Multiple sequence alignment - TraesCS4B01G082900

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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 TraesCS4B01G082900 chr4B 100.000 5002 0 0 1 5002 81992504 81997505 0.000000e+00 9238
1 TraesCS4B01G082900 chr4B 98.780 984 12 0 4019 5002 25738945 25737962 0.000000e+00 1751
2 TraesCS4B01G082900 chr4B 98.678 983 13 0 4020 5002 537395113 537396095 0.000000e+00 1744
3 TraesCS4B01G082900 chr4B 83.135 587 97 2 3016 3601 82007894 82008479 7.370000e-148 534
4 TraesCS4B01G082900 chr4B 80.510 549 91 12 1966 2509 82006770 82007307 1.680000e-109 407
5 TraesCS4B01G082900 chr4A 90.393 1603 126 13 639 2235 542043350 542041770 0.000000e+00 2082
6 TraesCS4B01G082900 chr4A 98.385 991 16 0 4012 5002 330724883 330723893 0.000000e+00 1742
7 TraesCS4B01G082900 chr4A 94.860 1109 48 1 2910 4018 542041074 542039975 0.000000e+00 1724
8 TraesCS4B01G082900 chr4A 87.460 622 48 14 2258 2852 542041716 542041098 0.000000e+00 689
9 TraesCS4B01G082900 chr4A 83.110 598 99 2 3005 3601 542034679 542034083 1.220000e-150 544
10 TraesCS4B01G082900 chr4A 80.769 546 88 15 1969 2509 542035829 542035296 1.300000e-110 411
11 TraesCS4B01G082900 chr4A 87.783 221 15 4 293 513 542044037 542043829 1.080000e-61 248
12 TraesCS4B01G082900 chr4A 91.096 146 13 0 3 148 542044206 542044061 1.100000e-46 198
13 TraesCS4B01G082900 chr4D 91.617 1515 77 21 2523 4014 55043507 55044994 0.000000e+00 2049
14 TraesCS4B01G082900 chr4D 87.848 1292 122 14 623 1912 55035906 55037164 0.000000e+00 1483
15 TraesCS4B01G082900 chr4D 91.353 532 42 2 1978 2509 55042873 55043400 0.000000e+00 725
16 TraesCS4B01G082900 chr4D 88.781 517 40 13 3 515 55035101 55035603 7.110000e-173 617
17 TraesCS4B01G082900 chr4D 84.157 587 91 2 3016 3601 55051087 55051672 7.270000e-158 568
18 TraesCS4B01G082900 chr4D 80.328 549 92 12 1966 2509 55049965 55050502 7.800000e-108 401
19 TraesCS4B01G082900 chr5B 98.881 983 11 0 4020 5002 459463112 459462130 0.000000e+00 1755
20 TraesCS4B01G082900 chr5B 98.779 983 12 0 4020 5002 336100242 336101224 0.000000e+00 1749
21 TraesCS4B01G082900 chr5B 87.861 173 16 1 3 170 604857510 604857338 1.100000e-46 198
22 TraesCS4B01G082900 chr5B 91.453 117 9 1 399 515 604857242 604857127 5.180000e-35 159
23 TraesCS4B01G082900 chr5A 98.779 983 12 0 4020 5002 149388535 149389517 0.000000e+00 1749
24 TraesCS4B01G082900 chr5A 90.000 120 11 1 396 515 611976715 611976597 2.410000e-33 154
25 TraesCS4B01G082900 chr1B 98.485 990 14 1 4013 5002 8634959 8635947 0.000000e+00 1744
26 TraesCS4B01G082900 chr1A 98.678 983 13 0 4020 5002 551794683 551795665 0.000000e+00 1744
27 TraesCS4B01G082900 chr3A 98.290 994 14 3 4010 5002 742248050 742247059 0.000000e+00 1738
28 TraesCS4B01G082900 chr6D 89.017 173 14 1 3 170 420225413 420225241 5.070000e-50 209
29 TraesCS4B01G082900 chr6D 87.931 174 14 3 3 170 28309754 28309582 1.100000e-46 198
30 TraesCS4B01G082900 chr6D 90.909 121 8 3 396 515 28309489 28309371 5.180000e-35 159
31 TraesCS4B01G082900 chr7A 88.439 173 15 2 3 170 47294390 47294218 2.360000e-48 204
32 TraesCS4B01G082900 chr7A 92.500 120 8 1 396 515 47294125 47294007 2.390000e-38 171
33 TraesCS4B01G082900 chr6A 87.861 173 16 1 3 170 29578269 29578441 1.100000e-46 198
34 TraesCS4B01G082900 chr6A 90.833 120 10 1 396 515 29578533 29578651 5.180000e-35 159
35 TraesCS4B01G082900 chr5D 87.861 173 16 1 3 170 441568773 441568601 1.100000e-46 198
36 TraesCS4B01G082900 chr5D 88.957 163 13 1 13 170 490431472 490431310 3.950000e-46 196
37 TraesCS4B01G082900 chr2B 81.982 222 38 2 1976 2196 432138199 432137979 2.380000e-43 187
38 TraesCS4B01G082900 chr7D 89.167 120 12 1 396 515 44716065 44715947 1.120000e-31 148


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 TraesCS4B01G082900 chr4B 81992504 81997505 5001 False 9238.0 9238 100.0000 1 5002 1 chr4B.!!$F1 5001
1 TraesCS4B01G082900 chr4B 25737962 25738945 983 True 1751.0 1751 98.7800 4019 5002 1 chr4B.!!$R1 983
2 TraesCS4B01G082900 chr4B 537395113 537396095 982 False 1744.0 1744 98.6780 4020 5002 1 chr4B.!!$F2 982
3 TraesCS4B01G082900 chr4B 82006770 82008479 1709 False 470.5 534 81.8225 1966 3601 2 chr4B.!!$F3 1635
4 TraesCS4B01G082900 chr4A 330723893 330724883 990 True 1742.0 1742 98.3850 4012 5002 1 chr4A.!!$R1 990
5 TraesCS4B01G082900 chr4A 542039975 542044206 4231 True 988.2 2082 90.3184 3 4018 5 chr4A.!!$R3 4015
