Multiple sequence alignment - TraesCS2D01G353900

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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 TraesCS2D01G353900 chr2D 100.000 2231 0 0 1 2231 452605709 452603479 0.000000e+00 4120
1 TraesCS2D01G353900 chr2D 93.542 542 35 0 1690 2231 452590922 452590381 0.000000e+00 808
2 TraesCS2D01G353900 chr2D 92.766 235 13 4 1 233 128892979 128892747 9.870000e-89 337
3 TraesCS2D01G353900 chr2A 93.492 1306 79 5 204 1506 596513992 596515294 0.000000e+00 1936
4 TraesCS2D01G353900 chr2A 95.872 218 7 2 1 216 468594931 468595148 3.520000e-93 351
5 TraesCS2D01G353900 chr2A 91.099 191 14 2 1505 1695 596526289 596526476 2.840000e-64 255
6 TraesCS2D01G353900 chr5D 94.963 536 25 2 1696 2231 222696300 222696833 0.000000e+00 839
7 TraesCS2D01G353900 chr5D 94.052 538 30 2 1695 2231 137726064 137726600 0.000000e+00 815
8 TraesCS2D01G353900 chr5D 93.358 542 36 0 1690 2231 65789363 65788822 0.000000e+00 802
9 TraesCS2D01G353900 chr5D 81.658 567 96 8 777 1339 152780802 152780240 4.340000e-127 464
10 TraesCS2D01G353900 chr3D 94.249 539 31 0 1693 2231 426787893 426788431 0.000000e+00 824
11 TraesCS2D01G353900 chr3D 93.186 543 36 1 1690 2231 612388213 612388755 0.000000e+00 797
12 TraesCS2D01G353900 chr3D 97.101 207 5 1 1 206 499769889 499770095 4.560000e-92 348
13 TraesCS2D01G353900 chr3D 81.267 363 64 4 956 1316 478125961 478126321 7.790000e-75 291
14 TraesCS2D01G353900 chr4D 93.923 543 32 1 1690 2231 476956181 476955639 0.000000e+00 819
15 TraesCS2D01G353900 chr4D 80.952 567 102 6 777 1339 384968749 384968185 5.650000e-121 444
16 TraesCS2D01G353900 chr4D 73.921 579 90 36 1671 2231 148350085 148350620 2.280000e-40 176
17 TraesCS2D01G353900 chr7D 93.843 536 33 0 1696 2231 351516807 351517342 0.000000e+00 808
18 TraesCS2D01G353900 chr7D 94.151 530 30 1 1702 2231 142678419 142677891 0.000000e+00 806
19 TraesCS2D01G353900 chr7D 95.000 220 9 2 1 218 326704558 326704777 5.900000e-91 344
20 TraesCS2D01G353900 chr4A 88.804 652 70 3 450 1098 17014291 17014942 0.000000e+00 797
21 TraesCS2D01G353900 chr4A 82.812 704 112 6 637 1336 547981492 547980794 2.430000e-174 621
22 TraesCS2D01G353900 chr1B 81.674 884 156 6 456 1336 359905255 359904375 0.000000e+00 730
23 TraesCS2D01G353900 chr1B 79.260 892 166 13 456 1335 550381951 550382835 2.450000e-169 604
24 TraesCS2D01G353900 chr1B 95.853 217 8 1 1 216 143199815 143200031 1.270000e-92 350
25 TraesCS2D01G353900 chr3B 80.068 883 170 6 456 1335 422326697 422325818 0.000000e+00 651
26 TraesCS2D01G353900 chr2B 88.525 366 36 3 1334 1695 532480593 532480230 2.630000e-119 438
27 TraesCS2D01G353900 chr2B 87.452 263 27 3 204 460 532480843 532480581 4.660000e-77 298
28 TraesCS2D01G353900 chr4B 79.455 550 100 12 795 1338 163806553 163806011 5.820000e-101 377
29 TraesCS2D01G353900 chr7B 86.310 336 45 1 996 1330 67810745 67811080 4.530000e-97 364
30 TraesCS2D01G353900 chr1A 96.729 214 4 3 1 212 515540816 515541028 9.800000e-94 353
31 TraesCS2D01G353900 chr1A 78.161 435 87 8 843 1273 276649126 276648696 1.020000e-68 270
32 TraesCS2D01G353900 chr7A 96.262 214 6 2 1 213 97420324 97420112 1.270000e-92 350
33 TraesCS2D01G353900 chr5A 95.853 217 8 1 1 216 433971888 433971672 1.270000e-92 350
34 TraesCS2D01G353900 chr6D 95.833 216 6 3 1 215 95023233 95023020 1.640000e-91 346
35 TraesCS2D01G353900 chr3A 80.174 459 89 2 878 1335 171214292 171213835 2.120000e-90 342
36 TraesCS2D01G353900 chrUn 100.000 56 0 0 1281 1336 76049029 76049084 1.090000e-18 104


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 TraesCS2D01G353900 chr2D 452603479 452605709 2230 True 4120 4120 100.0000 1 2231 1 chr2D.!!$R3 2230
1 TraesCS2D01G353900 chr2D 452590381 452590922 541 True 808 808 93.5420 1690 2231 1 chr2D.!!$R2 541
2 TraesCS2D01G353900 chr2A 596513992 596515294 1302 False 1936 1936 93.4920 204 1506 1 chr2A.!!$F2 1302
3 TraesCS2D01G353900 chr5D 222696300 222696833 533 False 839 839 94.9630 1696 2231 1 chr5D.!!$F2 535
4 TraesCS2D01G353900 chr5D 137726064 137726600 536 False 815 815 94.0520 1695 2231 1 chr5D.!!$F1 536
