Multiple sequence alignment - TraesCS3D01G448700

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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 TraesCS3D01G448700 chr3D 100.000 4881 0 0 1 4881 557501991 557497111 0.000000e+00 9014.0
1 TraesCS3D01G448700 chr3D 89.452 1242 95 17 3064 4295 557523894 557522679 0.000000e+00 1535.0
2 TraesCS3D01G448700 chr3D 89.130 1242 99 17 3064 4295 557559379 557558164 0.000000e+00 1513.0
3 TraesCS3D01G448700 chr3D 90.744 605 41 8 884 1478 557525100 557524501 0.000000e+00 793.0
4 TraesCS3D01G448700 chr3D 88.246 553 43 9 3744 4295 557589505 557588974 4.120000e-180 641.0
5 TraesCS3D01G448700 chr3D 88.690 504 53 3 4269 4770 557521837 557521336 3.230000e-171 612.0
6 TraesCS3D01G448700 chr3D 88.168 524 44 9 944 1456 554836750 554837266 4.180000e-170 608.0
7 TraesCS3D01G448700 chr3D 94.805 77 4 0 769 845 557525189 557525113 2.390000e-23 121.0
8 TraesCS3D01G448700 chr3D 94.805 77 4 0 769 845 557560323 557560247 2.390000e-23 121.0
9 TraesCS3D01G448700 chr3D 97.436 39 1 0 884 922 557560234 557560196 3.150000e-07 67.6
10 TraesCS3D01G448700 chr3A 93.203 1942 110 19 2945 4881 693206919 693204995 0.000000e+00 2835.0
11 TraesCS3D01G448700 chr3A 89.406 1718 142 23 3064 4769 693336837 693335148 0.000000e+00 2128.0
12 TraesCS3D01G448700 chr3A 94.903 1138 46 6 1820 2945 11511869 11513006 0.000000e+00 1770.0
13 TraesCS3D01G448700 chr3A 92.462 1048 65 6 745 1791 693207996 693206962 0.000000e+00 1485.0
14 TraesCS3D01G448700 chr3A 90.016 611 44 10 877 1476 693338160 693337556 0.000000e+00 774.0
15 TraesCS3D01G448700 chr3A 94.226 381 16 3 283 657 693245612 693245232 1.180000e-160 577.0
16 TraesCS3D01G448700 chr3A 93.525 278 18 0 2 279 693245961 693245684 9.770000e-112 414.0
17 TraesCS3D01G448700 chr3A 89.320 103 11 0 743 845 693338261 693338159 3.960000e-26 130.0
18 TraesCS3D01G448700 chr3A 82.576 132 19 3 1656 1785 498250662 498250791 3.990000e-21 113.0
19 TraesCS3D01G448700 chr3A 92.405 79 5 1 4803 4881 693335139 693335062 1.440000e-20 111.0
20 TraesCS3D01G448700 chr3A 81.295 139 22 3 1650 1786 343230430 343230566 5.170000e-20 110.0
21 TraesCS3D01G448700 chr3A 80.556 144 23 4 1640 1781 23366621 23366761 6.680000e-19 106.0
22 TraesCS3D01G448700 chr3A 95.455 66 3 0 160 225 693245676 693245611 6.680000e-19 106.0
23 TraesCS3D01G448700 chr3B 85.608 1876 192 29 3064 4877 739655244 739653385 0.000000e+00 1897.0
24 TraesCS3D01G448700 chr3B 85.991 1549 171 16 3364 4877 739600205 739598668 0.000000e+00 1616.0
25 TraesCS3D01G448700 chr3B 89.136 1169 108 14 3064 4216 739661450 739660285 0.000000e+00 1437.0
26 TraesCS3D01G448700 chr3B 90.732 1025 79 10 494 1512 739662754 739661740 0.000000e+00 1352.0
27 TraesCS3D01G448700 chr3B 90.254 985 70 9 494 1464 739656897 739655925 0.000000e+00 1264.0
28 TraesCS3D01G448700 chr3B 88.506 609 55 10 883 1478 739601904 739601298 0.000000e+00 723.0
29 TraesCS3D01G448700 chr3B 85.000 680 80 19 4212 4881 739660002 739659335 0.000000e+00 671.0
30 TraesCS3D01G448700 chr3B 86.827 539 56 7 930 1459 737922339 737921807 5.440000e-164 588.0
31 TraesCS3D01G448700 chr3B 88.710 62 5 2 3913 3972 75319944 75320005 1.880000e-09 75.0
32 TraesCS3D01G448700 chr3B 90.566 53 5 0 2985 3037 730257640 730257692 2.440000e-08 71.3
33 TraesCS3D01G448700 chr5D 95.763 1133 38 4 1823 2945 275171748 275170616 0.000000e+00 1818.0
34 TraesCS3D01G448700 chr5D 91.803 61 3 1 2957 3015 2789736 2789676 3.130000e-12 84.2
35 TraesCS3D01G448700 chr2D 95.419 1135 41 6 1822 2945 73126873 73125739 0.000000e+00 1797.0
36 TraesCS3D01G448700 chr2D 95.326 1134 41 6 1824 2945 621748803 621749936 0.000000e+00 1790.0
37 TraesCS3D01G448700 chr2D 78.010 191 25 12 4379 4559 584899446 584899629 2.400000e-18 104.0
38 TraesCS3D01G448700 chr1D 95.423 1136 39 7 1822 2945 60171817 60170683 0.000000e+00 1797.0
39 TraesCS3D01G448700 chr1D 95.326 1134 37 6 1823 2945 205134697 205133569 0.000000e+00 1786.0
40 TraesCS3D01G448700 chr1D 95.154 1135 43 6 1822 2945 247505759 247504626 0.000000e+00 1781.0
41 TraesCS3D01G448700 chr6D 95.004 1141 44 7 1816 2945 57791148 57790010 0.000000e+00 1779.0
42 TraesCS3D01G448700 chr6D 95.062 1134 45 5 1823 2945 142136692 142135559 0.000000e+00 1773.0
43 TraesCS3D01G448700 chr6D 81.671 371 51 12 4396 4755 8841407 8841043 4.780000e-75 292.0
44 TraesCS3D01G448700 chrUn 89.017 1211 97 17 3064 4264 395273956 395272772 0.000000e+00 1467.0
45 TraesCS3D01G448700 chrUn 90.422 877 65 10 3064 3931 252806371 252805505 0.000000e+00 1136.0
46 TraesCS3D01G448700 chrUn 90.597 553 38 7 884 1427 45144596 45144049 0.000000e+00 721.0
47 TraesCS3D01G448700 chrUn 87.884 553 45 9 3744 4295 463386773 463386242 8.920000e-177 630.0
48 TraesCS3D01G448700 chrUn 94.805 77 4 0 769 845 45144685 45144609 2.390000e-23 121.0
49 TraesCS3D01G448700 chrUn 94.805 77 4 0 769 845 388796785 388796861 2.390000e-23 121.0
50 TraesCS3D01G448700 chrUn 97.436 39 1 0 884 922 388796874 388796912 3.150000e-07 67.6
51 TraesCS3D01G448700 chr1A 81.884 138 21 3 1651 1786 108073063 108072928 3.990000e-21 113.0
