Multiple sequence alignment - TraesCS5D01G367700

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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 TraesCS5D01G367700 chr5D 100.000 3697 0 0 1 3697 444103522 444099826 0.000000e+00 6828.0
1 TraesCS5D01G367700 chr5D 93.891 933 32 4 2788 3695 422454796 422455728 0.000000e+00 1384.0
2 TraesCS5D01G367700 chr5B 93.806 1340 48 8 1416 2745 540914067 540912753 0.000000e+00 1982.0
3 TraesCS5D01G367700 chr5B 84.478 1121 116 31 135 1239 540915526 540914448 0.000000e+00 1053.0
4 TraesCS5D01G367700 chr5B 97.872 47 1 0 2740 2786 540912718 540912672 8.510000e-12 82.4
5 TraesCS5D01G367700 chr5B 100.000 42 0 0 2745 2786 540738985 540739026 1.100000e-10 78.7
6 TraesCS5D01G367700 chr5A 93.846 1300 42 8 1416 2707 561126880 561125611 0.000000e+00 1923.0
7 TraesCS5D01G367700 chr5A 87.452 263 16 12 833 1086 561127721 561127467 1.680000e-73 287.0
8 TraesCS5D01G367700 chr5A 79.534 386 69 7 118 502 533950938 533950562 2.190000e-67 267.0
9 TraesCS5D01G367700 chr5A 97.826 46 1 0 2741 2786 561125237 561125192 3.060000e-11 80.5
10 TraesCS5D01G367700 chr5A 95.238 42 0 1 84 125 262330885 262330846 8.570000e-07 65.8
11 TraesCS5D01G367700 chr3D 94.629 931 27 7 2790 3697 81850913 81849983 0.000000e+00 1421.0
12 TraesCS5D01G367700 chr3D 94.629 931 27 7 2790 3697 81852492 81851562 0.000000e+00 1421.0
13 TraesCS5D01G367700 chr3D 94.319 933 28 9 2790 3697 81857232 81856300 0.000000e+00 1406.0
14 TraesCS5D01G367700 chr3D 94.212 933 29 9 2790 3697 81854072 81853140 0.000000e+00 1400.0
15 TraesCS5D01G367700 chr3D 94.200 931 31 7 2790 3697 81849334 81848404 0.000000e+00 1399.0
16 TraesCS5D01G367700 chr3D 94.105 933 30 9 2790 3697 81855652 81854720 0.000000e+00 1395.0
17 TraesCS5D01G367700 chr3D 79.740 385 68 7 118 500 475021684 475021308 1.690000e-68 270.0
18 TraesCS5D01G367700 chr3D 81.994 311 48 6 118 426 32626701 32626397 1.320000e-64 257.0
19 TraesCS5D01G367700 chr3D 78.552 359 65 9 148 505 487586436 487586089 3.710000e-55 226.0
20 TraesCS5D01G367700 chr3D 87.500 168 11 6 3530 3697 495308762 495308605 6.300000e-43 185.0
21 TraesCS5D01G367700 chr6D 94.292 911 46 6 2790 3697 199213542 199214449 0.000000e+00 1389.0
22 TraesCS5D01G367700 chr6D 82.192 73 12 1 46 118 16181146 16181075 1.110000e-05 62.1
23 TraesCS5D01G367700 chr1D 93.878 931 31 9 2792 3697 348113633 348114562 0.000000e+00 1380.0
24 TraesCS5D01G367700 chr1D 86.567 67 5 2 51 117 114944506 114944444 1.840000e-08 71.3
25 TraesCS5D01G367700 chr7B 86.761 914 93 21 2794 3697 447450996 447450101 0.000000e+00 992.0
26 TraesCS5D01G367700 chr7B 80.942 955 90 58 2782 3697 413877134 413876233 0.000000e+00 671.0
27 TraesCS5D01G367700 chr4B 79.481 385 70 6 122 505 123457215 123456839 7.870000e-67 265.0
28 TraesCS5D01G367700 chr2D 82.428 313 44 8 140 450 375374769 375374466 2.830000e-66 263.0
29 TraesCS5D01G367700 chr2D 80.731 301 49 7 118 416 73464266 73463973 3.710000e-55 226.0
30 TraesCS5D01G367700 chr2D 85.366 82 12 0 36 117 339221338 339221257 6.580000e-13 86.1
31 TraesCS5D01G367700 chr2B 79.328 387 69 10 118 502 94653567 94653944 1.020000e-65 261.0
32 TraesCS5D01G367700 chr2B 87.000 100 12 1 25 123 439337001 439337100 1.090000e-20 111.0
33 TraesCS5D01G367700 chr3B 83.051 236 31 9 3468 3697 8497192 8496960 4.840000e-49 206.0
34 TraesCS5D01G367700 chr3B 84.416 154 15 8 3551 3697 20477855 20477704 3.850000e-30 143.0
35 TraesCS5D01G367700 chr7D 93.846 130 6 2 3569 3697 568822693 568822821 1.050000e-45 195.0
36 TraesCS5D01G367700 chr7D 88.554 166 9 6 3532 3697 108662376 108662221 3.770000e-45 193.0
37 TraesCS5D01G367700 chr3A 86.260 131 15 3 3569 3697 6645109 6644980 4.980000e-29 139.0
38 TraesCS5D01G367700 chr7A 86.813 91 12 0 28 118 126999179 126999269 6.530000e-18 102.0
39 TraesCS5D01G367700 chr6B 86.364 88 12 0 30 117 226015522 226015609 3.040000e-16 97.1
40 TraesCS5D01G367700 chr4A 85.714 91 13 0 28 118 164815426 164815336 3.040000e-16 97.1
41 TraesCS5D01G367700 chr1B 97.368 38 1 0 81 118 261653679 261653642 8.570000e-07 65.8


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 TraesCS5D01G367700 chr5D 444099826 444103522 3696 True 6828.000000 6828 100.000000 1 3697 1 chr5D.!!$R1 3696
1 TraesCS5D01G367700 chr5D 422454796 422455728 932 False 1384.000000 1384 93.891000 2788 3695 1 chr5D.!!$F1 907
2 TraesCS5D01G367700 chr5B 540912672 540915526 2854 True 1039.133333 1982 92.052000 135 2786 3 chr5B.!!$R1 2651
3 TraesCS5D01G367700 chr5A 561125192 561127721 2529 True 763.500000 1923 93.041333 833 2786 3 chr5A.!!$R3 1953
4 TraesCS5D01G367700 chr3D 81848404 81857232 8828 True 1407.000000 1421 94.349000 2790 3697 6 chr3D.!!$R5 907
5 TraesCS5D01G367700 chr6D 199213542 199214449 907 False 1389.000000 1389 94.292000 2790 3697 1 chr6D.!!$F1 907
6 TraesCS5D01G367700 chr1D 348113633 348114562 929 False 1380.000000 1380 93.878000 2792 3697 1 chr1D.!!$F1 905
7 TraesCS5D01G367700 chr7B 447450101 447450996 895 True 992.000000 992 86.761000 2794 3697 1 chr7B.!!$R2 903
8 TraesCS5D01G367700 chr7B 413876233 413877134 901 True 671.000000 671 80.942000 2782 3697 1 chr7B.!!$R1 915

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
713 723 0.096108 GCTTGCTAGCTCTTTGACGC 59.904 55.0 17.23 0.0 44.27 5.19 F
963 977 0.178958 AGTCGTCCCTGTCTTCCAGT 60.179 55.0 0.00 0.0 39.74 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3074 0.168788 CTGCCGCCTATGTTGTTGTG 59.831 55.000 0.0 0.0 0.00 3.33 R
