Multiple sequence alignment - TraesCS3D01G351200

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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 TraesCS3D01G351200 chr3D 100.000 3377 0 0 1 3377 462235667 462239043 0.000000e+00 6237.0
1 TraesCS3D01G351200 chr3D 98.246 342 6 0 3036 3377 253386968 253387309 1.730000e-167 599.0
2 TraesCS3D01G351200 chr3D 94.581 203 7 4 3032 3234 545055451 545055649 9.100000e-81 311.0
3 TraesCS3D01G351200 chr3D 85.350 314 22 11 2102 2400 138191037 138191341 1.520000e-78 303.0
4 TraesCS3D01G351200 chr3D 89.767 215 20 2 2424 2638 462244260 462244472 1.190000e-69 274.0
5 TraesCS3D01G351200 chr3D 90.000 50 5 0 2830 2879 462245090 462245139 7.820000e-07 65.8
6 TraesCS3D01G351200 chr3B 94.215 2299 112 10 598 2880 613805383 613807676 0.000000e+00 3489.0
7 TraesCS3D01G351200 chr3B 84.890 589 40 19 1 559 613804816 613805385 1.770000e-152 549.0
8 TraesCS3D01G351200 chr3B 88.350 103 6 2 2227 2325 201327952 201328052 5.920000e-23 119.0
9 TraesCS3D01G351200 chr3B 89.583 48 5 0 2830 2877 613808814 613808861 1.010000e-05 62.1
10 TraesCS3D01G351200 chr3A 96.650 1612 53 1 806 2416 605171962 605173573 0.000000e+00 2676.0
11 TraesCS3D01G351200 chr3A 89.446 578 32 14 2461 3035 605173573 605174124 0.000000e+00 702.0
12 TraesCS3D01G351200 chr3A 85.540 657 56 9 96 749 605171172 605171792 0.000000e+00 651.0
13 TraesCS3D01G351200 chr3A 88.837 215 23 1 2424 2638 605174650 605174863 2.580000e-66 263.0
14 TraesCS3D01G351200 chr3A 87.179 195 10 6 2108 2292 156266831 156267020 1.230000e-49 207.0
15 TraesCS3D01G351200 chr3A 90.000 50 5 0 2830 2879 605175590 605175639 7.820000e-07 65.8
16 TraesCS3D01G351200 chr3A 89.583 48 5 0 2830 2877 605177206 605177253 1.010000e-05 62.1
17 TraesCS3D01G351200 chr7D 97.399 346 9 0 3032 3377 43985938 43985593 1.040000e-164 590.0
18 TraesCS3D01G351200 chr7D 95.189 291 12 1 3034 3324 179491565 179491853 3.070000e-125 459.0
19 TraesCS3D01G351200 chr7D 93.750 256 8 5 3036 3290 426215591 426215343 8.850000e-101 377.0
20 TraesCS3D01G351200 chr2A 92.464 345 22 4 3036 3377 12357361 12357018 1.090000e-134 490.0
21 TraesCS3D01G351200 chrUn 94.118 255 10 2 3037 3290 402808148 402808398 1.900000e-102 383.0
22 TraesCS3D01G351200 chr5D 93.798 258 9 3 3036 3290 256742870 256742617 6.840000e-102 381.0
23 TraesCS3D01G351200 chr1A 89.591 269 18 10 3037 3298 208902121 208901856 1.940000e-87 333.0
24 TraesCS3D01G351200 chr7A 95.455 66 2 1 2971 3035 621572694 621572629 1.660000e-18 104.0
25 TraesCS3D01G351200 chr7A 89.855 69 4 3 2971 3036 6373938 6374006 6.000000e-13 86.1
26 TraesCS3D01G351200 chr7B 94.118 68 2 2 2970 3035 583472702 583472635 5.960000e-18 102.0
27 TraesCS3D01G351200 chr4A 87.805 82 5 4 2960 3036 737439606 737439525 1.290000e-14 91.6


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 TraesCS3D01G351200 chr3D 462235667 462239043 3376 False 6237.00 6237 100.000000 1 3377 1 chr3D.!!$F3 3376
1 TraesCS3D01G351200 chr3B 613804816 613808861 4045 False 1366.70 3489 89.562667 1 2880 3 chr3B.!!$F2 2879
2 TraesCS3D01G351200 chr3A 605171172 605177253 6081 False 736.65 2676 90.009333 96 3035 6 chr3A.!!$F2 2939

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
797 943 0.035056 CTCCCTCGGCAGTCCATTTT 60.035 55.0 0.00 0.0 0.0 1.82 F
798 944 0.035439 TCCCTCGGCAGTCCATTTTC 60.035 55.0 0.00 0.0 0.0 2.29 F
1419 1567 0.036388 TGCCGGAGAAGAATGTGGTC 60.036 55.0 5.05 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1816 0.321671 GCACACTGTCCTCCAAGCTA 59.678 55.0 0.0 0.0 0.0 3.32 R
1956 2104 0.390472 GTTTGGCACGAGAGAGGAGG 60.390 60.0 0.0 0.0 0.0 4.30 R
3313 3872 0.037447 AGGTTGGAAGGAAGAGCAGC 59.963 55.0 0.0 0.0 0.0 5.25 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
49 50 2.292569 CAGCATCTGCACTGTGTTTCTT 59.707 45.455 9.86 0.00 45.16 2.52
60 61 5.276270 CACTGTGTTTCTTTCTGGTGAATG 58.724 41.667 0.00 0.00 31.56 2.67
62 63 5.297776 ACTGTGTTTCTTTCTGGTGAATGAG 59.702 40.000 0.00 0.00 37.56 2.90
74 75 7.854557 TCTGGTGAATGAGAGTATTCATTTG 57.145 36.000 4.70 0.05 45.30 2.32
75 76 7.397221 TCTGGTGAATGAGAGTATTCATTTGT 58.603 34.615 4.70 0.00 45.30 2.83
78 79 8.298854 TGGTGAATGAGAGTATTCATTTGTTTG 58.701 33.333 4.70 0.00 45.30 2.93
79 80 8.299570 GGTGAATGAGAGTATTCATTTGTTTGT 58.700 33.333 4.70 0.00 45.30 2.83
80 81 9.121517 GTGAATGAGAGTATTCATTTGTTTGTG 57.878 33.333 4.70 0.00 45.30 3.33
82 83 8.408043 AATGAGAGTATTCATTTGTTTGTGGA 57.592 30.769 0.00 0.00 43.41 4.02
83 84 7.815840 TGAGAGTATTCATTTGTTTGTGGAA 57.184 32.000 0.00 0.00 0.00 3.53
84 85 7.648142 TGAGAGTATTCATTTGTTTGTGGAAC 58.352 34.615 0.00 0.00 38.78 3.62
85 86 7.502226 TGAGAGTATTCATTTGTTTGTGGAACT 59.498 33.333 0.00 0.00 39.08 3.01
86 87 7.875971 AGAGTATTCATTTGTTTGTGGAACTC 58.124 34.615 0.00 0.00 39.08 3.01
87 88 6.668323 AGTATTCATTTGTTTGTGGAACTCG 58.332 36.000 0.00 0.00 39.08 4.18
