Multiple sequence alignment - TraesCS5B01G163200

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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 TraesCS5B01G163200 chr5B 100.000 5506 0 0 1 5506 301205600 301200095 0.000000e+00 10168.0
1 TraesCS5B01G163200 chr5B 100.000 30 0 0 519 548 436556886 436556857 7.710000e-04 56.5
2 TraesCS5B01G163200 chr5D 92.347 3110 149 33 94 3185 267084276 267081238 0.000000e+00 4342.0
3 TraesCS5B01G163200 chr5D 93.305 1180 30 9 3899 5040 267080392 267079224 0.000000e+00 1696.0
4 TraesCS5B01G163200 chr5D 95.645 643 15 3 3169 3798 267081222 267080580 0.000000e+00 1020.0
5 TraesCS5B01G163200 chr5D 93.684 475 17 6 5035 5496 267079196 267078722 0.000000e+00 699.0
6 TraesCS5B01G163200 chr5A 93.459 2171 85 21 1036 3185 353598878 353601012 0.000000e+00 3169.0
7 TraesCS5B01G163200 chr5A 93.265 1648 44 23 3421 5040 353601334 353602942 0.000000e+00 2366.0
8 TraesCS5B01G163200 chr5A 89.759 498 12 12 5035 5496 353602970 353603464 7.890000e-168 601.0
9 TraesCS5B01G163200 chr5A 91.562 320 21 5 721 1038 353597151 353597466 2.360000e-118 436.0
10 TraesCS5B01G163200 chr5A 98.113 212 4 0 3169 3380 353601028 353601239 2.420000e-98 370.0
11 TraesCS5B01G163200 chr5A 88.832 197 22 0 2549 2745 666870188 666870384 5.510000e-60 243.0
12 TraesCS5B01G163200 chr5A 86.190 210 29 0 2546 2755 35158563 35158354 1.540000e-55 228.0
13 TraesCS5B01G163200 chr5A 90.323 93 5 2 3794 3886 560883478 560883390 9.690000e-23 119.0
14 TraesCS5B01G163200 chr2A 90.306 196 19 0 2550 2745 389187752 389187947 1.970000e-64 257.0
15 TraesCS5B01G163200 chr2A 91.398 93 4 2 3794 3886 65084815 65084903 2.080000e-24 124.0
16 TraesCS5B01G163200 chr7D 88.780 205 22 1 2542 2745 350957710 350957506 3.290000e-62 250.0
17 TraesCS5B01G163200 chr1A 89.231 195 21 0 2551 2745 20098305 20098499 1.530000e-60 244.0
18 TraesCS5B01G163200 chr1A 89.231 195 21 0 2551 2745 337147292 337147486 1.530000e-60 244.0
19 TraesCS5B01G163200 chr1A 88.462 104 7 2 3785 3888 335022185 335022283 2.690000e-23 121.0
20 TraesCS5B01G163200 chr1A 78.322 143 22 7 737 876 314438085 314437949 3.530000e-12 84.2
21 TraesCS5B01G163200 chr6B 88.177 203 22 2 2548 2748 147390466 147390264 1.980000e-59 241.0
22 TraesCS5B01G163200 chr3A 88.000 200 24 0 2546 2745 192874146 192874345 2.560000e-58 237.0
23 TraesCS5B01G163200 chr3A 83.568 213 35 0 2541 2753 81105699 81105487 3.360000e-47 200.0
24 TraesCS5B01G163200 chr3A 83.810 210 34 0 2551 2760 670412217 670412008 3.360000e-47 200.0
25 TraesCS5B01G163200 chr3A 90.323 93 5 2 3794 3886 657439697 657439785 9.690000e-23 119.0
26 TraesCS5B01G163200 chr1B 86.869 198 26 0 2548 2745 43189539 43189736 7.180000e-54 222.0
27 TraesCS5B01G163200 chr4A 85.514 214 28 3 2542 2755 112536114 112535904 2.580000e-53 220.0
28 TraesCS5B01G163200 chr7A 85.572 201 29 0 2545 2745 733452860 733453060 1.550000e-50 211.0
29 TraesCS5B01G163200 chr4B 79.468 263 46 8 194 452 645054339 645054597 4.380000e-41 180.0
30 TraesCS5B01G163200 chr2D 94.444 90 4 1 3793 3882 208540232 208540144 2.670000e-28 137.0
31 TraesCS5B01G163200 chr2D 77.114 201 27 12 676 872 453758816 453758631 1.260000e-16 99.0
32 TraesCS5B01G163200 chr2D 85.526 76 6 5 366 440 115938732 115938661 2.130000e-09 75.0
33 TraesCS5B01G163200 chr2B 90.196 102 5 3 3788 3888 142869612 142869515 1.610000e-25 128.0
34 TraesCS5B01G163200 chr2B 92.045 88 6 1 3795 3882 262903729 262903643 7.490000e-24 122.0
35 TraesCS5B01G163200 chr6A 90.323 93 5 2 3794 3886 508000861 508000949 9.690000e-23 119.0
36 TraesCS5B01G163200 chr4D 100.000 28 0 0 2013 2040 435644878 435644905 1.000000e-02 52.8
37 TraesCS5B01G163200 chr3B 100.000 28 0 0 2060 2087 3305815 3305842 1.000000e-02 52.8
38 TraesCS5B01G163200 chr3B 100.000 28 0 0 2060 2087 5411713 5411686 1.000000e-02 52.8


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 TraesCS5B01G163200 chr5B 301200095 301205600 5505 True 10168.00 10168 100.00000 1 5506 1 chr5B.!!$R1 5505
1 TraesCS5B01G163200 chr5D 267078722 267084276 5554 True 1939.25 4342 93.74525 94 5496 4 chr5D.!!$R1 5402
2 TraesCS5B01G163200 chr5A 353597151 353603464 6313 False 1388.40 3169 93.23160 721 5496 5 chr5A.!!$F2 4775

