Multiple sequence alignment - TraesCS5B01G272600

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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 TraesCS5B01G272600 chr5B 100.000 2880 0 0 390 3269 458144119 458146998 0.000000e+00 5319
1 TraesCS5B01G272600 chr5B 100.000 177 0 0 1 177 458143730 458143906 8.750000e-86 327
2 TraesCS5B01G272600 chr5A 91.526 2490 95 58 409 2859 482117908 482120320 0.000000e+00 3323
3 TraesCS5B01G272600 chr5A 92.718 412 23 4 2861 3269 482120481 482120888 3.630000e-164 588
4 TraesCS5B01G272600 chr5D 90.441 1475 74 37 1825 3269 381911008 381912445 0.000000e+00 1881
5 TraesCS5B01G272600 chr5D 94.476 887 17 12 565 1443 381909765 381910627 0.000000e+00 1338
6 TraesCS5B01G272600 chr5D 95.738 305 10 3 1445 1749 381910598 381910899 3.790000e-134 488
7 TraesCS5B01G272600 chrUn 100.000 393 0 0 988 1380 479539515 479539907 0.000000e+00 726
8 TraesCS5B01G272600 chr7D 84.364 275 41 2 1133 1406 220507332 220507605 5.380000e-68 268


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 TraesCS5B01G272600 chr5B 458143730 458146998 3268 False 2823.000000 5319 100.000000 1 3269 2 chr5B.!!$F1 3268
1 TraesCS5B01G272600 chr5A 482117908 482120888 2980 False 1955.500000 3323 92.122000 409 3269 2 chr5A.!!$F1 2860
2 TraesCS5B01G272600 chr5D 381909765 381912445 2680 False 1235.666667 1881 93.551667 565 3269 3 chr5D.!!$F1 2704

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
137 138 0.031585 TCCGTCCGAGATTTATGCCG 59.968 55.0 0.0 0.00 0.00 5.69 F
161 162 0.109153 GGTTGTAACCTCCGGGTGTT 59.891 55.0 0.0 8.24 46.67 3.32 F
743 745 0.114168 ACACCACTCCTCTCTGCTCT 59.886 55.0 0.0 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1833 0.671781 CCCGCTCCGATGGATCAATC 60.672 60.0 0.0 0.0 0.00 2.67 R
1826 1895 0.796927 GCCGTAGTTGAAGTTCCTGC 59.203 55.0 0.0 0.0 0.00 4.85 R
2355 2450 0.108207 CCCAAAATGGCACCAAAGCA 59.892 50.0 0.0 0.0 35.79 3.91 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
26 27 9.632638 AAGATACATATGAAAATTAGTGGTGCT 57.367 29.630 10.38 0.00 0.00 4.40
27 28 9.632638 AGATACATATGAAAATTAGTGGTGCTT 57.367 29.630 10.38 0.00 0.00 3.91
28 29 9.669353 GATACATATGAAAATTAGTGGTGCTTG 57.331 33.333 10.38 0.00 0.00 4.01
29 30 7.466746 ACATATGAAAATTAGTGGTGCTTGT 57.533 32.000 10.38 0.00 0.00 3.16
30 31 8.574251 ACATATGAAAATTAGTGGTGCTTGTA 57.426 30.769 10.38 0.00 0.00 2.41
31 32 9.189156 ACATATGAAAATTAGTGGTGCTTGTAT 57.811 29.630 10.38 0.00 0.00 2.29
35 36 8.630054 TGAAAATTAGTGGTGCTTGTATTACT 57.370 30.769 0.00 0.00 0.00 2.24
36 37 8.726988 TGAAAATTAGTGGTGCTTGTATTACTC 58.273 33.333 0.00 0.00 0.00 2.59
37 38 8.630054 AAAATTAGTGGTGCTTGTATTACTCA 57.370 30.769 0.00 0.00 0.00 3.41
38 39 8.807948 AAATTAGTGGTGCTTGTATTACTCAT 57.192 30.769 0.00 0.00 0.00 2.90
39 40 9.899661 AAATTAGTGGTGCTTGTATTACTCATA 57.100 29.630 0.00 0.00 0.00 2.15
41 42 9.712305 ATTAGTGGTGCTTGTATTACTCATATC 57.288 33.333 0.00 0.00 0.00 1.63
42 43 7.366847 AGTGGTGCTTGTATTACTCATATCT 57.633 36.000 0.00 0.00 0.00 1.98
43 44 7.212976 AGTGGTGCTTGTATTACTCATATCTG 58.787 38.462 0.00 0.00 0.00 2.90
44 45 7.069950 AGTGGTGCTTGTATTACTCATATCTGA 59.930 37.037 0.00 0.00 0.00 3.27
45 46 7.169982 GTGGTGCTTGTATTACTCATATCTGAC 59.830 40.741 0.00 0.00 0.00 3.51
46 47 7.069950 TGGTGCTTGTATTACTCATATCTGACT 59.930 37.037 0.00 0.00 0.00 3.41
47 48 8.577296 GGTGCTTGTATTACTCATATCTGACTA 58.423 37.037 0.00 0.00 0.00 2.59
64 65 8.894768 ATCTGACTATCAAAACTATGTAAGCC 57.105 34.615 0.00 0.00 0.00 4.35
65 66 7.847096 TCTGACTATCAAAACTATGTAAGCCA 58.153 34.615 0.00 0.00 0.00 4.75
66 67 8.486210 TCTGACTATCAAAACTATGTAAGCCAT 58.514 33.333 0.00 0.00 37.58 4.40
67 68 9.113838 CTGACTATCAAAACTATGTAAGCCATT 57.886 33.333 0.00 0.00 34.86 3.16
68 69 9.461312 TGACTATCAAAACTATGTAAGCCATTT 57.539 29.630 0.00 0.00 34.86 2.32
75 76 9.853555 CAAAACTATGTAAGCCATTTTATGTCA 57.146 29.630 0.00 0.00 34.86 3.58
78 79 9.855021 AACTATGTAAGCCATTTTATGTCAAAC 57.145 29.630 0.00 0.00 34.86 2.93
79 80 9.243105 ACTATGTAAGCCATTTTATGTCAAACT 57.757 29.630 0.00 0.00 34.86 2.66
82 83 8.586570 TGTAAGCCATTTTATGTCAAACTTTG 57.413 30.769 0.00 0.00 0.00 2.77
83 84 8.417106 TGTAAGCCATTTTATGTCAAACTTTGA 58.583 29.630 0.00 0.00 37.33 2.69
84 85 7.951530 AAGCCATTTTATGTCAAACTTTGAG 57.048 32.000 4.36 0.00 41.01 3.02
85 86 7.288810 AGCCATTTTATGTCAAACTTTGAGA 57.711 32.000 4.36 4.15 41.01 3.27
86 87 7.373493 AGCCATTTTATGTCAAACTTTGAGAG 58.627 34.615 4.36 0.00 41.01 3.20
87 88 7.231317 AGCCATTTTATGTCAAACTTTGAGAGA 59.769 33.333 4.36 0.00 41.01 3.10
88 89 7.867403 GCCATTTTATGTCAAACTTTGAGAGAA 59.133 33.333 4.36 4.70 41.01 2.87
89 90 9.185192 CCATTTTATGTCAAACTTTGAGAGAAC 57.815 33.333 7.93 0.00 41.01 3.01
90 91 9.734620 CATTTTATGTCAAACTTTGAGAGAACA 57.265 29.630 7.93 3.53 41.01 3.18
91 92 9.736023 ATTTTATGTCAAACTTTGAGAGAACAC 57.264 29.630 7.93 0.00 41.01 3.32
92 93 7.857734 TTATGTCAAACTTTGAGAGAACACA 57.142 32.000 4.36 0.00 41.01 3.72
