Multiple sequence alignment - TraesCS1B01G166000

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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 TraesCS1B01G166000 chr1B 100.000 4197 0 0 1 4197 289305940 289310136 0.000000e+00 7751.0
1 TraesCS1B01G166000 chr1B 95.270 148 7 0 2 149 666942559 666942706 7.020000e-58 235.0
2 TraesCS1B01G166000 chr1B 93.651 63 1 2 3899 3961 502217088 502217147 1.610000e-14 91.6
3 TraesCS1B01G166000 chr1D 94.475 3656 132 30 141 3751 201590102 201593732 0.000000e+00 5568.0
4 TraesCS1B01G166000 chr1D 92.674 273 16 1 3821 4089 201593656 201593928 1.410000e-104 390.0
5 TraesCS1B01G166000 chr1D 95.370 108 5 0 4090 4197 201594724 201594831 5.580000e-39 172.0
6 TraesCS1B01G166000 chr1D 92.188 64 5 0 3898 3961 56872840 56872903 1.610000e-14 91.6
7 TraesCS1B01G166000 chr1D 95.349 43 1 1 3907 3949 261215598 261215639 2.710000e-07 67.6
8 TraesCS1B01G166000 chr1A 94.958 3451 97 26 381 3783 255871659 255875080 0.000000e+00 5337.0
9 TraesCS1B01G166000 chr1A 89.545 220 17 5 141 356 255871240 255871457 1.490000e-69 274.0
10 TraesCS1B01G166000 chr1A 97.297 148 4 0 1 148 375615093 375615240 6.970000e-63 252.0
11 TraesCS1B01G166000 chr1A 91.463 82 7 0 3816 3897 255874967 255875048 3.430000e-21 113.0
12 TraesCS1B01G166000 chr1A 100.000 29 0 0 354 382 255871617 255871645 2.000000e-03 54.7
13 TraesCS1B01G166000 chr4B 98.077 156 3 0 1 156 145518328 145518483 5.350000e-69 272.0
14 TraesCS1B01G166000 chr2B 99.329 149 1 0 1 149 410189458 410189606 1.920000e-68 270.0
15 TraesCS1B01G166000 chr2B 90.244 41 3 1 3909 3949 66668159 66668120 8.000000e-03 52.8
16 TraesCS1B01G166000 chr5B 98.000 150 3 0 1 150 361487657 361487508 1.160000e-65 261.0
17 TraesCS1B01G166000 chr5B 85.517 145 21 0 1 145 439432315 439432459 7.270000e-33 152.0
18 TraesCS1B01G166000 chr4D 91.975 162 11 2 2 161 81331264 81331103 4.220000e-55 226.0
19 TraesCS1B01G166000 chr3B 94.326 141 8 0 2 142 466388426 466388566 2.540000e-52 217.0
20 TraesCS1B01G166000 chr4A 86.986 146 15 3 6 149 520149163 520149306 1.210000e-35 161.0
21 TraesCS1B01G166000 chr7A 91.935 62 3 2 4117 4176 532998325 532998386 7.480000e-13 86.1
22 TraesCS1B01G166000 chr5D 90.769 65 5 1 3898 3961 391789094 391789030 7.480000e-13 86.1
23 TraesCS1B01G166000 chr5D 86.364 66 6 3 3899 3961 563455616 563455681 7.530000e-08 69.4
24 TraesCS1B01G166000 chr3A 91.667 60 3 2 4119 4176 341045538 341045479 9.670000e-12 82.4
25 TraesCS1B01G166000 chr7B 89.552 67 2 2 4115 4176 374515250 374515184 3.480000e-11 80.5
26 TraesCS1B01G166000 chr7D 92.727 55 1 2 3898 3951 127344537 127344485 4.500000e-10 76.8
27 TraesCS1B01G166000 chr6D 84.615 78 9 2 4119 4193 388674245 388674168 1.620000e-09 75.0


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 TraesCS1B01G166000 chr1B 289305940 289310136 4196 False 7751.000000 7751 100.0000 1 4197 1 chr1B.!!$F1 4196
1 TraesCS1B01G166000 chr1D 201590102 201594831 4729 False 2043.333333 5568 94.1730 141 4197 3 chr1D.!!$F3 4056
2 TraesCS1B01G166000 chr1A 255871240 255875080 3840 False 1444.675000 5337 93.9915 141 3897 4 chr1A.!!$F2 3756

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
63 64 0.106419 AAAAAGGGACTGCGGGTTGA 60.106 50.0 0.00 0.0 40.86 3.18 F
64 65 0.106419 AAAAGGGACTGCGGGTTGAA 60.106 50.0 0.00 0.0 40.86 2.69 F
65 66 0.112412 AAAGGGACTGCGGGTTGAAT 59.888 50.0 0.00 0.0 40.86 2.57 F
123 124 0.389948 GACGGACGACCAGAAGCAAT 60.390 55.0 4.48 0.0 35.59 3.56 F
124 125 0.389948 ACGGACGACCAGAAGCAATC 60.390 55.0 4.48 0.0 35.59 2.67 F
129 130 0.443869 CGACCAGAAGCAATCGTTGG 59.556 55.0 0.00 0.0 0.00 3.77 F
2116 2324 0.554305 TCCTCCCCATAGACTACGCA 59.446 55.0 0.00 0.0 0.00 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1265 1.146358 GATTTCCGAGAACCGAGCGG 61.146 60.000 7.48 7.48 46.08 5.52 R
1197 1404 1.154225 GCACCGTGCACATAACTGC 60.154 57.895 18.79 11.07 44.26 4.40 R
1888 2096 2.027073 GAACACGTCGGATGCAGCA 61.027 57.895 3.51 0.00 0.00 4.41 R
1954 2162 4.478371 TCGCCATGGCTGCAGAGG 62.478 66.667 33.07 16.54 39.32 3.69 R
2147 2355 4.704833 TTGCTGCTCCGTCTGGGC 62.705 66.667 0.00 0.00 35.24 5.36 R
2588 2835 2.101582 GTCATGCTCTGTCCTACCGATT 59.898 50.000 0.00 0.00 0.00 3.34 R
3800 4065 0.242555 TCGACTGCAACTGCGTATGA 59.757 50.000 0.00 0.00 45.83 2.15 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 7.546250 TGGGCTTTTAATGAAAACATCCTAA 57.454 32.000 0.00 0.00 31.23 2.69
25 26 7.967908 TGGGCTTTTAATGAAAACATCCTAAA 58.032 30.769 0.00 0.00 31.23 1.85
26 27 7.875554 TGGGCTTTTAATGAAAACATCCTAAAC 59.124 33.333 0.00 0.00 31.23 2.01
27 28 7.062956 GGGCTTTTAATGAAAACATCCTAAACG 59.937 37.037 0.00 0.00 31.23 3.60
28 29 7.810759 GGCTTTTAATGAAAACATCCTAAACGA 59.189 33.333 0.00 0.00 31.23 3.85
29 30 9.187455 GCTTTTAATGAAAACATCCTAAACGAA 57.813 29.630 0.00 0.00 31.23 3.85
32 33 8.716619 TTAATGAAAACATCCTAAACGAAACG 57.283 30.769 0.00 0.00 0.00 3.60
33 34 5.738118 TGAAAACATCCTAAACGAAACGT 57.262 34.783 0.00 0.00 43.97 3.99
