Multiple sequence alignment - TraesCS5D01G127100

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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 TraesCS5D01G127100 chr5D 100.000 5209 0 0 1 5209 197155071 197149863 0.000000e+00 9620
1 TraesCS5D01G127100 chr5D 93.233 266 18 0 1496 1761 197153492 197153227 4.890000e-105 392
2 TraesCS5D01G127100 chr5D 93.233 266 18 0 1580 1845 197153576 197153311 4.890000e-105 392
3 TraesCS5D01G127100 chr5D 92.896 183 13 0 1496 1678 197153408 197153226 3.090000e-67 267
4 TraesCS5D01G127100 chr5D 92.896 183 13 0 1664 1846 197153576 197153394 3.090000e-67 267
5 TraesCS5D01G127100 chr5B 93.627 5084 145 64 250 5209 213248017 213253045 0.000000e+00 7428
6 TraesCS5D01G127100 chr5B 93.985 266 16 0 1580 1845 213249254 213249519 2.260000e-108 403
7 TraesCS5D01G127100 chr5B 93.609 266 17 0 1496 1761 213249338 213249603 1.050000e-106 398
8 TraesCS5D01G127100 chr5B 96.241 133 5 0 111 243 213247091 213247223 8.780000e-53 219
9 TraesCS5D01G127100 chr5A 93.060 3761 162 31 1497 5209 227922601 227926310 0.000000e+00 5408
10 TraesCS5D01G127100 chr5A 94.275 1642 81 5 205 1845 227921233 227922862 0.000000e+00 2499
11 TraesCS5D01G127100 chr5A 91.698 265 19 1 1580 1844 227922516 227922777 1.070000e-96 364
12 TraesCS5D01G127100 chr5A 95.789 95 3 1 1 95 216336454 216336547 9.030000e-33 152
13 TraesCS5D01G127100 chr4A 79.459 925 171 14 2454 3370 522294095 522295008 5.690000e-179 638
14 TraesCS5D01G127100 chr4D 79.351 925 172 14 2454 3370 70119063 70119976 2.650000e-177 632
15 TraesCS5D01G127100 chr4B 79.027 925 175 14 2454 3370 103772923 103773836 2.670000e-172 616
16 TraesCS5D01G127100 chr7D 79.167 528 102 5 2668 3194 492221175 492220655 4.960000e-95 359
17 TraesCS5D01G127100 chr7A 79.245 530 98 8 2668 3194 558756224 558755704 4.960000e-95 359
18 TraesCS5D01G127100 chr7B 78.302 530 103 8 2668 3194 521617128 521616608 1.080000e-86 331
19 TraesCS5D01G127100 chr1D 76.682 223 50 2 2852 3073 285442556 285442777 7.080000e-24 122


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 TraesCS5D01G127100 chr5D 197149863 197155071 5208 True 2187.6 9620 94.4516 1 5209 5 chr5D.!!$R1 5208
1 TraesCS5D01G127100 chr5B 213247091 213253045 5954 False 2112.0 7428 94.3655 111 5209 4 chr5B.!!$F1 5098
2 TraesCS5D01G127100 chr5A 227921233 227926310 5077 False 2757.0 5408 93.0110 205 5209 3 chr5A.!!$F2 5004
3 TraesCS5D01G127100 chr4A 522294095 522295008 913 False 638.0 638 79.4590 2454 3370 1 chr4A.!!$F1 916
4 TraesCS5D01G127100 chr4D 70119063 70119976 913 False 632.0 632 79.3510 2454 3370 1 chr4D.!!$F1 916
5 TraesCS5D01G127100 chr4B 103772923 103773836 913 False 616.0 616 79.0270 2454 3370 1 chr4B.!!$F1 916
6 TraesCS5D01G127100 chr7D 492220655 492221175 520 True 359.0 359 79.1670 2668 3194 1 chr7D.!!$R1 526
7 TraesCS5D01G127100 chr7A 558755704 558756224 520 True 359.0 359 79.2450 2668 3194 1 chr7A.!!$R1 526
8 TraesCS5D01G127100 chr7B 521616608 521617128 520 True 331.0 331 78.3020 2668 3194 1 chr7B.!!$R1 526

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
157 158 0.382873 TGTTCACTTTGCAGCTGCTG 59.617 50.0 36.61 26.56 42.66 4.41 F
602 1412 1.011968 CATGCGTGCTTGCTTTGCAT 61.012 50.0 11.65 11.65 46.43 3.96 F
1787 2682 0.171455 GACAAGAGCGACGAGGATGT 59.829 55.0 0.00 0.00 0.00 3.06 F
3392 4299 0.254462 TACCAATCAAGGCCGCATGA 59.746 50.0 10.68 10.68 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2662 0.171231 CATCCTCGTCGCTCTTGTCA 59.829 55.000 0.00 0.00 0.00 3.58 R
2378 3276 0.036022 GTGCTCCTTCCTGCTGTTCT 59.964 55.000 0.00 0.00 0.00 3.01 R
3395 4302 3.006323 AGCGATTCAACAAGAGACAGTCT 59.994 43.478 1.46 1.46 36.94 3.24 R
4773 5800 0.940126 GCGGTGATGATAACAGGCAG 59.060 55.000 0.00 0.00 0.00 4.85 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
18 19 3.660111 GGTGAAGCCCGTGTGTGC 61.660 66.667 0.00 0.00 0.00 4.57
19 20 4.012895 GTGAAGCCCGTGTGTGCG 62.013 66.667 0.00 0.00 0.00 5.34
20 21 4.539083 TGAAGCCCGTGTGTGCGT 62.539 61.111 0.00 0.00 0.00 5.24
21 22 4.012895 GAAGCCCGTGTGTGCGTG 62.013 66.667 0.00 0.00 0.00 5.34
22 23 4.849310 AAGCCCGTGTGTGCGTGT 62.849 61.111 0.00 0.00 0.00 4.49
23 24 4.849310 AGCCCGTGTGTGCGTGTT 62.849 61.111 0.00 0.00 0.00 3.32
