Multiple sequence alignment - TraesCS1D01G126900

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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 TraesCS1D01G126900 chr1D 100.000 3399 0 0 358 3756 138785260 138781862 0.000000e+00 6277.0
1 TraesCS1D01G126900 chr1D 100.000 130 0 0 1 130 138785617 138785488 1.350000e-59 241.0
2 TraesCS1D01G126900 chr1D 98.387 62 1 0 2106 2167 351064259 351064320 3.970000e-20 110.0
3 TraesCS1D01G126900 chr1B 97.140 1888 42 4 501 2384 200297780 200299659 0.000000e+00 3177.0
4 TraesCS1D01G126900 chr1B 96.125 1342 24 10 2396 3713 200299641 200300978 0.000000e+00 2165.0
5 TraesCS1D01G126900 chr1A 95.086 1852 57 21 551 2384 153337123 153338958 0.000000e+00 2885.0
6 TraesCS1D01G126900 chr1A 96.752 862 11 4 2865 3713 153339444 153340301 0.000000e+00 1421.0
7 TraesCS1D01G126900 chr1A 98.739 476 6 0 2397 2872 153338940 153339415 0.000000e+00 846.0
8 TraesCS1D01G126900 chr4A 91.954 87 5 2 1854 1940 521300853 521300937 1.830000e-23 121.0
9 TraesCS1D01G126900 chr7A 100.000 62 0 0 2106 2167 575311308 575311247 8.530000e-22 115.0
10 TraesCS1D01G126900 chr3B 100.000 62 0 0 2106 2167 822040407 822040346 8.530000e-22 115.0
11 TraesCS1D01G126900 chr3B 100.000 62 0 0 2106 2167 822068497 822068436 8.530000e-22 115.0
12 TraesCS1D01G126900 chr3B 92.593 54 2 2 2051 2104 581959219 581959270 4.020000e-10 76.8
13 TraesCS1D01G126900 chr3A 100.000 62 0 0 2106 2167 671093559 671093620 8.530000e-22 115.0
14 TraesCS1D01G126900 chr3A 94.444 54 2 1 2051 2104 585018029 585017977 8.650000e-12 82.4
15 TraesCS1D01G126900 chr6D 98.387 62 1 0 2106 2167 83950541 83950602 3.970000e-20 110.0
16 TraesCS1D01G126900 chr6D 96.721 61 1 1 1991 2051 429819876 429819935 2.390000e-17 100.0
17 TraesCS1D01G126900 chr4D 98.387 62 1 0 2106 2167 123583417 123583356 3.970000e-20 110.0
18 TraesCS1D01G126900 chr3D 94.444 54 1 2 2051 2104 444053635 444053686 8.650000e-12 82.4


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 TraesCS1D01G126900 chr1D 138781862 138785617 3755 True 3259.000000 6277 100.0000 1 3756 2 chr1D.!!$R1 3755
1 TraesCS1D01G126900 chr1B 200297780 200300978 3198 False 2671.000000 3177 96.6325 501 3713 2 chr1B.!!$F1 3212
2 TraesCS1D01G126900 chr1A 153337123 153340301 3178 False 1717.333333 2885 96.8590 551 3713 3 chr1A.!!$F1 3162

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
39 40 0.037303 ACATGTGGCACTTGGGAGAG 59.963 55.0 29.76 10.60 0.00 3.20 F
49 50 0.038159 CTTGGGAGAGTTCGCGTTCT 60.038 55.0 5.77 8.17 39.01 3.01 F
50 51 0.038526 TTGGGAGAGTTCGCGTTCTC 60.039 55.0 21.31 21.31 39.01 2.87 F
106 107 0.178912 ACCAAGGGACTACCGACCTT 60.179 55.0 0.00 0.00 46.96 3.50 F
1414 1427 0.320247 CCCGTGCAGATGGATAGCTC 60.320 60.0 0.00 0.00 0.00 4.09 F
1698 1711 1.508632 GTTCGTGCTTTCACTAGCCA 58.491 50.0 0.00 0.00 40.99 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1886 0.033109 AATTCTGTAAGGGGGCTGGC 60.033 55.000 0.00 0.0 0.00 4.85 R
2045 2076 0.032813 ATTGAGGGGTGGCCATTCTG 60.033 55.000 9.72 0.0 0.00 3.02 R
2101 2132 6.241223 TCCAAGACCCCTCATATAATAGGA 57.759 41.667 5.50 0.0 34.58 2.94 R
2252 2283 2.638480 AACTGCAGGACAAGCACTTA 57.362 45.000 19.93 0.0 37.02 2.24 R
2400 2431 2.293955 CAGTGAAACCACATGCACATCA 59.706 45.455 0.00 0.0 37.80 3.07 R
3714 3802 0.035343 TGTGTGAACAAACGGGGTGA 60.035 50.000 0.00 0.0 0.00 4.02 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
21 22 4.289529 GACATACACTTCGTTCGTGAAC 57.710 45.455 2.63 2.63 36.29 3.18
22 23 3.708890 ACATACACTTCGTTCGTGAACA 58.291 40.909 12.76 0.00 41.20 3.18
23 24 4.304110 ACATACACTTCGTTCGTGAACAT 58.696 39.130 12.76 0.00 41.20 2.71
24 25 4.149922 ACATACACTTCGTTCGTGAACATG 59.850 41.667 12.76 8.83 41.20 3.21
25 26 2.546778 ACACTTCGTTCGTGAACATGT 58.453 42.857 12.76 0.00 41.20 3.21
26 27 2.284150 ACACTTCGTTCGTGAACATGTG 59.716 45.455 19.00 19.00 41.20 3.21
27 28 1.864711 ACTTCGTTCGTGAACATGTGG 59.135 47.619 12.76 0.00 41.20 4.17
28 29 0.584396 TTCGTTCGTGAACATGTGGC 59.416 50.000 12.76 0.00 41.20 5.01
29 30 0.530870 TCGTTCGTGAACATGTGGCA 60.531 50.000 12.76 0.00 41.20 4.92
30 31 0.384230 CGTTCGTGAACATGTGGCAC 60.384 55.000 11.55 11.55 41.20 5.01
31 32 0.944386 GTTCGTGAACATGTGGCACT 59.056 50.000 19.83 0.00 40.84 4.40
32 33 1.333619 GTTCGTGAACATGTGGCACTT 59.666 47.619 19.83 9.98 40.84 3.16
33 34 0.943673 TCGTGAACATGTGGCACTTG 59.056 50.000 26.40 26.40 0.00 3.16
34 35 0.040157 CGTGAACATGTGGCACTTGG 60.040 55.000 29.76 17.27 0.00 3.61
35 36 0.314935 GTGAACATGTGGCACTTGGG 59.685 55.000 29.76 15.13 0.00 4.12
36 37 0.184692 TGAACATGTGGCACTTGGGA 59.815 50.000 29.76 14.96 0.00 4.37
37 38 0.883833 GAACATGTGGCACTTGGGAG 59.116 55.000 29.76 11.53 0.00 4.30
38 39 0.478072 AACATGTGGCACTTGGGAGA 59.522 50.000 29.76 6.27 0.00 3.71
39 40 0.037303 ACATGTGGCACTTGGGAGAG 59.963 55.000 29.76 10.60 0.00 3.20
40 41 0.037303 CATGTGGCACTTGGGAGAGT 59.963 55.000 22.05 0.00 0.00 3.24
41 42 0.773644 ATGTGGCACTTGGGAGAGTT 59.226 50.000 19.83 0.00 0.00 3.01
42 43 0.108585 TGTGGCACTTGGGAGAGTTC 59.891 55.000 19.83 0.00 0.00 3.01
43 44 0.951040 GTGGCACTTGGGAGAGTTCG 60.951 60.000 11.13 0.00 0.00 3.95
44 45 2.035442 GGCACTTGGGAGAGTTCGC 61.035 63.158 0.00 0.00 36.84 4.70
