Multiple sequence alignment - TraesCS6B01G049700

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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 TraesCS6B01G049700 chr6B 100.000 2653 0 0 595 3247 29267810 29270462 0.000000e+00 4900.0
1 TraesCS6B01G049700 chr6B 84.031 645 75 17 2103 2741 29559265 29559887 2.160000e-166 595.0
2 TraesCS6B01G049700 chr6B 100.000 300 0 0 1 300 29267216 29267515 3.660000e-154 555.0
3 TraesCS6B01G049700 chr6B 81.232 357 48 4 1052 1392 29285195 29285548 1.480000e-68 270.0
4 TraesCS6B01G049700 chr6B 78.538 424 69 12 2833 3247 29274983 29275393 3.210000e-65 259.0
5 TraesCS6B01G049700 chr6B 82.609 161 27 1 1665 1824 29560297 29560457 1.210000e-29 141.0
6 TraesCS6B01G049700 chr6B 92.941 85 4 2 35 118 472612075 472612158 4.400000e-24 122.0
7 TraesCS6B01G049700 chr6B 97.222 36 1 0 1 36 34316625 34316590 9.730000e-06 62.1
8 TraesCS6B01G049700 chr6B 97.143 35 0 1 3059 3092 59403548 59403582 1.260000e-04 58.4
9 TraesCS6B01G049700 chr6B 100.000 29 0 0 7 35 229527648 229527620 2.000000e-03 54.7
10 TraesCS6B01G049700 chr6A 93.448 1511 73 10 1743 3247 17398123 17399613 0.000000e+00 2218.0
11 TraesCS6B01G049700 chr6A 91.049 648 41 8 958 1604 17397499 17398130 0.000000e+00 859.0
12 TraesCS6B01G049700 chr6A 89.241 158 10 2 136 288 17396526 17396681 1.190000e-44 191.0
13 TraesCS6B01G049700 chr6A 77.517 298 29 5 648 907 17396665 17396962 9.390000e-31 145.0
14 TraesCS6B01G049700 chr6A 92.308 78 6 0 35 112 584511432 584511355 9.520000e-21 111.0
15 TraesCS6B01G049700 chr6A 96.552 58 2 0 892 949 17397405 17397462 2.670000e-16 97.1
16 TraesCS6B01G049700 chr6D 91.531 921 54 8 614 1519 16601296 16602207 0.000000e+00 1247.0
17 TraesCS6B01G049700 chr6D 86.200 1058 66 27 1571 2615 16602225 16603215 0.000000e+00 1072.0
18 TraesCS6B01G049700 chr6D 87.632 380 36 8 2870 3247 16605574 16605944 6.440000e-117 431.0
19 TraesCS6B01G049700 chr6D 86.496 274 34 1 1119 1392 16608568 16608838 6.810000e-77 298.0
20 TraesCS6B01G049700 chr6D 86.397 272 33 3 2608 2878 16603939 16604207 8.810000e-76 294.0
21 TraesCS6B01G049700 chr6D 93.939 165 9 1 136 300 16601155 16601318 6.960000e-62 248.0
22 TraesCS6B01G049700 chr6D 85.714 91 13 0 174 264 16636162 16636252 2.670000e-16 97.1
23 TraesCS6B01G049700 chr4A 77.989 527 92 17 999 1506 579523897 579523376 3.150000e-80 309.0
24 TraesCS6B01G049700 chr3A 77.336 578 87 29 987 1525 128086505 128085933 5.260000e-78 302.0
25 TraesCS6B01G049700 chr3A 84.783 92 13 1 2735 2825 491189419 491189510 1.240000e-14 91.6
26 TraesCS6B01G049700 chr3A 100.000 31 0 0 1 31 111554932 111554962 1.260000e-04 58.4
27 TraesCS6B01G049700 chr3B 76.976 582 92 26 987 1531 173324313 173323737 8.810000e-76 294.0
28 TraesCS6B01G049700 chr3B 86.905 84 11 0 2742 2825 818304770 818304687 9.590000e-16 95.3
29 TraesCS6B01G049700 chr3B 97.143 35 1 0 1 35 181496208 181496242 3.500000e-05 60.2
30 TraesCS6B01G049700 chr4B 82.203 354 46 9 999 1338 34571639 34571989 4.100000e-74 289.0
31 TraesCS6B01G049700 chr4B 94.737 38 1 1 1 37 544445365 544445328 1.260000e-04 58.4
32 TraesCS6B01G049700 chr3D 76.083 577 94 27 987 1525 121880891 121880321 8.940000e-66 261.0
33 TraesCS6B01G049700 chr3D 79.599 299 29 20 987 1256 121735416 121735121 5.530000e-43 185.0
34 TraesCS6B01G049700 chr3D 91.765 85 4 2 2742 2825 565081507 565081589 7.360000e-22 115.0
35 TraesCS6B01G049700 chr3D 97.059 34 1 0 3 36 57160236 57160269 1.260000e-04 58.4
36 TraesCS6B01G049700 chr2A 93.671 79 5 0 34 112 57166940 57166862 5.690000e-23 119.0
37 TraesCS6B01G049700 chr2A 94.595 74 4 0 35 108 650624400 650624327 7.360000e-22 115.0
38 TraesCS6B01G049700 chr2D 95.833 72 3 0 35 106 302248083 302248012 2.050000e-22 117.0
39 TraesCS6B01G049700 chr1A 94.595 74 4 0 35 108 82722814 82722741 7.360000e-22 115.0
40 TraesCS6B01G049700 chr1A 92.308 78 6 0 35 112 505489853 505489776 9.520000e-21 111.0
41 TraesCS6B01G049700 chr1A 82.955 88 14 1 2742 2828 494443687 494443774 9.660000e-11 78.7
42 TraesCS6B01G049700 chr7D 92.308 78 6 0 35 112 632404610 632404687 9.520000e-21 111.0
43 TraesCS6B01G049700 chr2B 84.956 113 10 4 1 109 22316943 22317052 1.230000e-19 108.0
44 TraesCS6B01G049700 chr2B 84.043 94 8 6 2741 2829 33942269 33942178 2.080000e-12 84.2
