Multiple sequence alignment - TraesCS6D01G149600

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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 TraesCS6D01G149600 chr6D 100.000 5314 0 0 1 5314 123154378 123159691 0.000000e+00 9814.0
1 TraesCS6D01G149600 chr6D 100.000 3103 0 0 5664 8766 123160041 123163143 0.000000e+00 5731.0
2 TraesCS6D01G149600 chr6D 76.549 226 38 13 6090 6310 103189035 103189250 9.300000e-20 110.0
3 TraesCS6D01G149600 chr6D 89.796 49 3 2 17 64 97016181 97016228 2.640000e-05 62.1
4 TraesCS6D01G149600 chr6B 96.944 3632 71 12 1698 5314 217166113 217169719 0.000000e+00 6056.0
5 TraesCS6D01G149600 chr6B 97.549 1999 36 4 5694 7682 217169921 217171916 0.000000e+00 3408.0
6 TraesCS6D01G149600 chr6B 94.753 953 38 5 581 1527 217164591 217165537 0.000000e+00 1472.0
7 TraesCS6D01G149600 chr6B 89.815 756 31 22 8036 8766 217172352 217173086 0.000000e+00 928.0
8 TraesCS6D01G149600 chr6B 95.541 157 7 0 532 688 217164213 217164369 1.460000e-62 252.0
9 TraesCS6D01G149600 chr6B 90.625 192 8 3 1529 1712 217165701 217165890 6.800000e-61 246.0
10 TraesCS6D01G149600 chr6B 91.018 167 14 1 7716 7882 217171916 217172081 3.180000e-54 224.0
11 TraesCS6D01G149600 chr6B 88.235 170 17 3 112 281 217163819 217163985 5.370000e-47 200.0
12 TraesCS6D01G149600 chr6B 93.496 123 5 2 7874 7994 217172234 217172355 6.990000e-41 180.0
13 TraesCS6D01G149600 chr6B 73.432 271 54 13 6048 6309 408259886 408260147 1.570000e-12 86.1
14 TraesCS6D01G149600 chr6A 97.370 3308 74 6 1675 4979 157966960 157963663 0.000000e+00 5614.0
15 TraesCS6D01G149600 chr6A 97.627 3118 53 10 5666 8766 157963670 157960557 0.000000e+00 5328.0
16 TraesCS6D01G149600 chr6A 90.346 1243 53 12 309 1514 157968462 157967250 0.000000e+00 1568.0
17 TraesCS6D01G149600 chr6A 93.642 173 9 1 1509 1681 157967150 157966980 3.140000e-64 257.0
18 TraesCS6D01G149600 chr6A 90.816 98 9 0 103 200 157971541 157971444 1.990000e-26 132.0
19 TraesCS6D01G149600 chr6A 90.000 50 4 1 29 77 198073759 198073710 7.350000e-06 63.9
20 TraesCS6D01G149600 chr7D 89.354 263 27 1 4594 4856 204870747 204871008 6.560000e-86 329.0
21 TraesCS6D01G149600 chr7D 88.168 262 26 3 4594 4854 436498943 436499200 3.070000e-79 307.0
22 TraesCS6D01G149600 chr7D 81.006 358 66 2 1041 1397 485831240 485831596 5.180000e-72 283.0
23 TraesCS6D01G149600 chr2A 80.000 435 72 14 4503 4927 743549123 743549552 3.070000e-79 307.0
24 TraesCS6D01G149600 chr2A 85.616 146 16 3 4344 4484 622265224 622265369 1.970000e-31 148.0
25 TraesCS6D01G149600 chr2A 83.916 143 18 3 4347 4484 746239608 746239750 1.990000e-26 132.0
26 TraesCS6D01G149600 chr2A 87.755 49 4 2 6262 6310 38592805 38592759 1.000000e-03 56.5
27 TraesCS6D01G149600 chr2A 92.500 40 2 1 6271 6310 80586406 80586368 1.000000e-03 56.5
28 TraesCS6D01G149600 chr7B 87.452 263 31 2 4594 4856 169295481 169295741 1.430000e-77 302.0
29 TraesCS6D01G149600 chr7B 81.111 360 62 5 1041 1397 513652191 513652547 5.180000e-72 283.0
30 TraesCS6D01G149600 chr3D 86.891 267 29 4 4594 4855 168185913 168185648 2.390000e-75 294.0
31 TraesCS6D01G149600 chr3D 86.232 276 33 5 4589 4862 590501242 590500970 2.390000e-75 294.0
32 TraesCS6D01G149600 chr7A 81.006 358 66 2 1041 1397 554390245 554390601 5.180000e-72 283.0
33 TraesCS6D01G149600 chr7A 76.768 495 100 11 3799 4288 554393550 554394034 6.750000e-66 263.0
34 TraesCS6D01G149600 chr7A 85.816 141 14 4 4344 4480 441920803 441920665 2.550000e-30 145.0
35 TraesCS6D01G149600 chr2D 78.571 434 79 14 4503 4927 611219392 611219820 3.120000e-69 274.0
36 TraesCS6D01G149600 chr3B 78.467 274 42 14 6043 6310 143254671 143254409 7.040000e-36 163.0
37 TraesCS6D01G149600 chr3B 76.000 275 56 9 6052 6326 456547831 456547567 5.520000e-27 134.0
38 TraesCS6D01G149600 chr3B 84.247 146 14 7 4345 4484 526205412 526205554 5.520000e-27 134.0
39 TraesCS6D01G149600 chr3B 74.016 254 48 13 6048 6293 76516574 76516331 4.360000e-13 87.9
40 TraesCS6D01G149600 chr3A 86.301 146 15 3 4344 4484 264950426 264950281 4.240000e-33 154.0
41 TraesCS6D01G149600 chr3A 78.761 226 34 12 6086 6309 83778044 83778257 1.190000e-28 139.0
