Multiple sequence alignment - TraesCS3B01G205900

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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 TraesCS3B01G205900 chr3B 100.000 7360 0 0 1 7360 240598158 240590799 0.000000e+00 13592.0
1 TraesCS3B01G205900 chr3B 88.312 77 7 1 142 216 723456098 723456022 2.830000e-14 91.6
2 TraesCS3B01G205900 chr3B 88.158 76 5 3 144 216 264012972 264013046 3.660000e-13 87.9
3 TraesCS3B01G205900 chr3B 94.231 52 1 2 4764 4813 482487834 482487885 2.200000e-10 78.7
4 TraesCS3B01G205900 chr3D 96.440 4775 122 22 245 5003 164994306 164989564 0.000000e+00 7832.0
5 TraesCS3B01G205900 chr3D 97.661 1197 23 3 5816 7012 164989439 164988248 0.000000e+00 2050.0
6 TraesCS3B01G205900 chr3D 88.400 500 51 3 1339 1838 55719999 55719507 4.920000e-166 595.0
7 TraesCS3B01G205900 chr3D 87.402 508 55 4 1329 1836 603818665 603819163 6.400000e-160 575.0
8 TraesCS3B01G205900 chr3D 92.761 373 18 5 6990 7360 164984736 164984371 1.410000e-146 531.0
9 TraesCS3B01G205900 chr3D 95.238 126 6 0 5598 5723 164989562 164989437 4.500000e-47 200.0
10 TraesCS3B01G205900 chr3A 95.940 4803 122 34 223 5004 206622612 206627362 0.000000e+00 7721.0
11 TraesCS3B01G205900 chr3A 96.941 1373 31 6 5813 7182 206627483 206628847 0.000000e+00 2292.0
12 TraesCS3B01G205900 chr3A 95.238 126 6 0 5598 5723 206627363 206627488 4.500000e-47 200.0
13 TraesCS3B01G205900 chr1D 95.274 529 21 3 1637 2165 65740992 65741516 0.000000e+00 835.0
14 TraesCS3B01G205900 chr1D 84.436 816 76 14 2842 3633 455097809 455097021 0.000000e+00 756.0
15 TraesCS3B01G205900 chr1D 82.615 696 67 21 2425 3114 422880050 422880697 3.850000e-157 566.0
16 TraesCS3B01G205900 chr1D 89.394 132 11 1 3100 3231 422880711 422880839 5.910000e-36 163.0
17 TraesCS3B01G205900 chr1D 92.308 104 8 0 5721 5824 420554541 420554644 1.650000e-31 148.0
18 TraesCS3B01G205900 chr7D 94.896 529 22 4 1637 2165 173527288 173527811 0.000000e+00 822.0
19 TraesCS3B01G205900 chr7D 88.755 498 49 3 1339 1836 578173934 578174424 2.940000e-168 603.0
20 TraesCS3B01G205900 chr2B 92.110 583 36 5 5014 5594 548233868 548233294 0.000000e+00 813.0
21 TraesCS3B01G205900 chr2B 91.267 584 41 4 5014 5595 587810430 587809855 0.000000e+00 787.0
22 TraesCS3B01G205900 chr2B 90.764 563 41 6 5036 5596 412050315 412050868 0.000000e+00 741.0
23 TraesCS3B01G205900 chr2B 90.411 73 5 1 146 216 216576668 216576740 2.190000e-15 95.3
24 TraesCS3B01G205900 chr5D 94.140 529 27 3 1637 2165 221498624 221499148 0.000000e+00 802.0
25 TraesCS3B01G205900 chr5D 94.140 529 25 5 1637 2165 237989 237467 0.000000e+00 800.0
26 TraesCS3B01G205900 chr5D 89.286 56 5 1 4769 4823 481255951 481255896 1.330000e-07 69.4
27 TraesCS3B01G205900 chrUn 93.750 528 29 3 1637 2164 144595951 144596474 0.000000e+00 789.0
28 TraesCS3B01G205900 chrUn 87.952 498 53 3 1339 1836 260711791 260711301 1.380000e-161 580.0
29 TraesCS3B01G205900 chrUn 87.629 97 11 1 1 96 247036277 247036373 2.170000e-20 111.0
30 TraesCS3B01G205900 chrUn 87.629 97 11 1 1 96 247045404 247045500 2.170000e-20 111.0
31 TraesCS3B01G205900 chrUn 87.629 97 11 1 1 96 377128189 377128285 2.170000e-20 111.0
32 TraesCS3B01G205900 chr1B 91.267 584 41 9 5013 5594 24036276 24036851 0.000000e+00 787.0
33 TraesCS3B01G205900 chr1B 90.411 584 46 9 5013 5594 24065069 24065644 0.000000e+00 760.0
34 TraesCS3B01G205900 chr1B 89.347 582 50 7 5014 5593 397616895 397617466 0.000000e+00 721.0
35 TraesCS3B01G205900 chr1B 83.333 102 16 1 2 102 291558457 291558356 7.860000e-15 93.5
36 TraesCS3B01G205900 chr4B 90.878 592 39 10 5014 5601 635106524 635107104 0.000000e+00 780.0
37 TraesCS3B01G205900 chr4B 91.667 108 9 0 5720 5827 621424794 621424687 4.600000e-32 150.0
38 TraesCS3B01G205900 chr4B 92.424 66 3 1 153 216 652887481 652887546 7.860000e-15 93.5
39 TraesCS3B01G205900 chr5B 93.371 528 31 3 1637 2164 328373 327850 0.000000e+00 778.0
40 TraesCS3B01G205900 chr5B 89.950 597 44 8 5009 5602 648778311 648777728 0.000000e+00 756.0
41 TraesCS3B01G205900 chr5B 95.000 100 5 0 5720 5819 316712703 316712604 2.750000e-34 158.0
42 TraesCS3B01G205900 chr5B 87.629 97 11 1 1 96 702139815 702139911 2.170000e-20 111.0
43 TraesCS3B01G205900 chr5B 85.567 97 13 1 1 96 464316085 464316181 4.700000e-17 100.0
44 TraesCS3B01G205900 chr5B 90.141 71 4 2 148 216 241165151 241165082 1.020000e-13 89.8
45 TraesCS3B01G205900 chr5B 82.759 87 15 0 1 87 435164548 435164462 2.200000e-10 78.7
46 TraesCS3B01G205900 chr5B 95.455 44 1 1 4778 4820 8970637 8970594 1.330000e-07 69.4
47 TraesCS3B01G205900 chr7A 93.195 529 32 3 1637 2165 622693730 622693206 0.000000e+00 774.0
48 TraesCS3B01G205900 chr7A 83.960 505 68 10 1339 1841 671294487 671293994 8.640000e-129 472.0
49 TraesCS3B01G205900 chr7A 96.809 94 2 1 5722 5814 7509924 7509831 9.890000e-34 156.0
50 TraesCS3B01G205900 chr7A 86.301 73 8 2 37 108 423563569 423563498 2.200000e-10 78.7
51 TraesCS3B01G205900 chr4A 90.256 585 43 8 5013 5595 726311484 726310912 0.000000e+00 752.0
52 TraesCS3B01G205900 chr4A 87.776 499 53 4 1339 1836 598469029 598468538 1.780000e-160 577.0
53 TraesCS3B01G205900 chr4A 84.554 505 65 6 1339 1841 447594373 447593880 8.580000e-134 488.0
54 TraesCS3B01G205900 chr4A 84.221 507 67 10 1337 1841 534420633 534420138 1.440000e-131 481.0
55 TraesCS3B01G205900 chr6D 84.447 778 71 13 2880 3633 197299673 197300424 0.000000e+00 721.0
