Multiple sequence alignment - TraesCS1A01G263000

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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 TraesCS1A01G263000 chr1A 100.000 4434 0 0 1 4434 458503600 458508033 0.000000e+00 8189.0
1 TraesCS1A01G263000 chr1A 79.310 116 21 3 318 431 488104345 488104231 1.320000e-10 78.7
2 TraesCS1A01G263000 chr1D 92.991 3481 158 36 817 4246 357432165 357435610 0.000000e+00 4998.0
3 TraesCS1A01G263000 chr1D 90.943 265 22 2 1 265 357430951 357431213 5.450000e-94 355.0
4 TraesCS1A01G263000 chr1D 86.667 330 26 9 475 789 357431849 357432175 2.540000e-92 350.0
5 TraesCS1A01G263000 chr1B 89.907 3339 230 44 689 3955 480818763 480822066 0.000000e+00 4200.0
6 TraesCS1A01G263000 chr1B 90.950 221 8 3 3965 4185 480822271 480822479 2.020000e-73 287.0
7 TraesCS1A01G263000 chr1B 85.833 240 30 4 1 239 480817167 480817403 7.360000e-63 252.0
8 TraesCS1A01G263000 chr1B 84.211 95 9 4 293 381 115952364 115952458 2.200000e-13 87.9
9 TraesCS1A01G263000 chr1B 88.889 72 6 2 4253 4324 480822485 480822554 2.200000e-13 87.9
10 TraesCS1A01G263000 chr5A 86.849 403 33 9 1389 1775 145748919 145748521 2.450000e-117 433.0
11 TraesCS1A01G263000 chr5A 96.774 31 1 0 272 302 22487571 22487541 8.000000e-03 52.8
12 TraesCS1A01G263000 chr3B 78.679 530 100 8 2900 3424 676894870 676895391 1.530000e-89 340.0
13 TraesCS1A01G263000 chr3A 77.799 527 110 5 2900 3424 649534962 649535483 7.160000e-83 318.0
14 TraesCS1A01G263000 chr3D 76.375 618 129 12 2814 3424 514647832 514648439 2.570000e-82 316.0
15 TraesCS1A01G263000 chr3D 82.759 116 11 4 284 393 477917359 477917247 1.310000e-15 95.3
16 TraesCS1A01G263000 chr5B 89.759 166 14 3 1389 1553 141953400 141953237 4.490000e-50 209.0
17 TraesCS1A01G263000 chr5B 83.962 106 11 6 296 395 586385906 586386011 3.650000e-16 97.1
18 TraesCS1A01G263000 chr4D 90.654 107 9 1 350 456 433111487 433111592 1.660000e-29 141.0
19 TraesCS1A01G263000 chr4A 84.483 116 10 3 278 386 48526401 48526287 1.690000e-19 108.0
20 TraesCS1A01G263000 chr4A 77.444 133 17 11 319 442 685322797 685322669 2.860000e-07 67.6
21 TraesCS1A01G263000 chr4A 96.970 33 1 0 274 306 45063028 45063060 6.200000e-04 56.5
22 TraesCS1A01G263000 chr5D 78.082 146 24 6 317 456 174279430 174279287 7.900000e-13 86.1
23 TraesCS1A01G263000 chr4B 84.444 90 10 4 315 402 433958034 433958121 7.900000e-13 86.1
24 TraesCS1A01G263000 chr2D 84.091 88 6 4 315 395 87817800 87817886 1.320000e-10 78.7
25 TraesCS1A01G263000 chr2D 85.897 78 5 4 315 386 88287466 88287389 1.320000e-10 78.7
26 TraesCS1A01G263000 chr2A 100.000 30 0 0 278 307 105600254 105600283 6.200000e-04 56.5


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 TraesCS1A01G263000 chr1A 458503600 458508033 4433 False 8189.000 8189 100.000000 1 4434 1 chr1A.!!$F1 4433
1 TraesCS1A01G263000 chr1D 357430951 357435610 4659 False 1901.000 4998 90.200333 1 4246 3 chr1D.!!$F1 4245
2 TraesCS1A01G263000 chr1B 480817167 480822554 5387 False 1206.725 4200 88.894750 1 4324 4 chr1B.!!$F2 4323
3 TraesCS1A01G263000 chr3B 676894870 676895391 521 False 340.000 340 78.679000 2900 3424 1 chr3B.!!$F1 524
4 TraesCS1A01G263000 chr3A 649534962 649535483 521 False 318.000 318 77.799000 2900 3424 1 chr3A.!!$F1 524
5 TraesCS1A01G263000 chr3D 514647832 514648439 607 False 316.000 316 76.375000 2814 3424 1 chr3D.!!$F1 610

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
925 2368 0.033601 ACTCCACTCGATCAGCCTCT 60.034 55.0 0.00 0.0 0.00 3.69 F
1678 3134 0.319469 GAATTGCGGTGTTTGGGTGG 60.319 55.0 0.00 0.0 0.00 4.61 F
2788 4287 0.473755 TTCCTGCAGAGTCAAAGGCA 59.526 50.0 17.39 0.0 34.66 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 3310 0.988439 ACACGCTTTTTGCAACAACG 59.012 45.0 0.0 8.53 43.06 4.10 R
3223 4722 0.537188 GCCCCACGAAGAATCTCAGA 59.463 55.0 0.0 0.00 0.00 3.27 R
3907 5436 0.031585 TGACACGACAGAAGGTTCCG 59.968 55.0 0.0 0.00 0.00 4.30 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
60 61 7.821595 TCGTCAACGATATCTTTACACAATT 57.178 32.000 0.22 0.00 44.22 2.32
61 62 8.246908 TCGTCAACGATATCTTTACACAATTT 57.753 30.769 0.22 0.00 44.22 1.82
62 63 8.714179 TCGTCAACGATATCTTTACACAATTTT 58.286 29.630 0.22 0.00 44.22 1.82
96 97 5.715439 TCATATGTTGAAGGGGTCTCATT 57.285 39.130 1.90 0.00 0.00 2.57
224 225 8.780846 TTGTGAACTCTGTTTAGTGAACTTTA 57.219 30.769 0.00 0.00 39.08 1.85
254 255 6.180472 GGGTTCTGATTCTTGGTAGATTCAA 58.820 40.000 0.00 0.00 39.19 2.69
265 266 6.655003 TCTTGGTAGATTCAAAGGTGTGATTC 59.345 38.462 0.00 0.00 0.00 2.52
266 267 5.253330 TGGTAGATTCAAAGGTGTGATTCC 58.747 41.667 0.00 0.00 31.25 3.01
271 272 6.176183 AGATTCAAAGGTGTGATTCCTGTAG 58.824 40.000 0.00 0.00 35.27 2.74
272 273 4.286297 TCAAAGGTGTGATTCCTGTAGG 57.714 45.455 0.00 0.00 35.27 3.18
273 274 3.650942 TCAAAGGTGTGATTCCTGTAGGT 59.349 43.478 0.00 0.00 35.27 3.08
274 275 4.841813 TCAAAGGTGTGATTCCTGTAGGTA 59.158 41.667 0.00 0.00 35.27 3.08
276 277 6.670464 TCAAAGGTGTGATTCCTGTAGGTATA 59.330 38.462 0.00 0.00 35.27 1.47
