Multiple sequence alignment - TraesCS1B01G414000

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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 TraesCS1B01G414000 chr1B 100.000 2798 0 0 1 2798 638989614 638986817 0.000000e+00 5168.0
1 TraesCS1B01G414000 chr1B 93.913 115 5 1 468 580 638938440 638938554 3.710000e-39 172.0
2 TraesCS1B01G414000 chr1D 92.700 1452 69 17 433 1860 463445281 463446719 0.000000e+00 2060.0
3 TraesCS1B01G414000 chr1D 82.440 541 69 10 2262 2798 463452765 463453283 1.530000e-122 449.0
4 TraesCS1B01G414000 chr1D 86.957 299 27 5 486 776 463490167 463489873 2.690000e-85 326.0
5 TraesCS1B01G414000 chr1D 80.296 406 71 8 2250 2650 19751412 19751813 5.860000e-77 298.0
6 TraesCS1B01G414000 chr1D 95.364 151 3 3 1085 1235 463489868 463489722 1.300000e-58 237.0
7 TraesCS1B01G414000 chr1D 88.587 184 8 7 1991 2167 463451996 463452173 7.850000e-51 211.0
8 TraesCS1B01G414000 chr1A 92.061 1436 61 26 466 1865 555799124 555797706 0.000000e+00 1971.0
9 TraesCS1B01G414000 chr1A 84.831 712 80 8 2091 2798 555797076 555796389 0.000000e+00 691.0
10 TraesCS1B01G414000 chr1A 80.372 484 64 19 119 583 555646544 555647015 3.450000e-89 339.0
11 TraesCS1B01G414000 chr1A 85.522 297 27 14 487 776 555642947 555643234 2.110000e-76 296.0
12 TraesCS1B01G414000 chr1A 80.539 334 30 7 131 462 555799461 555799161 1.010000e-54 224.0
13 TraesCS1B01G414000 chr1A 87.356 174 6 3 1087 1260 555644070 555644227 4.760000e-43 185.0
14 TraesCS1B01G414000 chr1A 86.782 174 7 3 1087 1260 555643240 555643397 2.210000e-41 180.0
15 TraesCS1B01G414000 chr1A 91.429 105 9 0 481 585 14486537 14486641 8.080000e-31 145.0
16 TraesCS1B01G414000 chr7A 89.637 386 23 6 1171 1549 666153541 666153916 2.520000e-130 475.0
17 TraesCS1B01G414000 chr7A 79.404 403 66 14 2256 2649 650054270 650054664 4.590000e-68 268.0
18 TraesCS1B01G414000 chr7A 91.045 201 10 4 1182 1375 701127430 701127231 5.940000e-67 265.0
19 TraesCS1B01G414000 chr3D 95.510 245 5 2 1171 1409 405820570 405820326 1.220000e-103 387.0
20 TraesCS1B01G414000 chr3D 92.683 41 2 1 2682 2721 357643070 357643030 1.080000e-04 58.4
21 TraesCS1B01G414000 chr6D 87.032 347 27 6 1171 1508 326170507 326170844 2.630000e-100 375.0
22 TraesCS1B01G414000 chr4D 83.130 409 55 12 2251 2650 320043382 320042979 7.370000e-96 361.0
23 TraesCS1B01G414000 chr4D 82.222 315 46 8 2335 2647 118324724 118325030 2.140000e-66 263.0
24 TraesCS1B01G414000 chr4D 97.297 37 0 1 2679 2714 50328013 50328049 8.370000e-06 62.1
25 TraesCS1B01G414000 chr2D 81.600 375 57 9 2250 2620 37248256 37248622 1.630000e-77 300.0
26 TraesCS1B01G414000 chr2D 83.951 324 40 10 2250 2568 561232185 561232501 1.630000e-77 300.0
27 TraesCS1B01G414000 chr2D 81.944 360 52 10 2257 2609 298839359 298839712 2.730000e-75 292.0
28 TraesCS1B01G414000 chr3B 91.542 201 9 3 1182 1375 701403913 701404112 1.280000e-68 270.0
29 TraesCS1B01G414000 chr5B 90.816 196 11 3 1182 1371 15682502 15682308 3.580000e-64 255.0
30 TraesCS1B01G414000 chr5B 89.796 196 13 3 1182 1371 7075770 7075576 7.740000e-61 244.0
31 TraesCS1B01G414000 chr3A 95.745 94 4 0 494 587 654325877 654325970 4.830000e-33 152.0
32 TraesCS1B01G414000 chr3A 93.069 101 6 1 485 585 647494846 647494945 2.250000e-31 147.0
33 TraesCS1B01G414000 chr5A 92.233 103 6 2 485 586 312754370 312754471 8.080000e-31 145.0
34 TraesCS1B01G414000 chr4A 97.222 36 1 0 2678 2713 571028227 571028262 8.370000e-06 62.1
35 TraesCS1B01G414000 chr7D 97.059 34 1 0 2685 2718 602073651 602073684 1.080000e-04 58.4
36 TraesCS1B01G414000 chr4B 97.143 35 0 1 2679 2712 24559689 24559723 1.080000e-04 58.4
37 TraesCS1B01G414000 chr6A 87.500 48 6 0 2676 2723 142072206 142072253 3.890000e-04 56.5
38 TraesCS1B01G414000 chr6A 100.000 28 0 0 2685 2712 142077853 142077880 5.000000e-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 TraesCS1B01G414000 chr1B 638986817 638989614 2797 True 5168 5168 100.000000 1 2798 1 chr1B.!!$R1 2797
1 TraesCS1B01G414000 chr1D 463445281 463446719 1438 False 2060 2060 92.700000 433 1860 1 chr1D.!!$F2 1427
2 TraesCS1B01G414000 chr1D 463451996 463453283 1287 False 330 449 85.513500 1991 2798 2 chr1D.!!$F3 807
3 TraesCS1B01G414000 chr1A 555796389 555799461 3072 True 962 1971 85.810333 131 2798 3 chr1A.!!$R1 2667
4 TraesCS1B01G414000 chr1A 555642947 555647015 4068 False 250 339 85.008000 119 1260 4 chr1A.!!$F2 1141

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
29 30 0.318614 GTGCGGTGGTTGTGGATTTG 60.319 55.0 0.00 0.0 0.0 2.32 F
