Multiple sequence alignment - TraesCS1B01G375100

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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 TraesCS1B01G375100 chr1B 100.000 3370 0 0 883 4252 605935739 605932370 0.000000e+00 6224.0
1 TraesCS1B01G375100 chr1B 100.000 598 0 0 1 598 605936621 605936024 0.000000e+00 1105.0
2 TraesCS1B01G375100 chr1B 93.333 45 3 0 2232 2276 605934354 605934310 2.740000e-07 67.6
3 TraesCS1B01G375100 chr1B 93.333 45 3 0 2268 2312 605934390 605934346 2.740000e-07 67.6
4 TraesCS1B01G375100 chr1D 92.188 1792 91 30 979 2737 445075572 445073797 0.000000e+00 2488.0
5 TraesCS1B01G375100 chr1D 92.979 1524 72 13 2739 4252 445073580 445072082 0.000000e+00 2189.0
6 TraesCS1B01G375100 chr1D 80.168 595 36 39 2 565 445076248 445075705 1.870000e-98 370.0
7 TraesCS1B01G375100 chr1D 79.835 243 30 14 7 233 445076887 445076648 4.400000e-35 159.0
8 TraesCS1B01G375100 chr1D 100.000 38 0 0 2268 2305 445074317 445074280 2.120000e-08 71.3
9 TraesCS1B01G375100 chr1A 90.847 1770 90 30 997 2737 540339607 540337881 0.000000e+00 2305.0
10 TraesCS1B01G375100 chr1A 92.116 1522 93 13 2739 4252 540337642 540336140 0.000000e+00 2121.0
11 TraesCS1B01G375100 chr1A 82.992 488 37 24 2 473 540340607 540340150 2.380000e-107 399.0
12 TraesCS1B01G375100 chr2D 90.196 51 4 1 1322 1371 61743 61693 9.870000e-07 65.8
13 TraesCS1B01G375100 chr2A 90.196 51 4 1 1322 1371 279346 279396 9.870000e-07 65.8
14 TraesCS1B01G375100 chr2A 100.000 32 0 0 1321 1352 86379765 86379796 4.590000e-05 60.2
15 TraesCS1B01G375100 chr7A 92.857 42 3 0 1322 1363 22332594 22332553 1.280000e-05 62.1
16 TraesCS1B01G375100 chr7A 90.476 42 4 0 1322 1363 21814837 21814796 5.940000e-04 56.5
17 TraesCS1B01G375100 chr7A 86.538 52 5 2 1322 1373 22140643 22140594 5.940000e-04 56.5
18 TraesCS1B01G375100 chr4A 92.857 42 3 0 1322 1363 711880262 711880303 1.280000e-05 62.1


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 TraesCS1B01G375100 chr1B 605932370 605936621 4251 True 1866.050000 6224 96.666500 1 4252 4 chr1B.!!$R1 4251
1 TraesCS1B01G375100 chr1D 445072082 445076887 4805 True 1055.460000 2488 89.034000 2 4252 5 chr1D.!!$R1 4250
2 TraesCS1B01G375100 chr1A 540336140 540340607 4467 True 1608.333333 2305 88.651667 2 4252 3 chr1A.!!$R1 4250

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
441 1102 0.099791 GAAGAGTCGAGCGAAGGGAG 59.900 60.000 0.00 0.0 0.00 4.30 F
543 1223 1.460497 GTCATCCTCCCTCCTCCCC 60.460 68.421 0.00 0.0 0.00 4.81 F
2280 3286 0.172803 AGGCGCTAGTCGTTACTTGG 59.827 55.000 7.64 0.0 41.07 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 2553 0.461548 TGTCCACATCGCTCATCTCC 59.538 55.0 0.0 0.0 0.00 3.71 R
2514 3539 0.449786 CAACCAAACAGACACGCACA 59.550 50.0 0.0 0.0 0.00 4.57 R
3428 4704 0.036022 GGCTCAAGGCTGAACTGACT 59.964 55.0 0.0 0.0 41.46 3.41 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 0.395036 CCATACCGACCAATTGCCCA 60.395 55.000 0.00 0.00 0.00 5.36
30 31 2.159393 CGACCAATTGCCCAGTACAATG 60.159 50.000 0.00 0.00 37.78 2.82
34 35 1.666209 ATTGCCCAGTACAATGCGCC 61.666 55.000 4.18 0.00 36.41 6.53
35 36 3.518068 GCCCAGTACAATGCGCCC 61.518 66.667 4.18 0.00 0.00 6.13
37 38 2.435938 CCAGTACAATGCGCCCGT 60.436 61.111 4.18 1.11 0.00 5.28
38 39 2.749865 CCAGTACAATGCGCCCGTG 61.750 63.158 4.18 2.22 0.00 4.94
39 40 3.124921 AGTACAATGCGCCCGTGC 61.125 61.111 4.18 2.62 0.00 5.34
70 71 0.251341 AACGGAGGCCATTTTGCTCT 60.251 50.000 5.01 0.00 0.00 4.09
72 73 0.677731 CGGAGGCCATTTTGCTCTGA 60.678 55.000 5.01 0.00 0.00 3.27
73 74 1.772836 GGAGGCCATTTTGCTCTGAT 58.227 50.000 5.01 0.00 0.00 2.90
75 76 0.822164 AGGCCATTTTGCTCTGATGC 59.178 50.000 5.01 0.00 0.00 3.91
81 82 3.444742 CCATTTTGCTCTGATGCCTTACA 59.555 43.478 0.00 0.00 0.00 2.41
85 86 2.436417 TGCTCTGATGCCTTACAAACC 58.564 47.619 0.00 0.00 0.00 3.27
90 91 2.156098 TGATGCCTTACAAACCCGAAC 58.844 47.619 0.00 0.00 0.00 3.95
92 93 0.885596 TGCCTTACAAACCCGAACGG 60.886 55.000 6.25 6.25 37.81 4.44
