Multiple sequence alignment - TraesCS1D01G289000

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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 TraesCS1D01G289000 chr1D 100.000 2195 0 0 1 2195 387192732 387194926 0.000000e+00 4054
1 TraesCS1D01G289000 chr1D 80.769 390 45 22 833 1200 387059958 387060339 5.970000e-71 278
2 TraesCS1D01G289000 chr1D 79.070 387 59 16 833 1202 386949632 386950013 1.680000e-61 246
3 TraesCS1D01G289000 chr1B 85.039 1798 125 85 149 1830 520468032 520469801 0.000000e+00 1698
4 TraesCS1D01G289000 chr1B 87.601 371 18 7 1829 2194 520469925 520470272 2.620000e-109 405
5 TraesCS1D01G289000 chr1B 79.854 412 61 14 802 1195 520390394 520390801 4.610000e-72 281
6 TraesCS1D01G289000 chr1B 79.854 412 58 14 809 1202 520374078 520374482 5.970000e-71 278
7 TraesCS1D01G289000 chr1B 87.069 232 25 3 992 1221 520399470 520399242 7.780000e-65 257
8 TraesCS1D01G289000 chr1B 79.834 362 29 20 170 508 520404885 520405225 7.890000e-55 224
9 TraesCS1D01G289000 chr1A 83.756 1182 92 41 719 1845 486953191 486954327 0.000000e+00 1027
10 TraesCS1D01G289000 chr1A 82.222 540 72 11 1672 2194 486954509 486955041 5.560000e-121 444
11 TraesCS1D01G289000 chr1A 82.059 340 35 11 157 472 486952740 486953077 1.290000e-67 267
12 TraesCS1D01G289000 chr1A 86.250 240 32 1 962 1200 486896836 486897075 2.160000e-65 259
13 TraesCS1D01G289000 chr1A 86.076 237 26 6 962 1191 486816868 486817104 4.680000e-62 248
14 TraesCS1D01G289000 chr7A 97.351 151 4 0 1 151 122331810 122331660 7.780000e-65 257
15 TraesCS1D01G289000 chr3A 96.753 154 5 0 1 154 15466488 15466335 7.780000e-65 257
16 TraesCS1D01G289000 chr5B 97.333 150 4 0 1 150 418917662 418917811 2.800000e-64 255
17 TraesCS1D01G289000 chr4B 94.578 166 7 1 1 166 636683939 636683776 2.800000e-64 255
18 TraesCS1D01G289000 chr4A 97.333 150 4 0 1 150 705545947 705546096 2.800000e-64 255
19 TraesCS1D01G289000 chr3B 97.333 150 4 0 1 150 172056898 172057047 2.800000e-64 255
20 TraesCS1D01G289000 chr2B 97.333 150 4 0 1 150 630735885 630736034 2.800000e-64 255
21 TraesCS1D01G289000 chr4D 95.333 150 7 0 1 150 418533961 418533812 2.820000e-59 239
22 TraesCS1D01G289000 chr7B 94.667 150 7 1 1 150 92126076 92126224 4.710000e-57 231


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 TraesCS1D01G289000 chr1D 387192732 387194926 2194 False 4054.000000 4054 100.000 1 2195 1 chr1D.!!$F3 2194
1 TraesCS1D01G289000 chr1B 520468032 520470272 2240 False 1051.500000 1698 86.320 149 2194 2 chr1B.!!$F4 2045
2 TraesCS1D01G289000 chr1A 486952740 486955041 2301 False 579.333333 1027 82.679 157 2194 3 chr1A.!!$F3 2037

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
120 121 0.175989 CTAGTCTGAAACTCGCCCCC 59.824 60.0 0.0 0.0 39.55 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1672 0.325933 AGGCAAGCACTATGTCTGCA 59.674 50.0 0.0 0.0 37.08 4.41 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
26 27 6.814343 AGCTGTTTACACTAACGAAAATACG 58.186 36.000 0.00 0.00 39.31 3.06
27 28 6.642131 AGCTGTTTACACTAACGAAAATACGA 59.358 34.615 0.00 0.00 37.03 3.43
28 29 6.946584 GCTGTTTACACTAACGAAAATACGAG 59.053 38.462 0.00 0.00 37.03 4.18
29 30 7.358683 GCTGTTTACACTAACGAAAATACGAGT 60.359 37.037 0.00 0.00 37.03 4.18
30 31 7.996002 TGTTTACACTAACGAAAATACGAGTC 58.004 34.615 0.00 0.00 37.03 3.36
31 32 7.114811 TGTTTACACTAACGAAAATACGAGTCC 59.885 37.037 0.00 0.00 37.03 3.85
32 33 4.161333 ACACTAACGAAAATACGAGTCCG 58.839 43.478 0.00 0.00 42.50 4.79
33 34 3.545078 CACTAACGAAAATACGAGTCCGG 59.455 47.826 0.00 0.00 40.78 5.14
34 35 2.000429 AACGAAAATACGAGTCCGGG 58.000 50.000 0.00 0.00 40.78 5.73
35 36 0.459063 ACGAAAATACGAGTCCGGGC 60.459 55.000 0.00 0.00 40.78 6.13
36 37 0.179119 CGAAAATACGAGTCCGGGCT 60.179 55.000 9.26 9.26 40.78 5.19
37 38 1.738030 CGAAAATACGAGTCCGGGCTT 60.738 52.381 11.49 0.00 40.78 4.35
38 39 2.480073 CGAAAATACGAGTCCGGGCTTA 60.480 50.000 11.49 0.00 40.78 3.09
39 40 3.725490 GAAAATACGAGTCCGGGCTTAT 58.275 45.455 11.49 1.30 40.78 1.73
40 41 2.814280 AATACGAGTCCGGGCTTATG 57.186 50.000 11.49 6.14 40.78 1.90
41 42 1.700955 ATACGAGTCCGGGCTTATGT 58.299 50.000 11.49 12.52 40.78 2.29
42 43 1.477553 TACGAGTCCGGGCTTATGTT 58.522 50.000 11.49 0.00 40.78 2.71
43 44 0.611714 ACGAGTCCGGGCTTATGTTT 59.388 50.000 11.49 0.00 40.78 2.83
44 45 1.287425 CGAGTCCGGGCTTATGTTTC 58.713 55.000 11.49 0.00 0.00 2.78
45 46 1.134788 CGAGTCCGGGCTTATGTTTCT 60.135 52.381 11.49 0.00 0.00 2.52
46 47 2.677037 CGAGTCCGGGCTTATGTTTCTT 60.677 50.000 11.49 0.00 0.00 2.52
