Multiple sequence alignment - TraesCS7A01G370200

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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 TraesCS7A01G370200 chr7A 100.000 5046 0 0 731 5776 543436492 543441537 0.000000e+00 9319
1 TraesCS7A01G370200 chr7A 100.000 341 0 0 1 341 543435762 543436102 1.060000e-176 630
2 TraesCS7A01G370200 chr7D 95.265 3062 110 19 731 3783 454675968 454672933 0.000000e+00 4819
3 TraesCS7A01G370200 chr7D 94.530 1499 35 6 3756 5212 454672934 454671441 0.000000e+00 2270
4 TraesCS7A01G370200 chr7B 91.236 2419 154 29 1853 4251 478859990 478857610 0.000000e+00 3240
5 TraesCS7A01G370200 chr7B 93.510 832 31 9 4401 5210 478857442 478856612 0.000000e+00 1216
6 TraesCS7A01G370200 chr7B 91.856 835 57 5 731 1561 478861199 478860372 0.000000e+00 1155
7 TraesCS7A01G370200 chr7B 92.958 213 12 2 1643 1855 478860373 478860164 2.020000e-79 307
8 TraesCS7A01G370200 chr7B 86.667 270 35 1 1 269 478888433 478888164 1.220000e-76 298
9 TraesCS7A01G370200 chr7B 91.250 80 4 2 4283 4362 478857611 478857535 7.920000e-19 106
10 TraesCS7A01G370200 chr6A 96.283 565 17 4 5213 5776 453909376 453909937 0.000000e+00 924
11 TraesCS7A01G370200 chr6A 95.070 568 21 4 5210 5776 86403442 86402881 0.000000e+00 887
12 TraesCS7A01G370200 chr5A 95.812 573 18 5 5208 5776 466022639 466023209 0.000000e+00 920
13 TraesCS7A01G370200 chr5A 94.415 573 27 4 5204 5776 604718385 604717818 0.000000e+00 876
14 TraesCS7A01G370200 chr5A 89.437 142 13 2 2047 2187 365931856 365931996 1.650000e-40 178
15 TraesCS7A01G370200 chr5A 86.408 103 14 0 2416 2518 365932249 365932351 4.730000e-21 113
16 TraesCS7A01G370200 chr3A 95.752 565 20 3 5213 5776 714771464 714770903 0.000000e+00 907
17 TraesCS7A01G370200 chr2A 95.431 569 21 4 5211 5776 81079025 81078459 0.000000e+00 902
18 TraesCS7A01G370200 chr1A 95.221 565 21 4 5212 5776 301861407 301861965 0.000000e+00 889
19 TraesCS7A01G370200 chr1A 94.346 566 19 5 5213 5776 77108907 77108353 0.000000e+00 856
20 TraesCS7A01G370200 chr4A 94.336 565 25 4 5213 5776 176543986 176544544 0.000000e+00 859
21 TraesCS7A01G370200 chr5B 92.188 128 10 0 2060 2187 314957977 314958104 1.280000e-41 182
22 TraesCS7A01G370200 chr5B 87.379 103 13 0 2416 2518 314958356 314958458 1.020000e-22 119
23 TraesCS7A01G370200 chr5D 91.406 128 11 0 2060 2187 277069024 277069151 5.950000e-40 176
24 TraesCS7A01G370200 chr5D 77.253 233 38 11 2416 2639 277069403 277069629 7.860000e-24 122


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 TraesCS7A01G370200 chr7A 543435762 543441537 5775 False 4974.5 9319 100.0000 1 5776 2 chr7A.!!$F1 5775
1 TraesCS7A01G370200 chr7D 454671441 454675968 4527 True 3544.5 4819 94.8975 731 5212 2 chr7D.!!$R1 4481
2 TraesCS7A01G370200 chr7B 478856612 478861199 4587 True 1204.8 3240 92.1620 731 5210 5 chr7B.!!$R2 4479
3 TraesCS7A01G370200 chr6A 453909376 453909937 561 False 924.0 924 96.2830 5213 5776 1 chr6A.!!$F1 563
4 TraesCS7A01G370200 chr6A 86402881 86403442 561 True 887.0 887 95.0700 5210 5776 1 chr6A.!!$R1 566
5 TraesCS7A01G370200 chr5A 466022639 466023209 570 False 920.0 920 95.8120 5208 5776 1 chr5A.!!$F1 568
6 TraesCS7A01G370200 chr5A 604717818 604718385 567 True 876.0 876 94.4150 5204 5776 1 chr5A.!!$R1 572
7 TraesCS7A01G370200 chr3A 714770903 714771464 561 True 907.0 907 95.7520 5213 5776 1 chr3A.!!$R1 563
8 TraesCS7A01G370200 chr2A 81078459 81079025 566 True 902.0 902 95.4310 5211 5776 1 chr2A.!!$R1 565
9 TraesCS7A01G370200 chr1A 301861407 301861965 558 False 889.0 889 95.2210 5212 5776 1 chr1A.!!$F1 564
10 TraesCS7A01G370200 chr1A 77108353 77108907 554 True 856.0 856 94.3460 5213 5776 1 chr1A.!!$R1 563
11 TraesCS7A01G370200 chr4A 176543986 176544544 558 False 859.0 859 94.3360 5213 5776 1 chr4A.!!$F1 563

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
154 155 0.035820 AATAAAGAGGTTGGCGGCGA 60.036 50.000 12.98 0.00 0.00 5.54 F
207 208 0.037160 GTCGGCCCTAAGGGTTTTGA 59.963 55.000 0.00 0.00 46.51 2.69 F
1213 1214 0.318762 AAGAGCGGTGTCAGGAGAAC 59.681 55.000 0.00 0.00 0.00 3.01 F
1224 1225 2.093106 TCAGGAGAACGTAGCTCTTCC 58.907 52.381 15.37 7.05 30.56 3.46 F
1667 1674 2.764010 ACAACTGAAAAGTGGGTTTCCC 59.236 45.455 0.00 0.00 45.71 3.97 F
3421 3618 0.331278 CCTGGCCAAATCCACTACCA 59.669 55.000 7.01 0.00 31.74 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 1138 0.984961 TGGAGCAGGAGATTCTGGGG 60.985 60.000 0.00 0.00 35.43 4.96 R
1932 2117 1.990799 CGAGAACACGAGCACCATTA 58.009 50.000 0.00 0.00 35.09 1.90 R
3031 3228 0.603707 TTCGGCAGCTTCCTGTCAAG 60.604 55.000 0.00 0.00 43.92 3.02 R
3204 3401 5.010282 ACCTTCAAGCATAAAGTTAGGTGG 58.990 41.667 0.00 0.00 33.71 4.61 R
3502 3701 3.009473 AGTTGTATCACAGAGGTTGGCAT 59.991 43.478 0.00 0.00 0.00 4.40 R
5086 5390 0.583438 CTCATCCATACGGCGCAAAG 59.417 55.000 10.83 1.82 0.00 2.77 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
25 26 7.840931 AGAAATAATAGAGGTTTGGCTTTTGG 58.159 34.615 0.00 0.00 0.00 3.28
26 27 7.673926 AGAAATAATAGAGGTTTGGCTTTTGGA 59.326 33.333 0.00 0.00 0.00 3.53
27 28 7.978099 AATAATAGAGGTTTGGCTTTTGGAT 57.022 32.000 0.00 0.00 0.00 3.41
