Multiple sequence alignment - TraesCS7A01G517100

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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 TraesCS7A01G517100 chr7A 100.000 3461 0 0 1 3461 701527382 701530842 0.000000e+00 6392
1 TraesCS7A01G517100 chr7A 90.361 83 8 0 1227 1309 175689115 175689197 3.650000e-20 110
2 TraesCS7A01G517100 chr7B 89.206 2946 183 49 592 3460 700826547 700829434 0.000000e+00 3554
3 TraesCS7A01G517100 chr7B 90.000 80 8 0 1230 1309 138469231 138469310 1.700000e-18 104
4 TraesCS7A01G517100 chr7D 92.523 2461 133 26 723 3154 611590652 611593090 0.000000e+00 3478
5 TraesCS7A01G517100 chr7D 92.884 267 14 3 3194 3460 611593163 611593424 1.950000e-102 383
6 TraesCS7A01G517100 chr7D 84.986 353 32 16 214 547 611590075 611590425 4.280000e-89 339
7 TraesCS7A01G517100 chr7D 90.909 187 14 3 340 524 611588757 611588942 7.420000e-62 248
8 TraesCS7A01G517100 chr7D 94.574 129 6 1 89 217 611589068 611589195 7.580000e-47 198
9 TraesCS7A01G517100 chr7D 91.566 83 7 0 1227 1309 173707536 173707618 7.850000e-22 115


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 TraesCS7A01G517100 chr7A 701527382 701530842 3460 False 6392.0 6392 100.0000 1 3461 1 chr7A.!!$F2 3460
1 TraesCS7A01G517100 chr7B 700826547 700829434 2887 False 3554.0 3554 89.2060 592 3460 1 chr7B.!!$F2 2868
2 TraesCS7A01G517100 chr7D 611588757 611593424 4667 False 929.2 3478 91.1752 89 3460 5 chr7D.!!$F2 3371

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
55 56 0.037605 GATGGGGTGTTCTCGACGTT 60.038 55.0 0.00 0.00 0.00 3.99 F
217 441 0.250814 AGACCGACCAAGTCTCGTCT 60.251 55.0 7.95 7.95 40.61 4.18 F
448 1565 0.251354 TGCCTCTACGTCTACGGTCT 59.749 55.0 7.50 0.00 44.95 3.85 F
1954 3190 0.447011 GCTCTGCGTAGTCGTGTACT 59.553 55.0 0.00 0.00 42.62 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 3270 0.321564 CCGTGCTGAACTTGATCCCA 60.322 55.000 0.0 0.0 0.00 4.37 R
2124 3360 2.203640 TCCACCGTCTGCCTCAGT 60.204 61.111 0.0 0.0 32.61 3.41 R
2323 3559 0.035630 CCTTCCTTGTCCAGCCTCAG 60.036 60.000 0.0 0.0 0.00 3.35 R
3188 4465 0.107703 CGGGTTGATTAGCTGCCTCA 60.108 55.000 0.0 0.0 0.00 3.86 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
24 25 2.354403 CGGATGAAAGGTTAGGTTCGGT 60.354 50.000 0.00 0.00 0.00 4.69
25 26 3.682696 GGATGAAAGGTTAGGTTCGGTT 58.317 45.455 0.00 0.00 0.00 4.44
26 27 4.077108 GGATGAAAGGTTAGGTTCGGTTT 58.923 43.478 0.00 0.00 0.00 3.27
27 28 4.155462 GGATGAAAGGTTAGGTTCGGTTTC 59.845 45.833 0.00 0.00 0.00 2.78
28 29 4.153673 TGAAAGGTTAGGTTCGGTTTCA 57.846 40.909 0.00 0.00 32.84 2.69
31 32 4.906065 AAGGTTAGGTTCGGTTTCAAAC 57.094 40.909 0.00 0.00 0.00 2.93
32 33 4.160642 AGGTTAGGTTCGGTTTCAAACT 57.839 40.909 0.00 0.00 0.00 2.66
35 36 1.687563 AGGTTCGGTTTCAAACTGGG 58.312 50.000 9.30 0.00 38.33 4.45
36 37 0.671796 GGTTCGGTTTCAAACTGGGG 59.328 55.000 9.30 0.00 38.33 4.96
37 38 1.682740 GTTCGGTTTCAAACTGGGGA 58.317 50.000 9.30 0.00 38.33 4.81
38 39 2.235891 GTTCGGTTTCAAACTGGGGAT 58.764 47.619 9.30 0.00 38.33 3.85
41 42 1.266178 GGTTTCAAACTGGGGATGGG 58.734 55.000 0.00 0.00 0.00 4.00
43 44 0.863956 TTTCAAACTGGGGATGGGGT 59.136 50.000 0.00 0.00 0.00 4.95
45 46 1.071314 TCAAACTGGGGATGGGGTGT 61.071 55.000 0.00 0.00 0.00 4.16
47 48 0.114364 AAACTGGGGATGGGGTGTTC 59.886 55.000 0.00 0.00 0.00 3.18
49 50 1.208165 ACTGGGGATGGGGTGTTCTC 61.208 60.000 0.00 0.00 0.00 2.87
50 51 2.257409 CTGGGGATGGGGTGTTCTCG 62.257 65.000 0.00 0.00 0.00 4.04
51 52 1.993391 GGGGATGGGGTGTTCTCGA 60.993 63.158 0.00 0.00 0.00 4.04
54 55 1.590147 GATGGGGTGTTCTCGACGT 59.410 57.895 0.00 0.00 0.00 4.34
55 56 0.037605 GATGGGGTGTTCTCGACGTT 60.038 55.000 0.00 0.00 0.00 3.99
56 57 0.320421 ATGGGGTGTTCTCGACGTTG 60.320 55.000 0.00 0.00 0.00 4.10
57 58 1.068585 GGGGTGTTCTCGACGTTGT 59.931 57.895 1.96 0.00 0.00 3.32
58 59 0.531311 GGGGTGTTCTCGACGTTGTT 60.531 55.000 1.96 0.00 0.00 2.83
60 61 1.537562 GGGTGTTCTCGACGTTGTTCT 60.538 52.381 1.96 0.00 0.00 3.01
61 62 2.199236 GGTGTTCTCGACGTTGTTCTT 58.801 47.619 1.96 0.00 0.00 2.52
62 63 2.218075 GGTGTTCTCGACGTTGTTCTTC 59.782 50.000 1.96 0.00 0.00 2.87
64 65 3.550678 GTGTTCTCGACGTTGTTCTTCTT 59.449 43.478 1.96 0.00 0.00 2.52
65 66 3.550275 TGTTCTCGACGTTGTTCTTCTTG 59.450 43.478 1.96 0.00 0.00 3.02