5 TraesCS2D01G353900 chr5D 65788822 65789363 541 True 802 802 93.3580 1690 2231 1 chr5D.!!$R1 541
6 TraesCS2D01G353900 chr5D 152780240 152780802 562 True 464 464 81.6580 777 1339 1 chr5D.!!$R2 562
7 TraesCS2D01G353900 chr3D 426787893 426788431 538 False 824 824 94.2490 1693 2231 1 chr3D.!!$F1 538
8 TraesCS2D01G353900 chr3D 612388213 612388755 542 False 797 797 93.1860 1690 2231 1 chr3D.!!$F4 541
9 TraesCS2D01G353900 chr4D 476955639 476956181 542 True 819 819 93.9230 1690 2231 1 chr4D.!!$R2 541
10 TraesCS2D01G353900 chr4D 384968185 384968749 564 True 444 444 80.9520 777 1339 1 chr4D.!!$R1 562
11 TraesCS2D01G353900 chr7D 351516807 351517342 535 False 808 808 93.8430 1696 2231 1 chr7D.!!$F2 535
12 TraesCS2D01G353900 chr7D 142677891 142678419 528 True 806 806 94.1510 1702 2231 1 chr7D.!!$R1 529
13 TraesCS2D01G353900 chr4A 17014291 17014942 651 False 797 797 88.8040 450 1098 1 chr4A.!!$F1 648
14 TraesCS2D01G353900 chr4A 547980794 547981492 698 True 621 621 82.8120 637 1336 1 chr4A.!!$R1 699
15 TraesCS2D01G353900 chr1B 359904375 359905255 880 True 730 730 81.6740 456 1336 1 chr1B.!!$R1 880
16 TraesCS2D01G353900 chr1B 550381951 550382835 884 False 604 604 79.2600 456 1335 1 chr1B.!!$F2 879
17 TraesCS2D01G353900 chr3B 422325818 422326697 879 True 651 651 80.0680 456 1335 1 chr3B.!!$R1 879
18 TraesCS2D01G353900 chr2B 532480230 532480843 613 True 368 438 87.9885 204 1695 2 chr2B.!!$R1 1491
19 TraesCS2D01G353900 chr4B 163806011 163806553 542 True 377 377 79.4550 795 1338 1 chr4B.!!$R1 543

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
353 359 0.318107 GCCGATTGCATTTCCATCCG 60.318 55.0 0.0 0.0 40.77 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1678 0.03759 GGGACACTTGGCACATGGTA 59.962 55.0 0.0 0.0 39.3 3.25 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
24 25 7.484035 CATGTCTATGGCTAGGAAACTTAAC 57.516 40.000 0.00 0.00 43.67 2.01
25 26 5.985911 TGTCTATGGCTAGGAAACTTAACC 58.014 41.667 0.00 0.00 43.67 2.85
26 27 5.486063 TGTCTATGGCTAGGAAACTTAACCA 59.514 40.000 0.00 0.00 43.67 3.67
27 28 6.157994 TGTCTATGGCTAGGAAACTTAACCAT 59.842 38.462 0.00 0.00 43.99 3.55
28 29 6.706716 GTCTATGGCTAGGAAACTTAACCATC 59.293 42.308 0.00 0.00 42.08 3.51
29 30 5.717119 ATGGCTAGGAAACTTAACCATCT 57.283 39.130 0.00 0.00 40.24 2.90
30 31 5.514500 TGGCTAGGAAACTTAACCATCTT 57.486 39.130 0.00 0.00 43.67 2.40
31 32 5.887754 TGGCTAGGAAACTTAACCATCTTT 58.112 37.500 0.00 0.00 43.67 2.52
32 33 5.710099 TGGCTAGGAAACTTAACCATCTTTG 59.290 40.000 0.00 0.00 43.67 2.77
33 34 5.944007 GGCTAGGAAACTTAACCATCTTTGA 59.056 40.000 0.00 0.00 43.67 2.69
34 35 6.603599 GGCTAGGAAACTTAACCATCTTTGAT 59.396 38.462 0.00 0.00 43.67 2.57
35 36 7.122799 GGCTAGGAAACTTAACCATCTTTGATT 59.877 37.037 0.00 0.00 43.67 2.57
36 37 9.174166 GCTAGGAAACTTAACCATCTTTGATTA 57.826 33.333 0.00 0.00 43.67 1.75
39 40 9.362151 AGGAAACTTAACCATCTTTGATTAACA 57.638 29.630 0.00 0.00 37.44 2.41
40 41 9.974980 GGAAACTTAACCATCTTTGATTAACAA 57.025 29.630 0.00 0.00 36.65 2.83
42 43 9.476202 AAACTTAACCATCTTTGATTAACAAGC 57.524 29.630 0.00 0.00 39.77 4.01
43 44 8.409358 ACTTAACCATCTTTGATTAACAAGCT 57.591 30.769 0.00 0.00 39.77 3.74
44 45 9.515226 ACTTAACCATCTTTGATTAACAAGCTA 57.485 29.630 0.00 0.00 39.77 3.32
45 46 9.994432 CTTAACCATCTTTGATTAACAAGCTAG 57.006 33.333 0.00 0.00 39.77 3.42
46 47 9.515226 TTAACCATCTTTGATTAACAAGCTAGT 57.485 29.630 0.00 0.00 39.77 2.57
47 48 7.617041 ACCATCTTTGATTAACAAGCTAGTC 57.383 36.000 0.00 0.00 39.77 2.59
48 49 7.168219 ACCATCTTTGATTAACAAGCTAGTCA 58.832 34.615 0.00 0.00 39.77 3.41
49 50 7.665559 ACCATCTTTGATTAACAAGCTAGTCAA 59.334 33.333 0.00 0.00 39.77 3.18
50 51 8.180267 CCATCTTTGATTAACAAGCTAGTCAAG 58.820 37.037 0.00 0.00 39.77 3.02
51 52 8.725148 CATCTTTGATTAACAAGCTAGTCAAGT 58.275 33.333 0.00 0.00 39.77 3.16
52 53 9.944376 ATCTTTGATTAACAAGCTAGTCAAGTA 57.056 29.630 0.00 0.00 39.77 2.24
53 54 9.424319 TCTTTGATTAACAAGCTAGTCAAGTAG 57.576 33.333 0.00 0.00 39.77 2.57
54 55 9.424319 CTTTGATTAACAAGCTAGTCAAGTAGA 57.576 33.333 0.00 0.00 39.77 2.59
