Multiple sequence alignment - TraesCS5A01G121500

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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 TraesCS5A01G121500 chr5A 100.000 3254 0 0 1 3254 262472784 262469531 0.000000e+00 6010.0
1 TraesCS5A01G121500 chr5A 94.426 305 16 1 2 305 434716536 434716840 4.920000e-128 468.0
2 TraesCS5A01G121500 chr5A 96.140 285 11 0 847 1131 705868591 705868875 1.770000e-127 466.0
3 TraesCS5A01G121500 chr2A 96.354 2962 92 7 305 3254 694744442 694741485 0.000000e+00 4857.0
4 TraesCS5A01G121500 chr2A 90.476 378 22 4 305 668 694745568 694745191 1.360000e-133 486.0
5 TraesCS5A01G121500 chr2A 94.408 304 17 0 2 305 714019041 714018738 4.920000e-128 468.0
6 TraesCS5A01G121500 chr7A 95.725 2971 98 12 302 3254 709138623 709135664 0.000000e+00 4756.0
7 TraesCS5A01G121500 chr1A 95.337 2166 88 4 305 2458 446217430 446219594 0.000000e+00 3428.0
8 TraesCS5A01G121500 chr1A 96.491 285 10 0 847 1131 444168370 444168086 3.800000e-129 472.0
9 TraesCS5A01G121500 chr3B 95.873 2108 59 2 1173 3254 73032259 73034364 0.000000e+00 3386.0
10 TraesCS5A01G121500 chr3B 97.419 1085 28 0 1173 2257 452562180 452561096 0.000000e+00 1849.0
11 TraesCS5A01G121500 chr3B 96.491 285 10 0 847 1131 73031977 73032261 3.800000e-129 472.0
12 TraesCS5A01G121500 chr3B 94.386 285 13 1 847 1131 452562459 452562178 4.990000e-118 435.0
13 TraesCS5A01G121500 chr3B 93.902 164 10 0 305 468 817237839 817237676 6.970000e-62 248.0
14 TraesCS5A01G121500 chr1D 96.274 1691 62 1 1564 3254 97786081 97784392 0.000000e+00 2772.0
15 TraesCS5A01G121500 chr1D 95.322 342 16 0 609 950 117323607 117323266 7.940000e-151 544.0
16 TraesCS5A01G121500 chr1D 83.960 505 58 14 936 1434 420557342 420556855 2.290000e-126 462.0
17 TraesCS5A01G121500 chr5D 95.740 1690 50 2 1564 3253 309068879 309067212 0.000000e+00 2702.0
18 TraesCS5A01G121500 chr5D 95.906 342 14 0 609 950 309069215 309068874 3.670000e-154 555.0
19 TraesCS5A01G121500 chr5D 95.410 305 12 2 2 305 136499957 136500260 4.880000e-133 484.0
20 TraesCS5A01G121500 chr5D 95.410 305 12 2 2 305 414740491 414740188 4.880000e-133 484.0
21 TraesCS5A01G121500 chr5D 95.082 305 14 1 2 305 547879715 547879411 2.270000e-131 479.0
22 TraesCS5A01G121500 chr4D 95.740 1690 50 2 1564 3253 77912520 77914187 0.000000e+00 2702.0
23 TraesCS5A01G121500 chr4D 96.188 341 13 0 610 950 77912185 77912525 2.840000e-155 558.0
24 TraesCS5A01G121500 chr4D 90.909 187 17 0 305 491 502955355 502955541 5.390000e-63 252.0
25 TraesCS5A01G121500 chr6D 95.621 1690 52 2 1564 3253 56195689 56197356 0.000000e+00 2691.0
26 TraesCS5A01G121500 chr6D 95.565 1691 49 10 1564 3253 75302472 75300807 0.000000e+00 2684.0
27 TraesCS5A01G121500 chr6D 95.322 342 16 0 609 950 75302808 75302467 7.940000e-151 544.0
28 TraesCS5A01G121500 chr3D 95.554 1687 53 2 1567 3253 149698763 149697099 0.000000e+00 2680.0
29 TraesCS5A01G121500 chr3D 95.614 342 15 0 609 950 149699102 149698761 1.710000e-152 549.0
30 TraesCS5A01G121500 chr3D 95.082 305 14 1 2 305 118523751 118524055 2.270000e-131 479.0
31 TraesCS5A01G121500 chr5B 95.023 1306 64 1 1564 2869 563525707 563524403 0.000000e+00 2050.0
32 TraesCS5A01G121500 chr5B 92.084 379 29 1 572 950 563526079 563525702 1.720000e-147 532.0
33 TraesCS5A01G121500 chr5B 100.000 28 0 0 530 557 478928719 478928692 6.000000e-03 52.8
34 TraesCS5A01G121500 chr4B 97.327 1085 29 0 1173 2257 629908303 629909387 0.000000e+00 1844.0
35 TraesCS5A01G121500 chr4B 97.327 1085 29 0 1173 2257 665901147 665902231 0.000000e+00 1844.0
36 TraesCS5A01G121500 chr4B 94.386 285 16 0 847 1131 629908021 629908305 3.850000e-119 438.0
37 TraesCS5A01G121500 chr4B 93.007 286 18 2 847 1131 665900863 665901147 1.810000e-112 416.0
38 TraesCS5A01G121500 chr1B 89.905 634 55 7 936 1568 568571712 568571087 0.000000e+00 808.0
39 TraesCS5A01G121500 chr7D 95.082 305 14 1 2 305 143714956 143715260 2.270000e-131 479.0
40 TraesCS5A01G121500 chr7D 94.805 308 11 5 2 305 529379356 529379662 2.940000e-130 475.0
41 TraesCS5A01G121500 chr7D 84.762 210 24 3 997 1202 11837903 11838108 1.530000e-48 204.0
42 TraesCS5A01G121500 chr2D 94.754 305 15 1 2 305 369011591 369011287 1.060000e-129 473.0
43 TraesCS5A01G121500 chr4A 96.113 283 11 0 849 1131 36003525 36003243 2.290000e-126 462.0
44 TraesCS5A01G121500 chr2B 94.737 285 15 0 847 1131 553880892 553881176 8.280000e-121 444.0
45 TraesCS5A01G121500 chr2B 87.209 86 8 3 488 572 98678261 98678344 9.610000e-16 95.3
46 TraesCS5A01G121500 chr7B 93.048 187 13 0 305 491 694938353 694938167 1.150000e-69 274.0
47 TraesCS5A01G121500 chr7B 92.262 168 13 0 301 468 166580867 166581034 4.200000e-59 239.0
48 TraesCS5A01G121500 chr7B 90.854 164 15 0 305 468 329029185 329029022 1.520000e-53 220.0
49 TraesCS5A01G121500 chr7B 100.000 29 0 0 529 557 244721691 244721719 2.000000e-03 54.7
50 TraesCS5A01G121500 chr7B 100.000 29 0 0 529 557 643112769 643112741 2.000000e-03 54.7
51 TraesCS5A01G121500 chr3A 88.333 120 12 2 942 1061 181044486 181044603 3.380000e-30 143.0
52 TraesCS5A01G121500 chr6B 100.000 28 0 0 530 557 159814207 159814180 6.000000e-03 52.8


