Multiple sequence alignment - TraesCS2B01G434600

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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 TraesCS2B01G434600 chr2B 100.000 5505 0 0 1 5505 624534843 624540347 0.000000e+00 10166.0
1 TraesCS2B01G434600 chr2B 98.734 79 0 1 5231 5308 624540035 624540113 7.440000e-29 139.0
2 TraesCS2B01G434600 chr2B 98.734 79 0 1 5193 5271 624540073 624540150 7.440000e-29 139.0
3 TraesCS2B01G434600 chr2B 97.619 42 0 1 5268 5308 624540035 624540076 2.750000e-08 71.3
4 TraesCS2B01G434600 chr2B 97.619 42 0 1 5193 5234 624540110 624540150 2.750000e-08 71.3
5 TraesCS2B01G434600 chr2D 92.653 4233 189 54 1 4164 527385297 527389476 0.000000e+00 5982.0
6 TraesCS2B01G434600 chr2D 90.533 1088 52 22 4161 5234 527391343 527392393 0.000000e+00 1391.0
7 TraesCS2B01G434600 chr2D 94.068 118 4 2 5388 5505 527392442 527392556 5.670000e-40 176.0
8 TraesCS2B01G434600 chr2D 97.115 104 2 1 5268 5370 527392352 527392455 2.040000e-39 174.0
9 TraesCS2B01G434600 chr2A 94.651 1832 67 14 1510 3328 672343902 672345715 0.000000e+00 2811.0
10 TraesCS2B01G434600 chr2A 92.344 1881 80 21 3329 5183 672345765 672347607 0.000000e+00 2617.0
11 TraesCS2B01G434600 chr2A 92.044 1458 71 14 42 1479 672342471 672343903 0.000000e+00 2008.0
12 TraesCS2B01G434600 chr2A 85.149 101 6 4 5268 5367 672347635 672347727 1.630000e-15 95.3
13 TraesCS2B01G434600 chr2A 100.000 29 0 0 1 29 672342443 672342471 3.000000e-03 54.7


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 TraesCS2B01G434600 chr2B 624534843 624540347 5504 False 2117.32 10166 98.54120 1 5505 5 chr2B.!!$F1 5504
1 TraesCS2B01G434600 chr2D 527385297 527392556 7259 False 1930.75 5982 93.59225 1 5505 4 chr2D.!!$F1 5504
2 TraesCS2B01G434600 chr2A 672342443 672347727 5284 False 1517.20 2811 92.83760 1 5367 5 chr2A.!!$F1 5366

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
976 1012 0.182537 TACTGCCATTCCCCAATCCG 59.817 55.000 0.00 0.00 0.00 4.18 F
1088 1124 0.313987 CGTTGATCCGATCCGATCCA 59.686 55.000 17.84 7.46 38.32 3.41 F
1621 1691 0.324943 TCCCAGAGGCTTGCTTACAC 59.675 55.000 0.00 0.00 0.00 2.90 F
2649 2732 0.767375 AGTTGGTCATGGAGCACACT 59.233 50.000 0.00 3.27 39.84 3.55 F
3104 3189 1.134946 GGCACATCAACTAATGGTGCC 59.865 52.381 17.05 17.05 44.48 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2471 0.327924 CCACCTGGACCAACTGCATA 59.672 55.000 0.00 0.0 37.39 3.14 R
2649 2732 2.642311 TCCAACAAGAAGAGTATGCCCA 59.358 45.455 0.00 0.0 0.00 5.36 R
3104 3189 3.317993 ACCTTCCTGGAATTTTGAACGTG 59.682 43.478 10.03 0.0 39.71 4.49 R
4294 6314 1.078848 AAGTCGCATGCTCTCCACC 60.079 57.895 17.13 0.0 0.00 4.61 R
4771 6798 1.059913 AAGAAGCACACCTGGCTAGT 58.940 50.000 0.00 0.0 41.66 2.57 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.064271 GCAACTGTGAGGAAACAACGTTA 59.936 43.478 0.00 0.00 0.00 3.18
65 66 1.156736 CTTTCCGGCTGACATTCGTT 58.843 50.000 0.00 0.00 0.00 3.85
81 82 9.093970 TGACATTCGTTAGATAACATTACCAAG 57.906 33.333 3.81 0.00 35.99 3.61
83 84 9.314321 ACATTCGTTAGATAACATTACCAAGAG 57.686 33.333 3.81 0.00 35.99 2.85
111 113 4.110036 ACAAGCAGTTTCACAAGTTTCC 57.890 40.909 0.00 0.00 0.00 3.13
138 140 3.305471 GGGAGACGAGTACAATGGCTATC 60.305 52.174 0.00 0.00 0.00 2.08
139 141 3.556513 GAGACGAGTACAATGGCTATCG 58.443 50.000 0.00 0.00 36.32 2.92
144 146 3.381949 GAGTACAATGGCTATCGTCCAC 58.618 50.000 0.00 0.00 36.26 4.02
146 148 2.315925 ACAATGGCTATCGTCCACAG 57.684 50.000 0.00 0.00 36.26 3.66
166 168 1.066152 GGGCAGGATCAAAATTCGAGC 59.934 52.381 0.00 0.00 0.00 5.03
171 173 4.797471 CAGGATCAAAATTCGAGCAAACA 58.203 39.130 0.00 0.00 0.00 2.83
196 210 3.182972 GCTTTCGCTACAACGTTACAGAA 59.817 43.478 0.00 0.20 0.00 3.02
197 211 4.685020 CTTTCGCTACAACGTTACAGAAC 58.315 43.478 0.00 0.00 0.00 3.01
198 212 3.352554 TCGCTACAACGTTACAGAACA 57.647 42.857 0.00 0.00 35.06 3.18
199 213 3.704512 TCGCTACAACGTTACAGAACAA 58.295 40.909 0.00 0.00 35.06 2.83
200 214 4.300803 TCGCTACAACGTTACAGAACAAT 58.699 39.130 0.00 0.00 35.06 2.71
201 215 5.459768 TCGCTACAACGTTACAGAACAATA 58.540 37.500 0.00 0.00 35.06 1.90
206 220 6.680055 ACAACGTTACAGAACAATAGTACG 57.320 37.500 0.00 0.00 35.06 3.67
286 303 2.655090 TCACATGGAAACTCTTGCCA 57.345 45.000 0.00 0.00 35.91 4.92
295 312 4.591498 TGGAAACTCTTGCCACTCTAGTAA 59.409 41.667 0.00 0.00 0.00 2.24
296 313 5.172205 GGAAACTCTTGCCACTCTAGTAAG 58.828 45.833 0.00 0.00 0.00 2.34