55 56 8.988064 TTGATTAACAAGCTAGTCAAGTAGAG 57.012 34.615 0.00 0.00 34.20 2.43
56 57 7.548097 TGATTAACAAGCTAGTCAAGTAGAGG 58.452 38.462 0.00 0.00 0.00 3.69
57 58 3.878160 ACAAGCTAGTCAAGTAGAGGC 57.122 47.619 0.00 0.00 0.00 4.70
58 59 3.165875 ACAAGCTAGTCAAGTAGAGGCA 58.834 45.455 0.00 0.00 0.00 4.75
59 60 3.772025 ACAAGCTAGTCAAGTAGAGGCAT 59.228 43.478 0.00 0.00 0.00 4.40
60 61 4.956700 ACAAGCTAGTCAAGTAGAGGCATA 59.043 41.667 0.00 0.00 0.00 3.14
61 62 5.163499 ACAAGCTAGTCAAGTAGAGGCATAC 60.163 44.000 0.00 0.00 0.00 2.39
62 63 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
63 64 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
64 65 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
65 66 5.182380 GCTAGTCAAGTAGAGGCATACTAGG 59.818 48.000 0.00 0.67 36.85 3.02
66 67 4.475345 AGTCAAGTAGAGGCATACTAGGG 58.525 47.826 3.23 0.00 34.90 3.53
67 68 4.168283 AGTCAAGTAGAGGCATACTAGGGA 59.832 45.833 3.23 0.66 34.90 4.20
68 69 4.278919 GTCAAGTAGAGGCATACTAGGGAC 59.721 50.000 3.23 7.70 34.90 4.46
69 70 4.079385 TCAAGTAGAGGCATACTAGGGACA 60.079 45.833 3.23 0.00 34.90 4.02
70 71 3.834938 AGTAGAGGCATACTAGGGACAC 58.165 50.000 0.00 0.00 34.21 3.67
71 72 3.464080 AGTAGAGGCATACTAGGGACACT 59.536 47.826 0.00 0.00 34.21 3.55
72 73 2.952116 AGAGGCATACTAGGGACACTC 58.048 52.381 0.00 0.00 0.00 3.51
73 74 2.516277 AGAGGCATACTAGGGACACTCT 59.484 50.000 0.00 0.00 0.00 3.24
74 75 2.625790 GAGGCATACTAGGGACACTCTG 59.374 54.545 0.00 0.00 0.00 3.35
75 76 2.023888 AGGCATACTAGGGACACTCTGT 60.024 50.000 0.00 0.00 0.00 3.41
76 77 2.766828 GGCATACTAGGGACACTCTGTT 59.233 50.000 0.00 0.00 0.00 3.16
77 78 3.197983 GGCATACTAGGGACACTCTGTTT 59.802 47.826 0.00 0.00 0.00 2.83
78 79 4.184629 GCATACTAGGGACACTCTGTTTG 58.815 47.826 0.00 0.00 0.00 2.93
79 80 4.322801 GCATACTAGGGACACTCTGTTTGT 60.323 45.833 0.00 0.00 0.00 2.83
80 81 5.411781 CATACTAGGGACACTCTGTTTGTC 58.588 45.833 0.00 0.00 42.35 3.18
81 82 3.577919 ACTAGGGACACTCTGTTTGTCT 58.422 45.455 0.00 0.00 42.63 3.41
82 83 4.737578 ACTAGGGACACTCTGTTTGTCTA 58.262 43.478 0.00 0.00 42.63 2.59
83 84 5.334421 ACTAGGGACACTCTGTTTGTCTAT 58.666 41.667 0.00 4.07 42.63 1.98
84 85 4.543590 AGGGACACTCTGTTTGTCTATG 57.456 45.455 9.96 0.00 42.63 2.23
85 86 3.904339 AGGGACACTCTGTTTGTCTATGT 59.096 43.478 9.96 0.00 42.63 2.29
86 87 5.084519 AGGGACACTCTGTTTGTCTATGTA 58.915 41.667 9.96 0.00 42.63 2.29
87 88 5.721960 AGGGACACTCTGTTTGTCTATGTAT 59.278 40.000 9.96 0.00 42.63 2.29
88 89 6.043411 GGGACACTCTGTTTGTCTATGTATC 58.957 44.000 9.96 0.00 42.63 2.24
89 90 6.043411 GGACACTCTGTTTGTCTATGTATCC 58.957 44.000 9.96 0.00 42.63 2.59
90 91 6.351033 GGACACTCTGTTTGTCTATGTATCCA 60.351 42.308 9.96 0.00 42.63 3.41
91 92 6.398918 ACACTCTGTTTGTCTATGTATCCAC 58.601 40.000 0.00 0.00 0.00 4.02
92 93 6.014584 ACACTCTGTTTGTCTATGTATCCACA 60.015 38.462 0.00 0.00 39.52 4.17
93 94 6.311445 CACTCTGTTTGTCTATGTATCCACAC 59.689 42.308 0.00 0.00 37.54 3.82
94 95 6.014584 ACTCTGTTTGTCTATGTATCCACACA 60.015 38.462 0.00 0.00 37.54 3.72
95 96 6.946340 TCTGTTTGTCTATGTATCCACACAT 58.054 36.000 0.00 0.00 41.88 3.21
96 97 6.818142 TCTGTTTGTCTATGTATCCACACATG 59.182 38.462 0.00 0.00 39.46 3.21
97 98 6.472016 TGTTTGTCTATGTATCCACACATGT 58.528 36.000 0.00 0.00 39.46 3.21
98 99 7.616313 TGTTTGTCTATGTATCCACACATGTA 58.384 34.615 0.00 0.00 39.46 2.29
99 100 7.547722 TGTTTGTCTATGTATCCACACATGTAC 59.452 37.037 0.00 0.00 39.46 2.90
100 101 7.418337 TTGTCTATGTATCCACACATGTACT 57.582 36.000 0.00 0.00 39.46 2.73
101 102 8.528044 TTGTCTATGTATCCACACATGTACTA 57.472 34.615 0.00 0.00 39.46 1.82
102 103 8.528044 TGTCTATGTATCCACACATGTACTAA 57.472 34.615 0.00 0.00 39.46 2.24
103 104 8.630037 TGTCTATGTATCCACACATGTACTAAG 58.370 37.037 0.00 0.00 39.46 2.18
104 105 8.630917 GTCTATGTATCCACACATGTACTAAGT 58.369 37.037 0.00 0.00 39.46 2.24
105 106 9.197306 TCTATGTATCCACACATGTACTAAGTT 57.803 33.333 0.00 0.00 39.46 2.66
106 107 9.817809 CTATGTATCCACACATGTACTAAGTTT 57.182 33.333 0.00 0.00 39.46 2.66
107 108 8.718102 ATGTATCCACACATGTACTAAGTTTC 57.282 34.615 0.00 0.00 37.74 2.78
108 109 7.101054 TGTATCCACACATGTACTAAGTTTCC 58.899 38.462 0.00 0.00 0.00 3.13