93 94 6.949352 ATGTCAAACTTTGAGAGAACACAT 57.051 33.333 4.36 1.51 41.01 3.21
94 95 9.554395 TTATGTCAAACTTTGAGAGAACACATA 57.446 29.630 4.36 5.45 41.01 2.29
95 96 8.627208 ATGTCAAACTTTGAGAGAACACATAT 57.373 30.769 4.36 0.00 41.01 1.78
96 97 9.725019 ATGTCAAACTTTGAGAGAACACATATA 57.275 29.630 4.36 0.00 41.01 0.86
97 98 9.725019 TGTCAAACTTTGAGAGAACACATATAT 57.275 29.630 4.36 0.00 41.01 0.86
104 105 9.190858 CTTTGAGAGAACACATATATAGACTGC 57.809 37.037 0.00 0.00 0.00 4.40
105 106 7.823745 TGAGAGAACACATATATAGACTGCA 57.176 36.000 0.00 0.00 0.00 4.41
106 107 7.880105 TGAGAGAACACATATATAGACTGCAG 58.120 38.462 13.48 13.48 0.00 4.41
107 108 7.503902 TGAGAGAACACATATATAGACTGCAGT 59.496 37.037 21.88 21.88 0.00 4.40
108 109 8.243961 AGAGAACACATATATAGACTGCAGTT 57.756 34.615 22.65 13.26 0.00 3.16
109 110 8.700051 AGAGAACACATATATAGACTGCAGTTT 58.300 33.333 22.65 18.57 0.00 2.66
110 111 8.654230 AGAACACATATATAGACTGCAGTTTG 57.346 34.615 22.65 12.04 0.00 2.93
111 112 7.712639 AGAACACATATATAGACTGCAGTTTGG 59.287 37.037 22.65 7.61 0.00 3.28
112 113 6.889198 ACACATATATAGACTGCAGTTTGGT 58.111 36.000 22.65 11.19 0.00 3.67
113 114 7.338710 ACACATATATAGACTGCAGTTTGGTT 58.661 34.615 22.65 9.13 0.00 3.67
114 115 8.482943 ACACATATATAGACTGCAGTTTGGTTA 58.517 33.333 22.65 11.04 0.00 2.85
115 116 8.982685 CACATATATAGACTGCAGTTTGGTTAG 58.017 37.037 22.65 10.51 0.00 2.34
116 117 8.150945 ACATATATAGACTGCAGTTTGGTTAGG 58.849 37.037 22.65 14.02 0.00 2.69
117 118 6.808321 ATATAGACTGCAGTTTGGTTAGGA 57.192 37.500 22.65 0.00 0.00 2.94
118 119 5.700402 ATAGACTGCAGTTTGGTTAGGAT 57.300 39.130 22.65 0.46 0.00 3.24
119 120 3.944087 AGACTGCAGTTTGGTTAGGATC 58.056 45.455 22.65 3.06 0.00 3.36
120 121 3.010420 GACTGCAGTTTGGTTAGGATCC 58.990 50.000 22.65 2.48 0.00 3.36
121 122 2.009774 CTGCAGTTTGGTTAGGATCCG 58.990 52.381 5.25 0.00 0.00 4.18
122 123 1.349688 TGCAGTTTGGTTAGGATCCGT 59.650 47.619 5.98 0.00 0.00 4.69
123 124 2.007608 GCAGTTTGGTTAGGATCCGTC 58.992 52.381 5.98 0.62 0.00 4.79
124 125 2.629051 CAGTTTGGTTAGGATCCGTCC 58.371 52.381 5.98 10.69 45.45 4.79
135 136 2.338500 GGATCCGTCCGAGATTTATGC 58.662 52.381 0.00 0.00 34.13 3.14
136 137 2.338500 GATCCGTCCGAGATTTATGCC 58.662 52.381 0.00 0.00 0.00 4.40
137 138 0.031585 TCCGTCCGAGATTTATGCCG 59.968 55.000 0.00 0.00 0.00 5.69
138 139 1.557443 CCGTCCGAGATTTATGCCGC 61.557 60.000 0.00 0.00 0.00 6.53
139 140 1.557443 CGTCCGAGATTTATGCCGCC 61.557 60.000 0.00 0.00 0.00 6.13
140 141 0.531974 GTCCGAGATTTATGCCGCCA 60.532 55.000 0.00 0.00 0.00 5.69
141 142 0.396435 TCCGAGATTTATGCCGCCAT 59.604 50.000 0.00 0.00 35.44 4.40
142 143 0.518636 CCGAGATTTATGCCGCCATG 59.481 55.000 0.00 0.00 32.85 3.66
143 144 0.518636 CGAGATTTATGCCGCCATGG 59.481 55.000 7.63 7.63 42.50 3.66
144 145 1.609208 GAGATTTATGCCGCCATGGT 58.391 50.000 14.67 0.00 41.21 3.55
145 146 1.956477 GAGATTTATGCCGCCATGGTT 59.044 47.619 14.67 0.00 41.21 3.67
146 147 1.682854 AGATTTATGCCGCCATGGTTG 59.317 47.619 14.67 6.37 41.21 3.77
147 148 1.408702 GATTTATGCCGCCATGGTTGT 59.591 47.619 14.67 0.00 41.21 3.32
148 149 2.130272 TTTATGCCGCCATGGTTGTA 57.870 45.000 14.67 4.70 41.21 2.41
149 150 2.130272 TTATGCCGCCATGGTTGTAA 57.870 45.000 14.67 3.65 41.21 2.41
150 151 1.384525 TATGCCGCCATGGTTGTAAC 58.615 50.000 14.67 0.00 41.21 2.50
159 160 4.707791 GGTTGTAACCTCCGGGTG 57.292 61.111 0.00 0.00 46.67 4.61
160 161 1.756665 GGTTGTAACCTCCGGGTGT 59.243 57.895 0.00 0.00 46.67 4.16
161 162 0.109153 GGTTGTAACCTCCGGGTGTT 59.891 55.000 0.00 8.24 46.67 3.32
162 163 1.232119 GTTGTAACCTCCGGGTGTTG 58.768 55.000 16.68 0.00 46.67 3.33
163 164 1.129917 TTGTAACCTCCGGGTGTTGA 58.870 50.000 16.68 3.95 46.67 3.18
164 165 0.682852 TGTAACCTCCGGGTGTTGAG 59.317 55.000 16.68 0.00 46.67 3.02
165 166 0.672711 GTAACCTCCGGGTGTTGAGC 60.673 60.000 16.68 6.20 46.67 4.26
166 167 1.122632 TAACCTCCGGGTGTTGAGCA 61.123 55.000 16.68 0.00 46.67 4.26
167 168 1.990160 AACCTCCGGGTGTTGAGCAA 61.990 55.000 0.00 0.00 46.67 3.91
168 169 1.228124 CCTCCGGGTGTTGAGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
169 170 0.821711 CCTCCGGGTGTTGAGCAAAA 60.822 55.000 0.00 0.00 0.00 2.44
170 171 1.028905 CTCCGGGTGTTGAGCAAAAA 58.971 50.000 0.00 0.00 0.00 1.94
171 172 1.613437 CTCCGGGTGTTGAGCAAAAAT 59.387 47.619 0.00 0.00 0.00 1.82
172 173 1.339610 TCCGGGTGTTGAGCAAAAATG 59.660 47.619 0.00 0.00 0.00 2.32
173 174 1.139163 CGGGTGTTGAGCAAAAATGC 58.861 50.000 0.00 0.00 0.00 3.56
175 176 2.030363 CGGGTGTTGAGCAAAAATGCTA 60.030 45.455 2.89 0.00 46.36 3.49
176 177 3.317150 GGGTGTTGAGCAAAAATGCTAC 58.683 45.455 2.89 0.28 46.36 3.58
431 432 7.118680 CGGGTGTTGAGTAATAGTACAAATGTT 59.881 37.037 2.81 0.00 32.12 2.71
467 468 8.463930 AATAAAAGTCAAGACAAATGTGGAGA 57.536 30.769 2.72 0.00 0.00 3.71
468 469 6.773976 AAAAGTCAAGACAAATGTGGAGAA 57.226 33.333 2.72 0.00 0.00 2.87
469 470 6.966534 AAAGTCAAGACAAATGTGGAGAAT 57.033 33.333 2.72 0.00 0.00 2.40
