Multiple sequence alignment - TraesCS4D01G280400

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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 TraesCS4D01G280400 chr4D 100.000 4835 0 0 1 4835 451290538 451285704 0.000000e+00 8929.0
1 TraesCS4D01G280400 chr4A 92.814 1642 43 14 2571 4200 15649271 15650849 0.000000e+00 2309.0
2 TraesCS4D01G280400 chr4A 94.619 762 30 4 547 1298 15647153 15647913 0.000000e+00 1170.0
3 TraesCS4D01G280400 chr4A 89.514 658 49 10 1920 2574 15648607 15649247 0.000000e+00 815.0
4 TraesCS4D01G280400 chr4A 86.929 482 50 11 89 563 15646663 15647138 3.310000e-146 529.0
5 TraesCS4D01G280400 chr4A 95.098 102 5 0 1505 1606 15648276 15648377 1.390000e-35 161.0
6 TraesCS4D01G280400 chr4A 90.526 95 5 1 1 91 15646370 15646464 6.570000e-24 122.0
7 TraesCS4D01G280400 chr4B 94.039 1124 39 13 3000 4117 564871985 564870884 0.000000e+00 1679.0
8 TraesCS4D01G280400 chr4B 88.900 964 52 25 353 1288 564875042 564874106 0.000000e+00 1136.0
9 TraesCS4D01G280400 chr4B 94.944 178 7 2 1 177 564880164 564879988 1.330000e-70 278.0
10 TraesCS4D01G280400 chr4B 86.387 191 11 6 169 354 564875347 564875167 1.370000e-45 195.0
11 TraesCS4D01G280400 chr6D 95.039 645 20 4 4201 4835 84301324 84301966 0.000000e+00 1003.0
12 TraesCS4D01G280400 chr6D 85.532 235 21 8 4201 4426 320674449 320674219 2.910000e-57 233.0
13 TraesCS4D01G280400 chr6D 88.112 143 12 4 1605 1745 178852318 178852179 1.080000e-36 165.0
14 TraesCS4D01G280400 chr3B 92.879 646 34 4 4201 4835 589554534 589553890 0.000000e+00 928.0
15 TraesCS4D01G280400 chr3B 91.538 650 28 10 4198 4835 25224884 25225518 0.000000e+00 870.0
16 TraesCS4D01G280400 chr5A 91.834 649 37 7 4199 4835 277843657 277844301 0.000000e+00 891.0
17 TraesCS4D01G280400 chr5A 82.296 514 58 17 4193 4682 580326219 580325715 9.680000e-112 414.0
18 TraesCS4D01G280400 chr5D 89.297 654 46 10 4201 4835 284193394 284192746 0.000000e+00 798.0
19 TraesCS4D01G280400 chr7A 89.094 651 53 6 4201 4834 711962589 711963238 0.000000e+00 793.0
20 TraesCS4D01G280400 chr7A 86.364 330 29 10 4201 4527 3052468 3052152 3.580000e-91 346.0
21 TraesCS4D01G280400 chr7A 86.111 324 12 4 4529 4834 3039522 3039214 7.810000e-83 318.0
22 TraesCS4D01G280400 chr1A 86.000 650 58 13 4207 4835 532322413 532321776 0.000000e+00 665.0
23 TraesCS4D01G280400 chr1A 92.683 123 9 0 1601 1723 65267155 65267033 1.380000e-40 178.0
24 TraesCS4D01G280400 chr5B 88.312 231 25 2 4201 4430 322173916 322173687 4.770000e-70 276.0
25 TraesCS4D01G280400 chr5B 91.603 131 8 3 1593 1722 31114746 31114618 1.380000e-40 178.0
26 TraesCS4D01G280400 chr5B 79.042 167 30 5 165 329 14249181 14249018 5.120000e-20 110.0
27 TraesCS4D01G280400 chr2A 82.372 312 35 10 4387 4680 770927564 770927255 2.230000e-63 254.0
28 TraesCS4D01G280400 chr2D 93.548 124 7 1 1600 1723 109700470 109700348 2.970000e-42 183.0
29 TraesCS4D01G280400 chr2D 92.742 124 9 0 1605 1728 586154926 586154803 3.840000e-41 180.0
30 TraesCS4D01G280400 chr6B 94.118 119 7 0 1604 1722 231349959 231349841 1.070000e-41 182.0
31 TraesCS4D01G280400 chr7B 92.188 128 9 1 1595 1722 81424980 81425106 3.840000e-41 180.0
32 TraesCS4D01G280400 chr7B 84.043 94 11 4 4464 4554 644447847 644447939 2.400000e-13 87.9
33 TraesCS4D01G280400 chr2B 90.769 130 11 1 1601 1729 712963795 712963666 6.430000e-39 172.0
34 TraesCS4D01G280400 chr2B 92.857 42 3 0 459 500 284067162 284067203 1.450000e-05 62.1
35 TraesCS4D01G280400 chr3A 89.630 135 13 1 1598 1731 522176553 522176687 2.310000e-38 171.0
36 TraesCS4D01G280400 chrUn 86.364 66 7 2 435 499 290654907 290654843 2.410000e-08 71.3


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 TraesCS4D01G280400 chr4D 451285704 451290538 4834 True 8929.000000 8929 100.000000 1 4835 1 chr4D.!!$R1 4834
1 TraesCS4D01G280400 chr4A 15646370 15650849 4479 False 851.000000 2309 91.583333 1 4200 6 chr4A.!!$F1 4199
2 TraesCS4D01G280400 chr4B 564870884 564875347 4463 True 1003.333333 1679 89.775333 169 4117 3 chr4B.!!$R2 3948
3 TraesCS4D01G280400 chr6D 84301324 84301966 642 False 1003.000000 1003 95.039000 4201 4835 1 chr6D.!!$F1 634
4 TraesCS4D01G280400 chr3B 589553890 589554534 644 True 928.000000 928 92.879000 4201 4835 1 chr3B.!!$R1 634
5 TraesCS4D01G280400 chr3B 25224884 25225518 634 False 870.000000 870 91.538000 4198 4835 1 chr3B.!!$F1 637
6 TraesCS4D01G280400 chr5A 277843657 277844301 644 False 891.000000 891 91.834000 4199 4835 1 chr5A.!!$F1 636
7 TraesCS4D01G280400 chr5A 580325715 580326219 504 True 414.000000 414 82.296000 4193 4682 1 chr5A.!!$R1 489
8 TraesCS4D01G280400 chr5D 284192746 284193394 648 True 798.000000 798 89.297000 4201 4835 1 chr5D.!!$R1 634
9 TraesCS4D01G280400 chr7A 711962589 711963238 649 False 793.000000 793 89.094000 4201 4834 1 chr7A.!!$F1 633
10 TraesCS4D01G280400 chr1A 532321776 532322413 637 True 665.000000 665 86.000000 4207 4835 1 chr1A.!!$R2 628