109 110 4.562082 TCCACACATGTACTAAGTTTCCG 58.438 43.478 0.00 0.00 0.00 4.30
110 111 3.682858 CCACACATGTACTAAGTTTCCGG 59.317 47.826 0.00 0.00 0.00 5.14
111 112 4.312443 CACACATGTACTAAGTTTCCGGT 58.688 43.478 0.00 0.00 0.00 5.28
112 113 4.753107 CACACATGTACTAAGTTTCCGGTT 59.247 41.667 0.00 0.00 0.00 4.44
113 114 5.927689 CACACATGTACTAAGTTTCCGGTTA 59.072 40.000 0.00 0.00 0.00 2.85
114 115 6.424509 CACACATGTACTAAGTTTCCGGTTAA 59.575 38.462 0.00 0.00 0.00 2.01
115 116 7.118680 CACACATGTACTAAGTTTCCGGTTAAT 59.881 37.037 0.00 0.00 0.00 1.40
116 117 8.313292 ACACATGTACTAAGTTTCCGGTTAATA 58.687 33.333 0.00 0.00 0.00 0.98
117 118 8.598075 CACATGTACTAAGTTTCCGGTTAATAC 58.402 37.037 0.00 0.00 0.00 1.89
118 119 8.313292 ACATGTACTAAGTTTCCGGTTAATACA 58.687 33.333 0.00 3.81 28.60 2.29
119 120 9.153721 CATGTACTAAGTTTCCGGTTAATACAA 57.846 33.333 0.00 0.00 28.05 2.41
120 121 9.895138 ATGTACTAAGTTTCCGGTTAATACAAT 57.105 29.630 0.00 0.00 28.05 2.71
121 122 9.723601 TGTACTAAGTTTCCGGTTAATACAATT 57.276 29.630 0.00 0.00 0.00 2.32
126 127 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
127 128 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
128 129 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
129 130 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
130 131 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
131 132 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
132 133 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
133 134 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
192 193 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
193 194 7.208064 ACAACTTTATTATTGCCTCTAGGGA 57.792 36.000 0.00 0.00 37.23 4.20
194 195 7.283329 ACAACTTTATTATTGCCTCTAGGGAG 58.717 38.462 0.00 0.00 36.70 4.30
195 196 7.127339 ACAACTTTATTATTGCCTCTAGGGAGA 59.873 37.037 0.00 0.00 41.86 3.71
196 197 7.880265 ACTTTATTATTGCCTCTAGGGAGAT 57.120 36.000 0.00 0.00 41.86 2.75
197 198 8.281529 ACTTTATTATTGCCTCTAGGGAGATT 57.718 34.615 0.00 0.00 41.86 2.40
198 199 8.728098 ACTTTATTATTGCCTCTAGGGAGATTT 58.272 33.333 0.00 0.00 41.86 2.17
199 200 9.225436 CTTTATTATTGCCTCTAGGGAGATTTC 57.775 37.037 0.00 0.00 41.86 2.17
200 201 5.568620 TTATTGCCTCTAGGGAGATTTCC 57.431 43.478 0.00 0.00 41.86 3.13
201 202 2.877154 TGCCTCTAGGGAGATTTCCT 57.123 50.000 1.74 0.00 43.49 3.36
202 203 3.136641 TGCCTCTAGGGAGATTTCCTT 57.863 47.619 1.74 0.00 43.49 3.36
285 291 5.922053 TCTGCTTCTACATGCACTAATCAT 58.078 37.500 0.00 0.00 35.20 2.45
304 310 6.904463 ATCATTTATGCATGCATCCAACTA 57.096 33.333 35.35 19.59 37.82 2.24
310 316 1.532505 GCATGCATCCAACTACTTGCG 60.533 52.381 14.21 0.00 37.92 4.85
311 317 1.739466 CATGCATCCAACTACTTGCGT 59.261 47.619 0.00 0.00 37.92 5.24
353 359 0.318107 GCCGATTGCATTTCCATCCG 60.318 55.000 0.00 0.00 40.77 4.18
361 367 1.680338 CATTTCCATCCGGGTCCTTC 58.320 55.000 0.00 0.00 38.11 3.46
396 402 6.558014 ACCCAGATCAGTCAGATATTCTTCAT 59.442 38.462 0.00 0.00 37.00 2.57
402 408 5.364735 TCAGTCAGATATTCTTCATGGCTGA 59.635 40.000 3.84 3.84 46.99 4.26
406 412 7.454066 AGTCAGATATTCTTCATGGCTGAGATA 59.546 37.037 0.00 0.00 31.00 1.98
464 470 2.771943 TCAAAATAGAGTCATCCGCCCT 59.228 45.455 0.00 0.00 0.00 5.19
479 485 1.429148 GCCCTAAAGACATCGCACCG 61.429 60.000 0.00 0.00 0.00 4.94
532 539 3.883744 CTGTTGCTTCCGCCCTCGT 62.884 63.158 0.00 0.00 34.43 4.18
690 697 3.334691 CTCTCAAGCGATGGGTTTTACA 58.665 45.455 0.00 0.00 0.00 2.41
703 710 2.625790 GGTTTTACACTGCCAACATGGA 59.374 45.455 0.00 0.00 40.96 3.41
712 719 1.423541 TGCCAACATGGACTACTTGGT 59.576 47.619 11.04 0.00 40.96 3.67
714 721 2.814097 GCCAACATGGACTACTTGGTGT 60.814 50.000 11.04 0.00 40.96 4.16
736 743 6.926272 GTGTAATTTGTTGGCCTTGTTCAATA 59.074 34.615 3.32 0.00 0.00 1.90
748 755 5.466393 GCCTTGTTCAATACAACTTGCAAAT 59.534 36.000 0.00 0.00 41.73 2.32
776 783 2.780924 AAGGCTTGGTCACCCCCA 60.781 61.111 0.00 0.00 0.00 4.96
779 786 1.229177 GGCTTGGTCACCCCCAAAT 60.229 57.895 0.00 0.00 43.68 2.32
780 787 1.543944 GGCTTGGTCACCCCCAAATG 61.544 60.000 0.00 0.00 43.68 2.32
