Multiple sequence alignment - TraesCS3B01G597000

Loading Multiple Alignment...

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 TraesCS3B01G597000 chr3B 100.000 4290 0 0 1 4290 819649047 819653336 0.000000e+00 7923.0
1 TraesCS3B01G597000 chr3B 96.747 1568 47 2 1 1567 819521397 819522961 0.000000e+00 2610.0
2 TraesCS3B01G597000 chr3B 93.539 1718 90 12 1819 3532 819381974 819383674 0.000000e+00 2538.0
3 TraesCS3B01G597000 chr3B 92.243 1534 107 6 2009 3533 819522960 819524490 0.000000e+00 2163.0
4 TraesCS3B01G597000 chr3B 92.210 1489 107 5 2032 3514 819299949 819301434 0.000000e+00 2098.0
5 TraesCS3B01G597000 chr3B 89.230 1662 130 29 1 1647 819380361 819381988 0.000000e+00 2032.0
6 TraesCS3B01G597000 chr3B 84.323 1550 197 18 2007 3531 819740852 819742380 0.000000e+00 1474.0
7 TraesCS3B01G597000 chr3B 97.059 578 16 1 920 1496 819298075 819298652 0.000000e+00 972.0
8 TraesCS3B01G597000 chr3B 93.384 529 34 1 3534 4062 787617836 787617309 0.000000e+00 782.0
9 TraesCS3B01G597000 chr3B 91.155 554 41 7 1 551 819296050 819296598 0.000000e+00 745.0
10 TraesCS3B01G597000 chr3B 87.358 530 63 4 959 1485 819740033 819740561 4.750000e-169 604.0
11 TraesCS3B01G597000 chr3B 96.522 230 8 0 4061 4290 819383666 819383895 8.710000e-102 381.0
12 TraesCS3B01G597000 chr3B 92.208 231 17 1 4061 4290 819524481 819524711 4.140000e-85 326.0
13 TraesCS3B01G597000 chr3B 91.026 234 14 3 4061 4290 819302191 819302421 4.170000e-80 309.0
14 TraesCS3B01G597000 chr3B 98.571 70 1 0 680 749 819296591 819296660 1.620000e-24 124.0
15 TraesCS3B01G597000 chr3D 92.833 1507 97 7 1923 3421 608951784 608953287 0.000000e+00 2174.0
16 TraesCS3B01G597000 chr3D 89.299 1654 131 17 1 1647 608949918 608951532 0.000000e+00 2032.0
17 TraesCS3B01G597000 chr3D 88.584 1603 122 22 1 1595 608980300 608981849 0.000000e+00 1890.0
18 TraesCS3B01G597000 chr3D 84.829 1549 189 19 2003 3531 609005391 609006913 0.000000e+00 1517.0
19 TraesCS3B01G597000 chr3D 86.736 1244 159 5 2145 3385 609286678 609285438 0.000000e+00 1378.0
20 TraesCS3B01G597000 chr3D 88.658 529 55 4 959 1483 609004575 609005102 1.300000e-179 640.0
21 TraesCS3B01G597000 chr3D 92.174 115 2 4 1819 1933 608981856 608981963 5.740000e-34 156.0
22 TraesCS3B01G597000 chr3D 91.304 115 3 4 1819 1933 608951518 608951625 2.670000e-32 150.0
23 TraesCS3B01G597000 chr3A 88.117 1498 129 18 1 1490 742331292 742332748 0.000000e+00 1735.0
24 TraesCS3B01G597000 chr3A 92.506 1201 81 5 2340 3533 742313762 742314960 0.000000e+00 1711.0
25 TraesCS3B01G597000 chr3A 84.238 1548 202 21 2003 3531 742356198 742357722 0.000000e+00 1469.0
26 TraesCS3B01G597000 chr3A 87.002 1154 139 10 2145 3293 742872387 742871240 0.000000e+00 1290.0
27 TraesCS3B01G597000 chr3A 89.348 629 43 12 616 1239 742277392 742278001 0.000000e+00 769.0
28 TraesCS3B01G597000 chr3A 92.697 534 29 6 1819 2352 742298540 742299063 0.000000e+00 761.0
29 TraesCS3B01G597000 chr3A 88.593 526 55 3 959 1483 742355389 742355910 6.050000e-178 634.0
30 TraesCS3B01G597000 chr3A 89.286 420 23 10 1230 1647 742298155 742298554 1.380000e-139 507.0
31 TraesCS3B01G597000 chr3A 95.238 42 1 1 1648 1689 62541909 62541949 9.960000e-07 65.8
32 TraesCS3B01G597000 chr2B 94.549 532 27 1 3534 4065 646065946 646065417 0.000000e+00 821.0
33 TraesCS3B01G597000 chr2B 93.962 530 27 4 3531 4059 73618410 73618935 0.000000e+00 797.0
34 TraesCS3B01G597000 chr2B 93.762 529 32 1 3534 4062 790772816 790772289 0.000000e+00 793.0
35 TraesCS3B01G597000 chr4D 94.173 532 31 0 3533 4064 68859089 68858558 0.000000e+00 811.0
36 TraesCS3B01G597000 chr6B 94.140 529 29 1 3534 4062 375789474 375788948 0.000000e+00 804.0
37 TraesCS3B01G597000 chr4B 93.974 531 31 1 3533 4063 632707872 632707343 0.000000e+00 802.0
38 TraesCS3B01G597000 chr1B 93.820 534 30 2 3530 4063 561632151 561632681 0.000000e+00 800.0
39 TraesCS3B01G597000 chr1B 93.916 526 31 1 3534 4059 74826822 74827346 0.000000e+00 793.0
40 TraesCS3B01G597000 chrUn 82.749 342 45 2 1 341 480923341 480923013 4.200000e-75 292.0
41 TraesCS3B01G597000 chr1D 76.471 374 68 14 13 372 295133397 295133030 7.330000e-43 185.0
42 TraesCS3B01G597000 chr5A 73.506 502 109 19 6 495 443726202 443725713 7.380000e-38 169.0
43 TraesCS3B01G597000 chr5A 87.143 70 7 2 1647 1715 672577394 672577462 1.280000e-10 78.7
44 TraesCS3B01G597000 chr2A 77.652 264 55 3 1 264 29943239 29943498 1.600000e-34 158.0
45 TraesCS3B01G597000 chr2A 78.161 261 39 11 653 907 1549019 1549267 2.670000e-32 150.0
46 TraesCS3B01G597000 chr4A 87.952 83 10 0 1 83 665706926 665706844 9.820000e-17 99.0