49 50 7.715264 ACGAAACGTTTTCTGACTTAAAAAG 57.285 32.000 15.89 0.00 36.35 2.27
50 51 6.744082 ACGAAACGTTTTCTGACTTAAAAAGG 59.256 34.615 15.89 0.00 36.35 3.11
51 52 6.195798 CGAAACGTTTTCTGACTTAAAAAGGG 59.804 38.462 15.89 0.00 35.58 3.95
52 53 6.762702 AACGTTTTCTGACTTAAAAAGGGA 57.237 33.333 0.00 0.00 35.58 4.20
53 54 6.127810 ACGTTTTCTGACTTAAAAAGGGAC 57.872 37.500 0.00 0.00 35.58 4.46
55 56 6.183360 ACGTTTTCTGACTTAAAAAGGGACTG 60.183 38.462 0.00 0.00 40.86 3.51
56 57 5.767816 TTTCTGACTTAAAAAGGGACTGC 57.232 39.130 0.00 0.00 40.86 4.40
57 58 3.399330 TCTGACTTAAAAAGGGACTGCG 58.601 45.455 0.00 0.00 40.86 5.18
58 59 2.484264 CTGACTTAAAAAGGGACTGCGG 59.516 50.000 0.00 0.00 40.86 5.69
59 60 1.810755 GACTTAAAAAGGGACTGCGGG 59.189 52.381 0.00 0.00 40.86 6.13
60 61 1.144298 ACTTAAAAAGGGACTGCGGGT 59.856 47.619 0.00 0.00 40.86 5.28
61 62 2.235891 CTTAAAAAGGGACTGCGGGTT 58.764 47.619 0.00 0.00 40.86 4.11
62 63 1.611519 TAAAAAGGGACTGCGGGTTG 58.388 50.000 0.00 0.00 40.86 3.77
63 64 0.106419 AAAAAGGGACTGCGGGTTGA 60.106 50.000 0.00 0.00 40.86 3.18
64 65 0.106419 AAAAGGGACTGCGGGTTGAA 60.106 50.000 0.00 0.00 40.86 2.69
65 66 0.112412 AAAGGGACTGCGGGTTGAAT 59.888 50.000 0.00 0.00 40.86 2.57
66 67 0.988832 AAGGGACTGCGGGTTGAATA 59.011 50.000 0.00 0.00 40.86 1.75
67 68 0.988832 AGGGACTGCGGGTTGAATAA 59.011 50.000 0.00 0.00 37.18 1.40
68 69 1.092348 GGGACTGCGGGTTGAATAAC 58.908 55.000 0.00 0.00 36.04 1.89
69 70 1.339727 GGGACTGCGGGTTGAATAACT 60.340 52.381 0.00 0.00 36.99 2.24
70 71 2.093341 GGGACTGCGGGTTGAATAACTA 60.093 50.000 0.00 0.00 36.99 2.24
71 72 3.602483 GGACTGCGGGTTGAATAACTAA 58.398 45.455 0.00 0.00 36.99 2.24
72 73 4.004982 GGACTGCGGGTTGAATAACTAAA 58.995 43.478 0.00 0.00 36.99 1.85
73 74 4.456566 GGACTGCGGGTTGAATAACTAAAA 59.543 41.667 0.00 0.00 36.99 1.52
74 75 5.366829 ACTGCGGGTTGAATAACTAAAAC 57.633 39.130 0.00 0.00 36.99 2.43
75 76 4.822896 ACTGCGGGTTGAATAACTAAAACA 59.177 37.500 0.00 0.00 36.99 2.83
76 77 5.110940 TGCGGGTTGAATAACTAAAACAC 57.889 39.130 0.00 0.00 36.99 3.32
77 78 4.023021 TGCGGGTTGAATAACTAAAACACC 60.023 41.667 0.00 0.00 36.99 4.16
78 79 4.023021 GCGGGTTGAATAACTAAAACACCA 60.023 41.667 0.00 0.00 36.99 4.17
79 80 5.695818 CGGGTTGAATAACTAAAACACCAG 58.304 41.667 0.00 0.00 36.99 4.00
80 81 5.335348 CGGGTTGAATAACTAAAACACCAGG 60.335 44.000 0.00 0.00 36.99 4.45
81 82 5.047590 GGGTTGAATAACTAAAACACCAGGG 60.048 44.000 0.00 0.00 36.99 4.45
82 83 5.771165 GGTTGAATAACTAAAACACCAGGGA 59.229 40.000 0.00 0.00 36.99 4.20
83 84 6.294342 GGTTGAATAACTAAAACACCAGGGAC 60.294 42.308 0.00 0.00 36.99 4.46
84 85 6.195600 TGAATAACTAAAACACCAGGGACT 57.804 37.500 0.00 0.00 43.88 3.85
85 86 6.607019 TGAATAACTAAAACACCAGGGACTT 58.393 36.000 0.00 0.00 34.60 3.01
86 87 7.064229 TGAATAACTAAAACACCAGGGACTTT 58.936 34.615 0.00 0.00 34.60 2.66
87 88 7.562088 TGAATAACTAAAACACCAGGGACTTTT 59.438 33.333 0.00 0.00 34.60 2.27
88 89 5.847111 AACTAAAACACCAGGGACTTTTC 57.153 39.130 0.00 0.00 34.60 2.29
89 90 5.125367 ACTAAAACACCAGGGACTTTTCT 57.875 39.130 0.00 0.00 34.60 2.52
90 91 4.887655 ACTAAAACACCAGGGACTTTTCTG 59.112 41.667 0.00 0.00 34.60 3.02
91 92 1.692411 AACACCAGGGACTTTTCTGC 58.308 50.000 0.00 0.00 34.60 4.26
92 93 0.550914 ACACCAGGGACTTTTCTGCA 59.449 50.000 0.00 0.00 34.60 4.41
93 94 1.064017 ACACCAGGGACTTTTCTGCAA 60.064 47.619 0.00 0.00 34.60 4.08
94 95 2.031120 CACCAGGGACTTTTCTGCAAA 58.969 47.619 0.00 0.00 34.60 3.68
95 96 2.430332 CACCAGGGACTTTTCTGCAAAA 59.570 45.455 0.00 0.00 34.60 2.44
107 108 4.959631 TTCTGCAAAAGTACTAACGACG 57.040 40.909 0.00 0.00 0.00 5.12
108 109 3.311106 TCTGCAAAAGTACTAACGACGG 58.689 45.455 0.00 0.00 0.00 4.79
109 110 3.004629 TCTGCAAAAGTACTAACGACGGA 59.995 43.478 0.00 0.00 0.00 4.69
110 111 3.052036 TGCAAAAGTACTAACGACGGAC 58.948 45.455 0.00 0.00 0.00 4.79
112 113 3.554524 CAAAAGTACTAACGACGGACGA 58.445 45.455 6.90 0.00 45.77 4.20
113 114 2.882742 AAGTACTAACGACGGACGAC 57.117 50.000 6.90 0.00 45.77 4.34
114 115 1.079503 AGTACTAACGACGGACGACC 58.920 55.000 6.90 0.00 45.77 4.79
115 116 0.796312 GTACTAACGACGGACGACCA 59.204 55.000 6.90 0.00 45.77 4.02
116 117 1.078709 TACTAACGACGGACGACCAG 58.921 55.000 6.90 0.00 45.77 4.00
117 118 0.603707 ACTAACGACGGACGACCAGA 60.604 55.000 6.90 0.00 45.77 3.86
118 119 0.518636 CTAACGACGGACGACCAGAA 59.481 55.000 6.90 0.00 45.77 3.02
119 120 0.518636 TAACGACGGACGACCAGAAG 59.481 55.000 6.90 0.00 45.77 2.85
120 121 2.504244 CGACGGACGACCAGAAGC 60.504 66.667 4.48 0.00 45.77 3.86
121 122 2.649034 GACGGACGACCAGAAGCA 59.351 61.111 4.48 0.00 35.59 3.91
122 123 1.006571 GACGGACGACCAGAAGCAA 60.007 57.895 4.48 0.00 35.59 3.91
123 124 0.389948 GACGGACGACCAGAAGCAAT 60.390 55.000 4.48 0.00 35.59 3.56
124 125 0.389948 ACGGACGACCAGAAGCAATC 60.390 55.000 4.48 0.00 35.59 2.67
125 126 1.413767 CGGACGACCAGAAGCAATCG 61.414 60.000 4.48 0.00 40.39 3.34
127 128 3.606886 ACGACCAGAAGCAATCGTT 57.393 47.368 0.00 0.00 44.98 3.85
128 129 1.148310 ACGACCAGAAGCAATCGTTG 58.852 50.000 0.00 0.00 44.98 4.10
129 130 0.443869 CGACCAGAAGCAATCGTTGG 59.556 55.000 0.00 0.00 0.00 3.77