781 788 0.831711 GCTTGGTCACCCCCAAATGT 60.832 55.000 0.00 0.00 43.68 2.71
830 844 1.179814 AGGATCTGGACGGCGGATAC 61.180 60.000 13.24 4.79 0.00 2.24
850 864 0.916086 ACTTCAGTGTTGTGGGTGGA 59.084 50.000 0.00 0.00 0.00 4.02
954 968 1.225704 CTGGATGGAGGTCCTTGCC 59.774 63.158 0.00 0.00 39.12 4.52
1001 1015 3.449018 ACTCTTTGGATGAGCTACGACAT 59.551 43.478 0.00 0.00 35.12 3.06
1010 1024 1.535896 GAGCTACGACATGGCGAGATA 59.464 52.381 31.27 8.99 40.44 1.98
1102 1116 2.358615 GGCTGGGAGATTTGGAAGGAAT 60.359 50.000 0.00 0.00 0.00 3.01
1116 1130 2.779755 AGGAATGGAATGCACGTGTA 57.220 45.000 18.38 14.09 0.00 2.90
1119 1133 4.016444 AGGAATGGAATGCACGTGTATTT 58.984 39.130 28.69 15.68 30.53 1.40
1124 1138 3.055021 TGGAATGCACGTGTATTTAGGGA 60.055 43.478 28.69 11.51 30.53 4.20
1133 1147 3.349927 GTGTATTTAGGGAAAAGGCGGT 58.650 45.455 0.00 0.00 0.00 5.68
1179 1193 9.368674 CATGCTATTAAAGAGGAGACATCTATG 57.631 37.037 0.00 0.00 0.00 2.23
1243 1257 2.235402 CGAAAGTAGGCCTTTGTCCCTA 59.765 50.000 12.58 0.00 43.47 3.53
1245 1259 4.625564 CGAAAGTAGGCCTTTGTCCCTATT 60.626 45.833 12.58 0.00 43.47 1.73
1252 1268 2.097629 GCCTTTGTCCCTATTTCGCTTC 59.902 50.000 0.00 0.00 0.00 3.86
1386 1407 8.041323 TGTTGGTGTTTTTCTTAAAGGCAAATA 58.959 29.630 0.00 0.00 0.00 1.40
1505 1526 3.947196 ACATGTCAAACTCAACAGAAGCA 59.053 39.130 0.00 0.00 0.00 3.91
1509 1530 4.217334 TGTCAAACTCAACAGAAGCACAAA 59.783 37.500 0.00 0.00 0.00 2.83
1526 1547 4.143137 GCACAAAAACCTCACAAACACAAG 60.143 41.667 0.00 0.00 0.00 3.16
1527 1548 4.388469 CACAAAAACCTCACAAACACAAGG 59.612 41.667 0.00 0.00 34.94 3.61
1532 1553 5.476091 AACCTCACAAACACAAGGAAAAA 57.524 34.783 0.00 0.00 32.99 1.94
1541 1562 5.948742 AACACAAGGAAAAAGGGAAATCA 57.051 34.783 0.00 0.00 0.00 2.57
1549 1570 0.329596 AAAGGGAAATCAGCTCCGCT 59.670 50.000 0.00 0.00 40.77 5.52
1565 1586 4.612943 CTCCGCTGAAACTAACTATCCTC 58.387 47.826 0.00 0.00 0.00 3.71
1569 1590 4.443621 GCTGAAACTAACTATCCTCCCAC 58.556 47.826 0.00 0.00 0.00 4.61
1574 1595 5.373812 AACTAACTATCCTCCCACCATTG 57.626 43.478 0.00 0.00 0.00 2.82
1575 1596 2.736670 AACTATCCTCCCACCATTGC 57.263 50.000 0.00 0.00 0.00 3.56
1576 1597 0.846693 ACTATCCTCCCACCATTGCC 59.153 55.000 0.00 0.00 0.00 4.52
1577 1598 0.846015 CTATCCTCCCACCATTGCCA 59.154 55.000 0.00 0.00 0.00 4.92
1601 1622 5.183140 AGAGAGAAGAAGTTGAGACTGCTAC 59.817 44.000 0.00 0.00 41.15 3.58
1602 1623 4.083003 AGAGAAGAAGTTGAGACTGCTACG 60.083 45.833 0.00 0.00 41.15 3.51
1620 1641 2.291043 GGGAGGAGCAGACCGGAAA 61.291 63.158 9.46 0.00 34.73 3.13
1627 1648 2.275318 GAGCAGACCGGAAATCTCAAG 58.725 52.381 9.46 0.00 0.00 3.02
1657 1678 2.354403 GCAAAGCAAGCATCCTCCAAAT 60.354 45.455 0.00 0.00 0.00 2.32
1675 1696 2.128771 ATACCATGTGCCAAGTGTCC 57.871 50.000 0.00 0.00 0.00 4.02
1676 1697 0.037590 TACCATGTGCCAAGTGTCCC 59.962 55.000 0.00 0.00 0.00 4.46
1683 1704 2.046892 CCAAGTGTCCCGCCTGAG 60.047 66.667 0.00 0.00 0.00 3.35
1837 1859 0.037734 AAGGCCGACTACCAAAAGGG 59.962 55.000 0.00 0.00 44.81 3.95
1879 1902 1.334599 CCGAAGAGAGCTACGAGATGC 60.335 57.143 0.00 0.00 0.00 3.91
1881 1904 1.953686 GAAGAGAGCTACGAGATGCCT 59.046 52.381 0.00 0.00 0.00 4.75
1895 1918 0.975040 ATGCCTGACTCGAGGAAGCT 60.975 55.000 18.41 0.00 34.69 3.74
1953 1977 1.536662 AAGGCCGACTCCCAGAAGT 60.537 57.895 0.00 0.00 0.00 3.01
2053 2077 2.537560 CGAATCCCGGAGCATGTGC 61.538 63.158 0.73 0.00 36.49 4.57
2084 2108 0.390735 GTCGTACGGGTCAGCCATTT 60.391 55.000 16.52 0.00 36.17 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.483640 GGTTAAGTTTCCTAGCCATAGACATG 59.516 42.308 0.00 0.00 0.00 3.21
2 3 5.486063 TGGTTAAGTTTCCTAGCCATAGACA 59.514 40.000 0.00 0.00 0.00 3.41
3 4 5.985911 TGGTTAAGTTTCCTAGCCATAGAC 58.014 41.667 0.00 0.00 0.00 2.59
5 6 6.831976 AGATGGTTAAGTTTCCTAGCCATAG 58.168 40.000 0.00 0.00 35.64 2.23
6 7 6.824958 AGATGGTTAAGTTTCCTAGCCATA 57.175 37.500 0.00 0.00 35.64 2.74
7 8 5.717119 AGATGGTTAAGTTTCCTAGCCAT 57.283 39.130 0.00 0.00 37.88 4.40
8 9 5.514500 AAGATGGTTAAGTTTCCTAGCCA 57.486 39.130 0.00 0.00 0.00 4.75
9 10 5.944007 TCAAAGATGGTTAAGTTTCCTAGCC 59.056 40.000 0.00 0.00 0.00 3.93
10 11 7.631717 ATCAAAGATGGTTAAGTTTCCTAGC 57.368 36.000 0.00 0.00 0.00 3.42