66 67 2.739292 TCTCGACGTTGTTCTTCTTGG 58.261 47.619 1.96 0.00 0.00 3.61
67 68 1.792949 CTCGACGTTGTTCTTCTTGGG 59.207 52.381 1.96 0.00 0.00 4.12
68 69 0.865769 CGACGTTGTTCTTCTTGGGG 59.134 55.000 0.00 0.00 0.00 4.96
71 72 1.770061 ACGTTGTTCTTCTTGGGGGTA 59.230 47.619 0.00 0.00 0.00 3.69
72 73 2.374170 ACGTTGTTCTTCTTGGGGGTAT 59.626 45.455 0.00 0.00 0.00 2.73
73 74 3.181437 ACGTTGTTCTTCTTGGGGGTATT 60.181 43.478 0.00 0.00 0.00 1.89
74 75 3.190535 CGTTGTTCTTCTTGGGGGTATTG 59.809 47.826 0.00 0.00 0.00 1.90
76 77 3.761897 TGTTCTTCTTGGGGGTATTGTG 58.238 45.455 0.00 0.00 0.00 3.33
77 78 3.139397 TGTTCTTCTTGGGGGTATTGTGT 59.861 43.478 0.00 0.00 0.00 3.72
78 79 4.351407 TGTTCTTCTTGGGGGTATTGTGTA 59.649 41.667 0.00 0.00 0.00 2.90
79 80 5.014755 TGTTCTTCTTGGGGGTATTGTGTAT 59.985 40.000 0.00 0.00 0.00 2.29
80 81 5.110814 TCTTCTTGGGGGTATTGTGTATG 57.889 43.478 0.00 0.00 0.00 2.39
81 82 4.785914 TCTTCTTGGGGGTATTGTGTATGA 59.214 41.667 0.00 0.00 0.00 2.15
83 84 5.110814 TCTTGGGGGTATTGTGTATGAAG 57.889 43.478 0.00 0.00 0.00 3.02
84 85 4.785914 TCTTGGGGGTATTGTGTATGAAGA 59.214 41.667 0.00 0.00 0.00 2.87
85 86 4.497291 TGGGGGTATTGTGTATGAAGAC 57.503 45.455 0.00 0.00 0.00 3.01
86 87 3.847184 TGGGGGTATTGTGTATGAAGACA 59.153 43.478 0.00 0.00 0.00 3.41
87 88 4.476846 TGGGGGTATTGTGTATGAAGACAT 59.523 41.667 0.00 0.00 40.16 3.06
88 89 4.821805 GGGGGTATTGTGTATGAAGACATG 59.178 45.833 0.00 0.00 37.87 3.21
89 90 4.821805 GGGGTATTGTGTATGAAGACATGG 59.178 45.833 0.00 0.00 37.87 3.66
90 91 5.397447 GGGGTATTGTGTATGAAGACATGGA 60.397 44.000 0.00 0.00 37.87 3.41
91 92 5.760253 GGGTATTGTGTATGAAGACATGGAG 59.240 44.000 0.00 0.00 37.87 3.86
92 93 6.349300 GGTATTGTGTATGAAGACATGGAGT 58.651 40.000 0.00 0.00 37.87 3.85
100 324 1.902508 GAAGACATGGAGTGGAGGTCA 59.097 52.381 0.00 0.00 0.00 4.02
108 332 1.072331 GGAGTGGAGGTCATGTGTTGT 59.928 52.381 0.00 0.00 0.00 3.32
128 352 2.415512 GTGATCCTTTGGTGCTCGTTAC 59.584 50.000 0.00 0.00 0.00 2.50
130 354 2.163818 TCCTTTGGTGCTCGTTACTG 57.836 50.000 0.00 0.00 0.00 2.74
158 382 1.153549 GAGCTTCAGGGGTGCTACG 60.154 63.158 0.00 0.00 37.16 3.51
167 391 1.206371 AGGGGTGCTACGTATGTTGTC 59.794 52.381 0.00 0.00 0.00 3.18
168 392 1.274596 GGGTGCTACGTATGTTGTCG 58.725 55.000 0.00 0.00 0.00 4.35
170 394 2.331194 GGTGCTACGTATGTTGTCGTT 58.669 47.619 0.00 0.00 40.70 3.85
172 396 2.091588 GTGCTACGTATGTTGTCGTTGG 59.908 50.000 0.00 0.00 40.70 3.77
173 397 2.288334 TGCTACGTATGTTGTCGTTGGT 60.288 45.455 0.00 0.00 40.70 3.67
174 398 2.091588 GCTACGTATGTTGTCGTTGGTG 59.908 50.000 0.00 0.00 40.70 4.17
175 399 0.863144 ACGTATGTTGTCGTTGGTGC 59.137 50.000 0.00 0.00 36.93 5.01
176 400 0.862490 CGTATGTTGTCGTTGGTGCA 59.138 50.000 0.00 0.00 0.00 4.57
177 401 1.261885 CGTATGTTGTCGTTGGTGCAA 59.738 47.619 0.00 0.00 0.00 4.08
217 441 0.250814 AGACCGACCAAGTCTCGTCT 60.251 55.000 7.95 7.95 40.61 4.18
218 442 0.597072 GACCGACCAAGTCTCGTCTT 59.403 55.000 0.00 0.00 31.41 3.01
219 443 0.314302 ACCGACCAAGTCTCGTCTTG 59.686 55.000 9.47 9.47 42.86 3.02
221 445 1.409412 CGACCAAGTCTCGTCTTGTG 58.591 55.000 13.24 9.14 42.01 3.33
222 446 1.784525 GACCAAGTCTCGTCTTGTGG 58.215 55.000 13.24 6.41 42.01 4.17
223 447 1.340248 GACCAAGTCTCGTCTTGTGGA 59.660 52.381 13.24 0.00 42.01 4.02
224 448 1.341531 ACCAAGTCTCGTCTTGTGGAG 59.658 52.381 13.24 0.00 42.01 3.86
225 449 1.341531 CCAAGTCTCGTCTTGTGGAGT 59.658 52.381 13.24 0.00 42.01 3.85
226 450 2.224066 CCAAGTCTCGTCTTGTGGAGTT 60.224 50.000 13.24 0.00 42.01 3.01
227 451 3.458189 CAAGTCTCGTCTTGTGGAGTTT 58.542 45.455 8.65 0.00 39.66 2.66
229 453 4.240175 AGTCTCGTCTTGTGGAGTTTAC 57.760 45.455 0.00 0.00 0.00 2.01
243 1350 6.262273 TGTGGAGTTTACCAAAAAGATCAGAC 59.738 38.462 0.00 0.00 41.87 3.51
267 1375 6.206048 ACCGTGAAATAAATTTCGAGGAGTTT 59.794 34.615 23.83 8.72 46.92 2.66
268 1376 6.523201 CCGTGAAATAAATTTCGAGGAGTTTG 59.477 38.462 17.20 0.92 46.92 2.93
271 1379 9.244799 GTGAAATAAATTTCGAGGAGTTTGTTT 57.755 29.630 10.09 1.34 46.92 2.83
278 1386 3.799366 TCGAGGAGTTTGTTTTGTGCTA 58.201 40.909 0.00 0.00 0.00 3.49
285 1393 6.811665 AGGAGTTTGTTTTGTGCTAAAGTTTC 59.188 34.615 0.00 0.00 0.00 2.78
296 1404 3.882888 TGCTAAAGTTTCCTGACAAGGTG 59.117 43.478 0.00 0.00 44.82 4.00
297 1405 3.253432 GCTAAAGTTTCCTGACAAGGTGG 59.747 47.826 0.00 0.00 44.82 4.61
