Multiple sequence alignment - TraesCS3A01G368900

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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 TraesCS3A01G368900 chr3A 100.000 2231 0 0 1 2231 619102331 619100101 0.000000e+00 4120.0
1 TraesCS3A01G368900 chr3A 76.772 254 56 3 489 740 552704653 552704905 2.990000e-29 139.0
2 TraesCS3A01G368900 chr3D 89.144 654 67 3 755 1405 475890267 475889615 0.000000e+00 811.0
3 TraesCS3A01G368900 chr3D 90.566 530 28 7 1711 2219 475883269 475882741 0.000000e+00 682.0
4 TraesCS3A01G368900 chr3D 90.186 377 24 2 380 756 475890670 475890307 1.550000e-131 479.0
5 TraesCS3A01G368900 chr3D 86.957 184 15 4 1711 1891 475890848 475890671 4.860000e-47 198.0
6 TraesCS3A01G368900 chr3D 90.991 111 10 0 1401 1511 475884416 475884306 1.380000e-32 150.0
7 TraesCS3A01G368900 chr3D 94.643 56 3 0 139 194 475890910 475890855 1.100000e-13 87.9
8 TraesCS3A01G368900 chr3B 91.037 569 35 4 191 757 633380116 633379562 0.000000e+00 754.0
9 TraesCS3A01G368900 chr3B 87.615 654 67 8 1006 1648 633378174 633377524 0.000000e+00 747.0
10 TraesCS3A01G368900 chr3B 87.782 532 26 17 1711 2231 633377525 633377022 8.880000e-164 586.0
11 TraesCS3A01G368900 chr3B 85.430 302 32 8 1711 2001 633380152 633379852 1.000000e-78 303.0
12 TraesCS3A01G368900 chr3B 86.822 258 31 3 755 1010 633379523 633379267 3.630000e-73 285.0
13 TraesCS3A01G368900 chr3B 96.429 56 2 0 139 194 633380214 633380159 2.360000e-15 93.5
14 TraesCS3A01G368900 chr1A 76.296 540 116 8 784 1316 337777979 337777445 6.070000e-71 278.0
15 TraesCS3A01G368900 chr1A 75.881 539 120 6 784 1316 337808503 337807969 1.310000e-67 267.0
16 TraesCS3A01G368900 chr1A 79.283 251 49 3 492 740 368200059 368199810 2.950000e-39 172.0
17 TraesCS3A01G368900 chr1A 81.507 146 24 3 1178 1321 64709776 64709632 1.400000e-22 117.0
18 TraesCS3A01G368900 chr2B 75.605 537 125 5 784 1316 40266918 40267452 6.110000e-66 261.0
19 TraesCS3A01G368900 chr2B 75.279 538 125 7 784 1316 40212706 40213240 1.320000e-62 250.0
20 TraesCS3A01G368900 chr2B 75.279 538 125 7 784 1316 40235112 40235646 1.320000e-62 250.0
21 TraesCS3A01G368900 chr2B 77.866 253 52 3 492 741 474408130 474407879 1.070000e-33 154.0
22 TraesCS3A01G368900 chr5A 92.754 138 9 1 1 138 491529741 491529605 4.860000e-47 198.0
23 TraesCS3A01G368900 chr1D 91.304 138 12 0 1 138 461382802 461382939 2.920000e-44 189.0
24 TraesCS3A01G368900 chr1D 96.774 31 1 0 1534 1564 429703165 429703135 4.000000e-03 52.8
25 TraesCS3A01G368900 chr1B 79.336 271 52 4 490 757 31768822 31768553 1.050000e-43 187.0
26 TraesCS3A01G368900 chr1B 92.000 50 2 2 1280 1329 325453174 325453127 3.980000e-08 69.4
27 TraesCS3A01G368900 chr7D 89.855 138 14 0 1 138 529761622 529761485 6.330000e-41 178.0
28 TraesCS3A01G368900 chr5D 89.855 138 14 0 1 138 541571467 541571330 6.330000e-41 178.0
29 TraesCS3A01G368900 chr4A 78.906 256 47 6 489 740 100650553 100650301 1.370000e-37 167.0
30 TraesCS3A01G368900 chr7B 78.486 251 51 3 492 740 337119318 337119069 6.380000e-36 161.0
31 TraesCS3A01G368900 chr7B 78.088 251 52 3 492 740 654028491 654028740 2.970000e-34 156.0
32 TraesCS3A01G368900 chr2D 100.000 28 0 0 1533 1560 634144821 634144794 4.000000e-03 52.8


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 TraesCS3A01G368900 chr3A 619100101 619102331 2230 True 4120.000000 4120 100.000000 1 2231 1 chr3A.!!$R1 2230
1 TraesCS3A01G368900 chr3D 475882741 475884416 1675 True 416.000000 682 90.778500 1401 2219 2 chr3D.!!$R1 818
2 TraesCS3A01G368900 chr3D 475889615 475890910 1295 True 393.975000 811 90.232500 139 1891 4 chr3D.!!$R2 1752
3 TraesCS3A01G368900 chr3B 633377022 633380214 3192 True 461.416667 754 89.185833 139 2231 6 chr3B.!!$R1 2092
4 TraesCS3A01G368900 chr1A 337777445 337777979 534 True 278.000000 278 76.296000 784 1316 1 chr1A.!!$R2 532
5 TraesCS3A01G368900 chr1A 337807969 337808503 534 True 267.000000 267 75.881000 784 1316 1 chr1A.!!$R3 532
6 TraesCS3A01G368900 chr2B 40266918 40267452 534 False 261.000000 261 75.605000 784 1316 1 chr2B.!!$F3 532
7 TraesCS3A01G368900 chr2B 40212706 40213240 534 False 250.000000 250 75.279000 784 1316 1 chr2B.!!$F1 532
8 TraesCS3A01G368900 chr2B 40235112 40235646 534 False 250.000000 250 75.279000 784 1316 1 chr2B.!!$F2 532

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
96 97 0.038251 TCGCTGAACATCGACTTGCT 60.038 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 3813 0.107831 TCAACTGGTTTCCTCACCCG 59.892 55.0 0.0 0.0 35.73 5.28 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
