Multiple sequence alignment - TraesCS6A01G153900

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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 TraesCS6A01G153900 chr6A 100.000 2264 0 0 1 2264 141863580 141861317 0.000000e+00 4181.0
1 TraesCS6A01G153900 chr6B 85.873 1444 127 28 45 1465 203692140 203690751 0.000000e+00 1465.0
2 TraesCS6A01G153900 chr6B 93.248 622 34 3 1647 2264 203690563 203689946 0.000000e+00 909.0
3 TraesCS6A01G153900 chr6B 91.346 104 9 0 1466 1569 203690686 203690583 2.340000e-30 143.0
4 TraesCS6A01G153900 chr6D 94.318 704 32 4 769 1465 114173315 114172613 0.000000e+00 1072.0
5 TraesCS6A01G153900 chr6D 90.865 613 27 4 1652 2264 114172420 114171837 0.000000e+00 795.0
6 TraesCS6A01G153900 chr6D 88.060 134 8 2 1466 1599 114172548 114172423 3.890000e-33 152.0
7 TraesCS6A01G153900 chr1D 92.500 40 3 0 143 182 364031378 364031417 8.730000e-05 58.4


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 TraesCS6A01G153900 chr6A 141861317 141863580 2263 True 4181 4181 100.000000 1 2264 1 chr6A.!!$R1 2263
1 TraesCS6A01G153900 chr6B 203689946 203692140 2194 True 839 1465 90.155667 45 2264 3 chr6B.!!$R1 2219
2 TraesCS6A01G153900 chr6D 114171837 114173315 1478 True 673 1072 91.081000 769 2264 3 chr6D.!!$R1 1495

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
854 870 0.04109 CCAACCTAGCCCAACCCAAT 59.959 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1884 0.87439 CATAGCCAACGCAACACACT 59.126 50.0 0.0 0.0 37.52 3.55 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
24 25 6.367374 TGGACTATCAAACAACCACTATCA 57.633 37.500 0.00 0.00 0.00 2.15
25 26 6.170506 TGGACTATCAAACAACCACTATCAC 58.829 40.000 0.00 0.00 0.00 3.06
26 27 5.585047 GGACTATCAAACAACCACTATCACC 59.415 44.000 0.00 0.00 0.00 4.02
27 28 6.121776 ACTATCAAACAACCACTATCACCA 57.878 37.500 0.00 0.00 0.00 4.17
28 29 6.539173 ACTATCAAACAACCACTATCACCAA 58.461 36.000 0.00 0.00 0.00 3.67
29 30 7.175104 ACTATCAAACAACCACTATCACCAAT 58.825 34.615 0.00 0.00 0.00 3.16
30 31 8.325787 ACTATCAAACAACCACTATCACCAATA 58.674 33.333 0.00 0.00 0.00 1.90
31 32 9.173021 CTATCAAACAACCACTATCACCAATAA 57.827 33.333 0.00 0.00 0.00 1.40
32 33 7.825331 TCAAACAACCACTATCACCAATAAA 57.175 32.000 0.00 0.00 0.00 1.40
33 34 8.239038 TCAAACAACCACTATCACCAATAAAA 57.761 30.769 0.00 0.00 0.00 1.52
34 35 8.865090 TCAAACAACCACTATCACCAATAAAAT 58.135 29.630 0.00 0.00 0.00 1.82
35 36 8.924691 CAAACAACCACTATCACCAATAAAATG 58.075 33.333 0.00 0.00 0.00 2.32
36 37 8.415950 AACAACCACTATCACCAATAAAATGA 57.584 30.769 0.00 0.00 0.00 2.57
37 38 8.593945 ACAACCACTATCACCAATAAAATGAT 57.406 30.769 0.00 0.00 36.95 2.45
38 39 8.686334 ACAACCACTATCACCAATAAAATGATC 58.314 33.333 0.00 0.00 34.86 2.92
39 40 7.823745 ACCACTATCACCAATAAAATGATCC 57.176 36.000 0.00 0.00 34.86 3.36
40 41 7.353525 ACCACTATCACCAATAAAATGATCCA 58.646 34.615 0.00 0.00 34.86 3.41
41 42 7.285401 ACCACTATCACCAATAAAATGATCCAC 59.715 37.037 0.00 0.00 34.86 4.02
42 43 7.503566 CCACTATCACCAATAAAATGATCCACT 59.496 37.037 0.00 0.00 34.86 4.00
43 44 8.347771 CACTATCACCAATAAAATGATCCACTG 58.652 37.037 0.00 0.00 34.86 3.66
60 61 2.095567 CACTGTGCCACTTCAATACTGC 60.096 50.000 0.00 0.00 0.00 4.40
63 64 2.154462 GTGCCACTTCAATACTGCAGT 58.846 47.619 25.12 25.12 28.00 4.40
64 65 2.160417 GTGCCACTTCAATACTGCAGTC 59.840 50.000 25.56 5.19 25.04 3.51
69 70 0.613260 TTCAATACTGCAGTCGGCCT 59.387 50.000 25.56 0.00 43.89 5.19
84 85 1.488527 GGCCTGACGTTATCGATGAC 58.511 55.000 8.54 9.44 40.62 3.06
85 86 1.202371 GGCCTGACGTTATCGATGACA 60.202 52.381 19.03 4.04 40.62 3.58
87 88 2.223502 GCCTGACGTTATCGATGACAGA 60.224 50.000 19.03 2.62 40.62 3.41
89 90 3.977579 CCTGACGTTATCGATGACAGATG 59.022 47.826 19.03 6.31 40.62 2.90
103 104 3.840078 TGACAGATGGGAAGTCTTCATGA 59.160 43.478 14.49 0.00 33.56 3.07
108 109 2.054021 TGGGAAGTCTTCATGACCACA 58.946 47.619 14.49 0.00 46.46 4.17
123 124 0.537143 CCACACTTGTAAGGCCAGCA 60.537 55.000 5.01 0.00 0.00 4.41
142 143 0.111832 ACCCTGGTGTCGTAGAGTCA 59.888 55.000 0.00 0.00 36.95 3.41
148 149 2.095415 TGGTGTCGTAGAGTCATCGTTG 60.095 50.000 0.00 0.00 36.95 4.10
161 162 6.875726 AGAGTCATCGTTGAATCAATCTGAAA 59.124 34.615 21.85 0.00 46.76 2.69
164 165 8.517878 AGTCATCGTTGAATCAATCTGAAAAAT 58.482 29.630 0.00 0.00 32.48 1.82
