Multiple sequence alignment - TraesCS4A01G042100

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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 TraesCS4A01G042100 chr4A 100.000 3675 0 0 1 3675 35569717 35566043 0.000000e+00 6787.0
1 TraesCS4A01G042100 chr4A 81.390 1381 227 24 1228 2587 35477826 35476455 0.000000e+00 1099.0
2 TraesCS4A01G042100 chr4D 91.003 3590 218 59 157 3675 434148398 434144843 0.000000e+00 4743.0
3 TraesCS4A01G042100 chr4D 80.890 1371 234 23 1237 2587 434030839 434029477 0.000000e+00 1055.0
4 TraesCS4A01G042100 chr4D 73.475 377 84 13 165 538 428378628 428378265 1.070000e-25 128.0
5 TraesCS4A01G042100 chr4B 93.961 2583 100 29 505 3059 532721318 532718764 0.000000e+00 3855.0
6 TraesCS4A01G042100 chr4B 81.621 1382 224 25 1227 2587 532582619 532581247 0.000000e+00 1118.0
7 TraesCS4A01G042100 chr4B 91.000 400 30 4 3274 3673 532717481 532717088 5.400000e-148 534.0
8 TraesCS4A01G042100 chr1A 75.026 977 193 40 1231 2186 580988492 580989438 4.420000e-109 405.0
9 TraesCS4A01G042100 chr1D 74.821 977 195 39 1231 2186 483972824 483973770 9.570000e-106 394.0
10 TraesCS4A01G042100 chr1B 74.821 977 195 38 1231 2186 673992409 673993355 9.570000e-106 394.0
11 TraesCS4A01G042100 chr1B 74.216 989 204 39 1231 2198 674004543 674003585 2.090000e-97 366.0
12 TraesCS4A01G042100 chr6D 93.631 157 10 0 1 157 341385719 341385875 6.140000e-58 235.0
13 TraesCS4A01G042100 chr5D 92.994 157 11 0 1 157 374698129 374698285 2.850000e-56 230.0
14 TraesCS4A01G042100 chr6A 73.822 382 83 15 157 532 391600232 391599862 6.400000e-28 135.0
15 TraesCS4A01G042100 chr3D 82.979 94 15 1 157 250 124478172 124478264 2.350000e-12 84.2


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 TraesCS4A01G042100 chr4A 35566043 35569717 3674 True 6787.0 6787 100.0000 1 3675 1 chr4A.!!$R2 3674
1 TraesCS4A01G042100 chr4A 35476455 35477826 1371 True 1099.0 1099 81.3900 1228 2587 1 chr4A.!!$R1 1359
2 TraesCS4A01G042100 chr4D 434144843 434148398 3555 True 4743.0 4743 91.0030 157 3675 1 chr4D.!!$R3 3518
3 TraesCS4A01G042100 chr4D 434029477 434030839 1362 True 1055.0 1055 80.8900 1237 2587 1 chr4D.!!$R2 1350
4 TraesCS4A01G042100 chr4B 532717088 532721318 4230 True 2194.5 3855 92.4805 505 3673 2 chr4B.!!$R2 3168
5 TraesCS4A01G042100 chr4B 532581247 532582619 1372 True 1118.0 1118 81.6210 1227 2587 1 chr4B.!!$R1 1360
6 TraesCS4A01G042100 chr1A 580988492 580989438 946 False 405.0 405 75.0260 1231 2186 1 chr1A.!!$F1 955
7 TraesCS4A01G042100 chr1D 483972824 483973770 946 False 394.0 394 74.8210 1231 2186 1 chr1D.!!$F1 955
8 TraesCS4A01G042100 chr1B 673992409 673993355 946 False 394.0 394 74.8210 1231 2186 1 chr1B.!!$F1 955
9 TraesCS4A01G042100 chr1B 674003585 674004543 958 True 366.0 366 74.2160 1231 2198 1 chr1B.!!$R1 967

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
495 496 0.039180 TGCCGGTGAAGTCTAGAGGA 59.961 55.0 1.9 0.0 0.00 3.71 F
1171 1192 0.036952 AGATCTTGCTCACCACCGTG 60.037 55.0 0.0 0.0 41.72 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 1962 2.203907 AGCAGCTCCCTCCACACT 60.204 61.111 0.00 0.00 0.0 3.55 R
2819 2870 2.037367 TAGAGCGCTGGGTGTCCT 59.963 61.111 18.48 6.14 0.0 3.85 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
17 18 2.640989 TGGTCGTTGTCGTCTCGG 59.359 61.111 0.00 0.00 38.33 4.63
18 19 2.804090 GGTCGTTGTCGTCTCGGC 60.804 66.667 0.00 0.00 38.33 5.54
19 20 3.164011 GTCGTTGTCGTCTCGGCG 61.164 66.667 0.00 0.00 38.33 6.46
20 21 3.653009 TCGTTGTCGTCTCGGCGT 61.653 61.111 6.85 0.00 38.33 5.68
21 22 2.728383 CGTTGTCGTCTCGGCGTT 60.728 61.111 6.85 0.00 32.50 4.84
22 23 2.844146 GTTGTCGTCTCGGCGTTG 59.156 61.111 6.85 1.06 32.50 4.10
23 24 1.947642 GTTGTCGTCTCGGCGTTGT 60.948 57.895 6.85 0.00 32.50 3.32
24 25 1.947146 TTGTCGTCTCGGCGTTGTG 60.947 57.895 6.85 0.00 32.50 3.33
25 26 3.103911 GTCGTCTCGGCGTTGTGG 61.104 66.667 6.85 0.00 0.00 4.17
26 27 3.289062 TCGTCTCGGCGTTGTGGA 61.289 61.111 6.85 0.00 0.00 4.02
27 28 2.805353 CGTCTCGGCGTTGTGGAG 60.805 66.667 6.85 0.00 0.00 3.86
28 29 3.112709 GTCTCGGCGTTGTGGAGC 61.113 66.667 6.85 0.00 0.00 4.70
42 43 3.386237 GAGCCGGCTCCTGTCTGT 61.386 66.667 40.99 12.50 37.11 3.41
43 44 3.363844 GAGCCGGCTCCTGTCTGTC 62.364 68.421 40.99 17.67 37.11 3.51
44 45 3.695606 GCCGGCTCCTGTCTGTCA 61.696 66.667 22.15 0.00 0.00 3.58
45 46 2.262915 CCGGCTCCTGTCTGTCAC 59.737 66.667 0.00 0.00 0.00 3.67
46 47 2.126307 CGGCTCCTGTCTGTCACG 60.126 66.667 0.00 0.00 0.00 4.35
47 48 2.262915 GGCTCCTGTCTGTCACGG 59.737 66.667 0.00 0.00 0.00 4.94
48 49 2.276116 GGCTCCTGTCTGTCACGGA 61.276 63.158 0.00 0.00 32.23 4.69