42 TraesCS6D01G149600 chrUn 85.616 146 15 5 4344 4484 79187213 79187069 1.970000e-31 148.0
43 TraesCS6D01G149600 chrUn 95.238 42 2 0 29 70 81901910 81901869 5.680000e-07 67.6
44 TraesCS6D01G149600 chr5D 78.571 238 38 11 6081 6309 5557726 5557959 2.550000e-30 145.0
45 TraesCS6D01G149600 chr5D 100.000 31 0 0 6089 6119 75282400 75282370 3.420000e-04 58.4
46 TraesCS6D01G149600 chr2B 83.974 156 19 4 4346 4498 775120766 775120614 2.550000e-30 145.0
47 TraesCS6D01G149600 chr2B 90.000 50 5 0 33 82 67908182 67908133 2.040000e-06 65.8
48 TraesCS6D01G149600 chr4B 97.674 43 1 0 28 70 47495741 47495783 3.390000e-09 75.0
49 TraesCS6D01G149600 chr4B 100.000 28 0 0 501 528 605505962 605505935 1.600000e-02 52.8
50 TraesCS6D01G149600 chr4B 100.000 28 0 0 501 528 621075498 621075525 1.600000e-02 52.8
51 TraesCS6D01G149600 chr5B 97.436 39 1 0 29 67 50276813 50276851 5.680000e-07 67.6
52 TraesCS6D01G149600 chr5B 95.238 42 2 0 29 70 659712710 659712669 5.680000e-07 67.6
53 TraesCS6D01G149600 chr1B 97.436 39 1 0 29 67 108209378 108209416 5.680000e-07 67.6
54 TraesCS6D01G149600 chr4A 86.885 61 5 3 30 88 32707482 32707541 2.040000e-06 65.8
55 TraesCS6D01G149600 chr1A 75.352 142 26 6 6045 6186 552109857 552109989 9.500000e-05 60.2


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 TraesCS6D01G149600 chr6D 123154378 123163143 8765 False 7772.500000 9814 100.000000 1 8766 2 chr6D.!!$F3 8765
1 TraesCS6D01G149600 chr6B 217163819 217173086 9267 False 1440.666667 6056 93.108444 112 8766 9 chr6B.!!$F2 8654
2 TraesCS6D01G149600 chr6A 157960557 157971541 10984 True 2579.800000 5614 93.960200 103 8766 5 chr6A.!!$R2 8663
3 TraesCS6D01G149600 chr7A 554390245 554394034 3789 False 273.000000 283 78.887000 1041 4288 2 chr7A.!!$F1 3247

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
397 3283 0.035458 CCTTGGCTCCGAGAGTGTTT 59.965 55.000 4.72 0.0 31.39 2.83 F
450 3337 0.039798 GTACGTCGTCAAGGAGTGCA 60.040 55.000 0.00 0.0 0.00 4.57 F
452 3339 0.597637 ACGTCGTCAAGGAGTGCAAG 60.598 55.000 0.00 0.0 0.00 4.01 F
2091 5887 1.182667 CCGTAGTGGTGTGGATCAGA 58.817 55.000 0.00 0.0 0.00 3.27 F
2135 5931 3.075005 GTCCCGAGCAGCCTACCA 61.075 66.667 0.00 0.0 0.00 3.25 F
4415 9241 4.073293 AGAGTGAAACAAGTGGTGGTAG 57.927 45.455 0.00 0.0 41.43 3.18 F
6076 10911 1.001378 CGTGAAGGTCTGGGCAAAAAG 60.001 52.381 0.00 0.0 0.00 2.27 F
7175 12016 2.161609 GGAGCCAGTAAACCGAAACATG 59.838 50.000 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 5887 0.179004 TCCGTGTTGCTTTGGGTCAT 60.179 50.000 0.00 0.00 0.00 3.06 R
2972 6786 1.067283 TGAGTCTGCAGTGAAGCTAGC 60.067 52.381 14.67 6.62 34.99 3.42 R
3344 7158 7.763613 AGAGGGATGAGGAAAGCATAATATTT 58.236 34.615 0.00 0.00 0.00 1.40 R
3476 7291 0.329596 CCCAAGGAAAGGAGTGGAGG 59.670 60.000 0.00 0.00 32.54 4.30 R
4473 9299 0.608856 TTGTGTCATGGCCGAGCATT 60.609 50.000 0.00 0.00 0.00 3.56 R
7088 11929 0.692756 TGTGTTCCAGTGGACCTCCA 60.693 55.000 12.69 3.38 45.30 3.86 R
7682 12527 0.450983 GAGCAGCAGCATTTCTGTCC 59.549 55.000 3.17 0.00 44.66 4.02 R
8491 13515 2.230130 TGTATTCCCCCTTGGCTTTG 57.770 50.000 0.00 0.00 0.00 2.77 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.303135 TGGAAGGCGTGTCGAGCT 61.303 61.111 0.00 0.00 34.52 4.09
18 19 2.048127 GGAAGGCGTGTCGAGCTT 60.048 61.111 0.00 0.00 34.52 3.74
19 20 1.668151 GGAAGGCGTGTCGAGCTTT 60.668 57.895 0.00 0.00 36.61 3.51
20 21 1.493311 GAAGGCGTGTCGAGCTTTG 59.507 57.895 0.00 0.00 34.01 2.77
21 22 1.901650 GAAGGCGTGTCGAGCTTTGG 61.902 60.000 0.00 0.00 34.01 3.28
22 23 2.660258 AAGGCGTGTCGAGCTTTGGT 62.660 55.000 0.00 0.00 32.61 3.67
23 24 2.668280 GGCGTGTCGAGCTTTGGTC 61.668 63.158 0.00 0.00 34.52 4.02
24 25 1.954146 GCGTGTCGAGCTTTGGTCA 60.954 57.895 0.00 0.00 0.00 4.02
25 26 1.891060 GCGTGTCGAGCTTTGGTCAG 61.891 60.000 0.00 0.00 0.00 3.51
26 27 1.284982 CGTGTCGAGCTTTGGTCAGG 61.285 60.000 0.00 0.00 0.00 3.86
27 28 0.951040 GTGTCGAGCTTTGGTCAGGG 60.951 60.000 0.00 0.00 0.00 4.45
28 29 2.035442 GTCGAGCTTTGGTCAGGGC 61.035 63.158 0.00 0.00 0.00 5.19
29 30 2.217038 TCGAGCTTTGGTCAGGGCT 61.217 57.895 0.00 0.00 37.77 5.19
30 31 0.902984 TCGAGCTTTGGTCAGGGCTA 60.903 55.000 0.00 0.00 35.01 3.93
