Multiple sequence alignment - TraesCS5A01G297400

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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 TraesCS5A01G297400 chr5A 100.000 3134 0 0 1 3134 505208629 505205496 0.000000e+00 5788.0
1 TraesCS5A01G297400 chr5A 84.290 331 26 13 553 869 505290162 505289844 1.830000e-77 300.0
2 TraesCS5A01G297400 chr5D 90.508 2718 166 47 137 2806 399633922 399631249 0.000000e+00 3506.0
3 TraesCS5A01G297400 chr5D 93.333 330 19 2 2807 3134 399631219 399630891 4.700000e-133 484.0
4 TraesCS5A01G297400 chr5B 89.173 2032 123 46 554 2547 479778948 479776976 0.000000e+00 2444.0
5 TraesCS5A01G297400 chr4D 84.286 140 18 3 2 137 80957896 80958035 1.960000e-27 134.0
6 TraesCS5A01G297400 chr6A 100.000 30 0 0 2947 2976 559166902 559166873 4.370000e-04 56.5


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 TraesCS5A01G297400 chr5A 505205496 505208629 3133 True 5788 5788 100.0000 1 3134 1 chr5A.!!$R1 3133
1 TraesCS5A01G297400 chr5D 399630891 399633922 3031 True 1995 3506 91.9205 137 3134 2 chr5D.!!$R1 2997
2 TraesCS5A01G297400 chr5B 479776976 479778948 1972 True 2444 2444 89.1730 554 2547 1 chr5B.!!$R1 1993

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
30 31 0.036732 TGGTGATCCACTGGCTTCAC 59.963 55.0 16.89 16.89 39.03 3.18 F
350 354 0.108396 TCTTACCAGCAGCAGCAACA 59.892 50.0 3.17 0.00 45.49 3.33 F
520 525 0.178998 GTGCTGCTGATGATGGGGAT 60.179 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2010 2.709125 TTCGTTGTCCTGCTCCACCG 62.709 60.000 0.0 0.0 0.0 4.94 R
2117 2184 1.513586 CGTCACGTCTCGCCTAACC 60.514 63.158 0.0 0.0 0.0 2.85 R
2299 2369 2.598589 CATGCAGCAAACACATGTACC 58.401 47.619 0.0 0.0 37.1 3.34 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 2.206576 AAGGAGCTGTTTGGTGATCC 57.793 50.000 0.00 0.00 0.00 3.36
20 21 1.067295 AGGAGCTGTTTGGTGATCCA 58.933 50.000 0.00 0.00 42.66 3.41
21 22 1.168714 GGAGCTGTTTGGTGATCCAC 58.831 55.000 0.00 0.00 44.22 4.02
22 23 1.271597 GGAGCTGTTTGGTGATCCACT 60.272 52.381 0.00 0.00 44.22 4.00
23 24 1.808945 GAGCTGTTTGGTGATCCACTG 59.191 52.381 0.00 0.00 44.22 3.66
24 25 0.883833 GCTGTTTGGTGATCCACTGG 59.116 55.000 0.00 0.00 44.22 4.00
25 26 0.883833 CTGTTTGGTGATCCACTGGC 59.116 55.000 0.00 0.00 44.22 4.85
26 27 0.478072 TGTTTGGTGATCCACTGGCT 59.522 50.000 0.00 0.00 44.22 4.75
27 28 1.133513 TGTTTGGTGATCCACTGGCTT 60.134 47.619 0.00 0.00 44.22 4.35
28 29 1.541588 GTTTGGTGATCCACTGGCTTC 59.458 52.381 0.00 0.00 44.22 3.86
29 30 0.770499 TTGGTGATCCACTGGCTTCA 59.230 50.000 0.00 0.00 44.22 3.02
30 31 0.036732 TGGTGATCCACTGGCTTCAC 59.963 55.000 16.89 16.89 39.03 3.18
31 32 0.678048 GGTGATCCACTGGCTTCACC 60.678 60.000 23.66 23.66 43.22 4.02
43 44 3.790152 GGCTTCACCAATTTGAGGATC 57.210 47.619 0.00 0.00 38.86 3.36
44 45 3.359950 GGCTTCACCAATTTGAGGATCT 58.640 45.455 0.00 0.00 38.86 2.75
45 46 3.129988 GGCTTCACCAATTTGAGGATCTG 59.870 47.826 0.00 0.00 38.86 2.90
46 47 3.428589 GCTTCACCAATTTGAGGATCTGC 60.429 47.826 0.00 0.00 34.92 4.26
47 48 3.438216 TCACCAATTTGAGGATCTGCA 57.562 42.857 0.00 0.00 34.92 4.41
48 49 3.349927 TCACCAATTTGAGGATCTGCAG 58.650 45.455 7.63 7.63 34.92 4.41
49 50 3.009363 TCACCAATTTGAGGATCTGCAGA 59.991 43.478 20.79 20.79 34.92 4.26
50 51 3.377485 CACCAATTTGAGGATCTGCAGAG 59.623 47.826 22.96 6.11 34.92 3.35
51 52 2.358267 CCAATTTGAGGATCTGCAGAGC 59.642 50.000 23.68 23.68 34.92 4.09
52 53 3.014623 CAATTTGAGGATCTGCAGAGCA 58.985 45.455 31.24 18.39 36.92 4.26
53 54 3.579534 ATTTGAGGATCTGCAGAGCAT 57.420 42.857 31.24 26.41 38.13 3.79
54 55 2.616634 TTGAGGATCTGCAGAGCATC 57.383 50.000 33.12 33.12 41.06 3.91
55 56 1.790818 TGAGGATCTGCAGAGCATCT 58.209 50.000 36.85 24.84 41.23 2.90
56 57 2.954792 TGAGGATCTGCAGAGCATCTA 58.045 47.619 36.85 24.63 41.23 1.98
57 58 3.508426 TGAGGATCTGCAGAGCATCTAT 58.492 45.455 36.85 17.58 41.23 1.98
58 59 3.902467 TGAGGATCTGCAGAGCATCTATT 59.098 43.478 36.85 14.33 41.23 1.73
59 60 4.021280 TGAGGATCTGCAGAGCATCTATTC 60.021 45.833 36.85 20.97 41.23 1.75
60 61 7.024499 TGAGGATCTGCAGAGCATCTATTCC 62.024 48.000 36.85 27.34 41.23 3.01
