Multiple sequence alignment - TraesCS5D01G230300

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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 TraesCS5D01G230300 chr5D 100.000 5915 0 0 1 5915 337306635 337300721 0.000000e+00 10924.0
1 TraesCS5D01G230300 chr5D 96.774 31 1 0 5291 5321 535200760 535200790 1.100000e-02 52.8
2 TraesCS5D01G230300 chr5A 93.996 4913 177 45 401 5238 438476375 438471506 0.000000e+00 7330.0
3 TraesCS5D01G230300 chr5A 86.889 450 42 9 5476 5915 438471261 438470819 6.890000e-134 488.0
4 TraesCS5D01G230300 chr5A 97.436 195 4 1 1 194 438476673 438476479 1.230000e-86 331.0
5 TraesCS5D01G230300 chr5B 96.157 3383 97 14 1933 5301 395924760 395921397 0.000000e+00 5496.0
6 TraesCS5D01G230300 chr5B 93.317 1242 39 17 344 1562 395926483 395925263 0.000000e+00 1794.0
7 TraesCS5D01G230300 chr5B 95.616 593 16 4 5332 5915 395921413 395920822 0.000000e+00 942.0
8 TraesCS5D01G230300 chr5B 91.371 394 23 6 1550 1939 395925241 395924855 4.060000e-146 529.0
9 TraesCS5D01G230300 chr5B 96.257 187 6 1 9 194 395926760 395926574 7.450000e-79 305.0
10 TraesCS5D01G230300 chr5B 85.799 169 22 2 1105 1272 680918703 680918870 1.690000e-40 178.0
11 TraesCS5D01G230300 chr2D 98.280 407 5 2 1 406 640258434 640258029 0.000000e+00 712.0
12 TraesCS5D01G230300 chr1A 85.929 533 75 0 4352 4884 256827136 256827668 2.390000e-158 569.0
13 TraesCS5D01G230300 chr1A 81.609 609 106 5 1940 2545 256824713 256825318 3.180000e-137 499.0
14 TraesCS5D01G230300 chr1A 84.463 354 48 5 3861 4212 256826666 256827014 5.680000e-90 342.0
15 TraesCS5D01G230300 chr1A 78.070 456 72 17 2978 3414 256825586 256826032 4.550000e-66 263.0
16 TraesCS5D01G230300 chr1A 84.496 258 38 2 2621 2877 256825322 256825578 2.740000e-63 254.0
17 TraesCS5D01G230300 chr1A 96.774 31 1 0 5291 5321 45537416 45537446 1.100000e-02 52.8
18 TraesCS5D01G230300 chr1D 85.366 533 78 0 4352 4884 202569645 202570177 2.410000e-153 553.0
19 TraesCS5D01G230300 chr1D 81.445 609 107 5 1940 2545 202567231 202567836 1.480000e-135 494.0
20 TraesCS5D01G230300 chr1D 83.514 370 54 5 3861 4228 202569173 202569537 7.340000e-89 339.0
21 TraesCS5D01G230300 chr1D 86.047 258 34 2 2621 2877 202567840 202568096 5.840000e-70 276.0
22 TraesCS5D01G230300 chr1D 78.174 449 70 19 2978 3414 202568104 202568536 1.640000e-65 261.0
23 TraesCS5D01G230300 chr1B 85.472 530 77 0 4352 4881 296502128 296502657 2.410000e-153 553.0
24 TraesCS5D01G230300 chr1B 81.938 609 104 5 1940 2545 296499678 296500283 1.470000e-140 510.0
25 TraesCS5D01G230300 chr1B 83.514 370 54 5 3861 4228 296501656 296502020 7.340000e-89 339.0
26 TraesCS5D01G230300 chr1B 84.884 258 37 2 2621 2877 296500287 296500543 5.880000e-65 259.0
27 TraesCS5D01G230300 chr1B 77.391 460 74 23 2978 3416 296500551 296501001 4.580000e-61 246.0
28 TraesCS5D01G230300 chr1B 76.250 240 55 2 2270 2508 122923382 122923144 6.220000e-25 126.0
29 TraesCS5D01G230300 chr1B 100.000 28 0 0 5294 5321 4616591 4616564 1.100000e-02 52.8
30 TraesCS5D01G230300 chr6A 83.266 496 80 1 4370 4865 47902465 47902957 2.510000e-123 453.0
31 TraesCS5D01G230300 chr6A 96.774 31 1 0 5291 5321 439517499 439517529 1.100000e-02 52.8
32 TraesCS5D01G230300 chr3B 79.563 504 97 4 4360 4863 525611444 525611941 7.290000e-94 355.0
33 TraesCS5D01G230300 chr7A 75.184 544 95 30 2237 2758 546709385 546709910 2.770000e-53 220.0
34 TraesCS5D01G230300 chr7B 73.123 759 147 45 2034 2757 466972726 466971990 9.980000e-53 219.0
35 TraesCS5D01G230300 chr7B 96.774 31 1 0 5291 5321 618520528 618520558 1.100000e-02 52.8
36 TraesCS5D01G230300 chr7B 96.774 31 1 0 5291 5321 708149027 708149057 1.100000e-02 52.8
37 TraesCS5D01G230300 chr7D 72.570 751 166 29 2034 2758 449061044 449060308 6.010000e-50 209.0
38 TraesCS5D01G230300 chr7D 73.973 438 97 15 4421 4848 14880893 14880463 1.710000e-35 161.0
39 TraesCS5D01G230300 chr4A 92.063 126 10 0 1147 1272 629365341 629365216 1.690000e-40 178.0
40 TraesCS5D01G230300 chr4A 73.804 439 98 16 4421 4849 721385380 721385811 2.210000e-34 158.0
41 TraesCS5D01G230300 chr4A 100.000 28 0 0 5294 5321 411853584 411853557 1.100000e-02 52.8
42 TraesCS5D01G230300 chr6B 96.774 31 1 0 5291 5321 391580785 391580815 1.100000e-02 52.8
43 TraesCS5D01G230300 chr3D 100.000 28 0 0 5294 5321 216612336 216612309 1.100000e-02 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 TraesCS5D01G230300 chr5D 337300721 337306635 5914 True 10924.000000 10924 100.000000 1 5915 1 chr5D.!!$R1 5914
1 TraesCS5D01G230300 chr5A 438470819 438476673 5854 True 2716.333333 7330 92.773667 1 5915 3 chr5A.!!$R1 5914
2 TraesCS5D01G230300 chr5B 395920822 395926760 5938 True 1813.200000 5496 94.543600 9 5915 5 chr5B.!!$R1 5906
