G401500 chr3B 82.540 126 20 1 2607 2732 46022563 46022440 3.210000e-20 110.0
40 TraesCS3D01G401500 chr3B 100.000 29 0 0 54 82 504655611 504655639 2.000000e-03 54.7
41 TraesCS3D01G401500 chr7A 100.000 29 0 0 1711 1739 303967860 303967832 2.000000e-03 54.7
42 TraesCS3D01G401500 chr5A 100.000 28 0 0 1715 1742 275080756 275080783 5.000000e-03 52.8
43 TraesCS3D01G401500 chr4D 94.286 35 0 2 52 84 386751311 386751345 5.000000e-03 52.8


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 TraesCS3D01G401500 chr3D 516192206 516195253 3047 True 5629.000000 5629 100.0000 1 3048 1 chr3D.!!$R2 3047
1 TraesCS3D01G401500 chr3D 515819222 515820302 1080 False 769.000000 769 80.6010 1546 2575 1 chr3D.!!$F1 1029
2 TraesCS3D01G401500 chr3A 651500295 651503231 2936 True 706.320000 1674 91.4594 159 3039 5 chr3A.!!$R2 2880
3 TraesCS3D01G401500 chr3A 650195340 650197416 2076 False 354.566667 798 89.2300 1332 3005 3 chr3A.!!$F2 1673
4 TraesCS3D01G401500 chr3B 678711031 678712332 1301 False 883.000000 883 79.9550 1302 2570 1 chr3B.!!$F7 1268
5 TraesCS3D01G401500 chr3B 679622120 679625828 3708 True 779.000000 1391 92.0242 247 3048 5 chr3B.!!$R14 2801


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
77 78 0.320697 AAACTTTCTCGGACGGAGGG 59.679 55.0 9.88 4.26 43.34 4.3 F
1193 2133 0.103572 GGTAGAAAGGCCGTATGCGA 59.896 55.0 4.21 0.00 42.61 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 2789 0.106419 TCCACTTTGGTTTCCGCCTT 60.106 50.000 0.0 0.0 39.03 4.35 R
2048 3061 1.988107 TCCACCAATCTTCCTGCTTCT 59.012 47.619 0.0 0.0 0.00 2.85 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 3.903876 CACTATGTGTTGGCATCGC 57.096 52.632 2.19 2.19 0.00 4.58
19 20 1.372582 CACTATGTGTTGGCATCGCT 58.627 50.000 10.19 0.00 0.00 4.93
20 21 1.739466 CACTATGTGTTGGCATCGCTT 59.261 47.619 10.19 6.69 0.00 4.68
21 22 2.935849 CACTATGTGTTGGCATCGCTTA 59.064 45.455 10.19 7.41 0.00 3.09
22 23 3.561310 CACTATGTGTTGGCATCGCTTAT 59.439 43.478 10.19 0.04 0.00 1.73
23 24 3.561310 ACTATGTGTTGGCATCGCTTATG 59.439 43.478 10.19 5.70 38.74 1.90
34 35 4.854361 CATCGCTTATGCCAGATACATC 57.146 45.455 0.00 0.00 35.36 3.06
35 36 3.319137 TCGCTTATGCCAGATACATCC 57.681 47.619 0.00 0.00 35.36 3.51
36 37 2.632512 TCGCTTATGCCAGATACATCCA 59.367 45.455 0.00 0.00 35.36 3.41
37 38 3.261643 TCGCTTATGCCAGATACATCCAT 59.738 43.478 0.00 0.00 35.36 3.41
38 39 4.005650 CGCTTATGCCAGATACATCCATT 58.994 43.478 0.00 0.00 35.36 3.16
39 40 4.456911 CGCTTATGCCAGATACATCCATTT 59.543 41.667 0.00 0.00 35.36 2.32
40 41 5.618418 CGCTTATGCCAGATACATCCATTTG 60.618 44.000 0.00 0.00 35.36 2.32
41 42 5.474532 GCTTATGCCAGATACATCCATTTGA 59.525 40.000 0.00 0.00 0.00 2.69
42 43 6.349115 GCTTATGCCAGATACATCCATTTGAG 60.349 42.308 0.00 0.00 0.00 3.02
43 44 3.824133 TGCCAGATACATCCATTTGAGG 58.176 45.455 0.00 0.00 0.00 3.86
44 45 3.152341 GCCAGATACATCCATTTGAGGG 58.848 50.000 0.00 0.00 0.00 4.30
45 46 3.181440 GCCAGATACATCCATTTGAGGGA 60.181 47.826 0.00 0.00 39.14 4.20
46 47 4.508047 GCCAGATACATCCATTTGAGGGAT 60.508 45.833 0.00 0.00 45.98 3.85
47 48 5.280676 GCCAGATACATCCATTTGAGGGATA 60.281 44.000 0.00 0.00 43.24 2.59
48 49 6.748045 GCCAGATACATCCATTTGAGGGATAA 60.748 42.308 0.00 0.00 43.24 1.75
49 50 7.233632 CCAGATACATCCATTTGAGGGATAAA 58.766 38.462 0.00 0.00 43.24 1.40
50 51 7.175641 CCAGATACATCCATTTGAGGGATAAAC 59.824 40.741 0.00 0.00 43.24 2.01
51 52 7.941238 CAGATACATCCATTTGAGGGATAAACT 59.059 37.037 0.00 0.00 43.24 2.66
52 53 8.506083 AGATACATCCATTTGAGGGATAAACTT 58.494 33.333 0.00 0.00 43.24 2.66
53 54 6.780457 ACATCCATTTGAGGGATAAACTTG 57.220 37.500 0.00 0.00 43.24 3.16