304 1412 4.993705 TTCCTGACAAGGTGGAAATAGT 57.006 40.909 0.00 0.00 44.82 2.12
307 1415 4.020218 TCCTGACAAGGTGGAAATAGTGAG 60.020 45.833 0.00 0.00 44.82 3.51
309 1417 3.907474 TGACAAGGTGGAAATAGTGAGGA 59.093 43.478 0.00 0.00 0.00 3.71
316 1424 2.239654 TGGAAATAGTGAGGAAGGCCAG 59.760 50.000 5.01 0.00 36.29 4.85
318 1426 1.216990 AATAGTGAGGAAGGCCAGGG 58.783 55.000 5.01 0.00 36.29 4.45
325 1433 2.684499 GGAAGGCCAGGGAAGGAGG 61.684 68.421 5.01 0.00 0.00 4.30
381 1490 3.125607 CGGACAATCGGATCGGGA 58.874 61.111 0.00 0.00 0.00 5.14
416 1525 3.423154 CGCTTCCCACGTGCCTTC 61.423 66.667 10.91 0.00 0.00 3.46
419 1528 4.323477 TTCCCACGTGCCTTCCCG 62.323 66.667 10.91 0.00 0.00 5.14
445 1562 1.948145 AGAATGCCTCTACGTCTACGG 59.052 52.381 7.50 0.00 44.95 4.02
446 1563 1.674962 GAATGCCTCTACGTCTACGGT 59.325 52.381 7.50 0.00 44.95 4.83
447 1564 1.307097 ATGCCTCTACGTCTACGGTC 58.693 55.000 7.50 0.00 44.95 4.79
448 1565 0.251354 TGCCTCTACGTCTACGGTCT 59.749 55.000 7.50 0.00 44.95 3.85
484 1608 2.884087 CTACAGTAGCGGCACACGGG 62.884 65.000 1.45 0.81 44.51 5.28
511 1635 3.252284 CCCACCTGCCAGTGAGGT 61.252 66.667 4.85 0.00 45.23 3.85
512 1636 2.348998 CCACCTGCCAGTGAGGTC 59.651 66.667 0.49 0.00 42.25 3.85
513 1637 2.047844 CACCTGCCAGTGAGGTCG 60.048 66.667 0.49 0.00 42.25 4.79
514 1638 2.203640 ACCTGCCAGTGAGGTCGA 60.204 61.111 0.00 0.00 39.89 4.20
515 1639 1.837051 ACCTGCCAGTGAGGTCGAA 60.837 57.895 0.00 0.00 39.89 3.71
516 1640 1.194781 ACCTGCCAGTGAGGTCGAAT 61.195 55.000 0.00 0.00 39.89 3.34
517 1641 0.460987 CCTGCCAGTGAGGTCGAATC 60.461 60.000 0.00 0.00 40.61 2.52
519 1643 1.519455 GCCAGTGAGGTCGAATCCG 60.519 63.158 0.00 0.00 40.61 4.18
550 1674 2.867472 CGCCCAACTTTACGCCTG 59.133 61.111 0.00 0.00 0.00 4.85
552 1676 2.989881 GCCCAACTTTACGCCTGGC 61.990 63.158 9.11 9.11 0.00 4.85
555 1679 0.671251 CCAACTTTACGCCTGGCAAA 59.329 50.000 20.29 11.49 0.00 3.68
556 1680 1.601914 CCAACTTTACGCCTGGCAAAC 60.602 52.381 20.29 0.00 0.00 2.93
557 1681 1.336755 CAACTTTACGCCTGGCAAACT 59.663 47.619 20.29 0.00 0.00 2.66
558 1682 1.235724 ACTTTACGCCTGGCAAACTC 58.764 50.000 20.29 0.00 0.00 3.01
559 1683 1.202770 ACTTTACGCCTGGCAAACTCT 60.203 47.619 20.29 0.00 0.00 3.24
625 1809 2.175499 TCCCTCCAATCCATCCATCAAC 59.825 50.000 0.00 0.00 0.00 3.18
654 1842 2.184830 CGATCCGTCTACCTCGCCA 61.185 63.158 0.00 0.00 0.00 5.69
670 1858 2.113433 CCAGGATCCTCGTCGACGT 61.113 63.158 34.40 17.98 40.80 4.34
686 1885 2.833582 GTCGATCCCTGCTCCGGA 60.834 66.667 2.93 2.93 0.00 5.14
687 1886 2.043349 TCGATCCCTGCTCCGGAA 60.043 61.111 5.23 0.00 31.75 4.30
706 1905 3.991536 GAGCACGCGGGTCTTCTCC 62.992 68.421 11.45 0.00 40.87 3.71
715 1914 4.083862 GTCTTCTCCGCCCCGCTT 62.084 66.667 0.00 0.00 0.00 4.68
716 1915 3.771160 TCTTCTCCGCCCCGCTTC 61.771 66.667 0.00 0.00 0.00 3.86
717 1916 3.775654 CTTCTCCGCCCCGCTTCT 61.776 66.667 0.00 0.00 0.00 2.85
718 1917 3.316573 CTTCTCCGCCCCGCTTCTT 62.317 63.158 0.00 0.00 0.00 2.52
719 1918 3.310860 TTCTCCGCCCCGCTTCTTC 62.311 63.158 0.00 0.00 0.00 2.87
720 1919 4.840005 CTCCGCCCCGCTTCTTCC 62.840 72.222 0.00 0.00 0.00 3.46
729 1928 4.803908 GCTTCTTCCCCCGCCCAG 62.804 72.222 0.00 0.00 0.00 4.45
742 1941 3.204827 CCCAGCCAAATCTCGCCG 61.205 66.667 0.00 0.00 0.00 6.46
762 1971 1.095600 GGAAGAACCGAGATTTGCCC 58.904 55.000 0.00 0.00 0.00 5.36
846 2055 3.547513 CGGGGGTCGGGATCTTCC 61.548 72.222 0.00 0.00 35.23 3.46
847 2056 2.040779 GGGGGTCGGGATCTTCCT 60.041 66.667 0.00 0.00 36.57 3.36
848 2057 1.693103 GGGGGTCGGGATCTTCCTT 60.693 63.158 0.00 0.00 36.57 3.36
1020 2241 3.600388 CATGGTGAACTCCAACTACTCC 58.400 50.000 0.00 0.00 41.09 3.85
1026 2247 0.679002 ACTCCAACTACTCCGCGCTA 60.679 55.000 5.56 0.00 0.00 4.26
1041 2262 2.490217 CTACCGCTGACCTCCACG 59.510 66.667 0.00 0.00 0.00 4.94
1176 2412 4.175489 GGCGAGCACGACGAGCTA 62.175 66.667 19.76 0.00 43.58 3.32
1347 2583 1.146930 CATCCTCGTCATGGGGGTG 59.853 63.158 0.00 0.00 0.00 4.61
1536 2772 2.183555 GACGTCATGTCCGGGTCC 59.816 66.667 11.55 0.00 42.04 4.46
1575 2811 4.803426 GACCAGCTCGTCGGCCAG 62.803 72.222 2.24 0.00 0.00 4.85
1617 2853 2.787994 CTGCTCATCCTGTTTGTCCTT 58.212 47.619 0.00 0.00 0.00 3.36
1656 2892 2.161486 GTGCGCGCTCGAGAAGATT 61.161 57.895 33.29 0.00 38.10 2.40
1743 2979 3.768185 GATCGCGGCGGTGAAGCTA 62.768 63.158 23.46 0.00 36.05 3.32
