Multiple sequence alignment - TraesCS6A01G268400

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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 TraesCS6A01G268400 chr6A 100.000 4701 0 0 1 4701 494882668 494877968 0.000000e+00 8682.0
1 TraesCS6A01G268400 chr6A 96.785 1244 39 1 2039 3282 495154071 495152829 0.000000e+00 2074.0
2 TraesCS6A01G268400 chr6A 92.229 1467 86 14 1843 3282 494046784 494048249 0.000000e+00 2052.0
3 TraesCS6A01G268400 chr6A 92.621 1423 75 11 1883 3282 493842324 493843739 0.000000e+00 2019.0
4 TraesCS6A01G268400 chr6A 94.458 1245 65 2 2038 3282 493756316 493757556 0.000000e+00 1914.0
5 TraesCS6A01G268400 chr6A 97.071 478 10 3 4226 4701 495152568 495152093 0.000000e+00 802.0
6 TraesCS6A01G268400 chr6A 95.483 487 18 1 1 487 495156159 495155677 0.000000e+00 774.0
7 TraesCS6A01G268400 chr6A 85.864 764 39 18 642 1368 495155685 495154954 0.000000e+00 749.0
8 TraesCS6A01G268400 chr6A 88.073 654 42 13 1415 2039 495154754 495154108 0.000000e+00 743.0
9 TraesCS6A01G268400 chr6A 96.218 238 6 3 3269 3505 493843774 493844009 2.050000e-103 387.0
10 TraesCS6A01G268400 chr6A 94.186 258 7 3 4226 4477 494048510 494048765 2.050000e-103 387.0
11 TraesCS6A01G268400 chr6A 96.930 228 6 1 3279 3505 495152786 495152559 9.550000e-102 381.0
12 TraesCS6A01G268400 chr6A 94.958 238 9 3 3269 3505 493757591 493757826 2.070000e-98 370.0
13 TraesCS6A01G268400 chr6A 90.777 206 18 1 1835 2039 493756075 493756280 1.670000e-69 274.0
14 TraesCS6A01G268400 chr6A 93.038 158 8 2 4226 4381 493757817 493757973 1.320000e-55 228.0
15 TraesCS6A01G268400 chr6A 82.955 264 31 10 4226 4477 493844000 493844261 4.730000e-55 226.0
16 TraesCS6A01G268400 chr6A 100.000 50 0 0 4652 4701 494873193 494873144 5.010000e-15 93.5
17 TraesCS6A01G268400 chr6A 98.000 50 1 0 4652 4701 495147298 495147249 2.330000e-13 87.9
18 TraesCS6A01G268400 chr6D 96.707 1245 40 1 2038 3282 349031429 349032672 0.000000e+00 2071.0
19 TraesCS6A01G268400 chr6D 96.064 1245 48 1 2038 3282 348861366 348862609 0.000000e+00 2026.0
20 TraesCS6A01G268400 chr6D 88.619 659 54 14 1400 2039 349030737 349031393 0.000000e+00 782.0
21 TraesCS6A01G268400 chr6D 84.695 673 59 13 1400 2039 348860669 348861330 2.390000e-177 632.0
22 TraesCS6A01G268400 chr6D 83.161 772 41 31 642 1377 348859770 348860488 1.440000e-174 623.0
23 TraesCS6A01G268400 chr6D 82.483 725 88 29 3504 4223 471175509 471176199 2.420000e-167 599.0
24 TraesCS6A01G268400 chr6D 81.289 807 42 35 642 1377 349029794 349030562 1.910000e-153 553.0
25 TraesCS6A01G268400 chr6D 87.822 427 19 12 4226 4651 348994997 348995391 1.980000e-128 470.0
26 TraesCS6A01G268400 chr6D 91.437 327 23 2 132 457 348857671 348857993 1.200000e-120 444.0
27 TraesCS6A01G268400 chr6D 87.626 396 29 6 14 402 349029374 349029756 4.320000e-120 442.0
28 TraesCS6A01G268400 chr6D 85.202 446 40 19 4226 4651 348862870 348863309 7.220000e-118 435.0
29 TraesCS6A01G268400 chr6D 92.517 294 15 3 4226 4513 350063089 350062797 9.410000e-112 414.0
30 TraesCS6A01G268400 chr6D 86.386 404 21 13 4249 4651 349176079 349176449 1.220000e-110 411.0
31 TraesCS6A01G268400 chr6D 97.368 228 5 1 3279 3505 350203812 350203585 2.050000e-103 387.0
32 TraesCS6A01G268400 chr6D 84.742 426 13 19 4226 4651 349032933 349033306 3.430000e-101 379.0
33 TraesCS6A01G268400 chr6D 97.297 222 6 0 3279 3500 348862652 348862873 1.230000e-100 377.0
34 TraesCS6A01G268400 chr6D 96.491 228 7 1 3279 3505 349032715 349032942 4.440000e-100 375.0
35 TraesCS6A01G268400 chr6D 92.941 255 15 2 4398 4651 348839085 348839337 7.430000e-98 368.0
36 TraesCS6A01G268400 chr6D 91.772 158 10 2 4226 4381 350203594 350203438 2.850000e-52 217.0
37 TraesCS6A01G268400 chr6D 85.646 209 20 5 1835 2039 350205296 350205094 1.330000e-50 211.0
38 TraesCS6A01G268400 chr6B 96.707 1245 40 1 2038 3282 529889880 529891123 0.000000e+00 2071.0
39 TraesCS6A01G268400 chr6B 95.984 1245 48 2 2039 3282 530852187 530850944 0.000000e+00 2021.0
40 TraesCS6A01G268400 chr6B 94.614 1244 66 1 2039 3282 529774054 529775296 0.000000e+00 1925.0
41 TraesCS6A01G268400 chr6B 82.586 781 38 38 642 1372 530853812 530853080 2.420000e-167 599.0
42 TraesCS6A01G268400 chr6B 84.330 619 64 21 1430 2039 530852819 530852225 4.080000e-160 575.0
43 TraesCS6A01G268400 chr6B 87.067 433 18 14 4226 4651 530850683 530850282 5.550000e-124 455.0
44 TraesCS6A01G268400 chr6B 95.798 238 7 3 3269 3505 529775331 529775566 9.550000e-102 381.0
45 TraesCS6A01G268400 chr6B 96.053 228 8 1 3279 3505 529891166 529891393 2.070000e-98 370.0
46 TraesCS6A01G268400 chr6B 96.847 222 6 1 3285 3505 530850895 530850674 2.070000e-98 370.0
47 TraesCS6A01G268400 chr6B 94.248 226 4 3 4226 4443 529891384 529891608 2.100000e-88 337.0
