Multiple sequence alignment - TraesCS4B01G001900

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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 TraesCS4B01G001900 chr4B 100.000 2393 0 0 1 2393 1081693 1079301 0.000000e+00 4420
1 TraesCS4B01G001900 chr4B 88.350 206 14 5 1199 1394 1066444 1066239 3.070000e-59 239
2 TraesCS4B01G001900 chr4B 82.390 159 17 3 2224 2376 1065851 1065698 6.940000e-26 128
3 TraesCS4B01G001900 chr4A 86.537 1805 98 67 660 2379 1076222 1077966 0.000000e+00 1853
4 TraesCS4B01G001900 chr4A 80.561 499 49 30 116 592 1075729 1076201 8.190000e-90 340
5 TraesCS4B01G001900 chr4A 79.091 220 19 15 1886 2092 1135139 1135344 2.500000e-25 126
6 TraesCS4B01G001900 chr4D 82.857 2170 137 97 309 2382 738328 740358 0.000000e+00 1729
7 TraesCS4B01G001900 chr4D 82.105 190 26 7 1042 1227 479525195 479525380 3.180000e-34 156
8 TraesCS4B01G001900 chr2D 84.483 174 25 2 1046 1218 528635714 528635886 1.140000e-38 171
9 TraesCS4B01G001900 chr2D 82.123 179 27 5 1048 1224 498532612 498532437 5.330000e-32 148
10 TraesCS4B01G001900 chr2A 84.483 174 25 2 1046 1218 673327382 673327554 1.140000e-38 171
11 TraesCS4B01G001900 chr2B 83.333 174 27 2 1046 1218 627073521 627073693 2.460000e-35 159
12 TraesCS4B01G001900 chr6A 82.022 178 32 0 1042 1219 454934514 454934691 4.120000e-33 152
13 TraesCS4B01G001900 chr1D 81.667 180 32 1 1045 1224 421226624 421226802 5.330000e-32 148


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 TraesCS4B01G001900 chr4B 1079301 1081693 2392 True 4420.0 4420 100.000 1 2393 1 chr4B.!!$R1 2392
1 TraesCS4B01G001900 chr4A 1075729 1077966 2237 False 1096.5 1853 83.549 116 2379 2 chr4A.!!$F2 2263
2 TraesCS4B01G001900 chr4D 738328 740358 2030 False 1729.0 1729 82.857 309 2382 1 chr4D.!!$F1 2073

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
42 43 0.037697 ATCGCTGCGAACACCAACTA 60.038 50.0 29.48 1.52 39.99 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1734 0.106669 AGGGTCGAGTCGATGGATGA 60.107 55.0 19.75 0.0 38.42 2.92 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
21 22 4.976540 ATATAGTCCAAGGGGTACAAGC 57.023 45.455 0.00 0.00 34.93 4.01
22 23 1.282382 TAGTCCAAGGGGTACAAGCC 58.718 55.000 0.00 0.00 34.93 4.35
23 24 0.770557 AGTCCAAGGGGTACAAGCCA 60.771 55.000 0.00 0.00 37.54 4.75
24 25 0.331616 GTCCAAGGGGTACAAGCCAT 59.668 55.000 0.00 0.00 37.54 4.40
25 26 0.623723 TCCAAGGGGTACAAGCCATC 59.376 55.000 0.00 0.00 37.54 3.51
26 27 0.748005 CCAAGGGGTACAAGCCATCG 60.748 60.000 0.00 0.00 37.54 3.84
27 28 1.077716 AAGGGGTACAAGCCATCGC 60.078 57.895 0.00 0.00 37.54 4.58
36 37 3.121030 AGCCATCGCTGCGAACAC 61.121 61.111 29.48 19.44 46.19 3.32
37 38 4.166011 GCCATCGCTGCGAACACC 62.166 66.667 29.48 13.45 39.99 4.16
38 39 2.741985 CCATCGCTGCGAACACCA 60.742 61.111 29.48 4.89 39.99 4.17
39 40 2.324330 CCATCGCTGCGAACACCAA 61.324 57.895 29.48 4.05 39.99 3.67
40 41 1.154413 CATCGCTGCGAACACCAAC 60.154 57.895 29.48 0.00 39.99 3.77
41 42 1.301716 ATCGCTGCGAACACCAACT 60.302 52.632 29.48 6.78 39.99 3.16
42 43 0.037697 ATCGCTGCGAACACCAACTA 60.038 50.000 29.48 1.52 39.99 2.24
43 44 0.666274 TCGCTGCGAACACCAACTAG 60.666 55.000 23.88 0.00 31.06 2.57
44 45 0.666274 CGCTGCGAACACCAACTAGA 60.666 55.000 18.66 0.00 0.00 2.43
45 46 1.508632 GCTGCGAACACCAACTAGAA 58.491 50.000 0.00 0.00 0.00 2.10
46 47 1.461127 GCTGCGAACACCAACTAGAAG 59.539 52.381 0.00 0.00 0.00 2.85
47 48 2.866460 GCTGCGAACACCAACTAGAAGA 60.866 50.000 0.00 0.00 0.00 2.87
48 49 2.989840 CTGCGAACACCAACTAGAAGAG 59.010 50.000 0.00 0.00 0.00 2.85
49 50 2.288825 TGCGAACACCAACTAGAAGAGG 60.289 50.000 0.00 0.00 0.00 3.69
50 51 2.338500 CGAACACCAACTAGAAGAGGC 58.662 52.381 0.00 0.00 0.00 4.70
51 52 2.338500 GAACACCAACTAGAAGAGGCG 58.662 52.381 0.00 0.00 0.00 5.52
52 53 1.629043 ACACCAACTAGAAGAGGCGA 58.371 50.000 0.00 0.00 0.00 5.54
53 54 1.272769 ACACCAACTAGAAGAGGCGAC 59.727 52.381 0.00 0.00 0.00 5.19
54 55 1.272490 CACCAACTAGAAGAGGCGACA 59.728 52.381 0.00 0.00 0.00 4.35
55 56 1.968493 ACCAACTAGAAGAGGCGACAA 59.032 47.619 0.00 0.00 0.00 3.18
56 57 2.028930 ACCAACTAGAAGAGGCGACAAG 60.029 50.000 0.00 0.00 0.00 3.16