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 TraesCS5A01G121500 chr5A 262469531 262472784 3253 True 6010.0 6010 100.0000 1 3254 1 chr5A.!!$R1 3253
1 TraesCS5A01G121500 chr2A 694741485 694745568 4083 True 2671.5 4857 93.4150 305 3254 2 chr2A.!!$R2 2949
2 TraesCS5A01G121500 chr7A 709135664 709138623 2959 True 4756.0 4756 95.7250 302 3254 1 chr7A.!!$R1 2952
3 TraesCS5A01G121500 chr1A 446217430 446219594 2164 False 3428.0 3428 95.3370 305 2458 1 chr1A.!!$F1 2153
4 TraesCS5A01G121500 chr3B 73031977 73034364 2387 False 1929.0 3386 96.1820 847 3254 2 chr3B.!!$F1 2407
5 TraesCS5A01G121500 chr3B 452561096 452562459 1363 True 1142.0 1849 95.9025 847 2257 2 chr3B.!!$R2 1410
6 TraesCS5A01G121500 chr1D 97784392 97786081 1689 True 2772.0 2772 96.2740 1564 3254 1 chr1D.!!$R1 1690
7 TraesCS5A01G121500 chr5D 309067212 309069215 2003 True 1628.5 2702 95.8230 609 3253 2 chr5D.!!$R3 2644
8 TraesCS5A01G121500 chr4D 77912185 77914187 2002 False 1630.0 2702 95.9640 610 3253 2 chr4D.!!$F2 2643
9 TraesCS5A01G121500 chr6D 56195689 56197356 1667 False 2691.0 2691 95.6210 1564 3253 1 chr6D.!!$F1 1689
10 TraesCS5A01G121500 chr6D 75300807 75302808 2001 True 1614.0 2684 95.4435 609 3253 2 chr6D.!!$R1 2644
11 TraesCS5A01G121500 chr3D 149697099 149699102 2003 True 1614.5 2680 95.5840 609 3253 2 chr3D.!!$R1 2644
12 TraesCS5A01G121500 chr5B 563524403 563526079 1676 True 1291.0 2050 93.5535 572 2869 2 chr5B.!!$R2 2297
13 TraesCS5A01G121500 chr4B 629908021 629909387 1366 False 1141.0 1844 95.8565 847 2257 2 chr4B.!!$F1 1410
14 TraesCS5A01G121500 chr4B 665900863 665902231 1368 False 1130.0 1844 95.1670 847 2257 2 chr4B.!!$F2 1410
15 TraesCS5A01G121500 chr1B 568571087 568571712 625 True 808.0 808 89.9050 936 1568 1 chr1B.!!$R1 632

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
293 294 0.033642 GCGCCAAGGGAGTAGGATAC 59.966 60.0 0.0 0.0 43.47 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 3510 1.272203 TGTGTGTCCCCACTTTGTGTT 60.272 47.619 0.0 0.0 42.34 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.814410 ACACACGTTCAGCTCGATG 58.186 52.632 0.00 1.36 0.00 3.84
19 20 0.313987 ACACACGTTCAGCTCGATGA 59.686 50.000 0.00 0.00 0.00 2.92
20 21 0.710567 CACACGTTCAGCTCGATGAC 59.289 55.000 0.00 0.00 0.00 3.06
21 22 0.729478 ACACGTTCAGCTCGATGACG 60.729 55.000 0.00 4.93 41.26 4.35
22 23 0.729478 CACGTTCAGCTCGATGACGT 60.729 55.000 0.00 5.49 37.39 4.34
23 24 0.454620 ACGTTCAGCTCGATGACGTC 60.455 55.000 9.11 9.11 40.69 4.34
24 25 1.134530 CGTTCAGCTCGATGACGTCC 61.135 60.000 14.12 0.00 40.69 4.79
25 26 0.802607 GTTCAGCTCGATGACGTCCC 60.803 60.000 14.12 3.95 40.69 4.46
26 27 1.248101 TTCAGCTCGATGACGTCCCA 61.248 55.000 14.12 0.00 40.69 4.37
27 28 1.517257 CAGCTCGATGACGTCCCAC 60.517 63.158 14.12 3.43 40.69 4.61
29 30 3.047718 GCTCGATGACGTCCCACGA 62.048 63.158 20.86 20.86 46.05 4.35
30 31 1.504900 CTCGATGACGTCCCACGAA 59.495 57.895 21.82 11.33 46.05 3.85
31 32 0.797249 CTCGATGACGTCCCACGAAC 60.797 60.000 21.82 1.35 46.05 3.95
32 33 1.211969 CGATGACGTCCCACGAACT 59.788 57.895 14.12 0.00 46.05 3.01
33 34 0.797249 CGATGACGTCCCACGAACTC 60.797 60.000 14.12 0.00 46.05 3.01
34 35 0.458025 GATGACGTCCCACGAACTCC 60.458 60.000 14.12 0.00 46.05 3.85
35 36 2.126580 GACGTCCCACGAACTCCG 60.127 66.667 3.51 0.00 46.05 4.63
36 37 2.595463 ACGTCCCACGAACTCCGA 60.595 61.111 2.48 0.00 46.05 4.55
37 38 1.930908 GACGTCCCACGAACTCCGAT 61.931 60.000 3.51 0.00 46.05 4.18
38 39 1.226603 CGTCCCACGAACTCCGATC 60.227 63.158 0.00 0.00 46.05 3.69
39 40 1.141234 GTCCCACGAACTCCGATCC 59.859 63.158 0.00 0.00 41.76 3.36
40 41 1.304630 TCCCACGAACTCCGATCCA 60.305 57.895 0.00 0.00 41.76 3.41
41 42 1.141881 CCCACGAACTCCGATCCAG 59.858 63.158 0.00 0.00 41.76 3.86
42 43 1.519455 CCACGAACTCCGATCCAGC 60.519 63.158 0.00 0.00 41.76 4.85
43 44 1.215382 CACGAACTCCGATCCAGCA 59.785 57.895 0.00 0.00 41.76 4.41
44 45 0.803768 CACGAACTCCGATCCAGCAG 60.804 60.000 0.00 0.00 41.76 4.24
45 46 0.965866 ACGAACTCCGATCCAGCAGA 60.966 55.000 0.00 0.00 41.76 4.26
46 47 0.248825 CGAACTCCGATCCAGCAGAG 60.249 60.000 0.00 0.00 41.76 3.35
47 48 0.529555 GAACTCCGATCCAGCAGAGC 60.530 60.000 0.00 0.00 0.00 4.09
48 49 0.975040 AACTCCGATCCAGCAGAGCT 60.975 55.000 0.00 0.00 40.77 4.09
49 50 0.975040 ACTCCGATCCAGCAGAGCTT 60.975 55.000 0.00 0.00 36.40 3.74
50 51 0.249405 CTCCGATCCAGCAGAGCTTC 60.249 60.000 0.00 0.00 36.40 3.86
51 52 0.972471 TCCGATCCAGCAGAGCTTCA 60.972 55.000 0.00 0.00 36.40 3.02
52 53 0.809241 CCGATCCAGCAGAGCTTCAC 60.809 60.000 0.00 0.00 36.40 3.18
53 54 0.108472 CGATCCAGCAGAGCTTCACA 60.108 55.000 0.00 0.00 36.40 3.58
54 55 1.654317 GATCCAGCAGAGCTTCACAG 58.346 55.000 0.00 0.00 36.40 3.66
55 56 1.206610 GATCCAGCAGAGCTTCACAGA 59.793 52.381 0.00 0.00 36.40 3.41
56 57 1.051008 TCCAGCAGAGCTTCACAGAA 58.949 50.000 0.00 0.00 36.40 3.02
57 58 1.001746 TCCAGCAGAGCTTCACAGAAG 59.998 52.381 2.48 2.48 36.40 2.85
58 59 1.001746 CCAGCAGAGCTTCACAGAAGA 59.998 52.381 10.72 0.00 36.40 2.87
59 60 2.339418 CAGCAGAGCTTCACAGAAGAG 58.661 52.381 10.72 0.00 36.40 2.85
60 61 1.969923 AGCAGAGCTTCACAGAAGAGT 59.030 47.619 10.72 0.00 33.89 3.24