130 131 1.523758 GACCAGAAGCAATCGTTGGT 58.476 50.000 3.92 3.92 44.43 3.67
201 205 4.242811 ACATCCAAGGGGCATCTTAGATA 58.757 43.478 0.00 0.00 0.00 1.98
258 262 3.728076 AAGACAACTAGACGCAGAACA 57.272 42.857 0.00 0.00 0.00 3.18
266 270 5.294050 ACTAGACGCAGAACAAGTAGTAC 57.706 43.478 0.00 0.00 0.00 2.73
297 301 5.296780 ACATTAATTCTTACTGCACCGGATG 59.703 40.000 9.46 3.68 0.00 3.51
352 518 4.942852 AGATCGCCAAAATTGTTGTCAAA 58.057 34.783 0.00 0.00 37.11 2.69
402 598 5.633601 CACGGTACATACATCGCTTAATCAT 59.366 40.000 0.00 0.00 0.00 2.45
415 613 5.592282 TCGCTTAATCATGAAGTCTCTCTCT 59.408 40.000 0.00 0.00 0.00 3.10
416 614 5.914635 CGCTTAATCATGAAGTCTCTCTCTC 59.085 44.000 0.00 0.00 0.00 3.20
417 615 6.238731 CGCTTAATCATGAAGTCTCTCTCTCT 60.239 42.308 0.00 0.00 0.00 3.10
418 616 7.141363 GCTTAATCATGAAGTCTCTCTCTCTC 58.859 42.308 0.00 0.00 0.00 3.20
419 617 7.013655 GCTTAATCATGAAGTCTCTCTCTCTCT 59.986 40.741 0.00 0.00 0.00 3.10
420 618 6.949352 AATCATGAAGTCTCTCTCTCTCTC 57.051 41.667 0.00 0.00 0.00 3.20
421 619 5.698741 TCATGAAGTCTCTCTCTCTCTCT 57.301 43.478 0.00 0.00 0.00 3.10
422 620 5.674525 TCATGAAGTCTCTCTCTCTCTCTC 58.325 45.833 0.00 0.00 0.00 3.20
423 621 5.426509 TCATGAAGTCTCTCTCTCTCTCTCT 59.573 44.000 0.00 0.00 0.00 3.10
424 622 5.089970 TGAAGTCTCTCTCTCTCTCTCTG 57.910 47.826 0.00 0.00 0.00 3.35
917 1115 4.016666 TCATCTCTTCCTCTTCCTCTTCCT 60.017 45.833 0.00 0.00 0.00 3.36
918 1116 5.194740 TCATCTCTTCCTCTTCCTCTTCCTA 59.805 44.000 0.00 0.00 0.00 2.94
919 1117 5.742562 TCTCTTCCTCTTCCTCTTCCTAT 57.257 43.478 0.00 0.00 0.00 2.57
921 1119 5.435041 TCTCTTCCTCTTCCTCTTCCTATCT 59.565 44.000 0.00 0.00 0.00 1.98
936 1134 1.069358 CTATCTCCCTCTGCGGTTTCC 59.931 57.143 0.00 0.00 0.00 3.13
937 1135 1.627297 ATCTCCCTCTGCGGTTTCCC 61.627 60.000 0.00 0.00 0.00 3.97
1030 1236 2.358267 GACGATCAGTCCTTCACCGTAT 59.642 50.000 6.47 0.00 43.95 3.06
1039 1245 6.070995 TCAGTCCTTCACCGTATGTAAATCTT 60.071 38.462 0.00 0.00 0.00 2.40
1462 1669 9.601217 GCTTAAATTCTCTCATCCTTAACAGTA 57.399 33.333 0.00 0.00 0.00 2.74
1515 1722 3.870633 ACTTCCACTGTTCTATCCGTC 57.129 47.619 0.00 0.00 0.00 4.79
1524 1731 2.841266 TGTTCTATCCGTCCCAATTCCA 59.159 45.455 0.00 0.00 0.00 3.53
1769 1976 1.879380 CGGAGTTGAGGCATGAAACAA 59.121 47.619 0.00 0.00 0.00 2.83
1783 1991 3.883744 AACAAGGGGCGCTGACGAG 62.884 63.158 7.64 0.00 43.93 4.18
1888 2096 2.584608 CTCTTCGGGGCGGTGAAT 59.415 61.111 0.00 0.00 0.00 2.57
2116 2324 0.554305 TCCTCCCCATAGACTACGCA 59.446 55.000 0.00 0.00 0.00 5.24
2587 2834 3.314045 ATTCGCCAAGAATCGCAATCGA 61.314 45.455 0.00 0.00 45.95 3.59
2588 2835 4.779037 ATTCGCCAAGAATCGCAATCGAA 61.779 43.478 0.00 0.00 45.95 3.71
2590 2837 7.437468 ATTCGCCAAGAATCGCAATCGAAAT 62.437 40.000 0.00 0.00 45.95 2.17
2701 2948 4.459089 GCCTGGAGGACACGAGCC 62.459 72.222 0.00 0.00 37.39 4.70
2800 3047 3.063510 TCAGCAAGAAGATCAAGGTGG 57.936 47.619 0.00 0.00 0.00 4.61
2827 3074 5.236911 CACCAAACCAAAATCAATCACCTTG 59.763 40.000 0.00 0.00 36.09 3.61
2828 3075 4.756135 CCAAACCAAAATCAATCACCTTGG 59.244 41.667 0.00 0.00 41.91 3.61
2873 3120 0.521735 CCGCTGACATATCCGATCGA 59.478 55.000 18.66 2.91 0.00 3.59
2877 3124 3.675225 CGCTGACATATCCGATCGAAAAT 59.325 43.478 18.66 9.59 0.00 1.82
3033 3280 6.316140 TGGTAAGTCTGGATCAAATTTCATCG 59.684 38.462 0.00 0.00 0.00 3.84
3240 3493 3.031013 CCCGCTAATTCCATTTTTCCCT 58.969 45.455 0.00 0.00 0.00 4.20
3458 3711 2.417719 CAGAGGAGTTGTGTACTTGGC 58.582 52.381 0.00 0.00 37.17 4.52
3524 3786 5.917447 GTCTTGCTCTTTTCCAATTCAACTC 59.083 40.000 0.00 0.00 0.00 3.01
3568 3830 0.886563 GGTAGACTATACCGGCGCAT 59.113 55.000 10.83 0.00 0.00 4.73
3662 3927 9.472361 GTACAGACAATTGTAAAAGTAGAGTCA 57.528 33.333 11.95 0.00 35.47 3.41
3663 3928 8.958119 ACAGACAATTGTAAAAGTAGAGTCAA 57.042 30.769 11.95 0.00 0.00 3.18
3708 3973 5.941555 AGTCATACTACTTTCTCCCCTTG 57.058 43.478 0.00 0.00 0.00 3.61
3709 3974 5.342866 AGTCATACTACTTTCTCCCCTTGT 58.657 41.667 0.00 0.00 0.00 3.16
3710 3975 5.187967 AGTCATACTACTTTCTCCCCTTGTG 59.812 44.000 0.00 0.00 0.00 3.33
3711 3976 4.469945 TCATACTACTTTCTCCCCTTGTGG 59.530 45.833 0.00 0.00 0.00 4.17
3712 3977 2.986050 ACTACTTTCTCCCCTTGTGGA 58.014 47.619 0.00 0.00 35.39 4.02
3713 3978 2.638363 ACTACTTTCTCCCCTTGTGGAC 59.362 50.000 0.00 0.00 35.39 4.02
3714 3979 0.771755 ACTTTCTCCCCTTGTGGACC 59.228 55.000 0.00 0.00 35.39 4.46
3715 3980 0.038310 CTTTCTCCCCTTGTGGACCC 59.962 60.000 0.00 0.00 35.39 4.46
3716 3981 1.432023 TTTCTCCCCTTGTGGACCCC 61.432 60.000 0.00 0.00 35.39 4.95
3717 3982 3.339093 CTCCCCTTGTGGACCCCC 61.339 72.222 0.00 0.00 35.39 5.40
3734 3999 2.361789 CCCCCGAATTCGTTTATGTGT 58.638 47.619 25.10 0.00 37.74 3.72
3735 4000 2.750712 CCCCCGAATTCGTTTATGTGTT 59.249 45.455 25.10 0.00 37.74 3.32
3736 4001 3.426963 CCCCCGAATTCGTTTATGTGTTG 60.427 47.826 25.10 6.75 37.74 3.33
3737 4002 3.168193 CCCGAATTCGTTTATGTGTTGC 58.832 45.455 25.10 0.00 37.74 4.17
3738 4003 3.365465 CCCGAATTCGTTTATGTGTTGCA 60.365 43.478 25.10 0.00 37.74 4.08