19 20 0.833949 CAGAGAGGGGCCTAGTTTCC 59.166 60.000 0.84 0.00 0.00 3.13
20 21 0.719623 AGAGAGGGGCCTAGTTTCCT 59.280 55.000 0.84 0.00 0.00 3.36
21 22 1.938069 AGAGAGGGGCCTAGTTTCCTA 59.062 52.381 0.84 0.00 0.00 2.94
22 23 2.524875 AGAGAGGGGCCTAGTTTCCTAT 59.475 50.000 0.84 0.00 0.00 2.57
23 24 2.635427 GAGAGGGGCCTAGTTTCCTATG 59.365 54.545 0.84 0.00 0.00 2.23
24 25 2.250273 AGAGGGGCCTAGTTTCCTATGA 59.750 50.000 0.84 0.00 0.00 2.15
25 26 3.116159 AGAGGGGCCTAGTTTCCTATGAT 60.116 47.826 0.84 0.00 0.00 2.45
26 27 4.109765 AGAGGGGCCTAGTTTCCTATGATA 59.890 45.833 0.84 0.00 0.00 2.15
27 28 5.033522 GAGGGGCCTAGTTTCCTATGATAT 58.966 45.833 0.84 0.00 0.00 1.63
28 29 4.785376 AGGGGCCTAGTTTCCTATGATATG 59.215 45.833 0.84 0.00 0.00 1.78
29 30 4.536489 GGGGCCTAGTTTCCTATGATATGT 59.464 45.833 0.84 0.00 0.00 2.29
30 31 5.338463 GGGGCCTAGTTTCCTATGATATGTC 60.338 48.000 0.84 0.00 0.00 3.06
31 32 5.485708 GGGCCTAGTTTCCTATGATATGTCT 59.514 44.000 0.84 0.00 0.00 3.41
32 33 6.668283 GGGCCTAGTTTCCTATGATATGTCTA 59.332 42.308 0.84 0.00 0.00 2.59
33 34 7.180408 GGGCCTAGTTTCCTATGATATGTCTAA 59.820 40.741 0.84 0.00 0.00 2.10
34 35 8.763601 GGCCTAGTTTCCTATGATATGTCTAAT 58.236 37.037 0.00 0.00 0.00 1.73
35 36 9.810545 GCCTAGTTTCCTATGATATGTCTAATC 57.189 37.037 0.00 0.00 0.00 1.75
40 41 9.868277 GTTTCCTATGATATGTCTAATCTCAGG 57.132 37.037 0.00 0.00 0.00 3.86
41 42 9.828691 TTTCCTATGATATGTCTAATCTCAGGA 57.171 33.333 0.00 0.00 34.75 3.86
42 43 8.815565 TCCTATGATATGTCTAATCTCAGGAC 57.184 38.462 0.00 0.00 33.15 3.85
43 44 8.394040 TCCTATGATATGTCTAATCTCAGGACA 58.606 37.037 0.00 0.00 42.85 4.02
44 45 9.029368 CCTATGATATGTCTAATCTCAGGACAA 57.971 37.037 0.00 0.00 42.14 3.18
48 49 9.770097 TGATATGTCTAATCTCAGGACAATTTC 57.230 33.333 0.00 0.00 42.14 2.17
49 50 9.995003 GATATGTCTAATCTCAGGACAATTTCT 57.005 33.333 0.00 0.00 42.14 2.52
50 51 9.775854 ATATGTCTAATCTCAGGACAATTTCTG 57.224 33.333 0.00 0.00 42.14 3.02
51 52 7.244886 TGTCTAATCTCAGGACAATTTCTGA 57.755 36.000 0.00 0.00 37.10 3.27
52 53 7.679783 TGTCTAATCTCAGGACAATTTCTGAA 58.320 34.615 0.00 0.00 39.23 3.02
53 54 7.821359 TGTCTAATCTCAGGACAATTTCTGAAG 59.179 37.037 0.00 0.00 39.23 3.02
54 55 5.893897 AATCTCAGGACAATTTCTGAAGC 57.106 39.130 0.00 0.00 39.23 3.86
55 56 4.356405 TCTCAGGACAATTTCTGAAGCA 57.644 40.909 0.00 0.00 39.23 3.91
56 57 4.717877 TCTCAGGACAATTTCTGAAGCAA 58.282 39.130 0.00 0.00 39.23 3.91
57 58 4.758674 TCTCAGGACAATTTCTGAAGCAAG 59.241 41.667 0.00 0.00 39.23 4.01
58 59 3.822735 TCAGGACAATTTCTGAAGCAAGG 59.177 43.478 0.00 0.00 37.11 3.61
59 60 3.571401 CAGGACAATTTCTGAAGCAAGGT 59.429 43.478 0.00 0.00 33.11 3.50
60 61 3.571401 AGGACAATTTCTGAAGCAAGGTG 59.429 43.478 0.00 0.00 0.00 4.00
61 62 3.319122 GGACAATTTCTGAAGCAAGGTGT 59.681 43.478 0.00 0.00 0.00 4.16
62 63 4.518970 GGACAATTTCTGAAGCAAGGTGTA 59.481 41.667 0.00 0.00 0.00 2.90
63 64 5.335191 GGACAATTTCTGAAGCAAGGTGTAG 60.335 44.000 0.00 0.00 0.00 2.74
64 65 4.022849 ACAATTTCTGAAGCAAGGTGTAGC 60.023 41.667 0.00 0.00 0.00 3.58
65 66 3.492102 TTTCTGAAGCAAGGTGTAGCT 57.508 42.857 0.00 0.00 44.31 3.32
66 67 2.462456 TCTGAAGCAAGGTGTAGCTG 57.538 50.000 0.00 0.00 41.70 4.24
67 68 1.970640 TCTGAAGCAAGGTGTAGCTGA 59.029 47.619 0.00 0.00 41.70 4.26
68 69 2.368548 TCTGAAGCAAGGTGTAGCTGAA 59.631 45.455 0.00 0.00 41.70 3.02
69 70 2.740981 CTGAAGCAAGGTGTAGCTGAAG 59.259 50.000 0.00 0.00 41.70 3.02
70 71 2.079925 GAAGCAAGGTGTAGCTGAAGG 58.920 52.381 0.00 0.00 41.70 3.46
71 72 0.322008 AGCAAGGTGTAGCTGAAGGC 60.322 55.000 0.00 0.00 40.13 4.35
90 91 3.691965 CGCATCGCTGAACATCGA 58.308 55.556 3.42 3.42 39.17 3.59
91 92 1.270968 CGCATCGCTGAACATCGAC 59.729 57.895 3.02 0.00 37.55 4.20
92 93 1.142185 CGCATCGCTGAACATCGACT 61.142 55.000 3.02 0.00 37.55 4.18
93 94 1.002366 GCATCGCTGAACATCGACTT 58.998 50.000 3.02 0.00 37.55 3.01
94 95 1.267235 GCATCGCTGAACATCGACTTG 60.267 52.381 3.02 1.13 37.55 3.16
95 96 1.002366 ATCGCTGAACATCGACTTGC 58.998 50.000 3.02 0.00 37.55 4.01
96 97 0.038251 TCGCTGAACATCGACTTGCT 60.038 50.000 0.00 0.00 0.00 3.91
97 98 0.368227 CGCTGAACATCGACTTGCTC 59.632 55.000 0.00 0.00 0.00 4.26
98 99 0.723981 GCTGAACATCGACTTGCTCC 59.276 55.000 0.00 0.00 0.00 4.70
99 100 1.941209 GCTGAACATCGACTTGCTCCA 60.941 52.381 0.00 0.00 0.00 3.86
100 101 2.416747 CTGAACATCGACTTGCTCCAA 58.583 47.619 0.00 0.00 0.00 3.53
101 102 2.807967 CTGAACATCGACTTGCTCCAAA 59.192 45.455 0.00 0.00 0.00 3.28
102 103 3.411446 TGAACATCGACTTGCTCCAAAT 58.589 40.909 0.00 0.00 0.00 2.32
