Multiple sequence alignment - TraesCS1B01G226900

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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 TraesCS1B01G226900 chr1B 100.000 3758 0 0 1 3758 407595479 407599236 0.000000e+00 6940.0
1 TraesCS1B01G226900 chr1D 92.308 1625 78 22 2155 3758 302074220 302075818 0.000000e+00 2265.0
2 TraesCS1B01G226900 chr1D 84.672 809 111 12 1159 1962 302072282 302073082 0.000000e+00 795.0
3 TraesCS1B01G226900 chr1D 83.817 241 30 6 922 1162 301980647 301980878 1.760000e-53 220.0
4 TraesCS1B01G226900 chr1A 91.728 1487 73 30 2155 3624 376754783 376756236 0.000000e+00 2019.0
5 TraesCS1B01G226900 chr1A 84.269 998 137 14 975 1964 376752013 376752998 0.000000e+00 955.0
6 TraesCS1B01G226900 chr1A 96.117 103 4 0 3656 3758 376756363 376756465 6.460000e-38 169.0
7 TraesCS1B01G226900 chr5B 90.990 899 77 4 1 896 115150834 115149937 0.000000e+00 1208.0
8 TraesCS1B01G226900 chr6B 91.186 885 75 3 1 882 440426285 440427169 0.000000e+00 1199.0
9 TraesCS1B01G226900 chr6B 90.417 887 81 4 13 896 346958256 346959141 0.000000e+00 1164.0
10 TraesCS1B01G226900 chr3B 90.798 902 76 7 1 896 346692742 346691842 0.000000e+00 1199.0
11 TraesCS1B01G226900 chr2B 90.747 897 78 5 3 896 71224189 71225083 0.000000e+00 1192.0
12 TraesCS1B01G226900 chr2B 89.989 899 85 5 1 896 14609395 14610291 0.000000e+00 1157.0
13 TraesCS1B01G226900 chr7B 89.889 900 86 5 1 896 423751667 423750769 0.000000e+00 1153.0
14 TraesCS1B01G226900 chr4B 90.045 894 83 6 8 896 298162856 298163748 0.000000e+00 1153.0
15 TraesCS1B01G226900 chr4D 90.101 889 81 7 11 896 329920060 329919176 0.000000e+00 1147.0
16 TraesCS1B01G226900 chr6D 97.297 37 1 0 1891 1927 58487623 58487587 3.130000e-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 TraesCS1B01G226900 chr1B 407595479 407599236 3757 False 6940.000000 6940 100.000000 1 3758 1 chr1B.!!$F1 3757
1 TraesCS1B01G226900 chr1D 302072282 302075818 3536 False 1530.000000 2265 88.490000 1159 3758 2 chr1D.!!$F2 2599
2 TraesCS1B01G226900 chr1A 376752013 376756465 4452 False 1047.666667 2019 90.704667 975 3758 3 chr1A.!!$F1 2783
3 TraesCS1B01G226900 chr5B 115149937 115150834 897 True 1208.000000 1208 90.990000 1 896 1 chr5B.!!$R1 895
4 TraesCS1B01G226900 chr6B 440426285 440427169 884 False 1199.000000 1199 91.186000 1 882 1 chr6B.!!$F2 881
5 TraesCS1B01G226900 chr6B 346958256 346959141 885 False 1164.000000 1164 90.417000 13 896 1 chr6B.!!$F1 883
6 TraesCS1B01G226900 chr3B 346691842 346692742 900 True 1199.000000 1199 90.798000 1 896 1 chr3B.!!$R1 895
7 TraesCS1B01G226900 chr2B 71224189 71225083 894 False 1192.000000 1192 90.747000 3 896 1 chr2B.!!$F2 893
8 TraesCS1B01G226900 chr2B 14609395 14610291 896 False 1157.000000 1157 89.989000 1 896 1 chr2B.!!$F1 895
9 TraesCS1B01G226900 chr7B 423750769 423751667 898 True 1153.000000 1153 89.889000 1 896 1 chr7B.!!$R1 895
10 TraesCS1B01G226900 chr4B 298162856 298163748 892 False 1153.000000 1153 90.045000 8 896 1 chr4B.!!$F1 888
11 TraesCS1B01G226900 chr4D 329919176 329920060 884 True 1147.000000 1147 90.101000 11 896 1 chr4D.!!$R1 885

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
931 940 0.325860 ACTCCCACACCCGCCTTATA 60.326 55.0 0.00 0.0 0.00 0.98 F
1355 1368 0.031994 GTGCACAAACACCCCACATC 59.968 55.0 13.17 0.0 34.35 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 3552 0.030908 CATTCCGGCCGACTAGAGAC 59.969 60.0 30.73 0.0 0.00 3.36 R
3257 5752 0.171007 CGTGCCCAGCATGTAAAAGG 59.829 55.0 0.55 0.0 41.91 3.11 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
124 125 2.030562 GTGGGTGTGGGTGTCGAG 59.969 66.667 0.00 0.00 0.00 4.04
190 191 4.680237 CACAGAGTGGCGGCCGAA 62.680 66.667 33.48 14.13 0.00 4.30
272 273 4.731853 TGATCTGGTGGCCGGGGA 62.732 66.667 2.18 0.00 0.00 4.81
347 348 2.372690 CCGAACACGAAGACCTGCG 61.373 63.158 0.00 0.00 0.00 5.18
426 427 4.438880 CGATCCTTCTGTCAACGATACAGT 60.439 45.833 13.43 0.00 43.88 3.55
435 436 2.826128 TCAACGATACAGTGGAGCTCTT 59.174 45.455 14.64 0.00 0.00 2.85
682 688 1.463674 CCTAGCAATGTTGTGGTCCC 58.536 55.000 0.00 0.00 0.00 4.46
695 702 1.606889 GGTCCCGCCTCCGATCTAT 60.607 63.158 0.00 0.00 36.29 1.98
854 863 2.238646 TCTTGTATCTTGACGGCCCATT 59.761 45.455 0.00 0.00 0.00 3.16
872 881 2.406596 TTAGTCCGGCCCACATTAAC 57.593 50.000 0.00 0.00 0.00 2.01
