Multiple sequence alignment - TraesCS2D01G281600

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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 TraesCS2D01G281600 chr2D 100.000 5816 0 0 1 5816 354749070 354743255 0.000000e+00 10741.0
1 TraesCS2D01G281600 chr2D 88.176 296 31 3 3110 3403 459825818 459826111 3.340000e-92 350.0
2 TraesCS2D01G281600 chr2D 80.503 159 31 0 3877 4035 459826173 459826331 7.910000e-24 122.0
3 TraesCS2D01G281600 chr2B 93.815 2603 101 27 934 3505 421712793 421710220 0.000000e+00 3860.0
4 TraesCS2D01G281600 chr2B 96.361 1209 38 6 3504 4710 421710059 421708855 0.000000e+00 1984.0
5 TraesCS2D01G281600 chr2B 93.638 613 29 5 5206 5816 421708332 421707728 0.000000e+00 907.0
6 TraesCS2D01G281600 chr2B 90.612 490 35 6 4729 5208 421708863 421708375 1.770000e-179 640.0
7 TraesCS2D01G281600 chr2B 87.667 300 32 4 3106 3403 541094901 541095197 1.550000e-90 344.0
8 TraesCS2D01G281600 chr2B 83.448 145 18 6 1208 1349 541093581 541093722 4.730000e-26 130.0
9 TraesCS2D01G281600 chr2B 82.000 150 27 0 3886 4035 541095272 541095421 1.700000e-25 128.0
10 TraesCS2D01G281600 chr2A 95.399 1717 43 16 3504 5208 474312262 474310570 0.000000e+00 2700.0
11 TraesCS2D01G281600 chr2A 94.129 1056 47 8 1804 2856 474314643 474313600 0.000000e+00 1592.0
12 TraesCS2D01G281600 chr2A 93.376 785 41 3 1025 1809 474315439 474314666 0.000000e+00 1151.0
13 TraesCS2D01G281600 chr2A 93.689 618 27 2 2841 3446 474313276 474312659 0.000000e+00 915.0
14 TraesCS2D01G281600 chr2A 92.628 624 33 6 5206 5816 474310528 474309905 0.000000e+00 885.0
15 TraesCS2D01G281600 chr2A 83.882 608 75 13 252 841 474324638 474324036 5.090000e-155 558.0
16 TraesCS2D01G281600 chr2A 88.000 300 31 4 3106 3403 602800113 602800409 3.340000e-92 350.0
17 TraesCS2D01G281600 chr2A 95.333 150 5 1 2414 2561 474313597 474313448 2.710000e-58 237.0
18 TraesCS2D01G281600 chr2A 81.132 159 30 0 3877 4035 602800475 602800633 1.700000e-25 128.0
19 TraesCS2D01G281600 chr2A 98.148 54 0 1 969 1021 474315522 474315469 6.210000e-15 93.5
20 TraesCS2D01G281600 chr3B 80.634 852 125 28 137 960 256198552 256197713 1.780000e-174 623.0
21 TraesCS2D01G281600 chr7B 79.180 927 140 29 78 964 12549880 12548967 1.400000e-165 593.0
22 TraesCS2D01G281600 chr7B 79.726 656 86 24 128 754 114397811 114398448 1.160000e-116 431.0
23 TraesCS2D01G281600 chr5D 80.093 859 119 28 137 962 309399927 309400766 5.020000e-165 592.0
24 TraesCS2D01G281600 chr5D 80.247 729 102 26 252 961 424199302 424198597 1.450000e-140 510.0
25 TraesCS2D01G281600 chr5B 79.695 852 137 24 138 962 9581 10423 3.020000e-162 582.0
26 TraesCS2D01G281600 chr5B 87.671 73 8 1 3498 3570 600083688 600083759 3.730000e-12 84.2
27 TraesCS2D01G281600 chr6B 79.415 855 129 27 137 967 49765185 49764354 1.420000e-155 560.0
28 TraesCS2D01G281600 chr6B 89.552 67 6 1 3505 3570 345580074 345580008 3.730000e-12 84.2
29 TraesCS2D01G281600 chr7D 79.201 851 127 31 137 961 628600580 628601406 3.960000e-151 545.0
30 TraesCS2D01G281600 chr6A 89.231 65 6 1 3505 3568 340097850 340097786 4.830000e-11 80.5


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 TraesCS2D01G281600 chr2D 354743255 354749070 5815 True 10741.000000 10741 100.000000 1 5816 1 chr2D.!!$R1 5815
1 TraesCS2D01G281600 chr2D 459825818 459826331 513 False 236.000000 350 84.339500 3110 4035 2 chr2D.!!$F1 925
2 TraesCS2D01G281600 chr2B 421707728 421712793 5065 True 1847.750000 3860 93.606500 934 5816 4 chr2B.!!$R1 4882
3 TraesCS2D01G281600 chr2B 541093581 541095421 1840 False 200.666667 344 84.371667 1208 4035 3 chr2B.!!$F1 2827
4 TraesCS2D01G281600 chr2A 474309905 474315522 5617 True 1081.928571 2700 94.671714 969 5816 7 chr2A.!!$R2 4847
5 TraesCS2D01G281600 chr2A 474324036 474324638 602 True 558.000000 558 83.882000 252 841 1 chr2A.!!$R1 589
6 TraesCS2D01G281600 chr2A 602800113 602800633 520 False 239.000000 350 84.566000 3106 4035 2 chr2A.!!$F1 929
7 TraesCS2D01G281600 chr3B 256197713 256198552 839 True 623.000000 623 80.634000 137 960 1 chr3B.!!$R1 823
