Multiple sequence alignment - TraesCS2A01G293700

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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 TraesCS2A01G293700 chr2A 100.000 3356 0 0 1 3356 504708106 504711461 0.000000e+00 6198.0
1 TraesCS2A01G293700 chr2A 100.000 147 0 0 3693 3839 504711798 504711944 4.890000e-69 272.0
2 TraesCS2A01G293700 chr2B 93.152 2614 119 31 764 3332 442914763 442917361 0.000000e+00 3781.0
3 TraesCS2A01G293700 chr2B 93.750 96 6 0 3744 3839 442917642 442917737 1.110000e-30 145.0
4 TraesCS2A01G293700 chr2D 92.843 2515 107 34 863 3332 373418515 373421001 0.000000e+00 3579.0
5 TraesCS2A01G293700 chr2D 88.889 207 19 3 669 873 373418290 373418494 6.370000e-63 252.0
6 TraesCS2A01G293700 chr2D 93.750 96 6 0 3744 3839 373421329 373421424 1.110000e-30 145.0
7 TraesCS2A01G293700 chr2D 83.784 148 22 2 3693 3839 325331753 325331607 5.170000e-29 139.0
8 TraesCS2A01G293700 chr2D 92.593 54 4 0 100 153 373416281 373416334 1.140000e-10 78.7
9 TraesCS2A01G293700 chr3D 76.845 393 66 18 155 533 585017207 585016826 8.410000e-47 198.0
10 TraesCS2A01G293700 chr6D 85.135 148 20 2 3693 3839 290949517 290949663 2.390000e-32 150.0
11 TraesCS2A01G293700 chr6D 96.078 51 2 0 3306 3356 128257071 128257021 2.460000e-12 84.2
12 TraesCS2A01G293700 chr6D 94.231 52 3 0 3305 3356 456406370 456406421 3.180000e-11 80.5
13 TraesCS2A01G293700 chr4D 85.156 128 19 0 3712 3839 269470245 269470372 8.650000e-27 132.0
14 TraesCS2A01G293700 chr7D 83.453 139 21 2 3693 3830 199077929 199078066 1.120000e-25 128.0
15 TraesCS2A01G293700 chr5B 82.639 144 18 5 3693 3830 46621502 46621360 1.870000e-23 121.0
16 TraesCS2A01G293700 chr4A 82.639 144 18 5 3693 3830 241655440 241655582 1.870000e-23 121.0
17 TraesCS2A01G293700 chr4A 94.000 50 3 0 3307 3356 323048620 323048571 4.110000e-10 76.8
18 TraesCS2A01G293700 chr1D 82.639 144 18 5 3693 3830 92974127 92973985 1.870000e-23 121.0
19 TraesCS2A01G293700 chr5D 96.000 50 1 1 3304 3353 298145755 298145803 3.180000e-11 80.5
20 TraesCS2A01G293700 chr7B 95.833 48 2 0 3308 3355 26882980 26882933 1.140000e-10 78.7
21 TraesCS2A01G293700 chr5A 94.118 51 3 0 3306 3356 330196305 330196355 1.140000e-10 78.7
22 TraesCS2A01G293700 chr6A 94.118 51 1 2 3307 3356 1683077 1683028 4.110000e-10 76.8
23 TraesCS2A01G293700 chr3B 92.453 53 4 0 3304 3356 774168315 774168367 4.110000e-10 76.8


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 TraesCS2A01G293700 chr2A 504708106 504711944 3838 False 3235.000 6198 100.00000 1 3839 2 chr2A.!!$F1 3838
1 TraesCS2A01G293700 chr2B 442914763 442917737 2974 False 1963.000 3781 93.45100 764 3839 2 chr2B.!!$F1 3075
2 TraesCS2A01G293700 chr2D 373416281 373421424 5143 False 1013.675 3579 92.01875 100 3839 4 chr2D.!!$F1 3739

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
676 830 0.037590 ATGAGTGGGCGCCTTTAACA 59.962 50.0 28.56 19.53 0.00 2.41 F
745 2193 0.039035 GGCCCCATTAACAGTCACCA 59.961 55.0 0.00 0.00 0.00 4.17 F
1029 2512 0.313043 TGAAGAAGGTGACGGACGTC 59.687 55.0 17.19 17.19 44.77 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 3077 0.606944 TCGGTAATGTTGGGGTGTGC 60.607 55.0 0.00 0.00 0.00 4.57 R
1676 3189 0.672342 GTTCATCCATGCATGCCTCC 59.328 55.0 21.69 2.63 0.00 4.30 R
3008 4536 0.326595 TGAAATAAGCTGGCGACCCA 59.673 50.0 0.00 0.00 39.32 4.51 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
19 20 4.738998 TGGCCTCCCCATGCGTTG 62.739 66.667 3.32 0.00 39.18 4.10
27 28 3.443045 CCATGCGTTGGGACAGCC 61.443 66.667 0.00 0.00 42.39 4.85
43 44 3.513225 CCCATTTAGGCAGGTGCG 58.487 61.111 0.00 0.00 43.26 5.34
44 45 1.378514 CCCATTTAGGCAGGTGCGT 60.379 57.895 2.33 2.33 43.26 5.24
45 46 1.656818 CCCATTTAGGCAGGTGCGTG 61.657 60.000 7.41 0.00 43.26 5.34
46 47 1.656818 CCATTTAGGCAGGTGCGTGG 61.657 60.000 7.41 1.86 43.26 4.94
47 48 0.960364 CATTTAGGCAGGTGCGTGGT 60.960 55.000 7.41 0.00 43.26 4.16
48 49 0.251165 ATTTAGGCAGGTGCGTGGTT 60.251 50.000 7.41 0.00 43.26 3.67
49 50 1.169661 TTTAGGCAGGTGCGTGGTTG 61.170 55.000 7.41 0.00 43.26 3.77
59 60 4.326766 CGTGGTTGCACGGGCTTG 62.327 66.667 12.74 0.00 44.01 4.01
60 61 3.216292 GTGGTTGCACGGGCTTGT 61.216 61.111 12.74 0.00 41.91 3.16
61 62 2.441164 TGGTTGCACGGGCTTGTT 60.441 55.556 12.74 0.00 41.91 2.83
62 63 2.027460 GGTTGCACGGGCTTGTTG 59.973 61.111 12.74 0.00 41.91 3.33
