Multiple sequence alignment - TraesCS3D01G068600

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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 TraesCS3D01G068600 chr3D 100.000 5717 0 0 1 5717 30240577 30234861 0.000000e+00 10558.0
1 TraesCS3D01G068600 chr3D 79.771 524 99 4 1658 2175 6950377 6950899 1.950000e-99 374.0
2 TraesCS3D01G068600 chr3A 91.854 3155 210 22 1657 4783 41993950 41990815 0.000000e+00 4359.0
3 TraesCS3D01G068600 chr3A 92.751 938 48 10 4781 5717 41990734 41989816 0.000000e+00 1338.0
4 TraesCS3D01G068600 chr3A 92.995 828 50 6 1 826 41999679 41998858 0.000000e+00 1201.0
5 TraesCS3D01G068600 chr3A 91.601 381 14 1 921 1301 41998684 41998322 1.420000e-140 510.0
6 TraesCS3D01G068600 chr3A 82.664 473 76 5 1749 2215 528524699 528524227 1.150000e-111 414.0
7 TraesCS3D01G068600 chr3A 78.230 565 110 11 1661 2215 657276547 657275986 3.280000e-92 350.0
8 TraesCS3D01G068600 chr3A 89.316 234 14 4 1293 1523 41994190 41993965 3.370000e-72 283.0
9 TraesCS3D01G068600 chr3A 80.463 389 50 10 5116 5490 701226625 701227001 2.030000e-69 274.0
10 TraesCS3D01G068600 chr3A 90.909 66 6 0 4977 5042 701226404 701226469 7.890000e-14 89.8
11 TraesCS3D01G068600 chr3A 83.516 91 13 2 2448 2538 49314414 49314502 3.670000e-12 84.2
12 TraesCS3D01G068600 chr3A 89.394 66 7 0 4977 5042 701226099 701226164 3.670000e-12 84.2
13 TraesCS3D01G068600 chr3A 97.297 37 0 1 2540 2575 41993002 41992966 1.720000e-05 62.1
14 TraesCS3D01G068600 chr3B 92.770 2379 101 27 2544 4904 52771117 52773442 0.000000e+00 3374.0
15 TraesCS3D01G068600 chr3B 94.549 1651 62 9 3415 5057 51815572 51813942 0.000000e+00 2525.0
16 TraesCS3D01G068600 chr3B 89.481 1445 101 22 1 1412 52769688 52771114 0.000000e+00 1779.0
17 TraesCS3D01G068600 chr3B 90.795 1032 75 7 2372 3387 51816596 51815569 0.000000e+00 1362.0
18 TraesCS3D01G068600 chr3B 90.261 729 51 13 132 854 51819113 51818399 0.000000e+00 935.0
19 TraesCS3D01G068600 chr3B 93.509 570 31 4 957 1523 51818068 51817502 0.000000e+00 843.0
20 TraesCS3D01G068600 chr3B 83.113 758 106 11 1628 2381 51817503 51816764 0.000000e+00 671.0
21 TraesCS3D01G068600 chr3B 79.221 539 102 8 1661 2190 688089663 688089126 3.250000e-97 366.0
22 TraesCS3D01G068600 chr3B 80.513 390 48 12 5116 5490 49411000 49410624 2.030000e-69 274.0
23 TraesCS3D01G068600 chr3B 93.548 62 3 1 1 61 51819173 51819112 2.190000e-14 91.6
24 TraesCS3D01G068600 chr3B 90.909 66 6 0 4977 5042 49411219 49411154 7.890000e-14 89.8
25 TraesCS3D01G068600 chr3B 87.013 77 10 0 2448 2524 197796307 197796383 2.840000e-13 87.9
26 TraesCS3D01G068600 chr3B 94.595 37 1 1 2540 2575 51816361 51816325 8.000000e-04 56.5
27 TraesCS3D01G068600 chr4A 87.965 1504 131 24 3497 4996 385781534 385780077 0.000000e+00 1729.0
28 TraesCS3D01G068600 chr4A 79.181 562 102 10 1661 2215 72971930 72972483 5.410000e-100 375.0
29 TraesCS3D01G068600 chr4B 89.575 777 70 5 3485 4259 207124209 207123442 0.000000e+00 976.0
30 TraesCS3D01G068600 chr4B 93.488 215 12 2 4241 4454 207118981 207118768 9.240000e-83 318.0
31 TraesCS3D01G068600 chr4B 83.929 280 33 5 2728 2997 207125365 207125088 2.040000e-64 257.0
32 TraesCS3D01G068600 chr4D 90.199 653 50 8 3858 4506 164905028 164904386 0.000000e+00 839.0
33 TraesCS3D01G068600 chr4D 86.500 200 27 0 4508 4707 164888427 164888228 2.680000e-53 220.0
34 TraesCS3D01G068600 chr7B 80.410 536 95 6 1665 2194 619093354 619093885 3.210000e-107 399.0
35 TraesCS3D01G068600 chr7B 87.342 237 26 4 5484 5717 479626278 479626043 9.440000e-68 268.0
36 TraesCS3D01G068600 chr2A 83.294 419 60 6 5043 5458 57807381 57806970 1.500000e-100 377.0
37 TraesCS3D01G068600 chr2A 94.643 112 6 0 1520 1631 379389057 379389168 2.120000e-39 174.0
38 TraesCS3D01G068600 chr2A 93.750 112 7 0 1520 1631 745015430 745015541 9.850000e-38 169.0
39 TraesCS3D01G068600 chr2A 92.982 114 8 0 1516 1629 39407396 39407509 3.540000e-37 167.0
40 TraesCS3D01G068600 chr2A 76.250 240 47 8 1661 1891 764823813 764823575 1.010000e-22 119.0
41 TraesCS3D01G068600 chr2A 87.013 77 9 1 2448 2524 293857789 293857864 1.020000e-12 86.1
42 TraesCS3D01G068600 chr2B 78.750 560 98 16 1657 2204 799282505 799281955 7.050000e-94 355.0
43 TraesCS3D01G068600 chr2B 93.043 115 7 1 1520 1634 693737239 693737126 3.540000e-37 167.0
44 TraesCS3D01G068600 chr2B 90.323 124 11 1 1522 1645 540156948 540156826 1.650000e-35 161.0
45 TraesCS3D01G068600 chr5B 77.679 560 111 12 1666 2215 498085312 498084757 4.270000e-86 329.0
46 TraesCS3D01G068600 chr5B 82.979 94 16 0 2448 2541 41473230 41473137 1.020000e-12 86.1
47 TraesCS3D01G068600 chr1B 91.139 237 15 6 5484 5717 36280356 36280123 3.320000e-82 316.0
48 TraesCS3D01G068600 chr6D 90.254 236 19 4 5484 5717 285746129 285745896 7.200000e-79 305.0
49 TraesCS3D01G068600 chr6D 89.083 229 22 3 5491 5717 448628470 448628697 1.210000e-71 281.0
