Multiple sequence alignment - TraesCS7B01G391800

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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 TraesCS7B01G391800 chr7B 100.000 4400 0 0 1 4400 658222698 658218299 0.000000e+00 8126.0
1 TraesCS7B01G391800 chr7B 88.924 316 26 4 170 476 658234041 658233726 8.930000e-102 381.0
2 TraesCS7B01G391800 chr7B 93.701 127 6 1 2 128 658275591 658275467 5.810000e-44 189.0
3 TraesCS7B01G391800 chr7A 89.270 2889 192 46 854 3665 678971558 678968711 0.000000e+00 3509.0
4 TraesCS7B01G391800 chr7A 89.815 540 31 12 301 824 678972203 678971672 0.000000e+00 671.0
5 TraesCS7B01G391800 chr7A 93.590 312 19 1 4089 4400 678966313 678966003 8.620000e-127 464.0
6 TraesCS7B01G391800 chr7A 87.385 325 23 11 2 311 678972702 678972381 1.500000e-94 357.0
7 TraesCS7B01G391800 chr7A 86.577 149 19 1 2109 2257 142308450 142308597 3.520000e-36 163.0
8 TraesCS7B01G391800 chr7A 85.235 149 21 1 2109 2257 172071875 172072022 7.620000e-33 152.0
9 TraesCS7B01G391800 chr7A 84.564 149 21 2 2109 2257 675742940 675742794 3.550000e-31 147.0
10 TraesCS7B01G391800 chr7A 87.705 122 14 1 2109 2230 667167399 667167279 1.650000e-29 141.0
11 TraesCS7B01G391800 chr7A 84.314 102 13 2 1685 1783 675743389 675743288 3.620000e-16 97.1
12 TraesCS7B01G391800 chr7D 88.962 2881 207 47 854 3663 587121266 587118426 0.000000e+00 3456.0
13 TraesCS7B01G391800 chr7D 85.064 857 71 27 1 824 587123914 587123082 0.000000e+00 821.0
14 TraesCS7B01G391800 chr7D 95.516 223 9 1 4178 4400 587118079 587117858 5.410000e-94 355.0
15 TraesCS7B01G391800 chr6B 86.501 563 42 11 2024 2574 720405712 720406252 4.900000e-164 588.0
16 TraesCS7B01G391800 chr6B 85.774 239 25 9 1369 1603 213157494 213157261 1.220000e-60 244.0
17 TraesCS7B01G391800 chr6D 85.833 240 23 9 1369 1603 121093273 121093040 1.220000e-60 244.0
18 TraesCS7B01G391800 chr6D 87.719 114 11 1 1673 1783 223690371 223690484 3.570000e-26 130.0
19 TraesCS7B01G391800 chr1D 80.058 346 43 22 1369 1709 11316755 11317079 2.650000e-57 233.0
20 TraesCS7B01G391800 chr1D 92.857 84 5 1 1867 1950 493747510 493747592 2.150000e-23 121.0
21 TraesCS7B01G391800 chr5D 84.390 205 25 6 1369 1572 30555570 30555768 1.250000e-45 195.0
22 TraesCS7B01G391800 chr5D 84.314 204 25 6 1370 1572 525777385 525777582 4.490000e-45 193.0
23 TraesCS7B01G391800 chr4D 83.173 208 28 6 1369 1575 287300413 287300212 2.700000e-42 183.0
24 TraesCS7B01G391800 chr2D 82.927 205 28 6 1369 1572 561922250 561922448 1.260000e-40 178.0
25 TraesCS7B01G391800 chr2D 87.097 124 12 4 1633 1753 561922559 561922681 2.130000e-28 137.0
26 TraesCS7B01G391800 chr2D 93.478 92 5 1 1867 1958 13209438 13209528 7.680000e-28 135.0
27 TraesCS7B01G391800 chr1B 83.010 206 26 6 1369 1572 346527791 346527989 1.260000e-40 178.0
28 TraesCS7B01G391800 chr6A 85.235 149 21 1 2109 2257 45045287 45045140 7.620000e-33 152.0
29 TraesCS7B01G391800 chr6A 86.275 102 11 3 1685 1783 514350975 514350874 1.670000e-19 108.0
30 TraesCS7B01G391800 chr6A 86.047 86 9 2 1701 1783 588757112 588757197 6.060000e-14 89.8
31 TraesCS7B01G391800 chr3A 94.048 84 4 1 1867 1950 411271672 411271590 4.620000e-25 126.0
32 TraesCS7B01G391800 chr3A 93.878 49 2 1 1867 1915 193870948 193870901 6.100000e-09 73.1
33 TraesCS7B01G391800 chr3D 91.304 92 6 2 1867 1958 168502726 168502815 1.660000e-24 124.0
34 TraesCS7B01G391800 chrUn 86.275 102 11 3 1685 1783 329059252 329059151 1.670000e-19 108.0
35 TraesCS7B01G391800 chr4A 86.275 102 11 1 1685 1783 504673704 504673603 1.670000e-19 108.0
36 TraesCS7B01G391800 chr5B 94.000 50 1 2 1867 1915 397292442 397292394 1.700000e-09 75.0
37 TraesCS7B01G391800 chr5A 93.878 49 2 1 1867 1915 510198936 510198983 6.100000e-09 73.1


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 TraesCS7B01G391800 chr7B 658218299 658222698 4399 True 8126.00 8126 100.000000 1 4400 1 chr7B.!!$R1 4399
1 TraesCS7B01G391800 chr7A 678966003 678972702 6699 True 1250.25 3509 90.015000 2 4400 4 chr7A.!!$R3 4398
2 TraesCS7B01G391800 chr7D 587117858 587123914 6056 True 1544.00 3456 89.847333 1 4400 3 chr7D.!!$R1 4399
3 TraesCS7B01G391800 chr6B 720405712 720406252 540 False 588.00 588 86.501000 2024 2574 1 chr6B.!!$F1 550

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
429 666 0.261991 AAGATCTGCCTCCGTCCCTA 59.738 55.0 0.00 0.00 0.00 3.53 F
1059 3133 0.251354 TGCAGCAGATCTGAAGTCCC 59.749 55.0 27.04 7.27 45.72 4.46 F
1932 4036 0.438830 GATCTGTGTGCGGACGTTTC 59.561 55.0 1.60 0.00 31.98 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 3440 0.244994 ACGCGCACTTCTTCATCTCT 59.755 50.000 5.73 0.00 0.00 3.10 R
2053 4157 1.003233 GCAGGTGAGACAGAACCCC 60.003 63.158 0.00 0.00 37.13 4.95 R
