Multiple sequence alignment - TraesCS2D01G186000

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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 TraesCS2D01G186000 chr2D 100.000 2498 0 0 1 2498 130986813 130989310 0.000000e+00 4614
1 TraesCS2D01G186000 chr2D 88.165 583 57 7 689 1263 131041860 131042438 0.000000e+00 684
2 TraesCS2D01G186000 chr2D 80.721 721 92 23 1247 1949 131042308 131042999 3.680000e-143 518
3 TraesCS2D01G186000 chr2D 82.333 583 83 7 812 1377 131124270 131124849 2.890000e-134 488
4 TraesCS2D01G186000 chr2D 83.648 477 65 5 858 1321 131134187 131134663 1.060000e-118 436
5 TraesCS2D01G186000 chr2D 83.172 309 29 15 103 389 131041425 131041732 6.850000e-66 261
6 TraesCS2D01G186000 chr2D 88.024 167 20 0 2331 2497 32430569 32430735 5.450000e-47 198
7 TraesCS2D01G186000 chr2D 90.066 151 11 4 1816 1963 131045494 131045643 2.540000e-45 193
8 TraesCS2D01G186000 chr2D 94.059 101 3 3 2220 2318 131047450 131047549 1.550000e-32 150
9 TraesCS2D01G186000 chr2B 89.586 1450 85 25 3 1434 184493690 184495091 0.000000e+00 1781
10 TraesCS2D01G186000 chr2B 84.993 733 63 24 1129 1856 184494867 184495557 0.000000e+00 701
11 TraesCS2D01G186000 chr2B 77.177 1091 180 46 515 1591 184634858 184635893 2.790000e-159 571
12 TraesCS2D01G186000 chr2B 76.923 1092 180 49 515 1591 184637146 184638180 2.810000e-154 555
13 TraesCS2D01G186000 chr2B 76.508 1094 181 53 515 1591 184611944 184612978 6.120000e-146 527
14 TraesCS2D01G186000 chr2B 79.866 745 110 20 851 1591 184572404 184573112 2.220000e-140 508
15 TraesCS2D01G186000 chr2B 89.513 267 28 0 1188 1454 184513658 184513924 3.080000e-89 339
16 TraesCS2D01G186000 chr2B 86.567 268 36 0 1185 1452 184572679 184572946 1.880000e-76 296
17 TraesCS2D01G186000 chr2B 86.567 268 36 0 1185 1452 184612546 184612813 1.880000e-76 296
18 TraesCS2D01G186000 chr2B 86.567 268 36 0 1185 1452 184635460 184635727 1.880000e-76 296
19 TraesCS2D01G186000 chr2B 85.448 268 38 1 1185 1452 184637748 184638014 6.800000e-71 278
20 TraesCS2D01G186000 chr2B 84.116 277 19 6 2044 2318 184496170 184496423 6.900000e-61 244
21 TraesCS2D01G186000 chr2B 89.474 95 8 2 1077 1170 184578917 184579010 4.360000e-23 119
22 TraesCS2D01G186000 chr2A 87.927 1433 89 34 3 1421 137128263 137129625 0.000000e+00 1611
23 TraesCS2D01G186000 chr2A 81.055 1156 123 50 1186 2303 137129357 137130454 0.000000e+00 833
24 TraesCS2D01G186000 chr2A 83.686 472 65 8 1186 1652 137212913 137213377 3.820000e-118 435
25 TraesCS2D01G186000 chrUn 86.792 265 35 0 1188 1452 476372002 476371738 1.880000e-76 296
26 TraesCS2D01G186000 chrUn 90.385 208 20 0 1247 1454 17496812 17496605 8.800000e-70 274
27 TraesCS2D01G186000 chrUn 90.385 208 20 0 1247 1454 302453936 302454143 8.800000e-70 274
28 TraesCS2D01G186000 chr6D 88.953 172 19 0 2326 2497 335056626 335056455 1.950000e-51 213
29 TraesCS2D01G186000 chr3B 89.286 168 17 1 2330 2497 24814385 24814219 2.520000e-50 209
30 TraesCS2D01G186000 chr3B 86.875 160 20 1 2339 2498 93954257 93954415 7.100000e-41 178
31 TraesCS2D01G186000 chr3B 86.875 160 20 1 2339 2498 93977425 93977583 7.100000e-41 178
32 TraesCS2D01G186000 chr1D 86.310 168 23 0 2327 2494 489963509 489963676 1.530000e-42 183
33 TraesCS2D01G186000 chr4B 86.145 166 22 1 2326 2491 168163114 168162950 7.100000e-41 178
34 TraesCS2D01G186000 chr5A 85.057 174 25 1 2325 2498 636578568 636578396 2.550000e-40 176
35 TraesCS2D01G186000 chr7A 85.119 168 25 0 2331 2498 303479667 303479834 3.300000e-39 172


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 TraesCS2D01G186000 chr2D 130986813 130989310 2497 False 4614.000000 4614 100.000000 1 2498 1 chr2D.!!$F2 2497
1 TraesCS2D01G186000 chr2D 131124270 131124849 579 False 488.000000 488 82.333000 812 1377 1 chr2D.!!$F3 565
2 TraesCS2D01G186000 chr2D 131041425 131047549 6124 False 361.200000 684 87.236600 103 2318 5 chr2D.!!$F5 2215
3 TraesCS2D01G186000 chr2B 184493690 184496423 2733 False 908.666667 1781 86.231667 3 2318 3 chr2B.!!$F3 2315
4 TraesCS2D01G186000 chr2B 184634858 184638180 3322 False 425.000000 571 81.528750 515 1591 4 chr2B.!!$F6 1076
5 TraesCS2D01G186000 chr2B 184611944 184612978 1034 False 411.500000 527 81.537500 515 1591 2 chr2B.!!$F5 1076
6 TraesCS2D01G186000 chr2B 184572404 184573112 708 False 402.000000 508 83.216500 851 1591 2 chr2B.!!$F4 740
7 TraesCS2D01G186000 chr2A 137128263 137130454 2191 False 1222.000000 1611 84.491000 3 2303 2 chr2A.!!$F2 2300

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
950 1029 0.387202 CCTGCTATCTCTCCCACACG 59.613 60.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 9551 0.107897 TGGTTCGGGTGATGAATCCG 60.108 55.0 0.0 0.0 44.59 4.18 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
