Multiple sequence alignment - TraesCS2D01G177500

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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 TraesCS2D01G177500 chr2D 100.000 7547 0 0 933 8479 121005315 120997769 0.000000e+00 13937.0
1 TraesCS2D01G177500 chr2D 100.000 478 0 0 1 478 121006247 121005770 0.000000e+00 883.0
2 TraesCS2D01G177500 chr2D 86.022 279 31 4 5355 5626 36785005 36784728 8.320000e-75 292.0
3 TraesCS2D01G177500 chr2D 84.791 263 26 8 5792 6043 80984282 80984541 1.410000e-62 252.0
4 TraesCS2D01G177500 chr2D 95.833 48 2 0 2058 2105 121004324 121004277 2.540000e-10 78.7
5 TraesCS2D01G177500 chr2D 87.500 64 8 0 5169 5232 185393900 185393963 3.280000e-09 75.0
6 TraesCS2D01G177500 chr2D 87.500 64 7 1 5710 5773 86080997 86080935 1.180000e-08 73.1
7 TraesCS2D01G177500 chr2A 96.198 3498 78 13 934 4421 125210370 125206918 0.000000e+00 5672.0
8 TraesCS2D01G177500 chr2A 94.149 2666 78 28 5321 7970 125206130 125203527 0.000000e+00 3988.0
9 TraesCS2D01G177500 chr2A 97.715 744 17 0 4535 5278 125206880 125206137 0.000000e+00 1280.0
10 TraesCS2D01G177500 chr2A 88.301 359 30 10 5355 5704 777401472 777401827 3.660000e-113 420.0
11 TraesCS2D01G177500 chr2A 83.777 413 30 14 2 398 125210941 125210550 2.910000e-94 357.0
12 TraesCS2D01G177500 chr2A 85.135 296 33 6 5355 5642 41211560 41211268 8.320000e-75 292.0
13 TraesCS2D01G177500 chr2A 85.663 279 32 4 5355 5626 41221418 41221141 3.870000e-73 287.0
14 TraesCS2D01G177500 chr2A 85.039 254 25 6 5802 6043 14942505 14942253 6.570000e-61 246.0
15 TraesCS2D01G177500 chr2A 92.361 144 6 4 8341 8479 125202939 125202796 5.190000e-47 200.0
16 TraesCS2D01G177500 chr2A 96.581 117 4 0 5241 5357 78848937 78848821 2.410000e-45 195.0
17 TraesCS2D01G177500 chr2A 94.262 122 7 0 5236 5357 502330486 502330365 4.040000e-43 187.0
18 TraesCS2D01G177500 chr2A 81.959 194 6 10 8114 8287 125203402 125203218 4.130000e-28 137.0
19 TraesCS2D01G177500 chr2A 92.063 63 4 1 8029 8091 125203516 125203455 4.220000e-13 87.9
20 TraesCS2D01G177500 chr2A 95.833 48 2 0 2058 2105 125209417 125209370 2.540000e-10 78.7
21 TraesCS2D01G177500 chr2A 97.674 43 1 0 4481 4523 125206905 125206863 3.280000e-09 75.0
22 TraesCS2D01G177500 chr2A 95.455 44 1 1 933 976 779538130 779538088 1.530000e-07 69.4
23 TraesCS2D01G177500 chr2A 85.938 64 8 1 5710 5773 86440627 86440565 5.490000e-07 67.6
24 TraesCS2D01G177500 chr2A 100.000 28 0 0 5712 5739 12365026 12364999 1.500000e-02 52.8
25 TraesCS2D01G177500 chr2B 97.102 2519 59 5 1705 4217 174400726 174398216 0.000000e+00 4235.0
26 TraesCS2D01G177500 chr2B 94.528 1261 47 8 7030 8271 174394407 174393150 0.000000e+00 1927.0
27 TraesCS2D01G177500 chr2B 96.709 1033 29 2 5973 7004 174395436 174394408 0.000000e+00 1714.0
28 TraesCS2D01G177500 chr2B 95.426 962 26 8 3867 4811 174397772 174396812 0.000000e+00 1517.0
29 TraesCS2D01G177500 chr2B 94.965 715 20 7 954 1668 174401425 174400727 0.000000e+00 1107.0
30 TraesCS2D01G177500 chr2B 93.789 322 19 1 1308 1629 698590110 698589790 4.600000e-132 483.0
31 TraesCS2D01G177500 chr2B 89.851 335 11 5 5608 5919 174395768 174395434 7.920000e-110 409.0
32 TraesCS2D01G177500 chr2B 93.536 263 11 1 5355 5611 174396141 174395879 3.710000e-103 387.0
33 TraesCS2D01G177500 chr2B 88.742 302 11 4 4959 5243 174396434 174396139 1.750000e-91 348.0
34 TraesCS2D01G177500 chr2B 97.872 141 3 0 8339 8479 174392254 174392114 2.360000e-60 244.0
35 TraesCS2D01G177500 chr2B 88.235 204 11 6 2 195 174426685 174426485 1.840000e-56 231.0
36 TraesCS2D01G177500 chr2B 86.538 208 9 11 12 204 174430055 174429852 2.400000e-50 211.0
37 TraesCS2D01G177500 chr2B 91.667 144 7 2 255 398 174402017 174401879 2.410000e-45 195.0
38 TraesCS2D01G177500 chr2B 83.962 106 11 4 2 102 174428915 174428811 7.010000e-16 97.1
39 TraesCS2D01G177500 chr2B 91.803 61 4 1 190 249 174402119 174402059 5.450000e-12 84.2
40 TraesCS2D01G177500 chr7D 94.890 861 30 8 1444 2298 155437384 155436532 0.000000e+00 1334.0
41 TraesCS2D01G177500 chr1D 94.658 805 29 8 1499 2298 9923049 9922254 0.000000e+00 1236.0
42 TraesCS2D01G177500 chr1D 93.415 820 28 10 1496 2298 10038174 10038984 0.000000e+00 1192.0
43 TraesCS2D01G177500 chr1D 90.345 145 8 2 5792 5935 328859857 328859718 1.450000e-42 185.0
44 TraesCS2D01G177500 chr1D 95.833 48 2 0 1924 1971 9922494 9922447 2.540000e-10 78.7
45 TraesCS2D01G177500 chr5B 94.103 780 41 4 995 1773 678890011 678890786 0.000000e+00 1181.0
46 TraesCS2D01G177500 chr5B 93.292 805 40 8 1499 2298 453115954 453115159 0.000000e+00 1175.0
47 TraesCS2D01G177500 chr5B 90.449 178 13 4 933 1107 11791280 11791456 1.840000e-56 231.0