49 50 1.214062 GCTCCTGTCTGTCACGGAG 59.786 63.158 12.42 12.42 40.78 4.63
50 51 1.244697 GCTCCTGTCTGTCACGGAGA 61.245 60.000 17.46 0.00 40.53 3.71
63 64 3.735029 GGAGACGCGACTCACCGT 61.735 66.667 32.99 3.18 40.85 4.83
67 68 2.354305 ACGCGACTCACCGTCAAC 60.354 61.111 15.93 0.00 42.98 3.18
68 69 3.103911 CGCGACTCACCGTCAACC 61.104 66.667 0.00 0.00 42.98 3.77
69 70 2.028484 GCGACTCACCGTCAACCA 59.972 61.111 0.00 0.00 42.98 3.67
70 71 2.308039 GCGACTCACCGTCAACCAC 61.308 63.158 0.00 0.00 42.98 4.16
71 72 1.066752 CGACTCACCGTCAACCACA 59.933 57.895 0.00 0.00 42.98 4.17
72 73 1.213094 CGACTCACCGTCAACCACAC 61.213 60.000 0.00 0.00 42.98 3.82
73 74 0.878961 GACTCACCGTCAACCACACC 60.879 60.000 0.00 0.00 42.37 4.16
74 75 1.597027 CTCACCGTCAACCACACCC 60.597 63.158 0.00 0.00 0.00 4.61
75 76 2.190843 CACCGTCAACCACACCCA 59.809 61.111 0.00 0.00 0.00 4.51
76 77 1.891919 CACCGTCAACCACACCCAG 60.892 63.158 0.00 0.00 0.00 4.45
77 78 2.978010 CCGTCAACCACACCCAGC 60.978 66.667 0.00 0.00 0.00 4.85
78 79 2.978010 CGTCAACCACACCCAGCC 60.978 66.667 0.00 0.00 0.00 4.85
79 80 2.515901 GTCAACCACACCCAGCCT 59.484 61.111 0.00 0.00 0.00 4.58
80 81 1.758592 GTCAACCACACCCAGCCTA 59.241 57.895 0.00 0.00 0.00 3.93
81 82 0.109723 GTCAACCACACCCAGCCTAA 59.890 55.000 0.00 0.00 0.00 2.69
82 83 1.072266 TCAACCACACCCAGCCTAAT 58.928 50.000 0.00 0.00 0.00 1.73
83 84 2.026636 GTCAACCACACCCAGCCTAATA 60.027 50.000 0.00 0.00 0.00 0.98
84 85 2.238646 TCAACCACACCCAGCCTAATAG 59.761 50.000 0.00 0.00 0.00 1.73
85 86 1.966845 ACCACACCCAGCCTAATAGT 58.033 50.000 0.00 0.00 0.00 2.12
86 87 1.559682 ACCACACCCAGCCTAATAGTG 59.440 52.381 0.00 0.00 34.61 2.74
87 88 1.837439 CCACACCCAGCCTAATAGTGA 59.163 52.381 0.00 0.00 32.76 3.41
88 89 2.238646 CCACACCCAGCCTAATAGTGAA 59.761 50.000 0.00 0.00 32.76 3.18
89 90 3.535561 CACACCCAGCCTAATAGTGAAG 58.464 50.000 0.00 0.00 32.76 3.02
90 91 2.505819 ACACCCAGCCTAATAGTGAAGG 59.494 50.000 0.00 0.00 35.86 3.46
91 92 2.127708 ACCCAGCCTAATAGTGAAGGG 58.872 52.381 0.00 0.00 40.88 3.95
92 93 1.202818 CCCAGCCTAATAGTGAAGGGC 60.203 57.143 0.00 0.00 42.74 5.19
95 96 1.598882 GCCTAATAGTGAAGGGCTGC 58.401 55.000 0.00 0.00 39.68 5.25
96 97 1.871080 CCTAATAGTGAAGGGCTGCG 58.129 55.000 0.00 0.00 0.00 5.18
97 98 1.139058 CCTAATAGTGAAGGGCTGCGT 59.861 52.381 0.00 0.00 0.00 5.24
98 99 2.364324 CCTAATAGTGAAGGGCTGCGTA 59.636 50.000 0.00 0.00 0.00 4.42
99 100 2.311124 AATAGTGAAGGGCTGCGTAC 57.689 50.000 0.00 0.00 0.00 3.67
100 101 0.102481 ATAGTGAAGGGCTGCGTACG 59.898 55.000 11.84 11.84 0.00 3.67
101 102 1.246056 TAGTGAAGGGCTGCGTACGT 61.246 55.000 17.90 0.00 0.00 3.57
102 103 2.048597 TGAAGGGCTGCGTACGTG 60.049 61.111 17.90 11.28 0.00 4.49
103 104 2.813908 GAAGGGCTGCGTACGTGG 60.814 66.667 17.90 10.87 0.00 4.94
125 126 4.286320 CGAGGAATCCGCCCCGAG 62.286 72.222 0.00 0.00 0.00 4.63
126 127 3.930012 GAGGAATCCGCCCCGAGG 61.930 72.222 0.00 0.00 0.00 4.63
138 139 4.457496 CCGAGGCGTCAGGCATGT 62.457 66.667 7.26 0.00 46.16 3.21
139 140 2.494445 CGAGGCGTCAGGCATGTA 59.506 61.111 7.26 0.00 46.16 2.29
140 141 1.153647 CGAGGCGTCAGGCATGTAA 60.154 57.895 7.26 0.00 46.16 2.41
141 142 0.530650 CGAGGCGTCAGGCATGTAAT 60.531 55.000 7.26 0.00 46.16 1.89
142 143 1.221414 GAGGCGTCAGGCATGTAATC 58.779 55.000 0.52 0.00 46.16 1.75
143 144 0.179045 AGGCGTCAGGCATGTAATCC 60.179 55.000 0.00 0.00 46.16 3.01
144 145 0.179045 GGCGTCAGGCATGTAATCCT 60.179 55.000 0.00 0.00 46.16 3.24
145 146 1.221414 GCGTCAGGCATGTAATCCTC 58.779 55.000 0.00 0.00 42.87 3.71
146 147 1.491670 CGTCAGGCATGTAATCCTCG 58.508 55.000 0.00 0.00 0.00 4.63
147 148 1.067060 CGTCAGGCATGTAATCCTCGA 59.933 52.381 0.00 0.00 0.00 4.04
148 149 2.748605 GTCAGGCATGTAATCCTCGAG 58.251 52.381 5.13 5.13 0.00 4.04
149 150 1.688735 TCAGGCATGTAATCCTCGAGG 59.311 52.381 26.32 26.32 0.00 4.63
171 172 1.205417 GGTCCAACCCTTGCATTGATG 59.795 52.381 0.00 0.00 30.04 3.07
177 178 2.880443 ACCCTTGCATTGATGTGAAGT 58.120 42.857 0.00 0.00 0.00 3.01
195 196 3.594603 AGTACCTGACACCAAATCTCG 57.405 47.619 0.00 0.00 0.00 4.04
201 202 3.329386 CTGACACCAAATCTCGTCACAT 58.671 45.455 0.00 0.00 34.78 3.21
205 206 5.084818 ACACCAAATCTCGTCACATGATA 57.915 39.130 0.00 0.00 0.00 2.15
206 207 5.487433 ACACCAAATCTCGTCACATGATAA 58.513 37.500 0.00 0.00 0.00 1.75
207 208 5.582269 ACACCAAATCTCGTCACATGATAAG 59.418 40.000 0.00 0.00 0.00 1.73
212 213 7.148423 CCAAATCTCGTCACATGATAAGAAACA 60.148 37.037 0.00 0.00 0.00 2.83
221 222 7.602644 GTCACATGATAAGAAACACTAACCTCA 59.397 37.037 0.00 0.00 0.00 3.86
222 223 8.321353 TCACATGATAAGAAACACTAACCTCAT 58.679 33.333 0.00 0.00 0.00 2.90