66 67 3.223661 GAGCATCTATTCCCCTGCG 57.776 57.895 0.00 0.00 39.57 5.18
67 68 0.952984 GAGCATCTATTCCCCTGCGC 60.953 60.000 0.00 0.00 39.57 6.09
68 69 1.968540 GCATCTATTCCCCTGCGCC 60.969 63.158 4.18 0.00 0.00 6.53
69 70 1.451504 CATCTATTCCCCTGCGCCA 59.548 57.895 4.18 0.00 0.00 5.69
70 71 0.604780 CATCTATTCCCCTGCGCCAG 60.605 60.000 4.18 1.92 0.00 4.85
71 72 2.403132 ATCTATTCCCCTGCGCCAGC 62.403 60.000 4.18 0.00 45.41 4.85
83 84 2.527442 GCGCCAGCACTTTTAACTAG 57.473 50.000 0.00 0.00 44.35 2.57
84 85 1.465856 GCGCCAGCACTTTTAACTAGC 60.466 52.381 0.00 0.00 44.35 3.42
85 86 1.201921 CGCCAGCACTTTTAACTAGCG 60.202 52.381 0.00 0.00 35.42 4.26
86 87 1.465856 GCCAGCACTTTTAACTAGCGC 60.466 52.381 0.00 0.00 0.00 5.92
87 88 2.076863 CCAGCACTTTTAACTAGCGCT 58.923 47.619 17.26 17.26 31.54 5.92
88 89 2.094417 CCAGCACTTTTAACTAGCGCTC 59.906 50.000 16.34 0.00 29.05 5.03
89 90 2.094417 CAGCACTTTTAACTAGCGCTCC 59.906 50.000 16.34 0.00 29.05 4.70
90 91 1.060698 GCACTTTTAACTAGCGCTCCG 59.939 52.381 16.34 9.49 0.00 4.63
102 103 3.706373 GCTCCGCCAACTCCAGGA 61.706 66.667 0.00 0.00 0.00 3.86
103 104 2.581354 CTCCGCCAACTCCAGGAG 59.419 66.667 15.72 15.72 43.43 3.69
104 105 3.672295 CTCCGCCAACTCCAGGAGC 62.672 68.421 17.31 2.00 42.99 4.70
107 108 2.125350 GCCAACTCCAGGAGCGAG 60.125 66.667 17.31 6.12 32.04 5.03
108 109 2.650116 GCCAACTCCAGGAGCGAGA 61.650 63.158 17.31 0.00 32.04 4.04
109 110 1.515020 CCAACTCCAGGAGCGAGAG 59.485 63.158 17.31 2.02 32.04 3.20
110 111 1.254284 CCAACTCCAGGAGCGAGAGT 61.254 60.000 17.31 0.00 42.58 3.24
111 112 0.108898 CAACTCCAGGAGCGAGAGTG 60.109 60.000 17.31 1.78 39.92 3.51
112 113 1.254284 AACTCCAGGAGCGAGAGTGG 61.254 60.000 17.31 0.00 39.92 4.00
113 114 1.379176 CTCCAGGAGCGAGAGTGGA 60.379 63.158 2.60 0.00 37.52 4.02
114 115 1.379176 TCCAGGAGCGAGAGTGGAG 60.379 63.158 0.00 0.00 34.03 3.86
115 116 2.493973 CAGGAGCGAGAGTGGAGC 59.506 66.667 0.00 0.00 0.00 4.70
116 117 3.137459 AGGAGCGAGAGTGGAGCG 61.137 66.667 0.00 0.00 35.78 5.03
117 118 4.200283 GGAGCGAGAGTGGAGCGG 62.200 72.222 0.00 0.00 35.78 5.52
118 119 4.200283 GAGCGAGAGTGGAGCGGG 62.200 72.222 0.00 0.00 35.78 6.13
121 122 3.522731 CGAGAGTGGAGCGGGGAG 61.523 72.222 0.00 0.00 0.00 4.30
122 123 3.151022 GAGAGTGGAGCGGGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
123 124 4.787280 AGAGTGGAGCGGGGAGGG 62.787 72.222 0.00 0.00 0.00 4.30
153 154 7.696017 ACAGGCCCTAAGTTTCTTAATCTTAA 58.304 34.615 0.00 0.00 0.00 1.85
181 185 6.266168 TGAAGAAAATTGGCGATAACACAT 57.734 33.333 0.00 0.00 0.00 3.21
195 199 6.400422 CGATAACACATACGCTAGTTTGTTC 58.600 40.000 0.00 0.00 39.85 3.18
202 206 7.095523 ACACATACGCTAGTTTGTTCGTTAAAT 60.096 33.333 0.00 0.00 39.85 1.40
204 208 7.742963 ACATACGCTAGTTTGTTCGTTAAATTG 59.257 33.333 0.00 0.00 39.00 2.32
294 298 0.331616 ATTTTGGAACCGGGCTAGCT 59.668 50.000 15.72 0.00 0.00 3.32
304 308 1.224870 GGGCTAGCTCCCTTTCCAC 59.775 63.158 15.72 0.00 43.13 4.02
349 353 0.519077 GTCTTACCAGCAGCAGCAAC 59.481 55.000 3.17 0.00 45.49 4.17
350 354 0.108396 TCTTACCAGCAGCAGCAACA 59.892 50.000 3.17 0.00 45.49 3.33
369 373 2.696504 GGGAGGGGAAAGGGGAGG 60.697 72.222 0.00 0.00 0.00 4.30
370 374 2.459710 GGAGGGGAAAGGGGAGGA 59.540 66.667 0.00 0.00 0.00 3.71
421 425 4.728882 GCATCAAGCAATACGTCAAGAAGG 60.729 45.833 0.00 0.00 44.79 3.46
495 500 3.474570 GGACGCCATCTCCTGCCT 61.475 66.667 0.00 0.00 0.00 4.75
520 525 0.178998 GTGCTGCTGATGATGGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
525 530 1.285667 TGCTGATGATGGGGATGTTGT 59.714 47.619 0.00 0.00 0.00 3.32
663 685 4.880426 TCGGCCATCTCCCTCCCC 62.880 72.222 2.24 0.00 0.00 4.81
671 693 4.806339 CTCCCTCCCCGCTTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
672 694 4.348495 TCCCTCCCCGCTTCCCTT 62.348 66.667 0.00 0.00 0.00 3.95
673 695 3.798511 CCCTCCCCGCTTCCCTTC 61.799 72.222 0.00 0.00 0.00 3.46
674 696 3.009115 CCTCCCCGCTTCCCTTCA 61.009 66.667 0.00 0.00 0.00 3.02
675 697 2.378634 CCTCCCCGCTTCCCTTCAT 61.379 63.158 0.00 0.00 0.00 2.57
676 698 1.153086 CTCCCCGCTTCCCTTCATG 60.153 63.158 0.00 0.00 0.00 3.07
677 699 2.124151 CCCCGCTTCCCTTCATGG 60.124 66.667 0.00 0.00 0.00 3.66
