Multiple sequence alignment - TraesCS7D01G006300

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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 TraesCS7D01G006300 chr7D 100.000 4353 0 0 1 4353 2905888 2901536 0.000000e+00 8039.0
1 TraesCS7D01G006300 chr7D 92.955 3506 224 17 857 4351 3552761 3549268 0.000000e+00 5084.0
2 TraesCS7D01G006300 chr7D 85.455 2035 214 44 1812 3815 2687464 2685481 0.000000e+00 2043.0
3 TraesCS7D01G006300 chr7D 81.881 2456 372 53 1923 4347 4009743 4007330 0.000000e+00 2002.0
4 TraesCS7D01G006300 chr7D 83.181 987 157 9 855 1836 2522575 2521593 0.000000e+00 894.0
5 TraesCS7D01G006300 chr7D 82.747 910 152 5 930 1836 3425076 3424169 0.000000e+00 806.0
6 TraesCS7D01G006300 chr7D 82.647 680 54 19 114 761 3553405 3552758 1.060000e-150 544.0
7 TraesCS7D01G006300 chr7D 83.060 366 30 20 377 719 2720077 2719721 1.970000e-78 303.0
8 TraesCS7D01G006300 chr7D 82.488 217 32 4 106 322 2721156 2720946 7.430000e-43 185.0
9 TraesCS7D01G006300 chr7D 86.441 118 11 2 705 822 2687735 2687623 1.640000e-24 124.0
10 TraesCS7D01G006300 chr7D 95.918 49 2 0 50 98 2721702 2721654 3.610000e-11 80.5
11 TraesCS7D01G006300 chr7A 91.378 3375 224 23 983 4351 3156010 3152697 0.000000e+00 4558.0
12 TraesCS7D01G006300 chr7A 81.111 3420 563 63 978 4347 3844174 3840788 0.000000e+00 2660.0
13 TraesCS7D01G006300 chr7A 96.390 1219 42 2 2399 3616 2685992 2684775 0.000000e+00 2006.0
14 TraesCS7D01G006300 chr7A 83.983 1898 268 19 2475 4347 2800440 2798554 0.000000e+00 1788.0
15 TraesCS7D01G006300 chr7A 91.065 1052 89 5 873 1920 2688527 2687477 0.000000e+00 1417.0
16 TraesCS7D01G006300 chr7A 82.612 1248 201 11 3110 4347 3803936 3802695 0.000000e+00 1088.0
17 TraesCS7D01G006300 chr7A 84.304 1013 143 10 854 1861 2806022 2805021 0.000000e+00 976.0
18 TraesCS7D01G006300 chr7A 91.089 505 44 1 3807 4311 2684780 2684277 0.000000e+00 682.0
19 TraesCS7D01G006300 chr7A 94.000 350 16 2 473 822 2689135 2688791 3.860000e-145 525.0
20 TraesCS7D01G006300 chr7A 91.460 363 21 5 1923 2279 2687442 2687084 1.410000e-134 490.0
21 TraesCS7D01G006300 chr7A 89.426 331 21 8 500 822 3156526 3156202 5.240000e-109 405.0
22 TraesCS7D01G006300 chr7A 93.382 136 8 1 820 954 2688666 2688531 2.650000e-47 200.0
23 TraesCS7D01G006300 chr7A 93.407 91 6 0 850 940 3156100 3156010 7.590000e-28 135.0
24 TraesCS7D01G006300 chr4A 81.699 3437 524 70 978 4351 739605578 739608972 0.000000e+00 2765.0
25 TraesCS7D01G006300 chr4A 81.452 3402 564 57 978 4347 742161107 742157741 0.000000e+00 2724.0
26 TraesCS7D01G006300 chr4A 84.506 2033 285 24 2330 4347 742021129 742023146 0.000000e+00 1982.0
27 TraesCS7D01G006300 chr4A 81.950 2277 351 47 2094 4347 740122932 740120693 0.000000e+00 1873.0
28 TraesCS7D01G006300 chr4A 83.248 1946 311 14 2409 4347 741422023 741423960 0.000000e+00 1773.0
29 TraesCS7D01G006300 chr4A 83.798 1901 270 22 2476 4347 739886473 739888364 0.000000e+00 1770.0
30 TraesCS7D01G006300 chr4A 81.451 2081 356 25 2279 4347 733805942 733808004 0.000000e+00 1677.0
31 TraesCS7D01G006300 chr4A 82.756 1183 193 10 3154 4331 741505836 741504660 0.000000e+00 1044.0
32 TraesCS7D01G006300 chr4A 85.151 862 124 4 854 1713 740442689 740441830 0.000000e+00 880.0
33 TraesCS7D01G006300 chr4A 82.579 884 150 4 978 1859 741420767 741421648 0.000000e+00 776.0
34 TraesCS7D01G006300 chr4A 93.220 413 21 4 1664 2073 740852629 740853037 6.230000e-168 601.0
35 TraesCS7D01G006300 chr4A 83.590 195 25 6 857 1044 740607096 740606902 4.470000e-40 176.0
36 TraesCS7D01G006300 chr1D 82.460 2041 325 28 2321 4347 464795424 464797445 0.000000e+00 1755.0


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 TraesCS7D01G006300 chr7D 2901536 2905888 4352 True 8039.000000 8039 100.000000 1 4353 1 chr7D.!!$R2 4352
1 TraesCS7D01G006300 chr7D 3549268 3553405 4137 True 2814.000000 5084 87.801000 114 4351 2 chr7D.!!$R7 4237
2 TraesCS7D01G006300 chr7D 4007330 4009743 2413 True 2002.000000 2002 81.881000 1923 4347 1 chr7D.!!$R4 2424
3 TraesCS7D01G006300 chr7D 2685481 2687735 2254 True 1083.500000 2043 85.948000 705 3815 2 chr7D.!!$R5 3110
4 TraesCS7D01G006300 chr7D 2521593 2522575 982 True 894.000000 894 83.181000 855 1836 1 chr7D.!!$R1 981
5 TraesCS7D01G006300 chr7D 3424169 3425076 907 True 806.000000 806 82.747000 930 1836 1 chr7D.!!$R3 906
6 TraesCS7D01G006300 chr7A 3840788 3844174 3386 True 2660.000000 2660 81.111000 978 4347 1 chr7A.!!$R4 3369
7 TraesCS7D01G006300 chr7A 2798554 2800440 1886 True 1788.000000 1788 83.983000 2475 4347 1 chr7A.!!$R1 1872
8 TraesCS7D01G006300 chr7A 3152697 3156526 3829 True 1699.333333 4558 91.403667 500 4351 3 chr7A.!!$R6 3851