31 32 0.179000 CGAGCTTTGGTCAGGGCTAT 59.821 55.000 0.00 0.00 35.01 2.97
32 33 1.407437 CGAGCTTTGGTCAGGGCTATT 60.407 52.381 0.00 0.00 35.01 1.73
33 34 2.293170 GAGCTTTGGTCAGGGCTATTC 58.707 52.381 0.00 0.00 35.01 1.75
34 35 1.064389 AGCTTTGGTCAGGGCTATTCC 60.064 52.381 0.00 0.00 32.94 3.01
45 46 2.413310 GGCTATTCCCTCCGTTTCAA 57.587 50.000 0.00 0.00 0.00 2.69
46 47 2.718563 GGCTATTCCCTCCGTTTCAAA 58.281 47.619 0.00 0.00 0.00 2.69
47 48 3.086282 GGCTATTCCCTCCGTTTCAAAA 58.914 45.455 0.00 0.00 0.00 2.44
48 49 3.699538 GGCTATTCCCTCCGTTTCAAAAT 59.300 43.478 0.00 0.00 0.00 1.82
49 50 4.885325 GGCTATTCCCTCCGTTTCAAAATA 59.115 41.667 0.00 0.00 0.00 1.40
50 51 5.008712 GGCTATTCCCTCCGTTTCAAAATAG 59.991 44.000 0.00 0.00 0.00 1.73
51 52 5.820947 GCTATTCCCTCCGTTTCAAAATAGA 59.179 40.000 0.00 0.00 30.43 1.98
52 53 6.486993 GCTATTCCCTCCGTTTCAAAATAGAT 59.513 38.462 0.00 0.00 30.43 1.98
53 54 6.699575 ATTCCCTCCGTTTCAAAATAGATG 57.300 37.500 0.00 0.00 0.00 2.90
54 55 5.429681 TCCCTCCGTTTCAAAATAGATGA 57.570 39.130 0.00 0.00 0.00 2.92
55 56 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
56 57 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
57 58 5.648092 CCCTCCGTTTCAAAATAGATGACTT 59.352 40.000 0.00 0.00 0.00 3.01
58 59 6.821665 CCCTCCGTTTCAAAATAGATGACTTA 59.178 38.462 0.00 0.00 0.00 2.24
59 60 7.335924 CCCTCCGTTTCAAAATAGATGACTTAA 59.664 37.037 0.00 0.00 0.00 1.85
60 61 8.175716 CCTCCGTTTCAAAATAGATGACTTAAC 58.824 37.037 0.00 0.00 0.00 2.01
61 62 8.842358 TCCGTTTCAAAATAGATGACTTAACT 57.158 30.769 0.00 0.00 0.00 2.24
62 63 9.280174 TCCGTTTCAAAATAGATGACTTAACTT 57.720 29.630 0.00 0.00 0.00 2.66
63 64 9.893305 CCGTTTCAAAATAGATGACTTAACTTT 57.107 29.630 0.00 0.00 0.00 2.66
125 126 2.941064 GCCCCGTTAAATCTTAGGTCAC 59.059 50.000 0.00 0.00 0.00 3.67
126 127 3.538591 CCCCGTTAAATCTTAGGTCACC 58.461 50.000 0.00 0.00 0.00 4.02
184 185 0.946221 CTGTTCGCTGGAGTGGACAC 60.946 60.000 0.00 0.00 38.98 3.67
185 186 1.668151 GTTCGCTGGAGTGGACACC 60.668 63.158 0.00 0.00 34.27 4.16
266 3104 2.494870 GTCGGGAAGCTAGTGAGGTAAA 59.505 50.000 0.00 0.00 31.56 2.01
296 3134 2.357154 GGTCCTGTTTGGCTGGATATGT 60.357 50.000 0.00 0.00 45.14 2.29
297 3135 2.945668 GTCCTGTTTGGCTGGATATGTC 59.054 50.000 0.00 0.00 45.14 3.06
298 3136 2.846206 TCCTGTTTGGCTGGATATGTCT 59.154 45.455 0.00 0.00 39.82 3.41
301 3139 2.846206 TGTTTGGCTGGATATGTCTCCT 59.154 45.455 0.00 0.00 36.20 3.69
302 3140 3.209410 GTTTGGCTGGATATGTCTCCTG 58.791 50.000 0.00 0.00 36.20 3.86
307 3145 3.383620 CTGGATATGTCTCCTGCACTC 57.616 52.381 0.00 0.00 36.20 3.51
308 3146 2.036992 CTGGATATGTCTCCTGCACTCC 59.963 54.545 0.00 0.00 36.20 3.85
309 3147 1.346068 GGATATGTCTCCTGCACTCCC 59.654 57.143 0.00 0.00 32.18 4.30
310 3148 2.324541 GATATGTCTCCTGCACTCCCT 58.675 52.381 0.00 0.00 0.00 4.20
311 3149 1.781786 TATGTCTCCTGCACTCCCTC 58.218 55.000 0.00 0.00 0.00 4.30
312 3150 1.326213 ATGTCTCCTGCACTCCCTCG 61.326 60.000 0.00 0.00 0.00 4.63
313 3151 1.679305 GTCTCCTGCACTCCCTCGA 60.679 63.158 0.00 0.00 0.00 4.04
314 3152 1.040339 GTCTCCTGCACTCCCTCGAT 61.040 60.000 0.00 0.00 0.00 3.59
316 3154 0.103937 CTCCTGCACTCCCTCGATTC 59.896 60.000 0.00 0.00 0.00 2.52
317 3155 0.614697 TCCTGCACTCCCTCGATTCA 60.615 55.000 0.00 0.00 0.00 2.57
324 3202 3.801698 CACTCCCTCGATTCATTGTCAT 58.198 45.455 0.00 0.00 0.00 3.06
327 3205 4.056740 CTCCCTCGATTCATTGTCATCAG 58.943 47.826 0.00 0.00 0.00 2.90
334 3220 2.967599 TCATTGTCATCAGACTCCCG 57.032 50.000 0.00 0.00 45.20 5.14
336 3222 1.134580 CATTGTCATCAGACTCCCGCT 60.135 52.381 0.00 0.00 45.20 5.52
342 3228 3.006323 GTCATCAGACTCCCGCTATCAAT 59.994 47.826 0.00 0.00 41.64 2.57
356 3242 4.037690 GCTATCAATTTCATGGTCGTTGC 58.962 43.478 0.00 0.00 0.00 4.17
357 3243 2.610219 TCAATTTCATGGTCGTTGCG 57.390 45.000 0.00 0.00 0.00 4.85
358 3244 1.876799 TCAATTTCATGGTCGTTGCGT 59.123 42.857 0.00 0.00 0.00 5.24
359 3245 2.095969 TCAATTTCATGGTCGTTGCGTC 60.096 45.455 0.00 0.00 0.00 5.19
360 3246 1.518325 ATTTCATGGTCGTTGCGTCA 58.482 45.000 0.00 0.00 0.00 4.35
361 3247 1.300481 TTTCATGGTCGTTGCGTCAA 58.700 45.000 0.00 0.00 0.00 3.18
362 3248 0.865111 TTCATGGTCGTTGCGTCAAG 59.135 50.000 0.00 0.00 0.00 3.02