28 29 5.921962 AATAGAGGTTTGGCTTTTGGATC 57.078 39.130 0.00 0.00 0.00 3.36
29 30 2.529632 AGAGGTTTGGCTTTTGGATCC 58.470 47.619 4.20 4.20 0.00 3.36
30 31 2.158325 AGAGGTTTGGCTTTTGGATCCA 60.158 45.455 11.44 11.44 0.00 3.41
31 32 2.833943 GAGGTTTGGCTTTTGGATCCAT 59.166 45.455 17.06 0.00 0.00 3.41
32 33 2.568509 AGGTTTGGCTTTTGGATCCATG 59.431 45.455 17.06 10.23 0.00 3.66
33 34 2.355007 GGTTTGGCTTTTGGATCCATGG 60.355 50.000 17.06 4.97 0.00 3.66
34 35 0.903942 TTGGCTTTTGGATCCATGGC 59.096 50.000 17.06 19.93 0.00 4.40
35 36 0.041535 TGGCTTTTGGATCCATGGCT 59.958 50.000 25.44 0.00 0.00 4.75
36 37 0.749049 GGCTTTTGGATCCATGGCTC 59.251 55.000 17.06 7.02 0.00 4.70
37 38 1.687368 GGCTTTTGGATCCATGGCTCT 60.687 52.381 17.06 0.00 0.00 4.09
38 39 2.105766 GCTTTTGGATCCATGGCTCTT 58.894 47.619 17.06 0.00 0.00 2.85
39 40 2.100418 GCTTTTGGATCCATGGCTCTTC 59.900 50.000 17.06 5.56 0.00 2.87
40 41 3.629087 CTTTTGGATCCATGGCTCTTCT 58.371 45.455 17.06 0.00 0.00 2.85
41 42 2.723322 TTGGATCCATGGCTCTTCTG 57.277 50.000 17.06 0.00 0.00 3.02
42 43 0.182061 TGGATCCATGGCTCTTCTGC 59.818 55.000 11.44 0.00 0.00 4.26
50 51 3.184683 GCTCTTCTGCCAGCGACG 61.185 66.667 0.00 0.00 0.00 5.12
51 52 2.568612 CTCTTCTGCCAGCGACGA 59.431 61.111 0.00 0.00 0.00 4.20
52 53 1.140589 CTCTTCTGCCAGCGACGAT 59.859 57.895 0.00 0.00 0.00 3.73
53 54 0.459237 CTCTTCTGCCAGCGACGATT 60.459 55.000 0.00 0.00 0.00 3.34
54 55 0.037326 TCTTCTGCCAGCGACGATTT 60.037 50.000 0.00 0.00 0.00 2.17
55 56 0.371645 CTTCTGCCAGCGACGATTTC 59.628 55.000 0.00 0.00 0.00 2.17
56 57 0.037326 TTCTGCCAGCGACGATTTCT 60.037 50.000 0.00 0.00 0.00 2.52
57 58 0.037326 TCTGCCAGCGACGATTTCTT 60.037 50.000 0.00 0.00 0.00 2.52
58 59 1.203758 TCTGCCAGCGACGATTTCTTA 59.796 47.619 0.00 0.00 0.00 2.10
59 60 2.159099 TCTGCCAGCGACGATTTCTTAT 60.159 45.455 0.00 0.00 0.00 1.73
60 61 2.201732 TGCCAGCGACGATTTCTTATC 58.798 47.619 0.00 0.00 0.00 1.75
61 62 2.159099 TGCCAGCGACGATTTCTTATCT 60.159 45.455 0.00 0.00 0.00 1.98
62 63 3.067601 TGCCAGCGACGATTTCTTATCTA 59.932 43.478 0.00 0.00 0.00 1.98
63 64 3.670991 GCCAGCGACGATTTCTTATCTAG 59.329 47.826 0.00 0.00 0.00 2.43
64 65 4.230657 CCAGCGACGATTTCTTATCTAGG 58.769 47.826 0.00 0.00 0.00 3.02
65 66 4.261656 CCAGCGACGATTTCTTATCTAGGT 60.262 45.833 0.00 0.00 0.00 3.08
66 67 4.677378 CAGCGACGATTTCTTATCTAGGTG 59.323 45.833 0.00 0.00 0.00 4.00
67 68 4.338682 AGCGACGATTTCTTATCTAGGTGT 59.661 41.667 0.00 0.00 0.00 4.16
68 69 5.041940 GCGACGATTTCTTATCTAGGTGTT 58.958 41.667 0.00 0.00 0.00 3.32
69 70 5.051641 GCGACGATTTCTTATCTAGGTGTTG 60.052 44.000 0.00 0.00 0.00 3.33
70 71 5.459107 CGACGATTTCTTATCTAGGTGTTGG 59.541 44.000 0.00 0.00 0.00 3.77
71 72 6.295719 ACGATTTCTTATCTAGGTGTTGGT 57.704 37.500 0.00 0.00 0.00 3.67
72 73 6.338937 ACGATTTCTTATCTAGGTGTTGGTC 58.661 40.000 0.00 0.00 0.00 4.02
73 74 5.753921 CGATTTCTTATCTAGGTGTTGGTCC 59.246 44.000 0.00 0.00 0.00 4.46
74 75 4.730949 TTCTTATCTAGGTGTTGGTCCG 57.269 45.455 0.00 0.00 0.00 4.79
75 76 3.028850 TCTTATCTAGGTGTTGGTCCGG 58.971 50.000 0.00 0.00 0.00 5.14
76 77 2.537633 TATCTAGGTGTTGGTCCGGT 57.462 50.000 0.00 0.00 0.00 5.28
77 78 2.537633 ATCTAGGTGTTGGTCCGGTA 57.462 50.000 0.00 0.00 0.00 4.02
78 79 1.843368 TCTAGGTGTTGGTCCGGTAG 58.157 55.000 0.00 0.00 0.00 3.18
79 80 0.822164 CTAGGTGTTGGTCCGGTAGG 59.178 60.000 0.00 0.00 39.46 3.18
80 81 0.409092 TAGGTGTTGGTCCGGTAGGA 59.591 55.000 0.00 0.00 46.11 2.94
88 89 2.443781 TCCGGTAGGACTGTGGCT 59.556 61.111 0.00 0.00 42.75 4.75
89 90 1.229082 TCCGGTAGGACTGTGGCTT 60.229 57.895 0.00 0.00 42.75 4.35
90 91 0.834687 TCCGGTAGGACTGTGGCTTT 60.835 55.000 0.00 0.00 42.75 3.51
91 92 0.673644 CCGGTAGGACTGTGGCTTTG 60.674 60.000 0.00 0.00 41.02 2.77
92 93 0.320374 CGGTAGGACTGTGGCTTTGA 59.680 55.000 0.00 0.00 0.00 2.69
93 94 1.066143 CGGTAGGACTGTGGCTTTGAT 60.066 52.381 0.00 0.00 0.00 2.57
94 95 2.359900 GGTAGGACTGTGGCTTTGATG 58.640 52.381 0.00 0.00 0.00 3.07
95 96 2.027192 GGTAGGACTGTGGCTTTGATGA 60.027 50.000 0.00 0.00 0.00 2.92
96 97 2.191128 AGGACTGTGGCTTTGATGAC 57.809 50.000 0.00 0.00 0.00 3.06
97 98 1.701847 AGGACTGTGGCTTTGATGACT 59.298 47.619 0.00 0.00 0.00 3.41
98 99 2.107204 AGGACTGTGGCTTTGATGACTT 59.893 45.455 0.00 0.00 0.00 3.01
99 100 3.327757 AGGACTGTGGCTTTGATGACTTA 59.672 43.478 0.00 0.00 0.00 2.24
100 101 4.018960 AGGACTGTGGCTTTGATGACTTAT 60.019 41.667 0.00 0.00 0.00 1.73
101 102 4.333926 GGACTGTGGCTTTGATGACTTATC 59.666 45.833 0.00 0.00 36.29 1.75
102 103 4.910195 ACTGTGGCTTTGATGACTTATCA 58.090 39.130 0.00 0.00 43.92 2.15
115 116 5.337578 TGACTTATCATCCACGATCAACA 57.662 39.130 0.00 0.00 0.00 3.33
116 117 5.729510 TGACTTATCATCCACGATCAACAA 58.270 37.500 0.00 0.00 0.00 2.83
117 118 5.580691 TGACTTATCATCCACGATCAACAAC 59.419 40.000 0.00 0.00 0.00 3.32
118 119 4.566759 ACTTATCATCCACGATCAACAACG 59.433 41.667 0.00 0.00 0.00 4.10
119 120 2.734276 TCATCCACGATCAACAACGA 57.266 45.000 0.00 0.00 0.00 3.85
120 121 3.033368 TCATCCACGATCAACAACGAA 57.967 42.857 0.00 0.00 0.00 3.85
121 122 3.394719 TCATCCACGATCAACAACGAAA 58.605 40.909 0.00 0.00 0.00 3.46
122 123 3.810386 TCATCCACGATCAACAACGAAAA 59.190 39.130 0.00 0.00 0.00 2.29