241 242 1.580059 TCACCCCAAGGAGATGGTAC 58.420 55.000 0.00 0.00 38.91 3.34
250 251 4.341235 CCAAGGAGATGGTACGAATCTACA 59.659 45.833 17.35 0.00 37.45 2.74
253 254 3.635373 GGAGATGGTACGAATCTACACCA 59.365 47.826 12.41 0.00 44.76 4.17
254 255 4.261656 GGAGATGGTACGAATCTACACCAG 60.262 50.000 12.41 0.00 43.94 4.00
255 256 2.953466 TGGTACGAATCTACACCAGC 57.047 50.000 0.00 0.00 36.15 4.85
259 260 3.368116 GGTACGAATCTACACCAGCACTT 60.368 47.826 0.00 0.00 0.00 3.16
261 262 1.920574 CGAATCTACACCAGCACTTCG 59.079 52.381 0.00 0.00 0.00 3.79
264 265 1.617322 TCTACACCAGCACTTCGTCT 58.383 50.000 0.00 0.00 0.00 4.18
270 271 2.228103 CACCAGCACTTCGTCTACTACA 59.772 50.000 0.00 0.00 0.00 2.74
273 274 3.378742 CCAGCACTTCGTCTACTACATCT 59.621 47.826 0.00 0.00 0.00 2.90
278 279 5.451662 GCACTTCGTCTACTACATCTAAACG 59.548 44.000 0.00 0.00 0.00 3.60
279 280 5.964168 CACTTCGTCTACTACATCTAAACGG 59.036 44.000 0.00 0.00 0.00 4.44
285 286 7.228108 TCGTCTACTACATCTAAACGGATGAAT 59.772 37.037 10.81 0.20 44.01 2.57
298 299 9.967346 CTAAACGGATGAATTAGAGTAAGATCA 57.033 33.333 0.00 0.00 0.00 2.92
303 304 7.309133 CGGATGAATTAGAGTAAGATCAGAGCT 60.309 40.741 0.00 0.00 0.00 4.09
331 332 8.190784 AGAAGACAAATTCAATGAAGAAACGTT 58.809 29.630 1.10 0.00 0.00 3.99
332 333 7.684062 AGACAAATTCAATGAAGAAACGTTG 57.316 32.000 0.00 0.00 37.90 4.10
336 337 4.582701 TTCAATGAAGAAACGTTGCCAT 57.417 36.364 0.00 0.00 36.90 4.40
337 338 5.697473 TTCAATGAAGAAACGTTGCCATA 57.303 34.783 0.00 0.00 36.90 2.74
367 368 1.394917 GTCGCACATGCAAGGACTAAG 59.605 52.381 4.49 0.00 42.21 2.18
372 373 4.229876 GCACATGCAAGGACTAAGAAAAC 58.770 43.478 0.00 0.00 41.59 2.43
373 374 4.261572 GCACATGCAAGGACTAAGAAAACA 60.262 41.667 0.00 0.00 41.59 2.83
374 375 5.565439 GCACATGCAAGGACTAAGAAAACAT 60.565 40.000 0.00 0.00 41.59 2.71
377 378 7.752239 CACATGCAAGGACTAAGAAAACATTAG 59.248 37.037 0.00 0.00 36.51 1.73
380 381 5.416013 GCAAGGACTAAGAAAACATTAGCCT 59.584 40.000 0.00 0.00 37.87 4.58
381 382 6.598064 GCAAGGACTAAGAAAACATTAGCCTA 59.402 38.462 8.24 0.00 36.55 3.93
382 383 7.283354 GCAAGGACTAAGAAAACATTAGCCTAT 59.717 37.037 8.24 0.00 36.55 2.57
383 384 9.832445 CAAGGACTAAGAAAACATTAGCCTATA 57.168 33.333 8.24 0.00 36.55 1.31
413 414 7.179966 TCTAATAACAGGAGGTAAGACACAGA 58.820 38.462 0.00 0.00 0.00 3.41
414 415 5.923733 ATAACAGGAGGTAAGACACAGAG 57.076 43.478 0.00 0.00 0.00 3.35
426 427 2.573915 AGACACAGAGATTTCCCTTCCC 59.426 50.000 0.00 0.00 0.00 3.97
431 432 0.183731 GAGATTTCCCTTCCCGCCAT 59.816 55.000 0.00 0.00 0.00 4.40
434 435 3.987954 TTTCCCTTCCCGCCATCGC 62.988 63.158 0.00 0.00 0.00 4.58
458 459 0.108138 CGAAGCCACAAGTAGAGGGG 60.108 60.000 0.00 0.00 0.00 4.79
459 460 1.276622 GAAGCCACAAGTAGAGGGGA 58.723 55.000 0.00 0.00 0.00 4.81
460 461 1.208293 GAAGCCACAAGTAGAGGGGAG 59.792 57.143 0.00 0.00 0.00 4.30
461 462 0.618968 AGCCACAAGTAGAGGGGAGG 60.619 60.000 0.00 0.00 0.00 4.30
462 463 1.908483 CCACAAGTAGAGGGGAGGC 59.092 63.158 0.00 0.00 0.00 4.70
463 464 1.517832 CACAAGTAGAGGGGAGGCG 59.482 63.158 0.00 0.00 0.00 5.52
465 466 0.252103 ACAAGTAGAGGGGAGGCGAA 60.252 55.000 0.00 0.00 0.00 4.70
466 467 1.123928 CAAGTAGAGGGGAGGCGAAT 58.876 55.000 0.00 0.00 0.00 3.34
468 469 0.470268 AGTAGAGGGGAGGCGAATCC 60.470 60.000 0.00 0.00 38.76 3.01
469 470 0.759436 GTAGAGGGGAGGCGAATCCA 60.759 60.000 8.41 0.00 41.52 3.41
470 471 0.759436 TAGAGGGGAGGCGAATCCAC 60.759 60.000 8.41 4.71 43.73 4.02
471 472 2.285368 AGGGGAGGCGAATCCACA 60.285 61.111 10.80 0.00 46.03 4.17
472 473 1.694169 AGGGGAGGCGAATCCACAT 60.694 57.895 10.80 0.00 46.03 3.21
473 474 0.399949 AGGGGAGGCGAATCCACATA 60.400 55.000 10.80 0.00 46.03 2.29
476 477 1.141053 GGGAGGCGAATCCACATACTT 59.859 52.381 8.41 0.00 41.52 2.24
488 489 1.732259 CACATACTTGCCGGTGAAGTC 59.268 52.381 20.33 0.00 35.30 3.01
490 491 2.829720 ACATACTTGCCGGTGAAGTCTA 59.170 45.455 20.33 8.36 35.30 2.59
494 495 0.895530 TTGCCGGTGAAGTCTAGAGG 59.104 55.000 1.90 0.00 0.00 3.69
495 496 0.039180 TGCCGGTGAAGTCTAGAGGA 59.961 55.000 1.90 0.00 0.00 3.71
496 497 1.183549 GCCGGTGAAGTCTAGAGGAA 58.816 55.000 1.90 0.00 0.00 3.36
498 499 2.028385 GCCGGTGAAGTCTAGAGGAAAA 60.028 50.000 1.90 0.00 0.00 2.29
518 519 0.618981 AGTTTGCCCTAGCCACCTAC 59.381 55.000 0.00 0.00 38.69 3.18
520 521 2.530958 TTTGCCCTAGCCACCTACGC 62.531 60.000 0.00 0.00 38.69 4.42
522 523 1.831286 GCCCTAGCCACCTACGCTA 60.831 63.158 0.00 0.00 37.79 4.26
538 541 1.409427 CGCTAGGGAGGAAAACGAGAT 59.591 52.381 0.00 0.00 0.00 2.75
549 552 2.080286 AAACGAGATGTCCAGGAACG 57.920 50.000 0.00 0.00 0.00 3.95