47 48 3.344515 GAGTCCGGGCTTATGTTTCTTT 58.655 45.455 11.49 0.00 0.00 2.52
48 49 3.081804 AGTCCGGGCTTATGTTTCTTTG 58.918 45.455 0.35 0.00 0.00 2.77
49 50 1.816224 TCCGGGCTTATGTTTCTTTGC 59.184 47.619 0.00 0.00 0.00 3.68
50 51 1.543802 CCGGGCTTATGTTTCTTTGCA 59.456 47.619 0.00 0.00 0.00 4.08
51 52 2.595386 CGGGCTTATGTTTCTTTGCAC 58.405 47.619 0.00 0.00 0.00 4.57
52 53 2.030363 CGGGCTTATGTTTCTTTGCACA 60.030 45.455 0.00 0.00 0.00 4.57
53 54 3.317150 GGGCTTATGTTTCTTTGCACAC 58.683 45.455 0.00 0.00 0.00 3.82
54 55 3.005791 GGGCTTATGTTTCTTTGCACACT 59.994 43.478 0.00 0.00 0.00 3.55
55 56 4.501400 GGGCTTATGTTTCTTTGCACACTT 60.501 41.667 0.00 0.00 0.00 3.16
56 57 5.049828 GGCTTATGTTTCTTTGCACACTTT 58.950 37.500 0.00 0.00 0.00 2.66
57 58 6.212955 GGCTTATGTTTCTTTGCACACTTTA 58.787 36.000 0.00 0.00 0.00 1.85
58 59 6.699642 GGCTTATGTTTCTTTGCACACTTTAA 59.300 34.615 0.00 0.00 0.00 1.52
59 60 7.223777 GGCTTATGTTTCTTTGCACACTTTAAA 59.776 33.333 0.00 0.00 0.00 1.52
60 61 8.055986 GCTTATGTTTCTTTGCACACTTTAAAC 58.944 33.333 0.00 0.00 0.00 2.01
61 62 9.301153 CTTATGTTTCTTTGCACACTTTAAACT 57.699 29.630 0.00 0.00 0.00 2.66
62 63 9.646427 TTATGTTTCTTTGCACACTTTAAACTT 57.354 25.926 0.00 0.00 0.00 2.66
64 65 9.816354 ATGTTTCTTTGCACACTTTAAACTTAT 57.184 25.926 0.00 0.00 0.00 1.73
65 66 9.081997 TGTTTCTTTGCACACTTTAAACTTATG 57.918 29.630 0.00 0.00 0.00 1.90
66 67 9.296400 GTTTCTTTGCACACTTTAAACTTATGA 57.704 29.630 0.00 0.00 0.00 2.15
67 68 9.515020 TTTCTTTGCACACTTTAAACTTATGAG 57.485 29.630 0.00 0.00 0.00 2.90
68 69 8.220755 TCTTTGCACACTTTAAACTTATGAGT 57.779 30.769 0.00 0.00 37.87 3.41
69 70 8.128582 TCTTTGCACACTTTAAACTTATGAGTG 58.871 33.333 0.00 0.00 42.48 3.51
70 71 7.561021 TTGCACACTTTAAACTTATGAGTGA 57.439 32.000 15.10 0.00 39.97 3.41
71 72 7.744087 TGCACACTTTAAACTTATGAGTGAT 57.256 32.000 15.10 0.00 39.97 3.06
72 73 7.806690 TGCACACTTTAAACTTATGAGTGATC 58.193 34.615 15.10 0.00 39.97 2.92
73 74 7.443879 TGCACACTTTAAACTTATGAGTGATCA 59.556 33.333 15.10 0.00 39.97 2.92
74 75 8.454106 GCACACTTTAAACTTATGAGTGATCAT 58.546 33.333 0.00 0.00 39.97 2.45
75 76 9.979270 CACACTTTAAACTTATGAGTGATCATC 57.021 33.333 0.00 0.00 39.97 2.92
76 77 9.167311 ACACTTTAAACTTATGAGTGATCATCC 57.833 33.333 0.00 0.00 39.97 3.51
77 78 8.331022 CACTTTAAACTTATGAGTGATCATCCG 58.669 37.037 0.00 0.00 39.97 4.18
78 79 8.258007 ACTTTAAACTTATGAGTGATCATCCGA 58.742 33.333 0.00 0.00 35.91 4.55
79 80 9.265901 CTTTAAACTTATGAGTGATCATCCGAT 57.734 33.333 0.00 0.00 35.91 4.18
80 81 8.593492 TTAAACTTATGAGTGATCATCCGATG 57.407 34.615 0.00 1.55 35.91 3.84
81 82 4.564041 ACTTATGAGTGATCATCCGATGC 58.436 43.478 0.00 0.00 33.99 3.91
82 83 2.469274 ATGAGTGATCATCCGATGCC 57.531 50.000 0.00 0.00 29.66 4.40
83 84 0.394192 TGAGTGATCATCCGATGCCC 59.606 55.000 0.00 0.00 29.66 5.36
84 85 0.394192 GAGTGATCATCCGATGCCCA 59.606 55.000 0.00 1.51 29.66 5.36
85 86 1.002888 GAGTGATCATCCGATGCCCAT 59.997 52.381 0.00 0.00 29.66 4.00
86 87 1.002888 AGTGATCATCCGATGCCCATC 59.997 52.381 0.00 3.01 34.56 3.51
87 88 1.058284 TGATCATCCGATGCCCATCA 58.942 50.000 3.25 5.48 37.69 3.07
88 89 1.002773 TGATCATCCGATGCCCATCAG 59.997 52.381 3.25 0.00 37.69 2.90
89 90 1.002888 GATCATCCGATGCCCATCAGT 59.997 52.381 3.25 0.00 37.69 3.41
90 91 0.394192 TCATCCGATGCCCATCAGTC 59.606 55.000 3.25 0.00 37.69 3.51
91 92 0.395686 CATCCGATGCCCATCAGTCT 59.604 55.000 8.79 0.00 37.69 3.24
92 93 1.620323 CATCCGATGCCCATCAGTCTA 59.380 52.381 8.79 0.00 37.69 2.59
93 94 2.015456 TCCGATGCCCATCAGTCTAT 57.985 50.000 8.79 0.00 37.69 1.98
94 95 3.169512 TCCGATGCCCATCAGTCTATA 57.830 47.619 8.79 0.00 37.69 1.31
95 96 3.506398 TCCGATGCCCATCAGTCTATAA 58.494 45.455 8.79 0.00 37.69 0.98
96 97 3.511540 TCCGATGCCCATCAGTCTATAAG 59.488 47.826 8.79 0.00 37.69 1.73
97 98 3.511540 CCGATGCCCATCAGTCTATAAGA 59.488 47.826 8.79 0.00 37.69 2.10
98 99 4.381398 CCGATGCCCATCAGTCTATAAGAG 60.381 50.000 8.79 0.00 37.69 2.85
99 100 4.502962 GATGCCCATCAGTCTATAAGAGC 58.497 47.826 3.48 0.00 37.74 4.09
100 101 3.581101 TGCCCATCAGTCTATAAGAGCT 58.419 45.455 0.00 0.00 0.00 4.09
101 102 3.576118 TGCCCATCAGTCTATAAGAGCTC 59.424 47.826 5.27 5.27 0.00 4.09
102 103 3.831911 GCCCATCAGTCTATAAGAGCTCT 59.168 47.826 11.45 11.45 0.00 4.09
103 104 5.013547 GCCCATCAGTCTATAAGAGCTCTA 58.986 45.833 18.59 6.01 0.00 2.43
104 105 5.125417 GCCCATCAGTCTATAAGAGCTCTAG 59.875 48.000 18.59 11.32 0.00 2.43
105 106 6.245408 CCCATCAGTCTATAAGAGCTCTAGT 58.755 44.000 18.59 11.27 0.00 2.57
106 107 6.374333 CCCATCAGTCTATAAGAGCTCTAGTC 59.626 46.154 18.59 8.82 0.00 2.59
107 108 7.168219 CCATCAGTCTATAAGAGCTCTAGTCT 58.832 42.308 18.59 11.05 0.00 3.24