678 700 2.830370 CCCGCTTCCCTTCATGGC 60.830 66.667 0.00 0.00 0.00 4.40
679 701 2.273449 CCGCTTCCCTTCATGGCT 59.727 61.111 0.00 0.00 0.00 4.75
680 702 1.379044 CCGCTTCCCTTCATGGCTT 60.379 57.895 0.00 0.00 0.00 4.35
681 703 1.379642 CCGCTTCCCTTCATGGCTTC 61.380 60.000 0.00 0.00 0.00 3.86
682 704 0.393537 CGCTTCCCTTCATGGCTTCT 60.394 55.000 0.00 0.00 0.00 2.85
683 705 1.844687 GCTTCCCTTCATGGCTTCTT 58.155 50.000 0.00 0.00 0.00 2.52
684 706 1.747924 GCTTCCCTTCATGGCTTCTTC 59.252 52.381 0.00 0.00 0.00 2.87
685 707 2.012673 CTTCCCTTCATGGCTTCTTCG 58.987 52.381 0.00 0.00 0.00 3.79
686 708 0.984230 TCCCTTCATGGCTTCTTCGT 59.016 50.000 0.00 0.00 0.00 3.85
687 709 1.066143 TCCCTTCATGGCTTCTTCGTC 60.066 52.381 0.00 0.00 0.00 4.20
688 710 1.373570 CCTTCATGGCTTCTTCGTCC 58.626 55.000 0.00 0.00 0.00 4.79
689 711 1.002366 CTTCATGGCTTCTTCGTCCG 58.998 55.000 0.00 0.00 0.00 4.79
690 712 1.019278 TTCATGGCTTCTTCGTCCGC 61.019 55.000 0.00 0.00 0.00 5.54
691 713 2.509336 ATGGCTTCTTCGTCCGCG 60.509 61.111 0.00 0.00 39.92 6.46
753 775 0.397535 GCCATGATCCCACCACCATT 60.398 55.000 0.00 0.00 0.00 3.16
754 776 1.405872 CCATGATCCCACCACCATTG 58.594 55.000 0.00 0.00 0.00 2.82
755 777 1.342275 CCATGATCCCACCACCATTGT 60.342 52.381 0.00 0.00 0.00 2.71
756 778 1.752498 CATGATCCCACCACCATTGTG 59.248 52.381 0.00 0.00 42.39 3.33
757 779 0.776810 TGATCCCACCACCATTGTGT 59.223 50.000 0.00 0.00 41.09 3.72
758 780 1.146774 TGATCCCACCACCATTGTGTT 59.853 47.619 0.00 0.00 41.09 3.32
764 786 1.367102 CCACCATTGTGTTGTGCCC 59.633 57.895 0.00 0.00 41.09 5.36
792 814 0.725117 GTCCGTTGACGCAATTAGGG 59.275 55.000 0.00 0.00 38.18 3.53
794 816 0.446222 CCGTTGACGCAATTAGGGTG 59.554 55.000 0.00 0.00 44.33 4.61
795 817 1.434555 CGTTGACGCAATTAGGGTGA 58.565 50.000 3.09 0.00 44.33 4.02
893 922 1.681538 TACATCGGAGCTCTGTCCTC 58.318 55.000 21.88 0.00 34.00 3.71
894 923 1.040339 ACATCGGAGCTCTGTCCTCC 61.040 60.000 21.88 0.00 44.35 4.30
895 924 0.754957 CATCGGAGCTCTGTCCTCCT 60.755 60.000 21.88 0.00 45.37 3.69
905 934 3.244491 GCTCTGTCCTCCTATCCTACGTA 60.244 52.174 0.00 0.00 0.00 3.57
908 937 2.224378 TGTCCTCCTATCCTACGTACGG 60.224 54.545 21.06 2.00 0.00 4.02
909 938 2.050144 TCCTCCTATCCTACGTACGGT 58.950 52.381 21.06 7.87 0.00 4.83
910 958 2.037772 TCCTCCTATCCTACGTACGGTC 59.962 54.545 21.06 0.00 0.00 4.79
911 959 2.421619 CTCCTATCCTACGTACGGTCC 58.578 57.143 21.06 0.00 0.00 4.46
921 969 0.456221 CGTACGGTCCTGCTTGATCT 59.544 55.000 7.57 0.00 0.00 2.75
922 970 1.534175 CGTACGGTCCTGCTTGATCTC 60.534 57.143 7.57 0.00 0.00 2.75
925 973 1.529309 GGTCCTGCTTGATCTCCCC 59.471 63.158 0.00 0.00 0.00 4.81
935 983 2.769621 ATCTCCCCATCGCTGCCA 60.770 61.111 0.00 0.00 0.00 4.92
938 986 3.008517 TCCCCATCGCTGCCAAGA 61.009 61.111 0.00 0.00 0.00 3.02
939 987 2.194056 CCCCATCGCTGCCAAGAT 59.806 61.111 0.00 0.00 0.00 2.40
940 988 1.454479 CCCCATCGCTGCCAAGATT 60.454 57.895 0.00 0.00 0.00 2.40
941 989 1.731433 CCCCATCGCTGCCAAGATTG 61.731 60.000 0.00 0.00 0.00 2.67
972 1021 1.367840 GGGAGGGACAATCGATCGG 59.632 63.158 16.41 1.30 0.00 4.18
973 1022 1.301009 GGAGGGACAATCGATCGGC 60.301 63.158 16.41 0.00 0.00 5.54
974 1023 1.661821 GAGGGACAATCGATCGGCG 60.662 63.158 16.41 0.00 42.69 6.46
1466 1515 3.796443 CGCCGAGGAAGACGACGA 61.796 66.667 0.00 0.00 38.71 4.20
1921 1988 1.220169 CGAGAAGCTCATCATGGCCG 61.220 60.000 0.00 0.00 0.00 6.13
2117 2184 2.148768 GTTCCTAACCAACTTGACGGG 58.851 52.381 0.00 0.00 0.00 5.28
2251 2320 3.887621 ATCGAAAGCTAAGCAGTGGTA 57.112 42.857 0.00 0.00 0.00 3.25
2277 2347 2.038557 AGACCACGAGTGCAAATAGGTT 59.961 45.455 0.00 0.00 0.00 3.50
2293 2363 9.748708 GCAAATAGGTTAATCATGAAGCAATTA 57.251 29.630 0.00 0.00 0.00 1.40
2299 2369 8.199449 AGGTTAATCATGAAGCAATTATTGTGG 58.801 33.333 0.00 0.00 0.00 4.17
2318 2388 1.545582 GGGTACATGTGTTTGCTGCAT 59.454 47.619 9.11 0.00 0.00 3.96
2325 2395 1.612950 TGTGTTTGCTGCATGGTTAGG 59.387 47.619 1.84 0.00 0.00 2.69
2329 2399 1.993956 TTGCTGCATGGTTAGGTTGT 58.006 45.000 1.84 0.00 0.00 3.32
2336 2406 4.942852 TGCATGGTTAGGTTGTGAAAAAG 58.057 39.130 0.00 0.00 0.00 2.27
2365 2435 2.582636 AGCATTCCCTAACCAATCACCT 59.417 45.455 0.00 0.00 0.00 4.00