32 33 2.807676 ACCTTTTGCATACTTCTGGGG 58.192 47.619 0.00 0.00 0.00 4.96
54 56 4.142227 GGCAAATGAGATGCTCAACAGAAT 60.142 41.667 0.78 0.00 44.04 2.40
79 81 3.206150 CTGGATGTAGGTTTTATGCGCT 58.794 45.455 9.73 0.00 0.00 5.92
94 96 1.937546 GCGCTGATTGGTGGAAAGGG 61.938 60.000 0.00 0.00 0.00 3.95
178 181 3.580458 CGTGAGAAGATTCCCTCCCATAT 59.420 47.826 0.00 0.00 0.00 1.78
179 182 4.562347 CGTGAGAAGATTCCCTCCCATATG 60.562 50.000 0.00 0.00 0.00 1.78
180 183 4.349342 GTGAGAAGATTCCCTCCCATATGT 59.651 45.833 1.24 0.00 0.00 2.29
225 248 8.647226 GTTTTAACCATCTCAATTTTGAATCGG 58.353 33.333 0.00 0.00 36.64 4.18
351 377 5.989477 TCCAGACTATATTGGTTGACAAGG 58.011 41.667 0.00 0.00 43.48 3.61
372 399 3.008485 GGCATCCCAAAAACCAAACCATA 59.992 43.478 0.00 0.00 0.00 2.74
400 428 1.290009 GTTGGAAGCATGTGCACCC 59.710 57.895 15.69 7.53 45.16 4.61
656 686 8.328146 GTTTTTGTTTTACTTCAGCATTCCTTC 58.672 33.333 0.00 0.00 0.00 3.46
698 756 5.359292 TGTGTCATAAGATCTCTCTCACAGG 59.641 44.000 0.00 0.00 0.00 4.00
747 805 2.359975 GTACCTGCCCTGCACACC 60.360 66.667 0.00 0.00 33.79 4.16
854 928 2.983136 CTCTGAAACGCAGTGTAGACAG 59.017 50.000 0.00 8.09 45.00 3.51
859 933 1.174783 ACGCAGTGTAGACAGGTAGG 58.825 55.000 0.00 0.00 42.51 3.18
862 936 1.204941 GCAGTGTAGACAGGTAGGTGG 59.795 57.143 0.00 0.00 0.00 4.61
950 1029 0.387202 CCTGCTATCTCTCCCACACG 59.613 60.000 0.00 0.00 0.00 4.49
951 1030 0.387202 CTGCTATCTCTCCCACACGG 59.613 60.000 0.00 0.00 0.00 4.94
953 1032 1.742768 CTATCTCTCCCACACGGCC 59.257 63.158 0.00 0.00 0.00 6.13
954 1033 1.001120 TATCTCTCCCACACGGCCA 59.999 57.895 2.24 0.00 0.00 5.36
955 1034 1.043116 TATCTCTCCCACACGGCCAG 61.043 60.000 2.24 0.00 0.00 4.85
973 1052 1.598130 GACTCAAACCGCACTGCCT 60.598 57.895 0.00 0.00 0.00 4.75
1024 1118 2.858646 GCTTTGAAAAACTCTGCCGTCC 60.859 50.000 0.00 0.00 0.00 4.79
1030 1124 0.832135 AAACTCTGCCGTCCTCCTCA 60.832 55.000 0.00 0.00 0.00 3.86
1058 1152 2.838736 TCTTCTCTCTTGTGTTGCCAC 58.161 47.619 0.00 0.00 42.19 5.01
1080 1174 2.169789 CAGTGCGGCGAGAATCCTG 61.170 63.158 12.98 2.21 0.00 3.86
1134 1228 4.021925 GAGGTGCCACCGCTTCCT 62.022 66.667 10.66 3.49 44.90 3.36
1155 1249 0.763035 AGGTAGAACTGCCACCGTTT 59.237 50.000 11.14 0.00 37.85 3.60
1170 1264 0.320073 CGTTTCCGGAAGTGCACCTA 60.320 55.000 17.97 0.00 0.00 3.08
1173 1267 2.125673 CCGGAAGTGCACCTACCG 60.126 66.667 28.02 28.02 42.67 4.02
1240 1334 0.035439 GCACTTGCCACCTAAGCCTA 60.035 55.000 0.00 0.00 34.31 3.93
1258 1409 1.073923 CTAAGTTGCCCAAGGTGGAGT 59.926 52.381 0.00 0.00 40.96 3.85
1263 1414 2.846532 CCCAAGGTGGAGTTGCCT 59.153 61.111 0.00 0.00 40.96 4.75
1272 1423 4.452733 GAGTTGCCTCCGGTCCCG 62.453 72.222 0.00 0.00 39.44 5.14
1282 1433 4.308458 CGGTCCCGGAAGTGCACA 62.308 66.667 21.04 0.00 35.56 4.57
1321 1472 2.281761 CCAAAGTGGAGCTGCCGT 60.282 61.111 1.53 0.00 40.96 5.68
1324 1475 3.883744 AAAGTGGAGCTGCCGTCGG 62.884 63.158 6.99 6.99 40.66 4.79
1335 3716 2.044650 CCGTCGGTCCCTGAGGTA 60.045 66.667 2.08 0.00 0.00 3.08
1368 3749 3.074281 CCGGAGTTGCCCAAGGTA 58.926 61.111 0.00 0.00 0.00 3.08
1380 3761 0.036732 CCAAGGTAGAGCTGCCAACA 59.963 55.000 7.37 0.00 37.85 3.33
1470 3884 0.250727 CCACTGTTCCCGTGTTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
1471 3885 0.874390 CACTGTTCCCGTGTTCCATG 59.126 55.000 0.00 0.00 0.00 3.66
1480 3894 1.677552 GTGTTCCATGTCCCGGAGT 59.322 57.895 0.73 0.00 33.01 3.85
1504 3918 1.937546 GCCCAAGCCGTGAGAATTGG 61.938 60.000 0.00 0.00 42.54 3.16
1528 3942 7.123397 TGGCTTATCAATATTGTTGCCTTGTTA 59.877 33.333 26.60 14.58 39.77 2.41
1591 4007 7.172361 TGTTGTGTCGATGATCTGATTGTTTAA 59.828 33.333 0.00 0.00 0.00 1.52
1606 4022 7.271511 TGATTGTTTAATTGTGGTTTTCAGCT 58.728 30.769 0.00 0.00 0.00 4.24
1681 4099 6.361433 TGTTCTCACAATTACCCTTTTCTCA 58.639 36.000 0.00 0.00 0.00 3.27
1695 4113 2.604046 TTCTCATAAGAGCCCTTCGC 57.396 50.000 0.00 0.00 41.81 4.70
1735 4157 2.825205 ACAACAATTTCACAGCAAGCC 58.175 42.857 0.00 0.00 0.00 4.35
1750 4172 3.146618 CAAGCCTTGATTGCATCTGTC 57.853 47.619 0.00 0.00 0.00 3.51
1752 4174 3.014304 AGCCTTGATTGCATCTGTCAT 57.986 42.857 0.00 0.00 0.00 3.06
1753 4175 3.362706 AGCCTTGATTGCATCTGTCATT 58.637 40.909 0.00 0.00 0.00 2.57
1754 4176 3.767673 AGCCTTGATTGCATCTGTCATTT 59.232 39.130 0.00 0.00 0.00 2.32
1755 4177 4.222145 AGCCTTGATTGCATCTGTCATTTT 59.778 37.500 0.00 0.00 0.00 1.82
1757 4179 5.063060 GCCTTGATTGCATCTGTCATTTTTC 59.937 40.000 0.00 0.00 0.00 2.29
1758 4180 5.579511 CCTTGATTGCATCTGTCATTTTTCC 59.420 40.000 0.00 0.00 0.00 3.13
1759 4181 5.725325 TGATTGCATCTGTCATTTTTCCA 57.275 34.783 0.00 0.00 0.00 3.53
1760 4182 6.099159 TGATTGCATCTGTCATTTTTCCAA 57.901 33.333 0.00 0.00 0.00 3.53
1761 4183 5.927689 TGATTGCATCTGTCATTTTTCCAAC 59.072 36.000 0.00 0.00 0.00 3.77