8 TraesCS2D01G281600 chr7B 12548967 12549880 913 True 593.000000 593 79.180000 78 964 1 chr7B.!!$R1 886
9 TraesCS2D01G281600 chr7B 114397811 114398448 637 False 431.000000 431 79.726000 128 754 1 chr7B.!!$F1 626
10 TraesCS2D01G281600 chr5D 309399927 309400766 839 False 592.000000 592 80.093000 137 962 1 chr5D.!!$F1 825
11 TraesCS2D01G281600 chr5D 424198597 424199302 705 True 510.000000 510 80.247000 252 961 1 chr5D.!!$R1 709
12 TraesCS2D01G281600 chr5B 9581 10423 842 False 582.000000 582 79.695000 138 962 1 chr5B.!!$F1 824
13 TraesCS2D01G281600 chr6B 49764354 49765185 831 True 560.000000 560 79.415000 137 967 1 chr6B.!!$R1 830
14 TraesCS2D01G281600 chr7D 628600580 628601406 826 False 545.000000 545 79.201000 137 961 1 chr7D.!!$F1 824

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
192 208 0.030603 GAGGTCCATCTCCCTCCCTT 60.031 60.000 0.00 0.0 41.22 3.95 F
412 469 0.034059 CTTCTCTGTGCAGTCCGGTT 59.966 55.000 0.00 0.0 0.00 4.44 F
645 717 0.106268 TTGGAGTGGTTGCCATGTGT 60.106 50.000 0.00 0.0 35.28 3.72 F
1026 1109 0.248054 CGCCACTTGTTGACACACAC 60.248 55.000 0.00 0.0 30.32 3.82 F
1027 1110 0.808125 GCCACTTGTTGACACACACA 59.192 50.000 0.00 0.0 30.32 3.72 F
1076 1185 1.452108 CCATTCCGCTTCACTCCCC 60.452 63.158 0.00 0.0 0.00 4.81 F
1077 1186 1.604378 CATTCCGCTTCACTCCCCT 59.396 57.895 0.00 0.0 0.00 4.79 F
1402 1514 2.430382 TTCCTCCGGCTGTGTTCGTC 62.430 60.000 0.00 0.0 0.00 4.20 F
3128 4137 1.007387 GAAGGTGGCACCAAAAGCG 60.007 57.895 36.28 0.0 41.95 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1169 0.618968 AGAGGGGAGTGAAGCGGAAT 60.619 55.000 0.00 0.00 0.00 3.01 R
2322 2584 1.002544 GACCTTGACAAGTGGAGGAGG 59.997 57.143 14.03 0.00 33.47 4.30 R
2629 3288 1.423584 TCAGCCAGAAGAACACCTCA 58.576 50.000 0.00 0.00 0.00 3.86 R
2856 3787 1.004394 CTTTCTTACCCTTCCGCCCTT 59.996 52.381 0.00 0.00 0.00 3.95 R
2862 3793 7.231925 TCCAAAACATTACTTTCTTACCCTTCC 59.768 37.037 0.00 0.00 0.00 3.46 R
3032 4041 7.715265 TTACACAAGTCTTCTGTTCATCTTC 57.285 36.000 0.00 0.00 0.00 2.87 R
3105 4114 3.244044 GCTTTTGGTGCCACCTTCAATAA 60.244 43.478 16.23 0.00 39.58 1.40 R
3242 4251 0.962356 CAGCTTGCCGGGAATCTGTT 60.962 55.000 26.01 4.32 0.00 3.16 R
4875 6266 2.156504 GCAAATGGATACTGATCGCTCG 59.843 50.000 0.00 0.00 32.28 5.03 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 2.741092 TCCCTGTGTTCGTCCTGC 59.259 61.111 0.00 0.00 0.00 4.85
18 19 1.837051 TCCCTGTGTTCGTCCTGCT 60.837 57.895 0.00 0.00 0.00 4.24
19 20 1.374758 CCCTGTGTTCGTCCTGCTC 60.375 63.158 0.00 0.00 0.00 4.26
20 21 1.668294 CCTGTGTTCGTCCTGCTCT 59.332 57.895 0.00 0.00 0.00 4.09
21 22 0.888619 CCTGTGTTCGTCCTGCTCTA 59.111 55.000 0.00 0.00 0.00 2.43
22 23 1.135257 CCTGTGTTCGTCCTGCTCTAG 60.135 57.143 0.00 0.00 0.00 2.43
23 24 1.813178 CTGTGTTCGTCCTGCTCTAGA 59.187 52.381 0.00 0.00 0.00 2.43
24 25 2.425312 CTGTGTTCGTCCTGCTCTAGAT 59.575 50.000 0.00 0.00 0.00 1.98
25 26 2.423892 TGTGTTCGTCCTGCTCTAGATC 59.576 50.000 0.00 0.00 0.00 2.75
26 27 2.685897 GTGTTCGTCCTGCTCTAGATCT 59.314 50.000 0.00 0.00 0.00 2.75
27 28 2.685388 TGTTCGTCCTGCTCTAGATCTG 59.315 50.000 5.18 0.00 0.00 2.90
28 29 2.946329 GTTCGTCCTGCTCTAGATCTGA 59.054 50.000 5.18 0.03 0.00 3.27
29 30 3.283259 TCGTCCTGCTCTAGATCTGAA 57.717 47.619 5.18 0.00 0.00 3.02
30 31 3.210227 TCGTCCTGCTCTAGATCTGAAG 58.790 50.000 5.18 3.63 0.00 3.02
31 32 2.293122 CGTCCTGCTCTAGATCTGAAGG 59.707 54.545 5.18 2.05 0.00 3.46
32 33 3.295973 GTCCTGCTCTAGATCTGAAGGT 58.704 50.000 5.18 0.00 0.00 3.50
33 34 3.068024 GTCCTGCTCTAGATCTGAAGGTG 59.932 52.174 5.18 0.00 0.00 4.00
34 35 2.224018 CCTGCTCTAGATCTGAAGGTGC 60.224 54.545 5.18 5.18 0.00 5.01
35 36 1.759445 TGCTCTAGATCTGAAGGTGCC 59.241 52.381 5.18 0.00 0.00 5.01
36 37 2.038659 GCTCTAGATCTGAAGGTGCCT 58.961 52.381 5.18 0.00 0.00 4.75
37 38 2.035832 GCTCTAGATCTGAAGGTGCCTC 59.964 54.545 5.18 0.00 0.00 4.70
38 39 2.627699 CTCTAGATCTGAAGGTGCCTCC 59.372 54.545 5.18 0.00 0.00 4.30
46 47 3.832175 AGGTGCCTCCTTCAGCAT 58.168 55.556 0.00 0.00 45.67 3.79
47 48 1.302285 AGGTGCCTCCTTCAGCATG 59.698 57.895 0.00 0.00 45.67 4.06
48 49 1.001641 GGTGCCTCCTTCAGCATGT 60.002 57.895 0.00 0.00 41.86 3.21
