Multiple sequence alignment - TraesCS7A01G310800

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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 TraesCS7A01G310800 chr7A 100.000 2381 0 0 1 2381 439729665 439732045 0.000000e+00 4397.0
1 TraesCS7A01G310800 chr7A 89.904 208 19 1 303 510 33147511 33147716 1.400000e-67 267.0
2 TraesCS7A01G310800 chr7A 87.671 73 6 2 1895 1964 30273079 30273151 5.450000e-12 82.4
3 TraesCS7A01G310800 chr7A 86.301 73 7 2 1895 1964 30242111 30242183 2.540000e-10 76.8
4 TraesCS7A01G310800 chr7A 97.143 35 0 1 1821 1854 30241791 30241825 9.190000e-05 58.4
5 TraesCS7A01G310800 chr7A 97.143 35 0 1 1821 1854 30272754 30272788 9.190000e-05 58.4
6 TraesCS7A01G310800 chr5D 95.656 1151 39 5 304 1445 296940149 296939001 0.000000e+00 1838.0
7 TraesCS7A01G310800 chr5D 97.660 940 13 2 1443 2381 296933865 296932934 0.000000e+00 1605.0
8 TraesCS7A01G310800 chr2D 86.314 738 68 17 749 1462 636741319 636742047 0.000000e+00 773.0
9 TraesCS7A01G310800 chr2D 86.314 738 68 17 749 1462 636887084 636886356 0.000000e+00 773.0
10 TraesCS7A01G310800 chr2D 75.078 963 164 45 755 1700 637345342 637344439 1.730000e-101 379.0
11 TraesCS7A01G310800 chr2D 77.318 604 93 30 755 1323 636946350 636945756 1.370000e-82 316.0
12 TraesCS7A01G310800 chr2D 91.071 224 20 0 83 306 49079182 49078959 1.070000e-78 303.0
13 TraesCS7A01G310800 chr2D 80.230 435 45 22 1283 1698 637355690 637355278 2.990000e-74 289.0
14 TraesCS7A01G310800 chr2D 75.051 489 81 28 749 1209 638330444 638330919 3.120000e-44 189.0
15 TraesCS7A01G310800 chr2D 82.400 125 18 3 1576 1699 636925901 636925780 3.240000e-19 106.0
16 TraesCS7A01G310800 chr2D 87.356 87 1 1 1890 1966 636939862 636939776 9.060000e-15 91.6
17 TraesCS7A01G310800 chr2D 100.000 46 0 0 1920 1965 638319793 638319838 4.220000e-13 86.1
18 TraesCS7A01G310800 chr2D 97.143 35 0 1 1821 1854 600579146 600579112 9.190000e-05 58.4
19 TraesCS7A01G310800 chr3D 92.619 420 25 5 298 714 576164188 576164604 1.220000e-167 599.0
20 TraesCS7A01G310800 chr3D 91.928 223 14 3 524 743 545170669 545170890 2.300000e-80 309.0
21 TraesCS7A01G310800 chr3D 90.338 207 18 1 304 510 310707531 310707327 1.080000e-68 270.0
22 TraesCS7A01G310800 chr2A 84.127 441 61 6 833 1266 762767814 762768252 3.660000e-113 418.0
23 TraesCS7A01G310800 chr2A 78.683 319 38 18 2000 2295 762847969 762847658 4.040000e-43 185.0
24 TraesCS7A01G310800 chr2A 79.279 222 23 11 1480 1700 762726588 762726787 1.480000e-27 134.0
25 TraesCS7A01G310800 chr2A 84.694 98 7 5 1782 1874 762726753 762726847 9.060000e-15 91.6
26 TraesCS7A01G310800 chr2A 100.000 44 0 0 1922 1965 763979777 763979734 5.450000e-12 82.4
27 TraesCS7A01G310800 chr5B 91.697 277 14 2 2094 2369 260781620 260781352 2.230000e-100 375.0
28 TraesCS7A01G310800 chr5B 92.308 195 14 1 304 498 6592220 6592413 2.330000e-70 276.0
29 TraesCS7A01G310800 chr2B 91.697 277 14 2 2094 2369 83118728 83118460 2.230000e-100 375.0
30 TraesCS7A01G310800 chr2B 91.336 277 15 2 2094 2369 219366823 219367091 1.040000e-98 370.0
31 TraesCS7A01G310800 chr2B 91.336 277 15 2 2094 2369 619036099 619035831 1.040000e-98 370.0
32 TraesCS7A01G310800 chr2B 90.614 277 17 2 2094 2369 650248425 650248693 2.250000e-95 359.0
33 TraesCS7A01G310800 chr2B 89.960 249 16 2 2094 2341 519566600 519566360 1.780000e-81 313.0
34 TraesCS7A01G310800 chr2B 80.075 266 32 12 989 1240 794767452 794767194 6.760000e-41 178.0
35 TraesCS7A01G310800 chr2B 81.768 181 27 4 1061 1241 797209833 797210007 1.910000e-31 147.0
36 TraesCS7A01G310800 chr2B 100.000 34 0 0 1821 1854 794675497 794675464 1.980000e-06 63.9
37 TraesCS7A01G310800 chr3B 91.336 277 15 2 2094 2369 304298502 304298770 1.040000e-98 370.0
38 TraesCS7A01G310800 chr3B 91.336 277 15 2 2094 2369 794681562 794681830 1.040000e-98 370.0
39 TraesCS7A01G310800 chr3B 90.614 277 16 3 2094 2369 125692155 125691888 2.250000e-95 359.0
40 TraesCS7A01G310800 chr3B 92.377 223 14 2 524 743 721054638 721054860 4.940000e-82 315.0
41 TraesCS7A01G310800 chr1B 91.221 262 14 2 2109 2369 638864101 638863848 4.870000e-92 348.0
42 TraesCS7A01G310800 chr6D 91.403 221 19 0 79 299 465334600 465334820 1.070000e-78 303.0
43 TraesCS7A01G310800 chr6D 92.537 201 14 1 303 503 201148756 201148955 1.080000e-73 287.0
44 TraesCS7A01G310800 chr6D 83.158 190 29 1 83 272 494098 494284 1.130000e-38 171.0
45 TraesCS7A01G310800 chr3A 91.480 223 15 3 524 743 681668860 681669081 1.070000e-78 303.0
46 TraesCS7A01G310800 chr1D 91.324 219 19 0 88 306 456775900 456775682 1.380000e-77 300.0
47 TraesCS7A01G310800 chr6B 90.865 208 18 1 303 510 99869104 99869310 6.480000e-71 278.0
48 TraesCS7A01G310800 chr6B 89.623 212 18 4 299 510 535372213 535372006 1.400000e-67 267.0
49 TraesCS7A01G310800 chr7D 91.045 201 17 1 304 504 207790364 207790165 1.080000e-68 270.0
50 TraesCS7A01G310800 chr7D 92.771 83 3 3 1 82 389185231 389185311 1.500000e-22 117.0
51 TraesCS7A01G310800 chr7D 87.671 73 6 2 1895 1964 29985948 29986020 5.450000e-12 82.4
52 TraesCS7A01G310800 chr4B 85.714 175 11 6 1886 2046 35913195 35913369 3.150000e-39 172.0
53 TraesCS7A01G310800 chrUn 91.525 59 4 1 1822 1879 234391164 234391222 1.960000e-11 80.5
54 TraesCS7A01G310800 chr4A 97.778 45 1 0 1920 1964 699188070 699188026 7.060000e-11 78.7
55 TraesCS7A01G310800 chr7B 100.000 34 0 0 1821 1854 746125018 746124985 1.980000e-06 63.9
56 TraesCS7A01G310800 chr7B 97.059 34 1 0 1821 1854 746126443 746126410 9.190000e-05 58.4