9 TraesCS7D01G006300 chr7A 3802695 3803936 1241 True 1088.000000 1088 82.612000 3110 4347 1 chr7A.!!$R3 1237
10 TraesCS7D01G006300 chr7A 2805021 2806022 1001 True 976.000000 976 84.304000 854 1861 1 chr7A.!!$R2 1007
11 TraesCS7D01G006300 chr7A 2684277 2689135 4858 True 886.666667 2006 92.897667 473 4311 6 chr7A.!!$R5 3838
12 TraesCS7D01G006300 chr4A 739605578 739608972 3394 False 2765.000000 2765 81.699000 978 4351 1 chr4A.!!$F2 3373
13 TraesCS7D01G006300 chr4A 742157741 742161107 3366 True 2724.000000 2724 81.452000 978 4347 1 chr4A.!!$R5 3369
14 TraesCS7D01G006300 chr4A 742021129 742023146 2017 False 1982.000000 1982 84.506000 2330 4347 1 chr4A.!!$F5 2017
15 TraesCS7D01G006300 chr4A 740120693 740122932 2239 True 1873.000000 1873 81.950000 2094 4347 1 chr4A.!!$R1 2253
16 TraesCS7D01G006300 chr4A 739886473 739888364 1891 False 1770.000000 1770 83.798000 2476 4347 1 chr4A.!!$F3 1871
17 TraesCS7D01G006300 chr4A 733805942 733808004 2062 False 1677.000000 1677 81.451000 2279 4347 1 chr4A.!!$F1 2068
18 TraesCS7D01G006300 chr4A 741420767 741423960 3193 False 1274.500000 1773 82.913500 978 4347 2 chr4A.!!$F6 3369
19 TraesCS7D01G006300 chr4A 741504660 741505836 1176 True 1044.000000 1044 82.756000 3154 4331 1 chr4A.!!$R4 1177
20 TraesCS7D01G006300 chr4A 740441830 740442689 859 True 880.000000 880 85.151000 854 1713 1 chr4A.!!$R2 859
21 TraesCS7D01G006300 chr1D 464795424 464797445 2021 False 1755.000000 1755 82.460000 2321 4347 1 chr1D.!!$F1 2026

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
106 107 0.035820 TCATTCCTACAACGGGTGGC 60.036 55.0 0.00 0.0 0.00 5.01 F
168 169 0.179015 TTGCTTTTGGGCCACGACTA 60.179 50.0 5.23 0.0 0.00 2.59 F
238 239 0.253044 CCATCACTGGGATTGTCCGT 59.747 55.0 0.00 0.0 39.04 4.69 F
593 616 0.321996 GGAAGAAGCAAGTCGGGAGT 59.678 55.0 0.00 0.0 0.00 3.85 F
1349 1595 0.591170 ACCAAGTTCATGAAACGCCG 59.409 50.0 10.35 0.0 43.02 6.46 F
2322 2664 0.106116 ATGTCTCTCTCCGGTACCCC 60.106 60.0 6.25 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 1518 0.546122 TGTGTGGCTTGTCTTCAGGT 59.454 50.000 0.00 0.0 0.00 4.00 R
1349 1595 0.935366 GATCTCGTCGCCGATGGAAC 60.935 60.000 6.46 0.0 43.27 3.62 R
1407 1653 1.285667 TGGACCCTGTACCTATCACGA 59.714 52.381 0.00 0.0 0.00 4.35 R
2297 2639 0.749049 CCGGAGAGAGACATGCATGA 59.251 55.000 32.75 0.0 0.00 3.07 R
3287 4711 4.142600 GGCATTAAGTGACCTTGCTTGTAG 60.143 45.833 0.00 0.0 31.89 2.74 R
4083 5528 1.304381 GCTTGGGGAATGCACCTGA 60.304 57.895 0.00 0.0 38.87 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.918712 ATGCTGCACTATGGAGTACC 57.081 50.000 3.57 0.00 38.17 3.34
20 21 1.866015 TGCTGCACTATGGAGTACCT 58.134 50.000 0.00 0.00 38.17 3.08
21 22 3.026707 TGCTGCACTATGGAGTACCTA 57.973 47.619 0.00 0.00 38.17 3.08
22 23 2.959030 TGCTGCACTATGGAGTACCTAG 59.041 50.000 0.00 0.00 38.17 3.02
23 24 3.223435 GCTGCACTATGGAGTACCTAGA 58.777 50.000 0.00 0.00 38.17 2.43
24 25 3.637229 GCTGCACTATGGAGTACCTAGAA 59.363 47.826 0.00 0.00 38.17 2.10
25 26 4.500035 GCTGCACTATGGAGTACCTAGAAC 60.500 50.000 0.00 0.00 38.17 3.01
26 27 4.868268 TGCACTATGGAGTACCTAGAACT 58.132 43.478 0.00 0.00 33.32 3.01
27 28 5.269991 TGCACTATGGAGTACCTAGAACTT 58.730 41.667 0.00 0.00 33.32 2.66
28 29 6.429151 TGCACTATGGAGTACCTAGAACTTA 58.571 40.000 0.00 0.00 33.32 2.24
29 30 6.320672 TGCACTATGGAGTACCTAGAACTTAC 59.679 42.308 0.00 0.00 33.32 2.34
30 31 6.513066 GCACTATGGAGTACCTAGAACTTACG 60.513 46.154 0.00 0.00 33.32 3.18
31 32 6.541641 CACTATGGAGTACCTAGAACTTACGT 59.458 42.308 0.00 0.00 33.32 3.57
32 33 7.712639 CACTATGGAGTACCTAGAACTTACGTA 59.287 40.741 0.00 0.00 33.32 3.57
33 34 8.435982 ACTATGGAGTACCTAGAACTTACGTAT 58.564 37.037 0.00 0.00 32.65 3.06
34 35 6.932356 TGGAGTACCTAGAACTTACGTATG 57.068 41.667 6.91 6.91 37.04 2.39
35 36 6.418101 TGGAGTACCTAGAACTTACGTATGT 58.582 40.000 8.22 8.22 37.04 2.29
36 37 7.564793 TGGAGTACCTAGAACTTACGTATGTA 58.435 38.462 13.83 0.00 37.04 2.29
37 38 7.495934 TGGAGTACCTAGAACTTACGTATGTAC 59.504 40.741 13.83 7.27 37.04 2.90
38 39 7.495934 GGAGTACCTAGAACTTACGTATGTACA 59.504 40.741 13.83 0.00 0.00 2.90
39 40 8.202745 AGTACCTAGAACTTACGTATGTACAC 57.797 38.462 13.83 9.09 0.00 2.90
40 41 7.824289 AGTACCTAGAACTTACGTATGTACACA 59.176 37.037 13.83 0.00 0.00 3.72
41 42 6.846350 ACCTAGAACTTACGTATGTACACAC 58.154 40.000 13.83 0.00 0.00 3.82
42 43 6.127897 ACCTAGAACTTACGTATGTACACACC 60.128 42.308 13.83 1.76 0.00 4.16
43 44 5.710513 AGAACTTACGTATGTACACACCA 57.289 39.130 13.83 0.00 0.00 4.17
44 45 5.706916 AGAACTTACGTATGTACACACCAG 58.293 41.667 13.83 0.00 0.00 4.00
45 46 3.841643 ACTTACGTATGTACACACCAGC 58.158 45.455 12.04 0.00 0.00 4.85
46 47 3.508793 ACTTACGTATGTACACACCAGCT 59.491 43.478 12.04 0.00 0.00 4.24