50 TraesCS3D01G068600 chr6A 90.830 229 18 3 5491 5717 77774275 77774048 2.590000e-78 303.0
51 TraesCS3D01G068600 chr6A 82.759 87 15 0 2448 2534 64537032 64536946 1.710000e-10 78.7
52 TraesCS3D01G068600 chr1D 88.608 237 23 4 5484 5717 271795270 271795505 9.380000e-73 285.0
53 TraesCS3D01G068600 chr1D 93.860 114 7 0 1518 1631 349256234 349256347 7.620000e-39 172.0
54 TraesCS3D01G068600 chr5A 89.083 229 21 4 5491 5717 32196577 32196351 1.210000e-71 281.0
55 TraesCS3D01G068600 chr5A 92.373 118 8 1 1522 1639 299273008 299272892 3.540000e-37 167.0
56 TraesCS3D01G068600 chr5A 88.550 131 13 2 1501 1630 414888601 414888472 2.130000e-34 158.0
57 TraesCS3D01G068600 chr6B 88.158 228 24 3 5492 5717 157945348 157945122 9.440000e-68 268.0
58 TraesCS3D01G068600 chr6B 82.667 225 28 8 5043 5260 700639627 700639407 7.560000e-44 189.0
59 TraesCS3D01G068600 chr7D 92.982 114 8 0 1516 1629 30960294 30960181 3.540000e-37 167.0
60 TraesCS3D01G068600 chrUn 87.013 77 10 0 2448 2524 224516036 224516112 2.840000e-13 87.9
61 TraesCS3D01G068600 chrUn 87.013 77 10 0 2448 2524 397217797 397217873 2.840000e-13 87.9


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 TraesCS3D01G068600 chr3D 30234861 30240577 5716 True 10558.000 10558 100.000000 1 5717 1 chr3D.!!$R1 5716
1 TraesCS3D01G068600 chr3D 6950377 6950899 522 False 374.000 374 79.771000 1658 2175 1 chr3D.!!$F1 517
2 TraesCS3D01G068600 chr3A 41989816 41994190 4374 True 1510.525 4359 92.804500 1293 5717 4 chr3A.!!$R3 4424
3 TraesCS3D01G068600 chr3A 41998322 41999679 1357 True 855.500 1201 92.298000 1 1301 2 chr3A.!!$R4 1300
4 TraesCS3D01G068600 chr3A 657275986 657276547 561 True 350.000 350 78.230000 1661 2215 1 chr3A.!!$R2 554
5 TraesCS3D01G068600 chr3B 52769688 52773442 3754 False 2576.500 3374 91.125500 1 4904 2 chr3B.!!$F2 4903
6 TraesCS3D01G068600 chr3B 51813942 51819173 5231 True 926.300 2525 91.481429 1 5057 7 chr3B.!!$R3 5056
7 TraesCS3D01G068600 chr3B 688089126 688089663 537 True 366.000 366 79.221000 1661 2190 1 chr3B.!!$R1 529
8 TraesCS3D01G068600 chr4A 385780077 385781534 1457 True 1729.000 1729 87.965000 3497 4996 1 chr4A.!!$R1 1499
9 TraesCS3D01G068600 chr4A 72971930 72972483 553 False 375.000 375 79.181000 1661 2215 1 chr4A.!!$F1 554
10 TraesCS3D01G068600 chr4B 207123442 207125365 1923 True 616.500 976 86.752000 2728 4259 2 chr4B.!!$R2 1531
11 TraesCS3D01G068600 chr4D 164904386 164905028 642 True 839.000 839 90.199000 3858 4506 1 chr4D.!!$R2 648
12 TraesCS3D01G068600 chr7B 619093354 619093885 531 False 399.000 399 80.410000 1665 2194 1 chr7B.!!$F1 529
13 TraesCS3D01G068600 chr2B 799281955 799282505 550 True 355.000 355 78.750000 1657 2204 1 chr2B.!!$R3 547
14 TraesCS3D01G068600 chr5B 498084757 498085312 555 True 329.000 329 77.679000 1666 2215 1 chr5B.!!$R2 549

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
90 92 0.040204 CTTGGGAAAGGAGCCATGGT 59.960 55.0 14.67 0.0 0.0 3.55 F
1797 2167 0.179045 GATTGTCGGGGCTGCATACT 60.179 55.0 0.50 0.0 0.0 2.12 F
2894 3477 0.107897 ACGAAAGCCATGCACGGATA 60.108 50.0 1.12 0.0 0.0 2.59 F
3677 4730 0.689623 AGGTCAGTTTGAGAGGCAGG 59.310 55.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2350 0.400213 TCAACGACAGGCCTGGAAAT 59.600 50.000 35.42 15.93 34.19 2.17 R
3300 4309 0.035458 GGTCCCAGTTCCAGACAGTG 59.965 60.000 0.00 0.00 31.99 3.66 R
4456 5531 1.739562 CCTCGCAGTCAGAAGGTGC 60.740 63.158 0.00 0.00 0.00 5.01 R
5463 6630 0.317938 CGAGAAAGGTAGATCCGGCG 60.318 60.000 0.00 0.00 41.99 6.46 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
70 72 3.659183 CCAAATCTTGTCCTGGGAGAT 57.341 47.619 0.00 0.00 0.00 2.75
90 92 0.040204 CTTGGGAAAGGAGCCATGGT 59.960 55.000 14.67 0.00 0.00 3.55
93 95 1.186200 GGGAAAGGAGCCATGGTTTC 58.814 55.000 14.67 14.46 0.00 2.78
94 96 1.272704 GGGAAAGGAGCCATGGTTTCT 60.273 52.381 19.43 13.50 0.00 2.52
316 319 9.188588 GATCGTGTTCGGTCATAGAATAATAAA 57.811 33.333 0.00 0.00 45.34 1.40
360 364 6.594788 AGAGCAATGCCTTTTCATTTAGAA 57.405 33.333 0.00 0.00 34.68 2.10
402 407 1.069049 GAGGTGCCATGTTTTGCAAGT 59.931 47.619 0.00 0.00 39.57 3.16
405 410 2.610232 GGTGCCATGTTTTGCAAGTAGG 60.610 50.000 0.00 0.23 39.57 3.18
524 529 3.628942 GCCATCTCAATGCATGTAAGACA 59.371 43.478 0.00 0.00 0.00 3.41
571 576 4.453480 AGGTTCCTTCCAAATGTTCTCA 57.547 40.909 0.00 0.00 0.00 3.27
591 596 4.635223 TCAATCAGGAAGTCAGACAACAG 58.365 43.478 2.66 0.00 0.00 3.16
688 695 7.492352 TCTAACTTAACAGAGCCAACTTTTC 57.508 36.000 0.00 0.00 0.00 2.29
733 740 1.134521 GGCCACGACTGTCATAATCCA 60.135 52.381 8.73 0.00 0.00 3.41
846 914 3.279434 CCCTAACCTGAAATGTGGTAGC 58.721 50.000 0.00 0.00 35.17 3.58
851 919 5.959618 AACCTGAAATGTGGTAGCTTTAC 57.040 39.130 0.00 0.00 35.17 2.01
868 1181 4.083484 GCTTTACGCAATTTACTCACTGGT 60.083 41.667 0.00 0.00 38.92 4.00