916 925 2.689034 CCCCCAGTCCAGGACTCC 60.689 72.222 20.30 0.00 41.37 3.85
917 926 2.689034 CCCCAGTCCAGGACTCCC 60.689 72.222 20.30 0.00 41.37 4.30
918 927 2.122729 CCCAGTCCAGGACTCCCA 59.877 66.667 20.30 0.00 41.37 4.37
919 928 2.294078 CCCAGTCCAGGACTCCCAC 61.294 68.421 20.30 0.00 41.37 4.61
920 929 1.536418 CCAGTCCAGGACTCCCACA 60.536 63.158 20.30 0.00 41.37 4.17
921 930 1.674057 CAGTCCAGGACTCCCACAC 59.326 63.158 20.30 0.00 41.37 3.82
922 931 1.536662 AGTCCAGGACTCCCACACC 60.537 63.158 17.31 0.00 38.71 4.16
923 932 2.203938 TCCAGGACTCCCACACCC 60.204 66.667 0.00 0.00 33.88 4.61
924 933 3.706373 CCAGGACTCCCACACCCG 61.706 72.222 0.00 0.00 33.88 5.28
925 934 4.394712 CAGGACTCCCACACCCGC 62.395 72.222 0.00 0.00 33.88 6.13
928 937 3.637273 GACTCCCACACCCGCCTT 61.637 66.667 0.00 0.00 0.00 4.35
929 938 2.203877 ACTCCCACACCCGCCTTA 60.204 61.111 0.00 0.00 0.00 2.69
930 939 1.615424 ACTCCCACACCCGCCTTAT 60.615 57.895 0.00 0.00 0.00 1.73
931 940 0.325860 ACTCCCACACCCGCCTTATA 60.326 55.000 0.00 0.00 0.00 0.98
932 941 1.056660 CTCCCACACCCGCCTTATAT 58.943 55.000 0.00 0.00 0.00 0.86
933 942 0.762418 TCCCACACCCGCCTTATATG 59.238 55.000 0.00 0.00 0.00 1.78
934 943 0.762418 CCCACACCCGCCTTATATGA 59.238 55.000 0.00 0.00 0.00 2.15
935 944 1.270839 CCCACACCCGCCTTATATGAG 60.271 57.143 0.00 0.00 0.00 2.90
936 945 1.416401 CCACACCCGCCTTATATGAGT 59.584 52.381 0.00 0.00 0.00 3.41
937 946 2.158813 CCACACCCGCCTTATATGAGTT 60.159 50.000 0.00 0.00 0.00 3.01
938 947 3.070446 CCACACCCGCCTTATATGAGTTA 59.930 47.826 0.00 0.00 0.00 2.24
939 948 4.262894 CCACACCCGCCTTATATGAGTTAT 60.263 45.833 0.00 0.00 0.00 1.89
940 949 5.046878 CCACACCCGCCTTATATGAGTTATA 60.047 44.000 0.00 0.00 0.00 0.98
941 950 6.351881 CCACACCCGCCTTATATGAGTTATAT 60.352 42.308 0.00 0.00 36.05 0.86
942 951 6.535150 CACACCCGCCTTATATGAGTTATATG 59.465 42.308 0.00 0.00 33.96 1.78
943 952 6.049149 CACCCGCCTTATATGAGTTATATGG 58.951 44.000 0.00 0.00 39.48 2.74
944 953 5.724854 ACCCGCCTTATATGAGTTATATGGT 59.275 40.000 0.00 0.00 39.03 3.55
945 954 6.899075 ACCCGCCTTATATGAGTTATATGGTA 59.101 38.462 0.00 0.00 39.03 3.25
946 955 7.567622 ACCCGCCTTATATGAGTTATATGGTAT 59.432 37.037 0.00 0.00 39.03 2.73
947 956 8.429641 CCCGCCTTATATGAGTTATATGGTATT 58.570 37.037 0.00 0.00 39.03 1.89
948 957 9.261180 CCGCCTTATATGAGTTATATGGTATTG 57.739 37.037 0.00 0.00 39.03 1.90
949 958 9.817809 CGCCTTATATGAGTTATATGGTATTGT 57.182 33.333 0.00 0.00 39.03 2.71
957 966 8.800370 TGAGTTATATGGTATTGTTCTTTGCA 57.200 30.769 0.00 0.00 0.00 4.08
958 967 9.407380 TGAGTTATATGGTATTGTTCTTTGCAT 57.593 29.630 0.00 0.00 0.00 3.96
964 973 9.754382 ATATGGTATTGTTCTTTGCATTTGATC 57.246 29.630 0.00 0.00 0.00 2.92
965 974 7.230849 TGGTATTGTTCTTTGCATTTGATCT 57.769 32.000 0.00 0.00 0.00 2.75
966 975 7.315142 TGGTATTGTTCTTTGCATTTGATCTC 58.685 34.615 0.00 0.00 0.00 2.75
967 976 7.177216 TGGTATTGTTCTTTGCATTTGATCTCT 59.823 33.333 0.00 0.00 0.00 3.10
968 977 8.031277 GGTATTGTTCTTTGCATTTGATCTCTT 58.969 33.333 0.00 0.00 0.00 2.85
969 978 9.415544 GTATTGTTCTTTGCATTTGATCTCTTT 57.584 29.630 0.00 0.00 0.00 2.52
970 979 7.703298 TTGTTCTTTGCATTTGATCTCTTTG 57.297 32.000 0.00 0.00 0.00 2.77
971 980 6.218019 TGTTCTTTGCATTTGATCTCTTTGG 58.782 36.000 0.00 0.00 0.00 3.28
972 981 6.040729 TGTTCTTTGCATTTGATCTCTTTGGA 59.959 34.615 0.00 0.00 0.00 3.53
973 982 6.263516 TCTTTGCATTTGATCTCTTTGGAG 57.736 37.500 0.00 0.00 40.73 3.86
984 993 2.705658 TCTCTTTGGAGGTTGCTTCAGA 59.294 45.455 0.00 0.00 39.86 3.27
1014 1026 0.178068 CTGGTATGGTTAGCGCACCT 59.822 55.000 16.94 6.34 37.75 4.00
1035 1047 0.034896 CCGGTGCAAGGTCTAGTTGT 59.965 55.000 0.00 0.00 0.00 3.32
1037 1049 1.540363 CGGTGCAAGGTCTAGTTGTGT 60.540 52.381 0.00 0.00 0.00 3.72
1041 1053 1.523758 CAAGGTCTAGTTGTGTGCCC 58.476 55.000 0.00 0.00 0.00 5.36
1045 1057 1.610886 GGTCTAGTTGTGTGCCCTTCC 60.611 57.143 0.00 0.00 0.00 3.46
1064 1076 2.711009 TCCCAATGGACATACCCAGATC 59.289 50.000 0.00 0.00 39.97 2.75
1077 1089 6.560304 ACATACCCAGATCATCTTAACCTCAT 59.440 38.462 0.00 0.00 0.00 2.90
1078 1090 5.559148 ACCCAGATCATCTTAACCTCATC 57.441 43.478 0.00 0.00 0.00 2.92
1079 1091 5.222870 ACCCAGATCATCTTAACCTCATCT 58.777 41.667 0.00 0.00 0.00 2.90
1080 1092 5.306678 ACCCAGATCATCTTAACCTCATCTC 59.693 44.000 0.00 0.00 0.00 2.75
1084 1096 4.286813 TCATCTTAACCTCATCTCCCCT 57.713 45.455 0.00 0.00 0.00 4.79