472 473 8.463930 AAGTCAAGACAAATGTGGAGAATTTA 57.536 30.769 2.72 0.00 0.00 1.40
477 478 4.352893 ACAAATGTGGAGAATTTAGGGGG 58.647 43.478 0.00 0.00 0.00 5.40
489 490 5.721480 AGAATTTAGGGGGTTTTCATGGAAG 59.279 40.000 0.00 0.00 0.00 3.46
513 514 2.812011 CCCTAGGTGCAAGTGTGTAAAC 59.188 50.000 8.29 0.00 0.00 2.01
514 515 3.496160 CCCTAGGTGCAAGTGTGTAAACT 60.496 47.826 8.29 0.00 0.00 2.66
515 516 4.262721 CCCTAGGTGCAAGTGTGTAAACTA 60.263 45.833 8.29 0.00 0.00 2.24
516 517 5.302360 CCTAGGTGCAAGTGTGTAAACTAA 58.698 41.667 0.00 0.00 0.00 2.24
517 518 5.761234 CCTAGGTGCAAGTGTGTAAACTAAA 59.239 40.000 0.00 0.00 0.00 1.85
533 534 2.064014 CTAAACCGTCGGTGGAACTTC 58.936 52.381 19.67 0.00 35.34 3.01
536 537 0.540365 ACCGTCGGTGGAACTTCCTA 60.540 55.000 18.08 0.00 37.46 2.94
552 553 7.985184 GGAACTTCCTAAATTTCCACTTGTTTT 59.015 33.333 0.00 0.00 41.53 2.43
683 684 1.188219 TCTTGCAGCTCTTCCCGTCT 61.188 55.000 0.00 0.00 0.00 4.18
684 685 0.739112 CTTGCAGCTCTTCCCGTCTC 60.739 60.000 0.00 0.00 0.00 3.36
708 710 1.228337 TCCCTCGTCTTGACGGACA 60.228 57.895 20.71 3.51 36.12 4.02
739 741 0.896019 ACCGACACCACTCCTCTCTG 60.896 60.000 0.00 0.00 0.00 3.35
740 742 1.214062 CGACACCACTCCTCTCTGC 59.786 63.158 0.00 0.00 0.00 4.26
741 743 1.247419 CGACACCACTCCTCTCTGCT 61.247 60.000 0.00 0.00 0.00 4.24
742 744 0.530288 GACACCACTCCTCTCTGCTC 59.470 60.000 0.00 0.00 0.00 4.26
743 745 0.114168 ACACCACTCCTCTCTGCTCT 59.886 55.000 0.00 0.00 0.00 4.09
744 746 0.817013 CACCACTCCTCTCTGCTCTC 59.183 60.000 0.00 0.00 0.00 3.20
882 884 4.166888 GGCAGCCCAGATCGAGCA 62.167 66.667 2.38 0.00 0.00 4.26
928 930 2.813901 AGATCGAGCTGAGCTGCC 59.186 61.111 13.71 0.00 43.03 4.85
981 998 4.504132 CCGGAGGCGAAGAAGAAG 57.496 61.111 0.00 0.00 46.14 2.85
982 999 1.890894 CCGGAGGCGAAGAAGAAGA 59.109 57.895 0.00 0.00 46.14 2.87
983 1000 0.246635 CCGGAGGCGAAGAAGAAGAA 59.753 55.000 0.00 0.00 46.14 2.52
984 1001 1.634702 CGGAGGCGAAGAAGAAGAAG 58.365 55.000 0.00 0.00 0.00 2.85
1417 1434 5.371526 AGACCTCATGTATGTATTGCTTGG 58.628 41.667 0.00 0.00 0.00 3.61
1419 1436 5.509498 ACCTCATGTATGTATTGCTTGGTT 58.491 37.500 0.00 0.00 0.00 3.67
1420 1437 5.590259 ACCTCATGTATGTATTGCTTGGTTC 59.410 40.000 0.00 0.00 0.00 3.62
1425 1442 8.584157 TCATGTATGTATTGCTTGGTTCTTTTT 58.416 29.630 0.00 0.00 0.00 1.94
1426 1443 8.863049 CATGTATGTATTGCTTGGTTCTTTTTC 58.137 33.333 0.00 0.00 0.00 2.29
1427 1444 8.177119 TGTATGTATTGCTTGGTTCTTTTTCT 57.823 30.769 0.00 0.00 0.00 2.52
1428 1445 8.637986 TGTATGTATTGCTTGGTTCTTTTTCTT 58.362 29.630 0.00 0.00 0.00 2.52
1429 1446 9.129209 GTATGTATTGCTTGGTTCTTTTTCTTC 57.871 33.333 0.00 0.00 0.00 2.87
1430 1447 6.512297 TGTATTGCTTGGTTCTTTTTCTTCC 58.488 36.000 0.00 0.00 0.00 3.46
1431 1448 5.876651 ATTGCTTGGTTCTTTTTCTTCCT 57.123 34.783 0.00 0.00 0.00 3.36
1432 1449 4.918810 TGCTTGGTTCTTTTTCTTCCTC 57.081 40.909 0.00 0.00 0.00 3.71
1433 1450 4.536765 TGCTTGGTTCTTTTTCTTCCTCT 58.463 39.130 0.00 0.00 0.00 3.69
1434 1451 4.956075 TGCTTGGTTCTTTTTCTTCCTCTT 59.044 37.500 0.00 0.00 0.00 2.85
1435 1452 5.067805 TGCTTGGTTCTTTTTCTTCCTCTTC 59.932 40.000 0.00 0.00 0.00 2.87
1436 1453 5.300539 GCTTGGTTCTTTTTCTTCCTCTTCT 59.699 40.000 0.00 0.00 0.00 2.85
1437 1454 6.183360 GCTTGGTTCTTTTTCTTCCTCTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
1438 1455 6.944234 TGGTTCTTTTTCTTCCTCTTCTTC 57.056 37.500 0.00 0.00 0.00 2.87
1439 1456 6.663734 TGGTTCTTTTTCTTCCTCTTCTTCT 58.336 36.000 0.00 0.00 0.00 2.85
1440 1457 7.119387 TGGTTCTTTTTCTTCCTCTTCTTCTT 58.881 34.615 0.00 0.00 0.00 2.52
1441 1458 7.283354 TGGTTCTTTTTCTTCCTCTTCTTCTTC 59.717 37.037 0.00 0.00 0.00 2.87
1442 1459 7.500892 GGTTCTTTTTCTTCCTCTTCTTCTTCT 59.499 37.037 0.00 0.00 0.00 2.85
1443 1460 9.549078 GTTCTTTTTCTTCCTCTTCTTCTTCTA 57.451 33.333 0.00 0.00 0.00 2.10
1451 1468 7.947890 TCTTCCTCTTCTTCTTCTACTTCTTCT 59.052 37.037 0.00 0.00 0.00 2.85
1454 1471 7.947890 TCCTCTTCTTCTTCTACTTCTTCTTCT 59.052 37.037 0.00 0.00 0.00 2.85
1506 1524 1.605712 GGCTCGATTCCGATTCCGATT 60.606 52.381 0.00 0.00 44.62 3.34
1754 1773 1.405821 CCGGTCTACTGGTAAGCTCAG 59.594 57.143 0.00 0.00 37.62 3.35
1772 1792 4.142227 GCTCAGCCATTCAGTTCATCAATT 60.142 41.667 0.00 0.00 0.00 2.32
1777 1797 4.619863 GCCATTCAGTTCATCAATTGCAGT 60.620 41.667 0.00 0.00 0.00 4.40
1780 1800 4.754372 TCAGTTCATCAATTGCAGTCAC 57.246 40.909 0.00 0.00 0.00 3.67
1786 1806 4.581868 TCATCAATTGCAGTCACTCATGA 58.418 39.130 0.00 0.00 0.00 3.07
1801 1821 2.135139 TCATGACACAGTTCTTGCGAC 58.865 47.619 0.00 0.00 0.00 5.19
1807 1833 1.205064 CAGTTCTTGCGACGCCTTG 59.795 57.895 18.69 7.42 0.00 3.61
1819 1845 1.528586 GACGCCTTGATTGATCCATCG 59.471 52.381 2.60 0.00 0.00 3.84
1823 1849 2.149578 CCTTGATTGATCCATCGGAGC 58.850 52.381 2.60 0.00 38.78 4.70
1826 1895 0.671781 GATTGATCCATCGGAGCGGG 60.672 60.000 0.00 0.00 41.58 6.13
2022 2091 1.202568 CAGCAAGAACGACACGCTG 59.797 57.895 0.00 0.00 43.55 5.18
2274 2343 3.652687 CCCTCAGGCTAGCACCAT 58.347 61.111 18.24 0.00 0.00 3.55