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 TraesCS7A01G310800 chr7A 439729665 439732045 2380 False 4397 4397 100.000 1 2381 1 chr7A.!!$F2 2380
1 TraesCS7A01G310800 chr5D 296939001 296940149 1148 True 1838 1838 95.656 304 1445 1 chr5D.!!$R2 1141
2 TraesCS7A01G310800 chr5D 296932934 296933865 931 True 1605 1605 97.660 1443 2381 1 chr5D.!!$R1 938
3 TraesCS7A01G310800 chr2D 636741319 636742047 728 False 773 773 86.314 749 1462 1 chr2D.!!$F1 713
4 TraesCS7A01G310800 chr2D 636886356 636887084 728 True 773 773 86.314 749 1462 1 chr2D.!!$R3 713
5 TraesCS7A01G310800 chr2D 637344439 637345342 903 True 379 379 75.078 755 1700 1 chr2D.!!$R7 945
6 TraesCS7A01G310800 chr2D 636945756 636946350 594 True 316 316 77.318 755 1323 1 chr2D.!!$R6 568

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
707 711 0.033228 CCAGAGCGATAGAAGCAGGG 59.967 60.0 0.0 0.0 37.01 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2242 0.249676 AGTCATGCTCTGCTGGAGTG 59.75 55.0 8.56 0.0 43.62 3.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.356882 TTTTTCTTAGGACAGCATTGACG 57.643 39.130 0.00 0.00 0.00 4.35
24 25 3.678056 TTCTTAGGACAGCATTGACGT 57.322 42.857 0.00 0.00 0.00 4.34
25 26 4.794278 TTCTTAGGACAGCATTGACGTA 57.206 40.909 0.00 0.00 0.00 3.57
26 27 4.371855 TCTTAGGACAGCATTGACGTAG 57.628 45.455 0.00 0.00 0.00 3.51
27 28 2.579207 TAGGACAGCATTGACGTAGC 57.421 50.000 0.00 0.00 0.00 3.58
28 29 0.108138 AGGACAGCATTGACGTAGCC 60.108 55.000 0.00 0.00 0.00 3.93
29 30 0.108138 GGACAGCATTGACGTAGCCT 60.108 55.000 0.00 0.00 0.00 4.58
30 31 1.281899 GACAGCATTGACGTAGCCTC 58.718 55.000 0.00 0.00 0.00 4.70
31 32 0.608130 ACAGCATTGACGTAGCCTCA 59.392 50.000 0.00 0.00 0.00 3.86
32 33 1.001974 ACAGCATTGACGTAGCCTCAA 59.998 47.619 0.00 0.00 32.24 3.02
33 34 2.076100 CAGCATTGACGTAGCCTCAAA 58.924 47.619 0.00 0.00 31.48 2.69
34 35 2.483877 CAGCATTGACGTAGCCTCAAAA 59.516 45.455 0.00 0.00 31.48 2.44
35 36 3.058293 CAGCATTGACGTAGCCTCAAAAA 60.058 43.478 0.00 0.00 31.48 1.94
36 37 3.758554 AGCATTGACGTAGCCTCAAAAAT 59.241 39.130 0.00 0.00 31.48 1.82
37 38 4.941263 AGCATTGACGTAGCCTCAAAAATA 59.059 37.500 0.00 0.00 31.48 1.40
38 39 5.414454 AGCATTGACGTAGCCTCAAAAATAA 59.586 36.000 0.00 0.00 31.48 1.40
39 40 5.739161 GCATTGACGTAGCCTCAAAAATAAG 59.261 40.000 0.00 0.00 31.48 1.73
40 41 6.403200 GCATTGACGTAGCCTCAAAAATAAGA 60.403 38.462 0.00 0.00 31.48 2.10
41 42 7.526608 CATTGACGTAGCCTCAAAAATAAGAA 58.473 34.615 0.00 0.00 31.48 2.52
42 43 7.499321 TTGACGTAGCCTCAAAAATAAGAAA 57.501 32.000 0.00 0.00 0.00 2.52
43 44 7.129109 TGACGTAGCCTCAAAAATAAGAAAG 57.871 36.000 0.00 0.00 0.00 2.62
44 45 6.932400 TGACGTAGCCTCAAAAATAAGAAAGA 59.068 34.615 0.00 0.00 0.00 2.52
45 46 7.442969 TGACGTAGCCTCAAAAATAAGAAAGAA 59.557 33.333 0.00 0.00 0.00 2.52
46 47 8.161699 ACGTAGCCTCAAAAATAAGAAAGAAA 57.838 30.769 0.00 0.00 0.00 2.52
47 48 8.290325 ACGTAGCCTCAAAAATAAGAAAGAAAG 58.710 33.333 0.00 0.00 0.00 2.62
48 49 8.504005 CGTAGCCTCAAAAATAAGAAAGAAAGA 58.496 33.333 0.00 0.00 0.00 2.52
63 64 7.664758 AGAAAGAAAGAAAATCACCATTGAGG 58.335 34.615 0.00 0.00 45.67 3.86
72 73 2.765969 CCATTGAGGTGGGTGGCT 59.234 61.111 0.00 0.00 35.55 4.75
73 74 1.379044 CCATTGAGGTGGGTGGCTC 60.379 63.158 0.00 0.00 35.55 4.70
74 75 1.379044 CATTGAGGTGGGTGGCTCC 60.379 63.158 0.00 0.00 0.00 4.70
75 76 2.971598 ATTGAGGTGGGTGGCTCCG 61.972 63.158 0.00 0.00 37.00 4.63
76 77 4.954118 TGAGGTGGGTGGCTCCGT 62.954 66.667 0.00 0.00 37.00 4.69
77 78 2.682494 GAGGTGGGTGGCTCCGTA 60.682 66.667 0.00 0.00 37.00 4.02
78 79 3.001406 AGGTGGGTGGCTCCGTAC 61.001 66.667 0.00 1.63 37.00 3.67
79 80 3.315949 GGTGGGTGGCTCCGTACA 61.316 66.667 11.86 0.00 37.00 2.90
80 81 2.745037 GTGGGTGGCTCCGTACAA 59.255 61.111 0.00 0.00 37.00 2.41
81 82 1.298667 GTGGGTGGCTCCGTACAAT 59.701 57.895 0.00 0.00 37.00 2.71
82 83 0.743345 GTGGGTGGCTCCGTACAATC 60.743 60.000 0.00 0.00 37.00 2.67
83 84 1.195442 TGGGTGGCTCCGTACAATCA 61.195 55.000 0.00 0.00 37.00 2.57
84 85 0.462047 GGGTGGCTCCGTACAATCAG 60.462 60.000 0.00 0.00 37.00 2.90
85 86 0.462047 GGTGGCTCCGTACAATCAGG 60.462 60.000 0.00 0.00 0.00 3.86
86 87 0.535335 GTGGCTCCGTACAATCAGGA 59.465 55.000 0.00 0.00 0.00 3.86
87 88 1.066430 GTGGCTCCGTACAATCAGGAA 60.066 52.381 0.00 0.00 33.10 3.36
88 89 1.066430 TGGCTCCGTACAATCAGGAAC 60.066 52.381 0.00 0.00 33.10 3.62
89 90 1.278238 GCTCCGTACAATCAGGAACG 58.722 55.000 0.00 0.00 33.10 3.95
93 94 1.278238 CGTACAATCAGGAACGGAGC 58.722 55.000 0.00 0.00 35.10 4.70
94 95 1.135083 CGTACAATCAGGAACGGAGCT 60.135 52.381 0.00 0.00 35.10 4.09
95 96 2.541556 GTACAATCAGGAACGGAGCTC 58.458 52.381 4.71 4.71 35.10 4.09
96 97 0.976641 ACAATCAGGAACGGAGCTCA 59.023 50.000 17.19 0.00 35.10 4.26
97 98 1.338200 ACAATCAGGAACGGAGCTCAC 60.338 52.381 17.19 4.01 35.10 3.51
98 99 0.108615 AATCAGGAACGGAGCTCACG 60.109 55.000 17.19 18.28 35.10 4.35
100 101 0.607217 TCAGGAACGGAGCTCACGTA 60.607 55.000 24.16 10.55 44.83 3.57
101 102 0.456312 CAGGAACGGAGCTCACGTAC 60.456 60.000 24.16 20.14 44.83 3.67
102 103 0.892358 AGGAACGGAGCTCACGTACA 60.892 55.000 24.16 0.00 44.83 2.90
103 104 0.038892 GGAACGGAGCTCACGTACAA 60.039 55.000 24.16 0.00 44.83 2.41
104 105 1.058404 GAACGGAGCTCACGTACAAC 58.942 55.000 24.16 14.87 44.83 3.32
105 106 0.319297 AACGGAGCTCACGTACAACC 60.319 55.000 24.16 1.86 44.83 3.77
106 107 1.287815 CGGAGCTCACGTACAACCA 59.712 57.895 17.19 0.00 0.00 3.67
107 108 1.007336 CGGAGCTCACGTACAACCAC 61.007 60.000 17.19 0.00 0.00 4.16