103 104 3.436704 TGAACATCGACTTGCTCCAAATC 59.563 43.478 0.00 0.00 0.00 2.17
104 105 3.340814 ACATCGACTTGCTCCAAATCT 57.659 42.857 0.00 0.00 0.00 2.40
105 106 3.679389 ACATCGACTTGCTCCAAATCTT 58.321 40.909 0.00 0.00 0.00 2.40
106 107 3.686726 ACATCGACTTGCTCCAAATCTTC 59.313 43.478 0.00 0.00 0.00 2.87
107 108 3.401033 TCGACTTGCTCCAAATCTTCA 57.599 42.857 0.00 0.00 0.00 3.02
108 109 3.738982 TCGACTTGCTCCAAATCTTCAA 58.261 40.909 0.00 0.00 0.00 2.69
109 110 4.133820 TCGACTTGCTCCAAATCTTCAAA 58.866 39.130 0.00 0.00 0.00 2.69
110 111 4.761739 TCGACTTGCTCCAAATCTTCAAAT 59.238 37.500 0.00 0.00 0.00 2.32
111 112 5.091431 CGACTTGCTCCAAATCTTCAAATC 58.909 41.667 0.00 0.00 0.00 2.17
112 113 5.397142 ACTTGCTCCAAATCTTCAAATCC 57.603 39.130 0.00 0.00 0.00 3.01
113 114 5.082425 ACTTGCTCCAAATCTTCAAATCCT 58.918 37.500 0.00 0.00 0.00 3.24
114 115 5.541484 ACTTGCTCCAAATCTTCAAATCCTT 59.459 36.000 0.00 0.00 0.00 3.36
115 116 6.721208 ACTTGCTCCAAATCTTCAAATCCTTA 59.279 34.615 0.00 0.00 0.00 2.69
116 117 6.764308 TGCTCCAAATCTTCAAATCCTTAG 57.236 37.500 0.00 0.00 0.00 2.18
117 118 5.126061 TGCTCCAAATCTTCAAATCCTTAGC 59.874 40.000 0.00 0.00 0.00 3.09
118 119 5.451103 GCTCCAAATCTTCAAATCCTTAGCC 60.451 44.000 0.00 0.00 0.00 3.93
119 120 5.579047 TCCAAATCTTCAAATCCTTAGCCA 58.421 37.500 0.00 0.00 0.00 4.75
120 121 5.418840 TCCAAATCTTCAAATCCTTAGCCAC 59.581 40.000 0.00 0.00 0.00 5.01
121 122 5.420104 CCAAATCTTCAAATCCTTAGCCACT 59.580 40.000 0.00 0.00 0.00 4.00
122 123 6.405176 CCAAATCTTCAAATCCTTAGCCACTC 60.405 42.308 0.00 0.00 0.00 3.51
123 124 3.861840 TCTTCAAATCCTTAGCCACTCG 58.138 45.455 0.00 0.00 0.00 4.18
124 125 3.513912 TCTTCAAATCCTTAGCCACTCGA 59.486 43.478 0.00 0.00 0.00 4.04
125 126 3.526931 TCAAATCCTTAGCCACTCGAG 57.473 47.619 11.84 11.84 0.00 4.04
126 127 2.832129 TCAAATCCTTAGCCACTCGAGT 59.168 45.455 13.58 13.58 0.00 4.18
127 128 3.119101 TCAAATCCTTAGCCACTCGAGTC 60.119 47.826 16.96 5.52 0.00 3.36
128 129 2.145397 ATCCTTAGCCACTCGAGTCA 57.855 50.000 16.96 0.00 0.00 3.41
129 130 2.145397 TCCTTAGCCACTCGAGTCAT 57.855 50.000 16.96 7.02 0.00 3.06
130 131 2.025155 TCCTTAGCCACTCGAGTCATC 58.975 52.381 16.96 7.60 0.00 2.92
131 132 2.028130 CCTTAGCCACTCGAGTCATCT 58.972 52.381 16.96 14.61 0.00 2.90
132 133 2.428890 CCTTAGCCACTCGAGTCATCTT 59.571 50.000 16.96 2.53 0.00 2.40
133 134 3.632604 CCTTAGCCACTCGAGTCATCTTA 59.367 47.826 16.96 6.00 0.00 2.10
134 135 4.261405 CCTTAGCCACTCGAGTCATCTTAG 60.261 50.000 16.96 14.46 0.00 2.18
135 136 2.729194 AGCCACTCGAGTCATCTTAGT 58.271 47.619 16.96 0.00 0.00 2.24
136 137 2.425312 AGCCACTCGAGTCATCTTAGTG 59.575 50.000 16.96 1.56 37.54 2.74
137 138 2.164624 GCCACTCGAGTCATCTTAGTGT 59.835 50.000 16.96 0.00 36.81 3.55
171 172 3.440023 TCCCCACTCCGAGGAGAT 58.560 61.111 24.53 7.21 44.53 2.75
183 184 3.004839 TCCGAGGAGATAAGAAGAATGCG 59.995 47.826 0.00 0.00 0.00 4.73
221 268 7.280356 AGAAAGAAAGCCACTAAAGTCAACTA 58.720 34.615 0.00 0.00 0.00 2.24
239 286 1.207329 CTACCAAAAGCCGTCCTAGCT 59.793 52.381 0.00 0.00 44.19 3.32
349 398 7.259882 ACATTGCACCAATATCACAAACTATG 58.740 34.615 0.00 0.00 32.35 2.23
364 413 3.611766 ACTATGTTAACCTCGCTTGCT 57.388 42.857 2.48 0.00 0.00 3.91
365 414 4.730949 ACTATGTTAACCTCGCTTGCTA 57.269 40.909 2.48 0.00 0.00 3.49
369 418 1.206371 GTTAACCTCGCTTGCTAGGGA 59.794 52.381 15.95 13.79 40.65 4.20
377 426 3.332034 TCGCTTGCTAGGGAAAACTTAC 58.668 45.455 12.27 0.00 40.05 2.34
427 476 5.612725 AGCAAAGGAGAAAATGGTTGAAA 57.387 34.783 0.00 0.00 0.00 2.69
519 568 1.376942 CTTGGCTGCAGGGTCTCAG 60.377 63.158 17.12 0.00 0.00 3.35
628 677 6.766467 GGATAACTCAAATCGATACCCAAAGT 59.234 38.462 0.00 0.00 0.00 2.66
630 679 4.906618 ACTCAAATCGATACCCAAAGTGT 58.093 39.130 0.00 0.00 0.00 3.55
670 719 2.436646 CAATTCGCGGCCCTCTGT 60.437 61.111 6.13 0.00 0.00 3.41
701 750 1.377366 GAGCGTCCTCATCCAGTCGA 61.377 60.000 0.00 0.00 38.03 4.20
714 763 1.338337 CCAGTCGAGCGTCAAGGATAT 59.662 52.381 0.00 0.00 0.00 1.63
745 794 0.517316 AGCTCGCAACGATGAAAACC 59.483 50.000 0.00 0.00 34.61 3.27
811 901 3.689347 TGCATGGCTAGTCACTCAAAAT 58.311 40.909 0.00 0.00 0.00 1.82
997 1088 1.128692 CGACTCTTTGGCATCGGTTTC 59.871 52.381 0.00 0.00 0.00 2.78
998 1089 2.151202 GACTCTTTGGCATCGGTTTCA 58.849 47.619 0.00 0.00 0.00 2.69
1054 2242 2.694628 AGCAATGCTCAACCAGTGAAAA 59.305 40.909 0.00 0.00 35.22 2.29
1056 2244 3.737663 GCAATGCTCAACCAGTGAAAACA 60.738 43.478 0.00 0.00 35.22 2.83
1097 2285 1.284785 TGTGGGATGGGAAATCTGGAC 59.715 52.381 0.00 0.00 0.00 4.02
