Multiple sequence alignment - TraesCS7A01G446200

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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 TraesCS7A01G446200 chr7A 100.000 3258 0 0 1 3258 641040330 641043587 0.000000e+00 6017.0
1 TraesCS7A01G446200 chr7A 94.203 69 2 1 128 194 621573290 621573222 1.600000e-18 104.0
2 TraesCS7A01G446200 chr7A 82.353 119 18 1 2727 2845 200235455 200235570 2.070000e-17 100.0
3 TraesCS7A01G446200 chr7A 84.545 110 7 5 366 472 712938846 712938948 2.070000e-17 100.0
4 TraesCS7A01G446200 chr7A 84.722 72 9 2 2880 2950 450619595 450619525 1.620000e-08 71.3
5 TraesCS7A01G446200 chr7B 93.576 1510 71 13 890 2389 601320653 601322146 0.000000e+00 2228.0
6 TraesCS7A01G446200 chr7B 89.677 155 12 2 194 347 601318406 601318557 9.220000e-46 195.0
7 TraesCS7A01G446200 chr7B 94.690 113 6 0 364 476 601320093 601320205 3.340000e-40 176.0
8 TraesCS7A01G446200 chr7B 88.235 136 11 5 212 344 693707507 693707640 1.210000e-34 158.0
9 TraesCS7A01G446200 chr7B 73.913 276 52 15 2299 2565 601325091 601325355 3.460000e-15 93.5
10 TraesCS7A01G446200 chr7D 92.130 953 37 18 1685 2612 554852400 554851461 0.000000e+00 1310.0
11 TraesCS7A01G446200 chr7D 93.342 736 44 2 895 1630 554853642 554852912 0.000000e+00 1083.0
12 TraesCS7A01G446200 chr7D 88.136 649 40 19 2614 3257 554851399 554850783 0.000000e+00 737.0
13 TraesCS7A01G446200 chr7D 93.103 348 16 6 1 347 554864744 554864404 1.350000e-138 503.0
14 TraesCS7A01G446200 chr7D 88.221 399 41 6 492 887 554854082 554853687 3.800000e-129 472.0
15 TraesCS7A01G446200 chr7D 96.364 110 4 0 367 476 554854177 554854068 7.180000e-42 182.0
16 TraesCS7A01G446200 chr7D 95.575 113 5 0 364 476 554864420 554864308 7.180000e-42 182.0
17 TraesCS7A01G446200 chr7D 95.556 45 1 1 2906 2950 118988705 118988662 1.620000e-08 71.3
18 TraesCS7A01G446200 chr6D 90.000 150 10 4 200 347 38168901 38169047 4.290000e-44 189.0
19 TraesCS7A01G446200 chr6B 81.347 193 13 4 3 195 528258256 528258425 5.670000e-28 135.0
20 TraesCS7A01G446200 chr6B 80.829 193 14 4 3 195 528274789 528274958 2.640000e-26 130.0
21 TraesCS7A01G446200 chr2B 84.559 136 16 5 212 344 94197754 94197621 2.640000e-26 130.0
22 TraesCS7A01G446200 chr2B 77.707 157 21 10 3100 3252 58788003 58788149 2.080000e-12 84.2
23 TraesCS7A01G446200 chr2B 91.071 56 5 0 140 195 66330552 66330497 3.490000e-10 76.8
24 TraesCS7A01G446200 chr2A 76.042 192 37 5 3069 3258 212633517 212633333 1.240000e-14 91.6
25 TraesCS7A01G446200 chr3A 86.585 82 10 1 2726 2807 20839371 20839451 4.480000e-14 89.8
26 TraesCS7A01G446200 chr3A 93.333 60 4 0 136 195 41103956 41104015 4.480000e-14 89.8
27 TraesCS7A01G446200 chr4A 100.000 39 0 0 376 414 37794463 37794425 4.510000e-09 73.1
28 TraesCS7A01G446200 chr1D 83.333 72 8 3 2880 2950 423305823 423305755 2.710000e-06 63.9
29 TraesCS7A01G446200 chr1D 100.000 28 0 0 2923 2950 240984005 240983978 6.000000e-03 52.8
30 TraesCS7A01G446200 chr1A 100.000 31 0 0 164 194 8006729 8006699 1.260000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G446200 chr7A 641040330 641043587 3257 False 6017.000 6017 100.0000 1 3258 1 chr7A.!!$F2 3257
1 TraesCS7A01G446200 chr7B 601318406 601325355 6949 False 673.125 2228 87.9640 194 2565 4 chr7B.!!$F2 2371
2 TraesCS7A01G446200 chr7D 554850783 554854177 3394 True 756.800 1310 91.6386 367 3257 5 chr7D.!!$R2 2890

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
88 89 0.030504 CTGTTGCAACGCATGGTCAA 59.969 50.0 23.79 2.80 38.76 3.18 F
1641 3265 0.034059 GTGCCGTGAGCTATAGCCAT 59.966 55.0 21.17 3.37 44.23 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 3787 0.594602 TCGTCCACGTAGTCCTGTTG 59.405 55.0 0.0 0.0 41.61 3.33 R
3064 7170 0.240945 GAAGTTGCGTGGGATTGGTG 59.759 55.0 0.0 0.0 0.00 4.17 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
33 34 9.569167 TTTTGAAGAGAGTATATGTTAGACACG 57.431 33.333 0.00 0.00 0.00 4.49
34 35 8.502105 TTGAAGAGAGTATATGTTAGACACGA 57.498 34.615 0.00 0.00 0.00 4.35
35 36 8.678593 TGAAGAGAGTATATGTTAGACACGAT 57.321 34.615 0.00 0.00 0.00 3.73
36 37 9.121658 TGAAGAGAGTATATGTTAGACACGATT 57.878 33.333 0.00 0.00 0.00 3.34
48 49 8.541133 TGTTAGACACGATTATTGTTGAATCA 57.459 30.769 0.00 0.00 33.66 2.57