111 112 0.321387 TTTTACGGCGGCCACACATA 60.321 50.0 20.71 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1019 1917 0.677731 CTTCTTCATGCTGCCCCGAA 60.678 55.0 0.0 0.0 0.0 4.30 R
2034 4412 0.823460 CTCTCTCCAGGCTCCAACTC 59.177 60.0 0.0 0.0 0.0 3.01 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
22 23 4.579384 CAGGGGTGCGGTGGTTGT 62.579 66.667 0.00 0.00 0.00 3.32
23 24 4.579384 AGGGGTGCGGTGGTTGTG 62.579 66.667 0.00 0.00 0.00 3.33
25 26 4.572571 GGGTGCGGTGGTTGTGGA 62.573 66.667 0.00 0.00 0.00 4.02
26 27 2.282180 GGTGCGGTGGTTGTGGAT 60.282 61.111 0.00 0.00 0.00 3.41
27 28 1.901464 GGTGCGGTGGTTGTGGATT 60.901 57.895 0.00 0.00 0.00 3.01
28 29 1.460273 GGTGCGGTGGTTGTGGATTT 61.460 55.000 0.00 0.00 0.00 2.17
29 30 0.318614 GTGCGGTGGTTGTGGATTTG 60.319 55.000 0.00 0.00 0.00 2.32
30 31 1.288752 GCGGTGGTTGTGGATTTGG 59.711 57.895 0.00 0.00 0.00 3.28
31 32 1.175983 GCGGTGGTTGTGGATTTGGA 61.176 55.000 0.00 0.00 0.00 3.53
32 33 0.881118 CGGTGGTTGTGGATTTGGAG 59.119 55.000 0.00 0.00 0.00 3.86
33 34 1.256812 GGTGGTTGTGGATTTGGAGG 58.743 55.000 0.00 0.00 0.00 4.30
34 35 0.603065 GTGGTTGTGGATTTGGAGGC 59.397 55.000 0.00 0.00 0.00 4.70
35 36 0.893270 TGGTTGTGGATTTGGAGGCG 60.893 55.000 0.00 0.00 0.00 5.52
36 37 0.608035 GGTTGTGGATTTGGAGGCGA 60.608 55.000 0.00 0.00 0.00 5.54
37 38 0.521735 GTTGTGGATTTGGAGGCGAC 59.478 55.000 0.00 0.00 0.00 5.19
38 39 0.953471 TTGTGGATTTGGAGGCGACG 60.953 55.000 0.00 0.00 0.00 5.12
39 40 2.106683 GTGGATTTGGAGGCGACGG 61.107 63.158 0.00 0.00 0.00 4.79
40 41 3.202706 GGATTTGGAGGCGACGGC 61.203 66.667 14.41 14.41 38.90 5.68
41 42 3.564027 GATTTGGAGGCGACGGCG 61.564 66.667 16.29 6.12 41.24 6.46
93 94 3.190391 GGTGGGGAGGGGTTGGTT 61.190 66.667 0.00 0.00 0.00 3.67
94 95 2.785776 GGTGGGGAGGGGTTGGTTT 61.786 63.158 0.00 0.00 0.00 3.27
95 96 1.234820 GTGGGGAGGGGTTGGTTTT 59.765 57.895 0.00 0.00 0.00 2.43
96 97 0.483770 GTGGGGAGGGGTTGGTTTTA 59.516 55.000 0.00 0.00 0.00 1.52
97 98 0.483770 TGGGGAGGGGTTGGTTTTAC 59.516 55.000 0.00 0.00 0.00 2.01
98 99 0.609957 GGGGAGGGGTTGGTTTTACG 60.610 60.000 0.00 0.00 0.00 3.18
99 100 0.609957 GGGAGGGGTTGGTTTTACGG 60.610 60.000 0.00 0.00 0.00 4.02
100 101 1.246056 GGAGGGGTTGGTTTTACGGC 61.246 60.000 0.00 0.00 0.00 5.68
101 102 1.579964 GAGGGGTTGGTTTTACGGCG 61.580 60.000 4.80 4.80 0.00 6.46
102 103 2.628696 GGGGTTGGTTTTACGGCGG 61.629 63.158 13.24 0.00 0.00 6.13
103 104 2.256158 GGTTGGTTTTACGGCGGC 59.744 61.111 13.24 0.00 0.00 6.53
104 105 2.256158 GTTGGTTTTACGGCGGCC 59.744 61.111 13.24 9.54 0.00 6.13
105 106 2.203308 TTGGTTTTACGGCGGCCA 60.203 55.556 20.71 8.53 0.00 5.36
106 107 2.553727 TTGGTTTTACGGCGGCCAC 61.554 57.895 20.71 8.90 0.00 5.01
107 108 2.979120 GGTTTTACGGCGGCCACA 60.979 61.111 20.71 2.15 0.00 4.17
108 109 2.253154 GTTTTACGGCGGCCACAC 59.747 61.111 20.71 3.62 0.00 3.82
109 110 2.203167 TTTTACGGCGGCCACACA 60.203 55.556 20.71 0.00 0.00 3.72
110 111 1.601197 TTTTACGGCGGCCACACAT 60.601 52.632 20.71 0.85 0.00 3.21
111 112 0.321387 TTTTACGGCGGCCACACATA 60.321 50.000 20.71 0.00 0.00 2.29
112 113 1.020333 TTTACGGCGGCCACACATAC 61.020 55.000 20.71 0.00 0.00 2.39
113 114 2.168666 TTACGGCGGCCACACATACA 62.169 55.000 20.71 0.00 0.00 2.29
114 115 2.839043 TACGGCGGCCACACATACAC 62.839 60.000 20.71 0.00 0.00 2.90
115 116 2.046314 GGCGGCCACACATACACT 60.046 61.111 15.62 0.00 0.00 3.55
116 117 2.398554 GGCGGCCACACATACACTG 61.399 63.158 15.62 0.00 0.00 3.66
117 118 1.671054 GCGGCCACACATACACTGT 60.671 57.895 2.24 0.00 39.20 3.55
118 119 0.390603 GCGGCCACACATACACTGTA 60.391 55.000 2.24 0.00 35.91 2.74
119 120 1.742411 GCGGCCACACATACACTGTAT 60.742 52.381 2.24 0.00 35.91 2.29
120 121 2.482316 GCGGCCACACATACACTGTATA 60.482 50.000 2.24 0.00 35.91 1.47
121 122 3.381045 CGGCCACACATACACTGTATAG 58.619 50.000 2.24 1.21 35.91 1.31
122 123 3.181479 CGGCCACACATACACTGTATAGT 60.181 47.826 2.24 1.78 35.91 2.12
123 124 4.679639 CGGCCACACATACACTGTATAGTT 60.680 45.833 2.24 0.00 35.91 2.24
124 125 4.570772 GGCCACACATACACTGTATAGTTG 59.429 45.833 0.00 3.06 35.91 3.16
125 126 4.034048 GCCACACATACACTGTATAGTTGC 59.966 45.833 1.19 7.53 35.91 4.17
126 127 5.175127 CCACACATACACTGTATAGTTGCA 58.825 41.667 1.19 0.00 35.91 4.08
127 128 5.817296 CCACACATACACTGTATAGTTGCAT 59.183 40.000 1.19 0.00 35.91 3.96
128 129 6.238184 CCACACATACACTGTATAGTTGCATG 60.238 42.308 1.19 0.00 35.91 4.06
129 130 5.817296 ACACATACACTGTATAGTTGCATGG 59.183 40.000 1.19 0.00 35.91 3.66
147 148 0.665835 GGTGCATGTTGTGTTTCGGA 59.334 50.000 0.00 0.00 0.00 4.55
148 149 1.599419 GGTGCATGTTGTGTTTCGGAC 60.599 52.381 0.00 0.00 0.00 4.79