56 TraesCS3B01G205900 chr6D 81.818 99 13 4 120 216 44846426 44846331 2.200000e-10 78.7
57 TraesCS3B01G205900 chr6D 93.750 48 2 1 4779 4825 32058932 32058885 3.680000e-08 71.3
58 TraesCS3B01G205900 chr2D 88.200 500 52 3 1339 1838 47826519 47826027 2.290000e-164 590.0
59 TraesCS3B01G205900 chr2D 88.000 500 53 3 1339 1838 399961974 399962466 1.060000e-162 584.0
60 TraesCS3B01G205900 chr2A 84.462 502 65 10 1339 1838 725017358 725017848 3.990000e-132 483.0
61 TraesCS3B01G205900 chr2A 91.509 106 9 0 5722 5827 416281081 416281186 5.950000e-31 147.0
62 TraesCS3B01G205900 chr2A 90.141 71 4 2 148 216 197535050 197535119 1.020000e-13 89.8
63 TraesCS3B01G205900 chr6A 84.263 502 65 11 1339 1838 583875963 583876452 1.860000e-130 477.0
64 TraesCS3B01G205900 chr6A 83.865 502 68 11 1339 1838 232182220 232182710 4.020000e-127 466.0
65 TraesCS3B01G205900 chr6A 94.898 98 4 1 5722 5819 599809025 599808929 1.280000e-32 152.0
66 TraesCS3B01G205900 chr6A 91.589 107 7 2 5722 5828 98239203 98239099 5.950000e-31 147.0
67 TraesCS3B01G205900 chr6A 87.097 62 5 3 4764 4822 54179420 54179481 4.770000e-07 67.6
68 TraesCS3B01G205900 chr6A 87.719 57 5 2 4769 4823 25690520 25690576 1.710000e-06 65.8
69 TraesCS3B01G205900 chr4D 93.137 102 7 0 5722 5823 323929573 323929674 4.600000e-32 150.0
70 TraesCS3B01G205900 chr7B 95.652 92 4 0 5722 5813 562993066 562993157 1.650000e-31 148.0
71 TraesCS3B01G205900 chr6B 87.654 81 6 3 139 216 713175784 713175863 2.830000e-14 91.6
72 TraesCS3B01G205900 chr1A 86.420 81 7 3 138 216 426017795 426017717 1.320000e-12 86.1
73 TraesCS3B01G205900 chr5A 90.909 55 5 0 45 99 279732439 279732493 2.850000e-09 75.0
74 TraesCS3B01G205900 chr5A 95.455 44 1 1 4778 4820 6929622 6929579 1.330000e-07 69.4


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 TraesCS3B01G205900 chr3B 240590799 240598158 7359 True 13592.000000 13592 100.000000 1 7360 1 chr3B.!!$R1 7359
1 TraesCS3B01G205900 chr3D 164984371 164994306 9935 True 2653.250000 7832 95.525000 245 7360 4 chr3D.!!$R2 7115
2 TraesCS3B01G205900 chr3A 206622612 206628847 6235 False 3404.333333 7721 96.039667 223 7182 3 chr3A.!!$F1 6959
3 TraesCS3B01G205900 chr1D 65740992 65741516 524 False 835.000000 835 95.274000 1637 2165 1 chr1D.!!$F1 528
4 TraesCS3B01G205900 chr1D 455097021 455097809 788 True 756.000000 756 84.436000 2842 3633 1 chr1D.!!$R1 791
5 TraesCS3B01G205900 chr1D 422880050 422880839 789 False 364.500000 566 86.004500 2425 3231 2 chr1D.!!$F3 806
6 TraesCS3B01G205900 chr7D 173527288 173527811 523 False 822.000000 822 94.896000 1637 2165 1 chr7D.!!$F1 528
7 TraesCS3B01G205900 chr2B 548233294 548233868 574 True 813.000000 813 92.110000 5014 5594 1 chr2B.!!$R1 580
8 TraesCS3B01G205900 chr2B 587809855 587810430 575 True 787.000000 787 91.267000 5014 5595 1 chr2B.!!$R2 581
9 TraesCS3B01G205900 chr2B 412050315 412050868 553 False 741.000000 741 90.764000 5036 5596 1 chr2B.!!$F2 560
10 TraesCS3B01G205900 chr5D 221498624 221499148 524 False 802.000000 802 94.140000 1637 2165 1 chr5D.!!$F1 528
11 TraesCS3B01G205900 chr5D 237467 237989 522 True 800.000000 800 94.140000 1637 2165 1 chr5D.!!$R1 528
12 TraesCS3B01G205900 chrUn 144595951 144596474 523 False 789.000000 789 93.750000 1637 2164 1 chrUn.!!$F1 527
13 TraesCS3B01G205900 chr1B 24036276 24036851 575 False 787.000000 787 91.267000 5013 5594 1 chr1B.!!$F1 581
14 TraesCS3B01G205900 chr1B 24065069 24065644 575 False 760.000000 760 90.411000 5013 5594 1 chr1B.!!$F2 581
15 TraesCS3B01G205900 chr1B 397616895 397617466 571 False 721.000000 721 89.347000 5014 5593 1 chr1B.!!$F3 579
16 TraesCS3B01G205900 chr4B 635106524 635107104 580 False 780.000000 780 90.878000 5014 5601 1 chr4B.!!$F1 587
17 TraesCS3B01G205900 chr5B 327850 328373 523 True 778.000000 778 93.371000 1637 2164 1 chr5B.!!$R1 527
18 TraesCS3B01G205900 chr5B 648777728 648778311 583 True 756.000000 756 89.950000 5009 5602 1 chr5B.!!$R6 593
19 TraesCS3B01G205900 chr7A 622693206 622693730 524 True 774.000000 774 93.195000 1637 2165 1 chr7A.!!$R3 528
20 TraesCS3B01G205900 chr4A 726310912 726311484 572 True 752.000000 752 90.256000 5013 5595 1 chr4A.!!$R4 582
21 TraesCS3B01G205900 chr6D 197299673 197300424 751 False 721.000000 721 84.447000 2880 3633 1 chr6D.!!$F1 753

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
41 42 0.377554 CGCCTACGTCTCGATTCAGT 59.622 55.000 0.00 0.0 33.53 3.41 F
43 44 1.132643 GCCTACGTCTCGATTCAGTGT 59.867 52.381 0.00 0.0 0.00 3.55 F
1165 1180 1.068588 GTGTGTTTTGGGAAAGGAGGC 59.931 52.381 0.00 0.0 0.00 4.70 F
3122 3202 1.202976 AGCAAACTGTTCAGGCAGGAT 60.203 47.619 12.29 0.0 40.59 3.24 F
3148 3228 3.521531 TGTATGGCTTATCACACCAAGGA 59.478 43.478 0.00 0.0 36.94 3.36 F
4728 4821 1.821666 GCCCTTTGAGCCTTGTTACCA 60.822 52.381 0.00 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1180 0.098025 AGCAAACGACACACAAACCG 59.902 50.0 0.00 0.00 0.00 4.44 R
1248 1263 1.056103 CGACTCTGCGAGAACACAAG 58.944 55.0 11.64 0.00 33.32 3.16 R
3148 3228 0.403271 AAGCAACTGCAGATGGAGGT 59.597 50.0 23.35 7.56 45.16 3.85 R
4158 4247 0.179124 GCGTTGGTGCAAAGAAACCA 60.179 50.0 0.00 0.00 44.72 3.67 R
4912 5005 1.435256 AACCTCCAGTAACCTGCACT 58.565 50.0 0.00 0.00 37.38 4.40 R
6482 6579 0.179051 CAGATGCTGAGAGGGGAAGC 60.179 60.0 0.00 0.00 37.46 3.86 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
