Multiple sequence alignment - TraesCS6B01G337500

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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 TraesCS6B01G337500 chr6B 100.000 2531 0 0 1 2531 594438440 594440970 0.000000e+00 4674.0
1 TraesCS6B01G337500 chr6B 89.655 58 5 1 1309 1365 504020548 504020491 3.490000e-09 73.1
2 TraesCS6B01G337500 chr6D 88.763 1504 71 43 680 2149 397629323 397630762 0.000000e+00 1751.0
3 TraesCS6B01G337500 chr6D 82.004 489 34 20 242 714 397628873 397629323 1.430000e-97 366.0
4 TraesCS6B01G337500 chr6D 85.463 227 23 6 2178 2397 397630752 397630975 7.040000e-56 228.0
5 TraesCS6B01G337500 chr6D 92.308 104 6 2 2423 2525 397635995 397636097 2.030000e-31 147.0
6 TraesCS6B01G337500 chr6D 97.500 40 1 0 1328 1367 102261455 102261494 4.520000e-08 69.4
7 TraesCS6B01G337500 chr6D 87.931 58 6 1 1309 1365 319250169 319250226 1.620000e-07 67.6
8 TraesCS6B01G337500 chr6A 86.430 1098 46 40 757 1793 543930913 543931968 0.000000e+00 1107.0
9 TraesCS6B01G337500 chr6A 83.915 659 67 23 1873 2504 543932022 543932668 6.030000e-166 593.0
10 TraesCS6B01G337500 chr6A 79.273 550 59 20 118 658 543930342 543930845 1.450000e-87 333.0
11 TraesCS6B01G337500 chr7A 82.991 341 41 10 1178 1505 148832512 148832176 2.460000e-75 292.0
12 TraesCS6B01G337500 chr7D 82.596 339 43 10 1178 1505 147579643 147579310 4.120000e-73 285.0
13 TraesCS6B01G337500 chr7D 78.947 228 36 9 1210 1428 634158823 634159047 7.300000e-31 145.0
14 TraesCS6B01G337500 chr7B 82.927 328 43 11 1178 1497 110353074 110352752 1.480000e-72 283.0
15 TraesCS6B01G337500 chr5A 97.674 86 2 0 1 86 678573891 678573976 5.640000e-32 148.0
16 TraesCS6B01G337500 chr5A 94.382 89 5 0 1 89 685875188 685875100 1.220000e-28 137.0
17 TraesCS6B01G337500 chr2D 95.556 90 4 0 1 90 398728138 398728227 7.300000e-31 145.0
18 TraesCS6B01G337500 chr4B 96.512 86 3 0 1 86 73100553 73100638 2.620000e-30 143.0
19 TraesCS6B01G337500 chr4A 96.552 87 2 1 1 86 2399751 2399665 2.620000e-30 143.0
20 TraesCS6B01G337500 chr4A 96.512 86 3 0 1 86 639055092 639055007 2.620000e-30 143.0
21 TraesCS6B01G337500 chr4A 88.750 80 9 0 12 91 718485847 718485768 5.760000e-17 99.0
22 TraesCS6B01G337500 chr3B 96.512 86 3 0 1 86 612035723 612035638 2.620000e-30 143.0
23 TraesCS6B01G337500 chr1A 96.512 86 3 0 1 86 124785867 124785952 2.620000e-30 143.0


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 TraesCS6B01G337500 chr6B 594438440 594440970 2530 False 4674.000000 4674 100.000 1 2531 1 chr6B.!!$F1 2530
1 TraesCS6B01G337500 chr6D 397628873 397630975 2102 False 781.666667 1751 85.410 242 2397 3 chr6D.!!$F4 2155
2 TraesCS6B01G337500 chr6A 543930342 543932668 2326 False 677.666667 1107 83.206 118 2504 3 chr6A.!!$F1 2386

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
82 83 0.038159 GTGTCGGCTGCTCAGTAGTT 60.038 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1669 0.039165 CTTTCCTTTTCCTGTGGCGC 60.039 55.0 0.0 0.0 0.0 6.53 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 1.070786 GGCACAAAGTGGAGGTCGA 59.929 57.895 0.00 0.00 33.64 4.20
26 27 1.228657 GCACAAAGTGGAGGTCGACC 61.229 60.000 27.67 27.67 33.64 4.79
27 28 0.944311 CACAAAGTGGAGGTCGACCG 60.944 60.000 28.26 14.08 42.08 4.79
28 29 2.027625 CAAAGTGGAGGTCGACCGC 61.028 63.158 28.12 28.12 42.08 5.68
30 31 2.436087 AAAGTGGAGGTCGACCGCTG 62.436 60.000 32.92 0.00 45.83 5.18
31 32 4.436998 GTGGAGGTCGACCGCTGG 62.437 72.222 32.92 0.00 42.08 4.85
32 33 4.671590 TGGAGGTCGACCGCTGGA 62.672 66.667 32.92 17.39 42.08 3.86
33 34 3.148279 GGAGGTCGACCGCTGGAT 61.148 66.667 32.92 14.64 42.08 3.41
34 35 2.413765 GAGGTCGACCGCTGGATC 59.586 66.667 28.62 16.29 42.08 3.36
35 36 2.362503 AGGTCGACCGCTGGATCA 60.363 61.111 28.26 0.00 42.08 2.92
36 37 1.945354 GAGGTCGACCGCTGGATCAA 61.945 60.000 28.62 0.00 42.08 2.57
37 38 1.079405 GGTCGACCGCTGGATCAAA 60.079 57.895 20.85 0.00 0.00 2.69
38 39 1.084370 GGTCGACCGCTGGATCAAAG 61.084 60.000 20.85 0.00 0.00 2.77
39 40 1.447838 TCGACCGCTGGATCAAAGC 60.448 57.895 9.09 9.09 37.31 3.51
40 41 1.741401 CGACCGCTGGATCAAAGCA 60.741 57.895 17.02 0.00 40.86 3.91
41 42 1.091771 CGACCGCTGGATCAAAGCAT 61.092 55.000 17.02 6.74 40.86 3.79
42 43 0.659957 GACCGCTGGATCAAAGCATC 59.340 55.000 17.02 11.03 40.86 3.91
43 44 1.091771 ACCGCTGGATCAAAGCATCG 61.092 55.000 17.02 8.06 40.86 3.84
44 45 1.091771 CCGCTGGATCAAAGCATCGT 61.092 55.000 17.02 0.00 40.86 3.73
45 46 0.302890 CGCTGGATCAAAGCATCGTC 59.697 55.000 17.02 0.00 40.86 4.20
46 47 0.659957 GCTGGATCAAAGCATCGTCC 59.340 55.000 13.25 0.00 40.52 4.79
47 48 2.013563 GCTGGATCAAAGCATCGTCCA 61.014 52.381 13.25 0.00 40.52 4.02
48 49 2.358957 CTGGATCAAAGCATCGTCCAA 58.641 47.619 0.00 0.00 38.41 3.53
49 50 2.947652 CTGGATCAAAGCATCGTCCAAT 59.052 45.455 0.00 0.00 38.41 3.16
50 51 2.684374 TGGATCAAAGCATCGTCCAATG 59.316 45.455 0.00 0.00 36.12 2.82
51 52 2.684881 GGATCAAAGCATCGTCCAATGT 59.315 45.455 0.00 0.00 0.00 2.71
52 53 3.129287 GGATCAAAGCATCGTCCAATGTT 59.871 43.478 0.00 0.00 0.00 2.71
53 54 3.829886 TCAAAGCATCGTCCAATGTTC 57.170 42.857 0.00 0.00 0.00 3.18
54 55 2.159430 TCAAAGCATCGTCCAATGTTCG 59.841 45.455 0.00 0.00 0.00 3.95
