Multiple sequence alignment - TraesCS2A01G037300

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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 TraesCS2A01G037300 chr2A 100.000 6449 0 0 1 6449 15875848 15882296 0.000000e+00 11910.0
1 TraesCS2A01G037300 chr2B 95.618 4404 121 21 2049 6431 24918373 24914021 0.000000e+00 6998.0
2 TraesCS2A01G037300 chr2B 89.791 1724 112 34 1 1687 24921760 24920064 0.000000e+00 2150.0
3 TraesCS2A01G037300 chr2B 91.184 397 18 6 1675 2060 24918954 24918564 2.060000e-144 523.0
4 TraesCS2A01G037300 chr7A 87.124 1196 109 25 357 1520 353260040 353261222 0.000000e+00 1314.0
5 TraesCS2A01G037300 chr7A 75.429 1400 296 40 3991 5369 701186541 701187913 2.540000e-178 636.0
6 TraesCS2A01G037300 chr7A 77.273 1078 199 34 2848 3895 701250898 701251959 5.570000e-165 592.0
7 TraesCS2A01G037300 chr7A 80.400 500 87 8 4887 5379 701252801 701253296 2.840000e-98 370.0
8 TraesCS2A01G037300 chr6A 86.789 1196 114 26 357 1520 214878818 214877635 0.000000e+00 1293.0
9 TraesCS2A01G037300 chr6A 87.578 161 10 5 1 161 31918351 31918501 1.850000e-40 178.0
10 TraesCS2A01G037300 chr1A 85.535 1196 108 27 357 1520 449794344 449793182 0.000000e+00 1190.0
11 TraesCS2A01G037300 chr1A 83.731 922 104 25 357 1246 42804869 42805776 0.000000e+00 830.0
12 TraesCS2A01G037300 chr2D 90.304 691 53 11 1 680 13680552 13679865 0.000000e+00 893.0
13 TraesCS2A01G037300 chr2D 74.444 180 41 3 5142 5320 478571 478746 8.970000e-09 73.1
14 TraesCS2A01G037300 chr7D 80.608 1052 187 14 2831 3872 611218389 611219433 0.000000e+00 797.0
15 TraesCS2A01G037300 chr7D 75.957 1410 286 38 3991 5369 611219440 611220827 0.000000e+00 676.0
16 TraesCS2A01G037300 chr7B 79.526 1055 193 19 2831 3872 700386979 700388023 0.000000e+00 730.0
17 TraesCS2A01G037300 chr7B 76.174 1406 286 41 3991 5370 700388030 700389412 0.000000e+00 695.0
18 TraesCS2A01G037300 chr6B 77.808 1086 213 23 2824 3895 5933295 5934366 0.000000e+00 645.0
19 TraesCS2A01G037300 chr6B 80.488 615 112 7 3255 3863 75520201 75519589 1.270000e-126 464.0
20 TraesCS2A01G037300 chr6D 77.416 1045 205 25 2827 3863 36077915 36076894 1.550000e-165 593.0
21 TraesCS2A01G037300 chr6D 71.698 1272 289 57 3993 5232 36076875 36075643 8.180000e-74 289.0
22 TraesCS2A01G037300 chr5D 76.536 1074 236 15 2827 3895 549584258 549585320 2.020000e-159 573.0
23 TraesCS2A01G037300 chr5D 71.840 973 211 47 3993 4941 27013813 27012880 3.030000e-53 220.0
24 TraesCS2A01G037300 chr5B 76.536 1074 236 15 2827 3895 701161221 701162283 2.020000e-159 573.0
25 TraesCS2A01G037300 chr4A 71.767 1392 324 52 3991 5348 47655890 47657246 4.820000e-86 329.0
26 TraesCS2A01G037300 chr4A 75.993 554 119 11 4798 5346 722930921 722931465 2.290000e-69 274.0


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 TraesCS2A01G037300 chr2A 15875848 15882296 6448 False 11910.000000 11910 100.000000 1 6449 1 chr2A.!!$F1 6448
1 TraesCS2A01G037300 chr2B 24914021 24921760 7739 True 3223.666667 6998 92.197667 1 6431 3 chr2B.!!$R1 6430
2 TraesCS2A01G037300 chr7A 353260040 353261222 1182 False 1314.000000 1314 87.124000 357 1520 1 chr7A.!!$F1 1163
3 TraesCS2A01G037300 chr7A 701186541 701187913 1372 False 636.000000 636 75.429000 3991 5369 1 chr7A.!!$F2 1378
4 TraesCS2A01G037300 chr7A 701250898 701253296 2398 False 481.000000 592 78.836500 2848 5379 2 chr7A.!!$F3 2531
5 TraesCS2A01G037300 chr6A 214877635 214878818 1183 True 1293.000000 1293 86.789000 357 1520 1 chr6A.!!$R1 1163
6 TraesCS2A01G037300 chr1A 449793182 449794344 1162 True 1190.000000 1190 85.535000 357 1520 1 chr1A.!!$R1 1163
7 TraesCS2A01G037300 chr1A 42804869 42805776 907 False 830.000000 830 83.731000 357 1246 1 chr1A.!!$F1 889
8 TraesCS2A01G037300 chr2D 13679865 13680552 687 True 893.000000 893 90.304000 1 680 1 chr2D.!!$R1 679
9 TraesCS2A01G037300 chr7D 611218389 611220827 2438 False 736.500000 797 78.282500 2831 5369 2 chr7D.!!$F1 2538
10 TraesCS2A01G037300 chr7B 700386979 700389412 2433 False 712.500000 730 77.850000 2831 5370 2 chr7B.!!$F1 2539
11 TraesCS2A01G037300 chr6B 5933295 5934366 1071 False 645.000000 645 77.808000 2824 3895 1 chr6B.!!$F1 1071
12 TraesCS2A01G037300 chr6B 75519589 75520201 612 True 464.000000 464 80.488000 3255 3863 1 chr6B.!!$R1 608
13 TraesCS2A01G037300 chr6D 36075643 36077915 2272 True 441.000000 593 74.557000 2827 5232 2 chr6D.!!$R1 2405
14 TraesCS2A01G037300 chr5D 549584258 549585320 1062 False 573.000000 573 76.536000 2827 3895 1 chr5D.!!$F1 1068
15 TraesCS2A01G037300 chr5D 27012880 27013813 933 True 220.000000 220 71.840000 3993 4941 1 chr5D.!!$R1 948
16 TraesCS2A01G037300 chr5B 701161221 701162283 1062 False 573.000000 573 76.536000 2827 3895 1 chr5B.!!$F1 1068
