Multiple sequence alignment - TraesCS4B01G278100

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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 TraesCS4B01G278100 chr4B 100.000 4170 0 0 1 4170 560011716 560015885 0.000000e+00 7701
1 TraesCS4B01G278100 chr4D 88.693 2494 201 43 1737 4170 447639875 447642347 0.000000e+00 2968
2 TraesCS4B01G278100 chr4D 92.054 1397 65 18 283 1642 447638290 447639677 0.000000e+00 1923
3 TraesCS4B01G278100 chr4D 83.077 260 37 6 2 259 447637824 447638078 3.240000e-56 230
4 TraesCS4B01G278100 chr4A 91.441 1776 129 15 1735 3497 19621795 19620030 0.000000e+00 2416
5 TraesCS4B01G278100 chr4A 93.529 1329 55 7 354 1651 19623296 19621968 0.000000e+00 1949
6 TraesCS4B01G278100 chr4A 82.508 303 38 9 2 300 19624864 19624573 6.920000e-63 252
7 TraesCS4B01G278100 chr4A 84.706 170 23 3 3518 3685 19585107 19584939 2.580000e-37 167
8 TraesCS4B01G278100 chr1A 89.427 227 24 0 1093 1319 550314237 550314011 1.900000e-73 287
9 TraesCS4B01G278100 chr1B 87.449 247 28 3 1093 1338 627929088 627928844 8.830000e-72 281
10 TraesCS4B01G278100 chr5D 85.714 231 29 4 1090 1318 495626196 495626424 1.500000e-59 241
11 TraesCS4B01G278100 chr5B 84.127 252 32 8 1090 1336 612679823 612680071 1.940000e-58 237
12 TraesCS4B01G278100 chr5A 84.211 247 34 4 1091 1333 619689721 619689966 6.970000e-58 235
13 TraesCS4B01G278100 chr2B 81.166 223 40 2 1090 1311 65370658 65370879 1.190000e-40 178
14 TraesCS4B01G278100 chr3B 78.814 236 42 7 1082 1311 678018408 678018641 7.220000e-33 152
15 TraesCS4B01G278100 chr3B 97.674 43 1 0 3066 3108 12396968 12397010 1.610000e-09 75
16 TraesCS4B01G278100 chr7B 97.674 43 1 0 3066 3108 192794676 192794634 1.610000e-09 75


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 TraesCS4B01G278100 chr4B 560011716 560015885 4169 False 7701 7701 100.000000 1 4170 1 chr4B.!!$F1 4169
1 TraesCS4B01G278100 chr4D 447637824 447642347 4523 False 1707 2968 87.941333 2 4170 3 chr4D.!!$F1 4168
2 TraesCS4B01G278100 chr4A 19620030 19624864 4834 True 1539 2416 89.159333 2 3497 3 chr4A.!!$R2 3495

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
137 141 0.251877 TGGATGGGTACGAGGTGTCA 60.252 55.0 0.00 0.00 0.00 3.58 F
1669 2952 0.383949 TTCTTGAAAAGTGCACCCGC 59.616 50.0 14.63 1.17 46.34 6.13 F
1755 3038 0.389426 ATGCCAGTGAACGACGGTAC 60.389 55.0 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 2996 0.375106 GAACCGCTTACTGCTGATGC 59.625 55.0 0.00 0.0 40.11 3.91 R
2916 4357 0.178950 TGGCTCACTCTGACTGGTCT 60.179 55.0 2.38 0.0 0.00 3.85 R
3445 4893 0.321298 TAGGCAACAGGCTTCGGTTC 60.321 55.0 0.00 0.0 44.01 3.62 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
33 34 1.292223 GCCTCTAGTTGTGCCACGA 59.708 57.895 0.00 0.00 0.00 4.35
39 40 1.464608 CTAGTTGTGCCACGACCATTG 59.535 52.381 11.64 0.00 32.87 2.82
40 41 1.371635 GTTGTGCCACGACCATTGC 60.372 57.895 3.68 0.00 0.00 3.56
41 42 2.902419 TTGTGCCACGACCATTGCG 61.902 57.895 0.00 0.00 0.00 4.85
42 43 3.353836 GTGCCACGACCATTGCGT 61.354 61.111 0.00 0.00 43.67 5.24
45 46 1.729131 GCCACGACCATTGCGTTTG 60.729 57.895 0.00 0.00 40.44 2.93
50 51 0.953471 CGACCATTGCGTTTGGAGGA 60.953 55.000 6.41 0.00 37.69 3.71
51 52 0.804989 GACCATTGCGTTTGGAGGAG 59.195 55.000 6.41 0.00 37.69 3.69
61 65 2.396651 TTTGGAGGAGGAGGACGGGT 62.397 60.000 0.00 0.00 0.00 5.28
79 83 2.222027 GGTTGTGAACTGGGAAGAGTG 58.778 52.381 0.00 0.00 0.00 3.51
110 114 1.862602 GAAAACGCACGGGCTCCAAT 61.863 55.000 8.62 0.00 38.10 3.16
130 134 5.416326 CCAATTAAGTTTTGGATGGGTACGA 59.584 40.000 0.61 0.00 45.35 3.43
137 141 0.251877 TGGATGGGTACGAGGTGTCA 60.252 55.000 0.00 0.00 0.00 3.58
149 153 2.279918 GTGTCAGACGCCAACGGT 60.280 61.111 2.32 0.00 46.04 4.83
204 208 2.193087 ATTTGTCGCCGGCCTAAGGT 62.193 55.000 23.46 0.00 0.00 3.50
205 209 2.400269 TTTGTCGCCGGCCTAAGGTT 62.400 55.000 23.46 0.00 0.00 3.50
206 210 2.818274 GTCGCCGGCCTAAGGTTG 60.818 66.667 23.46 3.72 0.00 3.77
209 213 1.969589 CGCCGGCCTAAGGTTGTTT 60.970 57.895 23.46 0.00 0.00 2.83
210 214 1.880894 GCCGGCCTAAGGTTGTTTC 59.119 57.895 18.11 0.00 0.00 2.78
