Multiple sequence alignment - TraesCS2A01G047800

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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 TraesCS2A01G047800 chr2A 100.000 3773 0 0 576 4348 18544199 18547971 0.000000e+00 6968.0
1 TraesCS2A01G047800 chr2A 84.254 2445 303 37 996 3398 18424978 18422574 0.000000e+00 2307.0
2 TraesCS2A01G047800 chr2A 91.823 905 44 11 3445 4348 266206171 266205296 0.000000e+00 1234.0
3 TraesCS2A01G047800 chr2A 100.000 186 0 0 1 186 18543624 18543809 1.160000e-90 344.0
4 TraesCS2A01G047800 chr2D 96.413 2899 72 6 576 3446 16765696 16762802 0.000000e+00 4748.0
5 TraesCS2A01G047800 chr2D 85.086 2454 291 41 996 3398 17011034 17013463 0.000000e+00 2435.0
6 TraesCS2A01G047800 chr2D 100.000 30 0 0 3445 3474 607748499 607748528 6.070000e-04 56.5
7 TraesCS2A01G047800 chr6D 85.620 2427 266 37 992 3353 27056847 27059255 0.000000e+00 2471.0
8 TraesCS2A01G047800 chr6D 79.287 869 125 26 3446 4309 16194971 16194153 1.370000e-154 556.0
9 TraesCS2A01G047800 chr6A 85.265 2450 280 47 992 3378 28410480 28412911 0.000000e+00 2449.0
10 TraesCS2A01G047800 chr2B 84.609 2456 302 38 996 3398 28883108 28885540 0.000000e+00 2372.0
11 TraesCS2A01G047800 chr2B 90.909 66 4 1 787 852 28753660 28753597 2.150000e-13 87.9
12 TraesCS2A01G047800 chr2B 93.750 48 3 0 1451 1498 28747947 28747900 6.030000e-09 73.1
13 TraesCS2A01G047800 chr6B 84.675 2447 290 37 1001 3377 49437836 49435405 0.000000e+00 2362.0
14 TraesCS2A01G047800 chr6B 84.792 2433 282 38 992 3353 49733987 49736402 0.000000e+00 2362.0
15 TraesCS2A01G047800 chr6B 86.931 1691 205 12 1540 3216 49306023 49307711 0.000000e+00 1884.0
16 TraesCS2A01G047800 chr6B 85.934 1301 155 13 2104 3377 49537617 49538916 0.000000e+00 1363.0
17 TraesCS2A01G047800 chr1D 95.916 906 28 4 3443 4345 188346356 188347255 0.000000e+00 1459.0
18 TraesCS2A01G047800 chr1D 92.513 187 8 1 3446 3632 184305694 184305514 3.330000e-66 263.0
19 TraesCS2A01G047800 chr1D 78.102 137 19 7 1108 1237 55428348 55428216 4.660000e-10 76.8
20 TraesCS2A01G047800 chr1D 86.567 67 6 2 1154 1220 55424623 55424560 2.170000e-08 71.3
21 TraesCS2A01G047800 chr3B 92.897 901 50 6 3446 4345 762974533 762975420 0.000000e+00 1297.0
22 TraesCS2A01G047800 chr3B 85.526 76 8 1 1124 1196 819507426 819507351 4.660000e-10 76.8
23 TraesCS2A01G047800 chr7B 91.790 877 55 7 3446 4321 749530649 749529789 0.000000e+00 1205.0
24 TraesCS2A01G047800 chr7B 100.000 30 0 0 3446 3475 379726034 379726063 6.070000e-04 56.5
25 TraesCS2A01G047800 chr5A 90.909 902 51 12 3446 4345 421864704 421865576 0.000000e+00 1182.0
26 TraesCS2A01G047800 chr3A 89.983 589 47 4 3446 4032 737803247 737803825 0.000000e+00 750.0
27 TraesCS2A01G047800 chr3A 100.000 32 0 0 3446 3477 628994183 628994214 4.700000e-05 60.2
28 TraesCS2A01G047800 chr3A 96.970 33 1 0 1153 1185 742240411 742240379 6.070000e-04 56.5
29 TraesCS2A01G047800 chr1B 79.078 846 122 27 3446 4287 12422284 12423078 8.280000e-147 531.0
30 TraesCS2A01G047800 chr1A 80.753 717 104 13 3595 4309 575457583 575458267 2.980000e-146 529.0
31 TraesCS2A01G047800 chr1A 86.567 67 6 2 1154 1220 54019049 54018986 2.170000e-08 71.3
32 TraesCS2A01G047800 chr3D 80.641 718 104 15 3595 4309 587654071 587654756 1.390000e-144 523.0
33 TraesCS2A01G047800 chr3D 85.333 75 8 1 1125 1196 608968354 608968280 1.680000e-09 75.0
34 TraesCS2A01G047800 chr4A 91.729 133 11 0 13 145 465224234 465224102 7.430000e-43 185.0
35 TraesCS2A01G047800 chr4A 100.000 32 0 0 3446 3477 659188169 659188138 4.700000e-05 60.2
36 TraesCS2A01G047800 chr5B 100.000 31 0 0 3444 3474 646245814 646245844 1.690000e-04 58.4


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 TraesCS2A01G047800 chr2A 18543624 18547971 4347 False 3656 6968 100.000 1 4348 2 chr2A.!!$F1 4347
1 TraesCS2A01G047800 chr2A 18422574 18424978 2404 True 2307 2307 84.254 996 3398 1 chr2A.!!$R1 2402
2 TraesCS2A01G047800 chr2A 266205296 266206171 875 True 1234 1234 91.823 3445 4348 1 chr2A.!!$R2 903
3 TraesCS2A01G047800 chr2D 16762802 16765696 2894 True 4748 4748 96.413 576 3446 1 chr2D.!!$R1 2870
4 TraesCS2A01G047800 chr2D 17011034 17013463 2429 False 2435 2435 85.086 996 3398 1 chr2D.!!$F1 2402
5 TraesCS2A01G047800 chr6D 27056847 27059255 2408 False 2471 2471 85.620 992 3353 1 chr6D.!!$F1 2361
6 TraesCS2A01G047800 chr6D 16194153 16194971 818 True 556 556 79.287 3446 4309 1 chr6D.!!$R1 863
