Multiple sequence alignment - TraesCS3D01G089400

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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 TraesCS3D01G089400 chr3D 100.000 2827 0 0 1 2827 45355195 45358021 0.000000e+00 5221.0
1 TraesCS3D01G089400 chr3D 91.573 178 15 0 1441 1618 514852535 514852712 2.180000e-61 246.0
2 TraesCS3D01G089400 chr3D 82.239 259 38 2 997 1255 50401166 50400916 1.710000e-52 217.0
3 TraesCS3D01G089400 chr3D 88.679 159 15 3 1451 1607 50400653 50400496 1.030000e-44 191.0
4 TraesCS3D01G089400 chr3D 90.541 74 7 0 105 178 156973422 156973495 6.450000e-17 99.0
5 TraesCS3D01G089400 chr3D 82.075 106 14 4 17 119 156973262 156973365 5.020000e-13 86.1
6 TraesCS3D01G089400 chr3A 90.449 1047 51 12 997 2012 57153930 57154958 0.000000e+00 1334.0
7 TraesCS3D01G089400 chr3A 88.754 329 23 8 1056 1384 57152609 57152923 9.500000e-105 390.0
8 TraesCS3D01G089400 chr3A 83.658 257 34 2 997 1253 57148964 57148716 4.710000e-58 235.0
9 TraesCS3D01G089400 chr3A 90.449 178 17 0 1441 1618 649567747 649567924 4.710000e-58 235.0
10 TraesCS3D01G089400 chr3A 82.692 260 37 2 997 1256 63476998 63476747 1.020000e-54 224.0
11 TraesCS3D01G089400 chr3A 89.937 159 16 0 1459 1617 15343454 15343612 3.690000e-49 206.0
12 TraesCS3D01G089400 chr3A 91.333 150 13 0 1458 1607 63476473 63476324 3.690000e-49 206.0
13 TraesCS3D01G089400 chr3A 80.377 265 41 7 997 1259 15343006 15343261 1.030000e-44 191.0
14 TraesCS3D01G089400 chr3A 92.308 65 5 0 1730 1794 15343712 15343776 3.000000e-15 93.5
15 TraesCS3D01G089400 chr3B 89.445 739 56 11 2088 2823 70907330 70908049 0.000000e+00 913.0
16 TraesCS3D01G089400 chr3B 89.250 707 34 18 1212 1888 70906173 70906867 0.000000e+00 846.0
17 TraesCS3D01G089400 chr3B 91.304 207 15 2 1888 2094 70906951 70907154 2.140000e-71 279.0
18 TraesCS3D01G089400 chr3B 91.573 178 13 2 1441 1618 677290014 677290189 7.820000e-61 244.0
19 TraesCS3D01G089400 chr3B 87.709 179 21 1 1 178 763034783 763034961 1.030000e-49 207.0
20 TraesCS3D01G089400 chr3B 91.333 150 13 0 1458 1607 79955623 79955474 3.690000e-49 206.0
21 TraesCS3D01G089400 chr3B 80.695 259 42 2 997 1255 79956139 79955889 7.990000e-46 195.0
22 TraesCS3D01G089400 chr3B 92.188 64 5 0 1730 1793 79955372 79955309 1.080000e-14 91.6
23 TraesCS3D01G089400 chr4D 87.964 781 80 14 173 947 279553416 279552644 0.000000e+00 909.0
24 TraesCS3D01G089400 chr4D 86.391 169 22 1 1 168 295001452 295001284 1.730000e-42 183.0
25 TraesCS3D01G089400 chr4D 86.538 104 8 6 12 114 443800651 443800553 2.980000e-20 110.0
26 TraesCS3D01G089400 chr5A 87.883 784 79 16 172 947 572035879 572036654 0.000000e+00 907.0
27 TraesCS3D01G089400 chr7D 87.852 782 82 13 172 947 100231083 100230309 0.000000e+00 905.0
28 TraesCS3D01G089400 chr7B 87.708 781 84 12 172 947 739480190 739479417 0.000000e+00 900.0
29 TraesCS3D01G089400 chr7B 87.580 781 87 10 172 947 168326461 168325686 0.000000e+00 896.0
30 TraesCS3D01G089400 chr6D 87.739 783 79 17 172 947 76058827 76058055 0.000000e+00 898.0
31 TraesCS3D01G089400 chr5D 87.580 781 83 14 174 947 406527537 406528310 0.000000e+00 893.0
32 TraesCS3D01G089400 chr1D 87.516 785 81 15 172 947 453607571 453606795 0.000000e+00 891.0
33 TraesCS3D01G089400 chr1D 87.484 783 81 17 173 947 457163976 457163203 0.000000e+00 887.0
34 TraesCS3D01G089400 chr1D 87.845 181 16 3 1 179 26143346 26143170 1.030000e-49 207.0
35 TraesCS3D01G089400 chr2B 87.709 179 21 1 1 178 734315853 734315675 1.030000e-49 207.0
36 TraesCS3D01G089400 chr2B 87.151 179 21 2 1 178 470477716 470477539 4.780000e-48 202.0
37 TraesCS3D01G089400 chr2B 83.708 178 26 3 2 178 568246330 568246505 6.270000e-37 165.0
38 TraesCS3D01G089400 chr2B 87.640 89 10 1 6 93 496978529 496978441 4.980000e-18 102.0
39 TraesCS3D01G089400 chr4A 88.820 161 18 0 1458 1618 625784771 625784611 6.180000e-47 198.0
40 TraesCS3D01G089400 chr4A 94.872 78 4 0 1720 1797 625640990 625641067 3.820000e-24 122.0
41 TraesCS3D01G089400 chr4A 89.062 64 7 0 1730 1793 625784506 625784443 2.330000e-11 80.5
