Multiple sequence alignment - TraesCS7B01G146900

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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 TraesCS7B01G146900 chr7B 100.000 9133 0 0 1 9133 192765165 192774297 0.000000e+00 16866.0
1 TraesCS7B01G146900 chr7B 89.549 421 39 3 2360 2775 652185401 652185821 6.280000e-146 529.0
2 TraesCS7B01G146900 chr7B 92.000 150 10 2 2079 2227 576919014 576919162 9.290000e-50 209.0
3 TraesCS7B01G146900 chr7D 93.100 4493 189 48 4096 8541 208552949 208548531 0.000000e+00 6468.0
4 TraesCS7B01G146900 chr7D 96.010 1253 43 5 827 2076 208554202 208552954 0.000000e+00 2030.0
5 TraesCS7B01G146900 chr7D 88.958 643 61 6 63 700 208554954 208554317 0.000000e+00 785.0
6 TraesCS7B01G146900 chr2A 99.058 2018 19 0 2075 4092 180227382 180225365 0.000000e+00 3622.0
7 TraesCS7B01G146900 chr2A 97.933 1742 20 7 2340 4081 192206701 192204976 0.000000e+00 3003.0
8 TraesCS7B01G146900 chr2A 98.052 154 3 0 2079 2232 192206855 192206702 1.510000e-67 268.0
9 TraesCS7B01G146900 chr5A 98.663 2019 24 2 2075 4092 435475494 435473478 0.000000e+00 3576.0
10 TraesCS7B01G146900 chr5A 94.385 837 43 3 3271 4103 610674768 610673932 0.000000e+00 1282.0
11 TraesCS7B01G146900 chr5A 99.160 595 5 0 8539 9133 328022894 328022300 0.000000e+00 1072.0
12 TraesCS7B01G146900 chr5A 89.506 162 16 1 2074 2234 518028596 518028435 4.320000e-48 204.0
13 TraesCS7B01G146900 chr7A 94.825 1913 70 10 4712 6603 221683736 221681832 0.000000e+00 2957.0
14 TraesCS7B01G146900 chr7A 93.371 1931 92 16 6639 8541 221681833 221679911 0.000000e+00 2824.0
15 TraesCS7B01G146900 chr7A 94.960 1369 52 9 725 2078 221686157 221684791 0.000000e+00 2130.0
16 TraesCS7B01G146900 chr7A 95.026 965 45 2 3130 4092 95891685 95892648 0.000000e+00 1513.0
17 TraesCS7B01G146900 chr7A 92.605 595 31 6 4120 4703 221684784 221684192 0.000000e+00 843.0
18 TraesCS7B01G146900 chr7A 92.289 402 27 2 3131 3532 33742147 33741750 1.330000e-157 568.0
19 TraesCS7B01G146900 chr7A 90.187 214 17 4 2802 3015 33742382 33742173 9.030000e-70 276.0
20 TraesCS7B01G146900 chr6A 95.440 965 41 2 3130 4092 428661952 428660989 0.000000e+00 1535.0
21 TraesCS7B01G146900 chr6A 99.161 596 5 0 8538 9133 11432286 11431691 0.000000e+00 1074.0
22 TraesCS7B01G146900 chr6A 90.419 167 16 0 2075 2241 428662879 428662713 4.290000e-53 220.0
23 TraesCS7B01G146900 chr6A 80.000 125 7 13 2886 3008 428662127 428662019 9.830000e-10 76.8
24 TraesCS7B01G146900 chr4B 95.026 965 45 2 3130 4092 240178895 240179858 0.000000e+00 1513.0
25 TraesCS7B01G146900 chr4B 87.406 397 39 5 2075 2460 240178009 240178405 6.510000e-121 446.0
26 TraesCS7B01G146900 chr4B 85.638 188 14 8 6579 6763 579470477 579470300 1.570000e-42 185.0
27 TraesCS7B01G146900 chr6B 99.496 595 3 0 8539 9133 391086455 391085861 0.000000e+00 1083.0
28 TraesCS7B01G146900 chr6B 88.957 163 12 3 2074 2232 131732036 131731876 7.230000e-46 196.0
29 TraesCS7B01G146900 chr6B 80.275 218 31 5 6584 6801 498563164 498562959 4.420000e-33 154.0
30 TraesCS7B01G146900 chr1A 98.993 596 6 0 8538 9133 12674183 12674778 0.000000e+00 1068.0
31 TraesCS7B01G146900 chr5B 98.992 595 6 0 8539 9133 682459365 682458771 0.000000e+00 1066.0
32 TraesCS7B01G146900 chr5B 83.019 265 23 5 6579 6843 316528826 316529068 4.290000e-53 220.0
33 TraesCS7B01G146900 chr4A 98.992 595 6 0 8539 9133 717461840 717461246 0.000000e+00 1066.0
34 TraesCS7B01G146900 chr2B 98.824 595 7 0 8539 9133 47196581 47195987 0.000000e+00 1061.0
35 TraesCS7B01G146900 chr2B 98.658 596 8 0 8538 9133 770072606 770073201 0.000000e+00 1057.0
36 TraesCS7B01G146900 chr2B 90.024 421 32 8 2352 2767 286517225 286517640 3.750000e-148 536.0
37 TraesCS7B01G146900 chr3B 98.497 599 9 0 8535 9133 820555331 820555929 0.000000e+00 1057.0
38 TraesCS7B01G146900 chr3B 81.787 291 29 7 6579 6868 717075741 717075474 1.190000e-53 222.0
39 TraesCS7B01G146900 chr3B 82.203 236 34 3 6636 6870 830298266 830298038 7.230000e-46 196.0
40 TraesCS7B01G146900 chr3B 81.944 216 26 4 6581 6795 816082281 816082078 4.380000e-38 171.0
41 TraesCS7B01G146900 chr3B 82.075 212 23 6 6583 6792 116078869 116078671 5.670000e-37 167.0
42 TraesCS7B01G146900 chr3A 94.575 553 28 1 3542 4092 353165460 353164908 0.000000e+00 854.0
43 TraesCS7B01G146900 chr6D 93.403 576 32 6 3521 4092 291635755 291636328 0.000000e+00 848.0
44 TraesCS7B01G146900 chr6D 90.299 402 37 2 2375 2775 21080690 21081090 8.120000e-145 525.0
45 TraesCS7B01G146900 chr6D 93.023 172 9 3 2802 2972 21081192 21081361 1.970000e-61 248.0
46 TraesCS7B01G146900 chr2D 87.925 530 47 10 2365 2892 648346606 648347120 7.840000e-170 608.0
47 TraesCS7B01G146900 chr4D 93.797 403 20 4 3131 3532 453322973 453323371 1.310000e-167 601.0
48 TraesCS7B01G146900 chr4D 91.244 217 12 6 2802 3015 453322735 453322947 1.160000e-73 289.0
49 TraesCS7B01G146900 chr4D 83.562 292 36 6 6578 6868 481411370 481411650 7.030000e-66 263.0
50 TraesCS7B01G146900 chr1D 90.714 420 35 3 2360 2775 202311353 202311772 2.880000e-154 556.0
51 TraesCS7B01G146900 chr1D 90.863 394 35 1 2383 2775 393435784 393436177 2.260000e-145 527.0
52 TraesCS7B01G146900 chr1D 90.783 217 13 6 2802 3015 393436278 393436490 5.400000e-72 283.0
53 TraesCS7B01G146900 chr1D 90.323 217 14 6 2802 3015 202311947 202312159 2.510000e-70 278.0