55 56 1.086696 AAGCATCGTCCAATGTTCGG 58.913 50.000 0.00 0.00 0.00 4.30
56 57 1.062525 GCATCGTCCAATGTTCGGC 59.937 57.895 0.00 0.00 0.00 5.54
57 58 1.721487 CATCGTCCAATGTTCGGCC 59.279 57.895 0.00 0.00 0.00 6.13
58 59 1.024046 CATCGTCCAATGTTCGGCCA 61.024 55.000 2.24 0.00 0.00 5.36
59 60 0.744414 ATCGTCCAATGTTCGGCCAG 60.744 55.000 2.24 0.00 0.00 4.85
60 61 1.671054 CGTCCAATGTTCGGCCAGT 60.671 57.895 2.24 0.00 0.00 4.00
61 62 1.875963 GTCCAATGTTCGGCCAGTG 59.124 57.895 2.24 0.00 0.00 3.66
62 63 3.277133 CCAATGTTCGGCCAGTGG 58.723 61.111 4.20 4.20 43.31 4.00
63 64 2.342650 CCAATGTTCGGCCAGTGGG 61.343 63.158 12.15 0.00 44.70 4.61
64 65 1.603455 CAATGTTCGGCCAGTGGGT 60.603 57.895 12.15 0.00 36.17 4.51
65 66 1.603455 AATGTTCGGCCAGTGGGTG 60.603 57.895 12.15 0.00 36.17 4.61
66 67 2.351924 AATGTTCGGCCAGTGGGTGT 62.352 55.000 12.15 0.00 36.17 4.16
67 68 2.668550 GTTCGGCCAGTGGGTGTC 60.669 66.667 12.15 0.00 36.17 3.67
68 69 4.308458 TTCGGCCAGTGGGTGTCG 62.308 66.667 12.15 0.00 36.17 4.35
74 75 4.320456 CAGTGGGTGTCGGCTGCT 62.320 66.667 0.00 0.00 0.00 4.24
75 76 4.008933 AGTGGGTGTCGGCTGCTC 62.009 66.667 0.00 0.00 0.00 4.26
76 77 4.314440 GTGGGTGTCGGCTGCTCA 62.314 66.667 0.00 0.00 0.00 4.26
77 78 4.007644 TGGGTGTCGGCTGCTCAG 62.008 66.667 0.00 0.00 0.00 3.35
78 79 4.008933 GGGTGTCGGCTGCTCAGT 62.009 66.667 0.00 0.00 0.00 3.41
79 80 2.646175 GGGTGTCGGCTGCTCAGTA 61.646 63.158 0.00 0.00 0.00 2.74
80 81 1.153745 GGTGTCGGCTGCTCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
81 82 1.587054 GTGTCGGCTGCTCAGTAGT 59.413 57.895 0.00 0.00 0.00 2.73
82 83 0.038159 GTGTCGGCTGCTCAGTAGTT 60.038 55.000 0.00 0.00 0.00 2.24
83 84 0.243907 TGTCGGCTGCTCAGTAGTTC 59.756 55.000 0.00 0.00 0.00 3.01
84 85 0.458716 GTCGGCTGCTCAGTAGTTCC 60.459 60.000 0.00 0.00 0.00 3.62
85 86 1.517257 CGGCTGCTCAGTAGTTCCG 60.517 63.158 0.00 0.00 0.00 4.30
86 87 1.890894 GGCTGCTCAGTAGTTCCGA 59.109 57.895 0.00 0.00 0.00 4.55
87 88 0.461961 GGCTGCTCAGTAGTTCCGAT 59.538 55.000 0.00 0.00 0.00 4.18
88 89 1.134670 GGCTGCTCAGTAGTTCCGATT 60.135 52.381 0.00 0.00 0.00 3.34
89 90 2.197577 GCTGCTCAGTAGTTCCGATTC 58.802 52.381 0.00 0.00 0.00 2.52
90 91 2.815478 CTGCTCAGTAGTTCCGATTCC 58.185 52.381 0.00 0.00 0.00 3.01
91 92 2.428890 CTGCTCAGTAGTTCCGATTCCT 59.571 50.000 0.00 0.00 0.00 3.36
92 93 2.832129 TGCTCAGTAGTTCCGATTCCTT 59.168 45.455 0.00 0.00 0.00 3.36
93 94 4.021229 TGCTCAGTAGTTCCGATTCCTTA 58.979 43.478 0.00 0.00 0.00 2.69
94 95 4.464951 TGCTCAGTAGTTCCGATTCCTTAA 59.535 41.667 0.00 0.00 0.00 1.85
95 96 5.128827 TGCTCAGTAGTTCCGATTCCTTAAT 59.871 40.000 0.00 0.00 0.00 1.40
96 97 5.692654 GCTCAGTAGTTCCGATTCCTTAATC 59.307 44.000 0.00 0.00 38.53 1.75
97 98 6.683110 GCTCAGTAGTTCCGATTCCTTAATCA 60.683 42.308 0.00 0.00 41.44 2.57
98 99 7.177832 TCAGTAGTTCCGATTCCTTAATCAA 57.822 36.000 0.00 0.00 41.44 2.57
99 100 7.792032 TCAGTAGTTCCGATTCCTTAATCAAT 58.208 34.615 0.00 0.00 41.44 2.57
100 101 8.920174 TCAGTAGTTCCGATTCCTTAATCAATA 58.080 33.333 0.00 0.00 41.44 1.90
101 102 9.197694 CAGTAGTTCCGATTCCTTAATCAATAG 57.802 37.037 0.00 0.00 41.44 1.73
102 103 9.144298 AGTAGTTCCGATTCCTTAATCAATAGA 57.856 33.333 0.00 0.00 41.44 1.98
103 104 9.413048 GTAGTTCCGATTCCTTAATCAATAGAG 57.587 37.037 0.00 0.00 41.44 2.43
104 105 7.445945 AGTTCCGATTCCTTAATCAATAGAGG 58.554 38.462 0.00 0.00 41.44 3.69
105 106 5.794894 TCCGATTCCTTAATCAATAGAGGC 58.205 41.667 0.00 0.00 41.44 4.70
106 107 4.627467 CCGATTCCTTAATCAATAGAGGCG 59.373 45.833 0.00 0.00 41.44 5.52
107 108 4.627467 CGATTCCTTAATCAATAGAGGCGG 59.373 45.833 0.00 0.00 41.44 6.13
108 109 5.552178 GATTCCTTAATCAATAGAGGCGGT 58.448 41.667 0.00 0.00 41.09 5.68
109 110 4.336889 TCCTTAATCAATAGAGGCGGTG 57.663 45.455 0.00 0.00 0.00 4.94
110 111 2.808543 CCTTAATCAATAGAGGCGGTGC 59.191 50.000 0.00 0.00 0.00 5.01
111 112 3.466836 CTTAATCAATAGAGGCGGTGCA 58.533 45.455 0.00 0.00 0.00 4.57
112 113 1.959042 AATCAATAGAGGCGGTGCAG 58.041 50.000 0.00 0.00 0.00 4.41
113 114 0.533755 ATCAATAGAGGCGGTGCAGC 60.534 55.000 5.64 5.64 0.00 5.25
114 115 1.153289 CAATAGAGGCGGTGCAGCT 60.153 57.895 14.92 0.00 37.29 4.24
115 116 1.153289 AATAGAGGCGGTGCAGCTG 60.153 57.895 14.92 10.11 37.29 4.24
166 167 2.871080 CGTTCGCAGCGCAAATGG 60.871 61.111 10.87 0.00 0.00 3.16
167 168 3.174573 GTTCGCAGCGCAAATGGC 61.175 61.111 10.87 3.90 39.90 4.40
168 169 3.668312 TTCGCAGCGCAAATGGCA 61.668 55.556 10.87 0.00 45.17 4.92
169 170 3.895102 TTCGCAGCGCAAATGGCAC 62.895 57.895 10.87 0.00 45.17 5.01
171 172 4.705519 GCAGCGCAAATGGCACGT 62.706 61.111 11.47 0.00 45.17 4.49
172 173 2.866750 CAGCGCAAATGGCACGTA 59.133 55.556 11.47 0.00 45.17 3.57
173 174 1.226101 CAGCGCAAATGGCACGTAG 60.226 57.895 11.47 0.00 45.17 3.51
174 175 1.375396 AGCGCAAATGGCACGTAGA 60.375 52.632 11.47 0.00 45.17 2.59
175 176 1.060937 GCGCAAATGGCACGTAGAG 59.939 57.895 0.30 0.00 45.17 2.43
176 177 1.715585 CGCAAATGGCACGTAGAGG 59.284 57.895 0.00 0.00 45.17 3.69
177 178 0.739462 CGCAAATGGCACGTAGAGGA 60.739 55.000 0.00 0.00 45.17 3.71
178 179 0.727398 GCAAATGGCACGTAGAGGAC 59.273 55.000 0.00 0.00 43.97 3.85
179 180 1.369625 CAAATGGCACGTAGAGGACC 58.630 55.000 0.00 0.00 0.00 4.46
180 181 1.066143 CAAATGGCACGTAGAGGACCT 60.066 52.381 0.00 0.00 0.00 3.85