108 109 7.119699 CCATCAGTCTATAAGAGCTCTAGTCTG 59.880 44.444 22.81 22.81 33.06 3.51
109 110 7.368198 TCAGTCTATAAGAGCTCTAGTCTGA 57.632 40.000 25.36 25.36 36.21 3.27
110 111 7.797062 TCAGTCTATAAGAGCTCTAGTCTGAA 58.203 38.462 26.23 16.33 35.89 3.02
111 112 8.268605 TCAGTCTATAAGAGCTCTAGTCTGAAA 58.731 37.037 26.23 13.79 35.89 2.69
112 113 8.342634 CAGTCTATAAGAGCTCTAGTCTGAAAC 58.657 40.741 23.74 13.48 33.36 2.78
113 114 8.272173 AGTCTATAAGAGCTCTAGTCTGAAACT 58.728 37.037 18.59 10.33 42.33 2.66
114 115 8.557029 GTCTATAAGAGCTCTAGTCTGAAACTC 58.443 40.741 18.59 0.00 39.55 3.01
115 116 4.695217 AAGAGCTCTAGTCTGAAACTCG 57.305 45.455 18.59 0.00 39.55 4.18
116 117 2.422127 AGAGCTCTAGTCTGAAACTCGC 59.578 50.000 16.50 0.00 39.55 5.03
117 118 1.474879 AGCTCTAGTCTGAAACTCGCC 59.525 52.381 0.00 0.00 39.55 5.54
118 119 1.470112 GCTCTAGTCTGAAACTCGCCC 60.470 57.143 0.00 0.00 39.55 6.13
119 120 1.135333 CTCTAGTCTGAAACTCGCCCC 59.865 57.143 0.00 0.00 39.55 5.80
120 121 0.175989 CTAGTCTGAAACTCGCCCCC 59.824 60.000 0.00 0.00 39.55 5.40
137 138 1.708341 CCCCCTATGCCAAATTCCTG 58.292 55.000 0.00 0.00 0.00 3.86
138 139 1.708341 CCCCTATGCCAAATTCCTGG 58.292 55.000 0.00 0.00 39.71 4.45
144 145 4.743018 CCAAATTCCTGGCTCCGT 57.257 55.556 0.00 0.00 0.00 4.69
145 146 2.482326 CCAAATTCCTGGCTCCGTC 58.518 57.895 0.00 0.00 0.00 4.79
146 147 1.032114 CCAAATTCCTGGCTCCGTCC 61.032 60.000 0.00 0.00 0.00 4.79
147 148 1.032114 CAAATTCCTGGCTCCGTCCC 61.032 60.000 0.00 0.00 0.00 4.46
166 167 6.208007 CCGTCCCTGACTGTATGTATGTATTA 59.792 42.308 0.00 0.00 0.00 0.98
366 407 4.154918 CCTTGGAGCTAGCTACAAACAAAG 59.845 45.833 35.80 25.80 45.23 2.77
373 414 4.214332 GCTAGCTACAAACAAAGCAGAGTT 59.786 41.667 7.70 0.00 41.32 3.01
381 422 0.716108 CAAAGCAGAGTTAGCCGTCG 59.284 55.000 0.00 0.00 0.00 5.12
405 446 0.461516 CACGTGCATGCATCTCTCCT 60.462 55.000 25.64 0.00 0.00 3.69
483 529 2.186384 CGGCTCTGCTCTTCCCTG 59.814 66.667 0.00 0.00 0.00 4.45
486 532 0.545646 GGCTCTGCTCTTCCCTGAAT 59.454 55.000 0.00 0.00 0.00 2.57
488 534 2.171448 GGCTCTGCTCTTCCCTGAATTA 59.829 50.000 0.00 0.00 0.00 1.40
490 536 4.064388 GCTCTGCTCTTCCCTGAATTATC 58.936 47.826 0.00 0.00 0.00 1.75
526 577 4.681942 CAGTTCAGTTCAACGAGAGGTAAG 59.318 45.833 0.00 0.00 0.00 2.34
527 578 3.936372 TCAGTTCAACGAGAGGTAAGG 57.064 47.619 0.00 0.00 0.00 2.69
528 579 3.228453 TCAGTTCAACGAGAGGTAAGGT 58.772 45.455 0.00 0.00 0.00 3.50
529 580 4.401022 TCAGTTCAACGAGAGGTAAGGTA 58.599 43.478 0.00 0.00 0.00 3.08
530 581 4.828939 TCAGTTCAACGAGAGGTAAGGTAA 59.171 41.667 0.00 0.00 0.00 2.85
594 645 5.917541 TTTTTCAACTCGAAAGACGCTAT 57.082 34.783 0.00 0.00 44.32 2.97
595 646 4.903638 TTTCAACTCGAAAGACGCTATG 57.096 40.909 0.00 0.00 38.72 2.23
596 647 2.876091 TCAACTCGAAAGACGCTATGG 58.124 47.619 0.00 0.00 42.26 2.74
598 649 2.853731 ACTCGAAAGACGCTATGGAG 57.146 50.000 0.00 0.00 42.26 3.86
601 652 1.063616 TCGAAAGACGCTATGGAGACG 59.936 52.381 0.00 0.00 42.26 4.18
602 653 1.202154 CGAAAGACGCTATGGAGACGT 60.202 52.381 0.00 0.00 37.88 4.34
603 654 2.452105 GAAAGACGCTATGGAGACGTC 58.548 52.381 7.70 7.70 45.00 4.34
614 665 1.178276 GGAGACGTCCAGATGACACT 58.822 55.000 13.01 0.00 44.71 3.55
628 679 9.647918 TCCAGATGACACTCTAAATATCTACTT 57.352 33.333 0.00 0.00 0.00 2.24
659 729 3.242867 TCTGGATTGACTGGTCAGAAGT 58.757 45.455 4.84 0.00 41.13 3.01
698 768 1.635817 GCACCCTGCCATCTCCCTTA 61.636 60.000 0.00 0.00 37.42 2.69
716 786 7.667219 TCTCCCTTAATATTCAATCATTCCAGC 59.333 37.037 0.00 0.00 0.00 4.85
730 800 2.199652 CCAGCCGTTTTTGGGAGCA 61.200 57.895 0.00 0.00 0.00 4.26
770 844 2.024751 TGGTTAAGGGCATAAGTTCCCC 60.025 50.000 0.00 0.00 43.67 4.81
805 879 1.468520 CTGTACAAACAAGATGGCCCG 59.531 52.381 0.00 0.00 34.49 6.13
831 908 4.399303 AGAGGTCAAAATATTCCGCCAAAG 59.601 41.667 0.00 0.00 0.00 2.77
843 920 3.843999 TCCGCCAAAGAAATTAACATGC 58.156 40.909 0.00 0.00 0.00 4.06
845 922 3.241701 CGCCAAAGAAATTAACATGCGT 58.758 40.909 0.00 0.00 35.22 5.24
852 929 0.732571 AATTAACATGCGTGGCGAGG 59.267 50.000 11.36 0.00 0.00 4.63
854 931 3.597675 TAACATGCGTGGCGAGGCA 62.598 57.895 18.31 18.31 46.49 4.75
862 939 1.212751 GTGGCGAGGCACCAAAATC 59.787 57.895 17.54 0.00 39.39 2.17
863 940 2.331893 TGGCGAGGCACCAAAATCG 61.332 57.895 0.00 0.00 38.19 3.34
867 944 0.443869 CGAGGCACCAAAATCGACAG 59.556 55.000 0.00 0.00 37.35 3.51
873 950 1.872952 CACCAAAATCGACAGAGCACA 59.127 47.619 0.00 0.00 0.00 4.57
875 952 1.466167 CCAAAATCGACAGAGCACAGG 59.534 52.381 0.00 0.00 0.00 4.00
876 953 1.466167 CAAAATCGACAGAGCACAGGG 59.534 52.381 0.00 0.00 0.00 4.45