52 TraesCS3D01G448700 chr1A 82.576 132 19 3 1656 1785 505408529 505408400 3.990000e-21 113.0
53 TraesCS3D01G448700 chr2B 82.677 127 18 3 1656 1780 627325220 627325096 5.170000e-20 110.0
54 TraesCS3D01G448700 chr6A 82.540 126 18 3 1656 1779 1815026 1814903 1.860000e-19 108.0
55 TraesCS3D01G448700 chr5A 83.761 117 15 3 1666 1780 581102066 581101952 1.860000e-19 108.0
56 TraesCS3D01G448700 chr5A 80.000 145 23 4 1647 1787 569701980 569702122 8.640000e-18 102.0
57 TraesCS3D01G448700 chr5A 84.286 70 5 5 2961 3030 503781255 503781192 4.080000e-06 63.9
58 TraesCS3D01G448700 chr4A 91.071 56 5 0 2985 3040 474495762 474495817 5.240000e-10 76.8
59 TraesCS3D01G448700 chr4A 89.286 56 3 1 2957 3012 625267782 625267834 3.150000e-07 67.6
60 TraesCS3D01G448700 chr2A 90.000 60 5 1 2957 3015 15012459 15012518 5.240000e-10 76.8
61 TraesCS3D01G448700 chr2A 87.931 58 5 1 3912 3969 513815620 513815675 3.150000e-07 67.6
62 TraesCS3D01G448700 chr7A 95.556 45 2 0 2993 3037 529327052 529327096 6.780000e-09 73.1
63 TraesCS3D01G448700 chr5B 92.000 50 4 0 2988 3037 598331132 598331083 2.440000e-08 71.3
64 TraesCS3D01G448700 chr1B 82.558 86 8 7 2957 3037 674916835 674916752 8.770000e-08 69.4


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 TraesCS3D01G448700 chr3D 557497111 557501991 4880 True 9014.000000 9014 100.000000 1 4881 1 chr3D.!!$R1 4880
1 TraesCS3D01G448700 chr3D 557521336 557525189 3853 True 765.250000 1535 90.922750 769 4770 4 chr3D.!!$R3 4001
2 TraesCS3D01G448700 chr3D 557588974 557589505 531 True 641.000000 641 88.246000 3744 4295 1 chr3D.!!$R2 551
3 TraesCS3D01G448700 chr3D 554836750 554837266 516 False 608.000000 608 88.168000 944 1456 1 chr3D.!!$F1 512
4 TraesCS3D01G448700 chr3D 557558164 557560323 2159 True 567.200000 1513 93.790333 769 4295 3 chr3D.!!$R4 3526
5 TraesCS3D01G448700 chr3A 693204995 693207996 3001 True 2160.000000 2835 92.832500 745 4881 2 chr3A.!!$R1 4136
6 TraesCS3D01G448700 chr3A 11511869 11513006 1137 False 1770.000000 1770 94.903000 1820 2945 1 chr3A.!!$F1 1125
7 TraesCS3D01G448700 chr3A 693335062 693338261 3199 True 785.750000 2128 90.286750 743 4881 4 chr3A.!!$R3 4138
8 TraesCS3D01G448700 chr3A 693245232 693245961 729 True 365.666667 577 94.402000 2 657 3 chr3A.!!$R2 655
9 TraesCS3D01G448700 chr3B 739653385 739662754 9369 True 1324.200000 1897 88.146000 494 4881 5 chr3B.!!$R3 4387
10 TraesCS3D01G448700 chr3B 739598668 739601904 3236 True 1169.500000 1616 87.248500 883 4877 2 chr3B.!!$R2 3994
11 TraesCS3D01G448700 chr3B 737921807 737922339 532 True 588.000000 588 86.827000 930 1459 1 chr3B.!!$R1 529
12 TraesCS3D01G448700 chr5D 275170616 275171748 1132 True 1818.000000 1818 95.763000 1823 2945 1 chr5D.!!$R2 1122
13 TraesCS3D01G448700 chr2D 73125739 73126873 1134 True 1797.000000 1797 95.419000 1822 2945 1 chr2D.!!$R1 1123
14 TraesCS3D01G448700 chr2D 621748803 621749936 1133 False 1790.000000 1790 95.326000 1824 2945 1 chr2D.!!$F2 1121
15 TraesCS3D01G448700 chr1D 60170683 60171817 1134 True 1797.000000 1797 95.423000 1822 2945 1 chr1D.!!$R1 1123
16 TraesCS3D01G448700 chr1D 205133569 205134697 1128 True 1786.000000 1786 95.326000 1823 2945 1 chr1D.!!$R2 1122
17 TraesCS3D01G448700 chr1D 247504626 247505759 1133 True 1781.000000 1781 95.154000 1822 2945 1 chr1D.!!$R3 1123
18 TraesCS3D01G448700 chr6D 57790010 57791148 1138 True 1779.000000 1779 95.004000 1816 2945 1 chr6D.!!$R2 1129
19 TraesCS3D01G448700 chr6D 142135559 142136692 1133 True 1773.000000 1773 95.062000 1823 2945 1 chr6D.!!$R3 1122
20 TraesCS3D01G448700 chrUn 395272772 395273956 1184 True 1467.000000 1467 89.017000 3064 4264 1 chrUn.!!$R2 1200
21 TraesCS3D01G448700 chrUn 252805505 252806371 866 True 1136.000000 1136 90.422000 3064 3931 1 chrUn.!!$R1 867
22 TraesCS3D01G448700 chrUn 463386242 463386773 531 True 630.000000 630 87.884000 3744 4295 1 chrUn.!!$R3 551
23 TraesCS3D01G448700 chrUn 45144049 45144685 636 True 421.000000 721 92.701000 769 1427 2 chrUn.!!$R4 658

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
707 776 0.027979 CAAAGTGGTGCTGACGTGTG 59.972 55.0 0.00 0.0 0.00 3.82 F
1884 8287 0.031585 GACGATGCATACGGCCACTA 59.968 55.0 18.34 0.0 43.89 2.74 F
2775 9239 0.810031 GACGATCATCAACACCCCGG 60.810 60.0 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 8453 0.403271 GTGGCTATGATGGGGCATCT 59.597 55.0 0.0 0.0 41.06 2.90 R
3472 10066 0.036952 ACTGAATCACTGGGTCTGCG 60.037 55.0 0.0 0.0 0.00 5.18 R
4136 10736 0.257328 TCAACACCTGGCTTCCACAA 59.743 50.0 0.0 0.0 0.00 3.33 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
17 18 3.181367 CTGCCCATTGTGCTCGAC 58.819 61.111 0.00 0.00 0.00 4.20
41 42 2.174969 GTGCCACGAACGGTGTGAA 61.175 57.895 4.84 0.00 45.52 3.18
69 70 2.443416 AGGAGTTAAATTGGCCGAACC 58.557 47.619 0.00 0.00 39.84 3.62
77 78 2.758207 TTGGCCGAACCCAAGGTCA 61.758 57.895 0.00 0.00 39.85 4.02
80 81 2.613506 GCCGAACCCAAGGTCAACG 61.614 63.158 0.00 0.00 33.12 4.10
111 112 2.798283 CGAGGTTGCGAGAACACTTTAA 59.202 45.455 0.00 0.00 0.00 1.52
145 146 1.459450 GCTGAATAGGGTTTGGCGAA 58.541 50.000 0.00 0.00 0.00 4.70
195 196 1.035139 AAACAAGCTTGGCAGAGGTG 58.965 50.000 29.18 2.89 0.00 4.00