48 TraesCS6A01G268400 chr6B 88.489 278 24 3 100 371 530858211 530857936 3.510000e-86 329.0
49 TraesCS6A01G268400 chr6B 85.759 316 20 12 4325 4618 564063637 564063325 1.270000e-80 311.0
50 TraesCS6A01G268400 chr6B 76.246 602 80 38 1452 2039 529773461 529774013 1.300000e-65 261.0
51 TraesCS6A01G268400 chr6B 92.405 158 9 2 4226 4381 529775557 529775713 6.120000e-54 222.0
52 TraesCS6A01G268400 chr6B 74.779 226 32 12 856 1058 530998940 530998717 1.400000e-10 78.7
53 TraesCS6A01G268400 chr3B 99.307 721 5 0 3503 4223 96866041 96865321 0.000000e+00 1304.0
54 TraesCS6A01G268400 chr3B 81.954 737 77 43 3501 4223 34064467 34065161 1.470000e-159 573.0
55 TraesCS6A01G268400 chr3B 81.511 741 89 35 3504 4223 813144076 813143363 2.460000e-157 566.0
56 TraesCS6A01G268400 chr3B 80.488 123 13 8 175 291 21860839 21860956 3.010000e-12 84.2
57 TraesCS6A01G268400 chr2A 99.037 727 5 2 3504 4230 761169819 761170543 0.000000e+00 1303.0
58 TraesCS6A01G268400 chr4A 98.750 720 8 1 3504 4223 711326843 711327561 0.000000e+00 1279.0
59 TraesCS6A01G268400 chr1B 98.750 720 7 2 3504 4223 78822572 78821855 0.000000e+00 1279.0
60 TraesCS6A01G268400 chr7B 89.919 744 44 10 3503 4224 663809445 663810179 0.000000e+00 929.0
61 TraesCS6A01G268400 chrUn 89.247 744 39 18 3503 4223 77585737 77586462 0.000000e+00 893.0
62 TraesCS6A01G268400 chrUn 87.681 138 12 4 503 640 282846281 282846413 6.300000e-34 156.0
63 TraesCS6A01G268400 chrUn 87.681 138 12 4 503 640 282853007 282853139 6.300000e-34 156.0
64 TraesCS6A01G268400 chrUn 88.148 135 11 4 506 640 295136443 295136314 6.300000e-34 156.0
65 TraesCS6A01G268400 chrUn 88.148 135 11 4 506 640 295141640 295141511 6.300000e-34 156.0
66 TraesCS6A01G268400 chrUn 88.148 135 11 4 506 640 304686841 304686712 6.300000e-34 156.0
67 TraesCS6A01G268400 chr1D 89.218 742 38 11 3504 4223 42812369 42811648 0.000000e+00 889.0
68 TraesCS6A01G268400 chr1D 98.000 50 1 0 4652 4701 475251622 475251573 2.330000e-13 87.9
69 TraesCS6A01G268400 chr7D 95.820 311 12 1 3894 4203 506881596 506881906 7.020000e-138 501.0
70 TraesCS6A01G268400 chr3D 82.781 151 15 5 487 637 389634832 389634971 1.780000e-24 124.0
71 TraesCS6A01G268400 chr3D 98.000 50 1 0 4652 4701 433808867 433808916 2.330000e-13 87.9
72 TraesCS6A01G268400 chr3D 98.000 50 1 0 4652 4701 433813713 433813762 2.330000e-13 87.9
73 TraesCS6A01G268400 chr7A 98.077 52 1 0 590 641 657522878 657522827 1.800000e-14 91.6
74 TraesCS6A01G268400 chr5B 98.039 51 1 0 4651 4701 641096339 641096289 6.480000e-14 89.8
75 TraesCS6A01G268400 chr4D 98.000 50 1 0 4652 4701 481078041 481078090 2.330000e-13 87.9
76 TraesCS6A01G268400 chr4D 96.000 50 2 0 4652 4701 481073183 481073232 1.080000e-11 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G268400 chr6A 494877968 494882668 4700 True 8682.000000 8682 100.000000 1 4701 1 chr6A.!!$R2 4700
1 TraesCS6A01G268400 chr6A 494046784 494048765 1981 False 1219.500000 2052 93.207500 1843 4477 2 chr6A.!!$F3 2634
2 TraesCS6A01G268400 chr6A 495152093 495156159 4066 True 920.500000 2074 93.367667 1 4701 6 chr6A.!!$R4 4700
3 TraesCS6A01G268400 chr6A 493842324 493844261 1937 False 877.333333 2019 90.598000 1883 4477 3 chr6A.!!$F2 2594
4 TraesCS6A01G268400 chr6A 493756075 493757973 1898 False 696.500000 1914 93.307750 1835 4381 4 chr6A.!!$F1 2546
5 TraesCS6A01G268400 chr6D 349029374 349033306 3932 False 767.000000 2071 89.245667 14 4651 6 chr6D.!!$F6 4637
6 TraesCS6A01G268400 chr6D 348857671 348863309 5638 False 756.166667 2026 89.642667 132 4651 6 chr6D.!!$F5 4519
7 TraesCS6A01G268400 chr6D 471175509 471176199 690 False 599.000000 599 82.483000 3504 4223 1 chr6D.!!$F4 719
8 TraesCS6A01G268400 chr6D 350203438 350205296 1858 True 271.666667 387 91.595333 1835 4381 3 chr6D.!!$R2 2546
9 TraesCS6A01G268400 chr6B 529889880 529891608 1728 False 926.000000 2071 95.669333 2038 4443 3 chr6B.!!$F2 2405
10 TraesCS6A01G268400 chr6B 530850282 530853812 3530 True 804.000000 2021 89.362800 642 4651 5 chr6B.!!$R4 4009
11 TraesCS6A01G268400 chr6B 529773461 529775713 2252 False 697.250000 1925 89.765750 1452 4381 4 chr6B.!!$F1 2929
12 TraesCS6A01G268400 chr3B 96865321 96866041 720 True 1304.000000 1304 99.307000 3503 4223 1 chr3B.!!$R1 720
13 TraesCS6A01G268400 chr3B 34064467 34065161 694 False 573.000000 573 81.954000 3501 4223 1 chr3B.!!$F2 722
14 TraesCS6A01G268400 chr3B 813143363 813144076 713 True 566.000000 566 81.511000 3504 4223 1 chr3B.!!$R2 719
15 TraesCS6A01G268400 chr2A 761169819 761170543 724 False 1303.000000 1303 99.037000 3504 4230 1 chr2A.!!$F1 726
16 TraesCS6A01G268400 chr4A 711326843 711327561 718 False 1279.000000 1279 98.750000 3504 4223 1 chr4A.!!$F1 719
17 TraesCS6A01G268400 chr1B 78821855 78822572 717 True 1279.000000 1279 98.750000 3504 4223 1 chr1B.!!$R1 719
