Multiple sequence alignment - TraesCS6D01G060100

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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 TraesCS6D01G060100 chr6D 100.000 2315 0 0 1 2315 28163627 28161313 0.000000e+00 4276.0
1 TraesCS6D01G060100 chr6D 87.313 402 31 13 910 1303 28028571 28028182 2.110000e-120 442.0
2 TraesCS6D01G060100 chr6D 82.195 483 52 14 963 1419 28065345 28064871 3.610000e-103 385.0
3 TraesCS6D01G060100 chr6B 90.374 1818 104 41 420 2197 52113473 52115259 0.000000e+00 2322.0
4 TraesCS6D01G060100 chr6B 88.249 417 43 5 912 1324 52152001 52152415 5.750000e-136 494.0
5 TraesCS6D01G060100 chr6B 85.270 482 48 14 870 1330 52060066 52059587 2.080000e-130 475.0
6 TraesCS6D01G060100 chr6B 94.922 256 12 1 1051 1306 51962019 51961765 1.290000e-107 399.0
7 TraesCS6D01G060100 chr6B 87.179 234 24 2 1005 1238 52188302 52188529 6.340000e-66 261.0
8 TraesCS6D01G060100 chr6B 100.000 29 0 0 811 839 52024565 52024537 1.000000e-03 54.7
9 TraesCS6D01G060100 chr6A 83.333 1200 118 45 172 1303 29794911 29796096 0.000000e+00 1033.0
10 TraesCS6D01G060100 chr6A 89.822 393 32 6 930 1320 29693003 29692617 4.440000e-137 497.0
11 TraesCS6D01G060100 chr6A 88.162 321 24 7 1418 1728 29809714 29810030 1.010000e-98 370.0
12 TraesCS6D01G060100 chrUn 90.057 352 29 4 974 1324 71734363 71734709 3.510000e-123 451.0
13 TraesCS6D01G060100 chrUn 86.916 321 28 7 1418 1728 71734998 71735314 4.730000e-92 348.0
14 TraesCS6D01G060100 chr3A 91.166 283 22 2 1917 2199 703960855 703961134 4.670000e-102 381.0
15 TraesCS6D01G060100 chr3A 96.154 52 1 1 1865 1915 8697964 8697913 1.470000e-12 84.2
16 TraesCS6D01G060100 chr3D 90.217 276 25 2 1917 2192 571689425 571689698 2.190000e-95 359.0
17 TraesCS6D01G060100 chr2B 95.000 60 2 1 1853 1911 760931729 760931670 2.450000e-15 93.5
18 TraesCS6D01G060100 chr2B 91.935 62 4 1 1862 1922 549025563 549025624 4.100000e-13 86.1
19 TraesCS6D01G060100 chr2A 95.000 60 2 1 1853 1911 27422800 27422741 2.450000e-15 93.5
20 TraesCS6D01G060100 chr5D 93.103 58 3 1 1862 1918 322958636 322958579 1.470000e-12 84.2
21 TraesCS6D01G060100 chr5B 91.935 62 1 4 1856 1915 710770159 710770100 1.470000e-12 84.2
22 TraesCS6D01G060100 chr5A 93.103 58 3 1 1862 1918 419685334 419685277 1.470000e-12 84.2
23 TraesCS6D01G060100 chr4B 88.235 68 6 2 1862 1927 405090306 405090373 1.910000e-11 80.5


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 TraesCS6D01G060100 chr6D 28161313 28163627 2314 True 4276.0 4276 100.0000 1 2315 1 chr6D.!!$R3 2314
1 TraesCS6D01G060100 chr6B 52113473 52115259 1786 False 2322.0 2322 90.3740 420 2197 1 chr6B.!!$F1 1777
2 TraesCS6D01G060100 chr6A 29794911 29796096 1185 False 1033.0 1033 83.3330 172 1303 1 chr6A.!!$F1 1131
3 TraesCS6D01G060100 chrUn 71734363 71735314 951 False 399.5 451 88.4865 974 1728 2 chrUn.!!$F1 754

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
135 136 0.105964 TAGTGATTTCGGCCATCGGG 59.894 55.0 2.24 0.0 39.77 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 2139 0.320508 GGACGGAGGGAGTGTGAAAC 60.321 60.0 0.0 0.0 37.35 2.78 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
20 21 3.611766 CGAGGATTGTAGGTGGTTTCT 57.388 47.619 0.00 0.00 0.00 2.52
21 22 3.522553 CGAGGATTGTAGGTGGTTTCTC 58.477 50.000 0.00 0.00 0.00 2.87
22 23 3.056107 CGAGGATTGTAGGTGGTTTCTCA 60.056 47.826 0.00 0.00 0.00 3.27
23 24 4.562757 CGAGGATTGTAGGTGGTTTCTCAA 60.563 45.833 0.00 0.00 0.00 3.02
24 25 4.652822 AGGATTGTAGGTGGTTTCTCAAC 58.347 43.478 0.00 0.00 0.00 3.18
37 38 4.566987 GTTTCTCAACCTACTACCAGTGG 58.433 47.826 7.91 7.91 0.00 4.00
38 39 3.537795 TCTCAACCTACTACCAGTGGT 57.462 47.619 20.91 20.91 40.16 4.16
39 40 3.853207 TCTCAACCTACTACCAGTGGTT 58.147 45.455 22.49 5.84 38.91 3.67
40 41 5.001833 TCTCAACCTACTACCAGTGGTTA 57.998 43.478 22.49 6.85 37.44 2.85
41 42 4.768968 TCTCAACCTACTACCAGTGGTTAC 59.231 45.833 22.49 0.00 37.44 2.50
42 43 4.482030 TCAACCTACTACCAGTGGTTACA 58.518 43.478 22.49 0.74 37.44 2.41
43 44 4.900652 TCAACCTACTACCAGTGGTTACAA 59.099 41.667 22.49 0.30 37.44 2.41
44 45 5.544948 TCAACCTACTACCAGTGGTTACAAT 59.455 40.000 22.49 4.47 37.44 2.71
45 46 6.043474 TCAACCTACTACCAGTGGTTACAATT 59.957 38.462 22.49 5.88 37.44 2.32
46 47 6.443995 ACCTACTACCAGTGGTTACAATTT 57.556 37.500 22.49 0.00 37.09 1.82
47 48 6.844829 ACCTACTACCAGTGGTTACAATTTT 58.155 36.000 22.49 0.00 37.09 1.82
48 49 7.292319 ACCTACTACCAGTGGTTACAATTTTT 58.708 34.615 22.49 0.00 37.09 1.94
129 130 9.797556 AATAAAAACTAATTAGTGATTTCGGCC 57.202 29.630 22.91 0.00 36.50 6.13
130 131 6.827586 AAAACTAATTAGTGATTTCGGCCA 57.172 33.333 18.70 0.00 36.50 5.36
131 132 7.404671 AAAACTAATTAGTGATTTCGGCCAT 57.595 32.000 18.70 0.00 36.50 4.40
132 133 6.619801 AACTAATTAGTGATTTCGGCCATC 57.380 37.500 18.70 0.00 36.50 3.51
133 134 4.750098 ACTAATTAGTGATTTCGGCCATCG 59.250 41.667 17.35 0.00 34.72 3.84
134 135 1.948104 TTAGTGATTTCGGCCATCGG 58.052 50.000 2.24 0.00 39.77 4.18
135 136 0.105964 TAGTGATTTCGGCCATCGGG 59.894 55.000 2.24 0.00 39.77 5.14