3622 5772 0.178861 AGGGTCCTATGGGCTATGGG 60.179 60.000 6.93 6.93 38.71 4.00 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
45 46 1.541233 CGTTCAACTCCTTGGCTCAGT 60.541 52.381 0.00 0.00 0.00 3.41
46 47 2.147150 GTTCAACTCCTTGGCTCAGTC 58.853 52.381 0.00 0.00 0.00 3.51
80 81 1.078759 GTCTCGCCGATGTTCAGTGG 61.079 60.000 0.00 0.00 0.00 4.00
156 157 3.758554 CGAGACCCAAAGACATTTCCATT 59.241 43.478 0.00 0.00 0.00 3.16
171 172 5.720371 TTTCCATTCCATTGTAACCACTG 57.280 39.130 0.00 0.00 0.00 3.66
173 174 3.091545 CCATTCCATTGTAACCACTGCT 58.908 45.455 0.00 0.00 0.00 4.24
174 175 3.511146 CCATTCCATTGTAACCACTGCTT 59.489 43.478 0.00 0.00 0.00 3.91
175 176 4.704540 CCATTCCATTGTAACCACTGCTTA 59.295 41.667 0.00 0.00 0.00 3.09
176 177 5.360714 CCATTCCATTGTAACCACTGCTTAT 59.639 40.000 0.00 0.00 0.00 1.73
177 178 6.460123 CCATTCCATTGTAACCACTGCTTATC 60.460 42.308 0.00 0.00 0.00 1.75
178 179 5.172687 TCCATTGTAACCACTGCTTATCA 57.827 39.130 0.00 0.00 0.00 2.15
180 181 4.201950 CCATTGTAACCACTGCTTATCAGC 60.202 45.833 0.00 0.00 46.76 4.26
181 182 2.985896 TGTAACCACTGCTTATCAGCC 58.014 47.619 0.00 0.00 46.74 4.85
182 183 1.933853 GTAACCACTGCTTATCAGCCG 59.066 52.381 0.00 0.00 46.74 5.52
183 184 1.026718 AACCACTGCTTATCAGCCGC 61.027 55.000 0.00 0.00 46.74 6.53
184 185 1.450134 CCACTGCTTATCAGCCGCA 60.450 57.895 0.00 0.00 46.74 5.69
185 186 1.709147 CCACTGCTTATCAGCCGCAC 61.709 60.000 0.00 0.00 46.74 5.34
186 187 0.742281 CACTGCTTATCAGCCGCACT 60.742 55.000 0.00 0.00 46.74 4.40
188 189 1.434622 CTGCTTATCAGCCGCACTGG 61.435 60.000 4.06 0.00 46.74 4.00
194 195 3.257933 CAGCCGCACTGGAGAAAC 58.742 61.111 0.00 0.00 43.19 2.78
195 196 1.597854 CAGCCGCACTGGAGAAACA 60.598 57.895 0.00 0.00 43.19 2.83
196 197 1.148273 AGCCGCACTGGAGAAACAA 59.852 52.632 0.00 0.00 42.00 2.83
197 198 1.166531 AGCCGCACTGGAGAAACAAC 61.167 55.000 0.00 0.00 42.00 3.32
198 199 1.949257 CCGCACTGGAGAAACAACC 59.051 57.895 0.00 0.00 42.00 3.77
199 200 1.515521 CCGCACTGGAGAAACAACCC 61.516 60.000 0.00 0.00 42.00 4.11
200 201 1.841663 CGCACTGGAGAAACAACCCG 61.842 60.000 0.00 0.00 0.00 5.28
201 202 0.818040 GCACTGGAGAAACAACCCGT 60.818 55.000 0.00 0.00 0.00 5.28
313 546 2.048222 AGCGACACACACCCATCG 60.048 61.111 0.00 0.00 37.63 3.84
316 549 1.218047 CGACACACACCCATCGGAT 59.782 57.895 0.00 0.00 0.00 4.18
385 618 4.143333 AACCGATCTGTCGCCGGG 62.143 66.667 2.18 0.00 46.83 5.73
423 656 0.811616 CCGGAAAAGATCTGCCTCCG 60.812 60.000 23.79 23.79 46.78 4.63
429 666 0.261991 AAGATCTGCCTCCGTCCCTA 59.738 55.000 0.00 0.00 0.00 3.53
633 878 1.159285 CTCTTTTCGCAGCCACATGA 58.841 50.000 0.00 0.00 0.00 3.07
669 923 3.007398 GGTGGCCAAGAGATGATAGTAGG 59.993 52.174 7.24 0.00 0.00 3.18
672 926 3.056179 GGCCAAGAGATGATAGTAGGAGC 60.056 52.174 0.00 0.00 0.00 4.70
674 928 3.823873 CCAAGAGATGATAGTAGGAGCGT 59.176 47.826 0.00 0.00 0.00 5.07
754 1018 2.079158 CAGATTTCACATCACGCCTGT 58.921 47.619 0.00 0.00 0.00 4.00
757 1021 3.195610 AGATTTCACATCACGCCTGTCTA 59.804 43.478 0.00 0.00 0.00 2.59
824 1096 1.078918 GCAGGCAAATCTTTGGGCC 60.079 57.895 0.00 0.00 46.77 5.80
828 1100 2.566833 GGCAAATCTTTGGGCCTTTT 57.433 45.000 4.53 0.00 43.09 2.27
829 1101 2.862541 GGCAAATCTTTGGGCCTTTTT 58.137 42.857 4.53 0.00 43.09 1.94
832 1104 5.009631 GGCAAATCTTTGGGCCTTTTTATT 58.990 37.500 4.53 0.00 43.09 1.40
833 1105 5.123820 GGCAAATCTTTGGGCCTTTTTATTC 59.876 40.000 4.53 0.00 43.09 1.75
834 1106 5.704978 GCAAATCTTTGGGCCTTTTTATTCA 59.295 36.000 4.53 0.00 38.57 2.57
835 1107 6.128200 GCAAATCTTTGGGCCTTTTTATTCAG 60.128 38.462 4.53 0.00 38.57 3.02
836 1108 6.933514 AATCTTTGGGCCTTTTTATTCAGA 57.066 33.333 4.53 0.00 0.00 3.27
837 1109 7.500629 AATCTTTGGGCCTTTTTATTCAGAT 57.499 32.000 4.53 0.00 0.00 2.90
838 1110 6.933514 TCTTTGGGCCTTTTTATTCAGATT 57.066 33.333 4.53 0.00 0.00 2.40
839 1111 7.315066 TCTTTGGGCCTTTTTATTCAGATTT 57.685 32.000 4.53 0.00 0.00 2.17
840 1112 8.429237 TCTTTGGGCCTTTTTATTCAGATTTA 57.571 30.769 4.53 0.00 0.00 1.40
841 1113 9.045745 TCTTTGGGCCTTTTTATTCAGATTTAT 57.954 29.630 4.53 0.00 0.00 1.40
974 3033 3.751518 GGCCACCGGATAACATAATCTT 58.248 45.455 9.46 0.00 0.00 2.40
1012 3071 2.549329 TGAATGCAATCCGATTCATCCG 59.451 45.455 0.00 0.00 32.51 4.18
1015 3074 2.416747 TGCAATCCGATTCATCCGATC 58.583 47.619 0.00 0.00 0.00 3.69
1016 3075 1.391485 GCAATCCGATTCATCCGATCG 59.609 52.381 8.51 8.51 37.54 3.69
1017 3076 2.677199 CAATCCGATTCATCCGATCGT 58.323 47.619 15.09 0.00 36.21 3.73
1018 3077 3.833442 CAATCCGATTCATCCGATCGTA 58.167 45.455 15.09 0.00 36.21 3.43
1019 3078 4.234574 CAATCCGATTCATCCGATCGTAA 58.765 43.478 15.09 1.75 36.21 3.18
1022 3086 4.978186 TCCGATTCATCCGATCGTAATAC 58.022 43.478 15.09 0.00 36.21 1.89