24 25 4.605967 GCCCGTGTGTGCGTGTTG 62.606 66.667 0.00 0.00 0.00 3.33
25 26 4.605967 CCCGTGTGTGCGTGTTGC 62.606 66.667 0.00 0.00 46.70 4.17
26 27 3.572539 CCGTGTGTGCGTGTTGCT 61.573 61.111 0.00 0.00 46.63 3.91
27 28 2.241190 CCGTGTGTGCGTGTTGCTA 61.241 57.895 0.00 0.00 46.63 3.49
28 29 1.083657 CGTGTGTGCGTGTTGCTAC 60.084 57.895 0.00 0.00 46.63 3.58
29 30 1.487452 CGTGTGTGCGTGTTGCTACT 61.487 55.000 0.00 0.00 46.63 2.57
30 31 1.493772 GTGTGTGCGTGTTGCTACTA 58.506 50.000 0.00 0.00 46.63 1.82
31 32 1.862201 GTGTGTGCGTGTTGCTACTAA 59.138 47.619 0.00 0.00 46.63 2.24
32 33 2.096909 GTGTGTGCGTGTTGCTACTAAG 60.097 50.000 0.00 0.00 46.63 2.18
33 34 2.132762 GTGTGCGTGTTGCTACTAAGT 58.867 47.619 0.00 0.00 46.63 2.24
34 35 2.542595 GTGTGCGTGTTGCTACTAAGTT 59.457 45.455 0.00 0.00 46.63 2.66
35 36 2.542178 TGTGCGTGTTGCTACTAAGTTG 59.458 45.455 0.00 0.00 46.63 3.16
36 37 2.096417 GTGCGTGTTGCTACTAAGTTGG 60.096 50.000 0.00 0.00 46.63 3.77
37 38 2.140717 GCGTGTTGCTACTAAGTTGGT 58.859 47.619 0.00 0.00 41.73 3.67
38 39 2.546789 GCGTGTTGCTACTAAGTTGGTT 59.453 45.455 0.00 0.00 41.73 3.67
39 40 3.002965 GCGTGTTGCTACTAAGTTGGTTT 59.997 43.478 0.00 0.00 41.73 3.27
40 41 4.523813 CGTGTTGCTACTAAGTTGGTTTG 58.476 43.478 0.00 0.00 0.00 2.93
41 42 4.271533 CGTGTTGCTACTAAGTTGGTTTGA 59.728 41.667 0.00 0.00 0.00 2.69
42 43 5.049680 CGTGTTGCTACTAAGTTGGTTTGAT 60.050 40.000 0.00 0.00 0.00 2.57
43 44 6.142817 GTGTTGCTACTAAGTTGGTTTGATG 58.857 40.000 0.00 0.00 0.00 3.07
44 45 5.825679 TGTTGCTACTAAGTTGGTTTGATGT 59.174 36.000 0.00 0.00 0.00 3.06
45 46 6.320164 TGTTGCTACTAAGTTGGTTTGATGTT 59.680 34.615 0.00 0.00 0.00 2.71
46 47 6.554334 TGCTACTAAGTTGGTTTGATGTTC 57.446 37.500 0.00 0.00 0.00 3.18
47 48 5.472137 TGCTACTAAGTTGGTTTGATGTTCC 59.528 40.000 0.00 0.00 0.00 3.62
48 49 5.705905 GCTACTAAGTTGGTTTGATGTTCCT 59.294 40.000 0.00 0.00 0.00 3.36
49 50 6.128254 GCTACTAAGTTGGTTTGATGTTCCTC 60.128 42.308 0.00 0.00 0.00 3.71
50 51 4.755123 ACTAAGTTGGTTTGATGTTCCTCG 59.245 41.667 0.00 0.00 0.00 4.63
51 52 3.208747 AGTTGGTTTGATGTTCCTCGT 57.791 42.857 0.00 0.00 0.00 4.18
52 53 4.345859 AGTTGGTTTGATGTTCCTCGTA 57.654 40.909 0.00 0.00 0.00 3.43
53 54 4.906618 AGTTGGTTTGATGTTCCTCGTAT 58.093 39.130 0.00 0.00 0.00 3.06
54 55 5.313712 AGTTGGTTTGATGTTCCTCGTATT 58.686 37.500 0.00 0.00 0.00 1.89
55 56 5.768164 AGTTGGTTTGATGTTCCTCGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
56 57 5.873179 TGGTTTGATGTTCCTCGTATTTC 57.127 39.130 0.00 0.00 0.00 2.17
57 58 5.556915 TGGTTTGATGTTCCTCGTATTTCT 58.443 37.500 0.00 0.00 0.00 2.52
58 59 5.642063 TGGTTTGATGTTCCTCGTATTTCTC 59.358 40.000 0.00 0.00 0.00 2.87
59 60 5.642063 GGTTTGATGTTCCTCGTATTTCTCA 59.358 40.000 0.00 0.00 0.00 3.27
60 61 6.148811 GGTTTGATGTTCCTCGTATTTCTCAA 59.851 38.462 0.00 0.00 0.00 3.02
61 62 6.721571 TTGATGTTCCTCGTATTTCTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
62 63 6.037786 TGATGTTCCTCGTATTTCTCAACT 57.962 37.500 0.00 0.00 0.00 3.16
63 64 6.464222 TGATGTTCCTCGTATTTCTCAACTT 58.536 36.000 0.00 0.00 0.00 2.66
64 65 6.368791 TGATGTTCCTCGTATTTCTCAACTTG 59.631 38.462 0.00 0.00 0.00 3.16
65 66 4.451096 TGTTCCTCGTATTTCTCAACTTGC 59.549 41.667 0.00 0.00 0.00 4.01
66 67 4.537135 TCCTCGTATTTCTCAACTTGCT 57.463 40.909 0.00 0.00 0.00 3.91
67 68 4.495422 TCCTCGTATTTCTCAACTTGCTC 58.505 43.478 0.00 0.00 0.00 4.26
68 69 4.220821 TCCTCGTATTTCTCAACTTGCTCT 59.779 41.667 0.00 0.00 0.00 4.09
69 70 4.564769 CCTCGTATTTCTCAACTTGCTCTC 59.435 45.833 0.00 0.00 0.00 3.20
70 71 4.166523 TCGTATTTCTCAACTTGCTCTCG 58.833 43.478 0.00 0.00 0.00 4.04
71 72 4.082949 TCGTATTTCTCAACTTGCTCTCGA 60.083 41.667 0.00 0.00 0.00 4.04
72 73 4.030753 CGTATTTCTCAACTTGCTCTCGAC 59.969 45.833 0.00 0.00 0.00 4.20
73 74 3.452755 TTTCTCAACTTGCTCTCGACA 57.547 42.857 0.00 0.00 0.00 4.35
74 75 3.452755 TTCTCAACTTGCTCTCGACAA 57.547 42.857 0.00 0.00 0.00 3.18
75 76 3.452755 TCTCAACTTGCTCTCGACAAA 57.547 42.857 0.00 0.00 0.00 2.83
76 77 3.792401 TCTCAACTTGCTCTCGACAAAA 58.208 40.909 0.00 0.00 0.00 2.44
77 78 3.555956 TCTCAACTTGCTCTCGACAAAAC 59.444 43.478 0.00 0.00 0.00 2.43
78 79 3.531538 TCAACTTGCTCTCGACAAAACT 58.468 40.909 0.00 0.00 0.00 2.66