1103 2291 3.555966 GATGGGAAATCTGGACGGAAAT 58.444 45.455 0.00 0.00 0.00 2.17
1121 2309 4.505922 GGAAATGAATGCACACGTTTTCAA 59.494 37.500 11.62 0.00 32.35 2.69
1130 2321 2.097466 CACACGTTTTCAAGAGCAAGGT 59.903 45.455 0.00 0.00 0.00 3.50
1205 2396 2.097466 CCATTGCGGGTGACAAGTATTC 59.903 50.000 0.00 0.00 0.00 1.75
1206 2397 2.552599 TTGCGGGTGACAAGTATTCA 57.447 45.000 0.00 0.00 0.00 2.57
1266 2459 2.554272 GTTTGGCGGCGTGTGTAG 59.446 61.111 9.37 0.00 0.00 2.74
1284 2477 7.078228 GTGTGTAGCAAAACTCCATTCTTAAG 58.922 38.462 0.00 0.00 0.00 1.85
1323 2516 8.829612 CAAGTCTTTTGCCTTGTTTCATAATTT 58.170 29.630 0.00 0.00 34.67 1.82
1367 2560 9.525409 GCGACTTATCCTTATTTCAAGTAGTTA 57.475 33.333 0.00 0.00 29.89 2.24
1427 2620 9.026074 GTTCGAGAAGTCTCCTAATTAATGAAG 57.974 37.037 2.75 0.00 39.79 3.02
1445 2638 7.440523 AATGAAGGAAGACAATAGTTGTGTC 57.559 36.000 0.00 0.00 45.52 3.67
1579 3691 5.999044 ACTATCCAATTCATGAGAGCAGTT 58.001 37.500 0.00 0.00 0.00 3.16
1582 3694 6.939132 ATCCAATTCATGAGAGCAGTTTAG 57.061 37.500 0.00 0.00 0.00 1.85
1605 3717 2.356793 GGCGGGCGAGATCATCTG 60.357 66.667 0.00 0.00 0.00 2.90
1616 3728 1.489230 AGATCATCTGCATGCTCACCA 59.511 47.619 20.33 0.13 28.88 4.17
1621 3733 1.748122 CTGCATGCTCACCACTCCC 60.748 63.158 20.33 0.00 0.00 4.30
1624 3736 1.985614 CATGCTCACCACTCCCAGA 59.014 57.895 0.00 0.00 0.00 3.86
1640 3752 5.191727 TCCCAGAGGATAAAAAGAATGCA 57.808 39.130 0.00 0.00 37.19 3.96
1648 3760 9.914131 AGAGGATAAAAAGAATGCAACTAAAAC 57.086 29.630 0.00 0.00 0.00 2.43
1655 3767 8.831715 AAAAGAATGCAACTAAAACCATTAGG 57.168 30.769 0.00 0.00 42.21 2.69
1662 3774 6.156519 GCAACTAAAACCATTAGGAAACCAG 58.843 40.000 0.84 0.00 38.69 4.00
1665 3777 7.907841 ACTAAAACCATTAGGAAACCAGTTT 57.092 32.000 0.00 0.00 38.69 2.66
1666 3778 8.313944 ACTAAAACCATTAGGAAACCAGTTTT 57.686 30.769 0.00 0.00 38.86 2.43
1667 3779 8.764558 ACTAAAACCATTAGGAAACCAGTTTTT 58.235 29.630 0.00 0.00 37.23 1.94
1687 3799 3.945981 TTTTGCGGGGAATTAGGAAAC 57.054 42.857 0.00 0.00 0.00 2.78
1688 3800 1.842052 TTGCGGGGAATTAGGAAACC 58.158 50.000 0.00 0.00 0.00 3.27
1689 3801 0.699399 TGCGGGGAATTAGGAAACCA 59.301 50.000 0.00 0.00 0.00 3.67
1690 3802 1.340600 TGCGGGGAATTAGGAAACCAG 60.341 52.381 0.00 0.00 0.00 4.00
1691 3803 1.340697 GCGGGGAATTAGGAAACCAGT 60.341 52.381 0.00 0.00 0.00 4.00
1692 3804 2.882643 GCGGGGAATTAGGAAACCAGTT 60.883 50.000 0.00 0.00 0.00 3.16
1693 3805 3.427573 CGGGGAATTAGGAAACCAGTTT 58.572 45.455 0.00 0.00 35.14 2.66
1694 3806 3.830178 CGGGGAATTAGGAAACCAGTTTT 59.170 43.478 0.00 0.00 32.11 2.43
1695 3807 4.282449 CGGGGAATTAGGAAACCAGTTTTT 59.718 41.667 0.00 0.00 32.11 1.94
1714 3826 0.747852 TTTTTGCGGGTGAGGAAACC 59.252 50.000 0.00 0.00 39.71 3.27
1715 3827 0.395862 TTTTGCGGGTGAGGAAACCA 60.396 50.000 0.00 0.00 42.47 3.67
1716 3828 0.821711 TTTGCGGGTGAGGAAACCAG 60.822 55.000 0.00 0.00 42.47 4.00
1717 3829 1.990160 TTGCGGGTGAGGAAACCAGT 61.990 55.000 0.00 0.00 42.47 4.00
1718 3830 1.228154 GCGGGTGAGGAAACCAGTT 60.228 57.895 0.00 0.00 42.47 3.16
1719 3831 1.515521 GCGGGTGAGGAAACCAGTTG 61.516 60.000 0.00 0.00 42.47 3.16
1720 3832 0.107831 CGGGTGAGGAAACCAGTTGA 59.892 55.000 0.00 0.00 42.47 3.18
1721 3833 1.605753 GGGTGAGGAAACCAGTTGAC 58.394 55.000 0.00 0.00 42.47 3.18
1722 3834 1.605753 GGTGAGGAAACCAGTTGACC 58.394 55.000 0.00 0.00 40.22 4.02
1760 3878 6.144563 GTGCTCAATAACCAAAGAAAGAAAGC 59.855 38.462 0.00 0.00 0.00 3.51
1772 3890 5.254339 AGAAAGAAAGCCACAAAAGTCAG 57.746 39.130 0.00 0.00 0.00 3.51
1774 3892 1.683385 AGAAAGCCACAAAAGTCAGCC 59.317 47.619 0.00 0.00 0.00 4.85
1775 3893 1.408702 GAAAGCCACAAAAGTCAGCCA 59.591 47.619 0.00 0.00 0.00 4.75
1789 3907 4.699522 GCCACCGAAAGCCGTCCT 62.700 66.667 0.00 0.00 36.31 3.85
1791 3909 1.153628 CCACCGAAAGCCGTCCTAG 60.154 63.158 0.00 0.00 36.31 3.02
1798 3916 1.068127 GAAAGCCGTCCTAGCCGAATA 59.932 52.381 2.01 0.00 0.00 1.75
1839 3958 3.898482 AGCAAGTACATGGTAAATCCCC 58.102 45.455 0.09 0.00 34.77 4.81
1844 3963 4.266714 AGTACATGGTAAATCCCCAAACG 58.733 43.478 0.00 0.00 35.14 3.60
1857 3976 1.524776 CCCAAACGAAAAACAATGGCG 59.475 47.619 0.00 0.00 0.00 5.69
1860 3979 0.598942 AACGAAAAACAATGGCGGCC 60.599 50.000 13.32 13.32 0.00 6.13
1898 4017 5.189928 TGCCGACCAATATCACAAACTATT 58.810 37.500 0.00 0.00 0.00 1.73
1918 4044 0.738412 TTAACGTCGCTTGCTAGGGC 60.738 55.000 7.35 2.60 34.50 5.19
1932 4058 4.917385 TGCTAGGGCAAAATTAGTCTTCA 58.083 39.130 0.00 0.00 46.36 3.02
1967 4096 2.997485 ACGCAAGCAAAGGAGAAATC 57.003 45.000 0.00 0.00 45.62 2.17