88 89 5.766150 ATTCATTTGTTTGTGGAACTCGA 57.234 34.783 0.00 0.00 39.08 4.04
89 90 4.545823 TCATTTGTTTGTGGAACTCGAC 57.454 40.909 0.00 0.00 39.08 4.20
90 91 4.196193 TCATTTGTTTGTGGAACTCGACT 58.804 39.130 0.00 0.00 39.08 4.18
92 93 5.465390 TCATTTGTTTGTGGAACTCGACTAG 59.535 40.000 0.00 0.00 39.08 2.57
93 94 3.380479 TGTTTGTGGAACTCGACTAGG 57.620 47.619 0.00 0.00 39.08 3.02
94 95 2.067013 GTTTGTGGAACTCGACTAGGC 58.933 52.381 0.00 0.00 38.04 3.93
98 99 0.824109 TGGAACTCGACTAGGCATGG 59.176 55.000 0.00 0.00 0.00 3.66
175 178 4.608948 ACTTAGATTTGCTATCCCTCCG 57.391 45.455 0.00 0.00 0.00 4.63
177 180 1.807814 AGATTTGCTATCCCTCCGGT 58.192 50.000 0.00 0.00 0.00 5.28
197 200 6.071896 TCCGGTGAATACAGAGATGTATGATC 60.072 42.308 0.00 0.00 35.40 2.92
229 243 1.674322 GTGGTGGTATGGCGCAAGT 60.674 57.895 10.83 0.00 41.68 3.16
234 248 0.673333 TGGTATGGCGCAAGTGTCAG 60.673 55.000 10.83 0.00 41.68 3.51
239 253 0.320050 TGGCGCAAGTGTCAGTGATA 59.680 50.000 10.83 0.00 41.68 2.15
266 282 6.509418 TGGTTTTTCCTATTGCTGATGTAC 57.491 37.500 0.00 0.00 37.07 2.90
267 283 6.007076 TGGTTTTTCCTATTGCTGATGTACA 58.993 36.000 0.00 0.00 37.07 2.90
295 312 2.886523 TGTTTGAAGAATCACCTGGCAG 59.113 45.455 7.75 7.75 34.61 4.85
411 441 4.083271 GCTAGTGGAGTGCTTTTGTTTAGG 60.083 45.833 0.00 0.00 0.00 2.69
412 442 4.164843 AGTGGAGTGCTTTTGTTTAGGA 57.835 40.909 0.00 0.00 0.00 2.94
458 488 9.158233 CATACAAAATGGAAAATTTGCTGATCT 57.842 29.630 0.00 0.00 39.55 2.75
533 563 4.022935 CGCATTGTACCATTTGATGCCTAT 60.023 41.667 0.00 0.00 39.83 2.57
534 564 5.181056 CGCATTGTACCATTTGATGCCTATA 59.819 40.000 0.00 0.00 39.83 1.31
579 609 4.019681 TCCATTCTATGAACCAAACGACCT 60.020 41.667 0.00 0.00 0.00 3.85
588 618 5.475719 TGAACCAAACGACCTACATAGAAG 58.524 41.667 0.00 0.00 0.00 2.85
591 621 5.721232 ACCAAACGACCTACATAGAAGAAG 58.279 41.667 0.00 0.00 0.00 2.85
597 627 9.503399 AAACGACCTACATAGAAGAAGAAAAAT 57.497 29.630 0.00 0.00 0.00 1.82
599 629 7.764901 ACGACCTACATAGAAGAAGAAAAATCC 59.235 37.037 0.00 0.00 0.00 3.01
622 652 8.852671 TCCAACCATCCAAATCCTATAAAATT 57.147 30.769 0.00 0.00 0.00 1.82
623 653 9.944079 TCCAACCATCCAAATCCTATAAAATTA 57.056 29.630 0.00 0.00 0.00 1.40
675 705 3.503363 ACAAGTGGAGATTGACGTACGTA 59.497 43.478 22.87 7.19 0.00 3.57
691 721 7.042590 TGACGTACGTACTTGTCATTTCAAAAT 60.043 33.333 22.87 0.00 36.50 1.82
705 735 9.410556 GTCATTTCAAAATATGCAGTAACAAGT 57.589 29.630 0.00 0.00 0.00 3.16
752 783 8.321353 TCTCTGTATTTTACACATCACTTGGAT 58.679 33.333 0.00 0.00 33.68 3.41
757 788 6.509418 TTTTACACATCACTTGGATAAGCC 57.491 37.500 0.00 0.00 37.43 4.35
767 913 4.608948 CTTGGATAAGCCTAGTCCGATT 57.391 45.455 0.00 0.00 35.15 3.34
768 914 4.561105 CTTGGATAAGCCTAGTCCGATTC 58.439 47.826 0.00 0.00 35.15 2.52
781 927 3.572255 AGTCCGATTCTTCTGCTATCTCC 59.428 47.826 0.00 0.00 0.00 3.71
782 928 2.894126 TCCGATTCTTCTGCTATCTCCC 59.106 50.000 0.00 0.00 0.00 4.30
785 931 3.365868 CGATTCTTCTGCTATCTCCCTCG 60.366 52.174 0.00 0.00 0.00 4.63
787 933 0.316841 CTTCTGCTATCTCCCTCGGC 59.683 60.000 0.00 0.00 0.00 5.54
788 934 0.397114 TTCTGCTATCTCCCTCGGCA 60.397 55.000 0.00 0.00 0.00 5.69
789 935 1.664873 CTGCTATCTCCCTCGGCAG 59.335 63.158 0.00 0.00 43.03 4.85
790 936 1.075970 TGCTATCTCCCTCGGCAGT 60.076 57.895 0.00 0.00 0.00 4.40
791 937 1.109920 TGCTATCTCCCTCGGCAGTC 61.110 60.000 0.00 0.00 0.00 3.51
795 941 0.692419 ATCTCCCTCGGCAGTCCATT 60.692 55.000 0.00 0.00 0.00 3.16
796 942 0.909610 TCTCCCTCGGCAGTCCATTT 60.910 55.000 0.00 0.00 0.00 2.32
797 943 0.035056 CTCCCTCGGCAGTCCATTTT 60.035 55.000 0.00 0.00 0.00 1.82
798 944 0.035439 TCCCTCGGCAGTCCATTTTC 60.035 55.000 0.00 0.00 0.00 2.29
799 945 1.032114 CCCTCGGCAGTCCATTTTCC 61.032 60.000 0.00 0.00 0.00 3.13
802 948 2.052104 CGGCAGTCCATTTTCCCCC 61.052 63.158 0.00 0.00 0.00 5.40
803 949 2.052104 GGCAGTCCATTTTCCCCCG 61.052 63.158 0.00 0.00 0.00 5.73
804 950 2.710902 GCAGTCCATTTTCCCCCGC 61.711 63.158 0.00 0.00 0.00 6.13
825 972 2.124151 CCCGGGCAAATCTCCCTG 60.124 66.667 8.08 0.00 41.69 4.45
828 975 1.678635 CGGGCAAATCTCCCTGCAA 60.679 57.895 0.00 0.00 41.69 4.08
842 990 2.203972 CTGCAACAATCCCTGCACCG 62.204 60.000 0.00 0.00 43.44 4.94
998 1146 4.400109 GCGTGACCTGCTCGACGA 62.400 66.667 0.00 0.00 35.64 4.20
1336 1484 0.453950 CAACGTCGTCTCCTACACCG 60.454 60.000 0.00 0.00 0.00 4.94
1419 1567 0.036388 TGCCGGAGAAGAATGTGGTC 60.036 55.000 5.05 0.00 0.00 4.02
1616 1764 1.888018 CCATCAAGCACTTGGGCAG 59.112 57.895 10.35 0.00 40.78 4.85
1650 1798 0.888619 TCGGCAATTCTCTCGTCAGT 59.111 50.000 0.00 0.00 0.00 3.41
1668 1816 3.266686 TTGCTATGCCAGGTGCGGT 62.267 57.895 0.00 0.00 45.60 5.68
1709 1857 1.197721 GGTCTTCACAAACATGGAGCG 59.802 52.381 0.00 0.00 0.00 5.03
1743 1891 0.534412 CCTGGAACGCTCTGATCTGT 59.466 55.000 0.00 0.00 0.00 3.41
1752 1900 1.139654 GCTCTGATCTGTGGGTATGCA 59.860 52.381 0.00 0.00 0.00 3.96