17 18 3.234730 GGGAGGGGCGATGACGAT 61.235 66.667 0.00 0.00 42.66 3.73
18 19 2.029666 GGAGGGGCGATGACGATG 59.970 66.667 0.00 0.00 42.66 3.84
19 20 2.029666 GAGGGGCGATGACGATGG 59.970 66.667 0.00 0.00 42.66 3.51
20 21 4.241555 AGGGGCGATGACGATGGC 62.242 66.667 0.00 0.00 42.66 4.40
27 28 3.841379 GATGACGATGGCGCGCCTA 62.841 63.158 45.79 33.27 42.48 3.93
28 29 4.865761 TGACGATGGCGCGCCTAC 62.866 66.667 45.79 35.71 42.48 3.18
32 33 4.570663 GATGGCGCGCCTACGTCT 62.571 66.667 45.79 25.12 42.83 4.18
33 34 4.570663 ATGGCGCGCCTACGTCTC 62.571 66.667 45.79 21.40 42.83 3.36
36 37 4.609247 GCGCGCCTACGTCTCGAT 62.609 66.667 23.24 0.00 42.83 3.59
37 38 2.024305 CGCGCCTACGTCTCGATT 59.976 61.111 0.00 0.00 42.83 3.34
38 39 2.004489 CGCGCCTACGTCTCGATTC 61.004 63.158 0.00 0.00 42.83 2.52
39 40 1.063649 GCGCCTACGTCTCGATTCA 59.936 57.895 0.00 0.00 42.83 2.57
40 41 0.930742 GCGCCTACGTCTCGATTCAG 60.931 60.000 0.00 0.00 42.83 3.02
41 42 0.377554 CGCCTACGTCTCGATTCAGT 59.622 55.000 0.00 0.00 33.53 3.41
42 43 1.828832 GCCTACGTCTCGATTCAGTG 58.171 55.000 0.00 0.00 0.00 3.66
43 44 1.132643 GCCTACGTCTCGATTCAGTGT 59.867 52.381 0.00 0.00 0.00 3.55
44 45 2.415625 GCCTACGTCTCGATTCAGTGTT 60.416 50.000 0.00 0.00 0.00 3.32
45 46 3.834610 CCTACGTCTCGATTCAGTGTTT 58.165 45.455 0.00 0.00 0.00 2.83
46 47 3.608506 CCTACGTCTCGATTCAGTGTTTG 59.391 47.826 0.00 0.00 0.00 2.93
47 48 3.093717 ACGTCTCGATTCAGTGTTTGT 57.906 42.857 0.00 0.00 0.00 2.83
48 49 4.233123 ACGTCTCGATTCAGTGTTTGTA 57.767 40.909 0.00 0.00 0.00 2.41
49 50 4.227538 ACGTCTCGATTCAGTGTTTGTAG 58.772 43.478 0.00 0.00 0.00 2.74
50 51 4.227538 CGTCTCGATTCAGTGTTTGTAGT 58.772 43.478 0.00 0.00 0.00 2.73
51 52 4.680110 CGTCTCGATTCAGTGTTTGTAGTT 59.320 41.667 0.00 0.00 0.00 2.24
52 53 5.387444 CGTCTCGATTCAGTGTTTGTAGTTG 60.387 44.000 0.00 0.00 0.00 3.16
53 54 5.462398 GTCTCGATTCAGTGTTTGTAGTTGT 59.538 40.000 0.00 0.00 0.00 3.32
54 55 5.690409 TCTCGATTCAGTGTTTGTAGTTGTC 59.310 40.000 0.00 0.00 0.00 3.18
55 56 4.443063 TCGATTCAGTGTTTGTAGTTGTCG 59.557 41.667 0.00 0.00 0.00 4.35
56 57 3.936902 TTCAGTGTTTGTAGTTGTCGC 57.063 42.857 0.00 0.00 0.00 5.19
57 58 3.173668 TCAGTGTTTGTAGTTGTCGCT 57.826 42.857 0.00 0.00 0.00 4.93
58 59 4.310357 TCAGTGTTTGTAGTTGTCGCTA 57.690 40.909 0.00 0.00 0.00 4.26
59 60 4.295870 TCAGTGTTTGTAGTTGTCGCTAG 58.704 43.478 0.00 0.00 0.00 3.42
60 61 3.428870 CAGTGTTTGTAGTTGTCGCTAGG 59.571 47.826 0.00 0.00 0.00 3.02
61 62 3.069158 AGTGTTTGTAGTTGTCGCTAGGT 59.931 43.478 0.00 0.00 0.00 3.08
62 63 3.183775 GTGTTTGTAGTTGTCGCTAGGTG 59.816 47.826 0.00 0.00 0.00 4.00
63 64 2.735134 GTTTGTAGTTGTCGCTAGGTGG 59.265 50.000 0.00 0.00 0.00 4.61
64 65 1.624336 TGTAGTTGTCGCTAGGTGGT 58.376 50.000 0.00 0.00 0.00 4.16
65 66 2.794103 TGTAGTTGTCGCTAGGTGGTA 58.206 47.619 0.00 0.00 0.00 3.25
66 67 2.489329 TGTAGTTGTCGCTAGGTGGTAC 59.511 50.000 0.00 0.00 0.00 3.34
67 68 1.624336 AGTTGTCGCTAGGTGGTACA 58.376 50.000 0.00 0.00 0.00 2.90
68 69 2.176889 AGTTGTCGCTAGGTGGTACAT 58.823 47.619 0.00 0.00 44.52 2.29
69 70 2.094182 AGTTGTCGCTAGGTGGTACATG 60.094 50.000 0.00 0.00 44.52 3.21
70 71 1.842052 TGTCGCTAGGTGGTACATGA 58.158 50.000 0.00 0.00 44.52 3.07
71 72 2.172679 TGTCGCTAGGTGGTACATGAA 58.827 47.619 0.00 0.00 44.52 2.57
72 73 2.764010 TGTCGCTAGGTGGTACATGAAT 59.236 45.455 0.00 0.00 44.52 2.57
73 74 3.181479 TGTCGCTAGGTGGTACATGAATC 60.181 47.826 0.00 0.00 44.52 2.52
74 75 3.068307 GTCGCTAGGTGGTACATGAATCT 59.932 47.826 0.00 0.00 44.52 2.40
75 76 4.277672 GTCGCTAGGTGGTACATGAATCTA 59.722 45.833 0.00 0.00 44.52 1.98
76 77 4.519350 TCGCTAGGTGGTACATGAATCTAG 59.481 45.833 0.00 2.83 44.52 2.43
77 78 4.519350 CGCTAGGTGGTACATGAATCTAGA 59.481 45.833 0.00 0.00 44.52 2.43
78 79 5.184096 CGCTAGGTGGTACATGAATCTAGAT 59.816 44.000 0.00 0.00 44.52 1.98
79 80 6.393990 GCTAGGTGGTACATGAATCTAGATG 58.606 44.000 5.86 0.00 44.52 2.90
80 81 6.015010 GCTAGGTGGTACATGAATCTAGATGT 60.015 42.308 5.86 3.90 44.52 3.06
81 82 7.176865 GCTAGGTGGTACATGAATCTAGATGTA 59.823 40.741 5.86 2.84 44.52 2.29
82 83 7.914427 AGGTGGTACATGAATCTAGATGTAA 57.086 36.000 5.86 0.00 44.52 2.41
83 84 8.497910 AGGTGGTACATGAATCTAGATGTAAT 57.502 34.615 5.86 0.00 44.52 1.89
84 85 8.938883 AGGTGGTACATGAATCTAGATGTAATT 58.061 33.333 5.86 0.00 44.52 1.40
85 86 9.561069 GGTGGTACATGAATCTAGATGTAATTT 57.439 33.333 5.86 0.00 44.52 1.82
163 164 9.809395 ATGATTGATGATGAATATTTCCTCTGT 57.191 29.630 0.00 0.00 0.00 3.41
210 211 9.250624 AGATCATTAAAGTAGTGATAAACGCTC 57.749 33.333 0.00 0.00 40.12 5.03
211 212 9.250624 GATCATTAAAGTAGTGATAAACGCTCT 57.749 33.333 0.00 0.00 40.12 4.09
212 213 8.997621 TCATTAAAGTAGTGATAAACGCTCTT 57.002 30.769 0.00 0.00 40.12 2.85
218 219 9.517609 AAAGTAGTGATAAACGCTCTTATACAG 57.482 33.333 0.00 0.00 40.12 2.74
219 220 8.447924 AGTAGTGATAAACGCTCTTATACAGA 57.552 34.615 0.00 0.00 40.12 3.41
237 238 4.430441 ACAGAGGGAGTAGATTGGAAGTT 58.570 43.478 0.00 0.00 0.00 2.66
323 324 1.608336 CGGACCACCACCTACCAGA 60.608 63.158 0.00 0.00 35.59 3.86
391 392 1.821759 CACGTTGTTGGTCCTGGCA 60.822 57.895 0.00 0.00 0.00 4.92
663 664 2.262915 CTCGGTCTCACCAGCCAC 59.737 66.667 0.00 0.00 38.47 5.01
717 718 2.338620 CTGTCCGAGCCACGACAA 59.661 61.111 2.48 0.00 45.77 3.18
867 871 2.742372 CGGAGGAAGCAACACCCG 60.742 66.667 0.00 0.00 0.00 5.28
898 904 1.452145 TTTTGCTTCGCTTTCGCCCT 61.452 50.000 0.00 0.00 35.26 5.19
1128 1143 1.423450 CGATGTGCGCAATTTCGGA 59.577 52.632 22.78 0.00 0.00 4.55