1024 3098 5.876460 TCCGATTCATCCGATCGTAATACTA 59.124 40.000 15.09 0.00 36.21 1.82
1059 3133 0.251354 TGCAGCAGATCTGAAGTCCC 59.749 55.000 27.04 7.27 45.72 4.46
1174 3248 1.626654 CCGCGTCACTGTCCATTCAC 61.627 60.000 4.92 0.00 0.00 3.18
1175 3249 1.781555 GCGTCACTGTCCATTCACG 59.218 57.895 0.00 0.00 0.00 4.35
1337 3415 2.107343 CACCACCACCGTGACGAA 59.893 61.111 6.54 0.00 43.14 3.85
1355 3433 3.385384 CAGACGGAGAGGCAGGCA 61.385 66.667 0.00 0.00 0.00 4.75
1417 3495 2.334946 GCCTTCATTCGGCAGCACA 61.335 57.895 0.00 0.00 46.77 4.57
1494 3578 3.782443 GGGTTCGGCGGTGATCCT 61.782 66.667 7.21 0.00 0.00 3.24
1591 3675 0.902531 CTACCCCGAAGCTTCCTTCA 59.097 55.000 20.62 1.95 46.25 3.02
1657 3741 4.401022 ACTGAATTTTCATCCTGTGCTCA 58.599 39.130 0.00 0.00 36.46 4.26
1838 3942 3.746492 GCTGTAGGTTAAGTCAACACCTG 59.254 47.826 0.11 0.00 41.28 4.00
1858 3962 1.061411 CGAGCAATCGCACATGTGG 59.939 57.895 26.55 16.47 42.27 4.17
1876 3980 1.271871 TGGACCGCAGTGGATTTCATT 60.272 47.619 7.13 0.00 42.00 2.57
1927 4031 1.357258 CTGCTGATCTGTGTGCGGAC 61.357 60.000 0.00 0.00 34.02 4.79
1932 4036 0.438830 GATCTGTGTGCGGACGTTTC 59.561 55.000 1.60 0.00 31.98 2.78
1960 4064 8.184848 GTCTGCTCCAAAATTCCTAAGATTTAC 58.815 37.037 0.00 0.00 0.00 2.01
1962 4066 8.415950 TGCTCCAAAATTCCTAAGATTTACAA 57.584 30.769 0.00 0.00 0.00 2.41
1991 4095 0.609662 CCAAAATTGCCCTGGTCCAG 59.390 55.000 12.40 12.40 0.00 3.86
2053 4157 3.634448 AGGAGATTGATAGAGACACACCG 59.366 47.826 0.00 0.00 0.00 4.94
2230 4337 6.421202 CAGATACAAGGCGAATAAGAAGGTAC 59.579 42.308 0.00 0.00 0.00 3.34
2231 4338 4.546829 ACAAGGCGAATAAGAAGGTACA 57.453 40.909 0.00 0.00 0.00 2.90
2233 4340 3.538634 AGGCGAATAAGAAGGTACACC 57.461 47.619 0.00 0.00 0.00 4.16
2237 4344 3.703420 CGAATAAGAAGGTACACCGAGG 58.297 50.000 0.00 0.00 42.08 4.63
2240 4347 2.005370 AAGAAGGTACACCGAGGTCA 57.995 50.000 0.00 0.00 42.08 4.02
2252 4359 1.284982 CGAGGTCAAAGCCTGTGTCG 61.285 60.000 0.00 0.00 39.34 4.35
2294 4411 2.490991 ACAAACTGCCTACCGTTTCTC 58.509 47.619 0.00 0.00 31.46 2.87
2436 4553 1.225704 CTGAATGCACTCCCTCCCC 59.774 63.158 0.00 0.00 0.00 4.81
2538 4657 2.932622 GCTTCTGACCATCGACATGTGT 60.933 50.000 1.15 0.00 0.00 3.72
2539 4658 2.368655 TCTGACCATCGACATGTGTG 57.631 50.000 1.15 0.00 0.00 3.82
2553 4672 0.612744 TGTGTGCCATCCTGATCGAA 59.387 50.000 0.00 0.00 0.00 3.71
2631 4750 2.591429 CAGCAGTTCACCACCGCA 60.591 61.111 0.00 0.00 0.00 5.69
2646 4765 1.299850 CGCAGTCACGGACAACAGA 60.300 57.895 6.78 0.00 34.60 3.41
2674 4793 7.068839 TCCTCAAATCAGATGTAGAGACCTTAC 59.931 40.741 8.05 0.00 0.00 2.34
2702 4821 4.883021 AGGTAACAGTCCTCCTCTGATA 57.117 45.455 0.00 0.00 41.41 2.15
2703 4822 4.798882 AGGTAACAGTCCTCCTCTGATAG 58.201 47.826 0.00 0.00 41.41 2.08
2704 4823 4.479056 AGGTAACAGTCCTCCTCTGATAGA 59.521 45.833 0.00 0.00 41.41 1.98
2795 4922 5.417580 GGTAAAAATGGCAGAAGACATGGTA 59.582 40.000 0.00 0.00 44.76 3.25
2804 4931 4.211125 CAGAAGACATGGTAGCTAGAGGA 58.789 47.826 0.00 0.00 0.00 3.71
2813 4940 2.809010 GCTAGAGGAGCGGTGTCC 59.191 66.667 0.00 0.00 42.62 4.02
2879 5006 2.746362 CAGGAAGATGTGACAAAGCCTC 59.254 50.000 0.00 0.00 0.00 4.70
2971 5098 7.559533 AGCTCTATCTCTTCAAGTTCAGACATA 59.440 37.037 0.00 0.00 0.00 2.29
2977 5104 3.232213 TCAAGTTCAGACATAGACGGC 57.768 47.619 0.00 0.00 0.00 5.68
3054 5181 1.078214 CGGCCAGATGTGTGGATGT 60.078 57.895 2.24 0.00 40.44 3.06
3061 5188 1.618343 AGATGTGTGGATGTCGTGTGA 59.382 47.619 0.00 0.00 0.00 3.58
3063 5190 0.750249 TGTGTGGATGTCGTGTGACT 59.250 50.000 0.00 0.00 45.70 3.41
3084 5211 3.750371 TCGGAGATTCACACCAAAACAT 58.250 40.909 0.00 0.00 0.00 2.71
3179 5306 5.715753 AGGTACTAAACTCTGAAGGTAGTGG 59.284 44.000 0.00 0.00 36.02 4.00
3205 5332 4.457834 ACTCTGTGTTCTGTATACTGGC 57.542 45.455 9.59 4.62 0.00 4.85
3228 5355 6.090898 GGCGAGTGGTGAATATATGTATTGAC 59.909 42.308 0.00 1.47 34.77 3.18
3245 5372 8.192068 TGTATTGACGTTCATGTATAACCAAG 57.808 34.615 0.00 0.00 0.00 3.61
3246 5373 7.820386 TGTATTGACGTTCATGTATAACCAAGT 59.180 33.333 0.00 0.00 0.00 3.16
3249 5376 6.224584 TGACGTTCATGTATAACCAAGTGAA 58.775 36.000 0.00 0.00 0.00 3.18
3285 5412 9.032420 GTCCATTAGTTATGTAACTTCTGCTAC 57.968 37.037 10.40 6.58 43.57 3.58
3296 5424 8.807667 TGTAACTTCTGCTACAAACTACTTAC 57.192 34.615 0.00 0.00 0.00 2.34
3331 5466 6.538742 TGTACAGAAAGCTTAACTATGCATCC 59.461 38.462 0.19 0.00 0.00 3.51
3332 5467 4.884164 ACAGAAAGCTTAACTATGCATCCC 59.116 41.667 0.19 0.00 0.00 3.85
3357 5492 4.018490 TGGTCGGTACTTTGATGTAGCTA 58.982 43.478 0.00 0.00 38.38 3.32
3369 5504 4.798574 TGATGTAGCTATGATGTACAGCG 58.201 43.478 6.63 0.00 36.15 5.18
3379 5514 4.450082 TGATGTACAGCGTCAGTGTATT 57.550 40.909 6.63 0.00 38.14 1.89
3380 5515 5.570234 TGATGTACAGCGTCAGTGTATTA 57.430 39.130 6.63 0.00 38.14 0.98
