Multiple sequence alignment - TraesCS5B01G416500

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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 TraesCS5B01G416500 chr5B 100.000 5508 0 0 1 5508 591140673 591146180 0.000000e+00 10172
1 TraesCS5B01G416500 chr5B 96.371 744 27 0 4765 5508 243862587 243863330 0.000000e+00 1225
2 TraesCS5B01G416500 chr5B 80.378 423 60 13 4325 4728 591152009 591152427 3.230000e-77 300
3 TraesCS5B01G416500 chr5B 90.741 162 10 4 1 157 491087804 491087643 1.550000e-50 211
4 TraesCS5B01G416500 chr5A 90.122 3685 202 51 153 3772 601468128 601471715 0.000000e+00 4639
5 TraesCS5B01G416500 chr5A 90.278 792 66 8 3776 4560 601500385 601501172 0.000000e+00 1026
6 TraesCS5B01G416500 chr5A 94.295 631 32 3 4121 4750 601472180 601472807 0.000000e+00 963
7 TraesCS5B01G416500 chr5A 91.304 161 8 3 1 157 349129252 349129094 1.200000e-51 215
8 TraesCS5B01G416500 chr5A 92.308 52 4 0 4065 4116 601472094 601472145 2.130000e-09 75
9 TraesCS5B01G416500 chr5D 91.616 2481 156 25 1325 3772 481948534 481950995 0.000000e+00 3382
10 TraesCS5B01G416500 chr5D 95.576 746 32 1 4763 5508 498550677 498549933 0.000000e+00 1194
11 TraesCS5B01G416500 chr5D 95.442 746 31 3 4763 5508 419009363 419008621 0.000000e+00 1186
12 TraesCS5B01G416500 chr5D 88.120 968 42 29 322 1263 481947151 481948071 0.000000e+00 1083
13 TraesCS5B01G416500 chr5D 93.968 630 35 2 4121 4750 481951248 481951874 0.000000e+00 950
14 TraesCS5B01G416500 chr5D 86.697 218 28 1 4322 4539 481973742 481973958 1.980000e-59 241
15 TraesCS5B01G416500 chr5D 84.507 142 16 4 3895 4032 481951049 481951188 9.620000e-28 135
16 TraesCS5B01G416500 chr5D 92.308 52 4 0 4065 4116 481951162 481951213 2.130000e-09 75
17 TraesCS5B01G416500 chr1B 96.237 744 28 0 4765 5508 94642235 94642978 0.000000e+00 1219
18 TraesCS5B01G416500 chr2B 95.979 746 29 1 4764 5508 116429805 116430550 0.000000e+00 1210
19 TraesCS5B01G416500 chr2B 91.250 160 10 2 1 156 6530306 6530147 1.200000e-51 215
20 TraesCS5B01G416500 chr1D 95.485 753 34 0 4756 5508 433294259 433293507 0.000000e+00 1203
21 TraesCS5B01G416500 chr1D 95.442 746 33 1 4763 5508 298512241 298511497 0.000000e+00 1188
22 TraesCS5B01G416500 chr1D 95.442 746 33 1 4763 5508 490401690 490400946 0.000000e+00 1188
23 TraesCS5B01G416500 chr3D 95.442 746 33 1 4763 5508 553398793 553399537 0.000000e+00 1188
24 TraesCS5B01G416500 chr3B 95.000 160 4 2 1 156 240267723 240267882 1.180000e-61 248
25 TraesCS5B01G416500 chr4B 93.082 159 8 3 1 156 437405052 437405210 4.290000e-56 230
26 TraesCS5B01G416500 chr6B 91.515 165 8 4 1 159 707003412 707003248 7.180000e-54 222
27 TraesCS5B01G416500 chr2D 91.875 160 10 3 1 157 91365702 91365543 2.580000e-53 220
28 TraesCS5B01G416500 chr7A 91.875 160 8 5 1 156 39311521 39311363 9.290000e-53 219
29 TraesCS5B01G416500 chr6A 89.535 172 10 6 1 166 592186939 592186770 1.550000e-50 211


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 TraesCS5B01G416500 chr5B 591140673 591146180 5507 False 10172.000000 10172 100.000000 1 5508 1 chr5B.!!$F2 5507
1 TraesCS5B01G416500 chr5B 243862587 243863330 743 False 1225.000000 1225 96.371000 4765 5508 1 chr5B.!!$F1 743
2 TraesCS5B01G416500 chr5A 601468128 601472807 4679 False 1892.333333 4639 92.241667 153 4750 3 chr5A.!!$F2 4597
3 TraesCS5B01G416500 chr5A 601500385 601501172 787 False 1026.000000 1026 90.278000 3776 4560 1 chr5A.!!$F1 784
4 TraesCS5B01G416500 chr5D 498549933 498550677 744 True 1194.000000 1194 95.576000 4763 5508 1 chr5D.!!$R2 745
5 TraesCS5B01G416500 chr5D 419008621 419009363 742 True 1186.000000 1186 95.442000 4763 5508 1 chr5D.!!$R1 745
6 TraesCS5B01G416500 chr5D 481947151 481951874 4723 False 1125.000000 3382 90.103800 322 4750 5 chr5D.!!$F2 4428
7 TraesCS5B01G416500 chr1B 94642235 94642978 743 False 1219.000000 1219 96.237000 4765 5508 1 chr1B.!!$F1 743
8 TraesCS5B01G416500 chr2B 116429805 116430550 745 False 1210.000000 1210 95.979000 4764 5508 1 chr2B.!!$F1 744
9 TraesCS5B01G416500 chr1D 433293507 433294259 752 True 1203.000000 1203 95.485000 4756 5508 1 chr1D.!!$R2 752
10 TraesCS5B01G416500 chr1D 298511497 298512241 744 True 1188.000000 1188 95.442000 4763 5508 1 chr1D.!!$R1 745
11 TraesCS5B01G416500 chr1D 490400946 490401690 744 True 1188.000000 1188 95.442000 4763 5508 1 chr1D.!!$R3 745
12 TraesCS5B01G416500 chr3D 553398793 553399537 744 False 1188.000000 1188 95.442000 4763 5508 1 chr3D.!!$F1 745

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
44 45 0.035458 GGTCAATAGATGGGGAGGCG 59.965 60.0 0.0 0.0 0.00 5.52 F
45 46 0.035458 GTCAATAGATGGGGAGGCGG 59.965 60.0 0.0 0.0 0.00 6.13 F
885 893 0.035630 CACCAGGAAGGAGCAAGGAG 60.036 60.0 0.0 0.0 41.22 3.69 F
2366 2845 0.033011 ACTATCCTCCTGCTCCACGT 60.033 55.0 0.0 0.0 0.00 4.49 F
2577 3056 0.104120 TCAGAATGCACGGGGTATCG 59.896 55.0 0.0 0.0 34.76 2.92 F
4017 4666 0.036671 GGTAACCGACCCCAAGACAG 60.037 60.0 0.0 0.0 43.25 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 1257 1.201414 AGGCGCGAAACCAAATTAAGG 59.799 47.619 12.10 0.0 0.00 2.69 R
1745 2209 1.615384 GCCTTGCATCTTCCTTCTGGT 60.615 52.381 0.00 0.0 34.23 4.00 R
2841 3328 0.034616 ACAAGCTGCACCACTCTCTC 59.965 55.000 1.02 0.0 0.00 3.20 R
3523 4017 0.244450 TGGCAGCAGCACTATTTTGC 59.756 50.000 2.65 0.0 44.61 3.68 R
4315 4994 0.318360 CGTATGCAGCGTTCGGGATA 60.318 55.000 5.76 0.0 0.00 2.59 R