17 TraesCS2A01G037300 chr4A 47655890 47657246 1356 False 329.000000 329 71.767000 3991 5348 1 chr4A.!!$F1 1357
18 TraesCS2A01G037300 chr4A 722930921 722931465 544 False 274.000000 274 75.993000 4798 5346 1 chr4A.!!$F2 548

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
900 940 1.135972 CCCTGATGCTTGAACGAAACG 60.136 52.381 0.00 0.00 0.00 3.60 F
1581 1630 0.884704 GTCTGCGAGCTTGAAACCCA 60.885 55.000 4.70 0.00 0.00 4.51 F
2212 3604 0.233590 CGACGCCGTCAAACAATTGA 59.766 50.000 18.40 0.00 43.18 2.57 F
3106 4504 0.037975 GGCAACAGGACCATTTGCAG 60.038 55.000 24.01 1.19 46.12 4.41 F
3904 5333 0.179018 AGCCAAGGTGGTCTCACAAC 60.179 55.000 0.00 0.00 45.32 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 3068 0.529555 TGCTTTTCTTTTGTGGCCGC 60.530 50.000 10.11 10.11 0.00 6.53 R
2433 3825 1.004918 AAGGTTCAACTCCTCCGCG 60.005 57.895 0.00 0.00 33.76 6.46 R
3372 4779 1.067516 CCCTTCCTTGTGTTTGTGCAG 59.932 52.381 0.00 0.00 0.00 4.41 R
4251 5692 1.348064 AGGATCCGTGTTCTCCACAA 58.652 50.000 5.98 0.00 44.78 3.33 R
5542 7013 0.393537 CAGCTGGTAAGGGCTCAAGG 60.394 60.000 5.57 0.00 36.59 3.61 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 3.367703 CCAACATCCTGCAATCCAAAGAC 60.368 47.826 0.00 0.00 0.00 3.01
70 71 2.441750 AGACCTGAAACAACAAGGGCTA 59.558 45.455 0.00 0.00 36.00 3.93
74 75 4.468153 ACCTGAAACAACAAGGGCTAAAAA 59.532 37.500 0.00 0.00 0.00 1.94
114 120 3.134804 GGGAGTATGTATGAACCTGCTGT 59.865 47.826 0.00 0.00 0.00 4.40
200 206 4.517285 ACATGTCCATATTGACGCTTCTT 58.483 39.130 0.00 0.00 38.11 2.52
203 209 4.769688 TGTCCATATTGACGCTTCTTGAT 58.230 39.130 2.76 0.00 38.11 2.57
218 224 4.991153 TCTTGATGAGAACATAGCGAGT 57.009 40.909 0.00 0.00 36.82 4.18
281 287 7.762588 TCTATAAGGAAGGAGAACCGAATAG 57.237 40.000 0.00 0.00 41.83 1.73
305 311 3.604875 AGCAATGCTTTGGATCTTTGG 57.395 42.857 0.00 0.00 33.89 3.28
308 314 3.056322 GCAATGCTTTGGATCTTTGGTCT 60.056 43.478 13.62 0.00 33.22 3.85
309 315 4.491676 CAATGCTTTGGATCTTTGGTCTG 58.508 43.478 4.44 0.00 0.00 3.51
310 316 3.228188 TGCTTTGGATCTTTGGTCTGT 57.772 42.857 0.00 0.00 0.00 3.41
311 317 2.886523 TGCTTTGGATCTTTGGTCTGTG 59.113 45.455 0.00 0.00 0.00 3.66
312 318 2.887152 GCTTTGGATCTTTGGTCTGTGT 59.113 45.455 0.00 0.00 0.00 3.72
317 324 4.136796 TGGATCTTTGGTCTGTGTTTCTG 58.863 43.478 0.00 0.00 0.00 3.02
335 342 9.760660 GTGTTTCTGTTGCTACTATTTATTCTG 57.239 33.333 0.00 0.00 0.00 3.02
355 362 8.633075 ATTCTGAACTTGTGTGTTTGTATTTG 57.367 30.769 0.00 0.00 0.00 2.32
459 467 3.832704 TGGCGTGACCAGTTATCTG 57.167 52.632 0.00 0.00 46.36 2.90
470 478 2.947652 CCAGTTATCTGTGGCATTGGAG 59.052 50.000 0.00 0.00 39.82 3.86
502 513 5.580691 CCTTCAGCACATAGTTGTTCGAATA 59.419 40.000 0.00 0.00 32.34 1.75
508 520 7.162546 CAGCACATAGTTGTTCGAATAAATTCG 59.837 37.037 12.70 16.93 46.33 3.34
531 543 2.843113 AGGAGCTGTAATTCAGAAGGCT 59.157 45.455 0.00 0.00 46.27 4.58
544 556 3.769300 TCAGAAGGCTATCTTGTGTGCTA 59.231 43.478 0.00 0.00 44.36 3.49
574 586 8.983307 TTTGTTTCGGTTGTATTTAGTTGTTT 57.017 26.923 0.00 0.00 0.00 2.83
625 638 4.940654 AGCTTTACTGGCAAAGAGAGATTC 59.059 41.667 1.67 0.00 37.66 2.52
665 679 1.402613 ACGGCTGTACCACAAACAAAC 59.597 47.619 0.00 0.00 39.03 2.93
679 693 6.472163 CCACAAACAAACACAACAAGACTATC 59.528 38.462 0.00 0.00 0.00 2.08
710 724 3.007182 TCCTGGTCGGTTAACTGGTTTAG 59.993 47.826 14.44 7.93 0.00 1.85
731 745 9.109393 GTTTAGGAATGTATGATTTGCTAGTGA 57.891 33.333 0.00 0.00 29.25 3.41
819 859 2.486548 GCAGAAAAGGAGGTACACCACA 60.487 50.000 10.24 0.00 43.22 4.17
832 872 6.779860 AGGTACACCACATTTTCTTACTGAT 58.220 36.000 0.38 0.00 38.89 2.90
833 873 6.655003 AGGTACACCACATTTTCTTACTGATG 59.345 38.462 0.38 0.00 38.89 3.07
834 874 6.653320 GGTACACCACATTTTCTTACTGATGA 59.347 38.462 0.00 0.00 35.64 2.92
853 893 9.935241 ACTGATGAAGTACATATAATCCATGTC 57.065 33.333 0.00 0.00 39.56 3.06
854 894 9.376075 CTGATGAAGTACATATAATCCATGTCC 57.624 37.037 0.00 0.00 39.56 4.02
855 895 8.879227 TGATGAAGTACATATAATCCATGTCCA 58.121 33.333 0.00 0.00 39.56 4.02
856 896 9.896645 GATGAAGTACATATAATCCATGTCCAT 57.103 33.333 0.00 0.00 39.56 3.41
871 911 9.784531 ATCCATGTCCATAGTGATTAAAGTTAG 57.215 33.333 0.00 0.00 0.00 2.34
877 917 8.870879 GTCCATAGTGATTAAAGTTAGACACAC 58.129 37.037 0.00 0.00 0.00 3.82
894 934 1.675641 ACGCCCCTGATGCTTGAAC 60.676 57.895 0.00 0.00 0.00 3.18
900 940 1.135972 CCCTGATGCTTGAACGAAACG 60.136 52.381 0.00 0.00 0.00 3.60
933 973 4.748892 CAGATTCTGCCGTCTAAAGAGAA 58.251 43.478 0.00 0.00 31.96 2.87
943 983 5.625721 GCCGTCTAAAGAGAAAAAGAAAAGC 59.374 40.000 0.00 0.00 31.96 3.51
1075 1119 1.636148 ACATGATGCCAAAAGCCAGT 58.364 45.000 0.00 0.00 42.71 4.00
1079 1123 1.075374 TGATGCCAAAAGCCAGTACCT 59.925 47.619 0.00 0.00 42.71 3.08