1165 1180 1.068588 GTGTGTTTTGGGAAAGGAGGC 59.931 52.381 0.00 0.00 0.00 4.70
1218 1233 1.799403 GATCTTCGATGCTGCCTGATG 59.201 52.381 0.00 0.00 0.00 3.07
1222 1237 2.713770 GATGCTGCCTGATGCGTG 59.286 61.111 0.00 0.00 45.60 5.34
1387 1402 4.753662 TGCGGCTACGGGGAGACT 62.754 66.667 0.00 0.00 41.36 3.24
1673 1690 3.632189 GTGAAACTTGATTGTGCAGTCC 58.368 45.455 0.00 0.00 0.00 3.85
1965 1982 4.429854 AGGAGCTTGGATTGAAGGTATC 57.570 45.455 0.00 0.00 33.83 2.24
2122 2139 4.142071 ACTCGCTCACACAGTGATATGAAT 60.142 41.667 7.81 0.00 41.94 2.57
2165 2182 5.562298 TTCCTTTAGAAGCTGGTACTTGT 57.438 39.130 0.00 0.00 0.00 3.16
2222 2240 5.172687 TGGTGGATTGCTTACAGTATCAA 57.827 39.130 0.00 0.00 0.00 2.57
2223 2241 5.565509 TGGTGGATTGCTTACAGTATCAAA 58.434 37.500 1.32 0.00 0.00 2.69
2574 2597 3.826157 CACCAAACATGTATCCACCAGTT 59.174 43.478 0.00 0.00 0.00 3.16
2652 2675 1.377856 GAGGCCTTCTGTTCTGCCC 60.378 63.158 6.77 0.00 45.14 5.36
3122 3202 1.202976 AGCAAACTGTTCAGGCAGGAT 60.203 47.619 12.29 0.00 40.59 3.24
3148 3228 3.521531 TGTATGGCTTATCACACCAAGGA 59.478 43.478 0.00 0.00 36.94 3.36
3213 3293 4.219288 GTCTTCTTCAACATGGCCTTCAAT 59.781 41.667 3.32 0.00 0.00 2.57
3325 3405 7.716560 TCCACATGTAAATACAATCATCCTCAG 59.283 37.037 0.00 0.00 39.99 3.35
3714 3798 5.357878 GTCAGAGGAATTATTGGTGAATGCA 59.642 40.000 0.00 0.00 0.00 3.96
3727 3816 3.613737 GGTGAATGCATTTGGATCAAACG 59.386 43.478 14.33 0.00 36.13 3.60
3849 3938 5.647658 CCATGTAATTGCACCTTCAAGTCTA 59.352 40.000 0.00 0.00 0.00 2.59
3850 3939 6.319658 CCATGTAATTGCACCTTCAAGTCTAT 59.680 38.462 0.00 0.00 0.00 1.98
3859 3948 5.491982 CACCTTCAAGTCTATGTTTAGCCT 58.508 41.667 0.00 0.00 0.00 4.58
4158 4247 9.893305 GTAGATTGTGTTTAGTGCAAGTTTAAT 57.107 29.630 0.00 0.00 0.00 1.40
4395 4484 6.541969 TGCATCTGTGTAAATTTGACATACG 58.458 36.000 0.00 0.00 0.00 3.06
4418 4507 8.157159 ACGAAGTTTAAAATTGCGAACATATG 57.843 30.769 19.40 0.00 37.78 1.78
4500 4593 8.821686 TTGAAGATGGAGGCTTTTATTAATGA 57.178 30.769 0.00 0.00 0.00 2.57
4506 4599 9.252962 GATGGAGGCTTTTATTAATGAAACATG 57.747 33.333 9.20 0.00 0.00 3.21
4550 4643 8.349245 TGTTTTCACTGTGTTTATCCAATACTG 58.651 33.333 7.79 0.00 33.33 2.74
4680 4773 6.340962 TCTTGATTCTTGACGAACTTAGGA 57.659 37.500 0.00 0.00 33.72 2.94
4728 4821 1.821666 GCCCTTTGAGCCTTGTTACCA 60.822 52.381 0.00 0.00 0.00 3.25
4741 4834 5.163652 GCCTTGTTACCACATTAGCCTAAAG 60.164 44.000 0.00 0.00 31.06 1.85
4749 4842 6.647229 ACCACATTAGCCTAAAGTACTAACC 58.353 40.000 0.00 0.00 0.00 2.85
4802 4895 9.467258 CAAAATCAGCGACAATTAATATGGATT 57.533 29.630 0.00 0.00 0.00 3.01
5004 5098 7.652105 TGTTAGCACCTATCAGTATCGATTTTC 59.348 37.037 1.71 0.00 0.00 2.29
5005 5099 5.542779 AGCACCTATCAGTATCGATTTTCC 58.457 41.667 1.71 0.00 0.00 3.13
5006 5100 4.691216 GCACCTATCAGTATCGATTTTCCC 59.309 45.833 1.71 0.00 0.00 3.97
5007 5101 5.511545 GCACCTATCAGTATCGATTTTCCCT 60.512 44.000 1.71 0.00 0.00 4.20
5081 5175 4.223144 ACCCCTAACTTTTTGATGTGCTT 58.777 39.130 0.00 0.00 0.00 3.91
5082 5176 4.653801 ACCCCTAACTTTTTGATGTGCTTT 59.346 37.500 0.00 0.00 0.00 3.51
5087 5181 8.711457 CCCTAACTTTTTGATGTGCTTTAATTG 58.289 33.333 0.00 0.00 0.00 2.32
5211 5306 9.932699 CAGAAGAGTGCAAATAAGATATCAAAG 57.067 33.333 5.32 0.00 0.00 2.77
5238 5333 8.995220 TGTTCATAAAAATATCACCTATACCGC 58.005 33.333 0.00 0.00 0.00 5.68
5239 5334 9.216117 GTTCATAAAAATATCACCTATACCGCT 57.784 33.333 0.00 0.00 0.00 5.52
5398 5494 9.807649 ATAGGTGATGCTTTTATGAACATTTTC 57.192 29.630 0.00 0.00 0.00 2.29
5570 5667 3.380479 TTTGAGTAGTGGGTTCGAGTG 57.620 47.619 0.00 0.00 0.00 3.51
5611 5708 5.575157 TGTCCCATATTTTTGTCTTAGCCA 58.425 37.500 0.00 0.00 0.00 4.75
5693 5790 3.119849 CCAAACTTATCTGGGAAAGCACG 60.120 47.826 0.00 0.00 0.00 5.34
5706 5803 4.574828 GGGAAAGCACGCTTCTCATAAATA 59.425 41.667 4.46 0.00 34.84 1.40
5718 5815 7.959651 CGCTTCTCATAAATATAATGTTCCTGC 59.040 37.037 0.00 0.00 0.00 4.85
5721 5818 9.851686 TTCTCATAAATATAATGTTCCTGCAGT 57.148 29.630 13.81 0.00 0.00 4.40
5726 5823 9.726438 ATAAATATAATGTTCCTGCAGTACTCC 57.274 33.333 13.81 0.00 0.00 3.85
5727 5824 2.789409 AATGTTCCTGCAGTACTCCC 57.211 50.000 13.81 0.00 0.00 4.30
5728 5825 1.958288 ATGTTCCTGCAGTACTCCCT 58.042 50.000 13.81 0.00 0.00 4.20
5729 5826 1.267121 TGTTCCTGCAGTACTCCCTC 58.733 55.000 13.81 0.00 0.00 4.30
5730 5827 0.537653 GTTCCTGCAGTACTCCCTCC 59.462 60.000 13.81 0.00 0.00 4.30
5731 5828 0.970937 TTCCTGCAGTACTCCCTCCG 60.971 60.000 13.81 0.00 0.00 4.63
5732 5829 1.682684 CCTGCAGTACTCCCTCCGT 60.683 63.158 13.81 0.00 0.00 4.69
5733 5830 1.668101 CCTGCAGTACTCCCTCCGTC 61.668 65.000 13.81 0.00 0.00 4.79
5734 5831 1.668101 CTGCAGTACTCCCTCCGTCC 61.668 65.000 5.25 0.00 0.00 4.79
5735 5832 2.424733 GCAGTACTCCCTCCGTCCC 61.425 68.421 0.00 0.00 0.00 4.46
5736 5833 1.000019 CAGTACTCCCTCCGTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
5737 5834 0.613853 CAGTACTCCCTCCGTCCCAA 60.614 60.000 0.00 0.00 0.00 4.12
5738 5835 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
5739 5836 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5740 5837 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