69 70 2.594529 CGACAAGCATGCGTTAAACT 57.405 45.000 13.01 0.00 0.00 2.66
70 71 3.715618 CGACAAGCATGCGTTAAACTA 57.284 42.857 13.01 0.00 0.00 2.24
71 72 3.659735 CGACAAGCATGCGTTAAACTAG 58.340 45.455 13.01 0.00 0.00 2.57
72 73 3.417185 GACAAGCATGCGTTAAACTAGC 58.583 45.455 13.01 0.00 0.00 3.42
73 74 2.811431 ACAAGCATGCGTTAAACTAGCA 59.189 40.909 13.01 0.00 45.46 3.49
80 81 4.678509 TGCGTTAAACTAGCATGGAAAG 57.321 40.909 0.00 0.00 35.81 2.62
81 82 4.069304 TGCGTTAAACTAGCATGGAAAGT 58.931 39.130 0.00 0.00 35.81 2.66
82 83 4.517453 TGCGTTAAACTAGCATGGAAAGTT 59.483 37.500 0.00 0.00 35.81 2.66
83 84 5.009210 TGCGTTAAACTAGCATGGAAAGTTT 59.991 36.000 0.00 5.19 43.75 2.66
84 85 5.918576 GCGTTAAACTAGCATGGAAAGTTTT 59.081 36.000 5.15 0.00 42.06 2.43
85 86 6.129194 GCGTTAAACTAGCATGGAAAGTTTTG 60.129 38.462 5.15 0.00 42.06 2.44
86 87 7.136119 CGTTAAACTAGCATGGAAAGTTTTGA 58.864 34.615 5.15 0.00 42.06 2.69
87 88 7.646130 CGTTAAACTAGCATGGAAAGTTTTGAA 59.354 33.333 5.15 0.00 42.06 2.69
88 89 8.968242 GTTAAACTAGCATGGAAAGTTTTGAAG 58.032 33.333 5.15 0.00 42.06 3.02
89 90 6.959639 AACTAGCATGGAAAGTTTTGAAGA 57.040 33.333 0.00 0.00 29.25 2.87
90 91 6.566197 ACTAGCATGGAAAGTTTTGAAGAG 57.434 37.500 0.00 0.00 0.00 2.85
91 92 4.248691 AGCATGGAAAGTTTTGAAGAGC 57.751 40.909 0.00 0.00 0.00 4.09
92 93 3.006217 AGCATGGAAAGTTTTGAAGAGCC 59.994 43.478 0.00 0.00 0.00 4.70
93 94 3.568538 CATGGAAAGTTTTGAAGAGCCG 58.431 45.455 0.00 0.00 0.00 5.52
94 95 1.336755 TGGAAAGTTTTGAAGAGCCGC 59.663 47.619 0.00 0.00 0.00 6.53
95 96 1.663161 GGAAAGTTTTGAAGAGCCGCG 60.663 52.381 0.00 0.00 0.00 6.46
96 97 1.002792 GAAAGTTTTGAAGAGCCGCGT 60.003 47.619 4.92 0.00 0.00 6.01
97 98 0.307760 AAGTTTTGAAGAGCCGCGTG 59.692 50.000 4.92 0.00 0.00 5.34
98 99 1.725973 GTTTTGAAGAGCCGCGTGC 60.726 57.895 4.92 8.57 41.71 5.34
99 100 2.183504 TTTTGAAGAGCCGCGTGCA 61.184 52.632 19.30 0.00 44.83 4.57
100 101 1.514678 TTTTGAAGAGCCGCGTGCAT 61.515 50.000 19.30 6.86 44.83 3.96
101 102 0.672091 TTTGAAGAGCCGCGTGCATA 60.672 50.000 19.30 0.00 44.83 3.14
102 103 0.461870 TTGAAGAGCCGCGTGCATAT 60.462 50.000 19.30 6.55 44.83 1.78
103 104 1.153597 TGAAGAGCCGCGTGCATATG 61.154 55.000 19.30 0.00 44.83 1.78
104 105 1.153369 AAGAGCCGCGTGCATATGT 60.153 52.632 19.30 0.87 44.83 2.29
105 106 0.744414 AAGAGCCGCGTGCATATGTT 60.744 50.000 19.30 3.78 44.83 2.71
106 107 0.104120 AGAGCCGCGTGCATATGTTA 59.896 50.000 19.30 0.00 44.83 2.41
107 108 1.148310 GAGCCGCGTGCATATGTTAT 58.852 50.000 19.30 0.00 44.83 1.89
108 109 1.531149 GAGCCGCGTGCATATGTTATT 59.469 47.619 19.30 0.00 44.83 1.40
109 110 1.264020 AGCCGCGTGCATATGTTATTG 59.736 47.619 19.30 0.00 44.83 1.90
110 111 1.002900 GCCGCGTGCATATGTTATTGT 60.003 47.619 13.61 0.00 40.77 2.71
111 112 2.638673 CCGCGTGCATATGTTATTGTG 58.361 47.619 4.92 0.00 0.00 3.33
112 113 2.031560 CCGCGTGCATATGTTATTGTGT 59.968 45.455 4.92 0.00 0.00 3.72
113 114 3.486708 CCGCGTGCATATGTTATTGTGTT 60.487 43.478 4.92 0.00 0.00 3.32
114 115 3.478159 CGCGTGCATATGTTATTGTGTTG 59.522 43.478 4.29 0.00 0.00 3.33
115 116 4.657055 GCGTGCATATGTTATTGTGTTGA 58.343 39.130 4.29 0.00 0.00 3.18
116 117 5.273170 GCGTGCATATGTTATTGTGTTGAT 58.727 37.500 4.29 0.00 0.00 2.57
117 118 5.396362 GCGTGCATATGTTATTGTGTTGATC 59.604 40.000 4.29 0.00 0.00 2.92
158 159 8.806146 ACTTGTTAACCAATGATTCAGCTTTAT 58.194 29.630 2.48 0.00 31.20 1.40
224 237 6.795098 AAAACCCAACAAAGAACAAAGAAC 57.205 33.333 0.00 0.00 0.00 3.01
225 238 5.476091 AACCCAACAAAGAACAAAGAACA 57.524 34.783 0.00 0.00 0.00 3.18
226 239 5.675684 ACCCAACAAAGAACAAAGAACAT 57.324 34.783 0.00 0.00 0.00 2.71
227 240 6.048732 ACCCAACAAAGAACAAAGAACATT 57.951 33.333 0.00 0.00 0.00 2.71
228 241 7.176589 ACCCAACAAAGAACAAAGAACATTA 57.823 32.000 0.00 0.00 0.00 1.90
229 242 7.616313 ACCCAACAAAGAACAAAGAACATTAA 58.384 30.769 0.00 0.00 0.00 1.40
255 268 6.405278 AAAACCTAGAAAATCACACCAAGG 57.595 37.500 0.00 0.00 0.00 3.61
260 273 5.711976 CCTAGAAAATCACACCAAGGAATGT 59.288 40.000 0.00 0.00 0.00 2.71
291 304 7.962918 GTCACAATGCTTTACAATACCTTGTAG 59.037 37.037 0.00 0.00 45.90 2.74