2901 3672 1.208358 CGCGAGTTGTCCTACGTGA 59.792 57.895 0.0 0.0 38.28 4.35 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
22 23 5.023533 ACATATTTGCTTAAGCCTCTCGA 57.976 39.130 24.30 1.62 41.18 4.04
23 24 5.615289 ACATATTTGCTTAAGCCTCTCGAT 58.385 37.500 24.30 11.12 41.18 3.59
24 25 5.698545 ACATATTTGCTTAAGCCTCTCGATC 59.301 40.000 24.30 0.00 41.18 3.69
25 26 3.610040 TTTGCTTAAGCCTCTCGATCA 57.390 42.857 24.30 0.00 41.18 2.92
26 27 3.610040 TTGCTTAAGCCTCTCGATCAA 57.390 42.857 24.30 6.02 41.18 2.57
27 28 3.827008 TGCTTAAGCCTCTCGATCAAT 57.173 42.857 24.30 0.00 41.18 2.57
28 29 3.722147 TGCTTAAGCCTCTCGATCAATC 58.278 45.455 24.30 0.00 41.18 2.67
29 30 3.386078 TGCTTAAGCCTCTCGATCAATCT 59.614 43.478 24.30 0.00 41.18 2.40
30 31 4.141846 TGCTTAAGCCTCTCGATCAATCTT 60.142 41.667 24.30 0.00 41.18 2.40
31 32 4.813697 GCTTAAGCCTCTCGATCAATCTTT 59.186 41.667 17.00 0.00 34.31 2.52
32 33 5.277250 GCTTAAGCCTCTCGATCAATCTTTG 60.277 44.000 17.00 0.00 34.31 2.77
33 34 2.559440 AGCCTCTCGATCAATCTTTGC 58.441 47.619 0.00 0.00 0.00 3.68
34 35 1.601430 GCCTCTCGATCAATCTTTGCC 59.399 52.381 0.00 0.00 0.00 4.52
35 36 2.910199 CCTCTCGATCAATCTTTGCCA 58.090 47.619 0.00 0.00 0.00 4.92
36 37 3.474600 CCTCTCGATCAATCTTTGCCAT 58.525 45.455 0.00 0.00 0.00 4.40
37 38 3.881688 CCTCTCGATCAATCTTTGCCATT 59.118 43.478 0.00 0.00 0.00 3.16
38 39 5.059161 CCTCTCGATCAATCTTTGCCATTA 58.941 41.667 0.00 0.00 0.00 1.90
39 40 5.704515 CCTCTCGATCAATCTTTGCCATTAT 59.295 40.000 0.00 0.00 0.00 1.28
40 41 6.206243 CCTCTCGATCAATCTTTGCCATTATT 59.794 38.462 0.00 0.00 0.00 1.40
41 42 7.255381 CCTCTCGATCAATCTTTGCCATTATTT 60.255 37.037 0.00 0.00 0.00 1.40
42 43 7.642669 TCTCGATCAATCTTTGCCATTATTTC 58.357 34.615 0.00 0.00 0.00 2.17
43 44 6.738114 TCGATCAATCTTTGCCATTATTTCC 58.262 36.000 0.00 0.00 0.00 3.13
44 45 5.922544 CGATCAATCTTTGCCATTATTTCCC 59.077 40.000 0.00 0.00 0.00 3.97
45 46 6.461370 CGATCAATCTTTGCCATTATTTCCCA 60.461 38.462 0.00 0.00 0.00 4.37
46 47 6.617782 TCAATCTTTGCCATTATTTCCCAA 57.382 33.333 0.00 0.00 0.00 4.12
47 48 7.197901 TCAATCTTTGCCATTATTTCCCAAT 57.802 32.000 0.00 0.00 0.00 3.16
48 49 7.631933 TCAATCTTTGCCATTATTTCCCAATT 58.368 30.769 0.00 0.00 0.00 2.32
49 50 7.553402 TCAATCTTTGCCATTATTTCCCAATTG 59.447 33.333 0.00 0.00 0.00 2.32
50 51 5.743117 TCTTTGCCATTATTTCCCAATTGG 58.257 37.500 18.21 18.21 0.00 3.16
51 52 3.557228 TGCCATTATTTCCCAATTGGC 57.443 42.857 19.75 4.79 41.18 4.52
52 53 3.113824 TGCCATTATTTCCCAATTGGCT 58.886 40.909 19.75 5.72 41.35 4.75
53 54 3.522750 TGCCATTATTTCCCAATTGGCTT 59.477 39.130 19.75 5.54 41.35 4.35
54 55 4.129380 GCCATTATTTCCCAATTGGCTTC 58.871 43.478 19.75 0.00 38.10 3.86
55 56 4.707105 CCATTATTTCCCAATTGGCTTCC 58.293 43.478 19.75 0.00 0.00 3.46
56 57 4.163839 CCATTATTTCCCAATTGGCTTCCA 59.836 41.667 19.75 0.57 0.00 3.53
70 71 6.855763 TTGGCTTCCAATAGTTCATGAATT 57.144 33.333 12.12 10.23 38.75 2.17
71 72 6.855763 TGGCTTCCAATAGTTCATGAATTT 57.144 33.333 12.12 6.06 0.00 1.82
72 73 7.953005 TGGCTTCCAATAGTTCATGAATTTA 57.047 32.000 12.12 8.13 0.00 1.40
73 74 8.359875 TGGCTTCCAATAGTTCATGAATTTAA 57.640 30.769 12.12 0.00 0.00 1.52
74 75 8.980596 TGGCTTCCAATAGTTCATGAATTTAAT 58.019 29.630 12.12 0.00 0.00 1.40
75 76 9.468532 GGCTTCCAATAGTTCATGAATTTAATC 57.531 33.333 12.12 0.00 0.00 1.75
76 77 9.468532 GCTTCCAATAGTTCATGAATTTAATCC 57.531 33.333 12.12 0.00 0.00 3.01
80 81 9.199982 CCAATAGTTCATGAATTTAATCCATGC 57.800 33.333 12.12 0.00 37.99 4.06
81 82 9.752961 CAATAGTTCATGAATTTAATCCATGCA 57.247 29.630 12.12 0.00 37.99 3.96
91 92 8.190122 TGAATTTAATCCATGCATATATTCCGC 58.810 33.333 0.00 0.00 0.00 5.54
92 93 7.643569 ATTTAATCCATGCATATATTCCGCA 57.356 32.000 0.00 0.00 40.50 5.69
93 94 6.682423 TTAATCCATGCATATATTCCGCAG 57.318 37.500 0.00 0.00 39.39 5.18
94 95 2.358957 TCCATGCATATATTCCGCAGC 58.641 47.619 0.00 0.00 39.39 5.25
95 96 2.086094 CCATGCATATATTCCGCAGCA 58.914 47.619 0.00 0.00 39.39 4.41
96 97 2.488937 CCATGCATATATTCCGCAGCAA 59.511 45.455 0.00 0.00 39.39 3.91
97 98 3.495193 CATGCATATATTCCGCAGCAAC 58.505 45.455 0.00 0.00 39.39 4.17
98 99 1.530720 TGCATATATTCCGCAGCAACG 59.469 47.619 0.00 0.00 0.00 4.10
99 100 1.725931 GCATATATTCCGCAGCAACGC 60.726 52.381 0.00 0.00 0.00 4.84
113 114 3.766691 ACGCGCGGGGTGTTATCT 61.767 61.111 35.22 5.42 35.33 1.98
114 115 2.414179 CGCGCGGGGTGTTATCTA 59.586 61.111 24.84 0.00 0.00 1.98
115 116 1.660575 CGCGCGGGGTGTTATCTAG 60.661 63.158 24.84 0.00 0.00 2.43
116 117 1.440476 GCGCGGGGTGTTATCTAGT 59.560 57.895 8.83 0.00 0.00 2.57
117 118 0.179092 GCGCGGGGTGTTATCTAGTT 60.179 55.000 8.83 0.00 0.00 2.24
118 119 1.741394 GCGCGGGGTGTTATCTAGTTT 60.741 52.381 8.83 0.00 0.00 2.66
119 120 2.624636 CGCGGGGTGTTATCTAGTTTT 58.375 47.619 0.00 0.00 0.00 2.43
120 121 3.784338 CGCGGGGTGTTATCTAGTTTTA 58.216 45.455 0.00 0.00 0.00 1.52
121 122 4.183101 CGCGGGGTGTTATCTAGTTTTAA 58.817 43.478 0.00 0.00 0.00 1.52
122 123 4.630940 CGCGGGGTGTTATCTAGTTTTAAA 59.369 41.667 0.00 0.00 0.00 1.52
123 124 5.295045 CGCGGGGTGTTATCTAGTTTTAAAT 59.705 40.000 0.00 0.00 0.00 1.40
124 125 6.479660 CGCGGGGTGTTATCTAGTTTTAAATA 59.520 38.462 0.00 0.00 0.00 1.40
125 126 7.011295 CGCGGGGTGTTATCTAGTTTTAAATAA 59.989 37.037 0.00 0.00 0.00 1.40
126 127 8.124823 GCGGGGTGTTATCTAGTTTTAAATAAC 58.875 37.037 0.00 3.82 35.90 1.89
127 128 8.330302 CGGGGTGTTATCTAGTTTTAAATAACG 58.670 37.037 0.00 0.00 37.39 3.18
128 129 8.615211 GGGGTGTTATCTAGTTTTAAATAACGG 58.385 37.037 0.00 0.00 37.39 4.44