7 TraesCS2A01G047800 chr6A 28410480 28412911 2431 False 2449 2449 85.265 992 3378 1 chr6A.!!$F1 2386
8 TraesCS2A01G047800 chr2B 28883108 28885540 2432 False 2372 2372 84.609 996 3398 1 chr2B.!!$F1 2402
9 TraesCS2A01G047800 chr6B 49435405 49437836 2431 True 2362 2362 84.675 1001 3377 1 chr6B.!!$R1 2376
10 TraesCS2A01G047800 chr6B 49733987 49736402 2415 False 2362 2362 84.792 992 3353 1 chr6B.!!$F3 2361
11 TraesCS2A01G047800 chr6B 49306023 49307711 1688 False 1884 1884 86.931 1540 3216 1 chr6B.!!$F1 1676
12 TraesCS2A01G047800 chr6B 49537617 49538916 1299 False 1363 1363 85.934 2104 3377 1 chr6B.!!$F2 1273
13 TraesCS2A01G047800 chr1D 188346356 188347255 899 False 1459 1459 95.916 3443 4345 1 chr1D.!!$F1 902
14 TraesCS2A01G047800 chr3B 762974533 762975420 887 False 1297 1297 92.897 3446 4345 1 chr3B.!!$F1 899
15 TraesCS2A01G047800 chr7B 749529789 749530649 860 True 1205 1205 91.790 3446 4321 1 chr7B.!!$R1 875
16 TraesCS2A01G047800 chr5A 421864704 421865576 872 False 1182 1182 90.909 3446 4345 1 chr5A.!!$F1 899
17 TraesCS2A01G047800 chr3A 737803247 737803825 578 False 750 750 89.983 3446 4032 1 chr3A.!!$F2 586
18 TraesCS2A01G047800 chr1B 12422284 12423078 794 False 531 531 79.078 3446 4287 1 chr1B.!!$F1 841
19 TraesCS2A01G047800 chr1A 575457583 575458267 684 False 529 529 80.753 3595 4309 1 chr1A.!!$F1 714
20 TraesCS2A01G047800 chr3D 587654071 587654756 685 False 523 523 80.641 3595 4309 1 chr3D.!!$F1 714

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
51 52 0.593128 AGCGCAATCAACGAAAAGCT 59.407 45.0 11.47 0.0 0.0 3.74 F
928 937 0.844661 TGTAGGTTGTGGGGGCTGAT 60.845 55.0 0.00 0.0 0.0 2.90 F
1503 1533 1.102154 CCACCAACAACAAGCTGACA 58.898 50.0 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1711 0.482887 CCCTCAAACCAACCCCTCTT 59.517 55.000 0.00 0.00 0.0 2.85 R
1755 1812 1.002134 CACCGGCTTGGAATCCACT 60.002 57.895 0.00 0.00 42.0 4.00 R
3418 3524 1.560611 AGTCGGTAGAGCTCTAGTGGT 59.439 52.381 23.87 5.31 0.0 4.16 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
22 23 5.902613 ATCTGGTTGTGGTTGTATGATTG 57.097 39.130 0.00 0.00 0.00 2.67
23 24 4.724399 TCTGGTTGTGGTTGTATGATTGT 58.276 39.130 0.00 0.00 0.00 2.71
24 25 5.870706 TCTGGTTGTGGTTGTATGATTGTA 58.129 37.500 0.00 0.00 0.00 2.41
25 26 6.480763 TCTGGTTGTGGTTGTATGATTGTAT 58.519 36.000 0.00 0.00 0.00 2.29
26 27 6.374053 TCTGGTTGTGGTTGTATGATTGTATG 59.626 38.462 0.00 0.00 0.00 2.39
27 28 6.007076 TGGTTGTGGTTGTATGATTGTATGT 58.993 36.000 0.00 0.00 0.00 2.29
28 29 6.491745 TGGTTGTGGTTGTATGATTGTATGTT 59.508 34.615 0.00 0.00 0.00 2.71
29 30 7.014711 TGGTTGTGGTTGTATGATTGTATGTTT 59.985 33.333 0.00 0.00 0.00 2.83
30 31 7.540745 GGTTGTGGTTGTATGATTGTATGTTTC 59.459 37.037 0.00 0.00 0.00 2.78
31 32 7.994425 TGTGGTTGTATGATTGTATGTTTCT 57.006 32.000 0.00 0.00 0.00 2.52
32 33 9.508642 TTGTGGTTGTATGATTGTATGTTTCTA 57.491 29.630 0.00 0.00 0.00 2.10
33 34 9.161629 TGTGGTTGTATGATTGTATGTTTCTAG 57.838 33.333 0.00 0.00 0.00 2.43
34 35 8.122952 GTGGTTGTATGATTGTATGTTTCTAGC 58.877 37.037 0.00 0.00 0.00 3.42
35 36 7.011016 TGGTTGTATGATTGTATGTTTCTAGCG 59.989 37.037 0.00 0.00 0.00 4.26
36 37 6.525121 TGTATGATTGTATGTTTCTAGCGC 57.475 37.500 0.00 0.00 0.00 5.92
37 38 6.045955 TGTATGATTGTATGTTTCTAGCGCA 58.954 36.000 11.47 0.00 0.00 6.09
38 39 6.536941 TGTATGATTGTATGTTTCTAGCGCAA 59.463 34.615 11.47 0.00 0.00 4.85
39 40 6.624352 ATGATTGTATGTTTCTAGCGCAAT 57.376 33.333 11.47 0.00 0.00 3.56
40 41 6.048073 TGATTGTATGTTTCTAGCGCAATC 57.952 37.500 11.47 5.95 40.32 2.67
41 42 5.584251 TGATTGTATGTTTCTAGCGCAATCA 59.416 36.000 11.47 8.71 44.40 2.57
42 43 5.871465 TTGTATGTTTCTAGCGCAATCAA 57.129 34.783 11.47 0.00 0.00 2.57
43 44 5.216566 TGTATGTTTCTAGCGCAATCAAC 57.783 39.130 11.47 7.90 0.00 3.18
44 45 2.873170 TGTTTCTAGCGCAATCAACG 57.127 45.000 11.47 0.00 0.00 4.10
45 46 2.409012 TGTTTCTAGCGCAATCAACGA 58.591 42.857 11.47 0.00 0.00 3.85
46 47 2.803386 TGTTTCTAGCGCAATCAACGAA 59.197 40.909 11.47 0.00 0.00 3.85
47 48 3.248841 TGTTTCTAGCGCAATCAACGAAA 59.751 39.130 11.47 4.53 0.00 3.46
48 49 4.215965 GTTTCTAGCGCAATCAACGAAAA 58.784 39.130 11.47 0.00 0.00 2.29
49 50 3.722555 TCTAGCGCAATCAACGAAAAG 57.277 42.857 11.47 0.00 0.00 2.27
50 51 2.159707 TCTAGCGCAATCAACGAAAAGC 60.160 45.455 11.47 0.00 0.00 3.51
51 52 0.593128 AGCGCAATCAACGAAAAGCT 59.407 45.000 11.47 0.00 0.00 3.74
52 53 1.804151 AGCGCAATCAACGAAAAGCTA 59.196 42.857 11.47 0.00 31.38 3.32
