Multiple sequence alignment - TraesCS4A01G202000

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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 TraesCS4A01G202000 chr4A 100.000 2594 0 0 1 2594 491714484 491711891 0.000000e+00 4791.0
1 TraesCS4A01G202000 chr7A 93.750 816 46 5 4 816 33005153 33004340 0.000000e+00 1219.0
2 TraesCS4A01G202000 chr7A 80.000 115 15 2 1888 1994 182723538 182723652 7.700000e-11 78.7
3 TraesCS4A01G202000 chr7A 86.364 66 6 3 2512 2576 671411237 671411174 4.630000e-08 69.4
4 TraesCS4A01G202000 chr1D 92.176 818 61 2 2 816 66686835 66687652 0.000000e+00 1153.0
5 TraesCS4A01G202000 chr3D 92.186 819 54 5 1 816 531259803 531258992 0.000000e+00 1149.0
6 TraesCS4A01G202000 chr3D 91.320 818 56 4 1 816 597139196 597138392 0.000000e+00 1103.0
7 TraesCS4A01G202000 chr3D 93.333 45 2 1 1826 1870 268520481 268520438 5.990000e-07 65.8
8 TraesCS4A01G202000 chr5A 91.707 820 60 5 1 816 211614143 211614958 0.000000e+00 1131.0
9 TraesCS4A01G202000 chr5A 91.320 818 66 2 1 816 679367900 679367086 0.000000e+00 1112.0
10 TraesCS4A01G202000 chr5A 78.431 204 34 6 1861 2055 426721238 426721036 9.750000e-25 124.0
11 TraesCS4A01G202000 chr6A 91.453 819 67 3 1 816 99769379 99768561 0.000000e+00 1122.0
12 TraesCS4A01G202000 chr4D 87.106 1047 55 26 817 1820 81917921 81916912 0.000000e+00 1112.0
13 TraesCS4A01G202000 chr4D 84.543 427 37 12 2171 2594 81916600 81916200 1.870000e-106 396.0
14 TraesCS4A01G202000 chr6D 91.320 818 63 2 1 816 116853835 116854646 0.000000e+00 1110.0
15 TraesCS4A01G202000 chr3A 91.198 818 65 3 1 815 653315561 653316374 0.000000e+00 1105.0
16 TraesCS4A01G202000 chr4B 86.275 663 58 18 817 1464 115555917 115555273 0.000000e+00 689.0
17 TraesCS4A01G202000 chr4B 86.622 299 20 10 2122 2419 115553700 115553421 1.940000e-81 313.0
18 TraesCS4A01G202000 chr4B 87.410 278 24 6 1521 1797 115555106 115554839 2.510000e-80 309.0
19 TraesCS4A01G202000 chr4B 93.333 165 10 1 2431 2594 115552097 115551933 2.580000e-60 243.0
20 TraesCS4A01G202000 chr4B 88.439 173 19 1 2139 2310 115554836 115554664 9.410000e-50 207.0
21 TraesCS4A01G202000 chr2B 90.000 100 10 0 2024 2123 683778587 683778488 2.090000e-26 130.0
22 TraesCS4A01G202000 chr5D 95.122 41 0 2 2525 2564 384745081 384745042 2.160000e-06 63.9


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 TraesCS4A01G202000 chr4A 491711891 491714484 2593 True 4791.0 4791 100.0000 1 2594 1 chr4A.!!$R1 2593
1 TraesCS4A01G202000 chr7A 33004340 33005153 813 True 1219.0 1219 93.7500 4 816 1 chr7A.!!$R1 812
2 TraesCS4A01G202000 chr1D 66686835 66687652 817 False 1153.0 1153 92.1760 2 816 1 chr1D.!!$F1 814
3 TraesCS4A01G202000 chr3D 531258992 531259803 811 True 1149.0 1149 92.1860 1 816 1 chr3D.!!$R2 815
4 TraesCS4A01G202000 chr3D 597138392 597139196 804 True 1103.0 1103 91.3200 1 816 1 chr3D.!!$R3 815
5 TraesCS4A01G202000 chr5A 211614143 211614958 815 False 1131.0 1131 91.7070 1 816 1 chr5A.!!$F1 815
6 TraesCS4A01G202000 chr5A 679367086 679367900 814 True 1112.0 1112 91.3200 1 816 1 chr5A.!!$R2 815
7 TraesCS4A01G202000 chr6A 99768561 99769379 818 True 1122.0 1122 91.4530 1 816 1 chr6A.!!$R1 815
8 TraesCS4A01G202000 chr4D 81916200 81917921 1721 True 754.0 1112 85.8245 817 2594 2 chr4D.!!$R1 1777
9 TraesCS4A01G202000 chr6D 116853835 116854646 811 False 1110.0 1110 91.3200 1 816 1 chr6D.!!$F1 815
10 TraesCS4A01G202000 chr3A 653315561 653316374 813 False 1105.0 1105 91.1980 1 815 1 chr3A.!!$F1 814
11 TraesCS4A01G202000 chr4B 115551933 115555917 3984 True 352.2 689 88.4158 817 2594 5 chr4B.!!$R1 1777

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
547 557 1.073319 TGGGGAAGAGTGTTGGGGA 60.073 57.895 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 3409 0.039074 GCTGCGTGCGACCTATATCT 60.039 55.0 0.0 0.0 0.0 1.98 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
541 551 1.132689 AGGAAGAGTGGGGAAGAGTGT 60.133 52.381 0.00 0.00 0.00 3.55
542 552 1.700186 GGAAGAGTGGGGAAGAGTGTT 59.300 52.381 0.00 0.00 0.00 3.32
547 557 1.073319 TGGGGAAGAGTGTTGGGGA 60.073 57.895 0.00 0.00 0.00 4.81
584 596 2.434702 GGAGAGGCCGGATAGAAAAAGA 59.565 50.000 5.05 0.00 0.00 2.52
603 615 4.033776 CCACCCTGTGCCACCGAT 62.034 66.667 0.00 0.00 31.34 4.18
685 697 1.532921 CCAAAAGCGACGCAAACTTGA 60.533 47.619 23.70 0.00 0.00 3.02
697 709 2.463589 AAACTTGAGCCGCGGATGGA 62.464 55.000 33.48 12.73 0.00 3.41
718 730 1.370609 TGAAAGCGGACACAAAACGA 58.629 45.000 0.00 0.00 0.00 3.85
770 784 7.060421 TGAACTCTCCTTTGTTCATTTTACCT 58.940 34.615 4.69 0.00 44.89 3.08
777 791 6.319152 TCCTTTGTTCATTTTACCTCAAACGA 59.681 34.615 0.00 0.00 0.00 3.85
805 819 2.442272 ACAGGATAGGGTCGCGCT 60.442 61.111 5.56 0.00 0.00 5.92
877 901 2.548067 CGAACCAAGTCAGCCAAGTACT 60.548 50.000 0.00 0.00 0.00 2.73
878 902 2.841442 ACCAAGTCAGCCAAGTACTC 57.159 50.000 0.00 0.00 0.00 2.59
879 903 2.047061 ACCAAGTCAGCCAAGTACTCA 58.953 47.619 0.00 0.00 0.00 3.41
880 904 2.438021 ACCAAGTCAGCCAAGTACTCAA 59.562 45.455 0.00 0.00 0.00 3.02
881 905 2.808543 CCAAGTCAGCCAAGTACTCAAC 59.191 50.000 0.00 0.00 0.00 3.18
882 906 3.495100 CCAAGTCAGCCAAGTACTCAACT 60.495 47.826 0.00 0.00 41.49 3.16