181 182 2.154567 AATGGCACGTAGAGGACCTA 57.845 50.000 0.00 0.00 0.00 3.08
204 205 3.043713 CCGCTCGCAACTGCTTCA 61.044 61.111 0.00 0.00 39.32 3.02
232 233 2.203126 GGCAGCAAGATCTCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
236 237 1.002274 AGCAAGATCTCCCGGTCCT 59.998 57.895 0.00 0.00 0.00 3.85
262 263 4.410743 GCAGGACAAAGCGCAGGC 62.411 66.667 11.47 0.00 40.37 4.85
263 264 4.093952 CAGGACAAAGCGCAGGCG 62.094 66.667 11.47 9.68 46.35 5.52
346 357 3.357079 CCACCTGGCGCACTTCAC 61.357 66.667 10.83 0.00 0.00 3.18
348 359 4.988598 ACCTGGCGCACTTCACCG 62.989 66.667 10.83 0.00 0.00 4.94
360 371 3.844099 GCACTTCACCGTTAATTAAAGCG 59.156 43.478 0.00 0.45 0.00 4.68
442 457 4.749976 TGTGACTAATAACGCACTATGCA 58.250 39.130 1.20 0.00 45.36 3.96
474 489 1.734388 AAACAACCGTGAAGCAGCCC 61.734 55.000 0.00 0.00 0.00 5.19
480 495 3.435186 GTGAAGCAGCCCGAAGCC 61.435 66.667 0.00 0.00 45.47 4.35
486 501 3.880846 CAGCCCGAAGCCGAATGC 61.881 66.667 0.00 0.00 45.47 3.56
500 515 3.817647 GCCGAATGCTTCTCCAATTCTAT 59.182 43.478 0.00 0.00 36.87 1.98
502 517 5.303971 CCGAATGCTTCTCCAATTCTATCT 58.696 41.667 0.00 0.00 0.00 1.98
503 518 5.178996 CCGAATGCTTCTCCAATTCTATCTG 59.821 44.000 0.00 0.00 0.00 2.90
543 561 1.194781 ACAGCCTGTTGATCGGACCT 61.195 55.000 0.00 0.00 0.00 3.85
544 562 0.824109 CAGCCTGTTGATCGGACCTA 59.176 55.000 0.00 0.00 0.00 3.08
545 563 1.115467 AGCCTGTTGATCGGACCTAG 58.885 55.000 0.00 0.00 0.00 3.02
546 564 0.824759 GCCTGTTGATCGGACCTAGT 59.175 55.000 0.00 0.00 0.00 2.57
547 565 2.029623 GCCTGTTGATCGGACCTAGTA 58.970 52.381 0.00 0.00 0.00 1.82
548 566 2.223758 GCCTGTTGATCGGACCTAGTAC 60.224 54.545 0.00 0.00 0.00 2.73
549 567 3.288964 CCTGTTGATCGGACCTAGTACT 58.711 50.000 0.00 0.00 0.00 2.73
550 568 4.458397 CCTGTTGATCGGACCTAGTACTA 58.542 47.826 1.89 1.89 0.00 1.82
551 569 4.515944 CCTGTTGATCGGACCTAGTACTAG 59.484 50.000 21.11 21.11 0.00 2.57
563 581 1.472188 AGTACTAGGAAGGACCGTGC 58.528 55.000 0.00 0.00 44.74 5.34
594 612 1.887198 ACGACTCCAAGTGGACAGTAG 59.113 52.381 0.00 0.00 39.78 2.57
595 613 1.887198 CGACTCCAAGTGGACAGTAGT 59.113 52.381 0.00 0.00 39.78 2.73
596 614 3.079578 CGACTCCAAGTGGACAGTAGTA 58.920 50.000 0.00 0.00 39.78 1.82
614 632 5.772169 AGTAGTACCAACGAGTAACCTCTTT 59.228 40.000 0.00 0.00 35.43 2.52
622 640 3.190874 CGAGTAACCTCTTTGCTGATCC 58.809 50.000 0.00 0.00 35.43 3.36
654 672 3.119566 CGAGGGAGAAAAGTAGTAAGCGT 60.120 47.826 0.00 0.00 0.00 5.07
662 680 7.175073 AGAAAAGTAGTAAGCGTGTCTTTTC 57.825 36.000 15.67 15.67 44.78 2.29
665 683 7.549615 AAAGTAGTAAGCGTGTCTTTTCTTT 57.450 32.000 0.00 0.00 36.25 2.52
667 685 5.695363 AGTAGTAAGCGTGTCTTTTCTTTCC 59.305 40.000 0.00 0.00 36.25 3.13
668 686 3.813724 AGTAAGCGTGTCTTTTCTTTCCC 59.186 43.478 0.00 0.00 36.25 3.97
669 687 2.341846 AGCGTGTCTTTTCTTTCCCA 57.658 45.000 0.00 0.00 0.00 4.37
670 688 2.863809 AGCGTGTCTTTTCTTTCCCAT 58.136 42.857 0.00 0.00 0.00 4.00
698 716 3.246226 GGATATAAGCAAGCGTGTCAGTG 59.754 47.826 0.59 0.00 0.00 3.66
748 799 0.180406 CGTTGGGTTGGGATAGAGGG 59.820 60.000 0.00 0.00 0.00 4.30
749 800 1.591768 GTTGGGTTGGGATAGAGGGA 58.408 55.000 0.00 0.00 0.00 4.20
750 801 2.136026 GTTGGGTTGGGATAGAGGGAT 58.864 52.381 0.00 0.00 0.00 3.85
751 802 1.819753 TGGGTTGGGATAGAGGGATG 58.180 55.000 0.00 0.00 0.00 3.51
752 803 1.068121 GGGTTGGGATAGAGGGATGG 58.932 60.000 0.00 0.00 0.00 3.51
908 962 3.770625 TGCACAACAGACCGAAGAA 57.229 47.368 0.00 0.00 0.00 2.52
909 963 2.031258 TGCACAACAGACCGAAGAAA 57.969 45.000 0.00 0.00 0.00 2.52
910 964 1.668751 TGCACAACAGACCGAAGAAAC 59.331 47.619 0.00 0.00 0.00 2.78
911 965 1.332904 GCACAACAGACCGAAGAAACG 60.333 52.381 0.00 0.00 0.00 3.60
912 966 0.935196 ACAACAGACCGAAGAAACGC 59.065 50.000 0.00 0.00 0.00 4.84
913 967 0.934496 CAACAGACCGAAGAAACGCA 59.066 50.000 0.00 0.00 0.00 5.24
914 968 0.935196 AACAGACCGAAGAAACGCAC 59.065 50.000 0.00 0.00 0.00 5.34
915 969 0.179094 ACAGACCGAAGAAACGCACA 60.179 50.000 0.00 0.00 0.00 4.57
916 970 0.508641 CAGACCGAAGAAACGCACAG 59.491 55.000 0.00 0.00 0.00 3.66
917 971 1.204312 GACCGAAGAAACGCACAGC 59.796 57.895 0.00 0.00 0.00 4.40
918 972 2.171489 GACCGAAGAAACGCACAGCC 62.171 60.000 0.00 0.00 0.00 4.85
919 973 2.170985 CGAAGAAACGCACAGCCG 59.829 61.111 0.00 0.00 0.00 5.52
920 974 2.127232 GAAGAAACGCACAGCCGC 60.127 61.111 0.00 0.00 0.00 6.53
921 975 2.892334 GAAGAAACGCACAGCCGCA 61.892 57.895 0.00 0.00 0.00 5.69
922 976 2.387125 GAAGAAACGCACAGCCGCAA 62.387 55.000 0.00 0.00 0.00 4.85
923 977 1.999071 AAGAAACGCACAGCCGCAAA 61.999 50.000 0.00 0.00 0.00 3.68
924 978 2.010817 GAAACGCACAGCCGCAAAG 61.011 57.895 0.00 0.00 0.00 2.77
925 979 2.387125 GAAACGCACAGCCGCAAAGA 62.387 55.000 0.00 0.00 0.00 2.52
940 994 0.396811 AAAGAGACCAGACCCAACCG 59.603 55.000 0.00 0.00 0.00 4.44
1101 1177 4.980592 TGCTGGCCCTCCTCCACA 62.981 66.667 0.00 0.00 0.00 4.17
1102 1178 3.415087 GCTGGCCCTCCTCCACAT 61.415 66.667 0.00 0.00 0.00 3.21
1116 1192 1.395826 CCACATCCTCCTCGTCCTCC 61.396 65.000 0.00 0.00 0.00 4.30
1117 1193 1.454111 ACATCCTCCTCGTCCTCCG 60.454 63.158 0.00 0.00 38.13 4.63
1118 1194 2.519780 ATCCTCCTCGTCCTCCGC 60.520 66.667 0.00 0.00 36.19 5.54
1119 1195 4.816984 TCCTCCTCGTCCTCCGCC 62.817 72.222 0.00 0.00 36.19 6.13