54 TraesCS7B01G146900 chr1D 91.558 154 7 5 2856 3007 202312475 202312624 3.340000e-49 207.0
55 TraesCS7B01G146900 chr1D 88.514 148 11 2 6728 6869 62141336 62141483 3.390000e-39 174.0
56 TraesCS7B01G146900 chr3D 83.904 292 23 7 6578 6868 540378664 540378932 3.270000e-64 257.0
57 TraesCS7B01G146900 chr3D 85.593 236 25 5 6636 6870 611967387 611967160 1.190000e-58 239.0
58 TraesCS7B01G146900 chr5D 82.724 301 27 7 6572 6870 324637297 324637574 2.550000e-60 244.0
59 TraesCS7B01G146900 chr1B 91.333 150 11 2 2079 2227 524489581 524489729 4.320000e-48 204.0
60 TraesCS7B01G146900 chr1B 86.667 150 12 5 2835 2984 625987302 625987443 9.490000e-35 159.0


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 TraesCS7B01G146900 chr7B 192765165 192774297 9132 False 16866.000000 16866 100.000000 1 9133 1 chr7B.!!$F1 9132
1 TraesCS7B01G146900 chr7D 208548531 208554954 6423 True 3094.333333 6468 92.689333 63 8541 3 chr7D.!!$R1 8478
2 TraesCS7B01G146900 chr2A 180225365 180227382 2017 True 3622.000000 3622 99.058000 2075 4092 1 chr2A.!!$R1 2017
3 TraesCS7B01G146900 chr2A 192204976 192206855 1879 True 1635.500000 3003 97.992500 2079 4081 2 chr2A.!!$R2 2002
4 TraesCS7B01G146900 chr5A 435473478 435475494 2016 True 3576.000000 3576 98.663000 2075 4092 1 chr5A.!!$R2 2017
5 TraesCS7B01G146900 chr5A 610673932 610674768 836 True 1282.000000 1282 94.385000 3271 4103 1 chr5A.!!$R4 832
6 TraesCS7B01G146900 chr5A 328022300 328022894 594 True 1072.000000 1072 99.160000 8539 9133 1 chr5A.!!$R1 594
7 TraesCS7B01G146900 chr7A 221679911 221686157 6246 True 2188.500000 2957 93.940250 725 8541 4 chr7A.!!$R2 7816
8 TraesCS7B01G146900 chr7A 95891685 95892648 963 False 1513.000000 1513 95.026000 3130 4092 1 chr7A.!!$F1 962
9 TraesCS7B01G146900 chr7A 33741750 33742382 632 True 422.000000 568 91.238000 2802 3532 2 chr7A.!!$R1 730
10 TraesCS7B01G146900 chr6A 11431691 11432286 595 True 1074.000000 1074 99.161000 8538 9133 1 chr6A.!!$R1 595
11 TraesCS7B01G146900 chr6A 428660989 428662879 1890 True 610.600000 1535 88.619667 2075 4092 3 chr6A.!!$R2 2017
12 TraesCS7B01G146900 chr4B 240178009 240179858 1849 False 979.500000 1513 91.216000 2075 4092 2 chr4B.!!$F1 2017
13 TraesCS7B01G146900 chr6B 391085861 391086455 594 True 1083.000000 1083 99.496000 8539 9133 1 chr6B.!!$R2 594
14 TraesCS7B01G146900 chr1A 12674183 12674778 595 False 1068.000000 1068 98.993000 8538 9133 1 chr1A.!!$F1 595
15 TraesCS7B01G146900 chr5B 682458771 682459365 594 True 1066.000000 1066 98.992000 8539 9133 1 chr5B.!!$R1 594
16 TraesCS7B01G146900 chr4A 717461246 717461840 594 True 1066.000000 1066 98.992000 8539 9133 1 chr4A.!!$R1 594
17 TraesCS7B01G146900 chr2B 47195987 47196581 594 True 1061.000000 1061 98.824000 8539 9133 1 chr2B.!!$R1 594
18 TraesCS7B01G146900 chr2B 770072606 770073201 595 False 1057.000000 1057 98.658000 8538 9133 1 chr2B.!!$F2 595
19 TraesCS7B01G146900 chr3B 820555331 820555929 598 False 1057.000000 1057 98.497000 8535 9133 1 chr3B.!!$F1 598
20 TraesCS7B01G146900 chr3A 353164908 353165460 552 True 854.000000 854 94.575000 3542 4092 1 chr3A.!!$R1 550
21 TraesCS7B01G146900 chr6D 291635755 291636328 573 False 848.000000 848 93.403000 3521 4092 1 chr6D.!!$F1 571
22 TraesCS7B01G146900 chr6D 21080690 21081361 671 False 386.500000 525 91.661000 2375 2972 2 chr6D.!!$F2 597
23 TraesCS7B01G146900 chr2D 648346606 648347120 514 False 608.000000 608 87.925000 2365 2892 1 chr2D.!!$F1 527
24 TraesCS7B01G146900 chr4D 453322735 453323371 636 False 445.000000 601 92.520500 2802 3532 2 chr4D.!!$F2 730
25 TraesCS7B01G146900 chr1D 393435784 393436490 706 False 405.000000 527 90.823000 2383 3015 2 chr1D.!!$F3 632
26 TraesCS7B01G146900 chr1D 202311353 202312624 1271 False 347.000000 556 90.865000 2360 3015 3 chr1D.!!$F2 655

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
55 56 0.178929 AACCGTCAGGGAGAGGAGTT 60.179 55.000 0.00 0.0 43.47 3.01 F
990 1044 0.252558 TAACGGCTTCCTCTTCCCCT 60.253 55.000 0.00 0.0 0.00 4.79 F
2868 3136 0.112412 AAACGGGAATTGAGGGCTGT 59.888 50.000 0.00 0.0 0.00 4.40 F
4094 4392 4.054780 CACGGGTATATGTGCTAGTTGT 57.945 45.455 0.00 0.0 0.00 3.32 F
4170 4468 0.239347 CAGTAACTGCCAGCAACTGC 59.761 55.000 12.46 0.0 42.49 4.40 F
5312 6070 0.098728 GCATGTCGGCGCACTTTAAT 59.901 50.000 10.83 0.0 0.00 1.40 F
5313 6071 1.329292 GCATGTCGGCGCACTTTAATA 59.671 47.619 10.83 0.0 0.00 0.98 F
6633 7415 0.108207 CTCAAGCTGATAGGGCAGGG 59.892 60.000 0.00 0.0 36.41 4.45 F
6785 7567 0.178975 AGACCTCCTGGCTCCGATAG 60.179 60.000 0.00 0.0 36.63 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2053 2.359900 CGGAGTAAGATTGCAAAGCCT 58.640 47.619 1.71 0.0 27.83 4.58 R
2963 3231 0.251653 TCGAGACTAACACCAGCCCT 60.252 55.000 0.00 0.0 0.00 5.19 R
4169 4467 0.819259 TGTTGTCAGAGGTTGCTGGC 60.819 55.000 0.00 0.0 40.82 4.85 R
5237 5995 1.407258 GTGCTGCACCCAGTTTTACAA 59.593 47.619 21.78 0.0 41.26 2.41 R
5899 6674 1.678101 GCAGCAGATATGGTCCCAAAC 59.322 52.381 0.00 0.0 0.00 2.93 R
6631 7413 0.106015 ATGCATAGCCCACCTTTCCC 60.106 55.000 0.00 0.0 0.00 3.97 R
6785 7567 0.165944 GTGTGTGCGGTTCTACATGC 59.834 55.000 0.00 0.0 0.00 4.06 R
8046 8843 0.929244 AGTTTGATCCATCCCCAGGG 59.071 55.000 0.00 0.0 0.00 4.45 R