878 1191 1.800805 ACTCACTGGTGCAAGAATCG 58.199 50.000 0.00 0.00 0.00 3.34
913 1226 1.232119 GTTTTCGTTCCATGGTCCGT 58.768 50.000 12.58 0.00 0.00 4.69
916 1229 2.495366 TTCGTTCCATGGTCCGTCGG 62.495 60.000 12.58 4.39 0.00 4.79
917 1230 2.818274 GTTCCATGGTCCGTCGGC 60.818 66.667 12.58 1.39 0.00 5.54
936 1271 3.565516 GGCGACTTCTTGTCAAATTTCC 58.434 45.455 0.00 0.00 45.60 3.13
942 1277 1.265635 TCTTGTCAAATTTCCGCCACG 59.734 47.619 0.00 0.00 0.00 4.94
1150 1508 2.765807 ACGCAGGGGAGAGGATGG 60.766 66.667 0.00 0.00 0.00 3.51
1256 1614 2.964740 TGATTGCGAGTCTTCTTCCTG 58.035 47.619 0.00 0.00 0.00 3.86
1296 1654 7.054491 ACTCCCATTTAAACATATTGCCATC 57.946 36.000 0.00 0.00 0.00 3.51
1366 1727 9.532697 GTAGTATTGTTTTGTGTTGTATAACCG 57.467 33.333 0.00 0.00 35.92 4.44
1384 1745 5.567138 AACCGAAATGCCATCTTTTCTAG 57.433 39.130 0.00 0.00 35.44 2.43
1423 1784 7.565680 CCTAGAGAAGTATACATGGTTTTGGT 58.434 38.462 5.50 0.00 0.00 3.67
1462 1823 8.532977 AACAAACGGAATTAGAAAAATGATGG 57.467 30.769 0.00 0.00 0.00 3.51
1477 1838 2.269023 TGATGGGAGCCTTCTTCTTCA 58.731 47.619 0.00 0.00 0.00 3.02
1531 1895 8.970859 AAAAATCATATGAACTACTCCCTCTG 57.029 34.615 9.99 0.00 0.00 3.35
1532 1896 7.682787 AAATCATATGAACTACTCCCTCTGT 57.317 36.000 9.99 0.00 0.00 3.41
1533 1897 7.682787 AATCATATGAACTACTCCCTCTGTT 57.317 36.000 9.99 0.00 0.00 3.16
1534 1898 7.682787 ATCATATGAACTACTCCCTCTGTTT 57.317 36.000 9.99 0.00 0.00 2.83
1535 1899 8.783660 ATCATATGAACTACTCCCTCTGTTTA 57.216 34.615 9.99 0.00 0.00 2.01
1536 1900 8.783660 TCATATGAACTACTCCCTCTGTTTAT 57.216 34.615 1.98 0.00 0.00 1.40
1537 1901 9.213777 TCATATGAACTACTCCCTCTGTTTATT 57.786 33.333 1.98 0.00 0.00 1.40
1538 1902 9.838339 CATATGAACTACTCCCTCTGTTTATTT 57.162 33.333 0.00 0.00 0.00 1.40
1548 1912 9.682465 ACTCCCTCTGTTTATTTTTATAAGACC 57.318 33.333 0.00 0.00 0.00 3.85
1549 1913 9.907229 CTCCCTCTGTTTATTTTTATAAGACCT 57.093 33.333 0.00 0.00 0.00 3.85
1565 1929 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
1566 1930 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
1567 1931 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
1568 1932 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
1569 1933 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
1571 1935 6.147581 CCTTGAAGACATTTCAGACAATGTG 58.852 40.000 12.82 2.31 45.55 3.21
1572 1936 6.238842 CCTTGAAGACATTTCAGACAATGTGT 60.239 38.462 12.82 8.23 45.55 3.72
1573 1937 7.041167 CCTTGAAGACATTTCAGACAATGTGTA 60.041 37.037 12.82 0.00 45.55 2.90
1574 1938 7.800155 TGAAGACATTTCAGACAATGTGTAA 57.200 32.000 12.82 3.20 45.55 2.41
1575 1939 8.219546 TGAAGACATTTCAGACAATGTGTAAA 57.780 30.769 12.82 0.00 45.55 2.01
1576 1940 8.681806 TGAAGACATTTCAGACAATGTGTAAAA 58.318 29.630 12.82 0.00 45.55 1.52
1577 1941 8.856490 AAGACATTTCAGACAATGTGTAAAAC 57.144 30.769 12.82 2.36 45.55 2.43
1578 1942 7.995289 AGACATTTCAGACAATGTGTAAAACA 58.005 30.769 12.82 0.00 45.55 2.83
1579 1943 8.465999 AGACATTTCAGACAATGTGTAAAACAA 58.534 29.630 12.82 0.00 45.55 2.83
1580 1944 8.406172 ACATTTCAGACAATGTGTAAAACAAC 57.594 30.769 0.00 0.00 44.19 3.32
1581 1945 7.491048 ACATTTCAGACAATGTGTAAAACAACC 59.509 33.333 0.00 0.00 44.19 3.77
1582 1946 6.767524 TTCAGACAATGTGTAAAACAACCT 57.232 33.333 0.00 0.00 43.61 3.50
1583 1947 7.867305 TTCAGACAATGTGTAAAACAACCTA 57.133 32.000 0.00 0.00 43.61 3.08
1584 1948 8.458573 TTCAGACAATGTGTAAAACAACCTAT 57.541 30.769 0.00 0.00 43.61 2.57
1585 1949 8.458573 TCAGACAATGTGTAAAACAACCTATT 57.541 30.769 0.00 0.00 43.61 1.73
1586 1950 8.908903 TCAGACAATGTGTAAAACAACCTATTT 58.091 29.630 0.00 0.00 43.61 1.40
1587 1951 9.528018 CAGACAATGTGTAAAACAACCTATTTT 57.472 29.630 0.00 0.00 43.61 1.82
1602 1966 9.458374 ACAACCTATTTTAAATTGTCTGAAACG 57.542 29.630 0.00 0.00 0.00 3.60
1603 1967 9.672086 CAACCTATTTTAAATTGTCTGAAACGA 57.328 29.630 0.00 0.00 0.00 3.85
1604 1968 9.673454 AACCTATTTTAAATTGTCTGAAACGAC 57.327 29.630 0.00 0.00 34.52 4.34
1605 1969 9.063615 ACCTATTTTAAATTGTCTGAAACGACT 57.936 29.630 0.00 0.00 35.00 4.18
1606 1970 9.893305 CCTATTTTAAATTGTCTGAAACGACTT 57.107 29.630 0.00 0.00 35.00 3.01
1613 1977 8.614994 AAATTGTCTGAAACGACTTACAAAAG 57.385 30.769 0.00 0.00 38.77 2.27
1615 1979 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
1616 1980 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
1617 1981 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
1618 1982 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
1619 1983 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
1620 1984 5.348179 TGAAACGACTTACAAAAGTGAACGA 59.652 36.000 0.00 0.00 46.09 3.85
1621 1985 5.783100 AACGACTTACAAAAGTGAACGAA 57.217 34.783 0.00 0.00 46.09 3.85
1622 1986 5.385396 ACGACTTACAAAAGTGAACGAAG 57.615 39.130 0.00 0.00 46.09 3.79
1623 1987 4.269363 ACGACTTACAAAAGTGAACGAAGG 59.731 41.667 0.00 0.00 46.09 3.46