277 278 6.481434 AAGGTGTGATTCCTGTAGGTATAC 57.519 41.667 0.00 0.00 35.27 1.47
278 279 4.900054 AGGTGTGATTCCTGTAGGTATACC 59.100 45.833 14.54 14.54 36.34 2.73
279 280 5.341793 AGGTGTGATTCCTGTAGGTATACCT 60.342 44.000 27.24 27.24 40.82 3.08
280 281 7.371412 AGGTGTGATTCCTGTAGGTATACCTG 61.371 46.154 31.07 16.30 39.29 4.00
288 289 2.868504 AGGTATACCTGGCCATGGG 58.131 57.895 24.01 16.10 46.55 4.00
319 320 4.760047 CCTGACGTTGCTCCCGGG 62.760 72.222 16.85 16.85 0.00 5.73
324 325 4.530857 CGTTGCTCCCGGGCCTAG 62.531 72.222 18.49 9.90 0.00 3.02
325 326 3.081409 GTTGCTCCCGGGCCTAGA 61.081 66.667 18.49 0.00 0.00 2.43
326 327 2.040884 TTGCTCCCGGGCCTAGAT 60.041 61.111 18.49 0.00 0.00 1.98
327 328 1.692749 TTGCTCCCGGGCCTAGATT 60.693 57.895 18.49 0.00 0.00 2.40
329 330 1.279025 TGCTCCCGGGCCTAGATTTT 61.279 55.000 18.49 0.00 0.00 1.82
331 332 0.837272 CTCCCGGGCCTAGATTTTGA 59.163 55.000 18.49 0.00 0.00 2.69
333 334 0.819666 CCCGGGCCTAGATTTTGAGC 60.820 60.000 8.08 0.00 0.00 4.26
334 335 0.819666 CCGGGCCTAGATTTTGAGCC 60.820 60.000 0.84 0.00 43.09 4.70
336 337 2.707902 GGCCTAGATTTTGAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
337 338 0.180406 GGCCTAGATTTTGAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
339 340 1.943340 GCCTAGATTTTGAGCCCGAAG 59.057 52.381 0.00 0.00 0.00 3.79
379 1512 4.513198 TTTTTGCGATTTACTGAAGGGG 57.487 40.909 0.00 0.00 0.00 4.79
381 1514 0.618458 TGCGATTTACTGAAGGGGCT 59.382 50.000 0.00 0.00 0.00 5.19
382 1515 1.300481 GCGATTTACTGAAGGGGCTC 58.700 55.000 0.00 0.00 0.00 4.70
384 1517 1.806623 CGATTTACTGAAGGGGCTCGG 60.807 57.143 0.00 0.00 0.00 4.63
385 1518 0.107165 ATTTACTGAAGGGGCTCGGC 60.107 55.000 0.00 0.00 0.00 5.54
410 1543 1.577421 CCCAACGGGCTTTTACACG 59.423 57.895 0.00 0.00 35.35 4.49
411 1544 1.167781 CCCAACGGGCTTTTACACGT 61.168 55.000 0.00 0.00 41.88 4.49
412 1545 0.040781 CCAACGGGCTTTTACACGTG 60.041 55.000 15.48 15.48 39.76 4.49
413 1546 0.659123 CAACGGGCTTTTACACGTGC 60.659 55.000 17.22 0.00 39.76 5.34
414 1547 0.816421 AACGGGCTTTTACACGTGCT 60.816 50.000 17.22 5.64 39.76 4.40
415 1548 1.206578 CGGGCTTTTACACGTGCTG 59.793 57.895 17.22 2.48 0.00 4.41
416 1549 1.579429 GGGCTTTTACACGTGCTGG 59.421 57.895 17.22 2.87 0.00 4.85
417 1550 1.170290 GGGCTTTTACACGTGCTGGT 61.170 55.000 17.22 0.00 0.00 4.00
418 1551 0.237498 GGCTTTTACACGTGCTGGTC 59.763 55.000 17.22 0.00 0.00 4.02
419 1552 0.941542 GCTTTTACACGTGCTGGTCA 59.058 50.000 17.22 0.00 0.00 4.02
420 1553 1.069906 GCTTTTACACGTGCTGGTCAG 60.070 52.381 17.22 5.61 0.00 3.51
421 1554 1.531149 CTTTTACACGTGCTGGTCAGG 59.469 52.381 17.22 0.00 36.67 3.86
422 1555 0.882927 TTTACACGTGCTGGTCAGGC 60.883 55.000 17.22 0.00 34.08 4.85
423 1556 1.754380 TTACACGTGCTGGTCAGGCT 61.754 55.000 17.22 0.00 34.08 4.58
424 1557 1.754380 TACACGTGCTGGTCAGGCTT 61.754 55.000 17.22 0.00 34.08 4.35
425 1558 2.281070 ACGTGCTGGTCAGGCTTG 60.281 61.111 0.00 0.00 34.08 4.01
426 1559 3.052082 CGTGCTGGTCAGGCTTGG 61.052 66.667 0.00 0.00 0.00 3.61
427 1560 2.113986 GTGCTGGTCAGGCTTGGT 59.886 61.111 0.00 0.00 0.00 3.67
428 1561 1.968540 GTGCTGGTCAGGCTTGGTC 60.969 63.158 0.00 0.00 0.00 4.02
429 1562 2.360475 GCTGGTCAGGCTTGGTCC 60.360 66.667 0.00 0.00 0.00 4.46
430 1563 2.900106 GCTGGTCAGGCTTGGTCCT 61.900 63.158 10.89 0.00 36.78 3.85
440 1573 4.227864 AGGCTTGGTCCTGATTTTCTAG 57.772 45.455 0.00 0.00 34.56 2.43
441 1574 3.054065 AGGCTTGGTCCTGATTTTCTAGG 60.054 47.826 0.00 0.00 34.56 3.02
442 1575 2.685388 GCTTGGTCCTGATTTTCTAGGC 59.315 50.000 0.00 0.00 34.00 3.93
443 1576 3.282885 CTTGGTCCTGATTTTCTAGGCC 58.717 50.000 0.00 0.00 34.00 5.19
444 1577 1.564348 TGGTCCTGATTTTCTAGGCCC 59.436 52.381 0.00 0.00 32.74 5.80
445 1578 1.475213 GGTCCTGATTTTCTAGGCCCG 60.475 57.143 0.00 0.00 34.00 6.13
446 1579 1.485066 GTCCTGATTTTCTAGGCCCGA 59.515 52.381 0.00 0.00 34.00 5.14
447 1580 1.485066 TCCTGATTTTCTAGGCCCGAC 59.515 52.381 0.00 0.00 34.00 4.79
448 1581 1.571919 CTGATTTTCTAGGCCCGACG 58.428 55.000 0.00 0.00 0.00 5.12
449 1582 0.461339 TGATTTTCTAGGCCCGACGC 60.461 55.000 0.00 0.00 0.00 5.19
462 1595 2.750237 GACGCCCGGGCTTGATTT 60.750 61.111 41.01 19.02 39.32 2.17
463 1596 2.282887 ACGCCCGGGCTTGATTTT 60.283 55.556 41.01 14.73 39.32 1.82
464 1597 1.873270 GACGCCCGGGCTTGATTTTT 61.873 55.000 41.01 15.76 39.32 1.94
486 1619 1.223487 GCCGGCCTCAGATAAACCA 59.777 57.895 18.11 0.00 0.00 3.67
487 1620 0.815615 GCCGGCCTCAGATAAACCAG 60.816 60.000 18.11 0.00 0.00 4.00
494 1627 2.436173 CCTCAGATAAACCAGGTCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
499 1632 4.656112 CAGATAAACCAGGTCCTCCTACAT 59.344 45.833 0.00 0.00 43.07 2.29
500 1633 4.656112 AGATAAACCAGGTCCTCCTACATG 59.344 45.833 0.00 0.00 43.07 3.21
552 1685 6.946009 GGAGGATAGAGTCTATCTAGCTTGTT 59.054 42.308 30.28 12.47 44.72 2.83
605 1750 6.255887 CGCTTGGGTGTTGTTTGTTTATTTTA 59.744 34.615 0.00 0.00 0.00 1.52
654 1801 6.037062 CGCATCAGGACTGTGTTATCAATTTA 59.963 38.462 0.00 0.00 0.00 1.40
698 2133 3.261643 TGGAAGCTCTGCTCTGTAATTCA 59.738 43.478 0.00 0.00 38.25 2.57
740 2177 2.177531 GCAAGTCCATGCGCTGTG 59.822 61.111 9.73 7.73 36.45 3.66