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
26 27 0.243636 GCAACGGGATCCACCAAAAG 59.756 55.000 15.23 0.00 41.2 2.27 F
1141 2558 0.030603 ATCCTCTTCTCCCTCCACCC 60.031 60.000 0.00 0.00 0.0 4.61 F
1580 3025 0.034896 GGTGGTGGTGACGTGATTCT 59.965 55.000 0.00 0.00 0.0 2.40 F
2227 3677 0.960364 CCGTGGGATTGTGAAGTGGG 60.960 60.000 0.00 0.00 0.0 4.61 F
3584 5130 1.888512 GGTGAACATGTGGCACAGAAT 59.111 47.619 26.04 13.57 41.8 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 2736 0.396556 GTGTCCTCCTCCTCCTCCTC 60.397 65.000 0.00 0.0 0.00 3.71 R
2175 3621 0.320073 TGCCCGCACACAAGTACTAC 60.320 55.000 0.00 0.0 0.00 2.73 R
3527 5072 0.606401 CACTTCACGGGATGGCAACT 60.606 55.000 5.46 0.0 37.61 3.16 R
3875 5511 3.107601 TGCCATCTAGCAAGTTACTCCT 58.892 45.455 0.00 0.0 40.56 3.69 R
5351 7107 0.032615 TCTGTGGGGTTTTGGTGCTT 60.033 50.000 0.00 0.0 0.00 3.91 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 2.825836 CTGGCTGGCAACGGGATC 60.826 66.667 5.14 0.00 45.89 3.36
18 19 4.424711 TGGCTGGCAACGGGATCC 62.425 66.667 1.92 1.92 45.89 3.36
19 20 4.424711 GGCTGGCAACGGGATCCA 62.425 66.667 15.23 0.00 45.89 3.41
20 21 3.134127 GCTGGCAACGGGATCCAC 61.134 66.667 15.23 1.85 45.89 4.02
21 22 2.438434 CTGGCAACGGGATCCACC 60.438 66.667 15.23 7.05 40.24 4.61
22 23 3.253061 TGGCAACGGGATCCACCA 61.253 61.111 15.23 9.66 41.20 4.17
23 24 2.034999 GGCAACGGGATCCACCAA 59.965 61.111 15.23 0.00 41.20 3.67
24 25 1.605165 GGCAACGGGATCCACCAAA 60.605 57.895 15.23 0.00 41.20 3.28
25 26 1.182385 GGCAACGGGATCCACCAAAA 61.182 55.000 15.23 0.00 41.20 2.44
26 27 0.243636 GCAACGGGATCCACCAAAAG 59.756 55.000 15.23 0.00 41.20 2.27
27 28 0.887933 CAACGGGATCCACCAAAAGG 59.112 55.000 15.23 0.00 41.20 3.11
28 29 0.774908 AACGGGATCCACCAAAAGGA 59.225 50.000 15.23 0.00 41.20 3.36
29 30 0.774908 ACGGGATCCACCAAAAGGAA 59.225 50.000 15.23 0.00 38.93 3.36
30 31 1.146152 ACGGGATCCACCAAAAGGAAA 59.854 47.619 15.23 0.00 38.93 3.13
31 32 2.243810 CGGGATCCACCAAAAGGAAAA 58.756 47.619 15.23 0.00 38.93 2.29
32 33 2.630580 CGGGATCCACCAAAAGGAAAAA 59.369 45.455 15.23 0.00 38.93 1.94
54 55 5.841957 AAAACTCAAAGATGCTCACAACT 57.158 34.783 0.00 0.00 0.00 3.16
55 56 5.429957 AAACTCAAAGATGCTCACAACTC 57.570 39.130 0.00 0.00 0.00 3.01
56 57 4.348863 ACTCAAAGATGCTCACAACTCT 57.651 40.909 0.00 0.00 0.00 3.24
57 58 5.474578 ACTCAAAGATGCTCACAACTCTA 57.525 39.130 0.00 0.00 0.00 2.43
58 59 6.047511 ACTCAAAGATGCTCACAACTCTAT 57.952 37.500 0.00 0.00 0.00 1.98
59 60 6.471146 ACTCAAAGATGCTCACAACTCTATT 58.529 36.000 0.00 0.00 0.00 1.73
60 61 6.593382 ACTCAAAGATGCTCACAACTCTATTC 59.407 38.462 0.00 0.00 0.00 1.75
61 62 5.877012 TCAAAGATGCTCACAACTCTATTCC 59.123 40.000 0.00 0.00 0.00 3.01
62 63 5.690464 AAGATGCTCACAACTCTATTCCT 57.310 39.130 0.00 0.00 0.00 3.36
63 64 6.798427 AAGATGCTCACAACTCTATTCCTA 57.202 37.500 0.00 0.00 0.00 2.94
64 65 6.403866 AGATGCTCACAACTCTATTCCTAG 57.596 41.667 0.00 0.00 0.00 3.02
65 66 5.304101 AGATGCTCACAACTCTATTCCTAGG 59.696 44.000 0.82 0.82 0.00 3.02
66 67 3.706594 TGCTCACAACTCTATTCCTAGGG 59.293 47.826 9.46 0.00 0.00 3.53
67 68 3.961408 GCTCACAACTCTATTCCTAGGGA 59.039 47.826 9.46 0.00 0.00 4.20
68 69 4.038642 GCTCACAACTCTATTCCTAGGGAG 59.961 50.000 9.46 9.98 31.21 4.30
69 70 5.205056 CTCACAACTCTATTCCTAGGGAGT 58.795 45.833 9.46 10.66 40.24 3.85
70 71 5.590818 TCACAACTCTATTCCTAGGGAGTT 58.409 41.667 19.71 19.71 45.96 3.01
71 72 6.023603 TCACAACTCTATTCCTAGGGAGTTT 58.976 40.000 21.76 13.77 43.65 2.66
72 73 7.186972 TCACAACTCTATTCCTAGGGAGTTTA 58.813 38.462 21.76 11.92 43.65 2.01
73 74 7.342284 TCACAACTCTATTCCTAGGGAGTTTAG 59.658 40.741 21.76 17.76 43.65 1.85
74 75 7.124448 CACAACTCTATTCCTAGGGAGTTTAGT 59.876 40.741 21.76 16.64 43.65 2.24
75 76 7.124448 ACAACTCTATTCCTAGGGAGTTTAGTG 59.876 40.741 21.76 16.10 43.65 2.74
76 77 6.743788 ACTCTATTCCTAGGGAGTTTAGTGT 58.256 40.000 9.46 3.65 35.82 3.55
77 78 7.190501 ACTCTATTCCTAGGGAGTTTAGTGTT 58.809 38.462 9.46 0.00 35.82 3.32
78 79 7.679025 ACTCTATTCCTAGGGAGTTTAGTGTTT 59.321 37.037 9.46 0.00 35.82 2.83
79 80 7.848128 TCTATTCCTAGGGAGTTTAGTGTTTG 58.152 38.462 9.46 0.00 31.21 2.93
80 81 5.899631 TTCCTAGGGAGTTTAGTGTTTGT 57.100 39.130 9.46 0.00 31.21 2.83