45 TraesCS6B01G049700 chr7A 88.506 87 8 2 2742 2828 501155581 501155497 1.590000e-18 104.0
46 TraesCS6B01G049700 chr7B 84.694 98 9 3 2742 2838 450642196 450642104 3.450000e-15 93.5
47 TraesCS6B01G049700 chr5A 84.615 78 3 3 1 77 151732687 151732756 5.810000e-08 69.4
48 TraesCS6B01G049700 chr5D 97.222 36 1 0 1 36 122204004 122203969 9.730000e-06 62.1


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 TraesCS6B01G049700 chr6B 29267216 29270462 3246 False 2727.500000 4900 100.000000 1 3247 2 chr6B.!!$F5 3246
1 TraesCS6B01G049700 chr6B 29559265 29560457 1192 False 368.000000 595 83.320000 1665 2741 2 chr6B.!!$F6 1076
2 TraesCS6B01G049700 chr6A 17396526 17399613 3087 False 702.020000 2218 89.561400 136 3247 5 chr6A.!!$F1 3111
3 TraesCS6B01G049700 chr6D 16601155 16608838 7683 False 598.333333 1247 88.699167 136 3247 6 chr6D.!!$F2 3111
4 TraesCS6B01G049700 chr4A 579523376 579523897 521 True 309.000000 309 77.989000 999 1506 1 chr4A.!!$R1 507
5 TraesCS6B01G049700 chr3A 128085933 128086505 572 True 302.000000 302 77.336000 987 1525 1 chr3A.!!$R1 538
6 TraesCS6B01G049700 chr3B 173323737 173324313 576 True 294.000000 294 76.976000 987 1531 1 chr3B.!!$R1 544
7 TraesCS6B01G049700 chr3D 121880321 121880891 570 True 261.000000 261 76.083000 987 1525 1 chr3D.!!$R2 538

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
964 1466 1.009675 AGTCATAAGCCCACCTACCCT 59.990 52.381 0.0 0.0 0.0 4.34 F
1436 2018 0.650512 CGGGCATATCGTTGTGTGAC 59.349 55.000 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
2211 2798 1.302033 CTTCTGCTGGGTGCTTCGT 60.302 57.895 0.0 0.0 43.37 3.85 R
2275 2862 2.364632 TGCTTCATCCCAATAACACCG 58.635 47.619 0.0 0.0 0.00 4.94 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
27 28 8.819643 AAGGAATATAAGAGCGTTTAGATCAC 57.180 34.615 0.00 0.00 37.82 3.06
28 29 8.184304 AGGAATATAAGAGCGTTTAGATCACT 57.816 34.615 0.00 0.00 37.82 3.41
29 30 9.298250 AGGAATATAAGAGCGTTTAGATCACTA 57.702 33.333 0.00 0.00 37.82 2.74
30 31 9.344309 GGAATATAAGAGCGTTTAGATCACTAC 57.656 37.037 0.00 0.00 37.82 2.73
31 32 8.951954 AATATAAGAGCGTTTAGATCACTACG 57.048 34.615 8.56 8.56 37.82 3.51
32 33 4.698583 AAGAGCGTTTAGATCACTACGT 57.301 40.909 12.81 0.00 37.82 3.57
33 34 4.698583 AGAGCGTTTAGATCACTACGTT 57.301 40.909 0.00 8.39 37.82 3.99
34 35 5.808042 AGAGCGTTTAGATCACTACGTTA 57.192 39.130 0.00 0.00 37.82 3.18
35 36 5.808403 AGAGCGTTTAGATCACTACGTTAG 58.192 41.667 0.00 0.00 37.82 2.34
36 37 5.583854 AGAGCGTTTAGATCACTACGTTAGA 59.416 40.000 0.00 0.00 37.82 2.10
37 38 6.093219 AGAGCGTTTAGATCACTACGTTAGAA 59.907 38.462 0.00 0.00 37.82 2.10
38 39 6.615088 AGCGTTTAGATCACTACGTTAGAAA 58.385 36.000 0.00 0.00 0.00 2.52
39 40 7.256286 AGCGTTTAGATCACTACGTTAGAAAT 58.744 34.615 0.00 0.00 0.00 2.17
40 41 8.400947 AGCGTTTAGATCACTACGTTAGAAATA 58.599 33.333 0.00 0.00 0.00 1.40
41 42 9.178427 GCGTTTAGATCACTACGTTAGAAATAT 57.822 33.333 0.00 0.00 0.00 1.28
67 68 8.638629 AAGAGTGTTTAGATCACTAGTGTAGT 57.361 34.615 21.99 9.94 44.68 2.73
81 82 6.733509 ACTAGTGTAGTGATCTAAACCCTCT 58.266 40.000 0.00 0.00 37.69 3.69
82 83 7.183460 ACTAGTGTAGTGATCTAAACCCTCTT 58.817 38.462 0.00 0.00 37.69 2.85
83 84 8.334734 ACTAGTGTAGTGATCTAAACCCTCTTA 58.665 37.037 0.00 0.00 37.69 2.10
84 85 9.357161 CTAGTGTAGTGATCTAAACCCTCTTAT 57.643 37.037 0.00 0.00 35.56 1.73
86 87 9.884814 AGTGTAGTGATCTAAACCCTCTTATAT 57.115 33.333 0.00 0.00 35.56 0.86
98 99 8.959705 AAACCCTCTTATATTTCTTTACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
99 100 7.063934 ACCCTCTTATATTTCTTTACGGAGG 57.936 40.000 0.00 0.00 37.96 4.30
101 102 7.299246 CCTCTTATATTTCTTTACGGAGGGA 57.701 40.000 0.00 0.00 35.53 4.20
102 103 7.379750 CCTCTTATATTTCTTTACGGAGGGAG 58.620 42.308 0.00 0.00 35.53 4.30
103 104 7.015389 CCTCTTATATTTCTTTACGGAGGGAGT 59.985 40.741 0.00 0.00 35.53 3.85
104 105 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
105 106 9.597681 TCTTATATTTCTTTACGGAGGGAGTAT 57.402 33.333 0.00 0.00 0.00 2.12
106 107 9.857957 CTTATATTTCTTTACGGAGGGAGTATC 57.142 37.037 0.00 0.00 0.00 2.24
107 108 7.850935 ATATTTCTTTACGGAGGGAGTATCA 57.149 36.000 0.00 0.00 36.25 2.15
108 109 4.996788 TTCTTTACGGAGGGAGTATCAC 57.003 45.455 0.00 0.00 40.51 3.06
109 110 3.972133 TCTTTACGGAGGGAGTATCACA 58.028 45.455 0.00 0.00 45.06 3.58
