Multiple sequence alignment - TraesCS3B01G300400

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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 TraesCS3B01G300400 chr3B 100.000 4246 0 0 1 4246 482001173 482005418 0.000000e+00 7841.0
1 TraesCS3B01G300400 chr3B 98.168 1201 22 0 1973 3173 675570292 675569092 0.000000e+00 2097.0
2 TraesCS3B01G300400 chr3B 96.293 1214 32 5 1973 3173 662806640 662805427 0.000000e+00 1980.0
3 TraesCS3B01G300400 chr3B 96.125 1213 33 3 1973 3173 662805424 662804214 0.000000e+00 1967.0
4 TraesCS3B01G300400 chr3B 98.583 988 14 0 2183 3170 685058341 685057354 0.000000e+00 1748.0
5 TraesCS3B01G300400 chr3B 93.145 919 59 4 2266 3182 141739412 141738496 0.000000e+00 1345.0
6 TraesCS3B01G300400 chr3B 100.000 175 0 0 4758 4932 482005930 482006104 1.710000e-84 324.0
7 TraesCS3B01G300400 chr3D 94.626 1563 61 12 245 1805 370617877 370619418 0.000000e+00 2399.0
8 TraesCS3B01G300400 chr3D 97.884 945 15 1 3170 4109 370619548 370620492 0.000000e+00 1629.0
9 TraesCS3B01G300400 chr3D 92.198 910 62 5 2266 3173 454525405 454526307 0.000000e+00 1279.0
10 TraesCS3B01G300400 chr3D 83.069 189 21 8 1956 2139 90306256 90306438 1.420000e-35 161.0
11 TraesCS3B01G300400 chr3D 80.137 146 16 7 1834 1972 370619418 370619557 4.060000e-16 97.1
12 TraesCS3B01G300400 chr3D 100.000 39 0 0 196 234 370617799 370617837 6.850000e-09 73.1
13 TraesCS3B01G300400 chr2B 95.337 1201 46 2 1973 3173 583524041 583522851 0.000000e+00 1899.0
14 TraesCS3B01G300400 chr7B 94.955 1209 50 7 1974 3173 55837667 55836461 0.000000e+00 1884.0
15 TraesCS3B01G300400 chr7B 89.091 275 21 6 1973 2240 544882877 544883149 2.850000e-87 333.0
16 TraesCS3B01G300400 chr3A 93.889 1260 43 12 569 1814 491521285 491522524 0.000000e+00 1869.0
17 TraesCS3B01G300400 chr3A 94.433 952 38 6 3171 4109 491522645 491523594 0.000000e+00 1450.0
18 TraesCS3B01G300400 chr3A 89.410 661 44 13 1972 2613 120173778 120174431 0.000000e+00 809.0
19 TraesCS3B01G300400 chr3A 93.534 232 13 1 277 508 491519630 491519859 1.310000e-90 344.0
20 TraesCS3B01G300400 chr3A 100.000 39 0 0 196 234 491519530 491519568 6.850000e-09 73.1
21 TraesCS3B01G300400 chr6A 90.128 1175 76 13 1960 3129 23445654 23446793 0.000000e+00 1491.0
22 TraesCS3B01G300400 chr6A 96.610 177 4 1 4758 4932 134944430 134944606 4.830000e-75 292.0
23 TraesCS3B01G300400 chr6A 96.341 82 3 0 1534 1615 88123502 88123583 8.610000e-28 135.0
24 TraesCS3B01G300400 chr6B 95.874 921 37 1 2253 3172 14309931 14310851 0.000000e+00 1489.0
25 TraesCS3B01G300400 chr6D 95.213 376 18 0 1284 1659 159013201 159012826 3.290000e-166 595.0
26 TraesCS3B01G300400 chr6D 90.152 132 9 1 1972 2099 412486400 412486269 8.490000e-38 169.0
27 TraesCS3B01G300400 chr7D 93.416 243 9 1 1281 1516 534658963 534658721 2.180000e-93 353.0
28 TraesCS3B01G300400 chr5D 89.583 288 14 4 1969 2240 410638469 410638756 7.850000e-93 351.0
29 TraesCS3B01G300400 chr1B 90.182 275 19 4 1973 2240 278474450 278474723 7.850000e-93 351.0
30 TraesCS3B01G300400 chr1B 83.051 118 18 2 1058 1174 638013768 638013884 6.750000e-19 106.0
31 TraesCS3B01G300400 chr5B 89.085 284 23 4 1964 2240 42140379 42140661 3.650000e-91 346.0
32 TraesCS3B01G300400 chr5B 96.571 175 4 1 4760 4932 532857152 532857326 6.250000e-74 289.0
33 TraesCS3B01G300400 chr5B 96.970 66 2 0 1451 1516 474747684 474747619 1.450000e-20 111.0
34 TraesCS3B01G300400 chr4B 88.929 280 17 8 1972 2240 371980099 371979823 2.850000e-87 333.0
35 TraesCS3B01G300400 chr2A 97.175 177 3 2 4758 4932 768624189 768624365 1.040000e-76 298.0
36 TraesCS3B01G300400 chrUn 96.610 177 4 1 4758 4932 316308637 316308813 4.830000e-75 292.0
37 TraesCS3B01G300400 chrUn 93.878 49 3 0 1970 2018 35418127 35418175 1.900000e-09 75.0
38 TraesCS3B01G300400 chr7A 96.610 177 4 1 4758 4932 27352833 27353009 4.830000e-75 292.0
39 TraesCS3B01G300400 chr5A 96.610 177 4 1 4758 4932 675294616 675294792 4.830000e-75 292.0
40 TraesCS3B01G300400 chr1A 96.610 177 4 1 4758 4932 516724444 516724620 4.830000e-75 292.0
41 TraesCS3B01G300400 chr1A 96.045 177 4 2 4758 4932 50135525 50135700 8.080000e-73 285.0
42 TraesCS3B01G300400 chr1A 96.045 177 4 2 4758 4932 516724119 516724294 8.080000e-73 285.0
43 TraesCS3B01G300400 chr1A 83.333 126 18 3 1058 1181 554887871 554887995 4.040000e-21 113.0
44 TraesCS3B01G300400 chr1A 93.939 66 4 0 1972 2037 441757688 441757753 3.140000e-17 100.0
45 TraesCS3B01G300400 chr1D 98.462 65 1 0 1452 1516 310145770 310145706 1.120000e-21 115.0
46 TraesCS3B01G300400 chr1D 82.540 126 19 3 1058 1181 463017432 463017556 1.880000e-19 108.0
47 TraesCS3B01G300400 chr4D 91.045 67 6 0 1973 2039 496335987 496335921 1.890000e-14 91.6
48 TraesCS3B01G300400 chr4D 93.333 60 4 0 1972 2031 454439774 454439833 6.800000e-14 89.8


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 TraesCS3B01G300400 chr3B 482001173 482006104 4931 False 4082.500 7841 100.00000 1 4932 2 chr3B.!!$F1 4931
1 TraesCS3B01G300400 chr3B 675569092 675570292 1200 True 2097.000 2097 98.16800 1973 3173 1 chr3B.!!$R2 1200
2 TraesCS3B01G300400 chr3B 662804214 662806640 2426 True 1973.500 1980 96.20900 1973 3173 2 chr3B.!!$R4 1200