81 82 5.899631 TCCTAGGGAGTTTAGTGTTTGTT 57.100 39.130 9.46 0.00 0.00 2.83
82 83 6.999705 TCCTAGGGAGTTTAGTGTTTGTTA 57.000 37.500 9.46 0.00 0.00 2.41
83 84 7.563724 TCCTAGGGAGTTTAGTGTTTGTTAT 57.436 36.000 9.46 0.00 0.00 1.89
84 85 7.391620 TCCTAGGGAGTTTAGTGTTTGTTATG 58.608 38.462 9.46 0.00 0.00 1.90
85 86 7.016858 TCCTAGGGAGTTTAGTGTTTGTTATGT 59.983 37.037 9.46 0.00 0.00 2.29
86 87 7.664318 CCTAGGGAGTTTAGTGTTTGTTATGTT 59.336 37.037 0.00 0.00 0.00 2.71
87 88 7.506328 AGGGAGTTTAGTGTTTGTTATGTTC 57.494 36.000 0.00 0.00 0.00 3.18
88 89 7.287810 AGGGAGTTTAGTGTTTGTTATGTTCT 58.712 34.615 0.00 0.00 0.00 3.01
89 90 7.444487 AGGGAGTTTAGTGTTTGTTATGTTCTC 59.556 37.037 0.00 0.00 0.00 2.87
90 91 7.444487 GGGAGTTTAGTGTTTGTTATGTTCTCT 59.556 37.037 0.00 0.00 0.00 3.10
91 92 9.485206 GGAGTTTAGTGTTTGTTATGTTCTCTA 57.515 33.333 0.00 0.00 0.00 2.43
130 131 3.739810 GGTAAGTTCGCTTTCTCGTCTTT 59.260 43.478 0.00 0.00 38.57 2.52
140 141 5.080068 GCTTTCTCGTCTTTATGGTTTTCG 58.920 41.667 0.00 0.00 0.00 3.46
163 164 3.007635 CTCCGTCCCTTTATGTTGGTTC 58.992 50.000 0.00 0.00 0.00 3.62
175 176 7.177392 CCTTTATGTTGGTTCTTTCCTCTTCAT 59.823 37.037 0.00 0.00 0.00 2.57
186 187 7.079451 TCTTTCCTCTTCATGTCCTTAGTTT 57.921 36.000 0.00 0.00 0.00 2.66
188 189 6.433847 TTCCTCTTCATGTCCTTAGTTTGA 57.566 37.500 0.00 0.00 0.00 2.69
208 209 9.471084 AGTTTGAAATAATCTAAACCAAAACGG 57.529 29.630 0.00 0.00 42.50 4.44
232 233 7.094549 CGGTATTTTCATTTCCTTGTCTTACCA 60.095 37.037 0.00 0.00 0.00 3.25
244 245 7.466804 TCCTTGTCTTACCAAAAACCATATCT 58.533 34.615 0.00 0.00 0.00 1.98
268 269 7.504922 TTGCATTAACGCAATCAATTCTTAC 57.495 32.000 4.57 0.00 46.61 2.34
318 319 9.309516 CAATGGAATCAAATCAAATCTTACCAG 57.690 33.333 0.00 0.00 0.00 4.00
328 329 4.534500 TCAAATCTTACCAGGCCTCAACTA 59.466 41.667 0.00 0.00 0.00 2.24
329 330 4.489306 AATCTTACCAGGCCTCAACTAC 57.511 45.455 0.00 0.00 0.00 2.73
332 333 3.844211 TCTTACCAGGCCTCAACTACAAT 59.156 43.478 0.00 0.00 0.00 2.71
336 337 4.993028 ACCAGGCCTCAACTACAATAAAA 58.007 39.130 0.00 0.00 0.00 1.52
337 338 4.765339 ACCAGGCCTCAACTACAATAAAAC 59.235 41.667 0.00 0.00 0.00 2.43
352 353 6.172630 ACAATAAAACTTTCCATGCAATCCC 58.827 36.000 0.00 0.00 0.00 3.85
391 394 7.227049 TCAACTCAAATCTTATCAAAACCCC 57.773 36.000 0.00 0.00 0.00 4.95
404 407 9.771534 CTTATCAAAACCCCAACTAAATGAAAA 57.228 29.630 0.00 0.00 0.00 2.29
408 411 7.766738 TCAAAACCCCAACTAAATGAAAACTTC 59.233 33.333 0.00 0.00 0.00 3.01
415 418 6.204882 CCAACTAAATGAAAACTTCTCCTCGT 59.795 38.462 0.00 0.00 0.00 4.18
421 424 4.377897 TGAAAACTTCTCCTCGTCTTTCC 58.622 43.478 0.00 0.00 0.00 3.13
425 428 3.090790 ACTTCTCCTCGTCTTTCCCTAC 58.909 50.000 0.00 0.00 0.00 3.18
426 429 2.140839 TCTCCTCGTCTTTCCCTACC 57.859 55.000 0.00 0.00 0.00 3.18
585 588 4.023193 AGTTGGGCTGTTTTTCTTATCACG 60.023 41.667 0.00 0.00 0.00 4.35
604 607 7.630242 ATCACGCATAATTTATATTGGAGGG 57.370 36.000 0.00 0.00 0.00 4.30
626 629 7.646884 AGGGATGAGAGTTTCTGGATATTTTT 58.353 34.615 0.00 0.00 0.00 1.94
645 648 4.668138 TTTTTGGACCCCAATAGCTAGT 57.332 40.909 0.00 0.00 43.55 2.57
649 652 3.393687 TGGACCCCAATAGCTAGTGAAT 58.606 45.455 22.20 7.10 0.00 2.57
655 658 4.202050 CCCCAATAGCTAGTGAATGTTTGC 60.202 45.833 22.20 0.00 0.00 3.68
661 664 3.750130 AGCTAGTGAATGTTTGCTGTGAG 59.250 43.478 0.00 0.00 0.00 3.51
667 670 1.913778 ATGTTTGCTGTGAGGCATCA 58.086 45.000 0.00 0.00 42.09 3.07
678 681 1.199789 TGAGGCATCACAATTGCGAAC 59.800 47.619 5.05 0.00 41.07 3.95
681 684 1.405469 GCATCACAATTGCGAACGCC 61.405 55.000 16.27 0.00 41.09 5.68
794 798 2.032030 CGTGTTCGCTTGAAGGAATTGT 60.032 45.455 0.00 0.00 30.72 2.71
802 806 4.872691 CGCTTGAAGGAATTGTCATACTCT 59.127 41.667 0.00 0.00 0.00 3.24
817 821 8.846943 TGTCATACTCTCAACACATAAATTGT 57.153 30.769 0.00 0.00 39.91 2.71
818 822 9.283768 TGTCATACTCTCAACACATAAATTGTT 57.716 29.630 0.00 0.00 36.00 2.83
825 829 5.980324 CAACACATAAATTGTTGCGAGAG 57.020 39.130 2.50 0.00 45.36 3.20
831 835 6.803320 CACATAAATTGTTGCGAGAGACATTT 59.197 34.615 0.00 0.00 36.00 2.32
833 837 2.686558 TTGTTGCGAGAGACATTTGC 57.313 45.000 0.00 0.00 0.00 3.68
837 841 3.812609 TGTTGCGAGAGACATTTGCTTTA 59.187 39.130 0.00 0.00 0.00 1.85