45 46 2.383527 GCACTTGGGAGAGTTCGCG 61.384 63.158 0.00 0.00 39.01 5.87
46 47 1.006102 CACTTGGGAGAGTTCGCGT 60.006 57.895 5.77 0.00 39.01 6.01
47 48 0.600255 CACTTGGGAGAGTTCGCGTT 60.600 55.000 5.77 0.00 39.01 4.84
48 49 0.319641 ACTTGGGAGAGTTCGCGTTC 60.320 55.000 5.77 2.76 39.01 3.95
49 50 0.038159 CTTGGGAGAGTTCGCGTTCT 60.038 55.000 5.77 8.17 39.01 3.01
50 51 0.038526 TTGGGAGAGTTCGCGTTCTC 60.039 55.000 21.31 21.31 39.01 2.87
53 54 2.726887 GAGAGTTCGCGTTCTCCAC 58.273 57.895 21.92 15.58 34.99 4.02
62 63 3.413522 CGTTCTCCACGTTCCTACC 57.586 57.895 0.00 0.00 44.49 3.18
63 64 0.455633 CGTTCTCCACGTTCCTACCG 60.456 60.000 0.00 0.00 44.49 4.02
64 65 0.735287 GTTCTCCACGTTCCTACCGC 60.735 60.000 0.00 0.00 0.00 5.68
65 66 0.896940 TTCTCCACGTTCCTACCGCT 60.897 55.000 0.00 0.00 0.00 5.52
66 67 1.153823 CTCCACGTTCCTACCGCTG 60.154 63.158 0.00 0.00 0.00 5.18
67 68 1.592400 CTCCACGTTCCTACCGCTGA 61.592 60.000 0.00 0.00 0.00 4.26
68 69 1.180456 TCCACGTTCCTACCGCTGAA 61.180 55.000 0.00 0.00 0.00 3.02
69 70 1.012486 CCACGTTCCTACCGCTGAAC 61.012 60.000 0.00 0.00 37.97 3.18
70 71 0.319211 CACGTTCCTACCGCTGAACA 60.319 55.000 0.00 0.00 40.65 3.18
71 72 0.038526 ACGTTCCTACCGCTGAACAG 60.039 55.000 0.00 0.00 40.65 3.16
72 73 0.038526 CGTTCCTACCGCTGAACAGT 60.039 55.000 3.77 0.00 40.65 3.55
73 74 1.604693 CGTTCCTACCGCTGAACAGTT 60.605 52.381 3.77 0.00 40.65 3.16
74 75 2.067013 GTTCCTACCGCTGAACAGTTC 58.933 52.381 6.32 6.32 40.41 3.01
75 76 1.334160 TCCTACCGCTGAACAGTTCA 58.666 50.000 15.39 15.39 38.17 3.18
76 77 1.000506 TCCTACCGCTGAACAGTTCAC 59.999 52.381 12.24 8.52 35.46 3.18
77 78 1.429463 CTACCGCTGAACAGTTCACC 58.571 55.000 12.24 5.21 35.46 4.02
78 79 0.319211 TACCGCTGAACAGTTCACCG 60.319 55.000 19.93 19.93 38.22 4.94
79 80 3.244105 CGCTGAACAGTTCACCGG 58.756 61.111 19.34 0.00 35.65 5.28
80 81 1.594293 CGCTGAACAGTTCACCGGT 60.594 57.895 19.34 0.00 35.65 5.28
81 82 1.831389 CGCTGAACAGTTCACCGGTG 61.831 60.000 29.26 29.26 35.65 4.94
82 83 0.814010 GCTGAACAGTTCACCGGTGT 60.814 55.000 32.74 13.92 35.46 4.16
83 84 1.663695 CTGAACAGTTCACCGGTGTT 58.336 50.000 32.74 20.01 37.12 3.32
84 85 2.828877 CTGAACAGTTCACCGGTGTTA 58.171 47.619 32.74 19.78 34.55 2.41
85 86 3.399330 CTGAACAGTTCACCGGTGTTAT 58.601 45.455 32.74 17.22 34.55 1.89
86 87 3.135225 TGAACAGTTCACCGGTGTTATG 58.865 45.455 32.74 27.69 34.55 1.90
87 88 3.181464 TGAACAGTTCACCGGTGTTATGA 60.181 43.478 32.74 11.90 34.55 2.15
88 89 2.762745 ACAGTTCACCGGTGTTATGAC 58.237 47.619 32.74 22.18 0.00 3.06
89 90 2.073816 CAGTTCACCGGTGTTATGACC 58.926 52.381 32.74 13.99 0.00 4.02
90 91 1.695242 AGTTCACCGGTGTTATGACCA 59.305 47.619 32.74 9.47 35.50 4.02
91 92 2.105134 AGTTCACCGGTGTTATGACCAA 59.895 45.455 32.74 15.22 35.50 3.67
92 93 2.465860 TCACCGGTGTTATGACCAAG 57.534 50.000 32.74 4.00 35.50 3.61
93 94 1.002659 TCACCGGTGTTATGACCAAGG 59.997 52.381 32.74 3.78 35.50 3.61
94 95 0.326927 ACCGGTGTTATGACCAAGGG 59.673 55.000 6.12 0.00 35.50 3.95
95 96 0.616371 CCGGTGTTATGACCAAGGGA 59.384 55.000 0.00 0.00 35.50 4.20
96 97 1.677820 CCGGTGTTATGACCAAGGGAC 60.678 57.143 0.00 0.00 35.50 4.46
98 99 2.498481 CGGTGTTATGACCAAGGGACTA 59.502 50.000 0.00 0.00 38.49 2.59
99 100 3.677976 CGGTGTTATGACCAAGGGACTAC 60.678 52.174 0.00 0.00 38.49 2.73
100 101 3.370209 GGTGTTATGACCAAGGGACTACC 60.370 52.174 0.00 0.00 38.49 3.18
101 102 2.498481 TGTTATGACCAAGGGACTACCG 59.502 50.000 0.00 0.00 46.96 4.02
102 103 2.762327 GTTATGACCAAGGGACTACCGA 59.238 50.000 0.00 0.00 46.96 4.69
103 104 1.192428 ATGACCAAGGGACTACCGAC 58.808 55.000 0.00 0.00 46.96 4.79
104 105 0.901580 TGACCAAGGGACTACCGACC 60.902 60.000 0.00 0.00 46.96 4.79
105 106 0.614134 GACCAAGGGACTACCGACCT 60.614 60.000 0.00 0.00 46.96 3.85
106 107 0.178912 ACCAAGGGACTACCGACCTT 60.179 55.000 0.00 0.00 46.96 3.50
107 108 1.077663 ACCAAGGGACTACCGACCTTA 59.922 52.381 0.00 0.00 46.96 2.69
108 109 1.755380 CCAAGGGACTACCGACCTTAG 59.245 57.143 0.00 0.00 46.96 2.18
109 110 2.454538 CAAGGGACTACCGACCTTAGT 58.545 52.381 0.00 0.00 46.96 2.24
110 111 2.830321 CAAGGGACTACCGACCTTAGTT 59.170 50.000 0.00 0.00 46.96 2.24
111 112 3.181393 AGGGACTACCGACCTTAGTTT 57.819 47.619 0.00 0.00 46.96 2.66
112 113 3.514539 AGGGACTACCGACCTTAGTTTT 58.485 45.455 0.00 0.00 46.96 2.43
113 114 3.513119 AGGGACTACCGACCTTAGTTTTC 59.487 47.826 0.00 0.00 46.96 2.29
114 115 3.505836 GGACTACCGACCTTAGTTTTCG 58.494 50.000 0.00 0.00 29.58 3.46
115 116 3.191371 GGACTACCGACCTTAGTTTTCGA 59.809 47.826 0.00 0.00 34.62 3.71
116 117 4.410448 GACTACCGACCTTAGTTTTCGAG 58.590 47.826 0.00 0.00 34.62 4.04
117 118 2.738013 ACCGACCTTAGTTTTCGAGG 57.262 50.000 0.00 0.00 34.62 4.63
118 119 2.242043 ACCGACCTTAGTTTTCGAGGA 58.758 47.619 0.00 0.00 34.62 3.71
119 120 2.230750 ACCGACCTTAGTTTTCGAGGAG 59.769 50.000 0.00 0.00 34.62 3.69
120 121 2.230750 CCGACCTTAGTTTTCGAGGAGT 59.769 50.000 0.00 0.00 34.62 3.85
121 122 3.305881 CCGACCTTAGTTTTCGAGGAGTT 60.306 47.826 0.00 0.00 34.62 3.01
122 123 4.304939 CGACCTTAGTTTTCGAGGAGTTT 58.695 43.478 0.00 0.00 34.62 2.66
123 124 4.385146 CGACCTTAGTTTTCGAGGAGTTTC 59.615 45.833 0.00 0.00 34.62 2.78
124 125 4.304939 ACCTTAGTTTTCGAGGAGTTTCG 58.695 43.478 0.00 0.00 41.79 3.46