3 TraesCS3B01G300400 chr3B 685057354 685058341 987 True 1748.000 1748 98.58300 2183 3170 1 chr3B.!!$R3 987
4 TraesCS3B01G300400 chr3B 141738496 141739412 916 True 1345.000 1345 93.14500 2266 3182 1 chr3B.!!$R1 916
5 TraesCS3B01G300400 chr3D 454525405 454526307 902 False 1279.000 1279 92.19800 2266 3173 1 chr3D.!!$F2 907
6 TraesCS3B01G300400 chr3D 370617799 370620492 2693 False 1049.550 2399 93.16175 196 4109 4 chr3D.!!$F3 3913
7 TraesCS3B01G300400 chr2B 583522851 583524041 1190 True 1899.000 1899 95.33700 1973 3173 1 chr2B.!!$R1 1200
8 TraesCS3B01G300400 chr7B 55836461 55837667 1206 True 1884.000 1884 94.95500 1974 3173 1 chr7B.!!$R1 1199
9 TraesCS3B01G300400 chr3A 491519530 491523594 4064 False 934.025 1869 95.46400 196 4109 4 chr3A.!!$F2 3913
10 TraesCS3B01G300400 chr3A 120173778 120174431 653 False 809.000 809 89.41000 1972 2613 1 chr3A.!!$F1 641
11 TraesCS3B01G300400 chr6A 23445654 23446793 1139 False 1491.000 1491 90.12800 1960 3129 1 chr6A.!!$F1 1169
12 TraesCS3B01G300400 chr6B 14309931 14310851 920 False 1489.000 1489 95.87400 2253 3172 1 chr6B.!!$F1 919
13 TraesCS3B01G300400 chr1A 516724119 516724620 501 False 288.500 292 96.32750 4758 4932 2 chr1A.!!$F4 174

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
157 158 0.177604 GCTGCAGGCACTACTCTGAT 59.822 55.000 17.12 0.0 41.35 2.90 F
720 2115 0.244994 GATCCAGTGACAGTGCTCGT 59.755 55.000 4.63 0.0 0.00 4.18 F
965 2372 0.317938 GATCGTGCTACCACCGCTAG 60.318 60.000 0.00 0.0 38.79 3.42 F
1447 2861 0.751643 ACGTCAAGCAGTTTGCCCTT 60.752 50.000 0.00 0.0 46.52 3.95 F
1700 3114 1.301479 GAGTTGGGTTCCTTCGCGT 60.301 57.895 5.77 0.0 0.00 6.01 F
2280 3733 1.821936 CTGTTGTTGCTTTGCCCCA 59.178 52.632 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 3386 0.169009 GCAGATCGTTGCCCTTTGTC 59.831 55.000 0.00 0.0 38.13 3.18 R
2263 3716 0.106335 CATGGGGCAAAGCAACAACA 59.894 50.000 0.00 0.0 0.00 3.33 R
2297 3750 1.474478 TCAACAAAAGCTTCAACCGCA 59.526 42.857 0.00 0.0 0.00 5.69 R
3007 5681 1.238439 CTCTCGGCCATCTCTCTCTC 58.762 60.000 2.24 0.0 0.00 3.20 R
3689 6384 0.472471 TTCGAGTCTTTGTTGGGCCT 59.528 50.000 4.53 0.0 0.00 5.19 R
4125 6823 0.600255 CGCGAGTTGGAAGGACTGTT 60.600 55.000 0.00 0.0 0.00 3.16 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
22 23 4.043073 GCTAGGTGTTTAGTCATCGTAGC 58.957 47.826 0.00 0.00 0.00 3.58
23 24 3.521947 AGGTGTTTAGTCATCGTAGCC 57.478 47.619 0.00 0.00 0.00 3.93
24 25 3.097614 AGGTGTTTAGTCATCGTAGCCT 58.902 45.455 0.00 0.00 0.00 4.58
25 26 3.119101 AGGTGTTTAGTCATCGTAGCCTG 60.119 47.826 0.00 0.00 0.00 4.85
26 27 3.187700 GTGTTTAGTCATCGTAGCCTGG 58.812 50.000 0.00 0.00 0.00 4.45
27 28 2.829720 TGTTTAGTCATCGTAGCCTGGT 59.170 45.455 0.00 0.00 0.00 4.00
28 29 3.259876 TGTTTAGTCATCGTAGCCTGGTT 59.740 43.478 0.00 0.00 0.00 3.67
29 30 4.251268 GTTTAGTCATCGTAGCCTGGTTT 58.749 43.478 0.00 0.00 0.00 3.27
30 31 4.546829 TTAGTCATCGTAGCCTGGTTTT 57.453 40.909 0.00 0.00 0.00 2.43
31 32 3.418684 AGTCATCGTAGCCTGGTTTTT 57.581 42.857 0.00 0.00 0.00 1.94
32 33 3.074412 AGTCATCGTAGCCTGGTTTTTG 58.926 45.455 0.00 0.00 0.00 2.44
33 34 1.810151 TCATCGTAGCCTGGTTTTTGC 59.190 47.619 0.00 0.00 0.00 3.68
34 35 1.135402 CATCGTAGCCTGGTTTTTGCC 60.135 52.381 0.00 0.00 0.00 4.52
35 36 1.209127 CGTAGCCTGGTTTTTGCCG 59.791 57.895 0.00 0.00 0.00 5.69
36 37 1.584495 GTAGCCTGGTTTTTGCCGG 59.416 57.895 0.00 0.00 34.71 6.13
37 38 1.151908 TAGCCTGGTTTTTGCCGGT 59.848 52.632 1.90 0.00 33.07 5.28
38 39 0.468400 TAGCCTGGTTTTTGCCGGTT 60.468 50.000 1.90 0.00 33.07 4.44
39 40 1.594021 GCCTGGTTTTTGCCGGTTG 60.594 57.895 1.90 0.00 33.07 3.77
40 41 1.819905 CCTGGTTTTTGCCGGTTGT 59.180 52.632 1.90 0.00 33.07 3.32
41 42 0.529555 CCTGGTTTTTGCCGGTTGTG 60.530 55.000 1.90 0.00 33.07 3.33
42 43 0.529555 CTGGTTTTTGCCGGTTGTGG 60.530 55.000 1.90 0.00 0.00 4.17
52 53 2.453983 CCGGTTGTGGCATCATTTTT 57.546 45.000 0.00 0.00 0.00 1.94
73 74 4.589216 TTTGCATCTTCTTCTTTGTGGG 57.411 40.909 0.00 0.00 0.00 4.61
74 75 1.888512 TGCATCTTCTTCTTTGTGGGC 59.111 47.619 0.00 0.00 0.00 5.36
75 76 2.165998 GCATCTTCTTCTTTGTGGGCT 58.834 47.619 0.00 0.00 0.00 5.19
76 77 2.163211 GCATCTTCTTCTTTGTGGGCTC 59.837 50.000 0.00 0.00 0.00 4.70
77 78 3.683802 CATCTTCTTCTTTGTGGGCTCT 58.316 45.455 0.00 0.00 0.00 4.09
78 79 3.131709 TCTTCTTCTTTGTGGGCTCTG 57.868 47.619 0.00 0.00 0.00 3.35
79 80 1.538950 CTTCTTCTTTGTGGGCTCTGC 59.461 52.381 0.00 0.00 0.00 4.26
80 81 0.767375 TCTTCTTTGTGGGCTCTGCT 59.233 50.000 0.00 0.00 0.00 4.24
81 82 1.143684 TCTTCTTTGTGGGCTCTGCTT 59.856 47.619 0.00 0.00 0.00 3.91
82 83 1.268899 CTTCTTTGTGGGCTCTGCTTG 59.731 52.381 0.00 0.00 0.00 4.01
83 84 0.183492 TCTTTGTGGGCTCTGCTTGT 59.817 50.000 0.00 0.00 0.00 3.16
84 85 0.313043 CTTTGTGGGCTCTGCTTGTG 59.687 55.000 0.00 0.00 0.00 3.33
85 86 0.395586 TTTGTGGGCTCTGCTTGTGT 60.396 50.000 0.00 0.00 0.00 3.72
86 87 1.102809 TTGTGGGCTCTGCTTGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
87 88 1.227943 GTGGGCTCTGCTTGTGTGA 60.228 57.895 0.00 0.00 0.00 3.58
88 89 1.227943 TGGGCTCTGCTTGTGTGAC 60.228 57.895 0.00 0.00 0.00 3.67