61 62 2.368221 AGCAGAGCTTCACAGAAGAGTT 59.632 45.455 10.72 0.00 33.89 3.01
62 63 2.736192 GCAGAGCTTCACAGAAGAGTTC 59.264 50.000 10.72 5.01 0.00 3.01
63 64 3.324993 CAGAGCTTCACAGAAGAGTTCC 58.675 50.000 10.72 0.00 0.00 3.62
64 65 2.029470 AGAGCTTCACAGAAGAGTTCCG 60.029 50.000 10.72 0.00 0.00 4.30
65 66 1.689273 AGCTTCACAGAAGAGTTCCGT 59.311 47.619 10.72 0.00 0.00 4.69
66 67 2.062519 GCTTCACAGAAGAGTTCCGTC 58.937 52.381 10.72 0.00 0.00 4.79
67 68 2.545952 GCTTCACAGAAGAGTTCCGTCA 60.546 50.000 10.72 0.00 0.00 4.35
68 69 3.312828 CTTCACAGAAGAGTTCCGTCAG 58.687 50.000 0.52 0.00 0.00 3.51
69 70 1.000163 TCACAGAAGAGTTCCGTCAGC 60.000 52.381 0.00 0.00 0.00 4.26
70 71 1.040646 ACAGAAGAGTTCCGTCAGCA 58.959 50.000 0.00 0.00 0.00 4.41
71 72 1.269831 ACAGAAGAGTTCCGTCAGCAC 60.270 52.381 0.00 0.00 0.00 4.40
72 73 0.039074 AGAAGAGTTCCGTCAGCACG 60.039 55.000 0.00 0.00 46.29 5.34
88 89 2.202743 CGACGGCGTGATGATGGT 60.203 61.111 21.19 0.00 0.00 3.55
89 90 2.516589 CGACGGCGTGATGATGGTG 61.517 63.158 21.19 0.00 0.00 4.17
90 91 1.153647 GACGGCGTGATGATGGTGA 60.154 57.895 21.19 0.00 0.00 4.02
91 92 0.530650 GACGGCGTGATGATGGTGAT 60.531 55.000 21.19 0.00 0.00 3.06
92 93 0.811219 ACGGCGTGATGATGGTGATG 60.811 55.000 13.76 0.00 0.00 3.07
93 94 0.530431 CGGCGTGATGATGGTGATGA 60.530 55.000 0.00 0.00 0.00 2.92
94 95 1.875157 CGGCGTGATGATGGTGATGAT 60.875 52.381 0.00 0.00 0.00 2.45
95 96 1.534163 GGCGTGATGATGGTGATGATG 59.466 52.381 0.00 0.00 0.00 3.07
96 97 2.216046 GCGTGATGATGGTGATGATGT 58.784 47.619 0.00 0.00 0.00 3.06
97 98 2.615447 GCGTGATGATGGTGATGATGTT 59.385 45.455 0.00 0.00 0.00 2.71
98 99 3.547413 GCGTGATGATGGTGATGATGTTG 60.547 47.826 0.00 0.00 0.00 3.33
99 100 3.547413 CGTGATGATGGTGATGATGTTGC 60.547 47.826 0.00 0.00 0.00 4.17
100 101 3.630769 GTGATGATGGTGATGATGTTGCT 59.369 43.478 0.00 0.00 0.00 3.91
101 102 4.818005 GTGATGATGGTGATGATGTTGCTA 59.182 41.667 0.00 0.00 0.00 3.49
102 103 4.818005 TGATGATGGTGATGATGTTGCTAC 59.182 41.667 0.00 0.00 0.00 3.58
103 104 3.544684 TGATGGTGATGATGTTGCTACC 58.455 45.455 0.00 0.00 0.00 3.18
104 105 2.022764 TGGTGATGATGTTGCTACCG 57.977 50.000 0.00 0.00 0.00 4.02
105 106 1.552792 TGGTGATGATGTTGCTACCGA 59.447 47.619 0.00 0.00 0.00 4.69
106 107 1.933853 GGTGATGATGTTGCTACCGAC 59.066 52.381 0.00 0.00 0.00 4.79
107 108 1.588404 GTGATGATGTTGCTACCGACG 59.412 52.381 0.00 0.00 0.00 5.12
108 109 0.577269 GATGATGTTGCTACCGACGC 59.423 55.000 0.00 0.00 0.00 5.19
109 110 0.108377 ATGATGTTGCTACCGACGCA 60.108 50.000 0.00 0.00 35.22 5.24
110 111 0.735978 TGATGTTGCTACCGACGCAG 60.736 55.000 0.00 0.00 38.80 5.18
111 112 1.421410 GATGTTGCTACCGACGCAGG 61.421 60.000 0.00 0.00 38.80 4.85
112 113 2.813908 GTTGCTACCGACGCAGGG 60.814 66.667 1.73 0.00 38.80 4.45
113 114 4.752879 TTGCTACCGACGCAGGGC 62.753 66.667 1.73 0.00 38.80 5.19
115 116 4.452733 GCTACCGACGCAGGGCTT 62.453 66.667 1.73 0.00 35.02 4.35
116 117 2.202756 CTACCGACGCAGGGCTTC 60.203 66.667 1.73 0.00 35.02 3.86
117 118 4.124351 TACCGACGCAGGGCTTCG 62.124 66.667 9.73 9.73 47.00 3.79
130 131 2.125512 CTTCGCCTAAGCACCGCT 60.126 61.111 0.00 0.00 42.56 5.52
131 132 1.141019 CTTCGCCTAAGCACCGCTA 59.859 57.895 0.00 0.00 38.25 4.26
132 133 0.249489 CTTCGCCTAAGCACCGCTAT 60.249 55.000 0.00 0.00 38.25 2.97
133 134 0.529773 TTCGCCTAAGCACCGCTATG 60.530 55.000 0.00 0.00 38.25 2.23
134 135 1.067416 CGCCTAAGCACCGCTATGA 59.933 57.895 0.00 0.00 38.25 2.15
135 136 0.319900 CGCCTAAGCACCGCTATGAT 60.320 55.000 0.00 0.00 38.25 2.45
136 137 1.067846 CGCCTAAGCACCGCTATGATA 60.068 52.381 0.00 0.00 38.25 2.15
137 138 2.417379 CGCCTAAGCACCGCTATGATAT 60.417 50.000 0.00 0.00 38.25 1.63
138 139 2.932614 GCCTAAGCACCGCTATGATATG 59.067 50.000 0.00 0.00 38.25 1.78
139 140 3.368427 GCCTAAGCACCGCTATGATATGA 60.368 47.826 0.00 0.00 38.25 2.15
140 141 4.177026 CCTAAGCACCGCTATGATATGAC 58.823 47.826 0.00 0.00 38.25 3.06
141 142 2.751166 AGCACCGCTATGATATGACC 57.249 50.000 0.00 0.00 36.99 4.02
142 143 1.067565 AGCACCGCTATGATATGACCG 60.068 52.381 0.00 0.00 36.99 4.79
143 144 1.067846 GCACCGCTATGATATGACCGA 60.068 52.381 0.00 0.00 0.00 4.69
144 145 2.868662 CACCGCTATGATATGACCGAG 58.131 52.381 0.00 0.00 0.00 4.63
145 146 1.819288 ACCGCTATGATATGACCGAGG 59.181 52.381 0.00 0.00 0.00 4.63
146 147 1.819288 CCGCTATGATATGACCGAGGT 59.181 52.381 0.00 0.00 0.00 3.85
147 148 2.416027 CCGCTATGATATGACCGAGGTG 60.416 54.545 0.00 0.00 0.00 4.00
148 149 2.416027 CGCTATGATATGACCGAGGTGG 60.416 54.545 0.00 0.00 46.41 4.61
149 150 2.826128 GCTATGATATGACCGAGGTGGA 59.174 50.000 0.00 0.00 42.00 4.02
150 151 3.258372 GCTATGATATGACCGAGGTGGAA 59.742 47.826 0.00 0.00 42.00 3.53
151 152 4.081420 GCTATGATATGACCGAGGTGGAAT 60.081 45.833 0.00 0.00 42.00 3.01
152 153 5.127194 GCTATGATATGACCGAGGTGGAATA 59.873 44.000 0.00 0.00 42.00 1.75
153 154 6.183360 GCTATGATATGACCGAGGTGGAATAT 60.183 42.308 0.00 0.85 42.00 1.28
154 155 5.405935 TGATATGACCGAGGTGGAATATG 57.594 43.478 0.00 0.00 42.00 1.78
155 156 4.222810 TGATATGACCGAGGTGGAATATGG 59.777 45.833 0.00 0.00 42.00 2.74
156 157 1.874129 TGACCGAGGTGGAATATGGT 58.126 50.000 0.00 0.00 42.00 3.55
157 158 1.484653 TGACCGAGGTGGAATATGGTG 59.515 52.381 0.00 0.00 42.00 4.17
