Multiple sequence alignment - TraesCS5A01G257900

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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 TraesCS5A01G257900 chr5A 100.000 4979 0 0 1 4979 473008822 473013800 0.000000e+00 9195.0
1 TraesCS5A01G257900 chr5D 92.547 4763 228 46 268 4979 370462178 370466864 0.000000e+00 6711.0
2 TraesCS5A01G257900 chr5B 91.105 4958 269 64 141 4979 439715058 439719962 0.000000e+00 6554.0
3 TraesCS5A01G257900 chr5B 91.364 220 19 0 1582 1801 688589695 688589476 8.100000e-78 302.0
4 TraesCS5A01G257900 chr5B 97.778 45 1 0 1488 1532 688590239 688590195 1.490000e-10 78.7
5 TraesCS5A01G257900 chr7B 77.100 2703 560 45 1298 3972 168074608 168077279 0.000000e+00 1507.0
6 TraesCS5A01G257900 chr7B 96.875 32 0 1 1437 1467 323817638 323817607 9.000000e-03 52.8
7 TraesCS5A01G257900 chr7D 77.009 2701 560 42 1298 3972 204109312 204111977 0.000000e+00 1491.0
8 TraesCS5A01G257900 chr7D 90.571 350 32 1 1446 1795 484694710 484694362 3.510000e-126 462.0
9 TraesCS5A01G257900 chr7A 76.707 2709 564 52 1306 3985 215934699 215937369 0.000000e+00 1445.0


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 TraesCS5A01G257900 chr5A 473008822 473013800 4978 False 9195 9195 100.000 1 4979 1 chr5A.!!$F1 4978
1 TraesCS5A01G257900 chr5D 370462178 370466864 4686 False 6711 6711 92.547 268 4979 1 chr5D.!!$F1 4711
2 TraesCS5A01G257900 chr5B 439715058 439719962 4904 False 6554 6554 91.105 141 4979 1 chr5B.!!$F1 4838
3 TraesCS5A01G257900 chr7B 168074608 168077279 2671 False 1507 1507 77.100 1298 3972 1 chr7B.!!$F1 2674
4 TraesCS5A01G257900 chr7D 204109312 204111977 2665 False 1491 1491 77.009 1298 3972 1 chr7D.!!$F1 2674
5 TraesCS5A01G257900 chr7A 215934699 215937369 2670 False 1445 1445 76.707 1306 3985 1 chr7A.!!$F1 2679

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
132 133 0.104777 TCCATCCATCCCTCTCCCAG 60.105 60.0 0.00 0.00 0.00 4.45 F
144 145 0.250234 TCTCCCAGCAGTGAAATCCG 59.750 55.0 0.00 0.00 0.00 4.18 F
245 246 0.258774 ACAGGGTACAATCCATGCCC 59.741 55.0 0.00 0.00 42.16 5.36 F
316 324 0.320421 TCGGTCTTCTTTCCTTGGCG 60.320 55.0 0.00 0.00 0.00 5.69 F
1091 1134 0.393537 GCCAAGTCCCTCACCATCAG 60.394 60.0 0.00 0.00 0.00 2.90 F
2249 2337 1.026718 AAGTGCAAGCGGCCTATGTC 61.027 55.0 0.00 0.00 43.89 3.06 F
2280 2368 0.241213 TTGATCCGGCGATCGATCTC 59.759 55.0 21.57 15.11 46.89 2.75 F
3540 3628 0.617413 AATCAGAGCCTCCTGTGGTG 59.383 55.0 0.00 0.00 33.42 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 1079 0.681243 GGGATGCTGTCCTTGGGTTC 60.681 60.000 8.33 0.0 46.91 3.62 R
2117 2205 1.135527 CACAATTAGGCATGGTGCTGG 59.864 52.381 1.64 0.0 44.28 4.85 R
2151 2239 3.555527 TCAGCAAATCCTCCATCTGAG 57.444 47.619 0.00 0.0 41.07 3.35 R
2249 2337 1.595382 GGATCAACCGATGCCTCCG 60.595 63.158 0.00 0.0 34.06 4.63 R
2280 2368 1.884926 GATCCCTTTCGCAGCCGAG 60.885 63.158 0.00 0.0 45.35 4.63 R
3880 3968 0.176680 ATGACCGTCCTGATGCTGAC 59.823 55.000 0.00 0.0 0.00 3.51 R
3964 4052 3.099362 CGTCGTCTCAGATTTTACTCCG 58.901 50.000 0.00 0.0 0.00 4.63 R
4525 4651 0.312416 ATCGGCGTGTCAGCTAGATC 59.688 55.000 6.85 0.0 37.29 2.75 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
25 26 4.794648 GCCATGGCAGGCGTACCA 62.795 66.667 32.08 0.00 46.12 3.25
26 27 2.824041 CCATGGCAGGCGTACCAC 60.824 66.667 0.00 0.00 39.19 4.16
27 28 2.824041 CATGGCAGGCGTACCACC 60.824 66.667 0.00 0.00 39.19 4.61
28 29 4.467084 ATGGCAGGCGTACCACCG 62.467 66.667 0.00 0.00 39.19 4.94
32 33 3.687102 CAGGCGTACCACCGGTGA 61.687 66.667 36.07 14.69 36.19 4.02
33 34 2.918802 AGGCGTACCACCGGTGAA 60.919 61.111 36.07 20.29 36.19 3.18
34 35 2.030862 GGCGTACCACCGGTGAAA 59.969 61.111 36.07 19.91 36.19 2.69
35 36 1.597578 GGCGTACCACCGGTGAAAA 60.598 57.895 36.07 17.24 36.19 2.29
36 37 1.570967 GCGTACCACCGGTGAAAAC 59.429 57.895 36.07 25.67 36.19 2.43
37 38 1.159098 GCGTACCACCGGTGAAAACA 61.159 55.000 36.07 12.43 36.19 2.83
38 39 1.515081 CGTACCACCGGTGAAAACAT 58.485 50.000 36.07 15.14 36.19 2.71
39 40 1.195900 CGTACCACCGGTGAAAACATG 59.804 52.381 36.07 18.96 36.19 3.21
40 41 2.496111 GTACCACCGGTGAAAACATGA 58.504 47.619 36.07 8.26 36.19 3.07
41 42 2.060050 ACCACCGGTGAAAACATGAA 57.940 45.000 36.07 0.00 32.98 2.57
42 43 2.593026 ACCACCGGTGAAAACATGAAT 58.407 42.857 36.07 4.77 32.98 2.57
43 44 2.962421 ACCACCGGTGAAAACATGAATT 59.038 40.909 36.07 0.00 32.98 2.17
44 45 3.005367 ACCACCGGTGAAAACATGAATTC 59.995 43.478 36.07 0.00 32.98 2.17
45 46 3.233578 CACCGGTGAAAACATGAATTCG 58.766 45.455 31.31 0.00 0.00 3.34
46 47 2.250188 CCGGTGAAAACATGAATTCGC 58.750 47.619 15.61 15.61 35.77 4.70
48 49 2.250188 GGTGAAAACATGAATTCGCCG 58.750 47.619 22.56 0.00 43.84 6.46