8245 9064 1.421410 GCGTTATGACTGACCCAGCG 61.421 60.000 0.00 0.0 34.37 5.18 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 3.116531 GTAGTTCACGGCACCGCC 61.117 66.667 9.43 0.00 46.75 6.13
36 37 3.672447 CGTGCCAATGCTGCCACA 61.672 61.111 0.00 0.00 38.71 4.17
37 38 2.735883 GTGCCAATGCTGCCACAA 59.264 55.556 0.00 0.00 38.71 3.33
38 39 1.665599 GTGCCAATGCTGCCACAAC 60.666 57.895 0.00 0.00 38.71 3.32
39 40 2.047939 GCCAATGCTGCCACAACC 60.048 61.111 0.00 0.00 33.53 3.77
40 41 2.259204 CCAATGCTGCCACAACCG 59.741 61.111 0.00 0.00 0.00 4.44
41 42 2.563798 CCAATGCTGCCACAACCGT 61.564 57.895 0.00 0.00 0.00 4.83
42 43 1.081242 CAATGCTGCCACAACCGTC 60.081 57.895 0.00 0.00 0.00 4.79
43 44 1.528076 AATGCTGCCACAACCGTCA 60.528 52.632 0.00 0.00 0.00 4.35
44 45 1.518056 AATGCTGCCACAACCGTCAG 61.518 55.000 0.00 0.00 0.00 3.51
45 46 3.357079 GCTGCCACAACCGTCAGG 61.357 66.667 0.00 0.00 45.13 3.86
46 47 2.669569 CTGCCACAACCGTCAGGG 60.670 66.667 0.00 0.00 43.47 4.45
47 48 3.164977 TGCCACAACCGTCAGGGA 61.165 61.111 0.00 0.00 43.47 4.20
48 49 2.358737 GCCACAACCGTCAGGGAG 60.359 66.667 0.00 0.00 43.47 4.30
49 50 2.879233 GCCACAACCGTCAGGGAGA 61.879 63.158 0.00 0.00 43.47 3.71
50 51 1.293498 CCACAACCGTCAGGGAGAG 59.707 63.158 0.00 0.00 43.47 3.20
51 52 1.293498 CACAACCGTCAGGGAGAGG 59.707 63.158 0.00 0.00 43.47 3.69
52 53 1.155390 ACAACCGTCAGGGAGAGGA 59.845 57.895 0.00 0.00 43.47 3.71
53 54 0.900647 ACAACCGTCAGGGAGAGGAG 60.901 60.000 0.00 0.00 43.47 3.69
54 55 0.900647 CAACCGTCAGGGAGAGGAGT 60.901 60.000 0.00 0.00 43.47 3.85
55 56 0.178929 AACCGTCAGGGAGAGGAGTT 60.179 55.000 0.00 0.00 43.47 3.01
56 57 0.900647 ACCGTCAGGGAGAGGAGTTG 60.901 60.000 0.00 0.00 43.47 3.16
57 58 1.216710 CGTCAGGGAGAGGAGTTGC 59.783 63.158 0.00 0.00 34.03 4.17
58 59 1.599576 GTCAGGGAGAGGAGTTGCC 59.400 63.158 0.00 0.00 0.00 4.52
59 60 1.158466 TCAGGGAGAGGAGTTGCCA 59.842 57.895 0.00 0.00 40.02 4.92
60 61 0.906756 TCAGGGAGAGGAGTTGCCAG 60.907 60.000 0.00 0.00 40.02 4.85
61 62 1.614824 AGGGAGAGGAGTTGCCAGG 60.615 63.158 0.00 0.00 40.02 4.45
62 63 1.613630 GGGAGAGGAGTTGCCAGGA 60.614 63.158 0.00 0.00 40.02 3.86
63 64 1.621672 GGGAGAGGAGTTGCCAGGAG 61.622 65.000 0.00 0.00 40.02 3.69
64 65 1.220477 GAGAGGAGTTGCCAGGAGC 59.780 63.158 0.00 0.00 44.14 4.70
65 66 1.229464 AGAGGAGTTGCCAGGAGCT 60.229 57.895 0.00 0.00 44.23 4.09
66 67 1.220477 GAGGAGTTGCCAGGAGCTC 59.780 63.158 4.71 4.71 44.23 4.09
67 68 1.229464 AGGAGTTGCCAGGAGCTCT 60.229 57.895 14.64 0.00 44.23 4.09
75 76 2.200081 TGCCAGGAGCTCTTTAATCCT 58.800 47.619 14.64 0.00 44.41 3.24
78 79 4.019858 GCCAGGAGCTCTTTAATCCTTTT 58.980 43.478 14.64 0.00 41.60 2.27
84 85 5.411669 GGAGCTCTTTAATCCTTTTCAACGA 59.588 40.000 14.64 0.00 0.00 3.85
94 95 2.160417 CCTTTTCAACGAGGATGAGTGC 59.840 50.000 0.00 0.00 34.91 4.40
95 96 1.808411 TTTCAACGAGGATGAGTGCC 58.192 50.000 0.00 0.00 0.00 5.01
100 101 4.056805 GAGGATGAGTGCCTCCCA 57.943 61.111 0.00 0.00 44.96 4.37
103 104 1.150081 GGATGAGTGCCTCCCATGG 59.850 63.158 4.14 4.14 0.00 3.66
144 145 4.278513 TTGACCCTGGGTTGCCGG 62.279 66.667 21.59 0.00 35.25 6.13
163 164 0.657951 GCGGCTATCTTCGACGAGAC 60.658 60.000 0.00 0.00 34.00 3.36
200 201 2.561419 CCAAAGACGTAGGAGGAAGACA 59.439 50.000 0.00 0.00 0.00 3.41
218 219 3.353836 CGTGGGGTGCCAAAGACG 61.354 66.667 0.00 0.00 0.00 4.18
229 230 0.656205 CCAAAGACGCGGTGAAAACG 60.656 55.000 12.47 0.00 0.00 3.60
265 266 1.225704 GATCAAGGAGGGCAGGTGG 59.774 63.158 0.00 0.00 0.00 4.61
272 273 3.850098 GAGGGCAGGTGGTGTGGTG 62.850 68.421 0.00 0.00 0.00 4.17
294 295 2.751036 CCGATGCACATGTGGCCA 60.751 61.111 26.55 17.14 0.00 5.36
309 310 2.124983 CCATGGACGGGAGCTGTG 60.125 66.667 5.56 0.00 0.00 3.66
314 315 2.811317 GACGGGAGCTGTGCGAAG 60.811 66.667 0.00 0.00 0.00 3.79
318 319 2.394563 GGGAGCTGTGCGAAGAAGC 61.395 63.158 0.00 0.00 37.20 3.86
326 327 2.390599 TGCGAAGAAGCGATGTGGC 61.391 57.895 0.00 0.00 40.67 5.01
350 351 4.777781 CGTAGCGACGGATCAACA 57.222 55.556 11.88 0.00 45.63 3.33
367 368 1.300156 CACGGATCCGACGATGCAT 60.300 57.895 39.55 12.74 42.83 3.96
391 392 1.031571 CAACCGGCATATGCTGTGGT 61.032 55.000 29.95 26.99 45.66 4.16
397 398 0.461870 GCATATGCTGTGGTCGGTCA 60.462 55.000 20.64 0.00 38.21 4.02
398 399 1.290203 CATATGCTGTGGTCGGTCAC 58.710 55.000 0.00 2.79 38.09 3.67
401 402 3.936203 GCTGTGGTCGGTCACCCA 61.936 66.667 0.00 0.00 46.18 4.51
493 497 1.633432 ACTACTGGTATTTGGCTGCCA 59.367 47.619 19.30 19.30 0.00 4.92
528 532 7.996098 TTTAAGTCACCTCTTCCATTTAAGG 57.004 36.000 0.00 0.00 34.94 2.69
529 533 5.584551 AAGTCACCTCTTCCATTTAAGGT 57.415 39.130 0.00 0.00 42.87 3.50
560 564 7.056635 CCCAACTGTACCAATCTGAATCTAAT 58.943 38.462 0.00 0.00 0.00 1.73
561 565 8.210946 CCCAACTGTACCAATCTGAATCTAATA 58.789 37.037 0.00 0.00 0.00 0.98
588 592 6.058833 TGTGTTCTTGCATAACTGAACCTTA 58.941 36.000 12.19 0.43 38.29 2.69
608 612 8.051901 ACCTTAAACGAAAATTATCTTCCCAG 57.948 34.615 0.00 0.00 0.00 4.45
622 627 4.628074 TCTTCCCAGTCTTTTACGAAGTG 58.372 43.478 0.00 0.00 45.73 3.16
633 638 6.910433 GTCTTTTACGAAGTGAGCAAATGAAA 59.090 34.615 0.00 0.00 45.73 2.69
674 679 2.440409 GGAGCAGTGGAATTGACACAT 58.560 47.619 11.25 0.00 41.21 3.21
675 680 3.609853 GGAGCAGTGGAATTGACACATA 58.390 45.455 11.25 0.00 41.21 2.29
676 681 3.375299 GGAGCAGTGGAATTGACACATAC 59.625 47.826 11.25 2.26 41.21 2.39
749 793 4.409218 GTACGCCGTGCTCCGACA 62.409 66.667 0.00 0.00 39.56 4.35