47 48 2.649331 ACGTATGTACACACCAGCTC 57.351 50.000 0.00 0.00 0.00 4.09
48 49 2.168496 ACGTATGTACACACCAGCTCT 58.832 47.619 0.00 0.00 0.00 4.09
49 50 2.163815 ACGTATGTACACACCAGCTCTC 59.836 50.000 0.00 0.00 0.00 3.20
50 51 2.791503 CGTATGTACACACCAGCTCTCG 60.792 54.545 0.00 0.00 0.00 4.04
51 52 1.545841 ATGTACACACCAGCTCTCGA 58.454 50.000 0.00 0.00 0.00 4.04
52 53 1.324383 TGTACACACCAGCTCTCGAA 58.676 50.000 0.00 0.00 0.00 3.71
53 54 1.684450 TGTACACACCAGCTCTCGAAA 59.316 47.619 0.00 0.00 0.00 3.46
54 55 2.101750 TGTACACACCAGCTCTCGAAAA 59.898 45.455 0.00 0.00 0.00 2.29
55 56 2.325583 ACACACCAGCTCTCGAAAAA 57.674 45.000 0.00 0.00 0.00 1.94
56 57 1.940613 ACACACCAGCTCTCGAAAAAC 59.059 47.619 0.00 0.00 0.00 2.43
57 58 1.264288 CACACCAGCTCTCGAAAAACC 59.736 52.381 0.00 0.00 0.00 3.27
58 59 0.512952 CACCAGCTCTCGAAAAACCG 59.487 55.000 0.00 0.00 0.00 4.44
59 60 0.391597 ACCAGCTCTCGAAAAACCGA 59.608 50.000 0.00 0.00 37.03 4.69
60 61 1.202604 ACCAGCTCTCGAAAAACCGAA 60.203 47.619 0.00 0.00 38.17 4.30
61 62 2.076863 CCAGCTCTCGAAAAACCGAAT 58.923 47.619 0.00 0.00 38.17 3.34
62 63 3.259064 CCAGCTCTCGAAAAACCGAATA 58.741 45.455 0.00 0.00 38.17 1.75
63 64 3.062234 CCAGCTCTCGAAAAACCGAATAC 59.938 47.826 0.00 0.00 38.17 1.89
64 65 3.678072 CAGCTCTCGAAAAACCGAATACA 59.322 43.478 0.00 0.00 38.17 2.29
65 66 4.151689 CAGCTCTCGAAAAACCGAATACAA 59.848 41.667 0.00 0.00 38.17 2.41
66 67 4.151867 AGCTCTCGAAAAACCGAATACAAC 59.848 41.667 0.00 0.00 38.17 3.32
67 68 4.625135 CTCTCGAAAAACCGAATACAACG 58.375 43.478 0.00 0.00 38.17 4.10
73 74 3.493213 CCGAATACAACGGGTGGC 58.507 61.111 0.00 0.00 45.65 5.01
74 75 1.078708 CCGAATACAACGGGTGGCT 60.079 57.895 0.00 0.00 45.65 4.75
75 76 1.366111 CCGAATACAACGGGTGGCTG 61.366 60.000 0.00 0.00 45.65 4.85
76 77 0.672401 CGAATACAACGGGTGGCTGT 60.672 55.000 0.00 0.00 0.00 4.40
77 78 0.802494 GAATACAACGGGTGGCTGTG 59.198 55.000 0.00 0.00 0.00 3.66
78 79 0.398696 AATACAACGGGTGGCTGTGA 59.601 50.000 0.00 0.00 0.00 3.58
79 80 0.398696 ATACAACGGGTGGCTGTGAA 59.601 50.000 0.00 0.00 0.00 3.18
80 81 0.398696 TACAACGGGTGGCTGTGAAT 59.601 50.000 0.00 0.00 0.00 2.57
81 82 0.889186 ACAACGGGTGGCTGTGAATC 60.889 55.000 0.00 0.00 0.00 2.52
82 83 0.888736 CAACGGGTGGCTGTGAATCA 60.889 55.000 0.00 0.00 0.00 2.57
83 84 0.606401 AACGGGTGGCTGTGAATCAG 60.606 55.000 0.00 0.00 46.12 2.90
84 85 1.746615 CGGGTGGCTGTGAATCAGG 60.747 63.158 0.00 0.00 43.78 3.86
85 86 1.380302 GGGTGGCTGTGAATCAGGT 59.620 57.895 0.00 0.00 43.78 4.00
86 87 0.251341 GGGTGGCTGTGAATCAGGTT 60.251 55.000 0.00 0.00 43.78 3.50
87 88 1.620822 GGTGGCTGTGAATCAGGTTT 58.379 50.000 0.00 0.00 43.78 3.27
88 89 1.541588 GGTGGCTGTGAATCAGGTTTC 59.458 52.381 0.00 0.00 43.78 2.78
89 90 2.229792 GTGGCTGTGAATCAGGTTTCA 58.770 47.619 0.00 0.00 43.78 2.69
90 91 2.821969 GTGGCTGTGAATCAGGTTTCAT 59.178 45.455 0.00 0.00 43.78 2.57
91 92 3.256631 GTGGCTGTGAATCAGGTTTCATT 59.743 43.478 0.00 0.00 43.78 2.57
92 93 3.507233 TGGCTGTGAATCAGGTTTCATTC 59.493 43.478 0.00 0.00 43.78 2.67
93 94 3.119352 GGCTGTGAATCAGGTTTCATTCC 60.119 47.826 0.00 0.00 43.78 3.01
94 95 3.760684 GCTGTGAATCAGGTTTCATTCCT 59.239 43.478 0.00 0.00 43.78 3.36
95 96 4.943705 GCTGTGAATCAGGTTTCATTCCTA 59.056 41.667 0.00 0.00 43.78 2.94
96 97 5.163713 GCTGTGAATCAGGTTTCATTCCTAC 60.164 44.000 0.00 0.00 43.78 3.18
97 98 5.875224 TGTGAATCAGGTTTCATTCCTACA 58.125 37.500 0.00 0.00 37.88 2.74
98 99 6.303054 TGTGAATCAGGTTTCATTCCTACAA 58.697 36.000 0.00 0.00 37.88 2.41
99 100 6.206634 TGTGAATCAGGTTTCATTCCTACAAC 59.793 38.462 0.00 0.00 37.88 3.32
100 101 5.411361 TGAATCAGGTTTCATTCCTACAACG 59.589 40.000 0.00 0.00 33.54 4.10
101 102 3.670625 TCAGGTTTCATTCCTACAACGG 58.329 45.455 0.00 0.00 33.54 4.44
102 103 2.747446 CAGGTTTCATTCCTACAACGGG 59.253 50.000 0.00 0.00 33.54 5.28
103 104 2.374170 AGGTTTCATTCCTACAACGGGT 59.626 45.455 0.00 0.00 33.04 5.28
104 105 2.486592 GGTTTCATTCCTACAACGGGTG 59.513 50.000 0.00 0.00 0.00 4.61
105 106 2.483014 TTCATTCCTACAACGGGTGG 57.517 50.000 0.00 0.00 0.00 4.61
106 107 0.035820 TCATTCCTACAACGGGTGGC 60.036 55.000 0.00 0.00 0.00 5.01
107 108 1.029947 CATTCCTACAACGGGTGGCC 61.030 60.000 0.00 0.00 0.00 5.36
108 109 2.530958 ATTCCTACAACGGGTGGCCG 62.531 60.000 0.00 0.00 39.31 6.13
110 111 2.433664 CTACAACGGGTGGCCGTC 60.434 66.667 0.00 0.00 46.11 4.79
111 112 3.229156 CTACAACGGGTGGCCGTCA 62.229 63.158 0.00 0.00 46.11 4.35
112 113 3.229156 TACAACGGGTGGCCGTCAG 62.229 63.158 0.00 0.00 46.11 3.51
127 128 2.002586 CGTCAGTGCCTGTTAATGGAG 58.997 52.381 2.16 0.00 32.61 3.86
136 137 0.455410 TGTTAATGGAGGCGCATTGC 59.545 50.000 10.83 2.11 45.38 3.56
138 139 1.134946 GTTAATGGAGGCGCATTGCTT 59.865 47.619 10.83 0.00 45.43 3.91