129 130 8.615211 GGGTGTTATCTAGTTTTAAATAACGGG 58.385 37.037 0.00 0.00 37.39 5.28
130 131 8.124823 GGTGTTATCTAGTTTTAAATAACGGGC 58.875 37.037 0.00 0.00 37.39 6.13
131 132 7.847564 GTGTTATCTAGTTTTAAATAACGGGCG 59.152 37.037 0.00 0.00 37.39 6.13
132 133 7.763528 TGTTATCTAGTTTTAAATAACGGGCGA 59.236 33.333 0.00 0.00 37.39 5.54
133 134 6.839820 ATCTAGTTTTAAATAACGGGCGAG 57.160 37.500 0.00 0.00 33.26 5.03
134 135 3.752412 AGTTTTAAATAACGGGCGAGC 57.248 42.857 0.00 0.00 33.26 5.03
135 136 2.094734 AGTTTTAAATAACGGGCGAGCG 59.905 45.455 0.00 0.00 33.26 5.03
136 137 1.008329 TTTAAATAACGGGCGAGCGG 58.992 50.000 0.00 0.00 0.00 5.52
137 138 0.175302 TTAAATAACGGGCGAGCGGA 59.825 50.000 0.00 0.00 0.00 5.54
166 167 1.341369 GCCGGCGTTGTGTTTAATGC 61.341 55.000 12.58 0.00 40.87 3.56
173 174 2.202557 GTGTTTAATGCCGCCCGC 60.203 61.111 0.00 0.00 38.31 6.13
216 217 3.440522 GCTGAATTAGGTTTCTCGGCTTT 59.559 43.478 0.00 0.00 0.00 3.51
221 222 0.602905 AGGTTTCTCGGCTTTCCACG 60.603 55.000 0.00 0.00 0.00 4.94
237 238 3.508840 CGCGGGTTCAATGGAGGC 61.509 66.667 0.00 0.00 0.00 4.70
246 247 3.442273 GGTTCAATGGAGGCGTTTGAATA 59.558 43.478 7.72 0.00 40.37 1.75
249 250 4.075682 TCAATGGAGGCGTTTGAATACAA 58.924 39.130 0.00 0.00 0.00 2.41
264 265 3.655276 ATACAACGAGGAGACGTGTTT 57.345 42.857 0.00 0.00 45.83 2.83
269 270 0.242825 CGAGGAGACGTGTTTAGCCA 59.757 55.000 0.00 0.00 0.00 4.75
276 277 2.561373 GTGTTTAGCCAGGCGTGC 59.439 61.111 5.55 0.00 0.00 5.34
279 280 2.359850 TTTAGCCAGGCGTGCAGG 60.360 61.111 5.55 1.01 0.00 4.85
316 317 1.210931 CTGTGTGCCGCTTCAATGG 59.789 57.895 0.00 0.00 0.00 3.16
342 343 1.679305 AGTGAGAGGTCGCATCCGT 60.679 57.895 0.00 0.00 35.46 4.69
363 364 0.445436 CTGAGCCGTCTTCAATGTGC 59.555 55.000 0.00 0.00 0.00 4.57
365 366 0.874390 GAGCCGTCTTCAATGTGCAA 59.126 50.000 0.00 0.00 0.00 4.08
366 367 0.877071 AGCCGTCTTCAATGTGCAAG 59.123 50.000 0.00 0.00 0.00 4.01
370 371 1.872952 CGTCTTCAATGTGCAAGGACA 59.127 47.619 0.00 0.00 0.00 4.02
382 383 1.702886 CAAGGACACACTCTACAGCG 58.297 55.000 0.00 0.00 0.00 5.18
396 397 2.114670 CAGCGGCATGAATTCGGGT 61.115 57.895 1.45 0.00 0.00 5.28
398 399 0.532862 AGCGGCATGAATTCGGGTAG 60.533 55.000 1.45 0.00 0.00 3.18
404 405 0.546122 ATGAATTCGGGTAGCTGGCA 59.454 50.000 0.00 0.00 0.00 4.92
405 406 0.546122 TGAATTCGGGTAGCTGGCAT 59.454 50.000 0.00 0.00 0.00 4.40
407 408 0.546122 AATTCGGGTAGCTGGCATCA 59.454 50.000 0.00 0.00 0.00 3.07
412 413 2.501128 GTAGCTGGCATCAGGCGA 59.499 61.111 0.00 0.00 46.16 5.54
440 441 3.440415 GGGCGAGGAAAAAGGCGG 61.440 66.667 0.00 0.00 0.00 6.13
445 447 0.948678 CGAGGAAAAAGGCGGTTTGA 59.051 50.000 0.00 0.00 0.00 2.69
452 454 1.534729 AAAGGCGGTTTGAGTGGATC 58.465 50.000 0.00 0.00 0.00 3.36
467 469 3.328931 AGTGGATCAATGTGGTCAGAAGT 59.671 43.478 0.00 0.00 0.00 3.01
479 481 4.643387 AGAAGTGGGCGTGGGTGC 62.643 66.667 0.00 0.00 0.00 5.01
488 490 2.357517 CGTGGGTGCTGTCTGGAC 60.358 66.667 0.00 0.00 36.19 4.02
497 499 4.243008 TGTCTGGACGCCCGCAAA 62.243 61.111 0.00 0.00 34.29 3.68
526 528 0.249657 TTTGCGGGACAAAACATGCC 60.250 50.000 0.00 0.00 45.22 4.40
527 529 2.093537 TTGCGGGACAAAACATGCCC 62.094 55.000 0.00 0.00 40.18 5.36
545 547 1.141881 CGGACCATCCTTCGGACTG 59.858 63.158 0.00 0.00 32.98 3.51
552 554 3.133003 ACCATCCTTCGGACTGATACAAG 59.867 47.826 0.00 0.00 32.98 3.16
557 559 0.968901 TCGGACTGATACAAGCCCGT 60.969 55.000 0.00 0.00 38.25 5.28
561 563 1.732259 GACTGATACAAGCCCGTGTTG 59.268 52.381 0.00 0.00 32.75 3.33
580 582 1.599518 GATGCCACACCAACGTCCA 60.600 57.895 0.00 0.00 0.00 4.02
592 594 3.445805 ACCAACGTCCAAACAGTTCAATT 59.554 39.130 0.00 0.00 0.00 2.32
649 651 8.168058 TGCCCTATAATACCCTAAAATTCCTTC 58.832 37.037 0.00 0.00 0.00 3.46
670 672 6.405842 CCTTCCAAAAGGCCTATCAATGTAAC 60.406 42.308 5.16 0.00 45.50 2.50
673 683 5.163519 CCAAAAGGCCTATCAATGTAACCAG 60.164 44.000 5.16 0.00 0.00 4.00
681 691 1.795872 TCAATGTAACCAGAACGCACG 59.204 47.619 0.00 0.00 0.00 5.34
696 706 1.261619 CGCACGTTTTCTTCAAGAGCT 59.738 47.619 0.00 0.00 0.00 4.09
697 707 2.286418 CGCACGTTTTCTTCAAGAGCTT 60.286 45.455 0.00 0.00 0.00 3.74
698 708 3.038710 GCACGTTTTCTTCAAGAGCTTG 58.961 45.455 3.87 3.87 41.71 4.01
699 709 3.038710 CACGTTTTCTTCAAGAGCTTGC 58.961 45.455 5.37 0.00 40.24 4.01
700 710 2.945668 ACGTTTTCTTCAAGAGCTTGCT 59.054 40.909 5.37 0.00 40.24 3.91
701 711 4.024893 CACGTTTTCTTCAAGAGCTTGCTA 60.025 41.667 5.37 0.00 40.24 3.49
702 712 4.212214 ACGTTTTCTTCAAGAGCTTGCTAG 59.788 41.667 5.37 5.80 40.24 3.42
713 723 0.096108 GCTTGCTAGCTCTTTGACGC 59.904 55.000 17.23 0.00 44.27 5.19
740 750 5.051816 CGTAAGTGTCCTGGTTTGTCTTTA 58.948 41.667 0.00 0.00 0.00 1.85
764 774 3.756117 GGAGAGAATCCTGGTTTGTTGT 58.244 45.455 0.00 0.00 45.64 3.32
777 787 1.025812 TTGTTGTGTAGGCCCAAACG 58.974 50.000 0.00 0.00 0.00 3.60
778 788 1.284715 GTTGTGTAGGCCCAAACGC 59.715 57.895 0.00 2.74 0.00 4.84
784 794 0.950071 GTAGGCCCAAACGCACGTTA 60.950 55.000 9.08 0.00 37.35 3.18
820 830 5.676953 CGTTATCCGCCTAAAAATTAGAGC 58.323 41.667 0.00 0.96 0.00 4.09
827 837 4.035675 CGCCTAAAAATTAGAGCAGGAAGG 59.964 45.833 0.00 0.00 0.00 3.46
887 897 0.381089 GACTCCACCTACCATCGTCG 59.619 60.000 0.00 0.00 0.00 5.12
888 898 0.323178 ACTCCACCTACCATCGTCGT 60.323 55.000 0.00 0.00 0.00 4.34
889 899 0.381089 CTCCACCTACCATCGTCGTC 59.619 60.000 0.00 0.00 0.00 4.20
951 965 1.681538 TAGATGAGCTGGAGTCGTCC 58.318 55.000 0.00 0.00 44.24 4.79
963 977 0.178958 AGTCGTCCCTGTCTTCCAGT 60.179 55.000 0.00 0.00 39.74 4.00