5057 5740 4.080129 ACGTGGTCCTTACTCACTCCTATA 60.080 45.833 0.00 0.0 0.00 1.31 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
28 29 9.959749 TTACAACAAGAGTTAATTTGATTGGTC 57.040 29.630 4.86 0.00 35.85 4.02
29 30 8.006298 ACAACAAGAGTTAATTTGATTGGTCA 57.994 30.769 4.86 0.00 35.85 4.02
30 31 8.474025 ACAACAAGAGTTAATTTGATTGGTCAA 58.526 29.630 4.86 0.00 38.17 3.18
31 32 9.480053 CAACAAGAGTTAATTTGATTGGTCAAT 57.520 29.630 0.00 0.00 38.99 2.57
37 38 9.956720 GAGTTAATTTGATTGGTCAATAGATGG 57.043 33.333 0.00 0.00 43.49 3.51
38 39 8.917088 AGTTAATTTGATTGGTCAATAGATGGG 58.083 33.333 0.00 0.00 43.49 4.00
39 40 6.736110 AATTTGATTGGTCAATAGATGGGG 57.264 37.500 0.00 0.00 43.49 4.96
40 41 5.464588 TTTGATTGGTCAATAGATGGGGA 57.535 39.130 0.00 0.00 43.49 4.81
41 42 4.712051 TGATTGGTCAATAGATGGGGAG 57.288 45.455 0.00 0.00 0.00 4.30
42 43 3.395607 TGATTGGTCAATAGATGGGGAGG 59.604 47.826 0.00 0.00 0.00 4.30
43 44 1.140312 TGGTCAATAGATGGGGAGGC 58.860 55.000 0.00 0.00 0.00 4.70
44 45 0.035458 GGTCAATAGATGGGGAGGCG 59.965 60.000 0.00 0.00 0.00 5.52
45 46 0.035458 GTCAATAGATGGGGAGGCGG 59.965 60.000 0.00 0.00 0.00 6.13
46 47 1.302832 CAATAGATGGGGAGGCGGC 60.303 63.158 0.00 0.00 0.00 6.53
47 48 2.529744 AATAGATGGGGAGGCGGCC 61.530 63.158 12.11 12.11 0.00 6.13
59 60 4.986708 GCGGCCCACCCCTGAAAA 62.987 66.667 0.00 0.00 0.00 2.29
60 61 2.037208 CGGCCCACCCCTGAAAAT 59.963 61.111 0.00 0.00 0.00 1.82
61 62 2.052104 CGGCCCACCCCTGAAAATC 61.052 63.158 0.00 0.00 0.00 2.17
62 63 1.078347 GGCCCACCCCTGAAAATCA 59.922 57.895 0.00 0.00 0.00 2.57
63 64 0.972471 GGCCCACCCCTGAAAATCAG 60.972 60.000 0.00 0.32 43.91 2.90
90 91 2.466846 GGGGGCAAGTTTATGATTGGT 58.533 47.619 0.00 0.00 0.00 3.67
91 92 2.837591 GGGGGCAAGTTTATGATTGGTT 59.162 45.455 0.00 0.00 0.00 3.67
92 93 4.027437 GGGGGCAAGTTTATGATTGGTTA 58.973 43.478 0.00 0.00 0.00 2.85
93 94 4.099419 GGGGGCAAGTTTATGATTGGTTAG 59.901 45.833 0.00 0.00 0.00 2.34
94 95 4.709886 GGGGCAAGTTTATGATTGGTTAGT 59.290 41.667 0.00 0.00 0.00 2.24
95 96 5.889289 GGGGCAAGTTTATGATTGGTTAGTA 59.111 40.000 0.00 0.00 0.00 1.82
96 97 6.039382 GGGGCAAGTTTATGATTGGTTAGTAG 59.961 42.308 0.00 0.00 0.00 2.57
97 98 6.826741 GGGCAAGTTTATGATTGGTTAGTAGA 59.173 38.462 0.00 0.00 0.00 2.59
98 99 7.502561 GGGCAAGTTTATGATTGGTTAGTAGAT 59.497 37.037 0.00 0.00 0.00 1.98
99 100 8.345565 GGCAAGTTTATGATTGGTTAGTAGATG 58.654 37.037 0.00 0.00 0.00 2.90
100 101 9.109393 GCAAGTTTATGATTGGTTAGTAGATGA 57.891 33.333 0.00 0.00 0.00 2.92
119 120 3.414486 AAAAACCTAGCCAGCGTGT 57.586 47.368 0.00 0.00 0.00 4.49
120 121 2.554370 AAAAACCTAGCCAGCGTGTA 57.446 45.000 0.00 0.00 0.00 2.90
121 122 2.554370 AAAACCTAGCCAGCGTGTAA 57.446 45.000 0.00 0.00 0.00 2.41
122 123 2.781681 AAACCTAGCCAGCGTGTAAT 57.218 45.000 0.00 0.00 0.00 1.89
123 124 2.781681 AACCTAGCCAGCGTGTAATT 57.218 45.000 0.00 0.00 0.00 1.40
124 125 2.024176 ACCTAGCCAGCGTGTAATTG 57.976 50.000 0.00 0.00 0.00 2.32
125 126 0.657840 CCTAGCCAGCGTGTAATTGC 59.342 55.000 0.00 0.00 0.00 3.56
126 127 0.301687 CTAGCCAGCGTGTAATTGCG 59.698 55.000 0.00 0.00 35.87 4.85
127 128 0.390603 TAGCCAGCGTGTAATTGCGT 60.391 50.000 0.00 0.00 35.87 5.24
128 129 1.511887 GCCAGCGTGTAATTGCGTG 60.512 57.895 0.00 0.00 35.87 5.34
129 130 1.866237 CCAGCGTGTAATTGCGTGT 59.134 52.632 0.00 0.00 35.87 4.49
130 131 1.072391 CCAGCGTGTAATTGCGTGTA 58.928 50.000 0.00 0.00 35.87 2.90
131 132 1.461512 CCAGCGTGTAATTGCGTGTAA 59.538 47.619 0.00 0.00 35.87 2.41
132 133 2.492001 CAGCGTGTAATTGCGTGTAAC 58.508 47.619 0.00 0.00 35.87 2.50
133 134 2.156891 CAGCGTGTAATTGCGTGTAACT 59.843 45.455 0.00 0.00 35.87 2.24
134 135 2.410730 AGCGTGTAATTGCGTGTAACTC 59.589 45.455 0.00 0.00 35.87 3.01
135 136 2.410730 GCGTGTAATTGCGTGTAACTCT 59.589 45.455 0.00 0.00 31.75 3.24
136 137 3.120786 GCGTGTAATTGCGTGTAACTCTT 60.121 43.478 0.00 0.00 31.75 2.85
137 138 4.609783 GCGTGTAATTGCGTGTAACTCTTT 60.610 41.667 0.00 0.00 31.75 2.52
138 139 4.838642 CGTGTAATTGCGTGTAACTCTTTG 59.161 41.667 0.00 0.00 31.75 2.77
139 140 5.557514 CGTGTAATTGCGTGTAACTCTTTGT 60.558 40.000 0.00 0.00 31.75 2.83
140 141 6.345961 CGTGTAATTGCGTGTAACTCTTTGTA 60.346 38.462 0.00 0.00 31.75 2.41
141 142 7.515643 GTGTAATTGCGTGTAACTCTTTGTAT 58.484 34.615 0.00 0.00 31.75 2.29
142 143 7.477422 GTGTAATTGCGTGTAACTCTTTGTATG 59.523 37.037 0.00 0.00 31.75 2.39
143 144 6.554334 AATTGCGTGTAACTCTTTGTATGT 57.446 33.333 0.00 0.00 31.75 2.29
144 145 5.994887 TTGCGTGTAACTCTTTGTATGTT 57.005 34.783 0.00 0.00 31.75 2.71
145 146 5.994887 TGCGTGTAACTCTTTGTATGTTT 57.005 34.783 0.00 0.00 31.75 2.83
146 147 7.479897 TTGCGTGTAACTCTTTGTATGTTTA 57.520 32.000 0.00 0.00 31.75 2.01
147 148 7.112528 TGCGTGTAACTCTTTGTATGTTTAG 57.887 36.000 0.00 0.00 31.75 1.85
148 149 6.013689 GCGTGTAACTCTTTGTATGTTTAGC 58.986 40.000 0.00 0.00 31.75 3.09
149 150 6.347079 GCGTGTAACTCTTTGTATGTTTAGCA 60.347 38.462 0.00 0.00 31.75 3.49
150 151 7.623506 GCGTGTAACTCTTTGTATGTTTAGCAT 60.624 37.037 0.00 0.00 36.70 3.79
151 152 8.227791 CGTGTAACTCTTTGTATGTTTAGCATT 58.772 33.333 0.00 0.00 35.02 3.56
178 179 3.006940 TCCACATACGATCCAACAAAGC 58.993 45.455 0.00 0.00 0.00 3.51
184 185 1.270094 ACGATCCAACAAAGCGTCTGA 60.270 47.619 0.00 0.00 0.00 3.27
190 194 1.939934 CAACAAAGCGTCTGAAGGTCA 59.060 47.619 0.00 0.00 0.00 4.02
198 202 1.633774 GTCTGAAGGTCAGGTCAGGA 58.366 55.000 5.46 0.00 44.39 3.86