141 142 1.473258 ATGGAGGCGCATTGCTTTTA 58.527 45.000 10.83 0.00 45.43 1.52
159 160 5.419239 TTTTATCCTCCATTGCTTTTGGG 57.581 39.130 1.20 0.00 34.85 4.12
162 163 1.193462 CCTCCATTGCTTTTGGGCCA 61.193 55.000 0.00 0.00 34.85 5.36
164 165 1.374505 CCATTGCTTTTGGGCCACG 60.375 57.895 5.23 0.00 0.00 4.94
165 166 1.664873 CATTGCTTTTGGGCCACGA 59.335 52.632 5.23 0.00 0.00 4.35
166 167 0.667184 CATTGCTTTTGGGCCACGAC 60.667 55.000 5.23 0.00 0.00 4.34
167 168 0.827507 ATTGCTTTTGGGCCACGACT 60.828 50.000 5.23 0.00 0.00 4.18
168 169 0.179015 TTGCTTTTGGGCCACGACTA 60.179 50.000 5.23 0.00 0.00 2.59
169 170 0.179015 TGCTTTTGGGCCACGACTAA 60.179 50.000 5.23 0.00 0.00 2.24
170 171 1.173913 GCTTTTGGGCCACGACTAAT 58.826 50.000 5.23 0.00 0.00 1.73
171 172 1.132453 GCTTTTGGGCCACGACTAATC 59.868 52.381 5.23 0.00 0.00 1.75
172 173 2.432444 CTTTTGGGCCACGACTAATCA 58.568 47.619 5.23 0.00 0.00 2.57
173 174 2.570415 TTTGGGCCACGACTAATCAA 57.430 45.000 5.23 0.00 0.00 2.57
174 175 2.799126 TTGGGCCACGACTAATCAAT 57.201 45.000 5.23 0.00 0.00 2.57
175 176 2.036958 TGGGCCACGACTAATCAATG 57.963 50.000 0.00 0.00 0.00 2.82
176 177 1.308998 GGGCCACGACTAATCAATGG 58.691 55.000 4.39 0.00 34.93 3.16
178 179 1.668419 GCCACGACTAATCAATGGCT 58.332 50.000 8.77 0.00 46.52 4.75
179 180 1.331756 GCCACGACTAATCAATGGCTG 59.668 52.381 8.77 0.00 46.52 4.85
221 222 2.092429 AGAAACCTTGTCTTCAGCACCA 60.092 45.455 0.00 0.00 0.00 4.17
238 239 0.253044 CCATCACTGGGATTGTCCGT 59.747 55.000 0.00 0.00 39.04 4.69
247 248 1.265454 GGATTGTCCGTGTCCCTCCT 61.265 60.000 0.00 0.00 0.00 3.69
255 256 0.458543 CGTGTCCCTCCTGATGAACG 60.459 60.000 0.00 0.00 0.00 3.95
258 259 1.612146 TCCCTCCTGATGAACGGCA 60.612 57.895 0.00 0.00 0.00 5.69
259 260 0.982852 TCCCTCCTGATGAACGGCAT 60.983 55.000 0.00 0.00 40.77 4.40
260 261 0.816825 CCCTCCTGATGAACGGCATG 60.817 60.000 0.00 0.00 37.34 4.06
272 273 1.375396 CGGCATGGTCCGTTGAAGA 60.375 57.895 3.80 0.00 44.18 2.87
273 274 0.953471 CGGCATGGTCCGTTGAAGAA 60.953 55.000 3.80 0.00 44.18 2.52
274 275 0.804989 GGCATGGTCCGTTGAAGAAG 59.195 55.000 0.00 0.00 0.00 2.85
276 277 1.882352 GCATGGTCCGTTGAAGAAGGT 60.882 52.381 0.00 0.00 0.00 3.50
278 279 1.961793 TGGTCCGTTGAAGAAGGTTG 58.038 50.000 0.00 0.00 0.00 3.77
279 280 1.487142 TGGTCCGTTGAAGAAGGTTGA 59.513 47.619 0.00 0.00 0.00 3.18
280 281 2.092861 TGGTCCGTTGAAGAAGGTTGAA 60.093 45.455 0.00 0.00 0.00 2.69
294 295 4.038271 AGGTTGAAAGATTGAGATGCCA 57.962 40.909 0.00 0.00 0.00 4.92
340 341 1.217057 ATGTTGGGCCTGGTGATCCT 61.217 55.000 4.53 0.00 34.23 3.24
360 361 3.495806 CCTTCATAGCTCTTCCATGTCCC 60.496 52.174 0.00 0.00 0.00 4.46
362 363 1.414181 CATAGCTCTTCCATGTCCCGT 59.586 52.381 0.00 0.00 0.00 5.28
363 364 0.824109 TAGCTCTTCCATGTCCCGTG 59.176 55.000 0.00 0.00 0.00 4.94
367 368 1.746615 CTTCCATGTCCCGTGGCAG 60.747 63.158 0.00 0.00 40.13 4.85
368 369 2.184020 CTTCCATGTCCCGTGGCAGA 62.184 60.000 0.00 0.00 36.20 4.26
385 386 2.545946 GCAGACGATATCCTCAAAAGCC 59.454 50.000 0.00 0.00 0.00 4.35
390 391 2.936498 CGATATCCTCAAAAGCCGTTGT 59.064 45.455 0.00 0.00 0.00 3.32
397 398 3.125316 CCTCAAAAGCCGTTGTGATAGTC 59.875 47.826 1.68 0.00 0.00 2.59
398 399 3.997021 CTCAAAAGCCGTTGTGATAGTCT 59.003 43.478 0.00 0.00 0.00 3.24
399 400 3.745975 TCAAAAGCCGTTGTGATAGTCTG 59.254 43.478 0.00 0.00 0.00 3.51
400 401 1.726853 AAGCCGTTGTGATAGTCTGC 58.273 50.000 0.00 0.00 0.00 4.26
401 402 0.898320 AGCCGTTGTGATAGTCTGCT 59.102 50.000 0.00 0.00 0.00 4.24
402 403 1.134965 AGCCGTTGTGATAGTCTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
403 404 1.404181 GCCGTTGTGATAGTCTGCTCA 60.404 52.381 0.00 0.00 0.00 4.26
446 447 6.588348 AAATTCTGCTTTCTTTTTCAACCG 57.412 33.333 0.00 0.00 0.00 4.44
447 448 3.708563 TCTGCTTTCTTTTTCAACCGG 57.291 42.857 0.00 0.00 0.00 5.28
448 449 3.283751 TCTGCTTTCTTTTTCAACCGGA 58.716 40.909 9.46 0.00 0.00 5.14
450 451 2.100087 TGCTTTCTTTTTCAACCGGACC 59.900 45.455 9.46 0.00 0.00 4.46
455 456 1.607148 CTTTTTCAACCGGACCTCACC 59.393 52.381 9.46 0.00 0.00 4.02
462 463 2.669240 CGGACCTCACCCCTTTCC 59.331 66.667 0.00 0.00 0.00 3.13
469 470 4.572007 GGACCTCACCCCTTTCCATTAATT 60.572 45.833 0.00 0.00 0.00 1.40
470 471 4.610333 ACCTCACCCCTTTCCATTAATTC 58.390 43.478 0.00 0.00 0.00 2.17
478 482 5.889289 CCCCTTTCCATTAATTCCTTAACGA 59.111 40.000 0.00 0.00 29.85 3.85
496 500 2.360483 ACGAAAACACATCACATGGCAA 59.640 40.909 0.00 0.00 33.60 4.52
583 606 1.073923 GACCAGAAAGGGGAAGAAGCA 59.926 52.381 0.00 0.00 43.89 3.91
593 616 0.321996 GGAAGAAGCAAGTCGGGAGT 59.678 55.000 0.00 0.00 0.00 3.85
653 676 9.737025 GTAGAAAGTGTTAATAGTTTGTAAGCG 57.263 33.333 9.48 0.00 0.00 4.68
723 754 8.050778 TCCTGAAAGATTTGCGTTATATGTTT 57.949 30.769 0.00 0.00 34.07 2.83