5741 5838 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5742 5839 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5743 5840 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5744 5841 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5745 5842 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5746 5843 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5747 5844 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5748 5845 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5749 5846 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5750 5847 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5751 5848 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5752 5849 4.700213 CCGTCCCAAAATAAGTGTCTCAAT 59.300 41.667 0.00 0.00 0.00 2.57
5753 5850 5.163754 CCGTCCCAAAATAAGTGTCTCAATC 60.164 44.000 0.00 0.00 0.00 2.67
5754 5851 5.643777 CGTCCCAAAATAAGTGTCTCAATCT 59.356 40.000 0.00 0.00 0.00 2.40
5755 5852 6.149474 CGTCCCAAAATAAGTGTCTCAATCTT 59.851 38.462 0.00 0.00 0.00 2.40
5756 5853 7.333423 CGTCCCAAAATAAGTGTCTCAATCTTA 59.667 37.037 0.00 0.00 0.00 2.10
5757 5854 8.669243 GTCCCAAAATAAGTGTCTCAATCTTAG 58.331 37.037 0.00 0.00 0.00 2.18
5758 5855 8.383175 TCCCAAAATAAGTGTCTCAATCTTAGT 58.617 33.333 0.00 0.00 0.00 2.24
5759 5856 9.667107 CCCAAAATAAGTGTCTCAATCTTAGTA 57.333 33.333 0.00 0.00 0.00 1.82
5767 5864 8.594881 AGTGTCTCAATCTTAGTACAACTTTG 57.405 34.615 0.00 0.00 0.00 2.77
5768 5865 7.171678 AGTGTCTCAATCTTAGTACAACTTTGC 59.828 37.037 0.00 0.00 0.00 3.68
5769 5866 6.989759 TGTCTCAATCTTAGTACAACTTTGCA 59.010 34.615 0.00 0.00 0.00 4.08
5770 5867 7.042051 TGTCTCAATCTTAGTACAACTTTGCAC 60.042 37.037 0.00 0.00 0.00 4.57
5771 5868 7.171678 GTCTCAATCTTAGTACAACTTTGCACT 59.828 37.037 0.00 0.65 38.32 4.40
5772 5869 8.364894 TCTCAATCTTAGTACAACTTTGCACTA 58.635 33.333 0.00 0.00 36.29 2.74
5773 5870 8.896320 TCAATCTTAGTACAACTTTGCACTAA 57.104 30.769 12.27 12.27 42.00 2.24
5774 5871 9.332502 TCAATCTTAGTACAACTTTGCACTAAA 57.667 29.630 13.37 7.41 42.98 1.85
5790 5887 8.495361 TTGCACTAAAGTTAGTACAAAGTTGA 57.505 30.769 12.43 0.00 41.56 3.18
5791 5888 7.912383 TGCACTAAAGTTAGTACAAAGTTGAC 58.088 34.615 3.46 0.00 41.82 3.18
5792 5889 7.549842 TGCACTAAAGTTAGTACAAAGTTGACA 59.450 33.333 3.46 0.00 41.82 3.58
5793 5890 7.849515 GCACTAAAGTTAGTACAAAGTTGACAC 59.150 37.037 3.46 0.00 41.82 3.67
5794 5891 8.875803 CACTAAAGTTAGTACAAAGTTGACACA 58.124 33.333 3.46 0.00 41.82 3.72
5795 5892 8.876790 ACTAAAGTTAGTACAAAGTTGACACAC 58.123 33.333 1.81 0.00 41.92 3.82
5796 5893 7.916914 AAAGTTAGTACAAAGTTGACACACT 57.083 32.000 0.00 0.00 0.00 3.55
5797 5894 7.916914 AAGTTAGTACAAAGTTGACACACTT 57.083 32.000 0.00 0.88 38.74 3.16
5798 5895 9.439500 AAAGTTAGTACAAAGTTGACACACTTA 57.561 29.630 0.00 0.00 35.87 2.24
5799 5896 9.609346 AAGTTAGTACAAAGTTGACACACTTAT 57.391 29.630 0.00 0.77 35.87 1.73
5800 5897 9.609346 AGTTAGTACAAAGTTGACACACTTATT 57.391 29.630 0.00 0.00 35.87 1.40
5804 5901 8.188139 AGTACAAAGTTGACACACTTATTTTGG 58.812 33.333 0.00 0.00 35.87 3.28
5805 5902 6.337356 ACAAAGTTGACACACTTATTTTGGG 58.663 36.000 0.00 0.00 35.87 4.12
5806 5903 6.153680 ACAAAGTTGACACACTTATTTTGGGA 59.846 34.615 0.00 0.00 35.87 4.37
5807 5904 5.767816 AGTTGACACACTTATTTTGGGAC 57.232 39.130 0.00 0.00 0.00 4.46
5808 5905 4.274950 AGTTGACACACTTATTTTGGGACG 59.725 41.667 0.00 0.00 0.00 4.79
5809 5906 3.142951 TGACACACTTATTTTGGGACGG 58.857 45.455 0.00 0.00 0.00 4.79
5810 5907 3.181453 TGACACACTTATTTTGGGACGGA 60.181 43.478 0.00 0.00 0.00 4.69
5811 5908 3.408634 ACACACTTATTTTGGGACGGAG 58.591 45.455 0.00 0.00 0.00 4.63
5812 5909 2.747446 CACACTTATTTTGGGACGGAGG 59.253 50.000 0.00 0.00 0.00 4.30
5813 5910 2.374170 ACACTTATTTTGGGACGGAGGT 59.626 45.455 0.00 0.00 0.00 3.85
5814 5911 3.181437 ACACTTATTTTGGGACGGAGGTT 60.181 43.478 0.00 0.00 0.00 3.50
6044 6141 3.058777 CACAGCATGGGTTTTGCAAATTC 60.059 43.478 13.65 9.30 43.62 2.17
6188 6285 4.837298 CCATCTCCATCATCTTCTGGTCTA 59.163 45.833 0.00 0.00 34.03 2.59
6368 6465 3.454082 GTGGAGAGTTCTGATCCCATTCT 59.546 47.826 0.00 0.00 31.73 2.40
6385 6482 6.982160 CCATTCTTGGGATGAAAATGGATA 57.018 37.500 6.58 0.00 46.00 2.59
6409 6506 6.949352 TTCAGAAAGCTTCTCAAGATGTTT 57.051 33.333 0.00 0.00 38.11 2.83
6907 7005 3.698250 TGGAACACTCGAACCCTTG 57.302 52.632 0.00 0.00 0.00 3.61
7026 10656 8.602328 CATTTTGTTCTTGCTGTGAATTTGTTA 58.398 29.630 0.00 0.00 0.00 2.41
7269 10903 2.945668 AGCGTGATCAAATTTAGGCCTC 59.054 45.455 9.68 0.00 0.00 4.70
7284 10918 1.743394 GGCCTCGTTTGATTTACAGGG 59.257 52.381 0.00 0.00 0.00 4.45
7296 10930 4.521256 TGATTTACAGGGTTGGTAAAGTGC 59.479 41.667 0.00 0.00 42.17 4.40
7304 10938 2.293399 GGTTGGTAAAGTGCAGGAACAG 59.707 50.000 0.00 0.00 0.00 3.16
7318 10952 4.323868 GCAGGAACAGGAAAACTAGAGGAT 60.324 45.833 0.00 0.00 0.00 3.24
7328 10962 5.072464 GGAAAACTAGAGGATTAGGATGCCT 59.928 44.000 0.00 0.00 37.71 4.75
7344 10978 1.144708 TGCCTTGTCCAGTGAAATCCA 59.855 47.619 0.00 0.00 0.00 3.41
7345 10979 2.225091 TGCCTTGTCCAGTGAAATCCAT 60.225 45.455 0.00 0.00 0.00 3.41
7346 10980 2.424956 GCCTTGTCCAGTGAAATCCATC 59.575 50.000 0.00 0.00 0.00 3.51
7347 10981 3.019564 CCTTGTCCAGTGAAATCCATCC 58.980 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.234730 ATCGTCATCGCCCCTCCC 61.235 66.667 0.00 0.00 36.96 4.30
1 2 2.029666 CATCGTCATCGCCCCTCC 59.970 66.667 0.00 0.00 36.96 4.30
2 3 2.029666 CCATCGTCATCGCCCCTC 59.970 66.667 0.00 0.00 36.96 4.30
3 4 4.241555 GCCATCGTCATCGCCCCT 62.242 66.667 0.00 0.00 36.96 4.79
19 20 4.609247 ATCGAGACGTAGGCGCGC 62.609 66.667 25.94 25.94 42.83 6.86
20 21 2.004489 GAATCGAGACGTAGGCGCG 61.004 63.158 0.00 0.00 42.83 6.86
21 22 0.930742 CTGAATCGAGACGTAGGCGC 60.931 60.000 0.00 0.00 42.83 6.53