1121 1197 4.824515 CTCCTCGTCCTCCGCCCT 62.825 72.222 0.00 0.00 36.19 5.19
1122 1198 4.816984 TCCTCGTCCTCCGCCCTC 62.817 72.222 0.00 0.00 36.19 4.30
1123 1199 4.824515 CCTCGTCCTCCGCCCTCT 62.825 72.222 0.00 0.00 36.19 3.69
1124 1200 3.213402 CTCGTCCTCCGCCCTCTC 61.213 72.222 0.00 0.00 36.19 3.20
1263 1354 1.092345 GCTGGAAGACCTTCATCCGC 61.092 60.000 11.38 4.66 37.08 5.54
1580 1695 3.127030 CACAGGAAAAGGAAAGGTATCGC 59.873 47.826 0.00 0.00 0.00 4.58
1585 1700 2.580966 AAGGAAAGGTATCGCTCGAC 57.419 50.000 0.00 0.00 0.00 4.20
1652 1779 0.757561 TCGGATGGTTCGGCTCCATA 60.758 55.000 6.85 0.00 44.52 2.74
1655 1782 1.048601 GATGGTTCGGCTCCATAGGA 58.951 55.000 6.85 0.00 44.52 2.94
1656 1783 0.759346 ATGGTTCGGCTCCATAGGAC 59.241 55.000 5.42 0.00 42.96 3.85
1657 1784 1.067582 GGTTCGGCTCCATAGGACG 59.932 63.158 0.00 0.00 0.00 4.79
1660 1787 2.520982 CGGCTCCATAGGACGGGA 60.521 66.667 0.00 0.00 0.00 5.14
1661 1788 1.908793 CGGCTCCATAGGACGGGAT 60.909 63.158 0.00 0.00 31.57 3.85
1662 1789 1.674057 GGCTCCATAGGACGGGATG 59.326 63.158 0.00 0.00 31.57 3.51
1663 1790 1.004440 GCTCCATAGGACGGGATGC 60.004 63.158 0.00 0.00 31.57 3.91
1711 1838 0.540923 CTTTCTCTCCTCCCCTGCTG 59.459 60.000 0.00 0.00 0.00 4.41
1740 1868 4.180817 TGATTGATTGTTCGTCGCTGTAT 58.819 39.130 0.00 0.00 0.00 2.29
1786 1914 2.842069 GCGATTGCTACATTCGTTGTCG 60.842 50.000 11.91 0.00 38.79 4.35
1793 1921 5.459768 TGCTACATTCGTTGTCGTACTTAA 58.540 37.500 0.00 0.00 39.87 1.85
1809 1950 5.470777 CGTACTTAATCAAGTTTTGTCCCCA 59.529 40.000 0.00 0.00 42.51 4.96
1833 1974 5.712217 TTACGGCTGATAATTTCTTCGTG 57.288 39.130 0.00 0.00 0.00 4.35
1840 1981 7.029563 GGCTGATAATTTCTTCGTGTTTGATT 58.970 34.615 0.00 0.00 0.00 2.57
1842 1983 8.915654 GCTGATAATTTCTTCGTGTTTGATTTT 58.084 29.630 0.00 0.00 0.00 1.82
1848 1989 4.854399 TCTTCGTGTTTGATTTTGCGAAT 58.146 34.783 0.00 0.00 37.64 3.34
1849 1990 4.674662 TCTTCGTGTTTGATTTTGCGAATG 59.325 37.500 0.00 0.00 37.64 2.67
1850 1991 3.304257 TCGTGTTTGATTTTGCGAATGG 58.696 40.909 0.00 0.00 0.00 3.16
1851 1992 3.049206 CGTGTTTGATTTTGCGAATGGT 58.951 40.909 0.00 0.00 0.00 3.55
1856 1997 3.296322 TGATTTTGCGAATGGTTGGTC 57.704 42.857 0.00 0.00 0.00 4.02
1870 2011 1.604278 GTTGGTCAGTGACTTCTTGGC 59.396 52.381 22.18 4.97 32.47 4.52
1967 2113 4.122143 AGAAGAAGAGGAATTCTGAGCG 57.878 45.455 5.23 0.00 39.47 5.03
2078 2228 2.506217 GATGCTTGTCGCGACCGA 60.506 61.111 34.34 22.18 43.27 4.69
2088 2238 2.177531 GCGACCGAGCACGTCTTA 59.822 61.111 2.18 0.00 37.88 2.10
2090 2240 1.513586 CGACCGAGCACGTCTTACC 60.514 63.158 2.18 0.00 37.88 2.85
2091 2241 1.582968 GACCGAGCACGTCTTACCA 59.417 57.895 2.18 0.00 37.88 3.25
2096 2246 1.199327 CGAGCACGTCTTACCAGAGAA 59.801 52.381 0.00 0.00 34.56 2.87
2098 2248 2.488545 GAGCACGTCTTACCAGAGAAGA 59.511 50.000 0.00 0.00 0.00 2.87
2102 2252 2.281140 GTCTTACCAGAGAAGACGGC 57.719 55.000 0.16 0.00 42.39 5.68
2103 2253 1.135053 GTCTTACCAGAGAAGACGGCC 60.135 57.143 0.00 0.00 42.39 6.13
2154 2309 2.040544 GGTGTTCCACGGCCTGATG 61.041 63.158 0.00 0.00 34.83 3.07
2175 2330 3.940221 TGCATGTGAACGATCATCAATCA 59.060 39.130 0.00 0.00 38.01 2.57
2206 2361 1.003003 TCGCTGTGAATTGGATGGTCA 59.997 47.619 0.00 0.00 0.00 4.02
2207 2362 1.811965 CGCTGTGAATTGGATGGTCAA 59.188 47.619 0.00 0.00 0.00 3.18
2208 2363 2.159476 CGCTGTGAATTGGATGGTCAAG 60.159 50.000 0.00 0.00 0.00 3.02
2209 2364 2.821969 GCTGTGAATTGGATGGTCAAGT 59.178 45.455 0.00 0.00 0.00 3.16
2212 2367 5.491070 CTGTGAATTGGATGGTCAAGTAGA 58.509 41.667 0.00 0.00 0.00 2.59
2235 2390 2.456942 TTGATGTGAATTCATCGCGC 57.543 45.000 12.12 0.00 44.82 6.86
2236 2391 0.657312 TGATGTGAATTCATCGCGCC 59.343 50.000 12.12 0.00 44.82 6.53
2249 2404 2.434185 GCGCCAACCGTGATCTGA 60.434 61.111 0.00 0.00 39.71 3.27
2259 2414 5.114780 CAACCGTGATCTGAAGAGAATCAT 58.885 41.667 0.00 0.00 37.82 2.45
2267 2424 1.554617 TGAAGAGAATCATGGACCGCA 59.445 47.619 0.00 0.00 37.82 5.69
2269 2426 0.179062 AGAGAATCATGGACCGCAGC 60.179 55.000 0.00 0.00 37.82 5.25
2285 2442 1.063174 GCAGCATCGAATTCCAGACAC 59.937 52.381 0.00 0.00 0.00 3.67
2290 2447 2.455674 TCGAATTCCAGACACACAGG 57.544 50.000 0.00 0.00 0.00 4.00
2291 2448 1.691976 TCGAATTCCAGACACACAGGT 59.308 47.619 0.00 0.00 0.00 4.00
2321 2478 3.963129 TGTTAACCTCCAACCATCCATC 58.037 45.455 2.48 0.00 0.00 3.51
2380 2538 0.108186 TACAGGTCGCATTGGAGCAG 60.108 55.000 6.97 2.68 36.90 4.24
2384 2542 0.881118 GGTCGCATTGGAGCAGAAAA 59.119 50.000 0.00 0.00 34.64 2.29
2388 2546 2.351418 TCGCATTGGAGCAGAAAATACG 59.649 45.455 0.00 0.00 0.00 3.06
2389 2547 2.095853 CGCATTGGAGCAGAAAATACGT 59.904 45.455 0.00 0.00 0.00 3.57
2390 2548 3.308595 CGCATTGGAGCAGAAAATACGTA 59.691 43.478 0.00 0.00 0.00 3.57
2391 2549 4.588278 GCATTGGAGCAGAAAATACGTAC 58.412 43.478 0.00 0.00 0.00 3.67
2393 2551 5.391523 GCATTGGAGCAGAAAATACGTACAA 60.392 40.000 0.00 0.00 0.00 2.41
2395 2553 5.600908 TGGAGCAGAAAATACGTACAAAC 57.399 39.130 0.00 0.00 0.00 2.93
2396 2554 5.302360 TGGAGCAGAAAATACGTACAAACT 58.698 37.500 0.00 0.00 0.00 2.66
2397 2555 6.457355 TGGAGCAGAAAATACGTACAAACTA 58.543 36.000 0.00 0.00 0.00 2.24
2398 2556 6.366877 TGGAGCAGAAAATACGTACAAACTAC 59.633 38.462 0.00 0.00 0.00 2.73
2399 2557 6.589139 GGAGCAGAAAATACGTACAAACTACT 59.411 38.462 0.00 0.00 0.00 2.57