49 50 8.440059 TGTTAGACACGATTATTGTTGAATCAC 58.560 33.333 0.00 0.00 33.66 3.06
50 51 8.656849 GTTAGACACGATTATTGTTGAATCACT 58.343 33.333 0.00 0.00 33.66 3.41
51 52 9.863845 TTAGACACGATTATTGTTGAATCACTA 57.136 29.630 0.00 0.00 33.66 2.74
52 53 8.771920 AGACACGATTATTGTTGAATCACTAA 57.228 30.769 0.00 0.00 33.66 2.24
53 54 9.214957 AGACACGATTATTGTTGAATCACTAAA 57.785 29.630 0.00 0.00 33.66 1.85
54 55 9.478019 GACACGATTATTGTTGAATCACTAAAG 57.522 33.333 0.00 0.00 33.66 1.85
55 56 8.999431 ACACGATTATTGTTGAATCACTAAAGT 58.001 29.630 0.00 0.00 33.66 2.66
72 73 9.809395 TCACTAAAGTATATAGTATGCCTCTGT 57.191 33.333 0.00 0.00 32.47 3.41
75 76 9.360093 CTAAAGTATATAGTATGCCTCTGTTGC 57.640 37.037 0.00 0.00 0.00 4.17
76 77 6.918067 AGTATATAGTATGCCTCTGTTGCA 57.082 37.500 0.00 0.00 43.97 4.08
77 78 7.303182 AGTATATAGTATGCCTCTGTTGCAA 57.697 36.000 0.00 0.00 42.92 4.08
78 79 7.155328 AGTATATAGTATGCCTCTGTTGCAAC 58.845 38.462 22.83 22.83 42.92 4.17
79 80 1.442769 AGTATGCCTCTGTTGCAACG 58.557 50.000 23.79 17.92 42.92 4.10
80 81 0.179189 GTATGCCTCTGTTGCAACGC 60.179 55.000 23.79 20.16 42.92 4.84
81 82 0.605050 TATGCCTCTGTTGCAACGCA 60.605 50.000 25.25 25.25 42.92 5.24
82 83 1.246056 ATGCCTCTGTTGCAACGCAT 61.246 50.000 26.85 26.85 42.92 4.73
83 84 1.443194 GCCTCTGTTGCAACGCATG 60.443 57.895 23.79 13.64 38.76 4.06
84 85 1.210931 CCTCTGTTGCAACGCATGG 59.789 57.895 23.79 17.98 38.76 3.66
85 86 1.518056 CCTCTGTTGCAACGCATGGT 61.518 55.000 23.79 0.00 38.76 3.55
86 87 0.110056 CTCTGTTGCAACGCATGGTC 60.110 55.000 23.79 0.00 38.76 4.02
87 88 0.817229 TCTGTTGCAACGCATGGTCA 60.817 50.000 23.79 3.60 38.76 4.02
88 89 0.030504 CTGTTGCAACGCATGGTCAA 59.969 50.000 23.79 2.80 38.76 3.18
89 90 0.672889 TGTTGCAACGCATGGTCAAT 59.327 45.000 23.79 0.00 38.76 2.57
90 91 1.335780 TGTTGCAACGCATGGTCAATC 60.336 47.619 23.79 0.00 38.76 2.67
91 92 0.957362 TTGCAACGCATGGTCAATCA 59.043 45.000 0.00 0.00 38.76 2.57
92 93 0.522626 TGCAACGCATGGTCAATCAG 59.477 50.000 0.00 0.00 31.71 2.90
93 94 0.523072 GCAACGCATGGTCAATCAGT 59.477 50.000 0.00 0.00 0.00 3.41
94 95 1.737236 GCAACGCATGGTCAATCAGTA 59.263 47.619 0.00 0.00 0.00 2.74
95 96 2.223112 GCAACGCATGGTCAATCAGTAG 60.223 50.000 0.00 0.00 0.00 2.57
96 97 3.261580 CAACGCATGGTCAATCAGTAGA 58.738 45.455 0.00 0.00 0.00 2.59
97 98 3.610040 ACGCATGGTCAATCAGTAGAA 57.390 42.857 0.00 0.00 0.00 2.10
98 99 4.142609 ACGCATGGTCAATCAGTAGAAT 57.857 40.909 0.00 0.00 0.00 2.40
99 100 5.276461 ACGCATGGTCAATCAGTAGAATA 57.724 39.130 0.00 0.00 0.00 1.75
100 101 5.858381 ACGCATGGTCAATCAGTAGAATAT 58.142 37.500 0.00 0.00 0.00 1.28
101 102 6.993079 ACGCATGGTCAATCAGTAGAATATA 58.007 36.000 0.00 0.00 0.00 0.86
102 103 7.615403 ACGCATGGTCAATCAGTAGAATATAT 58.385 34.615 0.00 0.00 0.00 0.86
103 104 8.749354 ACGCATGGTCAATCAGTAGAATATATA 58.251 33.333 0.00 0.00 0.00 0.86
104 105 9.755804 CGCATGGTCAATCAGTAGAATATATAT 57.244 33.333 0.00 0.00 0.00 0.86
167 168 8.412456 TGATTTATTTATATGCATTATGGCCCG 58.588 33.333 3.54 0.00 0.00 6.13
168 169 7.710676 TTTATTTATATGCATTATGGCCCGT 57.289 32.000 3.54 0.00 0.00 5.28
169 170 8.809468 TTTATTTATATGCATTATGGCCCGTA 57.191 30.769 3.54 0.00 0.00 4.02
170 171 6.942532 ATTTATATGCATTATGGCCCGTAG 57.057 37.500 3.54 0.00 0.00 3.51
171 172 2.107950 TATGCATTATGGCCCGTAGC 57.892 50.000 3.54 0.00 42.60 3.58
172 173 0.110295 ATGCATTATGGCCCGTAGCA 59.890 50.000 0.00 4.69 46.50 3.49
173 174 0.106967 TGCATTATGGCCCGTAGCAA 60.107 50.000 0.00 0.00 46.50 3.91
174 175 0.310854 GCATTATGGCCCGTAGCAAC 59.689 55.000 0.00 0.00 46.50 4.17
183 184 3.242474 CGTAGCAACGTACGGGCG 61.242 66.667 21.06 8.32 44.21 6.13
190 191 3.987404 ACGTACGGGCGTTCTACT 58.013 55.556 21.06 0.00 43.04 2.57
191 192 3.153024 ACGTACGGGCGTTCTACTA 57.847 52.632 21.06 0.00 43.04 1.82
192 193 1.009829 ACGTACGGGCGTTCTACTAG 58.990 55.000 21.06 0.00 43.04 2.57
197 198 2.648059 ACGGGCGTTCTACTAGTACAT 58.352 47.619 0.00 0.00 0.00 2.29
212 213 4.392921 AGTACATACAAGTAGCTGCCTG 57.607 45.455 0.00 0.00 0.00 4.85
213 214 2.029838 ACATACAAGTAGCTGCCTGC 57.970 50.000 0.00 0.00 43.29 4.85
255 256 5.066764 TGGTTTGTTTAGTGGTCTTAGTTGC 59.933 40.000 0.00 0.00 0.00 4.17
256 257 5.506815 GGTTTGTTTAGTGGTCTTAGTTGCC 60.507 44.000 0.00 0.00 0.00 4.52
258 259 4.385825 TGTTTAGTGGTCTTAGTTGCCTG 58.614 43.478 0.00 0.00 0.00 4.85