123 124 3.595709 TCCACGATCAACAACGAAAAC 57.404 42.857 0.00 0.00 0.00 2.43
124 125 2.288458 TCCACGATCAACAACGAAAACC 59.712 45.455 0.00 0.00 0.00 3.27
125 126 2.603652 CCACGATCAACAACGAAAACCC 60.604 50.000 0.00 0.00 0.00 4.11
126 127 1.262151 ACGATCAACAACGAAAACCCG 59.738 47.619 0.00 0.00 0.00 5.28
127 128 1.527736 CGATCAACAACGAAAACCCGA 59.472 47.619 0.00 0.00 0.00 5.14
128 129 2.660900 CGATCAACAACGAAAACCCGAC 60.661 50.000 0.00 0.00 0.00 4.79
129 130 2.027003 TCAACAACGAAAACCCGACT 57.973 45.000 0.00 0.00 0.00 4.18
130 131 2.358015 TCAACAACGAAAACCCGACTT 58.642 42.857 0.00 0.00 0.00 3.01
131 132 2.748532 TCAACAACGAAAACCCGACTTT 59.251 40.909 0.00 0.00 0.00 2.66
132 133 2.836479 ACAACGAAAACCCGACTTTG 57.164 45.000 0.00 0.00 0.00 2.77
133 134 1.402613 ACAACGAAAACCCGACTTTGG 59.597 47.619 0.00 0.00 0.00 3.28
134 135 0.382873 AACGAAAACCCGACTTTGGC 59.617 50.000 0.00 0.00 0.00 4.52
135 136 0.748729 ACGAAAACCCGACTTTGGCA 60.749 50.000 0.00 0.00 0.00 4.92
136 137 0.382515 CGAAAACCCGACTTTGGCAA 59.617 50.000 0.00 0.00 0.00 4.52
137 138 1.000717 CGAAAACCCGACTTTGGCAAT 60.001 47.619 0.00 0.00 0.00 3.56
138 139 2.226912 CGAAAACCCGACTTTGGCAATA 59.773 45.455 0.00 0.00 0.00 1.90
139 140 3.304794 CGAAAACCCGACTTTGGCAATAA 60.305 43.478 0.00 0.00 0.00 1.40
140 141 4.623002 GAAAACCCGACTTTGGCAATAAA 58.377 39.130 0.00 0.00 0.00 1.40
141 142 3.934457 AACCCGACTTTGGCAATAAAG 57.066 42.857 0.00 0.00 42.09 1.85
142 143 3.149005 ACCCGACTTTGGCAATAAAGA 57.851 42.857 0.00 0.00 39.46 2.52
143 144 3.081804 ACCCGACTTTGGCAATAAAGAG 58.918 45.455 0.00 0.00 39.46 2.85
144 145 2.423538 CCCGACTTTGGCAATAAAGAGG 59.576 50.000 0.00 5.39 39.46 3.69
145 146 3.081804 CCGACTTTGGCAATAAAGAGGT 58.918 45.455 0.00 0.00 39.46 3.85
146 147 3.506067 CCGACTTTGGCAATAAAGAGGTT 59.494 43.478 0.00 0.00 39.46 3.50
147 148 4.475944 CGACTTTGGCAATAAAGAGGTTG 58.524 43.478 0.00 0.00 39.46 3.77
148 149 4.615912 CGACTTTGGCAATAAAGAGGTTGG 60.616 45.833 0.00 0.00 39.46 3.77
151 152 0.455815 GGCAATAAAGAGGTTGGCGG 59.544 55.000 0.00 0.00 40.34 6.13
152 153 0.179137 GCAATAAAGAGGTTGGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
153 154 0.098728 CAATAAAGAGGTTGGCGGCG 59.901 55.000 0.51 0.51 0.00 6.46
154 155 0.035820 AATAAAGAGGTTGGCGGCGA 60.036 50.000 12.98 0.00 0.00 5.54
155 156 0.743345 ATAAAGAGGTTGGCGGCGAC 60.743 55.000 20.72 20.72 0.00 5.19
156 157 2.102109 TAAAGAGGTTGGCGGCGACA 62.102 55.000 28.49 13.60 0.00 4.35
157 158 4.681978 AGAGGTTGGCGGCGACAC 62.682 66.667 28.49 20.96 0.00 3.67
158 159 4.980805 GAGGTTGGCGGCGACACA 62.981 66.667 28.49 3.76 0.00 3.72
162 163 4.634703 TTGGCGGCGACACACCAT 62.635 61.111 18.66 0.00 30.85 3.55
164 165 4.760047 GGCGGCGACACACCATCT 62.760 66.667 12.98 0.00 0.00 2.90
165 166 2.183300 GCGGCGACACACCATCTA 59.817 61.111 12.98 0.00 0.00 1.98
166 167 2.165301 GCGGCGACACACCATCTAC 61.165 63.158 12.98 0.00 0.00 2.59
167 168 1.518572 CGGCGACACACCATCTACC 60.519 63.158 0.00 0.00 0.00 3.18
168 169 1.898154 GGCGACACACCATCTACCT 59.102 57.895 0.00 0.00 0.00 3.08
169 170 0.460284 GGCGACACACCATCTACCTG 60.460 60.000 0.00 0.00 0.00 4.00
170 171 0.246635 GCGACACACCATCTACCTGT 59.753 55.000 0.00 0.00 0.00 4.00
171 172 1.337823 GCGACACACCATCTACCTGTT 60.338 52.381 0.00 0.00 0.00 3.16
172 173 2.607187 CGACACACCATCTACCTGTTC 58.393 52.381 0.00 0.00 0.00 3.18
173 174 2.607187 GACACACCATCTACCTGTTCG 58.393 52.381 0.00 0.00 0.00 3.95
174 175 1.275291 ACACACCATCTACCTGTTCGG 59.725 52.381 0.00 0.00 39.35 4.30
175 176 0.902531 ACACCATCTACCTGTTCGGG 59.097 55.000 0.00 0.00 36.97 5.14
176 177 1.191535 CACCATCTACCTGTTCGGGA 58.808 55.000 4.54 0.00 36.97 5.14
177 178 1.137086 CACCATCTACCTGTTCGGGAG 59.863 57.143 4.54 0.00 46.13 4.30
191 192 1.476891 TCGGGAGAAAGAAGATGGTCG 59.523 52.381 0.00 0.00 34.75 4.79
192 193 1.471676 CGGGAGAAAGAAGATGGTCGG 60.472 57.143 0.00 0.00 0.00 4.79
193 194 1.657822 GGAGAAAGAAGATGGTCGGC 58.342 55.000 0.00 0.00 0.00 5.54
194 195 1.657822 GAGAAAGAAGATGGTCGGCC 58.342 55.000 0.00 0.00 0.00 6.13
195 196 0.253327 AGAAAGAAGATGGTCGGCCC 59.747 55.000 2.12 0.00 0.00 5.80
196 197 0.253327 GAAAGAAGATGGTCGGCCCT 59.747 55.000 2.12 0.00 0.00 5.19
197 198 1.485066 GAAAGAAGATGGTCGGCCCTA 59.515 52.381 2.12 0.00 0.00 3.53
198 199 1.580059 AAGAAGATGGTCGGCCCTAA 58.420 50.000 2.12 0.00 0.00 2.69
199 200 1.123928 AGAAGATGGTCGGCCCTAAG 58.876 55.000 2.12 0.00 0.00 2.18
200 201 0.106894 GAAGATGGTCGGCCCTAAGG 59.893 60.000 2.12 0.00 0.00 2.69
202 203 2.042261 ATGGTCGGCCCTAAGGGT 59.958 61.111 2.12 0.00 46.51 4.34
203 204 1.618447 ATGGTCGGCCCTAAGGGTT 60.618 57.895 2.12 0.00 46.51 4.11
204 205 1.212250 ATGGTCGGCCCTAAGGGTTT 61.212 55.000 2.12 0.00 46.51 3.27
205 206 1.381463 GGTCGGCCCTAAGGGTTTT 59.619 57.895 0.00 0.00 46.51 2.43
206 207 0.963856 GGTCGGCCCTAAGGGTTTTG 60.964 60.000 0.00 0.00 46.51 2.44
207 208 0.037160 GTCGGCCCTAAGGGTTTTGA 59.963 55.000 0.00 0.00 46.51 2.69
208 209 0.996583 TCGGCCCTAAGGGTTTTGAT 59.003 50.000 0.00 0.00 46.51 2.57
209 210 1.102978 CGGCCCTAAGGGTTTTGATG 58.897 55.000 0.00 0.00 46.51 3.07
210 211 1.615919 CGGCCCTAAGGGTTTTGATGT 60.616 52.381 0.00 0.00 46.51 3.06
211 212 2.356330 CGGCCCTAAGGGTTTTGATGTA 60.356 50.000 0.00 0.00 46.51 2.29