205 206 2.084844 GCAGAGGTGCGTGAAGATG 58.915 57.895 0.00 0.00 40.71 2.90
218 219 4.671377 CGTGAAGATGGAGAGAAGAAGAG 58.329 47.826 0.00 0.00 0.00 2.85
224 225 3.448093 TGGAGAGAAGAAGAGCAGAGA 57.552 47.619 0.00 0.00 0.00 3.10
241 242 4.358851 CAGAGAGCGGATCAAGTTAGAAG 58.641 47.826 0.00 0.00 0.00 2.85
245 246 3.971150 AGCGGATCAAGTTAGAAGATCG 58.029 45.455 0.00 0.00 39.17 3.69
256 257 5.455872 AGTTAGAAGATCGGGATTCTACCA 58.544 41.667 2.51 0.00 37.66 3.25
279 280 9.762381 ACCATATTATTTCCAACAAAAGGAGTA 57.238 29.630 0.00 0.00 36.33 2.59
287 356 5.640147 TCCAACAAAAGGAGTATTGACCAT 58.360 37.500 0.00 0.00 0.00 3.55
320 389 6.038603 TCCTTCTATGAATGCGGAATTCTTTG 59.961 38.462 10.02 5.24 44.42 2.77
340 409 1.124477 GGCCAATGGGGGACAACAAA 61.124 55.000 0.00 0.00 35.36 2.83
341 410 0.761802 GCCAATGGGGGACAACAAAA 59.238 50.000 0.00 0.00 37.04 2.44
342 411 1.141858 GCCAATGGGGGACAACAAAAA 59.858 47.619 0.00 0.00 37.04 1.94
360 429 2.793278 AAAACGCCAACATTGAGGAC 57.207 45.000 4.47 0.00 0.00 3.85
361 430 1.686355 AAACGCCAACATTGAGGACA 58.314 45.000 4.47 0.00 0.00 4.02
362 431 1.909700 AACGCCAACATTGAGGACAT 58.090 45.000 4.47 0.00 0.00 3.06
363 432 1.167851 ACGCCAACATTGAGGACATG 58.832 50.000 0.00 0.00 0.00 3.21
364 433 1.271325 ACGCCAACATTGAGGACATGA 60.271 47.619 0.00 0.00 0.00 3.07
365 434 1.811965 CGCCAACATTGAGGACATGAA 59.188 47.619 0.00 0.00 0.00 2.57
366 435 2.228582 CGCCAACATTGAGGACATGAAA 59.771 45.455 0.00 0.00 0.00 2.69
367 436 3.578688 GCCAACATTGAGGACATGAAAC 58.421 45.455 0.00 0.00 0.00 2.78
368 437 3.005684 GCCAACATTGAGGACATGAAACA 59.994 43.478 0.00 0.00 0.00 2.83
369 438 4.801891 CCAACATTGAGGACATGAAACAG 58.198 43.478 0.00 0.00 0.00 3.16
370 439 4.279169 CCAACATTGAGGACATGAAACAGT 59.721 41.667 0.00 0.00 0.00 3.55
371 440 5.221303 CCAACATTGAGGACATGAAACAGTT 60.221 40.000 0.00 0.00 0.00 3.16
372 441 5.695851 ACATTGAGGACATGAAACAGTTC 57.304 39.130 0.00 0.00 0.00 3.01
384 453 4.717877 TGAAACAGTTCATCTCCACATGT 58.282 39.130 0.00 0.00 38.88 3.21
385 454 4.516321 TGAAACAGTTCATCTCCACATGTG 59.484 41.667 19.31 19.31 38.88 3.21
386 455 2.430465 ACAGTTCATCTCCACATGTGC 58.570 47.619 20.81 4.05 0.00 4.57
387 456 2.224597 ACAGTTCATCTCCACATGTGCA 60.225 45.455 20.81 4.45 0.00 4.57
388 457 3.014623 CAGTTCATCTCCACATGTGCAT 58.985 45.455 20.81 8.66 0.00 3.96
389 458 3.442625 CAGTTCATCTCCACATGTGCATT 59.557 43.478 20.81 1.77 0.00 3.56
390 459 3.442625 AGTTCATCTCCACATGTGCATTG 59.557 43.478 20.81 13.72 0.00 2.82
391 460 1.746787 TCATCTCCACATGTGCATTGC 59.253 47.619 20.81 0.46 0.00 3.56
392 461 1.108776 ATCTCCACATGTGCATTGCC 58.891 50.000 20.81 0.00 0.00 4.52
393 462 0.038599 TCTCCACATGTGCATTGCCT 59.961 50.000 20.81 0.00 0.00 4.75
394 463 0.892755 CTCCACATGTGCATTGCCTT 59.107 50.000 20.81 0.00 0.00 4.35
395 464 0.889994 TCCACATGTGCATTGCCTTC 59.110 50.000 20.81 0.00 0.00 3.46
396 465 0.892755 CCACATGTGCATTGCCTTCT 59.107 50.000 20.81 0.00 0.00 2.85
397 466 2.093890 CCACATGTGCATTGCCTTCTA 58.906 47.619 20.81 0.00 0.00 2.10
398 467 2.691526 CCACATGTGCATTGCCTTCTAT 59.308 45.455 20.81 0.00 0.00 1.98
399 468 3.490249 CCACATGTGCATTGCCTTCTATG 60.490 47.826 20.81 6.23 0.00 2.23
400 469 2.691526 ACATGTGCATTGCCTTCTATGG 59.308 45.455 6.12 0.00 0.00 2.74
401 470 2.804986 TGTGCATTGCCTTCTATGGA 57.195 45.000 6.12 0.00 0.00 3.41
402 471 3.301794 TGTGCATTGCCTTCTATGGAT 57.698 42.857 6.12 0.00 30.14 3.41
403 472 2.953648 TGTGCATTGCCTTCTATGGATG 59.046 45.455 6.12 0.00 30.14 3.51
404 473 3.216800 GTGCATTGCCTTCTATGGATGA 58.783 45.455 6.12 0.00 30.14 2.92
405 474 3.004106 GTGCATTGCCTTCTATGGATGAC 59.996 47.826 6.12 0.00 30.14 3.06
406 475 2.555757 GCATTGCCTTCTATGGATGACC 59.444 50.000 0.00 0.00 0.00 4.02
407 476 3.749954 GCATTGCCTTCTATGGATGACCT 60.750 47.826 0.00 0.00 37.04 3.85
408 477 4.467769 CATTGCCTTCTATGGATGACCTT 58.532 43.478 0.00 0.00 37.04 3.50
409 478 3.845781 TGCCTTCTATGGATGACCTTC 57.154 47.619 0.00 0.00 37.04 3.46
410 479 3.114606 TGCCTTCTATGGATGACCTTCA 58.885 45.455 0.00 0.00 37.04 3.02
411 480 3.118261 TGCCTTCTATGGATGACCTTCAC 60.118 47.826 0.00 0.00 37.04 3.18
412 481 3.722147 CCTTCTATGGATGACCTTCACG 58.278 50.000 0.00 0.00 37.04 4.35
413 482 3.493350 CCTTCTATGGATGACCTTCACGG 60.493 52.174 0.00 0.00 37.04 4.94
423 492 2.859165 ACCTTCACGGTGATCACAAT 57.141 45.000 26.47 11.48 46.80 2.71
424 493 2.426522 ACCTTCACGGTGATCACAATG 58.573 47.619 26.47 21.81 46.80 2.82
425 494 1.131126 CCTTCACGGTGATCACAATGC 59.869 52.381 26.47 8.82 0.00 3.56
426 495 0.795698 TTCACGGTGATCACAATGCG 59.204 50.000 26.47 21.38 0.00 4.73
427 496 1.018752 TCACGGTGATCACAATGCGG 61.019 55.000 26.47 13.92 0.00 5.69
428 497 1.018752 CACGGTGATCACAATGCGGA 61.019 55.000 26.47 0.00 0.00 5.54
429 498 1.019278 ACGGTGATCACAATGCGGAC 61.019 55.000 26.47 6.31 0.00 4.79
430 499 1.018752 CGGTGATCACAATGCGGACA 61.019 55.000 26.47 0.00 0.00 4.02
431 500 1.382522 GGTGATCACAATGCGGACAT 58.617 50.000 26.47 0.00 38.49 3.06
432 501 1.064505 GGTGATCACAATGCGGACATG 59.935 52.381 26.47 0.00 36.36 3.21
433 502 2.009051 GTGATCACAATGCGGACATGA 58.991 47.619 21.07 0.00 36.36 3.07
434 503 2.615447 GTGATCACAATGCGGACATGAT 59.385 45.455 21.07 0.00 36.36 2.45