222 226 4.766375 CGTCCCATAGAACTACCACATTT 58.234 43.478 0.00 0.00 0.00 2.32
230 234 4.012374 AGAACTACCACATTTCAGGCATG 58.988 43.478 0.00 0.00 0.00 4.06
257 261 1.618837 TGTCCCACAGACTTCAGCTAC 59.381 52.381 0.00 0.00 46.46 3.58
293 297 0.178992 CACCCTGCCCAAAGACTTCA 60.179 55.000 0.00 0.00 0.00 3.02
301 305 5.297776 CCTGCCCAAAGACTTCAACTATATG 59.702 44.000 0.00 0.00 0.00 1.78
343 347 6.115446 TCTCATCAATAAGTGCGATTTTCCT 58.885 36.000 0.00 0.00 0.00 3.36
368 372 1.003349 TCCGCCTTCCGTTTTCCATTA 59.997 47.619 0.00 0.00 34.38 1.90
490 498 3.082579 GCCGGGAGCAGTTCGATCT 62.083 63.158 2.18 0.00 42.97 2.75
491 499 1.227089 CCGGGAGCAGTTCGATCTG 60.227 63.158 17.42 17.42 38.35 2.90
545 553 8.867112 TTATTCACGATATTTGTCCTAGTCAC 57.133 34.615 0.00 0.00 0.00 3.67
551 559 2.162338 TTTGTCCTAGTCACGGCCGG 62.162 60.000 31.76 18.67 0.00 6.13
552 560 4.509737 GTCCTAGTCACGGCCGGC 62.510 72.222 31.76 21.18 0.00 6.13
680 688 2.854300 ATTGACCAATCCCCACCGCC 62.854 60.000 0.00 0.00 0.00 6.13
691 699 2.556287 CACCGCCGCTTTGAGAAC 59.444 61.111 0.00 0.00 0.00 3.01
792 800 4.521559 TGGCCGGCCACAAAATTA 57.478 50.000 44.23 19.94 41.89 1.40
793 801 2.746697 TGGCCGGCCACAAAATTAA 58.253 47.368 44.23 19.08 41.89 1.40
878 886 4.785453 GCCGGCACCAGGAAGGAG 62.785 72.222 24.80 0.00 41.22 3.69
883 891 4.730487 CACCAGGAAGGAGCAAGG 57.270 61.111 0.00 0.00 41.22 3.61
884 892 2.069776 CACCAGGAAGGAGCAAGGA 58.930 57.895 0.00 0.00 41.22 3.36
885 893 0.035630 CACCAGGAAGGAGCAAGGAG 60.036 60.000 0.00 0.00 41.22 3.69
886 894 1.204113 ACCAGGAAGGAGCAAGGAGG 61.204 60.000 0.00 0.00 41.22 4.30
887 895 1.606531 CAGGAAGGAGCAAGGAGGG 59.393 63.158 0.00 0.00 0.00 4.30
888 896 1.617839 AGGAAGGAGCAAGGAGGGG 60.618 63.158 0.00 0.00 0.00 4.79
889 897 1.616628 GGAAGGAGCAAGGAGGGGA 60.617 63.158 0.00 0.00 0.00 4.81
890 898 1.208165 GGAAGGAGCAAGGAGGGGAA 61.208 60.000 0.00 0.00 0.00 3.97
891 899 0.698818 GAAGGAGCAAGGAGGGGAAA 59.301 55.000 0.00 0.00 0.00 3.13
892 900 0.701147 AAGGAGCAAGGAGGGGAAAG 59.299 55.000 0.00 0.00 0.00 2.62
893 901 1.210885 AGGAGCAAGGAGGGGAAAGG 61.211 60.000 0.00 0.00 0.00 3.11
901 909 3.001406 AGGGGAAAGGGGACGACG 61.001 66.667 0.00 0.00 0.00 5.12
951 959 3.447742 CAAGGTTTTCGCTGAAGCTTTT 58.552 40.909 0.00 0.00 41.40 2.27
952 960 3.355626 AGGTTTTCGCTGAAGCTTTTC 57.644 42.857 0.00 0.00 39.32 2.29
963 971 2.765699 TGAAGCTTTTCTGTTTTGGGCT 59.234 40.909 0.00 0.00 0.00 5.19
965 973 2.110578 AGCTTTTCTGTTTTGGGCTGT 58.889 42.857 0.00 0.00 0.00 4.40
966 974 2.501316 AGCTTTTCTGTTTTGGGCTGTT 59.499 40.909 0.00 0.00 0.00 3.16
1123 1167 4.662961 CAGGGTGAGCACGCACGA 62.663 66.667 18.04 0.00 45.43 4.35
1124 1168 4.664677 AGGGTGAGCACGCACGAC 62.665 66.667 18.04 0.00 45.43 4.34
1145 1189 1.530441 CGACGATTGCCATCTGCTTTG 60.530 52.381 0.00 0.00 42.00 2.77
1146 1190 1.470098 GACGATTGCCATCTGCTTTGT 59.530 47.619 0.00 0.00 42.00 2.83
1147 1191 2.677836 GACGATTGCCATCTGCTTTGTA 59.322 45.455 0.00 0.00 42.00 2.41
1244 1293 0.373716 CGCCTATGGTTTGTCGAAGC 59.626 55.000 0.00 0.00 36.29 3.86
1274 1323 1.493311 GCGAGCTGCACTGTTGTAC 59.507 57.895 1.02 0.00 45.45 2.90
1303 1656 3.777106 TGGTCAGATCAGCAAAGAACT 57.223 42.857 0.00 0.00 0.00 3.01
1361 1811 9.563898 TGTTGTAACTATCTTCGTACTGTTATG 57.436 33.333 0.00 0.00 0.00 1.90
1393 1843 5.565259 GCATACAAAAGATGTTGTCAAGTCG 59.435 40.000 0.00 0.00 43.63 4.18
1441 1891 1.448717 GAAGGTCCAGCTTCTCGCC 60.449 63.158 10.63 0.00 40.39 5.54
1472 1936 8.162245 CGGTAAGTACGGTTTAAAACTGAATAC 58.838 37.037 1.03 0.00 40.26 1.89
1473 1937 9.208022 GGTAAGTACGGTTTAAAACTGAATACT 57.792 33.333 1.03 1.84 40.26 2.12
1476 1940 9.940166 AAGTACGGTTTAAAACTGAATACTTTG 57.060 29.630 1.03 0.00 36.75 2.77
1477 1941 8.562052 AGTACGGTTTAAAACTGAATACTTTGG 58.438 33.333 1.03 0.00 40.26 3.28
1478 1942 7.337480 ACGGTTTAAAACTGAATACTTTGGT 57.663 32.000 1.03 0.00 40.26 3.67
1479 1943 7.197703 ACGGTTTAAAACTGAATACTTTGGTG 58.802 34.615 1.03 0.00 40.26 4.17
1480 1944 7.148035 ACGGTTTAAAACTGAATACTTTGGTGT 60.148 33.333 1.03 0.00 40.26 4.16
1481 1945 8.344098 CGGTTTAAAACTGAATACTTTGGTGTA 58.656 33.333 1.03 0.00 40.26 2.90
1512 1976 7.703058 TGACTCATCAACTATTAGTCTGTGA 57.297 36.000 0.00 0.00 38.92 3.58
1521 1985 6.163135 ACTATTAGTCTGTGAACTATGCCC 57.837 41.667 0.00 0.00 32.00 5.36
1585 2049 5.890334 TGTACCTTTGCACTTTTTCTTGAG 58.110 37.500 0.00 0.00 0.00 3.02
1586 2050 5.417580 TGTACCTTTGCACTTTTTCTTGAGT 59.582 36.000 0.00 0.00 0.00 3.41
1587 2051 5.405935 ACCTTTGCACTTTTTCTTGAGTT 57.594 34.783 0.00 0.00 0.00 3.01
1588 2052 5.170748 ACCTTTGCACTTTTTCTTGAGTTG 58.829 37.500 0.00 0.00 0.00 3.16
1590 2054 5.639082 CCTTTGCACTTTTTCTTGAGTTGTT 59.361 36.000 0.00 0.00 0.00 2.83
1591 2055 6.147656 CCTTTGCACTTTTTCTTGAGTTGTTT 59.852 34.615 0.00 0.00 0.00 2.83
1594 2058 6.092748 TGCACTTTTTCTTGAGTTGTTTCTC 58.907 36.000 0.00 0.00 35.28 2.87
1595 2059 6.071952 TGCACTTTTTCTTGAGTTGTTTCTCT 60.072 34.615 0.00 0.00 35.68 3.10
1596 2060 7.120579 TGCACTTTTTCTTGAGTTGTTTCTCTA 59.879 33.333 0.00 0.00 35.68 2.43
1597 2061 7.641802 GCACTTTTTCTTGAGTTGTTTCTCTAG 59.358 37.037 0.00 0.00 38.17 2.43
1599 2063 9.232473 ACTTTTTCTTGAGTTGTTTCTCTAGTT 57.768 29.630 0.00 0.00 38.07 2.24
1619 2083 9.314321 TCTAGTTTTCTTGAGTTGTTTCTGTAG 57.686 33.333 0.00 0.00 0.00 2.74
1721 2185 9.922305 GAACATATTTTCTTGTAGTGATGTAGC 57.078 33.333 0.00 0.00 0.00 3.58
1745 2209 2.427812 CCTGGCAATGCATTACATCACA 59.572 45.455 12.53 4.45 38.34 3.58