756 2198 5.048364 TGCGCTGTGTTTTCTGGTAATAAAT 60.048 36.000 9.73 0.00 0.00 1.40
779 2221 1.332195 AAAAGAAAGTCCAGCCAGCC 58.668 50.000 0.00 0.00 0.00 4.85
781 2223 0.538287 AAGAAAGTCCAGCCAGCCAC 60.538 55.000 0.00 0.00 0.00 5.01
782 2224 1.973812 GAAAGTCCAGCCAGCCACC 60.974 63.158 0.00 0.00 0.00 4.61
784 2226 2.703675 AAAGTCCAGCCAGCCACCAG 62.704 60.000 0.00 0.00 0.00 4.00
792 2234 4.371417 CAGCCACCAGCCCACCAT 62.371 66.667 0.00 0.00 45.47 3.55
793 2235 3.593680 AGCCACCAGCCCACCATT 61.594 61.111 0.00 0.00 45.47 3.16
794 2236 3.384532 GCCACCAGCCCACCATTG 61.385 66.667 0.00 0.00 34.35 2.82
834 2276 1.006998 TGCACCCAGGCCAGATAAAAT 59.993 47.619 5.01 0.00 0.00 1.82
899 2342 1.886542 GCCTTCCGAACCAAGAAACAT 59.113 47.619 0.00 0.00 0.00 2.71
925 2368 0.033601 ACTCCACTCGATCAGCCTCT 60.034 55.000 0.00 0.00 0.00 3.69
926 2369 0.667993 CTCCACTCGATCAGCCTCTC 59.332 60.000 0.00 0.00 0.00 3.20
927 2370 1.098129 TCCACTCGATCAGCCTCTCG 61.098 60.000 0.00 0.00 36.25 4.04
928 2371 1.299014 CACTCGATCAGCCTCTCGC 60.299 63.158 0.00 0.00 34.94 5.03
970 2413 2.687200 CATCTCCACCCCGACCCA 60.687 66.667 0.00 0.00 0.00 4.51
1016 2460 1.228552 ACATGTGGGCCCTCAACAC 60.229 57.895 29.35 16.26 35.75 3.32
1297 2748 2.610479 CGAGCTGGTGCAAAAGTAGAGA 60.610 50.000 0.00 0.00 42.74 3.10
1315 2766 0.521735 GACGGAATTGTGTGGCCTTC 59.478 55.000 3.32 0.00 0.00 3.46
1327 2781 2.750888 GGCCTTCGTGCGATTGGAC 61.751 63.158 14.86 10.10 0.00 4.02
1328 2782 1.741770 GCCTTCGTGCGATTGGACT 60.742 57.895 14.86 0.00 33.68 3.85
1330 2784 2.004583 CCTTCGTGCGATTGGACTTA 57.995 50.000 2.84 0.00 33.68 2.24
1343 2797 6.092259 GCGATTGGACTTAGAAAAGCTAGAAA 59.908 38.462 0.00 0.00 36.05 2.52
1351 2805 9.613957 GACTTAGAAAAGCTAGAAACATTTTCC 57.386 33.333 0.00 0.00 40.74 3.13
1353 2807 9.833182 CTTAGAAAAGCTAGAAACATTTTCCTC 57.167 33.333 0.00 0.00 40.74 3.71
1434 2888 1.991230 CTGTTGATTCCGGGGAGGT 59.009 57.895 0.00 0.00 41.99 3.85
1470 2924 1.446366 GTGGGGATTCGGGTCTAGC 59.554 63.158 0.00 0.00 0.00 3.42
1474 2928 1.258676 GGGATTCGGGTCTAGCTAGG 58.741 60.000 20.58 4.70 0.00 3.02
1494 2948 6.037720 GCTAGGAAAATTTGAAGAGTAGCTCC 59.962 42.308 0.00 0.00 0.00 4.70
1504 2958 2.040606 GTAGCTCCCCCTGACCCA 59.959 66.667 0.00 0.00 0.00 4.51
1543 2999 1.817357 TGATGCTGTTGGCTTCAGAG 58.183 50.000 12.16 0.00 45.85 3.35
1544 3000 1.348696 TGATGCTGTTGGCTTCAGAGA 59.651 47.619 12.16 0.73 45.85 3.10
1568 3024 3.439129 GGAAATTCGGAGAATCGGTGTTT 59.561 43.478 0.00 0.00 45.90 2.83
1588 3044 1.808411 ATTCTGGTGTAACTGGTGCG 58.192 50.000 0.00 0.00 36.74 5.34
1591 3047 1.841663 CTGGTGTAACTGGTGCGTGC 61.842 60.000 0.00 0.00 36.74 5.34
1635 3091 1.202557 AGGCGTGGTTTCGTGTTTAGA 60.203 47.619 0.00 0.00 0.00 2.10
1641 3097 4.549489 CGTGGTTTCGTGTTTAGAGTTGTC 60.549 45.833 0.00 0.00 0.00 3.18
1655 3111 5.312120 AGAGTTGTCGAATTGATCTACGT 57.688 39.130 0.00 0.00 0.00 3.57
1665 3121 5.449113 CGAATTGATCTACGTGTTGAATTGC 59.551 40.000 0.00 0.00 0.00 3.56
1675 3131 1.202463 TGTTGAATTGCGGTGTTTGGG 60.202 47.619 0.00 0.00 0.00 4.12
1678 3134 0.319469 GAATTGCGGTGTTTGGGTGG 60.319 55.000 0.00 0.00 0.00 4.61
1805 3261 6.724441 TGTATGAGGAAACTTCAGGTTCTCTA 59.276 38.462 4.61 0.00 44.43 2.43
1881 3337 2.650608 GCAAAAAGCGTGTACCAGAAG 58.349 47.619 0.00 0.00 0.00 2.85
1969 3425 3.643320 AGATAGCTCCGATGGATTGAACA 59.357 43.478 0.00 0.00 0.00 3.18
2087 3543 0.534203 AGGGTGGCACGTTTGTAGTG 60.534 55.000 12.17 0.00 42.15 2.74
2109 3596 4.706962 TGACAATCTGTAGAGCTCTTAGCA 59.293 41.667 23.84 16.85 45.56 3.49
2110 3597 5.163571 TGACAATCTGTAGAGCTCTTAGCAG 60.164 44.000 23.84 24.34 45.56 4.24
2111 3598 4.050553 CAATCTGTAGAGCTCTTAGCAGC 58.949 47.826 23.84 6.38 45.56 5.25
2162 3649 6.864560 TTCGACATTCACTTACGTAATCTG 57.135 37.500 8.76 7.55 0.00 2.90
2180 3667 3.117745 TCTGGACATTCATGATCACCCT 58.882 45.455 0.00 0.00 0.00 4.34
2181 3668 4.297768 TCTGGACATTCATGATCACCCTA 58.702 43.478 0.00 0.00 0.00 3.53
2191 3678 6.114187 TCATGATCACCCTATGACATTACC 57.886 41.667 0.00 0.00 41.24 2.85
2369 3858 8.461222 TGTTCCAAAGAAGATATAAATGCACAG 58.539 33.333 0.00 0.00 30.91 3.66
2461 3957 6.884295 TGATACTCCAAATGTAAGGTTCCAAG 59.116 38.462 0.00 0.00 0.00 3.61
2499 3996 4.946784 AGTTTTAGAGGCATTACGCAAG 57.053 40.909 0.00 0.00 45.17 4.01
2590 4089 6.966021 TCTCAAACCTTGTTACATTTACTGC 58.034 36.000 0.00 0.00 0.00 4.40
2626 4125 7.872993 TCAAGAGAGTTTCACACTGTTATTAGG 59.127 37.037 0.00 0.00 35.01 2.69
2712 4211 8.842358 TTGGGTTATATCATATCCGTCTTTTC 57.158 34.615 0.00 0.00 0.00 2.29
2788 4287 0.473755 TTCCTGCAGAGTCAAAGGCA 59.526 50.000 17.39 0.00 34.66 4.75
2794 4293 1.742268 GCAGAGTCAAAGGCATCCTTC 59.258 52.381 0.00 0.00 43.92 3.46
2805 4304 1.435408 GCATCCTTCGGAGAAGCAGC 61.435 60.000 0.00 4.47 45.90 5.25
2884 4383 1.186200 TGGTAGCTACTGAGGTGCTG 58.814 55.000 22.74 0.00 37.62 4.41
3214 4713 2.084610 TGAAGAGTGGTGCGATCAAG 57.915 50.000 0.00 0.00 0.00 3.02
3223 4722 0.103208 GTGCGATCAAGACCGAGGAT 59.897 55.000 0.00 0.00 0.00 3.24
3427 4926 2.213499 CAGAAACCGAAGCAAGACAGT 58.787 47.619 0.00 0.00 0.00 3.55
3438 4937 2.059541 GCAAGACAGTTCGTAGGTGTC 58.940 52.381 0.00 0.00 40.82 3.67