42 TraesCS3D01G089400 chr2A 80.541 185 17 10 12 178 142372680 142372863 1.060000e-24 124.0
43 TraesCS3D01G089400 chr5B 94.872 78 4 0 1720 1797 685218904 685218827 3.820000e-24 122.0
44 TraesCS3D01G089400 chr6A 90.411 73 7 0 105 177 614958019 614957947 2.320000e-16 97.1
45 TraesCS3D01G089400 chr7A 92.188 64 5 0 1730 1793 74677711 74677648 1.080000e-14 91.6


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 TraesCS3D01G089400 chr3D 45355195 45358021 2826 False 5221.000000 5221 100.000000 1 2827 1 chr3D.!!$F1 2826
1 TraesCS3D01G089400 chr3D 50400496 50401166 670 True 204.000000 217 85.459000 997 1607 2 chr3D.!!$R1 610
2 TraesCS3D01G089400 chr3A 57152609 57154958 2349 False 862.000000 1334 89.601500 997 2012 2 chr3A.!!$F3 1015
3 TraesCS3D01G089400 chr3A 63476324 63476998 674 True 215.000000 224 87.012500 997 1607 2 chr3A.!!$R2 610
4 TraesCS3D01G089400 chr3B 70906173 70908049 1876 False 679.333333 913 89.999667 1212 2823 3 chr3B.!!$F3 1611
5 TraesCS3D01G089400 chr4D 279552644 279553416 772 True 909.000000 909 87.964000 173 947 1 chr4D.!!$R1 774
6 TraesCS3D01G089400 chr5A 572035879 572036654 775 False 907.000000 907 87.883000 172 947 1 chr5A.!!$F1 775
7 TraesCS3D01G089400 chr7D 100230309 100231083 774 True 905.000000 905 87.852000 172 947 1 chr7D.!!$R1 775
8 TraesCS3D01G089400 chr7B 739479417 739480190 773 True 900.000000 900 87.708000 172 947 1 chr7B.!!$R2 775
9 TraesCS3D01G089400 chr7B 168325686 168326461 775 True 896.000000 896 87.580000 172 947 1 chr7B.!!$R1 775
10 TraesCS3D01G089400 chr6D 76058055 76058827 772 True 898.000000 898 87.739000 172 947 1 chr6D.!!$R1 775
11 TraesCS3D01G089400 chr5D 406527537 406528310 773 False 893.000000 893 87.580000 174 947 1 chr5D.!!$F1 773
12 TraesCS3D01G089400 chr1D 453606795 453607571 776 True 891.000000 891 87.516000 172 947 1 chr1D.!!$R2 775
13 TraesCS3D01G089400 chr1D 457163203 457163976 773 True 887.000000 887 87.484000 173 947 1 chr1D.!!$R3 774

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
137 138 0.108615 CATCGTTGTCGGCTTCCTCT 60.109 55.0 0.0 0.0 37.69 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2619 0.037303 CAGGTCTGGCTCCAACACAT 59.963 55.0 0.0 0.0 0.0 3.21 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
18 19 2.279120 GACTCCTGCATCGCCTCG 60.279 66.667 0.00 0.00 0.00 4.63
19 20 2.755876 ACTCCTGCATCGCCTCGA 60.756 61.111 0.00 0.00 41.13 4.04
20 21 2.279120 CTCCTGCATCGCCTCGAC 60.279 66.667 0.00 0.00 39.18 4.20
21 22 3.781770 CTCCTGCATCGCCTCGACC 62.782 68.421 0.00 0.00 39.18 4.79
51 52 2.510411 CCATGCGGTGGCCTATCA 59.490 61.111 3.32 0.00 42.12 2.15
53 54 1.153188 CATGCGGTGGCCTATCACA 60.153 57.895 3.32 0.00 39.27 3.58
54 55 1.146930 ATGCGGTGGCCTATCACAG 59.853 57.895 3.32 0.00 39.27 3.66
61 62 4.530857 GCCTATCACAGCCGCCGT 62.531 66.667 0.00 0.00 0.00 5.68
62 63 2.186903 CCTATCACAGCCGCCGTT 59.813 61.111 0.00 0.00 0.00 4.44
63 64 1.883084 CCTATCACAGCCGCCGTTC 60.883 63.158 0.00 0.00 0.00 3.95
64 65 1.153647 CTATCACAGCCGCCGTTCA 60.154 57.895 0.00 0.00 0.00 3.18
65 66 1.421410 CTATCACAGCCGCCGTTCAC 61.421 60.000 0.00 0.00 0.00 3.18
88 89 3.857038 GGCCCGCCCGTCAATCTA 61.857 66.667 0.00 0.00 0.00 1.98
89 90 2.588034 GCCCGCCCGTCAATCTAC 60.588 66.667 0.00 0.00 0.00 2.59
90 91 2.279252 CCCGCCCGTCAATCTACG 60.279 66.667 0.00 0.00 42.49 3.51
92 93 2.960129 CGCCCGTCAATCTACGCC 60.960 66.667 0.00 0.00 41.51 5.68
96 97 3.972803 CGTCAATCTACGCCGCGC 61.973 66.667 13.88 0.00 35.87 6.86
98 99 3.833645 TCAATCTACGCCGCGCCT 61.834 61.111 13.88 0.00 0.00 5.52
99 100 3.630148 CAATCTACGCCGCGCCTG 61.630 66.667 13.88 3.21 0.00 4.85
100 101 4.143333 AATCTACGCCGCGCCTGT 62.143 61.111 13.88 0.13 0.00 4.00
101 102 2.777972 AATCTACGCCGCGCCTGTA 61.778 57.895 13.88 1.54 0.00 2.74
102 103 2.948840 AATCTACGCCGCGCCTGTAC 62.949 60.000 13.88 0.00 0.00 2.90
126 127 2.047274 CCTGCCGACCATCGTTGT 60.047 61.111 0.00 0.00 38.40 3.32
132 133 4.278956 GACCATCGTTGTCGGCTT 57.721 55.556 0.00 0.00 37.69 4.35
134 135 1.359459 GACCATCGTTGTCGGCTTCC 61.359 60.000 0.00 0.00 37.69 3.46
137 138 0.108615 CATCGTTGTCGGCTTCCTCT 60.109 55.000 0.00 0.00 37.69 3.69