2275 2344 1.147824 CCCTCAGGCTAGCACCATG 59.852 63.158 18.24 9.42 0.00 3.66
2276 2345 1.630126 CCCTCAGGCTAGCACCATGT 61.630 60.000 18.24 0.00 0.00 3.21
2277 2346 0.254178 CCTCAGGCTAGCACCATGTT 59.746 55.000 18.24 0.00 0.00 2.71
2278 2347 1.376543 CTCAGGCTAGCACCATGTTG 58.623 55.000 18.24 3.09 0.00 3.33
2279 2348 0.677731 TCAGGCTAGCACCATGTTGC 60.678 55.000 18.24 7.21 43.34 4.17
2317 2408 4.764771 GCCATTGCCTGCTCCCCA 62.765 66.667 0.00 0.00 0.00 4.96
2339 2430 3.774959 CTACGCCGAGCTGCCGATT 62.775 63.158 11.24 0.00 0.00 3.34
2353 2448 0.994995 CCGATTCTTCAGCGTGTGAG 59.005 55.000 0.00 0.00 36.21 3.51
2354 2449 0.368227 CGATTCTTCAGCGTGTGAGC 59.632 55.000 0.00 0.00 36.21 4.26
2378 2473 0.972883 TTGGTGCCATTTTGGGTAGC 59.027 50.000 0.00 0.00 40.83 3.58
2379 2474 0.114168 TGGTGCCATTTTGGGTAGCT 59.886 50.000 0.00 0.00 41.01 3.32
2380 2475 0.532115 GGTGCCATTTTGGGTAGCTG 59.468 55.000 0.00 0.00 38.19 4.24
2381 2476 1.544724 GTGCCATTTTGGGTAGCTGA 58.455 50.000 0.00 0.00 38.19 4.26
2382 2477 2.102578 GTGCCATTTTGGGTAGCTGAT 58.897 47.619 0.00 0.00 38.19 2.90
2383 2478 2.099756 GTGCCATTTTGGGTAGCTGATC 59.900 50.000 0.00 0.00 38.19 2.92
2384 2479 1.683385 GCCATTTTGGGTAGCTGATCC 59.317 52.381 0.00 0.00 38.19 3.36
2385 2480 1.949525 CCATTTTGGGTAGCTGATCCG 59.050 52.381 0.00 0.00 32.67 4.18
2386 2481 2.421388 CCATTTTGGGTAGCTGATCCGA 60.421 50.000 0.00 0.00 32.67 4.55
2387 2482 2.691409 TTTTGGGTAGCTGATCCGAG 57.309 50.000 0.00 0.00 0.00 4.63
2388 2483 1.860641 TTTGGGTAGCTGATCCGAGA 58.139 50.000 0.00 0.00 0.00 4.04
2392 2487 0.313672 GGTAGCTGATCCGAGAGCTG 59.686 60.000 13.95 1.07 45.29 4.24
2408 2503 3.264193 AGAGCTGTGTATGTGAATTGGGA 59.736 43.478 0.00 0.00 0.00 4.37
2414 2509 6.723298 TGTGTATGTGAATTGGGAAAACTT 57.277 33.333 0.00 0.00 0.00 2.66
2448 2543 2.286365 ACCACGGTGTCCATTTTCAT 57.714 45.000 7.45 0.00 0.00 2.57
2456 2551 5.877564 ACGGTGTCCATTTTCATTTGTTTTT 59.122 32.000 0.00 0.00 0.00 1.94
2457 2552 6.183360 ACGGTGTCCATTTTCATTTGTTTTTG 60.183 34.615 0.00 0.00 0.00 2.44
2460 2555 8.026026 GGTGTCCATTTTCATTTGTTTTTGTTT 58.974 29.630 0.00 0.00 0.00 2.83
2461 2556 9.060547 GTGTCCATTTTCATTTGTTTTTGTTTC 57.939 29.630 0.00 0.00 0.00 2.78
2462 2557 8.786898 TGTCCATTTTCATTTGTTTTTGTTTCA 58.213 25.926 0.00 0.00 0.00 2.69
2491 2586 8.669946 TTTGTGTCACACATATGTCTAAAGAA 57.330 30.769 12.49 0.00 44.16 2.52
2656 2751 1.631405 TTTGTGAGGGGCCATCTTTG 58.369 50.000 20.14 0.00 0.00 2.77
2744 2840 2.313234 CTGTGTTTTGCTGCAGAATCG 58.687 47.619 20.43 0.00 0.00 3.34
2745 2841 1.055338 GTGTTTTGCTGCAGAATCGC 58.945 50.000 20.43 2.17 0.00 4.58
2746 2842 0.039256 TGTTTTGCTGCAGAATCGCC 60.039 50.000 20.43 0.00 0.00 5.54
2763 2859 1.465387 CGCCGTGTTTTACATGCCTAA 59.535 47.619 0.00 0.00 33.88 2.69
2801 2898 4.212214 GCTTAACGGGATCTTGCTAGAATG 59.788 45.833 0.99 0.00 33.20 2.67
2802 2899 5.601662 CTTAACGGGATCTTGCTAGAATGA 58.398 41.667 0.99 0.00 33.20 2.57
2803 2900 3.460857 ACGGGATCTTGCTAGAATGAC 57.539 47.619 0.99 0.00 33.20 3.06
2804 2901 2.766263 ACGGGATCTTGCTAGAATGACA 59.234 45.455 0.99 0.00 33.20 3.58
2805 2902 3.181471 ACGGGATCTTGCTAGAATGACAG 60.181 47.826 0.99 0.00 33.20 3.51
2808 2905 4.376146 GGATCTTGCTAGAATGACAGGAC 58.624 47.826 0.99 0.00 33.20 3.85
2813 2910 5.480422 TCTTGCTAGAATGACAGGACACTAA 59.520 40.000 0.00 0.00 0.00 2.24
2816 2913 5.422012 TGCTAGAATGACAGGACACTAATGA 59.578 40.000 0.00 0.00 0.00 2.57
2818 2915 6.989169 GCTAGAATGACAGGACACTAATGATT 59.011 38.462 0.00 0.00 0.00 2.57
2827 2924 8.268850 ACAGGACACTAATGATTTTCATGTAC 57.731 34.615 0.00 0.00 37.15 2.90
2859 2956 5.694006 CGAAGCTCTAGGGTTTAGAATCATG 59.306 44.000 0.00 0.00 35.61 3.07
2894 3150 8.706035 GTTCATGCATAGATATGGAAATTTTGC 58.294 33.333 0.00 0.00 37.57 3.68
2906 3162 6.357579 TGGAAATTTTGCTTCCATATGTGT 57.642 33.333 1.24 0.00 45.88 3.72
2914 3170 4.339748 TGCTTCCATATGTGTAAAGGCAA 58.660 39.130 1.24 0.00 0.00 4.52
2935 3191 5.621555 GCAAGGATCATGCTGGCAAATATAG 60.622 44.000 13.72 0.00 34.57 1.31
2936 3192 4.597004 AGGATCATGCTGGCAAATATAGG 58.403 43.478 0.00 0.00 0.00 2.57
2988 3248 2.437518 TAACGCACCGCCACTGCTAA 62.438 55.000 0.00 0.00 34.43 3.09
2994 3254 1.210155 CCGCCACTGCTAAAACTGC 59.790 57.895 0.00 0.00 34.43 4.40
3051 3311 4.447290 ACATACAGCACAACACAACAGTA 58.553 39.130 0.00 0.00 0.00 2.74
3176 3436 2.747686 GGTTCGACAGGGCTTCCA 59.252 61.111 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.632638 AGCACCACTAATTTTCATATGTATCTT 57.367 29.630 1.90 0.00 0.00 2.40
1 2 9.632638 AAGCACCACTAATTTTCATATGTATCT 57.367 29.630 1.90 0.00 0.00 1.98
2 3 9.669353 CAAGCACCACTAATTTTCATATGTATC 57.331 33.333 1.90 0.00 0.00 2.24
3 4 9.189156 ACAAGCACCACTAATTTTCATATGTAT 57.811 29.630 1.90 0.00 0.00 2.29
4 5 8.574251 ACAAGCACCACTAATTTTCATATGTA 57.426 30.769 1.90 0.00 0.00 2.29
5 6 7.466746 ACAAGCACCACTAATTTTCATATGT 57.533 32.000 1.90 0.00 0.00 2.29
9 10 9.243105 AGTAATACAAGCACCACTAATTTTCAT 57.757 29.630 0.00 0.00 0.00 2.57