3514 5013 3.450578 GAACCAGTGTACACGTCTCAAA 58.549 45.455 19.93 0.00 36.20 2.69
3520 5019 4.509970 CAGTGTACACGTCTCAAATGGAAA 59.490 41.667 19.93 0.00 36.20 3.13
3521 5020 4.750098 AGTGTACACGTCTCAAATGGAAAG 59.250 41.667 19.93 0.00 36.20 2.62
3522 5021 4.510340 GTGTACACGTCTCAAATGGAAAGT 59.490 41.667 10.84 0.00 0.00 2.66
3540 5039 1.789490 GTCGTTTACGGCGTAAATGC 58.211 50.000 39.72 32.91 41.81 3.56
3545 5044 3.243410 CGTTTACGGCGTAAATGCTATGA 59.757 43.478 36.84 18.75 39.64 2.15
3546 5045 4.511734 GTTTACGGCGTAAATGCTATGAC 58.488 43.478 37.86 24.12 39.64 3.06
3555 5054 4.965762 CGTAAATGCTATGACTCGTTCGTA 59.034 41.667 0.00 0.00 0.00 3.43
3601 5100 2.289072 CCCATAGGCGAAGTATCCAGTG 60.289 54.545 0.00 0.00 0.00 3.66
3607 5106 3.071479 GGCGAAGTATCCAGTGAAAACA 58.929 45.455 0.00 0.00 0.00 2.83
3632 5131 5.069119 GGTTTTCACTGGAAATCTGGAAACT 59.931 40.000 0.00 0.00 42.31 2.66
3633 5132 6.406961 GGTTTTCACTGGAAATCTGGAAACTT 60.407 38.462 0.00 0.00 42.31 2.66
3634 5133 6.790232 TTTCACTGGAAATCTGGAAACTTT 57.210 33.333 0.00 0.00 38.07 2.66
3682 5181 4.439968 TCACAGCTAAGAATCTGCAGATG 58.560 43.478 29.34 17.80 34.49 2.90
3683 5182 3.002451 CACAGCTAAGAATCTGCAGATGC 59.998 47.826 29.34 27.23 42.50 3.91
3793 5292 2.035312 CCCAAGCAGCCAAGCTCT 59.965 61.111 0.00 0.00 45.89 4.09
3794 5293 1.300963 CCCAAGCAGCCAAGCTCTA 59.699 57.895 0.00 0.00 45.89 2.43
3872 5401 1.375523 GTCCGTGCGGTCCAAATCT 60.376 57.895 10.60 0.00 36.47 2.40
3887 5416 1.106285 AATCTGCTTTTCATCGGCCC 58.894 50.000 0.00 0.00 0.00 5.80
3907 5436 3.004419 CCCGAAAGAACCTTTTGTCTTCC 59.996 47.826 0.00 0.00 0.00 3.46
4049 5774 3.686726 GTGATCCACTGAATCCACTGAAC 59.313 47.826 0.00 0.00 0.00 3.18
4069 5794 1.434622 CCATGCATCTCACGAGTGGC 61.435 60.000 0.00 0.00 0.00 5.01
4187 5912 8.061304 AGTACATTTTGGAATCCATAGAACCAT 58.939 33.333 1.39 0.00 34.19 3.55
4188 5913 7.116075 ACATTTTGGAATCCATAGAACCATG 57.884 36.000 1.39 1.48 34.19 3.66
4190 5915 3.882102 TGGAATCCATAGAACCATGGG 57.118 47.619 18.09 0.00 44.85 4.00
4191 5916 3.130450 TGGAATCCATAGAACCATGGGT 58.870 45.455 18.09 10.33 44.85 4.51
4196 5921 3.963129 TCCATAGAACCATGGGTTTCAC 58.037 45.455 18.09 0.00 46.95 3.18
4221 5946 1.604604 TGGAGTTGCTACACTTTGGC 58.395 50.000 0.13 0.00 0.00 4.52
4224 5949 1.946768 GAGTTGCTACACTTTGGCACA 59.053 47.619 0.13 0.00 35.62 4.57
4230 5955 1.072331 CTACACTTTGGCACAGGTCCT 59.928 52.381 5.53 0.00 42.39 3.85
4246 5975 3.767806 CTCTCAGCCAGCCGAGCA 61.768 66.667 0.00 0.00 0.00 4.26
4247 5976 3.719883 CTCTCAGCCAGCCGAGCAG 62.720 68.421 0.00 0.00 0.00 4.24
4248 5977 4.834453 CTCAGCCAGCCGAGCAGG 62.834 72.222 3.46 3.46 44.97 4.85
4253 5982 4.007644 CCAGCCGAGCAGGTCACA 62.008 66.667 0.00 0.00 43.70 3.58
4254 5983 2.740055 CAGCCGAGCAGGTCACAC 60.740 66.667 0.00 0.00 43.70 3.82
4255 5984 3.233980 AGCCGAGCAGGTCACACA 61.234 61.111 0.00 0.00 43.70 3.72
4256 5985 2.280797 GCCGAGCAGGTCACACAA 60.281 61.111 0.00 0.00 43.70 3.33
4257 5986 1.891919 GCCGAGCAGGTCACACAAA 60.892 57.895 0.00 0.00 43.70 2.83
4258 5987 1.237285 GCCGAGCAGGTCACACAAAT 61.237 55.000 0.00 0.00 43.70 2.32
4299 6028 3.027412 CTCTAGTGCATGTCCCTGTAGT 58.973 50.000 0.00 0.00 0.00 2.73
4303 6032 1.276421 GTGCATGTCCCTGTAGTCTGT 59.724 52.381 0.00 0.00 0.00 3.41
4310 6039 2.777459 CCCTGTAGTCTGTAGGGGAT 57.223 55.000 13.12 0.00 46.05 3.85
4316 6045 1.885049 AGTCTGTAGGGGATGTGCAT 58.115 50.000 0.00 0.00 0.00 3.96
4325 6054 3.159298 GGATGTGCATCCGTGTTCT 57.841 52.632 14.58 0.00 46.84 3.01
4326 6055 1.453155 GGATGTGCATCCGTGTTCTT 58.547 50.000 14.58 0.00 46.84 2.52
4327 6056 1.812571 GGATGTGCATCCGTGTTCTTT 59.187 47.619 14.58 0.00 46.84 2.52
4328 6057 2.228822 GGATGTGCATCCGTGTTCTTTT 59.771 45.455 14.58 0.00 46.84 2.27
4329 6058 3.305335 GGATGTGCATCCGTGTTCTTTTT 60.305 43.478 14.58 0.00 46.84 1.94
4354 6083 4.771590 TTTTTGAGAGTGATGTGCATCC 57.228 40.909 9.39 2.08 37.02 3.51
4355 6084 2.014335 TTGAGAGTGATGTGCATCCG 57.986 50.000 9.39 0.00 37.02 4.18
4356 6085 0.897621 TGAGAGTGATGTGCATCCGT 59.102 50.000 9.39 0.00 37.02 4.69
4357 6086 1.284657 GAGAGTGATGTGCATCCGTG 58.715 55.000 9.39 0.00 37.02 4.94
4358 6087 0.610174 AGAGTGATGTGCATCCGTGT 59.390 50.000 9.39 0.00 37.02 4.49
4359 6088 1.002430 AGAGTGATGTGCATCCGTGTT 59.998 47.619 9.39 0.00 37.02 3.32
4360 6089 1.129251 GAGTGATGTGCATCCGTGTTG 59.871 52.381 9.39 0.00 37.02 3.33
4361 6090 0.168788 GTGATGTGCATCCGTGTTGG 59.831 55.000 9.39 0.00 37.02 3.77
4369 6098 3.544772 TCCGTGTTGGAGCACTGA 58.455 55.556 0.00 0.00 43.74 3.41
4370 6099 1.367471 TCCGTGTTGGAGCACTGAG 59.633 57.895 0.00 0.00 43.74 3.35
4371 6100 2.320587 CCGTGTTGGAGCACTGAGC 61.321 63.158 0.00 0.00 42.00 4.26
4388 6117 4.933064 CGCATCGCTCTCCGTCCC 62.933 72.222 0.00 0.00 38.35 4.46
4389 6118 3.532155 GCATCGCTCTCCGTCCCT 61.532 66.667 0.00 0.00 38.35 4.20
4390 6119 2.415010 CATCGCTCTCCGTCCCTG 59.585 66.667 0.00 0.00 38.35 4.45
4391 6120 2.043852 ATCGCTCTCCGTCCCTGT 60.044 61.111 0.00 0.00 38.35 4.00
4392 6121 1.682684 ATCGCTCTCCGTCCCTGTT 60.683 57.895 0.00 0.00 38.35 3.16