1760 2224 2.479566 TCACACCAGAAGGAAGATGC 57.520 50.000 0.00 0.00 38.69 3.91
1761 2225 1.699083 TCACACCAGAAGGAAGATGCA 59.301 47.619 0.00 0.00 38.69 3.96
1762 2226 2.106338 TCACACCAGAAGGAAGATGCAA 59.894 45.455 0.00 0.00 38.69 4.08
1776 2240 4.708726 AGATGCAAGGCACATTTAGAAC 57.291 40.909 0.00 0.00 43.04 3.01
1794 2258 8.736751 TTTAGAACGCTTTAATTTGGAATGTC 57.263 30.769 0.00 0.00 0.00 3.06
1841 2305 7.962918 CACTAATCAGTGCATTGGTTTACTTAC 59.037 37.037 13.35 0.00 45.44 2.34
1873 2337 6.591062 TGCTGGAGACAATGATTAAAAATTGC 59.409 34.615 11.45 6.60 42.06 3.56
1917 2381 4.524328 TGTTGCTGAGAGAGACATACTTCA 59.476 41.667 0.00 0.00 0.00 3.02
1969 2435 8.211629 AGGGTATGTATGGATAGTTCAAACTTC 58.788 37.037 0.00 0.00 40.37 3.01
2037 2503 6.318648 TGTGGTGATTTTAGCCTGATTATCAC 59.681 38.462 0.00 0.00 40.50 3.06
2188 2666 4.462834 TGTGATCTTGTAACAGTCTCGGAT 59.537 41.667 0.00 0.00 0.00 4.18
2295 2774 4.253685 CGGAGCTGTATTTCCTCAAAGAA 58.746 43.478 0.00 0.00 0.00 2.52
2325 2804 5.703130 GGATCTGTGCCAATATTTACTCCTC 59.297 44.000 0.00 0.00 0.00 3.71
2327 2806 4.721776 TCTGTGCCAATATTTACTCCTCCT 59.278 41.667 0.00 0.00 0.00 3.69
2362 2841 3.636153 ACAAAACTATCCTCCTGCTCC 57.364 47.619 0.00 0.00 0.00 4.70
2366 2845 0.033011 ACTATCCTCCTGCTCCACGT 60.033 55.000 0.00 0.00 0.00 4.49
2438 2917 6.715464 CGCAAGGTATACCAACTTATGAAAG 58.285 40.000 23.87 0.00 38.89 2.62
2477 2956 3.868077 GCATGCTTAACTACTGGACTGAG 59.132 47.826 11.37 0.00 0.00 3.35
2530 3009 3.214328 GAACCTCTGCTTCAACTTTGGA 58.786 45.455 0.00 0.00 0.00 3.53
2537 3016 5.591099 TCTGCTTCAACTTTGGAAATGTTC 58.409 37.500 0.00 0.00 41.56 3.18
2543 3022 5.055812 TCAACTTTGGAAATGTTCATTGGC 58.944 37.500 0.00 0.00 41.56 4.52
2577 3056 0.104120 TCAGAATGCACGGGGTATCG 59.896 55.000 0.00 0.00 34.76 2.92
2671 3150 8.159447 TGGAAATACTGATCTATTCCCATGAAG 58.841 37.037 0.00 0.00 33.05 3.02
2677 3156 7.580910 ACTGATCTATTCCCATGAAGATGTTT 58.419 34.615 0.00 0.00 33.05 2.83
2678 3157 8.057623 ACTGATCTATTCCCATGAAGATGTTTT 58.942 33.333 0.00 0.00 33.05 2.43
2680 3159 8.906867 TGATCTATTCCCATGAAGATGTTTTTC 58.093 33.333 0.00 0.00 33.05 2.29
2681 3160 8.827832 ATCTATTCCCATGAAGATGTTTTTCA 57.172 30.769 0.00 0.00 38.76 2.69
2683 3162 9.258629 TCTATTCCCATGAAGATGTTTTTCAAT 57.741 29.630 0.00 0.00 38.01 2.57
2684 3163 9.880157 CTATTCCCATGAAGATGTTTTTCAATT 57.120 29.630 0.00 0.00 38.01 2.32
2685 3164 7.966246 TTCCCATGAAGATGTTTTTCAATTG 57.034 32.000 0.00 0.00 38.01 2.32
2686 3165 7.065120 TCCCATGAAGATGTTTTTCAATTGT 57.935 32.000 5.13 0.00 38.01 2.71
2687 3166 7.507829 TCCCATGAAGATGTTTTTCAATTGTT 58.492 30.769 5.13 0.00 38.01 2.83
2688 3167 7.441760 TCCCATGAAGATGTTTTTCAATTGTTG 59.558 33.333 5.13 0.00 38.01 3.33
2689 3168 7.308109 CCCATGAAGATGTTTTTCAATTGTTGG 60.308 37.037 5.13 0.00 38.01 3.77
2690 3169 7.308109 CCATGAAGATGTTTTTCAATTGTTGGG 60.308 37.037 5.13 0.00 38.01 4.12
2691 3170 6.882656 TGAAGATGTTTTTCAATTGTTGGGA 58.117 32.000 5.13 0.00 31.98 4.37
2713 3200 0.546598 GGTGTCGGGGATCTGGAAAT 59.453 55.000 0.00 0.00 0.00 2.17
2757 3244 7.672240 TGTTGTAATCAATGTACTGTCAGGTA 58.328 34.615 4.53 0.00 35.92 3.08
2761 3248 9.562408 TGTAATCAATGTACTGTCAGGTAAAAA 57.438 29.630 4.53 0.00 0.00 1.94
2801 3288 0.318441 TGCAGGAACTTCGTCAGGAG 59.682 55.000 0.00 0.00 34.60 3.69
2810 3297 0.809385 TTCGTCAGGAGGTCATCGTC 59.191 55.000 0.00 0.00 0.00 4.20
2831 3318 2.401766 CCTTGTGGATCAGTGCCGC 61.402 63.158 0.00 0.00 36.47 6.53
2841 3328 0.673333 TCAGTGCCGCACATACAAGG 60.673 55.000 24.97 5.86 36.74 3.61
2849 3336 2.534298 CGCACATACAAGGAGAGAGTG 58.466 52.381 0.00 0.00 0.00 3.51
2864 3351 1.202855 AGAGTGGTGCAGCTTGTCAAT 60.203 47.619 18.08 0.00 0.00 2.57
2880 3367 5.762825 TGTCAATAGTACCTCGTATGTCC 57.237 43.478 0.00 0.00 0.00 4.02
2909 3396 1.154413 CGCAGGCGCTTTAAGTGTG 60.154 57.895 7.64 0.01 35.30 3.82
2910 3397 1.442688 GCAGGCGCTTTAAGTGTGC 60.443 57.895 7.64 6.40 39.88 4.57
2911 3398 1.948508 CAGGCGCTTTAAGTGTGCA 59.051 52.632 7.64 0.00 42.10 4.57
2954 3442 9.837525 TGAAATTTTCTTTCATTTGTTGGTTTG 57.162 25.926 10.33 0.00 33.90 2.93
3129 3617 2.203070 ATCGCTCCATTCCACGCC 60.203 61.111 0.00 0.00 0.00 5.68
3133 3621 2.046023 CTCCATTCCACGCCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
3185 3673 3.492421 GGTTAGCACCATGTGTCAATG 57.508 47.619 0.00 0.00 43.61 2.82
3199 3687 7.095940 CCATGTGTCAATGATTTTGTTCAAGAC 60.096 37.037 0.00 0.00 36.27 3.01
3273 3761 8.951243 GTGCTTCCTAATTTGTTTATCTTCTCT 58.049 33.333 0.00 0.00 0.00 3.10
3448 3942 7.781324 ATACATCAAACCTGAACCTGAAAAT 57.219 32.000 0.00 0.00 34.49 1.82
3493 3987 4.284490 AGTGAATACTCAGCTTCAGACCAA 59.716 41.667 0.00 0.00 32.33 3.67
3523 4017 1.068748 GCACTTGCAGACATGTTCCAG 60.069 52.381 0.00 0.00 41.59 3.86
3602 4096 0.674581 CCCTGCATCTCGAGCAAACA 60.675 55.000 7.81 2.37 42.17 2.83
3620 4114 2.359602 CTGCTCCAGTGCACCCTG 60.360 66.667 14.63 6.13 38.12 4.45
3621 4115 3.170672 TGCTCCAGTGCACCCTGT 61.171 61.111 14.63 0.00 38.12 4.00
3622 4116 2.359230 GCTCCAGTGCACCCTGTC 60.359 66.667 14.63 0.00 0.00 3.51
3654 4148 4.214758 GCAACCCACTACTTATTCAAACGT 59.785 41.667 0.00 0.00 0.00 3.99
3746 4240 2.151202 GAGTGGATTCTCAACGGCAAA 58.849 47.619 0.00 0.00 34.88 3.68
3763 4257 5.941647 ACGGCAAACACTAAATTATGGTACT 59.058 36.000 0.00 0.00 0.00 2.73
3764 4258 7.104939 ACGGCAAACACTAAATTATGGTACTA 58.895 34.615 0.00 0.00 0.00 1.82