108 109 0.317479 GGAGCTCACGTACAACCACT 59.683 55.000 17.19 0.00 0.00 4.00
109 110 1.419374 GAGCTCACGTACAACCACTG 58.581 55.000 9.40 0.00 0.00 3.66
110 111 0.033504 AGCTCACGTACAACCACTGG 59.966 55.000 0.00 0.00 0.00 4.00
111 112 0.249741 GCTCACGTACAACCACTGGT 60.250 55.000 0.00 0.00 37.65 4.00
112 113 1.497991 CTCACGTACAACCACTGGTG 58.502 55.000 0.00 0.00 35.34 4.17
113 114 0.825410 TCACGTACAACCACTGGTGT 59.175 50.000 0.00 5.14 35.34 4.16
114 115 1.202440 TCACGTACAACCACTGGTGTC 60.202 52.381 0.00 0.00 35.34 3.67
115 116 0.825410 ACGTACAACCACTGGTGTCA 59.175 50.000 0.00 0.00 35.34 3.58
116 117 1.202486 ACGTACAACCACTGGTGTCAG 60.202 52.381 0.00 3.46 46.10 3.51
131 132 1.871080 GTCAGTTGACACCAGTGGAG 58.129 55.000 18.40 11.28 44.18 3.86
132 133 1.139058 GTCAGTTGACACCAGTGGAGT 59.861 52.381 18.40 15.28 44.18 3.85
133 134 1.837439 TCAGTTGACACCAGTGGAGTT 59.163 47.619 18.40 0.00 34.19 3.01
134 135 2.158957 TCAGTTGACACCAGTGGAGTTC 60.159 50.000 18.40 9.22 34.19 3.01
135 136 1.837439 AGTTGACACCAGTGGAGTTCA 59.163 47.619 18.40 11.82 34.19 3.18
136 137 2.158900 AGTTGACACCAGTGGAGTTCAG 60.159 50.000 18.40 0.68 34.19 3.02
137 138 0.106708 TGACACCAGTGGAGTTCAGC 59.893 55.000 18.40 2.52 34.19 4.26
138 139 0.946221 GACACCAGTGGAGTTCAGCG 60.946 60.000 18.40 0.00 34.19 5.18
139 140 1.069765 CACCAGTGGAGTTCAGCGT 59.930 57.895 18.40 0.00 0.00 5.07
140 141 0.532862 CACCAGTGGAGTTCAGCGTT 60.533 55.000 18.40 0.00 0.00 4.84
141 142 0.180406 ACCAGTGGAGTTCAGCGTTT 59.820 50.000 18.40 0.00 0.00 3.60
142 143 0.868406 CCAGTGGAGTTCAGCGTTTC 59.132 55.000 1.68 0.00 0.00 2.78
143 144 1.581934 CAGTGGAGTTCAGCGTTTCA 58.418 50.000 0.00 0.00 0.00 2.69
144 145 1.939934 CAGTGGAGTTCAGCGTTTCAA 59.060 47.619 0.00 0.00 0.00 2.69
145 146 2.549754 CAGTGGAGTTCAGCGTTTCAAT 59.450 45.455 0.00 0.00 0.00 2.57
146 147 3.003689 CAGTGGAGTTCAGCGTTTCAATT 59.996 43.478 0.00 0.00 0.00 2.32
147 148 4.213270 CAGTGGAGTTCAGCGTTTCAATTA 59.787 41.667 0.00 0.00 0.00 1.40
148 149 4.452455 AGTGGAGTTCAGCGTTTCAATTAG 59.548 41.667 0.00 0.00 0.00 1.73
149 150 3.188460 TGGAGTTCAGCGTTTCAATTAGC 59.812 43.478 0.00 0.00 0.00 3.09
150 151 3.188460 GGAGTTCAGCGTTTCAATTAGCA 59.812 43.478 0.00 0.00 0.00 3.49
151 152 4.142600 GGAGTTCAGCGTTTCAATTAGCAT 60.143 41.667 0.00 0.00 0.00 3.79
152 153 4.726416 AGTTCAGCGTTTCAATTAGCATG 58.274 39.130 0.00 0.00 0.00 4.06
153 154 3.135414 TCAGCGTTTCAATTAGCATGC 57.865 42.857 10.51 10.51 0.00 4.06
154 155 2.749076 TCAGCGTTTCAATTAGCATGCT 59.251 40.909 25.99 25.99 0.00 3.79
155 156 3.191162 TCAGCGTTTCAATTAGCATGCTT 59.809 39.130 28.02 5.63 0.00 3.91
156 157 4.394610 TCAGCGTTTCAATTAGCATGCTTA 59.605 37.500 28.02 18.49 0.00 3.09
157 158 5.094812 CAGCGTTTCAATTAGCATGCTTAA 58.905 37.500 28.02 17.49 0.00 1.85
158 159 5.745294 CAGCGTTTCAATTAGCATGCTTAAT 59.255 36.000 28.02 18.88 0.00 1.40
159 160 6.912051 CAGCGTTTCAATTAGCATGCTTAATA 59.088 34.615 28.02 4.26 0.00 0.98
160 161 7.431960 CAGCGTTTCAATTAGCATGCTTAATAA 59.568 33.333 28.02 14.63 0.00 1.40
161 162 7.973388 AGCGTTTCAATTAGCATGCTTAATAAA 59.027 29.630 28.02 14.21 0.00 1.40
162 163 8.755018 GCGTTTCAATTAGCATGCTTAATAAAT 58.245 29.630 28.02 16.00 0.00 1.40
173 174 9.709495 AGCATGCTTAATAAATTTTGTCTTTGA 57.291 25.926 16.30 0.00 0.00 2.69
174 175 9.745323 GCATGCTTAATAAATTTTGTCTTTGAC 57.255 29.630 11.37 0.00 0.00 3.18
175 176 9.941991 CATGCTTAATAAATTTTGTCTTTGACG 57.058 29.630 0.00 0.00 34.95 4.35
176 177 8.002433 TGCTTAATAAATTTTGTCTTTGACGC 57.998 30.769 0.00 0.00 34.95 5.19
177 178 7.115663 TGCTTAATAAATTTTGTCTTTGACGCC 59.884 33.333 0.00 0.00 34.95 5.68
178 179 7.115663 GCTTAATAAATTTTGTCTTTGACGCCA 59.884 33.333 0.00 0.00 34.95 5.69
179 180 8.514136 TTAATAAATTTTGTCTTTGACGCCAG 57.486 30.769 0.00 0.00 34.95 4.85
180 181 2.422276 ATTTTGTCTTTGACGCCAGC 57.578 45.000 0.00 0.00 34.95 4.85
181 182 0.383949 TTTTGTCTTTGACGCCAGCC 59.616 50.000 0.00 0.00 34.95 4.85
182 183 0.749818 TTTGTCTTTGACGCCAGCCA 60.750 50.000 0.00 0.00 34.95 4.75
183 184 1.165907 TTGTCTTTGACGCCAGCCAG 61.166 55.000 0.00 0.00 34.95 4.85
184 185 1.301716 GTCTTTGACGCCAGCCAGA 60.302 57.895 0.00 0.00 0.00 3.86
185 186 0.884704 GTCTTTGACGCCAGCCAGAA 60.885 55.000 0.00 0.00 0.00 3.02
186 187 0.179032 TCTTTGACGCCAGCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
187 188 0.239347 CTTTGACGCCAGCCAGAAAG 59.761 55.000 0.00 0.00 0.00 2.62
188 189 0.179032 TTTGACGCCAGCCAGAAAGA 60.179 50.000 0.00 0.00 0.00 2.52
189 190 0.036732 TTGACGCCAGCCAGAAAGAT 59.963 50.000 0.00 0.00 0.00 2.40
190 191 0.391661 TGACGCCAGCCAGAAAGATC 60.392 55.000 0.00 0.00 0.00 2.75
191 192 1.424493 GACGCCAGCCAGAAAGATCG 61.424 60.000 0.00 0.00 0.00 3.69
192 193 1.153568 CGCCAGCCAGAAAGATCGA 60.154 57.895 0.00 0.00 0.00 3.59
193 194 0.531532 CGCCAGCCAGAAAGATCGAT 60.532 55.000 0.00 0.00 0.00 3.59
194 195 1.673168 GCCAGCCAGAAAGATCGATT 58.327 50.000 0.00 0.00 0.00 3.34
195 196 1.332997 GCCAGCCAGAAAGATCGATTG 59.667 52.381 0.00 0.00 0.00 2.67
196 197 2.910199 CCAGCCAGAAAGATCGATTGA 58.090 47.619 0.00 0.00 0.00 2.57
197 198 2.611292 CCAGCCAGAAAGATCGATTGAC 59.389 50.000 0.00 0.00 0.00 3.18
198 199 3.264947 CAGCCAGAAAGATCGATTGACA 58.735 45.455 0.00 0.00 0.00 3.58
199 200 3.063180 CAGCCAGAAAGATCGATTGACAC 59.937 47.826 0.00 0.00 0.00 3.67
200 201 2.352960 GCCAGAAAGATCGATTGACACC 59.647 50.000 0.00 0.00 0.00 4.16
201 202 3.599343 CCAGAAAGATCGATTGACACCA 58.401 45.455 0.00 0.00 0.00 4.17
202 203 4.002982 CCAGAAAGATCGATTGACACCAA 58.997 43.478 0.00 0.00 36.61 3.67