2400 2558 7.201418 GGAGCAGAAAATACGTACAAACTACTC 60.201 40.741 0.00 5.56 0.00 2.59
2401 2559 7.376615 AGCAGAAAATACGTACAAACTACTCT 58.623 34.615 0.00 0.00 0.00 3.24
2402 2560 7.871463 AGCAGAAAATACGTACAAACTACTCTT 59.129 33.333 0.00 0.00 0.00 2.85
2403 2561 9.132521 GCAGAAAATACGTACAAACTACTCTTA 57.867 33.333 0.00 0.00 0.00 2.10
2409 2567 9.962783 AATACGTACAAACTACTCTTATCATCC 57.037 33.333 0.00 0.00 0.00 3.51
2435 2619 7.176690 CACTTTGAATGGTATAGTGGTTTCCTT 59.823 37.037 0.00 0.00 34.14 3.36
2454 2638 0.965866 TCCTGGAGTACGCAGACCAG 60.966 60.000 0.00 0.00 46.37 4.00
2479 2664 7.120579 AGCTTTGACAATATGAAAACCATACGA 59.879 33.333 0.00 0.00 40.29 3.43
2483 2668 8.950208 TGACAATATGAAAACCATACGACATA 57.050 30.769 0.00 0.00 40.29 2.29
2497 2682 7.092716 CCATACGACATACTCATCAATCATGA 58.907 38.462 0.00 0.00 39.39 3.07
2504 2689 8.198807 ACATACTCATCAATCATGATCAGGTA 57.801 34.615 9.06 7.35 44.53 3.08
2505 2690 8.823794 ACATACTCATCAATCATGATCAGGTAT 58.176 33.333 9.06 9.08 44.53 2.73
2506 2691 9.668497 CATACTCATCAATCATGATCAGGTATT 57.332 33.333 9.06 3.58 44.53 1.89
2507 2692 9.887629 ATACTCATCAATCATGATCAGGTATTC 57.112 33.333 9.06 0.00 44.53 1.75
2508 2693 7.742767 ACTCATCAATCATGATCAGGTATTCA 58.257 34.615 9.06 0.00 44.53 2.57
2509 2694 7.878644 ACTCATCAATCATGATCAGGTATTCAG 59.121 37.037 9.06 0.00 44.53 3.02
2510 2695 7.166167 TCATCAATCATGATCAGGTATTCAGG 58.834 38.462 9.06 0.00 44.53 3.86
2511 2696 6.505048 TCAATCATGATCAGGTATTCAGGT 57.495 37.500 9.06 0.00 0.00 4.00
2512 2697 6.293698 TCAATCATGATCAGGTATTCAGGTG 58.706 40.000 9.06 0.00 0.00 4.00
2513 2698 5.901413 ATCATGATCAGGTATTCAGGTGT 57.099 39.130 7.33 0.00 0.00 4.16
2514 2699 7.071071 TCAATCATGATCAGGTATTCAGGTGTA 59.929 37.037 9.06 0.00 0.00 2.90
2515 2700 7.565190 ATCATGATCAGGTATTCAGGTGTAT 57.435 36.000 7.33 0.00 0.00 2.29
2516 2701 6.762333 TCATGATCAGGTATTCAGGTGTATG 58.238 40.000 7.33 0.00 0.00 2.39
2517 2702 6.554605 TCATGATCAGGTATTCAGGTGTATGA 59.445 38.462 7.33 0.00 0.00 2.15
2518 2703 6.806668 TGATCAGGTATTCAGGTGTATGAA 57.193 37.500 0.00 0.00 43.04 2.57
2520 2705 8.491045 TGATCAGGTATTCAGGTGTATGAATA 57.509 34.615 5.31 5.31 45.75 1.75
2528 2713 7.792374 ATTCAGGTGTATGAATATGTGTGAC 57.208 36.000 0.25 0.00 45.75 3.67
2529 2714 6.293004 TCAGGTGTATGAATATGTGTGACA 57.707 37.500 0.00 0.00 0.00 3.58
2530 2715 6.888105 TCAGGTGTATGAATATGTGTGACAT 58.112 36.000 0.00 0.00 42.35 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.180456 CCTCCACTTTGTGCCATGCA 61.180 55.000 0.00 0.00 35.60 3.96
2 3 1.181098 ACCTCCACTTTGTGCCATGC 61.181 55.000 0.00 0.00 31.34 4.06
3 4 0.883833 GACCTCCACTTTGTGCCATG 59.116 55.000 0.00 0.00 31.34 3.66
4 5 0.606401 CGACCTCCACTTTGTGCCAT 60.606 55.000 0.00 0.00 31.34 4.40
5 6 1.227823 CGACCTCCACTTTGTGCCA 60.228 57.895 0.00 0.00 31.34 4.92
6 7 1.070786 TCGACCTCCACTTTGTGCC 59.929 57.895 0.00 0.00 31.34 5.01
10 11 2.027625 GCGGTCGACCTCCACTTTG 61.028 63.158 30.92 14.56 0.00 2.77
11 12 2.207924 AGCGGTCGACCTCCACTTT 61.208 57.895 30.92 5.20 0.00 2.66
14 15 4.436998 CCAGCGGTCGACCTCCAC 62.437 72.222 30.92 17.60 0.00 4.02
15 16 3.957435 ATCCAGCGGTCGACCTCCA 62.957 63.158 30.92 11.62 0.00 3.86
16 17 3.140225 GATCCAGCGGTCGACCTCC 62.140 68.421 30.92 21.24 0.00 4.30
18 19 1.541310 TTTGATCCAGCGGTCGACCT 61.541 55.000 30.92 12.42 0.00 3.85
19 20 1.079405 TTTGATCCAGCGGTCGACC 60.079 57.895 25.28 25.28 0.00 4.79
21 22 1.447838 GCTTTGATCCAGCGGTCGA 60.448 57.895 0.00 0.00 0.00 4.20
24 25 1.091771 CGATGCTTTGATCCAGCGGT 61.092 55.000 8.95 1.67 40.45 5.68
26 27 0.302890 GACGATGCTTTGATCCAGCG 59.697 55.000 5.92 5.92 45.30 5.18
27 28 0.659957 GGACGATGCTTTGATCCAGC 59.340 55.000 6.99 6.99 37.82 4.85
28 29 2.028420 TGGACGATGCTTTGATCCAG 57.972 50.000 0.00 0.00 34.50 3.86
29 30 2.488204 TTGGACGATGCTTTGATCCA 57.512 45.000 0.00 6.91 37.68 3.41
30 31 2.684881 ACATTGGACGATGCTTTGATCC 59.315 45.455 0.00 0.00 0.00 3.36
31 32 4.346129 GAACATTGGACGATGCTTTGATC 58.654 43.478 0.00 0.00 0.00 2.92
32 33 3.181507 CGAACATTGGACGATGCTTTGAT 60.182 43.478 0.00 0.00 0.00 2.57
33 34 2.159430 CGAACATTGGACGATGCTTTGA 59.841 45.455 0.00 0.00 0.00 2.69
34 35 2.508867 CGAACATTGGACGATGCTTTG 58.491 47.619 0.00 0.00 0.00 2.77
35 36 1.468520 CCGAACATTGGACGATGCTTT 59.531 47.619 0.00 0.00 0.00 3.51
36 37 1.086696 CCGAACATTGGACGATGCTT 58.913 50.000 0.00 0.00 0.00 3.91
37 38 1.369091 GCCGAACATTGGACGATGCT 61.369 55.000 0.00 0.00 0.00 3.79
38 39 1.062525 GCCGAACATTGGACGATGC 59.937 57.895 0.00 0.28 0.00 3.91
39 40 1.024046 TGGCCGAACATTGGACGATG 61.024 55.000 0.00 0.00 37.30 3.84
40 41 0.744414 CTGGCCGAACATTGGACGAT 60.744 55.000 0.00 0.00 37.30 3.73
41 42 1.375396 CTGGCCGAACATTGGACGA 60.375 57.895 0.00 0.00 37.30 4.20
42 43 1.671054 ACTGGCCGAACATTGGACG 60.671 57.895 0.00 0.00 37.30 4.79
43 44 1.586154 CCACTGGCCGAACATTGGAC 61.586 60.000 9.15 0.00 42.06 4.02
44 45 1.303236 CCACTGGCCGAACATTGGA 60.303 57.895 9.15 0.00 42.06 3.53
45 46 2.342650 CCCACTGGCCGAACATTGG 61.343 63.158 0.00 8.17 39.95 3.16
46 47 1.603455 ACCCACTGGCCGAACATTG 60.603 57.895 0.00 0.00 33.59 2.82
47 48 1.603455 CACCCACTGGCCGAACATT 60.603 57.895 0.00 0.00 33.59 2.71
48 49 2.034066 CACCCACTGGCCGAACAT 59.966 61.111 0.00 0.00 33.59 2.71