1085 1097 4.227197 TCATCTTAACCTCATCTCCCCTC 58.773 47.826 0.00 0.00 0.00 4.30
1086 1098 4.078336 TCATCTTAACCTCATCTCCCCTCT 60.078 45.833 0.00 0.00 0.00 3.69
1087 1099 3.917300 TCTTAACCTCATCTCCCCTCTC 58.083 50.000 0.00 0.00 0.00 3.20
1088 1100 2.777459 TAACCTCATCTCCCCTCTCC 57.223 55.000 0.00 0.00 0.00 3.71
1098 1111 0.398098 TCCCCTCTCCGGTTACCATC 60.398 60.000 0.00 0.00 0.00 3.51
1100 1113 0.464452 CCCTCTCCGGTTACCATCAC 59.536 60.000 0.00 0.00 0.00 3.06
1110 1123 3.631250 GGTTACCATCACCATCAACCAT 58.369 45.455 0.00 0.00 36.32 3.55
1113 1126 5.473504 GGTTACCATCACCATCAACCATATC 59.526 44.000 0.00 0.00 36.32 1.63
1123 1136 4.825634 CCATCAACCATATCAGCATCAACT 59.174 41.667 0.00 0.00 0.00 3.16
1225 1238 0.179001 CACCTCGGGAAAAACCACCT 60.179 55.000 0.00 0.00 41.20 4.00
1226 1239 0.554305 ACCTCGGGAAAAACCACCTT 59.446 50.000 0.00 0.00 41.20 3.50
1237 1250 0.697854 AACCACCTTCACCTCCACCT 60.698 55.000 0.00 0.00 0.00 4.00
1238 1251 1.376466 CCACCTTCACCTCCACCTG 59.624 63.158 0.00 0.00 0.00 4.00
1242 1255 0.322008 CCTTCACCTCCACCTGAAGC 60.322 60.000 2.45 0.00 41.40 3.86
1269 1282 3.388024 CCTTCAGGTCCGAAGATCCAATA 59.612 47.826 19.05 0.00 44.32 1.90
1294 1307 7.516198 AACCCACATATTCTTGAATATGAGC 57.484 36.000 32.67 0.00 42.77 4.26
1300 1313 6.146837 ACATATTCTTGAATATGAGCGCTGAC 59.853 38.462 32.67 0.38 42.77 3.51
1301 1314 3.525268 TCTTGAATATGAGCGCTGACA 57.475 42.857 18.48 8.29 0.00 3.58
1335 1348 4.396790 TCCATTGCCACGTTCCTTATAAAC 59.603 41.667 0.00 0.00 0.00 2.01
1347 1360 5.098218 TCCTTATAAACGTGCACAAACAC 57.902 39.130 18.64 0.00 37.19 3.32
1355 1368 0.031994 GTGCACAAACACCCCACATC 59.968 55.000 13.17 0.00 34.35 3.06
1359 1372 1.759445 CACAAACACCCCACATCCAAA 59.241 47.619 0.00 0.00 0.00 3.28
1360 1373 2.368221 CACAAACACCCCACATCCAAAT 59.632 45.455 0.00 0.00 0.00 2.32
1399 1412 1.890552 ACCTCTTCATCATGGCCTCT 58.109 50.000 3.32 0.00 0.00 3.69
1424 1437 3.408389 CTCGCTTCGAGCTTGAAGA 57.592 52.632 37.43 21.96 46.75 2.87
1428 1441 1.388431 CGCTTCGAGCTTGAAGACTTC 59.612 52.381 37.43 22.65 46.64 3.01
1434 1447 5.843673 TCGAGCTTGAAGACTTCTCATAT 57.156 39.130 16.02 0.00 0.00 1.78
1491 1504 1.950954 GCTCCTGCAGAAACCCTAACC 60.951 57.143 17.39 0.00 39.41 2.85
1499 1512 1.151744 AAACCCTAACCCCCTCCGT 60.152 57.895 0.00 0.00 0.00 4.69
1517 1531 1.198178 CGTCCCCAAAATACACCAACG 59.802 52.381 0.00 0.00 0.00 4.10
1524 1538 3.057806 CCAAAATACACCAACGAAGACCC 60.058 47.826 0.00 0.00 0.00 4.46
1536 1550 1.739067 GAAGACCCGGAACAATCCAG 58.261 55.000 0.73 0.00 46.97 3.86
1551 1565 1.358152 TCCAGGATCGTCCCTTGTTT 58.642 50.000 0.00 0.00 37.19 2.83
1555 1569 3.307480 CCAGGATCGTCCCTTGTTTAGTT 60.307 47.826 1.06 0.00 37.19 2.24
1566 1580 6.700081 GTCCCTTGTTTAGTTTGAATTGGTTC 59.300 38.462 0.00 0.00 34.85 3.62
1567 1581 6.381420 TCCCTTGTTTAGTTTGAATTGGTTCA 59.619 34.615 0.00 0.00 42.41 3.18
1610 1625 3.481453 GGGAAGAATTCTCTATGGTGGC 58.519 50.000 8.78 0.00 44.00 5.01
1613 1628 4.442706 GAAGAATTCTCTATGGTGGCGAA 58.557 43.478 8.78 0.00 43.23 4.70
1646 1661 2.498078 AGAGGAAAAGAGCCCTAACGAG 59.502 50.000 0.00 0.00 31.84 4.18
1674 1689 5.220491 GGAAGATAGCGTTGTTTAGCTTCAG 60.220 44.000 10.48 0.00 41.62 3.02
1675 1690 5.073311 AGATAGCGTTGTTTAGCTTCAGA 57.927 39.130 0.00 0.00 44.15 3.27
1677 1692 5.578727 AGATAGCGTTGTTTAGCTTCAGAAG 59.421 40.000 5.72 5.72 44.15 2.85
1724 1740 0.596341 GGATCGCCGCTCTCTTCTTC 60.596 60.000 0.00 0.00 0.00 2.87
1756 1772 1.153549 GTCATCGTGGTGCTCCTCC 60.154 63.158 6.34 0.00 34.23 4.30
1765 1781 0.757935 GGTGCTCCTCCCCGTGTATA 60.758 60.000 0.00 0.00 0.00 1.47
1780 1796 4.369182 CGTGTATAGGATCCAGGTGAAAC 58.631 47.826 15.82 2.43 0.00 2.78
1833 1849 4.940463 GCTACACGATGTTGTCCCTTATA 58.060 43.478 0.00 0.00 0.00 0.98
1872 1889 5.521696 TCTTAGGTGTTATAGGGTGTAGCA 58.478 41.667 0.00 0.00 0.00 3.49
1875 1892 4.295201 AGGTGTTATAGGGTGTAGCATGA 58.705 43.478 0.00 0.00 0.00 3.07
1880 1897 5.360429 TGTTATAGGGTGTAGCATGACGTTA 59.640 40.000 0.00 0.00 0.00 3.18
1884 1901 5.546621 AGGGTGTAGCATGACGTTATATT 57.453 39.130 0.00 0.00 0.00 1.28
1886 1903 4.384846 GGGTGTAGCATGACGTTATATTCG 59.615 45.833 0.00 0.00 0.00 3.34
1914 1931 0.966179 TGTGCTCTCTTTCGGTAGCA 59.034 50.000 0.00 0.00 42.41 3.49
1921 1938 2.033049 TCTCTTTCGGTAGCATAGTCGC 59.967 50.000 0.00 0.00 0.00 5.19
1947 1965 2.693069 CCCGCATGATCTGGTTATCTC 58.307 52.381 0.00 0.00 0.00 2.75