203 204 4.142816 CCAGAAAGATCGATTGACACCAAC 60.143 45.833 0.00 0.00 34.72 3.77
204 205 4.003648 AGAAAGATCGATTGACACCAACC 58.996 43.478 0.00 0.00 34.72 3.77
205 206 2.403252 AGATCGATTGACACCAACCC 57.597 50.000 0.00 0.00 34.72 4.11
206 207 1.006832 GATCGATTGACACCAACCCG 58.993 55.000 0.00 0.00 34.72 5.28
207 208 0.392461 ATCGATTGACACCAACCCGG 60.392 55.000 0.00 0.00 42.50 5.73
208 209 2.686816 CGATTGACACCAACCCGGC 61.687 63.158 0.00 0.00 39.03 6.13
209 210 2.282887 ATTGACACCAACCCGGCC 60.283 61.111 0.00 0.00 39.03 6.13
210 211 4.939368 TTGACACCAACCCGGCCG 62.939 66.667 21.04 21.04 39.03 6.13
230 231 3.758172 GGAAAGCCGCTCCACAAA 58.242 55.556 0.00 0.00 32.77 2.83
231 232 1.285950 GGAAAGCCGCTCCACAAAC 59.714 57.895 0.00 0.00 32.77 2.93
232 233 1.285950 GAAAGCCGCTCCACAAACC 59.714 57.895 0.00 0.00 0.00 3.27
233 234 2.142357 GAAAGCCGCTCCACAAACCC 62.142 60.000 0.00 0.00 0.00 4.11
234 235 2.920076 AAAGCCGCTCCACAAACCCA 62.920 55.000 0.00 0.00 0.00 4.51
235 236 2.909965 GCCGCTCCACAAACCCAA 60.910 61.111 0.00 0.00 0.00 4.12
236 237 2.494530 GCCGCTCCACAAACCCAAA 61.495 57.895 0.00 0.00 0.00 3.28
237 238 2.022240 GCCGCTCCACAAACCCAAAA 62.022 55.000 0.00 0.00 0.00 2.44
238 239 0.678950 CCGCTCCACAAACCCAAAAT 59.321 50.000 0.00 0.00 0.00 1.82
239 240 1.605202 CCGCTCCACAAACCCAAAATG 60.605 52.381 0.00 0.00 0.00 2.32
240 241 1.511850 GCTCCACAAACCCAAAATGC 58.488 50.000 0.00 0.00 0.00 3.56
241 242 1.877680 GCTCCACAAACCCAAAATGCC 60.878 52.381 0.00 0.00 0.00 4.40
242 243 1.415659 CTCCACAAACCCAAAATGCCA 59.584 47.619 0.00 0.00 0.00 4.92
243 244 1.415659 TCCACAAACCCAAAATGCCAG 59.584 47.619 0.00 0.00 0.00 4.85
244 245 1.228533 CACAAACCCAAAATGCCAGC 58.771 50.000 0.00 0.00 0.00 4.85
245 246 0.108396 ACAAACCCAAAATGCCAGCC 59.892 50.000 0.00 0.00 0.00 4.85
246 247 0.606130 CAAACCCAAAATGCCAGCCC 60.606 55.000 0.00 0.00 0.00 5.19
247 248 1.059006 AAACCCAAAATGCCAGCCCA 61.059 50.000 0.00 0.00 0.00 5.36
248 249 1.059006 AACCCAAAATGCCAGCCCAA 61.059 50.000 0.00 0.00 0.00 4.12
249 250 0.841594 ACCCAAAATGCCAGCCCAAT 60.842 50.000 0.00 0.00 0.00 3.16
250 251 0.328926 CCCAAAATGCCAGCCCAATT 59.671 50.000 0.00 0.00 0.00 2.32
251 252 1.558756 CCCAAAATGCCAGCCCAATTA 59.441 47.619 0.00 0.00 0.00 1.40
252 253 2.631267 CCAAAATGCCAGCCCAATTAC 58.369 47.619 0.00 0.00 0.00 1.89
253 254 2.027377 CCAAAATGCCAGCCCAATTACA 60.027 45.455 0.00 0.00 0.00 2.41
254 255 3.264104 CAAAATGCCAGCCCAATTACAG 58.736 45.455 0.00 0.00 0.00 2.74
255 256 2.236489 AATGCCAGCCCAATTACAGT 57.764 45.000 0.00 0.00 0.00 3.55
256 257 1.767759 ATGCCAGCCCAATTACAGTC 58.232 50.000 0.00 0.00 0.00 3.51
257 258 0.676466 TGCCAGCCCAATTACAGTCG 60.676 55.000 0.00 0.00 0.00 4.18
258 259 0.676782 GCCAGCCCAATTACAGTCGT 60.677 55.000 0.00 0.00 0.00 4.34
259 260 1.086696 CCAGCCCAATTACAGTCGTG 58.913 55.000 0.00 0.00 0.00 4.35
260 261 0.447801 CAGCCCAATTACAGTCGTGC 59.552 55.000 0.00 0.00 0.00 5.34
261 262 0.036164 AGCCCAATTACAGTCGTGCA 59.964 50.000 0.00 0.00 0.00 4.57
262 263 0.878416 GCCCAATTACAGTCGTGCAA 59.122 50.000 0.00 0.00 0.00 4.08
263 264 1.268352 GCCCAATTACAGTCGTGCAAA 59.732 47.619 0.00 0.00 0.00 3.68
264 265 2.920647 GCCCAATTACAGTCGTGCAAAC 60.921 50.000 0.00 0.00 0.00 2.93
265 266 2.292016 CCCAATTACAGTCGTGCAAACA 59.708 45.455 0.00 0.00 0.00 2.83
266 267 3.243234 CCCAATTACAGTCGTGCAAACAA 60.243 43.478 0.00 0.00 0.00 2.83
267 268 4.355437 CCAATTACAGTCGTGCAAACAAA 58.645 39.130 0.00 0.00 0.00 2.83
268 269 4.800993 CCAATTACAGTCGTGCAAACAAAA 59.199 37.500 0.00 0.00 0.00 2.44
269 270 5.289675 CCAATTACAGTCGTGCAAACAAAAA 59.710 36.000 0.00 0.00 0.00 1.94
270 271 6.402017 CAATTACAGTCGTGCAAACAAAAAG 58.598 36.000 0.00 0.00 0.00 2.27
271 272 2.874849 ACAGTCGTGCAAACAAAAAGG 58.125 42.857 0.00 0.00 0.00 3.11
272 273 1.587946 CAGTCGTGCAAACAAAAAGGC 59.412 47.619 0.00 0.00 0.00 4.35
273 274 1.476488 AGTCGTGCAAACAAAAAGGCT 59.524 42.857 0.00 0.00 0.00 4.58
274 275 1.587946 GTCGTGCAAACAAAAAGGCTG 59.412 47.619 0.00 0.00 0.00 4.85
275 276 1.474478 TCGTGCAAACAAAAAGGCTGA 59.526 42.857 0.00 0.00 0.00 4.26
276 277 1.587946 CGTGCAAACAAAAAGGCTGAC 59.412 47.619 0.00 0.00 0.00 3.51
277 278 1.587946 GTGCAAACAAAAAGGCTGACG 59.412 47.619 0.00 0.00 0.00 4.35
278 279 1.208259 GCAAACAAAAAGGCTGACGG 58.792 50.000 0.00 0.00 0.00 4.79
279 280 1.851658 CAAACAAAAAGGCTGACGGG 58.148 50.000 0.00 0.00 0.00 5.28
280 281 1.407258 CAAACAAAAAGGCTGACGGGA 59.593 47.619 0.00 0.00 0.00 5.14
281 282 1.770294 AACAAAAAGGCTGACGGGAA 58.230 45.000 0.00 0.00 0.00 3.97
282 283 1.318576 ACAAAAAGGCTGACGGGAAG 58.681 50.000 0.00 0.00 0.00 3.46
283 284 0.039165 CAAAAAGGCTGACGGGAAGC 60.039 55.000 0.00 0.00 40.06 3.86
295 296 3.284449 GGAAGCCCGCAACACGTT 61.284 61.111 0.00 0.00 41.42 3.99
296 297 1.962306 GGAAGCCCGCAACACGTTA 60.962 57.895 0.00 0.00 41.42 3.18
297 298 1.508808 GGAAGCCCGCAACACGTTAA 61.509 55.000 0.00 0.00 41.42 2.01
298 299 0.519961 GAAGCCCGCAACACGTTAAT 59.480 50.000 0.00 0.00 41.42 1.40
299 300 1.733360 GAAGCCCGCAACACGTTAATA 59.267 47.619 0.00 0.00 41.42 0.98
300 301 2.032680 AGCCCGCAACACGTTAATAT 57.967 45.000 0.00 0.00 41.42 1.28
301 302 1.668751 AGCCCGCAACACGTTAATATG 59.331 47.619 0.00 0.00 41.42 1.78
302 303 1.666700 GCCCGCAACACGTTAATATGA 59.333 47.619 0.00 0.00 41.42 2.15
306 307 3.863424 CCGCAACACGTTAATATGAGAGT 59.137 43.478 0.00 0.00 41.42 3.24
314 315 9.811995 AACACGTTAATATGAGAGTTAATAGCA 57.188 29.630 0.00 0.00 0.00 3.49
318 319 9.088512 CGTTAATATGAGAGTTAATAGCATCCC 57.911 37.037 0.00 0.00 0.00 3.85