759 806 4.803426 CTCCGACAGCACTCCGCC 62.803 72.222 0.00 0.00 44.04 6.13
767 814 2.279517 GCACTCCGCCGTATCCAG 60.280 66.667 0.00 0.00 32.94 3.86
775 822 3.151710 CCGTATCCAGGACCGGCA 61.152 66.667 14.86 0.00 33.20 5.69
777 824 2.125326 CGTATCCAGGACCGGCAGA 61.125 63.158 0.00 0.00 0.00 4.26
956 1010 2.456119 CGCCAGCAACCGTCTGATC 61.456 63.158 0.00 0.00 33.54 2.92
959 1013 0.742281 CCAGCAACCGTCTGATCCTG 60.742 60.000 0.00 0.00 33.54 3.86
990 1044 0.252558 TAACGGCTTCCTCTTCCCCT 60.253 55.000 0.00 0.00 0.00 4.79
1011 1066 3.260931 TCGTCTTCGAGTCCACGG 58.739 61.111 7.41 0.00 41.35 4.94
1012 1067 2.504244 CGTCTTCGAGTCCACGGC 60.504 66.667 0.00 0.00 39.71 5.68
1092 1149 2.496817 GCGCAACCACCACCAAAA 59.503 55.556 0.30 0.00 0.00 2.44
1136 1193 2.678580 TCCCGTGCATCCTCGTCA 60.679 61.111 0.00 0.00 0.00 4.35
1204 1261 1.928567 GTCCAACCATCCTCCCCCA 60.929 63.158 0.00 0.00 0.00 4.96
1257 1314 0.609681 AGAGTCCGAGAGCCGTCTTT 60.610 55.000 0.00 0.00 36.31 2.52
1426 1483 2.513026 GATGCCACCACAGCGAGACT 62.513 60.000 0.00 0.00 0.00 3.24
1656 1713 2.742116 CCACCAACGGGATCGGGAT 61.742 63.158 0.00 0.00 41.39 3.85
1733 1790 2.025887 CACTGCTCCCAGGTATTCCTTT 60.026 50.000 0.00 0.00 43.07 3.11
2022 2088 6.010850 TCTTACTCCGGCTCACATAATATCT 58.989 40.000 0.00 0.00 0.00 1.98
2480 2558 6.223852 TCTATCACTATCAGCCGAATTTTCC 58.776 40.000 0.00 0.00 0.00 3.13
2717 2795 3.878778 AGACAATAAGCAGCCTCGAATT 58.121 40.909 0.00 0.00 0.00 2.17
2868 3136 0.112412 AAACGGGAATTGAGGGCTGT 59.888 50.000 0.00 0.00 0.00 4.40
2963 3231 7.872138 AGGGTGGAGATCAAATATACTTGAAA 58.128 34.615 0.03 0.00 38.75 2.69
3008 3277 4.878439 ACAATTCTGTGTAGCGTTACTCA 58.122 39.130 10.88 11.81 33.30 3.41
3458 3750 5.557576 TGATGAGGATGGGAAGAAGTATG 57.442 43.478 0.00 0.00 0.00 2.39
3566 3858 5.884792 AGGGATTGTTTGTTCAAATGCAAAA 59.115 32.000 0.00 0.00 36.51 2.44
4094 4392 4.054780 CACGGGTATATGTGCTAGTTGT 57.945 45.455 0.00 0.00 0.00 3.32
4169 4467 1.597742 ACAGTAACTGCCAGCAACTG 58.402 50.000 19.85 19.85 42.53 3.16
4170 4468 0.239347 CAGTAACTGCCAGCAACTGC 59.761 55.000 12.46 0.00 42.49 4.40
4171 4469 0.890996 AGTAACTGCCAGCAACTGCC 60.891 55.000 0.00 0.00 43.38 4.85
4172 4470 1.150308 TAACTGCCAGCAACTGCCA 59.850 52.632 0.00 0.00 43.38 4.92
4173 4471 0.890542 TAACTGCCAGCAACTGCCAG 60.891 55.000 4.18 4.18 43.38 4.85
4223 4525 6.145535 GGAATCCTAAATCTTAAATGCTGCG 58.854 40.000 0.00 0.00 0.00 5.18
4243 4551 6.534436 GCTGCGAATTCAGTATCAGATATCAT 59.466 38.462 5.32 0.00 36.49 2.45
4331 4639 9.952188 GACCTCTTAAATGGCAAGAATAATTAC 57.048 33.333 0.00 0.00 31.84 1.89
4332 4640 8.621286 ACCTCTTAAATGGCAAGAATAATTACG 58.379 33.333 0.00 0.00 31.84 3.18
4340 4648 7.946655 TGGCAAGAATAATTACGACTAGATG 57.053 36.000 0.00 0.00 0.00 2.90
4418 4726 9.435688 AGAAACATACAAATAAAGGAAATTGCC 57.564 29.630 0.00 0.00 0.00 4.52
4444 4752 2.662006 GCTAGATGCAGACTGTGTGA 57.338 50.000 9.36 0.00 42.31 3.58
4445 4753 2.964740 GCTAGATGCAGACTGTGTGAA 58.035 47.619 9.36 0.00 42.31 3.18
4446 4754 3.329386 GCTAGATGCAGACTGTGTGAAA 58.671 45.455 9.36 0.00 42.31 2.69
4447 4755 3.937706 GCTAGATGCAGACTGTGTGAAAT 59.062 43.478 9.36 1.34 42.31 2.17
4450 4758 6.238049 GCTAGATGCAGACTGTGTGAAATAAG 60.238 42.308 9.36 1.57 42.31 1.73
4547 4855 3.120649 GGTTCAAGCGACTATGTTGTGTC 60.121 47.826 0.00 0.00 0.00 3.67
4596 4904 4.252242 CGATGTTTCGTGATGCGC 57.748 55.556 0.00 0.00 40.53 6.09
4672 4980 4.540359 ATTTGGCTTACACATGTGCATT 57.460 36.364 25.68 9.21 0.00 3.56
4704 5012 9.185192 CAAAGTTTACTTCCTCAAGCAATTTAG 57.815 33.333 0.00 0.00 34.61 1.85
4707 5015 7.724061 AGTTTACTTCCTCAAGCAATTTAGGAA 59.276 33.333 0.00 0.00 44.01 3.36
4710 5466 3.009723 TCCTCAAGCAATTTAGGAAGCG 58.990 45.455 0.00 0.00 35.20 4.68
4735 5491 1.202348 TGTCTCTCTGTACATGCCACG 59.798 52.381 0.00 0.00 0.00 4.94
4796 5552 6.723298 ATCATAGCAGGCTGTATATAGACC 57.277 41.667 17.16 0.78 0.00 3.85
4968 5726 0.694771 TCTGGGAAGCTGCAATCAGT 59.305 50.000 1.02 0.00 42.29 3.41
5061 5819 4.147826 CGAGATGTTATCACTGAGCAATCG 59.852 45.833 0.00 0.00 0.00 3.34
5085 5843 9.263538 TCGAACTGTTACATGTGTTAGTATTTT 57.736 29.630 9.11 0.00 0.00 1.82
5144 5902 4.841813 TGTTCTCAGGTTGAATGGGTACTA 59.158 41.667 0.00 0.00 0.00 1.82
5145 5903 5.308497 TGTTCTCAGGTTGAATGGGTACTAA 59.692 40.000 0.00 0.00 0.00 2.24
5312 6070 0.098728 GCATGTCGGCGCACTTTAAT 59.901 50.000 10.83 0.00 0.00 1.40
5313 6071 1.329292 GCATGTCGGCGCACTTTAATA 59.671 47.619 10.83 0.00 0.00 0.98
5314 6072 2.599848 GCATGTCGGCGCACTTTAATAG 60.600 50.000 10.83 0.00 0.00 1.73
5367 6126 7.512058 TGGTGCCATATTTCCATGGTATTAAAT 59.488 33.333 12.58 12.44 46.21 1.40
5426 6185 5.366829 TCATGAAGAAGCACATGAACTTG 57.633 39.130 0.00 0.00 46.10 3.16
5670 6429 5.046663 TGCATATGTTAGTTCCAGAGTCACA 60.047 40.000 4.29 0.00 0.00 3.58
5819 6591 3.744426 CGACAGTAGTTTGGGTGGTAAAG 59.256 47.826 0.00 0.00 0.00 1.85
5862 6634 5.701290 GTGCCTGATCTGTAGTTTGTTAGTT 59.299 40.000 0.00 0.00 0.00 2.24
5899 6674 6.258727 ACATAGATATCTTTGCTCGTTTGGTG 59.741 38.462 19.48 0.00 0.00 4.17
5952 6727 6.545298 AGGAGATCATTGCAATCTAAAACTCC 59.455 38.462 22.72 22.72 39.16 3.85
5977 6752 7.044496 TCCAAATCCTTTCCCTTTCTCTTAT 57.956 36.000 0.00 0.00 0.00 1.73
5978 6753 7.119387 TCCAAATCCTTTCCCTTTCTCTTATC 58.881 38.462 0.00 0.00 0.00 1.75
6103 6879 4.312443 CCTGAGCTTGCATTTTCAATTGT 58.688 39.130 5.13 0.00 0.00 2.71