53 54 2.225491 AGCGCAATCAACGAAAAGCTAA 59.775 40.909 11.47 0.00 31.38 3.09
54 55 3.119849 AGCGCAATCAACGAAAAGCTAAT 60.120 39.130 11.47 0.00 31.38 1.73
55 56 4.094294 AGCGCAATCAACGAAAAGCTAATA 59.906 37.500 11.47 0.00 31.38 0.98
56 57 4.791163 GCGCAATCAACGAAAAGCTAATAA 59.209 37.500 0.30 0.00 0.00 1.40
57 58 5.285134 GCGCAATCAACGAAAAGCTAATAAA 59.715 36.000 0.30 0.00 0.00 1.40
58 59 6.183359 GCGCAATCAACGAAAAGCTAATAAAA 60.183 34.615 0.30 0.00 0.00 1.52
59 60 7.618343 GCGCAATCAACGAAAAGCTAATAAAAA 60.618 33.333 0.30 0.00 0.00 1.94
60 61 8.372521 CGCAATCAACGAAAAGCTAATAAAAAT 58.627 29.630 0.00 0.00 0.00 1.82
65 66 9.337091 TCAACGAAAAGCTAATAAAAATACAGC 57.663 29.630 0.00 0.00 0.00 4.40
66 67 9.123709 CAACGAAAAGCTAATAAAAATACAGCA 57.876 29.630 0.00 0.00 34.65 4.41
67 68 8.669394 ACGAAAAGCTAATAAAAATACAGCAC 57.331 30.769 0.00 0.00 34.65 4.40
68 69 7.753580 ACGAAAAGCTAATAAAAATACAGCACC 59.246 33.333 0.00 0.00 34.65 5.01
69 70 7.044966 CGAAAAGCTAATAAAAATACAGCACCG 60.045 37.037 0.00 0.00 34.65 4.94
70 71 6.995511 AAGCTAATAAAAATACAGCACCGA 57.004 33.333 0.00 0.00 34.65 4.69
71 72 7.568199 AAGCTAATAAAAATACAGCACCGAT 57.432 32.000 0.00 0.00 34.65 4.18
72 73 7.568199 AGCTAATAAAAATACAGCACCGATT 57.432 32.000 0.00 0.00 34.65 3.34
73 74 7.639945 AGCTAATAAAAATACAGCACCGATTC 58.360 34.615 0.00 0.00 34.65 2.52
74 75 7.499232 AGCTAATAAAAATACAGCACCGATTCT 59.501 33.333 0.00 0.00 34.65 2.40
75 76 8.770828 GCTAATAAAAATACAGCACCGATTCTA 58.229 33.333 0.00 0.00 32.46 2.10
77 78 8.732746 AATAAAAATACAGCACCGATTCTAGT 57.267 30.769 0.00 0.00 0.00 2.57
78 79 6.663944 AAAAATACAGCACCGATTCTAGTC 57.336 37.500 0.00 0.00 0.00 2.59
79 80 4.323553 AATACAGCACCGATTCTAGTCC 57.676 45.455 0.00 0.00 0.00 3.85
80 81 1.557099 ACAGCACCGATTCTAGTCCA 58.443 50.000 0.00 0.00 0.00 4.02
81 82 1.899814 ACAGCACCGATTCTAGTCCAA 59.100 47.619 0.00 0.00 0.00 3.53
82 83 2.271800 CAGCACCGATTCTAGTCCAAC 58.728 52.381 0.00 0.00 0.00 3.77
83 84 1.899814 AGCACCGATTCTAGTCCAACA 59.100 47.619 0.00 0.00 0.00 3.33
84 85 2.301870 AGCACCGATTCTAGTCCAACAA 59.698 45.455 0.00 0.00 0.00 2.83
85 86 3.071479 GCACCGATTCTAGTCCAACAAA 58.929 45.455 0.00 0.00 0.00 2.83
86 87 3.689649 GCACCGATTCTAGTCCAACAAAT 59.310 43.478 0.00 0.00 0.00 2.32
87 88 4.156008 GCACCGATTCTAGTCCAACAAATT 59.844 41.667 0.00 0.00 0.00 1.82
88 89 5.353123 GCACCGATTCTAGTCCAACAAATTA 59.647 40.000 0.00 0.00 0.00 1.40
89 90 6.456988 GCACCGATTCTAGTCCAACAAATTAG 60.457 42.308 0.00 0.00 0.00 1.73
90 91 5.585047 ACCGATTCTAGTCCAACAAATTAGC 59.415 40.000 0.00 0.00 0.00 3.09
91 92 5.584649 CCGATTCTAGTCCAACAAATTAGCA 59.415 40.000 0.00 0.00 0.00 3.49
92 93 6.456988 CCGATTCTAGTCCAACAAATTAGCAC 60.457 42.308 0.00 0.00 0.00 4.40
93 94 6.092122 CGATTCTAGTCCAACAAATTAGCACA 59.908 38.462 0.00 0.00 0.00 4.57
94 95 6.554334 TTCTAGTCCAACAAATTAGCACAC 57.446 37.500 0.00 0.00 0.00 3.82
95 96 5.865085 TCTAGTCCAACAAATTAGCACACT 58.135 37.500 0.00 0.00 0.00 3.55
96 97 6.296026 TCTAGTCCAACAAATTAGCACACTT 58.704 36.000 0.00 0.00 0.00 3.16
97 98 5.186996 AGTCCAACAAATTAGCACACTTG 57.813 39.130 0.00 0.00 0.00 3.16
98 99 4.887071 AGTCCAACAAATTAGCACACTTGA 59.113 37.500 0.00 0.00 0.00 3.02
99 100 5.536161 AGTCCAACAAATTAGCACACTTGAT 59.464 36.000 0.00 0.00 0.00 2.57
100 101 5.858581 GTCCAACAAATTAGCACACTTGATC 59.141 40.000 0.00 0.00 0.00 2.92
101 102 5.769662 TCCAACAAATTAGCACACTTGATCT 59.230 36.000 0.00 0.00 0.00 2.75
102 103 6.939730 TCCAACAAATTAGCACACTTGATCTA 59.060 34.615 0.00 0.00 0.00 1.98
103 104 7.119699 TCCAACAAATTAGCACACTTGATCTAG 59.880 37.037 2.37 2.37 0.00 2.43
104 105 6.428385 ACAAATTAGCACACTTGATCTAGC 57.572 37.500 3.93 0.00 0.00 3.42
105 106 6.176183 ACAAATTAGCACACTTGATCTAGCT 58.824 36.000 3.93 0.00 36.20 3.32
106 107 7.331026 ACAAATTAGCACACTTGATCTAGCTA 58.669 34.615 3.93 0.00 33.83 3.32
107 108 7.824289 ACAAATTAGCACACTTGATCTAGCTAA 59.176 33.333 3.93 7.41 45.22 3.09
108 109 7.778470 AATTAGCACACTTGATCTAGCTAAC 57.222 36.000 3.93 0.00 44.33 2.34
109 110 3.775202 AGCACACTTGATCTAGCTAACG 58.225 45.455 3.93 0.00 0.00 3.18
110 111 2.860735 GCACACTTGATCTAGCTAACGG 59.139 50.000 3.93 0.00 0.00 4.44
111 112 3.676324 GCACACTTGATCTAGCTAACGGT 60.676 47.826 3.93 0.00 0.00 4.83
112 113 4.439700 GCACACTTGATCTAGCTAACGGTA 60.440 45.833 3.93 0.00 0.00 4.02
113 114 5.035443 CACACTTGATCTAGCTAACGGTAC 58.965 45.833 3.93 0.00 0.00 3.34
114 115 4.703575 ACACTTGATCTAGCTAACGGTACA 59.296 41.667 3.93 0.00 0.00 2.90
