Multiple sequence alignment - TraesCS3A01G312500

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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 TraesCS3A01G312500 chr3A 100.000 2928 0 0 1 2928 552318179 552315252 0.000000e+00 5408.0
1 TraesCS3A01G312500 chr3D 88.213 2842 196 50 145 2928 103873154 103875914 0.000000e+00 3264.0
2 TraesCS3A01G312500 chr3D 70.948 327 83 11 1563 1883 362856090 362856410 1.880000e-07 67.6
3 TraesCS3A01G312500 chr3D 76.190 126 23 7 1563 1684 362424014 362423892 3.150000e-05 60.2
4 TraesCS3A01G312500 chr3B 91.663 2051 122 29 171 2186 154484106 154486142 0.000000e+00 2795.0
5 TraesCS3A01G312500 chr3B 90.184 163 14 2 2766 2928 154487214 154487374 8.220000e-51 211.0
6 TraesCS3A01G312500 chr3B 76.800 125 24 5 1563 1684 472306319 472306197 6.770000e-07 65.8


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 TraesCS3A01G312500 chr3A 552315252 552318179 2927 True 5408 5408 100.0000 1 2928 1 chr3A.!!$R1 2927
1 TraesCS3A01G312500 chr3D 103873154 103875914 2760 False 3264 3264 88.2130 145 2928 1 chr3D.!!$F1 2783
2 TraesCS3A01G312500 chr3B 154484106 154487374 3268 False 1503 2795 90.9235 171 2928 2 chr3B.!!$F1 2757

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
103 104 0.038526 ACGTCACATTCGGAGGTCAC 60.039 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2001 0.099082 GTCGAGGAACGTGAGGCTAG 59.901 60.0 0.0 0.0 43.13 3.42 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.848272 ATTGTATTGTTGTTGAGGCCG 57.152 42.857 0.00 0.00 0.00 6.13
24 25 1.529226 TGTATTGTTGTTGAGGCCGG 58.471 50.000 0.00 0.00 0.00 6.13
25 26 1.072489 TGTATTGTTGTTGAGGCCGGA 59.928 47.619 5.05 0.00 0.00 5.14
26 27 2.290641 TGTATTGTTGTTGAGGCCGGAT 60.291 45.455 5.05 0.00 0.00 4.18
27 28 1.176527 ATTGTTGTTGAGGCCGGATG 58.823 50.000 5.05 0.00 0.00 3.51
28 29 0.179004 TTGTTGTTGAGGCCGGATGT 60.179 50.000 5.05 0.00 0.00 3.06
29 30 0.687920 TGTTGTTGAGGCCGGATGTA 59.312 50.000 5.05 0.00 0.00 2.29
30 31 1.072489 TGTTGTTGAGGCCGGATGTAA 59.928 47.619 5.05 0.00 0.00 2.41
31 32 2.290641 TGTTGTTGAGGCCGGATGTAAT 60.291 45.455 5.05 0.00 0.00 1.89
32 33 2.325583 TGTTGAGGCCGGATGTAATC 57.674 50.000 5.05 0.00 44.55 1.75
33 34 1.217882 GTTGAGGCCGGATGTAATCG 58.782 55.000 5.05 0.00 46.86 3.34
34 35 0.105964 TTGAGGCCGGATGTAATCGG 59.894 55.000 5.05 0.00 46.86 4.18
35 36 1.046472 TGAGGCCGGATGTAATCGGT 61.046 55.000 5.05 0.00 46.86 4.69
36 37 0.963962 GAGGCCGGATGTAATCGGTA 59.036 55.000 5.05 0.00 46.86 4.02
37 38 0.677842 AGGCCGGATGTAATCGGTAC 59.322 55.000 5.05 0.00 46.86 3.34
38 39 0.320160 GGCCGGATGTAATCGGTACC 60.320 60.000 5.05 0.16 46.86 3.34
39 40 0.390124 GCCGGATGTAATCGGTACCA 59.610 55.000 13.54 0.00 46.86 3.25
40 41 1.001633 GCCGGATGTAATCGGTACCAT 59.998 52.381 13.54 1.74 46.86 3.55
41 42 2.549349 GCCGGATGTAATCGGTACCATT 60.549 50.000 13.54 12.80 46.86 3.16
42 43 3.735591 CCGGATGTAATCGGTACCATTT 58.264 45.455 13.54 7.12 46.86 2.32
43 44 4.131596 CCGGATGTAATCGGTACCATTTT 58.868 43.478 13.54 4.51 46.86 1.82
44 45 4.212636 CCGGATGTAATCGGTACCATTTTC 59.787 45.833 13.54 3.32 46.86 2.29
45 46 4.212636 CGGATGTAATCGGTACCATTTTCC 59.787 45.833 13.54 14.42 46.86 3.13
46 47 5.374071 GGATGTAATCGGTACCATTTTCCT 58.626 41.667 13.54 0.00 46.86 3.36
47 48 5.826208 GGATGTAATCGGTACCATTTTCCTT 59.174 40.000 13.54 0.00 46.86 3.36
48 49 6.320418 GGATGTAATCGGTACCATTTTCCTTT 59.680 38.462 13.54 0.00 46.86 3.11
49 50 7.147966 GGATGTAATCGGTACCATTTTCCTTTT 60.148 37.037 13.54 0.00 46.86 2.27
50 51 7.527568 TGTAATCGGTACCATTTTCCTTTTT 57.472 32.000 13.54 0.00 30.94 1.94
51 52 7.371936 TGTAATCGGTACCATTTTCCTTTTTG 58.628 34.615 13.54 0.00 30.94 2.44
52 53 4.857509 TCGGTACCATTTTCCTTTTTGG 57.142 40.909 13.54 0.00 35.31 3.28
53 54 4.471548 TCGGTACCATTTTCCTTTTTGGA 58.528 39.130 13.54 0.00 44.51 3.53
54 55 5.081032 TCGGTACCATTTTCCTTTTTGGAT 58.919 37.500 13.54 0.00 45.68 3.41
55 56 5.047660 TCGGTACCATTTTCCTTTTTGGATG 60.048 40.000 13.54 0.00 45.68 3.51
56 57 5.487433 GGTACCATTTTCCTTTTTGGATGG 58.513 41.667 7.15 0.00 45.68 3.51
57 58 5.247337 GGTACCATTTTCCTTTTTGGATGGA 59.753 40.000 7.15 0.00 45.68 3.41
58 59 5.903198 ACCATTTTCCTTTTTGGATGGAA 57.097 34.783 7.14 0.00 45.68 3.53
59 60 6.259346 ACCATTTTCCTTTTTGGATGGAAA 57.741 33.333 7.14 0.00 45.68 3.13
66 67 8.900983 TTTCCTTTTTGGATGGAAAAACTATG 57.099 30.769 4.21 0.00 44.24 2.23