877 954 0.687354 AAATCGACAGAGCACAGGGT 59.313 50.000 0.00 0.00 0.00 4.34
878 955 0.687354 AATCGACAGAGCACAGGGTT 59.313 50.000 0.00 0.00 0.00 4.11
880 957 1.334160 TCGACAGAGCACAGGGTTTA 58.666 50.000 0.00 0.00 0.00 2.01
881 958 1.272490 TCGACAGAGCACAGGGTTTAG 59.728 52.381 0.00 0.00 0.00 1.85
934 1014 4.041567 TGTCCTCTTCACATTAAGCAAGGA 59.958 41.667 0.00 0.00 30.79 3.36
936 1016 5.123027 GTCCTCTTCACATTAAGCAAGGAAG 59.877 44.000 0.00 0.00 33.57 3.46
940 1020 4.771590 TCACATTAAGCAAGGAAGCAAG 57.228 40.909 0.00 0.00 36.85 4.01
957 1037 1.199789 CAAGCACAACACACACACACT 59.800 47.619 0.00 0.00 0.00 3.55
976 1071 6.097554 ACACACTCAGAAGAAGAAGAAGAAGA 59.902 38.462 0.00 0.00 0.00 2.87
979 1074 6.646240 CACTCAGAAGAAGAAGAAGAAGAAGG 59.354 42.308 0.00 0.00 0.00 3.46
993 1088 1.213296 AGAAGGACAACACAGGTGGT 58.787 50.000 4.24 0.00 32.44 4.16
1045 1140 1.745115 GGCATCAGCAACTACGGCA 60.745 57.895 0.00 0.00 44.61 5.69
1201 1296 1.997669 CGCCTACAACTGAACCTCTC 58.002 55.000 0.00 0.00 0.00 3.20
1220 1315 0.881118 CCCAAGTCCAAACCACATCG 59.119 55.000 0.00 0.00 0.00 3.84
1242 1342 2.096819 GTCGTCAGTCAAGGCTCTAGAG 59.903 54.545 15.85 15.85 0.00 2.43
1281 1385 6.354794 TGCTTCTACCTACTGTACATGTTT 57.645 37.500 2.30 0.00 0.00 2.83
1283 1387 7.898918 TGCTTCTACCTACTGTACATGTTTAA 58.101 34.615 2.30 0.00 0.00 1.52
1284 1388 7.816031 TGCTTCTACCTACTGTACATGTTTAAC 59.184 37.037 2.30 0.00 0.00 2.01
1286 1390 9.924650 CTTCTACCTACTGTACATGTTTAACTT 57.075 33.333 2.30 0.00 0.00 2.66
1336 1446 2.604912 TCCAACTAGCTGAGAGACCA 57.395 50.000 0.00 0.00 0.00 4.02
1339 1449 2.165437 CCAACTAGCTGAGAGACCACTC 59.835 54.545 0.00 0.00 42.90 3.51
1341 1451 2.442413 ACTAGCTGAGAGACCACTCAC 58.558 52.381 0.00 0.00 44.79 3.51
1342 1452 2.224892 ACTAGCTGAGAGACCACTCACA 60.225 50.000 0.00 0.00 44.79 3.58
1477 1609 1.005340 GCTGATCGTTCTTGCTCAGG 58.995 55.000 0.00 0.00 36.48 3.86
1489 1621 5.441718 TCTTGCTCAGGGTCTGATTTTAT 57.558 39.130 0.00 0.00 39.92 1.40
1491 1623 5.882557 TCTTGCTCAGGGTCTGATTTTATTC 59.117 40.000 0.00 0.00 39.92 1.75
1492 1624 5.178096 TGCTCAGGGTCTGATTTTATTCA 57.822 39.130 0.00 0.00 39.92 2.57
1512 1645 2.949644 CAGAAGAACAAGTTTCCCCGTT 59.050 45.455 0.00 0.00 0.00 4.44
1520 1653 1.919240 AGTTTCCCCGTTGATTTCCC 58.081 50.000 0.00 0.00 0.00 3.97
1522 1655 0.483328 TTTCCCCGTTGATTTCCCCA 59.517 50.000 0.00 0.00 0.00 4.96
1535 1668 2.232622 TCCCCAAAGGAAACCGTCA 58.767 52.632 0.00 0.00 43.78 4.35
1539 1672 3.010808 TCCCCAAAGGAAACCGTCAATAT 59.989 43.478 0.00 0.00 43.78 1.28
1563 1696 2.038952 AGACATAGTGCTTGCCTCAACA 59.961 45.455 0.00 0.00 0.00 3.33
1576 1709 4.334552 TGCCTCAACAGCAAGATAATGAA 58.665 39.130 0.00 0.00 37.28 2.57
1587 1720 5.402270 AGCAAGATAATGAAACGCAAAACAC 59.598 36.000 0.00 0.00 0.00 3.32
1588 1721 5.174761 GCAAGATAATGAAACGCAAAACACA 59.825 36.000 0.00 0.00 0.00 3.72
1589 1722 6.292061 GCAAGATAATGAAACGCAAAACACAA 60.292 34.615 0.00 0.00 0.00 3.33
1597 1730 5.065346 TGAAACGCAAAACACAACTCTCATA 59.935 36.000 0.00 0.00 0.00 2.15
1600 1733 4.515191 ACGCAAAACACAACTCTCATACAT 59.485 37.500 0.00 0.00 0.00 2.29
1601 1734 5.082059 CGCAAAACACAACTCTCATACATC 58.918 41.667 0.00 0.00 0.00 3.06
1609 1757 4.108336 CAACTCTCATACATCTCCACGTG 58.892 47.826 9.08 9.08 0.00 4.49
1654 1809 4.041740 TGATATTTTCTACGAGCGCTGT 57.958 40.909 18.48 16.28 0.00 4.40
1666 1821 2.328473 GAGCGCTGTCGATTGCATATA 58.672 47.619 18.48 0.00 38.10 0.86
1727 1882 3.771216 ACAGAACCTCAAATCAGGCAAT 58.229 40.909 0.00 0.00 36.98 3.56
1932 2487 2.749682 TGGAGACACCAATGCGCT 59.250 55.556 9.73 0.00 46.75 5.92
1938 2493 0.523072 GACACCAATGCGCTGAACAT 59.477 50.000 9.73 0.00 0.00 2.71
2017 2572 6.840780 AAATAGAATTTGGGTGTCTTGGAG 57.159 37.500 0.00 0.00 0.00 3.86
2049 2604 4.955925 TTCTTTGTCACGACACAAATGT 57.044 36.364 14.25 0.00 43.63 2.71
2055 2610 4.796369 TGTCACGACACAAATGTATACGA 58.204 39.130 0.00 0.00 39.95 3.43
2061 2616 4.321480 CGACACAAATGTATACGAACGTCA 59.679 41.667 2.45 0.00 39.95 4.35
2076 2631 4.550831 CGAACGTCATGGCATATCAGTTTC 60.551 45.833 0.00 0.00 0.00 2.78
2092 2647 0.944386 TTTCTTGCGCCTGAGTGAAC 59.056 50.000 4.18 0.00 0.00 3.18
2099 2654 1.202580 GCGCCTGAGTGAACCTGATAT 60.203 52.381 0.00 0.00 0.00 1.63
2152 2707 9.793252 AAATAGCATTGTTTACTAGCAAGAATG 57.207 29.630 15.66 15.66 37.74 2.67
2153 2708 6.824305 AGCATTGTTTACTAGCAAGAATGT 57.176 33.333 18.78 9.03 37.27 2.71
2194 2749 3.134804 ACACAAGCCAGACTAACTTGAGT 59.865 43.478 18.66 14.96 42.71 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.427012 CGTATTTTCGTTAGTGTAAACAGCTAA 58.573 33.333 0.00 0.00 0.00 3.09
1 2 7.807433 TCGTATTTTCGTTAGTGTAAACAGCTA 59.193 33.333 0.00 0.00 0.00 3.32