878 882 5.006358 ACGTTCGCTCAATAACATAACCATC 59.994 40.000 0.00 0.00 0.00 3.51
900 904 2.393271 TGTTTTTGCCCAACCACTTG 57.607 45.000 0.00 0.00 0.00 3.16
1141 2558 0.030603 ATCCTCTTCTCCCTCCACCC 60.031 60.000 0.00 0.00 0.00 4.61
1150 2567 3.011517 CCTCCACCCCCACTCCAG 61.012 72.222 0.00 0.00 0.00 3.86
1156 2573 4.351054 CCCCCACTCCAGCCACAC 62.351 72.222 0.00 0.00 0.00 3.82
1301 2734 4.790962 TCCCGACGAGGAGGACGG 62.791 72.222 0.00 0.00 45.00 4.79
1304 2737 4.790962 CGACGAGGAGGACGGGGA 62.791 72.222 0.00 0.00 34.93 4.81
1305 2738 2.829458 GACGAGGAGGACGGGGAG 60.829 72.222 0.00 0.00 34.93 4.30
1306 2739 4.444081 ACGAGGAGGACGGGGAGG 62.444 72.222 0.00 0.00 34.93 4.30
1307 2740 4.124943 CGAGGAGGACGGGGAGGA 62.125 72.222 0.00 0.00 0.00 3.71
1308 2741 2.123640 GAGGAGGACGGGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
1309 2742 3.742248 GAGGAGGACGGGGAGGAGG 62.742 73.684 0.00 0.00 0.00 4.30
1310 2743 3.752167 GGAGGACGGGGAGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
1311 2744 2.123640 GAGGACGGGGAGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
1312 2745 3.742248 GAGGACGGGGAGGAGGAGG 62.742 73.684 0.00 0.00 0.00 4.30
1325 2758 2.212794 GAGGAGGAGGAGGACACGGA 62.213 65.000 0.00 0.00 0.00 4.69
1326 2759 1.075896 GGAGGAGGAGGACACGGAT 60.076 63.158 0.00 0.00 0.00 4.18
1559 3001 0.158096 GTGCACACGTACGTTCTTCG 59.842 55.000 20.23 9.77 46.00 3.79
1560 3002 0.935831 TGCACACGTACGTTCTTCGG 60.936 55.000 20.23 8.98 44.69 4.30
1580 3025 0.034896 GGTGGTGGTGACGTGATTCT 59.965 55.000 0.00 0.00 0.00 2.40
1726 3171 1.450360 ATCCCTTCTCCTTATGGGCC 58.550 55.000 0.00 0.00 39.49 5.80
1824 3269 9.238368 TCCGAAGAAATAAAAGTGAAATGGTAT 57.762 29.630 0.00 0.00 0.00 2.73
1844 3289 2.514803 TGCAAGTAAGAAAAGAGGGGC 58.485 47.619 0.00 0.00 0.00 5.80
1845 3290 2.158534 TGCAAGTAAGAAAAGAGGGGCA 60.159 45.455 0.00 0.00 0.00 5.36
1923 3368 3.480470 CCTTCTCCTTTTCTCACTTGCA 58.520 45.455 0.00 0.00 0.00 4.08
1989 3434 3.134458 GCGAGTAAGGAAAGATGGGATG 58.866 50.000 0.00 0.00 0.00 3.51
2039 3484 9.619316 CGTTTCATAATTCTTGTCATGGTTTTA 57.381 29.630 0.00 0.00 0.00 1.52
2175 3621 5.933187 TCTATCTTCTCGAATCTTCTCCG 57.067 43.478 0.00 0.00 0.00 4.63
2227 3677 0.960364 CCGTGGGATTGTGAAGTGGG 60.960 60.000 0.00 0.00 0.00 4.61
2316 3766 7.840342 ATATATCGGATGAAGCTTCAACATC 57.160 36.000 31.55 23.42 41.13 3.06
2377 3827 4.248859 CGGAATAGCTGGATATCTGGTTG 58.751 47.826 2.05 0.00 0.00 3.77
2382 3832 7.120432 GGAATAGCTGGATATCTGGTTGAAATC 59.880 40.741 2.05 0.00 0.00 2.17
2394 3844 3.181459 TGGTTGAAATCTCCACTGTCGAA 60.181 43.478 0.00 0.00 0.00 3.71
2495 3945 3.520691 AGGACTGTTCTTTTTACCCCC 57.479 47.619 0.00 0.00 0.00 5.40
2501 3951 6.063496 ACTGTTCTTTTTACCCCCTCTATC 57.937 41.667 0.00 0.00 0.00 2.08
2558 4008 7.716799 AATTGAATACCTTGGAGCATTGTTA 57.283 32.000 0.00 0.00 0.00 2.41
2636 4086 2.684001 ATCGGCAAGTTAATCGGTCA 57.316 45.000 0.00 0.00 0.00 4.02
2637 4087 2.459060 TCGGCAAGTTAATCGGTCAA 57.541 45.000 0.00 0.00 0.00 3.18
2638 4088 2.980568 TCGGCAAGTTAATCGGTCAAT 58.019 42.857 0.00 0.00 0.00 2.57
2639 4089 3.340034 TCGGCAAGTTAATCGGTCAATT 58.660 40.909 0.00 0.00 0.00 2.32
2640 4090 4.505808 TCGGCAAGTTAATCGGTCAATTA 58.494 39.130 0.00 0.00 0.00 1.40
2641 4091 4.936411 TCGGCAAGTTAATCGGTCAATTAA 59.064 37.500 0.00 0.00 0.00 1.40
2642 4092 5.587043 TCGGCAAGTTAATCGGTCAATTAAT 59.413 36.000 0.00 0.00 34.54 1.40
2643 4093 5.907391 CGGCAAGTTAATCGGTCAATTAATC 59.093 40.000 0.00 0.00 34.54 1.75
2681 4131 7.113965 CGATTTATTAGTTTATCGGCTACACGT 59.886 37.037 0.00 0.00 36.99 4.49
2779 4229 4.724074 AACATTATCAGTTGGCCATGTG 57.276 40.909 6.09 7.49 0.00 3.21
2860 4310 7.015487 TGGAATTCAGATTTGAGTGGTCAATTT 59.985 33.333 7.93 0.00 42.41 1.82
2899 4349 5.880054 AATAACACTTGAAATCCACCTCG 57.120 39.130 0.00 0.00 0.00 4.63
3209 4698 3.619233 AACCAAACGACTTGTGTATGC 57.381 42.857 0.00 0.00 32.65 3.14
3255 4744 3.552890 GCAAGGTAGGTTTTTGCTCCAAG 60.553 47.826 1.51 0.00 42.84 3.61
3383 4872 9.778993 CCAGTAGAAAATCAATAAACACTCATG 57.221 33.333 0.00 0.00 0.00 3.07
3458 5003 7.581213 TTCAGTGGAGCTTTCAAATTTAAGA 57.419 32.000 5.11 0.00 0.00 2.10
3584 5130 1.888512 GGTGAACATGTGGCACAGAAT 59.111 47.619 26.04 13.57 41.80 2.40
3730 5276 7.944061 TCACCTTATAAGAATGAAATGGCATG 58.056 34.615 14.28 0.00 0.00 4.06