6173 6949 6.475596 AGTGCGGTTTATGGTAACTACTAT 57.524 37.500 0.00 0.00 37.61 2.12
6175 6951 7.428826 AGTGCGGTTTATGGTAACTACTATAC 58.571 38.462 0.00 0.00 30.75 1.47
6267 7045 8.879759 TCTAATGAGTTAAGCTTACCAAAATCG 58.120 33.333 5.45 0.00 0.00 3.34
6277 7055 2.649531 ACCAAAATCGGTCAACCAGA 57.350 45.000 0.00 0.00 32.11 3.86
6288 7066 3.421844 GGTCAACCAGAGCTAACCATTT 58.578 45.455 0.00 0.00 41.51 2.32
6383 7165 4.365514 TGATAGTTGATGTGGGTGTGTT 57.634 40.909 0.00 0.00 0.00 3.32
6475 7257 7.549134 TGTTTATAAGATGTCCAGCAGTGTTAG 59.451 37.037 0.00 0.00 0.00 2.34
6512 7294 7.611855 ACAGTATGATTTCCTTCCTACCAAAAG 59.388 37.037 0.00 0.00 39.69 2.27
6550 7332 5.466819 CATTCAACACAAGAACATGAGCAT 58.533 37.500 0.00 0.00 0.00 3.79
6599 7381 2.099652 TAGAACTGCACGCACCAGCT 62.100 55.000 0.00 0.00 39.10 4.24
6604 7386 1.904852 CTGCACGCACCAGCTAGTTG 61.905 60.000 0.00 0.00 39.10 3.16
6631 7413 3.003740 GCTCAAGCTGATAGGGCAG 57.996 57.895 0.00 0.00 38.91 4.85
6633 7415 0.108207 CTCAAGCTGATAGGGCAGGG 59.892 60.000 0.00 0.00 36.41 4.45
6634 7416 0.326522 TCAAGCTGATAGGGCAGGGA 60.327 55.000 0.00 0.00 36.41 4.20
6635 7417 0.548031 CAAGCTGATAGGGCAGGGAA 59.452 55.000 0.00 0.00 36.41 3.97
6636 7418 1.064463 CAAGCTGATAGGGCAGGGAAA 60.064 52.381 0.00 0.00 36.41 3.13
6637 7419 0.842635 AGCTGATAGGGCAGGGAAAG 59.157 55.000 0.00 0.00 36.41 2.62
6638 7420 0.179006 GCTGATAGGGCAGGGAAAGG 60.179 60.000 0.00 0.00 36.41 3.11
6680 7462 3.626924 ACTCCCCCTCACGTGTGC 61.627 66.667 16.51 0.00 0.00 4.57
6698 7480 2.696864 CCTCCCTCAGGCCTAAACA 58.303 57.895 3.98 0.00 34.56 2.83
6704 7486 1.561542 CCTCAGGCCTAAACATGGACT 59.438 52.381 3.98 0.00 45.41 3.85
6726 7508 6.753897 CTGAAAGTGGTCTGCAATTTTAAC 57.246 37.500 0.00 0.00 0.00 2.01
6727 7509 6.463995 TGAAAGTGGTCTGCAATTTTAACT 57.536 33.333 0.00 0.00 0.00 2.24
6728 7510 6.872920 TGAAAGTGGTCTGCAATTTTAACTT 58.127 32.000 0.00 0.00 0.00 2.66
6780 7562 0.907230 ACTCAAGACCTCCTGGCTCC 60.907 60.000 0.00 0.00 36.63 4.70
6785 7567 0.178975 AGACCTCCTGGCTCCGATAG 60.179 60.000 0.00 0.00 36.63 2.08
6801 7583 2.798145 CGATAGCATGTAGAACCGCACA 60.798 50.000 0.00 0.00 0.00 4.57
6807 7589 0.394938 TGTAGAACCGCACACACCAT 59.605 50.000 0.00 0.00 0.00 3.55
6848 7631 1.380380 CTGATGGGAAAGGTGGGCC 60.380 63.158 0.00 0.00 0.00 5.80
6907 7698 5.470098 ACTTGCATACTTTGTGAGTTTCGAT 59.530 36.000 0.00 0.00 39.86 3.59
6974 7769 4.577875 TGATTCATTTGTTTTCCCCATGC 58.422 39.130 0.00 0.00 0.00 4.06
7173 7969 1.376466 TTCAGCTGTGAAGGAGCCC 59.624 57.895 14.67 0.00 37.79 5.19
7379 8175 3.691609 GTGGAAAGGTTGAATCTAGGCTG 59.308 47.826 0.00 0.00 0.00 4.85
7466 8262 2.286713 CGTCGTGAATGGTCTTTTTGCA 60.287 45.455 0.00 0.00 0.00 4.08
7563 8359 1.525995 CACCTGGTTTCAGCCACGT 60.526 57.895 0.00 0.00 39.61 4.49
7741 8537 1.347707 AGGTCTCGGATGCTGAAACAA 59.652 47.619 0.00 0.00 0.00 2.83
7761 8557 2.839486 AGTGATTCTTGGCGTTGAGA 57.161 45.000 0.00 0.00 0.00 3.27
7766 8562 5.295292 AGTGATTCTTGGCGTTGAGATATTG 59.705 40.000 0.00 0.00 0.00 1.90
7772 8568 1.014352 GCGTTGAGATATTGGCCGTT 58.986 50.000 0.00 0.00 0.00 4.44
7777 8573 5.732247 GCGTTGAGATATTGGCCGTTAAAAT 60.732 40.000 0.00 0.00 0.00 1.82
7970 8767 3.842820 CTGCCAGATGTAGACCGATATG 58.157 50.000 0.00 0.00 0.00 1.78
8071 8881 4.535781 TGGGGATGGATCAAACTGTAATG 58.464 43.478 0.00 0.00 0.00 1.90
8072 8882 4.017591 TGGGGATGGATCAAACTGTAATGT 60.018 41.667 0.00 0.00 0.00 2.71
8073 8883 5.192722 TGGGGATGGATCAAACTGTAATGTA 59.807 40.000 0.00 0.00 0.00 2.29
8075 8885 6.777580 GGGGATGGATCAAACTGTAATGTAAT 59.222 38.462 0.00 0.00 0.00 1.89
8122 8933 0.307453 GTGTTGCAATGCGAGTGTCA 59.693 50.000 0.59 0.00 0.00 3.58
8141 8955 4.284550 GTGCCTCCCACTGCCCAA 62.285 66.667 0.00 0.00 41.35 4.12
8149 8963 0.251742 CCCACTGCCCAATTCCTGAA 60.252 55.000 0.00 0.00 0.00 3.02
8150 8964 1.620524 CCCACTGCCCAATTCCTGAAT 60.621 52.381 0.00 0.00 0.00 2.57
8176 8994 2.616960 TCTTGTGCACGGTGTATGATC 58.383 47.619 13.13 0.00 0.00 2.92
8201 9019 2.752354 CCATTATTTCTGCCAACGGACA 59.248 45.455 0.00 0.00 0.00 4.02
8232 9051 3.440173 CGCTGGTGTATCATTTTGGAAGT 59.560 43.478 0.00 0.00 0.00 3.01
8245 9064 1.814169 GGAAGTTGGGATCGACGGC 60.814 63.158 0.00 0.00 32.56 5.68
8248 9067 4.814294 GTTGGGATCGACGGCGCT 62.814 66.667 5.31 0.00 37.46 5.92
8320 9139 0.954449 CTGCTGCTGTTGCTGTAGCT 60.954 55.000 14.42 0.00 41.75 3.32
8322 9141 0.952497 GCTGCTGTTGCTGTAGCTCA 60.952 55.000 5.38 4.21 42.66 4.26
8342 9164 5.680922 GCTCACACTGTTGATGATAGTAGCT 60.681 44.000 0.00 0.00 30.37 3.32
8448 9270 2.447408 TTATCGCCCTCACCTACTGA 57.553 50.000 0.00 0.00 0.00 3.41
8450 9272 0.033011 ATCGCCCTCACCTACTGACT 60.033 55.000 0.00 0.00 0.00 3.41
8451 9273 0.251653 TCGCCCTCACCTACTGACTT 60.252 55.000 0.00 0.00 0.00 3.01
8459 9281 4.204012 CTCACCTACTGACTTAGCTAGCT 58.796 47.826 23.12 23.12 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.259204 CGGTTGTGGCAGCATTGG 59.741 61.111 0.00 0.00 0.00 3.16
24 25 1.081242 GACGGTTGTGGCAGCATTG 60.081 57.895 0.00 0.00 0.00 2.82
25 26 1.518056 CTGACGGTTGTGGCAGCATT 61.518 55.000 0.00 0.00 0.00 3.56
26 27 1.968017 CTGACGGTTGTGGCAGCAT 60.968 57.895 0.00 0.00 0.00 3.79
27 28 2.591429 CTGACGGTTGTGGCAGCA 60.591 61.111 0.00 0.00 0.00 4.41
28 29 3.357079 CCTGACGGTTGTGGCAGC 61.357 66.667 0.00 0.00 0.00 5.25
29 30 2.669569 CCCTGACGGTTGTGGCAG 60.670 66.667 0.00 0.00 0.00 4.85