3739 4004 3.845775 CCGAATTCGTTTATGTGTTGCAG 59.154 43.478 25.10 2.13 37.74 4.41
3740 4005 4.463209 CGAATTCGTTTATGTGTTGCAGT 58.537 39.130 19.67 0.00 34.11 4.40
3741 4006 4.909305 CGAATTCGTTTATGTGTTGCAGTT 59.091 37.500 19.67 0.00 34.11 3.16
3742 4007 5.164292 CGAATTCGTTTATGTGTTGCAGTTG 60.164 40.000 19.67 0.00 34.11 3.16
3743 4008 2.993545 TCGTTTATGTGTTGCAGTTGC 58.006 42.857 0.00 0.00 42.50 4.17
3762 4027 3.260483 GCCGCAGCTCATCGAGTG 61.260 66.667 0.00 0.00 35.50 3.51
3763 4028 2.182791 CCGCAGCTCATCGAGTGT 59.817 61.111 0.00 0.00 31.39 3.55
3764 4029 2.163390 CCGCAGCTCATCGAGTGTG 61.163 63.158 0.00 0.00 31.39 3.82
3765 4030 1.153958 CGCAGCTCATCGAGTGTGA 60.154 57.895 0.00 0.00 31.39 3.58
3766 4031 1.409227 CGCAGCTCATCGAGTGTGAC 61.409 60.000 0.00 0.00 31.39 3.67
3767 4032 1.080995 GCAGCTCATCGAGTGTGACC 61.081 60.000 0.00 0.00 31.39 4.02
3768 4033 0.244721 CAGCTCATCGAGTGTGACCA 59.755 55.000 0.00 0.00 31.39 4.02
3769 4034 0.529833 AGCTCATCGAGTGTGACCAG 59.470 55.000 0.00 0.00 31.39 4.00
3770 4035 0.528017 GCTCATCGAGTGTGACCAGA 59.472 55.000 0.00 0.00 31.39 3.86
3771 4036 1.067565 GCTCATCGAGTGTGACCAGAA 60.068 52.381 0.00 0.00 31.39 3.02
3772 4037 2.417924 GCTCATCGAGTGTGACCAGAAT 60.418 50.000 0.00 0.00 31.39 2.40
3773 4038 3.854666 CTCATCGAGTGTGACCAGAATT 58.145 45.455 0.00 0.00 0.00 2.17
3774 4039 3.849911 TCATCGAGTGTGACCAGAATTC 58.150 45.455 0.00 0.00 0.00 2.17
3775 4040 3.258123 TCATCGAGTGTGACCAGAATTCA 59.742 43.478 8.44 0.00 0.00 2.57
3776 4041 3.744238 TCGAGTGTGACCAGAATTCAA 57.256 42.857 8.44 0.00 0.00 2.69
3777 4042 4.066646 TCGAGTGTGACCAGAATTCAAA 57.933 40.909 8.44 0.00 0.00 2.69
3778 4043 4.058124 TCGAGTGTGACCAGAATTCAAAG 58.942 43.478 8.44 0.00 0.00 2.77
3779 4044 4.058124 CGAGTGTGACCAGAATTCAAAGA 58.942 43.478 8.44 0.00 0.00 2.52
3780 4045 4.151335 CGAGTGTGACCAGAATTCAAAGAG 59.849 45.833 8.44 0.00 0.00 2.85
3781 4046 4.392940 AGTGTGACCAGAATTCAAAGAGG 58.607 43.478 8.44 4.04 0.00 3.69
3782 4047 3.503748 GTGTGACCAGAATTCAAAGAGGG 59.496 47.826 8.44 1.94 0.00 4.30
3783 4048 3.394274 TGTGACCAGAATTCAAAGAGGGA 59.606 43.478 8.44 0.00 0.00 4.20
3784 4049 4.043310 TGTGACCAGAATTCAAAGAGGGAT 59.957 41.667 8.44 0.00 0.00 3.85
3785 4050 4.397417 GTGACCAGAATTCAAAGAGGGATG 59.603 45.833 8.44 0.00 0.00 3.51
3786 4051 3.950395 GACCAGAATTCAAAGAGGGATGG 59.050 47.826 8.44 5.68 0.00 3.51
3787 4052 2.692041 CCAGAATTCAAAGAGGGATGGC 59.308 50.000 8.44 0.00 0.00 4.40
3788 4053 2.357009 CAGAATTCAAAGAGGGATGGCG 59.643 50.000 8.44 0.00 0.00 5.69
3789 4054 2.025887 AGAATTCAAAGAGGGATGGCGT 60.026 45.455 8.44 0.00 0.00 5.68
3790 4055 2.044123 ATTCAAAGAGGGATGGCGTC 57.956 50.000 0.00 0.00 0.00 5.19
3791 4056 0.984230 TTCAAAGAGGGATGGCGTCT 59.016 50.000 6.67 0.00 0.00 4.18
3792 4057 0.984230 TCAAAGAGGGATGGCGTCTT 59.016 50.000 6.67 0.00 31.71 3.01
3793 4058 1.351017 TCAAAGAGGGATGGCGTCTTT 59.649 47.619 6.67 0.00 40.40 2.52
3794 4059 2.569853 TCAAAGAGGGATGGCGTCTTTA 59.430 45.455 6.67 0.00 38.24 1.85
3795 4060 3.199946 TCAAAGAGGGATGGCGTCTTTAT 59.800 43.478 6.67 0.00 38.24 1.40
3796 4061 2.918712 AGAGGGATGGCGTCTTTATG 57.081 50.000 6.67 0.00 0.00 1.90
3797 4062 2.119495 AGAGGGATGGCGTCTTTATGT 58.881 47.619 6.67 0.00 0.00 2.29
3798 4063 2.505819 AGAGGGATGGCGTCTTTATGTT 59.494 45.455 6.67 0.00 0.00 2.71
3799 4064 3.709653 AGAGGGATGGCGTCTTTATGTTA 59.290 43.478 6.67 0.00 0.00 2.41
3800 4065 4.348168 AGAGGGATGGCGTCTTTATGTTAT 59.652 41.667 6.67 0.00 0.00 1.89
3801 4066 4.642429 AGGGATGGCGTCTTTATGTTATC 58.358 43.478 6.67 0.00 0.00 1.75
3802 4067 4.102524 AGGGATGGCGTCTTTATGTTATCA 59.897 41.667 6.67 0.00 0.00 2.15
3803 4068 5.003804 GGGATGGCGTCTTTATGTTATCAT 58.996 41.667 6.67 0.00 38.00 2.45
3804 4069 6.013725 AGGGATGGCGTCTTTATGTTATCATA 60.014 38.462 6.67 0.00 35.70 2.15
3805 4070 6.092259 GGGATGGCGTCTTTATGTTATCATAC 59.908 42.308 6.67 0.00 36.42 2.39
3806 4071 6.183360 GGATGGCGTCTTTATGTTATCATACG 60.183 42.308 6.67 3.51 36.42 3.06
3811 4076 7.161829 CGTCTTTATGTTATCATACGCAGTT 57.838 36.000 0.00 0.00 45.11 3.16
3812 4077 7.057402 CGTCTTTATGTTATCATACGCAGTTG 58.943 38.462 0.00 0.00 45.11 3.16
3813 4078 6.846283 GTCTTTATGTTATCATACGCAGTTGC 59.154 38.462 0.00 0.00 45.11 4.17
3814 4079 6.536941 TCTTTATGTTATCATACGCAGTTGCA 59.463 34.615 4.84 0.00 45.11 4.08
3815 4080 4.801147 ATGTTATCATACGCAGTTGCAG 57.199 40.909 4.84 0.17 37.78 4.41
3816 4081 3.595173 TGTTATCATACGCAGTTGCAGT 58.405 40.909 4.84 5.98 37.78 4.40
3817 4082 3.616821 TGTTATCATACGCAGTTGCAGTC 59.383 43.478 4.84 0.00 37.78 3.51
3818 4083 1.280982 ATCATACGCAGTTGCAGTCG 58.719 50.000 4.84 0.00 37.78 4.18
3819 4084 0.242555 TCATACGCAGTTGCAGTCGA 59.757 50.000 4.84 0.00 37.78 4.20
3820 4085 1.135112 TCATACGCAGTTGCAGTCGAT 60.135 47.619 4.84 0.00 37.78 3.59
3821 4086 1.005662 CATACGCAGTTGCAGTCGATG 60.006 52.381 4.84 2.36 37.78 3.84
3833 4098 2.946564 CAGTCGATGCAGTTGTAGTCA 58.053 47.619 0.00 0.00 0.00 3.41
3834 4099 3.515630 CAGTCGATGCAGTTGTAGTCAT 58.484 45.455 0.00 0.00 0.00 3.06
3835 4100 4.672409 CAGTCGATGCAGTTGTAGTCATA 58.328 43.478 0.00 0.00 0.00 2.15