48 TraesCS2D01G177500 chr6B 90.640 844 62 8 933 1773 446282126 446282955 0.000000e+00 1105.0
49 TraesCS2D01G177500 chr6B 92.683 41 3 0 5710 5750 346804825 346804785 9.190000e-05 60.2
50 TraesCS2D01G177500 chr3A 91.449 690 46 8 1328 2013 570023102 570022422 0.000000e+00 935.0
51 TraesCS2D01G177500 chr3A 93.881 572 20 3 1728 2298 56495077 56495634 0.000000e+00 848.0
52 TraesCS2D01G177500 chr3A 92.767 318 21 1 1308 1625 59550146 59549831 7.760000e-125 459.0
53 TraesCS2D01G177500 chr3A 91.209 91 8 0 936 1026 570068751 570068661 3.210000e-24 124.0
54 TraesCS2D01G177500 chr3A 91.667 84 6 1 5053 5135 332556159 332556242 1.930000e-21 115.0
55 TraesCS2D01G177500 chr3A 95.455 44 1 1 933 976 71904632 71904674 1.530000e-07 69.4
56 TraesCS2D01G177500 chr7A 93.478 322 19 1 1308 1629 160398738 160398419 2.140000e-130 477.0
57 TraesCS2D01G177500 chr7A 87.187 359 32 10 5355 5704 39493892 39494245 6.170000e-106 396.0
58 TraesCS2D01G177500 chr7A 92.405 79 6 0 5058 5136 498590386 498590308 6.960000e-21 113.0
59 TraesCS2D01G177500 chr3B 93.478 322 19 1 1308 1629 727506367 727506686 2.140000e-130 477.0
60 TraesCS2D01G177500 chr3B 91.729 133 6 5 5227 5357 173371604 173371475 6.760000e-41 180.0
61 TraesCS2D01G177500 chr3B 91.667 132 8 3 5227 5357 173375814 173375685 6.760000e-41 180.0
62 TraesCS2D01G177500 chr4B 97.861 187 4 0 2112 2298 604267682 604267868 2.950000e-84 324.0
63 TraesCS2D01G177500 chr4B 97.326 187 5 0 2112 2298 546865831 546865645 1.370000e-82 318.0
64 TraesCS2D01G177500 chr4B 91.129 124 3 5 1762 1885 546865936 546865821 2.450000e-35 161.0
65 TraesCS2D01G177500 chr4B 95.349 43 2 0 5198 5240 20336907 20336865 1.530000e-07 69.4
66 TraesCS2D01G177500 chrUn 85.660 265 30 4 5355 5612 28695186 28694923 1.080000e-68 272.0
67 TraesCS2D01G177500 chrUn 90.541 74 7 0 5167 5240 28695259 28695186 1.950000e-16 99.0
68 TraesCS2D01G177500 chrUn 93.182 44 2 1 933 976 279159647 279159605 7.110000e-06 63.9
69 TraesCS2D01G177500 chr1A 84.528 265 33 4 5355 5612 67734594 67734331 1.090000e-63 255.0
70 TraesCS2D01G177500 chr1A 84.896 192 15 11 5524 5704 592765088 592765276 1.880000e-41 182.0
71 TraesCS2D01G177500 chr1B 91.724 145 11 1 5792 5935 589512896 589513040 5.190000e-47 200.0
72 TraesCS2D01G177500 chr1B 91.892 74 6 0 5167 5240 670290613 670290540 4.190000e-18 104.0
73 TraesCS2D01G177500 chr1B 90.566 53 5 0 5714 5766 387302008 387302060 4.250000e-08 71.3
74 TraesCS2D01G177500 chr1B 96.875 32 1 0 5716 5747 282836414 282836445 4.000000e-03 54.7
75 TraesCS2D01G177500 chr4A 95.798 119 5 0 5241 5359 340694804 340694686 8.690000e-45 193.0
76 TraesCS2D01G177500 chr4A 95.455 44 1 1 933 976 590625450 590625492 1.530000e-07 69.4
77 TraesCS2D01G177500 chr4A 95.349 43 2 0 5198 5240 591529480 591529438 1.530000e-07 69.4
78 TraesCS2D01G177500 chr4A 95.349 43 2 0 5198 5240 592515658 592515700 1.530000e-07 69.4
79 TraesCS2D01G177500 chr4A 95.455 44 1 1 933 976 604683939 604683981 1.530000e-07 69.4
80 TraesCS2D01G177500 chr3D 96.552 116 4 0 5242 5357 67711515 67711630 8.690000e-45 193.0
81 TraesCS2D01G177500 chr3D 95.726 117 5 0 5241 5357 279902326 279902210 1.120000e-43 189.0
82 TraesCS2D01G177500 chr3D 91.667 84 6 1 5053 5135 251316145 251316062 1.930000e-21 115.0
83 TraesCS2D01G177500 chr3D 92.308 78 6 0 5059 5136 127342719 127342796 2.500000e-20 111.0
84 TraesCS2D01G177500 chr3D 84.694 98 12 3 5039 5135 596889477 596889572 2.520000e-15 95.3
85 TraesCS2D01G177500 chr5A 94.958 119 6 0 5241 5359 115018753 115018635 4.040000e-43 187.0
86 TraesCS2D01G177500 chr5A 89.855 69 7 0 5164 5232 469650355 469650423 1.170000e-13 89.8
87 TraesCS2D01G177500 chr5D 92.969 128 8 1 5240 5367 349803571 349803697 1.450000e-42 185.0
88 TraesCS2D01G177500 chr6A 93.151 73 5 0 5064 5136 161148212 161148140 3.240000e-19 108.0
89 TraesCS2D01G177500 chr4D 91.139 79 7 0 5058 5136 28238569 28238491 3.240000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G177500 chr2D 120997769 121006247 8478 True 4966.233333 13937 98.611000 1 8479 3 chr2D.!!$R3 8478
1 TraesCS2D01G177500 chr2A 125202796 125210941 8145 True 1319.511111 5672 92.414333 2 8479 9 chr2A.!!$R9 8477
2 TraesCS2D01G177500 chr2B 174392114 174402119 10005 True 1106.109091 4235 93.836455 190 8479 11 chr2B.!!$R2 8289
3 TraesCS2D01G177500 chr7D 155436532 155437384 852 True 1334.000000 1334 94.890000 1444 2298 1 chr7D.!!$R1 854
4 TraesCS2D01G177500 chr1D 10038174 10038984 810 False 1192.000000 1192 93.415000 1496 2298 1 chr1D.!!$F1 802
5 TraesCS2D01G177500 chr1D 9922254 9923049 795 True 657.350000 1236 95.245500 1499 2298 2 chr1D.!!$R2 799
6 TraesCS2D01G177500 chr5B 678890011 678890786 775 False 1181.000000 1181 94.103000 995 1773 1 chr5B.!!$F2 778