67 68 6.463360 TCCTTTTTGGATGGAAAAACTATGC 58.537 36.000 0.00 0.00 40.56 3.14
68 69 6.042552 TCCTTTTTGGATGGAAAAACTATGCA 59.957 34.615 0.00 0.00 40.56 3.96
69 70 6.369615 CCTTTTTGGATGGAAAAACTATGCAG 59.630 38.462 0.00 0.00 38.73 4.41
70 71 4.454728 TTGGATGGAAAAACTATGCAGC 57.545 40.909 0.00 0.00 38.73 5.25
71 72 2.760092 TGGATGGAAAAACTATGCAGCC 59.240 45.455 0.00 0.00 43.95 4.85
72 73 3.026694 GGATGGAAAAACTATGCAGCCT 58.973 45.455 0.00 0.00 40.95 4.58
73 74 4.207165 GGATGGAAAAACTATGCAGCCTA 58.793 43.478 0.00 0.00 40.95 3.93
74 75 4.829492 GGATGGAAAAACTATGCAGCCTAT 59.171 41.667 0.00 0.00 40.95 2.57
75 76 5.302823 GGATGGAAAAACTATGCAGCCTATT 59.697 40.000 0.00 0.00 40.95 1.73
76 77 6.490040 GGATGGAAAAACTATGCAGCCTATTA 59.510 38.462 0.00 0.00 40.95 0.98
77 78 6.693315 TGGAAAAACTATGCAGCCTATTAC 57.307 37.500 0.00 0.00 0.00 1.89
78 79 6.423182 TGGAAAAACTATGCAGCCTATTACT 58.577 36.000 0.00 0.00 0.00 2.24
79 80 6.542370 TGGAAAAACTATGCAGCCTATTACTC 59.458 38.462 0.00 0.00 0.00 2.59
80 81 6.542370 GGAAAAACTATGCAGCCTATTACTCA 59.458 38.462 0.00 0.00 0.00 3.41
81 82 7.067008 GGAAAAACTATGCAGCCTATTACTCAA 59.933 37.037 0.00 0.00 0.00 3.02
82 83 7.559590 AAAACTATGCAGCCTATTACTCAAG 57.440 36.000 0.00 0.00 0.00 3.02
83 84 6.485830 AACTATGCAGCCTATTACTCAAGA 57.514 37.500 0.00 0.00 0.00 3.02
84 85 6.485830 ACTATGCAGCCTATTACTCAAGAA 57.514 37.500 0.00 0.00 0.00 2.52
85 86 6.284459 ACTATGCAGCCTATTACTCAAGAAC 58.716 40.000 0.00 0.00 0.00 3.01
86 87 3.521560 TGCAGCCTATTACTCAAGAACG 58.478 45.455 0.00 0.00 0.00 3.95
87 88 3.056107 TGCAGCCTATTACTCAAGAACGT 60.056 43.478 0.00 0.00 0.00 3.99
88 89 3.552294 GCAGCCTATTACTCAAGAACGTC 59.448 47.826 0.00 0.00 0.00 4.34
89 90 4.744570 CAGCCTATTACTCAAGAACGTCA 58.255 43.478 0.00 0.00 0.00 4.35
90 91 4.563184 CAGCCTATTACTCAAGAACGTCAC 59.437 45.833 0.00 0.00 0.00 3.67
91 92 4.219944 AGCCTATTACTCAAGAACGTCACA 59.780 41.667 0.00 0.00 0.00 3.58
92 93 5.105310 AGCCTATTACTCAAGAACGTCACAT 60.105 40.000 0.00 0.00 0.00 3.21
93 94 5.581085 GCCTATTACTCAAGAACGTCACATT 59.419 40.000 0.00 0.00 0.00 2.71
94 95 6.237861 GCCTATTACTCAAGAACGTCACATTC 60.238 42.308 0.00 0.00 0.00 2.67
95 96 5.763444 ATTACTCAAGAACGTCACATTCG 57.237 39.130 0.00 0.00 0.00 3.34
96 97 2.404215 ACTCAAGAACGTCACATTCGG 58.596 47.619 0.00 0.00 0.00 4.30
97 98 2.035449 ACTCAAGAACGTCACATTCGGA 59.965 45.455 0.00 0.00 0.00 4.55
98 99 2.663602 CTCAAGAACGTCACATTCGGAG 59.336 50.000 0.00 0.00 0.00 4.63
99 100 1.726791 CAAGAACGTCACATTCGGAGG 59.273 52.381 0.00 0.00 0.00 4.30
100 101 0.966920 AGAACGTCACATTCGGAGGT 59.033 50.000 0.00 0.00 35.10 3.85
101 102 1.067776 AGAACGTCACATTCGGAGGTC 60.068 52.381 0.00 0.00 32.70 3.85
102 103 0.677288 AACGTCACATTCGGAGGTCA 59.323 50.000 0.00 0.00 32.70 4.02
103 104 0.038526 ACGTCACATTCGGAGGTCAC 60.039 55.000 0.00 0.00 0.00 3.67
104 105 0.736325 CGTCACATTCGGAGGTCACC 60.736 60.000 0.00 0.00 0.00 4.02
105 106 0.320374 GTCACATTCGGAGGTCACCA 59.680 55.000 0.00 0.00 0.00 4.17
106 107 1.066143 GTCACATTCGGAGGTCACCAT 60.066 52.381 0.00 0.00 0.00 3.55
107 108 1.207089 TCACATTCGGAGGTCACCATC 59.793 52.381 0.00 0.00 0.00 3.51
108 109 1.208052 CACATTCGGAGGTCACCATCT 59.792 52.381 0.00 0.00 0.00 2.90
109 110 1.909302 ACATTCGGAGGTCACCATCTT 59.091 47.619 0.00 0.00 0.00 2.40
110 111 2.093447 ACATTCGGAGGTCACCATCTTC 60.093 50.000 0.00 0.00 0.00 2.87
111 112 1.639722 TTCGGAGGTCACCATCTTCA 58.360 50.000 0.00 0.00 0.00 3.02
112 113 0.895530 TCGGAGGTCACCATCTTCAC 59.104 55.000 0.00 0.00 0.00 3.18
113 114 0.608130 CGGAGGTCACCATCTTCACA 59.392 55.000 0.00 0.00 0.00 3.58
114 115 1.208052 CGGAGGTCACCATCTTCACAT 59.792 52.381 0.00 0.00 0.00 3.21
115 116 2.355108 CGGAGGTCACCATCTTCACATT 60.355 50.000 0.00 0.00 0.00 2.71
116 117 3.118775 CGGAGGTCACCATCTTCACATTA 60.119 47.826 0.00 0.00 0.00 1.90
117 118 4.622933 CGGAGGTCACCATCTTCACATTAA 60.623 45.833 0.00 0.00 0.00 1.40
118 119 5.440610 GGAGGTCACCATCTTCACATTAAT 58.559 41.667 0.00 0.00 0.00 1.40
119 120 6.591935 GGAGGTCACCATCTTCACATTAATA 58.408 40.000 0.00 0.00 0.00 0.98
120 121 7.227156 GGAGGTCACCATCTTCACATTAATAT 58.773 38.462 0.00 0.00 0.00 1.28
121 122 8.375506 GGAGGTCACCATCTTCACATTAATATA 58.624 37.037 0.00 0.00 0.00 0.86
122 123 9.950496 GAGGTCACCATCTTCACATTAATATAT 57.050 33.333 0.00 0.00 0.00 0.86
159 160 2.043115 GGGGGAAAGGTGAAAGGAAGAT 59.957 50.000 0.00 0.00 0.00 2.40