18 TraesCS6A01G268400 chr7B 663809445 663810179 734 False 929.000000 929 89.919000 3503 4224 1 chr7B.!!$F1 721
19 TraesCS6A01G268400 chrUn 77585737 77586462 725 False 893.000000 893 89.247000 3503 4223 1 chrUn.!!$F1 720
20 TraesCS6A01G268400 chr1D 42811648 42812369 721 True 889.000000 889 89.218000 3504 4223 1 chr1D.!!$R1 719

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
554 2318 0.097674 CGTGCAAATCCAGCAGCTAC 59.902 55.0 0.0 0.0 43.63 3.58 F
1626 3779 0.035317 AGAACCACGCTTCAGCATCA 59.965 50.0 0.0 0.0 42.21 3.07 F
2299 4549 1.550327 TGATGCTCGTCACCTTCTCT 58.450 50.0 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 4460 0.526524 CAGAAGGAGTCGGCGATGAC 60.527 60.000 14.79 6.20 39.21 3.06 R
2573 4823 0.247460 CGTTCTGCTGGATCCAGACA 59.753 55.000 40.29 32.53 46.30 3.41 R
4227 6594 1.819903 AGAAGAAGTAGTCGAGGTGGC 59.180 52.381 0.00 0.00 0.00 5.01 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
163 171 6.678568 AGATCTAGCAATGCTATGGTAGTT 57.321 37.500 15.97 15.34 46.46 2.24
233 241 3.318275 ACTTGCTATGTCCGATCGTATGT 59.682 43.478 15.09 0.00 0.00 2.29
258 266 4.496360 TGTGTTGAATTTATCTACGCCGA 58.504 39.130 0.00 0.00 41.63 5.54
370 378 5.163519 GCTCAAGATGCTCTAAGAGAAGAGT 60.164 44.000 14.21 0.00 44.13 3.24
371 379 6.206395 TCAAGATGCTCTAAGAGAAGAGTG 57.794 41.667 0.00 0.00 44.13 3.51
372 380 4.654091 AGATGCTCTAAGAGAAGAGTGC 57.346 45.455 0.00 0.00 44.13 4.40
373 381 2.929531 TGCTCTAAGAGAAGAGTGCG 57.070 50.000 0.00 0.00 44.13 5.34
384 392 2.028930 AGAAGAGTGCGTAGGAACTTGG 60.029 50.000 0.00 0.00 41.75 3.61
432 440 0.885196 TTATGGTTTTGGCAGCGTCC 59.115 50.000 0.00 0.00 0.00 4.79
485 2249 4.664150 CAAAGTTGGAGGTAAAAGGCAA 57.336 40.909 0.00 0.00 0.00 4.52
486 2250 4.620982 CAAAGTTGGAGGTAAAAGGCAAG 58.379 43.478 0.00 0.00 0.00 4.01
487 2251 2.239400 AGTTGGAGGTAAAAGGCAAGC 58.761 47.619 0.00 0.00 0.00 4.01
488 2252 1.068541 GTTGGAGGTAAAAGGCAAGCG 60.069 52.381 0.00 0.00 0.00 4.68
489 2253 0.398696 TGGAGGTAAAAGGCAAGCGA 59.601 50.000 0.00 0.00 0.00 4.93
490 2254 1.202830 TGGAGGTAAAAGGCAAGCGAA 60.203 47.619 0.00 0.00 0.00 4.70
491 2255 1.883926 GGAGGTAAAAGGCAAGCGAAA 59.116 47.619 0.00 0.00 0.00 3.46
492 2256 2.351447 GGAGGTAAAAGGCAAGCGAAAC 60.351 50.000 0.00 0.00 0.00 2.78
493 2257 2.292292 GAGGTAAAAGGCAAGCGAAACA 59.708 45.455 0.00 0.00 0.00 2.83
494 2258 2.293399 AGGTAAAAGGCAAGCGAAACAG 59.707 45.455 0.00 0.00 0.00 3.16
495 2259 2.051423 GTAAAAGGCAAGCGAAACAGC 58.949 47.619 0.00 0.00 37.41 4.40
502 2266 2.939022 AGCGAAACAGCTTCACGC 59.061 55.556 13.79 13.79 46.80 5.34
503 2267 1.887242 AGCGAAACAGCTTCACGCA 60.887 52.632 20.46 0.00 46.80 5.24
504 2268 1.722507 GCGAAACAGCTTCACGCAC 60.723 57.895 15.82 0.00 46.75 5.34
505 2269 1.437089 CGAAACAGCTTCACGCACG 60.437 57.895 0.00 0.00 42.61 5.34
506 2270 1.817217 CGAAACAGCTTCACGCACGA 61.817 55.000 0.00 0.00 42.61 4.35
507 2271 0.512952 GAAACAGCTTCACGCACGAT 59.487 50.000 0.00 0.00 42.61 3.73
508 2272 1.724623 GAAACAGCTTCACGCACGATA 59.275 47.619 0.00 0.00 42.61 2.92
509 2273 1.068474 AACAGCTTCACGCACGATAC 58.932 50.000 0.00 0.00 42.61 2.24
510 2274 0.243907 ACAGCTTCACGCACGATACT 59.756 50.000 0.00 0.00 42.61 2.12
511 2275 1.336887 ACAGCTTCACGCACGATACTT 60.337 47.619 0.00 0.00 42.61 2.24
512 2276 1.059692 CAGCTTCACGCACGATACTTG 59.940 52.381 0.00 0.00 42.61 3.16
513 2277 1.068474 GCTTCACGCACGATACTTGT 58.932 50.000 0.00 0.00 38.92 3.16
514 2278 2.094906 AGCTTCACGCACGATACTTGTA 60.095 45.455 0.00 0.00 42.61 2.41
515 2279 2.279136 GCTTCACGCACGATACTTGTAG 59.721 50.000 0.00 0.00 38.92 2.74
516 2280 1.904144 TCACGCACGATACTTGTAGC 58.096 50.000 0.00 0.00 0.00 3.58
517 2281 0.921347 CACGCACGATACTTGTAGCC 59.079 55.000 0.00 0.00 0.00 3.93
518 2282 0.524816 ACGCACGATACTTGTAGCCG 60.525 55.000 0.00 0.00 0.00 5.52
519 2283 0.248336 CGCACGATACTTGTAGCCGA 60.248 55.000 10.62 0.00 0.00 5.54
520 2284 1.197910 GCACGATACTTGTAGCCGAC 58.802 55.000 10.62 0.00 0.00 4.79
521 2285 1.836383 CACGATACTTGTAGCCGACC 58.164 55.000 10.62 0.00 0.00 4.79
522 2286 0.379669 ACGATACTTGTAGCCGACCG 59.620 55.000 10.62 0.00 0.00 4.79
523 2287 0.659427 CGATACTTGTAGCCGACCGA 59.341 55.000 0.00 0.00 0.00 4.69
524 2288 1.596464 CGATACTTGTAGCCGACCGAC 60.596 57.143 0.00 0.00 0.00 4.79
525 2289 0.743097 ATACTTGTAGCCGACCGACC 59.257 55.000 0.00 0.00 0.00 4.79
526 2290 1.315257 TACTTGTAGCCGACCGACCC 61.315 60.000 0.00 0.00 0.00 4.46
527 2291 2.601067 TTGTAGCCGACCGACCCA 60.601 61.111 0.00 0.00 0.00 4.51
528 2292 1.956629 CTTGTAGCCGACCGACCCAT 61.957 60.000 0.00 0.00 0.00 4.00
529 2293 2.106332 GTAGCCGACCGACCCATG 59.894 66.667 0.00 0.00 0.00 3.66
530 2294 3.845259 TAGCCGACCGACCCATGC 61.845 66.667 0.00 0.00 0.00 4.06
532 2296 4.856801 GCCGACCGACCCATGCAT 62.857 66.667 0.00 0.00 0.00 3.96