1949 1967 2.029918 CCGCATGATCTGGTTATCTCGA 60.030 50.000 0.00 0.00 0.00 4.04
1957 1975 4.347360 TCTGGTTATCTCGAGATCGGTA 57.653 45.455 30.49 11.37 40.29 4.02
1965 1983 8.671921 GGTTATCTCGAGATCGGTATTGTATAA 58.328 37.037 30.49 12.34 40.29 0.98
1966 1984 9.705471 GTTATCTCGAGATCGGTATTGTATAAG 57.295 37.037 30.49 0.00 40.29 1.73
1967 1985 6.738832 TCTCGAGATCGGTATTGTATAAGG 57.261 41.667 12.08 0.00 40.29 2.69
1970 3507 4.461781 CGAGATCGGTATTGTATAAGGGGT 59.538 45.833 0.00 0.00 35.37 4.95
1973 3510 7.237209 AGATCGGTATTGTATAAGGGGTTAC 57.763 40.000 0.00 0.00 0.00 2.50
1987 3524 4.513406 GGGGTTACCTCACCATTTCATA 57.487 45.455 0.00 0.00 38.79 2.15
1991 3528 5.365619 GGTTACCTCACCATTTCATATCGT 58.634 41.667 0.00 0.00 36.73 3.73
1995 3532 3.494626 CCTCACCATTTCATATCGTTCGG 59.505 47.826 0.00 0.00 0.00 4.30
1997 3534 2.032030 CACCATTTCATATCGTTCGGCC 60.032 50.000 0.00 0.00 0.00 6.13
1998 3535 1.194547 CCATTTCATATCGTTCGGCCG 59.805 52.381 22.12 22.12 0.00 6.13
1999 3536 1.864711 CATTTCATATCGTTCGGCCGT 59.135 47.619 27.15 7.91 0.00 5.68
2000 3537 1.282817 TTTCATATCGTTCGGCCGTG 58.717 50.000 27.15 14.46 0.00 4.94
2001 3538 0.173935 TTCATATCGTTCGGCCGTGT 59.826 50.000 27.15 10.18 0.00 4.49
2002 3539 1.023502 TCATATCGTTCGGCCGTGTA 58.976 50.000 27.15 9.28 0.00 2.90
2003 3540 1.126079 CATATCGTTCGGCCGTGTAC 58.874 55.000 27.15 19.67 0.00 2.90
2004 3541 1.027357 ATATCGTTCGGCCGTGTACT 58.973 50.000 27.15 11.11 0.00 2.73
2005 3542 0.810648 TATCGTTCGGCCGTGTACTT 59.189 50.000 27.15 13.43 0.00 2.24
2006 3543 0.734942 ATCGTTCGGCCGTGTACTTG 60.735 55.000 27.15 9.34 0.00 3.16
2007 3544 1.662446 CGTTCGGCCGTGTACTTGT 60.662 57.895 27.15 0.00 0.00 3.16
2008 3545 1.216941 CGTTCGGCCGTGTACTTGTT 61.217 55.000 27.15 0.00 0.00 2.83
2009 3546 0.939419 GTTCGGCCGTGTACTTGTTT 59.061 50.000 27.15 0.00 0.00 2.83
2010 3547 0.938713 TTCGGCCGTGTACTTGTTTG 59.061 50.000 27.15 0.00 0.00 2.93
2011 3548 0.104487 TCGGCCGTGTACTTGTTTGA 59.896 50.000 27.15 0.00 0.00 2.69
2012 3549 0.233848 CGGCCGTGTACTTGTTTGAC 59.766 55.000 19.50 0.00 0.00 3.18
2013 3550 1.589803 GGCCGTGTACTTGTTTGACT 58.410 50.000 0.00 0.00 0.00 3.41
2014 3551 1.944709 GGCCGTGTACTTGTTTGACTT 59.055 47.619 0.00 0.00 0.00 3.01
2015 3552 2.286772 GGCCGTGTACTTGTTTGACTTG 60.287 50.000 0.00 0.00 0.00 3.16
2016 3553 2.353579 GCCGTGTACTTGTTTGACTTGT 59.646 45.455 0.00 0.00 0.00 3.16
2017 3554 3.545426 GCCGTGTACTTGTTTGACTTGTC 60.545 47.826 0.00 0.00 0.00 3.18
2018 3555 3.869246 CCGTGTACTTGTTTGACTTGTCT 59.131 43.478 2.35 0.00 0.00 3.41
2019 3556 4.025979 CCGTGTACTTGTTTGACTTGTCTC 60.026 45.833 2.35 0.00 0.00 3.36
2048 3585 3.077359 CCGGAATGAATAAGGCAGATCC 58.923 50.000 0.00 0.00 0.00 3.36
2153 4536 1.334960 CGTGAGCACCAACAAACCATC 60.335 52.381 0.00 0.00 0.00 3.51
2294 4763 2.180159 AACAAGTATCCGCCGCCACT 62.180 55.000 0.00 0.00 0.00 4.00
2314 4783 1.230635 GCAGCTGTTTCTTCCTCGCA 61.231 55.000 16.64 0.00 0.00 5.10
2316 4785 1.808945 CAGCTGTTTCTTCCTCGCAAT 59.191 47.619 5.25 0.00 0.00 3.56
2320 4789 4.083271 AGCTGTTTCTTCCTCGCAATAAAC 60.083 41.667 0.00 0.00 0.00 2.01
2341 4811 1.734477 GTCGCGTGCTGACTGTCAT 60.734 57.895 11.45 0.00 33.54 3.06
2358 4834 0.673956 CATCTGTGCTGCTGCTGTCT 60.674 55.000 17.00 0.00 40.48 3.41
2468 4944 0.386478 GTACGTCGCGTCCAACTTCT 60.386 55.000 5.77 0.00 41.54 2.85
2586 5062 5.335976 GGTCATTTCACATCTTCAGAAACCC 60.336 44.000 0.00 0.00 34.47 4.11
2603 5079 2.187946 CTGTGGCTGACGATCCCC 59.812 66.667 0.00 0.00 0.00 4.81
2604 5080 3.391665 CTGTGGCTGACGATCCCCC 62.392 68.421 0.00 0.00 0.00 5.40
2605 5081 4.530857 GTGGCTGACGATCCCCCG 62.531 72.222 0.00 0.00 0.00 5.73
2622 5098 2.028294 CCCCGATCCATTCTCAGATGAG 60.028 54.545 3.33 3.33 43.36 2.90
2695 5171 4.241555 AGCCCATCGCGGACATCC 62.242 66.667 6.13 0.00 44.76 3.51
2755 5231 5.003096 AGGGTTTCATTCACTTCCAAGAT 57.997 39.130 0.00 0.00 0.00 2.40
2778 5264 0.615331 GGACTCAGCTGAACCCATCA 59.385 55.000 18.85 0.00 36.38 3.07
2997 5491 3.336468 ACAACACACCTAACGAACACAA 58.664 40.909 0.00 0.00 0.00 3.33
3006 5500 2.892373 AACGAACACAACCGCATATG 57.108 45.000 0.00 0.00 0.00 1.78
3011 5505 2.346099 ACACAACCGCATATGCAAAC 57.654 45.000 26.52 0.00 42.21 2.93
3047 5541 1.374758 CCTGAGCACACGGTCTTCC 60.375 63.158 0.00 0.00 40.44 3.46
3060 5554 1.584724 GTCTTCCCATTCCCTCTCCA 58.415 55.000 0.00 0.00 0.00 3.86
3110 5605 0.944386 AACAGCGCGTTCATCACTTT 59.056 45.000 8.43 0.00 29.27 2.66