6 TraesCS4B01G082900 chr4A 542034083 542035829 1746 True 477.5 544 81.9395 1969 3601 2 chr4A.!!$R2 1632
7 TraesCS4B01G082900 chr4D 55042873 55044994 2121 False 1387.0 2049 91.4850 1978 4014 2 chr4D.!!$F2 2036
8 TraesCS4B01G082900 chr4D 55035101 55037164 2063 False 1050.0 1483 88.3145 3 1912 2 chr4D.!!$F1 1909
9 TraesCS4B01G082900 chr4D 55049965 55051672 1707 False 484.5 568 82.2425 1966 3601 2 chr4D.!!$F3 1635
10 TraesCS4B01G082900 chr5B 459462130 459463112 982 True 1755.0 1755 98.8810 4020 5002 1 chr5B.!!$R1 982
11 TraesCS4B01G082900 chr5B 336100242 336101224 982 False 1749.0 1749 98.7790 4020 5002 1 chr5B.!!$F1 982
12 TraesCS4B01G082900 chr5A 149388535 149389517 982 False 1749.0 1749 98.7790 4020 5002 1 chr5A.!!$F1 982
13 TraesCS4B01G082900 chr1B 8634959 8635947 988 False 1744.0 1744 98.4850 4013 5002 1 chr1B.!!$F1 989
14 TraesCS4B01G082900 chr1A 551794683 551795665 982 False 1744.0 1744 98.6780 4020 5002 1 chr1A.!!$F1 982
15 TraesCS4B01G082900 chr3A 742247059 742248050 991 True 1738.0 1738 98.2900 4010 5002 1 chr3A.!!$R1 992

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
739 1132 0.244450 TTACTACGTTGTCCCGGCAG 59.756 55.0 5.77 0.0 0.00 4.85 F
1027 1420 0.029834 CCGCCACAATGCTAAGATGC 59.970 55.0 0.00 0.0 0.00 3.91 F
1816 2221 0.041576 GGAAAACGGTTCGTGTGCTC 60.042 55.0 0.00 0.0 39.99 4.26 F
2632 3229 0.324738 AGCGGGATCTCAAGTCAGGA 60.325 55.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 3210 0.324738 TCCTGACTTGAGATCCCGCT 60.325 55.000 0.00 0.0 0.00 5.52 R
2774 3371 1.760268 CGCGCTTCTTGCAGAGATCC 61.760 60.000 5.56 0.0 43.06 3.36 R
3638 4320 0.250513 ACCCGTGCTTCTCCTTCATC 59.749 55.000 0.00 0.0 0.00 2.92 R
4519 5201 1.203994 GTGCTCGGAAACAGGCTACTA 59.796 52.381 0.00 0.0 0.00 1.82 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
108 109 1.279271 ACTGGCCCAAGTCTACATCAC 59.721 52.381 0.00 0.00 0.00 3.06
160 161 0.875908 TGCCTCGCACGAATATGCTC 60.876 55.000 0.00 0.00 43.80 4.26
161 162 1.560860 GCCTCGCACGAATATGCTCC 61.561 60.000 0.00 0.00 43.80 4.70
164 165 1.789464 CTCGCACGAATATGCTCCTTC 59.211 52.381 0.00 0.00 43.80 3.46
203 204 5.814705 GGTCATTTTCTGATTGATCGAGAGT 59.185 40.000 0.00 0.00 35.97 3.24
204 205 6.314896 GGTCATTTTCTGATTGATCGAGAGTT 59.685 38.462 0.00 0.00 35.97 3.01
205 206 7.397970 GTCATTTTCTGATTGATCGAGAGTTC 58.602 38.462 0.00 0.00 35.97 3.01
218 219 2.600731 GAGAGTTCGACACACTGGATG 58.399 52.381 0.00 0.00 0.00 3.51
220 221 2.365617 AGAGTTCGACACACTGGATGTT 59.634 45.455 0.00 0.00 40.64 2.71
221 222 2.476619 GAGTTCGACACACTGGATGTTG 59.523 50.000 0.00 0.00 40.64 3.33
222 223 1.069906 GTTCGACACACTGGATGTTGC 60.070 52.381 0.00 0.00 40.64 4.17
223 224 0.392706 TCGACACACTGGATGTTGCT 59.607 50.000 0.00 0.00 40.64 3.91
224 225 1.616374 TCGACACACTGGATGTTGCTA 59.384 47.619 0.00 0.00 40.64 3.49
225 226 1.995484 CGACACACTGGATGTTGCTAG 59.005 52.381 0.00 0.00 40.64 3.42
226 227 1.734465 GACACACTGGATGTTGCTAGC 59.266 52.381 8.10 8.10 40.64 3.42
227 228 1.349026 ACACACTGGATGTTGCTAGCT 59.651 47.619 17.23 0.00 40.64 3.32
228 229 2.005451 CACACTGGATGTTGCTAGCTC 58.995 52.381 17.23 9.73 40.64 4.09
229 230 1.065854 ACACTGGATGTTGCTAGCTCC 60.066 52.381 17.23 14.65 38.98 4.70
243 244 0.680280 AGCTCCTTTCATGCCAGCTG 60.680 55.000 6.78 6.78 39.02 4.24
262 263 6.142817 CAGCTGTGTCCAAATTTTAGTGTAC 58.857 40.000 5.25 0.00 0.00 2.90
267 268 5.842327 GTGTCCAAATTTTAGTGTACGTTCG 59.158 40.000 0.00 0.00 0.00 3.95
271 272 5.406175 CCAAATTTTAGTGTACGTTCGAGGA 59.594 40.000 0.00 0.00 0.00 3.71
278 279 2.097142 GTGTACGTTCGAGGAGTAGCAT 59.903 50.000 0.00 0.00 0.00 3.79
280 281 3.940852 TGTACGTTCGAGGAGTAGCATAA 59.059 43.478 0.00 0.00 0.00 1.90
332 338 9.573133 TCTTGTAATATCATCATATAGCACGTG 57.427 33.333 12.28 12.28 0.00 4.49
333 339 9.358872 CTTGTAATATCATCATATAGCACGTGT 57.641 33.333 18.38 6.65 0.00 4.49
334 340 8.687824 TGTAATATCATCATATAGCACGTGTG 57.312 34.615 18.38 7.11 0.00 3.82
335 341 8.519526 TGTAATATCATCATATAGCACGTGTGA 58.480 33.333 18.38 12.71 0.00 3.58
336 342 9.353999 GTAATATCATCATATAGCACGTGTGAA 57.646 33.333 18.38 3.12 0.00 3.18
337 343 8.831715 AATATCATCATATAGCACGTGTGAAA 57.168 30.769 18.38 5.82 0.00 2.69
338 344 6.775939 ATCATCATATAGCACGTGTGAAAG 57.224 37.500 18.38 9.45 0.00 2.62
339 345 4.507756 TCATCATATAGCACGTGTGAAAGC 59.492 41.667 18.38 0.54 0.00 3.51
340 346 3.855858 TCATATAGCACGTGTGAAAGCA 58.144 40.909 18.38 0.00 0.00 3.91