136 137 2.186826 GTGATTTCGGCCATCGGGG 61.187 63.158 2.24 0.00 39.77 5.73
137 138 2.371259 TGATTTCGGCCATCGGGGA 61.371 57.895 2.24 0.00 40.01 4.81
138 139 1.073199 GATTTCGGCCATCGGGGAT 59.927 57.895 2.24 0.00 40.01 3.85
139 140 1.228245 ATTTCGGCCATCGGGGATG 60.228 57.895 2.24 0.00 40.01 3.51
140 141 4.562425 TTCGGCCATCGGGGATGC 62.562 66.667 2.24 0.00 38.59 3.91
142 143 4.996434 CGGCCATCGGGGATGCTC 62.996 72.222 2.24 0.00 38.59 4.26
143 144 3.564218 GGCCATCGGGGATGCTCT 61.564 66.667 0.00 0.00 38.59 4.09
144 145 2.512896 GCCATCGGGGATGCTCTT 59.487 61.111 0.08 0.00 38.59 2.85
145 146 1.895707 GCCATCGGGGATGCTCTTG 60.896 63.158 0.08 0.00 38.59 3.02
146 147 1.895707 CCATCGGGGATGCTCTTGC 60.896 63.158 0.08 0.00 38.59 4.01
147 148 1.895707 CATCGGGGATGCTCTTGCC 60.896 63.158 0.00 0.00 38.71 4.52
148 149 3.466791 ATCGGGGATGCTCTTGCCG 62.467 63.158 0.00 0.00 38.71 5.69
149 150 4.161295 CGGGGATGCTCTTGCCGA 62.161 66.667 0.00 0.00 38.71 5.54
150 151 2.203126 GGGGATGCTCTTGCCGAG 60.203 66.667 0.00 0.00 42.88 4.63
157 158 2.581953 CTCTTGCCGAGCGAGCTC 60.582 66.667 14.61 14.61 39.71 4.09
158 159 4.135153 TCTTGCCGAGCGAGCTCC 62.135 66.667 18.19 6.92 39.71 4.70
159 160 4.441695 CTTGCCGAGCGAGCTCCA 62.442 66.667 18.19 9.33 39.77 3.86
160 161 4.441695 TTGCCGAGCGAGCTCCAG 62.442 66.667 18.19 11.53 39.77 3.86
217 218 1.219124 CGTGGGAGGTGGTGATGAG 59.781 63.158 0.00 0.00 0.00 2.90
218 219 1.604378 GTGGGAGGTGGTGATGAGG 59.396 63.158 0.00 0.00 0.00 3.86
219 220 2.300967 TGGGAGGTGGTGATGAGGC 61.301 63.158 0.00 0.00 0.00 4.70
221 222 1.685224 GGAGGTGGTGATGAGGCAA 59.315 57.895 0.00 0.00 0.00 4.52
240 241 4.643387 AGCCTGGCGTGAACCCAC 62.643 66.667 13.96 0.00 39.86 4.61
273 274 1.226888 CTCGCCGGTGCTAGGTAAC 60.227 63.158 11.05 0.00 34.43 2.50
274 275 1.940883 CTCGCCGGTGCTAGGTAACA 61.941 60.000 11.05 0.00 34.75 2.41
275 276 1.079681 CGCCGGTGCTAGGTAACAA 60.080 57.895 0.00 0.00 34.75 2.83
283 284 3.304190 GGTGCTAGGTAACAACCGTTTTG 60.304 47.826 0.00 0.00 36.52 2.44
290 291 2.287393 AACAACCGTTTTGTCCAAGC 57.713 45.000 0.51 0.00 28.09 4.01
292 293 0.593773 CAACCGTTTTGTCCAAGCCG 60.594 55.000 0.00 0.00 0.00 5.52
293 294 1.033202 AACCGTTTTGTCCAAGCCGT 61.033 50.000 0.00 0.00 0.00 5.68
302 303 2.125106 CCAAGCCGTCACCCTAGC 60.125 66.667 0.00 0.00 0.00 3.42
325 326 0.552848 CATGTGGGCCCAACCTATCT 59.447 55.000 30.64 2.81 39.10 1.98
326 327 0.552848 ATGTGGGCCCAACCTATCTG 59.447 55.000 30.64 0.00 39.10 2.90
349 350 9.027202 TCTGAATGGGGTTTAAATTAACTAACC 57.973 33.333 0.00 0.00 39.41 2.85
350 351 7.828712 TGAATGGGGTTTAAATTAACTAACCG 58.171 34.615 0.00 0.00 40.71 4.44
351 352 6.778834 ATGGGGTTTAAATTAACTAACCGG 57.221 37.500 0.00 0.00 40.71 5.28
358 360 8.179615 GGTTTAAATTAACTAACCGGTCATCAG 58.820 37.037 8.04 5.70 31.64 2.90
359 361 8.938906 GTTTAAATTAACTAACCGGTCATCAGA 58.061 33.333 8.04 0.00 0.00 3.27
367 369 7.553881 ACTAACCGGTCATCAGAATATTTTG 57.446 36.000 8.04 0.00 0.00 2.44
368 370 4.900635 ACCGGTCATCAGAATATTTTGC 57.099 40.909 0.00 0.00 0.00 3.68
369 371 3.312421 ACCGGTCATCAGAATATTTTGCG 59.688 43.478 0.00 0.00 0.00 4.85
370 372 3.559655 CCGGTCATCAGAATATTTTGCGA 59.440 43.478 1.10 0.00 0.00 5.10
371 373 4.035091 CCGGTCATCAGAATATTTTGCGAA 59.965 41.667 1.10 0.00 0.00 4.70
372 374 5.448496 CCGGTCATCAGAATATTTTGCGAAA 60.448 40.000 0.53 0.53 0.00 3.46
373 375 5.678483 CGGTCATCAGAATATTTTGCGAAAG 59.322 40.000 5.18 0.00 0.00 2.62
374 376 6.456853 CGGTCATCAGAATATTTTGCGAAAGA 60.457 38.462 5.18 0.03 0.00 2.52
416 418 4.461081 TGTGCCAGCGAATAAATTAAAGGT 59.539 37.500 0.00 0.00 0.00 3.50
434 436 8.667076 TTAAAGGTTGTGGAGTAGTTTCTTAC 57.333 34.615 0.00 0.00 0.00 2.34
436 438 7.607615 AAGGTTGTGGAGTAGTTTCTTACTA 57.392 36.000 0.00 0.00 38.33 1.82
467 469 8.115490 ACCTGAATTATGATAGCTTTTATGCC 57.885 34.615 0.00 0.00 0.00 4.40
585 611 9.626045 GTCCTACTTAAATTTGTTTCATCTTGG 57.374 33.333 0.00 0.00 0.00 3.61
611 637 5.299531 CGTCCAAAGGTAGAGATCTGTATCA 59.700 44.000 12.36 0.00 34.28 2.15
613 639 6.322712 GTCCAAAGGTAGAGATCTGTATCAGT 59.677 42.308 12.36 0.00 34.28 3.41
614 640 6.547880 TCCAAAGGTAGAGATCTGTATCAGTC 59.452 42.308 12.36 0.00 34.28 3.51
615 641 6.549364 CCAAAGGTAGAGATCTGTATCAGTCT 59.451 42.308 12.36 0.00 34.28 3.24
616 642 7.424803 CAAAGGTAGAGATCTGTATCAGTCTG 58.575 42.308 12.36 0.00 34.28 3.51
624 652 5.825679 AGATCTGTATCAGTCTGGAGTACAC 59.174 44.000 0.00 0.00 34.28 2.90
661 689 2.232208 GCAAATTAACCTGCTGCCTCTT 59.768 45.455 0.00 0.00 35.62 2.85
689 717 1.271325 TGACAGCGACCATTTGTGGAT 60.271 47.619 0.73 0.00 0.00 3.41
704 732 6.773976 TTTGTGGATGATTTGACTAATCCC 57.226 37.500 7.09 3.40 41.68 3.85
705 733 5.449297 TGTGGATGATTTGACTAATCCCA 57.551 39.130 7.09 5.61 41.68 4.37
706 734 5.825532 TGTGGATGATTTGACTAATCCCAA 58.174 37.500 7.09 0.00 41.68 4.12
707 735 6.252233 TGTGGATGATTTGACTAATCCCAAA 58.748 36.000 7.09 1.67 41.68 3.28
708 736 6.723515 TGTGGATGATTTGACTAATCCCAAAA 59.276 34.615 7.09 0.00 41.68 2.44
718 746 7.353414 TGACTAATCCCAAAACAAATTGTCA 57.647 32.000 0.00 0.00 0.00 3.58