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
996 1373 1.112950 GCTACTTCTAGGCGGAGGTT 58.887 55.0 4.06 0.0 0.00 3.50 F
1339 1816 0.028770 TGCTGCCGAAACGTTTTCTG 59.971 50.0 15.89 11.9 0.00 3.02 F
1967 2696 0.107017 CAATTCCGGCCAGATGGAGT 60.107 55.0 2.24 0.0 37.39 3.85 F
2341 3075 0.107848 CATAACGTCTCACCACCCCC 60.108 60.0 0.00 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2723 0.036010 CCAGTCTCGGCCTTGTTGAT 60.036 55.0 0.00 0.0 0.00 2.57 R
2257 2991 0.463833 GGGGGTGCTTCTTCGTATGG 60.464 60.0 0.00 0.0 0.00 2.74 R
3045 4384 0.600518 TCCAAAACCACGCGATCGAA 60.601 50.0 21.57 0.0 39.41 3.71 R
3965 5307 1.769733 TAACACGTACGCTTCACACC 58.230 50.0 16.72 0.0 0.00 4.16 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
84 89 5.431765 AGATAAAATGTGAGTCAAGCCGAT 58.568 37.500 0.00 0.00 0.00 4.18
91 96 5.339008 TGTGAGTCAAGCCGATAGTTTAT 57.661 39.130 0.00 0.00 0.00 1.40
130 336 7.819415 AGCTTCCCTTACAAAGAAAAATATTGC 59.181 33.333 0.00 0.00 0.00 3.56
246 453 5.860716 GGAGACAGAAACATGAAGAAAATGC 59.139 40.000 0.00 0.00 0.00 3.56
247 454 6.294397 GGAGACAGAAACATGAAGAAAATGCT 60.294 38.462 0.00 0.00 0.00 3.79
291 498 5.357742 TGTTCTCTTAGCTGCAATATCCA 57.642 39.130 1.02 0.00 0.00 3.41
298 505 7.179872 TCTCTTAGCTGCAATATCCATCACTAT 59.820 37.037 1.02 0.00 0.00 2.12
418 757 6.686484 AGATAACATATCTATGTGTGCCCA 57.314 37.500 3.70 0.00 45.55 5.36
420 759 3.777106 ACATATCTATGTGTGCCCAGG 57.223 47.619 2.10 0.00 44.66 4.45
424 763 1.656587 TCTATGTGTGCCCAGGAAGT 58.343 50.000 0.00 0.00 0.00 3.01
430 769 2.640332 TGTGTGCCCAGGAAGTTATACA 59.360 45.455 0.00 0.00 0.00 2.29
456 795 9.950496 ATCATCCTATCCATATTAATTATCGCC 57.050 33.333 0.00 0.00 0.00 5.54
467 807 6.627395 ATTAATTATCGCCCAAACGAATGA 57.373 33.333 0.00 0.00 46.59 2.57
553 927 5.185828 GCAAAAATATGACTTGGAAGGGAGT 59.814 40.000 0.00 0.00 0.00 3.85
573 947 4.296690 AGTAGTAGTTTTGACGTGCAGAC 58.703 43.478 0.00 0.00 0.00 3.51
586 960 2.313172 GCAGACGCGCCATCCATAG 61.313 63.158 5.73 0.00 0.00 2.23
920 1296 2.802667 CGCCATCGACGGAAGCAAG 61.803 63.158 0.00 0.00 38.10 4.01
996 1373 1.112950 GCTACTTCTAGGCGGAGGTT 58.887 55.000 4.06 0.00 0.00 3.50
1144 1527 1.216930 ACCAGGTAAACCCAAGCACTT 59.783 47.619 0.00 0.00 36.42 3.16
1146 1529 3.081804 CCAGGTAAACCCAAGCACTTAG 58.918 50.000 0.00 0.00 36.42 2.18
1150 1533 4.227527 AGGTAAACCCAAGCACTTAGCTAT 59.772 41.667 0.00 0.00 45.84 2.97
1151 1534 5.861778 AGGTAAACCCAAGCACTTAGCTATG 60.862 44.000 5.13 5.13 45.84 2.23
1189 1598 0.463833 GGACGATGGGGGATGTGAAC 60.464 60.000 0.00 0.00 0.00 3.18
1191 1600 1.261938 ACGATGGGGGATGTGAACGA 61.262 55.000 0.00 0.00 0.00 3.85
1310 1729 5.562506 TCAGTTAGAACATACGACCTCTG 57.437 43.478 0.00 0.00 0.00 3.35
1321 1740 3.252974 ACGACCTCTGCTTCCTAAATG 57.747 47.619 0.00 0.00 0.00 2.32
1322 1741 1.936547 CGACCTCTGCTTCCTAAATGC 59.063 52.381 0.00 0.00 0.00 3.56
1327 1804 0.379669 CTGCTTCCTAAATGCTGCCG 59.620 55.000 0.00 0.00 0.00 5.69
1337 1814 1.766069 AATGCTGCCGAAACGTTTTC 58.234 45.000 15.89 8.28 0.00 2.29
1339 1816 0.028770 TGCTGCCGAAACGTTTTCTG 59.971 50.000 15.89 11.90 0.00 3.02
1344 1821 3.942739 TGCCGAAACGTTTTCTGTTTAG 58.057 40.909 15.89 0.00 39.51 1.85
1387 1881 8.202461 AGATTTCATTCAATATACCCGGTCTA 57.798 34.615 0.00 0.00 0.00 2.59
1389 1883 9.449719 GATTTCATTCAATATACCCGGTCTAAT 57.550 33.333 0.00 0.00 0.00 1.73
1390 1884 8.615878 TTTCATTCAATATACCCGGTCTAATG 57.384 34.615 0.00 0.00 0.00 1.90
1391 1885 6.707290 TCATTCAATATACCCGGTCTAATGG 58.293 40.000 0.00 0.00 0.00 3.16
1392 1886 6.499000 TCATTCAATATACCCGGTCTAATGGA 59.501 38.462 0.00 0.00 0.00 3.41
1438 1944 6.315642 TCGTTTAGAGTAGTTCAGATCGTCAT 59.684 38.462 0.00 0.00 0.00 3.06
1446 1952 2.995939 GTTCAGATCGTCATGCAAGACA 59.004 45.455 20.91 9.31 38.43 3.41
1455 1961 2.291465 GTCATGCAAGACAGTTTCTGCA 59.709 45.455 16.82 7.40 40.43 4.41
1456 1962 2.291465 TCATGCAAGACAGTTTCTGCAC 59.709 45.455 7.17 0.00 39.58 4.57
1457 1963 2.042686 TGCAAGACAGTTTCTGCACT 57.957 45.000 1.98 0.00 35.04 4.40
1458 1964 1.942657 TGCAAGACAGTTTCTGCACTC 59.057 47.619 1.98 0.00 35.04 3.51
1459 1965 1.942657 GCAAGACAGTTTCTGCACTCA 59.057 47.619 0.00 0.00 34.37 3.41
1460 1966 2.551459 GCAAGACAGTTTCTGCACTCAT 59.449 45.455 0.00 0.00 34.37 2.90
1461 1967 3.364764 GCAAGACAGTTTCTGCACTCATC 60.365 47.826 0.00 0.00 34.37 2.92
1462 1968 3.758755 AGACAGTTTCTGCACTCATCA 57.241 42.857 0.00 0.00 34.37 3.07
1463 1969 4.283363 AGACAGTTTCTGCACTCATCAT 57.717 40.909 0.00 0.00 34.37 2.45
1464 1970 4.649692 AGACAGTTTCTGCACTCATCATT 58.350 39.130 0.00 0.00 34.37 2.57
1465 1971 5.068636 AGACAGTTTCTGCACTCATCATTT 58.931 37.500 0.00 0.00 34.37 2.32
1466 1972 5.180868 AGACAGTTTCTGCACTCATCATTTC 59.819 40.000 0.00 0.00 34.37 2.17
1467 1973 4.823442 ACAGTTTCTGCACTCATCATTTCA 59.177 37.500 0.00 0.00 34.37 2.69
1468 1974 5.475909 ACAGTTTCTGCACTCATCATTTCAT 59.524 36.000 0.00 0.00 34.37 2.57