1087 1131 1.764571 AAGCCAGTACCTTCACCGCA 61.765 55.000 0.00 0.00 0.00 5.69
1170 1214 4.522114 TGACATGGAACTGTGAAGTTTCA 58.478 39.130 2.20 2.20 41.06 2.69
1213 1257 2.165301 GTGATATATCGCCGCCCGC 61.165 63.158 14.27 0.00 36.73 6.13
1246 1290 5.694995 TCTTGGGGACATCATTTCTTATCC 58.305 41.667 0.00 0.00 42.32 2.59
1265 1313 1.351017 CCCTGCAAGTGTTCTTCCCTA 59.649 52.381 0.00 0.00 0.00 3.53
1266 1314 2.025887 CCCTGCAAGTGTTCTTCCCTAT 60.026 50.000 0.00 0.00 0.00 2.57
1282 1330 3.846588 TCCCTATTTCTTGGAGACAGCTT 59.153 43.478 0.00 0.00 44.54 3.74
1340 1389 5.527951 TCCATGTTTTCTCATTGGTTTTCG 58.472 37.500 0.00 0.00 0.00 3.46
1359 1408 1.865970 CGCAGCTTCAGATCAGGATTC 59.134 52.381 0.00 0.00 0.00 2.52
1384 1433 3.381335 AGATCCGGCCTCCTTACTTTTA 58.619 45.455 0.00 0.00 0.00 1.52
1409 1458 3.218453 GGAGTGCAGAGATCTACAGCTA 58.782 50.000 12.86 0.49 0.00 3.32
1419 1468 3.392616 AGATCTACAGCTAATGGGTTGGG 59.607 47.826 0.00 0.00 0.00 4.12
1469 1518 3.118445 CCTCCTGGGAGTGATTTTCTCTC 60.118 52.174 14.63 0.00 40.44 3.20
1558 1607 9.865321 AGATCGCAAAGTAGTTAGTTGTTAATA 57.135 29.630 0.00 0.00 0.00 0.98
1569 1618 3.904571 AGTTGTTAATACACGTCTGCGA 58.095 40.909 0.00 0.00 42.00 5.10
1581 1630 0.884704 GTCTGCGAGCTTGAAACCCA 60.885 55.000 4.70 0.00 0.00 4.51
1631 1680 6.566564 GCACCCGTCATAATCATCATTTACAG 60.567 42.308 0.00 0.00 0.00 2.74
1637 1686 5.769662 TCATAATCATCATTTACAGCCCCAC 59.230 40.000 0.00 0.00 0.00 4.61
1644 1693 2.757894 TTTACAGCCCCACCAAAAGA 57.242 45.000 0.00 0.00 0.00 2.52
1733 2906 2.774234 CAGAAGCCTCCCCAGATTTCTA 59.226 50.000 0.00 0.00 0.00 2.10
1789 2962 6.258160 CGATTGAGAATGGTGTAATTTGGTC 58.742 40.000 0.00 0.00 0.00 4.02
1826 2999 5.469084 AGTCATTTCAAAAGACCGGTAGTTC 59.531 40.000 7.34 0.00 32.82 3.01
1848 3021 7.614583 AGTTCTGGTGTGATAAGCTAGTAACTA 59.385 37.037 0.00 0.00 0.00 2.24
1862 3035 8.068892 AGCTAGTAACTAACAGAAATACAGCT 57.931 34.615 0.00 0.00 31.92 4.24
1880 3053 1.880819 CTGGTGCCAGGCCAATGAAC 61.881 60.000 9.64 0.00 40.17 3.18
1895 3068 4.332819 CCAATGAACCCTTCTAGCTTTACG 59.667 45.833 0.00 0.00 0.00 3.18
1897 3070 1.925185 GAACCCTTCTAGCTTTACGCG 59.075 52.381 3.53 3.53 45.59 6.01
1905 3078 0.603172 TAGCTTTACGCGGCCACAAA 60.603 50.000 12.47 1.55 45.59 2.83
1906 3079 1.008309 GCTTTACGCGGCCACAAAA 60.008 52.632 12.47 0.00 0.00 2.44
1907 3080 1.001745 GCTTTACGCGGCCACAAAAG 61.002 55.000 12.47 7.37 0.00 2.27
1909 3082 1.002251 CTTTACGCGGCCACAAAAGAA 60.002 47.619 12.47 0.00 30.44 2.52
1910 3083 1.022735 TTACGCGGCCACAAAAGAAA 58.977 45.000 12.47 0.00 0.00 2.52
1911 3084 1.022735 TACGCGGCCACAAAAGAAAA 58.977 45.000 12.47 0.00 0.00 2.29
1912 3085 0.248866 ACGCGGCCACAAAAGAAAAG 60.249 50.000 12.47 0.00 0.00 2.27
1913 3086 1.548132 CGCGGCCACAAAAGAAAAGC 61.548 55.000 2.24 0.00 0.00 3.51
1915 3088 1.490621 CGGCCACAAAAGAAAAGCAG 58.509 50.000 2.24 0.00 0.00 4.24
1917 3090 2.288395 CGGCCACAAAAGAAAAGCAGAT 60.288 45.455 2.24 0.00 0.00 2.90
1920 3093 4.218417 GGCCACAAAAGAAAAGCAGATAGA 59.782 41.667 0.00 0.00 0.00 1.98
1921 3094 5.105595 GGCCACAAAAGAAAAGCAGATAGAT 60.106 40.000 0.00 0.00 0.00 1.98
1922 3095 6.095440 GGCCACAAAAGAAAAGCAGATAGATA 59.905 38.462 0.00 0.00 0.00 1.98
1923 3096 6.969473 GCCACAAAAGAAAAGCAGATAGATAC 59.031 38.462 0.00 0.00 0.00 2.24
1924 3097 7.362056 GCCACAAAAGAAAAGCAGATAGATACA 60.362 37.037 0.00 0.00 0.00 2.29
1925 3098 8.180267 CCACAAAAGAAAAGCAGATAGATACAG 58.820 37.037 0.00 0.00 0.00 2.74
1926 3099 8.725148 CACAAAAGAAAAGCAGATAGATACAGT 58.275 33.333 0.00 0.00 0.00 3.55
1951 3124 7.566760 AGGCAATCACACGATCATAAATTTA 57.433 32.000 0.00 0.00 0.00 1.40
2045 3227 3.269643 TGGAAGACCTAGGATCAGACTGA 59.730 47.826 17.98 7.80 37.04 3.41
2080 3465 3.500680 CACCACTTGTGGCGTTAGTTTAT 59.499 43.478 18.67 0.00 41.52 1.40
2091 3476 6.413818 GTGGCGTTAGTTTATTCATATGCAAC 59.586 38.462 0.00 0.00 0.00 4.17
2136 3528 9.976511 GTACCAAACTACTGATATAAGCATGTA 57.023 33.333 0.00 0.00 0.00 2.29
2144 3536 9.363763 CTACTGATATAAGCATGTATTGTGGAG 57.636 37.037 0.00 0.00 0.00 3.86
2177 3569 6.780457 AACAGCCATTTTATTACTGCAGAT 57.220 33.333 23.35 6.96 31.46 2.90
2212 3604 0.233590 CGACGCCGTCAAACAATTGA 59.766 50.000 18.40 0.00 43.18 2.57
2216 3608 2.292016 ACGCCGTCAAACAATTGATTGA 59.708 40.909 22.83 22.83 46.67 2.57
2336 3728 3.261897 AGAGCTACAGCAGAAGCCTTAAA 59.738 43.478 3.70 0.00 45.16 1.52
2346 3738 4.021981 GCAGAAGCCTTAAAATCCACAAGT 60.022 41.667 0.00 0.00 33.58 3.16
2364 3756 4.763793 ACAAGTGATCCTGACATGAAAAGG 59.236 41.667 0.00 3.09 0.00 3.11
2411 3803 5.833131 TGGATTGCTCCCTATGGAAAAATAC 59.167 40.000 0.00 0.00 41.17 1.89
2442 3834 3.798954 GAGGGCAATCGCGGAGGAG 62.799 68.421 6.13 0.00 39.92 3.69
2494 3886 5.369409 TGATGAGCAGGATGAAGAAGATT 57.631 39.130 0.00 0.00 39.69 2.40