160 161 3.092301 GGGGAAAGGTGAAAGGAAGATG 58.908 50.000 0.00 0.00 0.00 2.90
164 165 5.304357 GGGAAAGGTGAAAGGAAGATGAAAA 59.696 40.000 0.00 0.00 0.00 2.29
233 235 0.318441 TAGCAGTCAACGCTTGCTCT 59.682 50.000 0.99 0.00 40.96 4.09
236 238 1.136224 GCAGTCAACGCTTGCTCTAAC 60.136 52.381 0.00 0.00 0.00 2.34
250 252 1.923204 CTCTAACAGACACGCATGCTC 59.077 52.381 17.13 6.73 0.00 4.26
261 270 1.219124 GCATGCTCACCTCCTTCGA 59.781 57.895 11.37 0.00 0.00 3.71
262 271 0.809241 GCATGCTCACCTCCTTCGAG 60.809 60.000 11.37 0.00 35.72 4.04
270 279 3.991121 CTCACCTCCTTCGAGAAAAGAAC 59.009 47.826 0.00 0.00 38.52 3.01
326 338 0.670546 CGCCAACGAACTCCACTCAT 60.671 55.000 0.00 0.00 43.93 2.90
350 362 2.370519 TGTAAGCTGCTGACCTGGTTTA 59.629 45.455 14.51 0.00 35.24 2.01
359 371 5.674525 TGCTGACCTGGTTTAGATTAGATG 58.325 41.667 14.06 0.00 0.00 2.90
368 380 1.342074 TAGATTAGATGCCCTGCGCT 58.658 50.000 9.73 0.00 38.78 5.92
414 426 6.379133 TCTTCCTATTTGCTGCAATGATTTCT 59.621 34.615 16.77 0.00 0.00 2.52
460 472 0.250295 GCACCACAGCTCCACTTACA 60.250 55.000 0.00 0.00 0.00 2.41
463 475 2.744202 CACCACAGCTCCACTTACAATC 59.256 50.000 0.00 0.00 0.00 2.67
469 481 5.295292 CACAGCTCCACTTACAATCCATAAG 59.705 44.000 0.00 0.00 36.01 1.73
528 540 6.041979 ACTTGCCAATTCAACTAGGAACAAAT 59.958 34.615 0.00 0.00 0.00 2.32
537 549 4.124851 ACTAGGAACAAATAGGACGCAG 57.875 45.455 0.00 0.00 0.00 5.18
557 569 2.436911 AGTCCGTCCCCCATGTAATAAC 59.563 50.000 0.00 0.00 0.00 1.89
644 663 2.021457 CGACCTCTTCCTCTTCCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
658 677 3.870633 TCCTCTCGCTCCTTTCTTTAC 57.129 47.619 0.00 0.00 0.00 2.01
665 684 2.354203 CGCTCCTTTCTTTACTCAGCCT 60.354 50.000 0.00 0.00 0.00 4.58
686 705 3.716539 CTGCATGCATGGCCTGTGC 62.717 63.158 27.34 21.99 42.81 4.57
725 744 2.740055 CGCTCCGCTTGCTTCTGT 60.740 61.111 0.00 0.00 0.00 3.41
779 798 2.336809 CCGGCTCGCACTATCCTC 59.663 66.667 0.00 0.00 0.00 3.71
803 822 2.004733 CTTGCGCTGACATGATCAAGA 58.995 47.619 9.73 0.00 36.69 3.02
804 823 2.320745 TGCGCTGACATGATCAAGAT 57.679 45.000 9.73 0.00 36.69 2.40
805 824 2.207590 TGCGCTGACATGATCAAGATC 58.792 47.619 9.73 3.12 36.69 2.75
932 964 3.155167 CCCTCCACCGGTAGAGCC 61.155 72.222 22.99 0.00 0.00 4.70
943 983 2.025155 CGGTAGAGCCAGCGGATATAT 58.975 52.381 0.00 0.00 36.97 0.86
946 986 4.278669 CGGTAGAGCCAGCGGATATATAAT 59.721 45.833 0.00 0.00 36.97 1.28
949 989 2.797156 GAGCCAGCGGATATATAATGCG 59.203 50.000 0.00 0.00 35.94 4.73
976 1016 2.437180 CCTCATGCCGAGCAAGCA 60.437 61.111 2.68 0.00 43.62 3.91
990 1030 1.468736 GCAAGCAGCCAATAAGCACTC 60.469 52.381 0.00 0.00 37.23 3.51
991 1031 1.814394 CAAGCAGCCAATAAGCACTCA 59.186 47.619 0.00 0.00 34.23 3.41
992 1032 1.457346 AGCAGCCAATAAGCACTCAC 58.543 50.000 0.00 0.00 34.23 3.51
993 1033 1.004044 AGCAGCCAATAAGCACTCACT 59.996 47.619 0.00 0.00 34.23 3.41
1006 1046 0.330604 ACTCACTCCAGCAATGGCAT 59.669 50.000 0.00 0.00 44.61 4.40
1014 1054 0.752009 CAGCAATGGCATCTCAGGCT 60.752 55.000 0.00 2.63 44.61 4.58
1020 1060 2.657944 GCATCTCAGGCTCGCGAG 60.658 66.667 31.37 31.37 0.00 5.03
1212 1252 1.299165 CTACGCGTCCTTCATCCGG 60.299 63.158 18.63 0.00 0.00 5.14
1220 1260 2.354729 CTTCATCCGGGCCACCAA 59.645 61.111 4.39 0.00 36.13 3.67
1232 1272 0.895559 GCCACCAAGAAGTTCCCCAG 60.896 60.000 0.00 0.00 0.00 4.45
1302 1342 2.733301 CTCGCGCAGATCTCCCAT 59.267 61.111 8.75 0.00 0.00 4.00
1377 1417 2.102252 GTGCTACAAGGAGGAGATCAGG 59.898 54.545 0.00 0.00 0.00 3.86
1419 1459 4.643387 ACCGACAAGCAGTGGCCC 62.643 66.667 0.00 0.00 42.56 5.80
1486 1526 4.597507 TCTCATGGTACTGATAAATCCCCC 59.402 45.833 0.00 0.00 0.00 5.40
1490 1530 2.970640 GGTACTGATAAATCCCCCGAGT 59.029 50.000 0.00 0.00 0.00 4.18
1491 1531 3.006644 GGTACTGATAAATCCCCCGAGTC 59.993 52.174 0.00 0.00 0.00 3.36
1508 1548 3.125316 CGAGTCTACCTGCAAATTTCACC 59.875 47.826 0.00 0.00 0.00 4.02
1576 1640 2.833631 ACAGGAACTTCAACTACGGG 57.166 50.000 0.00 0.00 34.60 5.28
1639 1703 2.674380 CTGGTGGCCAACTGCTCC 60.674 66.667 24.13 11.90 40.92 4.70
1688 1752 3.866582 GGATGACGCCCAGGGAGG 61.867 72.222 10.89 1.84 37.03 4.30
1736 1800 4.840005 GCGAGTACTGCCCCAGCC 62.840 72.222 0.00 0.00 38.69 4.85
1798 1862 1.206578 CACCAACATCGTCAACGGC 59.793 57.895 2.31 0.00 40.29 5.68
1817 1881 1.375908 GGCCTCGAGTGCAACATCA 60.376 57.895 22.04 0.00 41.43 3.07
1822 1886 0.388520 TCGAGTGCAACATCACCGAG 60.389 55.000 0.00 0.00 41.43 4.63