297 314 5.279556 GGAAACTCTTGCCACTCTAGTAAGT 60.280 44.000 0.00 0.00 0.00 2.24
298 315 6.071503 GGAAACTCTTGCCACTCTAGTAAGTA 60.072 42.308 0.00 0.00 0.00 2.24
299 316 5.900865 ACTCTTGCCACTCTAGTAAGTAC 57.099 43.478 0.00 0.00 0.00 2.73
300 317 5.322754 ACTCTTGCCACTCTAGTAAGTACA 58.677 41.667 0.00 0.00 0.00 2.90
301 318 5.416326 ACTCTTGCCACTCTAGTAAGTACAG 59.584 44.000 0.00 0.00 0.00 2.74
302 319 5.322754 TCTTGCCACTCTAGTAAGTACAGT 58.677 41.667 0.00 0.00 0.00 3.55
303 320 6.479006 TCTTGCCACTCTAGTAAGTACAGTA 58.521 40.000 0.00 0.00 0.00 2.74
304 321 6.598457 TCTTGCCACTCTAGTAAGTACAGTAG 59.402 42.308 0.00 0.00 0.00 2.57
423 440 1.129917 ATCTCCTCCACCTGCAGATG 58.870 55.000 17.39 8.67 0.00 2.90
458 478 2.344917 CGGTGTAAAATTTGCCGCG 58.655 52.632 0.00 0.00 35.90 6.46
478 498 0.945099 TCCAGATCGAGAATCCGTCG 59.055 55.000 0.00 0.00 38.84 5.12
713 733 2.044946 CCTTGCCCTTCTTCCCGG 60.045 66.667 0.00 0.00 0.00 5.73
738 764 1.890979 CACCCAGCTCATCCATCGC 60.891 63.158 0.00 0.00 0.00 4.58
739 765 2.281345 CCCAGCTCATCCATCGCC 60.281 66.667 0.00 0.00 0.00 5.54
740 766 2.664185 CCAGCTCATCCATCGCCG 60.664 66.667 0.00 0.00 0.00 6.46
741 767 3.344215 CAGCTCATCCATCGCCGC 61.344 66.667 0.00 0.00 0.00 6.53
742 768 4.615815 AGCTCATCCATCGCCGCC 62.616 66.667 0.00 0.00 0.00 6.13
768 794 3.036084 CGCCGCCGCTAGGTTATG 61.036 66.667 0.00 0.00 40.50 1.90
802 828 0.595095 GCTCTGTGGGAGTTGCAAAG 59.405 55.000 0.00 0.00 43.62 2.77
820 846 3.878086 AAGTATGCACACACTGAAACG 57.122 42.857 0.00 0.00 0.00 3.60
904 930 2.113139 CCCGTTGCCAGTTCACCT 59.887 61.111 0.00 0.00 0.00 4.00
908 935 1.230635 CGTTGCCAGTTCACCTCCAG 61.231 60.000 0.00 0.00 0.00 3.86
923 950 0.325860 TCCAGCATAACGGGGTAGGT 60.326 55.000 0.00 0.00 33.79 3.08
976 1012 0.182537 TACTGCCATTCCCCAATCCG 59.817 55.000 0.00 0.00 0.00 4.18
986 1022 3.508840 CCAATCCGCCTCAACCGC 61.509 66.667 0.00 0.00 0.00 5.68
987 1023 3.508840 CAATCCGCCTCAACCGCC 61.509 66.667 0.00 0.00 0.00 6.13
988 1024 3.717294 AATCCGCCTCAACCGCCT 61.717 61.111 0.00 0.00 0.00 5.52
989 1025 3.682292 AATCCGCCTCAACCGCCTC 62.682 63.158 0.00 0.00 0.00 4.70
1088 1124 0.313987 CGTTGATCCGATCCGATCCA 59.686 55.000 17.84 7.46 38.32 3.41
1096 1132 2.357637 TCCGATCCGATCCAATTTTTGC 59.642 45.455 2.69 0.00 0.00 3.68
1147 1183 3.371097 GAGTCGCTGCGATTGGGGA 62.371 63.158 28.51 0.00 38.42 4.81
1155 1191 3.186909 GCTGCGATTGGGGAATTTTAAC 58.813 45.455 0.00 0.00 0.00 2.01
1270 1306 2.635338 GACGTGGTGAAAACCGGC 59.365 61.111 0.00 0.00 0.00 6.13
1481 1547 4.024048 GGTGAATGGCGACGATAAATGAAT 60.024 41.667 0.00 0.00 0.00 2.57
1488 1554 5.082059 GGCGACGATAAATGAATTATGCTG 58.918 41.667 0.00 0.00 34.30 4.41
1491 1557 6.073369 CGACGATAAATGAATTATGCTGGTG 58.927 40.000 0.00 0.00 34.30 4.17
1503 1569 1.360192 GCTGGTGCAGTGGTCAAAC 59.640 57.895 0.00 0.00 39.41 2.93
1508 1574 2.224281 TGGTGCAGTGGTCAAACTAGAG 60.224 50.000 0.00 0.00 0.00 2.43
1514 1580 4.310769 CAGTGGTCAAACTAGAGTGGAAG 58.689 47.826 0.00 0.00 0.00 3.46
1553 1623 9.777575 CCGATATTTAACCGAAGTTACAAAATT 57.222 29.630 0.00 0.00 38.19 1.82
1596 1666 9.398170 GTTGATTGATATGATATTTTTCCGGTG 57.602 33.333 0.00 0.00 0.00 4.94
1621 1691 0.324943 TCCCAGAGGCTTGCTTACAC 59.675 55.000 0.00 0.00 0.00 2.90
1636 1706 3.826729 GCTTACACAGAAACCAGGGATTT 59.173 43.478 0.00 0.00 0.00 2.17
1666 1736 9.236006 CCAATTATTCTGTAAGCAAGCCTATAT 57.764 33.333 0.00 0.00 0.00 0.86
1730 1807 3.189287 CAGGTACCAGACAGCAAAATGAC 59.811 47.826 15.94 0.00 0.00 3.06
1734 1811 3.489355 ACCAGACAGCAAAATGACATGA 58.511 40.909 0.00 0.00 0.00 3.07
1911 1991 9.632638 AACATGTATTATCAGGAGTGCTATTTT 57.367 29.630 0.00 0.00 0.00 1.82
1971 2051 1.781786 TGCCCTGGAGATCAGTACTC 58.218 55.000 0.00 0.00 41.83 2.59
1972 2052 1.289231 TGCCCTGGAGATCAGTACTCT 59.711 52.381 0.00 0.00 41.83 3.24
1973 2053 1.960689 GCCCTGGAGATCAGTACTCTC 59.039 57.143 0.00 0.00 41.83 3.20
2145 2226 6.377327 ACATCGTGAAAAACTGAAGACAAT 57.623 33.333 0.00 0.00 0.00 2.71
2154 2235 7.122055 TGAAAAACTGAAGACAATGGTAAGTGT 59.878 33.333 0.00 0.00 37.30 3.55
2229 2310 1.045407 AGTACTCGCCTGTTGTTCCA 58.955 50.000 0.00 0.00 0.00 3.53
2233 2314 3.134574 ACTCGCCTGTTGTTCCAATTA 57.865 42.857 0.00 0.00 0.00 1.40
2295 2376 6.460103 AGATATAGCAGAACCCCATGATTT 57.540 37.500 0.00 0.00 0.00 2.17
2310 2391 5.503498 CCATGATTTTGTGTTTGCAACTTG 58.497 37.500 0.00 0.00 0.00 3.16
2316 2398 7.600375 TGATTTTGTGTTTGCAACTTGTTTAGA 59.400 29.630 0.00 0.00 0.00 2.10
2362 2444 5.237344 GTGTGTATCCTGAATCAACCATAGC 59.763 44.000 0.00 0.00 0.00 2.97