63 64 2.027460 GTTGCACGGGCTTGTTGG 59.973 61.111 12.74 0.00 41.91 3.77
64 65 2.124109 TTGCACGGGCTTGTTGGA 60.124 55.556 12.74 0.00 41.91 3.53
65 66 2.485795 TTGCACGGGCTTGTTGGAC 61.486 57.895 12.74 0.00 41.91 4.02
66 67 4.025401 GCACGGGCTTGTTGGACG 62.025 66.667 0.00 0.00 36.96 4.79
67 68 3.353836 CACGGGCTTGTTGGACGG 61.354 66.667 0.00 0.00 0.00 4.79
68 69 4.636435 ACGGGCTTGTTGGACGGG 62.636 66.667 0.00 0.00 0.00 5.28
78 79 2.359354 TGGACGGGCCAATTCACG 60.359 61.111 0.00 0.00 45.87 4.35
79 80 2.046700 GGACGGGCCAATTCACGA 60.047 61.111 4.39 0.00 36.34 4.35
80 81 2.106683 GGACGGGCCAATTCACGAG 61.107 63.158 4.39 0.00 36.34 4.18
81 82 2.746277 ACGGGCCAATTCACGAGC 60.746 61.111 4.39 0.00 0.00 5.03
82 83 2.436646 CGGGCCAATTCACGAGCT 60.437 61.111 4.39 0.00 0.00 4.09
83 84 2.464459 CGGGCCAATTCACGAGCTC 61.464 63.158 4.39 2.73 0.00 4.09
84 85 2.115291 GGGCCAATTCACGAGCTCC 61.115 63.158 8.47 0.00 0.00 4.70
85 86 1.078143 GGCCAATTCACGAGCTCCT 60.078 57.895 8.47 0.00 0.00 3.69
86 87 0.678048 GGCCAATTCACGAGCTCCTT 60.678 55.000 8.47 0.00 0.00 3.36
87 88 0.729690 GCCAATTCACGAGCTCCTTC 59.270 55.000 8.47 0.00 0.00 3.46
88 89 1.373570 CCAATTCACGAGCTCCTTCC 58.626 55.000 8.47 0.00 0.00 3.46
89 90 1.002366 CAATTCACGAGCTCCTTCCG 58.998 55.000 8.47 0.00 0.00 4.30
90 91 0.608640 AATTCACGAGCTCCTTCCGT 59.391 50.000 8.47 0.00 36.95 4.69
91 92 0.608640 ATTCACGAGCTCCTTCCGTT 59.391 50.000 8.47 0.00 33.96 4.44
92 93 0.319555 TTCACGAGCTCCTTCCGTTG 60.320 55.000 8.47 0.00 33.96 4.10
93 94 1.176619 TCACGAGCTCCTTCCGTTGA 61.177 55.000 8.47 1.10 33.96 3.18
94 95 0.734253 CACGAGCTCCTTCCGTTGAG 60.734 60.000 8.47 0.00 33.96 3.02
95 96 0.894184 ACGAGCTCCTTCCGTTGAGA 60.894 55.000 8.47 0.00 32.03 3.27
96 97 0.179150 CGAGCTCCTTCCGTTGAGAG 60.179 60.000 8.47 0.00 0.00 3.20
97 98 4.193653 GCTCCTTCCGTTGAGAGC 57.806 61.111 0.00 0.00 44.36 4.09
98 99 1.594310 GCTCCTTCCGTTGAGAGCT 59.406 57.895 3.69 0.00 46.50 4.09
117 118 3.324993 GCTGAGTAGCTGAATATGCCTC 58.675 50.000 0.00 0.00 46.57 4.70
122 123 2.338577 AGCTGAATATGCCTCGCTTT 57.661 45.000 0.00 0.00 0.00 3.51
123 124 2.648059 AGCTGAATATGCCTCGCTTTT 58.352 42.857 0.00 0.00 0.00 2.27
153 154 2.755103 CTCCCTTTAACACCAGGCAATC 59.245 50.000 0.00 0.00 0.00 2.67
158 268 5.512921 CCCTTTAACACCAGGCAATCAAAAT 60.513 40.000 0.00 0.00 0.00 1.82
162 272 0.390209 ACCAGGCAATCAAAATGCGC 60.390 50.000 0.00 0.00 44.75 6.09
176 286 1.086696 ATGCGCGCTAGTTGTGAATT 58.913 45.000 33.29 0.00 0.00 2.17
177 287 0.165727 TGCGCGCTAGTTGTGAATTG 59.834 50.000 33.29 0.00 0.00 2.32
183 293 3.908382 GCGCTAGTTGTGAATTGAACAAG 59.092 43.478 0.00 0.00 38.17 3.16
194 304 4.518970 TGAATTGAACAAGCAACCTACCTC 59.481 41.667 0.00 0.00 0.00 3.85
195 305 2.163818 TGAACAAGCAACCTACCTCG 57.836 50.000 0.00 0.00 0.00 4.63
198 308 1.045407 ACAAGCAACCTACCTCGTCA 58.955 50.000 0.00 0.00 0.00 4.35
239 349 2.434843 CGCCACCCAGCAGGATCTA 61.435 63.158 0.00 0.00 39.89 1.98
246 356 4.215908 CACCCAGCAGGATCTAGTAAGTA 58.784 47.826 0.00 0.00 39.89 2.24
247 357 4.835615 CACCCAGCAGGATCTAGTAAGTAT 59.164 45.833 0.00 0.00 39.89 2.12
257 367 9.535878 CAGGATCTAGTAAGTATCAACCTTTTC 57.464 37.037 0.00 0.00 0.00 2.29
265 375 9.286170 AGTAAGTATCAACCTTTTCCTTCTTTC 57.714 33.333 0.00 0.00 0.00 2.62
266 376 7.526142 AAGTATCAACCTTTTCCTTCTTTCC 57.474 36.000 0.00 0.00 0.00 3.13
274 384 5.103473 ACCTTTTCCTTCTTTCCTTCTTCCT 60.103 40.000 0.00 0.00 0.00 3.36
337 447 6.647334 TGTTCTTGCTGGTTTGATGAATTA 57.353 33.333 0.00 0.00 0.00 1.40
339 449 7.092079 TGTTCTTGCTGGTTTGATGAATTATG 58.908 34.615 0.00 0.00 0.00 1.90
347 457 7.492020 GCTGGTTTGATGAATTATGTGCAAATA 59.508 33.333 0.00 0.00 0.00 1.40
353 463 9.738832 TTGATGAATTATGTGCAAATATGTGAG 57.261 29.630 0.00 0.00 0.00 3.51
359 469 8.638685 ATTATGTGCAAATATGTGAGCTTTTC 57.361 30.769 0.00 0.00 0.00 2.29
360 470 5.710513 TGTGCAAATATGTGAGCTTTTCT 57.289 34.783 0.00 0.00 0.00 2.52
361 471 6.816134 TGTGCAAATATGTGAGCTTTTCTA 57.184 33.333 0.00 0.00 0.00 2.10
362 472 7.213216 TGTGCAAATATGTGAGCTTTTCTAA 57.787 32.000 0.00 0.00 0.00 2.10
363 473 7.656412 TGTGCAAATATGTGAGCTTTTCTAAA 58.344 30.769 0.00 0.00 0.00 1.85
510 645 9.485206 AAATCCATGAACTCTTTCTCATTTTTG 57.515 29.630 0.00 0.00 29.69 2.44
515 650 9.856488 CATGAACTCTTTCTCATTTTTGATGAT 57.144 29.630 0.00 0.00 29.69 2.45
547 701 8.991026 TCAAAATCCATGAACATGTTTGAATTC 58.009 29.630 13.36 0.00 37.86 2.17