292 305 7.663905 TCACAATGCTTTACAATACCTTGTAGT 59.336 33.333 0.00 0.00 45.90 2.73
293 306 8.941977 CACAATGCTTTACAATACCTTGTAGTA 58.058 33.333 0.00 0.00 45.90 1.82
341 354 3.124466 GGCAACCCGCATCAATTTAAAAC 59.876 43.478 0.00 0.00 45.17 2.43
458 487 7.658179 ACTGAATAAGTGTTGTGTCTACATG 57.342 36.000 0.00 0.00 37.88 3.21
460 489 6.230472 TGAATAAGTGTTGTGTCTACATGCT 58.770 36.000 0.00 0.00 36.53 3.79
461 490 6.147656 TGAATAAGTGTTGTGTCTACATGCTG 59.852 38.462 0.00 0.00 36.53 4.41
462 491 2.146342 AGTGTTGTGTCTACATGCTGC 58.854 47.619 0.00 0.00 36.53 5.25
463 492 2.146342 GTGTTGTGTCTACATGCTGCT 58.854 47.619 0.00 0.00 36.53 4.24
464 493 3.006859 AGTGTTGTGTCTACATGCTGCTA 59.993 43.478 0.00 0.00 36.53 3.49
465 494 3.123621 GTGTTGTGTCTACATGCTGCTAC 59.876 47.826 0.00 0.00 36.53 3.58
466 495 3.006859 TGTTGTGTCTACATGCTGCTACT 59.993 43.478 0.00 0.00 36.53 2.57
467 496 3.236632 TGTGTCTACATGCTGCTACTG 57.763 47.619 0.00 0.00 0.00 2.74
468 497 1.929836 GTGTCTACATGCTGCTACTGC 59.070 52.381 0.00 0.00 40.20 4.40
469 498 1.134699 TGTCTACATGCTGCTACTGCC 60.135 52.381 0.00 0.00 38.71 4.85
489 518 7.897864 ACTGCCTATTTGCCTAATACTACTAG 58.102 38.462 0.00 0.00 0.00 2.57
491 520 7.014449 TGCCTATTTGCCTAATACTACTAGGA 58.986 38.462 0.00 0.00 38.63 2.94
492 521 7.178628 TGCCTATTTGCCTAATACTACTAGGAG 59.821 40.741 0.00 0.00 38.63 3.69
493 522 7.178805 GCCTATTTGCCTAATACTACTAGGAGT 59.821 40.741 13.42 13.42 38.63 3.85
494 523 9.750783 CCTATTTGCCTAATACTACTAGGAGTA 57.249 37.037 17.32 17.32 38.63 2.59
509 540 4.461450 AGGAGTAGCACATCTGGAGATA 57.539 45.455 0.00 0.00 32.63 1.98
512 543 5.843421 AGGAGTAGCACATCTGGAGATAATT 59.157 40.000 0.00 0.00 32.63 1.40
514 545 7.510685 AGGAGTAGCACATCTGGAGATAATTAA 59.489 37.037 0.00 0.00 32.63 1.40
653 700 3.118038 CAGGAGCCTGAGTAGAGTAGAGT 60.118 52.174 11.08 0.00 46.30 3.24
654 701 4.101898 CAGGAGCCTGAGTAGAGTAGAGTA 59.898 50.000 11.08 0.00 46.30 2.59
655 702 4.347000 AGGAGCCTGAGTAGAGTAGAGTAG 59.653 50.000 0.00 0.00 0.00 2.57
656 703 4.345837 GGAGCCTGAGTAGAGTAGAGTAGA 59.654 50.000 0.00 0.00 0.00 2.59
657 704 5.510861 GGAGCCTGAGTAGAGTAGAGTAGAG 60.511 52.000 0.00 0.00 0.00 2.43
658 705 4.966805 AGCCTGAGTAGAGTAGAGTAGAGT 59.033 45.833 0.00 0.00 0.00 3.24
721 768 1.039233 TACGCTACCCGGGAAGGAAG 61.039 60.000 32.02 16.50 45.00 3.46
722 769 2.908796 GCTACCCGGGAAGGAAGG 59.091 66.667 32.02 9.43 45.00 3.46
723 770 1.688187 GCTACCCGGGAAGGAAGGA 60.688 63.158 32.02 0.03 45.00 3.36
724 771 1.269703 GCTACCCGGGAAGGAAGGAA 61.270 60.000 32.02 0.00 45.00 3.36
807 854 2.191981 TATCCCTTTCCCACCCTCTC 57.808 55.000 0.00 0.00 0.00 3.20
828 875 3.079578 CCTTTTTAAACCCTCCGACTCC 58.920 50.000 0.00 0.00 0.00 3.85
866 913 2.493278 CAACCCTTCATCACCAACATCC 59.507 50.000 0.00 0.00 0.00 3.51
870 917 2.954318 CCTTCATCACCAACATCCATCC 59.046 50.000 0.00 0.00 0.00 3.51
871 918 3.623703 CTTCATCACCAACATCCATCCA 58.376 45.455 0.00 0.00 0.00 3.41
872 919 3.957508 TCATCACCAACATCCATCCAT 57.042 42.857 0.00 0.00 0.00 3.41
873 920 3.824133 TCATCACCAACATCCATCCATC 58.176 45.455 0.00 0.00 0.00 3.51
899 947 1.004745 GCACTTCATTCTCCCCCTTCA 59.995 52.381 0.00 0.00 0.00 3.02
900 948 2.555227 GCACTTCATTCTCCCCCTTCAA 60.555 50.000 0.00 0.00 0.00 2.69
901 949 3.084786 CACTTCATTCTCCCCCTTCAAC 58.915 50.000 0.00 0.00 0.00 3.18
911 959 0.038310 CCCCTTCAACTCCCTCCAAC 59.962 60.000 0.00 0.00 0.00 3.77
954 1018 1.501582 CTAGCTAGCTCCCCAAACCT 58.498 55.000 23.26 0.00 0.00 3.50
956 1020 0.547712 AGCTAGCTCCCCAAACCTCA 60.548 55.000 12.68 0.00 0.00 3.86
957 1021 0.548510 GCTAGCTCCCCAAACCTCAT 59.451 55.000 7.70 0.00 0.00 2.90
958 1022 1.064389 GCTAGCTCCCCAAACCTCATT 60.064 52.381 7.70 0.00 0.00 2.57
973 1037 2.162408 CCTCATTTTCCGGCTTCTTCAC 59.838 50.000 0.00 0.00 0.00 3.18
977 1041 2.631160 TTTCCGGCTTCTTCACTTCA 57.369 45.000 0.00 0.00 0.00 3.02
978 1042 2.859165 TTCCGGCTTCTTCACTTCAT 57.141 45.000 0.00 0.00 0.00 2.57
979 1043 2.859165 TCCGGCTTCTTCACTTCATT 57.141 45.000 0.00 0.00 0.00 2.57
980 1044 3.973206 TCCGGCTTCTTCACTTCATTA 57.027 42.857 0.00 0.00 0.00 1.90
981 1045 3.596214 TCCGGCTTCTTCACTTCATTAC 58.404 45.455 0.00 0.00 0.00 1.89
982 1046 3.260884 TCCGGCTTCTTCACTTCATTACT 59.739 43.478 0.00 0.00 0.00 2.24