2367 2449 2.357009 CCTGAATCAACCATAGCACTGC 59.643 50.000 0.00 0.00 0.00 4.40
2388 2471 9.744468 CACTGCTTTTAACTGGTTTATAACTTT 57.256 29.630 0.00 0.00 0.00 2.66
2536 2619 5.123820 CGGCATTTATGGTGGATGTAATAGG 59.876 44.000 0.00 0.00 0.00 2.57
2649 2732 0.767375 AGTTGGTCATGGAGCACACT 59.233 50.000 0.00 3.27 39.84 3.55
2679 2762 2.705658 TCTTCTTGTTGGAGAGAAGGCA 59.294 45.455 11.81 0.00 45.61 4.75
2958 3041 5.556915 TCCCATTTCAACTCTGTTAATCGT 58.443 37.500 0.00 0.00 0.00 3.73
3104 3189 1.134946 GGCACATCAACTAATGGTGCC 59.865 52.381 17.05 17.05 44.48 5.01
3185 3270 5.772672 TGACATTACAATTTAGTTGGCCACT 59.227 36.000 3.88 9.18 42.28 4.00
3256 3341 5.778161 TGTATGAACGACTGCTGTAATTG 57.222 39.130 0.00 0.00 0.00 2.32
3351 3485 2.271800 CACTGCCGAATCCTCTTGTAC 58.728 52.381 0.00 0.00 0.00 2.90
3762 3902 5.810074 CAGTTTTCCCTTTTTCGATGTTGTT 59.190 36.000 0.00 0.00 0.00 2.83
3978 4119 4.524714 TGTTGTTCTTCTTTCCCACAAACA 59.475 37.500 0.00 0.00 0.00 2.83
4102 4249 1.834263 CTTCCCCCTCTGTGGTCTTAG 59.166 57.143 0.00 0.00 0.00 2.18
4114 4261 5.601313 TCTGTGGTCTTAGTTGGAAGTTACT 59.399 40.000 0.00 0.00 0.00 2.24
4137 4284 8.372877 ACTTCCTAGGATATGATGGTATTCAG 57.627 38.462 13.57 4.03 0.00 3.02
4294 6314 7.529158 TGTGATGTTATTGCAGTTATCAAGTG 58.471 34.615 5.49 0.00 34.90 3.16
4345 6365 3.945434 GATGCTGCCGTGGATGCG 61.945 66.667 0.00 0.00 0.00 4.73
4351 6371 1.005037 TGCCGTGGATGCGATATCC 60.005 57.895 11.10 11.10 38.66 2.59
4420 6440 2.283145 ACAAGAAAGGAGTGCATGCT 57.717 45.000 20.33 0.00 0.00 3.79
4517 6537 5.435686 AACACCTTAACATAGGCAGATCA 57.564 39.130 0.00 0.00 38.99 2.92
4576 6597 8.660373 GTGTATTCCTTTATGTCAAGTTCTCTG 58.340 37.037 0.00 0.00 0.00 3.35
4732 6758 2.036346 AGAAAAGGCTGGAATTGCACAC 59.964 45.455 0.00 0.00 0.00 3.82
4769 6796 7.601130 TGTCTTGCAACTACGAGTTTAATGTAT 59.399 33.333 0.00 0.00 36.03 2.29
4770 6797 8.440833 GTCTTGCAACTACGAGTTTAATGTATT 58.559 33.333 0.00 0.00 36.03 1.89
4771 6798 9.642327 TCTTGCAACTACGAGTTTAATGTATTA 57.358 29.630 0.00 0.00 36.03 0.98
4815 6842 3.005155 AGCCATCTTCAGAGTTTTTGTGC 59.995 43.478 0.00 0.00 0.00 4.57
4897 6924 3.615155 CTTGAAGATTCCCAGAGAACCC 58.385 50.000 0.00 0.00 37.29 4.11
4942 6971 5.361905 CATTTGGTTTATTTCGCACGTTTG 58.638 37.500 0.00 0.00 0.00 2.93
5006 7036 6.605119 ACACCCATTTCTTATTCCTCTATGG 58.395 40.000 0.00 0.00 37.10 2.74
5008 7038 6.712547 CACCCATTTCTTATTCCTCTATGGAC 59.287 42.308 0.00 0.00 46.14 4.02
5061 7094 9.738832 TCAATCATTGTGTCTTGCATATTTATG 57.261 29.630 0.00 0.00 36.78 1.90
5079 7112 1.193323 TGGCCATAATGCAAGGTTGG 58.807 50.000 0.00 0.00 0.00 3.77
5088 7121 3.971404 ATGCAAGGTTGGCAGCATTGC 62.971 52.381 35.71 35.71 44.63 3.56
5112 7154 6.375455 GCTGAGGAAAAGGTTATCTTGATGAA 59.625 38.462 0.00 0.00 35.55 2.57
5140 7182 6.257849 TCGTATTAGGCAGCAAAGATTGTTAG 59.742 38.462 0.00 0.00 0.00 2.34
5141 7183 6.037172 CGTATTAGGCAGCAAAGATTGTTAGT 59.963 38.462 0.00 0.00 0.00 2.24
5142 7184 7.223971 CGTATTAGGCAGCAAAGATTGTTAGTA 59.776 37.037 0.00 0.00 0.00 1.82
5171 7213 7.936496 TTATCTGAATATGCTTTTGGTGTCA 57.064 32.000 0.00 0.00 0.00 3.58
5216 7276 1.068741 GACCTCGGGTTATTGCGATCT 59.931 52.381 0.00 0.00 35.25 2.75
5217 7277 1.485066 ACCTCGGGTTATTGCGATCTT 59.515 47.619 0.00 0.00 27.29 2.40
5218 7278 1.867233 CCTCGGGTTATTGCGATCTTG 59.133 52.381 0.00 0.00 0.00 3.02
5219 7279 2.550978 CTCGGGTTATTGCGATCTTGT 58.449 47.619 0.00 0.00 0.00 3.16
5220 7280 2.936498 CTCGGGTTATTGCGATCTTGTT 59.064 45.455 0.00 0.00 0.00 2.83
5221 7281 3.340034 TCGGGTTATTGCGATCTTGTTT 58.660 40.909 0.00 0.00 0.00 2.83
5222 7282 3.126171 TCGGGTTATTGCGATCTTGTTTG 59.874 43.478 0.00 0.00 0.00 2.93
5223 7283 3.179048 GGGTTATTGCGATCTTGTTTGC 58.821 45.455 0.00 0.00 0.00 3.68
5224 7284 3.366883 GGGTTATTGCGATCTTGTTTGCA 60.367 43.478 0.00 0.00 35.15 4.08
5225 7285 3.853671 GGTTATTGCGATCTTGTTTGCAG 59.146 43.478 0.00 0.00 38.75 4.41
5226 7286 2.642139 ATTGCGATCTTGTTTGCAGG 57.358 45.000 0.00 0.00 38.75 4.85
5227 7287 1.603456 TTGCGATCTTGTTTGCAGGA 58.397 45.000 0.00 0.00 38.75 3.86
5228 7288 1.159285 TGCGATCTTGTTTGCAGGAG 58.841 50.000 0.00 0.00 34.15 3.69
5229 7289 1.270785 TGCGATCTTGTTTGCAGGAGA 60.271 47.619 0.00 0.00 34.15 3.71
5230 7290 2.012673 GCGATCTTGTTTGCAGGAGAT 58.987 47.619 0.00 3.74 34.15 2.75
5231 7291 2.223203 GCGATCTTGTTTGCAGGAGATG 60.223 50.000 7.61 3.52 34.15 2.90
5232 7292 3.264947 CGATCTTGTTTGCAGGAGATGA 58.735 45.455 7.61 0.00 34.15 2.92
5233 7293 3.686241 CGATCTTGTTTGCAGGAGATGAA 59.314 43.478 7.61 0.00 34.15 2.57