3816 5377 9.725206 AAGGTACTCCCTCTGTAAAGAAATATA 57.275 33.333 0.00 0.00 45.47 0.86
3821 5382 9.397280 ACTCCCTCTGTAAAGAAATATAAAAGC 57.603 33.333 0.00 0.00 0.00 3.51
3824 5385 8.674607 CCCTCTGTAAAGAAATATAAAAGCGTT 58.325 33.333 0.00 0.00 0.00 4.84
3956 5597 4.265556 CCTTTTGTCGTAGCAGTTCTATCG 59.734 45.833 0.00 0.00 0.00 2.92
4243 5886 6.912591 CGTGGAAAGGTAAAAATAGCATGATC 59.087 38.462 0.00 0.00 0.00 2.92
4246 5889 7.147915 TGGAAAGGTAAAAATAGCATGATCACC 60.148 37.037 0.00 0.00 0.00 4.02
4252 5895 9.736023 GGTAAAAATAGCATGATCACCTTTTAG 57.264 33.333 0.00 0.00 0.00 1.85
4257 5900 4.122776 AGCATGATCACCTTTTAGCTACG 58.877 43.478 0.00 0.00 0.00 3.51
4487 6131 5.641709 GTCTCAAGCTTAAAGCATTTACCC 58.358 41.667 0.00 0.00 45.56 3.69
4698 6367 7.474474 AGCTAGGGTAGATATTAGATAGGCT 57.526 40.000 0.00 0.00 0.00 4.58
4748 6417 4.383649 GCATTTATCATATGTTTGCTGGCG 59.616 41.667 1.90 0.00 0.00 5.69
4841 6511 4.228912 CAAGCAAACCTTGTGTTCTAGG 57.771 45.455 0.00 0.00 44.74 3.02
4842 6512 3.857157 AGCAAACCTTGTGTTCTAGGA 57.143 42.857 0.00 0.00 38.52 2.94
4843 6513 3.744660 AGCAAACCTTGTGTTCTAGGAG 58.255 45.455 0.00 0.00 38.52 3.69
4920 6605 5.999600 AGCAAAGCTTTTTAAAAGATGCCAT 59.000 32.000 25.02 14.14 33.89 4.40
4949 6634 1.123038 GCAACTTCTTGCGAAAATGCG 59.877 47.619 0.00 0.00 43.42 4.73
5170 6894 6.968263 TTAATCAACACATCCAAAAGGTGA 57.032 33.333 0.00 0.00 36.42 4.02
5320 7044 8.445275 ACAACACTCAATACTAACATCACAAA 57.555 30.769 0.00 0.00 0.00 2.83
5351 7107 4.104102 AGGCGATCAAATATACTCCCCAAA 59.896 41.667 0.00 0.00 0.00 3.28
5496 7252 7.485913 CACATACAATTACTTCACAAATCAGGC 59.514 37.037 0.00 0.00 0.00 4.85
5497 7253 5.046910 ACAATTACTTCACAAATCAGGCG 57.953 39.130 0.00 0.00 0.00 5.52
5498 7254 3.764885 ATTACTTCACAAATCAGGCGC 57.235 42.857 0.00 0.00 0.00 6.53
5499 7255 1.075542 TACTTCACAAATCAGGCGCG 58.924 50.000 0.00 0.00 0.00 6.86
5500 7256 1.512734 CTTCACAAATCAGGCGCGC 60.513 57.895 25.94 25.94 0.00 6.86
5501 7257 3.307505 TTCACAAATCAGGCGCGCG 62.308 57.895 28.44 28.44 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.825836 GATCCCGTTGCCAGCCAG 60.826 66.667 0.00 0.00 0.00 4.85
2 3 4.424711 TGGATCCCGTTGCCAGCC 62.425 66.667 9.90 0.00 0.00 4.85
3 4 3.134127 GTGGATCCCGTTGCCAGC 61.134 66.667 9.90 0.00 31.18 4.85
4 5 2.438434 GGTGGATCCCGTTGCCAG 60.438 66.667 9.90 0.00 31.18 4.85
5 6 2.359015 TTTGGTGGATCCCGTTGCCA 62.359 55.000 9.90 7.11 34.77 4.92
6 7 1.182385 TTTTGGTGGATCCCGTTGCC 61.182 55.000 9.90 4.48 34.77 4.52
7 8 0.243636 CTTTTGGTGGATCCCGTTGC 59.756 55.000 9.90 0.00 34.77 4.17
8 9 0.887933 CCTTTTGGTGGATCCCGTTG 59.112 55.000 9.90 0.00 34.77 4.10
9 10 0.774908 TCCTTTTGGTGGATCCCGTT 59.225 50.000 9.90 0.00 41.38 4.44
10 11 0.774908 TTCCTTTTGGTGGATCCCGT 59.225 50.000 9.90 0.00 41.38 5.28
11 12 1.917872 TTTCCTTTTGGTGGATCCCG 58.082 50.000 9.90 0.00 41.38 5.14
31 32 6.096001 AGAGTTGTGAGCATCTTTGAGTTTTT 59.904 34.615 0.00 0.00 34.92 1.94
32 33 5.591877 AGAGTTGTGAGCATCTTTGAGTTTT 59.408 36.000 0.00 0.00 34.92 2.43
33 34 5.128919 AGAGTTGTGAGCATCTTTGAGTTT 58.871 37.500 0.00 0.00 34.92 2.66
34 35 4.712476 AGAGTTGTGAGCATCTTTGAGTT 58.288 39.130 0.00 0.00 34.92 3.01
35 36 4.348863 AGAGTTGTGAGCATCTTTGAGT 57.651 40.909 0.00 0.00 34.92 3.41
36 37 6.036953 GGAATAGAGTTGTGAGCATCTTTGAG 59.963 42.308 0.00 0.00 34.92 3.02
37 38 5.877012 GGAATAGAGTTGTGAGCATCTTTGA 59.123 40.000 0.00 0.00 34.92 2.69
38 39 5.879223 AGGAATAGAGTTGTGAGCATCTTTG 59.121 40.000 0.00 0.00 34.92 2.77
39 40 6.059787 AGGAATAGAGTTGTGAGCATCTTT 57.940 37.500 0.00 0.00 34.92 2.52
40 41 5.690464 AGGAATAGAGTTGTGAGCATCTT 57.310 39.130 0.00 0.00 34.92 2.40
41 42 5.304101 CCTAGGAATAGAGTTGTGAGCATCT 59.696 44.000 1.05 0.00 34.92 2.90
42 43 5.510520 CCCTAGGAATAGAGTTGTGAGCATC 60.511 48.000 11.48 0.00 0.00 3.91
43 44 4.346418 CCCTAGGAATAGAGTTGTGAGCAT 59.654 45.833 11.48 0.00 0.00 3.79
44 45 3.706594 CCCTAGGAATAGAGTTGTGAGCA 59.293 47.826 11.48 0.00 0.00 4.26
45 46 3.961408 TCCCTAGGAATAGAGTTGTGAGC 59.039 47.826 11.48 0.00 0.00 4.26
46 47 5.205056 ACTCCCTAGGAATAGAGTTGTGAG 58.795 45.833 11.48 6.05 36.16 3.51
47 48 5.208294 ACTCCCTAGGAATAGAGTTGTGA 57.792 43.478 11.48 0.00 36.16 3.58