1624 1988 4.318546 CGACTTACAAAAGTGAACGAAGGG 60.319 45.833 0.00 0.00 46.09 3.95
1625 1989 4.773013 ACTTACAAAAGTGAACGAAGGGA 58.227 39.130 0.00 0.00 44.40 4.20
1626 1990 4.814771 ACTTACAAAAGTGAACGAAGGGAG 59.185 41.667 0.00 0.00 44.40 4.30
1627 1991 3.277142 ACAAAAGTGAACGAAGGGAGT 57.723 42.857 0.00 0.00 0.00 3.85
1628 1992 4.411256 ACAAAAGTGAACGAAGGGAGTA 57.589 40.909 0.00 0.00 0.00 2.59
1629 1993 4.377897 ACAAAAGTGAACGAAGGGAGTAG 58.622 43.478 0.00 0.00 0.00 2.57
1630 1994 4.141779 ACAAAAGTGAACGAAGGGAGTAGT 60.142 41.667 0.00 0.00 0.00 2.73
1631 1995 4.684484 AAAGTGAACGAAGGGAGTAGTT 57.316 40.909 0.00 0.00 0.00 2.24
1677 2042 2.273557 GGTGATGCATGCAACCATTTC 58.726 47.619 28.84 19.78 0.00 2.17
1678 2043 2.093869 GGTGATGCATGCAACCATTTCT 60.094 45.455 28.84 10.89 0.00 2.52
1680 2045 3.615496 GTGATGCATGCAACCATTTCTTC 59.385 43.478 26.68 14.53 0.00 2.87
1685 2050 3.305094 GCATGCAACCATTTCTTCGATTG 59.695 43.478 14.21 0.00 0.00 2.67
1747 2113 1.434696 CATCATCTTGGCGGCAACC 59.565 57.895 21.79 0.00 0.00 3.77
1797 2167 0.179045 GATTGTCGGGGCTGCATACT 60.179 55.000 0.50 0.00 0.00 2.12
1884 2258 4.640855 ACACACCAGTCCGTCGCG 62.641 66.667 0.00 0.00 0.00 5.87
1909 2283 2.174107 CGAACACCGCATGCACAG 59.826 61.111 19.57 8.19 0.00 3.66
1931 2305 2.203280 CAAAGGCCGTCACCACCA 60.203 61.111 0.00 0.00 0.00 4.17
1933 2308 1.152830 AAAGGCCGTCACCACCATT 59.847 52.632 0.00 0.00 0.00 3.16
2090 2467 1.145598 CATGCTGCCGAGACTCCAT 59.854 57.895 0.00 0.00 0.00 3.41
2155 2532 1.384525 CCACTAGTCCCTCGAGTCTG 58.615 60.000 12.31 0.00 29.85 3.51
2163 2540 1.662608 CCTCGAGTCTGTGCACACT 59.337 57.895 17.42 13.02 0.00 3.55
2216 2596 3.318275 ACATAAGAGCACCGTCGTCATAT 59.682 43.478 0.00 0.00 0.00 1.78
2220 2600 1.852895 GAGCACCGTCGTCATATGAAC 59.147 52.381 7.07 2.06 0.00 3.18
2258 2638 1.505425 AAAACTTCCGGTGCGAGTAC 58.495 50.000 0.00 0.00 0.00 2.73
2271 2651 5.521010 CGGTGCGAGTACCTAAAATCATTTA 59.479 40.000 8.63 0.00 38.62 1.40
2361 2742 9.822185 GGGCACTGAAATTTATTTTTCTATCAT 57.178 29.630 0.00 0.00 36.71 2.45
2425 2998 2.029649 TGCTTGGACGTACTAACTGACC 60.030 50.000 0.00 0.00 0.00 4.02
2451 3024 6.653320 TGGAAATTCGATGCTTACAACTACTT 59.347 34.615 0.00 0.00 0.00 2.24
2470 3043 9.682465 AACTACTTCCTCTGTTTCTTTTTACTT 57.318 29.630 0.00 0.00 0.00 2.24
2603 3176 7.591421 AATTCCATGATGCATCTAATGACAA 57.409 32.000 26.32 16.98 0.00 3.18
2658 3231 5.403897 TTGACTTGAAGACAAAGCTTACG 57.596 39.130 7.58 0.00 35.49 3.18
2722 3295 6.806668 TTTTCTGTTCAGGGAAAAGGAAAT 57.193 33.333 0.00 0.00 31.53 2.17
2766 3339 7.200434 AGTCCCTAGCTGATTTTTCAGATAA 57.800 36.000 7.16 0.00 38.02 1.75
2813 3386 6.571605 TGGTGCATTAACATATTTGTGGATG 58.428 36.000 0.00 7.39 35.83 3.51
2855 3428 3.271250 CCAACTTGGTCCCTGATGG 57.729 57.895 0.00 0.00 31.35 3.51
2857 3430 1.340405 CCAACTTGGTCCCTGATGGAG 60.340 57.143 0.00 0.00 46.38 3.86
2872 3455 3.008923 TGATGGAGTATGAGCAACAACCA 59.991 43.478 0.00 0.00 0.00 3.67
2887 3470 1.244019 AACCAGGACGAAAGCCATGC 61.244 55.000 0.00 0.00 0.00 4.06
2894 3477 0.107897 ACGAAAGCCATGCACGGATA 60.108 50.000 1.12 0.00 0.00 2.59
2901 3484 0.937304 CCATGCACGGATAAGAACGG 59.063 55.000 0.00 0.00 0.00 4.44
2922 3505 3.751698 GGTTTGGGTGAGTATGACAGAAC 59.248 47.826 0.00 0.00 0.00 3.01
2924 3507 4.698201 TTGGGTGAGTATGACAGAACAA 57.302 40.909 0.00 0.00 0.00 2.83
3007 3973 1.673477 GGGCTTGCAAAAAGGGAGG 59.327 57.895 0.00 0.00 0.00 4.30
3017 3984 3.694072 GCAAAAAGGGAGGCAAAAAGTTT 59.306 39.130 0.00 0.00 0.00 2.66
3018 3985 4.157656 GCAAAAAGGGAGGCAAAAAGTTTT 59.842 37.500 0.00 0.00 0.00 2.43
3019 3986 5.676079 GCAAAAAGGGAGGCAAAAAGTTTTC 60.676 40.000 0.32 0.00 0.00 2.29
3129 4117 8.616942 TCATTTTTCGAACATGTCTCAAGTTTA 58.383 29.630 13.66 0.00 0.00 2.01
3161 4149 1.672030 CATGGTGCTGCGAGGAACA 60.672 57.895 0.00 0.00 37.75 3.18
3260 4269 6.109359 ACTATTAAGACAGCACATGGTTCTC 58.891 40.000 0.00 0.00 0.00 2.87
3300 4309 5.570589 GCTGACAAAATCATAGTTTGCTGAC 59.429 40.000 0.19 0.00 39.16 3.51
3341 4350 1.303309 GAAATGGGATGCTCACCTCG 58.697 55.000 0.00 0.00 0.00 4.63
3419 4428 4.819769 AGCTTTAGCACTCTTCTTCTCTG 58.180 43.478 4.33 0.00 45.16 3.35
3435 4444 8.672823 TTCTTCTCTGTATGGAATCAATCATG 57.327 34.615 0.00 0.00 0.00 3.07
3475 4484 5.580297 CAGCACCTTTCTTAGATCTTCAGTC 59.420 44.000 0.00 0.00 0.00 3.51
3506 4558 6.560003 ATCACAATCCTGGAACACTATACA 57.440 37.500 0.00 0.00 0.00 2.29
3635 4687 2.289547 ACTGTTGGGAAATCGACAAACG 59.710 45.455 0.00 0.00 44.09 3.60
3677 4730 0.689623 AGGTCAGTTTGAGAGGCAGG 59.310 55.000 0.00 0.00 0.00 4.85
3739 4792 7.116736 CAGGGTTAAGTGGTTCAGGTATTTAT 58.883 38.462 0.00 0.00 0.00 1.40
4216 5288 5.530915 CACACTGTAGAATTCCTTCAAACCA 59.469 40.000 0.65 0.00 33.56 3.67
4217 5289 6.207417 CACACTGTAGAATTCCTTCAAACCAT 59.793 38.462 0.65 0.00 33.56 3.55
4218 5290 7.390440 CACACTGTAGAATTCCTTCAAACCATA 59.610 37.037 0.65 0.00 33.56 2.74