115 116 5.163642 ACACTTGATCTAGCTAACGGTACAG 60.164 44.000 3.93 0.00 0.00 2.74
116 117 3.984508 TGATCTAGCTAACGGTACAGC 57.015 47.619 6.56 6.56 38.09 4.40
117 118 3.284617 TGATCTAGCTAACGGTACAGCA 58.715 45.455 14.74 3.33 40.36 4.41
118 119 3.889538 TGATCTAGCTAACGGTACAGCAT 59.110 43.478 14.74 2.72 40.36 3.79
119 120 4.341235 TGATCTAGCTAACGGTACAGCATT 59.659 41.667 14.74 1.11 40.36 3.56
120 121 4.041740 TCTAGCTAACGGTACAGCATTG 57.958 45.455 14.74 6.41 40.36 2.82
121 122 2.024176 AGCTAACGGTACAGCATTGG 57.976 50.000 14.74 0.00 40.36 3.16
122 123 1.553248 AGCTAACGGTACAGCATTGGA 59.447 47.619 14.74 0.00 40.36 3.53
123 124 1.933853 GCTAACGGTACAGCATTGGAG 59.066 52.381 9.16 0.00 37.73 3.86
124 125 2.677037 GCTAACGGTACAGCATTGGAGT 60.677 50.000 9.16 0.00 37.73 3.85
125 126 3.429822 GCTAACGGTACAGCATTGGAGTA 60.430 47.826 9.16 0.00 37.73 2.59
126 127 3.688694 AACGGTACAGCATTGGAGTAA 57.311 42.857 0.00 0.00 0.00 2.24
127 128 3.688694 ACGGTACAGCATTGGAGTAAA 57.311 42.857 0.00 0.00 0.00 2.01
128 129 3.332034 ACGGTACAGCATTGGAGTAAAC 58.668 45.455 0.00 0.00 0.00 2.01
129 130 3.244284 ACGGTACAGCATTGGAGTAAACA 60.244 43.478 0.00 0.00 0.00 2.83
130 131 3.370978 CGGTACAGCATTGGAGTAAACAG 59.629 47.826 0.00 0.00 0.00 3.16
131 132 4.324267 GGTACAGCATTGGAGTAAACAGT 58.676 43.478 0.00 0.00 0.00 3.55
132 133 4.760204 GGTACAGCATTGGAGTAAACAGTT 59.240 41.667 0.00 0.00 0.00 3.16
133 134 5.935789 GGTACAGCATTGGAGTAAACAGTTA 59.064 40.000 0.00 0.00 0.00 2.24
134 135 6.092259 GGTACAGCATTGGAGTAAACAGTTAG 59.908 42.308 0.00 0.00 0.00 2.34
135 136 5.865085 ACAGCATTGGAGTAAACAGTTAGA 58.135 37.500 0.00 0.00 0.00 2.10
136 137 5.934625 ACAGCATTGGAGTAAACAGTTAGAG 59.065 40.000 0.00 0.00 0.00 2.43
137 138 6.166279 CAGCATTGGAGTAAACAGTTAGAGA 58.834 40.000 0.00 0.00 0.00 3.10
138 139 6.820656 CAGCATTGGAGTAAACAGTTAGAGAT 59.179 38.462 0.00 0.00 0.00 2.75
139 140 6.820656 AGCATTGGAGTAAACAGTTAGAGATG 59.179 38.462 0.00 0.00 0.00 2.90
140 141 6.457528 GCATTGGAGTAAACAGTTAGAGATGC 60.458 42.308 0.00 0.00 0.00 3.91
141 142 5.738619 TGGAGTAAACAGTTAGAGATGCA 57.261 39.130 0.00 0.00 0.00 3.96
142 143 6.109156 TGGAGTAAACAGTTAGAGATGCAA 57.891 37.500 0.00 0.00 0.00 4.08
143 144 6.166279 TGGAGTAAACAGTTAGAGATGCAAG 58.834 40.000 0.00 0.00 0.00 4.01
144 145 5.582665 GGAGTAAACAGTTAGAGATGCAAGG 59.417 44.000 0.00 0.00 0.00 3.61
145 146 6.115448 AGTAAACAGTTAGAGATGCAAGGT 57.885 37.500 0.00 0.00 0.00 3.50
146 147 6.534634 AGTAAACAGTTAGAGATGCAAGGTT 58.465 36.000 0.00 0.00 0.00 3.50
147 148 7.676947 AGTAAACAGTTAGAGATGCAAGGTTA 58.323 34.615 0.00 0.00 0.00 2.85
148 149 8.154856 AGTAAACAGTTAGAGATGCAAGGTTAA 58.845 33.333 0.00 0.00 0.00 2.01
149 150 7.440523 AAACAGTTAGAGATGCAAGGTTAAG 57.559 36.000 0.00 0.00 0.00 1.85
150 151 5.491982 ACAGTTAGAGATGCAAGGTTAAGG 58.508 41.667 0.00 0.00 0.00 2.69
151 152 4.333926 CAGTTAGAGATGCAAGGTTAAGGC 59.666 45.833 0.00 0.00 0.00 4.35
152 153 4.226168 AGTTAGAGATGCAAGGTTAAGGCT 59.774 41.667 0.00 0.00 0.00 4.58
153 154 3.728385 AGAGATGCAAGGTTAAGGCTT 57.272 42.857 4.58 4.58 0.00 4.35
154 155 4.844349 AGAGATGCAAGGTTAAGGCTTA 57.156 40.909 2.04 2.04 0.00 3.09
155 156 4.775236 AGAGATGCAAGGTTAAGGCTTAG 58.225 43.478 7.09 0.00 0.00 2.18
156 157 3.879892 GAGATGCAAGGTTAAGGCTTAGG 59.120 47.826 7.09 0.00 0.00 2.69
157 158 3.267031 AGATGCAAGGTTAAGGCTTAGGT 59.733 43.478 7.09 0.00 0.00 3.08
158 159 4.473559 AGATGCAAGGTTAAGGCTTAGGTA 59.526 41.667 7.09 0.00 0.00 3.08
159 160 4.855298 TGCAAGGTTAAGGCTTAGGTAT 57.145 40.909 7.09 0.00 0.00 2.73
160 161 4.523083 TGCAAGGTTAAGGCTTAGGTATG 58.477 43.478 7.09 7.31 0.00 2.39
161 162 3.315470 GCAAGGTTAAGGCTTAGGTATGC 59.685 47.826 16.08 16.08 0.00 3.14
162 163 3.470645 AGGTTAAGGCTTAGGTATGCG 57.529 47.619 7.09 0.00 0.00 4.73
163 164 2.770232 AGGTTAAGGCTTAGGTATGCGT 59.230 45.455 7.09 0.00 0.00 5.24
164 165 3.962718 AGGTTAAGGCTTAGGTATGCGTA 59.037 43.478 7.09 0.00 0.00 4.42
165 166 4.591924 AGGTTAAGGCTTAGGTATGCGTAT 59.408 41.667 7.09 0.00 0.00 3.06
166 167 5.071384 AGGTTAAGGCTTAGGTATGCGTATT 59.929 40.000 7.09 0.00 0.00 1.89
167 168 5.761726 GGTTAAGGCTTAGGTATGCGTATTT 59.238 40.000 7.09 0.00 0.00 1.40
168 169 6.261603 GGTTAAGGCTTAGGTATGCGTATTTT 59.738 38.462 7.09 0.00 0.00 1.82
169 170 7.201758 GGTTAAGGCTTAGGTATGCGTATTTTT 60.202 37.037 7.09 0.00 0.00 1.94
617 618 4.641541 TCCAACCACATATCAAGCTTGATG 59.358 41.667 39.83 31.28 46.68 3.07
647 648 9.487790 AACAAATGGTAAAATCCTTGTGTATTG 57.512 29.630 0.00 0.00 33.69 1.90