1937 2001 2.192187 CCGTACTAGCCCGAGGGAC 61.192 68.421 13.28 3.38 37.50 4.46
1950 2014 0.456628 GAGGGACTAGCCTCACGTTC 59.543 60.000 10.61 0.00 41.55 3.95
1956 2020 0.099082 CTAGCCTCACGTTCCTCGAC 59.901 60.000 0.00 0.00 42.86 4.20
2124 2192 4.114073 CAAGTGAAATTGAAGCAAGCACA 58.886 39.130 0.00 0.00 31.29 4.57
2177 2245 6.439058 AGCTACACCAAGATTCTCTAAAGTCT 59.561 38.462 0.00 0.00 0.00 3.24
2203 2794 4.211374 GTGTCTAACTTCATTGTTCGCACT 59.789 41.667 0.00 0.00 0.00 4.40
2227 2818 8.015658 ACTTAATTGTGCTTTCTTGTATTCGAC 58.984 33.333 0.00 0.00 0.00 4.20
2265 2856 9.974980 TTTTATCTTTTGTGGGAAGTATTTGAC 57.025 29.630 0.00 0.00 0.00 3.18
2268 2859 6.801575 TCTTTTGTGGGAAGTATTTGACAAC 58.198 36.000 0.00 0.00 0.00 3.32
2269 2860 6.378564 TCTTTTGTGGGAAGTATTTGACAACA 59.621 34.615 0.00 0.00 0.00 3.33
2297 2888 2.069165 GAGGACAAGCCCCACAAGGT 62.069 60.000 0.00 0.00 37.37 3.50
2332 2923 3.525800 TTTAAAAGAGAGGGGCTTGCT 57.474 42.857 0.00 0.00 0.00 3.91
2335 2926 2.811542 AAAGAGAGGGGCTTGCTCGC 62.812 60.000 0.00 0.00 33.98 5.03
2357 2953 4.338400 GCCAATAAACTAAGGCCCTTACAG 59.662 45.833 0.00 0.00 41.25 2.74
2360 2956 6.833933 CCAATAAACTAAGGCCCTTACAGAAT 59.166 38.462 0.00 0.00 0.00 2.40
2377 2973 6.064846 ACAGAATGAGTGCAAAGTAAAGTG 57.935 37.500 0.00 0.00 39.69 3.16
2381 2977 4.893424 TGAGTGCAAAGTAAAGTGAACC 57.107 40.909 0.00 0.00 0.00 3.62
2385 2981 6.031751 AGTGCAAAGTAAAGTGAACCAAAA 57.968 33.333 0.00 0.00 0.00 2.44
2392 2988 9.360093 CAAAGTAAAGTGAACCAAAACATACAA 57.640 29.630 0.00 0.00 0.00 2.41
2394 2990 8.514330 AGTAAAGTGAACCAAAACATACAAGA 57.486 30.769 0.00 0.00 0.00 3.02
2404 3000 6.321181 ACCAAAACATACAAGATCACAAGTGT 59.679 34.615 0.00 0.00 0.00 3.55
2419 3015 1.157870 AGTGTCCGAACAAAGTGGCG 61.158 55.000 0.00 0.00 37.08 5.69
2421 3017 2.203084 TCCGAACAAAGTGGCGCA 60.203 55.556 10.83 0.00 0.00 6.09
2454 3050 3.898741 GCTAGACACTAGGCCTAGGAAAT 59.101 47.826 37.09 24.15 37.49 2.17
2457 3053 5.873146 AGACACTAGGCCTAGGAAATAAC 57.127 43.478 37.09 21.86 37.49 1.89
2459 3055 4.028825 ACACTAGGCCTAGGAAATAACGT 58.971 43.478 37.09 19.76 37.49 3.99
2479 3075 4.131088 GTCGCCCACGGAGAGTCC 62.131 72.222 0.00 0.00 40.63 3.85
2503 3099 5.089970 TGAATGGAAGAAGACGATCACAT 57.910 39.130 0.00 0.00 0.00 3.21
2513 3109 1.869767 GACGATCACATGATGGCTTCC 59.130 52.381 0.00 0.00 34.20 3.46
2514 3110 1.233019 CGATCACATGATGGCTTCCC 58.767 55.000 0.00 0.00 34.37 3.97
2515 3111 1.202734 CGATCACATGATGGCTTCCCT 60.203 52.381 0.00 0.00 34.37 4.20
2516 3112 2.228059 GATCACATGATGGCTTCCCTG 58.772 52.381 0.00 0.00 34.37 4.45
2517 3113 0.256752 TCACATGATGGCTTCCCTGG 59.743 55.000 0.00 0.00 0.00 4.45
2536 3132 0.527817 GCCTACATTGTCCCGTCTCG 60.528 60.000 0.00 0.00 0.00 4.04
2538 3134 1.681793 CCTACATTGTCCCGTCTCGAT 59.318 52.381 0.00 0.00 0.00 3.59
2584 3180 3.243168 TGCACAAAGATTGCTGACAAGAC 60.243 43.478 0.00 0.00 39.69 3.01
2598 3194 1.806542 ACAAGACGATCATGTTGTGGC 59.193 47.619 3.26 0.00 34.96 5.01
2600 3196 0.324614 AGACGATCATGTTGTGGCCA 59.675 50.000 0.00 0.00 0.00 5.36
2604 3200 1.676916 CGATCATGTTGTGGCCAGTCT 60.677 52.381 5.11 0.00 0.00 3.24
2606 3202 1.608055 TCATGTTGTGGCCAGTCTTG 58.392 50.000 5.11 8.39 0.00 3.02
2611 3207 1.476488 GTTGTGGCCAGTCTTGTTGTT 59.524 47.619 5.11 0.00 0.00 2.83
2614 3210 1.067060 GTGGCCAGTCTTGTTGTTTCC 59.933 52.381 5.11 0.00 0.00 3.13
2616 3212 1.398692 GCCAGTCTTGTTGTTTCCCA 58.601 50.000 0.00 0.00 0.00 4.37
2621 3217 3.803778 CAGTCTTGTTGTTTCCCAAATGC 59.196 43.478 0.00 0.00 34.07 3.56
2630 3226 6.097554 TGTTGTTTCCCAAATGCTCTCTAAAA 59.902 34.615 0.00 0.00 34.07 1.52
2639 3235 7.148340 CCCAAATGCTCTCTAAAACTGTAGAAG 60.148 40.741 0.00 0.00 29.74 2.85
2640 3236 7.148340 CCAAATGCTCTCTAAAACTGTAGAAGG 60.148 40.741 0.00 0.00 29.74 3.46
2642 3238 6.026947 TGCTCTCTAAAACTGTAGAAGGAC 57.973 41.667 0.00 0.00 29.74 3.85
2648 3244 7.709613 TCTCTAAAACTGTAGAAGGACAACAAC 59.290 37.037 0.00 0.00 29.74 3.32
2651 3247 9.321562 CTAAAACTGTAGAAGGACAACAACTTA 57.678 33.333 0.00 0.00 0.00 2.24
2667 3263 6.963049 ACAACTTAATACACAAGATCGGTC 57.037 37.500 0.00 0.00 0.00 4.79
2680 3276 2.158900 AGATCGGTCGGATGCTTGAATT 60.159 45.455 0.00 0.00 34.82 2.17
2700 3296 6.099557 TGAATTCAAGACCTTCCATTGGTTTT 59.900 34.615 5.45 0.00 38.03 2.43
2701 3297 5.529581 TTCAAGACCTTCCATTGGTTTTC 57.470 39.130 1.86 0.00 38.03 2.29
2716 3312 3.181467 TGGTTTTCAGCATTCCAAAGTGG 60.181 43.478 0.00 0.00 39.43 4.00