30 31 3.164977 TCCCTGACGGTTGTGGCA 61.165 61.111 0.00 0.00 0.00 4.92
31 32 2.358737 CTCCCTGACGGTTGTGGC 60.359 66.667 0.00 0.00 0.00 5.01
32 33 1.293498 CTCTCCCTGACGGTTGTGG 59.707 63.158 0.00 0.00 0.00 4.17
33 34 1.185618 TCCTCTCCCTGACGGTTGTG 61.186 60.000 0.00 0.00 0.00 3.33
34 35 0.900647 CTCCTCTCCCTGACGGTTGT 60.901 60.000 0.00 0.00 0.00 3.32
35 36 0.900647 ACTCCTCTCCCTGACGGTTG 60.901 60.000 0.00 0.00 0.00 3.77
36 37 0.178929 AACTCCTCTCCCTGACGGTT 60.179 55.000 0.00 0.00 0.00 4.44
37 38 0.900647 CAACTCCTCTCCCTGACGGT 60.901 60.000 0.00 0.00 0.00 4.83
38 39 1.893786 CAACTCCTCTCCCTGACGG 59.106 63.158 0.00 0.00 0.00 4.79
39 40 1.216710 GCAACTCCTCTCCCTGACG 59.783 63.158 0.00 0.00 0.00 4.35
40 41 1.194781 TGGCAACTCCTCTCCCTGAC 61.195 60.000 0.00 0.00 35.26 3.51
41 42 0.906756 CTGGCAACTCCTCTCCCTGA 60.907 60.000 0.00 0.00 35.26 3.86
42 43 1.601171 CTGGCAACTCCTCTCCCTG 59.399 63.158 0.00 0.00 35.26 4.45
43 44 1.614824 CCTGGCAACTCCTCTCCCT 60.615 63.158 0.00 0.00 35.26 4.20
44 45 1.613630 TCCTGGCAACTCCTCTCCC 60.614 63.158 0.00 0.00 35.26 4.30
45 46 1.904032 CTCCTGGCAACTCCTCTCC 59.096 63.158 0.00 0.00 35.26 3.71
46 47 1.220477 GCTCCTGGCAACTCCTCTC 59.780 63.158 0.00 0.00 41.35 3.20
47 48 1.229464 AGCTCCTGGCAACTCCTCT 60.229 57.895 0.00 0.00 44.79 3.69
48 49 1.220477 GAGCTCCTGGCAACTCCTC 59.780 63.158 0.87 0.00 44.79 3.71
49 50 0.839853 AAGAGCTCCTGGCAACTCCT 60.840 55.000 10.93 0.00 44.79 3.69
50 51 0.037447 AAAGAGCTCCTGGCAACTCC 59.963 55.000 10.93 0.00 44.79 3.85
51 52 2.770164 TAAAGAGCTCCTGGCAACTC 57.230 50.000 10.93 0.00 44.79 3.01
52 53 3.615155 GATTAAAGAGCTCCTGGCAACT 58.385 45.455 10.93 0.00 44.79 3.16
53 54 2.685388 GGATTAAAGAGCTCCTGGCAAC 59.315 50.000 10.93 0.00 44.79 4.17
54 55 2.578021 AGGATTAAAGAGCTCCTGGCAA 59.422 45.455 10.93 0.00 44.79 4.52
55 56 2.200081 AGGATTAAAGAGCTCCTGGCA 58.800 47.619 10.93 0.00 44.79 4.92
56 57 3.289407 AAGGATTAAAGAGCTCCTGGC 57.711 47.619 10.93 0.00 39.36 4.85
57 58 5.256474 TGAAAAGGATTAAAGAGCTCCTGG 58.744 41.667 10.93 0.00 39.36 4.45
58 59 6.616017 GTTGAAAAGGATTAAAGAGCTCCTG 58.384 40.000 10.93 0.00 39.36 3.86
59 60 5.412904 CGTTGAAAAGGATTAAAGAGCTCCT 59.587 40.000 10.93 0.00 41.19 3.69
60 61 5.411669 TCGTTGAAAAGGATTAAAGAGCTCC 59.588 40.000 10.93 0.00 35.54 4.70
61 62 6.402658 CCTCGTTGAAAAGGATTAAAGAGCTC 60.403 42.308 5.27 5.27 40.28 4.09
62 63 5.412904 CCTCGTTGAAAAGGATTAAAGAGCT 59.587 40.000 0.00 0.00 40.28 4.09
63 64 5.411669 TCCTCGTTGAAAAGGATTAAAGAGC 59.588 40.000 0.00 0.00 40.28 4.09
75 76 2.151202 GGCACTCATCCTCGTTGAAAA 58.849 47.619 0.00 0.00 0.00 2.29
78 79 2.671145 AGGCACTCATCCTCGTTGA 58.329 52.632 0.00 0.00 0.00 3.18
114 115 2.617274 GGTCAACCTCCTTGTGCGC 61.617 63.158 0.00 0.00 0.00 6.09
116 117 4.081050 GGGTCAACCTCCTTGTGC 57.919 61.111 0.00 0.00 35.85 4.57
144 145 0.657951 GTCTCGTCGAAGATAGCCGC 60.658 60.000 0.35 0.00 40.67 6.53
146 147 0.656785 ACGTCTCGTCGAAGATAGCC 59.343 55.000 0.35 0.00 40.67 3.93
148 149 3.092135 CACAACGTCTCGTCGAAGATAG 58.908 50.000 0.35 0.00 39.99 2.08
149 150 2.726989 GCACAACGTCTCGTCGAAGATA 60.727 50.000 0.35 0.00 39.99 1.98
187 188 0.531200 CCCACGTGTCTTCCTCCTAC 59.469 60.000 15.65 0.00 0.00 3.18
188 189 0.613853 CCCCACGTGTCTTCCTCCTA 60.614 60.000 15.65 0.00 0.00 2.94
189 190 1.913762 CCCCACGTGTCTTCCTCCT 60.914 63.158 15.65 0.00 0.00 3.69
200 201 2.203294 GTCTTTGGCACCCCACGT 60.203 61.111 0.00 0.00 41.97 4.49
211 212 1.259544 GCGTTTTCACCGCGTCTTTG 61.260 55.000 4.92 0.00 41.91 2.77
229 230 6.429385 CCTTGATCTACCTTATCCTTTCATGC 59.571 42.308 0.00 0.00 0.00 4.06
236 237 4.757692 CCCTCCTTGATCTACCTTATCCT 58.242 47.826 0.00 0.00 0.00 3.24
272 273 4.820744 ACATGTGCATCGGGGCCC 62.821 66.667 15.76 15.76 0.00 5.80
278 279 3.516806 ATGGCCACATGTGCATCG 58.483 55.556 20.81 7.87 35.57 3.84
294 295 4.457496 CGCACAGCTCCCGTCCAT 62.457 66.667 0.00 0.00 0.00 3.41
297 298 2.765250 TTCTTCGCACAGCTCCCGTC 62.765 60.000 0.00 0.00 0.00 4.79
305 306 0.094216 CACATCGCTTCTTCGCACAG 59.906 55.000 0.00 0.00 0.00 3.66
309 310 2.401195 GCCACATCGCTTCTTCGC 59.599 61.111 0.00 0.00 0.00 4.70
314 315 1.999051 CACTACGCCACATCGCTTC 59.001 57.895 0.00 0.00 0.00 3.86
350 351 1.300156 CATGCATCGTCGGATCCGT 60.300 57.895 32.15 11.81 40.74 4.69
367 368 2.123939 CATATGCCGGTTGCCCCA 60.124 61.111 1.90 0.00 40.16 4.96
373 374 0.748005 GACCACAGCATATGCCGGTT 60.748 55.000 26.20 12.67 43.38 4.44
374 375 1.153168 GACCACAGCATATGCCGGT 60.153 57.895 25.93 25.93 43.38 5.28
380 381 0.178068 GGTGACCGACCACAGCATAT 59.822 55.000 8.89 0.00 45.34 1.78
397 398 1.202698 GGCTAATGATTCGAGCTGGGT 60.203 52.381 0.00 0.00 36.43 4.51
398 399 1.071385 AGGCTAATGATTCGAGCTGGG 59.929 52.381 0.00 0.00 36.43 4.45
401 402 8.854614 ATTTTATTAGGCTAATGATTCGAGCT 57.145 30.769 26.16 2.83 36.43 4.09
470 474 2.872858 GCAGCCAAATACCAGTAGTAGC 59.127 50.000 0.00 0.00 33.42 3.58
476 480 0.112218 TGTGGCAGCCAAATACCAGT 59.888 50.000 18.28 0.00 34.18 4.00
493 497 6.006449 AGAGGTGACTTAAATCTTTGCATGT 58.994 36.000 0.00 0.00 44.43 3.21
505 509 7.086685 ACCTTAAATGGAAGAGGTGACTTAA 57.913 36.000 0.00 0.00 44.43 1.85
528 532 5.048991 CAGATTGGTACAGTTGGGTTTACAC 60.049 44.000 0.00 0.00 42.39 2.90
529 533 5.067273 CAGATTGGTACAGTTGGGTTTACA 58.933 41.667 0.00 0.00 42.39 2.41
534 538 4.289672 AGATTCAGATTGGTACAGTTGGGT 59.710 41.667 0.00 0.00 42.39 4.51