212 213 3.703921 GGCCCTAAGGGTTTTGATGTAA 58.296 45.455 0.00 0.00 46.51 2.41
213 214 4.286707 GGCCCTAAGGGTTTTGATGTAAT 58.713 43.478 0.00 0.00 46.51 1.89
214 215 5.451354 GGCCCTAAGGGTTTTGATGTAATA 58.549 41.667 0.00 0.00 46.51 0.98
215 216 6.075315 GGCCCTAAGGGTTTTGATGTAATAT 58.925 40.000 0.00 0.00 46.51 1.28
216 217 6.553476 GGCCCTAAGGGTTTTGATGTAATATT 59.447 38.462 0.00 0.00 46.51 1.28
217 218 7.070696 GGCCCTAAGGGTTTTGATGTAATATTT 59.929 37.037 0.00 0.00 46.51 1.40
218 219 8.482943 GCCCTAAGGGTTTTGATGTAATATTTT 58.517 33.333 0.00 0.00 46.51 1.82
246 247 7.575414 TTCATATTGTGTTTGTACTGTTGGT 57.425 32.000 0.00 0.00 0.00 3.67
247 248 7.575414 TCATATTGTGTTTGTACTGTTGGTT 57.425 32.000 0.00 0.00 0.00 3.67
248 249 8.001881 TCATATTGTGTTTGTACTGTTGGTTT 57.998 30.769 0.00 0.00 0.00 3.27
249 250 8.132362 TCATATTGTGTTTGTACTGTTGGTTTC 58.868 33.333 0.00 0.00 0.00 2.78
250 251 4.343811 TGTGTTTGTACTGTTGGTTTCG 57.656 40.909 0.00 0.00 0.00 3.46
251 252 3.752222 TGTGTTTGTACTGTTGGTTTCGT 59.248 39.130 0.00 0.00 0.00 3.85
252 253 4.215827 TGTGTTTGTACTGTTGGTTTCGTT 59.784 37.500 0.00 0.00 0.00 3.85
253 254 5.410746 TGTGTTTGTACTGTTGGTTTCGTTA 59.589 36.000 0.00 0.00 0.00 3.18
254 255 6.072838 TGTGTTTGTACTGTTGGTTTCGTTAA 60.073 34.615 0.00 0.00 0.00 2.01
255 256 6.968335 GTGTTTGTACTGTTGGTTTCGTTAAT 59.032 34.615 0.00 0.00 0.00 1.40
256 257 8.121708 GTGTTTGTACTGTTGGTTTCGTTAATA 58.878 33.333 0.00 0.00 0.00 0.98
257 258 8.336806 TGTTTGTACTGTTGGTTTCGTTAATAG 58.663 33.333 0.00 0.00 0.00 1.73
258 259 8.550376 GTTTGTACTGTTGGTTTCGTTAATAGA 58.450 33.333 0.00 0.00 0.00 1.98
259 260 8.836268 TTGTACTGTTGGTTTCGTTAATAGAT 57.164 30.769 0.00 0.00 0.00 1.98
260 261 8.836268 TGTACTGTTGGTTTCGTTAATAGATT 57.164 30.769 0.00 0.00 0.00 2.40
261 262 9.275398 TGTACTGTTGGTTTCGTTAATAGATTT 57.725 29.630 0.00 0.00 0.00 2.17
264 265 8.943002 ACTGTTGGTTTCGTTAATAGATTTAGG 58.057 33.333 0.00 0.00 0.00 2.69
265 266 8.851541 TGTTGGTTTCGTTAATAGATTTAGGT 57.148 30.769 0.00 0.00 0.00 3.08
266 267 9.287373 TGTTGGTTTCGTTAATAGATTTAGGTT 57.713 29.630 0.00 0.00 0.00 3.50
328 329 3.753294 TTTTTGTGTGGGTGTGTGTTT 57.247 38.095 0.00 0.00 0.00 2.83
329 330 4.866508 TTTTTGTGTGGGTGTGTGTTTA 57.133 36.364 0.00 0.00 0.00 2.01
330 331 4.442375 TTTTGTGTGGGTGTGTGTTTAG 57.558 40.909 0.00 0.00 0.00 1.85
331 332 2.045561 TGTGTGGGTGTGTGTTTAGG 57.954 50.000 0.00 0.00 0.00 2.69
332 333 1.314730 GTGTGGGTGTGTGTTTAGGG 58.685 55.000 0.00 0.00 0.00 3.53
333 334 0.920438 TGTGGGTGTGTGTTTAGGGT 59.080 50.000 0.00 0.00 0.00 4.34
334 335 1.314730 GTGGGTGTGTGTTTAGGGTG 58.685 55.000 0.00 0.00 0.00 4.61
335 336 1.134037 GTGGGTGTGTGTTTAGGGTGA 60.134 52.381 0.00 0.00 0.00 4.02
336 337 1.142060 TGGGTGTGTGTTTAGGGTGAG 59.858 52.381 0.00 0.00 0.00 3.51
337 338 1.142262 GGGTGTGTGTTTAGGGTGAGT 59.858 52.381 0.00 0.00 0.00 3.41
338 339 2.218603 GGTGTGTGTTTAGGGTGAGTG 58.781 52.381 0.00 0.00 0.00 3.51
339 340 2.420967 GGTGTGTGTTTAGGGTGAGTGT 60.421 50.000 0.00 0.00 0.00 3.55
340 341 2.870411 GTGTGTGTTTAGGGTGAGTGTC 59.130 50.000 0.00 0.00 0.00 3.67
989 990 1.811679 GAACAGGCTCGTAGCTGCC 60.812 63.158 4.64 4.64 44.56 4.85
1213 1214 0.318762 AAGAGCGGTGTCAGGAGAAC 59.681 55.000 0.00 0.00 0.00 3.01
1224 1225 2.093106 TCAGGAGAACGTAGCTCTTCC 58.907 52.381 15.37 7.05 30.56 3.46
1305 1306 8.318412 TCTGGTACTTCTATGCATGTAAAGAAA 58.682 33.333 10.16 0.00 0.00 2.52
1337 1338 4.730600 TTCGACATCACATCTTGTTGTG 57.269 40.909 5.69 5.69 46.70 3.33
1432 1433 5.611374 TCACCTTTTAGTATATGCTGCTCC 58.389 41.667 3.24 0.00 0.00 4.70
1434 1435 4.202472 ACCTTTTAGTATATGCTGCTCCCC 60.202 45.833 3.24 0.00 0.00 4.81
1440 1441 4.493618 AGTATATGCTGCTCCCCTTTCTA 58.506 43.478 0.00 0.00 0.00 2.10
1446 1447 2.814097 GCTGCTCCCCTTTCTAAACACA 60.814 50.000 0.00 0.00 0.00 3.72
1527 1532 4.273148 AGTTTATGACGCATAGGGGATC 57.727 45.455 0.00 0.00 0.00 3.36
1560 1565 4.566987 ACTTTGGAGTTTAGCGACTTAGG 58.433 43.478 0.00 0.00 29.87 2.69
1565 1570 3.305881 GGAGTTTAGCGACTTAGGTGTGT 60.306 47.826 0.00 0.00 0.00 3.72
1568 1573 3.476295 TTAGCGACTTAGGTGTGTACG 57.524 47.619 0.00 0.00 0.00 3.67
1621 1627 5.531122 TTCGTTATAGTCCTGATTCCTGG 57.469 43.478 0.00 0.00 0.00 4.45
1667 1674 2.764010 ACAACTGAAAAGTGGGTTTCCC 59.236 45.455 0.00 0.00 45.71 3.97
1700 1707 5.396750 TTTTATCGCTTGTTTGCCAAAAC 57.603 34.783 0.00 0.00 45.00 2.43
1713 1720 3.516615 TGCCAAAACGGTGAAAAAGAAG 58.483 40.909 0.00 0.00 36.97 2.85
1745 1752 6.094048 TGCTCTAAATCACATTACCTGAAAGC 59.906 38.462 0.00 0.00 0.00 3.51
1943 2128 6.586463 AGATTACGAATATGTAATGGTGCTCG 59.414 38.462 4.04 0.00 43.28 5.03
2225 2415 4.589216 TTCTGGAAGCTTTTGTTGATGG 57.411 40.909 0.00 0.00 0.00 3.51
2391 2581 8.893727 GCACCACATATTTCTAAACACTTATCT 58.106 33.333 0.00 0.00 0.00 1.98
2487 2677 4.443881 CCACTGGATGCTGTCTATGATTCA 60.444 45.833 0.00 0.00 0.00 2.57
2549 2739 6.809196 TGTGTATGTCCTTGTTTGTTTTTCAC 59.191 34.615 0.00 0.00 0.00 3.18
2715 2905 8.604640 TTCAAAACAACATCATGCACAATATT 57.395 26.923 0.00 0.00 0.00 1.28
2716 2906 8.019769 TCAAAACAACATCATGCACAATATTG 57.980 30.769 14.01 14.01 0.00 1.90
2717 2907 7.656542 TCAAAACAACATCATGCACAATATTGT 59.343 29.630 15.47 15.47 43.36 2.71