1956 2104 2.916111 CATTACGCTTGTGTTGTGGAC 58.084 47.619 0.00 0.00 0.00 4.02
1960 2108 1.507141 CGCTTGTGTTGTGGACCTCC 61.507 60.000 0.00 0.00 0.00 4.30
1962 2110 1.884235 CTTGTGTTGTGGACCTCCTC 58.116 55.000 0.00 0.00 36.82 3.71
2013 2161 1.348036 AGGTTTCTTGAGGACCTTCCG 59.652 52.381 0.00 0.00 40.83 4.30
2124 2272 4.025396 CGTATTCATGCACTTGATCCAGAC 60.025 45.833 0.00 0.00 0.00 3.51
2179 2327 0.538057 TTCTGCAGTTGGAAGCTGGG 60.538 55.000 14.67 0.00 34.73 4.45
2538 2686 7.448777 TCATCACTCATCAGGTTAGGTAGATAC 59.551 40.741 0.00 0.00 0.00 2.24
2539 2687 6.669631 TCACTCATCAGGTTAGGTAGATACA 58.330 40.000 0.00 0.00 0.00 2.29
2543 2691 8.670490 ACTCATCAGGTTAGGTAGATACAGATA 58.330 37.037 0.00 0.00 0.00 1.98
2558 2707 8.934507 AGATACAGATAGACTTTAACTTGTGC 57.065 34.615 0.00 0.00 0.00 4.57
2578 2727 1.271102 CGGTAGCAGGAGAATAGGAGC 59.729 57.143 0.00 0.00 0.00 4.70
2605 2754 3.325870 CTGATAAGACCAACAGCGAACA 58.674 45.455 0.00 0.00 0.00 3.18
2618 2767 2.609825 CGAACAGCAACTGCAGAGT 58.390 52.632 23.35 4.56 45.16 3.24
2620 2769 2.341257 CGAACAGCAACTGCAGAGTAT 58.659 47.619 23.35 0.01 45.16 2.12
2671 2830 1.547372 GCAGAGGATGGTGTTGCAAAT 59.453 47.619 0.00 0.00 34.99 2.32
2672 2831 2.754552 GCAGAGGATGGTGTTGCAAATA 59.245 45.455 0.00 0.00 34.99 1.40
2921 3120 5.467399 TGGGTTCGATTGTGTAAACAGTTAG 59.533 40.000 0.00 0.00 0.00 2.34
2922 3121 5.106830 GGGTTCGATTGTGTAAACAGTTAGG 60.107 44.000 0.00 0.00 0.00 2.69
2923 3122 5.697633 GGTTCGATTGTGTAAACAGTTAGGA 59.302 40.000 0.00 0.00 0.00 2.94
2924 3123 6.128634 GGTTCGATTGTGTAAACAGTTAGGAG 60.129 42.308 0.00 0.00 0.00 3.69
2925 3124 6.092955 TCGATTGTGTAAACAGTTAGGAGT 57.907 37.500 0.00 0.00 0.00 3.85
2926 3125 7.218228 TCGATTGTGTAAACAGTTAGGAGTA 57.782 36.000 0.00 0.00 0.00 2.59
2937 3136 8.474710 AAACAGTTAGGAGTACTAGAAAGACA 57.525 34.615 0.00 0.00 32.16 3.41
3078 3637 8.747538 AAGTCATGTACCCCTTTGTATTTATC 57.252 34.615 0.00 0.00 0.00 1.75
3079 3638 7.287810 AGTCATGTACCCCTTTGTATTTATCC 58.712 38.462 0.00 0.00 0.00 2.59
3080 3639 6.489022 GTCATGTACCCCTTTGTATTTATCCC 59.511 42.308 0.00 0.00 0.00 3.85
3081 3640 5.038651 TGTACCCCTTTGTATTTATCCCG 57.961 43.478 0.00 0.00 0.00 5.14
3083 3642 4.596354 ACCCCTTTGTATTTATCCCGTT 57.404 40.909 0.00 0.00 0.00 4.44
3084 3643 4.274978 ACCCCTTTGTATTTATCCCGTTG 58.725 43.478 0.00 0.00 0.00 4.10
3086 3645 5.044993 ACCCCTTTGTATTTATCCCGTTGTA 60.045 40.000 0.00 0.00 0.00 2.41
3087 3646 6.066032 CCCCTTTGTATTTATCCCGTTGTAT 58.934 40.000 0.00 0.00 0.00 2.29
3090 3649 8.780249 CCCTTTGTATTTATCCCGTTGTATAAG 58.220 37.037 0.00 0.00 0.00 1.73
3092 3651 8.680039 TTTGTATTTATCCCGTTGTATAAGGG 57.320 34.615 4.10 4.10 46.40 3.95
3109 3668 3.018423 AGGGGTTTCCTGCATATGTTC 57.982 47.619 4.29 0.00 46.07 3.18
3110 3669 2.031870 GGGGTTTCCTGCATATGTTCC 58.968 52.381 4.29 0.00 0.00 3.62
3113 3672 3.088532 GGTTTCCTGCATATGTTCCACA 58.911 45.455 4.29 0.00 0.00 4.17
3114 3673 3.119495 GGTTTCCTGCATATGTTCCACAC 60.119 47.826 4.29 0.00 0.00 3.82
3115 3674 2.418368 TCCTGCATATGTTCCACACC 57.582 50.000 4.29 0.00 0.00 4.16
3116 3675 1.915489 TCCTGCATATGTTCCACACCT 59.085 47.619 4.29 0.00 0.00 4.00
3117 3676 2.019249 CCTGCATATGTTCCACACCTG 58.981 52.381 4.29 0.00 0.00 4.00
3118 3677 2.618816 CCTGCATATGTTCCACACCTGT 60.619 50.000 4.29 0.00 0.00 4.00
3119 3678 3.370421 CCTGCATATGTTCCACACCTGTA 60.370 47.826 4.29 0.00 0.00 2.74
3120 3679 3.605634 TGCATATGTTCCACACCTGTAC 58.394 45.455 4.29 0.00 0.00 2.90
3121 3680 3.008485 TGCATATGTTCCACACCTGTACA 59.992 43.478 4.29 0.00 0.00 2.90
3122 3681 4.199310 GCATATGTTCCACACCTGTACAT 58.801 43.478 4.29 0.00 34.18 2.29
3123 3682 4.035558 GCATATGTTCCACACCTGTACATG 59.964 45.833 4.29 0.00 32.23 3.21
3125 3684 4.901197 ATGTTCCACACCTGTACATGTA 57.099 40.909 0.08 0.08 0.00 2.29
3126 3685 4.901197 TGTTCCACACCTGTACATGTAT 57.099 40.909 9.18 0.00 0.00 2.29
3128 3687 6.553953 TGTTCCACACCTGTACATGTATAT 57.446 37.500 9.18 0.00 0.00 0.86
3129 3688 7.663043 TGTTCCACACCTGTACATGTATATA 57.337 36.000 9.18 0.00 0.00 0.86
3130 3689 8.257602 TGTTCCACACCTGTACATGTATATAT 57.742 34.615 9.18 0.00 0.00 0.86
3134 3693 8.899771 TCCACACCTGTACATGTATATATATCG 58.100 37.037 9.18 0.00 0.00 2.92
3137 3696 7.145985 CACCTGTACATGTATATATATCGGCC 58.854 42.308 9.18 0.00 0.00 6.13
3138 3697 7.014326 CACCTGTACATGTATATATATCGGCCT 59.986 40.741 9.18 0.00 0.00 5.19
3140 3699 9.244292 CCTGTACATGTATATATATCGGCCTAT 57.756 37.037 9.18 0.00 0.00 2.57
3142 3701 9.020731 TGTACATGTATATATATCGGCCTATGG 57.979 37.037 9.18 0.00 0.00 2.74
3154 3713 2.907458 GCCTATGGCCTTATGGGAAT 57.093 50.000 9.43 0.00 44.06 3.01
3156 3715 3.621558 GCCTATGGCCTTATGGGAATAC 58.378 50.000 9.43 0.00 44.06 1.89
3157 3716 3.010138 GCCTATGGCCTTATGGGAATACA 59.990 47.826 9.43 0.00 44.06 2.29
3158 3717 4.508405 GCCTATGGCCTTATGGGAATACAA 60.508 45.833 9.43 0.00 44.06 2.41
3160 3719 4.814224 ATGGCCTTATGGGAATACAAGT 57.186 40.909 3.32 0.00 37.23 3.16