93 94 0.603439 GCCTTACAAACCCGAACGGA 60.603 55.000 15.07 0.00 37.50 4.69
139 141 1.741032 GAGCAGAGGCAGAGCACAC 60.741 63.158 0.00 0.00 44.61 3.82
141 143 2.653115 CAGAGGCAGAGCACACGA 59.347 61.111 0.00 0.00 0.00 4.35
146 148 0.108615 AGGCAGAGCACACGATGTAC 60.109 55.000 0.00 0.00 0.00 2.90
160 162 1.006813 ATGTACCAAGGCATCCCCAA 58.993 50.000 0.00 0.00 35.39 4.12
169 171 1.306296 GCATCCCCAAACTAGCCCA 59.694 57.895 0.00 0.00 0.00 5.36
175 177 1.176527 CCCAAACTAGCCCATGTGTG 58.823 55.000 0.00 0.00 0.00 3.82
176 178 0.527565 CCAAACTAGCCCATGTGTGC 59.472 55.000 0.00 0.00 0.00 4.57
177 179 0.527565 CAAACTAGCCCATGTGTGCC 59.472 55.000 0.00 0.00 0.00 5.01
178 180 0.405585 AAACTAGCCCATGTGTGCCT 59.594 50.000 0.00 0.00 0.00 4.75
179 181 0.405585 AACTAGCCCATGTGTGCCTT 59.594 50.000 0.00 0.00 0.00 4.35
182 184 0.698238 TAGCCCATGTGTGCCTTCTT 59.302 50.000 0.00 0.00 0.00 2.52
183 185 0.698238 AGCCCATGTGTGCCTTCTTA 59.302 50.000 0.00 0.00 0.00 2.10
184 186 1.075374 AGCCCATGTGTGCCTTCTTAA 59.925 47.619 0.00 0.00 0.00 1.85
185 187 2.102578 GCCCATGTGTGCCTTCTTAAT 58.897 47.619 0.00 0.00 0.00 1.40
186 188 3.053693 AGCCCATGTGTGCCTTCTTAATA 60.054 43.478 0.00 0.00 0.00 0.98
188 190 4.440112 GCCCATGTGTGCCTTCTTAATAAC 60.440 45.833 0.00 0.00 0.00 1.89
217 233 4.202050 CCATTTTCCCCTCGAGCATAAAAG 60.202 45.833 6.99 1.99 0.00 2.27
228 244 3.425359 CGAGCATAAAAGGCAAGTGACAG 60.425 47.826 0.00 0.00 0.00 3.51
247 903 5.813157 TGACAGATGTACGTTCTTGAAAACA 59.187 36.000 0.00 0.00 0.00 2.83
278 934 7.202526 AGTGACAAATGTATGTTGTTGAAAGG 58.797 34.615 0.00 0.00 39.29 3.11
306 967 0.238289 GTGACAAATCAGCACGGGTG 59.762 55.000 0.00 0.00 34.75 4.61
339 1000 3.782443 GGGGTGGCGTGAGGGTAG 61.782 72.222 0.00 0.00 0.00 3.18
340 1001 4.468689 GGGTGGCGTGAGGGTAGC 62.469 72.222 0.00 0.00 0.00 3.58
345 1006 1.153549 GGCGTGAGGGTAGCAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
351 1012 1.889530 GAGGGTAGCAGAAGCCGTGT 61.890 60.000 0.00 0.00 43.56 4.49
352 1013 1.448013 GGGTAGCAGAAGCCGTGTC 60.448 63.158 0.00 0.00 43.56 3.67
424 1085 2.280797 GCAGCAGACACACCGGAA 60.281 61.111 9.46 0.00 0.00 4.30
425 1086 2.320587 GCAGCAGACACACCGGAAG 61.321 63.158 9.46 1.96 0.00 3.46
426 1087 1.367471 CAGCAGACACACCGGAAGA 59.633 57.895 9.46 0.00 0.00 2.87
428 1089 1.115930 AGCAGACACACCGGAAGAGT 61.116 55.000 9.46 4.74 0.00 3.24
429 1090 0.667792 GCAGACACACCGGAAGAGTC 60.668 60.000 9.46 14.41 0.00 3.36
431 1092 0.536687 AGACACACCGGAAGAGTCGA 60.537 55.000 9.46 0.00 34.56 4.20
432 1093 0.109689 GACACACCGGAAGAGTCGAG 60.110 60.000 9.46 0.00 0.00 4.04
433 1094 1.444553 CACACCGGAAGAGTCGAGC 60.445 63.158 9.46 0.00 0.00 5.03
434 1095 2.202492 CACCGGAAGAGTCGAGCG 60.202 66.667 9.46 0.00 0.00 5.03
435 1096 2.359602 ACCGGAAGAGTCGAGCGA 60.360 61.111 9.46 0.00 0.00 4.93
436 1097 1.970114 ACCGGAAGAGTCGAGCGAA 60.970 57.895 9.46 0.00 0.00 4.70
437 1098 1.226435 CCGGAAGAGTCGAGCGAAG 60.226 63.158 0.00 0.00 0.00 3.79
438 1099 1.226435 CGGAAGAGTCGAGCGAAGG 60.226 63.158 0.00 0.00 0.00 3.46
439 1100 1.139947 GGAAGAGTCGAGCGAAGGG 59.860 63.158 0.00 0.00 0.00 3.95
440 1101 1.313812 GGAAGAGTCGAGCGAAGGGA 61.314 60.000 0.00 0.00 0.00 4.20
441 1102 0.099791 GAAGAGTCGAGCGAAGGGAG 59.900 60.000 0.00 0.00 0.00 4.30
536 1216 1.990060 CCACACCGTCATCCTCCCT 60.990 63.158 0.00 0.00 0.00 4.20
541 1221 1.834822 CCGTCATCCTCCCTCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
542 1222 1.834822 CGTCATCCTCCCTCCTCCC 60.835 68.421 0.00 0.00 0.00 4.30
543 1223 1.460497 GTCATCCTCCCTCCTCCCC 60.460 68.421 0.00 0.00 0.00 4.81
544 1224 2.122189 CATCCTCCCTCCTCCCCC 60.122 72.222 0.00 0.00 0.00 5.40
570 1250 4.394712 CTCCGCTCCACCCACCAC 62.395 72.222 0.00 0.00 0.00 4.16
573 1531 4.394712 CGCTCCACCCACCACTCC 62.395 72.222 0.00 0.00 0.00 3.85
574 1532 2.930562 GCTCCACCCACCACTCCT 60.931 66.667 0.00 0.00 0.00 3.69
950 1939 2.919856 AGTCGGCTGCTGACTGGT 60.920 61.111 36.13 17.95 46.83 4.00