575 578 8.331931 ACATATACTTCTTCCTTGGGTCATTA 57.668 34.615 0.00 0.00 0.00 1.90
590 593 7.220741 TGGGTCATTAATTTGTGAATCGAAA 57.779 32.000 0.00 0.00 0.00 3.46
689 697 6.813152 GCCCATATCAATTTCCCATTAATTCG 59.187 38.462 0.00 0.00 0.00 3.34
730 738 2.004583 AAGCGAGCGTGCACTTATTA 57.995 45.000 16.19 0.00 37.31 0.98
731 739 2.225068 AGCGAGCGTGCACTTATTAT 57.775 45.000 16.19 0.00 37.31 1.28
746 754 1.221414 ATTATTGCTTCCGCTCTCGC 58.779 50.000 0.00 0.00 36.97 5.03
796 804 3.368116 CCGTATATAAAAGAGGGCCGAGG 60.368 52.174 0.00 0.00 0.00 4.63
823 831 4.520492 AGAAATTTCACACACCACATCTCC 59.480 41.667 19.99 0.00 0.00 3.71
824 832 1.877637 TTTCACACACCACATCTCCG 58.122 50.000 0.00 0.00 0.00 4.63
825 833 0.756294 TTCACACACCACATCTCCGT 59.244 50.000 0.00 0.00 0.00 4.69
826 834 0.756294 TCACACACCACATCTCCGTT 59.244 50.000 0.00 0.00 0.00 4.44
831 839 1.066858 ACACCACATCTCCGTTGCTAG 60.067 52.381 0.00 0.00 0.00 3.42
837 845 0.246635 ATCTCCGTTGCTAGTTGCGT 59.753 50.000 0.00 0.00 46.63 5.24
839 847 1.352156 CTCCGTTGCTAGTTGCGTCC 61.352 60.000 0.00 0.00 46.63 4.79
841 849 1.626654 CCGTTGCTAGTTGCGTCCAG 61.627 60.000 0.00 0.00 46.63 3.86
892 900 1.883926 GCTAGCTAGCTAGAGACCCAC 59.116 57.143 42.59 25.24 46.56 4.61
931 939 0.107456 CAACTGAGCACACCAGGACT 59.893 55.000 0.00 0.00 36.03 3.85
932 940 1.344438 CAACTGAGCACACCAGGACTA 59.656 52.381 0.00 0.00 36.03 2.59
933 941 0.969894 ACTGAGCACACCAGGACTAC 59.030 55.000 0.00 0.00 36.03 2.73
955 963 2.061773 CAGTCGGTTAAGCACTGTGAG 58.938 52.381 12.86 4.59 34.08 3.51
981 989 1.608283 GCTAGGTTCAGGTCACCACAC 60.608 57.143 0.00 0.00 36.67 3.82
1000 1008 2.293318 ACGCCTCATCTCCAAGCCA 61.293 57.895 0.00 0.00 0.00 4.75
1001 1009 1.147824 CGCCTCATCTCCAAGCCAT 59.852 57.895 0.00 0.00 0.00 4.40
1003 1011 0.182061 GCCTCATCTCCAAGCCATGA 59.818 55.000 0.00 0.00 0.00 3.07
1004 1012 1.814634 GCCTCATCTCCAAGCCATGAG 60.815 57.143 0.00 0.00 42.20 2.90
1143 1161 4.383602 ACGCCGCAACGTGCATTC 62.384 61.111 0.00 0.00 45.36 2.67
1151 1169 1.667724 GCAACGTGCATTCTCAGCTAT 59.332 47.619 0.00 0.00 44.26 2.97
1152 1170 2.866156 GCAACGTGCATTCTCAGCTATA 59.134 45.455 0.00 0.00 44.26 1.31
1159 1177 5.345472 CGTGCATTCTCAGCTATAGATCTTG 59.655 44.000 0.00 0.00 0.00 3.02
1170 1191 1.557099 TAGATCTTGCTCACCACCGT 58.443 50.000 0.00 0.00 0.00 4.83
1171 1192 0.036952 AGATCTTGCTCACCACCGTG 60.037 55.000 0.00 0.00 41.72 4.94
1172 1193 1.639298 GATCTTGCTCACCACCGTGC 61.639 60.000 0.00 0.00 40.04 5.34
1183 1204 3.058160 ACCGTGCTGCATGAAGGC 61.058 61.111 22.79 0.00 0.00 4.35
1195 1218 1.913951 ATGAAGGCCGATGCTGTGGA 61.914 55.000 0.00 0.00 37.74 4.02
1214 1237 5.836009 GTGGATAACACGTACGTTAACTTG 58.164 41.667 20.23 9.04 40.85 3.16
1342 1377 1.068753 CATCTACTCGCTGCTGGGG 59.931 63.158 7.80 1.84 0.00 4.96
1396 1431 2.497293 CGGCGCTACACCATGGTA 59.503 61.111 19.28 1.27 0.00 3.25
1798 1833 0.335019 TCCTGAGGACCTCCGATTCA 59.665 55.000 19.11 0.00 42.08 2.57
2685 2735 1.547372 TCAGCAGTAACCCCGAGTAAC 59.453 52.381 0.00 0.00 0.00 2.50
2740 2791 1.752694 GTTGTGTGTGGTGTGGCCT 60.753 57.895 3.32 0.00 38.35 5.19
2743 2794 2.124362 TGTGTGGTGTGGCCTGTG 60.124 61.111 3.32 0.00 38.35 3.66
2744 2795 2.124320 GTGTGGTGTGGCCTGTGT 60.124 61.111 3.32 0.00 38.35 3.72
2745 2796 2.186826 GTGTGGTGTGGCCTGTGTC 61.187 63.158 3.32 0.00 38.35 3.67
2746 2797 2.594592 GTGGTGTGGCCTGTGTCC 60.595 66.667 3.32 0.00 38.35 4.02
2747 2798 3.093172 TGGTGTGGCCTGTGTCCA 61.093 61.111 3.32 2.86 38.35 4.02
2752 2803 1.529244 GTGGCCTGTGTCCAAAGCT 60.529 57.895 3.32 0.00 35.01 3.74
2819 2870 3.771216 ACAGACTTTAGGACGTAGGGAA 58.229 45.455 0.00 0.00 0.00 3.97
2844 2895 3.905678 CAGCGCTCTACGGGGAGG 61.906 72.222 7.13 0.00 43.93 4.30
2952 3007 3.134401 CGCAGCTTGTGACAGATCT 57.866 52.632 0.00 0.00 0.00 2.75
3029 3084 6.342906 TGGTATGTACAGGCTTGTGTTATAC 58.657 40.000 12.40 15.15 38.23 1.47
3030 3085 5.461078 GGTATGTACAGGCTTGTGTTATACG 59.539 44.000 12.40 0.00 38.23 3.06
3031 3086 3.852286 TGTACAGGCTTGTGTTATACGG 58.148 45.455 12.40 0.00 38.23 4.02
3032 3087 3.258872 TGTACAGGCTTGTGTTATACGGT 59.741 43.478 12.40 0.00 38.23 4.83
3033 3088 4.462132 TGTACAGGCTTGTGTTATACGGTA 59.538 41.667 12.40 0.00 38.23 4.02
3034 3089 4.748277 ACAGGCTTGTGTTATACGGTAT 57.252 40.909 0.00 5.87 35.83 2.73
3035 3090 5.857471 ACAGGCTTGTGTTATACGGTATA 57.143 39.130 0.00 3.76 35.83 1.47
3083 3166 8.806429 TTTAGTTGCATATTTTCCATCTCTGA 57.194 30.769 0.00 0.00 0.00 3.27
3084 3167 6.939132 AGTTGCATATTTTCCATCTCTGAG 57.061 37.500 0.00 0.00 0.00 3.35
3144 4108 5.468746 CCAGACGTAAGAAAAATTCCTGACA 59.531 40.000 0.00 0.00 43.62 3.58
3179 4150 4.034742 GCTAAACCGGTGTACATTACCATG 59.965 45.833 8.52 0.00 38.11 3.66