5234 7294 4.154737 CGATCTTGTTTGCAGGAGATGAAA 59.845 41.667 7.61 0.00 34.15 2.69
5235 7295 4.836125 TCTTGTTTGCAGGAGATGAAAC 57.164 40.909 0.00 0.00 33.34 2.78
5236 7296 3.569701 TCTTGTTTGCAGGAGATGAAACC 59.430 43.478 0.00 0.00 32.51 3.27
5237 7297 3.228188 TGTTTGCAGGAGATGAAACCT 57.772 42.857 0.00 0.00 36.92 3.50
5238 7298 3.149196 TGTTTGCAGGAGATGAAACCTC 58.851 45.455 0.00 0.00 33.91 3.85
5239 7299 2.099141 TTGCAGGAGATGAAACCTCG 57.901 50.000 0.00 0.00 33.91 4.63
5240 7300 0.250234 TGCAGGAGATGAAACCTCGG 59.750 55.000 0.00 0.00 33.91 4.63
5241 7301 0.462759 GCAGGAGATGAAACCTCGGG 60.463 60.000 0.00 0.00 33.91 5.14
5242 7302 0.905357 CAGGAGATGAAACCTCGGGT 59.095 55.000 0.00 0.00 37.65 5.28
5244 7304 2.500098 CAGGAGATGAAACCTCGGGTTA 59.500 50.000 8.48 0.00 46.20 2.85
5245 7305 3.134804 CAGGAGATGAAACCTCGGGTTAT 59.865 47.826 8.48 0.86 46.20 1.89
5246 7306 3.780850 AGGAGATGAAACCTCGGGTTATT 59.219 43.478 8.48 0.00 46.20 1.40
5247 7307 3.877508 GGAGATGAAACCTCGGGTTATTG 59.122 47.826 8.48 0.00 46.20 1.90
5248 7308 3.279434 AGATGAAACCTCGGGTTATTGC 58.721 45.455 8.48 1.35 46.20 3.56
5249 7309 1.444836 TGAAACCTCGGGTTATTGCG 58.555 50.000 8.48 0.00 46.20 4.85
5250 7310 1.002201 TGAAACCTCGGGTTATTGCGA 59.998 47.619 8.48 0.00 46.20 5.10
5251 7311 2.285977 GAAACCTCGGGTTATTGCGAT 58.714 47.619 8.48 0.00 46.20 4.58
5252 7312 1.949465 AACCTCGGGTTATTGCGATC 58.051 50.000 6.53 0.00 44.94 3.69
5253 7313 1.120530 ACCTCGGGTTATTGCGATCT 58.879 50.000 0.00 0.00 27.29 2.75
5254 7314 1.485066 ACCTCGGGTTATTGCGATCTT 59.515 47.619 0.00 0.00 27.29 2.40
5255 7315 1.867233 CCTCGGGTTATTGCGATCTTG 59.133 52.381 0.00 0.00 0.00 3.02
5256 7316 2.550978 CTCGGGTTATTGCGATCTTGT 58.449 47.619 0.00 0.00 0.00 3.16
5257 7317 2.936498 CTCGGGTTATTGCGATCTTGTT 59.064 45.455 0.00 0.00 0.00 2.83
5258 7318 3.340034 TCGGGTTATTGCGATCTTGTTT 58.660 40.909 0.00 0.00 0.00 2.83
5259 7319 3.126171 TCGGGTTATTGCGATCTTGTTTG 59.874 43.478 0.00 0.00 0.00 2.93
5260 7320 3.179048 GGGTTATTGCGATCTTGTTTGC 58.821 45.455 0.00 0.00 0.00 3.68
5261 7321 3.366883 GGGTTATTGCGATCTTGTTTGCA 60.367 43.478 0.00 0.00 35.15 4.08
5262 7322 3.853671 GGTTATTGCGATCTTGTTTGCAG 59.146 43.478 0.00 0.00 38.75 4.41
5263 7323 2.642139 ATTGCGATCTTGTTTGCAGG 57.358 45.000 0.00 0.00 38.75 4.85
5264 7324 1.603456 TTGCGATCTTGTTTGCAGGA 58.397 45.000 0.00 0.00 38.75 3.86
5265 7325 1.159285 TGCGATCTTGTTTGCAGGAG 58.841 50.000 0.00 0.00 34.15 3.69
5266 7326 1.270785 TGCGATCTTGTTTGCAGGAGA 60.271 47.619 0.00 0.00 34.15 3.71
5267 7327 2.012673 GCGATCTTGTTTGCAGGAGAT 58.987 47.619 0.00 3.74 34.15 2.75
5268 7328 2.223203 GCGATCTTGTTTGCAGGAGATG 60.223 50.000 7.61 3.52 34.15 2.90
5269 7329 3.264947 CGATCTTGTTTGCAGGAGATGA 58.735 45.455 7.61 0.00 34.15 2.92
5270 7330 3.686241 CGATCTTGTTTGCAGGAGATGAA 59.314 43.478 7.61 0.00 34.15 2.57
5271 7331 4.154737 CGATCTTGTTTGCAGGAGATGAAA 59.845 41.667 7.61 0.00 34.15 2.69
5272 7332 4.836125 TCTTGTTTGCAGGAGATGAAAC 57.164 40.909 0.00 0.00 33.34 2.78
5273 7333 3.569701 TCTTGTTTGCAGGAGATGAAACC 59.430 43.478 0.00 0.00 32.51 3.27
5274 7334 3.228188 TGTTTGCAGGAGATGAAACCT 57.772 42.857 0.00 0.00 36.92 3.50
5275 7335 3.149196 TGTTTGCAGGAGATGAAACCTC 58.851 45.455 0.00 0.00 33.91 3.85
5276 7336 2.099141 TTGCAGGAGATGAAACCTCG 57.901 50.000 0.00 0.00 33.91 4.63
5277 7337 0.250234 TGCAGGAGATGAAACCTCGG 59.750 55.000 0.00 0.00 33.91 4.63
5278 7338 0.462759 GCAGGAGATGAAACCTCGGG 60.463 60.000 0.00 0.00 33.91 5.14
5279 7339 0.905357 CAGGAGATGAAACCTCGGGT 59.095 55.000 0.00 0.00 37.65 5.28
5281 7341 2.500098 CAGGAGATGAAACCTCGGGTTA 59.500 50.000 8.48 0.00 46.20 2.85
5282 7342 3.134804 CAGGAGATGAAACCTCGGGTTAT 59.865 47.826 8.48 0.86 46.20 1.89
5283 7343 3.780850 AGGAGATGAAACCTCGGGTTATT 59.219 43.478 8.48 0.00 46.20 1.40
5284 7344 3.877508 GGAGATGAAACCTCGGGTTATTG 59.122 47.826 8.48 0.00 46.20 1.90
5285 7345 3.279434 AGATGAAACCTCGGGTTATTGC 58.721 45.455 8.48 1.35 46.20 3.56
5286 7346 1.444836 TGAAACCTCGGGTTATTGCG 58.555 50.000 8.48 0.00 46.20 4.85
5287 7347 1.002201 TGAAACCTCGGGTTATTGCGA 59.998 47.619 8.48 0.00 46.20 5.10
5288 7348 2.285977 GAAACCTCGGGTTATTGCGAT 58.714 47.619 8.48 0.00 46.20 4.58
5289 7349 1.949465 AACCTCGGGTTATTGCGATC 58.051 50.000 6.53 0.00 44.94 3.69
5320 7380 2.512885 GAGATGAATGCGTGTTGCTTG 58.487 47.619 0.00 0.00 46.63 4.01
5370 7430 3.187637 ACGAAATGAATGTGTACAACCCG 59.812 43.478 0.00 0.00 0.00 5.28