387 3273 1.886542 CAACAAAGGTACCTTGGCTCC 59.113 52.381 27.75 0.00 36.26 4.70
397 3283 0.035458 CCTTGGCTCCGAGAGTGTTT 59.965 55.000 4.72 0.00 31.39 2.83
433 3320 5.249852 AGGTGGTATTGAACTTTGCTAGGTA 59.750 40.000 0.00 0.00 0.00 3.08
445 3332 1.089920 GCTAGGTACGTCGTCAAGGA 58.910 55.000 0.00 0.00 0.00 3.36
446 3333 1.063764 GCTAGGTACGTCGTCAAGGAG 59.936 57.143 0.00 0.00 0.00 3.69
447 3334 2.354259 CTAGGTACGTCGTCAAGGAGT 58.646 52.381 0.00 0.00 0.00 3.85
448 3335 0.879765 AGGTACGTCGTCAAGGAGTG 59.120 55.000 0.00 0.00 0.00 3.51
449 3336 0.731855 GGTACGTCGTCAAGGAGTGC 60.732 60.000 0.00 0.00 0.00 4.40
450 3337 0.039798 GTACGTCGTCAAGGAGTGCA 60.040 55.000 0.00 0.00 0.00 4.57
451 3338 0.669619 TACGTCGTCAAGGAGTGCAA 59.330 50.000 0.00 0.00 0.00 4.08
452 3339 0.597637 ACGTCGTCAAGGAGTGCAAG 60.598 55.000 0.00 0.00 0.00 4.01
453 3340 1.284982 CGTCGTCAAGGAGTGCAAGG 61.285 60.000 0.00 0.00 0.00 3.61
473 3360 2.224402 GGAGTGCAGGAGAAAGACAACT 60.224 50.000 0.00 0.00 0.00 3.16
481 3368 4.151335 CAGGAGAAAGACAACTTCGACATG 59.849 45.833 0.00 0.00 35.05 3.21
519 3407 6.616237 TTTTCTATTTTCTACTCCCTCCGT 57.384 37.500 0.00 0.00 0.00 4.69
520 3408 6.616237 TTTCTATTTTCTACTCCCTCCGTT 57.384 37.500 0.00 0.00 0.00 4.44
521 3409 6.616237 TTCTATTTTCTACTCCCTCCGTTT 57.384 37.500 0.00 0.00 0.00 3.60
522 3410 6.218108 TCTATTTTCTACTCCCTCCGTTTC 57.782 41.667 0.00 0.00 0.00 2.78
523 3411 5.956563 TCTATTTTCTACTCCCTCCGTTTCT 59.043 40.000 0.00 0.00 0.00 2.52
524 3412 7.121382 TCTATTTTCTACTCCCTCCGTTTCTA 58.879 38.462 0.00 0.00 0.00 2.10
525 3413 6.616237 ATTTTCTACTCCCTCCGTTTCTAA 57.384 37.500 0.00 0.00 0.00 2.10
526 3414 6.423776 TTTTCTACTCCCTCCGTTTCTAAA 57.576 37.500 0.00 0.00 0.00 1.85
527 3415 6.616237 TTTCTACTCCCTCCGTTTCTAAAT 57.384 37.500 0.00 0.00 0.00 1.40
528 3416 5.593679 TCTACTCCCTCCGTTTCTAAATG 57.406 43.478 0.00 0.00 0.00 2.32
529 3417 5.021458 TCTACTCCCTCCGTTTCTAAATGT 58.979 41.667 0.00 0.00 0.00 2.71
530 3418 6.189859 TCTACTCCCTCCGTTTCTAAATGTA 58.810 40.000 0.00 0.00 0.00 2.29
578 3466 7.100458 ACGGTTCAATTTAGGTAGTACGTAT 57.900 36.000 0.00 0.00 0.00 3.06
693 3909 4.476628 GTTATCCTTAACCCGTTCCTGA 57.523 45.455 0.00 0.00 33.05 3.86
775 3991 3.936772 GAAAGCCATGACCCGCCCA 62.937 63.158 0.00 0.00 0.00 5.36
802 4018 3.186656 AACGGTCCCAAACCCCTCG 62.187 63.158 0.00 0.00 46.27 4.63
828 4044 2.956964 CCGCACGAATCTCGAGGC 60.957 66.667 13.56 5.79 43.74 4.70
888 4104 4.838152 TCGCGGGCAATCCTCTGC 62.838 66.667 6.13 0.00 41.85 4.26
983 4204 4.348495 TCCCGCCTCCCCTTTCCT 62.348 66.667 0.00 0.00 0.00 3.36
988 4209 1.307430 GCCTCCCCTTTCCTCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
1119 4340 2.844839 GGCTCCAGCGACCCCTAT 60.845 66.667 0.00 0.00 43.26 2.57
1515 4846 3.689347 TGCAAGCCTGAAATGTAGTCAT 58.311 40.909 0.00 0.00 35.59 3.06
1517 4848 3.181493 GCAAGCCTGAAATGTAGTCATGG 60.181 47.826 0.00 0.00 34.19 3.66
1527 5020 9.994432 CTGAAATGTAGTCATGGTAAAGAAATC 57.006 33.333 0.00 0.00 34.19 2.17
1664 5165 7.225011 AGTAGGAAATTTCTCCGAGAAGTTTT 58.775 34.615 24.42 19.89 41.96 2.43
1672 5173 5.135508 TCTCCGAGAAGTTTTCTAAGGTG 57.864 43.478 0.00 9.14 40.87 4.00
1673 5174 3.660865 TCCGAGAAGTTTTCTAAGGTGC 58.339 45.455 10.58 0.00 40.87 5.01
1855 5629 6.946009 ACCTAAAGGCTAAAAGTAAGCATTGA 59.054 34.615 0.00 0.00 42.63 2.57
1890 5665 7.565323 TTTAATTTTGCAGGTGAAATTTGCT 57.435 28.000 11.07 0.00 36.92 3.91
1962 5737 6.822667 ACATTCTGATGCAACTTATCAACA 57.177 33.333 0.00 0.00 36.72 3.33
2000 5775 7.885399 AGCTCAACTAGGTCAATTGAAACTAAT 59.115 33.333 10.35 3.26 32.19 1.73
2091 5887 1.182667 CCGTAGTGGTGTGGATCAGA 58.817 55.000 0.00 0.00 0.00 3.27
2135 5931 3.075005 GTCCCGAGCAGCCTACCA 61.075 66.667 0.00 0.00 0.00 3.25
2476 6290 9.590451 CATTATTAAACCAGCTGAATTGAATGT 57.410 29.630 17.39 0.00 0.00 2.71
2944 6758 6.112058 AGAAAATCAAAGTAGCTGAGCTAGG 58.888 40.000 15.54 5.30 42.11 3.02
2972 6786 5.261661 GCTAAATCGAGCAAAGACAAGATG 58.738 41.667 0.00 0.00 42.36 2.90
3476 7291 8.097038 TCATTCCCTTCATTGCTACTCATATAC 58.903 37.037 0.00 0.00 0.00 1.47
4415 9241 4.073293 AGAGTGAAACAAGTGGTGGTAG 57.927 45.455 0.00 0.00 41.43 3.18
4473 9299 1.039785 CCGGAGCAGAGAGACATGGA 61.040 60.000 0.00 0.00 0.00 3.41