1746 2982 2.434359 GCGGCGGTGAAGCTAGTT 60.434 61.111 9.78 0.00 37.29 2.24
1800 3036 2.803155 ATTTCAGCTCGAAGGCGGCA 62.803 55.000 13.08 0.00 36.56 5.69
1803 3039 2.045926 AGCTCGAAGGCGGCAATT 60.046 55.556 13.08 0.00 36.56 2.32
1806 3042 1.717937 CTCGAAGGCGGCAATTCTG 59.282 57.895 13.08 4.35 38.28 3.02
1812 3048 2.409870 GGCGGCAATTCTGGACCTG 61.410 63.158 3.07 0.00 0.00 4.00
1815 3051 1.651240 CGGCAATTCTGGACCTGCTG 61.651 60.000 2.99 0.36 35.13 4.41
1860 3096 2.620115 CGCCTACATCTGCCATTTCAAT 59.380 45.455 0.00 0.00 0.00 2.57
1915 3151 4.159693 AGACGCCTCAGAACATGTACAATA 59.840 41.667 0.00 0.00 0.00 1.90
1944 3180 2.986979 TCCACCGTGCTCTGCGTA 60.987 61.111 0.00 0.00 0.00 4.42
1954 3190 0.447011 GCTCTGCGTAGTCGTGTACT 59.553 55.000 0.00 0.00 42.62 2.73
1956 3192 1.062294 CTCTGCGTAGTCGTGTACTCC 59.938 57.143 0.00 0.00 39.80 3.85
1971 3207 2.764128 TCCCTGACCGCCATCTCC 60.764 66.667 0.00 0.00 0.00 3.71
2034 3270 1.489230 ACCAACTTCGACAAGGACCTT 59.511 47.619 0.00 0.00 33.37 3.50
2124 3360 2.214216 CCCGGTGGTCCACTTCTCA 61.214 63.158 21.40 0.00 34.40 3.27
2157 3393 2.637383 GGACTCGCTGGTCTTCGGT 61.637 63.158 6.03 0.00 36.55 4.69
2232 3468 1.519751 CCCTCATCTACCTCGGCTCG 61.520 65.000 0.00 0.00 0.00 5.03
2310 3546 1.404047 GCATTGGGTTTCATGTTCCCG 60.404 52.381 14.28 5.46 43.75 5.14
2316 3552 1.001393 TTTCATGTTCCCGGCCCTC 60.001 57.895 0.00 0.00 0.00 4.30
2319 3555 4.096003 ATGTTCCCGGCCCTCGTG 62.096 66.667 0.00 0.00 37.11 4.35
2340 3576 1.376466 GCTGAGGCTGGACAAGGAA 59.624 57.895 0.00 0.00 35.22 3.36
2421 3657 4.353437 GTCAGCGTCGTCGGGGTT 62.353 66.667 3.90 0.00 37.56 4.11
2514 3754 3.973973 AGGGCTTATTATACACAGGCTGA 59.026 43.478 23.66 0.00 32.51 4.26
2596 3843 6.615088 AGCAAAGCTCATACTACACATTTTG 58.385 36.000 0.00 0.00 30.62 2.44
2601 3848 7.133891 AGCTCATACTACACATTTTGTTCAC 57.866 36.000 0.00 0.00 39.91 3.18
2609 3856 3.317993 ACACATTTTGTTCACCTACAGGC 59.682 43.478 0.00 0.00 33.09 4.85
2610 3857 3.569701 CACATTTTGTTCACCTACAGGCT 59.430 43.478 0.00 0.00 39.32 4.58
2611 3858 4.759693 CACATTTTGTTCACCTACAGGCTA 59.240 41.667 0.00 0.00 39.32 3.93
2612 3859 5.240623 CACATTTTGTTCACCTACAGGCTAA 59.759 40.000 0.00 0.00 39.32 3.09
2613 3860 5.830991 ACATTTTGTTCACCTACAGGCTAAA 59.169 36.000 0.00 0.00 39.32 1.85
2614 3861 6.016276 ACATTTTGTTCACCTACAGGCTAAAG 60.016 38.462 0.00 0.00 39.32 1.85
2615 3862 4.967084 TTGTTCACCTACAGGCTAAAGA 57.033 40.909 0.00 0.00 39.32 2.52
2631 3878 3.733443 AAAGAGTTGTTTCATGGGTGC 57.267 42.857 0.00 0.00 0.00 5.01
2639 3887 0.040058 TTTCATGGGTGCTGGCTGAT 59.960 50.000 0.00 0.00 0.00 2.90
2768 4024 0.458543 TTCTGATCGAGGCAGCGAAC 60.459 55.000 11.97 5.04 44.22 3.95
2843 4099 5.125097 AGCTGCATTCAGAAAATCTACCTTG 59.875 40.000 1.02 0.00 42.95 3.61
2886 4142 7.496920 TCAGAAAACCTATCTCTGTGCATTATG 59.503 37.037 0.00 0.00 38.20 1.90
2902 4158 6.021232 GTGCATTATGTGATGAATGTTGTTCG 60.021 38.462 0.00 0.00 35.80 3.95
2953 4227 6.753180 TGACTCTGGATATTCTTGCAGTATC 58.247 40.000 0.00 0.00 36.54 2.24
2958 4232 8.668510 TCTGGATATTCTTGCAGTATCTTTTC 57.331 34.615 9.08 0.00 36.54 2.29
2977 4251 9.814899 ATCTTTTCATGGCTATCTATATTCTCG 57.185 33.333 0.00 0.00 0.00 4.04
2986 4260 6.529829 GGCTATCTATATTCTCGCTGAAACAG 59.470 42.308 0.00 0.00 38.29 3.16
2995 4269 4.744570 TCTCGCTGAAACAGTTATACAGG 58.255 43.478 13.37 6.97 33.43 4.00
3043 4317 9.045223 TCTGATACATATGTTTATGTGCTTCAC 57.955 33.333 14.77 0.00 46.22 3.18
3061 4336 7.698130 GTGCTTCACCTATTTACACATCATTTC 59.302 37.037 0.00 0.00 0.00 2.17
3108 4384 8.648557 AAGTTTTCTAATTTGAGAACCTTTGC 57.351 30.769 16.04 0.00 35.17 3.68
3149 4426 8.948145 TGTACTTTTTGCTACTTGTTCTTGTTA 58.052 29.630 0.00 0.00 0.00 2.41
3156 4433 9.502091 TTTGCTACTTGTTCTTGTTAGATATGT 57.498 29.630 0.00 0.00 0.00 2.29
3188 4465 8.753133 TGTCTATCATGTGTCTACTTTCTGATT 58.247 33.333 0.00 0.00 0.00 2.57
3209 4519 1.823899 GGCAGCTAATCAACCCGGG 60.824 63.158 22.25 22.25 0.00 5.73
3218 4528 1.913778 ATCAACCCGGGTTTTGTACC 58.086 50.000 36.59 0.00 46.99 3.34
3247 4557 8.671921 GGTTAATTGTCTGCCTATGATATGATG 58.328 37.037 0.00 0.00 0.00 3.07
3257 4567 5.110598 CCTATGATATGATGAGAGCTGCAC 58.889 45.833 1.02 0.00 0.00 4.57
3278 4591 7.272978 TGCACTCATAAATTCTACTCCTTACC 58.727 38.462 0.00 0.00 0.00 2.85
3294 4607 6.091718 TCCTTACCTTGTTAATTTTGTGGC 57.908 37.500 0.00 0.00 0.00 5.01