883 907 3.393089 AGTCAGCCAAGTACTCAACTG 57.607 47.619 11.02 11.02 38.88 3.16
971 995 4.845580 CGCGCCATGCCTTCTCCT 62.846 66.667 0.00 0.00 42.08 3.69
972 996 3.207669 GCGCCATGCCTTCTCCTG 61.208 66.667 0.00 0.00 37.76 3.86
973 997 2.586245 CGCCATGCCTTCTCCTGA 59.414 61.111 0.00 0.00 0.00 3.86
1004 1030 2.653726 CCTATAAATGCAGCCACCACA 58.346 47.619 0.00 0.00 0.00 4.17
1039 1065 2.256591 ACAAGCTGAGCCAACGCAG 61.257 57.895 0.00 0.00 45.59 5.18
1184 1210 3.073735 AGAGGCCGTGGAGCAGAG 61.074 66.667 0.00 0.00 0.00 3.35
1196 1222 2.886124 GCAGAGAGCGGCGGTAAC 60.886 66.667 13.22 9.31 0.00 2.50
1323 1355 2.092968 TCCCATAGTGATGCACCACTTC 60.093 50.000 21.35 0.00 44.32 3.01
1341 1373 0.042731 TCCCCTTCCATTCTCGTCCT 59.957 55.000 0.00 0.00 0.00 3.85
1354 1386 2.583520 GTCCTGGGCTGCTCTGAG 59.416 66.667 8.09 0.00 0.00 3.35
1355 1387 1.986757 GTCCTGGGCTGCTCTGAGA 60.987 63.158 9.28 1.09 0.00 3.27
1360 1392 0.107993 TGGGCTGCTCTGAGATTTCG 60.108 55.000 9.28 0.00 0.00 3.46
1367 1402 1.535015 GCTCTGAGATTTCGACCTCCG 60.535 57.143 9.28 1.51 40.25 4.63
1368 1403 1.066303 CTCTGAGATTTCGACCTCCGG 59.934 57.143 0.00 0.00 39.14 5.14
1371 1406 0.528684 GAGATTTCGACCTCCGGCTG 60.529 60.000 0.00 0.00 39.14 4.85
1384 1419 2.281761 GGCTGGTGTGGTCACTGG 60.282 66.667 2.66 0.00 43.41 4.00
1385 1420 2.281761 GCTGGTGTGGTCACTGGG 60.282 66.667 2.66 0.00 43.41 4.45
1406 1441 5.070180 TGGGATTTTGATGAAGCTTTTGTCA 59.930 36.000 0.00 2.78 0.00 3.58
1464 1499 6.432162 GGGCTAGATTATTTGATGAGCATTGA 59.568 38.462 0.00 0.00 0.00 2.57
1465 1500 7.361885 GGGCTAGATTATTTGATGAGCATTGAG 60.362 40.741 0.00 0.00 0.00 3.02
1467 1502 6.896021 AGATTATTTGATGAGCATTGAGGG 57.104 37.500 0.00 0.00 0.00 4.30
1468 1503 4.924305 TTATTTGATGAGCATTGAGGGC 57.076 40.909 0.00 0.00 0.00 5.19
1470 1505 3.650281 TTTGATGAGCATTGAGGGCTA 57.350 42.857 0.00 0.00 42.78 3.93
1471 1506 2.924757 TGATGAGCATTGAGGGCTAG 57.075 50.000 0.00 0.00 42.78 3.42
1472 1507 2.401568 TGATGAGCATTGAGGGCTAGA 58.598 47.619 0.00 0.00 42.78 2.43
1474 1509 3.393609 TGATGAGCATTGAGGGCTAGATT 59.606 43.478 0.00 0.00 42.78 2.40
1475 1510 4.594491 TGATGAGCATTGAGGGCTAGATTA 59.406 41.667 0.00 0.00 42.78 1.75
1476 1511 5.250082 TGATGAGCATTGAGGGCTAGATTAT 59.750 40.000 0.00 0.00 42.78 1.28
1479 1514 5.766670 TGAGCATTGAGGGCTAGATTATTTG 59.233 40.000 0.00 0.00 42.78 2.32
1480 1515 5.945310 AGCATTGAGGGCTAGATTATTTGA 58.055 37.500 0.00 0.00 40.47 2.69
1481 1516 6.550163 AGCATTGAGGGCTAGATTATTTGAT 58.450 36.000 0.00 0.00 40.47 2.57
1482 1517 6.433404 AGCATTGAGGGCTAGATTATTTGATG 59.567 38.462 0.00 0.00 40.47 3.07
1506 1647 6.897966 TGAGAATTGTATCTTGTACTCCCTCT 59.102 38.462 0.00 0.00 0.00 3.69
1511 1652 1.835494 TCTTGTACTCCCTCTGTCCG 58.165 55.000 0.00 0.00 0.00 4.79
1526 1675 5.880332 CCTCTGTCCGAAATTTCCTAATTCA 59.120 40.000 12.54 3.55 32.85 2.57
1556 1710 8.311836 CGGAGGGAGTATGTGTTAATATAATGT 58.688 37.037 0.00 0.00 0.00 2.71
1577 1731 8.742554 AATGTCATAAAAGTTCATTTCGGAAC 57.257 30.769 0.00 0.00 45.87 3.62
1641 1801 1.135083 CACGGTCAACTAGCACTAGGG 60.135 57.143 9.41 0.00 37.49 3.53
1658 1826 1.451504 GGCATCCCATGGATCGTCA 59.548 57.895 15.22 0.00 40.98 4.35
1659 1827 0.604780 GGCATCCCATGGATCGTCAG 60.605 60.000 15.22 0.00 40.98 3.51
1661 1829 1.002888 GCATCCCATGGATCGTCAGAT 59.997 52.381 15.22 2.08 40.98 2.90
1669 1837 4.382040 CCATGGATCGTCAGATATACCACC 60.382 50.000 5.56 0.00 37.19 4.61
1671 1839 4.416516 TGGATCGTCAGATATACCACCAT 58.583 43.478 0.00 0.00 37.19 3.55
1686 1854 5.007385 ACCACCATAGTCGTTCAATCTAC 57.993 43.478 0.00 0.00 0.00 2.59
1687 1855 4.464951 ACCACCATAGTCGTTCAATCTACA 59.535 41.667 0.00 0.00 0.00 2.74
1688 1856 5.043903 CCACCATAGTCGTTCAATCTACAG 58.956 45.833 0.00 0.00 0.00 2.74
1689 1857 5.394224 CCACCATAGTCGTTCAATCTACAGT 60.394 44.000 0.00 0.00 0.00 3.55
1695 1863 9.999009 CATAGTCGTTCAATCTACAGTAACTTA 57.001 33.333 0.00 0.00 0.00 2.24
1758 1926 1.451387 CGCACCAATCCAGTACCCC 60.451 63.158 0.00 0.00 0.00 4.95
1768 1936 0.035439 CCAGTACCCCAATCACGCTT 60.035 55.000 0.00 0.00 0.00 4.68
1797 3090 1.816224 GTTGCGGCAAAGGAGGATTTA 59.184 47.619 18.23 0.00 0.00 1.40
1809 3102 3.078837 GGAGGATTTAAGGCGTGTTTGA 58.921 45.455 0.00 0.00 0.00 2.69
1810 3103 3.694566 GGAGGATTTAAGGCGTGTTTGAT 59.305 43.478 0.00 0.00 0.00 2.57
1811 3104 4.879545 GGAGGATTTAAGGCGTGTTTGATA 59.120 41.667 0.00 0.00 0.00 2.15
1812 3105 5.007724 GGAGGATTTAAGGCGTGTTTGATAG 59.992 44.000 0.00 0.00 0.00 2.08
1813 3106 4.881850 AGGATTTAAGGCGTGTTTGATAGG 59.118 41.667 0.00 0.00 0.00 2.57
1814 3107 4.638865 GGATTTAAGGCGTGTTTGATAGGT 59.361 41.667 0.00 0.00 0.00 3.08
1815 3108 5.220796 GGATTTAAGGCGTGTTTGATAGGTC 60.221 44.000 0.00 0.00 0.00 3.85
1816 3109 2.851263 AAGGCGTGTTTGATAGGTCA 57.149 45.000 0.00 0.00 0.00 4.02
1817 3110 2.094762 AGGCGTGTTTGATAGGTCAC 57.905 50.000 0.00 0.00 33.11 3.67
1818 3111 1.346395 AGGCGTGTTTGATAGGTCACA 59.654 47.619 0.00 0.00 33.11 3.58
1819 3112 1.463444 GGCGTGTTTGATAGGTCACAC 59.537 52.381 0.00 0.00 35.96 3.82
1820 3113 2.139917 GCGTGTTTGATAGGTCACACA 58.860 47.619 0.00 0.00 41.41 3.72
1824 3117 4.681074 TGTTTGATAGGTCACACACTCA 57.319 40.909 0.00 0.00 39.44 3.41