4491 9317 1.002257 AATGCTCGGCCATGACACA 60.002 52.632 2.24 0.00 0.00 3.72
4923 9752 9.625747 TTGGAGTTGCAGATGTTGATATATTTA 57.374 29.630 0.00 0.00 0.00 1.40
4971 9800 4.020128 AGGTTGACTTAGGACAAAGCTAGG 60.020 45.833 0.00 0.00 0.00 3.02
4995 9824 9.312904 AGGAATTCAAATAATTTGGAACAGAGA 57.687 29.630 7.93 0.00 42.39 3.10
5023 9852 1.021390 GTTATGTGGTGCTGCTCGCT 61.021 55.000 0.00 0.00 40.11 4.93
5111 9940 1.938577 CAGTATACAGCTGCAGCCTTG 59.061 52.381 34.39 27.85 43.38 3.61
5176 10005 8.475331 AAGTGTAATTCGTCTTAGTACCATTG 57.525 34.615 0.00 0.00 0.00 2.82
5222 10051 4.081420 GGAAAGTGAAGAGGAGTCTGCATA 60.081 45.833 0.00 0.00 40.78 3.14
5247 10076 4.299586 TGGTTCATGGCAAATCAGTAGA 57.700 40.909 0.00 0.00 0.00 2.59
5281 10110 9.840427 AGTGACTATTAATTGTTTATTGCACAC 57.160 29.630 14.76 10.70 0.00 3.82
5691 10520 5.034554 TCAATCGAGAAACTGAACATTGC 57.965 39.130 0.00 0.00 0.00 3.56
5884 10716 4.340617 CAGAAGGACAGAGGTCTAGAAGT 58.659 47.826 0.00 0.00 43.77 3.01
5885 10717 4.770010 CAGAAGGACAGAGGTCTAGAAGTT 59.230 45.833 0.00 0.00 43.77 2.66
6045 10877 7.852945 GTCTACAGAGTTCAAACAAGACATTTG 59.147 37.037 0.00 0.00 38.21 2.32
6076 10911 1.001378 CGTGAAGGTCTGGGCAAAAAG 60.001 52.381 0.00 0.00 0.00 2.27
6079 10914 2.693074 TGAAGGTCTGGGCAAAAAGAAC 59.307 45.455 0.00 0.00 0.00 3.01
6122 10960 3.815856 TTGAAAGCATTTTGGAGCACA 57.184 38.095 0.00 0.00 39.27 4.57
6392 11232 5.103043 ACTCCCTCCATCTAGAAATGTAGGA 60.103 44.000 6.55 4.21 35.36 2.94
6637 11478 3.835378 TCACAATAACACAGCATGCAG 57.165 42.857 21.98 15.38 42.53 4.41
7017 11858 4.281941 TGTTTGGCACCTTGTATAATGCAA 59.718 37.500 0.00 0.00 39.92 4.08
7088 11929 2.842496 TGCCTTGATGGAGATGTTCTCT 59.158 45.455 4.65 0.00 42.95 3.10
7175 12016 2.161609 GGAGCCAGTAAACCGAAACATG 59.838 50.000 0.00 0.00 0.00 3.21
7358 12199 9.513906 CTTAGATAGTCAAGACTGGATCTGATA 57.486 37.037 18.90 8.62 42.52 2.15
7398 12242 4.151867 CGTCATATTGCAGGATCATGACAG 59.848 45.833 12.39 4.94 43.57 3.51
7782 12630 2.372040 TAACGCCGGTGCAGAACAGT 62.372 55.000 16.69 0.00 37.32 3.55
7786 12634 1.227527 CCGGTGCAGAACAGTGACA 60.228 57.895 0.00 0.00 0.00 3.58
7798 12646 6.554419 CAGAACAGTGACAAGATTGTTTGAA 58.446 36.000 0.00 0.00 42.43 2.69
7811 12659 3.878086 TGTTTGAATCTGTCGCTCAAC 57.122 42.857 0.00 0.00 0.00 3.18
7967 12978 5.118990 ACATGGATATGTTTTCTCCTCACG 58.881 41.667 0.00 0.00 45.01 4.35
8003 13014 8.038862 ATCAATCTGATGTTACCTTGATAGGT 57.961 34.615 2.01 2.01 45.50 3.08
8211 13234 8.928448 ACACATATAGTACCAGAATGACAGAAT 58.072 33.333 0.00 0.00 39.69 2.40
8262 13285 4.081406 ACCAAATGAGCAGTGCATTAAGA 58.919 39.130 19.20 0.00 35.06 2.10
8491 13515 3.013276 GCTCAAAGGCCAGTTACAAAC 57.987 47.619 5.01 0.00 0.00 2.93
8492 13516 2.360801 GCTCAAAGGCCAGTTACAAACA 59.639 45.455 5.01 0.00 0.00 2.83
8493 13517 3.181480 GCTCAAAGGCCAGTTACAAACAA 60.181 43.478 5.01 0.00 0.00 2.83
8494 13518 4.679372 GCTCAAAGGCCAGTTACAAACAAA 60.679 41.667 5.01 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.377628 AAAGCTCGACACGCCTTCCA 62.378 55.000 0.00 0.00 0.00 3.53
1 2 1.668151 AAAGCTCGACACGCCTTCC 60.668 57.895 0.00 0.00 0.00 3.46
2 3 1.493311 CAAAGCTCGACACGCCTTC 59.507 57.895 0.00 0.00 0.00 3.46
3 4 1.961277 CCAAAGCTCGACACGCCTT 60.961 57.895 0.00 0.00 0.00 4.35
4 5 2.357517 CCAAAGCTCGACACGCCT 60.358 61.111 0.00 0.00 0.00 5.52
5 6 2.665185 ACCAAAGCTCGACACGCC 60.665 61.111 0.00 0.00 0.00 5.68
6 7 1.891060 CTGACCAAAGCTCGACACGC 61.891 60.000 0.00 0.00 0.00 5.34
7 8 1.284982 CCTGACCAAAGCTCGACACG 61.285 60.000 0.00 0.00 0.00 4.49
8 9 0.951040 CCCTGACCAAAGCTCGACAC 60.951 60.000 0.00 0.00 0.00 3.67
9 10 1.371183 CCCTGACCAAAGCTCGACA 59.629 57.895 0.00 0.00 0.00 4.35
10 11 2.035442 GCCCTGACCAAAGCTCGAC 61.035 63.158 0.00 0.00 0.00 4.20
11 12 0.902984 TAGCCCTGACCAAAGCTCGA 60.903 55.000 0.00 0.00 36.79 4.04
12 13 0.179000 ATAGCCCTGACCAAAGCTCG 59.821 55.000 0.00 0.00 36.79 5.03
13 14 2.293170 GAATAGCCCTGACCAAAGCTC 58.707 52.381 0.00 0.00 36.79 4.09
14 15 1.064389 GGAATAGCCCTGACCAAAGCT 60.064 52.381 0.00 0.00 39.37 3.74
15 16 1.393603 GGAATAGCCCTGACCAAAGC 58.606 55.000 0.00 0.00 0.00 3.51
26 27 2.413310 TTGAAACGGAGGGAATAGCC 57.587 50.000 0.00 0.00 0.00 3.93