3766 4260 7.279313 CGGCAAACACTAAATTATGGTACTACT 59.721 37.037 0.00 0.00 0.00 2.57
3767 4261 8.953313 GGCAAACACTAAATTATGGTACTACTT 58.047 33.333 0.00 0.00 0.00 2.24
3780 4417 4.394300 TGGTACTACTTTCTCTCTACGTGC 59.606 45.833 0.00 0.00 0.00 5.34
3791 4428 0.038892 TCTACGTGCGGTTGTCTTCC 60.039 55.000 0.00 0.00 0.00 3.46
3794 4431 2.946762 GTGCGGTTGTCTTCCTGC 59.053 61.111 0.00 0.00 0.00 4.85
3795 4432 1.891919 GTGCGGTTGTCTTCCTGCA 60.892 57.895 0.00 0.00 34.31 4.41
3805 4443 3.930336 TGTCTTCCTGCAGATGTAGTTG 58.070 45.455 17.39 0.00 0.00 3.16
3932 4578 4.338012 TCCATGCACATTTGACAATCTCT 58.662 39.130 0.00 0.00 0.00 3.10
4017 4666 0.036671 GGTAACCGACCCCAAGACAG 60.037 60.000 0.00 0.00 43.25 3.51
4025 4674 0.468029 ACCCCAAGACAGCCAACTTG 60.468 55.000 0.00 0.00 41.85 3.16
4037 4686 1.869342 GCCAACTTGGTGCAATGTCAC 60.869 52.381 9.63 0.33 40.46 3.67
4048 4697 1.135489 GCAATGTCACTGCATCCACAG 60.135 52.381 0.42 0.00 43.59 3.66
4137 4816 3.964875 GCAGCAACCACCACCACG 61.965 66.667 0.00 0.00 0.00 4.94
4189 4868 4.188462 TGTACCCTAACTCGATGCAAATG 58.812 43.478 0.00 0.00 0.00 2.32
4200 4879 3.057596 TCGATGCAAATGAACCAAGGAAC 60.058 43.478 0.00 0.00 0.00 3.62
4293 4972 0.404040 ATGGCCGGTTATGGGTATGG 59.596 55.000 1.90 0.00 0.00 2.74
4297 4976 0.250727 CCGGTTATGGGTATGGGCAG 60.251 60.000 0.00 0.00 0.00 4.85
4306 4985 0.825010 GGTATGGGCAGCAATCTGGG 60.825 60.000 0.00 0.00 40.65 4.45
4309 4988 3.743017 GGGCAGCAATCTGGGGGA 61.743 66.667 0.00 0.00 40.65 4.81
4315 4994 2.307098 GCAGCAATCTGGGGGATACTAT 59.693 50.000 0.00 0.00 40.65 2.12
4333 5012 2.080286 ATATCCCGAACGCTGCATAC 57.920 50.000 0.00 0.00 0.00 2.39
4382 5061 2.012673 AGAGAATGAATGGAGCAACGC 58.987 47.619 0.00 0.00 0.00 4.84
4388 5067 2.051804 GAATGGAGCAACGCCATCCG 62.052 60.000 3.24 0.00 42.92 4.18
4407 5086 1.163554 GTTTCCCTGAAGCAGCAGAG 58.836 55.000 7.34 0.00 38.14 3.35
4420 5099 0.536687 AGCAGAGCAAAGCAAGCAGA 60.537 50.000 0.00 0.00 0.00 4.26
4427 5106 1.067516 GCAAAGCAAGCAGACCAGAAA 59.932 47.619 0.00 0.00 0.00 2.52
4456 5135 3.873361 TCTTTGGCGATCTTCTTAGCATG 59.127 43.478 0.00 0.00 0.00 4.06
4514 5193 3.335579 GTCGGTGGCTTGTAAGAAGAAT 58.664 45.455 0.00 0.00 0.00 2.40
4561 5240 1.266989 GCAGCAAAAGCTTTACCTCGT 59.733 47.619 13.10 0.00 0.00 4.18
4563 5242 3.058501 GCAGCAAAAGCTTTACCTCGTAA 60.059 43.478 13.10 0.00 0.00 3.18
4643 5322 7.901029 TGATGTAAATTCCATTTTTAGGCACA 58.099 30.769 0.00 0.00 33.82 4.57
4660 5339 3.561725 GGCACAGATACATACTGGAAAGC 59.438 47.826 0.00 0.00 39.38 3.51
4750 5430 8.458052 GTCATCAACATCCATGTGTACAAATAA 58.542 33.333 0.00 0.00 41.61 1.40
4751 5431 9.018582 TCATCAACATCCATGTGTACAAATAAA 57.981 29.630 0.00 0.00 41.61 1.40
4752 5432 9.292846 CATCAACATCCATGTGTACAAATAAAG 57.707 33.333 0.00 0.00 41.61 1.85
4753 5433 8.628630 TCAACATCCATGTGTACAAATAAAGA 57.371 30.769 0.00 0.00 41.61 2.52
4754 5434 8.511321 TCAACATCCATGTGTACAAATAAAGAC 58.489 33.333 0.00 0.00 41.61 3.01
4877 5558 0.315886 TTACAGCTCGCAAACGGAGA 59.684 50.000 0.00 0.00 40.63 3.71
4981 5664 1.151777 ATCCTGTTATGCGAACGCCG 61.152 55.000 16.27 0.00 41.09 6.46
4986 5669 4.858433 TATGCGAACGCCGTCCGG 62.858 66.667 16.27 0.24 42.52 5.14
5390 6073 2.363038 ACAACACTGCGAGTTACCTACA 59.637 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.006298 TGACCAATCAAATTAACTCTTGTTGT 57.994 30.769 0.00 0.00 37.59 3.32
5 6 8.870160 TTGACCAATCAAATTAACTCTTGTTG 57.130 30.769 0.00 0.00 41.99 3.33
20 21 3.395607 CCTCCCCATCTATTGACCAATCA 59.604 47.826 0.00 0.00 32.50 2.57
21 22 3.812167 GCCTCCCCATCTATTGACCAATC 60.812 52.174 0.00 0.00 32.50 2.67
22 23 2.108952 GCCTCCCCATCTATTGACCAAT 59.891 50.000 0.64 0.64 34.93 3.16
23 24 1.494721 GCCTCCCCATCTATTGACCAA 59.505 52.381 0.00 0.00 0.00 3.67
24 25 1.140312 GCCTCCCCATCTATTGACCA 58.860 55.000 0.00 0.00 0.00 4.02
25 26 0.035458 CGCCTCCCCATCTATTGACC 59.965 60.000 0.00 0.00 0.00 4.02
26 27 0.035458 CCGCCTCCCCATCTATTGAC 59.965 60.000 0.00 0.00 0.00 3.18
27 28 1.768684 GCCGCCTCCCCATCTATTGA 61.769 60.000 0.00 0.00 0.00 2.57
28 29 1.302832 GCCGCCTCCCCATCTATTG 60.303 63.158 0.00 0.00 0.00 1.90
29 30 2.529744 GGCCGCCTCCCCATCTATT 61.530 63.158 0.71 0.00 0.00 1.73
30 31 2.930562 GGCCGCCTCCCCATCTAT 60.931 66.667 0.71 0.00 0.00 1.98
42 43 4.986708 TTTTCAGGGGTGGGCCGC 62.987 66.667 9.05 9.05 46.91 6.53
43 44 2.037208 ATTTTCAGGGGTGGGCCG 59.963 61.111 0.00 0.00 34.97 6.13
44 45 0.972471 CTGATTTTCAGGGGTGGGCC 60.972 60.000 0.00 0.00 40.71 5.80
45 46 2.583472 CTGATTTTCAGGGGTGGGC 58.417 57.895 0.00 0.00 40.71 5.36
70 71 2.466846 ACCAATCATAAACTTGCCCCC 58.533 47.619 0.00 0.00 0.00 5.40
71 72 4.709886 ACTAACCAATCATAAACTTGCCCC 59.290 41.667 0.00 0.00 0.00 5.80
72 73 5.914898 ACTAACCAATCATAAACTTGCCC 57.085 39.130 0.00 0.00 0.00 5.36
73 74 7.859325 TCTACTAACCAATCATAAACTTGCC 57.141 36.000 0.00 0.00 0.00 4.52
74 75 9.109393 TCATCTACTAACCAATCATAAACTTGC 57.891 33.333 0.00 0.00 0.00 4.01
101 102 2.554370 TACACGCTGGCTAGGTTTTT 57.446 45.000 0.00 0.00 0.00 1.94
102 103 2.554370 TTACACGCTGGCTAGGTTTT 57.446 45.000 0.00 0.00 0.00 2.43
103 104 2.747446 CAATTACACGCTGGCTAGGTTT 59.253 45.455 0.00 0.00 0.00 3.27
104 105 2.356135 CAATTACACGCTGGCTAGGTT 58.644 47.619 0.00 0.00 0.00 3.50
105 106 2.012051 GCAATTACACGCTGGCTAGGT 61.012 52.381 0.00 0.00 0.00 3.08
106 107 0.657840 GCAATTACACGCTGGCTAGG 59.342 55.000 0.00 0.00 0.00 3.02
107 108 0.301687 CGCAATTACACGCTGGCTAG 59.698 55.000 0.00 0.00 0.00 3.42