533 2297 2.896854 CCGACCGACCCATGCATG 60.897 66.667 20.19 20.19 0.00 4.06
534 2298 2.186644 CGACCGACCCATGCATGA 59.813 61.111 28.31 0.00 0.00 3.07
535 2299 2.173669 CGACCGACCCATGCATGAC 61.174 63.158 28.31 16.45 0.00 3.06
536 2300 2.125147 ACCGACCCATGCATGACG 60.125 61.111 28.31 25.25 0.00 4.35
537 2301 2.125147 CCGACCCATGCATGACGT 60.125 61.111 28.31 21.66 0.00 4.34
538 2302 2.463620 CCGACCCATGCATGACGTG 61.464 63.158 28.31 17.32 34.83 4.49
548 2312 3.317608 CATGACGTGCAAATCCAGC 57.682 52.632 0.00 0.00 0.00 4.85
549 2313 0.522626 CATGACGTGCAAATCCAGCA 59.477 50.000 0.00 0.00 40.19 4.41
550 2314 0.806868 ATGACGTGCAAATCCAGCAG 59.193 50.000 0.00 0.00 43.63 4.24
551 2315 1.154150 GACGTGCAAATCCAGCAGC 60.154 57.895 0.00 0.00 43.63 5.25
552 2316 1.580845 GACGTGCAAATCCAGCAGCT 61.581 55.000 0.00 0.00 43.63 4.24
553 2317 0.321564 ACGTGCAAATCCAGCAGCTA 60.322 50.000 0.00 0.00 43.63 3.32
554 2318 0.097674 CGTGCAAATCCAGCAGCTAC 59.902 55.000 0.00 0.00 43.63 3.58
555 2319 1.457346 GTGCAAATCCAGCAGCTACT 58.543 50.000 0.00 0.00 43.63 2.57
556 2320 1.131883 GTGCAAATCCAGCAGCTACTG 59.868 52.381 7.00 7.00 43.63 2.74
566 2330 3.041874 CAGCTACTGCCGTTCTCAG 57.958 57.895 0.00 0.00 40.80 3.35
567 2331 0.459237 CAGCTACTGCCGTTCTCAGG 60.459 60.000 0.00 0.00 40.80 3.86
575 2339 3.384816 CCGTTCTCAGGCATATGCA 57.615 52.632 28.07 8.01 44.36 3.96
576 2340 1.888215 CCGTTCTCAGGCATATGCAT 58.112 50.000 28.07 19.95 44.36 3.96
582 2346 2.250646 CAGGCATATGCATGTCCGG 58.749 57.895 29.35 8.10 46.46 5.14
583 2347 1.601759 AGGCATATGCATGTCCGGC 60.602 57.895 28.07 8.95 44.36 6.13
584 2348 1.601759 GGCATATGCATGTCCGGCT 60.602 57.895 28.07 0.00 44.36 5.52
585 2349 1.577922 GCATATGCATGTCCGGCTG 59.422 57.895 22.84 0.00 41.59 4.85
586 2350 1.859427 GCATATGCATGTCCGGCTGG 61.859 60.000 22.84 4.71 41.59 4.85
587 2351 0.250424 CATATGCATGTCCGGCTGGA 60.250 55.000 11.27 11.27 43.88 3.86
597 2361 2.839486 TCCGGCTGGATTGTATCATC 57.161 50.000 11.27 0.00 40.17 2.92
598 2362 1.000843 TCCGGCTGGATTGTATCATCG 59.999 52.381 11.27 0.00 40.17 3.84
599 2363 1.270305 CCGGCTGGATTGTATCATCGT 60.270 52.381 5.28 0.00 37.49 3.73
600 2364 2.061773 CGGCTGGATTGTATCATCGTC 58.938 52.381 0.00 0.00 0.00 4.20
601 2365 2.288457 CGGCTGGATTGTATCATCGTCT 60.288 50.000 0.00 0.00 0.00 4.18
602 2366 3.057526 CGGCTGGATTGTATCATCGTCTA 60.058 47.826 0.00 0.00 0.00 2.59
603 2367 4.380973 CGGCTGGATTGTATCATCGTCTAT 60.381 45.833 0.00 0.00 0.00 1.98
604 2368 5.105752 GGCTGGATTGTATCATCGTCTATC 58.894 45.833 0.00 0.00 0.00 2.08
605 2369 5.105554 GGCTGGATTGTATCATCGTCTATCT 60.106 44.000 0.00 0.00 0.00 1.98
606 2370 6.095580 GGCTGGATTGTATCATCGTCTATCTA 59.904 42.308 0.00 0.00 0.00 1.98
607 2371 7.201866 GGCTGGATTGTATCATCGTCTATCTAT 60.202 40.741 0.00 0.00 0.00 1.98
608 2372 7.860373 GCTGGATTGTATCATCGTCTATCTATC 59.140 40.741 0.00 0.00 0.00 2.08
609 2373 8.807948 TGGATTGTATCATCGTCTATCTATCA 57.192 34.615 0.00 0.00 0.00 2.15
610 2374 9.413734 TGGATTGTATCATCGTCTATCTATCAT 57.586 33.333 0.00 0.00 0.00 2.45
611 2375 9.676195 GGATTGTATCATCGTCTATCTATCATG 57.324 37.037 0.00 0.00 0.00 3.07
612 2376 9.179552 GATTGTATCATCGTCTATCTATCATGC 57.820 37.037 0.00 0.00 0.00 4.06
613 2377 7.630242 TGTATCATCGTCTATCTATCATGCA 57.370 36.000 0.00 0.00 0.00 3.96
614 2378 8.055279 TGTATCATCGTCTATCTATCATGCAA 57.945 34.615 0.00 0.00 0.00 4.08
615 2379 8.522830 TGTATCATCGTCTATCTATCATGCAAA 58.477 33.333 0.00 0.00 0.00 3.68
616 2380 9.358872 GTATCATCGTCTATCTATCATGCAAAA 57.641 33.333 0.00 0.00 0.00 2.44
617 2381 7.643528 TCATCGTCTATCTATCATGCAAAAC 57.356 36.000 0.00 0.00 0.00 2.43
618 2382 7.436933 TCATCGTCTATCTATCATGCAAAACT 58.563 34.615 0.00 0.00 0.00 2.66
619 2383 7.928167 TCATCGTCTATCTATCATGCAAAACTT 59.072 33.333 0.00 0.00 0.00 2.66
620 2384 7.468922 TCGTCTATCTATCATGCAAAACTTG 57.531 36.000 0.00 0.00 0.00 3.16
621 2385 7.041721 TCGTCTATCTATCATGCAAAACTTGT 58.958 34.615 0.00 0.00 0.00 3.16
622 2386 7.222805 TCGTCTATCTATCATGCAAAACTTGTC 59.777 37.037 0.00 0.00 0.00 3.18
623 2387 7.340699 GTCTATCTATCATGCAAAACTTGTCG 58.659 38.462 0.00 0.00 0.00 4.35
624 2388 7.010552 GTCTATCTATCATGCAAAACTTGTCGT 59.989 37.037 0.00 0.00 0.00 4.34
625 2389 5.281693 TCTATCATGCAAAACTTGTCGTG 57.718 39.130 0.00 0.00 0.00 4.35
626 2390 3.988379 ATCATGCAAAACTTGTCGTGT 57.012 38.095 0.00 0.00 0.00 4.49
627 2391 3.063670 TCATGCAAAACTTGTCGTGTG 57.936 42.857 0.00 0.00 0.00 3.82
628 2392 2.421775 TCATGCAAAACTTGTCGTGTGT 59.578 40.909 0.00 0.00 0.00 3.72
629 2393 3.623510 TCATGCAAAACTTGTCGTGTGTA 59.376 39.130 0.00 0.00 0.00 2.90
630 2394 4.274705 TCATGCAAAACTTGTCGTGTGTAT 59.725 37.500 0.00 0.00 0.00 2.29
631 2395 5.467063 TCATGCAAAACTTGTCGTGTGTATA 59.533 36.000 0.00 0.00 0.00 1.47
632 2396 5.337219 TGCAAAACTTGTCGTGTGTATAG 57.663 39.130 0.00 0.00 0.00 1.31