27 28 4.983671 ATTTTGAAACGGAGGGAATAGC 57.016 40.909 0.00 0.00 0.00 2.97
28 29 7.715249 TCATCTATTTTGAAACGGAGGGAATAG 59.285 37.037 0.00 0.00 0.00 1.73
29 30 7.497909 GTCATCTATTTTGAAACGGAGGGAATA 59.502 37.037 0.00 0.00 0.00 1.75
30 31 6.318900 GTCATCTATTTTGAAACGGAGGGAAT 59.681 38.462 0.00 0.00 0.00 3.01
31 32 5.646360 GTCATCTATTTTGAAACGGAGGGAA 59.354 40.000 0.00 0.00 0.00 3.97
32 33 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
33 34 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
34 35 6.743575 AAGTCATCTATTTTGAAACGGAGG 57.256 37.500 0.00 0.00 0.00 4.30
35 36 8.936864 AGTTAAGTCATCTATTTTGAAACGGAG 58.063 33.333 0.00 0.00 0.00 4.63
36 37 8.842358 AGTTAAGTCATCTATTTTGAAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
37 38 9.893305 AAAGTTAAGTCATCTATTTTGAAACGG 57.107 29.630 0.00 0.00 0.00 4.44
79 80 8.523658 GCCTAAGATCCAAAAGTTAAGTCATTT 58.476 33.333 0.00 0.00 0.00 2.32
80 81 7.122799 GGCCTAAGATCCAAAAGTTAAGTCATT 59.877 37.037 0.00 0.00 0.00 2.57
81 82 6.603599 GGCCTAAGATCCAAAAGTTAAGTCAT 59.396 38.462 0.00 0.00 0.00 3.06
82 83 5.944007 GGCCTAAGATCCAAAAGTTAAGTCA 59.056 40.000 0.00 0.00 0.00 3.41
83 84 5.357314 GGGCCTAAGATCCAAAAGTTAAGTC 59.643 44.000 0.84 0.00 0.00 3.01
84 85 5.262009 GGGCCTAAGATCCAAAAGTTAAGT 58.738 41.667 0.84 0.00 0.00 2.24
85 86 4.645136 GGGGCCTAAGATCCAAAAGTTAAG 59.355 45.833 0.84 0.00 0.00 1.85
86 87 4.606210 GGGGCCTAAGATCCAAAAGTTAA 58.394 43.478 0.84 0.00 0.00 2.01
87 88 3.371166 CGGGGCCTAAGATCCAAAAGTTA 60.371 47.826 0.84 0.00 0.00 2.24
88 89 2.620627 CGGGGCCTAAGATCCAAAAGTT 60.621 50.000 0.84 0.00 0.00 2.66
89 90 1.064685 CGGGGCCTAAGATCCAAAAGT 60.065 52.381 0.84 0.00 0.00 2.66
90 91 1.064685 ACGGGGCCTAAGATCCAAAAG 60.065 52.381 0.84 0.00 0.00 2.27
91 92 0.996583 ACGGGGCCTAAGATCCAAAA 59.003 50.000 0.84 0.00 0.00 2.44
92 93 0.996583 AACGGGGCCTAAGATCCAAA 59.003 50.000 0.84 0.00 0.00 3.28
93 94 1.882308 TAACGGGGCCTAAGATCCAA 58.118 50.000 0.84 0.00 0.00 3.53
94 95 1.882308 TTAACGGGGCCTAAGATCCA 58.118 50.000 0.84 0.00 0.00 3.41
95 96 3.072622 AGATTTAACGGGGCCTAAGATCC 59.927 47.826 0.84 0.00 0.00 3.36
96 97 4.353383 AGATTTAACGGGGCCTAAGATC 57.647 45.455 0.84 0.43 0.00 2.75
97 98 4.790718 AAGATTTAACGGGGCCTAAGAT 57.209 40.909 0.84 0.00 0.00 2.40
98 99 4.102054 CCTAAGATTTAACGGGGCCTAAGA 59.898 45.833 0.84 0.00 0.00 2.10
99 100 4.141551 ACCTAAGATTTAACGGGGCCTAAG 60.142 45.833 0.84 0.00 0.00 2.18
100 101 3.781965 ACCTAAGATTTAACGGGGCCTAA 59.218 43.478 0.84 0.00 0.00 2.69
101 102 3.387012 ACCTAAGATTTAACGGGGCCTA 58.613 45.455 0.84 0.00 0.00 3.93
184 185 5.982890 AAGACCAAAATATGAACCACAGG 57.017 39.130 0.00 0.00 0.00 4.00
185 186 9.410556 CTAAAAAGACCAAAATATGAACCACAG 57.589 33.333 0.00 0.00 0.00 3.66
217 3055 3.374988 TGAACATGCTTTGCCGAATAGAG 59.625 43.478 0.00 0.00 0.00 2.43
218 3056 3.342719 TGAACATGCTTTGCCGAATAGA 58.657 40.909 0.00 0.00 0.00 1.98
219 3057 3.688272 CTGAACATGCTTTGCCGAATAG 58.312 45.455 0.00 0.00 0.00 1.73
220 3058 2.159393 GCTGAACATGCTTTGCCGAATA 60.159 45.455 0.00 0.00 0.00 1.75
221 3059 1.403249 GCTGAACATGCTTTGCCGAAT 60.403 47.619 0.00 0.00 0.00 3.34
266 3104 0.111253 CAAACAGGACCAAGGAGGCT 59.889 55.000 0.00 0.00 43.14 4.58
296 3134 0.324738 AATCGAGGGAGTGCAGGAGA 60.325 55.000 0.00 0.00 0.00 3.71
297 3135 0.103937 GAATCGAGGGAGTGCAGGAG 59.896 60.000 0.00 0.00 0.00 3.69
298 3136 0.614697 TGAATCGAGGGAGTGCAGGA 60.615 55.000 0.00 0.00 0.00 3.86
301 3139 1.278985 ACAATGAATCGAGGGAGTGCA 59.721 47.619 0.00 0.00 0.00 4.57
302 3140 1.936547 GACAATGAATCGAGGGAGTGC 59.063 52.381 0.00 0.00 0.00 4.40
303 3141 3.251479 TGACAATGAATCGAGGGAGTG 57.749 47.619 0.00 0.00 0.00 3.51
304 3142 3.452264 TGATGACAATGAATCGAGGGAGT 59.548 43.478 0.00 0.00 0.00 3.85
305 3143 4.056740 CTGATGACAATGAATCGAGGGAG 58.943 47.826 0.00 0.00 0.00 4.30
306 3144 3.706086 TCTGATGACAATGAATCGAGGGA 59.294 43.478 0.00 0.00 0.00 4.20
307 3145 3.806521 GTCTGATGACAATGAATCGAGGG 59.193 47.826 0.00 0.00 42.48 4.30
308 3146 4.691175 AGTCTGATGACAATGAATCGAGG 58.309 43.478 0.00 0.00 45.20 4.63
309 3147 4.744137 GGAGTCTGATGACAATGAATCGAG 59.256 45.833 0.00 0.00 45.20 4.04
310 3148 4.442052 GGGAGTCTGATGACAATGAATCGA 60.442 45.833 0.00 0.00 45.20 3.59