549 703 7.894376 AATCCATGAACATGTTTGAATTCAC 57.106 32.000 13.36 0.00 37.11 3.18
550 704 5.459768 TCCATGAACATGTTTGAATTCACG 58.540 37.500 13.36 0.00 37.11 4.35
558 712 7.406799 ACATGTTTGAATTCACGATTTTTCC 57.593 32.000 7.89 0.00 0.00 3.13
559 713 6.983307 ACATGTTTGAATTCACGATTTTTCCA 59.017 30.769 7.89 0.00 0.00 3.53
560 714 7.656948 ACATGTTTGAATTCACGATTTTTCCAT 59.343 29.630 7.89 0.00 0.00 3.41
610 764 0.368907 AAATGCGATCGAACGAACCG 59.631 50.000 21.57 14.27 35.09 4.44
634 788 7.631915 GAGAGGAAATAAAATCTCGCTCTAC 57.368 40.000 0.00 0.00 0.00 2.59
635 789 7.113658 AGAGGAAATAAAATCTCGCTCTACA 57.886 36.000 0.00 0.00 0.00 2.74
636 790 7.731054 AGAGGAAATAAAATCTCGCTCTACAT 58.269 34.615 0.00 0.00 0.00 2.29
637 791 7.655328 AGAGGAAATAAAATCTCGCTCTACATG 59.345 37.037 0.00 0.00 0.00 3.21
638 792 6.708054 AGGAAATAAAATCTCGCTCTACATGG 59.292 38.462 0.00 0.00 0.00 3.66
640 794 2.246719 AAATCTCGCTCTACATGGGC 57.753 50.000 0.00 0.00 0.00 5.36
643 797 1.068753 CTCGCTCTACATGGGCTGG 59.931 63.158 0.00 0.00 0.00 4.85
644 798 2.590007 CGCTCTACATGGGCTGGC 60.590 66.667 0.00 0.00 0.00 4.85
645 799 2.203266 GCTCTACATGGGCTGGCC 60.203 66.667 14.23 14.23 0.00 5.36
663 817 3.254629 CCACCAGGGTTGATGAGTG 57.745 57.895 0.00 0.00 0.00 3.51
664 818 0.322816 CCACCAGGGTTGATGAGTGG 60.323 60.000 0.00 0.00 38.89 4.00
666 820 1.379044 CCAGGGTTGATGAGTGGGC 60.379 63.158 0.00 0.00 0.00 5.36
667 821 1.746615 CAGGGTTGATGAGTGGGCG 60.747 63.158 0.00 0.00 0.00 6.13
668 822 3.134127 GGGTTGATGAGTGGGCGC 61.134 66.667 0.00 0.00 0.00 6.53
670 824 2.045926 GTTGATGAGTGGGCGCCT 60.046 61.111 28.56 6.33 0.00 5.52
671 825 1.675641 GTTGATGAGTGGGCGCCTT 60.676 57.895 28.56 12.70 0.00 4.35
672 826 1.074775 TTGATGAGTGGGCGCCTTT 59.925 52.632 28.56 12.29 0.00 3.11
676 830 0.037590 ATGAGTGGGCGCCTTTAACA 59.962 50.000 28.56 19.53 0.00 2.41
677 831 0.887387 TGAGTGGGCGCCTTTAACAC 60.887 55.000 28.56 24.15 0.00 3.32
679 833 0.688487 AGTGGGCGCCTTTAACACTA 59.312 50.000 27.24 0.00 40.31 2.74
680 834 0.800631 GTGGGCGCCTTTAACACTAC 59.199 55.000 28.56 5.64 0.00 2.73
682 836 0.800631 GGGCGCCTTTAACACTACAC 59.199 55.000 28.56 0.00 0.00 2.90
683 837 0.800631 GGCGCCTTTAACACTACACC 59.199 55.000 22.15 0.00 0.00 4.16
684 838 0.441145 GCGCCTTTAACACTACACCG 59.559 55.000 0.00 0.00 0.00 4.94
685 839 1.936203 GCGCCTTTAACACTACACCGA 60.936 52.381 0.00 0.00 0.00 4.69
687 841 2.410730 CGCCTTTAACACTACACCGAAG 59.589 50.000 0.00 0.00 0.00 3.79
688 842 3.656559 GCCTTTAACACTACACCGAAGA 58.343 45.455 0.00 0.00 0.00 2.87
695 2143 5.407407 AACACTACACCGAAGAGATGAAT 57.593 39.130 0.00 0.00 0.00 2.57
700 2148 2.834549 ACACCGAAGAGATGAATGGTCT 59.165 45.455 0.00 0.00 0.00 3.85
709 2157 4.499183 GAGATGAATGGTCTCTGTTTCGT 58.501 43.478 0.00 0.00 39.18 3.85
717 2165 0.400213 TCTCTGTTTCGTGGGCCAAT 59.600 50.000 8.40 0.00 0.00 3.16
730 2178 2.426406 GCCAATACCAAGCAGGCCC 61.426 63.158 0.00 0.00 43.14 5.80
745 2193 0.039035 GGCCCCATTAACAGTCACCA 59.961 55.000 0.00 0.00 0.00 4.17
754 2202 6.316390 CCCATTAACAGTCACCAGAGAAATAC 59.684 42.308 0.00 0.00 0.00 1.89
760 2208 3.193691 AGTCACCAGAGAAATACTCCACG 59.806 47.826 0.00 0.00 45.96 4.94
779 2227 1.377612 GCCCAGGGTAACGGAAAGT 59.622 57.895 7.55 0.00 37.60 2.66
798 2246 2.203480 TGCTCCACAGCCCCAAAC 60.203 61.111 0.00 0.00 46.26 2.93
930 2413 3.643792 ACAGGGACATATTACTCTGGAGC 59.356 47.826 9.64 0.00 38.74 4.70
945 2428 3.003763 AGCCTGGACCGAACTCCC 61.004 66.667 0.00 0.00 0.00 4.30
1029 2512 0.313043 TGAAGAAGGTGACGGACGTC 59.687 55.000 17.19 17.19 44.77 4.34
1175 2658 2.846827 CCAAGTTCTCCCAGGTATCCTT 59.153 50.000 0.00 0.00 0.00 3.36
1294 2777 4.863491 TCTTTACGTTTCGCTAGTCAACT 58.137 39.130 0.00 0.00 0.00 3.16
1323 2829 1.103398 CCGGGGATCTGCAAATCCAC 61.103 60.000 20.61 16.42 46.04 4.02
1333 2839 1.595093 GCAAATCCACGAACAGGGGG 61.595 60.000 0.00 0.00 45.91 5.40
1373 2879 2.357952 GCCTTTAGGATTTACTTGCCCG 59.642 50.000 0.00 0.00 37.39 6.13
1427 2934 7.896383 TTAGGGATTTGATGTTAGGATTTGG 57.104 36.000 0.00 0.00 0.00 3.28
1610 3119 4.039124 ACTGGAAAAGGTGTGGCTTATTTG 59.961 41.667 0.00 0.00 0.00 2.32
1614 3123 5.405935 AAAAGGTGTGGCTTATTTGATCC 57.594 39.130 0.00 0.00 0.00 3.36
1653 3162 6.261381 AGCATTGCTTTTGAACATGAAATTGT 59.739 30.769 5.03 0.00 33.89 2.71
1656 3165 9.372541 CATTGCTTTTGAACATGAAATTGTAAC 57.627 29.630 0.00 0.00 0.00 2.50