3836 4101 4.500837 CAGTCGATGCAGTTGTAGTCATAC 59.499 45.833 0.00 0.00 0.00 2.39
3837 4102 4.399618 AGTCGATGCAGTTGTAGTCATACT 59.600 41.667 0.00 0.00 32.75 2.12
3838 4103 5.589050 AGTCGATGCAGTTGTAGTCATACTA 59.411 40.000 0.00 0.00 32.75 1.82
3928 4193 5.465935 TGGCTTGGTTTCGTTAATGAAATC 58.534 37.500 22.33 21.95 39.80 2.17
3953 4218 0.179070 GATCACCCCCTCTTTCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
3954 4219 1.961180 ATCACCCCCTCTTTCGCTCG 61.961 60.000 0.00 0.00 0.00 5.03
4014 4283 3.771577 TTCAAAGAGGGAGGTGTCTTC 57.228 47.619 0.00 0.00 31.61 2.87
4027 4296 1.819288 GTGTCTTCATGTCTCCCGAGA 59.181 52.381 0.00 0.00 34.56 4.04
4048 4317 2.851071 CGAGGTCTCTCCCATCGCC 61.851 68.421 0.00 0.00 36.70 5.54
4107 5171 6.583806 GCAACCTACAATCAAAGAAATCACTG 59.416 38.462 0.00 0.00 0.00 3.66
4113 5177 5.168569 CAATCAAAGAAATCACTGCATGCT 58.831 37.500 20.33 0.00 0.00 3.79
4120 5184 4.945543 AGAAATCACTGCATGCTACATTGA 59.054 37.500 20.33 13.44 32.20 2.57
4162 5226 2.364002 GAGGGAGTGAATAGGAGACTGC 59.636 54.545 0.00 0.00 43.88 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.546250 TTAGGATGTTTTCATTAAAAGCCCA 57.454 32.000 0.00 0.00 41.05 5.36
2 3 7.810759 TCGTTTAGGATGTTTTCATTAAAAGCC 59.189 33.333 0.00 0.00 41.05 4.35
3 4 8.736751 TCGTTTAGGATGTTTTCATTAAAAGC 57.263 30.769 0.00 0.00 41.05 3.51
6 7 9.171701 CGTTTCGTTTAGGATGTTTTCATTAAA 57.828 29.630 0.00 0.00 41.05 1.52
7 8 8.344098 ACGTTTCGTTTAGGATGTTTTCATTAA 58.656 29.630 0.00 0.00 37.46 1.40
10 11 6.308371 ACGTTTCGTTTAGGATGTTTTCAT 57.692 33.333 0.00 0.00 39.24 2.57
11 12 5.738118 ACGTTTCGTTTAGGATGTTTTCA 57.262 34.783 0.00 0.00 36.35 2.69
25 26 6.744082 CCTTTTTAAGTCAGAAAACGTTTCGT 59.256 34.615 15.01 0.00 43.97 3.85
26 27 6.195798 CCCTTTTTAAGTCAGAAAACGTTTCG 59.804 38.462 15.01 6.37 0.00 3.46
27 28 7.219535 GTCCCTTTTTAAGTCAGAAAACGTTTC 59.780 37.037 15.01 8.08 0.00 2.78
28 29 7.031372 GTCCCTTTTTAAGTCAGAAAACGTTT 58.969 34.615 7.96 7.96 0.00 3.60
29 30 6.376299 AGTCCCTTTTTAAGTCAGAAAACGTT 59.624 34.615 0.00 0.00 0.00 3.99
30 31 5.884232 AGTCCCTTTTTAAGTCAGAAAACGT 59.116 36.000 0.00 0.00 0.00 3.99
31 32 6.199393 CAGTCCCTTTTTAAGTCAGAAAACG 58.801 40.000 0.00 0.00 0.00 3.60
32 33 5.977725 GCAGTCCCTTTTTAAGTCAGAAAAC 59.022 40.000 0.00 0.00 0.00 2.43
33 34 5.220970 CGCAGTCCCTTTTTAAGTCAGAAAA 60.221 40.000 0.00 0.00 0.00 2.29
34 35 4.274950 CGCAGTCCCTTTTTAAGTCAGAAA 59.725 41.667 0.00 0.00 0.00 2.52
35 36 3.813166 CGCAGTCCCTTTTTAAGTCAGAA 59.187 43.478 0.00 0.00 0.00 3.02
36 37 3.399330 CGCAGTCCCTTTTTAAGTCAGA 58.601 45.455 0.00 0.00 0.00 3.27
37 38 2.484264 CCGCAGTCCCTTTTTAAGTCAG 59.516 50.000 0.00 0.00 0.00 3.51
38 39 2.500229 CCGCAGTCCCTTTTTAAGTCA 58.500 47.619 0.00 0.00 0.00 3.41
39 40 1.810755 CCCGCAGTCCCTTTTTAAGTC 59.189 52.381 0.00 0.00 0.00 3.01
40 41 1.144298 ACCCGCAGTCCCTTTTTAAGT 59.856 47.619 0.00 0.00 0.00 2.24
41 42 1.905637 ACCCGCAGTCCCTTTTTAAG 58.094 50.000 0.00 0.00 0.00 1.85
42 43 1.957877 CAACCCGCAGTCCCTTTTTAA 59.042 47.619 0.00 0.00 0.00 1.52
43 44 1.143277 TCAACCCGCAGTCCCTTTTTA 59.857 47.619 0.00 0.00 0.00 1.52
44 45 0.106419 TCAACCCGCAGTCCCTTTTT 60.106 50.000 0.00 0.00 0.00 1.94
45 46 0.106419 TTCAACCCGCAGTCCCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
46 47 0.112412 ATTCAACCCGCAGTCCCTTT 59.888 50.000 0.00 0.00 0.00 3.11
47 48 0.988832 TATTCAACCCGCAGTCCCTT 59.011 50.000 0.00 0.00 0.00 3.95
48 49 0.988832 TTATTCAACCCGCAGTCCCT 59.011 50.000 0.00 0.00 0.00 4.20
49 50 1.092348 GTTATTCAACCCGCAGTCCC 58.908 55.000 0.00 0.00 0.00 4.46
50 51 2.109425 AGTTATTCAACCCGCAGTCC 57.891 50.000 0.00 0.00 35.05 3.85
51 52 5.049267 TGTTTTAGTTATTCAACCCGCAGTC 60.049 40.000 0.00 0.00 35.05 3.51
52 53 4.822896 TGTTTTAGTTATTCAACCCGCAGT 59.177 37.500 0.00 0.00 35.05 4.40
53 54 5.151389 GTGTTTTAGTTATTCAACCCGCAG 58.849 41.667 0.00 0.00 35.05 5.18
54 55 4.023021 GGTGTTTTAGTTATTCAACCCGCA 60.023 41.667 0.00 0.00 35.05 5.69
55 56 4.023021 TGGTGTTTTAGTTATTCAACCCGC 60.023 41.667 0.00 0.00 35.05 6.13
56 57 5.335348 CCTGGTGTTTTAGTTATTCAACCCG 60.335 44.000 0.00 0.00 35.05 5.28
57 58 5.047590 CCCTGGTGTTTTAGTTATTCAACCC 60.048 44.000 0.00 0.00 35.05 4.11
58 59 5.771165 TCCCTGGTGTTTTAGTTATTCAACC 59.229 40.000 0.00 0.00 35.05 3.77
59 60 6.489022 AGTCCCTGGTGTTTTAGTTATTCAAC 59.511 38.462 0.00 0.00 34.67 3.18
60 61 6.607019 AGTCCCTGGTGTTTTAGTTATTCAA 58.393 36.000 0.00 0.00 0.00 2.69
61 62 6.195600 AGTCCCTGGTGTTTTAGTTATTCA 57.804 37.500 0.00 0.00 0.00 2.57
62 63 7.520451 AAAGTCCCTGGTGTTTTAGTTATTC 57.480 36.000 0.00 0.00 0.00 1.75
63 64 7.783119 AGAAAAGTCCCTGGTGTTTTAGTTATT 59.217 33.333 0.00 0.00 0.00 1.40
64 65 7.230712 CAGAAAAGTCCCTGGTGTTTTAGTTAT 59.769 37.037 0.00 0.00 0.00 1.89
65 66 6.544564 CAGAAAAGTCCCTGGTGTTTTAGTTA 59.455 38.462 0.00 0.00 0.00 2.24
66 67 5.359860 CAGAAAAGTCCCTGGTGTTTTAGTT 59.640 40.000 0.00 0.00 0.00 2.24
67 68 4.887655 CAGAAAAGTCCCTGGTGTTTTAGT 59.112 41.667 0.00 0.00 0.00 2.24
68 69 4.261614 GCAGAAAAGTCCCTGGTGTTTTAG 60.262 45.833 0.00 0.00 0.00 1.85