5371 7431 3.187637 CGAAATGAATGTGTACAACCCGT 59.812 43.478 0.00 0.00 0.00 5.28
5372 7432 4.319911 CGAAATGAATGTGTACAACCCGTT 60.320 41.667 0.00 0.00 0.00 4.44
5373 7433 5.523438 AAATGAATGTGTACAACCCGTTT 57.477 34.783 0.00 0.00 0.00 3.60
5374 7434 4.759516 ATGAATGTGTACAACCCGTTTC 57.240 40.909 0.00 0.00 0.00 2.78
5377 7437 2.306341 TGTGTACAACCCGTTTCGAA 57.694 45.000 0.00 0.00 0.00 3.71
5378 7438 2.625737 TGTGTACAACCCGTTTCGAAA 58.374 42.857 6.47 6.47 0.00 3.46
5379 7439 3.005554 TGTGTACAACCCGTTTCGAAAA 58.994 40.909 13.10 0.00 0.00 2.29
5380 7440 3.063725 TGTGTACAACCCGTTTCGAAAAG 59.936 43.478 13.10 14.60 0.00 2.27
5381 7441 3.309410 GTGTACAACCCGTTTCGAAAAGA 59.691 43.478 22.90 1.37 0.00 2.52
5382 7442 3.937706 TGTACAACCCGTTTCGAAAAGAA 59.062 39.130 22.90 0.00 37.01 2.52
5383 7443 4.394300 TGTACAACCCGTTTCGAAAAGAAA 59.606 37.500 22.90 0.00 45.76 2.52
5405 7465 4.664150 AAAAATGTGTACAACCCACCAG 57.336 40.909 0.00 0.00 31.71 4.00
5406 7466 2.286365 AATGTGTACAACCCACCAGG 57.714 50.000 0.00 0.00 43.78 4.45
5407 7467 1.440618 ATGTGTACAACCCACCAGGA 58.559 50.000 0.00 0.00 39.89 3.86
5408 7468 0.470766 TGTGTACAACCCACCAGGAC 59.529 55.000 0.00 0.00 39.89 3.85
5409 7469 0.470766 GTGTACAACCCACCAGGACA 59.529 55.000 0.00 0.00 39.89 4.02
5493 7553 3.426787 TTGTTAGAAAATCGGCTCCCA 57.573 42.857 0.00 0.00 0.00 4.37
5497 7557 2.990066 AGAAAATCGGCTCCCAGTAG 57.010 50.000 0.00 0.00 0.00 2.57
5498 7558 2.188817 AGAAAATCGGCTCCCAGTAGT 58.811 47.619 0.00 0.00 0.00 2.73
5500 7560 3.132467 AGAAAATCGGCTCCCAGTAGTAC 59.868 47.826 0.00 0.00 0.00 2.73
5501 7561 1.411041 AATCGGCTCCCAGTAGTACC 58.589 55.000 0.00 0.00 0.00 3.34
5502 7562 0.260816 ATCGGCTCCCAGTAGTACCA 59.739 55.000 0.00 0.00 0.00 3.25
5503 7563 0.260816 TCGGCTCCCAGTAGTACCAT 59.739 55.000 0.00 0.00 0.00 3.55
5504 7564 1.120530 CGGCTCCCAGTAGTACCATT 58.879 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.537371 CGGAAAGGGGTTGACAAGCT 60.537 55.000 16.41 0.00 0.00 3.74
111 113 3.491619 CCATTGTACTCGTCTCCCAGATG 60.492 52.174 0.00 0.00 32.57 2.90
138 140 2.184020 TTGATCCTGCCCTGTGGACG 62.184 60.000 0.00 0.00 34.90 4.79
139 141 0.038166 TTTGATCCTGCCCTGTGGAC 59.962 55.000 0.00 0.00 34.90 4.02
144 146 2.357009 CTCGAATTTTGATCCTGCCCTG 59.643 50.000 0.00 0.00 0.00 4.45
146 148 1.066152 GCTCGAATTTTGATCCTGCCC 59.934 52.381 0.00 0.00 0.00 5.36
196 210 6.710597 ATCACATCTGTACCGTACTATTGT 57.289 37.500 10.03 7.47 0.00 2.71
197 211 9.692749 AATAATCACATCTGTACCGTACTATTG 57.307 33.333 10.03 6.93 0.00 1.90
198 212 9.692749 CAATAATCACATCTGTACCGTACTATT 57.307 33.333 10.03 0.56 0.00 1.73
199 213 7.813148 GCAATAATCACATCTGTACCGTACTAT 59.187 37.037 10.03 1.52 0.00 2.12
200 214 7.013942 AGCAATAATCACATCTGTACCGTACTA 59.986 37.037 10.03 0.00 0.00 1.82
201 215 5.983720 GCAATAATCACATCTGTACCGTACT 59.016 40.000 10.03 0.00 0.00 2.73
206 220 5.973565 GCAAAGCAATAATCACATCTGTACC 59.026 40.000 0.00 0.00 0.00 3.34
286 303 9.889128 CTAGGAAACTACTGTACTTACTAGAGT 57.111 37.037 13.99 0.00 43.67 3.24
295 312 8.697292 GGATTTGATCTAGGAAACTACTGTACT 58.303 37.037 0.00 0.00 43.67 2.73
296 313 8.475639 TGGATTTGATCTAGGAAACTACTGTAC 58.524 37.037 0.00 0.00 43.67 2.90
297 314 8.603898 TGGATTTGATCTAGGAAACTACTGTA 57.396 34.615 0.00 0.00 43.67 2.74
298 315 7.496346 TGGATTTGATCTAGGAAACTACTGT 57.504 36.000 0.00 0.00 43.67 3.55
299 316 7.443575 CCATGGATTTGATCTAGGAAACTACTG 59.556 40.741 5.56 0.00 43.67 2.74
300 317 7.512992 CCATGGATTTGATCTAGGAAACTACT 58.487 38.462 5.56 0.00 43.67 2.57
301 318 6.205658 GCCATGGATTTGATCTAGGAAACTAC 59.794 42.308 18.40 0.00 43.67 2.73
302 319 6.126507 TGCCATGGATTTGATCTAGGAAACTA 60.127 38.462 18.40 0.00 43.67 2.24
304 321 4.889409 TGCCATGGATTTGATCTAGGAAAC 59.111 41.667 18.40 0.00 0.00 2.78
423 440 2.472049 GCGCGTCTCTGTTTCTGC 59.528 61.111 8.43 0.00 0.00 4.26
432 450 0.441145 AATTTTACACCGCGCGTCTC 59.559 50.000 29.95 0.00 0.00 3.36
458 478 1.334239 CGACGGATTCTCGATCTGGAC 60.334 57.143 0.00 0.00 44.11 4.02
492 512 2.951475 AAGTCGCCGGAGCCAAAACA 62.951 55.000 5.05 0.00 34.57 2.83
664 684 3.485431 CTTGGAGCGAGTGCAGCG 61.485 66.667 4.63 4.63 46.23 5.18
667 687 3.939939 TGGCTTGGAGCGAGTGCA 61.940 61.111 0.00 0.00 43.62 4.57
719 739 1.890979 CGATGGATGAGCTGGGTGC 60.891 63.158 0.00 0.00 43.29 5.01
802 828 1.262950 TGCGTTTCAGTGTGTGCATAC 59.737 47.619 6.65 6.65 0.00 2.39
820 846 0.179181 CATGTCGGTGAGCATTGTGC 60.179 55.000 0.00 0.00 45.46 4.57
904 930 0.325860 ACCTACCCCGTTATGCTGGA 60.326 55.000 0.00 0.00 0.00 3.86