89 90 1.227943 GGGCTCTGCTTGTGTGACA 60.228 57.895 0.00 0.00 0.00 3.58
90 91 1.233285 GGGCTCTGCTTGTGTGACAG 61.233 60.000 0.00 0.00 0.00 3.51
91 92 0.533755 GGCTCTGCTTGTGTGACAGT 60.534 55.000 0.00 0.00 33.12 3.55
92 93 1.270305 GGCTCTGCTTGTGTGACAGTA 60.270 52.381 0.00 0.00 33.12 2.74
93 94 1.795286 GCTCTGCTTGTGTGACAGTAC 59.205 52.381 0.00 0.00 33.12 2.73
94 95 2.546795 GCTCTGCTTGTGTGACAGTACT 60.547 50.000 0.00 0.00 33.12 2.73
95 96 3.305403 GCTCTGCTTGTGTGACAGTACTA 60.305 47.826 0.00 0.00 33.12 1.82
96 97 4.480541 CTCTGCTTGTGTGACAGTACTAG 58.519 47.826 0.00 0.00 33.12 2.57
97 98 4.142038 TCTGCTTGTGTGACAGTACTAGA 58.858 43.478 0.00 0.00 33.12 2.43
98 99 4.023107 TCTGCTTGTGTGACAGTACTAGAC 60.023 45.833 0.00 0.00 33.12 2.59
99 100 3.005472 TGCTTGTGTGACAGTACTAGACC 59.995 47.826 0.00 0.00 0.00 3.85
100 101 3.614390 GCTTGTGTGACAGTACTAGACCC 60.614 52.174 0.00 0.00 0.00 4.46
101 102 2.156917 TGTGTGACAGTACTAGACCCG 58.843 52.381 0.00 0.00 0.00 5.28
102 103 2.224597 TGTGTGACAGTACTAGACCCGA 60.225 50.000 0.00 0.00 0.00 5.14
103 104 2.419324 GTGTGACAGTACTAGACCCGAG 59.581 54.545 0.00 0.00 0.00 4.63
104 105 2.015587 GTGACAGTACTAGACCCGAGG 58.984 57.143 0.00 0.00 0.00 4.63
105 106 1.632409 TGACAGTACTAGACCCGAGGT 59.368 52.381 0.00 0.00 39.44 3.85
115 116 3.908737 ACCCGAGGTCTTTTCTTCG 57.091 52.632 0.00 0.00 36.83 3.79
116 117 1.046204 ACCCGAGGTCTTTTCTTCGT 58.954 50.000 0.00 0.00 35.66 3.85
117 118 2.242043 ACCCGAGGTCTTTTCTTCGTA 58.758 47.619 0.00 0.00 35.66 3.43
118 119 2.830321 ACCCGAGGTCTTTTCTTCGTAT 59.170 45.455 0.00 0.00 35.66 3.06
119 120 3.260128 ACCCGAGGTCTTTTCTTCGTATT 59.740 43.478 0.00 0.00 35.66 1.89
120 121 4.251268 CCCGAGGTCTTTTCTTCGTATTT 58.749 43.478 0.00 0.00 35.66 1.40
121 122 4.694037 CCCGAGGTCTTTTCTTCGTATTTT 59.306 41.667 0.00 0.00 35.66 1.82
122 123 5.180680 CCCGAGGTCTTTTCTTCGTATTTTT 59.819 40.000 0.00 0.00 35.66 1.94
123 124 6.369615 CCCGAGGTCTTTTCTTCGTATTTTTA 59.630 38.462 0.00 0.00 35.66 1.52
124 125 7.065443 CCCGAGGTCTTTTCTTCGTATTTTTAT 59.935 37.037 0.00 0.00 35.66 1.40
125 126 8.448615 CCGAGGTCTTTTCTTCGTATTTTTATT 58.551 33.333 0.00 0.00 35.66 1.40
126 127 9.821662 CGAGGTCTTTTCTTCGTATTTTTATTT 57.178 29.630 0.00 0.00 33.42 1.40
146 147 9.487790 TTTATTTAATATAAATTGGCTGCAGGC 57.512 29.630 31.92 31.92 41.50 4.85
153 154 2.665000 TGGCTGCAGGCACTACTC 59.335 61.111 36.53 7.02 46.12 2.59
154 155 1.915266 TGGCTGCAGGCACTACTCT 60.915 57.895 36.53 0.00 46.12 3.24
155 156 1.449246 GGCTGCAGGCACTACTCTG 60.449 63.158 33.31 0.00 44.01 3.35
156 157 1.593787 GCTGCAGGCACTACTCTGA 59.406 57.895 17.12 0.00 41.35 3.27
157 158 0.177604 GCTGCAGGCACTACTCTGAT 59.822 55.000 17.12 0.00 41.35 2.90
158 159 1.937278 CTGCAGGCACTACTCTGATG 58.063 55.000 5.57 0.00 36.02 3.07
159 160 0.538584 TGCAGGCACTACTCTGATGG 59.461 55.000 0.00 0.00 36.02 3.51
160 161 0.826715 GCAGGCACTACTCTGATGGA 59.173 55.000 0.00 0.00 36.02 3.41
161 162 1.208052 GCAGGCACTACTCTGATGGAA 59.792 52.381 0.00 0.00 36.02 3.53
162 163 2.741228 GCAGGCACTACTCTGATGGAAG 60.741 54.545 0.00 0.00 36.02 3.46
163 164 1.484240 AGGCACTACTCTGATGGAAGC 59.516 52.381 0.00 0.00 36.02 3.86
164 165 1.208052 GGCACTACTCTGATGGAAGCA 59.792 52.381 0.00 0.00 0.00 3.91
179 180 3.673599 GCAGCGGCTTTCCTTCTT 58.326 55.556 0.00 0.00 36.96 2.52
180 181 1.959848 GCAGCGGCTTTCCTTCTTT 59.040 52.632 0.00 0.00 36.96 2.52
181 182 1.165270 GCAGCGGCTTTCCTTCTTTA 58.835 50.000 0.00 0.00 36.96 1.85
182 183 1.539827 GCAGCGGCTTTCCTTCTTTAA 59.460 47.619 0.00 0.00 36.96 1.52
183 184 2.030274 GCAGCGGCTTTCCTTCTTTAAA 60.030 45.455 0.00 0.00 36.96 1.52
184 185 3.826466 CAGCGGCTTTCCTTCTTTAAAG 58.174 45.455 9.04 9.04 36.09 1.85
185 186 3.502211 CAGCGGCTTTCCTTCTTTAAAGA 59.498 43.478 13.99 13.99 35.19 2.52
186 187 4.156739 CAGCGGCTTTCCTTCTTTAAAGAT 59.843 41.667 18.37 0.00 35.19 2.40
187 188 5.354234 CAGCGGCTTTCCTTCTTTAAAGATA 59.646 40.000 18.37 8.86 35.19 1.98
188 189 5.944007 AGCGGCTTTCCTTCTTTAAAGATAA 59.056 36.000 18.37 10.55 35.19 1.75
189 190 6.433093 AGCGGCTTTCCTTCTTTAAAGATAAA 59.567 34.615 18.37 16.21 35.19 1.40
190 191 7.122799 AGCGGCTTTCCTTCTTTAAAGATAAAT 59.877 33.333 18.37 3.14 35.19 1.40
191 192 8.403236 GCGGCTTTCCTTCTTTAAAGATAAATA 58.597 33.333 18.37 2.74 35.19 1.40
234 235 0.956633 CACAGTTGGTGCTGCTCAAT 59.043 50.000 0.00 0.00 41.36 2.57
235 236 2.153645 CACAGTTGGTGCTGCTCAATA 58.846 47.619 0.00 0.00 41.36 1.90
240 241 4.395854 CAGTTGGTGCTGCTCAATAACATA 59.604 41.667 0.00 0.00 0.00 2.29
241 242 4.637534 AGTTGGTGCTGCTCAATAACATAG 59.362 41.667 0.00 0.00 0.00 2.23
326 356 4.892934 TGCTACACAAAGGGTCAAGAAAAT 59.107 37.500 0.00 0.00 0.00 1.82
335 365 7.505585 ACAAAGGGTCAAGAAAATCATCAGTAA 59.494 33.333 0.00 0.00 0.00 2.24
444 474 1.990563 GCTTGCACGTATACGAAGTGT 59.009 47.619 30.77 5.87 45.73 3.55
497 527 1.021202 TTGCAAGACCAAACACGAGG 58.979 50.000 0.00 0.00 0.00 4.63
523 1895 5.689961 ACACAATAATTCCGCAAAAACTCAC 59.310 36.000 0.00 0.00 0.00 3.51
524 1896 5.920273 CACAATAATTCCGCAAAAACTCACT 59.080 36.000 0.00 0.00 0.00 3.41
541 1913 6.827586 ACTCACTCGAGAAAATCTCTTACT 57.172 37.500 21.68 0.00 41.26 2.24
560 1936 7.147976 TCTTACTGTGATGATCCAATACATCG 58.852 38.462 0.00 0.00 43.74 3.84