3383 5518 7.136772 TGATGTACAGCGTCAGTGTATTATAC 58.863 38.462 6.63 0.00 38.14 1.47
3384 5519 6.688637 TGTACAGCGTCAGTGTATTATACT 57.311 37.500 3.92 0.00 33.08 2.12
3385 5520 7.790823 TGTACAGCGTCAGTGTATTATACTA 57.209 36.000 3.92 0.00 33.08 1.82
3386 5521 7.633621 TGTACAGCGTCAGTGTATTATACTAC 58.366 38.462 3.92 1.28 33.08 2.73
3388 5523 5.826737 ACAGCGTCAGTGTATTATACTACCT 59.173 40.000 3.92 0.00 0.00 3.08
3398 5533 7.618512 AGTGTATTATACTACCTGTCTGTTGGT 59.381 37.037 3.92 0.00 40.12 3.67
3400 5535 3.611766 ATACTACCTGTCTGTTGGTGC 57.388 47.619 0.00 0.00 37.74 5.01
3460 5595 0.813610 CACCTCAACCGCACTCAACA 60.814 55.000 0.00 0.00 0.00 3.33
3468 5603 1.447317 CCGCACTCAACAACCAGCTT 61.447 55.000 0.00 0.00 0.00 3.74
3569 5719 7.092174 TGGACAATTAGGTAACCAGGTCATAAT 60.092 37.037 0.00 0.00 37.17 1.28
3617 5767 9.971922 ACAAAATTGAAGGAAGAATTAGACTTG 57.028 29.630 0.00 0.00 0.00 3.16
3619 5769 8.712228 AAATTGAAGGAAGAATTAGACTTGGT 57.288 30.769 0.00 0.00 0.00 3.67
3620 5770 7.929941 ATTGAAGGAAGAATTAGACTTGGTC 57.070 36.000 0.00 0.00 0.00 4.02
3621 5771 6.433847 TGAAGGAAGAATTAGACTTGGTCA 57.566 37.500 0.52 0.00 34.60 4.02
3622 5772 6.231211 TGAAGGAAGAATTAGACTTGGTCAC 58.769 40.000 0.52 0.00 34.60 3.67
3623 5773 5.167303 AGGAAGAATTAGACTTGGTCACC 57.833 43.478 0.00 0.00 34.60 4.02
3624 5774 4.019231 AGGAAGAATTAGACTTGGTCACCC 60.019 45.833 0.00 0.00 34.60 4.61
3625 5775 4.263331 GGAAGAATTAGACTTGGTCACCCA 60.263 45.833 0.00 0.00 39.65 4.51
3626 5776 5.501156 GAAGAATTAGACTTGGTCACCCAT 58.499 41.667 0.00 0.00 41.49 4.00
3627 5777 6.352737 GGAAGAATTAGACTTGGTCACCCATA 60.353 42.308 0.00 0.00 41.49 2.74
3628 5778 6.240549 AGAATTAGACTTGGTCACCCATAG 57.759 41.667 0.00 0.00 41.49 2.23
3667 5817 6.794534 AGGAAGAAATATTCAGGGTTTCACT 58.205 36.000 0.00 0.00 35.00 3.41
3668 5818 7.241628 AGGAAGAAATATTCAGGGTTTCACTT 58.758 34.615 0.00 0.00 35.00 3.16
3670 5820 8.367911 GGAAGAAATATTCAGGGTTTCACTTTT 58.632 33.333 0.00 0.00 35.00 2.27
3703 5853 5.745770 AGTGTTTCACTCTTGGATACATGCA 60.746 40.000 0.00 0.00 44.50 3.96
3704 5854 7.514697 AGTGTTTCACTCTTGGATACATGCAG 61.515 42.308 0.00 0.00 44.50 4.41
3713 5863 4.694760 TGGATACATGCAGCTAACTCAT 57.305 40.909 0.00 0.00 46.17 2.90
3714 5864 5.806654 TGGATACATGCAGCTAACTCATA 57.193 39.130 0.00 0.00 46.17 2.15
3715 5865 6.173427 TGGATACATGCAGCTAACTCATAA 57.827 37.500 0.00 0.00 46.17 1.90
3716 5866 5.991606 TGGATACATGCAGCTAACTCATAAC 59.008 40.000 0.00 0.00 46.17 1.89
3717 5867 5.991606 GGATACATGCAGCTAACTCATAACA 59.008 40.000 0.00 0.00 0.00 2.41
3718 5868 6.652481 GGATACATGCAGCTAACTCATAACAT 59.348 38.462 0.00 0.00 0.00 2.71
3719 5869 7.819415 GGATACATGCAGCTAACTCATAACATA 59.181 37.037 0.00 0.00 0.00 2.29
3720 5870 9.376075 GATACATGCAGCTAACTCATAACATAT 57.624 33.333 0.00 0.00 0.00 1.78
3721 5871 7.664082 ACATGCAGCTAACTCATAACATATC 57.336 36.000 0.00 0.00 0.00 1.63
3722 5872 7.448420 ACATGCAGCTAACTCATAACATATCT 58.552 34.615 0.00 0.00 0.00 1.98
3723 5873 7.601886 ACATGCAGCTAACTCATAACATATCTC 59.398 37.037 0.00 0.00 0.00 2.75
3724 5874 7.295322 TGCAGCTAACTCATAACATATCTCT 57.705 36.000 0.00 0.00 0.00 3.10
3725 5875 7.150640 TGCAGCTAACTCATAACATATCTCTG 58.849 38.462 0.00 0.00 0.00 3.35
3726 5876 7.151308 GCAGCTAACTCATAACATATCTCTGT 58.849 38.462 0.00 0.00 0.00 3.41
3727 5877 7.655328 GCAGCTAACTCATAACATATCTCTGTT 59.345 37.037 0.00 0.00 41.95 3.16
3728 5878 9.539825 CAGCTAACTCATAACATATCTCTGTTT 57.460 33.333 0.00 0.00 39.88 2.83
3760 5910 6.094881 TGGAAAAAGAGTTGTCCTACACAAAG 59.905 38.462 0.00 0.00 46.90 2.77
3761 5911 6.317893 GGAAAAAGAGTTGTCCTACACAAAGA 59.682 38.462 0.00 0.00 46.90 2.52
3808 5958 5.992217 AGAGTGGTACTGTTCTTGCTAAAAG 59.008 40.000 0.00 0.00 0.00 2.27
3820 5970 4.760204 TCTTGCTAAAAGAAGGTAACCAGC 59.240 41.667 0.00 0.00 37.17 4.85
3821 5971 3.418047 TGCTAAAAGAAGGTAACCAGCC 58.582 45.455 0.00 0.00 37.17 4.85
3824 5995 0.408309 AAAGAAGGTAACCAGCCCCC 59.592 55.000 0.00 0.00 37.17 5.40
3843 6014 2.513666 ACCACCAGCACACACACG 60.514 61.111 0.00 0.00 0.00 4.49
3844 6015 3.952675 CCACCAGCACACACACGC 61.953 66.667 0.00 0.00 0.00 5.34
3846 6017 3.202001 ACCAGCACACACACGCAC 61.202 61.111 0.00 0.00 0.00 5.34
3848 6019 2.023181 CAGCACACACACGCACAC 59.977 61.111 0.00 0.00 0.00 3.82
3849 6020 3.202001 AGCACACACACGCACACC 61.202 61.111 0.00 0.00 0.00 4.16
3851 6022 3.582120 CACACACACGCACACCCC 61.582 66.667 0.00 0.00 0.00 4.95
3866 6037 2.515398 CCCCCAGTGCACAGACAA 59.485 61.111 21.04 0.00 0.00 3.18
3871 6042 2.546373 CCCCAGTGCACAGACAATTTTG 60.546 50.000 21.04 4.73 0.00 2.44
3896 6067 9.890629 TGTAAGAAGATATGTGAAATAAGCAGT 57.109 29.630 0.00 0.00 0.00 4.40
3898 6069 7.798596 AGAAGATATGTGAAATAAGCAGTGG 57.201 36.000 0.00 0.00 0.00 4.00