138 139 0.173708 ATCGTTGTCGGCTTCCTCTC 59.826 55.000 0.00 0.00 37.69 3.20
140 141 1.446272 GTTGTCGGCTTCCTCTCGG 60.446 63.158 0.00 0.00 0.00 4.63
141 142 1.605451 TTGTCGGCTTCCTCTCGGA 60.605 57.895 0.00 0.00 37.60 4.55
143 144 2.047443 GTCGGCTTCCTCTCGGACT 61.047 63.158 0.00 0.00 39.60 3.85
144 145 1.749638 TCGGCTTCCTCTCGGACTC 60.750 63.158 0.00 0.00 39.60 3.36
145 146 2.776913 CGGCTTCCTCTCGGACTCC 61.777 68.421 0.00 0.00 39.60 3.85
258 260 0.816018 TGGACACCGCAATTGTCGTT 60.816 50.000 17.01 4.52 43.75 3.85
263 265 0.865769 ACCGCAATTGTCGTTGAGTC 59.134 50.000 17.01 0.00 0.00 3.36
264 266 1.148310 CCGCAATTGTCGTTGAGTCT 58.852 50.000 17.01 0.00 0.00 3.24
265 267 2.288579 ACCGCAATTGTCGTTGAGTCTA 60.289 45.455 17.01 0.00 0.00 2.59
298 301 0.179026 CCCTCCGACTCCTCGACATA 60.179 60.000 0.00 0.00 43.06 2.29
300 303 1.475392 CCTCCGACTCCTCGACATAGT 60.475 57.143 0.00 0.00 43.06 2.12
356 359 1.965930 GTGCTGGCAACACCGATGA 60.966 57.895 9.87 0.00 46.17 2.92
370 373 0.389817 CGATGAGTGCCTTCGTCCAA 60.390 55.000 2.29 0.00 37.57 3.53
390 393 2.995574 CGTATCCCCGGGCCTAGG 60.996 72.222 17.73 10.33 0.00 3.02
434 437 1.544691 ACTTCGTGTTCGCCTGTCTAT 59.455 47.619 0.00 0.00 36.96 1.98
487 490 2.949106 CGTGTACGACGTGTCCCT 59.051 61.111 11.56 0.00 43.50 4.20
532 535 2.014857 CCTCGTCAACATCGTCCTCTA 58.985 52.381 0.00 0.00 0.00 2.43
626 630 2.202797 CATCCTCGACACCGGCTG 60.203 66.667 0.00 1.20 36.24 4.85
663 667 1.082431 CACGGCATTTTTCGCACGA 60.082 52.632 0.00 0.00 0.00 4.35
690 694 4.752879 CCACGGCTACACCACCCG 62.753 72.222 0.00 0.00 46.97 5.28
731 736 2.033602 GGCACAAAGGGCTACCGT 59.966 61.111 0.00 0.00 43.47 4.83
789 795 1.590932 GCCTTCTGTGATGCATCGAT 58.409 50.000 21.34 0.00 0.00 3.59
806 814 0.529378 GATCGTTACGACTGTGGGGT 59.471 55.000 10.39 0.00 39.18 4.95
821 830 2.737376 GGTGTGTCCGTCGGCTTC 60.737 66.667 6.34 0.10 0.00 3.86
822 831 2.338984 GTGTGTCCGTCGGCTTCT 59.661 61.111 6.34 0.00 0.00 2.85
948 960 7.517614 TTTGTTCATGCCTTGACTTATACAA 57.482 32.000 0.00 0.00 32.84 2.41
949 961 7.701539 TTGTTCATGCCTTGACTTATACAAT 57.298 32.000 0.00 0.00 32.84 2.71
950 962 7.320443 TGTTCATGCCTTGACTTATACAATC 57.680 36.000 0.00 0.00 32.84 2.67
951 963 6.883756 TGTTCATGCCTTGACTTATACAATCA 59.116 34.615 0.00 0.00 32.84 2.57
952 964 7.392953 TGTTCATGCCTTGACTTATACAATCAA 59.607 33.333 0.00 0.00 32.84 2.57
953 965 7.320443 TCATGCCTTGACTTATACAATCAAC 57.680 36.000 0.00 0.00 0.00 3.18
954 966 5.794687 TGCCTTGACTTATACAATCAACG 57.205 39.130 0.00 0.00 0.00 4.10
955 967 5.483811 TGCCTTGACTTATACAATCAACGA 58.516 37.500 0.00 0.00 0.00 3.85
957 969 6.597672 TGCCTTGACTTATACAATCAACGATT 59.402 34.615 0.00 0.00 31.86 3.34
958 970 7.126398 GCCTTGACTTATACAATCAACGATTC 58.874 38.462 0.00 0.00 28.87 2.52
959 971 7.630924 CCTTGACTTATACAATCAACGATTCC 58.369 38.462 0.00 0.00 28.87 3.01
960 972 7.279981 CCTTGACTTATACAATCAACGATTCCA 59.720 37.037 0.00 0.00 28.87 3.53
961 973 7.534085 TGACTTATACAATCAACGATTCCAC 57.466 36.000 0.00 0.00 28.87 4.02
962 974 6.537301 TGACTTATACAATCAACGATTCCACC 59.463 38.462 0.00 0.00 28.87 4.61
963 975 5.522460 ACTTATACAATCAACGATTCCACCG 59.478 40.000 0.00 0.00 28.87 4.94
966 978 2.936498 ACAATCAACGATTCCACCGATC 59.064 45.455 0.00 0.00 28.87 3.69
969 981 2.100197 TCAACGATTCCACCGATCTCT 58.900 47.619 0.00 0.00 0.00 3.10
970 982 2.099263 TCAACGATTCCACCGATCTCTC 59.901 50.000 0.00 0.00 0.00 3.20
971 983 2.060050 ACGATTCCACCGATCTCTCT 57.940 50.000 0.00 0.00 0.00 3.10
972 984 3.210232 ACGATTCCACCGATCTCTCTA 57.790 47.619 0.00 0.00 0.00 2.43
974 986 3.754323 ACGATTCCACCGATCTCTCTATC 59.246 47.826 0.00 0.00 0.00 2.08
975 987 4.006989 CGATTCCACCGATCTCTCTATCT 58.993 47.826 0.00 0.00 0.00 1.98
980 992 4.349636 TCCACCGATCTCTCTATCTCTTCT 59.650 45.833 0.00 0.00 0.00 2.85
981 993 5.544562 TCCACCGATCTCTCTATCTCTTCTA 59.455 44.000 0.00 0.00 0.00 2.10
984 996 6.708502 CACCGATCTCTCTATCTCTTCTAACA 59.291 42.308 0.00 0.00 0.00 2.41
985 997 7.227711 CACCGATCTCTCTATCTCTTCTAACAA 59.772 40.741 0.00 0.00 0.00 2.83
986 998 7.942341 ACCGATCTCTCTATCTCTTCTAACAAT 59.058 37.037 0.00 0.00 0.00 2.71