971 985 2.498078 CCCTGTCTTCCAGTCTAGTTCC 59.502 54.545 0.00 0.00 39.74 3.62
972 986 2.164624 CCTGTCTTCCAGTCTAGTTCCG 59.835 54.545 0.00 0.00 39.74 4.30
992 1010 2.669569 CCCAAGCTCCACACCACG 60.670 66.667 0.00 0.00 0.00 4.94
993 1011 2.425592 CCAAGCTCCACACCACGA 59.574 61.111 0.00 0.00 0.00 4.35
994 1012 1.961277 CCAAGCTCCACACCACGAC 60.961 63.158 0.00 0.00 0.00 4.34
1014 1050 1.443828 GAGGATGGAGAAGGACGGC 59.556 63.158 0.00 0.00 0.00 5.68
1085 1121 1.614241 CCGATTCGGTTCTCCCCACT 61.614 60.000 17.08 0.00 42.73 4.00
1094 1130 3.083997 CTCCCCACTCCCCTTCCG 61.084 72.222 0.00 0.00 0.00 4.30
1105 1141 1.708551 TCCCCTTCCGTCCAATTTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1106 1142 2.109304 TCCCCTTCCGTCCAATTTCTTT 59.891 45.455 0.00 0.00 0.00 2.52
1110 1146 4.321230 CCCTTCCGTCCAATTTCTTTCTTG 60.321 45.833 0.00 0.00 0.00 3.02
1112 1148 5.472137 CCTTCCGTCCAATTTCTTTCTTGTA 59.528 40.000 0.00 0.00 0.00 2.41
1126 1213 8.848474 TTCTTTCTTGTAGACCAGAATTAAGG 57.152 34.615 0.00 0.00 0.00 2.69
1130 1217 4.216411 TGTAGACCAGAATTAAGGTGGC 57.784 45.455 6.05 0.00 38.50 5.01
1132 1219 3.636153 AGACCAGAATTAAGGTGGCTC 57.364 47.619 6.05 0.19 38.50 4.70
1169 1261 5.281314 TCCTATATCCCTAGGGCTGAATTC 58.719 45.833 24.42 0.00 39.08 2.17
1179 1271 2.174424 AGGGCTGAATTCTCCAATCCTC 59.826 50.000 15.80 2.07 0.00 3.71
1188 1280 1.036707 CTCCAATCCTCCTCGTCTCC 58.963 60.000 0.00 0.00 0.00 3.71
1189 1281 0.752009 TCCAATCCTCCTCGTCTCCG 60.752 60.000 0.00 0.00 0.00 4.63
1190 1282 1.038130 CCAATCCTCCTCGTCTCCGT 61.038 60.000 0.00 0.00 35.01 4.69
1191 1283 0.382515 CAATCCTCCTCGTCTCCGTC 59.617 60.000 0.00 0.00 35.01 4.79
1192 1284 0.256464 AATCCTCCTCGTCTCCGTCT 59.744 55.000 0.00 0.00 35.01 4.18
1193 1285 0.179040 ATCCTCCTCGTCTCCGTCTC 60.179 60.000 0.00 0.00 35.01 3.36
1194 1286 1.820481 CCTCCTCGTCTCCGTCTCC 60.820 68.421 0.00 0.00 35.01 3.71
1195 1287 2.125229 TCCTCGTCTCCGTCTCCG 60.125 66.667 0.00 0.00 35.01 4.63
1196 1288 2.436292 CCTCGTCTCCGTCTCCGT 60.436 66.667 0.00 0.00 35.01 4.69
1197 1289 2.462782 CCTCGTCTCCGTCTCCGTC 61.463 68.421 0.00 0.00 35.01 4.79
1198 1290 1.448189 CTCGTCTCCGTCTCCGTCT 60.448 63.158 0.00 0.00 35.01 4.18
1199 1291 1.422950 CTCGTCTCCGTCTCCGTCTC 61.423 65.000 0.00 0.00 35.01 3.36
1211 1303 2.026301 CGTCTCCGGCGGAATCTC 59.974 66.667 30.59 17.70 0.00 2.75
1217 1309 2.482333 CCGGCGGAATCTCTCGAGT 61.482 63.158 24.41 0.00 0.00 4.18
1256 1630 5.174395 CACGGATGGCCAAATGAATTTTAA 58.826 37.500 10.96 0.00 0.00 1.52
1322 1726 1.202417 GCTGCTGCCTCGATACAGTAA 60.202 52.381 14.26 5.03 36.26 2.24
1323 1727 2.464865 CTGCTGCCTCGATACAGTAAC 58.535 52.381 14.26 1.81 36.26 2.50
1324 1728 1.822371 TGCTGCCTCGATACAGTAACA 59.178 47.619 14.26 3.95 36.26 2.41
1325 1729 2.159240 TGCTGCCTCGATACAGTAACAG 60.159 50.000 14.26 0.00 36.26 3.16
1326 1730 2.159226 GCTGCCTCGATACAGTAACAGT 60.159 50.000 14.26 0.00 36.26 3.55
1327 1731 3.066342 GCTGCCTCGATACAGTAACAGTA 59.934 47.826 14.26 0.00 36.26 2.74
1345 1749 0.541392 TACTGTACATGGCCCTGCTG 59.459 55.000 8.09 0.00 0.00 4.41
1346 1750 1.300963 CTGTACATGGCCCTGCTGT 59.699 57.895 8.09 5.34 0.00 4.40
1347 1751 0.541392 CTGTACATGGCCCTGCTGTA 59.459 55.000 8.09 4.36 0.00 2.74
1348 1752 0.251916 TGTACATGGCCCTGCTGTAC 59.748 55.000 19.93 19.93 43.44 2.90
1353 1757 2.045926 GGCCCTGCTGTACCTGTG 60.046 66.667 0.00 0.00 0.00 3.66
1360 1764 1.743252 GCTGTACCTGTGCTCTGCC 60.743 63.158 0.00 0.00 0.00 4.85
1361 1765 1.673477 CTGTACCTGTGCTCTGCCA 59.327 57.895 0.00 0.00 0.00 4.92
1364 1768 1.207089 TGTACCTGTGCTCTGCCATAC 59.793 52.381 0.00 0.00 0.00 2.39
1380 1784 6.988580 TCTGCCATACTGAATGAATCTTACAG 59.011 38.462 0.00 0.00 37.86 2.74
1381 1785 6.888105 TGCCATACTGAATGAATCTTACAGA 58.112 36.000 0.00 0.00 37.86 3.41
1395 1799 7.823745 AATCTTACAGATTCAGTGTTGGTTT 57.176 32.000 0.00 0.00 40.75 3.27
1396 1800 7.823745 ATCTTACAGATTCAGTGTTGGTTTT 57.176 32.000 0.00 0.00 28.69 2.43
1397 1801 7.639113 TCTTACAGATTCAGTGTTGGTTTTT 57.361 32.000 0.00 0.00 0.00 1.94
1398 1802 8.740123 TCTTACAGATTCAGTGTTGGTTTTTA 57.260 30.769 0.00 0.00 0.00 1.52
1399 1803 8.617809 TCTTACAGATTCAGTGTTGGTTTTTAC 58.382 33.333 0.00 0.00 0.00 2.01
1400 1804 8.514330 TTACAGATTCAGTGTTGGTTTTTACT 57.486 30.769 0.00 0.00 0.00 2.24
1401 1805 7.404671 ACAGATTCAGTGTTGGTTTTTACTT 57.595 32.000 0.00 0.00 0.00 2.24
1402 1806 8.514330 ACAGATTCAGTGTTGGTTTTTACTTA 57.486 30.769 0.00 0.00 0.00 2.24
1403 1807 9.131791 ACAGATTCAGTGTTGGTTTTTACTTAT 57.868 29.630 0.00 0.00 0.00 1.73
1404 1808 9.965824 CAGATTCAGTGTTGGTTTTTACTTATT 57.034 29.630 0.00 0.00 0.00 1.40
1406 1810 9.113876 GATTCAGTGTTGGTTTTTACTTATTCG 57.886 33.333 0.00 0.00 0.00 3.34
1407 1811 7.789273 TCAGTGTTGGTTTTTACTTATTCGA 57.211 32.000 0.00 0.00 0.00 3.71
1408 1812 8.211116 TCAGTGTTGGTTTTTACTTATTCGAA 57.789 30.769 0.00 0.00 0.00 3.71
1409 1813 8.675504 TCAGTGTTGGTTTTTACTTATTCGAAA 58.324 29.630 0.00 0.00 0.00 3.46
1410 1814 9.291664 CAGTGTTGGTTTTTACTTATTCGAAAA 57.708 29.630 0.00 0.00 0.00 2.29
1411 1815 9.857957 AGTGTTGGTTTTTACTTATTCGAAAAA 57.142 25.926 0.00 0.00 31.42 1.94
1452 1856 2.507484 TCTGGTGCCAAATCTGAAGTG 58.493 47.619 0.00 0.00 0.00 3.16
1473 1877 3.251729 TGCTGAACATGCTGTTTCTCTTC 59.748 43.478 0.00 0.00 41.28 2.87
1475 1879 4.082895 GCTGAACATGCTGTTTCTCTTCAT 60.083 41.667 0.00 0.00 41.28 2.57
1476 1880 5.366829 TGAACATGCTGTTTCTCTTCATG 57.633 39.130 0.00 0.00 41.28 3.07
1480 1889 4.214971 ACATGCTGTTTCTCTTCATGTGTC 59.785 41.667 5.50 0.00 43.99 3.67