4393 6122 1.258445 ATCGCTCTCCGTCCCTGTTT 61.258 55.000 0.00 0.00 38.35 2.83
4394 6123 1.004918 CGCTCTCCGTCCCTGTTTT 60.005 57.895 0.00 0.00 0.00 2.43
4395 6124 0.245539 CGCTCTCCGTCCCTGTTTTA 59.754 55.000 0.00 0.00 0.00 1.52
4396 6125 1.723220 GCTCTCCGTCCCTGTTTTAC 58.277 55.000 0.00 0.00 0.00 2.01
4397 6126 1.675116 GCTCTCCGTCCCTGTTTTACC 60.675 57.143 0.00 0.00 0.00 2.85
4398 6127 1.900486 CTCTCCGTCCCTGTTTTACCT 59.100 52.381 0.00 0.00 0.00 3.08
4399 6128 2.302157 CTCTCCGTCCCTGTTTTACCTT 59.698 50.000 0.00 0.00 0.00 3.50
4400 6129 2.301009 TCTCCGTCCCTGTTTTACCTTC 59.699 50.000 0.00 0.00 0.00 3.46
4401 6130 1.001181 TCCGTCCCTGTTTTACCTTCG 59.999 52.381 0.00 0.00 0.00 3.79
4402 6131 1.001181 CCGTCCCTGTTTTACCTTCGA 59.999 52.381 0.00 0.00 0.00 3.71
4403 6132 2.354403 CCGTCCCTGTTTTACCTTCGAT 60.354 50.000 0.00 0.00 0.00 3.59
4404 6133 3.332034 CGTCCCTGTTTTACCTTCGATT 58.668 45.455 0.00 0.00 0.00 3.34
4405 6134 3.124636 CGTCCCTGTTTTACCTTCGATTG 59.875 47.826 0.00 0.00 0.00 2.67
4406 6135 3.078837 TCCCTGTTTTACCTTCGATTGC 58.921 45.455 0.00 0.00 0.00 3.56
4407 6136 2.159572 CCCTGTTTTACCTTCGATTGCG 60.160 50.000 0.00 0.00 39.35 4.85
4408 6137 2.739913 CCTGTTTTACCTTCGATTGCGA 59.260 45.455 0.00 0.00 46.33 5.10
4421 6150 5.086888 TCGATTGCGATCATTTCATCAAG 57.913 39.130 14.39 0.00 42.51 3.02
4422 6151 3.662645 CGATTGCGATCATTTCATCAAGC 59.337 43.478 14.39 0.00 40.82 4.01
4423 6152 4.554134 CGATTGCGATCATTTCATCAAGCT 60.554 41.667 14.39 0.00 40.82 3.74
4424 6153 3.685836 TGCGATCATTTCATCAAGCTG 57.314 42.857 0.00 0.00 0.00 4.24
4425 6154 3.272581 TGCGATCATTTCATCAAGCTGA 58.727 40.909 0.00 0.00 0.00 4.26
4426 6155 3.690628 TGCGATCATTTCATCAAGCTGAA 59.309 39.130 0.00 0.00 33.42 3.02
4427 6156 4.156373 TGCGATCATTTCATCAAGCTGAAA 59.844 37.500 1.81 1.81 46.13 2.69
4428 6157 4.498323 GCGATCATTTCATCAAGCTGAAAC 59.502 41.667 1.37 0.00 45.21 2.78
4429 6158 5.633927 CGATCATTTCATCAAGCTGAAACA 58.366 37.500 1.37 0.00 45.21 2.83
4430 6159 6.088173 CGATCATTTCATCAAGCTGAAACAA 58.912 36.000 1.37 0.00 45.21 2.83
4431 6160 6.033196 CGATCATTTCATCAAGCTGAAACAAC 59.967 38.462 1.37 0.00 45.21 3.32
4432 6161 6.146601 TCATTTCATCAAGCTGAAACAACA 57.853 33.333 1.37 0.00 45.21 3.33
4433 6162 6.210796 TCATTTCATCAAGCTGAAACAACAG 58.789 36.000 1.37 0.00 45.21 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.008613 TCAAAACTTCTATGTGTGAACAGCC 59.991 40.000 0.00 0.00 0.00 4.85
13 14 7.011950 ACGAATCAAAACTTCTATGTGTGAACA 59.988 33.333 0.00 0.00 0.00 3.18
89 90 5.112686 AGAGTAGAATTTGCCGAATGAGAC 58.887 41.667 0.00 0.00 0.00 3.36
96 97 6.459670 TGTGTATAGAGTAGAATTTGCCGA 57.540 37.500 0.00 0.00 0.00 5.54
224 225 2.289694 CCAAGAATCAGAACCCACGAGT 60.290 50.000 0.00 0.00 0.00 4.18
254 255 5.365895 GGTATACCTACAGGAATCACACCTT 59.634 44.000 15.09 0.00 38.94 3.50
265 266 2.097110 TGGCCAGGTATACCTACAGG 57.903 55.000 24.15 20.91 46.65 4.00
266 267 2.303022 CCATGGCCAGGTATACCTACAG 59.697 54.545 24.15 16.13 46.65 2.74
271 272 1.074951 GCCCATGGCCAGGTATACC 59.925 63.158 17.55 14.54 44.06 2.73
272 273 4.821935 GCCCATGGCCAGGTATAC 57.178 61.111 17.55 0.00 44.06 1.47
302 303 4.760047 CCCGGGAGCAACGTCAGG 62.760 72.222 18.48 0.00 0.00 3.86
307 308 4.530857 CTAGGCCCGGGAGCAACG 62.531 72.222 29.31 2.11 0.00 4.10
311 312 0.819666 CAAAATCTAGGCCCGGGAGC 60.820 60.000 29.31 10.00 0.00 4.70
312 313 0.837272 TCAAAATCTAGGCCCGGGAG 59.163 55.000 29.31 13.93 0.00 4.30
316 317 2.707902 GGCTCAAAATCTAGGCCCG 58.292 57.895 0.00 0.00 37.12 6.13
319 320 1.943340 CTTCGGGCTCAAAATCTAGGC 59.057 52.381 0.00 0.00 37.55 3.93
320 321 2.565841 CCTTCGGGCTCAAAATCTAGG 58.434 52.381 0.00 0.00 0.00 3.02
364 1497 1.571919 CGAGCCCCTTCAGTAAATCG 58.428 55.000 0.00 0.00 0.00 3.34
365 1498 1.954927 CCGAGCCCCTTCAGTAAATC 58.045 55.000 0.00 0.00 0.00 2.17
366 1499 0.107165 GCCGAGCCCCTTCAGTAAAT 60.107 55.000 0.00 0.00 0.00 1.40
393 1526 0.040781 CACGTGTAAAAGCCCGTTGG 60.041 55.000 7.58 0.00 0.00 3.77
395 1528 0.816421 AGCACGTGTAAAAGCCCGTT 60.816 50.000 18.38 0.00 0.00 4.44
396 1529 1.227734 AGCACGTGTAAAAGCCCGT 60.228 52.632 18.38 0.00 0.00 5.28
397 1530 1.206578 CAGCACGTGTAAAAGCCCG 59.793 57.895 18.38 0.00 0.00 6.13
398 1531 1.170290 ACCAGCACGTGTAAAAGCCC 61.170 55.000 18.38 0.00 0.00 5.19
400 1533 0.941542 TGACCAGCACGTGTAAAAGC 59.058 50.000 18.38 0.54 0.00 3.51
401 1534 1.531149 CCTGACCAGCACGTGTAAAAG 59.469 52.381 18.38 7.65 0.00 2.27
402 1535 1.588674 CCTGACCAGCACGTGTAAAA 58.411 50.000 18.38 0.00 0.00 1.52
403 1536 0.882927 GCCTGACCAGCACGTGTAAA 60.883 55.000 18.38 0.00 0.00 2.01
404 1537 1.301401 GCCTGACCAGCACGTGTAA 60.301 57.895 18.38 0.00 0.00 2.41
405 1538 1.754380 AAGCCTGACCAGCACGTGTA 61.754 55.000 18.38 0.00 0.00 2.90
406 1539 3.106986 AAGCCTGACCAGCACGTGT 62.107 57.895 18.38 0.68 0.00 4.49
407 1540 2.281070 AAGCCTGACCAGCACGTG 60.281 61.111 12.28 12.28 0.00 4.49
408 1541 2.281070 CAAGCCTGACCAGCACGT 60.281 61.111 0.00 0.00 0.00 4.49
409 1542 3.052082 CCAAGCCTGACCAGCACG 61.052 66.667 0.00 0.00 0.00 5.34
410 1543 1.968540 GACCAAGCCTGACCAGCAC 60.969 63.158 0.00 0.00 0.00 4.40