1987 4117 6.496338 AATCGATGAAGTTTCCCACTAAAC 57.504 37.500 0.00 0.00 39.22 2.01
1997 4127 6.885922 AGTTTCCCACTAAACTAAGCGATAT 58.114 36.000 0.32 0.00 45.53 1.63
1998 4128 8.015185 AGTTTCCCACTAAACTAAGCGATATA 57.985 34.615 0.32 0.00 45.53 0.86
1999 4129 8.648693 AGTTTCCCACTAAACTAAGCGATATAT 58.351 33.333 0.32 0.00 45.53 0.86
2116 4250 1.800315 CGCGTTCCACGAGGTACAG 60.800 63.158 9.16 3.51 46.05 2.74
2117 4251 2.092882 GCGTTCCACGAGGTACAGC 61.093 63.158 9.16 8.94 46.05 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.833949 GGAAACTAGGCCCCTCTCTG 59.166 60.000 0.00 0.00 0.00 3.35
1 2 0.719623 AGGAAACTAGGCCCCTCTCT 59.280 55.000 0.00 0.00 40.61 3.10
2 3 2.473576 TAGGAAACTAGGCCCCTCTC 57.526 55.000 0.00 0.00 43.67 3.20
14 15 9.868277 CCTGAGATTAGACATATCATAGGAAAC 57.132 37.037 0.00 0.00 33.08 2.78
15 16 9.828691 TCCTGAGATTAGACATATCATAGGAAA 57.171 33.333 0.00 0.00 35.40 3.13
16 17 9.249053 GTCCTGAGATTAGACATATCATAGGAA 57.751 37.037 0.00 0.00 37.75 3.36
17 18 8.394040 TGTCCTGAGATTAGACATATCATAGGA 58.606 37.037 0.00 0.00 35.67 2.94
18 19 8.586879 TGTCCTGAGATTAGACATATCATAGG 57.413 38.462 0.00 0.00 35.67 2.57
22 23 9.770097 GAAATTGTCCTGAGATTAGACATATCA 57.230 33.333 0.00 0.00 40.06 2.15
23 24 9.995003 AGAAATTGTCCTGAGATTAGACATATC 57.005 33.333 0.00 0.00 40.06 1.63
24 25 9.775854 CAGAAATTGTCCTGAGATTAGACATAT 57.224 33.333 0.00 0.00 40.06 1.78
25 26 8.981659 TCAGAAATTGTCCTGAGATTAGACATA 58.018 33.333 0.00 0.00 40.06 2.29
26 27 7.855375 TCAGAAATTGTCCTGAGATTAGACAT 58.145 34.615 0.00 0.00 40.06 3.06
27 28 7.244886 TCAGAAATTGTCCTGAGATTAGACA 57.755 36.000 0.00 0.00 38.70 3.41
28 29 7.201600 GCTTCAGAAATTGTCCTGAGATTAGAC 60.202 40.741 0.00 0.00 40.13 2.59
29 30 6.820656 GCTTCAGAAATTGTCCTGAGATTAGA 59.179 38.462 0.00 0.00 40.13 2.10
30 31 6.596888 TGCTTCAGAAATTGTCCTGAGATTAG 59.403 38.462 0.00 0.00 40.13 1.73
31 32 6.475504 TGCTTCAGAAATTGTCCTGAGATTA 58.524 36.000 0.00 0.00 40.13 1.75
32 33 5.319453 TGCTTCAGAAATTGTCCTGAGATT 58.681 37.500 0.00 0.00 40.13 2.40
33 34 4.914983 TGCTTCAGAAATTGTCCTGAGAT 58.085 39.130 0.00 0.00 40.13 2.75
34 35 4.356405 TGCTTCAGAAATTGTCCTGAGA 57.644 40.909 0.00 0.00 40.13 3.27
35 36 4.082895 CCTTGCTTCAGAAATTGTCCTGAG 60.083 45.833 0.00 0.00 40.13 3.35
36 37 3.822735 CCTTGCTTCAGAAATTGTCCTGA 59.177 43.478 0.00 0.00 37.61 3.86
37 38 3.571401 ACCTTGCTTCAGAAATTGTCCTG 59.429 43.478 0.00 0.00 0.00 3.86
38 39 3.571401 CACCTTGCTTCAGAAATTGTCCT 59.429 43.478 0.00 0.00 0.00 3.85
39 40 3.319122 ACACCTTGCTTCAGAAATTGTCC 59.681 43.478 0.00 0.00 0.00 4.02
40 41 4.574599 ACACCTTGCTTCAGAAATTGTC 57.425 40.909 0.00 0.00 0.00 3.18
41 42 4.022849 GCTACACCTTGCTTCAGAAATTGT 60.023 41.667 0.00 0.00 0.00 2.71
42 43 4.217118 AGCTACACCTTGCTTCAGAAATTG 59.783 41.667 0.00 0.00 35.86 2.32
43 44 4.217118 CAGCTACACCTTGCTTCAGAAATT 59.783 41.667 0.00 0.00 37.44 1.82
44 45 3.755378 CAGCTACACCTTGCTTCAGAAAT 59.245 43.478 0.00 0.00 37.44 2.17
45 46 3.141398 CAGCTACACCTTGCTTCAGAAA 58.859 45.455 0.00 0.00 37.44 2.52
46 47 2.368548 TCAGCTACACCTTGCTTCAGAA 59.631 45.455 0.00 0.00 37.44 3.02
47 48 1.970640 TCAGCTACACCTTGCTTCAGA 59.029 47.619 0.00 0.00 37.44 3.27
48 49 2.462456 TCAGCTACACCTTGCTTCAG 57.538 50.000 0.00 0.00 37.44 3.02
49 50 2.550855 CCTTCAGCTACACCTTGCTTCA 60.551 50.000 0.00 0.00 37.44 3.02
50 51 2.079925 CCTTCAGCTACACCTTGCTTC 58.920 52.381 0.00 0.00 37.44 3.86
51 52 1.884067 GCCTTCAGCTACACCTTGCTT 60.884 52.381 0.00 0.00 37.44 3.91
52 53 0.322008 GCCTTCAGCTACACCTTGCT 60.322 55.000 0.00 0.00 40.54 3.91
53 54 1.639298 CGCCTTCAGCTACACCTTGC 61.639 60.000 0.00 0.00 40.39 4.01
54 55 1.639298 GCGCCTTCAGCTACACCTTG 61.639 60.000 0.00 0.00 40.39 3.61
55 56 1.376037 GCGCCTTCAGCTACACCTT 60.376 57.895 0.00 0.00 40.39 3.50
56 57 2.266055 GCGCCTTCAGCTACACCT 59.734 61.111 0.00 0.00 40.39 4.00
57 58 3.188786 CGCGCCTTCAGCTACACC 61.189 66.667 0.00 0.00 40.39 4.16
58 59 3.854459 GCGCGCCTTCAGCTACAC 61.854 66.667 23.24 0.00 40.39 2.90
59 60 3.664025 ATGCGCGCCTTCAGCTACA 62.664 57.895 30.77 5.62 40.39 2.74
60 61 2.875786 GATGCGCGCCTTCAGCTAC 61.876 63.158 30.77 0.26 40.39 3.58
61 62 2.586079 GATGCGCGCCTTCAGCTA 60.586 61.111 30.77 7.41 40.39 3.32
73 74 1.142185 AGTCGATGTTCAGCGATGCG 61.142 55.000 15.61 0.00 38.91 4.73
74 75 1.002366 AAGTCGATGTTCAGCGATGC 58.998 50.000 15.61 4.93 38.91 3.91
75 76 1.267235 GCAAGTCGATGTTCAGCGATG 60.267 52.381 15.61 11.89 38.91 3.84
76 77 1.002366 GCAAGTCGATGTTCAGCGAT 58.998 50.000 15.61 0.00 38.91 4.58
77 78 0.038251 AGCAAGTCGATGTTCAGCGA 60.038 50.000 9.03 9.03 0.00 4.93