151 152 1.334960 GCATGTTGTGTTTCGGACAGG 60.335 52.381 0.00 0.00 39.39 4.00
162 163 0.400213 TCGGACAGGCTTTGAATGGT 59.600 50.000 0.00 0.00 0.00 3.55
165 166 1.273327 GGACAGGCTTTGAATGGTTGG 59.727 52.381 0.00 0.00 0.00 3.77
171 172 3.161866 GGCTTTGAATGGTTGGGACTTA 58.838 45.455 0.00 0.00 0.00 2.24
172 173 3.576550 GGCTTTGAATGGTTGGGACTTAA 59.423 43.478 0.00 0.00 0.00 1.85
173 174 4.321974 GGCTTTGAATGGTTGGGACTTAAG 60.322 45.833 0.00 0.00 0.00 1.85
174 175 4.809673 CTTTGAATGGTTGGGACTTAAGC 58.190 43.478 1.29 0.00 0.00 3.09
223 224 6.255215 CGACCATACATGTGAATTTGGTTAC 58.745 40.000 9.11 2.85 37.58 2.50
229 230 9.345517 CATACATGTGAATTTGGTTACTGAAAG 57.654 33.333 9.11 0.00 42.29 2.62
236 237 9.573133 GTGAATTTGGTTACTGAAAGATAATGG 57.427 33.333 0.00 0.00 37.43 3.16
259 260 4.587520 TGCCTCCAGAGGGAACAT 57.412 55.556 15.43 0.00 46.37 2.71
260 261 3.730116 TGCCTCCAGAGGGAACATA 57.270 52.632 15.43 0.00 46.37 2.29
261 262 1.965414 TGCCTCCAGAGGGAACATAA 58.035 50.000 15.43 0.00 46.37 1.90
262 263 2.274542 TGCCTCCAGAGGGAACATAAA 58.725 47.619 15.43 0.00 46.37 1.40
263 264 2.852449 TGCCTCCAGAGGGAACATAAAT 59.148 45.455 15.43 0.00 46.37 1.40
264 265 3.269381 TGCCTCCAGAGGGAACATAAATT 59.731 43.478 15.43 0.00 46.37 1.82
265 266 4.264352 TGCCTCCAGAGGGAACATAAATTT 60.264 41.667 15.43 0.00 46.37 1.82
266 267 5.044476 TGCCTCCAGAGGGAACATAAATTTA 60.044 40.000 15.43 0.00 46.37 1.40
267 268 6.860180 TGCCTCCAGAGGGAACATAAATTTAG 60.860 42.308 15.43 0.00 46.37 1.85
268 269 6.900194 CCTCCAGAGGGAACATAAATTTAGA 58.100 40.000 5.74 0.00 44.38 2.10
294 295 1.066929 CCAATAACCTTGCTGGCCAAC 60.067 52.381 7.01 1.82 40.22 3.77
295 296 1.895131 CAATAACCTTGCTGGCCAACT 59.105 47.619 7.01 0.00 40.22 3.16
307 308 2.037772 CTGGCCAACTGTGAGTAGTCTT 59.962 50.000 7.01 0.00 0.00 3.01
323 324 9.310449 TGAGTAGTCTTATAAGTTCACTTTCCT 57.690 33.333 12.19 5.93 37.40 3.36
324 325 9.791820 GAGTAGTCTTATAAGTTCACTTTCCTC 57.208 37.037 12.19 10.12 37.40 3.71
325 326 8.751242 AGTAGTCTTATAAGTTCACTTTCCTCC 58.249 37.037 12.19 0.00 37.40 4.30
336 337 4.858850 TCACTTTCCTCCACATTATGCAT 58.141 39.130 3.79 3.79 0.00 3.96
337 338 4.641541 TCACTTTCCTCCACATTATGCATG 59.358 41.667 10.16 0.00 39.07 4.06
338 339 3.382546 ACTTTCCTCCACATTATGCATGC 59.617 43.478 11.82 11.82 36.14 4.06
343 344 1.007038 CACATTATGCATGCGGGCC 60.007 57.895 14.09 0.00 36.14 5.80
345 346 1.042003 ACATTATGCATGCGGGCCAA 61.042 50.000 14.09 2.54 36.14 4.52
346 347 0.598158 CATTATGCATGCGGGCCAAC 60.598 55.000 14.09 0.00 0.00 3.77
350 351 4.424566 GCATGCGGGCCAACTGTG 62.425 66.667 4.39 0.00 0.00 3.66
359 360 1.963515 GGGCCAACTGTGACTCAAAAT 59.036 47.619 4.39 0.00 0.00 1.82
360 361 2.365293 GGGCCAACTGTGACTCAAAATT 59.635 45.455 4.39 0.00 0.00 1.82
361 362 3.181466 GGGCCAACTGTGACTCAAAATTT 60.181 43.478 4.39 0.00 0.00 1.82
362 363 4.441792 GGCCAACTGTGACTCAAAATTTT 58.558 39.130 0.00 0.00 0.00 1.82
363 364 4.875536 GGCCAACTGTGACTCAAAATTTTT 59.124 37.500 0.00 0.00 0.00 1.94
458 459 2.234908 AGATAGCTCTTGCAAACGACCT 59.765 45.455 0.00 0.00 42.74 3.85
463 464 3.630312 AGCTCTTGCAAACGACCTTTTTA 59.370 39.130 0.00 0.00 42.74 1.52
464 465 3.975035 GCTCTTGCAAACGACCTTTTTAG 59.025 43.478 0.00 0.00 39.41 1.85
492 527 7.576861 TCTAAAAGTAACCCAGAAAAACAGG 57.423 36.000 0.00 0.00 0.00 4.00
493 528 7.348033 TCTAAAAGTAACCCAGAAAAACAGGA 58.652 34.615 0.00 0.00 0.00 3.86
498 533 6.873997 AGTAACCCAGAAAAACAGGAAAAAG 58.126 36.000 0.00 0.00 0.00 2.27
499 534 5.755409 AACCCAGAAAAACAGGAAAAAGT 57.245 34.783 0.00 0.00 0.00 2.66
500 535 6.860790 AACCCAGAAAAACAGGAAAAAGTA 57.139 33.333 0.00 0.00 0.00 2.24
584 621 0.550914 ACACCACCCAGACATGTTGT 59.449 50.000 0.00 0.00 0.00 3.32
585 622 0.953727 CACCACCCAGACATGTTGTG 59.046 55.000 0.00 5.84 0.00 3.33
606 643 7.075674 TGTGTCTATACGTCGAACAATCTTA 57.924 36.000 0.00 0.00 0.00 2.10
609 646 9.100895 GTGTCTATACGTCGAACAATCTTATAC 57.899 37.037 0.00 0.00 0.00 1.47
670 725 4.760047 AAGCGCCACCAGCCTACG 62.760 66.667 2.29 0.00 38.78 3.51
674 729 2.820037 GCCACCAGCCTACGAAGC 60.820 66.667 0.00 0.00 34.35 3.86
716 775 4.117685 AGTTTATCAGTCGCGTATTTCCC 58.882 43.478 5.77 0.00 0.00 3.97
739 798 4.052608 TCAGTGCAAACGACGAAAAGATA 58.947 39.130 0.00 0.00 0.00 1.98
787 1678 6.573434 AGTTTCCTCCAAAGAACACAAATTC 58.427 36.000 0.00 0.00 0.00 2.17
796 1687 5.534207 AAGAACACAAATTCTGGCATGAA 57.466 34.783 0.00 0.00 38.95 2.57
799 1690 6.960448 AGAACACAAATTCTGGCATGAAGCA 61.960 40.000 0.00 0.00 39.27 3.91
813 1704 4.491676 CATGAAGCATCTGTCCAAAAAGG 58.508 43.478 0.00 0.00 39.47 3.11