1728 3243 5.518848 TCTTTGGCATGTTATATGCTTGG 57.481 39.130 13.28 3.06 44.02 3.61
2076 3603 9.555727 TTCCAAAGATTAAGAATTAGGATACCG 57.444 33.333 0.00 0.00 37.17 4.02
2105 3632 8.026607 TGTAACTTGCTTATAGTTCAAAATGCC 58.973 33.333 0.00 0.00 37.12 4.40
2129 3656 7.256547 GCCCCCTTCACAATATTATAGTAGTGA 60.257 40.741 9.36 2.32 34.54 3.41
2217 3744 5.711976 GCCCCTAGCAATATGTTGTATGATT 59.288 40.000 4.00 0.00 42.97 2.57
2218 3745 6.884295 GCCCCTAGCAATATGTTGTATGATTA 59.116 38.462 4.00 0.00 42.97 1.75
2351 3878 7.625185 GCTCATTCAATCTGTTTAACCTCTCAC 60.625 40.741 0.00 0.00 0.00 3.51
2424 3951 3.767711 TGACACTGTCACTCCTGAGTAT 58.232 45.455 7.84 0.00 40.20 2.12
2659 4186 5.568392 AGGAGATTGCTGAATTGAAAGAGT 58.432 37.500 0.00 0.00 0.00 3.24
2682 4209 3.394274 TGAAGGTGAGGTGGATCTTTGAA 59.606 43.478 0.00 0.00 0.00 2.69
2688 4215 6.015095 AGGTGAGGTGGATCTTTGAAAAATTC 60.015 38.462 0.00 0.00 0.00 2.17
2915 4443 3.393609 CCCTCTGGAATCTCATCATCCAA 59.606 47.826 0.00 0.00 42.41 3.53
2939 4467 4.160252 ACTTGGGTGAATTCCATAACATGC 59.840 41.667 2.27 0.00 33.82 4.06
2962 4490 1.613437 ACTGGGCTTGTTGAAATTCCG 59.387 47.619 0.00 0.00 0.00 4.30
2972 4500 6.567701 GCTTGTTGAAATTCCGACATAACTCA 60.568 38.462 0.00 0.00 31.10 3.41
2973 4501 6.480524 TGTTGAAATTCCGACATAACTCAG 57.519 37.500 0.00 0.00 0.00 3.35
3008 4536 7.363268 GCTTTCTGTTGGACCTCATCATTTTAT 60.363 37.037 0.00 0.00 0.00 1.40
3013 4541 4.792068 TGGACCTCATCATTTTATGGGTC 58.208 43.478 12.37 12.37 41.56 4.46
3028 4556 1.064758 TGGGTCGCCAGCTTATTTCAT 60.065 47.619 0.00 0.00 0.00 2.57
3095 4625 3.650281 TTCTGCTATGGCTTGATTCCA 57.350 42.857 1.68 0.00 39.59 3.53
3096 4626 3.650281 TCTGCTATGGCTTGATTCCAA 57.350 42.857 1.68 0.00 37.13 3.53
3117 4647 2.798283 ACATGTACCTTGTCGTTTGTCG 59.202 45.455 0.00 0.00 41.41 4.35
3137 4667 3.006217 TCGATGTGCTCATCCTTGATAGG 59.994 47.826 20.10 6.47 45.32 2.57
3142 4672 1.141657 GCTCATCCTTGATAGGCACCA 59.858 52.381 0.00 0.00 41.69 4.17
3155 4685 0.457443 GGCACCAATCTTTAGGCTGC 59.543 55.000 0.00 0.00 33.83 5.25
3156 4686 0.457443 GCACCAATCTTTAGGCTGCC 59.543 55.000 11.65 11.65 0.00 4.85
3157 4687 1.838112 CACCAATCTTTAGGCTGCCA 58.162 50.000 22.65 3.92 0.00 4.92
3177 4709 4.020485 GCCAGAGAGGAGTTAACCTAACAA 60.020 45.833 0.88 0.00 40.73 2.83
3188 4720 5.995897 AGTTAACCTAACAAGTGACATGTCC 59.004 40.000 22.85 13.88 41.07 4.02
3193 4725 5.175859 CCTAACAAGTGACATGTCCGTAAT 58.824 41.667 22.85 7.73 0.00 1.89
3194 4726 5.063438 CCTAACAAGTGACATGTCCGTAATG 59.937 44.000 22.85 15.68 0.00 1.90
3205 4737 3.000041 TGTCCGTAATGACATTGAGCAC 59.000 45.455 11.05 1.93 40.22 4.40
3222 4754 4.060900 GAGCACTTCTGATGACTGAAACA 58.939 43.478 0.00 0.00 34.54 2.83
3224 4756 5.798132 AGCACTTCTGATGACTGAAACATA 58.202 37.500 0.00 0.00 34.54 2.29
3234 4766 9.994432 CTGATGACTGAAACATACTTAAATTCC 57.006 33.333 0.00 0.00 0.00 3.01
3262 4796 3.590466 ATGACCCTGTTGGCTGGCC 62.590 63.158 4.43 4.43 37.83 5.36
3284 4818 1.134610 CCCAAGAAAATGGCATCCAGC 60.135 52.381 0.00 0.00 39.26 4.85
3300 4834 0.179197 CAGCAACTGAGCGCAATGAG 60.179 55.000 11.47 1.34 40.15 2.90
3315 4849 4.455606 GCAATGAGGCATACTACTTCCTT 58.544 43.478 0.00 0.00 0.00 3.36
3321 4856 2.223994 GGCATACTACTTCCTTCGTCCC 60.224 54.545 0.00 0.00 0.00 4.46
3323 4858 3.069729 GCATACTACTTCCTTCGTCCCAT 59.930 47.826 0.00 0.00 0.00 4.00
3324 4859 4.280174 GCATACTACTTCCTTCGTCCCATA 59.720 45.833 0.00 0.00 0.00 2.74
3328 4863 8.750298 CATACTACTTCCTTCGTCCCATAATAT 58.250 37.037 0.00 0.00 0.00 1.28
3329 4864 9.986157 ATACTACTTCCTTCGTCCCATAATATA 57.014 33.333 0.00 0.00 0.00 0.86
3330 4865 8.716674 ACTACTTCCTTCGTCCCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
3331 4866 8.804204 ACTACTTCCTTCGTCCCATAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
3332 4867 7.850935 ACTTCCTTCGTCCCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
3333 4868 7.897864 ACTTCCTTCGTCCCATAATATAAGAG 58.102 38.462 0.00 0.00 0.00 2.85
3334 4869 6.282199 TCCTTCGTCCCATAATATAAGAGC 57.718 41.667 0.00 0.00 0.00 4.09
3335 4870 5.103000 CCTTCGTCCCATAATATAAGAGCG 58.897 45.833 0.00 0.00 0.00 5.03
3337 4872 5.717078 TCGTCCCATAATATAAGAGCGTT 57.283 39.130 0.00 0.00 0.00 4.84
3338 4873 6.092955 TCGTCCCATAATATAAGAGCGTTT 57.907 37.500 0.00 0.00 0.00 3.60
3339 4874 6.518493 TCGTCCCATAATATAAGAGCGTTTT 58.482 36.000 0.00 0.00 0.00 2.43