2721 3317 2.101783 CAGCATTCCAAAGTGGCCATA 58.898 47.619 9.72 0.00 37.47 2.74
2730 3326 3.446873 CCAAAGTGGCCATACTAATGCAA 59.553 43.478 9.72 0.00 0.00 4.08
2731 3327 4.081752 CCAAAGTGGCCATACTAATGCAAA 60.082 41.667 9.72 0.00 0.00 3.68
2759 3355 7.341445 TCCCACCCAATAAATTTTTCTATCG 57.659 36.000 0.00 0.00 0.00 2.92
2779 3375 2.029110 CGTTTTTGTGGATCCCTTGCAT 60.029 45.455 9.90 0.00 0.00 3.96
2817 3413 0.988832 AAACCTAGCCGGATTCCACA 59.011 50.000 5.05 0.00 36.31 4.17
2833 3429 2.118404 ACAAGCAACCCGTGGTGTG 61.118 57.895 0.00 0.23 38.21 3.82
2836 3432 2.203153 GCAACCCGTGGTGTGTCT 60.203 61.111 0.00 0.00 35.34 3.41
2837 3433 2.251642 GCAACCCGTGGTGTGTCTC 61.252 63.158 0.00 0.00 35.34 3.36
2838 3434 1.954146 CAACCCGTGGTGTGTCTCG 60.954 63.158 0.00 0.00 35.34 4.04
2853 3449 2.688446 TGTCTCGGATCACACTCCATAC 59.312 50.000 0.00 0.00 34.78 2.39
2869 3465 6.545666 CACTCCATACAAATTTGGCCACTATA 59.454 38.462 21.74 4.23 32.80 1.31
2873 3469 7.230510 TCCATACAAATTTGGCCACTATACATC 59.769 37.037 21.74 0.00 32.80 3.06
2875 3471 6.849085 ACAAATTTGGCCACTATACATCAA 57.151 33.333 21.74 0.00 0.00 2.57
2905 3501 5.199024 TGTGGTCACAATTTTCATTGAGG 57.801 39.130 0.78 0.00 42.35 3.86
2908 3504 3.244976 GTCACAATTTTCATTGAGGCCG 58.755 45.455 0.00 0.00 42.35 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.505654 CCGGCCTCAACAACAATACAATATC 60.506 44.000 0.00 0.00 0.00 1.63
2 3 3.692101 CCGGCCTCAACAACAATACAATA 59.308 43.478 0.00 0.00 0.00 1.90
4 5 1.883275 CCGGCCTCAACAACAATACAA 59.117 47.619 0.00 0.00 0.00 2.41
6 7 1.816074 TCCGGCCTCAACAACAATAC 58.184 50.000 0.00 0.00 0.00 1.89
7 8 2.290641 ACATCCGGCCTCAACAACAATA 60.291 45.455 0.00 0.00 0.00 1.90
8 9 1.176527 CATCCGGCCTCAACAACAAT 58.823 50.000 0.00 0.00 0.00 2.71
9 10 0.179004 ACATCCGGCCTCAACAACAA 60.179 50.000 0.00 0.00 0.00 2.83
10 11 0.687920 TACATCCGGCCTCAACAACA 59.312 50.000 0.00 0.00 0.00 3.33
11 12 1.816074 TTACATCCGGCCTCAACAAC 58.184 50.000 0.00 0.00 0.00 3.32
12 13 2.639065 GATTACATCCGGCCTCAACAA 58.361 47.619 0.00 0.00 0.00 2.83
13 14 1.472552 CGATTACATCCGGCCTCAACA 60.473 52.381 0.00 0.00 0.00 3.33
14 15 1.217882 CGATTACATCCGGCCTCAAC 58.782 55.000 0.00 0.00 0.00 3.18
15 16 0.105964 CCGATTACATCCGGCCTCAA 59.894 55.000 0.00 0.00 39.22 3.02
16 17 1.745890 CCGATTACATCCGGCCTCA 59.254 57.895 0.00 0.00 39.22 3.86
17 18 4.675404 CCGATTACATCCGGCCTC 57.325 61.111 0.00 0.00 39.22 4.70
22 23 4.212636 GGAAAATGGTACCGATTACATCCG 59.787 45.833 7.57 0.00 31.46 4.18
23 24 5.374071 AGGAAAATGGTACCGATTACATCC 58.626 41.667 7.57 14.51 31.46 3.51
24 25 6.937436 AAGGAAAATGGTACCGATTACATC 57.063 37.500 7.57 7.76 31.46 3.06
25 26 7.712204 AAAAGGAAAATGGTACCGATTACAT 57.288 32.000 7.57 2.49 31.46 2.29
26 27 7.371936 CAAAAAGGAAAATGGTACCGATTACA 58.628 34.615 7.57 0.00 31.46 2.41
27 28 6.809689 CCAAAAAGGAAAATGGTACCGATTAC 59.190 38.462 7.57 2.84 41.22 1.89
28 29 6.720288 TCCAAAAAGGAAAATGGTACCGATTA 59.280 34.615 7.57 0.00 45.65 1.75
29 30 5.540719 TCCAAAAAGGAAAATGGTACCGATT 59.459 36.000 7.57 5.64 45.65 3.34
30 31 5.081032 TCCAAAAAGGAAAATGGTACCGAT 58.919 37.500 7.57 0.00 45.65 4.18
31 32 4.471548 TCCAAAAAGGAAAATGGTACCGA 58.528 39.130 7.57 0.00 45.65 4.69
32 33 4.857509 TCCAAAAAGGAAAATGGTACCG 57.142 40.909 7.57 0.00 45.65 4.02
44 45 6.229733 TGCATAGTTTTTCCATCCAAAAAGG 58.770 36.000 0.00 0.00 36.21 3.11
45 46 6.128472 GCTGCATAGTTTTTCCATCCAAAAAG 60.128 38.462 0.00 0.00 36.21 2.27
46 47 5.700373 GCTGCATAGTTTTTCCATCCAAAAA 59.300 36.000 0.00 0.00 33.72 1.94
47 48 5.237048 GCTGCATAGTTTTTCCATCCAAAA 58.763 37.500 0.00 0.00 0.00 2.44
48 49 4.322650 GGCTGCATAGTTTTTCCATCCAAA 60.323 41.667 0.50 0.00 0.00 3.28
49 50 3.195396 GGCTGCATAGTTTTTCCATCCAA 59.805 43.478 0.50 0.00 0.00 3.53
50 51 2.760092 GGCTGCATAGTTTTTCCATCCA 59.240 45.455 0.50 0.00 0.00 3.41
51 52 3.026694 AGGCTGCATAGTTTTTCCATCC 58.973 45.455 0.50 0.00 0.00 3.51
52 53 6.396829 AATAGGCTGCATAGTTTTTCCATC 57.603 37.500 0.50 0.00 0.00 3.51
53 54 7.062957 AGTAATAGGCTGCATAGTTTTTCCAT 58.937 34.615 0.00 0.00 0.00 3.41
54 55 6.423182 AGTAATAGGCTGCATAGTTTTTCCA 58.577 36.000 0.00 0.00 0.00 3.53
55 56 6.542370 TGAGTAATAGGCTGCATAGTTTTTCC 59.458 38.462 0.00 0.00 0.00 3.13
56 57 7.553881 TGAGTAATAGGCTGCATAGTTTTTC 57.446 36.000 0.00 0.00 0.00 2.29
57 58 7.829211 TCTTGAGTAATAGGCTGCATAGTTTTT 59.171 33.333 0.00 0.00 0.00 1.94
58 59 7.338710 TCTTGAGTAATAGGCTGCATAGTTTT 58.661 34.615 0.00 0.00 0.00 2.43