4219 5291 8.109634 ACACTGTAGAATTCCTTCAAACCATAT 58.890 33.333 0.65 0.00 33.56 1.78
4271 5343 6.093633 ACCGGCATAGAAAAGTGTATTTTCTC 59.906 38.462 16.49 5.61 44.75 2.87
4388 5461 4.104102 AGAACCAACTGACCACCATCTTTA 59.896 41.667 0.00 0.00 0.00 1.85
4456 5531 9.565090 TTACTGGAATTGATGATCCTTATGAAG 57.435 33.333 0.00 0.00 36.64 3.02
4518 5593 4.555262 ACACCCAAATGTTATCAAAAGCG 58.445 39.130 0.00 0.00 0.00 4.68
4527 5602 9.128107 CAAATGTTATCAAAAGCGACATAGTTT 57.872 29.630 0.00 0.00 31.24 2.66
4599 5678 0.321346 TCATTTCGCTGAGTGAGCCA 59.679 50.000 0.00 0.00 46.01 4.75
4689 5768 5.587844 GGCTGATCAAGTTGTGTCATATCTT 59.412 40.000 12.01 0.00 0.00 2.40
4713 5792 6.061441 TGAAGCAAATGAGTTCTTACAGGAA 58.939 36.000 0.00 0.00 0.00 3.36
4733 5812 6.096141 CAGGAATAGAGACGTATGCTATGGAT 59.904 42.308 0.00 0.00 0.00 3.41
4734 5813 6.096141 AGGAATAGAGACGTATGCTATGGATG 59.904 42.308 0.00 0.00 0.00 3.51
4785 5947 7.202093 CCAAGGGATGTGAAATATGAGGTAGTA 60.202 40.741 0.00 0.00 0.00 1.82
4816 5978 9.853177 TGTCTAGAAAGAGTGATGATAGTATGA 57.147 33.333 0.00 0.00 30.45 2.15
4821 5983 9.194972 AGAAAGAGTGATGATAGTATGAGAACA 57.805 33.333 0.00 0.00 0.00 3.18
4822 5984 9.979578 GAAAGAGTGATGATAGTATGAGAACAT 57.020 33.333 0.00 0.00 40.16 2.71
4916 6080 0.039798 GTGTGGCTGTGTGCATTGAG 60.040 55.000 0.00 0.00 45.15 3.02
4980 6145 5.570234 TCTAAACACACACAGGAAAAACC 57.430 39.130 0.00 0.00 39.35 3.27
5065 6232 7.540055 GCCATTAGCAATTTAATATGACTGAGC 59.460 37.037 0.00 0.00 42.97 4.26
5090 6257 2.618709 CTCCACCCGCAAAGGAATATTC 59.381 50.000 6.93 6.93 45.00 1.75
5116 6283 0.914644 CTGTGTCCCACTGATCCCAT 59.085 55.000 0.00 0.00 35.76 4.00
5137 6304 1.334869 CAATTGCGCTAATCCCTCCAC 59.665 52.381 9.73 0.00 0.00 4.02
5143 6310 2.811873 GCGCTAATCCCTCCACATCAAT 60.812 50.000 0.00 0.00 0.00 2.57
5144 6311 3.480470 CGCTAATCCCTCCACATCAATT 58.520 45.455 0.00 0.00 0.00 2.32
5145 6312 3.499918 CGCTAATCCCTCCACATCAATTC 59.500 47.826 0.00 0.00 0.00 2.17
5146 6313 3.823304 GCTAATCCCTCCACATCAATTCC 59.177 47.826 0.00 0.00 0.00 3.01
5147 6314 4.446889 GCTAATCCCTCCACATCAATTCCT 60.447 45.833 0.00 0.00 0.00 3.36
5148 6315 3.872459 ATCCCTCCACATCAATTCCTC 57.128 47.619 0.00 0.00 0.00 3.71
5149 6316 1.846439 TCCCTCCACATCAATTCCTCC 59.154 52.381 0.00 0.00 0.00 4.30
5150 6317 1.133668 CCCTCCACATCAATTCCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
5151 6318 1.133668 CCTCCACATCAATTCCTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
5152 6319 1.849039 CTCCACATCAATTCCTCCCCT 59.151 52.381 0.00 0.00 0.00 4.79
5153 6320 3.048600 CTCCACATCAATTCCTCCCCTA 58.951 50.000 0.00 0.00 0.00 3.53
5154 6321 2.777692 TCCACATCAATTCCTCCCCTAC 59.222 50.000 0.00 0.00 0.00 3.18
5155 6322 2.158608 CCACATCAATTCCTCCCCTACC 60.159 54.545 0.00 0.00 0.00 3.18
5156 6323 2.509548 CACATCAATTCCTCCCCTACCA 59.490 50.000 0.00 0.00 0.00 3.25
5157 6324 3.053693 CACATCAATTCCTCCCCTACCAA 60.054 47.826 0.00 0.00 0.00 3.67
5158 6325 3.053619 ACATCAATTCCTCCCCTACCAAC 60.054 47.826 0.00 0.00 0.00 3.77
5159 6326 2.638325 TCAATTCCTCCCCTACCAACA 58.362 47.619 0.00 0.00 0.00 3.33
5180 6347 4.796495 CCTAACCCAGCGCCCCAC 62.796 72.222 2.29 0.00 0.00 4.61
5222 6389 3.434641 CCATTCATTCATCGCTAATCGCT 59.565 43.478 0.00 0.00 38.27 4.93
5344 6511 1.588082 GCCGTTGGTTCTCGAGGTA 59.412 57.895 13.56 0.00 0.00 3.08
5406 6573 2.171237 TCACTAGCATAACCAGCAGCAT 59.829 45.455 0.00 0.00 0.00 3.79
5491 6658 4.840005 CCTTTCTCGCCGCTCCCC 62.840 72.222 0.00 0.00 0.00 4.81
5509 6676 1.804326 CGGGTTGGACGATGACGAC 60.804 63.158 0.00 0.00 42.66 4.34
5528 6695 1.521681 GCTATCGGCTTTGCTCGGT 60.522 57.895 0.00 0.00 38.06 4.69
5547 6714 1.068194 GTGTCGTGTCTCCTCTTGAGG 60.068 57.143 10.28 10.28 41.76 3.86
5552 6719 2.232452 CGTGTCTCCTCTTGAGGACATT 59.768 50.000 14.79 0.00 41.76 2.71
5556 6723 3.513515 GTCTCCTCTTGAGGACATTGTCT 59.486 47.826 14.79 2.95 41.76 3.41
5599 6766 0.598562 ACTCAGTGCTCGTGTAGGTG 59.401 55.000 0.00 0.00 0.00 4.00
5605 6772 1.375523 GCTCGTGTAGGTGGGTTGG 60.376 63.158 0.00 0.00 0.00 3.77
5678 6846 3.492102 AGTGTGTCAGGCAAGTTATGT 57.508 42.857 0.00 0.00 0.00 2.29
5691 6859 0.390735 GTTATGTCGGCCAACCTCGT 60.391 55.000 2.24 0.00 0.00 4.18
5703 6871 1.927174 CAACCTCGTAGGATTGAAGCG 59.073 52.381 7.76 0.00 37.67 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 0.332632 CCATGGCTCCTTTCCCAAGA 59.667 55.000 0.00 0.00 34.25 3.02
90 92 6.769512 AGGACAAGTATCACAAGCTAAGAAA 58.230 36.000 0.00 0.00 0.00 2.52
93 95 6.166279 TGAAGGACAAGTATCACAAGCTAAG 58.834 40.000 0.00 0.00 0.00 2.18
94 96 6.109156 TGAAGGACAAGTATCACAAGCTAA 57.891 37.500 0.00 0.00 0.00 3.09
140 142 6.774656 ACAGAAAACAAGGTGATTCTCAAGAT 59.225 34.615 0.00 0.00 29.56 2.40
162 164 7.417612 AGTGTGCATGTTTTTCTACTTTACAG 58.582 34.615 0.00 0.00 0.00 2.74
209 211 5.589855 ACAATCGAGAAATTGGTATGCATGA 59.410 36.000 10.16 0.00 40.28 3.07