951 1940 2.031163 GTCGGCTGCTGACTGGTT 59.969 61.111 29.44 0.00 36.86 3.67
952 1941 2.029844 GTCGGCTGCTGACTGGTTC 61.030 63.158 29.44 6.56 36.86 3.62
1377 2372 4.157120 GTATGCACGCCCGGGTCT 62.157 66.667 24.63 3.89 0.00 3.85
1406 2401 1.692749 TCCCCTCCCCTTGGATTCG 60.693 63.158 0.00 0.00 40.80 3.34
1413 2408 3.564027 CCTTGGATTCGTCGCCGC 61.564 66.667 0.00 0.00 0.00 6.53
1464 2462 4.047822 GTGATCTGACGATCTGTGGATTC 58.952 47.826 0.00 0.00 45.10 2.52
1467 2465 1.759445 CTGACGATCTGTGGATTCCCT 59.241 52.381 0.00 0.00 31.46 4.20
1609 2607 0.759436 ACGACCTCTTCACCAGGTGT 60.759 55.000 19.65 0.00 44.87 4.16
1618 2616 1.208706 TCACCAGGTGTTTCCAGACA 58.791 50.000 19.65 0.00 39.02 3.41
1699 2697 3.459378 GATCGCCGCGGAGAACGTA 62.459 63.158 34.86 13.02 46.52 3.57
1741 2739 3.024547 GGTAGTGTGCTCCTCTCATGTA 58.975 50.000 0.00 0.00 0.00 2.29
1753 2751 1.831106 TCTCATGTAGTGGTCGCCAAT 59.169 47.619 4.39 4.39 34.18 3.16
1829 2827 8.591940 TCTCAATTGATCAGAAGGTAGATATGG 58.408 37.037 8.96 0.00 0.00 2.74
1832 2830 9.347240 CAATTGATCAGAAGGTAGATATGGTTT 57.653 33.333 0.00 0.00 0.00 3.27
1854 2852 1.985473 TGAGCATCATGGTATTGGCC 58.015 50.000 0.00 0.00 42.56 5.36
1877 2878 2.502538 CAGCATCCATGATTTGGGGTTT 59.497 45.455 0.00 0.00 46.45 3.27
1880 2881 4.970640 AGCATCCATGATTTGGGGTTTATT 59.029 37.500 0.00 0.00 46.45 1.40
1881 2882 6.041865 CAGCATCCATGATTTGGGGTTTATTA 59.958 38.462 0.00 0.00 46.45 0.98
1882 2883 6.614906 AGCATCCATGATTTGGGGTTTATTAA 59.385 34.615 0.00 0.00 46.45 1.40
1883 2884 7.293062 AGCATCCATGATTTGGGGTTTATTAAT 59.707 33.333 0.00 0.00 46.45 1.40
1884 2885 7.603784 GCATCCATGATTTGGGGTTTATTAATC 59.396 37.037 0.00 0.00 46.45 1.75
1886 2887 8.248904 TCCATGATTTGGGGTTTATTAATCTG 57.751 34.615 0.00 0.00 46.45 2.90
2026 3027 5.178061 CGATCCATTGGTATGCAGCTATAA 58.822 41.667 1.86 0.00 0.00 0.98
2105 3109 4.095185 CACCCGTTGAGTTTGAAACTGTAA 59.905 41.667 16.25 7.69 43.03 2.41
2128 3132 9.869844 GTAATCATAGCAACATCAAAGTATGAC 57.130 33.333 0.00 0.00 41.93 3.06
2259 3265 6.655848 TCGTTACTTGGTACCATTTTAAGCAT 59.344 34.615 17.17 0.00 0.00 3.79
2273 3279 4.732106 GCATTAGGCGCTAGTCGT 57.268 55.556 7.64 0.00 41.07 4.34
2274 3280 2.973420 GCATTAGGCGCTAGTCGTT 58.027 52.632 7.64 1.44 41.07 3.85
2276 3282 1.785430 GCATTAGGCGCTAGTCGTTAC 59.215 52.381 7.64 0.00 41.07 2.50
2277 3283 2.543238 GCATTAGGCGCTAGTCGTTACT 60.543 50.000 7.64 0.00 41.07 2.24
2278 3284 3.703420 CATTAGGCGCTAGTCGTTACTT 58.297 45.455 7.64 0.00 41.07 2.24
2280 3286 0.172803 AGGCGCTAGTCGTTACTTGG 59.827 55.000 7.64 0.00 41.07 3.61
2282 3288 1.133025 GGCGCTAGTCGTTACTTGGTA 59.867 52.381 7.64 0.00 41.07 3.25
2283 3289 2.180397 GCGCTAGTCGTTACTTGGTAC 58.820 52.381 0.00 0.00 41.07 3.34
2284 3290 2.790387 CGCTAGTCGTTACTTGGTACC 58.210 52.381 4.43 4.43 37.15 3.34
2285 3291 2.162208 CGCTAGTCGTTACTTGGTACCA 59.838 50.000 11.60 11.60 37.15 3.25
2287 3293 4.676196 CGCTAGTCGTTACTTGGTACCATT 60.676 45.833 17.17 8.64 37.15 3.16
2288 3294 5.173664 GCTAGTCGTTACTTGGTACCATTT 58.826 41.667 17.17 8.25 37.15 2.32
2289 3295 5.640783 GCTAGTCGTTACTTGGTACCATTTT 59.359 40.000 17.17 5.53 37.15 1.82
2290 3296 6.813152 GCTAGTCGTTACTTGGTACCATTTTA 59.187 38.462 17.17 4.47 37.15 1.52
2291 3297 7.331687 GCTAGTCGTTACTTGGTACCATTTTAA 59.668 37.037 17.17 10.49 37.15 1.52
2292 3298 7.662604 AGTCGTTACTTGGTACCATTTTAAG 57.337 36.000 17.17 12.27 29.00 1.85
2293 3299 6.148315 AGTCGTTACTTGGTACCATTTTAAGC 59.852 38.462 17.17 3.52 29.00 3.09
2295 3301 6.148150 TCGTTACTTGGTACCATTTTAAGCAG 59.852 38.462 17.17 9.93 0.00 4.24
2334 3347 1.726853 GACAACAGAACGCCTAGCAT 58.273 50.000 0.00 0.00 0.00 3.79
2358 3371 1.233919 TCATGCTTGTGTGCGCTTAA 58.766 45.000 9.73 0.00 35.36 1.85
2359 3372 1.811965 TCATGCTTGTGTGCGCTTAAT 59.188 42.857 9.73 0.00 35.36 1.40
2398 3420 3.490526 CAGTGGCAAAATGCACACTTAAC 59.509 43.478 17.81 0.00 45.68 2.01
2399 3421 3.384467 AGTGGCAAAATGCACACTTAACT 59.616 39.130 15.85 0.00 45.68 2.24
2400 3422 4.499696 AGTGGCAAAATGCACACTTAACTC 60.500 41.667 15.85 0.00 45.68 3.01