1469 1975 6.656270 ACAGTTTCTGCACTCATCATTTCATA 59.344 34.615 0.00 0.00 34.37 2.15
1470 1976 7.148289 ACAGTTTCTGCACTCATCATTTCATAG 60.148 37.037 0.00 0.00 34.37 2.23
1471 1977 7.065443 CAGTTTCTGCACTCATCATTTCATAGA 59.935 37.037 0.00 0.00 0.00 1.98
1472 1978 7.774157 AGTTTCTGCACTCATCATTTCATAGAT 59.226 33.333 0.00 0.00 0.00 1.98
1473 1979 7.725818 TTCTGCACTCATCATTTCATAGATC 57.274 36.000 0.00 0.00 0.00 2.75
1474 1980 6.823497 TCTGCACTCATCATTTCATAGATCA 58.177 36.000 0.00 0.00 0.00 2.92
1475 1981 7.450903 TCTGCACTCATCATTTCATAGATCAT 58.549 34.615 0.00 0.00 0.00 2.45
1476 1982 7.937394 TCTGCACTCATCATTTCATAGATCATT 59.063 33.333 0.00 0.00 0.00 2.57
1477 1983 9.216117 CTGCACTCATCATTTCATAGATCATTA 57.784 33.333 0.00 0.00 0.00 1.90
1478 1984 9.563748 TGCACTCATCATTTCATAGATCATTAA 57.436 29.630 0.00 0.00 0.00 1.40
1609 2300 7.379098 GCAAAGGCCATATATTAAGTACTCC 57.621 40.000 5.01 0.00 0.00 3.85
1610 2301 6.374613 GCAAAGGCCATATATTAAGTACTCCC 59.625 42.308 5.01 0.00 0.00 4.30
1611 2302 7.690256 CAAAGGCCATATATTAAGTACTCCCT 58.310 38.462 5.01 0.00 0.00 4.20
1612 2303 7.497773 AAGGCCATATATTAAGTACTCCCTC 57.502 40.000 5.01 0.00 0.00 4.30
1613 2304 5.965091 AGGCCATATATTAAGTACTCCCTCC 59.035 44.000 5.01 0.00 0.00 4.30
1614 2305 5.724854 GGCCATATATTAAGTACTCCCTCCA 59.275 44.000 0.00 0.00 0.00 3.86
1615 2306 6.387220 GGCCATATATTAAGTACTCCCTCCAT 59.613 42.308 0.00 0.00 0.00 3.41
1616 2307 7.419172 GGCCATATATTAAGTACTCCCTCCATC 60.419 44.444 0.00 0.00 0.00 3.51
1617 2308 7.419172 GCCATATATTAAGTACTCCCTCCATCC 60.419 44.444 0.00 0.00 0.00 3.51
1618 2309 7.201920 CCATATATTAAGTACTCCCTCCATCCG 60.202 44.444 0.00 0.00 0.00 4.18
1619 2310 3.675348 TTAAGTACTCCCTCCATCCGA 57.325 47.619 0.00 0.00 0.00 4.55
1620 2311 2.544844 AAGTACTCCCTCCATCCGAA 57.455 50.000 0.00 0.00 0.00 4.30
1621 2312 2.544844 AGTACTCCCTCCATCCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
1622 2313 2.829023 AGTACTCCCTCCATCCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
1623 2314 3.178865 AGTACTCCCTCCATCCGAAAAA 58.821 45.455 0.00 0.00 0.00 1.94
1624 2315 2.789409 ACTCCCTCCATCCGAAAAAG 57.211 50.000 0.00 0.00 0.00 2.27
1625 2316 1.340114 ACTCCCTCCATCCGAAAAAGC 60.340 52.381 0.00 0.00 0.00 3.51
1626 2317 0.991920 TCCCTCCATCCGAAAAAGCT 59.008 50.000 0.00 0.00 0.00 3.74
1627 2318 1.354368 TCCCTCCATCCGAAAAAGCTT 59.646 47.619 0.00 0.00 0.00 3.74
1628 2319 1.474077 CCCTCCATCCGAAAAAGCTTG 59.526 52.381 0.00 0.00 0.00 4.01
1629 2320 2.162681 CCTCCATCCGAAAAAGCTTGT 58.837 47.619 0.00 0.00 0.00 3.16
1630 2321 2.162408 CCTCCATCCGAAAAAGCTTGTC 59.838 50.000 0.00 0.00 0.00 3.18
1631 2322 2.159382 TCCATCCGAAAAAGCTTGTCC 58.841 47.619 0.00 0.00 0.00 4.02
1632 2323 1.202348 CCATCCGAAAAAGCTTGTCCC 59.798 52.381 0.00 0.00 0.00 4.46
1633 2324 1.885887 CATCCGAAAAAGCTTGTCCCA 59.114 47.619 0.00 0.00 0.00 4.37
1634 2325 2.060050 TCCGAAAAAGCTTGTCCCAA 57.940 45.000 0.00 0.00 0.00 4.12
1635 2326 2.379972 TCCGAAAAAGCTTGTCCCAAA 58.620 42.857 0.00 0.00 0.00 3.28
1636 2327 2.100087 TCCGAAAAAGCTTGTCCCAAAC 59.900 45.455 0.00 0.00 0.00 2.93
1637 2328 2.100749 CCGAAAAAGCTTGTCCCAAACT 59.899 45.455 0.00 0.00 0.00 2.66
1638 2329 3.430236 CCGAAAAAGCTTGTCCCAAACTT 60.430 43.478 0.00 0.00 0.00 2.66
1639 2330 3.551485 CGAAAAAGCTTGTCCCAAACTTG 59.449 43.478 0.00 0.00 0.00 3.16
1640 2331 4.503910 GAAAAAGCTTGTCCCAAACTTGT 58.496 39.130 0.00 0.00 0.00 3.16
1641 2332 3.801114 AAAGCTTGTCCCAAACTTGTC 57.199 42.857 0.00 0.00 0.00 3.18
1642 2333 1.692411 AGCTTGTCCCAAACTTGTCC 58.308 50.000 0.00 0.00 0.00 4.02
1643 2334 0.673985 GCTTGTCCCAAACTTGTCCC 59.326 55.000 0.00 0.00 0.00 4.46
1644 2335 1.754201 GCTTGTCCCAAACTTGTCCCT 60.754 52.381 0.00 0.00 0.00 4.20
1645 2336 2.230660 CTTGTCCCAAACTTGTCCCTC 58.769 52.381 0.00 0.00 0.00 4.30
1646 2337 1.217916 TGTCCCAAACTTGTCCCTCA 58.782 50.000 0.00 0.00 0.00 3.86
1647 2338 1.566703 TGTCCCAAACTTGTCCCTCAA 59.433 47.619 0.00 0.00 34.61 3.02
1648 2339 2.024846 TGTCCCAAACTTGTCCCTCAAA 60.025 45.455 0.00 0.00 35.48 2.69
1649 2340 3.230976 GTCCCAAACTTGTCCCTCAAAT 58.769 45.455 0.00 0.00 35.48 2.32
1650 2341 3.005791 GTCCCAAACTTGTCCCTCAAATG 59.994 47.826 0.00 0.00 35.48 2.32
1651 2342 2.299867 CCCAAACTTGTCCCTCAAATGG 59.700 50.000 0.00 0.00 35.48 3.16
1652 2343 3.230134 CCAAACTTGTCCCTCAAATGGA 58.770 45.455 0.00 0.00 36.92 3.41
1653 2344 3.834231 CCAAACTTGTCCCTCAAATGGAT 59.166 43.478 0.00 0.00 36.92 3.41
1654 2345 4.322198 CCAAACTTGTCCCTCAAATGGATG 60.322 45.833 0.00 0.00 36.92 3.51
1655 2346 3.814504 ACTTGTCCCTCAAATGGATGT 57.185 42.857 0.00 0.00 35.48 3.06
1656 2347 4.927267 ACTTGTCCCTCAAATGGATGTA 57.073 40.909 0.00 0.00 35.48 2.29
1657 2348 5.456921 ACTTGTCCCTCAAATGGATGTAT 57.543 39.130 0.00 0.00 35.48 2.29
1658 2349 5.440610 ACTTGTCCCTCAAATGGATGTATC 58.559 41.667 0.00 0.00 35.48 2.24
1659 2350 5.192522 ACTTGTCCCTCAAATGGATGTATCT 59.807 40.000 0.00 0.00 35.48 1.98
1660 2351 6.386927 ACTTGTCCCTCAAATGGATGTATCTA 59.613 38.462 0.00 0.00 35.48 1.98