3161 3720 4.601406 TGGCCTTATGGGAATACAAGTT 57.399 40.909 3.32 0.00 37.23 2.66
3164 3723 3.699038 GCCTTATGGGAATACAAGTTGCA 59.301 43.478 1.81 0.00 37.23 4.08
3166 3725 5.534654 GCCTTATGGGAATACAAGTTGCATA 59.465 40.000 1.81 0.00 37.23 3.14
3167 3726 6.209391 GCCTTATGGGAATACAAGTTGCATAT 59.791 38.462 1.81 0.00 37.23 1.78
3168 3727 7.255942 GCCTTATGGGAATACAAGTTGCATATT 60.256 37.037 1.81 0.58 37.23 1.28
3171 3730 6.463995 TGGGAATACAAGTTGCATATTTCC 57.536 37.500 13.31 13.31 35.32 3.13
3173 3732 7.350382 TGGGAATACAAGTTGCATATTTCCTA 58.650 34.615 18.04 11.95 35.65 2.94
3175 3734 8.135529 GGGAATACAAGTTGCATATTTCCTAAC 58.864 37.037 13.07 0.00 32.93 2.34
3179 3738 6.866480 ACAAGTTGCATATTTCCTAACATGG 58.134 36.000 1.81 0.00 0.00 3.66
3180 3739 6.437162 ACAAGTTGCATATTTCCTAACATGGT 59.563 34.615 1.81 0.00 0.00 3.55
3182 3741 8.632679 CAAGTTGCATATTTCCTAACATGGTAT 58.367 33.333 0.00 0.00 0.00 2.73
3183 3742 8.766994 AGTTGCATATTTCCTAACATGGTATT 57.233 30.769 0.00 0.00 0.00 1.89
3184 3743 9.860650 AGTTGCATATTTCCTAACATGGTATTA 57.139 29.630 0.00 0.00 0.00 0.98
3189 3748 9.167311 CATATTTCCTAACATGGTATTAGAGCC 57.833 37.037 0.00 0.00 32.31 4.70
3190 3749 6.824958 TTTCCTAACATGGTATTAGAGCCT 57.175 37.500 0.00 0.00 32.31 4.58
3191 3750 6.824958 TTCCTAACATGGTATTAGAGCCTT 57.175 37.500 0.00 0.00 32.31 4.35
3192 3751 7.924358 TTCCTAACATGGTATTAGAGCCTTA 57.076 36.000 0.00 0.00 32.31 2.69
3195 3754 5.568620 AACATGGTATTAGAGCCTTAGGG 57.431 43.478 0.00 0.00 0.00 3.53
3196 3755 4.567857 ACATGGTATTAGAGCCTTAGGGT 58.432 43.478 1.19 1.19 35.46 4.34
3197 3756 4.975794 ACATGGTATTAGAGCCTTAGGGTT 59.024 41.667 3.86 0.00 31.55 4.11
3198 3757 5.432060 ACATGGTATTAGAGCCTTAGGGTTT 59.568 40.000 3.86 0.76 31.55 3.27
3199 3758 6.069029 ACATGGTATTAGAGCCTTAGGGTTTT 60.069 38.462 3.86 0.00 31.55 2.43
3200 3759 6.397217 TGGTATTAGAGCCTTAGGGTTTTT 57.603 37.500 3.86 0.00 31.55 1.94
3216 3775 4.615834 TTTTCCCGCACGCGCAAC 62.616 61.111 5.73 0.00 38.40 4.17
3233 3792 0.320374 AACTCGTGCTTTCCGATCCA 59.680 50.000 0.00 0.00 33.27 3.41
3234 3793 0.320374 ACTCGTGCTTTCCGATCCAA 59.680 50.000 0.00 0.00 33.27 3.53
3235 3794 1.066143 ACTCGTGCTTTCCGATCCAAT 60.066 47.619 0.00 0.00 33.27 3.16
3236 3795 1.594862 CTCGTGCTTTCCGATCCAATC 59.405 52.381 0.00 0.00 33.27 2.67
3237 3796 1.207089 TCGTGCTTTCCGATCCAATCT 59.793 47.619 0.00 0.00 0.00 2.40
3238 3797 1.594862 CGTGCTTTCCGATCCAATCTC 59.405 52.381 0.00 0.00 0.00 2.75
3240 3799 3.209410 GTGCTTTCCGATCCAATCTCAT 58.791 45.455 0.00 0.00 0.00 2.90
3241 3800 3.249559 GTGCTTTCCGATCCAATCTCATC 59.750 47.826 0.00 0.00 0.00 2.92
3242 3801 3.135348 TGCTTTCCGATCCAATCTCATCT 59.865 43.478 0.00 0.00 0.00 2.90
3244 3803 3.650070 TTCCGATCCAATCTCATCTCG 57.350 47.619 0.00 0.00 0.00 4.04
3245 3804 1.270826 TCCGATCCAATCTCATCTCGC 59.729 52.381 0.00 0.00 0.00 5.03
3247 3806 2.057316 CGATCCAATCTCATCTCGCAC 58.943 52.381 0.00 0.00 0.00 5.34
3248 3807 2.057316 GATCCAATCTCATCTCGCACG 58.943 52.381 0.00 0.00 0.00 5.34
3249 3808 0.528466 TCCAATCTCATCTCGCACGC 60.528 55.000 0.00 0.00 0.00 5.34
3250 3809 1.493950 CCAATCTCATCTCGCACGCC 61.494 60.000 0.00 0.00 0.00 5.68
3251 3810 1.589993 AATCTCATCTCGCACGCCG 60.590 57.895 0.00 0.00 38.61 6.46
3252 3811 4.854784 TCTCATCTCGCACGCCGC 62.855 66.667 0.00 0.00 36.73 6.53
3253 3812 4.862092 CTCATCTCGCACGCCGCT 62.862 66.667 0.00 0.00 39.08 5.52
3262 3821 4.749310 CACGCCGCTGCCTTCTCT 62.749 66.667 0.00 0.00 0.00 3.10
3263 3822 4.443266 ACGCCGCTGCCTTCTCTC 62.443 66.667 0.00 0.00 0.00 3.20
3264 3823 4.441695 CGCCGCTGCCTTCTCTCA 62.442 66.667 0.00 0.00 0.00 3.27
3265 3824 2.817396 GCCGCTGCCTTCTCTCAC 60.817 66.667 0.00 0.00 0.00 3.51
3266 3825 2.125350 CCGCTGCCTTCTCTCACC 60.125 66.667 0.00 0.00 0.00 4.02
3268 3827 2.125350 GCTGCCTTCTCTCACCGG 60.125 66.667 0.00 0.00 0.00 5.28
3270 3829 3.672295 CTGCCTTCTCTCACCGGCC 62.672 68.421 0.00 0.00 41.80 6.13
3271 3830 4.821589 GCCTTCTCTCACCGGCCG 62.822 72.222 21.04 21.04 36.56 6.13
3273 3832 4.821589 CTTCTCTCACCGGCCGGC 62.822 72.222 43.58 21.18 39.32 6.13
3290 3849 3.691342 CCGTCGCTGTCTTCCCCA 61.691 66.667 0.00 0.00 0.00 4.96
3291 3850 2.432628 CGTCGCTGTCTTCCCCAC 60.433 66.667 0.00 0.00 0.00 4.61
3292 3851 2.047179 GTCGCTGTCTTCCCCACC 60.047 66.667 0.00 0.00 0.00 4.61
3295 3854 2.352805 GCTGTCTTCCCCACCCAG 59.647 66.667 0.00 0.00 0.00 4.45
3296 3855 3.081554 CTGTCTTCCCCACCCAGG 58.918 66.667 0.00 0.00 37.03 4.45
3297 3856 1.847968 CTGTCTTCCCCACCCAGGT 60.848 63.158 0.00 0.00 34.66 4.00
3298 3857 2.129555 CTGTCTTCCCCACCCAGGTG 62.130 65.000 10.00 10.00 45.02 4.00
3299 3858 3.256960 TCTTCCCCACCCAGGTGC 61.257 66.667 11.52 0.00 44.16 5.01
3301 3860 4.938756 TTCCCCACCCAGGTGCCT 62.939 66.667 11.52 0.00 44.16 4.75
3305 3864 2.034687 CCACCCAGGTGCCTCTTG 59.965 66.667 11.52 0.00 44.16 3.02
3306 3865 2.674380 CACCCAGGTGCCTCTTGC 60.674 66.667 3.41 0.00 39.39 4.01