79 80 3.555956 TCAACTTGCTCTCGACAAAACTC 59.444 43.478 0.00 0.00 0.00 3.01
80 81 3.179443 ACTTGCTCTCGACAAAACTCA 57.821 42.857 0.00 0.00 0.00 3.41
81 82 3.733337 ACTTGCTCTCGACAAAACTCAT 58.267 40.909 0.00 0.00 0.00 2.90
82 83 3.496130 ACTTGCTCTCGACAAAACTCATG 59.504 43.478 0.00 0.00 0.00 3.07
83 84 2.416747 TGCTCTCGACAAAACTCATGG 58.583 47.619 0.00 0.00 0.00 3.66
84 85 1.129437 GCTCTCGACAAAACTCATGGC 59.871 52.381 0.00 0.00 0.00 4.40
85 86 2.416747 CTCTCGACAAAACTCATGGCA 58.583 47.619 0.00 0.00 0.00 4.92
86 87 2.414481 CTCTCGACAAAACTCATGGCAG 59.586 50.000 0.00 0.00 0.00 4.85
87 88 2.037121 TCTCGACAAAACTCATGGCAGA 59.963 45.455 0.00 0.00 0.00 4.26
88 89 2.807967 CTCGACAAAACTCATGGCAGAA 59.192 45.455 0.00 0.00 0.00 3.02
89 90 3.210227 TCGACAAAACTCATGGCAGAAA 58.790 40.909 0.00 0.00 0.00 2.52
90 91 3.003275 TCGACAAAACTCATGGCAGAAAC 59.997 43.478 0.00 0.00 0.00 2.78
91 92 3.243035 CGACAAAACTCATGGCAGAAACA 60.243 43.478 0.00 0.00 0.00 2.83
92 93 4.681744 GACAAAACTCATGGCAGAAACAA 58.318 39.130 0.00 0.00 0.00 2.83
93 94 4.685924 ACAAAACTCATGGCAGAAACAAG 58.314 39.130 0.00 0.00 0.00 3.16
94 95 4.160252 ACAAAACTCATGGCAGAAACAAGT 59.840 37.500 0.00 0.00 0.00 3.16
95 96 5.359576 ACAAAACTCATGGCAGAAACAAGTA 59.640 36.000 0.00 0.00 0.00 2.24
96 97 5.695851 AAACTCATGGCAGAAACAAGTAG 57.304 39.130 0.00 0.00 0.00 2.57
97 98 4.623932 ACTCATGGCAGAAACAAGTAGA 57.376 40.909 0.00 0.00 0.00 2.59
98 99 4.573900 ACTCATGGCAGAAACAAGTAGAG 58.426 43.478 0.00 0.00 0.00 2.43
99 100 3.937706 CTCATGGCAGAAACAAGTAGAGG 59.062 47.826 0.00 0.00 0.00 3.69
100 101 3.582647 TCATGGCAGAAACAAGTAGAGGA 59.417 43.478 0.00 0.00 0.00 3.71
101 102 3.685139 TGGCAGAAACAAGTAGAGGAG 57.315 47.619 0.00 0.00 0.00 3.69
102 103 2.303022 TGGCAGAAACAAGTAGAGGAGG 59.697 50.000 0.00 0.00 0.00 4.30
103 104 2.355209 GGCAGAAACAAGTAGAGGAGGG 60.355 54.545 0.00 0.00 0.00 4.30
104 105 2.567615 GCAGAAACAAGTAGAGGAGGGA 59.432 50.000 0.00 0.00 0.00 4.20
105 106 3.198853 GCAGAAACAAGTAGAGGAGGGAT 59.801 47.826 0.00 0.00 0.00 3.85
106 107 4.406003 GCAGAAACAAGTAGAGGAGGGATA 59.594 45.833 0.00 0.00 0.00 2.59
107 108 5.104900 GCAGAAACAAGTAGAGGAGGGATAA 60.105 44.000 0.00 0.00 0.00 1.75
108 109 6.408662 GCAGAAACAAGTAGAGGAGGGATAAT 60.409 42.308 0.00 0.00 0.00 1.28
109 110 7.569240 CAGAAACAAGTAGAGGAGGGATAATT 58.431 38.462 0.00 0.00 0.00 1.40
125 126 9.962783 GAGGGATAATTTCTTCAATTCAATCAG 57.037 33.333 0.00 0.00 36.43 2.90
140 141 9.071276 CAATTCAATCAGTTAGGGCTTATATGT 57.929 33.333 0.00 0.00 0.00 2.29
149 150 6.318900 AGTTAGGGCTTATATGTTCACTTTGC 59.681 38.462 0.00 0.00 0.00 3.68
157 158 0.382873 TGTTCACTTTGCAGCTGCTG 59.617 50.000 36.61 26.56 42.66 4.41
197 198 3.365364 GGTGAAAAGAAGAGAATGGCGTG 60.365 47.826 0.00 0.00 0.00 5.34
265 1053 3.118738 ACTGCCGTAGAAGTTATTGAGGG 60.119 47.826 0.00 0.00 0.00 4.30
422 1211 2.725723 CGCGATGTTTTTGCAACAAGAT 59.274 40.909 7.62 7.62 33.97 2.40
588 1398 1.953138 GGACGAGGAGATGCATGCG 60.953 63.158 14.09 2.36 0.00 4.73
589 1399 1.227089 GACGAGGAGATGCATGCGT 60.227 57.895 13.43 13.43 34.39 5.24
590 1400 1.485838 GACGAGGAGATGCATGCGTG 61.486 60.000 19.18 3.97 31.58 5.34
600 1410 3.152703 CATGCGTGCTTGCTTTGC 58.847 55.556 0.00 0.00 35.36 3.68
601 1411 1.662133 CATGCGTGCTTGCTTTGCA 60.662 52.632 0.00 8.72 40.23 4.08
602 1412 1.011968 CATGCGTGCTTGCTTTGCAT 61.012 50.000 11.65 11.65 46.43 3.96
603 1413 1.011968 ATGCGTGCTTGCTTTGCATG 61.012 50.000 14.92 11.90 44.02 4.06
604 1414 2.377310 GCGTGCTTGCTTTGCATGG 61.377 57.895 15.92 7.65 44.81 3.66
608 1418 2.266689 CTTGCTTTGCATGGCCCC 59.733 61.111 0.00 0.00 38.76 5.80
636 1446 4.086457 TCTTGTTGGGAAATAGAAAGGGC 58.914 43.478 0.00 0.00 0.00 5.19
754 1564 5.447413 CGGTGGTGCACGTCTATATATCTAG 60.447 48.000 11.45 0.00 34.83 2.43
799 1609 4.069232 CACCCTTCTCGCTCGCCA 62.069 66.667 0.00 0.00 0.00 5.69
1328 2142 1.971695 TCGACCAGAGCGCAGAGAA 60.972 57.895 11.47 0.00 0.00 2.87
1536 2350 3.774528 AAGAGCGCCGAGGATGCA 61.775 61.111 2.29 0.00 0.00 3.96
1558 2372 2.031012 CAGGCACGAACCAGAGCA 59.969 61.111 0.00 0.00 0.00 4.26
1589 2484 2.432628 CGACCAGAACACGGAGGC 60.433 66.667 0.00 0.00 0.00 4.70
1702 2597 1.590259 GACAAGAGCGCCGAGGATC 60.590 63.158 2.29 0.00 0.00 3.36