341 347 4.249661 TCATATAGCACGTGTGAAAGCAA 58.750 39.130 18.38 0.00 0.00 3.91
342 348 2.969443 ATAGCACGTGTGAAAGCAAC 57.031 45.000 18.38 0.00 0.00 4.17
343 349 1.948104 TAGCACGTGTGAAAGCAACT 58.052 45.000 18.38 4.61 0.00 3.16
349 355 1.603802 CGTGTGAAAGCAACTGTGGAT 59.396 47.619 0.00 0.00 0.00 3.41
354 360 0.675633 AAAGCAACTGTGGATGCACC 59.324 50.000 15.34 0.00 42.55 5.01
374 380 5.661458 CACCGGTTTATGACTAGTTGATCT 58.339 41.667 2.97 0.00 0.00 2.75
425 431 9.214957 CTGAATATACACGAAATAATGGCCTTA 57.785 33.333 3.32 0.19 0.00 2.69
459 465 2.370445 GCCCCTCTGCTCAAGCCTA 61.370 63.158 0.00 0.00 41.18 3.93
488 496 4.475135 GTCTCGGCCAGCCCTTCC 62.475 72.222 2.24 0.00 0.00 3.46
515 523 2.863740 CGCGATACAGATTGCAGGTTTA 59.136 45.455 0.00 0.00 41.99 2.01
516 524 3.308595 CGCGATACAGATTGCAGGTTTAA 59.691 43.478 0.00 0.00 41.99 1.52
544 637 5.747951 TTTTTGTGCCACCATTTCAAATC 57.252 34.783 0.00 0.00 0.00 2.17
545 638 4.412796 TTTGTGCCACCATTTCAAATCA 57.587 36.364 0.00 0.00 0.00 2.57
546 639 4.412796 TTGTGCCACCATTTCAAATCAA 57.587 36.364 0.00 0.00 0.00 2.57
559 652 9.426837 CCATTTCAAATCAATGTATGTTTGAGT 57.573 29.630 0.00 0.00 38.76 3.41
567 660 3.945981 TGTATGTTTGAGTGGTAGCGA 57.054 42.857 0.00 0.00 0.00 4.93
585 679 5.638596 AGCGAATTTTAGGGATCGTTTTT 57.361 34.783 0.00 0.00 37.60 1.94
655 1048 7.690952 TGGTAACTGTTGTTTACTTGAAACT 57.309 32.000 2.69 0.00 42.53 2.66
656 1049 8.789825 TGGTAACTGTTGTTTACTTGAAACTA 57.210 30.769 2.69 0.00 42.53 2.24
657 1050 9.398538 TGGTAACTGTTGTTTACTTGAAACTAT 57.601 29.630 2.69 0.00 42.53 2.12
658 1051 9.659830 GGTAACTGTTGTTTACTTGAAACTATG 57.340 33.333 2.69 0.00 46.53 2.23
661 1054 8.276252 ACTGTTGTTTACTTGAAACTATGTGT 57.724 30.769 2.23 0.00 46.53 3.72
662 1055 9.386010 ACTGTTGTTTACTTGAAACTATGTGTA 57.614 29.630 2.23 0.00 46.53 2.90
663 1056 9.646336 CTGTTGTTTACTTGAAACTATGTGTAC 57.354 33.333 2.23 0.00 46.53 2.90
664 1057 8.329583 TGTTGTTTACTTGAAACTATGTGTACG 58.670 33.333 2.23 0.00 46.53 3.67
665 1058 6.879962 TGTTTACTTGAAACTATGTGTACGC 58.120 36.000 0.00 0.00 46.53 4.42
666 1059 6.702723 TGTTTACTTGAAACTATGTGTACGCT 59.297 34.615 8.10 0.00 46.53 5.07
670 1063 5.867716 ACTTGAAACTATGTGTACGCTTAGG 59.132 40.000 24.88 13.38 0.00 2.69
684 1077 3.560068 ACGCTTAGGTGAACAAAGTTGAG 59.440 43.478 0.00 0.00 0.00 3.02
706 1099 7.259882 TGAGCTATAAATTTGCCATGTTTCAG 58.740 34.615 0.00 0.00 0.00 3.02
737 1130 1.070821 GTTTACTACGTTGTCCCGGC 58.929 55.000 5.77 0.00 0.00 6.13
739 1132 0.244450 TTACTACGTTGTCCCGGCAG 59.756 55.000 5.77 0.00 0.00 4.85
740 1133 0.895100 TACTACGTTGTCCCGGCAGT 60.895 55.000 5.77 0.00 33.60 4.40
749 1142 0.673956 GTCCCGGCAGTCTTTCTTCC 60.674 60.000 0.00 0.00 0.00 3.46
750 1143 0.836400 TCCCGGCAGTCTTTCTTCCT 60.836 55.000 0.00 0.00 0.00 3.36
755 1148 2.878406 CGGCAGTCTTTCTTCCTCAAAA 59.122 45.455 0.00 0.00 0.00 2.44
786 1179 5.750352 AAATTCCAGGATTCTGCACAAAT 57.250 34.783 0.00 0.00 39.61 2.32
787 1180 5.750352 AATTCCAGGATTCTGCACAAATT 57.250 34.783 0.00 0.00 39.61 1.82
790 1183 6.855763 TTCCAGGATTCTGCACAAATTATT 57.144 33.333 0.00 0.00 39.61 1.40
792 1185 7.243604 TCCAGGATTCTGCACAAATTATTTT 57.756 32.000 0.00 0.00 39.61 1.82
800 1193 7.517614 TCTGCACAAATTATTTTGGTGTCTA 57.482 32.000 13.17 0.00 45.34 2.59
818 1211 6.085573 GTGTCTAGATGTGATCTGATCATCG 58.914 44.000 22.09 6.70 42.04 3.84
832 1225 3.562557 TGATCATCGGAATGCATGAACTG 59.437 43.478 0.00 0.43 32.76 3.16
835 1228 3.871006 TCATCGGAATGCATGAACTGTAC 59.129 43.478 0.00 0.00 32.58 2.90
840 1233 4.436050 CGGAATGCATGAACTGTACTGAAC 60.436 45.833 0.00 1.09 0.00 3.18
842 1235 5.163814 GGAATGCATGAACTGTACTGAACTC 60.164 44.000 0.00 1.35 0.00 3.01
846 1239 4.390297 GCATGAACTGTACTGAACTCTTCC 59.610 45.833 6.77 0.00 0.00 3.46
852 1245 4.039366 ACTGTACTGAACTCTTCCAAGGAC 59.961 45.833 6.77 0.00 0.00 3.85
853 1246 3.964688 TGTACTGAACTCTTCCAAGGACA 59.035 43.478 0.00 0.00 27.54 4.02
854 1247 3.477210 ACTGAACTCTTCCAAGGACAC 57.523 47.619 0.00 0.00 0.00 3.67
862 1255 4.288105 ACTCTTCCAAGGACACATCTGAAT 59.712 41.667 0.00 0.00 0.00 2.57
870 1263 4.910195 AGGACACATCTGAATGTTGCTTA 58.090 39.130 0.19 0.00 43.74 3.09
873 1266 5.220931 GGACACATCTGAATGTTGCTTATCC 60.221 44.000 0.19 0.00 43.74 2.59
892 1285 8.663911 GCTTATCCTGATCTAATTATCTGCAAC 58.336 37.037 0.00 0.00 0.00 4.17
915 1308 1.661341 CAGGTTATGGAGCTGCACTC 58.339 55.000 11.23 3.75 45.85 3.51
969 1362 1.134670 CCTTCTCTTCGATCACCCCAC 60.135 57.143 0.00 0.00 0.00 4.61
1008 1401 1.635663 CCGTGGTTTCGATGGCTCAC 61.636 60.000 0.00 0.00 0.00 3.51