3 TraesCS5D01G230300 chr1A 256824713 256827668 2955 False 385.400000 569 82.913400 1940 4884 5 chr1A.!!$F2 2944
4 TraesCS5D01G230300 chr1D 202567231 202570177 2946 False 384.600000 553 82.909200 1940 4884 5 chr1D.!!$F1 2944
5 TraesCS5D01G230300 chr1B 296499678 296502657 2979 False 381.400000 553 82.639800 1940 4881 5 chr1B.!!$F1 2941
6 TraesCS5D01G230300 chr7A 546709385 546709910 525 False 220.000000 220 75.184000 2237 2758 1 chr7A.!!$F1 521
7 TraesCS5D01G230300 chr7B 466971990 466972726 736 True 219.000000 219 73.123000 2034 2757 1 chr7B.!!$R1 723
8 TraesCS5D01G230300 chr7D 449060308 449061044 736 True 209.000000 209 72.570000 2034 2758 1 chr7D.!!$R2 724

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
283 286 0.250124 TGTTCACCGGTGGCAAGTAG 60.250 55.000 33.4 6.33 0.00 2.57 F
284 287 0.250166 GTTCACCGGTGGCAAGTAGT 60.250 55.000 33.4 0.00 0.00 2.73 F
1635 1710 0.179000 GTTCCCGATGTCAGCAGGAT 59.821 55.000 0.0 0.00 0.00 3.24 F
1712 1788 1.207089 TCCGAGCCAGGTGACTAATTG 59.793 52.381 0.0 0.00 40.21 2.32 F
3497 3776 1.003233 AGGTAAGTTTCAGGGGAAGCG 59.997 52.381 0.0 0.00 39.03 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1710 0.106708 GAGAAGTCGCCATGGCCATA 59.893 55.000 30.79 13.97 37.98 2.74 R
1712 1788 3.198872 GGCATCAACCAGTAGAGTAAGC 58.801 50.000 0.00 0.00 0.00 3.09 R
2568 2758 0.171679 ATGTTCATGGCGACGTACGA 59.828 50.000 24.41 0.00 45.77 3.43 R
3603 3903 2.457366 ACCGCTTCTCGAAGTTCATT 57.543 45.000 3.32 0.00 41.67 2.57 R
5337 5874 1.546923 TGCTGCTGCTGTAATGCAAAT 59.453 42.857 17.00 0.00 42.83 2.32 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
156 159 1.126846 GAAAGGTGATGCGTCTCGTTG 59.873 52.381 14.59 0.00 0.00 4.10
194 197 3.010624 TCATACGAAACGAACCAACGA 57.989 42.857 0.00 0.00 37.03 3.85
195 198 3.379240 TCATACGAAACGAACCAACGAA 58.621 40.909 0.00 0.00 37.03 3.85
197 200 0.298411 ACGAAACGAACCAACGAACG 59.702 50.000 0.00 0.00 37.03 3.95
199 202 1.006183 CGAAACGAACCAACGAACGAA 60.006 47.619 0.14 0.00 37.03 3.85
200 203 2.356892 GAAACGAACCAACGAACGAAC 58.643 47.619 0.14 0.00 37.03 3.95
203 206 1.481819 CGAACCAACGAACGAACGGT 61.482 55.000 0.14 1.59 37.61 4.83
214 217 2.511600 GAACGGTCGATGCTGGGG 60.512 66.667 0.00 0.00 0.00 4.96
237 240 4.324991 GGGGGCTGAACGAACGGT 62.325 66.667 0.00 0.00 0.00 4.83
238 241 2.741211 GGGGCTGAACGAACGGTC 60.741 66.667 5.26 5.26 0.00 4.79
255 258 1.202568 GGTCGATGAGGACATGCATGA 60.203 52.381 32.75 10.72 38.70 3.07
259 262 2.543012 CGATGAGGACATGCATGAGTTC 59.457 50.000 32.75 23.03 36.82 3.01
275 278 1.953686 AGTTCCATTTGTTCACCGGTG 59.046 47.619 29.26 29.26 0.00 4.94
283 286 0.250124 TGTTCACCGGTGGCAAGTAG 60.250 55.000 33.40 6.33 0.00 2.57
284 287 0.250166 GTTCACCGGTGGCAAGTAGT 60.250 55.000 33.40 0.00 0.00 2.73
285 288 1.001181 GTTCACCGGTGGCAAGTAGTA 59.999 52.381 33.40 8.84 0.00 1.82
286 289 0.892755 TCACCGGTGGCAAGTAGTAG 59.107 55.000 33.40 4.12 0.00 2.57
299 302 3.810310 AGTAGTAGAACAGAGCCATGC 57.190 47.619 0.00 0.00 0.00 4.06
300 303 2.432510 AGTAGTAGAACAGAGCCATGCC 59.567 50.000 0.00 0.00 0.00 4.40
305 308 2.532843 AGAACAGAGCCATGCCATTTT 58.467 42.857 0.00 0.00 0.00 1.82
314 317 5.644636 AGAGCCATGCCATTTTATTTTTGTG 59.355 36.000 0.00 0.00 0.00 3.33
317 320 6.939163 AGCCATGCCATTTTATTTTTGTGTTA 59.061 30.769 0.00 0.00 0.00 2.41
318 321 7.446625 AGCCATGCCATTTTATTTTTGTGTTAA 59.553 29.630 0.00 0.00 0.00 2.01
319 322 7.536964 GCCATGCCATTTTATTTTTGTGTTAAC 59.463 33.333 0.00 0.00 0.00 2.01
321 324 8.562892 CATGCCATTTTATTTTTGTGTTAACCA 58.437 29.630 2.48 0.00 0.00 3.67
322 325 8.682936 TGCCATTTTATTTTTGTGTTAACCAT 57.317 26.923 2.48 0.00 0.00 3.55
323 326 9.125026 TGCCATTTTATTTTTGTGTTAACCATT 57.875 25.926 2.48 0.00 0.00 3.16
324 327 9.958234 GCCATTTTATTTTTGTGTTAACCATTT 57.042 25.926 2.48 0.00 0.00 2.32
332 335 6.777526 TTTGTGTTAACCATTTGCATAAGC 57.222 33.333 2.48 0.00 42.57 3.09
333 336 5.720371 TGTGTTAACCATTTGCATAAGCT 57.280 34.783 2.48 0.00 42.74 3.74
334 337 5.708948 TGTGTTAACCATTTGCATAAGCTC 58.291 37.500 2.48 0.00 42.74 4.09
335 338 5.476599 TGTGTTAACCATTTGCATAAGCTCT 59.523 36.000 2.48 0.00 42.74 4.09
336 339 5.801947 GTGTTAACCATTTGCATAAGCTCTG 59.198 40.000 2.48 0.00 42.74 3.35
337 340 5.709631 TGTTAACCATTTGCATAAGCTCTGA 59.290 36.000 2.48 0.00 42.74 3.27
338 341 6.377996 TGTTAACCATTTGCATAAGCTCTGAT 59.622 34.615 2.48 0.00 42.74 2.90
339 342 5.927281 AACCATTTGCATAAGCTCTGATT 57.073 34.783 0.00 0.00 42.74 2.57
340 343 5.927281 ACCATTTGCATAAGCTCTGATTT 57.073 34.783 0.00 0.00 42.74 2.17
341 344 5.657474 ACCATTTGCATAAGCTCTGATTTG 58.343 37.500 0.00 0.00 42.74 2.32
342 345 4.506654 CCATTTGCATAAGCTCTGATTTGC 59.493 41.667 0.00 0.00 42.74 3.68
