Multiple sequence alignment - TraesCS2D01G042500

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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 TraesCS2D01G042500 chr2D 100.000 3664 0 0 1 3664 15227745 15231408 0.000000e+00 6767
1 TraesCS2D01G042500 chr2D 99.622 3174 12 0 491 3664 15263946 15267119 0.000000e+00 5795
2 TraesCS2D01G042500 chr2D 99.695 1970 6 0 491 2460 15249038 15251007 0.000000e+00 3605
3 TraesCS2D01G042500 chr2D 99.349 1076 7 0 2589 3664 15251569 15252644 0.000000e+00 1949
4 TraesCS2D01G042500 chr2D 94.599 574 23 6 3097 3664 397664556 397663985 0.000000e+00 881
5 TraesCS2D01G042500 chr2D 98.182 495 5 4 1 491 19188591 19188097 0.000000e+00 861
6 TraesCS2D01G042500 chr2D 90.511 137 13 0 491 627 19849756 19849620 8.080000e-42 182
7 TraesCS2D01G042500 chr2D 88.276 145 6 5 617 760 15333464 15333598 2.930000e-36 163
8 TraesCS2D01G042500 chrUn 99.779 3174 7 0 491 3664 266171693 266168520 0.000000e+00 5823
9 TraesCS2D01G042500 chrUn 88.752 2676 161 54 492 3098 16444759 16442155 0.000000e+00 3145
10 TraesCS2D01G042500 chrUn 89.207 2585 163 48 492 3018 233477739 233475213 0.000000e+00 3121
11 TraesCS2D01G042500 chrUn 99.881 1687 2 0 1543 3229 379234394 379232708 0.000000e+00 3105
12 TraesCS2D01G042500 chrUn 99.822 1687 3 0 1543 3229 379211163 379209477 0.000000e+00 3099
13 TraesCS2D01G042500 chrUn 99.814 1076 2 0 2589 3664 344072929 344074004 0.000000e+00 1977
14 TraesCS2D01G042500 chrUn 86.276 1654 108 47 492 2083 366814511 366812915 0.000000e+00 1687
15 TraesCS2D01G042500 chrUn 99.667 600 2 0 491 1090 375770273 375769674 0.000000e+00 1098
16 TraesCS2D01G042500 chrUn 98.384 495 5 3 1 492 68038450 68038944 0.000000e+00 867
17 TraesCS2D01G042500 chrUn 94.030 134 8 0 491 624 16657106 16657239 1.720000e-48 204
18 TraesCS2D01G042500 chrUn 93.284 134 9 0 491 624 16611492 16611625 8.030000e-47 198
19 TraesCS2D01G042500 chr2A 93.085 2661 90 36 491 3098 17299595 17302214 0.000000e+00 3808
20 TraesCS2D01G042500 chr2A 88.751 1609 103 39 491 2063 20364958 20366524 0.000000e+00 1897
21 TraesCS2D01G042500 chr2B 92.886 2010 82 30 1103 3098 27287690 27289652 0.000000e+00 2863
22 TraesCS2D01G042500 chr2B 90.955 398 25 7 768 1160 27406651 27407042 3.240000e-145 525
23 TraesCS2D01G042500 chr2B 82.569 218 14 13 505 722 27249506 27249699 1.750000e-38 171
24 TraesCS2D01G042500 chr2B 82.569 218 14 13 505 722 27287100 27287293 1.750000e-38 171
25 TraesCS2D01G042500 chr6B 93.244 1939 106 19 1171 3098 549029331 549031255 0.000000e+00 2832
26 TraesCS2D01G042500 chr7B 91.478 1948 138 19 1171 3098 70339888 70341827 0.000000e+00 2652
27 TraesCS2D01G042500 chr6D 96.848 571 14 2 3098 3664 215532366 215532936 0.000000e+00 952
28 TraesCS2D01G042500 chr5D 96.106 565 16 4 3104 3664 305195445 305196007 0.000000e+00 917
29 TraesCS2D01G042500 chr5D 98.381 494 5 2 1 491 35892512 35893005 0.000000e+00 865
30 TraesCS2D01G042500 chr5D 97.800 500 7 4 1 496 439435553 439436052 0.000000e+00 859
31 TraesCS2D01G042500 chr7D 95.622 571 22 1 3097 3664 573900406 573900976 0.000000e+00 913
32 TraesCS2D01G042500 chr7D 95.304 575 21 2 3096 3664 102993160 102992586 0.000000e+00 907
33 TraesCS2D01G042500 chr7D 98.182 495 5 4 1 491 601817581 601817087 0.000000e+00 861
34 TraesCS2D01G042500 chr1D 98.583 494 4 3 1 491 430052965 430053458 0.000000e+00 870
35 TraesCS2D01G042500 chr3D 98.000 500 7 3 1 497 21352327 21351828 0.000000e+00 865
36 TraesCS2D01G042500 chr3D 98.377 493 5 3 1 491 564883570 564884061 0.000000e+00 863
37 TraesCS2D01G042500 chr4D 98.185 496 5 4 1 492 365201085 365201580 0.000000e+00 863


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 TraesCS2D01G042500 chr2D 15227745 15231408 3663 False 6767 6767 100.0000 1 3664 1 chr2D.!!$F1 3663
1 TraesCS2D01G042500 chr2D 15263946 15267119 3173 False 5795 5795 99.6220 491 3664 1 chr2D.!!$F2 3173
2 TraesCS2D01G042500 chr2D 15249038 15252644 3606 False 2777 3605 99.5220 491 3664 2 chr2D.!!$F4 3173
3 TraesCS2D01G042500 chr2D 397663985 397664556 571 True 881 881 94.5990 3097 3664 1 chr2D.!!$R3 567
4 TraesCS2D01G042500 chrUn 266168520 266171693 3173 True 5823 5823 99.7790 491 3664 1 chrUn.!!$R3 3173
5 TraesCS2D01G042500 chrUn 16442155 16444759 2604 True 3145 3145 88.7520 492 3098 1 chrUn.!!$R1 2606
6 TraesCS2D01G042500 chrUn 233475213 233477739 2526 True 3121 3121 89.2070 492 3018 1 chrUn.!!$R2 2526
7 TraesCS2D01G042500 chrUn 379232708 379234394 1686 True 3105 3105 99.8810 1543 3229 1 chrUn.!!$R7 1686
8 TraesCS2D01G042500 chrUn 379209477 379211163 1686 True 3099 3099 99.8220 1543 3229 1 chrUn.!!$R6 1686
9 TraesCS2D01G042500 chrUn 344072929 344074004 1075 False 1977 1977 99.8140 2589 3664 1 chrUn.!!$F4 1075
10 TraesCS2D01G042500 chrUn 366812915 366814511 1596 True 1687 1687 86.2760 492 2083 1 chrUn.!!$R4 1591
11 TraesCS2D01G042500 chrUn 375769674 375770273 599 True 1098 1098 99.6670 491 1090 1 chrUn.!!$R5 599