49 50 1.310933 GGTGCCTCCTTCAGCATGTG 61.311 60.000 0.00 0.00 41.86 3.21
50 51 0.607489 GTGCCTCCTTCAGCATGTGT 60.607 55.000 0.00 0.00 41.86 3.72
51 52 0.111061 TGCCTCCTTCAGCATGTGTT 59.889 50.000 0.00 0.00 37.40 3.32
52 53 1.350684 TGCCTCCTTCAGCATGTGTTA 59.649 47.619 0.00 0.00 37.40 2.41
53 54 2.025981 TGCCTCCTTCAGCATGTGTTAT 60.026 45.455 0.00 0.00 37.40 1.89
54 55 3.019564 GCCTCCTTCAGCATGTGTTATT 58.980 45.455 0.00 0.00 37.40 1.40
55 56 3.181493 GCCTCCTTCAGCATGTGTTATTG 60.181 47.826 0.00 0.00 37.40 1.90
56 57 3.181493 CCTCCTTCAGCATGTGTTATTGC 60.181 47.826 0.00 0.00 39.17 3.56
57 58 2.754552 TCCTTCAGCATGTGTTATTGCC 59.245 45.455 0.00 0.00 39.72 4.52
58 59 2.756760 CCTTCAGCATGTGTTATTGCCT 59.243 45.455 0.00 0.00 39.72 4.75
59 60 3.181493 CCTTCAGCATGTGTTATTGCCTC 60.181 47.826 0.00 0.00 39.72 4.70
60 61 3.354948 TCAGCATGTGTTATTGCCTCT 57.645 42.857 0.00 0.00 39.72 3.69
61 62 3.273434 TCAGCATGTGTTATTGCCTCTC 58.727 45.455 0.00 0.00 39.72 3.20
62 63 2.357009 CAGCATGTGTTATTGCCTCTCC 59.643 50.000 0.00 0.00 39.72 3.71
63 64 1.678101 GCATGTGTTATTGCCTCTCCC 59.322 52.381 0.00 0.00 32.66 4.30
64 65 2.945440 GCATGTGTTATTGCCTCTCCCA 60.945 50.000 0.00 0.00 32.66 4.37
65 66 2.787473 TGTGTTATTGCCTCTCCCAG 57.213 50.000 0.00 0.00 0.00 4.45
66 67 1.281867 TGTGTTATTGCCTCTCCCAGG 59.718 52.381 0.00 0.00 46.82 4.45
74 75 1.301293 CCTCTCCCAGGCTTTGTCC 59.699 63.158 0.00 0.00 34.56 4.02
75 76 1.078848 CTCTCCCAGGCTTTGTCCG 60.079 63.158 0.00 0.00 0.00 4.79
76 77 2.045926 CTCCCAGGCTTTGTCCGG 60.046 66.667 0.00 0.00 0.00 5.14
86 87 0.036164 CTTTGTCCGGGTCATGGTGA 59.964 55.000 0.00 0.00 0.00 4.02
92 93 2.123726 GGGTCATGGTGATGGGGC 60.124 66.667 0.00 0.00 0.00 5.80
94 95 2.272146 GTCATGGTGATGGGGCGT 59.728 61.111 0.00 0.00 0.00 5.68
95 96 1.524961 GTCATGGTGATGGGGCGTA 59.475 57.895 0.00 0.00 0.00 4.42
124 125 2.175715 GGATTGGGGTAATCTCTTGGCT 59.824 50.000 0.00 0.00 43.81 4.75
164 180 0.765135 TGTCGGTCCCCTTCCTGAAA 60.765 55.000 0.00 0.00 0.00 2.69
170 186 0.836400 TCCCCTTCCTGAAAGCGACT 60.836 55.000 0.00 0.00 33.29 4.18
171 187 0.902531 CCCCTTCCTGAAAGCGACTA 59.097 55.000 0.00 0.00 33.29 2.59
191 207 1.231751 TGAGGTCCATCTCCCTCCCT 61.232 60.000 3.41 0.00 45.56 4.20
192 208 0.030603 GAGGTCCATCTCCCTCCCTT 60.031 60.000 0.00 0.00 41.22 3.95
198 239 0.267356 CATCTCCCTCCCTTCCTCCT 59.733 60.000 0.00 0.00 0.00 3.69
203 244 1.398234 CCTCCCTTCCTCCTTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
206 247 0.196118 TCCCTTCCTCCTTCCCTTGT 59.804 55.000 0.00 0.00 0.00 3.16
211 252 0.104144 TCCTCCTTCCCTTGTTCCCA 60.104 55.000 0.00 0.00 0.00 4.37
226 267 2.558359 GTTCCCAGGTGAAAATCCACAG 59.442 50.000 0.00 0.00 38.74 3.66
227 268 0.890683 CCCAGGTGAAAATCCACAGC 59.109 55.000 0.00 0.00 38.74 4.40
266 320 1.798813 GGTGCTCTTAAAGGTGTCGTG 59.201 52.381 0.00 0.00 0.00 4.35
307 363 1.113788 TGGTCTGCAGCAAGCTTTTT 58.886 45.000 9.47 0.00 45.94 1.94
315 371 2.204237 CAGCAAGCTTTTTGGTGTTCC 58.796 47.619 7.73 0.00 41.46 3.62
323 379 1.561643 TTTTGGTGTTCCTGTTGGCA 58.438 45.000 0.00 0.00 34.23 4.92
341 397 1.915769 AGCGGCTCCTTCTTCCAGT 60.916 57.895 0.00 0.00 0.00 4.00
412 469 0.034059 CTTCTCTGTGCAGTCCGGTT 59.966 55.000 0.00 0.00 0.00 4.44
477 534 1.664873 GTCCCCTTTATGGCGAACTC 58.335 55.000 0.00 0.00 0.00 3.01
500 557 0.671796 ACGTCGATGGAAGTGTGTCA 59.328 50.000 9.90 0.00 33.47 3.58
540 597 1.928868 CCCTCCTGATGGCTTTGTTT 58.071 50.000 0.00 0.00 0.00 2.83
554 611 0.825425 TTGTTTCCCATTGCTCGCCA 60.825 50.000 0.00 0.00 0.00 5.69
583 640 1.169577 GAAGTGCTCTCGTCCTCTGA 58.830 55.000 0.00 0.00 0.00 3.27
619 690 3.042871 TGCATGCAATTTTTGTCCTCC 57.957 42.857 20.30 0.00 0.00 4.30
644 716 0.314935 GTTGGAGTGGTTGCCATGTG 59.685 55.000 0.00 0.00 35.28 3.21
645 717 0.106268 TTGGAGTGGTTGCCATGTGT 60.106 50.000 0.00 0.00 35.28 3.72
654 726 2.545742 GGTTGCCATGTGTTTTCAGGTC 60.546 50.000 0.00 0.00 0.00 3.85
670 742 1.696336 AGGTCTTCTTGCTTGCTCTGA 59.304 47.619 0.00 0.00 0.00 3.27
695 768 1.871126 GCAGCTCCACTTTGCCTTCC 61.871 60.000 0.00 0.00 31.79 3.46
699 772 1.856265 CTCCACTTTGCCTTCCGTGC 61.856 60.000 0.00 0.00 0.00 5.34