343 346 5.348986 CATTTGCATAAGCTCTGATTTGCT 58.651 37.500 0.00 0.00 42.74 3.91
344 347 4.365899 TTGCATAAGCTCTGATTTGCTG 57.634 40.909 0.00 0.00 42.74 4.41
345 348 3.349927 TGCATAAGCTCTGATTTGCTGT 58.650 40.909 0.61 0.00 42.74 4.40
346 349 4.516323 TGCATAAGCTCTGATTTGCTGTA 58.484 39.130 0.61 0.00 42.74 2.74
347 350 5.128205 TGCATAAGCTCTGATTTGCTGTAT 58.872 37.500 0.61 0.00 42.74 2.29
348 351 5.591472 TGCATAAGCTCTGATTTGCTGTATT 59.409 36.000 0.61 0.00 42.74 1.89
349 352 6.095860 TGCATAAGCTCTGATTTGCTGTATTT 59.904 34.615 0.61 0.00 42.74 1.40
350 353 6.636044 GCATAAGCTCTGATTTGCTGTATTTC 59.364 38.462 0.61 0.00 39.71 2.17
351 354 4.871993 AGCTCTGATTTGCTGTATTTCG 57.128 40.909 0.00 0.00 38.21 3.46
352 355 3.064545 AGCTCTGATTTGCTGTATTTCGC 59.935 43.478 0.00 0.00 38.21 4.70
353 356 3.601356 CTCTGATTTGCTGTATTTCGCG 58.399 45.455 0.00 0.00 0.00 5.87
373 376 2.354704 CGGGGAAACACATAAGCTCTCA 60.355 50.000 0.00 0.00 0.00 3.27
392 395 6.696148 GCTCTCAATTGCATGGAATTTTCTAG 59.304 38.462 21.12 16.09 0.00 2.43
394 397 8.806429 TCTCAATTGCATGGAATTTTCTAGTA 57.194 30.769 21.12 2.35 0.00 1.82
395 398 8.896744 TCTCAATTGCATGGAATTTTCTAGTAG 58.103 33.333 21.12 8.83 0.00 2.57
396 399 7.999679 TCAATTGCATGGAATTTTCTAGTAGG 58.000 34.615 21.12 8.18 0.00 3.18
397 400 7.833682 TCAATTGCATGGAATTTTCTAGTAGGA 59.166 33.333 21.12 10.19 0.00 2.94
398 401 7.814264 ATTGCATGGAATTTTCTAGTAGGAG 57.186 36.000 6.63 0.00 0.00 3.69
399 402 5.126067 TGCATGGAATTTTCTAGTAGGAGC 58.874 41.667 0.00 0.00 0.00 4.70
429 432 2.223144 TGTTTGATCGTGGCGAGAAAAG 59.777 45.455 0.00 0.00 39.91 2.27
430 433 1.438651 TTGATCGTGGCGAGAAAAGG 58.561 50.000 0.00 0.00 39.91 3.11
431 434 1.019278 TGATCGTGGCGAGAAAAGGC 61.019 55.000 0.00 0.00 39.91 4.35
432 435 0.741221 GATCGTGGCGAGAAAAGGCT 60.741 55.000 0.00 0.00 39.91 4.58
433 436 0.535335 ATCGTGGCGAGAAAAGGCTA 59.465 50.000 0.00 0.00 39.91 3.93
434 437 0.535335 TCGTGGCGAGAAAAGGCTAT 59.465 50.000 0.00 0.00 35.01 2.97
436 439 0.378610 GTGGCGAGAAAAGGCTATGC 59.621 55.000 0.00 0.00 35.01 3.14
448 451 2.009888 GCTATGCCACAGTTCGAGC 58.990 57.895 0.00 0.00 0.00 5.03
450 453 1.565305 CTATGCCACAGTTCGAGCTC 58.435 55.000 2.73 2.73 0.00 4.09
451 454 1.135915 CTATGCCACAGTTCGAGCTCT 59.864 52.381 12.85 0.00 0.00 4.09
452 455 1.186200 ATGCCACAGTTCGAGCTCTA 58.814 50.000 12.85 0.00 0.00 2.43
453 456 1.186200 TGCCACAGTTCGAGCTCTAT 58.814 50.000 12.85 0.00 0.00 1.98
454 457 1.134995 TGCCACAGTTCGAGCTCTATG 60.135 52.381 12.85 7.40 0.00 2.23
496 499 5.570589 CGTCCATTTCTTTTCAATTGCTCTC 59.429 40.000 0.00 0.00 0.00 3.20
816 835 0.454600 GACTCTATCGGACGCACCAA 59.545 55.000 0.43 0.00 38.90 3.67
1404 1434 2.184830 CATCACCGAGGCCATGCTG 61.185 63.158 5.01 0.00 0.00 4.41
1516 1546 1.374252 CGCTCCATGCCGGTATACC 60.374 63.158 12.27 12.27 38.78 2.73
1518 1548 0.396811 GCTCCATGCCGGTATACCTT 59.603 55.000 19.68 0.00 35.57 3.50
1519 1549 1.608283 GCTCCATGCCGGTATACCTTC 60.608 57.143 19.68 11.16 35.57 3.46
1520 1550 1.691976 CTCCATGCCGGTATACCTTCA 59.308 52.381 19.68 16.06 35.57 3.02
1521 1551 1.691976 TCCATGCCGGTATACCTTCAG 59.308 52.381 19.68 6.99 35.57 3.02
1522 1552 1.512926 CATGCCGGTATACCTTCAGC 58.487 55.000 19.68 15.98 0.00 4.26
1523 1553 1.070758 CATGCCGGTATACCTTCAGCT 59.929 52.381 19.68 1.22 0.00 4.24
1525 1555 0.750850 GCCGGTATACCTTCAGCTCA 59.249 55.000 19.68 0.00 0.00 4.26
1526 1556 1.538419 GCCGGTATACCTTCAGCTCAC 60.538 57.143 19.68 0.00 0.00 3.51
1528 1558 2.223829 CCGGTATACCTTCAGCTCACAG 60.224 54.545 19.68 0.00 0.00 3.66
1529 1559 2.799917 CGGTATACCTTCAGCTCACAGC 60.800 54.545 19.68 0.00 42.84 4.40
1548 1584 1.670380 GCTCTTCACTTCTCCGTGTCC 60.670 57.143 0.00 0.00 36.33 4.02
1563 1633 1.142748 GTCCAGCCCTCGATCACTG 59.857 63.158 0.00 0.00 0.00 3.66
1573 1643 2.417924 CCTCGATCACTGTAGCAGCTTT 60.418 50.000 0.00 0.00 34.37 3.51
1577 1647 5.043903 TCGATCACTGTAGCAGCTTTAATC 58.956 41.667 0.00 0.00 34.37 1.75
1580 1650 6.018425 CGATCACTGTAGCAGCTTTAATCAAT 60.018 38.462 0.00 0.00 34.37 2.57
1582 1652 6.845302 TCACTGTAGCAGCTTTAATCAATTG 58.155 36.000 0.00 0.00 34.37 2.32
1583 1653 6.430925 TCACTGTAGCAGCTTTAATCAATTGT 59.569 34.615 0.00 0.00 34.37 2.71
1585 1655 7.272084 CACTGTAGCAGCTTTAATCAATTGTTC 59.728 37.037 0.00 0.00 34.37 3.18
1586 1656 7.040478 ACTGTAGCAGCTTTAATCAATTGTTCA 60.040 33.333 0.00 0.00 34.37 3.18
1587 1657 7.829725 TGTAGCAGCTTTAATCAATTGTTCAT 58.170 30.769 0.00 0.00 0.00 2.57
1589 1659 6.927416 AGCAGCTTTAATCAATTGTTCATCA 58.073 32.000 5.13 0.00 0.00 3.07
1590 1660 7.553334 AGCAGCTTTAATCAATTGTTCATCAT 58.447 30.769 5.13 0.00 0.00 2.45
1591 1661 7.491372 AGCAGCTTTAATCAATTGTTCATCATG 59.509 33.333 5.13 0.00 0.00 3.07
1592 1662 7.618442 CAGCTTTAATCAATTGTTCATCATGC 58.382 34.615 5.13 2.75 0.00 4.06