311 3149 3.806521 GGGAGTCTGATGACAATGAATCG 59.193 47.826 0.00 0.00 45.20 3.34
312 3150 3.806521 CGGGAGTCTGATGACAATGAATC 59.193 47.826 0.00 0.00 45.20 2.52
313 3151 3.801698 CGGGAGTCTGATGACAATGAAT 58.198 45.455 0.00 0.00 45.20 2.57
314 3152 2.677902 GCGGGAGTCTGATGACAATGAA 60.678 50.000 0.00 0.00 45.20 2.57
316 3154 1.134580 AGCGGGAGTCTGATGACAATG 60.135 52.381 0.00 0.00 45.20 2.82
317 3155 1.198713 AGCGGGAGTCTGATGACAAT 58.801 50.000 0.00 0.00 45.20 2.71
324 3202 3.450817 TGAAATTGATAGCGGGAGTCTGA 59.549 43.478 0.00 0.00 0.00 3.27
327 3205 3.499918 CCATGAAATTGATAGCGGGAGTC 59.500 47.826 0.00 0.00 0.00 3.36
334 3220 4.037690 GCAACGACCATGAAATTGATAGC 58.962 43.478 0.00 0.00 0.00 2.97
336 3222 3.687212 ACGCAACGACCATGAAATTGATA 59.313 39.130 0.00 0.00 0.00 2.15
342 3228 1.262950 CTTGACGCAACGACCATGAAA 59.737 47.619 0.00 0.00 0.00 2.69
356 3242 0.041312 CCTTTGTTGACGGCTTGACG 60.041 55.000 0.00 0.00 40.31 4.35
357 3243 1.021968 ACCTTTGTTGACGGCTTGAC 58.978 50.000 0.00 0.00 0.00 3.18
358 3244 2.215196 GTACCTTTGTTGACGGCTTGA 58.785 47.619 0.00 0.00 0.00 3.02
359 3245 1.265905 GGTACCTTTGTTGACGGCTTG 59.734 52.381 4.06 0.00 0.00 4.01
360 3246 1.142262 AGGTACCTTTGTTGACGGCTT 59.858 47.619 9.21 0.00 0.00 4.35
361 3247 0.763035 AGGTACCTTTGTTGACGGCT 59.237 50.000 9.21 0.00 0.00 5.52
362 3248 1.265905 CAAGGTACCTTTGTTGACGGC 59.734 52.381 24.99 0.00 33.42 5.68
363 3249 1.877443 CCAAGGTACCTTTGTTGACGG 59.123 52.381 24.99 16.45 33.42 4.79
387 3273 7.115095 CACCTCTAGAACTTTAAAACACTCTCG 59.885 40.741 0.00 0.00 0.00 4.04
397 3283 8.877195 AGTTCAATACCACCTCTAGAACTTTAA 58.123 33.333 0.00 0.00 40.71 1.52
433 3320 0.597637 CTTGCACTCCTTGACGACGT 60.598 55.000 0.00 0.00 0.00 4.34
449 3336 2.224378 TGTCTTTCTCCTGCACTCCTTG 60.224 50.000 0.00 0.00 0.00 3.61
450 3337 2.050144 TGTCTTTCTCCTGCACTCCTT 58.950 47.619 0.00 0.00 0.00 3.36
451 3338 1.722034 TGTCTTTCTCCTGCACTCCT 58.278 50.000 0.00 0.00 0.00 3.69
452 3339 2.147150 GTTGTCTTTCTCCTGCACTCC 58.853 52.381 0.00 0.00 0.00 3.85
453 3340 3.118905 AGTTGTCTTTCTCCTGCACTC 57.881 47.619 0.00 0.00 0.00 3.51
500 3388 6.223351 AGAAACGGAGGGAGTAGAAAATAG 57.777 41.667 0.00 0.00 0.00 1.73
530 3418 8.013378 CGTCAAAAACGTCTTACATTTAGGAAT 58.987 33.333 0.00 0.00 46.42 3.01
775 3991 1.488705 TTGGGACCGTTGGATCTGCT 61.489 55.000 0.00 0.00 0.00 4.24
802 4018 0.876342 GATTCGTGCGGGATGAGGTC 60.876 60.000 0.00 0.00 0.00 3.85
846 4062 4.143618 CGTTTGAATTTTAGAGGCGTTTGC 60.144 41.667 0.00 0.00 41.71 3.68
858 4074 0.039888 CCCGCGACCGTTTGAATTTT 60.040 50.000 8.23 0.00 0.00 1.82
859 4075 1.577421 CCCGCGACCGTTTGAATTT 59.423 52.632 8.23 0.00 0.00 1.82
978 4199 1.267121 CGACCTTGGAGGAGAGGAAA 58.733 55.000 0.07 0.00 37.67 3.13
983 4204 1.379977 ATCGCGACCTTGGAGGAGA 60.380 57.895 12.93 0.00 37.67 3.71
988 4209 4.467084 GCCCATCGCGACCTTGGA 62.467 66.667 25.12 0.00 31.94 3.53
1144 4365 4.308458 CACCGTCGTCTTGGCCCA 62.308 66.667 0.00 0.00 0.00 5.36
1339 4560 4.840005 GAGCTGGTACCAGGCGGC 62.840 72.222 36.91 25.97 43.77 6.53
1413 4634 1.574392 GCGAAATGCGACGACGAAC 60.574 57.895 12.29 0.00 44.57 3.95
1527 5020 6.615088 TCGCGGTAGGTAGCTTAATTATTAG 58.385 40.000 6.13 0.00 0.00 1.73
1547 5040 0.302890 GACAGGATGCTCAATTCGCG 59.697 55.000 0.00 0.00 42.53 5.87
1548 5041 0.659957 GGACAGGATGCTCAATTCGC 59.340 55.000 0.00 0.00 42.53 4.70
1664 5165 3.006003 TGAACATGTACGTGCACCTTAGA 59.994 43.478 15.12 1.66 0.00 2.10
1672 5173 4.355543 AATTCCATGAACATGTACGTGC 57.644 40.909 15.12 0.00 37.11 5.34
1673 5174 6.377780 TCAAAATTCCATGAACATGTACGTG 58.622 36.000 13.64 13.64 37.11 4.49
1713 5240 0.819582 CTTGGCCCGATGCAAATTCT 59.180 50.000 0.00 0.00 43.89 2.40
1797 5561 2.550830 ACCAGCGACTTTCAACTGAT 57.449 45.000 0.00 0.00 31.67 2.90
1962 5737 1.375396 TTGAGCTGCACGGCGTATT 60.375 52.632 14.22 0.00 37.29 1.89
2000 5775 3.107402 ACTGCTGATAAGGAGGACTCA 57.893 47.619 3.28 0.00 0.00 3.41
2091 5887 0.179004 TCCGTGTTGCTTTGGGTCAT 60.179 50.000 0.00 0.00 0.00 3.06
2972 6786 1.067283 TGAGTCTGCAGTGAAGCTAGC 60.067 52.381 14.67 6.62 34.99 3.42
3344 7158 7.763613 AGAGGGATGAGGAAAGCATAATATTT 58.236 34.615 0.00 0.00 0.00 1.40