3492 5999 3.325870 TGCATCTTGGTTGAACTACTCG 58.674 45.455 0.00 0.00 0.00 4.18
3704 6316 2.034878 CATAGGGACTGCTGCAGACTA 58.965 52.381 34.28 27.99 41.52 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.939577 CGACCGAAGACCCATATGCG 60.940 60.000 0.00 0.00 0.00 4.73
9 10 2.038329 TCCCGACCGAAGACCCAT 59.962 61.111 0.00 0.00 0.00 4.00
42 43 2.606587 ATGAGCCCCGCTGGACTTT 61.607 57.895 0.00 0.00 39.88 2.66
79 80 1.048724 TAGATCCGGGGCAGGTCTTG 61.049 60.000 0.00 0.00 0.00 3.02
136 137 1.909302 TCTTTGGATCCCCTGTCAGAC 59.091 52.381 9.90 0.00 0.00 3.51
272 273 2.362736 TGAGCAGGTCGATAGTTACGT 58.637 47.619 0.00 0.00 37.40 3.57
396 397 0.755686 GACAGAAGGATCGATGGCCT 59.244 55.000 0.54 0.09 35.61 5.19
397 398 0.465705 TGACAGAAGGATCGATGGCC 59.534 55.000 0.54 0.00 0.00 5.36
426 427 3.347216 GGTGCTTTCATTAAGAGCTCCA 58.653 45.455 10.93 0.00 44.98 3.86
435 436 3.417101 ACCGACATTGGTGCTTTCATTA 58.583 40.909 0.00 0.00 41.85 1.90
678 684 1.596895 GGATAGATCGGAGGCGGGAC 61.597 65.000 0.00 0.00 0.00 4.46
682 688 0.808125 CAGAGGATAGATCGGAGGCG 59.192 60.000 0.00 0.00 0.00 5.52
695 702 4.831155 CCGGTGTCTATATAAACCAGAGGA 59.169 45.833 0.00 0.00 32.69 3.71
854 863 1.208535 CTGTTAATGTGGGCCGGACTA 59.791 52.381 7.57 0.00 0.00 2.59
899 908 2.689034 GGAGTCCTGGACTGGGGG 60.689 72.222 32.86 0.00 43.53 5.40
900 909 2.689034 GGGAGTCCTGGACTGGGG 60.689 72.222 32.86 0.00 43.53 4.96
901 910 2.122729 TGGGAGTCCTGGACTGGG 59.877 66.667 32.86 0.00 43.53 4.45
902 911 1.536418 TGTGGGAGTCCTGGACTGG 60.536 63.158 32.86 0.00 43.53 4.00
903 912 1.674057 GTGTGGGAGTCCTGGACTG 59.326 63.158 32.86 0.00 43.53 3.51
904 913 1.536662 GGTGTGGGAGTCCTGGACT 60.537 63.158 28.70 28.70 46.42 3.85
905 914 2.593956 GGGTGTGGGAGTCCTGGAC 61.594 68.421 19.20 19.20 0.00 4.02
906 915 2.203938 GGGTGTGGGAGTCCTGGA 60.204 66.667 9.58 0.00 0.00 3.86
907 916 3.706373 CGGGTGTGGGAGTCCTGG 61.706 72.222 9.58 0.00 0.00 4.45
908 917 4.394712 GCGGGTGTGGGAGTCCTG 62.395 72.222 9.58 0.00 0.00 3.86
911 920 1.623542 ATAAGGCGGGTGTGGGAGTC 61.624 60.000 0.00 0.00 0.00 3.36
912 921 0.325860 TATAAGGCGGGTGTGGGAGT 60.326 55.000 0.00 0.00 0.00 3.85
913 922 1.056660 ATATAAGGCGGGTGTGGGAG 58.943 55.000 0.00 0.00 0.00 4.30
914 923 0.762418 CATATAAGGCGGGTGTGGGA 59.238 55.000 0.00 0.00 0.00 4.37
915 924 0.762418 TCATATAAGGCGGGTGTGGG 59.238 55.000 0.00 0.00 0.00 4.61
916 925 1.416401 ACTCATATAAGGCGGGTGTGG 59.584 52.381 0.00 0.00 0.00 4.17
917 926 2.910688 ACTCATATAAGGCGGGTGTG 57.089 50.000 0.00 0.00 0.00 3.82
918 927 6.351881 CCATATAACTCATATAAGGCGGGTGT 60.352 42.308 0.00 0.00 30.76 4.16
919 928 6.049149 CCATATAACTCATATAAGGCGGGTG 58.951 44.000 0.00 0.00 30.76 4.61
920 929 5.724854 ACCATATAACTCATATAAGGCGGGT 59.275 40.000 0.00 0.00 38.40 5.28
921 930 6.235231 ACCATATAACTCATATAAGGCGGG 57.765 41.667 0.00 0.00 38.40 6.13
922 931 9.261180 CAATACCATATAACTCATATAAGGCGG 57.739 37.037 0.00 0.00 38.40 6.13
923 932 9.817809 ACAATACCATATAACTCATATAAGGCG 57.182 33.333 0.00 0.00 38.40 5.52
931 940 9.407380 TGCAAAGAACAATACCATATAACTCAT 57.593 29.630 0.00 0.00 0.00 2.90
932 941 8.800370 TGCAAAGAACAATACCATATAACTCA 57.200 30.769 0.00 0.00 0.00 3.41
938 947 9.754382 GATCAAATGCAAAGAACAATACCATAT 57.246 29.630 0.00 0.00 0.00 1.78
939 948 8.970020 AGATCAAATGCAAAGAACAATACCATA 58.030 29.630 0.00 0.00 0.00 2.74
940 949 7.844009 AGATCAAATGCAAAGAACAATACCAT 58.156 30.769 0.00 0.00 0.00 3.55
941 950 7.177216 AGAGATCAAATGCAAAGAACAATACCA 59.823 33.333 0.00 0.00 0.00 3.25
942 951 7.542025 AGAGATCAAATGCAAAGAACAATACC 58.458 34.615 0.00 0.00 0.00 2.73
943 952 8.976986 AAGAGATCAAATGCAAAGAACAATAC 57.023 30.769 0.00 0.00 0.00 1.89
944 953 9.414295 CAAAGAGATCAAATGCAAAGAACAATA 57.586 29.630 0.00 0.00 0.00 1.90
945 954 7.386848 CCAAAGAGATCAAATGCAAAGAACAAT 59.613 33.333 0.00 0.00 0.00 2.71
946 955 6.702723 CCAAAGAGATCAAATGCAAAGAACAA 59.297 34.615 0.00 0.00 0.00 2.83
947 956 6.040729 TCCAAAGAGATCAAATGCAAAGAACA 59.959 34.615 0.00 0.00 0.00 3.18
948 957 6.449698 TCCAAAGAGATCAAATGCAAAGAAC 58.550 36.000 0.00 0.00 0.00 3.01
949 958 6.294899 CCTCCAAAGAGATCAAATGCAAAGAA 60.295 38.462 0.00 0.00 43.39 2.52
950 959 5.184479 CCTCCAAAGAGATCAAATGCAAAGA 59.816 40.000 0.00 0.00 43.39 2.52
951 960 5.047519 ACCTCCAAAGAGATCAAATGCAAAG 60.048 40.000 0.00 0.00 43.39 2.77
952 961 4.834496 ACCTCCAAAGAGATCAAATGCAAA 59.166 37.500 0.00 0.00 43.39 3.68