69 70 3.634910 GCAGAAAAGTCCCTGGTGTTTTA 59.365 43.478 0.00 0.00 0.00 1.52
70 71 2.430694 GCAGAAAAGTCCCTGGTGTTTT 59.569 45.455 0.00 0.00 0.00 2.43
71 72 2.031870 GCAGAAAAGTCCCTGGTGTTT 58.968 47.619 0.00 0.00 0.00 2.83
72 73 1.064017 TGCAGAAAAGTCCCTGGTGTT 60.064 47.619 0.00 0.00 0.00 3.32
73 74 0.550914 TGCAGAAAAGTCCCTGGTGT 59.449 50.000 0.00 0.00 0.00 4.16
74 75 1.691196 TTGCAGAAAAGTCCCTGGTG 58.309 50.000 0.00 0.00 0.00 4.17
75 76 2.452600 TTTGCAGAAAAGTCCCTGGT 57.547 45.000 0.00 0.00 0.00 4.00
76 77 3.375782 CTTTTGCAGAAAAGTCCCTGG 57.624 47.619 3.17 0.00 42.17 4.45
84 85 5.276963 CCGTCGTTAGTACTTTTGCAGAAAA 60.277 40.000 0.00 0.00 0.00 2.29
85 86 4.209703 CCGTCGTTAGTACTTTTGCAGAAA 59.790 41.667 0.00 0.00 0.00 2.52
86 87 3.737266 CCGTCGTTAGTACTTTTGCAGAA 59.263 43.478 0.00 0.00 0.00 3.02
87 88 3.004629 TCCGTCGTTAGTACTTTTGCAGA 59.995 43.478 0.00 0.00 0.00 4.26
88 89 3.120782 GTCCGTCGTTAGTACTTTTGCAG 59.879 47.826 0.00 0.00 0.00 4.41
89 90 3.052036 GTCCGTCGTTAGTACTTTTGCA 58.948 45.455 0.00 0.00 0.00 4.08
90 91 2.089581 CGTCCGTCGTTAGTACTTTTGC 59.910 50.000 0.00 0.00 34.52 3.68
91 92 3.358993 GTCGTCCGTCGTTAGTACTTTTG 59.641 47.826 0.00 0.00 40.80 2.44
92 93 3.555518 GTCGTCCGTCGTTAGTACTTTT 58.444 45.455 0.00 0.00 40.80 2.27
93 94 2.095718 GGTCGTCCGTCGTTAGTACTTT 60.096 50.000 0.00 0.00 40.80 2.66
94 95 1.464997 GGTCGTCCGTCGTTAGTACTT 59.535 52.381 0.00 0.00 40.80 2.24
95 96 1.079503 GGTCGTCCGTCGTTAGTACT 58.920 55.000 0.00 0.00 40.80 2.73
96 97 0.796312 TGGTCGTCCGTCGTTAGTAC 59.204 55.000 0.00 0.00 40.80 2.73
97 98 1.078709 CTGGTCGTCCGTCGTTAGTA 58.921 55.000 0.00 0.00 40.80 1.82
98 99 0.603707 TCTGGTCGTCCGTCGTTAGT 60.604 55.000 0.00 0.00 40.80 2.24
99 100 0.518636 TTCTGGTCGTCCGTCGTTAG 59.481 55.000 0.00 0.00 40.80 2.34
100 101 0.518636 CTTCTGGTCGTCCGTCGTTA 59.481 55.000 0.00 0.00 40.80 3.18
101 102 1.285023 CTTCTGGTCGTCCGTCGTT 59.715 57.895 0.00 0.00 40.80 3.85
102 103 2.952245 CTTCTGGTCGTCCGTCGT 59.048 61.111 0.00 0.00 40.80 4.34
103 104 2.504244 GCTTCTGGTCGTCCGTCG 60.504 66.667 0.00 0.00 41.41 5.12
104 105 0.389948 ATTGCTTCTGGTCGTCCGTC 60.390 55.000 0.00 0.00 36.30 4.79
105 106 0.389948 GATTGCTTCTGGTCGTCCGT 60.390 55.000 0.00 0.00 36.30 4.69
106 107 1.413767 CGATTGCTTCTGGTCGTCCG 61.414 60.000 0.00 0.00 36.30 4.79
107 108 0.389948 ACGATTGCTTCTGGTCGTCC 60.390 55.000 0.00 0.00 43.01 4.79
108 109 1.126846 CAACGATTGCTTCTGGTCGTC 59.873 52.381 0.00 0.00 45.45 4.20
110 111 0.443869 CCAACGATTGCTTCTGGTCG 59.556 55.000 0.00 0.00 39.78 4.79
111 112 1.523758 ACCAACGATTGCTTCTGGTC 58.476 50.000 0.00 0.00 0.00 4.02
112 113 1.981256 AACCAACGATTGCTTCTGGT 58.019 45.000 0.00 0.00 0.00 4.00
113 114 4.701956 ATAAACCAACGATTGCTTCTGG 57.298 40.909 0.00 0.00 0.00 3.86
114 115 6.842163 ACTAATAAACCAACGATTGCTTCTG 58.158 36.000 0.00 0.00 0.00 3.02
115 116 7.280205 CCTACTAATAAACCAACGATTGCTTCT 59.720 37.037 0.00 0.00 0.00 2.85
116 117 7.065443 ACCTACTAATAAACCAACGATTGCTTC 59.935 37.037 0.00 0.00 0.00 3.86
117 118 6.882678 ACCTACTAATAAACCAACGATTGCTT 59.117 34.615 0.00 0.00 0.00 3.91
118 119 6.412214 ACCTACTAATAAACCAACGATTGCT 58.588 36.000 0.00 0.00 0.00 3.91
119 120 6.673154 ACCTACTAATAAACCAACGATTGC 57.327 37.500 0.00 0.00 0.00 3.56
168 169 3.511540 CCCCTTGGATGTCTTCTTTTTCC 59.488 47.826 0.00 0.00 0.00 3.13
169 170 3.056536 GCCCCTTGGATGTCTTCTTTTTC 60.057 47.826 0.00 0.00 0.00 2.29
230 234 3.746492 GCGTCTAGTTGTCTTTTCACCAT 59.254 43.478 0.00 0.00 0.00 3.55
231 235 3.128349 GCGTCTAGTTGTCTTTTCACCA 58.872 45.455 0.00 0.00 0.00 4.17
297 301 1.202568 GGCTTTTAGGGCATGCAATCC 60.203 52.381 21.36 11.86 0.00 3.01
352 518 5.446143 GCTAGCTAGCGATCCATATGTAT 57.554 43.478 28.89 0.00 39.82 2.29
402 598 4.532126 ACAGAGAGAGAGAGAGAGACTTCA 59.468 45.833 0.00 0.00 0.00 3.02
415 613 6.128035 CGATCTTTTCTTGAGACAGAGAGAGA 60.128 42.308 0.00 0.00 0.00 3.10
416 614 6.029607 CGATCTTTTCTTGAGACAGAGAGAG 58.970 44.000 0.00 0.00 0.00 3.20
417 615 5.105957 CCGATCTTTTCTTGAGACAGAGAGA 60.106 44.000 0.00 0.00 0.00 3.10
418 616 5.101628 CCGATCTTTTCTTGAGACAGAGAG 58.898 45.833 0.00 0.00 0.00 3.20
419 617 4.081972 CCCGATCTTTTCTTGAGACAGAGA 60.082 45.833 0.00 0.00 0.00 3.10
420 618 4.180057 CCCGATCTTTTCTTGAGACAGAG 58.820 47.826 0.00 0.00 0.00 3.35
421 619 3.617531 GCCCGATCTTTTCTTGAGACAGA 60.618 47.826 0.00 0.00 0.00 3.41
422 620 2.675348 GCCCGATCTTTTCTTGAGACAG 59.325 50.000 0.00 0.00 0.00 3.51
423 621 2.038426 TGCCCGATCTTTTCTTGAGACA 59.962 45.455 0.00 0.00 0.00 3.41
424 622 2.699954 TGCCCGATCTTTTCTTGAGAC 58.300 47.619 0.00 0.00 0.00 3.36
626 824 2.292455 CCTTGGGGAAGGAATGTCCAAT 60.292 50.000 0.00 0.00 42.62 3.16
917 1115 1.120530 GGAAACCGCAGAGGGAGATA 58.879 55.000 0.00 0.00 46.96 1.98
918 1116 1.627297 GGGAAACCGCAGAGGGAGAT 61.627 60.000 0.00 0.00 46.96 2.75
919 1117 2.291043 GGGAAACCGCAGAGGGAGA 61.291 63.158 0.00 0.00 46.96 3.71
936 1134 2.113860 TGCTTCGATCTTTTCTGGGG 57.886 50.000 0.00 0.00 0.00 4.96
937 1135 4.229876 GTTTTGCTTCGATCTTTTCTGGG 58.770 43.478 0.00 0.00 0.00 4.45