282 284 5.885465 AGGTTGAGAGTTTGAATCCATCTT 58.115 37.500 0.00 0.00 0.00 2.40
315 317 4.329638 TTTGCCTGGGAAATTAGGATGA 57.670 40.909 9.49 0.00 36.11 2.92
324 326 7.017056 CCTGGGAAATTAGGATGAGAAGAGTAT 59.983 40.741 0.00 0.00 36.11 2.12
328 330 9.267084 GGAAATTAGGATGAGAAGAGTATTGAC 57.733 37.037 0.00 0.00 0.00 3.18
334 336 6.045955 GGATGAGAAGAGTATTGACCAACTC 58.954 44.000 0.00 0.00 42.02 3.01
338 340 5.181748 AGAAGAGTATTGACCAACTCATGC 58.818 41.667 5.38 0.00 43.74 4.06
339 341 4.558226 AGAGTATTGACCAACTCATGCA 57.442 40.909 5.38 0.00 43.74 3.96
340 342 5.108187 AGAGTATTGACCAACTCATGCAT 57.892 39.130 0.00 0.00 43.74 3.96
341 343 6.239217 AGAGTATTGACCAACTCATGCATA 57.761 37.500 0.00 0.00 43.74 3.14
342 344 6.653020 AGAGTATTGACCAACTCATGCATAA 58.347 36.000 0.00 0.00 43.74 1.90
343 345 7.285566 AGAGTATTGACCAACTCATGCATAAT 58.714 34.615 0.00 0.00 43.74 1.28
344 346 8.432013 AGAGTATTGACCAACTCATGCATAATA 58.568 33.333 0.00 0.00 43.74 0.98
345 347 9.224267 GAGTATTGACCAACTCATGCATAATAT 57.776 33.333 0.00 0.00 41.46 1.28
346 348 9.578576 AGTATTGACCAACTCATGCATAATATT 57.421 29.630 0.00 0.00 0.00 1.28
347 349 9.831737 GTATTGACCAACTCATGCATAATATTC 57.168 33.333 0.00 0.00 0.00 1.75
348 350 6.882610 TGACCAACTCATGCATAATATTCC 57.117 37.500 0.00 0.00 0.00 3.01
349 351 5.769662 TGACCAACTCATGCATAATATTCCC 59.230 40.000 0.00 0.00 0.00 3.97
350 352 5.957132 ACCAACTCATGCATAATATTCCCT 58.043 37.500 0.00 0.00 0.00 4.20
351 353 6.006449 ACCAACTCATGCATAATATTCCCTC 58.994 40.000 0.00 0.00 0.00 4.30
352 354 5.122869 CCAACTCATGCATAATATTCCCTCG 59.877 44.000 0.00 0.00 0.00 4.63
353 355 4.256920 ACTCATGCATAATATTCCCTCGC 58.743 43.478 0.00 0.00 0.00 5.03
354 356 4.256110 CTCATGCATAATATTCCCTCGCA 58.744 43.478 0.00 0.00 0.00 5.10
355 357 4.650734 TCATGCATAATATTCCCTCGCAA 58.349 39.130 0.00 0.00 0.00 4.85
356 358 5.069318 TCATGCATAATATTCCCTCGCAAA 58.931 37.500 0.00 0.00 0.00 3.68
357 359 5.534278 TCATGCATAATATTCCCTCGCAAAA 59.466 36.000 0.00 0.00 0.00 2.44
358 360 5.843673 TGCATAATATTCCCTCGCAAAAA 57.156 34.783 0.00 0.00 0.00 1.94
471 2025 7.118101 GCAACCCATTAATTACGATACGGATAA 59.882 37.037 0.00 0.00 0.00 1.75
472 2026 9.158233 CAACCCATTAATTACGATACGGATAAT 57.842 33.333 0.00 0.00 0.00 1.28
473 2027 8.937634 ACCCATTAATTACGATACGGATAATC 57.062 34.615 0.00 0.00 0.00 1.75
474 2028 8.533657 ACCCATTAATTACGATACGGATAATCA 58.466 33.333 0.00 0.00 0.00 2.57
475 2029 9.542462 CCCATTAATTACGATACGGATAATCAT 57.458 33.333 0.00 0.00 0.00 2.45
509 2063 6.560253 AAAAGGATACGGATAATCATGCAC 57.440 37.500 0.00 0.00 46.39 4.57
527 2081 3.628942 TGCACAGAATTAGGATCACATGC 59.371 43.478 0.00 0.00 0.00 4.06
564 2119 1.083489 TTAAAGCGGTCCGATTGCAG 58.917 50.000 16.76 0.00 35.13 4.41
586 2141 7.281999 TGCAGAATCCAATCGTCATTAATTACA 59.718 33.333 0.99 0.00 0.00 2.41
592 2147 7.505258 TCCAATCGTCATTAATTACAGGATCA 58.495 34.615 0.00 0.00 0.00 2.92
595 2150 8.992073 CAATCGTCATTAATTACAGGATCATGA 58.008 33.333 15.42 0.00 0.00 3.07
610 2165 9.835389 ACAGGATCATGAAGAAAAATTGAAAAA 57.165 25.926 15.42 0.00 0.00 1.94
682 2239 1.603802 CATCGTCCGATCCAAAATGGG 59.396 52.381 0.00 0.00 38.32 4.00
720 2277 1.531883 GGATCAGTCGCAAAAATCCGC 60.532 52.381 0.00 0.00 0.00 5.54
724 2281 2.127042 TCGCAAAAATCCGCACGC 60.127 55.556 0.00 0.00 0.00 5.34
725 2282 3.171911 CGCAAAAATCCGCACGCC 61.172 61.111 0.00 0.00 0.00 5.68
736 2293 1.812093 CGCACGCCCGGATTTTAGA 60.812 57.895 0.73 0.00 0.00 2.10
819 2377 1.068402 TGCAACGCATCTGACAATTGG 60.068 47.619 10.83 0.00 31.71 3.16
836 2424 4.584327 ATTGGCAATTAATTACCTCGGC 57.416 40.909 16.73 9.77 0.00 5.54
841 2429 3.795488 GCAATTAATTACCTCGGCCTTGC 60.795 47.826 0.00 1.18 0.00 4.01
866 2454 7.253750 GCATGCTAAATCTTGTTTATTGTTCGG 60.254 37.037 11.37 0.00 0.00 4.30
925 2549 1.801178 CTTCGTGTTTCCCTTGCTCTC 59.199 52.381 0.00 0.00 0.00 3.20
926 2550 1.048601 TCGTGTTTCCCTTGCTCTCT 58.951 50.000 0.00 0.00 0.00 3.10
928 2552 1.270305 CGTGTTTCCCTTGCTCTCTGA 60.270 52.381 0.00 0.00 0.00 3.27
937 2561 2.364970 CCTTGCTCTCTGATCGATCCTT 59.635 50.000 22.31 0.00 0.00 3.36
945 2569 1.609072 CTGATCGATCCTTCCTACGCA 59.391 52.381 22.31 0.00 0.00 5.24
1435 3059 1.301401 TGCACGGCGTTCTTTAGCT 60.301 52.632 11.19 0.00 0.00 3.32
1440 3064 1.512098 GGCGTTCTTTAGCTTGCGC 60.512 57.895 0.00 0.00 43.46 6.09