411 1544 2.431683 GACCAAGCCTGACCAGCA 59.568 61.111 0.00 0.00 0.00 4.41
412 1545 2.360475 GGACCAAGCCTGACCAGC 60.360 66.667 0.00 0.00 0.00 4.85
413 1546 3.488423 AGGACCAAGCCTGACCAG 58.512 61.111 0.00 0.00 36.76 4.00
419 1552 3.054065 CCTAGAAAATCAGGACCAAGCCT 60.054 47.826 0.00 0.00 39.37 4.58
420 1553 3.282885 CCTAGAAAATCAGGACCAAGCC 58.717 50.000 0.00 0.00 33.42 4.35
421 1554 2.685388 GCCTAGAAAATCAGGACCAAGC 59.315 50.000 0.00 0.00 33.42 4.01
422 1555 3.282885 GGCCTAGAAAATCAGGACCAAG 58.717 50.000 0.00 0.00 33.38 3.61
423 1556 3.366052 GGCCTAGAAAATCAGGACCAA 57.634 47.619 0.00 0.00 33.38 3.67
426 1559 1.485066 TCGGGCCTAGAAAATCAGGAC 59.515 52.381 0.84 0.00 39.48 3.85
427 1560 1.485066 GTCGGGCCTAGAAAATCAGGA 59.515 52.381 0.84 0.00 33.42 3.86
428 1561 1.806623 CGTCGGGCCTAGAAAATCAGG 60.807 57.143 0.84 0.00 34.85 3.86
429 1562 1.571919 CGTCGGGCCTAGAAAATCAG 58.428 55.000 0.84 0.00 0.00 2.90
430 1563 0.461339 GCGTCGGGCCTAGAAAATCA 60.461 55.000 0.84 0.00 34.80 2.57
431 1564 2.308344 GCGTCGGGCCTAGAAAATC 58.692 57.895 0.84 0.00 34.80 2.17
432 1565 4.534401 GCGTCGGGCCTAGAAAAT 57.466 55.556 0.84 0.00 34.80 1.82
461 1594 3.669344 CTGAGGCCGGCGCAAAAA 61.669 61.111 22.54 1.23 36.38 1.94
462 1595 2.529454 TATCTGAGGCCGGCGCAAAA 62.529 55.000 22.54 12.14 36.38 2.44
463 1596 2.529454 TTATCTGAGGCCGGCGCAAA 62.529 55.000 22.54 8.55 36.38 3.68
464 1597 2.529454 TTTATCTGAGGCCGGCGCAA 62.529 55.000 22.54 11.94 36.38 4.85
465 1598 3.025189 TTTATCTGAGGCCGGCGCA 62.025 57.895 22.54 19.93 36.38 6.09
466 1599 2.203015 TTTATCTGAGGCCGGCGC 60.203 61.111 22.54 15.96 0.00 6.53
467 1600 1.887707 GGTTTATCTGAGGCCGGCG 60.888 63.158 22.54 6.52 0.00 6.46
468 1601 0.815615 CTGGTTTATCTGAGGCCGGC 60.816 60.000 21.18 21.18 0.00 6.13
469 1602 0.179045 CCTGGTTTATCTGAGGCCGG 60.179 60.000 0.00 0.00 0.00 6.13
470 1603 0.541863 ACCTGGTTTATCTGAGGCCG 59.458 55.000 0.00 0.00 0.00 6.13
471 1604 1.134068 GGACCTGGTTTATCTGAGGCC 60.134 57.143 0.00 0.00 0.00 5.19
472 1605 1.840635 AGGACCTGGTTTATCTGAGGC 59.159 52.381 0.00 0.00 0.00 4.70
473 1606 2.436173 GGAGGACCTGGTTTATCTGAGG 59.564 54.545 0.00 0.00 0.00 3.86
487 1620 5.552870 ACATAATGACATGTAGGAGGACC 57.447 43.478 0.00 0.00 37.37 4.46
494 1627 6.527722 GCAACCAACAACATAATGACATGTAG 59.472 38.462 0.00 0.00 38.19 2.74
499 1632 4.926140 TGCAACCAACAACATAATGACA 57.074 36.364 0.00 0.00 0.00 3.58
500 1633 7.881643 TTATTGCAACCAACAACATAATGAC 57.118 32.000 0.00 0.00 32.95 3.06
552 1685 6.265196 ACTTAGTGCAAATGAAACATCTCCAA 59.735 34.615 0.00 0.00 0.00 3.53
579 1713 0.174617 AACAAACAACACCCAAGCGG 59.825 50.000 0.00 0.00 37.81 5.52
605 1750 3.195825 CCTCCGATAACAAGAGGTTCAGT 59.804 47.826 0.00 0.00 41.96 3.41
710 2145 1.607801 GACTTGCTGCCCAAATCCCC 61.608 60.000 0.00 0.00 31.94 4.81
711 2146 1.607801 GGACTTGCTGCCCAAATCCC 61.608 60.000 0.00 0.00 42.58 3.85
779 2221 0.612732 ACATCAATGGTGGGCTGGTG 60.613 55.000 0.00 0.00 0.00 4.17
781 2223 0.612732 ACACATCAATGGTGGGCTGG 60.613 55.000 0.00 0.00 40.54 4.85
782 2224 2.019249 CTACACATCAATGGTGGGCTG 58.981 52.381 0.00 0.00 40.54 4.85
784 2226 2.017049 GACTACACATCAATGGTGGGC 58.983 52.381 0.00 0.00 40.54 5.36
785 2227 3.634397 AGACTACACATCAATGGTGGG 57.366 47.619 0.00 0.00 40.54 4.61
789 2231 4.256110 TCTGCAAGACTACACATCAATGG 58.744 43.478 0.00 0.00 38.67 3.16
813 2255 0.630673 TTTATCTGGCCTGGGTGCAT 59.369 50.000 10.07 0.00 0.00 3.96
834 2276 4.094294 CGACTTTCATCCGCCAAAAAGATA 59.906 41.667 0.00 0.00 33.85 1.98
899 2342 2.428530 CTGATCGAGTGGAGTGAATGGA 59.571 50.000 0.00 0.00 0.00 3.41
1297 2748 1.234615 CGAAGGCCACACAATTCCGT 61.235 55.000 5.01 0.00 0.00 4.69
1315 2766 3.725010 GCTTTTCTAAGTCCAATCGCACG 60.725 47.826 0.00 0.00 33.74 5.34
1327 2781 9.833182 GAGGAAAATGTTTCTAGCTTTTCTAAG 57.167 33.333 0.00 0.00 37.61 2.18
1328 2782 9.349713 TGAGGAAAATGTTTCTAGCTTTTCTAA 57.650 29.630 0.00 0.00 37.61 2.10
1330 2784 7.520614 CGTGAGGAAAATGTTTCTAGCTTTTCT 60.521 37.037 0.00 0.00 37.61 2.52
1351 2805 0.439985 CGACAGCATCAAACCGTGAG 59.560 55.000 0.00 0.00 40.43 3.51
1353 2807 1.497278 CCGACAGCATCAAACCGTG 59.503 57.895 0.00 0.00 0.00 4.94
1434 2888 3.476552 CCACCTTTCACTTGTCTGCTAA 58.523 45.455 0.00 0.00 0.00 3.09
1470 2924 6.540551 GGGAGCTACTCTTCAAATTTTCCTAG 59.459 42.308 0.00 0.00 0.00 3.02
1474 2928 4.399618 GGGGGAGCTACTCTTCAAATTTTC 59.600 45.833 0.00 0.00 0.00 2.29
1494 2948 2.044650 CTGCACATGGGTCAGGGG 60.045 66.667 10.49 0.00 0.00 4.79
1543 2999 3.248602 CACCGATTCTCCGAATTTCCATC 59.751 47.826 0.00 0.00 0.00 3.51
1544 3000 3.206150 CACCGATTCTCCGAATTTCCAT 58.794 45.455 0.00 0.00 0.00 3.41
1568 3024 2.300723 ACGCACCAGTTACACCAGAATA 59.699 45.455 0.00 0.00 0.00 1.75
1588 3044 1.039856 ACAATGGTTCCAAGGTGCAC 58.960 50.000 8.80 8.80 0.00 4.57
1591 3047 1.039068 TGCACAATGGTTCCAAGGTG 58.961 50.000 16.49 16.49 0.00 4.00
1635 3091 4.806330 ACACGTAGATCAATTCGACAACT 58.194 39.130 0.00 0.00 30.94 3.16
1641 3097 5.449113 GCAATTCAACACGTAGATCAATTCG 59.551 40.000 0.00 0.00 0.00 3.34
1655 3111 1.202463 CCCAAACACCGCAATTCAACA 60.202 47.619 0.00 0.00 0.00 3.33