211 215 0.891904 GCCGGCCTAAGGTTGTTTCA 60.892 55.000 18.11 0.00 0.00 2.69
212 216 1.165270 CCGGCCTAAGGTTGTTTCAG 58.835 55.000 0.00 0.00 0.00 3.02
213 217 1.271163 CCGGCCTAAGGTTGTTTCAGA 60.271 52.381 0.00 0.00 0.00 3.27
214 218 1.804748 CGGCCTAAGGTTGTTTCAGAC 59.195 52.381 0.00 0.00 0.00 3.51
215 219 2.808933 CGGCCTAAGGTTGTTTCAGACA 60.809 50.000 0.00 0.00 36.19 3.41
216 220 3.421844 GGCCTAAGGTTGTTTCAGACAT 58.578 45.455 0.00 0.00 38.26 3.06
218 222 3.440522 GCCTAAGGTTGTTTCAGACATCC 59.559 47.826 0.00 0.00 44.93 3.51
219 223 4.651778 CCTAAGGTTGTTTCAGACATCCA 58.348 43.478 8.49 0.00 46.33 3.41
220 224 5.070001 CCTAAGGTTGTTTCAGACATCCAA 58.930 41.667 8.49 0.00 46.33 3.53
221 225 4.918810 AAGGTTGTTTCAGACATCCAAC 57.081 40.909 8.49 0.00 46.33 3.77
426 1652 3.118702 TCTCACCGTACCAACAAACAGAA 60.119 43.478 0.00 0.00 0.00 3.02
428 1654 4.008330 TCACCGTACCAACAAACAGAAAA 58.992 39.130 0.00 0.00 0.00 2.29
546 1783 3.214123 CGCCGAGTATCCGACCCA 61.214 66.667 0.00 0.00 0.00 4.51
559 1796 1.101635 CGACCCAGAGTATCGGCTCA 61.102 60.000 5.62 0.00 42.67 4.26
803 2041 1.831652 CTGCCCAGAACCTTCCGTCT 61.832 60.000 0.00 0.00 0.00 4.18
806 2044 0.905357 CCCAGAACCTTCCGTCTCAT 59.095 55.000 0.00 0.00 0.00 2.90
1290 2540 1.952296 CACAGCAACTTCTCCAGCTTT 59.048 47.619 0.00 0.00 34.61 3.51
1392 2667 1.488957 CGAGTCGCTTGCTTGTGTC 59.511 57.895 0.00 0.00 0.00 3.67
1404 2679 2.244436 CTTGTGTCGCTGCAATCCCG 62.244 60.000 0.00 0.00 0.00 5.14
1442 2717 4.015872 ACCAAGATTTTAGCCGAGTTGA 57.984 40.909 0.00 0.00 0.00 3.18
1530 2807 2.897350 ACTGTGGTGGTGACTATGGTA 58.103 47.619 0.00 0.00 0.00 3.25
1568 2850 6.438186 TGGTATGCATCTGATTCTGGAATA 57.562 37.500 0.19 0.00 0.00 1.75
1573 2855 9.440773 GTATGCATCTGATTCTGGAATAACATA 57.559 33.333 0.19 0.00 0.00 2.29
1576 2858 9.358406 TGCATCTGATTCTGGAATAACATAAAT 57.642 29.630 0.00 0.00 0.00 1.40
1613 2896 8.931775 CAAAAATATAAGGTGGTTTAGTTTGGC 58.068 33.333 0.00 0.00 0.00 4.52
1642 2925 5.469084 GGGTACGAATTGTGAAAGAAGAGTT 59.531 40.000 0.00 0.00 0.00 3.01
1645 2928 6.211664 ACGAATTGTGAAAGAAGAGTTACG 57.788 37.500 0.00 0.00 0.00 3.18
1648 2931 6.786103 CGAATTGTGAAAGAAGAGTTACGTTC 59.214 38.462 0.00 0.00 0.00 3.95
1651 2934 7.548196 TTGTGAAAGAAGAGTTACGTTCATT 57.452 32.000 0.00 0.00 37.03 2.57
1652 2935 7.173863 TGTGAAAGAAGAGTTACGTTCATTC 57.826 36.000 0.00 9.77 37.03 2.67
1653 2936 6.984474 TGTGAAAGAAGAGTTACGTTCATTCT 59.016 34.615 14.58 0.00 37.03 2.40
1656 2939 7.709182 TGAAAGAAGAGTTACGTTCATTCTTGA 59.291 33.333 14.58 5.31 37.15 3.02
1657 2940 8.433421 AAAGAAGAGTTACGTTCATTCTTGAA 57.567 30.769 9.15 0.00 39.54 2.69
1658 2941 8.433421 AAGAAGAGTTACGTTCATTCTTGAAA 57.567 30.769 9.15 0.00 43.29 2.69
1659 2942 8.433421 AGAAGAGTTACGTTCATTCTTGAAAA 57.567 30.769 9.15 0.00 43.29 2.29
1661 2944 7.787725 AGAGTTACGTTCATTCTTGAAAAGT 57.212 32.000 0.00 0.00 46.34 2.66
1665 2948 4.351192 ACGTTCATTCTTGAAAAGTGCAC 58.649 39.130 9.40 9.40 46.34 4.57
1667 2950 4.051237 GTTCATTCTTGAAAAGTGCACCC 58.949 43.478 14.63 1.00 46.34 4.61
1668 2951 2.293122 TCATTCTTGAAAAGTGCACCCG 59.707 45.455 14.63 0.00 46.34 5.28
1669 2952 0.383949 TTCTTGAAAAGTGCACCCGC 59.616 50.000 14.63 1.17 46.34 6.13
1670 2953 0.749818 TCTTGAAAAGTGCACCCGCA 60.750 50.000 14.63 4.12 46.34 5.69
1693 2976 2.307934 AATGAAGAGGAAGAGCGAGC 57.692 50.000 0.00 0.00 0.00 5.03
1694 2977 1.484038 ATGAAGAGGAAGAGCGAGCT 58.516 50.000 0.00 0.00 0.00 4.09
1695 2978 0.814457 TGAAGAGGAAGAGCGAGCTC 59.186 55.000 16.63 16.63 43.03 4.09
1712 2995 4.615588 AGCTCTTTTACAGCTGTTCTCT 57.384 40.909 27.06 9.78 45.85 3.10
1713 2996 4.314121 AGCTCTTTTACAGCTGTTCTCTG 58.686 43.478 27.06 11.91 45.85 3.35
1714 2997 3.120373 GCTCTTTTACAGCTGTTCTCTGC 60.120 47.826 27.06 17.84 38.51 4.26
1715 2998 4.060900 CTCTTTTACAGCTGTTCTCTGCA 58.939 43.478 27.06 0.99 40.25 4.41
1716 2999 4.645535 TCTTTTACAGCTGTTCTCTGCAT 58.354 39.130 27.06 0.00 40.25 3.96
1717 3000 4.692625 TCTTTTACAGCTGTTCTCTGCATC 59.307 41.667 27.06 0.00 40.25 3.91
1748 3031 2.794910 CGGTTCTATATGCCAGTGAACG 59.205 50.000 0.00 0.00 38.20 3.95