12 TraesCS2D01G042500 chr2A 17299595 17302214 2619 False 3808 3808 93.0850 491 3098 1 chr2A.!!$F1 2607
13 TraesCS2D01G042500 chr2A 20364958 20366524 1566 False 1897 1897 88.7510 491 2063 1 chr2A.!!$F2 1572
14 TraesCS2D01G042500 chr2B 27287100 27289652 2552 False 1517 2863 87.7275 505 3098 2 chr2B.!!$F3 2593
15 TraesCS2D01G042500 chr6B 549029331 549031255 1924 False 2832 2832 93.2440 1171 3098 1 chr6B.!!$F1 1927
16 TraesCS2D01G042500 chr7B 70339888 70341827 1939 False 2652 2652 91.4780 1171 3098 1 chr7B.!!$F1 1927
17 TraesCS2D01G042500 chr6D 215532366 215532936 570 False 952 952 96.8480 3098 3664 1 chr6D.!!$F1 566
18 TraesCS2D01G042500 chr5D 305195445 305196007 562 False 917 917 96.1060 3104 3664 1 chr5D.!!$F2 560
19 TraesCS2D01G042500 chr7D 573900406 573900976 570 False 913 913 95.6220 3097 3664 1 chr7D.!!$F1 567
20 TraesCS2D01G042500 chr7D 102992586 102993160 574 True 907 907 95.3040 3096 3664 1 chr7D.!!$R1 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
279 280 0.037734 AAACCCTAAACCTGCGGAGG 59.962 55.0 22.94 22.94 46.21 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3411 4040 1.630878 GCAAGGGGAGAAGAAGAAGGA 59.369 52.381 0.0 0.0 0.0 3.36 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
27 28 9.825972 ATTGAAACTTGTTCGAAGTTGTATATG 57.174 29.630 0.00 0.00 40.10 1.78
28 29 7.802738 TGAAACTTGTTCGAAGTTGTATATGG 58.197 34.615 0.00 0.00 40.10 2.74
29 30 7.442969 TGAAACTTGTTCGAAGTTGTATATGGT 59.557 33.333 0.00 0.00 40.10 3.55
30 31 6.963049 ACTTGTTCGAAGTTGTATATGGTC 57.037 37.500 0.00 0.00 0.00 4.02
31 32 6.460781 ACTTGTTCGAAGTTGTATATGGTCA 58.539 36.000 0.00 0.00 0.00 4.02
32 33 7.103641 ACTTGTTCGAAGTTGTATATGGTCAT 58.896 34.615 0.00 0.00 0.00 3.06
33 34 7.277981 ACTTGTTCGAAGTTGTATATGGTCATC 59.722 37.037 0.00 0.00 0.00 2.92
34 35 6.046593 TGTTCGAAGTTGTATATGGTCATCC 58.953 40.000 0.00 0.00 0.00 3.51
47 48 4.860802 TGGTCATCCATCCTAATTGTGT 57.139 40.909 0.00 0.00 39.03 3.72
48 49 5.966853 TGGTCATCCATCCTAATTGTGTA 57.033 39.130 0.00 0.00 39.03 2.90
49 50 6.514012 TGGTCATCCATCCTAATTGTGTAT 57.486 37.500 0.00 0.00 39.03 2.29
50 51 6.298361 TGGTCATCCATCCTAATTGTGTATG 58.702 40.000 0.00 0.00 39.03 2.39
51 52 5.707298 GGTCATCCATCCTAATTGTGTATGG 59.293 44.000 0.00 0.00 38.76 2.74
53 54 6.998074 GTCATCCATCCTAATTGTGTATGGAA 59.002 38.462 14.01 1.68 46.73 3.53
54 55 7.502226 GTCATCCATCCTAATTGTGTATGGAAA 59.498 37.037 14.01 6.54 46.73 3.13
55 56 7.502226 TCATCCATCCTAATTGTGTATGGAAAC 59.498 37.037 14.01 0.00 46.73 2.78
56 57 6.969043 TCCATCCTAATTGTGTATGGAAACT 58.031 36.000 9.78 0.00 42.33 2.66
57 58 7.410174 TCCATCCTAATTGTGTATGGAAACTT 58.590 34.615 9.78 0.00 42.33 2.66
58 59 8.553153 TCCATCCTAATTGTGTATGGAAACTTA 58.447 33.333 9.78 0.00 42.33 2.24
59 60 9.354673 CCATCCTAATTGTGTATGGAAACTTAT 57.645 33.333 0.00 0.00 39.60 1.73
62 63 9.104965 TCCTAATTGTGTATGGAAACTTATTCG 57.895 33.333 0.00 0.00 0.00 3.34
63 64 9.104965 CCTAATTGTGTATGGAAACTTATTCGA 57.895 33.333 0.00 0.00 0.00 3.71
66 67 7.972832 TTGTGTATGGAAACTTATTCGAAGT 57.027 32.000 3.35 0.00 0.00 3.01
67 68 7.972832 TGTGTATGGAAACTTATTCGAAGTT 57.027 32.000 3.35 0.00 41.82 2.66
68 69 7.802738 TGTGTATGGAAACTTATTCGAAGTTG 58.197 34.615 3.35 0.00 40.10 3.16
69 70 7.442969 TGTGTATGGAAACTTATTCGAAGTTGT 59.557 33.333 3.35 0.00 40.10 3.32
70 71 8.928733 GTGTATGGAAACTTATTCGAAGTTGTA 58.071 33.333 3.35 0.00 40.10 2.41
71 72 9.661563 TGTATGGAAACTTATTCGAAGTTGTAT 57.338 29.630 3.35 1.74 40.10 2.29
75 76 9.104965 TGGAAACTTATTCGAAGTTGTATATGG 57.895 33.333 3.35 0.00 40.10 2.74
76 77 9.106070 GGAAACTTATTCGAAGTTGTATATGGT 57.894 33.333 3.35 0.00 40.10 3.55
78 79 9.661563 AAACTTATTCGAAGTTGTATATGGTCA 57.338 29.630 3.35 0.00 40.10 4.02
79 80 8.644318 ACTTATTCGAAGTTGTATATGGTCAC 57.356 34.615 3.35 0.00 0.00 3.67
80 81 7.709613 ACTTATTCGAAGTTGTATATGGTCACC 59.290 37.037 3.35 0.00 0.00 4.02
81 82 4.395959 TCGAAGTTGTATATGGTCACCC 57.604 45.455 0.00 0.00 0.00 4.61
82 83 3.120792 CGAAGTTGTATATGGTCACCCG 58.879 50.000 0.00 0.00 0.00 5.28
83 84 3.181484 CGAAGTTGTATATGGTCACCCGA 60.181 47.826 0.00 0.00 0.00 5.14
84 85 4.369182 GAAGTTGTATATGGTCACCCGAG 58.631 47.826 0.00 0.00 0.00 4.63
85 86 3.638860 AGTTGTATATGGTCACCCGAGA 58.361 45.455 0.00 0.00 0.00 4.04
86 87 4.223953 AGTTGTATATGGTCACCCGAGAT 58.776 43.478 0.00 0.00 0.00 2.75
87 88 4.654262 AGTTGTATATGGTCACCCGAGATT 59.346 41.667 0.00 0.00 0.00 2.40
88 89 4.600692 TGTATATGGTCACCCGAGATTG 57.399 45.455 0.00 0.00 0.00 2.67
89 90 4.219919 TGTATATGGTCACCCGAGATTGA 58.780 43.478 0.00 0.00 0.00 2.57
90 91 4.651962 TGTATATGGTCACCCGAGATTGAA 59.348 41.667 0.00 0.00 0.00 2.69
91 92 4.982241 ATATGGTCACCCGAGATTGAAT 57.018 40.909 0.00 0.00 0.00 2.57
92 93 6.495526 TGTATATGGTCACCCGAGATTGAATA 59.504 38.462 0.00 0.00 0.00 1.75
93 94 4.982241 ATGGTCACCCGAGATTGAATAT 57.018 40.909 0.00 0.00 0.00 1.28