1024 1417 0.323302 TCACCGCCACAATGCTAAGA 59.677 50.000 0.00 0.00 0.00 2.10
1027 1420 0.029834 CCGCCACAATGCTAAGATGC 59.970 55.000 0.00 0.00 0.00 3.91
1029 1422 1.105457 GCCACAATGCTAAGATGCCA 58.895 50.000 0.00 0.00 0.00 4.92
1032 1425 1.066605 CACAATGCTAAGATGCCAGGC 59.933 52.381 3.66 3.66 0.00 4.85
1036 1429 0.469917 TGCTAAGATGCCAGGCCTAC 59.530 55.000 3.98 0.20 0.00 3.18
1040 1433 0.978146 AAGATGCCAGGCCTACGAGT 60.978 55.000 3.98 0.00 0.00 4.18
1104 1497 2.787994 ACAGAGCAAGGTTTGAGGATG 58.212 47.619 0.00 0.00 0.00 3.51
1191 1584 0.810031 ACGCGTTAGATGTCATGGCC 60.810 55.000 5.58 0.00 0.00 5.36
1192 1585 1.821241 CGCGTTAGATGTCATGGCCG 61.821 60.000 0.00 0.00 0.00 6.13
1242 1635 0.249996 GCCAGCACAACCTTGCAAAT 60.250 50.000 0.00 0.00 45.62 2.32
1281 1674 4.082787 GCACACACCATTGTTATAGTTGCT 60.083 41.667 0.00 0.00 31.66 3.91
1368 1769 2.556144 AGCTGTGAGTTCATGCTTCA 57.444 45.000 6.73 0.00 35.92 3.02
1370 1771 3.418995 AGCTGTGAGTTCATGCTTCATT 58.581 40.909 6.73 0.00 35.92 2.57
1371 1772 3.825014 AGCTGTGAGTTCATGCTTCATTT 59.175 39.130 6.73 0.00 35.92 2.32
1372 1773 3.918591 GCTGTGAGTTCATGCTTCATTTG 59.081 43.478 0.00 0.00 0.00 2.32
1373 1774 4.558095 GCTGTGAGTTCATGCTTCATTTGT 60.558 41.667 0.00 0.00 0.00 2.83
1374 1775 4.862350 TGTGAGTTCATGCTTCATTTGTG 58.138 39.130 0.00 0.00 0.00 3.33
1375 1776 4.338964 TGTGAGTTCATGCTTCATTTGTGT 59.661 37.500 0.00 0.00 0.00 3.72
1376 1777 4.913924 GTGAGTTCATGCTTCATTTGTGTC 59.086 41.667 0.00 0.00 0.00 3.67
1377 1778 4.151258 AGTTCATGCTTCATTTGTGTCG 57.849 40.909 0.00 0.00 0.00 4.35
1378 1779 3.565482 AGTTCATGCTTCATTTGTGTCGT 59.435 39.130 0.00 0.00 0.00 4.34
1379 1780 4.754618 AGTTCATGCTTCATTTGTGTCGTA 59.245 37.500 0.00 0.00 0.00 3.43
1380 1781 5.238432 AGTTCATGCTTCATTTGTGTCGTAA 59.762 36.000 0.00 0.00 0.00 3.18
1397 1798 6.416455 GTGTCGTAAAAATTTGTCTTGCATCA 59.584 34.615 0.00 0.00 0.00 3.07
1398 1799 7.114811 GTGTCGTAAAAATTTGTCTTGCATCAT 59.885 33.333 0.00 0.00 0.00 2.45
1409 1810 4.100035 TGTCTTGCATCATAGATCTTCCGT 59.900 41.667 0.00 0.00 0.00 4.69
1427 1828 3.117434 CGTAGGATTTTTCAAGCCACG 57.883 47.619 0.00 0.00 41.40 4.94
1494 1895 0.100682 TAAGATGCCGACACTCGAGC 59.899 55.000 13.61 0.00 43.74 5.03
1538 1941 8.545472 ACAAAATTAGCACAGGAGGTACTATAA 58.455 33.333 0.00 0.00 41.55 0.98
1539 1942 9.391006 CAAAATTAGCACAGGAGGTACTATAAA 57.609 33.333 0.00 0.00 41.55 1.40
1545 1948 7.299134 AGCACAGGAGGTACTATAAACTAGAT 58.701 38.462 0.00 0.00 41.55 1.98
1549 1952 9.710818 ACAGGAGGTACTATAAACTAGATTGAA 57.289 33.333 0.00 0.00 41.55 2.69
1576 1979 7.725818 TGCATTGCAAATTAATTTCAACAGA 57.274 28.000 9.33 9.54 34.76 3.41
1612 2017 4.771577 TGAAAGAGAAGGCATGCCATTTTA 59.228 37.500 37.18 21.13 38.92 1.52
1613 2018 5.245751 TGAAAGAGAAGGCATGCCATTTTAA 59.754 36.000 37.18 18.81 38.92 1.52
1625 2030 3.704061 TGCCATTTTAATACAGGGGAAGC 59.296 43.478 0.00 0.00 0.00 3.86
1663 2068 1.760029 AGGGAAAAGGAGATCGAGAGC 59.240 52.381 0.00 0.00 0.00 4.09
1705 2110 6.294955 GCAAAATGAAGAAGAAGAATCCCTGT 60.295 38.462 0.00 0.00 0.00 4.00
1756 2161 0.179111 TGATAGTCGAAGGGCTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
1762 2167 2.434359 GAAGGGCTTGCGCTACGT 60.434 61.111 9.73 0.00 36.09 3.57
1766 2171 1.227147 GGGCTTGCGCTACGTATCA 60.227 57.895 9.73 0.00 36.09 2.15
1780 2185 0.180406 GTATCACTGCCGGGGATGTT 59.820 55.000 2.18 0.00 38.71 2.71
1816 2221 0.041576 GGAAAACGGTTCGTGTGCTC 60.042 55.000 0.00 0.00 39.99 4.26
1843 2248 4.569966 CCGATGACATCTCTTCTCTTTTGG 59.430 45.833 13.45 0.00 0.00 3.28
1869 2274 6.937436 AAAATTTTGACCTGTCTCGTACTT 57.063 33.333 1.75 0.00 0.00 2.24
1882 2287 7.384115 CCTGTCTCGTACTTAAAATGTTCTGAA 59.616 37.037 0.00 0.00 0.00 3.02
1934 2339 4.518217 CACGTTTTGTGTGAGATGAAGAC 58.482 43.478 0.00 0.00 43.88 3.01
1953 2358 5.066968 AGACTTAGTTAGCTGCTCTTGTC 57.933 43.478 4.91 10.06 0.00 3.18
1962 2367 8.375608 AGTTAGCTGCTCTTGTCATAAATATG 57.624 34.615 4.91 0.00 35.04 1.78
1963 2368 8.206867 AGTTAGCTGCTCTTGTCATAAATATGA 58.793 33.333 4.91 0.00 40.19 2.15
1964 2369 8.830580 GTTAGCTGCTCTTGTCATAAATATGAA 58.169 33.333 4.91 0.00 43.65 2.57
1999 2409 2.578586 ATCAGCCTTGACATGGGGCC 62.579 60.000 14.53 0.00 46.31 5.80
2064 2474 4.083057 GGCTGAAGAACTTGATGGAAGAAC 60.083 45.833 0.00 0.00 35.42 3.01
2111 2521 2.737252 GTTCCTCGATGAAGTTCACACC 59.263 50.000 7.96 0.00 0.00 4.16
2205 2662 5.163395 GGTGAAATTCAGGTACACCCAAAAA 60.163 40.000 0.00 0.00 43.29 1.94