987 999 8.792633 CCGATCTCTCTATCTCTTCTAACAATT 58.207 37.037 0.00 0.00 0.00 2.32
988 1000 9.825972 CGATCTCTCTATCTCTTCTAACAATTC 57.174 37.037 0.00 0.00 0.00 2.17
990 1002 9.653516 ATCTCTCTATCTCTTCTAACAATTCCA 57.346 33.333 0.00 0.00 0.00 3.53
992 1004 9.528018 CTCTCTATCTCTTCTAACAATTCCAAC 57.472 37.037 0.00 0.00 0.00 3.77
994 1006 7.265673 TCTATCTCTTCTAACAATTCCAACGG 58.734 38.462 0.00 0.00 0.00 4.44
995 1007 5.477607 TCTCTTCTAACAATTCCAACGGA 57.522 39.130 0.00 0.00 0.00 4.69
1080 1406 1.887198 GTCGTGGACTTCCTCTTCTCA 59.113 52.381 0.00 0.00 36.82 3.27
1088 1414 2.224917 ACTTCCTCTTCTCACTCCTCGT 60.225 50.000 0.00 0.00 0.00 4.18
1524 1961 3.326578 CCGTGACCCCCATGTCCA 61.327 66.667 0.00 0.00 34.25 4.02
1639 2078 2.416547 GTGGTGACCATTGTTGATCGAG 59.583 50.000 7.94 0.00 35.28 4.04
1700 2140 1.552226 GCACCGCATGATTGTTGATG 58.448 50.000 0.00 0.00 0.00 3.07
1710 2150 6.220930 GCATGATTGTTGATGGAGCATTAAT 58.779 36.000 0.00 0.00 0.00 1.40
1711 2151 6.704493 GCATGATTGTTGATGGAGCATTAATT 59.296 34.615 0.00 0.00 0.00 1.40
1712 2152 7.868922 GCATGATTGTTGATGGAGCATTAATTA 59.131 33.333 0.00 0.00 0.00 1.40
1713 2153 9.752961 CATGATTGTTGATGGAGCATTAATTAA 57.247 29.630 0.00 0.00 0.00 1.40
1714 2154 9.754382 ATGATTGTTGATGGAGCATTAATTAAC 57.246 29.630 0.00 0.00 0.00 2.01
1715 2155 8.196771 TGATTGTTGATGGAGCATTAATTAACC 58.803 33.333 0.00 0.00 0.00 2.85
1716 2156 7.473735 TTGTTGATGGAGCATTAATTAACCA 57.526 32.000 0.00 3.98 0.00 3.67
1799 2242 3.437795 GACGTCTTCCTCGCCGGA 61.438 66.667 5.05 0.00 41.06 5.14
1811 2254 3.512516 GCCGGATGCAAGACAGGC 61.513 66.667 5.05 14.36 40.77 4.85
1835 2278 0.317519 TGTACGACTGACACACGCAG 60.318 55.000 0.00 0.00 39.26 5.18
1837 2280 2.137425 TACGACTGACACACGCAGGG 62.137 60.000 0.00 0.00 37.69 4.45
1838 2281 2.357517 GACTGACACACGCAGGGG 60.358 66.667 0.00 0.00 37.69 4.79
1839 2282 4.626081 ACTGACACACGCAGGGGC 62.626 66.667 0.00 0.00 37.69 5.80
1840 2283 4.624364 CTGACACACGCAGGGGCA 62.624 66.667 0.00 0.00 41.24 5.36
1843 2303 4.722700 ACACACGCAGGGGCATCC 62.723 66.667 0.00 0.00 41.24 3.51
1862 2322 1.668294 CCGCCGATCCATCTAGCTT 59.332 57.895 0.00 0.00 0.00 3.74
1863 2323 0.668706 CCGCCGATCCATCTAGCTTG 60.669 60.000 0.00 0.00 0.00 4.01
1866 2326 1.051812 CCGATCCATCTAGCTTGGGT 58.948 55.000 3.08 0.00 34.85 4.51
1868 2328 1.967066 CGATCCATCTAGCTTGGGTCT 59.033 52.381 13.16 0.00 41.42 3.85
1913 2457 9.671862 AGTAGTAGATTAGCTTAATTAAGGGGT 57.328 33.333 23.37 10.11 33.95 4.95
1930 2478 4.706616 AGGGGTCTTCTATTTCCTGGTTA 58.293 43.478 0.00 0.00 0.00 2.85
2001 2549 5.065090 TGTTGATTTGTAGGAGATGCGATTG 59.935 40.000 0.00 0.00 0.00 2.67
2015 2563 3.286353 TGCGATTGATTATGCCCTTTCA 58.714 40.909 0.00 0.00 0.00 2.69
2021 2569 5.902613 TTGATTATGCCCTTTCAGTCTTG 57.097 39.130 0.00 0.00 0.00 3.02
2047 2595 1.540797 GCTGCTTTGGTTGCATTTCCA 60.541 47.619 0.00 0.00 39.86 3.53
2048 2596 2.137523 CTGCTTTGGTTGCATTTCCAC 58.862 47.619 5.47 0.00 39.86 4.02
2065 2613 4.819105 TCCACTGGACGTGATTAATTCT 57.181 40.909 0.00 0.00 46.81 2.40
2068 2616 4.032900 CCACTGGACGTGATTAATTCTTCG 59.967 45.833 0.00 0.00 46.81 3.79
2071 2619 3.196039 TGGACGTGATTAATTCTTCGGGA 59.804 43.478 0.00 0.00 0.00 5.14
2086 2634 1.685224 GGGATGTGTTGGAGCCAGA 59.315 57.895 0.00 0.00 0.00 3.86
2124 2855 0.936297 CTGTGGTCAAAAGCGCTTGC 60.936 55.000 25.80 13.92 39.58 4.01
2160 2891 1.919918 CTTTTGCGTTCTTGTTGCCA 58.080 45.000 0.00 0.00 0.00 4.92
2163 2894 0.100325 TTGCGTTCTTGTTGCCAGTG 59.900 50.000 0.00 0.00 0.00 3.66
2173 2904 3.229276 TGTTGCCAGTGTTTTTGACAG 57.771 42.857 0.00 0.00 39.39 3.51
2174 2905 2.560542 TGTTGCCAGTGTTTTTGACAGT 59.439 40.909 0.00 0.00 42.69 3.55
2209 2940 6.529477 GTCCACCTTGTAGACTATCGTTTAAC 59.471 42.308 0.00 0.00 0.00 2.01
2212 2943 7.310664 CACCTTGTAGACTATCGTTTAACTCA 58.689 38.462 0.00 0.00 0.00 3.41
2217 2948 5.579564 AGACTATCGTTTAACTCACCTCC 57.420 43.478 0.00 0.00 0.00 4.30
2218 2949 4.096081 AGACTATCGTTTAACTCACCTCCG 59.904 45.833 0.00 0.00 0.00 4.63
2219 2950 2.667473 ATCGTTTAACTCACCTCCGG 57.333 50.000 0.00 0.00 0.00 5.14
2293 3024 0.036010 CAAGATCTGGTGGGCGAACT 60.036 55.000 0.00 0.00 0.00 3.01