788 817 2.234414 TGTCACATACCCTACGTTTCCC 59.766 50.000 0.00 0.00 0.00 3.97
856 889 3.005554 ACTGCTCTCGTCATTTTGGATG 58.994 45.455 0.00 0.00 0.00 3.51
860 893 3.249559 GCTCTCGTCATTTTGGATGATCC 59.750 47.826 4.05 4.05 36.96 3.36
870 903 3.989600 TTGGATGATCCTCCTCTCTCT 57.010 47.619 16.86 0.00 37.46 3.10
871 904 3.524095 TGGATGATCCTCCTCTCTCTC 57.476 52.381 16.86 0.00 37.46 3.20
872 905 3.062889 TGGATGATCCTCCTCTCTCTCT 58.937 50.000 16.86 0.00 37.46 3.10
873 906 3.074390 TGGATGATCCTCCTCTCTCTCTC 59.926 52.174 16.86 0.00 37.46 3.20
878 914 0.628522 CCTCCTCTCTCTCTCCCACA 59.371 60.000 0.00 0.00 0.00 4.17
879 915 1.684869 CCTCCTCTCTCTCTCCCACAC 60.685 61.905 0.00 0.00 0.00 3.82
882 918 3.127250 TCCTCTCTCTCTCCCACACTAT 58.873 50.000 0.00 0.00 0.00 2.12
891 927 7.013220 TCTCTCTCCCACACTATAAAGCATAT 58.987 38.462 0.00 0.00 0.00 1.78
926 989 1.349627 GCAATCAGCACACGATCGG 59.650 57.895 20.98 10.92 44.79 4.18
970 1047 0.815734 TCAGTTCCCGTGCTAGCTAC 59.184 55.000 17.23 11.33 0.00 3.58
1056 1141 3.120979 CTACCTCGCGGTCGATGCA 62.121 63.158 6.13 0.00 44.21 3.96
1303 1388 4.233408 GCAAAGAGCAAAGCCACG 57.767 55.556 0.00 0.00 44.79 4.94
1354 1469 5.008415 TCTCTCGGTTTATCGATAGGTGAAC 59.992 44.000 5.09 7.14 44.20 3.18
1356 1471 5.125900 TCTCGGTTTATCGATAGGTGAACAA 59.874 40.000 15.87 0.93 46.47 2.83
1357 1472 5.345702 TCGGTTTATCGATAGGTGAACAAG 58.654 41.667 15.87 10.81 46.47 3.16
1358 1473 5.105635 TCGGTTTATCGATAGGTGAACAAGT 60.106 40.000 15.87 0.00 46.47 3.16
1378 1497 1.284491 TGTGATATGCTTTCTGGGCCA 59.716 47.619 5.85 5.85 0.00 5.36
1394 1513 6.412214 TCTGGGCCAGTTTATTTAGTTAGAC 58.588 40.000 31.60 0.00 32.61 2.59
1395 1514 6.214819 TCTGGGCCAGTTTATTTAGTTAGACT 59.785 38.462 31.60 0.00 32.61 3.24
1396 1515 6.786122 TGGGCCAGTTTATTTAGTTAGACTT 58.214 36.000 0.00 0.00 0.00 3.01
1397 1516 7.920227 TGGGCCAGTTTATTTAGTTAGACTTA 58.080 34.615 0.00 0.00 0.00 2.24
1398 1517 8.044908 TGGGCCAGTTTATTTAGTTAGACTTAG 58.955 37.037 0.00 0.00 0.00 2.18
1399 1518 8.262933 GGGCCAGTTTATTTAGTTAGACTTAGA 58.737 37.037 4.39 0.00 0.00 2.10
1400 1519 9.096160 GGCCAGTTTATTTAGTTAGACTTAGAC 57.904 37.037 0.00 0.00 0.00 2.59
1486 1772 3.227667 GCGTACGTGCGACTTTGT 58.772 55.556 30.16 0.00 0.00 2.83
1497 1783 4.318475 CGTGCGACTTTGTCACTTCAATTA 60.318 41.667 0.00 0.00 32.09 1.40
1548 1834 3.080300 TGGTTGTTCAGTGACCTGTTT 57.920 42.857 0.00 0.00 39.82 2.83
1602 1888 7.219726 GCAGCTATTTCAATTTTTCTCTAGTGC 59.780 37.037 0.00 0.00 0.00 4.40
1609 1895 4.749245 ATTTTTCTCTAGTGCCGTGTTG 57.251 40.909 0.00 0.00 0.00 3.33
1610 1896 2.163818 TTTCTCTAGTGCCGTGTTGG 57.836 50.000 0.00 0.00 42.50 3.77
1625 1919 1.072331 TGTTGGTGCTCCTTCTCTTCC 59.928 52.381 6.34 0.00 34.23 3.46
1631 1925 1.827969 TGCTCCTTCTCTTCCTACAGC 59.172 52.381 0.00 0.00 0.00 4.40
1637 1931 2.831685 TCTCTTCCTACAGCGCAAAA 57.168 45.000 11.47 0.00 0.00 2.44
1731 2025 2.040544 CAGTTTGGGCAGTAGCGGG 61.041 63.158 0.00 0.00 43.41 6.13
1773 2067 3.763897 CTGGGCACACCTTAAGCTAAAAT 59.236 43.478 0.00 0.00 41.11 1.82
1795 2089 8.419076 AAATTTGTTTTGGTCTATCACACAAC 57.581 30.769 0.00 0.00 0.00 3.32
1796 2090 6.516739 TTTGTTTTGGTCTATCACACAACA 57.483 33.333 0.00 0.00 36.01 3.33
1839 2133 2.665649 AGTCGTGTGGAATATTCGCA 57.334 45.000 9.32 8.08 0.00 5.10
1845 2139 3.242944 CGTGTGGAATATTCGCACTACTG 59.757 47.826 25.54 14.52 34.12 2.74
1851 2146 5.350365 TGGAATATTCGCACTACTGTTTCAC 59.650 40.000 9.32 0.00 0.00 3.18
1861 2156 0.393077 ACTGTTTCACACTCCCTCCG 59.607 55.000 0.00 0.00 0.00 4.63
1876 2171 4.273318 TCCCTCCGTCCTAAAGTTAGTAC 58.727 47.826 0.00 0.00 0.00 2.73
1889 2184 9.490379 CCTAAAGTTAGTACAAAGTTGAGTCAT 57.510 33.333 0.00 0.00 0.00 3.06
1902 2197 6.254281 AGTTGAGTCATTTATTTTGGGACG 57.746 37.500 0.00 0.00 33.84 4.79
1916 2220 1.499438 TGGGACGGAGGAGTAGATCAT 59.501 52.381 0.00 0.00 0.00 2.45
1988 2292 0.249868 GCCAGGCAACCAAACCTTTC 60.250 55.000 6.55 0.00 32.56 2.62
1992 2296 0.317519 GGCAACCAAACCTTTCGACG 60.318 55.000 0.00 0.00 0.00 5.12
2028 2332 4.666512 AGTCCAAGCTCCAATGTTTATGT 58.333 39.130 0.00 0.00 0.00 2.29
2034 2338 6.392354 CAAGCTCCAATGTTTATGTTCATGT 58.608 36.000 0.00 0.00 0.00 3.21
2038 2342 6.867816 GCTCCAATGTTTATGTTCATGTTCAA 59.132 34.615 0.00 0.00 0.00 2.69
2039 2343 7.546667 GCTCCAATGTTTATGTTCATGTTCAAT 59.453 33.333 0.00 0.00 0.00 2.57
2040 2344 9.426837 CTCCAATGTTTATGTTCATGTTCAATT 57.573 29.630 0.00 0.00 0.00 2.32
2146 2450 2.419297 GCATAACTGGACCCTGTCTCAG 60.419 54.545 0.00 9.64 37.11 3.35
2173 2477 6.552725 AGCTGTCTTCCTACATGATCTATTCA 59.447 38.462 0.00 0.00 39.12 2.57
2185 2489 8.824159 ACATGATCTATTCACCTTCTAAATCG 57.176 34.615 0.00 0.00 37.11 3.34
2197 2501 5.531287 ACCTTCTAAATCGTTTCACAAGCTT 59.469 36.000 0.00 0.00 0.00 3.74
2198 2502 6.039382 ACCTTCTAAATCGTTTCACAAGCTTT 59.961 34.615 0.00 0.00 0.00 3.51
2199 2503 6.578919 CCTTCTAAATCGTTTCACAAGCTTTC 59.421 38.462 0.00 0.00 0.00 2.62
2200 2504 6.861065 TCTAAATCGTTTCACAAGCTTTCT 57.139 33.333 0.00 0.00 0.00 2.52
2201 2505 7.956420 TCTAAATCGTTTCACAAGCTTTCTA 57.044 32.000 0.00 0.00 0.00 2.10