59 60 6.889198 TCTTGAGTAATAGGCTGCATAGTTT 58.111 36.000 0.00 0.00 0.00 2.66
60 61 6.485830 TCTTGAGTAATAGGCTGCATAGTT 57.514 37.500 0.00 0.00 0.00 2.24
61 62 6.284459 GTTCTTGAGTAATAGGCTGCATAGT 58.716 40.000 0.50 0.00 0.00 2.12
62 63 5.403766 CGTTCTTGAGTAATAGGCTGCATAG 59.596 44.000 0.50 0.00 0.00 2.23
63 64 5.163447 ACGTTCTTGAGTAATAGGCTGCATA 60.163 40.000 0.50 0.00 0.00 3.14
64 65 4.122776 CGTTCTTGAGTAATAGGCTGCAT 58.877 43.478 0.50 0.00 0.00 3.96
65 66 3.056107 ACGTTCTTGAGTAATAGGCTGCA 60.056 43.478 0.50 0.00 0.00 4.41
66 67 3.522553 ACGTTCTTGAGTAATAGGCTGC 58.477 45.455 0.00 0.00 0.00 5.25
67 68 4.563184 GTGACGTTCTTGAGTAATAGGCTG 59.437 45.833 0.00 0.00 0.00 4.85
68 69 4.219944 TGTGACGTTCTTGAGTAATAGGCT 59.780 41.667 0.00 0.00 0.00 4.58
69 70 4.491676 TGTGACGTTCTTGAGTAATAGGC 58.508 43.478 0.00 0.00 0.00 3.93
70 71 6.020599 CGAATGTGACGTTCTTGAGTAATAGG 60.021 42.308 14.85 0.00 0.00 2.57
71 72 6.020599 CCGAATGTGACGTTCTTGAGTAATAG 60.021 42.308 14.85 0.00 0.00 1.73
72 73 5.803461 CCGAATGTGACGTTCTTGAGTAATA 59.197 40.000 14.85 0.00 0.00 0.98
73 74 4.625742 CCGAATGTGACGTTCTTGAGTAAT 59.374 41.667 14.85 0.00 0.00 1.89
74 75 3.985279 CCGAATGTGACGTTCTTGAGTAA 59.015 43.478 14.85 0.00 0.00 2.24
75 76 3.253921 TCCGAATGTGACGTTCTTGAGTA 59.746 43.478 14.85 0.00 0.00 2.59
76 77 2.035449 TCCGAATGTGACGTTCTTGAGT 59.965 45.455 14.85 0.00 0.00 3.41
77 78 2.663602 CTCCGAATGTGACGTTCTTGAG 59.336 50.000 14.85 14.93 0.00 3.02
78 79 2.609491 CCTCCGAATGTGACGTTCTTGA 60.609 50.000 14.85 10.23 0.00 3.02
79 80 1.726791 CCTCCGAATGTGACGTTCTTG 59.273 52.381 14.85 6.75 0.00 3.02
80 81 1.343465 ACCTCCGAATGTGACGTTCTT 59.657 47.619 14.85 0.00 0.00 2.52
81 82 0.966920 ACCTCCGAATGTGACGTTCT 59.033 50.000 14.85 0.00 0.00 3.01
82 83 1.336517 TGACCTCCGAATGTGACGTTC 60.337 52.381 7.46 7.46 0.00 3.95
83 84 0.677288 TGACCTCCGAATGTGACGTT 59.323 50.000 0.00 0.00 0.00 3.99
84 85 0.038526 GTGACCTCCGAATGTGACGT 60.039 55.000 0.00 0.00 0.00 4.34
85 86 0.736325 GGTGACCTCCGAATGTGACG 60.736 60.000 0.00 0.00 0.00 4.35
86 87 0.320374 TGGTGACCTCCGAATGTGAC 59.680 55.000 2.11 0.00 0.00 3.67
87 88 1.207089 GATGGTGACCTCCGAATGTGA 59.793 52.381 2.11 0.00 0.00 3.58
88 89 1.208052 AGATGGTGACCTCCGAATGTG 59.792 52.381 2.11 0.00 0.00 3.21
89 90 1.573108 AGATGGTGACCTCCGAATGT 58.427 50.000 2.11 0.00 0.00 2.71
90 91 2.093500 TGAAGATGGTGACCTCCGAATG 60.093 50.000 2.11 0.00 0.00 2.67
91 92 2.093447 GTGAAGATGGTGACCTCCGAAT 60.093 50.000 2.11 0.00 0.00 3.34
92 93 1.275291 GTGAAGATGGTGACCTCCGAA 59.725 52.381 2.11 0.00 0.00 4.30
93 94 0.895530 GTGAAGATGGTGACCTCCGA 59.104 55.000 2.11 0.00 0.00 4.55
94 95 0.608130 TGTGAAGATGGTGACCTCCG 59.392 55.000 2.11 0.00 0.00 4.63
95 96 3.356529 AATGTGAAGATGGTGACCTCC 57.643 47.619 2.11 0.00 0.00 4.30
96 97 9.950496 ATATATTAATGTGAAGATGGTGACCTC 57.050 33.333 2.11 0.00 0.00 3.85
138 139 1.427753 TCTTCCTTTCACCTTTCCCCC 59.572 52.381 0.00 0.00 0.00 5.40
139 140 2.971901 TCTTCCTTTCACCTTTCCCC 57.028 50.000 0.00 0.00 0.00 4.81
140 141 4.034285 TCATCTTCCTTTCACCTTTCCC 57.966 45.455 0.00 0.00 0.00 3.97
141 142 6.405278 TTTTCATCTTCCTTTCACCTTTCC 57.595 37.500 0.00 0.00 0.00 3.13
164 165 2.413310 ATCACGGCCGACCTTTATTT 57.587 45.000 35.90 1.64 0.00 1.40
167 168 1.444836 CAAATCACGGCCGACCTTTA 58.555 50.000 35.90 10.25 0.00 1.85
233 235 1.428448 GTGAGCATGCGTGTCTGTTA 58.572 50.000 13.01 0.00 0.00 2.41
236 238 1.357258 GAGGTGAGCATGCGTGTCTG 61.357 60.000 13.01 0.00 0.00 3.51
250 252 3.728845 TGTTCTTTTCTCGAAGGAGGTG 58.271 45.455 0.00 0.00 40.85 4.00
261 270 7.189512 GCAATATAATGCGTCTGTTCTTTTCT 58.810 34.615 0.00 0.00 36.45 2.52
262 271 7.368750 GCAATATAATGCGTCTGTTCTTTTC 57.631 36.000 0.00 0.00 36.45 2.29
326 338 1.065926 CCAGGTCAGCAGCTTACATGA 60.066 52.381 20.42 0.02 0.00 3.07
350 362 4.787871 GCGCAGGGCATCTAATCT 57.212 55.556 0.30 0.00 42.87 2.40
395 407 8.780846 AAATTGAGAAATCATTGCAGCAAATA 57.219 26.923 12.97 3.39 0.00 1.40
397 409 6.148150 GGAAATTGAGAAATCATTGCAGCAAA 59.852 34.615 12.97 0.00 0.00 3.68
469 481 6.709846 ACAAATCCAGAAGATTCAGCTATAGC 59.290 38.462 17.33 17.33 44.75 2.97
537 549 2.804212 CGTTATTACATGGGGGACGGAC 60.804 54.545 0.00 0.00 0.00 4.79
557 569 1.657181 GGCGTCCAAGCAACAAACG 60.657 57.895 0.00 0.00 39.27 3.60
644 663 2.003301 GGCTGAGTAAAGAAAGGAGCG 58.997 52.381 0.00 0.00 0.00 5.03