562 1938 3.712162 GTGATGATCCAATACATCGCG 57.288 47.619 0.00 0.00 43.74 5.87
563 1939 2.413112 GTGATGATCCAATACATCGCGG 59.587 50.000 6.13 0.00 43.74 6.46
564 1940 2.037121 TGATGATCCAATACATCGCGGT 59.963 45.455 6.13 0.00 43.74 5.68
565 1941 2.613026 TGATCCAATACATCGCGGTT 57.387 45.000 6.13 0.00 0.00 4.44
567 1943 0.944386 ATCCAATACATCGCGGTTGC 59.056 50.000 6.13 0.00 37.91 4.17
587 1982 1.495584 GCTTTCTGTCGTGAACCGCA 61.496 55.000 0.00 0.00 36.19 5.69
720 2115 0.244994 GATCCAGTGACAGTGCTCGT 59.755 55.000 4.63 0.00 0.00 4.18
769 2164 4.715130 AGGCCCAGCTCACCGGTA 62.715 66.667 6.87 0.00 0.00 4.02
771 2166 2.125106 GCCCAGCTCACCGGTAAG 60.125 66.667 6.87 2.26 0.00 2.34
841 2243 1.158705 ACCCACCACCACTAGAGCT 59.841 57.895 0.00 0.00 0.00 4.09
848 2250 1.338337 CCACCACTAGAGCTATCACCG 59.662 57.143 0.00 0.00 0.00 4.94
855 2257 2.231215 AGAGCTATCACCGCATCAAC 57.769 50.000 0.00 0.00 0.00 3.18
917 2319 2.286294 CCAGCTAGTAATTCAGCTTGCG 59.714 50.000 6.44 0.00 45.80 4.85
951 2358 2.311463 CTCCCAGGTGATACAGATCGT 58.689 52.381 0.00 0.00 34.49 3.73
952 2359 2.031870 TCCCAGGTGATACAGATCGTG 58.968 52.381 1.23 0.00 34.49 4.35
953 2360 1.539065 CCCAGGTGATACAGATCGTGC 60.539 57.143 1.23 0.00 34.49 5.34
954 2361 1.410517 CCAGGTGATACAGATCGTGCT 59.589 52.381 1.23 0.00 34.49 4.40
955 2362 2.623416 CCAGGTGATACAGATCGTGCTA 59.377 50.000 1.23 0.00 34.49 3.49
956 2363 3.551046 CCAGGTGATACAGATCGTGCTAC 60.551 52.174 1.23 0.00 34.49 3.58
957 2364 2.623889 AGGTGATACAGATCGTGCTACC 59.376 50.000 0.00 0.00 34.49 3.18
958 2365 2.361119 GGTGATACAGATCGTGCTACCA 59.639 50.000 0.00 0.00 34.49 3.25
959 2366 3.372954 GTGATACAGATCGTGCTACCAC 58.627 50.000 1.23 0.00 38.62 4.16
960 2367 2.361119 TGATACAGATCGTGCTACCACC 59.639 50.000 1.23 0.00 38.79 4.61
961 2368 0.736636 TACAGATCGTGCTACCACCG 59.263 55.000 1.23 0.00 38.79 4.94
962 2369 1.878522 CAGATCGTGCTACCACCGC 60.879 63.158 0.00 0.00 38.79 5.68
963 2370 2.052690 AGATCGTGCTACCACCGCT 61.053 57.895 0.00 0.00 38.79 5.52
964 2371 0.750546 AGATCGTGCTACCACCGCTA 60.751 55.000 0.00 0.00 38.79 4.26
965 2372 0.317938 GATCGTGCTACCACCGCTAG 60.318 60.000 0.00 0.00 38.79 3.42
971 2378 1.442148 CTACCACCGCTAGGCCTTC 59.558 63.158 12.58 1.89 42.76 3.46
974 2381 2.187946 CACCGCTAGGCCTTCCAG 59.812 66.667 12.58 2.82 42.76 3.86
1293 2707 3.449227 CCTCCAGTACGCGCAGGA 61.449 66.667 5.73 7.69 0.00 3.86
1375 2789 1.376037 GTTCTCCAAGGACGGCCTG 60.376 63.158 12.91 4.91 46.28 4.85
1447 2861 0.751643 ACGTCAAGCAGTTTGCCCTT 60.752 50.000 0.00 0.00 46.52 3.95
1660 3074 1.746615 CCAGGGCAAGACGTCCATG 60.747 63.158 13.01 13.10 44.49 3.66
1700 3114 1.301479 GAGTTGGGTTCCTTCGCGT 60.301 57.895 5.77 0.00 0.00 6.01
1723 3137 5.355350 GTCTGCTAACCATCTAATGCAAACT 59.645 40.000 0.00 0.00 0.00 2.66
1852 3268 7.060633 CGACTAATATGTTTGAAAACTGTTGCC 59.939 37.037 7.39 0.00 39.59 4.52
1873 3289 8.458843 GTTGCCTCAGTAAATTTAATCAGCTAA 58.541 33.333 0.00 0.00 0.00 3.09
1874 3290 8.213518 TGCCTCAGTAAATTTAATCAGCTAAG 57.786 34.615 0.00 0.00 0.00 2.18
1875 3291 8.046708 TGCCTCAGTAAATTTAATCAGCTAAGA 58.953 33.333 0.00 0.00 0.00 2.10
1876 3292 8.555361 GCCTCAGTAAATTTAATCAGCTAAGAG 58.445 37.037 0.00 0.43 0.00 2.85
1893 3309 7.051422 GCTAAGAGCTTTTGTTGTCTAGTAC 57.949 40.000 0.00 0.00 38.45 2.73
1894 3310 6.869388 GCTAAGAGCTTTTGTTGTCTAGTACT 59.131 38.462 0.00 0.00 38.45 2.73
1895 3311 7.062488 GCTAAGAGCTTTTGTTGTCTAGTACTC 59.938 40.741 0.00 0.00 38.45 2.59
1896 3312 5.785243 AGAGCTTTTGTTGTCTAGTACTCC 58.215 41.667 0.00 0.00 0.00 3.85
1898 3314 6.720288 AGAGCTTTTGTTGTCTAGTACTCCTA 59.280 38.462 0.00 0.00 0.00 2.94
1899 3315 6.689554 AGCTTTTGTTGTCTAGTACTCCTAC 58.310 40.000 0.00 0.00 0.00 3.18
1900 3316 5.868258 GCTTTTGTTGTCTAGTACTCCTACC 59.132 44.000 0.00 0.00 0.00 3.18
1901 3317 6.295180 GCTTTTGTTGTCTAGTACTCCTACCT 60.295 42.308 0.00 0.00 0.00 3.08
1902 3318 6.585695 TTTGTTGTCTAGTACTCCTACCTG 57.414 41.667 0.00 0.00 0.00 4.00
1903 3319 5.509832 TGTTGTCTAGTACTCCTACCTGA 57.490 43.478 0.00 0.00 0.00 3.86
1904 3320 5.251764 TGTTGTCTAGTACTCCTACCTGAC 58.748 45.833 0.00 0.00 0.00 3.51
1917 3333 3.253432 CCTACCTGACAAAAAGTTGCCTC 59.747 47.826 0.00 0.00 38.39 4.70
1918 3334 2.733956 ACCTGACAAAAAGTTGCCTCA 58.266 42.857 0.00 0.00 38.39 3.86
1966 3386 8.992835 TGATCGAATCAGATACCATATCTTTG 57.007 34.615 0.00 0.00 33.59 2.77
1967 3387 8.806146 TGATCGAATCAGATACCATATCTTTGA 58.194 33.333 0.00 0.00 33.59 2.69
2042 3462 2.586792 GGCCGTTGGATCTGAGCT 59.413 61.111 0.00 0.00 0.00 4.09
2280 3733 1.821936 CTGTTGTTGCTTTGCCCCA 59.178 52.632 0.00 0.00 0.00 4.96
2297 3750 3.593680 ATGCAACAGCCCCACCCT 61.594 61.111 0.00 0.00 0.00 4.34
2655 5326 3.241836 CGAAAAACGAAAAGTTGCAACCC 60.242 43.478 25.62 11.64 43.37 4.11
3007 5681 2.370445 ATGGCAACGGGGAGAGAGG 61.370 63.158 0.00 0.00 42.51 3.69
3190 5871 5.477984 TCCCTTTGACAAATCAATTGAGGAG 59.522 40.000 14.54 8.10 44.36 3.69
3219 5900 2.831685 ACCATTAGTGCAGTGACGAA 57.168 45.000 3.69 0.00 0.00 3.85
3604 6299 8.948631 TCTAAGAACTAATGTCATGGACAATC 57.051 34.615 2.87 0.00 45.96 2.67
3644 6339 9.276590 CTTGTCAACTGAAGGCATTATATATGA 57.723 33.333 0.00 0.00 0.00 2.15
3689 6384 4.683832 GCAGATTCTAGCGTTCTTCCTAA 58.316 43.478 0.00 0.00 0.00 2.69