94 95 7.733773 ATATGGTCACCCGAGATTGAATATA 57.266 36.000 0.00 0.00 0.00 0.86
95 96 6.627087 ATGGTCACCCGAGATTGAATATAT 57.373 37.500 0.00 0.00 0.00 0.86
96 97 7.733773 ATGGTCACCCGAGATTGAATATATA 57.266 36.000 0.00 0.00 0.00 0.86
97 98 7.733773 TGGTCACCCGAGATTGAATATATAT 57.266 36.000 0.00 0.00 0.00 0.86
98 99 8.146053 TGGTCACCCGAGATTGAATATATATT 57.854 34.615 7.72 7.72 0.00 1.28
99 100 9.262240 TGGTCACCCGAGATTGAATATATATTA 57.738 33.333 7.97 0.00 0.00 0.98
128 129 7.880160 TTCCTCTTGAATTCTTCTTGTTTGA 57.120 32.000 7.05 0.00 0.00 2.69
129 130 7.880160 TCCTCTTGAATTCTTCTTGTTTGAA 57.120 32.000 7.05 0.00 0.00 2.69
130 131 8.292444 TCCTCTTGAATTCTTCTTGTTTGAAA 57.708 30.769 7.05 0.00 0.00 2.69
131 132 8.917088 TCCTCTTGAATTCTTCTTGTTTGAAAT 58.083 29.630 7.05 0.00 0.00 2.17
132 133 9.538508 CCTCTTGAATTCTTCTTGTTTGAAATT 57.461 29.630 7.05 0.00 0.00 1.82
141 142 9.761504 TTCTTCTTGTTTGAAATTTCATATGCA 57.238 25.926 21.10 13.98 37.00 3.96
142 143 9.932207 TCTTCTTGTTTGAAATTTCATATGCAT 57.068 25.926 21.10 3.79 37.00 3.96
143 144 9.967245 CTTCTTGTTTGAAATTTCATATGCATG 57.033 29.630 21.10 16.75 37.00 4.06
144 145 9.491675 TTCTTGTTTGAAATTTCATATGCATGT 57.508 25.926 21.10 0.00 37.00 3.21
173 174 9.809395 ATAGTAGCCTAGAATATGTGTACTGAA 57.191 33.333 0.00 0.00 0.00 3.02
174 175 8.534954 AGTAGCCTAGAATATGTGTACTGAAA 57.465 34.615 0.00 0.00 0.00 2.69
175 176 8.414778 AGTAGCCTAGAATATGTGTACTGAAAC 58.585 37.037 0.00 0.00 0.00 2.78
176 177 7.425224 AGCCTAGAATATGTGTACTGAAACT 57.575 36.000 0.00 0.00 0.00 2.66
177 178 7.852263 AGCCTAGAATATGTGTACTGAAACTT 58.148 34.615 0.00 0.00 0.00 2.66
178 179 7.982354 AGCCTAGAATATGTGTACTGAAACTTC 59.018 37.037 0.00 0.00 0.00 3.01
179 180 7.764443 GCCTAGAATATGTGTACTGAAACTTCA 59.236 37.037 0.00 0.00 35.57 3.02
180 181 9.823647 CCTAGAATATGTGTACTGAAACTTCAT 57.176 33.333 0.00 0.00 36.46 2.57
183 184 9.725019 AGAATATGTGTACTGAAACTTCATCAA 57.275 29.630 0.00 0.00 36.46 2.57
246 247 9.594478 AACACTACAAATTAAAAAGAAACCAGG 57.406 29.630 0.00 0.00 0.00 4.45
247 248 8.755028 ACACTACAAATTAAAAAGAAACCAGGT 58.245 29.630 0.00 0.00 0.00 4.00
248 249 9.594478 CACTACAAATTAAAAAGAAACCAGGTT 57.406 29.630 0.00 0.00 0.00 3.50
252 253 9.607988 ACAAATTAAAAAGAAACCAGGTTTAGG 57.392 29.630 18.08 0.00 35.77 2.69
253 254 9.051679 CAAATTAAAAAGAAACCAGGTTTAGGG 57.948 33.333 18.08 0.00 35.77 3.53
254 255 6.734502 TTAAAAAGAAACCAGGTTTAGGGG 57.265 37.500 18.08 0.00 35.77 4.79
255 256 2.992847 AAGAAACCAGGTTTAGGGGG 57.007 50.000 18.08 0.00 35.77 5.40
275 276 1.471287 GGCTAAAACCCTAAACCTGCG 59.529 52.381 0.00 0.00 0.00 5.18
276 277 1.471287 GCTAAAACCCTAAACCTGCGG 59.529 52.381 0.00 0.00 0.00 5.69
277 278 2.876892 GCTAAAACCCTAAACCTGCGGA 60.877 50.000 0.00 0.00 0.00 5.54
278 279 1.905637 AAAACCCTAAACCTGCGGAG 58.094 50.000 0.00 0.00 0.00 4.63
279 280 0.037734 AAACCCTAAACCTGCGGAGG 59.962 55.000 22.94 22.94 46.21 4.30
280 281 0.838987 AACCCTAAACCTGCGGAGGA 60.839 55.000 31.46 6.29 42.93 3.71
288 289 3.309582 CTGCGGAGGAGGCCTTTA 58.690 61.111 6.77 0.00 44.33 1.85
289 290 1.144936 CTGCGGAGGAGGCCTTTAG 59.855 63.158 6.77 0.00 44.33 1.85
290 291 1.612442 TGCGGAGGAGGCCTTTAGT 60.612 57.895 6.77 0.00 31.76 2.24
291 292 1.144276 GCGGAGGAGGCCTTTAGTC 59.856 63.158 6.77 0.92 31.76 2.59
292 293 1.823976 CGGAGGAGGCCTTTAGTCC 59.176 63.158 6.77 10.10 31.76 3.85
293 294 1.687297 CGGAGGAGGCCTTTAGTCCC 61.687 65.000 6.77 1.20 31.76 4.46
294 295 1.687297 GGAGGAGGCCTTTAGTCCCG 61.687 65.000 6.77 0.00 31.76 5.14
295 296 1.687297 GAGGAGGCCTTTAGTCCCGG 61.687 65.000 6.77 0.00 31.76 5.73
296 297 1.993948 GGAGGCCTTTAGTCCCGGT 60.994 63.158 6.77 0.00 0.00 5.28
297 298 1.559965 GGAGGCCTTTAGTCCCGGTT 61.560 60.000 6.77 0.00 0.00 4.44
298 299 1.197812 GAGGCCTTTAGTCCCGGTTA 58.802 55.000 6.77 0.00 0.00 2.85
299 300 1.138464 GAGGCCTTTAGTCCCGGTTAG 59.862 57.143 6.77 0.00 0.00 2.34
300 301 0.463295 GGCCTTTAGTCCCGGTTAGC 60.463 60.000 0.00 0.00 0.00 3.09
301 302 0.463295 GCCTTTAGTCCCGGTTAGCC 60.463 60.000 0.00 0.00 0.00 3.93
302 303 0.906775 CCTTTAGTCCCGGTTAGCCA 59.093 55.000 0.00 0.00 34.09 4.75
303 304 1.406477 CCTTTAGTCCCGGTTAGCCAC 60.406 57.143 0.00 0.00 34.09 5.01
304 305 0.247185 TTTAGTCCCGGTTAGCCACG 59.753 55.000 0.00 0.00 34.09 4.94
305 306 0.611618 TTAGTCCCGGTTAGCCACGA 60.612 55.000 0.00 0.00 34.09 4.35
306 307 1.033746 TAGTCCCGGTTAGCCACGAG 61.034 60.000 0.00 0.00 34.09 4.18
307 308 2.036098 TCCCGGTTAGCCACGAGA 59.964 61.111 0.00 0.00 34.09 4.04
308 309 1.607178 TCCCGGTTAGCCACGAGAA 60.607 57.895 0.00 0.00 34.09 2.87
309 310 1.447314 CCCGGTTAGCCACGAGAAC 60.447 63.158 0.00 0.00 34.09 3.01
310 311 1.447314 CCGGTTAGCCACGAGAACC 60.447 63.158 0.00 0.00 39.44 3.62
311 312 4.180496 GGTTAGCCACGAGAACCG 57.820 61.111 0.00 0.00 45.44 4.44
312 313 1.447314 GGTTAGCCACGAGAACCGG 60.447 63.158 0.00 0.00 43.93 5.28
313 314 1.447314 GTTAGCCACGAGAACCGGG 60.447 63.158 6.32 0.00 43.93 5.73
314 315 1.607178 TTAGCCACGAGAACCGGGA 60.607 57.895 6.32 0.00 46.66 5.14