10 11 8.630054 AGTAATACAAGCACCACTAATTTTCA 57.370 30.769 0.00 0.00 0.00 2.69
11 12 8.726988 TGAGTAATACAAGCACCACTAATTTTC 58.273 33.333 0.00 0.00 0.00 2.29
12 13 8.630054 TGAGTAATACAAGCACCACTAATTTT 57.370 30.769 0.00 0.00 0.00 1.82
13 14 8.807948 ATGAGTAATACAAGCACCACTAATTT 57.192 30.769 0.00 0.00 0.00 1.82
15 16 9.712305 GATATGAGTAATACAAGCACCACTAAT 57.288 33.333 0.00 0.00 0.00 1.73
16 17 8.924303 AGATATGAGTAATACAAGCACCACTAA 58.076 33.333 0.00 0.00 0.00 2.24
17 18 8.360390 CAGATATGAGTAATACAAGCACCACTA 58.640 37.037 0.00 0.00 0.00 2.74
18 19 7.069950 TCAGATATGAGTAATACAAGCACCACT 59.930 37.037 0.00 0.00 0.00 4.00
19 20 7.169982 GTCAGATATGAGTAATACAAGCACCAC 59.830 40.741 0.00 0.00 0.00 4.16
20 21 7.069950 AGTCAGATATGAGTAATACAAGCACCA 59.930 37.037 0.00 0.00 0.00 4.17
21 22 7.437748 AGTCAGATATGAGTAATACAAGCACC 58.562 38.462 0.00 0.00 0.00 5.01
38 39 9.982651 GGCTTACATAGTTTTGATAGTCAGATA 57.017 33.333 0.00 0.00 0.00 1.98
39 40 8.486210 TGGCTTACATAGTTTTGATAGTCAGAT 58.514 33.333 0.00 0.00 0.00 2.90
40 41 7.847096 TGGCTTACATAGTTTTGATAGTCAGA 58.153 34.615 0.00 0.00 0.00 3.27
41 42 8.668510 ATGGCTTACATAGTTTTGATAGTCAG 57.331 34.615 0.00 0.00 38.26 3.51
42 43 9.461312 AAATGGCTTACATAGTTTTGATAGTCA 57.539 29.630 0.00 0.00 39.40 3.41
49 50 9.853555 TGACATAAAATGGCTTACATAGTTTTG 57.146 29.630 0.00 0.00 39.40 2.44
52 53 9.855021 GTTTGACATAAAATGGCTTACATAGTT 57.145 29.630 0.00 0.00 39.40 2.24
53 54 9.243105 AGTTTGACATAAAATGGCTTACATAGT 57.757 29.630 0.00 0.00 39.40 2.12
56 57 9.206870 CAAAGTTTGACATAAAATGGCTTACAT 57.793 29.630 10.19 0.00 43.07 2.29
57 58 8.417106 TCAAAGTTTGACATAAAATGGCTTACA 58.583 29.630 14.35 0.00 39.69 2.41
58 59 8.810652 TCAAAGTTTGACATAAAATGGCTTAC 57.189 30.769 14.35 0.00 39.69 2.34
59 60 8.855110 TCTCAAAGTTTGACATAAAATGGCTTA 58.145 29.630 14.35 0.00 39.69 3.09
60 61 7.725251 TCTCAAAGTTTGACATAAAATGGCTT 58.275 30.769 14.35 0.00 39.69 4.35
61 62 7.231317 TCTCTCAAAGTTTGACATAAAATGGCT 59.769 33.333 14.35 0.00 39.69 4.75
62 63 7.370383 TCTCTCAAAGTTTGACATAAAATGGC 58.630 34.615 14.35 0.00 39.32 4.40
63 64 9.185192 GTTCTCTCAAAGTTTGACATAAAATGG 57.815 33.333 14.35 2.17 35.46 3.16
64 65 9.734620 TGTTCTCTCAAAGTTTGACATAAAATG 57.265 29.630 14.35 2.86 35.46 2.32
65 66 9.736023 GTGTTCTCTCAAAGTTTGACATAAAAT 57.264 29.630 14.35 0.00 35.46 1.82
66 67 8.735315 TGTGTTCTCTCAAAGTTTGACATAAAA 58.265 29.630 14.35 1.76 35.46 1.52
67 68 8.275015 TGTGTTCTCTCAAAGTTTGACATAAA 57.725 30.769 14.35 4.43 35.46 1.40
68 69 7.857734 TGTGTTCTCTCAAAGTTTGACATAA 57.142 32.000 14.35 6.03 35.46 1.90
69 70 9.725019 ATATGTGTTCTCTCAAAGTTTGACATA 57.275 29.630 14.35 17.03 35.46 2.29
70 71 6.949352 ATGTGTTCTCTCAAAGTTTGACAT 57.051 33.333 14.35 11.63 35.46 3.06
71 72 9.725019 ATATATGTGTTCTCTCAAAGTTTGACA 57.275 29.630 14.35 9.90 35.46 3.58
78 79 9.190858 GCAGTCTATATATGTGTTCTCTCAAAG 57.809 37.037 0.00 0.00 0.00 2.77
79 80 8.695456 TGCAGTCTATATATGTGTTCTCTCAAA 58.305 33.333 0.00 0.00 0.00 2.69
80 81 8.237811 TGCAGTCTATATATGTGTTCTCTCAA 57.762 34.615 0.00 0.00 0.00 3.02
81 82 7.503902 ACTGCAGTCTATATATGTGTTCTCTCA 59.496 37.037 15.25 0.00 0.00 3.27
82 83 7.881142 ACTGCAGTCTATATATGTGTTCTCTC 58.119 38.462 15.25 0.00 0.00 3.20
83 84 7.831691 ACTGCAGTCTATATATGTGTTCTCT 57.168 36.000 15.25 0.00 0.00 3.10
84 85 8.759641 CAAACTGCAGTCTATATATGTGTTCTC 58.240 37.037 21.95 0.00 0.00 2.87
85 86 7.712639 CCAAACTGCAGTCTATATATGTGTTCT 59.287 37.037 21.95 0.00 0.00 3.01
86 87 7.495934 ACCAAACTGCAGTCTATATATGTGTTC 59.504 37.037 21.95 0.00 0.00 3.18
87 88 7.338710 ACCAAACTGCAGTCTATATATGTGTT 58.661 34.615 21.95 2.75 0.00 3.32
88 89 6.889198 ACCAAACTGCAGTCTATATATGTGT 58.111 36.000 21.95 0.00 0.00 3.72
89 90 7.792374 AACCAAACTGCAGTCTATATATGTG 57.208 36.000 21.95 0.00 0.00 3.21
90 91 8.150945 CCTAACCAAACTGCAGTCTATATATGT 58.849 37.037 21.95 6.37 0.00 2.29
91 92 8.367911 TCCTAACCAAACTGCAGTCTATATATG 58.632 37.037 21.95 10.26 0.00 1.78
92 93 8.492415 TCCTAACCAAACTGCAGTCTATATAT 57.508 34.615 21.95 0.00 0.00 0.86
93 94 7.907841 TCCTAACCAAACTGCAGTCTATATA 57.092 36.000 21.95 10.23 0.00 0.86
94 95 6.808321 TCCTAACCAAACTGCAGTCTATAT 57.192 37.500 21.95 9.59 0.00 0.86
95 96 6.183360 GGATCCTAACCAAACTGCAGTCTATA 60.183 42.308 21.95 8.50 0.00 1.31
96 97 5.396884 GGATCCTAACCAAACTGCAGTCTAT 60.397 44.000 21.95 6.89 0.00 1.98
97 98 4.081087 GGATCCTAACCAAACTGCAGTCTA 60.081 45.833 21.95 6.16 0.00 2.59
98 99 3.307762 GGATCCTAACCAAACTGCAGTCT 60.308 47.826 21.95 2.13 0.00 3.24
99 100 3.010420 GGATCCTAACCAAACTGCAGTC 58.990 50.000 21.95 2.27 0.00 3.51
100 101 2.615493 CGGATCCTAACCAAACTGCAGT 60.615 50.000 15.25 15.25 0.00 4.40
101 102 2.009774 CGGATCCTAACCAAACTGCAG 58.990 52.381 13.48 13.48 0.00 4.41
102 103 1.349688 ACGGATCCTAACCAAACTGCA 59.650 47.619 10.75 0.00 0.00 4.41
103 104 2.007608 GACGGATCCTAACCAAACTGC 58.992 52.381 10.75 0.00 0.00 4.40
104 105 2.629051 GGACGGATCCTAACCAAACTG 58.371 52.381 10.75 0.00 42.45 3.16