3195 4166 9.391006 ACATTACCATGACGACAAACTAATATT 57.609 29.630 0.00 0.00 34.11 1.28
3209 4181 7.906527 ACAAACTAATATTGTCGTAAATTCGGC 59.093 33.333 0.00 0.00 36.28 5.54
3215 4187 7.739498 ATATTGTCGTAAATTCGGCCTAAAT 57.261 32.000 0.00 0.00 34.35 1.40
3301 4438 4.677182 ACTCTTTTGGCCCACTAATGAAT 58.323 39.130 0.00 0.00 0.00 2.57
3302 4439 4.463891 ACTCTTTTGGCCCACTAATGAATG 59.536 41.667 0.00 0.00 0.00 2.67
3328 4465 7.361713 GGGTGATGAGTTGTTTCATTCGAAATA 60.362 37.037 0.00 0.00 42.90 1.40
3334 4471 9.393249 TGAGTTGTTTCATTCGAAATAATTGTC 57.607 29.630 0.00 0.00 42.10 3.18
3363 4500 6.308015 AGAACTGTTTATATGTGCCTACCA 57.692 37.500 0.00 0.00 0.00 3.25
3376 4513 3.763897 GTGCCTACCAAATCCAGACAAAT 59.236 43.478 0.00 0.00 0.00 2.32
3377 4514 3.763360 TGCCTACCAAATCCAGACAAATG 59.237 43.478 0.00 0.00 0.00 2.32
3402 4539 5.437060 TGAAGTTCAAGTTTGAGCTACCTT 58.563 37.500 10.92 0.00 46.08 3.50
3406 4543 3.390135 TCAAGTTTGAGCTACCTTGTCG 58.610 45.455 11.58 0.00 36.53 4.35
3411 4548 2.060326 TGAGCTACCTTGTCGAAACG 57.940 50.000 0.00 0.00 0.00 3.60
3464 4601 7.568497 CGTGCAACTTGAAGAAAAAGAAAAACA 60.568 33.333 0.00 0.00 31.75 2.83
3490 4627 6.478344 TGATGTTTTGTTTCTTTCGGGAAATG 59.522 34.615 0.00 0.00 37.50 2.32
3492 4629 6.578023 TGTTTTGTTTCTTTCGGGAAATGAT 58.422 32.000 0.00 0.00 37.50 2.45
3493 4630 6.478344 TGTTTTGTTTCTTTCGGGAAATGATG 59.522 34.615 0.00 0.00 37.50 3.07
3554 4691 5.469084 GGGAAAACAAGAGAACAGTTCGTAT 59.531 40.000 7.68 0.00 34.02 3.06
3557 4694 4.500603 ACAAGAGAACAGTTCGTATCGT 57.499 40.909 7.68 0.81 34.02 3.73
3570 4707 5.798934 AGTTCGTATCGTCTGAACATGTAAC 59.201 40.000 0.00 0.00 43.36 2.50
3578 4715 4.523813 GTCTGAACATGTAACCGTTTGTG 58.476 43.478 0.00 0.00 0.00 3.33
3582 4719 2.566913 ACATGTAACCGTTTGTGCTCA 58.433 42.857 0.00 0.00 0.00 4.26
3629 4766 6.547141 ACAGTGTAAGGGCGTATATACTGTTA 59.453 38.462 17.31 1.36 46.00 2.41
3639 4776 9.962783 GGGCGTATATACTGTTAATATCTTAGG 57.037 37.037 11.05 0.00 0.00 2.69
3648 4785 6.156256 ACTGTTAATATCTTAGGTGAGCCACA 59.844 38.462 7.49 0.00 35.86 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.640989 CCGAGACGACAACGACCA 59.359 61.111 0.00 0.00 42.66 4.02
1 2 2.804090 GCCGAGACGACAACGACC 60.804 66.667 0.00 0.00 42.66 4.79
2 3 3.164011 CGCCGAGACGACAACGAC 61.164 66.667 0.00 0.00 42.66 4.34
3 4 3.185082 AACGCCGAGACGACAACGA 62.185 57.895 0.00 0.00 42.66 3.85
4 5 2.728383 AACGCCGAGACGACAACG 60.728 61.111 0.00 0.00 45.75 4.10
5 6 1.947642 ACAACGCCGAGACGACAAC 60.948 57.895 0.00 0.00 36.70 3.32
6 7 1.947146 CACAACGCCGAGACGACAA 60.947 57.895 0.00 0.00 36.70 3.18
7 8 2.354188 CACAACGCCGAGACGACA 60.354 61.111 0.00 0.00 36.70 4.35
8 9 3.103911 CCACAACGCCGAGACGAC 61.104 66.667 0.00 0.00 36.70 4.34
9 10 3.263503 CTCCACAACGCCGAGACGA 62.264 63.158 0.00 0.00 36.70 4.20
10 11 2.805353 CTCCACAACGCCGAGACG 60.805 66.667 0.00 0.00 39.50 4.18
11 12 3.112709 GCTCCACAACGCCGAGAC 61.113 66.667 0.00 0.00 0.00 3.36
12 13 4.373116 GGCTCCACAACGCCGAGA 62.373 66.667 0.00 0.00 36.45 4.04
25 26 3.363844 GACAGACAGGAGCCGGCTC 62.364 68.421 42.46 42.46 42.04 4.70
26 27 3.386237 GACAGACAGGAGCCGGCT 61.386 66.667 33.48 33.48 0.00 5.52
27 28 3.695606 TGACAGACAGGAGCCGGC 61.696 66.667 21.89 21.89 0.00 6.13
28 29 2.262915 GTGACAGACAGGAGCCGG 59.737 66.667 0.00 0.00 0.00 6.13
29 30 2.126307 CGTGACAGACAGGAGCCG 60.126 66.667 0.00 0.00 36.62 5.52
30 31 2.219325 CTCCGTGACAGACAGGAGCC 62.219 65.000 0.00 0.00 42.99 4.70
31 32 1.214062 CTCCGTGACAGACAGGAGC 59.786 63.158 0.00 0.00 42.99 4.70
33 34 1.235281 CGTCTCCGTGACAGACAGGA 61.235 60.000 4.31 0.00 45.60 3.86
34 35 1.210413 CGTCTCCGTGACAGACAGG 59.790 63.158 4.31 0.00 45.60 4.00
35 36 1.442857 GCGTCTCCGTGACAGACAG 60.443 63.158 4.31 0.00 45.60 3.51
36 37 2.643272 GCGTCTCCGTGACAGACA 59.357 61.111 4.31 0.00 45.60 3.41
43 44 2.502080 GTGAGTCGCGTCTCCGTG 60.502 66.667 26.45 0.00 45.74 4.94
44 45 3.735029 GGTGAGTCGCGTCTCCGT 61.735 66.667 26.45 0.00 36.15 4.69
45 46 4.813526 CGGTGAGTCGCGTCTCCG 62.814 72.222 26.45 23.44 44.53 4.63
46 47 3.664223 GACGGTGAGTCGCGTCTCC 62.664 68.421 26.45 16.99 40.43 3.71
47 48 2.202324 GACGGTGAGTCGCGTCTC 60.202 66.667 23.66 23.66 40.43 3.36
55 56 1.145377 GGTGTGGTTGACGGTGAGT 59.855 57.895 0.00 0.00 0.00 3.41
56 57 1.597027 GGGTGTGGTTGACGGTGAG 60.597 63.158 0.00 0.00 0.00 3.51
57 58 2.318519 CTGGGTGTGGTTGACGGTGA 62.319 60.000 0.00 0.00 0.00 4.02
58 59 1.891919 CTGGGTGTGGTTGACGGTG 60.892 63.158 0.00 0.00 0.00 4.94
59 60 2.508928 CTGGGTGTGGTTGACGGT 59.491 61.111 0.00 0.00 0.00 4.83
60 61 2.978010 GCTGGGTGTGGTTGACGG 60.978 66.667 0.00 0.00 0.00 4.79