177 178 8.084073 TCAATCTGAAAAATCTGACACCAAATC 58.916 33.333 0.00 0.00 0.00 2.17
178 179 7.771927 ATCTGAAAAATCTGACACCAAATCT 57.228 32.000 0.00 0.00 0.00 2.40
179 180 7.206981 TCTGAAAAATCTGACACCAAATCTC 57.793 36.000 0.00 0.00 0.00 2.75
181 182 5.530915 TGAAAAATCTGACACCAAATCTCGT 59.469 36.000 0.00 0.00 0.00 4.18
182 183 6.039270 TGAAAAATCTGACACCAAATCTCGTT 59.961 34.615 0.00 0.00 0.00 3.85
183 184 5.362556 AAATCTGACACCAAATCTCGTTG 57.637 39.130 0.00 0.00 0.00 4.10
184 185 3.469008 TCTGACACCAAATCTCGTTGT 57.531 42.857 0.00 0.00 0.00 3.32
185 186 3.804036 TCTGACACCAAATCTCGTTGTT 58.196 40.909 0.00 0.00 0.00 2.83
186 187 4.951254 TCTGACACCAAATCTCGTTGTTA 58.049 39.130 0.00 0.00 0.00 2.41
187 188 5.547465 TCTGACACCAAATCTCGTTGTTAT 58.453 37.500 0.00 0.00 0.00 1.89
188 189 5.408299 TCTGACACCAAATCTCGTTGTTATG 59.592 40.000 0.00 0.00 0.00 1.90
189 190 5.060506 TGACACCAAATCTCGTTGTTATGT 58.939 37.500 0.00 0.00 0.00 2.29
190 191 6.224584 TGACACCAAATCTCGTTGTTATGTA 58.775 36.000 0.00 0.00 0.00 2.29
191 192 6.876789 TGACACCAAATCTCGTTGTTATGTAT 59.123 34.615 0.00 0.00 0.00 2.29
192 193 7.072177 ACACCAAATCTCGTTGTTATGTATG 57.928 36.000 0.00 0.00 0.00 2.39
193 194 5.965334 CACCAAATCTCGTTGTTATGTATGC 59.035 40.000 0.00 0.00 0.00 3.14
194 195 5.645929 ACCAAATCTCGTTGTTATGTATGCA 59.354 36.000 0.00 0.00 0.00 3.96
195 196 5.965334 CCAAATCTCGTTGTTATGTATGCAC 59.035 40.000 0.00 0.00 0.00 4.57
196 197 5.389642 AATCTCGTTGTTATGTATGCACG 57.610 39.130 0.00 0.00 0.00 5.34
197 198 4.099380 TCTCGTTGTTATGTATGCACGA 57.901 40.909 0.00 0.00 0.00 4.35
198 199 3.855379 TCTCGTTGTTATGTATGCACGAC 59.145 43.478 0.00 0.00 0.00 4.34
199 200 3.576648 TCGTTGTTATGTATGCACGACA 58.423 40.909 5.78 5.78 0.00 4.35
200 201 3.610677 TCGTTGTTATGTATGCACGACAG 59.389 43.478 9.02 0.00 0.00 3.51
201 202 3.610677 CGTTGTTATGTATGCACGACAGA 59.389 43.478 9.02 2.02 0.00 3.41
215 216 2.363359 ACGACAGAAAACCCTAACTCGT 59.637 45.455 0.00 0.00 0.00 4.18
221 222 1.625511 AAACCCTAACTCGTCGACCT 58.374 50.000 10.58 0.00 0.00 3.85
229 230 2.750637 TCGTCGACCTGAGGAGCC 60.751 66.667 4.99 0.00 36.61 4.70
239 240 0.539051 CTGAGGAGCCGTCAGGAATT 59.461 55.000 13.76 0.00 41.02 2.17
244 245 2.007608 GGAGCCGTCAGGAATTTACAC 58.992 52.381 0.00 0.00 41.02 2.90
250 251 3.125316 CCGTCAGGAATTTACACTGAAGC 59.875 47.826 0.00 0.00 42.30 3.86
253 254 5.049405 CGTCAGGAATTTACACTGAAGCTTT 60.049 40.000 0.00 0.00 42.30 3.51
266 267 2.027192 TGAAGCTTTGTCTAATCCGCCT 60.027 45.455 0.00 0.00 0.00 5.52
270 271 2.464865 CTTTGTCTAATCCGCCTCGAG 58.535 52.381 5.13 5.13 0.00 4.04
282 284 1.597461 CCTCGAGGGGGAGTTTGAC 59.403 63.158 24.62 0.00 31.98 3.18
331 333 1.369209 CAATAAGCGCCGCCATTCG 60.369 57.895 4.98 0.00 38.08 3.34
359 361 7.222224 CCAAACGTAACATCTATGAGGACTAAC 59.778 40.741 0.00 0.00 0.00 2.34
371 373 4.030913 TGAGGACTAACATCCCTAACCTG 58.969 47.826 0.00 0.00 39.91 4.00
380 382 5.469210 ACATCCCTAACCTGTCTACTAGT 57.531 43.478 0.00 0.00 0.00 2.57
390 392 3.876914 CCTGTCTACTAGTCAGAGCTGAG 59.123 52.174 10.79 0.00 40.75 3.35
395 397 7.158697 TGTCTACTAGTCAGAGCTGAGATATC 58.841 42.308 0.00 0.00 40.75 1.63
405 407 6.209192 TCAGAGCTGAGATATCAGGATTCTTC 59.791 42.308 18.59 0.51 38.14 2.87
415 417 3.485764 GGATTCTTCCTCCTGCCAC 57.514 57.895 0.00 0.00 39.14 5.01
420 422 2.530151 TTCCTCCTGCCACCAGCT 60.530 61.111 0.00 0.00 44.23 4.24
421 423 2.134630 CTTCCTCCTGCCACCAGCTT 62.135 60.000 0.00 0.00 44.23 3.74
449 451 0.769873 ATAGGCAGAGGGGATGCAAG 59.230 55.000 0.00 0.00 45.68 4.01
454 456 1.895131 GCAGAGGGGATGCAAGAAAAA 59.105 47.619 0.00 0.00 43.31 1.94
472 474 1.473258 AAAGCTGCAACCTGTGAACA 58.527 45.000 1.02 0.00 0.00 3.18
482 484 4.990426 GCAACCTGTGAACATAATGCTTTT 59.010 37.500 7.04 0.00 0.00 2.27
492 494 9.875675 GTGAACATAATGCTTTTCTAGATGATC 57.124 33.333 0.00 0.00 0.00 2.92
532 539 4.041691 GCTCATAGGGGTATGGTATGTGTT 59.958 45.833 0.00 0.00 0.00 3.32
540 547 4.577283 GGGTATGGTATGTGTTTATGCGTT 59.423 41.667 0.00 0.00 0.00 4.84
541 548 5.277634 GGGTATGGTATGTGTTTATGCGTTC 60.278 44.000 0.00 0.00 0.00 3.95
545 554 6.597262 TGGTATGTGTTTATGCGTTCATAG 57.403 37.500 0.00 0.00 36.60 2.23
548 557 4.209307 TGTGTTTATGCGTTCATAGGGA 57.791 40.909 0.00 0.00 36.60 4.20