3340 4875 6.643770 TCGTCCCATAATATAAGAGCGTTTTC 59.356 38.462 0.00 0.00 0.00 2.29
3730 5265 7.737972 TGGTAGAAACGAAATGAAATTCTGA 57.262 32.000 0.00 0.00 33.67 3.27
3731 5266 8.335532 TGGTAGAAACGAAATGAAATTCTGAT 57.664 30.769 0.00 0.00 33.67 2.90
3732 5267 9.443323 TGGTAGAAACGAAATGAAATTCTGATA 57.557 29.630 0.00 0.00 33.67 2.15
3736 5271 8.462016 AGAAACGAAATGAAATTCTGATAAGGG 58.538 33.333 0.00 0.00 33.67 3.95
3737 5272 7.938140 AACGAAATGAAATTCTGATAAGGGA 57.062 32.000 0.00 0.00 33.67 4.20
3738 5273 7.938140 ACGAAATGAAATTCTGATAAGGGAA 57.062 32.000 0.00 0.00 33.67 3.97
3739 5274 8.525290 ACGAAATGAAATTCTGATAAGGGAAT 57.475 30.769 0.00 0.00 33.67 3.01
3740 5275 8.624776 ACGAAATGAAATTCTGATAAGGGAATC 58.375 33.333 0.00 0.00 33.67 2.52
3741 5276 8.623903 CGAAATGAAATTCTGATAAGGGAATCA 58.376 33.333 0.00 0.00 33.67 2.57
3759 5294 5.070047 GGAATCATTTGGCTGAATCCAGATT 59.930 40.000 4.84 0.00 42.46 2.40
3798 5333 1.164411 TTGGCTGGCACTACGATTTG 58.836 50.000 2.29 0.00 0.00 2.32
3811 5346 3.433306 ACGATTTGGAGGTGAAATCCA 57.567 42.857 0.00 0.00 45.15 3.41
3821 5356 1.895131 GGTGAAATCCATGCCAACACT 59.105 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.740822 AACGCATGGGGAGGCCAC 62.741 66.667 14.94 0.00 0.00 5.01
2 3 4.738998 CAACGCATGGGGAGGCCA 62.739 66.667 14.94 0.00 0.00 5.36
26 27 1.378514 ACGCACCTGCCTAAATGGG 60.379 57.895 0.00 0.00 37.91 4.00
27 28 1.656818 CCACGCACCTGCCTAAATGG 61.657 60.000 0.00 0.00 37.91 3.16
28 29 0.960364 ACCACGCACCTGCCTAAATG 60.960 55.000 0.00 0.00 37.91 2.32
29 30 0.251165 AACCACGCACCTGCCTAAAT 60.251 50.000 0.00 0.00 37.91 1.40
30 31 1.149627 AACCACGCACCTGCCTAAA 59.850 52.632 0.00 0.00 37.91 1.85
31 32 1.599518 CAACCACGCACCTGCCTAA 60.600 57.895 0.00 0.00 37.91 2.69
32 33 2.031919 CAACCACGCACCTGCCTA 59.968 61.111 0.00 0.00 37.91 3.93
43 44 2.781158 AACAAGCCCGTGCAACCAC 61.781 57.895 0.00 0.00 41.13 4.16
44 45 2.441164 AACAAGCCCGTGCAACCA 60.441 55.556 0.00 0.00 41.13 3.67
45 46 2.027460 CAACAAGCCCGTGCAACC 59.973 61.111 0.00 0.00 41.13 3.77
46 47 2.027460 CCAACAAGCCCGTGCAAC 59.973 61.111 0.00 0.00 41.13 4.17
47 48 2.124109 TCCAACAAGCCCGTGCAA 60.124 55.556 0.00 0.00 41.13 4.08
48 49 2.904866 GTCCAACAAGCCCGTGCA 60.905 61.111 0.00 0.00 41.13 4.57
49 50 4.025401 CGTCCAACAAGCCCGTGC 62.025 66.667 0.00 0.00 37.95 5.34
50 51 3.353836 CCGTCCAACAAGCCCGTG 61.354 66.667 0.00 0.00 0.00 4.94
51 52 4.636435 CCCGTCCAACAAGCCCGT 62.636 66.667 0.00 0.00 0.00 5.28
54 55 4.966787 TGGCCCGTCCAACAAGCC 62.967 66.667 0.00 0.00 43.21 4.35
61 62 2.359354 CGTGAATTGGCCCGTCCA 60.359 61.111 0.00 0.00 44.85 4.02
62 63 2.046700 TCGTGAATTGGCCCGTCC 60.047 61.111 0.00 0.00 0.00 4.79
63 64 2.750888 GCTCGTGAATTGGCCCGTC 61.751 63.158 0.00 0.00 0.00 4.79
64 65 2.746277 GCTCGTGAATTGGCCCGT 60.746 61.111 0.00 0.00 0.00 5.28
65 66 2.436646 AGCTCGTGAATTGGCCCG 60.437 61.111 0.00 0.00 0.00 6.13
66 67 2.115291 GGAGCTCGTGAATTGGCCC 61.115 63.158 7.83 0.00 0.00 5.80
67 68 0.678048 AAGGAGCTCGTGAATTGGCC 60.678 55.000 10.16 0.00 0.00 5.36
68 69 0.729690 GAAGGAGCTCGTGAATTGGC 59.270 55.000 10.16 0.00 0.00 4.52
69 70 1.373570 GGAAGGAGCTCGTGAATTGG 58.626 55.000 10.16 0.00 0.00 3.16
70 71 1.002366 CGGAAGGAGCTCGTGAATTG 58.998 55.000 10.16 0.00 0.00 2.32
71 72 0.608640 ACGGAAGGAGCTCGTGAATT 59.391 50.000 10.16 0.00 35.70 2.17
72 73 0.608640 AACGGAAGGAGCTCGTGAAT 59.391 50.000 10.16 0.00 37.20 2.57
73 74 0.319555 CAACGGAAGGAGCTCGTGAA 60.320 55.000 10.16 0.00 37.20 3.18
74 75 1.176619 TCAACGGAAGGAGCTCGTGA 61.177 55.000 10.16 0.00 37.20 4.35
75 76 0.734253 CTCAACGGAAGGAGCTCGTG 60.734 60.000 10.16 0.00 37.20 4.35
76 77 0.894184 TCTCAACGGAAGGAGCTCGT 60.894 55.000 7.83 5.12 38.89 4.18
77 78 0.179150 CTCTCAACGGAAGGAGCTCG 60.179 60.000 7.83 0.00 0.00 5.03
78 79 0.459411 GCTCTCAACGGAAGGAGCTC 60.459 60.000 4.71 4.71 45.15 4.09
79 80 1.594310 GCTCTCAACGGAAGGAGCT 59.406 57.895 12.92 0.00 45.15 4.09
80 81 4.193653 GCTCTCAACGGAAGGAGC 57.806 61.111 6.88 6.88 43.07 4.70
81 82 0.891373 TCAGCTCTCAACGGAAGGAG 59.109 55.000 0.00 0.00 0.00 3.69
82 83 0.891373 CTCAGCTCTCAACGGAAGGA 59.109 55.000 0.00 0.00 0.00 3.36
83 84 0.605589 ACTCAGCTCTCAACGGAAGG 59.394 55.000 0.00 0.00 0.00 3.46
84 85 2.733858 GCTACTCAGCTCTCAACGGAAG 60.734 54.545 0.00 0.00 44.93 3.46
85 86 1.202582 GCTACTCAGCTCTCAACGGAA 59.797 52.381 0.00 0.00 44.93 4.30