2592 3984 8.801715 TGTATGAAAAGTTTCTGCTGATTTTC 57.198 30.769 17.34 17.34 39.28 2.29
2709 4101 4.712337 GGAAGATTTCCCTACTCAGTGAGA 59.288 45.833 26.86 9.35 44.30 3.27
2748 4140 8.492673 TGATGTCCATTTCTACTTACATTGAC 57.507 34.615 0.00 0.00 0.00 3.18
2910 4302 7.491372 CCGACAACAGTTCTAGATTGCTTATTA 59.509 37.037 0.00 0.00 0.00 0.98
2929 4321 7.254017 GCTTATTATACTCAACGTTCCTGACAC 60.254 40.741 0.00 0.00 0.00 3.67
2948 4340 4.358851 ACACAACAATCACATCAAAACCG 58.641 39.130 0.00 0.00 0.00 4.44
3106 4504 0.037975 GGCAACAGGACCATTTGCAG 60.038 55.000 24.01 1.19 46.12 4.41
3107 4505 0.961019 GCAACAGGACCATTTGCAGA 59.039 50.000 19.98 0.00 44.17 4.26
3171 4569 6.827586 TCAGTTACCTCAAACAAACAAACT 57.172 33.333 0.00 0.00 0.00 2.66
3201 4599 5.820423 TGACATGTGTTATGTACCCAATAGC 59.180 40.000 1.15 0.00 31.52 2.97
3372 4779 4.012374 TGAGATTCCTTTGGCTTGATCAC 58.988 43.478 0.00 0.00 0.00 3.06
3392 4805 1.067516 CTGCACAAACACAAGGAAGGG 59.932 52.381 0.00 0.00 0.00 3.95
3487 4903 6.373495 TCCAAAGATGATTGAACTGATGACAG 59.627 38.462 0.00 0.00 39.93 3.51
3648 5071 1.210538 TGGATCTGCAGCTCCTTGAT 58.789 50.000 31.07 9.87 31.86 2.57
3789 5218 3.314635 CACTGCTTGAGAGTTTCAGCTTT 59.685 43.478 0.00 0.00 37.07 3.51
3898 5327 1.777272 AGAAGAAAGCCAAGGTGGTCT 59.223 47.619 0.00 0.00 40.46 3.85
3904 5333 0.179018 AGCCAAGGTGGTCTCACAAC 60.179 55.000 0.00 0.00 45.32 3.32
3918 5347 5.048013 GGTCTCACAACAAAGGAATAAAGGG 60.048 44.000 0.00 0.00 0.00 3.95
4247 5688 2.549633 GGAACCACAAGATCAATGCG 57.450 50.000 0.00 0.00 0.00 4.73
4251 5692 0.680921 CCACAAGATCAATGCGGGGT 60.681 55.000 0.00 0.00 0.00 4.95
4288 5729 5.393461 GGATCCTTTGACTTTAAGGCATGTG 60.393 44.000 0.00 0.00 41.59 3.21
4615 6059 8.200792 ACTTTGAGAGTATAGATGACAATGGAC 58.799 37.037 0.00 0.00 36.65 4.02
4623 6067 7.935755 AGTATAGATGACAATGGACATTTCAGG 59.064 37.037 12.14 0.00 29.55 3.86
4737 6184 3.434167 GCCTAGAATGGTGTCATGTGGAT 60.434 47.826 0.00 0.00 33.18 3.41
5260 6731 1.549243 TAAGCTCATGTGGGACGGCA 61.549 55.000 0.00 0.00 0.00 5.69
5275 6746 1.727511 CGGCATCGATGTTGGCCATT 61.728 55.000 25.47 0.00 46.75 3.16
5377 6848 6.813649 TGCAGATTGTTGTTCTTACTAGCTAG 59.186 38.462 19.44 19.44 0.00 3.42
5385 6856 6.606234 TGTTCTTACTAGCTAGACAGATCG 57.394 41.667 27.45 7.92 0.00 3.69
5387 6858 6.480651 TGTTCTTACTAGCTAGACAGATCGAG 59.519 42.308 27.45 11.49 0.00 4.04
5542 7013 2.630580 ACCTGTTCTCTTCTCACCACTC 59.369 50.000 0.00 0.00 0.00 3.51
5546 7017 3.070159 TGTTCTCTTCTCACCACTCCTTG 59.930 47.826 0.00 0.00 0.00 3.61
5563 7034 2.512515 GAGCCCTTACCAGCTGCG 60.513 66.667 8.66 4.27 40.11 5.18
5564 7035 4.785453 AGCCCTTACCAGCTGCGC 62.785 66.667 8.66 0.00 38.11 6.09
5616 7087 2.601504 GCTGCTACATGCGTCATGAATG 60.602 50.000 21.37 0.00 43.81 2.67
5658 7129 1.066908 TGTGTTAGCTTGGCTTTGTGC 59.933 47.619 0.00 0.00 40.44 4.57
5678 7149 4.183539 GCGTTAAGCAAGCACTATAGTG 57.816 45.455 25.68 25.68 46.43 2.74
5691 7162 4.748892 CACTATAGTGCTAGCTTGTGTGT 58.251 43.478 19.55 5.77 39.39 3.72
5692 7163 4.564372 CACTATAGTGCTAGCTTGTGTGTG 59.436 45.833 19.55 13.72 39.39 3.82
5693 7164 2.455674 TAGTGCTAGCTTGTGTGTGG 57.544 50.000 17.23 0.00 0.00 4.17
5694 7165 0.758734 AGTGCTAGCTTGTGTGTGGA 59.241 50.000 17.23 0.00 0.00 4.02
5695 7166 1.151668 GTGCTAGCTTGTGTGTGGAG 58.848 55.000 17.23 0.00 0.00 3.86
5696 7167 0.758734 TGCTAGCTTGTGTGTGGAGT 59.241 50.000 17.23 0.00 0.00 3.85
5697 7168 1.967779 TGCTAGCTTGTGTGTGGAGTA 59.032 47.619 17.23 0.00 0.00 2.59
5698 7169 2.567169 TGCTAGCTTGTGTGTGGAGTAT 59.433 45.455 17.23 0.00 0.00 2.12
5699 7170 2.932614 GCTAGCTTGTGTGTGGAGTATG 59.067 50.000 7.70 0.00 0.00 2.39
5700 7171 3.617531 GCTAGCTTGTGTGTGGAGTATGT 60.618 47.826 7.70 0.00 0.00 2.29
5701 7172 3.492102 AGCTTGTGTGTGGAGTATGTT 57.508 42.857 0.00 0.00 0.00 2.71
5702 7173 3.141398 AGCTTGTGTGTGGAGTATGTTG 58.859 45.455 0.00 0.00 0.00 3.33
5703 7174 2.226437 GCTTGTGTGTGGAGTATGTTGG 59.774 50.000 0.00 0.00 0.00 3.77
5704 7175 3.476552 CTTGTGTGTGGAGTATGTTGGT 58.523 45.455 0.00 0.00 0.00 3.67
5705 7176 3.569194 TGTGTGTGGAGTATGTTGGTT 57.431 42.857 0.00 0.00 0.00 3.67
5706 7177 3.892284 TGTGTGTGGAGTATGTTGGTTT 58.108 40.909 0.00 0.00 0.00 3.27
5707 7178 3.629855 TGTGTGTGGAGTATGTTGGTTTG 59.370 43.478 0.00 0.00 0.00 2.93
5708 7179 3.880490 GTGTGTGGAGTATGTTGGTTTGA 59.120 43.478 0.00 0.00 0.00 2.69
5709 7180 4.518970 GTGTGTGGAGTATGTTGGTTTGAT 59.481 41.667 0.00 0.00 0.00 2.57
5710 7181 4.518590 TGTGTGGAGTATGTTGGTTTGATG 59.481 41.667 0.00 0.00 0.00 3.07
5711 7182 4.518970 GTGTGGAGTATGTTGGTTTGATGT 59.481 41.667 0.00 0.00 0.00 3.06
5712 7183 4.759693 TGTGGAGTATGTTGGTTTGATGTC 59.240 41.667 0.00 0.00 0.00 3.06
5932 7403 5.981088 AGCAGATGTACATCTATCTCAGG 57.019 43.478 32.57 21.07 45.78 3.86
5944 7415 5.762179 TCTATCTCAGGTGGTGAAACAAT 57.238 39.130 0.00 0.00 39.98 2.71