54 55 5.658190 ACATCCATTTGAGGGATAAACTTGG 59.342 40.000 0.00 0.00 43.24 3.61
55 56 4.609301 TCCATTTGAGGGATAAACTTGGG 58.391 43.478 0.00 0.00 0.00 4.12
56 57 4.293634 TCCATTTGAGGGATAAACTTGGGA 59.706 41.667 0.00 0.00 0.00 4.37
57 58 4.402474 CCATTTGAGGGATAAACTTGGGAC 59.598 45.833 0.00 0.00 0.00 4.46
58 59 4.733077 TTTGAGGGATAAACTTGGGACA 57.267 40.909 0.00 0.00 0.00 4.02
71 72 2.249844 TGGGACAAACTTTCTCGGAC 57.750 50.000 0.00 0.00 31.92 4.79
72 73 1.145803 GGGACAAACTTTCTCGGACG 58.854 55.000 0.00 0.00 0.00 4.79
73 74 1.145803 GGACAAACTTTCTCGGACGG 58.854 55.000 0.00 0.00 0.00 4.79
74 75 1.269936 GGACAAACTTTCTCGGACGGA 60.270 52.381 0.00 0.00 0.00 4.69
75 76 2.059541 GACAAACTTTCTCGGACGGAG 58.940 52.381 3.68 3.68 44.58 4.63
76 77 1.270147 ACAAACTTTCTCGGACGGAGG 60.270 52.381 9.88 0.00 43.34 4.30
77 78 0.320697 AAACTTTCTCGGACGGAGGG 59.679 55.000 9.88 4.26 43.34 4.30
78 79 0.541296 AACTTTCTCGGACGGAGGGA 60.541 55.000 9.88 0.00 43.34 4.20
79 80 0.966370 ACTTTCTCGGACGGAGGGAG 60.966 60.000 9.88 10.00 43.34 4.30
80 81 0.966370 CTTTCTCGGACGGAGGGAGT 60.966 60.000 9.88 0.00 43.34 3.85
81 82 0.329261 TTTCTCGGACGGAGGGAGTA 59.671 55.000 9.88 0.00 43.34 2.59
82 83 0.393537 TTCTCGGACGGAGGGAGTAC 60.394 60.000 9.88 0.00 43.34 2.73
83 84 1.077930 CTCGGACGGAGGGAGTACA 60.078 63.158 2.13 0.00 39.22 2.90
84 85 0.465824 CTCGGACGGAGGGAGTACAT 60.466 60.000 2.13 0.00 39.22 2.29
85 86 0.750546 TCGGACGGAGGGAGTACATG 60.751 60.000 0.00 0.00 0.00 3.21
86 87 1.035932 CGGACGGAGGGAGTACATGT 61.036 60.000 2.69 2.69 0.00 3.21
87 88 1.192428 GGACGGAGGGAGTACATGTT 58.808 55.000 2.30 0.00 0.00 2.71
88 89 2.381911 GGACGGAGGGAGTACATGTTA 58.618 52.381 2.30 0.00 0.00 2.41
89 90 2.762327 GGACGGAGGGAGTACATGTTAA 59.238 50.000 2.30 0.00 0.00 2.01
90 91 3.429960 GGACGGAGGGAGTACATGTTAAC 60.430 52.174 2.30 0.00 0.00 2.01
91 92 3.167485 ACGGAGGGAGTACATGTTAACA 58.833 45.455 11.41 11.41 0.00 2.41
92 93 3.579586 ACGGAGGGAGTACATGTTAACAA 59.420 43.478 13.23 0.00 0.00 2.83
93 94 3.930848 CGGAGGGAGTACATGTTAACAAC 59.069 47.826 13.23 6.59 0.00 3.32
94 95 4.259356 GGAGGGAGTACATGTTAACAACC 58.741 47.826 13.23 9.05 0.00 3.77
95 96 4.263156 GGAGGGAGTACATGTTAACAACCA 60.263 45.833 13.23 0.00 0.00 3.67
96 97 5.497474 GAGGGAGTACATGTTAACAACCAT 58.503 41.667 13.23 7.18 0.00 3.55
97 98 5.887754 AGGGAGTACATGTTAACAACCATT 58.112 37.500 13.23 0.00 0.00 3.16
98 99 6.311735 AGGGAGTACATGTTAACAACCATTT 58.688 36.000 13.23 0.00 0.00 2.32
99 100 6.208599 AGGGAGTACATGTTAACAACCATTTG 59.791 38.462 13.23 7.70 38.83 2.32
100 101 5.861787 GGAGTACATGTTAACAACCATTTGC 59.138 40.000 13.23 0.00 36.00 3.68
101 102 6.398234 AGTACATGTTAACAACCATTTGCA 57.602 33.333 13.23 0.00 36.00 4.08
102 103 6.810911 AGTACATGTTAACAACCATTTGCAA 58.189 32.000 13.23 0.00 36.00 4.08
103 104 5.982465 ACATGTTAACAACCATTTGCAAC 57.018 34.783 13.23 0.00 36.00 4.17
104 105 4.505922 ACATGTTAACAACCATTTGCAACG 59.494 37.500 13.23 0.00 35.29 4.10
105 106 4.111375 TGTTAACAACCATTTGCAACGT 57.889 36.364 5.64 0.00 35.29 3.99
106 107 4.106197 TGTTAACAACCATTTGCAACGTC 58.894 39.130 5.64 0.00 35.29 4.34
107 108 2.949451 AACAACCATTTGCAACGTCA 57.051 40.000 0.00 0.00 36.00 4.35
108 109 2.949451 ACAACCATTTGCAACGTCAA 57.051 40.000 0.00 0.00 36.00 3.18
109 110 2.808244 ACAACCATTTGCAACGTCAAG 58.192 42.857 0.00 0.00 36.00 3.02
110 111 1.522258 CAACCATTTGCAACGTCAAGC 59.478 47.619 0.00 0.00 0.00 4.01
111 112 0.743688 ACCATTTGCAACGTCAAGCA 59.256 45.000 0.00 6.23 39.32 3.91
112 113 1.269206 ACCATTTGCAACGTCAAGCAG 60.269 47.619 0.00 2.80 42.39 4.24
