Multiple sequence alignment - TraesCS3B01G538900

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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 TraesCS3B01G538900 chr3B 100.000 3119 0 0 1 3119 778449825 778452943 0.000000e+00 5760.0
1 TraesCS3B01G538900 chr3D 90.386 1373 103 15 759 2115 582833615 582832256 0.000000e+00 1777.0
2 TraesCS3B01G538900 chr3D 90.372 914 69 10 2214 3119 582830467 582829565 0.000000e+00 1182.0
3 TraesCS3B01G538900 chr3D 92.857 98 4 3 630 725 582833700 582833604 4.190000e-29 139.0
4 TraesCS3B01G538900 chr4A 84.274 585 57 15 76 633 7467929 7468505 3.540000e-149 538.0
5 TraesCS3B01G538900 chr4A 83.986 587 56 18 76 633 589669801 589670378 2.130000e-146 529.0
6 TraesCS3B01G538900 chr7D 81.475 556 79 19 76 622 553599756 553599216 4.780000e-118 435.0
7 TraesCS3B01G538900 chr7D 72.832 346 70 17 1094 1433 509569525 509569852 2.560000e-16 97.1
8 TraesCS3B01G538900 chr7A 81.206 564 72 17 73 613 471552906 471553458 1.030000e-114 424.0
9 TraesCS3B01G538900 chr3A 84.375 384 49 10 259 633 60066626 60067007 1.770000e-97 366.0
10 TraesCS3B01G538900 chr5A 85.352 355 42 10 273 624 96987388 96987735 2.960000e-95 359.0
11 TraesCS3B01G538900 chr1A 88.077 260 22 8 273 529 568119418 568119165 1.820000e-77 300.0
12 TraesCS3B01G538900 chr5B 83.492 315 41 7 278 583 472298335 472298647 1.830000e-72 283.0
13 TraesCS3B01G538900 chr7B 82.111 341 48 10 273 606 600014010 600013676 2.370000e-71 279.0
14 TraesCS3B01G538900 chr2B 82.927 205 30 5 433 633 760122371 760122574 2.470000e-41 180.0


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 TraesCS3B01G538900 chr3B 778449825 778452943 3118 False 5760.000000 5760 100.000 1 3119 1 chr3B.!!$F1 3118
1 TraesCS3B01G538900 chr3D 582829565 582833700 4135 True 1032.666667 1777 91.205 630 3119 3 chr3D.!!$R1 2489
2 TraesCS3B01G538900 chr4A 7467929 7468505 576 False 538.000000 538 84.274 76 633 1 chr4A.!!$F1 557
3 TraesCS3B01G538900 chr4A 589669801 589670378 577 False 529.000000 529 83.986 76 633 1 chr4A.!!$F2 557
4 TraesCS3B01G538900 chr7D 553599216 553599756 540 True 435.000000 435 81.475 76 622 1 chr7D.!!$R1 546
5 TraesCS3B01G538900 chr7A 471552906 471553458 552 False 424.000000 424 81.206 73 613 1 chr7A.!!$F1 540

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
35 36 0.179029 AGACCCCAGTTTTGACCGTG 60.179 55.0 0.00 0.00 0.00 4.94 F
1149 1206 0.179134 ACAGCGTCCGCAAGATAGAC 60.179 55.0 14.70 0.00 44.88 2.59 F
1509 1579 0.390860 ACGAAGACAAGCAGTGCTCT 59.609 50.0 20.03 8.96 38.25 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1591 0.035056 ACGGAGCAAAGATCCTTGGG 60.035 55.0 6.20 0.0 35.75 4.12 R
2039 2109 0.320771 CTGGTAGGAGCGCACAGTTT 60.321 55.0 11.47 0.0 0.00 2.66 R
2449 4278 0.322456 AGCAAATCTAAGCACGGCCA 60.322 50.0 2.24 0.0 0.00 5.36 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
20 21 2.574450 TGACCGGTTTTGGTTTAGACC 58.426 47.619 9.42 0.00 44.01 3.85
21 22 1.881973 GACCGGTTTTGGTTTAGACCC 59.118 52.381 9.42 0.00 45.92 4.46
22 23 1.250328 CCGGTTTTGGTTTAGACCCC 58.750 55.000 0.00 0.00 45.92 4.95
23 24 1.479021 CCGGTTTTGGTTTAGACCCCA 60.479 52.381 0.00 0.00 45.92 4.96
24 25 1.883926 CGGTTTTGGTTTAGACCCCAG 59.116 52.381 0.00 0.00 45.92 4.45
25 26 2.750471 CGGTTTTGGTTTAGACCCCAGT 60.750 50.000 0.00 0.00 45.92 4.00
26 27 3.302161 GGTTTTGGTTTAGACCCCAGTT 58.698 45.455 0.00 0.00 45.92 3.16
27 28 3.707611 GGTTTTGGTTTAGACCCCAGTTT 59.292 43.478 0.00 0.00 45.92 2.66
28 29 4.162698 GGTTTTGGTTTAGACCCCAGTTTT 59.837 41.667 0.00 0.00 45.92 2.43
29 30 5.113383 GTTTTGGTTTAGACCCCAGTTTTG 58.887 41.667 0.00 0.00 45.92 2.44
30 31 3.955524 TGGTTTAGACCCCAGTTTTGA 57.044 42.857 0.00 0.00 45.92 2.69
31 32 3.558033 TGGTTTAGACCCCAGTTTTGAC 58.442 45.455 0.00 0.00 45.92 3.18
32 33 2.889045 GGTTTAGACCCCAGTTTTGACC 59.111 50.000 0.00 0.00 40.25 4.02
33 34 2.551032 GTTTAGACCCCAGTTTTGACCG 59.449 50.000 0.00 0.00 0.00 4.79
34 35 1.426751 TAGACCCCAGTTTTGACCGT 58.573 50.000 0.00 0.00 0.00 4.83
35 36 0.179029 AGACCCCAGTTTTGACCGTG 60.179 55.000 0.00 0.00 0.00 4.94
36 37 1.792118 GACCCCAGTTTTGACCGTGC 61.792 60.000 0.00 0.00 0.00 5.34
37 38 1.528309 CCCCAGTTTTGACCGTGCT 60.528 57.895 0.00 0.00 0.00 4.40
38 39 1.515521 CCCCAGTTTTGACCGTGCTC 61.516 60.000 0.00 0.00 0.00 4.26
39 40 0.817634 CCCAGTTTTGACCGTGCTCA 60.818 55.000 0.00 0.00 0.00 4.26
40 41 0.307760 CCAGTTTTGACCGTGCTCAC 59.692 55.000 0.00 0.00 0.00 3.51
41 42 1.299541 CAGTTTTGACCGTGCTCACT 58.700 50.000 0.00 0.00 0.00 3.41
42 43 1.261619 CAGTTTTGACCGTGCTCACTC 59.738 52.381 0.00 0.00 0.00 3.51
43 44 1.134521 AGTTTTGACCGTGCTCACTCA 60.135 47.619 0.00 0.00 0.00 3.41
44 45 1.668751 GTTTTGACCGTGCTCACTCAA 59.331 47.619 0.00 0.33 0.00 3.02
45 46 2.031258 TTTGACCGTGCTCACTCAAA 57.969 45.000 11.14 11.14 34.91 2.69
46 47 2.254546 TTGACCGTGCTCACTCAAAT 57.745 45.000 3.24 0.00 0.00 2.32