13 14 9.362151 TGTTAATCAAAGATGGTTAAGTTTCCT 57.638 29.630 0.00 0.00 41.55 3.36
14 15 9.974980 TTGTTAATCAAAGATGGTTAAGTTTCC 57.025 29.630 0.00 0.00 41.55 3.13
16 17 9.476202 GCTTGTTAATCAAAGATGGTTAAGTTT 57.524 29.630 0.00 0.00 41.55 2.66
17 18 8.860088 AGCTTGTTAATCAAAGATGGTTAAGTT 58.140 29.630 0.00 0.00 41.55 2.66
18 19 8.409358 AGCTTGTTAATCAAAGATGGTTAAGT 57.591 30.769 0.00 0.00 41.55 2.24
19 20 9.994432 CTAGCTTGTTAATCAAAGATGGTTAAG 57.006 33.333 0.00 0.00 41.55 1.85
20 21 9.515226 ACTAGCTTGTTAATCAAAGATGGTTAA 57.485 29.630 0.00 0.00 39.28 2.01
21 22 9.162764 GACTAGCTTGTTAATCAAAGATGGTTA 57.837 33.333 1.43 0.00 35.48 2.85
22 23 7.665559 TGACTAGCTTGTTAATCAAAGATGGTT 59.334 33.333 1.43 0.00 35.48 3.67
23 24 7.168219 TGACTAGCTTGTTAATCAAAGATGGT 58.832 34.615 1.43 3.58 35.48 3.55
24 25 7.615582 TGACTAGCTTGTTAATCAAAGATGG 57.384 36.000 1.43 0.00 35.48 3.51
25 26 8.725148 ACTTGACTAGCTTGTTAATCAAAGATG 58.275 33.333 6.01 0.00 35.48 2.90
26 27 8.854614 ACTTGACTAGCTTGTTAATCAAAGAT 57.145 30.769 6.01 0.00 35.48 2.40
27 28 9.424319 CTACTTGACTAGCTTGTTAATCAAAGA 57.576 33.333 6.01 0.00 35.48 2.52
28 29 9.424319 TCTACTTGACTAGCTTGTTAATCAAAG 57.576 33.333 6.01 5.13 35.48 2.77
29 30 9.424319 CTCTACTTGACTAGCTTGTTAATCAAA 57.576 33.333 6.01 0.00 35.48 2.69
30 31 8.035394 CCTCTACTTGACTAGCTTGTTAATCAA 58.965 37.037 6.01 3.53 34.61 2.57
31 32 7.548097 CCTCTACTTGACTAGCTTGTTAATCA 58.452 38.462 6.01 0.00 0.00 2.57
32 33 6.477360 GCCTCTACTTGACTAGCTTGTTAATC 59.523 42.308 6.01 0.00 0.00 1.75
33 34 6.070767 TGCCTCTACTTGACTAGCTTGTTAAT 60.071 38.462 6.01 1.00 0.00 1.40
34 35 5.245301 TGCCTCTACTTGACTAGCTTGTTAA 59.755 40.000 1.43 3.75 0.00 2.01
35 36 4.770531 TGCCTCTACTTGACTAGCTTGTTA 59.229 41.667 1.43 0.00 0.00 2.41
36 37 3.578716 TGCCTCTACTTGACTAGCTTGTT 59.421 43.478 1.43 0.00 0.00 2.83
37 38 3.165875 TGCCTCTACTTGACTAGCTTGT 58.834 45.455 0.00 0.00 0.00 3.16
38 39 3.876274 TGCCTCTACTTGACTAGCTTG 57.124 47.619 0.00 0.00 0.00 4.01
39 40 5.205056 AGTATGCCTCTACTTGACTAGCTT 58.795 41.667 0.00 0.00 0.00 3.74
40 41 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
41 42 5.182380 CCTAGTATGCCTCTACTTGACTAGC 59.818 48.000 0.00 0.00 35.60 3.42
42 43 5.708230 CCCTAGTATGCCTCTACTTGACTAG 59.292 48.000 0.00 0.00 36.32 2.57
43 44 5.371769 TCCCTAGTATGCCTCTACTTGACTA 59.628 44.000 0.00 0.00 33.96 2.59
44 45 4.168283 TCCCTAGTATGCCTCTACTTGACT 59.832 45.833 0.00 0.00 33.96 3.41
45 46 4.278919 GTCCCTAGTATGCCTCTACTTGAC 59.721 50.000 0.00 0.00 33.96 3.18
46 47 4.079385 TGTCCCTAGTATGCCTCTACTTGA 60.079 45.833 0.00 0.00 33.96 3.02
47 48 4.038162 GTGTCCCTAGTATGCCTCTACTTG 59.962 50.000 0.00 0.00 33.96 3.16
48 49 4.079096 AGTGTCCCTAGTATGCCTCTACTT 60.079 45.833 0.00 0.00 33.96 2.24
49 50 3.464080 AGTGTCCCTAGTATGCCTCTACT 59.536 47.826 0.00 0.00 36.04 2.57
50 51 3.822167 GAGTGTCCCTAGTATGCCTCTAC 59.178 52.174 0.00 0.00 0.00 2.59
51 52 3.722627 AGAGTGTCCCTAGTATGCCTCTA 59.277 47.826 0.00 0.00 0.00 2.43
52 53 2.516277 AGAGTGTCCCTAGTATGCCTCT 59.484 50.000 0.00 0.00 0.00 3.69
53 54 2.625790 CAGAGTGTCCCTAGTATGCCTC 59.374 54.545 0.00 0.00 0.00 4.70
54 55 2.023888 ACAGAGTGTCCCTAGTATGCCT 60.024 50.000 0.00 0.00 0.00 4.75
55 56 2.389715 ACAGAGTGTCCCTAGTATGCC 58.610 52.381 0.00 0.00 0.00 4.40
56 57 4.184629 CAAACAGAGTGTCCCTAGTATGC 58.815 47.826 0.00 0.00 0.00 3.14
57 58 5.186021 AGACAAACAGAGTGTCCCTAGTATG 59.814 44.000 1.08 0.00 45.39 2.39
58 59 5.334421 AGACAAACAGAGTGTCCCTAGTAT 58.666 41.667 1.08 0.00 45.39 2.12
59 60 4.737578 AGACAAACAGAGTGTCCCTAGTA 58.262 43.478 1.08 0.00 45.39 1.82
60 61 3.577919 AGACAAACAGAGTGTCCCTAGT 58.422 45.455 1.08 0.00 45.39 2.57
61 62 5.186021 ACATAGACAAACAGAGTGTCCCTAG 59.814 44.000 1.08 0.00 45.39 3.02
62 63 5.084519 ACATAGACAAACAGAGTGTCCCTA 58.915 41.667 1.08 0.00 45.39 3.53
63 64 3.904339 ACATAGACAAACAGAGTGTCCCT 59.096 43.478 1.08 0.00 45.39 4.20
64 65 4.273148 ACATAGACAAACAGAGTGTCCC 57.727 45.455 1.08 0.00 45.39 4.46
65 66 6.043411 GGATACATAGACAAACAGAGTGTCC 58.957 44.000 1.08 0.00 45.39 4.02
66 67 6.631016 TGGATACATAGACAAACAGAGTGTC 58.369 40.000 0.00 0.00 46.17 3.67