113 114 1.269206 CCATTTGCAACGTCAAGCAGT 60.269 47.619 0.00 2.34 42.39 4.40
114 115 2.462889 CATTTGCAACGTCAAGCAGTT 58.537 42.857 0.00 1.05 42.39 3.16
115 116 2.187351 TTTGCAACGTCAAGCAGTTC 57.813 45.000 0.00 0.00 42.39 3.01
116 117 1.090728 TTGCAACGTCAAGCAGTTCA 58.909 45.000 9.68 0.00 42.39 3.18
117 118 0.376852 TGCAACGTCAAGCAGTTCAC 59.623 50.000 6.23 0.00 35.51 3.18
118 119 0.376852 GCAACGTCAAGCAGTTCACA 59.623 50.000 0.00 0.00 0.00 3.58
119 120 1.202132 GCAACGTCAAGCAGTTCACAA 60.202 47.619 0.00 0.00 0.00 3.33
120 121 2.730715 GCAACGTCAAGCAGTTCACAAA 60.731 45.455 0.00 0.00 0.00 2.83
121 122 3.100817 CAACGTCAAGCAGTTCACAAAG 58.899 45.455 0.00 0.00 0.00 2.77
122 123 2.627945 ACGTCAAGCAGTTCACAAAGA 58.372 42.857 0.00 0.00 0.00 2.52
123 124 3.206150 ACGTCAAGCAGTTCACAAAGAT 58.794 40.909 0.00 0.00 0.00 2.40
124 125 3.002656 ACGTCAAGCAGTTCACAAAGATG 59.997 43.478 0.00 0.00 0.00 2.90
125 126 3.303406 GTCAAGCAGTTCACAAAGATGC 58.697 45.455 0.00 0.00 37.15 3.91
129 130 4.660789 AGCAGTTCACAAAGATGCTTTT 57.339 36.364 0.00 0.00 44.47 2.27
130 131 5.014808 AGCAGTTCACAAAGATGCTTTTT 57.985 34.783 0.00 0.00 44.47 1.94
151 152 4.708726 TTTTGTTTTGGTTTTGCATGGG 57.291 36.364 0.00 0.00 0.00 4.00
152 153 1.673168 TGTTTTGGTTTTGCATGGGC 58.327 45.000 0.00 0.00 41.68 5.36
189 190 2.296471 TGAGGAAGAACGGTCAGAAGTC 59.704 50.000 1.87 0.00 0.00 3.01
191 192 1.343465 GGAAGAACGGTCAGAAGTCCA 59.657 52.381 1.87 0.00 0.00 4.02
218 219 5.584253 ACTGTGAATGTATTCGTAGCTCT 57.416 39.130 0.00 0.00 39.62 4.09
229 230 2.562635 TCGTAGCTCTCGCTTGTATCT 58.437 47.619 0.00 0.00 46.47 1.98
242 243 5.577164 TCGCTTGTATCTTTCTTGTAGCTTC 59.423 40.000 0.00 0.00 0.00 3.86
264 300 5.924356 TCACTTGTAAATCAGGTTGACTCA 58.076 37.500 0.00 0.00 34.09 3.41
307 343 0.815734 GCTGCAACATCTCCATGCTT 59.184 50.000 0.00 0.00 40.66 3.91
351 388 3.820467 CAGGCCAATCTGTTAACAGTCAA 59.180 43.478 29.83 15.32 44.12 3.18
374 411 1.153066 TCACGTCCAGCCAAGCAAA 60.153 52.632 0.00 0.00 0.00 3.68
377 414 1.039856 ACGTCCAGCCAAGCAAATTT 58.960 45.000 0.00 0.00 0.00 1.82
435 509 2.761809 AGAGACAGCTTGAGATGGGAT 58.238 47.619 1.02 0.00 35.42 3.85
443 517 1.213678 CTTGAGATGGGATGCCTCCAA 59.786 52.381 10.44 0.00 44.08 3.53
494 568 3.895656 AGGAAAAACTTTACTGCCTTCCC 59.104 43.478 0.00 0.00 32.89 3.97
495 569 3.639561 GGAAAAACTTTACTGCCTTCCCA 59.360 43.478 0.00 0.00 0.00 4.37
496 570 4.100344 GGAAAAACTTTACTGCCTTCCCAA 59.900 41.667 0.00 0.00 0.00 4.12
497 571 5.395879 GGAAAAACTTTACTGCCTTCCCAAA 60.396 40.000 0.00 0.00 0.00 3.28
498 572 5.887214 AAAACTTTACTGCCTTCCCAAAT 57.113 34.783 0.00 0.00 0.00 2.32
499 573 5.887214 AAACTTTACTGCCTTCCCAAATT 57.113 34.783 0.00 0.00 0.00 1.82
500 574 5.887214 AACTTTACTGCCTTCCCAAATTT 57.113 34.783 0.00 0.00 0.00 1.82
502 576 4.653801 ACTTTACTGCCTTCCCAAATTTGT 59.346 37.500 16.73 0.00 0.00 2.83
503 577 5.130311 ACTTTACTGCCTTCCCAAATTTGTT 59.870 36.000 16.73 0.00 0.00 2.83
504 578 5.622346 TTACTGCCTTCCCAAATTTGTTT 57.378 34.783 16.73 0.00 0.00 2.83
507 581 3.983741 TGCCTTCCCAAATTTGTTTACG 58.016 40.909 16.73 1.25 0.00 3.18
552 1482 1.031029 ACGGAGGGAGAGCGTAGAAC 61.031 60.000 0.00 0.00 0.00 3.01
627 1559 0.755698 GGATCCGGGTGCTCTGTAGA 60.756 60.000 0.00 0.00 0.00 2.59
853 1785 1.160137 GGCATTGCCGGATCATCTAC 58.840 55.000 12.82 0.00 39.62 2.59
982 1916 2.208431 GATGCAGGATCCTCGTTTCTG 58.792 52.381 12.69 0.18 0.00 3.02
1050 1984 2.510238 AAGATGCGCTGCTCGGAC 60.510 61.111 9.73 0.00 42.53 4.79
1182 2122 5.665459 AGGATCGATTCTGTTGGTAGAAAG 58.335 41.667 5.09 0.00 39.87 2.62
1185 2125 2.678336 CGATTCTGTTGGTAGAAAGGCC 59.322 50.000 0.00 0.00 39.87 5.19