856 1747 6.074648 TGTTGTTTCAAGTTAGGATCCCAAT 58.925 36.000 8.55 0.00 0.00 3.16
857 1748 6.015519 TGTTGTTTCAAGTTAGGATCCCAATG 60.016 38.462 8.55 0.00 0.00 2.82
911 1802 4.717629 CTCTTCACGCCGACGCCA 62.718 66.667 0.00 0.00 45.53 5.69
998 1896 2.421424 CCTTATCAGCACACAAGAAGCC 59.579 50.000 0.00 0.00 0.00 4.35
1019 1917 2.868583 CGATGTCGGCATCTCAAGAAAT 59.131 45.455 26.18 0.00 46.96 2.17
1158 2056 3.731653 GAGCCGCCTCAGCTTCTCC 62.732 68.421 0.00 0.00 41.75 3.71
1733 4060 1.048160 TACCATCTCATCAGCCCGCA 61.048 55.000 0.00 0.00 0.00 5.69
1849 4180 2.517650 TCACTGACATGCGTGTAACA 57.482 45.000 12.53 5.90 39.09 2.41
1860 4191 1.401409 GCGTGTAACATGCATGTGCTT 60.401 47.619 31.98 19.27 44.78 3.91
1865 4196 2.736144 AACATGCATGTGCTTCAAGG 57.264 45.000 31.98 2.26 41.61 3.61
1866 4197 1.624336 ACATGCATGTGCTTCAAGGT 58.376 45.000 30.92 2.17 40.03 3.50
1867 4198 2.794103 ACATGCATGTGCTTCAAGGTA 58.206 42.857 30.92 0.00 40.03 3.08
1868 4199 2.751259 ACATGCATGTGCTTCAAGGTAG 59.249 45.455 30.92 0.13 40.03 3.18
1874 4243 5.759763 TGCATGTGCTTCAAGGTAGTATATG 59.240 40.000 6.55 0.00 42.66 1.78
1875 4244 5.760253 GCATGTGCTTCAAGGTAGTATATGT 59.240 40.000 0.00 0.00 38.21 2.29
1876 4245 6.929049 GCATGTGCTTCAAGGTAGTATATGTA 59.071 38.462 0.00 0.00 38.21 2.29
1877 4246 7.095607 GCATGTGCTTCAAGGTAGTATATGTAC 60.096 40.741 0.00 0.00 38.21 2.90
1884 4253 7.692460 TCAAGGTAGTATATGTACATACGGG 57.308 40.000 17.69 2.99 36.65 5.28
1889 4258 6.976925 GGTAGTATATGTACATACGGGATTGC 59.023 42.308 17.69 4.98 36.65 3.56
1895 4264 8.718102 ATATGTACATACGGGATTGCTAAATC 57.282 34.615 17.69 0.00 41.37 2.17
1900 4269 2.565841 ACGGGATTGCTAAATCTCAGC 58.434 47.619 0.00 0.00 42.61 4.26
1905 4282 1.737838 TTGCTAAATCTCAGCCGTGG 58.262 50.000 0.00 0.00 38.29 4.94
1908 4285 1.808133 GCTAAATCTCAGCCGTGGAGG 60.808 57.143 0.00 0.00 44.97 4.30
1917 4294 1.375523 GCCGTGGAGGTTGGTGTAG 60.376 63.158 0.00 0.00 43.70 2.74
1919 4296 0.902531 CCGTGGAGGTTGGTGTAGAT 59.097 55.000 0.00 0.00 34.51 1.98
1924 4301 4.083484 CGTGGAGGTTGGTGTAGATTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
1927 4304 6.040504 GTGGAGGTTGGTGTAGATTTTTCTTT 59.959 38.462 0.00 0.00 0.00 2.52
1928 4305 6.609616 TGGAGGTTGGTGTAGATTTTTCTTTT 59.390 34.615 0.00 0.00 0.00 2.27
1929 4306 7.780745 TGGAGGTTGGTGTAGATTTTTCTTTTA 59.219 33.333 0.00 0.00 0.00 1.52
1930 4307 8.635328 GGAGGTTGGTGTAGATTTTTCTTTTAA 58.365 33.333 0.00 0.00 0.00 1.52
1978 4356 7.194607 TCAGTCATTTGATTGAGACTTTGTC 57.805 36.000 2.02 0.00 39.17 3.18
1979 4357 6.767423 TCAGTCATTTGATTGAGACTTTGTCA 59.233 34.615 2.02 0.00 39.17 3.58
1980 4358 7.282901 TCAGTCATTTGATTGAGACTTTGTCAA 59.717 33.333 2.02 0.00 39.17 3.18
1981 4359 7.590322 CAGTCATTTGATTGAGACTTTGTCAAG 59.410 37.037 0.00 0.00 39.17 3.02
1982 4360 7.284034 AGTCATTTGATTGAGACTTTGTCAAGT 59.716 33.333 0.46 0.00 46.64 3.16
1983 4361 7.917505 GTCATTTGATTGAGACTTTGTCAAGTT 59.082 33.333 0.46 0.00 43.79 2.66
1984 4362 8.131100 TCATTTGATTGAGACTTTGTCAAGTTC 58.869 33.333 0.46 0.00 43.79 3.01
1985 4363 6.377327 TTGATTGAGACTTTGTCAAGTTCC 57.623 37.500 0.46 0.00 43.79 3.62
1986 4364 5.436175 TGATTGAGACTTTGTCAAGTTCCA 58.564 37.500 0.46 0.00 43.79 3.53
1987 4365 5.528690 TGATTGAGACTTTGTCAAGTTCCAG 59.471 40.000 0.46 0.00 43.79 3.86
1988 4366 4.487714 TGAGACTTTGTCAAGTTCCAGT 57.512 40.909 0.46 0.00 43.79 4.00
1989 4367 4.442706 TGAGACTTTGTCAAGTTCCAGTC 58.557 43.478 6.32 6.32 43.79 3.51
1992 4370 4.058817 GACTTTGTCAAGTTCCAGTCGAT 58.941 43.478 0.00 0.00 43.79 3.59
2003 4381 5.197451 AGTTCCAGTCGATTGAGATCTAGT 58.803 41.667 9.83 0.00 0.00 2.57
2008 4386 5.009510 CCAGTCGATTGAGATCTAGTCACAT 59.990 44.000 9.83 0.00 0.00 3.21
2010 4388 5.240623 AGTCGATTGAGATCTAGTCACATCC 59.759 44.000 0.00 0.00 0.00 3.51
2034 4412 3.009723 ACAGATATTGAACCGTGCTTGG 58.990 45.455 0.00 0.00 0.00 3.61
2046 4424 1.073722 TGCTTGGAGTTGGAGCCTG 59.926 57.895 0.00 0.00 35.59 4.85
2048 4426 2.069776 CTTGGAGTTGGAGCCTGGA 58.930 57.895 0.00 0.00 0.00 3.86
2057 4435 0.906756 TGGAGCCTGGAGAGAGTTGG 60.907 60.000 0.00 0.00 0.00 3.77
2163 4945 2.943033 GCGCCTTGTTGTATGGTTATCT 59.057 45.455 0.00 0.00 0.00 1.98
2164 4946 3.242739 GCGCCTTGTTGTATGGTTATCTG 60.243 47.826 0.00 0.00 0.00 2.90
2165 4947 3.312421 CGCCTTGTTGTATGGTTATCTGG 59.688 47.826 0.00 0.00 0.00 3.86
2166 4948 4.270008 GCCTTGTTGTATGGTTATCTGGT 58.730 43.478 0.00 0.00 0.00 4.00
2167 4949 4.335594 GCCTTGTTGTATGGTTATCTGGTC 59.664 45.833 0.00 0.00 0.00 4.02
2168 4950 5.745227 CCTTGTTGTATGGTTATCTGGTCT 58.255 41.667 0.00 0.00 0.00 3.85
2169 4951 5.586243 CCTTGTTGTATGGTTATCTGGTCTG 59.414 44.000 0.00 0.00 0.00 3.51