61 62 2.107041 TAGGCTGGGTGTGGTTGACG 62.107 60.000 0.00 0.00 0.00 4.35
62 63 0.109723 TTAGGCTGGGTGTGGTTGAC 59.890 55.000 0.00 0.00 0.00 3.18
63 64 1.072266 ATTAGGCTGGGTGTGGTTGA 58.928 50.000 0.00 0.00 0.00 3.18
64 65 2.026262 ACTATTAGGCTGGGTGTGGTTG 60.026 50.000 0.00 0.00 0.00 3.77
65 66 2.026262 CACTATTAGGCTGGGTGTGGTT 60.026 50.000 0.00 0.00 0.00 3.67
66 67 1.559682 CACTATTAGGCTGGGTGTGGT 59.440 52.381 0.00 0.00 0.00 4.16
67 68 1.837439 TCACTATTAGGCTGGGTGTGG 59.163 52.381 0.00 0.00 0.00 4.17
68 69 3.535561 CTTCACTATTAGGCTGGGTGTG 58.464 50.000 0.00 1.71 0.00 3.82
69 70 2.505819 CCTTCACTATTAGGCTGGGTGT 59.494 50.000 0.00 0.00 0.00 4.16
70 71 2.158755 CCCTTCACTATTAGGCTGGGTG 60.159 54.545 0.00 0.99 0.00 4.61
71 72 2.127708 CCCTTCACTATTAGGCTGGGT 58.872 52.381 0.00 0.00 0.00 4.51
72 73 1.202818 GCCCTTCACTATTAGGCTGGG 60.203 57.143 0.00 0.00 40.57 4.45
73 74 2.262423 GCCCTTCACTATTAGGCTGG 57.738 55.000 0.00 0.00 40.57 4.85
76 77 1.598882 GCAGCCCTTCACTATTAGGC 58.401 55.000 0.00 0.00 44.20 3.93
77 78 1.139058 ACGCAGCCCTTCACTATTAGG 59.861 52.381 0.00 0.00 0.00 2.69
78 79 2.604046 ACGCAGCCCTTCACTATTAG 57.396 50.000 0.00 0.00 0.00 1.73
79 80 2.223641 CGTACGCAGCCCTTCACTATTA 60.224 50.000 0.52 0.00 0.00 0.98
80 81 1.470979 CGTACGCAGCCCTTCACTATT 60.471 52.381 0.52 0.00 0.00 1.73
81 82 0.102481 CGTACGCAGCCCTTCACTAT 59.898 55.000 0.52 0.00 0.00 2.12
82 83 1.246056 ACGTACGCAGCCCTTCACTA 61.246 55.000 16.72 0.00 0.00 2.74
83 84 2.261671 CGTACGCAGCCCTTCACT 59.738 61.111 0.52 0.00 0.00 3.41
84 85 2.048503 ACGTACGCAGCCCTTCAC 60.049 61.111 16.72 0.00 0.00 3.18
85 86 2.048597 CACGTACGCAGCCCTTCA 60.049 61.111 16.72 0.00 0.00 3.02
86 87 2.813908 CCACGTACGCAGCCCTTC 60.814 66.667 16.72 0.00 0.00 3.46
109 110 3.930012 CCTCGGGGCGGATTCCTC 61.930 72.222 0.30 0.00 0.00 3.71
121 122 2.572095 TTACATGCCTGACGCCTCGG 62.572 60.000 0.00 0.00 36.24 4.63
122 123 0.530650 ATTACATGCCTGACGCCTCG 60.531 55.000 0.00 0.00 36.24 4.63
123 124 1.221414 GATTACATGCCTGACGCCTC 58.779 55.000 0.00 0.00 36.24 4.70
124 125 0.179045 GGATTACATGCCTGACGCCT 60.179 55.000 0.00 0.00 36.24 5.52
125 126 0.179045 AGGATTACATGCCTGACGCC 60.179 55.000 0.00 0.00 36.24 5.68
126 127 1.221414 GAGGATTACATGCCTGACGC 58.779 55.000 0.00 0.00 33.84 5.19
127 128 1.067060 TCGAGGATTACATGCCTGACG 59.933 52.381 0.00 0.00 33.84 4.35
128 129 2.546795 CCTCGAGGATTACATGCCTGAC 60.547 54.545 28.21 0.00 37.39 3.51
129 130 1.688735 CCTCGAGGATTACATGCCTGA 59.311 52.381 28.21 0.00 37.39 3.86
130 131 1.688735 TCCTCGAGGATTACATGCCTG 59.311 52.381 30.49 0.00 39.78 4.85
131 132 1.967066 CTCCTCGAGGATTACATGCCT 59.033 52.381 33.66 0.00 44.46 4.75
132 133 2.447244 CTCCTCGAGGATTACATGCC 57.553 55.000 33.66 0.00 44.46 4.40
143 144 0.905337 AAGGGTTGGACCTCCTCGAG 60.905 60.000 5.13 5.13 40.87 4.04
144 145 1.157751 AAGGGTTGGACCTCCTCGA 59.842 57.895 0.00 0.00 40.87 4.04
145 146 1.296715 CAAGGGTTGGACCTCCTCG 59.703 63.158 0.00 0.00 40.87 4.63
146 147 1.002011 GCAAGGGTTGGACCTCCTC 60.002 63.158 0.00 0.00 40.87 3.71
147 148 1.142688 ATGCAAGGGTTGGACCTCCT 61.143 55.000 0.00 0.00 40.87 3.69
148 149 0.251787 AATGCAAGGGTTGGACCTCC 60.252 55.000 0.00 0.00 40.87 4.30
149 150 0.890683 CAATGCAAGGGTTGGACCTC 59.109 55.000 0.00 0.00 40.87 3.85
150 151 0.482446 TCAATGCAAGGGTTGGACCT 59.518 50.000 0.00 0.00 44.56 3.85
151 152 1.205417 CATCAATGCAAGGGTTGGACC 59.795 52.381 0.00 0.00 37.60 4.46
152 153 1.895131 ACATCAATGCAAGGGTTGGAC 59.105 47.619 0.00 0.00 32.41 4.02
153 154 1.894466 CACATCAATGCAAGGGTTGGA 59.106 47.619 0.00 0.00 34.77 3.53
154 155 1.894466 TCACATCAATGCAAGGGTTGG 59.106 47.619 0.00 0.00 0.00 3.77
155 156 3.006110 ACTTCACATCAATGCAAGGGTTG 59.994 43.478 0.00 0.00 0.00 3.77
171 172 4.642429 AGATTTGGTGTCAGGTACTTCAC 58.358 43.478 0.00 0.00 39.06 3.18
177 178 2.894765 TGACGAGATTTGGTGTCAGGTA 59.105 45.455 0.00 0.00 36.50 3.08
195 196 7.602644 TGAGGTTAGTGTTTCTTATCATGTGAC 59.397 37.037 0.00 0.00 0.00 3.67
201 202 7.103641 GGTGATGAGGTTAGTGTTTCTTATCA 58.896 38.462 0.00 0.00 32.38 2.15
205 206 4.506802 GGGGTGATGAGGTTAGTGTTTCTT 60.507 45.833 0.00 0.00 0.00 2.52
206 207 3.009143 GGGGTGATGAGGTTAGTGTTTCT 59.991 47.826 0.00 0.00 0.00 2.52
207 208 3.244770 TGGGGTGATGAGGTTAGTGTTTC 60.245 47.826 0.00 0.00 0.00 2.78
212 213 1.916181 CCTTGGGGTGATGAGGTTAGT 59.084 52.381 0.00 0.00 0.00 2.24
221 222 2.127708 GTACCATCTCCTTGGGGTGAT 58.872 52.381 0.00 0.00 43.97 3.06
222 223 1.580059 GTACCATCTCCTTGGGGTGA 58.420 55.000 0.00 0.00 41.35 4.02
241 242 1.920574 CGAAGTGCTGGTGTAGATTCG 59.079 52.381 0.00 0.00 34.46 3.34