1186 2126 2.178912 TTCTGTTGGTAGAAAGGCCG 57.821 50.000 0.00 0.00 33.96 6.13
1193 2133 0.103572 GGTAGAAAGGCCGTATGCGA 59.896 55.000 4.21 0.00 42.61 5.10
1224 2166 1.887320 CGTTGCAATTCTGTGCTAGC 58.113 50.000 8.10 8.10 45.17 3.42
1265 2209 6.564709 TTTCTGTGATGTTTCTTGAGATGG 57.435 37.500 0.00 0.00 0.00 3.51
1286 2230 6.399639 TGGTTTCTTGTTCTGGGTAATTTC 57.600 37.500 0.00 0.00 0.00 2.17
1294 2238 5.636123 TGTTCTGGGTAATTTCTGCCTTAA 58.364 37.500 0.00 0.00 0.00 1.85
1295 2239 6.071984 TGTTCTGGGTAATTTCTGCCTTAAA 58.928 36.000 0.00 0.00 0.00 1.52
1296 2240 6.723977 TGTTCTGGGTAATTTCTGCCTTAAAT 59.276 34.615 0.00 0.00 0.00 1.40
1414 2359 5.102953 TCATCCAATCCCTGAACTAGTTG 57.897 43.478 14.14 0.00 0.00 3.16
1426 2371 4.523083 TGAACTAGTTGACATTATGGGGC 58.477 43.478 14.14 0.00 0.00 5.80
1512 2476 5.869753 TTTTAGATTGCAGCAGAGAGAAC 57.130 39.130 0.00 0.00 0.00 3.01
1513 2477 2.399916 AGATTGCAGCAGAGAGAACC 57.600 50.000 0.00 0.00 0.00 3.62
1514 2478 1.907936 AGATTGCAGCAGAGAGAACCT 59.092 47.619 0.00 0.00 0.00 3.50
1515 2479 2.008329 GATTGCAGCAGAGAGAACCTG 58.992 52.381 0.00 0.00 34.88 4.00
1516 2480 1.051008 TTGCAGCAGAGAGAACCTGA 58.949 50.000 0.00 0.00 33.65 3.86
1517 2481 1.273759 TGCAGCAGAGAGAACCTGAT 58.726 50.000 0.00 0.00 33.65 2.90
1518 2482 1.206610 TGCAGCAGAGAGAACCTGATC 59.793 52.381 0.00 0.00 33.65 2.92
1519 2483 1.481772 GCAGCAGAGAGAACCTGATCT 59.518 52.381 0.00 0.00 33.65 2.75
1520 2484 2.739287 GCAGCAGAGAGAACCTGATCTG 60.739 54.545 0.00 0.00 41.68 2.90
1521 2485 2.759535 CAGCAGAGAGAACCTGATCTGA 59.240 50.000 5.28 0.00 41.35 3.27
1522 2486 3.385433 CAGCAGAGAGAACCTGATCTGAT 59.615 47.826 5.28 0.00 41.35 2.90
1523 2487 3.638160 AGCAGAGAGAACCTGATCTGATC 59.362 47.826 10.72 10.72 41.35 2.92
1524 2488 3.638160 GCAGAGAGAACCTGATCTGATCT 59.362 47.826 17.82 4.60 41.35 2.75
1525 2489 4.099881 GCAGAGAGAACCTGATCTGATCTT 59.900 45.833 17.82 4.93 41.35 2.40
1526 2490 5.395546 GCAGAGAGAACCTGATCTGATCTTT 60.396 44.000 17.82 8.84 41.35 2.52
1527 2491 6.642430 CAGAGAGAACCTGATCTGATCTTTT 58.358 40.000 17.82 8.53 41.35 2.27
1528 2492 7.104939 CAGAGAGAACCTGATCTGATCTTTTT 58.895 38.462 17.82 8.21 41.35 1.94
1641 2613 0.855598 AAGGGATGGCAGCATGGTAT 59.144 50.000 4.64 0.00 35.86 2.73
1648 2620 2.786777 TGGCAGCATGGTATCATCATC 58.213 47.619 0.00 0.00 35.86 2.92
1786 2758 3.937706 CTGCTCCTAAACATGTCTCCAAG 59.062 47.826 0.00 0.00 0.00 3.61
1813 2789 3.118702 TGAAACGTTGGTTGGACAGTAGA 60.119 43.478 0.00 0.00 36.25 2.59
1892 2875 0.185175 AACCACTGACCCCAAGAACC 59.815 55.000 0.00 0.00 0.00 3.62
1913 2923 1.732259 CTGTACCCAGCAATTCGACAC 59.268 52.381 0.00 0.00 0.00 3.67
1965 2975 1.679680 CCCAGCATCATTCATGACACC 59.320 52.381 0.00 0.00 40.03 4.16
1993 3003 3.884350 ATGATGCTTGCTGCCGCG 61.884 61.111 0.00 0.00 42.00 6.46
2048 3061 4.074970 GGACTCTGAAAAGAAGCCATGAA 58.925 43.478 0.00 0.00 0.00 2.57
2260 3349 3.579709 GATGATATGATGCCGAGACGTT 58.420 45.455 0.00 0.00 0.00 3.99
2293 3386 2.101209 AAAAGTTGCACGTCTCCGCG 62.101 55.000 0.00 0.00 37.70 6.46
2368 3461 3.553917 TGATAATGTGAATGTACACGCCG 59.446 43.478 0.00 0.00 42.86 6.46
2379 3472 3.377439 TGTACACGCCGCTATAAGAATG 58.623 45.455 0.00 0.00 0.00 2.67
2421 3514 3.678072 CGTACTTCGGTGACATTGACATT 59.322 43.478 0.00 0.00 35.71 2.71
2422 3515 4.434198 CGTACTTCGGTGACATTGACATTG 60.434 45.833 0.00 0.00 35.71 2.82
2475 3611 7.155328 GGCCATGGACTATATATATGCTACAC 58.845 42.308 18.40 0.00 0.00 2.90
2504 3640 9.574516 AGTTAATAACTTATCTAGCCCCAAATG 57.425 33.333 0.00 0.00 39.04 2.32
2557 3693 5.991606 CAGAGTGAGTGGAAAGTTCAACATA 59.008 40.000 1.52 0.00 33.44 2.29