1767 2662 4.719106 ACGGAGGAGGCGACGACT 62.719 66.667 0.71 0.71 0.00 4.18
1778 2673 1.206831 CGACGACTGACAAGAGCGA 59.793 57.895 0.00 0.00 0.00 4.93
1787 2682 0.171455 GACAAGAGCGACGAGGATGT 59.829 55.000 0.00 0.00 0.00 3.06
2124 3019 2.347292 CCAAACGTTCGTCGACAAGAAG 60.347 50.000 17.16 5.37 42.86 2.85
2146 3041 2.429930 CGCCCAGGAACCAGACAA 59.570 61.111 0.00 0.00 0.00 3.18
2154 3049 2.800544 CAGGAACCAGACAACTACAACG 59.199 50.000 0.00 0.00 0.00 4.10
2213 3108 0.961019 ACGAACAGTAGTACCGCCAA 59.039 50.000 0.00 0.00 0.00 4.52
2781 3685 2.030562 ACGCAGTTCCTGAACGGG 59.969 61.111 11.23 12.35 37.78 5.28
2925 3832 2.616330 CGTGCTGGCCATGTCGTTT 61.616 57.895 5.51 0.00 0.00 3.60
3363 4270 3.315140 TCGGATGACCCCAACGCA 61.315 61.111 0.00 0.00 0.00 5.24
3392 4299 0.254462 TACCAATCAAGGCCGCATGA 59.746 50.000 10.68 10.68 0.00 3.07
3393 4300 0.396139 ACCAATCAAGGCCGCATGAT 60.396 50.000 13.83 13.83 37.88 2.45
3394 4301 0.031585 CCAATCAAGGCCGCATGATG 59.968 55.000 18.49 13.38 36.44 3.07
3395 4302 1.026584 CAATCAAGGCCGCATGATGA 58.973 50.000 18.49 9.00 36.44 2.92
3396 4303 1.001706 CAATCAAGGCCGCATGATGAG 60.002 52.381 18.49 12.36 36.44 2.90
3846 4796 1.071542 TGTGGGTGATGAACATCGTGT 59.928 47.619 9.71 0.00 40.63 4.49
3908 4858 0.846693 GGCTCTTGGGGATGTACCAT 59.153 55.000 0.00 0.00 41.20 3.55
4040 4990 3.917760 GACCGGATCCTCAGGCCG 61.918 72.222 9.46 2.79 44.42 6.13
4094 5044 2.043852 GCCGAGGAGGTGGAGAGA 60.044 66.667 0.00 0.00 43.70 3.10
4202 5152 0.823356 CCACCCAAGTCCAACCACTG 60.823 60.000 0.00 0.00 0.00 3.66
4215 5165 0.473886 ACCACTGGGCTAGGAACACT 60.474 55.000 2.02 0.00 37.90 3.55
4218 5168 2.180276 CACTGGGCTAGGAACACTACT 58.820 52.381 2.02 0.00 0.00 2.57
4243 5231 3.976942 CAGTACTTTGCAAACACATGAGC 59.023 43.478 8.05 0.00 0.00 4.26
4266 5254 5.051508 GCATGGCAGCAATAACGAAAATAAG 60.052 40.000 0.00 0.00 0.00 1.73
4313 5308 7.933215 AGTTTTGTACTTGTACAAGGAAACT 57.067 32.000 30.42 30.42 42.53 2.66
4330 5325 9.831737 CAAGGAAACTGTTAAGAACATTATCAG 57.168 33.333 0.00 4.82 42.68 2.90
4399 5394 4.041075 TGGCACTACAAAGTATCAACTCCA 59.959 41.667 0.00 0.00 33.75 3.86
4427 5422 1.774254 TCTCCTTCCTTCAGGCAACAA 59.226 47.619 0.00 0.00 41.41 2.83
4430 5425 3.944015 CTCCTTCCTTCAGGCAACAATAG 59.056 47.826 0.00 0.00 41.41 1.73
4432 5427 3.441572 CCTTCCTTCAGGCAACAATAGTG 59.558 47.826 0.00 0.00 41.41 2.74
4433 5428 4.326826 CTTCCTTCAGGCAACAATAGTGA 58.673 43.478 0.00 0.00 41.41 3.41
4434 5429 4.574674 TCCTTCAGGCAACAATAGTGAT 57.425 40.909 0.00 0.00 41.41 3.06
4435 5430 4.264253 TCCTTCAGGCAACAATAGTGATG 58.736 43.478 0.00 0.00 41.41 3.07
4440 5435 2.368439 GGCAACAATAGTGATGGCTCA 58.632 47.619 17.68 0.00 45.99 4.26
4441 5436 2.954318 GGCAACAATAGTGATGGCTCAT 59.046 45.455 17.68 0.00 45.99 2.90
4442 5437 3.004106 GGCAACAATAGTGATGGCTCATC 59.996 47.826 17.68 7.90 45.99 2.92
4451 5446 3.564053 TGATGGCTCATCATTACTGCA 57.436 42.857 12.22 0.00 44.60 4.41
4452 5447 4.094830 TGATGGCTCATCATTACTGCAT 57.905 40.909 12.22 0.00 44.60 3.96
4453 5448 3.818773 TGATGGCTCATCATTACTGCATG 59.181 43.478 12.22 0.00 44.60 4.06
4454 5449 3.564053 TGGCTCATCATTACTGCATGA 57.436 42.857 0.00 0.00 37.58 3.07
4455 5450 3.888583 TGGCTCATCATTACTGCATGAA 58.111 40.909 0.00 0.00 36.74 2.57
4456 5451 3.628942 TGGCTCATCATTACTGCATGAAC 59.371 43.478 0.00 0.00 36.74 3.18
4482 5477 3.568007 ACTGAAGCAAACATCGGCTAAAA 59.432 39.130 0.00 0.00 40.01 1.52
4490 5485 1.196808 ACATCGGCTAAAACACTTGCG 59.803 47.619 0.00 0.00 0.00 4.85
4515 5510 1.626686 AGGGACTGACTGACTGACTG 58.373 55.000 0.00 0.00 37.18 3.51
4516 5511 1.145945 AGGGACTGACTGACTGACTGA 59.854 52.381 0.00 0.00 37.18 3.41
4517 5512 1.271102 GGGACTGACTGACTGACTGAC 59.729 57.143 0.00 0.00 0.00 3.51
4518 5513 2.235016 GGACTGACTGACTGACTGACT 58.765 52.381 0.00 0.00 0.00 3.41
4519 5514 2.227865 GGACTGACTGACTGACTGACTC 59.772 54.545 0.00 0.00 0.00 3.36
4520 5515 3.146066 GACTGACTGACTGACTGACTCT 58.854 50.000 0.00 0.00 0.00 3.24
4521 5516 3.561143 ACTGACTGACTGACTGACTCTT 58.439 45.455 0.00 0.00 0.00 2.85
4539 5534 7.651808 TGACTCTTTTTGTTTCTCAATCATCC 58.348 34.615 0.00 0.00 35.84 3.51
4541 5536 7.655490 ACTCTTTTTGTTTCTCAATCATCCAG 58.345 34.615 0.00 0.00 35.84 3.86
4569 5580 9.716507 CATTAAGCTAGTACGTAAAATTGCATT 57.283 29.630 0.00 0.09 0.00 3.56