1661 2352 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
1662 2353 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
1663 2354 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
1664 2355 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
1665 2356 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
1666 2357 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
1667 2358 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
1668 2359 8.099537 CCTCAAATGGATGTATCTAGCACTAAT 58.900 37.037 0.00 0.00 0.00 1.73
1669 2360 9.499479 CTCAAATGGATGTATCTAGCACTAATT 57.501 33.333 0.00 0.00 0.00 1.40
1670 2361 9.851686 TCAAATGGATGTATCTAGCACTAATTT 57.148 29.630 0.00 0.00 0.00 1.82
1671 2362 9.888878 CAAATGGATGTATCTAGCACTAATTTG 57.111 33.333 0.00 0.00 0.00 2.32
1672 2363 9.851686 AAATGGATGTATCTAGCACTAATTTGA 57.148 29.630 0.00 0.00 0.00 2.69
1674 2365 8.837788 TGGATGTATCTAGCACTAATTTGATG 57.162 34.615 0.00 0.00 0.00 3.07
1675 2366 7.388776 TGGATGTATCTAGCACTAATTTGATGC 59.611 37.037 0.00 0.72 39.74 3.91
1695 2386 2.818432 GCTAGATGCATCCATTTGAGGG 59.182 50.000 23.06 0.00 42.31 4.30
1696 2387 3.497405 GCTAGATGCATCCATTTGAGGGA 60.497 47.826 23.06 0.00 42.31 4.20
1697 2388 2.941480 AGATGCATCCATTTGAGGGAC 58.059 47.619 23.06 0.00 37.23 4.46
1698 2389 2.242965 AGATGCATCCATTTGAGGGACA 59.757 45.455 23.06 0.00 37.23 4.02
1699 2390 2.601240 TGCATCCATTTGAGGGACAA 57.399 45.000 0.00 0.00 37.23 3.18
1700 2391 2.449464 TGCATCCATTTGAGGGACAAG 58.551 47.619 0.00 0.00 39.77 3.16
1701 2392 2.225091 TGCATCCATTTGAGGGACAAGT 60.225 45.455 0.00 0.00 39.77 3.16
1702 2393 2.827921 GCATCCATTTGAGGGACAAGTT 59.172 45.455 0.00 0.00 39.77 2.66
1703 2394 3.259123 GCATCCATTTGAGGGACAAGTTT 59.741 43.478 0.00 0.00 39.77 2.66
1704 2395 4.262592 GCATCCATTTGAGGGACAAGTTTT 60.263 41.667 0.00 0.00 39.77 2.43
1705 2396 5.742838 GCATCCATTTGAGGGACAAGTTTTT 60.743 40.000 0.00 0.00 39.77 1.94
1749 2440 9.482175 AATATACCATTACAAAAGCACCCTTAA 57.518 29.630 0.00 0.00 0.00 1.85
1751 2442 6.680148 ACCATTACAAAAGCACCCTTAAAT 57.320 33.333 0.00 0.00 0.00 1.40
1793 2484 3.751479 TCTTCATCATGTATCCACCGG 57.249 47.619 0.00 0.00 0.00 5.28
1799 2490 1.411246 TCATGTATCCACCGGTAGCAC 59.589 52.381 6.87 3.62 0.00 4.40
1828 2519 3.056536 AGCAAAGCTCGTTGTCATCTCTA 60.057 43.478 0.36 0.00 30.62 2.43
1834 2525 3.739519 GCTCGTTGTCATCTCTAGGCATT 60.740 47.826 0.00 0.00 0.00 3.56
1884 2575 8.588290 AGACTCATGATCTTGTAGAAGTAGTT 57.412 34.615 8.33 0.00 0.00 2.24
1891 2582 8.023021 TGATCTTGTAGAAGTAGTTGCCATAT 57.977 34.615 0.00 0.00 0.00 1.78
1955 2684 3.249687 GCCTATAGCCCCAATTCCG 57.750 57.895 0.00 0.00 34.35 4.30
1961 2690 4.440829 GCCCCAATTCCGGCCAGA 62.441 66.667 2.24 0.00 39.39 3.86
1963 2692 1.829533 CCCCAATTCCGGCCAGATG 60.830 63.158 2.24 0.00 0.00 2.90
1965 2694 1.227102 CCAATTCCGGCCAGATGGA 59.773 57.895 2.24 0.00 37.39 3.41
1966 2695 0.820891 CCAATTCCGGCCAGATGGAG 60.821 60.000 2.24 0.00 37.39 3.86
1967 2696 0.107017 CAATTCCGGCCAGATGGAGT 60.107 55.000 2.24 0.00 37.39 3.85
1968 2697 0.181350 AATTCCGGCCAGATGGAGTC 59.819 55.000 2.24 0.00 37.39 3.36
1969 2698 2.032860 ATTCCGGCCAGATGGAGTCG 62.033 60.000 2.24 3.14 37.39 4.18
1970 2699 4.227134 CCGGCCAGATGGAGTCGG 62.227 72.222 2.24 8.49 38.00 4.79
1971 2700 3.147595 CGGCCAGATGGAGTCGGA 61.148 66.667 2.24 0.00 37.39 4.55
1972 2701 2.721167 CGGCCAGATGGAGTCGGAA 61.721 63.158 2.24 0.00 37.39 4.30
1973 2702 1.832912 GGCCAGATGGAGTCGGAAT 59.167 57.895 2.18 0.00 37.39 3.01
1985 2717 2.352960 GAGTCGGAATGCAAATCTCACC 59.647 50.000 0.00 0.00 0.00 4.02
1991 2723 2.885135 ATGCAAATCTCACCCACTCA 57.115 45.000 0.00 0.00 0.00 3.41
1992 2724 2.885135 TGCAAATCTCACCCACTCAT 57.115 45.000 0.00 0.00 0.00 2.90
2026 2758 4.699522 GGTCAACCTTCGCCGGCT 62.700 66.667 26.68 0.86 0.00 5.52
2032 2764 2.582498 CCTTCGCCGGCTAGAACG 60.582 66.667 26.68 11.37 0.00 3.95
2051 2783 2.432510 ACGGGAGATGAAGGATCAAGAC 59.567 50.000 0.00 0.00 39.49 3.01
2055 2787 3.494048 GGAGATGAAGGATCAAGACGCAT 60.494 47.826 0.00 0.00 39.49 4.73
2074 2806 3.813240 GCATGGCCATGTTATCTGATCCT 60.813 47.826 39.08 3.55 40.80 3.24
2191 2924 0.393077 GACCCGGTGTGCTAGCATAT 59.607 55.000 22.51 1.93 0.00 1.78
2237 2971 9.265901 CTAAAGATAAAGATAGGGTGTCACATG 57.734 37.037 5.12 0.00 0.00 3.21
2257 2991 9.955208 TCACATGCTATAAAATCATGAATCAAC 57.045 29.630 0.00 0.00 39.80 3.18
2258 2992 9.188588 CACATGCTATAAAATCATGAATCAACC 57.811 33.333 0.00 0.00 39.80 3.77
2273 3007 2.695359 TCAACCATACGAAGAAGCACC 58.305 47.619 0.00 0.00 0.00 5.01
2341 3075 0.107848 CATAACGTCTCACCACCCCC 60.108 60.000 0.00 0.00 0.00 5.40
2391 3125 1.000739 CCCTACTACCACCGGACCA 59.999 63.158 9.46 0.00 0.00 4.02
2489 3223 0.536915 GAGGGTAGATAGTCCGCCGT 60.537 60.000 0.00 0.00 0.00 5.68
2519 3272 1.811359 AGTAGAAGAGAACGACCCGTG 59.189 52.381 0.00 0.00 39.99 4.94
2534 3287 2.231478 ACCCGTGCATATAGAAGATCGG 59.769 50.000 0.00 0.00 37.04 4.18