2952 4621 1.955778 TCAGTTGCCAACTTGTCATGG 59.044 47.619 7.51 0.00 40.46 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.372582 AGCGATGCCAACACATAGTG 58.627 50.000 0.00 0.00 39.75 2.74
1 2 2.113860 AAGCGATGCCAACACATAGT 57.886 45.000 0.00 0.00 0.00 2.12
2 3 4.137849 CATAAGCGATGCCAACACATAG 57.862 45.455 0.00 0.00 0.00 2.23
13 14 3.620374 GGATGTATCTGGCATAAGCGATG 59.380 47.826 0.00 0.00 43.41 3.84
14 15 3.261643 TGGATGTATCTGGCATAAGCGAT 59.738 43.478 0.00 0.00 43.41 4.58
15 16 2.632512 TGGATGTATCTGGCATAAGCGA 59.367 45.455 0.00 0.00 43.41 4.93
16 17 3.044235 TGGATGTATCTGGCATAAGCG 57.956 47.619 0.00 0.00 43.41 4.68
17 18 5.474532 TCAAATGGATGTATCTGGCATAAGC 59.525 40.000 0.00 0.00 41.10 3.09
18 19 6.150641 CCTCAAATGGATGTATCTGGCATAAG 59.849 42.308 0.00 0.00 0.00 1.73
19 20 6.005823 CCTCAAATGGATGTATCTGGCATAA 58.994 40.000 0.00 0.00 0.00 1.90
20 21 5.515359 CCCTCAAATGGATGTATCTGGCATA 60.515 44.000 0.00 0.00 0.00 3.14
21 22 4.404640 CCTCAAATGGATGTATCTGGCAT 58.595 43.478 0.00 0.00 0.00 4.40
22 23 3.435457 CCCTCAAATGGATGTATCTGGCA 60.435 47.826 0.00 0.00 0.00 4.92
23 24 3.152341 CCCTCAAATGGATGTATCTGGC 58.848 50.000 0.00 0.00 0.00 4.85
24 25 4.712051 TCCCTCAAATGGATGTATCTGG 57.288 45.455 0.00 0.00 0.00 3.86
25 26 7.941238 AGTTTATCCCTCAAATGGATGTATCTG 59.059 37.037 2.10 0.00 42.57 2.90
26 27 8.050316 AGTTTATCCCTCAAATGGATGTATCT 57.950 34.615 2.10 0.00 42.57 1.98
27 28 8.571336 CAAGTTTATCCCTCAAATGGATGTATC 58.429 37.037 2.10 0.00 42.57 2.24
28 29 7.506938 CCAAGTTTATCCCTCAAATGGATGTAT 59.493 37.037 2.10 0.00 42.57 2.29
29 30 6.833416 CCAAGTTTATCCCTCAAATGGATGTA 59.167 38.462 2.10 0.00 42.57 2.29
30 31 5.658190 CCAAGTTTATCCCTCAAATGGATGT 59.342 40.000 2.10 0.00 42.57 3.06
31 32 5.069516 CCCAAGTTTATCCCTCAAATGGATG 59.930 44.000 2.10 0.00 42.57 3.51
32 33 5.043432 TCCCAAGTTTATCCCTCAAATGGAT 60.043 40.000 0.00 0.00 44.71 3.41
33 34 4.293634 TCCCAAGTTTATCCCTCAAATGGA 59.706 41.667 0.00 0.00 36.05 3.41
34 35 4.402474 GTCCCAAGTTTATCCCTCAAATGG 59.598 45.833 0.00 0.00 0.00 3.16
35 36 5.016173 TGTCCCAAGTTTATCCCTCAAATG 58.984 41.667 0.00 0.00 0.00 2.32
36 37 5.269554 TGTCCCAAGTTTATCCCTCAAAT 57.730 39.130 0.00 0.00 0.00 2.32
37 38 4.733077 TGTCCCAAGTTTATCCCTCAAA 57.267 40.909 0.00 0.00 0.00 2.69
38 39 4.733077 TTGTCCCAAGTTTATCCCTCAA 57.267 40.909 0.00 0.00 0.00 3.02
39 40 4.105697 AGTTTGTCCCAAGTTTATCCCTCA 59.894 41.667 0.00 0.00 0.00 3.86
40 41 4.663334 AGTTTGTCCCAAGTTTATCCCTC 58.337 43.478 0.00 0.00 0.00 4.30
41 42 4.741928 AGTTTGTCCCAAGTTTATCCCT 57.258 40.909 0.00 0.00 0.00 4.20
42 43 5.538813 AGAAAGTTTGTCCCAAGTTTATCCC 59.461 40.000 0.00 0.00 0.00 3.85
43 44 6.567891 CGAGAAAGTTTGTCCCAAGTTTATCC 60.568 42.308 7.14 0.00 30.13 2.59
44 45 6.371389 CGAGAAAGTTTGTCCCAAGTTTATC 58.629 40.000 7.14 0.00 0.00 1.75
45 46 5.240844 CCGAGAAAGTTTGTCCCAAGTTTAT 59.759 40.000 7.14 0.00 0.00 1.40
46 47 4.577283 CCGAGAAAGTTTGTCCCAAGTTTA 59.423 41.667 7.14 0.00 0.00 2.01
47 48 3.380320 CCGAGAAAGTTTGTCCCAAGTTT 59.620 43.478 7.14 0.00 0.00 2.66
48 49 2.949644 CCGAGAAAGTTTGTCCCAAGTT 59.050 45.455 7.14 0.00 0.00 2.66
49 50 2.171870 TCCGAGAAAGTTTGTCCCAAGT 59.828 45.455 7.14 0.00 0.00 3.16
50 51 2.548480 GTCCGAGAAAGTTTGTCCCAAG 59.452 50.000 7.14 0.00 0.00 3.61
51 52 2.567985 GTCCGAGAAAGTTTGTCCCAA 58.432 47.619 7.14 0.00 0.00 4.12
52 53 1.539496 CGTCCGAGAAAGTTTGTCCCA 60.539 52.381 7.14 0.00 0.00 4.37
53 54 1.145803 CGTCCGAGAAAGTTTGTCCC 58.854 55.000 7.14 0.00 0.00 4.46
54 55 1.145803 CCGTCCGAGAAAGTTTGTCC 58.854 55.000 7.14 0.00 0.00 4.02
55 56 2.059541 CTCCGTCCGAGAAAGTTTGTC 58.940 52.381 2.68 2.68 41.63 3.18