110 111 4.543689 TCTTTACGGAGGGAGTATCACAT 58.456 43.478 0.00 0.00 45.06 3.21
111 112 5.698104 TCTTTACGGAGGGAGTATCACATA 58.302 41.667 0.00 0.00 45.06 2.29
112 113 6.131264 TCTTTACGGAGGGAGTATCACATAA 58.869 40.000 0.00 0.00 45.06 1.90
113 114 6.781014 TCTTTACGGAGGGAGTATCACATAAT 59.219 38.462 0.00 0.00 45.06 1.28
114 115 6.989155 TTACGGAGGGAGTATCACATAATT 57.011 37.500 0.00 0.00 45.06 1.40
115 116 5.888982 ACGGAGGGAGTATCACATAATTT 57.111 39.130 0.00 0.00 45.06 1.82
116 117 6.989155 ACGGAGGGAGTATCACATAATTTA 57.011 37.500 0.00 0.00 45.06 1.40
117 118 6.994221 ACGGAGGGAGTATCACATAATTTAG 58.006 40.000 0.00 0.00 45.06 1.85
118 119 6.014499 ACGGAGGGAGTATCACATAATTTAGG 60.014 42.308 0.00 0.00 45.06 2.69
119 120 6.574465 CGGAGGGAGTATCACATAATTTAGGG 60.574 46.154 0.00 0.00 45.06 3.53
120 121 6.500751 GGAGGGAGTATCACATAATTTAGGGA 59.499 42.308 0.00 0.00 45.06 4.20
121 122 7.310734 GGAGGGAGTATCACATAATTTAGGGAG 60.311 44.444 0.00 0.00 45.06 4.30
122 123 6.502158 AGGGAGTATCACATAATTTAGGGAGG 59.498 42.308 0.00 0.00 45.06 4.30
123 124 6.296489 GGGAGTATCACATAATTTAGGGAGGG 60.296 46.154 0.00 0.00 39.41 4.30
124 125 6.500751 GGAGTATCACATAATTTAGGGAGGGA 59.499 42.308 0.00 0.00 36.25 4.20
125 126 7.182930 GGAGTATCACATAATTTAGGGAGGGAT 59.817 40.741 0.00 0.00 36.25 3.85
126 127 8.152023 AGTATCACATAATTTAGGGAGGGATC 57.848 38.462 0.00 0.00 0.00 3.36
127 128 7.739444 AGTATCACATAATTTAGGGAGGGATCA 59.261 37.037 0.00 0.00 0.00 2.92
128 129 6.187727 TCACATAATTTAGGGAGGGATCAC 57.812 41.667 0.00 0.00 0.00 3.06
129 130 5.911178 TCACATAATTTAGGGAGGGATCACT 59.089 40.000 0.00 0.00 0.00 3.41
130 131 7.079700 TCACATAATTTAGGGAGGGATCACTA 58.920 38.462 0.00 0.00 0.00 2.74
131 132 7.570982 TCACATAATTTAGGGAGGGATCACTAA 59.429 37.037 0.00 0.00 0.00 2.24
132 133 8.386264 CACATAATTTAGGGAGGGATCACTAAT 58.614 37.037 0.00 0.00 0.00 1.73
133 134 8.386264 ACATAATTTAGGGAGGGATCACTAATG 58.614 37.037 0.00 0.25 0.00 1.90
134 135 6.848562 AATTTAGGGAGGGATCACTAATGT 57.151 37.500 0.00 0.00 0.00 2.71
146 147 7.620094 AGGGATCACTAATGTAGTCTTTACACT 59.380 37.037 0.00 0.00 36.76 3.55
192 198 6.091718 TGTGGTCTTTTGGTTTATTTAGGC 57.908 37.500 0.00 0.00 0.00 3.93
193 199 5.011227 TGTGGTCTTTTGGTTTATTTAGGCC 59.989 40.000 0.00 0.00 0.00 5.19
198 204 5.479027 TCTTTTGGTTTATTTAGGCCAGTCC 59.521 40.000 5.01 0.00 32.09 3.85
290 296 5.105473 TGGTTGTGTAGTCATAGGCTTACTC 60.105 44.000 0.00 0.00 0.00 2.59
620 626 5.344743 TTTGCAGGAAGTAGAGTCATAGG 57.655 43.478 0.00 0.00 0.00 2.57
621 627 2.695666 TGCAGGAAGTAGAGTCATAGGC 59.304 50.000 0.00 0.00 0.00 3.93
622 628 2.962421 GCAGGAAGTAGAGTCATAGGCT 59.038 50.000 0.00 0.00 0.00 4.58
623 629 3.386402 GCAGGAAGTAGAGTCATAGGCTT 59.614 47.826 0.00 0.00 0.00 4.35
624 630 4.585162 GCAGGAAGTAGAGTCATAGGCTTA 59.415 45.833 0.00 0.00 0.00 3.09
625 631 5.508320 GCAGGAAGTAGAGTCATAGGCTTAC 60.508 48.000 0.00 0.00 0.00 2.34
626 632 5.830991 CAGGAAGTAGAGTCATAGGCTTACT 59.169 44.000 0.00 0.00 0.00 2.24
627 633 6.016610 CAGGAAGTAGAGTCATAGGCTTACTC 60.017 46.154 13.47 13.47 39.95 2.59
629 635 6.548251 GGAAGTAGAGTCATAGGCTTACTCTT 59.452 42.308 23.36 11.92 45.94 2.85
630 636 7.068962 GGAAGTAGAGTCATAGGCTTACTCTTT 59.931 40.741 23.36 16.13 45.94 2.52
631 637 7.964666 AGTAGAGTCATAGGCTTACTCTTTT 57.035 36.000 23.36 13.88 45.94 2.27
632 638 8.368962 AGTAGAGTCATAGGCTTACTCTTTTT 57.631 34.615 23.36 12.19 45.94 1.94
670 676 4.130286 AGAGTCATAGGCTTACTGCAAC 57.870 45.455 0.00 0.00 45.15 4.17
691 698 7.386573 TGCAACGATCACTAATAAGAAACTGAA 59.613 33.333 0.00 0.00 0.00 3.02
700 707 8.993121 CACTAATAAGAAACTGAAAGAAGCTGA 58.007 33.333 0.00 0.00 37.43 4.26
788 807 3.422876 CACACTTCGCATGTCATTGTTTG 59.577 43.478 0.00 0.00 0.00 2.93
805 824 6.466308 TTGTTTGACTTGTCGATCATGTAG 57.534 37.500 0.00 0.00 35.12 2.74
816 835 6.062095 TGTCGATCATGTAGACTTGAGGATA 58.938 40.000 15.04 1.49 34.02 2.59
822 841 9.853555 GATCATGTAGACTTGAGGATATAACAG 57.146 37.037 4.77 0.00 34.23 3.16
825 869 7.348080 TGTAGACTTGAGGATATAACAGTGG 57.652 40.000 0.00 0.00 0.00 4.00
849 893 6.605594 GGGTAGGTAAAAATCATGGTCATTCA 59.394 38.462 0.00 0.00 0.00 2.57
852 896 9.520204 GTAGGTAAAAATCATGGTCATTCATTG 57.480 33.333 0.00 0.00 0.00 2.82
937 1439 4.263068 CCTCTATTGTCGGCCCAAATAGAT 60.263 45.833 21.12 1.54 0.00 1.98