326 327 3.651423 AGTTAATAGCATCCCAGGTACCC 59.349 47.826 8.74 0.00 0.00 3.69
336 337 1.564348 CCCAGGTACCCTAACTTGCAT 59.436 52.381 8.74 0.00 29.64 3.96
355 356 7.338703 ACTTGCATAGAATGTGATGATTCAGTT 59.661 33.333 0.00 0.00 35.16 3.16
356 357 7.634671 TGCATAGAATGTGATGATTCAGTTT 57.365 32.000 0.00 0.00 35.16 2.66
365 366 5.978919 TGTGATGATTCAGTTTCAAACTTGC 59.021 36.000 0.00 0.00 40.46 4.01
370 371 7.846644 TGATTCAGTTTCAAACTTGCAAAAT 57.153 28.000 0.00 0.00 40.46 1.82
380 381 5.580297 TCAAACTTGCAAAATTTGACTCCAC 59.420 36.000 24.41 0.00 37.41 4.02
420 421 6.950842 ACCTCATGTGATGATTTAGTCTCAA 58.049 36.000 0.00 0.00 38.85 3.02
421 422 7.046652 ACCTCATGTGATGATTTAGTCTCAAG 58.953 38.462 0.00 0.00 38.85 3.02
431 432 6.003326 TGATTTAGTCTCAAGCCAATCACAA 58.997 36.000 0.00 0.00 0.00 3.33
448 449 0.877071 CAACTCGACAATTGGCAGCT 59.123 50.000 12.81 0.00 0.00 4.24
453 454 1.003118 TCGACAATTGGCAGCTAGGTT 59.997 47.619 12.81 0.00 0.00 3.50
686 687 3.125658 ACCAAACCGCGATAAATGTGTAC 59.874 43.478 8.23 0.00 0.00 2.90
687 688 3.372822 CCAAACCGCGATAAATGTGTACT 59.627 43.478 8.23 0.00 0.00 2.73
707 711 0.033228 CCAGAGCGATAGAAGCAGGG 59.967 60.000 0.00 0.00 37.01 4.45
735 739 4.285020 TGCCATTGCCTTCCATATTGTTA 58.715 39.130 0.00 0.00 36.33 2.41
816 820 4.373116 GCTGCGTCCGGGAAGTGA 62.373 66.667 11.61 0.00 0.00 3.41
912 917 0.394565 GCGAAGTAGAGGCATGGGAT 59.605 55.000 0.00 0.00 0.00 3.85
958 963 1.202639 TGTTCGCAAGTGTGGTGATCT 60.203 47.619 0.00 0.00 39.48 2.75
1085 1127 4.394712 GGTGCAGGTCCTCGGTGG 62.395 72.222 0.00 0.00 37.10 4.61
1129 1171 2.146954 GACGACATCGGCGAAACAA 58.853 52.632 15.93 0.00 44.95 2.83
1281 1335 5.806654 ATGGCATTAATTGGGGTATTCAC 57.193 39.130 0.00 0.00 0.00 3.18
1471 1538 8.139989 GCAACAGGCTTATGAATCTGAATTAAT 58.860 33.333 0.64 0.00 40.25 1.40
1687 1754 7.895975 TGATGATTGCAGCTCATATTAGTAC 57.104 36.000 12.34 0.00 33.56 2.73
1966 2033 5.426504 TGATTGTTTCAAACTGCAACCAAT 58.573 33.333 1.10 0.00 0.00 3.16
1986 2053 3.836365 TTCTGGAATATGATCACGGCA 57.164 42.857 0.00 0.00 0.00 5.69
1993 2060 2.330440 TATGATCACGGCACTGCATT 57.670 45.000 0.00 0.00 0.00 3.56
2125 2192 7.822161 TGAGAGGAATCAAATTGTCTTTTCA 57.178 32.000 0.00 0.00 0.00 2.69
2172 2240 4.478206 CATCCTCTGCTTTCTCTTACCA 57.522 45.455 0.00 0.00 0.00 3.25
2173 2241 4.440880 CATCCTCTGCTTTCTCTTACCAG 58.559 47.826 0.00 0.00 0.00 4.00
2174 2242 2.234908 TCCTCTGCTTTCTCTTACCAGC 59.765 50.000 0.00 0.00 0.00 4.85
2175 2243 2.027745 CCTCTGCTTTCTCTTACCAGCA 60.028 50.000 0.00 0.00 39.98 4.41
2176 2244 2.999355 CTCTGCTTTCTCTTACCAGCAC 59.001 50.000 0.00 0.00 37.35 4.40
2177 2245 2.634940 TCTGCTTTCTCTTACCAGCACT 59.365 45.455 0.00 0.00 37.35 4.40
2210 2278 5.388111 CATGACTGTTACTGCATGTTTCTG 58.612 41.667 13.73 0.00 34.82 3.02
2250 2318 8.262227 TGAAGTTTCAGTAACAACTAAGGAGAA 58.738 33.333 0.00 0.00 39.30 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.819630 ACGTCAATGCTGTCCTAAGAAAAA 59.180 37.500 0.00 0.00 0.00 1.94
2 3 4.385825 ACGTCAATGCTGTCCTAAGAAAA 58.614 39.130 0.00 0.00 0.00 2.29
3 4 4.002906 ACGTCAATGCTGTCCTAAGAAA 57.997 40.909 0.00 0.00 0.00 2.52
4 5 3.678056 ACGTCAATGCTGTCCTAAGAA 57.322 42.857 0.00 0.00 0.00 2.52
5 6 3.428999 GCTACGTCAATGCTGTCCTAAGA 60.429 47.826 0.00 0.00 0.00 2.10
6 7 2.860735 GCTACGTCAATGCTGTCCTAAG 59.139 50.000 0.00 0.00 0.00 2.18
7 8 2.418197 GGCTACGTCAATGCTGTCCTAA 60.418 50.000 0.00 0.00 0.00 2.69
8 9 1.136305 GGCTACGTCAATGCTGTCCTA 59.864 52.381 0.00 0.00 0.00 2.94
9 10 0.108138 GGCTACGTCAATGCTGTCCT 60.108 55.000 0.00 0.00 0.00 3.85
10 11 0.108138 AGGCTACGTCAATGCTGTCC 60.108 55.000 0.00 0.00 0.00 4.02
11 12 1.281899 GAGGCTACGTCAATGCTGTC 58.718 55.000 0.00 0.00 0.00 3.51
12 13 0.608130 TGAGGCTACGTCAATGCTGT 59.392 50.000 0.00 0.00 0.00 4.40
13 14 1.725641 TTGAGGCTACGTCAATGCTG 58.274 50.000 0.00 0.00 34.10 4.41
14 15 2.472695 TTTGAGGCTACGTCAATGCT 57.527 45.000 0.00 0.00 37.92 3.79
15 16 3.552604 TTTTTGAGGCTACGTCAATGC 57.447 42.857 0.00 0.00 37.92 3.56
16 17 7.072177 TCTTATTTTTGAGGCTACGTCAATG 57.928 36.000 0.00 0.00 37.92 2.82
17 18 7.681939 TTCTTATTTTTGAGGCTACGTCAAT 57.318 32.000 0.00 0.00 37.92 2.57
18 19 7.442969 TCTTTCTTATTTTTGAGGCTACGTCAA 59.557 33.333 0.00 0.00 36.64 3.18
19 20 6.932400 TCTTTCTTATTTTTGAGGCTACGTCA 59.068 34.615 0.00 0.00 0.00 4.35
20 21 7.360575 TCTTTCTTATTTTTGAGGCTACGTC 57.639 36.000 0.00 0.00 0.00 4.34
21 22 7.739498 TTCTTTCTTATTTTTGAGGCTACGT 57.261 32.000 0.00 0.00 0.00 3.57
22 23 8.504005 TCTTTCTTTCTTATTTTTGAGGCTACG 58.496 33.333 0.00 0.00 0.00 3.51
37 38 8.146412 CCTCAATGGTGATTTTCTTTCTTTCTT 58.854 33.333 0.00 0.00 31.85 2.52
38 39 7.664758 CCTCAATGGTGATTTTCTTTCTTTCT 58.335 34.615 0.00 0.00 31.85 2.52
39 40 7.880059 CCTCAATGGTGATTTTCTTTCTTTC 57.120 36.000 0.00 0.00 31.85 2.62
55 56 1.379044 GAGCCACCCACCTCAATGG 60.379 63.158 0.00 0.00 42.93 3.16
56 57 1.379044 GGAGCCACCCACCTCAATG 60.379 63.158 0.00 0.00 0.00 2.82
57 58 2.971598 CGGAGCCACCCACCTCAAT 61.972 63.158 0.00 0.00 34.64 2.57
58 59 3.636231 CGGAGCCACCCACCTCAA 61.636 66.667 0.00 0.00 34.64 3.02
59 60 3.533079 TACGGAGCCACCCACCTCA 62.533 63.158 0.00 0.00 34.64 3.86
60 61 2.682494 TACGGAGCCACCCACCTC 60.682 66.667 0.00 0.00 34.64 3.85
61 62 3.001406 GTACGGAGCCACCCACCT 61.001 66.667 0.00 0.00 34.64 4.00
62 63 2.193087 ATTGTACGGAGCCACCCACC 62.193 60.000 0.00 0.00 34.64 4.61
63 64 0.743345 GATTGTACGGAGCCACCCAC 60.743 60.000 0.00 0.00 34.64 4.61
64 65 1.195442 TGATTGTACGGAGCCACCCA 61.195 55.000 0.00 0.00 34.64 4.51