315 316 1.880819 TTAGCCACGAGAACCGGGAC 61.881 60.000 6.32 0.00 46.66 4.46
316 317 2.776370 TAGCCACGAGAACCGGGACT 62.776 60.000 6.32 4.01 46.66 3.85
317 318 2.345760 GCCACGAGAACCGGGACTA 61.346 63.158 6.32 0.00 46.66 2.59
318 319 1.880819 GCCACGAGAACCGGGACTAA 61.881 60.000 6.32 0.00 46.66 2.24
319 320 0.604578 CCACGAGAACCGGGACTAAA 59.395 55.000 6.32 0.00 46.66 1.85
320 321 1.403780 CCACGAGAACCGGGACTAAAG 60.404 57.143 6.32 2.68 46.66 1.85
321 322 0.893447 ACGAGAACCGGGACTAAAGG 59.107 55.000 6.32 0.00 43.93 3.11
322 323 0.893447 CGAGAACCGGGACTAAAGGT 59.107 55.000 6.32 0.00 40.50 3.50
323 324 1.135170 CGAGAACCGGGACTAAAGGTC 60.135 57.143 6.32 0.00 43.79 3.85
331 332 1.521141 GACTAAAGGTCCTCCGCCC 59.479 63.158 0.00 0.00 38.93 6.13
332 333 1.969200 GACTAAAGGTCCTCCGCCCC 61.969 65.000 0.00 0.00 38.93 5.80
333 334 3.078836 TAAAGGTCCTCCGCCCCG 61.079 66.667 0.00 0.00 39.05 5.73
334 335 3.605412 TAAAGGTCCTCCGCCCCGA 62.605 63.158 0.00 0.00 39.05 5.14
366 367 4.636435 CCACGTGGACGGGCCTTT 62.636 66.667 31.31 0.00 42.34 3.11
367 368 2.344500 CACGTGGACGGGCCTTTA 59.656 61.111 7.95 0.00 44.95 1.85
368 369 1.740296 CACGTGGACGGGCCTTTAG 60.740 63.158 7.95 0.00 44.95 1.85
369 370 2.212110 ACGTGGACGGGCCTTTAGT 61.212 57.895 0.84 0.00 44.95 2.24
370 371 1.447314 CGTGGACGGGCCTTTAGTC 60.447 63.158 0.84 7.66 37.63 2.59
371 372 1.447314 GTGGACGGGCCTTTAGTCG 60.447 63.158 0.84 0.00 37.63 4.18
372 373 2.510918 GGACGGGCCTTTAGTCGC 60.511 66.667 0.84 0.00 35.87 5.19
373 374 2.884207 GACGGGCCTTTAGTCGCG 60.884 66.667 0.84 0.00 43.02 5.87
374 375 4.446413 ACGGGCCTTTAGTCGCGG 62.446 66.667 6.13 0.00 41.92 6.46
375 376 4.446413 CGGGCCTTTAGTCGCGGT 62.446 66.667 6.13 0.00 35.43 5.68
376 377 2.046604 GGGCCTTTAGTCGCGGTT 60.047 61.111 6.13 0.00 0.00 4.44
377 378 2.104859 GGGCCTTTAGTCGCGGTTC 61.105 63.158 6.13 0.00 0.00 3.62
378 379 2.450345 GGCCTTTAGTCGCGGTTCG 61.450 63.158 6.13 0.00 40.15 3.95
379 380 1.735559 GCCTTTAGTCGCGGTTCGT 60.736 57.895 6.13 0.00 39.67 3.85
380 381 0.456653 GCCTTTAGTCGCGGTTCGTA 60.457 55.000 6.13 0.00 39.67 3.43
381 382 1.981254 CCTTTAGTCGCGGTTCGTAA 58.019 50.000 6.13 0.00 39.67 3.18
382 383 1.916000 CCTTTAGTCGCGGTTCGTAAG 59.084 52.381 6.13 3.09 39.67 2.34
393 394 4.206958 TCGTAAGAGGCGCGACTA 57.793 55.556 18.29 0.00 45.01 2.59
394 395 2.470156 TCGTAAGAGGCGCGACTAA 58.530 52.632 18.29 0.00 45.01 2.24
395 396 0.804364 TCGTAAGAGGCGCGACTAAA 59.196 50.000 18.29 0.00 45.01 1.85
396 397 1.402968 TCGTAAGAGGCGCGACTAAAT 59.597 47.619 18.29 6.67 45.01 1.40
397 398 1.517276 CGTAAGAGGCGCGACTAAATG 59.483 52.381 18.29 4.75 43.02 2.32
398 399 1.859080 GTAAGAGGCGCGACTAAATGG 59.141 52.381 18.29 0.00 0.00 3.16
399 400 0.462047 AAGAGGCGCGACTAAATGGG 60.462 55.000 18.29 0.00 0.00 4.00
400 401 1.887707 GAGGCGCGACTAAATGGGG 60.888 63.158 18.29 0.00 0.00 4.96
401 402 2.900337 GGCGCGACTAAATGGGGG 60.900 66.667 12.10 0.00 0.00 5.40
416 417 4.770874 GGGGCCTTTAGTCGCGCA 62.771 66.667 8.75 0.00 39.53 6.09
417 418 2.513897 GGGCCTTTAGTCGCGCAT 60.514 61.111 8.75 0.00 37.82 4.73
418 419 1.227438 GGGCCTTTAGTCGCGCATA 60.227 57.895 8.75 0.00 37.82 3.14
419 420 0.602905 GGGCCTTTAGTCGCGCATAT 60.603 55.000 8.75 0.00 37.82 1.78
420 421 1.226746 GGCCTTTAGTCGCGCATATT 58.773 50.000 8.75 0.00 0.00 1.28
421 422 1.602377 GGCCTTTAGTCGCGCATATTT 59.398 47.619 8.75 0.00 0.00 1.40
422 423 2.803956 GGCCTTTAGTCGCGCATATTTA 59.196 45.455 8.75 0.00 0.00 1.40
423 424 3.120649 GGCCTTTAGTCGCGCATATTTAG 60.121 47.826 8.75 0.00 0.00 1.85
424 425 3.493503 GCCTTTAGTCGCGCATATTTAGT 59.506 43.478 8.75 0.00 0.00 2.24
425 426 4.376109 GCCTTTAGTCGCGCATATTTAGTC 60.376 45.833 8.75 0.00 0.00 2.59
426 427 4.150098 CCTTTAGTCGCGCATATTTAGTCC 59.850 45.833 8.75 0.00 0.00 3.85
427 428 2.150397 AGTCGCGCATATTTAGTCCC 57.850 50.000 8.75 0.00 0.00 4.46
428 429 0.782384 GTCGCGCATATTTAGTCCCG 59.218 55.000 8.75 0.00 0.00 5.14
429 430 0.319211 TCGCGCATATTTAGTCCCGG 60.319 55.000 8.75 0.00 0.00 5.73
430 431 0.599204 CGCGCATATTTAGTCCCGGT 60.599 55.000 8.75 0.00 0.00 5.28
431 432 1.589803 GCGCATATTTAGTCCCGGTT 58.410 50.000 0.30 0.00 0.00 4.44
432 433 1.263217 GCGCATATTTAGTCCCGGTTG 59.737 52.381 0.30 0.00 0.00 3.77
433 434 1.263217 CGCATATTTAGTCCCGGTTGC 59.737 52.381 0.00 0.00 0.00 4.17
434 435 2.294074 GCATATTTAGTCCCGGTTGCA 58.706 47.619 0.00 0.00 0.00 4.08
435 436 2.032924 GCATATTTAGTCCCGGTTGCAC 59.967 50.000 0.00 0.00 0.00 4.57
436 437 3.275143 CATATTTAGTCCCGGTTGCACA 58.725 45.455 0.00 0.00 0.00 4.57
437 438 1.821216 ATTTAGTCCCGGTTGCACAG 58.179 50.000 0.00 0.00 0.00 3.66
438 439 0.887387 TTTAGTCCCGGTTGCACAGC 60.887 55.000 0.00 0.00 0.00 4.40
439 440 2.741486 TTAGTCCCGGTTGCACAGCC 62.741 60.000 0.00 0.00 0.00 4.85
446 447 2.281900 GTTGCACAGCCGGGGTTA 60.282 61.111 2.18 0.00 0.00 2.85
447 448 1.899534 GTTGCACAGCCGGGGTTAA 60.900 57.895 2.18 0.00 0.00 2.01