3304 4617 7.067496 TGTTAATTTTGTGGCCCTGAAAATA 57.933 32.000 13.81 2.52 30.81 1.40
3313 4626 5.133221 GTGGCCCTGAAAATACATCTATGT 58.867 41.667 0.00 0.63 44.48 2.29
3314 4627 5.239525 GTGGCCCTGAAAATACATCTATGTC 59.760 44.000 0.00 0.00 41.97 3.06
3336 4649 7.284820 TGTCCATGATATGATGAATGTTGAGT 58.715 34.615 3.45 0.00 0.00 3.41
3394 4707 3.152341 AGCTTGTCATTTCAACTCTGGG 58.848 45.455 0.00 0.00 0.00 4.45
3401 4714 7.252612 TGTCATTTCAACTCTGGGTATTCTA 57.747 36.000 0.00 0.00 0.00 2.10
3403 4716 7.987458 TGTCATTTCAACTCTGGGTATTCTATC 59.013 37.037 0.00 0.00 0.00 2.08
3404 4717 8.207545 GTCATTTCAACTCTGGGTATTCTATCT 58.792 37.037 0.00 0.00 0.00 1.98
3405 4718 8.772250 TCATTTCAACTCTGGGTATTCTATCTT 58.228 33.333 0.00 0.00 0.00 2.40
3406 4719 9.401058 CATTTCAACTCTGGGTATTCTATCTTT 57.599 33.333 0.00 0.00 0.00 2.52
3407 4720 9.620259 ATTTCAACTCTGGGTATTCTATCTTTC 57.380 33.333 0.00 0.00 0.00 2.62
3431 4747 7.867921 TCTTTTTAGAATAACAGGGATGGCTA 58.132 34.615 0.00 0.00 0.00 3.93
3460 4776 2.268298 CATTGCAAGAAAGATGCCTGC 58.732 47.619 4.94 0.00 43.16 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.617263 CGAACCTAACCTTTCATCCGAAG 59.383 47.826 0.00 0.00 31.28 3.79
1 2 3.592059 CGAACCTAACCTTTCATCCGAA 58.408 45.455 0.00 0.00 0.00 4.30
2 3 2.093869 CCGAACCTAACCTTTCATCCGA 60.094 50.000 0.00 0.00 0.00 4.55
3 4 2.277084 CCGAACCTAACCTTTCATCCG 58.723 52.381 0.00 0.00 0.00 4.18
5 6 4.758165 TGAAACCGAACCTAACCTTTCATC 59.242 41.667 0.00 0.00 0.00 2.92
6 7 4.721132 TGAAACCGAACCTAACCTTTCAT 58.279 39.130 0.00 0.00 0.00 2.57
7 8 4.153673 TGAAACCGAACCTAACCTTTCA 57.846 40.909 0.00 0.00 0.00 2.69
8 9 5.066893 AGTTTGAAACCGAACCTAACCTTTC 59.933 40.000 4.14 0.00 0.00 2.62
9 10 4.951715 AGTTTGAAACCGAACCTAACCTTT 59.048 37.500 4.14 0.00 0.00 3.11
10 11 4.337274 CAGTTTGAAACCGAACCTAACCTT 59.663 41.667 4.14 0.00 0.00 3.50
11 12 3.881089 CAGTTTGAAACCGAACCTAACCT 59.119 43.478 4.14 0.00 0.00 3.50
13 14 3.004002 CCCAGTTTGAAACCGAACCTAAC 59.996 47.826 4.14 0.00 0.00 2.34
14 15 3.215975 CCCAGTTTGAAACCGAACCTAA 58.784 45.455 4.14 0.00 0.00 2.69
15 16 2.487625 CCCCAGTTTGAAACCGAACCTA 60.488 50.000 4.14 0.00 0.00 3.08
16 17 1.687563 CCCAGTTTGAAACCGAACCT 58.312 50.000 4.14 0.00 0.00 3.50
17 18 0.671796 CCCCAGTTTGAAACCGAACC 59.328 55.000 4.14 0.00 0.00 3.62
19 20 2.235016 CATCCCCAGTTTGAAACCGAA 58.765 47.619 4.14 0.00 0.00 4.30
20 21 1.546773 CCATCCCCAGTTTGAAACCGA 60.547 52.381 4.14 0.00 0.00 4.69
21 22 0.887933 CCATCCCCAGTTTGAAACCG 59.112 55.000 4.14 0.00 0.00 4.44
24 25 0.863956 ACCCCATCCCCAGTTTGAAA 59.136 50.000 0.00 0.00 0.00 2.69
25 26 0.114168 CACCCCATCCCCAGTTTGAA 59.886 55.000 0.00 0.00 0.00 2.69
26 27 1.071314 ACACCCCATCCCCAGTTTGA 61.071 55.000 0.00 0.00 0.00 2.69
27 28 0.178935 AACACCCCATCCCCAGTTTG 60.179 55.000 0.00 0.00 0.00 2.93
28 29 0.114364 GAACACCCCATCCCCAGTTT 59.886 55.000 0.00 0.00 0.00 2.66
31 32 1.609783 GAGAACACCCCATCCCCAG 59.390 63.158 0.00 0.00 0.00 4.45
32 33 2.297895 CGAGAACACCCCATCCCCA 61.298 63.158 0.00 0.00 0.00 4.96
35 36 1.153628 CGTCGAGAACACCCCATCC 60.154 63.158 0.00 0.00 0.00 3.51
36 37 0.037605 AACGTCGAGAACACCCCATC 60.038 55.000 0.00 0.00 0.00 3.51
37 38 0.320421 CAACGTCGAGAACACCCCAT 60.320 55.000 0.00 0.00 0.00 4.00
38 39 1.068417 CAACGTCGAGAACACCCCA 59.932 57.895 0.00 0.00 0.00 4.96
41 42 1.849097 AGAACAACGTCGAGAACACC 58.151 50.000 0.00 0.00 0.00 4.16
43 44 3.431922 AGAAGAACAACGTCGAGAACA 57.568 42.857 0.00 0.00 32.54 3.18
45 46 3.120792 CCAAGAAGAACAACGTCGAGAA 58.879 45.455 0.00 0.00 32.54 2.87
47 48 1.792949 CCCAAGAAGAACAACGTCGAG 59.207 52.381 0.00 0.00 32.54 4.04
49 50 0.865769 CCCCAAGAAGAACAACGTCG 59.134 55.000 0.00 0.00 32.54 5.12
50 51 1.235724 CCCCCAAGAAGAACAACGTC 58.764 55.000 0.00 0.00 0.00 4.34
51 52 0.549469 ACCCCCAAGAAGAACAACGT 59.451 50.000 0.00 0.00 0.00 3.99
54 55 4.148838 CACAATACCCCCAAGAAGAACAA 58.851 43.478 0.00 0.00 0.00 2.83
55 56 3.139397 ACACAATACCCCCAAGAAGAACA 59.861 43.478 0.00 0.00 0.00 3.18
56 57 3.763057 ACACAATACCCCCAAGAAGAAC 58.237 45.455 0.00 0.00 0.00 3.01
57 58 5.251932 TCATACACAATACCCCCAAGAAGAA 59.748 40.000 0.00 0.00 0.00 2.52
58 59 4.785914 TCATACACAATACCCCCAAGAAGA 59.214 41.667 0.00 0.00 0.00 2.87
60 61 5.251932 TCTTCATACACAATACCCCCAAGAA 59.748 40.000 0.00 0.00 0.00 2.52