105 106 1.206371 CGGACGGATCCTAACCAAACT 59.794 52.381 10.75 0.00 43.73 2.66
106 107 1.205417 TCGGACGGATCCTAACCAAAC 59.795 52.381 10.75 0.00 43.73 2.93
107 108 1.479323 CTCGGACGGATCCTAACCAAA 59.521 52.381 10.75 1.30 43.73 3.28
108 109 1.108776 CTCGGACGGATCCTAACCAA 58.891 55.000 10.75 0.00 43.73 3.67
109 110 0.256752 TCTCGGACGGATCCTAACCA 59.743 55.000 10.75 1.54 43.73 3.67
110 111 1.618487 ATCTCGGACGGATCCTAACC 58.382 55.000 10.75 9.19 43.73 2.85
111 112 3.729862 AAATCTCGGACGGATCCTAAC 57.270 47.619 10.75 0.64 43.73 2.34
112 113 4.321750 GCATAAATCTCGGACGGATCCTAA 60.322 45.833 10.75 0.00 43.73 2.69
113 114 3.192844 GCATAAATCTCGGACGGATCCTA 59.807 47.826 10.75 0.00 43.73 2.94
114 115 2.028930 GCATAAATCTCGGACGGATCCT 60.029 50.000 10.75 0.00 43.73 3.24
115 116 2.338500 GCATAAATCTCGGACGGATCC 58.662 52.381 0.00 0.00 42.28 3.36
116 117 2.338500 GGCATAAATCTCGGACGGATC 58.662 52.381 0.00 0.00 0.00 3.36
117 118 1.336887 CGGCATAAATCTCGGACGGAT 60.337 52.381 0.00 0.00 0.00 4.18
118 119 0.031585 CGGCATAAATCTCGGACGGA 59.968 55.000 0.00 0.00 0.00 4.69
119 120 1.557443 GCGGCATAAATCTCGGACGG 61.557 60.000 0.00 0.00 0.00 4.79
120 121 1.557443 GGCGGCATAAATCTCGGACG 61.557 60.000 3.07 0.00 0.00 4.79
121 122 0.531974 TGGCGGCATAAATCTCGGAC 60.532 55.000 7.97 0.00 0.00 4.79
122 123 0.396435 ATGGCGGCATAAATCTCGGA 59.604 50.000 24.59 0.00 0.00 4.55
123 124 0.518636 CATGGCGGCATAAATCTCGG 59.481 55.000 25.33 5.68 0.00 4.63
124 125 0.518636 CCATGGCGGCATAAATCTCG 59.481 55.000 25.33 10.12 0.00 4.04
125 126 1.609208 ACCATGGCGGCATAAATCTC 58.391 50.000 25.33 0.00 39.03 2.75
126 127 1.682854 CAACCATGGCGGCATAAATCT 59.317 47.619 25.33 0.00 39.03 2.40
127 128 1.408702 ACAACCATGGCGGCATAAATC 59.591 47.619 25.33 0.00 39.03 2.17
128 129 1.484038 ACAACCATGGCGGCATAAAT 58.516 45.000 25.33 10.01 39.03 1.40
129 130 2.130272 TACAACCATGGCGGCATAAA 57.870 45.000 25.33 3.70 39.03 1.40
130 131 1.746220 GTTACAACCATGGCGGCATAA 59.254 47.619 25.33 11.31 39.03 1.90
131 132 1.384525 GTTACAACCATGGCGGCATA 58.615 50.000 25.33 4.77 39.03 3.14
132 133 2.188912 GTTACAACCATGGCGGCAT 58.811 52.632 20.18 20.18 39.03 4.40
133 134 3.674906 GTTACAACCATGGCGGCA 58.325 55.556 16.34 16.34 39.03 5.69
151 152 1.028905 TTTTTGCTCAACACCCGGAG 58.971 50.000 0.73 0.00 0.00 4.63
152 153 1.339610 CATTTTTGCTCAACACCCGGA 59.660 47.619 0.73 0.00 0.00 5.14
153 154 1.782044 CATTTTTGCTCAACACCCGG 58.218 50.000 0.00 0.00 0.00 5.73
154 155 1.139163 GCATTTTTGCTCAACACCCG 58.861 50.000 0.00 0.00 0.00 5.28
155 156 2.531522 AGCATTTTTGCTCAACACCC 57.468 45.000 0.00 0.00 42.12 4.61
389 390 0.814010 CCCGCCAATGCTACACCTAC 60.814 60.000 0.00 0.00 34.43 3.18
390 391 1.268992 ACCCGCCAATGCTACACCTA 61.269 55.000 0.00 0.00 34.43 3.08
391 392 2.272146 CCCGCCAATGCTACACCT 59.728 61.111 0.00 0.00 34.43 4.00
392 393 2.045340 ACCCGCCAATGCTACACC 60.045 61.111 0.00 0.00 34.43 4.16
393 394 1.241315 AACACCCGCCAATGCTACAC 61.241 55.000 0.00 0.00 34.43 2.90
394 395 1.074072 AACACCCGCCAATGCTACA 59.926 52.632 0.00 0.00 34.43 2.74
395 396 0.958382 TCAACACCCGCCAATGCTAC 60.958 55.000 0.00 0.00 34.43 3.58
396 397 0.676466 CTCAACACCCGCCAATGCTA 60.676 55.000 0.00 0.00 34.43 3.49
397 398 1.973281 CTCAACACCCGCCAATGCT 60.973 57.895 0.00 0.00 34.43 3.79
398 399 0.958382 TACTCAACACCCGCCAATGC 60.958 55.000 0.00 0.00 0.00 3.56
399 400 1.529226 TTACTCAACACCCGCCAATG 58.471 50.000 0.00 0.00 0.00 2.82
400 401 2.507407 ATTACTCAACACCCGCCAAT 57.493 45.000 0.00 0.00 0.00 3.16
401 402 2.303600 ACTATTACTCAACACCCGCCAA 59.696 45.455 0.00 0.00 0.00 4.52
402 403 1.903860 ACTATTACTCAACACCCGCCA 59.096 47.619 0.00 0.00 0.00 5.69
403 404 2.685850 ACTATTACTCAACACCCGCC 57.314 50.000 0.00 0.00 0.00 6.13
404 405 4.114058 TGTACTATTACTCAACACCCGC 57.886 45.455 0.00 0.00 0.00 6.13
405 406 6.592607 ACATTTGTACTATTACTCAACACCCG 59.407 38.462 0.00 0.00 0.00 5.28
406 407 7.916914 ACATTTGTACTATTACTCAACACCC 57.083 36.000 0.00 0.00 0.00 4.61
407 408 8.780249 ACAACATTTGTACTATTACTCAACACC 58.220 33.333 0.00 0.00 43.27 4.16
438 439 9.743057 CCACATTTGTCTTGACTTTTATTTACA 57.257 29.630 2.35 0.00 0.00 2.41
444 445 7.873719 TTCTCCACATTTGTCTTGACTTTTA 57.126 32.000 2.35 0.00 0.00 1.52
445 446 6.773976 TTCTCCACATTTGTCTTGACTTTT 57.226 33.333 2.35 0.00 0.00 2.27
449 450 7.308435 CCTAAATTCTCCACATTTGTCTTGAC 58.692 38.462 0.00 0.00 0.00 3.18
451 452 6.350445 CCCCTAAATTCTCCACATTTGTCTTG 60.350 42.308 0.00 0.00 0.00 3.02
462 463 4.750833 TGAAAACCCCCTAAATTCTCCA 57.249 40.909 0.00 0.00 0.00 3.86
466 467 5.483937 ACTTCCATGAAAACCCCCTAAATTC 59.516 40.000 0.00 0.00 0.00 2.17
467 468 5.248248 CACTTCCATGAAAACCCCCTAAATT 59.752 40.000 0.00 0.00 0.00 1.82
468 469 4.777366 CACTTCCATGAAAACCCCCTAAAT 59.223 41.667 0.00 0.00 0.00 1.40
469 470 4.156477 CACTTCCATGAAAACCCCCTAAA 58.844 43.478 0.00 0.00 0.00 1.85
472 473 1.827245 GCACTTCCATGAAAACCCCCT 60.827 52.381 0.00 0.00 0.00 4.79