108 109 0.390603 ACGCAATTACACGCTGGCTA 60.391 50.000 0.00 0.00 0.00 3.93
109 110 1.671054 ACGCAATTACACGCTGGCT 60.671 52.632 0.00 0.00 0.00 4.75
110 111 1.511887 CACGCAATTACACGCTGGC 60.512 57.895 0.00 0.00 0.00 4.85
111 112 1.072391 TACACGCAATTACACGCTGG 58.928 50.000 0.00 0.00 0.00 4.85
112 113 2.156891 AGTTACACGCAATTACACGCTG 59.843 45.455 0.00 0.00 0.00 5.18
113 114 2.409975 AGTTACACGCAATTACACGCT 58.590 42.857 0.00 0.00 0.00 5.07
114 115 2.410730 AGAGTTACACGCAATTACACGC 59.589 45.455 0.00 0.00 0.00 5.34
115 116 4.640805 AAGAGTTACACGCAATTACACG 57.359 40.909 0.00 0.00 0.00 4.49
116 117 5.744490 ACAAAGAGTTACACGCAATTACAC 58.256 37.500 0.00 0.00 0.00 2.90
117 118 5.994887 ACAAAGAGTTACACGCAATTACA 57.005 34.783 0.00 0.00 0.00 2.41
118 119 7.515643 ACATACAAAGAGTTACACGCAATTAC 58.484 34.615 0.00 0.00 0.00 1.89
119 120 7.661127 ACATACAAAGAGTTACACGCAATTA 57.339 32.000 0.00 0.00 0.00 1.40
120 121 6.554334 ACATACAAAGAGTTACACGCAATT 57.446 33.333 0.00 0.00 0.00 2.32
121 122 6.554334 AACATACAAAGAGTTACACGCAAT 57.446 33.333 0.00 0.00 0.00 3.56
122 123 5.994887 AACATACAAAGAGTTACACGCAA 57.005 34.783 0.00 0.00 0.00 4.85
123 124 5.994887 AAACATACAAAGAGTTACACGCA 57.005 34.783 0.00 0.00 0.00 5.24
124 125 6.013689 GCTAAACATACAAAGAGTTACACGC 58.986 40.000 0.00 0.00 0.00 5.34
125 126 7.112528 TGCTAAACATACAAAGAGTTACACG 57.887 36.000 0.00 0.00 0.00 4.49
148 149 4.996758 TGGATCGTATGTGGAGCAATAATG 59.003 41.667 0.00 0.00 0.00 1.90
149 150 5.227569 TGGATCGTATGTGGAGCAATAAT 57.772 39.130 0.00 0.00 0.00 1.28
150 151 4.681074 TGGATCGTATGTGGAGCAATAA 57.319 40.909 0.00 0.00 0.00 1.40
151 152 4.141824 TGTTGGATCGTATGTGGAGCAATA 60.142 41.667 0.00 0.00 0.00 1.90
152 153 3.206150 GTTGGATCGTATGTGGAGCAAT 58.794 45.455 0.00 0.00 0.00 3.56
153 154 2.027653 TGTTGGATCGTATGTGGAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
154 155 1.552792 TGTTGGATCGTATGTGGAGCA 59.447 47.619 0.00 0.00 0.00 4.26
155 156 2.309528 TGTTGGATCGTATGTGGAGC 57.690 50.000 0.00 0.00 0.00 4.70
156 157 3.063997 GCTTTGTTGGATCGTATGTGGAG 59.936 47.826 0.00 0.00 0.00 3.86
157 158 3.006940 GCTTTGTTGGATCGTATGTGGA 58.993 45.455 0.00 0.00 0.00 4.02
160 161 2.671396 GACGCTTTGTTGGATCGTATGT 59.329 45.455 0.00 0.00 33.21 2.29
167 168 2.154462 CCTTCAGACGCTTTGTTGGAT 58.846 47.619 0.00 0.00 0.00 3.41
184 185 1.534235 ACGCTCCTGACCTGACCTT 60.534 57.895 0.00 0.00 0.00 3.50
190 194 0.757188 CTATGGGACGCTCCTGACCT 60.757 60.000 4.41 0.00 36.57 3.85
198 202 1.755380 GTGGTAGTTCTATGGGACGCT 59.245 52.381 0.00 0.00 0.00 5.07
222 226 1.477377 GGGACACATATGCATGCCTGA 60.477 52.381 16.68 0.00 35.39 3.86
245 249 7.976734 GTGACAAAGTATATGTAGCTGAAGTCT 59.023 37.037 0.00 0.00 0.00 3.24
257 261 4.566759 CAGGGTGTCGTGACAAAGTATATG 59.433 45.833 3.92 0.00 43.77 1.78
301 305 8.484641 TGATGAGAGAAACATGATGAAACTAC 57.515 34.615 0.00 0.00 0.00 2.73
318 322 6.259608 AGGAAAATCGCACTTATTGATGAGAG 59.740 38.462 0.00 0.00 0.00 3.20
350 354 3.434637 CAATAATGGAAAACGGAAGGCG 58.565 45.455 0.00 0.00 0.00 5.52
356 360 2.344142 GCAACGCAATAATGGAAAACGG 59.656 45.455 0.00 0.00 0.00 4.44
368 372 2.264813 GCTTCAATCATGCAACGCAAT 58.735 42.857 0.00 0.00 43.62 3.56
491 499 2.044832 CTAGAGTTGGCTGCGCATGC 62.045 60.000 12.24 16.90 43.20 4.06
492 500 0.742281 ACTAGAGTTGGCTGCGCATG 60.742 55.000 12.24 6.51 0.00 4.06
493 501 0.824109 TACTAGAGTTGGCTGCGCAT 59.176 50.000 12.24 0.00 0.00 4.73
551 559 0.451463 TTTGTTTAGTTAGCGCGCGC 60.451 50.000 45.10 45.10 42.33 6.86
552 560 1.510007 CTTTGTTTAGTTAGCGCGCG 58.490 50.000 28.44 28.44 0.00 6.86
553 561 1.461897 TCCTTTGTTTAGTTAGCGCGC 59.538 47.619 26.66 26.66 0.00 6.86
554 562 2.093783 CCTCCTTTGTTTAGTTAGCGCG 59.906 50.000 0.00 0.00 0.00 6.86
629 637 2.034179 TGTTATGTCCTATCGGTCTGCG 59.966 50.000 0.00 0.00 0.00 5.18
682 690 0.882927 TTGACCGGCGGTTCTCAAAG 60.883 55.000 34.58 2.21 35.25 2.77
691 699 1.135257 TGCATAATTTTTGACCGGCGG 60.135 47.619 27.06 27.06 0.00 6.13
732 740 5.521735 CCAGCTACATGTAGTCACAAGAATC 59.478 44.000 28.95 11.91 38.42 2.52
878 886 2.238701 TCCCCTTTCCCCTCCTTGC 61.239 63.158 0.00 0.00 0.00 4.01
879 887 1.691823 GTCCCCTTTCCCCTCCTTG 59.308 63.158 0.00 0.00 0.00 3.61
880 888 1.923909 CGTCCCCTTTCCCCTCCTT 60.924 63.158 0.00 0.00 0.00 3.36
881 889 2.285442 CGTCCCCTTTCCCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
882 890 2.285144 TCGTCCCCTTTCCCCTCC 60.285 66.667 0.00 0.00 0.00 4.30
883 891 2.987962 GTCGTCCCCTTTCCCCTC 59.012 66.667 0.00 0.00 0.00 4.30
884 892 3.001406 CGTCGTCCCCTTTCCCCT 61.001 66.667 0.00 0.00 0.00 4.79
885 893 1.907222 ATTCGTCGTCCCCTTTCCCC 61.907 60.000 0.00 0.00 0.00 4.81
886 894 0.035725 AATTCGTCGTCCCCTTTCCC 60.036 55.000 0.00 0.00 0.00 3.97
887 895 1.066358 AGAATTCGTCGTCCCCTTTCC 60.066 52.381 0.00 0.00 0.00 3.13
888 896 2.381725 AGAATTCGTCGTCCCCTTTC 57.618 50.000 0.00 0.00 0.00 2.62
889 897 2.224450 ACAAGAATTCGTCGTCCCCTTT 60.224 45.455 0.00 0.00 0.00 3.11
890 898 1.346722 ACAAGAATTCGTCGTCCCCTT 59.653 47.619 0.00 0.00 0.00 3.95
891 899 0.974383 ACAAGAATTCGTCGTCCCCT 59.026 50.000 0.00 0.00 0.00 4.79
892 900 1.076332 CACAAGAATTCGTCGTCCCC 58.924 55.000 0.00 0.00 0.00 4.81
893 901 1.076332 CCACAAGAATTCGTCGTCCC 58.924 55.000 0.00 0.00 0.00 4.46
901 909 1.883021 CGGGTGGCCACAAGAATTC 59.117 57.895 35.78 17.15 0.00 2.17
951 959 1.830477 AGCAAAACAGCCCAAAACAGA 59.170 42.857 0.00 0.00 34.23 3.41