7 TraesCS2D01G177500 chr5B 453115159 453115954 795 True 1175.000000 1175 93.292000 1499 2298 1 chr5B.!!$R1 799
8 TraesCS2D01G177500 chr6B 446282126 446282955 829 False 1105.000000 1105 90.640000 933 1773 1 chr6B.!!$F1 840
9 TraesCS2D01G177500 chr3A 570022422 570023102 680 True 935.000000 935 91.449000 1328 2013 1 chr3A.!!$R2 685
10 TraesCS2D01G177500 chr3A 56495077 56495634 557 False 848.000000 848 93.881000 1728 2298 1 chr3A.!!$F1 570

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
43 44 0.106268 TGGTTGCTTGCTCCTCCAAA 60.106 50.000 8.26 0.0 0.00 3.28 F
47 48 0.250901 TGCTTGCTCCTCCAAACTCC 60.251 55.000 0.00 0.0 0.00 3.85 F
153 164 0.333312 ACTCCACCAACAAACCACCA 59.667 50.000 0.00 0.0 0.00 4.17 F
473 531 0.399233 ATTTCCCTCTCCCTCTCCGG 60.399 60.000 0.00 0.0 0.00 5.14 F
1218 1278 1.141881 CAGCTACCAGCCCTACGTG 59.858 63.158 0.00 0.0 43.77 4.49 F
1413 1475 1.340399 TGAGGCCATCGGATTCTGCT 61.340 55.000 5.01 0.0 0.00 4.24 F
3228 3314 1.542472 CATGTGCAGCCTTCAACATCA 59.458 47.619 0.00 0.0 0.00 3.07 F
4894 6131 2.427506 CAAGTCCTGAAGTAAGGCCAC 58.572 52.381 5.01 0.0 37.24 5.01 F
5159 6413 0.693049 ACAAGCTTCTTGGGACGGAT 59.307 50.000 10.80 0.0 0.00 4.18 F
6999 8407 1.269723 GCAGCACAAAAAGTAGGTCCC 59.730 52.381 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1475 1.059838 CGATACGCTGACGACGACA 59.940 57.895 0.00 0.00 43.93 4.35 R
1485 1549 1.318576 GTCAACCCTCACCAAACTGG 58.681 55.000 0.00 0.00 45.02 4.00 R
1857 1925 1.478105 GTAAAGGCCAAGCAATCCAGG 59.522 52.381 5.01 0.00 0.00 4.45 R
2435 2516 4.349636 TCCATGGTTTGGTCTTCTACTTCA 59.650 41.667 12.58 0.00 46.52 3.02 R
3228 3314 6.879993 ACGTATCTCTATCGTCATAATCCTGT 59.120 38.462 0.00 0.00 32.26 4.00 R
3307 3393 0.588252 CACTGCGACAAGAAACCAGG 59.412 55.000 0.00 0.00 0.00 4.45 R
5148 6402 1.078426 GGACACCATCCGTCCCAAG 60.078 63.158 0.00 0.00 46.12 3.61 R
6460 7867 2.896044 TGCACAATTGGATTAACCTGCA 59.104 40.909 10.83 10.86 40.72 4.41 R
7165 8573 1.102809 TAATGGCTCATTGGCGCCTG 61.103 55.000 29.70 19.14 46.42 4.85 R
8287 10524 0.601841 CCCGGTTGCACGTCTTACTT 60.602 55.000 0.00 0.00 0.00 2.24 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
33 34 2.503895 AGGAAGGAGATGGTTGCTTG 57.496 50.000 0.00 0.00 0.00 4.01
43 44 0.106268 TGGTTGCTTGCTCCTCCAAA 60.106 50.000 8.26 0.00 0.00 3.28
47 48 0.250901 TGCTTGCTCCTCCAAACTCC 60.251 55.000 0.00 0.00 0.00 3.85
56 57 1.272092 CCTCCAAACTCCTGCCATTGA 60.272 52.381 0.00 0.00 0.00 2.57
57 58 1.815003 CTCCAAACTCCTGCCATTGAC 59.185 52.381 0.00 0.00 0.00 3.18
58 59 0.890683 CCAAACTCCTGCCATTGACC 59.109 55.000 0.00 0.00 0.00 4.02
73 84 7.924940 TGCCATTGACCTTCAAAATTTAAAAC 58.075 30.769 0.00 0.00 40.12 2.43
77 88 9.437045 CATTGACCTTCAAAATTTAAAACAAGC 57.563 29.630 0.00 0.00 40.12 4.01
80 91 9.877178 TGACCTTCAAAATTTAAAACAAGCTAA 57.123 25.926 0.00 0.00 0.00 3.09
95 106 5.971763 ACAAGCTAACACAAAAACAATGGA 58.028 33.333 0.00 0.00 0.00 3.41
106 117 7.280652 ACACAAAAACAATGGAAAGGAAATCAG 59.719 33.333 0.00 0.00 0.00 2.90
147 158 0.336737 ACCCCAACTCCACCAACAAA 59.663 50.000 0.00 0.00 0.00 2.83
148 159 0.750249 CCCCAACTCCACCAACAAAC 59.250 55.000 0.00 0.00 0.00 2.93
149 160 0.750249 CCCAACTCCACCAACAAACC 59.250 55.000 0.00 0.00 0.00 3.27
150 161 1.479709 CCAACTCCACCAACAAACCA 58.520 50.000 0.00 0.00 0.00 3.67
151 162 1.136110 CCAACTCCACCAACAAACCAC 59.864 52.381 0.00 0.00 0.00 4.16
152 163 1.136110 CAACTCCACCAACAAACCACC 59.864 52.381 0.00 0.00 0.00 4.61
153 164 0.333312 ACTCCACCAACAAACCACCA 59.667 50.000 0.00 0.00 0.00 4.17
154 165 1.063266 ACTCCACCAACAAACCACCAT 60.063 47.619 0.00 0.00 0.00 3.55
155 166 2.175931 ACTCCACCAACAAACCACCATA 59.824 45.455 0.00 0.00 0.00 2.74
156 167 3.226777 CTCCACCAACAAACCACCATAA 58.773 45.455 0.00 0.00 0.00 1.90
157 168 2.959707 TCCACCAACAAACCACCATAAC 59.040 45.455 0.00 0.00 0.00 1.89
158 169 2.695666 CCACCAACAAACCACCATAACA 59.304 45.455 0.00 0.00 0.00 2.41
159 170 3.133003 CCACCAACAAACCACCATAACAA 59.867 43.478 0.00 0.00 0.00 2.83
165 176 6.183360 CCAACAAACCACCATAACAAGTTACT 60.183 38.462 0.00 0.00 0.00 2.24
167 178 7.500720 ACAAACCACCATAACAAGTTACTAC 57.499 36.000 0.00 0.00 0.00 2.73
168 179 7.284820 ACAAACCACCATAACAAGTTACTACT 58.715 34.615 0.00 0.00 35.68 2.57
173 184 8.092687 ACCACCATAACAAGTTACTACTAACAG 58.907 37.037 0.00 0.00 35.56 3.16
176 187 6.255020 CCATAACAAGTTACTACTAACAGCCG 59.745 42.308 0.00 0.00 35.56 5.52
192 203 7.759450 TAACAGCCGGGTTAACAGGTTACTG 62.759 48.000 1.64 16.77 40.08 2.74
243 255 1.215423 AGAAAACCAACCAGCTCACCT 59.785 47.619 0.00 0.00 0.00 4.00
249 261 1.067516 CCAACCAGCTCACCTTTGTTG 59.932 52.381 0.00 0.00 35.22 3.33