2618 3398 2.795470 GCGTTTATGACTAGTAGCCAGC 59.205 50.000 0.00 0.00 0.00 4.85
2678 3458 4.821805 GGAGCAATGGATCCGATTAAAAGA 59.178 41.667 7.39 0.00 40.28 2.52
2701 3481 9.696917 AAGAAAGTGATGTTCCATTTGAAATAC 57.303 29.630 0.00 0.00 33.94 1.89
2702 3482 8.859090 AGAAAGTGATGTTCCATTTGAAATACA 58.141 29.630 0.00 0.00 33.94 2.29
2703 3483 9.474920 GAAAGTGATGTTCCATTTGAAATACAA 57.525 29.630 0.00 0.00 33.94 2.41
2732 3761 4.015872 ACGGCAAAAGAGATGTCCTAAA 57.984 40.909 0.00 0.00 0.00 1.85
2741 3770 9.565213 CAAAAGAGATGTCCTAAAATTTAGCTG 57.435 33.333 7.22 0.00 0.00 4.24
2944 4220 7.007723 TGTGACTGGAGGGTTTAACAAATAAT 58.992 34.615 0.00 0.00 0.00 1.28
2945 4221 8.164733 TGTGACTGGAGGGTTTAACAAATAATA 58.835 33.333 0.00 0.00 0.00 0.98
2946 4222 8.674607 GTGACTGGAGGGTTTAACAAATAATAG 58.325 37.037 0.00 0.00 0.00 1.73
2947 4223 8.387813 TGACTGGAGGGTTTAACAAATAATAGT 58.612 33.333 0.00 0.00 0.00 2.12
2948 4224 9.895138 GACTGGAGGGTTTAACAAATAATAGTA 57.105 33.333 0.00 0.00 0.00 1.82
2949 4225 9.901172 ACTGGAGGGTTTAACAAATAATAGTAG 57.099 33.333 0.00 0.00 0.00 2.57
2950 4226 9.901172 CTGGAGGGTTTAACAAATAATAGTAGT 57.099 33.333 0.00 0.00 0.00 2.73
2975 4251 0.249120 TGGACTTGTACATGAGCGGG 59.751 55.000 15.13 0.00 0.00 6.13
2998 4337 8.648097 CGGGAAATGATCTATAATTAACGACTG 58.352 37.037 0.00 0.00 0.00 3.51
3045 4384 0.832135 TGGAGAAGGACTTGGACGCT 60.832 55.000 0.00 0.00 0.00 5.07
3060 4399 2.726691 CGCTTCGATCGCGTGGTTT 61.727 57.895 18.07 0.00 45.13 3.27
3135 4474 3.121030 GTGATGAAGCAGCGCGGT 61.121 61.111 4.23 4.23 0.00 5.68
3807 5149 0.526211 TGTTCGAGGAGATCACACCG 59.474 55.000 0.00 0.00 32.13 4.94
3837 5179 2.319219 GCAGATGGCTTGCTAGCTC 58.681 57.895 19.45 10.35 46.90 4.09
3838 5180 0.179051 GCAGATGGCTTGCTAGCTCT 60.179 55.000 19.45 12.44 46.90 4.09
3885 5227 2.064762 CTGTGAGTGTGCAGTAGCTTC 58.935 52.381 0.00 0.00 42.74 3.86
3887 5229 1.795286 GTGAGTGTGCAGTAGCTTCAC 59.205 52.381 0.00 0.00 42.18 3.18
3895 5237 4.080919 TGTGCAGTAGCTTCACCAGAATAT 60.081 41.667 0.00 0.00 42.74 1.28
3965 5307 4.190001 ACTGCAGTAGCTTGATCAGAATG 58.810 43.478 20.16 0.00 42.74 2.67
4127 5474 7.701257 ATATACTACCACCCCTTTTATGTGT 57.299 36.000 0.00 0.00 0.00 3.72
4128 5475 8.802057 ATATACTACCACCCCTTTTATGTGTA 57.198 34.615 0.00 0.00 0.00 2.90
4129 5476 5.169992 ACTACCACCCCTTTTATGTGTAC 57.830 43.478 0.00 0.00 0.00 2.90
4130 5477 3.062122 ACCACCCCTTTTATGTGTACG 57.938 47.619 0.00 0.00 0.00 3.67
4131 5478 1.741145 CCACCCCTTTTATGTGTACGC 59.259 52.381 0.00 0.00 0.00 4.42
4132 5479 2.428491 CACCCCTTTTATGTGTACGCA 58.572 47.619 12.26 12.26 0.00 5.24
4133 5480 3.013921 CACCCCTTTTATGTGTACGCAT 58.986 45.455 24.28 24.28 0.00 4.73
4134 5481 3.013921 ACCCCTTTTATGTGTACGCATG 58.986 45.455 28.04 14.02 0.00 4.06
4135 5482 3.275143 CCCCTTTTATGTGTACGCATGA 58.725 45.455 28.04 19.37 0.00 3.07
4186 5533 1.475571 CGACCCAATCATCCATGCTGA 60.476 52.381 0.00 0.00 0.00 4.26
4188 5535 0.949397 CCCAATCATCCATGCTGACG 59.051 55.000 0.00 0.00 0.00 4.35
4196 5543 0.321346 TCCATGCTGACGTGTCATGT 59.679 50.000 15.62 0.00 39.13 3.21
4357 5715 1.000233 AAAATCCCGCTGGCCATGA 60.000 52.632 5.51 0.69 0.00 3.07
4403 5761 0.935898 GCATGGCAAGAGATCACTCG 59.064 55.000 0.00 0.00 46.64 4.18
4459 5818 7.091443 ACAAAAACTCCAAACGTTAAACATCA 58.909 30.769 0.00 0.00 0.00 3.07
4463 5822 4.210537 ACTCCAAACGTTAAACATCAGTCG 59.789 41.667 0.00 0.00 0.00 4.18
4590 5952 6.379133 ACAAAGTCACTTATGATAGGTCGGTA 59.621 38.462 0.00 0.00 37.14 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 70 4.579869 ACTATCGGCTTGACTCACATTTT 58.420 39.130 0.00 0.00 0.00 1.82
91 96 7.001674 TGTAAGGGAAGCTCACATTTTCTTTA 58.998 34.615 0.00 0.00 0.00 1.85
100 306 4.431416 TTCTTTGTAAGGGAAGCTCACA 57.569 40.909 0.00 0.00 0.00 3.58
102 308 6.976934 ATTTTTCTTTGTAAGGGAAGCTCA 57.023 33.333 0.00 0.00 0.00 4.26
109 315 7.148423 GCCAAGCAATATTTTTCTTTGTAAGGG 60.148 37.037 0.00 0.00 0.00 3.95
152 359 8.908786 ATTGTATATACCCTCATTGTGTCAAG 57.091 34.615 10.38 0.00 0.00 3.02
193 400 7.275779 CACTTCTGTATTTAGCTTACGTGACAT 59.724 37.037 0.00 0.00 0.00 3.06
271 478 5.994054 GTGATGGATATTGCAGCTAAGAGAA 59.006 40.000 0.00 0.00 0.00 2.87
374 713 4.581824 TCTTAAGTCCGCCACGTAATCTAT 59.418 41.667 1.63 0.00 29.78 1.98
418 757 8.923838 ATGGATAGGATGATGTATAACTTCCT 57.076 34.615 8.72 8.72 41.39 3.36
430 769 9.950496 GGCGATAATTAATATGGATAGGATGAT 57.050 33.333 0.00 0.00 0.00 2.45
456 795 6.662414 TTAGTGCTAGATTCATTCGTTTGG 57.338 37.500 0.00 0.00 0.00 3.28
522 863 9.859427 CTTCCAAGTCATATTTTTGCTGAAATA 57.141 29.630 7.28 7.28 36.30 1.40
526 867 5.185635 CCCTTCCAAGTCATATTTTTGCTGA 59.814 40.000 0.00 0.00 0.00 4.26
539 880 5.741962 AAACTACTACTCCCTTCCAAGTC 57.258 43.478 0.00 0.00 0.00 3.01
545 886 4.922103 CACGTCAAAACTACTACTCCCTTC 59.078 45.833 0.00 0.00 0.00 3.46
553 927 3.302555 CGTCTGCACGTCAAAACTACTA 58.697 45.455 0.00 0.00 41.42 1.82
781 1157 0.600255 GACGGCCGATCGGATGAATT 60.600 55.000 37.64 14.13 37.50 2.17