1517 1926 2.514824 GCAATGGAGGGCTCGGAC 60.515 66.667 0.00 0.00 0.00 4.79
1518 1927 3.036429 GCAATGGAGGGCTCGGACT 62.036 63.158 0.00 0.00 0.00 3.85
1519 1928 1.144936 CAATGGAGGGCTCGGACTC 59.855 63.158 0.00 0.00 0.00 3.36
1520 1929 2.427245 AATGGAGGGCTCGGACTCG 61.427 63.158 0.00 0.00 34.58 4.18
1522 1931 4.816984 GGAGGGCTCGGACTCGGA 62.817 72.222 0.00 0.00 36.95 4.55
1523 1932 3.213402 GAGGGCTCGGACTCGGAG 61.213 72.222 2.83 2.83 36.95 4.63
1524 1933 3.700831 GAGGGCTCGGACTCGGAGA 62.701 68.421 12.86 0.00 36.95 3.71
1525 1934 2.519780 GGGCTCGGACTCGGAGAT 60.520 66.667 12.86 0.00 33.89 2.75
1526 1935 2.557372 GGGCTCGGACTCGGAGATC 61.557 68.421 12.86 5.60 33.89 2.75
1527 1936 1.824329 GGCTCGGACTCGGAGATCA 60.824 63.158 12.86 0.00 33.89 2.92
1528 1937 1.357334 GCTCGGACTCGGAGATCAC 59.643 63.158 12.86 0.38 33.89 3.06
1529 1938 2.026522 CTCGGACTCGGAGATCACC 58.973 63.158 12.86 0.00 33.89 4.02
1530 1939 0.748367 CTCGGACTCGGAGATCACCA 60.748 60.000 12.86 0.00 33.89 4.17
1531 1940 0.748367 TCGGACTCGGAGATCACCAG 60.748 60.000 12.86 8.22 33.89 4.00
1532 1941 1.439644 GGACTCGGAGATCACCAGC 59.560 63.158 12.86 3.34 33.89 4.85
1533 1942 1.323271 GGACTCGGAGATCACCAGCA 61.323 60.000 12.86 0.00 33.89 4.41
1534 1943 0.532573 GACTCGGAGATCACCAGCAA 59.467 55.000 12.86 0.00 33.89 3.91
1535 1944 0.247736 ACTCGGAGATCACCAGCAAC 59.752 55.000 12.86 0.00 33.89 4.17
1536 1945 0.803768 CTCGGAGATCACCAGCAACG 60.804 60.000 9.99 0.00 33.89 4.10
1537 1946 1.811266 CGGAGATCACCAGCAACGG 60.811 63.158 9.99 0.00 0.00 4.44
1538 1947 1.596934 GGAGATCACCAGCAACGGA 59.403 57.895 4.05 0.00 0.00 4.69
1539 1948 0.460987 GGAGATCACCAGCAACGGAG 60.461 60.000 4.05 0.00 0.00 4.63
1540 1949 0.532573 GAGATCACCAGCAACGGAGA 59.467 55.000 0.00 0.00 0.00 3.71
1736 2145 3.346631 CTACTACAACGGCGGCGGT 62.347 63.158 35.05 28.52 0.00 5.68
1757 2166 1.138661 CAGAGCAAGTGGATCCTCTCC 59.861 57.143 16.50 10.75 45.19 3.71
1818 2227 2.022240 GCTCCCCTGCTACCTCTTCG 62.022 65.000 0.00 0.00 0.00 3.79
1924 2333 3.142838 GTACGCCTGGGCCTACGA 61.143 66.667 17.85 2.12 37.98 3.43
2208 2617 1.073768 GGAGCTCGTCTTCGACAAGC 61.074 60.000 7.83 0.00 41.35 4.01
2659 3074 2.014128 CAGAGAGAGAGGTTCGTCTCC 58.986 57.143 15.76 9.56 43.64 3.71
2678 3093 0.168788 CACAACAACATAGGCGGCAG 59.831 55.000 13.08 2.78 0.00 4.85
2718 3136 3.708451 TGCTATGGTTGTACTGGAGAGA 58.292 45.455 0.00 0.00 0.00 3.10
2732 3150 7.553402 TGTACTGGAGAGAAGTATAGTTCTGAC 59.447 40.741 24.42 17.10 36.89 3.51
2738 3156 6.408035 AGAGAAGTATAGTTCTGACTCGTGA 58.592 40.000 24.42 0.00 36.89 4.35
2901 3672 2.508526 GAGAGGGCTGATTTTGTGTGT 58.491 47.619 0.00 0.00 0.00 3.72
2979 3752 0.882484 TTCCGATGTCAGCGTTTGCA 60.882 50.000 9.95 0.00 46.23 4.08
3160 5544 5.440234 ACATGTATTTGTTGCCACGTTTA 57.560 34.783 0.00 0.00 0.00 2.01
3239 5623 1.916273 ACCGTAGTCCACATGCCCA 60.916 57.895 0.00 0.00 0.00 5.36
3246 5630 0.257039 GTCCACATGCCCATCTCCTT 59.743 55.000 0.00 0.00 0.00 3.36
3254 5638 0.259938 GCCCATCTCCTTTCCCACAT 59.740 55.000 0.00 0.00 0.00 3.21
3483 9034 0.034337 CAGCTGCAGTTGCCCAAAAT 59.966 50.000 18.01 0.00 41.18 1.82
3484 9035 0.034337 AGCTGCAGTTGCCCAAAATG 59.966 50.000 16.64 0.00 41.18 2.32
3485 9036 0.952010 GCTGCAGTTGCCCAAAATGG 60.952 55.000 16.64 0.00 41.18 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.698089 TGATCGAGAGGCTTAAGCAAATATG 59.302 40.000 27.83 13.01 44.36 1.78
4 5 4.142609 TGATCGAGAGGCTTAAGCAAAT 57.857 40.909 27.83 13.72 44.36 2.32
6 7 3.610040 TTGATCGAGAGGCTTAAGCAA 57.390 42.857 27.83 8.26 44.36 3.91
8 9 3.988819 AGATTGATCGAGAGGCTTAAGC 58.011 45.455 19.53 19.53 41.14 3.09
9 10 5.277250 GCAAAGATTGATCGAGAGGCTTAAG 60.277 44.000 0.00 0.00 0.00 1.85
10 11 4.572389 GCAAAGATTGATCGAGAGGCTTAA 59.428 41.667 0.00 0.00 0.00 1.85
11 12 4.122776 GCAAAGATTGATCGAGAGGCTTA 58.877 43.478 0.00 0.00 0.00 3.09
12 13 2.941720 GCAAAGATTGATCGAGAGGCTT 59.058 45.455 0.00 0.00 0.00 4.35
14 15 1.601430 GGCAAAGATTGATCGAGAGGC 59.399 52.381 0.00 0.00 0.00 4.70
15 16 2.910199 TGGCAAAGATTGATCGAGAGG 58.090 47.619 0.00 0.00 0.00 3.69
16 17 6.798315 ATAATGGCAAAGATTGATCGAGAG 57.202 37.500 0.00 0.00 0.00 3.20
17 18 7.255242 GGAAATAATGGCAAAGATTGATCGAGA 60.255 37.037 0.00 0.00 0.00 4.04
18 19 6.860023 GGAAATAATGGCAAAGATTGATCGAG 59.140 38.462 0.00 0.00 0.00 4.04
20 21 5.922544 GGGAAATAATGGCAAAGATTGATCG 59.077 40.000 0.00 0.00 0.00 3.69
21 22 6.819284 TGGGAAATAATGGCAAAGATTGATC 58.181 36.000 0.00 0.00 0.00 2.92
22 23 6.811634 TGGGAAATAATGGCAAAGATTGAT 57.188 33.333 0.00 0.00 0.00 2.57
23 24 6.617782 TTGGGAAATAATGGCAAAGATTGA 57.382 33.333 0.00 0.00 0.00 2.57
24 25 7.201750 CCAATTGGGAAATAATGGCAAAGATTG 60.202 37.037 17.36 0.00 40.01 2.67
25 26 6.829811 CCAATTGGGAAATAATGGCAAAGATT 59.170 34.615 17.36 0.00 40.01 2.40
26 27 6.358991 CCAATTGGGAAATAATGGCAAAGAT 58.641 36.000 17.36 0.00 40.01 2.40
27 28 5.743117 CCAATTGGGAAATAATGGCAAAGA 58.257 37.500 17.36 0.00 40.01 2.52
28 29 4.336153 GCCAATTGGGAAATAATGGCAAAG 59.664 41.667 25.73 0.00 40.57 2.77
29 30 4.018597 AGCCAATTGGGAAATAATGGCAAA 60.019 37.500 25.73 0.00 43.04 3.68
30 31 3.522750 AGCCAATTGGGAAATAATGGCAA 59.477 39.130 25.73 0.00 43.04 4.52
31 32 3.113824 AGCCAATTGGGAAATAATGGCA 58.886 40.909 25.73 0.00 43.04 4.92
32 33 3.843893 AGCCAATTGGGAAATAATGGC 57.156 42.857 25.73 8.12 40.01 4.40
33 34 4.163839 TGGAAGCCAATTGGGAAATAATGG 59.836 41.667 25.73 0.00 40.01 3.16
34 35 5.356291 TGGAAGCCAATTGGGAAATAATG 57.644 39.130 25.73 0.00 40.01 1.90