435 504 2.874086 TGATCACAATGCGGACATGATC 59.126 45.455 15.66 15.66 36.36 2.92
436 505 2.399916 TCACAATGCGGACATGATCA 57.600 45.000 0.00 0.00 36.36 2.92
437 506 2.709213 TCACAATGCGGACATGATCAA 58.291 42.857 0.00 0.00 36.36 2.57
438 507 3.080319 TCACAATGCGGACATGATCAAA 58.920 40.909 0.00 0.00 36.36 2.69
439 508 3.119884 TCACAATGCGGACATGATCAAAC 60.120 43.478 0.00 0.00 36.36 2.93
440 509 2.819019 ACAATGCGGACATGATCAAACA 59.181 40.909 0.00 0.00 36.36 2.83
441 510 3.173599 CAATGCGGACATGATCAAACAC 58.826 45.455 0.00 0.00 36.36 3.32
442 511 1.889545 TGCGGACATGATCAAACACA 58.110 45.000 0.00 0.00 0.00 3.72
443 512 2.435422 TGCGGACATGATCAAACACAT 58.565 42.857 0.00 0.00 0.00 3.21
444 513 2.162008 TGCGGACATGATCAAACACATG 59.838 45.455 0.00 0.00 46.11 3.21
451 520 4.348656 CATGATCAAACACATGTAGCTGC 58.651 43.478 0.00 0.00 38.98 5.25
452 521 2.416202 TGATCAAACACATGTAGCTGCG 59.584 45.455 0.00 0.00 0.00 5.18
453 522 1.155889 TCAAACACATGTAGCTGCGG 58.844 50.000 0.00 0.00 0.00 5.69
454 523 1.155889 CAAACACATGTAGCTGCGGA 58.844 50.000 0.00 0.00 0.00 5.54
455 524 1.739466 CAAACACATGTAGCTGCGGAT 59.261 47.619 0.00 0.00 0.00 4.18
456 525 1.656652 AACACATGTAGCTGCGGATC 58.343 50.000 0.00 0.00 0.00 3.36
457 526 0.536724 ACACATGTAGCTGCGGATCA 59.463 50.000 0.00 0.00 0.00 2.92
458 527 1.139654 ACACATGTAGCTGCGGATCAT 59.860 47.619 0.00 0.00 0.00 2.45
459 528 1.529865 CACATGTAGCTGCGGATCATG 59.470 52.381 16.57 16.57 40.80 3.07
460 529 1.413812 ACATGTAGCTGCGGATCATGA 59.586 47.619 21.89 0.00 39.07 3.07
461 530 2.067013 CATGTAGCTGCGGATCATGAG 58.933 52.381 14.30 0.00 38.35 2.90
462 531 1.402787 TGTAGCTGCGGATCATGAGA 58.597 50.000 0.09 0.00 0.00 3.27
463 532 1.339291 TGTAGCTGCGGATCATGAGAG 59.661 52.381 0.09 0.00 0.00 3.20
464 533 1.339610 GTAGCTGCGGATCATGAGAGT 59.660 52.381 0.09 0.00 0.00 3.24
465 534 0.104487 AGCTGCGGATCATGAGAGTG 59.896 55.000 0.09 0.00 0.00 3.51
466 535 0.179089 GCTGCGGATCATGAGAGTGT 60.179 55.000 0.09 0.00 0.00 3.55
467 536 1.850377 CTGCGGATCATGAGAGTGTC 58.150 55.000 0.09 0.00 0.00 3.67
468 537 0.461548 TGCGGATCATGAGAGTGTCC 59.538 55.000 0.09 1.59 0.00 4.02
469 538 3.559015 CGGATCATGAGAGTGTCCG 57.441 57.895 17.64 17.64 44.72 4.79
471 540 2.500509 GGATCATGAGAGTGTCCGAC 57.499 55.000 0.09 0.00 0.00 4.79
472 541 1.751351 GGATCATGAGAGTGTCCGACA 59.249 52.381 0.09 0.00 0.00 4.35
482 551 1.807226 TGTCCGACACATAGCTCCG 59.193 57.895 0.00 0.00 0.00 4.63
483 552 1.065928 GTCCGACACATAGCTCCGG 59.934 63.158 0.00 0.00 41.36 5.14
484 553 2.125326 TCCGACACATAGCTCCGGG 61.125 63.158 0.00 0.00 40.48 5.73
485 554 2.417516 CGACACATAGCTCCGGGG 59.582 66.667 0.00 0.00 0.00 5.73
486 555 2.822399 GACACATAGCTCCGGGGG 59.178 66.667 1.90 0.00 0.00 5.40
487 556 1.760875 GACACATAGCTCCGGGGGA 60.761 63.158 1.90 0.00 0.00 4.81
488 557 1.074471 ACACATAGCTCCGGGGGAT 60.074 57.895 1.90 0.00 0.00 3.85
489 558 1.122019 ACACATAGCTCCGGGGGATC 61.122 60.000 1.90 0.00 0.00 3.36
490 559 1.121407 CACATAGCTCCGGGGGATCA 61.121 60.000 1.90 0.00 0.00 2.92
491 560 0.833834 ACATAGCTCCGGGGGATCAG 60.834 60.000 1.90 0.00 0.00 2.90
492 561 0.833834 CATAGCTCCGGGGGATCAGT 60.834 60.000 1.90 0.00 0.00 3.41
508 577 6.385033 GGGATCAGTATAATTGCAGCAAATC 58.615 40.000 12.97 7.71 0.00 2.17
510 579 7.303998 GGATCAGTATAATTGCAGCAAATCTC 58.696 38.462 12.97 2.53 0.00 2.75
561 630 1.748493 TGGCAAACCAAAGATATCGGC 59.252 47.619 0.00 0.00 45.37 5.54
596 665 1.021968 GTCCCGCTGTCTTTGTTGTT 58.978 50.000 0.00 0.00 0.00 2.83
606 675 6.033341 GCTGTCTTTGTTGTTTGTTCATACA 58.967 36.000 0.00 0.00 0.00 2.29
624 693 7.684317 TCATACAGGGGAGACATTACAATTA 57.316 36.000 0.00 0.00 0.00 1.40
625 694 7.506114 TCATACAGGGGAGACATTACAATTAC 58.494 38.462 0.00 0.00 0.00 1.89
631 700 7.993183 CAGGGGAGACATTACAATTACTATGTT 59.007 37.037 0.00 0.00 31.76 2.71
672 741 6.267496 ACATTTAGTGATTAACTTGTGGGC 57.733 37.500 0.00 0.00 40.56 5.36
673 742 5.772672 ACATTTAGTGATTAACTTGTGGGCA 59.227 36.000 0.00 0.00 40.56 5.36
690 759 2.494059 GGCAGTTACTTCAGCTGACAA 58.506 47.619 18.03 8.21 42.87 3.18
697 766 2.292267 ACTTCAGCTGACAAAGTGGTG 58.708 47.619 18.03 1.11 32.22 4.17
707 776 0.027979 CAAAGTGGTGCTGACGTGTG 59.972 55.000 0.00 0.00 0.00 3.82
708 777 1.714899 AAAGTGGTGCTGACGTGTGC 61.715 55.000 0.00 0.00 0.00 4.57
710 779 2.588596 TGGTGCTGACGTGTGCAG 60.589 61.111 11.65 5.43 40.06 4.41
711 780 2.280119 GGTGCTGACGTGTGCAGA 60.280 61.111 11.65 0.00 40.06 4.26
712 781 1.887242 GGTGCTGACGTGTGCAGAA 60.887 57.895 11.65 0.00 40.06 3.02
713 782 1.276844 GTGCTGACGTGTGCAGAAC 59.723 57.895 11.65 5.32 40.06 3.01
715 784 2.943345 GCTGACGTGTGCAGAACGG 61.943 63.158 21.90 8.84 45.20 4.44
722 796 1.003839 TGTGCAGAACGGACATCCC 60.004 57.895 0.00 0.00 41.63 3.85
726 800 1.899437 GCAGAACGGACATCCCTCCA 61.899 60.000 0.00 0.00 0.00 3.86
738 812 5.480422 GGACATCCCTCCAAATTTGTTTAGT 59.520 40.000 16.73 6.09 0.00 2.24
776 850 0.671472 TCACATCTGCCTTGCGTCAG 60.671 55.000 0.00 0.00 0.00 3.51
1059 1140 1.280421 AGAAATGGAGAGCACCCAGAC 59.720 52.381 0.00 0.00 37.08 3.51
1133 1223 0.107831 GTGCTGGTACAAGGTGGTCA 59.892 55.000 0.00 0.00 38.70 4.02
1509 7662 5.013547 CACCCGATCTCTATATCAGTTCCT 58.986 45.833 0.00 0.00 0.00 3.36