3775 6470 1.336125 GTGCTCTTCTTTGCAGCAGTT 59.664 47.619 0.00 0.00 43.75 3.16
4051 6749 8.743085 ATCTATTCTGCAGAATCTTTTAGCAA 57.257 30.769 38.37 20.45 43.17 3.91
4109 6807 6.801539 TGGATTTGAAATGTGTAGAGTGTC 57.198 37.500 0.00 0.00 0.00 3.67
4110 6808 5.705441 TGGATTTGAAATGTGTAGAGTGTCC 59.295 40.000 0.00 0.00 0.00 4.02
4111 6809 5.940470 GGATTTGAAATGTGTAGAGTGTCCT 59.060 40.000 0.00 0.00 0.00 3.85
4112 6810 6.092807 GGATTTGAAATGTGTAGAGTGTCCTC 59.907 42.308 0.00 0.00 38.04 3.71
4113 6811 5.545063 TTGAAATGTGTAGAGTGTCCTCA 57.455 39.130 0.00 0.00 40.40 3.86
4114 6812 5.545063 TGAAATGTGTAGAGTGTCCTCAA 57.455 39.130 0.00 0.00 40.40 3.02
4115 6813 5.924356 TGAAATGTGTAGAGTGTCCTCAAA 58.076 37.500 0.00 0.00 40.40 2.69
4116 6814 5.758296 TGAAATGTGTAGAGTGTCCTCAAAC 59.242 40.000 0.00 0.00 40.40 2.93
4117 6815 5.552870 AATGTGTAGAGTGTCCTCAAACT 57.447 39.130 0.00 0.00 40.40 2.66
4118 6816 4.585955 TGTGTAGAGTGTCCTCAAACTC 57.414 45.455 0.00 0.00 42.61 3.01
4119 6817 3.004419 TGTGTAGAGTGTCCTCAAACTCG 59.996 47.826 0.00 0.00 46.05 4.18
4120 6818 3.004524 GTGTAGAGTGTCCTCAAACTCGT 59.995 47.826 0.00 0.00 46.05 4.18
4121 6819 3.252701 TGTAGAGTGTCCTCAAACTCGTC 59.747 47.826 0.00 0.00 46.05 4.20
4122 6820 2.307768 AGAGTGTCCTCAAACTCGTCA 58.692 47.619 0.00 0.00 46.05 4.35
4123 6821 2.294791 AGAGTGTCCTCAAACTCGTCAG 59.705 50.000 0.00 0.00 46.05 3.51
4124 6822 1.341531 AGTGTCCTCAAACTCGTCAGG 59.658 52.381 0.00 0.00 0.00 3.86
4125 6823 1.340248 GTGTCCTCAAACTCGTCAGGA 59.660 52.381 0.00 0.00 32.30 3.86
4126 6824 2.036387 TGTCCTCAAACTCGTCAGGAA 58.964 47.619 0.00 0.00 36.78 3.36
4127 6825 2.223971 TGTCCTCAAACTCGTCAGGAAC 60.224 50.000 0.00 0.00 36.78 3.62
4128 6826 2.036387 TCCTCAAACTCGTCAGGAACA 58.964 47.619 0.00 0.00 31.78 3.18
4129 6827 2.035961 TCCTCAAACTCGTCAGGAACAG 59.964 50.000 0.00 0.00 31.78 3.16
4130 6828 2.224066 CCTCAAACTCGTCAGGAACAGT 60.224 50.000 0.00 0.00 0.00 3.55
4131 6829 3.053455 CTCAAACTCGTCAGGAACAGTC 58.947 50.000 0.00 0.00 0.00 3.51
4132 6830 2.135933 CAAACTCGTCAGGAACAGTCC 58.864 52.381 0.00 0.00 45.35 3.85
4142 6840 1.797025 GGAACAGTCCTTCCAACTCG 58.203 55.000 0.00 0.00 41.24 4.18
4143 6841 1.149148 GAACAGTCCTTCCAACTCGC 58.851 55.000 0.00 0.00 0.00 5.03
4144 6842 0.600255 AACAGTCCTTCCAACTCGCG 60.600 55.000 0.00 0.00 0.00 5.87
4145 6843 2.048127 AGTCCTTCCAACTCGCGC 60.048 61.111 0.00 0.00 0.00 6.86
4146 6844 2.048127 GTCCTTCCAACTCGCGCT 60.048 61.111 5.56 0.00 0.00 5.92
4147 6845 1.214589 GTCCTTCCAACTCGCGCTA 59.785 57.895 5.56 0.00 0.00 4.26
4148 6846 0.802607 GTCCTTCCAACTCGCGCTAG 60.803 60.000 7.49 7.49 0.00 3.42
4149 6847 1.519455 CCTTCCAACTCGCGCTAGG 60.519 63.158 14.02 0.03 0.00 3.02
4150 6848 1.519455 CTTCCAACTCGCGCTAGGG 60.519 63.158 14.02 5.92 0.00 3.53
4151 6849 2.227089 CTTCCAACTCGCGCTAGGGT 62.227 60.000 14.02 0.00 0.00 4.34
4152 6850 1.823169 TTCCAACTCGCGCTAGGGTT 61.823 55.000 14.02 4.18 34.69 4.11
4153 6851 1.810030 CCAACTCGCGCTAGGGTTC 60.810 63.158 14.02 0.00 31.40 3.62
4154 6852 1.810030 CAACTCGCGCTAGGGTTCC 60.810 63.158 14.02 0.00 31.40 3.62
4155 6853 3.015312 AACTCGCGCTAGGGTTCCC 62.015 63.158 14.02 0.00 26.14 3.97
4156 6854 4.222847 CTCGCGCTAGGGTTCCCC 62.223 72.222 5.56 0.00 45.90 4.81
4240 6938 4.101448 CCCCCTCCGTCTTGGCTG 62.101 72.222 0.00 0.00 37.80 4.85
4241 6939 4.785453 CCCCTCCGTCTTGGCTGC 62.785 72.222 0.00 0.00 37.80 5.25
4242 6940 4.785453 CCCTCCGTCTTGGCTGCC 62.785 72.222 12.87 12.87 37.80 4.85
4243 6941 3.710722 CCTCCGTCTTGGCTGCCT 61.711 66.667 21.03 0.00 37.80 4.75
4244 6942 2.125350 CTCCGTCTTGGCTGCCTC 60.125 66.667 21.03 6.92 37.80 4.70
4245 6943 3.997064 CTCCGTCTTGGCTGCCTCG 62.997 68.421 21.03 17.29 37.80 4.63
4879 7904 0.606401 CCCTGCATGGTCTCGTTGTT 60.606 55.000 0.00 0.00 0.00 2.83
4884 7909 0.865111 CATGGTCTCGTTGTTTGCGA 59.135 50.000 0.00 0.00 36.85 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.043073 GCTACGATGACTAAACACCTAGC 58.957 47.826 0.00 0.00 0.00 3.42
1 2 4.338682 AGGCTACGATGACTAAACACCTAG 59.661 45.833 0.00 0.00 0.00 3.02
2 3 4.097437 CAGGCTACGATGACTAAACACCTA 59.903 45.833 0.00 0.00 0.00 3.08
3 4 3.097614 AGGCTACGATGACTAAACACCT 58.902 45.455 0.00 0.00 0.00 4.00
4 5 3.187700 CAGGCTACGATGACTAAACACC 58.812 50.000 0.00 0.00 0.00 4.16
5 6 3.187700 CCAGGCTACGATGACTAAACAC 58.812 50.000 0.00 0.00 0.00 3.32
6 7 2.829720 ACCAGGCTACGATGACTAAACA 59.170 45.455 0.00 0.00 0.00 2.83
7 8 3.521947 ACCAGGCTACGATGACTAAAC 57.478 47.619 0.00 0.00 0.00 2.01
8 9 4.546829 AAACCAGGCTACGATGACTAAA 57.453 40.909 0.00 0.00 0.00 1.85
9 10 4.546829 AAAACCAGGCTACGATGACTAA 57.453 40.909 0.00 0.00 0.00 2.24
10 11 4.250464 CAAAAACCAGGCTACGATGACTA 58.750 43.478 0.00 0.00 0.00 2.59
11 12 3.074412 CAAAAACCAGGCTACGATGACT 58.926 45.455 0.00 0.00 0.00 3.41
12 13 2.414161 GCAAAAACCAGGCTACGATGAC 60.414 50.000 0.00 0.00 0.00 3.06
13 14 1.810151 GCAAAAACCAGGCTACGATGA 59.190 47.619 0.00 0.00 0.00 2.92
14 15 1.135402 GGCAAAAACCAGGCTACGATG 60.135 52.381 0.00 0.00 0.00 3.84
15 16 1.173913 GGCAAAAACCAGGCTACGAT 58.826 50.000 0.00 0.00 0.00 3.73
16 17 1.231958 CGGCAAAAACCAGGCTACGA 61.232 55.000 0.00 0.00 0.00 3.43