2458 3480 7.106239 TCATTTATGGAAACCTGAAGTCTCTC 58.894 38.462 0.00 0.00 0.00 3.20
2475 3497 0.321564 CTCGGGCTGTTTGGATGACA 60.322 55.000 0.00 0.00 0.00 3.58
2508 3533 2.577449 CCAAAATATGGGCGTTGACC 57.423 50.000 0.00 0.00 46.27 4.02
2509 3534 1.202245 CCAAAATATGGGCGTTGACCG 60.202 52.381 0.00 0.00 46.27 4.79
2518 3543 4.012895 CGTTGACCGCCAGTGTGC 62.013 66.667 0.00 0.00 0.00 4.57
2535 3560 1.358759 GCGTGTCTGTTTGGTTGGG 59.641 57.895 0.00 0.00 0.00 4.12
2555 3580 3.632604 GGGAGCCAAAATTTCTAGCCTAC 59.367 47.826 0.00 0.00 0.00 3.18
2587 3612 2.289547 TGGTCGCTAGTTTGTTTTCTGC 59.710 45.455 0.00 0.00 0.00 4.26
2607 3632 2.825836 CAACGCCAGGGCAGATCC 60.826 66.667 11.42 0.00 42.06 3.36
2695 3721 1.064685 CCAAACGGCCCCTCTATTCTT 60.065 52.381 0.00 0.00 0.00 2.52
2705 3731 4.089361 CCCCTCTATTCTTTTGGCTGTTT 58.911 43.478 0.00 0.00 0.00 2.83
2712 3738 7.725251 TCTATTCTTTTGGCTGTTTTCATGTT 58.275 30.769 0.00 0.00 0.00 2.71
2713 3739 8.855110 TCTATTCTTTTGGCTGTTTTCATGTTA 58.145 29.630 0.00 0.00 0.00 2.41
2723 3749 6.349280 GGCTGTTTTCATGTTATAAGTGCTGA 60.349 38.462 0.00 0.00 0.00 4.26
2737 3763 3.754965 AGTGCTGACTGCCTCAATTTTA 58.245 40.909 1.50 0.00 42.00 1.52
2771 4045 4.002982 TGTGCCACTCAAATCTGATGTAC 58.997 43.478 0.00 0.00 0.00 2.90
2772 4046 4.002982 GTGCCACTCAAATCTGATGTACA 58.997 43.478 0.00 0.00 0.00 2.90
2813 4087 8.109634 ACAACATCATAGGGATTTAGTTGAACT 58.890 33.333 2.37 2.37 38.63 3.01
2940 4216 6.162079 CGATACTTGAAGCCATACATCATCT 58.838 40.000 0.00 0.00 0.00 2.90
2966 4242 2.436911 ACCAGAAGTTACGGTTGTTCCT 59.563 45.455 0.00 0.00 0.00 3.36
3065 4341 4.049640 GCACGCCGGCAAATCCAA 62.050 61.111 28.98 0.00 34.01 3.53
3170 4446 1.135139 GACTATCTGACGAGGCTTGCA 59.865 52.381 0.37 0.21 0.00 4.08
3171 4447 1.759445 ACTATCTGACGAGGCTTGCAT 59.241 47.619 0.37 0.00 0.00 3.96
3197 4473 4.786425 AGAAAGGAAGCCAGGACAATATC 58.214 43.478 0.00 0.00 0.00 1.63
3200 4476 3.118531 AGGAAGCCAGGACAATATCACT 58.881 45.455 0.00 0.00 0.00 3.41
3411 4687 4.772100 CCCCTGTTTTCTGTTCATATGGTT 59.228 41.667 2.13 0.00 0.00 3.67
3443 4720 2.141517 CAGTCAGTCAGTTCAGCCTTG 58.858 52.381 0.00 0.00 0.00 3.61
3482 4761 1.291877 CCTTGCCGTCAGTGTACAGC 61.292 60.000 0.00 0.00 0.00 4.40
3550 4829 9.573133 GATTTAACATGTTTCTATCACCTTTGG 57.427 33.333 17.78 0.00 0.00 3.28
3570 4849 5.086104 TGGTGAATTACAGCTTCTACTCC 57.914 43.478 0.00 0.00 45.86 3.85
3596 4875 2.751806 CAAAGAATGGAGAAGAGGGTGC 59.248 50.000 0.00 0.00 0.00 5.01
3599 4878 1.280421 GAATGGAGAAGAGGGTGCTGT 59.720 52.381 0.00 0.00 0.00 4.40
3636 4915 0.882042 AAGAGACGCACCACTGCTTG 60.882 55.000 0.00 0.00 41.77 4.01
3689 4968 4.830826 AGAAATTCTCGGTGAAAACACC 57.169 40.909 9.07 9.07 41.68 4.16
3690 4969 4.204012 AGAAATTCTCGGTGAAAACACCA 58.796 39.130 17.53 5.98 45.23 4.17
3695 4974 6.642707 ATTCTCGGTGAAAACACCATTAAA 57.357 33.333 17.53 7.70 45.23 1.52
3726 5005 5.990386 TCCTATCTTCTACTACTGTGCTACG 59.010 44.000 0.00 0.00 0.00 3.51
3735 5014 8.531622 TCTACTACTGTGCTACGAGAATATAC 57.468 38.462 0.00 0.00 0.00 1.47
3840 5119 3.829601 TGGTTTTCACGAATAAAGGGCAT 59.170 39.130 0.00 0.00 0.00 4.40
3951 5234 3.297134 ACAGAGGTGAAAAAGGAGCAA 57.703 42.857 0.00 0.00 0.00 3.91
3952 5235 2.952310 ACAGAGGTGAAAAAGGAGCAAC 59.048 45.455 0.00 0.00 0.00 4.17
3975 5258 3.291383 TTGTTCCAAAGGGGCGCG 61.291 61.111 0.00 0.00 36.21 6.86
3989 5272 1.653094 GGCGCGAACAATGGAATCCA 61.653 55.000 12.10 3.67 38.19 3.41
3994 5277 2.378038 CGAACAATGGAATCCATGGGT 58.622 47.619 20.09 14.50 44.40 4.51
3995 5278 2.358898 CGAACAATGGAATCCATGGGTC 59.641 50.000 22.07 22.07 45.65 4.46
3996 5279 3.635591 GAACAATGGAATCCATGGGTCT 58.364 45.455 24.10 7.54 45.65 3.85
3997 5280 3.763557 ACAATGGAATCCATGGGTCTT 57.236 42.857 20.09 3.24 44.40 3.01
3998 5281 3.635591 ACAATGGAATCCATGGGTCTTC 58.364 45.455 20.09 12.27 44.40 2.87
3999 5282 3.270433 ACAATGGAATCCATGGGTCTTCT 59.730 43.478 20.09 0.00 44.40 2.85
4000 5283 4.264532 ACAATGGAATCCATGGGTCTTCTT 60.265 41.667 20.09 0.00 44.40 2.52