2 3 6.642131 TCGTATTTTCGTTAGTGTAAACAGCT 59.358 34.615 0.00 0.00 0.00 4.24
3 4 6.810286 TCGTATTTTCGTTAGTGTAAACAGC 58.190 36.000 0.00 0.00 0.00 4.40
4 5 8.000285 ACTCGTATTTTCGTTAGTGTAAACAG 58.000 34.615 0.00 0.00 0.00 3.16
5 6 7.114811 GGACTCGTATTTTCGTTAGTGTAAACA 59.885 37.037 0.00 0.00 0.00 2.83
6 7 7.440281 GGACTCGTATTTTCGTTAGTGTAAAC 58.560 38.462 0.00 0.00 0.00 2.01
7 8 6.305399 CGGACTCGTATTTTCGTTAGTGTAAA 59.695 38.462 0.00 0.00 0.00 2.01
8 9 5.794945 CGGACTCGTATTTTCGTTAGTGTAA 59.205 40.000 0.00 0.00 0.00 2.41
9 10 5.323900 CGGACTCGTATTTTCGTTAGTGTA 58.676 41.667 0.00 0.00 0.00 2.90
10 11 4.161333 CGGACTCGTATTTTCGTTAGTGT 58.839 43.478 0.00 0.00 0.00 3.55
11 12 3.545078 CCGGACTCGTATTTTCGTTAGTG 59.455 47.826 0.00 0.00 33.95 2.74
12 13 3.428045 CCCGGACTCGTATTTTCGTTAGT 60.428 47.826 0.73 0.00 33.95 2.24
13 14 3.111098 CCCGGACTCGTATTTTCGTTAG 58.889 50.000 0.73 0.00 33.95 2.34
14 15 2.735126 GCCCGGACTCGTATTTTCGTTA 60.735 50.000 0.73 0.00 33.95 3.18
15 16 2.000429 CCCGGACTCGTATTTTCGTT 58.000 50.000 0.73 0.00 33.95 3.85
16 17 0.459063 GCCCGGACTCGTATTTTCGT 60.459 55.000 0.73 0.00 33.95 3.85
17 18 0.179119 AGCCCGGACTCGTATTTTCG 60.179 55.000 0.73 0.00 33.95 3.46
18 19 2.019948 AAGCCCGGACTCGTATTTTC 57.980 50.000 0.73 0.00 33.95 2.29
19 20 3.118519 ACATAAGCCCGGACTCGTATTTT 60.119 43.478 0.73 0.00 33.95 1.82
20 21 2.433239 ACATAAGCCCGGACTCGTATTT 59.567 45.455 0.73 0.00 33.95 1.40
21 22 2.037144 ACATAAGCCCGGACTCGTATT 58.963 47.619 0.73 0.00 33.95 1.89
22 23 1.700955 ACATAAGCCCGGACTCGTAT 58.299 50.000 0.73 0.00 33.95 3.06
23 24 1.477553 AACATAAGCCCGGACTCGTA 58.522 50.000 0.73 0.00 33.95 3.43
24 25 0.611714 AAACATAAGCCCGGACTCGT 59.388 50.000 0.73 0.00 33.95 4.18
25 26 1.134788 AGAAACATAAGCCCGGACTCG 60.135 52.381 0.73 0.00 0.00 4.18
26 27 2.693267 AGAAACATAAGCCCGGACTC 57.307 50.000 0.73 0.00 0.00 3.36
27 28 3.081804 CAAAGAAACATAAGCCCGGACT 58.918 45.455 0.73 0.00 0.00 3.85
28 29 2.415491 GCAAAGAAACATAAGCCCGGAC 60.415 50.000 0.73 0.00 0.00 4.79
29 30 1.816224 GCAAAGAAACATAAGCCCGGA 59.184 47.619 0.73 0.00 0.00 5.14
30 31 1.543802 TGCAAAGAAACATAAGCCCGG 59.456 47.619 0.00 0.00 0.00 5.73
31 32 2.030363 TGTGCAAAGAAACATAAGCCCG 60.030 45.455 0.00 0.00 0.00 6.13
32 33 3.005791 AGTGTGCAAAGAAACATAAGCCC 59.994 43.478 0.00 0.00 0.00 5.19
33 34 4.243007 AGTGTGCAAAGAAACATAAGCC 57.757 40.909 0.00 0.00 0.00 4.35
34 35 7.692908 TTAAAGTGTGCAAAGAAACATAAGC 57.307 32.000 0.00 0.00 0.00 3.09
35 36 9.301153 AGTTTAAAGTGTGCAAAGAAACATAAG 57.699 29.630 0.00 0.00 0.00 1.73
36 37 9.646427 AAGTTTAAAGTGTGCAAAGAAACATAA 57.354 25.926 0.00 0.00 0.00 1.90
38 39 9.816354 ATAAGTTTAAAGTGTGCAAAGAAACAT 57.184 25.926 0.00 0.00 0.00 2.71
39 40 9.081997 CATAAGTTTAAAGTGTGCAAAGAAACA 57.918 29.630 0.00 0.00 0.00 2.83
40 41 9.296400 TCATAAGTTTAAAGTGTGCAAAGAAAC 57.704 29.630 0.00 0.00 0.00 2.78
41 42 9.515020 CTCATAAGTTTAAAGTGTGCAAAGAAA 57.485 29.630 0.00 0.00 0.00 2.52
42 43 8.682710 ACTCATAAGTTTAAAGTGTGCAAAGAA 58.317 29.630 0.00 0.00 28.74 2.52
43 44 8.128582 CACTCATAAGTTTAAAGTGTGCAAAGA 58.871 33.333 0.00 0.00 34.14 2.52
44 45 8.128582 TCACTCATAAGTTTAAAGTGTGCAAAG 58.871 33.333 13.16 0.00 38.71 2.77
45 46 7.990917 TCACTCATAAGTTTAAAGTGTGCAAA 58.009 30.769 13.16 0.00 38.71 3.68
46 47 7.561021 TCACTCATAAGTTTAAAGTGTGCAA 57.439 32.000 13.16 0.00 38.71 4.08
47 48 7.443879 TGATCACTCATAAGTTTAAAGTGTGCA 59.556 33.333 13.16 0.00 38.71 4.57
48 49 7.806690 TGATCACTCATAAGTTTAAAGTGTGC 58.193 34.615 13.16 9.38 38.71 4.57
49 50 9.979270 GATGATCACTCATAAGTTTAAAGTGTG 57.021 33.333 0.00 0.69 42.27 3.82
50 51 9.167311 GGATGATCACTCATAAGTTTAAAGTGT 57.833 33.333 0.00 0.00 42.27 3.55
51 52 8.331022 CGGATGATCACTCATAAGTTTAAAGTG 58.669 37.037 0.00 9.67 42.27 3.16
52 53 8.258007 TCGGATGATCACTCATAAGTTTAAAGT 58.742 33.333 0.00 0.00 42.27 2.66
53 54 8.648557 TCGGATGATCACTCATAAGTTTAAAG 57.351 34.615 0.00 0.00 42.27 1.85
54 55 9.045223 CATCGGATGATCACTCATAAGTTTAAA 57.955 33.333 12.67 0.00 42.27 1.52
55 56 7.171508 GCATCGGATGATCACTCATAAGTTTAA 59.828 37.037 21.69 0.00 42.27 1.52
56 57 6.646653 GCATCGGATGATCACTCATAAGTTTA 59.353 38.462 21.69 0.00 42.27 2.01
57 58 5.468072 GCATCGGATGATCACTCATAAGTTT 59.532 40.000 21.69 0.00 42.27 2.66
58 59 4.993584 GCATCGGATGATCACTCATAAGTT 59.006 41.667 21.69 0.00 42.27 2.66
59 60 4.562347 GGCATCGGATGATCACTCATAAGT 60.562 45.833 21.69 0.00 42.27 2.24
60 61 3.931468 GGCATCGGATGATCACTCATAAG 59.069 47.826 21.69 0.00 42.27 1.73
61 62 3.306989 GGGCATCGGATGATCACTCATAA 60.307 47.826 21.69 0.00 42.27 1.90