1749 3032 3.490249 CGGTTCTATATGCCAGTGAACGA 60.490 47.826 0.00 0.00 38.20 3.85
1750 3033 3.802685 GGTTCTATATGCCAGTGAACGAC 59.197 47.826 0.00 0.00 38.20 4.34
1752 3035 2.034179 TCTATATGCCAGTGAACGACGG 59.966 50.000 0.00 0.00 0.00 4.79
1755 3038 0.389426 ATGCCAGTGAACGACGGTAC 60.389 55.000 0.00 0.00 0.00 3.34
1756 3039 1.735559 GCCAGTGAACGACGGTACC 60.736 63.158 0.16 0.16 0.00 3.34
1778 3214 4.853196 CCGTGATTCTTATTGCTTTGTGTG 59.147 41.667 0.00 0.00 0.00 3.82
1781 3217 6.636447 CGTGATTCTTATTGCTTTGTGTGAAA 59.364 34.615 0.00 0.00 0.00 2.69
1786 3222 7.094508 TCTTATTGCTTTGTGTGAAACTTGA 57.905 32.000 0.00 0.00 38.04 3.02
1791 3227 7.697352 TTGCTTTGTGTGAAACTTGAATATG 57.303 32.000 0.00 0.00 38.04 1.78
1797 3233 9.509855 TTTGTGTGAAACTTGAATATGTACAAC 57.490 29.630 0.00 0.00 38.04 3.32
1838 3274 8.748380 AAGCTGCAAACTAGAATTATTTGTTC 57.252 30.769 1.02 0.00 36.04 3.18
1842 3279 9.132521 CTGCAAACTAGAATTATTTGTTCTTGG 57.867 33.333 0.00 0.00 37.18 3.61
1852 3289 4.590850 ATTTGTTCTTGGCTCTGGTTTC 57.409 40.909 0.00 0.00 0.00 2.78
1872 3309 3.942829 TCAAGGGTGAACATAGCTTGAG 58.057 45.455 0.00 0.00 0.00 3.02
1893 3330 6.993079 TGAGCTCTTCAACAGACTACAATAA 58.007 36.000 16.19 0.00 31.34 1.40
1898 3335 9.372369 GCTCTTCAACAGACTACAATAACTATT 57.628 33.333 0.00 0.00 0.00 1.73
1924 3363 4.391523 GGTACTAGTACAGTAGCGGATAGC 59.608 50.000 29.38 8.05 45.52 2.97
1938 3377 4.241681 GCGGATAGCTAGGATTCTTTCAG 58.758 47.826 0.00 0.00 44.04 3.02
1957 3396 5.053978 TCAGTATCTCTGCCACTATCTGA 57.946 43.478 0.00 0.00 43.32 3.27
1959 3398 5.709631 TCAGTATCTCTGCCACTATCTGATC 59.290 44.000 0.00 0.00 43.32 2.92
1963 3402 1.067669 TCTGCCACTATCTGATCACGC 59.932 52.381 0.00 0.00 0.00 5.34
1974 3413 0.396435 TGATCACGCAAAGTCAGGGT 59.604 50.000 0.00 0.00 0.00 4.34
1981 3420 1.197721 CGCAAAGTCAGGGTGAATCAC 59.802 52.381 4.51 4.51 0.00 3.06
2007 3446 5.952347 GGATTCAAAGGGAAATAGAGGTTGT 59.048 40.000 0.00 0.00 39.39 3.32
2008 3447 6.437477 GGATTCAAAGGGAAATAGAGGTTGTT 59.563 38.462 0.00 0.00 39.39 2.83
2057 3496 8.250332 GTGCATGAAACCTTATTTCCTGAATTA 58.750 33.333 0.00 0.00 0.00 1.40
2058 3497 8.250332 TGCATGAAACCTTATTTCCTGAATTAC 58.750 33.333 0.00 0.00 0.00 1.89
2062 3501 9.449719 TGAAACCTTATTTCCTGAATTACTCTC 57.550 33.333 0.00 0.00 0.00 3.20
2063 3502 9.674068 GAAACCTTATTTCCTGAATTACTCTCT 57.326 33.333 0.00 0.00 0.00 3.10
2064 3503 9.454859 AAACCTTATTTCCTGAATTACTCTCTG 57.545 33.333 0.00 0.00 0.00 3.35
2090 3531 0.622665 AGAACAAGGAGATGCTGGGG 59.377 55.000 0.00 0.00 0.00 4.96
2092 3533 0.846427 AACAAGGAGATGCTGGGGGA 60.846 55.000 0.00 0.00 0.00 4.81
2101 3542 1.771255 GATGCTGGGGGACTGAATAGT 59.229 52.381 0.00 0.00 40.66 2.12
2115 3556 4.141756 ACTGAATAGTCTGCATCTCCTTGG 60.142 45.833 0.00 0.00 28.79 3.61
2139 3580 9.114952 TGGCGAACATATTTAATTTCTGACATA 57.885 29.630 0.00 0.00 0.00 2.29
2277 3718 9.796180 AGTATACTACTACCTATTCTTCCACTG 57.204 37.037 2.75 0.00 37.23 3.66
2311 3752 3.380320 GGGCATAACACTATGTGAAACCC 59.620 47.826 4.61 4.50 37.76 4.11
2410 3851 3.561725 AGTTGTTCTGCTACTCTTTGTGC 59.438 43.478 0.00 0.00 0.00 4.57
2450 3891 9.793252 AATAAATATGTGACTTGTTCTGCAATC 57.207 29.630 0.00 0.00 36.36 2.67
2494 3935 1.407299 CCAGACAGATGGGAATTCGCA 60.407 52.381 25.29 25.29 43.04 5.10
2551 3992 9.762933 CTTCTAAAGATGATAAAGAGAAGGAGG 57.237 37.037 0.00 0.00 36.41 4.30
2552 3993 8.846423 TCTAAAGATGATAAAGAGAAGGAGGT 57.154 34.615 0.00 0.00 0.00 3.85
2650 4091 3.326747 AGAAATCGAAGTGCTAAAGCGT 58.673 40.909 0.00 0.00 45.83 5.07
2791 4232 2.335712 GGGTTTCCTGGCAAGAGCG 61.336 63.158 0.00 0.00 43.41 5.03
2916 4357 2.592993 CGTTCCTTGGCCCTGAGGA 61.593 63.158 13.90 13.90 40.22 3.71
3026 4467 0.536915 GATCAGGAAGGGCATGGAGC 60.537 60.000 0.00 0.00 44.65 4.70
3127 4568 4.446023 GGAATGAGGGATGAAGCTGAGATT 60.446 45.833 0.00 0.00 0.00 2.40
3128 4569 4.792513 ATGAGGGATGAAGCTGAGATTT 57.207 40.909 0.00 0.00 0.00 2.17
3195 4636 5.163713 GCAAAAGCTGGGTCATCTAAGTAAG 60.164 44.000 0.00 0.00 0.00 2.34
3213 4654 6.472686 AGTAAGAGCGATCCAAAATCTACT 57.527 37.500 0.00 0.00 0.00 2.57