983 1047 4.464951 TCCGGCTTCTTCACTTCATTACTA 59.535 41.667 0.00 0.00 0.00 1.82
984 1048 4.806247 CCGGCTTCTTCACTTCATTACTAG 59.194 45.833 0.00 0.00 0.00 2.57
985 1049 5.411781 CGGCTTCTTCACTTCATTACTAGT 58.588 41.667 0.00 0.00 0.00 2.57
986 1050 5.869888 CGGCTTCTTCACTTCATTACTAGTT 59.130 40.000 0.00 0.00 0.00 2.24
989 1053 9.216117 GGCTTCTTCACTTCATTACTAGTTTAA 57.784 33.333 0.00 0.00 0.00 1.52
1026 1092 2.058675 CGGAGAAGGTTCTGGTGGT 58.941 57.895 0.00 0.00 37.73 4.16
1279 1345 1.605058 CCAGGGTTCCTCATCGTCGT 61.605 60.000 0.00 0.00 0.00 4.34
1281 1347 1.141234 GGGTTCCTCATCGTCGTCC 59.859 63.158 0.00 0.00 0.00 4.79
1293 1359 2.029844 GTCGTCCAGGCAGCAGAAC 61.030 63.158 0.00 0.00 0.00 3.01
1380 1449 2.022129 GCTCCACGACCACGACAAG 61.022 63.158 0.00 0.00 42.66 3.16
1381 1450 1.372997 CTCCACGACCACGACAAGG 60.373 63.158 0.00 0.00 42.66 3.61
1382 1451 2.357034 CCACGACCACGACAAGGG 60.357 66.667 0.00 0.00 42.66 3.95
1393 1462 1.140252 ACGACAAGGGCAACAAGTAGT 59.860 47.619 0.00 0.00 39.74 2.73
1394 1463 1.531149 CGACAAGGGCAACAAGTAGTG 59.469 52.381 0.00 0.00 39.74 2.74
1395 1464 1.880027 GACAAGGGCAACAAGTAGTGG 59.120 52.381 0.00 0.00 39.74 4.00
1396 1465 1.493022 ACAAGGGCAACAAGTAGTGGA 59.507 47.619 0.00 0.00 39.74 4.02
1397 1466 2.108250 ACAAGGGCAACAAGTAGTGGAT 59.892 45.455 0.00 0.00 39.74 3.41
1398 1467 2.749621 CAAGGGCAACAAGTAGTGGATC 59.250 50.000 0.00 0.00 39.74 3.36
1399 1468 1.066143 AGGGCAACAAGTAGTGGATCG 60.066 52.381 0.00 0.00 39.74 3.69
1400 1469 1.066430 GGGCAACAAGTAGTGGATCGA 60.066 52.381 0.00 0.00 39.74 3.59
1401 1470 2.420129 GGGCAACAAGTAGTGGATCGAT 60.420 50.000 0.00 0.00 39.74 3.59
1402 1471 2.866762 GGCAACAAGTAGTGGATCGATC 59.133 50.000 17.36 17.36 0.00 3.69
1510 1599 6.294620 GGATGCAATCTACACTACCTACCTAC 60.295 46.154 0.00 0.00 44.71 3.18
1610 1736 5.767816 CATTCTGATGCATGAGGATTTCA 57.232 39.130 13.49 0.00 40.85 2.69
1643 1769 6.208994 ACTCGACCCTCTACCATATATTTGAC 59.791 42.308 0.00 0.00 0.00 3.18
1647 1773 4.504858 CCTCTACCATATATTTGACGGGC 58.495 47.826 0.00 0.00 0.00 6.13
1655 1781 0.677288 TATTTGACGGGCCGATCGAT 59.323 50.000 35.78 22.36 0.00 3.59
1656 1782 0.600255 ATTTGACGGGCCGATCGATC 60.600 55.000 35.78 19.91 0.00 3.69
1669 1795 1.599071 GATCGATCGATTTGCAGCCAA 59.401 47.619 29.89 0.00 34.60 4.52
1684 1810 4.900652 TGCAGCCAATAATAATCCAATGGT 59.099 37.500 0.00 0.00 0.00 3.55
1690 1816 7.510001 AGCCAATAATAATCCAATGGTTGATGA 59.490 33.333 0.00 0.00 0.00 2.92
1711 1841 6.851222 TGAGTTTTCAGTCTCAAATGACTC 57.149 37.500 0.00 0.00 44.56 3.36
1712 1842 6.348498 TGAGTTTTCAGTCTCAAATGACTCA 58.652 36.000 0.95 0.95 44.56 3.41
1749 1879 9.378551 TGCCTACATTTTCAGTTATTACAGTAG 57.621 33.333 0.00 0.00 0.00 2.57
1968 2128 2.306219 ACCTACCTGGAAGCTTCTTTCC 59.694 50.000 25.05 10.81 45.59 3.13
2173 2395 1.713005 ATTCAGGGGCTGCGATGGAT 61.713 55.000 0.00 0.00 0.00 3.41
2174 2396 2.593725 CAGGGGCTGCGATGGATG 60.594 66.667 0.00 0.00 0.00 3.51
2175 2397 3.882326 AGGGGCTGCGATGGATGG 61.882 66.667 0.00 0.00 0.00 3.51
2177 2399 2.433446 GGGCTGCGATGGATGGAT 59.567 61.111 0.00 0.00 0.00 3.41
2178 2400 1.970114 GGGCTGCGATGGATGGATG 60.970 63.158 0.00 0.00 0.00 3.51
2180 2402 1.071987 GCTGCGATGGATGGATGGA 59.928 57.895 0.00 0.00 0.00 3.41
2181 2403 0.322277 GCTGCGATGGATGGATGGAT 60.322 55.000 0.00 0.00 0.00 3.41
2182 2404 1.450025 CTGCGATGGATGGATGGATG 58.550 55.000 0.00 0.00 0.00 3.51
2183 2405 0.037160 TGCGATGGATGGATGGATGG 59.963 55.000 0.00 0.00 0.00 3.51
2184 2406 0.325933 GCGATGGATGGATGGATGGA 59.674 55.000 0.00 0.00 0.00 3.41
2185 2407 1.064906 GCGATGGATGGATGGATGGAT 60.065 52.381 0.00 0.00 0.00 3.41
2186 2408 2.640184 CGATGGATGGATGGATGGATG 58.360 52.381 0.00 0.00 0.00 3.51
2187 2409 2.682858 CGATGGATGGATGGATGGATGG 60.683 54.545 0.00 0.00 0.00 3.51
2188 2410 1.078115 TGGATGGATGGATGGATGGG 58.922 55.000 0.00 0.00 0.00 4.00
2189 2411 1.375610 GGATGGATGGATGGATGGGA 58.624 55.000 0.00 0.00 0.00 4.37
2190 2412 1.284198 GGATGGATGGATGGATGGGAG 59.716 57.143 0.00 0.00 0.00 4.30
2191 2413 0.702902 ATGGATGGATGGATGGGAGC 59.297 55.000 0.00 0.00 0.00 4.70