17 18 1.209127 CGGCAAAAACCAGGCTACG 59.791 57.895 0.00 0.00 0.00 3.51
18 19 1.176619 ACCGGCAAAAACCAGGCTAC 61.177 55.000 0.00 0.00 0.00 3.58
19 20 0.468400 AACCGGCAAAAACCAGGCTA 60.468 50.000 0.00 0.00 0.00 3.93
20 21 1.760480 AACCGGCAAAAACCAGGCT 60.760 52.632 0.00 0.00 0.00 4.58
21 22 1.594021 CAACCGGCAAAAACCAGGC 60.594 57.895 0.00 0.00 0.00 4.85
22 23 0.529555 CACAACCGGCAAAAACCAGG 60.530 55.000 0.00 0.00 0.00 4.45
23 24 0.529555 CCACAACCGGCAAAAACCAG 60.530 55.000 0.00 0.00 0.00 4.00
24 25 1.517832 CCACAACCGGCAAAAACCA 59.482 52.632 0.00 0.00 0.00 3.67
25 26 4.429213 CCACAACCGGCAAAAACC 57.571 55.556 0.00 0.00 0.00 3.27
33 34 2.453983 AAAAATGATGCCACAACCGG 57.546 45.000 0.00 0.00 0.00 5.28
50 51 5.358922 CCCACAAAGAAGAAGATGCAAAAA 58.641 37.500 0.00 0.00 0.00 1.94
51 52 4.740334 GCCCACAAAGAAGAAGATGCAAAA 60.740 41.667 0.00 0.00 0.00 2.44
52 53 3.243839 GCCCACAAAGAAGAAGATGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
53 54 2.297033 GCCCACAAAGAAGAAGATGCAA 59.703 45.455 0.00 0.00 0.00 4.08
54 55 1.888512 GCCCACAAAGAAGAAGATGCA 59.111 47.619 0.00 0.00 0.00 3.96
55 56 2.163211 GAGCCCACAAAGAAGAAGATGC 59.837 50.000 0.00 0.00 0.00 3.91
56 57 3.439476 CAGAGCCCACAAAGAAGAAGATG 59.561 47.826 0.00 0.00 0.00 2.90
57 58 3.683802 CAGAGCCCACAAAGAAGAAGAT 58.316 45.455 0.00 0.00 0.00 2.40
58 59 2.811873 GCAGAGCCCACAAAGAAGAAGA 60.812 50.000 0.00 0.00 0.00 2.87
59 60 1.538950 GCAGAGCCCACAAAGAAGAAG 59.461 52.381 0.00 0.00 0.00 2.85
60 61 1.143684 AGCAGAGCCCACAAAGAAGAA 59.856 47.619 0.00 0.00 0.00 2.52
61 62 0.767375 AGCAGAGCCCACAAAGAAGA 59.233 50.000 0.00 0.00 0.00 2.87
62 63 1.268899 CAAGCAGAGCCCACAAAGAAG 59.731 52.381 0.00 0.00 0.00 2.85
63 64 1.321474 CAAGCAGAGCCCACAAAGAA 58.679 50.000 0.00 0.00 0.00 2.52
64 65 0.183492 ACAAGCAGAGCCCACAAAGA 59.817 50.000 0.00 0.00 0.00 2.52
65 66 0.313043 CACAAGCAGAGCCCACAAAG 59.687 55.000 0.00 0.00 0.00 2.77
66 67 0.395586 ACACAAGCAGAGCCCACAAA 60.396 50.000 0.00 0.00 0.00 2.83
67 68 1.102809 CACACAAGCAGAGCCCACAA 61.103 55.000 0.00 0.00 0.00 3.33
68 69 1.526686 CACACAAGCAGAGCCCACA 60.527 57.895 0.00 0.00 0.00 4.17
69 70 1.227943 TCACACAAGCAGAGCCCAC 60.228 57.895 0.00 0.00 0.00 4.61
70 71 1.227943 GTCACACAAGCAGAGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
71 72 1.227943 TGTCACACAAGCAGAGCCC 60.228 57.895 0.00 0.00 0.00 5.19
72 73 0.533755 ACTGTCACACAAGCAGAGCC 60.534 55.000 0.00 0.00 34.60 4.70
73 74 1.795286 GTACTGTCACACAAGCAGAGC 59.205 52.381 0.00 0.00 34.60 4.09
74 75 3.377346 AGTACTGTCACACAAGCAGAG 57.623 47.619 0.00 0.00 34.60 3.35
75 76 4.023107 GTCTAGTACTGTCACACAAGCAGA 60.023 45.833 5.39 0.00 34.60 4.26
76 77 4.230657 GTCTAGTACTGTCACACAAGCAG 58.769 47.826 5.39 0.00 36.41 4.24
77 78 3.005472 GGTCTAGTACTGTCACACAAGCA 59.995 47.826 5.39 0.00 0.00 3.91
78 79 3.576648 GGTCTAGTACTGTCACACAAGC 58.423 50.000 5.39 0.00 0.00 4.01
79 80 3.366070 CGGGTCTAGTACTGTCACACAAG 60.366 52.174 5.39 0.00 0.00 3.16
80 81 2.555325 CGGGTCTAGTACTGTCACACAA 59.445 50.000 5.39 0.00 0.00 3.33
81 82 2.156917 CGGGTCTAGTACTGTCACACA 58.843 52.381 5.39 0.00 0.00 3.72
82 83 2.419324 CTCGGGTCTAGTACTGTCACAC 59.581 54.545 5.39 0.00 0.00 3.82
83 84 2.617276 CCTCGGGTCTAGTACTGTCACA 60.617 54.545 5.39 0.00 0.00 3.58
84 85 2.015587 CCTCGGGTCTAGTACTGTCAC 58.984 57.143 5.39 0.00 0.00 3.67
85 86 1.632409 ACCTCGGGTCTAGTACTGTCA 59.368 52.381 5.39 0.00 0.00 3.58
86 87 2.416680 ACCTCGGGTCTAGTACTGTC 57.583 55.000 5.39 0.00 0.00 3.51
97 98 1.046204 ACGAAGAAAAGACCTCGGGT 58.954 50.000 0.00 0.00 39.44 5.28
98 99 3.521947 ATACGAAGAAAAGACCTCGGG 57.478 47.619 0.00 0.00 0.00 5.14
99 100 5.857822 AAAATACGAAGAAAAGACCTCGG 57.142 39.130 0.00 0.00 0.00 4.63
100 101 9.821662 AAATAAAAATACGAAGAAAAGACCTCG 57.178 29.630 0.00 0.00 0.00 4.63
120 121 9.487790 GCCTGCAGCCAATTTATATTAAATAAA 57.512 29.630 8.66 5.74 34.35 1.40
121 122 8.646004 TGCCTGCAGCCAATTTATATTAAATAA 58.354 29.630 8.66 0.00 42.71 1.40
122 123 8.087750 GTGCCTGCAGCCAATTTATATTAAATA 58.912 33.333 8.66 0.00 42.71 1.40
123 124 6.930722 GTGCCTGCAGCCAATTTATATTAAAT 59.069 34.615 8.66 0.00 42.71 1.40
124 125 6.098124 AGTGCCTGCAGCCAATTTATATTAAA 59.902 34.615 8.66 0.00 42.71 1.52
125 126 5.598005 AGTGCCTGCAGCCAATTTATATTAA 59.402 36.000 8.66 0.00 42.71 1.40
126 127 5.139727 AGTGCCTGCAGCCAATTTATATTA 58.860 37.500 8.66 0.00 42.71 0.98
127 128 3.962718 AGTGCCTGCAGCCAATTTATATT 59.037 39.130 8.66 0.00 42.71 1.28
128 129 3.569491 AGTGCCTGCAGCCAATTTATAT 58.431 40.909 8.66 0.00 42.71 0.86
129 130 3.017048 AGTGCCTGCAGCCAATTTATA 57.983 42.857 8.66 0.00 42.71 0.98
130 131 1.856629 AGTGCCTGCAGCCAATTTAT 58.143 45.000 8.66 0.00 42.71 1.40
131 132 2.091541 GTAGTGCCTGCAGCCAATTTA 58.908 47.619 8.66 0.00 42.71 1.40
132 133 0.890683 GTAGTGCCTGCAGCCAATTT 59.109 50.000 8.66 0.00 42.71 1.82
133 134 0.038744 AGTAGTGCCTGCAGCCAATT 59.961 50.000 8.66 0.00 42.71 2.32
134 135 0.393537 GAGTAGTGCCTGCAGCCAAT 60.394 55.000 8.66 5.30 42.71 3.16
135 136 1.003355 GAGTAGTGCCTGCAGCCAA 60.003 57.895 8.66 0.00 42.71 4.52
136 137 1.915266 AGAGTAGTGCCTGCAGCCA 60.915 57.895 8.66 0.00 42.71 4.75
137 138 1.449246 CAGAGTAGTGCCTGCAGCC 60.449 63.158 8.66 0.00 42.71 4.85