1524 7679 2.644798 AGTTCCTTATGTTGGTGAGGCT 59.355 45.455 0.00 0.00 0.00 4.58
1661 8041 7.769044 ACAACACTATGAACATATTACCTCCAC 59.231 37.037 0.00 0.00 0.00 4.02
1662 8042 7.676683 ACACTATGAACATATTACCTCCACT 57.323 36.000 0.00 0.00 0.00 4.00
1733 8136 5.289595 TGAAACATGTCTAGATACATCCGC 58.710 41.667 0.00 0.00 38.01 5.54
1755 8158 6.316390 CCGCCTCTAGACAAATTTAAGACAAT 59.684 38.462 0.00 0.00 0.00 2.71
1791 8194 8.993121 ACAGAGCGAATATATTCCAAAATGTAG 58.007 33.333 17.83 3.94 33.28 2.74
1792 8195 8.993121 CAGAGCGAATATATTCCAAAATGTAGT 58.007 33.333 17.83 0.00 33.28 2.73
1794 8197 9.209175 GAGCGAATATATTCCAAAATGTAGTCT 57.791 33.333 17.83 4.64 33.80 3.24
1795 8198 9.209175 AGCGAATATATTCCAAAATGTAGTCTC 57.791 33.333 17.83 0.00 33.80 3.36
1796 8199 9.209175 GCGAATATATTCCAAAATGTAGTCTCT 57.791 33.333 17.83 0.00 33.80 3.10
1810 8213 8.937207 AATGTAGTCTCTAATATTACCTCCGT 57.063 34.615 0.00 0.00 0.00 4.69
1811 8214 7.976135 TGTAGTCTCTAATATTACCTCCGTC 57.024 40.000 0.00 0.00 0.00 4.79
1812 8215 7.743749 TGTAGTCTCTAATATTACCTCCGTCT 58.256 38.462 0.00 0.00 0.00 4.18
1813 8216 7.877097 TGTAGTCTCTAATATTACCTCCGTCTC 59.123 40.741 0.00 0.00 0.00 3.36
1814 8217 6.839454 AGTCTCTAATATTACCTCCGTCTCA 58.161 40.000 0.00 0.00 0.00 3.27
1815 8218 7.288560 AGTCTCTAATATTACCTCCGTCTCAA 58.711 38.462 0.00 0.00 0.00 3.02
1816 8219 7.778853 AGTCTCTAATATTACCTCCGTCTCAAA 59.221 37.037 0.00 0.00 0.00 2.69
1817 8220 8.578151 GTCTCTAATATTACCTCCGTCTCAAAT 58.422 37.037 0.00 0.00 0.00 2.32
1818 8221 9.144298 TCTCTAATATTACCTCCGTCTCAAATT 57.856 33.333 0.00 0.00 0.00 1.82
1884 8287 0.031585 GACGATGCATACGGCCACTA 59.968 55.000 18.34 0.00 43.89 2.74
1961 8365 3.614092 CACCATCTAGGCAACATCTGTT 58.386 45.455 0.00 0.00 43.14 3.16
2001 8405 1.302431 CAGTGGTGCCGAATGTCCA 60.302 57.895 0.00 0.00 0.00 4.02
2017 8421 3.692690 TGTCCAAGCCTAATACCAAACC 58.307 45.455 0.00 0.00 0.00 3.27
2044 8453 2.877786 CGCACCATAACATCTAATGCCA 59.122 45.455 0.00 0.00 0.00 4.92
2056 8465 0.852155 TAATGCCAGATGCCCCATCA 59.148 50.000 7.83 0.00 42.72 3.07
2132 8541 1.815421 CCGCCTTCTTCCACCGATG 60.815 63.158 0.00 0.00 0.00 3.84
2302 8711 4.049186 GTCAATGACGCGGTAGATACAAT 58.951 43.478 12.47 0.00 0.00 2.71
2342 8751 1.079197 CACACCATCGCCACTGCTA 60.079 57.895 0.00 0.00 34.43 3.49
2381 8790 1.842562 CATCCACAACATCTCTCCCCT 59.157 52.381 0.00 0.00 0.00 4.79
2775 9239 0.810031 GACGATCATCAACACCCCGG 60.810 60.000 0.00 0.00 0.00 5.73
2873 9339 4.320456 CGCAGCCACCACCTCACT 62.320 66.667 0.00 0.00 0.00 3.41
2985 9452 4.089361 TGTCCAGATACGGATGCATCTAT 58.911 43.478 25.28 16.11 37.41 1.98
2986 9453 4.158579 TGTCCAGATACGGATGCATCTATC 59.841 45.833 25.28 22.51 37.41 2.08
3045 9565 9.932207 TTCAGAACGGAATGAGTACTAATAAAA 57.068 29.630 0.00 0.00 0.00 1.52
3046 9566 9.582431 TCAGAACGGAATGAGTACTAATAAAAG 57.418 33.333 0.00 0.00 0.00 2.27
3047 9567 9.367444 CAGAACGGAATGAGTACTAATAAAAGT 57.633 33.333 0.00 0.00 0.00 2.66
3048 9568 9.939802 AGAACGGAATGAGTACTAATAAAAGTT 57.060 29.630 0.00 0.00 0.00 2.66
3397 9991 9.736414 ATTGATCTCCCATAATGAACTAATCTG 57.264 33.333 0.00 0.00 0.00 2.90
3457 10051 9.760926 AGATATACTATAGCAATGAACTCTCCA 57.239 33.333 0.00 0.00 0.00 3.86
3472 10066 4.715713 ACTCTCCACCTTACCAACTTTTC 58.284 43.478 0.00 0.00 0.00 2.29
3520 10118 0.925558 TGATGCAGGATTTGGCCCTA 59.074 50.000 0.00 0.00 31.64 3.53
3685 10283 1.541147 CAGCGTTGGATGGTGATGTTT 59.459 47.619 0.00 0.00 34.73 2.83
3693 10291 0.916086 ATGGTGATGTTTAGCCCCGA 59.084 50.000 0.00 0.00 0.00 5.14
3786 10384 3.797039 CTCTGGTCAAGATCGCCAATAA 58.203 45.455 3.69 0.00 33.29 1.40
3848 10446 5.794687 AATCAATGTATGTGTGTACACCG 57.205 39.130 22.91 1.19 45.88 4.94
3982 10581 9.483916 CGGATGTATCTAACACCAAAACATATA 57.516 33.333 0.00 0.00 42.09 0.86
4084 10684 9.859427 AGTTCAACACAAATATGTCAAATATGG 57.141 29.630 0.00 0.00 37.82 2.74
4118 10718 5.825679 TGATGGGATTACTTATTGGAAACCG 59.174 40.000 0.00 0.00 0.00 4.44
4136 10736 7.997107 GAAACCGTTCCAATAAAAGAAACTT 57.003 32.000 0.00 0.00 0.00 2.66
4186 10786 9.838339 CCAAAAAGATAGGACACTGATATTAGT 57.162 33.333 0.00 0.00 0.00 2.24
4314 11786 0.263765 TCCTCAACGCCCCTACCTAT 59.736 55.000 0.00 0.00 0.00 2.57
4438 11914 4.789784 TGTGCTAAGAAATAAAACGCCAC 58.210 39.130 0.00 0.00 0.00 5.01
4696 12205 7.795482 TGATAAGTAAATTTACCATGGTCCG 57.205 36.000 23.76 0.00 34.19 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.957395 AAGTCGAGCACAATGGGCAG 60.957 55.000 11.17 3.07 0.00 4.85
5 6 1.069022 CACCCAAAGTCGAGCACAATG 60.069 52.381 0.00 0.00 0.00 2.82
17 18 2.637025 CGTTCGTGGCACCCAAAG 59.363 61.111 12.86 3.87 34.18 2.77
69 70 0.326927 ACATACCCCGTTGACCTTGG 59.673 55.000 0.00 0.00 0.00 3.61
77 78 1.833787 AACCTCGCACATACCCCGTT 61.834 55.000 0.00 0.00 0.00 4.44
80 81 2.112815 GCAACCTCGCACATACCCC 61.113 63.158 0.00 0.00 0.00 4.95
127 128 2.017049 CCTTCGCCAAACCCTATTCAG 58.983 52.381 0.00 0.00 0.00 3.02
134 135 1.006220 CAAAGCCTTCGCCAAACCC 60.006 57.895 0.00 0.00 34.57 4.11
145 146 0.685097 TCGCTCTTACACCAAAGCCT 59.315 50.000 0.00 0.00 0.00 4.58
149 150 1.070134 ACAGCTCGCTCTTACACCAAA 59.930 47.619 0.00 0.00 0.00 3.28
195 196 2.949451 TCTTCTCTCCATCTTCACGC 57.051 50.000 0.00 0.00 0.00 5.34