3899 6070 7.341805 AGAAGATATGTGAAATAAGCAGTGGT 58.658 34.615 0.00 0.00 0.00 4.16
3900 6071 6.932356 AGATATGTGAAATAAGCAGTGGTG 57.068 37.500 0.00 0.00 0.00 4.17
3911 6082 2.066340 CAGTGGTGCTTAGGGTCCA 58.934 57.895 0.00 0.00 0.00 4.02
3912 6083 4.716003 GTGGTGCTTAGGGTCCAC 57.284 61.111 0.00 0.00 42.40 4.02
3913 6084 2.067197 GTGGTGCTTAGGGTCCACT 58.933 57.895 6.02 0.00 44.57 4.00
3914 6085 0.036294 GTGGTGCTTAGGGTCCACTC 60.036 60.000 6.02 0.00 44.57 3.51
3915 6086 1.198759 TGGTGCTTAGGGTCCACTCC 61.199 60.000 0.00 0.00 0.00 3.85
3916 6087 0.910088 GGTGCTTAGGGTCCACTCCT 60.910 60.000 0.00 0.00 38.36 3.69
3917 6088 0.250513 GTGCTTAGGGTCCACTCCTG 59.749 60.000 0.00 0.00 35.92 3.86
3918 6089 1.222113 GCTTAGGGTCCACTCCTGC 59.778 63.158 0.00 0.00 35.92 4.85
3919 6090 1.268283 GCTTAGGGTCCACTCCTGCT 61.268 60.000 0.00 0.00 35.92 4.24
3920 6091 1.280457 CTTAGGGTCCACTCCTGCTT 58.720 55.000 0.00 0.00 35.92 3.91
3936 6107 7.174253 CACTCCTGCTTGTTGTAATAAGGTAAA 59.826 37.037 3.79 0.00 0.00 2.01
3942 6113 9.871238 TGCTTGTTGTAATAAGGTAAAACAAAA 57.129 25.926 3.79 0.00 39.54 2.44
4022 6200 7.650834 AACAAACAATATGGGAAATTCAACG 57.349 32.000 0.00 0.00 0.00 4.10
4035 6221 8.885722 TGGGAAATTCAACGAGTATAATTGTAC 58.114 33.333 4.29 4.29 0.00 2.90
4040 6226 7.903452 TTCAACGAGTATAATTGTACGCTAG 57.097 36.000 12.77 6.31 0.00 3.42
4067 6253 6.070251 TGAGAAGTATGCAATTCTACTGGGAA 60.070 38.462 10.99 0.00 35.93 3.97
4074 6260 3.736126 GCAATTCTACTGGGAATGCAAGC 60.736 47.826 0.00 0.00 36.24 4.01
4076 6262 0.901827 TCTACTGGGAATGCAAGCGA 59.098 50.000 0.00 0.00 0.00 4.93
4078 6264 2.092968 TCTACTGGGAATGCAAGCGATT 60.093 45.455 0.00 0.00 0.00 3.34
4079 6265 2.418368 ACTGGGAATGCAAGCGATTA 57.582 45.000 0.00 0.00 0.00 1.75
4081 6267 2.292267 CTGGGAATGCAAGCGATTAGT 58.708 47.619 0.00 0.00 0.00 2.24
4082 6268 2.684881 CTGGGAATGCAAGCGATTAGTT 59.315 45.455 0.00 0.00 0.00 2.24
4083 6269 3.876914 CTGGGAATGCAAGCGATTAGTTA 59.123 43.478 0.00 0.00 0.00 2.24
4084 6270 4.460263 TGGGAATGCAAGCGATTAGTTAT 58.540 39.130 0.00 0.00 0.00 1.89
4086 6272 6.058833 TGGGAATGCAAGCGATTAGTTATTA 58.941 36.000 0.00 0.00 0.00 0.98
4087 6273 6.544197 TGGGAATGCAAGCGATTAGTTATTAA 59.456 34.615 0.00 0.00 0.00 1.40
4128 8341 9.624697 GTATTGAGACATCTAGAGAGCATAAAG 57.375 37.037 0.00 0.00 0.00 1.85
4129 8342 6.083098 TGAGACATCTAGAGAGCATAAAGC 57.917 41.667 0.00 0.00 46.19 3.51
4202 8415 0.474184 ATAGAGGAATTGTGCCCCCG 59.526 55.000 0.00 0.00 0.00 5.73
4212 8425 4.669809 TGCCCCCGCCGATTGTTT 62.670 61.111 0.00 0.00 0.00 2.83
4217 8430 1.288752 CCCGCCGATTGTTTGCTTT 59.711 52.632 0.00 0.00 0.00 3.51
4318 8531 4.310022 TGGAAAGGGTTGACCGAATAAT 57.690 40.909 0.00 0.00 46.96 1.28
4325 8538 6.749036 AGGGTTGACCGAATAATAATCTCT 57.251 37.500 0.00 0.00 46.96 3.10
4341 8554 3.482156 TCTCTGAAAAGTGAAGCTGCT 57.518 42.857 0.00 0.00 0.00 4.24
4382 8595 1.531602 ACTTGCAGCACCTTTCCCC 60.532 57.895 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.699399 AGACGGAAGGACTGAGGAGA 59.301 55.000 0.00 0.00 0.00 3.71
46 47 1.099689 GAGACGGAAGGACTGAGGAG 58.900 60.000 0.00 0.00 0.00 3.69
80 81 0.158928 CGTCGTCGTTTGTCTCTTGC 59.841 55.000 0.00 0.00 0.00 4.01
141 142 7.331687 GGTTACAATGGAATGGAAATGTCTTTG 59.668 37.037 0.00 0.00 0.00 2.77
142 143 7.016072 TGGTTACAATGGAATGGAAATGTCTTT 59.984 33.333 0.00 0.00 0.00 2.52
156 157 5.172687 TGATAAGCAGTGGTTACAATGGA 57.827 39.130 16.61 0.00 42.60 3.41
177 178 1.165907 TTGTTTCTCCAGTGCGGCTG 61.166 55.000 0.00 1.55 44.63 4.85
178 179 1.148273 TTGTTTCTCCAGTGCGGCT 59.852 52.632 0.00 0.00 33.14 5.52
179 180 1.282875 GTTGTTTCTCCAGTGCGGC 59.717 57.895 0.00 0.00 33.14 6.53
180 181 1.515521 GGGTTGTTTCTCCAGTGCGG 61.516 60.000 0.00 0.00 0.00 5.69
181 182 1.841663 CGGGTTGTTTCTCCAGTGCG 61.842 60.000 0.00 0.00 0.00 5.34
182 183 0.818040 ACGGGTTGTTTCTCCAGTGC 60.818 55.000 0.00 0.00 31.58 4.40
183 184 1.226746 GACGGGTTGTTTCTCCAGTG 58.773 55.000 0.00 0.00 32.80 3.66
184 185 0.108019 GGACGGGTTGTTTCTCCAGT 59.892 55.000 0.00 0.00 35.09 4.00
185 186 0.949105 CGGACGGGTTGTTTCTCCAG 60.949 60.000 0.00 0.00 0.00 3.86
186 187 1.070105 CGGACGGGTTGTTTCTCCA 59.930 57.895 0.00 0.00 0.00 3.86
188 189 2.322830 GCCGGACGGGTTGTTTCTC 61.323 63.158 5.05 0.00 38.44 2.87
313 546 4.312443 TCGGCTTTTGTTATCCGATATCC 58.688 43.478 0.00 0.00 44.99 2.59
605 850 0.321653 TGCGAAAAGAGGGGAAGAGC 60.322 55.000 0.00 0.00 0.00 4.09
633 878 1.078001 CCACCCGAGCCGGTTAAAT 60.078 57.895 1.90 0.00 46.80 1.40
655 900 3.254657 GCAACGCTCCTACTATCATCTCT 59.745 47.826 0.00 0.00 0.00 3.10
669 923 0.512952 CCACAGTAACAGCAACGCTC 59.487 55.000 0.00 0.00 36.40 5.03
672 926 0.586319 CACCCACAGTAACAGCAACG 59.414 55.000 0.00 0.00 0.00 4.10
674 928 0.840617 TCCACCCACAGTAACAGCAA 59.159 50.000 0.00 0.00 0.00 3.91