2210 2667 5.523438 TTCAGGTACACCCAAAAATGTTC 57.477 39.130 0.00 0.00 36.42 3.18
2211 2668 4.798882 TCAGGTACACCCAAAAATGTTCT 58.201 39.130 0.00 0.00 36.42 3.01
2215 2672 6.002082 AGGTACACCCAAAAATGTTCTACTC 58.998 40.000 0.00 0.00 36.42 2.59
2269 2757 2.730090 CGCTGATGAAAAATTGCTCGCT 60.730 45.455 0.00 0.00 0.00 4.93
2411 2899 5.618236 TGATGAAGCCATAGGAATTCTCAG 58.382 41.667 5.23 0.00 32.09 3.35
2463 2951 3.003068 ACAAACTCCGATATACCGACGAG 59.997 47.826 0.00 0.00 0.00 4.18
2535 3058 4.871557 TGGTTTCAGTATATTTCCGTTCCG 59.128 41.667 0.00 0.00 0.00 4.30
2574 3171 3.273919 CTGCCTTCTGTTTGCAGTAAC 57.726 47.619 2.69 0.00 45.69 2.50
2632 3229 0.324738 AGCGGGATCTCAAGTCAGGA 60.325 55.000 0.00 0.00 0.00 3.86
2649 3246 2.102420 CAGGATACGTCATGGCAAGGTA 59.898 50.000 0.00 0.00 46.39 3.08
2665 3262 6.945435 TGGCAAGGTAAACATTTTCTCTCATA 59.055 34.615 0.00 0.00 0.00 2.15
2666 3263 7.615365 TGGCAAGGTAAACATTTTCTCTCATAT 59.385 33.333 0.00 0.00 0.00 1.78
2667 3264 7.917505 GGCAAGGTAAACATTTTCTCTCATATG 59.082 37.037 0.00 0.00 0.00 1.78
2735 3332 7.488187 TTCATGATCCGAGAATCTGAATTTC 57.512 36.000 0.00 0.00 30.33 2.17
2774 3371 2.900546 ACAGGTACCTGAGGAAGTCAAG 59.099 50.000 41.87 16.27 46.30 3.02
2854 3451 2.866762 AGAATTTCGAGCTGGTAATCGC 59.133 45.455 0.00 0.00 38.79 4.58
2863 3464 2.159028 AGCTGGTAATCGCCTTCTCTTC 60.159 50.000 0.00 0.00 0.00 2.87
2867 3468 2.036089 GGTAATCGCCTTCTCTTCCGAT 59.964 50.000 0.00 0.00 41.63 4.18
2885 3486 3.566742 CCGATCAATCAATCAATCAGCCA 59.433 43.478 0.00 0.00 0.00 4.75
2886 3487 4.037089 CCGATCAATCAATCAATCAGCCAA 59.963 41.667 0.00 0.00 0.00 4.52
2887 3488 5.450826 CCGATCAATCAATCAATCAGCCAAA 60.451 40.000 0.00 0.00 0.00 3.28
2889 3490 6.198403 CGATCAATCAATCAATCAGCCAAAAG 59.802 38.462 0.00 0.00 0.00 2.27
2890 3491 6.593268 TCAATCAATCAATCAGCCAAAAGA 57.407 33.333 0.00 0.00 0.00 2.52
2891 3492 6.627243 TCAATCAATCAATCAGCCAAAAGAG 58.373 36.000 0.00 0.00 0.00 2.85
2960 3588 9.333724 CATTATGATGCTATATGATTACAGGCA 57.666 33.333 0.00 0.00 0.00 4.75
3465 4147 2.022129 GTGGTGCTGTTCGACGAGG 61.022 63.158 0.00 0.00 0.00 4.63
3566 4248 1.302271 GGTGGACTTCCGGAACACC 60.302 63.158 29.33 29.33 43.98 4.16
3584 4266 3.133542 ACACCATCATCATCATGACGTCT 59.866 43.478 17.92 0.00 42.05 4.18
3637 4319 1.519455 GCGTGATGGTCGAGAAGGG 60.519 63.158 0.00 0.00 0.00 3.95
3638 4320 1.141881 CGTGATGGTCGAGAAGGGG 59.858 63.158 0.00 0.00 0.00 4.79
3942 4624 2.121538 GCCAAGGAAGGGGATTCGC 61.122 63.158 0.00 0.00 38.95 4.70
3948 4630 0.179070 GGAAGGGGATTCGCTGACTC 60.179 60.000 0.00 0.00 38.95 3.36
3955 4637 2.609244 GGGATTCGCTGACTCTAGATGC 60.609 54.545 0.00 0.00 0.00 3.91
3960 4642 1.596709 CGCTGACTCTAGATGCTGACG 60.597 57.143 0.00 0.00 0.00 4.35
3965 4647 0.382158 CTCTAGATGCTGACGCCGAA 59.618 55.000 0.00 0.00 34.43 4.30
4056 4738 2.520968 GGAACCAGCACACCCCTT 59.479 61.111 0.00 0.00 0.00 3.95
4210 4892 0.035056 AGATTGCGCCTACAAGCCTT 60.035 50.000 4.18 0.00 36.61 4.35
4438 5120 3.288092 GTTGAGACAAACCCAACTCCTT 58.712 45.455 0.00 0.00 37.69 3.36
4519 5201 3.673594 GCTTCAGTACTGCTACGTGACAT 60.674 47.826 18.45 0.00 0.00 3.06
4708 5390 5.468409 TGAACTGAACATAACGAAGAATGCA 59.532 36.000 0.00 0.00 0.00 3.96
4867 5549 3.152341 CAGGAGACAAAAGCTCACCATT 58.848 45.455 0.00 0.00 34.07 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.401153 GCGACTTGAGATTACGTTCAGAAAAT 60.401 38.462 0.00 0.00 0.00 1.82
108 109 2.502538 TGTATCGTGTTAAGGGAAGGGG 59.497 50.000 0.00 0.00 0.00 4.79
160 161 2.170607 ACCATCGGTTACTCATGGAAGG 59.829 50.000 16.32 2.02 39.73 3.46
161 162 3.118775 TGACCATCGGTTACTCATGGAAG 60.119 47.826 16.32 0.00 39.73 3.46
164 165 2.979814 TGACCATCGGTTACTCATGG 57.020 50.000 10.26 10.26 42.59 3.66
203 204 1.202639 AGCAACATCCAGTGTGTCGAA 60.203 47.619 0.00 0.00 41.14 3.71
204 205 0.392706 AGCAACATCCAGTGTGTCGA 59.607 50.000 0.00 0.00 41.14 4.20
205 206 1.995484 CTAGCAACATCCAGTGTGTCG 59.005 52.381 0.00 0.00 41.14 4.35
207 208 1.349026 AGCTAGCAACATCCAGTGTGT 59.651 47.619 18.83 0.00 41.14 3.72
208 209 2.005451 GAGCTAGCAACATCCAGTGTG 58.995 52.381 18.83 0.00 41.14 3.82
209 210 1.065854 GGAGCTAGCAACATCCAGTGT 60.066 52.381 18.83 0.00 44.84 3.55
210 211 1.209019 AGGAGCTAGCAACATCCAGTG 59.791 52.381 18.83 0.00 34.08 3.66
211 212 1.577736 AGGAGCTAGCAACATCCAGT 58.422 50.000 18.83 0.00 34.08 4.00
212 213 2.706339 AAGGAGCTAGCAACATCCAG 57.294 50.000 18.83 0.00 34.08 3.86
213 214 2.305635 TGAAAGGAGCTAGCAACATCCA 59.694 45.455 18.83 5.15 34.08 3.41