49 50 3.469863 GACACCCACTGGCCGAACA 62.470 63.158 0.00 0.00 33.59 3.18
50 51 2.668550 GACACCCACTGGCCGAAC 60.669 66.667 0.00 0.00 33.59 3.95
51 52 4.308458 CGACACCCACTGGCCGAA 62.308 66.667 0.00 0.00 33.59 4.30
57 58 4.320456 AGCAGCCGACACCCACTG 62.320 66.667 0.00 0.00 0.00 3.66
58 59 4.008933 GAGCAGCCGACACCCACT 62.009 66.667 0.00 0.00 0.00 4.00
59 60 4.314440 TGAGCAGCCGACACCCAC 62.314 66.667 0.00 0.00 0.00 4.61
60 61 4.007644 CTGAGCAGCCGACACCCA 62.008 66.667 0.00 0.00 0.00 4.51
61 62 2.564553 CTACTGAGCAGCCGACACCC 62.565 65.000 0.00 0.00 0.00 4.61
62 63 1.153745 CTACTGAGCAGCCGACACC 60.154 63.158 0.00 0.00 0.00 4.16
63 64 0.038159 AACTACTGAGCAGCCGACAC 60.038 55.000 0.00 0.00 0.00 3.67
64 65 0.243907 GAACTACTGAGCAGCCGACA 59.756 55.000 0.00 0.00 0.00 4.35
65 66 0.458716 GGAACTACTGAGCAGCCGAC 60.459 60.000 0.00 0.00 0.00 4.79
66 67 1.890894 GGAACTACTGAGCAGCCGA 59.109 57.895 0.00 0.00 0.00 5.54
67 68 1.517257 CGGAACTACTGAGCAGCCG 60.517 63.158 0.00 0.00 0.00 5.52
68 69 0.461961 ATCGGAACTACTGAGCAGCC 59.538 55.000 0.00 0.00 37.31 4.85
69 70 2.197577 GAATCGGAACTACTGAGCAGC 58.802 52.381 0.00 0.00 37.31 5.25
70 71 2.428890 AGGAATCGGAACTACTGAGCAG 59.571 50.000 0.00 0.00 37.31 4.24
71 72 2.457598 AGGAATCGGAACTACTGAGCA 58.542 47.619 0.00 0.00 37.31 4.26
72 73 3.528597 AAGGAATCGGAACTACTGAGC 57.471 47.619 0.00 0.00 37.31 4.26
73 74 6.806751 TGATTAAGGAATCGGAACTACTGAG 58.193 40.000 0.00 0.00 43.92 3.35
74 75 6.785337 TGATTAAGGAATCGGAACTACTGA 57.215 37.500 0.00 0.00 43.92 3.41
75 76 9.197694 CTATTGATTAAGGAATCGGAACTACTG 57.802 37.037 0.00 0.00 43.92 2.74
76 77 9.144298 TCTATTGATTAAGGAATCGGAACTACT 57.856 33.333 0.00 0.00 43.92 2.57
77 78 9.413048 CTCTATTGATTAAGGAATCGGAACTAC 57.587 37.037 0.00 0.00 43.92 2.73
78 79 8.585881 CCTCTATTGATTAAGGAATCGGAACTA 58.414 37.037 0.00 0.00 43.92 2.24
79 80 7.445945 CCTCTATTGATTAAGGAATCGGAACT 58.554 38.462 0.00 0.00 43.92 3.01
80 81 6.147985 GCCTCTATTGATTAAGGAATCGGAAC 59.852 42.308 0.00 0.00 43.92 3.62
81 82 6.231211 GCCTCTATTGATTAAGGAATCGGAA 58.769 40.000 0.00 0.00 43.92 4.30
82 83 5.566826 CGCCTCTATTGATTAAGGAATCGGA 60.567 44.000 0.00 0.00 43.92 4.55
83 84 4.627467 CGCCTCTATTGATTAAGGAATCGG 59.373 45.833 0.00 0.00 43.92 4.18
84 85 4.627467 CCGCCTCTATTGATTAAGGAATCG 59.373 45.833 0.00 0.00 43.92 3.34
85 86 5.409826 CACCGCCTCTATTGATTAAGGAATC 59.590 44.000 0.00 0.00 41.72 2.52
86 87 5.308825 CACCGCCTCTATTGATTAAGGAAT 58.691 41.667 0.00 0.00 0.00 3.01
87 88 4.703897 CACCGCCTCTATTGATTAAGGAA 58.296 43.478 0.00 0.00 0.00 3.36
88 89 3.494398 GCACCGCCTCTATTGATTAAGGA 60.494 47.826 0.00 0.00 0.00 3.36
89 90 2.808543 GCACCGCCTCTATTGATTAAGG 59.191 50.000 0.00 0.00 0.00 2.69
90 91 3.466836 TGCACCGCCTCTATTGATTAAG 58.533 45.455 0.00 0.00 0.00 1.85
91 92 3.466836 CTGCACCGCCTCTATTGATTAA 58.533 45.455 0.00 0.00 0.00 1.40
92 93 2.806745 GCTGCACCGCCTCTATTGATTA 60.807 50.000 0.00 0.00 0.00 1.75
93 94 1.959042 CTGCACCGCCTCTATTGATT 58.041 50.000 0.00 0.00 0.00 2.57
94 95 0.533755 GCTGCACCGCCTCTATTGAT 60.534 55.000 0.00 0.00 0.00 2.57
95 96 1.153369 GCTGCACCGCCTCTATTGA 60.153 57.895 0.00 0.00 0.00 2.57
96 97 1.153289 AGCTGCACCGCCTCTATTG 60.153 57.895 1.02 0.00 0.00 1.90
97 98 1.153289 CAGCTGCACCGCCTCTATT 60.153 57.895 0.00 0.00 0.00 1.73
98 99 2.503061 CAGCTGCACCGCCTCTAT 59.497 61.111 0.00 0.00 0.00 1.98
99 100 4.457496 GCAGCTGCACCGCCTCTA 62.457 66.667 33.36 0.00 41.59 2.43
109 110 0.942884 GAGGTTTTGCTTGCAGCTGC 60.943 55.000 31.89 31.89 42.97 5.25
110 111 0.662374 CGAGGTTTTGCTTGCAGCTG 60.662 55.000 10.11 10.11 42.97 4.24
111 112 1.103398 ACGAGGTTTTGCTTGCAGCT 61.103 50.000 9.12 0.00 42.97 4.24
112 113 0.936297 CACGAGGTTTTGCTTGCAGC 60.936 55.000 0.00 1.70 42.82 5.25
113 114 0.936297 GCACGAGGTTTTGCTTGCAG 60.936 55.000 0.00 0.00 35.74 4.41
114 115 1.065600 GCACGAGGTTTTGCTTGCA 59.934 52.632 0.00 0.00 35.74 4.08
115 116 1.661509 GGCACGAGGTTTTGCTTGC 60.662 57.895 0.00 0.00 38.85 4.01
116 117 4.633980 GGCACGAGGTTTTGCTTG 57.366 55.556 0.00 0.00 38.85 4.01
148 149 2.127270 CATTTGCGCTGCGAACGT 60.127 55.556 28.07 2.95 34.53 3.99
166 167 0.100861 GTGCTAGGTCCTCTACGTGC 59.899 60.000 0.00 0.00 0.00 5.34
167 168 0.377554 CGTGCTAGGTCCTCTACGTG 59.622 60.000 0.00 0.00 0.00 4.49
168 169 1.375098 GCGTGCTAGGTCCTCTACGT 61.375 60.000 18.16 0.00 0.00 3.57
169 170 1.355916 GCGTGCTAGGTCCTCTACG 59.644 63.158 14.69 14.69 0.00 3.51
170 171 1.734748 GGCGTGCTAGGTCCTCTAC 59.265 63.158 0.00 0.00 0.00 2.59
171 172 1.822613 CGGCGTGCTAGGTCCTCTA 60.823 63.158 0.00 0.00 0.00 2.43
172 173 3.141488 CGGCGTGCTAGGTCCTCT 61.141 66.667 0.00 0.00 0.00 3.69
173 174 4.874977 GCGGCGTGCTAGGTCCTC 62.875 72.222 9.37 0.00 41.73 3.71
215 216 2.203126 CCGGGAGATCTTGCTGCC 60.203 66.667 0.00 0.00 42.39 4.85
271 272 4.065281 CTGGGACACGTCGGGGTC 62.065 72.222 0.00 5.08 0.00 4.46
279 280 2.743928 GAAGCTGGCTGGGACACG 60.744 66.667 0.00 0.00 0.00 4.49
346 357 3.095738 CGCCTTTCGCTTTAATTAACGG 58.904 45.455 0.00 0.00 34.21 4.44
360 371 3.561310 TGATCACATTATCTGCGCCTTTC 59.439 43.478 4.18 0.00 0.00 2.62
400 412 5.131475 TCACATGAGATTCAGATTCATCCCA 59.869 40.000 0.00 0.00 29.48 4.37
442 457 2.673833 GGTTGTTTCTGACGACGATCT 58.326 47.619 0.00 0.00 42.63 2.75