2718 2908 7.966246 AAACAACATCATGCACAATATTGTT 57.034 28.000 18.50 11.71 39.91 2.83
2719 2909 9.486497 AAAACAACATCATGCACAATATTGTTA 57.514 25.926 18.50 11.05 39.91 2.41
2720 2910 9.656040 AAACAACATCATGCACAATATTGTTAT 57.344 25.926 18.50 12.76 39.91 1.89
2721 2911 8.637281 ACAACATCATGCACAATATTGTTATG 57.363 30.769 23.99 23.99 39.91 1.90
2870 3061 3.495331 TGAGGTGGTAACGGTAGTAACA 58.505 45.455 0.00 0.00 42.51 2.41
2906 3102 4.819105 TTAGTGGTAGGTCATCCTTGTG 57.181 45.455 0.00 0.00 42.12 3.33
2925 3122 7.404688 TCCTTGTGGCAATATATATTAGCCCTA 59.595 37.037 27.80 20.18 38.22 3.53
3031 3228 8.930760 GTTGGACTAATATATGAATCTGCTCAC 58.069 37.037 0.00 0.00 0.00 3.51
3157 3354 3.489908 ACATTTATGTTTGCACACGCACA 60.490 39.130 0.00 0.00 39.93 4.57
3204 3401 4.893424 TGTAGCACCTTCACTGAAAAAC 57.107 40.909 0.00 0.00 0.00 2.43
3421 3618 0.331278 CCTGGCCAAATCCACTACCA 59.669 55.000 7.01 0.00 31.74 3.25
3502 3701 6.183360 CCTTCTAGCATGAATCTCAATGCAAA 60.183 38.462 10.00 1.52 42.06 3.68
3592 3791 0.883833 ACCTTCTTTTCCTGCATGCG 59.116 50.000 14.09 7.87 0.00 4.73
3746 3947 6.748132 TCTGCCCAGCTTAATAAAATAATGC 58.252 36.000 0.00 0.00 0.00 3.56
3783 4012 7.885399 AGAACCTCATAGCCATTATATTTCACC 59.115 37.037 0.00 0.00 0.00 4.02
4574 4857 5.106277 CCGACTCCTTCCCTTGTTTTATTTC 60.106 44.000 0.00 0.00 0.00 2.17
4576 4859 5.711698 ACTCCTTCCCTTGTTTTATTTCCA 58.288 37.500 0.00 0.00 0.00 3.53
4811 5095 3.275999 CCTATTTTTCCCGATTCACCGT 58.724 45.455 0.00 0.00 0.00 4.83
5080 5384 5.338632 TGGATGGTTGGGATCGTACTATAT 58.661 41.667 0.00 0.00 0.00 0.86
5086 5390 6.377429 TGGTTGGGATCGTACTATATGAGATC 59.623 42.308 0.00 0.00 37.55 2.75
5162 5474 5.523916 GCTCTCTTGAACTCTGTTTTGTACA 59.476 40.000 0.00 0.00 34.95 2.90
5184 5496 6.957631 ACATGTACTGATTGGGTTAGATCAA 58.042 36.000 0.00 0.00 32.33 2.57
5310 5622 4.532834 TGCAACCTCCAACTCTTAAAACT 58.467 39.130 0.00 0.00 0.00 2.66
5328 5640 2.407562 ACTGGCCAAAATTCAACCCTT 58.592 42.857 7.01 0.00 0.00 3.95
5333 5645 2.371841 GCCAAAATTCAACCCTTCCCTT 59.628 45.455 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.673926 TCCAAAAGCCAAACCTCTATTATTTCT 59.326 33.333 0.00 0.00 0.00 2.52
1 2 7.836842 TCCAAAAGCCAAACCTCTATTATTTC 58.163 34.615 0.00 0.00 0.00 2.17
5 6 5.891551 GGATCCAAAAGCCAAACCTCTATTA 59.108 40.000 6.95 0.00 0.00 0.98
6 7 4.711846 GGATCCAAAAGCCAAACCTCTATT 59.288 41.667 6.95 0.00 0.00 1.73
7 8 4.264352 TGGATCCAAAAGCCAAACCTCTAT 60.264 41.667 13.46 0.00 0.00 1.98
8 9 3.075283 TGGATCCAAAAGCCAAACCTCTA 59.925 43.478 13.46 0.00 0.00 2.43
9 10 2.158325 TGGATCCAAAAGCCAAACCTCT 60.158 45.455 13.46 0.00 0.00 3.69
10 11 2.247358 TGGATCCAAAAGCCAAACCTC 58.753 47.619 13.46 0.00 0.00 3.85
11 12 2.397044 TGGATCCAAAAGCCAAACCT 57.603 45.000 13.46 0.00 0.00 3.50
12 13 2.355007 CCATGGATCCAAAAGCCAAACC 60.355 50.000 20.67 0.00 34.95 3.27
13 14 2.936553 GCCATGGATCCAAAAGCCAAAC 60.937 50.000 20.67 0.00 34.95 2.93
14 15 1.278699 GCCATGGATCCAAAAGCCAAA 59.721 47.619 20.67 0.00 34.95 3.28
15 16 0.903942 GCCATGGATCCAAAAGCCAA 59.096 50.000 20.67 0.00 34.95 4.52
16 17 0.041535 AGCCATGGATCCAAAAGCCA 59.958 50.000 20.67 0.00 35.91 4.75
17 18 0.749049 GAGCCATGGATCCAAAAGCC 59.251 55.000 20.67 11.60 0.00 4.35
18 19 1.772836 AGAGCCATGGATCCAAAAGC 58.227 50.000 26.11 20.69 0.00 3.51
19 20 3.380637 CAGAAGAGCCATGGATCCAAAAG 59.619 47.826 26.11 11.50 0.00 2.27
20 21 3.359033 CAGAAGAGCCATGGATCCAAAA 58.641 45.455 26.11 0.00 0.00 2.44
21 22 2.947243 GCAGAAGAGCCATGGATCCAAA 60.947 50.000 26.11 0.00 0.00 3.28
22 23 1.409241 GCAGAAGAGCCATGGATCCAA 60.409 52.381 26.11 1.96 0.00 3.53
23 24 0.182061 GCAGAAGAGCCATGGATCCA 59.818 55.000 26.11 18.88 0.00 3.41
24 25 3.018479 GCAGAAGAGCCATGGATCC 57.982 57.895 26.11 12.13 0.00 3.36
33 34 2.897641 ATCGTCGCTGGCAGAAGAGC 62.898 60.000 20.86 1.38 30.40 4.09
34 35 0.459237 AATCGTCGCTGGCAGAAGAG 60.459 55.000 20.86 6.41 30.40 2.85
35 36 0.037326 AAATCGTCGCTGGCAGAAGA 60.037 50.000 20.86 13.83 0.00 2.87
36 37 0.371645 GAAATCGTCGCTGGCAGAAG 59.628 55.000 20.86 11.47 0.00 2.85
37 38 0.037326 AGAAATCGTCGCTGGCAGAA 60.037 50.000 20.86 1.66 0.00 3.02
38 39 0.037326 AAGAAATCGTCGCTGGCAGA 60.037 50.000 20.86 0.00 0.00 4.26
39 40 1.640428 TAAGAAATCGTCGCTGGCAG 58.360 50.000 10.94 10.94 0.00 4.85
40 41 2.159099 AGATAAGAAATCGTCGCTGGCA 60.159 45.455 0.00 0.00 0.00 4.92
41 42 2.474816 AGATAAGAAATCGTCGCTGGC 58.525 47.619 0.00 0.00 0.00 4.85
42 43 4.230657 CCTAGATAAGAAATCGTCGCTGG 58.769 47.826 0.00 0.00 0.00 4.85
43 44 4.677378 CACCTAGATAAGAAATCGTCGCTG 59.323 45.833 0.00 0.00 0.00 5.18
44 45 4.338682 ACACCTAGATAAGAAATCGTCGCT 59.661 41.667 0.00 0.00 0.00 4.93
45 46 4.608951 ACACCTAGATAAGAAATCGTCGC 58.391 43.478 0.00 0.00 0.00 5.19
46 47 5.459107 CCAACACCTAGATAAGAAATCGTCG 59.541 44.000 0.00 0.00 0.00 5.12
47 48 6.338937 ACCAACACCTAGATAAGAAATCGTC 58.661 40.000 0.00 0.00 0.00 4.20
48 49 6.295719 ACCAACACCTAGATAAGAAATCGT 57.704 37.500 0.00 0.00 0.00 3.73
49 50 5.753921 GGACCAACACCTAGATAAGAAATCG 59.246 44.000 0.00 0.00 0.00 3.34
50 51 5.753921 CGGACCAACACCTAGATAAGAAATC 59.246 44.000 0.00 0.00 0.00 2.17
51 52 5.396436 CCGGACCAACACCTAGATAAGAAAT 60.396 44.000 0.00 0.00 0.00 2.17
52 53 4.081309 CCGGACCAACACCTAGATAAGAAA 60.081 45.833 0.00 0.00 0.00 2.52