67 68 6.605471 TGGATACATAGACAAACAGAGTGT 57.395 37.500 0.00 0.00 46.17 3.55
84 85 6.255020 CGGAAACTTAGTACATGTGTGGATAC 59.745 42.308 9.11 0.00 0.00 2.24
85 86 6.334989 CGGAAACTTAGTACATGTGTGGATA 58.665 40.000 9.11 0.00 0.00 2.59
86 87 5.175859 CGGAAACTTAGTACATGTGTGGAT 58.824 41.667 9.11 0.00 0.00 3.41
87 88 4.561938 CCGGAAACTTAGTACATGTGTGGA 60.562 45.833 9.11 0.00 0.00 4.02
88 89 3.682858 CCGGAAACTTAGTACATGTGTGG 59.317 47.826 9.11 0.00 0.00 4.17
89 90 4.312443 ACCGGAAACTTAGTACATGTGTG 58.688 43.478 9.46 0.00 0.00 3.82
90 91 4.612264 ACCGGAAACTTAGTACATGTGT 57.388 40.909 9.46 0.00 0.00 3.72
91 92 7.605410 ATTAACCGGAAACTTAGTACATGTG 57.395 36.000 9.46 0.00 0.00 3.21
92 93 8.313292 TGTATTAACCGGAAACTTAGTACATGT 58.687 33.333 9.46 2.69 0.00 3.21
93 94 8.706492 TGTATTAACCGGAAACTTAGTACATG 57.294 34.615 9.46 0.00 0.00 3.21
94 95 9.895138 ATTGTATTAACCGGAAACTTAGTACAT 57.105 29.630 9.46 2.28 29.53 2.29
95 96 9.723601 AATTGTATTAACCGGAAACTTAGTACA 57.276 29.630 9.46 10.88 28.23 2.90
100 101 9.101655 GCTAGAATTGTATTAACCGGAAACTTA 57.898 33.333 9.46 0.00 0.00 2.24
101 102 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
102 103 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
103 104 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
104 105 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
105 106 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
106 107 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
107 108 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
166 167 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
167 168 8.774183 TCCCTAGAGGCAATAATAAAGTTGTTA 58.226 33.333 0.00 0.00 34.51 2.41
168 169 7.639378 TCCCTAGAGGCAATAATAAAGTTGTT 58.361 34.615 0.00 0.00 34.51 2.83
169 170 7.127339 TCTCCCTAGAGGCAATAATAAAGTTGT 59.873 37.037 0.00 0.00 40.83 3.32
170 171 7.509546 TCTCCCTAGAGGCAATAATAAAGTTG 58.490 38.462 0.00 0.00 40.83 3.16
171 172 7.691993 TCTCCCTAGAGGCAATAATAAAGTT 57.308 36.000 0.00 0.00 40.83 2.66
172 173 7.880265 ATCTCCCTAGAGGCAATAATAAAGT 57.120 36.000 0.00 0.00 40.83 2.66
173 174 9.225436 GAAATCTCCCTAGAGGCAATAATAAAG 57.775 37.037 0.00 0.00 40.83 1.85
174 175 8.164070 GGAAATCTCCCTAGAGGCAATAATAAA 58.836 37.037 0.00 0.00 40.83 1.40
175 176 7.517604 AGGAAATCTCCCTAGAGGCAATAATAA 59.482 37.037 0.00 0.00 43.64 1.40
176 177 7.025620 AGGAAATCTCCCTAGAGGCAATAATA 58.974 38.462 0.00 0.00 43.64 0.98
177 178 5.854481 AGGAAATCTCCCTAGAGGCAATAAT 59.146 40.000 0.00 0.00 43.64 1.28
178 179 5.227593 AGGAAATCTCCCTAGAGGCAATAA 58.772 41.667 0.00 0.00 43.64 1.40
179 180 4.832492 AGGAAATCTCCCTAGAGGCAATA 58.168 43.478 0.00 0.00 43.64 1.90
180 181 3.674477 AGGAAATCTCCCTAGAGGCAAT 58.326 45.455 0.00 0.00 43.64 3.56
181 182 3.136641 AGGAAATCTCCCTAGAGGCAA 57.863 47.619 0.00 0.00 43.64 4.52
182 183 2.877154 AGGAAATCTCCCTAGAGGCA 57.123 50.000 0.00 0.00 43.64 4.75
183 184 3.041946 TGAAGGAAATCTCCCTAGAGGC 58.958 50.000 0.00 0.00 43.64 4.70
184 185 7.676043 TGTATATGAAGGAAATCTCCCTAGAGG 59.324 40.741 0.00 0.00 43.64 3.69
185 186 8.657387 TGTATATGAAGGAAATCTCCCTAGAG 57.343 38.462 0.00 0.00 43.64 2.43
188 189 9.494055 CCTATGTATATGAAGGAAATCTCCCTA 57.506 37.037 0.00 0.00 43.64 3.53
189 190 7.964293 ACCTATGTATATGAAGGAAATCTCCCT 59.036 37.037 4.69 0.00 43.64 4.20
190 191 8.043710 CACCTATGTATATGAAGGAAATCTCCC 58.956 40.741 4.69 0.00 43.64 4.30
191 192 7.550906 GCACCTATGTATATGAAGGAAATCTCC 59.449 40.741 4.69 0.00 42.81 3.71
192 193 7.276658 CGCACCTATGTATATGAAGGAAATCTC 59.723 40.741 4.69 0.00 33.16 2.75
193 194 7.099764 CGCACCTATGTATATGAAGGAAATCT 58.900 38.462 4.69 0.00 33.16 2.40
194 195 6.874134 ACGCACCTATGTATATGAAGGAAATC 59.126 38.462 4.69 0.00 33.16 2.17
195 196 6.769512 ACGCACCTATGTATATGAAGGAAAT 58.230 36.000 4.69 0.00 33.16 2.17
196 197 6.169557 ACGCACCTATGTATATGAAGGAAA 57.830 37.500 4.69 0.00 33.16 3.13
197 198 5.801531 ACGCACCTATGTATATGAAGGAA 57.198 39.130 4.69 0.00 33.16 3.36
198 199 5.184479 GGTACGCACCTATGTATATGAAGGA 59.816 44.000 0.00 0.00 42.11 3.36
199 200 5.408356 GGTACGCACCTATGTATATGAAGG 58.592 45.833 0.00 0.00 42.11 3.46