49 50 2.351350 GGTGAAAACATGAATTCGCCGT 60.351 45.455 22.56 0.00 43.84 5.68
50 51 2.656422 GTGAAAACATGAATTCGCCGTG 59.344 45.455 0.00 0.17 31.50 4.94
51 52 1.648681 GAAAACATGAATTCGCCGTGC 59.351 47.619 0.00 0.00 0.00 5.34
52 53 0.109319 AAACATGAATTCGCCGTGCC 60.109 50.000 0.00 0.00 0.00 5.01
53 54 2.023181 CATGAATTCGCCGTGCCG 59.977 61.111 0.04 0.00 0.00 5.69
76 77 2.895865 CCGGCTCAGCATGCAGAG 60.896 66.667 29.92 29.92 34.76 3.35
77 78 2.895865 CGGCTCAGCATGCAGAGG 60.896 66.667 33.10 18.71 34.76 3.69
78 79 3.210528 GGCTCAGCATGCAGAGGC 61.211 66.667 38.15 38.15 44.70 4.70
79 80 3.210528 GCTCAGCATGCAGAGGCC 61.211 66.667 33.10 18.71 40.13 5.19
80 81 2.271173 CTCAGCATGCAGAGGCCA 59.729 61.111 27.49 0.44 40.13 5.36
81 82 1.820056 CTCAGCATGCAGAGGCCAG 60.820 63.158 27.49 7.01 40.13 4.85
82 83 2.829003 CAGCATGCAGAGGCCAGG 60.829 66.667 21.98 0.00 40.13 4.45
83 84 4.816984 AGCATGCAGAGGCCAGGC 62.817 66.667 21.98 1.26 40.13 4.85
96 97 2.159327 GCCAGGCCATTGATTAATGC 57.841 50.000 5.01 1.26 41.87 3.56
97 98 1.413445 GCCAGGCCATTGATTAATGCA 59.587 47.619 5.01 0.00 41.87 3.96
98 99 2.038033 GCCAGGCCATTGATTAATGCAT 59.962 45.455 5.01 0.00 41.87 3.96
99 100 3.659786 CCAGGCCATTGATTAATGCATG 58.340 45.455 5.01 8.07 41.87 4.06
100 101 3.064207 CAGGCCATTGATTAATGCATGC 58.936 45.455 11.82 11.82 41.87 4.06
101 102 2.038033 AGGCCATTGATTAATGCATGCC 59.962 45.455 16.68 16.35 43.60 4.40
102 103 2.063266 GCCATTGATTAATGCATGCCG 58.937 47.619 16.68 0.00 41.87 5.69
103 104 2.546373 GCCATTGATTAATGCATGCCGT 60.546 45.455 16.68 5.24 41.87 5.68
104 105 3.054166 CCATTGATTAATGCATGCCGTG 58.946 45.455 16.68 1.88 41.87 4.94
105 106 3.491276 CCATTGATTAATGCATGCCGTGT 60.491 43.478 16.68 0.00 41.87 4.49
106 107 3.419264 TTGATTAATGCATGCCGTGTC 57.581 42.857 16.68 7.67 0.00 3.67
107 108 1.330213 TGATTAATGCATGCCGTGTCG 59.670 47.619 16.68 0.00 0.00 4.35
108 109 1.330521 GATTAATGCATGCCGTGTCGT 59.669 47.619 16.68 0.00 0.00 4.34
109 110 2.011540 TTAATGCATGCCGTGTCGTA 57.988 45.000 16.68 0.00 0.00 3.43
110 111 2.232756 TAATGCATGCCGTGTCGTAT 57.767 45.000 16.68 0.00 0.00 3.06
111 112 0.657312 AATGCATGCCGTGTCGTATG 59.343 50.000 16.68 0.00 0.00 2.39
112 113 1.159713 ATGCATGCCGTGTCGTATGG 61.160 55.000 16.68 0.00 38.58 2.74
113 114 1.813753 GCATGCCGTGTCGTATGGT 60.814 57.895 6.36 0.00 37.79 3.55
114 115 1.762222 GCATGCCGTGTCGTATGGTC 61.762 60.000 6.36 0.00 37.79 4.02
115 116 1.143183 ATGCCGTGTCGTATGGTCC 59.857 57.895 3.34 0.00 37.79 4.46
116 117 1.609635 ATGCCGTGTCGTATGGTCCA 61.610 55.000 0.00 0.00 37.79 4.02
117 118 1.143183 GCCGTGTCGTATGGTCCAT 59.857 57.895 9.88 9.88 37.79 3.41
118 119 0.874607 GCCGTGTCGTATGGTCCATC 60.875 60.000 7.92 0.00 37.79 3.51
119 120 0.249322 CCGTGTCGTATGGTCCATCC 60.249 60.000 7.92 0.00 0.00 3.51
128 129 3.247424 TGGTCCATCCATCCCTCTC 57.753 57.895 0.00 0.00 41.93 3.20
129 130 0.400525 TGGTCCATCCATCCCTCTCC 60.401 60.000 0.00 0.00 41.93 3.71
130 131 1.130678 GGTCCATCCATCCCTCTCCC 61.131 65.000 0.00 0.00 35.97 4.30
131 132 0.400525 GTCCATCCATCCCTCTCCCA 60.401 60.000 0.00 0.00 0.00 4.37
132 133 0.104777 TCCATCCATCCCTCTCCCAG 60.105 60.000 0.00 0.00 0.00 4.45
133 134 1.759881 CATCCATCCCTCTCCCAGC 59.240 63.158 0.00 0.00 0.00 4.85
134 135 1.058428 CATCCATCCCTCTCCCAGCA 61.058 60.000 0.00 0.00 0.00 4.41
135 136 0.767446 ATCCATCCCTCTCCCAGCAG 60.767 60.000 0.00 0.00 0.00 4.24
136 137 1.692042 CCATCCCTCTCCCAGCAGT 60.692 63.158 0.00 0.00 0.00 4.40
137 138 1.525923 CATCCCTCTCCCAGCAGTG 59.474 63.158 0.00 0.00 0.00 3.66
138 139 0.979709 CATCCCTCTCCCAGCAGTGA 60.980 60.000 0.00 0.00 0.00 3.41
139 140 0.252881 ATCCCTCTCCCAGCAGTGAA 60.253 55.000 0.00 0.00 0.00 3.18
144 145 0.250234 TCTCCCAGCAGTGAAATCCG 59.750 55.000 0.00 0.00 0.00 4.18
150 151 2.271800 CAGCAGTGAAATCCGAGTACC 58.728 52.381 0.00 0.00 0.00 3.34
178 179 1.923148 CCTCCATTAACAACCCCCTCT 59.077 52.381 0.00 0.00 0.00 3.69
182 183 2.524306 CATTAACAACCCCCTCTTGCA 58.476 47.619 0.00 0.00 0.00 4.08
183 184 2.990740 TTAACAACCCCCTCTTGCAT 57.009 45.000 0.00 0.00 0.00 3.96
189 190 2.568509 CAACCCCCTCTTGCATTTCATT 59.431 45.455 0.00 0.00 0.00 2.57
210 211 9.773328 TTCATTTCATCTCGTTTCATTCAATAC 57.227 29.630 0.00 0.00 0.00 1.89
219 220 7.606073 TCTCGTTTCATTCAATACATTTCCTGA 59.394 33.333 0.00 0.00 0.00 3.86
240 241 0.767998 TGTGCACAGGGTACAATCCA 59.232 50.000 17.42 0.00 39.28 3.41
241 242 1.354031 TGTGCACAGGGTACAATCCAT 59.646 47.619 17.42 0.00 39.28 3.41
242 243 1.745087 GTGCACAGGGTACAATCCATG 59.255 52.381 13.17 0.00 43.73 3.66
243 244 0.740737 GCACAGGGTACAATCCATGC 59.259 55.000 0.00 0.00 42.16 4.06
244 245 1.392589 CACAGGGTACAATCCATGCC 58.607 55.000 0.00 0.00 42.16 4.40