3361 4805 4.814771 GTGGTATAAATACTGTCCCTGCAC 59.185 45.833 0.46 0.00 33.81 4.57
3372 4816 1.226802 CCCTGCACTCTCATCGACG 60.227 63.158 0.00 0.00 0.00 5.12
3377 4821 0.992802 GCACTCTCATCGACGGTTTC 59.007 55.000 0.00 0.00 0.00 2.78
3389 4833 3.119602 TCGACGGTTTCTTACTCTGATGG 60.120 47.826 0.00 0.00 0.00 3.51
3405 4853 6.038825 ACTCTGATGGTCTTAGTTCATACTCG 59.961 42.308 0.00 0.00 35.78 4.18
3416 4864 1.227380 CATACTCGGGCCTGCTGAC 60.227 63.158 6.73 0.00 0.00 3.51
3422 4870 1.377725 CGGGCCTGCTGACTGAATT 60.378 57.895 0.84 0.00 0.00 2.17
3441 4889 8.150296 ACTGAATTATTTTTCTGGGTTTGGAAG 58.850 33.333 0.00 0.00 0.00 3.46
3445 4893 1.703411 TTTCTGGGTTTGGAAGCTGG 58.297 50.000 0.00 0.00 0.00 4.85
3457 4905 1.301677 GAAGCTGGAACCGAAGCCTG 61.302 60.000 0.00 0.00 40.42 4.85
3471 4937 2.680913 GCCTGTTGCCTAGTGTGCG 61.681 63.158 0.00 0.00 0.00 5.34
3489 4955 7.243487 AGTGTGCGTTGTAATCATTTAATCTG 58.757 34.615 0.00 0.00 0.00 2.90
3530 4996 7.819415 TGATACCTCTATTGTATATTGCAGTGC 59.181 37.037 8.58 8.58 0.00 4.40
3535 5001 9.224267 CCTCTATTGTATATTGCAGTGCTAATT 57.776 33.333 17.60 3.38 0.00 1.40
3567 5033 1.091537 ATGGTTGTATTGCGGTTCCG 58.908 50.000 6.90 6.90 0.00 4.30
3569 5035 0.674269 GGTTGTATTGCGGTTCCGGA 60.674 55.000 13.16 0.00 0.00 5.14
3571 5037 1.329599 GTTGTATTGCGGTTCCGGATC 59.670 52.381 4.15 3.92 0.00 3.36
3572 5038 0.537653 TGTATTGCGGTTCCGGATCA 59.462 50.000 4.15 0.00 0.00 2.92
3573 5039 1.140052 TGTATTGCGGTTCCGGATCAT 59.860 47.619 4.15 4.50 0.00 2.45
3575 5041 2.631160 ATTGCGGTTCCGGATCATTA 57.369 45.000 4.15 0.00 0.00 1.90
3576 5042 2.631160 TTGCGGTTCCGGATCATTAT 57.369 45.000 4.15 0.00 0.00 1.28
3577 5043 1.877637 TGCGGTTCCGGATCATTATG 58.122 50.000 4.15 0.00 0.00 1.90
3578 5044 1.140052 TGCGGTTCCGGATCATTATGT 59.860 47.619 4.15 0.00 0.00 2.29
3579 5045 1.531149 GCGGTTCCGGATCATTATGTG 59.469 52.381 4.15 0.00 0.00 3.21
3580 5046 1.531149 CGGTTCCGGATCATTATGTGC 59.469 52.381 4.15 0.00 0.00 4.57
3581 5047 2.806745 CGGTTCCGGATCATTATGTGCT 60.807 50.000 4.15 0.00 0.00 4.40
3582 5048 3.554129 CGGTTCCGGATCATTATGTGCTA 60.554 47.826 4.15 0.00 0.00 3.49
3583 5049 4.579869 GGTTCCGGATCATTATGTGCTAT 58.420 43.478 4.15 0.00 0.00 2.97
3585 5051 6.349300 GGTTCCGGATCATTATGTGCTATAT 58.651 40.000 4.15 0.00 0.00 0.86
3586 5052 6.823689 GGTTCCGGATCATTATGTGCTATATT 59.176 38.462 4.15 0.00 0.00 1.28
3587 5053 7.985184 GGTTCCGGATCATTATGTGCTATATTA 59.015 37.037 4.15 0.00 0.00 0.98
3589 5055 8.533569 TCCGGATCATTATGTGCTATATTAGA 57.466 34.615 0.00 0.00 0.00 2.10
3590 5056 8.977412 TCCGGATCATTATGTGCTATATTAGAA 58.023 33.333 0.00 0.00 0.00 2.10
3591 5057 9.599866 CCGGATCATTATGTGCTATATTAGAAA 57.400 33.333 0.00 0.00 0.00 2.52
3649 5115 7.123397 TGAACTCTACTGATCTTAGTTCATGCT 59.877 37.037 17.20 0.00 46.65 3.79
3651 5117 6.605194 ACTCTACTGATCTTAGTTCATGCTCA 59.395 38.462 0.00 0.00 32.19 4.26
3655 5121 3.453717 TGATCTTAGTTCATGCTCAGGCT 59.546 43.478 0.00 0.00 39.59 4.58
3656 5122 3.257469 TCTTAGTTCATGCTCAGGCTG 57.743 47.619 8.58 8.58 39.59 4.85
3657 5123 2.568956 TCTTAGTTCATGCTCAGGCTGT 59.431 45.455 15.27 0.00 39.59 4.40
3658 5124 2.680312 TAGTTCATGCTCAGGCTGTC 57.320 50.000 15.27 8.39 39.59 3.51
3659 5125 0.390866 AGTTCATGCTCAGGCTGTCG 60.391 55.000 15.27 8.23 39.59 4.35
3660 5126 1.078918 TTCATGCTCAGGCTGTCGG 60.079 57.895 15.27 7.39 39.59 4.79
3661 5127 1.543944 TTCATGCTCAGGCTGTCGGA 61.544 55.000 15.27 8.72 39.59 4.55
3663 5129 0.463295 CATGCTCAGGCTGTCGGAAT 60.463 55.000 15.27 3.65 39.59 3.01
3671 5139 2.947652 CAGGCTGTCGGAATGAATGATT 59.052 45.455 6.28 0.00 0.00 2.57
3672 5140 4.129380 CAGGCTGTCGGAATGAATGATTA 58.871 43.478 6.28 0.00 0.00 1.75
3695 5163 6.622833 ATTTCTTGGTTTTGGAATTTGCAG 57.377 33.333 0.00 0.00 0.00 4.41
3712 5180 4.855596 GCTGAAGCTTTTCTGCGG 57.144 55.556 0.00 0.00 36.46 5.69
3748 5216 7.551262 TGTACTTGATATATTTTGGTGAACGCT 59.449 33.333 0.00 0.00 0.00 5.07
3753 5221 7.269316 TGATATATTTTGGTGAACGCTAGACA 58.731 34.615 0.00 0.00 0.00 3.41
3760 5228 4.053295 TGGTGAACGCTAGACAAACTAAC 58.947 43.478 0.00 0.00 0.00 2.34