1762 4184 5.534207 TTGCATCTGTCATTTTTCCAACT 57.466 34.783 0.00 0.00 0.00 3.16
1763 4185 6.647334 TTGCATCTGTCATTTTTCCAACTA 57.353 33.333 0.00 0.00 0.00 2.24
1764 4186 6.012658 TGCATCTGTCATTTTTCCAACTAC 57.987 37.500 0.00 0.00 0.00 2.73
1765 4187 5.534278 TGCATCTGTCATTTTTCCAACTACA 59.466 36.000 0.00 0.00 0.00 2.74
1766 4188 6.040278 TGCATCTGTCATTTTTCCAACTACAA 59.960 34.615 0.00 0.00 0.00 2.41
1767 4189 6.922957 GCATCTGTCATTTTTCCAACTACAAA 59.077 34.615 0.00 0.00 0.00 2.83
1768 4190 7.437862 GCATCTGTCATTTTTCCAACTACAAAA 59.562 33.333 0.00 0.00 0.00 2.44
1769 4191 8.755018 CATCTGTCATTTTTCCAACTACAAAAC 58.245 33.333 0.00 0.00 0.00 2.43
1770 4192 7.831753 TCTGTCATTTTTCCAACTACAAAACA 58.168 30.769 0.00 0.00 0.00 2.83
1771 4193 8.474025 TCTGTCATTTTTCCAACTACAAAACAT 58.526 29.630 0.00 0.00 0.00 2.71
1778 4200 6.969993 TTCCAACTACAAAACATAAAGCCT 57.030 33.333 0.00 0.00 0.00 4.58
1820 4242 4.638304 TCAACCTGTCCTAGCTTTAACAC 58.362 43.478 0.00 0.00 0.00 3.32
1847 4270 7.598278 TGATATTTACAACCCACACATTGTTC 58.402 34.615 0.00 0.00 39.67 3.18
1856 4279 5.197451 ACCCACACATTGTTCTTGAGTTTA 58.803 37.500 0.00 0.00 0.00 2.01
1858 4281 5.204833 CCACACATTGTTCTTGAGTTTACG 58.795 41.667 0.00 0.00 0.00 3.18
1859 4282 4.670621 CACACATTGTTCTTGAGTTTACGC 59.329 41.667 0.00 0.00 0.00 4.42
1892 7429 1.599047 CGGATGAGCAAGAGGGTGT 59.401 57.895 0.00 0.00 0.00 4.16
1930 7468 0.465460 TCACACTGTTCTTGGGTGCC 60.465 55.000 0.00 0.00 34.70 5.01
1935 7473 2.067932 CTGTTCTTGGGTGCCTGGGA 62.068 60.000 0.00 0.00 0.00 4.37
1952 7490 3.309506 AGTGGCAGCTCACTCGCT 61.310 61.111 9.94 0.00 43.82 4.93
1957 7495 1.510480 GGCAGCTCACTCGCTTGTTT 61.510 55.000 0.00 0.00 38.41 2.83
1969 7507 1.629013 GCTTGTTTTATGGCCGCTTC 58.371 50.000 0.00 0.00 0.00 3.86
1970 7508 1.202348 GCTTGTTTTATGGCCGCTTCT 59.798 47.619 0.00 0.00 0.00 2.85
1972 7510 3.860754 GCTTGTTTTATGGCCGCTTCTTT 60.861 43.478 0.00 0.00 0.00 2.52
1973 7511 3.569250 TGTTTTATGGCCGCTTCTTTC 57.431 42.857 0.00 0.00 0.00 2.62
1974 7512 2.095466 TGTTTTATGGCCGCTTCTTTCG 60.095 45.455 0.00 0.00 0.00 3.46
1976 7514 1.816074 TTATGGCCGCTTCTTTCGTT 58.184 45.000 0.00 0.00 0.00 3.85
1977 7515 1.083489 TATGGCCGCTTCTTTCGTTG 58.917 50.000 0.00 0.00 0.00 4.10
1978 7516 0.605319 ATGGCCGCTTCTTTCGTTGA 60.605 50.000 0.00 0.00 0.00 3.18
1979 7517 1.206831 GGCCGCTTCTTTCGTTGAC 59.793 57.895 0.00 0.00 0.00 3.18
1982 7520 0.790814 CCGCTTCTTTCGTTGACCTC 59.209 55.000 0.00 0.00 0.00 3.85
1983 7521 1.497991 CGCTTCTTTCGTTGACCTCA 58.502 50.000 0.00 0.00 0.00 3.86
1987 7546 2.814280 TCTTTCGTTGACCTCACCTC 57.186 50.000 0.00 0.00 0.00 3.85
1998 7557 4.232091 TGACCTCACCTCCTTTTAACTCT 58.768 43.478 0.00 0.00 0.00 3.24
1999 7558 4.040461 TGACCTCACCTCCTTTTAACTCTG 59.960 45.833 0.00 0.00 0.00 3.35
2005 7564 5.306937 TCACCTCCTTTTAACTCTGATGTCA 59.693 40.000 0.00 0.00 0.00 3.58
2006 7565 6.013379 TCACCTCCTTTTAACTCTGATGTCAT 60.013 38.462 0.00 0.00 0.00 3.06
2008 7567 7.824289 CACCTCCTTTTAACTCTGATGTCATAA 59.176 37.037 0.00 0.00 0.00 1.90
2032 7591 3.857157 TGAAAGGAAGTAGCCAACTGT 57.143 42.857 0.00 0.00 38.88 3.55
2033 7592 3.476552 TGAAAGGAAGTAGCCAACTGTG 58.523 45.455 0.00 0.00 38.88 3.66
2034 7593 3.135712 TGAAAGGAAGTAGCCAACTGTGA 59.864 43.478 0.00 0.00 38.88 3.58
2037 7596 5.499004 AAGGAAGTAGCCAACTGTGAATA 57.501 39.130 0.00 0.00 38.88 1.75
2038 7597 5.700402 AGGAAGTAGCCAACTGTGAATAT 57.300 39.130 0.00 0.00 38.88 1.28
2039 7598 6.808321 AGGAAGTAGCCAACTGTGAATATA 57.192 37.500 0.00 0.00 38.88 0.86
2041 7600 7.220030 AGGAAGTAGCCAACTGTGAATATATG 58.780 38.462 0.00 0.00 38.88 1.78
2042 7601 7.071196 AGGAAGTAGCCAACTGTGAATATATGA 59.929 37.037 0.00 0.00 38.88 2.15
2065 7777 0.032130 GCATCGAGCGAATGGAGGTA 59.968 55.000 0.00 0.00 0.00 3.08
2083 7795 1.827969 GTAGCAGTGATCTGGGTGTCT 59.172 52.381 0.00 0.00 41.57 3.41
2088 7800 3.447586 GCAGTGATCTGGGTGTCTAAGTA 59.552 47.826 0.00 0.00 41.57 2.24
2096 7808 4.082408 TCTGGGTGTCTAAGTATCAACACG 60.082 45.833 0.00 0.00 42.24 4.49
2097 7809 3.056393 TGGGTGTCTAAGTATCAACACGG 60.056 47.826 0.00 0.00 42.24 4.94
2098 7810 3.518590 GGTGTCTAAGTATCAACACGGG 58.481 50.000 0.00 0.00 42.24 5.28
2118 7830 1.449246 GCCGCTGATGAAGAGTGCT 60.449 57.895 0.00 0.00 0.00 4.40
2159 7872 1.616159 ACTCCGGATTTTGGTGTTGG 58.384 50.000 3.57 0.00 29.28 3.77
2160 7873 0.887933 CTCCGGATTTTGGTGTTGGG 59.112 55.000 3.57 0.00 0.00 4.12
2166 9284 1.684450 GATTTTGGTGTTGGGTTCGGT 59.316 47.619 0.00 0.00 0.00 4.69
2170 9288 3.292159 GTGTTGGGTTCGGTGGGC 61.292 66.667 0.00 0.00 0.00 5.36
2175 9293 1.182385 TTGGGTTCGGTGGGCAAATC 61.182 55.000 0.00 0.00 0.00 2.17
2199 9317 6.493115 TCATGTCCCAATTTGTTCTTGTGTAT 59.507 34.615 0.00 0.00 0.00 2.29
2295 9417 4.502604 GCTCAACTCTTAAGTACCACACCA 60.503 45.833 1.63 0.00 33.48 4.17
2324 9446 5.890110 CGAACACATCGCTAGTGATATTT 57.110 39.130 18.16 11.26 45.89 1.40