953 962 4.410099 ACCTCCAAAGAGATCAAATGCAA 58.590 39.130 0.00 0.00 43.39 4.08
954 963 4.038271 ACCTCCAAAGAGATCAAATGCA 57.962 40.909 0.00 0.00 43.39 3.96
955 964 4.741342 CAACCTCCAAAGAGATCAAATGC 58.259 43.478 0.00 0.00 43.39 3.56
956 965 4.461781 AGCAACCTCCAAAGAGATCAAATG 59.538 41.667 0.00 0.00 43.39 2.32
957 966 4.670765 AGCAACCTCCAAAGAGATCAAAT 58.329 39.130 0.00 0.00 43.39 2.32
958 967 4.104383 AGCAACCTCCAAAGAGATCAAA 57.896 40.909 0.00 0.00 43.39 2.69
959 968 3.795688 AGCAACCTCCAAAGAGATCAA 57.204 42.857 0.00 0.00 43.39 2.57
960 969 3.072915 TGAAGCAACCTCCAAAGAGATCA 59.927 43.478 0.00 0.00 43.39 2.92
961 970 3.679389 TGAAGCAACCTCCAAAGAGATC 58.321 45.455 0.00 0.00 43.39 2.75
962 971 3.328931 TCTGAAGCAACCTCCAAAGAGAT 59.671 43.478 0.00 0.00 43.39 2.75
963 972 2.705658 TCTGAAGCAACCTCCAAAGAGA 59.294 45.455 0.00 0.00 43.39 3.10
964 973 3.072944 CTCTGAAGCAACCTCCAAAGAG 58.927 50.000 0.00 0.00 40.09 2.85
965 974 2.224621 CCTCTGAAGCAACCTCCAAAGA 60.225 50.000 0.00 0.00 0.00 2.52
966 975 2.157738 CCTCTGAAGCAACCTCCAAAG 58.842 52.381 0.00 0.00 0.00 2.77
967 976 1.202927 CCCTCTGAAGCAACCTCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
968 977 0.401738 CCCTCTGAAGCAACCTCCAA 59.598 55.000 0.00 0.00 0.00 3.53
969 978 1.492133 CCCCTCTGAAGCAACCTCCA 61.492 60.000 0.00 0.00 0.00 3.86
970 979 1.301293 CCCCTCTGAAGCAACCTCC 59.699 63.158 0.00 0.00 0.00 4.30
971 980 1.301293 CCCCCTCTGAAGCAACCTC 59.699 63.158 0.00 0.00 0.00 3.85
972 981 3.500635 CCCCCTCTGAAGCAACCT 58.499 61.111 0.00 0.00 0.00 3.50
994 1003 1.436983 GGTGCGCTAACCATACCAGC 61.437 60.000 9.73 0.00 40.22 4.85
995 1004 0.178068 AGGTGCGCTAACCATACCAG 59.822 55.000 18.19 0.00 43.20 4.00
1027 1039 0.690762 GGGAAGGGCACACAACTAGA 59.309 55.000 0.00 0.00 0.00 2.43
1029 1041 0.847373 TTGGGAAGGGCACACAACTA 59.153 50.000 0.00 0.00 0.00 2.24
1035 1047 3.599602 TCCATTGGGAAGGGCACA 58.400 55.556 2.09 0.00 41.32 4.57
1045 1057 3.862877 TGATCTGGGTATGTCCATTGG 57.137 47.619 0.00 0.00 36.05 3.16
1064 1076 4.230455 AGAGGGGAGATGAGGTTAAGATG 58.770 47.826 0.00 0.00 0.00 2.90
1077 1089 1.309006 GGTAACCGGAGAGGGGAGA 59.691 63.158 9.46 0.00 46.96 3.71
1078 1090 0.398664 ATGGTAACCGGAGAGGGGAG 60.399 60.000 9.46 0.00 46.96 4.30
1079 1091 0.398098 GATGGTAACCGGAGAGGGGA 60.398 60.000 9.46 0.00 46.96 4.81
1080 1092 0.689745 TGATGGTAACCGGAGAGGGG 60.690 60.000 9.46 0.00 46.96 4.79
1084 1096 1.760613 GATGGTGATGGTAACCGGAGA 59.239 52.381 9.46 0.00 40.86 3.71
1085 1097 1.484653 TGATGGTGATGGTAACCGGAG 59.515 52.381 9.46 0.00 40.86 4.63
1086 1098 1.574263 TGATGGTGATGGTAACCGGA 58.426 50.000 9.46 0.00 40.86 5.14
1087 1099 2.014128 GTTGATGGTGATGGTAACCGG 58.986 52.381 0.00 0.00 40.86 5.28
1088 1100 2.014128 GGTTGATGGTGATGGTAACCG 58.986 52.381 0.00 0.00 40.86 4.44
1098 1111 4.139038 TGATGCTGATATGGTTGATGGTG 58.861 43.478 0.00 0.00 0.00 4.17
1100 1113 4.825634 AGTTGATGCTGATATGGTTGATGG 59.174 41.667 0.00 0.00 0.00 3.51
1110 1123 5.946942 AGAGGAAGAAGTTGATGCTGATA 57.053 39.130 0.00 0.00 0.00 2.15
1113 1126 3.688673 GGAAGAGGAAGAAGTTGATGCTG 59.311 47.826 0.00 0.00 0.00 4.41
1123 1136 7.560796 AGTTTATGAAGAGGAAGAGGAAGAA 57.439 36.000 0.00 0.00 0.00 2.52
1167 1180 5.545588 GTCAAGGCTGCTCAGATAATGATA 58.454 41.667 0.00 0.00 37.28 2.15
1182 1195 4.021925 GGGCTGGTCGTCAAGGCT 62.022 66.667 10.27 0.00 0.00 4.58
1225 1238 0.687354 GAGCTTCAGGTGGAGGTGAA 59.313 55.000 0.00 0.00 0.00 3.18
1226 1239 0.178921 AGAGCTTCAGGTGGAGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
1237 1250 1.625818 GGACCTGAAGGAAGAGCTTCA 59.374 52.381 11.90 0.00 41.20 3.02
1238 1251 1.404851 CGGACCTGAAGGAAGAGCTTC 60.405 57.143 2.62 1.62 38.94 3.86
1242 1255 2.171840 TCTTCGGACCTGAAGGAAGAG 58.828 52.381 19.35 1.98 44.38 2.85
1294 1307 1.470632 GGACTTCATCCTCTGTCAGCG 60.471 57.143 0.00 0.00 45.22 5.18
1335 1348 1.733402 ATGTGGGGTGTTTGTGCACG 61.733 55.000 13.13 0.00 40.08 5.34
1340 1353 2.166907 TTTGGATGTGGGGTGTTTGT 57.833 45.000 0.00 0.00 0.00 2.83
1347 1360 2.523325 TGGTGTATTTGGATGTGGGG 57.477 50.000 0.00 0.00 0.00 4.96
1355 1368 4.283212 AGGTTGTCCAATTGGTGTATTTGG 59.717 41.667 23.76 0.00 39.88 3.28
1359 1372 5.014202 GGTTAGGTTGTCCAATTGGTGTAT 58.986 41.667 23.76 9.17 36.34 2.29
1360 1373 4.105057 AGGTTAGGTTGTCCAATTGGTGTA 59.895 41.667 23.76 8.94 36.34 2.90
1399 1412 3.099438 CTCGAAGCGAGCGAGGTA 58.901 61.111 15.12 0.00 46.75 3.08