803 822 1.950484 GCCACCATCGGTTGACTTGAT 60.950 52.381 0.00 0.00 31.02 2.57
804 823 0.605319 GCCACCATCGGTTGACTTGA 60.605 55.000 0.00 0.00 31.02 3.02
805 824 1.875963 GCCACCATCGGTTGACTTG 59.124 57.895 0.00 0.00 31.02 3.16
806 825 1.671054 CGCCACCATCGGTTGACTT 60.671 57.895 0.00 0.00 31.02 3.01
807 826 2.047274 CGCCACCATCGGTTGACT 60.047 61.111 0.00 0.00 31.02 3.41
808 827 3.799755 GCGCCACCATCGGTTGAC 61.800 66.667 0.00 0.00 31.02 3.18
895 926 2.584608 GTGAGGACACGGGGATGG 59.415 66.667 0.00 0.00 37.28 3.51
903 935 4.083862 GGAGGGGCGTGAGGACAC 62.084 72.222 0.00 0.00 42.88 3.67
916 948 2.363795 TGGCTCTACCGGTGGAGG 60.364 66.667 38.97 25.09 43.94 4.30
928 960 2.797156 CGCATTATATATCCGCTGGCTC 59.203 50.000 0.00 0.00 0.00 4.70
929 961 2.826428 CGCATTATATATCCGCTGGCT 58.174 47.619 0.00 0.00 0.00 4.75
932 964 2.034591 CGTGCGCATTATATATCCGCTG 60.035 50.000 15.91 10.01 44.44 5.18
943 983 3.483665 GGACACGCGTGCGCATTA 61.484 61.111 37.35 0.00 44.19 1.90
966 1006 0.379669 CTTATTGGCTGCTTGCTCGG 59.620 55.000 0.00 0.00 42.39 4.63
976 1016 1.630369 TGGAGTGAGTGCTTATTGGCT 59.370 47.619 0.00 0.00 0.00 4.75
990 1030 1.022735 GAGATGCCATTGCTGGAGTG 58.977 55.000 0.00 0.00 46.37 3.51
991 1031 0.622136 TGAGATGCCATTGCTGGAGT 59.378 50.000 0.00 0.00 46.37 3.85
992 1032 1.309950 CTGAGATGCCATTGCTGGAG 58.690 55.000 0.00 0.00 46.37 3.86
993 1033 0.106868 CCTGAGATGCCATTGCTGGA 60.107 55.000 0.00 0.00 46.37 3.86
1026 1066 4.856607 GCGACGGCGAGGAGGAAG 62.857 72.222 18.90 0.00 40.82 3.46
1129 1169 1.133407 GAACAGGGACGAGTAGAGCTG 59.867 57.143 0.00 0.00 0.00 4.24
1212 1252 1.606601 GGGGAACTTCTTGGTGGCC 60.607 63.158 0.00 0.00 0.00 5.36
1220 1260 2.067197 CCGAACCTGGGGAACTTCT 58.933 57.895 0.00 0.00 0.00 2.85
1377 1417 3.479370 CAGTAGTTGCTCTGCGGC 58.521 61.111 0.00 0.00 34.00 6.53
1419 1459 2.125106 GACTTGCCGGGGTAGCAG 60.125 66.667 2.18 0.00 42.17 4.24
1486 1526 3.125316 GGTGAAATTTGCAGGTAGACTCG 59.875 47.826 0.00 0.00 0.00 4.18
1490 1530 3.517296 TGGGTGAAATTTGCAGGTAGA 57.483 42.857 0.00 0.00 0.00 2.59
1491 1531 3.119029 CCATGGGTGAAATTTGCAGGTAG 60.119 47.826 2.85 0.00 0.00 3.18
1521 1561 0.244994 GGTCAGAGATCAGCACGTGT 59.755 55.000 18.38 0.68 0.00 4.49
1523 1563 0.814457 GAGGTCAGAGATCAGCACGT 59.186 55.000 0.00 0.00 0.00 4.49
1524 1564 1.102154 AGAGGTCAGAGATCAGCACG 58.898 55.000 0.00 0.00 0.00 5.34
1525 1565 1.136695 CCAGAGGTCAGAGATCAGCAC 59.863 57.143 0.00 0.00 0.00 4.40
1526 1566 1.482954 CCAGAGGTCAGAGATCAGCA 58.517 55.000 0.00 0.00 0.00 4.41
1528 1568 0.752054 GGCCAGAGGTCAGAGATCAG 59.248 60.000 0.00 0.00 0.00 2.90
1529 1569 1.039785 CGGCCAGAGGTCAGAGATCA 61.040 60.000 2.24 0.00 0.00 2.92
1530 1570 1.739049 CGGCCAGAGGTCAGAGATC 59.261 63.158 2.24 0.00 0.00 2.75
1531 1571 1.760086 CCGGCCAGAGGTCAGAGAT 60.760 63.158 2.24 0.00 0.00 2.75
1532 1572 2.363018 CCGGCCAGAGGTCAGAGA 60.363 66.667 2.24 0.00 0.00 3.10
1639 1703 2.503375 GTCTGGTACGCCGTGTCG 60.503 66.667 0.00 0.00 37.67 4.35
1798 1862 2.434884 ATGTTGCACTCGAGGCCG 60.435 61.111 18.41 5.88 37.07 6.13
1937 2001 0.099082 GTCGAGGAACGTGAGGCTAG 59.901 60.000 0.00 0.00 43.13 3.42
1950 2014 1.079336 GGTTTTCTCCCGGTCGAGG 60.079 63.158 0.00 0.00 0.00 4.63
1956 2020 0.546598 AGGCTATGGTTTTCTCCCGG 59.453 55.000 0.00 0.00 0.00 5.73
2078 2146 8.185003 TGTTGATAGTACGATCAATGTTCTTG 57.815 34.615 27.21 0.00 45.21 3.02
2081 2149 8.110612 CACTTGTTGATAGTACGATCAATGTTC 58.889 37.037 27.21 17.66 45.21 3.18
2124 2192 8.533657 TCAATTTGCTCAGGATATTTGTCATTT 58.466 29.630 0.00 0.00 0.00 2.32
2177 2245 4.084745 GCGAACAATGAAGTTAGACACGAA 60.085 41.667 0.00 0.00 0.00 3.85
2203 2794 7.866729 TGTCGAATACAAGAAAGCACAATTAA 58.133 30.769 0.00 0.00 34.29 1.40
2243 2834 7.069331 TGTTGTCAAATACTTCCCACAAAAGAT 59.931 33.333 0.00 0.00 0.00 2.40
2244 2835 6.378564 TGTTGTCAAATACTTCCCACAAAAGA 59.621 34.615 0.00 0.00 0.00 2.52
2245 2836 6.568869 TGTTGTCAAATACTTCCCACAAAAG 58.431 36.000 0.00 0.00 0.00 2.27
2251 2842 7.560368 ACAATTTTGTTGTCAAATACTTCCCA 58.440 30.769 0.00 0.00 42.14 4.37
2262 2853 6.459573 GCTTGTCCTCTACAATTTTGTTGTCA 60.460 38.462 0.63 0.00 46.81 3.58
2265 2856 5.222631 GGCTTGTCCTCTACAATTTTGTTG 58.777 41.667 0.63 0.00 46.81 3.33
2268 2859 3.193479 GGGGCTTGTCCTCTACAATTTTG 59.807 47.826 0.00 0.00 46.81 2.44
2269 2860 3.181423 TGGGGCTTGTCCTCTACAATTTT 60.181 43.478 0.00 0.00 46.81 1.82
2332 2923 1.562475 AGGGCCTTAGTTTATTGGCGA 59.438 47.619 0.00 0.00 45.75 5.54