47 48 2.254546 TGACCGTGCTCACTCAAATT 57.745 45.000 0.00 0.00 0.00 1.82
48 49 2.143122 TGACCGTGCTCACTCAAATTC 58.857 47.619 0.00 0.00 0.00 2.17
49 50 1.126846 GACCGTGCTCACTCAAATTCG 59.873 52.381 0.00 0.00 0.00 3.34
50 51 0.179215 CCGTGCTCACTCAAATTCGC 60.179 55.000 0.00 0.00 0.00 4.70
51 52 0.512518 CGTGCTCACTCAAATTCGCA 59.487 50.000 0.00 0.00 0.00 5.10
52 53 1.129251 CGTGCTCACTCAAATTCGCAT 59.871 47.619 0.00 0.00 0.00 4.73
53 54 2.348362 CGTGCTCACTCAAATTCGCATA 59.652 45.455 0.00 0.00 0.00 3.14
54 55 3.181521 CGTGCTCACTCAAATTCGCATAA 60.182 43.478 0.00 0.00 0.00 1.90
55 56 4.494690 CGTGCTCACTCAAATTCGCATAAT 60.495 41.667 0.00 0.00 0.00 1.28
56 57 5.335127 GTGCTCACTCAAATTCGCATAATT 58.665 37.500 0.00 0.00 0.00 1.40
57 58 5.801947 GTGCTCACTCAAATTCGCATAATTT 59.198 36.000 1.84 1.84 0.00 1.82
58 59 6.308766 GTGCTCACTCAAATTCGCATAATTTT 59.691 34.615 4.45 0.00 0.00 1.82
59 60 6.867816 TGCTCACTCAAATTCGCATAATTTTT 59.132 30.769 4.45 0.00 0.00 1.94
60 61 7.148771 TGCTCACTCAAATTCGCATAATTTTTG 60.149 33.333 4.45 3.98 0.00 2.44
61 62 7.148755 GCTCACTCAAATTCGCATAATTTTTGT 60.149 33.333 4.45 4.45 0.00 2.83
62 63 9.340695 CTCACTCAAATTCGCATAATTTTTGTA 57.659 29.630 4.45 0.00 0.00 2.41
63 64 9.853555 TCACTCAAATTCGCATAATTTTTGTAT 57.146 25.926 4.45 0.00 0.00 2.29
73 74 9.891828 TCGCATAATTTTTGTATATCCATGAAC 57.108 29.630 0.00 0.00 0.00 3.18
74 75 9.897744 CGCATAATTTTTGTATATCCATGAACT 57.102 29.630 0.00 0.00 0.00 3.01
93 97 7.789273 TGAACTTTTTCAAATCCACGTAGTA 57.211 32.000 0.00 0.00 37.47 1.82
104 108 7.446013 TCAAATCCACGTAGTATTTTCAAGGTT 59.554 33.333 0.00 0.00 41.61 3.50
108 112 5.467399 CCACGTAGTATTTTCAAGGTTGTGA 59.533 40.000 0.00 0.00 41.61 3.58
109 113 6.148811 CCACGTAGTATTTTCAAGGTTGTGAT 59.851 38.462 0.00 0.00 41.61 3.06
110 114 7.308348 CCACGTAGTATTTTCAAGGTTGTGATT 60.308 37.037 0.00 0.00 41.61 2.57
447 495 4.216687 TCCAAATCCGCGTACTTTTTCAAT 59.783 37.500 4.92 0.00 0.00 2.57
450 499 5.365403 AATCCGCGTACTTTTTCAATTCA 57.635 34.783 4.92 0.00 0.00 2.57
485 534 9.965824 TTTCTAATTCATGAACTCTTTCCAAAC 57.034 29.630 11.07 0.00 0.00 2.93
558 610 9.883142 TGGATTTGAAAAACTACATGAACTTTT 57.117 25.926 0.00 0.00 0.00 2.27
572 624 5.482686 TGAACTTTTAAAAAGTACGCGGT 57.517 34.783 12.47 0.00 0.00 5.68
613 666 5.108385 ACTTGGAAAAAGTACGCAGATTG 57.892 39.130 0.00 0.00 0.00 2.67
615 668 2.817258 TGGAAAAAGTACGCAGATTGGG 59.183 45.455 0.00 0.00 36.28 4.12
621 675 5.722021 AAAGTACGCAGATTGGGAAAAAT 57.278 34.783 0.00 0.00 34.12 1.82
624 678 3.757745 ACGCAGATTGGGAAAAATACG 57.242 42.857 0.00 0.00 34.12 3.06
628 682 4.241681 GCAGATTGGGAAAAATACGCAAA 58.758 39.130 0.00 0.00 41.81 3.68
633 687 7.956943 CAGATTGGGAAAAATACGCAAATTTTC 59.043 33.333 6.49 6.11 41.81 2.29
713 767 1.985614 TGGCAGAGATCCACCACTG 59.014 57.895 0.00 0.00 0.00 3.66
714 768 4.215349 GCAGAGATCCACCACTGC 57.785 61.111 0.00 0.00 46.25 4.40
715 769 1.451028 GCAGAGATCCACCACTGCC 60.451 63.158 0.00 0.00 46.46 4.85
716 770 1.153489 CAGAGATCCACCACTGCCG 60.153 63.158 0.00 0.00 0.00 5.69
717 771 2.512515 GAGATCCACCACTGCCGC 60.513 66.667 0.00 0.00 0.00 6.53
718 772 3.005539 AGATCCACCACTGCCGCT 61.006 61.111 0.00 0.00 0.00 5.52
719 773 2.821366 GATCCACCACTGCCGCTG 60.821 66.667 0.00 0.00 0.00 5.18
720 774 4.415150 ATCCACCACTGCCGCTGG 62.415 66.667 2.06 0.00 34.62 4.85
723 777 4.007644 CACCACTGCCGCTGGAGA 62.008 66.667 3.13 0.00 32.55 3.71
724 778 3.699894 ACCACTGCCGCTGGAGAG 61.700 66.667 3.13 0.00 32.55 3.20
725 779 4.463879 CCACTGCCGCTGGAGAGG 62.464 72.222 3.13 0.65 38.10 3.69
726 780 3.385384 CACTGCCGCTGGAGAGGA 61.385 66.667 3.13 0.00 37.14 3.71
727 781 3.386237 ACTGCCGCTGGAGAGGAC 61.386 66.667 3.13 0.00 37.14 3.85
728 782 4.504916 CTGCCGCTGGAGAGGACG 62.505 72.222 0.00 0.00 37.14 4.79
733 787 4.154347 GCTGGAGAGGACGCCCTG 62.154 72.222 0.00 0.00 44.53 4.45
734 788 3.465403 CTGGAGAGGACGCCCTGG 61.465 72.222 0.00 0.00 44.53 4.45
756 810 3.104843 CTAGTTCAGCTATGGCCAGTC 57.895 52.381 13.05 2.13 39.73 3.51
757 811 1.279496 AGTTCAGCTATGGCCAGTCA 58.721 50.000 13.05 0.00 39.73 3.41
784 838 3.467226 GAGTCGGATTGGCGGGGA 61.467 66.667 0.00 0.00 0.00 4.81
785 839 3.447025 GAGTCGGATTGGCGGGGAG 62.447 68.421 0.00 0.00 0.00 4.30
786 840 4.547367 GTCGGATTGGCGGGGAGG 62.547 72.222 0.00 0.00 0.00 4.30
812 866 0.533755 CCTGAGTCCAATCCGATGGC 60.534 60.000 0.00 0.00 40.46 4.40
828 882 3.910104 GCGGATTCGTTCGCGGTC 61.910 66.667 6.13 0.00 42.48 4.79
829 883 3.604202 CGGATTCGTTCGCGGTCG 61.604 66.667 6.13 11.96 41.70 4.79
830 884 3.910104 GGATTCGTTCGCGGTCGC 61.910 66.667 6.13 5.16 41.70 5.19
856 910 3.381590 GGGAATTTAGGTGCCAATCTGAC 59.618 47.826 0.00 0.00 0.00 3.51
864 918 2.096496 GGTGCCAATCTGACTCGAATTG 59.904 50.000 0.66 0.66 0.00 2.32
933 987 4.959596 TTTCTTACTCTACGCAGTCGAT 57.040 40.909 0.00 0.00 43.93 3.59