737 746 2.151202 ACTTGTGAAAGTGCGTATGGG 58.849 47.619 0.00 0.00 0.00 4.00
843 852 2.440409 CCCCTCTGTTCTTGTTCATGG 58.560 52.381 0.00 0.00 0.00 3.66
905 914 2.749441 GCAGGAAGCAGCCACTCC 60.749 66.667 0.00 0.00 44.79 3.85
918 927 1.671742 CACTCCCGCTGTAGGTTGT 59.328 57.895 0.00 0.00 0.00 3.32
922 931 2.046314 CCGCTGTAGGTTGTGGGG 60.046 66.667 0.00 0.00 0.00 4.96
925 934 2.907179 GCTGTAGGTTGTGGGGGCT 61.907 63.158 0.00 0.00 0.00 5.19
926 935 1.002134 CTGTAGGTTGTGGGGGCTG 60.002 63.158 0.00 0.00 0.00 4.85
927 936 1.462432 TGTAGGTTGTGGGGGCTGA 60.462 57.895 0.00 0.00 0.00 4.26
928 937 0.844661 TGTAGGTTGTGGGGGCTGAT 60.845 55.000 0.00 0.00 0.00 2.90
966 975 6.465894 GGACATGCCTATAAGGTATTGGAGTT 60.466 42.308 0.00 0.00 38.73 3.01
968 977 7.354312 ACATGCCTATAAGGTATTGGAGTTTT 58.646 34.615 0.00 0.00 38.73 2.43
977 986 3.933332 GGTATTGGAGTTTTGGAGAGACG 59.067 47.826 0.00 0.00 0.00 4.18
1083 1103 4.382320 GTTACGGCCGGTGCAGGA 62.382 66.667 31.76 3.55 40.13 3.86
1401 1431 2.640989 CAGTTCGTCGTCACGGGA 59.359 61.111 0.00 0.00 46.70 5.14
1431 1461 2.351276 GTCACGCTGGTTGGGGAT 59.649 61.111 0.00 0.00 0.00 3.85
1503 1533 1.102154 CCACCAACAACAAGCTGACA 58.898 50.000 0.00 0.00 0.00 3.58
1695 1752 2.027073 CTACGCCGTGCTGCTCAAA 61.027 57.895 0.00 0.00 0.00 2.69
1755 1812 0.871722 CCGTCGTCCTTGATTTTGCA 59.128 50.000 0.00 0.00 0.00 4.08
1965 2022 2.355837 GACGAGTGTGCGCTTCCA 60.356 61.111 9.73 0.00 33.86 3.53
2388 2476 1.274358 TGATCATCCCCTTGGTGGAGA 60.274 52.381 0.00 2.82 38.35 3.71
2393 2481 1.879575 TCCCCTTGGTGGAGATACAG 58.120 55.000 0.00 0.00 38.35 2.74
2405 2493 2.173569 GGAGATACAGAAGGCCACCAAT 59.826 50.000 5.01 0.00 0.00 3.16
2489 2577 3.127533 GACCTGCATGTCGTGGCC 61.128 66.667 6.36 0.00 0.00 5.36
2673 2761 4.060900 CCTTTACCATCATCTCCATGTCG 58.939 47.826 0.00 0.00 0.00 4.35
2760 2848 1.729586 AACCTACCTTCACTCAGCCA 58.270 50.000 0.00 0.00 0.00 4.75
3048 3136 0.036294 CGAGGAGGAAACCCTTGTCC 60.036 60.000 0.00 0.00 33.25 4.02
3417 3523 4.445735 CCTTGACGGGATGTAAATATGGGT 60.446 45.833 0.00 0.00 0.00 4.51
3418 3524 5.221762 CCTTGACGGGATGTAAATATGGGTA 60.222 44.000 0.00 0.00 0.00 3.69
3454 3560 7.164122 TCTACCGACTGAGAAAACTAGTAAGA 58.836 38.462 0.00 0.00 0.00 2.10
3617 3723 3.744660 TCTTTCCTTGACTTCCTCTTGC 58.255 45.455 0.00 0.00 0.00 4.01
3699 3806 3.580193 GCATGTGCTAGCGCCAGG 61.580 66.667 24.82 18.26 38.21 4.45
3732 3841 3.767902 AGCAAAGAAGCAGAGAAGACT 57.232 42.857 0.00 0.00 36.85 3.24
3790 3902 0.954452 GTGCAAAGTGAGGAAGGGTG 59.046 55.000 0.00 0.00 0.00 4.61
3800 3930 2.711009 TGAGGAAGGGTGTCAACTTCAT 59.289 45.455 16.19 11.37 43.70 2.57
3827 3957 6.117975 ACTAATCCAGGAAAAAGGTAACGA 57.882 37.500 0.00 0.00 46.39 3.85
3853 3983 5.317808 TCCGGATGTTTCATTGTTTCCTAA 58.682 37.500 0.00 0.00 0.00 2.69
4093 4225 0.549950 CTCTCAGGGGAATGTGCCAT 59.450 55.000 0.00 0.00 0.00 4.40
4270 4416 0.733150 GGCTAAATGAACCAGCCGAC 59.267 55.000 0.00 0.00 44.99 4.79
4329 4476 0.473755 TTGTCATCCATGGCGCCTAT 59.526 50.000 29.70 16.59 34.48 2.57
4345 4492 5.105716 GGCGCCTATATCTAACTCTTCATCA 60.106 44.000 22.15 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.724399 ACAATCATACAACCACAACCAGA 58.276 39.130 0.00 0.00 0.00 3.86
2 3 6.150976 ACATACAATCATACAACCACAACCAG 59.849 38.462 0.00 0.00 0.00 4.00
3 4 6.007076 ACATACAATCATACAACCACAACCA 58.993 36.000 0.00 0.00 0.00 3.67
5 6 8.296713 AGAAACATACAATCATACAACCACAAC 58.703 33.333 0.00 0.00 0.00 3.32
6 7 8.402798 AGAAACATACAATCATACAACCACAA 57.597 30.769 0.00 0.00 0.00 3.33
7 8 7.994425 AGAAACATACAATCATACAACCACA 57.006 32.000 0.00 0.00 0.00 4.17
8 9 8.122952 GCTAGAAACATACAATCATACAACCAC 58.877 37.037 0.00 0.00 0.00 4.16
9 10 7.011016 CGCTAGAAACATACAATCATACAACCA 59.989 37.037 0.00 0.00 0.00 3.67
10 11 7.345192 CGCTAGAAACATACAATCATACAACC 58.655 38.462 0.00 0.00 0.00 3.77
11 12 6.846283 GCGCTAGAAACATACAATCATACAAC 59.154 38.462 0.00 0.00 0.00 3.32
12 13 6.536941 TGCGCTAGAAACATACAATCATACAA 59.463 34.615 9.73 0.00 0.00 2.41
13 14 6.045955 TGCGCTAGAAACATACAATCATACA 58.954 36.000 9.73 0.00 0.00 2.29
14 15 6.525121 TGCGCTAGAAACATACAATCATAC 57.475 37.500 9.73 0.00 0.00 2.39
15 16 7.440856 TGATTGCGCTAGAAACATACAATCATA 59.559 33.333 9.73 0.00 43.99 2.15
16 17 6.260714 TGATTGCGCTAGAAACATACAATCAT 59.739 34.615 9.73 0.00 43.99 2.45
17 18 5.584251 TGATTGCGCTAGAAACATACAATCA 59.416 36.000 9.73 8.09 45.61 2.57
18 19 6.048073 TGATTGCGCTAGAAACATACAATC 57.952 37.500 9.73 5.35 41.28 2.67