47 TraesCS3B01G597000 chr5D 89.286 56 4 2 1659 1712 417734322 417734267 7.700000e-08 69.4
48 TraesCS3B01G597000 chr5D 81.081 74 11 2 650 721 104445879 104445951 5.990000e-04 56.5
49 TraesCS3B01G597000 chr7B 82.667 75 10 3 298 370 221894891 221894964 3.580000e-06 63.9
50 TraesCS3B01G597000 chr5B 81.429 70 10 2 654 721 113822280 113822348 2.000000e-03 54.7


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 TraesCS3B01G597000 chr3B 819649047 819653336 4289 False 7923.000000 7923 100.000000 1 4290 1 chr3B.!!$F1 4289
1 TraesCS3B01G597000 chr3B 819521397 819524711 3314 False 1699.666667 2610 93.732667 1 4290 3 chr3B.!!$F4 4289
2 TraesCS3B01G597000 chr3B 819380361 819383895 3534 False 1650.333333 2538 93.097000 1 4290 3 chr3B.!!$F3 4289
3 TraesCS3B01G597000 chr3B 819740033 819742380 2347 False 1039.000000 1474 85.840500 959 3531 2 chr3B.!!$F5 2572
4 TraesCS3B01G597000 chr3B 819296050 819302421 6371 False 849.600000 2098 94.004200 1 4290 5 chr3B.!!$F2 4289
5 TraesCS3B01G597000 chr3B 787617309 787617836 527 True 782.000000 782 93.384000 3534 4062 1 chr3B.!!$R1 528
6 TraesCS3B01G597000 chr3D 608949918 608953287 3369 False 1452.000000 2174 91.145333 1 3421 3 chr3D.!!$F1 3420
7 TraesCS3B01G597000 chr3D 609285438 609286678 1240 True 1378.000000 1378 86.736000 2145 3385 1 chr3D.!!$R1 1240
8 TraesCS3B01G597000 chr3D 609004575 609006913 2338 False 1078.500000 1517 86.743500 959 3531 2 chr3D.!!$F3 2572
9 TraesCS3B01G597000 chr3D 608980300 608981963 1663 False 1023.000000 1890 90.379000 1 1933 2 chr3D.!!$F2 1932
10 TraesCS3B01G597000 chr3A 742331292 742332748 1456 False 1735.000000 1735 88.117000 1 1490 1 chr3A.!!$F4 1489
11 TraesCS3B01G597000 chr3A 742313762 742314960 1198 False 1711.000000 1711 92.506000 2340 3533 1 chr3A.!!$F3 1193
12 TraesCS3B01G597000 chr3A 742871240 742872387 1147 True 1290.000000 1290 87.002000 2145 3293 1 chr3A.!!$R1 1148
13 TraesCS3B01G597000 chr3A 742355389 742357722 2333 False 1051.500000 1469 86.415500 959 3531 2 chr3A.!!$F6 2572
14 TraesCS3B01G597000 chr3A 742277392 742278001 609 False 769.000000 769 89.348000 616 1239 1 chr3A.!!$F2 623
15 TraesCS3B01G597000 chr3A 742298155 742299063 908 False 634.000000 761 90.991500 1230 2352 2 chr3A.!!$F5 1122
16 TraesCS3B01G597000 chr2B 646065417 646065946 529 True 821.000000 821 94.549000 3534 4065 1 chr2B.!!$R1 531
17 TraesCS3B01G597000 chr2B 73618410 73618935 525 False 797.000000 797 93.962000 3531 4059 1 chr2B.!!$F1 528
18 TraesCS3B01G597000 chr2B 790772289 790772816 527 True 793.000000 793 93.762000 3534 4062 1 chr2B.!!$R2 528
19 TraesCS3B01G597000 chr4D 68858558 68859089 531 True 811.000000 811 94.173000 3533 4064 1 chr4D.!!$R1 531
20 TraesCS3B01G597000 chr6B 375788948 375789474 526 True 804.000000 804 94.140000 3534 4062 1 chr6B.!!$R1 528
21 TraesCS3B01G597000 chr4B 632707343 632707872 529 True 802.000000 802 93.974000 3533 4063 1 chr4B.!!$R1 530
22 TraesCS3B01G597000 chr1B 561632151 561632681 530 False 800.000000 800 93.820000 3530 4063 1 chr1B.!!$F2 533
23 TraesCS3B01G597000 chr1B 74826822 74827346 524 False 793.000000 793 93.916000 3534 4059 1 chr1B.!!$F1 525

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
213 214 1.060937 GCGCACCAGAATAGCAACG 59.939 57.895 0.3 0.0 0.0 4.10 F
1743 4002 0.036858 TGCCAACATCAATCGTCGGA 60.037 50.000 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 4062 0.032678 AATGCGAGCGGGAGTAGATG 59.967 55.0 0.00 0.0 0.00 2.90 R
3444 6043 0.390124 CAACATGCAGGTGCCAAGTT 59.610 50.0 4.03 0.0 41.18 2.66 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
102 103 4.736896 GGAGCGAACCGAAGCCGT 62.737 66.667 0.00 0.00 0.00 5.68
104 105 4.295119 AGCGAACCGAAGCCGTGT 62.295 61.111 0.00 0.00 0.00 4.49
213 214 1.060937 GCGCACCAGAATAGCAACG 59.939 57.895 0.30 0.00 0.00 4.10
215 216 1.290203 CGCACCAGAATAGCAACGAT 58.710 50.000 0.00 0.00 0.00 3.73
437 442 2.036475 CCATCTTGAGGGACCTATCACG 59.964 54.545 0.00 0.00 31.30 4.35
581 588 4.825422 TGGTTGTGTGCTTCATTGAAAAA 58.175 34.783 0.01 0.00 0.00 1.94
677 688 6.887545 ACCCATTTCCATTAACTGAATAACGA 59.112 34.615 0.00 0.00 0.00 3.85
859 875 1.412710 AGAACAGGTTCACAAGCGAGA 59.587 47.619 14.06 0.00 41.84 4.04
1042 2341 1.925455 CTCCTCTCCCAGCCCCAAA 60.925 63.158 0.00 0.00 0.00 3.28
1125 2433 0.771127 ACAAAGGGCTCAAGCTACCA 59.229 50.000 1.46 0.00 41.70 3.25
1485 2814 3.264897 CGCCAGCATCAGGTACGC 61.265 66.667 0.00 0.00 0.00 4.42
1595 3815 2.758979 TCCACTCCAACGTATTCTCCTC 59.241 50.000 0.00 0.00 0.00 3.71
1625 3845 6.589830 AAATCTCGATTTATGTGTTCTCCG 57.410 37.500 3.19 0.00 39.08 4.63
1632 3891 6.256975 TCGATTTATGTGTTCTCCGGTATTTG 59.743 38.462 0.00 0.00 0.00 2.32