1593 1663 7.276878 CAGCTTTAATCAATTGTTCATCATGCA 59.723 33.333 5.13 0.00 0.00 3.96
1594 1664 7.985184 AGCTTTAATCAATTGTTCATCATGCAT 59.015 29.630 5.13 0.00 0.00 3.96
1635 1710 0.179000 GTTCCCGATGTCAGCAGGAT 59.821 55.000 0.00 0.00 0.00 3.24
1662 1737 1.682684 GGCGACTTCTCCTCCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
1712 1788 1.207089 TCCGAGCCAGGTGACTAATTG 59.793 52.381 0.00 0.00 40.21 2.32
1766 1842 1.279840 GCAGTTCCTCGTGTTGTGC 59.720 57.895 0.00 0.00 0.00 4.57
1804 1880 8.188799 AGTTAGCAACATGAATTTGATGATGAG 58.811 33.333 9.65 0.00 0.00 2.90
2301 2480 2.029369 GTGACGGCCAACACGGTA 59.971 61.111 12.41 0.00 36.97 4.02
2568 2758 4.558538 ACGTACTACAACAACTCTTCGT 57.441 40.909 0.00 0.00 0.00 3.85
2906 3110 1.797025 CACCGTCCCTTCTTCTTCAC 58.203 55.000 0.00 0.00 0.00 3.18
2928 3133 3.301906 CAGCTTCGTCGTAAATGTCAGAG 59.698 47.826 0.00 0.00 0.00 3.35
2947 3152 2.545946 GAGCTCAGAACGTTTCTTGCTT 59.454 45.455 9.40 5.60 42.95 3.91
3205 3424 4.033684 CGACGTAAGCCTATACAGTTCAC 58.966 47.826 0.00 0.00 45.62 3.18
3206 3425 4.437794 CGACGTAAGCCTATACAGTTCACA 60.438 45.833 0.00 0.00 45.62 3.58
3245 3470 3.194542 GCATAGTCTAGTAGAGCCATGGG 59.805 52.174 15.13 0.00 0.00 4.00
3462 3741 3.338250 AAGGATGGGCTGCCGGAA 61.338 61.111 13.40 0.00 0.00 4.30
3497 3776 1.003233 AGGTAAGTTTCAGGGGAAGCG 59.997 52.381 0.00 0.00 39.03 4.68
3603 3903 1.588239 AGGAGCAGATGATGTCCCAA 58.412 50.000 0.00 0.00 32.53 4.12
3773 4079 3.836562 GACTGGGGTTTAGAGGTACAGAA 59.163 47.826 0.00 0.00 0.00 3.02
3789 4095 5.858581 GGTACAGAAAAACAGCACAATGATC 59.141 40.000 0.00 0.00 0.00 2.92
3792 4098 4.682860 CAGAAAAACAGCACAATGATCACC 59.317 41.667 0.00 0.00 0.00 4.02
3793 4099 2.995466 AAACAGCACAATGATCACCG 57.005 45.000 0.00 0.00 0.00 4.94
3804 4112 2.084610 TGATCACCGCTTCAGACAAG 57.915 50.000 0.00 0.00 0.00 3.16
3814 4122 3.935203 CGCTTCAGACAAGTCCACATATT 59.065 43.478 0.00 0.00 0.00 1.28
3824 4132 7.557719 AGACAAGTCCACATATTTAATTCCAGG 59.442 37.037 0.00 0.00 0.00 4.45
4149 4600 1.080498 ACCATCTACCCCTTCACCTCA 59.920 52.381 0.00 0.00 0.00 3.86
4152 4603 2.233305 TCTACCCCTTCACCTCACTC 57.767 55.000 0.00 0.00 0.00 3.51
4821 5351 2.104859 CATCTGGTCCGTGCTGCTG 61.105 63.158 0.00 0.00 0.00 4.41
4908 5438 0.961857 TGAAGCAGTGCGGCATCAAT 60.962 50.000 10.00 0.00 38.42 2.57
5062 5593 4.982241 AGAATTGAACAGAGGACCAGAA 57.018 40.909 0.00 0.00 0.00 3.02
5142 5679 2.747989 GGGTAGCTGGTAAGTTTTGCTC 59.252 50.000 0.00 0.00 35.47 4.26
5174 5711 8.581253 AAGCCTAATGTAGCTAAGAAAAACAT 57.419 30.769 0.00 0.00 38.74 2.71
5177 5714 8.889717 GCCTAATGTAGCTAAGAAAAACATGTA 58.110 33.333 0.00 0.00 31.44 2.29
5245 5782 3.808728 TGCAGGATAAGCAGAATACCAC 58.191 45.455 0.00 0.00 37.02 4.16
5247 5784 4.199310 GCAGGATAAGCAGAATACCACAA 58.801 43.478 0.00 0.00 0.00 3.33
5248 5785 4.823989 GCAGGATAAGCAGAATACCACAAT 59.176 41.667 0.00 0.00 0.00 2.71
5249 5786 5.997746 GCAGGATAAGCAGAATACCACAATA 59.002 40.000 0.00 0.00 0.00 1.90
5304 5841 5.404466 TCAAAGGAATTTGCATTACCTGG 57.596 39.130 0.00 0.00 32.23 4.45
5305 5842 4.222588 TCAAAGGAATTTGCATTACCTGGG 59.777 41.667 0.00 0.00 32.23 4.45
5306 5843 3.473113 AGGAATTTGCATTACCTGGGT 57.527 42.857 0.00 0.00 0.00 4.51
5307 5844 3.099141 AGGAATTTGCATTACCTGGGTG 58.901 45.455 2.07 0.00 0.00 4.61
5308 5845 3.096092 GGAATTTGCATTACCTGGGTGA 58.904 45.455 2.07 0.00 0.00 4.02
5309 5846 3.706086 GGAATTTGCATTACCTGGGTGAT 59.294 43.478 2.07 0.00 0.00 3.06
5310 5847 4.441913 GGAATTTGCATTACCTGGGTGATG 60.442 45.833 16.90 16.90 42.61 3.07
5311 5848 3.448093 TTTGCATTACCTGGGTGATGA 57.552 42.857 22.97 9.50 42.42 2.92
5312 5849 3.448093 TTGCATTACCTGGGTGATGAA 57.552 42.857 22.97 13.41 42.42 2.57
5313 5850 3.003394 TGCATTACCTGGGTGATGAAG 57.997 47.619 22.97 3.20 42.42 3.02
5314 5851 2.575735 TGCATTACCTGGGTGATGAAGA 59.424 45.455 22.97 7.61 42.42 2.87
5315 5852 3.010027 TGCATTACCTGGGTGATGAAGAA 59.990 43.478 22.97 6.99 42.42 2.52
5316 5853 4.016444 GCATTACCTGGGTGATGAAGAAA 58.984 43.478 22.97 0.22 42.42 2.52
5317 5854 4.462483 GCATTACCTGGGTGATGAAGAAAA 59.538 41.667 22.97 0.00 42.42 2.29
5318 5855 5.127682 GCATTACCTGGGTGATGAAGAAAAT 59.872 40.000 22.97 1.78 42.42 1.82
5319 5856 6.681368 GCATTACCTGGGTGATGAAGAAAATC 60.681 42.308 22.97 4.45 42.42 2.17
5320 5857 3.347216 ACCTGGGTGATGAAGAAAATCG 58.653 45.455 0.00 0.00 0.00 3.34
5321 5858 3.244911 ACCTGGGTGATGAAGAAAATCGT 60.245 43.478 0.00 0.00 0.00 3.73
5322 5859 3.758554 CCTGGGTGATGAAGAAAATCGTT 59.241 43.478 0.00 0.00 0.00 3.85
5323 5860 4.142600 CCTGGGTGATGAAGAAAATCGTTC 60.143 45.833 0.00 0.00 0.00 3.95
5324 5861 3.435327 TGGGTGATGAAGAAAATCGTTCG 59.565 43.478 0.00 0.00 0.00 3.95
5325 5862 3.682858 GGGTGATGAAGAAAATCGTTCGA 59.317 43.478 0.00 0.00 0.00 3.71