78 79 0.368227 GAGCAAGTCGATGTTCAGCG 59.632 55.000 4.04 4.04 31.60 5.18
79 80 0.723981 GGAGCAAGTCGATGTTCAGC 59.276 55.000 5.42 0.00 32.76 4.26
80 81 2.084610 TGGAGCAAGTCGATGTTCAG 57.915 50.000 5.42 0.00 32.76 3.02
81 82 2.542020 TTGGAGCAAGTCGATGTTCA 57.458 45.000 5.42 0.00 32.76 3.18
82 83 3.686726 AGATTTGGAGCAAGTCGATGTTC 59.313 43.478 0.00 0.00 35.67 3.18
83 84 3.679389 AGATTTGGAGCAAGTCGATGTT 58.321 40.909 0.00 0.00 35.67 2.71
84 85 3.340814 AGATTTGGAGCAAGTCGATGT 57.659 42.857 0.00 0.00 35.67 3.06
85 86 3.686241 TGAAGATTTGGAGCAAGTCGATG 59.314 43.478 0.00 0.00 35.67 3.84
86 87 3.942829 TGAAGATTTGGAGCAAGTCGAT 58.057 40.909 0.00 0.00 35.67 3.59
87 88 3.401033 TGAAGATTTGGAGCAAGTCGA 57.599 42.857 0.00 0.00 35.67 4.20
88 89 4.488126 TTTGAAGATTTGGAGCAAGTCG 57.512 40.909 0.00 0.00 35.67 4.18
89 90 5.184671 AGGATTTGAAGATTTGGAGCAAGTC 59.815 40.000 0.00 0.00 31.63 3.01
90 91 5.082425 AGGATTTGAAGATTTGGAGCAAGT 58.918 37.500 0.00 0.00 0.00 3.16
91 92 5.656213 AGGATTTGAAGATTTGGAGCAAG 57.344 39.130 0.00 0.00 0.00 4.01
92 93 6.350445 GCTAAGGATTTGAAGATTTGGAGCAA 60.350 38.462 0.00 0.00 0.00 3.91
93 94 5.126061 GCTAAGGATTTGAAGATTTGGAGCA 59.874 40.000 0.00 0.00 0.00 4.26
94 95 5.451103 GGCTAAGGATTTGAAGATTTGGAGC 60.451 44.000 0.00 0.00 0.00 4.70
95 96 5.653769 TGGCTAAGGATTTGAAGATTTGGAG 59.346 40.000 0.00 0.00 0.00 3.86
96 97 5.418840 GTGGCTAAGGATTTGAAGATTTGGA 59.581 40.000 0.00 0.00 0.00 3.53
97 98 5.420104 AGTGGCTAAGGATTTGAAGATTTGG 59.580 40.000 0.00 0.00 0.00 3.28
98 99 6.521151 AGTGGCTAAGGATTTGAAGATTTG 57.479 37.500 0.00 0.00 0.00 2.32
99 100 5.355350 CGAGTGGCTAAGGATTTGAAGATTT 59.645 40.000 0.00 0.00 0.00 2.17
100 101 4.878397 CGAGTGGCTAAGGATTTGAAGATT 59.122 41.667 0.00 0.00 0.00 2.40
101 102 4.162320 TCGAGTGGCTAAGGATTTGAAGAT 59.838 41.667 0.00 0.00 0.00 2.40
102 103 3.513912 TCGAGTGGCTAAGGATTTGAAGA 59.486 43.478 0.00 0.00 0.00 2.87
103 104 3.861840 TCGAGTGGCTAAGGATTTGAAG 58.138 45.455 0.00 0.00 0.00 3.02
104 105 3.260884 ACTCGAGTGGCTAAGGATTTGAA 59.739 43.478 19.30 0.00 0.00 2.69
105 106 2.832129 ACTCGAGTGGCTAAGGATTTGA 59.168 45.455 19.30 0.00 0.00 2.69
106 107 3.190874 GACTCGAGTGGCTAAGGATTTG 58.809 50.000 25.58 0.00 0.00 2.32
107 108 2.832129 TGACTCGAGTGGCTAAGGATTT 59.168 45.455 25.58 0.00 0.00 2.17
108 109 2.457598 TGACTCGAGTGGCTAAGGATT 58.542 47.619 25.58 0.00 0.00 3.01
109 110 2.145397 TGACTCGAGTGGCTAAGGAT 57.855 50.000 25.58 0.00 0.00 3.24
110 111 2.025155 GATGACTCGAGTGGCTAAGGA 58.975 52.381 25.58 0.00 0.00 3.36
111 112 2.028130 AGATGACTCGAGTGGCTAAGG 58.972 52.381 25.58 0.00 0.00 2.69
112 113 3.791973 AAGATGACTCGAGTGGCTAAG 57.208 47.619 25.58 0.00 0.00 2.18
113 114 4.096532 CACTAAGATGACTCGAGTGGCTAA 59.903 45.833 25.58 3.31 36.85 3.09
114 115 3.628032 CACTAAGATGACTCGAGTGGCTA 59.372 47.826 25.58 6.84 36.85 3.93
115 116 2.425312 CACTAAGATGACTCGAGTGGCT 59.575 50.000 25.58 13.89 36.85 4.75
116 117 2.164624 ACACTAAGATGACTCGAGTGGC 59.835 50.000 25.58 10.31 40.88 5.01
117 118 3.440522 TCACACTAAGATGACTCGAGTGG 59.559 47.826 25.58 0.99 40.88 4.00
118 119 4.393371 TCTCACACTAAGATGACTCGAGTG 59.607 45.833 25.58 9.14 41.60 3.51
119 120 4.580868 TCTCACACTAAGATGACTCGAGT 58.419 43.478 20.18 20.18 0.00 4.18
120 121 5.295540 TGATCTCACACTAAGATGACTCGAG 59.704 44.000 11.84 11.84 33.64 4.04
121 122 5.186198 TGATCTCACACTAAGATGACTCGA 58.814 41.667 0.00 0.00 33.64 4.04
122 123 5.491635 TGATCTCACACTAAGATGACTCG 57.508 43.478 0.00 0.00 33.64 4.18
123 124 7.254387 GCAAATGATCTCACACTAAGATGACTC 60.254 40.741 0.00 0.00 33.64 3.36
124 125 6.538021 GCAAATGATCTCACACTAAGATGACT 59.462 38.462 0.00 0.00 33.64 3.41
125 126 6.314648 TGCAAATGATCTCACACTAAGATGAC 59.685 38.462 0.00 0.00 33.64 3.06
126 127 6.408869 TGCAAATGATCTCACACTAAGATGA 58.591 36.000 0.00 0.00 33.64 2.92
127 128 6.673154 TGCAAATGATCTCACACTAAGATG 57.327 37.500 0.00 0.00 33.64 2.90
128 129 6.238676 GCATGCAAATGATCTCACACTAAGAT 60.239 38.462 14.21 0.00 36.19 2.40
129 130 5.065602 GCATGCAAATGATCTCACACTAAGA 59.934 40.000 14.21 0.00 0.00 2.10
130 131 5.066117 AGCATGCAAATGATCTCACACTAAG 59.934 40.000 21.98 0.00 0.00 2.18
131 132 4.945543 AGCATGCAAATGATCTCACACTAA 59.054 37.500 21.98 0.00 0.00 2.24
132 133 4.520179 AGCATGCAAATGATCTCACACTA 58.480 39.130 21.98 0.00 0.00 2.74
133 134 3.353557 AGCATGCAAATGATCTCACACT 58.646 40.909 21.98 0.00 0.00 3.55
134 135 3.488721 GGAGCATGCAAATGATCTCACAC 60.489 47.826 21.98 0.00 37.16 3.82
135 136 2.686405 GGAGCATGCAAATGATCTCACA 59.314 45.455 21.98 0.00 37.16 3.58