2339 3070 1.162800 GGTGGGCTCATGAAGATCGC 61.163 60.000 0.00 0.00 0.00 4.58
2340 3071 0.462581 GTGGGCTCATGAAGATCGCA 60.463 55.000 6.27 3.64 33.60 5.10
2349 3080 1.886777 GAAGATCGCAGCTCCCAGC 60.887 63.158 0.00 0.00 42.84 4.85
2369 3100 2.452813 CCGACGAGGTGCCAAATCG 61.453 63.158 0.00 0.00 42.04 3.34
2370 3101 2.785258 GACGAGGTGCCAAATCGC 59.215 61.111 0.00 0.00 40.02 4.58
2435 3166 6.041637 GGTTTCCAAAGATTTTAACCTGACCT 59.958 38.462 0.00 0.00 33.84 3.85
2437 3168 7.669089 TTCCAAAGATTTTAACCTGACCTTT 57.331 32.000 0.00 0.00 0.00 3.11
2444 3175 5.447624 TTTTAACCTGACCTTTAGCAAGC 57.552 39.130 0.00 0.00 0.00 4.01
2452 3183 0.181350 CCTTTAGCAAGCGGAGGGAT 59.819 55.000 0.00 0.00 0.00 3.85
2491 3222 1.654954 AATCGACGACGGAGGTGAGG 61.655 60.000 7.55 0.00 40.21 3.86
2493 3224 4.131088 GACGACGGAGGTGAGGGC 62.131 72.222 0.00 0.00 0.00 5.19
2502 3233 3.050275 GGTGAGGGCGCTGAACAC 61.050 66.667 8.56 10.33 0.00 3.32
2511 3242 1.991430 CGCTGAACACGAAGATCCG 59.009 57.895 0.00 0.00 0.00 4.18
2581 3312 1.323412 CTCTGACTAGCGCTACCCAT 58.677 55.000 14.45 0.00 0.00 4.00
2591 3322 2.819595 CTACCCATGCGCGTTGCT 60.820 61.111 8.43 0.00 46.63 3.91
2603 3334 1.959899 GCGTTGCTCCACTGTCGATG 61.960 60.000 0.00 0.00 0.00 3.84
2610 3341 2.349886 GCTCCACTGTCGATGTCAAATC 59.650 50.000 0.00 0.00 0.00 2.17
2615 3346 0.742990 TGTCGATGTCAAATCCGGCC 60.743 55.000 0.00 0.00 0.00 6.13
2623 3354 4.109675 AAATCCGGCCGACCCCTG 62.110 66.667 30.73 8.93 0.00 4.45
2653 3384 3.506096 CGAGTCCGCGACTAGCCA 61.506 66.667 8.23 0.00 43.53 4.75
2677 3408 2.989571 AGATTCAGAGGGGAAACAAGGT 59.010 45.455 0.00 0.00 0.00 3.50
2678 3409 2.656947 TTCAGAGGGGAAACAAGGTG 57.343 50.000 0.00 0.00 0.00 4.00
2679 3410 0.110486 TCAGAGGGGAAACAAGGTGC 59.890 55.000 0.00 0.00 0.00 5.01
2680 3411 0.178992 CAGAGGGGAAACAAGGTGCA 60.179 55.000 0.00 0.00 0.00 4.57
2681 3412 0.111253 AGAGGGGAAACAAGGTGCAG 59.889 55.000 0.00 0.00 0.00 4.41
2716 3448 2.378886 TCAGACCTTCTCTGTGGAGGTA 59.621 50.000 9.62 0.00 46.09 3.08
2717 3449 3.165875 CAGACCTTCTCTGTGGAGGTAA 58.834 50.000 9.62 0.00 41.60 2.85
2718 3450 3.578716 CAGACCTTCTCTGTGGAGGTAAA 59.421 47.826 9.62 0.00 41.60 2.01
2719 3451 4.223923 CAGACCTTCTCTGTGGAGGTAAAT 59.776 45.833 9.62 0.00 41.60 1.40
2720 3452 4.468153 AGACCTTCTCTGTGGAGGTAAATC 59.532 45.833 9.62 0.00 39.86 2.17
2721 3453 3.519913 ACCTTCTCTGTGGAGGTAAATCC 59.480 47.826 7.93 0.00 39.86 3.01
2724 3456 4.620086 TCTCTGTGGAGGTAAATCCCTA 57.380 45.455 0.00 0.00 38.72 3.53
2734 3466 5.605488 GGAGGTAAATCCCTACTTGGTCATA 59.395 44.000 0.00 0.00 34.03 2.15
2749 3481 8.413309 ACTTGGTCATATTTATTGATGATGGG 57.587 34.615 0.00 0.00 34.69 4.00
2759 3491 6.771934 TTATTGATGATGGGGGTGTACATA 57.228 37.500 0.00 0.00 0.00 2.29
2774 3506 7.419287 GGGGTGTACATAGTATAATGGTGTTCA 60.419 40.741 0.00 0.00 0.00 3.18
2823 3555 8.016301 TGATTATGAGATCTAGGGTGCATATC 57.984 38.462 0.00 0.27 0.00 1.63
2824 3556 7.620888 TGATTATGAGATCTAGGGTGCATATCA 59.379 37.037 0.00 2.55 0.00 2.15
2825 3557 7.797121 TTATGAGATCTAGGGTGCATATCAA 57.203 36.000 0.00 0.00 0.00 2.57
2826 3558 5.474578 TGAGATCTAGGGTGCATATCAAC 57.525 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.755876 TCGAGGCGATGCAGGAGT 60.756 61.111 0.00 0.00 0.00 3.85
3 4 2.279120 GTCGAGGCGATGCAGGAG 60.279 66.667 0.00 0.00 38.42 3.69
4 5 3.838271 GGTCGAGGCGATGCAGGA 61.838 66.667 0.00 0.00 38.42 3.86
36 37 1.146930 CTGTGATAGGCCACCGCAT 59.853 57.895 5.01 0.00 36.26 4.73
37 38 2.584064 CTGTGATAGGCCACCGCA 59.416 61.111 5.01 5.27 36.26 5.69
38 39 2.897350 GCTGTGATAGGCCACCGC 60.897 66.667 5.01 0.00 39.39 5.68
45 46 1.883084 GAACGGCGGCTGTGATAGG 60.883 63.158 16.38 0.00 0.00 2.57
47 48 1.447140 GTGAACGGCGGCTGTGATA 60.447 57.895 16.38 2.02 0.00 2.15
48 49 2.742372 GTGAACGGCGGCTGTGAT 60.742 61.111 16.38 0.00 0.00 3.06
72 73 2.588034 GTAGATTGACGGGCGGGC 60.588 66.667 0.00 0.00 0.00 6.13
74 75 2.960129 GCGTAGATTGACGGGCGG 60.960 66.667 0.00 0.00 43.13 6.13
76 77 2.960129 CGGCGTAGATTGACGGGC 60.960 66.667 0.00 0.00 43.13 6.13
77 78 2.960129 GCGGCGTAGATTGACGGG 60.960 66.667 9.37 0.00 43.13 5.28