48 49 5.941555 AACTCCCTAGGAATAGAGTTGTG 57.058 43.478 22.87 4.09 45.39 3.33
49 50 7.124448 CACTAAACTCCCTAGGAATAGAGTTGT 59.876 40.741 23.73 17.63 46.17 3.32
50 51 7.124448 ACACTAAACTCCCTAGGAATAGAGTTG 59.876 40.741 23.73 17.11 46.17 3.16
52 53 6.743788 ACACTAAACTCCCTAGGAATAGAGT 58.256 40.000 11.48 11.46 41.25 3.24
53 54 7.663043 AACACTAAACTCCCTAGGAATAGAG 57.337 40.000 11.48 10.76 0.00 2.43
54 55 7.456902 ACAAACACTAAACTCCCTAGGAATAGA 59.543 37.037 11.48 0.00 0.00 1.98
55 56 7.621796 ACAAACACTAAACTCCCTAGGAATAG 58.378 38.462 11.48 7.27 0.00 1.73
56 57 7.563724 ACAAACACTAAACTCCCTAGGAATA 57.436 36.000 11.48 0.00 0.00 1.75
57 58 6.449830 ACAAACACTAAACTCCCTAGGAAT 57.550 37.500 11.48 0.00 0.00 3.01
58 59 5.899631 ACAAACACTAAACTCCCTAGGAA 57.100 39.130 11.48 0.00 0.00 3.36
59 60 5.899631 AACAAACACTAAACTCCCTAGGA 57.100 39.130 11.48 0.00 0.00 2.94
60 61 7.166167 ACATAACAAACACTAAACTCCCTAGG 58.834 38.462 0.06 0.06 0.00 3.02
61 62 8.617290 AACATAACAAACACTAAACTCCCTAG 57.383 34.615 0.00 0.00 0.00 3.02
62 63 8.434392 AGAACATAACAAACACTAAACTCCCTA 58.566 33.333 0.00 0.00 0.00 3.53
63 64 7.287810 AGAACATAACAAACACTAAACTCCCT 58.712 34.615 0.00 0.00 0.00 4.20
64 65 7.444487 AGAGAACATAACAAACACTAAACTCCC 59.556 37.037 0.00 0.00 0.00 4.30
65 66 8.379457 AGAGAACATAACAAACACTAAACTCC 57.621 34.615 0.00 0.00 0.00 3.85
82 83 8.919145 CCACTCTCCTTTAATAGTAGAGAACAT 58.081 37.037 11.47 0.00 37.66 2.71
83 84 7.342284 CCCACTCTCCTTTAATAGTAGAGAACA 59.658 40.741 11.47 0.00 37.66 3.18
84 85 7.342541 ACCCACTCTCCTTTAATAGTAGAGAAC 59.657 40.741 11.47 0.00 37.66 3.01
85 86 7.420029 ACCCACTCTCCTTTAATAGTAGAGAA 58.580 38.462 11.47 0.00 37.66 2.87
86 87 6.982899 ACCCACTCTCCTTTAATAGTAGAGA 58.017 40.000 11.47 0.00 37.66 3.10
87 88 8.763984 TTACCCACTCTCCTTTAATAGTAGAG 57.236 38.462 0.00 0.00 39.65 2.43
88 89 8.342270 ACTTACCCACTCTCCTTTAATAGTAGA 58.658 37.037 0.00 0.00 0.00 2.59
89 90 8.536340 ACTTACCCACTCTCCTTTAATAGTAG 57.464 38.462 0.00 0.00 0.00 2.57
90 91 8.906238 AACTTACCCACTCTCCTTTAATAGTA 57.094 34.615 0.00 0.00 0.00 1.82
91 92 7.363617 CGAACTTACCCACTCTCCTTTAATAGT 60.364 40.741 0.00 0.00 0.00 2.12
92 93 6.979238 CGAACTTACCCACTCTCCTTTAATAG 59.021 42.308 0.00 0.00 0.00 1.73
101 102 2.745515 AAGCGAACTTACCCACTCTC 57.254 50.000 0.00 0.00 33.13 3.20
107 108 1.991264 GACGAGAAAGCGAACTTACCC 59.009 52.381 0.00 0.00 34.05 3.69
140 141 2.027469 ACCAACATAAAGGGACGGAGAC 60.027 50.000 0.00 0.00 0.00 3.36
163 164 6.936900 TCAAACTAAGGACATGAAGAGGAAAG 59.063 38.462 0.00 0.00 0.00 2.62
205 206 6.894339 AAGACAAGGAAATGAAAATACCGT 57.106 33.333 0.00 0.00 0.00 4.83
208 209 9.974980 TTTGGTAAGACAAGGAAATGAAAATAC 57.025 29.630 0.00 0.00 0.00 1.89
232 233 6.393990 TGCGTTAATGCAAGATATGGTTTTT 58.606 32.000 19.88 0.00 43.02 1.94
268 269 9.462174 TTGAGTTATTGCAGAACATGTTTTTAG 57.538 29.630 13.36 4.52 0.00 1.85
318 319 6.015772 TGGAAAGTTTTATTGTAGTTGAGGCC 60.016 38.462 0.00 0.00 0.00 5.19
328 329 6.172630 GGGATTGCATGGAAAGTTTTATTGT 58.827 36.000 2.94 0.00 0.00 2.71
329 330 5.585844 GGGGATTGCATGGAAAGTTTTATTG 59.414 40.000 2.94 0.00 0.00 1.90
332 333 4.424842 AGGGGATTGCATGGAAAGTTTTA 58.575 39.130 2.94 0.00 0.00 1.52
336 337 2.311542 TGTAGGGGATTGCATGGAAAGT 59.688 45.455 2.94 0.00 0.00 2.66
337 338 2.689983 GTGTAGGGGATTGCATGGAAAG 59.310 50.000 2.94 0.00 0.00 2.62
352 353 7.447374 TTTGAGTTGATTTGGTATGTGTAGG 57.553 36.000 0.00 0.00 0.00 3.18
382 385 7.189079 AGTTTTCATTTAGTTGGGGTTTTGA 57.811 32.000 0.00 0.00 0.00 2.69
391 394 7.171678 AGACGAGGAGAAGTTTTCATTTAGTTG 59.828 37.037 0.00 0.00 0.00 3.16
404 407 2.312424 AGGGAAAGACGAGGAGAAGT 57.688 50.000 0.00 0.00 0.00 3.01
408 411 1.112950 GGGTAGGGAAAGACGAGGAG 58.887 60.000 0.00 0.00 0.00 3.69
415 418 7.219601 TGATTTGATAATGGGTAGGGAAAGA 57.780 36.000 0.00 0.00 0.00 2.52
464 467 9.181805 CTAATTGTGTCTGACATATACCTTACG 57.818 37.037 14.37 0.00 33.40 3.18
499 502 1.332028 GCGTGCGTGCATATTACAGTC 60.332 52.381 0.00 0.00 34.15 3.51
503 506 1.278637 GGGCGTGCGTGCATATTAC 59.721 57.895 0.00 0.00 36.28 1.89
535 538 6.486993 CCAACTCCCTATTTAGCTAATTGTCC 59.513 42.308 7.08 0.00 0.00 4.02
585 588 9.118300 CTCTCATCCCTCCAATATAAATTATGC 57.882 37.037 0.00 0.00 0.00 3.14
600 603 6.432403 AATATCCAGAAACTCTCATCCCTC 57.568 41.667 0.00 0.00 0.00 4.30