250 262 2.023673 CAACCAGCTCACCTTTGTTGA 58.976 47.619 0.00 0.00 36.51 3.18
251 263 2.426738 CAACCAGCTCACCTTTGTTGAA 59.573 45.455 0.00 0.00 36.51 2.69
252 264 2.733956 ACCAGCTCACCTTTGTTGAAA 58.266 42.857 0.00 0.00 0.00 2.69
253 265 3.096092 ACCAGCTCACCTTTGTTGAAAA 58.904 40.909 0.00 0.00 0.00 2.29
317 375 1.128692 GAAAACCATCCGCGAGACAAG 59.871 52.381 8.23 0.00 0.00 3.16
324 382 1.153823 CCGCGAGACAAGGAACGAT 60.154 57.895 8.23 0.00 0.00 3.73
344 402 5.013236 CGATTTAACGACGAATCAAACCAG 58.987 41.667 0.00 0.00 33.00 4.00
391 449 1.485066 TCCTTATTCTCACCGCCTTCC 59.515 52.381 0.00 0.00 0.00 3.46
402 460 4.704833 GCCTTCCGCAGCCTGTCA 62.705 66.667 0.00 0.00 37.47 3.58
403 461 2.743928 CCTTCCGCAGCCTGTCAC 60.744 66.667 0.00 0.00 0.00 3.67
404 462 2.743928 CTTCCGCAGCCTGTCACC 60.744 66.667 0.00 0.00 0.00 4.02
405 463 4.329545 TTCCGCAGCCTGTCACCC 62.330 66.667 0.00 0.00 0.00 4.61
409 467 4.729918 GCAGCCTGTCACCCCCAG 62.730 72.222 0.00 0.00 0.00 4.45
410 468 4.729918 CAGCCTGTCACCCCCAGC 62.730 72.222 0.00 0.00 0.00 4.85
411 469 4.990910 AGCCTGTCACCCCCAGCT 62.991 66.667 0.00 0.00 0.00 4.24
412 470 4.416738 GCCTGTCACCCCCAGCTC 62.417 72.222 0.00 0.00 0.00 4.09
413 471 4.087892 CCTGTCACCCCCAGCTCG 62.088 72.222 0.00 0.00 0.00 5.03
414 472 4.767255 CTGTCACCCCCAGCTCGC 62.767 72.222 0.00 0.00 0.00 5.03
442 500 4.344865 GCCTCCTCGCAACCCCAA 62.345 66.667 0.00 0.00 0.00 4.12
466 524 1.773653 AGCTCATCATTTCCCTCTCCC 59.226 52.381 0.00 0.00 0.00 4.30
467 525 1.773653 GCTCATCATTTCCCTCTCCCT 59.226 52.381 0.00 0.00 0.00 4.20
468 526 2.224499 GCTCATCATTTCCCTCTCCCTC 60.224 54.545 0.00 0.00 0.00 4.30
469 527 3.316501 CTCATCATTTCCCTCTCCCTCT 58.683 50.000 0.00 0.00 0.00 3.69
470 528 3.312890 TCATCATTTCCCTCTCCCTCTC 58.687 50.000 0.00 0.00 0.00 3.20
471 529 2.182516 TCATTTCCCTCTCCCTCTCC 57.817 55.000 0.00 0.00 0.00 3.71
472 530 0.755686 CATTTCCCTCTCCCTCTCCG 59.244 60.000 0.00 0.00 0.00 4.63
473 531 0.399233 ATTTCCCTCTCCCTCTCCGG 60.399 60.000 0.00 0.00 0.00 5.14
1218 1278 1.141881 CAGCTACCAGCCCTACGTG 59.858 63.158 0.00 0.00 43.77 4.49
1413 1475 1.340399 TGAGGCCATCGGATTCTGCT 61.340 55.000 5.01 0.00 0.00 4.24
1485 1549 1.681538 TGGCTCGTCTCAGTAGGATC 58.318 55.000 0.00 0.00 0.00 3.36
1669 1733 7.328005 CGTAAGTTCTAGACAAGTAAAAGGGAC 59.672 40.741 0.00 0.00 0.00 4.46
1696 1764 9.578439 ACACCTTCAGTTATAAACGAATAGTAC 57.422 33.333 0.00 0.00 36.23 2.73
1839 1907 4.891168 TGCATTATCTCATTTGGACATGCT 59.109 37.500 0.00 0.00 35.47 3.79
1840 1908 5.009310 TGCATTATCTCATTTGGACATGCTC 59.991 40.000 0.00 0.00 35.47 4.26
1841 1909 5.009310 GCATTATCTCATTTGGACATGCTCA 59.991 40.000 0.00 0.00 33.47 4.26
1842 1910 6.436261 CATTATCTCATTTGGACATGCTCAC 58.564 40.000 0.00 0.00 0.00 3.51
1843 1911 3.421919 TCTCATTTGGACATGCTCACA 57.578 42.857 0.00 0.00 0.00 3.58
1844 1912 3.959293 TCTCATTTGGACATGCTCACAT 58.041 40.909 0.00 0.00 36.79 3.21
2435 2516 8.535335 AGAATGTCATACAATACTCAAGTGACT 58.465 33.333 0.00 0.00 36.40 3.41
3074 3160 7.512992 TGATTTTCCAGGCATTTTAAAGGAAA 58.487 30.769 11.17 11.17 41.77 3.13
3118 3204 9.825109 TGATGAACGTAAATTACTAATCCATCA 57.175 29.630 13.71 13.71 0.00 3.07
3228 3314 1.542472 CATGTGCAGCCTTCAACATCA 59.458 47.619 0.00 0.00 0.00 3.07
3307 3393 7.968956 GGAATAGAAAGGTTAGCTGCTTTTTAC 59.031 37.037 7.79 1.47 0.00 2.01
3320 3406 5.257082 TGCTTTTTACCTGGTTTCTTGTC 57.743 39.130 3.84 0.00 0.00 3.18
3388 3474 4.976224 TGAGATCTGCACATGGAAAATG 57.024 40.909 0.00 0.00 0.00 2.32
3477 3563 6.751888 TGTTATCATGATACCGCGATAAGATG 59.248 38.462 15.10 1.14 32.51 2.90
4398 5283 6.646240 GTCTCTTATTTCTGGCATCTGATCTC 59.354 42.308 0.00 0.00 0.00 2.75
4437 5322 5.388578 GCGTAAAAGAGCTTACAGACAACTC 60.389 44.000 0.00 0.00 32.30 3.01
4514 5441 6.123651 TGGTAGTATGGTGTGTTTGTTTTCT 58.876 36.000 0.00 0.00 0.00 2.52
4515 5442 7.281098 TGGTAGTATGGTGTGTTTGTTTTCTA 58.719 34.615 0.00 0.00 0.00 2.10
4516 5443 7.774157 TGGTAGTATGGTGTGTTTGTTTTCTAA 59.226 33.333 0.00 0.00 0.00 2.10
4517 5444 8.789762 GGTAGTATGGTGTGTTTGTTTTCTAAT 58.210 33.333 0.00 0.00 0.00 1.73
4520 5447 9.131791 AGTATGGTGTGTTTGTTTTCTAATTCT 57.868 29.630 0.00 0.00 0.00 2.40
4521 5448 9.744468 GTATGGTGTGTTTGTTTTCTAATTCTT 57.256 29.630 0.00 0.00 0.00 2.52
4523 5450 9.665719 ATGGTGTGTTTGTTTTCTAATTCTTTT 57.334 25.926 0.00 0.00 0.00 2.27
4524 5451 9.495572 TGGTGTGTTTGTTTTCTAATTCTTTTT 57.504 25.926 0.00 0.00 0.00 1.94
4703 5630 6.183361 ACCCCATTGCTTTCATTTACTTGAAA 60.183 34.615 0.31 0.31 41.92 2.69
4811 5740 8.292448 GTGTTTTGAGTGATGGCCATATATTAG 58.708 37.037 20.84 0.00 0.00 1.73
4813 5742 9.502091 GTTTTGAGTGATGGCCATATATTAGTA 57.498 33.333 20.84 0.00 0.00 1.82
4860 6097 6.399639 ACGTCAATGTTCCCACTTAAAAAT 57.600 33.333 0.00 0.00 0.00 1.82