1039 1245 7.004555 AGCGGTAAATTATATCATGGTCAGA 57.995 36.000 0.00 0.00 0.00 3.27
1059 1265 1.146358 GATTTCCGAGAACCGAGCGG 61.146 60.000 7.48 7.48 46.08 5.52
1197 1404 1.154225 GCACCGTGCACATAACTGC 60.154 57.895 18.79 11.07 44.26 4.40
1400 1607 2.102252 GCGGTCCTGATCAGAATTCTCT 59.898 50.000 24.62 0.00 0.00 3.10
1433 1640 7.888021 TGTTAAGGATGAGAGAATTTAAGCCAA 59.112 33.333 0.00 0.00 0.00 4.52
1462 1669 2.788515 CGTATGCCGGGGAATGTTT 58.211 52.632 2.18 0.00 0.00 2.83
1769 1976 3.626924 AAACTCGTCAGCGCCCCT 61.627 61.111 2.29 0.00 38.14 4.79
1783 1991 3.447742 CTCCTGCAAGAAACCAACAAAC 58.552 45.455 0.00 0.00 34.07 2.93
1888 2096 2.027073 GAACACGTCGGATGCAGCA 61.027 57.895 3.51 0.00 0.00 4.41
1954 2162 4.478371 TCGCCATGGCTGCAGAGG 62.478 66.667 33.07 16.54 39.32 3.69
2147 2355 4.704833 TTGCTGCTCCGTCTGGGC 62.705 66.667 0.00 0.00 35.24 5.36
2587 2834 2.766263 TCATGCTCTGTCCTACCGATTT 59.234 45.455 0.00 0.00 0.00 2.17
2588 2835 2.101582 GTCATGCTCTGTCCTACCGATT 59.898 50.000 0.00 0.00 0.00 3.34
2590 2837 1.103803 GTCATGCTCTGTCCTACCGA 58.896 55.000 0.00 0.00 0.00 4.69
2591 2838 0.103208 GGTCATGCTCTGTCCTACCG 59.897 60.000 0.00 0.00 31.12 4.02
2592 2839 0.103208 CGGTCATGCTCTGTCCTACC 59.897 60.000 0.00 0.00 31.56 3.18
2800 3047 2.629336 TTGATTTTGGTTTGGTGGGC 57.371 45.000 0.00 0.00 0.00 5.36
2813 3060 4.399303 GGATCGTTCCAAGGTGATTGATTT 59.601 41.667 7.68 0.00 41.83 2.17
2850 3097 1.591594 CGGATATGTCAGCGGCGTT 60.592 57.895 9.37 0.00 0.00 4.84
2873 3120 0.165944 GCACGCGTACTGCAGATTTT 59.834 50.000 23.35 0.00 46.97 1.82
2964 3211 0.962489 GTGATCCGATCTCCGTGGAT 59.038 55.000 9.78 0.00 45.02 3.41
2972 3219 1.135139 CGTGGTTCTGTGATCCGATCT 59.865 52.381 9.78 0.00 0.00 2.75
3240 3493 4.633175 TCTGCACGTGTAAAATAGGTTGA 58.367 39.130 18.38 0.00 0.00 3.18
3524 3786 3.063510 TCCCTGCAATTCTCAGAGTTG 57.936 47.619 5.54 5.54 33.40 3.16
3539 3801 4.942483 CGGTATAGTCTACCTGTATCCCTG 59.058 50.000 3.45 0.00 35.49 4.45
3578 3840 7.164662 GCAACAATTCCCGATTACGTATTTTAC 59.835 37.037 0.00 0.00 37.88 2.01
3580 3842 6.031471 GCAACAATTCCCGATTACGTATTTT 58.969 36.000 0.00 0.00 37.88 1.82
3581 3843 5.355910 AGCAACAATTCCCGATTACGTATTT 59.644 36.000 0.00 0.00 37.88 1.40
3588 3850 2.441410 TGCAGCAACAATTCCCGATTA 58.559 42.857 0.00 0.00 0.00 1.75
3592 3854 2.094803 TGTATTGCAGCAACAATTCCCG 60.095 45.455 10.85 0.00 40.64 5.14
3593 3855 3.591196 TGTATTGCAGCAACAATTCCC 57.409 42.857 10.85 0.00 40.64 3.97
3594 3856 8.870160 TTATAATGTATTGCAGCAACAATTCC 57.130 30.769 10.85 0.00 40.64 3.01
3638 3903 8.958119 TTGACTCTACTTTTACAATTGTCTGT 57.042 30.769 15.85 11.77 0.00 3.41
3662 3927 1.931172 GTTGCACCGACACGCTATATT 59.069 47.619 0.00 0.00 0.00 1.28
3663 3928 1.136305 AGTTGCACCGACACGCTATAT 59.864 47.619 0.00 0.00 0.00 0.86
3665 3930 1.014044 CAGTTGCACCGACACGCTAT 61.014 55.000 0.00 0.00 0.00 2.97
3714 3979 2.361789 ACACATAAACGAATTCGGGGG 58.638 47.619 29.79 17.02 44.95 5.40
3715 3980 3.753842 CAACACATAAACGAATTCGGGG 58.246 45.455 29.79 16.05 44.95 5.73
3716 3981 3.168193 GCAACACATAAACGAATTCGGG 58.832 45.455 29.79 16.11 44.95 5.14
3717 3982 3.816091 TGCAACACATAAACGAATTCGG 58.184 40.909 29.79 15.05 44.95 4.30
3718 3983 4.463209 ACTGCAACACATAAACGAATTCG 58.537 39.130 25.64 25.64 46.33 3.34
3719 3984 5.387342 GCAACTGCAACACATAAACGAATTC 60.387 40.000 0.00 0.00 41.59 2.17
3720 3985 4.444056 GCAACTGCAACACATAAACGAATT 59.556 37.500 0.00 0.00 41.59 2.17
3721 3986 3.980775 GCAACTGCAACACATAAACGAAT 59.019 39.130 0.00 0.00 41.59 3.34
3722 3987 3.367607 GCAACTGCAACACATAAACGAA 58.632 40.909 0.00 0.00 41.59 3.85
3723 3988 2.993545 GCAACTGCAACACATAAACGA 58.006 42.857 0.00 0.00 41.59 3.85
3745 4010 3.260483 CACTCGATGAGCTGCGGC 61.260 66.667 10.33 10.33 39.06 6.53
3746 4011 2.163390 CACACTCGATGAGCTGCGG 61.163 63.158 0.00 0.00 32.04 5.69
3747 4012 1.153958 TCACACTCGATGAGCTGCG 60.154 57.895 0.00 0.00 32.04 5.18
3748 4013 1.080995 GGTCACACTCGATGAGCTGC 61.081 60.000 8.97 0.00 40.61 5.25
3749 4014 0.244721 TGGTCACACTCGATGAGCTG 59.755 55.000 15.44 0.00 43.47 4.24
3750 4015 0.529833 CTGGTCACACTCGATGAGCT 59.470 55.000 15.44 0.00 43.47 4.09
3751 4016 0.528017 TCTGGTCACACTCGATGAGC 59.472 55.000 9.25 9.25 43.39 4.26
3752 4017 3.516981 ATTCTGGTCACACTCGATGAG 57.483 47.619 0.00 0.00 35.52 2.90
3753 4018 3.258123 TGAATTCTGGTCACACTCGATGA 59.742 43.478 7.05 0.00 0.00 2.92
3754 4019 3.588955 TGAATTCTGGTCACACTCGATG 58.411 45.455 7.05 0.00 0.00 3.84
3755 4020 3.961480 TGAATTCTGGTCACACTCGAT 57.039 42.857 7.05 0.00 0.00 3.59
3756 4021 3.744238 TTGAATTCTGGTCACACTCGA 57.256 42.857 7.05 0.00 0.00 4.04
3757 4022 4.058124 TCTTTGAATTCTGGTCACACTCG 58.942 43.478 7.05 0.00 0.00 4.18
3758 4023 4.453819 CCTCTTTGAATTCTGGTCACACTC 59.546 45.833 7.05 0.00 0.00 3.51
3759 4024 4.392940 CCTCTTTGAATTCTGGTCACACT 58.607 43.478 7.05 0.00 0.00 3.55
3760 4025 3.503748 CCCTCTTTGAATTCTGGTCACAC 59.496 47.826 7.05 0.00 0.00 3.82
3761 4026 3.394274 TCCCTCTTTGAATTCTGGTCACA 59.606 43.478 7.05 0.00 0.00 3.58
3762 4027 4.021102 TCCCTCTTTGAATTCTGGTCAC 57.979 45.455 7.05 0.00 0.00 3.67