245 246 0.258774 ACAGGGTACAATCCATGCCC 59.741 55.000 0.00 0.00 42.16 5.36
246 247 0.468029 CAGGGTACAATCCATGCCCC 60.468 60.000 0.00 0.00 41.67 5.80
247 248 1.152546 GGGTACAATCCATGCCCCC 60.153 63.158 0.00 0.00 37.48 5.40
248 249 1.528309 GGTACAATCCATGCCCCCG 60.528 63.158 0.00 0.00 0.00 5.73
249 250 1.529796 GTACAATCCATGCCCCCGA 59.470 57.895 0.00 0.00 0.00 5.14
250 251 0.818040 GTACAATCCATGCCCCCGAC 60.818 60.000 0.00 0.00 0.00 4.79
251 252 0.986019 TACAATCCATGCCCCCGACT 60.986 55.000 0.00 0.00 0.00 4.18
252 253 1.526917 CAATCCATGCCCCCGACTC 60.527 63.158 0.00 0.00 0.00 3.36
265 266 2.444895 GACTCCCCTCCCGAGCAT 60.445 66.667 0.00 0.00 0.00 3.79
293 301 3.225069 ATTGGCGTTGCTGCAACCC 62.225 57.895 32.70 31.16 40.82 4.11
298 306 2.946762 GTTGCTGCAACCCGTCTC 59.053 61.111 30.11 7.62 38.30 3.36
314 322 2.689646 GTCTCGGTCTTCTTTCCTTGG 58.310 52.381 0.00 0.00 0.00 3.61
315 323 1.002087 TCTCGGTCTTCTTTCCTTGGC 59.998 52.381 0.00 0.00 0.00 4.52
316 324 0.320421 TCGGTCTTCTTTCCTTGGCG 60.320 55.000 0.00 0.00 0.00 5.69
336 344 0.540923 GCAGCTCTCATCTTCTGGGT 59.459 55.000 0.00 0.00 0.00 4.51
337 345 1.743091 GCAGCTCTCATCTTCTGGGTG 60.743 57.143 0.00 0.00 0.00 4.61
341 349 2.903798 CTCTCATCTTCTGGGTGCTTC 58.096 52.381 0.00 0.00 0.00 3.86
366 374 2.659428 CCTTTTGATGTCATCTCCCCC 58.341 52.381 13.90 0.00 0.00 5.40
367 375 2.292267 CTTTTGATGTCATCTCCCCCG 58.708 52.381 13.90 0.00 0.00 5.73
398 406 1.178534 TTTCTCCCCTGCTTTTGCCG 61.179 55.000 0.00 0.00 46.87 5.69
436 444 2.029623 CCTCCATTTCCAAGGCAGATG 58.970 52.381 0.00 0.00 0.00 2.90
442 450 1.558167 TTCCAAGGCAGATGGCGGTA 61.558 55.000 0.26 0.00 46.16 4.02
445 453 2.746375 AAGGCAGATGGCGGTAGGG 61.746 63.158 0.26 0.00 46.16 3.53
448 456 2.505982 CAGATGGCGGTAGGGGTG 59.494 66.667 0.00 0.00 0.00 4.61
450 458 2.766651 GATGGCGGTAGGGGTGGA 60.767 66.667 0.00 0.00 0.00 4.02
451 459 2.768344 ATGGCGGTAGGGGTGGAG 60.768 66.667 0.00 0.00 0.00 3.86
452 460 3.635869 ATGGCGGTAGGGGTGGAGT 62.636 63.158 0.00 0.00 0.00 3.85
453 461 2.042639 GGCGGTAGGGGTGGAGTA 60.043 66.667 0.00 0.00 0.00 2.59
454 462 2.429767 GGCGGTAGGGGTGGAGTAC 61.430 68.421 0.00 0.00 0.00 2.73
455 463 1.380920 GCGGTAGGGGTGGAGTACT 60.381 63.158 0.00 0.00 0.00 2.73
456 464 0.974525 GCGGTAGGGGTGGAGTACTT 60.975 60.000 0.00 0.00 0.00 2.24
457 465 0.822164 CGGTAGGGGTGGAGTACTTG 59.178 60.000 0.00 0.00 0.00 3.16
503 511 7.307219 CGACTCCCAAAGTTTCTTTACTTGTAG 60.307 40.741 0.00 0.00 38.74 2.74
507 515 7.716560 TCCCAAAGTTTCTTTACTTGTAGTACC 59.283 37.037 0.00 0.00 38.33 3.34
508 516 7.499895 CCCAAAGTTTCTTTACTTGTAGTACCA 59.500 37.037 0.00 0.00 38.33 3.25
509 517 8.557029 CCAAAGTTTCTTTACTTGTAGTACCAG 58.443 37.037 0.00 0.00 38.33 4.00
511 519 8.658499 AAGTTTCTTTACTTGTAGTACCAGTG 57.342 34.615 15.50 1.61 37.00 3.66
524 532 0.492276 ACCAGTGGTACCTCCTCCTT 59.508 55.000 14.87 0.00 32.11 3.36
525 533 0.905357 CCAGTGGTACCTCCTCCTTG 59.095 60.000 14.36 3.44 37.07 3.61
526 534 1.552486 CCAGTGGTACCTCCTCCTTGA 60.552 57.143 14.36 0.00 37.07 3.02
527 535 1.550976 CAGTGGTACCTCCTCCTTGAC 59.449 57.143 14.36 0.00 37.07 3.18
530 538 1.196012 GGTACCTCCTCCTTGACTGG 58.804 60.000 4.06 0.00 0.00 4.00
562 570 1.717032 CGGGACAAGATCATAGGGGA 58.283 55.000 0.00 0.00 0.00 4.81
567 575 3.716872 GGACAAGATCATAGGGGAAGGAA 59.283 47.826 0.00 0.00 0.00 3.36
568 576 4.202409 GGACAAGATCATAGGGGAAGGAAG 60.202 50.000 0.00 0.00 0.00 3.46
569 577 4.375313 ACAAGATCATAGGGGAAGGAAGT 58.625 43.478 0.00 0.00 0.00 3.01
570 578 5.538877 ACAAGATCATAGGGGAAGGAAGTA 58.461 41.667 0.00 0.00 0.00 2.24
678 691 4.410400 CCGGGGCAGGTGTTCTCC 62.410 72.222 0.00 0.00 0.00 3.71
684 697 2.948720 GCAGGTGTTCTCCGAGCCT 61.949 63.158 0.00 0.00 0.00 4.58
685 698 1.216710 CAGGTGTTCTCCGAGCCTC 59.783 63.158 0.00 0.00 0.00 4.70
705 726 3.730761 CAGCTCTGCCGCCACAAC 61.731 66.667 0.00 0.00 0.00 3.32
710 731 3.490759 CTGCCGCCACAACGCTAG 61.491 66.667 0.00 0.00 0.00 3.42
732 753 1.153353 GCACCGTCGGATTCTTGAAA 58.847 50.000 20.51 0.00 0.00 2.69
734 755 2.683968 CACCGTCGGATTCTTGAAAGA 58.316 47.619 20.51 0.00 0.00 2.52
751 772 5.553123 TGAAAGACCTTCGCTGGTAATTAA 58.447 37.500 0.00 0.00 41.00 1.40
764 785 6.490534 GCTGGTAATTAACTTGCTCAATCTC 58.509 40.000 1.50 0.00 0.00 2.75
783 804 4.985538 TCTCTGCCTATTTGGTTTGAACT 58.014 39.130 0.00 0.00 38.35 3.01
788 809 6.016276 TCTGCCTATTTGGTTTGAACTTTCTC 60.016 38.462 0.00 0.00 38.35 2.87
848 872 2.449464 TGTTCTTGCCCTGAATCCATG 58.551 47.619 0.00 0.00 0.00 3.66
849 873 1.753073 GTTCTTGCCCTGAATCCATGG 59.247 52.381 4.97 4.97 0.00 3.66
850 874 1.002069 TCTTGCCCTGAATCCATGGT 58.998 50.000 12.58 0.00 31.59 3.55
851 875 1.108776 CTTGCCCTGAATCCATGGTG 58.891 55.000 12.58 0.00 31.59 4.17