1633 3892 5.554822 TTTATGTGTTCTCCGGTATTTGC 57.445 39.130 0.00 0.00 0.00 3.68
1634 3893 2.552599 TGTGTTCTCCGGTATTTGCA 57.447 45.000 0.00 0.00 0.00 4.08
1635 3894 3.066291 TGTGTTCTCCGGTATTTGCAT 57.934 42.857 0.00 0.00 0.00 3.96
1636 3895 3.417101 TGTGTTCTCCGGTATTTGCATT 58.583 40.909 0.00 0.00 0.00 3.56
1637 3896 3.190327 TGTGTTCTCCGGTATTTGCATTG 59.810 43.478 0.00 0.00 0.00 2.82
1638 3897 3.190535 GTGTTCTCCGGTATTTGCATTGT 59.809 43.478 0.00 0.00 0.00 2.71
1639 3898 3.190327 TGTTCTCCGGTATTTGCATTGTG 59.810 43.478 0.00 0.00 0.00 3.33
1640 3899 3.066291 TCTCCGGTATTTGCATTGTGT 57.934 42.857 0.00 0.00 0.00 3.72
1641 3900 4.209307 TCTCCGGTATTTGCATTGTGTA 57.791 40.909 0.00 0.00 0.00 2.90
1642 3901 4.776349 TCTCCGGTATTTGCATTGTGTAT 58.224 39.130 0.00 0.00 0.00 2.29
1643 3902 5.189928 TCTCCGGTATTTGCATTGTGTATT 58.810 37.500 0.00 0.00 0.00 1.89
1644 3903 5.650266 TCTCCGGTATTTGCATTGTGTATTT 59.350 36.000 0.00 0.00 0.00 1.40
1645 3904 5.885881 TCCGGTATTTGCATTGTGTATTTC 58.114 37.500 0.00 0.00 0.00 2.17
1646 3905 5.650266 TCCGGTATTTGCATTGTGTATTTCT 59.350 36.000 0.00 0.00 0.00 2.52
1647 3906 6.151985 TCCGGTATTTGCATTGTGTATTTCTT 59.848 34.615 0.00 0.00 0.00 2.52
1648 3907 6.811170 CCGGTATTTGCATTGTGTATTTCTTT 59.189 34.615 0.00 0.00 0.00 2.52
1649 3908 7.330700 CCGGTATTTGCATTGTGTATTTCTTTT 59.669 33.333 0.00 0.00 0.00 2.27
1650 3909 8.707839 CGGTATTTGCATTGTGTATTTCTTTTT 58.292 29.630 0.00 0.00 0.00 1.94
1655 3914 8.939201 TTGCATTGTGTATTTCTTTTTCTTCA 57.061 26.923 0.00 0.00 0.00 3.02
1656 3915 8.939201 TGCATTGTGTATTTCTTTTTCTTCAA 57.061 26.923 0.00 0.00 0.00 2.69
1657 3916 9.033481 TGCATTGTGTATTTCTTTTTCTTCAAG 57.967 29.630 0.00 0.00 0.00 3.02
1658 3917 9.248291 GCATTGTGTATTTCTTTTTCTTCAAGA 57.752 29.630 0.00 0.00 0.00 3.02
1663 3922 9.582223 GTGTATTTCTTTTTCTTCAAGAGTACG 57.418 33.333 0.00 0.00 31.88 3.67
1664 3923 8.280497 TGTATTTCTTTTTCTTCAAGAGTACGC 58.720 33.333 0.00 0.00 31.88 4.42
1665 3924 5.668558 TTCTTTTTCTTCAAGAGTACGCC 57.331 39.130 0.00 0.00 31.84 5.68
1666 3925 4.699637 TCTTTTTCTTCAAGAGTACGCCA 58.300 39.130 0.00 0.00 0.00 5.69
1667 3926 5.120399 TCTTTTTCTTCAAGAGTACGCCAA 58.880 37.500 0.00 0.00 0.00 4.52
1668 3927 5.763204 TCTTTTTCTTCAAGAGTACGCCAAT 59.237 36.000 0.00 0.00 0.00 3.16
1669 3928 5.356882 TTTTCTTCAAGAGTACGCCAATG 57.643 39.130 0.00 0.00 0.00 2.82
1670 3929 3.953712 TCTTCAAGAGTACGCCAATGA 57.046 42.857 0.00 0.00 0.00 2.57
1671 3930 4.471904 TCTTCAAGAGTACGCCAATGAT 57.528 40.909 0.00 0.00 0.00 2.45
1672 3931 4.183865 TCTTCAAGAGTACGCCAATGATG 58.816 43.478 0.00 0.00 0.00 3.07
1673 3932 3.610040 TCAAGAGTACGCCAATGATGT 57.390 42.857 0.00 0.00 0.00 3.06
1674 3933 4.729227 TCAAGAGTACGCCAATGATGTA 57.271 40.909 0.00 0.00 0.00 2.29
1675 3934 4.430007 TCAAGAGTACGCCAATGATGTAC 58.570 43.478 6.81 6.81 38.94 2.90
1676 3935 3.454371 AGAGTACGCCAATGATGTACC 57.546 47.619 10.04 4.44 39.36 3.34
1677 3936 2.764010 AGAGTACGCCAATGATGTACCA 59.236 45.455 10.04 0.00 39.36 3.25
1678 3937 3.388024 AGAGTACGCCAATGATGTACCAT 59.612 43.478 10.04 0.00 39.36 3.55
1679 3938 4.587262 AGAGTACGCCAATGATGTACCATA 59.413 41.667 10.04 0.00 39.36 2.74
1680 3939 5.246203 AGAGTACGCCAATGATGTACCATAT 59.754 40.000 10.04 0.00 39.36 1.78
1681 3940 5.865085 AGTACGCCAATGATGTACCATATT 58.135 37.500 10.04 0.00 39.36 1.28
1682 3941 6.296026 AGTACGCCAATGATGTACCATATTT 58.704 36.000 10.04 0.00 39.36 1.40
1683 3942 6.770785 AGTACGCCAATGATGTACCATATTTT 59.229 34.615 10.04 0.00 39.36 1.82
1684 3943 6.463995 ACGCCAATGATGTACCATATTTTT 57.536 33.333 0.00 0.00 0.00 1.94
1685 3944 7.575414 ACGCCAATGATGTACCATATTTTTA 57.425 32.000 0.00 0.00 0.00 1.52
1686 3945 8.177119 ACGCCAATGATGTACCATATTTTTAT 57.823 30.769 0.00 0.00 0.00 1.40
1687 3946 9.290988 ACGCCAATGATGTACCATATTTTTATA 57.709 29.630 0.00 0.00 0.00 0.98
1688 3947 9.773328 CGCCAATGATGTACCATATTTTTATAG 57.227 33.333 0.00 0.00 0.00 1.31
1714 3973 9.952188 GAAGGTAGCAAATAATTACAAGAATCC 57.048 33.333 0.00 0.00 0.00 3.01
1715 3974 9.700831 AAGGTAGCAAATAATTACAAGAATCCT 57.299 29.630 0.00 0.00 0.00 3.24
1719 3978 8.958119 AGCAAATAATTACAAGAATCCTACGA 57.042 30.769 0.00 0.00 0.00 3.43
1720 3979 9.561069 AGCAAATAATTACAAGAATCCTACGAT 57.439 29.630 0.00 0.00 0.00 3.73
1726 3985 6.844696 TTACAAGAATCCTACGATTGATGC 57.155 37.500 0.00 0.00 38.88 3.91
1727 3986 4.130118 ACAAGAATCCTACGATTGATGCC 58.870 43.478 0.00 0.00 38.88 4.40
1728 3987 4.129380 CAAGAATCCTACGATTGATGCCA 58.871 43.478 0.00 0.00 38.88 4.92
1729 3988 4.422073 AGAATCCTACGATTGATGCCAA 57.578 40.909 0.00 0.00 38.88 4.52
1730 3989 4.130118 AGAATCCTACGATTGATGCCAAC 58.870 43.478 0.00 0.00 38.88 3.77
1731 3990 3.558931 ATCCTACGATTGATGCCAACA 57.441 42.857 0.00 0.00 34.72 3.33