3771 5239 4.134563 AGACAAACTAACGCACAATTCCT 58.865 39.130 0.00 0.00 0.00 3.36
3773 5241 3.059188 ACAAACTAACGCACAATTCCTCG 60.059 43.478 0.00 0.00 0.00 4.63
3789 5257 4.192429 TCCTCGTGCATATATGTGGATG 57.808 45.455 14.14 6.82 0.00 3.51
3819 5287 3.508793 ACCTTCCAGAATGATGCTGTTTG 59.491 43.478 0.00 0.00 39.69 2.93
3845 5313 8.974060 AACCTGAAATTTACATATACACGGAT 57.026 30.769 0.00 0.00 0.00 4.18
3850 5318 9.772973 TGAAATTTACATATACACGGATTAGCT 57.227 29.630 0.00 0.00 0.00 3.32
3864 5332 7.014230 ACACGGATTAGCTAAAATGCCATTATT 59.986 33.333 10.85 0.00 0.00 1.40
3974 5457 9.403583 ACTAAGTTGAACAAAATAGAGGAAACA 57.596 29.630 0.00 0.00 0.00 2.83
3975 5458 9.665264 CTAAGTTGAACAAAATAGAGGAAACAC 57.335 33.333 0.00 0.00 0.00 3.32
3976 5459 7.639113 AGTTGAACAAAATAGAGGAAACACA 57.361 32.000 0.00 0.00 0.00 3.72
3977 5460 7.707104 AGTTGAACAAAATAGAGGAAACACAG 58.293 34.615 0.00 0.00 0.00 3.66
3979 5462 7.639113 TGAACAAAATAGAGGAAACACAGTT 57.361 32.000 0.00 0.00 0.00 3.16
3980 5463 8.062065 TGAACAAAATAGAGGAAACACAGTTT 57.938 30.769 0.00 0.00 0.00 2.66
3982 5465 9.665264 GAACAAAATAGAGGAAACACAGTTTAG 57.335 33.333 0.00 0.00 0.00 1.85
3984 5467 9.403583 ACAAAATAGAGGAAACACAGTTTAGAA 57.596 29.630 0.00 0.00 0.00 2.10
4052 5545 6.140737 CGAAGTGAATTATTAAATGAAGCCGC 59.859 38.462 0.00 0.00 0.00 6.53
4053 5546 6.699575 AGTGAATTATTAAATGAAGCCGCT 57.300 33.333 0.00 0.00 0.00 5.52
4057 5550 7.649306 GTGAATTATTAAATGAAGCCGCTCAAT 59.351 33.333 0.00 0.00 0.00 2.57
4058 5551 8.845227 TGAATTATTAAATGAAGCCGCTCAATA 58.155 29.630 0.00 0.00 0.00 1.90
4059 5552 9.846248 GAATTATTAAATGAAGCCGCTCAATAT 57.154 29.630 0.00 0.00 0.00 1.28
4065 5558 7.935338 AAATGAAGCCGCTCAATATTTTATG 57.065 32.000 0.00 0.00 0.00 1.90
4066 5559 5.437289 TGAAGCCGCTCAATATTTTATGG 57.563 39.130 0.00 0.00 0.00 2.74
4076 5569 7.710475 CGCTCAATATTTTATGGGGAAAAATGT 59.290 33.333 4.49 0.00 37.19 2.71
4077 5570 8.829612 GCTCAATATTTTATGGGGAAAAATGTG 58.170 33.333 4.49 3.49 37.19 3.21
4085 5578 9.632638 TTTTATGGGGAAAAATGTGAATTGAAA 57.367 25.926 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.609131 CCTCCTCCAAACGCAATGGT 60.609 55.000 2.15 0.00 39.09 3.55
39 40 1.079057 GTCCTCCTCCTCCAAACGC 60.079 63.158 0.00 0.00 0.00 4.84
40 41 1.215647 CGTCCTCCTCCTCCAAACG 59.784 63.158 0.00 0.00 0.00 3.60
41 42 1.597461 CCGTCCTCCTCCTCCAAAC 59.403 63.158 0.00 0.00 0.00 2.93
42 43 1.612442 CCCGTCCTCCTCCTCCAAA 60.612 63.158 0.00 0.00 0.00 3.28
45 46 2.039137 AACCCGTCCTCCTCCTCC 59.961 66.667 0.00 0.00 0.00 4.30
50 51 0.763223 AGTTCACAACCCGTCCTCCT 60.763 55.000 0.00 0.00 0.00 3.69
51 52 0.602905 CAGTTCACAACCCGTCCTCC 60.603 60.000 0.00 0.00 0.00 4.30
61 65 1.142870 CCCACTCTTCCCAGTTCACAA 59.857 52.381 0.00 0.00 0.00 3.33
79 83 1.211709 CGTTTTCACAATCCGCCCC 59.788 57.895 0.00 0.00 0.00 5.80
110 114 4.041938 ACCTCGTACCCATCCAAAACTTAA 59.958 41.667 0.00 0.00 0.00 1.85
130 134 2.029073 CGTTGGCGTCTGACACCT 59.971 61.111 15.30 0.00 27.57 4.00
137 141 4.657824 CGTCCACCGTTGGCGTCT 62.658 66.667 7.47 0.00 43.56 4.18
149 153 0.877071 GGTAGTTCAGACGACGTCCA 59.123 55.000 23.76 8.73 32.82 4.02
157 161 1.478916 GCTCTCCAGGGTAGTTCAGAC 59.521 57.143 0.00 0.00 0.00 3.51
159 163 1.754226 GAGCTCTCCAGGGTAGTTCAG 59.246 57.143 6.43 0.00 0.00 3.02
160 164 1.853963 GAGCTCTCCAGGGTAGTTCA 58.146 55.000 6.43 0.00 0.00 3.18
204 208 3.304911 TGGGTTGGATGTCTGAAACAA 57.695 42.857 0.00 0.00 42.37 2.83
205 209 3.304911 TTGGGTTGGATGTCTGAAACA 57.695 42.857 0.00 0.00 43.51 2.83
206 210 4.664150 TTTTGGGTTGGATGTCTGAAAC 57.336 40.909 0.00 0.00 0.00 2.78
209 213 4.081406 CTCATTTTGGGTTGGATGTCTGA 58.919 43.478 0.00 0.00 0.00 3.27
210 214 3.194116 CCTCATTTTGGGTTGGATGTCTG 59.806 47.826 0.00 0.00 0.00 3.51
211 215 3.434309 CCTCATTTTGGGTTGGATGTCT 58.566 45.455 0.00 0.00 0.00 3.41
212 216 2.497273 CCCTCATTTTGGGTTGGATGTC 59.503 50.000 0.00 0.00 39.82 3.06
213 217 2.539302 CCCTCATTTTGGGTTGGATGT 58.461 47.619 0.00 0.00 39.82 3.06
280 284 1.894466 TCATCAAATTGCCCCTGTGTG 59.106 47.619 0.00 0.00 0.00 3.82
281 285 2.173519 CTCATCAAATTGCCCCTGTGT 58.826 47.619 0.00 0.00 0.00 3.72