211 213 7.566760 TTACAATCGAGAAATTGGTATGCAT 57.433 32.000 3.79 3.79 40.28 3.96
264 266 7.881643 ATTAACTCAATTTTACATGCGCAAA 57.118 28.000 17.11 3.42 0.00 3.68
316 319 3.140325 TGCCGATTCCTTGACTTCTTT 57.860 42.857 0.00 0.00 0.00 2.52
322 326 0.729690 GCTCTTGCCGATTCCTTGAC 59.270 55.000 0.00 0.00 0.00 3.18
360 364 7.624077 ACCTCTGTACATTAACCCTCTATTTCT 59.376 37.037 0.00 0.00 0.00 2.52
402 407 2.496070 TCTTGCTAAAGCTTCGCTCCTA 59.504 45.455 18.05 0.00 38.25 2.94
405 410 4.348198 AATTCTTGCTAAAGCTTCGCTC 57.652 40.909 18.05 2.56 38.25 5.03
442 447 3.117963 CCCCTCGACTCTTCCTAAGACTA 60.118 52.174 0.00 0.00 33.12 2.59
524 529 3.190535 CGTCCAATTTTTCAACGGGATCT 59.809 43.478 0.00 0.00 0.00 2.75
571 576 3.406764 GCTGTTGTCTGACTTCCTGATT 58.593 45.455 9.51 0.00 0.00 2.57
591 596 1.227853 AGAAACACACCCTCACCGC 60.228 57.895 0.00 0.00 0.00 5.68
603 608 7.227049 ACACAAAAGGAAAAAGAGAGAAACA 57.773 32.000 0.00 0.00 0.00 2.83
642 649 0.035820 TTTATGACACGTGGGGCTCC 60.036 55.000 21.57 0.00 0.00 4.70
688 695 1.813859 CCAAGGCTGACATGGCATG 59.186 57.895 25.31 25.31 34.73 4.06
733 740 6.115446 TGATCGCTTTGATTAAATCTGACCT 58.885 36.000 0.00 0.00 37.47 3.85
846 914 5.382303 CACCAGTGAGTAAATTGCGTAAAG 58.618 41.667 0.00 0.00 0.00 1.85
851 919 1.535028 TGCACCAGTGAGTAAATTGCG 59.465 47.619 0.99 0.00 0.00 4.85
868 1181 8.290325 CGTCTATATATATAGCCGATTCTTGCA 58.710 37.037 22.59 2.36 39.26 4.08
878 1191 9.230932 GGAACGAAAACGTCTATATATATAGCC 57.769 37.037 20.69 11.72 36.47 3.93
898 1211 2.569657 CGACGGACCATGGAACGA 59.430 61.111 29.62 0.00 0.00 3.85
907 1220 3.278592 AAGAAGTCGCCGACGGACC 62.279 63.158 20.50 3.73 40.63 4.46
919 1232 2.955660 TGGCGGAAATTTGACAAGAAGT 59.044 40.909 0.00 0.00 0.00 3.01
1256 1614 2.608090 GGGAGTATTAACTGCAACGAGC 59.392 50.000 0.00 0.00 45.33 5.03
1275 1633 6.819284 ACAGATGGCAATATGTTTAAATGGG 58.181 36.000 0.00 0.00 34.57 4.00
1296 1654 9.318041 CGTTGTCAAAAGAAGATGTATTAACAG 57.682 33.333 0.00 0.00 39.49 3.16
1412 1773 9.810545 TTTTTCTAGTTTCTAACCAAAACCATG 57.189 29.630 0.00 0.00 37.33 3.66
1462 1823 4.486125 AGAAGATGAAGAAGAAGGCTCC 57.514 45.455 0.00 0.00 0.00 4.70
1523 1887 9.907229 AGGTCTTATAAAAATAAACAGAGGGAG 57.093 33.333 0.00 0.00 0.00 4.30
1539 1903 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
1540 1904 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
1541 1905 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
1542 1906 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
1543 1907 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
1544 1908 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
1545 1909 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
1546 1910 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
1547 1911 6.147581 CACATTGTCTGAAATGTCTTCAAGG 58.852 40.000 12.25 0.00 45.47 3.61
1548 1912 6.732154 ACACATTGTCTGAAATGTCTTCAAG 58.268 36.000 12.25 6.29 45.47 3.02
1549 1913 6.698008 ACACATTGTCTGAAATGTCTTCAA 57.302 33.333 12.25 0.00 45.47 2.69
1550 1914 7.800155 TTACACATTGTCTGAAATGTCTTCA 57.200 32.000 12.25 0.00 45.47 3.02
1551 1915 8.958043 GTTTTACACATTGTCTGAAATGTCTTC 58.042 33.333 12.25 0.00 45.47 2.87
1552 1916 8.465999 TGTTTTACACATTGTCTGAAATGTCTT 58.534 29.630 12.25 7.68 45.47 3.01
1553 1917 7.995289 TGTTTTACACATTGTCTGAAATGTCT 58.005 30.769 12.25 6.84 45.47 3.41
1554 1918 8.531530 GTTGTTTTACACATTGTCTGAAATGTC 58.468 33.333 12.25 5.04 45.47 3.06
1556 1920 7.706179 AGGTTGTTTTACACATTGTCTGAAATG 59.294 33.333 9.50 9.50 42.21 2.32
1557 1921 7.781056 AGGTTGTTTTACACATTGTCTGAAAT 58.219 30.769 0.00 0.00 34.43 2.17
1558 1922 7.164230 AGGTTGTTTTACACATTGTCTGAAA 57.836 32.000 0.00 0.00 34.43 2.69
1559 1923 6.767524 AGGTTGTTTTACACATTGTCTGAA 57.232 33.333 0.00 0.00 34.43 3.02
1560 1924 8.458573 AATAGGTTGTTTTACACATTGTCTGA 57.541 30.769 0.00 0.00 34.43 3.27
1561 1925 9.528018 AAAATAGGTTGTTTTACACATTGTCTG 57.472 29.630 0.00 0.00 34.43 3.51
1576 1940 9.458374 CGTTTCAGACAATTTAAAATAGGTTGT 57.542 29.630 4.25 4.25 35.87 3.32
1577 1941 9.672086 TCGTTTCAGACAATTTAAAATAGGTTG 57.328 29.630 0.00 0.00 0.00 3.77
1578 1942 9.673454 GTCGTTTCAGACAATTTAAAATAGGTT 57.327 29.630 0.00 0.00 40.65 3.50
1579 1943 9.063615 AGTCGTTTCAGACAATTTAAAATAGGT 57.936 29.630 0.00 0.00 43.24 3.08
1580 1944 9.893305 AAGTCGTTTCAGACAATTTAAAATAGG 57.107 29.630 0.00 0.00 43.24 2.57
1587 1951 9.710979 CTTTTGTAAGTCGTTTCAGACAATTTA 57.289 29.630 0.00 0.00 43.24 1.40
1588 1952 8.241367 ACTTTTGTAAGTCGTTTCAGACAATTT 58.759 29.630 0.00 0.00 40.60 1.82
1589 1953 7.696453 CACTTTTGTAAGTCGTTTCAGACAATT 59.304 33.333 0.00 0.00 42.67 2.32
1590 1954 7.065324 TCACTTTTGTAAGTCGTTTCAGACAAT 59.935 33.333 0.00 0.00 42.67 2.71
1591 1955 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
1592 1956 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