5326 5863 4.153475 GGGTGATGAAGAAAATCGTTCGAA 59.847 41.667 0.00 0.00 0.00 3.71
5327 5864 5.334569 GGGTGATGAAGAAAATCGTTCGAAA 60.335 40.000 0.00 0.00 0.00 3.46
5328 5865 6.140110 GGTGATGAAGAAAATCGTTCGAAAA 58.860 36.000 0.00 0.00 0.00 2.29
5329 5866 6.635239 GGTGATGAAGAAAATCGTTCGAAAAA 59.365 34.615 0.00 0.00 0.00 1.94
5330 5867 7.149128 GGTGATGAAGAAAATCGTTCGAAAAAG 60.149 37.037 0.00 0.00 0.00 2.27
5331 5868 7.586300 GTGATGAAGAAAATCGTTCGAAAAAGA 59.414 33.333 0.00 0.01 0.00 2.52
5332 5869 8.126074 TGATGAAGAAAATCGTTCGAAAAAGAA 58.874 29.630 0.00 0.00 0.00 2.52
5333 5870 8.850454 ATGAAGAAAATCGTTCGAAAAAGAAA 57.150 26.923 0.00 0.00 0.00 2.52
5334 5871 8.322906 TGAAGAAAATCGTTCGAAAAAGAAAG 57.677 30.769 0.00 0.00 0.00 2.62
5335 5872 7.431084 TGAAGAAAATCGTTCGAAAAAGAAAGG 59.569 33.333 0.00 0.00 31.97 3.11
5336 5873 7.023197 AGAAAATCGTTCGAAAAAGAAAGGA 57.977 32.000 0.00 0.00 31.97 3.36
5337 5874 7.477494 AGAAAATCGTTCGAAAAAGAAAGGAA 58.523 30.769 0.00 0.00 31.97 3.36
5387 5963 5.200483 CACTTTGCTAAGGGGATCCAATAA 58.800 41.667 15.23 0.00 35.61 1.40
5391 5967 4.792068 TGCTAAGGGGATCCAATAAAGTG 58.208 43.478 15.23 0.00 34.83 3.16
5425 6001 7.931578 TCAAAGACTTTAAACTTGGAACTGA 57.068 32.000 0.00 0.00 0.00 3.41
5431 6007 8.749354 AGACTTTAAACTTGGAACTGAAAATGT 58.251 29.630 0.00 0.00 0.00 2.71
5464 6105 6.774656 AGAATTCTGATATCCACCAAACCATC 59.225 38.462 7.30 0.00 0.00 3.51
5584 6231 2.024273 TGGGGTTGGTTAAGGTGACAAA 60.024 45.455 0.00 0.00 0.00 2.83
5591 6238 3.391296 TGGTTAAGGTGACAAAGAGAGCT 59.609 43.478 0.00 0.00 0.00 4.09
5663 6310 9.413734 CCATATCTTTCAGTATCTTTTTCCCTT 57.586 33.333 0.00 0.00 0.00 3.95
5901 6557 7.336176 AGGGGATGTTTAATACTCTTTCGTTTC 59.664 37.037 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 197 1.736645 CCAGCATCGACCGTTCGTT 60.737 57.895 1.29 0.00 46.01 3.85
195 198 2.126071 CCAGCATCGACCGTTCGT 60.126 61.111 1.29 0.00 46.01 3.85
197 200 2.511600 CCCCAGCATCGACCGTTC 60.512 66.667 0.00 0.00 0.00 3.95
220 223 4.324991 ACCGTTCGTTCAGCCCCC 62.325 66.667 0.00 0.00 0.00 5.40
221 224 2.741211 GACCGTTCGTTCAGCCCC 60.741 66.667 0.00 0.00 0.00 5.80
222 225 2.830704 ATCGACCGTTCGTTCAGCCC 62.831 60.000 1.29 0.00 46.01 5.19
223 226 1.445582 ATCGACCGTTCGTTCAGCC 60.446 57.895 1.29 0.00 46.01 4.85
224 227 0.731514 TCATCGACCGTTCGTTCAGC 60.732 55.000 1.29 0.00 46.01 4.26
225 228 1.260206 CTCATCGACCGTTCGTTCAG 58.740 55.000 1.29 0.00 46.01 3.02
226 229 0.109458 CCTCATCGACCGTTCGTTCA 60.109 55.000 1.29 0.00 46.01 3.18
227 230 0.169672 TCCTCATCGACCGTTCGTTC 59.830 55.000 1.29 0.00 46.01 3.95
228 231 0.109412 GTCCTCATCGACCGTTCGTT 60.109 55.000 1.29 0.00 46.01 3.85
229 232 1.239296 TGTCCTCATCGACCGTTCGT 61.239 55.000 1.29 0.00 46.01 3.85
231 234 1.560923 CATGTCCTCATCGACCGTTC 58.439 55.000 0.00 0.00 31.15 3.95
232 235 0.460284 GCATGTCCTCATCGACCGTT 60.460 55.000 0.00 0.00 31.15 4.44
233 236 1.141881 GCATGTCCTCATCGACCGT 59.858 57.895 0.00 0.00 31.15 4.83
234 237 0.249615 ATGCATGTCCTCATCGACCG 60.250 55.000 0.00 0.00 31.15 4.79
235 238 1.202568 TCATGCATGTCCTCATCGACC 60.203 52.381 25.43 0.00 31.15 4.79
236 239 2.133553 CTCATGCATGTCCTCATCGAC 58.866 52.381 25.43 0.00 31.15 4.20
237 240 1.758862 ACTCATGCATGTCCTCATCGA 59.241 47.619 25.43 2.73 31.15 3.59
238 241 2.235845 ACTCATGCATGTCCTCATCG 57.764 50.000 25.43 8.12 31.15 3.84
239 242 2.877168 GGAACTCATGCATGTCCTCATC 59.123 50.000 25.43 15.21 31.15 2.92
240 243 2.240414 TGGAACTCATGCATGTCCTCAT 59.760 45.455 26.43 11.39 34.21 2.90
255 258 1.953686 CACCGGTGAACAAATGGAACT 59.046 47.619 31.31 0.00 0.00 3.01
259 262 1.288752 GCCACCGGTGAACAAATGG 59.711 57.895 36.07 17.54 0.00 3.16
275 278 2.233922 TGGCTCTGTTCTACTACTTGCC 59.766 50.000 0.00 0.00 38.42 4.52
283 286 2.338577 ATGGCATGGCTCTGTTCTAC 57.661 50.000 21.08 0.00 0.00 2.59
284 287 3.370840 AAATGGCATGGCTCTGTTCTA 57.629 42.857 21.08 0.00 0.00 2.10
285 288 2.226962 AAATGGCATGGCTCTGTTCT 57.773 45.000 21.08 0.00 0.00 3.01
286 289 4.660789 ATAAAATGGCATGGCTCTGTTC 57.339 40.909 21.08 0.00 0.00 3.18
314 317 6.194796 TCAGAGCTTATGCAAATGGTTAAC 57.805 37.500 3.16 0.00 42.74 2.01
317 320 5.927281 AATCAGAGCTTATGCAAATGGTT 57.073 34.783 3.16 0.00 42.74 3.67
318 321 5.657474 CAAATCAGAGCTTATGCAAATGGT 58.343 37.500 3.16 0.00 42.74 3.55
319 322 4.506654 GCAAATCAGAGCTTATGCAAATGG 59.493 41.667 3.16 0.00 42.74 3.16
321 324 5.105473 ACAGCAAATCAGAGCTTATGCAAAT 60.105 36.000 3.16 0.00 39.50 2.32
322 325 4.219070 ACAGCAAATCAGAGCTTATGCAAA 59.781 37.500 3.16 0.00 39.50 3.68
323 326 3.760151 ACAGCAAATCAGAGCTTATGCAA 59.240 39.130 3.16 0.00 39.50 4.08
324 327 3.349927 ACAGCAAATCAGAGCTTATGCA 58.650 40.909 3.16 0.00 39.50 3.96
325 328 5.686159 ATACAGCAAATCAGAGCTTATGC 57.314 39.130 0.00 0.00 39.50 3.14