48 49 6.855763 AAATTCATGAACTATTGGAAGCCA 57.144 33.333 11.07 0.00 0.00 4.75
49 50 9.468532 GATTAAATTCATGAACTATTGGAAGCC 57.531 33.333 11.07 0.00 0.00 4.35
50 51 9.468532 GGATTAAATTCATGAACTATTGGAAGC 57.531 33.333 11.07 3.19 0.00 3.86
54 55 9.199982 GCATGGATTAAATTCATGAACTATTGG 57.800 33.333 11.07 0.00 40.28 3.16
55 56 9.752961 TGCATGGATTAAATTCATGAACTATTG 57.247 29.630 11.07 1.13 40.28 1.90
65 66 8.190122 GCGGAATATATGCATGGATTAAATTCA 58.810 33.333 20.25 0.34 0.00 2.57
66 67 8.190122 TGCGGAATATATGCATGGATTAAATTC 58.810 33.333 10.16 11.58 32.86 2.17
67 68 8.065473 TGCGGAATATATGCATGGATTAAATT 57.935 30.769 10.16 3.22 32.86 1.82
68 69 7.643569 TGCGGAATATATGCATGGATTAAAT 57.356 32.000 10.16 0.00 32.86 1.40
69 70 6.404623 GCTGCGGAATATATGCATGGATTAAA 60.405 38.462 10.16 0.00 38.07 1.52
70 71 5.066375 GCTGCGGAATATATGCATGGATTAA 59.934 40.000 10.16 0.00 38.07 1.40
71 72 4.576053 GCTGCGGAATATATGCATGGATTA 59.424 41.667 10.16 0.00 38.07 1.75
72 73 3.379372 GCTGCGGAATATATGCATGGATT 59.621 43.478 10.16 8.51 38.07 3.01
73 74 2.947652 GCTGCGGAATATATGCATGGAT 59.052 45.455 10.16 4.68 38.07 3.41
74 75 2.290197 TGCTGCGGAATATATGCATGGA 60.290 45.455 10.16 0.00 38.07 3.41
75 76 2.086094 TGCTGCGGAATATATGCATGG 58.914 47.619 10.16 0.00 38.07 3.66
76 77 3.495193 GTTGCTGCGGAATATATGCATG 58.505 45.455 10.16 0.00 38.07 4.06
77 78 2.160219 CGTTGCTGCGGAATATATGCAT 59.840 45.455 3.79 3.79 38.07 3.96
78 79 1.530720 CGTTGCTGCGGAATATATGCA 59.469 47.619 0.00 0.00 37.07 3.96
79 80 1.725931 GCGTTGCTGCGGAATATATGC 60.726 52.381 0.00 0.00 0.00 3.14
80 81 2.232239 GCGTTGCTGCGGAATATATG 57.768 50.000 0.00 0.00 0.00 1.78
94 95 3.090960 GATAACACCCCGCGCGTTG 62.091 63.158 29.95 23.32 0.00 4.10
95 96 1.947597 TAGATAACACCCCGCGCGTT 61.948 55.000 29.95 18.17 0.00 4.84
96 97 2.345880 CTAGATAACACCCCGCGCGT 62.346 60.000 29.95 11.67 0.00 6.01
97 98 1.660575 CTAGATAACACCCCGCGCG 60.661 63.158 25.67 25.67 0.00 6.86
98 99 0.179092 AACTAGATAACACCCCGCGC 60.179 55.000 0.00 0.00 0.00 6.86
99 100 2.304751 AAACTAGATAACACCCCGCG 57.695 50.000 0.00 0.00 0.00 6.46
100 101 6.688637 ATTTAAAACTAGATAACACCCCGC 57.311 37.500 0.00 0.00 0.00 6.13
101 102 8.330302 CGTTATTTAAAACTAGATAACACCCCG 58.670 37.037 0.00 0.00 35.66 5.73
102 103 8.615211 CCGTTATTTAAAACTAGATAACACCCC 58.385 37.037 0.00 0.00 35.66 4.95
103 104 8.615211 CCCGTTATTTAAAACTAGATAACACCC 58.385 37.037 0.00 0.00 35.66 4.61
104 105 8.124823 GCCCGTTATTTAAAACTAGATAACACC 58.875 37.037 0.00 0.00 35.66 4.16
105 106 7.847564 CGCCCGTTATTTAAAACTAGATAACAC 59.152 37.037 0.00 0.00 35.66 3.32
106 107 7.763528 TCGCCCGTTATTTAAAACTAGATAACA 59.236 33.333 0.00 0.00 35.66 2.41
107 108 8.130307 TCGCCCGTTATTTAAAACTAGATAAC 57.870 34.615 0.00 0.00 33.67 1.89
108 109 7.042523 GCTCGCCCGTTATTTAAAACTAGATAA 60.043 37.037 0.00 0.00 0.00 1.75
109 110 6.421801 GCTCGCCCGTTATTTAAAACTAGATA 59.578 38.462 0.00 0.00 0.00 1.98
110 111 5.235831 GCTCGCCCGTTATTTAAAACTAGAT 59.764 40.000 0.00 0.00 0.00 1.98
111 112 4.567959 GCTCGCCCGTTATTTAAAACTAGA 59.432 41.667 0.00 0.00 0.00 2.43
112 113 4.549489 CGCTCGCCCGTTATTTAAAACTAG 60.549 45.833 0.00 0.00 0.00 2.57
113 114 3.306703 CGCTCGCCCGTTATTTAAAACTA 59.693 43.478 0.00 0.00 0.00 2.24
114 115 2.094734 CGCTCGCCCGTTATTTAAAACT 59.905 45.455 0.00 0.00 0.00 2.66
115 116 2.433808 CGCTCGCCCGTTATTTAAAAC 58.566 47.619 0.00 0.00 0.00 2.43
116 117 1.397692 CCGCTCGCCCGTTATTTAAAA 59.602 47.619 0.00 0.00 0.00 1.52
117 118 1.008329 CCGCTCGCCCGTTATTTAAA 58.992 50.000 0.00 0.00 0.00 1.52
118 119 0.175302 TCCGCTCGCCCGTTATTTAA 59.825 50.000 0.00 0.00 0.00 1.52
119 120 0.175302 TTCCGCTCGCCCGTTATTTA 59.825 50.000 0.00 0.00 0.00 1.40
120 121 1.078988 TTCCGCTCGCCCGTTATTT 60.079 52.632 0.00 0.00 0.00 1.40
121 122 1.520787 CTTCCGCTCGCCCGTTATT 60.521 57.895 0.00 0.00 0.00 1.40
122 123 2.106332 CTTCCGCTCGCCCGTTAT 59.894 61.111 0.00 0.00 0.00 1.89
123 124 4.137872 CCTTCCGCTCGCCCGTTA 62.138 66.667 0.00 0.00 0.00 3.18
127 128 3.607370 AAGTTCCTTCCGCTCGCCC 62.607 63.158 0.00 0.00 0.00 6.13
128 129 2.047179 AAGTTCCTTCCGCTCGCC 60.047 61.111 0.00 0.00 0.00 5.54
129 130 2.391389 CCAAGTTCCTTCCGCTCGC 61.391 63.158 0.00 0.00 0.00 5.03
130 131 2.391389 GCCAAGTTCCTTCCGCTCG 61.391 63.158 0.00 0.00 0.00 5.03
131 132 2.041115 GGCCAAGTTCCTTCCGCTC 61.041 63.158 0.00 0.00 0.00 5.03
132 133 2.034221 GGCCAAGTTCCTTCCGCT 59.966 61.111 0.00 0.00 0.00 5.52
133 134 3.431725 CGGCCAAGTTCCTTCCGC 61.432 66.667 2.24 0.00 33.36 5.54
134 135 2.746277 CCGGCCAAGTTCCTTCCG 60.746 66.667 2.24 0.00 39.79 4.30
135 136 3.062466 GCCGGCCAAGTTCCTTCC 61.062 66.667 18.11 0.00 0.00 3.46
136 137 3.431725 CGCCGGCCAAGTTCCTTC 61.432 66.667 23.46 0.00 0.00 3.46
137 138 3.785122 AACGCCGGCCAAGTTCCTT 62.785 57.895 23.46 0.00 0.00 3.36
153 154 0.731174 CGGGCGGCATTAAACACAAC 60.731 55.000 12.47 0.00 0.00 3.32
182 183 0.949105 AATTCAGCCACACGTCGTCC 60.949 55.000 0.00 0.00 0.00 4.79
183 184 1.654105 CTAATTCAGCCACACGTCGTC 59.346 52.381 0.00 0.00 0.00 4.20
184 185 1.671850 CCTAATTCAGCCACACGTCGT 60.672 52.381 0.00 0.00 0.00 4.34
185 186 0.999406 CCTAATTCAGCCACACGTCG 59.001 55.000 0.00 0.00 0.00 5.12
196 197 4.007659 GGAAAGCCGAGAAACCTAATTCA 58.992 43.478 0.00 0.00 0.00 2.57
216 217 2.359354 CCATTGAACCCGCGTGGA 60.359 61.111 18.79 0.00 37.49 4.02
221 222 3.508840 CGCCTCCATTGAACCCGC 61.509 66.667 0.00 0.00 0.00 6.13
237 238 3.059044 CGTCTCCTCGTTGTATTCAAACG 59.941 47.826 2.45 2.45 35.20 3.60