259 260 6.051074 TCATCCGTTTAGATGTAGTAGACGA 58.949 40.000 0.00 0.00 43.46 4.20
273 274 9.967346 CTGATCTTACTCTAATTCATCCGTTTA 57.033 33.333 0.00 0.00 0.00 2.01
278 279 7.895759 AGCTCTGATCTTACTCTAATTCATCC 58.104 38.462 0.00 0.00 0.00 3.51
285 286 9.116067 GTCTTCTAAGCTCTGATCTTACTCTAA 57.884 37.037 0.00 0.00 0.00 2.10
293 294 7.619050 TGAATTTGTCTTCTAAGCTCTGATCT 58.381 34.615 0.00 0.00 0.00 2.75
297 298 8.037382 TCATTGAATTTGTCTTCTAAGCTCTG 57.963 34.615 0.00 0.00 0.00 3.35
298 299 8.627208 TTCATTGAATTTGTCTTCTAAGCTCT 57.373 30.769 0.00 0.00 0.00 4.09
303 304 9.663904 CGTTTCTTCATTGAATTTGTCTTCTAA 57.336 29.630 0.00 0.00 0.00 2.10
331 332 3.445687 ACGCTCGGACGTATGGCA 61.446 61.111 1.73 0.00 46.19 4.92
348 349 1.275010 TCTTAGTCCTTGCATGTGCGA 59.725 47.619 0.01 0.00 45.83 5.10
388 389 7.179966 TCTGTGTCTTACCTCCTGTTATTAGA 58.820 38.462 0.00 0.00 0.00 2.10
398 399 4.383226 GGGAAATCTCTGTGTCTTACCTCC 60.383 50.000 0.00 0.00 0.00 4.30
399 400 4.468153 AGGGAAATCTCTGTGTCTTACCTC 59.532 45.833 0.00 0.00 0.00 3.85
407 408 1.279271 CGGGAAGGGAAATCTCTGTGT 59.721 52.381 0.00 0.00 0.00 3.72
410 411 0.464554 GGCGGGAAGGGAAATCTCTG 60.465 60.000 0.00 0.00 0.00 3.35
413 414 0.183731 GATGGCGGGAAGGGAAATCT 59.816 55.000 0.00 0.00 0.00 2.40
414 415 1.166531 CGATGGCGGGAAGGGAAATC 61.167 60.000 0.00 0.00 0.00 2.17
441 442 1.280457 CTCCCCTCTACTTGTGGCTT 58.720 55.000 0.00 0.00 0.00 4.35
445 446 0.970937 TCGCCTCCCCTCTACTTGTG 60.971 60.000 0.00 0.00 0.00 3.33
446 447 0.252103 TTCGCCTCCCCTCTACTTGT 60.252 55.000 0.00 0.00 0.00 3.16
449 450 0.470268 GGATTCGCCTCCCCTCTACT 60.470 60.000 0.00 0.00 0.00 2.57
450 451 0.759436 TGGATTCGCCTCCCCTCTAC 60.759 60.000 1.25 0.00 37.63 2.59
451 452 0.759436 GTGGATTCGCCTCCCCTCTA 60.759 60.000 1.25 0.00 37.63 2.43
453 454 1.700042 ATGTGGATTCGCCTCCCCTC 61.700 60.000 1.25 0.00 37.63 4.30
458 459 1.599542 GCAAGTATGTGGATTCGCCTC 59.400 52.381 0.00 0.00 37.63 4.70
459 460 1.668419 GCAAGTATGTGGATTCGCCT 58.332 50.000 0.00 0.00 37.63 5.52
460 461 0.663153 GGCAAGTATGTGGATTCGCC 59.337 55.000 0.00 0.00 37.10 5.54
461 462 0.304705 CGGCAAGTATGTGGATTCGC 59.695 55.000 0.00 0.00 0.00 4.70
462 463 0.937304 CCGGCAAGTATGTGGATTCG 59.063 55.000 0.00 0.00 0.00 3.34
463 464 1.670811 CACCGGCAAGTATGTGGATTC 59.329 52.381 0.00 0.00 0.00 2.52
465 466 0.908910 TCACCGGCAAGTATGTGGAT 59.091 50.000 0.00 0.00 0.00 3.41
466 467 0.687920 TTCACCGGCAAGTATGTGGA 59.312 50.000 0.00 0.00 0.00 4.02
468 469 1.732259 GACTTCACCGGCAAGTATGTG 59.268 52.381 17.28 0.00 34.10 3.21
469 470 1.623811 AGACTTCACCGGCAAGTATGT 59.376 47.619 17.28 5.11 34.10 2.29
470 471 2.386661 AGACTTCACCGGCAAGTATG 57.613 50.000 17.28 0.26 34.10 2.39
471 472 3.362706 TCTAGACTTCACCGGCAAGTAT 58.637 45.455 17.28 16.61 34.10 2.12
472 473 2.753452 CTCTAGACTTCACCGGCAAGTA 59.247 50.000 17.28 4.69 34.10 2.24
473 474 1.546476 CTCTAGACTTCACCGGCAAGT 59.454 52.381 17.28 17.28 36.77 3.16
476 477 0.039180 TCCTCTAGACTTCACCGGCA 59.961 55.000 0.00 0.00 0.00 5.69
488 489 4.396478 GCTAGGGCAAACTTTTTCCTCTAG 59.604 45.833 9.49 9.49 38.54 2.43
490 491 3.157881 GCTAGGGCAAACTTTTTCCTCT 58.842 45.455 0.00 0.00 38.54 3.69
494 495 2.288825 GGTGGCTAGGGCAAACTTTTTC 60.289 50.000 0.00 0.00 40.46 2.29
495 496 1.691976 GGTGGCTAGGGCAAACTTTTT 59.308 47.619 0.00 0.00 40.46 1.94
496 497 1.133167 AGGTGGCTAGGGCAAACTTTT 60.133 47.619 0.00 0.00 35.57 2.27
498 499 1.004394 GTAGGTGGCTAGGGCAAACTT 59.996 52.381 0.00 0.00 35.57 2.66
518 519 0.815734 TCTCGTTTTCCTCCCTAGCG 59.184 55.000 0.00 0.00 0.00 4.26
520 521 3.181474 GGACATCTCGTTTTCCTCCCTAG 60.181 52.174 0.00 0.00 0.00 3.02
522 523 1.555533 GGACATCTCGTTTTCCTCCCT 59.444 52.381 0.00 0.00 0.00 4.20
549 552 6.235231 TGACCCAAGGAAGAAGTATATGTC 57.765 41.667 0.00 0.00 0.00 3.06
575 578 7.920151 TGAACAAGTGATTTCGATTCACAAATT 59.080 29.630 23.26 15.97 44.73 1.82
590 593 2.029380 TCGGTCGTCATGAACAAGTGAT 60.029 45.455 0.00 0.00 32.01 3.06
596 599 3.915536 TGTATTTCGGTCGTCATGAACA 58.084 40.909 0.00 0.00 32.01 3.18
689 697 3.685836 AGCGGCAAATTTACGTATTCC 57.314 42.857 1.45 0.00 0.00 3.01
746 754 2.874086 TGCTGTTGATCACTGAACACAG 59.126 45.455 15.57 15.57 37.63 3.66
777 785 5.006896 TCTCCTCGGCCCTCTTTTATATA 57.993 43.478 0.00 0.00 0.00 0.86
796 804 5.499139 TGTGGTGTGTGAAATTTCTTCTC 57.501 39.130 18.64 12.40 0.00 2.87
823 831 1.781555 CTGGACGCAACTAGCAACG 59.218 57.895 0.00 0.00 46.13 4.10
824 832 1.497722 GCTGGACGCAACTAGCAAC 59.502 57.895 9.81 0.00 46.13 4.17
825 833 3.966215 GCTGGACGCAACTAGCAA 58.034 55.556 9.81 0.00 46.13 3.91
892 900 8.935844 TCAGTTGCTCTATTATTGTTTGTACTG 58.064 33.333 0.00 0.00 0.00 2.74