920 1296 6.184789 AGGAGCTAGCTAGATACCTAATGAC 58.815 44.000 25.15 2.49 0.00 3.06
976 1353 0.033405 ACCTCCGCCTAGAAGTAGCA 60.033 55.000 0.00 0.00 0.00 3.49
996 1373 0.982852 ATCCGGCCTGAACCATCTCA 60.983 55.000 0.00 0.00 0.00 3.27
1146 1529 8.150945 TCCAGAAAATGAATAGGAGTACATAGC 58.849 37.037 0.00 0.00 0.00 2.97
1148 1531 8.141909 CGTCCAGAAAATGAATAGGAGTACATA 58.858 37.037 0.00 0.00 0.00 2.29
1150 1533 6.153851 TCGTCCAGAAAATGAATAGGAGTACA 59.846 38.462 0.00 0.00 0.00 2.90
1151 1534 6.570692 TCGTCCAGAAAATGAATAGGAGTAC 58.429 40.000 0.00 0.00 0.00 2.73
1204 1613 4.770010 GGTGAGATAGATTCGATCCTTCCT 59.230 45.833 3.45 0.00 0.00 3.36
1298 1707 4.386867 TTTAGGAAGCAGAGGTCGTATG 57.613 45.455 0.00 0.00 0.00 2.39
1299 1708 4.740934 GCATTTAGGAAGCAGAGGTCGTAT 60.741 45.833 0.00 0.00 0.00 3.06
1303 1722 2.941720 CAGCATTTAGGAAGCAGAGGTC 59.058 50.000 0.00 0.00 0.00 3.85
1310 1729 1.094785 TTCGGCAGCATTTAGGAAGC 58.905 50.000 0.00 0.00 0.00 3.86
1321 1740 0.028902 ACAGAAAACGTTTCGGCAGC 59.971 50.000 15.01 0.44 0.00 5.25
1322 1741 2.468532 AACAGAAAACGTTTCGGCAG 57.531 45.000 15.01 6.67 0.00 4.85
1327 1804 6.250089 TCCGTTTCTAAACAGAAAACGTTTC 58.750 36.000 15.01 8.08 39.20 2.78
1337 1814 9.339492 CTAACTAACTACTCCGTTTCTAAACAG 57.661 37.037 6.41 0.00 38.81 3.16
1344 1821 8.976986 TGAAATCTAACTAACTACTCCGTTTC 57.023 34.615 0.00 0.00 0.00 2.78
1358 1852 8.437575 ACCGGGTATATTGAATGAAATCTAACT 58.562 33.333 6.32 0.00 0.00 2.24
1382 1876 0.846693 ACCAGCCCATCCATTAGACC 59.153 55.000 0.00 0.00 0.00 3.85
1387 1881 2.042639 GCCACCAGCCCATCCATT 60.043 61.111 0.00 0.00 34.35 3.16
1438 1944 1.942657 GAGTGCAGAAACTGTCTTGCA 59.057 47.619 8.98 8.98 37.77 4.08
1446 1952 7.108194 TCTATGAAATGATGAGTGCAGAAACT 58.892 34.615 0.00 0.00 0.00 2.66
1465 1971 8.972127 GCTACTCTGGGTATTAATGATCTATGA 58.028 37.037 0.00 0.00 0.00 2.15
1466 1972 8.976353 AGCTACTCTGGGTATTAATGATCTATG 58.024 37.037 0.00 0.00 0.00 2.23
1467 1973 9.196139 GAGCTACTCTGGGTATTAATGATCTAT 57.804 37.037 0.00 0.00 0.00 1.98
1468 1974 8.394822 AGAGCTACTCTGGGTATTAATGATCTA 58.605 37.037 0.00 0.00 39.62 1.98
1469 1975 7.245292 AGAGCTACTCTGGGTATTAATGATCT 58.755 38.462 0.00 0.00 39.62 2.75
1470 1976 7.475137 AGAGCTACTCTGGGTATTAATGATC 57.525 40.000 0.00 0.00 39.62 2.92
1471 1977 7.038658 GGAAGAGCTACTCTGGGTATTAATGAT 60.039 40.741 0.00 0.00 40.28 2.45
1472 1978 6.267928 GGAAGAGCTACTCTGGGTATTAATGA 59.732 42.308 0.00 0.00 40.28 2.57
1473 1979 6.042093 TGGAAGAGCTACTCTGGGTATTAATG 59.958 42.308 0.00 0.00 40.28 1.90
1474 1980 6.143915 TGGAAGAGCTACTCTGGGTATTAAT 58.856 40.000 0.00 0.00 40.28 1.40
1475 1981 5.525484 TGGAAGAGCTACTCTGGGTATTAA 58.475 41.667 0.00 0.00 40.28 1.40
1476 1982 5.138758 TGGAAGAGCTACTCTGGGTATTA 57.861 43.478 0.00 0.00 40.28 0.98
1477 1983 3.964031 CTGGAAGAGCTACTCTGGGTATT 59.036 47.826 0.00 0.00 40.28 1.89
1478 1984 3.571590 CTGGAAGAGCTACTCTGGGTAT 58.428 50.000 0.00 0.00 40.28 2.73
1479 1985 2.950874 GCTGGAAGAGCTACTCTGGGTA 60.951 54.545 0.00 0.00 45.21 3.69
1607 2298 0.991920 AGCTTTTTCGGATGGAGGGA 59.008 50.000 0.00 0.00 0.00 4.20
1608 2299 1.474077 CAAGCTTTTTCGGATGGAGGG 59.526 52.381 0.00 0.00 0.00 4.30
1609 2300 2.162408 GACAAGCTTTTTCGGATGGAGG 59.838 50.000 0.00 0.00 0.00 4.30
1610 2301 2.162408 GGACAAGCTTTTTCGGATGGAG 59.838 50.000 0.00 0.00 0.00 3.86
1611 2302 2.159382 GGACAAGCTTTTTCGGATGGA 58.841 47.619 0.00 0.00 0.00 3.41
1612 2303 1.202348 GGGACAAGCTTTTTCGGATGG 59.798 52.381 0.00 0.00 0.00 3.51
1613 2304 1.885887 TGGGACAAGCTTTTTCGGATG 59.114 47.619 0.00 0.00 31.92 3.51
1614 2305 2.286365 TGGGACAAGCTTTTTCGGAT 57.714 45.000 0.00 0.00 31.92 4.18
1615 2306 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
1625 2316 3.939454 TTGAGGGACAAGTTTGGGACAAG 60.939 47.826 0.00 0.00 37.48 3.16
1626 2317 2.024846 TTGAGGGACAAGTTTGGGACAA 60.025 45.455 0.00 0.00 37.48 3.18
1627 2318 1.217916 TGAGGGACAAGTTTGGGACA 58.782 50.000 0.00 0.00 0.00 4.02
1628 2319 2.358322 TTGAGGGACAAGTTTGGGAC 57.642 50.000 0.00 0.00 34.20 4.46
1629 2320 3.230134 CATTTGAGGGACAAGTTTGGGA 58.770 45.455 0.00 0.00 39.77 4.37
1630 2321 2.299867 CCATTTGAGGGACAAGTTTGGG 59.700 50.000 0.00 0.00 39.77 4.12
1631 2322 3.230134 TCCATTTGAGGGACAAGTTTGG 58.770 45.455 0.00 0.00 39.77 3.28
1632 2323 4.281688 ACATCCATTTGAGGGACAAGTTTG 59.718 41.667 0.00 0.00 39.77 2.93
1633 2324 4.482990 ACATCCATTTGAGGGACAAGTTT 58.517 39.130 0.00 0.00 39.77 2.66
1634 2325 4.118168 ACATCCATTTGAGGGACAAGTT 57.882 40.909 0.00 0.00 39.77 2.66
1635 2326 3.814504 ACATCCATTTGAGGGACAAGT 57.185 42.857 0.00 0.00 39.77 3.16
1636 2327 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
1637 2328 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
1638 2329 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
1639 2330 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
1640 2331 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
1641 2332 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