158 159 0.837272 ACCGAGGTGGAATATGGTGG 59.163 55.000 0.00 0.00 42.00 4.61
159 160 1.128200 CCGAGGTGGAATATGGTGGA 58.872 55.000 0.00 0.00 42.00 4.02
160 161 1.070758 CCGAGGTGGAATATGGTGGAG 59.929 57.143 0.00 0.00 42.00 3.86
161 162 1.070758 CGAGGTGGAATATGGTGGAGG 59.929 57.143 0.00 0.00 0.00 4.30
162 163 1.421646 GAGGTGGAATATGGTGGAGGG 59.578 57.143 0.00 0.00 0.00 4.30
163 164 0.478507 GGTGGAATATGGTGGAGGGG 59.521 60.000 0.00 0.00 0.00 4.79
164 165 0.478507 GTGGAATATGGTGGAGGGGG 59.521 60.000 0.00 0.00 0.00 5.40
165 166 1.360393 TGGAATATGGTGGAGGGGGC 61.360 60.000 0.00 0.00 0.00 5.80
166 167 1.360393 GGAATATGGTGGAGGGGGCA 61.360 60.000 0.00 0.00 0.00 5.36
167 168 0.178990 GAATATGGTGGAGGGGGCAC 60.179 60.000 0.00 0.00 0.00 5.01
182 183 2.591429 CACCGCACACAGCTGGAA 60.591 61.111 19.93 0.00 42.61 3.53
183 184 1.968017 CACCGCACACAGCTGGAAT 60.968 57.895 19.93 0.00 42.61 3.01
184 185 0.673333 CACCGCACACAGCTGGAATA 60.673 55.000 19.93 0.00 42.61 1.75
185 186 0.391661 ACCGCACACAGCTGGAATAG 60.392 55.000 19.93 6.23 42.61 1.73
186 187 0.108186 CCGCACACAGCTGGAATAGA 60.108 55.000 19.93 0.00 42.61 1.98
187 188 1.473965 CCGCACACAGCTGGAATAGAT 60.474 52.381 19.93 0.00 42.61 1.98
188 189 1.863454 CGCACACAGCTGGAATAGATC 59.137 52.381 19.93 0.00 42.61 2.75
189 190 2.739609 CGCACACAGCTGGAATAGATCA 60.740 50.000 19.93 0.00 42.61 2.92
190 191 3.273434 GCACACAGCTGGAATAGATCAA 58.727 45.455 19.93 0.00 41.15 2.57
191 192 3.064545 GCACACAGCTGGAATAGATCAAC 59.935 47.826 19.93 0.00 41.15 3.18
192 193 4.256110 CACACAGCTGGAATAGATCAACA 58.744 43.478 19.93 0.00 0.00 3.33
193 194 4.331992 CACACAGCTGGAATAGATCAACAG 59.668 45.833 19.93 0.00 0.00 3.16
194 195 4.223700 ACACAGCTGGAATAGATCAACAGA 59.776 41.667 19.93 0.00 0.00 3.41
195 196 5.104610 ACACAGCTGGAATAGATCAACAGAT 60.105 40.000 19.93 0.00 0.00 2.90
196 197 5.466058 CACAGCTGGAATAGATCAACAGATC 59.534 44.000 19.93 0.00 38.74 2.75
197 198 5.129980 ACAGCTGGAATAGATCAACAGATCA 59.870 40.000 19.93 0.00 40.49 2.92
198 199 6.053650 CAGCTGGAATAGATCAACAGATCAA 58.946 40.000 5.57 0.00 40.49 2.57
199 200 6.018098 CAGCTGGAATAGATCAACAGATCAAC 60.018 42.308 5.57 0.00 40.49 3.18
200 201 6.054295 GCTGGAATAGATCAACAGATCAACT 58.946 40.000 8.06 0.00 40.49 3.16
201 202 6.541641 GCTGGAATAGATCAACAGATCAACTT 59.458 38.462 8.06 0.00 40.49 2.66
202 203 7.466996 GCTGGAATAGATCAACAGATCAACTTG 60.467 40.741 8.06 0.00 40.49 3.16
203 204 7.397221 TGGAATAGATCAACAGATCAACTTGT 58.603 34.615 8.06 0.00 40.49 3.16
204 205 7.335171 TGGAATAGATCAACAGATCAACTTGTG 59.665 37.037 8.06 0.00 40.49 3.33
205 206 7.335422 GGAATAGATCAACAGATCAACTTGTGT 59.665 37.037 8.06 0.00 40.49 3.72
206 207 5.936686 AGATCAACAGATCAACTTGTGTG 57.063 39.130 8.06 0.00 40.49 3.82
207 208 5.371526 AGATCAACAGATCAACTTGTGTGT 58.628 37.500 8.06 0.00 40.49 3.72
208 209 5.468072 AGATCAACAGATCAACTTGTGTGTC 59.532 40.000 8.06 0.00 40.49 3.67
209 210 3.876914 TCAACAGATCAACTTGTGTGTCC 59.123 43.478 0.00 0.00 0.00 4.02
210 211 3.845781 ACAGATCAACTTGTGTGTCCT 57.154 42.857 0.00 0.00 0.00 3.85
211 212 3.470709 ACAGATCAACTTGTGTGTCCTG 58.529 45.455 0.00 0.00 0.00 3.86
212 213 2.810274 CAGATCAACTTGTGTGTCCTGG 59.190 50.000 0.00 0.00 0.00 4.45
213 214 2.154462 GATCAACTTGTGTGTCCTGGG 58.846 52.381 0.00 0.00 0.00 4.45
214 215 0.182537 TCAACTTGTGTGTCCTGGGG 59.817 55.000 0.00 0.00 0.00 4.96
215 216 0.106719 CAACTTGTGTGTCCTGGGGT 60.107 55.000 0.00 0.00 0.00 4.95
216 217 0.106719 AACTTGTGTGTCCTGGGGTG 60.107 55.000 0.00 0.00 0.00 4.61
217 218 1.898574 CTTGTGTGTCCTGGGGTGC 60.899 63.158 0.00 0.00 0.00 5.01
218 219 3.429372 TTGTGTGTCCTGGGGTGCC 62.429 63.158 0.00 0.00 0.00 5.01
219 220 4.660938 GTGTGTCCTGGGGTGCCC 62.661 72.222 0.00 0.00 45.71 5.36
232 233 4.881381 TGCCCCCTGCCCCCATAT 62.881 66.667 0.00 0.00 40.16 1.78
233 234 2.534272 GCCCCCTGCCCCCATATA 60.534 66.667 0.00 0.00 0.00 0.86
234 235 1.935931 GCCCCCTGCCCCCATATAT 60.936 63.158 0.00 0.00 0.00 0.86
235 236 1.937924 GCCCCCTGCCCCCATATATC 61.938 65.000 0.00 0.00 0.00 1.63
236 237 0.552367 CCCCCTGCCCCCATATATCA 60.552 60.000 0.00 0.00 0.00 2.15
237 238 1.381867 CCCCTGCCCCCATATATCAA 58.618 55.000 0.00 0.00 0.00 2.57
238 239 1.285962 CCCCTGCCCCCATATATCAAG 59.714 57.143 0.00 0.00 0.00 3.02
239 240 1.285962 CCCTGCCCCCATATATCAAGG 59.714 57.143 0.00 0.00 0.00 3.61
240 241 2.278245 CCTGCCCCCATATATCAAGGA 58.722 52.381 0.00 0.00 0.00 3.36
241 242 2.240667 CCTGCCCCCATATATCAAGGAG 59.759 54.545 0.00 0.00 0.00 3.69
242 243 1.635487 TGCCCCCATATATCAAGGAGC 59.365 52.381 0.00 0.00 0.00 4.70
243 244 1.635487 GCCCCCATATATCAAGGAGCA 59.365 52.381 0.00 0.00 0.00 4.26
244 245 2.041620 GCCCCCATATATCAAGGAGCAA 59.958 50.000 0.00 0.00 0.00 3.91
245 246 3.875369 GCCCCCATATATCAAGGAGCAAG 60.875 52.174 0.00 0.00 0.00 4.01
246 247 3.308688 CCCCCATATATCAAGGAGCAAGG 60.309 52.174 0.00 0.00 0.00 3.61
247 248 3.308688 CCCCATATATCAAGGAGCAAGGG 60.309 52.174 0.00 0.00 0.00 3.95
248 249 3.588842 CCCATATATCAAGGAGCAAGGGA 59.411 47.826 0.00 0.00 34.49 4.20
249 250 4.324099 CCCATATATCAAGGAGCAAGGGAG 60.324 50.000 0.00 0.00 34.49 4.30
250 251 4.324099 CCATATATCAAGGAGCAAGGGAGG 60.324 50.000 0.00 0.00 0.00 4.30