486 501 4.327982 TCCGCAGATAGAATTGGAGAAG 57.672 45.455 0.00 0.00 0.00 2.85
500 515 6.813649 GTGCATCTTCTATTATTATCCGCAGA 59.186 38.462 0.00 0.00 0.00 4.26
502 517 6.463360 TGTGCATCTTCTATTATTATCCGCA 58.537 36.000 0.00 0.00 0.00 5.69
503 518 6.456181 GCTGTGCATCTTCTATTATTATCCGC 60.456 42.308 0.00 0.00 0.00 5.54
543 561 2.648059 GCACGGTCCTTCCTAGTACTA 58.352 52.381 1.89 1.89 0.00 1.82
544 562 1.472188 GCACGGTCCTTCCTAGTACT 58.528 55.000 0.00 0.00 0.00 2.73
545 563 0.459078 GGCACGGTCCTTCCTAGTAC 59.541 60.000 0.00 0.00 0.00 2.73
546 564 0.040058 TGGCACGGTCCTTCCTAGTA 59.960 55.000 0.00 0.00 0.00 1.82
547 565 0.617820 ATGGCACGGTCCTTCCTAGT 60.618 55.000 0.00 0.00 0.00 2.57
548 566 0.179073 CATGGCACGGTCCTTCCTAG 60.179 60.000 0.00 0.00 0.00 3.02
549 567 0.907704 ACATGGCACGGTCCTTCCTA 60.908 55.000 0.00 0.00 0.00 2.94
550 568 1.779061 AACATGGCACGGTCCTTCCT 61.779 55.000 0.00 0.00 0.00 3.36
551 569 0.893727 AAACATGGCACGGTCCTTCC 60.894 55.000 0.00 0.00 0.00 3.46
552 570 1.816074 TAAACATGGCACGGTCCTTC 58.184 50.000 0.00 0.00 0.00 3.46
553 571 2.290641 TGATAAACATGGCACGGTCCTT 60.291 45.455 0.00 0.00 0.00 3.36
554 572 1.280710 TGATAAACATGGCACGGTCCT 59.719 47.619 0.00 0.00 0.00 3.85
555 573 1.400494 GTGATAAACATGGCACGGTCC 59.600 52.381 0.00 0.00 0.00 4.46
556 574 2.825086 GTGATAAACATGGCACGGTC 57.175 50.000 0.00 0.00 0.00 4.79
563 581 4.093408 CACTTGGAGTCGTGATAAACATGG 59.907 45.833 0.00 0.00 36.29 3.66
654 672 5.012239 CCTGATGATGGGAAAGAAAAGACA 58.988 41.667 0.00 0.00 0.00 3.41
662 680 6.479006 TGCTTATATCCTGATGATGGGAAAG 58.521 40.000 0.00 0.00 35.08 2.62
665 683 5.572271 GCTTGCTTATATCCTGATGATGGGA 60.572 44.000 0.00 0.00 34.76 4.37
667 685 4.331992 CGCTTGCTTATATCCTGATGATGG 59.668 45.833 0.00 0.00 34.76 3.51
668 686 4.934001 ACGCTTGCTTATATCCTGATGATG 59.066 41.667 0.00 0.00 34.76 3.07
669 687 4.934001 CACGCTTGCTTATATCCTGATGAT 59.066 41.667 0.00 0.00 37.49 2.45
670 688 4.202253 ACACGCTTGCTTATATCCTGATGA 60.202 41.667 0.00 0.00 0.00 2.92
718 737 0.531200 AACCCAACGTTCGCCAAAAA 59.469 45.000 0.00 0.00 0.00 1.94
719 738 0.179134 CAACCCAACGTTCGCCAAAA 60.179 50.000 0.00 0.00 29.93 2.44
720 739 1.433879 CAACCCAACGTTCGCCAAA 59.566 52.632 0.00 0.00 29.93 3.28
721 740 2.482333 CCAACCCAACGTTCGCCAA 61.482 57.895 0.00 0.00 29.93 4.52
752 803 4.796495 AATTCGCGGGGCCCTGAC 62.796 66.667 36.08 23.34 0.00 3.51
766 817 2.046314 CTGACGTGGGCCGGAATT 60.046 61.111 5.05 0.00 42.24 2.17
836 887 3.095922 CCTTTTATCGGGAGGCCAC 57.904 57.895 5.01 0.00 0.00 5.01
895 949 0.935196 GTGCGTTTCTTCGGTCTGTT 59.065 50.000 0.00 0.00 0.00 3.16
908 962 2.896801 CTCTTTGCGGCTGTGCGTT 61.897 57.895 0.00 0.00 37.81 4.84
909 963 3.349006 CTCTTTGCGGCTGTGCGT 61.349 61.111 0.00 0.00 37.81 5.24
910 964 3.043713 TCTCTTTGCGGCTGTGCG 61.044 61.111 0.00 0.00 37.81 5.34
911 965 2.558313 GTCTCTTTGCGGCTGTGC 59.442 61.111 0.00 0.00 0.00 4.57
912 966 1.572085 CTGGTCTCTTTGCGGCTGTG 61.572 60.000 0.00 0.00 0.00 3.66
913 967 1.302033 CTGGTCTCTTTGCGGCTGT 60.302 57.895 0.00 0.00 0.00 4.40
914 968 1.004560 TCTGGTCTCTTTGCGGCTG 60.005 57.895 0.00 0.00 0.00 4.85
915 969 1.004440 GTCTGGTCTCTTTGCGGCT 60.004 57.895 0.00 0.00 0.00 5.52
916 970 2.035442 GGTCTGGTCTCTTTGCGGC 61.035 63.158 0.00 0.00 0.00 6.53
917 971 1.376037 GGGTCTGGTCTCTTTGCGG 60.376 63.158 0.00 0.00 0.00 5.69
918 972 0.250295 TTGGGTCTGGTCTCTTTGCG 60.250 55.000 0.00 0.00 0.00 4.85
919 973 1.239347 GTTGGGTCTGGTCTCTTTGC 58.761 55.000 0.00 0.00 0.00 3.68
920 974 1.878102 CGGTTGGGTCTGGTCTCTTTG 60.878 57.143 0.00 0.00 0.00 2.77
921 975 0.396811 CGGTTGGGTCTGGTCTCTTT 59.603 55.000 0.00 0.00 0.00 2.52
922 976 2.058675 CGGTTGGGTCTGGTCTCTT 58.941 57.895 0.00 0.00 0.00 2.85
923 977 2.584391 GCGGTTGGGTCTGGTCTCT 61.584 63.158 0.00 0.00 0.00 3.10
924 978 2.047179 GCGGTTGGGTCTGGTCTC 60.047 66.667 0.00 0.00 0.00 3.36
925 979 2.185310 GATGCGGTTGGGTCTGGTCT 62.185 60.000 0.00 0.00 0.00 3.85
1099 1175 4.688770 GGAGGACGAGGAGGATGT 57.311 61.111 0.00 0.00 0.00 3.06
1120 1196 4.803426 GACGCGCTGGTGGGAGAG 62.803 72.222 5.73 0.00 0.00 3.20
1554 1669 0.039165 CTTTCCTTTTCCTGTGGCGC 60.039 55.000 0.00 0.00 0.00 6.53
1556 1671 1.704641 ACCTTTCCTTTTCCTGTGGC 58.295 50.000 0.00 0.00 0.00 5.01
1564 1679 3.259902 GTCGAGCGATACCTTTCCTTTT 58.740 45.455 0.00 0.00 0.00 2.27
1580 1695 1.068417 TTTGACCACCACCGTCGAG 59.932 57.895 0.00 0.00 32.68 4.04
1585 1700 1.384525 TTGAAGTTTGACCACCACCG 58.615 50.000 0.00 0.00 0.00 4.94
1652 1779 3.550431 CCATCCGCATCCCGTCCT 61.550 66.667 0.00 0.00 34.38 3.85
1656 1783 3.612247 GATCCCCATCCGCATCCCG 62.612 68.421 0.00 0.00 0.00 5.14
1657 1784 2.352805 GATCCCCATCCGCATCCC 59.647 66.667 0.00 0.00 0.00 3.85
1660 1787 0.535102 GAAACGATCCCCATCCGCAT 60.535 55.000 0.00 0.00 0.00 4.73
1661 1788 1.153249 GAAACGATCCCCATCCGCA 60.153 57.895 0.00 0.00 0.00 5.69
1662 1789 0.463833 AAGAAACGATCCCCATCCGC 60.464 55.000 0.00 0.00 0.00 5.54
1663 1790 1.940613 GAAAGAAACGATCCCCATCCG 59.059 52.381 0.00 0.00 0.00 4.18
1711 1838 2.684881 ACGAACAATCAATCATGGGAGC 59.315 45.455 0.00 0.00 0.00 4.70
1716 1843 3.181517 ACAGCGACGAACAATCAATCATG 60.182 43.478 0.00 0.00 0.00 3.07
1740 1868 9.788960 GCTTCTCTTCTTCTTTGTTTTTCTTTA 57.211 29.630 0.00 0.00 0.00 1.85