2202 2506 8.373048 TCTAAATCGTTTCACAAGCTTTCTAA 57.627 30.769 0.00 0.00 0.00 2.10
2203 2507 8.832521 TCTAAATCGTTTCACAAGCTTTCTAAA 58.167 29.630 0.00 0.00 0.00 1.85
2204 2508 9.612620 CTAAATCGTTTCACAAGCTTTCTAAAT 57.387 29.630 0.00 0.00 0.00 1.40
2205 2509 8.507470 AAATCGTTTCACAAGCTTTCTAAATC 57.493 30.769 0.00 0.00 0.00 2.17
2206 2510 5.675970 TCGTTTCACAAGCTTTCTAAATCG 58.324 37.500 0.00 4.92 0.00 3.34
2207 2511 5.235616 TCGTTTCACAAGCTTTCTAAATCGT 59.764 36.000 0.00 0.00 0.00 3.73
2208 2512 5.907391 CGTTTCACAAGCTTTCTAAATCGTT 59.093 36.000 0.00 0.00 0.00 3.85
2209 2513 6.413818 CGTTTCACAAGCTTTCTAAATCGTTT 59.586 34.615 0.00 0.00 0.00 3.60
2210 2514 7.356476 CGTTTCACAAGCTTTCTAAATCGTTTC 60.356 37.037 0.00 0.00 0.00 2.78
2211 2515 6.612247 TCACAAGCTTTCTAAATCGTTTCA 57.388 33.333 0.00 0.00 0.00 2.69
2212 2516 6.427150 TCACAAGCTTTCTAAATCGTTTCAC 58.573 36.000 0.00 0.00 0.00 3.18
2213 2517 6.037720 TCACAAGCTTTCTAAATCGTTTCACA 59.962 34.615 0.00 0.00 0.00 3.58
2214 2518 6.690957 CACAAGCTTTCTAAATCGTTTCACAA 59.309 34.615 0.00 0.00 0.00 3.33
2215 2519 6.912591 ACAAGCTTTCTAAATCGTTTCACAAG 59.087 34.615 0.00 0.00 0.00 3.16
2216 2520 5.452777 AGCTTTCTAAATCGTTTCACAAGC 58.547 37.500 0.00 0.00 35.41 4.01
2217 2521 5.239525 AGCTTTCTAAATCGTTTCACAAGCT 59.760 36.000 0.00 0.00 39.64 3.74
2218 2522 5.340667 GCTTTCTAAATCGTTTCACAAGCTG 59.659 40.000 0.00 0.00 32.99 4.24
2219 2523 5.356882 TTCTAAATCGTTTCACAAGCTGG 57.643 39.130 0.00 0.00 0.00 4.85
2220 2524 4.385825 TCTAAATCGTTTCACAAGCTGGT 58.614 39.130 0.00 0.00 0.00 4.00
2221 2525 4.819630 TCTAAATCGTTTCACAAGCTGGTT 59.180 37.500 0.00 0.00 0.00 3.67
2222 2526 3.626028 AATCGTTTCACAAGCTGGTTC 57.374 42.857 0.00 0.00 0.00 3.62
2223 2527 1.305201 TCGTTTCACAAGCTGGTTCC 58.695 50.000 0.00 0.00 0.00 3.62
2224 2528 1.134220 TCGTTTCACAAGCTGGTTCCT 60.134 47.619 0.00 0.00 0.00 3.36
2225 2529 1.002468 CGTTTCACAAGCTGGTTCCTG 60.002 52.381 0.00 0.00 0.00 3.86
2226 2530 1.032014 TTTCACAAGCTGGTTCCTGC 58.968 50.000 11.81 11.81 0.00 4.85
2227 2531 0.183492 TTCACAAGCTGGTTCCTGCT 59.817 50.000 15.65 15.65 41.76 4.24
2228 2532 0.183492 TCACAAGCTGGTTCCTGCTT 59.817 50.000 23.57 23.57 46.81 3.91
2230 2534 3.769201 AAGCTGGTTCCTGCTTGC 58.231 55.556 26.74 8.50 45.10 4.01
2231 2535 1.152694 AAGCTGGTTCCTGCTTGCA 60.153 52.632 26.74 0.00 45.10 4.08
2232 2536 1.177256 AAGCTGGTTCCTGCTTGCAG 61.177 55.000 26.74 15.02 45.10 4.41
2233 2537 1.900498 GCTGGTTCCTGCTTGCAGT 60.900 57.895 19.49 0.00 0.00 4.40
2234 2538 1.954528 CTGGTTCCTGCTTGCAGTG 59.045 57.895 19.49 11.92 0.00 3.66
2235 2539 0.535780 CTGGTTCCTGCTTGCAGTGA 60.536 55.000 19.49 13.75 0.00 3.41
2236 2540 0.535780 TGGTTCCTGCTTGCAGTGAG 60.536 55.000 19.49 6.47 0.00 3.51
2237 2541 0.250467 GGTTCCTGCTTGCAGTGAGA 60.250 55.000 19.49 8.55 0.00 3.27
2238 2542 1.597742 GTTCCTGCTTGCAGTGAGAA 58.402 50.000 19.49 13.36 0.00 2.87
2239 2543 1.949525 GTTCCTGCTTGCAGTGAGAAA 59.050 47.619 19.49 5.12 0.00 2.52
2240 2544 1.888215 TCCTGCTTGCAGTGAGAAAG 58.112 50.000 19.49 4.52 0.00 2.62
2241 2545 0.879765 CCTGCTTGCAGTGAGAAAGG 59.120 55.000 19.49 0.92 0.00 3.11
2242 2546 0.240411 CTGCTTGCAGTGAGAAAGGC 59.760 55.000 13.89 0.00 0.00 4.35
2243 2547 1.174712 TGCTTGCAGTGAGAAAGGCC 61.175 55.000 0.00 0.00 0.00 5.19
2244 2548 1.871126 GCTTGCAGTGAGAAAGGCCC 61.871 60.000 0.00 0.00 0.00 5.80
2245 2549 0.538057 CTTGCAGTGAGAAAGGCCCA 60.538 55.000 0.00 0.00 0.00 5.36
2246 2550 0.106268 TTGCAGTGAGAAAGGCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
2247 2551 0.112995 TGCAGTGAGAAAGGCCCAAT 59.887 50.000 0.00 0.00 0.00 3.16
2248 2552 1.260544 GCAGTGAGAAAGGCCCAATT 58.739 50.000 0.00 0.00 0.00 2.32
2249 2553 1.067354 GCAGTGAGAAAGGCCCAATTG 60.067 52.381 0.00 0.00 0.00 2.32
2250 2554 1.547372 CAGTGAGAAAGGCCCAATTGG 59.453 52.381 18.21 18.21 37.09 3.16
2264 2568 4.387598 CCCAATTGGCAAGAAAATGTTCA 58.612 39.130 19.75 0.00 36.09 3.18
2265 2569 4.820716 CCCAATTGGCAAGAAAATGTTCAA 59.179 37.500 19.75 0.00 36.09 2.69
2266 2570 5.298777 CCCAATTGGCAAGAAAATGTTCAAA 59.701 36.000 19.75 0.00 36.09 2.69
2267 2571 6.016108 CCCAATTGGCAAGAAAATGTTCAAAT 60.016 34.615 19.75 0.00 36.09 2.32
2268 2572 7.427214 CCAATTGGCAAGAAAATGTTCAAATT 58.573 30.769 12.53 0.00 36.09 1.82
2269 2573 7.380065 CCAATTGGCAAGAAAATGTTCAAATTG 59.620 33.333 12.53 6.21 36.09 2.32
2270 2574 6.374565 TTGGCAAGAAAATGTTCAAATTGG 57.625 33.333 0.00 0.00 36.09 3.16
2271 2575 4.275443 TGGCAAGAAAATGTTCAAATTGGC 59.725 37.500 12.96 12.96 39.99 4.52
2272 2576 4.320421 GGCAAGAAAATGTTCAAATTGGCC 60.320 41.667 10.08 0.00 36.65 5.36
2273 2577 4.320421 GCAAGAAAATGTTCAAATTGGCCC 60.320 41.667 0.00 0.00 36.09 5.80
2274 2578 4.703379 AGAAAATGTTCAAATTGGCCCA 57.297 36.364 0.00 0.00 36.09 5.36
2275 2579 4.644498 AGAAAATGTTCAAATTGGCCCAG 58.356 39.130 0.00 0.00 36.09 4.45
2276 2580 4.102996 AGAAAATGTTCAAATTGGCCCAGT 59.897 37.500 0.00 0.00 36.09 4.00
2277 2581 3.683365 AATGTTCAAATTGGCCCAGTC 57.317 42.857 0.00 0.00 0.00 3.51
2278 2582 2.079170 TGTTCAAATTGGCCCAGTCA 57.921 45.000 0.00 0.00 0.00 3.41