125 126 3.678548 CCTTAGTTTTCGAGGAGTTTCGG 59.321 47.826 0.00 0.00 40.83 4.30
126 127 4.553323 CTTAGTTTTCGAGGAGTTTCGGA 58.447 43.478 0.00 0.00 40.83 4.55
127 128 3.679824 AGTTTTCGAGGAGTTTCGGAT 57.320 42.857 0.00 0.00 40.83 4.18
128 129 3.586892 AGTTTTCGAGGAGTTTCGGATC 58.413 45.455 0.00 0.00 40.83 3.36
129 130 2.667473 TTTCGAGGAGTTTCGGATCC 57.333 50.000 0.00 0.00 40.83 3.36
379 380 4.400120 ACCGTTGTATATCTCTCTCTCCC 58.600 47.826 0.00 0.00 0.00 4.30
380 381 4.105057 ACCGTTGTATATCTCTCTCTCCCT 59.895 45.833 0.00 0.00 0.00 4.20
381 382 4.698304 CCGTTGTATATCTCTCTCTCCCTC 59.302 50.000 0.00 0.00 0.00 4.30
382 383 5.514136 CCGTTGTATATCTCTCTCTCCCTCT 60.514 48.000 0.00 0.00 0.00 3.69
383 384 5.642063 CGTTGTATATCTCTCTCTCCCTCTC 59.358 48.000 0.00 0.00 0.00 3.20
384 385 5.414789 TGTATATCTCTCTCTCCCTCTCG 57.585 47.826 0.00 0.00 0.00 4.04
385 386 4.841813 TGTATATCTCTCTCTCCCTCTCGT 59.158 45.833 0.00 0.00 0.00 4.18
386 387 6.017830 TGTATATCTCTCTCTCCCTCTCGTA 58.982 44.000 0.00 0.00 0.00 3.43
387 388 6.670464 TGTATATCTCTCTCTCCCTCTCGTAT 59.330 42.308 0.00 0.00 0.00 3.06
388 389 7.840210 TGTATATCTCTCTCTCCCTCTCGTATA 59.160 40.741 0.00 0.00 0.00 1.47
389 390 7.931015 ATATCTCTCTCTCCCTCTCGTATAT 57.069 40.000 0.00 0.00 0.00 0.86
390 391 6.636454 ATCTCTCTCTCCCTCTCGTATATT 57.364 41.667 0.00 0.00 0.00 1.28
391 392 6.442541 TCTCTCTCTCCCTCTCGTATATTT 57.557 41.667 0.00 0.00 0.00 1.40
392 393 7.556416 TCTCTCTCTCCCTCTCGTATATTTA 57.444 40.000 0.00 0.00 0.00 1.40
393 394 8.153221 TCTCTCTCTCCCTCTCGTATATTTAT 57.847 38.462 0.00 0.00 0.00 1.40
394 395 9.269494 TCTCTCTCTCCCTCTCGTATATTTATA 57.731 37.037 0.00 0.00 0.00 0.98
395 396 9.321562 CTCTCTCTCCCTCTCGTATATTTATAC 57.678 40.741 0.00 0.00 36.15 1.47
396 397 8.823794 TCTCTCTCCCTCTCGTATATTTATACA 58.176 37.037 8.13 0.00 38.72 2.29
397 398 9.621629 CTCTCTCCCTCTCGTATATTTATACAT 57.378 37.037 8.13 0.00 38.72 2.29
398 399 9.616156 TCTCTCCCTCTCGTATATTTATACATC 57.384 37.037 8.13 0.00 38.72 3.06
399 400 9.621629 CTCTCCCTCTCGTATATTTATACATCT 57.378 37.037 8.13 0.00 38.72 2.90
400 401 9.976776 TCTCCCTCTCGTATATTTATACATCTT 57.023 33.333 8.13 0.00 38.72 2.40
402 403 8.967918 TCCCTCTCGTATATTTATACATCTTGG 58.032 37.037 8.13 3.63 38.72 3.61
403 404 8.967918 CCCTCTCGTATATTTATACATCTTGGA 58.032 37.037 8.13 0.00 38.72 3.53
418 419 7.741554 ACATCTTGGAAGATAAGTAGAGGTT 57.258 36.000 1.53 0.00 43.65 3.50
419 420 7.560368 ACATCTTGGAAGATAAGTAGAGGTTG 58.440 38.462 1.53 0.00 43.65 3.77
420 421 6.546428 TCTTGGAAGATAAGTAGAGGTTGG 57.454 41.667 0.00 0.00 0.00 3.77
421 422 6.023603 TCTTGGAAGATAAGTAGAGGTTGGT 58.976 40.000 0.00 0.00 0.00 3.67
422 423 5.934402 TGGAAGATAAGTAGAGGTTGGTC 57.066 43.478 0.00 0.00 0.00 4.02
423 424 5.590818 TGGAAGATAAGTAGAGGTTGGTCT 58.409 41.667 0.00 0.00 0.00 3.85
424 425 6.738635 TGGAAGATAAGTAGAGGTTGGTCTA 58.261 40.000 0.00 0.00 0.00 2.59
425 426 6.606395 TGGAAGATAAGTAGAGGTTGGTCTAC 59.394 42.308 3.30 3.30 46.47 2.59
432 433 5.259832 GTAGAGGTTGGTCTACCATGTAC 57.740 47.826 1.96 0.00 46.97 2.90
433 434 3.105283 AGAGGTTGGTCTACCATGTACC 58.895 50.000 11.91 11.91 46.97 3.34
434 435 3.200958 AGGTTGGTCTACCATGTACCT 57.799 47.619 15.39 15.39 45.36 3.08
438 439 6.930068 GGTTGGTCTACCATGTACCTATAT 57.070 41.667 12.38 0.00 46.97 0.86
440 441 8.605325 GGTTGGTCTACCATGTACCTATATAT 57.395 38.462 12.38 0.00 46.97 0.86
441 442 8.475639 GGTTGGTCTACCATGTACCTATATATG 58.524 40.741 12.38 0.00 46.97 1.78
442 443 9.032624 GTTGGTCTACCATGTACCTATATATGT 57.967 37.037 1.96 0.00 46.97 2.29
443 444 8.589701 TGGTCTACCATGTACCTATATATGTG 57.410 38.462 0.00 0.00 42.01 3.21
444 445 7.123697 TGGTCTACCATGTACCTATATATGTGC 59.876 40.741 0.00 0.80 42.01 4.57
445 446 7.123697 GGTCTACCATGTACCTATATATGTGCA 59.876 40.741 10.43 10.43 35.64 4.57
446 447 8.696374 GTCTACCATGTACCTATATATGTGCAT 58.304 37.037 13.41 13.41 38.15 3.96
447 448 9.267071 TCTACCATGTACCTATATATGTGCATT 57.733 33.333 15.59 8.15 35.94 3.56
450 451 8.821817 ACCATGTACCTATATATGTGCATTACA 58.178 33.333 15.59 6.22 44.87 2.41
465 466 6.487689 TGCATTACACACACGATTAATGAA 57.512 33.333 0.00 0.00 34.98 2.57
466 467 7.082700 TGCATTACACACACGATTAATGAAT 57.917 32.000 0.00 0.00 34.98 2.57
467 468 7.534282 TGCATTACACACACGATTAATGAATT 58.466 30.769 0.00 0.00 34.98 2.17
468 469 8.669243 TGCATTACACACACGATTAATGAATTA 58.331 29.630 0.00 0.00 34.98 1.40
469 470 9.663904 GCATTACACACACGATTAATGAATTAT 57.336 29.630 0.00 0.00 34.98 1.28
472 473 7.857734 ACACACACGATTAATGAATTATGGA 57.142 32.000 0.00 0.00 0.00 3.41
473 474 8.450578 ACACACACGATTAATGAATTATGGAT 57.549 30.769 0.00 0.00 0.00 3.41
474 475 8.344831 ACACACACGATTAATGAATTATGGATG 58.655 33.333 0.00 0.00 0.00 3.51
475 476 7.324375 CACACACGATTAATGAATTATGGATGC 59.676 37.037 0.00 0.00 0.00 3.91
476 477 7.013178 ACACACGATTAATGAATTATGGATGCA 59.987 33.333 0.00 0.00 0.00 3.96
477 478 7.324375 CACACGATTAATGAATTATGGATGCAC 59.676 37.037 0.00 0.00 0.00 4.57
478 479 7.013178 ACACGATTAATGAATTATGGATGCACA 59.987 33.333 0.00 0.00 0.00 4.57
479 480 7.324375 CACGATTAATGAATTATGGATGCACAC 59.676 37.037 0.00 0.00 0.00 3.82
480 481 7.013178 ACGATTAATGAATTATGGATGCACACA 59.987 33.333 0.00 0.00 0.00 3.72
481 482 7.861872 CGATTAATGAATTATGGATGCACACAA 59.138 33.333 0.00 0.00 0.00 3.33