251 252 2.568546 TATCAAGGAGCAAGGGAGGA 57.431 50.000 0.00 0.00 0.00 3.71
252 253 1.211456 ATCAAGGAGCAAGGGAGGAG 58.789 55.000 0.00 0.00 0.00 3.69
253 254 0.911525 TCAAGGAGCAAGGGAGGAGG 60.912 60.000 0.00 0.00 0.00 4.30
254 255 0.911525 CAAGGAGCAAGGGAGGAGGA 60.912 60.000 0.00 0.00 0.00 3.71
255 256 0.620121 AAGGAGCAAGGGAGGAGGAG 60.620 60.000 0.00 0.00 0.00 3.69
256 257 2.069430 GGAGCAAGGGAGGAGGAGG 61.069 68.421 0.00 0.00 0.00 4.30
257 258 2.690510 AGCAAGGGAGGAGGAGGC 60.691 66.667 0.00 0.00 0.00 4.70
258 259 3.803162 GCAAGGGAGGAGGAGGCC 61.803 72.222 0.00 0.00 0.00 5.19
259 260 3.474570 CAAGGGAGGAGGAGGCCG 61.475 72.222 0.00 0.00 0.00 6.13
260 261 4.806339 AAGGGAGGAGGAGGCCGG 62.806 72.222 0.00 0.00 0.00 6.13
290 291 3.458163 CGCGCCAAGGGAGTAGGA 61.458 66.667 0.00 0.00 34.27 2.94
291 292 2.797278 CGCGCCAAGGGAGTAGGAT 61.797 63.158 0.00 0.00 34.27 3.24
292 293 1.461091 CGCGCCAAGGGAGTAGGATA 61.461 60.000 0.00 0.00 34.27 2.59
293 294 0.033642 GCGCCAAGGGAGTAGGATAC 59.966 60.000 0.00 0.00 43.47 2.24
294 295 0.680061 CGCCAAGGGAGTAGGATACC 59.320 60.000 0.00 0.00 44.47 2.73
295 296 1.758123 CGCCAAGGGAGTAGGATACCT 60.758 57.143 0.00 0.00 44.47 3.08
296 297 2.490351 CGCCAAGGGAGTAGGATACCTA 60.490 54.545 0.00 0.00 44.47 3.08
332 333 5.334421 ACTCCTAATGTCTCAGTTGGTAGT 58.666 41.667 0.00 0.00 0.00 2.73
333 334 5.419471 ACTCCTAATGTCTCAGTTGGTAGTC 59.581 44.000 0.00 0.00 0.00 2.59
364 365 4.157105 CGGATTTTATTTTCGTCCCACCTT 59.843 41.667 0.00 0.00 0.00 3.50
402 414 0.044244 CTTCCTCCCACCTTCCCCTA 59.956 60.000 0.00 0.00 0.00 3.53
408 420 2.298661 CCACCTTCCCCTAAGCCGT 61.299 63.158 0.00 0.00 33.49 5.68
512 524 6.770286 AATTACAGATCCCACCTATCATGT 57.230 37.500 0.00 0.00 0.00 3.21
590 1728 0.035458 CGCAAACAACTCCTCTCCCT 59.965 55.000 0.00 0.00 0.00 4.20
606 1744 2.196925 CCTGATAGCCCTCTCGCGT 61.197 63.158 5.77 0.00 0.00 6.01
839 1977 0.535553 GAGAGGTAGATCGAGGCGGT 60.536 60.000 0.00 0.00 0.00 5.68
970 2108 2.490115 TGCCTTTGTTTCTGTTTCGTGT 59.510 40.909 0.00 0.00 0.00 4.49
1067 2205 1.794785 GCGTCGTCATGTTCGTCGA 60.795 57.895 24.45 12.93 40.70 4.20
1111 2249 4.338879 ACTAACCTCGGTTACTTGCTCTA 58.661 43.478 4.47 0.00 39.31 2.43
1246 2425 4.217983 TGATGTTTAAGCACATGTGATGCA 59.782 37.500 29.80 19.03 45.92 3.96
1588 2767 1.699083 TCTGATTGTGCCTCCAAGACA 59.301 47.619 0.00 0.00 0.00 3.41
1782 2961 3.189287 GCACGAATTGGACTGAGAAATGT 59.811 43.478 0.00 0.00 0.00 2.71
1874 3053 5.739161 GCATTATTTTGCTGCAGTGTAGTAC 59.261 40.000 16.64 0.00 39.57 2.73
1924 3103 6.072199 AGCAAAAGGACTAGATGAAGGATT 57.928 37.500 0.00 0.00 0.00 3.01
2161 3361 4.555709 TTGGGTGCGGCAACTCGT 62.556 61.111 18.73 0.00 0.00 4.18
2190 3391 2.091333 AGACAATCTTTTGTGGTGGGGT 60.091 45.455 0.00 0.00 46.01 4.95
2283 3510 2.173782 TGTAGAAAGGAGGTGGTTGCAA 59.826 45.455 0.00 0.00 0.00 4.08
2387 3614 0.465097 CGCTCTCCTCCATGCCAAAT 60.465 55.000 0.00 0.00 0.00 2.32
2836 4064 9.950496 TCTTTCTGTTGATTCTTATAGAGCTTT 57.050 29.630 0.00 0.00 0.00 3.51
2856 4084 2.743718 CAAGAGGGCGTCACCTGT 59.256 61.111 10.15 0.00 42.10 4.00
2881 4109 3.708403 TCACTTGCATTGACCTCTCAT 57.292 42.857 0.00 0.00 0.00 2.90
2974 4202 4.165565 TCGACTCATAGTTCCCTTCCTCTA 59.834 45.833 0.00 0.00 0.00 2.43
3031 4259 3.317455 TTCATCAGGCCCATTATTGCT 57.683 42.857 0.00 0.00 0.00 3.91
3184 4417 8.275040 ACTACTTGCATGAATTTTAGACCCTAT 58.725 33.333 6.60 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.313987 TCATCGAGCTGAACGTGTGT 59.686 50.000 0.00 0.00 0.00 3.72
2 3 0.729478 CGTCATCGAGCTGAACGTGT 60.729 55.000 0.00 0.00 39.71 4.49
3 4 0.729478 ACGTCATCGAGCTGAACGTG 60.729 55.000 12.23 3.66 40.62 4.49
4 5 0.454620 GACGTCATCGAGCTGAACGT 60.455 55.000 11.55 12.62 40.62 3.99
5 6 1.134530 GGACGTCATCGAGCTGAACG 61.135 60.000 18.91 0.00 40.62 3.95
7 8 1.248101 TGGGACGTCATCGAGCTGAA 61.248 55.000 18.91 0.00 40.62 3.02
8 9 1.677633 TGGGACGTCATCGAGCTGA 60.678 57.895 18.91 0.00 40.62 4.26
9 10 1.517257 GTGGGACGTCATCGAGCTG 60.517 63.158 18.91 0.00 40.62 4.24
10 11 2.885861 GTGGGACGTCATCGAGCT 59.114 61.111 18.91 0.00 40.62 4.09
11 12 2.537792 TTCGTGGGACGTCATCGAGC 62.538 60.000 18.91 0.00 43.14 5.03
12 13 0.797249 GTTCGTGGGACGTCATCGAG 60.797 60.000 18.91 4.47 43.14 4.04
13 14 1.210931 GTTCGTGGGACGTCATCGA 59.789 57.895 18.91 19.14 43.14 3.59
14 15 0.797249 GAGTTCGTGGGACGTCATCG 60.797 60.000 18.91 17.24 43.14 3.84
15 16 0.458025 GGAGTTCGTGGGACGTCATC 60.458 60.000 18.91 9.49 43.14 2.92
16 17 1.590147 GGAGTTCGTGGGACGTCAT 59.410 57.895 18.91 0.00 43.14 3.06
17 18 2.911484 CGGAGTTCGTGGGACGTCA 61.911 63.158 18.91 0.00 43.14 4.35
18 19 1.930908 ATCGGAGTTCGTGGGACGTC 61.931 60.000 7.13 7.13 43.14 4.34
19 20 1.930908 GATCGGAGTTCGTGGGACGT 61.931 60.000 0.00 0.00 43.14 4.34
20 21 1.226603 GATCGGAGTTCGTGGGACG 60.227 63.158 0.00 0.00 44.19 4.79
21 22 1.141234 GGATCGGAGTTCGTGGGAC 59.859 63.158 0.00 0.00 40.32 4.46
22 23 1.304630 TGGATCGGAGTTCGTGGGA 60.305 57.895 0.00 0.00 40.32 4.37
23 24 1.141881 CTGGATCGGAGTTCGTGGG 59.858 63.158 0.00 0.00 40.32 4.61
24 25 1.519455 GCTGGATCGGAGTTCGTGG 60.519 63.158 0.00 0.00 40.32 4.94
25 26 0.803768 CTGCTGGATCGGAGTTCGTG 60.804 60.000 0.00 0.00 40.32 4.35