724 755 8.519526 TCCTGAAAGATTTGCGTTATATGTTTT 58.480 29.630 0.00 0.00 34.07 2.43
725 756 9.139174 CCTGAAAGATTTGCGTTATATGTTTTT 57.861 29.630 0.00 0.00 34.07 1.94
875 1033 4.304110 GTGTCCACACAAATTCGAGTAGA 58.696 43.478 4.92 0.00 45.75 2.59
878 1036 3.932710 TCCACACAAATTCGAGTAGATGC 59.067 43.478 0.00 0.00 0.00 3.91
886 1044 4.810191 ATTCGAGTAGATGCCTTATCCC 57.190 45.455 0.00 0.00 36.40 3.85
981 1227 4.696479 ACATTATTGCACCCAAAAACCA 57.304 36.364 0.00 0.00 34.05 3.67
1077 1323 3.857157 AAGGAGGAGTACAAACTGCAA 57.143 42.857 0.00 0.00 45.91 4.08
1098 1344 4.471904 AAGAAGCGTCAAGGATGATGTA 57.528 40.909 1.61 0.00 43.28 2.29
1212 1458 1.183549 GGGCTAACGAGGTCAGAGAA 58.816 55.000 0.00 0.00 0.00 2.87
1266 1512 2.124983 CTGGTGCATGTCGAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
1272 1518 2.989639 CATGTCGAGGGGCCTGAA 59.010 61.111 0.84 0.00 0.00 3.02
1303 1549 1.338973 AGCCACACATGCTCAAACAAG 59.661 47.619 0.00 0.00 32.41 3.16
1349 1595 0.591170 ACCAAGTTCATGAAACGCCG 59.409 50.000 10.35 0.00 43.02 6.46
1351 1597 1.001815 CCAAGTTCATGAAACGCCGTT 60.002 47.619 10.35 0.00 43.02 4.44
1428 1674 2.091499 TCGTGATAGGTACAGGGTCCAT 60.091 50.000 0.00 0.00 0.00 3.41
1453 1699 6.722590 TGAGGTGGTCACTAATCTAGTTGTTA 59.277 38.462 0.93 0.00 36.76 2.41
1461 1707 7.117379 GTCACTAATCTAGTTGTTACAACCACC 59.883 40.741 22.64 0.04 36.76 4.61
1503 1749 6.779860 AGCTCTATACAAGGACCAAAAAGAA 58.220 36.000 0.00 0.00 0.00 2.52
1559 1805 2.488528 CCAAGATGATGAGTGATGGGGG 60.489 54.545 0.00 0.00 0.00 5.40
1567 1813 1.274126 TGAGTGATGGGGGTGGTGATA 60.274 52.381 0.00 0.00 0.00 2.15
1614 1860 3.662759 ATTTTTGGATTCGGAGGCCTA 57.337 42.857 4.42 0.00 0.00 3.93
1654 1900 5.461078 GCCAAAGCAATGTATGATAAGCTTG 59.539 40.000 9.86 0.00 41.01 4.01
1661 1907 5.663795 ATGTATGATAAGCTTGAAGCACG 57.336 39.130 20.45 0.00 45.56 5.34
1685 1931 4.389890 TTGATTGCAGTGCTTTTGTTCT 57.610 36.364 17.60 0.00 0.00 3.01
1686 1932 4.389890 TGATTGCAGTGCTTTTGTTCTT 57.610 36.364 17.60 0.00 0.00 2.52
1920 2170 7.122799 TGCGATAAAGAGGTATGCATCTACTAT 59.877 37.037 0.19 0.00 34.31 2.12
1921 2171 8.622157 GCGATAAAGAGGTATGCATCTACTATA 58.378 37.037 0.19 0.00 34.31 1.31
2157 2492 4.345859 TGGGACTTACTGTCGAATGTTT 57.654 40.909 0.00 0.00 46.24 2.83
2167 2503 4.821805 ACTGTCGAATGTTTCCTCACATTT 59.178 37.500 0.81 0.00 45.55 2.32
2171 2507 7.970384 TGTCGAATGTTTCCTCACATTTATAC 58.030 34.615 0.81 1.78 45.55 1.47
2241 2581 2.158957 TGGAGGTATCTGGATTGCGAAC 60.159 50.000 0.00 0.00 0.00 3.95
2315 2657 2.200067 GTTCATGCATGTCTCTCTCCG 58.800 52.381 25.43 0.00 0.00 4.63
2322 2664 0.106116 ATGTCTCTCTCCGGTACCCC 60.106 60.000 6.25 0.00 0.00 4.95
2395 2738 2.032550 GGTTGACATTCATGCATCCTCG 59.967 50.000 0.00 0.00 0.00 4.63
2572 3966 5.648092 GTGTACTAATTGTGGAAGCAGGATT 59.352 40.000 0.00 0.00 0.00 3.01
2961 4359 8.922237 TCTGAGCATATATCCTAAAGATCATCC 58.078 37.037 0.00 0.00 36.33 3.51
2967 4365 8.986847 CATATATCCTAAAGATCATCCGATTGC 58.013 37.037 0.00 0.00 36.33 3.56
3040 4438 6.045106 AGGAACCAGGGTTAAGACTATTTGAA 59.955 38.462 3.19 0.00 38.60 2.69
3258 4680 4.395854 TCGTAGGCTAGTTGTTCATCGTAA 59.604 41.667 0.00 0.00 0.00 3.18
3287 4711 0.250234 TCTGGCTAGCACATCCACAC 59.750 55.000 18.24 0.00 0.00 3.82
3350 4774 4.060205 GTTGCCATCACTTTCATGCTTTT 58.940 39.130 0.00 0.00 0.00 2.27
3398 4822 3.214328 GGCCCCACTAATTCACACTATG 58.786 50.000 0.00 0.00 0.00 2.23
3685 5115 5.825679 AGTTGGTATGCACTCAAACTTTGTA 59.174 36.000 6.85 0.00 0.00 2.41
3774 5207 7.563188 TGGTAATATTGCAATGAATAGTTGGGT 59.437 33.333 22.27 0.00 0.00 4.51
3780 5213 3.763897 GCAATGAATAGTTGGGTGGAGTT 59.236 43.478 0.00 0.00 0.00 3.01
3914 5353 3.133464 GTGCTGCGCATGGCCTAA 61.133 61.111 12.24 0.00 41.91 2.69
4043 5482 0.468771 AGCTTGTTGCCCTTCAGCTT 60.469 50.000 0.00 0.00 44.23 3.74
4068 5510 3.709834 TGGTCAGCTCTCCACCATA 57.290 52.632 2.60 0.00 35.16 2.74
4083 5528 0.682855 CCATAACACCATGGGCGGTT 60.683 55.000 18.09 18.45 41.63 4.44
4130 5575 1.295792 TCAAGACACAAGCAACGACC 58.704 50.000 0.00 0.00 0.00 4.79
4156 5601 5.745476 GCTCATTTCAAGAGGGAGATATGCT 60.745 44.000 0.00 0.00 33.72 3.79
4351 5798 0.323360 TATGTGCTTCCCAACTGCCC 60.323 55.000 0.00 0.00 0.00 5.36
4352 5799 2.085343 ATGTGCTTCCCAACTGCCCT 62.085 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.866015 AGGTACTCCATAGTGCAGCA 58.134 50.000 0.00 0.00 39.87 4.41
2 3 3.223435 TCTAGGTACTCCATAGTGCAGC 58.777 50.000 0.00 0.00 39.87 5.25
5 6 5.855740 AAGTTCTAGGTACTCCATAGTGC 57.144 43.478 0.00 0.00 41.75 4.40
26 27 3.760151 AGAGCTGGTGTGTACATACGTAA 59.240 43.478 15.51 4.38 0.00 3.18
27 28 3.349927 AGAGCTGGTGTGTACATACGTA 58.650 45.455 15.51 0.00 0.00 3.57
28 29 2.163815 GAGAGCTGGTGTGTACATACGT 59.836 50.000 15.51 0.00 0.00 3.57