964 1466 1.009675 AGTCATAAGCCCACCTACCCT 59.990 52.381 0.00 0.00 0.00 4.34
966 1468 2.241430 GTCATAAGCCCACCTACCCTTT 59.759 50.000 0.00 0.00 0.00 3.11
969 1471 1.725169 AAGCCCACCTACCCTTTGCA 61.725 55.000 0.00 0.00 0.00 4.08
970 1472 1.228737 GCCCACCTACCCTTTGCAA 60.229 57.895 0.00 0.00 0.00 4.08
1128 1685 2.840651 GTTCCTCTGGATCCTTTCTCCA 59.159 50.000 14.23 0.00 40.49 3.86
1139 1696 3.399330 TCCTTTCTCCATGTTCGTTGTC 58.601 45.455 0.00 0.00 0.00 3.18
1339 1899 1.021968 GTGCGTGTTCTCCCTGTTTT 58.978 50.000 0.00 0.00 0.00 2.43
1380 1959 8.992073 ACATTCCTTTGATTTAATTTTGCAGAC 58.008 29.630 0.00 0.00 0.00 3.51
1396 1977 2.632377 CAGACGGCTTGATATGGTTGT 58.368 47.619 0.00 0.00 0.00 3.32
1424 2006 2.093921 TGATCGTGTTTCTTCGGGCATA 60.094 45.455 0.00 0.00 0.00 3.14
1434 2016 1.327460 CTTCGGGCATATCGTTGTGTG 59.673 52.381 0.00 0.00 0.00 3.82
1436 2018 0.650512 CGGGCATATCGTTGTGTGAC 59.349 55.000 0.00 0.00 0.00 3.67
1449 2031 2.833794 TGTGTGACTGTAGAGTTTGGC 58.166 47.619 0.00 0.00 30.16 4.52
1461 2043 6.734137 TGTAGAGTTTGGCTATGTTTTGTTG 58.266 36.000 0.00 0.00 0.00 3.33
1464 2046 5.594317 AGAGTTTGGCTATGTTTTGTTGTCT 59.406 36.000 0.00 0.00 0.00 3.41
1468 2050 5.699097 TGGCTATGTTTTGTTGTCTAACC 57.301 39.130 0.00 0.00 35.92 2.85
1477 2059 3.417069 TGTTGTCTAACCCTGTGATGG 57.583 47.619 0.00 0.00 35.92 3.51
1506 2088 7.338449 TGGATAAGAGTAATTGGGTTAGTTTGC 59.662 37.037 0.00 0.00 0.00 3.68
1519 2101 6.601613 TGGGTTAGTTTGCTATTAGATGGTTG 59.398 38.462 0.00 0.00 0.00 3.77
1520 2102 6.039382 GGGTTAGTTTGCTATTAGATGGTTGG 59.961 42.308 0.00 0.00 0.00 3.77
1531 2113 9.116067 GCTATTAGATGGTTGGTGTGTATAAAA 57.884 33.333 0.00 0.00 0.00 1.52
1560 2142 9.743581 ATAAATGATGCCTGATATGTACATGAA 57.256 29.630 18.81 0.00 0.00 2.57
1561 2143 7.444629 AATGATGCCTGATATGTACATGAAC 57.555 36.000 18.81 9.68 0.00 3.18
1562 2144 5.308014 TGATGCCTGATATGTACATGAACC 58.692 41.667 18.81 5.32 0.00 3.62
1564 2146 4.450976 TGCCTGATATGTACATGAACCAC 58.549 43.478 18.81 4.89 0.00 4.16
1565 2147 4.080638 TGCCTGATATGTACATGAACCACA 60.081 41.667 18.81 7.36 0.00 4.17
1566 2148 5.065914 GCCTGATATGTACATGAACCACAT 58.934 41.667 18.81 1.55 40.17 3.21
1567 2149 5.180117 GCCTGATATGTACATGAACCACATC 59.820 44.000 18.81 11.37 37.07 3.06
1568 2150 6.290605 CCTGATATGTACATGAACCACATCA 58.709 40.000 18.81 14.99 37.07 3.07
1569 2151 6.938596 CCTGATATGTACATGAACCACATCAT 59.061 38.462 18.81 0.00 40.64 2.45
1572 2154 9.187996 TGATATGTACATGAACCACATCATTTT 57.812 29.630 18.81 0.00 37.96 1.82
1581 2163 5.293814 TGAACCACATCATTTTGTTTTGCAG 59.706 36.000 0.00 0.00 0.00 4.41
1635 2218 7.176589 AGGAAATTTGTAAACACTTTGGTGA 57.823 32.000 0.00 0.00 45.61 4.02
1636 2219 7.264947 AGGAAATTTGTAAACACTTTGGTGAG 58.735 34.615 0.00 0.00 45.61 3.51
1662 2245 3.028130 TCGACAATATAGCCCAGTGTCA 58.972 45.455 9.93 0.00 38.80 3.58
1666 2249 5.615289 GACAATATAGCCCAGTGTCAAGAT 58.385 41.667 5.75 0.00 38.74 2.40
1673 2256 2.027192 GCCCAGTGTCAAGATCCTGTTA 60.027 50.000 0.00 0.00 0.00 2.41
1675 2258 3.254060 CCAGTGTCAAGATCCTGTTACG 58.746 50.000 0.00 0.00 0.00 3.18
1703 2286 9.540538 TTTAATCCCATGGAGAAATGTTCTTAA 57.459 29.630 15.22 6.16 40.87 1.85
1741 2324 9.396022 TGTAAGAAAATGAAATAGATCAGACCC 57.604 33.333 0.00 0.00 31.76 4.46
1796 2379 4.251268 TCTGTGATTTCTGATGCACTGAG 58.749 43.478 0.00 0.00 35.33 3.35
1939 2524 4.459390 TGCTAGTAAATACCGTGAGCAA 57.541 40.909 0.00 0.00 35.63 3.91
2011 2597 9.613428 CATTTCAGATATTCCAGGTTACTAACA 57.387 33.333 1.40 0.00 0.00 2.41
2014 2600 8.141298 TCAGATATTCCAGGTTACTAACACAA 57.859 34.615 1.40 0.00 0.00 3.33
2019 2605 4.575885 TCCAGGTTACTAACACAAGCATC 58.424 43.478 1.40 0.00 0.00 3.91
2098 2684 5.091261 GTGAGTTCACATGGTAGAATCCT 57.909 43.478 7.37 0.00 45.75 3.24
2099 2685 6.222038 GTGAGTTCACATGGTAGAATCCTA 57.778 41.667 7.37 0.00 45.75 2.94
2100 2686 6.640518 GTGAGTTCACATGGTAGAATCCTAA 58.359 40.000 7.37 0.00 45.75 2.69
2101 2687 7.275920 GTGAGTTCACATGGTAGAATCCTAAT 58.724 38.462 7.37 0.00 45.75 1.73
2110 2696 8.376270 ACATGGTAGAATCCTAATTAACTAGCC 58.624 37.037 0.00 0.00 0.00 3.93
2122 2709 8.429641 CCTAATTAACTAGCCATGTTTCCTCTA 58.570 37.037 0.00 0.00 0.00 2.43
2275 2862 3.123050 GTGTCCACTTTGAAAACCATGC 58.877 45.455 0.00 0.00 0.00 4.06
2391 2989 4.450419 GCGCTCTTGATCTTGCAGTATTAT 59.550 41.667 0.00 0.00 0.00 1.28