6000 7473 1.662629 CAGCGTTCTTGCTATCACCAG 59.337 52.381 0.00 0.00 45.23 4.00
6018 7491 3.118811 ACCAGAGTGCTTCTAATGAGAGC 60.119 47.826 0.00 0.00 33.83 4.09
6028 7501 6.536582 TGCTTCTAATGAGAGCAATGAGTAAC 59.463 38.462 2.67 0.00 34.77 2.50
6029 7502 6.760770 GCTTCTAATGAGAGCAATGAGTAACT 59.239 38.462 0.00 0.00 31.77 2.24
6112 7593 1.760029 TCATAGTGTATTCCAGCGGCA 59.240 47.619 1.45 0.00 0.00 5.69
6125 7606 1.377202 GCGGCAATTCACCAGAGGA 60.377 57.895 0.00 0.00 0.00 3.71
6126 7607 0.960364 GCGGCAATTCACCAGAGGAA 60.960 55.000 0.00 0.00 0.00 3.36
6295 7776 2.203337 GCACACCCTCCAGCACAA 60.203 61.111 0.00 0.00 0.00 3.33
6300 7781 0.466189 CACCCTCCAGCACAACAAGT 60.466 55.000 0.00 0.00 0.00 3.16
6370 7854 6.748132 AGTTTTAAGCAAGCAAAGCAATAGA 58.252 32.000 0.00 0.00 0.00 1.98
6392 7876 6.934056 AGAACATGCTTATGCCAAATTTGTA 58.066 32.000 16.73 6.17 38.71 2.41
6393 7877 7.385267 AGAACATGCTTATGCCAAATTTGTAA 58.615 30.769 16.73 8.19 38.71 2.41
6418 7902 3.302375 TTGCGCCACAAAATGCAAT 57.698 42.105 4.18 0.00 41.95 3.56
6425 7909 4.290155 CGCCACAAAATGCAATACTATCC 58.710 43.478 0.00 0.00 0.00 2.59
6431 7915 8.292448 CCACAAAATGCAATACTATCCAGATAC 58.708 37.037 0.00 0.00 0.00 2.24
6432 7916 8.011673 CACAAAATGCAATACTATCCAGATACG 58.988 37.037 0.00 0.00 0.00 3.06
6433 7917 7.931407 ACAAAATGCAATACTATCCAGATACGA 59.069 33.333 0.00 0.00 0.00 3.43
6434 7918 8.773645 CAAAATGCAATACTATCCAGATACGAA 58.226 33.333 0.00 0.00 0.00 3.85
6435 7919 8.902540 AAATGCAATACTATCCAGATACGAAA 57.097 30.769 0.00 0.00 0.00 3.46
6436 7920 7.891183 ATGCAATACTATCCAGATACGAAAC 57.109 36.000 0.00 0.00 0.00 2.78
6437 7921 7.050970 TGCAATACTATCCAGATACGAAACT 57.949 36.000 0.00 0.00 0.00 2.66
6438 7922 6.923508 TGCAATACTATCCAGATACGAAACTG 59.076 38.462 0.00 0.00 0.00 3.16
6439 7923 6.128795 GCAATACTATCCAGATACGAAACTGC 60.129 42.308 0.00 0.00 33.40 4.40
6440 7924 4.323553 ACTATCCAGATACGAAACTGCC 57.676 45.455 0.00 0.00 33.40 4.85
6441 7925 3.961408 ACTATCCAGATACGAAACTGCCT 59.039 43.478 0.00 0.00 33.40 4.75
6442 7926 2.961526 TCCAGATACGAAACTGCCTC 57.038 50.000 0.00 0.00 33.40 4.70
6443 7927 2.176045 TCCAGATACGAAACTGCCTCA 58.824 47.619 0.00 0.00 33.40 3.86
6444 7928 2.094182 TCCAGATACGAAACTGCCTCAC 60.094 50.000 0.00 0.00 33.40 3.51
6445 7929 2.353704 CCAGATACGAAACTGCCTCACA 60.354 50.000 0.00 0.00 33.40 3.58
6446 7930 3.525537 CAGATACGAAACTGCCTCACAT 58.474 45.455 0.00 0.00 0.00 3.21
6447 7931 4.441495 CCAGATACGAAACTGCCTCACATA 60.441 45.833 0.00 0.00 33.40 2.29
6448 7932 4.504461 CAGATACGAAACTGCCTCACATAC 59.496 45.833 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.611374 TCAGGTCTTACAGTTTTCTTCCTG 58.389 41.667 0.00 0.00 40.55 3.86
52 53 4.664150 TTTTAGCCCTTGTTGTTTCAGG 57.336 40.909 0.00 0.00 0.00 3.86
74 75 4.018960 ACTCCCAGATAAGTGACAGCATTT 60.019 41.667 0.00 0.00 0.00 2.32
200 206 2.481969 GGCACTCGCTATGTTCTCATCA 60.482 50.000 0.00 0.00 38.60 3.07
203 209 0.894835 TGGCACTCGCTATGTTCTCA 59.105 50.000 0.00 0.00 38.60 3.27
218 224 0.320374 CCTGGTTACTCGTCTTGGCA 59.680 55.000 0.00 0.00 0.00 4.92
281 287 5.751990 CCAAAGATCCAAAGCATTGCTAATC 59.248 40.000 12.39 12.16 38.25 1.75
305 311 6.787085 AATAGTAGCAACAGAAACACAGAC 57.213 37.500 0.00 0.00 0.00 3.51
308 314 9.502091 AGAATAAATAGTAGCAACAGAAACACA 57.498 29.630 0.00 0.00 0.00 3.72
309 315 9.760660 CAGAATAAATAGTAGCAACAGAAACAC 57.239 33.333 0.00 0.00 0.00 3.32
310 316 9.719355 TCAGAATAAATAGTAGCAACAGAAACA 57.281 29.630 0.00 0.00 0.00 2.83
317 324 9.760660 CACAAGTTCAGAATAAATAGTAGCAAC 57.239 33.333 0.00 0.00 0.00 4.17
335 342 6.885735 AAGCAAATACAAACACACAAGTTC 57.114 33.333 0.00 0.00 0.00 3.01
355 362 0.037447 ACAGCCTCCTCCTGAAAAGC 59.963 55.000 0.00 0.00 34.47 3.51
441 448 3.832704 CAGATAACTGGTCACGCCA 57.167 52.632 0.00 0.00 46.95 5.69
459 467 2.755929 GAGTCGACTCCAATGCCAC 58.244 57.895 31.24 6.83 37.02 5.01
470 478 0.247736 ATGTGCTGAAGGGAGTCGAC 59.752 55.000 7.70 7.70 0.00 4.20
478 486 3.325870 TCGAACAACTATGTGCTGAAGG 58.674 45.455 0.00 0.00 40.46 3.46
502 513 6.173339 TCTGAATTACAGCTCCTTCGAATTT 58.827 36.000 0.00 0.00 45.38 1.82
508 520 3.625313 GCCTTCTGAATTACAGCTCCTTC 59.375 47.826 0.00 0.00 45.38 3.46
510 522 2.843113 AGCCTTCTGAATTACAGCTCCT 59.157 45.455 0.00 0.00 45.38 3.69
531 543 9.767684 CGAAACAAAATTATAGCACACAAGATA 57.232 29.630 0.00 0.00 0.00 1.98
600 613 5.683876 TCTCTCTTTGCCAGTAAAGCTAT 57.316 39.130 3.62 0.00 37.53 2.97
625 638 9.237846 CAGCCGTACATGTATATATGATTGTAG 57.762 37.037 15.59 1.82 0.00 2.74
665 679 6.312426 GGAGAACAGATGATAGTCTTGTTGTG 59.688 42.308 0.00 0.00 0.00 3.33
679 693 0.898320 ACCGACCAGGAGAACAGATG 59.102 55.000 0.00 0.00 45.00 2.90
710 724 8.844244 AGAAATCACTAGCAAATCATACATTCC 58.156 33.333 0.00 0.00 0.00 3.01