344 561 1.004504 GCCTCAAATGATCGCTTCGTC 60.005 52.381 0.00 0.00 0.00 4.20
346 563 1.009078 TGCCTCAAATGATCGCTTCG 58.991 50.000 4.80 0.00 0.00 3.79
426 1652 6.233434 TCTCAAGTAGTGCTCATGTCATTTT 58.767 36.000 0.00 0.00 0.00 1.82
428 1654 5.411831 TCTCAAGTAGTGCTCATGTCATT 57.588 39.130 0.00 0.00 0.00 2.57
546 1783 1.135915 CTTGCAGTGAGCCGATACTCT 59.864 52.381 0.00 0.00 44.83 3.24
686 1924 2.515901 GGGTGTGGCTGAGGTTGT 59.484 61.111 0.00 0.00 0.00 3.32
785 2023 1.827399 GAGACGGAAGGTTCTGGGCA 61.827 60.000 3.64 0.00 37.89 5.36
1052 2302 4.465446 CCTCCTCCTCCTCCGGCA 62.465 72.222 0.00 0.00 0.00 5.69
1290 2540 2.280797 GTGTTGAGCTGGCGGACA 60.281 61.111 0.00 0.00 0.00 4.02
1392 2667 1.645455 CAAGATCGGGATTGCAGCG 59.355 57.895 0.00 0.00 0.00 5.18
1404 2679 6.500684 TCTTGGTTCTACAAATGCAAGATC 57.499 37.500 0.00 0.00 0.00 2.75
1442 2717 3.930336 TGTCGTTCATCTCTTGCTCAAT 58.070 40.909 0.00 0.00 0.00 2.57
1576 2858 9.680315 CCACCTTATATTTTTGTTTTTGTACGA 57.320 29.630 0.00 0.00 0.00 3.43
1599 2882 2.223947 CCCAGTTGCCAAACTAAACCAC 60.224 50.000 0.00 0.00 45.07 4.16
1605 2888 1.693062 TCGTACCCAGTTGCCAAACTA 59.307 47.619 0.00 0.00 45.07 2.24
1613 2896 4.513692 TCTTTCACAATTCGTACCCAGTTG 59.486 41.667 0.00 0.00 0.00 3.16
1642 2925 5.504994 GGTGCACTTTTCAAGAATGAACGTA 60.505 40.000 17.98 0.00 45.01 3.57
1645 2928 4.051237 GGGTGCACTTTTCAAGAATGAAC 58.949 43.478 17.98 0.00 45.01 3.18
1648 2931 2.664916 CGGGTGCACTTTTCAAGAATG 58.335 47.619 17.98 0.00 0.00 2.67
1651 2934 2.029743 GCGGGTGCACTTTTCAAGA 58.970 52.632 17.98 0.00 42.15 3.02
1652 2935 4.633980 GCGGGTGCACTTTTCAAG 57.366 55.556 17.98 1.95 42.15 3.02
1671 2954 3.438434 GCTCGCTCTTCCTCTTCATTTTT 59.562 43.478 0.00 0.00 0.00 1.94
1672 2955 3.006247 GCTCGCTCTTCCTCTTCATTTT 58.994 45.455 0.00 0.00 0.00 1.82
1673 2956 2.235898 AGCTCGCTCTTCCTCTTCATTT 59.764 45.455 0.00 0.00 0.00 2.32
1674 2957 1.830477 AGCTCGCTCTTCCTCTTCATT 59.170 47.619 0.00 0.00 0.00 2.57
1675 2958 1.408702 GAGCTCGCTCTTCCTCTTCAT 59.591 52.381 11.49 0.00 39.80 2.57
1676 2959 0.814457 GAGCTCGCTCTTCCTCTTCA 59.186 55.000 11.49 0.00 39.80 3.02
1677 2960 3.641031 GAGCTCGCTCTTCCTCTTC 57.359 57.895 11.49 0.00 39.80 2.87
1686 2969 1.658095 CAGCTGTAAAAGAGCTCGCTC 59.342 52.381 8.37 10.83 45.24 5.03
1687 2970 1.001406 ACAGCTGTAAAAGAGCTCGCT 59.999 47.619 20.16 6.12 45.24 4.93
1688 2971 1.433534 ACAGCTGTAAAAGAGCTCGC 58.566 50.000 20.16 3.58 45.24 5.03
1689 2972 3.321497 AGAACAGCTGTAAAAGAGCTCG 58.679 45.455 22.01 0.00 45.24 5.03
1690 2973 4.388469 CAGAGAACAGCTGTAAAAGAGCTC 59.612 45.833 22.01 16.33 45.24 4.09
1692 2975 3.120373 GCAGAGAACAGCTGTAAAAGAGC 60.120 47.826 22.01 16.01 35.81 4.09
1693 2976 4.060900 TGCAGAGAACAGCTGTAAAAGAG 58.939 43.478 22.01 10.05 35.81 2.85
1694 2977 4.071961 TGCAGAGAACAGCTGTAAAAGA 57.928 40.909 22.01 0.00 35.81 2.52
1695 2978 4.453478 TGATGCAGAGAACAGCTGTAAAAG 59.547 41.667 22.01 10.58 35.81 2.27
1696 2979 4.388485 TGATGCAGAGAACAGCTGTAAAA 58.612 39.130 22.01 2.26 35.81 1.52
1697 2980 3.999001 CTGATGCAGAGAACAGCTGTAAA 59.001 43.478 22.01 1.14 35.81 2.01
1698 2981 3.593096 CTGATGCAGAGAACAGCTGTAA 58.407 45.455 22.01 0.39 35.81 2.41
1699 2982 3.242549 CTGATGCAGAGAACAGCTGTA 57.757 47.619 22.01 2.09 35.81 2.74
1700 2983 2.096220 CTGATGCAGAGAACAGCTGT 57.904 50.000 15.25 15.25 35.81 4.40
1713 2996 0.375106 GAACCGCTTACTGCTGATGC 59.625 55.000 0.00 0.00 40.11 3.91
1714 2997 2.015736 AGAACCGCTTACTGCTGATG 57.984 50.000 0.00 0.00 40.11 3.07
1715 2998 5.473931 CATATAGAACCGCTTACTGCTGAT 58.526 41.667 0.00 0.00 40.11 2.90
1716 2999 4.796290 GCATATAGAACCGCTTACTGCTGA 60.796 45.833 0.00 0.00 40.11 4.26
1717 3000 3.430218 GCATATAGAACCGCTTACTGCTG 59.570 47.826 0.00 0.00 40.11 4.41
1721 3004 3.641906 ACTGGCATATAGAACCGCTTACT 59.358 43.478 0.00 0.00 0.00 2.24
1739 3022 1.443194 CGGTACCGTCGTTCACTGG 60.443 63.158 26.39 0.00 34.35 4.00
1750 3033 3.454375 AGCAATAAGAATCACGGTACCG 58.546 45.455 32.22 32.22 46.03 4.02
1752 3035 6.021596 CACAAAGCAATAAGAATCACGGTAC 58.978 40.000 0.00 0.00 0.00 3.34