908 935 2.169978 AGAAGAACCTACCCCGTTATGC 59.830 50.000 0.00 0.00 0.00 3.14
923 950 2.110899 ACTGAGAGGTGGGAGAGAAGAA 59.889 50.000 0.00 0.00 0.00 2.52
986 1022 2.599597 CCATGGAAGCTGGGGAGG 59.400 66.667 5.56 0.00 0.00 4.30
987 1023 2.123982 GCCATGGAAGCTGGGGAG 60.124 66.667 18.40 0.00 34.16 4.30
988 1024 2.614969 AGCCATGGAAGCTGGGGA 60.615 61.111 18.40 0.00 39.69 4.81
989 1025 2.123982 GAGCCATGGAAGCTGGGG 60.124 66.667 18.40 0.00 41.75 4.96
1088 1124 5.115480 ACAAAATCGACCTGTGCAAAAATT 58.885 33.333 0.00 0.00 0.00 1.82
1096 1132 2.286833 ACACGAACAAAATCGACCTGTG 59.713 45.455 3.47 0.00 45.48 3.66
1147 1183 1.203075 TCCACGGCCTGGGTTAAAATT 60.203 47.619 17.89 0.00 41.06 1.82
1428 1471 7.917505 GTGCTCCCACTAAAATTGAAATGATAG 59.082 37.037 0.00 0.00 38.93 2.08
1488 1554 2.224305 ACTCTAGTTTGACCACTGCACC 60.224 50.000 0.00 0.00 0.00 5.01
1491 1557 2.037251 TCCACTCTAGTTTGACCACTGC 59.963 50.000 0.00 0.00 0.00 4.40
1499 1565 4.021016 AGCAGGTACTTCCACTCTAGTTTG 60.021 45.833 0.00 0.00 34.60 2.93
1503 1569 5.916661 TTTAGCAGGTACTTCCACTCTAG 57.083 43.478 0.00 0.00 34.60 2.43
1508 1574 2.740447 CGGTTTTAGCAGGTACTTCCAC 59.260 50.000 0.00 0.00 34.60 4.02
1514 1580 7.517259 CGGTTAAATATCGGTTTTAGCAGGTAC 60.517 40.741 0.00 0.00 0.00 3.34
1553 1623 2.847449 TCAACCTCCCGGGAATGAAATA 59.153 45.455 26.68 3.99 38.76 1.40
1559 1629 1.295020 TCAATCAACCTCCCGGGAAT 58.705 50.000 26.68 13.40 38.76 3.01
1596 1666 1.676967 CAAGCCTCTGGGAGTTGCC 60.677 63.158 0.00 0.00 33.58 4.52
1621 1691 3.230134 TGGTCAAAATCCCTGGTTTCTG 58.770 45.455 0.00 0.00 0.00 3.02
1636 1706 6.350110 GGCTTGCTTACAGAATAATTGGTCAA 60.350 38.462 0.00 0.00 0.00 3.18
1890 1969 9.765795 AGTGTAAAATAGCACTCCTGATAATAC 57.234 33.333 0.00 0.00 41.58 1.89
1971 2051 8.873215 TTCTCATAGTTAAATTAAGCTCCGAG 57.127 34.615 0.00 0.00 0.00 4.63
1972 2052 9.661563 TTTTCTCATAGTTAAATTAAGCTCCGA 57.338 29.630 0.00 0.00 0.00 4.55
2145 2226 2.914695 AACCGCAACTACACTTACCA 57.085 45.000 0.00 0.00 0.00 3.25
2263 2344 5.467063 GGGTTCTGCTATATCTTTAGTGCAC 59.533 44.000 9.40 9.40 0.00 4.57
2310 2391 9.476202 AAAAATAGGCAAGTTGTGAATCTAAAC 57.524 29.630 4.48 0.00 0.00 2.01
2316 2398 5.990996 CACCAAAAATAGGCAAGTTGTGAAT 59.009 36.000 4.48 0.00 0.00 2.57
2362 2444 9.744468 AAAGTTATAAACCAGTTAAAAGCAGTG 57.256 29.630 0.00 0.00 0.00 3.66
2388 2471 0.327924 CCACCTGGACCAACTGCATA 59.672 55.000 0.00 0.00 37.39 3.14
2423 2506 4.443621 GAGCATCTAAGGTAGTTTCACCC 58.556 47.826 0.00 0.00 39.62 4.61
2536 2619 7.347448 CAGTTTTCTTAAGCAAAAAGAATGCC 58.653 34.615 1.70 0.00 44.91 4.40
2649 2732 2.642311 TCCAACAAGAAGAGTATGCCCA 59.358 45.455 0.00 0.00 0.00 5.36
2679 2762 5.005094 CCCATTGAAATTGCAAAGGATGTT 58.995 37.500 20.06 0.00 38.54 2.71
2958 3041 4.356405 AGAGATTGTGTCATGGTTGTGA 57.644 40.909 0.00 0.00 0.00 3.58
3050 3135 4.832266 TGACCCATCTTAACAAAAGCACAT 59.168 37.500 0.00 0.00 0.00 3.21
3104 3189 3.317993 ACCTTCCTGGAATTTTGAACGTG 59.682 43.478 10.03 0.00 39.71 4.49
3351 3485 9.534565 AAATATACCAGCGCATAGTATCAATAG 57.465 33.333 11.47 0.00 0.00 1.73
3598 3737 9.208022 TGATATACATATCAAAAGGAAGCTTCG 57.792 33.333 19.91 6.18 44.36 3.79
3697 3836 9.849607 CGTCATTATGTTGTCAAATATACAGAC 57.150 33.333 0.00 0.00 0.00 3.51
3762 3902 6.869206 AGAGGTAAATAGCTGTTCCACTTA 57.131 37.500 0.00 0.00 33.58 2.24
3952 4093 5.730296 TGTGGGAAAGAAGAACAACAAAA 57.270 34.783 0.00 0.00 0.00 2.44
4114 4261 6.156949 GGCTGAATACCATCATATCCTAGGAA 59.843 42.308 17.30 5.83 0.00 3.36
4137 4284 6.655078 ACCAAATTAGAATATGGACATGGC 57.345 37.500 0.00 0.00 36.75 4.40
4294 6314 1.078848 AAGTCGCATGCTCTCCACC 60.079 57.895 17.13 0.00 0.00 4.61
4345 6365 6.586844 GGTACTTACGAGCAATTCTGGATATC 59.413 42.308 0.00 0.00 0.00 1.63
4351 6371 3.857052 TGGGTACTTACGAGCAATTCTG 58.143 45.455 0.00 0.00 0.00 3.02
4420 6440 4.818863 CATCCATGGCACGCCCCA 62.819 66.667 6.96 0.00 39.65 4.96
4517 6537 8.185003 GCGAATCAGCCTTTTGTTTTAATAAT 57.815 30.769 0.00 0.00 0.00 1.28
4576 6597 2.035066 GCATTACCATGGGAGTGAATGC 59.965 50.000 23.17 23.09 41.47 3.56
4732 6758 4.737054 AGTTGCAAGACAAAAGTTGACTG 58.263 39.130 0.00 0.00 40.82 3.51
4769 6796 2.257207 AGAAGCACACCTGGCTAGTAA 58.743 47.619 0.00 0.00 41.66 2.24
4770 6797 1.938585 AGAAGCACACCTGGCTAGTA 58.061 50.000 0.00 0.00 41.66 1.82
4771 6798 1.059913 AAGAAGCACACCTGGCTAGT 58.940 50.000 0.00 0.00 41.66 2.57
4795 6822 3.558505 CGCACAAAAACTCTGAAGATGG 58.441 45.455 0.00 0.00 0.00 3.51
4815 6842 3.320541 AGCTCTGAAGATGACCTATTCCG 59.679 47.826 0.00 0.00 0.00 4.30