1825 3118 4.377021 TGTTTGATAGGTCACACACTCAC 58.623 43.478 0.00 0.00 39.44 3.51
1826 3119 4.141824 TGTTTGATAGGTCACACACTCACA 60.142 41.667 0.00 0.00 39.44 3.58
1827 3120 3.660501 TGATAGGTCACACACTCACAC 57.339 47.619 0.00 0.00 0.00 3.82
1828 3121 3.230976 TGATAGGTCACACACTCACACT 58.769 45.455 0.00 0.00 0.00 3.55
1829 3122 4.403734 TGATAGGTCACACACTCACACTA 58.596 43.478 0.00 0.00 0.00 2.74
1830 3123 4.459337 TGATAGGTCACACACTCACACTAG 59.541 45.833 0.00 0.00 0.00 2.57
1831 3124 2.667470 AGGTCACACACTCACACTAGT 58.333 47.619 0.00 0.00 0.00 2.57
1832 3125 2.623889 AGGTCACACACTCACACTAGTC 59.376 50.000 0.00 0.00 0.00 2.59
1833 3126 2.288273 GGTCACACACTCACACTAGTCC 60.288 54.545 0.00 0.00 0.00 3.85
1834 3127 2.623889 GTCACACACTCACACTAGTCCT 59.376 50.000 0.00 0.00 0.00 3.85
1835 3128 2.623416 TCACACACTCACACTAGTCCTG 59.377 50.000 0.00 0.00 0.00 3.86
1836 3129 1.964223 ACACACTCACACTAGTCCTGG 59.036 52.381 0.00 0.00 0.00 4.45
1837 3130 0.969894 ACACTCACACTAGTCCTGGC 59.030 55.000 0.00 0.00 0.00 4.85
1838 3131 0.247736 CACTCACACTAGTCCTGGCC 59.752 60.000 0.00 0.00 0.00 5.36
1839 3132 0.178932 ACTCACACTAGTCCTGGCCA 60.179 55.000 4.71 4.71 0.00 5.36
1840 3133 1.198713 CTCACACTAGTCCTGGCCAT 58.801 55.000 5.51 0.00 0.00 4.40
1841 3134 0.904649 TCACACTAGTCCTGGCCATG 59.095 55.000 5.51 2.84 0.00 3.66
1842 3135 0.107508 CACACTAGTCCTGGCCATGG 60.108 60.000 5.51 7.63 0.00 3.66
1843 3136 1.274703 ACACTAGTCCTGGCCATGGG 61.275 60.000 15.13 4.96 0.00 4.00
1860 3153 4.050934 GCAACCCGGCCCGAAAAG 62.051 66.667 3.71 0.00 0.00 2.27
1861 3154 3.370231 CAACCCGGCCCGAAAAGG 61.370 66.667 3.71 0.00 40.63 3.11
1871 3164 2.983791 CGAAAAGGCCCGGACCTA 59.016 61.111 10.84 0.00 39.93 3.08
1872 3165 1.153429 CGAAAAGGCCCGGACCTAG 60.153 63.158 10.84 0.00 39.93 3.02
1873 3166 1.610554 CGAAAAGGCCCGGACCTAGA 61.611 60.000 10.84 0.00 39.93 2.43
1874 3167 0.837940 GAAAAGGCCCGGACCTAGAT 59.162 55.000 10.84 0.00 39.93 1.98
1875 3168 1.212195 GAAAAGGCCCGGACCTAGATT 59.788 52.381 10.84 5.89 39.93 2.40
1876 3169 1.296002 AAAGGCCCGGACCTAGATTT 58.704 50.000 10.84 0.00 39.93 2.17
1877 3170 1.296002 AAGGCCCGGACCTAGATTTT 58.704 50.000 10.84 0.00 39.93 1.82
1878 3171 0.546598 AGGCCCGGACCTAGATTTTG 59.453 55.000 7.93 0.00 38.67 2.44
1879 3172 0.544697 GGCCCGGACCTAGATTTTGA 59.455 55.000 0.73 0.00 0.00 2.69
1880 3173 1.475213 GGCCCGGACCTAGATTTTGAG 60.475 57.143 0.73 0.00 0.00 3.02
1881 3174 1.954927 CCCGGACCTAGATTTTGAGC 58.045 55.000 0.73 0.00 0.00 4.26
1882 3175 1.475213 CCCGGACCTAGATTTTGAGCC 60.475 57.143 0.73 0.00 0.00 4.70
1883 3176 1.475213 CCGGACCTAGATTTTGAGCCC 60.475 57.143 0.00 0.00 0.00 5.19
1884 3177 1.806623 CGGACCTAGATTTTGAGCCCG 60.807 57.143 0.00 0.00 0.00 6.13
1885 3178 1.485066 GGACCTAGATTTTGAGCCCGA 59.515 52.381 0.00 0.00 0.00 5.14
1886 3179 2.093128 GGACCTAGATTTTGAGCCCGAA 60.093 50.000 0.00 0.00 0.00 4.30
1887 3180 3.198872 GACCTAGATTTTGAGCCCGAAG 58.801 50.000 0.00 0.00 0.00 3.79
1888 3181 2.838202 ACCTAGATTTTGAGCCCGAAGA 59.162 45.455 0.00 0.00 0.00 2.87
1889 3182 3.198872 CCTAGATTTTGAGCCCGAAGAC 58.801 50.000 0.00 0.00 0.00 3.01
1890 3183 2.115343 AGATTTTGAGCCCGAAGACC 57.885 50.000 0.00 0.00 0.00 3.85
1891 3184 0.727398 GATTTTGAGCCCGAAGACCG 59.273 55.000 0.00 0.00 38.18 4.79
1911 3204 3.733960 GCCGGGCCTGTCGTTTTC 61.734 66.667 11.58 0.00 0.00 2.29
1912 3205 2.281208 CCGGGCCTGTCGTTTTCA 60.281 61.111 11.58 0.00 0.00 2.69
1913 3206 2.613506 CCGGGCCTGTCGTTTTCAC 61.614 63.158 11.58 0.00 0.00 3.18
1928 3221 5.043189 GTTTTCACGATTTACTGAAGGGG 57.957 43.478 0.00 0.00 0.00 4.79
1929 3222 2.396590 TCACGATTTACTGAAGGGGC 57.603 50.000 0.00 0.00 0.00 5.80
1930 3223 1.065709 TCACGATTTACTGAAGGGGCC 60.066 52.381 0.00 0.00 0.00 5.80
1931 3224 0.255033 ACGATTTACTGAAGGGGCCC 59.745 55.000 17.12 17.12 0.00 5.80
1932 3225 0.814010 CGATTTACTGAAGGGGCCCG 60.814 60.000 18.95 5.08 0.00 6.13
1933 3226 0.544697 GATTTACTGAAGGGGCCCGA 59.455 55.000 18.95 4.15 0.00 5.14
1934 3227 0.255033 ATTTACTGAAGGGGCCCGAC 59.745 55.000 18.95 15.82 0.00 4.79
1935 3228 0.838987 TTTACTGAAGGGGCCCGACT 60.839 55.000 18.95 4.92 0.00 4.18
1936 3229 1.262640 TTACTGAAGGGGCCCGACTC 61.263 60.000 18.95 15.74 0.00 3.36
1937 3230 2.449967 TACTGAAGGGGCCCGACTCA 62.450 60.000 18.95 19.44 0.00 3.41
1938 3231 2.528127 TGAAGGGGCCCGACTCAA 60.528 61.111 18.95 3.96 0.00 3.02
1939 3232 2.269241 GAAGGGGCCCGACTCAAG 59.731 66.667 18.95 0.00 0.00 3.02
1940 3233 3.330720 AAGGGGCCCGACTCAAGG 61.331 66.667 18.95 0.00 0.00 3.61
1946 3239 4.452733 CCCGACTCAAGGCCCGAC 62.453 72.222 0.00 0.00 0.00 4.79
1947 3240 3.691342 CCGACTCAAGGCCCGACA 61.691 66.667 0.00 0.00 0.00 4.35
1948 3241 2.125912 CGACTCAAGGCCCGACAG 60.126 66.667 0.00 0.00 0.00 3.51
1949 3242 2.266055 GACTCAAGGCCCGACAGG 59.734 66.667 0.00 0.00 39.47 4.00
1962 3255 4.718940 CCCGACAGGCTTTATCATTTTT 57.281 40.909 0.00 0.00 35.76 1.94
1963 3256 4.423732 CCCGACAGGCTTTATCATTTTTG 58.576 43.478 0.00 0.00 35.76 2.44
1964 3257 4.423732 CCGACAGGCTTTATCATTTTTGG 58.576 43.478 0.00 0.00 0.00 3.28
1965 3258 4.423732 CGACAGGCTTTATCATTTTTGGG 58.576 43.478 0.00 0.00 0.00 4.12
1966 3259 4.183865 GACAGGCTTTATCATTTTTGGGC 58.816 43.478 0.00 0.00 0.00 5.36