326 329 6.849811 CGAAATACAGCAAATCAGAGCTTATG 59.150 38.462 0.00 0.00 39.50 1.90
327 330 6.512415 GCGAAATACAGCAAATCAGAGCTTAT 60.512 38.462 0.00 0.00 39.50 1.73
328 331 5.220662 GCGAAATACAGCAAATCAGAGCTTA 60.221 40.000 0.00 0.00 39.50 3.09
329 332 4.437930 GCGAAATACAGCAAATCAGAGCTT 60.438 41.667 0.00 0.00 39.50 3.74
330 333 3.064545 GCGAAATACAGCAAATCAGAGCT 59.935 43.478 0.00 0.00 42.94 4.09
331 334 3.357897 GCGAAATACAGCAAATCAGAGC 58.642 45.455 0.00 0.00 0.00 4.09
332 335 3.544834 CCGCGAAATACAGCAAATCAGAG 60.545 47.826 8.23 0.00 0.00 3.35
333 336 2.351418 CCGCGAAATACAGCAAATCAGA 59.649 45.455 8.23 0.00 0.00 3.27
334 337 2.539547 CCCGCGAAATACAGCAAATCAG 60.540 50.000 8.23 0.00 0.00 2.90
335 338 1.400142 CCCGCGAAATACAGCAAATCA 59.600 47.619 8.23 0.00 0.00 2.57
336 339 1.268539 CCCCGCGAAATACAGCAAATC 60.269 52.381 8.23 0.00 0.00 2.17
337 340 0.738389 CCCCGCGAAATACAGCAAAT 59.262 50.000 8.23 0.00 0.00 2.32
338 341 0.321741 TCCCCGCGAAATACAGCAAA 60.322 50.000 8.23 0.00 0.00 3.68
339 342 0.321741 TTCCCCGCGAAATACAGCAA 60.322 50.000 8.23 0.00 0.00 3.91
340 343 0.321741 TTTCCCCGCGAAATACAGCA 60.322 50.000 8.23 0.00 35.49 4.41
341 344 0.098200 GTTTCCCCGCGAAATACAGC 59.902 55.000 8.23 0.00 42.38 4.40
342 345 1.129811 GTGTTTCCCCGCGAAATACAG 59.870 52.381 8.23 0.00 46.39 2.74
343 346 1.158434 GTGTTTCCCCGCGAAATACA 58.842 50.000 8.23 1.97 46.39 2.29
344 347 1.158434 TGTGTTTCCCCGCGAAATAC 58.842 50.000 8.23 9.69 46.97 1.89
345 348 2.116827 ATGTGTTTCCCCGCGAAATA 57.883 45.000 8.23 0.00 42.38 1.40
346 349 2.116827 TATGTGTTTCCCCGCGAAAT 57.883 45.000 8.23 0.00 42.38 2.17
347 350 1.807742 CTTATGTGTTTCCCCGCGAAA 59.192 47.619 8.23 0.00 38.16 3.46
348 351 1.444836 CTTATGTGTTTCCCCGCGAA 58.555 50.000 8.23 0.00 0.00 4.70
349 352 1.022451 GCTTATGTGTTTCCCCGCGA 61.022 55.000 8.23 0.00 0.00 5.87
350 353 1.024579 AGCTTATGTGTTTCCCCGCG 61.025 55.000 0.00 0.00 0.00 6.46
351 354 0.733150 GAGCTTATGTGTTTCCCCGC 59.267 55.000 0.00 0.00 0.00 6.13
352 355 2.280628 GAGAGCTTATGTGTTTCCCCG 58.719 52.381 0.00 0.00 0.00 5.73
353 356 3.350219 TGAGAGCTTATGTGTTTCCCC 57.650 47.619 0.00 0.00 0.00 4.81
359 362 4.097437 CCATGCAATTGAGAGCTTATGTGT 59.903 41.667 10.34 0.00 0.00 3.72
373 376 7.201857 GCTCCTACTAGAAAATTCCATGCAATT 60.202 37.037 0.00 0.00 0.00 2.32
392 395 1.165270 AACATGCCAAACGCTCCTAC 58.835 50.000 0.00 0.00 38.78 3.18
394 397 0.314935 CAAACATGCCAAACGCTCCT 59.685 50.000 0.00 0.00 38.78 3.69
395 398 0.313672 TCAAACATGCCAAACGCTCC 59.686 50.000 0.00 0.00 38.78 4.70
396 399 2.253603 GATCAAACATGCCAAACGCTC 58.746 47.619 0.00 0.00 38.78 5.03
397 400 1.401409 CGATCAAACATGCCAAACGCT 60.401 47.619 0.00 0.00 38.78 5.07
398 401 0.984109 CGATCAAACATGCCAAACGC 59.016 50.000 0.00 0.00 38.31 4.84
399 402 1.978097 CACGATCAAACATGCCAAACG 59.022 47.619 0.00 0.00 0.00 3.60
412 415 1.019278 GCCTTTTCTCGCCACGATCA 61.019 55.000 0.00 0.00 34.61 2.92
430 433 0.460987 AGCTCGAACTGTGGCATAGC 60.461 55.000 11.50 0.00 0.00 2.97
431 434 1.135915 AGAGCTCGAACTGTGGCATAG 59.864 52.381 9.94 9.94 0.00 2.23
432 435 1.186200 AGAGCTCGAACTGTGGCATA 58.814 50.000 8.37 0.00 0.00 3.14
433 436 1.186200 TAGAGCTCGAACTGTGGCAT 58.814 50.000 8.37 0.00 0.00 4.40
434 437 1.134995 CATAGAGCTCGAACTGTGGCA 60.135 52.381 8.37 0.00 0.00 4.92
436 439 2.425312 AGACATAGAGCTCGAACTGTGG 59.575 50.000 8.37 0.00 31.32 4.17
437 440 3.773860 AGACATAGAGCTCGAACTGTG 57.226 47.619 8.37 1.90 0.00 3.66
438 441 3.310227 CGTAGACATAGAGCTCGAACTGT 59.690 47.826 8.37 10.33 0.00 3.55
439 442 3.303461 CCGTAGACATAGAGCTCGAACTG 60.303 52.174 8.37 7.15 0.00 3.16
441 444 2.031857 CCCGTAGACATAGAGCTCGAAC 60.032 54.545 8.37 0.00 0.00 3.95
442 445 2.158856 TCCCGTAGACATAGAGCTCGAA 60.159 50.000 8.37 0.53 0.00 3.71
444 447 1.532007 GTCCCGTAGACATAGAGCTCG 59.468 57.143 8.37 0.00 45.55 5.03
454 457 1.226888 GCGTCCATGTCCCGTAGAC 60.227 63.158 0.00 0.00 46.51 2.59
496 499 5.421056 TGGTGATTGGTGAGTAGTACCTTAG 59.579 44.000 0.00 0.00 39.01 2.18
724 734 3.515286 TGAGCCGGGTCGATCGAC 61.515 66.667 34.70 34.70 43.87 4.20
802 821 1.149361 GCGATTTGGTGCGTCCGATA 61.149 55.000 0.00 0.00 39.52 2.92
930 949 2.852075 GGGTGTGGAGGTGGTGGA 60.852 66.667 0.00 0.00 0.00 4.02
1218 1248 3.160585 CAGTTCTGGGTGCCCTCA 58.839 61.111 8.91 0.00 36.94 3.86
1404 1434 1.884926 GTAGCTCATCCTGCCGTGC 60.885 63.158 0.00 0.00 0.00 5.34
1521 1551 2.336667 GAGAAGTGAAGAGCTGTGAGC 58.663 52.381 0.00 0.00 42.84 4.26
1522 1552 2.670789 CGGAGAAGTGAAGAGCTGTGAG 60.671 54.545 0.00 0.00 0.00 3.51
1523 1553 1.270826 CGGAGAAGTGAAGAGCTGTGA 59.729 52.381 0.00 0.00 0.00 3.58
1525 1555 1.000283 CACGGAGAAGTGAAGAGCTGT 60.000 52.381 0.00 0.00 44.43 4.40