2419 2491 3.489047 CGGTTTGAAAATGCGACAATTGT 59.511 39.130 11.78 11.78 0.00 2.71
2423 2495 6.019479 GGTTTGAAAATGCGACAATTGTGTTA 60.019 34.615 17.58 1.60 38.41 2.41
2429 2501 6.597262 AATGCGACAATTGTGTTATCGATA 57.403 33.333 17.58 0.00 38.41 2.92
2478 2550 5.615289 GCCCTCAAGATCAAGCTATTTCTA 58.385 41.667 0.00 0.00 0.00 2.10
2518 2592 3.434319 GTCAGCACACGGGCATGG 61.434 66.667 0.00 0.00 35.83 3.66
2542 2616 1.149627 TTGGCTACCGTGGCAACTT 59.850 52.632 9.29 0.00 45.43 2.66
2551 2625 1.270625 CCGTGGCAACTTACAAGAGGA 60.271 52.381 0.00 0.00 37.61 3.71
2554 2628 1.073284 TGGCAACTTACAAGAGGACCC 59.927 52.381 0.00 0.00 37.61 4.46
2557 2631 2.779506 CAACTTACAAGAGGACCCCAC 58.220 52.381 0.00 0.00 0.00 4.61
2559 2633 1.132495 ACTTACAAGAGGACCCCACCT 60.132 52.381 0.00 0.00 43.64 4.00
2560 2634 1.279271 CTTACAAGAGGACCCCACCTG 59.721 57.143 0.00 0.00 40.73 4.00
2570 2644 0.923358 ACCCCACCTGTCAGTTTCAA 59.077 50.000 0.00 0.00 0.00 2.69
2579 2653 3.312421 CCTGTCAGTTTCAACGTCAATGT 59.688 43.478 0.00 0.00 0.00 2.71
2580 2654 4.271590 TGTCAGTTTCAACGTCAATGTG 57.728 40.909 0.00 0.00 0.00 3.21
2589 2663 7.853929 AGTTTCAACGTCAATGTGTGTTTATAC 59.146 33.333 0.00 0.00 0.00 1.47
2590 2664 6.846325 TCAACGTCAATGTGTGTTTATACA 57.154 33.333 0.00 0.00 32.26 2.29
2603 2677 7.758076 TGTGTGTTTATACAGAGTTTAGATCGG 59.242 37.037 0.00 0.00 34.24 4.18
2612 2686 4.096532 CAGAGTTTAGATCGGTCTGTAGCA 59.903 45.833 8.91 0.00 35.87 3.49
2617 2691 2.613739 GATCGGTCTGTAGCAGCGCA 62.614 60.000 11.47 0.00 0.00 6.09
2618 2692 2.890847 ATCGGTCTGTAGCAGCGCAC 62.891 60.000 11.47 0.00 0.00 5.34
2621 2695 2.997315 TCTGTAGCAGCGCACCCT 60.997 61.111 11.47 4.80 0.00 4.34
2623 2697 1.218047 CTGTAGCAGCGCACCCTAA 59.782 57.895 11.47 0.00 0.00 2.69
2636 2710 2.359900 CACCCTAATCTTGGTGCTGAC 58.640 52.381 0.00 0.00 44.98 3.51
2638 2712 2.290323 ACCCTAATCTTGGTGCTGACAC 60.290 50.000 0.00 0.00 46.66 3.67
2655 2729 7.429920 GTGCTGACACGTAAAAATTACAGAAAA 59.570 33.333 0.00 0.00 36.98 2.29
2658 2732 8.789881 TGACACGTAAAAATTACAGAAAATGG 57.210 30.769 0.00 0.00 0.00 3.16
2671 2745 4.156008 ACAGAAAATGGTACCAATTCGCTC 59.844 41.667 25.94 16.88 33.74 5.03
2672 2746 4.155826 CAGAAAATGGTACCAATTCGCTCA 59.844 41.667 25.94 2.41 33.74 4.26
2677 2751 1.732259 GGTACCAATTCGCTCACACTG 59.268 52.381 7.15 0.00 0.00 3.66
2680 2754 0.957395 CCAATTCGCTCACACTGCCT 60.957 55.000 0.00 0.00 0.00 4.75
2689 2763 2.357009 GCTCACACTGCCTCAATTATGG 59.643 50.000 0.00 0.00 0.00 2.74
2690 2764 3.614092 CTCACACTGCCTCAATTATGGT 58.386 45.455 0.00 0.00 0.00 3.55
2693 2767 4.225042 TCACACTGCCTCAATTATGGTACT 59.775 41.667 0.00 0.00 0.00 2.73
2737 2811 4.372656 AGAGAGTCGAAGAAAACCTTGTG 58.627 43.478 0.00 0.00 39.69 3.33
2741 2815 5.064834 AGAGTCGAAGAAAACCTTGTGAAAC 59.935 40.000 0.00 0.00 39.69 2.78
2744 2818 3.064271 CGAAGAAAACCTTGTGAAACGGA 59.936 43.478 0.00 0.00 42.39 4.69
2746 2820 5.588240 GAAGAAAACCTTGTGAAACGGATT 58.412 37.500 0.00 0.00 42.39 3.01
2759 2833 5.648960 GTGAAACGGATTGGAAGGGTAATAA 59.351 40.000 0.00 0.00 0.00 1.40
2763 2837 5.434408 ACGGATTGGAAGGGTAATAAGAAC 58.566 41.667 0.00 0.00 0.00 3.01
2768 2842 6.584185 TTGGAAGGGTAATAAGAACTTTGC 57.416 37.500 0.00 0.00 0.00 3.68
2774 2848 4.379082 GGGTAATAAGAACTTTGCGTGTGG 60.379 45.833 0.00 0.00 0.00 4.17
2821 2924 2.605837 TAGTTGTTTGGCGAGTGACA 57.394 45.000 0.00 0.00 0.00 3.58
2845 2948 3.266772 AGTGCTCTTTGGGGTTATCATCA 59.733 43.478 0.00 0.00 0.00 3.07
2863 2966 5.487433 TCATCATTTCCTAGCAACTTTCGA 58.513 37.500 0.00 0.00 0.00 3.71
2870 2973 4.385825 TCCTAGCAACTTTCGAAACATGT 58.614 39.130 6.47 0.56 0.00 3.21
2915 3018 8.607441 TGAGAGAATGATTATAAATTCGGTGG 57.393 34.615 4.86 0.00 37.77 4.61
2925 3028 1.604604 AATTCGGTGGTGTTGTCCAG 58.395 50.000 0.00 0.00 38.23 3.86
2967 3070 4.707210 ATGGCAAAACGAACATTTTTCG 57.293 36.364 3.52 3.52 46.36 3.46
3003 3106 1.613437 CGGGAACATGGCAGTTTCTTT 59.387 47.619 9.88 0.00 0.00 2.52
3029 3132 4.378774 CAATCCTGGCAATTTTCACAACA 58.621 39.130 0.00 0.00 0.00 3.33
3037 3140 7.804129 CCTGGCAATTTTCACAACAAAATTATG 59.196 33.333 4.10 0.00 41.82 1.90
3039 3142 8.680903 TGGCAATTTTCACAACAAAATTATGTT 58.319 25.926 4.10 0.00 41.82 2.71