931 939 2.363038 ACAGTGCTTAACCGACTGTGTA 59.637 45.455 0.00 0.00 46.66 2.90
932 940 1.138266 ACAGTGCTTAACCGACTGTGT 59.862 47.619 0.00 0.00 46.66 3.72
933 941 1.865865 ACAGTGCTTAACCGACTGTG 58.134 50.000 0.00 0.00 46.66 3.66
955 963 2.094442 GTGACCTGAACCTAGCTCACTC 60.094 54.545 0.00 0.00 32.86 3.51
981 989 1.817099 GGCTTGGAGATGAGGCGTG 60.817 63.158 0.00 0.00 0.00 5.34
1133 1151 4.655762 TCTATAGCTGAGAATGCACGTT 57.344 40.909 0.00 0.00 0.00 3.99
1143 1161 4.280425 TGGTGAGCAAGATCTATAGCTGAG 59.720 45.833 18.52 0.00 37.48 3.35
1151 1169 1.557099 ACGGTGGTGAGCAAGATCTA 58.443 50.000 0.00 0.00 0.00 1.98
1152 1170 2.366469 ACGGTGGTGAGCAAGATCT 58.634 52.632 0.00 0.00 0.00 2.75
1170 1191 2.116533 CATCGGCCTTCATGCAGCA 61.117 57.895 0.00 0.00 0.00 4.41
1171 1192 2.719979 CATCGGCCTTCATGCAGC 59.280 61.111 0.00 0.00 0.00 5.25
1172 1193 1.822613 AGCATCGGCCTTCATGCAG 60.823 57.895 24.93 0.00 46.70 4.41
1183 1204 0.930310 CGTGTTATCCACAGCATCGG 59.070 55.000 0.00 0.00 44.78 4.18
1195 1218 7.462109 TCAAACAAGTTAACGTACGTGTTAT 57.538 32.000 23.57 8.75 45.55 1.89
1204 1227 4.347813 GCACACATCAAACAAGTTAACGT 58.652 39.130 0.00 0.00 0.00 3.99
1205 1228 3.417321 CGCACACATCAAACAAGTTAACG 59.583 43.478 0.00 0.00 0.00 3.18
1206 1229 4.593157 TCGCACACATCAAACAAGTTAAC 58.407 39.130 0.00 0.00 0.00 2.01
1208 1231 3.303725 GCTCGCACACATCAAACAAGTTA 60.304 43.478 0.00 0.00 0.00 2.24
1209 1232 2.541588 GCTCGCACACATCAAACAAGTT 60.542 45.455 0.00 0.00 0.00 2.66
1210 1233 1.002468 GCTCGCACACATCAAACAAGT 60.002 47.619 0.00 0.00 0.00 3.16
1211 1234 1.002576 TGCTCGCACACATCAAACAAG 60.003 47.619 0.00 0.00 0.00 3.16
1214 1237 0.867746 TCTGCTCGCACACATCAAAC 59.132 50.000 0.00 0.00 0.00 2.93
1921 1962 2.203907 AGCAGCTCCCTCCACACT 60.204 61.111 0.00 0.00 0.00 3.55
2509 2556 4.360405 ATGAACACCCACCCGGCC 62.360 66.667 0.00 0.00 33.26 6.13
2740 2791 3.674997 GTCCAAGATAGCTTTGGACACA 58.325 45.455 30.91 7.16 43.77 3.72
2743 2794 2.673368 CACGTCCAAGATAGCTTTGGAC 59.327 50.000 28.07 28.07 42.50 4.02
2744 2795 2.565391 TCACGTCCAAGATAGCTTTGGA 59.435 45.455 13.31 13.31 32.53 3.53
2745 2796 2.972625 TCACGTCCAAGATAGCTTTGG 58.027 47.619 9.08 9.08 30.14 3.28
2746 2797 4.872691 AGATTCACGTCCAAGATAGCTTTG 59.127 41.667 0.00 0.00 30.14 2.77
2747 2798 5.091261 AGATTCACGTCCAAGATAGCTTT 57.909 39.130 0.00 0.00 30.14 3.51
2752 2803 7.825331 AATCTAGAGATTCACGTCCAAGATA 57.175 36.000 0.00 0.00 40.49 1.98
2819 2870 2.037367 TAGAGCGCTGGGTGTCCT 59.963 61.111 18.48 6.14 0.00 3.85
2844 2895 4.143242 CGTGCGGAATATCATGTGATCTTC 60.143 45.833 10.84 10.84 37.10 2.87
3074 3157 5.811613 CAGTTTAGAAGAAGCTCAGAGATGG 59.188 44.000 0.00 0.00 0.00 3.51
3120 4084 5.468746 TGTCAGGAATTTTTCTTACGTCTGG 59.531 40.000 0.00 0.00 0.00 3.86
3121 4085 6.539649 TGTCAGGAATTTTTCTTACGTCTG 57.460 37.500 0.00 0.00 0.00 3.51
3144 4108 3.055602 ACCGGTTTAGCTAATCCGAAGTT 60.056 43.478 39.15 24.68 46.24 2.66
3165 4134 5.407387 AGTTTGTCGTCATGGTAATGTACAC 59.593 40.000 0.00 0.00 35.15 2.90
3195 4166 5.883503 AAATTTAGGCCGAATTTACGACA 57.116 34.783 23.13 0.00 35.54 4.35
3268 4405 4.145052 GGCCAAAAGAGTAATCATAGGGG 58.855 47.826 0.00 0.00 0.00 4.79
3301 4438 3.501828 CGAATGAAACAACTCATCACCCA 59.498 43.478 0.00 0.00 34.90 4.51
3302 4439 3.751175 TCGAATGAAACAACTCATCACCC 59.249 43.478 0.00 0.00 34.90 4.61
3363 4500 7.111247 TGAACTTCAACATTTGTCTGGATTT 57.889 32.000 0.00 0.00 0.00 2.17
3376 4513 5.065988 GGTAGCTCAAACTTGAACTTCAACA 59.934 40.000 0.00 0.00 35.44 3.33
3377 4514 5.297029 AGGTAGCTCAAACTTGAACTTCAAC 59.703 40.000 0.00 0.00 35.44 3.18
3402 4539 2.794910 CAAGAGAGCTTTCGTTTCGACA 59.205 45.455 0.00 0.00 34.89 4.35
3406 4543 3.050619 TCGACAAGAGAGCTTTCGTTTC 58.949 45.455 0.00 0.00 36.70 2.78
3411 4548 2.734276 AGGTCGACAAGAGAGCTTTC 57.266 50.000 18.91 0.00 43.01 2.62
3464 4601 5.782893 TCCCGAAAGAAACAAAACATCAT 57.217 34.783 0.00 0.00 0.00 2.45
3490 4627 5.399858 ACTACGTCACATACTTCACACATC 58.600 41.667 0.00 0.00 0.00 3.06
3492 4629 4.841443 ACTACGTCACATACTTCACACA 57.159 40.909 0.00 0.00 0.00 3.72
3493 4630 6.199531 TGAAAACTACGTCACATACTTCACAC 59.800 38.462 0.00 0.00 0.00 3.82
3554 4691 3.374220 AACGGTTACATGTTCAGACGA 57.626 42.857 2.30 0.00 0.00 4.20
3557 4694 3.002862 GCACAAACGGTTACATGTTCAGA 59.997 43.478 2.30 0.00 0.00 3.27
3570 4707 8.988934 ACTTACATTATATATGAGCACAAACGG 58.011 33.333 0.00 0.00 0.00 4.44
3629 4766 6.084738 TCCTATGTGGCTCACCTAAGATATT 58.915 40.000 0.00 0.00 36.63 1.28
3639 4776 5.822519 TCAACATTTATCCTATGTGGCTCAC 59.177 40.000 0.00 0.00 36.41 3.51
3648 4785 8.494433 TCTGCTTAACCTCAACATTTATCCTAT 58.506 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.