852 876 0.703488 TTGCCCTGAATCCATGGTGA 59.297 50.000 12.58 0.00 31.59 4.02
853 877 0.703488 TGCCCTGAATCCATGGTGAA 59.297 50.000 12.58 0.00 31.59 3.18
854 878 1.106285 GCCCTGAATCCATGGTGAAC 58.894 55.000 12.58 3.03 31.59 3.18
855 879 1.616725 GCCCTGAATCCATGGTGAACA 60.617 52.381 12.58 7.47 31.59 3.18
856 880 2.951787 GCCCTGAATCCATGGTGAACAT 60.952 50.000 12.58 0.00 41.57 2.71
857 881 2.954318 CCCTGAATCCATGGTGAACATC 59.046 50.000 12.58 3.28 37.84 3.06
858 882 3.623703 CCTGAATCCATGGTGAACATCA 58.376 45.455 12.58 7.52 37.84 3.07
860 884 4.647853 CCTGAATCCATGGTGAACATCATT 59.352 41.667 12.58 0.79 37.84 2.57
861 885 5.221185 CCTGAATCCATGGTGAACATCATTC 60.221 44.000 12.58 11.12 37.84 2.67
862 886 4.646040 TGAATCCATGGTGAACATCATTCC 59.354 41.667 12.58 0.00 37.84 3.01
864 888 3.623703 TCCATGGTGAACATCATTCCTG 58.376 45.455 12.58 0.00 37.84 3.86
865 889 3.266513 TCCATGGTGAACATCATTCCTGA 59.733 43.478 12.58 0.00 37.84 3.86
877 901 4.305539 TCATTCCTGATGAACACATGGT 57.694 40.909 0.00 0.00 41.73 3.55
879 903 6.005066 TCATTCCTGATGAACACATGGTAT 57.995 37.500 0.00 0.00 41.73 2.73
880 904 6.057533 TCATTCCTGATGAACACATGGTATC 58.942 40.000 0.00 0.00 41.73 2.24
881 905 5.434182 TTCCTGATGAACACATGGTATCA 57.566 39.130 0.00 0.00 0.00 2.15
882 906 5.027293 TCCTGATGAACACATGGTATCAG 57.973 43.478 14.23 14.23 42.59 2.90
884 908 4.813161 CCTGATGAACACATGGTATCAGTC 59.187 45.833 17.09 10.06 41.82 3.51
885 909 4.769688 TGATGAACACATGGTATCAGTCC 58.230 43.478 0.00 0.00 0.00 3.85
887 911 2.093711 TGAACACATGGTATCAGTCCGG 60.094 50.000 0.00 0.00 0.00 5.14
888 912 1.860641 ACACATGGTATCAGTCCGGA 58.139 50.000 0.00 0.00 0.00 5.14
889 913 2.184533 ACACATGGTATCAGTCCGGAA 58.815 47.619 5.23 0.00 0.00 4.30
891 915 3.199946 ACACATGGTATCAGTCCGGAAAT 59.800 43.478 5.23 2.74 0.00 2.17
892 916 4.199310 CACATGGTATCAGTCCGGAAATT 58.801 43.478 5.23 0.00 0.00 1.82
893 917 4.640201 CACATGGTATCAGTCCGGAAATTT 59.360 41.667 5.23 0.00 0.00 1.82
894 918 4.640201 ACATGGTATCAGTCCGGAAATTTG 59.360 41.667 5.23 2.65 0.00 2.32
895 919 4.561500 TGGTATCAGTCCGGAAATTTGA 57.438 40.909 5.23 8.75 0.00 2.69
897 921 5.505780 TGGTATCAGTCCGGAAATTTGATT 58.494 37.500 20.36 9.97 31.49 2.57
898 922 5.588648 TGGTATCAGTCCGGAAATTTGATTC 59.411 40.000 20.36 16.60 31.49 2.52
900 924 4.301072 TCAGTCCGGAAATTTGATTCCT 57.699 40.909 5.23 0.00 45.54 3.36
901 925 5.429681 TCAGTCCGGAAATTTGATTCCTA 57.570 39.130 5.23 0.00 45.54 2.94
902 926 5.183228 TCAGTCCGGAAATTTGATTCCTAC 58.817 41.667 5.23 3.27 45.54 3.18
923 957 7.618117 TCCTACTCTGTATTTTCTGTGTGGATA 59.382 37.037 0.00 0.00 0.00 2.59
942 976 4.202409 GGATATCTGACAGGAAAAGGAGGG 60.202 50.000 1.81 0.00 0.00 4.30
966 1000 4.260375 CCGAATTCCTATGAAGTTCTTGCG 60.260 45.833 4.17 0.00 33.05 4.85
1044 1078 2.724520 ATCATTTCCTGATGCGCCC 58.275 52.632 4.18 0.00 43.15 6.13
1045 1079 1.168407 ATCATTTCCTGATGCGCCCG 61.168 55.000 4.18 0.00 43.15 6.13
1046 1080 1.819208 CATTTCCTGATGCGCCCGA 60.819 57.895 4.18 0.00 0.00 5.14
1047 1081 1.077787 ATTTCCTGATGCGCCCGAA 60.078 52.632 4.18 0.00 0.00 4.30
1057 1100 4.323477 CGCCCGAACCCAAGGACA 62.323 66.667 0.00 0.00 0.00 4.02
1058 1101 2.359975 GCCCGAACCCAAGGACAG 60.360 66.667 0.00 0.00 0.00 3.51
1091 1134 0.393537 GCCAAGTCCCTCACCATCAG 60.394 60.000 0.00 0.00 0.00 2.90
1528 1613 2.277373 GGAGCTGCGACGTCTACG 60.277 66.667 14.70 1.88 46.33 3.51
1686 1771 2.203070 ATCATCTGTTCGGCGGCC 60.203 61.111 9.54 9.54 0.00 6.13
1795 1880 1.078426 CCCATCCTGTTCGACACCC 60.078 63.158 0.00 0.00 0.00 4.61
2069 2154 1.933247 CTTGCTGAGATCGAGGGAAC 58.067 55.000 0.00 0.00 0.00 3.62
2071 2156 1.590259 GCTGAGATCGAGGGAACGC 60.590 63.158 0.00 0.00 0.00 4.84
2083 2168 1.959226 GGAACGCTCTTCGGTTGCA 60.959 57.895 0.00 0.00 38.87 4.08
2102 2190 1.521681 CCGGGGAAGTCGAAGATGC 60.522 63.158 0.00 0.00 40.67 3.91
2103 2191 1.521681 CGGGGAAGTCGAAGATGCC 60.522 63.158 0.00 0.00 40.67 4.40
2151 2239 4.876107 CCTAATTGTGTATCCAGTGGTGTC 59.124 45.833 9.54 1.36 0.00 3.67
2249 2337 1.026718 AAGTGCAAGCGGCCTATGTC 61.027 55.000 0.00 0.00 43.89 3.06
2280 2368 0.241213 TTGATCCGGCGATCGATCTC 59.759 55.000 21.57 15.11 46.89 2.75
2355 2443 2.309613 AGATTCAGGTGCAACAGCAAA 58.690 42.857 3.64 0.00 40.49 3.68
2363 2451 2.029649 GGTGCAACAGCAAAGATCATGT 60.030 45.455 0.00 0.00 40.49 3.21
2364 2452 3.553508 GGTGCAACAGCAAAGATCATGTT 60.554 43.478 0.00 0.00 40.49 2.71
2379 2467 6.128486 AGATCATGTTAATGGCAATGTGGTA 58.872 36.000 0.00 0.00 34.30 3.25
2416 2504 1.377202 GGCATTGGCAAGACGGAGA 60.377 57.895 5.96 0.00 43.71 3.71
2433 2521 1.820519 GAGATGGCATTGGAGTTTGCA 59.179 47.619 0.00 0.00 40.66 4.08
2593 2681 1.085893 GAGCTTTGAGGAGCAAGAGC 58.914 55.000 0.00 0.00 45.12 4.09