214 215 2.991250 TGAAAGGAGCTAGCAACATCC 58.009 47.619 18.83 14.88 0.00 3.51
215 216 3.243002 GCATGAAAGGAGCTAGCAACATC 60.243 47.826 18.83 5.24 0.00 3.06
216 217 2.686915 GCATGAAAGGAGCTAGCAACAT 59.313 45.455 18.83 5.34 0.00 2.71
217 218 2.086869 GCATGAAAGGAGCTAGCAACA 58.913 47.619 18.83 7.63 0.00 3.33
218 219 1.403323 GGCATGAAAGGAGCTAGCAAC 59.597 52.381 18.83 9.11 0.00 4.17
220 221 0.620030 TGGCATGAAAGGAGCTAGCA 59.380 50.000 18.83 0.00 0.00 3.49
221 222 1.307097 CTGGCATGAAAGGAGCTAGC 58.693 55.000 6.62 6.62 30.26 3.42
222 223 1.134159 AGCTGGCATGAAAGGAGCTAG 60.134 52.381 0.00 0.00 38.23 3.42
223 224 0.914644 AGCTGGCATGAAAGGAGCTA 59.085 50.000 0.00 0.00 38.23 3.32
224 225 0.680280 CAGCTGGCATGAAAGGAGCT 60.680 55.000 5.57 0.00 40.67 4.09
225 226 0.964358 ACAGCTGGCATGAAAGGAGC 60.964 55.000 19.93 0.00 0.00 4.70
226 227 0.809385 CACAGCTGGCATGAAAGGAG 59.191 55.000 19.93 0.00 0.00 3.69
227 228 0.111061 ACACAGCTGGCATGAAAGGA 59.889 50.000 19.93 0.00 0.00 3.36
228 229 0.524862 GACACAGCTGGCATGAAAGG 59.475 55.000 19.93 0.00 0.00 3.11
229 230 0.524862 GGACACAGCTGGCATGAAAG 59.475 55.000 19.93 0.00 0.00 2.62
243 244 5.842327 CGAACGTACACTAAAATTTGGACAC 59.158 40.000 0.00 0.00 0.00 3.67
262 263 5.629849 CCTAAATTATGCTACTCCTCGAACG 59.370 44.000 0.00 0.00 0.00 3.95
267 268 8.926092 AAAATCCCTAAATTATGCTACTCCTC 57.074 34.615 0.00 0.00 0.00 3.71
327 329 1.531677 CCACAGTTGCTTTCACACGTG 60.532 52.381 15.48 15.48 0.00 4.49
332 338 1.337703 TGCATCCACAGTTGCTTTCAC 59.662 47.619 0.00 0.00 39.12 3.18
333 339 1.337703 GTGCATCCACAGTTGCTTTCA 59.662 47.619 0.00 0.00 41.67 2.69
334 340 1.336240 GGTGCATCCACAGTTGCTTTC 60.336 52.381 0.00 0.00 43.88 2.62
335 341 0.675633 GGTGCATCCACAGTTGCTTT 59.324 50.000 0.00 0.00 43.88 3.51
336 342 1.518056 CGGTGCATCCACAGTTGCTT 61.518 55.000 0.00 0.00 43.88 3.91
337 343 1.968017 CGGTGCATCCACAGTTGCT 60.968 57.895 0.00 0.00 43.88 3.91
338 344 2.562912 CGGTGCATCCACAGTTGC 59.437 61.111 0.00 0.00 43.88 4.17
339 345 1.172180 AACCGGTGCATCCACAGTTG 61.172 55.000 8.52 0.00 43.88 3.16
340 346 0.467290 AAACCGGTGCATCCACAGTT 60.467 50.000 8.52 0.00 43.88 3.16
341 347 0.398696 TAAACCGGTGCATCCACAGT 59.601 50.000 8.52 0.00 43.88 3.55
342 348 1.401552 CATAAACCGGTGCATCCACAG 59.598 52.381 8.52 0.00 43.88 3.66
343 349 1.003696 TCATAAACCGGTGCATCCACA 59.996 47.619 8.52 0.00 43.88 4.17
349 355 3.007074 TCAACTAGTCATAAACCGGTGCA 59.993 43.478 8.52 0.00 0.00 4.57
374 380 8.049117 AGAGAACCTGTCAATGCAAGATAATTA 58.951 33.333 0.00 0.00 0.00 1.40
459 465 1.073199 CCGAGACTTGGGCCAGTTT 59.927 57.895 6.23 2.42 0.00 2.66
488 496 1.457303 GCAATCTGTATCGCGCTTAGG 59.543 52.381 5.56 0.00 0.00 2.69
539 632 7.485913 GCTACCACTCAAACATACATTGATTTG 59.514 37.037 0.00 0.00 36.30 2.32
540 633 7.538575 GCTACCACTCAAACATACATTGATTT 58.461 34.615 0.00 0.00 36.30 2.17
542 635 5.294306 CGCTACCACTCAAACATACATTGAT 59.706 40.000 0.00 0.00 36.30 2.57
543 636 4.629634 CGCTACCACTCAAACATACATTGA 59.370 41.667 0.00 0.00 35.60 2.57
544 637 4.629634 TCGCTACCACTCAAACATACATTG 59.370 41.667 0.00 0.00 0.00 2.82
545 638 4.827692 TCGCTACCACTCAAACATACATT 58.172 39.130 0.00 0.00 0.00 2.71
546 639 4.465632 TCGCTACCACTCAAACATACAT 57.534 40.909 0.00 0.00 0.00 2.29
559 652 3.133362 ACGATCCCTAAAATTCGCTACCA 59.867 43.478 0.00 0.00 35.08 3.25
560 653 3.725490 ACGATCCCTAAAATTCGCTACC 58.275 45.455 0.00 0.00 35.08 3.18
655 1048 4.787260 TGTTCACCTAAGCGTACACATA 57.213 40.909 0.00 0.00 0.00 2.29
656 1049 3.671008 TGTTCACCTAAGCGTACACAT 57.329 42.857 0.00 0.00 0.00 3.21
657 1050 3.455990 TTGTTCACCTAAGCGTACACA 57.544 42.857 0.00 0.00 0.00 3.72
658 1051 3.805971 ACTTTGTTCACCTAAGCGTACAC 59.194 43.478 0.00 0.00 0.00 2.90
659 1052 4.062677 ACTTTGTTCACCTAAGCGTACA 57.937 40.909 0.00 0.00 0.00 2.90
660 1053 4.508861 TCAACTTTGTTCACCTAAGCGTAC 59.491 41.667 0.00 0.00 0.00 3.67
661 1054 4.695396 TCAACTTTGTTCACCTAAGCGTA 58.305 39.130 0.00 0.00 0.00 4.42
662 1055 3.537580 TCAACTTTGTTCACCTAAGCGT 58.462 40.909 0.00 0.00 0.00 5.07
663 1056 3.607078 GCTCAACTTTGTTCACCTAAGCG 60.607 47.826 0.00 0.00 0.00 4.68
664 1057 3.565902 AGCTCAACTTTGTTCACCTAAGC 59.434 43.478 0.00 0.00 0.00 3.09
665 1058 8.547967 TTATAGCTCAACTTTGTTCACCTAAG 57.452 34.615 0.00 0.00 0.00 2.18
666 1059 8.911918 TTTATAGCTCAACTTTGTTCACCTAA 57.088 30.769 0.00 0.00 0.00 2.69
670 1063 8.427774 GCAAATTTATAGCTCAACTTTGTTCAC 58.572 33.333 17.58 5.36 31.69 3.18