1424 1437 8.980832 ATTAGGGAAGGTGATATATGAGAAGT 57.019 34.615 0.00 0.00 0.00 3.01
1428 1441 6.607600 TCGGATTAGGGAAGGTGATATATGAG 59.392 42.308 0.00 0.00 0.00 2.90
1434 1447 5.213519 TCTTTCGGATTAGGGAAGGTGATA 58.786 41.667 0.00 0.00 0.00 2.15
1463 1476 1.267574 TTCTGCAGGAGCCTGGTAGG 61.268 60.000 15.13 0.00 43.77 3.18
1491 1504 0.106868 GTATTTTGGGGACGGAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
1499 1512 2.953284 TCGTTGGTGTATTTTGGGGA 57.047 45.000 0.00 0.00 0.00 4.81
1517 1531 1.739067 CTGGATTGTTCCGGGTCTTC 58.261 55.000 0.00 0.00 45.89 2.87
1524 1538 1.571919 GACGATCCTGGATTGTTCCG 58.428 55.000 26.45 18.96 45.89 4.30
1536 1550 4.320870 TCAAACTAAACAAGGGACGATCC 58.679 43.478 0.00 0.00 35.23 3.36
1551 1565 5.534654 CCTCCAACTGAACCAATTCAAACTA 59.465 40.000 0.00 0.00 44.28 2.24
1555 1569 4.177537 TCCTCCAACTGAACCAATTCAA 57.822 40.909 0.00 0.00 44.28 2.69
1566 1580 2.507058 TCCCATCTGATTCCTCCAACTG 59.493 50.000 0.00 0.00 0.00 3.16
1567 1581 2.776536 CTCCCATCTGATTCCTCCAACT 59.223 50.000 0.00 0.00 0.00 3.16
1610 1625 1.067669 TCCTCTCAATGGCGATCTTCG 59.932 52.381 0.00 0.00 43.89 3.79
1613 1628 3.198635 TCTTTTCCTCTCAATGGCGATCT 59.801 43.478 0.00 0.00 0.00 2.75
1621 1636 4.624125 CGTTAGGGCTCTTTTCCTCTCAAT 60.624 45.833 0.00 0.00 34.75 2.57
1622 1637 3.306780 CGTTAGGGCTCTTTTCCTCTCAA 60.307 47.826 0.00 0.00 34.75 3.02
1646 1661 2.693267 AACAACGCTATCTTCCCCTC 57.307 50.000 0.00 0.00 0.00 4.30
1674 1689 3.821600 TCGGCACATCTATCTAGTCCTTC 59.178 47.826 0.00 0.00 0.00 3.46
1675 1690 3.833732 TCGGCACATCTATCTAGTCCTT 58.166 45.455 0.00 0.00 0.00 3.36
1677 1692 4.792521 AATCGGCACATCTATCTAGTCC 57.207 45.455 0.00 0.00 0.00 3.85
1724 1740 3.961474 CGATGACGTCTTCAAGTCTTG 57.039 47.619 25.61 6.21 37.92 3.02
1738 1754 1.153549 GGAGGAGCACCACGATGAC 60.154 63.158 2.07 0.00 38.94 3.06
1741 1757 3.083997 GGGGAGGAGCACCACGAT 61.084 66.667 2.07 0.00 41.00 3.73
1756 1772 1.618837 CACCTGGATCCTATACACGGG 59.381 57.143 14.23 1.08 0.00 5.28
1765 1781 1.760405 AAGGGTTTCACCTGGATCCT 58.240 50.000 14.23 0.00 40.87 3.24
1790 1806 2.125512 GCCGCTGACGAGTCCAAT 60.126 61.111 0.34 0.00 43.93 3.16
1814 1830 4.766375 CCTTATAAGGGACAACATCGTGT 58.234 43.478 22.09 0.00 42.66 4.49
1816 1832 3.740141 CGCCTTATAAGGGACAACATCGT 60.740 47.826 28.81 0.00 46.56 3.73
1824 1840 3.126343 CACAACAACGCCTTATAAGGGAC 59.874 47.826 28.81 14.71 46.56 4.46
1833 1849 1.981256 AAGATCCACAACAACGCCTT 58.019 45.000 0.00 0.00 0.00 4.35
1872 1889 5.786264 AGAAGGACCGAATATAACGTCAT 57.214 39.130 0.00 0.00 0.00 3.06
1875 1892 5.107133 CACAAGAAGGACCGAATATAACGT 58.893 41.667 0.00 0.00 0.00 3.99
1880 1897 3.452627 AGAGCACAAGAAGGACCGAATAT 59.547 43.478 0.00 0.00 0.00 1.28
1884 1901 0.603569 GAGAGCACAAGAAGGACCGA 59.396 55.000 0.00 0.00 0.00 4.69
1886 1903 2.849294 AAGAGAGCACAAGAAGGACC 57.151 50.000 0.00 0.00 0.00 4.46
1929 1947 3.057946 TCTCGAGATAACCAGATCATGCG 60.058 47.826 12.08 0.00 0.00 4.73
1932 1950 4.397730 CCGATCTCGAGATAACCAGATCAT 59.602 45.833 27.36 1.85 40.90 2.45
1938 1956 4.825634 ACAATACCGATCTCGAGATAACCA 59.174 41.667 27.36 13.73 43.02 3.67
1947 1965 4.461781 ACCCCTTATACAATACCGATCTCG 59.538 45.833 0.00 0.00 39.44 4.04
1949 1967 6.212187 GGTAACCCCTTATACAATACCGATCT 59.788 42.308 0.00 0.00 0.00 2.75
1957 1975 5.041015 TGGTGAGGTAACCCCTTATACAAT 58.959 41.667 0.00 0.00 46.51 2.71
1966 1984 2.891191 TGAAATGGTGAGGTAACCCC 57.109 50.000 0.00 0.00 39.70 4.95
1967 1985 4.755123 CGATATGAAATGGTGAGGTAACCC 59.245 45.833 0.00 0.00 39.70 4.11
1970 3507 5.751509 CGAACGATATGAAATGGTGAGGTAA 59.248 40.000 0.00 0.00 0.00 2.85
1973 3510 3.494626 CCGAACGATATGAAATGGTGAGG 59.505 47.826 0.00 0.00 0.00 3.86
1978 3515 1.194547 CGGCCGAACGATATGAAATGG 59.805 52.381 24.07 0.00 35.47 3.16
1982 3519 0.173935 ACACGGCCGAACGATATGAA 59.826 50.000 35.90 0.00 37.61 2.57
1987 3524 0.734942 CAAGTACACGGCCGAACGAT 60.735 55.000 35.90 16.97 37.61 3.73
1991 3528 0.938713 CAAACAAGTACACGGCCGAA 59.061 50.000 35.90 14.32 0.00 4.30
1995 3532 2.353579 ACAAGTCAAACAAGTACACGGC 59.646 45.455 0.00 0.00 0.00 5.68
1997 3534 4.804139 AGAGACAAGTCAAACAAGTACACG 59.196 41.667 2.72 0.00 0.00 4.49
1998 3535 6.979238 ACTAGAGACAAGTCAAACAAGTACAC 59.021 38.462 0.00 0.00 0.00 2.90
1999 3536 7.108841 ACTAGAGACAAGTCAAACAAGTACA 57.891 36.000 0.00 0.00 0.00 2.90
2000 3537 6.360148 CGACTAGAGACAAGTCAAACAAGTAC 59.640 42.308 0.00 0.00 42.91 2.73