2325 9447 5.894952 CGAACACATCGCTAGTGATATTTC 58.105 41.667 18.16 17.16 45.89 2.17
2326 9448 5.386424 CGAACACATCGCTAGTGATATTTCG 60.386 44.000 25.62 25.62 45.89 3.46
2327 9449 4.299155 ACACATCGCTAGTGATATTTCGG 58.701 43.478 18.16 7.83 40.16 4.30
2328 9450 4.037565 ACACATCGCTAGTGATATTTCGGA 59.962 41.667 18.16 0.00 40.16 4.55
2329 9451 5.164233 CACATCGCTAGTGATATTTCGGAT 58.836 41.667 18.16 0.00 39.30 4.18
2330 9452 5.061435 CACATCGCTAGTGATATTTCGGATG 59.939 44.000 18.16 7.26 39.30 3.51
2331 9453 3.575630 TCGCTAGTGATATTTCGGATGC 58.424 45.455 0.70 0.00 0.00 3.91
2332 9454 2.342651 CGCTAGTGATATTTCGGATGCG 59.657 50.000 0.00 0.00 0.00 4.73
2333 9455 2.668457 GCTAGTGATATTTCGGATGCGG 59.332 50.000 6.82 0.00 0.00 5.69
2334 9456 1.512926 AGTGATATTTCGGATGCGGC 58.487 50.000 6.82 0.00 0.00 6.53
2335 9457 0.163788 GTGATATTTCGGATGCGGCG 59.836 55.000 6.82 0.51 0.00 6.46
2336 9458 0.948623 TGATATTTCGGATGCGGCGG 60.949 55.000 9.78 0.00 0.00 6.13
2337 9459 0.669318 GATATTTCGGATGCGGCGGA 60.669 55.000 9.78 6.17 0.00 5.54
2338 9460 0.949105 ATATTTCGGATGCGGCGGAC 60.949 55.000 9.78 0.15 0.00 4.79
2339 9461 2.299503 TATTTCGGATGCGGCGGACA 62.300 55.000 9.78 0.00 0.00 4.02
2340 9462 2.940890 ATTTCGGATGCGGCGGACAT 62.941 55.000 9.78 4.02 0.00 3.06
2341 9463 3.673956 TTCGGATGCGGCGGACATT 62.674 57.895 9.78 0.00 0.00 2.71
2342 9464 2.279851 CGGATGCGGCGGACATTA 60.280 61.111 9.78 0.00 0.00 1.90
2343 9465 2.310233 CGGATGCGGCGGACATTAG 61.310 63.158 9.78 0.00 0.00 1.73
2344 9466 1.069090 GGATGCGGCGGACATTAGA 59.931 57.895 9.78 0.00 0.00 2.10
2345 9467 1.222115 GGATGCGGCGGACATTAGAC 61.222 60.000 9.78 0.00 0.00 2.59
2346 9468 0.529773 GATGCGGCGGACATTAGACA 60.530 55.000 9.78 0.00 0.00 3.41
2347 9469 0.530650 ATGCGGCGGACATTAGACAG 60.531 55.000 9.78 0.00 0.00 3.51
2348 9470 1.153628 GCGGCGGACATTAGACAGT 60.154 57.895 9.78 0.00 0.00 3.55
2349 9471 0.739813 GCGGCGGACATTAGACAGTT 60.740 55.000 9.78 0.00 0.00 3.16
2350 9472 1.278238 CGGCGGACATTAGACAGTTC 58.722 55.000 0.00 0.00 0.00 3.01
2351 9473 1.653151 GGCGGACATTAGACAGTTCC 58.347 55.000 0.00 0.00 0.00 3.62
2352 9474 1.278238 GCGGACATTAGACAGTTCCG 58.722 55.000 4.94 4.94 41.58 4.30
2353 9475 1.278238 CGGACATTAGACAGTTCCGC 58.722 55.000 0.00 0.00 32.53 5.54
2354 9476 1.653151 GGACATTAGACAGTTCCGCC 58.347 55.000 0.00 0.00 0.00 6.13
2355 9477 1.653151 GACATTAGACAGTTCCGCCC 58.347 55.000 0.00 0.00 0.00 6.13
2356 9478 1.207329 GACATTAGACAGTTCCGCCCT 59.793 52.381 0.00 0.00 0.00 5.19
2357 9479 2.429610 GACATTAGACAGTTCCGCCCTA 59.570 50.000 0.00 0.00 0.00 3.53
2358 9480 3.039011 ACATTAGACAGTTCCGCCCTAT 58.961 45.455 0.00 0.00 0.00 2.57
2359 9481 3.069729 ACATTAGACAGTTCCGCCCTATC 59.930 47.826 0.00 0.00 0.00 2.08
2360 9482 2.447408 TAGACAGTTCCGCCCTATCA 57.553 50.000 0.00 0.00 0.00 2.15
2361 9483 0.824759 AGACAGTTCCGCCCTATCAC 59.175 55.000 0.00 0.00 0.00 3.06
2362 9484 0.535335 GACAGTTCCGCCCTATCACA 59.465 55.000 0.00 0.00 0.00 3.58
2363 9485 0.537188 ACAGTTCCGCCCTATCACAG 59.463 55.000 0.00 0.00 0.00 3.66
2364 9486 0.537188 CAGTTCCGCCCTATCACAGT 59.463 55.000 0.00 0.00 0.00 3.55
2365 9487 0.824759 AGTTCCGCCCTATCACAGTC 59.175 55.000 0.00 0.00 0.00 3.51
2366 9488 0.179081 GTTCCGCCCTATCACAGTCC 60.179 60.000 0.00 0.00 0.00 3.85
2367 9489 0.325296 TTCCGCCCTATCACAGTCCT 60.325 55.000 0.00 0.00 0.00 3.85
2368 9490 0.755698 TCCGCCCTATCACAGTCCTC 60.756 60.000 0.00 0.00 0.00 3.71
2369 9491 0.757188 CCGCCCTATCACAGTCCTCT 60.757 60.000 0.00 0.00 0.00 3.69
2370 9492 1.478837 CCGCCCTATCACAGTCCTCTA 60.479 57.143 0.00 0.00 0.00 2.43
2371 9493 2.520069 CGCCCTATCACAGTCCTCTAT 58.480 52.381 0.00 0.00 0.00 1.98
2372 9494 2.230025 CGCCCTATCACAGTCCTCTATG 59.770 54.545 0.00 0.00 0.00 2.23
2373 9495 3.235200 GCCCTATCACAGTCCTCTATGT 58.765 50.000 0.00 0.00 0.00 2.29
2374 9496 3.006323 GCCCTATCACAGTCCTCTATGTG 59.994 52.174 0.00 0.00 46.52 3.21
2383 9505 6.090483 ACAGTCCTCTATGTGATATTTCGG 57.910 41.667 0.00 0.00 0.00 4.30
2384 9506 5.833667 ACAGTCCTCTATGTGATATTTCGGA 59.166 40.000 0.00 0.00 0.00 4.55
2385 9507 6.495181 ACAGTCCTCTATGTGATATTTCGGAT 59.505 38.462 0.00 0.00 0.00 4.18
2386 9508 7.032580 CAGTCCTCTATGTGATATTTCGGATC 58.967 42.308 0.00 0.00 0.00 3.36
2387 9509 6.153680 AGTCCTCTATGTGATATTTCGGATCC 59.846 42.308 0.00 0.00 0.00 3.36
2388 9510 6.153680 GTCCTCTATGTGATATTTCGGATCCT 59.846 42.308 10.75 0.00 0.00 3.24
2389 9511 7.339721 GTCCTCTATGTGATATTTCGGATCCTA 59.660 40.741 10.75 0.00 0.00 2.94
2390 9512 7.558081 TCCTCTATGTGATATTTCGGATCCTAG 59.442 40.741 10.75 0.14 0.00 3.02
2391 9513 7.101652 TCTATGTGATATTTCGGATCCTAGC 57.898 40.000 10.75 0.00 0.00 3.42
2392 9514 4.174411 TGTGATATTTCGGATCCTAGCG 57.826 45.455 10.75 0.00 0.00 4.26
2393 9515 3.824443 TGTGATATTTCGGATCCTAGCGA 59.176 43.478 10.75 0.00 0.00 4.93