2170 4952 6.367374 TTGTTGTATGGTTATCTGGTCTGA 57.633 37.500 0.00 0.00 0.00 3.27
2171 4953 5.977635 TGTTGTATGGTTATCTGGTCTGAG 58.022 41.667 0.00 0.00 0.00 3.35
2194 4976 4.271049 GTGGTATGTCATGCATGTAGTGTC 59.729 45.833 25.43 13.10 38.47 3.67
2195 4977 4.162131 TGGTATGTCATGCATGTAGTGTCT 59.838 41.667 25.43 7.95 38.47 3.41
2196 4978 5.362430 TGGTATGTCATGCATGTAGTGTCTA 59.638 40.000 25.43 8.99 38.47 2.59
2197 4979 6.041979 TGGTATGTCATGCATGTAGTGTCTAT 59.958 38.462 25.43 11.61 38.47 1.98
2198 4980 6.931281 GGTATGTCATGCATGTAGTGTCTATT 59.069 38.462 25.43 2.76 38.47 1.73
2231 5532 8.709272 AAGAACTACTCCCTCTATACCATAAC 57.291 38.462 0.00 0.00 0.00 1.89
2239 5540 7.397761 ACTCCCTCTATACCATAACATAAGAGC 59.602 40.741 0.00 0.00 0.00 4.09
2248 5549 7.209471 ACCATAACATAAGAGCGTTTTTCAA 57.791 32.000 0.00 0.00 0.00 2.69
2273 5574 1.448540 CGATTCGGTGCTCAGGCTT 60.449 57.895 0.00 0.00 39.59 4.35
2284 5585 0.036732 CTCAGGCTTAGTTGCACCCA 59.963 55.000 0.00 0.00 34.04 4.51
2292 5593 2.779755 TAGTTGCACCCACGATGAAT 57.220 45.000 0.00 0.00 0.00 2.57
2302 5603 5.501715 CACCCACGATGAATAGAAAATTCG 58.498 41.667 0.00 0.00 0.00 3.34
2306 5607 7.067008 ACCCACGATGAATAGAAAATTCGAAAT 59.933 33.333 0.00 0.00 0.00 2.17
2388 5690 1.956477 AGGTGCGCTCAAAATTTCAGT 59.044 42.857 9.73 0.00 0.00 3.41
2399 5701 6.346040 GCTCAAAATTTCAGTTCATTTGGACG 60.346 38.462 0.00 0.00 33.08 4.79
2401 5703 7.038659 TCAAAATTTCAGTTCATTTGGACGTT 58.961 30.769 0.00 0.00 33.08 3.99
2408 5710 5.818336 TCAGTTCATTTGGACGTTTGAGTAA 59.182 36.000 0.00 0.00 0.00 2.24
2412 5714 4.753107 TCATTTGGACGTTTGAGTAACTCC 59.247 41.667 0.00 0.00 35.93 3.85
2413 5715 2.825861 TGGACGTTTGAGTAACTCCC 57.174 50.000 0.00 0.00 35.19 4.30
2476 5778 5.062683 CGGTTCATGTATTGTTCTGACTCAG 59.937 44.000 0.00 0.00 0.00 3.35
2535 5837 2.421073 TGATCTGAAATTTGGAGCGCAG 59.579 45.455 11.47 0.00 0.00 5.18
2557 5961 4.877823 AGCTCACGCATCAAATTATCTTCA 59.122 37.500 0.00 0.00 39.10 3.02
2635 6163 0.178767 CCGGATGCAGATGAACCTGA 59.821 55.000 0.00 0.00 36.29 3.86
2714 6245 7.396623 ACACTCTTATATTATAAGACGGAGGGG 59.603 40.741 18.17 13.20 31.09 4.79
2729 6260 7.655403 AGACGGAGGGGGTAATATATGTAATA 58.345 38.462 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.579384 ACAACCACCGCACCCCTG 62.579 66.667 0.00 0.00 0.00 4.45
8 9 3.860930 ATCCACAACCACCGCACCC 62.861 63.158 0.00 0.00 0.00 4.61
9 10 1.460273 AAATCCACAACCACCGCACC 61.460 55.000 0.00 0.00 0.00 5.01
10 11 0.318614 CAAATCCACAACCACCGCAC 60.319 55.000 0.00 0.00 0.00 5.34
11 12 1.459455 CCAAATCCACAACCACCGCA 61.459 55.000 0.00 0.00 0.00 5.69
12 13 1.175983 TCCAAATCCACAACCACCGC 61.176 55.000 0.00 0.00 0.00 5.68
13 14 0.881118 CTCCAAATCCACAACCACCG 59.119 55.000 0.00 0.00 0.00 4.94
14 15 1.256812 CCTCCAAATCCACAACCACC 58.743 55.000 0.00 0.00 0.00 4.61
15 16 0.603065 GCCTCCAAATCCACAACCAC 59.397 55.000 0.00 0.00 0.00 4.16
16 17 0.893270 CGCCTCCAAATCCACAACCA 60.893 55.000 0.00 0.00 0.00 3.67
17 18 0.608035 TCGCCTCCAAATCCACAACC 60.608 55.000 0.00 0.00 0.00 3.77
18 19 0.521735 GTCGCCTCCAAATCCACAAC 59.478 55.000 0.00 0.00 0.00 3.32
19 20 0.953471 CGTCGCCTCCAAATCCACAA 60.953 55.000 0.00 0.00 0.00 3.33
20 21 1.375396 CGTCGCCTCCAAATCCACA 60.375 57.895 0.00 0.00 0.00 4.17
21 22 2.106683 CCGTCGCCTCCAAATCCAC 61.107 63.158 0.00 0.00 0.00 4.02
22 23 2.267642 CCGTCGCCTCCAAATCCA 59.732 61.111 0.00 0.00 0.00 3.41
23 24 3.202706 GCCGTCGCCTCCAAATCC 61.203 66.667 0.00 0.00 0.00 3.01
24 25 3.564027 CGCCGTCGCCTCCAAATC 61.564 66.667 0.00 0.00 0.00 2.17
76 77 2.320830 AAAACCAACCCCTCCCCACC 62.321 60.000 0.00 0.00 0.00 4.61
77 78 0.483770 TAAAACCAACCCCTCCCCAC 59.516 55.000 0.00 0.00 0.00 4.61
78 79 0.483770 GTAAAACCAACCCCTCCCCA 59.516 55.000 0.00 0.00 0.00 4.96
79 80 0.609957 CGTAAAACCAACCCCTCCCC 60.610 60.000 0.00 0.00 0.00 4.81
80 81 0.609957 CCGTAAAACCAACCCCTCCC 60.610 60.000 0.00 0.00 0.00 4.30
81 82 1.246056 GCCGTAAAACCAACCCCTCC 61.246 60.000 0.00 0.00 0.00 4.30
82 83 1.579964 CGCCGTAAAACCAACCCCTC 61.580 60.000 0.00 0.00 0.00 4.30
83 84 1.601477 CGCCGTAAAACCAACCCCT 60.601 57.895 0.00 0.00 0.00 4.79
84 85 2.628696 CCGCCGTAAAACCAACCCC 61.629 63.158 0.00 0.00 0.00 4.95
85 86 2.956194 CCGCCGTAAAACCAACCC 59.044 61.111 0.00 0.00 0.00 4.11
86 87 2.256158 GCCGCCGTAAAACCAACC 59.744 61.111 0.00 0.00 0.00 3.77
87 88 2.256158 GGCCGCCGTAAAACCAAC 59.744 61.111 0.00 0.00 0.00 3.77
88 89 2.203308 TGGCCGCCGTAAAACCAA 60.203 55.556 4.58 0.00 0.00 3.67
89 90 2.979120 GTGGCCGCCGTAAAACCA 60.979 61.111 4.45 0.00 0.00 3.67