19 20 6.258160 GTTGATTGCGCTAGAAACATACAAT 58.742 36.000 9.73 0.00 0.00 2.71
20 21 5.627172 GTTGATTGCGCTAGAAACATACAA 58.373 37.500 9.73 0.00 0.00 2.41
21 22 4.201676 CGTTGATTGCGCTAGAAACATACA 60.202 41.667 9.73 0.00 0.00 2.29
22 23 4.032445 TCGTTGATTGCGCTAGAAACATAC 59.968 41.667 9.73 1.18 0.00 2.39
23 24 4.177783 TCGTTGATTGCGCTAGAAACATA 58.822 39.130 9.73 0.00 0.00 2.29
24 25 3.000041 TCGTTGATTGCGCTAGAAACAT 59.000 40.909 9.73 0.00 0.00 2.71
25 26 2.409012 TCGTTGATTGCGCTAGAAACA 58.591 42.857 9.73 0.00 0.00 2.83
26 27 3.449322 TTCGTTGATTGCGCTAGAAAC 57.551 42.857 9.73 9.03 0.00 2.78
27 28 4.463209 CTTTTCGTTGATTGCGCTAGAAA 58.537 39.130 9.73 4.00 0.00 2.52
28 29 3.666902 GCTTTTCGTTGATTGCGCTAGAA 60.667 43.478 9.73 0.00 0.00 2.10
29 30 2.159707 GCTTTTCGTTGATTGCGCTAGA 60.160 45.455 9.73 0.00 0.00 2.43
30 31 2.159653 AGCTTTTCGTTGATTGCGCTAG 60.160 45.455 9.73 0.00 0.00 3.42
31 32 1.804151 AGCTTTTCGTTGATTGCGCTA 59.196 42.857 9.73 0.00 0.00 4.26
32 33 0.593128 AGCTTTTCGTTGATTGCGCT 59.407 45.000 9.73 0.00 0.00 5.92
33 34 2.241259 TAGCTTTTCGTTGATTGCGC 57.759 45.000 0.00 0.00 0.00 6.09
34 35 6.846870 TTTATTAGCTTTTCGTTGATTGCG 57.153 33.333 0.00 0.00 0.00 4.85
39 40 9.337091 GCTGTATTTTTATTAGCTTTTCGTTGA 57.663 29.630 0.00 0.00 0.00 3.18
40 41 9.123709 TGCTGTATTTTTATTAGCTTTTCGTTG 57.876 29.630 0.00 0.00 35.50 4.10
41 42 9.124807 GTGCTGTATTTTTATTAGCTTTTCGTT 57.875 29.630 0.00 0.00 35.50 3.85
42 43 7.753580 GGTGCTGTATTTTTATTAGCTTTTCGT 59.246 33.333 0.00 0.00 35.50 3.85
43 44 7.044966 CGGTGCTGTATTTTTATTAGCTTTTCG 60.045 37.037 0.00 0.00 35.50 3.46
44 45 7.966204 TCGGTGCTGTATTTTTATTAGCTTTTC 59.034 33.333 0.00 0.00 35.50 2.29
45 46 7.822658 TCGGTGCTGTATTTTTATTAGCTTTT 58.177 30.769 0.00 0.00 35.50 2.27
46 47 7.385778 TCGGTGCTGTATTTTTATTAGCTTT 57.614 32.000 0.00 0.00 35.50 3.51
47 48 6.995511 TCGGTGCTGTATTTTTATTAGCTT 57.004 33.333 0.00 0.00 35.50 3.74
48 49 7.499232 AGAATCGGTGCTGTATTTTTATTAGCT 59.501 33.333 0.00 0.00 35.50 3.32
49 50 7.639945 AGAATCGGTGCTGTATTTTTATTAGC 58.360 34.615 0.00 0.00 35.06 3.09
51 52 9.826574 ACTAGAATCGGTGCTGTATTTTTATTA 57.173 29.630 0.00 0.00 0.00 0.98
52 53 8.732746 ACTAGAATCGGTGCTGTATTTTTATT 57.267 30.769 0.00 0.00 0.00 1.40
53 54 7.441458 GGACTAGAATCGGTGCTGTATTTTTAT 59.559 37.037 0.00 0.00 0.00 1.40
54 55 6.759827 GGACTAGAATCGGTGCTGTATTTTTA 59.240 38.462 0.00 0.00 0.00 1.52
55 56 5.585047 GGACTAGAATCGGTGCTGTATTTTT 59.415 40.000 0.00 0.00 0.00 1.94
56 57 5.116882 GGACTAGAATCGGTGCTGTATTTT 58.883 41.667 0.00 0.00 0.00 1.82
57 58 4.161565 TGGACTAGAATCGGTGCTGTATTT 59.838 41.667 0.00 0.00 0.00 1.40
58 59 3.704566 TGGACTAGAATCGGTGCTGTATT 59.295 43.478 0.00 0.00 0.00 1.89
59 60 3.296854 TGGACTAGAATCGGTGCTGTAT 58.703 45.455 0.00 0.00 0.00 2.29
60 61 2.730382 TGGACTAGAATCGGTGCTGTA 58.270 47.619 0.00 0.00 0.00 2.74
61 62 1.557099 TGGACTAGAATCGGTGCTGT 58.443 50.000 0.00 0.00 0.00 4.40
62 63 2.271800 GTTGGACTAGAATCGGTGCTG 58.728 52.381 0.00 0.00 0.00 4.41
63 64 1.899814 TGTTGGACTAGAATCGGTGCT 59.100 47.619 0.00 0.00 0.00 4.40
64 65 2.380084 TGTTGGACTAGAATCGGTGC 57.620 50.000 0.00 0.00 0.00 5.01
65 66 5.880054 AATTTGTTGGACTAGAATCGGTG 57.120 39.130 0.00 0.00 0.00 4.94
66 67 5.585047 GCTAATTTGTTGGACTAGAATCGGT 59.415 40.000 0.00 0.00 0.00 4.69
67 68 5.584649 TGCTAATTTGTTGGACTAGAATCGG 59.415 40.000 0.00 0.00 0.00 4.18
68 69 6.092122 TGTGCTAATTTGTTGGACTAGAATCG 59.908 38.462 0.00 0.00 0.00 3.34
69 70 7.119846 AGTGTGCTAATTTGTTGGACTAGAATC 59.880 37.037 0.00 0.00 0.00 2.52
70 71 6.942576 AGTGTGCTAATTTGTTGGACTAGAAT 59.057 34.615 0.00 0.00 0.00 2.40
71 72 6.296026 AGTGTGCTAATTTGTTGGACTAGAA 58.704 36.000 0.00 0.00 0.00 2.10
72 73 5.865085 AGTGTGCTAATTTGTTGGACTAGA 58.135 37.500 0.00 0.00 0.00 2.43
73 74 6.204688 TCAAGTGTGCTAATTTGTTGGACTAG 59.795 38.462 0.00 0.00 0.00 2.57
74 75 6.058833 TCAAGTGTGCTAATTTGTTGGACTA 58.941 36.000 0.00 0.00 0.00 2.59
75 76 4.887071 TCAAGTGTGCTAATTTGTTGGACT 59.113 37.500 0.00 0.00 0.00 3.85
76 77 5.181690 TCAAGTGTGCTAATTTGTTGGAC 57.818 39.130 0.00 0.00 0.00 4.02
77 78 5.769662 AGATCAAGTGTGCTAATTTGTTGGA 59.230 36.000 0.00 0.00 0.00 3.53
78 79 6.017400 AGATCAAGTGTGCTAATTTGTTGG 57.983 37.500 0.00 0.00 0.00 3.77
79 80 6.744537 GCTAGATCAAGTGTGCTAATTTGTTG 59.255 38.462 0.00 0.00 0.00 3.33
80 81 6.656693 AGCTAGATCAAGTGTGCTAATTTGTT 59.343 34.615 0.00 0.00 0.00 2.83
81 82 6.176183 AGCTAGATCAAGTGTGCTAATTTGT 58.824 36.000 0.00 0.00 0.00 2.83