86 87 0.811915 GCTACTCAGCTCTCAACGGA 59.188 55.000 0.00 0.00 44.93 4.69
87 88 3.337398 GCTACTCAGCTCTCAACGG 57.663 57.895 0.00 0.00 44.93 4.44
97 98 3.573598 CGAGGCATATTCAGCTACTCAG 58.426 50.000 0.00 0.00 0.00 3.35
98 99 2.288457 GCGAGGCATATTCAGCTACTCA 60.288 50.000 0.00 0.00 0.00 3.41
114 115 3.190874 GGAGTGACTATGAAAAGCGAGG 58.809 50.000 0.00 0.00 0.00 4.63
117 118 3.252974 AGGGAGTGACTATGAAAAGCG 57.747 47.619 0.00 0.00 0.00 4.68
122 123 5.308497 TGGTGTTAAAGGGAGTGACTATGAA 59.692 40.000 0.00 0.00 0.00 2.57
123 124 4.841813 TGGTGTTAAAGGGAGTGACTATGA 59.158 41.667 0.00 0.00 0.00 2.15
153 154 0.976963 CACAACTAGCGCGCATTTTG 59.023 50.000 35.10 30.09 0.00 2.44
158 268 0.165727 CAATTCACAACTAGCGCGCA 59.834 50.000 35.10 18.19 0.00 6.09
162 272 3.908382 GCTTGTTCAATTCACAACTAGCG 59.092 43.478 10.19 0.00 40.07 4.26
176 286 1.414919 ACGAGGTAGGTTGCTTGTTCA 59.585 47.619 0.00 0.00 0.00 3.18
177 287 2.067013 GACGAGGTAGGTTGCTTGTTC 58.933 52.381 0.00 0.00 0.00 3.18
183 293 3.139029 CCTTGACGAGGTAGGTTGC 57.861 57.895 0.00 0.00 40.95 4.17
194 304 0.892755 TACACCAGCCTACCTTGACG 59.107 55.000 0.00 0.00 0.00 4.35
195 305 2.614734 GGTTACACCAGCCTACCTTGAC 60.615 54.545 0.00 0.00 38.42 3.18
198 308 1.737199 TGGTTACACCAGCCTACCTT 58.263 50.000 0.00 0.00 44.79 3.50
231 341 9.535878 GAAAAGGTTGATACTTACTAGATCCTG 57.464 37.037 0.00 0.00 0.00 3.86
239 349 9.286170 GAAAGAAGGAAAAGGTTGATACTTACT 57.714 33.333 0.00 0.00 0.00 2.24
246 356 6.377080 AGAAGGAAAGAAGGAAAAGGTTGAT 58.623 36.000 0.00 0.00 0.00 2.57
247 357 5.766590 AGAAGGAAAGAAGGAAAAGGTTGA 58.233 37.500 0.00 0.00 0.00 3.18
321 431 4.746729 TGCACATAATTCATCAAACCAGC 58.253 39.130 0.00 0.00 0.00 4.85
328 438 7.863877 GCTCACATATTTGCACATAATTCATCA 59.136 33.333 0.00 0.00 0.00 3.07
337 447 6.276832 AGAAAAGCTCACATATTTGCACAT 57.723 33.333 0.00 0.00 0.00 3.21
339 449 8.519492 TTTTAGAAAAGCTCACATATTTGCAC 57.481 30.769 0.00 0.00 0.00 4.57
481 616 8.413309 AATGAGAAAGAGTTCATGGATTTTGA 57.587 30.769 0.00 0.00 36.09 2.69
482 617 9.485206 AAAATGAGAAAGAGTTCATGGATTTTG 57.515 29.630 0.00 0.00 36.09 2.44
486 621 8.413309 TCAAAAATGAGAAAGAGTTCATGGAT 57.587 30.769 0.00 0.00 36.09 3.41
488 623 8.301720 TCATCAAAAATGAGAAAGAGTTCATGG 58.698 33.333 0.00 0.00 36.09 3.66
489 624 9.856488 ATCATCAAAAATGAGAAAGAGTTCATG 57.144 29.630 0.00 0.00 36.09 3.07
527 681 5.240403 TCGTGAATTCAAACATGTTCATGGA 59.760 36.000 12.39 2.29 37.88 3.41
603 757 5.731591 AGATTTTATTTCCTCTCGGTTCGT 58.268 37.500 0.00 0.00 0.00 3.85
604 758 6.275305 GAGATTTTATTTCCTCTCGGTTCG 57.725 41.667 0.00 0.00 0.00 3.95
610 764 7.203910 TGTAGAGCGAGATTTTATTTCCTCTC 58.796 38.462 0.00 0.00 31.54 3.20
625 779 1.068753 CCAGCCCATGTAGAGCGAG 59.931 63.158 0.00 0.00 0.00 5.03
626 780 3.094062 GCCAGCCCATGTAGAGCGA 62.094 63.158 0.00 0.00 0.00 4.93
645 799 0.322816 CCACTCATCAACCCTGGTGG 60.323 60.000 0.00 0.00 38.26 4.61
646 800 0.322816 CCCACTCATCAACCCTGGTG 60.323 60.000 0.00 0.00 34.71 4.17
647 801 2.078452 CCCACTCATCAACCCTGGT 58.922 57.895 0.00 0.00 0.00 4.00
648 802 1.379044 GCCCACTCATCAACCCTGG 60.379 63.158 0.00 0.00 0.00 4.45
649 803 1.746615 CGCCCACTCATCAACCCTG 60.747 63.158 0.00 0.00 0.00 4.45
650 804 2.671070 CGCCCACTCATCAACCCT 59.329 61.111 0.00 0.00 0.00 4.34
651 805 3.134127 GCGCCCACTCATCAACCC 61.134 66.667 0.00 0.00 0.00 4.11
652 806 3.134127 GGCGCCCACTCATCAACC 61.134 66.667 18.11 0.00 0.00 3.77
653 807 1.244019 AAAGGCGCCCACTCATCAAC 61.244 55.000 26.15 0.00 0.00 3.18
654 808 0.326595 TAAAGGCGCCCACTCATCAA 59.673 50.000 26.15 0.00 0.00 2.57
656 810 0.733150 GTTAAAGGCGCCCACTCATC 59.267 55.000 26.15 4.24 0.00 2.92
659 813 0.605589 AGTGTTAAAGGCGCCCACTC 60.606 55.000 26.15 15.33 30.94 3.51
660 814 0.688487 TAGTGTTAAAGGCGCCCACT 59.312 50.000 29.74 29.74 39.53 4.00
661 815 0.800631 GTAGTGTTAAAGGCGCCCAC 59.199 55.000 26.15 23.04 0.00 4.61
662 816 0.397187 TGTAGTGTTAAAGGCGCCCA 59.603 50.000 26.15 11.09 0.00 5.36
663 817 0.800631 GTGTAGTGTTAAAGGCGCCC 59.199 55.000 26.15 7.94 0.00 6.13
664 818 0.800631 GGTGTAGTGTTAAAGGCGCC 59.199 55.000 21.89 21.89 0.00 6.53
666 820 2.068837 TCGGTGTAGTGTTAAAGGCG 57.931 50.000 0.00 0.00 0.00 5.52
667 821 3.656559 TCTTCGGTGTAGTGTTAAAGGC 58.343 45.455 0.00 0.00 0.00 4.35
668 822 5.130292 TCTCTTCGGTGTAGTGTTAAAGG 57.870 43.478 0.00 0.00 0.00 3.11
670 824 6.335471 TCATCTCTTCGGTGTAGTGTTAAA 57.665 37.500 0.00 0.00 0.00 1.52