4591 5602 1.768275 CACCCCAGTGCCATAGTATCA 59.232 52.381 0.00 0.00 37.14 2.15
4662 5676 4.186159 GCCTAACATTAGAGTTTACCGCA 58.814 43.478 0.00 0.00 32.47 5.69
4773 5800 3.615155 AGCCCTCTAGAATCTTGCAAAC 58.385 45.455 0.00 0.00 0.00 2.93
4799 5826 1.134220 GTTATCATCACCGCCCTTCCA 60.134 52.381 0.00 0.00 0.00 3.53
5013 6040 5.235516 AGTCCAAAACTCTAACCATACACG 58.764 41.667 0.00 0.00 30.02 4.49
5044 6071 6.175471 ACTCACTTCATGCTCATCAAACATA 58.825 36.000 0.00 0.00 0.00 2.29
5121 6150 7.324354 ACTTCTAAACTAAGCCAACGAAAAA 57.676 32.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.660111 GCACACACGGGCTTCACC 61.660 66.667 0.00 0.00 37.93 4.02
2 3 4.012895 CGCACACACGGGCTTCAC 62.013 66.667 0.00 0.00 0.00 3.18
3 4 4.539083 ACGCACACACGGGCTTCA 62.539 61.111 0.00 0.00 37.37 3.02
4 5 4.012895 CACGCACACACGGGCTTC 62.013 66.667 0.00 0.00 37.37 3.86
5 6 4.849310 ACACGCACACACGGGCTT 62.849 61.111 0.00 0.00 41.17 4.35
6 7 4.849310 AACACGCACACACGGGCT 62.849 61.111 0.00 0.00 41.17 5.19
7 8 4.605967 CAACACGCACACACGGGC 62.606 66.667 0.00 0.00 41.17 6.13
8 9 4.605967 GCAACACGCACACACGGG 62.606 66.667 0.00 0.00 43.76 5.28
9 10 2.241190 TAGCAACACGCACACACGG 61.241 57.895 0.00 0.00 46.13 4.94
10 11 1.083657 GTAGCAACACGCACACACG 60.084 57.895 0.00 0.00 46.13 4.49
11 12 1.493772 TAGTAGCAACACGCACACAC 58.506 50.000 0.00 0.00 46.13 3.82
12 13 2.131972 CTTAGTAGCAACACGCACACA 58.868 47.619 0.00 0.00 46.13 3.72
13 14 2.132762 ACTTAGTAGCAACACGCACAC 58.867 47.619 0.00 0.00 46.13 3.82
14 15 2.519377 ACTTAGTAGCAACACGCACA 57.481 45.000 0.00 0.00 46.13 4.57
15 16 2.096417 CCAACTTAGTAGCAACACGCAC 60.096 50.000 0.00 0.00 46.13 5.34
16 17 2.139917 CCAACTTAGTAGCAACACGCA 58.860 47.619 0.00 0.00 46.13 5.24
17 18 2.140717 ACCAACTTAGTAGCAACACGC 58.859 47.619 0.00 0.00 42.91 5.34
18 19 4.271533 TCAAACCAACTTAGTAGCAACACG 59.728 41.667 0.00 0.00 0.00 4.49
19 20 5.744666 TCAAACCAACTTAGTAGCAACAC 57.255 39.130 0.00 0.00 0.00 3.32
20 21 5.825679 ACATCAAACCAACTTAGTAGCAACA 59.174 36.000 0.00 0.00 0.00 3.33
21 22 6.313744 ACATCAAACCAACTTAGTAGCAAC 57.686 37.500 0.00 0.00 0.00 4.17
22 23 6.016610 GGAACATCAAACCAACTTAGTAGCAA 60.017 38.462 0.00 0.00 0.00 3.91
23 24 5.472137 GGAACATCAAACCAACTTAGTAGCA 59.528 40.000 0.00 0.00 0.00 3.49
24 25 5.705905 AGGAACATCAAACCAACTTAGTAGC 59.294 40.000 0.00 0.00 0.00 3.58
25 26 6.090898 CGAGGAACATCAAACCAACTTAGTAG 59.909 42.308 0.00 0.00 0.00 2.57
26 27 5.929992 CGAGGAACATCAAACCAACTTAGTA 59.070 40.000 0.00 0.00 0.00 1.82
27 28 4.755123 CGAGGAACATCAAACCAACTTAGT 59.245 41.667 0.00 0.00 0.00 2.24
28 29 4.755123 ACGAGGAACATCAAACCAACTTAG 59.245 41.667 0.00 0.00 0.00 2.18
29 30 4.710324 ACGAGGAACATCAAACCAACTTA 58.290 39.130 0.00 0.00 0.00 2.24
30 31 3.551846 ACGAGGAACATCAAACCAACTT 58.448 40.909 0.00 0.00 0.00 2.66
31 32 3.208747 ACGAGGAACATCAAACCAACT 57.791 42.857 0.00 0.00 0.00 3.16
32 33 5.622770 AATACGAGGAACATCAAACCAAC 57.377 39.130 0.00 0.00 0.00 3.77
33 34 6.001460 AGAAATACGAGGAACATCAAACCAA 58.999 36.000 0.00 0.00 0.00 3.67
34 35 5.556915 AGAAATACGAGGAACATCAAACCA 58.443 37.500 0.00 0.00 0.00 3.67
35 36 5.642063 TGAGAAATACGAGGAACATCAAACC 59.358 40.000 0.00 0.00 0.00 3.27
36 37 6.721571 TGAGAAATACGAGGAACATCAAAC 57.278 37.500 0.00 0.00 0.00 2.93
37 38 6.934645 AGTTGAGAAATACGAGGAACATCAAA 59.065 34.615 0.00 0.00 0.00 2.69
38 39 6.464222 AGTTGAGAAATACGAGGAACATCAA 58.536 36.000 0.00 0.00 0.00 2.57
39 40 6.037786 AGTTGAGAAATACGAGGAACATCA 57.962 37.500 0.00 0.00 0.00 3.07
40 41 6.673316 GCAAGTTGAGAAATACGAGGAACATC 60.673 42.308 7.16 0.00 0.00 3.06
41 42 5.122396 GCAAGTTGAGAAATACGAGGAACAT 59.878 40.000 7.16 0.00 0.00 2.71
42 43 4.451096 GCAAGTTGAGAAATACGAGGAACA 59.549 41.667 7.16 0.00 0.00 3.18
43 44 4.691216 AGCAAGTTGAGAAATACGAGGAAC 59.309 41.667 7.16 0.00 0.00 3.62
44 45 4.894784 AGCAAGTTGAGAAATACGAGGAA 58.105 39.130 7.16 0.00 0.00 3.36
45 46 4.220821 AGAGCAAGTTGAGAAATACGAGGA 59.779 41.667 7.16 0.00 0.00 3.71
46 47 4.499183 AGAGCAAGTTGAGAAATACGAGG 58.501 43.478 7.16 0.00 0.00 4.63
47 48 4.264145 CGAGAGCAAGTTGAGAAATACGAG 59.736 45.833 7.16 0.00 0.00 4.18
48 49 4.082949 TCGAGAGCAAGTTGAGAAATACGA 60.083 41.667 7.16 5.13 0.00 3.43