56 57 1.270147 CCTCCGTCCGAGAAAGTTTGT 60.270 52.381 0.00 0.00 41.63 2.83
57 58 1.429463 CCTCCGTCCGAGAAAGTTTG 58.571 55.000 0.00 0.00 41.63 2.93
58 59 0.320697 CCCTCCGTCCGAGAAAGTTT 59.679 55.000 0.00 0.00 41.63 2.66
59 60 0.541296 TCCCTCCGTCCGAGAAAGTT 60.541 55.000 0.00 0.00 41.63 2.66
60 61 0.966370 CTCCCTCCGTCCGAGAAAGT 60.966 60.000 0.00 0.00 41.63 2.66
61 62 0.966370 ACTCCCTCCGTCCGAGAAAG 60.966 60.000 0.00 0.00 41.63 2.62
62 63 0.329261 TACTCCCTCCGTCCGAGAAA 59.671 55.000 0.00 0.00 41.63 2.52
63 64 0.393537 GTACTCCCTCCGTCCGAGAA 60.394 60.000 0.00 0.00 41.63 2.87
64 65 1.222936 GTACTCCCTCCGTCCGAGA 59.777 63.158 0.00 0.00 41.63 4.04
65 66 0.465824 ATGTACTCCCTCCGTCCGAG 60.466 60.000 0.00 0.00 38.46 4.63
66 67 0.750546 CATGTACTCCCTCCGTCCGA 60.751 60.000 0.00 0.00 0.00 4.55
67 68 1.035932 ACATGTACTCCCTCCGTCCG 61.036 60.000 0.00 0.00 0.00 4.79
68 69 1.192428 AACATGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
69 70 3.194116 TGTTAACATGTACTCCCTCCGTC 59.806 47.826 3.59 0.00 0.00 4.79
70 71 3.167485 TGTTAACATGTACTCCCTCCGT 58.833 45.455 3.59 0.00 0.00 4.69
71 72 3.880047 TGTTAACATGTACTCCCTCCG 57.120 47.619 3.59 0.00 0.00 4.63
72 73 4.259356 GGTTGTTAACATGTACTCCCTCC 58.741 47.826 9.56 0.00 0.00 4.30
73 74 4.901868 TGGTTGTTAACATGTACTCCCTC 58.098 43.478 9.56 0.00 0.00 4.30
74 75 4.986054 TGGTTGTTAACATGTACTCCCT 57.014 40.909 9.56 0.00 0.00 4.20
75 76 6.386654 CAAATGGTTGTTAACATGTACTCCC 58.613 40.000 9.56 0.00 0.00 4.30
76 77 5.861787 GCAAATGGTTGTTAACATGTACTCC 59.138 40.000 9.56 6.37 37.06 3.85
77 78 6.442952 TGCAAATGGTTGTTAACATGTACTC 58.557 36.000 9.56 0.63 37.06 2.59
78 79 6.398234 TGCAAATGGTTGTTAACATGTACT 57.602 33.333 9.56 0.00 37.06 2.73
79 80 6.345408 CGTTGCAAATGGTTGTTAACATGTAC 60.345 38.462 9.56 4.72 37.06 2.90
80 81 5.687730 CGTTGCAAATGGTTGTTAACATGTA 59.312 36.000 9.56 0.09 37.06 2.29
81 82 4.505922 CGTTGCAAATGGTTGTTAACATGT 59.494 37.500 9.56 0.00 37.06 3.21
82 83 4.505922 ACGTTGCAAATGGTTGTTAACATG 59.494 37.500 9.56 4.71 37.08 3.21
83 84 4.688021 ACGTTGCAAATGGTTGTTAACAT 58.312 34.783 9.56 0.00 37.08 2.71
84 85 4.106197 GACGTTGCAAATGGTTGTTAACA 58.894 39.130 3.59 3.59 37.08 2.41
85 86 4.106197 TGACGTTGCAAATGGTTGTTAAC 58.894 39.130 0.00 0.00 37.08 2.01
86 87 4.371855 TGACGTTGCAAATGGTTGTTAA 57.628 36.364 0.00 0.00 37.08 2.01
87 88 4.355437 CTTGACGTTGCAAATGGTTGTTA 58.645 39.130 0.00 0.00 37.08 2.41
88 89 2.949451 TGACGTTGCAAATGGTTGTT 57.051 40.000 0.00 0.00 37.08 2.83
89 90 2.808244 CTTGACGTTGCAAATGGTTGT 58.192 42.857 0.00 0.00 37.08 3.32
90 91 1.522258 GCTTGACGTTGCAAATGGTTG 59.478 47.619 0.00 0.00 37.08 3.77
91 92 1.135915 TGCTTGACGTTGCAAATGGTT 59.864 42.857 0.00 0.00 37.08 3.67
92 93 0.743688 TGCTTGACGTTGCAAATGGT 59.256 45.000 0.00 0.00 37.08 3.55
93 94 1.269206 ACTGCTTGACGTTGCAAATGG 60.269 47.619 0.00 0.00 38.81 3.16
94 95 2.124011 ACTGCTTGACGTTGCAAATG 57.876 45.000 0.00 0.00 38.81 2.32
95 96 2.098934 TGAACTGCTTGACGTTGCAAAT 59.901 40.909 0.00 0.00 38.81 2.32
96 97 1.470494 TGAACTGCTTGACGTTGCAAA 59.530 42.857 0.00 0.00 38.81 3.68
97 98 1.090728 TGAACTGCTTGACGTTGCAA 58.909 45.000 11.71 0.00 38.81 4.08
98 99 0.376852 GTGAACTGCTTGACGTTGCA 59.623 50.000 10.49 10.49 37.63 4.08
99 100 0.376852 TGTGAACTGCTTGACGTTGC 59.623 50.000 0.00 0.00 0.00 4.17
100 101 2.823196 TTGTGAACTGCTTGACGTTG 57.177 45.000 0.00 0.00 0.00 4.10
101 102 3.006940 TCTTTGTGAACTGCTTGACGTT 58.993 40.909 0.00 0.00 0.00 3.99
102 103 2.627945 TCTTTGTGAACTGCTTGACGT 58.372 42.857 0.00 0.00 0.00 4.34
103 104 3.548587 CATCTTTGTGAACTGCTTGACG 58.451 45.455 0.00 0.00 0.00 4.35