762 776 8.812972 TCAAACATAGGTACTGTCTCTAATTGT 58.187 33.333 0.00 0.00 41.52 2.71
763 777 9.307121 CTCAAACATAGGTACTGTCTCTAATTG 57.693 37.037 0.00 0.00 41.52 2.32
764 778 9.256228 TCTCAAACATAGGTACTGTCTCTAATT 57.744 33.333 0.00 0.00 41.52 1.40
766 780 8.645814 TTCTCAAACATAGGTACTGTCTCTAA 57.354 34.615 0.00 0.00 41.52 2.10
778 817 6.053650 TCTGCAGATCATTCTCAAACATAGG 58.946 40.000 13.74 0.00 0.00 2.57
853 893 7.464178 GCGTGTGTCTAACTTTAATCACTATGG 60.464 40.741 0.00 0.00 0.00 2.74
854 894 7.391786 GCGTGTGTCTAACTTTAATCACTATG 58.608 38.462 0.00 0.00 0.00 2.23
855 895 6.534079 GGCGTGTGTCTAACTTTAATCACTAT 59.466 38.462 0.00 0.00 0.00 2.12
856 896 5.865552 GGCGTGTGTCTAACTTTAATCACTA 59.134 40.000 0.00 0.00 0.00 2.74
857 897 4.689345 GGCGTGTGTCTAACTTTAATCACT 59.311 41.667 0.00 0.00 0.00 3.41
858 898 4.142966 GGGCGTGTGTCTAACTTTAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
871 911 3.127533 GCATCAGGGGCGTGTGTC 61.128 66.667 0.00 0.00 0.00 3.67
877 917 2.753966 CGTTCAAGCATCAGGGGCG 61.754 63.158 0.00 0.00 36.08 6.13
921 961 8.122952 TCTTGCTTTTCTTTTTCTCTTTAGACG 58.877 33.333 0.00 0.00 0.00 4.18
958 998 9.342308 TGTGATATCTCTTGTCTTTTTGTTCTT 57.658 29.630 3.98 0.00 0.00 2.52
971 1011 7.767659 TGTTGATCCTCTTTGTGATATCTCTTG 59.232 37.037 3.98 0.00 0.00 3.02
1041 1084 5.236047 GGCATCATGTTGCTTTTGTTGTTTA 59.764 36.000 24.11 0.00 42.38 2.01
1045 1088 3.132160 TGGCATCATGTTGCTTTTGTTG 58.868 40.909 24.11 0.00 42.38 3.33
1075 1119 1.071814 GGGTGTTGCGGTGAAGGTA 59.928 57.895 0.00 0.00 0.00 3.08
1079 1123 2.589442 GACGGGTGTTGCGGTGAA 60.589 61.111 0.00 0.00 0.00 3.18
1087 1131 3.109592 TTTCGGCAGGACGGGTGTT 62.110 57.895 0.00 0.00 0.00 3.32
1155 1199 9.567848 TTAAGACAAAATGAAACTTCACAGTTC 57.432 29.630 0.00 0.00 42.89 3.01
1159 1203 7.831753 TGGTTAAGACAAAATGAAACTTCACA 58.168 30.769 0.00 0.00 40.49 3.58
1170 1214 7.607991 ACTCGATCATCTTGGTTAAGACAAAAT 59.392 33.333 0.00 0.00 45.17 1.82
1213 1257 1.003118 TGTCCCCAAGAAATCCAGTCG 59.997 52.381 0.00 0.00 0.00 4.18
1246 1290 2.859165 TAGGGAAGAACACTTGCAGG 57.141 50.000 0.00 0.00 34.46 4.85
1265 1313 4.565236 CCTCTGAAGCTGTCTCCAAGAAAT 60.565 45.833 0.00 0.00 0.00 2.17
1266 1314 3.244353 CCTCTGAAGCTGTCTCCAAGAAA 60.244 47.826 0.00 0.00 0.00 2.52
1282 1330 2.105649 TGTGCAATTGTGGTACCTCTGA 59.894 45.455 14.36 3.38 0.00 3.27
1340 1389 2.873472 CTGAATCCTGATCTGAAGCTGC 59.127 50.000 0.38 0.00 0.00 5.25
1375 1424 4.894784 TCTGCACTCCCTGTAAAAGTAAG 58.105 43.478 0.00 0.00 0.00 2.34
1384 1433 2.291865 TGTAGATCTCTGCACTCCCTGT 60.292 50.000 0.00 0.00 33.67 4.00
1409 1458 4.535692 AGAAACAAATATGCCCAACCCATT 59.464 37.500 0.00 0.00 0.00 3.16
1419 1468 6.470235 CGGAAAGTCATGAGAAACAAATATGC 59.530 38.462 0.00 0.00 0.00 3.14
1469 1518 5.711976 AGGTTCCCAAGACATATTGAACTTG 59.288 40.000 0.00 0.00 36.24 3.16
1558 1607 0.529773 TTTCAAGCTCGCAGACGTGT 60.530 50.000 0.00 0.00 41.18 4.49
1569 1618 2.689983 CAACAAGACTGGGTTTCAAGCT 59.310 45.455 0.00 0.00 0.00 3.74
1581 1630 1.542915 GATGCACATGCCAACAAGACT 59.457 47.619 0.49 0.00 41.18 3.24
1611 1660 5.106555 GGGGCTGTAAATGATGATTATGACG 60.107 44.000 0.00 0.00 0.00 4.35
1631 1680 1.484653 ACTTGTTTCTTTTGGTGGGGC 59.515 47.619 0.00 0.00 0.00 5.80
1680 1729 8.755977 GCCCCAAGCTACACTAGTATATTATAA 58.244 37.037 0.00 0.00 38.99 0.98
1687 1736 2.047830 GGCCCCAAGCTACACTAGTAT 58.952 52.381 0.00 0.00 43.05 2.12
1688 1737 1.007963 AGGCCCCAAGCTACACTAGTA 59.992 52.381 0.00 0.00 43.05 1.82
1689 1738 0.252742 AGGCCCCAAGCTACACTAGT 60.253 55.000 0.00 0.00 43.05 2.57
1691 1740 0.546747 ACAGGCCCCAAGCTACACTA 60.547 55.000 0.00 0.00 43.05 2.74
1733 2906 7.759489 TTGTAGAATTTGCTTTATCCACAGT 57.241 32.000 0.00 0.00 0.00 3.55
1789 2962 3.371898 TGAAATGACTGCATCACTAAGCG 59.628 43.478 0.00 0.00 41.24 4.68
1826 2999 7.544622 TGTTAGTTACTAGCTTATCACACCAG 58.455 38.462 7.68 0.00 0.00 4.00
1848 3021 2.162681 GGCACCAGCTGTATTTCTGTT 58.837 47.619 13.81 0.00 41.70 3.16
1862 3035 1.907807 GTTCATTGGCCTGGCACCA 60.908 57.895 22.05 7.32 34.65 4.17
1880 3053 1.152383 GCCGCGTAAAGCTAGAAGGG 61.152 60.000 4.92 0.00 45.59 3.95
1895 3068 0.529555 TGCTTTTCTTTTGTGGCCGC 60.530 50.000 10.11 10.11 0.00 6.53
1897 3070 2.888834 TCTGCTTTTCTTTTGTGGCC 57.111 45.000 0.00 0.00 0.00 5.36
1905 3078 7.147655 TGCCTACTGTATCTATCTGCTTTTCTT 60.148 37.037 0.00 0.00 0.00 2.52
1906 3079 6.325028 TGCCTACTGTATCTATCTGCTTTTCT 59.675 38.462 0.00 0.00 0.00 2.52
1907 3080 6.516718 TGCCTACTGTATCTATCTGCTTTTC 58.483 40.000 0.00 0.00 0.00 2.29
1909 3082 6.485830 TTGCCTACTGTATCTATCTGCTTT 57.514 37.500 0.00 0.00 0.00 3.51
1910 3083 6.268617 TGATTGCCTACTGTATCTATCTGCTT 59.731 38.462 10.42 0.00 0.00 3.91
1911 3084 5.777223 TGATTGCCTACTGTATCTATCTGCT 59.223 40.000 10.42 0.00 0.00 4.24
1912 3085 5.866633 GTGATTGCCTACTGTATCTATCTGC 59.133 44.000 10.42 0.00 0.00 4.26