90 91 2.979120 TGTGGCCGCCGTAAAACC 60.979 61.111 15.15 0.00 0.00 3.27
91 92 1.858372 ATGTGTGGCCGCCGTAAAAC 61.858 55.000 15.15 4.40 0.00 2.43
92 93 0.321387 TATGTGTGGCCGCCGTAAAA 60.321 50.000 15.15 0.00 0.00 1.52
93 94 1.020333 GTATGTGTGGCCGCCGTAAA 61.020 55.000 15.15 0.00 0.00 2.01
94 95 1.448189 GTATGTGTGGCCGCCGTAA 60.448 57.895 15.15 0.00 0.00 3.18
95 96 2.184836 GTATGTGTGGCCGCCGTA 59.815 61.111 15.15 8.15 0.00 4.02
96 97 4.010224 TGTATGTGTGGCCGCCGT 62.010 61.111 15.15 9.18 0.00 5.68
97 98 3.496131 GTGTATGTGTGGCCGCCG 61.496 66.667 15.15 0.00 0.00 6.46
98 99 2.046314 AGTGTATGTGTGGCCGCC 60.046 61.111 15.15 1.04 0.00 6.13
99 100 0.390603 TACAGTGTATGTGTGGCCGC 60.391 55.000 10.11 10.11 43.80 6.53
100 101 2.309528 ATACAGTGTATGTGTGGCCG 57.690 50.000 15.07 0.00 43.80 6.13
101 102 4.402056 ACTATACAGTGTATGTGTGGCC 57.598 45.455 23.36 0.00 43.80 5.36
102 103 4.034048 GCAACTATACAGTGTATGTGTGGC 59.966 45.833 23.36 23.15 43.80 5.01
103 104 5.175127 TGCAACTATACAGTGTATGTGTGG 58.825 41.667 23.36 18.83 43.80 4.17
104 105 6.238184 CCATGCAACTATACAGTGTATGTGTG 60.238 42.308 23.36 17.66 43.80 3.82
105 106 5.817296 CCATGCAACTATACAGTGTATGTGT 59.183 40.000 23.36 18.22 43.80 3.72
106 107 5.817296 ACCATGCAACTATACAGTGTATGTG 59.183 40.000 23.36 18.24 43.80 3.21
107 108 5.817296 CACCATGCAACTATACAGTGTATGT 59.183 40.000 23.36 16.28 46.45 2.29
108 109 5.277490 GCACCATGCAACTATACAGTGTATG 60.277 44.000 23.36 15.73 44.26 2.39
109 110 4.816385 GCACCATGCAACTATACAGTGTAT 59.184 41.667 19.36 19.36 44.26 2.29
110 111 4.188462 GCACCATGCAACTATACAGTGTA 58.812 43.478 5.24 5.24 44.26 2.90
111 112 3.009723 GCACCATGCAACTATACAGTGT 58.990 45.455 0.00 0.00 44.26 3.55
112 113 3.680642 GCACCATGCAACTATACAGTG 57.319 47.619 0.00 0.00 44.26 3.66
124 125 1.794116 GAAACACAACATGCACCATGC 59.206 47.619 5.19 0.00 44.80 4.06
125 126 2.052891 CGAAACACAACATGCACCATG 58.947 47.619 3.80 3.80 46.18 3.66
126 127 1.000385 CCGAAACACAACATGCACCAT 60.000 47.619 0.00 0.00 0.00 3.55
127 128 0.383590 CCGAAACACAACATGCACCA 59.616 50.000 0.00 0.00 0.00 4.17
128 129 0.665835 TCCGAAACACAACATGCACC 59.334 50.000 0.00 0.00 0.00 5.01
129 130 1.064803 TGTCCGAAACACAACATGCAC 59.935 47.619 0.00 0.00 31.20 4.57
147 148 1.133199 TCCCAACCATTCAAAGCCTGT 60.133 47.619 0.00 0.00 0.00 4.00
148 149 1.273327 GTCCCAACCATTCAAAGCCTG 59.727 52.381 0.00 0.00 0.00 4.85
151 152 4.809673 CTTAAGTCCCAACCATTCAAAGC 58.190 43.478 0.00 0.00 0.00 3.51
162 163 8.478877 TGAATGTTTTTAAAGCTTAAGTCCCAA 58.521 29.630 0.00 0.00 0.00 4.12
165 166 7.858879 TCGTGAATGTTTTTAAAGCTTAAGTCC 59.141 33.333 0.00 0.00 0.00 3.85
171 172 7.480810 ACTTCTCGTGAATGTTTTTAAAGCTT 58.519 30.769 0.00 0.00 0.00 3.74
172 173 7.027778 ACTTCTCGTGAATGTTTTTAAAGCT 57.972 32.000 0.00 0.00 0.00 3.74
173 174 7.547119 CAACTTCTCGTGAATGTTTTTAAAGC 58.453 34.615 0.00 0.00 0.00 3.51
174 175 7.547119 GCAACTTCTCGTGAATGTTTTTAAAG 58.453 34.615 0.00 0.00 0.00 1.85
245 246 8.213679 TCATCTAAATTTATGTTCCCTCTGGAG 58.786 37.037 0.00 0.00 43.07 3.86
246 247 8.101309 TCATCTAAATTTATGTTCCCTCTGGA 57.899 34.615 0.00 0.00 39.54 3.86
247 248 8.752005 TTCATCTAAATTTATGTTCCCTCTGG 57.248 34.615 0.00 0.00 0.00 3.86
249 250 9.190317 GGTTTCATCTAAATTTATGTTCCCTCT 57.810 33.333 0.00 0.00 0.00 3.69
250 251 8.966868 TGGTTTCATCTAAATTTATGTTCCCTC 58.033 33.333 0.00 0.00 0.00 4.30
251 252 8.893563 TGGTTTCATCTAAATTTATGTTCCCT 57.106 30.769 0.00 0.00 0.00 4.20
260 261 9.435688 GCAAGGTTATTGGTTTCATCTAAATTT 57.564 29.630 0.00 0.00 0.00 1.82
261 262 8.815912 AGCAAGGTTATTGGTTTCATCTAAATT 58.184 29.630 0.00 0.00 0.00 1.82
262 263 8.253113 CAGCAAGGTTATTGGTTTCATCTAAAT 58.747 33.333 0.00 0.00 0.00 1.40
263 264 7.309744 CCAGCAAGGTTATTGGTTTCATCTAAA 60.310 37.037 0.00 0.00 0.00 1.85
264 265 6.152661 CCAGCAAGGTTATTGGTTTCATCTAA 59.847 38.462 0.00 0.00 0.00 2.10
265 266 5.652014 CCAGCAAGGTTATTGGTTTCATCTA 59.348 40.000 0.00 0.00 0.00 1.98
266 267 4.463891 CCAGCAAGGTTATTGGTTTCATCT 59.536 41.667 0.00 0.00 0.00 2.90
267 268 4.747810 CCAGCAAGGTTATTGGTTTCATC 58.252 43.478 0.00 0.00 0.00 2.92
268 269 3.055891 GCCAGCAAGGTTATTGGTTTCAT 60.056 43.478 0.00 0.00 40.61 2.57
294 295 9.915629 AAAGTGAACTTATAAGACTACTCACAG 57.084 33.333 19.38 0.00 34.61 3.66
295 296 9.909644 GAAAGTGAACTTATAAGACTACTCACA 57.090 33.333 19.38 4.58 34.61 3.58
307 308 9.613428 CATAATGTGGAGGAAAGTGAACTTATA 57.387 33.333 0.00 0.00 34.61 0.98
325 326 1.007038 GGCCCGCATGCATAATGTG 60.007 57.895 19.57 0.00 44.89 3.21
336 337 3.825160 GAGTCACAGTTGGCCCGCA 62.825 63.158 0.00 0.00 0.00 5.69
337 338 3.050275 GAGTCACAGTTGGCCCGC 61.050 66.667 0.00 0.00 0.00 6.13