61 62 4.785914 TCTTCATACACAATACCCCCAAGA 59.214 41.667 0.00 0.00 0.00 3.02
62 63 4.881850 GTCTTCATACACAATACCCCCAAG 59.118 45.833 0.00 0.00 0.00 3.61
64 65 3.847184 TGTCTTCATACACAATACCCCCA 59.153 43.478 0.00 0.00 0.00 4.96
65 66 4.497291 TGTCTTCATACACAATACCCCC 57.503 45.455 0.00 0.00 0.00 5.40
66 67 4.821805 CCATGTCTTCATACACAATACCCC 59.178 45.833 0.00 0.00 32.47 4.95
67 68 5.680619 TCCATGTCTTCATACACAATACCC 58.319 41.667 0.00 0.00 32.47 3.69
68 69 6.258727 CACTCCATGTCTTCATACACAATACC 59.741 42.308 0.00 0.00 32.47 2.73
71 72 5.045651 TCCACTCCATGTCTTCATACACAAT 60.046 40.000 0.00 0.00 32.47 2.71
72 73 4.285775 TCCACTCCATGTCTTCATACACAA 59.714 41.667 0.00 0.00 32.47 3.33
73 74 3.837731 TCCACTCCATGTCTTCATACACA 59.162 43.478 0.00 0.00 32.47 3.72
74 75 4.437239 CTCCACTCCATGTCTTCATACAC 58.563 47.826 0.00 0.00 32.47 2.90
76 77 3.452627 ACCTCCACTCCATGTCTTCATAC 59.547 47.826 0.00 0.00 32.47 2.39
77 78 3.706594 GACCTCCACTCCATGTCTTCATA 59.293 47.826 0.00 0.00 32.47 2.15
78 79 2.503356 GACCTCCACTCCATGTCTTCAT 59.497 50.000 0.00 0.00 34.21 2.57
79 80 1.902508 GACCTCCACTCCATGTCTTCA 59.097 52.381 0.00 0.00 0.00 3.02
80 81 1.902508 TGACCTCCACTCCATGTCTTC 59.097 52.381 0.00 0.00 0.00 2.87
81 82 2.030027 TGACCTCCACTCCATGTCTT 57.970 50.000 0.00 0.00 0.00 3.01
83 84 1.556911 ACATGACCTCCACTCCATGTC 59.443 52.381 0.00 0.00 44.17 3.06
84 85 1.661463 ACATGACCTCCACTCCATGT 58.339 50.000 0.00 0.00 43.13 3.21
85 86 1.280133 ACACATGACCTCCACTCCATG 59.720 52.381 0.00 0.00 41.40 3.66
86 87 1.661463 ACACATGACCTCCACTCCAT 58.339 50.000 0.00 0.00 0.00 3.41
87 88 1.072173 CAACACATGACCTCCACTCCA 59.928 52.381 0.00 0.00 0.00 3.86
88 89 1.072331 ACAACACATGACCTCCACTCC 59.928 52.381 0.00 0.00 0.00 3.85
89 90 2.146342 CACAACACATGACCTCCACTC 58.854 52.381 0.00 0.00 0.00 3.51
90 91 1.768275 TCACAACACATGACCTCCACT 59.232 47.619 0.00 0.00 0.00 4.00
91 92 2.254546 TCACAACACATGACCTCCAC 57.745 50.000 0.00 0.00 0.00 4.02
92 93 2.290260 GGATCACAACACATGACCTCCA 60.290 50.000 0.00 0.00 0.00 3.86
100 324 2.297033 GCACCAAAGGATCACAACACAT 59.703 45.455 0.00 0.00 0.00 3.21
108 332 2.301870 AGTAACGAGCACCAAAGGATCA 59.698 45.455 0.00 0.00 0.00 2.92
130 354 0.322008 CCTGAAGCTCAACCTGGGAC 60.322 60.000 0.00 0.00 0.00 4.46
158 382 2.603652 GGTTGCACCAACGACAACATAC 60.604 50.000 7.33 0.00 44.36 2.39
172 396 1.210155 GGCATCGTCTTGGTTGCAC 59.790 57.895 0.00 0.00 36.82 4.57
173 397 0.537143 AAGGCATCGTCTTGGTTGCA 60.537 50.000 0.00 0.00 36.82 4.08
174 398 0.598065 AAAGGCATCGTCTTGGTTGC 59.402 50.000 0.00 0.00 0.00 4.17
175 399 2.154462 AGAAAGGCATCGTCTTGGTTG 58.846 47.619 0.00 0.00 0.00 3.77
176 400 2.427506 GAGAAAGGCATCGTCTTGGTT 58.572 47.619 0.00 0.00 0.00 3.67
177 401 1.673033 CGAGAAAGGCATCGTCTTGGT 60.673 52.381 0.00 0.00 34.30 3.67
217 441 6.831353 TCTGATCTTTTTGGTAAACTCCACAA 59.169 34.615 0.00 0.00 37.20 3.33
218 442 6.262273 GTCTGATCTTTTTGGTAAACTCCACA 59.738 38.462 0.00 0.00 37.20 4.17
219 443 6.294010 GGTCTGATCTTTTTGGTAAACTCCAC 60.294 42.308 0.00 0.00 37.20 4.02
221 445 5.106673 CGGTCTGATCTTTTTGGTAAACTCC 60.107 44.000 0.00 0.00 0.00 3.85
222 446 5.469084 ACGGTCTGATCTTTTTGGTAAACTC 59.531 40.000 0.00 0.00 0.00 3.01
223 447 5.238650 CACGGTCTGATCTTTTTGGTAAACT 59.761 40.000 0.00 0.00 0.00 2.66
224 448 5.237779 TCACGGTCTGATCTTTTTGGTAAAC 59.762 40.000 0.00 0.00 0.00 2.01
225 449 5.369833 TCACGGTCTGATCTTTTTGGTAAA 58.630 37.500 0.00 0.00 0.00 2.01
226 450 4.963373 TCACGGTCTGATCTTTTTGGTAA 58.037 39.130 0.00 0.00 0.00 2.85
227 451 4.610605 TCACGGTCTGATCTTTTTGGTA 57.389 40.909 0.00 0.00 0.00 3.25
229 453 4.829064 TTTCACGGTCTGATCTTTTTGG 57.171 40.909 0.00 0.00 0.00 3.28
243 1350 5.796350 ACTCCTCGAAATTTATTTCACGG 57.204 39.130 13.81 12.24 44.83 4.94
267 1375 5.184096 TGTCAGGAAACTTTAGCACAAAACA 59.816 36.000 0.00 0.00 40.21 2.83
268 1376 5.646606 TGTCAGGAAACTTTAGCACAAAAC 58.353 37.500 0.00 0.00 40.21 2.43
271 1379 4.338118 CCTTGTCAGGAAACTTTAGCACAA 59.662 41.667 0.00 0.00 44.19 3.33
278 1386 3.662759 TCCACCTTGTCAGGAAACTTT 57.337 42.857 0.00 0.00 44.19 2.66
296 1404 2.422093 CCTGGCCTTCCTCACTATTTCC 60.422 54.545 3.32 0.00 0.00 3.13
297 1405 2.422093 CCCTGGCCTTCCTCACTATTTC 60.422 54.545 3.32 0.00 0.00 2.17
304 1412 1.925455 CCTTCCCTGGCCTTCCTCA 60.925 63.158 3.32 0.00 0.00 3.86