952 960 1.935199 CAGCAAAACAGCCCAAAACAG 59.065 47.619 0.00 0.00 34.23 3.16
963 971 1.412079 ATCAACCAGCCAGCAAAACA 58.588 45.000 0.00 0.00 0.00 2.83
965 973 2.423185 CGATATCAACCAGCCAGCAAAA 59.577 45.455 3.12 0.00 0.00 2.44
966 974 2.016318 CGATATCAACCAGCCAGCAAA 58.984 47.619 3.12 0.00 0.00 3.68
1122 1166 1.766143 GCAGATGGCAATCGTCGGTC 61.766 60.000 0.00 0.00 43.97 4.79
1123 1167 1.815421 GCAGATGGCAATCGTCGGT 60.815 57.895 0.00 0.00 43.97 4.69
1124 1168 3.017323 GCAGATGGCAATCGTCGG 58.983 61.111 0.00 0.00 43.97 4.79
1209 1257 1.201414 AGGCGCGAAACCAAATTAAGG 59.799 47.619 12.10 0.00 0.00 2.69
1244 1293 2.790387 GCAGCTCGCAAAGATTTAAGG 58.210 47.619 3.64 0.00 41.79 2.69
1272 1321 5.012664 TGCTGATCTGACCAAAAGGTAAGTA 59.987 40.000 3.42 0.00 0.00 2.24
1274 1323 4.326826 TGCTGATCTGACCAAAAGGTAAG 58.673 43.478 3.42 0.00 0.00 2.34
1290 1643 5.013183 AGGTACTTGGTAGTTCTTTGCTGAT 59.987 40.000 0.00 0.00 35.78 2.90
1361 1811 6.151144 ACAACATCTTTTGTATGCCTAGGAAC 59.849 38.462 14.75 7.69 37.96 3.62
1485 1949 8.651588 CACAGACTAATAGTTGATGAGTCAAAC 58.348 37.037 0.00 0.00 45.68 2.93
1512 1976 8.934697 TCAAATAGACTAATAGTGGGCATAGTT 58.065 33.333 0.00 0.00 0.00 2.24
1585 2049 8.451748 ACAACTCAAGAAAACTAGAGAAACAAC 58.548 33.333 0.00 0.00 32.59 3.32
1586 2050 8.561738 ACAACTCAAGAAAACTAGAGAAACAA 57.438 30.769 0.00 0.00 32.59 2.83
1587 2051 8.561738 AACAACTCAAGAAAACTAGAGAAACA 57.438 30.769 0.00 0.00 32.59 2.83
1588 2052 9.491934 GAAACAACTCAAGAAAACTAGAGAAAC 57.508 33.333 0.00 0.00 32.59 2.78
1590 2054 8.883731 CAGAAACAACTCAAGAAAACTAGAGAA 58.116 33.333 0.00 0.00 32.59 2.87
1591 2055 8.041323 ACAGAAACAACTCAAGAAAACTAGAGA 58.959 33.333 0.00 0.00 32.59 3.10
1594 2058 9.099454 ACTACAGAAACAACTCAAGAAAACTAG 57.901 33.333 0.00 0.00 0.00 2.57
1595 2059 9.444600 AACTACAGAAACAACTCAAGAAAACTA 57.555 29.630 0.00 0.00 0.00 2.24
1596 2060 7.923414 ACTACAGAAACAACTCAAGAAAACT 57.077 32.000 0.00 0.00 0.00 2.66
1597 2061 8.234546 TCAACTACAGAAACAACTCAAGAAAAC 58.765 33.333 0.00 0.00 0.00 2.43
1599 2063 7.915293 TCAACTACAGAAACAACTCAAGAAA 57.085 32.000 0.00 0.00 0.00 2.52
1600 2064 9.261180 CTATCAACTACAGAAACAACTCAAGAA 57.739 33.333 0.00 0.00 0.00 2.52
1619 2083 1.863454 CAGCTCATCGTGGCTATCAAC 59.137 52.381 0.00 0.00 37.00 3.18
1721 2185 3.119065 TGATGTAATGCATTGCCAGGTTG 60.119 43.478 22.27 0.00 38.06 3.77
1745 2209 1.615384 GCCTTGCATCTTCCTTCTGGT 60.615 52.381 0.00 0.00 34.23 4.00
1760 2224 3.559238 AAGCGTTCTAAATGTGCCTTG 57.441 42.857 0.00 0.00 0.00 3.61
1761 2225 5.699097 TTAAAGCGTTCTAAATGTGCCTT 57.301 34.783 0.00 0.00 0.00 4.35
1762 2226 5.897377 ATTAAAGCGTTCTAAATGTGCCT 57.103 34.783 0.00 0.00 0.00 4.75
1841 2305 6.506500 AATCATTGTCTCCAGCAACTAAAG 57.493 37.500 0.00 0.00 0.00 1.85
2009 2475 3.826524 TCAGGCTAAAATCACCACACAA 58.173 40.909 0.00 0.00 0.00 3.33
2019 2485 9.391006 TCTTTTACGTGATAATCAGGCTAAAAT 57.609 29.630 0.00 0.00 35.83 1.82
2174 2652 3.994392 TCTGCAAAATCCGAGACTGTTAC 59.006 43.478 0.00 0.00 0.00 2.50
2242 2720 9.601217 GCTGAGTGGAGATTAGAGTTTAATTAA 57.399 33.333 0.00 0.00 0.00 1.40
2295 2774 6.549433 AAATATTGGCACAGATCCATTTGT 57.451 33.333 0.00 0.00 42.39 2.83
2325 2804 2.136298 TGTAGAGGCTGAGTCTGAGG 57.864 55.000 0.00 0.00 0.00 3.86
2327 2806 3.898123 AGTTTTGTAGAGGCTGAGTCTGA 59.102 43.478 0.00 0.00 0.00 3.27
2366 2845 2.230994 GAGCCTCGTGGTCAGCATCA 62.231 60.000 5.26 0.00 41.24 3.07
2415 2894 7.625828 ACTTTCATAAGTTGGTATACCTTGC 57.374 36.000 22.41 12.11 41.85 4.01
2435 2914 8.917088 AGCATGCCTATTGTATGATAAAACTTT 58.083 29.630 15.66 0.00 39.21 2.66
2453 2932 2.840651 AGTCCAGTAGTTAAGCATGCCT 59.159 45.455 15.66 3.39 0.00 4.75
2477 2956 8.134895 TCAAATAAGCGTATCCAAATTTGATCC 58.865 33.333 19.86 3.77 38.02 3.36
2486 2965 7.857734 TCAGATTTCAAATAAGCGTATCCAA 57.142 32.000 0.00 0.00 0.00 3.53
2489 2968 7.920738 AGGTTCAGATTTCAAATAAGCGTATC 58.079 34.615 0.00 0.00 0.00 2.24
2494 2973 6.032717 GCAGAGGTTCAGATTTCAAATAAGC 58.967 40.000 0.00 0.00 0.00 3.09
2530 3009 1.276989 CCAGGCTGCCAATGAACATTT 59.723 47.619 22.65 0.00 0.00 2.32
2537 3016 0.466739 TATCTGCCAGGCTGCCAATG 60.467 55.000 22.65 11.30 0.00 2.82
2543 3022 2.924757 TCTGAATATCTGCCAGGCTG 57.075 50.000 14.15 13.09 0.00 4.85
2577 3056 1.993370 CATCTCCGAAAGAACGTCCAC 59.007 52.381 0.00 0.00 37.61 4.02
2646 3125 8.378565 TCTTCATGGGAATAGATCAGTATTTCC 58.621 37.037 5.44 5.44 38.24 3.13
2671 3150 4.447389 CGGTCCCAACAATTGAAAAACATC 59.553 41.667 13.59 0.00 0.00 3.06
2677 3156 1.683917 CACCGGTCCCAACAATTGAAA 59.316 47.619 13.59 0.00 0.00 2.69
2678 3157 1.323412 CACCGGTCCCAACAATTGAA 58.677 50.000 13.59 0.00 0.00 2.69
2680 3159 0.596082 GACACCGGTCCCAACAATTG 59.404 55.000 2.59 3.24 38.12 2.32
2681 3160 0.887387 CGACACCGGTCCCAACAATT 60.887 55.000 2.59 0.00 41.13 2.32
2683 3162 2.109387 CGACACCGGTCCCAACAA 59.891 61.111 2.59 0.00 41.13 2.83
2713 3200 7.169158 ACAACAATTGAAAAACTTCAGAGGA 57.831 32.000 13.59 0.00 31.87 3.71
2772 3259 3.242543 CGAAGTTCCTGCATATTCAGTGC 60.243 47.826 1.63 0.00 42.81 4.40
2773 3260 3.935203 ACGAAGTTCCTGCATATTCAGTG 59.065 43.478 1.63 0.00 37.78 3.66
2810 3297 1.021390 GGCACTGATCCACAAGGTCG 61.021 60.000 0.00 0.00 35.89 4.79
2831 3318 3.854666 CACCACTCTCTCCTTGTATGTG 58.145 50.000 0.00 0.00 0.00 3.21
2841 3328 0.034616 ACAAGCTGCACCACTCTCTC 59.965 55.000 1.02 0.00 0.00 3.20
2849 3336 2.678336 GGTACTATTGACAAGCTGCACC 59.322 50.000 1.02 0.00 0.00 5.01
2864 3351 2.954318 GCAAGGGACATACGAGGTACTA 59.046 50.000 0.00 0.00 41.55 1.82