735 810 2.917227 CCTTTGGCGCAACCCCTT 60.917 61.111 10.83 0.00 37.83 3.95
741 816 2.361230 GCGCAACCCCTTTAGCCT 60.361 61.111 0.30 0.00 0.00 4.58
833 909 2.037847 GCCTTGGGGTTGCATCCT 59.962 61.111 13.47 0.00 34.45 3.24
846 922 5.508320 GGGTTGCATCCTCGTTTTTCTTTTA 60.508 40.000 13.47 0.00 0.00 1.52
848 924 6.089417 GGTTGCATCCTCGTTTTTCTTTTATG 59.911 38.462 6.56 0.00 0.00 1.90
894 971 6.496911 TCTTATAATCCTGATCGGTTGATGGA 59.503 38.462 0.00 0.00 34.09 3.41
900 977 3.313526 CCTGATCGGTTGATGGATTTGTC 59.686 47.826 0.00 0.00 34.09 3.18
905 982 5.058149 TCGGTTGATGGATTTGTCAATTG 57.942 39.130 0.00 0.00 36.79 2.32
913 990 5.766150 TGGATTTGTCAATTGAAAGTCGT 57.234 34.783 10.35 0.00 0.00 4.34
925 1003 3.057019 TGAAAGTCGTGTGAAATCGAGG 58.943 45.455 0.00 0.00 36.76 4.63
943 1022 0.831307 GGCCTACTCGGATTGGTTCT 59.169 55.000 0.00 0.00 33.16 3.01
1021 1104 1.514678 GGATGCGCCACTTGTTGACA 61.515 55.000 4.18 0.00 36.34 3.58
1022 1105 0.385974 GATGCGCCACTTGTTGACAC 60.386 55.000 4.18 0.00 0.00 3.67
1023 1106 1.100463 ATGCGCCACTTGTTGACACA 61.100 50.000 4.18 0.00 0.00 3.72
1024 1107 1.298339 GCGCCACTTGTTGACACAC 60.298 57.895 0.00 0.00 30.32 3.82
1025 1108 1.987704 GCGCCACTTGTTGACACACA 61.988 55.000 0.00 0.00 30.32 3.72
1026 1109 0.248054 CGCCACTTGTTGACACACAC 60.248 55.000 0.00 0.00 30.32 3.82
1027 1110 0.808125 GCCACTTGTTGACACACACA 59.192 50.000 0.00 0.00 30.32 3.72
1028 1111 1.467374 GCCACTTGTTGACACACACAC 60.467 52.381 0.00 0.00 30.32 3.82
1029 1112 1.809547 CCACTTGTTGACACACACACA 59.190 47.619 0.00 0.00 30.32 3.72
1030 1113 2.414029 CCACTTGTTGACACACACACAC 60.414 50.000 0.00 0.00 30.32 3.82
1031 1114 2.225255 CACTTGTTGACACACACACACA 59.775 45.455 0.00 0.00 30.32 3.72
1032 1115 2.225491 ACTTGTTGACACACACACACAC 59.775 45.455 0.00 0.00 30.32 3.82
1033 1116 1.884235 TGTTGACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
1034 1117 1.533299 TGTTGACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
1067 1176 2.586792 GCTCCAGTCCATTCCGCT 59.413 61.111 0.00 0.00 0.00 5.52
1076 1185 1.452108 CCATTCCGCTTCACTCCCC 60.452 63.158 0.00 0.00 0.00 4.81
1077 1186 1.604378 CATTCCGCTTCACTCCCCT 59.396 57.895 0.00 0.00 0.00 4.79
1402 1514 2.430382 TTCCTCCGGCTGTGTTCGTC 62.430 60.000 0.00 0.00 0.00 4.20
1593 1799 8.917088 AGAATTACCCTATCCATTGTTGAAATG 58.083 33.333 0.00 0.00 0.00 2.32
1641 1847 9.790297 ATAGTCCATATATCACCCTTGATTACT 57.210 33.333 0.00 0.00 39.66 2.24
1658 1864 8.621532 TTGATTACTAGCACAAGAAAGATGTT 57.378 30.769 0.00 0.00 0.00 2.71
1661 1867 7.596749 TTACTAGCACAAGAAAGATGTTAGC 57.403 36.000 0.00 0.00 32.22 3.09
1663 1869 5.872070 ACTAGCACAAGAAAGATGTTAGCTC 59.128 40.000 0.00 0.00 33.62 4.09
1718 1924 6.773976 AGCAATAGTTAAGCTGGCAATTTA 57.226 33.333 0.00 0.00 37.20 1.40
1778 1984 7.332926 TGTGCAAATAATTAAAATTGGACGCAT 59.667 29.630 19.14 0.00 44.09 4.73
1796 2002 3.551046 CGCATAGCCGACTTGAAGAGTAT 60.551 47.826 0.00 0.00 39.19 2.12
1826 2088 4.994217 AAGAACAACTCTAGCTCAGAAAGC 59.006 41.667 0.00 0.00 42.11 3.51
2339 2994 3.492102 TTTCCTCCTCCACTTGTCAAG 57.508 47.619 11.17 11.17 0.00 3.02
2372 3027 8.279103 GCTCTTATTTTTCAGATAGATTCGGTG 58.721 37.037 0.00 0.00 0.00 4.94
2408 3063 9.739276 AATGTTTTGGTGAGTAATCTTATGAGA 57.261 29.630 0.00 0.00 36.09 3.27
2629 3288 9.906660 ATTGTTTGTTTTACATCATATGAACGT 57.093 25.926 9.99 12.31 0.00 3.99
2835 3494 6.370166 GTGCAAGCTAAGATAGTTTTCACTCT 59.630 38.462 8.61 0.00 39.00 3.24
2836 3495 6.936900 TGCAAGCTAAGATAGTTTTCACTCTT 59.063 34.615 0.00 0.00 34.06 2.85
2837 3496 7.118390 TGCAAGCTAAGATAGTTTTCACTCTTC 59.882 37.037 0.00 0.00 34.06 2.87
2838 3497 7.118390 GCAAGCTAAGATAGTTTTCACTCTTCA 59.882 37.037 0.00 0.00 34.06 3.02
2839 3498 8.655092 CAAGCTAAGATAGTTTTCACTCTTCAG 58.345 37.037 0.00 0.00 34.06 3.02
2862 3793 6.533012 CAGACTGTATATCATAATGAAGGGCG 59.467 42.308 0.00 0.00 0.00 6.13
2928 3926 8.196771 CCTTTTGTAAGATATTTGCAGCCATTA 58.803 33.333 0.00 0.00 32.92 1.90
3062 4071 8.450578 TGAACAGAAGACTTGTGTAATTGATT 57.549 30.769 17.49 1.17 35.96 2.57
3066 4075 9.125026 ACAGAAGACTTGTGTAATTGATTTTCT 57.875 29.630 15.85 0.00 35.14 2.52