2279 2583 1.962807 TGTTCAAATTGGCCCAGTCAG 59.037 47.619 0.00 0.00 0.00 3.51
2280 2584 2.238521 GTTCAAATTGGCCCAGTCAGA 58.761 47.619 0.00 0.00 0.00 3.27
2281 2585 2.205022 TCAAATTGGCCCAGTCAGAG 57.795 50.000 0.00 0.00 0.00 3.35
2282 2586 0.529378 CAAATTGGCCCAGTCAGAGC 59.471 55.000 0.00 0.00 0.00 4.09
2283 2587 0.112995 AAATTGGCCCAGTCAGAGCA 59.887 50.000 0.00 0.00 0.00 4.26
2284 2588 0.610232 AATTGGCCCAGTCAGAGCAC 60.610 55.000 0.00 0.00 0.00 4.40
2285 2589 2.809861 ATTGGCCCAGTCAGAGCACG 62.810 60.000 0.00 0.00 0.00 5.34
2286 2590 4.008933 GGCCCAGTCAGAGCACGT 62.009 66.667 0.00 0.00 0.00 4.49
2287 2591 2.031163 GCCCAGTCAGAGCACGTT 59.969 61.111 0.00 0.00 0.00 3.99
2288 2592 2.029844 GCCCAGTCAGAGCACGTTC 61.030 63.158 0.00 0.00 0.00 3.95
2289 2593 1.734477 CCCAGTCAGAGCACGTTCG 60.734 63.158 0.00 0.00 0.00 3.95
2290 2594 1.007271 CCAGTCAGAGCACGTTCGT 60.007 57.895 0.00 0.00 0.00 3.85
2291 2595 0.597637 CCAGTCAGAGCACGTTCGTT 60.598 55.000 0.00 0.00 0.00 3.85
2292 2596 0.778815 CAGTCAGAGCACGTTCGTTC 59.221 55.000 0.00 0.00 0.00 3.95
2293 2597 0.318784 AGTCAGAGCACGTTCGTTCC 60.319 55.000 0.00 0.00 0.00 3.62
2294 2598 0.596600 GTCAGAGCACGTTCGTTCCA 60.597 55.000 0.00 0.00 0.00 3.53
2295 2599 0.318699 TCAGAGCACGTTCGTTCCAG 60.319 55.000 0.00 0.00 0.00 3.86
2296 2600 1.664965 AGAGCACGTTCGTTCCAGC 60.665 57.895 0.00 0.00 0.00 4.85
2297 2601 3.000080 GAGCACGTTCGTTCCAGCG 62.000 63.158 0.00 0.00 0.00 5.18
2298 2602 4.072088 GCACGTTCGTTCCAGCGG 62.072 66.667 0.00 0.00 0.00 5.52
2299 2603 2.660552 CACGTTCGTTCCAGCGGT 60.661 61.111 0.00 0.00 0.00 5.68
2300 2604 1.372004 CACGTTCGTTCCAGCGGTA 60.372 57.895 0.00 0.00 0.00 4.02
2301 2605 0.734942 CACGTTCGTTCCAGCGGTAT 60.735 55.000 0.00 0.00 0.00 2.73
2302 2606 0.810648 ACGTTCGTTCCAGCGGTATA 59.189 50.000 0.00 0.00 0.00 1.47
2303 2607 1.406539 ACGTTCGTTCCAGCGGTATAT 59.593 47.619 0.00 0.00 0.00 0.86
2304 2608 2.159198 ACGTTCGTTCCAGCGGTATATT 60.159 45.455 0.00 0.00 0.00 1.28
2305 2609 2.470257 CGTTCGTTCCAGCGGTATATTC 59.530 50.000 0.00 0.00 0.00 1.75
2306 2610 2.798847 GTTCGTTCCAGCGGTATATTCC 59.201 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.056107 TGAGAAACCACCTACAATCCTCG 60.056 47.826 0.00 0.00 0.00 4.63
1 2 4.553330 TGAGAAACCACCTACAATCCTC 57.447 45.455 0.00 0.00 0.00 3.71
2 3 4.506802 GGTTGAGAAACCACCTACAATCCT 60.507 45.833 2.75 0.00 42.38 3.24
4 5 4.652822 AGGTTGAGAAACCACCTACAATC 58.347 43.478 10.11 0.00 45.23 2.67
5 6 4.724279 AGGTTGAGAAACCACCTACAAT 57.276 40.909 10.11 0.00 45.23 2.71
9 10 4.774200 GGTAGTAGGTTGAGAAACCACCTA 59.226 45.833 10.11 6.36 45.23 3.08
10 11 3.581770 GGTAGTAGGTTGAGAAACCACCT 59.418 47.826 10.11 7.21 45.23 4.00
11 12 3.325716 TGGTAGTAGGTTGAGAAACCACC 59.674 47.826 10.11 8.68 45.23 4.61
12 13 4.040095 ACTGGTAGTAGGTTGAGAAACCAC 59.960 45.833 10.11 6.33 45.23 4.16
13 14 4.039973 CACTGGTAGTAGGTTGAGAAACCA 59.960 45.833 10.11 0.00 45.23 3.67
14 15 4.562963 CCACTGGTAGTAGGTTGAGAAACC 60.563 50.000 0.00 0.00 43.15 3.27
15 16 4.040095 ACCACTGGTAGTAGGTTGAGAAAC 59.960 45.833 0.00 0.00 32.11 2.78
16 17 4.228824 ACCACTGGTAGTAGGTTGAGAAA 58.771 43.478 0.00 0.00 32.11 2.52
17 18 3.853207 ACCACTGGTAGTAGGTTGAGAA 58.147 45.455 0.00 0.00 32.11 2.87
18 19 3.537795 ACCACTGGTAGTAGGTTGAGA 57.462 47.619 0.00 0.00 32.11 3.27
19 20 4.525487 TGTAACCACTGGTAGTAGGTTGAG 59.475 45.833 17.93 0.00 38.82 3.02
20 21 4.482030 TGTAACCACTGGTAGTAGGTTGA 58.518 43.478 17.93 8.24 38.82 3.18
21 22 4.877378 TGTAACCACTGGTAGTAGGTTG 57.123 45.455 17.93 0.00 38.82 3.77
22 23 6.443995 AATTGTAACCACTGGTAGTAGGTT 57.556 37.500 0.00 15.16 40.30 3.50
23 24 6.443995 AAATTGTAACCACTGGTAGTAGGT 57.556 37.500 0.00 0.00 33.12 3.08
24 25 7.754851 AAAAATTGTAACCACTGGTAGTAGG 57.245 36.000 0.00 0.00 33.12 3.18
103 104 9.797556 GGCCGAAATCACTAATTAGTTTTTATT 57.202 29.630 15.60 10.03 33.46 1.40
104 105 8.962679 TGGCCGAAATCACTAATTAGTTTTTAT 58.037 29.630 15.60 4.83 33.46 1.40
105 106 8.338072 TGGCCGAAATCACTAATTAGTTTTTA 57.662 30.769 15.60 2.70 33.46 1.52
106 107 7.222000 TGGCCGAAATCACTAATTAGTTTTT 57.778 32.000 15.60 16.63 33.46 1.94
107 108 6.827586 TGGCCGAAATCACTAATTAGTTTT 57.172 33.333 15.60 14.03 33.46 2.43
108 109 6.238374 CGATGGCCGAAATCACTAATTAGTTT 60.238 38.462 15.60 7.98 41.76 2.66
109 110 5.236478 CGATGGCCGAAATCACTAATTAGTT 59.764 40.000 15.60 1.14 41.76 2.24
110 111 4.750098 CGATGGCCGAAATCACTAATTAGT 59.250 41.667 12.50 12.50 41.76 2.24
111 112 4.152402 CCGATGGCCGAAATCACTAATTAG 59.848 45.833 11.05 11.05 41.76 1.73
112 113 4.062293 CCGATGGCCGAAATCACTAATTA 58.938 43.478 0.00 0.00 41.76 1.40
113 114 2.878406 CCGATGGCCGAAATCACTAATT 59.122 45.455 0.00 0.00 41.76 1.40
114 115 2.494059 CCGATGGCCGAAATCACTAAT 58.506 47.619 0.00 0.00 41.76 1.73
115 116 1.474320 CCCGATGGCCGAAATCACTAA 60.474 52.381 0.00 0.00 41.76 2.24
116 117 0.105964 CCCGATGGCCGAAATCACTA 59.894 55.000 0.00 0.00 41.76 2.74
117 118 1.153168 CCCGATGGCCGAAATCACT 60.153 57.895 0.00 0.00 41.76 3.41
118 119 2.186826 CCCCGATGGCCGAAATCAC 61.187 63.158 0.00 0.00 41.76 3.06