2445 3043 6.984474 TGTCTACAGTTTTTCTCTGTTACAGG 59.016 38.462 12.79 3.67 42.50 4.00
2488 3087 1.523758 AAAGTGATTCGGCTCACACC 58.476 50.000 16.93 0.00 46.45 4.16
2653 3993 4.497340 CGTGCCAAATTACAGTTGACACTT 60.497 41.667 2.69 0.00 37.25 3.16
2670 4010 9.865484 GTTGACACTTTATTTGACTCTTTCTAC 57.135 33.333 0.00 0.00 0.00 2.59
2709 4073 2.035632 AGCTAGAGTGCGCTATTCCTT 58.964 47.619 9.73 0.00 38.13 3.36
2710 4074 2.131183 GCTAGAGTGCGCTATTCCTTG 58.869 52.381 9.73 0.00 0.00 3.61
2711 4075 2.223829 GCTAGAGTGCGCTATTCCTTGA 60.224 50.000 9.73 0.00 0.00 3.02
2712 4076 3.553922 GCTAGAGTGCGCTATTCCTTGAT 60.554 47.826 9.73 0.00 0.00 2.57
2713 4077 3.550437 AGAGTGCGCTATTCCTTGATT 57.450 42.857 9.73 0.00 0.00 2.57
2714 4078 4.672587 AGAGTGCGCTATTCCTTGATTA 57.327 40.909 9.73 0.00 0.00 1.75
2715 4079 4.626042 AGAGTGCGCTATTCCTTGATTAG 58.374 43.478 9.73 0.00 0.00 1.73
2716 4080 4.100189 AGAGTGCGCTATTCCTTGATTAGT 59.900 41.667 9.73 0.00 0.00 2.24
2717 4081 4.372656 AGTGCGCTATTCCTTGATTAGTC 58.627 43.478 9.73 0.00 0.00 2.59
2718 4082 4.100189 AGTGCGCTATTCCTTGATTAGTCT 59.900 41.667 9.73 0.00 0.00 3.24
2719 4083 4.446051 GTGCGCTATTCCTTGATTAGTCTC 59.554 45.833 9.73 0.00 0.00 3.36
2720 4084 3.991121 GCGCTATTCCTTGATTAGTCTCC 59.009 47.826 0.00 0.00 0.00 3.71
2721 4085 4.262249 GCGCTATTCCTTGATTAGTCTCCT 60.262 45.833 0.00 0.00 0.00 3.69
2727 4091 6.627087 TTCCTTGATTAGTCTCCTCAATGT 57.373 37.500 0.00 0.00 0.00 2.71
2750 4114 2.766828 AGTGCTACATTGTACTCCCTCC 59.233 50.000 0.00 0.00 0.00 4.30
2755 4119 4.038883 GCTACATTGTACTCCCTCCGTATT 59.961 45.833 0.00 0.00 0.00 1.89
2768 4132 9.151177 ACTCCCTCCGTATTAAAATATAAGACA 57.849 33.333 0.00 0.00 0.00 3.41
2831 4196 7.973048 TTTGATACAGAGGGAGTAGTTATGT 57.027 36.000 0.00 0.00 0.00 2.29
2868 4233 5.246656 AGTTGAAAAATTGGATGGCTGATCA 59.753 36.000 0.00 0.00 31.91 2.92
2893 5630 6.205101 ACAATTAAGTAGTACGTCTGAGGG 57.795 41.667 0.00 0.00 0.00 4.30
2939 5678 3.678806 CGTATGTCAACATGGCTACCAGT 60.679 47.826 5.89 0.00 36.75 4.00
2952 5715 7.990314 ACATGGCTACCAGTAAAACAAAATTTT 59.010 29.630 0.00 0.00 36.75 1.82
2953 5716 7.778470 TGGCTACCAGTAAAACAAAATTTTG 57.222 32.000 25.73 25.73 43.62 2.44
3117 5881 6.648192 CAAGATTCCAGAATACTGAAGACCT 58.352 40.000 0.00 0.00 46.03 3.85
3170 5934 8.523658 AGAATATAAACCTTCTCCTGTTTTTGC 58.476 33.333 0.00 0.00 36.23 3.68
3176 5941 3.315191 CCTTCTCCTGTTTTTGCGAAGAA 59.685 43.478 0.00 0.00 31.90 2.52
3178 5943 4.552166 TCTCCTGTTTTTGCGAAGAAAG 57.448 40.909 0.00 0.00 0.00 2.62
3208 5973 2.805099 AGAACAGAAGAAGCAAAGCGAG 59.195 45.455 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.184304 AGTGATCTAAACGCTCTTATATTCCT 57.816 34.615 0.00 0.00 0.00 3.36
4 5 9.344309 GTAGTGATCTAAACGCTCTTATATTCC 57.656 37.037 0.00 0.00 0.00 3.01
5 6 9.053135 CGTAGTGATCTAAACGCTCTTATATTC 57.947 37.037 0.00 0.00 0.00 1.75
6 7 8.566260 ACGTAGTGATCTAAACGCTCTTATATT 58.434 33.333 12.20 0.00 42.51 1.28
7 8 8.097078 ACGTAGTGATCTAAACGCTCTTATAT 57.903 34.615 12.20 0.00 42.51 0.86
8 9 7.488187 ACGTAGTGATCTAAACGCTCTTATA 57.512 36.000 12.20 0.00 42.51 0.98
9 10 6.374565 ACGTAGTGATCTAAACGCTCTTAT 57.625 37.500 12.20 0.00 42.51 1.73
10 11 5.808042 ACGTAGTGATCTAAACGCTCTTA 57.192 39.130 12.20 0.00 42.51 2.10
11 12 4.698583 ACGTAGTGATCTAAACGCTCTT 57.301 40.909 12.20 0.00 42.51 2.85
12 13 4.698583 AACGTAGTGATCTAAACGCTCT 57.301 40.909 12.20 0.00 45.00 4.09
13 14 5.804173 TCTAACGTAGTGATCTAAACGCTC 58.196 41.667 12.20 0.00 45.00 5.03
14 15 5.808042 TCTAACGTAGTGATCTAAACGCT 57.192 39.130 12.20 5.28 45.00 5.07
15 16 6.859715 TTTCTAACGTAGTGATCTAAACGC 57.140 37.500 12.20 0.00 45.00 4.84
41 42 9.736414 ACTACACTAGTGATCTAAACACTCTTA 57.264 33.333 29.30 5.03 45.58 2.10
42 43 8.638629 ACTACACTAGTGATCTAAACACTCTT 57.361 34.615 29.30 4.06 45.58 2.85
57 58 6.733509 AGAGGGTTTAGATCACTACACTAGT 58.266 40.000 0.00 0.00 40.28 2.57
58 59 7.648039 AAGAGGGTTTAGATCACTACACTAG 57.352 40.000 0.00 0.00 32.04 2.57
60 61 9.884814 ATATAAGAGGGTTTAGATCACTACACT 57.115 33.333 0.00 0.00 32.04 3.55
73 74 7.991460 CCTCCGTAAAGAAATATAAGAGGGTTT 59.009 37.037 0.00 0.00 0.00 3.27
74 75 7.419865 CCCTCCGTAAAGAAATATAAGAGGGTT 60.420 40.741 12.22 0.00 39.53 4.11
75 76 6.042897 CCCTCCGTAAAGAAATATAAGAGGGT 59.957 42.308 12.22 0.00 39.53 4.34
76 77 6.269307 TCCCTCCGTAAAGAAATATAAGAGGG 59.731 42.308 13.91 13.91 44.19 4.30