78 79 3.320078 CGCGGCGTAGATTGACGG 61.320 66.667 15.36 0.00 43.13 4.79
79 80 3.972803 GCGCGGCGTAGATTGACG 61.973 66.667 24.46 1.30 45.70 4.35
83 84 2.777972 TACAGGCGCGGCGTAGATT 61.778 57.895 27.74 5.36 0.00 2.40
84 85 3.214123 TACAGGCGCGGCGTAGAT 61.214 61.111 27.74 14.02 0.00 1.98
85 86 4.183686 GTACAGGCGCGGCGTAGA 62.184 66.667 27.57 14.49 0.00 2.59
107 108 4.778143 AACGATGGTCGGCAGGGC 62.778 66.667 4.28 0.00 45.59 5.19
108 109 2.819595 CAACGATGGTCGGCAGGG 60.820 66.667 4.28 0.00 45.59 4.45
110 111 3.474806 GACAACGATGGTCGGCAG 58.525 61.111 4.28 0.00 45.59 4.85
117 118 1.079127 AGGAAGCCGACAACGATGG 60.079 57.895 0.00 0.00 42.66 3.51
118 119 0.108615 AGAGGAAGCCGACAACGATG 60.109 55.000 0.00 0.00 42.66 3.84
119 120 0.173708 GAGAGGAAGCCGACAACGAT 59.826 55.000 0.00 0.00 42.66 3.73
174 175 1.454479 GGTCGGGTAGATGACGGGA 60.454 63.158 0.00 0.00 35.95 5.14
176 177 1.035932 AGTGGTCGGGTAGATGACGG 61.036 60.000 0.00 0.00 35.95 4.79
177 178 0.815734 AAGTGGTCGGGTAGATGACG 59.184 55.000 0.00 0.00 35.95 4.35
258 260 2.563179 GGCCAACAGAGAAGTAGACTCA 59.437 50.000 0.00 0.00 36.91 3.41
263 265 1.208293 GAGGGGCCAACAGAGAAGTAG 59.792 57.143 4.39 0.00 0.00 2.57
264 266 1.276622 GAGGGGCCAACAGAGAAGTA 58.723 55.000 4.39 0.00 0.00 2.24
265 267 1.492993 GGAGGGGCCAACAGAGAAGT 61.493 60.000 4.39 0.00 36.34 3.01
289 291 2.286477 CGAGCTGTACACTATGTCGAGG 60.286 54.545 0.00 0.00 0.00 4.63
298 301 1.290324 CCTGCACGAGCTGTACACT 59.710 57.895 6.36 0.00 42.74 3.55
300 303 1.289066 GACCTGCACGAGCTGTACA 59.711 57.895 6.36 0.00 42.74 2.90
370 373 2.710237 CTAGGCCCGGGGATACGTCT 62.710 65.000 25.28 3.68 37.60 4.18
376 379 2.122369 CTTCCTAGGCCCGGGGAT 60.122 66.667 25.28 6.88 0.00 3.85
473 476 1.809567 AACCCAGGGACACGTCGTAC 61.810 60.000 14.54 0.00 0.00 3.67
532 535 3.584868 GAAGTAGTGTGCGCCGGGT 62.585 63.158 4.18 0.00 0.00 5.28
626 630 1.352156 GGTCGATGTTGAGTCGTGGC 61.352 60.000 0.00 0.00 39.91 5.01
629 633 0.386858 CGTGGTCGATGTTGAGTCGT 60.387 55.000 0.00 0.00 39.91 4.34
636 640 1.243902 AAAATGCCGTGGTCGATGTT 58.756 45.000 0.00 0.00 39.71 2.71
663 667 1.028868 GTAGCCGTGGTCGAGGTAGT 61.029 60.000 0.00 0.00 39.71 2.73
748 753 0.534203 GGCTGGAGTGAAAACCGACA 60.534 55.000 0.00 0.00 0.00 4.35
789 795 1.108727 ACACCCCACAGTCGTAACGA 61.109 55.000 0.00 0.00 0.00 3.85
806 814 1.461091 AAGAGAAGCCGACGGACACA 61.461 55.000 20.50 0.00 0.00 3.72
821 830 3.699038 AGACTGGAGAAGAATCCGAAGAG 59.301 47.826 0.00 0.00 42.77 2.85
822 831 3.697045 GAGACTGGAGAAGAATCCGAAGA 59.303 47.826 0.00 0.00 42.77 2.87
916 928 5.183904 GTCAAGGCATGAACAAATCCTAAGT 59.816 40.000 0.00 0.00 40.50 2.24
931 943 6.112734 TCGTTGATTGTATAAGTCAAGGCAT 58.887 36.000 0.00 0.00 37.54 4.40
948 960 2.695666 AGAGATCGGTGGAATCGTTGAT 59.304 45.455 0.00 0.00 0.00 2.57
949 961 2.099263 GAGAGATCGGTGGAATCGTTGA 59.901 50.000 0.00 0.00 0.00 3.18
950 962 2.099921 AGAGAGATCGGTGGAATCGTTG 59.900 50.000 0.00 0.00 0.00 4.10
951 963 2.379972 AGAGAGATCGGTGGAATCGTT 58.620 47.619 0.00 0.00 0.00 3.85
952 964 2.060050 AGAGAGATCGGTGGAATCGT 57.940 50.000 0.00 0.00 0.00 3.73
953 965 4.006989 AGATAGAGAGATCGGTGGAATCG 58.993 47.826 0.00 0.00 0.00 3.34
954 966 5.253330 AGAGATAGAGAGATCGGTGGAATC 58.747 45.833 0.00 0.00 0.00 2.52
955 967 5.255397 AGAGATAGAGAGATCGGTGGAAT 57.745 43.478 0.00 0.00 0.00 3.01
957 969 4.349636 AGAAGAGATAGAGAGATCGGTGGA 59.650 45.833 0.00 0.00 0.00 4.02
958 970 4.651778 AGAAGAGATAGAGAGATCGGTGG 58.348 47.826 0.00 0.00 0.00 4.61
959 971 6.708502 TGTTAGAAGAGATAGAGAGATCGGTG 59.291 42.308 0.00 0.00 0.00 4.94
960 972 6.833041 TGTTAGAAGAGATAGAGAGATCGGT 58.167 40.000 0.00 0.00 0.00 4.69
961 973 7.737972 TTGTTAGAAGAGATAGAGAGATCGG 57.262 40.000 0.00 0.00 0.00 4.18
962 974 9.825972 GAATTGTTAGAAGAGATAGAGAGATCG 57.174 37.037 0.00 0.00 0.00 3.69
966 978 9.528018 GTTGGAATTGTTAGAAGAGATAGAGAG 57.472 37.037 0.00 0.00 0.00 3.20
969 981 7.123697 TCCGTTGGAATTGTTAGAAGAGATAGA 59.876 37.037 0.00 0.00 0.00 1.98
970 982 7.265673 TCCGTTGGAATTGTTAGAAGAGATAG 58.734 38.462 0.00 0.00 0.00 2.08
971 983 7.123697 TCTCCGTTGGAATTGTTAGAAGAGATA 59.876 37.037 0.00 0.00 0.00 1.98