482 483 9.701098 GATTAATGAATTATGGATGCACACAAT 57.299 29.630 0.00 0.00 0.00 2.71
483 484 9.701098 ATTAATGAATTATGGATGCACACAATC 57.299 29.630 0.00 0.00 0.00 2.67
484 485 5.518848 TGAATTATGGATGCACACAATCC 57.481 39.130 0.00 0.00 35.12 3.01
485 486 4.341806 TGAATTATGGATGCACACAATCCC 59.658 41.667 0.88 0.00 33.65 3.85
486 487 3.668141 TTATGGATGCACACAATCCCT 57.332 42.857 0.88 0.00 33.65 4.20
487 488 2.537633 ATGGATGCACACAATCCCTT 57.462 45.000 0.88 0.00 33.65 3.95
488 489 1.838112 TGGATGCACACAATCCCTTC 58.162 50.000 0.88 0.00 33.65 3.46
489 490 1.355381 TGGATGCACACAATCCCTTCT 59.645 47.619 0.88 0.00 33.65 2.85
490 491 2.225091 TGGATGCACACAATCCCTTCTT 60.225 45.455 0.88 0.00 33.65 2.52
491 492 2.827921 GGATGCACACAATCCCTTCTTT 59.172 45.455 0.00 0.00 0.00 2.52
492 493 3.119352 GGATGCACACAATCCCTTCTTTC 60.119 47.826 0.00 0.00 0.00 2.62
493 494 2.238521 TGCACACAATCCCTTCTTTCC 58.761 47.619 0.00 0.00 0.00 3.13
494 495 1.546029 GCACACAATCCCTTCTTTCCC 59.454 52.381 0.00 0.00 0.00 3.97
495 496 1.812571 CACACAATCCCTTCTTTCCCG 59.187 52.381 0.00 0.00 0.00 5.14
496 497 0.811281 CACAATCCCTTCTTTCCCGC 59.189 55.000 0.00 0.00 0.00 6.13
497 498 0.404040 ACAATCCCTTCTTTCCCGCA 59.596 50.000 0.00 0.00 0.00 5.69
498 499 0.811281 CAATCCCTTCTTTCCCGCAC 59.189 55.000 0.00 0.00 0.00 5.34
499 500 0.676782 AATCCCTTCTTTCCCGCACG 60.677 55.000 0.00 0.00 0.00 5.34
517 518 1.069500 ACGCATGTTACTTTGAACGCC 60.069 47.619 0.00 0.00 31.59 5.68
998 1007 1.553704 GGTGGGTATCCGAGTTTCTGT 59.446 52.381 0.00 0.00 35.24 3.41
1149 1158 3.537206 GAACCAGTGCACCTCCGCT 62.537 63.158 14.63 0.00 0.00 5.52
1161 1170 1.140589 CTCCGCTCTCGTCAAGCAT 59.859 57.895 7.10 0.00 39.81 3.79
1312 1321 5.548056 GGTATTTCCTGGATCTGGGATTCTA 59.452 44.000 0.00 0.27 0.00 2.10
1327 1336 3.366374 GGATTCTAGTTTTGCTGCGCTTT 60.366 43.478 9.73 0.00 0.00 3.51
1399 1412 0.684153 CAATGGCCCAAATCTCCCGT 60.684 55.000 0.00 0.00 0.00 5.28
1414 1427 0.320247 CCCGTGCAGATGGATAGCTC 60.320 60.000 0.00 0.00 0.00 4.09
1421 1434 4.820716 GTGCAGATGGATAGCTCTTTCATT 59.179 41.667 0.00 0.00 0.00 2.57
1698 1711 1.508632 GTTCGTGCTTTCACTAGCCA 58.491 50.000 0.00 0.00 40.99 4.75
1855 1886 7.798596 ACTTTGTCTGCCATATTAGAATGAG 57.201 36.000 0.00 0.00 0.00 2.90
2100 2131 6.940298 AGTACCGATTGGATCAAGAAGAAAAA 59.060 34.615 5.81 0.00 39.21 1.94
2101 2132 6.840780 ACCGATTGGATCAAGAAGAAAAAT 57.159 33.333 5.81 0.00 39.21 1.82
2163 2194 3.584868 GACGAAGGTCACCGGGGTG 62.585 68.421 11.66 11.66 46.64 4.61
2326 2357 5.183228 AGGAACACGGTCATAATAGTTTGG 58.817 41.667 0.00 0.00 0.00 3.28
2376 2407 5.016051 TCTCTAGAAGGAACATGATGTGC 57.984 43.478 0.00 0.00 0.00 4.57
2377 2408 4.467438 TCTCTAGAAGGAACATGATGTGCA 59.533 41.667 5.81 0.00 0.00 4.57
2378 2409 5.129980 TCTCTAGAAGGAACATGATGTGCAT 59.870 40.000 5.81 0.00 37.85 3.96
2392 2423 7.585579 ATGATGTGCATGTGGTATGATAAAA 57.414 32.000 0.00 0.00 35.42 1.52
2393 2424 7.401955 TGATGTGCATGTGGTATGATAAAAA 57.598 32.000 0.00 0.00 0.00 1.94
2508 2539 8.804912 ATGATCTTTAAGCTTCTGTTTGATCT 57.195 30.769 0.00 0.00 31.88 2.75
2534 2565 3.411446 TGATCTGATGCGTTTCCACTTT 58.589 40.909 0.00 0.00 0.00 2.66
3231 3303 3.555168 CCGTAGTCAAAGGATATGAGGGC 60.555 52.174 0.00 0.00 0.00 5.19
3383 3455 2.164624 ACGAGGACGAGGAAAGAAGATG 59.835 50.000 0.00 0.00 42.66 2.90
3401 3473 5.743636 AGATGATCCTTCTATGCTTCTCC 57.256 43.478 0.00 0.00 0.00 3.71
3415 3487 3.012518 GCTTCTCCTTCATGCTTGCTTA 58.987 45.455 0.00 0.00 0.00 3.09
3713 3801 9.434420 TTTGCAAGAAAAAGATCTTCAAGAAAA 57.566 25.926 8.78 1.13 37.56 2.29
3714 3802 9.603921 TTGCAAGAAAAAGATCTTCAAGAAAAT 57.396 25.926 8.78 0.00 37.56 1.82
3715 3803 9.252962 TGCAAGAAAAAGATCTTCAAGAAAATC 57.747 29.630 8.78 0.00 37.56 2.17
3716 3804 9.252962 GCAAGAAAAAGATCTTCAAGAAAATCA 57.747 29.630 8.78 0.00 37.56 2.57
3718 3806 9.755804 AAGAAAAAGATCTTCAAGAAAATCACC 57.244 29.630 8.78 0.00 34.60 4.02
3719 3807 8.363390 AGAAAAAGATCTTCAAGAAAATCACCC 58.637 33.333 8.78 0.00 0.00 4.61
3720 3808 6.596309 AAAGATCTTCAAGAAAATCACCCC 57.404 37.500 8.78 0.00 0.00 4.95
3721 3809 4.265073 AGATCTTCAAGAAAATCACCCCG 58.735 43.478 0.00 0.00 0.00 5.73
3722 3810 3.502123 TCTTCAAGAAAATCACCCCGT 57.498 42.857 0.00 0.00 0.00 5.28
3723 3811 3.827722 TCTTCAAGAAAATCACCCCGTT 58.172 40.909 0.00 0.00 0.00 4.44
3724 3812 4.211920 TCTTCAAGAAAATCACCCCGTTT 58.788 39.130 0.00 0.00 0.00 3.60
3725 3813 4.037446 TCTTCAAGAAAATCACCCCGTTTG 59.963 41.667 0.00 0.00 0.00 2.93
3726 3814 3.292460 TCAAGAAAATCACCCCGTTTGT 58.708 40.909 0.00 0.00 0.00 2.83
3727 3815 3.702045 TCAAGAAAATCACCCCGTTTGTT 59.298 39.130 0.00 0.00 0.00 2.83
3728 3816 4.048504 CAAGAAAATCACCCCGTTTGTTC 58.951 43.478 0.00 0.00 0.00 3.18
3729 3817 3.292460 AGAAAATCACCCCGTTTGTTCA 58.708 40.909 0.00 0.00 0.00 3.18
3730 3818 3.067601 AGAAAATCACCCCGTTTGTTCAC 59.932 43.478 0.00 0.00 0.00 3.18
3731 3819 2.060050 AATCACCCCGTTTGTTCACA 57.940 45.000 0.00 0.00 0.00 3.58
3732 3820 1.314730 ATCACCCCGTTTGTTCACAC 58.685 50.000 0.00 0.00 0.00 3.82
3733 3821 0.035343 TCACCCCGTTTGTTCACACA 60.035 50.000 0.00 0.00 0.00 3.72
3734 3822 0.811915 CACCCCGTTTGTTCACACAA 59.188 50.000 0.00 0.00 41.39 3.33
3735 3823 0.812549 ACCCCGTTTGTTCACACAAC 59.187 50.000 0.00 0.00 42.87 3.32
3736 3824 0.248296 CCCCGTTTGTTCACACAACG 60.248 55.000 14.89 14.89 42.87 4.10