2634 2722 3.007398 TGAAGAGAGAGCTTTTCAGGGAC 59.993 47.826 0.00 0.00 39.50 4.46
2931 3019 1.008538 GCTGTGGCTTGTTGGTTCG 60.009 57.895 0.00 0.00 35.22 3.95
3540 3628 0.617413 AATCAGAGCCTCCTGTGGTG 59.383 55.000 0.00 0.00 33.42 4.17
3693 3781 4.415332 GCGGAGAAGTCGGTCGCA 62.415 66.667 0.00 0.00 44.87 5.10
3857 3945 2.051345 CGGGTTGTTTGACAGCGC 60.051 61.111 0.00 0.00 38.53 5.92
3981 4069 4.401837 AGGTACCGGAGTAAAATCTGAGAC 59.598 45.833 9.46 0.00 0.00 3.36
4123 4211 9.177608 GATCACTGAGATAGCTAGTCTGATTAT 57.822 37.037 15.58 8.31 37.00 1.28
4124 4212 8.334263 TCACTGAGATAGCTAGTCTGATTATG 57.666 38.462 15.58 7.04 0.00 1.90
4125 4213 8.160106 TCACTGAGATAGCTAGTCTGATTATGA 58.840 37.037 15.58 8.62 0.00 2.15
4126 4214 8.959548 CACTGAGATAGCTAGTCTGATTATGAT 58.040 37.037 15.58 0.00 0.00 2.45
4127 4215 9.177608 ACTGAGATAGCTAGTCTGATTATGATC 57.822 37.037 15.58 0.00 0.00 2.92
4171 4261 5.983118 ACAACTTATTTAACCAACTTGCTGC 59.017 36.000 0.00 0.00 0.00 5.25
4196 4286 6.017770 CGTACAGTCCAGTCTCCTAAATCTAG 60.018 46.154 0.00 0.00 0.00 2.43
4283 4399 5.536538 CCTGGAGATGTTATGTGCTAGTAGA 59.463 44.000 0.00 0.00 0.00 2.59
4325 4441 7.099764 TGCTGAACATTTTACTCCTAGAAGAG 58.900 38.462 0.00 0.00 39.91 2.85
4327 4443 7.276878 GCTGAACATTTTACTCCTAGAAGAGAC 59.723 40.741 3.32 0.00 37.33 3.36
4344 4460 3.829601 AGAGACTGTAACTCCAGTGAAGG 59.170 47.826 0.00 0.00 45.46 3.46
4420 4543 1.203287 GCAGTCTTCCCTTGCAATTCC 59.797 52.381 0.00 0.00 37.75 3.01
4439 4562 4.471904 TCCGATGCTGAATTTAGTCTGT 57.528 40.909 0.00 0.00 0.00 3.41
4443 4566 5.985530 CCGATGCTGAATTTAGTCTGTCATA 59.014 40.000 0.00 0.00 0.00 2.15
4484 4607 2.864946 GCACAGAGTAGCAGACATGATG 59.135 50.000 0.00 0.00 0.00 3.07
4525 4651 2.415168 TGCTTCTTCCTTATCGCAAACG 59.585 45.455 0.00 0.00 42.01 3.60
4572 4698 0.395724 ATGGATGGGGAAACGAAGGC 60.396 55.000 0.00 0.00 0.00 4.35
4630 4763 4.634443 TGATCATGCATCAAGTCTGAACTG 59.366 41.667 0.00 0.00 38.68 3.16
4654 4806 0.390078 CAGCTCTCTGCAGTCACTGG 60.390 60.000 14.67 0.00 45.94 4.00
4722 4881 8.737175 GTGCATTCTCATCCATGATATAAATGT 58.263 33.333 0.00 0.00 36.02 2.71
4753 4912 1.117142 ATGCTTGCCTGGTTGTGCTT 61.117 50.000 0.00 0.00 0.00 3.91
4840 4999 1.006571 GGCTTCTTCGACACCGTCA 60.007 57.895 0.00 0.00 37.05 4.35
4854 5013 1.012086 CCGTCATGGACATCAAGCAG 58.988 55.000 0.00 0.00 42.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.824041 GTGGTACGCCTGCCATGG 60.824 66.667 7.63 7.63 37.09 3.66
18 19 1.159098 TGTTTTCACCGGTGGTACGC 61.159 55.000 33.40 19.54 32.11 4.42
19 20 1.195900 CATGTTTTCACCGGTGGTACG 59.804 52.381 33.40 8.81 32.11 3.67
20 21 2.496111 TCATGTTTTCACCGGTGGTAC 58.504 47.619 33.40 25.85 32.11 3.34
21 22 2.932855 TCATGTTTTCACCGGTGGTA 57.067 45.000 33.40 19.42 32.11 3.25
22 23 2.060050 TTCATGTTTTCACCGGTGGT 57.940 45.000 33.40 10.72 35.62 4.16
23 24 3.574614 GAATTCATGTTTTCACCGGTGG 58.425 45.455 33.40 16.05 0.00 4.61
24 25 3.233578 CGAATTCATGTTTTCACCGGTG 58.766 45.455 29.26 29.26 0.00 4.94
25 26 2.351350 GCGAATTCATGTTTTCACCGGT 60.351 45.455 0.00 0.00 0.00 5.28
26 27 2.250188 GCGAATTCATGTTTTCACCGG 58.750 47.619 0.00 0.00 0.00 5.28
27 28 2.250188 GGCGAATTCATGTTTTCACCG 58.750 47.619 6.22 0.00 0.00 4.94
28 29 2.250188 CGGCGAATTCATGTTTTCACC 58.750 47.619 0.00 8.45 0.00 4.02
29 30 2.656422 CACGGCGAATTCATGTTTTCAC 59.344 45.455 16.62 2.14 0.00 3.18
30 31 2.920227 GCACGGCGAATTCATGTTTTCA 60.920 45.455 16.62 0.00 0.00 2.69
31 32 1.648681 GCACGGCGAATTCATGTTTTC 59.351 47.619 16.62 0.00 0.00 2.29
32 33 1.668628 GGCACGGCGAATTCATGTTTT 60.669 47.619 16.62 0.00 0.00 2.43
33 34 0.109319 GGCACGGCGAATTCATGTTT 60.109 50.000 16.62 0.00 0.00 2.83
34 35 1.506262 GGCACGGCGAATTCATGTT 59.494 52.632 16.62 0.00 0.00 2.71
35 36 3.187058 GGCACGGCGAATTCATGT 58.813 55.556 16.62 0.00 0.00 3.21
59 60 2.895865 CTCTGCATGCTGAGCCGG 60.896 66.667 32.99 16.82 35.75 6.13
60 61 2.895865 CCTCTGCATGCTGAGCCG 60.896 66.667 36.19 24.98 39.62 5.52
61 62 3.210528 GCCTCTGCATGCTGAGCC 61.211 66.667 36.19 27.87 39.62 4.70
62 63 3.210528 GGCCTCTGCATGCTGAGC 61.211 66.667 36.19 30.63 39.62 4.26
63 64 1.820056 CTGGCCTCTGCATGCTGAG 60.820 63.158 35.19 35.19 40.13 3.35
64 65 2.271173 CTGGCCTCTGCATGCTGA 59.729 61.111 23.75 23.75 40.13 4.26
65 66 2.829003 CCTGGCCTCTGCATGCTG 60.829 66.667 20.33 18.97 40.13 4.41
66 67 4.816984 GCCTGGCCTCTGCATGCT 62.817 66.667 20.33 0.00 40.13 3.79
77 78 1.413445 TGCATTAATCAATGGCCTGGC 59.587 47.619 11.05 11.05 41.64 4.85
78 79 3.659786 CATGCATTAATCAATGGCCTGG 58.340 45.455 3.32 0.00 41.64 4.45
79 80 3.064207 GCATGCATTAATCAATGGCCTG 58.936 45.455 14.21 0.00 41.64 4.85
80 81 2.038033 GGCATGCATTAATCAATGGCCT 59.962 45.455 21.36 0.00 40.79 5.19