2394 9516 4.279922 TGTGATATTTCGGATCCTAGCGAA 59.720 41.667 10.75 5.30 0.00 4.70
2395 9517 5.221362 TGTGATATTTCGGATCCTAGCGAAA 60.221 40.000 16.14 16.14 35.33 3.46
2396 9518 5.346281 GTGATATTTCGGATCCTAGCGAAAG 59.654 44.000 17.91 0.00 34.54 2.62
2397 9519 2.596904 TTTCGGATCCTAGCGAAAGG 57.403 50.000 10.75 0.00 38.06 3.11
2398 9520 0.750850 TTCGGATCCTAGCGAAAGGG 59.249 55.000 10.75 0.00 37.24 3.95
2399 9521 0.396695 TCGGATCCTAGCGAAAGGGT 60.397 55.000 10.75 0.00 37.24 4.34
2400 9522 1.133699 TCGGATCCTAGCGAAAGGGTA 60.134 52.381 10.75 0.00 37.24 3.69
2401 9523 1.000496 CGGATCCTAGCGAAAGGGTAC 60.000 57.143 10.75 0.00 37.24 3.34
2402 9524 1.000496 GGATCCTAGCGAAAGGGTACG 60.000 57.143 3.84 0.00 37.24 3.67
2409 9531 3.340727 CGAAAGGGTACGCCAGTAG 57.659 57.895 6.27 0.00 36.17 2.57
2410 9532 0.179119 CGAAAGGGTACGCCAGTAGG 60.179 60.000 6.27 0.00 36.17 3.18
2411 9533 0.177373 GAAAGGGTACGCCAGTAGGG 59.823 60.000 6.27 0.00 40.85 3.53
2420 9542 3.316029 CCAGTAGGGCGGCCTTAA 58.684 61.111 37.40 17.26 0.00 1.85
2421 9543 1.837090 CCAGTAGGGCGGCCTTAAT 59.163 57.895 37.40 19.25 0.00 1.40
2422 9544 0.250338 CCAGTAGGGCGGCCTTAATC 60.250 60.000 37.40 22.20 0.00 1.75
2423 9545 0.600255 CAGTAGGGCGGCCTTAATCG 60.600 60.000 37.40 16.28 0.00 3.34
2442 9564 2.515901 CCCCCGGATTCATCACCC 59.484 66.667 0.73 0.00 0.00 4.61
2443 9565 2.111043 CCCCGGATTCATCACCCG 59.889 66.667 0.73 0.00 42.64 5.28
2444 9566 2.439960 CCCCGGATTCATCACCCGA 61.440 63.158 0.73 0.00 45.58 5.14
2445 9567 1.524961 CCCGGATTCATCACCCGAA 59.475 57.895 0.73 0.00 45.58 4.30
2446 9568 0.814010 CCCGGATTCATCACCCGAAC 60.814 60.000 0.73 0.00 45.58 3.95
2447 9569 0.814010 CCGGATTCATCACCCGAACC 60.814 60.000 0.00 0.00 45.58 3.62
2448 9570 0.107897 CGGATTCATCACCCGAACCA 60.108 55.000 0.00 0.00 45.58 3.67
2449 9571 1.677518 CGGATTCATCACCCGAACCAA 60.678 52.381 0.00 0.00 45.58 3.67
2450 9572 2.654863 GGATTCATCACCCGAACCAAT 58.345 47.619 0.00 0.00 0.00 3.16
2451 9573 2.618709 GGATTCATCACCCGAACCAATC 59.381 50.000 0.00 0.00 0.00 2.67
2461 9583 1.794222 GAACCAATCGGCCTTCACG 59.206 57.895 0.00 0.00 34.57 4.35
2462 9584 0.672401 GAACCAATCGGCCTTCACGA 60.672 55.000 0.00 0.00 45.19 4.35
2463 9585 0.250553 AACCAATCGGCCTTCACGAA 60.251 50.000 0.00 0.00 44.20 3.85
2464 9586 0.250553 ACCAATCGGCCTTCACGAAA 60.251 50.000 0.00 0.00 44.20 3.46
2465 9587 0.447801 CCAATCGGCCTTCACGAAAG 59.552 55.000 0.00 0.00 44.20 2.62
2480 9602 6.995511 TCACGAAAGGAAGGTATATTTTGG 57.004 37.500 0.00 0.00 0.00 3.28
2481 9603 6.713276 TCACGAAAGGAAGGTATATTTTGGA 58.287 36.000 0.00 0.00 0.00 3.53
2482 9604 7.343357 TCACGAAAGGAAGGTATATTTTGGAT 58.657 34.615 0.00 0.00 0.00 3.41
2483 9605 7.282224 TCACGAAAGGAAGGTATATTTTGGATG 59.718 37.037 0.00 0.00 0.00 3.51
2484 9606 6.546034 ACGAAAGGAAGGTATATTTTGGATGG 59.454 38.462 0.00 0.00 0.00 3.51
2485 9607 6.016276 CGAAAGGAAGGTATATTTTGGATGGG 60.016 42.308 0.00 0.00 0.00 4.00
2486 9608 6.606241 AAGGAAGGTATATTTTGGATGGGA 57.394 37.500 0.00 0.00 0.00 4.37
2487 9609 6.803587 AGGAAGGTATATTTTGGATGGGAT 57.196 37.500 0.00 0.00 0.00 3.85
2488 9610 6.794534 AGGAAGGTATATTTTGGATGGGATC 58.205 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.505258 AGTATGCAAAAGGTAAACCACAAATT 58.495 30.769 1.26 0.00 38.89 1.82
1 2 7.061566 AGTATGCAAAAGGTAAACCACAAAT 57.938 32.000 1.26 0.00 38.89 2.32
3 4 6.322712 AGAAGTATGCAAAAGGTAAACCACAA 59.677 34.615 1.26 0.00 38.89 3.33
6 7 5.242838 CCAGAAGTATGCAAAAGGTAAACCA 59.757 40.000 1.26 0.00 38.89 3.67
7 8 5.336451 CCCAGAAGTATGCAAAAGGTAAACC 60.336 44.000 0.00 0.00 0.00 3.27
8 9 5.336451 CCCCAGAAGTATGCAAAAGGTAAAC 60.336 44.000 0.00 0.00 0.00 2.01
9 10 4.770010 CCCCAGAAGTATGCAAAAGGTAAA 59.230 41.667 0.00 0.00 0.00 2.01
15 16 2.300956 TGCCCCAGAAGTATGCAAAA 57.699 45.000 0.00 0.00 0.00 2.44
32 33 4.430137 TTCTGTTGAGCATCTCATTTGC 57.570 40.909 0.00 0.00 40.39 3.68
54 56 4.634004 CGCATAAAACCTACATCCAGTGAA 59.366 41.667 0.00 0.00 0.00 3.18
79 81 1.075374 CTGTCCCCTTTCCACCAATCA 59.925 52.381 0.00 0.00 0.00 2.57
94 96 1.359848 CACCACTTATCACGCTGTCC 58.640 55.000 0.00 0.00 0.00 4.02
178 181 4.460263 ACCTTGATAGCACAAGAACAACA 58.540 39.130 16.09 0.00 46.85 3.33
179 182 5.438761 AACCTTGATAGCACAAGAACAAC 57.561 39.130 16.09 0.00 46.85 3.32
180 183 6.463995 AAAACCTTGATAGCACAAGAACAA 57.536 33.333 16.09 0.00 46.85 2.83
351 377 2.629336 TGGTTTGGTTTTTGGGATGC 57.371 45.000 0.00 0.00 0.00 3.91
601 631 3.011949 GCCGAAGCAAAAACAATCTGA 57.988 42.857 0.00 0.00 39.53 3.27
656 686 4.187594 CACAAGCAAGTGTATATCAGCG 57.812 45.455 0.81 0.00 34.83 5.18
747 805 3.490759 GGACACCGTGCAGATGCG 61.491 66.667 0.00 0.00 45.83 4.73
848 922 1.626825 GTTTGGCCACCTACCTGTCTA 59.373 52.381 3.88 0.00 0.00 2.59
854 928 1.339929 CAACAAGTTTGGCCACCTACC 59.660 52.381 3.88 0.00 0.00 3.18