3004 3492 2.853542 TGGCTGAGCAACCCCTCA 60.854 61.111 6.82 0.00 39.42 3.86
3090 3578 1.831652 CTGCTTCTCCACCGGAACCT 61.832 60.000 9.46 0.00 0.00 3.50
3129 3617 5.412594 TCTTTTGTAGTATCTGGCTTTGCTG 59.587 40.000 0.00 0.00 0.00 4.41
3133 3621 6.003950 TGCTTCTTTTGTAGTATCTGGCTTT 58.996 36.000 0.00 0.00 0.00 3.51
3199 3687 9.803315 TTGCTAGTGTATGTTTCTAGTAGAATG 57.197 33.333 13.34 0.00 33.67 2.67
3273 3761 4.214310 TGCTGAAGACCTGGAAAAATGAA 58.786 39.130 0.00 0.00 0.00 2.57
3277 3765 3.631250 AGTTGCTGAAGACCTGGAAAAA 58.369 40.909 0.00 0.00 0.00 1.94
3282 3770 3.258372 TGTAGTAGTTGCTGAAGACCTGG 59.742 47.826 0.00 0.00 0.00 4.45
3353 3847 3.128242 GCTTTTGCACTGCTAGATGATGT 59.872 43.478 1.98 0.00 46.58 3.06
3397 3891 2.824341 TCCACTAAGGAGGTCGAAACTC 59.176 50.000 9.31 9.31 43.07 3.01
3421 3915 4.935205 TCAGGTTCAGGTTTGATGTATTCG 59.065 41.667 0.00 0.00 32.27 3.34
3424 3918 7.781324 ATTTTCAGGTTCAGGTTTGATGTAT 57.219 32.000 0.00 0.00 32.27 2.29
3493 3987 3.573538 TGTCTGCAAGTGCCAATACATTT 59.426 39.130 0.00 0.00 41.18 2.32
3505 3999 1.242076 GCTGGAACATGTCTGCAAGT 58.758 50.000 0.00 0.00 38.20 3.16
3523 4017 0.244450 TGGCAGCAGCACTATTTTGC 59.756 50.000 2.65 0.00 44.61 3.68
3602 4096 2.851102 AGGGTGCACTGGAGCAGT 60.851 61.111 17.98 0.00 46.69 4.40
3763 4257 2.430465 ACCGCACGTAGAGAGAAAGTA 58.570 47.619 0.00 0.00 0.00 2.24
3764 4258 1.245732 ACCGCACGTAGAGAGAAAGT 58.754 50.000 0.00 0.00 0.00 2.66
3766 4260 1.338973 ACAACCGCACGTAGAGAGAAA 59.661 47.619 0.00 0.00 0.00 2.52
3767 4261 0.956633 ACAACCGCACGTAGAGAGAA 59.043 50.000 0.00 0.00 0.00 2.87
3769 4263 0.522180 AGACAACCGCACGTAGAGAG 59.478 55.000 0.00 0.00 0.00 3.20
3774 4268 0.319211 CAGGAAGACAACCGCACGTA 60.319 55.000 0.00 0.00 0.00 3.57
3780 4417 1.081892 CATCTGCAGGAAGACAACCG 58.918 55.000 15.13 0.00 0.00 4.44
3791 4428 6.145209 GCACATATACTCAACTACATCTGCAG 59.855 42.308 7.63 7.63 0.00 4.41
3794 4431 9.351570 CTATGCACATATACTCAACTACATCTG 57.648 37.037 0.00 0.00 0.00 2.90
3795 4432 9.301897 TCTATGCACATATACTCAACTACATCT 57.698 33.333 0.00 0.00 0.00 2.90
3890 4533 7.281549 GCATGGAGCTATTTGAAATGGAATTTT 59.718 33.333 5.40 0.00 43.38 1.82
3891 4534 6.764560 GCATGGAGCTATTTGAAATGGAATTT 59.235 34.615 5.40 0.00 45.04 1.82
3892 4535 6.126997 TGCATGGAGCTATTTGAAATGGAATT 60.127 34.615 5.40 0.00 45.94 2.17
3893 4536 5.364446 TGCATGGAGCTATTTGAAATGGAAT 59.636 36.000 5.40 0.00 45.94 3.01
3932 4578 5.198207 TCGATCCTCTACACCTGTCAATTA 58.802 41.667 0.00 0.00 0.00 1.40
4007 4656 2.344535 CAAGTTGGCTGTCTTGGGG 58.655 57.895 0.00 0.00 37.83 4.96
4017 4666 0.388659 TGACATTGCACCAAGTTGGC 59.611 50.000 22.25 9.43 42.67 4.52
4037 4686 1.880894 CAGGTTGCTGTGGATGCAG 59.119 57.895 0.00 0.00 41.71 4.41
4060 4709 1.907807 TGCTGATTGGGGTTGCACC 60.908 57.895 0.00 0.00 37.60 5.01
4137 4816 1.439353 CTGCATGTCCGGCACATACC 61.439 60.000 16.04 11.84 44.60 2.73
4148 4827 2.513897 GCCCCCGTACTGCATGTC 60.514 66.667 0.00 0.00 0.00 3.06
4174 4853 4.155826 CCTTGGTTCATTTGCATCGAGTTA 59.844 41.667 0.00 0.00 0.00 2.24
4177 4856 2.749076 TCCTTGGTTCATTTGCATCGAG 59.251 45.455 0.00 0.00 0.00 4.04
4189 4868 0.608035 TCATGCCCGTTCCTTGGTTC 60.608 55.000 0.00 0.00 0.00 3.62
4233 4912 7.339466 ACTGTTGATAGTTCATCCCATAAAACC 59.661 37.037 0.00 0.00 32.09 3.27
4293 4972 0.538287 GTATCCCCCAGATTGCTGCC 60.538 60.000 0.00 0.00 40.91 4.85
4297 4976 5.297569 GGATATAGTATCCCCCAGATTGC 57.702 47.826 4.93 0.00 36.33 3.56
4309 4988 2.823747 TGCAGCGTTCGGGATATAGTAT 59.176 45.455 0.00 0.00 0.00 2.12
4315 4994 0.318360 CGTATGCAGCGTTCGGGATA 60.318 55.000 5.76 0.00 0.00 2.59
4327 5006 1.866471 GCACTGGTATACGCGTATGCA 60.866 52.381 36.60 25.21 42.97 3.96
4333 5012 1.930503 TCATTTGCACTGGTATACGCG 59.069 47.619 3.53 3.53 0.00 6.01
4382 5061 0.322456 TGCTTCAGGGAAACGGATGG 60.322 55.000 0.00 0.00 0.00 3.51
4388 5067 1.163554 CTCTGCTGCTTCAGGGAAAC 58.836 55.000 0.00 0.00 36.69 2.78
4393 5072 0.522180 CTTTGCTCTGCTGCTTCAGG 59.478 55.000 0.00 0.03 34.91 3.86
4407 5086 0.670162 TTCTGGTCTGCTTGCTTTGC 59.330 50.000 0.00 0.00 0.00 3.68
4420 5099 2.222027 CCAAAGAGCGAGTTTTCTGGT 58.778 47.619 0.00 0.00 0.00 4.00
4456 5135 0.604578 TGCTCTGCTTCATTTTGGCC 59.395 50.000 0.00 0.00 0.00 5.36
4514 5193 0.921166 ATCATGCATCCACTCCACCA 59.079 50.000 0.00 0.00 0.00 4.17
4563 5242 9.640963 GCCAAATAGAATTATGTACTACGAGAT 57.359 33.333 0.00 0.00 0.00 2.75
4643 5322 6.058183 GTCCATTGCTTTCCAGTATGTATCT 58.942 40.000 0.00 0.00 0.00 1.98
4660 5339 7.219322 TCATACAGGAATCATACAGTCCATTG 58.781 38.462 0.00 0.00 42.25 2.82
4704 5383 9.083080 TGATGACACTACAAAATTCGTACTATG 57.917 33.333 0.00 0.00 0.00 2.23
4706 5385 8.918658 GTTGATGACACTACAAAATTCGTACTA 58.081 33.333 0.00 0.00 0.00 1.82
4877 5558 8.770438 TTTTCAGTTCTATGTGCTTTGTTTTT 57.230 26.923 0.00 0.00 0.00 1.94
4931 5614 8.802267 GTCTAGAGAGCTTGTCCTTATTATCAT 58.198 37.037 0.00 0.00 0.00 2.45
4981 5664 4.124970 GGTTATATTCAACCAGTCCGGAC 58.875 47.826 27.67 27.67 46.14 4.79
5057 5740 4.080129 ACGTGGTCCTTACTCACTCCTATA 60.080 45.833 0.00 0.00 0.00 1.31
5165 5848 6.043854 TGTGCGTTATTATGGGCTATATGA 57.956 37.500 0.00 0.00 0.00 2.15
5390 6073 5.148651 ACAACTTACTTAAGAGGCGATGT 57.851 39.130 10.09 4.36 37.08 3.06
5455 6138 6.350696 GGTTAAGGTTCCTTTGCGGATTAAAT 60.351 38.462 9.46 0.00 42.70 1.40


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

AutoCloner maintained by Alex Coulton.