119 120 1.705002 ATCCCCGATGGCCGAAATCA 61.705 55.000 0.00 0.00 41.76 2.57
120 121 1.073199 ATCCCCGATGGCCGAAATC 59.927 57.895 0.00 0.00 41.76 2.17
121 122 1.228245 CATCCCCGATGGCCGAAAT 60.228 57.895 0.00 0.00 41.76 2.17
122 123 2.191908 CATCCCCGATGGCCGAAA 59.808 61.111 0.00 0.00 41.76 3.46
123 124 4.562425 GCATCCCCGATGGCCGAA 62.562 66.667 0.00 0.00 40.10 4.30
125 126 4.996434 GAGCATCCCCGATGGCCG 62.996 72.222 0.00 0.00 40.10 6.13
126 127 3.125376 AAGAGCATCCCCGATGGCC 62.125 63.158 0.00 0.00 40.10 5.36
127 128 1.895707 CAAGAGCATCCCCGATGGC 60.896 63.158 3.94 0.00 40.10 4.40
128 129 1.895707 GCAAGAGCATCCCCGATGG 60.896 63.158 3.94 0.00 40.10 3.51
129 130 1.895707 GGCAAGAGCATCCCCGATG 60.896 63.158 0.00 0.00 44.61 3.84
130 131 2.512896 GGCAAGAGCATCCCCGAT 59.487 61.111 0.00 0.00 44.61 4.18
131 132 4.161295 CGGCAAGAGCATCCCCGA 62.161 66.667 0.00 0.00 42.13 5.14
132 133 4.161295 TCGGCAAGAGCATCCCCG 62.161 66.667 0.00 0.00 44.61 5.73
133 134 2.203126 CTCGGCAAGAGCATCCCC 60.203 66.667 0.00 0.00 44.61 4.81
141 142 4.135153 GGAGCTCGCTCGGCAAGA 62.135 66.667 7.83 0.00 43.59 3.02
142 143 4.441695 TGGAGCTCGCTCGGCAAG 62.442 66.667 7.83 0.00 43.59 4.01
143 144 4.441695 CTGGAGCTCGCTCGGCAA 62.442 66.667 7.83 0.00 43.59 4.52
169 170 3.892581 GGGGCTACGCTGCAATGC 61.893 66.667 0.00 0.00 34.04 3.56
170 171 2.438254 TGGGGCTACGCTGCAATG 60.438 61.111 0.00 0.00 34.04 2.82
171 172 2.124570 CTGGGGCTACGCTGCAAT 60.125 61.111 0.00 0.00 34.04 3.56
172 173 4.408821 CCTGGGGCTACGCTGCAA 62.409 66.667 0.00 0.00 34.04 4.08
200 201 1.604378 CCTCATCACCACCTCCCAC 59.396 63.158 0.00 0.00 0.00 4.61
201 202 2.300967 GCCTCATCACCACCTCCCA 61.301 63.158 0.00 0.00 0.00 4.37
207 208 2.475666 GCTCTTGCCTCATCACCAC 58.524 57.895 0.00 0.00 0.00 4.16
218 219 2.669569 TTCACGCCAGGCTCTTGC 60.670 61.111 10.54 0.00 38.76 4.01
219 220 2.328099 GGTTCACGCCAGGCTCTTG 61.328 63.158 10.54 3.98 0.00 3.02
221 222 4.021925 GGGTTCACGCCAGGCTCT 62.022 66.667 10.54 0.00 0.00 4.09
231 232 2.739671 GTACCGGCGTGGGTTCAC 60.740 66.667 6.01 0.00 44.64 3.18
258 259 1.022982 GGTTGTTACCTAGCACCGGC 61.023 60.000 0.00 0.00 41.53 6.13
261 262 2.174363 AACGGTTGTTACCTAGCACC 57.826 50.000 0.00 0.00 42.66 5.01
273 274 0.593773 CGGCTTGGACAAAACGGTTG 60.594 55.000 0.00 0.00 0.00 3.77
274 275 1.033202 ACGGCTTGGACAAAACGGTT 61.033 50.000 11.08 0.00 0.00 4.44
275 276 1.441732 GACGGCTTGGACAAAACGGT 61.442 55.000 11.08 5.67 0.00 4.83
283 284 1.218316 CTAGGGTGACGGCTTGGAC 59.782 63.158 0.00 0.00 0.00 4.02
290 291 2.367202 ATGTGGGCTAGGGTGACGG 61.367 63.158 0.00 0.00 0.00 4.79
292 293 0.392998 CACATGTGGGCTAGGGTGAC 60.393 60.000 18.51 0.00 0.00 3.67
293 294 1.561769 CCACATGTGGGCTAGGGTGA 61.562 60.000 33.56 0.00 46.81 4.02
325 326 7.093858 CCGGTTAGTTAATTTAAACCCCATTCA 60.094 37.037 0.00 0.00 38.52 2.57
326 327 7.093814 ACCGGTTAGTTAATTTAAACCCCATTC 60.094 37.037 0.00 0.00 38.52 2.67
349 350 4.794248 TCGCAAAATATTCTGATGACCG 57.206 40.909 0.00 0.00 0.00 4.79
350 351 6.785191 TCTTTCGCAAAATATTCTGATGACC 58.215 36.000 0.00 0.00 0.00 4.02
351 352 8.847444 ATTCTTTCGCAAAATATTCTGATGAC 57.153 30.769 0.00 0.00 0.00 3.06
383 385 3.328382 TCGCTGGCACATACTACTTTT 57.672 42.857 0.00 0.00 38.20 2.27
386 388 4.665833 TTATTCGCTGGCACATACTACT 57.334 40.909 0.00 0.00 38.20 2.57
387 389 5.924475 ATTTATTCGCTGGCACATACTAC 57.076 39.130 0.00 0.00 38.20 2.73
388 390 8.439993 TTTAATTTATTCGCTGGCACATACTA 57.560 30.769 0.00 0.00 38.20 1.82
390 392 6.636850 CCTTTAATTTATTCGCTGGCACATAC 59.363 38.462 0.00 0.00 38.20 2.39
391 393 6.320164 ACCTTTAATTTATTCGCTGGCACATA 59.680 34.615 0.00 0.00 38.20 2.29
392 394 5.127031 ACCTTTAATTTATTCGCTGGCACAT 59.873 36.000 0.00 0.00 38.20 3.21
393 395 4.461081 ACCTTTAATTTATTCGCTGGCACA 59.539 37.500 0.00 0.00 0.00 4.57
394 396 4.993905 ACCTTTAATTTATTCGCTGGCAC 58.006 39.130 0.00 0.00 0.00 5.01
395 397 5.047660 ACAACCTTTAATTTATTCGCTGGCA 60.048 36.000 0.00 0.00 0.00 4.92
396 398 5.288472 CACAACCTTTAATTTATTCGCTGGC 59.712 40.000 0.00 0.00 0.00 4.85
397 399 5.804979 CCACAACCTTTAATTTATTCGCTGG 59.195 40.000 0.00 0.00 0.00 4.85
400 402 6.617879 ACTCCACAACCTTTAATTTATTCGC 58.382 36.000 0.00 0.00 0.00 4.70
434 436 8.140112 AGCTATCATAATTCAGGTTAGGGTAG 57.860 38.462 0.00 0.00 34.08 3.18
436 438 7.394144 AAGCTATCATAATTCAGGTTAGGGT 57.606 36.000 0.00 0.00 0.00 4.34
560 585 9.362151 ACCAAGATGAAACAAATTTAAGTAGGA 57.638 29.630 0.00 0.00 0.00 2.94
585 611 3.444388 ACAGATCTCTACCTTTGGACGAC 59.556 47.826 0.00 0.00 0.00 4.34
593 619 6.068010 CCAGACTGATACAGATCTCTACCTT 58.932 44.000 3.32 0.00 35.18 3.50
595 621 5.626142 TCCAGACTGATACAGATCTCTACC 58.374 45.833 3.32 0.00 35.18 3.18
611 637 1.700955 ACGGTTGTGTACTCCAGACT 58.299 50.000 0.00 0.00 0.00 3.24
613 639 1.536766 CGTACGGTTGTGTACTCCAGA 59.463 52.381 7.57 0.00 42.00 3.86
614 640 1.401931 CCGTACGGTTGTGTACTCCAG 60.402 57.143 26.39 0.00 42.00 3.86
615 641 0.597568 CCGTACGGTTGTGTACTCCA 59.402 55.000 26.39 0.00 42.00 3.86
616 642 0.881118 TCCGTACGGTTGTGTACTCC 59.119 55.000 32.16 0.00 42.00 3.85