4002 5285 4.402616 TGGAATCCATGGGTCTTCTTTT 57.597 40.909 13.02 0.00 0.00 2.27
4003 5286 4.750941 TGGAATCCATGGGTCTTCTTTTT 58.249 39.130 13.02 0.00 0.00 1.94
4078 5361 5.889853 AGAGGCTATTTGATTCTTCATGCAA 59.110 36.000 0.00 0.00 0.00 4.08
4083 5366 7.416664 GGCTATTTGATTCTTCATGCAAGGTTA 60.417 37.037 0.00 0.00 32.22 2.85
4125 5409 2.224018 TGCAAACAGAAGGGAACAATGC 60.224 45.455 0.00 0.00 0.00 3.56
4127 5411 3.858503 GCAAACAGAAGGGAACAATGCTC 60.859 47.826 0.00 0.00 0.00 4.26
4130 5414 3.152341 ACAGAAGGGAACAATGCTCAAG 58.848 45.455 0.00 0.00 0.00 3.02
4132 5416 3.571401 CAGAAGGGAACAATGCTCAAGTT 59.429 43.478 0.00 0.00 0.00 2.66
4140 5424 5.915196 GGAACAATGCTCAAGTTAACACTTC 59.085 40.000 8.61 0.00 41.69 3.01
4141 5425 5.095691 ACAATGCTCAAGTTAACACTTCG 57.904 39.130 8.61 0.00 41.69 3.79
4142 5426 4.814234 ACAATGCTCAAGTTAACACTTCGA 59.186 37.500 8.61 0.00 41.69 3.71
4143 5427 5.295787 ACAATGCTCAAGTTAACACTTCGAA 59.704 36.000 8.61 0.00 41.69 3.71
4144 5428 4.789095 TGCTCAAGTTAACACTTCGAAC 57.211 40.909 8.61 0.00 41.69 3.95
4145 5429 4.185394 TGCTCAAGTTAACACTTCGAACA 58.815 39.130 8.61 0.00 41.69 3.18
4146 5430 4.270084 TGCTCAAGTTAACACTTCGAACAG 59.730 41.667 8.61 0.00 41.69 3.16
4164 5462 5.108780 CGAACAGCAAACAGTTTTGATTACG 60.109 40.000 4.95 1.26 44.38 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.944709 GGCAATTGGTCGGTATGGTAC 59.055 52.381 7.72 0.00 0.00 3.34
1 2 1.134037 GGGCAATTGGTCGGTATGGTA 60.134 52.381 7.72 0.00 0.00 3.25
2 3 0.395173 GGGCAATTGGTCGGTATGGT 60.395 55.000 7.72 0.00 0.00 3.55
4 5 1.024271 CTGGGCAATTGGTCGGTATG 58.976 55.000 7.72 0.00 0.00 2.39
5 6 0.623723 ACTGGGCAATTGGTCGGTAT 59.376 50.000 7.72 0.00 0.00 2.73
6 7 1.065998 GTACTGGGCAATTGGTCGGTA 60.066 52.381 7.72 0.00 0.00 4.02
7 8 0.322187 GTACTGGGCAATTGGTCGGT 60.322 55.000 7.72 0.36 0.00 4.69
8 9 0.322098 TGTACTGGGCAATTGGTCGG 60.322 55.000 7.72 0.00 0.00 4.79
9 10 1.529226 TTGTACTGGGCAATTGGTCG 58.471 50.000 7.72 0.00 0.00 4.79
10 11 2.417243 GCATTGTACTGGGCAATTGGTC 60.417 50.000 7.72 0.00 34.68 4.02
22 23 3.124921 GCACGGGCGCATTGTACT 61.125 61.111 10.83 0.00 0.00 2.73
38 39 4.038080 CCGTTCCGTGCCCTTTGC 62.038 66.667 0.00 0.00 41.77 3.68
39 40 2.281208 TCCGTTCCGTGCCCTTTG 60.281 61.111 0.00 0.00 0.00 2.77
40 41 2.032071 CTCCGTTCCGTGCCCTTT 59.968 61.111 0.00 0.00 0.00 3.11
45 46 4.778143 ATGGCCTCCGTTCCGTGC 62.778 66.667 3.32 0.00 0.00 5.34
46 47 1.241315 AAAATGGCCTCCGTTCCGTG 61.241 55.000 3.32 0.00 30.58 4.94
47 48 1.074248 AAAATGGCCTCCGTTCCGT 59.926 52.632 3.32 0.00 30.58 4.69
48 49 1.506262 CAAAATGGCCTCCGTTCCG 59.494 57.895 3.32 0.00 30.58 4.30
70 71 2.156098 GTTCGGGTTTGTAAGGCATCA 58.844 47.619 0.00 0.00 0.00 3.07
72 73 1.161843 CGTTCGGGTTTGTAAGGCAT 58.838 50.000 0.00 0.00 0.00 4.40
73 74 0.885596 CCGTTCGGGTTTGTAAGGCA 60.886 55.000 3.04 0.00 0.00 4.75
75 76 1.435577 CTCCGTTCGGGTTTGTAAGG 58.564 55.000 11.37 0.00 37.00 2.69
81 82 0.542702 TACTCCCTCCGTTCGGGTTT 60.543 55.000 11.37 0.00 42.56 3.27
85 86 2.768492 CGGTACTCCCTCCGTTCGG 61.768 68.421 4.74 4.74 41.58 4.30
90 91 1.734137 CATGTCGGTACTCCCTCCG 59.266 63.158 0.00 0.00 46.93 4.63
120 122 2.508887 GTGCTCTGCCTCTGCTCG 60.509 66.667 0.00 0.00 38.71 5.03
139 141 0.535102 GGGGATGCCTTGGTACATCG 60.535 60.000 2.19 0.00 42.94 3.84
141 143 1.006813 TTGGGGATGCCTTGGTACAT 58.993 50.000 2.19 0.00 39.30 2.29
146 148 1.767759 CTAGTTTGGGGATGCCTTGG 58.232 55.000 2.19 0.00 0.00 3.61
160 162 0.405585 AAGGCACACATGGGCTAGTT 59.594 50.000 6.00 0.00 45.56 2.24
169 171 5.321102 TGGTGTTATTAAGAAGGCACACAT 58.679 37.500 5.44 0.00 36.96 3.21
175 177 6.715347 AATGGATGGTGTTATTAAGAAGGC 57.285 37.500 0.00 0.00 0.00 4.35
176 178 8.197439 GGAAAATGGATGGTGTTATTAAGAAGG 58.803 37.037 0.00 0.00 0.00 3.46
177 179 8.197439 GGGAAAATGGATGGTGTTATTAAGAAG 58.803 37.037 0.00 0.00 0.00 2.85
178 180 7.125053 GGGGAAAATGGATGGTGTTATTAAGAA 59.875 37.037 0.00 0.00 0.00 2.52
179 181 6.609616 GGGGAAAATGGATGGTGTTATTAAGA 59.390 38.462 0.00 0.00 0.00 2.10