49 50 4.030753 GTCGAGAGCAAGTTGAGAAATACG 59.969 45.833 7.16 2.90 0.00 3.06
50 51 4.923871 TGTCGAGAGCAAGTTGAGAAATAC 59.076 41.667 7.16 0.00 0.00 1.89
51 52 5.134202 TGTCGAGAGCAAGTTGAGAAATA 57.866 39.130 7.16 0.00 0.00 1.40
52 53 3.995199 TGTCGAGAGCAAGTTGAGAAAT 58.005 40.909 7.16 0.00 0.00 2.17
53 54 3.452755 TGTCGAGAGCAAGTTGAGAAA 57.547 42.857 7.16 0.00 0.00 2.52
54 55 3.452755 TTGTCGAGAGCAAGTTGAGAA 57.547 42.857 7.16 0.00 0.00 2.87
55 56 3.452755 TTTGTCGAGAGCAAGTTGAGA 57.547 42.857 7.16 0.00 0.00 3.27
56 57 3.557595 AGTTTTGTCGAGAGCAAGTTGAG 59.442 43.478 7.16 0.00 0.00 3.02
57 58 3.531538 AGTTTTGTCGAGAGCAAGTTGA 58.468 40.909 7.16 0.00 0.00 3.18
58 59 3.309682 TGAGTTTTGTCGAGAGCAAGTTG 59.690 43.478 0.00 0.00 0.00 3.16
59 60 3.531538 TGAGTTTTGTCGAGAGCAAGTT 58.468 40.909 0.00 0.00 0.00 2.66
60 61 3.179443 TGAGTTTTGTCGAGAGCAAGT 57.821 42.857 0.00 0.00 0.00 3.16
61 62 3.120408 CCATGAGTTTTGTCGAGAGCAAG 60.120 47.826 0.00 0.00 0.00 4.01
62 63 2.807967 CCATGAGTTTTGTCGAGAGCAA 59.192 45.455 0.00 0.00 0.00 3.91
63 64 2.416747 CCATGAGTTTTGTCGAGAGCA 58.583 47.619 0.00 0.00 0.00 4.26
64 65 1.129437 GCCATGAGTTTTGTCGAGAGC 59.871 52.381 0.00 0.00 0.00 4.09
65 66 2.414481 CTGCCATGAGTTTTGTCGAGAG 59.586 50.000 0.00 0.00 0.00 3.20
66 67 2.037121 TCTGCCATGAGTTTTGTCGAGA 59.963 45.455 0.00 0.00 0.00 4.04
67 68 2.416747 TCTGCCATGAGTTTTGTCGAG 58.583 47.619 0.00 0.00 0.00 4.04
68 69 2.542020 TCTGCCATGAGTTTTGTCGA 57.458 45.000 0.00 0.00 0.00 4.20
69 70 3.243035 TGTTTCTGCCATGAGTTTTGTCG 60.243 43.478 0.00 0.00 0.00 4.35
70 71 4.305989 TGTTTCTGCCATGAGTTTTGTC 57.694 40.909 0.00 0.00 0.00 3.18
71 72 4.160252 ACTTGTTTCTGCCATGAGTTTTGT 59.840 37.500 0.00 0.00 0.00 2.83
72 73 4.685924 ACTTGTTTCTGCCATGAGTTTTG 58.314 39.130 0.00 0.00 0.00 2.44
73 74 5.827797 TCTACTTGTTTCTGCCATGAGTTTT 59.172 36.000 0.00 0.00 0.00 2.43
74 75 5.376625 TCTACTTGTTTCTGCCATGAGTTT 58.623 37.500 0.00 0.00 0.00 2.66
75 76 4.973168 TCTACTTGTTTCTGCCATGAGTT 58.027 39.130 0.00 0.00 0.00 3.01
76 77 4.564406 CCTCTACTTGTTTCTGCCATGAGT 60.564 45.833 0.00 0.00 0.00 3.41
77 78 3.937706 CCTCTACTTGTTTCTGCCATGAG 59.062 47.826 0.00 0.00 0.00 2.90
78 79 3.582647 TCCTCTACTTGTTTCTGCCATGA 59.417 43.478 0.00 0.00 0.00 3.07
79 80 3.937706 CTCCTCTACTTGTTTCTGCCATG 59.062 47.826 0.00 0.00 0.00 3.66
80 81 3.054802 CCTCCTCTACTTGTTTCTGCCAT 60.055 47.826 0.00 0.00 0.00 4.40
81 82 2.303022 CCTCCTCTACTTGTTTCTGCCA 59.697 50.000 0.00 0.00 0.00 4.92
82 83 2.355209 CCCTCCTCTACTTGTTTCTGCC 60.355 54.545 0.00 0.00 0.00 4.85
83 84 2.567615 TCCCTCCTCTACTTGTTTCTGC 59.432 50.000 0.00 0.00 0.00 4.26
84 85 6.546428 TTATCCCTCCTCTACTTGTTTCTG 57.454 41.667 0.00 0.00 0.00 3.02
85 86 7.757242 AATTATCCCTCCTCTACTTGTTTCT 57.243 36.000 0.00 0.00 0.00 2.52
86 87 8.268605 AGAAATTATCCCTCCTCTACTTGTTTC 58.731 37.037 0.00 0.00 0.00 2.78
87 88 8.164057 AGAAATTATCCCTCCTCTACTTGTTT 57.836 34.615 0.00 0.00 0.00 2.83
88 89 7.757242 AGAAATTATCCCTCCTCTACTTGTT 57.243 36.000 0.00 0.00 0.00 2.83
89 90 7.403231 TGAAGAAATTATCCCTCCTCTACTTGT 59.597 37.037 0.00 0.00 0.00 3.16
90 91 7.796054 TGAAGAAATTATCCCTCCTCTACTTG 58.204 38.462 0.00 0.00 0.00 3.16
91 92 7.996758 TGAAGAAATTATCCCTCCTCTACTT 57.003 36.000 0.00 0.00 0.00 2.24
92 93 7.996758 TTGAAGAAATTATCCCTCCTCTACT 57.003 36.000 0.00 0.00 0.00 2.57
93 94 9.278978 GAATTGAAGAAATTATCCCTCCTCTAC 57.721 37.037 0.00 0.00 38.64 2.59
94 95 9.003145 TGAATTGAAGAAATTATCCCTCCTCTA 57.997 33.333 0.00 0.00 38.64 2.43
95 96 7.876371 TGAATTGAAGAAATTATCCCTCCTCT 58.124 34.615 0.00 0.00 38.64 3.69
96 97 8.525290 TTGAATTGAAGAAATTATCCCTCCTC 57.475 34.615 0.00 0.00 38.64 3.71
97 98 9.140874 GATTGAATTGAAGAAATTATCCCTCCT 57.859 33.333 0.00 0.00 38.64 3.69
98 99 8.917088 TGATTGAATTGAAGAAATTATCCCTCC 58.083 33.333 0.00 0.00 38.64 4.30
99 100 9.962783 CTGATTGAATTGAAGAAATTATCCCTC 57.037 33.333 0.00 0.00 38.64 4.30
100 101 9.484806 ACTGATTGAATTGAAGAAATTATCCCT 57.515 29.630 0.00 0.00 38.64 4.20
106 107 8.037166 GCCCTAACTGATTGAATTGAAGAAATT 58.963 33.333 0.00 0.00 41.33 1.82
107 108 7.398332 AGCCCTAACTGATTGAATTGAAGAAAT 59.602 33.333 0.00 0.00 0.00 2.17
108 109 6.721208 AGCCCTAACTGATTGAATTGAAGAAA 59.279 34.615 0.00 0.00 0.00 2.52
109 110 6.248433 AGCCCTAACTGATTGAATTGAAGAA 58.752 36.000 0.00 0.00 0.00 2.52