338 339 0.817634 TTTGAGTCACAGTTGGCCCG 60.818 55.000 0.00 0.00 0.00 6.13
406 407 6.151985 TGGCTAACTGTCAACTTTTTCTTTCA 59.848 34.615 0.00 0.00 0.00 2.69
408 409 6.524101 TGGCTAACTGTCAACTTTTTCTTT 57.476 33.333 0.00 0.00 0.00 2.52
426 427 4.321304 GCAAGAGCTATCTCGTTATGGCTA 60.321 45.833 9.73 0.00 42.97 3.93
463 464 9.293404 GTTTTTCTGGGTTACTTTTAGATACCT 57.707 33.333 0.00 0.00 0.00 3.08
464 465 9.070179 TGTTTTTCTGGGTTACTTTTAGATACC 57.930 33.333 0.00 0.00 0.00 2.73
481 516 9.665264 GACATACTACTTTTTCCTGTTTTTCTG 57.335 33.333 0.00 0.00 0.00 3.02
488 523 7.104290 GGCTTAGACATACTACTTTTTCCTGT 58.896 38.462 0.00 0.00 0.00 4.00
492 527 6.539103 CCTGGGCTTAGACATACTACTTTTTC 59.461 42.308 0.00 0.00 0.00 2.29
493 528 6.012771 ACCTGGGCTTAGACATACTACTTTTT 60.013 38.462 0.00 0.00 0.00 1.94
498 533 4.499357 CGAACCTGGGCTTAGACATACTAC 60.499 50.000 0.00 0.00 0.00 2.73
499 534 3.635373 CGAACCTGGGCTTAGACATACTA 59.365 47.826 0.00 0.00 0.00 1.82
500 535 2.431057 CGAACCTGGGCTTAGACATACT 59.569 50.000 0.00 0.00 0.00 2.12
584 621 9.049523 AGTATAAGATTGTTCGACGTATAGACA 57.950 33.333 0.00 0.00 0.00 3.41
585 622 9.875675 AAGTATAAGATTGTTCGACGTATAGAC 57.124 33.333 0.00 0.00 0.00 2.59
606 643 9.311425 AGGACTGTCCCTATATAGGATAAGTAT 57.689 37.037 27.58 15.56 46.63 2.12
609 646 7.644062 TGAGGACTGTCCCTATATAGGATAAG 58.356 42.308 27.58 21.24 46.63 1.73
620 657 5.144159 ACAGATAATGAGGACTGTCCCTA 57.856 43.478 22.81 12.69 38.95 3.53
623 660 5.983540 AGAAACAGATAATGAGGACTGTCC 58.016 41.667 19.20 19.20 41.73 4.02
625 662 6.102663 CGAAGAAACAGATAATGAGGACTGT 58.897 40.000 0.00 0.00 43.92 3.55
716 775 2.284150 TCTTTTCGTCGTTTGCACTGAG 59.716 45.455 0.00 0.00 0.00 3.35
787 1678 1.022735 GGACAGATGCTTCATGCCAG 58.977 55.000 2.07 0.00 42.00 4.85
796 1687 1.615392 GTGCCTTTTTGGACAGATGCT 59.385 47.619 0.00 0.00 38.35 3.79
799 1690 3.771216 AGATGTGCCTTTTTGGACAGAT 58.229 40.909 0.00 0.00 38.35 2.90
813 1704 3.564511 ACATGCGTTGTTTTAGATGTGC 58.435 40.909 0.00 0.00 33.74 4.57
837 1728 5.640147 ACACATTGGGATCCTAACTTGAAA 58.360 37.500 21.11 0.00 0.00 2.69
840 1731 5.256474 AGAACACATTGGGATCCTAACTTG 58.744 41.667 13.44 14.63 0.00 3.16
856 1747 2.818487 CGCACGGCACAAGAACACA 61.818 57.895 0.00 0.00 0.00 3.72
857 1748 2.052237 CGCACGGCACAAGAACAC 60.052 61.111 0.00 0.00 0.00 3.32
910 1801 4.814147 AGTGAGGCGATGATATATGTGTG 58.186 43.478 0.00 0.00 0.00 3.82
911 1802 4.524328 TGAGTGAGGCGATGATATATGTGT 59.476 41.667 0.00 0.00 0.00 3.72
1012 1910 0.819582 ATGCTGCCCCGAATTTCTTG 59.180 50.000 0.00 0.00 0.00 3.02
1019 1917 0.677731 CTTCTTCATGCTGCCCCGAA 60.678 55.000 0.00 0.00 0.00 4.30
1158 2056 2.048222 TGGTTCTGCTCCGCGAAG 60.048 61.111 8.23 0.00 0.00 3.79
1584 3891 1.299089 CGTCATCGTCCGCATGCTA 60.299 57.895 17.13 0.06 0.00 3.49
1633 3940 2.817423 CGCTGATCCCTTCTTGCGC 61.817 63.158 0.00 0.00 39.58 6.09
1684 4011 4.722700 CTTGGAGCCCACCACCCG 62.723 72.222 0.00 0.00 39.85 5.28
1849 4180 3.077484 ACTACCTTGAAGCACATGCAT 57.923 42.857 6.64 0.00 45.16 3.96
1860 4191 7.460910 TCCCGTATGTACATATACTACCTTGA 58.539 38.462 18.27 1.68 32.58 3.02
1865 4196 7.769220 AGCAATCCCGTATGTACATATACTAC 58.231 38.462 18.27 7.19 32.58 2.73
1866 4197 7.949690 AGCAATCCCGTATGTACATATACTA 57.050 36.000 18.27 6.20 32.58 1.82
1867 4198 6.852420 AGCAATCCCGTATGTACATATACT 57.148 37.500 18.27 0.00 32.58 2.12
1868 4199 8.991243 TTTAGCAATCCCGTATGTACATATAC 57.009 34.615 18.27 8.61 0.00 1.47
1874 4243 6.220930 TGAGATTTAGCAATCCCGTATGTAC 58.779 40.000 0.00 0.00 39.95 2.90
1875 4244 6.413783 TGAGATTTAGCAATCCCGTATGTA 57.586 37.500 0.00 0.00 39.95 2.29
1876 4245 5.290493 TGAGATTTAGCAATCCCGTATGT 57.710 39.130 0.00 0.00 39.95 2.29
1877 4246 4.153117 GCTGAGATTTAGCAATCCCGTATG 59.847 45.833 0.00 0.00 39.95 2.39
1884 4253 2.289002 CCACGGCTGAGATTTAGCAATC 59.711 50.000 0.00 0.00 42.88 2.67
1889 4258 1.482593 ACCTCCACGGCTGAGATTTAG 59.517 52.381 0.00 0.00 35.61 1.85
1895 4264 2.046892 CCAACCTCCACGGCTGAG 60.047 66.667 0.00 0.00 35.61 3.35
1900 4269 0.902531 ATCTACACCAACCTCCACGG 59.097 55.000 0.00 0.00 39.35 4.94
1953 4330 7.041576 TGACAAAGTCTCAATCAAATGACTGAG 60.042 37.037 14.06 14.06 46.40 3.35
1956 4334 7.284034 ACTTGACAAAGTCTCAATCAAATGACT 59.716 33.333 0.00 0.00 43.34 3.41
1961 4339 6.376864 TGGAACTTGACAAAGTCTCAATCAAA 59.623 34.615 0.00 0.00 46.15 2.69
1966 4344 4.843728 ACTGGAACTTGACAAAGTCTCAA 58.156 39.130 0.00 0.00 46.15 3.02
1972 4350 4.511454 TCAATCGACTGGAACTTGACAAAG 59.489 41.667 0.00 0.00 39.49 2.77
1973 4351 4.447290 TCAATCGACTGGAACTTGACAAA 58.553 39.130 0.00 0.00 0.00 2.83