972 984 6.049955 TCCGTTGGAATTGTTAGAAGAGAT 57.950 37.500 0.00 0.00 0.00 2.75
974 986 5.479306 TCTCCGTTGGAATTGTTAGAAGAG 58.521 41.667 0.00 0.00 0.00 2.85
975 987 5.477607 TCTCCGTTGGAATTGTTAGAAGA 57.522 39.130 0.00 0.00 0.00 2.87
980 992 3.410631 TGCTCTCCGTTGGAATTGTTA 57.589 42.857 0.00 0.00 0.00 2.41
981 993 2.270352 TGCTCTCCGTTGGAATTGTT 57.730 45.000 0.00 0.00 0.00 2.83
984 996 2.787473 TCATGCTCTCCGTTGGAATT 57.213 45.000 0.00 0.00 0.00 2.17
985 997 2.636830 CTTCATGCTCTCCGTTGGAAT 58.363 47.619 0.00 0.00 0.00 3.01
986 998 1.945819 GCTTCATGCTCTCCGTTGGAA 60.946 52.381 0.00 0.00 38.95 3.53
987 999 0.391661 GCTTCATGCTCTCCGTTGGA 60.392 55.000 0.00 0.00 38.95 3.53
988 1000 2.093216 GCTTCATGCTCTCCGTTGG 58.907 57.895 0.00 0.00 38.95 3.77
1062 1388 1.889829 AGTGAGAAGAGGAAGTCCACG 59.110 52.381 0.00 0.00 38.89 4.94
1080 1406 4.680537 ACGGGCAGGACGAGGAGT 62.681 66.667 0.00 0.00 34.93 3.85
1148 1474 3.200593 TAGAGGTCGCCGACTCGC 61.201 66.667 17.76 9.06 32.47 5.03
1149 1475 2.708255 GTAGAGGTCGCCGACTCG 59.292 66.667 17.76 0.00 32.47 4.18
1150 1476 2.708255 CGTAGAGGTCGCCGACTC 59.292 66.667 17.76 12.20 32.47 3.36
1151 1477 3.507009 GCGTAGAGGTCGCCGACT 61.507 66.667 17.76 2.92 46.61 4.18
1175 1501 2.701780 GGAGCCGTCGAGCTTCTGA 61.702 63.158 9.18 0.00 45.15 3.27
1492 1929 2.511600 CGGCGAGGTTGTCCATCC 60.512 66.667 0.00 0.00 35.89 3.51
1524 1961 0.622738 AGGGTGATGCTGGAGATGGT 60.623 55.000 0.00 0.00 0.00 3.55
1639 2078 9.757227 GAGAGAGATGGTATTATATTGGTATGC 57.243 37.037 0.00 0.00 0.00 3.14
1689 2129 8.196771 GGTTAATTAATGCTCCATCAACAATCA 58.803 33.333 0.31 0.00 0.00 2.57
1700 2140 9.598517 TCAAATCAATTGGTTAATTAATGCTCC 57.401 29.630 3.93 0.00 39.62 4.70
1710 2150 6.164876 CCTGCACATCAAATCAATTGGTTAA 58.835 36.000 3.93 0.00 39.62 2.01
1711 2151 5.337410 CCCTGCACATCAAATCAATTGGTTA 60.337 40.000 3.93 0.00 39.62 2.85
1712 2152 4.563993 CCCTGCACATCAAATCAATTGGTT 60.564 41.667 5.42 0.78 39.62 3.67
1713 2153 3.055675 CCCTGCACATCAAATCAATTGGT 60.056 43.478 5.42 0.00 39.62 3.67
1714 2154 3.055675 ACCCTGCACATCAAATCAATTGG 60.056 43.478 5.42 0.00 39.62 3.16
1715 2155 4.196626 ACCCTGCACATCAAATCAATTG 57.803 40.909 0.00 0.00 40.58 2.32
1716 2156 4.895668 AACCCTGCACATCAAATCAATT 57.104 36.364 0.00 0.00 0.00 2.32
1799 2242 3.650950 ACCGGGCCTGTCTTGCAT 61.651 61.111 11.58 0.00 0.00 3.96
1811 2254 1.080974 GTGTCAGTCGTACACCGGG 60.081 63.158 6.32 0.00 41.10 5.73
1838 2281 4.335647 ATGGATCGGCGGGGATGC 62.336 66.667 7.21 0.00 35.55 3.91
1839 2282 1.257750 TAGATGGATCGGCGGGGATG 61.258 60.000 7.21 0.00 0.00 3.51
1840 2283 0.972983 CTAGATGGATCGGCGGGGAT 60.973 60.000 7.21 0.00 0.00 3.85
1843 2303 1.821061 AAGCTAGATGGATCGGCGGG 61.821 60.000 7.21 0.00 36.25 6.13
1913 2457 7.450014 TGCAACATTTAACCAGGAAATAGAAGA 59.550 33.333 0.00 0.00 0.00 2.87
1962 2510 8.370493 ACAAATCAACATCCAATCGATACTAG 57.630 34.615 0.00 0.00 0.00 2.57
1968 2516 5.739959 TCCTACAAATCAACATCCAATCGA 58.260 37.500 0.00 0.00 0.00 3.59
1973 2521 4.883585 GCATCTCCTACAAATCAACATCCA 59.116 41.667 0.00 0.00 0.00 3.41
2001 2549 5.447818 CGAACAAGACTGAAAGGGCATAATC 60.448 44.000 0.00 0.00 39.30 1.75
2015 2563 1.331756 CAAAGCAGCACGAACAAGACT 59.668 47.619 0.00 0.00 0.00 3.24
2021 2569 1.208642 GCAACCAAAGCAGCACGAAC 61.209 55.000 0.00 0.00 0.00 3.95
2047 2595 4.181578 CCGAAGAATTAATCACGTCCAGT 58.818 43.478 0.00 0.00 0.00 4.00
2048 2596 3.555956 CCCGAAGAATTAATCACGTCCAG 59.444 47.826 0.00 0.00 0.00 3.86
2065 2613 1.002624 GGCTCCAACACATCCCGAA 60.003 57.895 0.00 0.00 0.00 4.30
2068 2616 0.678048 GTCTGGCTCCAACACATCCC 60.678 60.000 0.00 0.00 0.00 3.85
2071 2619 0.037303 CAGGTCTGGCTCCAACACAT 59.963 55.000 0.00 0.00 0.00 3.21
2086 2634 4.815489 TCGAGAGTCGAACCAGGT 57.185 55.556 0.00 0.00 46.90 4.00
2160 2891 3.443681 CCCAGAACACTGTCAAAAACACT 59.556 43.478 0.00 0.00 33.24 3.55
2163 2894 3.192633 ACACCCAGAACACTGTCAAAAAC 59.807 43.478 0.00 0.00 0.00 2.43
2173 2904 4.475527 GGTGGACACCCAGAACAC 57.524 61.111 10.38 0.00 44.55 3.32
2231 2962 0.040067 CGAAAGCTCCAACAACTGCC 60.040 55.000 0.00 0.00 0.00 4.85
2287 3018 0.517316 GTCACCAATGTGGAGTTCGC 59.483 55.000 0.18 0.00 40.96 4.70