62 63 2.234661 GGGCATCGGATGATCACTCATA 59.765 50.000 21.69 0.00 42.27 2.15
63 64 1.002888 GGGCATCGGATGATCACTCAT 59.997 52.381 21.69 0.00 44.93 2.90
64 65 0.394192 GGGCATCGGATGATCACTCA 59.606 55.000 21.69 0.00 35.41 3.41
65 66 0.394192 TGGGCATCGGATGATCACTC 59.606 55.000 21.69 4.33 30.49 3.51
66 67 1.002888 GATGGGCATCGGATGATCACT 59.997 52.381 21.69 8.32 30.49 3.41
67 68 1.271001 TGATGGGCATCGGATGATCAC 60.271 52.381 21.69 6.54 40.63 3.06
68 69 1.002773 CTGATGGGCATCGGATGATCA 59.997 52.381 21.69 18.16 44.92 2.92
69 70 1.002888 ACTGATGGGCATCGGATGATC 59.997 52.381 21.69 14.89 44.92 2.92
70 71 1.002888 GACTGATGGGCATCGGATGAT 59.997 52.381 21.69 6.28 44.92 2.45
71 72 0.394192 GACTGATGGGCATCGGATGA 59.606 55.000 21.69 1.11 44.92 2.92
72 73 0.395686 AGACTGATGGGCATCGGATG 59.604 55.000 13.63 13.63 44.92 3.51
73 74 2.015456 TAGACTGATGGGCATCGGAT 57.985 50.000 0.00 0.00 44.92 4.18
74 75 2.015456 ATAGACTGATGGGCATCGGA 57.985 50.000 0.00 0.00 44.92 4.55
75 76 3.511540 TCTTATAGACTGATGGGCATCGG 59.488 47.826 0.00 0.00 46.89 4.18
76 77 4.742417 CTCTTATAGACTGATGGGCATCG 58.258 47.826 0.00 0.00 40.63 3.84
77 78 4.222588 AGCTCTTATAGACTGATGGGCATC 59.777 45.833 0.00 0.00 38.29 3.91
78 79 4.166539 AGCTCTTATAGACTGATGGGCAT 58.833 43.478 0.00 0.00 0.00 4.40
79 80 3.576118 GAGCTCTTATAGACTGATGGGCA 59.424 47.826 6.43 0.00 0.00 5.36
80 81 3.831911 AGAGCTCTTATAGACTGATGGGC 59.168 47.826 11.45 0.00 0.00 5.36
81 82 6.245408 ACTAGAGCTCTTATAGACTGATGGG 58.755 44.000 23.84 0.00 0.00 4.00
82 83 7.119699 CAGACTAGAGCTCTTATAGACTGATGG 59.880 44.444 26.78 10.15 39.85 3.51
83 84 7.877612 TCAGACTAGAGCTCTTATAGACTGATG 59.122 40.741 28.19 14.68 40.70 3.07
84 85 7.973402 TCAGACTAGAGCTCTTATAGACTGAT 58.027 38.462 28.19 7.21 40.70 2.90
85 86 7.368198 TCAGACTAGAGCTCTTATAGACTGA 57.632 40.000 28.19 28.19 42.14 3.41
86 87 8.342634 GTTTCAGACTAGAGCTCTTATAGACTG 58.657 40.741 25.75 25.75 39.25 3.51
87 88 8.272173 AGTTTCAGACTAGAGCTCTTATAGACT 58.728 37.037 23.84 15.61 36.65 3.24
88 89 8.446599 AGTTTCAGACTAGAGCTCTTATAGAC 57.553 38.462 23.84 13.52 36.65 2.59
89 90 7.439955 CGAGTTTCAGACTAGAGCTCTTATAGA 59.560 40.741 23.84 11.15 39.19 1.98
90 91 7.572759 CGAGTTTCAGACTAGAGCTCTTATAG 58.427 42.308 23.84 15.94 39.19 1.31
91 92 6.017770 GCGAGTTTCAGACTAGAGCTCTTATA 60.018 42.308 23.84 2.49 39.19 0.98
92 93 5.220970 GCGAGTTTCAGACTAGAGCTCTTAT 60.221 44.000 23.84 10.58 39.19 1.73
93 94 4.095185 GCGAGTTTCAGACTAGAGCTCTTA 59.905 45.833 23.84 7.12 39.19 2.10
94 95 3.119637 GCGAGTTTCAGACTAGAGCTCTT 60.120 47.826 23.84 4.14 39.19 2.85
95 96 2.422127 GCGAGTTTCAGACTAGAGCTCT 59.578 50.000 22.17 22.17 39.19 4.09
96 97 2.478879 GGCGAGTTTCAGACTAGAGCTC 60.479 54.545 5.27 5.27 39.19 4.09
97 98 1.474879 GGCGAGTTTCAGACTAGAGCT 59.525 52.381 0.00 0.00 39.19 4.09
98 99 1.470112 GGGCGAGTTTCAGACTAGAGC 60.470 57.143 0.00 0.00 39.19 4.09
99 100 1.135333 GGGGCGAGTTTCAGACTAGAG 59.865 57.143 0.00 0.00 39.19 2.43
100 101 1.183549 GGGGCGAGTTTCAGACTAGA 58.816 55.000 0.00 0.00 39.19 2.43
101 102 0.175989 GGGGGCGAGTTTCAGACTAG 59.824 60.000 0.00 0.00 39.19 2.57
102 103 2.283824 GGGGGCGAGTTTCAGACTA 58.716 57.895 0.00 0.00 39.19 2.59
103 104 3.069778 GGGGGCGAGTTTCAGACT 58.930 61.111 0.00 0.00 42.70 3.24
118 119 1.708341 CAGGAATTTGGCATAGGGGG 58.292 55.000 0.00 0.00 0.00 5.40
119 120 1.708341 CCAGGAATTTGGCATAGGGG 58.292 55.000 0.00 0.00 0.00 4.79
127 128 1.032114 GGACGGAGCCAGGAATTTGG 61.032 60.000 0.00 0.00 41.35 3.28
128 129 1.032114 GGGACGGAGCCAGGAATTTG 61.032 60.000 0.00 0.00 0.00 2.32
129 130 1.208165 AGGGACGGAGCCAGGAATTT 61.208 55.000 0.00 0.00 0.00 1.82
130 131 1.616628 AGGGACGGAGCCAGGAATT 60.617 57.895 0.00 0.00 0.00 2.17
131 132 2.041265 AGGGACGGAGCCAGGAAT 59.959 61.111 0.00 0.00 0.00 3.01
132 133 3.003173 CAGGGACGGAGCCAGGAA 61.003 66.667 0.00 0.00 0.00 3.36
133 134 3.992641 TCAGGGACGGAGCCAGGA 61.993 66.667 0.00 0.00 0.00 3.86
134 135 3.775654 GTCAGGGACGGAGCCAGG 61.776 72.222 0.00 0.00 30.07 4.45
135 136 2.681778 AGTCAGGGACGGAGCCAG 60.682 66.667 0.00 0.00 37.67 4.85
136 137 2.435120 TACAGTCAGGGACGGAGCCA 62.435 60.000 3.59 0.00 37.67 4.75
137 138 1.043673 ATACAGTCAGGGACGGAGCC 61.044 60.000 3.59 0.00 37.67 4.70
138 139 0.103208 CATACAGTCAGGGACGGAGC 59.897 60.000 3.59 0.00 37.67 4.70
139 140 1.475403 ACATACAGTCAGGGACGGAG 58.525 55.000 3.59 0.00 37.67 4.63
140 141 2.812836 TACATACAGTCAGGGACGGA 57.187 50.000 3.59 0.00 37.67 4.69
141 142 2.693591 ACATACATACAGTCAGGGACGG 59.306 50.000 0.00 0.00 37.67 4.79
142 143 5.707242 ATACATACATACAGTCAGGGACG 57.293 43.478 0.00 0.00 37.67 4.79