4894 6131 2.427506 CAAGTCCTGAAGTAAGGCCAC 58.572 52.381 5.01 0.00 37.24 5.01
4944 6181 3.135348 CCACATAGCCAATCTTCTCCTCA 59.865 47.826 0.00 0.00 0.00 3.86
5096 6333 8.514594 CCTAAAATGCTTGTCTTAGATTTGTCA 58.485 33.333 0.00 0.00 0.00 3.58
5148 6402 4.335874 TGTCTAGATACGGAGACAAGCTTC 59.664 45.833 0.00 0.00 46.93 3.86
5159 6413 0.693049 ACAAGCTTCTTGGGACGGAT 59.307 50.000 10.80 0.00 0.00 4.18
5250 6504 4.436079 ACCTGTTTATTGGTACTCCCTCT 58.564 43.478 0.00 0.00 34.36 3.69
5278 6532 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
5280 6534 7.414098 CGGAAATACTTGTCCTAGAAATGGTTG 60.414 40.741 0.00 0.00 0.00 3.77
5281 6535 7.393515 GGAAATACTTGTCCTAGAAATGGTTGT 59.606 37.037 0.00 0.00 0.00 3.32
5283 6537 9.975218 AAATACTTGTCCTAGAAATGGTTGTAT 57.025 29.630 0.00 0.00 0.00 2.29
5284 6538 9.614792 AATACTTGTCCTAGAAATGGTTGTATC 57.385 33.333 0.00 0.00 0.00 2.24
5285 6539 7.259088 ACTTGTCCTAGAAATGGTTGTATCT 57.741 36.000 0.00 0.00 0.00 1.98
5286 6540 8.375493 ACTTGTCCTAGAAATGGTTGTATCTA 57.625 34.615 0.00 0.00 0.00 1.98
5287 6541 8.478877 ACTTGTCCTAGAAATGGTTGTATCTAG 58.521 37.037 0.00 0.00 40.55 2.43
5288 6542 8.603898 TTGTCCTAGAAATGGTTGTATCTAGA 57.396 34.615 9.60 0.00 42.48 2.43
5289 6543 8.008513 TGTCCTAGAAATGGTTGTATCTAGAC 57.991 38.462 9.60 7.06 42.48 2.59
5290 6544 7.839705 TGTCCTAGAAATGGTTGTATCTAGACT 59.160 37.037 9.60 0.00 42.48 3.24
5291 6545 8.697292 GTCCTAGAAATGGTTGTATCTAGACTT 58.303 37.037 9.60 0.00 42.48 3.01
5292 6546 8.696374 TCCTAGAAATGGTTGTATCTAGACTTG 58.304 37.037 9.60 0.00 42.48 3.16
5293 6547 8.478877 CCTAGAAATGGTTGTATCTAGACTTGT 58.521 37.037 9.60 0.00 42.48 3.16
5294 6548 9.877178 CTAGAAATGGTTGTATCTAGACTTGTT 57.123 33.333 0.00 0.00 42.48 2.83
5296 6550 9.574516 AGAAATGGTTGTATCTAGACTTGTTTT 57.425 29.630 0.00 0.00 0.00 2.43
5534 6788 4.096833 GCAAACATCTCCATTGATGCTACA 59.903 41.667 4.63 0.00 45.51 2.74
5544 6798 4.443881 CCATTGATGCTACAGGACATCTCA 60.444 45.833 4.78 0.00 42.57 3.27
5586 6840 5.953183 TGCATGTTAATCACATCACCTTTC 58.047 37.500 0.00 0.00 43.17 2.62
5724 7115 5.881923 TGTGTTATACTACCTCCATTCCC 57.118 43.478 0.00 0.00 0.00 3.97
5884 7281 6.634805 ACAGATGTGGATTAGACTGTACTTG 58.365 40.000 0.00 0.00 36.94 3.16
6188 7585 3.845781 ACGGACATGCCTCTTGATAAT 57.154 42.857 0.00 0.00 0.00 1.28
6215 7612 9.458374 GTAAAATGCTCAAACTTTGCTACTTTA 57.542 29.630 0.00 0.00 0.00 1.85
6364 7771 5.152804 GCTGAGAAGTTCTGCATTTCTTTC 58.847 41.667 10.90 0.00 46.58 2.62
6460 7867 2.022718 ACTGGAGAGAAAGGTGAGCT 57.977 50.000 0.00 0.00 0.00 4.09
6646 8053 6.121590 ACATAGTTGTTCCATGCATCATACA 58.878 36.000 0.00 0.00 29.55 2.29
6963 8371 4.663636 GTACACAAGCATGGTTGTACTC 57.336 45.455 35.38 24.68 40.69 2.59
6999 8407 1.269723 GCAGCACAAAAAGTAGGTCCC 59.730 52.381 0.00 0.00 0.00 4.46
7005 8413 4.082949 GCACAAAAAGTAGGTCCCACATAC 60.083 45.833 0.00 0.00 35.77 2.39
7010 8418 7.827729 ACAAAAAGTAGGTCCCACATACTATTC 59.172 37.037 1.67 0.00 43.89 1.75
7076 8484 5.119931 TGCATATCGCTGTTTCTTTTGTT 57.880 34.783 0.00 0.00 43.06 2.83
7241 8649 1.975407 CAAAGCAGCCACCAGGGAG 60.975 63.158 0.00 0.00 40.01 4.30
7282 8690 1.202582 CGACGAGAAACCACTGGAGAT 59.797 52.381 0.71 0.00 0.00 2.75
7369 8777 1.443194 GCATCAAGGCGTGCAACAG 60.443 57.895 0.00 0.00 40.94 3.16
7395 8803 1.672356 GACCAGTGCGCCATCTTGT 60.672 57.895 4.18 2.73 0.00 3.16
7409 8817 1.893808 CTTGTTGGCGCAGGTCTGT 60.894 57.895 10.83 0.00 0.00 3.41
7488 8896 1.716826 CGAGTCGTAGTGAGAGCCCC 61.717 65.000 3.82 0.00 0.00 5.80
7571 8979 3.526931 TCAAGAATGATCAGACCGTCC 57.473 47.619 0.09 0.00 0.00 4.79
7582 8990 0.316204 AGACCGTCCTTGGTTGTACG 59.684 55.000 0.00 0.00 44.01 3.67
7657 9065 5.336372 CCCAAATGTTCGGATGAGCTTTTTA 60.336 40.000 0.00 0.00 32.76 1.52
7796 9210 2.644992 CCGCCTTTGCCAAGTCAC 59.355 61.111 0.00 0.00 0.00 3.67
7852 9266 5.460748 GTGTTTAAGGTCCAATTGTTTTCGG 59.539 40.000 4.43 0.00 0.00 4.30
7947 9361 5.084519 AGCCGTCAATGGTATAAGAGGATA 58.915 41.667 0.00 0.00 0.00 2.59
7948 9362 5.721960 AGCCGTCAATGGTATAAGAGGATAT 59.278 40.000 0.00 0.00 0.00 1.63
8002 9421 4.352298 ACTCTGAACCTCTCCCATTTTCTT 59.648 41.667 0.00 0.00 0.00 2.52
8061 9480 4.407621 TCTTCGAATTATTGTGGCCCTAGA 59.592 41.667 0.00 0.00 0.00 2.43
8084 9503 3.918591 GTCATACAGTAACACCGTGTCTG 59.081 47.826 15.44 15.44 0.00 3.51
8121 9570 2.478539 GCAATGCAACCTAAGTAGCAGC 60.479 50.000 0.00 0.00 40.71 5.25
8178 9635 3.066342 GCATGGAGCACGTAGTAGTAGAA 59.934 47.826 0.00 0.00 41.61 2.10
8250 9721 2.353858 CAAGCACAATGCCTGGGAA 58.646 52.632 0.00 0.00 46.52 3.97
8287 10524 1.805539 CCGTCGATGCGCAAGAAGA 60.806 57.895 25.01 15.61 43.02 2.87
8289 10526 0.024238 CGTCGATGCGCAAGAAGAAG 59.976 55.000 17.11 10.08 43.02 2.85
8290 10527 1.071605 GTCGATGCGCAAGAAGAAGT 58.928 50.000 17.11 0.00 43.02 3.01