82 83 6.674694 AGCTAGATCAAGTGTGCTAATTTG 57.325 37.500 0.00 0.00 0.00 2.32
83 84 7.010552 CGTTAGCTAGATCAAGTGTGCTAATTT 59.989 37.037 8.19 0.00 42.39 1.82
84 85 6.477033 CGTTAGCTAGATCAAGTGTGCTAATT 59.523 38.462 8.19 0.00 42.39 1.40
85 86 5.980116 CGTTAGCTAGATCAAGTGTGCTAAT 59.020 40.000 8.19 0.00 42.39 1.73
86 87 5.340803 CGTTAGCTAGATCAAGTGTGCTAA 58.659 41.667 0.00 0.00 39.63 3.09
87 88 4.202020 CCGTTAGCTAGATCAAGTGTGCTA 60.202 45.833 0.00 0.00 32.72 3.49
88 89 3.429547 CCGTTAGCTAGATCAAGTGTGCT 60.430 47.826 0.00 0.00 34.92 4.40
89 90 2.860735 CCGTTAGCTAGATCAAGTGTGC 59.139 50.000 0.00 0.00 0.00 4.57
90 91 4.111375 ACCGTTAGCTAGATCAAGTGTG 57.889 45.455 0.00 0.00 0.00 3.82
91 92 4.703575 TGTACCGTTAGCTAGATCAAGTGT 59.296 41.667 0.00 0.00 0.00 3.55
92 93 5.244785 TGTACCGTTAGCTAGATCAAGTG 57.755 43.478 0.00 0.00 0.00 3.16
93 94 4.202030 GCTGTACCGTTAGCTAGATCAAGT 60.202 45.833 0.00 0.00 36.99 3.16
94 95 4.202020 TGCTGTACCGTTAGCTAGATCAAG 60.202 45.833 0.00 0.00 40.52 3.02
95 96 3.697542 TGCTGTACCGTTAGCTAGATCAA 59.302 43.478 0.00 0.00 40.52 2.57
96 97 3.284617 TGCTGTACCGTTAGCTAGATCA 58.715 45.455 0.00 0.00 40.52 2.92
97 98 3.984508 TGCTGTACCGTTAGCTAGATC 57.015 47.619 0.00 0.00 40.52 2.75
98 99 4.501571 CCAATGCTGTACCGTTAGCTAGAT 60.502 45.833 0.00 0.00 40.52 1.98
99 100 3.181479 CCAATGCTGTACCGTTAGCTAGA 60.181 47.826 0.00 0.00 40.52 2.43
100 101 3.123804 CCAATGCTGTACCGTTAGCTAG 58.876 50.000 4.74 0.00 40.52 3.42
101 102 2.761767 TCCAATGCTGTACCGTTAGCTA 59.238 45.455 4.74 0.00 40.52 3.32
102 103 1.553248 TCCAATGCTGTACCGTTAGCT 59.447 47.619 4.74 0.00 40.52 3.32
103 104 1.933853 CTCCAATGCTGTACCGTTAGC 59.066 52.381 0.00 0.00 40.29 3.09
104 105 3.247006 ACTCCAATGCTGTACCGTTAG 57.753 47.619 0.00 0.00 0.00 2.34
105 106 4.804868 TTACTCCAATGCTGTACCGTTA 57.195 40.909 0.00 0.00 0.00 3.18
106 107 3.688694 TTACTCCAATGCTGTACCGTT 57.311 42.857 0.00 0.00 0.00 4.44
107 108 3.244284 TGTTTACTCCAATGCTGTACCGT 60.244 43.478 0.00 0.00 0.00 4.83
108 109 3.331150 TGTTTACTCCAATGCTGTACCG 58.669 45.455 0.00 0.00 0.00 4.02
109 110 4.324267 ACTGTTTACTCCAATGCTGTACC 58.676 43.478 0.00 0.00 0.00 3.34
110 111 5.941948 AACTGTTTACTCCAATGCTGTAC 57.058 39.130 0.00 0.00 0.00 2.90
111 112 6.999950 TCTAACTGTTTACTCCAATGCTGTA 58.000 36.000 0.00 0.00 0.00 2.74
112 113 5.865085 TCTAACTGTTTACTCCAATGCTGT 58.135 37.500 0.00 0.00 0.00 4.40
113 114 6.166279 TCTCTAACTGTTTACTCCAATGCTG 58.834 40.000 0.00 0.00 0.00 4.41
114 115 6.360370 TCTCTAACTGTTTACTCCAATGCT 57.640 37.500 0.00 0.00 0.00 3.79
115 116 6.457528 GCATCTCTAACTGTTTACTCCAATGC 60.458 42.308 0.00 2.85 0.00 3.56
116 117 6.595326 TGCATCTCTAACTGTTTACTCCAATG 59.405 38.462 0.00 0.00 0.00 2.82
117 118 6.711277 TGCATCTCTAACTGTTTACTCCAAT 58.289 36.000 0.00 0.00 0.00 3.16
118 119 6.109156 TGCATCTCTAACTGTTTACTCCAA 57.891 37.500 0.00 0.00 0.00 3.53
119 120 5.738619 TGCATCTCTAACTGTTTACTCCA 57.261 39.130 0.00 0.00 0.00 3.86
120 121 5.582665 CCTTGCATCTCTAACTGTTTACTCC 59.417 44.000 0.00 0.00 0.00 3.85
121 122 6.166982 ACCTTGCATCTCTAACTGTTTACTC 58.833 40.000 0.00 0.00 0.00 2.59
122 123 6.115448 ACCTTGCATCTCTAACTGTTTACT 57.885 37.500 0.00 0.00 0.00 2.24
123 124 6.803154 AACCTTGCATCTCTAACTGTTTAC 57.197 37.500 0.00 0.00 0.00 2.01
124 125 7.606456 CCTTAACCTTGCATCTCTAACTGTTTA 59.394 37.037 0.00 0.00 0.00 2.01
125 126 6.431234 CCTTAACCTTGCATCTCTAACTGTTT 59.569 38.462 0.00 0.00 0.00 2.83
126 127 5.940470 CCTTAACCTTGCATCTCTAACTGTT 59.060 40.000 0.00 0.00 0.00 3.16
127 128 5.491982 CCTTAACCTTGCATCTCTAACTGT 58.508 41.667 0.00 0.00 0.00 3.55
128 129 4.333926 GCCTTAACCTTGCATCTCTAACTG 59.666 45.833 0.00 0.00 0.00 3.16
129 130 4.226168 AGCCTTAACCTTGCATCTCTAACT 59.774 41.667 0.00 0.00 0.00 2.24
130 131 4.518249 AGCCTTAACCTTGCATCTCTAAC 58.482 43.478 0.00 0.00 0.00 2.34
131 132 4.844349 AGCCTTAACCTTGCATCTCTAA 57.156 40.909 0.00 0.00 0.00 2.10
132 133 4.844349 AAGCCTTAACCTTGCATCTCTA 57.156 40.909 0.00 0.00 0.00 2.43
133 134 3.728385 AAGCCTTAACCTTGCATCTCT 57.272 42.857 0.00 0.00 0.00 3.10
134 135 3.879892 CCTAAGCCTTAACCTTGCATCTC 59.120 47.826 0.00 0.00 0.00 2.75
135 136 3.267031 ACCTAAGCCTTAACCTTGCATCT 59.733 43.478 0.00 0.00 0.00 2.90
136 137 3.621558 ACCTAAGCCTTAACCTTGCATC 58.378 45.455 0.00 0.00 0.00 3.91
137 138 3.739401 ACCTAAGCCTTAACCTTGCAT 57.261 42.857 0.00 0.00 0.00 3.96
138 139 4.523083 CATACCTAAGCCTTAACCTTGCA 58.477 43.478 0.00 0.00 0.00 4.08