448 449 1.075836 TTGCACAGCCGGGGTTAAT 59.924 52.632 2.18 0.00 0.00 1.40
449 450 1.247419 TTGCACAGCCGGGGTTAATG 61.247 55.000 2.18 0.00 0.00 1.90
450 451 2.414785 GCACAGCCGGGGTTAATGG 61.415 63.158 2.18 0.00 0.00 3.16
454 455 2.043349 GCCGGGGTTAATGGCCTT 60.043 61.111 3.32 0.00 43.06 4.35
455 456 1.684391 GCCGGGGTTAATGGCCTTT 60.684 57.895 3.32 6.72 43.06 3.11
456 457 1.955495 GCCGGGGTTAATGGCCTTTG 61.955 60.000 13.96 0.00 43.06 2.77
457 458 1.515487 CGGGGTTAATGGCCTTTGC 59.485 57.895 13.96 6.67 0.00 3.68
458 459 1.515487 GGGGTTAATGGCCTTTGCG 59.485 57.895 13.96 0.00 38.85 4.85
459 460 0.968393 GGGGTTAATGGCCTTTGCGA 60.968 55.000 13.96 0.00 38.85 5.10
460 461 0.892063 GGGTTAATGGCCTTTGCGAA 59.108 50.000 13.96 0.00 38.85 4.70
461 462 1.403647 GGGTTAATGGCCTTTGCGAAC 60.404 52.381 13.96 9.94 38.85 3.95
462 463 1.403647 GGTTAATGGCCTTTGCGAACC 60.404 52.381 13.96 14.67 38.85 3.62
463 464 0.523966 TTAATGGCCTTTGCGAACCG 59.476 50.000 13.96 0.00 38.85 4.44
464 465 1.309499 TAATGGCCTTTGCGAACCGG 61.309 55.000 13.96 0.00 38.85 5.28
467 468 3.733960 GCCTTTGCGAACCGGGAC 61.734 66.667 6.32 0.00 0.00 4.46
468 469 2.032071 CCTTTGCGAACCGGGACT 59.968 61.111 6.32 0.00 0.00 3.85
469 470 1.294138 CCTTTGCGAACCGGGACTA 59.706 57.895 6.32 0.00 0.00 2.59
470 471 0.320946 CCTTTGCGAACCGGGACTAA 60.321 55.000 6.32 0.00 0.00 2.24
471 472 1.515081 CTTTGCGAACCGGGACTAAA 58.485 50.000 6.32 0.00 0.00 1.85
472 473 1.463444 CTTTGCGAACCGGGACTAAAG 59.537 52.381 6.32 6.26 0.00 1.85
473 474 0.320946 TTGCGAACCGGGACTAAAGG 60.321 55.000 6.32 0.00 0.00 3.11
474 475 2.104859 GCGAACCGGGACTAAAGGC 61.105 63.158 6.32 0.00 0.00 4.35
475 476 1.294138 CGAACCGGGACTAAAGGCA 59.706 57.895 6.32 0.00 0.00 4.75
476 477 0.107848 CGAACCGGGACTAAAGGCAT 60.108 55.000 6.32 0.00 0.00 4.40
477 478 1.137479 CGAACCGGGACTAAAGGCATA 59.863 52.381 6.32 0.00 0.00 3.14
478 479 2.224209 CGAACCGGGACTAAAGGCATAT 60.224 50.000 6.32 0.00 0.00 1.78
479 480 3.743269 CGAACCGGGACTAAAGGCATATT 60.743 47.826 6.32 0.00 0.00 1.28
480 481 3.945640 ACCGGGACTAAAGGCATATTT 57.054 42.857 6.32 0.00 0.00 1.40
481 482 4.245251 ACCGGGACTAAAGGCATATTTT 57.755 40.909 6.32 0.00 0.00 1.82
482 483 4.204799 ACCGGGACTAAAGGCATATTTTC 58.795 43.478 6.32 0.00 0.00 2.29
483 484 4.079958 ACCGGGACTAAAGGCATATTTTCT 60.080 41.667 6.32 0.00 0.00 2.52
484 485 5.131475 ACCGGGACTAAAGGCATATTTTCTA 59.869 40.000 6.32 0.00 0.00 2.10
485 486 5.469084 CCGGGACTAAAGGCATATTTTCTAC 59.531 44.000 0.00 0.00 0.00 2.59
486 487 6.289064 CGGGACTAAAGGCATATTTTCTACT 58.711 40.000 0.00 0.00 0.00 2.57
487 488 7.439381 CGGGACTAAAGGCATATTTTCTACTA 58.561 38.462 0.00 0.00 0.00 1.82
488 489 7.599245 CGGGACTAAAGGCATATTTTCTACTAG 59.401 40.741 0.00 0.00 0.00 2.57
489 490 8.430431 GGGACTAAAGGCATATTTTCTACTAGT 58.570 37.037 0.00 0.00 0.00 2.57
3411 4040 1.275002 TGCCTTATCCTCCCCTTCCTT 60.275 52.381 0.00 0.00 0.00 3.36
3650 4283 0.821301 TGGTGATGAAGTTGCGGCAA 60.821 50.000 12.11 12.11 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.825972 CATATACAACTTCGAACAAGTTTCAAT 57.174 29.630 0.00 0.00 38.32 2.57
2 3 8.286800 CCATATACAACTTCGAACAAGTTTCAA 58.713 33.333 0.00 0.00 38.32 2.69
4 5 7.803724 ACCATATACAACTTCGAACAAGTTTC 58.196 34.615 0.00 0.00 38.32 2.78
6 7 6.932400 TGACCATATACAACTTCGAACAAGTT 59.068 34.615 0.00 0.00 40.80 2.66
7 8 6.460781 TGACCATATACAACTTCGAACAAGT 58.539 36.000 0.00 0.00 0.00 3.16
8 9 6.961359 TGACCATATACAACTTCGAACAAG 57.039 37.500 0.00 0.00 0.00 3.16
9 10 6.537301 GGATGACCATATACAACTTCGAACAA 59.463 38.462 0.00 0.00 35.97 2.83
10 11 6.046593 GGATGACCATATACAACTTCGAACA 58.953 40.000 0.00 0.00 35.97 3.18
11 12 6.046593 TGGATGACCATATACAACTTCGAAC 58.953 40.000 0.00 0.00 41.77 3.95
12 13 6.228616 TGGATGACCATATACAACTTCGAA 57.771 37.500 0.00 0.00 41.77 3.71
13 14 5.862678 TGGATGACCATATACAACTTCGA 57.137 39.130 0.00 0.00 41.77 3.71
27 28 5.707298 CCATACACAATTAGGATGGATGACC 59.293 44.000 13.65 0.00 39.61 4.02
28 29 6.533730 TCCATACACAATTAGGATGGATGAC 58.466 40.000 16.39 0.00 40.86 3.06
29 30 6.762077 TCCATACACAATTAGGATGGATGA 57.238 37.500 16.39 0.28 40.86 2.92
30 31 7.503566 AGTTTCCATACACAATTAGGATGGATG 59.496 37.037 19.49 9.53 44.20 3.51
31 32 7.586349 AGTTTCCATACACAATTAGGATGGAT 58.414 34.615 19.49 7.23 44.20 3.41
32 33 6.969043 AGTTTCCATACACAATTAGGATGGA 58.031 36.000 16.39 16.39 43.36 3.41
33 34 7.645058 AAGTTTCCATACACAATTAGGATGG 57.355 36.000 12.96 12.96 38.75 3.51
36 37 9.104965 CGAATAAGTTTCCATACACAATTAGGA 57.895 33.333 0.00 0.00 0.00 2.94
37 38 9.104965 TCGAATAAGTTTCCATACACAATTAGG 57.895 33.333 0.00 0.00 0.00 2.69
40 41 9.010029 ACTTCGAATAAGTTTCCATACACAATT 57.990 29.630 0.00 0.00 0.00 2.32
41 42 8.561738 ACTTCGAATAAGTTTCCATACACAAT 57.438 30.769 0.00 0.00 0.00 2.71
42 43 7.972832 ACTTCGAATAAGTTTCCATACACAA 57.027 32.000 0.00 0.00 0.00 3.33
43 44 7.442969 ACAACTTCGAATAAGTTTCCATACACA 59.557 33.333 0.00 0.00 38.32 3.72
44 45 7.803724 ACAACTTCGAATAAGTTTCCATACAC 58.196 34.615 0.00 0.00 38.32 2.90