2192 2414 0.698542 TGGATGGATGGATGGGAGCA 60.699 55.000 0.00 0.00 0.00 4.26
2193 2415 0.479815 GGATGGATGGATGGGAGCAA 59.520 55.000 0.00 0.00 0.00 3.91
2194 2416 1.613836 GATGGATGGATGGGAGCAAC 58.386 55.000 0.00 0.00 0.00 4.17
2217 2439 1.276138 TGCATGAAGCTTCTCGGAAGA 59.724 47.619 26.09 5.44 45.94 2.87
2232 2458 0.790814 GAAGACGGAACCTGCTTTCG 59.209 55.000 0.00 0.00 0.00 3.46
2286 2516 0.951040 GTACACAGCACACCTCTGCC 60.951 60.000 0.00 0.00 37.96 4.85
2287 2517 2.434658 TACACAGCACACCTCTGCCG 62.435 60.000 0.00 0.00 37.96 5.69
2288 2518 3.550431 ACAGCACACCTCTGCCGT 61.550 61.111 0.00 0.00 37.96 5.68
2299 2535 0.737715 CTCTGCCGTTCTGCTGGTAC 60.738 60.000 0.00 0.00 0.00 3.34
2369 2611 3.433615 GTGTAACTGCACAGACTCAATCC 59.566 47.826 4.31 0.00 39.07 3.01
2382 2624 4.233287 AGACTCAATCCCCTACTCCTACTT 59.767 45.833 0.00 0.00 0.00 2.24
2383 2625 4.548669 ACTCAATCCCCTACTCCTACTTC 58.451 47.826 0.00 0.00 0.00 3.01
2384 2626 4.016479 ACTCAATCCCCTACTCCTACTTCA 60.016 45.833 0.00 0.00 0.00 3.02
2385 2627 4.547671 TCAATCCCCTACTCCTACTTCAG 58.452 47.826 0.00 0.00 0.00 3.02
2386 2628 4.016479 TCAATCCCCTACTCCTACTTCAGT 60.016 45.833 0.00 0.00 0.00 3.41
2387 2629 3.666345 TCCCCTACTCCTACTTCAGTC 57.334 52.381 0.00 0.00 0.00 3.51
2388 2630 3.199671 TCCCCTACTCCTACTTCAGTCT 58.800 50.000 0.00 0.00 0.00 3.24
2389 2631 3.053544 TCCCCTACTCCTACTTCAGTCTG 60.054 52.174 0.00 0.00 0.00 3.51
2390 2632 3.309265 CCCCTACTCCTACTTCAGTCTGT 60.309 52.174 0.00 0.00 0.00 3.41
2391 2633 4.079901 CCCCTACTCCTACTTCAGTCTGTA 60.080 50.000 0.00 0.00 0.00 2.74
2392 2634 4.883006 CCCTACTCCTACTTCAGTCTGTAC 59.117 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.844497 GGCTTGTACCCCTTGGACTAT 59.156 52.381 0.00 0.00 34.81 2.12
3 4 1.282382 GGCTTGTACCCCTTGGACTA 58.718 55.000 0.00 0.00 34.81 2.59
4 5 0.770557 TGGCTTGTACCCCTTGGACT 60.771 55.000 0.00 0.00 34.81 3.85
5 6 0.331616 ATGGCTTGTACCCCTTGGAC 59.668 55.000 0.00 0.00 34.81 4.02
6 7 0.623723 GATGGCTTGTACCCCTTGGA 59.376 55.000 0.00 0.00 34.81 3.53
7 8 0.748005 CGATGGCTTGTACCCCTTGG 60.748 60.000 0.00 0.00 37.80 3.61
8 9 1.376609 GCGATGGCTTGTACCCCTTG 61.377 60.000 0.00 0.00 35.83 3.61
9 10 1.077716 GCGATGGCTTGTACCCCTT 60.078 57.895 0.00 0.00 35.83 3.95
10 11 2.590092 GCGATGGCTTGTACCCCT 59.410 61.111 0.00 0.00 35.83 4.79
20 21 4.166011 GGTGTTCGCAGCGATGGC 62.166 66.667 20.32 12.54 35.23 4.40
26 27 1.461127 CTTCTAGTTGGTGTTCGCAGC 59.539 52.381 0.00 0.00 45.17 5.25
27 28 2.989840 CTCTTCTAGTTGGTGTTCGCAG 59.010 50.000 0.00 0.00 0.00 5.18
28 29 2.288825 CCTCTTCTAGTTGGTGTTCGCA 60.289 50.000 0.00 0.00 0.00 5.10
29 30 2.338500 CCTCTTCTAGTTGGTGTTCGC 58.662 52.381 0.00 0.00 0.00 4.70
30 31 2.338500 GCCTCTTCTAGTTGGTGTTCG 58.662 52.381 0.00 0.00 0.00 3.95
31 32 2.029290 TCGCCTCTTCTAGTTGGTGTTC 60.029 50.000 0.00 0.00 0.00 3.18
32 33 1.968493 TCGCCTCTTCTAGTTGGTGTT 59.032 47.619 0.00 0.00 0.00 3.32
33 34 1.272769 GTCGCCTCTTCTAGTTGGTGT 59.727 52.381 0.00 0.00 0.00 4.16
34 35 1.272490 TGTCGCCTCTTCTAGTTGGTG 59.728 52.381 0.00 0.00 0.00 4.17
35 36 1.629043 TGTCGCCTCTTCTAGTTGGT 58.371 50.000 0.00 0.00 0.00 3.67
36 37 2.611518 CTTGTCGCCTCTTCTAGTTGG 58.388 52.381 0.00 0.00 0.00 3.77
37 38 1.996191 GCTTGTCGCCTCTTCTAGTTG 59.004 52.381 0.00 0.00 0.00 3.16
38 39 1.618837 TGCTTGTCGCCTCTTCTAGTT 59.381 47.619 0.00 0.00 38.05 2.24
39 40 1.257743 TGCTTGTCGCCTCTTCTAGT 58.742 50.000 0.00 0.00 38.05 2.57
40 41 2.200067 CATGCTTGTCGCCTCTTCTAG 58.800 52.381 0.00 0.00 38.05 2.43
41 42 1.740380 GCATGCTTGTCGCCTCTTCTA 60.740 52.381 11.37 0.00 38.05 2.10
42 43 1.023513 GCATGCTTGTCGCCTCTTCT 61.024 55.000 11.37 0.00 38.05 2.85
43 44 1.427020 GCATGCTTGTCGCCTCTTC 59.573 57.895 11.37 0.00 38.05 2.87
44 45 2.393768 CGCATGCTTGTCGCCTCTT 61.394 57.895 17.13 0.00 38.05 2.85
45 46 2.816958 CGCATGCTTGTCGCCTCT 60.817 61.111 17.13 0.00 38.05 3.69
46 47 1.358725 TAACGCATGCTTGTCGCCTC 61.359 55.000 17.13 0.00 38.05 4.70
47 48 0.953471 TTAACGCATGCTTGTCGCCT 60.953 50.000 17.13 0.00 38.05 5.52
48 49 0.109964 TTTAACGCATGCTTGTCGCC 60.110 50.000 17.13 0.00 38.05 5.54
49 50 0.974836 GTTTAACGCATGCTTGTCGC 59.025 50.000 17.13 0.00 39.77 5.19