77 78 7.015389 ACTCCCTCCGTAAAGAAATATAAGAGG 59.985 40.741 0.00 0.00 0.00 3.69
78 79 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
79 80 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
80 81 9.857957 GATACTCCCTCCGTAAAGAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
81 82 9.370930 TGATACTCCCTCCGTAAAGAAATATAA 57.629 33.333 0.00 0.00 0.00 0.98
82 83 8.800332 GTGATACTCCCTCCGTAAAGAAATATA 58.200 37.037 0.00 0.00 0.00 0.86
83 84 7.289317 TGTGATACTCCCTCCGTAAAGAAATAT 59.711 37.037 0.00 0.00 0.00 1.28
84 85 6.608405 TGTGATACTCCCTCCGTAAAGAAATA 59.392 38.462 0.00 0.00 0.00 1.40
85 86 5.424252 TGTGATACTCCCTCCGTAAAGAAAT 59.576 40.000 0.00 0.00 0.00 2.17
86 87 4.773674 TGTGATACTCCCTCCGTAAAGAAA 59.226 41.667 0.00 0.00 0.00 2.52
87 88 4.346730 TGTGATACTCCCTCCGTAAAGAA 58.653 43.478 0.00 0.00 0.00 2.52
88 89 3.972133 TGTGATACTCCCTCCGTAAAGA 58.028 45.455 0.00 0.00 0.00 2.52
89 90 4.939052 ATGTGATACTCCCTCCGTAAAG 57.061 45.455 0.00 0.00 0.00 1.85
90 91 6.989155 ATTATGTGATACTCCCTCCGTAAA 57.011 37.500 0.00 0.00 0.00 2.01
91 92 6.989155 AATTATGTGATACTCCCTCCGTAA 57.011 37.500 0.00 0.00 0.00 3.18
92 93 6.989155 AAATTATGTGATACTCCCTCCGTA 57.011 37.500 0.00 0.00 0.00 4.02
93 94 5.888982 AAATTATGTGATACTCCCTCCGT 57.111 39.130 0.00 0.00 0.00 4.69
94 95 6.398918 CCTAAATTATGTGATACTCCCTCCG 58.601 44.000 0.00 0.00 0.00 4.63
95 96 6.500751 TCCCTAAATTATGTGATACTCCCTCC 59.499 42.308 0.00 0.00 0.00 4.30
96 97 7.310734 CCTCCCTAAATTATGTGATACTCCCTC 60.311 44.444 0.00 0.00 0.00 4.30
97 98 6.502158 CCTCCCTAAATTATGTGATACTCCCT 59.498 42.308 0.00 0.00 0.00 4.20
98 99 6.296489 CCCTCCCTAAATTATGTGATACTCCC 60.296 46.154 0.00 0.00 0.00 4.30
99 100 6.500751 TCCCTCCCTAAATTATGTGATACTCC 59.499 42.308 0.00 0.00 0.00 3.85
100 101 7.554959 TCCCTCCCTAAATTATGTGATACTC 57.445 40.000 0.00 0.00 0.00 2.59
101 102 7.739444 TGATCCCTCCCTAAATTATGTGATACT 59.261 37.037 0.00 0.00 0.00 2.12
102 103 7.824779 GTGATCCCTCCCTAAATTATGTGATAC 59.175 40.741 0.00 0.00 0.00 2.24
103 104 7.739444 AGTGATCCCTCCCTAAATTATGTGATA 59.261 37.037 0.00 0.00 0.00 2.15
104 105 6.564152 AGTGATCCCTCCCTAAATTATGTGAT 59.436 38.462 0.00 0.00 0.00 3.06
105 106 5.911178 AGTGATCCCTCCCTAAATTATGTGA 59.089 40.000 0.00 0.00 0.00 3.58
106 107 6.192970 AGTGATCCCTCCCTAAATTATGTG 57.807 41.667 0.00 0.00 0.00 3.21
107 108 7.947782 TTAGTGATCCCTCCCTAAATTATGT 57.052 36.000 0.00 0.00 0.00 2.29
108 109 8.386264 ACATTAGTGATCCCTCCCTAAATTATG 58.614 37.037 0.00 0.00 0.00 1.90
109 110 8.525729 ACATTAGTGATCCCTCCCTAAATTAT 57.474 34.615 0.00 0.00 0.00 1.28
110 111 7.947782 ACATTAGTGATCCCTCCCTAAATTA 57.052 36.000 0.00 0.00 0.00 1.40
111 112 6.848562 ACATTAGTGATCCCTCCCTAAATT 57.151 37.500 0.00 0.00 0.00 1.82
112 113 7.082972 ACTACATTAGTGATCCCTCCCTAAAT 58.917 38.462 0.00 0.00 37.69 1.40
113 114 6.449956 ACTACATTAGTGATCCCTCCCTAAA 58.550 40.000 0.00 0.00 37.69 1.85
114 115 6.039415 ACTACATTAGTGATCCCTCCCTAA 57.961 41.667 0.00 0.00 37.69 2.69
115 116 5.375956 AGACTACATTAGTGATCCCTCCCTA 59.624 44.000 0.00 0.00 39.59 3.53
116 117 4.171044 AGACTACATTAGTGATCCCTCCCT 59.829 45.833 0.00 0.00 39.59 4.20
117 118 4.484912 AGACTACATTAGTGATCCCTCCC 58.515 47.826 0.00 0.00 39.59 4.30
118 119 6.487299 AAAGACTACATTAGTGATCCCTCC 57.513 41.667 0.00 0.00 39.59 4.30
119 120 7.921745 GTGTAAAGACTACATTAGTGATCCCTC 59.078 40.741 0.00 0.00 39.59 4.30
120 121 7.620094 AGTGTAAAGACTACATTAGTGATCCCT 59.380 37.037 0.00 0.00 39.59 4.20
121 122 7.783042 AGTGTAAAGACTACATTAGTGATCCC 58.217 38.462 0.00 0.00 39.59 3.85
122 123 8.688151 AGAGTGTAAAGACTACATTAGTGATCC 58.312 37.037 0.00 0.00 39.59 3.36
123 124 9.724839 GAGAGTGTAAAGACTACATTAGTGATC 57.275 37.037 0.00 0.00 39.59 2.92
124 125 9.469097 AGAGAGTGTAAAGACTACATTAGTGAT 57.531 33.333 0.00 0.00 39.59 3.06
125 126 8.865420 AGAGAGTGTAAAGACTACATTAGTGA 57.135 34.615 0.00 0.00 39.59 3.41
171 172 5.148502 TGGCCTAAATAAACCAAAAGACCA 58.851 37.500 3.32 0.00 0.00 4.02
192 198 5.887598 TCAATGGAAGTATCATTTGGACTGG 59.112 40.000 0.00 0.00 33.08 4.00
193 199 6.375174 TGTCAATGGAAGTATCATTTGGACTG 59.625 38.462 0.00 0.00 32.97 3.51
198 204 8.272545 TCTCTTGTCAATGGAAGTATCATTTG 57.727 34.615 0.00 0.00 33.08 2.32
596 602 6.173339 CCTATGACTCTACTTCCTGCAAAAA 58.827 40.000 0.00 0.00 0.00 1.94