736 996 2.350522 AGACAGGCGTGATGTGAAATC 58.649 47.619 14.38 0.00 0.00 2.17
754 1018 1.153647 CTCATGCAACGGCGGTAGA 60.154 57.895 13.24 0.00 45.35 2.59
806 1078 1.078918 GGCCCAAAGATTTGCCTGC 60.079 57.895 0.00 2.77 40.77 4.85
883 2942 4.918275 CGTCGATCGTACGAAGATCTCGA 61.918 52.174 27.59 27.59 43.75 4.04
894 2953 1.931612 GTGGTCGCGTCGATCGTAC 60.932 63.158 15.94 10.90 40.17 3.67
974 3033 8.800370 TTGCATTCAGTTATCTTATTGGTACA 57.200 30.769 0.00 0.00 0.00 2.90
1036 3110 3.368843 GGACTTCAGATCTGCTGCAAGTA 60.369 47.826 21.22 0.74 44.52 2.24
1041 3115 0.809241 CGGGACTTCAGATCTGCTGC 60.809 60.000 18.36 7.71 44.52 5.25
1042 3116 0.820226 TCGGGACTTCAGATCTGCTG 59.180 55.000 18.36 14.36 46.31 4.41
1059 3133 1.401018 GGCGACTTTTCATTGGGTTCG 60.401 52.381 0.00 0.00 0.00 3.95
1175 3249 3.529533 AGATGAATATGATAGCGGCTGC 58.470 45.455 13.86 10.33 43.24 5.25
1337 3415 3.386237 GCCTGCCTCTCCGTCTGT 61.386 66.667 0.00 0.00 0.00 3.41
1355 3433 2.094286 CACTTCTTCATCTCTGACGGCT 60.094 50.000 0.00 0.00 0.00 5.52
1360 3438 1.733718 CGCGCACTTCTTCATCTCTGA 60.734 52.381 8.75 0.00 0.00 3.27
1362 3440 0.244994 ACGCGCACTTCTTCATCTCT 59.755 50.000 5.73 0.00 0.00 3.10
1458 3542 2.776072 CCGTCGTCGTTTCCATGC 59.224 61.111 0.71 0.00 35.01 4.06
1488 3572 4.166888 GCTCTGGCGCCAGGATCA 62.167 66.667 46.58 31.09 43.75 2.92
1657 3741 2.348998 CTCCAGGGCGTTCTGCTT 59.651 61.111 2.31 0.00 45.43 3.91
1699 3783 2.358737 GCCTTCGGACCACCACAG 60.359 66.667 0.00 0.00 35.59 3.66
1858 3962 2.083774 TCAATGAAATCCACTGCGGTC 58.916 47.619 0.00 0.00 35.57 4.79
1876 3980 9.191995 GTTTCTCTTTTGTTCAGAAGTTTTTCA 57.808 29.630 3.66 0.00 35.70 2.69
1932 4036 1.826385 AGGAATTTTGGAGCAGACGG 58.174 50.000 0.00 0.00 0.00 4.79
1991 4095 8.191446 TCAGTCAGTGTAGTTCTATTTCTATGC 58.809 37.037 0.00 0.00 0.00 3.14
2053 4157 1.003233 GCAGGTGAGACAGAACCCC 60.003 63.158 0.00 0.00 37.13 4.95
2230 4337 1.071471 ACAGGCTTTGACCTCGGTG 59.929 57.895 0.00 0.00 38.26 4.94
2231 4338 1.071471 CACAGGCTTTGACCTCGGT 59.929 57.895 0.00 0.00 38.26 4.69
2233 4340 1.284982 CGACACAGGCTTTGACCTCG 61.285 60.000 7.81 2.76 38.26 4.63
2237 4344 1.527311 GAACTCGACACAGGCTTTGAC 59.473 52.381 7.81 0.00 0.00 3.18
2240 4347 1.139058 ACAGAACTCGACACAGGCTTT 59.861 47.619 0.00 0.00 0.00 3.51
2294 4411 9.603921 AGGCAATTCATTAATTCATTGTAAAGG 57.396 29.630 14.02 0.00 32.87 3.11
2420 4537 2.190578 CGGGGAGGGAGTGCATTC 59.809 66.667 0.00 0.00 0.00 2.67
2421 4538 4.115199 GCGGGGAGGGAGTGCATT 62.115 66.667 0.00 0.00 0.00 3.56
2453 4572 7.308951 GCAACAAGGCTACAAGGAAGTAATTTA 60.309 37.037 0.00 0.00 0.00 1.40
2461 4580 1.616159 GGCAACAAGGCTACAAGGAA 58.384 50.000 0.00 0.00 40.24 3.36
2538 4657 3.766644 CTGTTCGATCAGGATGGCA 57.233 52.632 14.54 0.00 36.16 4.92
2553 4672 2.548480 GCTTTTAAGTTGCTCGACCTGT 59.452 45.455 0.00 0.00 0.00 4.00
2631 4750 1.971357 AGGATTCTGTTGTCCGTGACT 59.029 47.619 5.77 0.00 39.54 3.41
2646 4765 6.614906 AGGTCTCTACATCTGATTTGAGGATT 59.385 38.462 9.79 0.00 0.00 3.01
2674 4793 3.195825 AGGAGGACTGTTACCTTGATTCG 59.804 47.826 0.00 0.00 37.93 3.34
2691 4810 7.416964 TCTTTCTTTCTTCTATCAGAGGAGG 57.583 40.000 0.00 0.00 31.73 4.30
2702 4821 8.655901 AGAGGTGACTATTTCTTTCTTTCTTCT 58.344 33.333 0.00 0.00 44.43 2.85
2703 4822 8.840833 AGAGGTGACTATTTCTTTCTTTCTTC 57.159 34.615 0.00 0.00 44.43 2.87
2744 4863 5.066375 CGGAGCCAATTTCAGATGTTTATGA 59.934 40.000 0.00 0.00 0.00 2.15
2813 4940 1.812922 CTGCTGTCCTAAGCCGCAG 60.813 63.158 0.00 0.00 42.83 5.18
2820 4947 1.134699 CAATCCGAGCTGCTGTCCTAA 60.135 52.381 7.01 0.00 0.00 2.69
2971 5098 2.356313 CAGTGCTTCGTGCCGTCT 60.356 61.111 1.30 0.00 42.00 4.18
2977 5104 1.723542 CTAGACTTGCAGTGCTTCGTG 59.276 52.381 17.60 4.45 0.00 4.35
3054 5181 1.530323 TGAATCTCCGAGTCACACGA 58.470 50.000 0.00 0.00 31.64 4.35
3061 5188 3.139077 GTTTTGGTGTGAATCTCCGAGT 58.861 45.455 0.00 0.00 32.86 4.18
3063 5190 3.201353 TGTTTTGGTGTGAATCTCCGA 57.799 42.857 0.00 0.00 32.86 4.55
3084 5211 6.757947 GTGTTCGTTACTATACATAAAGGCCA 59.242 38.462 5.01 0.00 0.00 5.36
3179 5306 7.251994 CCAGTATACAGAACACAGAGTAGTTC 58.748 42.308 5.50 0.00 43.33 3.01
3205 5332 6.861572 ACGTCAATACATATATTCACCACTCG 59.138 38.462 0.00 0.00 0.00 4.18
3228 5355 7.526608 ACAATTCACTTGGTTATACATGAACG 58.473 34.615 0.00 0.00 39.30 3.95
3238 5365 5.304686 ACAGAGGACAATTCACTTGGTTA 57.695 39.130 0.00 0.00 39.30 2.85
3245 5372 5.491982 ACTAATGGACAGAGGACAATTCAC 58.508 41.667 0.00 0.00 0.00 3.18
3246 5373 5.762179 ACTAATGGACAGAGGACAATTCA 57.238 39.130 0.00 0.00 0.00 2.57
3249 5376 7.200434 ACATAACTAATGGACAGAGGACAAT 57.800 36.000 0.00 0.00 40.16 2.71
3285 5412 9.701098 TGTACAAGTATGGAAGTAAGTAGTTTG 57.299 33.333 0.00 0.00 0.00 2.93
3295 5423 6.115448 AGCTTTCTGTACAAGTATGGAAGT 57.885 37.500 0.00 0.00 0.00 3.01