3737 3825 0.248296 CCCGTTTGTTCACACAACGG 60.248 55.000 24.44 24.44 46.87 4.44
3739 3827 2.748461 CGTTTGTTCACACAACGGAT 57.252 45.000 14.39 0.00 42.87 4.18
3740 3828 3.059634 CGTTTGTTCACACAACGGATT 57.940 42.857 14.39 0.00 42.87 3.01
3741 3829 3.430931 CGTTTGTTCACACAACGGATTT 58.569 40.909 14.39 0.00 42.87 2.17
3742 3830 3.239483 CGTTTGTTCACACAACGGATTTG 59.761 43.478 14.39 0.00 42.87 2.32
3743 3831 3.428746 TTGTTCACACAACGGATTTGG 57.571 42.857 0.00 0.00 38.03 3.28
3744 3832 2.644676 TGTTCACACAACGGATTTGGA 58.355 42.857 0.00 0.00 39.84 3.53
3745 3833 2.356382 TGTTCACACAACGGATTTGGAC 59.644 45.455 0.00 0.00 39.84 4.02
3746 3834 2.333688 TCACACAACGGATTTGGACA 57.666 45.000 0.00 0.00 39.84 4.02
3747 3835 2.644676 TCACACAACGGATTTGGACAA 58.355 42.857 0.00 0.00 39.84 3.18
3748 3836 3.218453 TCACACAACGGATTTGGACAAT 58.782 40.909 0.00 0.00 39.84 2.71
3749 3837 3.004210 TCACACAACGGATTTGGACAATG 59.996 43.478 0.00 0.00 39.84 2.82
3750 3838 2.955660 ACACAACGGATTTGGACAATGT 59.044 40.909 0.00 0.00 39.84 2.71
3751 3839 4.023622 CACACAACGGATTTGGACAATGTA 60.024 41.667 0.00 0.00 39.84 2.29
3752 3840 4.580995 ACACAACGGATTTGGACAATGTAA 59.419 37.500 0.00 0.00 39.84 2.41
3753 3841 4.915085 CACAACGGATTTGGACAATGTAAC 59.085 41.667 0.00 0.00 39.84 2.50
3754 3842 4.022676 ACAACGGATTTGGACAATGTAACC 60.023 41.667 0.00 0.00 39.84 2.85
3755 3843 3.757270 ACGGATTTGGACAATGTAACCA 58.243 40.909 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.732219 TGTTCACGAACGAAGTGTATGTC 59.268 43.478 5.51 0.00 45.00 3.06
1 2 3.708890 TGTTCACGAACGAAGTGTATGT 58.291 40.909 5.51 0.00 45.00 2.29
2 3 4.149922 ACATGTTCACGAACGAAGTGTATG 59.850 41.667 5.51 4.53 45.00 2.39
3 4 4.149922 CACATGTTCACGAACGAAGTGTAT 59.850 41.667 15.32 0.00 45.00 2.29
4 5 3.487942 CACATGTTCACGAACGAAGTGTA 59.512 43.478 15.32 0.00 45.00 2.90
5 6 2.284150 CACATGTTCACGAACGAAGTGT 59.716 45.455 15.32 10.44 45.00 3.55
6 7 2.348498 CCACATGTTCACGAACGAAGTG 60.348 50.000 16.06 16.06 45.00 3.16
8 9 1.398451 GCCACATGTTCACGAACGAAG 60.398 52.381 0.00 1.00 43.94 3.79
9 10 0.584396 GCCACATGTTCACGAACGAA 59.416 50.000 0.00 0.00 43.94 3.85
10 11 0.530870 TGCCACATGTTCACGAACGA 60.531 50.000 0.00 0.00 43.94 3.85
11 12 0.384230 GTGCCACATGTTCACGAACG 60.384 55.000 11.01 0.00 43.94 3.95
12 13 0.944386 AGTGCCACATGTTCACGAAC 59.056 50.000 17.45 2.89 41.50 3.95
13 14 1.333308 CAAGTGCCACATGTTCACGAA 59.667 47.619 17.45 0.00 35.97 3.85
14 15 0.943673 CAAGTGCCACATGTTCACGA 59.056 50.000 17.45 0.00 35.97 4.35
15 16 0.040157 CCAAGTGCCACATGTTCACG 60.040 55.000 17.45 8.34 35.97 4.35
16 17 0.314935 CCCAAGTGCCACATGTTCAC 59.685 55.000 16.35 16.35 0.00 3.18
17 18 0.184692 TCCCAAGTGCCACATGTTCA 59.815 50.000 0.00 0.00 0.00 3.18
18 19 0.883833 CTCCCAAGTGCCACATGTTC 59.116 55.000 0.00 0.00 0.00 3.18
19 20 0.478072 TCTCCCAAGTGCCACATGTT 59.522 50.000 0.00 0.00 0.00 2.71
20 21 0.037303 CTCTCCCAAGTGCCACATGT 59.963 55.000 0.00 0.00 0.00 3.21
21 22 0.037303 ACTCTCCCAAGTGCCACATG 59.963 55.000 0.00 0.00 0.00 3.21
22 23 0.773644 AACTCTCCCAAGTGCCACAT 59.226 50.000 0.00 0.00 0.00 3.21
23 24 0.108585 GAACTCTCCCAAGTGCCACA 59.891 55.000 0.00 0.00 0.00 4.17
24 25 0.951040 CGAACTCTCCCAAGTGCCAC 60.951 60.000 0.00 0.00 0.00 5.01
25 26 1.371183 CGAACTCTCCCAAGTGCCA 59.629 57.895 0.00 0.00 0.00 4.92
26 27 2.035442 GCGAACTCTCCCAAGTGCC 61.035 63.158 0.00 0.00 0.00 5.01
27 28 2.383527 CGCGAACTCTCCCAAGTGC 61.384 63.158 0.00 0.00 0.00 4.40
28 29 0.600255 AACGCGAACTCTCCCAAGTG 60.600 55.000 15.93 0.00 0.00 3.16
29 30 0.319641 GAACGCGAACTCTCCCAAGT 60.320 55.000 15.93 0.00 0.00 3.16
30 31 0.038159 AGAACGCGAACTCTCCCAAG 60.038 55.000 15.93 0.00 0.00 3.61
31 32 0.038526 GAGAACGCGAACTCTCCCAA 60.039 55.000 15.93 0.00 33.36 4.12
32 33 1.585006 GAGAACGCGAACTCTCCCA 59.415 57.895 15.93 0.00 33.36 4.37
33 34 4.480031 GAGAACGCGAACTCTCCC 57.520 61.111 15.93 0.00 33.36 4.30
35 36 2.726887 GTGGAGAACGCGAACTCTC 58.273 57.895 25.75 23.58 37.87 3.20
36 37 4.968197 GTGGAGAACGCGAACTCT 57.032 55.556 25.75 18.72 34.11 3.24
45 46 0.735287 GCGGTAGGAACGTGGAGAAC 60.735 60.000 0.00 0.00 0.00 3.01
46 47 0.896940 AGCGGTAGGAACGTGGAGAA 60.897 55.000 0.00 0.00 0.00 2.87
47 48 1.303888 AGCGGTAGGAACGTGGAGA 60.304 57.895 0.00 0.00 0.00 3.71
48 49 1.153823 CAGCGGTAGGAACGTGGAG 60.154 63.158 0.00 0.00 0.00 3.86
49 50 1.180456 TTCAGCGGTAGGAACGTGGA 61.180 55.000 0.00 0.00 0.00 4.02
50 51 1.012486 GTTCAGCGGTAGGAACGTGG 61.012 60.000 2.57 0.00 34.69 4.94
51 52 0.319211 TGTTCAGCGGTAGGAACGTG 60.319 55.000 11.67 0.00 44.85 4.49
52 53 0.038526 CTGTTCAGCGGTAGGAACGT 60.039 55.000 11.67 0.00 44.85 3.99
53 54 0.038526 ACTGTTCAGCGGTAGGAACG 60.039 55.000 11.67 9.41 44.85 3.95
54 55 2.067013 GAACTGTTCAGCGGTAGGAAC 58.933 52.381 15.34 10.04 42.82 3.62
55 56 1.689813 TGAACTGTTCAGCGGTAGGAA 59.310 47.619 18.69 0.00 35.19 3.36
56 57 1.000506 GTGAACTGTTCAGCGGTAGGA 59.999 52.381 22.61 0.00 41.01 2.94
57 58 1.429463 GTGAACTGTTCAGCGGTAGG 58.571 55.000 22.61 0.00 41.01 3.18
58 59 1.429463 GGTGAACTGTTCAGCGGTAG 58.571 55.000 29.70 0.00 46.56 3.18
59 60 3.599412 GGTGAACTGTTCAGCGGTA 57.401 52.632 29.70 4.63 46.56 4.02
60 61 4.456806 GGTGAACTGTTCAGCGGT 57.543 55.556 29.70 0.00 46.56 5.68