4876 6903 3.615155 GGGTTCTCTGGGAATCTTCAAG 58.385 50.000 0.00 0.00 35.50 3.02
4897 6924 3.373748 GCAAAAACAACAACAAAGGAGGG 59.626 43.478 0.00 0.00 0.00 4.30
4942 6971 4.762251 ACAAACTTAGGTTGATGAAGGAGC 59.238 41.667 17.62 0.00 35.63 4.70
4949 6979 4.037923 ACTGCCAACAAACTTAGGTTGATG 59.962 41.667 17.62 14.78 45.50 3.07
5088 7121 7.066766 CCTTCATCAAGATAACCTTTTCCTCAG 59.933 40.741 0.00 0.00 31.42 3.35
5092 7125 6.183360 CGACCTTCATCAAGATAACCTTTTCC 60.183 42.308 0.00 0.00 31.42 3.13
5093 7126 6.371825 ACGACCTTCATCAAGATAACCTTTTC 59.628 38.462 0.00 0.00 31.42 2.29
5112 7154 2.500098 TCTTTGCTGCCTAATACGACCT 59.500 45.455 0.00 0.00 0.00 3.85
5149 7191 6.127535 CCTTGACACCAAAAGCATATTCAGAT 60.128 38.462 0.00 0.00 0.00 2.90
5166 7208 3.715628 AAAACACAGCATCCTTGACAC 57.284 42.857 0.00 0.00 0.00 3.67
5171 7213 2.041701 AGCCAAAAACACAGCATCCTT 58.958 42.857 0.00 0.00 0.00 3.36
5216 7276 3.565307 AGGTTTCATCTCCTGCAAACAA 58.435 40.909 0.00 0.00 31.79 2.83
5217 7277 3.149196 GAGGTTTCATCTCCTGCAAACA 58.851 45.455 0.00 0.00 33.83 2.83
5218 7278 2.160417 CGAGGTTTCATCTCCTGCAAAC 59.840 50.000 0.00 0.00 33.83 2.93
5219 7279 2.426522 CGAGGTTTCATCTCCTGCAAA 58.573 47.619 0.00 0.00 33.83 3.68
5220 7280 1.339055 CCGAGGTTTCATCTCCTGCAA 60.339 52.381 0.00 0.00 33.83 4.08
5221 7281 0.250234 CCGAGGTTTCATCTCCTGCA 59.750 55.000 0.00 0.00 33.83 4.41
5222 7282 0.462759 CCCGAGGTTTCATCTCCTGC 60.463 60.000 0.00 0.00 33.83 4.85
5223 7283 0.905357 ACCCGAGGTTTCATCTCCTG 59.095 55.000 0.00 0.00 33.83 3.86
5224 7284 1.657804 AACCCGAGGTTTCATCTCCT 58.342 50.000 2.81 0.00 44.33 3.69
5225 7285 3.840124 ATAACCCGAGGTTTCATCTCC 57.160 47.619 12.63 0.00 44.33 3.71
5226 7286 3.312697 GCAATAACCCGAGGTTTCATCTC 59.687 47.826 12.63 0.00 44.33 2.75
5227 7287 3.279434 GCAATAACCCGAGGTTTCATCT 58.721 45.455 12.63 0.00 44.33 2.90
5228 7288 2.031683 CGCAATAACCCGAGGTTTCATC 59.968 50.000 12.63 2.28 44.33 2.92
5229 7289 2.014128 CGCAATAACCCGAGGTTTCAT 58.986 47.619 12.63 0.62 44.33 2.57
5230 7290 1.002201 TCGCAATAACCCGAGGTTTCA 59.998 47.619 12.63 0.00 44.33 2.69
5231 7291 1.729284 TCGCAATAACCCGAGGTTTC 58.271 50.000 12.63 2.01 44.33 2.78
5232 7292 2.093128 AGATCGCAATAACCCGAGGTTT 60.093 45.455 12.63 0.00 44.33 3.27
5234 7294 1.120530 AGATCGCAATAACCCGAGGT 58.879 50.000 0.00 0.00 36.86 3.85
5235 7295 1.867233 CAAGATCGCAATAACCCGAGG 59.133 52.381 0.00 0.00 36.86 4.63
5236 7296 2.550978 ACAAGATCGCAATAACCCGAG 58.449 47.619 0.00 0.00 36.86 4.63
5237 7297 2.684001 ACAAGATCGCAATAACCCGA 57.316 45.000 0.00 0.00 37.91 5.14
5238 7298 3.425404 CAAACAAGATCGCAATAACCCG 58.575 45.455 0.00 0.00 0.00 5.28
5239 7299 3.179048 GCAAACAAGATCGCAATAACCC 58.821 45.455 0.00 0.00 0.00 4.11
5240 7300 3.832276 TGCAAACAAGATCGCAATAACC 58.168 40.909 0.00 0.00 0.00 2.85
5241 7301 3.853671 CCTGCAAACAAGATCGCAATAAC 59.146 43.478 0.00 0.00 33.21 1.89
5242 7302 3.755905 TCCTGCAAACAAGATCGCAATAA 59.244 39.130 0.00 0.00 33.21 1.40
5243 7303 3.342719 TCCTGCAAACAAGATCGCAATA 58.657 40.909 0.00 0.00 33.21 1.90
5244 7304 2.161855 TCCTGCAAACAAGATCGCAAT 58.838 42.857 0.00 0.00 33.21 3.56
5245 7305 1.536766 CTCCTGCAAACAAGATCGCAA 59.463 47.619 0.00 0.00 33.21 4.85
5246 7306 1.159285 CTCCTGCAAACAAGATCGCA 58.841 50.000 0.00 0.00 0.00 5.10
5247 7307 1.442769 TCTCCTGCAAACAAGATCGC 58.557 50.000 0.00 0.00 0.00 4.58
5248 7308 3.264947 TCATCTCCTGCAAACAAGATCG 58.735 45.455 0.00 0.00 0.00 3.69
5249 7309 5.397326 GTTTCATCTCCTGCAAACAAGATC 58.603 41.667 0.00 0.00 31.14 2.75
5250 7310 4.219288 GGTTTCATCTCCTGCAAACAAGAT 59.781 41.667 0.00 0.00 31.79 2.40
5251 7311 3.569701 GGTTTCATCTCCTGCAAACAAGA 59.430 43.478 0.00 0.00 31.79 3.02
5252 7312 3.571401 AGGTTTCATCTCCTGCAAACAAG 59.429 43.478 0.00 0.00 31.79 3.16
5253 7313 3.565307 AGGTTTCATCTCCTGCAAACAA 58.435 40.909 0.00 0.00 31.79 2.83
5254 7314 3.149196 GAGGTTTCATCTCCTGCAAACA 58.851 45.455 0.00 0.00 33.83 2.83
5255 7315 2.160417 CGAGGTTTCATCTCCTGCAAAC 59.840 50.000 0.00 0.00 33.83 2.93
5256 7316 2.426522 CGAGGTTTCATCTCCTGCAAA 58.573 47.619 0.00 0.00 33.83 3.68
5257 7317 1.339055 CCGAGGTTTCATCTCCTGCAA 60.339 52.381 0.00 0.00 33.83 4.08
5258 7318 0.250234 CCGAGGTTTCATCTCCTGCA 59.750 55.000 0.00 0.00 33.83 4.41
5259 7319 0.462759 CCCGAGGTTTCATCTCCTGC 60.463 60.000 0.00 0.00 33.83 4.85
5260 7320 0.905357 ACCCGAGGTTTCATCTCCTG 59.095 55.000 0.00 0.00 33.83 3.86
5261 7321 1.657804 AACCCGAGGTTTCATCTCCT 58.342 50.000 2.81 0.00 44.33 3.69