1665 3121 4.596585 AGGCCCACCCAAACACCG 62.597 66.667 0.00 0.00 36.11 4.94
1678 3134 0.769247 ACGGTATATTGGGGAAGGCC 59.231 55.000 0.00 0.00 0.00 5.19
1695 3151 5.334414 GCCAAGCTATCAAAGAATATGGACG 60.334 44.000 0.00 0.00 0.00 4.79
1854 3310 0.988439 ACACGCTTTTTGCAACAACG 59.012 45.000 0.00 8.53 43.06 4.10
1951 3407 2.749621 GTTTGTTCAATCCATCGGAGCT 59.250 45.455 0.00 0.00 34.05 4.09
1969 3425 6.923199 AGATTTTGATTCATCAGGTGGTTT 57.077 33.333 0.00 0.00 38.19 3.27
2087 3543 5.255710 TGCTAAGAGCTCTACAGATTGTC 57.744 43.478 18.59 5.00 42.97 3.18
2109 3596 8.926092 AGTTGATTAAGACCTAAAGAAAAGCT 57.074 30.769 0.00 0.00 0.00 3.74
2162 3649 4.999950 GTCATAGGGTGATCATGAATGTCC 59.000 45.833 0.00 0.00 39.48 4.02
2180 3667 6.446909 TGGCAGATAATGGGTAATGTCATA 57.553 37.500 0.00 0.00 0.00 2.15
2181 3668 5.323382 TGGCAGATAATGGGTAATGTCAT 57.677 39.130 0.00 0.00 0.00 3.06
2191 3678 9.305925 GTTCTTTATTTTCTTGGCAGATAATGG 57.694 33.333 10.48 4.62 33.92 3.16
2286 3773 9.284968 GCCATAACAGATGTTGGTATTAGTATT 57.715 33.333 8.46 0.00 37.60 1.89
2287 3774 8.660435 AGCCATAACAGATGTTGGTATTAGTAT 58.340 33.333 8.46 0.00 37.60 2.12
2288 3775 7.931407 CAGCCATAACAGATGTTGGTATTAGTA 59.069 37.037 8.46 0.00 37.60 1.82
2289 3776 6.767902 CAGCCATAACAGATGTTGGTATTAGT 59.232 38.462 8.46 0.00 37.60 2.24
2304 3791 1.677576 GCATTAGCAGCAGCCATAACA 59.322 47.619 0.00 0.00 43.56 2.41
2305 3792 1.952296 AGCATTAGCAGCAGCCATAAC 59.048 47.619 0.00 0.00 45.49 1.89
2369 3858 2.225491 TGCAACGCCTAATTGAAGACAC 59.775 45.455 0.00 0.00 0.00 3.67
2441 3930 6.648879 TTTCTTGGAACCTTACATTTGGAG 57.351 37.500 0.00 0.00 0.00 3.86
2442 3931 7.610580 ATTTTCTTGGAACCTTACATTTGGA 57.389 32.000 0.00 0.00 0.00 3.53
2443 3932 9.942850 AATATTTTCTTGGAACCTTACATTTGG 57.057 29.630 0.00 0.00 0.00 3.28
2499 3996 2.463047 AGGTACCAGAGAGGATCCAC 57.537 55.000 15.82 8.01 41.22 4.02
2590 4089 6.486657 TGTGAAACTCTCTTGAAGGGTATTTG 59.513 38.462 0.00 0.00 37.91 2.32
2642 4141 6.038356 TGCTTTGCTTCTCTTTTCTTTTCAG 58.962 36.000 0.00 0.00 0.00 3.02
2741 4240 7.732593 ACTTGGATCTACTAATAGCTCCTGATT 59.267 37.037 3.04 0.00 42.18 2.57
2755 4254 2.906389 TGCAGGAACACTTGGATCTACT 59.094 45.455 0.00 0.00 0.00 2.57
2793 4292 2.343758 GGTGTGCTGCTTCTCCGA 59.656 61.111 0.00 0.00 0.00 4.55
2794 4293 2.031012 TGGTGTGCTGCTTCTCCG 59.969 61.111 0.00 0.00 0.00 4.63
2805 4304 1.805869 CTTCTGAGGAAGCTGGTGTG 58.194 55.000 0.00 0.00 41.80 3.82
3169 4668 1.229464 ACCAGCCTTCTCCAGCTCT 60.229 57.895 0.00 0.00 37.18 4.09
3214 4713 3.304391 CGAAGAATCTCAGATCCTCGGTC 60.304 52.174 5.48 0.00 0.00 4.79
3223 4722 0.537188 GCCCCACGAAGAATCTCAGA 59.463 55.000 0.00 0.00 0.00 3.27
3349 4848 1.216710 CTCGGTCCAGAGGCAAGAC 59.783 63.158 3.57 0.00 34.74 3.01
3427 4926 2.872557 CGGAGCGACACCTACGAA 59.127 61.111 0.00 0.00 41.70 3.85
3514 5013 1.073177 CGCCGTAAACGACTTTCCAT 58.927 50.000 3.65 0.00 43.02 3.41
3520 5019 1.391144 GCATTTACGCCGTAAACGACT 59.609 47.619 23.19 6.19 40.16 4.18
3521 5020 1.391144 AGCATTTACGCCGTAAACGAC 59.609 47.619 23.19 15.32 40.16 4.34
3522 5021 1.712401 AGCATTTACGCCGTAAACGA 58.288 45.000 23.19 3.42 40.16 3.85
3540 5039 7.320797 GCTTATTACAGTACGAACGAGTCATAG 59.679 40.741 0.14 0.00 0.00 2.23
3545 5044 5.557891 AGCTTATTACAGTACGAACGAGT 57.442 39.130 0.14 0.00 0.00 4.18
3546 5045 6.307318 ACAAAGCTTATTACAGTACGAACGAG 59.693 38.462 0.00 0.00 0.00 4.18
3607 5106 4.453480 TCCAGATTTCCAGTGAAAACCT 57.547 40.909 0.00 0.00 43.37 3.50
3619 5118 7.386025 CCATGAAGGAAAAAGTTTCCAGATTTC 59.614 37.037 19.27 14.33 41.00 2.17
3632 5131 5.271598 AGCATATGGACCATGAAGGAAAAA 58.728 37.500 17.73 0.00 41.22 1.94
3633 5132 4.870636 AGCATATGGACCATGAAGGAAAA 58.129 39.130 17.73 0.00 41.22 2.29
3634 5133 4.464008 GAGCATATGGACCATGAAGGAAA 58.536 43.478 17.73 0.00 41.22 3.13
3682 5181 1.958205 CCGCCTATGCAGCAGTAGC 60.958 63.158 0.00 2.04 42.56 3.58
3683 5182 1.958205 GCCGCCTATGCAGCAGTAG 60.958 63.158 0.00 3.28 40.71 2.57
3710 5209 4.634883 CAGCTTCAACACTATGCAGAATCT 59.365 41.667 0.00 0.00 0.00 2.40
3711 5210 4.201891 CCAGCTTCAACACTATGCAGAATC 60.202 45.833 0.00 0.00 0.00 2.52
3722 5221 6.210287 ACTATACTACTCCAGCTTCAACAC 57.790 41.667 0.00 0.00 0.00 3.32
3757 5256 2.356125 GGGCCAAGCTCTTCTGATAACA 60.356 50.000 4.39 0.00 0.00 2.41
3829 5328 5.887035 AGCGGACAGGGTATATACTAATCTC 59.113 44.000 12.54 2.24 0.00 2.75
3841 5340 3.066190 CGGACAGCGGACAGGGTA 61.066 66.667 0.00 0.00 0.00 3.69
3872 5401 0.891449 TTTCGGGCCGATGAAAAGCA 60.891 50.000 31.59 9.34 35.23 3.91
3887 5416 3.303791 CCGGAAGACAAAAGGTTCTTTCG 60.304 47.826 0.00 5.25 39.95 3.46
3907 5436 0.031585 TGACACGACAGAAGGTTCCG 59.968 55.000 0.00 0.00 0.00 4.30
4049 5774 0.812811 CCACTCGTGAGATGCATGGG 60.813 60.000 2.46 0.00 40.01 4.00
4069 5794 1.728971 GTTCGTGAACCAGATGCAGAG 59.271 52.381 1.21 0.00 35.36 3.35
4187 5912 3.094484 ACTCCAAAGTTGTGAAACCCA 57.906 42.857 0.00 0.00 34.36 4.51
4209 5934 0.875059 GACCTGTGCCAAAGTGTAGC 59.125 55.000 0.00 0.00 0.00 3.58
4221 5946 1.595882 CTGGCTGAGAGGACCTGTG 59.404 63.158 0.00 0.00 0.00 3.66
4224 5949 2.686835 GGCTGGCTGAGAGGACCT 60.687 66.667 0.00 0.00 0.00 3.85