3060 3165 4.130286 TGCCCGTTTTTGAAGAATTTGT 57.870 36.364 0.00 0.00 0.00 2.83
3083 3188 4.325741 TCATAAAAACATTCGCAAATGCCG 59.674 37.500 0.00 0.00 45.16 5.69
3088 3193 1.378514 ATTCGCAAATGCCGTCCCT 60.379 52.632 0.00 0.00 37.91 4.20
3098 3203 2.566570 GCCGTCCCTCCTAGCTAGC 61.567 68.421 15.74 6.62 0.00 3.42
3103 3208 1.338655 GTCCCTCCTAGCTAGCGAAAG 59.661 57.143 15.74 8.35 0.00 2.62
3106 3211 2.223852 CCCTCCTAGCTAGCGAAAGTTC 60.224 54.545 15.74 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.425066 TGGATCACCAAACAGCTCCTT 59.575 47.619 0.00 0.00 43.91 3.36
1 2 1.067295 TGGATCACCAAACAGCTCCT 58.933 50.000 0.00 0.00 43.91 3.69
2 3 3.650647 TGGATCACCAAACAGCTCC 57.349 52.632 0.00 0.00 43.91 4.70
11 12 0.036732 GTGAAGCCAGTGGATCACCA 59.963 55.000 26.46 13.06 44.76 4.17
12 13 0.678048 GGTGAAGCCAGTGGATCACC 60.678 60.000 33.91 33.91 46.17 4.02
13 14 0.036732 TGGTGAAGCCAGTGGATCAC 59.963 55.000 27.82 27.82 43.61 3.06
14 15 2.462301 TGGTGAAGCCAGTGGATCA 58.538 52.632 15.20 13.63 43.61 2.92
23 24 3.129988 CAGATCCTCAAATTGGTGAAGCC 59.870 47.826 0.00 0.00 37.90 4.35
24 25 3.428589 GCAGATCCTCAAATTGGTGAAGC 60.429 47.826 0.00 0.00 0.00 3.86
25 26 3.760151 TGCAGATCCTCAAATTGGTGAAG 59.240 43.478 0.00 0.00 0.00 3.02
26 27 3.760151 CTGCAGATCCTCAAATTGGTGAA 59.240 43.478 8.42 0.00 0.00 3.18
27 28 3.009363 TCTGCAGATCCTCAAATTGGTGA 59.991 43.478 13.74 0.00 0.00 4.02
28 29 3.349927 TCTGCAGATCCTCAAATTGGTG 58.650 45.455 13.74 0.00 0.00 4.17
29 30 3.618351 CTCTGCAGATCCTCAAATTGGT 58.382 45.455 18.63 0.00 0.00 3.67
30 31 2.358267 GCTCTGCAGATCCTCAAATTGG 59.642 50.000 18.63 1.60 0.00 3.16
31 32 3.014623 TGCTCTGCAGATCCTCAAATTG 58.985 45.455 18.63 2.16 33.32 2.32
32 33 3.361281 TGCTCTGCAGATCCTCAAATT 57.639 42.857 18.63 0.00 33.32 1.82
33 34 3.136809 AGATGCTCTGCAGATCCTCAAAT 59.863 43.478 18.63 1.70 43.65 2.32
34 35 2.504585 AGATGCTCTGCAGATCCTCAAA 59.495 45.455 18.63 0.00 43.65 2.69
35 36 2.117051 AGATGCTCTGCAGATCCTCAA 58.883 47.619 18.63 0.00 43.65 3.02
36 37 1.790818 AGATGCTCTGCAGATCCTCA 58.209 50.000 18.63 13.01 43.65 3.86
37 38 4.497300 GAATAGATGCTCTGCAGATCCTC 58.503 47.826 18.63 15.37 43.65 3.71
38 39 3.261390 GGAATAGATGCTCTGCAGATCCT 59.739 47.826 18.63 13.59 43.65 3.24
39 40 3.598299 GGAATAGATGCTCTGCAGATCC 58.402 50.000 18.63 14.62 43.65 3.36
40 41 3.598299 GGGAATAGATGCTCTGCAGATC 58.402 50.000 18.63 14.36 43.65 2.75
41 42 2.305343 GGGGAATAGATGCTCTGCAGAT 59.695 50.000 18.63 1.53 43.65 2.90
42 43 1.696336 GGGGAATAGATGCTCTGCAGA 59.304 52.381 17.19 17.19 43.65 4.26
43 44 1.698532 AGGGGAATAGATGCTCTGCAG 59.301 52.381 7.63 7.63 43.65 4.41
44 45 1.419012 CAGGGGAATAGATGCTCTGCA 59.581 52.381 0.00 0.00 41.43 4.41
45 46 2.181954 CAGGGGAATAGATGCTCTGC 57.818 55.000 0.00 0.00 41.43 4.26
47 48 0.683973 CGCAGGGGAATAGATGCTCT 59.316 55.000 0.00 0.00 36.52 4.09
48 49 0.952984 GCGCAGGGGAATAGATGCTC 60.953 60.000 0.30 0.00 36.52 4.26
49 50 1.072159 GCGCAGGGGAATAGATGCT 59.928 57.895 0.30 0.00 36.52 3.79
50 51 1.968540 GGCGCAGGGGAATAGATGC 60.969 63.158 10.83 0.00 35.32 3.91
51 52 0.604780 CTGGCGCAGGGGAATAGATG 60.605 60.000 10.83 0.00 0.00 2.90
52 53 1.757306 CTGGCGCAGGGGAATAGAT 59.243 57.895 10.83 0.00 0.00 1.98
53 54 3.106986 GCTGGCGCAGGGGAATAGA 62.107 63.158 10.83 0.00 35.78 1.98
54 55 2.592861 GCTGGCGCAGGGGAATAG 60.593 66.667 10.83 0.00 35.78 1.73
55 56 3.407083 TGCTGGCGCAGGGGAATA 61.407 61.111 10.83 0.00 42.25 1.75
63 64 1.804151 CTAGTTAAAAGTGCTGGCGCA 59.196 47.619 10.83 0.00 45.60 6.09
64 65 1.465856 GCTAGTTAAAAGTGCTGGCGC 60.466 52.381 0.00 0.00 0.00 6.53
65 66 2.527442 GCTAGTTAAAAGTGCTGGCG 57.473 50.000 0.00 0.00 0.00 5.69
66 67 1.465856 GCGCTAGTTAAAAGTGCTGGC 60.466 52.381 14.36 3.56 45.01 4.85
67 68 2.527442 GCGCTAGTTAAAAGTGCTGG 57.473 50.000 14.36 0.00 45.01 4.85
86 87 2.581354 CTCCTGGAGTTGGCGGAG 59.419 66.667 15.76 0.00 37.33 4.63
87 88 3.706373 GCTCCTGGAGTTGGCGGA 61.706 66.667 23.92 0.00 31.39 5.54
89 90 3.997064 CTCGCTCCTGGAGTTGGCG 62.997 68.421 23.92 21.09 45.93 5.69
90 91 2.125350 CTCGCTCCTGGAGTTGGC 60.125 66.667 23.92 10.35 31.39 4.52