633 2397 4.148891 GCAAAACTTGTCGTGTGTATAGC 58.851 43.478 0.00 0.00 0.00 2.97
634 2398 4.319190 GCAAAACTTGTCGTGTGTATAGCA 60.319 41.667 0.00 0.00 0.00 3.49
683 2451 2.751166 TGAAGGAAGAAAGAGGAGCG 57.249 50.000 0.00 0.00 0.00 5.03
700 2468 1.878088 AGCGTGACTCTACTTCGACAA 59.122 47.619 0.00 0.00 0.00 3.18
713 2481 9.140286 CTCTACTTCGACAATTTTCAGTTGATA 57.860 33.333 0.00 0.00 0.00 2.15
728 2496 4.081420 CAGTTGATAGAGGTGTAGGTGCTT 60.081 45.833 0.00 0.00 0.00 3.91
736 2504 3.939592 GAGGTGTAGGTGCTTAACATTCC 59.060 47.826 0.00 0.00 0.00 3.01
830 2601 2.432628 CACCGTTCGTGCTCCTCC 60.433 66.667 0.00 0.00 35.18 4.30
831 2602 2.915659 ACCGTTCGTGCTCCTCCA 60.916 61.111 0.00 0.00 0.00 3.86
832 2603 2.342279 CCGTTCGTGCTCCTCCAA 59.658 61.111 0.00 0.00 0.00 3.53
833 2604 1.301401 CCGTTCGTGCTCCTCCAAA 60.301 57.895 0.00 0.00 0.00 3.28
834 2605 0.673644 CCGTTCGTGCTCCTCCAAAT 60.674 55.000 0.00 0.00 0.00 2.32
835 2606 0.721718 CGTTCGTGCTCCTCCAAATC 59.278 55.000 0.00 0.00 0.00 2.17
836 2607 1.808411 GTTCGTGCTCCTCCAAATCA 58.192 50.000 0.00 0.00 0.00 2.57
837 2608 2.151202 GTTCGTGCTCCTCCAAATCAA 58.849 47.619 0.00 0.00 0.00 2.57
838 2609 2.099141 TCGTGCTCCTCCAAATCAAG 57.901 50.000 0.00 0.00 0.00 3.02
839 2610 1.089920 CGTGCTCCTCCAAATCAAGG 58.910 55.000 0.00 0.00 0.00 3.61
840 2611 1.339055 CGTGCTCCTCCAAATCAAGGA 60.339 52.381 0.00 0.00 39.38 3.36
841 2612 2.681976 CGTGCTCCTCCAAATCAAGGAT 60.682 50.000 0.00 0.00 40.83 3.24
842 2613 3.359950 GTGCTCCTCCAAATCAAGGATT 58.640 45.455 0.00 0.00 40.83 3.01
843 2614 3.379688 GTGCTCCTCCAAATCAAGGATTC 59.620 47.826 0.00 0.00 40.83 2.52
844 2615 2.615912 GCTCCTCCAAATCAAGGATTCG 59.384 50.000 0.00 0.00 40.83 3.34
845 2616 3.682718 GCTCCTCCAAATCAAGGATTCGA 60.683 47.826 0.00 0.00 40.83 3.71
987 2759 8.141909 TCACCTATAAACTGAATGGATACGAAG 58.858 37.037 0.00 0.00 42.51 3.79
1071 2860 3.241900 CGTTTGACAGAATCAGCTCATCG 60.242 47.826 0.00 0.00 38.99 3.84
1200 3002 1.734117 GCCAAGCAAATCACCACGC 60.734 57.895 0.00 0.00 0.00 5.34
1214 3038 7.948278 AATCACCACGCTTCTATTATTACTC 57.052 36.000 0.00 0.00 0.00 2.59
1279 3114 1.676635 GCATGCAACCTGAGCCTGA 60.677 57.895 14.21 0.00 30.48 3.86
1280 3115 1.654954 GCATGCAACCTGAGCCTGAG 61.655 60.000 14.21 0.00 30.48 3.35
1281 3116 1.378250 ATGCAACCTGAGCCTGAGC 60.378 57.895 0.00 0.00 40.32 4.26
1282 3117 2.749441 GCAACCTGAGCCTGAGCC 60.749 66.667 0.00 0.00 41.25 4.70
1293 3143 3.847602 CTGAGCCTGCTAGCCGCT 61.848 66.667 22.47 22.47 40.11 5.52
1323 3173 1.440353 CGAAACTTCGCGGCTTTGG 60.440 57.895 6.13 0.00 44.26 3.28
1324 3174 1.652563 GAAACTTCGCGGCTTTGGT 59.347 52.632 6.13 0.00 0.00 3.67
1380 3244 4.403137 GCGCACGCATGAGCCAAA 62.403 61.111 10.65 0.00 45.12 3.28
1445 3544 1.327764 CAAACTTCCGCTTCCGATAGC 59.672 52.381 0.00 0.00 37.80 2.97
1456 3555 0.395724 TCCGATAGCCACAGAGCTCA 60.396 55.000 17.77 0.00 43.67 4.26
1521 3621 1.813859 CCCGAGGTAACGATCAGCA 59.186 57.895 0.00 0.00 46.39 4.41
1522 3622 0.389391 CCCGAGGTAACGATCAGCAT 59.611 55.000 0.00 0.00 46.39 3.79
1523 3623 1.603172 CCCGAGGTAACGATCAGCATC 60.603 57.143 0.00 0.00 46.39 3.91
1549 3671 2.445654 CCCTCCTCCTCCTCCTGC 60.446 72.222 0.00 0.00 0.00 4.85
1570 3693 3.056328 GCCCCCTGTTCGTTCTGC 61.056 66.667 0.00 0.00 0.00 4.26
1626 3779 0.035317 AGAACCACGCTTCAGCATCA 59.965 50.000 0.00 0.00 42.21 3.07
1640 3793 4.392047 TCAGCATCAGTCAACACAAGAAT 58.608 39.130 0.00 0.00 0.00 2.40
1645 3798 5.625251 CATCAGTCAACACAAGAATAGCAC 58.375 41.667 0.00 0.00 0.00 4.40
1801 4006 2.298610 CTGCAGCATCACATCCAGAAT 58.701 47.619 0.00 0.00 0.00 2.40
2147 4397 3.164977 TCCACGGCACCAACCTCA 61.165 61.111 0.00 0.00 0.00 3.86
2266 4516 2.751913 CCTCGTCTCCCTCGTCGTG 61.752 68.421 0.00 0.00 0.00 4.35
2299 4549 1.550327 TGATGCTCGTCACCTTCTCT 58.450 50.000 0.00 0.00 0.00 3.10
2401 4651 4.090057 GCAGACCGTGGCTTTCGC 62.090 66.667 0.00 0.00 0.00 4.70
2573 4823 1.079127 CATCTCCGGCGTGTTCCTT 60.079 57.895 6.01 0.00 0.00 3.36
2756 5006 1.800586 TGCAAGAAGATCAGCGTCAAC 59.199 47.619 0.00 0.00 0.00 3.18
2795 5045 2.709170 CCTCTACGAGGTCAGCGAT 58.291 57.895 1.71 0.00 44.25 4.58
2831 5081 2.741985 CCCAAGATCGCGCACACA 60.742 61.111 8.75 0.00 0.00 3.72
2966 5216 3.397613 GATCCTGCTCCGCCTGCTT 62.398 63.158 0.00 0.00 0.00 3.91
2972 5222 3.458163 CTCCGCCTGCTTCCCGTA 61.458 66.667 0.00 0.00 0.00 4.02
3002 5252 2.126618 GTCGTCGTGTCATCGGCA 60.127 61.111 0.00 0.00 35.00 5.69
3136 5386 0.905357 ACATGGGTGCTCCTCTACAC 59.095 55.000 4.53 0.00 36.20 2.90
3364 5660 3.799755 GCGCCGGACACCATGAAC 61.800 66.667 5.05 0.00 0.00 3.18
4431 6842 5.892119 TGAACAGTAACTAGCTAGTAGCCAT 59.108 40.000 26.29 13.06 43.77 4.40
4663 7084 5.348724 ACATGCGAGTAGTGTAGAAATTGTG 59.651 40.000 0.00 0.00 0.00 3.33