125 126 6.094881 TGCAAAGTGAACATATAAGCCCTAAC 59.905 38.462 0.00 0.00 0.00 2.34
140 141 1.391577 TTCAGCAGCTGCAAAGTGAA 58.608 45.000 38.24 32.29 45.16 3.18
149 150 0.600057 GTCCCCTTTTTCAGCAGCTG 59.400 55.000 17.10 17.10 0.00 4.24
157 158 2.037121 CACCACCATTGTCCCCTTTTTC 59.963 50.000 0.00 0.00 0.00 2.29
197 198 7.519488 GCACTAAACCCAACAACTAAACTAGTC 60.519 40.741 0.00 0.00 38.26 2.59
265 1053 9.160496 AGCATATATAGCAAGCTAACTGAAATC 57.840 33.333 5.81 0.00 33.06 2.17
422 1211 3.569701 GCAAAACTCTGGGTGAATTCTCA 59.430 43.478 7.05 2.21 0.00 3.27
588 1398 2.030958 GGCCATGCAAAGCAAGCAC 61.031 57.895 12.75 5.42 45.95 4.40
589 1399 2.344500 GGCCATGCAAAGCAAGCA 59.656 55.556 12.75 0.23 43.62 3.91
590 1400 2.435410 GGGCCATGCAAAGCAAGC 60.435 61.111 4.39 8.36 43.62 4.01
591 1401 1.833787 AAGGGGCCATGCAAAGCAAG 61.834 55.000 4.39 0.00 43.62 4.01
592 1402 1.842465 AAGGGGCCATGCAAAGCAA 60.842 52.632 4.39 0.00 43.62 3.91
593 1403 2.203818 AAGGGGCCATGCAAAGCA 60.204 55.556 4.39 0.00 44.86 3.91
594 1404 2.266689 CAAGGGGCCATGCAAAGC 59.733 61.111 4.39 2.80 0.00 3.51
595 1405 1.833787 AAGCAAGGGGCCATGCAAAG 61.834 55.000 28.26 3.84 46.50 2.77
596 1406 1.829523 GAAGCAAGGGGCCATGCAAA 61.830 55.000 28.26 0.00 46.50 3.68
597 1407 2.203818 AAGCAAGGGGCCATGCAA 60.204 55.556 28.26 0.00 46.50 4.08
598 1408 2.681064 GAAGCAAGGGGCCATGCA 60.681 61.111 28.26 0.00 46.50 3.96
599 1409 1.986210 AAGAAGCAAGGGGCCATGC 60.986 57.895 21.89 21.89 46.50 4.06
600 1410 0.901580 ACAAGAAGCAAGGGGCCATG 60.902 55.000 4.39 4.83 46.50 3.66
601 1411 0.178924 AACAAGAAGCAAGGGGCCAT 60.179 50.000 4.39 0.00 46.50 4.40
602 1412 1.114722 CAACAAGAAGCAAGGGGCCA 61.115 55.000 4.39 0.00 46.50 5.36
603 1413 1.667722 CAACAAGAAGCAAGGGGCC 59.332 57.895 0.00 0.00 46.50 5.80
604 1414 1.667722 CCAACAAGAAGCAAGGGGC 59.332 57.895 0.00 0.00 45.30 5.80
608 1418 5.964958 TCTATTTCCCAACAAGAAGCAAG 57.035 39.130 0.00 0.00 0.00 4.01
636 1446 4.811557 GTCTTTGAAATGGATCTACCGGAG 59.188 45.833 9.46 0.60 42.61 4.63
844 1655 2.124736 AATGACCGGGCACGATGG 60.125 61.111 15.41 0.00 44.60 3.51
1096 1907 2.722201 GCCCCACGAAGAGGACGAT 61.722 63.158 0.00 0.00 42.26 3.73
1245 2056 1.813862 GCCTTGTCTGTTGCCTGTGTA 60.814 52.381 0.00 0.00 0.00 2.90
1391 2205 2.263021 TTCTTGGACGGCGACTCGA 61.263 57.895 16.62 2.71 0.00 4.04
1522 2336 4.957684 CGATGCATCCTCGGCGCT 62.958 66.667 20.87 0.00 32.58 5.92
1536 2350 1.079819 CTGGTTCGTGCCTGTCGAT 60.080 57.895 0.00 0.00 37.18 3.59
1702 2597 3.103911 GTTCGTGCCTGTCGACGG 61.104 66.667 17.81 17.81 37.05 4.79
1767 2662 0.171231 CATCCTCGTCGCTCTTGTCA 59.829 55.000 0.00 0.00 0.00 3.58
1778 2673 0.320771 GCCTGTTGACACATCCTCGT 60.321 55.000 0.00 0.00 30.39 4.18
1787 2682 1.102154 CTGGTTTGTGCCTGTTGACA 58.898 50.000 0.00 0.00 0.00 3.58
2124 3019 3.901797 CTGGTTCCTGGGCGTGTCC 62.902 68.421 0.00 0.00 0.00 4.02
2146 3041 2.555757 GTGTGTCCTCTACCGTTGTAGT 59.444 50.000 0.16 0.00 44.08 2.73
2154 3049 3.074675 TCAGAGAGTGTGTCCTCTACC 57.925 52.381 0.00 0.00 41.85 3.18
2213 3108 2.665603 GCCTCTCTTCGCCTTGGT 59.334 61.111 0.00 0.00 0.00 3.67
2378 3276 0.036022 GTGCTCCTTCCTGCTGTTCT 59.964 55.000 0.00 0.00 0.00 3.01
2781 3685 4.865761 TCGATGTAGTGCGGCGCC 62.866 66.667 30.82 19.07 0.00 6.53
3392 4299 5.167121 CGATTCAACAAGAGACAGTCTCAT 58.833 41.667 28.76 17.09 45.73 2.90
3393 4300 4.550422 CGATTCAACAAGAGACAGTCTCA 58.450 43.478 28.76 9.77 45.73 3.27
3394 4301 3.366422 GCGATTCAACAAGAGACAGTCTC 59.634 47.826 21.47 21.47 43.70 3.36
3395 4302 3.006323 AGCGATTCAACAAGAGACAGTCT 59.994 43.478 1.46 1.46 36.94 3.24
3396 4303 3.321497 AGCGATTCAACAAGAGACAGTC 58.679 45.455 0.00 0.00 0.00 3.51
3626 4539 3.710722 CGCCTCCCTCCAGTGCTT 61.711 66.667 0.00 0.00 0.00 3.91
3737 4650 3.578716 GGAAAGGAAAGGAAAGGAAAGGG 59.421 47.826 0.00 0.00 0.00 3.95
3908 4858 2.203640 AGGGACTCGCACCAGTCA 60.204 61.111 9.11 0.00 44.18 3.41
4040 4990 0.682292 GGACGATCATCTTCCCCTCC 59.318 60.000 0.00 0.00 29.30 4.30
4094 5044 2.100252 CCAATGCAGAGATTTGGCGATT 59.900 45.455 3.18 0.00 34.03 3.34
4202 5152 2.694109 CTGGTAGTAGTGTTCCTAGCCC 59.306 54.545 0.00 0.00 32.12 5.19
4215 5165 5.672503 TGTGTTTGCAAAGTACTGGTAGTA 58.327 37.500 13.26 0.00 0.00 1.82