551 560 3.563808 TGTTTATGCGTTCATAGGGATGC 59.436 43.478 0.00 0.00 36.60 3.91
558 567 2.731451 CGTTCATAGGGATGCGTGTATG 59.269 50.000 0.00 0.00 32.62 2.39
559 568 2.455674 TCATAGGGATGCGTGTATGC 57.544 50.000 0.00 0.00 32.62 3.14
566 575 3.056536 AGGGATGCGTGTATGCTAGTATG 60.057 47.826 3.24 0.00 35.36 2.39
569 578 5.394224 GGGATGCGTGTATGCTAGTATGTAT 60.394 44.000 3.24 0.00 35.36 2.29
570 579 5.516696 GGATGCGTGTATGCTAGTATGTATG 59.483 44.000 3.24 0.00 35.36 2.39
572 581 5.699839 TGCGTGTATGCTAGTATGTATGAG 58.300 41.667 3.24 0.00 35.36 2.90
582 591 5.692204 GCTAGTATGTATGAGCATTCGTGTT 59.308 40.000 0.00 0.00 34.96 3.32
585 594 5.874810 AGTATGTATGAGCATTCGTGTTTGT 59.125 36.000 0.00 0.00 0.00 2.83
586 595 7.039270 AGTATGTATGAGCATTCGTGTTTGTA 58.961 34.615 0.00 0.00 0.00 2.41
587 596 5.524511 TGTATGAGCATTCGTGTTTGTAC 57.475 39.130 0.00 0.00 0.00 2.90
591 600 5.778161 TGAGCATTCGTGTTTGTACTATG 57.222 39.130 0.00 0.00 0.00 2.23
592 601 5.234752 TGAGCATTCGTGTTTGTACTATGT 58.765 37.500 0.00 0.00 0.00 2.29
595 604 5.699001 AGCATTCGTGTTTGTACTATGTTGA 59.301 36.000 0.00 0.00 0.00 3.18
596 605 6.203915 AGCATTCGTGTTTGTACTATGTTGAA 59.796 34.615 0.00 0.00 0.00 2.69
683 692 2.742053 GTGAAAAGAGCTGCGGTGATAA 59.258 45.455 0.00 0.00 0.00 1.75
684 693 3.375299 GTGAAAAGAGCTGCGGTGATAAT 59.625 43.478 0.00 0.00 0.00 1.28
685 694 4.570772 GTGAAAAGAGCTGCGGTGATAATA 59.429 41.667 0.00 0.00 0.00 0.98
686 695 5.237344 GTGAAAAGAGCTGCGGTGATAATAT 59.763 40.000 0.00 0.00 0.00 1.28
687 696 5.466728 TGAAAAGAGCTGCGGTGATAATATC 59.533 40.000 0.00 0.00 0.00 1.63
694 703 6.441274 AGCTGCGGTGATAATATCAATTTTG 58.559 36.000 4.30 0.00 41.69 2.44
695 704 6.039717 AGCTGCGGTGATAATATCAATTTTGT 59.960 34.615 4.30 0.00 41.69 2.83
696 705 6.697019 GCTGCGGTGATAATATCAATTTTGTT 59.303 34.615 4.30 0.00 41.69 2.83
698 707 8.994429 TGCGGTGATAATATCAATTTTGTTTT 57.006 26.923 4.30 0.00 41.69 2.43
764 776 0.966920 CGTCTTGGGGCGGTATATCT 59.033 55.000 0.00 0.00 0.00 1.98
767 779 3.613432 CGTCTTGGGGCGGTATATCTAAC 60.613 52.174 0.00 0.00 0.00 2.34
779 791 4.222145 GGTATATCTAACGAGATGGCCCAA 59.778 45.833 0.00 0.00 42.66 4.12
841 857 0.413434 ATTTAAGCCCAGCCCAACCT 59.587 50.000 0.00 0.00 0.00 3.50
843 859 0.623723 TTAAGCCCAGCCCAACCTAG 59.376 55.000 0.00 0.00 0.00 3.02
854 870 0.041090 CCAACCTAGCCCAACCCAAT 59.959 55.000 0.00 0.00 0.00 3.16
855 871 1.286553 CCAACCTAGCCCAACCCAATA 59.713 52.381 0.00 0.00 0.00 1.90
867 883 2.616842 CAACCCAATACAATACTCCGCC 59.383 50.000 0.00 0.00 0.00 6.13
872 888 3.186409 CCAATACAATACTCCGCCGATTG 59.814 47.826 0.00 0.00 36.77 2.67
1050 1069 3.264897 GCGATGAAGGTGCGCGAT 61.265 61.111 12.10 0.00 41.37 4.58
1068 1087 2.357760 GTGCCGGCGTACCTCAAA 60.358 61.111 23.90 0.00 0.00 2.69
1295 1314 3.186047 CGCGCAGGTTAGGGTTCG 61.186 66.667 8.75 0.00 0.00 3.95
1302 1321 2.934553 GCAGGTTAGGGTTCGATTGTAC 59.065 50.000 0.00 0.00 0.00 2.90
1343 1362 1.153369 CCGGTGGTGCGATGAGATT 60.153 57.895 0.00 0.00 0.00 2.40
1399 1420 5.059955 CGATTGGCGTGTGGTTTAATTTAAC 59.940 40.000 0.00 0.00 34.64 2.01
1489 1574 6.533819 CAATTGTGCATTTGAATCACTTGT 57.466 33.333 0.00 0.00 0.00 3.16
1506 1591 5.376854 ACTTGTGTAGTGGCAATTGATTC 57.623 39.130 10.34 0.00 35.19 2.52
1550 1635 4.130118 GGAACTGTATGCGGATCTGAATT 58.870 43.478 5.48 0.00 0.00 2.17
1552 1637 5.177696 GGAACTGTATGCGGATCTGAATTAC 59.822 44.000 5.48 4.11 0.00 1.89
1555 1640 4.631131 TGTATGCGGATCTGAATTACCTG 58.369 43.478 5.48 0.00 0.00 4.00
1558 1643 1.884235 CGGATCTGAATTACCTGGGC 58.116 55.000 0.00 0.00 0.00 5.36
1562 1647 3.181458 GGATCTGAATTACCTGGGCGTTA 60.181 47.826 0.00 0.00 0.00 3.18
1563 1648 4.505039 GGATCTGAATTACCTGGGCGTTAT 60.505 45.833 0.00 0.00 0.00 1.89
1564 1649 4.067972 TCTGAATTACCTGGGCGTTATC 57.932 45.455 0.00 0.00 0.00 1.75
1565 1650 3.709653 TCTGAATTACCTGGGCGTTATCT 59.290 43.478 0.00 0.00 0.00 1.98
1566 1651 3.804036 TGAATTACCTGGGCGTTATCTG 58.196 45.455 0.00 0.00 0.00 2.90
1567 1652 3.199071 TGAATTACCTGGGCGTTATCTGT 59.801 43.478 0.00 0.00 0.00 3.41
1568 1653 3.926058 ATTACCTGGGCGTTATCTGTT 57.074 42.857 0.00 0.00 0.00 3.16
1569 1654 5.104859 TGAATTACCTGGGCGTTATCTGTTA 60.105 40.000 0.00 0.00 0.00 2.41
1570 1655 4.822685 TTACCTGGGCGTTATCTGTTAA 57.177 40.909 0.00 0.00 0.00 2.01
1594 1679 6.897706 TCTGTTTCACATCCATTTCATTCA 57.102 33.333 0.00 0.00 0.00 2.57