81 82 2.419667 GGCATGCATTAATCAATGGCC 58.580 47.619 21.36 0.00 41.64 5.36
82 83 2.063266 CGGCATGCATTAATCAATGGC 58.937 47.619 21.36 17.37 41.64 4.40
83 84 3.054166 CACGGCATGCATTAATCAATGG 58.946 45.455 21.36 0.00 41.64 3.16
84 85 3.708890 ACACGGCATGCATTAATCAATG 58.291 40.909 21.36 5.98 43.79 2.82
85 86 3.548616 CGACACGGCATGCATTAATCAAT 60.549 43.478 21.36 0.00 0.00 2.57
86 87 2.223226 CGACACGGCATGCATTAATCAA 60.223 45.455 21.36 0.00 0.00 2.57
87 88 1.330213 CGACACGGCATGCATTAATCA 59.670 47.619 21.36 0.00 0.00 2.57
88 89 1.330521 ACGACACGGCATGCATTAATC 59.669 47.619 21.36 8.91 0.00 1.75
89 90 1.378531 ACGACACGGCATGCATTAAT 58.621 45.000 21.36 0.00 0.00 1.40
90 91 2.011540 TACGACACGGCATGCATTAA 57.988 45.000 21.36 0.00 0.00 1.40
91 92 1.864082 CATACGACACGGCATGCATTA 59.136 47.619 21.36 0.00 0.00 1.90
92 93 0.657312 CATACGACACGGCATGCATT 59.343 50.000 21.36 1.55 0.00 3.56
93 94 1.159713 CCATACGACACGGCATGCAT 61.160 55.000 21.36 3.56 0.00 3.96
94 95 1.813337 CCATACGACACGGCATGCA 60.813 57.895 21.36 0.00 0.00 3.96
95 96 1.762222 GACCATACGACACGGCATGC 61.762 60.000 9.90 9.90 0.00 4.06
96 97 1.151777 GGACCATACGACACGGCATG 61.152 60.000 0.00 0.00 0.00 4.06
97 98 1.143183 GGACCATACGACACGGCAT 59.857 57.895 0.00 0.00 0.00 4.40
98 99 1.609635 ATGGACCATACGACACGGCA 61.610 55.000 4.75 0.00 0.00 5.69
99 100 0.874607 GATGGACCATACGACACGGC 60.875 60.000 7.05 0.00 0.00 5.68
100 101 0.249322 GGATGGACCATACGACACGG 60.249 60.000 7.05 0.00 38.79 4.94
101 102 0.458260 TGGATGGACCATACGACACG 59.542 55.000 12.26 0.00 44.64 4.49
111 112 1.130678 GGGAGAGGGATGGATGGACC 61.131 65.000 0.00 0.00 39.54 4.46
112 113 0.400525 TGGGAGAGGGATGGATGGAC 60.401 60.000 0.00 0.00 0.00 4.02
113 114 0.104777 CTGGGAGAGGGATGGATGGA 60.105 60.000 0.00 0.00 0.00 3.41
114 115 1.776975 GCTGGGAGAGGGATGGATGG 61.777 65.000 0.00 0.00 0.00 3.51
115 116 1.058428 TGCTGGGAGAGGGATGGATG 61.058 60.000 0.00 0.00 0.00 3.51
116 117 0.767446 CTGCTGGGAGAGGGATGGAT 60.767 60.000 0.00 0.00 0.00 3.41
117 118 1.383664 CTGCTGGGAGAGGGATGGA 60.384 63.158 0.00 0.00 0.00 3.41
118 119 1.692042 ACTGCTGGGAGAGGGATGG 60.692 63.158 0.00 0.00 0.00 3.51
119 120 0.979709 TCACTGCTGGGAGAGGGATG 60.980 60.000 0.00 0.00 0.00 3.51
120 121 0.252881 TTCACTGCTGGGAGAGGGAT 60.253 55.000 0.00 0.00 0.00 3.85
121 122 0.473694 TTTCACTGCTGGGAGAGGGA 60.474 55.000 0.00 0.00 0.00 4.20
122 123 0.622665 ATTTCACTGCTGGGAGAGGG 59.377 55.000 0.00 0.00 0.00 4.30
123 124 1.407989 GGATTTCACTGCTGGGAGAGG 60.408 57.143 0.00 0.00 0.00 3.69
124 125 1.741732 CGGATTTCACTGCTGGGAGAG 60.742 57.143 0.00 0.00 0.00 3.20
125 126 0.250234 CGGATTTCACTGCTGGGAGA 59.750 55.000 0.00 0.00 0.00 3.71
126 127 0.250234 TCGGATTTCACTGCTGGGAG 59.750 55.000 0.00 0.00 0.00 4.30
127 128 0.250234 CTCGGATTTCACTGCTGGGA 59.750 55.000 0.00 0.00 0.00 4.37
128 129 0.036010 ACTCGGATTTCACTGCTGGG 60.036 55.000 0.00 0.00 0.00 4.45
129 130 2.271800 GTACTCGGATTTCACTGCTGG 58.728 52.381 0.00 0.00 0.00 4.85
130 131 2.271800 GGTACTCGGATTTCACTGCTG 58.728 52.381 0.00 0.00 0.00 4.41
131 132 1.899814 TGGTACTCGGATTTCACTGCT 59.100 47.619 0.00 0.00 0.00 4.24
132 133 2.271800 CTGGTACTCGGATTTCACTGC 58.728 52.381 0.00 0.00 0.00 4.40
133 134 2.233922 ACCTGGTACTCGGATTTCACTG 59.766 50.000 0.00 0.00 0.00 3.66
134 135 2.537143 ACCTGGTACTCGGATTTCACT 58.463 47.619 0.00 0.00 0.00 3.41
135 136 3.446516 AGTACCTGGTACTCGGATTTCAC 59.553 47.826 29.36 6.76 44.86 3.18
136 137 3.705051 AGTACCTGGTACTCGGATTTCA 58.295 45.455 29.36 0.00 44.86 2.69
178 179 6.445475 TGAAACGAGATGAAATGAAATGCAA 58.555 32.000 0.00 0.00 0.00 4.08
182 183 9.865321 ATTGAATGAAACGAGATGAAATGAAAT 57.135 25.926 0.00 0.00 0.00 2.17
189 190 9.773328 GAAATGTATTGAATGAAACGAGATGAA 57.227 29.630 0.00 0.00 0.00 2.57
209 210 3.928727 CTGTGCACAATCAGGAAATGT 57.071 42.857 21.98 0.00 0.00 2.71
219 220 2.224992 TGGATTGTACCCTGTGCACAAT 60.225 45.455 21.98 9.41 43.65 2.71
247 248 2.978298 TATGCTCGGGAGGGGAGTCG 62.978 65.000 0.00 0.00 30.28 4.18
248 249 1.152525 TATGCTCGGGAGGGGAGTC 60.153 63.158 0.00 0.00 30.28 3.36
249 250 1.152440 CTATGCTCGGGAGGGGAGT 60.152 63.158 0.00 0.00 30.28 3.85
250 251 2.578714 GCTATGCTCGGGAGGGGAG 61.579 68.421 0.00 0.00 30.28 4.30
251 252 2.524394 GCTATGCTCGGGAGGGGA 60.524 66.667 0.00 0.00 32.55 4.81
252 253 2.177594 GATGCTATGCTCGGGAGGGG 62.178 65.000 0.00 0.00 0.00 4.79
257 258 2.398252 ATGATGATGCTATGCTCGGG 57.602 50.000 0.00 0.00 0.00 5.14
259 260 2.159558 GCCAATGATGATGCTATGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
265 266 1.334556 GCAACGCCAATGATGATGCTA 59.665 47.619 0.00 0.00 0.00 3.49
293 301 2.329379 CAAGGAAAGAAGACCGAGACG 58.671 52.381 0.00 0.00 0.00 4.18
298 306 1.298859 CCGCCAAGGAAAGAAGACCG 61.299 60.000 0.00 0.00 45.00 4.79