136 137 2.034305 GGGAGCATGCAAATGATCTCAC 59.966 50.000 21.98 2.80 37.39 3.51
137 138 2.304092 GGGAGCATGCAAATGATCTCA 58.696 47.619 21.98 0.00 37.39 3.27
171 172 8.780846 TTTGGTTTATAGTCGCATTCTTCTTA 57.219 30.769 0.00 0.00 0.00 2.10
183 184 7.808381 GTGGCTTTCTTTCTTTGGTTTATAGTC 59.192 37.037 0.00 0.00 0.00 2.59
221 268 0.321653 CAGCTAGGACGGCTTTTGGT 60.322 55.000 0.00 0.00 38.03 3.67
239 286 5.333299 CATTGAAATGCTTCCTGGATTCA 57.667 39.130 0.00 1.03 35.62 2.57
266 313 7.924947 GGGGAGTTACATTGTATGTAGTACTTC 59.075 40.741 0.00 0.00 45.58 3.01
349 398 1.206371 TCCCTAGCAAGCGAGGTTAAC 59.794 52.381 17.97 0.00 37.16 2.01
364 413 5.286760 AGGAGGAGAGTAAGTTTTCCCTA 57.713 43.478 0.00 0.00 0.00 3.53
365 414 4.149090 AGGAGGAGAGTAAGTTTTCCCT 57.851 45.455 0.00 0.00 0.00 4.20
377 426 7.575343 GCGTAGGTAAATTATGTAGGAGGAGAG 60.575 44.444 0.00 0.00 0.00 3.20
457 506 9.971922 GCCTTAAAAGATGTTGCTATTATCATT 57.028 29.630 0.00 0.00 0.00 2.57
458 507 9.135189 TGCCTTAAAAGATGTTGCTATTATCAT 57.865 29.630 0.00 0.00 0.00 2.45
459 508 8.518430 TGCCTTAAAAGATGTTGCTATTATCA 57.482 30.769 0.00 0.00 0.00 2.15
460 509 9.801873 TTTGCCTTAAAAGATGTTGCTATTATC 57.198 29.630 0.00 0.00 0.00 1.75
463 512 9.506018 AATTTTGCCTTAAAAGATGTTGCTATT 57.494 25.926 0.00 0.00 41.26 1.73
464 513 9.506018 AAATTTTGCCTTAAAAGATGTTGCTAT 57.494 25.926 0.00 0.00 41.26 2.97
465 514 8.900983 AAATTTTGCCTTAAAAGATGTTGCTA 57.099 26.923 0.00 0.00 41.26 3.49
466 515 7.806409 AAATTTTGCCTTAAAAGATGTTGCT 57.194 28.000 0.00 0.00 41.26 3.91
519 568 1.909700 TGGAGCAATGTCTTTGGGTC 58.090 50.000 1.08 0.00 35.75 4.46
628 677 1.300931 GTGCTCAAGCGTCAGGACA 60.301 57.895 0.00 0.00 45.83 4.02
630 679 1.758440 AAGGTGCTCAAGCGTCAGGA 61.758 55.000 0.00 0.00 45.83 3.86
670 719 1.734477 GACGCTCGCAAGCTTCTCA 60.734 57.895 0.00 0.00 46.91 3.27
689 738 0.171231 TTGACGCTCGACTGGATGAG 59.829 55.000 0.00 0.00 35.30 2.90
701 750 5.012046 TCCACATAATGATATCCTTGACGCT 59.988 40.000 0.00 0.00 0.00 5.07
714 763 2.677836 GTTGCGAGCTTCCACATAATGA 59.322 45.455 0.00 0.00 0.00 2.57
745 794 6.163476 TGTAACATGTAAGCTTAGTGGAGTG 58.837 40.000 18.16 9.56 0.00 3.51
811 901 6.454223 AGCTTATCCATAGCCCAAATTCTA 57.546 37.500 0.00 0.00 39.47 2.10
840 930 1.202533 CGTAGTTTGGCCATCCTCGAT 60.203 52.381 6.09 0.00 0.00 3.59
943 1033 2.094286 ACTGAGCAAGGAGAACATCTCG 60.094 50.000 1.58 0.00 44.28 4.04
947 1037 5.690464 ATAAGACTGAGCAAGGAGAACAT 57.310 39.130 0.00 0.00 0.00 2.71
957 1047 4.276183 GTCGTGGAGATATAAGACTGAGCA 59.724 45.833 0.00 0.00 0.00 4.26
997 1088 4.085733 TCCCACCAAGATTTAACCATGTG 58.914 43.478 0.00 0.00 0.00 3.21
998 1089 4.396357 TCCCACCAAGATTTAACCATGT 57.604 40.909 0.00 0.00 0.00 3.21
1054 2242 6.015010 ACAAGTAGCAGTAGAGAAGACAATGT 60.015 38.462 0.00 0.00 0.00 2.71
1056 2244 6.393990 CACAAGTAGCAGTAGAGAAGACAAT 58.606 40.000 0.00 0.00 0.00 2.71
1097 2285 2.330231 AACGTGTGCATTCATTTCCG 57.670 45.000 0.00 0.00 0.00 4.30
1103 2291 3.791789 GCTCTTGAAAACGTGTGCATTCA 60.792 43.478 0.00 0.00 0.00 2.57
1205 2396 4.870426 ACTCTCGTGGCATTACATTACTTG 59.130 41.667 0.00 0.00 0.00 3.16
1206 2397 5.086104 ACTCTCGTGGCATTACATTACTT 57.914 39.130 0.00 0.00 0.00 2.24
1284 2477 9.476202 AGGCAAAAGACTTGTCATTTTTATTAC 57.524 29.630 3.49 0.00 0.00 1.89
1289 2482 6.667007 CAAGGCAAAAGACTTGTCATTTTT 57.333 33.333 2.95 0.18 39.30 1.94
1330 2523 3.879295 AGGATAAGTCGCATCAACCAATG 59.121 43.478 0.00 0.00 0.00 2.82
1367 2560 3.845781 TTCACTTCAAGAAGCCTGACT 57.154 42.857 9.62 0.00 41.99 3.41
1405 2598 9.541143 CTTCCTTCATTAATTAGGAGACTTCTC 57.459 37.037 13.26 0.00 43.67 2.87
1408 2601 8.826765 TGTCTTCCTTCATTAATTAGGAGACTT 58.173 33.333 24.35 0.00 43.67 3.01
1427 2620 6.016276 ACATTTGGACACAACTATTGTCTTCC 60.016 38.462 10.22 10.22 43.23 3.46
1445 2638 9.906660 TTCTTTTAAGCAACTACATACATTTGG 57.093 29.630 0.00 0.00 0.00 3.28
1547 3659 7.015682 TCTCATGAATTGGATAGTACTCCCTTC 59.984 40.741 0.00 4.27 34.12 3.46
1548 3660 6.846505 TCTCATGAATTGGATAGTACTCCCTT 59.153 38.462 0.00 0.00 34.12 3.95
1560 3672 6.053632 TCTAAACTGCTCTCATGAATTGGA 57.946 37.500 0.00 0.00 0.00 3.53
1579 3691 3.060020 CTCGCCCGCCGAACTCTAA 62.060 63.158 0.00 0.00 46.81 2.10
1582 3694 4.208686 ATCTCGCCCGCCGAACTC 62.209 66.667 0.00 0.00 46.81 3.01
1605 3717 1.748122 CTGGGAGTGGTGAGCATGC 60.748 63.158 10.51 10.51 0.00 4.06
1616 3728 5.196695 GCATTCTTTTTATCCTCTGGGAGT 58.803 41.667 0.00 0.00 45.86 3.85
1621 3733 9.912634 TTTTAGTTGCATTCTTTTTATCCTCTG 57.087 29.630 0.00 0.00 0.00 3.35
1624 3736 8.646900 TGGTTTTAGTTGCATTCTTTTTATCCT 58.353 29.630 0.00 0.00 0.00 3.24