988 1042 1.351683 GCCGGAGAGGAGGTAGATAGA 59.648 57.143 5.05 0.00 45.00 1.98
1005 1059 2.349297 AGAAACTCGACGACATGTCC 57.651 50.000 20.03 6.16 45.23 4.02
1019 1073 0.957395 ATGTCCAAGCGGCAGTTGAG 60.957 55.000 1.45 0.00 0.00 3.02
1149 1206 0.179134 ACAGCGTCCGCAAGATAGAC 60.179 55.000 14.70 0.00 44.88 2.59
1197 1254 4.773117 GCCGACCTGGACGACGAC 62.773 72.222 19.67 0.00 42.00 4.34
1221 1278 2.288643 GAGCCCCTCCCAGATCCT 59.711 66.667 0.00 0.00 0.00 3.24
1264 1321 4.704833 ACTGCCGCCTGTCGCATT 62.705 61.111 0.00 0.00 37.30 3.56
1290 1347 1.274596 CGTACGGCACCAACATACTC 58.725 55.000 7.57 0.00 0.00 2.59
1300 1357 0.659427 CAACATACTCGCCATGCTGG 59.341 55.000 0.00 0.00 41.55 4.85
1350 1413 2.411806 CCCCGTATTCGACACAAAAACG 60.412 50.000 0.00 0.00 39.71 3.60
1353 1416 2.894000 CGTATTCGACACAAAAACGCTG 59.106 45.455 0.00 0.00 39.71 5.18
1389 1452 2.646175 CCATCCGGACGTCCACAGT 61.646 63.158 32.80 13.59 35.14 3.55
1394 1457 3.936203 GGACGTCCACAGTGCCCA 61.936 66.667 29.75 0.00 35.64 5.36
1408 1471 2.597217 CCCAGCCCTTGTTCGCAA 60.597 61.111 0.00 0.00 35.53 4.85
1412 1475 1.152963 AGCCCTTGTTCGCAACAGT 60.153 52.632 2.73 0.00 43.27 3.55
1455 1518 2.073816 GTGGGATACTCCACGTTTGTG 58.926 52.381 0.00 0.00 46.31 3.33
1487 1557 1.755395 CACTCCCCGGACCATACGA 60.755 63.158 0.73 0.00 0.00 3.43
1488 1558 1.755783 ACTCCCCGGACCATACGAC 60.756 63.158 0.73 0.00 0.00 4.34
1499 1569 1.536766 ACCATACGACGACGAAGACAA 59.463 47.619 15.32 0.00 42.66 3.18
1506 1576 1.215655 ACGACGAAGACAAGCAGTGC 61.216 55.000 7.13 7.13 0.00 4.40
1509 1579 0.390860 ACGAAGACAAGCAGTGCTCT 59.609 50.000 20.03 8.96 38.25 4.09
1516 1586 1.072806 ACAAGCAGTGCTCTTGGATCA 59.927 47.619 20.03 0.00 43.77 2.92
1520 1590 2.818432 AGCAGTGCTCTTGGATCAAAAG 59.182 45.455 13.14 0.00 30.62 2.27
1521 1591 2.670509 GCAGTGCTCTTGGATCAAAAGC 60.671 50.000 8.18 9.02 0.00 3.51
1543 1613 2.426522 CAAGGATCTTTGCTCCGTTCA 58.573 47.619 4.46 0.00 37.88 3.18
1545 1615 3.356529 AGGATCTTTGCTCCGTTCAAT 57.643 42.857 0.00 0.00 37.88 2.57
1549 1619 2.857483 TCTTTGCTCCGTTCAATTCCA 58.143 42.857 0.00 0.00 0.00 3.53
1550 1620 3.420893 TCTTTGCTCCGTTCAATTCCAT 58.579 40.909 0.00 0.00 0.00 3.41
1551 1621 3.826157 TCTTTGCTCCGTTCAATTCCATT 59.174 39.130 0.00 0.00 0.00 3.16
1553 1623 1.818060 TGCTCCGTTCAATTCCATTGG 59.182 47.619 0.00 0.00 40.61 3.16
1554 1624 1.818674 GCTCCGTTCAATTCCATTGGT 59.181 47.619 1.86 0.00 40.61 3.67
1557 1627 3.226777 TCCGTTCAATTCCATTGGTGTT 58.773 40.909 1.86 0.00 40.61 3.32
1578 1648 1.827789 GTCCTTTGCAGTGCACCCA 60.828 57.895 19.58 8.58 38.71 4.51
1640 1710 1.347707 CTTCCTGGACACCAAGTGCTA 59.652 52.381 0.00 0.00 39.64 3.49
1669 1739 2.663196 GCGTAGGCAAGTGGGTCT 59.337 61.111 1.75 0.00 39.62 3.85
1698 1768 4.650085 GGCCAGGCCTACTAGGAT 57.350 61.111 24.99 0.00 46.69 3.24
1767 1837 2.182791 CACGTCTGCTCCTGCGAT 59.817 61.111 0.00 0.00 43.34 4.58
1796 1866 3.187700 CCCTGTCTGATTACGCTACAAC 58.812 50.000 0.00 0.00 0.00 3.32
1799 1869 3.904571 TGTCTGATTACGCTACAACGTT 58.095 40.909 0.00 0.00 45.75 3.99
1835 1905 2.347490 GAAGCTTGGCGAGGACCA 59.653 61.111 2.10 0.00 38.16 4.02
1836 1906 1.743252 GAAGCTTGGCGAGGACCAG 60.743 63.158 2.10 0.00 41.82 4.00
1849 1919 3.612371 GACCAGCTCTTCGACGCGT 62.612 63.158 13.85 13.85 0.00 6.01
1894 1964 2.284331 TTCTCTACCTGGGCGGCA 60.284 61.111 12.47 0.00 35.61 5.69
1959 2029 1.840635 GAGCCTTTAGGACCCTGTGAT 59.159 52.381 0.00 0.00 37.39 3.06
1962 2032 4.662349 GCCTTTAGGACCCTGTGATGGG 62.662 59.091 0.00 0.00 43.59 4.00
2043 2113 4.295119 AGGACGACGCGGCAAACT 62.295 61.111 14.85 2.37 36.10 2.66
2045 2115 3.335534 GACGACGCGGCAAACTGT 61.336 61.111 14.85 0.00 33.63 3.55
2088 2158 7.545362 CGAAGGACATGAATTTAATGAGTCT 57.455 36.000 0.00 0.00 0.00 3.24
2096 2166 9.846248 ACATGAATTTAATGAGTCTTGCTTAAC 57.154 29.630 0.00 0.00 0.00 2.01
2129 3945 6.127619 GCTTTCTGGATGTAGCCAAGTTATTT 60.128 38.462 0.00 0.00 37.52 1.40
2132 3948 7.391148 TCTGGATGTAGCCAAGTTATTTTTC 57.609 36.000 0.00 0.00 37.52 2.29
2134 3950 7.669722 TCTGGATGTAGCCAAGTTATTTTTCTT 59.330 33.333 0.00 0.00 37.52 2.52
2135 3951 8.871629 TGGATGTAGCCAAGTTATTTTTCTTA 57.128 30.769 0.00 0.00 34.31 2.10
2166 3989 7.013655 ACCATGTATTATGAGCCAAATGTTCTC 59.986 37.037 0.00 0.00 0.00 2.87
2225 4048 9.733556 TTAAACCATGTATTATGAGTCAAGTGT 57.266 29.630 0.00 0.00 0.00 3.55
2226 4049 8.635765 AAACCATGTATTATGAGTCAAGTGTT 57.364 30.769 0.00 0.00 0.00 3.32
2227 4050 7.849804 ACCATGTATTATGAGTCAAGTGTTC 57.150 36.000 0.00 0.00 0.00 3.18
2228 4051 7.624549 ACCATGTATTATGAGTCAAGTGTTCT 58.375 34.615 0.00 0.00 0.00 3.01
2229 4052 7.766278 ACCATGTATTATGAGTCAAGTGTTCTC 59.234 37.037 0.00 0.00 0.00 2.87
2230 4053 7.984050 CCATGTATTATGAGTCAAGTGTTCTCT 59.016 37.037 0.00 0.00 0.00 3.10
2231 4054 9.376075 CATGTATTATGAGTCAAGTGTTCTCTT 57.624 33.333 0.00 0.00 0.00 2.85
2232 4055 8.988064 TGTATTATGAGTCAAGTGTTCTCTTC 57.012 34.615 0.00 0.00 0.00 2.87