3296 5424 8.443937 GTTAAGCTTTCTGTACAAGTATGGAAG 58.556 37.037 3.20 0.00 0.00 3.46
3316 5451 2.290641 CCAACGGGATGCATAGTTAAGC 59.709 50.000 0.00 0.00 35.59 3.09
3332 5467 2.409975 ACATCAAAGTACCGACCAACG 58.590 47.619 0.00 0.00 42.18 4.10
3343 5478 6.703607 GCTGTACATCATAGCTACATCAAAGT 59.296 38.462 0.00 0.00 38.31 2.66
3357 5492 4.655762 ATACACTGACGCTGTACATCAT 57.344 40.909 0.00 0.00 0.00 2.45
3369 5504 8.223177 ACAGACAGGTAGTATAATACACTGAC 57.777 38.462 23.58 19.61 32.66 3.51
3379 5514 4.159693 CAGCACCAACAGACAGGTAGTATA 59.840 45.833 0.00 0.00 36.07 1.47
3380 5515 3.055819 CAGCACCAACAGACAGGTAGTAT 60.056 47.826 0.00 0.00 36.07 2.12
3383 5518 1.609061 CCAGCACCAACAGACAGGTAG 60.609 57.143 0.00 0.00 36.07 3.18
3384 5519 0.396435 CCAGCACCAACAGACAGGTA 59.604 55.000 0.00 0.00 36.07 3.08
3385 5520 1.149174 CCAGCACCAACAGACAGGT 59.851 57.895 0.00 0.00 39.10 4.00
3386 5521 2.263741 GCCAGCACCAACAGACAGG 61.264 63.158 0.00 0.00 0.00 4.00
3388 5523 1.526686 CTGCCAGCACCAACAGACA 60.527 57.895 0.00 0.00 31.67 3.41
3398 5533 1.601759 GCCTTCAGAACTGCCAGCA 60.602 57.895 0.00 0.00 0.00 4.41
3400 5535 0.250640 AGTGCCTTCAGAACTGCCAG 60.251 55.000 0.00 0.00 0.00 4.85
3421 5556 4.142687 GGTGTGAGGTTTACATCATTTCCG 60.143 45.833 0.24 0.00 38.98 4.30
3460 5595 5.047377 TCACAGTTTTCTTTTCAAGCTGGTT 60.047 36.000 0.00 0.00 36.93 3.67
3569 5719 9.703892 TTTGTTCAACAAGAGAAGAAAATTTCA 57.296 25.926 8.55 0.00 39.53 2.69
3592 5742 9.415544 CCAAGTCTAATTCTTCCTTCAATTTTG 57.584 33.333 0.00 0.00 0.00 2.44
3619 5769 1.729586 GTCCTATGGGCTATGGGTGA 58.270 55.000 12.85 0.00 38.50 4.02
3620 5770 0.693049 GGTCCTATGGGCTATGGGTG 59.307 60.000 12.85 0.00 38.50 4.61
3621 5771 0.475828 GGGTCCTATGGGCTATGGGT 60.476 60.000 12.85 0.00 38.50 4.51
3622 5772 0.178861 AGGGTCCTATGGGCTATGGG 60.179 60.000 6.93 6.93 38.71 4.00
3623 5773 2.642171 TAGGGTCCTATGGGCTATGG 57.358 55.000 0.00 0.00 0.00 2.74
3624 5774 2.840651 CCTTAGGGTCCTATGGGCTATG 59.159 54.545 16.88 0.00 39.06 2.23
3625 5775 2.733637 TCCTTAGGGTCCTATGGGCTAT 59.266 50.000 21.61 0.00 41.47 2.97
3626 5776 2.158154 TCCTTAGGGTCCTATGGGCTA 58.842 52.381 21.61 6.84 41.47 3.93
3627 5777 0.949582 TCCTTAGGGTCCTATGGGCT 59.050 55.000 21.61 0.53 41.47 5.19
3628 5778 1.700186 CTTCCTTAGGGTCCTATGGGC 59.300 57.143 21.61 0.00 41.47 5.36
3680 5830 4.455533 TGCATGTATCCAAGAGTGAAACAC 59.544 41.667 0.00 0.00 41.43 3.32
3682 5832 4.437930 GCTGCATGTATCCAAGAGTGAAAC 60.438 45.833 0.00 0.00 0.00 2.78
3684 5834 3.054875 AGCTGCATGTATCCAAGAGTGAA 60.055 43.478 1.02 0.00 0.00 3.18
3686 5836 2.915349 AGCTGCATGTATCCAAGAGTG 58.085 47.619 1.02 0.00 0.00 3.51
3687 5837 4.163078 AGTTAGCTGCATGTATCCAAGAGT 59.837 41.667 1.02 0.00 0.00 3.24
3688 5838 4.701765 AGTTAGCTGCATGTATCCAAGAG 58.298 43.478 1.02 0.00 0.00 2.85
3691 5841 4.486125 TGAGTTAGCTGCATGTATCCAA 57.514 40.909 1.02 0.00 0.00 3.53
3693 5843 5.991606 TGTTATGAGTTAGCTGCATGTATCC 59.008 40.000 1.02 0.00 0.00 2.59
3694 5844 7.664082 ATGTTATGAGTTAGCTGCATGTATC 57.336 36.000 1.02 0.00 0.00 2.24
3695 5845 9.376075 GATATGTTATGAGTTAGCTGCATGTAT 57.624 33.333 1.02 0.00 0.00 2.29
3699 5849 7.818446 CAGAGATATGTTATGAGTTAGCTGCAT 59.182 37.037 1.02 0.00 0.00 3.96
3727 5877 6.210584 AGGACAACTCTTTTTCCAGACAAAAA 59.789 34.615 0.00 0.00 34.72 1.94
3728 5878 5.714806 AGGACAACTCTTTTTCCAGACAAAA 59.285 36.000 0.00 0.00 0.00 2.44
3729 5879 5.261216 AGGACAACTCTTTTTCCAGACAAA 58.739 37.500 0.00 0.00 0.00 2.83
3730 5880 4.855340 AGGACAACTCTTTTTCCAGACAA 58.145 39.130 0.00 0.00 0.00 3.18
3731 5881 4.503714 AGGACAACTCTTTTTCCAGACA 57.496 40.909 0.00 0.00 0.00 3.41
3732 5882 5.236695 GTGTAGGACAACTCTTTTTCCAGAC 59.763 44.000 0.00 0.00 0.00 3.51
3733 5883 5.104693 TGTGTAGGACAACTCTTTTTCCAGA 60.105 40.000 0.00 0.00 0.00 3.86
3734 5884 5.123227 TGTGTAGGACAACTCTTTTTCCAG 58.877 41.667 0.00 0.00 0.00 3.86
3735 5885 5.105567 TGTGTAGGACAACTCTTTTTCCA 57.894 39.130 0.00 0.00 0.00 3.53
3736 5886 6.317893 TCTTTGTGTAGGACAACTCTTTTTCC 59.682 38.462 0.00 0.00 44.53 3.13
3737 5887 7.316544 TCTTTGTGTAGGACAACTCTTTTTC 57.683 36.000 0.00 0.00 44.53 2.29
3738 5888 7.610305 TCTTCTTTGTGTAGGACAACTCTTTTT 59.390 33.333 0.00 0.00 44.53 1.94
3739 5889 7.110155 TCTTCTTTGTGTAGGACAACTCTTTT 58.890 34.615 0.00 0.00 44.53 2.27
3740 5890 6.650120 TCTTCTTTGTGTAGGACAACTCTTT 58.350 36.000 0.00 0.00 44.53 2.52
3741 5891 6.235231 TCTTCTTTGTGTAGGACAACTCTT 57.765 37.500 0.00 0.00 44.53 2.85
3742 5892 5.871396 TCTTCTTTGTGTAGGACAACTCT 57.129 39.130 0.00 0.00 44.53 3.24
3743 5893 6.920569 TTTCTTCTTTGTGTAGGACAACTC 57.079 37.500 0.00 0.00 44.53 3.01
3787 5937 6.293462 CCTTCTTTTAGCAAGAACAGTACCAC 60.293 42.308 0.00 0.00 33.20 4.16
3790 5940 6.862711 ACCTTCTTTTAGCAAGAACAGTAC 57.137 37.500 0.00 0.00 33.20 2.73