477 478 2.755103 CCTAGGGCACTTCCATGAAAAC 59.245 50.000 0.00 0.00 36.21 2.43
489 490 1.073199 ACACTTGCACCTAGGGCAC 59.927 57.895 20.55 7.57 41.75 5.01
513 514 2.064014 GAAGTTCCACCGACGGTTTAG 58.936 52.381 19.02 9.52 31.02 1.85
514 515 1.270252 GGAAGTTCCACCGACGGTTTA 60.270 52.381 19.02 5.25 36.28 2.01
515 516 0.533531 GGAAGTTCCACCGACGGTTT 60.534 55.000 19.02 8.91 36.28 3.27
516 517 1.070275 GGAAGTTCCACCGACGGTT 59.930 57.895 19.02 0.43 36.28 4.44
517 518 0.540365 TAGGAAGTTCCACCGACGGT 60.540 55.000 23.87 15.37 39.61 4.83
558 559 5.244402 TCCGTGTTTCTCATACTACCTCAAA 59.756 40.000 0.00 0.00 0.00 2.69
559 560 4.768448 TCCGTGTTTCTCATACTACCTCAA 59.232 41.667 0.00 0.00 0.00 3.02
560 561 4.338012 TCCGTGTTTCTCATACTACCTCA 58.662 43.478 0.00 0.00 0.00 3.86
561 562 4.978083 TCCGTGTTTCTCATACTACCTC 57.022 45.455 0.00 0.00 0.00 3.85
562 563 5.934402 ATTCCGTGTTTCTCATACTACCT 57.066 39.130 0.00 0.00 0.00 3.08
563 564 6.592607 TGAAATTCCGTGTTTCTCATACTACC 59.407 38.462 0.00 0.00 36.71 3.18
571 572 4.489679 AAGCTGAAATTCCGTGTTTCTC 57.510 40.909 0.00 0.00 36.71 2.87
683 684 0.408309 TCAAGACGAGGGAGGAAGGA 59.592 55.000 0.00 0.00 0.00 3.36
684 685 0.533032 GTCAAGACGAGGGAGGAAGG 59.467 60.000 0.00 0.00 0.00 3.46
882 884 2.756283 CTTCTCGGGAGCTCGGGT 60.756 66.667 7.83 0.00 31.63 5.28
971 988 5.226396 TGCTCTTCTTCTTCTTCTTCTTCG 58.774 41.667 0.00 0.00 0.00 3.79
973 990 6.825610 TCTTGCTCTTCTTCTTCTTCTTCTT 58.174 36.000 0.00 0.00 0.00 2.52
974 991 6.418057 TCTTGCTCTTCTTCTTCTTCTTCT 57.582 37.500 0.00 0.00 0.00 2.85
975 992 6.928492 TCTTCTTGCTCTTCTTCTTCTTCTTC 59.072 38.462 0.00 0.00 0.00 2.87
976 993 6.825610 TCTTCTTGCTCTTCTTCTTCTTCTT 58.174 36.000 0.00 0.00 0.00 2.52
979 996 6.767456 TCATCTTCTTGCTCTTCTTCTTCTT 58.233 36.000 0.00 0.00 0.00 2.52
980 997 6.357579 TCATCTTCTTGCTCTTCTTCTTCT 57.642 37.500 0.00 0.00 0.00 2.85
981 998 6.402442 GCTTCATCTTCTTGCTCTTCTTCTTC 60.402 42.308 0.00 0.00 0.00 2.87
982 999 5.412286 GCTTCATCTTCTTGCTCTTCTTCTT 59.588 40.000 0.00 0.00 0.00 2.52
983 1000 4.937015 GCTTCATCTTCTTGCTCTTCTTCT 59.063 41.667 0.00 0.00 0.00 2.85
984 1001 4.201705 CGCTTCATCTTCTTGCTCTTCTTC 60.202 45.833 0.00 0.00 0.00 2.87
1417 1434 8.445275 AGAAGAAGAAGAGGAAGAAAAAGAAC 57.555 34.615 0.00 0.00 0.00 3.01
1419 1436 8.929487 AGTAGAAGAAGAAGAGGAAGAAAAAGA 58.071 33.333 0.00 0.00 0.00 2.52
1420 1437 9.554395 AAGTAGAAGAAGAAGAGGAAGAAAAAG 57.446 33.333 0.00 0.00 0.00 2.27
1425 1442 7.947890 AGAAGAAGTAGAAGAAGAAGAGGAAGA 59.052 37.037 0.00 0.00 0.00 2.87
1426 1443 8.122472 AGAAGAAGTAGAAGAAGAAGAGGAAG 57.878 38.462 0.00 0.00 0.00 3.46
1427 1444 8.485578 AAGAAGAAGTAGAAGAAGAAGAGGAA 57.514 34.615 0.00 0.00 0.00 3.36
1428 1445 7.947890 AGAAGAAGAAGTAGAAGAAGAAGAGGA 59.052 37.037 0.00 0.00 0.00 3.71
1429 1446 8.122472 AGAAGAAGAAGTAGAAGAAGAAGAGG 57.878 38.462 0.00 0.00 0.00 3.69
1430 1447 9.626045 GAAGAAGAAGAAGTAGAAGAAGAAGAG 57.374 37.037 0.00 0.00 0.00 2.85
1431 1448 9.362151 AGAAGAAGAAGAAGTAGAAGAAGAAGA 57.638 33.333 0.00 0.00 0.00 2.87
1432 1449 9.981114 AAGAAGAAGAAGAAGTAGAAGAAGAAG 57.019 33.333 0.00 0.00 0.00 2.85
1433 1450 9.974980 GAAGAAGAAGAAGAAGTAGAAGAAGAA 57.025 33.333 0.00 0.00 0.00 2.52
1434 1451 9.362151 AGAAGAAGAAGAAGAAGTAGAAGAAGA 57.638 33.333 0.00 0.00 0.00 2.87
1435 1452 9.981114 AAGAAGAAGAAGAAGAAGTAGAAGAAG 57.019 33.333 0.00 0.00 0.00 2.85
1436 1453 9.974980 GAAGAAGAAGAAGAAGAAGTAGAAGAA 57.025 33.333 0.00 0.00 0.00 2.52
1437 1454 9.362151 AGAAGAAGAAGAAGAAGAAGTAGAAGA 57.638 33.333 0.00 0.00 0.00 2.87
1438 1455 9.981114 AAGAAGAAGAAGAAGAAGAAGTAGAAG 57.019 33.333 0.00 0.00 0.00 2.85
1439 1456 9.974980 GAAGAAGAAGAAGAAGAAGAAGTAGAA 57.025 33.333 0.00 0.00 0.00 2.10
1440 1457 9.362151 AGAAGAAGAAGAAGAAGAAGAAGTAGA 57.638 33.333 0.00 0.00 0.00 2.59
1441 1458 9.981114 AAGAAGAAGAAGAAGAAGAAGAAGTAG 57.019 33.333 0.00 0.00 0.00 2.57
1442 1459 9.974980 GAAGAAGAAGAAGAAGAAGAAGAAGTA 57.025 33.333 0.00 0.00 0.00 2.24
1443 1460 8.704668 AGAAGAAGAAGAAGAAGAAGAAGAAGT 58.295 33.333 0.00 0.00 0.00 3.01
1451 1468 8.147704 GGAGAAGAAGAAGAAGAAGAAGAAGAA 58.852 37.037 0.00 0.00 0.00 2.52
1454 1471 6.451393 CGGAGAAGAAGAAGAAGAAGAAGAA 58.549 40.000 0.00 0.00 0.00 2.52
1506 1524 1.592400 GCAGAGCAAGGCAGCAATCA 61.592 55.000 4.78 0.00 36.85 2.57
1754 1773 3.852286 TGCAATTGATGAACTGAATGGC 58.148 40.909 10.34 0.00 0.00 4.40
1777 1797 3.133691 GCAAGAACTGTGTCATGAGTGA 58.866 45.455 0.00 0.00 0.00 3.41
1780 1800 2.869358 CGCAAGAACTGTGTCATGAG 57.131 50.000 0.00 0.00 43.02 2.90
1801 1821 0.870393 CCGATGGATCAATCAAGGCG 59.130 55.000 10.75 0.00 0.00 5.52
1807 1833 0.671781 CCCGCTCCGATGGATCAATC 60.672 60.000 0.00 0.00 0.00 2.67
1819 1845 2.436824 GAAGTTCCTGCCCGCTCC 60.437 66.667 0.00 0.00 0.00 4.70
1823 1849 1.439679 GTAGTTGAAGTTCCTGCCCG 58.560 55.000 0.00 0.00 0.00 6.13
1826 1895 0.796927 GCCGTAGTTGAAGTTCCTGC 59.203 55.000 0.00 0.00 0.00 4.85
1983 2052 1.149627 CTTCCACACCCCCGTGAAA 59.850 57.895 0.00 0.00 43.14 2.69