3763 4028 4.568380 CCATCCCTCTTTGAATTCTGGTCA 60.568 45.833 7.05 0.00 0.00 4.02
3764 4029 3.950395 CCATCCCTCTTTGAATTCTGGTC 59.050 47.826 7.05 0.00 0.00 4.02
3765 4030 3.879321 GCCATCCCTCTTTGAATTCTGGT 60.879 47.826 7.05 0.00 0.00 4.00
3766 4031 2.692041 GCCATCCCTCTTTGAATTCTGG 59.308 50.000 7.05 3.76 0.00 3.86
3767 4032 2.357009 CGCCATCCCTCTTTGAATTCTG 59.643 50.000 7.05 0.00 0.00 3.02
3768 4033 2.025887 ACGCCATCCCTCTTTGAATTCT 60.026 45.455 7.05 0.00 0.00 2.40
3769 4034 2.356069 GACGCCATCCCTCTTTGAATTC 59.644 50.000 0.00 0.00 0.00 2.17
3770 4035 2.025887 AGACGCCATCCCTCTTTGAATT 60.026 45.455 0.00 0.00 0.00 2.17
3771 4036 1.561542 AGACGCCATCCCTCTTTGAAT 59.438 47.619 0.00 0.00 0.00 2.57
3772 4037 0.984230 AGACGCCATCCCTCTTTGAA 59.016 50.000 0.00 0.00 0.00 2.69
3773 4038 0.984230 AAGACGCCATCCCTCTTTGA 59.016 50.000 0.00 0.00 0.00 2.69
3774 4039 1.826385 AAAGACGCCATCCCTCTTTG 58.174 50.000 0.00 0.00 33.83 2.77
3775 4040 3.054361 ACATAAAGACGCCATCCCTCTTT 60.054 43.478 0.00 0.00 37.82 2.52
3776 4041 2.505819 ACATAAAGACGCCATCCCTCTT 59.494 45.455 0.00 0.00 0.00 2.85
3777 4042 2.119495 ACATAAAGACGCCATCCCTCT 58.881 47.619 0.00 0.00 0.00 3.69
3778 4043 2.622064 ACATAAAGACGCCATCCCTC 57.378 50.000 0.00 0.00 0.00 4.30
3779 4044 4.102524 TGATAACATAAAGACGCCATCCCT 59.897 41.667 0.00 0.00 0.00 4.20
3780 4045 4.385825 TGATAACATAAAGACGCCATCCC 58.614 43.478 0.00 0.00 0.00 3.85
3781 4046 6.183360 CGTATGATAACATAAAGACGCCATCC 60.183 42.308 0.00 0.00 40.13 3.51
3782 4047 6.669977 GCGTATGATAACATAAAGACGCCATC 60.670 42.308 15.96 0.00 46.15 3.51
3783 4048 5.120208 GCGTATGATAACATAAAGACGCCAT 59.880 40.000 15.96 0.00 46.15 4.40
3784 4049 4.446385 GCGTATGATAACATAAAGACGCCA 59.554 41.667 15.96 0.00 46.15 5.69
3785 4050 4.942765 GCGTATGATAACATAAAGACGCC 58.057 43.478 15.96 3.53 46.15 5.68
3787 4052 6.749216 ACTGCGTATGATAACATAAAGACG 57.251 37.500 0.00 0.00 40.13 4.18
3788 4053 6.846283 GCAACTGCGTATGATAACATAAAGAC 59.154 38.462 0.00 0.00 40.13 3.01
3789 4054 6.536941 TGCAACTGCGTATGATAACATAAAGA 59.463 34.615 0.00 0.00 45.83 2.52
3790 4055 6.714492 TGCAACTGCGTATGATAACATAAAG 58.286 36.000 0.00 0.00 45.83 1.85
3791 4056 6.315144 ACTGCAACTGCGTATGATAACATAAA 59.685 34.615 0.00 0.00 45.83 1.40
3792 4057 5.815222 ACTGCAACTGCGTATGATAACATAA 59.185 36.000 0.00 0.00 45.83 1.90
3793 4058 5.356426 ACTGCAACTGCGTATGATAACATA 58.644 37.500 0.00 0.00 45.83 2.29
3794 4059 4.191544 ACTGCAACTGCGTATGATAACAT 58.808 39.130 0.00 0.00 45.83 2.71
3795 4060 3.595173 ACTGCAACTGCGTATGATAACA 58.405 40.909 0.00 0.00 45.83 2.41
3796 4061 3.301835 CGACTGCAACTGCGTATGATAAC 60.302 47.826 0.00 0.00 45.83 1.89
3797 4062 2.857748 CGACTGCAACTGCGTATGATAA 59.142 45.455 0.00 0.00 45.83 1.75
3798 4063 2.098443 TCGACTGCAACTGCGTATGATA 59.902 45.455 0.00 0.00 45.83 2.15
3799 4064 1.135112 TCGACTGCAACTGCGTATGAT 60.135 47.619 0.00 0.00 45.83 2.45
3800 4065 0.242555 TCGACTGCAACTGCGTATGA 59.757 50.000 0.00 0.00 45.83 2.15
3801 4066 1.005662 CATCGACTGCAACTGCGTATG 60.006 52.381 0.00 0.00 45.83 2.39
3802 4067 1.280982 CATCGACTGCAACTGCGTAT 58.719 50.000 0.00 0.00 45.83 3.06
3803 4068 2.736890 CATCGACTGCAACTGCGTA 58.263 52.632 0.00 0.00 45.83 4.42
3804 4069 3.554232 CATCGACTGCAACTGCGT 58.446 55.556 0.00 0.00 45.83 5.24
3813 4078 2.946564 TGACTACAACTGCATCGACTG 58.053 47.619 0.00 0.00 0.00 3.51
3814 4079 3.876274 ATGACTACAACTGCATCGACT 57.124 42.857 0.00 0.00 0.00 4.18
3815 4080 4.673441 AGTATGACTACAACTGCATCGAC 58.327 43.478 0.00 0.00 0.00 4.20
3816 4081 4.983671 AGTATGACTACAACTGCATCGA 57.016 40.909 0.00 0.00 0.00 3.59
3828 4093 5.363005 GCAAGGGGAGAAAGTAGTATGACTA 59.637 44.000 0.00 0.00 0.00 2.59
3829 4094 4.162509 GCAAGGGGAGAAAGTAGTATGACT 59.837 45.833 0.00 0.00 0.00 3.41
3830 4095 4.443621 GCAAGGGGAGAAAGTAGTATGAC 58.556 47.826 0.00 0.00 0.00 3.06
3831 4096 3.132289 CGCAAGGGGAGAAAGTAGTATGA 59.868 47.826 0.00 0.00 0.00 2.15
3832 4097 3.458189 CGCAAGGGGAGAAAGTAGTATG 58.542 50.000 0.00 0.00 0.00 2.39
3833 4098 3.821421 CGCAAGGGGAGAAAGTAGTAT 57.179 47.619 0.00 0.00 0.00 2.12
3885 4150 4.445453 CCAGATAACATTGCTGCTGTAGA 58.555 43.478 0.00 0.00 0.00 2.59
3888 4153 1.747355 GCCAGATAACATTGCTGCTGT 59.253 47.619 0.00 0.00 0.00 4.40
3893 4158 3.091633 ACCAAGCCAGATAACATTGCT 57.908 42.857 0.00 0.00 0.00 3.91
3961 4226 0.740868 TGATGAGTTGCGGCTGTAGC 60.741 55.000 0.00 0.00 41.14 3.58
3962 4227 1.662629 CTTGATGAGTTGCGGCTGTAG 59.337 52.381 0.00 0.00 0.00 2.74
3963 4228 1.001974 ACTTGATGAGTTGCGGCTGTA 59.998 47.619 0.00 0.00 33.92 2.74
4027 4296 0.464735 CGATGGGAGAGACCTCGAGT 60.465 60.000 12.31 0.00 40.33 4.18
4030 4299 2.725008 GCGATGGGAGAGACCTCG 59.275 66.667 0.00 0.00 40.33 4.63
4048 4317 1.775869 CGATCTGATGGGTCATGTCG 58.224 55.000 0.00 0.00 35.94 4.35
4095 5159 5.909621 ATGTAGCATGCAGTGATTTCTTT 57.090 34.783 21.98 0.00 31.11 2.52
4107 5171 3.561310 TCGATCCTTTCAATGTAGCATGC 59.439 43.478 10.51 10.51 0.00 4.06
4113 5177 5.097742 ACCACATCGATCCTTTCAATGTA 57.902 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.