1732 3991 3.558931 TCCTACGATTGATGCCAACAT 57.441 42.857 0.00 0.00 39.98 2.71
1742 4001 1.016627 ATGCCAACATCAATCGTCGG 58.983 50.000 0.00 0.00 0.00 4.79
1743 4002 0.036858 TGCCAACATCAATCGTCGGA 60.037 50.000 0.00 0.00 0.00 4.55
1744 4003 1.083489 GCCAACATCAATCGTCGGAA 58.917 50.000 0.00 0.00 0.00 4.30
1745 4004 1.202031 GCCAACATCAATCGTCGGAAC 60.202 52.381 0.00 0.00 0.00 3.62
1746 4005 2.073056 CCAACATCAATCGTCGGAACA 58.927 47.619 0.00 0.00 0.00 3.18
1747 4006 2.159707 CCAACATCAATCGTCGGAACAC 60.160 50.000 0.00 0.00 0.00 3.32
1748 4007 1.722011 ACATCAATCGTCGGAACACC 58.278 50.000 0.00 0.00 0.00 4.16
1749 4008 1.006832 CATCAATCGTCGGAACACCC 58.993 55.000 0.00 0.00 0.00 4.61
1750 4009 0.611200 ATCAATCGTCGGAACACCCA 59.389 50.000 0.00 0.00 34.14 4.51
1751 4010 0.320073 TCAATCGTCGGAACACCCAC 60.320 55.000 0.00 0.00 34.14 4.61
1752 4011 0.601576 CAATCGTCGGAACACCCACA 60.602 55.000 0.00 0.00 34.14 4.17
1753 4012 0.601841 AATCGTCGGAACACCCACAC 60.602 55.000 0.00 0.00 34.14 3.82
1754 4013 2.444700 ATCGTCGGAACACCCACACC 62.445 60.000 0.00 0.00 34.14 4.16
1755 4014 2.506962 GTCGGAACACCCACACCA 59.493 61.111 0.00 0.00 34.14 4.17
1756 4015 1.153127 GTCGGAACACCCACACCAA 60.153 57.895 0.00 0.00 34.14 3.67
1757 4016 1.153127 TCGGAACACCCACACCAAC 60.153 57.895 0.00 0.00 34.14 3.77
1758 4017 2.190841 CGGAACACCCACACCAACC 61.191 63.158 0.00 0.00 34.14 3.77
1759 4018 1.076632 GGAACACCCACACCAACCA 60.077 57.895 0.00 0.00 34.14 3.67
1760 4019 0.684805 GGAACACCCACACCAACCAA 60.685 55.000 0.00 0.00 34.14 3.67
1761 4020 1.187087 GAACACCCACACCAACCAAA 58.813 50.000 0.00 0.00 0.00 3.28
1762 4021 1.550976 GAACACCCACACCAACCAAAA 59.449 47.619 0.00 0.00 0.00 2.44
1763 4022 1.872773 ACACCCACACCAACCAAAAT 58.127 45.000 0.00 0.00 0.00 1.82
1764 4023 2.192263 ACACCCACACCAACCAAAATT 58.808 42.857 0.00 0.00 0.00 1.82
1765 4024 2.169561 ACACCCACACCAACCAAAATTC 59.830 45.455 0.00 0.00 0.00 2.17
1766 4025 2.433970 CACCCACACCAACCAAAATTCT 59.566 45.455 0.00 0.00 0.00 2.40
1767 4026 3.639094 CACCCACACCAACCAAAATTCTA 59.361 43.478 0.00 0.00 0.00 2.10
1768 4027 3.639561 ACCCACACCAACCAAAATTCTAC 59.360 43.478 0.00 0.00 0.00 2.59
1769 4028 3.305064 CCCACACCAACCAAAATTCTACG 60.305 47.826 0.00 0.00 0.00 3.51
1770 4029 3.305064 CCACACCAACCAAAATTCTACGG 60.305 47.826 0.00 0.00 0.00 4.02
1771 4030 2.295070 ACACCAACCAAAATTCTACGGC 59.705 45.455 0.00 0.00 0.00 5.68
1772 4031 2.556622 CACCAACCAAAATTCTACGGCT 59.443 45.455 0.00 0.00 0.00 5.52
1773 4032 3.754323 CACCAACCAAAATTCTACGGCTA 59.246 43.478 0.00 0.00 0.00 3.93
1774 4033 4.216687 CACCAACCAAAATTCTACGGCTAA 59.783 41.667 0.00 0.00 0.00 3.09
1775 4034 4.216902 ACCAACCAAAATTCTACGGCTAAC 59.783 41.667 0.00 0.00 0.00 2.34
1776 4035 4.457949 CCAACCAAAATTCTACGGCTAACT 59.542 41.667 0.00 0.00 0.00 2.24
1777 4036 5.048294 CCAACCAAAATTCTACGGCTAACTT 60.048 40.000 0.00 0.00 0.00 2.66
1778 4037 6.443792 CAACCAAAATTCTACGGCTAACTTT 58.556 36.000 0.00 0.00 0.00 2.66
1779 4038 6.644248 ACCAAAATTCTACGGCTAACTTTT 57.356 33.333 0.00 0.00 0.00 2.27
1780 4039 6.675026 ACCAAAATTCTACGGCTAACTTTTC 58.325 36.000 0.00 0.00 0.00 2.29
1781 4040 6.263617 ACCAAAATTCTACGGCTAACTTTTCA 59.736 34.615 0.00 0.00 0.00 2.69
1782 4041 6.581166 CCAAAATTCTACGGCTAACTTTTCAC 59.419 38.462 0.00 0.00 0.00 3.18
1783 4042 6.870971 AAATTCTACGGCTAACTTTTCACA 57.129 33.333 0.00 0.00 0.00 3.58
1784 4043 6.870971 AATTCTACGGCTAACTTTTCACAA 57.129 33.333 0.00 0.00 0.00 3.33
1785 4044 6.870971 ATTCTACGGCTAACTTTTCACAAA 57.129 33.333 0.00 0.00 0.00 2.83
1786 4045 6.870971 TTCTACGGCTAACTTTTCACAAAT 57.129 33.333 0.00 0.00 0.00 2.32
1787 4046 6.476243 TCTACGGCTAACTTTTCACAAATC 57.524 37.500 0.00 0.00 0.00 2.17
1788 4047 6.228258 TCTACGGCTAACTTTTCACAAATCT 58.772 36.000 0.00 0.00 0.00 2.40
1789 4048 7.380536 TCTACGGCTAACTTTTCACAAATCTA 58.619 34.615 0.00 0.00 0.00 1.98
1790 4049 8.038944 TCTACGGCTAACTTTTCACAAATCTAT 58.961 33.333 0.00 0.00 0.00 1.98
1791 4050 7.073342 ACGGCTAACTTTTCACAAATCTATC 57.927 36.000 0.00 0.00 0.00 2.08
1792 4051 6.879458 ACGGCTAACTTTTCACAAATCTATCT 59.121 34.615 0.00 0.00 0.00 1.98
1793 4052 8.038944 ACGGCTAACTTTTCACAAATCTATCTA 58.961 33.333 0.00 0.00 0.00 1.98
1794 4053 8.543774 CGGCTAACTTTTCACAAATCTATCTAG 58.456 37.037 0.00 0.00 0.00 2.43
1795 4054 9.384764 GGCTAACTTTTCACAAATCTATCTAGT 57.615 33.333 0.00 0.00 0.00 2.57
1799 4058 8.779354 ACTTTTCACAAATCTATCTAGTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
1800 4059 7.824779 ACTTTTCACAAATCTATCTAGTCCACC 59.175 37.037 0.00 0.00 0.00 4.61
1801 4060 5.871396 TCACAAATCTATCTAGTCCACCC 57.129 43.478 0.00 0.00 0.00 4.61