65 66 0.462047 CTGATTGTACGGAGCCACCC 60.462 60.000 0.00 0.00 34.64 4.61
66 67 0.462047 CCTGATTGTACGGAGCCACC 60.462 60.000 0.00 0.00 0.00 4.61
67 68 0.535335 TCCTGATTGTACGGAGCCAC 59.465 55.000 0.00 0.00 0.00 5.01
68 69 1.066430 GTTCCTGATTGTACGGAGCCA 60.066 52.381 0.00 0.00 0.00 4.75
69 70 1.653151 GTTCCTGATTGTACGGAGCC 58.347 55.000 0.00 0.00 0.00 4.70
70 71 1.278238 CGTTCCTGATTGTACGGAGC 58.722 55.000 0.00 0.00 0.00 4.70
74 75 1.135083 AGCTCCGTTCCTGATTGTACG 60.135 52.381 0.00 0.00 0.00 3.67
75 76 2.094182 TGAGCTCCGTTCCTGATTGTAC 60.094 50.000 12.15 0.00 0.00 2.90
76 77 2.094182 GTGAGCTCCGTTCCTGATTGTA 60.094 50.000 12.15 0.00 0.00 2.41
77 78 0.976641 TGAGCTCCGTTCCTGATTGT 59.023 50.000 12.15 0.00 0.00 2.71
78 79 1.363744 GTGAGCTCCGTTCCTGATTG 58.636 55.000 12.15 0.00 0.00 2.67
79 80 0.108615 CGTGAGCTCCGTTCCTGATT 60.109 55.000 12.15 0.00 0.00 2.57
80 81 1.251527 ACGTGAGCTCCGTTCCTGAT 61.252 55.000 20.13 1.39 34.28 2.90
81 82 0.607217 TACGTGAGCTCCGTTCCTGA 60.607 55.000 27.31 12.32 39.60 3.86
82 83 0.456312 GTACGTGAGCTCCGTTCCTG 60.456 60.000 27.31 7.28 39.60 3.86
83 84 0.892358 TGTACGTGAGCTCCGTTCCT 60.892 55.000 27.31 11.39 39.60 3.36
84 85 0.038892 TTGTACGTGAGCTCCGTTCC 60.039 55.000 27.31 20.17 39.60 3.62
85 86 1.058404 GTTGTACGTGAGCTCCGTTC 58.942 55.000 27.31 23.30 39.60 3.95
86 87 0.319297 GGTTGTACGTGAGCTCCGTT 60.319 55.000 27.31 15.71 39.60 4.44
87 88 1.288127 GGTTGTACGTGAGCTCCGT 59.712 57.895 26.03 26.03 42.06 4.69
88 89 1.007336 GTGGTTGTACGTGAGCTCCG 61.007 60.000 19.02 19.02 0.00 4.63
89 90 0.317479 AGTGGTTGTACGTGAGCTCC 59.683 55.000 12.15 1.40 0.00 4.70
90 91 1.419374 CAGTGGTTGTACGTGAGCTC 58.581 55.000 6.82 6.82 0.00 4.09
91 92 0.033504 CCAGTGGTTGTACGTGAGCT 59.966 55.000 0.00 0.00 0.00 4.09
92 93 0.249741 ACCAGTGGTTGTACGTGAGC 60.250 55.000 9.70 0.00 27.29 4.26
93 94 1.202486 ACACCAGTGGTTGTACGTGAG 60.202 52.381 13.62 0.00 31.02 3.51
94 95 0.825410 ACACCAGTGGTTGTACGTGA 59.175 50.000 13.62 0.00 31.02 4.35
95 96 1.214367 GACACCAGTGGTTGTACGTG 58.786 55.000 13.62 1.62 31.02 4.49
96 97 0.825410 TGACACCAGTGGTTGTACGT 59.175 50.000 13.62 7.05 31.02 3.57
97 98 1.497991 CTGACACCAGTGGTTGTACG 58.502 55.000 13.62 3.20 35.70 3.67
112 113 1.139058 ACTCCACTGGTGTCAACTGAC 59.861 52.381 1.22 2.78 44.97 3.51
113 114 1.496060 ACTCCACTGGTGTCAACTGA 58.504 50.000 1.22 0.00 0.00 3.41
114 115 2.213499 GAACTCCACTGGTGTCAACTG 58.787 52.381 3.23 0.00 0.00 3.16
115 116 1.837439 TGAACTCCACTGGTGTCAACT 59.163 47.619 3.23 0.00 0.00 3.16
116 117 2.213499 CTGAACTCCACTGGTGTCAAC 58.787 52.381 3.23 0.62 0.00 3.18
117 118 1.475034 GCTGAACTCCACTGGTGTCAA 60.475 52.381 3.23 0.00 0.00 3.18
118 119 0.106708 GCTGAACTCCACTGGTGTCA 59.893 55.000 3.23 3.57 0.00 3.58
119 120 0.946221 CGCTGAACTCCACTGGTGTC 60.946 60.000 3.23 0.00 0.00 3.67
120 121 1.069765 CGCTGAACTCCACTGGTGT 59.930 57.895 0.00 0.00 0.00 4.16
121 122 0.532862 AACGCTGAACTCCACTGGTG 60.533 55.000 0.00 0.00 0.00 4.17
122 123 0.180406 AAACGCTGAACTCCACTGGT 59.820 50.000 0.00 0.00 0.00 4.00
123 124 0.868406 GAAACGCTGAACTCCACTGG 59.132 55.000 0.00 0.00 0.00 4.00
124 125 1.581934 TGAAACGCTGAACTCCACTG 58.418 50.000 0.00 0.00 0.00 3.66
125 126 2.325583 TTGAAACGCTGAACTCCACT 57.674 45.000 0.00 0.00 0.00 4.00
126 127 3.626028 AATTGAAACGCTGAACTCCAC 57.374 42.857 0.00 0.00 0.00 4.02
127 128 3.188460 GCTAATTGAAACGCTGAACTCCA 59.812 43.478 0.00 0.00 0.00 3.86
128 129 3.188460 TGCTAATTGAAACGCTGAACTCC 59.812 43.478 0.00 0.00 0.00 3.85
129 130 4.404507 TGCTAATTGAAACGCTGAACTC 57.595 40.909 0.00 0.00 0.00 3.01
130 131 4.726416 CATGCTAATTGAAACGCTGAACT 58.274 39.130 0.00 0.00 0.00 3.01
131 132 3.301642 GCATGCTAATTGAAACGCTGAAC 59.698 43.478 11.37 0.00 0.00 3.18
132 133 3.191162 AGCATGCTAATTGAAACGCTGAA 59.809 39.130 21.21 0.00 0.00 3.02
133 134 2.749076 AGCATGCTAATTGAAACGCTGA 59.251 40.909 21.21 0.00 0.00 4.26
134 135 3.141002 AGCATGCTAATTGAAACGCTG 57.859 42.857 21.21 0.00 0.00 5.18
135 136 3.855689 AAGCATGCTAATTGAAACGCT 57.144 38.095 23.00 0.00 0.00 5.07
136 137 7.678194 TTATTAAGCATGCTAATTGAAACGC 57.322 32.000 23.00 0.00 0.00 4.84
147 148 9.709495 TCAAAGACAAAATTTATTAAGCATGCT 57.291 25.926 16.30 16.30 0.00 3.79
148 149 9.745323 GTCAAAGACAAAATTTATTAAGCATGC 57.255 29.630 10.51 10.51 32.09 4.06
149 150 9.941991 CGTCAAAGACAAAATTTATTAAGCATG 57.058 29.630 0.00 0.00 32.09 4.06
150 151 8.647226 GCGTCAAAGACAAAATTTATTAAGCAT 58.353 29.630 0.00 0.00 32.09 3.79
151 152 7.115663 GGCGTCAAAGACAAAATTTATTAAGCA 59.884 33.333 0.00 0.00 32.09 3.91
152 153 7.115663 TGGCGTCAAAGACAAAATTTATTAAGC 59.884 33.333 0.00 0.00 32.09 3.09
153 154 8.514136 TGGCGTCAAAGACAAAATTTATTAAG 57.486 30.769 0.00 0.00 32.09 1.85
154 155 7.115663 GCTGGCGTCAAAGACAAAATTTATTAA 59.884 33.333 0.00 0.00 32.09 1.40
155 156 6.584563 GCTGGCGTCAAAGACAAAATTTATTA 59.415 34.615 0.00 0.00 32.09 0.98
156 157 5.405269 GCTGGCGTCAAAGACAAAATTTATT 59.595 36.000 0.00 0.00 32.09 1.40
157 158 4.923281 GCTGGCGTCAAAGACAAAATTTAT 59.077 37.500 0.00 0.00 32.09 1.40
158 159 4.295051 GCTGGCGTCAAAGACAAAATTTA 58.705 39.130 0.00 0.00 32.09 1.40
159 160 3.123050 GCTGGCGTCAAAGACAAAATTT 58.877 40.909 0.00 0.00 32.09 1.82
160 161 2.545742 GGCTGGCGTCAAAGACAAAATT 60.546 45.455 0.00 0.00 32.09 1.82
161 162 1.000274 GGCTGGCGTCAAAGACAAAAT 60.000 47.619 0.00 0.00 32.09 1.82
162 163 0.383949 GGCTGGCGTCAAAGACAAAA 59.616 50.000 0.00 0.00 32.09 2.44
163 164 0.749818 TGGCTGGCGTCAAAGACAAA 60.750 50.000 0.00 0.00 32.09 2.83