53 54 3.449737 CCGGACCAACACCTAGATAAGAA 59.550 47.826 0.00 0.00 0.00 2.52
54 55 3.028850 CCGGACCAACACCTAGATAAGA 58.971 50.000 0.00 0.00 0.00 2.10
55 56 2.764572 ACCGGACCAACACCTAGATAAG 59.235 50.000 9.46 0.00 0.00 1.73
56 57 2.823959 ACCGGACCAACACCTAGATAA 58.176 47.619 9.46 0.00 0.00 1.75
57 58 2.537633 ACCGGACCAACACCTAGATA 57.462 50.000 9.46 0.00 0.00 1.98
58 59 2.385803 CTACCGGACCAACACCTAGAT 58.614 52.381 9.46 0.00 0.00 1.98
59 60 1.617804 CCTACCGGACCAACACCTAGA 60.618 57.143 9.46 0.00 0.00 2.43
60 61 0.822164 CCTACCGGACCAACACCTAG 59.178 60.000 9.46 0.00 0.00 3.02
61 62 0.409092 TCCTACCGGACCAACACCTA 59.591 55.000 9.46 0.00 33.30 3.08
62 63 1.156803 TCCTACCGGACCAACACCT 59.843 57.895 9.46 0.00 33.30 4.00
63 64 3.795905 TCCTACCGGACCAACACC 58.204 61.111 9.46 0.00 33.30 4.16
71 72 0.834687 AAAGCCACAGTCCTACCGGA 60.835 55.000 9.46 0.00 36.83 5.14
72 73 0.673644 CAAAGCCACAGTCCTACCGG 60.674 60.000 0.00 0.00 0.00 5.28
73 74 0.320374 TCAAAGCCACAGTCCTACCG 59.680 55.000 0.00 0.00 0.00 4.02
74 75 2.027192 TCATCAAAGCCACAGTCCTACC 60.027 50.000 0.00 0.00 0.00 3.18
75 76 3.003480 GTCATCAAAGCCACAGTCCTAC 58.997 50.000 0.00 0.00 0.00 3.18
76 77 2.906389 AGTCATCAAAGCCACAGTCCTA 59.094 45.455 0.00 0.00 0.00 2.94
77 78 1.701847 AGTCATCAAAGCCACAGTCCT 59.298 47.619 0.00 0.00 0.00 3.85
78 79 2.191128 AGTCATCAAAGCCACAGTCC 57.809 50.000 0.00 0.00 0.00 3.85
79 80 4.937620 TGATAAGTCATCAAAGCCACAGTC 59.062 41.667 0.00 0.00 40.80 3.51
80 81 4.910195 TGATAAGTCATCAAAGCCACAGT 58.090 39.130 0.00 0.00 40.80 3.55
93 94 5.337578 TGTTGATCGTGGATGATAAGTCA 57.662 39.130 0.00 0.00 39.04 3.41
94 95 5.276395 CGTTGTTGATCGTGGATGATAAGTC 60.276 44.000 0.00 0.00 0.00 3.01
95 96 4.566759 CGTTGTTGATCGTGGATGATAAGT 59.433 41.667 0.00 0.00 0.00 2.24
96 97 4.803613 TCGTTGTTGATCGTGGATGATAAG 59.196 41.667 0.00 0.00 0.00 1.73
97 98 4.749976 TCGTTGTTGATCGTGGATGATAA 58.250 39.130 0.00 0.00 0.00 1.75
98 99 4.379339 TCGTTGTTGATCGTGGATGATA 57.621 40.909 0.00 0.00 0.00 2.15
99 100 3.245518 TCGTTGTTGATCGTGGATGAT 57.754 42.857 0.00 0.00 0.00 2.45
100 101 2.734276 TCGTTGTTGATCGTGGATGA 57.266 45.000 0.00 0.00 0.00 2.92
101 102 3.804518 TTTCGTTGTTGATCGTGGATG 57.195 42.857 0.00 0.00 0.00 3.51
102 103 3.058501 GGTTTTCGTTGTTGATCGTGGAT 60.059 43.478 0.00 0.00 0.00 3.41
103 104 2.288458 GGTTTTCGTTGTTGATCGTGGA 59.712 45.455 0.00 0.00 0.00 4.02
104 105 2.603652 GGGTTTTCGTTGTTGATCGTGG 60.604 50.000 0.00 0.00 0.00 4.94
105 106 2.646250 GGGTTTTCGTTGTTGATCGTG 58.354 47.619 0.00 0.00 0.00 4.35
106 107 1.262151 CGGGTTTTCGTTGTTGATCGT 59.738 47.619 0.00 0.00 0.00 3.73
107 108 1.527736 TCGGGTTTTCGTTGTTGATCG 59.472 47.619 0.00 0.00 0.00 3.69
108 109 2.546789 AGTCGGGTTTTCGTTGTTGATC 59.453 45.455 0.00 0.00 0.00 2.92
109 110 2.567985 AGTCGGGTTTTCGTTGTTGAT 58.432 42.857 0.00 0.00 0.00 2.57
110 111 2.027003 AGTCGGGTTTTCGTTGTTGA 57.973 45.000 0.00 0.00 0.00 3.18
111 112 2.836479 AAGTCGGGTTTTCGTTGTTG 57.164 45.000 0.00 0.00 0.00 3.33
112 113 2.159352 CCAAAGTCGGGTTTTCGTTGTT 60.159 45.455 0.00 0.00 0.00 2.83
113 114 1.402613 CCAAAGTCGGGTTTTCGTTGT 59.597 47.619 0.00 0.00 0.00 3.32
114 115 1.862411 GCCAAAGTCGGGTTTTCGTTG 60.862 52.381 0.00 0.00 0.00 4.10
115 116 0.382873 GCCAAAGTCGGGTTTTCGTT 59.617 50.000 0.00 0.00 0.00 3.85
116 117 0.748729 TGCCAAAGTCGGGTTTTCGT 60.749 50.000 0.00 0.00 0.00 3.85
117 118 0.382515 TTGCCAAAGTCGGGTTTTCG 59.617 50.000 0.00 0.00 0.00 3.46
118 119 2.812358 ATTGCCAAAGTCGGGTTTTC 57.188 45.000 0.00 0.00 0.00 2.29
119 120 4.342665 TCTTTATTGCCAAAGTCGGGTTTT 59.657 37.500 3.39 0.00 36.94 2.43
120 121 3.892588 TCTTTATTGCCAAAGTCGGGTTT 59.107 39.130 3.39 0.00 36.94 3.27
121 122 3.492337 TCTTTATTGCCAAAGTCGGGTT 58.508 40.909 3.39 0.00 36.94 4.11
122 123 3.081804 CTCTTTATTGCCAAAGTCGGGT 58.918 45.455 3.39 0.00 36.94 5.28
123 124 2.423538 CCTCTTTATTGCCAAAGTCGGG 59.576 50.000 3.39 0.00 36.94 5.14
124 125 3.081804 ACCTCTTTATTGCCAAAGTCGG 58.918 45.455 3.39 7.04 36.94 4.79
125 126 4.475944 CAACCTCTTTATTGCCAAAGTCG 58.524 43.478 3.39 0.00 36.94 4.18
126 127 4.809673 CCAACCTCTTTATTGCCAAAGTC 58.190 43.478 3.39 0.00 36.94 3.01
127 128 3.006859 GCCAACCTCTTTATTGCCAAAGT 59.993 43.478 3.39 0.00 36.94 2.66
128 129 3.588955 GCCAACCTCTTTATTGCCAAAG 58.411 45.455 0.00 0.00 36.95 2.77
129 130 2.029470 CGCCAACCTCTTTATTGCCAAA 60.029 45.455 0.00 0.00 0.00 3.28
130 131 1.543802 CGCCAACCTCTTTATTGCCAA 59.456 47.619 0.00 0.00 0.00 4.52
131 132 1.173043 CGCCAACCTCTTTATTGCCA 58.827 50.000 0.00 0.00 0.00 4.92
132 133 0.455815 CCGCCAACCTCTTTATTGCC 59.544 55.000 0.00 0.00 0.00 4.52
133 134 0.179137 GCCGCCAACCTCTTTATTGC 60.179 55.000 0.00 0.00 0.00 3.56
134 135 0.098728 CGCCGCCAACCTCTTTATTG 59.901 55.000 0.00 0.00 0.00 1.90
135 136 0.035820 TCGCCGCCAACCTCTTTATT 60.036 50.000 0.00 0.00 0.00 1.40
136 137 0.743345 GTCGCCGCCAACCTCTTTAT 60.743 55.000 0.00 0.00 0.00 1.40
137 138 1.375013 GTCGCCGCCAACCTCTTTA 60.375 57.895 0.00 0.00 0.00 1.85
138 139 2.668550 GTCGCCGCCAACCTCTTT 60.669 61.111 0.00 0.00 0.00 2.52
139 140 3.936203 TGTCGCCGCCAACCTCTT 61.936 61.111 0.00 0.00 0.00 2.85
140 141 4.681978 GTGTCGCCGCCAACCTCT 62.682 66.667 0.00 0.00 0.00 3.69