1521 3145 2.046892 GATGGCCACGTGCTCACT 60.047 61.111 8.16 0.00 40.92 3.41
1623 3247 1.985116 GGGCGTCCTCTTCCTCTGT 60.985 63.158 0.00 0.00 0.00 3.41
1635 3259 0.684479 TCCTCTGTGCCGTGAGCTAT 60.684 55.000 0.00 0.00 44.23 2.97
1636 3260 1.032794 CCTCTGTGCCGTGAGCTATA 58.967 55.000 0.00 0.00 44.23 1.31
1637 3261 1.000827 CCTCTGTGCCGTGAGCTATAG 60.001 57.143 0.00 0.00 44.23 1.31
1641 3265 0.034059 GTGCCGTGAGCTATAGCCAT 59.966 55.000 21.17 3.37 44.23 4.40
1665 3289 3.756783 CCCGTCCCCTCCCTCTCT 61.757 72.222 0.00 0.00 0.00 3.10
1668 3292 2.284151 GTCCCCTCCCTCTCTCCC 59.716 72.222 0.00 0.00 0.00 4.30
1687 3311 7.020827 TCTCCCTTCTTGAATTAACTGTGAT 57.979 36.000 0.00 0.00 0.00 3.06
1708 3786 5.694910 TGATGTGATGAACTGATGATCGATG 59.305 40.000 0.54 0.00 0.00 3.84
1709 3787 3.805971 TGTGATGAACTGATGATCGATGC 59.194 43.478 0.54 0.00 0.00 3.91
1710 3788 3.805971 GTGATGAACTGATGATCGATGCA 59.194 43.478 0.54 0.83 0.00 3.96
2026 4116 2.283173 GCCAAGGGGAAGGTGGTG 60.283 66.667 0.00 0.00 35.59 4.17
2215 4305 2.768834 GGACCTTGCCGAGTTCATC 58.231 57.895 0.00 0.00 0.00 2.92
2251 4341 1.450312 CTTGGGCATCACCGTCTCC 60.450 63.158 0.00 0.00 40.62 3.71
2343 4436 3.118629 TGTCACACTCTGCAGAAACTCTT 60.119 43.478 18.85 0.00 0.00 2.85
2344 4437 4.099419 TGTCACACTCTGCAGAAACTCTTA 59.901 41.667 18.85 0.00 0.00 2.10
2370 4463 2.995283 TGGAGTTCAGAGATTGCCATG 58.005 47.619 0.00 0.00 0.00 3.66
2400 4493 4.749099 CAGTTCTCTGTTTCTCTTCCTGTG 59.251 45.833 0.00 0.00 36.97 3.66
2405 4498 6.304624 TCTCTGTTTCTCTTCCTGTGTAGTA 58.695 40.000 0.00 0.00 0.00 1.82
2406 4499 6.431543 TCTCTGTTTCTCTTCCTGTGTAGTAG 59.568 42.308 0.00 0.00 0.00 2.57
2437 4530 7.433680 ACTGTTATTTTGATTTGGAGTGGAAC 58.566 34.615 0.00 0.00 0.00 3.62
2459 4554 5.258051 ACTTCTTGGTGGTTTGAACTTGTA 58.742 37.500 0.00 0.00 0.00 2.41
2469 4564 6.363357 GTGGTTTGAACTTGTATTTGATCAGC 59.637 38.462 0.00 0.00 0.00 4.26
2516 4612 1.005748 GCCTTCAGTTTGGCTTGGC 60.006 57.895 0.00 0.00 45.26 4.52
2623 4727 9.599866 ACATTATGCTTTCTAATTTTTAAGCCC 57.400 29.630 12.61 0.00 41.67 5.19
2624 4728 9.598517 CATTATGCTTTCTAATTTTTAAGCCCA 57.401 29.630 12.61 2.29 41.67 5.36
2625 4729 8.996024 TTATGCTTTCTAATTTTTAAGCCCAC 57.004 30.769 12.61 0.00 41.67 4.61
2630 4795 7.602265 GCTTTCTAATTTTTAAGCCCACAATCA 59.398 33.333 0.00 0.00 37.59 2.57
2631 4796 9.487790 CTTTCTAATTTTTAAGCCCACAATCAA 57.512 29.630 0.00 0.00 0.00 2.57
2646 4811 5.887598 CCACAATCAATTGAGGTCTCCAATA 59.112 40.000 14.54 0.00 41.65 1.90
2716 4881 6.426646 TTCTTATAAGGAGCCCTCTCATTC 57.573 41.667 12.54 0.00 41.79 2.67
2717 4882 5.467738 TCTTATAAGGAGCCCTCTCATTCA 58.532 41.667 12.54 0.00 41.79 2.57
2718 4883 5.905331 TCTTATAAGGAGCCCTCTCATTCAA 59.095 40.000 12.54 0.00 41.79 2.69
2719 4884 6.560304 TCTTATAAGGAGCCCTCTCATTCAAT 59.440 38.462 12.54 0.00 41.79 2.57
2720 4885 5.659849 ATAAGGAGCCCTCTCATTCAATT 57.340 39.130 0.00 0.00 41.79 2.32
2721 4886 3.574354 AGGAGCCCTCTCATTCAATTC 57.426 47.619 0.00 0.00 41.13 2.17
2722 4887 3.121688 AGGAGCCCTCTCATTCAATTCT 58.878 45.455 0.00 0.00 41.13 2.40
2723 4888 3.526841 AGGAGCCCTCTCATTCAATTCTT 59.473 43.478 0.00 0.00 41.13 2.52
2724 4889 4.017683 AGGAGCCCTCTCATTCAATTCTTT 60.018 41.667 0.00 0.00 41.13 2.52
2725 4890 5.192522 AGGAGCCCTCTCATTCAATTCTTTA 59.807 40.000 0.00 0.00 41.13 1.85
2875 5041 1.738350 CTTCAAGGAGCATGCTCACAG 59.262 52.381 40.37 29.67 44.40 3.66
2881 5065 3.428532 AGGAGCATGCTCACAGATTTTT 58.571 40.909 40.37 16.42 44.40 1.94
2908 5092 8.900983 AAAGCCTCATAGTTAATTCAGATCTC 57.099 34.615 0.00 0.00 0.00 2.75
2909 5093 7.003402 AGCCTCATAGTTAATTCAGATCTCC 57.997 40.000 0.00 0.00 0.00 3.71
3061 7167 4.522789 AGTTACAATTTTGAGCGGGTCAAT 59.477 37.500 21.76 10.26 44.89 2.57
3064 7170 3.244976 CAATTTTGAGCGGGTCAATGAC 58.755 45.455 21.76 4.51 44.89 3.06
3071 7177 0.451783 GCGGGTCAATGACACCAATC 59.548 55.000 15.86 0.00 35.35 2.67
3096 7202 1.339151 GCAACTTCTCACCACCTAGGG 60.339 57.143 14.81 1.73 43.89 3.53
3101 7207 3.072622 ACTTCTCACCACCTAGGGAAAAC 59.927 47.826 14.81 0.00 43.89 2.43
3107 7213 1.268625 CCACCTAGGGAAAACAAACGC 59.731 52.381 14.81 0.00 0.00 4.84
3108 7214 1.268625 CACCTAGGGAAAACAAACGCC 59.731 52.381 14.81 0.00 0.00 5.68
3109 7215 1.133730 ACCTAGGGAAAACAAACGCCA 60.134 47.619 14.81 0.00 0.00 5.69