601 604 6.838401 AAATATCCAGAAACTCTCATCCCT 57.162 37.500 0.00 0.00 0.00 4.20
602 605 7.888250 AAAAATATCCAGAAACTCTCATCCC 57.112 36.000 0.00 0.00 0.00 3.85
642 645 2.813754 GCCTCACAGCAAACATTCACTA 59.186 45.455 0.00 0.00 0.00 2.74
645 648 1.689984 TGCCTCACAGCAAACATTCA 58.310 45.000 0.00 0.00 40.56 2.57
661 664 1.405469 GCGTTCGCAATTGTGATGCC 61.405 55.000 25.01 15.36 40.72 4.40
667 670 3.241701 CATAAAAGGCGTTCGCAATTGT 58.758 40.909 18.46 10.13 0.00 2.71
717 720 7.254387 CCAGAATTCGTCATGCTTTTTGAAAAA 60.254 33.333 2.83 2.83 0.00 1.94
722 725 3.365820 GCCAGAATTCGTCATGCTTTTTG 59.634 43.478 0.00 0.00 0.00 2.44
728 731 2.634982 TTTGCCAGAATTCGTCATGC 57.365 45.000 0.00 0.77 0.00 4.06
729 732 3.899734 TGTTTTGCCAGAATTCGTCATG 58.100 40.909 0.00 0.00 0.00 3.07
730 733 4.582701 TTGTTTTGCCAGAATTCGTCAT 57.417 36.364 0.00 0.00 0.00 3.06
731 734 4.097135 TCTTTGTTTTGCCAGAATTCGTCA 59.903 37.500 0.00 0.00 0.00 4.35
732 735 4.606961 TCTTTGTTTTGCCAGAATTCGTC 58.393 39.130 0.00 0.00 0.00 4.20
733 736 4.647424 TCTTTGTTTTGCCAGAATTCGT 57.353 36.364 0.00 0.00 0.00 3.85
734 737 6.529463 AATTCTTTGTTTTGCCAGAATTCG 57.471 33.333 0.00 0.00 40.42 3.34
735 738 8.615211 AGAAAATTCTTTGTTTTGCCAGAATTC 58.385 29.630 0.00 0.00 42.53 2.17
817 821 3.188460 GGTAAAGCAAATGTCTCTCGCAA 59.812 43.478 0.00 0.00 0.00 4.85
818 822 2.742053 GGTAAAGCAAATGTCTCTCGCA 59.258 45.455 0.00 0.00 0.00 5.10
825 829 3.253230 GGTGCATGGTAAAGCAAATGTC 58.747 45.455 0.00 0.00 43.20 3.06
831 835 0.676466 CTCGGGTGCATGGTAAAGCA 60.676 55.000 0.00 0.00 38.65 3.91
833 837 1.705337 CGCTCGGGTGCATGGTAAAG 61.705 60.000 0.00 0.00 0.00 1.85
837 841 4.015406 TTCGCTCGGGTGCATGGT 62.015 61.111 0.00 0.00 0.00 3.55
878 882 2.984562 AGTGGTTGGGCAAAAACAAAG 58.015 42.857 0.00 0.00 0.00 2.77
900 904 3.077901 CGCTCGTCGTCGTATCGC 61.078 66.667 1.33 0.95 38.33 4.58
922 926 4.326766 CACCTGTTTGCGTGCCCG 62.327 66.667 0.00 0.00 37.07 6.13
923 927 3.977244 CCACCTGTTTGCGTGCCC 61.977 66.667 0.00 0.00 0.00 5.36
924 928 4.645921 GCCACCTGTTTGCGTGCC 62.646 66.667 0.00 0.00 0.00 5.01
1141 2558 2.033141 CTGTGTGGCTGGAGTGGG 59.967 66.667 0.00 0.00 0.00 4.61
1150 2567 2.595463 TGCCTTGCTCTGTGTGGC 60.595 61.111 0.00 0.00 43.49 5.01
1156 2573 1.807886 GATTGCCTGCCTTGCTCTG 59.192 57.895 0.00 0.00 0.00 3.35
1298 2731 3.756783 CCTCCTCCTCCTCCCCGT 61.757 72.222 0.00 0.00 0.00 5.28
1299 2732 3.430497 TCCTCCTCCTCCTCCCCG 61.430 72.222 0.00 0.00 0.00 5.73
1300 2733 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1301 2734 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1302 2735 1.231928 GTCCTCCTCCTCCTCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
1303 2736 0.396556 GTGTCCTCCTCCTCCTCCTC 60.397 65.000 0.00 0.00 0.00 3.71
1304 2737 1.700985 GTGTCCTCCTCCTCCTCCT 59.299 63.158 0.00 0.00 0.00 3.69
1305 2738 1.755008 CGTGTCCTCCTCCTCCTCC 60.755 68.421 0.00 0.00 0.00 4.30
1306 2739 1.755008 CCGTGTCCTCCTCCTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
1307 2740 1.585651 ATCCGTGTCCTCCTCCTCCT 61.586 60.000 0.00 0.00 0.00 3.69
1308 2741 1.075896 ATCCGTGTCCTCCTCCTCC 60.076 63.158 0.00 0.00 0.00 4.30
1309 2742 2.022240 GCATCCGTGTCCTCCTCCTC 62.022 65.000 0.00 0.00 0.00 3.71
1310 2743 2.060980 GCATCCGTGTCCTCCTCCT 61.061 63.158 0.00 0.00 0.00 3.69
1311 2744 2.501610 GCATCCGTGTCCTCCTCC 59.498 66.667 0.00 0.00 0.00 4.30
1312 2745 2.501610 GGCATCCGTGTCCTCCTC 59.498 66.667 0.00 0.00 0.00 3.71
1391 2824 2.217038 AGCGGCTCCTCACTTTCCA 61.217 57.895 0.00 0.00 0.00 3.53
1396 2829 4.079850 CTGCAGCGGCTCCTCACT 62.080 66.667 10.92 0.00 41.91 3.41
1559 3001 2.406002 AATCACGTCACCACCACCCC 62.406 60.000 0.00 0.00 0.00 4.95
1560 3002 0.953960 GAATCACGTCACCACCACCC 60.954 60.000 0.00 0.00 0.00 4.61
1580 3025 5.534654 ACCTGGAGAAATCAAAACGAATCAA 59.465 36.000 0.00 0.00 0.00 2.57
1726 3171 1.106285 GTTTAGCCAAGGATGCCCAG 58.894 55.000 0.00 0.00 33.88 4.45
1824 3269 2.158534 TGCCCCTCTTTTCTTACTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
1844 3289 7.716998 AGTTAGAGTTGATAGCCCATGTTATTG 59.283 37.037 0.00 0.00 0.00 1.90
1845 3290 7.806180 AGTTAGAGTTGATAGCCCATGTTATT 58.194 34.615 0.00 0.00 0.00 1.40