45 46 7.972832 ACAACTTCGAATAAGTTTCCATACA 57.027 32.000 0.00 0.00 38.32 2.29
49 50 9.104965 CCATATACAACTTCGAATAAGTTTCCA 57.895 33.333 0.00 0.00 38.32 3.53
50 51 9.106070 ACCATATACAACTTCGAATAAGTTTCC 57.894 33.333 0.00 0.00 38.32 3.13
52 53 9.661563 TGACCATATACAACTTCGAATAAGTTT 57.338 29.630 0.00 0.00 38.32 2.66
53 54 9.095065 GTGACCATATACAACTTCGAATAAGTT 57.905 33.333 0.00 0.00 40.80 2.66
54 55 7.709613 GGTGACCATATACAACTTCGAATAAGT 59.290 37.037 0.00 0.00 0.00 2.24
55 56 8.073355 GGTGACCATATACAACTTCGAATAAG 57.927 38.462 0.00 0.00 0.00 1.73
115 116 9.761504 TGCATATGAAATTTCAAACAAGAAGAA 57.238 25.926 23.91 1.93 41.13 2.52
116 117 9.932207 ATGCATATGAAATTTCAAACAAGAAGA 57.068 25.926 23.91 4.00 41.13 2.87
117 118 9.967245 CATGCATATGAAATTTCAAACAAGAAG 57.033 29.630 23.91 9.77 41.13 2.85
118 119 9.491675 ACATGCATATGAAATTTCAAACAAGAA 57.508 25.926 23.91 8.45 41.13 2.52
147 148 9.809395 TTCAGTACACATATTCTAGGCTACTAT 57.191 33.333 0.00 0.00 0.00 2.12
148 149 9.636789 TTTCAGTACACATATTCTAGGCTACTA 57.363 33.333 0.00 0.00 0.00 1.82
149 150 8.414778 GTTTCAGTACACATATTCTAGGCTACT 58.585 37.037 0.00 0.00 0.00 2.57
150 151 8.414778 AGTTTCAGTACACATATTCTAGGCTAC 58.585 37.037 0.00 0.00 0.00 3.58
151 152 8.534954 AGTTTCAGTACACATATTCTAGGCTA 57.465 34.615 0.00 0.00 0.00 3.93
152 153 7.425224 AGTTTCAGTACACATATTCTAGGCT 57.575 36.000 0.00 0.00 0.00 4.58
153 154 7.764443 TGAAGTTTCAGTACACATATTCTAGGC 59.236 37.037 0.00 0.00 32.50 3.93
154 155 9.823647 ATGAAGTTTCAGTACACATATTCTAGG 57.176 33.333 0.00 0.00 41.08 3.02
157 158 9.725019 TTGATGAAGTTTCAGTACACATATTCT 57.275 29.630 0.00 0.00 41.08 2.40
220 221 9.594478 CCTGGTTTCTTTTTAATTTGTAGTGTT 57.406 29.630 0.00 0.00 0.00 3.32
221 222 8.755028 ACCTGGTTTCTTTTTAATTTGTAGTGT 58.245 29.630 0.00 0.00 0.00 3.55
222 223 9.594478 AACCTGGTTTCTTTTTAATTTGTAGTG 57.406 29.630 6.18 0.00 0.00 2.74
226 227 9.607988 CCTAAACCTGGTTTCTTTTTAATTTGT 57.392 29.630 26.95 2.11 37.01 2.83
227 228 9.051679 CCCTAAACCTGGTTTCTTTTTAATTTG 57.948 33.333 26.95 2.02 37.01 2.32
228 229 8.215050 CCCCTAAACCTGGTTTCTTTTTAATTT 58.785 33.333 26.95 2.76 37.01 1.82
229 230 7.202149 CCCCCTAAACCTGGTTTCTTTTTAATT 60.202 37.037 26.95 3.28 37.01 1.40
230 231 6.271391 CCCCCTAAACCTGGTTTCTTTTTAAT 59.729 38.462 26.95 4.03 37.01 1.40
231 232 5.603395 CCCCCTAAACCTGGTTTCTTTTTAA 59.397 40.000 26.95 8.17 37.01 1.52
232 233 5.149239 CCCCCTAAACCTGGTTTCTTTTTA 58.851 41.667 26.95 8.87 37.01 1.52
233 234 3.971305 CCCCCTAAACCTGGTTTCTTTTT 59.029 43.478 26.95 6.26 37.01 1.94
234 235 3.583228 CCCCCTAAACCTGGTTTCTTTT 58.417 45.455 26.95 7.01 37.01 2.27
235 236 3.254093 CCCCCTAAACCTGGTTTCTTT 57.746 47.619 26.95 7.40 37.01 2.52
236 237 2.992847 CCCCCTAAACCTGGTTTCTT 57.007 50.000 26.95 7.77 37.01 2.52
255 256 1.471287 CGCAGGTTTAGGGTTTTAGCC 59.529 52.381 0.00 0.00 35.59 3.93
256 257 2.913777 CGCAGGTTTAGGGTTTTAGC 57.086 50.000 0.00 0.00 0.00 3.09
271 272 1.144936 CTAAAGGCCTCCTCCGCAG 59.855 63.158 5.23 0.00 30.89 5.18
272 273 1.612442 ACTAAAGGCCTCCTCCGCA 60.612 57.895 5.23 0.00 30.89 5.69
273 274 1.144276 GACTAAAGGCCTCCTCCGC 59.856 63.158 5.23 0.00 30.89 5.54
274 275 1.687297 GGGACTAAAGGCCTCCTCCG 61.687 65.000 5.23 0.00 30.89 4.63
275 276 1.687297 CGGGACTAAAGGCCTCCTCC 61.687 65.000 5.23 7.60 30.89 4.30
276 277 1.687297 CCGGGACTAAAGGCCTCCTC 61.687 65.000 5.23 0.00 30.89 3.71
277 278 1.689582 CCGGGACTAAAGGCCTCCT 60.690 63.158 5.23 0.00 33.87 3.69
278 279 1.559965 AACCGGGACTAAAGGCCTCC 61.560 60.000 5.23 1.56 0.00 4.30
279 280 1.138464 CTAACCGGGACTAAAGGCCTC 59.862 57.143 5.23 0.00 0.00 4.70
280 281 1.201424 CTAACCGGGACTAAAGGCCT 58.799 55.000 6.32 0.00 0.00 5.19
281 282 0.463295 GCTAACCGGGACTAAAGGCC 60.463 60.000 6.32 0.00 0.00 5.19
282 283 0.463295 GGCTAACCGGGACTAAAGGC 60.463 60.000 6.32 1.99 0.00 4.35
283 284 0.906775 TGGCTAACCGGGACTAAAGG 59.093 55.000 6.32 0.00 39.70 3.11
284 285 1.738030 CGTGGCTAACCGGGACTAAAG 60.738 57.143 6.32 0.00 39.70 1.85
285 286 0.247185 CGTGGCTAACCGGGACTAAA 59.753 55.000 6.32 0.00 39.70 1.85
286 287 0.611618 TCGTGGCTAACCGGGACTAA 60.612 55.000 6.32 0.00 39.70 2.24
287 288 1.001020 TCGTGGCTAACCGGGACTA 60.001 57.895 6.32 0.00 39.70 2.59
288 289 2.283388 TCGTGGCTAACCGGGACT 60.283 61.111 6.32 0.00 39.70 3.85
289 290 1.880819 TTCTCGTGGCTAACCGGGAC 61.881 60.000 6.32 0.00 39.70 4.46
290 291 1.607178 TTCTCGTGGCTAACCGGGA 60.607 57.895 6.32 0.00 39.70 5.14
291 292 1.447314 GTTCTCGTGGCTAACCGGG 60.447 63.158 6.32 0.00 39.70 5.73
292 293 1.447314 GGTTCTCGTGGCTAACCGG 60.447 63.158 0.00 0.00 39.70 5.28
293 294 4.180496 GGTTCTCGTGGCTAACCG 57.820 61.111 0.00 0.00 39.70 4.44
294 295 1.447314 CCGGTTCTCGTGGCTAACC 60.447 63.158 0.00 0.00 39.44 2.85
295 296 1.447314 CCCGGTTCTCGTGGCTAAC 60.447 63.158 0.00 0.00 37.11 2.34
296 297 1.607178 TCCCGGTTCTCGTGGCTAA 60.607 57.895 0.00 0.00 37.11 3.09
297 298 2.036098 TCCCGGTTCTCGTGGCTA 59.964 61.111 0.00 0.00 37.11 3.93