3110 7216 1.957877 CCTAGGGAAAACAAACGCCAA 59.042 47.619 0.00 0.00 0.00 4.52
3111 7217 2.560981 CCTAGGGAAAACAAACGCCAAT 59.439 45.455 0.00 0.00 0.00 3.16
3112 7218 3.759618 CCTAGGGAAAACAAACGCCAATA 59.240 43.478 0.00 0.00 0.00 1.90
3113 7219 4.401202 CCTAGGGAAAACAAACGCCAATAT 59.599 41.667 0.00 0.00 0.00 1.28
3114 7220 4.186856 AGGGAAAACAAACGCCAATATG 57.813 40.909 0.00 0.00 0.00 1.78
3116 7222 3.677596 GGGAAAACAAACGCCAATATGTG 59.322 43.478 0.00 0.00 0.00 3.21
3122 7514 5.484173 ACAAACGCCAATATGTGATACTG 57.516 39.130 0.00 0.00 0.00 2.74
3165 7557 5.491070 ACATACAGCTATCAGCACAGAAAA 58.509 37.500 0.38 0.00 45.56 2.29
3167 7559 4.959596 ACAGCTATCAGCACAGAAAATG 57.040 40.909 0.38 0.00 45.56 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.569167 CGTGTCTAACATATACTCTCTTCAAAA 57.431 33.333 0.00 0.00 0.00 2.44
8 9 8.953313 TCGTGTCTAACATATACTCTCTTCAAA 58.047 33.333 0.00 0.00 0.00 2.69
9 10 8.502105 TCGTGTCTAACATATACTCTCTTCAA 57.498 34.615 0.00 0.00 0.00 2.69
10 11 8.678593 ATCGTGTCTAACATATACTCTCTTCA 57.321 34.615 0.00 0.00 0.00 3.02
22 23 9.161629 TGATTCAACAATAATCGTGTCTAACAT 57.838 29.630 0.00 0.00 36.35 2.71
23 24 8.440059 GTGATTCAACAATAATCGTGTCTAACA 58.560 33.333 0.00 0.00 36.35 2.41
24 25 8.656849 AGTGATTCAACAATAATCGTGTCTAAC 58.343 33.333 0.00 0.00 36.35 2.34
25 26 8.771920 AGTGATTCAACAATAATCGTGTCTAA 57.228 30.769 0.00 0.00 36.35 2.10
26 27 9.863845 TTAGTGATTCAACAATAATCGTGTCTA 57.136 29.630 0.00 0.00 36.35 2.59
27 28 8.771920 TTAGTGATTCAACAATAATCGTGTCT 57.228 30.769 0.00 0.00 36.35 3.41
28 29 9.478019 CTTTAGTGATTCAACAATAATCGTGTC 57.522 33.333 0.00 0.00 36.35 3.67
29 30 8.999431 ACTTTAGTGATTCAACAATAATCGTGT 58.001 29.630 0.00 0.00 36.35 4.49
46 47 9.809395 ACAGAGGCATACTATATACTTTAGTGA 57.191 33.333 0.00 0.00 32.35 3.41
49 50 9.360093 GCAACAGAGGCATACTATATACTTTAG 57.640 37.037 0.00 0.00 0.00 1.85
50 51 8.866093 TGCAACAGAGGCATACTATATACTTTA 58.134 33.333 0.00 0.00 36.11 1.85
51 52 7.735917 TGCAACAGAGGCATACTATATACTTT 58.264 34.615 0.00 0.00 36.11 2.66
52 53 7.303182 TGCAACAGAGGCATACTATATACTT 57.697 36.000 0.00 0.00 36.11 2.24
53 54 6.918067 TGCAACAGAGGCATACTATATACT 57.082 37.500 0.00 0.00 36.11 2.12
54 55 6.089551 CGTTGCAACAGAGGCATACTATATAC 59.910 42.308 28.01 0.00 41.58 1.47
55 56 6.156519 CGTTGCAACAGAGGCATACTATATA 58.843 40.000 28.01 0.00 41.58 0.86
56 57 4.991056 CGTTGCAACAGAGGCATACTATAT 59.009 41.667 28.01 0.00 41.58 0.86
57 58 4.368315 CGTTGCAACAGAGGCATACTATA 58.632 43.478 28.01 0.00 41.58 1.31
58 59 3.198068 CGTTGCAACAGAGGCATACTAT 58.802 45.455 28.01 0.00 41.58 2.12
59 60 2.616960 CGTTGCAACAGAGGCATACTA 58.383 47.619 28.01 0.00 41.58 1.82
60 61 1.442769 CGTTGCAACAGAGGCATACT 58.557 50.000 28.01 0.00 41.58 2.12
61 62 0.179189 GCGTTGCAACAGAGGCATAC 60.179 55.000 28.01 0.00 41.58 2.39
62 63 0.605050 TGCGTTGCAACAGAGGCATA 60.605 50.000 28.01 6.74 41.58 3.14
63 64 1.246056 ATGCGTTGCAACAGAGGCAT 61.246 50.000 26.85 26.85 43.62 4.40
64 65 1.898094 ATGCGTTGCAACAGAGGCA 60.898 52.632 28.01 26.48 43.62 4.75
65 66 1.443194 CATGCGTTGCAACAGAGGC 60.443 57.895 28.01 22.17 43.62 4.70
66 67 1.210931 CCATGCGTTGCAACAGAGG 59.789 57.895 28.01 18.97 43.62 3.69
67 68 0.110056 GACCATGCGTTGCAACAGAG 60.110 55.000 28.01 13.80 43.62 3.35
68 69 0.817229 TGACCATGCGTTGCAACAGA 60.817 50.000 28.01 14.54 43.62 3.41
69 70 0.030504 TTGACCATGCGTTGCAACAG 59.969 50.000 28.01 20.60 43.62 3.16
70 71 0.672889 ATTGACCATGCGTTGCAACA 59.327 45.000 28.01 11.26 43.62 3.33
71 72 1.335780 TGATTGACCATGCGTTGCAAC 60.336 47.619 19.89 19.89 43.62 4.17
72 73 0.957362 TGATTGACCATGCGTTGCAA 59.043 45.000 0.00 0.00 43.62 4.08
73 74 0.522626 CTGATTGACCATGCGTTGCA 59.477 50.000 0.00 0.00 44.86 4.08
74 75 0.523072 ACTGATTGACCATGCGTTGC 59.477 50.000 0.00 0.00 0.00 4.17
75 76 3.261580 TCTACTGATTGACCATGCGTTG 58.738 45.455 0.00 0.00 0.00 4.10
76 77 3.610040 TCTACTGATTGACCATGCGTT 57.390 42.857 0.00 0.00 0.00 4.84
77 78 3.610040 TTCTACTGATTGACCATGCGT 57.390 42.857 0.00 0.00 0.00 5.24
78 79 9.755804 ATATATATTCTACTGATTGACCATGCG 57.244 33.333 0.00 0.00 0.00 4.73
141 142 8.412456 CGGGCCATAATGCATATAAATAAATCA 58.588 33.333 4.39 0.00 0.00 2.57
142 143 8.413229 ACGGGCCATAATGCATATAAATAAATC 58.587 33.333 4.39 0.00 0.00 2.17