3128 4137 1.007387 GAAGGTGGCACCAAAAGCG 60.007 57.895 36.28 0.00 41.95 4.68
3242 4251 3.669536 TGACATTGTTATTGTGGCGAGA 58.330 40.909 0.00 0.00 0.00 4.04
3254 4263 1.521681 GGCGAGAACAGATTCCCGG 60.522 63.158 0.00 0.00 36.62 5.73
3418 4427 0.188342 AGATGGCCCACCTGTGTTTT 59.812 50.000 0.00 0.00 36.63 2.43
3637 5026 7.894753 TGCCAATGAATTTGATTAGGATACA 57.105 32.000 0.00 0.00 37.53 2.29
3739 5128 3.492309 GGATGTGTCATCTGTGGCTCTAG 60.492 52.174 9.16 0.00 0.00 2.43
3836 5225 3.591023 TCAATTCGCCTGTGAATTCGTA 58.409 40.909 14.07 3.07 44.55 3.43
3841 5230 5.365403 TTCGCCTGTGAATTCGTATTTTT 57.635 34.783 0.04 0.00 0.00 1.94
4039 5429 6.806739 GCAATGGAGGTTTGTTCTTTACATAC 59.193 38.462 0.00 0.00 37.80 2.39
4085 5475 3.938963 ACAGCGTTCTCTTTTCAGTTTCA 59.061 39.130 0.00 0.00 0.00 2.69
4537 5927 1.188863 TACTCTAGGGTTCAACCGCC 58.811 55.000 0.00 0.00 39.83 6.13
4618 6008 4.274459 GTGAGCCATGATGATTTCTACCAC 59.726 45.833 0.00 0.00 0.00 4.16
4714 6104 1.131303 ACCCCCGAGTGGTGAATTCA 61.131 55.000 3.38 3.38 33.94 2.57
4715 6105 0.676782 CCCCCGAGTGGTGAATTCAC 60.677 60.000 27.16 27.16 45.72 3.18
4753 6143 2.086869 GTTAGCAGTGCATGGACATGT 58.913 47.619 20.21 0.00 40.80 3.21
4760 6150 4.096231 GCAGTGCATGGACATGTAAATACA 59.904 41.667 20.21 0.00 40.80 2.29
4964 6355 2.159099 TCGCGTTTATCTTGAGGCAGAT 60.159 45.455 5.77 0.00 37.31 2.90
4970 6361 6.425504 CGTTTATCTTGAGGCAGATGATTTC 58.574 40.000 0.00 0.00 35.08 2.17
5182 6588 0.529555 GGCAGCAGGACTCGAGATTC 60.530 60.000 21.68 7.00 0.00 2.52
5185 6591 1.941734 GCAGGACTCGAGATTCGCG 60.942 63.158 21.68 0.00 40.21 5.87
5195 6602 1.287425 GAGATTCGCGTCGGGAATTT 58.713 50.000 30.64 26.68 43.47 1.82
5296 6749 3.045601 ACATTGTAGTGCCTGTCTGAC 57.954 47.619 0.00 0.00 0.00 3.51
5351 6805 6.323203 ACACAAAATGTTCTTCCTCTCATG 57.677 37.500 0.00 0.00 38.98 3.07
5372 6837 0.315251 GTTCACAAAAGCTCCAGCCC 59.685 55.000 0.00 0.00 43.38 5.19
5405 6870 1.514678 TTGTGTCGCATGGAGCCAAC 61.515 55.000 0.00 0.00 41.38 3.77
5596 7062 2.862541 CCTGGACCTGAACAACAATCA 58.137 47.619 0.00 0.00 0.00 2.57
5607 7073 6.639686 CCTGAACAACAATCAAAGTCTCATTG 59.360 38.462 0.00 0.00 34.29 2.82
5609 7075 7.420002 TGAACAACAATCAAAGTCTCATTGAG 58.580 34.615 7.38 7.38 39.92 3.02
5610 7076 6.949352 ACAACAATCAAAGTCTCATTGAGT 57.051 33.333 13.23 0.00 39.92 3.41
5614 7080 9.390795 CAACAATCAAAGTCTCATTGAGTAAAG 57.609 33.333 13.23 2.41 39.92 1.85
5623 7089 7.038659 AGTCTCATTGAGTAAAGTATCTGCAC 58.961 38.462 13.23 0.17 0.00 4.57
5627 7093 7.330262 TCATTGAGTAAAGTATCTGCACATCA 58.670 34.615 0.00 0.00 0.00 3.07
5652 7118 7.847711 ACATCTAGGTTGCAGACTAGAATAT 57.152 36.000 24.35 14.55 46.12 1.28
5653 7119 7.665690 ACATCTAGGTTGCAGACTAGAATATG 58.334 38.462 24.35 20.88 46.12 1.78
5732 7198 7.222031 GGCCCGATTTTTACAGAAACATATTTC 59.778 37.037 0.00 0.00 44.02 2.17
5780 7246 1.244816 GGCCCTGTACAAACCAAGTC 58.755 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.816863 GAGCAGGACGAACACAGGGA 61.817 60.000 0.00 0.00 0.00 4.20
1 2 1.374758 GAGCAGGACGAACACAGGG 60.375 63.158 0.00 0.00 0.00 4.45
2 3 0.888619 TAGAGCAGGACGAACACAGG 59.111 55.000 0.00 0.00 0.00 4.00
3 4 1.813178 TCTAGAGCAGGACGAACACAG 59.187 52.381 0.00 0.00 0.00 3.66
4 5 1.905637 TCTAGAGCAGGACGAACACA 58.094 50.000 0.00 0.00 0.00 3.72
5 6 2.685897 AGATCTAGAGCAGGACGAACAC 59.314 50.000 11.20 0.00 0.00 3.32
6 7 2.685388 CAGATCTAGAGCAGGACGAACA 59.315 50.000 11.20 0.00 0.00 3.18
7 8 2.946329 TCAGATCTAGAGCAGGACGAAC 59.054 50.000 11.20 0.00 0.00 3.95
8 9 3.283259 TCAGATCTAGAGCAGGACGAA 57.717 47.619 11.20 0.00 0.00 3.85
9 10 3.210227 CTTCAGATCTAGAGCAGGACGA 58.790 50.000 11.20 0.00 0.00 4.20
10 11 2.293122 CCTTCAGATCTAGAGCAGGACG 59.707 54.545 11.20 5.14 0.00 4.79
11 12 3.068024 CACCTTCAGATCTAGAGCAGGAC 59.932 52.174 17.22 0.00 0.00 3.85
12 13 3.295093 CACCTTCAGATCTAGAGCAGGA 58.705 50.000 17.22 8.72 0.00 3.86
13 14 2.224018 GCACCTTCAGATCTAGAGCAGG 60.224 54.545 11.20 10.79 0.00 4.85
14 15 2.224018 GGCACCTTCAGATCTAGAGCAG 60.224 54.545 11.20 1.83 0.00 4.24
15 16 1.759445 GGCACCTTCAGATCTAGAGCA 59.241 52.381 11.20 0.00 0.00 4.26
16 17 2.035832 GAGGCACCTTCAGATCTAGAGC 59.964 54.545 0.00 0.00 0.00 4.09