1967 3260 3.055167 ACAGGCTTTATCATTTTTGGGCC 60.055 43.478 0.00 0.00 38.71 5.80
1968 3261 3.055240 CAGGCTTTATCATTTTTGGGCCA 60.055 43.478 0.00 0.00 40.61 5.36
1969 3262 3.198417 AGGCTTTATCATTTTTGGGCCAG 59.802 43.478 6.23 0.00 40.61 4.85
1970 3263 3.534554 GCTTTATCATTTTTGGGCCAGG 58.465 45.455 6.23 0.00 0.00 4.45
1971 3264 3.534554 CTTTATCATTTTTGGGCCAGGC 58.465 45.455 6.23 1.26 0.00 4.85
1972 3265 2.548464 TATCATTTTTGGGCCAGGCT 57.452 45.000 12.43 0.00 0.00 4.58
1973 3266 1.660242 ATCATTTTTGGGCCAGGCTT 58.340 45.000 12.43 0.00 0.00 4.35
1974 3267 0.686224 TCATTTTTGGGCCAGGCTTG 59.314 50.000 12.43 4.28 0.00 4.01
1997 3290 2.193786 AAAAACAGGCCCGACGGT 59.806 55.556 13.94 0.00 0.00 4.83
1998 3291 1.895231 AAAAACAGGCCCGACGGTC 60.895 57.895 13.94 0.00 0.00 4.79
1999 3292 4.675029 AAACAGGCCCGACGGTCG 62.675 66.667 22.88 22.88 39.51 4.79
2022 3315 3.874873 GGCTTGGGCGCAAAAATC 58.125 55.556 17.59 6.87 39.81 2.17
2023 3316 1.005156 GGCTTGGGCGCAAAAATCA 60.005 52.632 17.59 0.00 39.81 2.57
2024 3317 1.015607 GGCTTGGGCGCAAAAATCAG 61.016 55.000 17.59 5.61 39.81 2.90
2025 3318 1.015607 GCTTGGGCGCAAAAATCAGG 61.016 55.000 17.59 5.06 0.00 3.86
2026 3319 1.005156 TTGGGCGCAAAAATCAGGC 60.005 52.632 14.56 0.00 0.00 4.85
2027 3320 2.125552 GGGCGCAAAAATCAGGCC 60.126 61.111 10.83 0.00 43.01 5.19
2028 3321 2.649129 GGGCGCAAAAATCAGGCCT 61.649 57.895 10.83 0.00 44.69 5.19
2029 3322 1.446618 GGCGCAAAAATCAGGCCTG 60.447 57.895 27.87 27.87 40.59 4.85
2030 3323 1.586028 GCGCAAAAATCAGGCCTGA 59.414 52.632 36.73 36.73 44.59 3.86
2031 3324 0.733909 GCGCAAAAATCAGGCCTGAC 60.734 55.000 37.39 21.77 43.11 3.51
2032 3325 0.454957 CGCAAAAATCAGGCCTGACG 60.455 55.000 37.39 28.68 43.11 4.35
2033 3326 0.109132 GCAAAAATCAGGCCTGACGG 60.109 55.000 37.39 23.48 43.11 4.79
2034 3327 1.247567 CAAAAATCAGGCCTGACGGT 58.752 50.000 37.39 22.26 43.11 4.83
2035 3328 1.200020 CAAAAATCAGGCCTGACGGTC 59.800 52.381 37.39 0.00 43.11 4.79
2036 3329 0.673644 AAAATCAGGCCTGACGGTCG 60.674 55.000 37.39 7.75 43.11 4.79
2037 3330 2.521958 AAATCAGGCCTGACGGTCGG 62.522 60.000 37.39 6.89 43.11 4.79
2060 3353 4.850822 GCTCGGGCCTAGGTTTAC 57.149 61.111 11.31 0.00 0.00 2.01
2061 3354 2.209475 GCTCGGGCCTAGGTTTACT 58.791 57.895 11.31 0.00 0.00 2.24
2062 3355 0.179081 GCTCGGGCCTAGGTTTACTG 60.179 60.000 11.31 4.17 0.00 2.74
2063 3356 0.179081 CTCGGGCCTAGGTTTACTGC 60.179 60.000 11.31 0.00 0.00 4.40
2064 3357 1.153229 CGGGCCTAGGTTTACTGCC 60.153 63.158 11.31 2.81 41.42 4.85
2065 3358 1.623542 CGGGCCTAGGTTTACTGCCT 61.624 60.000 11.31 0.00 41.84 4.75
2066 3359 0.180642 GGGCCTAGGTTTACTGCCTC 59.819 60.000 11.31 0.00 41.84 4.70
2067 3360 0.179081 GGCCTAGGTTTACTGCCTCG 60.179 60.000 11.31 0.00 39.05 4.63
2068 3361 0.179081 GCCTAGGTTTACTGCCTCGG 60.179 60.000 11.31 0.00 40.70 4.63
2069 3362 0.464452 CCTAGGTTTACTGCCTCGGG 59.536 60.000 0.00 0.00 35.87 5.14
2079 3372 2.124695 GCCTCGGGCTTTGGTAGG 60.125 66.667 7.58 0.00 46.69 3.18
2085 3378 2.824489 GGCTTTGGTAGGCTCGGC 60.824 66.667 0.00 0.00 45.60 5.54
2086 3379 2.046314 GCTTTGGTAGGCTCGGCA 60.046 61.111 0.00 0.00 0.00 5.69
2087 3380 2.399356 GCTTTGGTAGGCTCGGCAC 61.399 63.158 0.00 0.00 0.00 5.01
2112 3405 4.256180 GGCCCGGCCTGGTAGATG 62.256 72.222 22.31 0.00 46.69 2.90
2113 3406 4.256180 GCCCGGCCTGGTAGATGG 62.256 72.222 15.45 0.00 35.15 3.51
2136 3429 0.039074 GATATAGGTCGCACGCAGCT 60.039 55.000 0.00 0.00 42.61 4.24
2200 3775 2.141535 ACATCGAATTCCTAGCGAGC 57.858 50.000 0.00 0.00 37.48 5.03
2261 3836 1.142314 GCCATGCATGCCATTCGTT 59.858 52.632 21.69 0.00 29.71 3.85
2266 3841 0.246910 TGCATGCCATTCGTTTGCAT 59.753 45.000 16.68 0.00 46.09 3.96
2282 3857 2.082366 CATGCGTTGGAAAGCGTGC 61.082 57.895 6.58 0.00 42.40 5.34
2292 3867 1.098050 GAAAGCGTGCAAGATGGGAT 58.902 50.000 2.99 0.00 0.00 3.85
2318 3893 4.543689 TCGACCATTACTCCTTACTCCAT 58.456 43.478 0.00 0.00 0.00 3.41
2329 3904 3.055385 TCCTTACTCCATTCCTTTCACCG 60.055 47.826 0.00 0.00 0.00 4.94
2330 3905 3.307480 CCTTACTCCATTCCTTTCACCGT 60.307 47.826 0.00 0.00 0.00 4.83
2331 3906 2.474410 ACTCCATTCCTTTCACCGTC 57.526 50.000 0.00 0.00 0.00 4.79
2332 3907 1.003233 ACTCCATTCCTTTCACCGTCC 59.997 52.381 0.00 0.00 0.00 4.79
2333 3908 1.003118 CTCCATTCCTTTCACCGTCCA 59.997 52.381 0.00 0.00 0.00 4.02
2334 3909 1.422024 TCCATTCCTTTCACCGTCCAA 59.578 47.619 0.00 0.00 0.00 3.53
2335 3910 2.158593 TCCATTCCTTTCACCGTCCAAA 60.159 45.455 0.00 0.00 0.00 3.28
2351 3926 4.970003 CGTCCAAAGTTCAAACTGTCATTC 59.030 41.667 0.00 0.00 39.66 2.67
2360 3935 6.769822 AGTTCAAACTGTCATTCACATCTCTT 59.230 34.615 0.00 0.00 37.98 2.85
2361 3936 6.791887 TCAAACTGTCATTCACATCTCTTC 57.208 37.500 0.00 0.00 33.23 2.87
2362 3937 5.702670 TCAAACTGTCATTCACATCTCTTCC 59.297 40.000 0.00 0.00 33.23 3.46
2363 3938 5.495926 AACTGTCATTCACATCTCTTCCT 57.504 39.130 0.00 0.00 33.23 3.36
2364 3939 5.495926 ACTGTCATTCACATCTCTTCCTT 57.504 39.130 0.00 0.00 33.23 3.36
2365 3940 5.874093 ACTGTCATTCACATCTCTTCCTTT 58.126 37.500 0.00 0.00 33.23 3.11
2366 3941 5.704515 ACTGTCATTCACATCTCTTCCTTTG 59.295 40.000 0.00 0.00 33.23 2.77
2379 3954 3.960755 TCTTCCTTTGTGTGTGAGAGAGA 59.039 43.478 0.00 0.00 0.00 3.10