22 23 0.377554 ACTGAATCGAGACGTAGGCG 59.622 55.000 0.00 0.00 44.93 5.52
23 24 1.132643 ACACTGAATCGAGACGTAGGC 59.867 52.381 0.00 0.00 0.00 3.93
24 25 3.489180 AACACTGAATCGAGACGTAGG 57.511 47.619 0.00 0.00 0.00 3.18
25 26 4.227538 ACAAACACTGAATCGAGACGTAG 58.772 43.478 0.00 0.00 0.00 3.51
26 27 4.233123 ACAAACACTGAATCGAGACGTA 57.767 40.909 0.00 0.00 0.00 3.57
27 28 3.093717 ACAAACACTGAATCGAGACGT 57.906 42.857 0.00 0.00 0.00 4.34
28 29 4.227538 ACTACAAACACTGAATCGAGACG 58.772 43.478 0.00 0.00 0.00 4.18
29 30 5.462398 ACAACTACAAACACTGAATCGAGAC 59.538 40.000 0.00 0.00 0.00 3.36
30 31 5.597806 ACAACTACAAACACTGAATCGAGA 58.402 37.500 0.00 0.00 0.00 4.04
31 32 5.387444 CGACAACTACAAACACTGAATCGAG 60.387 44.000 0.00 0.00 0.00 4.04
32 33 4.443063 CGACAACTACAAACACTGAATCGA 59.557 41.667 0.00 0.00 0.00 3.59
33 34 4.688063 CGACAACTACAAACACTGAATCG 58.312 43.478 0.00 0.00 0.00 3.34
34 35 4.211374 AGCGACAACTACAAACACTGAATC 59.789 41.667 0.00 0.00 0.00 2.52
35 36 4.127171 AGCGACAACTACAAACACTGAAT 58.873 39.130 0.00 0.00 0.00 2.57
36 37 3.527533 AGCGACAACTACAAACACTGAA 58.472 40.909 0.00 0.00 0.00 3.02
37 38 3.173668 AGCGACAACTACAAACACTGA 57.826 42.857 0.00 0.00 0.00 3.41
38 39 3.428870 CCTAGCGACAACTACAAACACTG 59.571 47.826 0.00 0.00 0.00 3.66
39 40 3.069158 ACCTAGCGACAACTACAAACACT 59.931 43.478 0.00 0.00 0.00 3.55
40 41 3.183775 CACCTAGCGACAACTACAAACAC 59.816 47.826 0.00 0.00 0.00 3.32
41 42 3.386486 CACCTAGCGACAACTACAAACA 58.614 45.455 0.00 0.00 0.00 2.83
42 43 2.735134 CCACCTAGCGACAACTACAAAC 59.265 50.000 0.00 0.00 0.00 2.93
43 44 2.366266 ACCACCTAGCGACAACTACAAA 59.634 45.455 0.00 0.00 0.00 2.83
44 45 1.965643 ACCACCTAGCGACAACTACAA 59.034 47.619 0.00 0.00 0.00 2.41
45 46 1.624336 ACCACCTAGCGACAACTACA 58.376 50.000 0.00 0.00 0.00 2.74
46 47 2.489329 TGTACCACCTAGCGACAACTAC 59.511 50.000 0.00 0.00 0.00 2.73
47 48 2.794103 TGTACCACCTAGCGACAACTA 58.206 47.619 0.00 0.00 0.00 2.24
48 49 1.624336 TGTACCACCTAGCGACAACT 58.376 50.000 0.00 0.00 0.00 3.16
49 50 2.094390 TCATGTACCACCTAGCGACAAC 60.094 50.000 0.00 0.00 0.00 3.32
50 51 2.172679 TCATGTACCACCTAGCGACAA 58.827 47.619 0.00 0.00 0.00 3.18
51 52 1.842052 TCATGTACCACCTAGCGACA 58.158 50.000 0.00 0.00 0.00 4.35
52 53 2.953466 TTCATGTACCACCTAGCGAC 57.047 50.000 0.00 0.00 0.00 5.19
53 54 3.296854 AGATTCATGTACCACCTAGCGA 58.703 45.455 0.00 0.00 0.00 4.93
54 55 3.735237 AGATTCATGTACCACCTAGCG 57.265 47.619 0.00 0.00 0.00 4.26
55 56 6.015010 ACATCTAGATTCATGTACCACCTAGC 60.015 42.308 1.33 0.00 31.20 3.42
56 57 7.531857 ACATCTAGATTCATGTACCACCTAG 57.468 40.000 1.33 0.00 31.20 3.02
57 58 9.601810 ATTACATCTAGATTCATGTACCACCTA 57.398 33.333 1.33 0.00 35.63 3.08
58 59 7.914427 TTACATCTAGATTCATGTACCACCT 57.086 36.000 1.33 0.00 35.63 4.00
59 60 9.561069 AAATTACATCTAGATTCATGTACCACC 57.439 33.333 1.33 0.00 35.63 4.61
137 138 9.809395 ACAGAGGAAATATTCATCATCAATCAT 57.191 29.630 7.40 0.00 42.56 2.45
184 185 9.250624 GAGCGTTTATCACTACTTTAATGATCT 57.749 33.333 0.00 0.00 34.86 2.75
185 186 9.250624 AGAGCGTTTATCACTACTTTAATGATC 57.749 33.333 0.00 0.00 34.86 2.92
186 187 9.601217 AAGAGCGTTTATCACTACTTTAATGAT 57.399 29.630 0.00 0.00 36.95 2.45
187 188 8.997621 AAGAGCGTTTATCACTACTTTAATGA 57.002 30.769 0.00 0.00 0.00 2.57
192 193 9.517609 CTGTATAAGAGCGTTTATCACTACTTT 57.482 33.333 0.00 0.00 0.00 2.66
193 194 8.900781 TCTGTATAAGAGCGTTTATCACTACTT 58.099 33.333 0.00 0.00 0.00 2.24
194 195 8.447924 TCTGTATAAGAGCGTTTATCACTACT 57.552 34.615 0.00 0.00 0.00 2.57
195 196 8.716619 CTCTGTATAAGAGCGTTTATCACTAC 57.283 38.462 0.00 0.00 45.93 2.73
209 210 7.162973 TCCAATCTACTCCCTCTGTATAAGA 57.837 40.000 0.00 0.00 0.00 2.10
210 211 7.507616 ACTTCCAATCTACTCCCTCTGTATAAG 59.492 40.741 0.00 0.00 0.00 1.73
211 212 7.363031 ACTTCCAATCTACTCCCTCTGTATAA 58.637 38.462 0.00 0.00 0.00 0.98
212 213 6.923670 ACTTCCAATCTACTCCCTCTGTATA 58.076 40.000 0.00 0.00 0.00 1.47
213 214 5.782925 ACTTCCAATCTACTCCCTCTGTAT 58.217 41.667 0.00 0.00 0.00 2.29
214 215 5.208294 ACTTCCAATCTACTCCCTCTGTA 57.792 43.478 0.00 0.00 0.00 2.74
215 216 4.067944 ACTTCCAATCTACTCCCTCTGT 57.932 45.455 0.00 0.00 0.00 3.41
216 217 6.546428 TTAACTTCCAATCTACTCCCTCTG 57.454 41.667 0.00 0.00 0.00 3.35
217 218 7.569599 TTTTAACTTCCAATCTACTCCCTCT 57.430 36.000 0.00 0.00 0.00 3.69
247 248 9.787435 TTTATCTTTTCCTGTGTACTGTATGTT 57.213 29.630 0.00 0.00 0.00 2.71
249 250 8.380644 CGTTTATCTTTTCCTGTGTACTGTATG 58.619 37.037 0.00 0.00 0.00 2.39
251 252 7.436118 ACGTTTATCTTTTCCTGTGTACTGTA 58.564 34.615 0.00 0.00 0.00 2.74
257 258 9.511144 CTTAAAAACGTTTATCTTTTCCTGTGT 57.489 29.630 15.03 0.00 0.00 3.72
258 259 9.724839 TCTTAAAAACGTTTATCTTTTCCTGTG 57.275 29.630 15.03 0.00 0.00 3.66
261 262 9.908152 CCATCTTAAAAACGTTTATCTTTTCCT 57.092 29.630 15.03 0.00 0.00 3.36
262 263 9.902196 TCCATCTTAAAAACGTTTATCTTTTCC 57.098 29.630 15.03 0.00 0.00 3.13
323 324 3.290710 GGTGCATGGATAGTTTGGTGAT 58.709 45.455 0.00 0.00 0.00 3.06
867 871 2.281234 CGAAGCAAAATCTCTCGCTCTC 59.719 50.000 0.00 0.00 32.37 3.20
898 904 2.038007 AGAGGGAGGCTCGAGCAA 59.962 61.111 36.27 0.00 44.36 3.91
976 982 1.997874 AGCTCCCCGAATGCTCCTT 60.998 57.895 0.00 0.00 30.41 3.36
1077 1092 2.267961 GGTGTACCTTCCAGGCCG 59.732 66.667 0.00 0.00 39.63 6.13
1092 1107 4.796495 GGGCCGGAATTGAGCGGT 62.796 66.667 5.05 0.00 0.00 5.68
1165 1180 0.098025 AGCAAACGACACACAAACCG 59.902 50.000 0.00 0.00 0.00 4.44