26 27 0.965866 TCTGCTGGATCGGAGTTCGT 60.966 55.000 0.00 0.00 40.32 3.85
27 28 0.248825 CTCTGCTGGATCGGAGTTCG 60.249 60.000 0.00 0.00 35.32 3.95
28 29 0.529555 GCTCTGCTGGATCGGAGTTC 60.530 60.000 2.12 0.00 40.67 3.01
29 30 0.975040 AGCTCTGCTGGATCGGAGTT 60.975 55.000 0.00 0.00 40.67 3.01
30 31 0.975040 AAGCTCTGCTGGATCGGAGT 60.975 55.000 0.00 0.00 39.62 3.85
31 32 0.249405 GAAGCTCTGCTGGATCGGAG 60.249 60.000 0.00 0.00 39.62 4.63
32 33 0.972471 TGAAGCTCTGCTGGATCGGA 60.972 55.000 0.00 0.00 39.62 4.55
33 34 0.809241 GTGAAGCTCTGCTGGATCGG 60.809 60.000 0.00 0.00 39.62 4.18
34 35 0.108472 TGTGAAGCTCTGCTGGATCG 60.108 55.000 0.00 0.00 39.62 3.69
35 36 1.206610 TCTGTGAAGCTCTGCTGGATC 59.793 52.381 0.00 0.00 39.62 3.36
36 37 1.273759 TCTGTGAAGCTCTGCTGGAT 58.726 50.000 0.00 0.00 39.62 3.41
37 38 1.001746 CTTCTGTGAAGCTCTGCTGGA 59.998 52.381 0.00 0.00 39.62 3.86
38 39 1.001746 TCTTCTGTGAAGCTCTGCTGG 59.998 52.381 2.71 0.00 39.62 4.85
39 40 2.288948 ACTCTTCTGTGAAGCTCTGCTG 60.289 50.000 2.71 0.00 39.62 4.41
40 41 1.969923 ACTCTTCTGTGAAGCTCTGCT 59.030 47.619 2.71 0.00 42.56 4.24
41 42 2.453983 ACTCTTCTGTGAAGCTCTGC 57.546 50.000 2.71 0.00 0.00 4.26
42 43 3.324993 GGAACTCTTCTGTGAAGCTCTG 58.675 50.000 2.71 0.00 0.00 3.35
43 44 2.029470 CGGAACTCTTCTGTGAAGCTCT 60.029 50.000 2.71 0.00 0.00 4.09
44 45 2.333014 CGGAACTCTTCTGTGAAGCTC 58.667 52.381 2.71 0.62 0.00 4.09
45 46 2.447244 CGGAACTCTTCTGTGAAGCT 57.553 50.000 2.71 0.00 0.00 3.74
52 53 1.423395 GTGCTGACGGAACTCTTCTG 58.577 55.000 0.00 0.00 41.86 3.02
53 54 0.039074 CGTGCTGACGGAACTCTTCT 60.039 55.000 0.00 0.00 42.18 2.85
54 55 0.039437 TCGTGCTGACGGAACTCTTC 60.039 55.000 0.00 0.00 46.11 2.87
55 56 0.318784 GTCGTGCTGACGGAACTCTT 60.319 55.000 0.00 0.00 46.11 2.85
56 57 1.286260 GTCGTGCTGACGGAACTCT 59.714 57.895 0.00 0.00 46.11 3.24
57 58 3.843985 GTCGTGCTGACGGAACTC 58.156 61.111 0.00 0.00 46.11 3.01
71 72 2.202743 ACCATCATCACGCCGTCG 60.203 61.111 0.00 0.00 42.43 5.12
72 73 0.530650 ATCACCATCATCACGCCGTC 60.531 55.000 0.00 0.00 0.00 4.79
73 74 0.811219 CATCACCATCATCACGCCGT 60.811 55.000 0.00 0.00 0.00 5.68
74 75 0.530431 TCATCACCATCATCACGCCG 60.530 55.000 0.00 0.00 0.00 6.46
75 76 1.534163 CATCATCACCATCATCACGCC 59.466 52.381 0.00 0.00 0.00 5.68
76 77 2.216046 ACATCATCACCATCATCACGC 58.784 47.619 0.00 0.00 0.00 5.34
77 78 3.547413 GCAACATCATCACCATCATCACG 60.547 47.826 0.00 0.00 0.00 4.35
78 79 3.630769 AGCAACATCATCACCATCATCAC 59.369 43.478 0.00 0.00 0.00 3.06
79 80 3.893521 AGCAACATCATCACCATCATCA 58.106 40.909 0.00 0.00 0.00 3.07
80 81 4.214971 GGTAGCAACATCATCACCATCATC 59.785 45.833 0.00 0.00 0.00 2.92
81 82 4.139786 GGTAGCAACATCATCACCATCAT 58.860 43.478 0.00 0.00 0.00 2.45
82 83 3.544684 GGTAGCAACATCATCACCATCA 58.455 45.455 0.00 0.00 0.00 3.07
83 84 2.545526 CGGTAGCAACATCATCACCATC 59.454 50.000 0.00 0.00 0.00 3.51
84 85 2.170397 TCGGTAGCAACATCATCACCAT 59.830 45.455 0.00 0.00 0.00 3.55
85 86 1.552792 TCGGTAGCAACATCATCACCA 59.447 47.619 0.00 0.00 0.00 4.17
86 87 1.933853 GTCGGTAGCAACATCATCACC 59.066 52.381 0.00 0.00 0.00 4.02
87 88 1.588404 CGTCGGTAGCAACATCATCAC 59.412 52.381 0.00 0.00 0.00 3.06
88 89 1.921243 CGTCGGTAGCAACATCATCA 58.079 50.000 0.00 0.00 0.00 3.07
89 90 0.577269 GCGTCGGTAGCAACATCATC 59.423 55.000 0.00 0.00 34.19 2.92
90 91 0.108377 TGCGTCGGTAGCAACATCAT 60.108 50.000 0.00 0.00 42.18 2.45
91 92 0.735978 CTGCGTCGGTAGCAACATCA 60.736 55.000 0.00 0.00 44.67 3.07
92 93 1.421410 CCTGCGTCGGTAGCAACATC 61.421 60.000 0.00 0.00 44.67 3.06
93 94 1.447838 CCTGCGTCGGTAGCAACAT 60.448 57.895 0.00 0.00 44.67 2.71
94 95 2.048597 CCTGCGTCGGTAGCAACA 60.049 61.111 0.00 0.00 44.67 3.33
95 96 2.813908 CCCTGCGTCGGTAGCAAC 60.814 66.667 0.00 0.00 44.67 4.17
96 97 4.752879 GCCCTGCGTCGGTAGCAA 62.753 66.667 0.00 0.00 44.67 3.91
98 99 4.452733 AAGCCCTGCGTCGGTAGC 62.453 66.667 0.00 0.00 0.00 3.58
99 100 2.202756 GAAGCCCTGCGTCGGTAG 60.203 66.667 0.00 0.00 0.00 3.18
113 114 0.249489 ATAGCGGTGCTTAGGCGAAG 60.249 55.000 2.68 2.68 40.44 3.79
114 115 0.529773 CATAGCGGTGCTTAGGCGAA 60.530 55.000 0.00 0.00 40.44 4.70
115 116 1.067416 CATAGCGGTGCTTAGGCGA 59.933 57.895 0.00 0.00 40.44 5.54
116 117 0.319900 ATCATAGCGGTGCTTAGGCG 60.320 55.000 0.00 0.00 40.44 5.52
117 118 2.743636 TATCATAGCGGTGCTTAGGC 57.256 50.000 0.00 0.00 40.44 3.93
118 119 4.177026 GTCATATCATAGCGGTGCTTAGG 58.823 47.826 0.00 0.00 40.44 2.69
119 120 4.177026 GGTCATATCATAGCGGTGCTTAG 58.823 47.826 0.00 0.00 40.44 2.18
120 121 3.366985 CGGTCATATCATAGCGGTGCTTA 60.367 47.826 0.00 0.00 40.44 3.09
121 122 2.610479 CGGTCATATCATAGCGGTGCTT 60.610 50.000 0.00 0.00 40.44 3.91
122 123 1.067565 CGGTCATATCATAGCGGTGCT 60.068 52.381 0.00 0.00 43.41 4.40
123 124 1.067846 TCGGTCATATCATAGCGGTGC 60.068 52.381 0.00 0.00 37.22 5.01
124 125 2.416027 CCTCGGTCATATCATAGCGGTG 60.416 54.545 0.00 0.00 37.22 4.94
125 126 1.819288 CCTCGGTCATATCATAGCGGT 59.181 52.381 0.00 0.00 37.22 5.68
126 127 1.819288 ACCTCGGTCATATCATAGCGG 59.181 52.381 0.00 0.00 37.22 5.52
127 128 2.416027 CCACCTCGGTCATATCATAGCG 60.416 54.545 0.00 0.00 37.92 4.26
128 129 2.826128 TCCACCTCGGTCATATCATAGC 59.174 50.000 0.00 0.00 35.57 2.97