205 206 2.099756 GCTCTCTGCTCTTCTTCTCTCC 59.900 54.545 0.00 0.00 38.95 3.71
218 219 2.099921 TCTAACTTGATCCGCTCTCTGC 59.900 50.000 0.00 0.00 38.57 4.26
224 225 3.243569 CCGATCTTCTAACTTGATCCGCT 60.244 47.826 0.00 0.00 34.70 5.52
241 242 8.265055 TGGAAATAATATGGTAGAATCCCGATC 58.735 37.037 0.00 0.00 0.00 3.69
245 246 8.934023 TGTTGGAAATAATATGGTAGAATCCC 57.066 34.615 0.00 0.00 0.00 3.85
279 280 4.091549 AGAAGGAAATGCACATGGTCAAT 58.908 39.130 0.00 0.00 0.00 2.57
280 281 3.499338 AGAAGGAAATGCACATGGTCAA 58.501 40.909 0.00 0.00 0.00 3.18
287 356 4.201940 CGCATTCATAGAAGGAAATGCACA 60.202 41.667 16.37 0.00 32.91 4.57
320 389 2.683572 GTTGTCCCCCATTGGCCC 60.684 66.667 0.00 0.00 0.00 5.80
340 409 2.428890 TGTCCTCAATGTTGGCGTTTTT 59.571 40.909 0.00 0.00 0.00 1.94
341 410 2.028130 TGTCCTCAATGTTGGCGTTTT 58.972 42.857 0.00 0.00 0.00 2.43
342 411 1.686355 TGTCCTCAATGTTGGCGTTT 58.314 45.000 0.00 0.00 0.00 3.60
343 412 1.541147 CATGTCCTCAATGTTGGCGTT 59.459 47.619 0.00 0.00 0.00 4.84
344 413 1.167851 CATGTCCTCAATGTTGGCGT 58.832 50.000 0.00 0.00 0.00 5.68
345 414 1.452110 TCATGTCCTCAATGTTGGCG 58.548 50.000 0.00 0.00 0.00 5.69
346 415 3.005684 TGTTTCATGTCCTCAATGTTGGC 59.994 43.478 0.00 0.00 0.00 4.52
347 416 4.279169 ACTGTTTCATGTCCTCAATGTTGG 59.721 41.667 0.00 0.00 0.00 3.77
348 417 5.443185 ACTGTTTCATGTCCTCAATGTTG 57.557 39.130 0.00 0.00 0.00 3.33
349 418 5.593909 TGAACTGTTTCATGTCCTCAATGTT 59.406 36.000 0.00 0.00 36.79 2.71
350 419 5.132502 TGAACTGTTTCATGTCCTCAATGT 58.867 37.500 0.00 0.00 36.79 2.71
351 420 5.694231 TGAACTGTTTCATGTCCTCAATG 57.306 39.130 0.00 0.00 36.79 2.82
362 431 4.516321 CACATGTGGAGATGAACTGTTTCA 59.484 41.667 18.51 0.00 45.93 2.69
363 432 4.614535 GCACATGTGGAGATGAACTGTTTC 60.615 45.833 26.55 0.78 0.00 2.78
364 433 3.254166 GCACATGTGGAGATGAACTGTTT 59.746 43.478 26.55 0.00 0.00 2.83
365 434 2.816087 GCACATGTGGAGATGAACTGTT 59.184 45.455 26.55 0.00 0.00 3.16
366 435 2.224597 TGCACATGTGGAGATGAACTGT 60.225 45.455 26.55 0.00 0.00 3.55
367 436 2.429478 TGCACATGTGGAGATGAACTG 58.571 47.619 26.55 0.00 0.00 3.16
368 437 2.865119 TGCACATGTGGAGATGAACT 57.135 45.000 26.55 0.00 0.00 3.01
369 438 3.766151 CAATGCACATGTGGAGATGAAC 58.234 45.455 26.55 8.29 33.50 3.18
370 439 2.164827 GCAATGCACATGTGGAGATGAA 59.835 45.455 28.45 1.50 33.50 2.57
371 440 1.746787 GCAATGCACATGTGGAGATGA 59.253 47.619 28.45 0.00 33.50 2.92
372 441 1.202371 GGCAATGCACATGTGGAGATG 60.202 52.381 26.55 24.61 33.50 2.90
373 442 1.108776 GGCAATGCACATGTGGAGAT 58.891 50.000 26.55 14.51 33.50 2.75
374 443 0.038599 AGGCAATGCACATGTGGAGA 59.961 50.000 26.55 0.00 33.50 3.71
375 444 0.892755 AAGGCAATGCACATGTGGAG 59.107 50.000 26.55 14.39 33.50 3.86
376 445 0.889994 GAAGGCAATGCACATGTGGA 59.110 50.000 26.55 24.83 34.81 4.02
377 446 0.892755 AGAAGGCAATGCACATGTGG 59.107 50.000 26.55 11.38 0.00 4.17
378 447 3.490249 CCATAGAAGGCAATGCACATGTG 60.490 47.826 21.83 21.83 0.00 3.21
379 448 2.691526 CCATAGAAGGCAATGCACATGT 59.308 45.455 7.79 0.00 0.00 3.21
380 449 2.953648 TCCATAGAAGGCAATGCACATG 59.046 45.455 7.79 2.49 0.00 3.21
381 450 3.301794 TCCATAGAAGGCAATGCACAT 57.698 42.857 7.79 0.00 0.00 3.21
382 451 2.804986 TCCATAGAAGGCAATGCACA 57.195 45.000 7.79 0.00 0.00 4.57
383 452 3.004106 GTCATCCATAGAAGGCAATGCAC 59.996 47.826 7.79 0.00 0.00 4.57
384 453 3.216800 GTCATCCATAGAAGGCAATGCA 58.783 45.455 7.79 0.00 0.00 3.96
385 454 2.555757 GGTCATCCATAGAAGGCAATGC 59.444 50.000 0.00 0.00 0.00 3.56
386 455 4.096190 AGGTCATCCATAGAAGGCAATG 57.904 45.455 0.00 0.00 35.89 2.82
387 456 4.166725 TGAAGGTCATCCATAGAAGGCAAT 59.833 41.667 0.00 0.00 35.89 3.56
388 457 3.523157 TGAAGGTCATCCATAGAAGGCAA 59.477 43.478 0.00 0.00 35.89 4.52
389 458 3.114606 TGAAGGTCATCCATAGAAGGCA 58.885 45.455 0.00 0.00 35.89 4.75
390 459 3.471680 GTGAAGGTCATCCATAGAAGGC 58.528 50.000 0.00 0.00 35.89 4.35
391 460 3.493350 CCGTGAAGGTCATCCATAGAAGG 60.493 52.174 0.00 0.00 35.89 3.46
392 461 3.722147 CCGTGAAGGTCATCCATAGAAG 58.278 50.000 0.00 0.00 35.89 2.85
393 462 3.819564 CCGTGAAGGTCATCCATAGAA 57.180 47.619 0.00 0.00 35.89 2.10
406 475 1.201954 CGCATTGTGATCACCGTGAAG 60.202 52.381 22.85 13.84 0.00 3.02
407 476 0.795698 CGCATTGTGATCACCGTGAA 59.204 50.000 22.85 10.84 0.00 3.18
408 477 1.018752 CCGCATTGTGATCACCGTGA 61.019 55.000 22.85 3.10 0.00 4.35
409 478 1.018752 TCCGCATTGTGATCACCGTG 61.019 55.000 22.85 20.20 0.00 4.94
410 479 1.019278 GTCCGCATTGTGATCACCGT 61.019 55.000 22.85 8.74 0.00 4.83
411 480 1.018752 TGTCCGCATTGTGATCACCG 61.019 55.000 22.85 17.55 0.00 4.94
412 481 1.064505 CATGTCCGCATTGTGATCACC 59.935 52.381 22.85 6.58 31.99 4.02
413 482 2.009051 TCATGTCCGCATTGTGATCAC 58.991 47.619 19.27 19.27 31.99 3.06
414 483 2.399916 TCATGTCCGCATTGTGATCA 57.600 45.000 0.00 0.00 31.99 2.92
415 484 2.874086 TGATCATGTCCGCATTGTGATC 59.126 45.455 0.00 6.69 34.89 2.92
416 485 2.921821 TGATCATGTCCGCATTGTGAT 58.078 42.857 0.00 0.00 31.99 3.06
417 486 2.399916 TGATCATGTCCGCATTGTGA 57.600 45.000 0.00 0.00 31.99 3.58
418 487 3.173599 GTTTGATCATGTCCGCATTGTG 58.826 45.455 0.00 0.00 31.99 3.33