164 165 1.153066 TGGCTGGCGTCAAAGACAA 60.153 52.632 0.00 0.00 32.09 3.18
165 166 1.597854 CTGGCTGGCGTCAAAGACA 60.598 57.895 0.00 0.00 32.09 3.41
166 167 0.884704 TTCTGGCTGGCGTCAAAGAC 60.885 55.000 0.00 0.00 0.00 3.01
167 168 0.179032 TTTCTGGCTGGCGTCAAAGA 60.179 50.000 0.00 0.00 0.00 2.52
168 169 0.239347 CTTTCTGGCTGGCGTCAAAG 59.761 55.000 0.00 1.27 0.00 2.77
169 170 0.179032 TCTTTCTGGCTGGCGTCAAA 60.179 50.000 0.00 0.00 0.00 2.69
170 171 0.036732 ATCTTTCTGGCTGGCGTCAA 59.963 50.000 0.00 0.00 0.00 3.18
171 172 0.391661 GATCTTTCTGGCTGGCGTCA 60.392 55.000 0.00 0.00 0.00 4.35
172 173 1.424493 CGATCTTTCTGGCTGGCGTC 61.424 60.000 0.00 0.00 0.00 5.19
173 174 1.448540 CGATCTTTCTGGCTGGCGT 60.449 57.895 0.00 0.00 0.00 5.68
174 175 0.531532 ATCGATCTTTCTGGCTGGCG 60.532 55.000 0.00 0.00 0.00 5.69
175 176 1.332997 CAATCGATCTTTCTGGCTGGC 59.667 52.381 0.00 0.00 0.00 4.85
176 177 2.611292 GTCAATCGATCTTTCTGGCTGG 59.389 50.000 0.00 0.00 0.00 4.85
177 178 3.063180 GTGTCAATCGATCTTTCTGGCTG 59.937 47.826 0.00 0.00 0.00 4.85
178 179 3.265791 GTGTCAATCGATCTTTCTGGCT 58.734 45.455 0.00 0.00 0.00 4.75
179 180 2.352960 GGTGTCAATCGATCTTTCTGGC 59.647 50.000 0.00 0.00 0.00 4.85
180 181 3.599343 TGGTGTCAATCGATCTTTCTGG 58.401 45.455 0.00 0.00 0.00 3.86
181 182 4.142816 GGTTGGTGTCAATCGATCTTTCTG 60.143 45.833 0.00 0.00 35.10 3.02
182 183 4.003648 GGTTGGTGTCAATCGATCTTTCT 58.996 43.478 0.00 0.00 35.10 2.52
183 184 3.127030 GGGTTGGTGTCAATCGATCTTTC 59.873 47.826 0.00 0.00 34.91 2.62
184 185 3.081804 GGGTTGGTGTCAATCGATCTTT 58.918 45.455 0.00 0.00 34.91 2.52
185 186 2.711542 GGGTTGGTGTCAATCGATCTT 58.288 47.619 0.00 0.00 34.91 2.40
186 187 1.405526 CGGGTTGGTGTCAATCGATCT 60.406 52.381 0.00 0.00 34.91 2.75
187 188 1.006832 CGGGTTGGTGTCAATCGATC 58.993 55.000 0.00 0.00 34.91 3.69
188 189 0.392461 CCGGGTTGGTGTCAATCGAT 60.392 55.000 0.00 0.00 34.91 3.59
189 190 1.004320 CCGGGTTGGTGTCAATCGA 60.004 57.895 0.00 0.00 34.91 3.59
190 191 2.686816 GCCGGGTTGGTGTCAATCG 61.687 63.158 2.18 0.00 41.21 3.34
191 192 2.340328 GGCCGGGTTGGTGTCAATC 61.340 63.158 2.18 0.00 41.21 2.67
192 193 2.282887 GGCCGGGTTGGTGTCAAT 60.283 61.111 2.18 0.00 41.21 2.57
193 194 4.939368 CGGCCGGGTTGGTGTCAA 62.939 66.667 20.10 0.00 41.21 3.18
213 214 1.285950 GTTTGTGGAGCGGCTTTCC 59.714 57.895 2.97 2.10 35.20 3.13
214 215 1.285950 GGTTTGTGGAGCGGCTTTC 59.714 57.895 2.97 0.24 0.00 2.62
215 216 2.200337 GGGTTTGTGGAGCGGCTTT 61.200 57.895 2.97 0.00 0.00 3.51
216 217 2.597510 GGGTTTGTGGAGCGGCTT 60.598 61.111 2.97 0.00 0.00 4.35
217 218 2.920076 TTTGGGTTTGTGGAGCGGCT 62.920 55.000 0.00 0.00 0.00 5.52
218 219 2.022240 TTTTGGGTTTGTGGAGCGGC 62.022 55.000 0.00 0.00 0.00 6.53
219 220 0.678950 ATTTTGGGTTTGTGGAGCGG 59.321 50.000 0.00 0.00 0.00 5.52
220 221 1.782044 CATTTTGGGTTTGTGGAGCG 58.218 50.000 0.00 0.00 0.00 5.03
221 222 1.511850 GCATTTTGGGTTTGTGGAGC 58.488 50.000 0.00 0.00 0.00 4.70
222 223 1.415659 TGGCATTTTGGGTTTGTGGAG 59.584 47.619 0.00 0.00 0.00 3.86
223 224 1.415659 CTGGCATTTTGGGTTTGTGGA 59.584 47.619 0.00 0.00 0.00 4.02
224 225 1.881591 CTGGCATTTTGGGTTTGTGG 58.118 50.000 0.00 0.00 0.00 4.17
225 226 1.228533 GCTGGCATTTTGGGTTTGTG 58.771 50.000 0.00 0.00 0.00 3.33
226 227 0.108396 GGCTGGCATTTTGGGTTTGT 59.892 50.000 0.00 0.00 0.00 2.83
227 228 0.606130 GGGCTGGCATTTTGGGTTTG 60.606 55.000 2.88 0.00 0.00 2.93
228 229 1.059006 TGGGCTGGCATTTTGGGTTT 61.059 50.000 2.88 0.00 0.00 3.27
229 230 1.059006 TTGGGCTGGCATTTTGGGTT 61.059 50.000 2.88 0.00 0.00 4.11
230 231 0.841594 ATTGGGCTGGCATTTTGGGT 60.842 50.000 2.88 0.00 0.00 4.51
231 232 0.328926 AATTGGGCTGGCATTTTGGG 59.671 50.000 2.88 0.00 0.00 4.12
232 233 2.027377 TGTAATTGGGCTGGCATTTTGG 60.027 45.455 2.88 0.00 0.00 3.28
233 234 3.264104 CTGTAATTGGGCTGGCATTTTG 58.736 45.455 2.88 0.00 0.00 2.44
234 235 2.905736 ACTGTAATTGGGCTGGCATTTT 59.094 40.909 2.88 0.00 0.00 1.82
235 236 2.497273 GACTGTAATTGGGCTGGCATTT 59.503 45.455 2.88 0.00 0.00 2.32
236 237 2.102578 GACTGTAATTGGGCTGGCATT 58.897 47.619 2.88 0.00 0.00 3.56
237 238 1.767759 GACTGTAATTGGGCTGGCAT 58.232 50.000 2.88 0.00 0.00 4.40
238 239 0.676466 CGACTGTAATTGGGCTGGCA 60.676 55.000 2.88 0.00 0.00 4.92
239 240 0.676782 ACGACTGTAATTGGGCTGGC 60.677 55.000 0.00 0.00 0.00 4.85
240 241 1.086696 CACGACTGTAATTGGGCTGG 58.913 55.000 0.00 0.00 0.00 4.85
241 242 0.447801 GCACGACTGTAATTGGGCTG 59.552 55.000 0.00 0.00 28.79 4.85
242 243 0.036164 TGCACGACTGTAATTGGGCT 59.964 50.000 0.00 0.00 33.08 5.19
243 244 0.878416 TTGCACGACTGTAATTGGGC 59.122 50.000 0.00 0.00 32.43 5.36
244 245 2.292016 TGTTTGCACGACTGTAATTGGG 59.708 45.455 0.00 0.00 0.00 4.12
245 246 3.617540 TGTTTGCACGACTGTAATTGG 57.382 42.857 0.00 0.00 0.00 3.16
246 247 5.940603 TTTTGTTTGCACGACTGTAATTG 57.059 34.783 0.00 0.00 0.00 2.32
247 248 5.518487 CCTTTTTGTTTGCACGACTGTAATT 59.482 36.000 0.00 0.00 0.00 1.40
248 249 5.040635 CCTTTTTGTTTGCACGACTGTAAT 58.959 37.500 0.00 0.00 0.00 1.89
249 250 4.416620 CCTTTTTGTTTGCACGACTGTAA 58.583 39.130 0.00 0.00 0.00 2.41
250 251 3.732471 GCCTTTTTGTTTGCACGACTGTA 60.732 43.478 0.00 0.00 0.00 2.74
251 252 2.874849 CCTTTTTGTTTGCACGACTGT 58.125 42.857 0.00 0.00 0.00 3.55
252 253 1.587946 GCCTTTTTGTTTGCACGACTG 59.412 47.619 0.00 0.00 0.00 3.51
253 254 1.476488 AGCCTTTTTGTTTGCACGACT 59.524 42.857 0.00 0.00 0.00 4.18
254 255 1.587946 CAGCCTTTTTGTTTGCACGAC 59.412 47.619 0.00 0.00 0.00 4.34
255 256 1.474478 TCAGCCTTTTTGTTTGCACGA 59.526 42.857 0.00 0.00 0.00 4.35