859 933 1.665169 CTTTGCAACAAGTTTGGCCAC 59.335 47.619 3.88 0.00 0.00 5.01
862 936 0.301388 CGCTTTGCAACAAGTTTGGC 59.699 50.000 0.00 0.00 0.00 4.52
904 980 3.733337 CTTGCTACTTATAGGGTGCAGG 58.267 50.000 0.00 2.85 0.00 4.85
950 1029 2.281484 TGCGGTTTGAGTCTGGCC 60.281 61.111 0.00 0.00 0.00 5.36
951 1030 1.598130 AGTGCGGTTTGAGTCTGGC 60.598 57.895 0.00 0.00 0.00 4.85
953 1032 1.571460 GCAGTGCGGTTTGAGTCTG 59.429 57.895 0.00 0.00 0.00 3.51
954 1033 1.598130 GGCAGTGCGGTTTGAGTCT 60.598 57.895 9.45 0.00 0.00 3.24
955 1034 0.320421 TAGGCAGTGCGGTTTGAGTC 60.320 55.000 9.45 0.00 0.00 3.36
1024 1118 1.068434 GAGAAGAAGCCCGATGAGGAG 59.932 57.143 0.00 0.00 45.00 3.69
1030 1124 2.093764 CACAAGAGAGAAGAAGCCCGAT 60.094 50.000 0.00 0.00 0.00 4.18
1134 1228 1.636148 ACGGTGGCAGTTCTACCTTA 58.364 50.000 0.00 0.00 43.52 2.69
1155 1249 3.384348 GGTAGGTGCACTTCCGGA 58.616 61.111 17.98 0.00 0.00 5.14
1240 1334 0.261696 AACTCCACCTTGGGCAACTT 59.738 50.000 0.00 0.00 38.32 2.66
1272 1423 2.639327 GGGTGGCATGTGCACTTCC 61.639 63.158 19.41 15.79 44.36 3.46
1275 1426 1.904865 CTTGGGTGGCATGTGCACT 60.905 57.895 19.41 0.15 44.36 4.40
1282 1433 4.431131 CTCCGGCTTGGGTGGCAT 62.431 66.667 0.00 0.00 38.76 4.40
1321 1472 1.304713 GGTGTACCTCAGGGACCGA 60.305 63.158 2.59 0.00 36.25 4.69
1324 1475 1.597461 GCAGGTGTACCTCAGGGAC 59.403 63.158 0.00 0.00 46.65 4.46
1329 1480 2.221299 GGGTGGCAGGTGTACCTCA 61.221 63.158 0.00 0.00 46.65 3.86
1335 3716 4.603535 GGCTTGGGTGGCAGGTGT 62.604 66.667 0.00 0.00 0.00 4.16
1368 3749 1.377725 CGGGAATGTTGGCAGCTCT 60.378 57.895 2.28 0.00 0.00 4.09
1380 3761 0.394352 GCATGTGAACCTCCGGGAAT 60.394 55.000 0.00 0.00 36.25 3.01
1396 3777 4.431131 CTCCGGCTTGGGTGGCAT 62.431 66.667 0.00 0.00 38.76 4.40
1486 3900 1.937546 GCCAATTCTCACGGCTTGGG 61.938 60.000 0.00 0.00 42.78 4.12
1494 3908 9.241317 CAACAATATTGATAAGCCAATTCTCAC 57.759 33.333 22.16 0.00 37.81 3.51
1528 3942 0.553819 ACGAGGAGCAGAGGAGGTAT 59.446 55.000 0.00 0.00 0.00 2.73
1591 4007 4.644685 ACAACACTAGCTGAAAACCACAAT 59.355 37.500 0.00 0.00 0.00 2.71
1681 4099 3.733337 CATACTTGCGAAGGGCTCTTAT 58.267 45.455 0.00 0.00 44.05 1.73
1695 4113 2.062971 AAGGAGGGCATGCATACTTG 57.937 50.000 21.36 0.00 0.00 3.16
1708 4126 4.278170 TGCTGTGAAATTGTTGTAAGGAGG 59.722 41.667 0.00 0.00 0.00 4.30
1709 4127 5.437289 TGCTGTGAAATTGTTGTAAGGAG 57.563 39.130 0.00 0.00 0.00 3.69
1750 4172 9.862585 GCTTTATGTTTTGTAGTTGGAAAAATG 57.137 29.630 0.00 0.00 0.00 2.32
1752 4174 8.261522 AGGCTTTATGTTTTGTAGTTGGAAAAA 58.738 29.630 0.00 0.00 0.00 1.94
1753 4175 7.787028 AGGCTTTATGTTTTGTAGTTGGAAAA 58.213 30.769 0.00 0.00 0.00 2.29
1754 4176 7.354751 AGGCTTTATGTTTTGTAGTTGGAAA 57.645 32.000 0.00 0.00 0.00 3.13
1755 4177 6.969993 AGGCTTTATGTTTTGTAGTTGGAA 57.030 33.333 0.00 0.00 0.00 3.53
1757 4179 8.138712 TGTTTAGGCTTTATGTTTTGTAGTTGG 58.861 33.333 0.00 0.00 0.00 3.77
1758 4180 9.691362 ATGTTTAGGCTTTATGTTTTGTAGTTG 57.309 29.630 0.00 0.00 0.00 3.16
1802 4224 3.260884 TCAGGTGTTAAAGCTAGGACAGG 59.739 47.826 0.00 0.00 33.90 4.00
1804 4226 6.808321 ATATCAGGTGTTAAAGCTAGGACA 57.192 37.500 0.00 0.00 33.90 4.02
1820 4242 6.152661 ACAATGTGTGGGTTGTAAATATCAGG 59.847 38.462 0.00 0.00 36.83 3.86
1847 4270 7.591006 TTAAGACTATTGGCGTAAACTCAAG 57.409 36.000 0.00 0.00 0.00 3.02
1856 4279 2.159014 TCCGCATTAAGACTATTGGCGT 60.159 45.455 0.00 0.00 0.00 5.68
1858 4281 4.065088 TCATCCGCATTAAGACTATTGGC 58.935 43.478 0.00 0.00 0.00 4.52
1859 4282 4.153117 GCTCATCCGCATTAAGACTATTGG 59.847 45.833 0.00 0.00 0.00 3.16
1892 7429 2.972021 TGATTCTGGTGACACCTTGAGA 59.028 45.455 24.81 16.36 39.58 3.27
1930 7468 2.046507 GTGAGCTGCCACTCCCAG 60.047 66.667 12.17 0.00 35.72 4.45
1949 7487 0.109319 AAGCGGCCATAAAACAAGCG 60.109 50.000 2.24 0.00 0.00 4.68
1950 7488 1.202348 AGAAGCGGCCATAAAACAAGC 59.798 47.619 2.24 0.00 0.00 4.01
1952 7490 3.610585 CGAAAGAAGCGGCCATAAAACAA 60.611 43.478 2.24 0.00 0.00 2.83
1957 7495 1.466950 CAACGAAAGAAGCGGCCATAA 59.533 47.619 2.24 0.00 0.00 1.90
1969 7507 1.344763 AGGAGGTGAGGTCAACGAAAG 59.655 52.381 0.00 0.00 38.92 2.62
1970 7508 1.420430 AGGAGGTGAGGTCAACGAAA 58.580 50.000 0.00 0.00 38.92 3.46
1972 7510 1.420430 AAAGGAGGTGAGGTCAACGA 58.580 50.000 0.00 0.00 38.92 3.85
1973 7511 2.256117 AAAAGGAGGTGAGGTCAACG 57.744 50.000 0.00 0.00 38.92 4.10
1974 7512 4.715713 AGTTAAAAGGAGGTGAGGTCAAC 58.284 43.478 0.00 0.00 0.00 3.18
1976 7514 4.040461 CAGAGTTAAAAGGAGGTGAGGTCA 59.960 45.833 0.00 0.00 0.00 4.02
1977 7515 4.283722 TCAGAGTTAAAAGGAGGTGAGGTC 59.716 45.833 0.00 0.00 0.00 3.85
1978 7516 4.232091 TCAGAGTTAAAAGGAGGTGAGGT 58.768 43.478 0.00 0.00 0.00 3.85
1979 7517 4.891992 TCAGAGTTAAAAGGAGGTGAGG 57.108 45.455 0.00 0.00 0.00 3.86
1982 7520 5.551233 TGACATCAGAGTTAAAAGGAGGTG 58.449 41.667 0.00 0.00 0.00 4.00