1600 1685 3.028850 ACATCCATTTCATTCAGCCAGG 58.971 45.455 0.00 0.00 0.00 4.45
1601 1686 2.148446 TCCATTTCATTCAGCCAGGG 57.852 50.000 0.00 0.00 0.00 4.45
1602 1687 1.358787 TCCATTTCATTCAGCCAGGGT 59.641 47.619 0.00 0.00 0.00 4.34
1603 1688 2.580322 TCCATTTCATTCAGCCAGGGTA 59.420 45.455 0.00 0.00 0.00 3.69
1604 1689 3.205056 TCCATTTCATTCAGCCAGGGTAT 59.795 43.478 0.00 0.00 0.00 2.73
1605 1690 4.415179 TCCATTTCATTCAGCCAGGGTATA 59.585 41.667 0.00 0.00 0.00 1.47
1606 1691 4.763793 CCATTTCATTCAGCCAGGGTATAG 59.236 45.833 0.00 0.00 0.00 1.31
1607 1692 5.380043 CATTTCATTCAGCCAGGGTATAGT 58.620 41.667 0.00 0.00 0.00 2.12
1608 1693 5.450818 TTTCATTCAGCCAGGGTATAGTT 57.549 39.130 0.00 0.00 0.00 2.24
1609 1694 5.450818 TTCATTCAGCCAGGGTATAGTTT 57.549 39.130 0.00 0.00 0.00 2.66
1610 1695 4.780815 TCATTCAGCCAGGGTATAGTTTG 58.219 43.478 0.00 0.00 0.00 2.93
1611 1696 3.644966 TTCAGCCAGGGTATAGTTTGG 57.355 47.619 0.00 0.00 0.00 3.28
1616 1701 2.643551 CCAGGGTATAGTTTGGCACTG 58.356 52.381 0.00 0.00 35.97 3.66
1617 1702 2.026262 CCAGGGTATAGTTTGGCACTGT 60.026 50.000 0.00 0.00 35.97 3.55
1618 1703 3.270877 CAGGGTATAGTTTGGCACTGTC 58.729 50.000 0.00 0.00 35.97 3.51
1619 1704 3.055094 CAGGGTATAGTTTGGCACTGTCT 60.055 47.826 0.00 0.00 35.97 3.41
1620 1705 3.587506 AGGGTATAGTTTGGCACTGTCTT 59.412 43.478 0.00 0.00 35.97 3.01
1621 1706 3.939592 GGGTATAGTTTGGCACTGTCTTC 59.060 47.826 0.00 0.00 35.97 2.87
1622 1707 4.323562 GGGTATAGTTTGGCACTGTCTTCT 60.324 45.833 0.00 0.00 35.97 2.85
1623 1708 4.631813 GGTATAGTTTGGCACTGTCTTCTG 59.368 45.833 0.00 0.00 35.97 3.02
1624 1709 4.623932 ATAGTTTGGCACTGTCTTCTGA 57.376 40.909 0.00 0.00 35.97 3.27
1625 1710 2.843701 AGTTTGGCACTGTCTTCTGAG 58.156 47.619 0.00 0.00 32.83 3.35
1626 1711 2.171448 AGTTTGGCACTGTCTTCTGAGT 59.829 45.455 0.00 0.00 32.83 3.41
1627 1712 2.945668 GTTTGGCACTGTCTTCTGAGTT 59.054 45.455 0.00 0.00 0.00 3.01
1628 1713 3.281727 TTGGCACTGTCTTCTGAGTTT 57.718 42.857 0.00 0.00 0.00 2.66
1629 1714 3.281727 TGGCACTGTCTTCTGAGTTTT 57.718 42.857 0.00 0.00 0.00 2.43
1630 1715 4.415881 TGGCACTGTCTTCTGAGTTTTA 57.584 40.909 0.00 0.00 0.00 1.52
1631 1716 4.127171 TGGCACTGTCTTCTGAGTTTTAC 58.873 43.478 0.00 0.00 0.00 2.01
1632 1717 4.141711 TGGCACTGTCTTCTGAGTTTTACT 60.142 41.667 0.00 0.00 0.00 2.24
1633 1718 5.069914 TGGCACTGTCTTCTGAGTTTTACTA 59.930 40.000 0.00 0.00 0.00 1.82
1634 1719 5.635700 GGCACTGTCTTCTGAGTTTTACTAG 59.364 44.000 0.00 0.00 0.00 2.57
1635 1720 6.217294 GCACTGTCTTCTGAGTTTTACTAGT 58.783 40.000 0.00 0.00 0.00 2.57
1636 1721 7.368833 GCACTGTCTTCTGAGTTTTACTAGTA 58.631 38.462 0.00 0.00 0.00 1.82
1637 1722 8.030106 GCACTGTCTTCTGAGTTTTACTAGTAT 58.970 37.037 2.79 0.00 0.00 2.12
1650 1735 9.490379 AGTTTTACTAGTATATATTGCACCAGC 57.510 33.333 2.79 0.00 42.57 4.85
1664 1749 1.469703 CACCAGCGATGCAAATTCTCA 59.530 47.619 0.00 0.00 0.00 3.27
1665 1750 2.095110 CACCAGCGATGCAAATTCTCAA 60.095 45.455 0.00 0.00 0.00 3.02
1666 1751 2.756760 ACCAGCGATGCAAATTCTCAAT 59.243 40.909 0.00 0.00 0.00 2.57
1667 1752 3.113322 CCAGCGATGCAAATTCTCAATG 58.887 45.455 0.00 0.00 0.00 2.82
1694 1779 6.205658 AGACATCCTTGAGCTTTACAAAGTTC 59.794 38.462 10.57 10.57 43.78 3.01
1697 1782 5.305585 TCCTTGAGCTTTACAAAGTTCGAT 58.694 37.500 12.13 0.00 45.63 3.59
1712 1797 7.985184 ACAAAGTTCGATCACTTATATGGCTTA 59.015 33.333 3.01 0.00 35.87 3.09
1717 1802 7.754851 TCGATCACTTATATGGCTTACACTA 57.245 36.000 0.00 0.00 0.00 2.74
1719 1804 8.244113 TCGATCACTTATATGGCTTACACTATG 58.756 37.037 0.00 0.00 0.00 2.23
1738 1823 8.847196 ACACTATGCTGTTATAGTTCTCGAATA 58.153 33.333 0.00 0.00 40.86 1.75
1744 1829 7.710907 TGCTGTTATAGTTCTCGAATAGCAAAT 59.289 33.333 12.16 0.00 41.27 2.32
1779 1865 5.641783 TGACACATTTGTTGGGTATCATG 57.358 39.130 0.00 0.00 43.89 3.07
1791 1877 8.028652 TGTTGGGTATCATGTGTGATTATAGA 57.971 34.615 0.00 0.00 42.37 1.98
1794 1880 8.434589 TGGGTATCATGTGTGATTATAGATCA 57.565 34.615 0.00 0.00 42.37 2.92
1833 1919 3.545703 GCTATGCATAGTTTGGGACTGT 58.454 45.455 29.62 0.00 39.48 3.55
1880 1966 0.971386 ACTGCAGGCCATCTTTTTGG 59.029 50.000 19.93 0.00 39.94 3.28
1965 2051 7.007546 GCGTAAGATCTATTAGCTGTATTCACG 59.992 40.741 0.00 0.00 43.02 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.653320 GTGATAGTGGTTGTTTGATAGTCCAA 59.347 38.462 0.00 0.00 0.00 3.53