1593 1957 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
1594 1958 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
1595 1959 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
1596 1960 5.348179 TCGTTCACTTTTGTAAGTCGTTTCA 59.652 36.000 0.00 0.00 42.67 2.69
1597 1961 5.788467 TCGTTCACTTTTGTAAGTCGTTTC 58.212 37.500 0.00 0.00 42.67 2.78
1598 1962 5.783100 TCGTTCACTTTTGTAAGTCGTTT 57.217 34.783 0.00 0.00 42.67 3.60
1599 1963 5.220529 CCTTCGTTCACTTTTGTAAGTCGTT 60.221 40.000 0.00 0.00 42.67 3.85
1600 1964 4.269363 CCTTCGTTCACTTTTGTAAGTCGT 59.731 41.667 0.00 0.00 42.67 4.34
1601 1965 4.318546 CCCTTCGTTCACTTTTGTAAGTCG 60.319 45.833 0.00 0.00 42.67 4.18
1602 1966 4.812626 TCCCTTCGTTCACTTTTGTAAGTC 59.187 41.667 0.00 0.00 42.67 3.01
1603 1967 4.773013 TCCCTTCGTTCACTTTTGTAAGT 58.227 39.130 0.00 0.00 45.40 2.24
1604 1968 4.814771 ACTCCCTTCGTTCACTTTTGTAAG 59.185 41.667 0.00 0.00 37.40 2.34
1605 1969 4.773013 ACTCCCTTCGTTCACTTTTGTAA 58.227 39.130 0.00 0.00 0.00 2.41
1606 1970 4.411256 ACTCCCTTCGTTCACTTTTGTA 57.589 40.909 0.00 0.00 0.00 2.41
1607 1971 3.277142 ACTCCCTTCGTTCACTTTTGT 57.723 42.857 0.00 0.00 0.00 2.83
1608 1972 4.377897 ACTACTCCCTTCGTTCACTTTTG 58.622 43.478 0.00 0.00 0.00 2.44
1609 1973 4.684484 ACTACTCCCTTCGTTCACTTTT 57.316 40.909 0.00 0.00 0.00 2.27
1610 1974 4.684484 AACTACTCCCTTCGTTCACTTT 57.316 40.909 0.00 0.00 0.00 2.66
1611 1975 4.684484 AAACTACTCCCTTCGTTCACTT 57.316 40.909 0.00 0.00 0.00 3.16
1612 1976 4.684484 AAAACTACTCCCTTCGTTCACT 57.316 40.909 0.00 0.00 0.00 3.41
1651 2015 4.820744 GCATGCATCACCCCGGGT 62.821 66.667 21.85 2.03 35.62 5.28
1677 2042 5.869753 AAGGTCTTGATGAACAATCGAAG 57.130 39.130 0.00 0.00 38.22 3.79
1678 2043 6.227522 TGTAAGGTCTTGATGAACAATCGAA 58.772 36.000 0.00 0.00 38.22 3.71
1680 2045 6.480524 TTGTAAGGTCTTGATGAACAATCG 57.519 37.500 0.00 0.00 38.22 3.34
1747 2113 1.595466 ACTGGATAGGAGTAGCGACG 58.405 55.000 0.00 0.00 0.00 5.12
1797 2167 2.040947 TGGGCTTTGGTGTGATGTATGA 59.959 45.455 0.00 0.00 0.00 2.15
1836 2207 0.671472 GCAATTCAGCTTGGTTGGGC 60.671 55.000 0.00 0.00 0.00 5.36
1912 2286 4.025401 GTGGTGACGGCCTTTGCG 62.025 66.667 0.00 0.00 38.85 4.85
1916 2290 0.469144 AAAATGGTGGTGACGGCCTT 60.469 50.000 0.00 0.00 0.00 4.35
1931 2305 5.582953 TCTGAAGATGGATTGGTGGAAAAT 58.417 37.500 0.00 0.00 0.00 1.82
1933 2308 4.592942 CTCTGAAGATGGATTGGTGGAAA 58.407 43.478 0.00 0.00 0.00 3.13
1974 2350 0.400213 TCAACGACAGGCCTGGAAAT 59.600 50.000 35.42 15.93 34.19 2.17
1977 2353 2.741092 GTCAACGACAGGCCTGGA 59.259 61.111 35.42 20.12 32.09 3.86
2090 2467 1.340308 CCCTGTGATGCCTCAATGACA 60.340 52.381 0.00 0.00 31.85 3.58
2099 2476 3.134127 GGCGTTCCCTGTGATGCC 61.134 66.667 0.00 0.00 37.61 4.40
2135 2512 0.256464 AGACTCGAGGGACTAGTGGG 59.744 60.000 18.41 0.00 41.55 4.61
2155 2532 3.184986 GCATCATTTTTGGAAGTGTGCAC 59.815 43.478 10.75 10.75 33.78 4.57
2163 2540 2.035910 TGGGGGCATCATTTTTGGAA 57.964 45.000 0.00 0.00 0.00 3.53
2197 2577 2.946990 TCATATGACGACGGTGCTCTTA 59.053 45.455 0.00 0.00 0.00 2.10
2216 2596 9.862371 TTTTAACTTTTCAATGCTAACAGTTCA 57.138 25.926 0.00 0.00 0.00 3.18
2271 2651 8.141268 CGTGGCATATTTTTACTTTGGGAATAT 58.859 33.333 0.00 0.00 0.00 1.28
2325 2705 2.198827 TTCAGTGCCCGTGATTCATT 57.801 45.000 0.00 0.00 0.00 2.57
2329 2709 5.659440 AATAAATTTCAGTGCCCGTGATT 57.341 34.783 0.00 0.00 0.00 2.57
2372 2753 5.975939 GGAAGCACTCATTTATGATTCAAGC 59.024 40.000 4.81 0.00 41.83 4.01
2425 2998 5.551760 AGTTGTAAGCATCGAATTTCCAG 57.448 39.130 0.00 0.00 0.00 3.86
2451 3024 6.767524 TGCAAAGTAAAAAGAAACAGAGGA 57.232 33.333 0.00 0.00 0.00 3.71
2583 3156 8.141909 AGAAAATTGTCATTAGATGCATCATGG 58.858 33.333 27.81 14.13 0.00 3.66
2641 3214 2.939756 TGCACGTAAGCTTTGTCTTCAA 59.060 40.909 3.20 0.00 45.62 2.69
2644 3217 2.802816 CTCTGCACGTAAGCTTTGTCTT 59.197 45.455 3.20 0.00 45.62 3.01
2672 3245 4.168101 TGAATGGTACTCCCTCTGTTTCT 58.832 43.478 0.00 0.00 0.00 2.52
2685 3258 7.214467 TGAACAGAAAAGGATTGAATGGTAC 57.786 36.000 0.00 0.00 0.00 3.34
2688 3261 5.337009 CCCTGAACAGAAAAGGATTGAATGG 60.337 44.000 3.19 0.00 32.43 3.16
2722 3295 9.713684 AGGGACTAATAAAATGGATTGAATGAA 57.286 29.630 0.00 0.00 36.02 2.57
2741 3314 6.814954 ATCTGAAAAATCAGCTAGGGACTA 57.185 37.500 0.97 0.00 37.50 2.59
2766 3339 3.384146 TGTGTTGCACATGGTGAGAAATT 59.616 39.130 0.00 0.00 39.62 1.82
2813 3386 2.299013 GGGTTGGTTTTGAGGATTGGAC 59.701 50.000 0.00 0.00 0.00 4.02
2848 3421 3.548745 TGTTGCTCATACTCCATCAGG 57.451 47.619 0.00 0.00 0.00 3.86
2854 3427 2.027192 TCCTGGTTGTTGCTCATACTCC 60.027 50.000 0.00 0.00 0.00 3.85
2855 3428 3.003480 GTCCTGGTTGTTGCTCATACTC 58.997 50.000 0.00 0.00 0.00 2.59
2857 3430 1.732259 CGTCCTGGTTGTTGCTCATAC 59.268 52.381 0.00 0.00 0.00 2.39
2872 3455 2.034879 CGTGCATGGCTTTCGTCCT 61.035 57.895 0.00 0.00 0.00 3.85