560 564 8.046708 AGGTTCAGTTATGCAAGAACACATATA 58.953 33.333 15.07 0.00 41.49 0.86
561 565 6.886459 AGGTTCAGTTATGCAAGAACACATAT 59.114 34.615 15.07 0.00 41.49 1.78
579 583 9.556030 GGAAGATAATTTTCGTTTAAGGTTCAG 57.444 33.333 0.00 0.00 0.00 3.02
588 592 7.761038 AAGACTGGGAAGATAATTTTCGTTT 57.239 32.000 0.00 0.00 0.00 3.60
608 612 5.985781 TCATTTGCTCACTTCGTAAAAGAC 58.014 37.500 0.00 0.00 0.00 3.01
622 627 7.396540 TCCTCCTAGAATTTTTCATTTGCTC 57.603 36.000 0.00 0.00 0.00 4.26
633 638 3.000727 CGCAACGTTCCTCCTAGAATTT 58.999 45.455 0.00 0.00 0.00 1.82
674 679 0.179121 CGCCGCTGGACAAGTATGTA 60.179 55.000 0.00 0.00 40.74 2.29
675 680 1.447838 CGCCGCTGGACAAGTATGT 60.448 57.895 0.00 0.00 44.25 2.29
676 681 2.813179 GCGCCGCTGGACAAGTATG 61.813 63.158 0.00 0.00 0.00 2.39
749 793 2.758327 TGGATACGGCGGAGTGCT 60.758 61.111 13.24 0.00 45.43 4.40
759 806 1.464376 ATCTGCCGGTCCTGGATACG 61.464 60.000 14.42 14.42 42.51 3.06
775 822 4.271816 AATCGAGGCGCGCGATCT 62.272 61.111 37.18 28.70 44.62 2.75
824 878 2.240500 GGAGACATCGCATCGCCAC 61.241 63.158 0.00 0.00 36.17 5.01
873 927 1.344438 CCTTTTGCCTTTTGGGTCTCC 59.656 52.381 0.00 0.00 40.82 3.71
920 974 0.389817 CGCGGTTGGTCATTCTCTGA 60.390 55.000 0.00 0.00 0.00 3.27
956 1010 4.690719 TTACGCGTGGTGGGCAGG 62.691 66.667 24.59 0.00 0.00 4.85
1081 1138 3.124686 CCGTGGTTTTGGTGGTGG 58.875 61.111 0.00 0.00 0.00 4.61
1136 1193 2.431942 GTGGACGGCGAACACGAT 60.432 61.111 16.62 0.00 34.93 3.73
1216 1273 2.370445 ATGGGTCTGAGCTTCGGGG 61.370 63.158 6.83 0.00 0.00 5.73
1426 1483 3.214253 CAGATCGAGCTGCCCAGA 58.786 61.111 18.91 0.00 0.00 3.86
1656 1713 2.743538 GCGCTCTCATGGTGTGCA 60.744 61.111 0.00 0.00 42.37 4.57
1733 1790 5.361427 TGAAACAAAGTCAGTTATCACGGA 58.639 37.500 0.00 0.00 0.00 4.69
1839 1902 6.928979 TTCCGTACTCTTCAATTTTGTGAA 57.071 33.333 0.00 0.00 36.15 3.18
1934 2000 7.265599 TCCTCTAATTCCTCACAATTTACCA 57.734 36.000 0.00 0.00 0.00 3.25
1987 2053 2.359900 CGGAGTAAGATTGCAAAGCCT 58.640 47.619 1.71 0.00 27.83 4.58
2022 2088 3.005472 CACGAGTGGAGTGAAAAGAGGTA 59.995 47.826 0.00 0.00 41.83 3.08
2192 2258 3.451526 GAACGTGCTATTAGTACCACCC 58.548 50.000 6.37 0.00 0.00 4.61
2868 3136 7.885009 TGATTCCTTCTTAAATCATGCATGA 57.115 32.000 30.47 30.47 37.06 3.07
2963 3231 0.251653 TCGAGACTAACACCAGCCCT 60.252 55.000 0.00 0.00 0.00 5.19
3008 3277 9.237187 GATTTCTTCTCAAATAAGTTTCCCTCT 57.763 33.333 0.00 0.00 0.00 3.69
3458 3750 4.333926 GGTCTATGTGCTCCAGTTGAAATC 59.666 45.833 0.00 0.00 0.00 2.17
4018 4316 5.056480 CCGAAATATCTAGCAACATGTCCA 58.944 41.667 0.00 0.00 0.00 4.02
4117 4415 7.890655 ACTATGGCTTAGATCCTTTTCTTTTGT 59.109 33.333 13.76 0.00 0.00 2.83
4169 4467 0.819259 TGTTGTCAGAGGTTGCTGGC 60.819 55.000 0.00 0.00 40.82 4.85
4170 4468 1.679139 TTGTTGTCAGAGGTTGCTGG 58.321 50.000 0.00 0.00 36.55 4.85
4171 4469 3.607775 CGATTTGTTGTCAGAGGTTGCTG 60.608 47.826 0.00 0.00 37.24 4.41
4172 4470 2.549754 CGATTTGTTGTCAGAGGTTGCT 59.450 45.455 0.00 0.00 0.00 3.91
4173 4471 2.290641 ACGATTTGTTGTCAGAGGTTGC 59.709 45.455 0.00 0.00 0.00 4.17
4243 4551 3.706594 GGGGAGAGAATACACATCACTCA 59.293 47.826 0.00 0.00 36.58 3.41
4249 4557 5.467738 TCATACAGGGGAGAGAATACACAT 58.532 41.667 0.00 0.00 0.00 3.21
4303 4611 9.920946 AATTATTCTTGCCATTTAAGAGGTCTA 57.079 29.630 0.00 0.00 35.74 2.59
4307 4615 8.836413 TCGTAATTATTCTTGCCATTTAAGAGG 58.164 33.333 0.00 0.00 35.74 3.69
4309 4617 9.391006 AGTCGTAATTATTCTTGCCATTTAAGA 57.609 29.630 0.00 0.00 32.64 2.10
4445 4753 9.675464 TCCCACAAATTATTCGTTCTACTTATT 57.325 29.630 0.00 0.00 0.00 1.40
4446 4754 9.675464 TTCCCACAAATTATTCGTTCTACTTAT 57.325 29.630 0.00 0.00 0.00 1.73
4447 4755 9.158233 CTTCCCACAAATTATTCGTTCTACTTA 57.842 33.333 0.00 0.00 0.00 2.24
4450 4758 7.373778 ACTTCCCACAAATTATTCGTTCTAC 57.626 36.000 0.00 0.00 0.00 2.59
4547 4855 8.755941 CAATATGAGTGACCTATTTGAACTACG 58.244 37.037 0.00 0.00 0.00 3.51
4596 4904 5.368989 CAGTTACCAAATAGGGGCTCTAAG 58.631 45.833 0.00 0.00 43.89 2.18
4672 4980 4.724399 TGAGGAAGTAAACTTTGGCATCA 58.276 39.130 0.00 0.00 36.11 3.07
4704 5012 0.885196 AGAGAGACACAGACGCTTCC 59.115 55.000 0.00 0.00 0.00 3.46
4707 5015 1.807742 GTACAGAGAGACACAGACGCT 59.192 52.381 0.00 0.00 0.00 5.07
4710 5466 3.506810 GCATGTACAGAGAGACACAGAC 58.493 50.000 0.33 0.00 0.00 3.51
4968 5726 8.556589 TCCATGGAAGATAGGAATTTGAAACTA 58.443 33.333 13.46 0.00 0.00 2.24
4988 5746 3.879295 CACATAGGCTTACAACTCCATGG 59.121 47.826 4.97 4.97 0.00 3.66
5085 5843 7.037153 AGGTAAAACTCCCCACACTGATTATAA 60.037 37.037 0.00 0.00 0.00 0.98
5144 5902 9.070179 GCTAATAGTAGAACTAGGCTCTTACTT 57.930 37.037 0.38 0.00 33.66 2.24
5145 5903 8.219178 TGCTAATAGTAGAACTAGGCTCTTACT 58.781 37.037 0.38 6.67 33.66 2.24
5237 5995 1.407258 GTGCTGCACCCAGTTTTACAA 59.593 47.619 21.78 0.00 41.26 2.41
5670 6429 7.610305 ACAACATTAGGACGATCAGGTAAATTT 59.390 33.333 0.00 0.00 0.00 1.82
5819 6591 6.036517 CAGGCACATAACTCTCAAGTTGATAC 59.963 42.308 5.91 0.00 45.37 2.24
5899 6674 1.678101 GCAGCAGATATGGTCCCAAAC 59.322 52.381 0.00 0.00 0.00 2.93
5952 6727 4.928263 AGAGAAAGGGAAAGGATTTGGAG 58.072 43.478 0.00 0.00 39.27 3.86
5977 6752 7.615757 TCTGTAGGAGATGTAGAACAGAAATGA 59.384 37.037 0.74 0.00 40.10 2.57
5978 6753 7.776107 TCTGTAGGAGATGTAGAACAGAAATG 58.224 38.462 0.74 0.00 40.10 2.32
6267 7045 2.789409 ATGGTTAGCTCTGGTTGACC 57.211 50.000 0.00 0.00 0.00 4.02