182 184 6.098716 AGGGGAAAATGGATGGTGTTATTA 57.901 37.500 0.00 0.00 0.00 0.98
183 185 4.959080 AGGGGAAAATGGATGGTGTTATT 58.041 39.130 0.00 0.00 0.00 1.40
184 186 4.546674 GAGGGGAAAATGGATGGTGTTAT 58.453 43.478 0.00 0.00 0.00 1.89
185 187 3.623703 CGAGGGGAAAATGGATGGTGTTA 60.624 47.826 0.00 0.00 0.00 2.41
186 188 2.820178 GAGGGGAAAATGGATGGTGTT 58.180 47.619 0.00 0.00 0.00 3.32
188 190 1.064758 TCGAGGGGAAAATGGATGGTG 60.065 52.381 0.00 0.00 0.00 4.17
217 233 2.080286 ACGTACATCTGTCACTTGCC 57.920 50.000 0.00 0.00 0.00 4.52
228 244 5.113529 CGCTTTGTTTTCAAGAACGTACATC 59.886 40.000 0.00 0.00 41.09 3.06
247 903 5.008613 ACAACATACATTTGTCACTCGCTTT 59.991 36.000 0.00 0.00 31.30 3.51
278 934 4.207841 GTGCTGATTTGTCACTTGCTTTTC 59.792 41.667 0.00 0.00 0.00 2.29
306 967 2.922779 CCCCCGTACACTTGTTCAC 58.077 57.895 0.00 0.00 0.00 3.18
330 991 1.153549 CGGCTTCTGCTACCCTCAC 60.154 63.158 0.00 0.00 39.59 3.51
331 992 1.609501 ACGGCTTCTGCTACCCTCA 60.610 57.895 0.00 0.00 39.59 3.86
333 994 1.889530 GACACGGCTTCTGCTACCCT 61.890 60.000 0.00 0.00 39.59 4.34
334 995 1.448013 GACACGGCTTCTGCTACCC 60.448 63.158 0.00 0.00 39.59 3.69
335 996 1.448013 GGACACGGCTTCTGCTACC 60.448 63.158 0.00 0.00 39.59 3.18
336 997 1.448013 GGGACACGGCTTCTGCTAC 60.448 63.158 0.00 0.00 39.59 3.58
337 998 2.978824 GGGACACGGCTTCTGCTA 59.021 61.111 0.00 0.00 39.59 3.49
338 999 4.379243 CGGGACACGGCTTCTGCT 62.379 66.667 0.00 0.00 39.42 4.24
352 1013 2.246761 TTATGTCTTGTCGCCCCGGG 62.247 60.000 15.80 15.80 0.00 5.73
424 1085 1.751162 CCTCCCTTCGCTCGACTCT 60.751 63.158 0.00 0.00 0.00 3.24
425 1086 1.720694 CTCCTCCCTTCGCTCGACTC 61.721 65.000 0.00 0.00 0.00 3.36
426 1087 1.751162 CTCCTCCCTTCGCTCGACT 60.751 63.158 0.00 0.00 0.00 4.18
428 1089 1.001269 TTCTCCTCCCTTCGCTCGA 60.001 57.895 0.00 0.00 0.00 4.04
429 1090 1.032657 TCTTCTCCTCCCTTCGCTCG 61.033 60.000 0.00 0.00 0.00 5.03
431 1092 1.190643 CTTCTTCTCCTCCCTTCGCT 58.809 55.000 0.00 0.00 0.00 4.93
432 1093 1.134936 GTCTTCTTCTCCTCCCTTCGC 60.135 57.143 0.00 0.00 0.00 4.70
433 1094 1.478916 GGTCTTCTTCTCCTCCCTTCG 59.521 57.143 0.00 0.00 0.00 3.79
434 1095 2.499693 CAGGTCTTCTTCTCCTCCCTTC 59.500 54.545 0.00 0.00 0.00 3.46
435 1096 2.545810 CAGGTCTTCTTCTCCTCCCTT 58.454 52.381 0.00 0.00 0.00 3.95
436 1097 1.899438 GCAGGTCTTCTTCTCCTCCCT 60.899 57.143 0.00 0.00 0.00 4.20
437 1098 0.539518 GCAGGTCTTCTTCTCCTCCC 59.460 60.000 0.00 0.00 0.00 4.30
438 1099 0.539518 GGCAGGTCTTCTTCTCCTCC 59.460 60.000 0.00 0.00 0.00 4.30
439 1100 0.539518 GGGCAGGTCTTCTTCTCCTC 59.460 60.000 0.00 0.00 0.00 3.71
440 1101 1.261238 CGGGCAGGTCTTCTTCTCCT 61.261 60.000 0.00 0.00 0.00 3.69
441 1102 1.219393 CGGGCAGGTCTTCTTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
525 1205 1.460497 GGGGAGGAGGGAGGATGAC 60.460 68.421 0.00 0.00 0.00 3.06
546 1226 3.775654 GTGGAGCGGAGGAGGGTG 61.776 72.222 0.00 0.00 0.00 4.61
550 1230 3.775654 GTGGGTGGAGCGGAGGAG 61.776 72.222 0.00 0.00 0.00 3.69
553 1233 4.394712 GTGGTGGGTGGAGCGGAG 62.395 72.222 0.00 0.00 0.00 4.63
554 1234 4.954118 AGTGGTGGGTGGAGCGGA 62.954 66.667 0.00 0.00 0.00 5.54
555 1235 4.394712 GAGTGGTGGGTGGAGCGG 62.395 72.222 0.00 0.00 0.00 5.52
556 1236 4.394712 GGAGTGGTGGGTGGAGCG 62.395 72.222 0.00 0.00 0.00 5.03
557 1237 2.930562 AGGAGTGGTGGGTGGAGC 60.931 66.667 0.00 0.00 0.00 4.70
882 1849 3.752816 GAGGGGTACGGGAGGGAGG 62.753 73.684 0.00 0.00 0.00 4.30
883 1850 2.123382 GAGGGGTACGGGAGGGAG 60.123 72.222 0.00 0.00 0.00 4.30
884 1851 3.759101 GGAGGGGTACGGGAGGGA 61.759 72.222 0.00 0.00 0.00 4.20
971 1963 1.814169 GCTAAAGAACCTCCGCCCG 60.814 63.158 0.00 0.00 0.00 6.13
972 1964 1.814169 CGCTAAAGAACCTCCGCCC 60.814 63.158 0.00 0.00 0.00 6.13
973 1965 1.079336 ACGCTAAAGAACCTCCGCC 60.079 57.895 0.00 0.00 0.00 6.13
974 1966 1.411493 CGACGCTAAAGAACCTCCGC 61.411 60.000 0.00 0.00 0.00 5.54
975 1967 0.801067 CCGACGCTAAAGAACCTCCG 60.801 60.000 0.00 0.00 0.00 4.63
976 1968 1.082679 GCCGACGCTAAAGAACCTCC 61.083 60.000 0.00 0.00 0.00 4.30