2233 4056 8.807118 TGTATTATGAGTCAAGTGTTCTCTTCT 58.193 33.333 0.00 0.00 0.00 2.85
2234 4057 9.081997 GTATTATGAGTCAAGTGTTCTCTTCTG 57.918 37.037 0.00 0.00 0.00 3.02
2235 4058 5.543507 ATGAGTCAAGTGTTCTCTTCTGT 57.456 39.130 0.00 0.00 0.00 3.41
2236 4059 5.344743 TGAGTCAAGTGTTCTCTTCTGTT 57.655 39.130 0.00 0.00 0.00 3.16
2237 4060 5.734720 TGAGTCAAGTGTTCTCTTCTGTTT 58.265 37.500 0.00 0.00 0.00 2.83
2238 4061 6.873997 TGAGTCAAGTGTTCTCTTCTGTTTA 58.126 36.000 0.00 0.00 0.00 2.01
2239 4062 7.500992 TGAGTCAAGTGTTCTCTTCTGTTTAT 58.499 34.615 0.00 0.00 0.00 1.40
2240 4063 7.987458 TGAGTCAAGTGTTCTCTTCTGTTTATT 59.013 33.333 0.00 0.00 0.00 1.40
2241 4064 8.738645 AGTCAAGTGTTCTCTTCTGTTTATTT 57.261 30.769 0.00 0.00 0.00 1.40
2242 4065 9.178758 AGTCAAGTGTTCTCTTCTGTTTATTTT 57.821 29.630 0.00 0.00 0.00 1.82
2243 4066 9.788960 GTCAAGTGTTCTCTTCTGTTTATTTTT 57.211 29.630 0.00 0.00 0.00 1.94
2271 4094 7.291566 TCAAGTTAAATTTGGTACTTCCCTGA 58.708 34.615 0.00 0.69 34.77 3.86
2283 4106 5.593095 GGTACTTCCCTGAGTTTGAAAGTTT 59.407 40.000 0.00 0.00 0.00 2.66
2289 4115 5.949354 TCCCTGAGTTTGAAAGTTTTCAGAA 59.051 36.000 13.47 3.71 46.68 3.02
2301 4127 8.744652 TGAAAGTTTTCAGAATCCAGTTGTAAA 58.255 29.630 3.28 0.00 41.88 2.01
2302 4128 9.750125 GAAAGTTTTCAGAATCCAGTTGTAAAT 57.250 29.630 0.00 0.00 37.15 1.40
2303 4129 9.533253 AAAGTTTTCAGAATCCAGTTGTAAATG 57.467 29.630 0.00 0.00 0.00 2.32
2305 4131 8.695456 AGTTTTCAGAATCCAGTTGTAAATGTT 58.305 29.630 0.00 0.00 0.00 2.71
2306 4132 9.959749 GTTTTCAGAATCCAGTTGTAAATGTTA 57.040 29.630 0.00 0.00 0.00 2.41
2307 4133 9.959749 TTTTCAGAATCCAGTTGTAAATGTTAC 57.040 29.630 0.00 0.00 0.00 2.50
2311 4140 9.559958 CAGAATCCAGTTGTAAATGTTACAATC 57.440 33.333 14.70 8.57 39.30 2.67
2367 4196 8.893563 AAATTTCATTACCCAGAAATAGTGGA 57.106 30.769 0.00 0.00 42.02 4.02
2370 4199 5.376625 TCATTACCCAGAAATAGTGGATGC 58.623 41.667 0.00 0.00 37.23 3.91
2416 4245 1.280421 GACAGGCAAGATTCTCTGGGT 59.720 52.381 6.00 0.00 0.00 4.51
2424 4253 4.559502 GCAAGATTCTCTGGGTTTGTTTCC 60.560 45.833 0.00 0.00 0.00 3.13
2429 4258 4.935352 TCTCTGGGTTTGTTTCCAATTG 57.065 40.909 0.00 0.00 31.97 2.32
2438 4267 6.048509 GGTTTGTTTCCAATTGTCATTGTCT 58.951 36.000 4.43 0.00 38.58 3.41
2442 4271 6.734137 TGTTTCCAATTGTCATTGTCTACAC 58.266 36.000 4.43 0.00 38.58 2.90
2446 4275 4.379813 CCAATTGTCATTGTCTACACAGCC 60.380 45.833 4.43 0.00 38.58 4.85
2449 4278 2.305635 TGTCATTGTCTACACAGCCCAT 59.694 45.455 0.00 0.00 32.71 4.00
2467 4296 0.740737 ATGGCCGTGCTTAGATTTGC 59.259 50.000 0.00 0.00 0.00 3.68
2472 4301 2.030946 GCCGTGCTTAGATTTGCTACAG 59.969 50.000 0.00 0.00 0.00 2.74
2477 4306 5.403766 CGTGCTTAGATTTGCTACAGGATAG 59.596 44.000 0.00 0.00 0.00 2.08
2480 4309 7.495934 GTGCTTAGATTTGCTACAGGATAGAAA 59.504 37.037 0.00 0.00 0.00 2.52
2481 4310 7.712639 TGCTTAGATTTGCTACAGGATAGAAAG 59.287 37.037 0.00 0.00 0.00 2.62
2623 4452 4.586884 AGTTAGACCGACACATCTCTACA 58.413 43.478 0.00 0.00 0.00 2.74
2641 4470 6.065976 TCTACACAAGATGAATGGGAATGT 57.934 37.500 0.00 0.00 0.00 2.71
2708 4537 5.095145 TGGACTGATTCTTCTGAAGGATG 57.905 43.478 15.81 5.33 35.44 3.51
2709 4538 4.533707 TGGACTGATTCTTCTGAAGGATGT 59.466 41.667 15.81 8.45 35.44 3.06
2713 4542 6.638610 ACTGATTCTTCTGAAGGATGTACTG 58.361 40.000 15.81 8.18 35.44 2.74
2726 4555 4.020485 AGGATGTACTGTAAACCCTGTGAC 60.020 45.833 0.00 0.00 0.00 3.67
2739 4568 2.550208 CCCTGTGACGCTAAGGTTTTCT 60.550 50.000 0.00 0.00 0.00 2.52
2747 4576 7.174253 TGTGACGCTAAGGTTTTCTTTATCATT 59.826 33.333 0.00 0.00 36.93 2.57
2748 4577 8.021396 GTGACGCTAAGGTTTTCTTTATCATTT 58.979 33.333 0.00 0.00 36.93 2.32
2761 4590 9.458374 TTTCTTTATCATTTCACGGTTTCTTTC 57.542 29.630 0.00 0.00 0.00 2.62
2764 4593 4.829064 TCATTTCACGGTTTCTTTCCTG 57.171 40.909 0.00 0.00 0.00 3.86
2767 4596 2.270352 TCACGGTTTCTTTCCTGCAT 57.730 45.000 0.00 0.00 0.00 3.96
2786 4615 8.271458 TCCTGCATATAAACTCCTGTAAATTCA 58.729 33.333 0.00 0.00 0.00 2.57
2789 4618 8.673711 TGCATATAAACTCCTGTAAATTCACAC 58.326 33.333 0.00 0.00 0.00 3.82
2798 4627 7.936847 ACTCCTGTAAATTCACACTACAAATGA 59.063 33.333 0.00 0.00 0.00 2.57
2799 4628 8.094798 TCCTGTAAATTCACACTACAAATGAC 57.905 34.615 0.00 0.00 0.00 3.06
2844 4673 9.901172 TTTGAATATTCCTAGTCTTCCTTTACC 57.099 33.333 12.90 0.00 0.00 2.85
2849 4678 4.362677 TCCTAGTCTTCCTTTACCATGCT 58.637 43.478 0.00 0.00 0.00 3.79
2850 4679 4.406003 TCCTAGTCTTCCTTTACCATGCTC 59.594 45.833 0.00 0.00 0.00 4.26
2851 4680 4.162320 CCTAGTCTTCCTTTACCATGCTCA 59.838 45.833 0.00 0.00 0.00 4.26
2863 4692 4.098914 ACCATGCTCAGGTTTACTTGAA 57.901 40.909 0.00 0.00 35.33 2.69
2876 4705 0.980423 ACTTGAACCTCAGCCCTCTC 59.020 55.000 0.00 0.00 0.00 3.20
2877 4706 0.108424 CTTGAACCTCAGCCCTCTCG 60.108 60.000 0.00 0.00 0.00 4.04
2883 4712 4.704103 TCAGCCCTCTCGCCAGGT 62.704 66.667 0.00 0.00 0.00 4.00