2293 3024 2.158559 CCAATTCGTCACCAATGTGGA 58.841 47.619 0.18 0.00 40.96 4.02
2314 3045 1.852157 TTCATGAGCCCACCCACCTC 61.852 60.000 0.00 0.00 0.00 3.85
2349 3080 3.622060 ATTTGGCACCTCGTCGGGG 62.622 63.158 10.39 10.39 40.11 5.73
2357 3088 2.690778 GCTTCGCGATTTGGCACCT 61.691 57.895 10.88 0.00 0.00 4.00
2369 3100 1.643832 CGGCAAATCTAGGCTTCGC 59.356 57.895 0.00 0.00 0.00 4.70
2370 3101 1.089481 TGCGGCAAATCTAGGCTTCG 61.089 55.000 0.00 0.00 0.00 3.79
2377 3108 1.013596 CGACCAATGCGGCAAATCTA 58.986 50.000 6.82 0.00 39.03 1.98
2435 3166 0.908910 TCATCCCTCCGCTTGCTAAA 59.091 50.000 0.00 0.00 0.00 1.85
2437 3168 1.402896 CCTCATCCCTCCGCTTGCTA 61.403 60.000 0.00 0.00 0.00 3.49
2444 3175 1.915078 AAGTTGGCCTCATCCCTCCG 61.915 60.000 3.32 0.00 0.00 4.63
2491 3222 1.696832 GGATCTTCGTGTTCAGCGCC 61.697 60.000 2.29 0.00 0.00 6.53
2493 3224 1.413767 CCGGATCTTCGTGTTCAGCG 61.414 60.000 0.00 0.00 0.00 5.18
2494 3225 1.696832 GCCGGATCTTCGTGTTCAGC 61.697 60.000 5.05 0.00 0.00 4.26
2497 3228 1.814169 GGGCCGGATCTTCGTGTTC 60.814 63.158 5.05 0.00 0.00 3.18
2502 3233 3.151958 ATGTCGGGCCGGATCTTCG 62.152 63.158 27.98 2.26 0.00 3.79
2535 3266 2.598565 TCCAGATGGGATCTACCTTCG 58.401 52.381 0.00 0.00 42.15 3.79
2581 3312 4.908687 ACAGTGGAGCAACGCGCA 62.909 61.111 5.73 0.00 46.13 6.09
2584 3315 1.738099 ATCGACAGTGGAGCAACGC 60.738 57.895 0.00 0.00 0.00 4.84
2585 3316 0.667487 ACATCGACAGTGGAGCAACG 60.667 55.000 0.00 0.00 0.00 4.10
2591 3322 2.673893 CGGATTTGACATCGACAGTGGA 60.674 50.000 0.00 0.00 0.00 4.02
2603 3334 2.822701 GGGTCGGCCGGATTTGAC 60.823 66.667 27.83 14.98 34.97 3.18
2623 3354 1.522302 GGACTCGCGGTACCCTATCC 61.522 65.000 6.13 3.02 0.00 2.59
2624 3355 1.849976 CGGACTCGCGGTACCCTATC 61.850 65.000 6.13 0.00 0.00 2.08
2639 3370 0.389426 TCTTTTGGCTAGTCGCGGAC 60.389 55.000 6.13 3.09 40.44 4.79
2641 3372 1.327764 GAATCTTTTGGCTAGTCGCGG 59.672 52.381 6.13 0.00 40.44 6.46
2642 3373 1.999735 TGAATCTTTTGGCTAGTCGCG 59.000 47.619 0.00 0.00 40.44 5.87
2643 3374 3.262420 TCTGAATCTTTTGGCTAGTCGC 58.738 45.455 0.00 0.00 38.13 5.19
2645 3376 4.195416 CCCTCTGAATCTTTTGGCTAGTC 58.805 47.826 0.00 0.00 0.00 2.59
2646 3377 3.054065 CCCCTCTGAATCTTTTGGCTAGT 60.054 47.826 0.00 0.00 0.00 2.57
2647 3378 3.200825 TCCCCTCTGAATCTTTTGGCTAG 59.799 47.826 0.00 0.00 0.00 3.42
2648 3379 3.189606 TCCCCTCTGAATCTTTTGGCTA 58.810 45.455 0.00 0.00 0.00 3.93
2649 3380 1.995542 TCCCCTCTGAATCTTTTGGCT 59.004 47.619 0.00 0.00 0.00 4.75
2650 3381 2.514458 TCCCCTCTGAATCTTTTGGC 57.486 50.000 0.00 0.00 0.00 4.52
2651 3382 4.151883 TGTTTCCCCTCTGAATCTTTTGG 58.848 43.478 0.00 0.00 0.00 3.28
2652 3383 5.279156 CCTTGTTTCCCCTCTGAATCTTTTG 60.279 44.000 0.00 0.00 0.00 2.44
2653 3384 4.835056 CCTTGTTTCCCCTCTGAATCTTTT 59.165 41.667 0.00 0.00 0.00 2.27
2677 3408 1.771854 TGAACCTGGGTAAACTCTGCA 59.228 47.619 0.00 0.00 0.00 4.41
2678 3409 2.038557 TCTGAACCTGGGTAAACTCTGC 59.961 50.000 0.00 0.00 0.00 4.26
2679 3410 3.557264 GGTCTGAACCTGGGTAAACTCTG 60.557 52.174 0.00 0.00 42.80 3.35
2680 3411 2.638363 GGTCTGAACCTGGGTAAACTCT 59.362 50.000 0.00 0.00 42.80 3.24
2681 3412 3.055209 GGTCTGAACCTGGGTAAACTC 57.945 52.381 0.00 0.00 42.80 3.01
2718 3450 9.745018 CATCAATAAATATGACCAAGTAGGGAT 57.255 33.333 0.00 0.00 43.89 3.85
2719 3451 8.944138 TCATCAATAAATATGACCAAGTAGGGA 58.056 33.333 0.00 0.00 43.89 4.20
2720 3452 9.745018 ATCATCAATAAATATGACCAAGTAGGG 57.255 33.333 0.00 0.00 43.89 3.53
2724 3456 7.452501 CCCCATCATCAATAAATATGACCAAGT 59.547 37.037 0.00 0.00 35.06 3.16
2734 3466 6.024563 TGTACACCCCCATCATCAATAAAT 57.975 37.500 0.00 0.00 0.00 1.40
2749 3481 7.502696 TGAACACCATTATACTATGTACACCC 58.497 38.462 0.00 0.00 0.00 4.61
2785 3517 8.335484 AGATCTCATAATCATCACCTCTAGCTA 58.665 37.037 0.00 0.00 0.00 3.32
2786 3518 7.184161 AGATCTCATAATCATCACCTCTAGCT 58.816 38.462 0.00 0.00 0.00 3.32
2787 3519 7.408756 AGATCTCATAATCATCACCTCTAGC 57.591 40.000 0.00 0.00 0.00 3.42
2788 3520 9.123902 CCTAGATCTCATAATCATCACCTCTAG 57.876 40.741 0.00 0.00 32.17 2.43


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

AutoCloner maintained by Alex Coulton.