2398 5279 8.675705 AGAGAGAGGAAAAGAAAAGAAAAGAG 57.324 34.615 0.00 0.00 0.00 2.85
2528 5412 3.006003 GTGGTTATTTTTCTTTGCGGGGA 59.994 43.478 0.00 0.00 0.00 4.81
2584 5468 5.082425 ACAATGAAAGGGCAAGAGATTCTT 58.918 37.500 0.00 0.00 37.14 2.52
2585 5469 6.248433 ACAATGAAAGGGCAAGAGATTCTTA 58.752 36.000 0.00 0.00 33.78 2.10
2591 5475 9.561069 TGAAAGGGCAAGAGATTCTTAATATAC 57.439 33.333 0.00 0.00 33.78 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 208 2.743938 GCCGACAGATACACGAATGAT 58.256 47.619 0.00 0.00 0.00 2.45
208 209 1.533129 CGCCGACAGATACACGAATGA 60.533 52.381 0.00 0.00 0.00 2.57
365 366 2.707849 CGGATCCGGTCGGTCTTGT 61.708 63.158 26.95 0.00 36.47 3.16
446 447 1.381327 CGTCCAGCCTCTTCCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
567 578 1.212195 GGGTCTTTTTCTATCCGGCCT 59.788 52.381 0.00 0.00 0.00 5.19
570 581 2.640184 GGTGGGTCTTTTTCTATCCGG 58.360 52.381 0.00 0.00 0.00 5.14
685 697 1.077787 TTTCAATCCATCCGCGGCT 60.078 52.632 23.51 8.48 0.00 5.52
697 709 2.356382 TCGTTTTGTGTCCGCTTTCAAT 59.644 40.909 0.00 0.00 0.00 2.57
718 730 2.099098 CGGGAGCAAACAGACTTTTGTT 59.901 45.455 10.04 5.91 42.82 2.83
747 759 7.060421 TGAGGTAAAATGAACAAAGGAGAGTT 58.940 34.615 0.00 0.00 0.00 3.01
754 768 7.979115 TTCGTTTGAGGTAAAATGAACAAAG 57.021 32.000 0.00 0.00 39.15 2.77
770 784 2.029369 CCGGTCCCGTTCGTTTGA 59.971 61.111 4.84 0.00 37.81 2.69
777 791 1.000739 TATCCTGTCCGGTCCCGTT 59.999 57.895 0.00 0.00 37.81 4.44
805 819 1.061546 GGACTTACCCCAACTCCACA 58.938 55.000 0.00 0.00 0.00 4.17
877 901 2.916702 AGCACATGTCAGTCAGTTGA 57.083 45.000 0.00 0.00 0.00 3.18
878 902 5.410746 AGATTAAGCACATGTCAGTCAGTTG 59.589 40.000 0.00 0.00 0.00 3.16
879 903 5.555017 AGATTAAGCACATGTCAGTCAGTT 58.445 37.500 0.00 0.00 0.00 3.16
880 904 5.157940 AGATTAAGCACATGTCAGTCAGT 57.842 39.130 0.00 0.00 0.00 3.41
881 905 4.569966 GGAGATTAAGCACATGTCAGTCAG 59.430 45.833 0.00 0.00 0.00 3.51
882 906 4.020307 TGGAGATTAAGCACATGTCAGTCA 60.020 41.667 0.00 0.00 0.00 3.41
883 907 4.331168 GTGGAGATTAAGCACATGTCAGTC 59.669 45.833 0.00 0.00 0.00 3.51
970 994 5.104982 GCATTTATAGGGAGGAGGAGATCAG 60.105 48.000 0.00 0.00 0.00 2.90
971 995 4.780021 GCATTTATAGGGAGGAGGAGATCA 59.220 45.833 0.00 0.00 0.00 2.92
972 996 4.780021 TGCATTTATAGGGAGGAGGAGATC 59.220 45.833 0.00 0.00 0.00 2.75
973 997 4.767908 TGCATTTATAGGGAGGAGGAGAT 58.232 43.478 0.00 0.00 0.00 2.75
1004 1030 1.971481 TGTGTTGCTGTGATGCTCTT 58.029 45.000 0.00 0.00 0.00 2.85
1063 1089 5.619981 GCACCATATTTGATATTTCCCTCGC 60.620 44.000 0.00 0.00 0.00 5.03
1064 1090 5.707298 AGCACCATATTTGATATTTCCCTCG 59.293 40.000 0.00 0.00 0.00 4.63
1066 1092 5.776716 CCAGCACCATATTTGATATTTCCCT 59.223 40.000 0.00 0.00 0.00 4.20
1068 1094 5.567423 GCCCAGCACCATATTTGATATTTCC 60.567 44.000 0.00 0.00 0.00 3.13
1070 1096 4.900652 TGCCCAGCACCATATTTGATATTT 59.099 37.500 0.00 0.00 31.71 1.40
1071 1097 4.482030 TGCCCAGCACCATATTTGATATT 58.518 39.130 0.00 0.00 31.71 1.28
1072 1098 4.116782 TGCCCAGCACCATATTTGATAT 57.883 40.909 0.00 0.00 31.71 1.63
1073 1099 3.591695 TGCCCAGCACCATATTTGATA 57.408 42.857 0.00 0.00 31.71 2.15
1074 1100 2.457813 TGCCCAGCACCATATTTGAT 57.542 45.000 0.00 0.00 31.71 2.57
1075 1101 2.033372 CATGCCCAGCACCATATTTGA 58.967 47.619 0.00 0.00 43.04 2.69
1076 1102 2.033372 TCATGCCCAGCACCATATTTG 58.967 47.619 0.00 0.00 43.04 2.32
1152 1178 1.457455 CTCTGCTCCCTCTCCTCCC 60.457 68.421 0.00 0.00 0.00 4.30
1184 1210 2.202756 CCTCTGTTACCGCCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
1280 1309 0.176910 CCCGCTCCTCTTCTTCTTCC 59.823 60.000 0.00 0.00 0.00 3.46
1305 1337 2.292267 GGGAAGTGGTGCATCACTATG 58.708 52.381 32.00 0.00 46.17 2.23
1323 1355 0.179000 CAGGACGAGAATGGAAGGGG 59.821 60.000 0.00 0.00 0.00 4.79
1341 1373 0.107993 CGAAATCTCAGAGCAGCCCA 60.108 55.000 0.00 0.00 0.00 5.36
1367 1402 2.281761 CCAGTGACCACACCAGCC 60.282 66.667 2.78 0.00 46.99 4.85
1368 1403 2.129555 ATCCCAGTGACCACACCAGC 62.130 60.000 2.78 0.00 46.99 4.85
1371 1406 1.613437 CAAAATCCCAGTGACCACACC 59.387 52.381 2.78 0.00 46.99 4.16
1384 1419 5.119743 GCTGACAAAAGCTTCATCAAAATCC 59.880 40.000 0.00 0.00 40.20 3.01
1385 1420 5.693104 TGCTGACAAAAGCTTCATCAAAATC 59.307 36.000 0.00 0.00 43.90 2.17
1464 1499 8.223330 ACAATTCTCATCAAATAATCTAGCCCT 58.777 33.333 0.00 0.00 0.00 5.19
1465 1500 8.401490 ACAATTCTCATCAAATAATCTAGCCC 57.599 34.615 0.00 0.00 0.00 5.19
1476 1511 9.383519 GGAGTACAAGATACAATTCTCATCAAA 57.616 33.333 0.00 0.00 0.00 2.69
1479 1514 7.731054 AGGGAGTACAAGATACAATTCTCATC 58.269 38.462 0.00 0.00 0.00 2.92
1480 1515 7.566879 AGAGGGAGTACAAGATACAATTCTCAT 59.433 37.037 0.00 0.00 0.00 2.90
1481 1516 6.897966 AGAGGGAGTACAAGATACAATTCTCA 59.102 38.462 0.00 0.00 0.00 3.27
1482 1517 7.147811 ACAGAGGGAGTACAAGATACAATTCTC 60.148 40.741 0.00 0.00 0.00 2.87
1492 1527 1.353358 TCGGACAGAGGGAGTACAAGA 59.647 52.381 0.00 0.00 0.00 3.02
1493 1528 1.835494 TCGGACAGAGGGAGTACAAG 58.165 55.000 0.00 0.00 0.00 3.16
1506 1647 6.128391 CGTCTTGAATTAGGAAATTTCGGACA 60.128 38.462 11.95 4.12 35.41 4.02
1511 1652 6.183360 CCCTCCGTCTTGAATTAGGAAATTTC 60.183 42.308 9.83 9.83 35.41 2.17