2894 4723 2.031516 CGCCAGGTTCAGTCAGCAG 61.032 63.158 0.00 0.00 0.00 4.24
2895 4724 1.673665 GCCAGGTTCAGTCAGCAGG 60.674 63.158 0.00 0.00 0.00 4.85
2896 4725 2.061220 CCAGGTTCAGTCAGCAGGA 58.939 57.895 0.00 0.00 0.00 3.86
2897 4726 0.036577 CCAGGTTCAGTCAGCAGGAG 60.037 60.000 0.00 0.00 0.00 3.69
2898 4727 0.683973 CAGGTTCAGTCAGCAGGAGT 59.316 55.000 0.00 0.00 0.00 3.85
2901 4730 0.394565 GTTCAGTCAGCAGGAGTGGT 59.605 55.000 11.81 0.00 45.36 4.16
2919 4748 2.220586 TGGGTCATCAACGGCCTCA 61.221 57.895 0.00 0.00 0.00 3.86
2964 4793 2.664567 GTTGCAAACGGCCATATGC 58.335 52.632 14.82 14.82 43.89 3.14
2969 4798 0.027979 CAAACGGCCATATGCTCACG 59.972 55.000 2.24 1.40 40.92 4.35
3038 4867 4.448537 ACTCTTGATTGAGAGGTCTTCG 57.551 45.455 6.82 0.00 45.93 3.79
3056 4885 6.257193 GGTCTTCGTCGAATTAAACCATGTAT 59.743 38.462 8.36 0.00 0.00 2.29
3075 4904 2.601240 TGGGATGAGCCAAATGTTCA 57.399 45.000 0.00 0.00 38.95 3.18
3084 4913 4.402155 TGAGCCAAATGTTCACTTCTGTTT 59.598 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.889045 GGTCAAAACTGGGGTCTAAACC 59.111 50.000 0.00 0.00 45.65 3.27
12 13 2.551032 CGGTCAAAACTGGGGTCTAAAC 59.449 50.000 0.00 0.00 0.00 2.01
13 14 2.173143 ACGGTCAAAACTGGGGTCTAAA 59.827 45.455 0.00 0.00 35.97 1.85
14 15 1.770061 ACGGTCAAAACTGGGGTCTAA 59.230 47.619 0.00 0.00 35.97 2.10
15 16 1.071071 CACGGTCAAAACTGGGGTCTA 59.929 52.381 0.00 0.00 35.97 2.59
16 17 0.179029 CACGGTCAAAACTGGGGTCT 60.179 55.000 0.00 0.00 35.97 3.85
17 18 1.792118 GCACGGTCAAAACTGGGGTC 61.792 60.000 0.00 0.00 35.55 4.46
18 19 1.826487 GCACGGTCAAAACTGGGGT 60.826 57.895 0.00 0.00 35.55 4.95
19 20 1.515521 GAGCACGGTCAAAACTGGGG 61.516 60.000 0.00 0.00 35.55 4.96
20 21 0.817634 TGAGCACGGTCAAAACTGGG 60.818 55.000 0.00 0.00 38.30 4.45
21 22 0.307760 GTGAGCACGGTCAAAACTGG 59.692 55.000 0.00 0.00 35.97 4.00
22 23 1.261619 GAGTGAGCACGGTCAAAACTG 59.738 52.381 0.00 0.00 37.81 3.16
23 24 1.134521 TGAGTGAGCACGGTCAAAACT 60.135 47.619 0.00 0.00 36.20 2.66
24 25 1.295792 TGAGTGAGCACGGTCAAAAC 58.704 50.000 0.00 0.00 36.20 2.43
25 26 2.031258 TTGAGTGAGCACGGTCAAAA 57.969 45.000 0.00 0.00 36.20 2.44
26 27 2.031258 TTTGAGTGAGCACGGTCAAA 57.969 45.000 11.62 11.62 34.91 2.69
27 28 2.254546 ATTTGAGTGAGCACGGTCAA 57.745 45.000 0.00 2.35 36.20 3.18
28 29 2.143122 GAATTTGAGTGAGCACGGTCA 58.857 47.619 0.00 0.00 36.20 4.02
29 30 1.126846 CGAATTTGAGTGAGCACGGTC 59.873 52.381 0.00 0.00 36.20 4.79
30 31 1.148310 CGAATTTGAGTGAGCACGGT 58.852 50.000 0.00 0.00 36.20 4.83
31 32 0.179215 GCGAATTTGAGTGAGCACGG 60.179 55.000 0.00 0.00 36.20 4.94
32 33 0.512518 TGCGAATTTGAGTGAGCACG 59.487 50.000 0.00 0.00 36.20 5.34
33 34 2.907910 ATGCGAATTTGAGTGAGCAC 57.092 45.000 0.00 0.00 37.44 4.40
34 35 5.565592 AATTATGCGAATTTGAGTGAGCA 57.434 34.783 0.00 0.00 39.02 4.26
35 36 6.875926 AAAATTATGCGAATTTGAGTGAGC 57.124 33.333 9.24 0.00 30.94 4.26
36 37 8.231304 ACAAAAATTATGCGAATTTGAGTGAG 57.769 30.769 9.24 1.67 35.52 3.51
37 38 9.853555 ATACAAAAATTATGCGAATTTGAGTGA 57.146 25.926 16.31 7.80 35.52 3.41
47 48 9.891828 GTTCATGGATATACAAAAATTATGCGA 57.108 29.630 0.00 0.00 0.00 5.10
48 49 9.897744 AGTTCATGGATATACAAAAATTATGCG 57.102 29.630 0.00 0.00 0.00 4.73
62 63 7.975616 CGTGGATTTGAAAAAGTTCATGGATAT 59.024 33.333 0.00 0.00 43.29 1.63
63 64 7.040062 ACGTGGATTTGAAAAAGTTCATGGATA 60.040 33.333 0.00 0.00 43.29 2.59
64 65 6.158598 CGTGGATTTGAAAAAGTTCATGGAT 58.841 36.000 0.00 0.00 43.29 3.41
65 66 5.068460 ACGTGGATTTGAAAAAGTTCATGGA 59.932 36.000 0.00 0.00 43.29 3.41
66 67 5.288804 ACGTGGATTTGAAAAAGTTCATGG 58.711 37.500 0.00 0.00 43.29 3.66
67 68 7.138736 ACTACGTGGATTTGAAAAAGTTCATG 58.861 34.615 5.70 0.00 43.29 3.07
68 69 7.272037 ACTACGTGGATTTGAAAAAGTTCAT 57.728 32.000 5.70 0.00 43.29 2.57
69 70 6.687081 ACTACGTGGATTTGAAAAAGTTCA 57.313 33.333 5.70 0.00 42.12 3.18
70 71 9.673454 AAATACTACGTGGATTTGAAAAAGTTC 57.327 29.630 5.70 0.00 0.00 3.01
72 73 9.673454 GAAAATACTACGTGGATTTGAAAAAGT 57.327 29.630 5.70 0.00 0.00 2.66
73 74 9.672086 TGAAAATACTACGTGGATTTGAAAAAG 57.328 29.630 5.70 0.00 0.00 2.27
318 362 5.781818 AGTTCATGGATTGGAAAAGGAACAT 59.218 36.000 0.00 0.00 36.69 2.71
367 411 7.925483 TGGACTTGAAAAATTATGTCAACTTGG 59.075 33.333 0.00 0.00 0.00 3.61
416 464 1.135402 ACGCGGATTTGGATTTCTTGC 60.135 47.619 12.47 0.00 0.00 4.01
417 465 2.919666 ACGCGGATTTGGATTTCTTG 57.080 45.000 12.47 0.00 0.00 3.02
480 529 7.573916 TTCATATTTGCGTACATTTGTTTGG 57.426 32.000 0.00 0.00 0.00 3.28
529 579 8.306761 AGTTCATGTAGTTTTTCAAATCCATCC 58.693 33.333 0.00 0.00 0.00 3.51
530 580 9.696917 AAGTTCATGTAGTTTTTCAAATCCATC 57.303 29.630 0.00 0.00 0.00 3.51
586 638 3.690139 TGCGTACTTTTTCCAAGTTCACA 59.310 39.130 0.00 0.00 0.00 3.58
615 668 7.014702 CCATGTGGAAAATTTGCGTATTTTTC 58.985 34.615 11.30 11.30 37.72 2.29
621 675 2.353208 GGCCATGTGGAAAATTTGCGTA 60.353 45.455 0.00 0.00 37.39 4.42