104 105 3.004106 AGCATCTTTGTGAACTGCTTGAC 59.996 43.478 0.00 0.00 40.08 3.18
105 106 3.216800 AGCATCTTTGTGAACTGCTTGA 58.783 40.909 0.00 0.00 40.08 3.02
106 107 3.637998 AGCATCTTTGTGAACTGCTTG 57.362 42.857 0.00 0.00 40.08 4.01
108 109 4.660789 AAAAGCATCTTTGTGAACTGCT 57.339 36.364 0.00 0.00 44.62 4.24
129 130 4.619160 GCCCATGCAAAACCAAAACAAAAA 60.619 37.500 0.00 0.00 37.47 1.94
130 131 3.119352 GCCCATGCAAAACCAAAACAAAA 60.119 39.130 0.00 0.00 37.47 2.44
131 132 2.424956 GCCCATGCAAAACCAAAACAAA 59.575 40.909 0.00 0.00 37.47 2.83
132 133 2.019984 GCCCATGCAAAACCAAAACAA 58.980 42.857 0.00 0.00 37.47 2.83
133 134 1.065199 TGCCCATGCAAAACCAAAACA 60.065 42.857 0.00 0.00 46.66 2.83
134 135 1.673168 TGCCCATGCAAAACCAAAAC 58.327 45.000 0.00 0.00 46.66 2.43
145 146 4.392940 AGTAATTATCTCTGTGCCCATGC 58.607 43.478 0.00 0.00 38.26 4.06
146 147 6.057533 TCAAGTAATTATCTCTGTGCCCATG 58.942 40.000 0.00 0.00 0.00 3.66
147 148 6.252599 TCAAGTAATTATCTCTGTGCCCAT 57.747 37.500 0.00 0.00 0.00 4.00
148 149 5.396772 CCTCAAGTAATTATCTCTGTGCCCA 60.397 44.000 0.00 0.00 0.00 5.36
149 150 5.059833 CCTCAAGTAATTATCTCTGTGCCC 58.940 45.833 0.00 0.00 0.00 5.36
150 151 5.918608 TCCTCAAGTAATTATCTCTGTGCC 58.081 41.667 0.00 0.00 0.00 5.01
151 152 7.268586 TCTTCCTCAAGTAATTATCTCTGTGC 58.731 38.462 0.00 0.00 0.00 4.57
152 153 9.092876 GTTCTTCCTCAAGTAATTATCTCTGTG 57.907 37.037 0.00 0.00 0.00 3.66
153 154 7.976734 CGTTCTTCCTCAAGTAATTATCTCTGT 59.023 37.037 0.00 0.00 0.00 3.41
154 155 7.436673 CCGTTCTTCCTCAAGTAATTATCTCTG 59.563 40.741 0.00 0.00 0.00 3.35
155 156 7.124448 ACCGTTCTTCCTCAAGTAATTATCTCT 59.876 37.037 0.00 0.00 0.00 3.10
156 157 7.266400 ACCGTTCTTCCTCAAGTAATTATCTC 58.734 38.462 0.00 0.00 0.00 2.75
157 158 7.093465 TGACCGTTCTTCCTCAAGTAATTATCT 60.093 37.037 0.00 0.00 0.00 1.98
191 192 6.034591 GCTACGAATACATTCACAGTACTGT 58.965 40.000 22.95 22.95 46.17 3.55
218 219 5.073311 AGCTACAAGAAAGATACAAGCGA 57.927 39.130 0.00 0.00 34.01 4.93
229 230 8.445275 TGATTTACAAGTGAAGCTACAAGAAA 57.555 30.769 0.00 0.00 0.00 2.52
242 243 6.618287 TTGAGTCAACCTGATTTACAAGTG 57.382 37.500 0.08 0.00 0.00 3.16
275 311 1.134946 GTTGCAGCACACCTTCTTGTT 59.865 47.619 0.00 0.00 0.00 2.83
283 319 0.890542 TGGAGATGTTGCAGCACACC 60.891 55.000 5.00 10.16 0.00 4.16
307 343 7.044798 CCTGAACCAACAAAATTACTGGAAAA 58.955 34.615 0.00 0.00 32.97 2.29
351 388 0.036952 CTTGGCTGGACGTGACAGAT 60.037 55.000 18.20 0.00 38.20 2.90
374 411 7.978975 CGGGTGTTAATTGATATGGACAAAAAT 59.021 33.333 0.00 0.00 0.00 1.82
377 414 6.181190 TCGGGTGTTAATTGATATGGACAAA 58.819 36.000 0.00 0.00 0.00 2.83
443 517 5.984926 TCGTTTCGTACCAACAAATTAGAGT 59.015 36.000 4.04 0.00 0.00 3.24
494 568 9.026074 ACAGTGGTATTTTCGTAAACAAATTTG 57.974 29.630 16.67 16.67 0.00 2.32
498 572 9.719279 CTTTACAGTGGTATTTTCGTAAACAAA 57.281 29.630 0.00 0.00 0.00 2.83
499 573 7.856894 GCTTTACAGTGGTATTTTCGTAAACAA 59.143 33.333 0.00 0.00 0.00 2.83
500 574 7.012138 TGCTTTACAGTGGTATTTTCGTAAACA 59.988 33.333 0.00 0.00 0.00 2.83
502 576 7.227116 AGTGCTTTACAGTGGTATTTTCGTAAA 59.773 33.333 0.00 0.00 0.00 2.01
503 577 6.707161 AGTGCTTTACAGTGGTATTTTCGTAA 59.293 34.615 0.00 0.00 0.00 3.18
504 578 6.225318 AGTGCTTTACAGTGGTATTTTCGTA 58.775 36.000 0.00 0.00 0.00 3.43
507 581 6.966021 TCAAGTGCTTTACAGTGGTATTTTC 58.034 36.000 0.00 0.00 30.18 2.29
523 1452 1.115467 CTCCCTCCGTATCAAGTGCT 58.885 55.000 0.00 0.00 0.00 4.40
552 1482 4.878971 TGTAATGTATCCATTCGTTGGTGG 59.121 41.667 6.97 0.54 46.52 4.61
627 1559 4.881850 CCTGGAATTATCAACGGCTACTTT 59.118 41.667 0.00 0.00 0.00 2.66