64 65 1.663695 AACACCGGTGAACTGTTCAG 58.336 50.000 40.21 13.91 41.01 3.02
65 66 2.983907 TAACACCGGTGAACTGTTCA 57.016 45.000 40.21 18.69 37.33 3.18
66 67 3.185797 GTCATAACACCGGTGAACTGTTC 59.814 47.826 40.21 22.16 30.76 3.18
67 68 3.135994 GTCATAACACCGGTGAACTGTT 58.864 45.455 40.21 24.86 32.85 3.16
68 69 2.549349 GGTCATAACACCGGTGAACTGT 60.549 50.000 40.21 18.84 0.00 3.55
69 70 2.073816 GGTCATAACACCGGTGAACTG 58.926 52.381 40.21 28.87 0.00 3.16
70 71 1.695242 TGGTCATAACACCGGTGAACT 59.305 47.619 40.21 24.49 39.62 3.01
71 72 2.172851 TGGTCATAACACCGGTGAAC 57.827 50.000 40.21 25.32 39.62 3.18
72 73 2.551287 CCTTGGTCATAACACCGGTGAA 60.551 50.000 40.21 26.66 39.62 3.18
73 74 1.002659 CCTTGGTCATAACACCGGTGA 59.997 52.381 40.21 20.46 39.62 4.02
74 75 1.448985 CCTTGGTCATAACACCGGTG 58.551 55.000 32.83 32.83 39.62 4.94
75 76 0.326927 CCCTTGGTCATAACACCGGT 59.673 55.000 0.00 0.00 39.62 5.28
76 77 0.616371 TCCCTTGGTCATAACACCGG 59.384 55.000 0.00 0.00 39.62 5.28
77 78 1.278127 AGTCCCTTGGTCATAACACCG 59.722 52.381 0.00 0.00 39.62 4.94
78 79 3.370209 GGTAGTCCCTTGGTCATAACACC 60.370 52.174 0.00 0.00 36.90 4.16
79 80 3.677976 CGGTAGTCCCTTGGTCATAACAC 60.678 52.174 0.00 0.00 0.00 3.32
80 81 2.498481 CGGTAGTCCCTTGGTCATAACA 59.502 50.000 0.00 0.00 0.00 2.41
81 82 2.762327 TCGGTAGTCCCTTGGTCATAAC 59.238 50.000 0.00 0.00 0.00 1.89
82 83 2.762327 GTCGGTAGTCCCTTGGTCATAA 59.238 50.000 0.00 0.00 0.00 1.90
83 84 2.381911 GTCGGTAGTCCCTTGGTCATA 58.618 52.381 0.00 0.00 0.00 2.15
84 85 1.192428 GTCGGTAGTCCCTTGGTCAT 58.808 55.000 0.00 0.00 0.00 3.06
85 86 0.901580 GGTCGGTAGTCCCTTGGTCA 60.902 60.000 0.00 0.00 0.00 4.02
86 87 0.614134 AGGTCGGTAGTCCCTTGGTC 60.614 60.000 0.00 0.00 0.00 4.02
87 88 0.178912 AAGGTCGGTAGTCCCTTGGT 60.179 55.000 0.00 0.00 37.21 3.67
88 89 1.755380 CTAAGGTCGGTAGTCCCTTGG 59.245 57.143 0.00 0.00 38.95 3.61
89 90 2.454538 ACTAAGGTCGGTAGTCCCTTG 58.545 52.381 0.00 0.00 38.95 3.61
90 91 2.915657 ACTAAGGTCGGTAGTCCCTT 57.084 50.000 0.00 0.00 41.38 3.95
91 92 2.915657 AACTAAGGTCGGTAGTCCCT 57.084 50.000 0.00 0.00 31.32 4.20
92 93 3.674410 CGAAAACTAAGGTCGGTAGTCCC 60.674 52.174 0.00 0.00 31.32 4.46
93 94 3.191371 TCGAAAACTAAGGTCGGTAGTCC 59.809 47.826 0.00 0.00 35.51 3.85
94 95 4.410448 CTCGAAAACTAAGGTCGGTAGTC 58.590 47.826 0.00 0.00 35.51 2.59
95 96 3.192212 CCTCGAAAACTAAGGTCGGTAGT 59.808 47.826 0.00 0.00 35.51 2.73
96 97 3.441572 TCCTCGAAAACTAAGGTCGGTAG 59.558 47.826 0.00 0.00 35.51 3.18
97 98 3.420893 TCCTCGAAAACTAAGGTCGGTA 58.579 45.455 0.00 0.00 35.51 4.02
98 99 2.230750 CTCCTCGAAAACTAAGGTCGGT 59.769 50.000 0.00 0.00 35.51 4.69
99 100 2.230750 ACTCCTCGAAAACTAAGGTCGG 59.769 50.000 0.00 0.00 35.51 4.79
100 101 3.572604 ACTCCTCGAAAACTAAGGTCG 57.427 47.619 0.00 0.00 36.12 4.79
101 102 4.385146 CGAAACTCCTCGAAAACTAAGGTC 59.615 45.833 0.00 0.00 41.44 3.85
102 103 4.304939 CGAAACTCCTCGAAAACTAAGGT 58.695 43.478 0.00 0.00 41.44 3.50
103 104 3.678548 CCGAAACTCCTCGAAAACTAAGG 59.321 47.826 0.00 0.00 41.44 2.69
104 105 4.553323 TCCGAAACTCCTCGAAAACTAAG 58.447 43.478 0.00 0.00 41.44 2.18
105 106 4.589216 TCCGAAACTCCTCGAAAACTAA 57.411 40.909 0.00 0.00 41.44 2.24
106 107 4.381292 GGATCCGAAACTCCTCGAAAACTA 60.381 45.833 0.00 0.00 41.44 2.24
107 108 3.586892 GATCCGAAACTCCTCGAAAACT 58.413 45.455 0.00 0.00 41.44 2.66
108 109 2.671888 GGATCCGAAACTCCTCGAAAAC 59.328 50.000 0.00 0.00 41.44 2.43
109 110 2.968675 GGATCCGAAACTCCTCGAAAA 58.031 47.619 0.00 0.00 41.44 2.29
110 111 2.667473 GGATCCGAAACTCCTCGAAA 57.333 50.000 0.00 0.00 41.44 3.46
357 358 4.105057 AGGGAGAGAGAGATATACAACGGT 59.895 45.833 0.00 0.00 0.00 4.83
358 359 4.658063 AGGGAGAGAGAGATATACAACGG 58.342 47.826 0.00 0.00 0.00 4.44
359 360 5.556915 AGAGGGAGAGAGAGATATACAACG 58.443 45.833 0.00 0.00 0.00 4.10
360 361 5.642063 CGAGAGGGAGAGAGAGATATACAAC 59.358 48.000 0.00 0.00 0.00 3.32
361 362 5.308497 ACGAGAGGGAGAGAGAGATATACAA 59.692 44.000 0.00 0.00 0.00 2.41
362 363 4.841813 ACGAGAGGGAGAGAGAGATATACA 59.158 45.833 0.00 0.00 0.00 2.29
363 364 5.416271 ACGAGAGGGAGAGAGAGATATAC 57.584 47.826 0.00 0.00 0.00 1.47
364 365 9.442062 AATATACGAGAGGGAGAGAGAGATATA 57.558 37.037 0.00 0.00 0.00 0.86
365 366 7.931015 ATATACGAGAGGGAGAGAGAGATAT 57.069 40.000 0.00 0.00 0.00 1.63
366 367 7.743116 AATATACGAGAGGGAGAGAGAGATA 57.257 40.000 0.00 0.00 0.00 1.98
367 368 6.636454 AATATACGAGAGGGAGAGAGAGAT 57.364 41.667 0.00 0.00 0.00 2.75
368 369 6.442541 AAATATACGAGAGGGAGAGAGAGA 57.557 41.667 0.00 0.00 0.00 3.10
369 370 9.321562 GTATAAATATACGAGAGGGAGAGAGAG 57.678 40.741 0.00 0.00 30.42 3.20
370 371 8.823794 TGTATAAATATACGAGAGGGAGAGAGA 58.176 37.037 6.20 0.00 41.04 3.10
371 372 9.621629 ATGTATAAATATACGAGAGGGAGAGAG 57.378 37.037 6.20 0.00 41.04 3.20
372 373 9.616156 GATGTATAAATATACGAGAGGGAGAGA 57.384 37.037 6.20 0.00 41.04 3.10
373 374 9.621629 AGATGTATAAATATACGAGAGGGAGAG 57.378 37.037 6.20 0.00 41.04 3.20
374 375 9.976776 AAGATGTATAAATATACGAGAGGGAGA 57.023 33.333 6.20 0.00 41.04 3.71
376 377 8.967918 CCAAGATGTATAAATATACGAGAGGGA 58.032 37.037 6.20 0.00 41.04 4.20
377 378 8.967918 TCCAAGATGTATAAATATACGAGAGGG 58.032 37.037 6.20 5.54 41.04 4.30
392 393 9.440761 AACCTCTACTTATCTTCCAAGATGTAT 57.559 33.333 11.44 0.60 45.01 2.29