2887 3470 1.735571 CCCAAACCGTTCTTATCCGTG 59.264 52.381 0.00 0.00 0.00 4.94
2894 3477 3.071892 TCATACTCACCCAAACCGTTCTT 59.928 43.478 0.00 0.00 0.00 2.52
2901 3484 4.385825 TGTTCTGTCATACTCACCCAAAC 58.614 43.478 0.00 0.00 0.00 2.93
2922 3505 1.406539 ACAAGCCAAACTCAGCTGTTG 59.593 47.619 14.67 10.95 39.87 3.33
2924 3507 1.312815 GACAAGCCAAACTCAGCTGT 58.687 50.000 14.67 0.00 39.87 4.40
3007 3973 6.237728 CCCTGTCGTTTAAGAAAACTTTTTGC 60.238 38.462 0.00 0.00 42.39 3.68
3017 3984 6.016108 CCAAATAAACCCCTGTCGTTTAAGAA 60.016 38.462 0.00 0.00 38.72 2.52
3018 3985 5.474189 CCAAATAAACCCCTGTCGTTTAAGA 59.526 40.000 0.00 0.00 38.72 2.10
3019 3986 5.474189 TCCAAATAAACCCCTGTCGTTTAAG 59.526 40.000 0.00 0.00 38.72 1.85
3161 4149 1.846007 TGGTTTTGTCAGCACCAACT 58.154 45.000 3.26 0.00 37.66 3.16
3260 4269 1.149174 AGCACCAACCAGTCCACAG 59.851 57.895 0.00 0.00 0.00 3.66
3300 4309 0.035458 GGTCCCAGTTCCAGACAGTG 59.965 60.000 0.00 0.00 31.99 3.66
3341 4350 2.093890 TGGTTGCATGGACATGTCATC 58.906 47.619 26.47 11.33 40.80 2.92
3419 4428 5.048921 CACTCTGCCATGATTGATTCCATAC 60.049 44.000 0.00 0.00 0.00 2.39
3435 4444 0.381089 GCTGATTCATGCACTCTGCC 59.619 55.000 0.00 0.00 44.23 4.85
3475 4484 5.416639 TGTTCCAGGATTGTGATTTCTCATG 59.583 40.000 0.00 0.00 32.98 3.07
3635 4687 2.229792 TGGACAGTCATGCCAAAGAAC 58.770 47.619 2.17 0.00 32.08 3.01
3677 4730 4.762251 ACAACCCTTCTGATTTAGCAGTTC 59.238 41.667 0.00 0.00 37.20 3.01
4150 5208 8.969121 TGAATGTAGAATTGTGCAGTAATTTG 57.031 30.769 9.50 0.00 0.00 2.32
4218 5290 9.261035 ACCTTGATAATAAGATCGACCAGATAT 57.739 33.333 0.00 0.00 40.26 1.63
4219 5291 8.651589 ACCTTGATAATAAGATCGACCAGATA 57.348 34.615 0.00 0.00 40.26 1.98
4271 5343 4.827284 AGTGGGACATTCAAAAACACCTAG 59.173 41.667 0.00 0.00 44.52 3.02
4456 5531 1.739562 CCTCGCAGTCAGAAGGTGC 60.740 63.158 0.00 0.00 0.00 5.01
4539 5614 3.176924 AGGAACCTCTTACAGAGCAGA 57.823 47.619 0.00 0.00 40.98 4.26
4689 5768 5.620206 TCCTGTAAGAACTCATTTGCTTCA 58.380 37.500 0.00 0.00 34.07 3.02
4713 5792 7.468141 TTTCATCCATAGCATACGTCTCTAT 57.532 36.000 0.00 0.00 0.00 1.98
4935 6099 4.692228 ACTTTACAAAATGCAAGTGGGTG 58.308 39.130 0.00 0.00 0.00 4.61
4942 6107 8.865001 GTGTGTTTAGAACTTTACAAAATGCAA 58.135 29.630 0.00 0.00 0.00 4.08
4980 6145 5.243730 TCAGGGTGGCTTTAAGAAAGAAATG 59.756 40.000 3.15 0.00 41.02 2.32
5065 6232 3.726517 CTTTGCGGGTGGAGTGCG 61.727 66.667 0.00 0.00 0.00 5.34
5080 6247 0.535102 CAGCGGGCGGAATATTCCTT 60.535 55.000 27.86 7.55 45.33 3.36
5116 6283 1.211703 TGGAGGGATTAGCGCAATTGA 59.788 47.619 11.47 0.00 0.00 2.57
5137 6304 3.053693 TGTTGGTAGGGGAGGAATTGATG 60.054 47.826 0.00 0.00 0.00 3.07
5143 6310 1.920351 GGAATGTTGGTAGGGGAGGAA 59.080 52.381 0.00 0.00 0.00 3.36
5144 6311 1.591768 GGAATGTTGGTAGGGGAGGA 58.408 55.000 0.00 0.00 0.00 3.71
5145 6312 0.551396 GGGAATGTTGGTAGGGGAGG 59.449 60.000 0.00 0.00 0.00 4.30
5146 6313 1.596496 AGGGAATGTTGGTAGGGGAG 58.404 55.000 0.00 0.00 0.00 4.30
5147 6314 2.848071 GTTAGGGAATGTTGGTAGGGGA 59.152 50.000 0.00 0.00 0.00 4.81
5148 6315 2.092049 GGTTAGGGAATGTTGGTAGGGG 60.092 54.545 0.00 0.00 0.00 4.79
5149 6316 2.092049 GGGTTAGGGAATGTTGGTAGGG 60.092 54.545 0.00 0.00 0.00 3.53
5150 6317 2.578940 TGGGTTAGGGAATGTTGGTAGG 59.421 50.000 0.00 0.00 0.00 3.18
5151 6318 3.886123 CTGGGTTAGGGAATGTTGGTAG 58.114 50.000 0.00 0.00 0.00 3.18
5152 6319 2.025699 GCTGGGTTAGGGAATGTTGGTA 60.026 50.000 0.00 0.00 0.00 3.25
5153 6320 1.272480 GCTGGGTTAGGGAATGTTGGT 60.272 52.381 0.00 0.00 0.00 3.67
5154 6321 1.474330 GCTGGGTTAGGGAATGTTGG 58.526 55.000 0.00 0.00 0.00 3.77
5155 6322 1.094785 CGCTGGGTTAGGGAATGTTG 58.905 55.000 0.00 0.00 41.61 3.33
5156 6323 0.679960 GCGCTGGGTTAGGGAATGTT 60.680 55.000 0.00 0.00 41.61 2.71
5157 6324 1.077716 GCGCTGGGTTAGGGAATGT 60.078 57.895 0.00 0.00 41.61 2.71
5158 6325 1.823899 GGCGCTGGGTTAGGGAATG 60.824 63.158 7.64 0.00 41.61 2.67
5159 6326 2.595655 GGCGCTGGGTTAGGGAAT 59.404 61.111 7.64 0.00 41.61 3.01
5344 6511 4.869861 GTGTTGTTTTGGCTCTGTTCAAAT 59.130 37.500 0.00 0.00 33.58 2.32
5406 6573 3.583276 CTACGAAGCGGCACCCACA 62.583 63.158 1.45 0.00 0.00 4.17
5433 6600 2.426024 GACGTGTGGCTCACCTCTATTA 59.574 50.000 13.55 0.00 43.51 0.98
5462 6629 0.597898 GAGAAAGGTAGATCCGGCGC 60.598 60.000 0.00 0.00 41.99 6.53
5463 6630 0.317938 CGAGAAAGGTAGATCCGGCG 60.318 60.000 0.00 0.00 41.99 6.46
5491 6658 1.804326 GTCGTCATCGTCCAACCCG 60.804 63.158 0.00 0.00 38.33 5.28
5547 6714 5.746245 CCGAGTCTATCTTCAAGACAATGTC 59.254 44.000 5.02 5.02 44.77 3.06
5552 6719 4.332828 TGACCGAGTCTATCTTCAAGACA 58.667 43.478 6.06 0.00 44.77 3.41
5556 6723 3.948473 CCTCTGACCGAGTCTATCTTCAA 59.052 47.826 5.77 0.00 38.11 2.69
5678 6846 0.974010 AATCCTACGAGGTTGGCCGA 60.974 55.000 0.00 0.00 40.50 5.54
5691 6859 3.769739 ACATATGCCGCTTCAATCCTA 57.230 42.857 1.58 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.