91 92 1.254284 ACTCTCGCTCCTGGAGTTGG 61.254 60.000 23.92 13.96 37.04 3.77
92 93 0.108898 CACTCTCGCTCCTGGAGTTG 60.109 60.000 23.92 16.79 38.12 3.16
93 94 1.254284 CCACTCTCGCTCCTGGAGTT 61.254 60.000 23.92 0.59 38.12 3.01
94 95 1.680651 CCACTCTCGCTCCTGGAGT 60.681 63.158 23.92 1.78 40.42 3.85
95 96 1.379176 TCCACTCTCGCTCCTGGAG 60.379 63.158 19.55 19.55 0.00 3.86
96 97 1.379176 CTCCACTCTCGCTCCTGGA 60.379 63.158 0.00 0.00 0.00 3.86
97 98 3.074999 GCTCCACTCTCGCTCCTGG 62.075 68.421 0.00 0.00 0.00 4.45
98 99 2.493973 GCTCCACTCTCGCTCCTG 59.506 66.667 0.00 0.00 0.00 3.86
99 100 3.137459 CGCTCCACTCTCGCTCCT 61.137 66.667 0.00 0.00 0.00 3.69
100 101 4.200283 CCGCTCCACTCTCGCTCC 62.200 72.222 0.00 0.00 0.00 4.70
101 102 4.200283 CCCGCTCCACTCTCGCTC 62.200 72.222 0.00 0.00 0.00 5.03
104 105 3.522731 CTCCCCGCTCCACTCTCG 61.523 72.222 0.00 0.00 0.00 4.04
105 106 3.151022 CCTCCCCGCTCCACTCTC 61.151 72.222 0.00 0.00 0.00 3.20
106 107 4.787280 CCCTCCCCGCTCCACTCT 62.787 72.222 0.00 0.00 0.00 3.24
124 125 1.003233 AGAAACTTAGGGCCTGTTCGG 59.997 52.381 18.53 3.95 0.00 4.30
125 126 2.474410 AGAAACTTAGGGCCTGTTCG 57.526 50.000 18.53 3.92 0.00 3.95
126 127 6.181190 AGATTAAGAAACTTAGGGCCTGTTC 58.819 40.000 18.53 13.84 0.00 3.18
127 128 6.140968 AGATTAAGAAACTTAGGGCCTGTT 57.859 37.500 18.53 10.15 0.00 3.16
128 129 5.780958 AGATTAAGAAACTTAGGGCCTGT 57.219 39.130 18.53 2.84 0.00 4.00
129 130 7.201741 GCTTAAGATTAAGAAACTTAGGGCCTG 60.202 40.741 18.53 2.03 42.05 4.85
130 131 6.829298 GCTTAAGATTAAGAAACTTAGGGCCT 59.171 38.462 12.58 12.58 42.05 5.19
131 132 6.039493 GGCTTAAGATTAAGAAACTTAGGGCC 59.961 42.308 14.96 0.00 42.05 5.80
132 133 6.829298 AGGCTTAAGATTAAGAAACTTAGGGC 59.171 38.462 14.96 13.25 43.47 5.19
133 134 8.678199 CAAGGCTTAAGATTAAGAAACTTAGGG 58.322 37.037 14.96 3.08 42.05 3.53
134 135 9.449719 TCAAGGCTTAAGATTAAGAAACTTAGG 57.550 33.333 14.96 0.00 42.05 2.69
153 154 2.238521 TCGCCAATTTTCTTCAAGGCT 58.761 42.857 0.00 0.00 39.91 4.58
181 185 7.405469 TCAATTTAACGAACAAACTAGCGTA 57.595 32.000 0.00 0.00 35.74 4.42
195 199 7.510428 AGCTGCAACAATAATCAATTTAACG 57.490 32.000 1.02 0.00 0.00 3.18
202 206 6.374053 TGTTAGCTAGCTGCAACAATAATCAA 59.626 34.615 27.68 5.56 45.94 2.57
204 208 6.363577 TGTTAGCTAGCTGCAACAATAATC 57.636 37.500 27.68 3.67 45.94 1.75
294 298 1.075601 ATGCAAGGAGTGGAAAGGGA 58.924 50.000 0.00 0.00 0.00 4.20
304 308 1.002033 GCATTTCCGCTATGCAAGGAG 60.002 52.381 0.00 0.00 45.93 3.69
325 329 1.811679 GCTGCTGGTAAGACGCTCC 60.812 63.158 0.00 0.00 0.00 4.70
349 353 3.023735 CCCCTTTCCCCTCCCCTG 61.024 72.222 0.00 0.00 0.00 4.45
350 354 3.224269 TCCCCTTTCCCCTCCCCT 61.224 66.667 0.00 0.00 0.00 4.79
369 373 2.892425 CCGAGATGCAACCCGCTC 60.892 66.667 0.00 0.00 43.06 5.03
410 414 0.874607 GTGTCACGCCTTCTTGACGT 60.875 55.000 0.00 0.00 42.42 4.34
466 470 2.499205 GCGTCCGTCCATGGATGA 59.501 61.111 31.81 21.48 46.14 2.92
495 500 2.476821 CATCATCAGCAGCACGATACA 58.523 47.619 0.00 0.00 0.00 2.29
520 525 3.540617 TGTTTCAAGCAGAGCTACAACA 58.459 40.909 0.00 0.00 38.25 3.33
525 530 2.416547 GCGATTGTTTCAAGCAGAGCTA 59.583 45.455 0.00 0.00 38.25 3.32
640 662 4.222847 GGAGATGGCCGACGGTCC 62.223 72.222 17.38 17.35 0.00 4.46
654 676 4.806339 AGGGAAGCGGGGAGGGAG 62.806 72.222 0.00 0.00 0.00 4.30
663 685 0.393537 AGAAGCCATGAAGGGAAGCG 60.394 55.000 0.00 0.00 38.09 4.68
664 686 1.747924 GAAGAAGCCATGAAGGGAAGC 59.252 52.381 0.00 0.00 38.09 3.86
671 693 1.019278 GCGGACGAAGAAGCCATGAA 61.019 55.000 0.00 0.00 0.00 2.57
672 694 1.447838 GCGGACGAAGAAGCCATGA 60.448 57.895 0.00 0.00 0.00 3.07
673 695 2.802667 CGCGGACGAAGAAGCCATG 61.803 63.158 0.00 0.00 43.93 3.66
674 696 2.509336 CGCGGACGAAGAAGCCAT 60.509 61.111 0.00 0.00 43.93 4.40
723 745 2.436596 GATCATGGCATGGGGAGGGG 62.437 65.000 26.15 0.00 0.00 4.79
726 748 1.076192 GGGATCATGGCATGGGGAG 59.924 63.158 26.15 1.25 0.00 4.30
753 775 2.826287 CGTGTGGGGCACAACACA 60.826 61.111 26.00 10.74 46.28 3.72
754 776 2.826738 ACGTGTGGGGCACAACAC 60.827 61.111 17.25 17.25 46.28 3.32
755 777 2.515057 GACGTGTGGGGCACAACA 60.515 61.111 0.00 0.00 46.28 3.33
756 778 3.645975 CGACGTGTGGGGCACAAC 61.646 66.667 0.00 0.00 46.28 3.32