141 142 4.980805 TGTGTCGCCGCCAACCTC 62.981 66.667 0.00 0.00 0.00 3.85
147 148 3.365291 TAGATGGTGTGTCGCCGCC 62.365 63.158 0.00 0.00 36.72 6.13
148 149 2.165301 GTAGATGGTGTGTCGCCGC 61.165 63.158 0.00 0.00 36.72 6.53
149 150 1.518572 GGTAGATGGTGTGTCGCCG 60.519 63.158 0.00 0.00 36.72 6.46
150 151 0.460284 CAGGTAGATGGTGTGTCGCC 60.460 60.000 0.00 0.00 34.12 5.54
151 152 0.246635 ACAGGTAGATGGTGTGTCGC 59.753 55.000 0.00 0.00 0.00 5.19
152 153 2.607187 GAACAGGTAGATGGTGTGTCG 58.393 52.381 0.00 0.00 0.00 4.35
153 154 2.607187 CGAACAGGTAGATGGTGTGTC 58.393 52.381 0.00 0.00 0.00 3.67
154 155 1.275291 CCGAACAGGTAGATGGTGTGT 59.725 52.381 0.00 0.00 34.51 3.72
155 156 1.405526 CCCGAACAGGTAGATGGTGTG 60.406 57.143 0.00 0.00 38.74 3.82
156 157 0.902531 CCCGAACAGGTAGATGGTGT 59.097 55.000 0.00 0.00 38.74 4.16
157 158 1.137086 CTCCCGAACAGGTAGATGGTG 59.863 57.143 0.00 0.00 38.74 4.17
158 159 1.006758 TCTCCCGAACAGGTAGATGGT 59.993 52.381 0.00 0.00 38.74 3.55
159 160 1.776662 TCTCCCGAACAGGTAGATGG 58.223 55.000 0.00 0.00 38.74 3.51
160 161 3.447586 TCTTTCTCCCGAACAGGTAGATG 59.552 47.826 0.00 0.00 38.74 2.90
161 162 3.709587 TCTTTCTCCCGAACAGGTAGAT 58.290 45.455 0.00 0.00 38.74 1.98
162 163 3.165087 TCTTTCTCCCGAACAGGTAGA 57.835 47.619 0.00 0.00 38.74 2.59
163 164 3.510360 TCTTCTTTCTCCCGAACAGGTAG 59.490 47.826 0.00 0.00 38.74 3.18
164 165 3.503365 TCTTCTTTCTCCCGAACAGGTA 58.497 45.455 0.00 0.00 38.74 3.08
165 166 2.326428 TCTTCTTTCTCCCGAACAGGT 58.674 47.619 0.00 0.00 38.74 4.00
166 167 3.265791 CATCTTCTTTCTCCCGAACAGG 58.734 50.000 0.00 0.00 40.63 4.00
167 168 3.265791 CCATCTTCTTTCTCCCGAACAG 58.734 50.000 0.00 0.00 0.00 3.16
168 169 2.637872 ACCATCTTCTTTCTCCCGAACA 59.362 45.455 0.00 0.00 0.00 3.18
169 170 3.263261 GACCATCTTCTTTCTCCCGAAC 58.737 50.000 0.00 0.00 0.00 3.95
170 171 2.094182 CGACCATCTTCTTTCTCCCGAA 60.094 50.000 0.00 0.00 0.00 4.30
171 172 1.476891 CGACCATCTTCTTTCTCCCGA 59.523 52.381 0.00 0.00 0.00 5.14
172 173 1.471676 CCGACCATCTTCTTTCTCCCG 60.472 57.143 0.00 0.00 0.00 5.14
173 174 1.744114 GCCGACCATCTTCTTTCTCCC 60.744 57.143 0.00 0.00 0.00 4.30
174 175 1.657822 GCCGACCATCTTCTTTCTCC 58.342 55.000 0.00 0.00 0.00 3.71
175 176 1.657822 GGCCGACCATCTTCTTTCTC 58.342 55.000 0.00 0.00 35.26 2.87
176 177 0.253327 GGGCCGACCATCTTCTTTCT 59.747 55.000 0.00 0.00 39.85 2.52
177 178 0.253327 AGGGCCGACCATCTTCTTTC 59.747 55.000 0.00 0.00 43.89 2.62
178 179 1.580059 TAGGGCCGACCATCTTCTTT 58.420 50.000 0.00 0.00 43.89 2.52
179 180 1.486726 CTTAGGGCCGACCATCTTCTT 59.513 52.381 0.00 0.00 43.89 2.52
180 181 1.123928 CTTAGGGCCGACCATCTTCT 58.876 55.000 0.00 0.00 43.89 2.85
181 182 0.106894 CCTTAGGGCCGACCATCTTC 59.893 60.000 0.00 0.00 43.89 2.87
182 183 1.345715 CCCTTAGGGCCGACCATCTT 61.346 60.000 3.52 0.00 43.89 2.40
183 184 1.766461 CCCTTAGGGCCGACCATCT 60.766 63.158 3.52 0.00 43.89 2.90
184 185 2.829592 CCCTTAGGGCCGACCATC 59.170 66.667 3.52 0.00 43.89 3.51
220 221 8.637986 ACCAACAGTACAAACACAATATGAAAT 58.362 29.630 0.00 0.00 0.00 2.17
221 222 8.001881 ACCAACAGTACAAACACAATATGAAA 57.998 30.769 0.00 0.00 0.00 2.69
222 223 7.575414 ACCAACAGTACAAACACAATATGAA 57.425 32.000 0.00 0.00 0.00 2.57
223 224 7.575414 AACCAACAGTACAAACACAATATGA 57.425 32.000 0.00 0.00 0.00 2.15
224 225 7.112844 CGAAACCAACAGTACAAACACAATATG 59.887 37.037 0.00 0.00 0.00 1.78
225 226 7.136119 CGAAACCAACAGTACAAACACAATAT 58.864 34.615 0.00 0.00 0.00 1.28
226 227 6.093771 ACGAAACCAACAGTACAAACACAATA 59.906 34.615 0.00 0.00 0.00 1.90
227 228 5.106078 ACGAAACCAACAGTACAAACACAAT 60.106 36.000 0.00 0.00 0.00 2.71
228 229 4.215827 ACGAAACCAACAGTACAAACACAA 59.784 37.500 0.00 0.00 0.00 3.33
229 230 3.752222 ACGAAACCAACAGTACAAACACA 59.248 39.130 0.00 0.00 0.00 3.72
230 231 4.345271 ACGAAACCAACAGTACAAACAC 57.655 40.909 0.00 0.00 0.00 3.32
231 232 6.492007 TTAACGAAACCAACAGTACAAACA 57.508 33.333 0.00 0.00 0.00 2.83
232 233 8.550376 TCTATTAACGAAACCAACAGTACAAAC 58.450 33.333 0.00 0.00 0.00 2.93
233 234 8.659925 TCTATTAACGAAACCAACAGTACAAA 57.340 30.769 0.00 0.00 0.00 2.83
234 235 8.836268 ATCTATTAACGAAACCAACAGTACAA 57.164 30.769 0.00 0.00 0.00 2.41
235 236 8.836268 AATCTATTAACGAAACCAACAGTACA 57.164 30.769 0.00 0.00 0.00 2.90
238 239 8.943002 CCTAAATCTATTAACGAAACCAACAGT 58.057 33.333 0.00 0.00 0.00 3.55
239 240 8.943002 ACCTAAATCTATTAACGAAACCAACAG 58.057 33.333 0.00 0.00 0.00 3.16
240 241 8.851541 ACCTAAATCTATTAACGAAACCAACA 57.148 30.769 0.00 0.00 0.00 3.33
308 309 3.753294 AAACACACACCCACACAAAAA 57.247 38.095 0.00 0.00 0.00 1.94
309 310 3.193691 CCTAAACACACACCCACACAAAA 59.806 43.478 0.00 0.00 0.00 2.44
310 311 2.755655 CCTAAACACACACCCACACAAA 59.244 45.455 0.00 0.00 0.00 2.83
311 312 2.370349 CCTAAACACACACCCACACAA 58.630 47.619 0.00 0.00 0.00 3.33
312 313 1.408961 CCCTAAACACACACCCACACA 60.409 52.381 0.00 0.00 0.00 3.72
313 314 1.314730 CCCTAAACACACACCCACAC 58.685 55.000 0.00 0.00 0.00 3.82
314 315 0.920438 ACCCTAAACACACACCCACA 59.080 50.000 0.00 0.00 0.00 4.17
315 316 1.134037 TCACCCTAAACACACACCCAC 60.134 52.381 0.00 0.00 0.00 4.61
316 317 1.142060 CTCACCCTAAACACACACCCA 59.858 52.381 0.00 0.00 0.00 4.51