314 322 1.143620 AGAAGATGAGAGCTGCCGC 59.856 57.895 0.00 0.00 0.00 6.53
315 323 0.530211 CCAGAAGATGAGAGCTGCCG 60.530 60.000 0.00 0.00 0.00 5.69
316 324 0.179051 CCCAGAAGATGAGAGCTGCC 60.179 60.000 0.00 0.00 0.00 4.85
336 344 1.259609 CATCAAAAGGCAGGGAAGCA 58.740 50.000 0.00 0.00 35.83 3.91
337 345 1.203287 GACATCAAAAGGCAGGGAAGC 59.797 52.381 0.00 0.00 0.00 3.86
341 349 2.686915 GAGATGACATCAAAAGGCAGGG 59.313 50.000 17.57 0.00 0.00 4.45
366 374 0.727398 GGAGAAAAACAGATCGGGCG 59.273 55.000 0.00 0.00 0.00 6.13
367 375 1.095600 GGGAGAAAAACAGATCGGGC 58.904 55.000 0.00 0.00 0.00 6.13
409 417 0.618458 TTGGAAATGGAGGAGACCCG 59.382 55.000 0.00 0.00 37.58 5.28
410 418 1.064389 CCTTGGAAATGGAGGAGACCC 60.064 57.143 0.00 0.00 0.00 4.46
436 444 2.042639 TACTCCACCCCTACCGCC 60.043 66.667 0.00 0.00 0.00 6.13
442 450 1.349067 GTCACAAGTACTCCACCCCT 58.651 55.000 0.00 0.00 0.00 4.79
445 453 3.181469 TGAACTGTCACAAGTACTCCACC 60.181 47.826 0.00 0.00 0.00 4.61
448 456 4.025979 CGTTTGAACTGTCACAAGTACTCC 60.026 45.833 0.00 0.00 31.90 3.85
450 458 3.869246 CCGTTTGAACTGTCACAAGTACT 59.131 43.478 0.00 0.00 31.90 2.73
451 459 3.545426 GCCGTTTGAACTGTCACAAGTAC 60.545 47.826 0.00 0.00 31.90 2.73
452 460 2.610374 GCCGTTTGAACTGTCACAAGTA 59.390 45.455 0.00 0.00 31.90 2.24
453 461 1.400494 GCCGTTTGAACTGTCACAAGT 59.600 47.619 0.00 0.00 31.90 3.16
454 462 1.268539 GGCCGTTTGAACTGTCACAAG 60.269 52.381 0.00 0.00 31.90 3.16
455 463 0.736053 GGCCGTTTGAACTGTCACAA 59.264 50.000 0.00 0.00 31.90 3.33
456 464 0.393132 TGGCCGTTTGAACTGTCACA 60.393 50.000 0.00 0.00 31.90 3.58
457 465 0.028902 GTGGCCGTTTGAACTGTCAC 59.971 55.000 7.16 7.16 40.51 3.67
507 515 1.550976 GTCAAGGAGGAGGTACCACTG 59.449 57.143 15.94 1.83 42.04 3.66
508 516 1.433592 AGTCAAGGAGGAGGTACCACT 59.566 52.381 15.94 11.94 42.04 4.00
509 517 1.550976 CAGTCAAGGAGGAGGTACCAC 59.449 57.143 15.94 7.91 42.04 4.16
511 519 1.196012 CCAGTCAAGGAGGAGGTACC 58.804 60.000 2.73 2.73 39.35 3.34
524 532 2.752358 CTCCCAAGCAGCCAGTCA 59.248 61.111 0.00 0.00 0.00 3.41
543 551 1.717032 TCCCCTATGATCTTGTCCCG 58.283 55.000 0.00 0.00 0.00 5.14
646 659 4.200283 CGGCCGACAGGAGAGCTC 62.200 72.222 24.07 5.27 41.02 4.09
710 731 4.814294 AGAATCCGACGGTGCCGC 62.814 66.667 14.79 2.98 44.19 6.53
711 732 2.125673 AAGAATCCGACGGTGCCG 60.126 61.111 14.79 9.29 46.03 5.69
732 753 4.820894 AGTTAATTACCAGCGAAGGTCT 57.179 40.909 2.22 0.00 42.06 3.85
734 755 3.439129 GCAAGTTAATTACCAGCGAAGGT 59.561 43.478 4.58 4.58 45.72 3.50
751 772 4.500499 AATAGGCAGAGATTGAGCAAGT 57.500 40.909 0.00 0.00 0.00 3.16
764 785 6.089249 AGAAAGTTCAAACCAAATAGGCAG 57.911 37.500 0.00 0.00 43.14 4.85
783 804 4.992688 ACAAAACATGAACTTGCGAGAAA 58.007 34.783 8.31 0.00 0.00 2.52
788 809 5.701029 AAGAAACAAAACATGAACTTGCG 57.299 34.783 0.00 0.00 0.00 4.85
848 872 4.701651 TGTTCATCAGGAATGATGTTCACC 59.298 41.667 15.69 0.00 43.87 4.02
849 873 5.181811 TGTGTTCATCAGGAATGATGTTCAC 59.818 40.000 23.78 23.78 43.87 3.18
850 874 5.315348 TGTGTTCATCAGGAATGATGTTCA 58.685 37.500 15.69 13.06 43.87 3.18
851 875 5.885230 TGTGTTCATCAGGAATGATGTTC 57.115 39.130 15.69 11.20 43.87 3.18
852 876 5.126545 CCATGTGTTCATCAGGAATGATGTT 59.873 40.000 15.69 0.00 43.87 2.71
853 877 4.643334 CCATGTGTTCATCAGGAATGATGT 59.357 41.667 15.69 0.00 43.87 3.06
854 878 4.643334 ACCATGTGTTCATCAGGAATGATG 59.357 41.667 11.18 11.18 43.87 3.07
855 879 4.863548 ACCATGTGTTCATCAGGAATGAT 58.136 39.130 0.00 0.00 43.87 2.45
856 880 4.305539 ACCATGTGTTCATCAGGAATGA 57.694 40.909 0.00 0.00 42.76 2.57
857 881 5.824097 TGATACCATGTGTTCATCAGGAATG 59.176 40.000 0.00 0.00 37.93 2.67
858 882 6.005066 TGATACCATGTGTTCATCAGGAAT 57.995 37.500 0.00 0.00 37.93 3.01
860 884 4.471025 ACTGATACCATGTGTTCATCAGGA 59.529 41.667 19.96 0.00 44.41 3.86
861 885 4.774124 ACTGATACCATGTGTTCATCAGG 58.226 43.478 19.96 10.22 44.41 3.86
862 886 4.813161 GGACTGATACCATGTGTTCATCAG 59.187 45.833 17.07 17.07 45.21 2.90
864 888 3.804325 CGGACTGATACCATGTGTTCATC 59.196 47.826 0.00 0.00 31.15 2.92
865 889 3.432186 CCGGACTGATACCATGTGTTCAT 60.432 47.826 0.00 0.00 34.21 2.57
869 893 1.860641 TCCGGACTGATACCATGTGT 58.139 50.000 0.00 0.00 0.00 3.72
870 894 2.979814 TTCCGGACTGATACCATGTG 57.020 50.000 1.83 0.00 0.00 3.21
871 895 4.503714 AATTTCCGGACTGATACCATGT 57.496 40.909 1.83 0.00 0.00 3.21
872 896 4.881273 TCAAATTTCCGGACTGATACCATG 59.119 41.667 1.83 0.00 0.00 3.66
875 899 5.008712 GGAATCAAATTTCCGGACTGATACC 59.991 44.000 1.83 6.28 36.12 2.73
891 915 9.219603 CACAGAAAATACAGAGTAGGAATCAAA 57.780 33.333 0.00 0.00 0.00 2.69
892 916 8.375506 ACACAGAAAATACAGAGTAGGAATCAA 58.624 33.333 0.00 0.00 0.00 2.57