1802 4061 5.277250 TCACAAATCTATCTAGTCCACCCA 58.723 41.667 0.00 0.00 0.00 4.51
1803 4062 5.128827 TCACAAATCTATCTAGTCCACCCAC 59.871 44.000 0.00 0.00 0.00 4.61
1804 4063 5.030147 ACAAATCTATCTAGTCCACCCACA 58.970 41.667 0.00 0.00 0.00 4.17
1805 4064 5.667626 ACAAATCTATCTAGTCCACCCACAT 59.332 40.000 0.00 0.00 0.00 3.21
1806 4065 6.183361 ACAAATCTATCTAGTCCACCCACATC 60.183 42.308 0.00 0.00 0.00 3.06
1807 4066 4.816048 TCTATCTAGTCCACCCACATCT 57.184 45.455 0.00 0.00 0.00 2.90
1808 4067 5.924769 TCTATCTAGTCCACCCACATCTA 57.075 43.478 0.00 0.00 0.00 1.98
1809 4068 5.632118 TCTATCTAGTCCACCCACATCTAC 58.368 45.833 0.00 0.00 0.00 2.59
1810 4069 4.544564 ATCTAGTCCACCCACATCTACT 57.455 45.455 0.00 0.00 0.00 2.57
1811 4070 3.899726 TCTAGTCCACCCACATCTACTC 58.100 50.000 0.00 0.00 0.00 2.59
1812 4071 1.867363 AGTCCACCCACATCTACTCC 58.133 55.000 0.00 0.00 0.00 3.85
1813 4072 0.831307 GTCCACCCACATCTACTCCC 59.169 60.000 0.00 0.00 0.00 4.30
1814 4073 0.686441 TCCACCCACATCTACTCCCG 60.686 60.000 0.00 0.00 0.00 5.14
1815 4074 1.144057 CACCCACATCTACTCCCGC 59.856 63.158 0.00 0.00 0.00 6.13
1816 4075 1.001760 ACCCACATCTACTCCCGCT 59.998 57.895 0.00 0.00 0.00 5.52
1817 4076 1.043673 ACCCACATCTACTCCCGCTC 61.044 60.000 0.00 0.00 0.00 5.03
1854 4155 0.315059 GCACACAGAAACACGACACG 60.315 55.000 0.00 0.00 0.00 4.49
1855 4156 0.315059 CACACAGAAACACGACACGC 60.315 55.000 0.00 0.00 0.00 5.34
1856 4157 0.738063 ACACAGAAACACGACACGCA 60.738 50.000 0.00 0.00 0.00 5.24
1857 4158 0.371989 CACAGAAACACGACACGCAA 59.628 50.000 0.00 0.00 0.00 4.85
1859 4160 0.042188 CAGAAACACGACACGCAAGG 60.042 55.000 0.00 0.00 46.39 3.61
1860 4161 1.368850 GAAACACGACACGCAAGGC 60.369 57.895 0.00 0.00 46.39 4.35
1982 4452 6.090898 GTGCATAGAAGTACAAGGTACAACTG 59.909 42.308 9.01 0.00 0.00 3.16
2005 4475 3.420893 CATAGAAGAACAAGGCCCACAA 58.579 45.455 0.00 0.00 0.00 3.33
2085 4642 8.827677 GCACACGTCCTAATAAAATAAGAGATT 58.172 33.333 0.00 0.00 0.00 2.40
2121 4678 7.829211 AGTTGTGCATAGTATAAAACCTCATGT 59.171 33.333 0.00 0.00 0.00 3.21
2122 4679 9.104965 GTTGTGCATAGTATAAAACCTCATGTA 57.895 33.333 0.00 0.00 0.00 2.29
2123 4680 9.845740 TTGTGCATAGTATAAAACCTCATGTAT 57.154 29.630 0.00 0.00 0.00 2.29
2182 4739 2.359230 AGCACCTTGAGCGGCTTC 60.359 61.111 2.97 0.00 37.01 3.86
2273 4830 0.250081 TGGCGACATGTACAACAGCA 60.250 50.000 0.00 0.00 33.40 4.41
2300 4857 0.385390 CCCACACCACAAGAACTTGC 59.615 55.000 13.50 0.00 44.03 4.01
2402 4966 1.002624 GACCAAATCACCGGCCTCA 60.003 57.895 0.00 0.00 0.00 3.86
2419 4983 4.104417 ACCTCTCGTCGTGAGCGC 62.104 66.667 16.91 0.00 44.86 5.92
2501 5065 0.033504 TGTCAAGCCTCAGAACGGTC 59.966 55.000 0.00 0.00 0.00 4.79
2541 5105 5.128663 TCATCGATCTATGGAAGGACAACAA 59.871 40.000 7.33 0.00 0.00 2.83
2570 5134 3.494924 CCTCAACATCACAAGAGACCACA 60.495 47.826 0.00 0.00 0.00 4.17
2626 5190 4.056740 GCCTCTACATCATGTCATGTCTG 58.943 47.826 12.54 12.97 38.07 3.51
2802 5376 3.252284 CAGGGCTGTGGTGGGAGT 61.252 66.667 0.00 0.00 0.00 3.85
2803 5377 2.450502 AGGGCTGTGGTGGGAGTT 60.451 61.111 0.00 0.00 0.00 3.01
3226 5800 0.252881 TGAGCATGGAGGAGGAAGGT 60.253 55.000 0.00 0.00 0.00 3.50
3631 6980 0.460311 AATAACGAGTGGAGCCGAGG 59.540 55.000 0.00 0.00 0.00 4.63
3666 7015 5.186996 TCGTTTACAGGACGAGTTAAACT 57.813 39.130 0.00 0.00 43.79 2.66
3687 7036 2.447443 AGCCGATCTCACAAGTACTCA 58.553 47.619 0.00 0.00 0.00 3.41
3732 7081 7.587037 AAAAGAATCAGTGTTTCTTGATGGA 57.413 32.000 23.50 0.00 41.38 3.41
3789 7140 2.361610 CAAGGCCCAACCGCTCAT 60.362 61.111 0.00 0.00 46.52 2.90
3837 7188 5.633601 CACGTACATGACCATATATGTCCAC 59.366 44.000 11.73 1.38 38.41 4.02
3847 7198 7.988028 TGACCATATATGTCCACGTTAAATTCA 59.012 33.333 11.73 0.00 0.00 2.57
4050 7402 3.587933 GGCTCGACTCGGCTCGAT 61.588 66.667 5.92 0.00 41.71 3.59
4059 7411 1.961180 CTCGGCTCGATTTCCACCCT 61.961 60.000 0.00 0.00 34.61 4.34
4065 7417 3.181458 GGCTCGATTTCCACCCTTACATA 60.181 47.826 0.00 0.00 0.00 2.29
4066 7418 4.505039 GGCTCGATTTCCACCCTTACATAT 60.505 45.833 0.00 0.00 0.00 1.78
4067 7419 5.279809 GGCTCGATTTCCACCCTTACATATA 60.280 44.000 0.00 0.00 0.00 0.86
4068 7420 5.869888 GCTCGATTTCCACCCTTACATATAG 59.130 44.000 0.00 0.00 0.00 1.31
4069 7421 6.295123 GCTCGATTTCCACCCTTACATATAGA 60.295 42.308 0.00 0.00 0.00 1.98
4081 7433 9.719433 ACCCTTACATATAGAGGTACAAACTTA 57.281 33.333 0.00 0.00 0.00 2.24
4230 7583 6.530120 ACACACACCATTAAGACTGAACATA 58.470 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.220821 GGTGATCTACGGACATGGATGTAT 59.779 45.833 0.00 0.00 41.95 2.29
102 103 0.327924 AAGGGGCGATGATGACAACA 59.672 50.000 0.00 0.00 0.00 3.33
104 105 0.107214 GGAAGGGGCGATGATGACAA 60.107 55.000 0.00 0.00 0.00 3.18