853 1785 3.151022 GGAGAGGAGGGCTGACGG 61.151 72.222 0.00 0.00 0.00 4.79
982 1916 3.119955 GCCATCTACAAAAGTTTCGACCC 60.120 47.826 0.00 0.00 0.00 4.46
1050 1984 0.863538 CTGAATCGTCGGACAGCGAG 60.864 60.000 9.10 0.00 40.56 5.03
1130 2070 4.230657 GAGAATTCGACAGGATCATACCG 58.769 47.826 0.00 0.00 34.73 4.02
1182 2122 3.123621 CAGAAGATAAATCGCATACGGCC 59.876 47.826 0.00 0.00 40.31 6.13
1185 2125 3.425525 ACGCAGAAGATAAATCGCATACG 59.574 43.478 0.00 0.00 42.01 3.06
1186 2126 4.974103 ACGCAGAAGATAAATCGCATAC 57.026 40.909 0.00 0.00 0.00 2.39
1193 2133 6.032094 CAGAATTGCAACGCAGAAGATAAAT 58.968 36.000 0.00 0.00 40.61 1.40
1265 2209 5.920840 GCAGAAATTACCCAGAACAAGAAAC 59.079 40.000 0.00 0.00 0.00 2.78
1384 2329 6.154021 AGTTCAGGGATTGGATGAAAATTCAG 59.846 38.462 1.98 0.00 41.08 3.02
1414 2359 4.021544 TGAGTTGTTTTGCCCCATAATGTC 60.022 41.667 0.00 0.00 0.00 3.06
1426 2371 7.543868 TGTCTATTGGTTTTGTGAGTTGTTTTG 59.456 33.333 0.00 0.00 0.00 2.44
1533 2497 2.466846 TCAGATCAGGTTCCATTCGGA 58.533 47.619 0.00 0.00 40.60 4.55
1534 2498 2.988010 TCAGATCAGGTTCCATTCGG 57.012 50.000 0.00 0.00 0.00 4.30
1535 2499 4.056740 CAGATCAGATCAGGTTCCATTCG 58.943 47.826 13.14 0.00 0.00 3.34
1536 2500 5.033589 ACAGATCAGATCAGGTTCCATTC 57.966 43.478 13.14 0.00 0.00 2.67
1537 2501 5.426509 TGTACAGATCAGATCAGGTTCCATT 59.573 40.000 13.14 0.00 0.00 3.16
1538 2502 4.964897 TGTACAGATCAGATCAGGTTCCAT 59.035 41.667 13.14 0.00 0.00 3.41
1539 2503 4.352893 TGTACAGATCAGATCAGGTTCCA 58.647 43.478 13.14 7.80 0.00 3.53
1540 2504 5.105146 AGTTGTACAGATCAGATCAGGTTCC 60.105 44.000 13.14 5.70 0.00 3.62
1541 2505 5.971763 AGTTGTACAGATCAGATCAGGTTC 58.028 41.667 13.14 8.59 0.00 3.62
1542 2506 7.563188 AGATAGTTGTACAGATCAGATCAGGTT 59.437 37.037 13.14 0.00 0.00 3.50
1543 2507 7.066142 AGATAGTTGTACAGATCAGATCAGGT 58.934 38.462 13.14 12.07 0.00 4.00
1584 2550 2.970974 GAACCTTGTGCGCTCTGCC 61.971 63.158 9.73 0.00 45.60 4.85
1621 2587 1.517238 TACCATGCTGCCATCCCTTA 58.483 50.000 0.00 0.00 0.00 2.69
1641 2613 3.586100 TTCTGTTTCCGTCGATGATGA 57.414 42.857 6.11 0.00 0.00 2.92
1648 2620 1.860676 TCCAGTTTCTGTTTCCGTCG 58.139 50.000 0.00 0.00 0.00 5.12
1786 2758 0.666374 CCAACCAACGTTTCACCTCC 59.334 55.000 0.00 0.00 0.00 4.30
1813 2789 0.106419 TCCACTTTGGTTTCCGCCTT 60.106 50.000 0.00 0.00 39.03 4.35
1864 2845 0.827507 GGTCAGTGGTTGTGGCCATT 60.828 55.000 9.72 0.00 41.08 3.16
1892 2875 1.338674 TGTCGAATTGCTGGGTACAGG 60.339 52.381 0.00 0.00 45.04 4.00
1913 2923 4.202040 TGCACTGTTTTCATCAGAACCTTG 60.202 41.667 0.00 0.00 36.81 3.61
1965 2975 2.159421 GCAAGCATCATGTCCACAAGAG 60.159 50.000 0.00 0.00 0.00 2.85
2008 3018 3.011517 TTGGCCTGCTCCTCCTCC 61.012 66.667 3.32 0.00 0.00 4.30
2009 3019 2.588989 CTTGGCCTGCTCCTCCTC 59.411 66.667 3.32 0.00 0.00 3.71
2048 3061 1.988107 TCCACCAATCTTCCTGCTTCT 59.012 47.619 0.00 0.00 0.00 2.85
2260 3349 4.274705 TGCAACTTTTAGCATTCAACGAGA 59.725 37.500 0.00 0.00 35.51 4.04
2293 3386 6.266103 AGAGGAGAGATCATGAGAGAAATGAC 59.734 42.308 0.09 0.00 36.89 3.06
2379 3472 7.818642 AGTACGCACTTACAGATCTATAATCC 58.181 38.462 0.00 0.00 0.00 3.01
2421 3514 4.400529 TGCTTATGAATCGGCTAAGTCA 57.599 40.909 0.00 0.00 0.00 3.41
2422 3515 4.752101 ACATGCTTATGAATCGGCTAAGTC 59.248 41.667 0.00 0.00 0.00 3.01
2504 3640 2.338577 ATGGCATGGCAGTCTTCTAC 57.661 50.000 27.02 0.00 0.00 2.59
2575 3711 6.109359 ACTAGTTGCCTGAAATCATACAGAC 58.891 40.000 0.00 0.00 36.38 3.51
2975 4645 3.609103 CACCAGTTGCACAAGAACTAC 57.391 47.619 0.00 0.00 32.27 2.73



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

AutoCloner maintained by Alex Coulton.