1 2 6.170506 GTGATAGTGGTTGTTTGATAGTCCA 58.829 40.000 0.00 0.00 0.00 4.02
2 3 5.585047 GGTGATAGTGGTTGTTTGATAGTCC 59.415 44.000 0.00 0.00 0.00 3.85
3 4 6.170506 TGGTGATAGTGGTTGTTTGATAGTC 58.829 40.000 0.00 0.00 0.00 2.59
4 5 6.121776 TGGTGATAGTGGTTGTTTGATAGT 57.878 37.500 0.00 0.00 0.00 2.12
5 6 7.630242 ATTGGTGATAGTGGTTGTTTGATAG 57.370 36.000 0.00 0.00 0.00 2.08
6 7 9.521841 TTTATTGGTGATAGTGGTTGTTTGATA 57.478 29.630 0.00 0.00 0.00 2.15
7 8 8.415950 TTTATTGGTGATAGTGGTTGTTTGAT 57.584 30.769 0.00 0.00 0.00 2.57
8 9 7.825331 TTTATTGGTGATAGTGGTTGTTTGA 57.175 32.000 0.00 0.00 0.00 2.69
9 10 8.924691 CATTTTATTGGTGATAGTGGTTGTTTG 58.075 33.333 0.00 0.00 0.00 2.93
10 11 8.865090 TCATTTTATTGGTGATAGTGGTTGTTT 58.135 29.630 0.00 0.00 0.00 2.83
11 12 8.415950 TCATTTTATTGGTGATAGTGGTTGTT 57.584 30.769 0.00 0.00 0.00 2.83
12 13 8.593945 ATCATTTTATTGGTGATAGTGGTTGT 57.406 30.769 0.00 0.00 31.21 3.32
13 14 8.137437 GGATCATTTTATTGGTGATAGTGGTTG 58.863 37.037 0.00 0.00 33.03 3.77
14 15 7.838696 TGGATCATTTTATTGGTGATAGTGGTT 59.161 33.333 0.00 0.00 33.03 3.67
15 16 7.285401 GTGGATCATTTTATTGGTGATAGTGGT 59.715 37.037 0.00 0.00 33.03 4.16
16 17 7.503566 AGTGGATCATTTTATTGGTGATAGTGG 59.496 37.037 0.00 0.00 33.03 4.00
17 18 8.347771 CAGTGGATCATTTTATTGGTGATAGTG 58.652 37.037 0.00 0.00 33.03 2.74
18 19 8.055181 ACAGTGGATCATTTTATTGGTGATAGT 58.945 33.333 0.00 0.00 33.03 2.12
19 20 8.347771 CACAGTGGATCATTTTATTGGTGATAG 58.652 37.037 0.00 0.00 33.03 2.08
20 21 7.201812 GCACAGTGGATCATTTTATTGGTGATA 60.202 37.037 1.84 0.00 33.03 2.15
21 22 6.406177 GCACAGTGGATCATTTTATTGGTGAT 60.406 38.462 1.84 0.00 35.42 3.06
22 23 5.105797 GCACAGTGGATCATTTTATTGGTGA 60.106 40.000 1.84 0.00 0.00 4.02
23 24 5.104374 GCACAGTGGATCATTTTATTGGTG 58.896 41.667 1.84 0.00 0.00 4.17
24 25 4.160252 GGCACAGTGGATCATTTTATTGGT 59.840 41.667 1.84 0.00 0.00 3.67
25 26 4.160065 TGGCACAGTGGATCATTTTATTGG 59.840 41.667 1.84 0.00 0.00 3.16
26 27 5.104374 GTGGCACAGTGGATCATTTTATTG 58.896 41.667 13.86 0.00 41.80 1.90
27 28 5.018809 AGTGGCACAGTGGATCATTTTATT 58.981 37.500 21.41 0.00 42.47 1.40
28 29 4.603131 AGTGGCACAGTGGATCATTTTAT 58.397 39.130 21.41 0.00 42.47 1.40
29 30 4.032960 AGTGGCACAGTGGATCATTTTA 57.967 40.909 21.41 0.00 42.47 1.52
30 31 2.880443 AGTGGCACAGTGGATCATTTT 58.120 42.857 21.41 0.00 42.47 1.82
31 32 2.592102 AGTGGCACAGTGGATCATTT 57.408 45.000 21.41 0.00 42.47 2.32
32 33 2.224843 TGAAGTGGCACAGTGGATCATT 60.225 45.455 21.41 1.12 43.84 2.57
33 34 1.352017 TGAAGTGGCACAGTGGATCAT 59.648 47.619 21.41 0.00 43.84 2.45
34 35 0.764271 TGAAGTGGCACAGTGGATCA 59.236 50.000 21.41 10.67 43.84 2.92
35 36 1.896220 TTGAAGTGGCACAGTGGATC 58.104 50.000 21.41 8.28 43.84 3.36
36 37 2.592102 ATTGAAGTGGCACAGTGGAT 57.408 45.000 21.41 4.15 43.84 3.41
37 38 2.371841 AGTATTGAAGTGGCACAGTGGA 59.628 45.455 21.41 1.72 43.84 4.02
38 39 2.485426 CAGTATTGAAGTGGCACAGTGG 59.515 50.000 21.41 0.00 43.84 4.00
39 40 2.095567 GCAGTATTGAAGTGGCACAGTG 60.096 50.000 21.41 11.71 43.84 3.66
41 42 2.153645 TGCAGTATTGAAGTGGCACAG 58.846 47.619 21.41 0.00 41.80 3.66
42 43 2.153645 CTGCAGTATTGAAGTGGCACA 58.846 47.619 21.41 0.00 0.00 4.57
43 44 2.154462 ACTGCAGTATTGAAGTGGCAC 58.846 47.619 20.16 10.29 41.87 5.01
60 61 3.197103 TCGATAACGTCAGGCCGACTG 62.197 57.143 20.38 16.59 42.98 3.51
63 64 0.030235 CATCGATAACGTCAGGCCGA 59.970 55.000 0.00 0.00 40.69 5.54
64 65 0.030235 TCATCGATAACGTCAGGCCG 59.970 55.000 0.00 0.00 40.69 6.13
69 70 3.243401 CCCATCTGTCATCGATAACGTCA 60.243 47.826 0.00 0.00 40.69 4.35
72 73 3.643159 TCCCATCTGTCATCGATAACG 57.357 47.619 0.00 0.00 41.26 3.18
73 74 4.950050 ACTTCCCATCTGTCATCGATAAC 58.050 43.478 0.00 0.00 0.00 1.89
76 77 3.303938 AGACTTCCCATCTGTCATCGAT 58.696 45.455 0.00 0.00 33.56 3.59
84 85 3.054875 TGGTCATGAAGACTTCCCATCTG 60.055 47.826 12.66 3.30 46.72 2.90
85 86 3.054802 GTGGTCATGAAGACTTCCCATCT 60.055 47.826 12.66 0.00 46.72 2.90
87 88 2.644299 TGTGGTCATGAAGACTTCCCAT 59.356 45.455 12.66 0.00 46.72 4.00
89 90 2.039084 AGTGTGGTCATGAAGACTTCCC 59.961 50.000 12.66 6.97 46.72 3.97
103 104 0.537371 GCTGGCCTTACAAGTGTGGT 60.537 55.000 3.32 0.00 0.00 4.16
108 109 1.074951 GGGTGCTGGCCTTACAAGT 59.925 57.895 3.32 0.00 0.00 3.16