143 144 8.305046 ACGGGCCATAATGCATATAAATAAAT 57.695 30.769 4.39 0.00 0.00 1.40
144 145 7.710676 ACGGGCCATAATGCATATAAATAAA 57.289 32.000 4.39 0.00 0.00 1.40
145 146 7.012894 GCTACGGGCCATAATGCATATAAATAA 59.987 37.037 4.39 0.00 34.27 1.40
146 147 6.485313 GCTACGGGCCATAATGCATATAAATA 59.515 38.462 4.39 0.00 34.27 1.40
147 148 5.299279 GCTACGGGCCATAATGCATATAAAT 59.701 40.000 4.39 0.00 34.27 1.40
148 149 4.638421 GCTACGGGCCATAATGCATATAAA 59.362 41.667 4.39 0.00 34.27 1.40
149 150 4.196193 GCTACGGGCCATAATGCATATAA 58.804 43.478 4.39 0.00 34.27 0.98
150 151 3.198853 TGCTACGGGCCATAATGCATATA 59.801 43.478 4.39 0.00 40.92 0.86
151 152 2.026356 TGCTACGGGCCATAATGCATAT 60.026 45.455 4.39 0.00 40.92 1.78
152 153 1.349357 TGCTACGGGCCATAATGCATA 59.651 47.619 4.39 0.00 40.92 3.14
153 154 0.110295 TGCTACGGGCCATAATGCAT 59.890 50.000 4.39 0.00 40.92 3.96
154 155 0.106967 TTGCTACGGGCCATAATGCA 60.107 50.000 4.39 5.24 40.92 3.96
155 156 0.310854 GTTGCTACGGGCCATAATGC 59.689 55.000 4.39 2.23 40.92 3.56
156 157 0.586319 CGTTGCTACGGGCCATAATG 59.414 55.000 13.04 0.00 43.94 1.90
157 158 3.000815 CGTTGCTACGGGCCATAAT 57.999 52.632 13.04 0.00 43.94 1.28
158 159 4.524869 CGTTGCTACGGGCCATAA 57.475 55.556 13.04 0.00 43.94 1.90
167 168 2.126346 ACGCCCGTACGTTGCTAC 60.126 61.111 20.29 0.00 45.75 3.58
174 175 1.009829 ACTAGTAGAACGCCCGTACG 58.990 55.000 8.69 8.69 39.50 3.67
175 176 2.936498 TGTACTAGTAGAACGCCCGTAC 59.064 50.000 1.87 0.00 0.00 3.67
176 177 3.260475 TGTACTAGTAGAACGCCCGTA 57.740 47.619 1.87 0.00 0.00 4.02
177 178 2.113860 TGTACTAGTAGAACGCCCGT 57.886 50.000 1.87 0.00 0.00 5.28
178 179 3.561310 TGTATGTACTAGTAGAACGCCCG 59.439 47.826 1.87 0.00 0.00 6.13
179 180 5.067023 ACTTGTATGTACTAGTAGAACGCCC 59.933 44.000 1.87 0.00 39.76 6.13
180 181 6.129053 ACTTGTATGTACTAGTAGAACGCC 57.871 41.667 1.87 0.00 39.76 5.68
187 188 6.262496 CAGGCAGCTACTTGTATGTACTAGTA 59.738 42.308 11.89 11.89 41.30 1.82
188 189 5.067936 CAGGCAGCTACTTGTATGTACTAGT 59.932 44.000 0.00 0.00 43.00 2.57
189 190 5.524284 CAGGCAGCTACTTGTATGTACTAG 58.476 45.833 0.00 0.00 35.61 2.57
190 191 4.202121 GCAGGCAGCTACTTGTATGTACTA 60.202 45.833 0.00 0.00 41.15 1.82
191 192 3.430929 GCAGGCAGCTACTTGTATGTACT 60.431 47.826 0.00 0.00 41.15 2.73
192 193 2.866762 GCAGGCAGCTACTTGTATGTAC 59.133 50.000 0.00 0.00 41.15 2.90
212 213 1.128692 CACGCTAACCAACTAGCAAGC 59.871 52.381 3.73 0.00 43.84 4.01
213 214 1.732259 CCACGCTAACCAACTAGCAAG 59.268 52.381 3.73 0.00 43.84 4.01
214 215 1.071071 ACCACGCTAACCAACTAGCAA 59.929 47.619 3.73 0.00 43.84 3.91
255 256 4.006319 GGATTCAAACTCTCAACCTCAGG 58.994 47.826 0.00 0.00 0.00 3.86
256 257 4.645535 TGGATTCAAACTCTCAACCTCAG 58.354 43.478 0.00 0.00 0.00 3.35
258 259 5.495640 AGATGGATTCAAACTCTCAACCTC 58.504 41.667 0.00 0.00 0.00 3.85
299 301 6.245890 ACTCTTCTCATCCTAATTTCCCAG 57.754 41.667 0.00 0.00 0.00 4.45
315 317 5.181748 GCATGAGTTGGTCAATACTCTTCT 58.818 41.667 0.00 0.00 41.05 2.85
324 326 6.265196 GGGAATATTATGCATGAGTTGGTCAA 59.735 38.462 10.16 0.00 39.19 3.18
328 330 5.122869 CGAGGGAATATTATGCATGAGTTGG 59.877 44.000 10.16 0.00 0.00 3.77
334 336 5.375417 TTTGCGAGGGAATATTATGCATG 57.625 39.130 10.16 0.00 0.00 4.06
360 362 8.815912 ACCTCCTAATTTTATGCATGAGTTTTT 58.184 29.630 10.16 0.00 0.00 1.94
361 363 8.253113 CACCTCCTAATTTTATGCATGAGTTTT 58.747 33.333 10.16 0.00 0.00 2.43
362 364 7.615365 TCACCTCCTAATTTTATGCATGAGTTT 59.385 33.333 10.16 1.49 0.00 2.66
363 365 7.067494 GTCACCTCCTAATTTTATGCATGAGTT 59.933 37.037 10.16 3.82 0.00 3.01
364 366 6.543831 GTCACCTCCTAATTTTATGCATGAGT 59.456 38.462 10.16 0.00 0.00 3.41
365 367 6.016777 GGTCACCTCCTAATTTTATGCATGAG 60.017 42.308 10.16 4.44 0.00 2.90
427 1981 3.380479 TGCCTTAATTATCTCGACCCG 57.620 47.619 0.00 0.00 0.00 5.28
485 2039 6.545666 TGTGCATGATTATCCGTATCCTTTTT 59.454 34.615 0.00 0.00 0.00 1.94
486 2040 6.061441 TGTGCATGATTATCCGTATCCTTTT 58.939 36.000 0.00 0.00 0.00 2.27
487 2041 5.620206 TGTGCATGATTATCCGTATCCTTT 58.380 37.500 0.00 0.00 0.00 3.11
488 2042 5.012046 TCTGTGCATGATTATCCGTATCCTT 59.988 40.000 0.00 0.00 0.00 3.36
489 2043 4.528206 TCTGTGCATGATTATCCGTATCCT 59.472 41.667 0.00 0.00 0.00 3.24
490 2044 4.820897 TCTGTGCATGATTATCCGTATCC 58.179 43.478 0.00 0.00 0.00 2.59