129 130 5.667539 ATTCCACCTCGGTCATATCATAG 57.332 43.478 0.00 0.00 35.57 2.23
130 131 6.098266 CCATATTCCACCTCGGTCATATCATA 59.902 42.308 0.00 0.00 35.57 2.15
131 132 5.104776 CCATATTCCACCTCGGTCATATCAT 60.105 44.000 0.00 0.00 35.57 2.45
132 133 4.222810 CCATATTCCACCTCGGTCATATCA 59.777 45.833 0.00 0.00 35.57 2.15
133 134 4.223032 ACCATATTCCACCTCGGTCATATC 59.777 45.833 0.00 0.00 35.57 1.63
134 135 4.020218 CACCATATTCCACCTCGGTCATAT 60.020 45.833 0.00 0.00 35.57 1.78
135 136 3.323691 CACCATATTCCACCTCGGTCATA 59.676 47.826 0.00 0.00 35.57 2.15
136 137 2.104792 CACCATATTCCACCTCGGTCAT 59.895 50.000 0.00 0.00 35.57 3.06
137 138 1.484653 CACCATATTCCACCTCGGTCA 59.515 52.381 0.00 0.00 35.57 4.02
138 139 1.202651 CCACCATATTCCACCTCGGTC 60.203 57.143 0.00 0.00 35.57 4.79
139 140 0.837272 CCACCATATTCCACCTCGGT 59.163 55.000 0.00 0.00 35.57 4.69
140 141 1.070758 CTCCACCATATTCCACCTCGG 59.929 57.143 0.00 0.00 0.00 4.63
141 142 1.070758 CCTCCACCATATTCCACCTCG 59.929 57.143 0.00 0.00 0.00 4.63
142 143 1.421646 CCCTCCACCATATTCCACCTC 59.578 57.143 0.00 0.00 0.00 3.85
143 144 1.522900 CCCTCCACCATATTCCACCT 58.477 55.000 0.00 0.00 0.00 4.00
144 145 0.478507 CCCCTCCACCATATTCCACC 59.521 60.000 0.00 0.00 0.00 4.61
145 146 0.478507 CCCCCTCCACCATATTCCAC 59.521 60.000 0.00 0.00 0.00 4.02
146 147 1.360393 GCCCCCTCCACCATATTCCA 61.360 60.000 0.00 0.00 0.00 3.53
147 148 1.360393 TGCCCCCTCCACCATATTCC 61.360 60.000 0.00 0.00 0.00 3.01
148 149 0.178990 GTGCCCCCTCCACCATATTC 60.179 60.000 0.00 0.00 0.00 1.75
149 150 1.930520 GTGCCCCCTCCACCATATT 59.069 57.895 0.00 0.00 0.00 1.28
150 151 3.674278 GTGCCCCCTCCACCATAT 58.326 61.111 0.00 0.00 0.00 1.78
169 170 2.910199 TGATCTATTCCAGCTGTGTGC 58.090 47.619 13.81 0.00 43.29 4.57
170 171 4.256110 TGTTGATCTATTCCAGCTGTGTG 58.744 43.478 13.81 0.00 0.00 3.82
171 172 4.223700 TCTGTTGATCTATTCCAGCTGTGT 59.776 41.667 13.81 0.24 0.00 3.72
172 173 4.763073 TCTGTTGATCTATTCCAGCTGTG 58.237 43.478 13.81 4.33 0.00 3.66
173 174 5.129980 TGATCTGTTGATCTATTCCAGCTGT 59.870 40.000 13.81 0.00 46.84 4.40
174 175 5.608449 TGATCTGTTGATCTATTCCAGCTG 58.392 41.667 6.78 6.78 46.84 4.24
175 176 5.883685 TGATCTGTTGATCTATTCCAGCT 57.116 39.130 7.42 0.00 46.84 4.24
176 177 6.054295 AGTTGATCTGTTGATCTATTCCAGC 58.946 40.000 7.42 0.00 46.84 4.85
177 178 7.551974 ACAAGTTGATCTGTTGATCTATTCCAG 59.448 37.037 10.54 0.00 46.84 3.86
178 179 7.335171 CACAAGTTGATCTGTTGATCTATTCCA 59.665 37.037 10.54 0.00 46.84 3.53
179 180 7.335422 ACACAAGTTGATCTGTTGATCTATTCC 59.665 37.037 10.54 0.00 46.84 3.01
180 181 8.173775 CACACAAGTTGATCTGTTGATCTATTC 58.826 37.037 10.54 0.00 46.84 1.75
181 182 7.663081 ACACACAAGTTGATCTGTTGATCTATT 59.337 33.333 10.54 0.00 46.84 1.73
182 183 7.164122 ACACACAAGTTGATCTGTTGATCTAT 58.836 34.615 10.54 0.00 46.84 1.98
183 184 6.524734 ACACACAAGTTGATCTGTTGATCTA 58.475 36.000 10.54 0.00 46.84 1.98
184 185 5.371526 ACACACAAGTTGATCTGTTGATCT 58.628 37.500 10.54 0.00 46.84 2.75
185 186 5.334414 GGACACACAAGTTGATCTGTTGATC 60.334 44.000 10.54 1.89 46.89 2.92
186 187 4.516698 GGACACACAAGTTGATCTGTTGAT 59.483 41.667 10.54 0.00 35.26 2.57
187 188 3.876914 GGACACACAAGTTGATCTGTTGA 59.123 43.478 10.54 0.00 0.00 3.18
188 189 3.879295 AGGACACACAAGTTGATCTGTTG 59.121 43.478 10.54 0.00 0.00 3.33
189 190 3.879295 CAGGACACACAAGTTGATCTGTT 59.121 43.478 10.54 0.00 0.00 3.16
190 191 3.470709 CAGGACACACAAGTTGATCTGT 58.529 45.455 10.54 7.16 0.00 3.41
191 192 2.810274 CCAGGACACACAAGTTGATCTG 59.190 50.000 10.54 0.00 0.00 2.90
192 193 2.224621 CCCAGGACACACAAGTTGATCT 60.225 50.000 10.54 0.00 0.00 2.75
193 194 2.154462 CCCAGGACACACAAGTTGATC 58.846 52.381 10.54 1.59 0.00 2.92
194 195 1.202927 CCCCAGGACACACAAGTTGAT 60.203 52.381 10.54 0.00 0.00 2.57
195 196 0.182537 CCCCAGGACACACAAGTTGA 59.817 55.000 10.54 0.00 0.00 3.18
196 197 0.106719 ACCCCAGGACACACAAGTTG 60.107 55.000 0.00 0.00 0.00 3.16
197 198 0.106719 CACCCCAGGACACACAAGTT 60.107 55.000 0.00 0.00 0.00 2.66
198 199 1.531748 CACCCCAGGACACACAAGT 59.468 57.895 0.00 0.00 0.00 3.16
199 200 1.898574 GCACCCCAGGACACACAAG 60.899 63.158 0.00 0.00 0.00 3.16
200 201 2.194597 GCACCCCAGGACACACAA 59.805 61.111 0.00 0.00 0.00 3.33
201 202 3.884774 GGCACCCCAGGACACACA 61.885 66.667 0.00 0.00 0.00 3.72
216 217 1.935931 ATATATGGGGGCAGGGGGC 60.936 63.158 0.00 0.00 43.74 5.80
217 218 0.552367 TGATATATGGGGGCAGGGGG 60.552 60.000 0.00 0.00 0.00 5.40
218 219 1.285962 CTTGATATATGGGGGCAGGGG 59.714 57.143 0.00 0.00 0.00 4.79
219 220 1.285962 CCTTGATATATGGGGGCAGGG 59.714 57.143 0.00 0.00 0.00 4.45
220 221 2.240667 CTCCTTGATATATGGGGGCAGG 59.759 54.545 0.00 0.00 0.00 4.85
221 222 2.356535 GCTCCTTGATATATGGGGGCAG 60.357 54.545 13.08 4.17 0.00 4.85
222 223 1.635487 GCTCCTTGATATATGGGGGCA 59.365 52.381 13.08 0.00 0.00 5.36
223 224 1.635487 TGCTCCTTGATATATGGGGGC 59.365 52.381 11.73 11.73 0.00 5.80
224 225 3.308688 CCTTGCTCCTTGATATATGGGGG 60.309 52.174 0.00 0.00 0.00 5.40
225 226 3.308688 CCCTTGCTCCTTGATATATGGGG 60.309 52.174 0.00 0.00 0.00 4.96
226 227 3.588842 TCCCTTGCTCCTTGATATATGGG 59.411 47.826 0.00 0.00 0.00 4.00