1526 1675 2.233305 ACACATACTCCCTCCGTCTT 57.767 50.000 0.00 0.00 0.00 3.01
1556 1710 7.012894 ACAGTGTTCCGAAATGAACTTTTATGA 59.987 33.333 5.61 0.00 43.96 2.15
1593 1752 9.590451 CTATTTTCCATGAGCATGTGTTTTAAT 57.410 29.630 9.39 3.83 37.11 1.40
1598 1757 5.711506 TGACTATTTTCCATGAGCATGTGTT 59.288 36.000 9.39 0.00 37.11 3.32
1600 1759 5.575957 GTGACTATTTTCCATGAGCATGTG 58.424 41.667 9.39 2.05 37.11 3.21
1601 1760 4.333649 CGTGACTATTTTCCATGAGCATGT 59.666 41.667 9.39 0.00 37.11 3.21
1641 1801 0.394192 TCTGACGATCCATGGGATGC 59.606 55.000 13.02 0.00 43.27 3.91
1649 1817 3.839778 TGGTGGTATATCTGACGATCCA 58.160 45.455 0.00 0.00 0.00 3.41
1654 1822 4.454847 ACGACTATGGTGGTATATCTGACG 59.545 45.833 0.00 0.00 32.76 4.35
1658 1826 6.971726 TTGAACGACTATGGTGGTATATCT 57.028 37.500 0.00 0.00 33.37 1.98
1659 1827 7.603651 AGATTGAACGACTATGGTGGTATATC 58.396 38.462 0.00 2.13 33.37 1.63
1661 1829 6.971726 AGATTGAACGACTATGGTGGTATA 57.028 37.500 0.00 0.00 33.37 1.47
1669 1837 8.912787 AAGTTACTGTAGATTGAACGACTATG 57.087 34.615 0.00 0.00 0.00 2.23
1758 1926 1.531149 ACCGAAACTGAAGCGTGATTG 59.469 47.619 0.00 0.00 0.00 2.67
1768 1936 1.377366 TTTGCCGCAACCGAAACTGA 61.377 50.000 4.98 0.00 36.29 3.41
1797 3090 2.224426 TGTGACCTATCAAACACGCCTT 60.224 45.455 0.00 0.00 36.31 4.35
1809 3102 4.408276 ACTAGTGTGAGTGTGTGACCTAT 58.592 43.478 0.00 0.00 0.00 2.57
1810 3103 3.819337 GACTAGTGTGAGTGTGTGACCTA 59.181 47.826 0.00 0.00 0.00 3.08
1811 3104 2.623889 GACTAGTGTGAGTGTGTGACCT 59.376 50.000 0.00 0.00 0.00 3.85
1812 3105 2.288273 GGACTAGTGTGAGTGTGTGACC 60.288 54.545 0.00 0.00 0.00 4.02
1813 3106 2.623889 AGGACTAGTGTGAGTGTGTGAC 59.376 50.000 0.00 0.00 0.00 3.67
1814 3107 2.623416 CAGGACTAGTGTGAGTGTGTGA 59.377 50.000 0.00 0.00 0.00 3.58
1815 3108 2.288457 CCAGGACTAGTGTGAGTGTGTG 60.288 54.545 0.00 0.00 0.00 3.82
1816 3109 1.964223 CCAGGACTAGTGTGAGTGTGT 59.036 52.381 0.00 0.00 0.00 3.72
1817 3110 1.337260 GCCAGGACTAGTGTGAGTGTG 60.337 57.143 0.00 0.00 0.00 3.82
1818 3111 0.969894 GCCAGGACTAGTGTGAGTGT 59.030 55.000 0.00 0.00 0.00 3.55
1819 3112 0.247736 GGCCAGGACTAGTGTGAGTG 59.752 60.000 0.00 0.00 0.00 3.51
1820 3113 0.178932 TGGCCAGGACTAGTGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
1821 3114 1.134580 CATGGCCAGGACTAGTGTGAG 60.135 57.143 13.35 0.00 0.00 3.51
1822 3115 0.904649 CATGGCCAGGACTAGTGTGA 59.095 55.000 13.35 0.00 0.00 3.58
1823 3116 0.107508 CCATGGCCAGGACTAGTGTG 60.108 60.000 21.32 4.37 0.00 3.82
1824 3117 1.274703 CCCATGGCCAGGACTAGTGT 61.275 60.000 21.32 0.00 0.00 3.55
1825 3118 1.528824 CCCATGGCCAGGACTAGTG 59.471 63.158 21.32 6.06 0.00 2.74
1826 3119 2.378634 GCCCATGGCCAGGACTAGT 61.379 63.158 21.32 0.00 44.06 2.57
1827 3120 2.512896 GCCCATGGCCAGGACTAG 59.487 66.667 21.32 5.63 44.06 2.57
1843 3136 4.050934 CTTTTCGGGCCGGGTTGC 62.051 66.667 27.98 0.00 0.00 4.17
1844 3137 3.370231 CCTTTTCGGGCCGGGTTG 61.370 66.667 27.98 13.94 0.00 3.77
1853 3146 2.588856 CTAGGTCCGGGCCTTTTCGG 62.589 65.000 36.78 14.66 46.89 4.30
1854 3147 1.153429 CTAGGTCCGGGCCTTTTCG 60.153 63.158 36.78 15.84 39.94 3.46
1855 3148 0.837940 ATCTAGGTCCGGGCCTTTTC 59.162 55.000 36.78 0.68 39.94 2.29
1856 3149 1.296002 AATCTAGGTCCGGGCCTTTT 58.704 50.000 36.78 21.56 39.94 2.27
1857 3150 1.296002 AAATCTAGGTCCGGGCCTTT 58.704 50.000 36.78 19.94 39.94 3.11
1858 3151 1.064685 CAAAATCTAGGTCCGGGCCTT 60.065 52.381 36.78 13.74 39.94 4.35
1859 3152 0.546598 CAAAATCTAGGTCCGGGCCT 59.453 55.000 33.93 33.93 42.43 5.19
1860 3153 0.544697 TCAAAATCTAGGTCCGGGCC 59.455 55.000 20.43 20.43 0.00 5.80
1861 3154 1.954927 CTCAAAATCTAGGTCCGGGC 58.045 55.000 0.00 0.00 0.00 6.13
1862 3155 1.475213 GGCTCAAAATCTAGGTCCGGG 60.475 57.143 0.00 0.00 0.00 5.73
1863 3156 1.475213 GGGCTCAAAATCTAGGTCCGG 60.475 57.143 0.00 0.00 0.00 5.14
1864 3157 1.806623 CGGGCTCAAAATCTAGGTCCG 60.807 57.143 0.00 0.00 0.00 4.79
1865 3158 1.485066 TCGGGCTCAAAATCTAGGTCC 59.515 52.381 0.00 0.00 0.00 4.46
1866 3159 2.981859 TCGGGCTCAAAATCTAGGTC 57.018 50.000 0.00 0.00 0.00 3.85
1867 3160 2.838202 TCTTCGGGCTCAAAATCTAGGT 59.162 45.455 0.00 0.00 0.00 3.08
1868 3161 3.198872 GTCTTCGGGCTCAAAATCTAGG 58.801 50.000 0.00 0.00 0.00 3.02
1869 3162 3.198872 GGTCTTCGGGCTCAAAATCTAG 58.801 50.000 0.00 0.00 0.00 2.43
1870 3163 2.418197 CGGTCTTCGGGCTCAAAATCTA 60.418 50.000 0.00 0.00 34.75 1.98
1871 3164 1.676014 CGGTCTTCGGGCTCAAAATCT 60.676 52.381 0.00 0.00 34.75 2.40
1872 3165 0.727398 CGGTCTTCGGGCTCAAAATC 59.273 55.000 0.00 0.00 34.75 2.17
1873 3166 2.854522 CGGTCTTCGGGCTCAAAAT 58.145 52.632 0.00 0.00 34.75 1.82
1874 3167 4.371975 CGGTCTTCGGGCTCAAAA 57.628 55.556 0.00 0.00 34.75 2.44
1894 3187 3.733960 GAAAACGACAGGCCCGGC 61.734 66.667 0.00 0.00 0.00 6.13
1895 3188 2.281208 TGAAAACGACAGGCCCGG 60.281 61.111 0.00 0.00 0.00 5.73
1896 3189 2.943653 GTGAAAACGACAGGCCCG 59.056 61.111 0.00 0.00 0.00 6.13
1897 3190 0.953960 ATCGTGAAAACGACAGGCCC 60.954 55.000 0.00 0.00 45.30 5.80
1898 3191 0.872388 AATCGTGAAAACGACAGGCC 59.128 50.000 2.69 0.00 45.30 5.19
1899 3192 2.681152 AAATCGTGAAAACGACAGGC 57.319 45.000 2.69 0.00 45.30 4.85
1900 3193 4.446385 TCAGTAAATCGTGAAAACGACAGG 59.554 41.667 2.69 0.00 45.30 4.00