29 30 2.791503 CGAGAGCTGGTGTGTACATACG 60.792 54.545 15.51 5.18 0.00 3.06
30 31 2.422479 TCGAGAGCTGGTGTGTACATAC 59.578 50.000 13.90 13.90 0.00 2.39
31 32 2.718563 TCGAGAGCTGGTGTGTACATA 58.281 47.619 0.00 0.00 0.00 2.29
32 33 1.545841 TCGAGAGCTGGTGTGTACAT 58.454 50.000 0.00 0.00 0.00 2.29
33 34 1.324383 TTCGAGAGCTGGTGTGTACA 58.676 50.000 0.00 0.00 0.00 2.90
34 35 2.433868 TTTCGAGAGCTGGTGTGTAC 57.566 50.000 0.00 0.00 0.00 2.90
35 36 3.128349 GTTTTTCGAGAGCTGGTGTGTA 58.872 45.455 0.00 0.00 0.00 2.90
36 37 1.940613 GTTTTTCGAGAGCTGGTGTGT 59.059 47.619 0.00 0.00 0.00 3.72
37 38 1.264288 GGTTTTTCGAGAGCTGGTGTG 59.736 52.381 0.00 0.00 0.00 3.82
38 39 1.594331 GGTTTTTCGAGAGCTGGTGT 58.406 50.000 0.00 0.00 0.00 4.16
39 40 0.512952 CGGTTTTTCGAGAGCTGGTG 59.487 55.000 0.00 0.00 0.00 4.17
40 41 0.391597 TCGGTTTTTCGAGAGCTGGT 59.608 50.000 0.00 0.00 34.82 4.00
41 42 1.508632 TTCGGTTTTTCGAGAGCTGG 58.491 50.000 0.00 0.00 40.42 4.85
42 43 3.678072 TGTATTCGGTTTTTCGAGAGCTG 59.322 43.478 0.00 0.00 40.42 4.24
43 44 3.921677 TGTATTCGGTTTTTCGAGAGCT 58.078 40.909 0.00 0.00 40.42 4.09
44 45 4.392216 GTTGTATTCGGTTTTTCGAGAGC 58.608 43.478 0.00 0.00 40.42 4.09
45 46 4.433805 CCGTTGTATTCGGTTTTTCGAGAG 60.434 45.833 0.00 0.00 42.62 3.20
46 47 3.429543 CCGTTGTATTCGGTTTTTCGAGA 59.570 43.478 0.00 0.00 42.62 4.04
47 48 3.423907 CCCGTTGTATTCGGTTTTTCGAG 60.424 47.826 3.78 0.00 45.63 4.04
48 49 2.479656 CCCGTTGTATTCGGTTTTTCGA 59.520 45.455 3.78 0.00 45.63 3.71
49 50 2.223845 ACCCGTTGTATTCGGTTTTTCG 59.776 45.455 3.78 0.00 45.63 3.46
50 51 3.557508 CACCCGTTGTATTCGGTTTTTC 58.442 45.455 3.78 0.00 45.63 2.29
51 52 2.293955 CCACCCGTTGTATTCGGTTTTT 59.706 45.455 3.78 0.00 45.63 1.94
52 53 1.881324 CCACCCGTTGTATTCGGTTTT 59.119 47.619 3.78 0.00 45.63 2.43
53 54 1.525941 CCACCCGTTGTATTCGGTTT 58.474 50.000 3.78 0.00 45.63 3.27
54 55 0.956902 GCCACCCGTTGTATTCGGTT 60.957 55.000 3.78 0.00 45.63 4.44
55 56 1.376295 GCCACCCGTTGTATTCGGT 60.376 57.895 3.78 0.00 45.63 4.69
56 57 1.078708 AGCCACCCGTTGTATTCGG 60.079 57.895 0.00 0.00 46.49 4.30
57 58 0.672401 ACAGCCACCCGTTGTATTCG 60.672 55.000 0.00 0.00 33.59 3.34
58 59 0.802494 CACAGCCACCCGTTGTATTC 59.198 55.000 0.00 0.00 33.59 1.75
59 60 0.398696 TCACAGCCACCCGTTGTATT 59.601 50.000 0.00 0.00 33.59 1.89
60 61 0.398696 TTCACAGCCACCCGTTGTAT 59.601 50.000 0.00 0.00 33.59 2.29
61 62 0.398696 ATTCACAGCCACCCGTTGTA 59.601 50.000 0.00 0.00 33.59 2.41
62 63 0.889186 GATTCACAGCCACCCGTTGT 60.889 55.000 0.00 0.00 36.14 3.32
63 64 0.888736 TGATTCACAGCCACCCGTTG 60.889 55.000 0.00 0.00 0.00 4.10
64 65 0.606401 CTGATTCACAGCCACCCGTT 60.606 55.000 0.00 0.00 39.86 4.44
65 66 1.003355 CTGATTCACAGCCACCCGT 60.003 57.895 0.00 0.00 39.86 5.28
66 67 1.746615 CCTGATTCACAGCCACCCG 60.747 63.158 0.00 0.00 44.52 5.28
67 68 0.251341 AACCTGATTCACAGCCACCC 60.251 55.000 0.00 0.00 44.52 4.61
68 69 1.541588 GAAACCTGATTCACAGCCACC 59.458 52.381 0.00 0.00 44.52 4.61
69 70 2.229792 TGAAACCTGATTCACAGCCAC 58.770 47.619 0.00 0.00 44.52 5.01
70 71 2.655090 TGAAACCTGATTCACAGCCA 57.345 45.000 0.00 0.00 44.52 4.75
71 72 3.119352 GGAATGAAACCTGATTCACAGCC 60.119 47.826 0.00 0.00 44.52 4.85
72 73 3.760684 AGGAATGAAACCTGATTCACAGC 59.239 43.478 0.00 0.00 44.52 4.40
73 74 5.939883 TGTAGGAATGAAACCTGATTCACAG 59.060 40.000 0.00 0.00 41.78 3.66
74 75 5.875224 TGTAGGAATGAAACCTGATTCACA 58.125 37.500 0.00 0.00 41.78 3.58
75 76 6.612306 GTTGTAGGAATGAAACCTGATTCAC 58.388 40.000 0.00 0.00 41.78 3.18
76 77 5.411361 CGTTGTAGGAATGAAACCTGATTCA 59.589 40.000 0.00 0.00 43.03 2.57
77 78 5.163754 CCGTTGTAGGAATGAAACCTGATTC 60.164 44.000 0.00 0.00 38.31 2.52
78 79 4.700213 CCGTTGTAGGAATGAAACCTGATT 59.300 41.667 0.00 0.00 38.31 2.57
79 80 4.261801 CCGTTGTAGGAATGAAACCTGAT 58.738 43.478 0.00 0.00 38.31 2.90
80 81 3.558321 CCCGTTGTAGGAATGAAACCTGA 60.558 47.826 0.00 0.00 38.31 3.86
81 82 2.747446 CCCGTTGTAGGAATGAAACCTG 59.253 50.000 0.00 0.00 38.31 4.00
82 83 2.374170 ACCCGTTGTAGGAATGAAACCT 59.626 45.455 0.00 0.00 41.05 3.50
83 84 2.486592 CACCCGTTGTAGGAATGAAACC 59.513 50.000 0.00 0.00 0.00 3.27
84 85 2.486592 CCACCCGTTGTAGGAATGAAAC 59.513 50.000 0.00 0.00 0.00 2.78
85 86 2.785562 CCACCCGTTGTAGGAATGAAA 58.214 47.619 0.00 0.00 0.00 2.69
86 87 1.612199 GCCACCCGTTGTAGGAATGAA 60.612 52.381 0.00 0.00 0.00 2.57
87 88 0.035820 GCCACCCGTTGTAGGAATGA 60.036 55.000 0.00 0.00 0.00 2.57
88 89 1.029947 GGCCACCCGTTGTAGGAATG 61.030 60.000 0.00 0.00 0.00 2.67
89 90 1.301954 GGCCACCCGTTGTAGGAAT 59.698 57.895 0.00 0.00 0.00 3.01
90 91 2.751688 GGCCACCCGTTGTAGGAA 59.248 61.111 0.00 0.00 0.00 3.36
127 128 1.269257 GGAGGATAAAAGCAATGCGCC 60.269 52.381 4.18 0.00 44.04 6.53
136 137 5.422145 CCCAAAAGCAATGGAGGATAAAAG 58.578 41.667 4.19 0.00 40.56 2.27