307 1415 2.684499 CCTCCTTCCCTGGCCTTCC 61.684 68.421 3.32 0.00 0.00 3.46
309 1417 3.342477 GCCTCCTTCCCTGGCCTT 61.342 66.667 3.32 0.00 40.71 4.35
381 1490 3.842923 CCGGCCGAGCACATCTCT 61.843 66.667 30.73 0.00 39.70 3.10
414 1523 1.482593 GAGGCATTCTCTTCTCGGGAA 59.517 52.381 0.00 0.00 39.38 3.97
415 1524 1.115467 GAGGCATTCTCTTCTCGGGA 58.885 55.000 0.00 0.00 39.38 5.14
416 1525 3.677002 GAGGCATTCTCTTCTCGGG 57.323 57.895 0.00 0.00 39.38 5.14
428 1545 1.134159 AGACCGTAGACGTAGAGGCAT 60.134 52.381 0.85 0.00 37.74 4.40
445 1562 3.217743 CGCGGGTAGGAGGGAGAC 61.218 72.222 0.00 0.00 0.00 3.36
446 1563 3.736224 ACGCGGGTAGGAGGGAGA 61.736 66.667 12.47 0.00 0.00 3.71
447 1564 3.528370 CACGCGGGTAGGAGGGAG 61.528 72.222 12.47 0.00 0.00 4.30
484 1608 4.115199 CAGGTGGGGGCAGTAGGC 62.115 72.222 0.00 0.00 43.74 3.93
487 1611 4.992982 TGGCAGGTGGGGGCAGTA 62.993 66.667 0.00 0.00 35.74 2.74
492 1616 4.039092 CTCACTGGCAGGTGGGGG 62.039 72.222 20.34 1.15 37.75 5.40
511 1635 2.024868 CAACCACGTGCGGATTCGA 61.025 57.895 10.91 0.00 39.00 3.71
512 1636 2.474266 CAACCACGTGCGGATTCG 59.526 61.111 10.91 0.00 39.81 3.34
513 1637 1.964373 ACCAACCACGTGCGGATTC 60.964 57.895 19.89 0.00 0.00 2.52
514 1638 2.112297 ACCAACCACGTGCGGATT 59.888 55.556 19.89 5.54 0.00 3.01
515 1639 2.668212 CACCAACCACGTGCGGAT 60.668 61.111 19.89 0.00 0.00 4.18
547 1671 1.889170 GGAAGGAAAGAGTTTGCCAGG 59.111 52.381 0.00 0.00 0.00 4.45
548 1672 1.889170 GGGAAGGAAAGAGTTTGCCAG 59.111 52.381 0.00 0.00 33.11 4.85
550 1674 1.889170 CAGGGAAGGAAAGAGTTTGCC 59.111 52.381 0.00 0.00 33.05 4.52
552 1676 4.718961 TCTTCAGGGAAGGAAAGAGTTTG 58.281 43.478 6.17 0.00 39.82 2.93
555 1679 4.202514 CCTTTCTTCAGGGAAGGAAAGAGT 60.203 45.833 20.18 0.00 36.80 3.24
556 1680 4.331108 CCTTTCTTCAGGGAAGGAAAGAG 58.669 47.826 20.18 12.74 36.80 2.85
557 1681 4.373156 CCTTTCTTCAGGGAAGGAAAGA 57.627 45.455 20.18 0.00 36.80 2.52
581 1747 3.052642 AGAGATCTGAGCCCTCTTCTTCT 60.053 47.826 0.00 0.00 33.86 2.85
583 1749 3.403228 AGAGATCTGAGCCCTCTTCTT 57.597 47.619 0.00 0.00 33.86 2.52
586 1752 2.397597 GGAAGAGATCTGAGCCCTCTT 58.602 52.381 13.34 13.34 46.43 2.85
654 1842 2.172372 CGACGTCGACGAGGATCCT 61.172 63.158 41.52 16.13 43.02 3.24
670 1858 2.043349 TTCCGGAGCAGGGATCGA 60.043 61.111 3.34 0.00 32.58 3.59
686 1885 2.048127 GAAGACCCGCGTGCTCTT 60.048 61.111 4.92 7.63 0.00 2.85
687 1886 2.992114 AGAAGACCCGCGTGCTCT 60.992 61.111 4.92 0.00 0.00 4.09
720 1919 4.447342 AGATTTGGCTGGGCGGGG 62.447 66.667 0.00 0.00 0.00 5.73
721 1920 2.830370 GAGATTTGGCTGGGCGGG 60.830 66.667 0.00 0.00 0.00 6.13
728 1927 2.876368 CTTCCCGGCGAGATTTGGCT 62.876 60.000 9.30 0.00 0.00 4.75
729 1928 2.437716 TTCCCGGCGAGATTTGGC 60.438 61.111 9.30 0.00 0.00 4.52
742 1941 1.095600 GGCAAATCTCGGTTCTTCCC 58.904 55.000 0.00 0.00 0.00 3.97
792 2001 2.359975 CTCACGGGAAACAGGCCC 60.360 66.667 0.00 0.00 42.41 5.80
797 2006 0.036388 GAGATGCCTCACGGGAAACA 60.036 55.000 0.00 0.00 39.24 2.83
799 2008 1.602237 GGAGATGCCTCACGGGAAA 59.398 57.895 0.00 0.00 41.20 3.13
898 2107 5.565509 GAGATTAGGGGGAAAATGGAGATC 58.434 45.833 0.00 0.00 0.00 2.75
934 2155 0.179163 GCGGCAAAGAAATCCTTCCG 60.179 55.000 0.00 0.00 42.12 4.30
963 2184 3.661131 CGAGGCGGATCGACGGAT 61.661 66.667 0.00 0.00 45.56 4.18
1041 2262 2.894387 GACTGCAGCTCGATGGCC 60.894 66.667 15.27 0.00 0.00 5.36
1212 2448 3.760035 GAGACGCCCGAGCCTTCA 61.760 66.667 0.00 0.00 34.57 3.02
1317 2553 2.835431 AGGATGGAGACGAGGCCG 60.835 66.667 0.00 0.00 42.50 6.13
1536 2772 2.360350 ACGCCCATGTGCTTGAGG 60.360 61.111 0.00 0.00 0.00 3.86
1617 2853 3.948719 GGGGCGAGGAACACCACA 61.949 66.667 0.00 0.00 0.00 4.17
1656 2892 2.965783 GACAGGCTCAGCGAGTCA 59.034 61.111 13.55 0.00 36.65 3.41
1743 2979 2.359230 GCGAGCTTGCCCTCAACT 60.359 61.111 15.66 0.00 0.00 3.16
1779 3015 0.740868 CCGCCTTCGAGCTGAAATCA 60.741 55.000 0.00 0.00 35.79 2.57
1812 3048 0.546122 TGATGGGTATCACCACCAGC 59.454 55.000 0.00 0.00 44.72 4.85
1815 3051 2.487265 GGTCATGATGGGTATCACCACC 60.487 54.545 0.00 0.00 45.54 4.61
1860 3096 0.673333 CGTTGTAGATGGGCTGCACA 60.673 55.000 7.21 7.21 39.03 4.57
1915 3151 2.502492 CGGTGGAGATCCGGCTGAT 61.502 63.158 0.00 0.00 43.68 2.90
1944 3180 0.959372 CGGTCAGGGAGTACACGACT 60.959 60.000 0.00 0.00 42.90 4.18
1954 3190 2.764128 GGAGATGGCGGTCAGGGA 60.764 66.667 0.00 0.00 0.00 4.20