393 394 8.696374 CAACCTCTACTTATCTTCCAAGATGTA 58.304 37.037 11.44 5.90 45.01 2.29
394 395 7.365117 CCAACCTCTACTTATCTTCCAAGATGT 60.365 40.741 11.44 5.13 45.01 3.06
395 396 6.989169 CCAACCTCTACTTATCTTCCAAGATG 59.011 42.308 11.44 0.00 45.01 2.90
396 397 6.674419 ACCAACCTCTACTTATCTTCCAAGAT 59.326 38.462 7.01 7.01 46.85 2.40
397 398 6.023603 ACCAACCTCTACTTATCTTCCAAGA 58.976 40.000 0.00 0.00 39.78 3.02
398 399 6.155393 AGACCAACCTCTACTTATCTTCCAAG 59.845 42.308 0.00 0.00 0.00 3.61
399 400 6.023603 AGACCAACCTCTACTTATCTTCCAA 58.976 40.000 0.00 0.00 0.00 3.53
400 401 5.590818 AGACCAACCTCTACTTATCTTCCA 58.409 41.667 0.00 0.00 0.00 3.53
401 402 6.040729 GGTAGACCAACCTCTACTTATCTTCC 59.959 46.154 6.37 0.00 41.68 3.46
402 403 6.606395 TGGTAGACCAACCTCTACTTATCTTC 59.394 42.308 0.00 0.00 44.35 2.87
403 404 6.500336 TGGTAGACCAACCTCTACTTATCTT 58.500 40.000 0.00 0.00 44.35 2.40
404 405 6.088541 TGGTAGACCAACCTCTACTTATCT 57.911 41.667 0.00 0.00 44.35 1.98
408 409 9.624645 AGGTACATGGTAGACCAACCTCTACTT 62.625 44.444 15.14 2.23 46.56 2.24
409 410 8.243093 AGGTACATGGTAGACCAACCTCTACT 62.243 46.154 15.14 2.90 46.56 2.57
410 411 6.102443 AGGTACATGGTAGACCAACCTCTAC 61.102 48.000 15.14 6.81 46.56 2.59
411 412 4.016851 AGGTACATGGTAGACCAACCTCTA 60.017 45.833 15.14 0.00 46.56 2.43
412 413 3.246021 AGGTACATGGTAGACCAACCTCT 60.246 47.826 15.14 4.18 46.56 3.69
413 414 3.105283 AGGTACATGGTAGACCAACCTC 58.895 50.000 15.14 4.04 46.56 3.85
419 420 7.123697 TGCACATATATAGGTACATGGTAGACC 59.876 40.741 0.00 0.00 0.00 3.85
420 421 8.063200 TGCACATATATAGGTACATGGTAGAC 57.937 38.462 0.00 0.00 0.00 2.59
421 422 8.838649 ATGCACATATATAGGTACATGGTAGA 57.161 34.615 11.50 0.00 0.00 2.59
424 425 8.821817 TGTAATGCACATATATAGGTACATGGT 58.178 33.333 12.72 3.01 30.04 3.55
425 426 9.098355 GTGTAATGCACATATATAGGTACATGG 57.902 37.037 12.72 0.00 46.91 3.66
442 443 6.487689 TTCATTAATCGTGTGTGTAATGCA 57.512 33.333 0.00 0.00 35.07 3.96
443 444 7.969387 AATTCATTAATCGTGTGTGTAATGC 57.031 32.000 0.00 0.00 35.07 3.56
446 447 9.384764 TCCATAATTCATTAATCGTGTGTGTAA 57.615 29.630 0.00 0.00 0.00 2.41
447 448 8.950208 TCCATAATTCATTAATCGTGTGTGTA 57.050 30.769 0.00 0.00 0.00 2.90
448 449 7.857734 TCCATAATTCATTAATCGTGTGTGT 57.142 32.000 0.00 0.00 0.00 3.72
449 450 7.324375 GCATCCATAATTCATTAATCGTGTGTG 59.676 37.037 0.00 0.00 0.00 3.82
450 451 7.013178 TGCATCCATAATTCATTAATCGTGTGT 59.987 33.333 0.00 0.00 0.00 3.72
451 452 7.324375 GTGCATCCATAATTCATTAATCGTGTG 59.676 37.037 0.00 0.00 0.00 3.82
452 453 7.013178 TGTGCATCCATAATTCATTAATCGTGT 59.987 33.333 0.00 0.00 0.00 4.49
453 454 7.324375 GTGTGCATCCATAATTCATTAATCGTG 59.676 37.037 0.00 0.00 0.00 4.35
454 455 7.013178 TGTGTGCATCCATAATTCATTAATCGT 59.987 33.333 0.00 0.00 0.00 3.73
455 456 7.361894 TGTGTGCATCCATAATTCATTAATCG 58.638 34.615 0.00 0.00 0.00 3.34
456 457 9.701098 ATTGTGTGCATCCATAATTCATTAATC 57.299 29.630 0.00 0.00 0.00 1.75
457 458 9.701098 GATTGTGTGCATCCATAATTCATTAAT 57.299 29.630 0.00 0.00 0.00 1.40
458 459 8.143193 GGATTGTGTGCATCCATAATTCATTAA 58.857 33.333 0.00 0.00 34.69 1.40
459 460 7.255906 GGGATTGTGTGCATCCATAATTCATTA 60.256 37.037 5.68 0.00 36.22 1.90
460 461 6.463331 GGGATTGTGTGCATCCATAATTCATT 60.463 38.462 5.68 0.00 36.22 2.57
461 462 5.011329 GGGATTGTGTGCATCCATAATTCAT 59.989 40.000 5.68 0.00 36.22 2.57
462 463 4.341806 GGGATTGTGTGCATCCATAATTCA 59.658 41.667 5.68 0.00 36.22 2.57
463 464 4.586001 AGGGATTGTGTGCATCCATAATTC 59.414 41.667 5.68 1.76 36.22 2.17
464 465 4.549668 AGGGATTGTGTGCATCCATAATT 58.450 39.130 5.68 0.00 36.22 1.40
465 466 4.188937 AGGGATTGTGTGCATCCATAAT 57.811 40.909 5.68 2.67 36.22 1.28
466 467 3.668141 AGGGATTGTGTGCATCCATAA 57.332 42.857 5.68 0.00 36.22 1.90
467 468 3.202818 AGAAGGGATTGTGTGCATCCATA 59.797 43.478 5.68 0.00 36.22 2.74
468 469 2.024655 AGAAGGGATTGTGTGCATCCAT 60.025 45.455 5.68 0.00 36.22 3.41
469 470 1.355381 AGAAGGGATTGTGTGCATCCA 59.645 47.619 5.68 0.00 36.22 3.41
470 471 2.134789 AGAAGGGATTGTGTGCATCC 57.865 50.000 0.00 0.00 0.00 3.51
471 472 3.119352 GGAAAGAAGGGATTGTGTGCATC 60.119 47.826 0.00 0.00 0.00 3.91
472 473 2.827921 GGAAAGAAGGGATTGTGTGCAT 59.172 45.455 0.00 0.00 0.00 3.96
473 474 2.238521 GGAAAGAAGGGATTGTGTGCA 58.761 47.619 0.00 0.00 0.00 4.57
474 475 1.546029 GGGAAAGAAGGGATTGTGTGC 59.454 52.381 0.00 0.00 0.00 4.57
475 476 1.812571 CGGGAAAGAAGGGATTGTGTG 59.187 52.381 0.00 0.00 0.00 3.82
476 477 1.886655 GCGGGAAAGAAGGGATTGTGT 60.887 52.381 0.00 0.00 0.00 3.72
477 478 0.811281 GCGGGAAAGAAGGGATTGTG 59.189 55.000 0.00 0.00 0.00 3.33
478 479 0.404040 TGCGGGAAAGAAGGGATTGT 59.596 50.000 0.00 0.00 0.00 2.71
479 480 0.811281 GTGCGGGAAAGAAGGGATTG 59.189 55.000 0.00 0.00 0.00 2.67
480 481 0.676782 CGTGCGGGAAAGAAGGGATT 60.677 55.000 0.00 0.00 0.00 3.01
481 482 1.078426 CGTGCGGGAAAGAAGGGAT 60.078 57.895 0.00 0.00 0.00 3.85
482 483 2.345991 CGTGCGGGAAAGAAGGGA 59.654 61.111 0.00 0.00 0.00 4.20
483 484 3.431725 GCGTGCGGGAAAGAAGGG 61.432 66.667 0.00 0.00 0.00 3.95
484 485 2.040544 ATGCGTGCGGGAAAGAAGG 61.041 57.895 0.00 0.00 0.00 3.46
485 486 1.135315 CATGCGTGCGGGAAAGAAG 59.865 57.895 0.00 0.00 0.00 2.85
486 487 1.169661 AACATGCGTGCGGGAAAGAA 61.170 50.000 5.64 0.00 0.00 2.52