419 488 2.819019 TGTTTGATCATGTCCGCATTGT 59.181 40.909 0.00 0.00 31.99 2.71
420 489 3.173599 GTGTTTGATCATGTCCGCATTG 58.826 45.455 0.00 0.00 31.99 2.82
421 490 2.819019 TGTGTTTGATCATGTCCGCATT 59.181 40.909 0.00 0.00 31.99 3.56
422 491 2.435422 TGTGTTTGATCATGTCCGCAT 58.565 42.857 0.00 0.00 35.32 4.73
423 492 1.889545 TGTGTTTGATCATGTCCGCA 58.110 45.000 0.00 0.00 0.00 5.69
424 493 2.789208 CATGTGTTTGATCATGTCCGC 58.211 47.619 0.00 0.00 37.31 5.54
429 498 4.348656 GCAGCTACATGTGTTTGATCATG 58.651 43.478 9.11 0.00 44.56 3.07
430 499 3.064408 CGCAGCTACATGTGTTTGATCAT 59.936 43.478 9.11 0.00 0.00 2.45
431 500 2.416202 CGCAGCTACATGTGTTTGATCA 59.584 45.455 9.11 0.00 0.00 2.92
432 501 2.223112 CCGCAGCTACATGTGTTTGATC 60.223 50.000 9.11 0.00 0.00 2.92
433 502 1.739466 CCGCAGCTACATGTGTTTGAT 59.261 47.619 9.11 0.00 0.00 2.57
434 503 1.155889 CCGCAGCTACATGTGTTTGA 58.844 50.000 9.11 0.00 0.00 2.69
435 504 1.155889 TCCGCAGCTACATGTGTTTG 58.844 50.000 9.11 4.83 0.00 2.93
436 505 2.009774 GATCCGCAGCTACATGTGTTT 58.990 47.619 9.11 0.00 0.00 2.83
437 506 1.066215 TGATCCGCAGCTACATGTGTT 60.066 47.619 9.11 0.00 0.00 3.32
438 507 0.536724 TGATCCGCAGCTACATGTGT 59.463 50.000 9.11 0.00 0.00 3.72
439 508 1.529865 CATGATCCGCAGCTACATGTG 59.470 52.381 9.11 0.00 35.22 3.21
440 509 1.413812 TCATGATCCGCAGCTACATGT 59.586 47.619 2.69 2.69 39.18 3.21
441 510 2.067013 CTCATGATCCGCAGCTACATG 58.933 52.381 0.00 0.00 39.40 3.21
442 511 1.966354 TCTCATGATCCGCAGCTACAT 59.034 47.619 0.00 0.00 0.00 2.29
443 512 1.339291 CTCTCATGATCCGCAGCTACA 59.661 52.381 0.00 0.00 0.00 2.74
444 513 1.339610 ACTCTCATGATCCGCAGCTAC 59.660 52.381 0.00 0.00 0.00 3.58
445 514 1.339291 CACTCTCATGATCCGCAGCTA 59.661 52.381 0.00 0.00 0.00 3.32
446 515 0.104487 CACTCTCATGATCCGCAGCT 59.896 55.000 0.00 0.00 0.00 4.24
447 516 0.179089 ACACTCTCATGATCCGCAGC 60.179 55.000 0.00 0.00 0.00 5.25
448 517 1.537776 GGACACTCTCATGATCCGCAG 60.538 57.143 0.00 0.00 0.00 5.18
449 518 0.461548 GGACACTCTCATGATCCGCA 59.538 55.000 0.00 0.00 0.00 5.69
450 519 0.596083 CGGACACTCTCATGATCCGC 60.596 60.000 18.81 0.00 45.13 5.54
451 520 3.559015 CGGACACTCTCATGATCCG 57.441 57.895 17.64 17.64 45.61 4.18
452 521 1.751351 TGTCGGACACTCTCATGATCC 59.249 52.381 6.76 0.00 0.00 3.36
453 522 2.803451 GTGTCGGACACTCTCATGATC 58.197 52.381 29.09 3.45 45.27 2.92
454 523 2.949451 GTGTCGGACACTCTCATGAT 57.051 50.000 29.09 0.00 45.27 2.45
464 533 1.663379 CCGGAGCTATGTGTCGGACA 61.663 60.000 6.76 6.76 42.94 4.02
465 534 1.065928 CCGGAGCTATGTGTCGGAC 59.934 63.158 0.00 0.00 42.94 4.79
466 535 2.125326 CCCGGAGCTATGTGTCGGA 61.125 63.158 0.73 0.00 42.94 4.55
467 536 2.417516 CCCGGAGCTATGTGTCGG 59.582 66.667 0.73 0.00 40.32 4.79
468 537 2.417516 CCCCGGAGCTATGTGTCG 59.582 66.667 0.73 0.00 0.00 4.35
469 538 1.122019 ATCCCCCGGAGCTATGTGTC 61.122 60.000 0.73 0.00 34.05 3.67
470 539 1.074471 ATCCCCCGGAGCTATGTGT 60.074 57.895 0.73 0.00 34.05 3.72
471 540 1.121407 TGATCCCCCGGAGCTATGTG 61.121 60.000 0.73 0.00 39.11 3.21
472 541 0.833834 CTGATCCCCCGGAGCTATGT 60.834 60.000 0.73 0.00 39.11 2.29
473 542 0.833834 ACTGATCCCCCGGAGCTATG 60.834 60.000 0.73 0.00 39.11 2.23
474 543 0.784495 TACTGATCCCCCGGAGCTAT 59.216 55.000 0.73 0.00 39.11 2.97
475 544 0.784495 ATACTGATCCCCCGGAGCTA 59.216 55.000 0.73 0.00 39.11 3.32
476 545 0.784495 TATACTGATCCCCCGGAGCT 59.216 55.000 0.73 0.00 39.11 4.09
477 546 1.640917 TTATACTGATCCCCCGGAGC 58.359 55.000 0.73 0.00 38.78 4.70
478 547 3.619979 GCAATTATACTGATCCCCCGGAG 60.620 52.174 0.73 0.00 34.05 4.63
479 548 2.304761 GCAATTATACTGATCCCCCGGA 59.695 50.000 0.73 0.00 35.55 5.14
480 549 2.039746 TGCAATTATACTGATCCCCCGG 59.960 50.000 0.00 0.00 0.00 5.73
481 550 3.338249 CTGCAATTATACTGATCCCCCG 58.662 50.000 0.00 0.00 0.00 5.73
482 551 3.084786 GCTGCAATTATACTGATCCCCC 58.915 50.000 0.00 0.00 0.00 5.40
483 552 3.754965 TGCTGCAATTATACTGATCCCC 58.245 45.455 0.00 0.00 0.00 4.81
484 553 5.772825 TTTGCTGCAATTATACTGATCCC 57.227 39.130 16.77 0.00 0.00 3.85
485 554 7.174599 AGAGATTTGCTGCAATTATACTGATCC 59.825 37.037 16.77 7.57 0.00 3.36
486 555 8.097078 AGAGATTTGCTGCAATTATACTGATC 57.903 34.615 16.77 12.74 0.00 2.92
487 556 7.718314 TGAGAGATTTGCTGCAATTATACTGAT 59.282 33.333 16.77 3.71 0.00 2.90
488 557 7.049754 TGAGAGATTTGCTGCAATTATACTGA 58.950 34.615 16.77 4.37 0.00 3.41
489 558 7.255491 TGAGAGATTTGCTGCAATTATACTG 57.745 36.000 16.77 0.00 0.00 2.74
490 559 7.555554 AGTTGAGAGATTTGCTGCAATTATACT 59.444 33.333 16.77 11.68 0.00 2.12
491 560 7.701445 AGTTGAGAGATTTGCTGCAATTATAC 58.299 34.615 16.77 5.35 0.00 1.47
492 561 7.772292 AGAGTTGAGAGATTTGCTGCAATTATA 59.228 33.333 16.77 0.90 0.00 0.98
561 630 2.716217 GGGACAATCTCCTTTCTGGTG 58.284 52.381 0.00 0.00 39.39 4.17
581 650 3.497118 TGAACAAACAACAAAGACAGCG 58.503 40.909 0.00 0.00 0.00 5.18
596 665 4.927267 AATGTCTCCCCTGTATGAACAA 57.073 40.909 0.00 0.00 34.49 2.83
606 675 7.691993 ACATAGTAATTGTAATGTCTCCCCT 57.308 36.000 0.00 0.00 0.00 4.79
624 693 7.812669 GTGCAGGCTAATTTTGTTAAACATAGT 59.187 33.333 0.00 0.00 0.00 2.12
625 694 7.812191 TGTGCAGGCTAATTTTGTTAAACATAG 59.188 33.333 0.00 0.00 0.00 2.23
631 700 8.364142 ACTAAATGTGCAGGCTAATTTTGTTAA 58.636 29.630 9.05 0.00 28.22 2.01