3821 5971 4.974721 GTGTGCTGGTGGTGGGGG 62.975 72.222 0.00 0.00 0.00 5.40
3824 5995 2.124362 TGTGTGTGCTGGTGGTGG 60.124 61.111 0.00 0.00 0.00 4.61
3829 6000 3.202001 GTGCGTGTGTGTGCTGGT 61.202 61.111 0.00 0.00 0.00 4.00
3831 6002 2.023181 GTGTGCGTGTGTGTGCTG 59.977 61.111 0.00 0.00 0.00 4.41
3832 6003 3.202001 GGTGTGCGTGTGTGTGCT 61.202 61.111 0.00 0.00 0.00 4.40
3849 6020 0.540365 AATTGTCTGTGCACTGGGGG 60.540 55.000 21.80 6.05 0.00 5.40
3851 6022 2.101249 ACAAAATTGTCTGTGCACTGGG 59.899 45.455 21.80 10.63 36.50 4.45
3853 6024 5.820131 TCTTACAAAATTGTCTGTGCACTG 58.180 37.500 19.41 18.10 42.35 3.66
3854 6025 6.318648 TCTTCTTACAAAATTGTCTGTGCACT 59.681 34.615 19.41 0.00 42.35 4.40
3855 6026 6.494842 TCTTCTTACAAAATTGTCTGTGCAC 58.505 36.000 10.75 10.75 42.35 4.57
3856 6027 6.691754 TCTTCTTACAAAATTGTCTGTGCA 57.308 33.333 1.37 0.00 42.35 4.57
3857 6028 9.282247 CATATCTTCTTACAAAATTGTCTGTGC 57.718 33.333 1.37 0.00 42.35 4.57
3892 6063 1.377333 GGACCCTAAGCACCACTGC 60.377 63.158 0.00 0.00 44.63 4.40
3893 6064 0.321653 GTGGACCCTAAGCACCACTG 60.322 60.000 0.00 0.00 46.14 3.66
3894 6065 2.067197 GTGGACCCTAAGCACCACT 58.933 57.895 0.00 0.00 46.14 4.00
3895 6066 4.716003 GTGGACCCTAAGCACCAC 57.284 61.111 0.00 0.00 44.23 4.16
3896 6067 1.198759 GGAGTGGACCCTAAGCACCA 61.199 60.000 0.00 0.00 0.00 4.17
3897 6068 0.910088 AGGAGTGGACCCTAAGCACC 60.910 60.000 0.00 0.00 30.92 5.01
3898 6069 0.250513 CAGGAGTGGACCCTAAGCAC 59.749 60.000 0.00 0.00 31.64 4.40
3899 6070 1.553690 GCAGGAGTGGACCCTAAGCA 61.554 60.000 0.00 0.00 31.64 3.91
3900 6071 1.222113 GCAGGAGTGGACCCTAAGC 59.778 63.158 0.00 0.00 31.64 3.09
3901 6072 1.065854 CAAGCAGGAGTGGACCCTAAG 60.066 57.143 0.00 0.00 31.64 2.18
3902 6073 0.984230 CAAGCAGGAGTGGACCCTAA 59.016 55.000 0.00 0.00 31.64 2.69
3903 6074 0.178903 ACAAGCAGGAGTGGACCCTA 60.179 55.000 0.00 0.00 31.64 3.53
3904 6075 1.062488 AACAAGCAGGAGTGGACCCT 61.062 55.000 0.00 0.00 0.00 4.34
3905 6076 0.890996 CAACAAGCAGGAGTGGACCC 60.891 60.000 0.00 0.00 0.00 4.46
3906 6077 0.179018 ACAACAAGCAGGAGTGGACC 60.179 55.000 0.00 0.00 0.00 4.46
3907 6078 2.543777 TACAACAAGCAGGAGTGGAC 57.456 50.000 0.00 0.00 0.00 4.02
3908 6079 3.788227 ATTACAACAAGCAGGAGTGGA 57.212 42.857 0.00 0.00 0.00 4.02
3909 6080 4.396166 CCTTATTACAACAAGCAGGAGTGG 59.604 45.833 0.00 0.00 0.00 4.00
3910 6081 5.003804 ACCTTATTACAACAAGCAGGAGTG 58.996 41.667 0.00 0.00 0.00 3.51
3911 6082 5.242795 ACCTTATTACAACAAGCAGGAGT 57.757 39.130 0.00 0.00 0.00 3.85
3912 6083 7.681939 TTTACCTTATTACAACAAGCAGGAG 57.318 36.000 0.00 0.00 0.00 3.69
3913 6084 7.502895 TGTTTTACCTTATTACAACAAGCAGGA 59.497 33.333 0.00 0.00 0.00 3.86
3914 6085 7.653647 TGTTTTACCTTATTACAACAAGCAGG 58.346 34.615 0.00 0.00 0.00 4.85
3915 6086 9.522804 TTTGTTTTACCTTATTACAACAAGCAG 57.477 29.630 0.00 0.00 35.97 4.24
3916 6087 9.871238 TTTTGTTTTACCTTATTACAACAAGCA 57.129 25.926 0.00 0.00 35.97 3.91
3965 6138 9.613428 CAAGTAATCTGGTTGACCTTTATATCA 57.387 33.333 1.34 0.00 36.82 2.15
3966 6139 9.832445 TCAAGTAATCTGGTTGACCTTTATATC 57.168 33.333 1.34 0.00 36.82 1.63
4022 6200 9.549509 CTTCTCATCTAGCGTACAATTATACTC 57.450 37.037 0.00 0.00 0.00 2.59
4035 6221 5.925397 AGAATTGCATACTTCTCATCTAGCG 59.075 40.000 0.00 0.00 0.00 4.26
4040 6226 6.426328 CCCAGTAGAATTGCATACTTCTCATC 59.574 42.308 9.26 4.13 33.83 2.92
4096 8309 9.231297 GCTCTCTAGATGTCTCAATACTTCTAT 57.769 37.037 0.00 0.00 36.26 1.98
4101 8314 8.932434 TTATGCTCTCTAGATGTCTCAATACT 57.068 34.615 0.00 0.00 0.00 2.12
4106 8319 5.278218 CGCTTTATGCTCTCTAGATGTCTCA 60.278 44.000 0.00 0.00 40.11 3.27
4119 8332 1.009829 CACTGTCCCGCTTTATGCTC 58.990 55.000 0.00 0.00 40.11 4.26
4128 8341 1.134521 TGTATGGAATCACTGTCCCGC 60.135 52.381 0.00 0.00 33.89 6.13
4129 8342 2.550978 GTGTATGGAATCACTGTCCCG 58.449 52.381 0.00 0.00 33.89 5.14
4130 8343 2.093658 ACGTGTATGGAATCACTGTCCC 60.094 50.000 0.00 0.00 33.89 4.46
4131 8344 3.247006 ACGTGTATGGAATCACTGTCC 57.753 47.619 0.00 0.00 35.55 4.02
4132 8345 4.264614 CGTAACGTGTATGGAATCACTGTC 59.735 45.833 0.00 0.00 33.07 3.51
4137 8350 4.437772 TGTCGTAACGTGTATGGAATCA 57.562 40.909 0.00 0.00 0.00 2.57
4202 8415 2.053627 CAGTGAAAGCAAACAATCGGC 58.946 47.619 0.00 0.00 0.00 5.54
4212 8425 7.575414 TTAAGTTGGAATAACAGTGAAAGCA 57.425 32.000 0.00 0.00 0.00 3.91
4318 8531 5.555017 AGCAGCTTCACTTTTCAGAGATTA 58.445 37.500 0.00 0.00 0.00 1.75
4325 8538 4.067896 CCTAGAAGCAGCTTCACTTTTCA 58.932 43.478 32.20 10.57 42.37 2.69
4336 8549 0.905357 TTGGACTCCCTAGAAGCAGC 59.095 55.000 0.00 0.00 0.00 5.25
4341 8554 0.620700 GCCCCTTGGACTCCCTAGAA 60.621 60.000 0.00 0.00 37.47 2.10


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

AutoCloner maintained by Alex Coulton.