138 139 3.197549 GCCCAAAAGCAATGGAGGATAAA 59.802 43.478 4.19 0.00 40.56 1.40
141 142 1.197812 GCCCAAAAGCAATGGAGGAT 58.802 50.000 4.19 0.00 40.56 3.24
162 163 2.009774 GCACAGCCATTGATTAGTCGT 58.990 47.619 0.00 0.00 0.00 4.34
164 165 3.539604 AGAGCACAGCCATTGATTAGTC 58.460 45.455 0.00 0.00 0.00 2.59
165 166 3.054875 TGAGAGCACAGCCATTGATTAGT 60.055 43.478 0.00 0.00 0.00 2.24
166 167 3.311871 GTGAGAGCACAGCCATTGATTAG 59.688 47.826 0.00 0.00 44.51 1.73
167 168 3.273434 GTGAGAGCACAGCCATTGATTA 58.727 45.455 0.00 0.00 44.51 1.75
168 169 2.089980 GTGAGAGCACAGCCATTGATT 58.910 47.619 0.00 0.00 44.51 2.57
169 170 1.681166 GGTGAGAGCACAGCCATTGAT 60.681 52.381 0.00 0.00 46.96 2.57
170 171 0.321919 GGTGAGAGCACAGCCATTGA 60.322 55.000 0.00 0.00 46.96 2.57
171 172 1.642037 CGGTGAGAGCACAGCCATTG 61.642 60.000 0.00 0.00 46.96 2.82
172 173 1.376424 CGGTGAGAGCACAGCCATT 60.376 57.895 0.00 0.00 46.96 3.16
173 174 2.236223 CTCGGTGAGAGCACAGCCAT 62.236 60.000 0.00 0.00 46.96 4.40
174 175 2.917227 TCGGTGAGAGCACAGCCA 60.917 61.111 0.00 0.00 46.96 4.75
175 176 2.125753 CTCGGTGAGAGCACAGCC 60.126 66.667 0.00 0.00 46.96 4.85
221 222 0.984230 ACACGGACAATCCCAGTGAT 59.016 50.000 9.14 0.00 35.88 3.06
228 229 1.221021 GGAGGGACACGGACAATCC 59.779 63.158 0.00 0.00 0.00 3.01
233 234 0.970937 TCATCAGGAGGGACACGGAC 60.971 60.000 0.00 0.00 0.00 4.79
238 239 1.899437 GCCGTTCATCAGGAGGGACA 61.899 60.000 0.00 0.00 0.00 4.02
247 248 1.449423 CGGACCATGCCGTTCATCA 60.449 57.895 3.80 0.00 46.07 3.07
255 256 0.804989 CTTCTTCAACGGACCATGCC 59.195 55.000 0.00 0.00 0.00 4.40
258 259 2.105821 TCAACCTTCTTCAACGGACCAT 59.894 45.455 0.00 0.00 0.00 3.55
259 260 1.487142 TCAACCTTCTTCAACGGACCA 59.513 47.619 0.00 0.00 0.00 4.02
260 261 2.249844 TCAACCTTCTTCAACGGACC 57.750 50.000 0.00 0.00 0.00 4.46
272 273 4.410099 TGGCATCTCAATCTTTCAACCTT 58.590 39.130 0.00 0.00 0.00 3.50
273 274 4.038271 TGGCATCTCAATCTTTCAACCT 57.962 40.909 0.00 0.00 0.00 3.50
274 275 4.789012 TTGGCATCTCAATCTTTCAACC 57.211 40.909 0.00 0.00 0.00 3.77
276 277 4.943093 TCGATTGGCATCTCAATCTTTCAA 59.057 37.500 13.43 0.00 46.41 2.69
278 279 5.490139 TTCGATTGGCATCTCAATCTTTC 57.510 39.130 13.43 0.00 46.41 2.62
279 280 5.649395 TCTTTCGATTGGCATCTCAATCTTT 59.351 36.000 13.43 0.00 46.41 2.52
280 281 5.188434 TCTTTCGATTGGCATCTCAATCTT 58.812 37.500 13.43 0.00 46.41 2.40
294 295 5.543507 ATGTCTCCATAGCTCTTTCGATT 57.456 39.130 0.00 0.00 0.00 3.34
300 301 5.071519 ACATAGCAATGTCTCCATAGCTCTT 59.928 40.000 0.00 0.00 42.92 2.85
302 303 4.892433 ACATAGCAATGTCTCCATAGCTC 58.108 43.478 0.00 0.00 42.92 4.09
321 322 1.217057 AGGATCACCAGGCCCAACAT 61.217 55.000 0.00 0.00 38.94 2.71
322 323 1.434513 AAGGATCACCAGGCCCAACA 61.435 55.000 0.00 0.00 38.94 3.33
340 341 2.103094 CGGGACATGGAAGAGCTATGAA 59.897 50.000 0.00 0.00 37.65 2.57
362 363 3.797039 CTTTTGAGGATATCGTCTGCCA 58.203 45.455 22.32 4.11 0.00 4.92
363 364 2.545946 GCTTTTGAGGATATCGTCTGCC 59.454 50.000 22.32 6.66 0.00 4.85
367 368 2.822764 ACGGCTTTTGAGGATATCGTC 58.177 47.619 16.75 16.75 0.00 4.20
368 369 2.936498 CAACGGCTTTTGAGGATATCGT 59.064 45.455 0.00 0.00 0.00 3.73
372 373 3.410631 TCACAACGGCTTTTGAGGATA 57.589 42.857 5.04 0.00 0.00 2.59
385 386 2.919859 CAGTGAGCAGACTATCACAACG 59.080 50.000 17.67 6.35 46.63 4.10
399 400 2.761304 AAAGGCCTCCAGCAGTGAGC 62.761 60.000 5.23 0.00 46.50 4.26
400 401 0.615331 TAAAGGCCTCCAGCAGTGAG 59.385 55.000 5.23 0.00 46.50 3.51
401 402 1.064003 TTAAAGGCCTCCAGCAGTGA 58.936 50.000 5.23 0.00 46.50 3.41
402 403 1.909700 TTTAAAGGCCTCCAGCAGTG 58.090 50.000 5.23 0.00 46.50 3.66
403 404 2.675658 TTTTAAAGGCCTCCAGCAGT 57.324 45.000 5.23 0.00 46.50 4.40
430 431 2.361119 AGGTCCGGTTGAAAAAGAAAGC 59.639 45.455 0.00 0.00 0.00 3.51
435 436 1.607148 GGTGAGGTCCGGTTGAAAAAG 59.393 52.381 0.00 0.00 0.00 2.27
446 447 0.704664 AATGGAAAGGGGTGAGGTCC 59.295 55.000 0.00 0.00 0.00 4.46
447 448 3.732048 TTAATGGAAAGGGGTGAGGTC 57.268 47.619 0.00 0.00 0.00 3.85
448 449 4.572007 GGAATTAATGGAAAGGGGTGAGGT 60.572 45.833 0.00 0.00 0.00 3.85
450 451 4.871822 AGGAATTAATGGAAAGGGGTGAG 58.128 43.478 0.00 0.00 0.00 3.51
455 456 7.399245 TTCGTTAAGGAATTAATGGAAAGGG 57.601 36.000 6.50 0.00 0.00 3.95
462 463 9.619316 TGATGTGTTTTCGTTAAGGAATTAATG 57.381 29.630 11.14 0.00 0.00 1.90
469 470 5.049060 CCATGTGATGTGTTTTCGTTAAGGA 60.049 40.000 0.00 0.00 0.00 3.36
470 471 5.153513 CCATGTGATGTGTTTTCGTTAAGG 58.846 41.667 0.00 0.00 0.00 2.69
478 482 2.100584 ACGTTGCCATGTGATGTGTTTT 59.899 40.909 0.00 0.00 0.00 2.43
496 500 2.023414 TTGGAGACTTGCACGGACGT 62.023 55.000 0.00 0.00 0.00 4.34
556 579 0.329596 CCCCTTTCTGGTCTCCTTGG 59.670 60.000 0.00 0.00 0.00 3.61