644 713 6.803320 CACAAGTTAATCACTAAATGTGCAGG 59.197 38.462 0.00 0.00 45.81 4.85
672 741 4.024556 CCACTTTGTCAGCTGAAGTAACTG 60.025 45.833 20.19 9.50 32.69 3.16
673 742 4.130118 CCACTTTGTCAGCTGAAGTAACT 58.870 43.478 20.19 0.00 32.69 2.24
690 759 2.180204 GCACACGTCAGCACCACTT 61.180 57.895 4.00 0.00 0.00 3.16
697 766 2.546321 CGTTCTGCACACGTCAGC 59.454 61.111 5.65 1.92 32.80 4.26
707 776 1.153349 GGAGGGATGTCCGTTCTGC 60.153 63.158 0.00 0.00 41.52 4.26
708 777 0.613260 TTGGAGGGATGTCCGTTCTG 59.387 55.000 2.04 0.00 39.81 3.02
710 779 2.420058 ATTTGGAGGGATGTCCGTTC 57.580 50.000 0.00 0.00 39.81 3.95
711 780 2.825532 CAAATTTGGAGGGATGTCCGTT 59.174 45.455 10.49 0.00 39.81 4.44
712 781 2.225017 ACAAATTTGGAGGGATGTCCGT 60.225 45.455 21.74 0.00 39.81 4.69
713 782 2.446435 ACAAATTTGGAGGGATGTCCG 58.554 47.619 21.74 0.00 39.81 4.79
715 784 6.590234 ACTAAACAAATTTGGAGGGATGTC 57.410 37.500 21.74 0.00 31.09 3.06
776 850 0.861837 CACGAGACTTTGACTGGTGC 59.138 55.000 0.00 0.00 37.31 5.01
934 1009 3.840468 TGCTCGAACGCTTATCAGTTAA 58.160 40.909 0.00 0.00 0.00 2.01
1059 1140 0.606401 ATGGTTCCTCACGCTGTTGG 60.606 55.000 0.00 0.00 0.00 3.77
1204 1294 2.643272 GAGTGCACCTCGTCGACA 59.357 61.111 17.16 1.87 0.00 4.35
1488 7641 7.340743 ACATAAGGAACTGATATAGAGATCGGG 59.659 40.741 0.00 0.00 40.86 5.14
1491 7644 9.868277 CCAACATAAGGAACTGATATAGAGATC 57.132 37.037 0.00 0.00 40.86 2.75
1509 7662 0.403655 TGCCAGCCTCACCAACATAA 59.596 50.000 0.00 0.00 0.00 1.90
1524 7679 3.701205 TTGACTAAGATGAGCTTGCCA 57.299 42.857 0.00 0.00 37.42 4.92
1698 8078 9.817809 TCTAGACATGTTTCATTGTTAGATACC 57.182 33.333 0.00 0.00 0.00 2.73
1709 8089 5.928839 GCGGATGTATCTAGACATGTTTCAT 59.071 40.000 0.00 0.00 40.18 2.57
1710 8090 5.289595 GCGGATGTATCTAGACATGTTTCA 58.710 41.667 0.00 0.00 40.18 2.69
1711 8091 4.686554 GGCGGATGTATCTAGACATGTTTC 59.313 45.833 0.00 0.00 40.18 2.78
1755 8158 9.817809 GAATATATTCGCTCTGTCCCATATTAA 57.182 33.333 9.65 0.00 0.00 1.40
1791 8194 7.507733 TTGAGACGGAGGTAATATTAGAGAC 57.492 40.000 0.00 0.00 0.00 3.36
1792 8195 8.707796 ATTTGAGACGGAGGTAATATTAGAGA 57.292 34.615 0.00 0.00 0.00 3.10
1797 8200 9.901172 AAACTAATTTGAGACGGAGGTAATATT 57.099 29.630 0.00 0.00 0.00 1.28
1800 8203 8.631480 AAAAACTAATTTGAGACGGAGGTAAT 57.369 30.769 0.00 0.00 0.00 1.89
1961 8365 0.714180 TCAAGGGGGTAGGAGTAGCA 59.286 55.000 0.00 0.00 0.00 3.49
2001 8405 3.706600 TGTCGGTTTGGTATTAGGCTT 57.293 42.857 0.00 0.00 0.00 4.35
2017 8421 2.473816 AGATGTTATGGTGCGATGTCG 58.526 47.619 0.00 0.00 43.27 4.35
2044 8453 0.403271 GTGGCTATGATGGGGCATCT 59.597 55.000 0.00 0.00 41.06 2.90
2056 8465 1.048601 CAGTCCCGGTATGTGGCTAT 58.951 55.000 0.00 0.00 0.00 2.97
2132 8541 1.118838 AGTACCTGCTCTGGAGATGC 58.881 55.000 1.35 0.00 0.00 3.91
2201 8610 3.449227 CGCAGGGTGGTCGAGCTA 61.449 66.667 16.64 0.00 0.00 3.32
2342 8751 4.704103 TGGGCTCCGAGTGGCTCT 62.704 66.667 0.00 0.00 34.14 4.09
2636 9100 0.742505 TCGCGGATTTCGGATAGTGT 59.257 50.000 6.13 0.00 39.69 3.55
2640 9104 2.295070 TCATCTTCGCGGATTTCGGATA 59.705 45.455 6.13 0.00 39.69 2.59
2967 9434 4.725790 TGGATAGATGCATCCGTATCTG 57.274 45.455 23.06 0.00 46.51 2.90
2985 9452 7.942894 TCTTAGATTTGTCTAGATACGGATGGA 59.057 37.037 0.00 0.00 0.00 3.41
2986 9453 8.112016 TCTTAGATTTGTCTAGATACGGATGG 57.888 38.462 0.00 0.00 0.00 3.51
3137 9661 4.464597 GGAGTTACAGAGTCAGAGACCAAT 59.535 45.833 0.00 0.00 32.18 3.16
3397 9991 9.390795 CGAATATTTTGGAGAATCATGTTGATC 57.609 33.333 0.00 0.00 35.76 2.92
3455 10049 1.950909 TGCGAAAAGTTGGTAAGGTGG 59.049 47.619 0.00 0.00 0.00 4.61
3457 10051 2.876550 GTCTGCGAAAAGTTGGTAAGGT 59.123 45.455 0.00 0.00 0.00 3.50
3472 10066 0.036952 ACTGAATCACTGGGTCTGCG 60.037 55.000 0.00 0.00 0.00 5.18
3520 10118 1.070601 GGCCTCACCAACATTTTTGCT 59.929 47.619 0.00 0.00 38.86 3.91
3693 10291 0.748729 GATCTCCTCGACCTCCGTGT 60.749 60.000 0.00 0.00 39.75 4.49
3786 10384 9.649167 ATCGTACACTTTAGCAAGTATTTAAGT 57.351 29.630 0.00 0.00 41.69 2.24
4084 10684 9.512588 AATAAGTAATCCCATCATGATCAGAAC 57.487 33.333 4.86 2.23 0.00 3.01
4118 10718 8.710835 TTCCACAAAGTTTCTTTTATTGGAAC 57.289 30.769 16.96 0.00 36.94 3.62
4136 10736 0.257328 TCAACACCTGGCTTCCACAA 59.743 50.000 0.00 0.00 0.00 3.33
4184 10784 1.270465 CCCCAGACCGAACGTTTAACT 60.270 52.381 0.46 0.00 0.00 2.24
4186 10786 1.001181 CTCCCCAGACCGAACGTTTAA 59.999 52.381 0.46 0.00 0.00 1.52
4235 10835 9.512435 GAAATCAATTGTCAAGGAGTAATGATG 57.488 33.333 5.13 0.00 0.00 3.07
4428 11904 6.040166 TGGTTTATTAAGTTGGTGGCGTTTTA 59.960 34.615 0.00 0.00 0.00 1.52
4429 11905 5.163437 TGGTTTATTAAGTTGGTGGCGTTTT 60.163 36.000 0.00 0.00 0.00 2.43
4433 11909 3.754323 TCTGGTTTATTAAGTTGGTGGCG 59.246 43.478 0.00 0.00 0.00 5.69
4438 11914 7.659390 TGGCAATTTTCTGGTTTATTAAGTTGG 59.341 33.333 0.00 0.00 0.00 3.77
4502 11980 4.269183 ACAGATGGAAATTGCCACGAATA 58.731 39.130 7.53 0.00 41.56 1.75
4696 12205 4.463891 TCAAGGGAATTTTCTGCCTTCATC 59.536 41.667 0.00 0.00 29.80 2.92
4791 12300 5.501252 GCGCTCATGGCAAATTTTATTTCTG 60.501 40.000 0.00 0.00 41.91 3.02


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

AutoCloner maintained by Alex Coulton.