1642 2333 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
1643 2334 9.499479 AATTAGTGCTAGATACATCCATTTGAG 57.501 33.333 0.00 0.00 0.00 3.02
1644 2335 9.851686 AAATTAGTGCTAGATACATCCATTTGA 57.148 29.630 0.00 0.00 0.00 2.69
1645 2336 9.888878 CAAATTAGTGCTAGATACATCCATTTG 57.111 33.333 0.00 2.71 0.00 2.32
1646 2337 9.851686 TCAAATTAGTGCTAGATACATCCATTT 57.148 29.630 0.00 0.00 0.00 2.32
1648 2339 9.445878 CATCAAATTAGTGCTAGATACATCCAT 57.554 33.333 0.00 0.00 0.00 3.41
1649 2340 7.388776 GCATCAAATTAGTGCTAGATACATCCA 59.611 37.037 0.00 0.00 36.02 3.41
1650 2341 7.605691 AGCATCAAATTAGTGCTAGATACATCC 59.394 37.037 9.58 0.00 46.54 3.51
1651 2342 8.545229 AGCATCAAATTAGTGCTAGATACATC 57.455 34.615 9.58 0.00 46.54 3.06
1659 2350 6.791887 GCATCTAGCATCAAATTAGTGCTA 57.208 37.500 14.73 14.73 46.54 3.49
1674 2365 2.818432 CCCTCAAATGGATGCATCTAGC 59.182 50.000 25.28 10.32 45.96 3.42
1675 2366 4.070716 GTCCCTCAAATGGATGCATCTAG 58.929 47.826 25.28 8.89 33.65 2.43
1676 2367 3.459227 TGTCCCTCAAATGGATGCATCTA 59.541 43.478 25.28 20.79 33.65 1.98
1677 2368 2.242965 TGTCCCTCAAATGGATGCATCT 59.757 45.455 25.28 4.53 33.65 2.90
1678 2369 2.658285 TGTCCCTCAAATGGATGCATC 58.342 47.619 18.81 18.81 33.65 3.91
1679 2370 2.832643 TGTCCCTCAAATGGATGCAT 57.167 45.000 0.00 0.00 33.65 3.96
1680 2371 2.225091 ACTTGTCCCTCAAATGGATGCA 60.225 45.455 0.00 0.00 35.48 3.96
1681 2372 2.450476 ACTTGTCCCTCAAATGGATGC 58.550 47.619 0.00 0.00 35.48 3.91
1682 2373 5.473066 AAAACTTGTCCCTCAAATGGATG 57.527 39.130 0.00 0.00 35.48 3.51
1702 2393 8.722622 ATATTCTACTCCCTCTATCCGAAAAA 57.277 34.615 0.00 0.00 0.00 1.94
1703 2394 9.240734 GTATATTCTACTCCCTCTATCCGAAAA 57.759 37.037 0.00 0.00 0.00 2.29
1704 2395 7.833183 GGTATATTCTACTCCCTCTATCCGAAA 59.167 40.741 0.00 0.00 0.00 3.46
1705 2396 7.037080 TGGTATATTCTACTCCCTCTATCCGAA 60.037 40.741 0.00 0.00 0.00 4.30
1706 2397 6.446110 TGGTATATTCTACTCCCTCTATCCGA 59.554 42.308 0.00 0.00 0.00 4.55
1707 2398 6.660800 TGGTATATTCTACTCCCTCTATCCG 58.339 44.000 0.00 0.00 0.00 4.18
1712 2403 9.670442 TTTGTAATGGTATATTCTACTCCCTCT 57.330 33.333 0.00 0.00 0.00 3.69
1715 2406 9.000486 GCTTTTGTAATGGTATATTCTACTCCC 58.000 37.037 0.00 0.00 0.00 4.30
1716 2407 9.555727 TGCTTTTGTAATGGTATATTCTACTCC 57.444 33.333 0.00 0.00 0.00 3.85
1793 2484 2.227968 CTTTGCTCACGGCGTGCTAC 62.228 60.000 33.59 23.89 45.43 3.58
1828 2519 2.185350 CCGCTGAGACGAATGCCT 59.815 61.111 0.00 0.00 34.06 4.75
1834 2525 1.372997 GTTTGCTCCGCTGAGACGA 60.373 57.895 9.60 0.00 41.42 4.20
1860 2551 7.221838 GCAACTACTTCTACAAGATCATGAGTC 59.778 40.741 4.68 0.00 33.34 3.36
1914 2605 2.644992 CCAGTGTTTTCCTGGCGC 59.355 61.111 0.00 0.00 42.81 6.53
1950 2679 1.832912 GACTCCATCTGGCCGGAAT 59.167 57.895 20.61 4.41 34.44 3.01
1955 2684 0.533755 CATTCCGACTCCATCTGGCC 60.534 60.000 0.00 0.00 34.44 5.36
1961 2690 3.209410 GAGATTTGCATTCCGACTCCAT 58.791 45.455 0.00 0.00 0.00 3.41
1963 2692 2.352960 GTGAGATTTGCATTCCGACTCC 59.647 50.000 0.00 0.00 0.00 3.85
1965 2694 2.359900 GGTGAGATTTGCATTCCGACT 58.640 47.619 0.00 0.00 0.00 4.18
1966 2695 1.401905 GGGTGAGATTTGCATTCCGAC 59.598 52.381 0.00 0.00 0.00 4.79
1967 2696 1.004161 TGGGTGAGATTTGCATTCCGA 59.996 47.619 0.00 0.00 0.00 4.55
1968 2697 1.133025 GTGGGTGAGATTTGCATTCCG 59.867 52.381 0.00 0.00 0.00 4.30
1969 2698 2.424956 GAGTGGGTGAGATTTGCATTCC 59.575 50.000 0.00 0.00 0.00 3.01
1970 2699 3.084039 TGAGTGGGTGAGATTTGCATTC 58.916 45.455 0.00 0.00 0.00 2.67
1971 2700 3.159213 TGAGTGGGTGAGATTTGCATT 57.841 42.857 0.00 0.00 0.00 3.56
1972 2701 2.885135 TGAGTGGGTGAGATTTGCAT 57.115 45.000 0.00 0.00 0.00 3.96
1973 2702 2.040145 TGATGAGTGGGTGAGATTTGCA 59.960 45.455 0.00 0.00 0.00 4.08
1985 2717 0.321564 TCGGCCTTGTTGATGAGTGG 60.322 55.000 0.00 0.00 0.00 4.00
1991 2723 0.036010 CCAGTCTCGGCCTTGTTGAT 60.036 55.000 0.00 0.00 0.00 2.57
1992 2724 1.371183 CCAGTCTCGGCCTTGTTGA 59.629 57.895 0.00 0.00 0.00 3.18
2025 2757 3.891977 TGATCCTTCATCTCCCGTTCTAG 59.108 47.826 0.00 0.00 31.92 2.43
2026 2758 3.910989 TGATCCTTCATCTCCCGTTCTA 58.089 45.455 0.00 0.00 31.92 2.10
2032 2764 2.804933 GCGTCTTGATCCTTCATCTCCC 60.805 54.545 0.00 0.00 31.92 4.30
2051 2783 1.596603 TCAGATAACATGGCCATGCG 58.403 50.000 39.74 22.15 42.39 4.73
2055 2787 3.047857 TGAGGATCAGATAACATGGCCA 58.952 45.455 8.56 8.56 42.56 5.36
2116 2849 5.338708 CCATGATCTAGTTCTTTGGGTCTGT 60.339 44.000 12.20 0.00 0.00 3.41
2123 2856 4.878397 GGTGTCCCATGATCTAGTTCTTTG 59.122 45.833 0.00 1.16 0.00 2.77
2124 2857 4.785376 AGGTGTCCCATGATCTAGTTCTTT 59.215 41.667 0.00 0.00 0.00 2.52
2146 2879 1.045350 TCTCTGGATTCGCCCCTGAG 61.045 60.000 13.96 13.96 45.52 3.35
2147 2880 1.001631 TCTCTGGATTCGCCCCTGA 59.998 57.895 0.00 0.00 34.97 3.86
2207 2940 8.651389 TGACACCCTATCTTTATCTTTAGATGG 58.349 37.037 2.51 0.00 36.05 3.51
2225 2958 5.754782 TGATTTTATAGCATGTGACACCCT 58.245 37.500 2.45 0.00 0.00 4.34