227 228 4.324099 CCTCCCTTGCTCCTTGATATATGG 60.324 50.000 0.00 0.00 0.00 2.74
228 229 4.533707 TCCTCCCTTGCTCCTTGATATATG 59.466 45.833 0.00 0.00 0.00 1.78
229 230 4.767908 TCCTCCCTTGCTCCTTGATATAT 58.232 43.478 0.00 0.00 0.00 0.86
230 231 4.163427 CTCCTCCCTTGCTCCTTGATATA 58.837 47.826 0.00 0.00 0.00 0.86
231 232 2.978278 CTCCTCCCTTGCTCCTTGATAT 59.022 50.000 0.00 0.00 0.00 1.63
232 233 2.402564 CTCCTCCCTTGCTCCTTGATA 58.597 52.381 0.00 0.00 0.00 2.15
233 234 1.211456 CTCCTCCCTTGCTCCTTGAT 58.789 55.000 0.00 0.00 0.00 2.57
234 235 0.911525 CCTCCTCCCTTGCTCCTTGA 60.912 60.000 0.00 0.00 0.00 3.02
235 236 0.911525 TCCTCCTCCCTTGCTCCTTG 60.912 60.000 0.00 0.00 0.00 3.61
236 237 0.620121 CTCCTCCTCCCTTGCTCCTT 60.620 60.000 0.00 0.00 0.00 3.36
237 238 1.002792 CTCCTCCTCCCTTGCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
238 239 2.069430 CCTCCTCCTCCCTTGCTCC 61.069 68.421 0.00 0.00 0.00 4.70
239 240 2.741055 GCCTCCTCCTCCCTTGCTC 61.741 68.421 0.00 0.00 0.00 4.26
240 241 2.690510 GCCTCCTCCTCCCTTGCT 60.691 66.667 0.00 0.00 0.00 3.91
241 242 3.803162 GGCCTCCTCCTCCCTTGC 61.803 72.222 0.00 0.00 0.00 4.01
242 243 3.474570 CGGCCTCCTCCTCCCTTG 61.475 72.222 0.00 0.00 0.00 3.61
243 244 4.806339 CCGGCCTCCTCCTCCCTT 62.806 72.222 0.00 0.00 0.00 3.95
273 274 1.461091 TATCCTACTCCCTTGGCGCG 61.461 60.000 0.00 0.00 0.00 6.86
274 275 0.033642 GTATCCTACTCCCTTGGCGC 59.966 60.000 0.00 0.00 0.00 6.53
275 276 0.680061 GGTATCCTACTCCCTTGGCG 59.320 60.000 0.00 0.00 0.00 5.69
276 277 2.104669 AGGTATCCTACTCCCTTGGC 57.895 55.000 0.00 0.00 28.47 4.52
285 286 7.675619 AGTAGAGACTAGGAGTAGGTATCCTAC 59.324 44.444 15.65 15.65 45.58 3.18
286 287 7.778781 AGTAGAGACTAGGAGTAGGTATCCTA 58.221 42.308 0.00 1.98 45.58 2.94
288 289 6.070596 GGAGTAGAGACTAGGAGTAGGTATCC 60.071 50.000 0.00 0.00 35.45 2.59
289 290 6.727697 AGGAGTAGAGACTAGGAGTAGGTATC 59.272 46.154 0.00 0.00 35.45 2.24
290 291 6.636985 AGGAGTAGAGACTAGGAGTAGGTAT 58.363 44.000 0.00 0.00 35.45 2.73
291 292 6.041910 AGGAGTAGAGACTAGGAGTAGGTA 57.958 45.833 0.00 0.00 35.45 3.08
292 293 4.899486 AGGAGTAGAGACTAGGAGTAGGT 58.101 47.826 0.00 0.00 35.45 3.08
293 294 6.999705 TTAGGAGTAGAGACTAGGAGTAGG 57.000 45.833 0.00 0.00 35.45 3.18
294 295 7.970102 ACATTAGGAGTAGAGACTAGGAGTAG 58.030 42.308 0.00 0.00 35.45 2.57
295 296 7.790798 AGACATTAGGAGTAGAGACTAGGAGTA 59.209 40.741 0.00 0.00 35.45 2.59
296 297 6.618196 AGACATTAGGAGTAGAGACTAGGAGT 59.382 42.308 0.00 0.00 35.45 3.85
297 298 7.074653 AGACATTAGGAGTAGAGACTAGGAG 57.925 44.000 0.00 0.00 35.45 3.69
298 299 6.616137 TGAGACATTAGGAGTAGAGACTAGGA 59.384 42.308 0.00 0.00 35.45 2.94
299 300 6.833041 TGAGACATTAGGAGTAGAGACTAGG 58.167 44.000 0.00 0.00 35.45 3.02
300 301 7.506114 ACTGAGACATTAGGAGTAGAGACTAG 58.494 42.308 0.00 0.00 35.45 2.57
344 345 5.419788 GGGTAAGGTGGGACGAAAATAAAAT 59.580 40.000 0.00 0.00 0.00 1.82
348 349 2.093553 CGGGTAAGGTGGGACGAAAATA 60.094 50.000 0.00 0.00 0.00 1.40
402 414 1.770294 TCCTTGGTTTTTCACGGCTT 58.230 45.000 0.00 0.00 0.00 4.35
408 420 2.168728 CGGGGTTTTCCTTGGTTTTTCA 59.831 45.455 0.00 0.00 40.46 2.69
491 503 6.575244 AAACATGATAGGTGGGATCTGTAA 57.425 37.500 0.00 0.00 0.00 2.41
492 504 6.575244 AAAACATGATAGGTGGGATCTGTA 57.425 37.500 0.00 0.00 0.00 2.74
606 1744 1.899437 CGGCTCAAGGAACCCTAGCA 61.899 60.000 9.27 0.00 37.06 3.49
631 1769 2.043852 ATCGAGGAGCTCCGGTGT 60.044 61.111 26.95 9.79 42.08 4.16
905 2043 4.680237 CCCTCGTTGCCGCAGACA 62.680 66.667 0.00 0.00 0.00 3.41
970 2108 2.664851 CGTGAAGACGGCCTGCAA 60.665 61.111 0.00 0.00 42.18 4.08
995 2133 1.077501 CCGGGATCCAGCATGTTGT 60.078 57.895 15.23 0.00 0.00 3.32
1067 2205 1.701847 AGTGAGACTGACCCTGCAATT 59.298 47.619 0.00 0.00 0.00 2.32
1147 2326 4.051922 GCTACAAGCAATCATACGTAGCT 58.948 43.478 11.12 0.46 45.22 3.32
1152 2331 7.818493 ATATACAGCTACAAGCAATCATACG 57.182 36.000 1.22 0.00 45.56 3.06
1246 2425 3.198635 CAGTTCCCATGACACCTATGAGT 59.801 47.826 0.00 0.00 0.00 3.41
1291 2470 3.763097 TTTTGCTTGGCTATCATGACG 57.237 42.857 0.00 0.00 0.00 4.35
1782 2961 4.127918 TGGTCTTCTCCTCCTCTGTTAA 57.872 45.455 0.00 0.00 0.00 2.01
1924 3103 8.879342 ATTTCCACGTGTTTTTAAATCAATGA 57.121 26.923 15.65 0.00 0.00 2.57
2161 3361 3.250762 CACAAAAGATTGTCTTCGAGCCA 59.749 43.478 0.00 0.00 46.78 4.75
2283 3510 1.272203 TGTGTGTCCCCACTTTGTGTT 60.272 47.619 0.00 0.00 42.34 3.32
2387 3614 0.546747 ACCTCCGAACCAAGGATCCA 60.547 55.000 15.82 0.00 37.13 3.41
2415 3642 4.669318 GATAGAAAGGTTGTCATCGTCGA 58.331 43.478 0.00 0.00 0.00 4.20
2464 3691 3.762293 GTGGTGGCATCAACAGCA 58.238 55.556 0.00 0.00 41.90 4.41
2836 4064 2.281484 GGTGACGCCCTCTTGCAA 60.281 61.111 0.00 0.00 0.00 4.08
2841 4069 3.314331 CCACAGGTGACGCCCTCT 61.314 66.667 0.08 0.00 38.26 3.69
2871 4099 2.143876 TGGTGATCGATGAGAGGTCA 57.856 50.000 0.54 0.00 37.02 4.02
2881 4109 2.388526 ATCCTCAGGATGGTGATCGA 57.611 50.000 4.99 0.00 41.43 3.59
3031 4259 5.111989 GCAAGATGAACAGACTATGTAGCA 58.888 41.667 0.00 0.00 43.00 3.49
3155 4383 8.736244 GGGTCTAAAATTCATGCAAGTAGTTAA 58.264 33.333 0.00 0.00 0.00 2.01
3157 4385 6.948309 AGGGTCTAAAATTCATGCAAGTAGTT 59.052 34.615 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.