1901 3194 5.570262 TCAGTAAATCGTGAAAACGACAG 57.430 39.130 2.69 0.00 45.30 3.51
1902 3195 5.050634 CCTTCAGTAAATCGTGAAAACGACA 60.051 40.000 2.69 0.00 45.30 4.35
1903 3196 5.371629 CCTTCAGTAAATCGTGAAAACGAC 58.628 41.667 2.69 0.00 45.30 4.34
1904 3197 4.449743 CCCTTCAGTAAATCGTGAAAACGA 59.550 41.667 3.16 3.16 46.58 3.85
1905 3198 4.378046 CCCCTTCAGTAAATCGTGAAAACG 60.378 45.833 0.00 0.00 32.36 3.60
1906 3199 4.615223 GCCCCTTCAGTAAATCGTGAAAAC 60.615 45.833 0.00 0.00 32.36 2.43
1907 3200 3.504520 GCCCCTTCAGTAAATCGTGAAAA 59.495 43.478 0.00 0.00 32.36 2.29
1908 3201 3.078837 GCCCCTTCAGTAAATCGTGAAA 58.921 45.455 0.00 0.00 32.36 2.69
1909 3202 2.617021 GGCCCCTTCAGTAAATCGTGAA 60.617 50.000 0.00 0.00 0.00 3.18
1910 3203 1.065709 GGCCCCTTCAGTAAATCGTGA 60.066 52.381 0.00 0.00 0.00 4.35
1911 3204 1.379527 GGCCCCTTCAGTAAATCGTG 58.620 55.000 0.00 0.00 0.00 4.35
1912 3205 0.255033 GGGCCCCTTCAGTAAATCGT 59.745 55.000 12.23 0.00 0.00 3.73
1913 3206 0.814010 CGGGCCCCTTCAGTAAATCG 60.814 60.000 18.66 0.00 0.00 3.34
1914 3207 0.544697 TCGGGCCCCTTCAGTAAATC 59.455 55.000 18.66 0.00 0.00 2.17
1915 3208 0.255033 GTCGGGCCCCTTCAGTAAAT 59.745 55.000 18.66 0.00 0.00 1.40
1916 3209 0.838987 AGTCGGGCCCCTTCAGTAAA 60.839 55.000 18.66 0.00 0.00 2.01
1917 3210 1.229400 AGTCGGGCCCCTTCAGTAA 60.229 57.895 18.66 0.00 0.00 2.24
1918 3211 1.684734 GAGTCGGGCCCCTTCAGTA 60.685 63.158 18.66 0.00 0.00 2.74
1919 3212 3.003763 GAGTCGGGCCCCTTCAGT 61.004 66.667 18.66 0.00 0.00 3.41
1920 3213 2.527951 CTTGAGTCGGGCCCCTTCAG 62.528 65.000 18.66 0.58 0.00 3.02
1921 3214 2.528127 TTGAGTCGGGCCCCTTCA 60.528 61.111 18.66 14.81 0.00 3.02
1922 3215 2.269241 CTTGAGTCGGGCCCCTTC 59.731 66.667 18.66 12.10 0.00 3.46
1923 3216 3.330720 CCTTGAGTCGGGCCCCTT 61.331 66.667 18.66 0.46 0.00 3.95
1929 3222 4.452733 GTCGGGCCTTGAGTCGGG 62.453 72.222 0.84 0.00 0.00 5.14
1930 3223 3.649277 CTGTCGGGCCTTGAGTCGG 62.649 68.421 0.84 0.00 0.00 4.79
1931 3224 2.125912 CTGTCGGGCCTTGAGTCG 60.126 66.667 0.84 0.00 0.00 4.18
1932 3225 2.266055 CCTGTCGGGCCTTGAGTC 59.734 66.667 0.84 0.00 0.00 3.36
1941 3234 4.423732 CAAAAATGATAAAGCCTGTCGGG 58.576 43.478 0.00 0.00 38.36 5.14
1942 3235 4.423732 CCAAAAATGATAAAGCCTGTCGG 58.576 43.478 0.00 0.00 0.00 4.79
1943 3236 4.423732 CCCAAAAATGATAAAGCCTGTCG 58.576 43.478 0.00 0.00 0.00 4.35
1944 3237 4.183865 GCCCAAAAATGATAAAGCCTGTC 58.816 43.478 0.00 0.00 0.00 3.51
1945 3238 3.055167 GGCCCAAAAATGATAAAGCCTGT 60.055 43.478 0.00 0.00 36.22 4.00
1946 3239 3.055240 TGGCCCAAAAATGATAAAGCCTG 60.055 43.478 0.00 0.00 39.90 4.85
1947 3240 3.180507 TGGCCCAAAAATGATAAAGCCT 58.819 40.909 0.00 0.00 39.90 4.58
1948 3241 3.534554 CTGGCCCAAAAATGATAAAGCC 58.465 45.455 0.00 0.00 39.64 4.35
1949 3242 3.534554 CCTGGCCCAAAAATGATAAAGC 58.465 45.455 0.00 0.00 0.00 3.51
1950 3243 3.198417 AGCCTGGCCCAAAAATGATAAAG 59.802 43.478 16.57 0.00 0.00 1.85
1951 3244 3.180507 AGCCTGGCCCAAAAATGATAAA 58.819 40.909 16.57 0.00 0.00 1.40
1952 3245 2.831565 AGCCTGGCCCAAAAATGATAA 58.168 42.857 16.57 0.00 0.00 1.75
1953 3246 2.500910 CAAGCCTGGCCCAAAAATGATA 59.499 45.455 16.57 0.00 0.00 2.15
1954 3247 1.279846 CAAGCCTGGCCCAAAAATGAT 59.720 47.619 16.57 0.00 0.00 2.45
1955 3248 0.686224 CAAGCCTGGCCCAAAAATGA 59.314 50.000 16.57 0.00 0.00 2.57
1956 3249 0.321830 CCAAGCCTGGCCCAAAAATG 60.322 55.000 16.57 3.48 35.39 2.32
1957 3250 2.068915 CCAAGCCTGGCCCAAAAAT 58.931 52.632 16.57 0.00 35.39 1.82
1958 3251 3.560989 CCAAGCCTGGCCCAAAAA 58.439 55.556 16.57 0.00 35.39 1.94
1980 3273 1.895231 GACCGTCGGGCCTGTTTTT 60.895 57.895 17.28 0.00 36.48 1.94
1981 3274 2.281276 GACCGTCGGGCCTGTTTT 60.281 61.111 17.28 0.00 36.48 2.43
1982 3275 4.675029 CGACCGTCGGGCCTGTTT 62.675 66.667 17.28 0.00 36.00 2.83
2002 3295 2.453379 ATTTTTGCGCCCAAGCCCAG 62.453 55.000 4.18 0.00 36.02 4.45
2003 3296 2.447586 GATTTTTGCGCCCAAGCCCA 62.448 55.000 4.18 0.00 36.02 5.36
2004 3297 1.741401 GATTTTTGCGCCCAAGCCC 60.741 57.895 4.18 0.00 36.02 5.19
2005 3298 1.005156 TGATTTTTGCGCCCAAGCC 60.005 52.632 4.18 0.00 36.02 4.35
2006 3299 1.015607 CCTGATTTTTGCGCCCAAGC 61.016 55.000 4.18 0.00 37.71 4.01
2007 3300 1.015607 GCCTGATTTTTGCGCCCAAG 61.016 55.000 4.18 0.00 31.52 3.61
2008 3301 1.005156 GCCTGATTTTTGCGCCCAA 60.005 52.632 4.18 0.00 0.00 4.12
2009 3302 2.656055 GCCTGATTTTTGCGCCCA 59.344 55.556 4.18 0.00 0.00 5.36
2010 3303 2.125552 GGCCTGATTTTTGCGCCC 60.126 61.111 4.18 0.00 33.30 6.13
2011 3304 1.446618 CAGGCCTGATTTTTGCGCC 60.447 57.895 29.88 0.00 40.03 6.53
2012 3305 0.733909 GTCAGGCCTGATTTTTGCGC 60.734 55.000 37.07 18.51 42.18 6.09
2013 3306 0.454957 CGTCAGGCCTGATTTTTGCG 60.455 55.000 37.07 28.71 42.18 4.85
2014 3307 0.109132 CCGTCAGGCCTGATTTTTGC 60.109 55.000 37.07 21.95 42.18 3.68
2015 3308 1.200020 GACCGTCAGGCCTGATTTTTG 59.800 52.381 37.07 23.93 42.18 2.44
2016 3309 1.534729 GACCGTCAGGCCTGATTTTT 58.465 50.000 37.07 21.69 42.18 1.94
2017 3310 0.673644 CGACCGTCAGGCCTGATTTT 60.674 55.000 37.07 23.48 42.18 1.82
2018 3311 1.079127 CGACCGTCAGGCCTGATTT 60.079 57.895 37.07 23.84 42.18 2.17
2019 3312 2.579201 CGACCGTCAGGCCTGATT 59.421 61.111 37.07 24.20 42.18 2.57