757 779 4.164087 ACGACGTGTGGGGCACAA 62.164 61.111 0.00 0.00 46.28 3.33
807 829 2.656069 CGGCGGGGAAGAAGAAGGA 61.656 63.158 0.00 0.00 0.00 3.36
810 832 2.966732 ATGCGGCGGGGAAGAAGAA 61.967 57.895 9.78 0.00 0.00 2.52
811 833 3.399181 ATGCGGCGGGGAAGAAGA 61.399 61.111 9.78 0.00 0.00 2.87
812 834 3.204827 CATGCGGCGGGGAAGAAG 61.205 66.667 9.78 0.00 0.00 2.85
893 922 2.149578 CAGGACCGTACGTAGGATAGG 58.850 57.143 16.52 7.92 0.00 2.57
894 923 1.534595 GCAGGACCGTACGTAGGATAG 59.465 57.143 16.52 2.95 0.00 2.08
895 924 1.141657 AGCAGGACCGTACGTAGGATA 59.858 52.381 16.52 0.00 0.00 2.59
905 934 1.617947 GGGAGATCAAGCAGGACCGT 61.618 60.000 0.00 0.00 0.00 4.83
908 937 0.842635 ATGGGGAGATCAAGCAGGAC 59.157 55.000 0.00 0.00 0.00 3.85
909 938 1.135094 GATGGGGAGATCAAGCAGGA 58.865 55.000 0.00 0.00 0.00 3.86
910 958 0.250209 CGATGGGGAGATCAAGCAGG 60.250 60.000 0.00 0.00 0.00 4.85
911 959 0.883814 GCGATGGGGAGATCAAGCAG 60.884 60.000 0.00 0.00 0.00 4.24
921 969 1.925285 AATCTTGGCAGCGATGGGGA 61.925 55.000 1.46 0.00 0.00 4.81
922 970 1.454479 AATCTTGGCAGCGATGGGG 60.454 57.895 1.46 0.00 0.00 4.96
935 983 0.179062 CGCCAGCTAGAGCCAATCTT 60.179 55.000 0.00 0.00 43.38 2.40
938 986 2.507944 CCGCCAGCTAGAGCCAAT 59.492 61.111 0.00 0.00 43.38 3.16
939 987 3.785859 CCCGCCAGCTAGAGCCAA 61.786 66.667 0.00 0.00 43.38 4.52
940 988 4.777854 TCCCGCCAGCTAGAGCCA 62.778 66.667 0.00 0.00 43.38 4.75
941 989 3.922640 CTCCCGCCAGCTAGAGCC 61.923 72.222 0.00 0.00 43.38 4.70
943 991 3.230245 CCCTCCCGCCAGCTAGAG 61.230 72.222 0.00 0.22 0.00 2.43
944 992 3.751018 TCCCTCCCGCCAGCTAGA 61.751 66.667 0.00 0.00 0.00 2.43
945 993 3.541713 GTCCCTCCCGCCAGCTAG 61.542 72.222 0.00 0.00 0.00 3.42
984 1033 3.782443 ATTGGAGACCGGCCGACC 61.782 66.667 30.73 23.02 0.00 4.79
985 1034 2.511600 CATTGGAGACCGGCCGAC 60.512 66.667 30.73 20.31 0.00 4.79
986 1035 2.682136 TCATTGGAGACCGGCCGA 60.682 61.111 30.73 4.34 0.00 5.54
987 1036 2.511600 GTCATTGGAGACCGGCCG 60.512 66.667 21.04 21.04 32.36 6.13
989 1038 1.810030 GTCGTCATTGGAGACCGGC 60.810 63.158 0.00 0.00 35.07 6.13
990 1039 1.516386 CGTCGTCATTGGAGACCGG 60.516 63.158 0.00 0.00 35.07 5.28
991 1040 1.516386 CCGTCGTCATTGGAGACCG 60.516 63.158 0.00 0.00 35.07 4.79
992 1041 1.810030 GCCGTCGTCATTGGAGACC 60.810 63.158 0.00 0.00 35.07 3.85
993 1042 2.158959 CGCCGTCGTCATTGGAGAC 61.159 63.158 0.00 3.41 35.19 3.36
994 1043 2.180769 CGCCGTCGTCATTGGAGA 59.819 61.111 0.00 0.00 0.00 3.71
995 1044 3.554692 GCGCCGTCGTCATTGGAG 61.555 66.667 0.00 0.00 38.14 3.86
1477 1526 4.539881 GCGCGTCTCCTCGTCCTC 62.540 72.222 8.43 0.00 0.00 3.71
1943 2010 2.709125 TTCGTTGTCCTGCTCCACCG 62.709 60.000 0.00 0.00 0.00 4.94
2117 2184 1.513586 CGTCACGTCTCGCCTAACC 60.514 63.158 0.00 0.00 0.00 2.85
2202 2270 9.474920 GTTCTAACCATCAAATCAAATGTGAAA 57.525 29.630 0.00 0.00 37.30 2.69
2212 2280 8.964420 TTTCGATTTGTTCTAACCATCAAATC 57.036 30.769 15.14 15.14 45.64 2.17
2251 2320 5.354234 CCTATTTGCACTCGTGGTCTTAATT 59.646 40.000 0.00 0.00 0.00 1.40
2277 2347 7.658525 ACCCACAATAATTGCTTCATGATTA 57.341 32.000 0.00 0.00 0.00 1.75
2293 2363 3.005684 CAGCAAACACATGTACCCACAAT 59.994 43.478 0.00 0.00 38.42 2.71
2299 2369 2.598589 CATGCAGCAAACACATGTACC 58.401 47.619 0.00 0.00 37.10 3.34
2318 2388 5.009610 GCATCTCTTTTTCACAACCTAACCA 59.990 40.000 0.00 0.00 0.00 3.67
2325 2395 4.362279 TGCTTGCATCTCTTTTTCACAAC 58.638 39.130 0.00 0.00 0.00 3.32
2329 2399 4.322198 GGGAATGCTTGCATCTCTTTTTCA 60.322 41.667 8.64 0.00 0.00 2.69
2336 2406 2.620585 GGTTAGGGAATGCTTGCATCTC 59.379 50.000 8.64 8.43 0.00 2.75
2365 2435 9.709495 ACAGAGCAAAATGAAAATATGCTAAAA 57.291 25.926 0.00 0.00 46.58 1.52
2419 2491 9.051679 CCTCCACACAAATTTATATCGATAACA 57.948 33.333 9.61 0.00 0.00 2.41
2423 2495 5.473504 GCCCTCCACACAAATTTATATCGAT 59.526 40.000 2.16 2.16 0.00 3.59
2429 2501 4.346418 TGTTTGCCCTCCACACAAATTTAT 59.654 37.500 0.00 0.00 35.87 1.40
2460 2532 5.174035 CGGTCGTAGAAATAGCTTGATCTTG 59.826 44.000 0.00 0.00 39.69 3.02
2532 2606 1.798813 GTCCTCTTGTAAGTTGCCACG 59.201 52.381 0.00 0.00 0.00 4.94
2539 2613 1.132495 AGGTGGGGTCCTCTTGTAAGT 60.132 52.381 0.00 0.00 31.32 2.24