143 144 8.803235 TGATAATACATACATACAGTCAGGGAC 58.197 37.037 0.00 0.00 0.00 4.46
144 145 8.950007 TGATAATACATACATACAGTCAGGGA 57.050 34.615 0.00 0.00 0.00 4.20
145 146 9.025041 TCTGATAATACATACATACAGTCAGGG 57.975 37.037 0.00 0.00 32.44 4.45
166 167 7.306866 GCGCGTCTCTTCTTAATTAATTCTGAT 60.307 37.037 8.43 0.00 0.00 2.90
196 197 0.384669 GACCTTATCCTGACCCGACG 59.615 60.000 0.00 0.00 0.00 5.12
197 198 1.136500 GTGACCTTATCCTGACCCGAC 59.864 57.143 0.00 0.00 0.00 4.79
248 250 2.156051 GACACCTGACCTCCACCGAC 62.156 65.000 0.00 0.00 0.00 4.79
299 305 0.320247 CTCGCTTGAGCTTGAGGTGT 60.320 55.000 1.07 0.00 39.32 4.16
366 407 3.248171 CGCGACGGCTAACTCTGC 61.248 66.667 0.00 0.00 36.88 4.26
381 422 3.723364 GATGCATGCACGTGACCGC 62.723 63.158 25.37 17.45 37.70 5.68
405 446 2.027561 CCCATTGACTGTTTCCGTCCTA 60.028 50.000 0.00 0.00 0.00 2.94
445 486 3.184581 CGAGCGTGGATTAAGATTAAGCC 59.815 47.826 11.76 11.76 46.58 4.35
483 529 4.935808 ACTGAACGAACCACCAGATAATTC 59.064 41.667 0.00 0.00 0.00 2.17
486 532 4.202274 TGAACTGAACGAACCACCAGATAA 60.202 41.667 0.00 0.00 0.00 1.75
488 534 2.104111 TGAACTGAACGAACCACCAGAT 59.896 45.455 0.00 0.00 0.00 2.90
490 536 1.867233 CTGAACTGAACGAACCACCAG 59.133 52.381 0.00 0.00 0.00 4.00
526 577 0.788391 CTCACGTTTGCTCCGTTACC 59.212 55.000 0.00 0.00 36.17 2.85
527 578 0.788391 CCTCACGTTTGCTCCGTTAC 59.212 55.000 0.00 0.00 36.17 2.50
528 579 0.320073 CCCTCACGTTTGCTCCGTTA 60.320 55.000 0.00 0.00 36.17 3.18
529 580 1.597027 CCCTCACGTTTGCTCCGTT 60.597 57.895 0.00 0.00 36.17 4.44
530 581 1.466025 TACCCTCACGTTTGCTCCGT 61.466 55.000 0.00 0.00 39.52 4.69
577 628 2.854777 CTCCATAGCGTCTTTCGAGTTG 59.145 50.000 0.00 0.00 42.86 3.16
581 632 1.063616 CGTCTCCATAGCGTCTTTCGA 59.936 52.381 0.00 0.00 42.86 3.71
582 633 1.202154 ACGTCTCCATAGCGTCTTTCG 60.202 52.381 0.00 0.00 43.12 3.46
584 635 1.134560 GGACGTCTCCATAGCGTCTTT 59.865 52.381 16.46 0.00 44.47 2.52
585 636 0.739561 GGACGTCTCCATAGCGTCTT 59.260 55.000 16.46 0.00 44.47 3.01
586 637 0.393944 TGGACGTCTCCATAGCGTCT 60.394 55.000 16.46 0.00 42.15 4.18
587 638 0.029567 CTGGACGTCTCCATAGCGTC 59.970 60.000 16.46 7.65 46.18 5.19
588 639 0.393944 TCTGGACGTCTCCATAGCGT 60.394 55.000 16.46 0.00 46.18 5.07
590 641 1.957177 TCATCTGGACGTCTCCATAGC 59.043 52.381 16.46 0.00 46.18 2.97
591 642 3.634568 GTCATCTGGACGTCTCCATAG 57.365 52.381 16.46 6.73 46.18 2.23
602 653 9.647918 AAGTAGATATTTAGAGTGTCATCTGGA 57.352 33.333 0.00 0.00 0.00 3.86
628 679 5.188434 CCAGTCAATCCAGAGCTAATGAAA 58.812 41.667 0.00 0.00 0.00 2.69
629 680 4.225942 ACCAGTCAATCCAGAGCTAATGAA 59.774 41.667 0.00 0.00 0.00 2.57
630 681 3.776969 ACCAGTCAATCCAGAGCTAATGA 59.223 43.478 0.00 0.00 0.00 2.57
631 682 4.125703 GACCAGTCAATCCAGAGCTAATG 58.874 47.826 0.00 0.00 0.00 1.90
632 683 3.776969 TGACCAGTCAATCCAGAGCTAAT 59.223 43.478 0.00 0.00 36.53 1.73
635 686 1.554160 CTGACCAGTCAATCCAGAGCT 59.446 52.381 1.58 0.00 39.39 4.09
636 687 1.552337 TCTGACCAGTCAATCCAGAGC 59.448 52.381 1.58 0.00 39.39 4.09
637 688 3.260380 ACTTCTGACCAGTCAATCCAGAG 59.740 47.826 1.58 0.00 39.39 3.35
659 729 3.276857 GCATCTTTGAAGCATCCAGAGA 58.723 45.455 0.00 0.00 0.00 3.10
698 768 6.469782 AAACGGCTGGAATGATTGAATATT 57.530 33.333 0.00 0.00 0.00 1.28
716 786 0.597377 GTGCTTGCTCCCAAAAACGG 60.597 55.000 0.00 0.00 0.00 4.44
730 800 0.107017 ACAAGAGTGCCACTGTGCTT 60.107 50.000 0.00 0.00 0.00 3.91
805 879 3.315470 GGCGGAATATTTTGACCTCTTCC 59.685 47.826 0.00 0.00 0.00 3.46
831 908 2.440501 CTCGCCACGCATGTTAATTTC 58.559 47.619 0.00 0.00 0.00 2.17
843 920 2.527547 GATTTTGGTGCCTCGCCACG 62.528 60.000 0.00 0.00 44.22 4.94
845 922 2.331893 CGATTTTGGTGCCTCGCCA 61.332 57.895 0.00 0.00 42.73 5.69
852 929 0.874390 TGCTCTGTCGATTTTGGTGC 59.126 50.000 0.00 0.00 0.00 5.01
854 931 2.146342 CTGTGCTCTGTCGATTTTGGT 58.854 47.619 0.00 0.00 0.00 3.67
857 934 1.072331 ACCCTGTGCTCTGTCGATTTT 59.928 47.619 0.00 0.00 0.00 1.82
858 935 0.687354 ACCCTGTGCTCTGTCGATTT 59.313 50.000 0.00 0.00 0.00 2.17
859 936 0.687354 AACCCTGTGCTCTGTCGATT 59.313 50.000 0.00 0.00 0.00 3.34
862 939 1.000955 ACTAAACCCTGTGCTCTGTCG 59.999 52.381 0.00 0.00 0.00 4.35
863 940 2.841442 ACTAAACCCTGTGCTCTGTC 57.159 50.000 0.00 0.00 0.00 3.51
867 944 0.796927 GCGAACTAAACCCTGTGCTC 59.203 55.000 0.00 0.00 0.00 4.26
873 950 7.370905 AGTATTTATAGGCGAACTAAACCCT 57.629 36.000 0.00 0.00 34.79 4.34
875 952 9.926751 GAAAAGTATTTATAGGCGAACTAAACC 57.073 33.333 0.00 0.00 37.28 3.27
878 955 9.101655 GGTGAAAAGTATTTATAGGCGAACTAA 57.898 33.333 0.00 0.00 37.28 2.24
880 957 6.257193 CGGTGAAAAGTATTTATAGGCGAACT 59.743 38.462 0.00 0.00 37.28 3.01