491 2045 6.974932 ATTCTGTGCATGATTATCCGTATC 57.025 37.500 0.00 0.00 0.00 2.24
492 2046 7.550551 CCTAATTCTGTGCATGATTATCCGTAT 59.449 37.037 0.00 0.00 0.00 3.06
493 2047 6.873605 CCTAATTCTGTGCATGATTATCCGTA 59.126 38.462 0.00 0.00 0.00 4.02
494 2048 5.702670 CCTAATTCTGTGCATGATTATCCGT 59.297 40.000 0.00 0.00 0.00 4.69
495 2049 5.934043 TCCTAATTCTGTGCATGATTATCCG 59.066 40.000 0.00 0.00 0.00 4.18
496 2050 7.609146 TGATCCTAATTCTGTGCATGATTATCC 59.391 37.037 0.00 0.00 0.00 2.59
497 2051 8.449397 GTGATCCTAATTCTGTGCATGATTATC 58.551 37.037 0.00 0.00 0.00 1.75
498 2052 7.940688 TGTGATCCTAATTCTGTGCATGATTAT 59.059 33.333 0.00 0.00 0.00 1.28
499 2053 7.281841 TGTGATCCTAATTCTGTGCATGATTA 58.718 34.615 0.00 0.00 0.00 1.75
500 2054 6.124340 TGTGATCCTAATTCTGTGCATGATT 58.876 36.000 0.00 0.00 0.00 2.57
509 2063 8.484641 AATATACGCATGTGATCCTAATTCTG 57.515 34.615 14.43 0.00 0.00 3.02
527 2081 7.061905 CCGCTTTAACTGTGATCCTAATATACG 59.938 40.741 0.00 0.00 0.00 3.06
564 2119 8.378172 TCCTGTAATTAATGACGATTGGATTC 57.622 34.615 0.00 0.00 0.00 2.52
631 2186 0.996462 TGCGATTTTAACTCGAGCGG 59.004 50.000 13.61 0.00 38.38 5.52
682 2239 1.726322 CGAACGATCCGGATCTCGC 60.726 63.158 35.31 23.91 38.42 5.03
705 2262 1.206578 CGTGCGGATTTTTGCGACT 59.793 52.632 0.00 0.00 0.00 4.18
708 2265 3.171911 GGCGTGCGGATTTTTGCG 61.172 61.111 0.00 0.00 0.00 4.85
720 2277 3.434637 CAAAATCTAAAATCCGGGCGTG 58.565 45.455 0.00 0.00 0.00 5.34
724 2281 4.464069 TTGGCAAAATCTAAAATCCGGG 57.536 40.909 0.00 0.00 0.00 5.73
725 2282 6.983474 AAATTGGCAAAATCTAAAATCCGG 57.017 33.333 3.01 0.00 0.00 5.14
792 2350 2.202650 GATGCGTTGCACATGGCC 60.203 61.111 0.00 0.00 43.04 5.36
819 2377 3.795488 GCAAGGCCGAGGTAATTAATTGC 60.795 47.826 11.05 9.30 34.46 3.56
836 2424 7.546667 ACAATAAACAAGATTTAGCATGCAAGG 59.453 33.333 21.98 2.67 0.00 3.61
841 2429 7.253750 GCCGAACAATAAACAAGATTTAGCATG 60.254 37.037 0.00 0.00 0.00 4.06
911 2535 2.093973 TCGATCAGAGAGCAAGGGAAAC 60.094 50.000 0.00 0.00 0.00 2.78
914 2538 1.959985 GATCGATCAGAGAGCAAGGGA 59.040 52.381 20.52 0.00 0.00 4.20
925 2549 1.609072 TGCGTAGGAAGGATCGATCAG 59.391 52.381 25.93 8.03 0.00 2.90
926 2550 1.609072 CTGCGTAGGAAGGATCGATCA 59.391 52.381 25.93 2.12 0.00 2.92
928 2552 0.315568 GCTGCGTAGGAAGGATCGAT 59.684 55.000 0.00 0.00 0.00 3.59
980 2604 2.730524 GCTCTCCTCCTGGACCAGC 61.731 68.421 16.72 0.00 37.46 4.85
983 2607 0.179936 CATTGCTCTCCTCCTGGACC 59.820 60.000 0.00 0.00 37.46 4.46
985 2609 1.630126 GCCATTGCTCTCCTCCTGGA 61.630 60.000 0.00 0.00 36.21 3.86
1146 2770 4.681978 AGGAAGTCGTGCACCGCC 62.682 66.667 12.15 5.66 36.19 6.13
1317 2941 2.479198 GCGAACGCCTTAACCAGC 59.521 61.111 8.03 0.00 34.56 4.85
1320 2944 3.493440 CCCGCGAACGCCTTAACC 61.493 66.667 8.23 0.00 38.22 2.85
1515 3139 2.821366 CACCCGATGGCAGTGAGC 60.821 66.667 0.00 0.00 44.65 4.26
1549 3173 3.260483 CAGGAGCTGCGCGATGAC 61.260 66.667 12.10 0.00 0.00 3.06
1623 3247 0.758734 AATGGCTATAGCTCACGGCA 59.241 50.000 23.53 12.47 44.79 5.69
1635 3259 1.342672 GGACGGGGGAGAAATGGCTA 61.343 60.000 0.00 0.00 0.00 3.93
1636 3260 2.680370 GGACGGGGGAGAAATGGCT 61.680 63.158 0.00 0.00 0.00 4.75
1637 3261 2.124278 GGACGGGGGAGAAATGGC 60.124 66.667 0.00 0.00 0.00 4.40
1641 3265 2.285144 GAGGGGACGGGGGAGAAA 60.285 66.667 0.00 0.00 0.00 2.52
1665 3289 6.430925 CACATCACAGTTAATTCAAGAAGGGA 59.569 38.462 0.00 0.00 0.00 4.20
1668 3292 8.724229 TCATCACATCACAGTTAATTCAAGAAG 58.276 33.333 0.00 0.00 0.00 2.85
1687 3311 3.805971 GCATCGATCATCAGTTCATCACA 59.194 43.478 0.00 0.00 0.00 3.58
1708 3786 1.007336 CGTCCACGTAGTCCTGTTGC 61.007 60.000 0.00 0.00 41.61 4.17
1709 3787 0.594602 TCGTCCACGTAGTCCTGTTG 59.405 55.000 0.00 0.00 41.61 3.33
1710 3788 0.595095 GTCGTCCACGTAGTCCTGTT 59.405 55.000 0.00 0.00 41.61 3.16
1905 3995 0.860618 GTAGTCGTCCACGTCGATGC 60.861 60.000 4.06 0.00 39.45 3.91
2026 4116 4.864334 CCCTGGTCGATGCTGGCC 62.864 72.222 0.00 0.00 0.00 5.36
2215 4305 3.815569 GAGATCCACGAGGCGAGCG 62.816 68.421 0.00 0.00 33.74 5.03
2271 4364 1.135915 ACAGATCACGGAGAGATGCAC 59.864 52.381 0.00 0.00 38.11 4.57
2343 4436 5.003804 GCAATCTCTGAACTCCAAGGTTTA 58.996 41.667 0.00 0.00 0.00 2.01
2344 4437 3.823304 GCAATCTCTGAACTCCAAGGTTT 59.177 43.478 0.00 0.00 0.00 3.27
2400 4493 9.893305 AATCAAAATAACAGTTTGTGCTACTAC 57.107 29.630 0.00 0.00 37.28 2.73