50 51 2.594529 AGTTTAACGCATGCTTGTCG 57.405 45.000 17.13 12.45 0.00 4.35
51 52 3.120338 TGCTAGTTTAACGCATGCTTGTC 60.120 43.478 17.13 1.48 0.00 3.18
52 53 2.811431 TGCTAGTTTAACGCATGCTTGT 59.189 40.909 17.13 4.01 0.00 3.16
53 54 3.469899 TGCTAGTTTAACGCATGCTTG 57.530 42.857 17.13 3.27 0.00 4.01
58 59 4.700213 ACTTTCCATGCTAGTTTAACGCAT 59.300 37.500 4.97 4.97 44.53 4.73
59 60 4.069304 ACTTTCCATGCTAGTTTAACGCA 58.931 39.130 0.63 0.63 38.14 5.24
60 61 4.680171 ACTTTCCATGCTAGTTTAACGC 57.320 40.909 0.00 0.00 0.00 4.84
61 62 7.136119 TCAAAACTTTCCATGCTAGTTTAACG 58.864 34.615 14.46 9.15 40.24 3.18
62 63 8.865590 TTCAAAACTTTCCATGCTAGTTTAAC 57.134 30.769 14.46 0.00 40.24 2.01
63 64 8.908903 TCTTCAAAACTTTCCATGCTAGTTTAA 58.091 29.630 14.46 8.42 40.24 1.52
64 65 8.458573 TCTTCAAAACTTTCCATGCTAGTTTA 57.541 30.769 14.46 2.94 40.24 2.01
65 66 7.346751 TCTTCAAAACTTTCCATGCTAGTTT 57.653 32.000 10.47 10.47 42.24 2.66
66 67 6.515696 GCTCTTCAAAACTTTCCATGCTAGTT 60.516 38.462 0.00 0.00 33.76 2.24
67 68 5.048434 GCTCTTCAAAACTTTCCATGCTAGT 60.048 40.000 0.00 0.00 0.00 2.57
68 69 5.397326 GCTCTTCAAAACTTTCCATGCTAG 58.603 41.667 0.00 0.00 0.00 3.42
69 70 4.218417 GGCTCTTCAAAACTTTCCATGCTA 59.782 41.667 0.00 0.00 0.00 3.49
70 71 3.006217 GGCTCTTCAAAACTTTCCATGCT 59.994 43.478 0.00 0.00 0.00 3.79
71 72 3.320626 GGCTCTTCAAAACTTTCCATGC 58.679 45.455 0.00 0.00 0.00 4.06
72 73 3.568538 CGGCTCTTCAAAACTTTCCATG 58.431 45.455 0.00 0.00 0.00 3.66
73 74 2.029918 GCGGCTCTTCAAAACTTTCCAT 60.030 45.455 0.00 0.00 0.00 3.41
74 75 1.336755 GCGGCTCTTCAAAACTTTCCA 59.663 47.619 0.00 0.00 0.00 3.53
75 76 1.663161 CGCGGCTCTTCAAAACTTTCC 60.663 52.381 0.00 0.00 0.00 3.13
76 77 1.002792 ACGCGGCTCTTCAAAACTTTC 60.003 47.619 12.47 0.00 0.00 2.62
77 78 1.021968 ACGCGGCTCTTCAAAACTTT 58.978 45.000 12.47 0.00 0.00 2.66
78 79 0.307760 CACGCGGCTCTTCAAAACTT 59.692 50.000 12.47 0.00 0.00 2.66
79 80 1.941812 CACGCGGCTCTTCAAAACT 59.058 52.632 12.47 0.00 0.00 2.66
80 81 1.725973 GCACGCGGCTCTTCAAAAC 60.726 57.895 12.47 0.00 40.25 2.43
81 82 1.514678 ATGCACGCGGCTCTTCAAAA 61.515 50.000 12.47 0.00 45.15 2.44
82 83 0.672091 TATGCACGCGGCTCTTCAAA 60.672 50.000 12.47 0.00 45.15 2.69
83 84 0.461870 ATATGCACGCGGCTCTTCAA 60.462 50.000 12.47 0.00 45.15 2.69
84 85 1.143838 ATATGCACGCGGCTCTTCA 59.856 52.632 12.47 0.00 45.15 3.02
85 86 1.154205 ACATATGCACGCGGCTCTTC 61.154 55.000 12.47 0.00 45.15 2.87
86 87 0.744414 AACATATGCACGCGGCTCTT 60.744 50.000 12.47 3.58 45.15 2.85
87 88 0.104120 TAACATATGCACGCGGCTCT 59.896 50.000 12.47 5.83 45.15 4.09
88 89 1.148310 ATAACATATGCACGCGGCTC 58.852 50.000 12.47 0.00 45.15 4.70
89 90 1.264020 CAATAACATATGCACGCGGCT 59.736 47.619 12.47 4.14 45.15 5.52
90 91 1.002900 ACAATAACATATGCACGCGGC 60.003 47.619 12.47 12.14 45.13 6.53
91 92 2.031560 ACACAATAACATATGCACGCGG 59.968 45.455 12.47 0.00 0.00 6.46
92 93 3.317744 ACACAATAACATATGCACGCG 57.682 42.857 3.53 3.53 0.00 6.01
93 94 4.657055 TCAACACAATAACATATGCACGC 58.343 39.130 1.58 0.00 0.00 5.34
94 95 6.485393 TGATCAACACAATAACATATGCACG 58.515 36.000 1.58 0.00 0.00 5.34
102 103 9.883142 TCTACACATATGATCAACACAATAACA 57.117 29.630 10.38 0.00 0.00 2.41
203 205 5.476091 TGTTCTTTGTTCTTTGTTGGGTT 57.524 34.783 0.00 0.00 0.00 4.11
205 218 8.485976 TTTAATGTTCTTTGTTCTTTGTTGGG 57.514 30.769 0.00 0.00 0.00 4.12
236 249 5.711976 ACATTCCTTGGTGTGATTTTCTAGG 59.288 40.000 0.00 0.00 0.00 3.02
255 268 3.542712 AGCATTGTGACAACGACATTC 57.457 42.857 0.00 0.00 0.00 2.67
260 273 4.884458 TTGTAAAGCATTGTGACAACGA 57.116 36.364 0.00 0.00 0.00 3.85
293 306 8.573035 CGTAAATGTGGGGCTGTAAATTATTAT 58.427 33.333 0.00 0.00 0.00 1.28
306 319 1.214325 GTTGCCGTAAATGTGGGGC 59.786 57.895 0.00 0.00 45.76 5.80
307 320 1.600511 GGGTTGCCGTAAATGTGGGG 61.601 60.000 0.00 0.00 0.00 4.96
327 340 3.677596 CGTGGTGGGTTTTAAATTGATGC 59.322 43.478 0.00 0.00 0.00 3.91
341 354 1.394618 TTTCTGGAAAACGTGGTGGG 58.605 50.000 0.00 0.00 0.00 4.61
397 419 5.369685 TCAAAGGACACATACGTACGTAA 57.630 39.130 29.91 14.89 33.99 3.18
458 487 0.665298 GGCAAATAGGCAGTAGCAGC 59.335 55.000 0.00 0.00 44.61 5.25