1246 1261 2.055100 GACTCTGCGAGAACACAAGAC 58.945 52.381 11.64 0.00 33.32 3.01
1248 1263 1.056103 CGACTCTGCGAGAACACAAG 58.944 55.000 11.64 0.00 33.32 3.16
1387 1402 2.281900 GGGTGGTTGTAGCGGCAA 60.282 61.111 1.45 0.00 0.00 4.52
1442 1457 4.264442 TGGGGGAAATAAAATCGGGAGAAA 60.264 41.667 0.00 0.00 45.37 2.52
1673 1690 1.282248 ATCAACGACAGCAACCGACG 61.282 55.000 0.00 0.00 0.00 5.12
1929 1946 6.042093 TCCAAGCTCCTTGAATAGGTAGTATG 59.958 42.308 6.54 0.00 43.42 2.39
1953 1970 7.148755 GCACAAAACATGTTGATACCTTCAATC 60.149 37.037 12.82 0.00 45.77 2.67
1965 1982 5.783100 AAAACAGAGCACAAAACATGTTG 57.217 34.783 12.82 3.65 41.46 3.33
2436 2455 3.327757 ACTCTTTCTCACCCTGCATAACA 59.672 43.478 0.00 0.00 0.00 2.41
2574 2597 2.485479 GGAAGAGACAGGCAGTTGTTGA 60.485 50.000 0.00 0.00 0.00 3.18
2652 2675 0.751643 AGCCCGGGAAAAATGATCCG 60.752 55.000 29.31 0.00 41.90 4.18
3122 3202 5.109500 TGGTGTGATAAGCCATACAATGA 57.891 39.130 0.00 0.00 30.96 2.57
3148 3228 0.403271 AAGCAACTGCAGATGGAGGT 59.597 50.000 23.35 7.56 45.16 3.85
3213 3293 6.015856 TGGAAAGACAACTTCTTGTTTGTCAA 60.016 34.615 14.93 0.00 44.41 3.18
3325 3405 3.286353 GGACCTAGGTGTACTCAGGTAC 58.714 54.545 22.10 0.00 46.06 3.34
3591 3671 8.492415 TGATTACTACTTCCCTAACTATGCAT 57.508 34.615 3.79 3.79 0.00 3.96
3592 3672 7.907841 TGATTACTACTTCCCTAACTATGCA 57.092 36.000 0.00 0.00 0.00 3.96
3714 3798 4.695455 ACTTGATCGACGTTTGATCCAAAT 59.305 37.500 21.75 9.22 41.22 2.32
3727 3816 7.705325 TCTTTAAAGTATGGCTACTTGATCGAC 59.295 37.037 14.74 0.00 45.40 4.20
3849 3938 8.179509 AGTCGACTATACAATAGGCTAAACAT 57.820 34.615 18.46 0.00 0.00 2.71
3850 3939 7.578310 AGTCGACTATACAATAGGCTAAACA 57.422 36.000 18.46 0.00 0.00 2.83
3994 4083 8.758829 ACACTGTCCTACACATAATATTCTTCA 58.241 33.333 0.00 0.00 33.23 3.02
4073 4162 3.249799 CACAAGGTCAAAACTCGTATGCA 59.750 43.478 0.00 0.00 0.00 3.96
4124 4213 6.223852 CACTAAACACAATCTACACTGGACT 58.776 40.000 0.00 0.00 0.00 3.85
4158 4247 0.179124 GCGTTGGTGCAAAGAAACCA 60.179 50.000 0.00 0.00 44.72 3.67
4395 4484 9.341899 AGACATATGTTCGCAATTTTAAACTTC 57.658 29.630 10.30 0.00 0.00 3.01
4463 4552 6.825721 GCCTCCATCTTCAAAGAATTAAGAGA 59.174 38.462 0.00 0.00 38.77 3.10
4464 4553 6.827762 AGCCTCCATCTTCAAAGAATTAAGAG 59.172 38.462 0.00 0.27 38.77 2.85
4465 4554 6.725364 AGCCTCCATCTTCAAAGAATTAAGA 58.275 36.000 0.00 0.00 38.77 2.10
4466 4555 7.401955 AAGCCTCCATCTTCAAAGAATTAAG 57.598 36.000 0.00 0.00 38.77 1.85
4506 4599 3.581024 ACACAATCATGGATGTGTTGC 57.419 42.857 23.30 0.00 42.03 4.17
4574 4667 4.690748 CACATACACGAGATTGTCCAAAGT 59.309 41.667 0.00 0.00 0.00 2.66
4578 4671 3.953712 ACACATACACGAGATTGTCCA 57.046 42.857 0.00 0.00 0.00 4.02
4622 4715 5.019785 AGTCAGAGGTAGTTTCGTTTTGT 57.980 39.130 0.00 0.00 0.00 2.83
4680 4773 4.895668 ATGCCAAGAACAAACATCCATT 57.104 36.364 0.00 0.00 0.00 3.16
4728 4821 5.423290 ACGGGTTAGTACTTTAGGCTAATGT 59.577 40.000 23.87 23.87 0.00 2.71
4741 4834 8.159344 ACTAGTGATGTTATACGGGTTAGTAC 57.841 38.462 0.00 0.00 0.00 2.73
4802 4895 6.472887 CAATACAAACTTTCTACTCCCTCCA 58.527 40.000 0.00 0.00 0.00 3.86
4912 5005 1.435256 AACCTCCAGTAACCTGCACT 58.565 50.000 0.00 0.00 37.38 4.40
5081 5175 5.770685 AATGCTTTTTAGGGGCCAATTAA 57.229 34.783 4.39 0.00 0.00 1.40
5082 5176 5.770685 AAATGCTTTTTAGGGGCCAATTA 57.229 34.783 4.39 0.00 0.00 1.40
5192 5286 9.793252 ATGAACACTTTGATATCTTATTTGCAC 57.207 29.630 3.98 0.00 0.00 4.57
5236 5331 7.007543 ACGTAAATGACATGCACGTATAGCG 62.008 44.000 20.23 0.00 43.39 4.26
5237 5332 4.208460 ACGTAAATGACATGCACGTATAGC 59.792 41.667 20.23 0.00 43.39 2.97
5238 5333 5.883328 ACGTAAATGACATGCACGTATAG 57.117 39.130 20.23 0.19 43.39 1.31
5239 5334 5.805994 TGAACGTAAATGACATGCACGTATA 59.194 36.000 21.31 13.70 44.34 1.47
5240 5335 4.627900 TGAACGTAAATGACATGCACGTAT 59.372 37.500 21.31 14.29 44.34 3.06
5241 5336 3.988517 TGAACGTAAATGACATGCACGTA 59.011 39.130 21.31 9.60 44.34 3.57
5242 5337 2.803386 TGAACGTAAATGACATGCACGT 59.197 40.909 17.44 17.44 46.82 4.49
5243 5338 3.447752 TGAACGTAAATGACATGCACG 57.552 42.857 16.42 16.42 38.52 5.34
5347 5442 6.193514 TGCAATGTCATTTACGTTCATGAT 57.806 33.333 11.34 0.00 35.02 2.45
5437 5533 8.783833 TTGACCAAAACTTTGAAAATTCATGA 57.216 26.923 3.72 0.00 40.55 3.07
5438 5534 9.276397 GTTTGACCAAAACTTTGAAAATTCATG 57.724 29.630 3.72 0.00 44.10 3.07
5543 5640 5.012354 TCGAACCCACTACTCAAATTTACCT 59.988 40.000 0.00 0.00 0.00 3.08
5570 5667 1.895131 ACATTCACATTTGTGCCCCTC 59.105 47.619 5.81 0.00 45.25 4.30
5596 5693 5.806654 ACCATTGTGGCTAAGACAAAAAT 57.193 34.783 0.00 0.00 42.67 1.82
5693 5790 8.786898 TGCAGGAACATTATATTTATGAGAAGC 58.213 33.333 4.94 0.00 0.00 3.86
5706 5803 4.040755 AGGGAGTACTGCAGGAACATTAT 58.959 43.478 19.93 0.00 0.00 1.28
5718 5815 0.613853 TTGGGACGGAGGGAGTACTG 60.614 60.000 0.00 0.00 0.00 2.74
5720 5817 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
5721 5818 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
5722 5819 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
5723 5820 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5724 5821 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5725 5822 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5726 5823 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5727 5824 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5728 5825 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5729 5826 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5730 5827 5.643777 AGATTGAGACACTTATTTTGGGACG 59.356 40.000 0.00 0.00 0.00 4.79