1983 7521 5.825593 TGACATCAGAGTTAAAAGGAGGT 57.174 39.130 0.00 0.00 0.00 3.85
1987 7546 8.454106 CAAGGTTATGACATCAGAGTTAAAAGG 58.546 37.037 0.00 0.00 0.00 3.11
1998 7557 6.542821 ACTTCCTTTCAAGGTTATGACATCA 58.457 36.000 5.48 0.00 46.54 3.07
1999 7558 7.201652 GCTACTTCCTTTCAAGGTTATGACATC 60.202 40.741 5.48 0.00 46.54 3.06
2005 7564 5.514500 TGGCTACTTCCTTTCAAGGTTAT 57.486 39.130 5.48 0.00 46.54 1.89
2006 7565 4.986054 TGGCTACTTCCTTTCAAGGTTA 57.014 40.909 5.48 0.00 46.54 2.85
2008 7567 3.138468 AGTTGGCTACTTCCTTTCAAGGT 59.862 43.478 5.48 0.00 46.54 3.50
2022 7581 7.015195 TGCTAGTCATATATTCACAGTTGGCTA 59.985 37.037 0.00 0.00 0.00 3.93
2023 7582 6.183361 TGCTAGTCATATATTCACAGTTGGCT 60.183 38.462 0.00 0.00 0.00 4.75
2032 7591 5.354234 TCGCTCGATGCTAGTCATATATTCA 59.646 40.000 5.53 0.00 40.11 2.57
2033 7592 5.811588 TCGCTCGATGCTAGTCATATATTC 58.188 41.667 5.53 0.00 40.11 1.75
2034 7593 5.819825 TCGCTCGATGCTAGTCATATATT 57.180 39.130 5.53 0.00 40.11 1.28
2037 7596 4.419280 CATTCGCTCGATGCTAGTCATAT 58.581 43.478 5.53 0.00 40.11 1.78
2038 7597 3.366374 CCATTCGCTCGATGCTAGTCATA 60.366 47.826 5.53 0.00 40.11 2.15
2039 7598 2.608998 CCATTCGCTCGATGCTAGTCAT 60.609 50.000 5.53 0.06 40.11 3.06
2041 7600 1.001268 TCCATTCGCTCGATGCTAGTC 60.001 52.381 5.53 0.00 40.11 2.59
2042 7601 1.000827 CTCCATTCGCTCGATGCTAGT 60.001 52.381 5.53 0.00 40.11 2.57
2065 7777 2.238084 TAGACACCCAGATCACTGCT 57.762 50.000 0.00 0.00 42.25 4.24
2083 7795 0.460635 GGCGCCCGTGTTGATACTTA 60.461 55.000 18.11 0.00 0.00 2.24
2096 7808 4.838152 TCTTCATCAGCGGCGCCC 62.838 66.667 30.40 14.23 0.00 6.13
2097 7809 3.267860 CTCTTCATCAGCGGCGCC 61.268 66.667 30.40 19.07 0.00 6.53
2098 7810 2.510238 ACTCTTCATCAGCGGCGC 60.510 61.111 26.86 26.86 0.00 6.53
2111 7823 2.736670 AAAAAGTGGTCCAGCACTCT 57.263 45.000 11.69 0.00 0.00 3.24
2159 7872 0.173255 CATGATTTGCCCACCGAACC 59.827 55.000 0.00 0.00 0.00 3.62
2160 7873 0.887933 ACATGATTTGCCCACCGAAC 59.112 50.000 0.00 0.00 0.00 3.95
2166 9284 2.250921 ATTGGGACATGATTTGCCCA 57.749 45.000 0.00 5.35 44.75 5.36
2170 9288 6.707161 ACAAGAACAAATTGGGACATGATTTG 59.293 34.615 12.74 12.74 46.22 2.32
2175 9293 4.947645 ACACAAGAACAAATTGGGACATG 58.052 39.130 0.00 0.00 39.30 3.21
2199 9317 7.953005 TTTGGCAAACCTATAGATTTCATCA 57.047 32.000 8.93 0.00 36.63 3.07
2217 9337 8.627208 TTATTATTTGGCTTTTGAATTTGGCA 57.373 26.923 0.00 0.00 0.00 4.92
2295 9417 4.175599 CGATGTGTTCGCTCTGCT 57.824 55.556 0.00 0.00 41.69 4.24
2318 9440 0.669318 TCCGCCGCATCCGAAATATC 60.669 55.000 0.00 0.00 36.29 1.63
2319 9441 0.949105 GTCCGCCGCATCCGAAATAT 60.949 55.000 0.00 0.00 36.29 1.28
2320 9442 1.593209 GTCCGCCGCATCCGAAATA 60.593 57.895 0.00 0.00 36.29 1.40
2321 9443 2.895372 GTCCGCCGCATCCGAAAT 60.895 61.111 0.00 0.00 36.29 2.17
2322 9444 3.673956 ATGTCCGCCGCATCCGAAA 62.674 57.895 0.00 0.00 36.29 3.46
2323 9445 2.299503 TAATGTCCGCCGCATCCGAA 62.300 55.000 0.00 0.00 36.29 4.30
2324 9446 2.693250 CTAATGTCCGCCGCATCCGA 62.693 60.000 0.00 0.00 36.29 4.55
2325 9447 2.279851 TAATGTCCGCCGCATCCG 60.280 61.111 0.00 0.00 0.00 4.18
2326 9448 1.069090 TCTAATGTCCGCCGCATCC 59.931 57.895 0.00 0.00 0.00 3.51
2327 9449 0.529773 TGTCTAATGTCCGCCGCATC 60.530 55.000 0.00 0.00 0.00 3.91
2328 9450 0.530650 CTGTCTAATGTCCGCCGCAT 60.531 55.000 0.00 0.00 0.00 4.73
2329 9451 1.153647 CTGTCTAATGTCCGCCGCA 60.154 57.895 0.00 0.00 0.00 5.69
2330 9452 0.739813 AACTGTCTAATGTCCGCCGC 60.740 55.000 0.00 0.00 0.00 6.53
2331 9453 1.278238 GAACTGTCTAATGTCCGCCG 58.722 55.000 0.00 0.00 0.00 6.46
2332 9454 1.653151 GGAACTGTCTAATGTCCGCC 58.347 55.000 0.00 0.00 0.00 6.13
2333 9455 1.278238 CGGAACTGTCTAATGTCCGC 58.722 55.000 3.70 0.00 32.53 5.54
2334 9456 1.278238 GCGGAACTGTCTAATGTCCG 58.722 55.000 11.03 11.03 41.58 4.79
2335 9457 1.653151 GGCGGAACTGTCTAATGTCC 58.347 55.000 0.00 0.00 0.00 4.02
2336 9458 1.207329 AGGGCGGAACTGTCTAATGTC 59.793 52.381 0.00 0.00 0.00 3.06
2337 9459 1.276622 AGGGCGGAACTGTCTAATGT 58.723 50.000 0.00 0.00 0.00 2.71
2338 9460 3.069586 TGATAGGGCGGAACTGTCTAATG 59.930 47.826 0.00 0.00 0.00 1.90
2339 9461 3.069729 GTGATAGGGCGGAACTGTCTAAT 59.930 47.826 0.00 0.00 0.00 1.73
2340 9462 2.429610 GTGATAGGGCGGAACTGTCTAA 59.570 50.000 0.00 0.00 0.00 2.10
2341 9463 2.029623 GTGATAGGGCGGAACTGTCTA 58.970 52.381 0.00 0.00 0.00 2.59
2342 9464 0.824759 GTGATAGGGCGGAACTGTCT 59.175 55.000 0.00 0.00 0.00 3.41
2343 9465 0.535335 TGTGATAGGGCGGAACTGTC 59.465 55.000 0.00 0.00 0.00 3.51
2344 9466 0.537188 CTGTGATAGGGCGGAACTGT 59.463 55.000 0.00 0.00 0.00 3.55
2345 9467 0.537188 ACTGTGATAGGGCGGAACTG 59.463 55.000 0.00 0.00 0.00 3.16
2346 9468 0.824759 GACTGTGATAGGGCGGAACT 59.175 55.000 0.00 0.00 0.00 3.01
2347 9469 0.179081 GGACTGTGATAGGGCGGAAC 60.179 60.000 0.00 0.00 0.00 3.62