1755 3038 4.853196 CACACAAAGCAATAAGAATCACGG 59.147 41.667 0.00 0.00 0.00 4.94
1756 3039 5.688823 TCACACAAAGCAATAAGAATCACG 58.311 37.500 0.00 0.00 0.00 4.35
1765 3201 9.409312 CATATTCAAGTTTCACACAAAGCAATA 57.591 29.630 0.00 0.00 0.00 1.90
1766 3202 7.927629 ACATATTCAAGTTTCACACAAAGCAAT 59.072 29.630 0.00 0.00 0.00 3.56
1768 3204 6.804677 ACATATTCAAGTTTCACACAAAGCA 58.195 32.000 0.00 0.00 0.00 3.91
1769 3205 7.860373 TGTACATATTCAAGTTTCACACAAAGC 59.140 33.333 0.00 0.00 0.00 3.51
1791 3227 7.021790 GCTTCTTTGCTGGTAATTAGTTGTAC 58.978 38.462 0.00 0.00 0.00 2.90
1838 3274 1.251251 CCCTTGAAACCAGAGCCAAG 58.749 55.000 0.00 0.00 36.64 3.61
1842 3279 1.609072 GTTCACCCTTGAAACCAGAGC 59.391 52.381 0.00 0.00 43.52 4.09
1852 3289 2.421424 GCTCAAGCTATGTTCACCCTTG 59.579 50.000 0.00 0.00 38.21 3.61
1872 3309 8.934507 ATAGTTATTGTAGTCTGTTGAAGAGC 57.065 34.615 0.00 0.00 34.84 4.09
1893 3330 7.605691 CCGCTACTGTACTAGTACCATAATAGT 59.394 40.741 26.41 22.49 41.76 2.12
1898 3335 5.551305 TCCGCTACTGTACTAGTACCATA 57.449 43.478 26.41 17.99 40.89 2.74
1899 3336 4.428294 TCCGCTACTGTACTAGTACCAT 57.572 45.455 26.41 17.85 40.89 3.55
1900 3337 3.912496 TCCGCTACTGTACTAGTACCA 57.088 47.619 26.41 15.21 40.89 3.25
1912 3349 8.921789 CTGAAAGAATCCTAGCTATCCGCTACT 61.922 44.444 0.00 0.00 42.58 2.57
1913 3350 6.844080 CTGAAAGAATCCTAGCTATCCGCTAC 60.844 46.154 0.00 0.00 42.58 3.58
1914 3351 5.184096 CTGAAAGAATCCTAGCTATCCGCTA 59.816 44.000 0.00 0.00 42.58 4.26
1915 3352 4.021544 CTGAAAGAATCCTAGCTATCCGCT 60.022 45.833 0.00 0.00 45.72 5.52
1916 3353 4.241681 CTGAAAGAATCCTAGCTATCCGC 58.758 47.826 0.00 0.00 34.07 5.54
1938 3377 5.618863 CGTGATCAGATAGTGGCAGAGATAC 60.619 48.000 0.00 0.00 0.00 2.24
1957 3396 0.396435 TCACCCTGACTTTGCGTGAT 59.604 50.000 0.00 0.00 0.00 3.06
1959 3398 1.197721 GATTCACCCTGACTTTGCGTG 59.802 52.381 0.00 0.00 0.00 5.34
1963 3402 2.816087 CCAGTGATTCACCCTGACTTTG 59.184 50.000 13.14 2.74 34.49 2.77
1981 3420 5.760131 ACCTCTATTTCCCTTTGAATCCAG 58.240 41.667 0.00 0.00 31.67 3.86
1989 3428 3.832490 GGCAACAACCTCTATTTCCCTTT 59.168 43.478 0.00 0.00 0.00 3.11
1991 3430 3.087370 GGCAACAACCTCTATTTCCCT 57.913 47.619 0.00 0.00 0.00 4.20
2014 3453 1.304713 ACATGCCTCTGCCAAAGGG 60.305 57.895 0.00 0.00 36.33 3.95
2037 3476 9.674068 AGAGAGTAATTCAGGAAATAAGGTTTC 57.326 33.333 0.00 0.00 0.00 2.78
2062 3501 4.629200 GCATCTCCTTGTTCTGAAGTACAG 59.371 45.833 0.00 0.00 46.97 2.74
2063 3502 4.284490 AGCATCTCCTTGTTCTGAAGTACA 59.716 41.667 0.00 0.00 0.00 2.90
2064 3503 4.629200 CAGCATCTCCTTGTTCTGAAGTAC 59.371 45.833 0.00 0.00 0.00 2.73
2092 3533 4.141756 CCAAGGAGATGCAGACTATTCAGT 60.142 45.833 0.00 0.00 37.87 3.41
2101 3542 0.391661 GTTCGCCAAGGAGATGCAGA 60.392 55.000 0.00 0.00 0.00 4.26
2139 3580 6.127026 ACACAGTAAGAAGTTGGAGAAAGAGT 60.127 38.462 0.00 0.00 0.00 3.24
2277 3718 9.410556 CATAGTGTTATGCCCAAATTTATAAGC 57.589 33.333 0.00 0.00 30.98 3.09
2311 3752 9.236691 GCATACTTCACACAATATAAAATGGTG 57.763 33.333 0.00 0.00 35.66 4.17
2450 3891 4.253685 TCGATCTTTCTAAAACCCTGCAG 58.746 43.478 6.78 6.78 0.00 4.41
2494 3935 1.530323 CCCGAATGAAACCCTCGTTT 58.470 50.000 0.00 0.00 44.99 3.60
2551 3992 5.070981 TGATGAAGGGAGATAGGACAATGAC 59.929 44.000 0.00 0.00 0.00 3.06
2552 3993 5.070981 GTGATGAAGGGAGATAGGACAATGA 59.929 44.000 0.00 0.00 0.00 2.57
2650 4091 1.933500 GCGAGTAAGGCGTTCTTGTCA 60.934 52.381 0.00 0.00 36.93 3.58
2791 4232 6.043854 AGAAAGAAGTCAGGGTTCTGTATC 57.956 41.667 0.00 0.00 41.59 2.24
2916 4357 0.178950 TGGCTCACTCTGACTGGTCT 60.179 55.000 2.38 0.00 0.00 3.85
3026 4467 0.608130 TTCCGACCACCTCTGTCATG 59.392 55.000 0.00 0.00 32.91 3.07
3127 4568 3.791320 TCTCCTCCTTTCCAGCTCTAAA 58.209 45.455 0.00 0.00 0.00 1.85
3128 4569 3.474798 TCTCCTCCTTTCCAGCTCTAA 57.525 47.619 0.00 0.00 0.00 2.10
3177 4618 3.723260 GCTCTTACTTAGATGACCCAGC 58.277 50.000 0.00 0.00 30.92 4.85
3178 4619 3.632604 TCGCTCTTACTTAGATGACCCAG 59.367 47.826 0.00 0.00 30.92 4.45
3195 4636 7.653713 TGAATTCTAGTAGATTTTGGATCGCTC 59.346 37.037 7.05 0.00 0.00 5.03