3327 3886 3.902318 GCTGCTGCTCTTCCTTCC 58.098 61.111 8.53 0.00 36.03 3.46
3329 3888 0.607489 GCTGCTGCTCTTCCTTCCAA 60.607 55.000 8.53 0.00 36.03 3.53
3330 3889 1.163554 CTGCTGCTCTTCCTTCCAAC 58.836 55.000 0.00 0.00 0.00 3.77
3331 3890 0.250901 TGCTGCTCTTCCTTCCAACC 60.251 55.000 0.00 0.00 0.00 3.77
3332 3891 0.037447 GCTGCTCTTCCTTCCAACCT 59.963 55.000 0.00 0.00 0.00 3.50
3333 3892 1.818642 CTGCTCTTCCTTCCAACCTG 58.181 55.000 0.00 0.00 0.00 4.00
3334 3893 0.250901 TGCTCTTCCTTCCAACCTGC 60.251 55.000 0.00 0.00 0.00 4.85
3335 3894 0.037447 GCTCTTCCTTCCAACCTGCT 59.963 55.000 0.00 0.00 0.00 4.24
3337 3896 0.401738 TCTTCCTTCCAACCTGCTGG 59.598 55.000 8.29 8.29 37.87 4.85
3338 3897 0.610232 CTTCCTTCCAACCTGCTGGG 60.610 60.000 14.82 4.64 37.06 4.45
3339 3898 2.677875 CCTTCCAACCTGCTGGGC 60.678 66.667 14.82 0.00 39.10 5.36
3340 3899 2.437897 CTTCCAACCTGCTGGGCT 59.562 61.111 14.82 0.00 39.10 5.19
3341 3900 1.975407 CTTCCAACCTGCTGGGCTG 60.975 63.158 14.82 10.35 39.10 4.85
3342 3901 4.666253 TCCAACCTGCTGGGCTGC 62.666 66.667 14.82 0.00 39.10 5.25
3343 3902 4.673375 CCAACCTGCTGGGCTGCT 62.673 66.667 14.82 0.00 39.10 4.24
3344 3903 3.371063 CAACCTGCTGGGCTGCTG 61.371 66.667 14.82 0.00 39.10 4.41
3348 3907 3.518998 CTGCTGGGCTGCTGCATC 61.519 66.667 17.89 9.29 41.91 3.91
3351 3910 3.138798 CTGGGCTGCTGCATCCAC 61.139 66.667 22.57 13.00 41.91 4.02
3352 3911 4.746309 TGGGCTGCTGCATCCACC 62.746 66.667 22.57 13.44 41.91 4.61
3353 3912 4.746309 GGGCTGCTGCATCCACCA 62.746 66.667 22.57 0.00 41.91 4.17
3354 3913 3.138798 GGCTGCTGCATCCACCAG 61.139 66.667 17.11 0.00 41.91 4.00
3355 3914 3.138798 GCTGCTGCATCCACCAGG 61.139 66.667 11.11 0.00 39.41 4.45
3356 3915 3.138798 CTGCTGCATCCACCAGGC 61.139 66.667 1.31 0.00 33.74 4.85
3357 3916 3.931190 CTGCTGCATCCACCAGGCA 62.931 63.158 1.31 0.00 35.96 4.75
3358 3917 3.446570 GCTGCATCCACCAGGCAC 61.447 66.667 0.00 0.00 33.34 5.01
3359 3918 3.129502 CTGCATCCACCAGGCACG 61.130 66.667 0.00 0.00 33.34 5.34
3360 3919 3.907260 CTGCATCCACCAGGCACGT 62.907 63.158 0.00 0.00 33.34 4.49
3361 3920 3.434319 GCATCCACCAGGCACGTG 61.434 66.667 12.28 12.28 33.74 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.456280 CTGCTCTCATAAGCCTTCTGAC 58.544 50.000 0.00 0.00 41.77 3.51
49 50 7.884877 ACAAATGAATACTCTCATTCACCAGAA 59.115 33.333 0.90 0.00 45.22 3.02
60 61 7.875971 AGTTCCACAAACAAATGAATACTCTC 58.124 34.615 0.00 0.00 40.56 3.20
62 63 6.797033 CGAGTTCCACAAACAAATGAATACTC 59.203 38.462 0.00 0.00 40.56 2.59
74 75 2.067013 GCCTAGTCGAGTTCCACAAAC 58.933 52.381 0.00 0.00 38.21 2.93
75 76 1.689813 TGCCTAGTCGAGTTCCACAAA 59.310 47.619 0.00 0.00 0.00 2.83
78 79 1.471676 CCATGCCTAGTCGAGTTCCAC 60.472 57.143 0.00 0.00 0.00 4.02
79 80 0.824109 CCATGCCTAGTCGAGTTCCA 59.176 55.000 0.00 0.00 0.00 3.53
80 81 0.105039 CCCATGCCTAGTCGAGTTCC 59.895 60.000 0.00 0.00 0.00 3.62
82 83 1.972660 GCCCCATGCCTAGTCGAGTT 61.973 60.000 0.00 0.00 0.00 3.01
83 84 2.435693 GCCCCATGCCTAGTCGAGT 61.436 63.158 0.00 0.00 0.00 4.18
84 85 1.690219 AAGCCCCATGCCTAGTCGAG 61.690 60.000 0.00 0.00 42.71 4.04
85 86 1.689233 AAGCCCCATGCCTAGTCGA 60.689 57.895 0.00 0.00 42.71 4.20
86 87 1.524621 CAAGCCCCATGCCTAGTCG 60.525 63.158 0.00 0.00 42.71 4.18
87 88 0.464554 GACAAGCCCCATGCCTAGTC 60.465 60.000 0.00 0.00 42.71 2.59
88 89 1.207488 TGACAAGCCCCATGCCTAGT 61.207 55.000 0.00 0.00 42.71 2.57
89 90 0.749454 GTGACAAGCCCCATGCCTAG 60.749 60.000 0.00 0.00 42.71 3.02
90 91 1.302949 GTGACAAGCCCCATGCCTA 59.697 57.895 0.00 0.00 42.71 3.93
92 93 3.443045 CGTGACAAGCCCCATGCC 61.443 66.667 0.00 0.00 42.71 4.40
93 94 4.120331 GCGTGACAAGCCCCATGC 62.120 66.667 1.44 0.00 38.01 4.06
94 95 2.672651 TGCGTGACAAGCCCCATG 60.673 61.111 10.95 0.00 0.00 3.66
98 99 2.743928 CTCCTGCGTGACAAGCCC 60.744 66.667 10.95 0.00 0.00 5.19
108 109 1.135575 GCTGACAAAAATCCTCCTGCG 60.136 52.381 0.00 0.00 0.00 5.18
175 178 6.914259 TCGATCATACATCTCTGTATTCACC 58.086 40.000 0.00 0.00 44.42 4.02
177 180 8.031277 CCATTCGATCATACATCTCTGTATTCA 58.969 37.037 0.00 0.00 44.42 2.57
197 200 2.901840 CCACCGCATCCCCATTCG 60.902 66.667 0.00 0.00 0.00 3.34
229 243 6.068010 AGGAAAAACCAACATATCACTGACA 58.932 36.000 0.00 0.00 42.04 3.58
234 248 7.489113 CAGCAATAGGAAAAACCAACATATCAC 59.511 37.037 0.00 0.00 42.04 3.06
239 253 6.014327 ACATCAGCAATAGGAAAAACCAACAT 60.014 34.615 0.00 0.00 42.04 2.71
266 282 7.117236 CCAGGTGATTCTTCAAACATTTCATTG 59.883 37.037 0.00 0.00 32.48 2.82
267 283 7.156673 CCAGGTGATTCTTCAAACATTTCATT 58.843 34.615 0.00 0.00 32.48 2.57
295 312 2.686235 CATGAGATCCAGGCTCGAATC 58.314 52.381 0.00 0.00 35.15 2.52
411 441 3.264947 GGGAAAAGAAGGCATTTGCATC 58.735 45.455 4.74 2.48 44.36 3.91
412 442 2.638855 TGGGAAAAGAAGGCATTTGCAT 59.361 40.909 4.74 0.00 44.36 3.96
463 493 8.983789 TCCACCATAACAGAAATATGTACAGTA 58.016 33.333 0.33 0.00 31.70 2.74