2405 4498 7.271511 TCCAAATCAAAATAACAGTTTGTGCT 58.728 30.769 0.00 0.00 37.28 4.40
2406 4499 7.224557 ACTCCAAATCAAAATAACAGTTTGTGC 59.775 33.333 0.00 0.00 37.28 4.57
2416 4509 8.477419 AGAAGTTCCACTCCAAATCAAAATAA 57.523 30.769 0.00 0.00 0.00 1.40
2437 4530 4.718940 ACAAGTTCAAACCACCAAGAAG 57.281 40.909 0.00 0.00 0.00 2.85
2440 4535 6.568869 TCAAATACAAGTTCAAACCACCAAG 58.431 36.000 0.00 0.00 0.00 3.61
2450 4545 8.791327 TTCATAGCTGATCAAATACAAGTTCA 57.209 30.769 0.00 0.00 0.00 3.18
2459 4554 7.893124 AGAAACCATTCATAGCTGATCAAAT 57.107 32.000 0.00 0.00 38.06 2.32
2512 4608 2.161855 CTCTGCAGTTTATGGTGCCAA 58.838 47.619 14.67 0.00 39.04 4.52
2513 4609 1.825090 CTCTGCAGTTTATGGTGCCA 58.175 50.000 14.67 0.00 39.04 4.92
2514 4610 0.453390 GCTCTGCAGTTTATGGTGCC 59.547 55.000 14.67 0.00 39.04 5.01
2515 4611 1.399791 GAGCTCTGCAGTTTATGGTGC 59.600 52.381 14.67 6.61 40.29 5.01
2516 4612 2.703416 TGAGCTCTGCAGTTTATGGTG 58.297 47.619 16.19 0.00 0.00 4.17
2600 4704 8.589338 TGTGGGCTTAAAAATTAGAAAGCATAA 58.411 29.630 16.04 3.49 44.81 1.90
2612 4716 6.880529 CCTCAATTGATTGTGGGCTTAAAAAT 59.119 34.615 8.96 0.00 43.89 1.82
2614 4718 5.792741 CCTCAATTGATTGTGGGCTTAAAA 58.207 37.500 8.96 0.00 43.89 1.52
2615 4719 5.404466 CCTCAATTGATTGTGGGCTTAAA 57.596 39.130 8.96 0.00 43.89 1.52
2623 4727 5.909621 ATTGGAGACCTCAATTGATTGTG 57.090 39.130 8.96 0.00 38.84 3.33
2624 4728 8.717717 TCTATATTGGAGACCTCAATTGATTGT 58.282 33.333 8.96 9.43 38.84 2.71
2625 4729 9.217278 CTCTATATTGGAGACCTCAATTGATTG 57.783 37.037 8.96 6.10 36.40 2.67
2690 4855 4.656112 TGAGAGGGCTCCTTATAAGAAAGG 59.344 45.833 14.28 0.00 46.35 3.11
2691 4856 5.878406 TGAGAGGGCTCCTTATAAGAAAG 57.122 43.478 14.28 11.36 40.55 2.62
2694 4859 5.467738 TGAATGAGAGGGCTCCTTATAAGA 58.532 41.667 14.28 0.00 40.55 2.10
2695 4860 5.815233 TGAATGAGAGGGCTCCTTATAAG 57.185 43.478 5.43 5.43 40.55 1.73
2696 4861 6.770286 ATTGAATGAGAGGGCTCCTTATAA 57.230 37.500 0.00 0.00 40.55 0.98
2697 4862 6.560304 AGAATTGAATGAGAGGGCTCCTTATA 59.440 38.462 0.00 0.00 40.55 0.98
2698 4863 5.372066 AGAATTGAATGAGAGGGCTCCTTAT 59.628 40.000 0.00 0.00 40.55 1.73
2720 4885 8.474831 GCCCTTTAAAATAAGGAAGCATAAAGA 58.525 33.333 4.02 0.00 46.28 2.52
2721 4886 8.478066 AGCCCTTTAAAATAAGGAAGCATAAAG 58.522 33.333 4.02 0.00 46.28 1.85
2722 4887 8.374184 AGCCCTTTAAAATAAGGAAGCATAAA 57.626 30.769 4.02 0.00 46.28 1.40
2723 4888 7.617723 TGAGCCCTTTAAAATAAGGAAGCATAA 59.382 33.333 4.02 0.00 46.28 1.90
2724 4889 7.122715 TGAGCCCTTTAAAATAAGGAAGCATA 58.877 34.615 4.02 0.00 46.28 3.14
2725 4890 5.957774 TGAGCCCTTTAAAATAAGGAAGCAT 59.042 36.000 4.02 0.00 46.28 3.79
2778 4943 3.138304 CCGGTCAAAATTGAGTGACTCA 58.862 45.455 11.93 11.93 43.06 3.41
2882 5066 9.988815 GAGATCTGAATTAACTATGAGGCTTTA 57.011 33.333 0.00 0.00 0.00 1.85
2886 5070 6.763355 TGGAGATCTGAATTAACTATGAGGC 58.237 40.000 0.00 0.00 0.00 4.70
2909 5093 2.548057 CGGGTGATCCAATTCCGTATTG 59.452 50.000 0.00 1.60 42.73 1.90
2914 5098 1.967319 AATCGGGTGATCCAATTCCG 58.033 50.000 0.00 0.00 41.80 4.30
2973 7078 5.425196 AATTAGGCAGCATGGTGAATTTT 57.575 34.783 28.34 11.11 35.86 1.82
3061 7167 1.149401 TTGCGTGGGATTGGTGTCA 59.851 52.632 0.00 0.00 0.00 3.58
3064 7170 0.240945 GAAGTTGCGTGGGATTGGTG 59.759 55.000 0.00 0.00 0.00 4.17
3071 7177 1.227823 TGGTGAGAAGTTGCGTGGG 60.228 57.895 0.00 0.00 0.00 4.61
3096 7202 7.008266 CAGTATCACATATTGGCGTTTGTTTTC 59.992 37.037 0.00 0.00 0.00 2.29
3101 7207 5.484173 ACAGTATCACATATTGGCGTTTG 57.516 39.130 0.00 0.00 0.00 2.93
3107 7213 5.610398 TGGTGCTACAGTATCACATATTGG 58.390 41.667 14.93 0.00 32.69 3.16
3108 7214 7.734924 ATTGGTGCTACAGTATCACATATTG 57.265 36.000 14.93 0.00 32.69 1.90
3146 7538 4.330250 ACATTTTCTGTGCTGATAGCTGT 58.670 39.130 0.00 0.00 42.97 4.40
3149 7541 4.337763 CGAACATTTTCTGTGCTGATAGC 58.662 43.478 0.00 0.00 42.82 2.97
3153 7545 1.946081 TGCGAACATTTTCTGTGCTGA 59.054 42.857 0.00 0.00 38.39 4.26
3156 7548 2.118228 TGTGCGAACATTTTCTGTGC 57.882 45.000 0.00 0.00 38.39 4.57
3159 7551 7.914871 TCCATATTTATGTGCGAACATTTTCTG 59.085 33.333 15.80 6.58 31.82 3.02
3165 7557 7.509141 TCAATCCATATTTATGTGCGAACAT 57.491 32.000 14.84 14.84 31.82 2.71


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

AutoCloner maintained by Alex Coulton.