1526 1556 1.000283 ACACGGAGAAGTGAAGAGCTG 60.000 52.381 0.00 0.00 44.43 4.24
1528 1558 1.670380 GGACACGGAGAAGTGAAGAGC 60.670 57.143 4.00 0.00 44.43 4.09
1529 1559 1.613925 TGGACACGGAGAAGTGAAGAG 59.386 52.381 4.00 0.00 44.43 2.85
1548 1584 0.249238 GCTACAGTGATCGAGGGCTG 60.249 60.000 0.00 10.18 35.31 4.85
1563 1633 7.970061 TGATGAACAATTGATTAAAGCTGCTAC 59.030 33.333 13.59 0.00 0.00 3.58
1577 1647 8.874816 TGAATTGTTATGCATGATGAACAATTG 58.125 29.630 34.30 3.24 37.03 2.32
1580 1650 7.036829 CCTGAATTGTTATGCATGATGAACAA 58.963 34.615 21.61 21.61 37.03 2.83
1582 1652 6.474427 CACCTGAATTGTTATGCATGATGAAC 59.526 38.462 10.16 6.28 0.00 3.18
1583 1653 6.377712 TCACCTGAATTGTTATGCATGATGAA 59.622 34.615 10.16 0.00 0.00 2.57
1585 1655 6.139048 TCACCTGAATTGTTATGCATGATG 57.861 37.500 10.16 0.00 0.00 3.07
1586 1656 5.221185 GCTCACCTGAATTGTTATGCATGAT 60.221 40.000 10.16 0.00 0.00 2.45
1587 1657 4.096833 GCTCACCTGAATTGTTATGCATGA 59.903 41.667 10.16 0.00 0.00 3.07
1589 1659 3.065786 CGCTCACCTGAATTGTTATGCAT 59.934 43.478 3.79 3.79 0.00 3.96
1590 1660 2.419673 CGCTCACCTGAATTGTTATGCA 59.580 45.455 0.00 0.00 0.00 3.96
1591 1661 2.223340 CCGCTCACCTGAATTGTTATGC 60.223 50.000 0.00 0.00 0.00 3.14
1592 1662 2.223340 GCCGCTCACCTGAATTGTTATG 60.223 50.000 0.00 0.00 0.00 1.90
1593 1663 2.017049 GCCGCTCACCTGAATTGTTAT 58.983 47.619 0.00 0.00 0.00 1.89
1594 1664 1.448985 GCCGCTCACCTGAATTGTTA 58.551 50.000 0.00 0.00 0.00 2.41
1602 1677 2.811317 GAACTCGCCGCTCACCTG 60.811 66.667 0.00 0.00 0.00 4.00
1635 1710 0.106708 GAGAAGTCGCCATGGCCATA 59.893 55.000 30.79 13.97 37.98 2.74
1712 1788 3.198872 GGCATCAACCAGTAGAGTAAGC 58.801 50.000 0.00 0.00 0.00 3.09
1766 1842 4.065088 TGTTGCTAACTTGAGCTTACCAG 58.935 43.478 0.00 0.00 43.27 4.00
1804 1880 3.741476 CCACTTTGCGCTCCCTGC 61.741 66.667 9.73 0.00 38.57 4.85
2301 2480 2.043852 ACGGCGAGGATGGAGAGT 60.044 61.111 16.62 0.00 0.00 3.24
2568 2758 0.171679 ATGTTCATGGCGACGTACGA 59.828 50.000 24.41 0.00 45.77 3.43
2906 3110 3.242518 TCTGACATTTACGACGAAGCTG 58.757 45.455 0.00 0.00 0.00 4.24
2928 3133 3.495001 AGTAAGCAAGAAACGTTCTGAGC 59.505 43.478 0.00 4.40 40.59 4.26
2947 3152 6.100004 GTCGGTCAAAATTCAGAGATCAGTA 58.900 40.000 0.00 0.00 0.00 2.74
3205 3424 7.658982 AGACTATGCATAATGTAGGTGTGATTG 59.341 37.037 8.00 0.00 0.00 2.67
3206 3425 7.739825 AGACTATGCATAATGTAGGTGTGATT 58.260 34.615 8.00 0.00 0.00 2.57
3245 3470 3.008049 ACCAGGAACTACCAATGTCAGAC 59.992 47.826 0.00 0.00 42.04 3.51
3497 3776 2.888834 AACCCAAATGTTCAGTGTGC 57.111 45.000 0.00 0.00 0.00 4.57
3603 3903 2.457366 ACCGCTTCTCGAAGTTCATT 57.543 45.000 3.32 0.00 41.67 2.57
3773 4079 2.607771 GCGGTGATCATTGTGCTGTTTT 60.608 45.455 0.00 0.00 0.00 2.43
3789 4095 0.249868 TGGACTTGTCTGAAGCGGTG 60.250 55.000 0.61 0.00 0.00 4.94
3792 4098 1.800805 ATGTGGACTTGTCTGAAGCG 58.199 50.000 0.61 0.00 0.00 4.68
3793 4099 5.886960 AAATATGTGGACTTGTCTGAAGC 57.113 39.130 0.61 0.00 0.00 3.86
3804 4112 6.239036 GGAAGCCTGGAATTAAATATGTGGAC 60.239 42.308 0.00 0.00 0.00 4.02
3814 4122 6.073447 TCATTACTGGAAGCCTGGAATTAA 57.927 37.500 0.00 0.00 34.43 1.40
3824 4132 4.333926 GGAACACAGATCATTACTGGAAGC 59.666 45.833 0.00 0.00 37.60 3.86
4241 4769 2.889512 AGGAGGACAAATGGGGAAAAC 58.110 47.619 0.00 0.00 0.00 2.43
4821 5351 1.835693 CAGGGAGAAGATGGAGGCC 59.164 63.158 0.00 0.00 0.00 5.19
4887 5417 2.281692 ATGCCGCACTGCTTCACA 60.282 55.556 0.00 0.00 0.00 3.58
4908 5438 5.747483 CAGAACTCCTGATGCCTCAGCAA 62.747 52.174 13.07 3.33 45.63 3.91
4920 5450 3.405831 TGCACAATCTTCAGAACTCCTG 58.594 45.455 0.00 0.00 44.27 3.86
4921 5451 3.777106 TGCACAATCTTCAGAACTCCT 57.223 42.857 0.00 0.00 0.00 3.69
4922 5452 4.574013 CCTATGCACAATCTTCAGAACTCC 59.426 45.833 0.00 0.00 0.00 3.85
5062 5593 5.988310 TCATTCTTGCTTGACATCCAAAT 57.012 34.783 0.00 0.00 33.76 2.32
5101 5637 2.676839 CCACAAGAGCAATCACAGCTAG 59.323 50.000 0.00 0.00 43.58 3.42
5142 5679 8.213518 TCTTAGCTACATTAGGCTTTGATTTG 57.786 34.615 0.00 0.00 39.65 2.32
5180 5717 9.628746 AAACTTTACGTTCAAAACACAAGTAAT 57.371 25.926 0.00 0.00 33.90 1.89
5189 5726 9.151752 GCTACTCTTAAACTTTACGTTCAAAAC 57.848 33.333 0.00 0.00 33.90 2.43
5238 5775 8.736244 GTTTGGTGAATACTGTATTGTGGTATT 58.264 33.333 17.21 0.00 38.39 1.89
5243 5780 6.567687 TGGTTTGGTGAATACTGTATTGTG 57.432 37.500 17.21 0.00 0.00 3.33
5244 5781 6.945435 TGATGGTTTGGTGAATACTGTATTGT 59.055 34.615 17.21 0.00 0.00 2.71
5245 5782 7.389803 TGATGGTTTGGTGAATACTGTATTG 57.610 36.000 17.21 0.00 0.00 1.90
5247 5784 9.693739 TTTATGATGGTTTGGTGAATACTGTAT 57.306 29.630 0.00 0.00 0.00 2.29
5248 5785 9.693739 ATTTATGATGGTTTGGTGAATACTGTA 57.306 29.630 0.00 0.00 0.00 2.74
5249 5786 8.469200 CATTTATGATGGTTTGGTGAATACTGT 58.531 33.333 0.00 0.00 0.00 3.55