246 247 2.861360 GCTAAACACGTCTCCTCGTTGT 60.861 50.000 0.00 0.00 42.27 3.32
249 250 0.243095 GGCTAAACACGTCTCCTCGT 59.757 55.000 0.00 0.00 45.10 4.18
299 300 3.353600 CCATTGAAGCGGCACACA 58.646 55.556 1.45 0.00 0.00 3.72
316 317 3.363844 GACCTCTCACTGCCTCCGC 62.364 68.421 0.00 0.00 0.00 5.54
318 319 2.888863 CGACCTCTCACTGCCTCC 59.111 66.667 0.00 0.00 0.00 4.30
342 343 0.976641 ACATTGAAGACGGCTCAGGA 59.023 50.000 0.00 0.00 0.00 3.86
363 364 1.670087 CCGCTGTAGAGTGTGTCCTTG 60.670 57.143 0.00 0.00 0.00 3.61
365 366 1.878656 GCCGCTGTAGAGTGTGTCCT 61.879 60.000 0.00 0.00 0.00 3.85
366 367 1.446272 GCCGCTGTAGAGTGTGTCC 60.446 63.158 0.00 0.00 0.00 4.02
370 371 0.608130 TTCATGCCGCTGTAGAGTGT 59.392 50.000 0.00 0.00 0.00 3.55
376 377 0.813610 CCCGAATTCATGCCGCTGTA 60.814 55.000 6.22 0.00 0.00 2.74
382 383 0.947244 CAGCTACCCGAATTCATGCC 59.053 55.000 6.22 0.00 0.00 4.40
396 397 1.329913 TTCTCGCCTGATGCCAGCTA 61.330 55.000 0.00 0.00 39.07 3.32
398 399 2.124983 TTCTCGCCTGATGCCAGC 60.125 61.111 0.00 0.00 39.07 4.85
404 405 2.103042 GCGCTTGTTCTCGCCTGAT 61.103 57.895 0.00 0.00 45.01 2.90
405 406 2.738521 GCGCTTGTTCTCGCCTGA 60.739 61.111 0.00 0.00 45.01 3.86
433 434 1.202879 TGATCCACTCAAACCGCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
434 435 0.400213 TGATCCACTCAAACCGCCTT 59.600 50.000 0.00 0.00 0.00 4.35
440 441 3.820467 TGACCACATTGATCCACTCAAAC 59.180 43.478 0.00 0.00 46.62 2.93
445 447 3.328931 ACTTCTGACCACATTGATCCACT 59.671 43.478 0.00 0.00 0.00 4.00
452 454 0.883833 GCCCACTTCTGACCACATTG 59.116 55.000 0.00 0.00 0.00 2.82
479 481 4.680237 TTGCGGGCGTCCAGACAG 62.680 66.667 6.96 0.00 0.00 3.51
522 524 2.919043 GAAGGATGGTCCGGGCAT 59.081 61.111 9.07 0.00 42.75 4.40
523 525 3.781307 CGAAGGATGGTCCGGGCA 61.781 66.667 9.07 0.00 42.75 5.36
545 547 1.670811 CATCCAACACGGGCTTGTATC 59.329 52.381 0.00 0.00 34.36 2.24
552 554 3.747976 GTGGCATCCAACACGGGC 61.748 66.667 0.00 0.00 34.18 6.13
561 563 2.332654 GGACGTTGGTGTGGCATCC 61.333 63.158 0.00 0.00 0.00 3.51
580 582 4.992319 TCGTACATCCGAATTGAACTGTTT 59.008 37.500 0.00 0.00 33.15 2.83
649 651 4.709397 TGGTTACATTGATAGGCCTTTTGG 59.291 41.667 12.58 0.00 44.18 3.28
657 659 4.034048 GTGCGTTCTGGTTACATTGATAGG 59.966 45.833 0.00 0.00 0.00 2.57
670 672 1.329292 TGAAGAAAACGTGCGTTCTGG 59.671 47.619 10.46 0.00 37.35 3.86
673 683 3.280775 CTCTTGAAGAAAACGTGCGTTC 58.719 45.455 10.46 0.00 37.35 3.95
681 691 4.471373 GCTAGCAAGCTCTTGAAGAAAAC 58.529 43.478 10.63 0.00 45.85 2.43
696 706 1.148310 GTGCGTCAAAGAGCTAGCAA 58.852 50.000 18.83 0.00 36.32 3.91
697 707 0.033366 TGTGCGTCAAAGAGCTAGCA 59.967 50.000 18.83 0.00 0.00 3.49
698 708 0.440371 GTGTGCGTCAAAGAGCTAGC 59.560 55.000 6.62 6.62 0.00 3.42
699 709 0.710567 CGTGTGCGTCAAAGAGCTAG 59.289 55.000 0.00 0.00 0.00 3.42
700 710 2.809181 CGTGTGCGTCAAAGAGCTA 58.191 52.632 0.00 0.00 0.00 3.32
701 711 3.630204 CGTGTGCGTCAAAGAGCT 58.370 55.556 0.00 0.00 0.00 4.09
719 729 7.236019 TCCTATAAAGACAAACCAGGACACTTA 59.764 37.037 0.00 0.00 0.00 2.24
724 734 6.154706 TCTCTCCTATAAAGACAAACCAGGAC 59.845 42.308 0.00 0.00 0.00 3.85
764 774 2.666862 CGTGCGTTTGGGCCTACA 60.667 61.111 4.53 0.00 0.00 2.74
798 808 6.293462 CCTGCTCTAATTTTTAGGCGGATAAC 60.293 42.308 13.53 0.00 0.00 1.89
805 815 4.339530 CCCTTCCTGCTCTAATTTTTAGGC 59.660 45.833 0.00 0.00 0.00 3.93
809 819 4.202673 TGGTCCCTTCCTGCTCTAATTTTT 60.203 41.667 0.00 0.00 0.00 1.94
813 823 2.270434 TGGTCCCTTCCTGCTCTAAT 57.730 50.000 0.00 0.00 0.00 1.73
814 824 2.038863 TTGGTCCCTTCCTGCTCTAA 57.961 50.000 0.00 0.00 0.00 2.10
820 830 2.239400 GGTTTCTTTGGTCCCTTCCTG 58.761 52.381 0.00 0.00 0.00 3.86
827 837 2.018515 TGAACGTGGTTTCTTTGGTCC 58.981 47.619 0.00 0.00 0.00 4.46
887 897 7.915923 TGAAGATTGATTGATCTGTACTACGAC 59.084 37.037 0.00 0.00 36.53 4.34
888 898 7.996385 TGAAGATTGATTGATCTGTACTACGA 58.004 34.615 0.00 0.00 36.53 3.43
889 899 8.634475 TTGAAGATTGATTGATCTGTACTACG 57.366 34.615 0.00 0.00 36.53 3.51
963 977 2.666098 GCTTGGGGGCGGAACTAGA 61.666 63.158 0.00 0.00 0.00 2.43
992 1010 0.747852 GTCCTTCTCCATCCTCCGTC 59.252 60.000 0.00 0.00 0.00 4.79
993 1011 1.038130 CGTCCTTCTCCATCCTCCGT 61.038 60.000 0.00 0.00 0.00 4.69
994 1012 1.736586 CGTCCTTCTCCATCCTCCG 59.263 63.158 0.00 0.00 0.00 4.63
1085 1121 1.368374 AGAAATTGGACGGAAGGGGA 58.632 50.000 0.00 0.00 0.00 4.81
1094 1130 6.710744 TCTGGTCTACAAGAAAGAAATTGGAC 59.289 38.462 0.00 0.00 0.00 4.02
1105 1141 6.472887 CCACCTTAATTCTGGTCTACAAGAA 58.527 40.000 2.47 2.47 33.75 2.52
1106 1142 5.570844 GCCACCTTAATTCTGGTCTACAAGA 60.571 44.000 0.00 0.00 33.75 3.02
1110 1146 4.443621 GAGCCACCTTAATTCTGGTCTAC 58.556 47.826 0.00 0.00 33.75 2.59
1112 1148 2.093447 CGAGCCACCTTAATTCTGGTCT 60.093 50.000 0.00 0.00 33.75 3.85
1124 1211 1.882989 GAGCAGAGAACGAGCCACCT 61.883 60.000 0.00 0.00 0.00 4.00
1126 1213 1.446966 GGAGCAGAGAACGAGCCAC 60.447 63.158 0.00 0.00 0.00 5.01
1130 1217 1.110442 AGGATGGAGCAGAGAACGAG 58.890 55.000 0.00 0.00 0.00 4.18
1132 1219 4.142271 GGATATAGGATGGAGCAGAGAACG 60.142 50.000 0.00 0.00 0.00 3.95
1169 1261 1.036707 GGAGACGAGGAGGATTGGAG 58.963 60.000 0.00 0.00 0.00 3.86
1195 1287 1.360911 GAGAGATTCCGCCGGAGAC 59.639 63.158 5.05 4.67 31.21 3.36
1196 1288 2.187493 CGAGAGATTCCGCCGGAGA 61.187 63.158 5.05 0.00 31.21 3.71
1197 1289 2.123988 CTCGAGAGATTCCGCCGGAG 62.124 65.000 6.58 0.00 40.84 4.63
1198 1290 2.124445 TCGAGAGATTCCGCCGGA 60.124 61.111 5.05 0.00 33.31 5.14
1199 1291 2.333225 CTCGAGAGATTCCGCCGG 59.667 66.667 6.58 0.00 40.84 6.13