123 124 0.111832 TGACTCTACGACACCAGGGT 59.888 55.000 0.00 0.00 0.00 4.34
132 133 4.957759 TGATTCAACGATGACTCTACGA 57.042 40.909 12.96 0.00 36.49 3.43
142 143 8.733458 TCAGATTTTTCAGATTGATTCAACGAT 58.267 29.630 0.15 0.00 0.00 3.73
148 149 7.596494 TGGTGTCAGATTTTTCAGATTGATTC 58.404 34.615 0.00 0.00 0.00 2.52
161 162 4.821805 ACAACGAGATTTGGTGTCAGATTT 59.178 37.500 0.00 0.00 0.00 2.17
164 165 3.469008 ACAACGAGATTTGGTGTCAGA 57.531 42.857 0.00 0.00 0.00 3.27
177 178 3.610677 TGTCGTGCATACATAACAACGAG 59.389 43.478 0.00 0.00 0.00 4.18
178 179 3.576648 TGTCGTGCATACATAACAACGA 58.423 40.909 0.00 0.00 0.00 3.85
179 180 3.610677 TCTGTCGTGCATACATAACAACG 59.389 43.478 5.43 0.00 0.00 4.10
181 182 6.367421 GTTTTCTGTCGTGCATACATAACAA 58.633 36.000 5.43 1.74 0.00 2.83
182 183 5.106869 GGTTTTCTGTCGTGCATACATAACA 60.107 40.000 17.05 6.33 0.00 2.41
183 184 5.321516 GGTTTTCTGTCGTGCATACATAAC 58.678 41.667 5.43 9.49 0.00 1.89
184 185 4.393680 GGGTTTTCTGTCGTGCATACATAA 59.606 41.667 5.43 2.84 0.00 1.90
185 186 3.936453 GGGTTTTCTGTCGTGCATACATA 59.064 43.478 5.43 0.00 0.00 2.29
186 187 2.747446 GGGTTTTCTGTCGTGCATACAT 59.253 45.455 5.43 0.00 0.00 2.29
187 188 2.147958 GGGTTTTCTGTCGTGCATACA 58.852 47.619 4.94 4.94 0.00 2.29
188 189 2.423577 AGGGTTTTCTGTCGTGCATAC 58.576 47.619 0.00 0.00 0.00 2.39
189 190 2.851263 AGGGTTTTCTGTCGTGCATA 57.149 45.000 0.00 0.00 0.00 3.14
190 191 2.812011 GTTAGGGTTTTCTGTCGTGCAT 59.188 45.455 0.00 0.00 0.00 3.96
191 192 2.158871 AGTTAGGGTTTTCTGTCGTGCA 60.159 45.455 0.00 0.00 0.00 4.57
192 193 2.479275 GAGTTAGGGTTTTCTGTCGTGC 59.521 50.000 0.00 0.00 0.00 5.34
193 194 2.729882 CGAGTTAGGGTTTTCTGTCGTG 59.270 50.000 0.00 0.00 0.00 4.35
194 195 2.363359 ACGAGTTAGGGTTTTCTGTCGT 59.637 45.455 0.00 0.00 34.74 4.34
195 196 2.985139 GACGAGTTAGGGTTTTCTGTCG 59.015 50.000 0.00 0.00 0.00 4.35
196 197 2.985139 CGACGAGTTAGGGTTTTCTGTC 59.015 50.000 0.00 0.00 0.00 3.51
197 198 2.624838 TCGACGAGTTAGGGTTTTCTGT 59.375 45.455 0.00 0.00 0.00 3.41
198 199 2.985139 GTCGACGAGTTAGGGTTTTCTG 59.015 50.000 0.00 0.00 0.00 3.02
199 200 2.029560 GGTCGACGAGTTAGGGTTTTCT 60.030 50.000 9.92 0.00 0.00 2.52
200 201 2.029560 AGGTCGACGAGTTAGGGTTTTC 60.030 50.000 9.92 0.00 0.00 2.29
201 202 1.966354 AGGTCGACGAGTTAGGGTTTT 59.034 47.619 9.92 0.00 0.00 2.43
215 216 2.750637 GACGGCTCCTCAGGTCGA 60.751 66.667 10.02 0.00 0.00 4.20
221 222 0.984230 AAATTCCTGACGGCTCCTCA 59.016 50.000 0.00 0.00 0.00 3.86
229 230 3.997021 AGCTTCAGTGTAAATTCCTGACG 59.003 43.478 0.00 0.00 35.10 4.35
239 240 5.637810 CGGATTAGACAAAGCTTCAGTGTAA 59.362 40.000 17.88 17.88 0.00 2.41
244 245 2.352960 GGCGGATTAGACAAAGCTTCAG 59.647 50.000 0.00 0.00 0.00 3.02
250 251 2.464865 CTCGAGGCGGATTAGACAAAG 58.535 52.381 3.91 0.00 0.00 2.77
253 254 1.107538 CCCTCGAGGCGGATTAGACA 61.108 60.000 26.87 0.00 0.00 3.41
266 267 1.228644 TCGTCAAACTCCCCCTCGA 60.229 57.895 0.00 0.00 0.00 4.04
270 271 1.739371 CGATTCTCGTCAAACTCCCCC 60.739 57.143 0.00 0.00 34.72 5.40
282 284 1.368641 TTTCCATGCACCGATTCTCG 58.631 50.000 0.00 0.00 40.07 4.04
295 297 6.348540 GCTTATTGTTCGAGTCAGTTTTCCAT 60.349 38.462 0.00 0.00 0.00 3.41
296 298 5.049680 GCTTATTGTTCGAGTCAGTTTTCCA 60.050 40.000 0.00 0.00 0.00 3.53
297 299 5.383130 GCTTATTGTTCGAGTCAGTTTTCC 58.617 41.667 0.00 0.00 0.00 3.13
298 300 5.073478 CGCTTATTGTTCGAGTCAGTTTTC 58.927 41.667 0.00 0.00 0.00 2.29
301 303 2.412089 GCGCTTATTGTTCGAGTCAGTT 59.588 45.455 0.00 0.00 0.00 3.16
331 333 5.519206 GTCCTCATAGATGTTACGTTTGGAC 59.481 44.000 0.00 0.00 33.51 4.02
341 343 6.146760 AGGGATGTTAGTCCTCATAGATGTT 58.853 40.000 0.00 0.00 38.38 2.71
342 344 5.721225 AGGGATGTTAGTCCTCATAGATGT 58.279 41.667 0.00 0.00 38.38 3.06
344 346 6.726764 GGTTAGGGATGTTAGTCCTCATAGAT 59.273 42.308 0.00 0.00 38.38 1.98
345 347 6.075984 GGTTAGGGATGTTAGTCCTCATAGA 58.924 44.000 0.00 0.00 38.38 1.98
346 348 6.015010 CAGGTTAGGGATGTTAGTCCTCATAG 60.015 46.154 0.00 0.00 38.38 2.23
359 361 5.446860 TGACTAGTAGACAGGTTAGGGATG 58.553 45.833 3.59 0.00 0.00 3.51
371 373 7.158697 TGATATCTCAGCTCTGACTAGTAGAC 58.841 42.308 3.59 0.00 35.46 2.59
380 382 5.643176 AGAATCCTGATATCTCAGCTCTGA 58.357 41.667 3.98 0.00 46.39 3.27
405 407 2.045536 GAAGCTGGTGGCAGGAGG 60.046 66.667 0.00 0.00 44.79 4.30