2001 3538 6.436261 CGACTAGAGACAAGTCAAACAAGTA 58.564 40.000 0.00 0.00 42.91 2.24
2002 3539 5.282510 CGACTAGAGACAAGTCAAACAAGT 58.717 41.667 0.00 0.00 42.91 3.16
2003 3540 4.681942 CCGACTAGAGACAAGTCAAACAAG 59.318 45.833 0.00 0.00 42.91 3.16
2004 3541 4.617959 CCGACTAGAGACAAGTCAAACAA 58.382 43.478 0.00 0.00 42.91 2.83
2005 3542 3.552273 GCCGACTAGAGACAAGTCAAACA 60.552 47.826 0.00 0.00 42.91 2.83
2006 3543 2.987821 GCCGACTAGAGACAAGTCAAAC 59.012 50.000 0.00 0.00 42.91 2.93
2007 3544 2.029290 GGCCGACTAGAGACAAGTCAAA 60.029 50.000 0.00 0.00 42.91 2.69
2008 3545 1.544691 GGCCGACTAGAGACAAGTCAA 59.455 52.381 0.00 0.00 42.91 3.18
2009 3546 1.174783 GGCCGACTAGAGACAAGTCA 58.825 55.000 0.00 0.00 42.91 3.41
2010 3547 0.099082 CGGCCGACTAGAGACAAGTC 59.901 60.000 24.07 0.00 40.01 3.01
2011 3548 1.313812 CCGGCCGACTAGAGACAAGT 61.314 60.000 30.73 0.00 0.00 3.16
2012 3549 1.030488 TCCGGCCGACTAGAGACAAG 61.030 60.000 30.73 4.77 0.00 3.16
2013 3550 0.609957 TTCCGGCCGACTAGAGACAA 60.610 55.000 30.73 0.00 0.00 3.18
2014 3551 0.395311 ATTCCGGCCGACTAGAGACA 60.395 55.000 30.73 0.00 0.00 3.41
2015 3552 0.030908 CATTCCGGCCGACTAGAGAC 59.969 60.000 30.73 0.00 0.00 3.36
2016 3553 0.106868 TCATTCCGGCCGACTAGAGA 60.107 55.000 30.73 11.67 0.00 3.10
2017 3554 0.744874 TTCATTCCGGCCGACTAGAG 59.255 55.000 30.73 8.93 0.00 2.43
2018 3555 1.410004 ATTCATTCCGGCCGACTAGA 58.590 50.000 30.73 16.43 0.00 2.43
2019 3556 3.318017 CTTATTCATTCCGGCCGACTAG 58.682 50.000 30.73 14.13 0.00 2.57
2118 4492 1.363807 CACGCTGTGTGGAGACTGA 59.636 57.895 13.38 0.00 45.21 3.41
2131 4505 1.724582 GGTTTGTTGGTGCTCACGCT 61.725 55.000 0.00 0.00 36.97 5.07
2146 4520 1.079127 CCTCCGAGTGCGATGGTTT 60.079 57.895 0.00 0.00 40.82 3.27
2294 4763 1.230635 GCGAGGAAGAAACAGCTGCA 61.231 55.000 15.27 0.00 0.00 4.41
2299 4768 4.151689 TCGTTTATTGCGAGGAAGAAACAG 59.848 41.667 21.07 15.41 37.03 3.16
2320 4789 3.168604 CAGTCAGCACGCGACTCG 61.169 66.667 15.93 5.17 41.80 4.18
2326 4795 0.668706 ACAGATGACAGTCAGCACGC 60.669 55.000 20.72 2.35 34.77 5.34
2327 4796 1.066136 CACAGATGACAGTCAGCACG 58.934 55.000 20.72 13.20 34.77 5.34
2330 4799 1.077123 CAGCACAGATGACAGTCAGC 58.923 55.000 11.05 11.05 31.96 4.26
2333 4803 1.077123 CAGCAGCACAGATGACAGTC 58.923 55.000 0.00 0.00 0.00 3.51
2341 4811 0.602106 GAAGACAGCAGCAGCACAGA 60.602 55.000 3.17 0.00 45.49 3.41
2441 4917 2.256158 CGCGACGTACAGGACCAA 59.744 61.111 0.00 0.00 0.00 3.67
2552 5028 3.006940 TGTGAAATGACCATAGCGGAAC 58.993 45.455 0.00 0.00 38.63 3.62
2586 5062 2.187946 GGGGATCGTCAGCCACAG 59.812 66.667 0.00 0.00 0.00 3.66
2603 5079 2.036862 TGCTCATCTGAGAATGGATCGG 59.963 50.000 11.34 0.00 44.74 4.18
2604 5080 3.058450 GTGCTCATCTGAGAATGGATCG 58.942 50.000 11.34 0.00 44.74 3.69
2605 5081 3.058450 CGTGCTCATCTGAGAATGGATC 58.942 50.000 11.34 0.00 44.74 3.36
2661 5137 1.068753 CTCGATGGCTTGATCCGCT 59.931 57.895 4.39 0.00 0.00 5.52
2663 5139 1.958205 GGCTCGATGGCTTGATCCG 60.958 63.158 0.00 0.00 38.32 4.18
2664 5140 1.599240 GGGCTCGATGGCTTGATCC 60.599 63.158 8.00 0.00 41.48 3.36
2695 5171 1.081556 TTGTTCATCCGGTCGATGCG 61.082 55.000 0.00 0.00 46.93 4.73
2700 5176 2.293677 TGAGATTGTTCATCCGGTCG 57.706 50.000 0.00 0.00 31.20 4.79
2713 5189 1.825090 TGCTCGCCAAACATGAGATT 58.175 45.000 0.00 0.00 31.31 2.40
2755 5231 0.615331 GGGTTCAGCTGAGTCCATCA 59.385 55.000 28.68 9.53 36.21 3.07
2825 5314 6.404074 CCACTTCAGTAATGAATCTTGGAAGC 60.404 42.308 17.25 0.00 35.19 3.86
2826 5315 6.404074 GCCACTTCAGTAATGAATCTTGGAAG 60.404 42.308 22.69 7.37 37.21 3.46
2997 5491 2.770589 GCCGGTTTGCATATGCGGT 61.771 57.895 22.21 0.00 45.83 5.68
3006 5500 1.212751 GATTGGTGAGCCGGTTTGC 59.787 57.895 1.90 0.00 37.67 3.68
3011 5505 3.197790 CTGCGATTGGTGAGCCGG 61.198 66.667 0.00 0.00 37.67 6.13
3047 5541 1.221840 CGTGGTGGAGAGGGAATGG 59.778 63.158 0.00 0.00 0.00 3.16
3110 5605 0.886043 TCGACGTGGAGTTCGAGGAA 60.886 55.000 0.00 0.00 32.01 3.36
3257 5752 0.171007 CGTGCCCAGCATGTAAAAGG 59.829 55.000 0.55 0.00 41.91 3.11
3466 5973 7.145932 AGTAGTTCAACCAAGATGCAAATAC 57.854 36.000 0.00 0.00 0.00 1.89
3478 5985 5.466819 CATTGTAGACGAGTAGTTCAACCA 58.533 41.667 0.00 0.00 0.00 3.67
3492 5999 2.084546 GGTCACCCTTGCATTGTAGAC 58.915 52.381 0.00 0.00 0.00 2.59
3704 6316 9.362151 TCCACTTATTTAAATCACTTCAAAGGT 57.638 29.630 3.39 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.