1913 3086 6.865726 GTGTGATTGCCTACTGTATCTATCTG 59.134 42.308 10.42 0.00 0.00 2.90
1915 3088 5.859114 CGTGTGATTGCCTACTGTATCTATC 59.141 44.000 0.00 0.00 0.00 2.08
1917 3090 4.885325 TCGTGTGATTGCCTACTGTATCTA 59.115 41.667 0.00 0.00 0.00 1.98
1920 3093 4.099419 TGATCGTGTGATTGCCTACTGTAT 59.901 41.667 0.00 0.00 34.09 2.29
1921 3094 3.445805 TGATCGTGTGATTGCCTACTGTA 59.554 43.478 0.00 0.00 34.09 2.74
1922 3095 2.233676 TGATCGTGTGATTGCCTACTGT 59.766 45.455 0.00 0.00 34.09 3.55
1923 3096 2.892374 TGATCGTGTGATTGCCTACTG 58.108 47.619 0.00 0.00 34.09 2.74
1924 3097 3.827008 ATGATCGTGTGATTGCCTACT 57.173 42.857 0.00 0.00 34.09 2.57
1925 3098 5.984233 TTTATGATCGTGTGATTGCCTAC 57.016 39.130 0.00 0.00 34.09 3.18
1926 3099 7.566760 AAATTTATGATCGTGTGATTGCCTA 57.433 32.000 0.00 0.00 34.09 3.93
1951 3124 2.283298 CTGCCTACGCACTCAATTGAT 58.717 47.619 8.96 0.00 41.12 2.57
2012 3192 4.020218 CCTAGGTCTTCCAGACATGTTGAA 60.020 45.833 0.00 3.11 46.79 2.69
2045 3227 3.579586 ACAAGTGGTGCCATCAAAATCAT 59.420 39.130 0.00 0.00 0.00 2.45
2080 3465 6.984474 GGTTGTACTAGCTAGTTGCATATGAA 59.016 38.462 30.40 12.12 45.94 2.57
2091 3476 6.590068 TGGTACTCTAGGTTGTACTAGCTAG 58.410 44.000 27.24 27.24 44.00 3.42
2136 3528 6.044287 TGGCTGTTATATATGACCTCCACAAT 59.956 38.462 11.47 0.00 0.00 2.71
2177 3569 2.876091 CGTCGTCAAGATCCTTTGCTA 58.124 47.619 0.00 0.00 0.00 3.49
2212 3604 5.156355 GTCGCATTCACACAAAAGATCAAT 58.844 37.500 0.00 0.00 0.00 2.57
2216 3608 2.095768 CGGTCGCATTCACACAAAAGAT 60.096 45.455 0.00 0.00 0.00 2.40
2246 3638 3.124128 GCAAAATGCTTTAGCTTTGCCTC 59.876 43.478 21.45 4.52 46.98 4.70
2325 3717 5.385198 TCACTTGTGGATTTTAAGGCTTCT 58.615 37.500 1.30 0.00 0.00 2.85
2326 3718 5.705609 TCACTTGTGGATTTTAAGGCTTC 57.294 39.130 1.30 0.00 0.00 3.86
2336 3728 4.019051 TCATGTCAGGATCACTTGTGGATT 60.019 41.667 0.00 0.00 0.00 3.01
2346 3738 3.438216 TGCCTTTTCATGTCAGGATCA 57.562 42.857 10.62 0.00 0.00 2.92
2364 3756 6.097356 CACATGGATAATTCTGCCAATATGC 58.903 40.000 0.00 0.00 34.95 3.14
2411 3803 2.441532 CCCTCTGCATGGCCCTTG 60.442 66.667 0.00 0.00 0.00 3.61
2433 3825 1.004918 AAGGTTCAACTCCTCCGCG 60.005 57.895 0.00 0.00 33.76 6.46
2442 3834 4.737054 CCATTACATGCTGAAGGTTCAAC 58.263 43.478 0.00 0.00 36.64 3.18
2494 3886 6.625267 AGCTCTCATCTACCCCTCTAAAATA 58.375 40.000 0.00 0.00 0.00 1.40
2592 3984 4.942363 ATCTTCATCTCCCCCATAATGG 57.058 45.455 0.00 0.00 37.25 3.16
2638 4030 1.210967 ACCAAACGGACCAACTTCAGA 59.789 47.619 0.00 0.00 0.00 3.27
2709 4101 8.599624 AAATGGACATCAACTTATGAAATCCT 57.400 30.769 10.75 0.00 42.57 3.24
2748 4140 1.071385 GGGCCAGAGTAGATGGTCATG 59.929 57.143 4.39 0.00 44.58 3.07
2910 4302 4.056050 GTTGTGTCAGGAACGTTGAGTAT 58.944 43.478 5.00 0.00 0.00 2.12
2929 4321 3.670055 GCTCGGTTTTGATGTGATTGTTG 59.330 43.478 0.00 0.00 0.00 3.33
3106 4504 5.256352 GTTTTCTCGCCGATTCAAATACTC 58.744 41.667 0.00 0.00 0.00 2.59
3107 4505 4.094442 GGTTTTCTCGCCGATTCAAATACT 59.906 41.667 0.00 0.00 0.00 2.12
3372 4779 1.067516 CCCTTCCTTGTGTTTGTGCAG 59.932 52.381 0.00 0.00 0.00 4.41
3392 4805 5.221322 GGAAAAATTGATCCTCTGCCATACC 60.221 44.000 3.13 0.00 32.75 2.73
3466 4882 7.566569 AGATCTGTCATCAGTTCAATCATCTT 58.433 34.615 0.00 0.00 40.73 2.40
3487 4903 7.016661 TCCCTTTGTATTTATCTCCCTGAGATC 59.983 40.741 9.74 0.00 45.03 2.75
3648 5071 2.539338 GCGAGTGTTGCCGGACAAA 61.539 57.895 5.05 0.00 40.82 2.83
3789 5218 1.155859 AGCTGGGCCAAAACCATCA 59.844 52.632 8.04 0.00 37.38 3.07
3898 5327 6.836527 TCTTTCCCTTTATTCCTTTGTTGTGA 59.163 34.615 0.00 0.00 0.00 3.58
3904 5333 6.650807 GCCTTTTCTTTCCCTTTATTCCTTTG 59.349 38.462 0.00 0.00 0.00 2.77
3918 5347 2.820059 CCACCTTGGCCTTTTCTTTC 57.180 50.000 3.32 0.00 0.00 2.62
3974 5403 4.987912 TGGCTTTTAATTCCTTTTTCTGCG 59.012 37.500 0.00 0.00 0.00 5.18
4247 5688 1.599797 CCGTGTTCTCCACAACCCC 60.600 63.158 0.00 0.00 44.78 4.95
4251 5692 1.348064 AGGATCCGTGTTCTCCACAA 58.652 50.000 5.98 0.00 44.78 3.33
4288 5729 3.421844 ACCTTCCATCTGTAAAGGCAAC 58.578 45.455 0.39 0.00 42.76 4.17
4340 5781 4.604490 TGGAGGAGTTAGGGTAAATTTGGT 59.396 41.667 0.00 0.00 0.00 3.67
4615 6059 7.733402 ATGTCAAAACAAAATCCCTGAAATG 57.267 32.000 0.00 0.00 39.30 2.32
4623 6067 9.437045 GATTGAACAAATGTCAAAACAAAATCC 57.563 29.630 0.00 0.00 39.30 3.01
5260 6731 1.813862 CGGGTAATGGCCAACATCGAT 60.814 52.381 10.96 0.00 39.40 3.59
5377 6848 5.907197 TTTTGACACTTTCTCGATCTGTC 57.093 39.130 2.86 2.86 33.30 3.51
5483 6954 4.785453 GCAGGCCGACCTCCCTTG 62.785 72.222 0.00 0.00 46.34 3.61
5542 7013 0.393537 CAGCTGGTAAGGGCTCAAGG 60.394 60.000 5.57 0.00 36.59 3.61
5546 7017 2.512515 CGCAGCTGGTAAGGGCTC 60.513 66.667 17.12 0.00 36.59 4.70
5563 7034 4.864247 ACTTCAAAGTTCAAACACACATGC 59.136 37.500 0.00 0.00 35.21 4.06