2237 2971 9.546909 CGTATGGTTGATTCATGATTTTATAGC 57.453 33.333 0.00 0.00 0.00 2.97
2257 2991 0.463833 GGGGGTGCTTCTTCGTATGG 60.464 60.000 0.00 0.00 0.00 2.74
2258 2992 0.810031 CGGGGGTGCTTCTTCGTATG 60.810 60.000 0.00 0.00 0.00 2.39
2262 2996 1.302192 TTTCGGGGGTGCTTCTTCG 60.302 57.895 0.00 0.00 0.00 3.79
2341 3075 8.943909 ATAAAGTTAGGTTTTATCTCCAGTCG 57.056 34.615 0.00 0.00 0.00 4.18
2422 3156 1.320344 CCCTCCGTCTGTCATTCCGA 61.320 60.000 0.00 0.00 0.00 4.55
2452 3186 0.761323 TCTTTCCCGGTGAGACCACA 60.761 55.000 0.00 0.00 44.93 4.17
2489 3223 2.000803 TCTCTTCTACTCCACCAGGGA 58.999 52.381 0.00 0.00 45.89 4.20
2501 3254 0.524862 GCACGGGTCGTTCTCTTCTA 59.475 55.000 0.00 0.00 38.32 2.10
2519 3272 2.275318 GGCAGCCGATCTTCTATATGC 58.725 52.381 0.00 0.00 0.00 3.14
2641 3421 0.970427 TGCTCCGCCTCATAGTGTGA 60.970 55.000 0.00 0.00 35.05 3.58
2643 3423 0.833287 ATTGCTCCGCCTCATAGTGT 59.167 50.000 0.00 0.00 0.00 3.55
2701 3481 3.737266 TCTCTTTTGCCGTACGTACTTTG 59.263 43.478 22.55 12.24 0.00 2.77
2702 3482 3.981211 TCTCTTTTGCCGTACGTACTTT 58.019 40.909 22.55 0.00 0.00 2.66
2703 3483 3.648339 TCTCTTTTGCCGTACGTACTT 57.352 42.857 22.55 0.00 0.00 2.24
2704 3484 3.057033 ACATCTCTTTTGCCGTACGTACT 60.057 43.478 22.55 0.00 0.00 2.73
2705 3485 3.248266 ACATCTCTTTTGCCGTACGTAC 58.752 45.455 15.90 15.90 0.00 3.67
2706 3486 3.504863 GACATCTCTTTTGCCGTACGTA 58.495 45.455 15.21 0.00 0.00 3.57
2708 3737 1.659098 GGACATCTCTTTTGCCGTACG 59.341 52.381 8.69 8.69 0.00 3.67
2732 3761 5.473504 ACGAAAAGTGATCACCAGCTAAATT 59.526 36.000 22.21 4.60 0.00 1.82
2741 3770 5.179368 TGAAGAATGACGAAAAGTGATCACC 59.821 40.000 22.21 6.01 0.00 4.02
2806 4059 9.886132 AGTAATTATTTCTCGTTACATGGAACT 57.114 29.630 18.59 1.32 31.24 3.01
2899 4175 9.998106 AGTCACAGAATTTTGTTACTACACTAT 57.002 29.630 12.82 0.00 34.63 2.12
2900 4176 9.256477 CAGTCACAGAATTTTGTTACTACACTA 57.744 33.333 13.77 0.00 34.26 2.74
2901 4177 7.226720 CCAGTCACAGAATTTTGTTACTACACT 59.773 37.037 13.77 1.81 34.26 3.55
2902 4178 7.225931 TCCAGTCACAGAATTTTGTTACTACAC 59.774 37.037 13.77 0.00 34.26 2.90
2903 4179 7.276658 TCCAGTCACAGAATTTTGTTACTACA 58.723 34.615 13.77 3.51 34.26 2.74
2904 4180 7.095187 CCTCCAGTCACAGAATTTTGTTACTAC 60.095 40.741 13.77 4.71 34.26 2.73
2905 4181 6.934645 CCTCCAGTCACAGAATTTTGTTACTA 59.065 38.462 13.77 1.97 34.26 1.82
2944 4220 9.856162 TCATGTACAAGTCCATACATACTACTA 57.144 33.333 0.00 0.00 39.47 1.82
2945 4221 8.762481 TCATGTACAAGTCCATACATACTACT 57.238 34.615 0.00 0.00 39.47 2.57
2946 4222 7.595502 GCTCATGTACAAGTCCATACATACTAC 59.404 40.741 0.00 0.00 39.47 2.73
2947 4223 7.521585 CGCTCATGTACAAGTCCATACATACTA 60.522 40.741 0.00 0.00 39.47 1.82
2948 4224 6.516718 GCTCATGTACAAGTCCATACATACT 58.483 40.000 0.00 0.00 39.47 2.12
2949 4225 5.402568 CGCTCATGTACAAGTCCATACATAC 59.597 44.000 0.00 0.00 39.47 2.39
2950 4226 5.508994 CCGCTCATGTACAAGTCCATACATA 60.509 44.000 0.00 0.00 39.47 2.29
2951 4227 4.371786 CGCTCATGTACAAGTCCATACAT 58.628 43.478 0.00 0.00 41.63 2.29
2952 4228 3.430236 CCGCTCATGTACAAGTCCATACA 60.430 47.826 0.00 0.00 35.82 2.29
2998 4337 8.045176 AGCTGATGAACCAGTTTATTAGAAAC 57.955 34.615 10.15 0.00 36.57 2.78
3010 4349 2.762887 TCTCCACTAGCTGATGAACCAG 59.237 50.000 0.00 0.00 37.23 4.00
3045 4384 0.600518 TCCAAAACCACGCGATCGAA 60.601 50.000 21.57 0.00 39.41 3.71
3060 4399 1.138883 CGTCTCGATCGCCTTCCAA 59.861 57.895 11.09 0.00 0.00 3.53
3701 5043 3.209812 CCATCTCGTCGGCCTCGA 61.210 66.667 16.62 16.62 43.86 4.04
3726 5068 2.759114 CTGGCCACCATGTCCAGT 59.241 61.111 0.00 0.00 41.76 4.00
3807 5149 1.817099 CATCTGCTCCCTGCCGAAC 60.817 63.158 0.00 0.00 38.36 3.95
3837 5179 7.939782 TCTATTGAGTTCTCATGAGCTTCTAG 58.060 38.462 18.36 12.17 33.86 2.43
3838 5180 7.888250 TCTATTGAGTTCTCATGAGCTTCTA 57.112 36.000 18.36 11.56 33.86 2.10
3885 5227 3.935203 ACGAGCTTCACAATATTCTGGTG 59.065 43.478 0.00 0.00 0.00 4.17
3887 5229 4.183865 TCACGAGCTTCACAATATTCTGG 58.816 43.478 0.00 0.00 0.00 3.86
3895 5237 2.100749 TGAGTTCTCACGAGCTTCACAA 59.899 45.455 0.00 0.00 30.22 3.33
3965 5307 1.769733 TAACACGTACGCTTCACACC 58.230 50.000 16.72 0.00 0.00 4.16
4115 5462 4.955925 TTCATGCGTACACATAAAAGGG 57.044 40.909 0.00 0.00 0.00 3.95
4122 5469 8.629158 ACCAAAAATATATTCATGCGTACACAT 58.371 29.630 0.00 0.00 0.00 3.21
4123 5470 7.990917 ACCAAAAATATATTCATGCGTACACA 58.009 30.769 0.00 0.00 0.00 3.72
4124 5471 9.938670 TTACCAAAAATATATTCATGCGTACAC 57.061 29.630 0.00 0.00 0.00 2.90
4186 5533 2.032528 CCTGCCCACATGACACGT 59.967 61.111 0.00 0.00 0.00 4.49
4188 5535 3.064324 GCCCTGCCCACATGACAC 61.064 66.667 0.00 0.00 0.00 3.67
4403 5761 7.569591 GCATATGTTTGTCGCCTATAGAAGAAC 60.570 40.741 4.29 0.00 0.00 3.01
4459 5818 5.651387 TCAGATGTTTCTCAAGATCGACT 57.349 39.130 0.00 0.00 37.68 4.18
4463 5822 8.538856 CGAGTTATTCAGATGTTTCTCAAGATC 58.461 37.037 0.00 0.00 33.65 2.75


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

AutoCloner maintained by Alex Coulton.