139 140 3.315470 GCATACCTAAGCCTTAACCTTGC 59.685 47.826 0.00 0.00 0.00 4.01
140 141 3.560068 CGCATACCTAAGCCTTAACCTTG 59.440 47.826 0.00 0.00 0.00 3.61
141 142 3.199289 ACGCATACCTAAGCCTTAACCTT 59.801 43.478 0.00 0.00 0.00 3.50
142 143 2.770232 ACGCATACCTAAGCCTTAACCT 59.230 45.455 0.00 0.00 0.00 3.50
143 144 3.189618 ACGCATACCTAAGCCTTAACC 57.810 47.619 0.00 0.00 0.00 2.85
144 145 6.856135 AAATACGCATACCTAAGCCTTAAC 57.144 37.500 0.00 0.00 0.00 2.01
145 146 7.868906 AAAAATACGCATACCTAAGCCTTAA 57.131 32.000 0.00 0.00 0.00 1.85
597 598 6.124340 TGATCATCAAGCTTGATATGTGGTT 58.876 36.000 35.25 20.15 45.62 3.67
610 611 7.887996 TTTTACCATTTGTTGATCATCAAGC 57.112 32.000 16.57 0.00 37.00 4.01
617 618 7.872483 ACACAAGGATTTTACCATTTGTTGATC 59.128 33.333 0.00 0.00 29.81 2.92
675 676 7.087639 GTGCATACAAACAAGCATTACCTTAA 58.912 34.615 0.00 0.00 39.43 1.85
708 709 6.864342 ACGCACTTTCACAAGTATATCTAGT 58.136 36.000 0.00 0.00 41.69 2.57
758 767 6.000840 TGCCTCAAGTTTCAATACACATGTA 58.999 36.000 0.00 0.00 34.67 2.29
767 776 2.353406 GCTGCATGCCTCAAGTTTCAAT 60.353 45.455 16.68 0.00 35.15 2.57
770 779 3.413522 GCTGCATGCCTCAAGTTTC 57.586 52.632 16.68 0.00 35.15 2.78
843 852 2.039084 AGACCAAGACCAAGACCATGAC 59.961 50.000 0.00 0.00 0.00 3.06
887 896 2.350514 GAGTGGCTGCTTCCTGCT 59.649 61.111 0.00 0.00 43.37 4.24
905 914 2.046314 CCCCACAACCTACAGCGG 60.046 66.667 0.00 0.00 0.00 5.52
910 919 0.331616 AATCAGCCCCCACAACCTAC 59.668 55.000 0.00 0.00 0.00 3.18
918 927 3.721575 ACAAGTATATCAATCAGCCCCCA 59.278 43.478 0.00 0.00 0.00 4.96
922 931 5.368145 TGTCCACAAGTATATCAATCAGCC 58.632 41.667 0.00 0.00 0.00 4.85
925 934 5.764686 GGCATGTCCACAAGTATATCAATCA 59.235 40.000 0.00 0.00 34.01 2.57
926 935 6.000219 AGGCATGTCCACAAGTATATCAATC 59.000 40.000 8.58 0.00 37.29 2.67
927 936 5.945310 AGGCATGTCCACAAGTATATCAAT 58.055 37.500 8.58 0.00 37.29 2.57
928 937 5.372343 AGGCATGTCCACAAGTATATCAA 57.628 39.130 8.58 0.00 37.29 2.57
966 975 2.480244 CGCAGATGATCGTCTCTCCAAA 60.480 50.000 14.75 0.00 0.00 3.28
968 977 0.665298 CGCAGATGATCGTCTCTCCA 59.335 55.000 14.75 0.00 0.00 3.86
977 986 2.203112 TGGCTGCCGCAGATGATC 60.203 61.111 24.80 5.49 38.10 2.92
1431 1461 4.476410 CCGCTGCTGTCGTCGCTA 62.476 66.667 0.00 0.00 0.00 4.26
1648 1705 2.002018 AACCAACCCCTCTTGGCGAA 62.002 55.000 0.00 0.00 44.19 4.70
1654 1711 0.482887 CCCTCAAACCAACCCCTCTT 59.517 55.000 0.00 0.00 0.00 2.85
1695 1752 2.439883 GAGTACCCGGGCGAGTCT 60.440 66.667 24.08 11.88 0.00 3.24
1755 1812 1.002134 CACCGGCTTGGAATCCACT 60.002 57.895 0.00 0.00 42.00 4.00
1826 1883 1.673337 GCATGTCTGCTCTGGCACA 60.673 57.895 0.00 0.00 45.32 4.57
1965 2022 4.393155 TCGCCGAAGCACATGCCT 62.393 61.111 0.00 0.00 43.38 4.75
2174 2258 4.009675 TGCCTGCACTTAAACCTGAATAG 58.990 43.478 0.00 0.00 0.00 1.73
2388 2476 6.667414 TCAAAATTATTGGTGGCCTTCTGTAT 59.333 34.615 3.32 0.00 0.00 2.29
2393 2481 5.146010 TGTCAAAATTATTGGTGGCCTTC 57.854 39.130 3.32 0.00 0.00 3.46
2405 2493 3.743911 TCTCGCGAGCTTTGTCAAAATTA 59.256 39.130 30.97 5.73 0.00 1.40
2489 2577 1.734465 GCGACCTTGGACTTCTTGATG 59.266 52.381 0.00 0.00 0.00 3.07
2673 2761 1.753073 CAGGGATGGCATGGTTTCTTC 59.247 52.381 3.81 0.00 0.00 2.87
2760 2848 2.097110 TGGACTATAGGGAACGCCAT 57.903 50.000 4.43 0.00 35.15 4.40
3230 3318 3.070878 TCGGGATAAAGCTATCATGCACA 59.929 43.478 0.00 0.00 36.40 4.57
3248 3354 2.742053 CACAACCACTTGATACTTCGGG 59.258 50.000 0.00 0.00 0.00 5.14
3417 3523 2.770802 AGTCGGTAGAGCTCTAGTGGTA 59.229 50.000 23.87 0.00 0.00 3.25
3418 3524 1.560611 AGTCGGTAGAGCTCTAGTGGT 59.439 52.381 23.87 5.31 0.00 4.16
3432 3538 6.837471 ATCTTACTAGTTTTCTCAGTCGGT 57.163 37.500 0.00 0.00 0.00 4.69
3563 3669 3.316588 TGAAGGATCTCATCGAGTGTAGC 59.683 47.826 0.00 0.00 0.00 3.58
3617 3723 2.420022 GTGGGTCGAGGAAAATGATGTG 59.580 50.000 0.00 0.00 0.00 3.21
3699 3806 0.387239 CTTTGCTAAAGCGCACCCAC 60.387 55.000 11.47 0.00 45.83 4.61
3732 3841 9.788889 ATTGATCTTGCATTGTCTCTATTATCA 57.211 29.630 0.00 0.00 0.00 2.15
3790 3902 6.098409 TCCTGGATTAGTCCTATGAAGTTGAC 59.902 42.308 5.79 0.00 45.32 3.18
3800 3930 7.580109 CGTTACCTTTTTCCTGGATTAGTCCTA 60.580 40.741 5.79 0.00 45.32 2.94
3853 3983 2.945668 GCTCGGCAGAACCAATAGAATT 59.054 45.455 0.00 0.00 39.03 2.17
3989 4120 8.730680 GCTACCAATTTTGATTCTTGTTCTCTA 58.269 33.333 0.00 0.00 0.00 2.43
4093 4225 1.685224 GAAGGATGGGTGCTGGACA 59.315 57.895 0.77 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.