298 299 2.776370 TAGTCCCGGTTCTCGTGGCT 62.776 60.000 0.00 0.00 37.11 4.75
299 300 1.880819 TTAGTCCCGGTTCTCGTGGC 61.881 60.000 0.00 0.00 37.11 5.01
300 301 0.604578 TTTAGTCCCGGTTCTCGTGG 59.395 55.000 0.00 0.00 37.11 4.94
301 302 1.403780 CCTTTAGTCCCGGTTCTCGTG 60.404 57.143 0.00 0.00 37.11 4.35
302 303 0.893447 CCTTTAGTCCCGGTTCTCGT 59.107 55.000 0.00 0.00 37.11 4.18
303 304 0.893447 ACCTTTAGTCCCGGTTCTCG 59.107 55.000 0.00 0.00 38.88 4.04
304 305 2.669300 GACCTTTAGTCCCGGTTCTC 57.331 55.000 0.00 0.00 39.84 2.87
313 314 1.521141 GGGCGGAGGACCTTTAGTC 59.479 63.158 0.00 0.00 45.51 2.59
314 315 1.993948 GGGGCGGAGGACCTTTAGT 60.994 63.158 0.00 0.00 43.03 2.24
315 316 2.908796 GGGGCGGAGGACCTTTAG 59.091 66.667 0.00 0.00 43.03 1.85
316 317 3.078836 CGGGGCGGAGGACCTTTA 61.079 66.667 0.00 0.00 43.03 1.85
349 350 3.242897 TAAAGGCCCGTCCACGTGG 62.243 63.158 29.26 29.26 37.29 4.94
350 351 1.740296 CTAAAGGCCCGTCCACGTG 60.740 63.158 9.08 9.08 37.29 4.49
351 352 2.163601 GACTAAAGGCCCGTCCACGT 62.164 60.000 0.00 0.00 37.29 4.49
352 353 1.447314 GACTAAAGGCCCGTCCACG 60.447 63.158 0.00 0.00 37.29 4.94
353 354 1.447314 CGACTAAAGGCCCGTCCAC 60.447 63.158 0.00 0.00 37.29 4.02
354 355 2.975536 CGACTAAAGGCCCGTCCA 59.024 61.111 0.00 0.00 37.29 4.02
355 356 2.510918 GCGACTAAAGGCCCGTCC 60.511 66.667 0.00 0.00 0.00 4.79
356 357 2.884207 CGCGACTAAAGGCCCGTC 60.884 66.667 0.00 0.02 0.00 4.79
357 358 4.446413 CCGCGACTAAAGGCCCGT 62.446 66.667 8.23 0.00 0.00 5.28
358 359 3.945304 AACCGCGACTAAAGGCCCG 62.945 63.158 8.23 0.00 0.00 6.13
359 360 2.046604 AACCGCGACTAAAGGCCC 60.047 61.111 8.23 0.00 0.00 5.80
360 361 2.450345 CGAACCGCGACTAAAGGCC 61.450 63.158 8.23 0.00 44.57 5.19
361 362 0.456653 TACGAACCGCGACTAAAGGC 60.457 55.000 8.23 0.00 44.57 4.35
362 363 1.916000 CTTACGAACCGCGACTAAAGG 59.084 52.381 8.23 0.00 44.57 3.11
363 364 2.844804 CTCTTACGAACCGCGACTAAAG 59.155 50.000 8.23 3.58 44.57 1.85
364 365 2.414559 CCTCTTACGAACCGCGACTAAA 60.415 50.000 8.23 0.00 44.57 1.85
365 366 1.131126 CCTCTTACGAACCGCGACTAA 59.869 52.381 8.23 0.00 44.57 2.24
366 367 0.729116 CCTCTTACGAACCGCGACTA 59.271 55.000 8.23 0.00 44.57 2.59
367 368 1.505353 CCTCTTACGAACCGCGACT 59.495 57.895 8.23 0.00 44.57 4.18
368 369 2.157073 GCCTCTTACGAACCGCGAC 61.157 63.158 8.23 0.00 44.57 5.19
369 370 2.180017 GCCTCTTACGAACCGCGA 59.820 61.111 8.23 0.00 44.57 5.87
371 372 3.551915 GCGCCTCTTACGAACCGC 61.552 66.667 0.00 0.00 33.61 5.68
372 373 3.245315 CGCGCCTCTTACGAACCG 61.245 66.667 0.00 0.00 0.00 4.44
373 374 2.157073 GTCGCGCCTCTTACGAACC 61.157 63.158 0.00 0.00 37.60 3.62
374 375 0.097674 TAGTCGCGCCTCTTACGAAC 59.902 55.000 0.00 0.00 37.60 3.95
375 376 0.804364 TTAGTCGCGCCTCTTACGAA 59.196 50.000 0.00 0.00 37.60 3.85
376 377 0.804364 TTTAGTCGCGCCTCTTACGA 59.196 50.000 0.00 0.00 0.00 3.43
377 378 1.517276 CATTTAGTCGCGCCTCTTACG 59.483 52.381 0.00 0.00 0.00 3.18
378 379 1.859080 CCATTTAGTCGCGCCTCTTAC 59.141 52.381 0.00 0.00 0.00 2.34
379 380 1.202486 CCCATTTAGTCGCGCCTCTTA 60.202 52.381 0.00 0.00 0.00 2.10
380 381 0.462047 CCCATTTAGTCGCGCCTCTT 60.462 55.000 0.00 0.00 0.00 2.85
381 382 1.144057 CCCATTTAGTCGCGCCTCT 59.856 57.895 0.00 2.63 0.00 3.69
382 383 1.887707 CCCCATTTAGTCGCGCCTC 60.888 63.158 0.00 0.00 0.00 4.70
383 384 2.189521 CCCCATTTAGTCGCGCCT 59.810 61.111 0.00 0.00 0.00 5.52
384 385 2.900337 CCCCCATTTAGTCGCGCC 60.900 66.667 0.00 0.00 0.00 6.53
399 400 2.653953 TATGCGCGACTAAAGGCCCC 62.654 60.000 12.10 0.00 0.00 5.80
400 401 0.602905 ATATGCGCGACTAAAGGCCC 60.603 55.000 12.10 0.00 0.00 5.80
401 402 1.226746 AATATGCGCGACTAAAGGCC 58.773 50.000 12.10 0.00 0.00 5.19
402 403 3.493503 ACTAAATATGCGCGACTAAAGGC 59.506 43.478 12.10 0.00 0.00 4.35
403 404 4.150098 GGACTAAATATGCGCGACTAAAGG 59.850 45.833 12.10 0.00 0.00 3.11
404 405 4.150098 GGGACTAAATATGCGCGACTAAAG 59.850 45.833 12.10 0.00 0.00 1.85
405 406 4.053295 GGGACTAAATATGCGCGACTAAA 58.947 43.478 12.10 0.00 0.00 1.85
406 407 3.645884 GGGACTAAATATGCGCGACTAA 58.354 45.455 12.10 0.00 0.00 2.24
407 408 2.351060 CGGGACTAAATATGCGCGACTA 60.351 50.000 12.10 0.00 38.72 2.59
408 409 1.602165 CGGGACTAAATATGCGCGACT 60.602 52.381 12.10 0.00 38.72 4.18
409 410 0.782384 CGGGACTAAATATGCGCGAC 59.218 55.000 12.10 0.88 38.72 5.19
410 411 0.319211 CCGGGACTAAATATGCGCGA 60.319 55.000 12.10 0.00 38.72 5.87
411 412 0.599204 ACCGGGACTAAATATGCGCG 60.599 55.000 6.32 0.00 36.61 6.86
412 413 1.263217 CAACCGGGACTAAATATGCGC 59.737 52.381 6.32 0.00 0.00 6.09
413 414 1.263217 GCAACCGGGACTAAATATGCG 59.737 52.381 6.32 0.00 0.00 4.73
414 415 2.032924 GTGCAACCGGGACTAAATATGC 59.967 50.000 6.32 2.60 34.56 3.14
415 416 3.275143 TGTGCAACCGGGACTAAATATG 58.725 45.455 6.32 0.00 38.87 1.78
416 417 3.541632 CTGTGCAACCGGGACTAAATAT 58.458 45.455 6.32 0.00 38.87 1.28
417 418 2.937873 GCTGTGCAACCGGGACTAAATA 60.938 50.000 6.32 0.00 38.87 1.40