407 409 4.020617 CGGAAGCTGGTGGCAGGA 62.021 66.667 0.00 0.00 44.79 3.86
410 412 2.032528 CTTCGGAAGCTGGTGGCA 59.967 61.111 4.57 0.00 44.79 4.92
420 422 1.134401 CCTCTGCCTATTGCTTCGGAA 60.134 52.381 0.00 0.00 42.00 4.30
421 423 0.465705 CCTCTGCCTATTGCTTCGGA 59.534 55.000 0.00 0.00 42.00 4.55
430 432 0.769873 CTTGCATCCCCTCTGCCTAT 59.230 55.000 0.00 0.00 38.89 2.57
434 436 1.549203 TTTTCTTGCATCCCCTCTGC 58.451 50.000 0.00 0.00 40.10 4.26
454 456 1.696063 ATGTTCACAGGTTGCAGCTT 58.304 45.000 0.00 0.00 0.00 3.74
456 458 3.504863 CATTATGTTCACAGGTTGCAGC 58.495 45.455 0.00 0.00 0.00 5.25
457 459 3.192001 AGCATTATGTTCACAGGTTGCAG 59.808 43.478 11.24 0.00 33.15 4.41
466 468 9.875675 GATCATCTAGAAAAGCATTATGTTCAC 57.124 33.333 0.00 0.00 0.00 3.18
496 498 9.930158 ATACCCCTATGAGCTTTGTTTAATTAA 57.070 29.630 0.00 0.00 0.00 1.40
497 499 9.349713 CATACCCCTATGAGCTTTGTTTAATTA 57.650 33.333 0.00 0.00 32.66 1.40
500 502 6.126409 CCATACCCCTATGAGCTTTGTTTAA 58.874 40.000 0.00 0.00 32.66 1.52
507 514 4.287067 CACATACCATACCCCTATGAGCTT 59.713 45.833 0.00 0.00 32.66 3.74
517 524 4.131596 ACGCATAAACACATACCATACCC 58.868 43.478 0.00 0.00 0.00 3.69
532 539 2.224185 ACGCATCCCTATGAACGCATAA 60.224 45.455 0.00 0.00 36.60 1.90
540 547 1.970640 AGCATACACGCATCCCTATGA 59.029 47.619 0.00 0.00 34.84 2.15
541 548 2.462456 AGCATACACGCATCCCTATG 57.538 50.000 0.00 0.00 36.09 2.23
545 554 3.254060 CATACTAGCATACACGCATCCC 58.746 50.000 0.00 0.00 0.00 3.85
548 557 6.267496 TCATACATACTAGCATACACGCAT 57.733 37.500 0.00 0.00 0.00 4.73
551 560 5.699839 TGCTCATACATACTAGCATACACG 58.300 41.667 0.00 0.00 39.92 4.49
558 567 5.223382 ACACGAATGCTCATACATACTAGC 58.777 41.667 0.00 0.00 35.51 3.42
559 568 7.222805 ACAAACACGAATGCTCATACATACTAG 59.777 37.037 0.00 0.00 0.00 2.57
566 575 5.779806 AGTACAAACACGAATGCTCATAC 57.220 39.130 0.00 0.00 0.00 2.39
569 578 5.234752 ACATAGTACAAACACGAATGCTCA 58.765 37.500 0.00 0.00 0.00 4.26
570 579 5.779806 ACATAGTACAAACACGAATGCTC 57.220 39.130 0.00 0.00 0.00 4.26
572 581 5.922546 TCAACATAGTACAAACACGAATGC 58.077 37.500 0.00 0.00 0.00 3.56
672 681 8.633075 AAACAAAATTGATATTATCACCGCAG 57.367 30.769 5.86 0.66 39.39 5.18
738 747 2.721167 CGCCCCAAGACGGATCTGA 61.721 63.158 9.00 0.00 36.56 3.27
739 748 2.202932 CGCCCCAAGACGGATCTG 60.203 66.667 0.00 0.00 36.56 2.90
753 765 3.734293 GCCATCTCGTTAGATATACCGCC 60.734 52.174 0.00 0.00 40.65 6.13
757 769 5.169295 GTTGGGCCATCTCGTTAGATATAC 58.831 45.833 7.26 0.00 40.65 1.47
764 776 4.133820 CAATATGTTGGGCCATCTCGTTA 58.866 43.478 7.26 0.00 0.00 3.18
779 791 2.365582 GCCTTCGGTTGACCAATATGT 58.634 47.619 0.51 0.00 35.14 2.29
841 857 4.141344 GGAGTATTGTATTGGGTTGGGCTA 60.141 45.833 0.00 0.00 0.00 3.93
843 859 2.956333 GGAGTATTGTATTGGGTTGGGC 59.044 50.000 0.00 0.00 0.00 5.36
854 870 1.539496 GGCAATCGGCGGAGTATTGTA 60.539 52.381 16.93 0.00 46.16 2.41
855 871 0.814010 GGCAATCGGCGGAGTATTGT 60.814 55.000 16.93 0.00 46.16 2.71
867 883 2.336667 GATTTGTTTGGGTGGCAATCG 58.663 47.619 0.00 0.00 0.00 3.34
872 888 1.676968 GGGGATTTGTTTGGGTGGC 59.323 57.895 0.00 0.00 0.00 5.01
1011 1030 1.472276 GGATCTCGTTGTACAGCGCG 61.472 60.000 25.08 20.00 34.98 6.86
1050 1069 3.166490 TTTGAGGTACGCCGGCACA 62.166 57.895 28.98 10.55 40.50 4.57
1085 1104 1.603172 CGGTGCTCTTCTTCACGTTCT 60.603 52.381 0.00 0.00 34.20 3.01
1195 1214 4.162690 CAGGCCCACGAGGTAGGC 62.163 72.222 0.00 0.00 46.37 3.93
1197 1216 4.162690 GGCAGGCCCACGAGGTAG 62.163 72.222 0.00 0.00 38.26 3.18
1302 1321 3.609853 TCGGATCAGGAAACAGAAATGG 58.390 45.455 0.00 0.00 0.00 3.16
1343 1362 3.021177 GGGTTCAATCCCCGGAAAATA 57.979 47.619 0.73 0.00 41.54 1.40
1381 1400 8.453320 ACCTTATAGTTAAATTAAACCACACGC 58.547 33.333 0.00 0.00 0.00 5.34
1385 1404 8.667463 TGCGACCTTATAGTTAAATTAAACCAC 58.333 33.333 0.00 0.00 0.00 4.16
1399 1420 2.394708 CACGTCCATGCGACCTTATAG 58.605 52.381 8.25 0.00 38.36 1.31
1489 1574 3.937814 AGACGAATCAATTGCCACTACA 58.062 40.909 0.00 0.00 0.00 2.74
1506 1591 4.910357 CCACTATTGGCGGTCATATAGACG 60.910 50.000 14.43 7.96 41.47 4.18
1539 1624 1.873903 CGCCCAGGTAATTCAGATCCG 60.874 57.143 0.00 0.00 0.00 4.18
1550 1635 4.652421 AGATTAACAGATAACGCCCAGGTA 59.348 41.667 0.00 0.00 0.00 3.08
1552 1637 3.809832 CAGATTAACAGATAACGCCCAGG 59.190 47.826 0.00 0.00 0.00 4.45