684 1077 8.652810 ATTCTGAAACATGGCAAATTTATAGC 57.347 30.769 0.00 0.00 0.00 2.97
714 1107 3.119173 CCGGGACAACGTAGTAAACCATA 60.119 47.826 0.00 0.00 45.00 2.74
716 1109 1.000731 CCGGGACAACGTAGTAAACCA 59.999 52.381 0.00 0.00 45.00 3.67
723 1116 1.445582 GACTGCCGGGACAACGTAG 60.446 63.158 2.18 0.00 0.00 3.51
727 1120 0.250338 AGAAAGACTGCCGGGACAAC 60.250 55.000 2.18 0.00 0.00 3.32
730 1123 0.673956 GGAAGAAAGACTGCCGGGAC 60.674 60.000 2.18 0.00 34.16 4.46
732 1125 4.303257 GGAAGAAAGACTGCCGGG 57.697 61.111 2.18 0.00 34.16 5.73
765 1158 5.750352 AATTTGTGCAGAATCCTGGAATT 57.250 34.783 0.00 0.00 42.47 2.17
766 1159 7.427989 AATAATTTGTGCAGAATCCTGGAAT 57.572 32.000 0.00 0.00 42.47 3.01
786 1179 8.539544 TCAGATCACATCTAGACACCAAAATAA 58.460 33.333 0.00 0.00 37.58 1.40
787 1180 8.078060 TCAGATCACATCTAGACACCAAAATA 57.922 34.615 0.00 0.00 37.58 1.40
790 1183 6.155049 TGATCAGATCACATCTAGACACCAAA 59.845 38.462 9.21 0.00 37.58 3.28
792 1185 5.203528 TGATCAGATCACATCTAGACACCA 58.796 41.667 9.21 0.00 37.58 4.17
800 1193 5.480205 CATTCCGATGATCAGATCACATCT 58.520 41.667 15.67 0.00 43.01 2.90
818 1211 4.697352 AGTTCAGTACAGTTCATGCATTCC 59.303 41.667 0.00 0.00 0.00 3.01
832 1225 4.202223 TGTGTCCTTGGAAGAGTTCAGTAC 60.202 45.833 0.00 0.00 0.00 2.73
835 1228 3.475566 TGTGTCCTTGGAAGAGTTCAG 57.524 47.619 0.00 0.00 0.00 3.02
840 1233 3.969287 TCAGATGTGTCCTTGGAAGAG 57.031 47.619 0.00 0.00 0.00 2.85
842 1235 4.330250 ACATTCAGATGTGTCCTTGGAAG 58.670 43.478 0.00 0.00 44.64 3.46
846 1239 3.504906 AGCAACATTCAGATGTGTCCTTG 59.495 43.478 0.00 0.00 45.58 3.61
852 1245 5.587443 TCAGGATAAGCAACATTCAGATGTG 59.413 40.000 0.00 0.00 45.58 3.21
854 1247 6.711194 AGATCAGGATAAGCAACATTCAGATG 59.289 38.462 0.00 0.00 39.25 2.90
862 1255 9.716531 CAGATAATTAGATCAGGATAAGCAACA 57.283 33.333 0.00 0.00 0.00 3.33
870 1263 6.044754 TGGGTTGCAGATAATTAGATCAGGAT 59.955 38.462 0.00 0.00 0.00 3.24
873 1266 6.057533 TGTGGGTTGCAGATAATTAGATCAG 58.942 40.000 0.00 0.00 0.00 2.90
892 1285 0.749454 GCAGCTCCATAACCTGTGGG 60.749 60.000 0.00 0.00 37.34 4.61
900 1293 4.521075 GCGAGTGCAGCTCCATAA 57.479 55.556 9.71 0.00 41.10 1.90
915 1308 3.357079 GTTCCTGCCACCACTGCG 61.357 66.667 0.00 0.00 0.00 5.18
942 1335 1.961180 ATCGAAGAGAAGGTGGCCCG 61.961 60.000 0.00 0.00 43.63 6.13
969 1362 1.146263 GGGACGCCTCCTGGTTATG 59.854 63.158 1.57 0.00 36.68 1.90
990 1383 1.635663 GGTGAGCCATCGAAACCACG 61.636 60.000 0.00 0.00 34.09 4.94
1008 1401 0.029834 GCATCTTAGCATTGTGGCGG 59.970 55.000 0.00 0.00 39.27 6.13
1024 1417 1.749334 GCTACTCGTAGGCCTGGCAT 61.749 60.000 22.05 17.16 33.87 4.40
1027 1420 1.320344 TGTGCTACTCGTAGGCCTGG 61.320 60.000 17.99 7.51 33.87 4.45
1029 1422 1.654954 CGTGTGCTACTCGTAGGCCT 61.655 60.000 11.78 11.78 33.87 5.19
1032 1425 4.379221 GCGTGTGCTACTCGTAGG 57.621 61.111 6.26 0.00 37.41 3.18
1080 1473 2.551459 CCTCAAACCTTGCTCTGTTGAG 59.449 50.000 5.02 5.02 42.96 3.02
1104 1497 2.649331 TTTTCCCTCTCGACGATGAC 57.351 50.000 0.00 0.00 0.00 3.06
1191 1584 1.004277 GTGTCTCCTCTTGTGCGACG 61.004 60.000 0.00 0.00 0.00 5.12
1192 1585 1.004277 CGTGTCTCCTCTTGTGCGAC 61.004 60.000 0.00 0.00 0.00 5.19
1242 1635 0.521867 GTGCGACGATACGTGCTACA 60.522 55.000 0.00 0.00 41.37 2.74
1333 1726 8.698973 ACTCACAGCTAGACATACATAAGTAT 57.301 34.615 0.00 0.00 41.57 2.12
1368 1769 7.276658 TGCAAGACAAATTTTTACGACACAAAT 59.723 29.630 0.00 0.00 0.00 2.32
1370 1771 6.093404 TGCAAGACAAATTTTTACGACACAA 58.907 32.000 0.00 0.00 0.00 3.33
1371 1772 5.641709 TGCAAGACAAATTTTTACGACACA 58.358 33.333 0.00 0.00 0.00 3.72
1372 1773 6.416455 TGATGCAAGACAAATTTTTACGACAC 59.584 34.615 0.00 0.00 0.00 3.67
1373 1774 6.499172 TGATGCAAGACAAATTTTTACGACA 58.501 32.000 0.00 0.00 0.00 4.35
1374 1775 6.984740 TGATGCAAGACAAATTTTTACGAC 57.015 33.333 0.00 0.00 0.00 4.34
1375 1776 8.726068 TCTATGATGCAAGACAAATTTTTACGA 58.274 29.630 0.00 0.00 0.00 3.43
1376 1777 8.894409 TCTATGATGCAAGACAAATTTTTACG 57.106 30.769 0.00 0.00 0.00 3.18
1380 1781 9.798994 GAAGATCTATGATGCAAGACAAATTTT 57.201 29.630 0.00 0.00 0.00 1.82
1397 1798 7.442666 GCTTGAAAAATCCTACGGAAGATCTAT 59.557 37.037 0.00 0.00 34.34 1.98
1398 1799 6.761714 GCTTGAAAAATCCTACGGAAGATCTA 59.238 38.462 0.00 0.00 34.34 1.98
1409 1810 1.466950 CGCGTGGCTTGAAAAATCCTA 59.533 47.619 0.00 0.00 0.00 2.94
1427 1828 4.025401 CCAACGGCTTGACCACGC 62.025 66.667 0.00 0.00 39.03 5.34
1439 1840 1.011242 CACAACACGAGCACCAACG 60.011 57.895 0.00 0.00 0.00 4.10