893 917 7.819415 CACACAGAAAATACAGAGTAGGAATCA 59.181 37.037 0.00 0.00 0.00 2.57
894 918 7.278868 CCACACAGAAAATACAGAGTAGGAATC 59.721 40.741 0.00 0.00 0.00 2.52
895 919 7.038302 TCCACACAGAAAATACAGAGTAGGAAT 60.038 37.037 0.00 0.00 0.00 3.01
897 921 5.778241 TCCACACAGAAAATACAGAGTAGGA 59.222 40.000 0.00 0.00 0.00 2.94
898 922 6.037786 TCCACACAGAAAATACAGAGTAGG 57.962 41.667 0.00 0.00 0.00 3.18
900 924 9.201989 AGATATCCACACAGAAAATACAGAGTA 57.798 33.333 0.00 0.00 0.00 2.59
901 925 7.984050 CAGATATCCACACAGAAAATACAGAGT 59.016 37.037 0.00 0.00 0.00 3.24
902 926 8.200120 TCAGATATCCACACAGAAAATACAGAG 58.800 37.037 0.00 0.00 0.00 3.35
923 957 1.283321 GCCCTCCTTTTCCTGTCAGAT 59.717 52.381 0.00 0.00 0.00 2.90
942 976 4.496507 GCAAGAACTTCATAGGAATTCGGC 60.497 45.833 0.00 4.03 31.55 5.54
966 1000 7.565323 AATTTAATCTGTTGGAGATCTCAGC 57.435 36.000 23.85 13.08 40.89 4.26
1044 1078 1.026718 GGATGCTGTCCTTGGGTTCG 61.027 60.000 1.94 0.00 44.16 3.95
1045 1079 0.681243 GGGATGCTGTCCTTGGGTTC 60.681 60.000 8.33 0.00 46.91 3.62
1046 1080 1.384191 GGGATGCTGTCCTTGGGTT 59.616 57.895 8.33 0.00 46.91 4.11
1047 1081 2.616458 GGGGATGCTGTCCTTGGGT 61.616 63.158 8.33 0.00 46.91 4.51
1550 1635 4.678743 AAAACCTGGCGAGGGGGC 62.679 66.667 19.90 0.00 44.84 5.80
1566 1651 2.598394 GCCTTGAGCCACCTGCAA 60.598 61.111 0.00 0.00 44.83 4.08
1686 1771 2.047274 ACCACCACGATGCCGAAG 60.047 61.111 0.00 0.00 39.50 3.79
2083 2168 1.898154 CATCTTCGACTTCCCCGGT 59.102 57.895 0.00 0.00 0.00 5.28
2117 2205 1.135527 CACAATTAGGCATGGTGCTGG 59.864 52.381 1.64 0.00 44.28 4.85
2151 2239 3.555527 TCAGCAAATCCTCCATCTGAG 57.444 47.619 0.00 0.00 41.07 3.35
2249 2337 1.595382 GGATCAACCGATGCCTCCG 60.595 63.158 0.00 0.00 34.06 4.63
2280 2368 1.884926 GATCCCTTTCGCAGCCGAG 60.885 63.158 0.00 0.00 45.35 4.63
2355 2443 4.957954 ACCACATTGCCATTAACATGATCT 59.042 37.500 0.00 0.00 31.07 2.75
2363 2451 4.648307 TGATGCATACCACATTGCCATTAA 59.352 37.500 0.00 0.00 38.08 1.40
2364 2452 4.213513 TGATGCATACCACATTGCCATTA 58.786 39.130 0.00 0.00 38.08 1.90
2416 2504 2.431782 GGTATGCAAACTCCAATGCCAT 59.568 45.455 0.00 0.00 41.87 4.40
2433 2521 2.112898 CCGCTGTGAGTACCGGTAT 58.887 57.895 19.19 6.93 36.18 2.73
2593 2681 2.892852 TCACCCTTTGAAAAGCATCCAG 59.107 45.455 0.00 0.00 34.69 3.86
2634 2722 2.309528 TTATGAGCAAGTAGGGCACG 57.690 50.000 0.00 0.00 0.00 5.34
2765 2853 2.231964 TGAATTGGCTCAAGGTTCATGC 59.768 45.455 0.00 0.00 0.00 4.06
3019 3107 3.244875 TGCCATAAGTTGTCATCACCAGT 60.245 43.478 0.00 0.00 0.00 4.00
3265 3353 0.250295 TGCGGCTGTAGAAAGCAGTT 60.250 50.000 0.00 0.00 45.43 3.16
3540 3628 2.357034 TCGACCGGCTTGAGTTGC 60.357 61.111 0.00 0.00 0.00 4.17
3693 3781 2.454336 TCAGGTCCTGTATCCGTGAT 57.546 50.000 18.65 0.00 32.61 3.06
3780 3868 2.510012 TTCAGCAGCGCCATCTCG 60.510 61.111 2.29 0.00 0.00 4.04
3857 3945 3.385384 TCCTGCACAGCTCCTCCG 61.385 66.667 0.00 0.00 0.00 4.63
3880 3968 0.176680 ATGACCGTCCTGATGCTGAC 59.823 55.000 0.00 0.00 0.00 3.51
3964 4052 3.099362 CGTCGTCTCAGATTTTACTCCG 58.901 50.000 0.00 0.00 0.00 4.63
4123 4211 7.038048 GTCAAGTTACACATGATCTCAGATCA 58.962 38.462 19.88 19.88 28.08 2.92
4124 4212 7.038048 TGTCAAGTTACACATGATCTCAGATC 58.962 38.462 7.83 7.83 28.08 2.75
4125 4213 6.939622 TGTCAAGTTACACATGATCTCAGAT 58.060 36.000 0.00 0.00 28.08 2.90
4126 4214 6.345096 TGTCAAGTTACACATGATCTCAGA 57.655 37.500 0.00 0.00 28.08 3.27
4127 4215 6.648310 AGTTGTCAAGTTACACATGATCTCAG 59.352 38.462 0.00 0.00 28.08 3.35
4171 4261 4.641094 AGATTTAGGAGACTGGACTGTACG 59.359 45.833 0.00 0.00 43.88 3.67
4208 4298 7.385752 TCCAATTTGCTCAGAATTTCATCAAAC 59.614 33.333 0.00 0.00 0.00 2.93
4327 4443 7.439655 GCTAAATATCCTTCACTGGAGTTACAG 59.560 40.741 0.00 0.00 44.03 2.74
4344 4460 7.992754 AATCACAGATCCCTTGCTAAATATC 57.007 36.000 0.00 0.00 0.00 1.63
4420 4543 5.980698 ATGACAGACTAAATTCAGCATCG 57.019 39.130 0.00 0.00 0.00 3.84
4439 4562 4.225942 AGGAGAACTTTGCTGGTGATATGA 59.774 41.667 0.00 0.00 0.00 2.15
4443 4566 2.787994 CAGGAGAACTTTGCTGGTGAT 58.212 47.619 0.00 0.00 33.40 3.06
4525 4651 0.312416 ATCGGCGTGTCAGCTAGATC 59.688 55.000 6.85 0.00 37.29 2.75
4532 4658 0.865111 TCACAAAATCGGCGTGTCAG 59.135 50.000 6.85 0.00 32.42 3.51
4533 4659 0.865111 CTCACAAAATCGGCGTGTCA 59.135 50.000 6.85 0.00 32.42 3.58
4535 4661 1.464608 CATCTCACAAAATCGGCGTGT 59.535 47.619 6.85 0.00 32.42 4.49
4630 4763 2.187424 CTGCAGAGAGCTGAGGGC 59.813 66.667 8.42 0.00 45.17 5.19
4654 4806 2.738314 GTTGCCAACCAGCATGAATTTC 59.262 45.455 0.00 0.00 43.64 2.17
4679 4831 3.005205 ACTGCGTGTGAGCATTTGA 57.995 47.368 0.00 0.00 46.97 2.69
4890 5049 1.079750 GTCGTGGAAGAGGGACAGC 60.080 63.158 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.