6288 7066 3.688235 TGATTGATGAGACATGCCACAA 58.312 40.909 0.00 0.00 0.00 3.33
6383 7165 7.732025 TGTTCTGATAAGGAGTTACAAACAGA 58.268 34.615 0.00 0.00 0.00 3.41
6512 7294 7.653647 TGTGTTGAATGGGAAACATAAGTTAC 58.346 34.615 0.00 0.00 39.40 2.50
6550 7332 0.251354 GGCAGAACTGAGCAGATGGA 59.749 55.000 4.21 0.00 0.00 3.41
6629 7411 0.753111 GCATAGCCCACCTTTCCCTG 60.753 60.000 0.00 0.00 0.00 4.45
6631 7413 0.106015 ATGCATAGCCCACCTTTCCC 60.106 55.000 0.00 0.00 0.00 3.97
6633 7415 5.334879 CGTATAAATGCATAGCCCACCTTTC 60.335 44.000 0.00 0.00 0.00 2.62
6634 7416 4.518970 CGTATAAATGCATAGCCCACCTTT 59.481 41.667 0.00 0.00 0.00 3.11
6635 7417 4.072131 CGTATAAATGCATAGCCCACCTT 58.928 43.478 0.00 0.00 0.00 3.50
6636 7418 3.072476 ACGTATAAATGCATAGCCCACCT 59.928 43.478 0.00 0.00 0.00 4.00
6637 7419 3.408634 ACGTATAAATGCATAGCCCACC 58.591 45.455 0.00 0.00 0.00 4.61
6638 7420 4.062293 TGACGTATAAATGCATAGCCCAC 58.938 43.478 0.00 0.00 0.00 4.61
6680 7462 1.133976 CATGTTTAGGCCTGAGGGAGG 60.134 57.143 17.99 0.00 46.13 4.30
6698 7480 1.421268 TGCAGACCACTTTCAGTCCAT 59.579 47.619 0.00 0.00 33.29 3.41
6704 7486 6.463995 AGTTAAAATTGCAGACCACTTTCA 57.536 33.333 0.00 0.00 0.00 2.69
6724 7506 7.589587 GCTGGCGCAATTTAAAAATAAAAAGTT 59.410 29.630 10.83 0.00 35.78 2.66
6725 7507 7.075121 GCTGGCGCAATTTAAAAATAAAAAGT 58.925 30.769 10.83 0.00 35.78 2.66
6726 7508 6.522855 GGCTGGCGCAATTTAAAAATAAAAAG 59.477 34.615 10.83 0.00 38.10 2.27
6727 7509 6.374578 GGCTGGCGCAATTTAAAAATAAAAA 58.625 32.000 10.83 0.00 38.10 1.94
6728 7510 5.389935 CGGCTGGCGCAATTTAAAAATAAAA 60.390 36.000 11.55 0.00 38.10 1.52
6780 7562 1.787155 GTGCGGTTCTACATGCTATCG 59.213 52.381 0.00 0.00 0.00 2.92
6785 7567 0.165944 GTGTGTGCGGTTCTACATGC 59.834 55.000 0.00 0.00 0.00 4.06
6796 7578 0.884259 TGAACTGGATGGTGTGTGCG 60.884 55.000 0.00 0.00 0.00 5.34
6801 7583 0.850100 TTGGGTGAACTGGATGGTGT 59.150 50.000 0.00 0.00 0.00 4.16
6807 7589 1.214175 TGAGCTTTTGGGTGAACTGGA 59.786 47.619 0.00 0.00 0.00 3.86
6848 7631 8.334632 TCAATACTGTTGACGTATAAATGCATG 58.665 33.333 0.00 0.00 0.00 4.06
6883 7674 4.814234 TCGAAACTCACAAAGTATGCAAGT 59.186 37.500 0.00 0.00 37.17 3.16
6924 7715 7.174946 TGGACAAGAATGATTTCACTCCTTAAC 59.825 37.037 0.00 0.00 34.08 2.01
6974 7769 8.706936 GTCATATCTGTTACAGACAAGCATATG 58.293 37.037 17.92 18.05 43.63 1.78
7173 7969 3.922171 ATTTCTAAGGGACTGAGCAGG 57.078 47.619 2.20 0.00 40.86 4.85
7263 8059 1.526887 GCACGATCCCATCCTCCAA 59.473 57.895 0.00 0.00 0.00 3.53
7379 8175 2.926778 ATACCTCCTGCTCATTGCTC 57.073 50.000 0.00 0.00 43.37 4.26
7466 8262 1.003928 TGCTCCTTCATGCTCATGTGT 59.996 47.619 9.41 0.00 39.72 3.72
7563 8359 8.908786 ATTATCTCAAGAACTTTTGTGTCTGA 57.091 30.769 0.00 0.00 0.00 3.27
7741 8537 3.126001 TCTCAACGCCAAGAATCACTT 57.874 42.857 0.00 0.00 39.70 3.16
7772 8568 2.080693 ACAATGCTCGTGGCGATTTTA 58.919 42.857 0.00 0.00 45.43 1.52
7777 8573 3.252964 CAACAATGCTCGTGGCGA 58.747 55.556 0.00 0.00 45.43 5.54
7852 8649 2.965831 AGAGTGCTCTCCAACTGTAACA 59.034 45.455 12.06 0.00 41.26 2.41
7880 8677 2.675844 CGGGCGTGACTGAATGAATAAA 59.324 45.455 0.00 0.00 0.00 1.40
8046 8843 0.929244 AGTTTGATCCATCCCCAGGG 59.071 55.000 0.00 0.00 0.00 4.45
8071 8881 8.379902 CGTTCAAGCCCAAATGATAAAAATTAC 58.620 33.333 0.00 0.00 0.00 1.89
8072 8882 8.091449 ACGTTCAAGCCCAAATGATAAAAATTA 58.909 29.630 0.00 0.00 0.00 1.40
8073 8883 6.934083 ACGTTCAAGCCCAAATGATAAAAATT 59.066 30.769 0.00 0.00 0.00 1.82
8075 8885 5.848406 ACGTTCAAGCCCAAATGATAAAAA 58.152 33.333 0.00 0.00 0.00 1.94
8083 8893 3.620821 CACAAAAACGTTCAAGCCCAAAT 59.379 39.130 0.00 0.00 0.00 2.32
8122 8933 3.971702 GGGCAGTGGGAGGCACTT 61.972 66.667 0.00 0.00 41.55 3.16
8141 8955 6.623549 CGTGCACAAGAATGTTATTCAGGAAT 60.624 38.462 18.64 0.00 37.82 3.01
8149 8963 3.146066 ACACCGTGCACAAGAATGTTAT 58.854 40.909 18.64 0.00 37.82 1.89
8150 8964 2.566913 ACACCGTGCACAAGAATGTTA 58.433 42.857 18.64 0.00 37.82 2.41
8176 8994 2.480073 CGTTGGCAGAAATAATGGGCAG 60.480 50.000 0.00 0.00 37.13 4.85
8212 9031 5.336690 CCCAACTTCCAAAATGATACACCAG 60.337 44.000 0.00 0.00 0.00 4.00
8213 9032 4.526262 CCCAACTTCCAAAATGATACACCA 59.474 41.667 0.00 0.00 0.00 4.17
8232 9051 4.812476 CAGCGCCGTCGATCCCAA 62.812 66.667 2.29 0.00 38.10 4.12
8245 9064 1.421410 GCGTTATGACTGACCCAGCG 61.421 60.000 0.00 0.00 34.37 5.18
8248 9067 1.447140 GCGCGTTATGACTGACCCA 60.447 57.895 8.43 0.00 0.00 4.51
8320 9139 5.921962 AGCTACTATCATCAACAGTGTGA 57.078 39.130 0.00 0.00 0.00 3.58
8322 9141 7.786030 ACAATAGCTACTATCATCAACAGTGT 58.214 34.615 0.00 0.00 0.00 3.55
8342 9164 4.283337 TGATACCGTCCAGGAAGACAATA 58.717 43.478 3.53 0.00 45.00 1.90
8448 9270 1.819288 TCAAGACGCAGCTAGCTAAGT 59.181 47.619 18.86 19.62 42.61 2.24
8450 9272 3.526931 ATTCAAGACGCAGCTAGCTAA 57.473 42.857 18.86 5.80 42.61 3.09
8451 9273 3.526931 AATTCAAGACGCAGCTAGCTA 57.473 42.857 18.86 0.00 42.61 3.32
8459 9281 1.804151 CTCCGGAAAATTCAAGACGCA 59.196 47.619 5.23 0.00 0.00 5.24
8486 9308 3.901797 AACGCCGGCCTTCTTCCAG 62.902 63.158 23.46 5.65 0.00 3.86
8509 9332 4.639171 GCCCACAACCCAAACGCG 62.639 66.667 3.53 3.53 0.00 6.01
8957 9780 1.667722 CGGATGAGCATGGGATCGA 59.332 57.895 0.00 0.00 30.14 3.59
8965 9788 0.390492 TCAAGATCGCGGATGAGCAT 59.610 50.000 6.13 0.00 36.85 3.79


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

AutoCloner maintained by Alex Coulton.