5290 5827 3.979911 TCATCACCCAGGTAATGCAAAT 58.020 40.909 0.00 0.00 0.00 2.32
5291 5828 3.448093 TCATCACCCAGGTAATGCAAA 57.552 42.857 0.00 0.00 0.00 3.68
5292 5829 3.010027 TCTTCATCACCCAGGTAATGCAA 59.990 43.478 0.00 0.00 0.00 4.08
5293 5830 2.575735 TCTTCATCACCCAGGTAATGCA 59.424 45.455 0.00 0.00 0.00 3.96
5294 5831 3.281727 TCTTCATCACCCAGGTAATGC 57.718 47.619 0.00 0.00 0.00 3.56
5295 5832 6.458751 CGATTTTCTTCATCACCCAGGTAATG 60.459 42.308 0.00 0.00 0.00 1.90
5296 5833 5.590259 CGATTTTCTTCATCACCCAGGTAAT 59.410 40.000 0.00 0.00 0.00 1.89
5297 5834 4.941263 CGATTTTCTTCATCACCCAGGTAA 59.059 41.667 0.00 0.00 0.00 2.85
5298 5835 4.019681 ACGATTTTCTTCATCACCCAGGTA 60.020 41.667 0.00 0.00 0.00 3.08
5299 5836 3.244911 ACGATTTTCTTCATCACCCAGGT 60.245 43.478 0.00 0.00 0.00 4.00
5300 5837 3.347216 ACGATTTTCTTCATCACCCAGG 58.653 45.455 0.00 0.00 0.00 4.45
5301 5838 4.436050 CGAACGATTTTCTTCATCACCCAG 60.436 45.833 0.00 0.00 0.00 4.45
5302 5839 3.435327 CGAACGATTTTCTTCATCACCCA 59.565 43.478 0.00 0.00 0.00 4.51
5303 5840 3.682858 TCGAACGATTTTCTTCATCACCC 59.317 43.478 0.00 0.00 0.00 4.61
5304 5841 4.921470 TCGAACGATTTTCTTCATCACC 57.079 40.909 0.00 0.00 0.00 4.02
5305 5842 7.586300 TCTTTTTCGAACGATTTTCTTCATCAC 59.414 33.333 0.00 0.00 0.00 3.06
5306 5843 7.635423 TCTTTTTCGAACGATTTTCTTCATCA 58.365 30.769 0.00 0.00 0.00 3.07
5307 5844 8.488979 TTCTTTTTCGAACGATTTTCTTCATC 57.511 30.769 0.00 0.00 0.00 2.92
5308 5845 8.850454 TTTCTTTTTCGAACGATTTTCTTCAT 57.150 26.923 0.00 0.00 0.00 2.57
5309 5846 7.431084 CCTTTCTTTTTCGAACGATTTTCTTCA 59.569 33.333 0.00 0.00 0.00 3.02
5310 5847 7.642586 TCCTTTCTTTTTCGAACGATTTTCTTC 59.357 33.333 0.00 0.00 0.00 2.87
5311 5848 7.477494 TCCTTTCTTTTTCGAACGATTTTCTT 58.523 30.769 0.00 0.00 0.00 2.52
5312 5849 7.023197 TCCTTTCTTTTTCGAACGATTTTCT 57.977 32.000 0.00 0.00 0.00 2.52
5313 5850 7.673810 TTCCTTTCTTTTTCGAACGATTTTC 57.326 32.000 0.00 0.00 0.00 2.29
5314 5851 8.642908 AATTCCTTTCTTTTTCGAACGATTTT 57.357 26.923 0.00 0.00 0.00 1.82
5315 5852 8.539674 CAAATTCCTTTCTTTTTCGAACGATTT 58.460 29.630 0.00 0.00 0.00 2.17
5316 5853 7.306574 GCAAATTCCTTTCTTTTTCGAACGATT 60.307 33.333 0.00 0.00 0.00 3.34
5317 5854 6.143919 GCAAATTCCTTTCTTTTTCGAACGAT 59.856 34.615 0.00 0.00 0.00 3.73
5318 5855 5.457473 GCAAATTCCTTTCTTTTTCGAACGA 59.543 36.000 0.00 0.00 0.00 3.85
5319 5856 5.231147 TGCAAATTCCTTTCTTTTTCGAACG 59.769 36.000 0.00 0.00 0.00 3.95
5320 5857 6.582437 TGCAAATTCCTTTCTTTTTCGAAC 57.418 33.333 0.00 0.00 0.00 3.95
5321 5858 7.784633 AATGCAAATTCCTTTCTTTTTCGAA 57.215 28.000 0.00 0.00 0.00 3.71
5322 5859 7.923344 TGTAATGCAAATTCCTTTCTTTTTCGA 59.077 29.630 0.00 0.00 0.00 3.71
5323 5860 8.071122 TGTAATGCAAATTCCTTTCTTTTTCG 57.929 30.769 0.00 0.00 0.00 3.46
5324 5861 8.011673 GCTGTAATGCAAATTCCTTTCTTTTTC 58.988 33.333 0.00 0.00 0.00 2.29
5325 5862 7.498570 TGCTGTAATGCAAATTCCTTTCTTTTT 59.501 29.630 0.00 0.00 40.29 1.94
5326 5863 6.991531 TGCTGTAATGCAAATTCCTTTCTTTT 59.008 30.769 0.00 0.00 40.29 2.27
5327 5864 6.523840 TGCTGTAATGCAAATTCCTTTCTTT 58.476 32.000 0.00 0.00 40.29 2.52
5328 5865 6.100404 TGCTGTAATGCAAATTCCTTTCTT 57.900 33.333 0.00 0.00 40.29 2.52
5329 5866 5.717119 CTGCTGTAATGCAAATTCCTTTCT 58.283 37.500 0.00 0.00 42.83 2.52
5330 5867 4.328169 GCTGCTGTAATGCAAATTCCTTTC 59.672 41.667 0.00 0.00 42.83 2.62
5331 5868 4.248058 GCTGCTGTAATGCAAATTCCTTT 58.752 39.130 0.00 0.00 42.83 3.11
5332 5869 3.258872 TGCTGCTGTAATGCAAATTCCTT 59.741 39.130 0.00 0.00 42.83 3.36
5333 5870 2.827322 TGCTGCTGTAATGCAAATTCCT 59.173 40.909 0.00 0.00 42.83 3.36
5334 5871 3.184541 CTGCTGCTGTAATGCAAATTCC 58.815 45.455 0.00 0.00 42.83 3.01
5335 5872 2.601763 GCTGCTGCTGTAATGCAAATTC 59.398 45.455 8.53 0.00 42.83 2.17
5336 5873 2.028839 TGCTGCTGCTGTAATGCAAATT 60.029 40.909 17.00 0.00 42.83 1.82
5337 5874 1.546923 TGCTGCTGCTGTAATGCAAAT 59.453 42.857 17.00 0.00 42.83 2.32
5391 5967 8.926715 AGTTTAAAGTCTTTGAATTGTGGAAC 57.073 30.769 8.14 0.00 37.35 3.62
5431 6007 7.164122 GGTGGATATCAGAATTCTGCTTCATA 58.836 38.462 27.45 19.89 43.46 2.15
5464 6105 4.963276 CACCTGTGTGGGTACATTTATG 57.037 45.455 0.00 0.00 39.39 1.90
5584 6231 4.382901 CCAGATTTTGTAGCTGAGCTCTCT 60.383 45.833 11.68 13.98 40.44 3.10
5591 6238 3.253188 GTGTTGCCAGATTTTGTAGCTGA 59.747 43.478 0.00 0.00 0.00 4.26
5757 6404 1.132500 ATAGTGCACTTCTAGCCCCC 58.868 55.000 27.06 0.00 0.00 5.40
5831 6486 4.752101 GTGCAGATAACAACTCAACAGAGT 59.248 41.667 0.00 0.00 44.25 3.24
5833 6488 4.702831 TGTGCAGATAACAACTCAACAGA 58.297 39.130 0.00 0.00 0.00 3.41
5837 6492 3.475575 TGCTGTGCAGATAACAACTCAA 58.524 40.909 3.02 0.00 33.32 3.02


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

AutoCloner maintained by Alex Coulton.