1555 1640 5.353123 TGAAACAGATTAACAGATAACGCCC 59.647 40.000 0.00 0.00 0.00 6.13
1600 1685 4.631813 CAGAAGACAGTGCCAAACTATACC 59.368 45.833 0.00 0.00 36.83 2.73
1601 1686 5.479306 TCAGAAGACAGTGCCAAACTATAC 58.521 41.667 0.00 0.00 36.83 1.47
1602 1687 5.246203 ACTCAGAAGACAGTGCCAAACTATA 59.754 40.000 0.00 0.00 36.83 1.31
1603 1688 4.040952 ACTCAGAAGACAGTGCCAAACTAT 59.959 41.667 0.00 0.00 36.83 2.12
1604 1689 3.388024 ACTCAGAAGACAGTGCCAAACTA 59.612 43.478 0.00 0.00 36.83 2.24
1605 1690 2.171448 ACTCAGAAGACAGTGCCAAACT 59.829 45.455 0.00 0.00 40.93 2.66
1606 1691 2.565841 ACTCAGAAGACAGTGCCAAAC 58.434 47.619 0.00 0.00 0.00 2.93
1607 1692 3.281727 AACTCAGAAGACAGTGCCAAA 57.718 42.857 0.00 0.00 0.00 3.28
1608 1693 3.281727 AAACTCAGAAGACAGTGCCAA 57.718 42.857 0.00 0.00 0.00 4.52
1609 1694 3.281727 AAAACTCAGAAGACAGTGCCA 57.718 42.857 0.00 0.00 0.00 4.92
1610 1695 4.381411 AGTAAAACTCAGAAGACAGTGCC 58.619 43.478 0.00 0.00 0.00 5.01
1611 1696 6.217294 ACTAGTAAAACTCAGAAGACAGTGC 58.783 40.000 0.00 0.00 0.00 4.40
1624 1709 9.490379 GCTGGTGCAATATATACTAGTAAAACT 57.510 33.333 6.70 0.00 39.41 2.66
1625 1710 8.433126 CGCTGGTGCAATATATACTAGTAAAAC 58.567 37.037 6.70 0.00 39.64 2.43
1626 1711 8.361889 TCGCTGGTGCAATATATACTAGTAAAA 58.638 33.333 6.70 0.00 39.64 1.52
1627 1712 7.888424 TCGCTGGTGCAATATATACTAGTAAA 58.112 34.615 6.70 0.00 39.64 2.01
1628 1713 7.457024 TCGCTGGTGCAATATATACTAGTAA 57.543 36.000 6.70 0.00 39.64 2.24
1629 1714 7.480810 CATCGCTGGTGCAATATATACTAGTA 58.519 38.462 4.77 4.77 39.64 1.82
1630 1715 5.977489 TCGCTGGTGCAATATATACTAGT 57.023 39.130 0.00 0.00 39.64 2.57
1631 1716 5.233050 GCATCGCTGGTGCAATATATACTAG 59.767 44.000 8.59 0.00 42.08 2.57
1632 1717 5.109210 GCATCGCTGGTGCAATATATACTA 58.891 41.667 8.59 0.00 42.08 1.82
1633 1718 3.935203 GCATCGCTGGTGCAATATATACT 59.065 43.478 8.59 0.00 42.08 2.12
1634 1719 4.264543 GCATCGCTGGTGCAATATATAC 57.735 45.455 8.59 0.00 42.08 1.47
1643 1728 0.171903 AGAATTTGCATCGCTGGTGC 59.828 50.000 6.82 6.82 42.81 5.01
1644 1729 1.469703 TGAGAATTTGCATCGCTGGTG 59.530 47.619 0.00 0.00 0.00 4.17
1645 1730 1.825090 TGAGAATTTGCATCGCTGGT 58.175 45.000 0.00 0.00 0.00 4.00
1646 1731 2.925578 TTGAGAATTTGCATCGCTGG 57.074 45.000 0.00 0.00 0.00 4.85
1647 1732 4.023739 TCATTGAGAATTTGCATCGCTG 57.976 40.909 0.00 0.00 0.00 5.18
1648 1733 4.397103 TCTTCATTGAGAATTTGCATCGCT 59.603 37.500 0.00 0.00 35.25 4.93
1649 1734 4.498323 GTCTTCATTGAGAATTTGCATCGC 59.502 41.667 0.00 0.00 35.25 4.58
1650 1735 5.633927 TGTCTTCATTGAGAATTTGCATCG 58.366 37.500 0.00 0.00 35.25 3.84
1664 1749 6.240894 TGTAAAGCTCAAGGATGTCTTCATT 58.759 36.000 0.00 0.00 34.06 2.57
1665 1750 5.809001 TGTAAAGCTCAAGGATGTCTTCAT 58.191 37.500 0.00 0.00 36.95 2.57
1666 1751 5.227569 TGTAAAGCTCAAGGATGTCTTCA 57.772 39.130 0.00 0.00 32.41 3.02
1667 1752 6.205658 ACTTTGTAAAGCTCAAGGATGTCTTC 59.794 38.462 4.35 0.00 39.63 2.87
1694 1779 7.009631 GCATAGTGTAAGCCATATAAGTGATCG 59.990 40.741 0.00 0.00 0.00 3.69
1697 1782 7.154656 CAGCATAGTGTAAGCCATATAAGTGA 58.845 38.462 0.00 0.00 0.00 3.41
1712 1797 6.694877 TCGAGAACTATAACAGCATAGTGT 57.305 37.500 0.00 0.00 40.14 3.55
1717 1802 6.749139 TGCTATTCGAGAACTATAACAGCAT 58.251 36.000 0.00 0.00 30.88 3.79
1719 1804 7.464830 TTTGCTATTCGAGAACTATAACAGC 57.535 36.000 0.00 0.00 0.00 4.40
1738 1823 5.750067 GTGTCATTCAACAGTTTCATTTGCT 59.250 36.000 0.00 0.00 0.00 3.91
1744 1829 6.629128 ACAAATGTGTCATTCAACAGTTTCA 58.371 32.000 0.00 0.00 29.49 2.69
1798 1884 0.874390 CATAGCCAACGCAACACACT 59.126 50.000 0.00 0.00 37.52 3.55
1833 1919 1.977854 AGGTTGATACAGCTGTCACCA 59.022 47.619 25.56 16.46 0.00 4.17
1842 1928 5.700832 TGCAGTAACTTGAAGGTTGATACAG 59.299 40.000 0.00 0.00 0.00 2.74
1880 1966 7.546667 ACTTCATAAATGCACAAAATGGTGATC 59.453 33.333 0.00 0.00 41.32 2.92
1965 2051 7.790823 TTGACCTAACCTACTAACACAAAAC 57.209 36.000 0.00 0.00 0.00 2.43
2088 2177 5.633182 TCAAAAGTGTCAAACTCTGCAAAAC 59.367 36.000 0.00 0.00 38.56 2.43
2189 2278 8.956426 GGTTCTGTCAAAACTATCATGGAATTA 58.044 33.333 0.00 0.00 0.00 1.40
2237 2326 4.209307 TGTAAGTCACACTGTTGTTCCA 57.791 40.909 0.00 0.00 31.66 3.53


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

AutoCloner maintained by Alex Coulton.