17 18 2.627699 GGAGGCACCTTCAGATCTAGAG 59.372 54.545 0.00 0.00 35.41 2.43
18 19 2.672098 GGAGGCACCTTCAGATCTAGA 58.328 52.381 0.00 0.00 35.41 2.43
30 31 1.001641 ACATGCTGAAGGAGGCACC 60.002 57.895 0.00 0.00 41.39 5.01
31 32 0.607489 ACACATGCTGAAGGAGGCAC 60.607 55.000 0.00 0.00 41.39 5.01
32 33 0.111061 AACACATGCTGAAGGAGGCA 59.889 50.000 0.00 0.00 42.80 4.75
33 34 2.113860 TAACACATGCTGAAGGAGGC 57.886 50.000 0.00 0.00 0.00 4.70
34 35 3.181493 GCAATAACACATGCTGAAGGAGG 60.181 47.826 0.00 0.00 39.46 4.30
35 36 3.181493 GGCAATAACACATGCTGAAGGAG 60.181 47.826 0.00 0.00 42.20 3.69
36 37 2.754552 GGCAATAACACATGCTGAAGGA 59.245 45.455 0.00 0.00 42.20 3.36
37 38 2.756760 AGGCAATAACACATGCTGAAGG 59.243 45.455 0.00 0.00 42.20 3.46
38 39 3.693085 AGAGGCAATAACACATGCTGAAG 59.307 43.478 0.00 0.00 42.20 3.02
39 40 3.689347 AGAGGCAATAACACATGCTGAA 58.311 40.909 0.00 0.00 42.20 3.02
40 41 3.273434 GAGAGGCAATAACACATGCTGA 58.727 45.455 0.00 0.00 42.20 4.26
41 42 2.357009 GGAGAGGCAATAACACATGCTG 59.643 50.000 0.00 0.00 42.20 4.41
42 43 2.648059 GGAGAGGCAATAACACATGCT 58.352 47.619 0.00 0.00 42.20 3.79
43 44 1.678101 GGGAGAGGCAATAACACATGC 59.322 52.381 0.00 0.00 41.82 4.06
44 45 2.947652 CTGGGAGAGGCAATAACACATG 59.052 50.000 0.00 0.00 0.00 3.21
45 46 2.092212 CCTGGGAGAGGCAATAACACAT 60.092 50.000 0.00 0.00 34.01 3.21
46 47 1.281867 CCTGGGAGAGGCAATAACACA 59.718 52.381 0.00 0.00 34.01 3.72
47 48 2.044123 CCTGGGAGAGGCAATAACAC 57.956 55.000 0.00 0.00 34.01 3.32
56 57 1.301293 GGACAAAGCCTGGGAGAGG 59.699 63.158 0.00 0.00 46.13 3.69
57 58 1.078848 CGGACAAAGCCTGGGAGAG 60.079 63.158 0.00 0.00 0.00 3.20
58 59 2.592993 CCGGACAAAGCCTGGGAGA 61.593 63.158 0.00 0.00 0.00 3.71
59 60 2.045926 CCGGACAAAGCCTGGGAG 60.046 66.667 0.00 0.00 0.00 4.30
60 61 3.646715 CCCGGACAAAGCCTGGGA 61.647 66.667 0.73 0.00 41.41 4.37
61 62 3.920093 GACCCGGACAAAGCCTGGG 62.920 68.421 0.73 5.52 43.21 4.45
62 63 2.359975 GACCCGGACAAAGCCTGG 60.360 66.667 0.73 0.00 38.20 4.45
63 64 1.002134 ATGACCCGGACAAAGCCTG 60.002 57.895 0.73 0.00 0.00 4.85
64 65 1.002134 CATGACCCGGACAAAGCCT 60.002 57.895 0.73 0.00 0.00 4.58
65 66 2.046285 CCATGACCCGGACAAAGCC 61.046 63.158 0.73 0.00 0.00 4.35
66 67 1.303317 ACCATGACCCGGACAAAGC 60.303 57.895 0.73 0.00 0.00 3.51
67 68 0.036164 TCACCATGACCCGGACAAAG 59.964 55.000 0.73 1.49 0.00 2.77
68 69 0.695924 ATCACCATGACCCGGACAAA 59.304 50.000 0.73 0.00 0.00 2.83
69 70 0.035534 CATCACCATGACCCGGACAA 60.036 55.000 0.73 0.00 30.57 3.18
70 71 1.601703 CATCACCATGACCCGGACA 59.398 57.895 0.73 2.81 30.57 4.02
71 72 1.153168 CCATCACCATGACCCGGAC 60.153 63.158 0.73 0.00 30.57 4.79
72 73 2.374525 CCCATCACCATGACCCGGA 61.375 63.158 0.73 0.00 30.57 5.14
73 74 2.192979 CCCATCACCATGACCCGG 59.807 66.667 0.00 0.00 30.57 5.73
74 75 2.192979 CCCCATCACCATGACCCG 59.807 66.667 0.00 0.00 30.57 5.28
75 76 2.123726 GCCCCATCACCATGACCC 60.124 66.667 0.00 0.00 30.57 4.46
76 77 1.978455 TACGCCCCATCACCATGACC 61.978 60.000 0.00 0.00 30.57 4.02
92 93 1.447643 CCCAATCCAGGGCTCTACG 59.552 63.158 0.00 0.00 43.10 3.51
107 108 0.918983 CCAGCCAAGAGATTACCCCA 59.081 55.000 0.00 0.00 0.00 4.96
150 166 0.673956 GTCGCTTTCAGGAAGGGGAC 60.674 60.000 19.96 19.96 46.75 4.46
164 180 2.235016 GAGATGGACCTCATAGTCGCT 58.765 52.381 0.00 0.00 37.66 4.93
191 207 1.073098 GGGAACAAGGGAAGGAGGAA 58.927 55.000 0.00 0.00 0.00 3.36
192 208 0.104144 TGGGAACAAGGGAAGGAGGA 60.104 55.000 0.00 0.00 37.44 3.71
198 239 1.227249 TTCACCTGGGAACAAGGGAA 58.773 50.000 0.00 0.00 42.06 3.97
203 244 2.962421 GTGGATTTTCACCTGGGAACAA 59.038 45.455 0.00 0.00 42.06 2.83
206 247 2.875296 CTGTGGATTTTCACCTGGGAA 58.125 47.619 0.00 0.00 36.87 3.97
211 252 0.779997 AGGGCTGTGGATTTTCACCT 59.220 50.000 0.00 0.00 36.87 4.00
241 282 0.963962 ACCTTTAAGAGCACCGTCGA 59.036 50.000 0.00 0.00 0.00 4.20
266 320 1.328279 CTCCTTCCCACAAACCCAAC 58.672 55.000 0.00 0.00 0.00 3.77
307 363 1.827789 GCTGCCAACAGGAACACCA 60.828 57.895 0.00 0.00 44.63 4.17
323 379 1.915769 ACTGGAAGAAGGAGCCGCT 60.916 57.895 0.00 0.00 37.43 5.52
341 397 3.625897 CACAGCGGGGAGTCACCA 61.626 66.667 13.09 0.00 41.20 4.17