5564 7035 5.863397 ACACTTCAAAGTTCAAACACACATG 59.137 36.000 0.00 0.00 37.08 3.21
5565 7036 5.863397 CACACTTCAAAGTTCAAACACACAT 59.137 36.000 0.00 0.00 37.08 3.21
5616 7087 5.008911 ACACCTTGGTAAAAACATACCGTTC 59.991 40.000 0.00 0.00 46.94 3.95
5678 7149 2.743636 TACTCCACACACAAGCTAGC 57.256 50.000 6.62 6.62 0.00 3.42
5691 7162 5.003160 CAGACATCAAACCAACATACTCCA 58.997 41.667 0.00 0.00 0.00 3.86
5692 7163 4.142600 GCAGACATCAAACCAACATACTCC 60.143 45.833 0.00 0.00 0.00 3.85
5693 7164 4.697352 AGCAGACATCAAACCAACATACTC 59.303 41.667 0.00 0.00 0.00 2.59
5694 7165 4.655963 AGCAGACATCAAACCAACATACT 58.344 39.130 0.00 0.00 0.00 2.12
5695 7166 5.156355 CAAGCAGACATCAAACCAACATAC 58.844 41.667 0.00 0.00 0.00 2.39
5696 7167 4.826733 ACAAGCAGACATCAAACCAACATA 59.173 37.500 0.00 0.00 0.00 2.29
5697 7168 3.638160 ACAAGCAGACATCAAACCAACAT 59.362 39.130 0.00 0.00 0.00 2.71
5698 7169 3.023119 ACAAGCAGACATCAAACCAACA 58.977 40.909 0.00 0.00 0.00 3.33
5699 7170 3.715628 ACAAGCAGACATCAAACCAAC 57.284 42.857 0.00 0.00 0.00 3.77
5700 7171 7.446931 TCTTATTACAAGCAGACATCAAACCAA 59.553 33.333 0.00 0.00 0.00 3.67
5701 7172 6.939730 TCTTATTACAAGCAGACATCAAACCA 59.060 34.615 0.00 0.00 0.00 3.67
5702 7173 7.377766 TCTTATTACAAGCAGACATCAAACC 57.622 36.000 0.00 0.00 0.00 3.27
5703 7174 7.414540 CCCTCTTATTACAAGCAGACATCAAAC 60.415 40.741 0.00 0.00 0.00 2.93
5704 7175 6.599244 CCCTCTTATTACAAGCAGACATCAAA 59.401 38.462 0.00 0.00 0.00 2.69
5705 7176 6.115446 CCCTCTTATTACAAGCAGACATCAA 58.885 40.000 0.00 0.00 0.00 2.57
5706 7177 5.189736 ACCCTCTTATTACAAGCAGACATCA 59.810 40.000 0.00 0.00 0.00 3.07
5707 7178 5.525378 CACCCTCTTATTACAAGCAGACATC 59.475 44.000 0.00 0.00 0.00 3.06
5708 7179 5.045578 ACACCCTCTTATTACAAGCAGACAT 60.046 40.000 0.00 0.00 0.00 3.06
5709 7180 4.286032 ACACCCTCTTATTACAAGCAGACA 59.714 41.667 0.00 0.00 0.00 3.41
5710 7181 4.631813 CACACCCTCTTATTACAAGCAGAC 59.368 45.833 0.00 0.00 0.00 3.51
5711 7182 4.832248 CACACCCTCTTATTACAAGCAGA 58.168 43.478 0.00 0.00 0.00 4.26
5712 7183 3.375299 GCACACCCTCTTATTACAAGCAG 59.625 47.826 0.00 0.00 0.00 4.24
5765 7236 2.735134 ACTCGCTGAATTTACGGTTCAC 59.265 45.455 0.00 0.00 32.55 3.18
5969 7442 3.687698 GCAAGAACGCTGAAAATAGGGTA 59.312 43.478 0.00 0.00 42.22 3.69
6000 7473 5.114780 TCATTGCTCTCATTAGAAGCACTC 58.885 41.667 0.00 0.00 36.36 3.51
6018 7491 8.289939 TGGACTAAGGTACTAGTTACTCATTG 57.710 38.462 0.00 0.00 38.49 2.82
6028 7501 7.393796 TCTTGTCTTCTTGGACTAAGGTACTAG 59.606 40.741 0.00 0.00 35.69 2.57
6029 7502 7.236529 TCTTGTCTTCTTGGACTAAGGTACTA 58.763 38.462 0.00 0.00 35.69 1.82
6095 7576 3.202906 GAATTGCCGCTGGAATACACTA 58.797 45.455 0.00 0.00 0.00 2.74
6096 7577 2.017049 GAATTGCCGCTGGAATACACT 58.983 47.619 0.00 0.00 0.00 3.55
6097 7578 1.742831 TGAATTGCCGCTGGAATACAC 59.257 47.619 0.00 0.00 0.00 2.90
6098 7579 1.742831 GTGAATTGCCGCTGGAATACA 59.257 47.619 0.00 0.00 0.00 2.29
6099 7580 1.065551 GGTGAATTGCCGCTGGAATAC 59.934 52.381 0.00 0.00 0.00 1.89
6100 7581 1.340502 TGGTGAATTGCCGCTGGAATA 60.341 47.619 0.00 0.00 0.00 1.75
6101 7582 0.611618 TGGTGAATTGCCGCTGGAAT 60.612 50.000 0.00 0.00 0.00 3.01
6102 7583 1.228398 TGGTGAATTGCCGCTGGAA 60.228 52.632 0.00 0.00 0.00 3.53
6103 7584 1.675310 CTGGTGAATTGCCGCTGGA 60.675 57.895 0.00 0.00 0.00 3.86
6104 7585 1.651240 CTCTGGTGAATTGCCGCTGG 61.651 60.000 0.00 0.00 0.00 4.85
6105 7586 1.651240 CCTCTGGTGAATTGCCGCTG 61.651 60.000 0.00 0.00 0.00 5.18
6106 7587 1.377725 CCTCTGGTGAATTGCCGCT 60.378 57.895 0.00 0.00 0.00 5.52
6112 7593 5.126707 GCATCTTCATTTCCTCTGGTGAATT 59.873 40.000 0.00 0.00 30.97 2.17
6125 7606 3.763360 TGAAATCACCGGCATCTTCATTT 59.237 39.130 0.00 0.00 0.00 2.32
6126 7607 3.355378 TGAAATCACCGGCATCTTCATT 58.645 40.909 0.00 0.00 0.00 2.57
6200 7681 3.240069 GAACTGCACTGCTTTGCTATTG 58.760 45.455 10.83 2.90 43.41 1.90
6203 7684 1.238439 GGAACTGCACTGCTTTGCTA 58.762 50.000 10.83 0.00 43.41 3.49
6240 7721 1.894466 TGGTCGAACGGAGAACCATAA 59.106 47.619 0.00 0.00 35.59 1.90
6281 7762 0.466189 ACTTGTTGTGCTGGAGGGTG 60.466 55.000 0.00 0.00 0.00 4.61
6285 7766 4.516698 ACAGATTTACTTGTTGTGCTGGAG 59.483 41.667 0.00 0.00 0.00 3.86
6370 7854 6.371271 GGTTACAAATTTGGCATAAGCATGTT 59.629 34.615 21.74 0.00 44.61 2.71
6392 7876 0.247736 TTTGTGGCGCAACTTTGGTT 59.752 45.000 17.46 0.00 36.72 3.67
6393 7877 0.247736 TTTTGTGGCGCAACTTTGGT 59.752 45.000 17.46 0.00 36.72 3.67
6404 7888 5.067674 TCTGGATAGTATTGCATTTTGTGGC 59.932 40.000 0.00 0.00 0.00 5.01
6418 7902 5.138276 AGGCAGTTTCGTATCTGGATAGTA 58.862 41.667 2.81 0.00 32.94 1.82
6425 7909 2.959516 TGTGAGGCAGTTTCGTATCTG 58.040 47.619 0.00 0.00 35.12 2.90


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

AutoCloner maintained by Alex Coulton.