671 825 5.970317 TCATCTCTTCGGTGTAGTGTTAA 57.030 39.130 0.00 0.00 0.00 2.01
672 826 5.970317 TTCATCTCTTCGGTGTAGTGTTA 57.030 39.130 0.00 0.00 0.00 2.41
676 830 3.769844 ACCATTCATCTCTTCGGTGTAGT 59.230 43.478 0.00 0.00 0.00 2.73
677 831 4.098654 AGACCATTCATCTCTTCGGTGTAG 59.901 45.833 0.00 0.00 0.00 2.74
679 833 2.834549 AGACCATTCATCTCTTCGGTGT 59.165 45.455 0.00 0.00 0.00 4.16
680 834 3.452474 GAGACCATTCATCTCTTCGGTG 58.548 50.000 0.00 0.00 39.67 4.94
687 841 4.328440 CACGAAACAGAGACCATTCATCTC 59.672 45.833 0.00 0.00 42.57 2.75
688 842 4.248859 CACGAAACAGAGACCATTCATCT 58.751 43.478 0.00 0.00 0.00 2.90
695 2143 1.070786 GCCCACGAAACAGAGACCA 59.929 57.895 0.00 0.00 0.00 4.02
700 2148 1.612199 GGTATTGGCCCACGAAACAGA 60.612 52.381 0.00 0.00 0.00 3.41
708 2156 1.322538 CCTGCTTGGTATTGGCCCAC 61.323 60.000 0.00 0.00 0.00 4.61
709 2157 1.000233 CCTGCTTGGTATTGGCCCA 60.000 57.895 0.00 0.00 0.00 5.36
717 2165 1.003646 TTAATGGGGCCTGCTTGGTA 58.996 50.000 0.84 0.00 38.35 3.25
730 2178 7.106239 AGTATTTCTCTGGTGACTGTTAATGG 58.894 38.462 0.00 0.00 0.00 3.16
745 2193 0.831307 GGGCCGTGGAGTATTTCTCT 59.169 55.000 0.00 0.00 42.40 3.10
754 2202 3.006728 TTACCCTGGGCCGTGGAG 61.007 66.667 14.08 9.51 0.00 3.86
760 2208 1.378119 CTTTCCGTTACCCTGGGCC 60.378 63.158 14.08 0.00 0.00 5.80
798 2246 2.270923 TCATCAAAACGATCTCAGCCG 58.729 47.619 0.00 0.00 29.21 5.52
860 2309 2.022762 CGCTAAAATGACGGGCGC 59.977 61.111 0.00 0.00 39.42 6.53
930 2413 1.823169 TTTCGGGAGTTCGGTCCAGG 61.823 60.000 2.42 0.00 38.52 4.45
945 2428 4.766007 CTGTGTGACTCTTGATTGTTTCG 58.234 43.478 0.00 0.00 0.00 3.46
1098 2581 1.704641 GGAGGTTGGCAAACTCCTTT 58.295 50.000 43.11 15.04 36.48 3.11
1306 2789 0.107214 TCGTGGATTTGCAGATCCCC 60.107 55.000 28.36 19.05 44.12 4.81
1316 2799 1.304134 GCCCCCTGTTCGTGGATTT 60.304 57.895 0.00 0.00 0.00 2.17
1317 2800 2.075355 TTGCCCCCTGTTCGTGGATT 62.075 55.000 0.00 0.00 0.00 3.01
1323 2829 1.134946 GATTTGATTGCCCCCTGTTCG 59.865 52.381 0.00 0.00 0.00 3.95
1333 2839 2.177173 GCGAAACCGAGATTTGATTGC 58.823 47.619 0.00 0.00 0.00 3.56
1427 2934 1.028905 CTCATGTCTCGACCTCCTCC 58.971 60.000 0.00 0.00 0.00 4.30
1568 3077 0.606944 TCGGTAATGTTGGGGTGTGC 60.607 55.000 0.00 0.00 0.00 4.57
1676 3189 0.672342 GTTCATCCATGCATGCCTCC 59.328 55.000 21.69 2.63 0.00 4.30
1728 3243 7.661127 AACAAACAAACAGGGTTAAACTTTC 57.339 32.000 0.00 0.00 0.00 2.62
1840 3367 0.798776 CTTTGGTTCCTGCAGTAGCG 59.201 55.000 13.81 0.00 46.23 4.26
1886 3413 3.758554 CCACAACTTTCGATCCAATTCCT 59.241 43.478 0.00 0.00 0.00 3.36
1892 3419 5.097742 ACATATCCACAACTTTCGATCCA 57.902 39.130 0.00 0.00 0.00 3.41
2105 3632 9.658799 CATCACTACTATAATATTGTGAAGGGG 57.341 37.037 7.79 0.00 37.85 4.79
2217 3744 9.288576 CATAGCAGGATTGAAATTCCTAACATA 57.711 33.333 0.00 0.00 31.73 2.29
2218 3745 7.781693 ACATAGCAGGATTGAAATTCCTAACAT 59.218 33.333 0.00 0.00 31.73 2.71
2351 3878 4.253685 AGTTCCGTTGATTGGTGTATCAG 58.746 43.478 0.00 0.00 36.03 2.90
2424 3951 3.507233 CCAGAGCATCAAACTTTGGCTTA 59.493 43.478 6.69 0.00 37.82 3.09
2548 4075 9.814899 TGCATTTTCAAAAGAAAGTTCATAAGA 57.185 25.926 0.00 0.00 0.00 2.10
2659 4186 3.394274 TCAAAGATCCACCTCACCTTCAA 59.606 43.478 0.00 0.00 0.00 2.69
2682 4209 4.929819 AAAGCAACTGGTACCGAATTTT 57.070 36.364 7.57 0.62 0.00 1.82
2688 4215 3.749088 TGAATGTAAAGCAACTGGTACCG 59.251 43.478 7.57 4.79 0.00 4.02
2887 4415 3.988976 TGAGATTCCAGAGGGACAAAG 57.011 47.619 0.00 0.00 44.89 2.77
2915 4443 5.337491 GCATGTTATGGAATTCACCCAAGTT 60.337 40.000 7.93 0.00 37.22 2.66
2939 4467 1.247567 ATTTCAACAAGCCCAGTCCG 58.752 50.000 0.00 0.00 0.00 4.79
2962 4490 6.734104 AAGCACAAAGATCTGAGTTATGTC 57.266 37.500 0.00 0.00 0.00 3.06
2972 4500 4.276926 GTCCAACAGAAAGCACAAAGATCT 59.723 41.667 0.00 0.00 0.00 2.75
2973 4501 4.540824 GTCCAACAGAAAGCACAAAGATC 58.459 43.478 0.00 0.00 0.00 2.75
3008 4536 0.326595 TGAAATAAGCTGGCGACCCA 59.673 50.000 0.00 0.00 39.32 4.51
3013 4541 6.651755 AAATTTCAATGAAATAAGCTGGCG 57.348 33.333 20.05 0.00 40.77 5.69
3049 4577 4.580580 CCTCTTGTACAAAGGAGCAAAGTT 59.419 41.667 22.32 0.00 31.44 2.66
3051 4579 4.389374 TCCTCTTGTACAAAGGAGCAAAG 58.611 43.478 24.04 11.36 34.26 2.77
3095 4625 3.246699 CGACAAACGACAAGGTACATGTT 59.753 43.478 2.30 0.00 41.73 2.71
3096 4626 2.798283 CGACAAACGACAAGGTACATGT 59.202 45.455 2.69 2.69 45.55 3.21