977 1969 1.082679 GGCCGACGCTAAAGAACCTC 61.083 60.000 0.00 0.00 34.44 3.85
1354 2349 3.845259 GGGCGTGCATACCTCGGA 61.845 66.667 7.78 0.00 0.00 4.55
1435 2433 0.467474 ATCGTCAGATCACGGGGCTA 60.467 55.000 5.83 0.00 40.35 3.93
1467 2465 4.578898 ACACCTGCGCGACGACAA 62.579 61.111 12.10 0.00 0.00 3.18
1555 2553 0.461548 TGTCCACATCGCTCATCTCC 59.538 55.000 0.00 0.00 0.00 3.71
1618 2616 3.352524 GACACCTCGTCGTCCACT 58.647 61.111 0.00 0.00 34.19 4.00
1723 2721 2.495270 CACTACATGAGAGGAGCACACT 59.505 50.000 0.00 0.00 0.00 3.55
1829 2827 5.104374 CCAATACCATGATGCTCACAAAAC 58.896 41.667 0.00 0.00 0.00 2.43
1832 2830 2.689471 GCCAATACCATGATGCTCACAA 59.311 45.455 0.00 0.00 0.00 3.33
1880 2881 8.347004 TGAAACAACAAGGCATAATCAGATTA 57.653 30.769 5.29 5.29 0.00 1.75
1881 2882 7.230849 TGAAACAACAAGGCATAATCAGATT 57.769 32.000 0.20 0.20 0.00 2.40
1882 2883 6.626623 GCTGAAACAACAAGGCATAATCAGAT 60.627 38.462 0.00 0.00 35.05 2.90
1883 2884 5.335897 GCTGAAACAACAAGGCATAATCAGA 60.336 40.000 0.00 0.00 35.05 3.27
1884 2885 4.860907 GCTGAAACAACAAGGCATAATCAG 59.139 41.667 0.00 0.00 35.92 2.90
1886 2887 4.082026 AGGCTGAAACAACAAGGCATAATC 60.082 41.667 0.00 0.00 0.00 1.75
2076 3077 1.071071 CAAACTCAACGGGTGGTCCTA 59.929 52.381 0.00 0.00 0.00 2.94
2105 3109 6.293081 GCGTCATACTTTGATGTTGCTATGAT 60.293 38.462 0.00 0.00 42.42 2.45
2143 3148 3.202906 CATTTACCACTATCACACCGGG 58.797 50.000 6.32 0.00 0.00 5.73
2181 3186 6.420903 GCTACTTTCCTGGATTTCAAACAAAC 59.579 38.462 0.00 0.00 0.00 2.93
2259 3265 2.159338 CCAAGTAACGACTAGCGCCTAA 60.159 50.000 2.29 0.00 46.04 2.69
2270 3276 5.996513 TGCTTAAAATGGTACCAAGTAACGA 59.003 36.000 20.76 1.28 0.00 3.85
2271 3277 6.072893 ACTGCTTAAAATGGTACCAAGTAACG 60.073 38.462 20.76 7.87 0.00 3.18
2273 3279 7.608761 CCTACTGCTTAAAATGGTACCAAGTAA 59.391 37.037 20.76 15.37 0.00 2.24
2274 3280 7.107542 CCTACTGCTTAAAATGGTACCAAGTA 58.892 38.462 20.76 17.08 0.00 2.24
2276 3282 5.163652 GCCTACTGCTTAAAATGGTACCAAG 60.164 44.000 20.76 12.51 36.87 3.61
2277 3283 4.703093 GCCTACTGCTTAAAATGGTACCAA 59.297 41.667 20.76 0.00 36.87 3.67
2278 3284 4.266714 GCCTACTGCTTAAAATGGTACCA 58.733 43.478 18.99 18.99 36.87 3.25
2280 3286 3.242641 GCGCCTACTGCTTAAAATGGTAC 60.243 47.826 0.00 0.00 38.05 3.34
2282 3288 1.743394 GCGCCTACTGCTTAAAATGGT 59.257 47.619 0.00 0.00 38.05 3.55
2283 3289 2.017049 AGCGCCTACTGCTTAAAATGG 58.983 47.619 2.29 0.00 40.48 3.16
2284 3290 3.303395 GCTAGCGCCTACTGCTTAAAATG 60.303 47.826 2.29 0.00 43.71 2.32
2285 3291 2.872858 GCTAGCGCCTACTGCTTAAAAT 59.127 45.455 2.29 0.00 43.71 1.82
2287 3293 1.935933 GCTAGCGCCTACTGCTTAAA 58.064 50.000 2.29 0.00 43.71 1.52
2288 3294 3.661745 GCTAGCGCCTACTGCTTAA 57.338 52.632 2.29 0.00 43.71 1.85
2334 3347 1.135717 GCGCACACAAGCATGATTACA 60.136 47.619 0.30 0.00 0.00 2.41
2348 3361 2.284150 GCGTATCTCAATTAAGCGCACA 59.716 45.455 11.47 0.00 42.44 4.57
2358 3371 2.695666 ACTGCCTAGTGCGTATCTCAAT 59.304 45.455 0.00 0.00 45.60 2.57
2359 3372 2.100197 ACTGCCTAGTGCGTATCTCAA 58.900 47.619 0.00 0.00 45.60 3.02
2434 3456 6.036517 CGAGAGACTTCAGGTTTCCATAAATG 59.963 42.308 0.00 0.00 30.31 2.32
2458 3480 2.174334 CTGTCATCCAAACAGCCCG 58.826 57.895 0.00 0.00 37.88 6.13
2509 3534 1.714899 AAACAGACACGCACACTGGC 61.715 55.000 0.00 0.00 36.17 4.85
2514 3539 0.449786 CAACCAAACAGACACGCACA 59.550 50.000 0.00 0.00 0.00 4.57
2518 3543 0.944386 CTCCCAACCAAACAGACACG 59.056 55.000 0.00 0.00 0.00 4.49
2535 3560 3.242772 GCGTAGGCTAGAAATTTTGGCTC 60.243 47.826 15.29 9.22 36.69 4.70
2607 3632 0.247655 CGATGAAATTCACCGCCACG 60.248 55.000 0.00 0.00 0.00 4.94
2615 3640 5.170021 CCAAAAAGATGGCGATGAAATTCA 58.830 37.500 0.00 0.00 32.78 2.57
2630 3655 0.816018 TCGCGGACAAGCCAAAAAGA 60.816 50.000 6.13 0.00 35.94 2.52
2678 3704 2.620627 CCAAAAGAATAGAGGGGCCGTT 60.621 50.000 0.00 0.00 0.00 4.44
2695 3721 6.644592 GCACTTATAACATGAAAACAGCCAAA 59.355 34.615 0.00 0.00 0.00 3.28
2705 3731 5.801350 GCAGTCAGCACTTATAACATGAA 57.199 39.130 0.00 0.00 44.79 2.57