3282 4723 8.244113 CCGCAATACAATCAGTCTATGACTATA 58.756 37.037 0.00 0.00 41.37 1.31
3361 4805 4.095185 AGAGTAAGAAACCGTCGATGAGAG 59.905 45.833 6.11 0.00 0.00 3.20
3372 4816 6.937392 ACTAAGACCATCAGAGTAAGAAACC 58.063 40.000 0.00 0.00 0.00 3.27
3377 4821 8.908903 AGTATGAACTAAGACCATCAGAGTAAG 58.091 37.037 0.00 0.00 32.84 2.34
3389 4833 2.694109 AGGCCCGAGTATGAACTAAGAC 59.306 50.000 0.00 0.00 35.56 3.01
3405 4853 2.355010 ATAATTCAGTCAGCAGGCCC 57.645 50.000 0.00 0.00 0.00 5.80
3416 4864 7.118245 GCTTCCAAACCCAGAAAAATAATTCAG 59.882 37.037 0.00 0.00 0.00 3.02
3422 4870 4.283212 CCAGCTTCCAAACCCAGAAAAATA 59.717 41.667 0.00 0.00 0.00 1.40
3441 4889 1.600916 AACAGGCTTCGGTTCCAGC 60.601 57.895 0.00 0.00 35.07 4.85
3445 4893 0.321298 TAGGCAACAGGCTTCGGTTC 60.321 55.000 0.00 0.00 44.01 3.62
3457 4905 1.504359 TACAACGCACACTAGGCAAC 58.496 50.000 0.00 0.00 0.00 4.17
3509 4975 8.783833 ATTAGCACTGCAATATACAATAGAGG 57.216 34.615 3.30 0.00 0.00 3.69
3546 5012 2.678836 CGGAACCGCAATACAACCATTA 59.321 45.455 0.00 0.00 0.00 1.90
3561 5027 2.851195 AGCACATAATGATCCGGAACC 58.149 47.619 9.01 3.91 0.00 3.62
3590 5056 9.238368 TGTCGATAAGAATTAAGGGATGTTTTT 57.762 29.630 0.00 0.00 32.17 1.94
3591 5057 8.801882 TGTCGATAAGAATTAAGGGATGTTTT 57.198 30.769 0.00 0.00 32.17 2.43
3592 5058 8.801882 TTGTCGATAAGAATTAAGGGATGTTT 57.198 30.769 0.00 0.00 32.17 2.83
3593 5059 8.980481 ATTGTCGATAAGAATTAAGGGATGTT 57.020 30.769 0.02 0.00 32.17 2.71
3594 5060 8.980481 AATTGTCGATAAGAATTAAGGGATGT 57.020 30.769 0.02 0.00 32.17 3.06
3628 5094 6.040278 CCTGAGCATGAACTAAGATCAGTAGA 59.960 42.308 0.00 0.00 42.50 2.59
3631 5097 4.682859 GCCTGAGCATGAACTAAGATCAGT 60.683 45.833 0.00 0.00 42.50 3.41
3632 5098 3.808726 GCCTGAGCATGAACTAAGATCAG 59.191 47.826 0.00 0.00 43.37 2.90
3635 5101 3.199508 ACAGCCTGAGCATGAACTAAGAT 59.800 43.478 0.00 0.00 43.56 2.40
3649 5115 1.554617 TCATTCATTCCGACAGCCTGA 59.445 47.619 0.00 0.00 0.00 3.86
3651 5117 3.287867 AATCATTCATTCCGACAGCCT 57.712 42.857 0.00 0.00 0.00 4.58
3655 5121 7.339212 ACCAAGAAATAATCATTCATTCCGACA 59.661 33.333 0.00 0.00 0.00 4.35
3656 5122 7.707104 ACCAAGAAATAATCATTCATTCCGAC 58.293 34.615 0.00 0.00 0.00 4.79
3657 5123 7.880160 ACCAAGAAATAATCATTCATTCCGA 57.120 32.000 0.00 0.00 0.00 4.55
3658 5124 8.931385 AAACCAAGAAATAATCATTCATTCCG 57.069 30.769 0.00 0.00 0.00 4.30
3671 5139 6.204495 GCTGCAAATTCCAAAACCAAGAAATA 59.796 34.615 0.00 0.00 0.00 1.40
3672 5140 5.008911 GCTGCAAATTCCAAAACCAAGAAAT 59.991 36.000 0.00 0.00 0.00 2.17
3695 5163 1.211190 CCCGCAGAAAAGCTTCAGC 59.789 57.895 0.00 0.65 39.89 4.26
3740 5208 4.289529 CGTTAGTTTGTCTAGCGTTCAC 57.710 45.455 3.68 0.00 44.35 3.18
3748 5216 5.302360 AGGAATTGTGCGTTAGTTTGTCTA 58.698 37.500 0.00 0.00 0.00 2.59
3753 5221 3.059188 CACGAGGAATTGTGCGTTAGTTT 60.059 43.478 0.00 0.00 34.37 2.66
3771 5239 4.082026 CCTCTCATCCACATATATGCACGA 60.082 45.833 12.79 6.09 0.00 4.35
3773 5241 4.223700 TCCCTCTCATCCACATATATGCAC 59.776 45.833 12.79 0.00 0.00 4.57
3781 5249 2.277008 AGGTTCCCTCTCATCCACAT 57.723 50.000 0.00 0.00 0.00 3.21
3802 5270 3.508793 AGGTTCAAACAGCATCATTCTGG 59.491 43.478 0.00 0.00 35.94 3.86
3805 5273 4.771590 TCAGGTTCAAACAGCATCATTC 57.228 40.909 0.00 0.00 0.00 2.67
3819 5287 8.428186 TCCGTGTATATGTAAATTTCAGGTTC 57.572 34.615 0.00 0.00 0.00 3.62
3840 5308 7.524717 AATAATGGCATTTTAGCTAATCCGT 57.475 32.000 19.21 5.42 34.17 4.69
3956 5439 9.665264 CTAAACTGTGTTTCCTCTATTTTGTTC 57.335 33.333 0.00 0.00 0.00 3.18
4027 5520 6.140737 GCGGCTTCATTTAATAATTCACTTCG 59.859 38.462 0.00 0.00 0.00 3.79
4058 5551 9.804977 TTCAATTCACATTTTTCCCCATAAAAT 57.195 25.926 0.00 0.00 36.03 1.82
4059 5552 9.632638 TTTCAATTCACATTTTTCCCCATAAAA 57.367 25.926 0.00 0.00 0.00 1.52
4064 5557 6.491714 TCTTTCAATTCACATTTTTCCCCA 57.508 33.333 0.00 0.00 0.00 4.96
4065 5558 7.800155 TTTCTTTCAATTCACATTTTTCCCC 57.200 32.000 0.00 0.00 0.00 4.81
4120 5617 9.991906 TTCCCGTATTTTAATTACTCATAGGAG 57.008 33.333 2.12 2.12 46.96 3.69
4141 5639 7.306749 GCATAGCAATAACATTTTGAATTCCCG 60.307 37.037 2.27 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.