8291 10528 2.259618 GTCGATGCGCAAGAAGAAGTA 58.740 47.619 17.11 0.00 43.02 2.24
8292 10529 2.666508 GTCGATGCGCAAGAAGAAGTAA 59.333 45.455 17.11 0.00 43.02 2.24
8293 10530 2.923655 TCGATGCGCAAGAAGAAGTAAG 59.076 45.455 17.11 0.00 43.02 2.34
8303 10703 3.391049 AGAAGAAGTAAGACGTGCAACC 58.609 45.455 0.00 0.00 0.00 3.77
8320 10720 4.994756 CGGGCAAGTGGGGGCTTT 62.995 66.667 0.00 0.00 0.00 3.51
8321 10721 2.997315 GGGCAAGTGGGGGCTTTC 60.997 66.667 0.00 0.00 0.00 2.62
8322 10722 2.118294 GGCAAGTGGGGGCTTTCT 59.882 61.111 0.00 0.00 0.00 2.52
8323 10723 1.533994 GGCAAGTGGGGGCTTTCTT 60.534 57.895 0.00 0.00 0.00 2.52
8324 10724 1.536073 GGCAAGTGGGGGCTTTCTTC 61.536 60.000 0.00 0.00 0.00 2.87
8325 10725 1.866853 GCAAGTGGGGGCTTTCTTCG 61.867 60.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.359900 CAACCATCTCCTTCCTTTCGG 58.640 52.381 0.00 0.00 0.00 4.30
10 11 1.740025 GCAACCATCTCCTTCCTTTCG 59.260 52.381 0.00 0.00 0.00 3.46
19 20 0.034670 AGGAGCAAGCAACCATCTCC 60.035 55.000 10.01 0.00 42.68 3.71
33 34 1.377856 GGCAGGAGTTTGGAGGAGC 60.378 63.158 0.00 0.00 0.00 4.70
43 44 1.067295 TGAAGGTCAATGGCAGGAGT 58.933 50.000 0.00 0.00 0.00 3.85
47 48 7.727331 TTTAAATTTTGAAGGTCAATGGCAG 57.273 32.000 0.00 0.00 36.11 4.85
56 57 9.660180 TGTTAGCTTGTTTTAAATTTTGAAGGT 57.340 25.926 0.00 0.97 0.00 3.50
57 58 9.914923 GTGTTAGCTTGTTTTAAATTTTGAAGG 57.085 29.630 0.00 0.00 0.00 3.46
73 84 6.900568 TTCCATTGTTTTTGTGTTAGCTTG 57.099 33.333 0.00 0.00 0.00 4.01
77 88 8.485976 TTTCCTTTCCATTGTTTTTGTGTTAG 57.514 30.769 0.00 0.00 0.00 2.34
80 91 7.108847 TGATTTCCTTTCCATTGTTTTTGTGT 58.891 30.769 0.00 0.00 0.00 3.72
91 102 4.670765 AGCACTTCTGATTTCCTTTCCAT 58.329 39.130 0.00 0.00 0.00 3.41
95 106 3.505293 GCTGAGCACTTCTGATTTCCTTT 59.495 43.478 0.00 0.00 0.00 3.11
106 117 2.259505 GCATCTTTGCTGAGCACTTC 57.740 50.000 6.64 0.00 45.77 3.01
129 140 0.750249 GTTTGTTGGTGGAGTTGGGG 59.250 55.000 0.00 0.00 0.00 4.96
147 158 7.965718 TGTTAGTAGTAACTTGTTATGGTGGT 58.034 34.615 18.87 0.00 39.55 4.16
148 159 7.064253 GCTGTTAGTAGTAACTTGTTATGGTGG 59.936 40.741 18.87 0.62 39.55 4.61
149 160 7.064253 GGCTGTTAGTAGTAACTTGTTATGGTG 59.936 40.741 18.87 1.77 39.55 4.17
150 161 7.101700 GGCTGTTAGTAGTAACTTGTTATGGT 58.898 38.462 18.87 0.00 39.55 3.55
151 162 6.255020 CGGCTGTTAGTAGTAACTTGTTATGG 59.745 42.308 18.87 3.73 39.55 2.74
152 163 6.255020 CCGGCTGTTAGTAGTAACTTGTTATG 59.745 42.308 18.87 5.31 39.55 1.90
153 164 6.335777 CCGGCTGTTAGTAGTAACTTGTTAT 58.664 40.000 18.87 0.00 39.55 1.89
154 165 5.336690 CCCGGCTGTTAGTAGTAACTTGTTA 60.337 44.000 18.87 0.70 39.55 2.41
155 166 4.562143 CCCGGCTGTTAGTAGTAACTTGTT 60.562 45.833 18.87 0.00 39.55 2.83
156 167 3.056322 CCCGGCTGTTAGTAGTAACTTGT 60.056 47.826 18.87 0.00 39.55 3.16
157 168 3.056322 ACCCGGCTGTTAGTAGTAACTTG 60.056 47.826 18.87 13.27 39.55 3.16
158 169 3.168292 ACCCGGCTGTTAGTAGTAACTT 58.832 45.455 18.87 0.00 39.55 2.66
159 170 2.812658 ACCCGGCTGTTAGTAGTAACT 58.187 47.619 18.87 0.00 39.55 2.24
165 176 2.234414 CCTGTTAACCCGGCTGTTAGTA 59.766 50.000 2.48 0.00 32.63 1.82
167 178 1.002773 ACCTGTTAACCCGGCTGTTAG 59.997 52.381 2.48 0.00 32.63 2.34
168 179 1.058284 ACCTGTTAACCCGGCTGTTA 58.942 50.000 2.48 0.00 0.00 2.41
173 184 1.002315 TCAGTAACCTGTTAACCCGGC 59.998 52.381 2.48 0.00 39.82 6.13
176 187 4.711399 AGTTGTCAGTAACCTGTTAACCC 58.289 43.478 2.48 0.00 39.82 4.11
192 203 4.841443 AATAAAACCCGGTTGAGTTGTC 57.159 40.909 2.79 0.00 0.00 3.18
198 209 9.563748 CTTTCCTATATAATAAAACCCGGTTGA 57.436 33.333 2.79 0.00 0.00 3.18
243 255 9.956720 TTCTTTTGCTTTTCAATTTTCAACAAA 57.043 22.222 0.00 0.00 34.12 2.83
249 261 8.962857 TGGTTTTCTTTTGCTTTTCAATTTTC 57.037 26.923 0.00 0.00 34.12 2.29
250 262 7.541783 GCTGGTTTTCTTTTGCTTTTCAATTTT 59.458 29.630 0.00 0.00 34.12 1.82
251 263 7.028962 GCTGGTTTTCTTTTGCTTTTCAATTT 58.971 30.769 0.00 0.00 34.12 1.82
252 264 6.375174 AGCTGGTTTTCTTTTGCTTTTCAATT 59.625 30.769 0.00 0.00 34.12 2.32
253 265 5.882000 AGCTGGTTTTCTTTTGCTTTTCAAT 59.118 32.000 0.00 0.00 34.12 2.57
304 362 1.153823 CGTTCCTTGTCTCGCGGAT 60.154 57.895 6.13 0.00 0.00 4.18
317 375 4.828291 TGATTCGTCGTTAAATCGTTCC 57.172 40.909 0.00 0.00 35.16 3.62
324 382 3.058777 GCCTGGTTTGATTCGTCGTTAAA 60.059 43.478 0.00 0.00 0.00 1.52
425 483 4.344865 TTGGGGTTGCGAGGAGGC 62.345 66.667 0.00 0.00 0.00 4.70
426 484 2.359975 GTTGGGGTTGCGAGGAGG 60.360 66.667 0.00 0.00 0.00 4.30
427 485 2.359975 GGTTGGGGTTGCGAGGAG 60.360 66.667 0.00 0.00 0.00 3.69
428 486 3.961414 GGGTTGGGGTTGCGAGGA 61.961 66.667 0.00 0.00 0.00 3.71
429 487 4.278513 TGGGTTGGGGTTGCGAGG 62.279 66.667 0.00 0.00 0.00 4.63
430 488 2.672996 CTGGGTTGGGGTTGCGAG 60.673 66.667 0.00 0.00 0.00 5.03