464 494 7.857456 TCCACCATAACAGAAATATGTACAGT 58.143 34.615 0.33 0.00 31.70 3.55
465 495 8.731275 TTCCACCATAACAGAAATATGTACAG 57.269 34.615 0.33 0.00 31.70 2.74
466 496 9.693739 AATTCCACCATAACAGAAATATGTACA 57.306 29.630 0.00 0.00 31.70 2.90
467 497 9.950680 CAATTCCACCATAACAGAAATATGTAC 57.049 33.333 0.00 0.00 31.70 2.90
483 513 5.080337 TGTTAAATGGTAGCAATTCCACCA 58.920 37.500 0.00 5.11 45.96 4.17
547 577 9.919416 TTTGGTTCATAGAATGGAATCATTAGA 57.081 29.630 0.00 0.00 43.08 2.10
579 609 9.753674 ATGGTTGGATTTTTCTTCTTCTATGTA 57.246 29.630 0.00 0.00 0.00 2.29
588 618 6.595326 GGATTTGGATGGTTGGATTTTTCTTC 59.405 38.462 0.00 0.00 0.00 2.87
591 621 6.053632 AGGATTTGGATGGTTGGATTTTTC 57.946 37.500 0.00 0.00 0.00 2.29
597 627 8.852671 AATTTTATAGGATTTGGATGGTTGGA 57.147 30.769 0.00 0.00 0.00 3.53
622 652 8.400947 GCTCAAGTGCTTATCTGATTCAAAATA 58.599 33.333 0.00 0.00 0.00 1.40
623 653 7.122353 AGCTCAAGTGCTTATCTGATTCAAAAT 59.878 33.333 0.00 0.00 40.93 1.82
624 654 6.432162 AGCTCAAGTGCTTATCTGATTCAAAA 59.568 34.615 0.00 0.00 40.93 2.44
634 664 3.254060 TGTTCGAGCTCAAGTGCTTATC 58.746 45.455 15.40 0.00 44.17 1.75
675 705 9.410556 GTTACTGCATATTTTGAAATGACAAGT 57.589 29.630 0.00 2.07 0.00 3.16
705 735 7.335924 CAGAGACGGGGTTTGAAAATTATAGAA 59.664 37.037 0.00 0.00 0.00 2.10
752 783 3.068307 GCAGAAGAATCGGACTAGGCTTA 59.932 47.826 0.00 0.00 0.00 3.09
755 786 1.410882 AGCAGAAGAATCGGACTAGGC 59.589 52.381 0.00 0.00 0.00 3.93
757 788 5.106317 GGAGATAGCAGAAGAATCGGACTAG 60.106 48.000 0.00 0.00 0.00 2.57
765 911 2.896685 CCGAGGGAGATAGCAGAAGAAT 59.103 50.000 0.00 0.00 0.00 2.40
766 912 2.311463 CCGAGGGAGATAGCAGAAGAA 58.689 52.381 0.00 0.00 0.00 2.52
767 913 1.988293 CCGAGGGAGATAGCAGAAGA 58.012 55.000 0.00 0.00 0.00 2.87
768 914 0.316841 GCCGAGGGAGATAGCAGAAG 59.683 60.000 0.00 0.00 0.00 2.85
781 927 1.032114 GGGAAAATGGACTGCCGAGG 61.032 60.000 0.00 0.00 36.79 4.63
782 928 1.032114 GGGGAAAATGGACTGCCGAG 61.032 60.000 0.00 0.00 36.79 4.63
785 931 2.052104 CGGGGGAAAATGGACTGCC 61.052 63.158 0.00 0.00 0.00 4.85
787 933 2.052104 GGCGGGGGAAAATGGACTG 61.052 63.158 0.00 0.00 0.00 3.51
788 934 2.359011 GGCGGGGGAAAATGGACT 59.641 61.111 0.00 0.00 0.00 3.85
789 935 2.036572 TGGCGGGGGAAAATGGAC 59.963 61.111 0.00 0.00 0.00 4.02
790 936 2.036572 GTGGCGGGGGAAAATGGA 59.963 61.111 0.00 0.00 0.00 3.41
791 937 3.074369 GGTGGCGGGGGAAAATGG 61.074 66.667 0.00 0.00 0.00 3.16
804 950 2.440247 GAGATTTGCCCGGGGTGG 60.440 66.667 25.28 0.00 37.55 4.61
825 972 2.568090 CGGTGCAGGGATTGTTGC 59.432 61.111 0.00 0.00 40.67 4.17
828 975 3.545124 TTCGCGGTGCAGGGATTGT 62.545 57.895 6.13 0.00 33.07 2.71
985 1133 1.696832 GGCATTTCGTCGAGCAGGTC 61.697 60.000 7.20 0.00 0.00 3.85
1114 1262 1.782028 AAGGTGAACTCGTTTGGCGC 61.782 55.000 0.00 0.00 41.07 6.53
1220 1368 1.141881 CCCACGAAGACGATGGAGG 59.858 63.158 0.00 0.00 40.40 4.30
1419 1567 0.936764 CGATCATCGCGTTCCAGGAG 60.937 60.000 5.77 0.00 31.14 3.69
1578 1726 2.508891 CGACGCATGGACGCTTCTC 61.509 63.158 0.00 0.00 36.19 2.87
1650 1798 1.904990 TACCGCACCTGGCATAGCAA 61.905 55.000 0.00 0.00 45.17 3.91
1668 1816 0.321671 GCACACTGTCCTCCAAGCTA 59.678 55.000 0.00 0.00 0.00 3.32
1709 1857 1.909302 TCCAGGAGACCACATTCTTCC 59.091 52.381 0.00 0.00 0.00 3.46
1743 1891 2.042297 TCTCCCATTTTGTGCATACCCA 59.958 45.455 0.00 0.00 0.00 4.51
1752 1900 1.002857 CCTCCCCTCTCCCATTTTGT 58.997 55.000 0.00 0.00 0.00 2.83
1956 2104 0.390472 GTTTGGCACGAGAGAGGAGG 60.390 60.000 0.00 0.00 0.00 4.30
2013 2161 2.278330 CCCAAGGCCTGGCTCAAAC 61.278 63.158 19.68 0.61 44.90 2.93
2124 2272 5.655488 AGAAGGATGTATGAAGAAGTGTCG 58.345 41.667 0.00 0.00 0.00 4.35
2179 2327 2.159184 TCCTGATCATTGACGCACTCTC 60.159 50.000 0.00 0.00 0.00 3.20
2492 2640 6.753744 TGATGAACATGACTAATTGACTCTCG 59.246 38.462 0.00 0.00 0.00 4.04
2538 2686 4.929808 ACCGCACAAGTTAAAGTCTATCTG 59.070 41.667 0.00 0.00 0.00 2.90
2539 2687 5.148651 ACCGCACAAGTTAAAGTCTATCT 57.851 39.130 0.00 0.00 0.00 1.98
2543 2691 3.064931 GCTACCGCACAAGTTAAAGTCT 58.935 45.455 0.00 0.00 35.78 3.24
2557 2706 1.271102 CTCCTATTCTCCTGCTACCGC 59.729 57.143 0.00 0.00 0.00 5.68
2558 2707 1.271102 GCTCCTATTCTCCTGCTACCG 59.729 57.143 0.00 0.00 0.00 4.02
2605 2754 2.168106 CTCCAGATACTCTGCAGTTGCT 59.832 50.000 14.67 2.72 42.98 3.91
2696 2855 1.871126 GCACCCTGAAAGCCTTGAGC 61.871 60.000 0.00 0.00 44.25 4.26
2921 3120 3.429684 GCCAGCTGTCTTTCTAGTACTCC 60.430 52.174 13.81 0.00 0.00 3.85
2922 3121 3.429684 GGCCAGCTGTCTTTCTAGTACTC 60.430 52.174 13.81 0.00 0.00 2.59
2923 3122 2.498078 GGCCAGCTGTCTTTCTAGTACT 59.502 50.000 13.81 0.00 0.00 2.73
2924 3123 2.498078 AGGCCAGCTGTCTTTCTAGTAC 59.502 50.000 13.81 0.00 0.00 2.73
2925 3124 2.821437 AGGCCAGCTGTCTTTCTAGTA 58.179 47.619 13.81 0.00 0.00 1.82
2926 3125 1.650528 AGGCCAGCTGTCTTTCTAGT 58.349 50.000 13.81 0.00 0.00 2.57
2937 3136 4.666512 TCTAAGAATTCAAAAGGCCAGCT 58.333 39.130 5.01 0.00 0.00 4.24