418 419 1.821216 CTGTGCAACCGGGACTAAAT 58.179 50.000 6.32 0.00 38.87 1.40
419 420 0.887387 GCTGTGCAACCGGGACTAAA 60.887 55.000 6.32 0.00 38.87 1.85
420 421 1.302192 GCTGTGCAACCGGGACTAA 60.302 57.895 6.32 0.00 38.87 2.24
421 422 2.345991 GCTGTGCAACCGGGACTA 59.654 61.111 6.32 0.00 38.87 2.59
422 423 4.643387 GGCTGTGCAACCGGGACT 62.643 66.667 6.32 0.00 38.87 3.85
428 429 3.853698 TAACCCCGGCTGTGCAACC 62.854 63.158 0.00 0.00 34.36 3.77
429 430 1.248101 ATTAACCCCGGCTGTGCAAC 61.248 55.000 0.00 0.00 37.35 4.17
430 431 1.075836 ATTAACCCCGGCTGTGCAA 59.924 52.632 0.00 0.00 0.00 4.08
431 432 1.677300 CATTAACCCCGGCTGTGCA 60.677 57.895 0.00 0.00 0.00 4.57
432 433 2.414785 CCATTAACCCCGGCTGTGC 61.415 63.158 0.00 0.00 0.00 4.57
433 434 2.414785 GCCATTAACCCCGGCTGTG 61.415 63.158 0.00 0.00 42.78 3.66
434 435 2.044352 GCCATTAACCCCGGCTGT 60.044 61.111 0.00 0.00 42.78 4.40
435 436 2.833121 GGCCATTAACCCCGGCTG 60.833 66.667 0.00 0.00 45.50 4.85
436 437 2.163021 AAAGGCCATTAACCCCGGCT 62.163 55.000 5.01 0.00 45.50 5.52
437 438 1.684391 AAAGGCCATTAACCCCGGC 60.684 57.895 5.01 0.00 45.47 6.13
438 439 1.955495 GCAAAGGCCATTAACCCCGG 61.955 60.000 5.01 0.00 0.00 5.73
439 440 1.515487 GCAAAGGCCATTAACCCCG 59.485 57.895 5.01 0.00 0.00 5.73
440 441 0.968393 TCGCAAAGGCCATTAACCCC 60.968 55.000 5.01 0.00 36.38 4.95
441 442 0.892063 TTCGCAAAGGCCATTAACCC 59.108 50.000 5.01 0.00 36.38 4.11
442 443 1.403647 GGTTCGCAAAGGCCATTAACC 60.404 52.381 5.01 6.83 36.38 2.85
443 444 1.731098 CGGTTCGCAAAGGCCATTAAC 60.731 52.381 5.01 0.33 36.38 2.01
444 445 0.523966 CGGTTCGCAAAGGCCATTAA 59.476 50.000 5.01 0.00 36.38 1.40
445 446 1.309499 CCGGTTCGCAAAGGCCATTA 61.309 55.000 5.01 0.00 36.38 1.90
446 447 2.635443 CCGGTTCGCAAAGGCCATT 61.635 57.895 5.01 0.00 36.38 3.16
447 448 3.061848 CCGGTTCGCAAAGGCCAT 61.062 61.111 5.01 0.00 36.38 4.40
450 451 2.791501 TAGTCCCGGTTCGCAAAGGC 62.792 60.000 0.00 0.00 0.00 4.35
451 452 0.320946 TTAGTCCCGGTTCGCAAAGG 60.321 55.000 0.00 0.00 0.00 3.11
452 453 1.463444 CTTTAGTCCCGGTTCGCAAAG 59.537 52.381 0.00 5.06 0.00 2.77
453 454 1.515081 CTTTAGTCCCGGTTCGCAAA 58.485 50.000 0.00 0.00 0.00 3.68
454 455 0.320946 CCTTTAGTCCCGGTTCGCAA 60.321 55.000 0.00 0.00 0.00 4.85
455 456 1.294138 CCTTTAGTCCCGGTTCGCA 59.706 57.895 0.00 0.00 0.00 5.10
456 457 2.104859 GCCTTTAGTCCCGGTTCGC 61.105 63.158 0.00 0.00 0.00 4.70
457 458 0.107848 ATGCCTTTAGTCCCGGTTCG 60.108 55.000 0.00 0.00 0.00 3.95
458 459 2.994186 TATGCCTTTAGTCCCGGTTC 57.006 50.000 0.00 0.00 0.00 3.62
459 460 3.945640 AATATGCCTTTAGTCCCGGTT 57.054 42.857 0.00 0.00 0.00 4.44
460 461 3.945640 AAATATGCCTTTAGTCCCGGT 57.054 42.857 0.00 0.00 0.00 5.28
461 462 4.461198 AGAAAATATGCCTTTAGTCCCGG 58.539 43.478 0.00 0.00 0.00 5.73
462 463 6.289064 AGTAGAAAATATGCCTTTAGTCCCG 58.711 40.000 0.00 0.00 0.00 5.14
463 464 8.430431 ACTAGTAGAAAATATGCCTTTAGTCCC 58.570 37.037 3.59 0.00 0.00 4.46
464 465 9.262358 CACTAGTAGAAAATATGCCTTTAGTCC 57.738 37.037 3.59 0.00 0.00 3.85
465 466 9.262358 CCACTAGTAGAAAATATGCCTTTAGTC 57.738 37.037 3.59 0.00 0.00 2.59
466 467 8.211629 CCCACTAGTAGAAAATATGCCTTTAGT 58.788 37.037 3.59 0.00 0.00 2.24
467 468 8.429641 TCCCACTAGTAGAAAATATGCCTTTAG 58.570 37.037 3.59 0.00 0.00 1.85
468 469 8.326765 TCCCACTAGTAGAAAATATGCCTTTA 57.673 34.615 3.59 0.00 0.00 1.85
469 470 7.092399 ACTCCCACTAGTAGAAAATATGCCTTT 60.092 37.037 3.59 0.00 0.00 3.11
470 471 6.387220 ACTCCCACTAGTAGAAAATATGCCTT 59.613 38.462 3.59 0.00 0.00 4.35
471 472 5.905913 ACTCCCACTAGTAGAAAATATGCCT 59.094 40.000 3.59 0.00 0.00 4.75
472 473 6.176014 ACTCCCACTAGTAGAAAATATGCC 57.824 41.667 3.59 0.00 0.00 4.40
475 476 9.824216 TGCTATACTCCCACTAGTAGAAAATAT 57.176 33.333 3.59 0.00 35.50 1.28
476 477 9.075678 GTGCTATACTCCCACTAGTAGAAAATA 57.924 37.037 3.59 0.00 35.50 1.40
477 478 7.563924 TGTGCTATACTCCCACTAGTAGAAAAT 59.436 37.037 3.59 0.00 35.50 1.82
478 479 6.893554 TGTGCTATACTCCCACTAGTAGAAAA 59.106 38.462 3.59 0.00 35.50 2.29
479 480 6.429151 TGTGCTATACTCCCACTAGTAGAAA 58.571 40.000 3.59 0.00 35.50 2.52
480 481 6.009908 TGTGCTATACTCCCACTAGTAGAA 57.990 41.667 3.59 0.00 35.50 2.10
481 482 5.641789 TGTGCTATACTCCCACTAGTAGA 57.358 43.478 3.59 0.00 35.50 2.59
482 483 6.096423 TGTTTGTGCTATACTCCCACTAGTAG 59.904 42.308 0.00 0.00 35.50 2.57
483 484 5.953548 TGTTTGTGCTATACTCCCACTAGTA 59.046 40.000 0.00 0.00 36.44 1.82
484 485 4.775780 TGTTTGTGCTATACTCCCACTAGT 59.224 41.667 0.00 0.00 0.00 2.57
485 486 5.339008 TGTTTGTGCTATACTCCCACTAG 57.661 43.478 0.00 0.00 0.00 2.57
486 487 4.382685 GCTGTTTGTGCTATACTCCCACTA 60.383 45.833 0.00 0.00 0.00 2.74
487 488 3.619979 GCTGTTTGTGCTATACTCCCACT 60.620 47.826 0.00 0.00 0.00 4.00
488 489 2.678336 GCTGTTTGTGCTATACTCCCAC 59.322 50.000 0.00 0.00 0.00 4.61
489 490 2.304470 TGCTGTTTGTGCTATACTCCCA 59.696 45.455 0.00 0.00 0.00 4.37
3411 4040 1.630878 GCAAGGGGAGAAGAAGAAGGA 59.369 52.381 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.