4687 7108 1.064357 GAAGCGTTCTACCCTCTCGAG 59.936 57.143 5.93 5.93 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 8.773645 CATTGCTAGATCTAGATAGATACCTCG 58.226 40.741 30.06 3.47 42.79 4.63
163 171 7.424803 CAAGTTCACAAAATATGGACACTTCA 58.575 34.615 0.00 0.00 0.00 3.02
233 241 6.757478 TCGGCGTAGATAAATTCAACACATAA 59.243 34.615 6.85 0.00 0.00 1.90
255 263 1.990799 TGCAACGTAGATCAACTCGG 58.009 50.000 0.00 0.00 0.00 4.63
258 266 4.456280 TCTCATGCAACGTAGATCAACT 57.544 40.909 0.00 0.00 0.00 3.16
329 337 1.071699 GAGCCGGACATAGCCCATTTA 59.928 52.381 5.05 0.00 0.00 1.40
370 378 0.179043 TGCAACCAAGTTCCTACGCA 60.179 50.000 0.00 0.00 0.00 5.24
371 379 0.517316 CTGCAACCAAGTTCCTACGC 59.483 55.000 0.00 0.00 0.00 4.42
372 380 1.156736 CCTGCAACCAAGTTCCTACG 58.843 55.000 0.00 0.00 0.00 3.51
373 381 2.152016 GTCCTGCAACCAAGTTCCTAC 58.848 52.381 0.00 0.00 0.00 3.18
384 392 1.889545 AAGAAGCTCAGTCCTGCAAC 58.110 50.000 0.00 0.00 0.00 4.17
432 440 3.529252 CTCCACAAGAGAGCACTGG 57.471 57.895 0.00 0.00 46.50 4.00
478 2242 2.419057 AGCTGTTTCGCTTGCCTTT 58.581 47.368 0.00 0.00 36.74 3.11
479 2243 4.164258 AGCTGTTTCGCTTGCCTT 57.836 50.000 0.00 0.00 36.74 4.35
485 2249 2.939022 GCGTGAAGCTGTTTCGCT 59.061 55.556 14.37 0.00 42.79 4.93
495 2259 2.279136 GCTACAAGTATCGTGCGTGAAG 59.721 50.000 0.00 0.00 0.00 3.02
496 2260 2.256174 GCTACAAGTATCGTGCGTGAA 58.744 47.619 0.00 0.00 0.00 3.18
497 2261 1.468565 GGCTACAAGTATCGTGCGTGA 60.469 52.381 0.00 0.00 0.00 4.35
498 2262 0.921347 GGCTACAAGTATCGTGCGTG 59.079 55.000 0.00 0.00 0.00 5.34
499 2263 0.524816 CGGCTACAAGTATCGTGCGT 60.525 55.000 0.00 0.00 0.00 5.24
500 2264 0.248336 TCGGCTACAAGTATCGTGCG 60.248 55.000 0.00 0.00 0.00 5.34
501 2265 1.197910 GTCGGCTACAAGTATCGTGC 58.802 55.000 0.00 0.00 0.00 5.34
502 2266 1.836383 GGTCGGCTACAAGTATCGTG 58.164 55.000 0.00 0.00 0.00 4.35
503 2267 0.379669 CGGTCGGCTACAAGTATCGT 59.620 55.000 0.00 0.00 0.00 3.73
504 2268 0.659427 TCGGTCGGCTACAAGTATCG 59.341 55.000 0.00 0.00 0.00 2.92
505 2269 1.268948 GGTCGGTCGGCTACAAGTATC 60.269 57.143 0.00 0.00 0.00 2.24
506 2270 0.743097 GGTCGGTCGGCTACAAGTAT 59.257 55.000 0.00 0.00 0.00 2.12
507 2271 1.315257 GGGTCGGTCGGCTACAAGTA 61.315 60.000 0.00 0.00 0.00 2.24
508 2272 2.643232 GGGTCGGTCGGCTACAAGT 61.643 63.158 0.00 0.00 0.00 3.16
509 2273 1.956629 ATGGGTCGGTCGGCTACAAG 61.957 60.000 0.00 0.00 0.00 3.16
510 2274 1.985662 ATGGGTCGGTCGGCTACAA 60.986 57.895 0.00 0.00 0.00 2.41
511 2275 2.363276 ATGGGTCGGTCGGCTACA 60.363 61.111 0.00 0.00 0.00 2.74
512 2276 2.106332 CATGGGTCGGTCGGCTAC 59.894 66.667 0.00 0.00 0.00 3.58
513 2277 3.845259 GCATGGGTCGGTCGGCTA 61.845 66.667 0.00 0.00 0.00 3.93
515 2279 4.856801 ATGCATGGGTCGGTCGGC 62.857 66.667 0.00 0.00 0.00 5.54
516 2280 2.896854 CATGCATGGGTCGGTCGG 60.897 66.667 19.40 0.00 0.00 4.79
517 2281 2.173669 GTCATGCATGGGTCGGTCG 61.174 63.158 25.97 0.00 0.00 4.79
518 2282 2.173669 CGTCATGCATGGGTCGGTC 61.174 63.158 25.97 7.67 0.00 4.79
519 2283 2.125147 CGTCATGCATGGGTCGGT 60.125 61.111 25.97 0.00 0.00 4.69
520 2284 2.125147 ACGTCATGCATGGGTCGG 60.125 61.111 25.97 13.00 0.00 4.79
521 2285 3.092403 CACGTCATGCATGGGTCG 58.908 61.111 25.97 25.71 0.00 4.79
530 2294 0.522626 TGCTGGATTTGCACGTCATG 59.477 50.000 0.00 0.00 35.31 3.07
531 2295 0.806868 CTGCTGGATTTGCACGTCAT 59.193 50.000 0.00 0.00 36.37 3.06
532 2296 1.855213 GCTGCTGGATTTGCACGTCA 61.855 55.000 0.00 0.00 36.37 4.35
533 2297 1.154150 GCTGCTGGATTTGCACGTC 60.154 57.895 0.00 0.00 36.37 4.34
534 2298 0.321564 TAGCTGCTGGATTTGCACGT 60.322 50.000 13.43 0.00 36.37 4.49
535 2299 0.097674 GTAGCTGCTGGATTTGCACG 59.902 55.000 13.43 0.00 36.37 5.34
536 2300 1.131883 CAGTAGCTGCTGGATTTGCAC 59.868 52.381 22.82 0.00 36.37 4.57
537 2301 1.456296 CAGTAGCTGCTGGATTTGCA 58.544 50.000 22.82 0.00 38.81 4.08
549 2313 1.893786 CCTGAGAACGGCAGTAGCT 59.106 57.895 0.00 0.00 41.70 3.32
550 2314 1.811679 GCCTGAGAACGGCAGTAGC 60.812 63.158 0.00 0.00 46.77 3.58
551 2315 4.504132 GCCTGAGAACGGCAGTAG 57.496 61.111 0.00 0.00 46.77 2.57
557 2321 1.534163 CATGCATATGCCTGAGAACGG 59.466 52.381 23.90 0.00 38.67 4.44
558 2322 2.216046 ACATGCATATGCCTGAGAACG 58.784 47.619 31.67 11.03 38.67 3.95
559 2323 2.551459 GGACATGCATATGCCTGAGAAC 59.449 50.000 31.67 20.31 38.67 3.01
560 2324 2.807837 CGGACATGCATATGCCTGAGAA 60.808 50.000 31.67 12.13 38.67 2.87
561 2325 1.270465 CGGACATGCATATGCCTGAGA 60.270 52.381 31.67 12.83 38.67 3.27
562 2326 1.154197 CGGACATGCATATGCCTGAG 58.846 55.000 31.67 20.35 38.67 3.35
563 2327 0.250424 CCGGACATGCATATGCCTGA 60.250 55.000 31.67 13.53 38.67 3.86
564 2328 1.859427 GCCGGACATGCATATGCCTG 61.859 60.000 25.72 25.72 41.49 4.85
565 2329 1.601759 GCCGGACATGCATATGCCT 60.602 57.895 24.54 12.64 41.18 4.75
566 2330 1.601759 AGCCGGACATGCATATGCC 60.602 57.895 24.54 9.08 41.18 4.40