3052 3611 9.841295 GATAAATACAAAGGGGTACATGACTTA 57.159 33.333 0.00 0.00 0.00 2.24
3053 3612 7.778382 GGATAAATACAAAGGGGTACATGACTT 59.222 37.037 0.00 0.00 0.00 3.01
3055 3614 6.489022 GGGATAAATACAAAGGGGTACATGAC 59.511 42.308 0.00 0.00 0.00 3.06
3056 3615 6.607019 GGGATAAATACAAAGGGGTACATGA 58.393 40.000 0.00 0.00 0.00 3.07
3057 3616 5.472137 CGGGATAAATACAAAGGGGTACATG 59.528 44.000 0.00 0.00 0.00 3.21
3062 3621 4.264038 ACAACGGGATAAATACAAAGGGGT 60.264 41.667 0.00 0.00 0.00 4.95
3063 3622 4.274978 ACAACGGGATAAATACAAAGGGG 58.725 43.478 0.00 0.00 0.00 4.79
3064 3623 8.680039 TTATACAACGGGATAAATACAAAGGG 57.320 34.615 0.00 0.00 0.00 3.95
3066 3625 8.780249 CCCTTATACAACGGGATAAATACAAAG 58.220 37.037 0.00 0.00 40.55 2.77
3067 3626 7.720515 CCCCTTATACAACGGGATAAATACAAA 59.279 37.037 0.00 0.00 40.55 2.83
3069 3628 6.329723 ACCCCTTATACAACGGGATAAATACA 59.670 38.462 0.00 0.00 40.55 2.29
3070 3629 6.772605 ACCCCTTATACAACGGGATAAATAC 58.227 40.000 0.00 0.00 40.55 1.89
3071 3630 7.391388 AACCCCTTATACAACGGGATAAATA 57.609 36.000 0.00 0.00 40.55 1.40
3072 3631 5.917545 ACCCCTTATACAACGGGATAAAT 57.082 39.130 0.00 0.00 40.55 1.40
3074 3633 5.397786 GGAAACCCCTTATACAACGGGATAA 60.398 44.000 0.00 0.00 40.55 1.75
3075 3634 4.102996 GGAAACCCCTTATACAACGGGATA 59.897 45.833 0.00 0.00 40.55 2.59
3077 3636 2.239402 GGAAACCCCTTATACAACGGGA 59.761 50.000 0.00 0.00 40.55 5.14
3078 3637 2.240414 AGGAAACCCCTTATACAACGGG 59.760 50.000 0.00 0.00 44.85 5.28
3079 3638 3.275999 CAGGAAACCCCTTATACAACGG 58.724 50.000 0.00 0.00 44.85 4.44
3080 3639 2.681344 GCAGGAAACCCCTTATACAACG 59.319 50.000 0.00 0.00 44.85 4.10
3081 3640 3.692690 TGCAGGAAACCCCTTATACAAC 58.307 45.455 0.00 0.00 44.85 3.32
3083 3642 5.133660 ACATATGCAGGAAACCCCTTATACA 59.866 40.000 1.58 0.00 44.85 2.29
3084 3643 5.631119 ACATATGCAGGAAACCCCTTATAC 58.369 41.667 1.58 0.00 44.85 1.47
3086 3645 4.814224 ACATATGCAGGAAACCCCTTAT 57.186 40.909 1.58 0.00 44.85 1.73
3087 3646 4.532834 GAACATATGCAGGAAACCCCTTA 58.467 43.478 1.58 0.00 44.85 2.69
3090 3649 2.031870 GGAACATATGCAGGAAACCCC 58.968 52.381 1.58 0.00 0.00 4.95
3092 3651 3.088532 TGTGGAACATATGCAGGAAACC 58.911 45.455 1.58 0.00 45.67 3.27
3108 3667 8.899771 CGATATATATACATGTACAGGTGTGGA 58.100 37.037 22.69 9.13 0.00 4.02
3109 3668 8.135529 CCGATATATATACATGTACAGGTGTGG 58.864 40.741 22.69 8.15 0.00 4.17
3110 3669 7.648112 GCCGATATATATACATGTACAGGTGTG 59.352 40.741 22.69 8.01 0.00 3.82
3113 3672 7.067421 AGGCCGATATATATACATGTACAGGT 58.933 38.462 18.23 18.23 0.00 4.00
3114 3673 7.526142 AGGCCGATATATATACATGTACAGG 57.474 40.000 7.96 5.87 0.00 4.00
3116 3675 9.020731 CCATAGGCCGATATATATACATGTACA 57.979 37.037 7.96 0.00 0.00 2.90
3117 3676 7.974501 GCCATAGGCCGATATATATACATGTAC 59.025 40.741 7.96 0.00 44.06 2.90
3118 3677 8.063200 GCCATAGGCCGATATATATACATGTA 57.937 38.462 8.27 8.27 44.06 2.29
3119 3678 6.936279 GCCATAGGCCGATATATATACATGT 58.064 40.000 2.69 2.69 44.06 3.21
3137 3696 5.880901 ACTTGTATTCCCATAAGGCCATAG 58.119 41.667 5.01 0.00 34.51 2.23
3138 3697 5.922960 ACTTGTATTCCCATAAGGCCATA 57.077 39.130 5.01 0.00 34.51 2.74
3140 3699 4.277476 CAACTTGTATTCCCATAAGGCCA 58.723 43.478 5.01 0.00 34.51 5.36
3141 3700 3.068165 GCAACTTGTATTCCCATAAGGCC 59.932 47.826 0.00 0.00 34.51 5.19
3142 3701 3.699038 TGCAACTTGTATTCCCATAAGGC 59.301 43.478 0.00 0.00 34.51 4.35
3143 3702 7.765695 ATATGCAACTTGTATTCCCATAAGG 57.234 36.000 0.00 0.00 0.00 2.69
3144 3703 9.683069 GAAATATGCAACTTGTATTCCCATAAG 57.317 33.333 0.00 0.00 0.00 1.73
3145 3704 8.637986 GGAAATATGCAACTTGTATTCCCATAA 58.362 33.333 0.00 0.00 0.00 1.90
3146 3705 8.004215 AGGAAATATGCAACTTGTATTCCCATA 58.996 33.333 0.00 0.00 0.00 2.74
3147 3706 6.840705 AGGAAATATGCAACTTGTATTCCCAT 59.159 34.615 0.00 0.00 0.00 4.00
3149 3708 6.715347 AGGAAATATGCAACTTGTATTCCC 57.285 37.500 0.00 0.00 0.00 3.97
3150 3709 8.682710 TGTTAGGAAATATGCAACTTGTATTCC 58.317 33.333 0.00 0.96 0.00 3.01
3153 3712 8.632679 CCATGTTAGGAAATATGCAACTTGTAT 58.367 33.333 0.00 0.00 33.98 2.29
3154 3713 7.613801 ACCATGTTAGGAAATATGCAACTTGTA 59.386 33.333 0.00 0.00 33.98 2.41
3156 3715 6.866480 ACCATGTTAGGAAATATGCAACTTG 58.134 36.000 0.00 0.00 33.98 3.16
3157 3716 8.766994 ATACCATGTTAGGAAATATGCAACTT 57.233 30.769 0.00 0.00 33.98 2.66
3158 3717 8.766994 AATACCATGTTAGGAAATATGCAACT 57.233 30.769 0.00 0.00 33.98 3.16
3161 3720 9.725019 CTCTAATACCATGTTAGGAAATATGCA 57.275 33.333 0.00 0.00 33.98 3.96
3164 3723 9.117223 AGGCTCTAATACCATGTTAGGAAATAT 57.883 33.333 0.00 0.00 31.59 1.28
3166 3725 7.394144 AGGCTCTAATACCATGTTAGGAAAT 57.606 36.000 0.00 0.00 31.59 2.17
3167 3726 6.824958 AGGCTCTAATACCATGTTAGGAAA 57.175 37.500 0.00 0.00 31.59 3.13
3168 3727 6.824958 AAGGCTCTAATACCATGTTAGGAA 57.175 37.500 0.00 0.00 31.59 3.36
3171 3730 6.270231 ACCCTAAGGCTCTAATACCATGTTAG 59.730 42.308 0.00 0.00 36.11 2.34