597 603 5.734720 CCTATGACTCTACTTCCTGCAAAA 58.265 41.667 0.00 0.00 0.00 2.44
598 604 4.383118 GCCTATGACTCTACTTCCTGCAAA 60.383 45.833 0.00 0.00 0.00 3.68
599 605 3.133003 GCCTATGACTCTACTTCCTGCAA 59.867 47.826 0.00 0.00 0.00 4.08
600 606 2.695666 GCCTATGACTCTACTTCCTGCA 59.304 50.000 0.00 0.00 0.00 4.41
601 607 2.962421 AGCCTATGACTCTACTTCCTGC 59.038 50.000 0.00 0.00 0.00 4.85
602 608 5.830991 AGTAAGCCTATGACTCTACTTCCTG 59.169 44.000 0.00 0.00 0.00 3.86
603 609 6.020881 AGTAAGCCTATGACTCTACTTCCT 57.979 41.667 0.00 0.00 0.00 3.36
604 610 6.066032 AGAGTAAGCCTATGACTCTACTTCC 58.934 44.000 2.01 0.00 46.30 3.46
635 641 6.173339 CCTATGACTCTACTTCCTGCAAAAA 58.827 40.000 0.00 0.00 0.00 1.94
636 642 5.734720 CCTATGACTCTACTTCCTGCAAAA 58.265 41.667 0.00 0.00 0.00 2.44
637 643 4.383118 GCCTATGACTCTACTTCCTGCAAA 60.383 45.833 0.00 0.00 0.00 3.68
638 644 3.133003 GCCTATGACTCTACTTCCTGCAA 59.867 47.826 0.00 0.00 0.00 4.08
639 645 2.695666 GCCTATGACTCTACTTCCTGCA 59.304 50.000 0.00 0.00 0.00 4.41
640 646 2.962421 AGCCTATGACTCTACTTCCTGC 59.038 50.000 0.00 0.00 0.00 4.85
641 647 5.830991 AGTAAGCCTATGACTCTACTTCCTG 59.169 44.000 0.00 0.00 0.00 3.86
642 648 5.830991 CAGTAAGCCTATGACTCTACTTCCT 59.169 44.000 0.00 0.00 0.00 3.36
643 649 5.508320 GCAGTAAGCCTATGACTCTACTTCC 60.508 48.000 0.00 0.00 37.23 3.46
644 650 5.067936 TGCAGTAAGCCTATGACTCTACTTC 59.932 44.000 0.00 0.00 44.83 3.01
645 651 4.956700 TGCAGTAAGCCTATGACTCTACTT 59.043 41.667 0.00 0.00 44.83 2.24
646 652 4.537751 TGCAGTAAGCCTATGACTCTACT 58.462 43.478 0.00 0.00 44.83 2.57
647 653 4.920640 TGCAGTAAGCCTATGACTCTAC 57.079 45.455 0.00 0.00 44.83 2.59
648 654 4.202020 CGTTGCAGTAAGCCTATGACTCTA 60.202 45.833 0.00 0.00 44.83 2.43
649 655 3.429547 CGTTGCAGTAAGCCTATGACTCT 60.430 47.826 0.00 0.00 44.83 3.24
650 656 2.860735 CGTTGCAGTAAGCCTATGACTC 59.139 50.000 0.00 0.00 44.83 3.36
691 698 1.295792 TTTTGTCGCGTCAGCTTCTT 58.704 45.000 5.77 0.00 42.32 2.52
700 707 1.206578 CGCTCCAATTTTGTCGCGT 59.793 52.632 5.77 0.00 38.91 6.01
788 807 5.641709 TCAAGTCTACATGATCGACAAGTC 58.358 41.667 0.00 0.00 32.58 3.01
805 824 5.615925 ACCCACTGTTATATCCTCAAGTC 57.384 43.478 0.00 0.00 0.00 3.01
816 835 7.559897 CCATGATTTTTACCTACCCACTGTTAT 59.440 37.037 0.00 0.00 0.00 1.89
822 841 5.258051 TGACCATGATTTTTACCTACCCAC 58.742 41.667 0.00 0.00 0.00 4.61
825 869 7.639113 TGAATGACCATGATTTTTACCTACC 57.361 36.000 0.00 0.00 0.00 3.18
937 1439 2.092429 GGTGGGCTTATGACTTGGATGA 60.092 50.000 0.00 0.00 0.00 2.92
1139 1696 3.425938 GAATTCAGCCGCGCTCGTG 62.426 63.158 5.56 0.00 36.40 4.35
1285 1845 2.170985 CGAACTTCTTGCGCCGTG 59.829 61.111 4.18 0.00 0.00 4.94
1380 1959 1.202290 GCCAACAACCATATCAAGCCG 60.202 52.381 0.00 0.00 0.00 5.52
1396 1977 3.616821 CGAAGAAACACGATCATAGCCAA 59.383 43.478 0.00 0.00 0.00 4.52
1424 2006 4.585955 AACTCTACAGTCACACAACGAT 57.414 40.909 0.00 0.00 29.93 3.73
1434 2016 6.204882 ACAAAACATAGCCAAACTCTACAGTC 59.795 38.462 0.00 0.00 29.93 3.51
1436 2018 6.560253 ACAAAACATAGCCAAACTCTACAG 57.440 37.500 0.00 0.00 0.00 2.74
1449 2031 6.485313 TCACAGGGTTAGACAACAAAACATAG 59.515 38.462 0.00 0.00 36.29 2.23
1468 2050 4.848357 ACTCTTATCCAAACCATCACAGG 58.152 43.478 0.00 0.00 0.00 4.00
1477 2059 8.803397 ACTAACCCAATTACTCTTATCCAAAC 57.197 34.615 0.00 0.00 0.00 2.93
1519 2101 9.893305 GGCATCATTTATAGTTTTATACACACC 57.107 33.333 0.00 0.00 0.00 4.16
1534 2116 9.743581 TTCATGTACATATCAGGCATCATTTAT 57.256 29.630 8.32 0.00 0.00 1.40
1535 2117 9.002600 GTTCATGTACATATCAGGCATCATTTA 57.997 33.333 8.32 0.00 0.00 1.40
1536 2118 7.040201 GGTTCATGTACATATCAGGCATCATTT 60.040 37.037 8.32 0.00 0.00 2.32
1537 2119 6.432162 GGTTCATGTACATATCAGGCATCATT 59.568 38.462 8.32 0.00 0.00 2.57
1551 2133 6.647334 ACAAAATGATGTGGTTCATGTACA 57.353 33.333 0.00 0.00 36.48 2.90
1552 2134 7.945033 AAACAAAATGATGTGGTTCATGTAC 57.055 32.000 0.00 0.00 36.48 2.90
1555 2137 6.137415 GCAAAACAAAATGATGTGGTTCATG 58.863 36.000 0.00 0.00 36.48 3.07
1556 2138 5.821470 TGCAAAACAAAATGATGTGGTTCAT 59.179 32.000 0.00 0.00 37.96 2.57
1558 2140 5.523188 TCTGCAAAACAAAATGATGTGGTTC 59.477 36.000 0.00 0.00 32.81 3.62
1559 2141 5.426504 TCTGCAAAACAAAATGATGTGGTT 58.573 33.333 0.00 0.00 32.81 3.67
1560 2142 5.021033 TCTGCAAAACAAAATGATGTGGT 57.979 34.783 0.00 0.00 32.81 4.16