4218 5168 5.126779 TCATGTGTTTGCAAAGTACTGGTA 58.873 37.500 13.26 0.00 0.00 3.25
4243 5231 5.051508 GCTTATTTTCGTTATTGCTGCCATG 60.052 40.000 0.00 0.00 0.00 3.66
4266 5254 4.579869 TGTGAACAAGAAGAATCCTAGGC 58.420 43.478 2.96 0.00 0.00 3.93
4313 5308 8.999431 GTTTCAGACCTGATAATGTTCTTAACA 58.001 33.333 0.01 0.00 41.77 2.41
4330 5325 3.093717 TCGAGTGTTGAGTTTCAGACC 57.906 47.619 0.00 0.00 0.00 3.85
4399 5394 4.809007 GCCTGAAGGAAGGAGATGTTCTTT 60.809 45.833 0.00 0.00 40.02 2.52
4432 5427 4.070009 TCATGCAGTAATGATGAGCCATC 58.930 43.478 0.00 7.90 40.88 3.51
4433 5428 4.094830 TCATGCAGTAATGATGAGCCAT 57.905 40.909 0.00 0.00 31.58 4.40
4434 5429 3.564053 TCATGCAGTAATGATGAGCCA 57.436 42.857 0.00 0.00 31.58 4.75
4435 5430 3.628942 TGTTCATGCAGTAATGATGAGCC 59.371 43.478 12.83 6.96 36.48 4.70
4437 5432 7.272731 CAGTTTTGTTCATGCAGTAATGATGAG 59.727 37.037 0.00 0.00 36.48 2.90
4438 5433 7.040548 TCAGTTTTGTTCATGCAGTAATGATGA 60.041 33.333 0.00 0.00 36.48 2.92
4440 5435 7.218228 TCAGTTTTGTTCATGCAGTAATGAT 57.782 32.000 0.00 0.00 36.48 2.45
4441 5436 6.631971 TCAGTTTTGTTCATGCAGTAATGA 57.368 33.333 0.00 0.00 34.75 2.57
4442 5437 6.129009 GCTTCAGTTTTGTTCATGCAGTAATG 60.129 38.462 0.00 0.00 0.00 1.90
4444 5439 5.163571 TGCTTCAGTTTTGTTCATGCAGTAA 60.164 36.000 0.00 0.00 0.00 2.24
4445 5440 4.337836 TGCTTCAGTTTTGTTCATGCAGTA 59.662 37.500 0.00 0.00 0.00 2.74
4446 5441 3.130869 TGCTTCAGTTTTGTTCATGCAGT 59.869 39.130 0.00 0.00 0.00 4.40
4447 5442 3.708890 TGCTTCAGTTTTGTTCATGCAG 58.291 40.909 0.00 0.00 0.00 4.41
4448 5443 3.797451 TGCTTCAGTTTTGTTCATGCA 57.203 38.095 0.00 0.00 0.00 3.96
4449 5444 4.329528 TGTTTGCTTCAGTTTTGTTCATGC 59.670 37.500 0.00 0.00 0.00 4.06
4450 5445 6.560799 CGATGTTTGCTTCAGTTTTGTTCATG 60.561 38.462 0.00 0.00 0.00 3.07
4451 5446 5.459762 CGATGTTTGCTTCAGTTTTGTTCAT 59.540 36.000 0.00 0.00 0.00 2.57
4452 5447 4.797868 CGATGTTTGCTTCAGTTTTGTTCA 59.202 37.500 0.00 0.00 0.00 3.18
4453 5448 4.207019 CCGATGTTTGCTTCAGTTTTGTTC 59.793 41.667 0.00 0.00 0.00 3.18
4454 5449 4.111916 CCGATGTTTGCTTCAGTTTTGTT 58.888 39.130 0.00 0.00 0.00 2.83
4455 5450 3.705604 CCGATGTTTGCTTCAGTTTTGT 58.294 40.909 0.00 0.00 0.00 2.83
4456 5451 2.472488 GCCGATGTTTGCTTCAGTTTTG 59.528 45.455 0.00 0.00 0.00 2.44
4482 5477 1.623811 AGTCCCTGTTATCGCAAGTGT 59.376 47.619 0.00 0.00 39.48 3.55
4490 5485 3.764434 TCAGTCAGTCAGTCCCTGTTATC 59.236 47.826 0.00 0.00 32.61 1.75
4515 5510 7.651808 TGGATGATTGAGAAACAAAAAGAGTC 58.348 34.615 0.00 0.00 42.03 3.36
4516 5511 7.255730 CCTGGATGATTGAGAAACAAAAAGAGT 60.256 37.037 0.00 0.00 42.03 3.24
4517 5512 7.088905 CCTGGATGATTGAGAAACAAAAAGAG 58.911 38.462 0.00 0.00 42.03 2.85
4518 5513 6.517194 GCCTGGATGATTGAGAAACAAAAAGA 60.517 38.462 0.00 0.00 42.03 2.52
4519 5514 5.636543 GCCTGGATGATTGAGAAACAAAAAG 59.363 40.000 0.00 0.00 42.03 2.27
4520 5515 5.070180 TGCCTGGATGATTGAGAAACAAAAA 59.930 36.000 0.00 0.00 42.03 1.94
4521 5516 4.588106 TGCCTGGATGATTGAGAAACAAAA 59.412 37.500 0.00 0.00 42.03 2.44
4539 5534 6.897259 TTTTACGTACTAGCTTAATGCCTG 57.103 37.500 0.00 0.00 44.23 4.85
4541 5536 6.631636 GCAATTTTACGTACTAGCTTAATGCC 59.368 38.462 0.00 0.00 44.23 4.40
4569 5580 2.553911 TACTATGGCACTGGGGTGTA 57.446 50.000 0.00 0.00 44.65 2.90
4591 5602 9.103861 GCTCTGTAAGATTTTGTTAGATAGCTT 57.896 33.333 0.00 0.00 45.62 3.74
4614 5628 2.083002 CTGGAAGGCTCTTCTTTGCTC 58.917 52.381 12.71 0.00 0.00 4.26
4662 5676 7.308830 GCCTTTGAGTGTTTTATGATGTCTCTT 60.309 37.037 0.00 0.00 0.00 2.85
4752 5779 3.265479 AGTTTGCAAGATTCTAGAGGGCT 59.735 43.478 0.00 0.00 0.00 5.19
4773 5800 0.940126 GCGGTGATGATAACAGGCAG 59.060 55.000 0.00 0.00 0.00 4.85
4977 6004 4.164030 AGTTTTGGACTTGGCAGGAAAATT 59.836 37.500 2.65 0.00 33.92 1.82
5013 6040 5.300969 TGAGCATGAAGTGAGTTAATTGC 57.699 39.130 0.00 0.00 0.00 3.56
5044 6071 6.367969 GTCGTTGTCACCTTGTATAAATGTCT 59.632 38.462 0.00 0.00 0.00 3.41
5121 6150 4.522022 CCTTTGGCACTTTCAGAATCTCTT 59.478 41.667 0.00 0.00 0.00 2.85
5124 6153 3.571401 CACCTTTGGCACTTTCAGAATCT 59.429 43.478 0.00 0.00 0.00 2.40
5125 6154 3.305608 CCACCTTTGGCACTTTCAGAATC 60.306 47.826 0.00 0.00 35.56 2.52


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

AutoCloner maintained by Alex Coulton.