2335 2926 5.751586 TCTGTAAGGGCCTTAGTTTATTGG 58.248 41.667 26.03 9.96 0.00 3.16
2345 2936 2.619074 GCACTCATTCTGTAAGGGCCTT 60.619 50.000 24.44 24.44 33.23 4.35
2357 2953 5.915196 GGTTCACTTTACTTTGCACTCATTC 59.085 40.000 0.00 0.00 0.00 2.67
2360 2956 4.265893 TGGTTCACTTTACTTTGCACTCA 58.734 39.130 0.00 0.00 0.00 3.41
2377 2973 7.379529 CACTTGTGATCTTGTATGTTTTGGTTC 59.620 37.037 0.00 0.00 0.00 3.62
2381 2977 6.857964 GGACACTTGTGATCTTGTATGTTTTG 59.142 38.462 7.83 0.00 0.00 2.44
2385 2981 4.021456 TCGGACACTTGTGATCTTGTATGT 60.021 41.667 7.83 0.00 0.00 2.29
2392 2988 3.469008 TTGTTCGGACACTTGTGATCT 57.531 42.857 0.00 0.00 34.98 2.75
2394 2990 3.312421 CACTTTGTTCGGACACTTGTGAT 59.688 43.478 14.41 0.00 34.87 3.06
2404 3000 1.573829 GATGCGCCACTTTGTTCGGA 61.574 55.000 4.18 0.00 0.00 4.55
2444 3040 2.558378 GACCCACGTTATTTCCTAGGC 58.442 52.381 2.96 0.00 0.00 3.93
2479 3075 3.868077 GTGATCGTCTTCTTCCATTCAGG 59.132 47.826 0.00 0.00 39.47 3.86
2513 3109 1.153168 CGGGACAATGTAGGCCAGG 60.153 63.158 5.01 0.00 0.00 4.45
2514 3110 0.462047 GACGGGACAATGTAGGCCAG 60.462 60.000 5.01 0.00 0.00 4.85
2515 3111 0.907704 AGACGGGACAATGTAGGCCA 60.908 55.000 5.01 0.00 0.00 5.36
2516 3112 0.179081 GAGACGGGACAATGTAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
2517 3113 0.527817 CGAGACGGGACAATGTAGGC 60.528 60.000 0.00 0.00 0.00 3.93
2519 3115 2.732366 CATCGAGACGGGACAATGTAG 58.268 52.381 0.00 0.00 0.00 2.74
2520 3116 1.202371 GCATCGAGACGGGACAATGTA 60.202 52.381 0.00 0.00 0.00 2.29
2521 3117 0.460284 GCATCGAGACGGGACAATGT 60.460 55.000 0.00 0.00 0.00 2.71
2536 3132 2.103042 AAGCTCTTCGTGCCGCATC 61.103 57.895 0.00 0.00 0.00 3.91
2538 3134 3.043713 CAAGCTCTTCGTGCCGCA 61.044 61.111 0.00 0.00 0.00 5.69
2579 3175 1.131126 GGCCACAACATGATCGTCTTG 59.869 52.381 0.00 1.75 0.00 3.02
2584 3180 0.729116 GACTGGCCACAACATGATCG 59.271 55.000 0.00 0.00 0.00 3.69
2598 3194 4.370917 CATTTGGGAAACAACAAGACTGG 58.629 43.478 0.00 0.00 39.19 4.00
2600 3196 3.706086 AGCATTTGGGAAACAACAAGACT 59.294 39.130 0.00 0.00 39.19 3.24
2604 3200 3.960102 AGAGAGCATTTGGGAAACAACAA 59.040 39.130 0.00 0.00 39.19 2.83
2606 3202 5.705609 TTAGAGAGCATTTGGGAAACAAC 57.294 39.130 0.00 0.00 39.19 3.32
2611 3207 5.385198 ACAGTTTTAGAGAGCATTTGGGAA 58.615 37.500 0.00 0.00 0.00 3.97
2614 3210 7.148340 CCTTCTACAGTTTTAGAGAGCATTTGG 60.148 40.741 0.00 0.00 29.67 3.28
2616 3212 7.604545 GTCCTTCTACAGTTTTAGAGAGCATTT 59.395 37.037 0.00 0.00 29.67 2.32
2621 3217 7.434492 TGTTGTCCTTCTACAGTTTTAGAGAG 58.566 38.462 0.00 0.00 29.67 3.20
2630 3226 8.426489 TGTATTAAGTTGTTGTCCTTCTACAGT 58.574 33.333 0.00 0.00 33.88 3.55
2639 3235 7.234384 CGATCTTGTGTATTAAGTTGTTGTCC 58.766 38.462 0.00 0.00 0.00 4.02
2640 3236 7.095355 ACCGATCTTGTGTATTAAGTTGTTGTC 60.095 37.037 0.00 0.00 0.00 3.18
2642 3238 7.129109 ACCGATCTTGTGTATTAAGTTGTTG 57.871 36.000 0.00 0.00 0.00 3.33
2648 3244 4.928601 TCCGACCGATCTTGTGTATTAAG 58.071 43.478 0.00 0.00 0.00 1.85
2651 3247 3.717707 CATCCGACCGATCTTGTGTATT 58.282 45.455 0.00 0.00 0.00 1.89
2680 3276 4.541705 TGAAAACCAATGGAAGGTCTTGA 58.458 39.130 6.16 0.00 38.76 3.02
2700 3296 0.178967 TGGCCACTTTGGAATGCTGA 60.179 50.000 0.00 0.00 40.96 4.26
2701 3297 0.899720 ATGGCCACTTTGGAATGCTG 59.100 50.000 8.16 0.00 40.96 4.41
2753 3349 4.837093 AGGGATCCACAAAAACGATAGA 57.163 40.909 15.23 0.00 41.38 1.98
2759 3355 3.683365 ATGCAAGGGATCCACAAAAAC 57.317 42.857 15.23 0.00 0.00 2.43
2769 3365 7.564660 TGAATTCCATAAACTTATGCAAGGGAT 59.435 33.333 2.27 0.00 39.30 3.85
2779 3375 7.775053 AGGTTTGCTGAATTCCATAAACTTA 57.225 32.000 19.19 0.00 34.69 2.24
2817 3413 1.822186 GACACACCACGGGTTGCTT 60.822 57.895 0.00 0.00 31.02 3.91
2833 3429 2.688446 TGTATGGAGTGTGATCCGAGAC 59.312 50.000 0.00 0.00 42.77 3.36
2836 3432 4.753516 ATTTGTATGGAGTGTGATCCGA 57.246 40.909 0.00 0.00 42.77 4.55
2837 3433 5.449041 CCAAATTTGTATGGAGTGTGATCCG 60.449 44.000 16.73 0.00 42.77 4.18
2838 3434 5.679638 GCCAAATTTGTATGGAGTGTGATCC 60.680 44.000 16.73 0.00 39.12 3.36
2853 3449 8.034215 TCTTTTGATGTATAGTGGCCAAATTTG 58.966 33.333 7.24 11.40 0.00 2.32
2869 3465 7.523293 TTGTGACCACATATTCTTTTGATGT 57.477 32.000 3.47 0.00 41.52 3.06
2873 3469 9.258826 TGAAAATTGTGACCACATATTCTTTTG 57.741 29.630 3.47 0.00 41.52 2.44


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

AutoCloner maintained by Alex Coulton.