3173 3732 4.975794 ACCCTAAGGCTCTAATACCATGTT 59.024 41.667 0.00 0.00 36.11 2.71
3175 3734 5.568620 AACCCTAAGGCTCTAATACCATG 57.431 43.478 0.00 0.00 36.11 3.66
3177 3736 6.397217 AAAAACCCTAAGGCTCTAATACCA 57.603 37.500 0.00 0.00 36.11 3.25
3214 3773 0.320374 TGGATCGGAAAGCACGAGTT 59.680 50.000 0.00 0.00 44.24 3.01
3216 3775 1.594862 GATTGGATCGGAAAGCACGAG 59.405 52.381 0.00 0.00 44.24 4.18
3217 3776 1.207089 AGATTGGATCGGAAAGCACGA 59.793 47.619 0.00 0.00 45.19 4.35
3218 3777 1.594862 GAGATTGGATCGGAAAGCACG 59.405 52.381 0.00 0.00 0.00 5.34
3221 3780 3.737850 AGATGAGATTGGATCGGAAAGC 58.262 45.455 0.00 0.00 0.00 3.51
3222 3781 3.986572 CGAGATGAGATTGGATCGGAAAG 59.013 47.826 0.00 0.00 0.00 2.62
3223 3782 3.800261 GCGAGATGAGATTGGATCGGAAA 60.800 47.826 0.00 0.00 0.00 3.13
3226 3785 1.000171 TGCGAGATGAGATTGGATCGG 60.000 52.381 0.00 0.00 0.00 4.18
3227 3786 2.057316 GTGCGAGATGAGATTGGATCG 58.943 52.381 0.00 0.00 0.00 3.69
3229 3788 1.871408 GCGTGCGAGATGAGATTGGAT 60.871 52.381 0.00 0.00 0.00 3.41
3230 3789 0.528466 GCGTGCGAGATGAGATTGGA 60.528 55.000 0.00 0.00 0.00 3.53
3231 3790 1.493950 GGCGTGCGAGATGAGATTGG 61.494 60.000 0.00 0.00 0.00 3.16
3233 3792 1.589993 CGGCGTGCGAGATGAGATT 60.590 57.895 0.00 0.00 0.00 2.40
3234 3793 2.026734 CGGCGTGCGAGATGAGAT 59.973 61.111 0.00 0.00 0.00 2.75
3235 3794 4.854784 GCGGCGTGCGAGATGAGA 62.855 66.667 9.37 0.00 0.00 3.27
3245 3804 4.749310 AGAGAAGGCAGCGGCGTG 62.749 66.667 9.37 6.94 42.47 5.34
3247 3806 4.441695 TGAGAGAAGGCAGCGGCG 62.442 66.667 0.51 0.51 42.47 6.46
3248 3807 2.817396 GTGAGAGAAGGCAGCGGC 60.817 66.667 0.00 0.00 40.13 6.53
3249 3808 2.125350 GGTGAGAGAAGGCAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
3251 3810 2.125350 CCGGTGAGAGAAGGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
3256 3815 4.821589 GCCGGCCGGTGAGAGAAG 62.822 72.222 42.53 16.82 37.65 2.85
3273 3832 3.691342 TGGGGAAGACAGCGACGG 61.691 66.667 0.00 0.00 0.00 4.79
3274 3833 2.432628 GTGGGGAAGACAGCGACG 60.433 66.667 0.00 0.00 0.00 5.12
3275 3834 2.047179 GGTGGGGAAGACAGCGAC 60.047 66.667 0.00 0.00 0.00 5.19
3276 3835 3.319198 GGGTGGGGAAGACAGCGA 61.319 66.667 0.00 0.00 37.22 4.93
3277 3836 3.612247 CTGGGTGGGGAAGACAGCG 62.612 68.421 0.00 0.00 37.22 5.18
3278 3837 2.352805 CTGGGTGGGGAAGACAGC 59.647 66.667 0.00 0.00 35.71 4.40
3279 3838 1.847968 ACCTGGGTGGGGAAGACAG 60.848 63.158 0.00 0.00 41.11 3.51
3281 3840 2.757077 CACCTGGGTGGGGAAGAC 59.243 66.667 11.62 0.00 43.63 3.01
3282 3841 3.256960 GCACCTGGGTGGGGAAGA 61.257 66.667 19.69 0.00 43.63 2.87
3283 3842 4.366684 GGCACCTGGGTGGGGAAG 62.367 72.222 19.69 0.00 43.63 3.46
3284 3843 4.938756 AGGCACCTGGGTGGGGAA 62.939 66.667 19.69 0.00 43.63 3.97
3287 3846 3.260100 AAGAGGCACCTGGGTGGG 61.260 66.667 19.69 0.00 45.49 4.61
3288 3847 2.034687 CAAGAGGCACCTGGGTGG 59.965 66.667 19.69 3.86 45.49 4.61
3298 3857 1.080705 CAGCAGCTTTGCAAGAGGC 60.081 57.895 0.00 6.14 45.13 4.70
3299 3858 1.080705 GCAGCAGCTTTGCAAGAGG 60.081 57.895 13.66 0.00 41.17 3.69
3310 3869 0.607489 TTGGAAGGAAGAGCAGCAGC 60.607 55.000 0.00 0.00 42.56 5.25
3311 3870 1.163554 GTTGGAAGGAAGAGCAGCAG 58.836 55.000 0.00 0.00 0.00 4.24
3312 3871 0.250901 GGTTGGAAGGAAGAGCAGCA 60.251 55.000 0.00 0.00 0.00 4.41
3313 3872 0.037447 AGGTTGGAAGGAAGAGCAGC 59.963 55.000 0.00 0.00 0.00 5.25
3314 3873 1.818642 CAGGTTGGAAGGAAGAGCAG 58.181 55.000 0.00 0.00 0.00 4.24
3317 3876 1.612726 CCAGCAGGTTGGAAGGAAGAG 60.613 57.143 0.00 0.00 40.87 2.85
3318 3877 0.401738 CCAGCAGGTTGGAAGGAAGA 59.598 55.000 0.00 0.00 40.87 2.87
3319 3878 0.610232 CCCAGCAGGTTGGAAGGAAG 60.610 60.000 3.51 0.00 40.87 3.46
3320 3879 1.460255 CCCAGCAGGTTGGAAGGAA 59.540 57.895 3.51 0.00 40.87 3.36
3321 3880 3.170362 CCCAGCAGGTTGGAAGGA 58.830 61.111 3.51 0.00 40.87 3.36
3322 3881 2.677875 GCCCAGCAGGTTGGAAGG 60.678 66.667 3.51 0.00 40.87 3.46
3326 3885 4.673375 AGCAGCCCAGCAGGTTGG 62.673 66.667 10.86 0.00 46.57 3.77
3331 3890 3.518998 GATGCAGCAGCCCAGCAG 61.519 66.667 0.00 0.00 42.14 4.24
3334 3893 3.138798 GTGGATGCAGCAGCCCAG 61.139 66.667 26.95 0.00 39.46 4.45
3335 3894 4.746309 GGTGGATGCAGCAGCCCA 62.746 66.667 26.95 19.76 39.46 5.36
3337 3896 3.138798 CTGGTGGATGCAGCAGCC 61.139 66.667 29.46 23.57 42.58 4.85
3338 3897 3.138798 CCTGGTGGATGCAGCAGC 61.139 66.667 33.34 0.62 46.06 5.25
3339 3898 3.138798 GCCTGGTGGATGCAGCAG 61.139 66.667 32.22 32.22 46.72 4.24
3340 3899 3.969119 TGCCTGGTGGATGCAGCA 61.969 61.111 18.42 18.42 34.57 4.41
3341 3900 3.446570 GTGCCTGGTGGATGCAGC 61.447 66.667 9.74 9.74 35.33 5.25
3342 3901 3.129502 CGTGCCTGGTGGATGCAG 61.130 66.667 0.00 0.00 35.33 4.41
3343 3902 3.952508 ACGTGCCTGGTGGATGCA 61.953 61.111 0.00 0.00 34.57 3.96
3344 3903 3.434319 CACGTGCCTGGTGGATGC 61.434 66.667 0.82 0.00 34.57 3.91


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

AutoCloner maintained by Alex Coulton.