487 488 0.320858 TAACATGCGTGCGGGAAAGA 60.321 50.000 5.64 0.00 0.00 2.52
488 489 0.179200 GTAACATGCGTGCGGGAAAG 60.179 55.000 5.64 0.00 0.00 2.62
489 490 0.604243 AGTAACATGCGTGCGGGAAA 60.604 50.000 5.64 0.00 0.00 3.13
490 491 0.604243 AAGTAACATGCGTGCGGGAA 60.604 50.000 5.64 0.00 0.00 3.97
491 492 0.604243 AAAGTAACATGCGTGCGGGA 60.604 50.000 5.64 0.00 0.00 5.14
492 493 0.454285 CAAAGTAACATGCGTGCGGG 60.454 55.000 5.64 0.00 0.00 6.13
493 494 0.515127 TCAAAGTAACATGCGTGCGG 59.485 50.000 5.64 0.00 0.00 5.69
494 495 1.969256 GTTCAAAGTAACATGCGTGCG 59.031 47.619 5.64 0.00 0.00 5.34
495 496 1.969256 CGTTCAAAGTAACATGCGTGC 59.031 47.619 5.64 0.00 0.00 5.34
496 497 1.969256 GCGTTCAAAGTAACATGCGTG 59.031 47.619 3.82 3.82 0.00 5.34
497 498 1.069500 GGCGTTCAAAGTAACATGCGT 60.069 47.619 0.00 0.00 0.00 5.24
498 499 1.069568 TGGCGTTCAAAGTAACATGCG 60.070 47.619 0.00 0.00 0.00 4.73
499 500 2.584791 CTGGCGTTCAAAGTAACATGC 58.415 47.619 0.00 0.00 0.00 4.06
517 518 1.267806 GGCGGATAATCATGGTTGCTG 59.732 52.381 0.08 0.00 0.00 4.41
654 663 6.340522 GGCATGTGTAGGCAAAAATATCTTT 58.659 36.000 0.00 0.00 34.74 2.52
812 821 2.822643 ATCTGCGGGGTGAAGGGAGA 62.823 60.000 0.00 0.00 32.63 3.71
994 1003 2.659063 CGAGGCCCACCATGACAGA 61.659 63.158 0.00 0.00 39.06 3.41
998 1007 2.063979 CCTACGAGGCCCACCATGA 61.064 63.158 0.00 0.00 39.06 3.07
1149 1158 2.483714 GGCCTTGATATGCTTGACGAGA 60.484 50.000 0.00 0.00 0.00 4.04
1161 1170 2.041430 TGGACGGGGGCCTTGATA 59.959 61.111 0.84 0.00 0.00 2.15
1327 1336 0.871722 CCGAACAAGATCGCCAAACA 59.128 50.000 0.00 0.00 41.40 2.83
1399 1412 4.701651 ATGAAAGAGCTATCCATCTGCA 57.298 40.909 0.00 0.00 0.00 4.41
1414 1427 0.238289 AACAGTCCGCGCAATGAAAG 59.762 50.000 3.71 0.00 0.00 2.62
1421 1434 0.882484 TGAATCAAACAGTCCGCGCA 60.882 50.000 8.75 0.00 0.00 6.09
1698 1711 7.762159 GCACTAGTAAGAAGTAGAGCAAGAAAT 59.238 37.037 0.00 0.00 41.93 2.17
1828 1859 9.851686 TCATTCTAATATGGCAGACAAAGTTAT 57.148 29.630 0.00 0.00 0.00 1.89
1855 1886 0.033109 AATTCTGTAAGGGGGCTGGC 60.033 55.000 0.00 0.00 0.00 4.85
2045 2076 0.032813 ATTGAGGGGTGGCCATTCTG 60.033 55.000 9.72 0.00 0.00 3.02
2100 2131 6.826727 TCCAAGACCCCTCATATAATAGGAT 58.173 40.000 5.50 0.00 34.58 3.24
2101 2132 6.241223 TCCAAGACCCCTCATATAATAGGA 57.759 41.667 5.50 0.00 34.58 2.94
2252 2283 2.638480 AACTGCAGGACAAGCACTTA 57.362 45.000 19.93 0.00 37.02 2.24
2326 2357 3.952535 ACAACGCAAGAAAATCACACTC 58.047 40.909 0.00 0.00 43.62 3.51
2399 2430 3.057104 CAGTGAAACCACATGCACATCAT 60.057 43.478 0.00 0.00 37.80 2.45
2400 2431 2.293955 CAGTGAAACCACATGCACATCA 59.706 45.455 0.00 0.00 37.80 3.07
2401 2432 2.294233 ACAGTGAAACCACATGCACATC 59.706 45.455 0.00 0.00 37.80 3.06
2417 2448 4.756642 TCTTGCAAGGTTCAAGATACAGTG 59.243 41.667 25.73 0.00 43.34 3.66
2508 2539 5.069119 AGTGGAAACGCATCAGATCAGTATA 59.931 40.000 0.00 0.00 45.56 1.47
2534 2565 8.539544 TGTTATGATGGATGAGTAGTTCTGAAA 58.460 33.333 0.00 0.00 0.00 2.69
3231 3303 5.868801 ACCAAAAATTGCTGAAACGGATATG 59.131 36.000 0.00 0.00 0.00 1.78
3383 3455 5.543507 TGAAGGAGAAGCATAGAAGGATC 57.456 43.478 0.00 0.00 0.00 3.36
3415 3487 5.709164 ACTTCAAATCAATGTGAGCTTAGCT 59.291 36.000 6.37 6.37 43.88 3.32
3420 3492 6.183360 TGTTTGACTTCAAATCAATGTGAGCT 60.183 34.615 7.63 0.00 46.12 4.09
3500 3587 3.199727 TGCCTTGGCTTATCTACACATGA 59.800 43.478 13.18 0.00 0.00 3.07
3574 3662 4.519540 TTTGCCCAGCATAGACTTTTTC 57.480 40.909 0.00 0.00 38.76 2.29
3713 3801 1.314730 GTGTGAACAAACGGGGTGAT 58.685 50.000 0.00 0.00 0.00 3.06
3714 3802 0.035343 TGTGTGAACAAACGGGGTGA 60.035 50.000 0.00 0.00 0.00 4.02
3715 3803 0.811915 TTGTGTGAACAAACGGGGTG 59.188 50.000 0.00 0.00 0.00 4.61
3716 3804 0.812549 GTTGTGTGAACAAACGGGGT 59.187 50.000 0.00 0.00 0.00 4.95
3717 3805 0.248296 CGTTGTGTGAACAAACGGGG 60.248 55.000 16.28 0.00 0.00 5.73
3718 3806 0.248296 CCGTTGTGTGAACAAACGGG 60.248 55.000 25.56 15.62 38.90 5.28
3719 3807 0.727970 TCCGTTGTGTGAACAAACGG 59.272 50.000 26.42 26.42 41.26 4.44
3720 3808 2.748461 ATCCGTTGTGTGAACAAACG 57.252 45.000 16.75 16.75 0.00 3.60
3721 3809 3.549873 CCAAATCCGTTGTGTGAACAAAC 59.450 43.478 0.00 0.00 35.23 2.93
3722 3810 3.444034 TCCAAATCCGTTGTGTGAACAAA 59.556 39.130 0.00 0.00 35.23 2.83
3723 3811 3.017442 TCCAAATCCGTTGTGTGAACAA 58.983 40.909 0.00 0.00 35.23 2.83
3724 3812 2.356382 GTCCAAATCCGTTGTGTGAACA 59.644 45.455 0.00 0.00 35.23 3.18
3725 3813 2.356382 TGTCCAAATCCGTTGTGTGAAC 59.644 45.455 0.00 0.00 35.23 3.18
3726 3814 2.644676 TGTCCAAATCCGTTGTGTGAA 58.355 42.857 0.00 0.00 35.23 3.18
3727 3815 2.333688 TGTCCAAATCCGTTGTGTGA 57.666 45.000 0.00 0.00 35.23 3.58
3728 3816 3.243367 ACATTGTCCAAATCCGTTGTGTG 60.243 43.478 0.00 0.00 35.23 3.82
3729 3817 2.955660 ACATTGTCCAAATCCGTTGTGT 59.044 40.909 0.00 0.00 35.23 3.72
3730 3818 3.641437 ACATTGTCCAAATCCGTTGTG 57.359 42.857 0.00 0.00 35.23 3.33
3731 3819 4.022676 GGTTACATTGTCCAAATCCGTTGT 60.023 41.667 0.00 0.00 35.23 3.32
3732 3820 4.022762 TGGTTACATTGTCCAAATCCGTTG 60.023 41.667 0.00 0.00 36.94 4.10
3733 3821 4.145807 TGGTTACATTGTCCAAATCCGTT 58.854 39.130 0.00 0.00 0.00 4.44
3734 3822 3.757270 TGGTTACATTGTCCAAATCCGT 58.243 40.909 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.