2723 3749 6.888632 AGAGATGTGAATAAAATTGAGGCAGT 59.111 34.615 0.00 0.00 0.00 4.40
2940 4216 4.263435 ACAACCGTAACTTCTGGTTTTGA 58.737 39.130 0.00 0.00 43.23 2.69
2966 4242 1.134367 CAGTCGTCATCTTTAGCCCGA 59.866 52.381 0.00 0.00 0.00 5.14
3011 4287 1.728426 GTTCGACACGACGTCCCAG 60.728 63.158 10.58 2.35 42.07 4.45
3050 4326 2.596046 TGTTGGATTTGCCGGCGT 60.596 55.556 23.90 10.63 40.66 5.68
3065 4341 1.745087 CTGTTGTTCTTGTGCCACTGT 59.255 47.619 0.00 0.00 0.00 3.55
3149 4425 1.407258 GCAAGCCTCGTCAGATAGTCT 59.593 52.381 0.00 0.00 0.00 3.24
3170 4446 3.181429 TGTCCTGGCTTCCTTTCTTCAAT 60.181 43.478 0.00 0.00 0.00 2.57
3171 4447 2.174639 TGTCCTGGCTTCCTTTCTTCAA 59.825 45.455 0.00 0.00 0.00 2.69
3383 4659 4.715534 TGAACAGAAAACAGGGGATACA 57.284 40.909 0.00 0.00 39.74 2.29
3384 4660 6.263168 CCATATGAACAGAAAACAGGGGATAC 59.737 42.308 3.65 0.00 0.00 2.24
3411 4687 8.539544 TGAACTGACTGACTGGATAATATTTCA 58.460 33.333 0.00 0.00 0.00 2.69
3420 4696 1.277557 GGCTGAACTGACTGACTGGAT 59.722 52.381 0.00 0.00 0.00 3.41
3428 4704 0.036022 GGCTCAAGGCTGAACTGACT 59.964 55.000 0.00 0.00 41.46 3.41
3443 4720 1.589716 GACACAACATGCCAGGGCTC 61.590 60.000 12.19 0.00 42.51 4.70
3512 4791 9.774742 GAAACATGTTAAATCTTACTGTCATCC 57.225 33.333 12.39 0.00 0.00 3.51
3550 4829 5.351740 GGTTGGAGTAGAAGCTGTAATTCAC 59.648 44.000 0.00 0.00 0.00 3.18
3570 4849 3.760684 CCTCTTCTCCATTCTTTGGGTTG 59.239 47.826 0.00 0.00 46.45 3.77
3606 4885 0.809241 GCGTCTCTTCTCAGGGCATG 60.809 60.000 0.00 0.00 0.00 4.06
3689 4968 9.512588 AGTAGAAGATAGGATGCCATTTTAATG 57.487 33.333 0.00 0.00 36.17 1.90
3695 4974 6.784969 ACAGTAGTAGAAGATAGGATGCCATT 59.215 38.462 0.00 0.00 0.00 3.16
3726 5005 4.760715 TCGCTCTAGGGTGTGTATATTCTC 59.239 45.833 2.44 0.00 0.00 2.87
3735 5014 2.351244 TGCCTCGCTCTAGGGTGTG 61.351 63.158 2.44 0.06 37.11 3.82
3767 5046 1.518792 GAGTAGTTCGCCGGCCTTC 60.519 63.158 23.46 10.33 0.00 3.46
3840 5119 3.062466 CGGTGGAGAGCGACCTGA 61.062 66.667 0.00 0.00 46.19 3.86
3975 5258 3.635591 AGACCCATGGATTCCATTGTTC 58.364 45.455 15.22 10.46 42.23 3.18
4011 5294 5.013079 TGGATGATGATTCCAGGTATGTACC 59.987 44.000 0.81 0.81 46.82 3.34
4012 5295 6.114187 TGGATGATGATTCCAGGTATGTAC 57.886 41.667 0.00 0.00 38.35 2.90
4037 5320 2.039613 CCTCTCCAGCTTTTCAGTCCTT 59.960 50.000 0.00 0.00 0.00 3.36
4039 5322 1.948144 GCCTCTCCAGCTTTTCAGTCC 60.948 57.143 0.00 0.00 0.00 3.85
4078 5361 4.223700 TCACATCAAGCATGAGAGTAACCT 59.776 41.667 0.00 0.00 39.39 3.50
4083 5366 4.001652 CAGTTCACATCAAGCATGAGAGT 58.998 43.478 0.00 0.00 39.39 3.24
4117 5401 5.621228 CGAAGTGTTAACTTGAGCATTGTTC 59.379 40.000 7.22 0.00 46.84 3.18
4123 5407 4.185394 TGTTCGAAGTGTTAACTTGAGCA 58.815 39.130 7.22 2.01 46.84 4.26
4125 5409 4.270084 TGCTGTTCGAAGTGTTAACTTGAG 59.730 41.667 7.22 0.00 46.84 3.02
4127 5411 4.530094 TGCTGTTCGAAGTGTTAACTTG 57.470 40.909 7.22 0.00 46.84 3.16
4130 5414 4.654015 TGTTTGCTGTTCGAAGTGTTAAC 58.346 39.130 0.00 0.00 0.00 2.01
4132 5416 3.936453 ACTGTTTGCTGTTCGAAGTGTTA 59.064 39.130 0.00 0.00 0.00 2.41
4140 5424 5.108780 CGTAATCAAAACTGTTTGCTGTTCG 60.109 40.000 6.53 5.38 43.30 3.95
4141 5425 5.331532 GCGTAATCAAAACTGTTTGCTGTTC 60.332 40.000 6.53 0.00 43.30 3.18
4142 5426 4.502645 GCGTAATCAAAACTGTTTGCTGTT 59.497 37.500 6.53 3.22 43.30 3.16
4143 5427 4.041723 GCGTAATCAAAACTGTTTGCTGT 58.958 39.130 6.53 0.00 43.30 4.40
4144 5428 3.425193 GGCGTAATCAAAACTGTTTGCTG 59.575 43.478 6.53 2.67 43.30 4.41
4145 5429 3.638484 GGCGTAATCAAAACTGTTTGCT 58.362 40.909 6.53 0.00 43.30 3.91
4146 5430 2.403698 CGGCGTAATCAAAACTGTTTGC 59.596 45.455 6.53 3.93 43.30 3.68
4164 5462 1.953559 TGTTGATAGGCTGAATCGGC 58.046 50.000 5.30 5.30 34.56 5.54
4211 5509 5.778241 TGGTATGTACTGGGACGATATGAAT 59.222 40.000 0.00 0.00 0.00 2.57
4212 5510 5.141910 TGGTATGTACTGGGACGATATGAA 58.858 41.667 0.00 0.00 0.00 2.57
4217 5515 3.371965 AGTTGGTATGTACTGGGACGAT 58.628 45.455 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.