567 2331 1.577922 CAGCCGGACATGCATATGC 59.422 57.895 21.09 21.09 37.85 3.14
568 2332 0.250424 TCCAGCCGGACATGCATATG 60.250 55.000 5.05 0.00 35.91 1.78
569 2333 0.694771 ATCCAGCCGGACATGCATAT 59.305 50.000 5.05 0.00 46.79 1.78
570 2334 0.473755 AATCCAGCCGGACATGCATA 59.526 50.000 5.05 0.00 46.79 3.14
571 2335 1.105167 CAATCCAGCCGGACATGCAT 61.105 55.000 5.05 0.00 46.79 3.96
572 2336 1.750018 CAATCCAGCCGGACATGCA 60.750 57.895 5.05 0.00 46.79 3.96
573 2337 0.463654 TACAATCCAGCCGGACATGC 60.464 55.000 5.05 0.00 46.79 4.06
574 2338 2.146342 GATACAATCCAGCCGGACATG 58.854 52.381 5.05 0.00 46.79 3.21
575 2339 1.768275 TGATACAATCCAGCCGGACAT 59.232 47.619 5.05 0.00 46.79 3.06
576 2340 1.199615 TGATACAATCCAGCCGGACA 58.800 50.000 5.05 0.00 46.79 4.02
577 2341 2.417719 GATGATACAATCCAGCCGGAC 58.582 52.381 5.05 0.00 46.79 4.79
579 2343 1.270305 ACGATGATACAATCCAGCCGG 60.270 52.381 0.00 0.00 0.00 6.13
580 2344 2.061773 GACGATGATACAATCCAGCCG 58.938 52.381 0.00 0.00 0.00 5.52
581 2345 3.393089 AGACGATGATACAATCCAGCC 57.607 47.619 0.00 0.00 0.00 4.85
582 2346 5.960113 AGATAGACGATGATACAATCCAGC 58.040 41.667 0.00 0.00 0.00 4.85
583 2347 8.897752 TGATAGATAGACGATGATACAATCCAG 58.102 37.037 0.00 0.00 0.00 3.86
584 2348 8.807948 TGATAGATAGACGATGATACAATCCA 57.192 34.615 0.00 0.00 0.00 3.41
585 2349 9.676195 CATGATAGATAGACGATGATACAATCC 57.324 37.037 0.00 0.00 0.00 3.01
586 2350 9.179552 GCATGATAGATAGACGATGATACAATC 57.820 37.037 0.00 0.00 0.00 2.67
587 2351 8.689972 TGCATGATAGATAGACGATGATACAAT 58.310 33.333 0.00 0.00 0.00 2.71
588 2352 8.055279 TGCATGATAGATAGACGATGATACAA 57.945 34.615 0.00 0.00 0.00 2.41
589 2353 7.630242 TGCATGATAGATAGACGATGATACA 57.370 36.000 0.00 0.00 0.00 2.29
590 2354 8.917415 TTTGCATGATAGATAGACGATGATAC 57.083 34.615 0.00 0.00 0.00 2.24
591 2355 9.358872 GTTTTGCATGATAGATAGACGATGATA 57.641 33.333 0.00 0.00 0.00 2.15
592 2356 8.093307 AGTTTTGCATGATAGATAGACGATGAT 58.907 33.333 0.00 0.00 0.00 2.45
593 2357 7.436933 AGTTTTGCATGATAGATAGACGATGA 58.563 34.615 0.00 0.00 0.00 2.92
594 2358 7.649370 AGTTTTGCATGATAGATAGACGATG 57.351 36.000 0.00 0.00 0.00 3.84
595 2359 7.712639 ACAAGTTTTGCATGATAGATAGACGAT 59.287 33.333 0.00 0.00 0.00 3.73
596 2360 7.041721 ACAAGTTTTGCATGATAGATAGACGA 58.958 34.615 0.00 0.00 0.00 4.20
597 2361 7.239166 ACAAGTTTTGCATGATAGATAGACG 57.761 36.000 0.00 0.00 0.00 4.18
598 2362 7.010552 ACGACAAGTTTTGCATGATAGATAGAC 59.989 37.037 0.00 0.00 0.00 2.59
599 2363 7.010460 CACGACAAGTTTTGCATGATAGATAGA 59.990 37.037 0.00 0.00 0.00 1.98
600 2364 7.121911 CACGACAAGTTTTGCATGATAGATAG 58.878 38.462 0.00 0.00 0.00 2.08
601 2365 6.593770 ACACGACAAGTTTTGCATGATAGATA 59.406 34.615 0.00 0.00 0.00 1.98
602 2366 5.412594 ACACGACAAGTTTTGCATGATAGAT 59.587 36.000 0.00 0.00 0.00 1.98
603 2367 4.754618 ACACGACAAGTTTTGCATGATAGA 59.245 37.500 0.00 0.00 0.00 1.98
604 2368 4.847757 CACACGACAAGTTTTGCATGATAG 59.152 41.667 0.00 0.00 0.00 2.08
605 2369 4.274705 ACACACGACAAGTTTTGCATGATA 59.725 37.500 0.00 0.00 0.00 2.15
606 2370 3.066621 ACACACGACAAGTTTTGCATGAT 59.933 39.130 0.00 0.00 0.00 2.45
607 2371 2.421775 ACACACGACAAGTTTTGCATGA 59.578 40.909 0.00 0.00 0.00 3.07
608 2372 2.796304 ACACACGACAAGTTTTGCATG 58.204 42.857 0.00 0.00 0.00 4.06
609 2373 4.829064 ATACACACGACAAGTTTTGCAT 57.171 36.364 0.00 0.00 0.00 3.96
610 2374 4.319190 GCTATACACACGACAAGTTTTGCA 60.319 41.667 0.00 0.00 0.00 4.08
611 2375 4.148891 GCTATACACACGACAAGTTTTGC 58.851 43.478 0.00 0.00 0.00 3.68
612 2376 5.337219 TGCTATACACACGACAAGTTTTG 57.663 39.130 0.00 0.00 0.00 2.44
626 2390 4.014569 TGCCTTTGAGTTGTGCTATACA 57.985 40.909 0.00 0.00 37.56 2.29
627 2391 4.695455 TCTTGCCTTTGAGTTGTGCTATAC 59.305 41.667 0.00 0.00 0.00 1.47
628 2392 4.905429 TCTTGCCTTTGAGTTGTGCTATA 58.095 39.130 0.00 0.00 0.00 1.31
629 2393 3.754965 TCTTGCCTTTGAGTTGTGCTAT 58.245 40.909 0.00 0.00 0.00 2.97
630 2394 3.207265 TCTTGCCTTTGAGTTGTGCTA 57.793 42.857 0.00 0.00 0.00 3.49
631 2395 2.057137 TCTTGCCTTTGAGTTGTGCT 57.943 45.000 0.00 0.00 0.00 4.40
632 2396 2.544486 CCTTCTTGCCTTTGAGTTGTGC 60.544 50.000 0.00 0.00 0.00 4.57
633 2397 2.951642 TCCTTCTTGCCTTTGAGTTGTG 59.048 45.455 0.00 0.00 0.00 3.33
634 2398 3.297134 TCCTTCTTGCCTTTGAGTTGT 57.703 42.857 0.00 0.00 0.00 3.32
635 2399 4.098501 ACTTTCCTTCTTGCCTTTGAGTTG 59.901 41.667 0.00 0.00 0.00 3.16
636 2400 4.281657 ACTTTCCTTCTTGCCTTTGAGTT 58.718 39.130 0.00 0.00 0.00 3.01
637 2401 3.885901 GACTTTCCTTCTTGCCTTTGAGT 59.114 43.478 0.00 0.00 0.00 3.41
638 2402 4.023365 CAGACTTTCCTTCTTGCCTTTGAG 60.023 45.833 0.00 0.00 0.00 3.02
639 2403 3.885297 CAGACTTTCCTTCTTGCCTTTGA 59.115 43.478 0.00 0.00 0.00 2.69
640 2404 3.005155 CCAGACTTTCCTTCTTGCCTTTG 59.995 47.826 0.00 0.00 0.00 2.77
683 2451 6.421202 ACTGAAAATTGTCGAAGTAGAGTCAC 59.579 38.462 0.00 0.00 0.00 3.67