624 678 1.271271 TGGGCCATGTGGAAAATTTGC 60.271 47.619 0.00 0.00 37.39 3.68
628 682 0.983467 GGTTGGGCCATGTGGAAAAT 59.017 50.000 7.26 0.00 37.39 1.82
633 687 2.362889 GGAGGTTGGGCCATGTGG 60.363 66.667 7.26 0.00 40.61 4.17
664 718 1.203313 GGGTTTCGTCTTTCGTGCG 59.797 57.895 0.00 0.00 40.80 5.34
716 770 4.154347 CAGGGCGTCCTCTCCAGC 62.154 72.222 5.00 0.00 42.67 4.85
717 771 3.465403 CCAGGGCGTCCTCTCCAG 61.465 72.222 5.00 0.00 42.67 3.86
736 790 2.432146 TGACTGGCCATAGCTGAACTAG 59.568 50.000 5.51 0.00 39.73 2.57
737 791 2.432146 CTGACTGGCCATAGCTGAACTA 59.568 50.000 5.51 0.00 39.73 2.24
738 792 1.209019 CTGACTGGCCATAGCTGAACT 59.791 52.381 5.51 0.00 39.73 3.01
739 793 1.661341 CTGACTGGCCATAGCTGAAC 58.339 55.000 5.51 0.00 39.73 3.18
740 794 0.107508 GCTGACTGGCCATAGCTGAA 60.108 55.000 22.51 0.23 39.73 3.02
741 795 1.524002 GCTGACTGGCCATAGCTGA 59.476 57.895 22.51 0.00 39.73 4.26
742 796 4.137879 GCTGACTGGCCATAGCTG 57.862 61.111 22.51 13.30 39.73 4.24
752 806 2.268280 CTCCCAGCTGGCTGACTG 59.732 66.667 28.39 12.73 46.30 3.51
753 807 2.203907 ACTCCCAGCTGGCTGACT 60.204 61.111 28.39 6.30 46.30 3.41
754 808 2.267324 GACTCCCAGCTGGCTGAC 59.733 66.667 28.39 17.04 46.30 3.51
755 809 3.385384 CGACTCCCAGCTGGCTGA 61.385 66.667 28.39 18.68 46.30 4.26
756 810 4.463879 CCGACTCCCAGCTGGCTG 62.464 72.222 28.39 22.34 43.26 4.85
757 811 3.991924 ATCCGACTCCCAGCTGGCT 62.992 63.158 28.39 11.48 0.00 4.75
762 816 2.514824 GCCAATCCGACTCCCAGC 60.515 66.667 0.00 0.00 0.00 4.85
784 838 1.415672 TTGGACTCAGGGAAACGCCT 61.416 55.000 0.00 0.00 36.66 5.52
785 839 0.322546 ATTGGACTCAGGGAAACGCC 60.323 55.000 0.00 0.00 0.00 5.68
786 840 1.087501 GATTGGACTCAGGGAAACGC 58.912 55.000 0.00 0.00 0.00 4.84
787 841 1.739067 GGATTGGACTCAGGGAAACG 58.261 55.000 0.00 0.00 0.00 3.60
788 842 1.278127 TCGGATTGGACTCAGGGAAAC 59.722 52.381 0.00 0.00 0.00 2.78
789 843 1.651737 TCGGATTGGACTCAGGGAAA 58.348 50.000 0.00 0.00 0.00 3.13
790 844 1.486310 CATCGGATTGGACTCAGGGAA 59.514 52.381 0.00 0.00 0.00 3.97
791 845 1.123077 CATCGGATTGGACTCAGGGA 58.877 55.000 0.00 0.00 0.00 4.20
792 846 0.107456 CCATCGGATTGGACTCAGGG 59.893 60.000 0.00 0.00 39.25 4.45
795 849 1.143838 CGCCATCGGATTGGACTCA 59.856 57.895 9.68 0.00 39.25 3.41
812 866 3.604202 CGACCGCGAACGAATCCG 61.604 66.667 8.23 0.00 43.93 4.18
832 886 2.039418 GATTGGCACCTAAATTCCCCC 58.961 52.381 0.00 0.00 0.00 5.40
833 887 2.695147 CAGATTGGCACCTAAATTCCCC 59.305 50.000 0.00 0.00 0.00 4.81
834 888 3.381590 GTCAGATTGGCACCTAAATTCCC 59.618 47.826 0.00 0.00 0.00 3.97
835 889 4.273318 AGTCAGATTGGCACCTAAATTCC 58.727 43.478 0.00 0.00 0.00 3.01
836 890 4.034510 CGAGTCAGATTGGCACCTAAATTC 59.965 45.833 0.00 0.00 0.00 2.17
837 891 3.941483 CGAGTCAGATTGGCACCTAAATT 59.059 43.478 0.00 0.00 0.00 1.82
838 892 3.197766 TCGAGTCAGATTGGCACCTAAAT 59.802 43.478 0.00 0.00 0.00 1.40
839 893 2.565391 TCGAGTCAGATTGGCACCTAAA 59.435 45.455 0.00 0.00 0.00 1.85
840 894 2.176045 TCGAGTCAGATTGGCACCTAA 58.824 47.619 0.00 0.00 0.00 2.69
842 896 0.976641 TTCGAGTCAGATTGGCACCT 59.023 50.000 0.00 0.00 0.00 4.00
843 897 2.029838 ATTCGAGTCAGATTGGCACC 57.970 50.000 0.00 0.00 0.00 5.01
844 898 3.002791 TCAATTCGAGTCAGATTGGCAC 58.997 45.455 12.83 0.00 0.00 5.01
845 899 3.264947 CTCAATTCGAGTCAGATTGGCA 58.735 45.455 12.83 0.00 36.94 4.92
856 910 2.208431 GAGATGGCACCTCAATTCGAG 58.792 52.381 3.30 0.00 41.89 4.04
869 923 2.441822 AATAGGCGAGGCGAGATGGC 62.442 60.000 0.00 0.00 45.27 4.40
933 987 3.864160 TTGCAAGCGAGCGAGCAGA 62.864 57.895 14.64 6.59 38.35 4.26
981 1035 5.007430 GGACATGTCGTCGAGTTTCTATCTA 59.993 44.000 19.33 0.00 46.42 1.98
988 1042 2.404215 CTTGGACATGTCGTCGAGTTT 58.596 47.619 19.33 0.00 46.42 2.66
1005 1059 2.192608 GAAGCCTCAACTGCCGCTTG 62.193 60.000 7.54 0.00 41.48 4.01
1149 1206 2.202570 GGGTCCATGTCGTCGACG 60.203 66.667 31.30 31.30 41.45 5.12
1181 1238 4.456253 CGTCGTCGTCCAGGTCGG 62.456 72.222 6.24 0.00 0.00 4.79
1221 1278 1.373748 GTAGAAGCGCACAACCGGA 60.374 57.895 9.46 0.00 0.00 5.14
1323 1386 1.227468 GTCGAATACGGGGAAGGCC 60.227 63.158 0.00 0.00 40.21 5.19
1333 1396 3.223157 CCAGCGTTTTTGTGTCGAATAC 58.777 45.455 0.00 0.00 0.00 1.89
1385 1448 2.983725 GAACAAGGGCTGGGCACTGT 62.984 60.000 0.00 0.00 43.87 3.55
1394 1457 1.152963 ACTGTTGCGAACAAGGGCT 60.153 52.632 0.00 0.00 41.61 5.19
1421 1484 1.053424 TCCCACCGTCAAGTAAAGCT 58.947 50.000 0.00 0.00 0.00 3.74
1455 1518 1.446966 GAGTGGCAAGGAGTCGAGC 60.447 63.158 0.00 0.00 0.00 5.03
1487 1557 1.215655 GCACTGCTTGTCTTCGTCGT 61.216 55.000 0.00 0.00 0.00 4.34
1488 1558 0.941463 AGCACTGCTTGTCTTCGTCG 60.941 55.000 0.00 0.00 33.89 5.12
1499 1569 2.574006 TTTGATCCAAGAGCACTGCT 57.426 45.000 2.22 2.22 43.88 4.24
1509 1579 2.692709 TCCTTGGGCTTTTGATCCAA 57.307 45.000 0.00 0.00 38.13 3.53
1516 1586 2.564504 GAGCAAAGATCCTTGGGCTTTT 59.435 45.455 6.20 0.00 30.00 2.27