213 214 1.303309 CTTCTGTTCATGGGGCGATC 58.697 55.000 0.00 0.00 0.00 3.69
215 216 1.377202 GCTTCTGTTCATGGGGCGA 60.377 57.895 0.00 0.00 0.00 5.54
437 442 1.421480 ATACTCGGGAAGGTAAGGCC 58.579 55.000 0.00 0.00 37.58 5.19
495 501 1.605992 CTGGAGGGCTCATGCTTCA 59.394 57.895 0.00 0.00 39.59 3.02
677 688 9.981114 CTTAAACTCTGGATGGTTTTGTATTTT 57.019 29.630 0.00 0.00 37.01 1.82
786 797 1.537348 CCAGGTGTCGTCGAGTTTTCA 60.537 52.381 0.00 0.00 0.00 2.69
859 875 5.175388 AGCGTCCCCTTAGAAACTTATTT 57.825 39.130 0.00 0.00 0.00 1.40
1042 2341 0.998145 AGGAGGAGAAGCTGCCATTT 59.002 50.000 0.00 0.00 0.00 2.32
1485 2814 2.429571 GCTGCACGCATGGTTGTG 60.430 61.111 0.00 0.00 38.92 3.33
1603 3823 5.050490 CCGGAGAACACATAAATCGAGATT 58.950 41.667 0.00 0.00 0.00 2.40
1607 3827 3.880047 ACCGGAGAACACATAAATCGA 57.120 42.857 9.46 0.00 0.00 3.59
1613 3833 4.209307 TGCAAATACCGGAGAACACATA 57.791 40.909 9.46 0.00 0.00 2.29
1632 3891 9.248291 TCTTGAAGAAAAAGAAATACACAATGC 57.752 29.630 0.00 0.00 30.79 3.56
1637 3896 9.582223 CGTACTCTTGAAGAAAAAGAAATACAC 57.418 33.333 0.00 0.00 33.40 2.90
1638 3897 8.280497 GCGTACTCTTGAAGAAAAAGAAATACA 58.720 33.333 0.00 0.00 33.40 2.29
1639 3898 7.745155 GGCGTACTCTTGAAGAAAAAGAAATAC 59.255 37.037 0.00 0.00 33.40 1.89
1640 3899 7.442969 TGGCGTACTCTTGAAGAAAAAGAAATA 59.557 33.333 0.00 0.00 33.40 1.40
1641 3900 6.262273 TGGCGTACTCTTGAAGAAAAAGAAAT 59.738 34.615 0.00 0.00 33.40 2.17
1642 3901 5.587043 TGGCGTACTCTTGAAGAAAAAGAAA 59.413 36.000 0.00 0.00 33.40 2.52
1643 3902 5.120399 TGGCGTACTCTTGAAGAAAAAGAA 58.880 37.500 0.00 0.00 33.40 2.52
1644 3903 4.699637 TGGCGTACTCTTGAAGAAAAAGA 58.300 39.130 0.00 0.00 32.80 2.52
1645 3904 5.418310 TTGGCGTACTCTTGAAGAAAAAG 57.582 39.130 0.00 0.00 0.00 2.27
1646 3905 5.529430 TCATTGGCGTACTCTTGAAGAAAAA 59.471 36.000 0.00 0.00 0.00 1.94
1647 3906 5.060506 TCATTGGCGTACTCTTGAAGAAAA 58.939 37.500 0.00 0.00 0.00 2.29
1648 3907 4.637276 TCATTGGCGTACTCTTGAAGAAA 58.363 39.130 0.00 0.00 0.00 2.52
1649 3908 4.265904 TCATTGGCGTACTCTTGAAGAA 57.734 40.909 0.00 0.00 0.00 2.52
1650 3909 3.953712 TCATTGGCGTACTCTTGAAGA 57.046 42.857 0.00 0.00 0.00 2.87
1651 3910 3.935203 ACATCATTGGCGTACTCTTGAAG 59.065 43.478 0.00 0.00 0.00 3.02
1652 3911 3.937814 ACATCATTGGCGTACTCTTGAA 58.062 40.909 0.00 0.00 0.00 2.69
1653 3912 3.610040 ACATCATTGGCGTACTCTTGA 57.390 42.857 0.00 0.00 0.00 3.02
1654 3913 3.555956 GGTACATCATTGGCGTACTCTTG 59.444 47.826 12.97 0.00 36.56 3.02
1655 3914 3.196901 TGGTACATCATTGGCGTACTCTT 59.803 43.478 12.97 0.00 36.56 2.85
1656 3915 2.764010 TGGTACATCATTGGCGTACTCT 59.236 45.455 12.97 0.00 36.56 3.24
1657 3916 3.173668 TGGTACATCATTGGCGTACTC 57.826 47.619 12.97 7.02 36.56 2.59
1688 3947 9.952188 GGATTCTTGTAATTATTTGCTACCTTC 57.048 33.333 0.00 0.00 0.00 3.46
1689 3948 9.700831 AGGATTCTTGTAATTATTTGCTACCTT 57.299 29.630 0.00 0.00 0.00 3.50
1694 3953 8.958119 TCGTAGGATTCTTGTAATTATTTGCT 57.042 30.769 0.00 0.00 0.00 3.91
1700 3959 8.988934 GCATCAATCGTAGGATTCTTGTAATTA 58.011 33.333 7.68 0.00 40.90 1.40
1701 3960 7.041098 GGCATCAATCGTAGGATTCTTGTAATT 60.041 37.037 7.68 0.00 40.90 1.40
1702 3961 6.428159 GGCATCAATCGTAGGATTCTTGTAAT 59.572 38.462 7.68 0.00 40.90 1.89
1703 3962 5.758296 GGCATCAATCGTAGGATTCTTGTAA 59.242 40.000 7.68 0.00 40.90 2.41
1704 3963 5.163353 TGGCATCAATCGTAGGATTCTTGTA 60.163 40.000 7.68 1.53 40.90 2.41
1705 3964 4.130118 GGCATCAATCGTAGGATTCTTGT 58.870 43.478 7.68 0.00 40.90 3.16
1706 3965 4.129380 TGGCATCAATCGTAGGATTCTTG 58.871 43.478 7.68 9.34 40.90 3.02
1707 3966 4.422073 TGGCATCAATCGTAGGATTCTT 57.578 40.909 7.68 0.00 40.90 2.52
1708 3967 4.130118 GTTGGCATCAATCGTAGGATTCT 58.870 43.478 7.68 0.00 40.90 2.40
1709 3968 3.876914 TGTTGGCATCAATCGTAGGATTC 59.123 43.478 7.68 0.00 40.90 2.52
1710 3969 3.884895 TGTTGGCATCAATCGTAGGATT 58.115 40.909 4.83 4.83 43.62 3.01
1711 3970 3.558931 TGTTGGCATCAATCGTAGGAT 57.441 42.857 0.00 0.00 35.10 3.24
1712 3971 3.558931 ATGTTGGCATCAATCGTAGGA 57.441 42.857 1.83 0.00 35.10 2.94
1723 3982 1.016627 CCGACGATTGATGTTGGCAT 58.983 50.000 0.00 0.00 34.22 4.40
1724 3983 0.036858 TCCGACGATTGATGTTGGCA 60.037 50.000 0.00 0.00 40.19 4.92
1725 3984 1.083489 TTCCGACGATTGATGTTGGC 58.917 50.000 0.00 0.00 40.19 4.52
1726 3985 2.073056 TGTTCCGACGATTGATGTTGG 58.927 47.619 0.00 0.00 41.50 3.77
1727 3986 2.159707 GGTGTTCCGACGATTGATGTTG 60.160 50.000 0.00 0.00 0.00 3.33
1728 3987 2.073816 GGTGTTCCGACGATTGATGTT 58.926 47.619 0.00 0.00 0.00 2.71
1729 3988 1.674817 GGGTGTTCCGACGATTGATGT 60.675 52.381 0.00 0.00 33.83 3.06
1730 3989 1.006832 GGGTGTTCCGACGATTGATG 58.993 55.000 0.00 0.00 33.83 3.07
1731 3990 0.611200 TGGGTGTTCCGACGATTGAT 59.389 50.000 0.00 0.00 38.76 2.57