138 139 0.177604 ATCAGAGTAGTGCCTGCAGC 59.822 55.000 8.66 4.57 44.14 5.25
139 140 1.472904 CCATCAGAGTAGTGCCTGCAG 60.473 57.143 6.78 6.78 0.00 4.41
140 141 0.538584 CCATCAGAGTAGTGCCTGCA 59.461 55.000 0.00 0.00 0.00 4.41
141 142 0.826715 TCCATCAGAGTAGTGCCTGC 59.173 55.000 0.00 0.00 0.00 4.85
142 143 2.741228 GCTTCCATCAGAGTAGTGCCTG 60.741 54.545 0.00 0.00 0.00 4.85
143 144 1.484240 GCTTCCATCAGAGTAGTGCCT 59.516 52.381 0.00 0.00 0.00 4.75
144 145 1.208052 TGCTTCCATCAGAGTAGTGCC 59.792 52.381 0.00 0.00 0.00 5.01
145 146 2.548875 CTGCTTCCATCAGAGTAGTGC 58.451 52.381 0.00 0.00 33.54 4.40
146 147 2.548875 GCTGCTTCCATCAGAGTAGTG 58.451 52.381 0.00 0.00 33.54 2.74
147 148 1.135915 CGCTGCTTCCATCAGAGTAGT 59.864 52.381 0.00 0.00 33.54 2.73
148 149 1.537776 CCGCTGCTTCCATCAGAGTAG 60.538 57.143 0.00 0.00 33.54 2.57
149 150 0.461548 CCGCTGCTTCCATCAGAGTA 59.538 55.000 0.00 0.00 33.54 2.59
150 151 1.220206 CCGCTGCTTCCATCAGAGT 59.780 57.895 0.00 0.00 33.54 3.24
151 152 2.178890 GCCGCTGCTTCCATCAGAG 61.179 63.158 0.00 0.00 33.54 3.35
152 153 2.124983 GCCGCTGCTTCCATCAGA 60.125 61.111 0.00 0.00 33.54 3.27
162 163 1.165270 TAAAGAAGGAAAGCCGCTGC 58.835 50.000 0.00 0.00 39.96 5.25
163 164 3.502211 TCTTTAAAGAAGGAAAGCCGCTG 59.498 43.478 15.57 0.00 39.96 5.18
164 165 3.751518 TCTTTAAAGAAGGAAAGCCGCT 58.248 40.909 15.57 0.00 39.96 5.52
165 166 4.703645 ATCTTTAAAGAAGGAAAGCCGC 57.296 40.909 21.26 0.00 38.77 6.53
234 235 3.381272 GGTACTGTACACCGGCTATGTTA 59.619 47.826 18.79 0.00 0.00 2.41
235 236 2.167075 GGTACTGTACACCGGCTATGTT 59.833 50.000 18.79 0.00 0.00 2.71
316 346 9.646427 AGTAGACTTACTGATGATTTTCTTGAC 57.354 33.333 0.00 0.00 38.69 3.18
361 391 7.042187 TCGCTAAACCACGAAACAAGTAAATTA 60.042 33.333 0.00 0.00 34.93 1.40
362 392 5.910723 CGCTAAACCACGAAACAAGTAAATT 59.089 36.000 0.00 0.00 0.00 1.82
375 405 2.149606 AAACGCGTCGCTAAACCACG 62.150 55.000 14.44 0.00 36.60 4.94
450 480 9.177608 CAAATGGGTTCTTATCTTATTGACTGA 57.822 33.333 0.00 0.00 0.00 3.41
497 527 6.858993 TGAGTTTTTGCGGAATTATTGTGTAC 59.141 34.615 0.00 0.00 0.00 2.90
541 1913 3.059166 CGCGATGTATTGGATCATCACA 58.941 45.455 0.00 0.00 39.99 3.58
561 1937 2.170985 CGACAGAAAGCGCAACCG 59.829 61.111 11.47 0.00 37.57 4.44
562 1938 1.082756 CACGACAGAAAGCGCAACC 60.083 57.895 11.47 0.00 0.00 3.77
563 1939 0.303493 TTCACGACAGAAAGCGCAAC 59.697 50.000 11.47 0.00 0.00 4.17
564 1940 0.303493 GTTCACGACAGAAAGCGCAA 59.697 50.000 11.47 0.00 0.00 4.85
565 1941 1.495584 GGTTCACGACAGAAAGCGCA 61.496 55.000 11.47 0.00 0.00 6.09
587 1982 1.783250 GCCTCGATCCATTCCCCCAT 61.783 60.000 0.00 0.00 0.00 4.00
720 2115 1.599071 CAGCGAGCTTTTGTCTTGTGA 59.401 47.619 0.00 0.00 0.00 3.58
769 2164 9.851686 TGTGATTGTATGCTTAAGATATTCCTT 57.148 29.630 6.67 0.00 0.00 3.36
841 2243 0.529773 GCCTCGTTGATGCGGTGATA 60.530 55.000 0.00 0.00 0.00 2.15
848 2250 1.086634 GTCCTCTGCCTCGTTGATGC 61.087 60.000 0.00 0.00 0.00 3.91
917 2319 2.582978 GGAGCCAGTAACCGGACC 59.417 66.667 9.46 0.00 0.00 4.46
951 2358 3.467226 GGCCTAGCGGTGGTAGCA 61.467 66.667 0.00 0.00 37.01 3.49
952 2359 2.646117 GAAGGCCTAGCGGTGGTAGC 62.646 65.000 5.16 0.00 32.94 3.58
953 2360 1.442148 GAAGGCCTAGCGGTGGTAG 59.558 63.158 5.16 0.00 33.92 3.18
954 2361 2.062177 GGAAGGCCTAGCGGTGGTA 61.062 63.158 5.16 0.00 0.00 3.25
955 2362 3.400054 GGAAGGCCTAGCGGTGGT 61.400 66.667 5.16 0.00 0.00 4.16
956 2363 3.391665 CTGGAAGGCCTAGCGGTGG 62.392 68.421 5.16 0.00 34.31 4.61
957 2364 2.187946 CTGGAAGGCCTAGCGGTG 59.812 66.667 5.16 0.00 34.31 4.94
971 2378 4.530857 GATCCACCGACGCCCTGG 62.531 72.222 0.00 0.00 0.00 4.45
1516 2930 1.073897 GGCCTGCTTGACAAGGACT 59.926 57.895 16.80 0.00 0.00 3.85
1660 3074 3.222603 ACCTGTGGTGAAATCAAAGGTC 58.777 45.455 0.00 0.00 46.87 3.85
1700 3114 5.500234 AGTTTGCATTAGATGGTTAGCAGA 58.500 37.500 0.00 0.00 33.14 4.26
1818 3234 9.737427 TTTTCAAACATATTAGTCGCAGAAAAA 57.263 25.926 0.00 0.00 39.69 1.94
1819 3235 9.176181 GTTTTCAAACATATTAGTCGCAGAAAA 57.824 29.630 0.00 0.00 37.25 2.29
1820 3236 8.564574 AGTTTTCAAACATATTAGTCGCAGAAA 58.435 29.630 5.26 0.00 41.30 2.52
1821 3237 8.015087 CAGTTTTCAAACATATTAGTCGCAGAA 58.985 33.333 5.26 0.00 41.30 3.02
1822 3238 7.172532 ACAGTTTTCAAACATATTAGTCGCAGA 59.827 33.333 5.26 0.00 41.30 4.26
1823 3239 7.298122 ACAGTTTTCAAACATATTAGTCGCAG 58.702 34.615 5.26 0.00 41.30 5.18
1824 3240 7.197071 ACAGTTTTCAAACATATTAGTCGCA 57.803 32.000 5.26 0.00 41.30 5.10
1825 3241 7.409343 GCAACAGTTTTCAAACATATTAGTCGC 60.409 37.037 5.26 0.00 41.30 5.19
1826 3242 7.060633 GGCAACAGTTTTCAAACATATTAGTCG 59.939 37.037 5.26 0.00 41.30 4.18
1827 3243 8.082242 AGGCAACAGTTTTCAAACATATTAGTC 58.918 33.333 5.26 0.00 41.30 2.59
1828 3244 7.951591 AGGCAACAGTTTTCAAACATATTAGT 58.048 30.769 5.26 0.00 41.30 2.24
1829 3245 8.081633 TGAGGCAACAGTTTTCAAACATATTAG 58.918 33.333 5.26 0.00 41.30 1.73
1830 3246 7.946207 TGAGGCAACAGTTTTCAAACATATTA 58.054 30.769 5.26 0.00 41.30 0.98
1831 3247 6.815089 TGAGGCAACAGTTTTCAAACATATT 58.185 32.000 5.26 0.00 41.30 1.28
1832 3248 6.403866 TGAGGCAACAGTTTTCAAACATAT 57.596 33.333 5.26 0.00 41.30 1.78
1833 3249 5.830912 CTGAGGCAACAGTTTTCAAACATA 58.169 37.500 5.26 0.00 41.30 2.29