1520 1590 1.379642 CGGAGCAAAGATCCTTGGGC 61.380 60.000 6.20 0.00 35.75 5.36
1521 1591 0.035056 ACGGAGCAAAGATCCTTGGG 60.035 55.000 6.20 0.00 35.75 4.12
1526 1596 3.181496 GGAATTGAACGGAGCAAAGATCC 60.181 47.826 0.00 0.00 34.38 3.36
1543 1613 3.575805 AGGACACAACACCAATGGAATT 58.424 40.909 6.16 0.00 36.63 2.17
1545 1615 2.746279 AGGACACAACACCAATGGAA 57.254 45.000 6.16 0.00 0.00 3.53
1549 1619 2.101249 CTGCAAAGGACACAACACCAAT 59.899 45.455 0.00 0.00 0.00 3.16
1550 1620 1.476085 CTGCAAAGGACACAACACCAA 59.524 47.619 0.00 0.00 0.00 3.67
1551 1621 1.102154 CTGCAAAGGACACAACACCA 58.898 50.000 0.00 0.00 0.00 4.17
1553 1623 1.798813 GCACTGCAAAGGACACAACAC 60.799 52.381 0.00 0.00 0.00 3.32
1554 1624 0.455410 GCACTGCAAAGGACACAACA 59.545 50.000 0.00 0.00 0.00 3.33
1557 1627 1.383456 GGTGCACTGCAAAGGACACA 61.383 55.000 17.98 0.00 41.47 3.72
1578 1648 3.066203 AGACGAAAAGCAAATGGTCGTTT 59.934 39.130 0.00 0.00 44.36 3.60
1640 1710 2.056906 GCCTACGCCCATCCAGGAAT 62.057 60.000 0.00 0.00 41.22 3.01
1694 1764 2.733301 CATCGAGCTCGCCATCCT 59.267 61.111 30.97 8.14 39.60 3.24
1695 1765 3.040763 GCATCGAGCTCGCCATCC 61.041 66.667 30.97 7.14 41.15 3.51
1722 1792 3.058160 CCTTTGTGGCGGCAGAGG 61.058 66.667 13.91 16.39 34.97 3.69
1744 1814 4.148825 GGAGCAGACGTGGCCGAT 62.149 66.667 0.00 0.00 37.88 4.18
1785 1855 2.043411 GTCGACAACGTTGTAGCGTAA 58.957 47.619 32.39 15.27 45.00 3.18
1796 1866 3.487202 CCGGCATGGTCGACAACG 61.487 66.667 18.91 12.88 41.26 4.10
1799 1869 4.015406 AAGCCGGCATGGTCGACA 62.015 61.111 31.54 3.91 41.21 4.35
1824 1894 2.604686 AAGAGCTGGTCCTCGCCA 60.605 61.111 2.76 0.00 36.95 5.69
1825 1895 2.185608 GAAGAGCTGGTCCTCGCC 59.814 66.667 2.76 0.00 36.95 5.54
1835 1905 2.097918 CGTACGCGTCGAAGAGCT 59.902 61.111 18.63 0.00 36.95 4.09
1836 1906 2.097160 TCGTACGCGTCGAAGAGC 59.903 61.111 24.28 0.21 36.95 4.09
1845 1915 4.746951 TGCCTGTCGTCGTACGCG 62.747 66.667 20.77 20.77 42.21 6.01
1849 1919 2.632544 CCAGGTGCCTGTCGTCGTA 61.633 63.158 16.15 0.00 42.15 3.43
1894 1964 1.407936 ATGAGGCAGTAGTCGCTGAT 58.592 50.000 0.00 0.00 38.70 2.90
1984 2054 8.438047 ATCATACTTGAGACCAAACTTGGTGAC 61.438 40.741 18.73 12.01 46.92 3.67
2039 2109 0.320771 CTGGTAGGAGCGCACAGTTT 60.321 55.000 11.47 0.00 0.00 2.66
2043 2113 0.970427 TCATCTGGTAGGAGCGCACA 60.970 55.000 11.47 0.00 0.00 4.57
2045 2115 1.676678 GGTCATCTGGTAGGAGCGCA 61.677 60.000 11.47 0.00 0.00 6.09
2079 2149 6.166279 CACAGGAGTTAAGCAAGACTCATTA 58.834 40.000 13.16 0.00 43.14 1.90
2086 2156 1.699634 AGCCACAGGAGTTAAGCAAGA 59.300 47.619 0.00 0.00 0.00 3.02
2087 2157 2.191128 AGCCACAGGAGTTAAGCAAG 57.809 50.000 0.00 0.00 0.00 4.01
2088 2158 2.656947 AAGCCACAGGAGTTAAGCAA 57.343 45.000 0.00 0.00 0.00 3.91
2096 2166 1.004044 ACATCCAGAAAGCCACAGGAG 59.996 52.381 0.00 0.00 0.00 3.69
2135 3951 9.985730 CATTTGGCTCATAATACATGGTTTAAT 57.014 29.630 0.00 0.00 0.00 1.40
2138 3954 7.422465 ACATTTGGCTCATAATACATGGTTT 57.578 32.000 0.00 0.00 0.00 3.27
2140 3956 6.835488 AGAACATTTGGCTCATAATACATGGT 59.165 34.615 0.00 0.00 0.00 3.55
2148 3964 6.240894 ACAGAAGAGAACATTTGGCTCATAA 58.759 36.000 0.00 0.00 0.00 1.90
2149 3965 5.809001 ACAGAAGAGAACATTTGGCTCATA 58.191 37.500 0.00 0.00 0.00 2.15
2199 4022 9.733556 ACACTTGACTCATAATACATGGTTTAA 57.266 29.630 0.00 0.00 0.00 1.52
2200 4023 9.733556 AACACTTGACTCATAATACATGGTTTA 57.266 29.630 0.00 0.00 0.00 2.01
2201 4024 8.635765 AACACTTGACTCATAATACATGGTTT 57.364 30.769 0.00 0.00 0.00 3.27
2202 4025 8.103305 AGAACACTTGACTCATAATACATGGTT 58.897 33.333 0.00 0.00 0.00 3.67
2203 4026 7.624549 AGAACACTTGACTCATAATACATGGT 58.375 34.615 0.00 0.00 0.00 3.55
2204 4027 7.984050 AGAGAACACTTGACTCATAATACATGG 59.016 37.037 0.00 0.00 33.69 3.66
2205 4028 8.939201 AGAGAACACTTGACTCATAATACATG 57.061 34.615 0.00 0.00 33.69 3.21
2206 4029 9.593134 GAAGAGAACACTTGACTCATAATACAT 57.407 33.333 0.00 0.00 33.69 2.29
2207 4030 8.807118 AGAAGAGAACACTTGACTCATAATACA 58.193 33.333 0.00 0.00 33.69 2.29
2208 4031 9.081997 CAGAAGAGAACACTTGACTCATAATAC 57.918 37.037 0.00 0.00 33.69 1.89
2209 4032 8.807118 ACAGAAGAGAACACTTGACTCATAATA 58.193 33.333 0.00 0.00 33.69 0.98
2210 4033 7.675062 ACAGAAGAGAACACTTGACTCATAAT 58.325 34.615 0.00 0.00 33.69 1.28
2211 4034 7.055667 ACAGAAGAGAACACTTGACTCATAA 57.944 36.000 0.00 0.00 33.69 1.90
2212 4035 6.656632 ACAGAAGAGAACACTTGACTCATA 57.343 37.500 0.00 0.00 33.69 2.15
2213 4036 5.543507 ACAGAAGAGAACACTTGACTCAT 57.456 39.130 0.00 0.00 33.69 2.90
2214 4037 5.344743 AACAGAAGAGAACACTTGACTCA 57.655 39.130 0.00 0.00 33.69 3.41
2215 4038 7.954788 ATAAACAGAAGAGAACACTTGACTC 57.045 36.000 0.00 0.00 0.00 3.36
2216 4039 8.738645 AAATAAACAGAAGAGAACACTTGACT 57.261 30.769 0.00 0.00 0.00 3.41
2217 4040 9.788960 AAAAATAAACAGAAGAGAACACTTGAC 57.211 29.630 0.00 0.00 0.00 3.18
2242 4065 9.602568 GGGAAGTACCAAATTTAACTTGAAAAA 57.397 29.630 14.18 0.00 41.20 1.94