2348 9470 0.325296 AGGACTGTGATAGGGCGGAA 60.325 55.000 0.00 0.00 0.00 4.30
2349 9471 0.755698 GAGGACTGTGATAGGGCGGA 60.756 60.000 0.00 0.00 0.00 5.54
2350 9472 0.757188 AGAGGACTGTGATAGGGCGG 60.757 60.000 0.00 0.00 0.00 6.13
2351 9473 1.982660 TAGAGGACTGTGATAGGGCG 58.017 55.000 0.00 0.00 0.00 6.13
2352 9474 3.006323 CACATAGAGGACTGTGATAGGGC 59.994 52.174 0.00 0.00 44.35 5.19
2353 9475 4.474394 TCACATAGAGGACTGTGATAGGG 58.526 47.826 1.47 0.00 45.01 3.53
2359 9481 5.923114 CCGAAATATCACATAGAGGACTGTG 59.077 44.000 0.00 0.00 43.24 3.66
2360 9482 5.833667 TCCGAAATATCACATAGAGGACTGT 59.166 40.000 0.00 0.00 0.00 3.55
2361 9483 6.332735 TCCGAAATATCACATAGAGGACTG 57.667 41.667 0.00 0.00 0.00 3.51
2362 9484 6.153680 GGATCCGAAATATCACATAGAGGACT 59.846 42.308 0.00 0.00 0.00 3.85
2363 9485 6.153680 AGGATCCGAAATATCACATAGAGGAC 59.846 42.308 5.98 0.00 0.00 3.85
2364 9486 6.256819 AGGATCCGAAATATCACATAGAGGA 58.743 40.000 5.98 0.00 0.00 3.71
2365 9487 6.537453 AGGATCCGAAATATCACATAGAGG 57.463 41.667 5.98 0.00 0.00 3.69
2366 9488 7.199766 GCTAGGATCCGAAATATCACATAGAG 58.800 42.308 5.98 0.00 0.00 2.43
2367 9489 6.183360 CGCTAGGATCCGAAATATCACATAGA 60.183 42.308 5.98 0.00 0.00 1.98
2368 9490 5.974158 CGCTAGGATCCGAAATATCACATAG 59.026 44.000 5.98 0.00 0.00 2.23
2369 9491 5.650703 TCGCTAGGATCCGAAATATCACATA 59.349 40.000 5.98 0.00 0.00 2.29
2370 9492 4.462834 TCGCTAGGATCCGAAATATCACAT 59.537 41.667 5.98 0.00 0.00 3.21
2371 9493 3.824443 TCGCTAGGATCCGAAATATCACA 59.176 43.478 5.98 0.00 0.00 3.58
2372 9494 4.436242 TCGCTAGGATCCGAAATATCAC 57.564 45.455 5.98 0.00 0.00 3.06
2373 9495 5.462530 TTTCGCTAGGATCCGAAATATCA 57.537 39.130 5.98 0.00 45.21 2.15
2379 9501 0.750850 CCCTTTCGCTAGGATCCGAA 59.249 55.000 5.98 3.14 41.17 4.30
2380 9502 0.396695 ACCCTTTCGCTAGGATCCGA 60.397 55.000 5.98 0.00 37.50 4.55
2381 9503 1.000496 GTACCCTTTCGCTAGGATCCG 60.000 57.143 5.98 0.00 37.50 4.18
2382 9504 1.000496 CGTACCCTTTCGCTAGGATCC 60.000 57.143 2.48 2.48 37.50 3.36
2383 9505 2.418983 CGTACCCTTTCGCTAGGATC 57.581 55.000 4.41 0.00 37.50 3.36
2391 9513 0.179119 CCTACTGGCGTACCCTTTCG 60.179 60.000 2.61 0.00 33.59 3.46
2392 9514 0.177373 CCCTACTGGCGTACCCTTTC 59.823 60.000 2.61 0.00 33.59 2.62
2393 9515 2.293877 CCCTACTGGCGTACCCTTT 58.706 57.895 2.61 0.00 33.59 3.11
2394 9516 4.045469 CCCTACTGGCGTACCCTT 57.955 61.111 2.61 0.00 33.59 3.95
2403 9525 0.250338 GATTAAGGCCGCCCTACTGG 60.250 60.000 5.55 0.00 41.90 4.00
2404 9526 0.600255 CGATTAAGGCCGCCCTACTG 60.600 60.000 5.55 0.00 41.90 2.74
2405 9527 1.746517 CGATTAAGGCCGCCCTACT 59.253 57.895 5.55 0.00 41.90 2.57
2406 9528 1.959738 GCGATTAAGGCCGCCCTAC 60.960 63.158 5.55 0.00 45.06 3.18
2407 9529 2.424302 GCGATTAAGGCCGCCCTA 59.576 61.111 5.55 0.00 45.06 3.53
2425 9547 2.515901 GGGTGATGAATCCGGGGG 59.484 66.667 0.00 0.00 0.00 5.40
2426 9548 1.978455 TTCGGGTGATGAATCCGGGG 61.978 60.000 0.00 0.00 43.54 5.73
2427 9549 0.814010 GTTCGGGTGATGAATCCGGG 60.814 60.000 0.00 0.00 43.54 5.73
2428 9550 0.814010 GGTTCGGGTGATGAATCCGG 60.814 60.000 0.00 0.00 43.54 5.14
2429 9551 0.107897 TGGTTCGGGTGATGAATCCG 60.108 55.000 0.00 0.00 44.59 4.18
2430 9552 2.122783 TTGGTTCGGGTGATGAATCC 57.877 50.000 0.00 0.00 0.00 3.01
2431 9553 2.287915 CGATTGGTTCGGGTGATGAATC 59.712 50.000 0.00 0.00 44.28 2.52
2432 9554 2.288666 CGATTGGTTCGGGTGATGAAT 58.711 47.619 0.00 0.00 44.28 2.57
2433 9555 1.732941 CGATTGGTTCGGGTGATGAA 58.267 50.000 0.00 0.00 44.28 2.57
2434 9556 3.451793 CGATTGGTTCGGGTGATGA 57.548 52.632 0.00 0.00 44.28 2.92
2443 9565 0.672401 TCGTGAAGGCCGATTGGTTC 60.672 55.000 0.00 0.00 37.67 3.62
2444 9566 0.250553 TTCGTGAAGGCCGATTGGTT 60.251 50.000 0.00 0.00 37.67 3.67
2445 9567 0.250553 TTTCGTGAAGGCCGATTGGT 60.251 50.000 0.00 0.00 37.67 3.67
2446 9568 0.447801 CTTTCGTGAAGGCCGATTGG 59.552 55.000 0.00 0.00 33.81 3.16
2447 9569 3.975992 CTTTCGTGAAGGCCGATTG 57.024 52.632 0.00 0.00 33.81 2.67
2455 9577 7.335924 TCCAAAATATACCTTCCTTTCGTGAAG 59.664 37.037 0.00 0.00 39.13 3.02
2456 9578 7.169591 TCCAAAATATACCTTCCTTTCGTGAA 58.830 34.615 0.00 0.00 0.00 3.18
2457 9579 6.713276 TCCAAAATATACCTTCCTTTCGTGA 58.287 36.000 0.00 0.00 0.00 4.35
2458 9580 6.995511 TCCAAAATATACCTTCCTTTCGTG 57.004 37.500 0.00 0.00 0.00 4.35
2459 9581 6.546034 CCATCCAAAATATACCTTCCTTTCGT 59.454 38.462 0.00 0.00 0.00 3.85
2460 9582 6.016276 CCCATCCAAAATATACCTTCCTTTCG 60.016 42.308 0.00 0.00 0.00 3.46
2461 9583 7.066781 TCCCATCCAAAATATACCTTCCTTTC 58.933 38.462 0.00 0.00 0.00 2.62
2462 9584 6.992235 TCCCATCCAAAATATACCTTCCTTT 58.008 36.000 0.00 0.00 0.00 3.11
2463 9585 6.606241 TCCCATCCAAAATATACCTTCCTT 57.394 37.500 0.00 0.00 0.00 3.36
2464 9586 6.794534 GATCCCATCCAAAATATACCTTCCT 58.205 40.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.