689 717 9.270640 CAATTTGTTTTGGGATTAGTCAAATCA 57.729 29.630 0.00 0.00 45.05 2.57
704 732 6.418819 GTCTGATGTCCTGACAATTTGTTTTG 59.581 38.462 3.79 0.00 45.41 2.44
705 733 6.461509 GGTCTGATGTCCTGACAATTTGTTTT 60.462 38.462 3.79 0.00 45.41 2.43
706 734 5.010012 GGTCTGATGTCCTGACAATTTGTTT 59.990 40.000 3.79 0.00 45.41 2.83
707 735 4.520492 GGTCTGATGTCCTGACAATTTGTT 59.480 41.667 3.79 0.00 45.41 2.83
708 736 4.074970 GGTCTGATGTCCTGACAATTTGT 58.925 43.478 0.63 0.63 45.41 2.83
718 746 0.344790 AGGATGGGGTCTGATGTCCT 59.655 55.000 0.00 0.00 0.00 3.85
788 817 4.302455 AGTTCAGACGTTCAGTTCAGATG 58.698 43.478 0.00 0.00 0.00 2.90
856 889 1.780309 TGGGAGAGAGAGAGGAGGATC 59.220 57.143 0.00 0.00 0.00 3.36
860 893 1.284785 AGTGTGGGAGAGAGAGAGGAG 59.715 57.143 0.00 0.00 0.00 3.69
870 903 5.513094 GCCATATGCTTTATAGTGTGGGAGA 60.513 44.000 0.00 0.00 36.87 3.71
871 904 4.697352 GCCATATGCTTTATAGTGTGGGAG 59.303 45.833 0.00 0.00 36.87 4.30
872 905 4.103943 TGCCATATGCTTTATAGTGTGGGA 59.896 41.667 0.00 0.00 42.00 4.37
873 906 4.397420 TGCCATATGCTTTATAGTGTGGG 58.603 43.478 0.00 0.00 42.00 4.61
878 914 6.243900 AGCTTCATGCCATATGCTTTATAGT 58.756 36.000 0.00 0.00 44.23 2.12
879 915 6.598457 AGAGCTTCATGCCATATGCTTTATAG 59.402 38.462 0.00 0.00 44.23 1.31
882 918 4.722220 AGAGCTTCATGCCATATGCTTTA 58.278 39.130 0.00 0.00 44.23 1.85
891 927 1.077930 GCTGGAGAGCTTCATGCCA 60.078 57.895 0.00 0.00 42.52 4.92
898 934 0.327259 TGCTGATTGCTGGAGAGCTT 59.673 50.000 0.00 0.00 46.39 3.74
900 936 0.675837 TGTGCTGATTGCTGGAGAGC 60.676 55.000 0.00 0.00 46.44 4.09
915 951 1.439353 ATTGATGGCCGATCGTGTGC 61.439 55.000 15.09 10.32 33.17 4.57
921 984 2.023673 TGGTTTGATTGATGGCCGATC 58.976 47.619 0.00 3.10 36.42 3.69
926 989 3.928375 GTGTTGATGGTTTGATTGATGGC 59.072 43.478 0.00 0.00 0.00 4.40
970 1047 0.727793 GTTTATGTGCGTTGCGTGGG 60.728 55.000 0.00 0.00 0.00 4.61
1056 1141 2.203938 TTTCCTCTGTCGCCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
1201 1286 2.886124 GCCGTAGCCGAACTGCTC 60.886 66.667 0.00 0.00 41.68 4.26
1285 1370 1.372128 CGTGGCTTTGCTCTTTGCC 60.372 57.895 0.00 0.00 45.10 4.52
1288 1373 2.572290 AGTTACGTGGCTTTGCTCTTT 58.428 42.857 0.00 0.00 0.00 2.52
1303 1388 7.907214 AGACAAATCACAATCACCTAGTTAC 57.093 36.000 0.00 0.00 0.00 2.50
1354 1469 3.181493 GCCCAGAAAGCATATCACACTTG 60.181 47.826 0.00 0.00 0.00 3.16
1356 1471 2.648059 GCCCAGAAAGCATATCACACT 58.352 47.619 0.00 0.00 0.00 3.55
1357 1472 1.678101 GGCCCAGAAAGCATATCACAC 59.322 52.381 0.00 0.00 0.00 3.82
1358 1473 1.284491 TGGCCCAGAAAGCATATCACA 59.716 47.619 0.00 0.00 0.00 3.58
1394 1513 6.401153 GCACTACGAATTGTTCCTTGTCTAAG 60.401 42.308 0.00 0.00 0.00 2.18
1395 1514 5.407387 GCACTACGAATTGTTCCTTGTCTAA 59.593 40.000 0.00 0.00 0.00 2.10
1396 1515 4.927425 GCACTACGAATTGTTCCTTGTCTA 59.073 41.667 0.00 0.00 0.00 2.59
1397 1516 3.746492 GCACTACGAATTGTTCCTTGTCT 59.254 43.478 0.00 0.00 0.00 3.41
1398 1517 4.066710 GCACTACGAATTGTTCCTTGTC 57.933 45.455 0.00 0.00 0.00 3.18
1473 1759 0.928229 GAAGTGACAAAGTCGCACGT 59.072 50.000 12.56 0.00 44.42 4.49
1476 1762 4.319477 GCTAATTGAAGTGACAAAGTCGCA 60.319 41.667 12.56 0.00 44.42 5.10
1477 1763 4.083802 AGCTAATTGAAGTGACAAAGTCGC 60.084 41.667 2.65 2.65 42.60 5.19
1478 1764 5.597813 AGCTAATTGAAGTGACAAAGTCG 57.402 39.130 0.00 0.00 34.95 4.18
1479 1765 6.365247 TCGTAGCTAATTGAAGTGACAAAGTC 59.635 38.462 0.00 0.00 33.44 3.01
1480 1766 6.220930 TCGTAGCTAATTGAAGTGACAAAGT 58.779 36.000 0.00 0.00 33.44 2.66
1481 1767 6.706055 TCGTAGCTAATTGAAGTGACAAAG 57.294 37.500 0.00 0.00 33.44 2.77
1486 1772 6.020971 TCAGTTCGTAGCTAATTGAAGTGA 57.979 37.500 24.33 24.33 44.30 3.41
1497 1783 1.405821 AGCGCTATTCAGTTCGTAGCT 59.594 47.619 8.99 0.00 38.87 3.32
1548 1834 3.455990 AATGTTGATTTGCACTGCACA 57.544 38.095 2.26 0.00 38.71 4.57
1575 1861 7.427606 CACTAGAGAAAAATTGAAATAGCTGCG 59.572 37.037 0.00 0.00 0.00 5.18
1602 1888 0.951040 GAGAAGGAGCACCAACACGG 60.951 60.000 2.07 0.00 42.50 4.94
1609 1895 2.167487 CTGTAGGAAGAGAAGGAGCACC 59.833 54.545 0.00 0.00 0.00 5.01
1610 1896 2.418060 GCTGTAGGAAGAGAAGGAGCAC 60.418 54.545 0.00 0.00 0.00 4.40
1625 1919 3.796178 ACAAATGTTGTTTTGCGCTGTAG 59.204 39.130 9.73 0.00 42.22 2.74
1631 1925 4.838665 AAGTGACAAATGTTGTTTTGCG 57.161 36.364 0.00 0.00 45.52 4.85
1773 2067 6.071896 TGTGTTGTGTGATAGACCAAAACAAA 60.072 34.615 0.00 0.00 33.50 2.83
1824 2118 4.181578 ACAGTAGTGCGAATATTCCACAC 58.818 43.478 25.73 23.43 33.58 3.82
1845 2139 0.320508 GGACGGAGGGAGTGTGAAAC 60.321 60.000 0.00 0.00 37.35 2.78
1851 2146 1.558233 ACTTTAGGACGGAGGGAGTG 58.442 55.000 0.00 0.00 0.00 3.51
1861 2156 8.883954 ACTCAACTTTGTACTAACTTTAGGAC 57.116 34.615 4.60 4.60 43.49 3.85
1876 2171 7.114811 CGTCCCAAAATAAATGACTCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
1889 2184 4.778958 TCTACTCCTCCGTCCCAAAATAAA 59.221 41.667 0.00 0.00 0.00 1.40
1946 2250 7.500892 TGGCTAGTGTTTAGAGATTTGTTTGAA 59.499 33.333 0.00 0.00 0.00 2.69
1958 2262 2.290071 GGTTGCCTGGCTAGTGTTTAGA 60.290 50.000 21.03 0.00 0.00 2.10