5731 5828 7.454260 AAGATTGAGACACTTATTTTGGGAC 57.546 36.000 0.00 0.00 0.00 4.46
5732 5829 8.383175 ACTAAGATTGAGACACTTATTTTGGGA 58.617 33.333 0.00 0.00 0.00 4.37
5733 5830 8.567285 ACTAAGATTGAGACACTTATTTTGGG 57.433 34.615 0.00 0.00 0.00 4.12
5741 5838 9.046296 CAAAGTTGTACTAAGATTGAGACACTT 57.954 33.333 0.00 0.00 0.00 3.16
5742 5839 7.171678 GCAAAGTTGTACTAAGATTGAGACACT 59.828 37.037 0.00 0.00 0.00 3.55
5743 5840 7.042051 TGCAAAGTTGTACTAAGATTGAGACAC 60.042 37.037 0.00 0.00 0.00 3.67
5744 5841 6.989759 TGCAAAGTTGTACTAAGATTGAGACA 59.010 34.615 0.00 0.00 0.00 3.41
5745 5842 7.291567 GTGCAAAGTTGTACTAAGATTGAGAC 58.708 38.462 5.17 0.00 40.10 3.36
5746 5843 7.421530 GTGCAAAGTTGTACTAAGATTGAGA 57.578 36.000 5.17 0.00 40.10 3.27
5767 5864 7.849515 GTGTCAACTTTGTACTAACTTTAGTGC 59.150 37.037 11.24 10.37 43.44 4.40
5768 5865 8.875803 TGTGTCAACTTTGTACTAACTTTAGTG 58.124 33.333 11.24 0.00 43.44 2.74
5769 5866 8.876790 GTGTGTCAACTTTGTACTAACTTTAGT 58.123 33.333 6.85 6.85 45.39 2.24
5770 5867 9.095065 AGTGTGTCAACTTTGTACTAACTTTAG 57.905 33.333 0.00 0.00 36.82 1.85
5771 5868 9.439500 AAGTGTGTCAACTTTGTACTAACTTTA 57.561 29.630 0.00 0.00 37.05 1.85
5772 5869 7.916914 AGTGTGTCAACTTTGTACTAACTTT 57.083 32.000 0.00 0.00 0.00 2.66
5773 5870 7.916914 AAGTGTGTCAACTTTGTACTAACTT 57.083 32.000 0.00 0.00 37.05 2.66
5774 5871 9.609346 AATAAGTGTGTCAACTTTGTACTAACT 57.391 29.630 0.00 0.00 40.77 2.24
5778 5875 8.188139 CCAAAATAAGTGTGTCAACTTTGTACT 58.812 33.333 0.00 0.00 40.77 2.73
5779 5876 7.434013 CCCAAAATAAGTGTGTCAACTTTGTAC 59.566 37.037 5.95 0.00 40.77 2.90
5780 5877 7.339721 TCCCAAAATAAGTGTGTCAACTTTGTA 59.660 33.333 5.95 0.00 40.77 2.41
5781 5878 6.153680 TCCCAAAATAAGTGTGTCAACTTTGT 59.846 34.615 5.95 0.00 40.77 2.83
5782 5879 6.475402 GTCCCAAAATAAGTGTGTCAACTTTG 59.525 38.462 5.95 0.00 40.77 2.77
5783 5880 6.569780 GTCCCAAAATAAGTGTGTCAACTTT 58.430 36.000 5.95 0.00 40.77 2.66
5784 5881 5.220970 CGTCCCAAAATAAGTGTGTCAACTT 60.221 40.000 0.00 0.00 42.89 2.66
5785 5882 4.274950 CGTCCCAAAATAAGTGTGTCAACT 59.725 41.667 0.00 0.00 0.00 3.16
5786 5883 4.533222 CGTCCCAAAATAAGTGTGTCAAC 58.467 43.478 0.00 0.00 0.00 3.18
5787 5884 3.566322 CCGTCCCAAAATAAGTGTGTCAA 59.434 43.478 0.00 0.00 0.00 3.18
5788 5885 3.142951 CCGTCCCAAAATAAGTGTGTCA 58.857 45.455 0.00 0.00 0.00 3.58
5789 5886 3.404899 TCCGTCCCAAAATAAGTGTGTC 58.595 45.455 0.00 0.00 0.00 3.67
5790 5887 3.408634 CTCCGTCCCAAAATAAGTGTGT 58.591 45.455 0.00 0.00 0.00 3.72
5791 5888 2.747446 CCTCCGTCCCAAAATAAGTGTG 59.253 50.000 0.00 0.00 0.00 3.82
5792 5889 2.374170 ACCTCCGTCCCAAAATAAGTGT 59.626 45.455 0.00 0.00 0.00 3.55
5793 5890 3.067684 ACCTCCGTCCCAAAATAAGTG 57.932 47.619 0.00 0.00 0.00 3.16
5794 5891 3.181437 ACAACCTCCGTCCCAAAATAAGT 60.181 43.478 0.00 0.00 0.00 2.24
5795 5892 3.418047 ACAACCTCCGTCCCAAAATAAG 58.582 45.455 0.00 0.00 0.00 1.73
5796 5893 3.512219 ACAACCTCCGTCCCAAAATAA 57.488 42.857 0.00 0.00 0.00 1.40
5797 5894 3.583966 ACTACAACCTCCGTCCCAAAATA 59.416 43.478 0.00 0.00 0.00 1.40
5798 5895 2.374170 ACTACAACCTCCGTCCCAAAAT 59.626 45.455 0.00 0.00 0.00 1.82
5799 5896 1.770061 ACTACAACCTCCGTCCCAAAA 59.230 47.619 0.00 0.00 0.00 2.44
5800 5897 1.426751 ACTACAACCTCCGTCCCAAA 58.573 50.000 0.00 0.00 0.00 3.28
5801 5898 1.345415 GAACTACAACCTCCGTCCCAA 59.655 52.381 0.00 0.00 0.00 4.12
5802 5899 0.971386 GAACTACAACCTCCGTCCCA 59.029 55.000 0.00 0.00 0.00 4.37
5803 5900 0.971386 TGAACTACAACCTCCGTCCC 59.029 55.000 0.00 0.00 0.00 4.46
5804 5901 3.329929 AATGAACTACAACCTCCGTCC 57.670 47.619 0.00 0.00 0.00 4.79
5805 5902 4.083484 CCAAAATGAACTACAACCTCCGTC 60.083 45.833 0.00 0.00 0.00 4.79
5806 5903 3.818773 CCAAAATGAACTACAACCTCCGT 59.181 43.478 0.00 0.00 0.00 4.69
5807 5904 3.365969 GCCAAAATGAACTACAACCTCCG 60.366 47.826 0.00 0.00 0.00 4.63
5808 5905 3.826729 AGCCAAAATGAACTACAACCTCC 59.173 43.478 0.00 0.00 0.00 4.30
5809 5906 4.798574 CAGCCAAAATGAACTACAACCTC 58.201 43.478 0.00 0.00 0.00 3.85
5810 5907 3.005791 GCAGCCAAAATGAACTACAACCT 59.994 43.478 0.00 0.00 0.00 3.50
5811 5908 3.243704 TGCAGCCAAAATGAACTACAACC 60.244 43.478 0.00 0.00 0.00 3.77
5812 5909 3.976169 TGCAGCCAAAATGAACTACAAC 58.024 40.909 0.00 0.00 0.00 3.32
5813 5910 4.099266 ACTTGCAGCCAAAATGAACTACAA 59.901 37.500 0.00 0.00 0.00 2.41
5814 5911 3.636300 ACTTGCAGCCAAAATGAACTACA 59.364 39.130 0.00 0.00 0.00 2.74
6044 6141 0.179140 CAAATTTGCATCCGGGACCG 60.179 55.000 5.01 3.25 39.44 4.79
6368 6465 8.606754 TTTCTGAATATCCATTTTCATCCCAA 57.393 30.769 0.00 0.00 31.83 4.12
6385 6482 7.521871 AAACATCTTGAGAAGCTTTCTGAAT 57.478 32.000 0.00 0.00 40.87 2.57
6482 6579 0.179051 CAGATGCTGAGAGGGGAAGC 60.179 60.000 0.00 0.00 37.46 3.86
6755 6852 0.679640 TTGCCGAACCCAATAGCCTG 60.680 55.000 0.00 0.00 0.00 4.85
7246 10880 4.523083 AGGCCTAAATTTGATCACGCTTA 58.477 39.130 1.29 0.00 0.00 3.09
7269 10903 5.692613 TTACCAACCCTGTAAATCAAACG 57.307 39.130 0.00 0.00 0.00 3.60
7284 10918 2.293399 CCTGTTCCTGCACTTTACCAAC 59.707 50.000 0.00 0.00 0.00 3.77
7296 10930 4.891992 TCCTCTAGTTTTCCTGTTCCTG 57.108 45.455 0.00 0.00 0.00 3.86
7304 10938 5.072464 AGGCATCCTAATCCTCTAGTTTTCC 59.928 44.000 0.00 0.00 28.47 3.13
7318 10952 2.265367 TCACTGGACAAGGCATCCTAA 58.735 47.619 4.40 0.00 37.13 2.69
7328 10962 2.378208 TGGGATGGATTTCACTGGACAA 59.622 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.