3137 4667 0.457443 GGCAGCCTAAAGATTGGTGC 59.543 55.000 3.29 4.47 33.13 5.01
3142 4672 2.172293 CCTCTCTGGCAGCCTAAAGATT 59.828 50.000 14.15 0.00 0.00 2.40
3155 4685 5.246429 ACTTGTTAGGTTAACTCCTCTCTGG 59.754 44.000 5.42 0.00 39.38 3.86
3156 4686 6.015350 TCACTTGTTAGGTTAACTCCTCTCTG 60.015 42.308 5.42 0.00 39.38 3.35
3157 4687 6.015265 GTCACTTGTTAGGTTAACTCCTCTCT 60.015 42.308 5.42 0.00 39.38 3.10
3177 4709 3.953712 TGTCATTACGGACATGTCACT 57.046 42.857 26.47 13.17 42.56 3.41
3188 4720 4.627035 TCAGAAGTGCTCAATGTCATTACG 59.373 41.667 0.00 0.00 0.00 3.18
3193 4725 3.999001 GTCATCAGAAGTGCTCAATGTCA 59.001 43.478 0.00 0.00 0.00 3.58
3194 4726 4.093115 CAGTCATCAGAAGTGCTCAATGTC 59.907 45.833 0.00 0.00 0.00 3.06
3201 4733 4.077300 TGTTTCAGTCATCAGAAGTGCT 57.923 40.909 0.00 0.00 0.00 4.40
3222 4754 8.462016 GTCATTGCAGTTCAGGAATTTAAGTAT 58.538 33.333 0.00 0.00 0.00 2.12
3224 4756 6.294731 GGTCATTGCAGTTCAGGAATTTAAGT 60.295 38.462 0.00 0.00 0.00 2.24
3234 4766 1.901591 ACAGGGTCATTGCAGTTCAG 58.098 50.000 0.00 0.00 0.00 3.02
3262 4796 2.429610 CTGGATGCCATTTTCTTGGGAG 59.570 50.000 0.00 0.00 40.73 4.30
3284 4818 1.136147 GCCTCATTGCGCTCAGTTG 59.864 57.895 9.73 0.00 0.00 3.16
3287 4821 0.585357 GTATGCCTCATTGCGCTCAG 59.415 55.000 9.73 0.00 0.00 3.35
3292 4826 2.802816 GGAAGTAGTATGCCTCATTGCG 59.197 50.000 0.00 0.00 0.00 4.85
3300 4834 2.223994 GGGACGAAGGAAGTAGTATGCC 60.224 54.545 0.00 0.00 0.00 4.40
3315 4849 5.717078 AACGCTCTTATATTATGGGACGA 57.283 39.130 0.00 0.00 0.00 4.20
3321 4856 8.062231 AGTGTCGAAAACGCTCTTATATTATG 57.938 34.615 0.00 0.00 45.69 1.90
3324 4859 9.178427 GTATAGTGTCGAAAACGCTCTTATATT 57.822 33.333 0.00 0.00 45.69 1.28
3328 4863 6.187125 AGTATAGTGTCGAAAACGCTCTTA 57.813 37.500 0.00 0.00 45.69 2.10
3329 4864 5.056894 AGTATAGTGTCGAAAACGCTCTT 57.943 39.130 0.00 0.00 45.69 2.85
3330 4865 4.698583 AGTATAGTGTCGAAAACGCTCT 57.301 40.909 0.00 0.00 45.69 4.09
3705 5240 8.335532 TCAGAATTTCATTTCGTTTCTACCAT 57.664 30.769 0.00 0.00 0.00 3.55
3712 5247 8.348285 TCCCTTATCAGAATTTCATTTCGTTT 57.652 30.769 0.00 0.00 0.00 3.60
3713 5248 7.938140 TCCCTTATCAGAATTTCATTTCGTT 57.062 32.000 0.00 0.00 0.00 3.85
3715 5250 8.623903 TGATTCCCTTATCAGAATTTCATTTCG 58.376 33.333 0.00 0.00 32.91 3.46
3720 5255 8.698210 CCAAATGATTCCCTTATCAGAATTTCA 58.302 33.333 0.00 0.00 37.91 2.69
3721 5256 7.654923 GCCAAATGATTCCCTTATCAGAATTTC 59.345 37.037 0.00 0.00 37.91 2.17
3722 5257 7.346436 AGCCAAATGATTCCCTTATCAGAATTT 59.654 33.333 0.00 0.00 37.91 1.82
3723 5258 6.842807 AGCCAAATGATTCCCTTATCAGAATT 59.157 34.615 0.00 0.00 37.91 2.17
3724 5259 6.267014 CAGCCAAATGATTCCCTTATCAGAAT 59.733 38.462 0.00 0.00 37.91 2.40
3725 5260 5.595542 CAGCCAAATGATTCCCTTATCAGAA 59.404 40.000 0.00 0.00 37.91 3.02
3726 5261 5.103982 TCAGCCAAATGATTCCCTTATCAGA 60.104 40.000 0.00 0.00 37.91 3.27
3727 5262 5.135383 TCAGCCAAATGATTCCCTTATCAG 58.865 41.667 0.00 0.00 37.91 2.90
3728 5263 5.128033 TCAGCCAAATGATTCCCTTATCA 57.872 39.130 0.00 0.00 38.78 2.15
3729 5264 6.294955 GGATTCAGCCAAATGATTCCCTTATC 60.295 42.308 6.44 0.00 41.07 1.75
3730 5265 5.541484 GGATTCAGCCAAATGATTCCCTTAT 59.459 40.000 6.44 0.00 41.07 1.73
3731 5266 4.895297 GGATTCAGCCAAATGATTCCCTTA 59.105 41.667 6.44 0.00 41.07 2.69
3732 5267 3.708121 GGATTCAGCCAAATGATTCCCTT 59.292 43.478 6.44 0.00 41.07 3.95
3733 5268 3.303049 GGATTCAGCCAAATGATTCCCT 58.697 45.455 6.44 0.00 41.07 4.20
3734 5269 3.033184 TGGATTCAGCCAAATGATTCCC 58.967 45.455 12.61 0.00 44.04 3.97
3735 5270 3.956199 TCTGGATTCAGCCAAATGATTCC 59.044 43.478 0.00 9.60 44.54 3.01
3736 5271 5.786264 ATCTGGATTCAGCCAAATGATTC 57.214 39.130 0.00 0.00 40.69 2.52
3737 5272 5.070047 GGAATCTGGATTCAGCCAAATGATT 59.930 40.000 20.41 0.00 46.77 2.57
3738 5273 4.587684 GGAATCTGGATTCAGCCAAATGAT 59.412 41.667 20.41 0.00 46.77 2.45
3739 5274 3.956199 GGAATCTGGATTCAGCCAAATGA 59.044 43.478 20.41 0.00 46.77 2.57
3740 5275 3.702548 TGGAATCTGGATTCAGCCAAATG 59.297 43.478 20.41 0.00 46.77 2.32
3741 5276 3.985127 TGGAATCTGGATTCAGCCAAAT 58.015 40.909 20.41 0.00 46.77 2.32
3742 5277 3.454719 TGGAATCTGGATTCAGCCAAA 57.545 42.857 20.41 1.70 46.77 3.28
3798 5333 1.478105 GTTGGCATGGATTTCACCTCC 59.522 52.381 0.00 0.00 0.00 4.30
3811 5346 4.832266 TGTTCCTCATTTTAGTGTTGGCAT 59.168 37.500 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.