256 257 1.587946 GTCAGCCTTTTTGTTTGCACG 59.412 47.619 0.00 0.00 0.00 5.34
257 258 1.587946 CGTCAGCCTTTTTGTTTGCAC 59.412 47.619 0.00 0.00 0.00 4.57
258 259 1.470632 CCGTCAGCCTTTTTGTTTGCA 60.471 47.619 0.00 0.00 0.00 4.08
259 260 1.208259 CCGTCAGCCTTTTTGTTTGC 58.792 50.000 0.00 0.00 0.00 3.68
260 261 1.407258 TCCCGTCAGCCTTTTTGTTTG 59.593 47.619 0.00 0.00 0.00 2.93
261 262 1.770294 TCCCGTCAGCCTTTTTGTTT 58.230 45.000 0.00 0.00 0.00 2.83
262 263 1.681264 CTTCCCGTCAGCCTTTTTGTT 59.319 47.619 0.00 0.00 0.00 2.83
263 264 1.318576 CTTCCCGTCAGCCTTTTTGT 58.681 50.000 0.00 0.00 0.00 2.83
264 265 0.039165 GCTTCCCGTCAGCCTTTTTG 60.039 55.000 0.00 0.00 0.00 2.44
265 266 2.341452 GCTTCCCGTCAGCCTTTTT 58.659 52.632 0.00 0.00 0.00 1.94
266 267 4.081050 GCTTCCCGTCAGCCTTTT 57.919 55.556 0.00 0.00 0.00 2.27
278 279 1.508808 TTAACGTGTTGCGGGCTTCC 61.509 55.000 0.00 0.00 46.52 3.46
279 280 0.519961 ATTAACGTGTTGCGGGCTTC 59.480 50.000 0.00 0.00 46.52 3.86
280 281 1.810959 TATTAACGTGTTGCGGGCTT 58.189 45.000 0.00 0.00 46.52 4.35
281 282 1.668751 CATATTAACGTGTTGCGGGCT 59.331 47.619 0.00 0.00 46.52 5.19
282 283 1.666700 TCATATTAACGTGTTGCGGGC 59.333 47.619 0.00 0.00 46.52 6.13
283 284 3.191669 TCTCATATTAACGTGTTGCGGG 58.808 45.455 0.00 0.00 46.52 6.13
284 285 3.863424 ACTCTCATATTAACGTGTTGCGG 59.137 43.478 0.00 0.00 46.52 5.69
288 289 9.811995 TGCTATTAACTCTCATATTAACGTGTT 57.188 29.630 0.00 0.00 0.00 3.32
289 290 9.982651 ATGCTATTAACTCTCATATTAACGTGT 57.017 29.630 0.00 0.00 0.00 4.49
291 292 9.640963 GGATGCTATTAACTCTCATATTAACGT 57.359 33.333 0.00 0.00 0.00 3.99
292 293 9.088512 GGGATGCTATTAACTCTCATATTAACG 57.911 37.037 0.00 0.00 0.00 3.18
293 294 9.944376 TGGGATGCTATTAACTCTCATATTAAC 57.056 33.333 0.00 0.00 0.00 2.01
295 296 8.762645 CCTGGGATGCTATTAACTCTCATATTA 58.237 37.037 0.00 0.00 0.00 0.98
296 297 7.238514 ACCTGGGATGCTATTAACTCTCATATT 59.761 37.037 0.00 0.00 0.00 1.28
297 298 6.732862 ACCTGGGATGCTATTAACTCTCATAT 59.267 38.462 0.00 0.00 0.00 1.78
298 299 6.084738 ACCTGGGATGCTATTAACTCTCATA 58.915 40.000 0.00 0.00 0.00 2.15
299 300 4.910304 ACCTGGGATGCTATTAACTCTCAT 59.090 41.667 0.00 0.00 0.00 2.90
300 301 4.298626 ACCTGGGATGCTATTAACTCTCA 58.701 43.478 0.00 0.00 0.00 3.27
301 302 4.965200 ACCTGGGATGCTATTAACTCTC 57.035 45.455 0.00 0.00 0.00 3.20
302 303 4.593634 GGTACCTGGGATGCTATTAACTCT 59.406 45.833 4.06 0.00 0.00 3.24
326 327 8.833493 TGAATCATCACATTCTATGCAAGTTAG 58.167 33.333 0.00 0.00 34.35 2.34
336 337 9.288576 AGTTTGAAACTGAATCATCACATTCTA 57.711 29.630 10.18 0.00 41.01 2.10
355 356 6.091986 GTGGAGTCAAATTTTGCAAGTTTGAA 59.908 34.615 28.56 18.02 41.77 2.69
356 357 5.580297 GTGGAGTCAAATTTTGCAAGTTTGA 59.420 36.000 25.62 25.62 38.95 2.69
365 366 4.081697 GGGGTATGGTGGAGTCAAATTTTG 60.082 45.833 2.59 2.59 0.00 2.44
370 371 1.748732 TGGGGTATGGTGGAGTCAAA 58.251 50.000 0.00 0.00 0.00 2.69
380 381 0.039618 AGGTGCAAGTTGGGGTATGG 59.960 55.000 4.75 0.00 0.00 2.74
417 418 2.143122 GTCGAGTTGTGATTGGCTTGA 58.857 47.619 0.00 0.00 0.00 3.02
420 421 2.254546 TTGTCGAGTTGTGATTGGCT 57.745 45.000 0.00 0.00 0.00 4.75
421 422 3.236816 CAATTGTCGAGTTGTGATTGGC 58.763 45.455 0.00 0.00 0.00 4.52
431 432 1.406069 CCTAGCTGCCAATTGTCGAGT 60.406 52.381 4.43 0.00 0.00 4.18
494 495 3.963129 TGGGGTATAGGAAAAACAGCAG 58.037 45.455 0.00 0.00 0.00 4.24
498 499 4.525100 GCAAGTTGGGGTATAGGAAAAACA 59.475 41.667 4.75 0.00 0.00 2.83
504 505 2.645297 TGTTGCAAGTTGGGGTATAGGA 59.355 45.455 0.00 0.00 0.00 2.94
686 687 1.000385 CCTGCTTCTATCGCTCTGGAG 60.000 57.143 0.00 0.00 0.00 3.86
687 688 1.035923 CCTGCTTCTATCGCTCTGGA 58.964 55.000 0.00 0.00 0.00 3.86
707 711 0.247460 GGAAGGCAATGGCAAAGACC 59.753 55.000 10.05 1.09 43.71 3.85
735 739 0.264359 AGGAGCCCTACAGAGCAGAT 59.736 55.000 0.00 0.00 28.47 2.90
803 807 0.388649 CAGACTTCACTTCCCGGACG 60.389 60.000 0.73 0.00 0.00 4.79
816 820 1.595382 GCGTGAGTGCACCAGACTT 60.595 57.895 14.63 0.00 42.09 3.01
1229 1271 1.000607 GGTCGCGAGCATCCTTGTATA 60.001 52.381 31.60 0.00 0.00 1.47
1281 1335 2.123982 GGCTGCCATCCTTGAGGG 60.124 66.667 15.17 0.00 36.49 4.30
1471 1538 4.038522 TGGAAATCAAGCCGAATTGTTTGA 59.961 37.500 0.00 0.00 34.42 2.69
1478 1545 5.975693 TTTTACTGGAAATCAAGCCGAAT 57.024 34.783 0.00 0.00 0.00 3.34
1623 1690 8.209584 AGTCTGAGTCATGCATACTGATTAAAT 58.790 33.333 0.00 0.00 0.00 1.40
1687 1754 3.963383 AAGCTTCGGGCAATAATTACG 57.037 42.857 0.00 0.00 44.79 3.18
1817 1884 3.396276 TGTTAATCCAGAAACCTCACCCA 59.604 43.478 0.00 0.00 0.00 4.51
1966 2033 3.134623 AGTGCCGTGATCATATTCCAGAA 59.865 43.478 0.00 0.00 0.00 3.02
1993 2060 4.681244 GCATGATAATCAAAAGGCAGGCAA 60.681 41.667 0.00 0.00 33.78 4.52
2072 2139 2.119457 CAAGAAGGCAAAACTGAACGC 58.881 47.619 0.00 0.00 0.00 4.84
2074 2141 4.743493 TCAACAAGAAGGCAAAACTGAAC 58.257 39.130 0.00 0.00 0.00 3.18
2170 2238 2.436292 GCTCTGCTGGAGTGCTGG 60.436 66.667 14.71 0.00 43.62 4.85
2171 2239 1.078356 ATGCTCTGCTGGAGTGCTG 60.078 57.895 20.88 1.91 43.62 4.41
2172 2240 1.078356 CATGCTCTGCTGGAGTGCT 60.078 57.895 20.88 6.98 43.62 4.40
2173 2241 1.078637 TCATGCTCTGCTGGAGTGC 60.079 57.895 15.04 15.04 43.62 4.40
2174 2242 0.249676 AGTCATGCTCTGCTGGAGTG 59.750 55.000 8.56 0.00 43.62 3.51
2175 2243 0.249676 CAGTCATGCTCTGCTGGAGT 59.750 55.000 8.56 0.00 43.62 3.85
2176 2244 0.249676 ACAGTCATGCTCTGCTGGAG 59.750 55.000 14.56 3.48 44.49 3.86
2177 2245 0.689055 AACAGTCATGCTCTGCTGGA 59.311 50.000 14.56 0.00 36.50 3.86


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

AutoCloner maintained by Alex Coulton.