1494 1895 6.978343 TTTTGTAAGATTCGTCCCATACTG 57.022 37.500 0.00 0.00 0.00 2.74
1538 1941 9.826574 AATTTGCAATGCATATTCAATCTAGTT 57.173 25.926 16.19 0.00 35.89 2.24
1551 1954 8.325421 TCTGTTGAAATTAATTTGCAATGCAT 57.675 26.923 17.98 0.00 38.76 3.96
1575 1978 9.133627 GCCTTCTCTTTCAACATTCTTATTTTC 57.866 33.333 0.00 0.00 0.00 2.29
1576 1979 8.641541 TGCCTTCTCTTTCAACATTCTTATTTT 58.358 29.630 0.00 0.00 0.00 1.82
1600 2005 3.640967 TCCCCTGTATTAAAATGGCATGC 59.359 43.478 9.90 9.90 0.00 4.06
1612 2017 1.490910 GGTGCTAGCTTCCCCTGTATT 59.509 52.381 17.23 0.00 0.00 1.89
1613 2018 1.132500 GGTGCTAGCTTCCCCTGTAT 58.868 55.000 17.23 0.00 0.00 2.29
1625 2030 1.673033 CCTTCCGACAACAGGTGCTAG 60.673 57.143 0.00 0.00 0.00 3.42
1663 2068 1.154225 GCCCAAGATTTGCGTGACG 60.154 57.895 0.00 0.00 0.00 4.35
1705 2110 1.306141 ACCGGGCTCTCCAATCAGA 60.306 57.895 6.32 0.00 34.36 3.27
1756 2161 1.299926 CCCGGCAGTGATACGTAGC 60.300 63.158 3.32 3.32 0.00 3.58
1762 2167 0.468226 GAACATCCCCGGCAGTGATA 59.532 55.000 0.00 0.00 0.00 2.15
1766 2171 2.610859 AGGAACATCCCCGGCAGT 60.611 61.111 0.00 0.00 37.19 4.40
1780 2185 5.451242 CGTTTTCCCTTGAATTGTTTCAGGA 60.451 40.000 0.01 0.00 42.60 3.86
1816 2221 1.336440 AGAAGAGATGTCATCGGAGCG 59.664 52.381 7.18 0.00 0.00 5.03
1843 2248 5.358298 ACGAGACAGGTCAAAATTTTAGC 57.642 39.130 2.44 2.83 0.00 3.09
1882 2287 8.451908 ACTGCTAAAACTACAGAAATTCAAGT 57.548 30.769 0.00 0.00 35.38 3.16
1919 2324 6.209589 AGCTAACTAAGTCTTCATCTCACACA 59.790 38.462 0.00 0.00 0.00 3.72
1932 2337 4.810790 TGACAAGAGCAGCTAACTAAGTC 58.189 43.478 0.00 2.62 0.00 3.01
1934 2339 7.834068 TTTATGACAAGAGCAGCTAACTAAG 57.166 36.000 0.00 0.00 0.00 2.18
1953 2358 8.571461 ACCTGCCATGATAGTTCATATTTATG 57.429 34.615 0.00 0.00 40.70 1.90
1962 2367 4.453819 GCTGATAACCTGCCATGATAGTTC 59.546 45.833 0.00 0.00 34.12 3.01
1963 2368 4.392940 GCTGATAACCTGCCATGATAGTT 58.607 43.478 0.00 0.00 34.12 2.24
1964 2369 4.013267 GCTGATAACCTGCCATGATAGT 57.987 45.455 0.00 0.00 34.12 2.12
1999 2409 0.325602 TTTGGTACCGGCAACTAGGG 59.674 55.000 7.57 0.00 0.00 3.53
2064 2474 1.813513 ACCTCGCCATTCTGTTTGAG 58.186 50.000 0.00 0.00 0.00 3.02
2215 2672 7.406405 GGCATGACCAATTGACCAACTATGG 62.406 48.000 7.12 8.58 45.56 2.74
2250 2707 3.829948 ACAGCGAGCAATTTTTCATCAG 58.170 40.909 0.00 0.00 0.00 2.90
2269 2757 5.464057 CGATACACTGACAACCAAAGTTACA 59.536 40.000 0.00 0.00 33.27 2.41
2355 2843 2.576615 AGAACTTTCACAGGCTGGAAC 58.423 47.619 20.34 7.51 0.00 3.62
2411 2899 3.023045 TACCCCTCCTGGAGCCCTC 62.023 68.421 18.51 0.00 35.39 4.30
2493 2981 4.950050 ACCATCGAAACCTGATGTATCTC 58.050 43.478 0.00 0.00 41.28 2.75
2494 2982 5.359194 AACCATCGAAACCTGATGTATCT 57.641 39.130 0.00 0.00 41.28 1.98
2613 3210 0.324738 TCCTGACTTGAGATCCCGCT 60.325 55.000 0.00 0.00 0.00 5.52
2632 3229 3.945346 TGTTTACCTTGCCATGACGTAT 58.055 40.909 0.00 0.00 0.00 3.06
2670 3267 9.671279 CAGGATTACATTTAGGTGCATCATATA 57.329 33.333 0.00 0.00 0.00 0.86
2735 3332 5.784177 ACCTGTCAGTGTCAGTATAGTTTG 58.216 41.667 14.92 1.66 0.00 2.93
2774 3371 1.760268 CGCGCTTCTTGCAGAGATCC 61.760 60.000 5.56 0.00 43.06 3.36
2863 3464 3.566742 TGGCTGATTGATTGATTGATCGG 59.433 43.478 0.00 0.00 0.00 4.18
2867 3468 6.593268 TCTTTTGGCTGATTGATTGATTGA 57.407 33.333 0.00 0.00 0.00 2.57
2913 3541 7.650834 AATGGAAATTGTAAACGAAATGTGG 57.349 32.000 0.00 0.00 0.00 4.17
3465 4147 2.811317 CCTGTGCGCCTTCTCGAC 60.811 66.667 4.18 0.00 0.00 4.20
3522 4204 4.379243 CTTGCCGTCCGTCAGCCT 62.379 66.667 0.00 0.00 0.00 4.58
3566 4248 7.071313 GGCGTTAGACGTCATGATGATGATG 62.071 48.000 21.75 12.25 46.84 3.07
3637 4319 0.462759 CCCGTGCTTCTCCTTCATCC 60.463 60.000 0.00 0.00 0.00 3.51
3638 4320 0.250513 ACCCGTGCTTCTCCTTCATC 59.749 55.000 0.00 0.00 0.00 2.92
3942 4624 2.118228 GCGTCAGCATCTAGAGTCAG 57.882 55.000 0.00 0.00 44.35 3.51
3955 4637 2.809601 CGTTCCCTTCGGCGTCAG 60.810 66.667 6.85 4.19 0.00 3.51
3960 4642 2.741211 GACCACGTTCCCTTCGGC 60.741 66.667 0.00 0.00 0.00 5.54
4126 4808 7.015389 GGAGGGTGTTAGACTATGTATAGCTTT 59.985 40.741 0.00 0.00 33.68 3.51
4210 4892 2.147958 CTTTACCGCTGCCACAGTTTA 58.852 47.619 0.00 0.00 33.43 2.01
4519 5201 1.203994 GTGCTCGGAAACAGGCTACTA 59.796 52.381 0.00 0.00 0.00 1.82
4708 5390 3.434309 ACTCATTGGGCTGCTGTTAAAT 58.566 40.909 0.00 0.00 0.00 1.40
4867 5549 4.530710 ACCGACAAGATAACAGCTGTTA 57.469 40.909 34.82 34.82 43.71 2.41


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

AutoCloner maintained by Alex Coulton.