881 958 6.036408 ACGGTGAAAAGTATTTATAGGCGAAC 59.964 38.462 0.00 0.00 37.28 3.95
934 1014 0.887247 TGTGTGTGTTGTGCTTGCTT 59.113 45.000 0.00 0.00 0.00 3.91
936 1016 0.109365 TGTGTGTGTGTTGTGCTTGC 60.109 50.000 0.00 0.00 0.00 4.01
940 1020 0.801872 TGAGTGTGTGTGTGTTGTGC 59.198 50.000 0.00 0.00 0.00 4.57
957 1037 6.325028 TGTCCTTCTTCTTCTTCTTCTTCTGA 59.675 38.462 0.00 0.00 0.00 3.27
976 1071 0.106719 CCACCACCTGTGTTGTCCTT 60.107 55.000 0.00 0.00 43.85 3.36
979 1074 1.166531 GCTCCACCACCTGTGTTGTC 61.167 60.000 0.00 0.00 43.85 3.18
993 1088 2.993008 GAGTGCTCCATGGCTCCA 59.007 61.111 6.96 0.35 0.00 3.86
1045 1140 2.888863 CCTCTTCTCCTTCGCGCT 59.111 61.111 5.56 0.00 0.00 5.92
1050 1145 2.736826 CGGGGGCCTCTTCTCCTTC 61.737 68.421 0.52 0.00 0.00 3.46
1183 1278 1.066071 GGGAGAGGTTCAGTTGTAGGC 60.066 57.143 0.00 0.00 0.00 3.93
1201 1296 0.881118 CGATGTGGTTTGGACTTGGG 59.119 55.000 0.00 0.00 0.00 4.12
1220 1315 1.133407 CTAGAGCCTTGACTGACGACC 59.867 57.143 0.00 0.00 0.00 4.79
1242 1342 3.748298 GAAGCATTTCTTCTTGTACCGC 58.252 45.455 0.00 0.00 45.99 5.68
1336 1446 5.112129 ACTCAAAAACCCTAGTTGTGAGT 57.888 39.130 10.28 10.28 46.85 3.41
1339 1449 5.105917 ACAACACTCAAAAACCCTAGTTGTG 60.106 40.000 0.00 0.00 44.40 3.33
1341 1451 5.576447 ACAACACTCAAAAACCCTAGTTG 57.424 39.130 0.00 0.00 40.48 3.16
1342 1452 6.599356 AAACAACACTCAAAAACCCTAGTT 57.401 33.333 0.00 0.00 38.03 2.24
1432 1543 7.064134 CGTTGCATCTCTACTTTGTAATAACCA 59.936 37.037 0.00 0.00 0.00 3.67
1433 1544 7.399523 CGTTGCATCTCTACTTTGTAATAACC 58.600 38.462 0.00 0.00 0.00 2.85
1489 1621 3.211045 CGGGGAAACTTGTTCTTCTGAA 58.789 45.455 0.00 0.00 0.00 3.02
1491 1623 2.572290 ACGGGGAAACTTGTTCTTCTG 58.428 47.619 0.00 0.00 0.00 3.02
1492 1624 2.949644 CAACGGGGAAACTTGTTCTTCT 59.050 45.455 0.00 0.00 0.00 2.85
1496 1628 4.295870 GAAATCAACGGGGAAACTTGTTC 58.704 43.478 0.00 0.00 0.00 3.18
1520 1653 3.192422 TGCATATTGACGGTTTCCTTTGG 59.808 43.478 0.00 0.00 0.00 3.28
1522 1655 4.156008 GTCTGCATATTGACGGTTTCCTTT 59.844 41.667 0.00 0.00 0.00 3.11
1533 1666 4.274214 GCAAGCACTATGTCTGCATATTGA 59.726 41.667 8.48 0.00 39.28 2.57
1535 1668 3.567164 GGCAAGCACTATGTCTGCATATT 59.433 43.478 0.00 0.00 37.01 1.28
1539 1672 0.325933 AGGCAAGCACTATGTCTGCA 59.674 50.000 0.00 0.00 37.08 4.41
1563 1696 5.402270 GTGTTTTGCGTTTCATTATCTTGCT 59.598 36.000 0.00 0.00 0.00 3.91
1576 1709 4.334203 TGTATGAGAGTTGTGTTTTGCGTT 59.666 37.500 0.00 0.00 0.00 4.84
1587 1720 4.108336 CACGTGGAGATGTATGAGAGTTG 58.892 47.826 7.95 0.00 0.00 3.16
1588 1721 3.429547 GCACGTGGAGATGTATGAGAGTT 60.430 47.826 18.88 0.00 0.00 3.01
1589 1722 2.099921 GCACGTGGAGATGTATGAGAGT 59.900 50.000 18.88 0.00 0.00 3.24
1597 1730 1.270785 TGTTGATGCACGTGGAGATGT 60.271 47.619 18.88 0.00 0.00 3.06
1600 1733 2.183478 AATGTTGATGCACGTGGAGA 57.817 45.000 18.88 2.17 0.00 3.71
1601 1734 2.226200 TGAAATGTTGATGCACGTGGAG 59.774 45.455 18.88 0.00 0.00 3.86
1609 1757 9.970395 TCATAATCCTATTTGAAATGTTGATGC 57.030 29.630 0.00 0.00 0.00 3.91
1646 1801 1.143305 ATATGCAATCGACAGCGCTC 58.857 50.000 7.13 0.00 37.46 5.03
1654 1809 7.090808 GTGGAGTATCAGTTATATGCAATCGA 58.909 38.462 0.00 0.00 36.25 3.59
1666 1821 8.367660 TCTATTCTCTTTGTGGAGTATCAGTT 57.632 34.615 0.00 0.00 36.25 3.16
1727 1882 2.229675 AAGCGCAGATCATGAATCGA 57.770 45.000 11.47 0.00 39.55 3.59
1845 2000 6.099159 ACAAGAACAGTAGAGGTTTAGTCC 57.901 41.667 0.00 0.00 0.00 3.85
1846 2001 8.574737 TCTAACAAGAACAGTAGAGGTTTAGTC 58.425 37.037 0.00 0.00 0.00 2.59
1848 2003 9.760077 TTTCTAACAAGAACAGTAGAGGTTTAG 57.240 33.333 0.00 0.00 0.00 1.85
1932 2487 9.361315 CAAGATCAAAAGCATTATCAATGTTCA 57.639 29.630 0.00 0.00 41.01 3.18
1938 2493 6.927416 ACTGCAAGATCAAAAGCATTATCAA 58.073 32.000 0.00 0.00 37.43 2.57
2006 2561 2.037772 AGATGTGTGACTCCAAGACACC 59.962 50.000 7.01 1.00 39.53 4.16
2017 2572 4.270084 TCGTGACAAAGAAAGATGTGTGAC 59.730 41.667 0.00 0.00 0.00 3.67
2049 2604 5.048294 ACTGATATGCCATGACGTTCGTATA 60.048 40.000 0.00 0.00 0.00 1.47
2055 2610 4.517285 AGAAACTGATATGCCATGACGTT 58.483 39.130 0.00 0.00 0.00 3.99
2061 2616 2.033801 GCGCAAGAAACTGATATGCCAT 59.966 45.455 0.30 0.00 43.02 4.40
2076 2631 1.302033 AGGTTCACTCAGGCGCAAG 60.302 57.895 10.83 5.88 43.44 4.01
2130 2685 6.207417 ACACATTCTTGCTAGTAAACAATGCT 59.793 34.615 17.75 8.32 0.00 3.79
2151 2706 7.220740 TGTGTCAGTTCTATCCAAATTACACA 58.779 34.615 0.00 0.00 40.62 3.72
2152 2707 7.667043 TGTGTCAGTTCTATCCAAATTACAC 57.333 36.000 0.00 0.00 35.31 2.90
2153 2708 7.094805 GCTTGTGTCAGTTCTATCCAAATTACA 60.095 37.037 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.