412 469 3.980989 CGTCGACCCACCGGACAA 61.981 66.667 9.46 0.00 0.00 3.18
465 522 0.241749 ACGTGACGAGTTCGCCATAA 59.758 50.000 13.70 0.00 44.43 1.90
477 534 0.386858 ACACTTCCATCGACGTGACG 60.387 55.000 2.24 2.24 39.93 4.35
481 538 0.671796 TGACACACTTCCATCGACGT 59.328 50.000 0.00 0.00 0.00 4.34
485 542 2.416547 GACCAATGACACACTTCCATCG 59.583 50.000 0.00 0.00 0.00 3.84
500 557 1.033746 CGAGCCATGCCAAGACCAAT 61.034 55.000 0.00 0.00 0.00 3.16
529 586 1.980036 AGCAATGGGAAACAAAGCCAT 59.020 42.857 0.00 0.00 34.58 4.40
540 597 1.451927 GACATGGCGAGCAATGGGA 60.452 57.895 15.98 0.00 31.81 4.37
554 611 3.056250 ACGAGAGCACTTCATGAAGACAT 60.056 43.478 36.15 22.17 40.79 3.06
583 640 1.216710 GCAAGCCGCAGACTCTAGT 59.783 57.895 0.00 0.00 41.79 2.57
619 690 2.021722 CAACCACTCCAACACACCG 58.978 57.895 0.00 0.00 0.00 4.94
644 716 3.067320 AGCAAGCAAGAAGACCTGAAAAC 59.933 43.478 0.00 0.00 0.00 2.43
645 717 3.290710 AGCAAGCAAGAAGACCTGAAAA 58.709 40.909 0.00 0.00 0.00 2.29
654 726 3.597255 TCTCATCAGAGCAAGCAAGAAG 58.403 45.455 0.00 0.00 41.81 2.85
670 742 1.949547 GCAAAGTGGAGCTGCTCTCAT 60.950 52.381 27.09 11.65 43.70 2.90
699 772 1.475441 GAAGAAGCTCGCCATCGACG 61.475 60.000 0.00 0.00 40.21 5.12
858 934 9.664332 GATCAGGATTATAAGAGCACAACATAT 57.336 33.333 0.00 0.00 0.00 1.78
882 959 5.418524 TCAATTGACAAATCCATCAACCGAT 59.581 36.000 3.38 0.00 37.64 4.18
883 960 4.764308 TCAATTGACAAATCCATCAACCGA 59.236 37.500 3.38 0.00 37.64 4.69
894 971 6.130298 TCACACGACTTTCAATTGACAAAT 57.870 33.333 7.89 0.00 0.00 2.32
900 977 5.439828 TCGATTTCACACGACTTTCAATTG 58.560 37.500 0.00 0.00 33.62 2.32
905 982 2.159827 GCCTCGATTTCACACGACTTTC 60.160 50.000 0.00 0.00 34.82 2.62
913 990 2.961526 GAGTAGGCCTCGATTTCACA 57.038 50.000 9.68 0.00 0.00 3.58
925 1003 3.306156 GGATAGAACCAATCCGAGTAGGC 60.306 52.174 0.00 0.00 40.77 3.93
1021 1104 1.810151 GTTGAAGGTGTGTGTGTGTGT 59.190 47.619 0.00 0.00 0.00 3.72
1022 1105 1.132262 GGTTGAAGGTGTGTGTGTGTG 59.868 52.381 0.00 0.00 0.00 3.82
1023 1106 1.004277 AGGTTGAAGGTGTGTGTGTGT 59.996 47.619 0.00 0.00 0.00 3.72
1024 1107 1.670811 GAGGTTGAAGGTGTGTGTGTG 59.329 52.381 0.00 0.00 0.00 3.82
1025 1108 1.559682 AGAGGTTGAAGGTGTGTGTGT 59.440 47.619 0.00 0.00 0.00 3.72
1026 1109 2.213499 GAGAGGTTGAAGGTGTGTGTG 58.787 52.381 0.00 0.00 0.00 3.82
1027 1110 1.202533 CGAGAGGTTGAAGGTGTGTGT 60.203 52.381 0.00 0.00 0.00 3.72
1028 1111 1.502231 CGAGAGGTTGAAGGTGTGTG 58.498 55.000 0.00 0.00 0.00 3.82
1029 1112 3.989104 CGAGAGGTTGAAGGTGTGT 57.011 52.632 0.00 0.00 0.00 3.72
1060 1169 0.618968 AGAGGGGAGTGAAGCGGAAT 60.619 55.000 0.00 0.00 0.00 3.01
1067 1176 3.760035 GCGCGAGAGGGGAGTGAA 61.760 66.667 12.10 0.00 45.27 3.18
1076 1185 2.411290 GAGGAGGAAGCGCGAGAG 59.589 66.667 12.10 0.00 0.00 3.20
1077 1186 3.141488 GGAGGAGGAAGCGCGAGA 61.141 66.667 12.10 0.00 0.00 4.04
1402 1514 1.833434 TTTTACTGCAACGACCGCGG 61.833 55.000 26.86 26.86 43.17 6.46
1593 1799 1.882623 CCTCCTTCCAGTGAGCAAAAC 59.117 52.381 0.00 0.00 0.00 2.43
1641 1847 5.793817 TGAGCTAACATCTTTCTTGTGCTA 58.206 37.500 0.00 0.00 29.50 3.49
1658 1864 6.152323 AGTTACGTCCAGATAAACTTGAGCTA 59.848 38.462 0.00 0.00 0.00 3.32
1696 1902 7.492344 ACAATAAATTGCCAGCTTAACTATTGC 59.508 33.333 2.60 0.00 41.38 3.56
1778 1984 6.296803 TCATAGATACTCTTCAAGTCGGCTA 58.703 40.000 0.00 0.00 39.55 3.93
1796 2002 7.394641 TCTGAGCTAGAGTTGTTCTTTCATAGA 59.605 37.037 0.00 0.00 37.36 1.98
1826 2088 7.406799 ACTCGGAAAAACATTTGCATTTTAG 57.593 32.000 0.00 0.00 0.00 1.85
1853 2115 2.991250 AGCAGCATTTACCGAGAACAT 58.009 42.857 0.00 0.00 0.00 2.71
1983 2245 8.846211 CCTGGAAAAGTTCAGTATGTAAAAAGA 58.154 33.333 0.00 0.00 37.40 2.52
2261 2523 1.186917 TTCCAGCCAACCCAGCATTG 61.187 55.000 0.00 0.00 0.00 2.82
2322 2584 1.002544 GACCTTGACAAGTGGAGGAGG 59.997 57.143 14.03 0.00 33.47 4.30
2339 2994 6.749923 ATCTGAAAAATAAGAGCAGTGACC 57.250 37.500 0.00 0.00 0.00 4.02
2408 3063 6.377912 AGGAGTTACAGCCTATTATGAGAGT 58.622 40.000 0.00 0.00 31.31 3.24
2610 3269 7.148474 ACACCTCACGTTCATATGATGTAAAAC 60.148 37.037 6.17 0.00 0.00 2.43
2629 3288 1.423584 TCAGCCAGAAGAACACCTCA 58.576 50.000 0.00 0.00 0.00 3.86