1640 3752 7.907841 AACTGGTTTCCTAATGGTTTTAGTT 57.092 32.000 0.00 0.00 34.23 2.24
1666 3778 3.007074 GGTTTCCTAATTCCCCGCAAAAA 59.993 43.478 0.00 0.00 0.00 1.94
1667 3779 2.563620 GGTTTCCTAATTCCCCGCAAAA 59.436 45.455 0.00 0.00 0.00 2.44
1668 3780 2.172679 GGTTTCCTAATTCCCCGCAAA 58.827 47.619 0.00 0.00 0.00 3.68
1670 3782 0.699399 TGGTTTCCTAATTCCCCGCA 59.301 50.000 0.00 0.00 0.00 5.69
1671 3783 1.340697 ACTGGTTTCCTAATTCCCCGC 60.341 52.381 0.00 0.00 0.00 6.13
1672 3784 2.801077 ACTGGTTTCCTAATTCCCCG 57.199 50.000 0.00 0.00 0.00 5.73
1673 3785 5.818678 AAAAACTGGTTTCCTAATTCCCC 57.181 39.130 0.00 0.00 31.45 4.81
1695 3807 0.747852 GGTTTCCTCACCCGCAAAAA 59.252 50.000 0.00 0.00 0.00 1.94
1696 3808 0.395862 TGGTTTCCTCACCCGCAAAA 60.396 50.000 0.00 0.00 35.73 2.44
1697 3809 0.821711 CTGGTTTCCTCACCCGCAAA 60.822 55.000 0.00 0.00 35.73 3.68
1698 3810 1.228124 CTGGTTTCCTCACCCGCAA 60.228 57.895 0.00 0.00 35.73 4.85
1699 3811 1.990160 AACTGGTTTCCTCACCCGCA 61.990 55.000 0.00 0.00 35.73 5.69
1700 3812 1.228154 AACTGGTTTCCTCACCCGC 60.228 57.895 0.00 0.00 35.73 6.13
1701 3813 0.107831 TCAACTGGTTTCCTCACCCG 59.892 55.000 0.00 0.00 35.73 5.28
1702 3814 1.605753 GTCAACTGGTTTCCTCACCC 58.394 55.000 0.00 0.00 35.73 4.61
1703 3815 1.143073 AGGTCAACTGGTTTCCTCACC 59.857 52.381 2.61 0.00 37.34 4.02
1704 3816 2.618709 CAAGGTCAACTGGTTTCCTCAC 59.381 50.000 7.19 0.00 0.00 3.51
1705 3817 2.422803 CCAAGGTCAACTGGTTTCCTCA 60.423 50.000 7.19 0.00 0.00 3.86
1706 3818 2.158667 TCCAAGGTCAACTGGTTTCCTC 60.159 50.000 7.19 0.00 0.00 3.71
1707 3819 1.850345 TCCAAGGTCAACTGGTTTCCT 59.150 47.619 0.00 2.61 0.00 3.36
1708 3820 2.358322 TCCAAGGTCAACTGGTTTCC 57.642 50.000 0.00 0.00 0.00 3.13
1709 3821 7.881775 ATTATATCCAAGGTCAACTGGTTTC 57.118 36.000 0.00 0.00 0.00 2.78
1710 3822 8.557450 ACTATTATATCCAAGGTCAACTGGTTT 58.443 33.333 0.00 0.00 0.00 3.27
1711 3823 7.993183 CACTATTATATCCAAGGTCAACTGGTT 59.007 37.037 0.00 0.00 0.00 3.67
1712 3824 7.509546 CACTATTATATCCAAGGTCAACTGGT 58.490 38.462 0.00 0.00 0.00 4.00
1713 3825 6.428159 GCACTATTATATCCAAGGTCAACTGG 59.572 42.308 0.00 0.00 0.00 4.00
1714 3826 7.220030 AGCACTATTATATCCAAGGTCAACTG 58.780 38.462 0.00 0.00 0.00 3.16
1715 3827 7.071196 TGAGCACTATTATATCCAAGGTCAACT 59.929 37.037 0.00 0.00 30.47 3.16
1716 3828 7.217200 TGAGCACTATTATATCCAAGGTCAAC 58.783 38.462 0.00 0.00 30.47 3.18
1717 3829 7.373617 TGAGCACTATTATATCCAAGGTCAA 57.626 36.000 0.00 0.00 30.47 3.18
1718 3830 6.994421 TGAGCACTATTATATCCAAGGTCA 57.006 37.500 0.00 0.00 0.00 4.02
1719 3831 9.944376 TTATTGAGCACTATTATATCCAAGGTC 57.056 33.333 0.00 0.00 0.00 3.85
1720 3832 9.726438 GTTATTGAGCACTATTATATCCAAGGT 57.274 33.333 0.00 0.00 0.00 3.50
1721 3833 9.167311 GGTTATTGAGCACTATTATATCCAAGG 57.833 37.037 0.00 0.00 0.00 3.61
1722 3834 9.725019 TGGTTATTGAGCACTATTATATCCAAG 57.275 33.333 0.00 0.00 0.00 3.61
1760 3878 0.817634 TCGGTGGCTGACTTTTGTGG 60.818 55.000 0.00 0.00 0.00 4.17
1772 3890 3.305177 TAGGACGGCTTTCGGTGGC 62.305 63.158 0.00 0.00 44.45 5.01
1774 3892 1.810030 GCTAGGACGGCTTTCGGTG 60.810 63.158 0.00 0.00 44.45 4.94
1775 3893 2.577593 GCTAGGACGGCTTTCGGT 59.422 61.111 0.00 0.00 44.45 4.69
1789 3907 3.838244 AATGCTTCCTGTATTCGGCTA 57.162 42.857 0.00 0.00 0.00 3.93
1791 3909 2.682856 TGAAATGCTTCCTGTATTCGGC 59.317 45.455 0.00 0.00 30.66 5.54
1798 3916 3.056322 GCTTCCATTGAAATGCTTCCTGT 60.056 43.478 0.00 0.00 35.08 4.00
1839 3958 1.070909 GCCGCCATTGTTTTTCGTTTG 60.071 47.619 0.00 0.00 0.00 2.93
1844 3963 0.241481 TACGGCCGCCATTGTTTTTC 59.759 50.000 28.58 0.00 0.00 2.29
1898 4017 1.717194 CCCTAGCAAGCGACGTTAAA 58.283 50.000 0.00 0.00 0.00 1.52
1932 4058 4.679905 GCTTGCGTAGGTAATTCTGTAGGT 60.680 45.833 0.00 0.00 0.00 3.08
1967 4096 6.402226 GCTTAGTTTAGTGGGAAACTTCATCG 60.402 42.308 6.84 0.00 45.30 3.84
2010 4140 2.884894 AAGACGTCGGGATTATCACC 57.115 50.000 10.46 0.00 0.00 4.02
2011 4141 4.205792 CGTAAAAGACGTCGGGATTATCAC 59.794 45.833 10.46 0.00 46.86 3.06
2056 4190 0.406750 TGCCCATCCATCCATCCATC 59.593 55.000 0.00 0.00 0.00 3.51
2057 4191 0.408309 CTGCCCATCCATCCATCCAT 59.592 55.000 0.00 0.00 0.00 3.41
2058 4192 1.848400 CTGCCCATCCATCCATCCA 59.152 57.895 0.00 0.00 0.00 3.41
2059 4193 1.605738 GCTGCCCATCCATCCATCC 60.606 63.158 0.00 0.00 0.00 3.51
2125 4259 2.400896 TTTTCTTGCGTTCCGGCAGC 62.401 55.000 0.00 2.06 44.94 5.25
2130 4264 0.378962 TGGTGTTTTCTTGCGTTCCG 59.621 50.000 0.00 0.00 0.00 4.30
2131 4265 1.835121 GTGGTGTTTTCTTGCGTTCC 58.165 50.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.