285 291 5.679382 GCAAGTAGTTGGATGCATGCATAAA 60.679 40.000 32.27 24.89 38.63 1.40
310 316 7.706607 GGCTGGATAAATTCTTATCAACCAAAC 59.293 37.037 7.08 0.00 43.63 2.93
311 317 7.416213 CGGCTGGATAAATTCTTATCAACCAAA 60.416 37.037 7.08 0.00 43.63 3.28
361 367 5.989477 TGACTGATCTGGGTACTAAATTGG 58.011 41.667 4.49 0.00 0.00 3.16
464 470 6.671614 AATATTTTCGGTGCGATGTCTTTA 57.328 33.333 0.00 0.00 35.23 1.85
479 485 7.155328 TCTTCCTGGATAGCTCGAATATTTTC 58.845 38.462 0.00 0.00 0.00 2.29
524 531 0.456221 AGTTGTCATCTACGAGGGCG 59.544 55.000 0.00 0.00 44.79 6.13
558 565 2.354821 GAGATAATCCCGCGCTTGTTTT 59.645 45.455 5.56 0.00 0.00 2.43
560 567 1.139058 AGAGATAATCCCGCGCTTGTT 59.861 47.619 5.56 0.00 0.00 2.83
690 697 2.553028 CCAAGTAGTCCATGTTGGCAGT 60.553 50.000 0.00 0.00 37.47 4.40
703 710 4.279922 GGCCAACAAATTACACCAAGTAGT 59.720 41.667 0.00 0.00 33.43 2.73
712 719 5.344743 TTGAACAAGGCCAACAAATTACA 57.655 34.783 5.01 0.00 0.00 2.41
714 721 7.055667 TGTATTGAACAAGGCCAACAAATTA 57.944 32.000 5.01 0.00 34.29 1.40
736 743 6.403866 TCCAGACAATAATTTGCAAGTTGT 57.596 33.333 16.66 16.47 36.22 3.32
748 755 3.073798 TGACCAAGCCTTCCAGACAATAA 59.926 43.478 0.00 0.00 0.00 1.40
841 855 0.621082 TCACAGTTTGTCCACCCACA 59.379 50.000 0.00 0.00 0.00 4.17
850 864 2.297033 GTGGGCATCAATCACAGTTTGT 59.703 45.455 0.00 0.00 0.00 2.83
954 968 0.904649 TGACATCCAGGTGTAGCCAG 59.095 55.000 0.00 0.00 40.61 4.85
1001 1015 1.072173 CATCCCACCAATATCTCGCCA 59.928 52.381 0.00 0.00 0.00 5.69
1102 1116 3.055021 TCCCTAAATACACGTGCATTCCA 60.055 43.478 17.22 5.59 0.00 3.53
1116 1130 1.182667 GCACCGCCTTTTCCCTAAAT 58.817 50.000 0.00 0.00 0.00 1.40
1119 1133 2.353573 GGCACCGCCTTTTCCCTA 59.646 61.111 0.00 0.00 46.69 3.53
1133 1147 2.011548 GCACGATCACCAATACAGGCA 61.012 52.381 0.00 0.00 0.00 4.75
1140 1154 2.330440 TAGCATGCACGATCACCAAT 57.670 45.000 21.98 0.00 0.00 3.16
1252 1268 2.230940 CGACATTACAGCCTCGCCG 61.231 63.158 0.00 0.00 0.00 6.46
1257 1273 5.995897 AGTAAGTTTTTCGACATTACAGCCT 59.004 36.000 0.00 0.00 0.00 4.58
1351 1368 2.259875 AAACACCAACACACGCACGG 62.260 55.000 0.00 0.00 0.00 4.94
1456 1477 2.113986 GTGTGAGCTTGGCCCTGT 59.886 61.111 0.00 0.00 0.00 4.00
1505 1526 4.282195 TCCTTGTGTTTGTGAGGTTTTTGT 59.718 37.500 0.00 0.00 0.00 2.83
1509 1530 5.476091 TTTTCCTTGTGTTTGTGAGGTTT 57.524 34.783 0.00 0.00 0.00 3.27
1526 1547 2.164422 CGGAGCTGATTTCCCTTTTTCC 59.836 50.000 0.00 0.00 0.00 3.13
1527 1548 3.494045 CGGAGCTGATTTCCCTTTTTC 57.506 47.619 0.00 0.00 0.00 2.29
1549 1570 4.431378 TGGTGGGAGGATAGTTAGTTTCA 58.569 43.478 0.00 0.00 0.00 2.69
1565 1586 0.329261 TTCTCTCTGGCAATGGTGGG 59.671 55.000 0.00 0.00 0.00 4.61
1569 1590 3.347077 ACTTCTTCTCTCTGGCAATGG 57.653 47.619 0.00 0.00 0.00 3.16
1574 1595 3.258123 AGTCTCAACTTCTTCTCTCTGGC 59.742 47.826 0.00 0.00 28.74 4.85
1575 1596 4.808558 CAGTCTCAACTTCTTCTCTCTGG 58.191 47.826 0.00 0.00 31.71 3.86
1576 1597 4.022068 AGCAGTCTCAACTTCTTCTCTCTG 60.022 45.833 0.00 0.00 31.71 3.35
1577 1598 4.151883 AGCAGTCTCAACTTCTTCTCTCT 58.848 43.478 0.00 0.00 31.71 3.10
1602 1623 1.627297 ATTTCCGGTCTGCTCCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
1614 1635 3.199880 ACCTATGCTTGAGATTTCCGG 57.800 47.619 0.00 0.00 0.00 5.14
1650 1671 3.091545 ACTTGGCACATGGTATTTGGAG 58.908 45.455 0.00 0.00 39.30 3.86
1657 1678 0.037590 GGGACACTTGGCACATGGTA 59.962 55.000 0.00 0.00 39.30 3.25
1837 1859 2.273179 GGTTTTTGAGGCCGGGTCC 61.273 63.158 2.18 0.00 0.00 4.46
1879 1902 1.515020 CCAGCTTCCTCGAGTCAGG 59.485 63.158 12.31 0.00 34.40 3.86
1881 1904 2.650116 GGCCAGCTTCCTCGAGTCA 61.650 63.158 12.31 0.00 0.00 3.41
1887 1910 1.970352 CTCTCAGGGCCAGCTTCCTC 61.970 65.000 6.18 0.00 0.00 3.71
1953 1977 4.329545 GGGTGCAGTCTTGGCCGA 62.330 66.667 0.00 0.00 0.00 5.54
2053 2077 4.710695 TACGACGCACTGTGCCCG 62.711 66.667 28.42 28.42 41.12 6.13
2056 2080 3.467119 CCGTACGACGCACTGTGC 61.467 66.667 22.38 22.38 40.91 4.57
2101 2125 2.480419 GTCACAGTCAACATGGCTACAC 59.520 50.000 0.00 0.00 26.99 2.90


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

AutoCloner maintained by Alex Coulton.