723 754 4.877378 AATTTCATCAGCCTGCAGAAAA 57.123 36.364 17.39 4.39 32.65 2.29
724 755 4.562082 CAAATTTCATCAGCCTGCAGAAA 58.438 39.130 17.39 6.38 33.33 2.52
725 756 3.615592 GCAAATTTCATCAGCCTGCAGAA 60.616 43.478 17.39 0.00 0.00 3.02
726 757 2.094390 GCAAATTTCATCAGCCTGCAGA 60.094 45.455 17.39 0.00 0.00 4.26
826 984 0.767375 GCCAGCTATTCATCCAGGGA 59.233 55.000 0.00 0.00 0.00 4.20
875 1033 1.981495 GGCTACAGAGGGATAAGGCAT 59.019 52.381 0.00 0.00 33.30 4.40
878 1036 2.683768 ACAGGCTACAGAGGGATAAGG 58.316 52.381 0.00 0.00 0.00 2.69
886 1044 6.717289 AGATAGGATAGTACAGGCTACAGAG 58.283 44.000 0.00 0.00 0.00 3.35
1077 1323 3.340814 ACATCATCCTTGACGCTTCTT 57.659 42.857 0.00 0.00 33.85 2.52
1098 1344 3.119173 CCAGCTCTCTCTCGAGATGTTTT 60.119 47.826 17.03 0.00 43.86 2.43
1197 1443 3.567164 ACGAAAGTTCTCTGACCTCGTTA 59.433 43.478 0.00 0.00 46.40 3.18
1266 1512 0.877743 GCTTGTCTTCAGGTTCAGGC 59.122 55.000 0.00 0.00 0.00 4.85
1272 1518 0.546122 TGTGTGGCTTGTCTTCAGGT 59.454 50.000 0.00 0.00 0.00 4.00
1303 1549 1.303309 CCGCCCATCTTCTTCATGAC 58.697 55.000 0.00 0.00 0.00 3.06
1349 1595 0.935366 GATCTCGTCGCCGATGGAAC 60.935 60.000 6.46 0.00 43.27 3.62
1351 1597 1.381165 TTGATCTCGTCGCCGATGGA 61.381 55.000 6.46 3.36 43.27 3.41
1407 1653 1.285667 TGGACCCTGTACCTATCACGA 59.714 52.381 0.00 0.00 0.00 4.35
1428 1674 5.084519 ACAACTAGATTAGTGACCACCTCA 58.915 41.667 0.00 0.00 39.39 3.86
1438 1684 6.161381 CGGTGGTTGTAACAACTAGATTAGT 58.839 40.000 6.51 0.00 41.73 2.24
1461 1707 1.868519 GCTAATAGGCGAGGGTCAACG 60.869 57.143 0.00 0.00 0.00 4.10
1503 1749 3.346315 TGAATCATCAATGCCAACGAGT 58.654 40.909 0.00 0.00 30.99 4.18
1559 1805 1.463444 GTTGCTTGGACGTATCACCAC 59.537 52.381 0.00 0.00 35.81 4.16
1567 1813 2.550830 ATCTTGAGTTGCTTGGACGT 57.449 45.000 0.00 0.00 0.00 4.34
1639 1885 5.359756 TCGTGCTTCAAGCTTATCATACAT 58.640 37.500 11.57 0.00 42.97 2.29
1654 1900 2.912967 CACTGCAATCAAATCGTGCTTC 59.087 45.455 0.00 0.00 39.09 3.86
1661 1907 5.464389 AGAACAAAAGCACTGCAATCAAATC 59.536 36.000 3.30 0.00 0.00 2.17
1685 1931 1.610554 GCTAGGGTGGCGTCCTACAA 61.611 60.000 2.08 0.00 35.92 2.41
1686 1932 2.056223 GCTAGGGTGGCGTCCTACA 61.056 63.158 2.08 0.00 35.92 2.74
1848 2097 4.785914 TCATCCAACTCCCCATTTACTACA 59.214 41.667 0.00 0.00 0.00 2.74
2026 2328 1.760613 GACCATAGTCCATCCGAACCA 59.239 52.381 0.00 0.00 37.00 3.67
2157 2492 9.739276 AAGTTCAAGAATGTATAAATGTGAGGA 57.261 29.630 0.00 0.00 0.00 3.71
2167 2503 9.952188 CTATCGTCAGAAGTTCAAGAATGTATA 57.048 33.333 5.50 0.00 0.00 1.47
2171 2507 7.490725 ACATCTATCGTCAGAAGTTCAAGAATG 59.509 37.037 5.50 5.14 0.00 2.67
2224 2564 4.636206 AGAAAAGTTCGCAATCCAGATACC 59.364 41.667 0.00 0.00 34.02 2.73
2297 2639 0.749049 CCGGAGAGAGACATGCATGA 59.251 55.000 32.75 0.00 0.00 3.07
2322 2664 9.300681 TGGCATTATAGAATAAAGAAATGGAGG 57.699 33.333 0.00 0.00 0.00 4.30
2405 3794 6.867662 ACAAGGCATCTAAGTATGTAATGC 57.132 37.500 0.00 0.00 41.49 3.56
2451 3842 7.894753 TCACCATCCATAATGCAAAAGATAA 57.105 32.000 0.00 0.00 33.71 1.75
2572 3966 5.170748 TCGAGTATACGAGTAGTTGTGACA 58.829 41.667 0.22 0.00 37.37 3.58
2951 4349 4.191544 TCTTTCGCAATCGGATGATCTTT 58.808 39.130 0.00 0.00 32.24 2.52
2961 4359 7.011773 CCATATCAAACTATCTTTCGCAATCG 58.988 38.462 0.00 0.00 0.00 3.34
2967 4365 8.292448 CCCATTTCCATATCAAACTATCTTTCG 58.708 37.037 0.00 0.00 0.00 3.46
3040 4438 5.127491 TCGTTGAAGTACCTTTCACCAATT 58.873 37.500 0.00 0.00 36.84 2.32
3287 4711 4.142600 GGCATTAAGTGACCTTGCTTGTAG 60.143 45.833 0.00 0.00 31.89 2.74
3350 4774 3.396260 AGCTAGGACACGCAAAACTTA 57.604 42.857 0.00 0.00 0.00 2.24
3398 4822 4.418392 CCAACATGCTCAAGACAATTAGC 58.582 43.478 0.00 0.00 35.51 3.09
3685 5115 4.074970 CTGTCAGCTTACCCAATTCTGTT 58.925 43.478 0.00 0.00 0.00 3.16
3780 5213 4.700213 GGATCTTGCTTAGTTTGGCTACAA 59.300 41.667 0.00 0.00 34.07 2.41
3793 5226 5.426689 TGTCTATGACTTGGATCTTGCTT 57.573 39.130 0.00 0.00 33.15 3.91
3914 5353 3.175710 ACCAGCCCGGGTTCTTGT 61.176 61.111 24.63 10.77 38.19 3.16
4017 5456 1.600916 GGGCAACAAGCTCTCGGTT 60.601 57.895 0.00 0.00 41.91 4.44
4018 5457 2.032681 GGGCAACAAGCTCTCGGT 59.967 61.111 0.00 0.00 41.91 4.69
4043 5482 2.028112 GTGGAGAGCTGACCATGTGTTA 60.028 50.000 10.97 0.00 38.48 2.41
4068 5510 1.603455 CTGAACCGCCCATGGTGTT 60.603 57.895 11.73 10.92 42.89 3.32
4083 5528 1.304381 GCTTGGGGAATGCACCTGA 60.304 57.895 0.00 0.00 38.87 3.86
4130 5575 3.623906 TCTCCCTCTTGAAATGAGCAG 57.376 47.619 0.00 0.00 36.84 4.24
4156 5601 4.263068 GGAACTCAAGAGATTCAAGGACCA 60.263 45.833 3.73 0.00 0.00 4.02
4249 5694 4.843516 AGACTTTGACTTCCTGAAGGAGAT 59.156 41.667 11.34 0.00 46.36 2.75
4331 5778 1.686115 GGGCAGTTGGGAAGCACATAT 60.686 52.381 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.