431 489 4.966787 GCTGGGTTGGGGTTGCGA 62.967 66.667 0.00 0.00 0.00 5.10
432 490 4.974721 AGCTGGGTTGGGGTTGCG 62.975 66.667 0.00 0.00 0.00 4.85
433 491 2.991540 GAGCTGGGTTGGGGTTGC 60.992 66.667 0.00 0.00 0.00 4.17
434 492 0.967380 GATGAGCTGGGTTGGGGTTG 60.967 60.000 0.00 0.00 0.00 3.77
435 493 1.384191 GATGAGCTGGGTTGGGGTT 59.616 57.895 0.00 0.00 0.00 4.11
436 494 1.217057 ATGATGAGCTGGGTTGGGGT 61.217 55.000 0.00 0.00 0.00 4.95
437 495 0.032813 AATGATGAGCTGGGTTGGGG 60.033 55.000 0.00 0.00 0.00 4.96
438 496 1.753073 GAAATGATGAGCTGGGTTGGG 59.247 52.381 0.00 0.00 0.00 4.12
439 497 1.753073 GGAAATGATGAGCTGGGTTGG 59.247 52.381 0.00 0.00 0.00 3.77
440 498 1.753073 GGGAAATGATGAGCTGGGTTG 59.247 52.381 0.00 0.00 0.00 3.77
441 499 1.642762 AGGGAAATGATGAGCTGGGTT 59.357 47.619 0.00 0.00 0.00 4.11
442 500 1.213926 GAGGGAAATGATGAGCTGGGT 59.786 52.381 0.00 0.00 0.00 4.51
993 1051 0.107654 CGAAGTCCTCCATGGGGAAC 60.108 60.000 15.22 1.44 44.38 3.62
1413 1475 1.059838 CGATACGCTGACGACGACA 59.940 57.895 0.00 0.00 43.93 4.35
1485 1549 1.318576 GTCAACCCTCACCAAACTGG 58.681 55.000 0.00 0.00 45.02 4.00
1640 1704 9.420551 CCTTTTACTTGTCTAGAACTTACGAAT 57.579 33.333 0.00 0.00 0.00 3.34
1669 1733 8.475331 ACTATTCGTTTATAACTGAAGGTGTG 57.525 34.615 5.20 0.00 31.31 3.82
1845 1913 2.163815 GCAATCCAGGATGCTGATATGC 59.836 50.000 16.85 17.10 31.97 3.14
1846 1914 3.687125 AGCAATCCAGGATGCTGATATG 58.313 45.455 16.85 11.57 36.15 1.78
1857 1925 1.478105 GTAAAGGCCAAGCAATCCAGG 59.522 52.381 5.01 0.00 0.00 4.45
2435 2516 4.349636 TCCATGGTTTGGTCTTCTACTTCA 59.650 41.667 12.58 0.00 46.52 3.02
3228 3314 6.879993 ACGTATCTCTATCGTCATAATCCTGT 59.120 38.462 0.00 0.00 32.26 4.00
3307 3393 0.588252 CACTGCGACAAGAAACCAGG 59.412 55.000 0.00 0.00 0.00 4.45
3320 3406 4.614555 TTAAATGAACTATGGCACTGCG 57.385 40.909 0.00 0.00 0.00 5.18
3357 3443 2.485814 GTGCAGATCTCAACCAAGGAAC 59.514 50.000 0.00 0.00 0.00 3.62
3388 3474 7.057264 AGAGATCCCTGCCTTTAAAATAGAAC 58.943 38.462 0.00 0.00 0.00 3.01
4071 4954 1.452953 ATGCCATCGCCTTGCATGAG 61.453 55.000 0.00 0.00 43.66 2.90
4343 5226 6.716898 TGCAATATAGAAAGATCAGATGCG 57.283 37.500 0.00 0.00 0.00 4.73
4476 5361 9.921637 CACCATACTACCAAATAACAAAAACAT 57.078 29.630 0.00 0.00 0.00 2.71
4477 5362 8.915036 ACACCATACTACCAAATAACAAAAACA 58.085 29.630 0.00 0.00 0.00 2.83
4478 5363 9.187455 CACACCATACTACCAAATAACAAAAAC 57.813 33.333 0.00 0.00 0.00 2.43
4479 5364 8.915036 ACACACCATACTACCAAATAACAAAAA 58.085 29.630 0.00 0.00 0.00 1.94
4487 5385 6.969993 AACAAACACACCATACTACCAAAT 57.030 33.333 0.00 0.00 0.00 2.32
4527 5454 8.962111 GCAAAGAATTAGAAAACAAAGTCTGAG 58.038 33.333 0.00 0.00 31.03 3.35
4528 5455 8.465999 TGCAAAGAATTAGAAAACAAAGTCTGA 58.534 29.630 0.00 0.00 31.03 3.27
4529 5456 8.633075 TGCAAAGAATTAGAAAACAAAGTCTG 57.367 30.769 0.00 0.00 31.03 3.51
4530 5457 9.087424 GTTGCAAAGAATTAGAAAACAAAGTCT 57.913 29.630 0.00 0.00 31.83 3.24
4531 5458 8.328146 GGTTGCAAAGAATTAGAAAACAAAGTC 58.672 33.333 0.00 0.00 0.00 3.01
4532 5459 7.279981 GGGTTGCAAAGAATTAGAAAACAAAGT 59.720 33.333 0.00 0.00 0.00 2.66
4533 5460 7.279758 TGGGTTGCAAAGAATTAGAAAACAAAG 59.720 33.333 0.00 0.00 0.00 2.77
4534 5461 7.065204 GTGGGTTGCAAAGAATTAGAAAACAAA 59.935 33.333 0.00 0.00 0.00 2.83
4535 5462 6.536941 GTGGGTTGCAAAGAATTAGAAAACAA 59.463 34.615 0.00 0.00 0.00 2.83
4536 5463 6.045955 GTGGGTTGCAAAGAATTAGAAAACA 58.954 36.000 0.00 0.00 0.00 2.83
4537 5464 6.280643 AGTGGGTTGCAAAGAATTAGAAAAC 58.719 36.000 0.00 0.00 0.00 2.43
4538 5465 6.097554 TGAGTGGGTTGCAAAGAATTAGAAAA 59.902 34.615 0.00 0.00 0.00 2.29
4539 5466 5.596361 TGAGTGGGTTGCAAAGAATTAGAAA 59.404 36.000 0.00 0.00 0.00 2.52
4540 5467 5.009610 GTGAGTGGGTTGCAAAGAATTAGAA 59.990 40.000 0.00 0.00 0.00 2.10
4541 5468 4.518970 GTGAGTGGGTTGCAAAGAATTAGA 59.481 41.667 0.00 0.00 0.00 2.10
4542 5469 4.520492 AGTGAGTGGGTTGCAAAGAATTAG 59.480 41.667 0.00 0.00 0.00 1.73
4703 5630 6.006275 AGGGCACATCATACTGTTTTCTAT 57.994 37.500 0.00 0.00 0.00 1.98
4784 5713 2.064434 TGGCCATCACTCAAAACACA 57.936 45.000 0.00 0.00 0.00 3.72
4860 6097 3.967326 CAGGACTTGGGTAGATACATGGA 59.033 47.826 0.00 0.00 0.00 3.41
4894 6131 6.311690 TGCTTTTGTTCCCTTTAAGAAAAACG 59.688 34.615 0.00 0.00 33.01 3.60
4944 6181 7.603180 TCTCAGCTTATATTGATGTGGTACT 57.397 36.000 0.00 0.00 0.00 2.73
5148 6402 1.078426 GGACACCATCCGTCCCAAG 60.078 63.158 0.00 0.00 46.12 3.61
5159 6413 9.559732 CAAATCAGTGATATAAATAGGACACCA 57.440 33.333 5.94 0.00 0.00 4.17
5250 6504 4.346730 TCTAGGACAAGTATTTCCGGACA 58.653 43.478 1.83 0.00 36.95 4.02
5307 6561 8.772250 TGTCCTAGAAATGGATAAAAGAGATGT 58.228 33.333 0.00 0.00 35.87 3.06
5308 6562 9.618890 TTGTCCTAGAAATGGATAAAAGAGATG 57.381 33.333 0.00 0.00 35.87 2.90