1732 3991 0.320073 GTGGGTGTTCCGACGATTGA 60.320 55.000 0.00 0.00 38.76 2.57
1733 3992 0.601576 TGTGGGTGTTCCGACGATTG 60.602 55.000 0.00 0.00 43.85 2.67
1734 3993 0.601841 GTGTGGGTGTTCCGACGATT 60.602 55.000 0.00 0.00 43.85 3.34
1735 3994 1.005394 GTGTGGGTGTTCCGACGAT 60.005 57.895 0.00 0.00 43.85 3.73
1736 3995 2.418356 GTGTGGGTGTTCCGACGA 59.582 61.111 0.00 0.00 43.85 4.20
1737 3996 2.663852 GGTGTGGGTGTTCCGACG 60.664 66.667 0.00 0.00 43.85 5.12
1738 3997 1.153127 TTGGTGTGGGTGTTCCGAC 60.153 57.895 0.00 0.00 41.78 4.79
1739 3998 1.153127 GTTGGTGTGGGTGTTCCGA 60.153 57.895 0.00 0.00 38.76 4.55
1740 3999 2.190841 GGTTGGTGTGGGTGTTCCG 61.191 63.158 0.00 0.00 38.76 4.30
1741 4000 0.684805 TTGGTTGGTGTGGGTGTTCC 60.685 55.000 0.00 0.00 0.00 3.62
1742 4001 1.187087 TTTGGTTGGTGTGGGTGTTC 58.813 50.000 0.00 0.00 0.00 3.18
1743 4002 1.645710 TTTTGGTTGGTGTGGGTGTT 58.354 45.000 0.00 0.00 0.00 3.32
1744 4003 1.872773 ATTTTGGTTGGTGTGGGTGT 58.127 45.000 0.00 0.00 0.00 4.16
1745 4004 2.433970 AGAATTTTGGTTGGTGTGGGTG 59.566 45.455 0.00 0.00 0.00 4.61
1746 4005 2.758130 AGAATTTTGGTTGGTGTGGGT 58.242 42.857 0.00 0.00 0.00 4.51
1747 4006 3.305064 CGTAGAATTTTGGTTGGTGTGGG 60.305 47.826 0.00 0.00 0.00 4.61
1748 4007 3.305064 CCGTAGAATTTTGGTTGGTGTGG 60.305 47.826 0.00 0.00 0.00 4.17
1749 4008 3.855524 GCCGTAGAATTTTGGTTGGTGTG 60.856 47.826 0.00 0.00 0.00 3.82
1750 4009 2.295070 GCCGTAGAATTTTGGTTGGTGT 59.705 45.455 0.00 0.00 0.00 4.16
1751 4010 2.556622 AGCCGTAGAATTTTGGTTGGTG 59.443 45.455 0.00 0.00 0.00 4.17
1752 4011 2.871453 AGCCGTAGAATTTTGGTTGGT 58.129 42.857 0.00 0.00 0.00 3.67
1753 4012 4.457949 AGTTAGCCGTAGAATTTTGGTTGG 59.542 41.667 0.00 0.00 0.00 3.77
1754 4013 5.622770 AGTTAGCCGTAGAATTTTGGTTG 57.377 39.130 0.00 0.00 0.00 3.77
1755 4014 6.644248 AAAGTTAGCCGTAGAATTTTGGTT 57.356 33.333 0.00 0.00 0.00 3.67
1756 4015 6.263617 TGAAAAGTTAGCCGTAGAATTTTGGT 59.736 34.615 0.00 0.00 0.00 3.67
1757 4016 6.581166 GTGAAAAGTTAGCCGTAGAATTTTGG 59.419 38.462 0.00 0.00 0.00 3.28
1758 4017 7.136119 TGTGAAAAGTTAGCCGTAGAATTTTG 58.864 34.615 0.00 0.00 0.00 2.44
1759 4018 7.266922 TGTGAAAAGTTAGCCGTAGAATTTT 57.733 32.000 0.00 0.00 0.00 1.82
1760 4019 6.870971 TGTGAAAAGTTAGCCGTAGAATTT 57.129 33.333 0.00 0.00 0.00 1.82
1761 4020 6.870971 TTGTGAAAAGTTAGCCGTAGAATT 57.129 33.333 0.00 0.00 0.00 2.17
1762 4021 6.870971 TTTGTGAAAAGTTAGCCGTAGAAT 57.129 33.333 0.00 0.00 0.00 2.40
1763 4022 6.708949 AGATTTGTGAAAAGTTAGCCGTAGAA 59.291 34.615 0.00 0.00 0.00 2.10
1764 4023 6.228258 AGATTTGTGAAAAGTTAGCCGTAGA 58.772 36.000 0.00 0.00 0.00 2.59
1765 4024 6.481954 AGATTTGTGAAAAGTTAGCCGTAG 57.518 37.500 0.00 0.00 0.00 3.51
1766 4025 8.038944 AGATAGATTTGTGAAAAGTTAGCCGTA 58.961 33.333 0.00 0.00 0.00 4.02
1767 4026 6.879458 AGATAGATTTGTGAAAAGTTAGCCGT 59.121 34.615 0.00 0.00 0.00 5.68
1768 4027 7.308782 AGATAGATTTGTGAAAAGTTAGCCG 57.691 36.000 0.00 0.00 0.00 5.52
1769 4028 9.384764 ACTAGATAGATTTGTGAAAAGTTAGCC 57.615 33.333 0.00 0.00 0.00 3.93
1773 4032 9.220767 GTGGACTAGATAGATTTGTGAAAAGTT 57.779 33.333 0.00 0.00 0.00 2.66
1774 4033 7.824779 GGTGGACTAGATAGATTTGTGAAAAGT 59.175 37.037 0.00 0.00 0.00 2.66
1775 4034 7.281100 GGGTGGACTAGATAGATTTGTGAAAAG 59.719 40.741 0.00 0.00 0.00 2.27
1776 4035 7.110155 GGGTGGACTAGATAGATTTGTGAAAA 58.890 38.462 0.00 0.00 0.00 2.29
1777 4036 6.214615 TGGGTGGACTAGATAGATTTGTGAAA 59.785 38.462 0.00 0.00 0.00 2.69
1778 4037 5.724370 TGGGTGGACTAGATAGATTTGTGAA 59.276 40.000 0.00 0.00 0.00 3.18
1779 4038 5.128827 GTGGGTGGACTAGATAGATTTGTGA 59.871 44.000 0.00 0.00 0.00 3.58
1780 4039 5.104941 TGTGGGTGGACTAGATAGATTTGTG 60.105 44.000 0.00 0.00 0.00 3.33
1781 4040 5.030147 TGTGGGTGGACTAGATAGATTTGT 58.970 41.667 0.00 0.00 0.00 2.83
1782 4041 5.614324 TGTGGGTGGACTAGATAGATTTG 57.386 43.478 0.00 0.00 0.00 2.32
1783 4042 6.146760 AGATGTGGGTGGACTAGATAGATTT 58.853 40.000 0.00 0.00 0.00 2.17
1784 4043 5.721225 AGATGTGGGTGGACTAGATAGATT 58.279 41.667 0.00 0.00 0.00 2.40
1785 4044 5.346782 AGATGTGGGTGGACTAGATAGAT 57.653 43.478 0.00 0.00 0.00 1.98
1786 4045 4.816048 AGATGTGGGTGGACTAGATAGA 57.184 45.455 0.00 0.00 0.00 1.98
1787 4046 5.636123 AGTAGATGTGGGTGGACTAGATAG 58.364 45.833 0.00 0.00 0.00 2.08
1788 4047 5.457778 GGAGTAGATGTGGGTGGACTAGATA 60.458 48.000 0.00 0.00 0.00 1.98
1789 4048 4.475345 GAGTAGATGTGGGTGGACTAGAT 58.525 47.826 0.00 0.00 0.00 1.98
1790 4049 3.372784 GGAGTAGATGTGGGTGGACTAGA 60.373 52.174 0.00 0.00 0.00 2.43
1791 4050 2.959707 GGAGTAGATGTGGGTGGACTAG 59.040 54.545 0.00 0.00 0.00 2.57
1792 4051 2.358932 GGGAGTAGATGTGGGTGGACTA 60.359 54.545 0.00 0.00 0.00 2.59