1786 1914 6.887626 TGGGGACAAAACTTGATTAAGTAC 57.112 37.500 2.94 0.00 41.50 2.73
1809 1950 6.315393 ACACGAAGAAATTATCAGCCGTAATT 59.685 34.615 0.00 0.00 34.20 1.40
1833 1974 3.807071 ACCAACCATTCGCAAAATCAAAC 59.193 39.130 0.00 0.00 0.00 2.93
1840 1981 1.336440 CACTGACCAACCATTCGCAAA 59.664 47.619 0.00 0.00 0.00 3.68
1842 1983 0.107643 TCACTGACCAACCATTCGCA 59.892 50.000 0.00 0.00 0.00 5.10
1843 1984 0.517316 GTCACTGACCAACCATTCGC 59.483 55.000 0.00 0.00 0.00 4.70
1848 1989 2.421388 CCAAGAAGTCACTGACCAACCA 60.421 50.000 5.51 0.00 32.18 3.67
1849 1990 2.222027 CCAAGAAGTCACTGACCAACC 58.778 52.381 5.51 0.00 32.18 3.77
1850 1991 1.604278 GCCAAGAAGTCACTGACCAAC 59.396 52.381 5.51 0.00 32.18 3.77
1851 1992 1.810031 CGCCAAGAAGTCACTGACCAA 60.810 52.381 5.51 0.00 32.18 3.67
1856 1997 1.891060 GCGACGCCAAGAAGTCACTG 61.891 60.000 9.14 0.00 37.23 3.66
1870 2011 1.104579 GCGAAATTGCTAATGCGACG 58.895 50.000 0.00 0.00 43.34 5.12
1967 2113 3.057526 ACACGCCAAGCTTTTAGAATTCC 60.058 43.478 0.00 0.00 0.00 3.01
2078 2228 2.229302 GTCTTCTCTGGTAAGACGTGCT 59.771 50.000 0.00 0.00 42.35 4.40
2088 2238 2.600769 ACGGCCGTCTTCTCTGGT 60.601 61.111 28.70 0.00 0.00 4.00
2090 2240 0.526524 GATCACGGCCGTCTTCTCTG 60.527 60.000 31.80 16.17 0.00 3.35
2091 2241 0.681564 AGATCACGGCCGTCTTCTCT 60.682 55.000 31.80 23.10 0.00 3.10
2096 2246 1.079819 CACAAGATCACGGCCGTCT 60.080 57.895 31.80 20.78 0.00 4.18
2098 2248 1.374252 GTCACAAGATCACGGCCGT 60.374 57.895 28.70 28.70 0.00 5.68
2102 2252 0.371301 CATGCGTCACAAGATCACGG 59.629 55.000 4.90 0.00 34.04 4.94
2103 2253 1.059692 GACATGCGTCACAAGATCACG 59.940 52.381 0.00 0.00 42.13 4.35
2142 2297 2.438975 ACATGCATCAGGCCGTGG 60.439 61.111 0.00 0.00 43.89 4.94
2149 2304 3.558418 TGATGATCGTTCACATGCATCAG 59.442 43.478 0.00 0.00 37.71 2.90
2154 2309 4.034858 AGTGATTGATGATCGTTCACATGC 59.965 41.667 21.73 3.71 39.27 4.06
2175 2330 1.617322 TCACAGCGAGGAGTAACAGT 58.383 50.000 0.00 0.00 0.00 3.55
2206 2361 8.824781 CGATGAATTCACATCAATTCTCTACTT 58.175 33.333 11.07 0.00 44.57 2.24
2207 2362 7.042187 GCGATGAATTCACATCAATTCTCTACT 60.042 37.037 11.07 0.00 44.57 2.57
2208 2363 7.068341 GCGATGAATTCACATCAATTCTCTAC 58.932 38.462 11.07 0.00 44.57 2.59
2209 2364 6.074142 CGCGATGAATTCACATCAATTCTCTA 60.074 38.462 11.07 0.00 44.57 2.43
2212 2367 4.787563 GCGCGATGAATTCACATCAATTCT 60.788 41.667 12.10 0.00 44.57 2.40
2235 2390 3.319137 TTCTCTTCAGATCACGGTTGG 57.681 47.619 0.00 0.00 0.00 3.77
2236 2391 4.498241 TGATTCTCTTCAGATCACGGTTG 58.502 43.478 0.00 0.00 0.00 3.77
2248 2403 2.208431 CTGCGGTCCATGATTCTCTTC 58.792 52.381 0.00 0.00 0.00 2.87
2249 2404 1.745141 GCTGCGGTCCATGATTCTCTT 60.745 52.381 0.00 0.00 0.00 2.85
2259 2414 1.078497 AATTCGATGCTGCGGTCCA 60.078 52.632 0.00 0.00 0.00 4.02
2267 2424 2.289631 TGTGTGTCTGGAATTCGATGCT 60.290 45.455 0.00 0.00 0.00 3.79
2269 2426 2.674852 CCTGTGTGTCTGGAATTCGATG 59.325 50.000 0.00 0.00 37.33 3.84
2285 2442 4.037923 AGGTTAACATCAAGCAAACCTGTG 59.962 41.667 8.10 0.00 46.24 3.66
2290 2447 4.846779 TGGAGGTTAACATCAAGCAAAC 57.153 40.909 20.75 3.44 0.00 2.93
2291 2448 4.038642 GGTTGGAGGTTAACATCAAGCAAA 59.961 41.667 20.75 5.33 0.00 3.68
2321 2478 1.502231 CATTCTATTCTGGTCCGGCG 58.498 55.000 0.00 0.00 0.00 6.46
2384 2542 9.128404 TGGATGATAAGAGTAGTTTGTACGTAT 57.872 33.333 0.00 0.00 0.00 3.06
2388 2546 9.654663 AAAGTGGATGATAAGAGTAGTTTGTAC 57.345 33.333 0.00 0.00 0.00 2.90
2389 2547 9.653287 CAAAGTGGATGATAAGAGTAGTTTGTA 57.347 33.333 0.00 0.00 0.00 2.41
2390 2548 8.375506 TCAAAGTGGATGATAAGAGTAGTTTGT 58.624 33.333 0.00 0.00 32.04 2.83
2391 2549 8.777865 TCAAAGTGGATGATAAGAGTAGTTTG 57.222 34.615 0.00 0.00 0.00 2.93
2393 2551 9.388506 CATTCAAAGTGGATGATAAGAGTAGTT 57.611 33.333 0.00 0.00 0.00 2.24
2395 2553 7.989741 ACCATTCAAAGTGGATGATAAGAGTAG 59.010 37.037 0.00 0.00 39.12 2.57
2396 2554 7.861629 ACCATTCAAAGTGGATGATAAGAGTA 58.138 34.615 0.00 0.00 39.12 2.59
2397 2555 6.725364 ACCATTCAAAGTGGATGATAAGAGT 58.275 36.000 0.00 0.00 39.12 3.24
2398 2556 8.915057 ATACCATTCAAAGTGGATGATAAGAG 57.085 34.615 0.00 0.00 39.12 2.85
2400 2558 9.784531 ACTATACCATTCAAAGTGGATGATAAG 57.215 33.333 0.00 0.00 39.12 1.73
2401 2559 9.559732 CACTATACCATTCAAAGTGGATGATAA 57.440 33.333 0.00 0.00 39.12 1.75
2409 2567 6.659242 AGGAAACCACTATACCATTCAAAGTG 59.341 38.462 0.00 0.00 37.81 3.16
2435 2619 0.965866 CTGGTCTGCGTACTCCAGGA 60.966 60.000 10.08 0.00 42.38 3.86
2445 2629 0.877071 ATTGTCAAAGCTGGTCTGCG 59.123 50.000 0.00 0.00 38.13 5.18
2447 2631 5.885230 TTCATATTGTCAAAGCTGGTCTG 57.115 39.130 0.00 0.00 0.00 3.51
2454 2638 7.218204 GTCGTATGGTTTTCATATTGTCAAAGC 59.782 37.037 0.00 0.00 40.15 3.51
2479 2664 7.075851 ACCTGATCATGATTGATGAGTATGT 57.924 36.000 10.14 0.00 44.54 2.29
2483 2668 7.742767 TGAATACCTGATCATGATTGATGAGT 58.257 34.615 10.14 5.05 44.54 3.41
2497 2682 8.884323 ACATATTCATACACCTGAATACCTGAT 58.116 33.333 8.28 0.00 45.84 2.90
2504 2689 7.337938 TGTCACACATATTCATACACCTGAAT 58.662 34.615 4.85 4.85 45.44 2.57
2505 2690 6.706295 TGTCACACATATTCATACACCTGAA 58.294 36.000 0.00 0.00 39.35 3.02
2506 2691 6.293004 TGTCACACATATTCATACACCTGA 57.707 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.