5309 6563 9.844257 CTTGTCCTAGAAATGGATAAAAGAGAT 57.156 33.333 0.00 0.00 34.98 2.75
5310 6564 8.826765 ACTTGTCCTAGAAATGGATAAAAGAGA 58.173 33.333 0.00 0.00 34.98 3.10
5316 6570 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
5317 6571 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
5318 6572 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
5319 6573 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
5442 6696 9.484806 ACTCTCAATTGATCCTGGATTAAAAAT 57.515 29.630 16.64 9.24 0.00 1.82
5534 6788 6.944290 TCACTTCAAAATCATTGAGATGTCCT 59.056 34.615 0.00 0.00 36.96 3.85
5544 6798 6.015688 ACATGCAGACTCACTTCAAAATCATT 60.016 34.615 0.00 0.00 0.00 2.57
5884 7281 7.326454 TGGTGATATAGAAGATGATAAGCAGC 58.674 38.462 0.00 0.00 0.00 5.25
5998 7395 4.144297 CACCTGAACAGAATGGAAAAGGA 58.856 43.478 3.19 0.00 43.62 3.36
6048 7445 7.344612 TCCAGATATACATAAAGGACACTGTGT 59.655 37.037 14.23 14.23 0.00 3.72
6188 7585 7.038154 AGTAGCAAAGTTTGAGCATTTTACA 57.962 32.000 19.82 0.00 0.00 2.41
6229 7626 6.261603 GCACAAGTATCCTGATGAATCAATCA 59.738 38.462 0.00 0.00 43.67 2.57
6230 7627 6.261603 TGCACAAGTATCCTGATGAATCAATC 59.738 38.462 0.00 0.00 36.18 2.67
6231 7628 6.124340 TGCACAAGTATCCTGATGAATCAAT 58.876 36.000 0.00 0.00 36.18 2.57
6232 7629 5.499313 TGCACAAGTATCCTGATGAATCAA 58.501 37.500 0.00 0.00 36.18 2.57
6364 7771 4.107622 GCGAAAATCTGGAAACCATGATG 58.892 43.478 0.00 0.00 30.82 3.07
6460 7867 2.896044 TGCACAATTGGATTAACCTGCA 59.104 40.909 10.83 10.86 40.72 4.41
6646 8053 7.114095 TCAACAACCCTTTTACTTGTCTACTT 58.886 34.615 0.00 0.00 0.00 2.24
6711 8118 5.099575 GCTTTTCACGGTTCTTCAGAAAAA 58.900 37.500 0.00 0.00 37.62 1.94
6713 8120 3.945285 AGCTTTTCACGGTTCTTCAGAAA 59.055 39.130 0.00 0.00 35.58 2.52
6999 8407 7.436673 CCTCGAAAGGAAAGAGAATAGTATGTG 59.563 40.741 0.00 0.00 46.67 3.21
7005 8413 4.123506 GCCCTCGAAAGGAAAGAGAATAG 58.876 47.826 5.34 0.00 46.67 1.73
7010 8418 1.276421 TCTGCCCTCGAAAGGAAAGAG 59.724 52.381 5.34 0.00 46.67 2.85
7165 8573 1.102809 TAATGGCTCATTGGCGCCTG 61.103 55.000 29.70 19.14 46.42 4.85
7241 8649 1.433534 CGAAAGCTGTGAGGAGGTTC 58.566 55.000 0.00 0.00 32.49 3.62
7254 8662 1.130009 GTTTCTCGTCGCCGAAAGC 59.870 57.895 8.99 0.00 43.69 3.51
7255 8663 0.942410 TGGTTTCTCGTCGCCGAAAG 60.942 55.000 8.99 0.00 43.69 2.62
7282 8690 4.635765 CCGCCTTCTTGAATATCTTCAACA 59.364 41.667 2.34 0.00 44.46 3.33
7369 8777 2.740714 GCGCACTGGTCGTTCATCC 61.741 63.158 0.30 0.00 0.00 3.51
7488 8896 4.439700 CCACTCTAGTTATGTACACACCCG 60.440 50.000 0.00 0.00 0.00 5.28
7565 8973 0.032540 GTCGTACAACCAAGGACGGT 59.967 55.000 0.00 0.00 42.71 4.83
7571 8979 2.828877 TGGACAAGTCGTACAACCAAG 58.171 47.619 0.00 0.00 34.62 3.61
7582 8990 6.237942 CGAAGTTGTATCATCATGGACAAGTC 60.238 42.308 11.81 9.07 35.03 3.01
7775 9189 3.977244 CTTGGCAAAGGCGGCGTT 61.977 61.111 9.37 3.90 42.47 4.84
7796 9210 2.653890 CAAGTCAAATCACAAGCCACG 58.346 47.619 0.00 0.00 0.00 4.94
7852 9266 2.546789 GCATACCGCCCAAGTGTATTAC 59.453 50.000 0.00 0.00 32.94 1.89
7947 9361 5.763204 CAGTTTAACACACACAGGTCCTTAT 59.237 40.000 0.00 0.00 0.00 1.73
7948 9362 5.120399 CAGTTTAACACACACAGGTCCTTA 58.880 41.667 0.00 0.00 0.00 2.69
8002 9421 4.759693 ACATGAAATTGTAGCGAAGAACCA 59.240 37.500 0.00 0.00 0.00 3.67
8061 9480 3.825014 AGACACGGTGTTACTGTATGACT 59.175 43.478 15.94 0.63 35.04 3.41
8233 9702 1.648116 ATTTCCCAGGCATTGTGCTT 58.352 45.000 1.64 0.00 44.28 3.91
8250 9721 2.416701 CGGAAAACATTTGGCGCCTATT 60.417 45.455 29.70 14.14 0.00 1.73
8287 10524 0.601841 CCCGGTTGCACGTCTTACTT 60.602 55.000 0.00 0.00 0.00 2.24
8289 10526 2.674084 GCCCGGTTGCACGTCTTAC 61.674 63.158 0.00 0.00 0.00 2.34
8290 10527 2.357760 GCCCGGTTGCACGTCTTA 60.358 61.111 0.00 0.00 0.00 2.10
8291 10528 4.555709 TGCCCGGTTGCACGTCTT 62.556 61.111 0.00 0.00 36.04 3.01
8292 10529 4.555709 TTGCCCGGTTGCACGTCT 62.556 61.111 4.74 0.00 41.88 4.18
8293 10530 4.025401 CTTGCCCGGTTGCACGTC 62.025 66.667 4.74 0.00 41.88 4.34
8303 10703 4.994756 AAAGCCCCCACTTGCCCG 62.995 66.667 0.00 0.00 0.00 6.13
8329 10729 2.203070 CATGCCAGGTAGTCCGGC 60.203 66.667 0.00 11.14 46.05 6.13
8330 10730 2.505982 CCATGCCAGGTAGTCCGG 59.494 66.667 0.00 0.00 39.05 5.14
8332 10732 2.919043 CCCCATGCCAGGTAGTCC 59.081 66.667 0.00 0.00 0.00 3.85
8333 10733 2.193248 GCCCCATGCCAGGTAGTC 59.807 66.667 0.00 0.00 0.00 2.59
8334 10734 2.613696 TGCCCCATGCCAGGTAGT 60.614 61.111 0.00 0.00 40.16 2.73
8335 10735 2.124151 GTGCCCCATGCCAGGTAG 60.124 66.667 0.00 0.00 40.16 3.18
8336 10736 4.108299 CGTGCCCCATGCCAGGTA 62.108 66.667 0.00 0.00 40.16 3.08


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

AutoCloner maintained by Alex Coulton.