1793 4052 1.622725 GGGAGTAGATGTGGGTGGACT 60.623 57.143 0.00 0.00 0.00 3.85
1794 4053 0.831307 GGGAGTAGATGTGGGTGGAC 59.169 60.000 0.00 0.00 0.00 4.02
1795 4054 0.686441 CGGGAGTAGATGTGGGTGGA 60.686 60.000 0.00 0.00 0.00 4.02
1796 4055 1.823295 CGGGAGTAGATGTGGGTGG 59.177 63.158 0.00 0.00 0.00 4.61
1797 4056 1.144057 GCGGGAGTAGATGTGGGTG 59.856 63.158 0.00 0.00 0.00 4.61
1798 4057 1.001760 AGCGGGAGTAGATGTGGGT 59.998 57.895 0.00 0.00 0.00 4.51
1799 4058 1.742768 GAGCGGGAGTAGATGTGGG 59.257 63.158 0.00 0.00 0.00 4.61
1800 4059 1.360551 CGAGCGGGAGTAGATGTGG 59.639 63.158 0.00 0.00 0.00 4.17
1801 4060 1.299468 GCGAGCGGGAGTAGATGTG 60.299 63.158 0.00 0.00 0.00 3.21
1802 4061 1.109920 ATGCGAGCGGGAGTAGATGT 61.110 55.000 0.00 0.00 0.00 3.06
1803 4062 0.032678 AATGCGAGCGGGAGTAGATG 59.967 55.000 0.00 0.00 0.00 2.90
1804 4063 0.032678 CAATGCGAGCGGGAGTAGAT 59.967 55.000 0.00 0.00 0.00 1.98
1805 4064 1.320344 ACAATGCGAGCGGGAGTAGA 61.320 55.000 0.00 0.00 0.00 2.59
1806 4065 1.141881 ACAATGCGAGCGGGAGTAG 59.858 57.895 0.00 0.00 0.00 2.57
1807 4066 1.153647 CACAATGCGAGCGGGAGTA 60.154 57.895 0.00 0.00 0.00 2.59
1808 4067 1.884075 TACACAATGCGAGCGGGAGT 61.884 55.000 0.00 0.00 0.00 3.85
1809 4068 0.530650 ATACACAATGCGAGCGGGAG 60.531 55.000 0.00 0.00 0.00 4.30
1810 4069 0.107897 AATACACAATGCGAGCGGGA 60.108 50.000 0.00 0.00 0.00 5.14
1811 4070 0.732571 AAATACACAATGCGAGCGGG 59.267 50.000 0.00 0.00 0.00 6.13
1812 4071 1.665679 AGAAATACACAATGCGAGCGG 59.334 47.619 0.00 0.00 0.00 5.52
1813 4072 4.508971 CTTAGAAATACACAATGCGAGCG 58.491 43.478 0.00 0.00 0.00 5.03
1814 4073 4.201812 TGCTTAGAAATACACAATGCGAGC 60.202 41.667 0.00 0.00 0.00 5.03
1815 4074 5.163864 TGTGCTTAGAAATACACAATGCGAG 60.164 40.000 0.00 0.00 39.91 5.03
1816 4075 4.693095 TGTGCTTAGAAATACACAATGCGA 59.307 37.500 0.00 0.00 39.91 5.10
1817 4076 4.788100 GTGTGCTTAGAAATACACAATGCG 59.212 41.667 0.00 0.00 44.02 4.73
1867 4168 6.842163 AGCACATTATAGTGTTACAGTTTGC 58.158 36.000 0.00 0.00 41.52 3.68
1872 4173 7.609760 TTTGGAGCACATTATAGTGTTACAG 57.390 36.000 0.00 0.00 43.14 2.74
1982 4452 1.340991 TGGGCCTTGTTCTTCTATGCC 60.341 52.381 4.53 0.00 33.59 4.40
2085 4642 4.905429 ACTATGCACAACTTGTATCCACA 58.095 39.130 0.00 0.00 32.04 4.17
2096 4653 7.985476 ACATGAGGTTTTATACTATGCACAAC 58.015 34.615 0.00 0.00 0.00 3.32
2121 4678 5.818678 GACCATGGGTCCAATACAGTATA 57.181 43.478 18.09 0.00 46.19 1.47
2122 4679 4.706842 GACCATGGGTCCAATACAGTAT 57.293 45.455 18.09 0.00 46.19 2.12
2273 4830 2.099405 CTTGTGGTGTGGGAACTTGTT 58.901 47.619 0.00 0.00 0.00 2.83
2402 4966 4.104417 GCGCTCACGACGAGAGGT 62.104 66.667 21.28 0.00 45.45 3.85
2541 5105 0.405198 TGTGATGTTGAGGGTGCCAT 59.595 50.000 0.00 0.00 0.00 4.40
2570 5134 6.663093 TGACTTACAAATATGTTGCCCTTGAT 59.337 34.615 0.00 0.00 41.05 2.57
2802 5376 1.180456 TGGTCGCACCCTCTCGTTAA 61.180 55.000 3.33 0.00 37.50 2.01
2803 5377 1.592400 CTGGTCGCACCCTCTCGTTA 61.592 60.000 3.33 0.00 37.50 3.18
3121 5695 0.970427 TGGCCGTGCTCATAGACAGA 60.970 55.000 0.00 0.00 0.00 3.41
3202 5776 3.903530 TCCTCCTCCATGCTCACTATA 57.096 47.619 0.00 0.00 0.00 1.31
3226 5800 4.906060 GTCTTTAGGAGGGGGATAAGCTTA 59.094 45.833 8.99 8.99 0.00 3.09
3402 5990 9.485206 TTGTCTTTCAAGGTAATAGACTGTTAC 57.515 33.333 12.38 12.38 36.91 2.50
3405 5993 7.119846 GCATTGTCTTTCAAGGTAATAGACTGT 59.880 37.037 0.00 0.00 39.61 3.55
3442 6041 1.993956 ACATGCAGGTGCCAAGTTTA 58.006 45.000 1.71 0.00 41.18 2.01
3443 6042 1.122227 AACATGCAGGTGCCAAGTTT 58.878 45.000 4.03 0.00 41.18 2.66
3444 6043 0.390124 CAACATGCAGGTGCCAAGTT 59.610 50.000 4.03 0.00 41.18 2.66
3622 6971 4.198028 TCTTAAACTAAACCTCGGCTCC 57.802 45.455 0.00 0.00 0.00 4.70
3631 6980 8.158445 CGTCCTGTAAACGATCTTAAACTAAAC 58.842 37.037 0.00 0.00 42.62 2.01
3666 7015 3.617284 TGAGTACTTGTGAGATCGGCTA 58.383 45.455 0.00 0.00 0.00 3.93
3687 7036 6.639632 TTTACCGAGCCTAACGAGTTATAT 57.360 37.500 0.00 0.00 0.00 0.86
3812 7163 4.625742 GGACATATATGGTCATGTACGTGC 59.374 45.833 16.96 0.00 35.55 5.34
4050 7402 7.134162 TGTACCTCTATATGTAAGGGTGGAAA 58.866 38.462 0.00 0.00 34.31 3.13
4065 7417 7.234988 ACTTGTCCACTAAGTTTGTACCTCTAT 59.765 37.037 0.00 0.00 34.91 1.98
4066 7418 6.552350 ACTTGTCCACTAAGTTTGTACCTCTA 59.448 38.462 0.00 0.00 34.91 2.43
4067 7419 5.365895 ACTTGTCCACTAAGTTTGTACCTCT 59.634 40.000 0.00 0.00 34.91 3.69
4068 7420 5.608449 ACTTGTCCACTAAGTTTGTACCTC 58.392 41.667 0.00 0.00 34.91 3.85
4069 7421 5.625568 ACTTGTCCACTAAGTTTGTACCT 57.374 39.130 0.00 0.00 34.91 3.08
4081 7433 2.104170 GCTCTAGGCTACTTGTCCACT 58.896 52.381 0.00 0.00 38.06 4.00
4230 7583 8.530804 AGGCAGCTTATTCATCTTTTCTAATT 57.469 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.