467 496 7.178805 ACTCCTAGTAGTATTAGGCAAATAGGC 59.821 40.741 12.79 0.00 44.61 3.93
468 497 8.653036 ACTCCTAGTAGTATTAGGCAAATAGG 57.347 38.462 12.79 0.00 38.05 2.57
489 518 5.736951 ATTATCTCCAGATGTGCTACTCC 57.263 43.478 0.00 0.00 36.05 3.85
521 552 8.194769 ACACCAAAGTTTTATACACCTTTTCTG 58.805 33.333 0.00 0.00 0.00 3.02
527 558 7.308951 GCATACACACCAAAGTTTTATACACCT 60.309 37.037 0.00 0.00 0.00 4.00
528 559 6.804783 GCATACACACCAAAGTTTTATACACC 59.195 38.462 0.00 0.00 0.00 4.16
529 560 7.364200 TGCATACACACCAAAGTTTTATACAC 58.636 34.615 0.00 0.00 0.00 2.90
530 561 7.511959 TGCATACACACCAAAGTTTTATACA 57.488 32.000 0.00 0.00 0.00 2.29
531 562 7.009174 GCATGCATACACACCAAAGTTTTATAC 59.991 37.037 14.21 0.00 0.00 1.47
533 564 5.868801 GCATGCATACACACCAAAGTTTTAT 59.131 36.000 14.21 0.00 0.00 1.40
535 566 4.057432 GCATGCATACACACCAAAGTTTT 58.943 39.130 14.21 0.00 0.00 2.43
574 605 9.155975 GTCCTCGTATGCATTTCAAATCTATAT 57.844 33.333 3.54 0.00 0.00 0.86
575 606 8.367911 AGTCCTCGTATGCATTTCAAATCTATA 58.632 33.333 3.54 0.00 0.00 1.31
576 607 7.220030 AGTCCTCGTATGCATTTCAAATCTAT 58.780 34.615 3.54 0.00 0.00 1.98
637 684 7.504911 ACTCTACTCTACTCTACTCTACTCAGG 59.495 44.444 0.00 0.00 0.00 3.86
638 685 8.461249 ACTCTACTCTACTCTACTCTACTCAG 57.539 42.308 0.00 0.00 0.00 3.35
639 686 9.565090 CTACTCTACTCTACTCTACTCTACTCA 57.435 40.741 0.00 0.00 0.00 3.41
640 687 9.784531 TCTACTCTACTCTACTCTACTCTACTC 57.215 40.741 0.00 0.00 0.00 2.59
641 688 9.790344 CTCTACTCTACTCTACTCTACTCTACT 57.210 40.741 0.00 0.00 0.00 2.57
644 691 9.790344 CTACTCTACTCTACTCTACTCTACTCT 57.210 40.741 0.00 0.00 0.00 3.24
646 693 7.449704 GCCTACTCTACTCTACTCTACTCTACT 59.550 44.444 0.00 0.00 0.00 2.57
647 694 7.231317 TGCCTACTCTACTCTACTCTACTCTAC 59.769 44.444 0.00 0.00 0.00 2.59
648 695 7.231317 GTGCCTACTCTACTCTACTCTACTCTA 59.769 44.444 0.00 0.00 0.00 2.43
721 768 1.014352 CCAACGAATCCGACCATTCC 58.986 55.000 0.00 0.00 39.50 3.01
722 769 1.014352 CCCAACGAATCCGACCATTC 58.986 55.000 0.00 0.00 39.50 2.67
723 770 0.616371 TCCCAACGAATCCGACCATT 59.384 50.000 0.00 0.00 39.50 3.16
724 771 0.616371 TTCCCAACGAATCCGACCAT 59.384 50.000 0.00 0.00 39.50 3.55
767 814 2.676748 TGTCAATATTTGGGGATGGGC 58.323 47.619 0.00 0.00 0.00 5.36
772 819 6.544327 AAGGGATATGTCAATATTTGGGGA 57.456 37.500 0.00 0.00 0.00 4.81
807 854 3.079578 GGAGTCGGAGGGTTTAAAAAGG 58.920 50.000 0.00 0.00 0.00 3.11
866 913 2.927028 TGAAGTGCTGATGGATGGATG 58.073 47.619 0.00 0.00 0.00 3.51
870 917 3.564644 GGAGAATGAAGTGCTGATGGATG 59.435 47.826 0.00 0.00 0.00 3.51
871 918 3.434739 GGGAGAATGAAGTGCTGATGGAT 60.435 47.826 0.00 0.00 0.00 3.41
872 919 2.092753 GGGAGAATGAAGTGCTGATGGA 60.093 50.000 0.00 0.00 0.00 3.41
873 920 2.295885 GGGAGAATGAAGTGCTGATGG 58.704 52.381 0.00 0.00 0.00 3.51
899 947 1.134438 GGTGGAGGTTGGAGGGAGTT 61.134 60.000 0.00 0.00 0.00 3.01
900 948 1.539124 GGTGGAGGTTGGAGGGAGT 60.539 63.158 0.00 0.00 0.00 3.85
901 949 0.916358 ATGGTGGAGGTTGGAGGGAG 60.916 60.000 0.00 0.00 0.00 4.30
911 959 1.219124 CAGTGGTCGATGGTGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
945 993 0.894835 CCGGAAAATGAGGTTTGGGG 59.105 55.000 0.00 0.00 0.00 4.96
949 1013 2.876581 AGAAGCCGGAAAATGAGGTTT 58.123 42.857 5.05 0.00 0.00 3.27
954 1018 3.140325 AGTGAAGAAGCCGGAAAATGA 57.860 42.857 5.05 0.00 0.00 2.57
956 1020 3.486383 TGAAGTGAAGAAGCCGGAAAAT 58.514 40.909 5.05 0.00 0.00 1.82
957 1021 2.925724 TGAAGTGAAGAAGCCGGAAAA 58.074 42.857 5.05 0.00 0.00 2.29
958 1022 2.631160 TGAAGTGAAGAAGCCGGAAA 57.369 45.000 5.05 0.00 0.00 3.13
980 1044 8.428063 CCTCCATGATCTCAAGATTAAACTAGT 58.572 37.037 0.00 0.00 34.37 2.57
981 1045 7.877097 CCCTCCATGATCTCAAGATTAAACTAG 59.123 40.741 0.00 0.00 34.37 2.57
982 1046 7.690301 GCCCTCCATGATCTCAAGATTAAACTA 60.690 40.741 0.00 0.00 34.37 2.24
983 1047 6.599445 CCCTCCATGATCTCAAGATTAAACT 58.401 40.000 0.00 0.00 34.37 2.66
984 1048 5.240403 GCCCTCCATGATCTCAAGATTAAAC 59.760 44.000 0.00 0.00 34.37 2.01
985 1049 5.380043 GCCCTCCATGATCTCAAGATTAAA 58.620 41.667 0.00 0.00 34.37 1.52
986 1050 4.503817 CGCCCTCCATGATCTCAAGATTAA 60.504 45.833 0.00 0.00 34.37 1.40
989 1053 1.347050 CGCCCTCCATGATCTCAAGAT 59.653 52.381 0.00 0.00 37.51 2.40