2542 2616 0.192566 ACAGGTGGGGTCCTCTTGTA 59.807 55.000 2.65 0.00 35.99 2.41
2551 2625 0.923358 TTGAAACTGACAGGTGGGGT 59.077 50.000 7.51 0.00 0.00 4.95
2554 2628 1.597663 GACGTTGAAACTGACAGGTGG 59.402 52.381 7.51 0.00 0.00 4.61
2557 2631 3.312421 ACATTGACGTTGAAACTGACAGG 59.688 43.478 7.51 0.00 0.00 4.00
2559 2633 3.687212 ACACATTGACGTTGAAACTGACA 59.313 39.130 0.00 0.00 0.00 3.58
2560 2634 4.028383 CACACATTGACGTTGAAACTGAC 58.972 43.478 0.00 0.00 0.00 3.51
2570 2644 6.220930 ACTCTGTATAAACACACATTGACGT 58.779 36.000 0.00 0.00 0.00 4.34
2579 2653 7.833786 ACCGATCTAAACTCTGTATAAACACA 58.166 34.615 0.00 0.00 0.00 3.72
2580 2654 8.189460 AGACCGATCTAAACTCTGTATAAACAC 58.811 37.037 0.00 0.00 31.46 3.32
2589 2663 4.096532 TGCTACAGACCGATCTAAACTCTG 59.903 45.833 0.00 0.00 35.48 3.35
2590 2664 4.270834 TGCTACAGACCGATCTAAACTCT 58.729 43.478 0.00 0.00 32.25 3.24
2603 2677 1.945354 TAGGGTGCGCTGCTACAGAC 61.945 60.000 9.73 0.00 32.44 3.51
2612 2686 1.991230 ACCAAGATTAGGGTGCGCT 59.009 52.632 9.73 0.00 35.67 5.92
2617 2691 1.985159 TGTCAGCACCAAGATTAGGGT 59.015 47.619 0.00 0.00 38.10 4.34
2618 2692 2.359900 GTGTCAGCACCAAGATTAGGG 58.640 52.381 0.00 0.00 39.61 3.53
2621 2695 2.831685 ACGTGTCAGCACCAAGATTA 57.168 45.000 0.00 0.00 42.39 1.75
2623 2697 2.831685 TTACGTGTCAGCACCAAGAT 57.168 45.000 0.00 0.00 42.39 2.40
2631 2705 7.901874 TTTTCTGTAATTTTTACGTGTCAGC 57.098 32.000 0.00 0.00 0.00 4.26
2636 2710 9.120422 GGTACCATTTTCTGTAATTTTTACGTG 57.880 33.333 7.15 0.00 0.00 4.49
2638 2712 9.680315 TTGGTACCATTTTCTGTAATTTTTACG 57.320 29.630 17.17 0.00 0.00 3.18
2650 2724 4.156008 GTGAGCGAATTGGTACCATTTTCT 59.844 41.667 24.58 21.14 0.00 2.52
2655 2729 2.027192 AGTGTGAGCGAATTGGTACCAT 60.027 45.455 17.17 0.30 0.00 3.55
2658 2732 1.128692 GCAGTGTGAGCGAATTGGTAC 59.871 52.381 0.00 0.00 0.00 3.34
2671 2745 4.517285 AGTACCATAATTGAGGCAGTGTG 58.483 43.478 0.00 0.00 0.00 3.82
2672 2746 4.844349 AGTACCATAATTGAGGCAGTGT 57.156 40.909 0.00 0.00 0.00 3.55
2677 2751 5.530915 TGCACATTAGTACCATAATTGAGGC 59.469 40.000 0.00 0.00 0.00 4.70
2693 2767 9.210329 TCTCTTAAACGAGTTAATTGCACATTA 57.790 29.630 0.00 0.00 31.22 1.90
2737 2811 6.117488 TCTTATTACCCTTCCAATCCGTTTC 58.883 40.000 0.00 0.00 0.00 2.78
2741 2815 5.681639 AGTTCTTATTACCCTTCCAATCCG 58.318 41.667 0.00 0.00 0.00 4.18
2744 2818 6.127730 CGCAAAGTTCTTATTACCCTTCCAAT 60.128 38.462 0.00 0.00 0.00 3.16
2746 2820 4.698304 CGCAAAGTTCTTATTACCCTTCCA 59.302 41.667 0.00 0.00 0.00 3.53
2759 2833 7.675962 TTAATATAACCACACGCAAAGTTCT 57.324 32.000 0.00 0.00 0.00 3.01
2821 2924 2.375174 TGATAACCCCAAAGAGCACTGT 59.625 45.455 0.00 0.00 0.00 3.55
2845 2948 6.016276 ACATGTTTCGAAAGTTGCTAGGAAAT 60.016 34.615 11.66 0.00 0.00 2.17
2863 2966 6.690530 CATGAAGGGTGTATGAAACATGTTT 58.309 36.000 23.49 23.49 41.10 2.83
2870 2973 4.661222 TCAAGCATGAAGGGTGTATGAAA 58.339 39.130 0.00 0.00 30.99 2.69
2915 3018 0.042448 GAACGTTCGCTGGACAACAC 60.042 55.000 13.36 0.00 0.00 3.32
2925 3028 1.300697 ACCTCCACTGAACGTTCGC 60.301 57.895 22.48 1.71 0.00 4.70
3003 3106 4.282957 TGTGAAAATTGCCAGGATTGCTTA 59.717 37.500 0.00 0.00 0.00 3.09
3029 3132 6.763610 TCTTCAAAAACGGGCAACATAATTTT 59.236 30.769 0.00 0.00 39.74 1.82
3037 3140 4.331443 ACAAATTCTTCAAAAACGGGCAAC 59.669 37.500 0.00 0.00 0.00 4.17
3039 3142 4.116238 GACAAATTCTTCAAAAACGGGCA 58.884 39.130 0.00 0.00 0.00 5.36
3040 3143 4.116238 TGACAAATTCTTCAAAAACGGGC 58.884 39.130 0.00 0.00 0.00 6.13
3041 3144 7.938563 TTATGACAAATTCTTCAAAAACGGG 57.061 32.000 0.00 0.00 0.00 5.28
3060 3165 4.325741 CGGCATTTGCGAATGTTTTTATGA 59.674 37.500 24.39 0.00 43.67 2.15
3070 3175 1.376609 GAGGGACGGCATTTGCGAAT 61.377 55.000 0.00 0.00 43.26 3.34
3083 3188 1.338655 CTTTCGCTAGCTAGGAGGGAC 59.661 57.143 22.10 3.45 35.79 4.46
3088 3193 2.846039 CGAACTTTCGCTAGCTAGGA 57.154 50.000 22.10 14.20 44.26 2.94
3103 3208 3.329929 AGACCCCAATAGACAACGAAC 57.670 47.619 0.00 0.00 0.00 3.95
3106 3211 3.700038 ACTCTAGACCCCAATAGACAACG 59.300 47.826 0.00 0.00 0.00 4.10
3108 3213 4.942944 TGACTCTAGACCCCAATAGACAA 58.057 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.