1834 3250 4.685924 CTGAGGCAACAGTTTTCAAACAT 58.314 39.130 5.26 0.00 41.30 2.71
1835 3251 4.108699 CTGAGGCAACAGTTTTCAAACA 57.891 40.909 5.26 0.00 41.30 2.83
1873 3289 5.540719 AGGAGTACTAGACAACAAAAGCTCT 59.459 40.000 0.00 0.00 0.00 4.09
1874 3290 5.785243 AGGAGTACTAGACAACAAAAGCTC 58.215 41.667 0.00 0.00 0.00 4.09
1875 3291 5.810080 AGGAGTACTAGACAACAAAAGCT 57.190 39.130 0.00 0.00 0.00 3.74
1876 3292 5.868258 GGTAGGAGTACTAGACAACAAAAGC 59.132 44.000 0.00 0.00 30.77 3.51
1878 3294 6.779049 TCAGGTAGGAGTACTAGACAACAAAA 59.221 38.462 0.00 0.00 30.77 2.44
1879 3295 6.208204 GTCAGGTAGGAGTACTAGACAACAAA 59.792 42.308 0.00 0.00 35.14 2.83
1880 3296 5.709164 GTCAGGTAGGAGTACTAGACAACAA 59.291 44.000 0.00 0.00 35.14 2.83
1882 3298 5.251764 TGTCAGGTAGGAGTACTAGACAAC 58.748 45.833 0.00 0.00 38.64 3.32
1883 3299 5.509832 TGTCAGGTAGGAGTACTAGACAA 57.490 43.478 0.00 0.00 38.64 3.18
1885 3301 6.830873 TTTTGTCAGGTAGGAGTACTAGAC 57.169 41.667 0.00 0.00 35.38 2.59
1886 3302 7.008941 ACTTTTTGTCAGGTAGGAGTACTAGA 58.991 38.462 0.00 0.00 30.77 2.43
1890 3306 5.049612 GCAACTTTTTGTCAGGTAGGAGTAC 60.050 44.000 0.00 0.00 34.90 2.73
1891 3307 5.061179 GCAACTTTTTGTCAGGTAGGAGTA 58.939 41.667 0.00 0.00 34.90 2.59
1892 3308 3.883489 GCAACTTTTTGTCAGGTAGGAGT 59.117 43.478 0.00 0.00 34.90 3.85
1893 3309 3.253432 GGCAACTTTTTGTCAGGTAGGAG 59.747 47.826 0.00 0.00 37.29 3.69
1894 3310 3.219281 GGCAACTTTTTGTCAGGTAGGA 58.781 45.455 0.00 0.00 37.29 2.94
1895 3311 3.643159 GGCAACTTTTTGTCAGGTAGG 57.357 47.619 0.00 0.00 37.29 3.18
1904 3320 9.336850 ATCACACTGATCTGAGGCAACTTTTTG 62.337 40.741 6.60 0.00 39.39 2.44
1966 3386 0.169009 GCAGATCGTTGCCCTTTGTC 59.831 55.000 0.00 0.00 38.13 3.18
1967 3387 1.577328 CGCAGATCGTTGCCCTTTGT 61.577 55.000 1.66 0.00 41.01 2.83
2042 3462 2.727392 CGGATCCAACGGCCCACTA 61.727 63.158 13.41 0.00 0.00 2.74
2263 3716 0.106335 CATGGGGCAAAGCAACAACA 59.894 50.000 0.00 0.00 0.00 3.33
2280 3733 3.593680 AGGGTGGGGCTGTTGCAT 61.594 61.111 0.00 0.00 41.91 3.96
2297 3750 1.474478 TCAACAAAAGCTTCAACCGCA 59.526 42.857 0.00 0.00 0.00 5.69
2655 5326 4.731480 GCGGTTGTAACTTTTGTAACTGTG 59.269 41.667 0.00 0.00 31.07 3.66
3007 5681 1.238439 CTCTCGGCCATCTCTCTCTC 58.762 60.000 2.24 0.00 0.00 3.20
3190 5871 4.081697 ACTGCACTAATGGTTAAAATGCCC 60.082 41.667 0.00 0.00 0.00 5.36
3219 5900 8.517878 CAAGAAAATAATGACTTGGTGACTGAT 58.482 33.333 0.00 0.00 36.92 2.90
3604 6299 6.483307 TCAGTTGACAAGATTTTACTGACCAG 59.517 38.462 0.00 0.00 37.62 4.00
3644 6339 8.887036 TGCGAAGTTACACATATATTCAGATT 57.113 30.769 0.00 0.00 0.00 2.40
3689 6384 0.472471 TTCGAGTCTTTGTTGGGCCT 59.528 50.000 4.53 0.00 0.00 5.19
3775 6470 5.640147 ACTTTGATCCCCAAGACAATGTTA 58.360 37.500 3.97 0.00 35.94 2.41
4051 6749 4.575885 GATAGACTAGTCTCGCAGATCCT 58.424 47.826 28.42 3.96 40.93 3.24
4109 6807 2.224066 ACTGTTCCTGACGAGTTTGAGG 60.224 50.000 0.00 0.00 0.00 3.86
4110 6808 3.053455 GACTGTTCCTGACGAGTTTGAG 58.947 50.000 0.00 0.00 0.00 3.02
4111 6809 2.223971 GGACTGTTCCTGACGAGTTTGA 60.224 50.000 0.00 0.00 39.13 2.69
4112 6810 2.135933 GGACTGTTCCTGACGAGTTTG 58.864 52.381 0.00 0.00 39.13 2.93
4113 6811 2.528041 GGACTGTTCCTGACGAGTTT 57.472 50.000 0.00 0.00 39.13 2.66
4123 6821 1.797025 CGAGTTGGAAGGACTGTTCC 58.203 55.000 0.00 0.00 45.63 3.62
4124 6822 1.149148 GCGAGTTGGAAGGACTGTTC 58.851 55.000 0.00 0.00 0.00 3.18
4125 6823 0.600255 CGCGAGTTGGAAGGACTGTT 60.600 55.000 0.00 0.00 0.00 3.16
4126 6824 1.006102 CGCGAGTTGGAAGGACTGT 60.006 57.895 0.00 0.00 0.00 3.55
4127 6825 2.383527 GCGCGAGTTGGAAGGACTG 61.384 63.158 12.10 0.00 0.00 3.51
4128 6826 1.248785 TAGCGCGAGTTGGAAGGACT 61.249 55.000 12.10 0.00 0.00 3.85
4129 6827 0.802607 CTAGCGCGAGTTGGAAGGAC 60.803 60.000 12.10 0.00 0.00 3.85
4130 6828 1.511305 CTAGCGCGAGTTGGAAGGA 59.489 57.895 12.10 0.00 0.00 3.36
4131 6829 1.519455 CCTAGCGCGAGTTGGAAGG 60.519 63.158 12.10 0.46 0.00 3.46
4132 6830 1.519455 CCCTAGCGCGAGTTGGAAG 60.519 63.158 12.10 0.00 0.00 3.46
4133 6831 1.823169 AACCCTAGCGCGAGTTGGAA 61.823 55.000 12.10 0.00 0.00 3.53
4134 6832 2.221906 GAACCCTAGCGCGAGTTGGA 62.222 60.000 12.10 0.00 0.00 3.53
4135 6833 1.810030 GAACCCTAGCGCGAGTTGG 60.810 63.158 12.10 13.27 0.00 3.77
4136 6834 1.810030 GGAACCCTAGCGCGAGTTG 60.810 63.158 12.10 9.47 0.00 3.16
4137 6835 2.577593 GGAACCCTAGCGCGAGTT 59.422 61.111 12.10 11.46 0.00 3.01
4223 6921 4.101448 CAGCCAAGACGGAGGGGG 62.101 72.222 0.00 0.00 36.56 5.40
4224 6922 4.785453 GCAGCCAAGACGGAGGGG 62.785 72.222 0.00 0.00 36.56 4.79
4225 6923 4.785453 GGCAGCCAAGACGGAGGG 62.785 72.222 6.55 0.00 36.56 4.30
4226 6924 3.672295 GAGGCAGCCAAGACGGAGG 62.672 68.421 15.80 0.00 36.56 4.30
4227 6925 2.125350 GAGGCAGCCAAGACGGAG 60.125 66.667 15.80 0.00 36.56 4.63
4228 6926 4.069232 CGAGGCAGCCAAGACGGA 62.069 66.667 15.80 0.00 36.56 4.69
4863 7886 0.310543 GCAAACAACGAGACCATGCA 59.689 50.000 0.00 0.00 32.80 3.96
4879 7904 4.717629 CTCCTCACCGCGTCGCAA 62.718 66.667 18.75 0.00 0.00 4.85
4884 7909 4.361971 TCCTCCTCCTCACCGCGT 62.362 66.667 4.92 0.00 0.00 6.01


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

AutoCloner maintained by Alex Coulton.