990 1054 0.755079 CGCCCTCCATGATCTCAAGA 59.245 55.000 0.00 0.00 0.00 3.02
991 1055 0.250209 CCGCCCTCCATGATCTCAAG 60.250 60.000 0.00 0.00 0.00 3.02
1269 1335 1.226802 CTGCCTGGACGACGATGAG 60.227 63.158 0.00 0.00 0.00 2.90
1279 1345 2.752358 CTGGTTCTGCTGCCTGGA 59.248 61.111 0.00 0.00 0.00 3.86
1281 1347 2.281970 TGCTGGTTCTGCTGCCTG 60.282 61.111 0.00 0.00 0.00 4.85
1380 1449 1.066430 TCGATCCACTACTTGTTGCCC 60.066 52.381 0.00 0.00 0.00 5.36
1381 1450 2.380084 TCGATCCACTACTTGTTGCC 57.620 50.000 0.00 0.00 0.00 4.52
1382 1451 3.521560 TGATCGATCCACTACTTGTTGC 58.478 45.455 22.31 0.00 0.00 4.17
1411 1480 7.683437 ACAGTAGGTATTATCATCGATCGAA 57.317 36.000 23.50 6.97 0.00 3.71
1510 1599 2.872245 CCTAATATATGGCCGGAATGCG 59.128 50.000 5.05 0.00 0.00 4.73
1607 1733 0.744874 GGGTCGAGTCGATGGATGAA 59.255 55.000 19.75 0.00 38.42 2.57
1608 1734 0.106669 AGGGTCGAGTCGATGGATGA 60.107 55.000 19.75 0.00 38.42 2.92
1609 1735 0.312416 GAGGGTCGAGTCGATGGATG 59.688 60.000 19.75 0.00 38.42 3.51
1610 1736 0.183971 AGAGGGTCGAGTCGATGGAT 59.816 55.000 19.75 5.37 38.42 3.41
1655 1781 5.534278 TGGATTATTATTGGCTGCAAATCGA 59.466 36.000 5.33 0.00 0.00 3.59
1656 1782 5.771469 TGGATTATTATTGGCTGCAAATCG 58.229 37.500 5.33 0.00 0.00 3.34
1657 1783 7.118680 CCATTGGATTATTATTGGCTGCAAATC 59.881 37.037 5.33 1.09 0.00 2.17
1684 1810 7.500227 AGTCATTTGAGACTGAAAACTCATCAA 59.500 33.333 0.00 0.00 46.58 2.57
1710 1840 2.431454 TGTAGGCATTGCGATTGTTGA 58.569 42.857 1.91 0.00 0.00 3.18
1711 1841 2.917701 TGTAGGCATTGCGATTGTTG 57.082 45.000 1.91 0.00 0.00 3.33
1712 1842 4.454728 AAATGTAGGCATTGCGATTGTT 57.545 36.364 1.91 0.00 43.89 2.83
1803 1946 6.682746 ACGAGGATCATTCACAGTATATGTC 58.317 40.000 0.00 0.00 35.55 3.06
1933 2093 1.134610 GGTAGGTTCCATGTACACCGG 60.135 57.143 0.00 0.00 35.54 5.28
1934 2094 1.829222 AGGTAGGTTCCATGTACACCG 59.171 52.381 0.00 0.00 35.54 4.94
1935 2095 2.093128 CCAGGTAGGTTCCATGTACACC 60.093 54.545 0.00 0.00 0.00 4.16
1936 2096 2.835764 TCCAGGTAGGTTCCATGTACAC 59.164 50.000 0.00 0.00 39.02 2.90
1937 2097 3.193395 TCCAGGTAGGTTCCATGTACA 57.807 47.619 0.00 0.00 39.02 2.90
1938 2098 3.681874 GCTTCCAGGTAGGTTCCATGTAC 60.682 52.174 0.00 0.00 39.02 2.90
1939 2099 2.504175 GCTTCCAGGTAGGTTCCATGTA 59.496 50.000 0.00 0.00 39.02 2.29
1940 2100 1.282157 GCTTCCAGGTAGGTTCCATGT 59.718 52.381 0.00 0.00 39.02 3.21
1941 2101 1.561542 AGCTTCCAGGTAGGTTCCATG 59.438 52.381 0.00 0.00 39.02 3.66
1968 2128 5.779529 ACTTCCCTTTGCAATGCATATAG 57.220 39.130 9.39 7.12 38.76 1.31
2173 2395 0.698542 TGCTCCCATCCATCCATCCA 60.699 55.000 0.00 0.00 0.00 3.41
2174 2396 0.479815 TTGCTCCCATCCATCCATCC 59.520 55.000 0.00 0.00 0.00 3.51
2175 2397 1.613836 GTTGCTCCCATCCATCCATC 58.386 55.000 0.00 0.00 0.00 3.51
2177 2399 1.614711 GGTTGCTCCCATCCATCCA 59.385 57.895 0.00 0.00 32.20 3.41
2178 2400 1.526917 CGGTTGCTCCCATCCATCC 60.527 63.158 0.00 0.00 31.51 3.51
2180 2402 1.077501 CACGGTTGCTCCCATCCAT 60.078 57.895 0.00 0.00 31.51 3.41
2181 2403 2.350895 CACGGTTGCTCCCATCCA 59.649 61.111 0.00 0.00 31.51 3.41
2182 2404 3.134127 GCACGGTTGCTCCCATCC 61.134 66.667 0.00 0.00 46.17 3.51
2191 2413 0.877071 AGAAGCTTCATGCACGGTTG 59.123 50.000 27.57 0.00 45.94 3.77
2192 2414 1.160137 GAGAAGCTTCATGCACGGTT 58.840 50.000 27.57 3.93 45.94 4.44
2193 2415 1.016130 CGAGAAGCTTCATGCACGGT 61.016 55.000 27.57 4.70 45.94 4.83
2194 2416 1.699656 CCGAGAAGCTTCATGCACGG 61.700 60.000 27.57 24.81 45.94 4.94
2217 2439 2.613390 GAACGAAAGCAGGTTCCGT 58.387 52.632 0.00 0.00 37.23 4.69
2286 2516 2.892374 TGATGATGTACCAGCAGAACG 58.108 47.619 0.00 0.00 31.88 3.95
2287 2517 5.824904 AATTGATGATGTACCAGCAGAAC 57.175 39.130 0.00 0.00 31.88 3.01
2288 2518 5.822519 GGTAATTGATGATGTACCAGCAGAA 59.177 40.000 0.00 0.00 36.74 3.02
2299 2535 1.661178 GCGCGCAGGTAATTGATGATG 60.661 52.381 29.10 0.00 0.00 3.07
2359 2599 3.794971 AGTAGGAGTAGGGGATTGAGTCT 59.205 47.826 0.00 0.00 0.00 3.24
2360 2600 4.187506 AGTAGGAGTAGGGGATTGAGTC 57.812 50.000 0.00 0.00 0.00 3.36
2369 2611 3.970842 ACAGACTGAAGTAGGAGTAGGG 58.029 50.000 10.08 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.