3476 7291 0.329596 CCCAAGGAAAGGAGTGGAGG 59.670 60.000 0.00 0.00 32.54 4.30
4111 8936 8.082242 AGTAAATACTTTGTGCTGAAAATGACC 58.918 33.333 0.00 0.00 31.13 4.02
4415 9241 2.160013 GCTACGTTCGTGTCATGTGTTC 60.160 50.000 8.14 0.00 0.00 3.18
4473 9299 0.608856 TTGTGTCATGGCCGAGCATT 60.609 50.000 0.00 0.00 0.00 3.56
4491 9317 8.352942 AGAACTTCAAATAATTCTTCTGCGTTT 58.647 29.630 0.00 0.00 0.00 3.60
4599 9425 4.330944 TGCAGACTAAAGAGAAACGGAA 57.669 40.909 0.00 0.00 0.00 4.30
4818 9646 7.792508 CGTTTCTTTTTACTCCGCATATATGAC 59.207 37.037 17.10 6.95 0.00 3.06
4923 9752 6.601332 TCTTTAAGTTTGACCAAGTCCAGAT 58.399 36.000 0.00 0.00 0.00 2.90
4995 9824 3.055819 CAGCACCACATAACCTGTACTCT 60.056 47.826 0.00 0.00 35.91 3.24
5133 9962 9.814899 ATTACACTTCTAATCTGATGAAGACAG 57.185 33.333 19.01 13.29 39.42 3.51
5153 9982 7.037438 TCCAATGGTACTAAGACGAATTACAC 58.963 38.462 0.00 0.00 0.00 2.90
5161 9990 2.431057 AGGCTCCAATGGTACTAAGACG 59.569 50.000 0.00 0.00 0.00 4.18
5176 10005 5.008712 CCTTTATGGAACGAAATAAGGCTCC 59.991 44.000 0.00 0.00 38.35 4.70
5247 10076 7.916914 AACAATTAATAGTCACTTAGCCGTT 57.083 32.000 0.00 0.00 0.00 4.44
5281 10110 8.875803 TCTGTTATAAATTACGGCAACTGTTAG 58.124 33.333 0.00 0.00 0.00 2.34
5663 10492 9.612620 AATGTTCAGTTTCTCGATTGATTTTAC 57.387 29.630 0.00 0.00 0.00 2.01
5664 10493 9.611284 CAATGTTCAGTTTCTCGATTGATTTTA 57.389 29.630 0.00 0.00 0.00 1.52
5665 10494 7.115378 GCAATGTTCAGTTTCTCGATTGATTTT 59.885 33.333 0.00 0.00 0.00 1.82
5666 10495 6.583806 GCAATGTTCAGTTTCTCGATTGATTT 59.416 34.615 0.00 0.00 0.00 2.17
5667 10496 6.088824 GCAATGTTCAGTTTCTCGATTGATT 58.911 36.000 0.00 0.00 0.00 2.57
5668 10497 5.181811 TGCAATGTTCAGTTTCTCGATTGAT 59.818 36.000 0.00 0.00 0.00 2.57
5669 10498 4.514816 TGCAATGTTCAGTTTCTCGATTGA 59.485 37.500 0.00 0.00 0.00 2.57
5670 10499 4.786507 TGCAATGTTCAGTTTCTCGATTG 58.213 39.130 0.00 0.00 0.00 2.67
5671 10500 5.633830 ATGCAATGTTCAGTTTCTCGATT 57.366 34.783 0.00 0.00 0.00 3.34
6045 10877 2.744202 AGACCTTCACGAATGTCATTGC 59.256 45.455 14.86 0.00 38.07 3.56
6076 10911 6.986904 ATAGTCTTTTTGGAGAATCGGTTC 57.013 37.500 0.00 0.00 34.37 3.62
6079 10914 8.296713 TCAAAAATAGTCTTTTTGGAGAATCGG 58.703 33.333 20.19 0.00 44.86 4.18
6122 10960 6.715264 AGGTCTGGACGAAAATAACAAAATCT 59.285 34.615 0.00 0.00 0.00 2.40
6251 11089 7.609918 TGCTCCAGCTATGAACACTAAAAATAA 59.390 33.333 0.00 0.00 42.66 1.40
6319 11157 5.593909 TGCTCATACAATTTGGGGAATAGTG 59.406 40.000 0.78 0.00 0.00 2.74
6324 11162 5.010922 GCATATGCTCATACAATTTGGGGAA 59.989 40.000 20.64 0.00 38.21 3.97
6669 11510 4.451900 AGACGTCAGATTTTCCAAAGTGT 58.548 39.130 19.50 0.00 0.00 3.55
7017 11858 8.860088 AGAGGTTTAAACAGATGCTTTTACAAT 58.140 29.630 19.57 0.00 0.00 2.71
7088 11929 0.692756 TGTGTTCCAGTGGACCTCCA 60.693 55.000 12.69 3.38 45.30 3.86
7175 12016 1.118838 AGCTGATCTGCCTCTGGTAC 58.881 55.000 19.74 0.00 0.00 3.34
7358 12199 4.235939 TGACGTACATGCAAGCATTTTT 57.764 36.364 4.52 0.00 33.90 1.94
7398 12242 6.805760 GGATCTGCAATTTTGAAGAGAAAGAC 59.194 38.462 7.08 0.00 45.67 3.01
7682 12527 0.450983 GAGCAGCAGCATTTCTGTCC 59.549 55.000 3.17 0.00 44.66 4.02
7731 12579 4.203226 TGGAACAACATTGCAGAAGTACA 58.797 39.130 0.00 0.00 31.92 2.90
7782 12630 5.560760 GCGACAGATTCAAACAATCTTGTCA 60.561 40.000 17.47 0.00 41.31 3.58
7786 12634 4.756642 TGAGCGACAGATTCAAACAATCTT 59.243 37.500 0.00 0.00 34.96 2.40
7798 12646 8.035394 TCTTTTAATCTTAGTTGAGCGACAGAT 58.965 33.333 0.00 0.00 0.00 2.90
7967 12978 1.118033 CAGATTGATCAAATGCGCGC 58.882 50.000 27.26 27.26 0.00 6.86
8003 13014 4.705023 TGTATACACAGCTCTGCTTGAGTA 59.295 41.667 0.08 4.33 44.41 2.59
8211 13234 3.646611 TGATGGTCGTACGAACTTGAA 57.353 42.857 31.45 13.93 32.08 2.69
8262 13285 5.365895 AGTGTACCAGTTTCCTGTAGTTCTT 59.634 40.000 0.00 0.00 36.95 2.52
8317 13340 4.153835 GCTTCATGTAGCAATAGCCATCTC 59.846 45.833 18.39 0.00 43.56 2.75
8491 13515 2.230130 TGTATTCCCCCTTGGCTTTG 57.770 50.000 0.00 0.00 0.00 2.77
8492 13516 3.268034 TTTGTATTCCCCCTTGGCTTT 57.732 42.857 0.00 0.00 0.00 3.51
8493 13517 3.268034 TTTTGTATTCCCCCTTGGCTT 57.732 42.857 0.00 0.00 0.00 4.35
8494 13518 3.106827 CATTTTGTATTCCCCCTTGGCT 58.893 45.455 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.