1956 3192 4.227134 CCGGAGATGGCGGTCAGG 62.227 72.222 0.00 0.00 0.00 3.86
1971 3207 2.890371 CCGAACAGGAGGTACCCG 59.110 66.667 8.74 2.64 45.00 5.28
2034 3270 0.321564 CCGTGCTGAACTTGATCCCA 60.322 55.000 0.00 0.00 0.00 4.37
2124 3360 2.203640 TCCACCGTCTGCCTCAGT 60.204 61.111 0.00 0.00 32.61 3.41
2232 3468 3.480470 CCAGATGTTGGGTATCATGGTC 58.520 50.000 0.00 0.00 43.75 4.02
2295 3531 2.348104 GGCCGGGAACATGAAACCC 61.348 63.158 2.18 8.08 40.17 4.11
2319 3555 4.704833 TTGTCCAGCCTCAGCGCC 62.705 66.667 2.29 0.00 46.67 6.53
2322 3558 0.676151 CTTCCTTGTCCAGCCTCAGC 60.676 60.000 0.00 0.00 40.32 4.26
2323 3559 0.035630 CCTTCCTTGTCCAGCCTCAG 60.036 60.000 0.00 0.00 0.00 3.35
2421 3657 0.598158 GGCTGTACACGTTTCCGACA 60.598 55.000 0.00 0.00 37.88 4.35
2514 3754 5.179452 AGTGTATTCTGGCAGTGGTAATT 57.821 39.130 15.27 0.00 0.00 1.40
2588 3835 3.569701 AGCCTGTAGGTGAACAAAATGTG 59.430 43.478 0.00 0.00 37.57 3.21
2596 3843 4.538746 ACTCTTTAGCCTGTAGGTGAAC 57.461 45.455 0.00 0.00 37.57 3.18
2601 3848 5.305585 TGAAACAACTCTTTAGCCTGTAGG 58.694 41.667 0.00 0.00 38.53 3.18
2609 3856 4.520492 AGCACCCATGAAACAACTCTTTAG 59.480 41.667 0.00 0.00 0.00 1.85
2610 3857 4.278170 CAGCACCCATGAAACAACTCTTTA 59.722 41.667 0.00 0.00 0.00 1.85
2611 3858 3.068590 CAGCACCCATGAAACAACTCTTT 59.931 43.478 0.00 0.00 0.00 2.52
2612 3859 2.624838 CAGCACCCATGAAACAACTCTT 59.375 45.455 0.00 0.00 0.00 2.85
2613 3860 2.233271 CAGCACCCATGAAACAACTCT 58.767 47.619 0.00 0.00 0.00 3.24
2614 3861 1.270550 CCAGCACCCATGAAACAACTC 59.729 52.381 0.00 0.00 0.00 3.01
2615 3862 1.331214 CCAGCACCCATGAAACAACT 58.669 50.000 0.00 0.00 0.00 3.16
2631 3878 2.424601 CCACCAACAACATATCAGCCAG 59.575 50.000 0.00 0.00 0.00 4.85
2639 3887 3.168035 AGAATGCCCACCAACAACATA 57.832 42.857 0.00 0.00 0.00 2.29
2722 3978 6.611613 AGACCCAGGATACACATGTATATG 57.388 41.667 0.25 7.02 40.99 1.78
2723 3979 7.479579 AGTAGACCCAGGATACACATGTATAT 58.520 38.462 0.00 0.00 40.99 0.86
2724 3980 6.860034 AGTAGACCCAGGATACACATGTATA 58.140 40.000 0.00 0.00 40.99 1.47
2843 4099 9.597999 GGTTTTCTGAATGCAAAATTCATTAAC 57.402 29.630 1.85 6.77 37.40 2.01
2886 4142 5.106555 ACATTCTCCGAACAACATTCATCAC 60.107 40.000 0.00 0.00 0.00 3.06
2926 4182 5.016051 TGCAAGAATATCCAGAGTCAGAC 57.984 43.478 0.00 0.00 0.00 3.51
2953 4227 7.763528 AGCGAGAATATAGATAGCCATGAAAAG 59.236 37.037 0.00 0.00 0.00 2.27
2958 4232 6.141560 TCAGCGAGAATATAGATAGCCATG 57.858 41.667 0.00 0.00 0.00 3.66
2977 4251 4.253685 TCTGCCTGTATAACTGTTTCAGC 58.746 43.478 0.00 3.82 34.37 4.26
2986 4260 7.550906 ACTCTTTCTCAAATCTGCCTGTATAAC 59.449 37.037 0.00 0.00 0.00 1.89
3043 4317 8.400947 CACTTGGAGAAATGATGTGTAAATAGG 58.599 37.037 0.00 0.00 0.00 2.57
3061 4336 5.693769 TTAATTCTAGTCCCCACTTGGAG 57.306 43.478 0.00 0.00 37.39 3.86
3108 4384 7.115378 GCAAAAAGTACATCAAAGAATCTGGTG 59.885 37.037 0.00 0.00 0.00 4.17
3188 4465 0.107703 CGGGTTGATTAGCTGCCTCA 60.108 55.000 0.00 0.00 0.00 3.86
3209 4519 6.368213 CAGACAATTAACCTCGGTACAAAAC 58.632 40.000 0.00 0.00 0.00 2.43
3218 4528 4.693283 TCATAGGCAGACAATTAACCTCG 58.307 43.478 0.00 0.00 31.79 4.63
3247 4557 6.279882 AGTAGAATTTATGAGTGCAGCTCTC 58.720 40.000 16.25 16.25 44.41 3.20
3257 4567 9.892130 AACAAGGTAAGGAGTAGAATTTATGAG 57.108 33.333 0.00 0.00 0.00 2.90
3278 4591 4.599047 TCAGGGCCACAAAATTAACAAG 57.401 40.909 6.18 0.00 0.00 3.16
3294 4607 7.226441 TCATGGACATAGATGTATTTTCAGGG 58.774 38.462 0.00 0.00 41.95 4.45
3304 4617 9.614792 CATTCATCATATCATGGACATAGATGT 57.385 33.333 0.00 0.00 45.16 3.06
3313 4626 7.994334 TGAACTCAACATTCATCATATCATGGA 59.006 33.333 0.00 0.00 31.11 3.41
3314 4627 8.161699 TGAACTCAACATTCATCATATCATGG 57.838 34.615 0.00 0.00 31.11 3.66
3403 4716 7.976175 GCCATCCCTGTTATTCTAAAAAGAAAG 59.024 37.037 0.00 0.00 0.00 2.62
3404 4717 7.673926 AGCCATCCCTGTTATTCTAAAAAGAAA 59.326 33.333 0.00 0.00 0.00 2.52
3405 4718 7.182060 AGCCATCCCTGTTATTCTAAAAAGAA 58.818 34.615 0.00 0.00 0.00 2.52
3406 4719 6.731467 AGCCATCCCTGTTATTCTAAAAAGA 58.269 36.000 0.00 0.00 0.00 2.52
3407 4720 7.013369 GGTAGCCATCCCTGTTATTCTAAAAAG 59.987 40.741 0.00 0.00 0.00 2.27
3431 4747 2.361610 CTTGCAATGGAGCCGGGT 60.362 61.111 5.45 5.45 0.00 5.28


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

AutoCloner maintained by Alex Coulton.