317 318 1.142262 ACTCACCCTAAACACACACCC 59.858 52.381 0.00 0.00 0.00 4.61
318 319 2.218603 CACTCACCCTAAACACACACC 58.781 52.381 0.00 0.00 0.00 4.16
319 320 2.870411 GACACTCACCCTAAACACACAC 59.130 50.000 0.00 0.00 0.00 3.82
320 321 3.188159 GACACTCACCCTAAACACACA 57.812 47.619 0.00 0.00 0.00 3.72
1062 1063 2.588314 GAGGCGAGCATGCTCTGG 60.588 66.667 37.44 26.75 40.69 3.86
1137 1138 0.984961 TGGAGCAGGAGATTCTGGGG 60.985 60.000 0.00 0.00 35.43 4.96
1213 1214 2.105128 CAGCCCGGAAGAGCTACG 59.895 66.667 0.73 0.00 37.18 3.51
1337 1338 6.687105 CGATCCAATAAAACCGAAACAGAATC 59.313 38.462 0.00 0.00 0.00 2.52
1403 1404 9.219603 GCAGCATATACTAAAAGGTGAATGATA 57.780 33.333 0.00 0.00 0.00 2.15
1432 1433 4.086706 ACCTGACTGTGTTTAGAAAGGG 57.913 45.455 0.00 0.00 32.05 3.95
1434 1435 6.662616 CATGAACCTGACTGTGTTTAGAAAG 58.337 40.000 0.00 0.00 0.00 2.62
1440 1441 2.653726 TGCATGAACCTGACTGTGTTT 58.346 42.857 0.00 0.00 0.00 2.83
1446 1447 2.573462 AGTGGTATGCATGAACCTGACT 59.427 45.455 17.55 11.55 36.67 3.41
1527 1532 5.526010 AAACTCCAAAGTAAGCGAATACG 57.474 39.130 0.00 0.00 37.38 3.06
1560 1565 7.766219 AGGTTCAAATATATCACGTACACAC 57.234 36.000 0.00 0.00 0.00 3.82
1608 1614 4.906618 TGTAGTTTTCCAGGAATCAGGAC 58.093 43.478 1.58 0.00 32.62 3.85
1621 1627 7.303634 TGCCGATAAGAGAATTGTAGTTTTC 57.696 36.000 0.00 0.00 0.00 2.29
1667 1674 3.107642 AGCGATAAAATACAGTCCCCG 57.892 47.619 0.00 0.00 0.00 5.73
1700 1707 3.052036 CAACATGGCTTCTTTTTCACCG 58.948 45.455 0.00 0.00 0.00 4.94
1713 1720 4.644103 ATGTGATTTAGAGCAACATGGC 57.356 40.909 0.00 0.00 0.00 4.40
1745 1752 2.565841 GGGTAGTAAGCTGAATGCCAG 58.434 52.381 8.01 0.00 45.67 4.85
1763 1770 2.971901 ACTTTTGAAGTACCCTGGGG 57.028 50.000 18.88 7.87 40.69 4.96
1803 1810 9.880157 TTACTGATTAGTAGGTACAATGAAACC 57.120 33.333 0.00 2.15 40.33 3.27
1932 2117 1.990799 CGAGAACACGAGCACCATTA 58.009 50.000 0.00 0.00 35.09 1.90
2225 2415 8.682936 AAGGTACAATTATCCATGAGACAATC 57.317 34.615 0.00 0.00 0.00 2.67
2289 2479 3.189702 TCCGTGATTCGTCAAATTTTCCC 59.810 43.478 0.00 0.00 37.94 3.97
2391 2581 9.081997 CAACAGCAAATTAGTCAACTGTAAAAA 57.918 29.630 0.00 0.00 37.38 1.94
2487 2677 0.905357 CTTCAGGAACATCCTCCGGT 59.095 55.000 0.00 0.00 45.66 5.28
2549 2739 6.446781 ACAATGTTCATCAGAAAGCCATAG 57.553 37.500 0.00 0.00 35.08 2.23
2715 2905 6.514947 ACACGACTAACCTTAACACATAACA 58.485 36.000 0.00 0.00 0.00 2.41
2716 2906 8.427774 GTTACACGACTAACCTTAACACATAAC 58.572 37.037 0.00 0.00 0.00 1.89
2717 2907 8.140628 TGTTACACGACTAACCTTAACACATAA 58.859 33.333 0.00 0.00 0.00 1.90
2718 2908 7.656412 TGTTACACGACTAACCTTAACACATA 58.344 34.615 0.00 0.00 0.00 2.29
2719 2909 6.514947 TGTTACACGACTAACCTTAACACAT 58.485 36.000 0.00 0.00 0.00 3.21
2720 2910 5.900425 TGTTACACGACTAACCTTAACACA 58.100 37.500 0.00 0.00 0.00 3.72
2721 2911 6.826893 TTGTTACACGACTAACCTTAACAC 57.173 37.500 0.00 0.00 31.04 3.32
2925 3122 0.905809 TGCTTTGCAATGAGGCCCAT 60.906 50.000 15.97 0.00 34.76 4.00
3031 3228 0.603707 TTCGGCAGCTTCCTGTCAAG 60.604 55.000 0.00 0.00 43.92 3.02
3157 3354 7.734924 AAATATTGAGTACGATGTCATGCAT 57.265 32.000 0.00 0.00 41.24 3.96
3204 3401 5.010282 ACCTTCAAGCATAAAGTTAGGTGG 58.990 41.667 0.00 0.00 33.71 4.61
3381 3578 7.628580 GCCAGGGAAAAATACAGTATGAAAGAC 60.629 40.741 0.00 0.00 39.69 3.01
3421 3618 8.391075 TGAAAAGGTCTCAAATTAAATCGAGT 57.609 30.769 0.00 0.00 0.00 4.18
3502 3701 3.009473 AGTTGTATCACAGAGGTTGGCAT 59.991 43.478 0.00 0.00 0.00 4.40
3592 3791 6.677913 TGCAAACTAAAGCTAAAATGAGACC 58.322 36.000 0.00 0.00 0.00 3.85
3765 3966 5.179452 AGGCGGTGAAATATAATGGCTAT 57.821 39.130 0.00 0.00 0.00 2.97
3783 4012 5.234116 GCAAAATATTTTAACCCATGAGGCG 59.766 40.000 12.98 0.00 40.58 5.52
4014 4243 8.071122 TGTTCAAAAATGTGCTTTAGTATTGC 57.929 30.769 0.00 0.00 0.00 3.56
4082 4311 8.644374 AAGCAAGTACCTACATAAATTTGGAA 57.356 30.769 0.00 0.00 0.00 3.53
4266 4495 9.512435 CCAAGAAAATAGTGATTGATTGCTTAG 57.488 33.333 0.00 0.00 0.00 2.18
4267 4496 9.241919 TCCAAGAAAATAGTGATTGATTGCTTA 57.758 29.630 0.00 0.00 0.00 3.09
4268 4497 8.125978 TCCAAGAAAATAGTGATTGATTGCTT 57.874 30.769 0.00 0.00 0.00 3.91
4269 4498 7.707624 TCCAAGAAAATAGTGATTGATTGCT 57.292 32.000 0.00 0.00 0.00 3.91
4270 4499 7.977853 ACATCCAAGAAAATAGTGATTGATTGC 59.022 33.333 0.00 0.00 0.00 3.56
4271 4500 9.865321 AACATCCAAGAAAATAGTGATTGATTG 57.135 29.630 0.00 0.00 0.00 2.67
4398 4666 7.017551 AGGACCTACATATGCATCCAAGAAATA 59.982 37.037 0.19 0.00 0.00 1.40
4618 4901 3.979948 TCTGTTCAACATGCCAACATTG 58.020 40.909 0.00 0.00 32.87 2.82
4811 5095 4.158394 GCTCCTTATTCAACAATCAAGCCA 59.842 41.667 0.00 0.00 0.00 4.75
5080 5384 1.570813 CATACGGCGCAAAGATCTCA 58.429 50.000 10.83 0.00 0.00 3.27
5086 5390 0.583438 CTCATCCATACGGCGCAAAG 59.417 55.000 10.83 1.82 0.00 2.77
5162 5474 7.056635 CCTTTGATCTAACCCAATCAGTACAT 58.943 38.462 0.00 0.00 33.66 2.29
5184 5496 2.610438 ACCCAATCAGCATTGACCTT 57.390 45.000 0.00 0.00 41.97 3.50
5310 5622 1.696884 GGAAGGGTTGAATTTTGGCCA 59.303 47.619 0.00 0.00 0.00 5.36
5658 5984 3.252458 CGAAAATTTTCCCTCGGTCACTT 59.748 43.478 22.15 0.00 33.68 3.16
5715 6042 0.462225 TTCGACTTTTCCACCGTGCA 60.462 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.