4246 5975 1.408702 GTGGTGCAATTTGTGTGACCT 59.591 47.619 0.00 0.00 34.53 3.85
4247 5976 1.537990 GGTGGTGCAATTTGTGTGACC 60.538 52.381 0.00 0.00 34.20 4.02
4248 5977 1.408702 AGGTGGTGCAATTTGTGTGAC 59.591 47.619 0.00 0.00 0.00 3.67
4249 5978 1.680735 GAGGTGGTGCAATTTGTGTGA 59.319 47.619 0.00 0.00 0.00 3.58
4250 5979 1.269726 GGAGGTGGTGCAATTTGTGTG 60.270 52.381 0.00 0.00 0.00 3.82
4251 5980 1.039856 GGAGGTGGTGCAATTTGTGT 58.960 50.000 0.00 0.00 0.00 3.72
4252 5981 1.039068 TGGAGGTGGTGCAATTTGTG 58.961 50.000 0.00 0.00 0.00 3.33
4253 5982 1.039856 GTGGAGGTGGTGCAATTTGT 58.960 50.000 0.00 0.00 0.00 2.83
4254 5983 1.039068 TGTGGAGGTGGTGCAATTTG 58.961 50.000 0.00 0.00 0.00 2.32
4255 5984 1.039856 GTGTGGAGGTGGTGCAATTT 58.960 50.000 0.00 0.00 0.00 1.82
4256 5985 0.106268 TGTGTGGAGGTGGTGCAATT 60.106 50.000 0.00 0.00 0.00 2.32
4257 5986 0.112995 ATGTGTGGAGGTGGTGCAAT 59.887 50.000 0.00 0.00 0.00 3.56
4258 5987 0.537143 GATGTGTGGAGGTGGTGCAA 60.537 55.000 0.00 0.00 0.00 4.08
4308 6037 3.559238 AAAAGAACACGGATGCACATC 57.441 42.857 1.86 1.86 37.11 3.06
4333 6062 3.189080 CGGATGCACATCACTCTCAAAAA 59.811 43.478 12.43 0.00 39.54 1.94
4334 6063 2.743664 CGGATGCACATCACTCTCAAAA 59.256 45.455 12.43 0.00 39.54 2.44
4335 6064 2.289631 ACGGATGCACATCACTCTCAAA 60.290 45.455 12.43 0.00 39.54 2.69
4336 6065 1.276138 ACGGATGCACATCACTCTCAA 59.724 47.619 12.43 0.00 39.54 3.02
4337 6066 0.897621 ACGGATGCACATCACTCTCA 59.102 50.000 12.43 0.00 39.54 3.27
4338 6067 1.284657 CACGGATGCACATCACTCTC 58.715 55.000 12.43 0.00 39.54 3.20
4339 6068 0.610174 ACACGGATGCACATCACTCT 59.390 50.000 12.43 0.00 39.54 3.24
4340 6069 1.129251 CAACACGGATGCACATCACTC 59.871 52.381 12.43 0.00 39.54 3.51
4341 6070 1.159285 CAACACGGATGCACATCACT 58.841 50.000 12.43 0.00 39.54 3.41
4342 6071 0.168788 CCAACACGGATGCACATCAC 59.831 55.000 12.43 1.81 39.54 3.06
4343 6072 0.036022 TCCAACACGGATGCACATCA 59.964 50.000 12.43 0.00 39.64 3.07
4344 6073 0.729116 CTCCAACACGGATGCACATC 59.271 55.000 1.86 1.86 45.19 3.06
4345 6074 1.308069 GCTCCAACACGGATGCACAT 61.308 55.000 0.00 0.00 45.19 3.21
4346 6075 1.965930 GCTCCAACACGGATGCACA 60.966 57.895 0.00 0.00 45.19 4.57
4347 6076 1.965930 TGCTCCAACACGGATGCAC 60.966 57.895 0.00 0.00 45.19 4.57
4348 6077 1.965930 GTGCTCCAACACGGATGCA 60.966 57.895 0.00 0.00 45.19 3.96
4349 6078 1.672356 AGTGCTCCAACACGGATGC 60.672 57.895 0.00 0.00 45.19 3.91
4350 6079 0.320683 TCAGTGCTCCAACACGGATG 60.321 55.000 0.00 0.00 45.19 3.51
4351 6080 0.036952 CTCAGTGCTCCAACACGGAT 60.037 55.000 0.00 0.00 45.19 4.18
4352 6081 1.367471 CTCAGTGCTCCAACACGGA 59.633 57.895 0.00 0.00 45.45 4.69
4353 6082 2.320587 GCTCAGTGCTCCAACACGG 61.321 63.158 0.00 0.00 45.45 4.94
4354 6083 2.661566 CGCTCAGTGCTCCAACACG 61.662 63.158 0.00 0.00 45.45 4.49
4355 6084 2.959357 GCGCTCAGTGCTCCAACAC 61.959 63.158 1.89 0.00 41.02 3.32
4356 6085 2.666190 GCGCTCAGTGCTCCAACA 60.666 61.111 1.89 0.00 40.11 3.33
4357 6086 1.975363 GATGCGCTCAGTGCTCCAAC 61.975 60.000 12.40 0.00 40.03 3.77
4358 6087 1.742880 GATGCGCTCAGTGCTCCAA 60.743 57.895 12.40 0.00 40.03 3.53
4359 6088 2.125391 GATGCGCTCAGTGCTCCA 60.125 61.111 12.40 0.00 40.03 3.86
4360 6089 3.260483 CGATGCGCTCAGTGCTCC 61.260 66.667 12.40 2.06 40.03 4.70
4371 6100 4.933064 GGGACGGAGAGCGATGCG 62.933 72.222 3.74 3.74 40.19 4.73
4372 6101 3.532155 AGGGACGGAGAGCGATGC 61.532 66.667 0.00 0.00 0.00 3.91
4373 6102 1.949847 AACAGGGACGGAGAGCGATG 61.950 60.000 0.00 0.00 0.00 3.84
4374 6103 1.258445 AAACAGGGACGGAGAGCGAT 61.258 55.000 0.00 0.00 0.00 4.58
4375 6104 1.469335 AAAACAGGGACGGAGAGCGA 61.469 55.000 0.00 0.00 0.00 4.93
4376 6105 0.245539 TAAAACAGGGACGGAGAGCG 59.754 55.000 0.00 0.00 0.00 5.03
4377 6106 1.675116 GGTAAAACAGGGACGGAGAGC 60.675 57.143 0.00 0.00 0.00 4.09
4378 6107 1.900486 AGGTAAAACAGGGACGGAGAG 59.100 52.381 0.00 0.00 0.00 3.20
4379 6108 2.019807 AGGTAAAACAGGGACGGAGA 57.980 50.000 0.00 0.00 0.00 3.71
4380 6109 2.696506 GAAGGTAAAACAGGGACGGAG 58.303 52.381 0.00 0.00 0.00 4.63
4381 6110 1.001181 CGAAGGTAAAACAGGGACGGA 59.999 52.381 0.00 0.00 0.00 4.69
4382 6111 1.001181 TCGAAGGTAAAACAGGGACGG 59.999 52.381 0.00 0.00 0.00 4.79
4383 6112 2.443887 TCGAAGGTAAAACAGGGACG 57.556 50.000 0.00 0.00 0.00 4.79
4384 6113 3.119955 GCAATCGAAGGTAAAACAGGGAC 60.120 47.826 0.00 0.00 0.00 4.46
4385 6114 3.078837 GCAATCGAAGGTAAAACAGGGA 58.921 45.455 0.00 0.00 0.00 4.20
4386 6115 2.159572 CGCAATCGAAGGTAAAACAGGG 60.160 50.000 0.00 0.00 38.10 4.45
4387 6116 2.739913 TCGCAATCGAAGGTAAAACAGG 59.260 45.455 0.00 0.00 42.44 4.00
4400 6129 3.662645 GCTTGATGAAATGATCGCAATCG 59.337 43.478 0.00 0.00 34.39 3.34
4401 6130 4.675565 CAGCTTGATGAAATGATCGCAATC 59.324 41.667 0.00 0.00 0.00 2.67
4402 6131 4.337274 TCAGCTTGATGAAATGATCGCAAT 59.663 37.500 0.00 0.00 0.00 3.56
4403 6132 3.690628 TCAGCTTGATGAAATGATCGCAA 59.309 39.130 0.00 0.00 0.00 4.85
4404 6133 3.272581 TCAGCTTGATGAAATGATCGCA 58.727 40.909 0.00 0.00 0.00 5.10
4405 6134 3.957671 TCAGCTTGATGAAATGATCGC 57.042 42.857 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.