2006 2075 1.488957 CTCAGCGTGTCGTTCTTGC 59.511 57.895 0.00 0.00 0.00 4.01
2259 2328 1.376543 CAACATGGTGCTAGCCTGAG 58.623 55.000 13.29 0.90 0.00 3.35
2262 2331 4.326255 GCAACATGGTGCTAGCCT 57.674 55.556 28.48 0.00 41.51 4.58
2274 2343 8.822855 CGTGGTAAGAATATTTATACAGCAACA 58.177 33.333 11.45 1.34 0.00 3.33
2275 2344 7.797123 GCGTGGTAAGAATATTTATACAGCAAC 59.203 37.037 11.45 5.59 0.00 4.17
2276 2345 7.041644 GGCGTGGTAAGAATATTTATACAGCAA 60.042 37.037 17.15 2.79 0.00 3.91
2277 2346 6.425721 GGCGTGGTAAGAATATTTATACAGCA 59.574 38.462 17.15 6.41 0.00 4.41
2278 2347 6.425721 TGGCGTGGTAAGAATATTTATACAGC 59.574 38.462 11.45 11.89 0.00 4.40
2279 2348 7.956420 TGGCGTGGTAAGAATATTTATACAG 57.044 36.000 11.45 5.77 0.00 2.74
2283 2367 6.294508 GGCAATGGCGTGGTAAGAATATTTAT 60.295 38.462 0.00 0.00 42.47 1.40
2284 2368 5.009210 GGCAATGGCGTGGTAAGAATATTTA 59.991 40.000 0.00 0.00 42.47 1.40
2286 2370 3.317993 GGCAATGGCGTGGTAAGAATATT 59.682 43.478 0.00 0.00 42.47 1.28
2327 2418 2.295692 CTGAAGAATCGGCAGCTCG 58.704 57.895 0.00 0.00 0.00 5.03
2335 2426 0.368227 GCTCACACGCTGAAGAATCG 59.632 55.000 0.00 0.00 0.00 3.34
2346 2441 1.280746 CACCAAAGCAGCTCACACG 59.719 57.895 0.00 0.00 0.00 4.49
2353 2448 0.869730 CAAAATGGCACCAAAGCAGC 59.130 50.000 0.00 0.00 35.83 5.25
2354 2449 1.515081 CCAAAATGGCACCAAAGCAG 58.485 50.000 0.00 0.00 35.83 4.24
2355 2450 0.108207 CCCAAAATGGCACCAAAGCA 59.892 50.000 0.00 0.00 35.79 3.91
2378 2473 2.360483 ACATACACAGCTCTCGGATCAG 59.640 50.000 0.00 0.00 0.00 2.90
2379 2474 2.099756 CACATACACAGCTCTCGGATCA 59.900 50.000 0.00 0.00 0.00 2.92
2380 2475 2.359214 TCACATACACAGCTCTCGGATC 59.641 50.000 0.00 0.00 0.00 3.36
2381 2476 2.379005 TCACATACACAGCTCTCGGAT 58.621 47.619 0.00 0.00 0.00 4.18
2382 2477 1.834188 TCACATACACAGCTCTCGGA 58.166 50.000 0.00 0.00 0.00 4.55
2383 2478 2.654749 TTCACATACACAGCTCTCGG 57.345 50.000 0.00 0.00 0.00 4.63
2384 2479 3.308053 CCAATTCACATACACAGCTCTCG 59.692 47.826 0.00 0.00 0.00 4.04
2385 2480 3.624861 CCCAATTCACATACACAGCTCTC 59.375 47.826 0.00 0.00 0.00 3.20
2386 2481 3.264193 TCCCAATTCACATACACAGCTCT 59.736 43.478 0.00 0.00 0.00 4.09
2387 2482 3.609853 TCCCAATTCACATACACAGCTC 58.390 45.455 0.00 0.00 0.00 4.09
2388 2483 3.719268 TCCCAATTCACATACACAGCT 57.281 42.857 0.00 0.00 0.00 4.24
2392 2487 7.328493 GCTAAAGTTTTCCCAATTCACATACAC 59.672 37.037 0.00 0.00 0.00 2.90
2408 2503 3.026707 ACACACCCAGGCTAAAGTTTT 57.973 42.857 0.00 0.00 0.00 2.43
2414 2509 3.167291 TGGTACACACCCAGGCTAA 57.833 52.632 0.00 0.00 45.11 3.09
2491 2586 5.112686 GCCTATGTTCAGTTCGAATTCTCT 58.887 41.667 0.00 0.00 35.63 3.10
2625 2720 2.426024 CCCTCACAAATGGCTCAATCAG 59.574 50.000 0.00 0.00 0.00 2.90
2656 2751 1.200020 CTTCCTTGGATCACGTTTGCC 59.800 52.381 0.00 0.00 0.00 4.52
2744 2840 3.562567 TTTAGGCATGTAAAACACGGC 57.437 42.857 0.00 0.00 37.11 5.68
2786 2882 4.141846 TGTCCTGTCATTCTAGCAAGATCC 60.142 45.833 0.00 0.00 0.00 3.36
2787 2883 4.808364 GTGTCCTGTCATTCTAGCAAGATC 59.192 45.833 0.00 0.00 0.00 2.75
2790 2886 4.199432 AGTGTCCTGTCATTCTAGCAAG 57.801 45.455 0.00 0.00 0.00 4.01
2801 2898 7.383102 ACATGAAAATCATTAGTGTCCTGTC 57.617 36.000 0.00 0.00 34.28 3.51
2802 2899 7.882791 TGTACATGAAAATCATTAGTGTCCTGT 59.117 33.333 0.00 0.00 34.28 4.00
2803 2900 8.267620 TGTACATGAAAATCATTAGTGTCCTG 57.732 34.615 0.00 0.00 34.28 3.86
2804 2901 8.321353 TCTGTACATGAAAATCATTAGTGTCCT 58.679 33.333 0.00 0.00 34.28 3.85
2805 2902 8.492673 TCTGTACATGAAAATCATTAGTGTCC 57.507 34.615 0.00 0.00 34.28 4.02
2813 2910 7.087409 TCGCATTTCTGTACATGAAAATCAT 57.913 32.000 18.18 5.67 37.65 2.45
2816 2913 5.801947 GCTTCGCATTTCTGTACATGAAAAT 59.198 36.000 18.18 12.20 37.05 1.82
2818 2915 4.455533 AGCTTCGCATTTCTGTACATGAAA 59.544 37.500 17.19 17.19 37.74 2.69
2827 2924 2.208431 CCCTAGAGCTTCGCATTTCTG 58.792 52.381 0.00 0.00 0.00 3.02
2834 2931 3.521947 TTCTAAACCCTAGAGCTTCGC 57.478 47.619 0.00 0.00 0.00 4.70
2859 2956 5.998454 ATCTATGCATGAACAACACTAGC 57.002 39.130 10.16 0.00 0.00 3.42
2894 3150 5.192927 TCCTTGCCTTTACACATATGGAAG 58.807 41.667 7.80 5.70 27.47 3.46
2899 3155 5.242393 GCATGATCCTTGCCTTTACACATAT 59.758 40.000 0.00 0.00 33.95 1.78
2900 3156 4.580167 GCATGATCCTTGCCTTTACACATA 59.420 41.667 0.00 0.00 33.95 2.29
2901 3157 3.382546 GCATGATCCTTGCCTTTACACAT 59.617 43.478 0.00 0.00 33.95 3.21
2906 3162 2.658285 CCAGCATGATCCTTGCCTTTA 58.342 47.619 12.65 0.00 41.06 1.85
2914 3170 4.290459 TCCTATATTTGCCAGCATGATCCT 59.710 41.667 0.00 0.00 39.69 3.24
2988 3248 4.679373 ATCTATCGAGACATGGCAGTTT 57.321 40.909 0.00 0.00 33.41 2.66
2994 3254 9.173021 ACTCTTCTATTATCTATCGAGACATGG 57.827 37.037 0.00 0.00 33.41 3.66
3051 3311 4.287552 AGATACAGAAATGTCGGTAGGGT 58.712 43.478 2.29 0.00 37.76 4.34
3089 3349 4.570772 GTCGTGCAAGATTAGATGCCTTTA 59.429 41.667 5.42 0.00 41.87 1.85
3176 3436 6.688578 AGTTGACTGAATGTTGTAGTATCGT 58.311 36.000 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.