1902 3347 3.480470 TGCAAGTGAGAAAAGGAGAAGG 58.520 45.455 0.00 0.00 0.00 3.46
1923 3368 2.684881 CGGACAAGCAAGAAGGCATATT 59.315 45.455 0.00 0.00 35.83 1.28
2039 3484 2.351706 TCCTGCCGTGGTTTTAGTTT 57.648 45.000 0.00 0.00 0.00 2.66
2055 3501 2.706190 CTCCCTCCGTTCCATAATTCCT 59.294 50.000 0.00 0.00 0.00 3.36
2175 3621 0.320073 TGCCCGCACACAAGTACTAC 60.320 55.000 0.00 0.00 0.00 2.73
2227 3677 1.338020 CTCAACTTGGACAAGGCAACC 59.662 52.381 15.72 0.00 42.53 3.77
2377 3827 5.869888 ACAAGTATTCGACAGTGGAGATTTC 59.130 40.000 0.00 0.00 0.00 2.17
2382 3832 3.679980 CCAACAAGTATTCGACAGTGGAG 59.320 47.826 0.00 0.00 0.00 3.86
2394 3844 4.648651 ACCTTCGTTAAGCCAACAAGTAT 58.351 39.130 0.33 0.00 36.92 2.12
2495 3945 9.182933 GCTAAAAGTTAGGAATACACGATAGAG 57.817 37.037 0.00 0.00 41.38 2.43
2501 3951 7.772332 ATCAGCTAAAAGTTAGGAATACACG 57.228 36.000 0.00 0.00 0.00 4.49
2532 3982 7.716799 ACAATGCTCCAAGGTATTCAATTTA 57.283 32.000 0.00 0.00 0.00 1.40
2603 4053 6.115448 ACTTGCCGATTAGCCTATTAATCT 57.885 37.500 0.00 0.00 37.72 2.40
2640 4090 9.010029 ACTAATAAATCGGCCGATTAATTGATT 57.990 29.630 44.22 34.52 43.26 2.57
2641 4091 8.561738 ACTAATAAATCGGCCGATTAATTGAT 57.438 30.769 44.22 32.02 43.26 2.57
2642 4092 7.972832 ACTAATAAATCGGCCGATTAATTGA 57.027 32.000 44.22 29.11 43.26 2.57
2681 4131 7.270047 CGATTAATCCCTACTTGTAAGGTCAA 58.730 38.462 9.87 0.00 31.70 3.18
2817 4267 8.422973 TGAATTCCAACAAGTTTCTCAAATTG 57.577 30.769 2.27 0.00 0.00 2.32
2860 4310 2.363306 ATTTGTGTGTCCTCTTGCCA 57.637 45.000 0.00 0.00 0.00 4.92
3044 4501 3.480470 ACAACTGAGCAACATAACAGCT 58.520 40.909 0.00 0.00 42.17 4.24
3209 4698 4.513692 TGTACCTTCAAGATGTTTTGACGG 59.486 41.667 9.04 9.04 46.40 4.79
3419 4964 7.452813 AGCTCCACTGAATAAAGGAAGAAAAAT 59.547 33.333 0.00 0.00 0.00 1.82
3458 5003 7.881775 AAAAAGACACACCTCAAGTTATTCT 57.118 32.000 0.00 0.00 0.00 2.40
3527 5072 0.606401 CACTTCACGGGATGGCAACT 60.606 55.000 5.46 0.00 37.61 3.16
3584 5130 8.436778 TCCAGATAAAAGAATCCGATTCCATTA 58.563 33.333 16.09 14.94 40.13 1.90
3730 5276 8.535690 AAGTTATCAGTTAGTAAAGAGTGTGC 57.464 34.615 0.00 0.00 0.00 4.57
3816 5377 8.324163 ACTTCAGTGATCTAATAAACGCTTTT 57.676 30.769 0.00 0.00 0.00 2.27
3818 5379 8.251721 ACTACTTCAGTGATCTAATAAACGCTT 58.748 33.333 0.00 0.00 35.62 4.68
3872 5508 4.141824 GCCATCTAGCAAGTTACTCCTTCT 60.142 45.833 0.00 0.00 0.00 2.85
3875 5511 3.107601 TGCCATCTAGCAAGTTACTCCT 58.892 45.455 0.00 0.00 40.56 3.69
4136 5779 3.944015 GTCAGGGGAAGAAATGACTCATG 59.056 47.826 0.00 0.00 39.15 3.07
4243 5886 2.806244 ACAGCAACGTAGCTAAAAGGTG 59.194 45.455 0.00 4.80 44.54 4.00
4246 5889 4.844267 ACAAACAGCAACGTAGCTAAAAG 58.156 39.130 0.00 0.00 44.54 2.27
4252 5895 2.116366 CCAAACAAACAGCAACGTAGC 58.884 47.619 0.00 0.00 0.00 3.58
4257 5900 1.289276 CAGGCCAAACAAACAGCAAC 58.711 50.000 5.01 0.00 0.00 4.17
4323 5967 1.077930 AGCCAGTTCGATGCTGCAT 60.078 52.632 16.20 16.20 33.23 3.96
4661 6330 6.173339 TCTACCCTAGCTTCAAAAATGACTG 58.827 40.000 0.00 0.00 0.00 3.51
4663 6332 8.910351 ATATCTACCCTAGCTTCAAAAATGAC 57.090 34.615 0.00 0.00 0.00 3.06
4698 6367 5.276461 ACGGTGAGAATATAACTCATGCA 57.724 39.130 13.23 0.00 44.41 3.96
4796 6466 9.515226 TTGCCAGACTGATTTTTATTTAGTACT 57.485 29.630 3.32 0.00 0.00 2.73
4797 6467 9.774742 CTTGCCAGACTGATTTTTATTTAGTAC 57.225 33.333 3.32 0.00 0.00 2.73
4810 6480 1.202976 AGGTTTGCTTGCCAGACTGAT 60.203 47.619 3.32 0.00 0.00 2.90
4837 6507 8.840321 CCAATTGACAATACCAAATACTCCTAG 58.160 37.037 7.12 0.00 0.00 3.02
4838 6508 8.553153 TCCAATTGACAATACCAAATACTCCTA 58.447 33.333 7.12 0.00 0.00 2.94
4839 6509 7.410174 TCCAATTGACAATACCAAATACTCCT 58.590 34.615 7.12 0.00 0.00 3.69
4840 6510 7.639113 TCCAATTGACAATACCAAATACTCC 57.361 36.000 7.12 0.00 0.00 3.85
4841 6511 9.125026 AGATCCAATTGACAATACCAAATACTC 57.875 33.333 7.12 0.00 0.00 2.59
4842 6512 8.906867 CAGATCCAATTGACAATACCAAATACT 58.093 33.333 7.12 0.00 0.00 2.12
4843 6513 8.686334 ACAGATCCAATTGACAATACCAAATAC 58.314 33.333 7.12 0.00 0.00 1.89
5170 6894 4.574674 TGAGTGGGCAAATCTCACTTAT 57.425 40.909 0.00 0.00 41.24 1.73
5320 7044 6.291377 AGTATATTTGATCGCCTGATGTTGT 58.709 36.000 0.00 0.00 34.09 3.32
5351 7107 0.032615 TCTGTGGGGTTTTGGTGCTT 60.033 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.