2243 4066 8.983789 AGGGAAGTACCAAATTTAACTTGAAAA 58.016 29.630 14.18 0.00 41.20 2.29
2244 4067 8.417884 CAGGGAAGTACCAAATTTAACTTGAAA 58.582 33.333 14.18 0.00 41.20 2.69
2245 4068 7.780745 TCAGGGAAGTACCAAATTTAACTTGAA 59.219 33.333 14.18 0.00 41.20 2.69
2246 4069 7.291566 TCAGGGAAGTACCAAATTTAACTTGA 58.708 34.615 14.18 6.54 41.20 3.02
2247 4070 7.230712 ACTCAGGGAAGTACCAAATTTAACTTG 59.769 37.037 14.18 4.87 41.20 3.16
2248 4071 7.295340 ACTCAGGGAAGTACCAAATTTAACTT 58.705 34.615 10.77 10.77 41.20 2.66
2249 4072 6.849151 ACTCAGGGAAGTACCAAATTTAACT 58.151 36.000 0.00 0.00 41.20 2.24
2266 4089 5.835113 TCTGAAAACTTTCAAACTCAGGG 57.165 39.130 6.36 0.00 45.61 4.45
2271 4094 7.410120 ACTGGATTCTGAAAACTTTCAAACT 57.590 32.000 6.36 0.00 45.61 2.66
2283 4106 8.684386 TGTAACATTTACAACTGGATTCTGAA 57.316 30.769 0.00 0.00 0.00 3.02
2301 4127 9.295825 TGAACTTCCAAACATAGATTGTAACAT 57.704 29.630 0.00 0.00 37.68 2.71
2302 4128 8.684386 TGAACTTCCAAACATAGATTGTAACA 57.316 30.769 0.00 0.00 37.68 2.41
2303 4129 9.959749 TTTGAACTTCCAAACATAGATTGTAAC 57.040 29.630 0.00 0.00 37.68 2.50
2347 4176 5.132648 AGCATCCACTATTTCTGGGTAATGA 59.867 40.000 0.00 0.00 0.00 2.57
2370 4199 3.263602 CAACAGATTGTGTGCAGTGAG 57.736 47.619 0.00 0.00 40.26 3.51
2384 4213 5.738619 TCTTGCCTGTCTATAACAACAGA 57.261 39.130 4.16 0.00 44.54 3.41
2424 4253 9.900090 CATGGGCTGTGTAGACAATGACAATTG 62.900 44.444 3.24 3.24 45.00 2.32
2429 4258 2.472695 TGGGCTGTGTAGACAATGAC 57.527 50.000 0.00 0.00 31.64 3.06
2446 4275 1.066002 CAAATCTAAGCACGGCCATGG 59.934 52.381 7.63 7.63 0.00 3.66
2449 4278 0.322456 AGCAAATCTAAGCACGGCCA 60.322 50.000 2.24 0.00 0.00 5.36
2457 4286 9.823647 TTCTTTCTATCCTGTAGCAAATCTAAG 57.176 33.333 0.00 0.00 0.00 2.18
2467 4296 7.981789 TGTGTGCTAATTCTTTCTATCCTGTAG 59.018 37.037 0.00 0.00 0.00 2.74
2623 4452 5.539574 TGAACAACATTCCCATTCATCTTGT 59.460 36.000 0.00 0.00 0.00 3.16
2708 4537 2.064014 GCGTCACAGGGTTTACAGTAC 58.936 52.381 0.00 0.00 0.00 2.73
2709 4538 1.965643 AGCGTCACAGGGTTTACAGTA 59.034 47.619 0.00 0.00 0.00 2.74
2713 4542 2.289257 ACCTTAGCGTCACAGGGTTTAC 60.289 50.000 0.00 0.00 31.19 2.01
2726 4555 7.216317 CGTGAAATGATAAAGAAAACCTTAGCG 59.784 37.037 0.00 0.00 34.00 4.26
2739 4568 7.367285 CAGGAAAGAAACCGTGAAATGATAAA 58.633 34.615 0.00 0.00 0.00 1.40
2747 4576 2.045561 TGCAGGAAAGAAACCGTGAA 57.954 45.000 0.00 0.00 0.00 3.18
2748 4577 2.270352 ATGCAGGAAAGAAACCGTGA 57.730 45.000 0.00 0.00 0.00 4.35
2761 4590 8.345565 GTGAATTTACAGGAGTTTATATGCAGG 58.654 37.037 0.00 0.00 0.00 4.85
2764 4593 8.893727 AGTGTGAATTTACAGGAGTTTATATGC 58.106 33.333 2.84 0.00 0.00 3.14
2810 4639 9.793259 AAGACTAGGAATATTCAAAACACTGAA 57.207 29.630 17.07 0.00 39.56 3.02
2811 4640 9.436957 GAAGACTAGGAATATTCAAAACACTGA 57.563 33.333 17.07 0.00 0.00 3.41
2812 4641 8.669243 GGAAGACTAGGAATATTCAAAACACTG 58.331 37.037 17.07 2.68 0.00 3.66
2813 4642 8.606830 AGGAAGACTAGGAATATTCAAAACACT 58.393 33.333 17.07 6.37 0.00 3.55
2814 4643 8.794335 AGGAAGACTAGGAATATTCAAAACAC 57.206 34.615 17.07 4.22 0.00 3.32
2815 4644 9.807921 AAAGGAAGACTAGGAATATTCAAAACA 57.192 29.630 17.07 0.00 0.00 2.83
2821 4650 9.495572 CATGGTAAAGGAAGACTAGGAATATTC 57.504 37.037 6.93 6.93 0.00 1.75
2823 4652 7.293535 AGCATGGTAAAGGAAGACTAGGAATAT 59.706 37.037 0.00 0.00 0.00 1.28
2824 4653 6.615726 AGCATGGTAAAGGAAGACTAGGAATA 59.384 38.462 0.00 0.00 0.00 1.75
2825 4654 5.430089 AGCATGGTAAAGGAAGACTAGGAAT 59.570 40.000 0.00 0.00 0.00 3.01
2828 4657 4.162320 TGAGCATGGTAAAGGAAGACTAGG 59.838 45.833 0.00 0.00 0.00 3.02
2844 4673 4.425577 GGTTCAAGTAAACCTGAGCATG 57.574 45.455 0.00 0.00 44.45 4.06
2863 4692 4.704103 TGGCGAGAGGGCTGAGGT 62.704 66.667 0.00 0.00 42.84 3.85
2876 4705 2.031012 TGCTGACTGAACCTGGCG 59.969 61.111 0.00 0.00 0.00 5.69
2877 4706 1.673665 CCTGCTGACTGAACCTGGC 60.674 63.158 0.00 0.00 0.00 4.85
2883 4712 0.394192 CACCACTCCTGCTGACTGAA 59.606 55.000 0.00 0.00 0.00 3.02
2894 4723 0.673644 CGTTGATGACCCACCACTCC 60.674 60.000 0.00 0.00 0.00 3.85
2895 4724 0.673644 CCGTTGATGACCCACCACTC 60.674 60.000 0.00 0.00 0.00 3.51
2896 4725 1.374947 CCGTTGATGACCCACCACT 59.625 57.895 0.00 0.00 0.00 4.00
2897 4726 2.332654 GCCGTTGATGACCCACCAC 61.333 63.158 0.00 0.00 0.00 4.16
2898 4727 2.033448 GCCGTTGATGACCCACCA 59.967 61.111 0.00 0.00 0.00 4.17
2901 4730 1.561769 ATGAGGCCGTTGATGACCCA 61.562 55.000 0.00 0.00 0.00 4.51
2919 4748 5.535753 TCATCCTCATCGTGTATGTTGAT 57.464 39.130 0.00 0.00 36.89 2.57
3005 4834 5.911752 TCAATCAAGAGTAAGATGCTCCTC 58.088 41.667 0.00 0.00 33.69 3.71
3038 4867 6.485313 TCATCCCATACATGGTTTAATTCGAC 59.515 38.462 7.46 0.00 46.65 4.20
3056 4885 2.170166 GTGAACATTTGGCTCATCCCA 58.830 47.619 0.00 0.00 0.00 4.37
3058 4887 3.760684 AGAAGTGAACATTTGGCTCATCC 59.239 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.