1561 2143 5.697178 TCATCTGCAAAACAAAATGATGTGG 59.303 36.000 6.67 0.00 32.06 4.17
1562 2144 6.772770 TCATCTGCAAAACAAAATGATGTG 57.227 33.333 6.67 0.00 32.06 3.21
1564 2146 6.203145 TGGTTCATCTGCAAAACAAAATGATG 59.797 34.615 0.00 0.00 31.63 3.07
1565 2147 6.203338 GTGGTTCATCTGCAAAACAAAATGAT 59.797 34.615 0.00 0.00 0.00 2.45
1566 2148 5.523188 GTGGTTCATCTGCAAAACAAAATGA 59.477 36.000 0.00 0.00 0.00 2.57
1567 2149 5.293814 TGTGGTTCATCTGCAAAACAAAATG 59.706 36.000 0.00 0.00 0.00 2.32
1568 2150 5.426504 TGTGGTTCATCTGCAAAACAAAAT 58.573 33.333 0.00 0.00 0.00 1.82
1569 2151 4.825422 TGTGGTTCATCTGCAAAACAAAA 58.175 34.783 0.00 0.00 0.00 2.44
1572 2154 4.241590 GATGTGGTTCATCTGCAAAACA 57.758 40.909 0.00 0.00 46.64 2.83
1612 2195 6.019075 GCTCACCAAAGTGTTTACAAATTTCC 60.019 38.462 0.00 0.00 44.83 3.13
1620 2203 4.377431 CGATCAGCTCACCAAAGTGTTTAC 60.377 45.833 0.00 0.00 44.83 2.01
1630 2213 4.559502 GCTATATTGTCGATCAGCTCACCA 60.560 45.833 0.00 0.00 0.00 4.17
1631 2214 3.923461 GCTATATTGTCGATCAGCTCACC 59.077 47.826 0.00 0.00 0.00 4.02
1635 2218 2.899900 TGGGCTATATTGTCGATCAGCT 59.100 45.455 0.00 0.00 0.00 4.24
1636 2219 3.257393 CTGGGCTATATTGTCGATCAGC 58.743 50.000 0.00 0.00 0.00 4.26
1662 2245 6.895782 TGGGATTAAATCGTAACAGGATCTT 58.104 36.000 0.00 0.00 0.00 2.40
1666 2249 5.131308 TCCATGGGATTAAATCGTAACAGGA 59.869 40.000 13.02 0.00 0.00 3.86
1673 2256 6.129179 ACATTTCTCCATGGGATTAAATCGT 58.871 36.000 13.02 10.16 30.12 3.73
1675 2258 8.242729 AGAACATTTCTCCATGGGATTAAATC 57.757 34.615 13.02 2.54 34.07 2.17
1775 2358 3.181509 GCTCAGTGCATCAGAAATCACAG 60.182 47.826 0.00 0.00 42.31 3.66
1796 2379 7.814587 AGTTCTTTCAAATGTATTTAAGCCAGC 59.185 33.333 0.00 0.00 0.00 4.85
1894 2477 7.569957 GCAATTGAGACATCCAACAAATGTTTC 60.570 37.037 10.34 0.00 37.47 2.78
1939 2524 7.011482 CCGTCTAGCTGCTGTTATTTAGAAAAT 59.989 37.037 13.43 0.00 0.00 1.82
2099 2685 9.700831 AAATAGAGGAAACATGGCTAGTTAATT 57.299 29.630 0.00 0.00 0.00 1.40
2146 2733 9.193806 ACTTTCTCTGCATCATAAATTAACCAT 57.806 29.630 0.00 0.00 0.00 3.55
2211 2798 1.302033 CTTCTGCTGGGTGCTTCGT 60.302 57.895 0.00 0.00 43.37 3.85
2275 2862 2.364632 TGCTTCATCCCAATAACACCG 58.635 47.619 0.00 0.00 0.00 4.94
2391 2989 9.989296 TTTCAGAATCCCAAATCTAATAAGGAA 57.011 29.630 0.00 0.00 0.00 3.36
2568 3181 4.917385 TGCATCTCCTCTCTCTATAGGAC 58.083 47.826 0.00 0.00 36.97 3.85
2569 3182 5.508567 CATGCATCTCCTCTCTCTATAGGA 58.491 45.833 0.00 0.00 39.63 2.94
2670 4010 5.496133 AGCTGATCGATGAATTTTCTTGG 57.504 39.130 0.54 0.00 0.00 3.61
2709 4073 6.155221 AGCACTTACATTGAGGAGACTAATCA 59.845 38.462 0.00 0.00 44.43 2.57
2710 4074 6.578023 AGCACTTACATTGAGGAGACTAATC 58.422 40.000 0.00 0.00 44.43 1.75
2711 4075 6.552445 AGCACTTACATTGAGGAGACTAAT 57.448 37.500 0.00 0.00 44.43 1.73
2712 4076 6.436218 TGTAGCACTTACATTGAGGAGACTAA 59.564 38.462 0.00 0.00 37.93 2.24
2713 4077 5.949952 TGTAGCACTTACATTGAGGAGACTA 59.050 40.000 0.00 0.00 37.93 2.59
2714 4078 4.772624 TGTAGCACTTACATTGAGGAGACT 59.227 41.667 0.00 0.00 39.66 3.24
2715 4079 5.073311 TGTAGCACTTACATTGAGGAGAC 57.927 43.478 0.00 0.00 37.35 3.36
2727 4091 4.404715 GGAGGGAGTACAATGTAGCACTTA 59.595 45.833 0.00 0.00 0.00 2.24
2815 4180 9.710818 TCAGTATTTTACATAACTACTCCCTCT 57.289 33.333 0.00 0.00 0.00 3.69
2831 4196 9.474920 CCAATTTTTCAACTGCTCAGTATTTTA 57.525 29.630 2.62 0.00 41.58 1.52
2838 4203 4.927425 CCATCCAATTTTTCAACTGCTCAG 59.073 41.667 0.00 0.00 0.00 3.35
2868 4233 7.776969 TCCCTCAGACGTACTACTTAATTGTAT 59.223 37.037 0.00 0.00 0.00 2.29
2952 5715 9.383519 GTCATTTTACAAGGAAGATATGTCTCA 57.616 33.333 0.00 0.00 32.15 3.27
2953 5716 8.831550 GGTCATTTTACAAGGAAGATATGTCTC 58.168 37.037 0.00 0.00 32.15 3.36
3017 5780 8.860088 AGCAAGAAAACACATAGGAAGTAAATT 58.140 29.630 0.00 0.00 0.00 1.82
3021 5784 6.530120 TCAGCAAGAAAACACATAGGAAGTA 58.470 36.000 0.00 0.00 0.00 2.24
3022 5785 5.376625 TCAGCAAGAAAACACATAGGAAGT 58.623 37.500 0.00 0.00 0.00 3.01
3154 5918 2.878406 TCTTCGCAAAAACAGGAGAAGG 59.122 45.455 0.00 0.00 40.11 3.46
3170 5934 6.715464 TCTGTTCTTTTAGTTGCTTTCTTCG 58.285 36.000 0.00 0.00 0.00 3.79
3176 5941 6.095440 TGCTTCTTCTGTTCTTTTAGTTGCTT 59.905 34.615 0.00 0.00 0.00 3.91
3178 5943 5.821204 TGCTTCTTCTGTTCTTTTAGTTGC 58.179 37.500 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.