1974 4352 4.058124 CTCAATCGACTGGAACTTGACAA 58.942 43.478 0.00 0.00 0.00 3.18
1975 4353 3.320826 TCTCAATCGACTGGAACTTGACA 59.679 43.478 0.00 0.00 0.00 3.58
1976 4354 3.914312 TCTCAATCGACTGGAACTTGAC 58.086 45.455 0.00 0.00 0.00 3.18
1977 4355 4.464244 AGATCTCAATCGACTGGAACTTGA 59.536 41.667 0.00 0.00 36.97 3.02
1978 4356 4.753233 AGATCTCAATCGACTGGAACTTG 58.247 43.478 0.00 0.00 36.97 3.16
1979 4357 5.654650 ACTAGATCTCAATCGACTGGAACTT 59.345 40.000 0.00 0.00 36.97 2.66
1980 4358 5.197451 ACTAGATCTCAATCGACTGGAACT 58.803 41.667 0.00 0.00 36.97 3.01
1981 4359 5.066634 TGACTAGATCTCAATCGACTGGAAC 59.933 44.000 0.00 0.00 36.97 3.62
1982 4360 5.066634 GTGACTAGATCTCAATCGACTGGAA 59.933 44.000 0.00 0.00 36.97 3.53
1983 4361 4.576873 GTGACTAGATCTCAATCGACTGGA 59.423 45.833 0.00 0.00 36.97 3.86
1984 4362 4.336713 TGTGACTAGATCTCAATCGACTGG 59.663 45.833 0.00 0.00 36.97 4.00
1985 4363 5.491635 TGTGACTAGATCTCAATCGACTG 57.508 43.478 0.00 0.00 36.97 3.51
1986 4364 5.240623 GGATGTGACTAGATCTCAATCGACT 59.759 44.000 0.00 0.00 36.97 4.18
1987 4365 5.009110 TGGATGTGACTAGATCTCAATCGAC 59.991 44.000 0.00 0.00 36.97 4.20
1988 4366 5.133221 TGGATGTGACTAGATCTCAATCGA 58.867 41.667 0.00 0.00 36.97 3.59
1989 4367 5.444663 TGGATGTGACTAGATCTCAATCG 57.555 43.478 0.00 0.00 36.97 3.34
1992 4370 7.062957 TCTGTATGGATGTGACTAGATCTCAA 58.937 38.462 0.00 0.00 34.59 3.02
2003 4381 6.183360 ACGGTTCAATATCTGTATGGATGTGA 60.183 38.462 0.00 0.00 0.00 3.58
2008 4386 4.100963 AGCACGGTTCAATATCTGTATGGA 59.899 41.667 0.00 0.00 0.00 3.41
2010 4388 5.277490 CCAAGCACGGTTCAATATCTGTATG 60.277 44.000 0.00 0.00 0.00 2.39
2034 4412 0.823460 CTCTCTCCAGGCTCCAACTC 59.177 60.000 0.00 0.00 0.00 3.01
2046 4424 3.579151 ACAGTTTACTCCCAACTCTCTCC 59.421 47.826 0.00 0.00 31.83 3.71
2048 4426 3.967987 ACACAGTTTACTCCCAACTCTCT 59.032 43.478 0.00 0.00 31.83 3.10
2057 4435 2.294074 TGCCACAACACAGTTTACTCC 58.706 47.619 0.00 0.00 0.00 3.85
2124 4906 3.191371 GGCGCATATATTCCCCTTTCTTG 59.809 47.826 10.83 0.00 0.00 3.02
2163 4945 2.093500 GCATGACATACCACTCAGACCA 60.093 50.000 0.00 0.00 0.00 4.02
2164 4946 2.093500 TGCATGACATACCACTCAGACC 60.093 50.000 0.00 0.00 0.00 3.85
2165 4947 3.251479 TGCATGACATACCACTCAGAC 57.749 47.619 0.00 0.00 0.00 3.51
2166 4948 3.198417 ACATGCATGACATACCACTCAGA 59.802 43.478 32.75 0.00 36.64 3.27
2167 4949 3.538591 ACATGCATGACATACCACTCAG 58.461 45.455 32.75 1.29 36.64 3.35
2168 4950 3.632643 ACATGCATGACATACCACTCA 57.367 42.857 32.75 0.00 36.64 3.41
2169 4951 4.509230 CACTACATGCATGACATACCACTC 59.491 45.833 32.75 0.00 36.64 3.51
2170 4952 4.080919 ACACTACATGCATGACATACCACT 60.081 41.667 32.75 9.69 36.64 4.00
2171 4953 4.191544 ACACTACATGCATGACATACCAC 58.808 43.478 32.75 0.00 36.64 4.16
2205 4987 9.804977 GTTATGGTATAGAGGGAGTAGTTCTTA 57.195 37.037 0.00 0.00 0.00 2.10
2221 5522 9.602568 TGAAAAACGCTCTTATGTTATGGTATA 57.397 29.630 0.00 0.00 0.00 1.47
2222 5523 8.500753 TGAAAAACGCTCTTATGTTATGGTAT 57.499 30.769 0.00 0.00 0.00 2.73
2224 5525 6.811253 TGAAAAACGCTCTTATGTTATGGT 57.189 33.333 0.00 0.00 0.00 3.55
2231 5532 4.846137 CCTCGTTTGAAAAACGCTCTTATG 59.154 41.667 17.88 4.73 42.80 1.90
2239 5540 2.309898 ATCGCCTCGTTTGAAAAACG 57.690 45.000 16.87 16.87 44.29 3.60
2248 5549 2.813908 GCACCGAATCGCCTCGTT 60.814 61.111 0.00 0.00 37.11 3.85
2273 5574 2.779755 ATTCATCGTGGGTGCAACTA 57.220 45.000 0.00 0.00 36.74 2.24
2328 5629 8.231692 TCTTCCATGCAAAATAAATTATCGGA 57.768 30.769 0.00 0.00 0.00 4.55
2337 5638 8.034215 CACCAACTTATCTTCCATGCAAAATAA 58.966 33.333 0.00 0.00 0.00 1.40
2338 5639 7.395772 TCACCAACTTATCTTCCATGCAAAATA 59.604 33.333 0.00 0.00 0.00 1.40
2339 5640 6.211184 TCACCAACTTATCTTCCATGCAAAAT 59.789 34.615 0.00 0.00 0.00 1.82
2378 5680 7.547370 TCAAACGTCCAAATGAACTGAAATTTT 59.453 29.630 0.00 0.00 0.00 1.82
2388 5690 5.237779 GGAGTTACTCAAACGTCCAAATGAA 59.762 40.000 14.72 0.00 43.29 2.57
2399 5701 1.886886 TTGCCGGGAGTTACTCAAAC 58.113 50.000 14.72 3.08 38.46 2.93
2401 5703 2.642154 TTTTGCCGGGAGTTACTCAA 57.358 45.000 14.72 0.00 31.08 3.02
2453 5755 5.934625 ACTGAGTCAGAACAATACATGAACC 59.065 40.000 26.86 0.00 35.18 3.62
2594 6065 6.148948 CGGTGAAGAGAAAATGCACAATAAA 58.851 36.000 0.00 0.00 0.00 1.40
2635 6163 7.613022 TGAAAAATGTAGATCCATTTCTGAGCT 59.387 33.333 9.50 0.00 42.63 4.09
2703 6234 4.759953 ACATATATTACCCCCTCCGTCTT 58.240 43.478 0.00 0.00 0.00 3.01
2770 6301 3.939592 GGTCCTTCCGAAAGATTTACCTG 59.060 47.826 0.00 0.00 34.14 4.00


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

AutoCloner maintained by Alex Coulton.