700 2468 7.106239 CACCTACACCTCTATCAACTGAAAAT 58.894 38.462 0.00 0.00 0.00 1.82
713 2481 4.323562 GGAATGTTAAGCACCTACACCTCT 60.324 45.833 0.00 0.00 0.00 3.69
728 2496 3.343617 GGCTAGCACTTGTGGAATGTTA 58.656 45.455 18.24 0.00 0.00 2.41
824 2595 4.142609 TCGAATCCTTGATTTGGAGGAG 57.857 45.455 4.63 0.00 44.77 3.69
828 2599 4.371786 CTCGATCGAATCCTTGATTTGGA 58.628 43.478 19.92 0.00 34.98 3.53
829 2600 3.496130 CCTCGATCGAATCCTTGATTTGG 59.504 47.826 19.92 8.18 34.98 3.28
830 2601 3.496130 CCCTCGATCGAATCCTTGATTTG 59.504 47.826 19.92 2.47 35.41 2.32
831 2602 3.495100 CCCCTCGATCGAATCCTTGATTT 60.495 47.826 19.92 0.00 31.89 2.17
832 2603 2.037772 CCCCTCGATCGAATCCTTGATT 59.962 50.000 19.92 0.00 34.71 2.57
833 2604 1.620819 CCCCTCGATCGAATCCTTGAT 59.379 52.381 19.92 0.00 0.00 2.57
834 2605 1.040646 CCCCTCGATCGAATCCTTGA 58.959 55.000 19.92 0.00 0.00 3.02
835 2606 0.034059 CCCCCTCGATCGAATCCTTG 59.966 60.000 19.92 6.04 0.00 3.61
836 2607 0.398664 ACCCCCTCGATCGAATCCTT 60.399 55.000 19.92 0.74 0.00 3.36
837 2608 0.828343 GACCCCCTCGATCGAATCCT 60.828 60.000 19.92 0.42 0.00 3.24
838 2609 1.113517 TGACCCCCTCGATCGAATCC 61.114 60.000 19.92 6.04 0.00 3.01
839 2610 0.750850 TTGACCCCCTCGATCGAATC 59.249 55.000 19.92 11.70 0.00 2.52
840 2611 1.200519 TTTGACCCCCTCGATCGAAT 58.799 50.000 19.92 2.28 0.00 3.34
841 2612 1.200519 ATTTGACCCCCTCGATCGAA 58.799 50.000 19.92 0.58 0.00 3.71
842 2613 1.684983 GTATTTGACCCCCTCGATCGA 59.315 52.381 18.32 18.32 0.00 3.59
843 2614 1.411246 TGTATTTGACCCCCTCGATCG 59.589 52.381 9.36 9.36 0.00 3.69
844 2615 2.434702 AGTGTATTTGACCCCCTCGATC 59.565 50.000 0.00 0.00 0.00 3.69
845 2616 2.170607 CAGTGTATTTGACCCCCTCGAT 59.829 50.000 0.00 0.00 0.00 3.59
987 2759 3.372954 CAAGGCTGCGTGTACTAGTATC 58.627 50.000 5.75 2.26 0.00 2.24
1071 2860 0.390998 GTGCAGAGGCTGAGAAGGAC 60.391 60.000 0.00 0.00 41.91 3.85
1214 3038 3.517602 TCCACAGTCGGATTGTTTATCG 58.482 45.455 3.12 0.00 33.82 2.92
1319 3169 1.373748 GCACGACTCCGCTACCAAA 60.374 57.895 0.00 0.00 39.95 3.28
1321 3171 4.111016 CGCACGACTCCGCTACCA 62.111 66.667 0.00 0.00 39.95 3.25
1323 3173 4.112341 ACCGCACGACTCCGCTAC 62.112 66.667 0.00 0.00 39.95 3.58
1324 3174 4.111016 CACCGCACGACTCCGCTA 62.111 66.667 0.00 0.00 39.95 4.26
1445 3544 1.875813 GTCGCGATGAGCTCTGTGG 60.876 63.158 14.06 6.32 45.59 4.17
1521 3621 2.366167 AGGAGGGCAAGAGCGGAT 60.366 61.111 0.00 0.00 43.41 4.18
1522 3622 3.077556 GAGGAGGGCAAGAGCGGA 61.078 66.667 0.00 0.00 43.41 5.54
1523 3623 4.168291 GGAGGAGGGCAAGAGCGG 62.168 72.222 0.00 0.00 43.41 5.52
1529 3645 2.041265 GGAGGAGGAGGAGGGCAA 59.959 66.667 0.00 0.00 0.00 4.52
1531 3647 2.445654 CAGGAGGAGGAGGAGGGC 60.446 72.222 0.00 0.00 0.00 5.19
1570 3693 5.474532 TCAGTTTTCATTGTGATCCTCCTTG 59.525 40.000 0.00 0.00 0.00 3.61
1626 3779 5.679734 CAAGTGCTATTCTTGTGTTGACT 57.320 39.130 0.00 0.00 37.90 3.41
1645 3798 2.359900 GGTCTAATGGAGGTGCACAAG 58.640 52.381 20.43 4.03 0.00 3.16
1801 4006 6.252967 ACAAAATGCATCTGTATTGACGAA 57.747 33.333 11.61 0.00 30.82 3.85
1838 4043 7.817962 GGAATTGTTAGCAACTAGAACAGACTA 59.182 37.037 0.00 0.00 37.44 2.59
1840 4045 6.651225 AGGAATTGTTAGCAACTAGAACAGAC 59.349 38.462 0.00 0.00 37.44 3.51
1849 4054 5.473066 AATTGCAGGAATTGTTAGCAACT 57.527 34.783 0.00 0.00 46.43 3.16
2147 4397 2.742372 GACGTTGGATGCGCTGGT 60.742 61.111 9.73 0.00 0.00 4.00
2210 4460 0.526524 CAGAAGGAGTCGGCGATGAC 60.527 60.000 14.79 6.20 39.21 3.06
2266 4516 0.601311 GCATCATGCCGAGGAGGTAC 60.601 60.000 0.00 0.00 43.70 3.34
2375 4625 4.427661 ACGGTCTGCGAGCTCAGC 62.428 66.667 15.40 17.75 34.19 4.26
2401 4651 4.143333 CCACGAGGTACAGCCCCG 62.143 72.222 0.00 0.00 38.26 5.73
2573 4823 0.247460 CGTTCTGCTGGATCCAGACA 59.753 55.000 40.29 32.53 46.30 3.41
2669 4919 1.771073 GCATGCGGCGCTTGTACATA 61.771 55.000 36.88 16.93 36.33 2.29
2699 4949 2.186384 CAGAGGCTCTTGAGCGGG 59.814 66.667 15.90 0.00 35.24 6.13
2795 5045 1.735376 GCTGGGGCGAGTCGATCTTA 61.735 60.000 18.61 0.00 0.00 2.10
2831 5081 1.784525 CGAGGAACTTGAAGTCGCTT 58.215 50.000 0.00 0.00 44.22 4.68
2924 5174 1.893919 GCTCCTCCACCTGAGTCACC 61.894 65.000 0.00 0.00 39.65 4.02
2972 5222 1.141881 GACGACGCTGGTGATCCAT 59.858 57.895 0.00 0.00 43.43 3.41
2988 5238 0.924090 GAGAATGCCGATGACACGAC 59.076 55.000 0.00 0.00 35.09 4.34
3002 5252 2.350522 GTGGTGTTCATCTGCGAGAAT 58.649 47.619 0.00 0.00 0.00 2.40
3639 5935 2.657237 CCGGACCGAGCTTTCAGT 59.343 61.111 17.49 0.00 0.00 3.41
4224 6591 1.957765 GAAGTAGTCGAGGTGGCCCC 61.958 65.000 0.00 0.03 0.00 5.80
4227 6594 1.819903 AGAAGAAGTAGTCGAGGTGGC 59.180 52.381 0.00 0.00 0.00 5.01
4663 7084 0.108281 GAGGGTAGAACGCTTCCACC 60.108 60.000 6.74 6.74 41.76 4.61


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

AutoCloner maintained by Alex Coulton.