2742 3401 7.439157 TGTCCAGTGAATGAGATTAAAGTTG 57.561 36.000 0.00 0.00 0.00 3.16
2791 3450 6.291648 TGCACTATCCAAATATGCCAAAAA 57.708 33.333 0.00 0.00 35.37 1.94
2792 3451 5.929058 TGCACTATCCAAATATGCCAAAA 57.071 34.783 0.00 0.00 35.37 2.44
2795 3454 3.318839 GCTTGCACTATCCAAATATGCCA 59.681 43.478 0.00 0.00 35.37 4.92
2835 3494 8.097038 GCCCTTCATTATGATATACAGTCTGAA 58.903 37.037 6.91 0.00 0.00 3.02
2836 3495 7.577616 CGCCCTTCATTATGATATACAGTCTGA 60.578 40.741 6.91 0.00 0.00 3.27
2837 3496 6.533012 CGCCCTTCATTATGATATACAGTCTG 59.467 42.308 0.00 0.00 0.00 3.51
2838 3497 6.351371 CCGCCCTTCATTATGATATACAGTCT 60.351 42.308 0.00 0.00 0.00 3.24
2839 3498 5.812642 CCGCCCTTCATTATGATATACAGTC 59.187 44.000 0.00 0.00 0.00 3.51
2856 3787 1.004394 CTTTCTTACCCTTCCGCCCTT 59.996 52.381 0.00 0.00 0.00 3.95
2862 3793 7.231925 TCCAAAACATTACTTTCTTACCCTTCC 59.768 37.037 0.00 0.00 0.00 3.46
3024 4033 9.784531 AAGTCTTCTGTTCATCTTCTTTGATAA 57.215 29.630 0.00 0.00 0.00 1.75
3032 4041 7.715265 TTACACAAGTCTTCTGTTCATCTTC 57.285 36.000 0.00 0.00 0.00 2.87
3105 4114 3.244044 GCTTTTGGTGCCACCTTCAATAA 60.244 43.478 16.23 0.00 39.58 1.40
3242 4251 0.962356 CAGCTTGCCGGGAATCTGTT 60.962 55.000 26.01 4.32 0.00 3.16
3254 4263 4.474113 CTTCATCAAGAGAAACAGCTTGC 58.526 43.478 0.00 0.00 40.89 4.01
3418 4427 8.085909 TGAATGACTAACTCGAGTATGACAAAA 58.914 33.333 20.39 8.16 0.00 2.44
3421 4430 6.753107 TGAATGACTAACTCGAGTATGACA 57.247 37.500 20.39 19.33 0.00 3.58
3464 4473 9.837681 TGTTATCCTAGGTAATCTCAATGGATA 57.162 33.333 9.08 0.00 35.13 2.59
3739 5128 8.616076 AGAAGTAATCACAAGCATAAATGTAGC 58.384 33.333 0.00 0.00 0.00 3.58
3841 5230 7.693533 TCCTCATCTAAGTACTAGAGAGGAA 57.306 40.000 24.56 13.28 45.77 3.36
3842 5231 6.616137 TGTCCTCATCTAAGTACTAGAGAGGA 59.384 42.308 23.92 23.92 46.09 3.71
3876 5266 2.095059 GCAGAACAAAGCACAGGGTATG 60.095 50.000 0.00 0.00 0.00 2.39
4085 5475 7.566760 TGGCATCATGTATTTAAATTCGTCT 57.433 32.000 5.91 0.00 0.00 4.18
4418 5808 6.916440 TGCATATCAAATATTCATGTGCTCC 58.084 36.000 20.44 3.71 36.08 4.70
4537 5927 8.041323 AGTGTACTGTTTATCTTCCTGGTAATG 58.959 37.037 0.00 0.00 0.00 1.90
4618 6008 7.542890 AGTCATGTCTACATTGAACAGAGTAG 58.457 38.462 0.00 0.00 33.61 2.57
4735 6125 3.625649 TTACATGTCCATGCACTGCTA 57.374 42.857 0.00 0.00 42.39 3.49
4875 6266 2.156504 GCAAATGGATACTGATCGCTCG 59.843 50.000 0.00 0.00 32.28 5.03
4964 6355 6.680810 CCTCATTTACAACTTGCTGAAATCA 58.319 36.000 0.00 0.00 0.00 2.57
4970 6361 2.414559 CCGCCTCATTTACAACTTGCTG 60.415 50.000 0.00 0.00 0.00 4.41
5102 6500 5.296035 ACTTCAACTTACTACAAACACTGGC 59.704 40.000 0.00 0.00 0.00 4.85
5182 6588 1.423845 CTCCAAAATTCCCGACGCG 59.576 57.895 3.53 3.53 0.00 6.01
5185 6591 4.712122 TTAATGCTCCAAAATTCCCGAC 57.288 40.909 0.00 0.00 0.00 4.79
5195 6602 7.408756 AAGATGCTTGTATTTAATGCTCCAA 57.591 32.000 0.00 0.00 0.00 3.53
5296 6749 5.295045 GCCCAAATAGAAATTGCTCCATTTG 59.705 40.000 12.24 12.24 34.62 2.32
5351 6805 1.268079 GGCTGGAGCTTTTGTGAACTC 59.732 52.381 0.00 0.00 41.70 3.01
5596 7062 8.097038 TGCAGATACTTTACTCAATGAGACTTT 58.903 33.333 18.20 0.00 33.32 2.66
5607 7073 6.968131 TGTTGATGTGCAGATACTTTACTC 57.032 37.500 0.00 0.00 0.00 2.59
5609 7075 7.545362 AGATGTTGATGTGCAGATACTTTAC 57.455 36.000 0.00 0.00 0.00 2.01
5610 7076 7.928167 CCTAGATGTTGATGTGCAGATACTTTA 59.072 37.037 0.00 0.00 0.00 1.85
5614 7080 5.605534 ACCTAGATGTTGATGTGCAGATAC 58.394 41.667 0.00 0.00 0.00 2.24
5623 7089 4.511527 AGTCTGCAACCTAGATGTTGATG 58.488 43.478 14.00 6.98 46.77 3.07
5627 7093 6.552445 ATTCTAGTCTGCAACCTAGATGTT 57.448 37.500 17.97 7.84 0.00 2.71
5652 7118 6.493115 ACACCATGTTTTCCTATGATCAAACA 59.507 34.615 10.04 10.04 41.93 2.83
5653 7119 6.924111 ACACCATGTTTTCCTATGATCAAAC 58.076 36.000 0.00 0.00 0.00 2.93
5672 7138 1.765904 TCAAGTGAGCAGGTAACACCA 59.234 47.619 0.00 0.00 41.95 4.17
5711 7177 8.758829 AGGGGGAAATATGTTTCTGTAAAAATC 58.241 33.333 13.76 0.00 42.66 2.17
5732 7198 6.755542 AGTCAGAAAATATCTTCTAGGGGG 57.244 41.667 0.00 0.00 35.73 5.40


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

AutoCloner maintained by Alex Coulton.