1203 1295 1.746220 AGGAACACTCGAGAGATTCCG 59.254 52.381 26.49 9.82 44.44 4.30
1211 1303 2.125912 CGGCCAGGAACACTCGAG 60.126 66.667 11.84 11.84 0.00 4.04
1239 1331 6.166984 TGTCAGTTAAAATTCATTTGGCCA 57.833 33.333 0.00 0.00 32.27 5.36
1303 1707 2.159240 TGTTACTGTATCGAGGCAGCAG 60.159 50.000 16.04 9.85 36.26 4.24
1322 1726 1.555075 CAGGGCCATGTACAGTACTGT 59.445 52.381 30.13 30.13 46.87 3.55
1323 1727 1.743772 GCAGGGCCATGTACAGTACTG 60.744 57.143 21.44 21.44 0.00 2.74
1324 1728 0.541863 GCAGGGCCATGTACAGTACT 59.458 55.000 20.22 0.00 0.00 2.73
1325 1729 0.541863 AGCAGGGCCATGTACAGTAC 59.458 55.000 20.22 3.49 0.00 2.73
1326 1730 0.541392 CAGCAGGGCCATGTACAGTA 59.459 55.000 20.22 0.00 0.00 2.74
1327 1731 1.300963 CAGCAGGGCCATGTACAGT 59.699 57.895 20.22 0.00 0.00 3.55
1345 1749 1.482593 AGTATGGCAGAGCACAGGTAC 59.517 52.381 0.00 0.00 0.00 3.34
1346 1750 1.482182 CAGTATGGCAGAGCACAGGTA 59.518 52.381 0.00 0.00 0.00 3.08
1347 1751 0.251354 CAGTATGGCAGAGCACAGGT 59.749 55.000 0.00 0.00 0.00 4.00
1348 1752 0.538584 TCAGTATGGCAGAGCACAGG 59.461 55.000 0.00 0.00 36.16 4.00
1353 1757 4.387598 AGATTCATTCAGTATGGCAGAGC 58.612 43.478 0.00 0.00 36.16 4.09
1380 1784 9.113876 CGAATAAGTAAAAACCAACACTGAATC 57.886 33.333 0.00 0.00 0.00 2.52
1381 1785 8.842280 TCGAATAAGTAAAAACCAACACTGAAT 58.158 29.630 0.00 0.00 0.00 2.57
1411 1815 8.372459 ACCAGAAACCAAAAACTAACTCTTTTT 58.628 29.630 0.00 0.00 32.23 1.94
1412 1816 7.817478 CACCAGAAACCAAAAACTAACTCTTTT 59.183 33.333 0.00 0.00 0.00 2.27
1413 1817 7.320399 CACCAGAAACCAAAAACTAACTCTTT 58.680 34.615 0.00 0.00 0.00 2.52
1414 1818 6.627287 GCACCAGAAACCAAAAACTAACTCTT 60.627 38.462 0.00 0.00 0.00 2.85
1418 1822 4.116961 GGCACCAGAAACCAAAAACTAAC 58.883 43.478 0.00 0.00 0.00 2.34
1428 1832 2.238521 TCAGATTTGGCACCAGAAACC 58.761 47.619 0.00 0.00 0.00 3.27
1492 1901 1.941999 GCCCTCCATTGCTGCAACTC 61.942 60.000 18.51 0.00 0.00 3.01
1517 1926 0.803768 CGTTGCTGGTGATCTCCGAG 60.804 60.000 9.20 8.61 0.00 4.63
1518 1927 1.215382 CGTTGCTGGTGATCTCCGA 59.785 57.895 9.20 0.00 0.00 4.55
1519 1928 1.811266 CCGTTGCTGGTGATCTCCG 60.811 63.158 9.20 5.51 0.00 4.63
1520 1929 0.460987 CTCCGTTGCTGGTGATCTCC 60.461 60.000 6.88 6.88 0.00 3.71
1521 1930 0.532573 TCTCCGTTGCTGGTGATCTC 59.467 55.000 0.00 0.00 0.00 2.75
1522 1931 0.247736 GTCTCCGTTGCTGGTGATCT 59.752 55.000 0.00 0.00 34.34 2.75
1523 1932 0.247736 AGTCTCCGTTGCTGGTGATC 59.752 55.000 0.00 0.00 34.34 2.92
1524 1933 0.247736 GAGTCTCCGTTGCTGGTGAT 59.752 55.000 0.00 0.00 34.34 3.06
1525 1934 1.666011 GAGTCTCCGTTGCTGGTGA 59.334 57.895 0.00 0.00 0.00 4.02
1526 1935 1.734477 CGAGTCTCCGTTGCTGGTG 60.734 63.158 0.00 0.00 0.00 4.17
1527 1936 2.651361 CGAGTCTCCGTTGCTGGT 59.349 61.111 0.00 0.00 0.00 4.00
1528 1937 2.125912 CCGAGTCTCCGTTGCTGG 60.126 66.667 0.00 0.00 0.00 4.85
1529 1938 1.153939 CTCCGAGTCTCCGTTGCTG 60.154 63.158 0.00 0.00 0.00 4.41
1530 1939 0.681564 ATCTCCGAGTCTCCGTTGCT 60.682 55.000 0.00 0.00 0.00 3.91
1531 1940 0.248702 GATCTCCGAGTCTCCGTTGC 60.249 60.000 0.00 0.00 0.00 4.17
1532 1941 1.095600 TGATCTCCGAGTCTCCGTTG 58.904 55.000 0.00 0.00 0.00 4.10
1533 1942 1.096416 GTGATCTCCGAGTCTCCGTT 58.904 55.000 0.00 0.00 0.00 4.44
1534 1943 0.748729 GGTGATCTCCGAGTCTCCGT 60.749 60.000 0.00 0.00 0.00 4.69
1535 1944 0.748367 TGGTGATCTCCGAGTCTCCG 60.748 60.000 9.20 0.00 32.15 4.63
1536 1945 1.028905 CTGGTGATCTCCGAGTCTCC 58.971 60.000 9.20 4.24 0.00 3.71
1537 1946 0.383949 GCTGGTGATCTCCGAGTCTC 59.616 60.000 9.20 0.00 0.00 3.36
1538 1947 0.323816 TGCTGGTGATCTCCGAGTCT 60.324 55.000 9.20 0.00 0.00 3.24
1539 1948 0.532573 TTGCTGGTGATCTCCGAGTC 59.467 55.000 9.20 5.50 0.00 3.36
1540 1949 0.247736 GTTGCTGGTGATCTCCGAGT 59.752 55.000 9.20 0.00 0.00 4.18
1736 2145 2.106566 GAGAGGATCCACTTGCTCTGA 58.893 52.381 15.82 0.00 43.53 3.27
2208 2617 4.680237 TCCGCCGTTGCTGAGGTG 62.680 66.667 0.00 0.00 37.74 4.00
2557 2969 1.649664 CAGCGACAGGATCTTGAAGG 58.350 55.000 12.40 1.37 0.00 3.46
2659 3074 0.168788 CTGCCGCCTATGTTGTTGTG 59.831 55.000 0.00 0.00 0.00 3.33
2718 3136 6.093771 ACGAATCACGAGTCAGAACTATACTT 59.906 38.462 0.00 0.00 45.77 2.24
2732 3150 5.017484 TCAATTTCAACACGAATCACGAG 57.983 39.130 0.00 0.00 45.77 4.18
2738 3156 7.022055 TGTACACTTCAATTTCAACACGAAT 57.978 32.000 0.00 0.00 32.32 3.34
2786 3557 3.002144 GTGGGCGTTAGTGTTTTCGTTTA 59.998 43.478 0.00 0.00 0.00 2.01
2787 3558 2.015587 TGGGCGTTAGTGTTTTCGTTT 58.984 42.857 0.00 0.00 0.00 3.60
2788 3559 1.331447 GTGGGCGTTAGTGTTTTCGTT 59.669 47.619 0.00 0.00 0.00 3.85
2901 3672 1.208358 CGCGAGTTGTCCTACGTGA 59.792 57.895 0.00 0.00 38.28 4.35
3026 3799 1.573108 GAGATGGGGGACAGAAGTCA 58.427 55.000 0.00 0.00 46.80 3.41
3132 5515 4.782019 GGCAACAAATACATGTTCAGGA 57.218 40.909 2.30 0.00 41.44 3.86
3239 5623 4.946160 TTTGGTATGTGGGAAAGGAGAT 57.054 40.909 0.00 0.00 0.00 2.75
3246 5630 5.186256 TGATAGCTTTTGGTATGTGGGAA 57.814 39.130 0.00 0.00 42.49 3.97
3254 5638 4.027674 TGGCAACTGATAGCTTTTGGTA 57.972 40.909 0.00 0.00 35.29 3.25
3483 9034 4.329545 GGTCAAGTGCCGGAGCCA 62.330 66.667 5.05 0.00 38.69 4.75
3484 9035 4.021925 AGGTCAAGTGCCGGAGCC 62.022 66.667 5.05 0.00 38.69 4.70
3485 9036 2.743928 CAGGTCAAGTGCCGGAGC 60.744 66.667 5.05 0.00 40.48 4.70
3486 9037 1.079543 CTCAGGTCAAGTGCCGGAG 60.080 63.158 5.05 7.23 40.72 4.63
3568 9122 1.337703 GAAACTGCAGTTGCCATGTCA 59.662 47.619 31.73 0.00 41.18 3.58


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

AutoCloner maintained by Alex Coulton.