5262 7322 3.840124 ATAACCCGAGGTTTCATCTCC 57.160 47.619 12.63 0.00 44.33 3.71
5263 7323 3.312697 GCAATAACCCGAGGTTTCATCTC 59.687 47.826 12.63 0.00 44.33 2.75
5264 7324 3.279434 GCAATAACCCGAGGTTTCATCT 58.721 45.455 12.63 0.00 44.33 2.90
5265 7325 2.031683 CGCAATAACCCGAGGTTTCATC 59.968 50.000 12.63 2.28 44.33 2.92
5266 7326 2.014128 CGCAATAACCCGAGGTTTCAT 58.986 47.619 12.63 0.62 44.33 2.57
5267 7327 1.002201 TCGCAATAACCCGAGGTTTCA 59.998 47.619 12.63 0.00 44.33 2.69
5268 7328 1.729284 TCGCAATAACCCGAGGTTTC 58.271 50.000 12.63 2.01 44.33 2.78
5269 7329 2.093128 AGATCGCAATAACCCGAGGTTT 60.093 45.455 12.63 0.00 44.33 3.27
5271 7331 1.120530 AGATCGCAATAACCCGAGGT 58.879 50.000 0.00 0.00 36.86 3.85
5272 7332 1.867233 CAAGATCGCAATAACCCGAGG 59.133 52.381 0.00 0.00 36.86 4.63
5273 7333 2.550978 ACAAGATCGCAATAACCCGAG 58.449 47.619 0.00 0.00 36.86 4.63
5274 7334 2.684001 ACAAGATCGCAATAACCCGA 57.316 45.000 0.00 0.00 37.91 5.14
5275 7335 3.425404 CAAACAAGATCGCAATAACCCG 58.575 45.455 0.00 0.00 0.00 5.28
5276 7336 3.179048 GCAAACAAGATCGCAATAACCC 58.821 45.455 0.00 0.00 0.00 4.11
5277 7337 3.832276 TGCAAACAAGATCGCAATAACC 58.168 40.909 0.00 0.00 0.00 2.85
5278 7338 3.853671 CCTGCAAACAAGATCGCAATAAC 59.146 43.478 0.00 0.00 33.21 1.89
5279 7339 3.755905 TCCTGCAAACAAGATCGCAATAA 59.244 39.130 0.00 0.00 33.21 1.40
5280 7340 3.342719 TCCTGCAAACAAGATCGCAATA 58.657 40.909 0.00 0.00 33.21 1.90
5281 7341 2.161855 TCCTGCAAACAAGATCGCAAT 58.838 42.857 0.00 0.00 33.21 3.56
5282 7342 1.536766 CTCCTGCAAACAAGATCGCAA 59.463 47.619 0.00 0.00 33.21 4.85
5283 7343 1.159285 CTCCTGCAAACAAGATCGCA 58.841 50.000 0.00 0.00 0.00 5.10
5284 7344 1.442769 TCTCCTGCAAACAAGATCGC 58.557 50.000 0.00 0.00 0.00 4.58
5285 7345 3.264947 TCATCTCCTGCAAACAAGATCG 58.735 45.455 0.00 0.00 0.00 3.69
5286 7346 5.579718 CATTCATCTCCTGCAAACAAGATC 58.420 41.667 0.00 0.00 0.00 2.75
5287 7347 4.142227 GCATTCATCTCCTGCAAACAAGAT 60.142 41.667 0.00 0.00 35.96 2.40
5288 7348 3.192001 GCATTCATCTCCTGCAAACAAGA 59.808 43.478 0.00 0.00 35.96 3.02
5289 7349 3.508762 GCATTCATCTCCTGCAAACAAG 58.491 45.455 0.00 0.00 35.96 3.16
5320 7380 2.654877 TCGCAACCCGACTTCTCC 59.345 61.111 0.00 0.00 41.89 3.71
5384 7444 3.386402 CCTGGTGGGTTGTACACATTTTT 59.614 43.478 0.00 0.00 40.54 1.94
5385 7445 2.962421 CCTGGTGGGTTGTACACATTTT 59.038 45.455 0.00 0.00 40.54 1.82
5386 7446 2.175931 TCCTGGTGGGTTGTACACATTT 59.824 45.455 0.00 0.00 40.54 2.32
5387 7447 1.777878 TCCTGGTGGGTTGTACACATT 59.222 47.619 0.00 0.00 40.54 2.71
5388 7448 1.073284 GTCCTGGTGGGTTGTACACAT 59.927 52.381 0.00 0.00 40.54 3.21
5389 7449 0.470766 GTCCTGGTGGGTTGTACACA 59.529 55.000 0.00 0.00 40.54 3.72
5390 7450 0.470766 TGTCCTGGTGGGTTGTACAC 59.529 55.000 0.00 0.00 38.10 2.90
5391 7451 0.762418 CTGTCCTGGTGGGTTGTACA 59.238 55.000 0.00 0.00 36.25 2.90
5392 7452 0.036306 CCTGTCCTGGTGGGTTGTAC 59.964 60.000 0.00 0.00 36.25 2.90
5393 7453 0.104882 TCCTGTCCTGGTGGGTTGTA 60.105 55.000 0.00 0.00 36.25 2.41
5394 7454 0.991355 TTCCTGTCCTGGTGGGTTGT 60.991 55.000 0.00 0.00 36.25 3.32
5395 7455 0.184933 TTTCCTGTCCTGGTGGGTTG 59.815 55.000 0.00 0.00 36.25 3.77
5396 7456 0.478507 CTTTCCTGTCCTGGTGGGTT 59.521 55.000 0.00 0.00 36.25 4.11
5397 7457 0.401395 TCTTTCCTGTCCTGGTGGGT 60.401 55.000 0.00 0.00 36.25 4.51
5398 7458 0.771127 TTCTTTCCTGTCCTGGTGGG 59.229 55.000 0.00 0.00 0.00 4.61
5399 7459 2.158608 AGTTTCTTTCCTGTCCTGGTGG 60.159 50.000 0.00 0.00 0.00 4.61
5400 7460 3.214696 AGTTTCTTTCCTGTCCTGGTG 57.785 47.619 0.00 0.00 0.00 4.17
5401 7461 3.555966 CAAGTTTCTTTCCTGTCCTGGT 58.444 45.455 0.00 0.00 0.00 4.00
5402 7462 2.887152 CCAAGTTTCTTTCCTGTCCTGG 59.113 50.000 0.00 0.00 0.00 4.45
5403 7463 3.820557 TCCAAGTTTCTTTCCTGTCCTG 58.179 45.455 0.00 0.00 0.00 3.86
5404 7464 4.731313 ATCCAAGTTTCTTTCCTGTCCT 57.269 40.909 0.00 0.00 0.00 3.85
5405 7465 8.575649 TTATTATCCAAGTTTCTTTCCTGTCC 57.424 34.615 0.00 0.00 0.00 4.02
5406 7466 9.841880 GTTTATTATCCAAGTTTCTTTCCTGTC 57.158 33.333 0.00 0.00 0.00 3.51
5407 7467 9.588096 AGTTTATTATCCAAGTTTCTTTCCTGT 57.412 29.630 0.00 0.00 0.00 4.00
5409 7469 9.807921 TGAGTTTATTATCCAAGTTTCTTTCCT 57.192 29.630 0.00 0.00 0.00 3.36
5439 7499 0.183492 ACAGCAAGCCCAACTCTCAA 59.817 50.000 0.00 0.00 0.00 3.02
5451 7511 6.201425 ACAAATGCATTTAGTGAAACAGCAAG 59.799 34.615 23.69 9.19 40.34 4.01
5483 7543 0.260816 TGGTACTACTGGGAGCCGAT 59.739 55.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.