2020 3313 3.461773 CCGACCGTCAGGCCTGAT 61.462 66.667 37.07 22.76 42.18 2.90
2043 3336 0.179081 CAGTAAACCTAGGCCCGAGC 60.179 60.000 9.30 0.00 38.76 5.03
2044 3337 0.179081 GCAGTAAACCTAGGCCCGAG 60.179 60.000 9.30 0.00 0.00 4.63
2045 3338 1.619807 GGCAGTAAACCTAGGCCCGA 61.620 60.000 9.30 0.00 38.70 5.14
2046 3339 1.153229 GGCAGTAAACCTAGGCCCG 60.153 63.158 9.30 0.00 38.70 6.13
2047 3340 0.180642 GAGGCAGTAAACCTAGGCCC 59.819 60.000 9.30 0.00 45.72 5.80
2048 3341 0.179081 CGAGGCAGTAAACCTAGGCC 60.179 60.000 9.30 1.78 44.92 5.19
2049 3342 0.179081 CCGAGGCAGTAAACCTAGGC 60.179 60.000 9.30 0.00 42.25 3.93
2050 3343 0.464452 CCCGAGGCAGTAAACCTAGG 59.536 60.000 7.41 7.41 46.56 3.02
2063 3356 2.124695 GCCTACCAAAGCCCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
2064 3357 1.153349 GAGCCTACCAAAGCCCGAG 60.153 63.158 0.00 0.00 0.00 4.63
2065 3358 2.987125 GAGCCTACCAAAGCCCGA 59.013 61.111 0.00 0.00 0.00 5.14
2066 3359 2.511600 CGAGCCTACCAAAGCCCG 60.512 66.667 0.00 0.00 0.00 6.13
2067 3360 2.124695 CCGAGCCTACCAAAGCCC 60.125 66.667 0.00 0.00 0.00 5.19
2068 3361 2.824489 GCCGAGCCTACCAAAGCC 60.824 66.667 0.00 0.00 0.00 4.35
2069 3362 2.046314 TGCCGAGCCTACCAAAGC 60.046 61.111 0.00 0.00 0.00 3.51
2070 3363 2.100631 CGTGCCGAGCCTACCAAAG 61.101 63.158 0.00 0.00 0.00 2.77
2071 3364 2.047655 CGTGCCGAGCCTACCAAA 60.048 61.111 0.00 0.00 0.00 3.28
2072 3365 2.501223 CTTCGTGCCGAGCCTACCAA 62.501 60.000 0.00 0.00 37.14 3.67
2073 3366 2.992689 TTCGTGCCGAGCCTACCA 60.993 61.111 0.00 0.00 37.14 3.25
2074 3367 2.202756 CTTCGTGCCGAGCCTACC 60.203 66.667 0.00 0.00 37.14 3.18
2075 3368 2.886124 GCTTCGTGCCGAGCCTAC 60.886 66.667 0.00 0.00 37.14 3.18
2096 3389 4.256180 CCATCTACCAGGCCGGGC 62.256 72.222 23.25 22.67 40.22 6.13
2097 3390 4.256180 GCCATCTACCAGGCCGGG 62.256 72.222 21.67 21.67 45.18 5.73
2104 3397 4.353777 GACCTATATCTGGCCATCTACCA 58.646 47.826 5.51 0.00 35.40 3.25
2105 3398 3.381908 CGACCTATATCTGGCCATCTACC 59.618 52.174 5.51 0.00 0.00 3.18
2106 3399 3.181485 GCGACCTATATCTGGCCATCTAC 60.181 52.174 5.51 0.00 0.00 2.59
2107 3400 3.024547 GCGACCTATATCTGGCCATCTA 58.975 50.000 5.51 0.49 0.00 1.98
2108 3401 1.827969 GCGACCTATATCTGGCCATCT 59.172 52.381 5.51 0.00 0.00 2.90
2109 3402 1.550524 TGCGACCTATATCTGGCCATC 59.449 52.381 5.51 0.00 0.00 3.51
2110 3403 1.276421 GTGCGACCTATATCTGGCCAT 59.724 52.381 5.51 0.00 0.00 4.40
2111 3404 0.679505 GTGCGACCTATATCTGGCCA 59.320 55.000 4.71 4.71 0.00 5.36
2112 3405 0.388649 CGTGCGACCTATATCTGGCC 60.389 60.000 0.00 0.00 0.00 5.36
2113 3406 1.009389 GCGTGCGACCTATATCTGGC 61.009 60.000 0.00 0.00 0.00 4.85
2114 3407 0.313987 TGCGTGCGACCTATATCTGG 59.686 55.000 0.00 0.00 0.00 3.86
2115 3408 1.691127 CTGCGTGCGACCTATATCTG 58.309 55.000 0.00 0.00 0.00 2.90
2116 3409 0.039074 GCTGCGTGCGACCTATATCT 60.039 55.000 0.00 0.00 0.00 1.98
2117 3410 2.435741 GCTGCGTGCGACCTATATC 58.564 57.895 0.00 0.00 0.00 1.63
2118 3411 4.655527 GCTGCGTGCGACCTATAT 57.344 55.556 0.00 0.00 0.00 0.86
2136 3429 2.291209 TTTGCATCTCCAAAGCCTGA 57.709 45.000 0.00 0.00 31.55 3.86
2261 3836 1.371512 CGCTTTCCAACGCATGCAA 60.372 52.632 19.57 0.15 0.00 4.08
2266 3841 2.660553 CTTGCACGCTTTCCAACGCA 62.661 55.000 0.00 0.00 0.00 5.24
2282 3857 3.751479 TGGTCGATACATCCCATCTTG 57.249 47.619 0.00 0.00 0.00 3.02
2292 3867 5.533903 GGAGTAAGGAGTAATGGTCGATACA 59.466 44.000 0.00 0.00 0.00 2.29
2318 3893 2.721425 ACTTTGGACGGTGAAAGGAA 57.279 45.000 11.79 0.00 34.12 3.36
2329 3904 5.743872 GTGAATGACAGTTTGAACTTTGGAC 59.256 40.000 0.00 0.00 37.08 4.02
2330 3905 5.417266 TGTGAATGACAGTTTGAACTTTGGA 59.583 36.000 0.00 0.00 37.08 3.53
2331 3906 5.649557 TGTGAATGACAGTTTGAACTTTGG 58.350 37.500 0.00 0.00 37.08 3.28
2332 3907 7.198390 AGATGTGAATGACAGTTTGAACTTTG 58.802 34.615 0.00 0.00 38.23 2.77
2333 3908 7.284034 AGAGATGTGAATGACAGTTTGAACTTT 59.716 33.333 0.00 0.00 38.23 2.66
2334 3909 6.769822 AGAGATGTGAATGACAGTTTGAACTT 59.230 34.615 0.00 0.00 38.23 2.66
2335 3910 6.294473 AGAGATGTGAATGACAGTTTGAACT 58.706 36.000 0.00 0.00 38.23 3.01
2351 3926 4.129380 TCACACACAAAGGAAGAGATGTG 58.871 43.478 3.41 3.41 46.52 3.21
2360 3935 2.630098 CCTCTCTCTCACACACAAAGGA 59.370 50.000 0.00 0.00 0.00 3.36
2361 3936 2.630098 TCCTCTCTCTCACACACAAAGG 59.370 50.000 0.00 0.00 0.00 3.11
2362 3937 4.327982 TTCCTCTCTCTCACACACAAAG 57.672 45.455 0.00 0.00 0.00 2.77
2363 3938 4.753516 TTTCCTCTCTCTCACACACAAA 57.246 40.909 0.00 0.00 0.00 2.83
2364 3939 4.405680 TCTTTTCCTCTCTCTCACACACAA 59.594 41.667 0.00 0.00 0.00 3.33
2365 3940 3.960755 TCTTTTCCTCTCTCTCACACACA 59.039 43.478 0.00 0.00 0.00 3.72
2366 3941 4.592485 TCTTTTCCTCTCTCTCACACAC 57.408 45.455 0.00 0.00 0.00 3.82
2379 3954 9.856488 GTGTTTACTCTTTTCTTTTCTTTTCCT 57.144 29.630 0.00 0.00 0.00 3.36
2428 5309 3.810310 ATTTGTCGGTTGCCTGAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
2429 5310 3.305064 GCTATTTGTCGGTTGCCTGAAAA 60.305 43.478 0.00 0.00 0.00 2.29
2506 5390 3.006003 TCCCCGCAAAGAAAAATAACCAC 59.994 43.478 0.00 0.00 0.00 4.16
2570 5454 6.969828 CCGTATATTAAGAATCTCTTGCCC 57.030 41.667 0.00 0.00 37.29 5.36


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

AutoCloner maintained by Alex Coulton.