1992 2296 3.546218 GCTTGGACTTTTCACGTTGAGAC 60.546 47.826 0.00 0.00 0.00 3.36
2038 2342 3.408634 CGTAAGACCCACAACCAAGAAT 58.591 45.455 0.00 0.00 43.02 2.40
2039 2343 2.485835 CCGTAAGACCCACAACCAAGAA 60.486 50.000 0.00 0.00 43.02 2.52
2040 2344 1.071071 CCGTAAGACCCACAACCAAGA 59.929 52.381 0.00 0.00 43.02 3.02
2173 2477 5.063880 AGCTTGTGAAACGATTTAGAAGGT 58.936 37.500 6.08 6.08 42.39 3.50
2185 2489 7.431084 TGAAACGATTTAGAAAGCTTGTGAAAC 59.569 33.333 0.00 0.00 37.35 2.78
2197 2501 4.819630 ACCAGCTTGTGAAACGATTTAGAA 59.180 37.500 0.00 0.00 42.39 2.10
2198 2502 4.385825 ACCAGCTTGTGAAACGATTTAGA 58.614 39.130 0.00 0.00 42.39 2.10
2199 2503 4.749245 ACCAGCTTGTGAAACGATTTAG 57.251 40.909 0.00 0.00 42.39 1.85
2200 2504 4.023536 GGAACCAGCTTGTGAAACGATTTA 60.024 41.667 0.00 0.00 42.39 1.40
2201 2505 3.243401 GGAACCAGCTTGTGAAACGATTT 60.243 43.478 0.00 0.00 42.39 2.17
2202 2506 2.293399 GGAACCAGCTTGTGAAACGATT 59.707 45.455 0.00 0.00 42.39 3.34
2203 2507 1.880027 GGAACCAGCTTGTGAAACGAT 59.120 47.619 0.00 0.00 42.39 3.73
2204 2508 1.134220 AGGAACCAGCTTGTGAAACGA 60.134 47.619 0.00 0.00 42.39 3.85
2205 2509 1.002468 CAGGAACCAGCTTGTGAAACG 60.002 52.381 0.00 0.00 42.39 3.60
2206 2510 1.269257 GCAGGAACCAGCTTGTGAAAC 60.269 52.381 1.04 0.00 37.35 2.78
2207 2511 1.032014 GCAGGAACCAGCTTGTGAAA 58.968 50.000 1.04 0.00 0.00 2.69
2208 2512 0.183492 AGCAGGAACCAGCTTGTGAA 59.817 50.000 4.94 0.00 36.85 3.18
2209 2513 0.183492 AAGCAGGAACCAGCTTGTGA 59.817 50.000 19.65 0.00 46.00 3.58
2210 2514 2.724520 AAGCAGGAACCAGCTTGTG 58.275 52.632 19.65 0.00 46.00 3.33
2214 2518 1.602888 CTGCAAGCAGGAACCAGCT 60.603 57.895 14.10 4.94 42.00 4.24
2215 2519 2.960170 CTGCAAGCAGGAACCAGC 59.040 61.111 14.10 0.00 40.17 4.85
2224 2528 1.174712 GGCCTTTCTCACTGCAAGCA 61.175 55.000 0.00 0.00 37.60 3.91
2225 2529 1.583477 GGCCTTTCTCACTGCAAGC 59.417 57.895 0.00 0.00 37.60 4.01
2226 2530 0.538057 TGGGCCTTTCTCACTGCAAG 60.538 55.000 4.53 0.00 42.29 4.01
2227 2531 0.106268 TTGGGCCTTTCTCACTGCAA 60.106 50.000 4.53 0.00 0.00 4.08
2228 2532 0.112995 ATTGGGCCTTTCTCACTGCA 59.887 50.000 4.53 0.00 0.00 4.41
2229 2533 1.067354 CAATTGGGCCTTTCTCACTGC 60.067 52.381 4.53 0.00 0.00 4.40
2230 2534 1.547372 CCAATTGGGCCTTTCTCACTG 59.453 52.381 17.36 0.00 0.00 3.66
2231 2535 1.928868 CCAATTGGGCCTTTCTCACT 58.071 50.000 17.36 0.00 0.00 3.41
2241 2545 5.280940 TGAACATTTTCTTGCCAATTGGGC 61.281 41.667 25.73 17.55 46.91 5.36
2242 2546 4.387598 TGAACATTTTCTTGCCAATTGGG 58.612 39.130 25.73 9.65 34.33 4.12
2243 2547 6.374565 TTTGAACATTTTCTTGCCAATTGG 57.625 33.333 20.81 20.81 33.63 3.16
2244 2548 7.380065 CCAATTTGAACATTTTCTTGCCAATTG 59.620 33.333 0.00 0.00 32.36 2.32
2245 2549 7.427214 CCAATTTGAACATTTTCTTGCCAATT 58.573 30.769 0.00 0.00 32.36 2.32
2246 2550 6.515365 GCCAATTTGAACATTTTCTTGCCAAT 60.515 34.615 0.00 0.00 32.36 3.16
2247 2551 5.221009 GCCAATTTGAACATTTTCTTGCCAA 60.221 36.000 0.00 0.00 32.36 4.52
2248 2552 4.275443 GCCAATTTGAACATTTTCTTGCCA 59.725 37.500 0.00 0.00 32.36 4.92
2249 2553 4.320421 GGCCAATTTGAACATTTTCTTGCC 60.320 41.667 0.00 0.00 32.36 4.52
2250 2554 4.320421 GGGCCAATTTGAACATTTTCTTGC 60.320 41.667 4.39 0.00 32.36 4.01
2251 2555 4.820716 TGGGCCAATTTGAACATTTTCTTG 59.179 37.500 2.13 0.00 32.36 3.02
2252 2556 5.046288 TGGGCCAATTTGAACATTTTCTT 57.954 34.783 2.13 0.00 32.36 2.52
2253 2557 4.102996 ACTGGGCCAATTTGAACATTTTCT 59.897 37.500 8.04 0.00 32.36 2.52
2254 2558 4.388485 ACTGGGCCAATTTGAACATTTTC 58.612 39.130 8.04 0.00 0.00 2.29
2255 2559 4.141528 TGACTGGGCCAATTTGAACATTTT 60.142 37.500 8.04 0.00 0.00 1.82
2256 2560 3.390639 TGACTGGGCCAATTTGAACATTT 59.609 39.130 8.04 0.00 0.00 2.32
2257 2561 2.971330 TGACTGGGCCAATTTGAACATT 59.029 40.909 8.04 0.00 0.00 2.71
2258 2562 2.564062 CTGACTGGGCCAATTTGAACAT 59.436 45.455 8.04 0.00 0.00 2.71
2259 2563 1.962807 CTGACTGGGCCAATTTGAACA 59.037 47.619 8.04 1.81 0.00 3.18
2260 2564 2.229784 CTCTGACTGGGCCAATTTGAAC 59.770 50.000 8.04 0.00 0.00 3.18
2261 2565 2.517959 CTCTGACTGGGCCAATTTGAA 58.482 47.619 8.04 0.00 0.00 2.69
2262 2566 1.887956 GCTCTGACTGGGCCAATTTGA 60.888 52.381 8.04 3.22 0.00 2.69
2263 2567 0.529378 GCTCTGACTGGGCCAATTTG 59.471 55.000 8.04 0.00 0.00 2.32
2264 2568 0.112995 TGCTCTGACTGGGCCAATTT 59.887 50.000 8.04 0.00 0.00 1.82
2265 2569 0.610232 GTGCTCTGACTGGGCCAATT 60.610 55.000 8.04 0.00 0.00 2.32
2266 2570 1.001641 GTGCTCTGACTGGGCCAAT 60.002 57.895 8.04 0.00 0.00 3.16
2267 2571 2.431683 GTGCTCTGACTGGGCCAA 59.568 61.111 8.04 0.00 0.00 4.52
2268 2572 4.007644 CGTGCTCTGACTGGGCCA 62.008 66.667 5.85 5.85 0.00 5.36
2269 2573 3.537206 AACGTGCTCTGACTGGGCC 62.537 63.158 0.00 0.00 0.00 5.80
2270 2574 2.029844 GAACGTGCTCTGACTGGGC 61.030 63.158 0.00 0.00 0.00 5.36
2271 2575 1.734477 CGAACGTGCTCTGACTGGG 60.734 63.158 0.00 0.00 0.00 4.45
2272 2576 0.597637 AACGAACGTGCTCTGACTGG 60.598 55.000 0.00 0.00 0.00 4.00
2273 2577 0.778815 GAACGAACGTGCTCTGACTG 59.221 55.000 0.00 0.00 0.00 3.51
2274 2578 0.318784 GGAACGAACGTGCTCTGACT 60.319 55.000 5.32 0.00 0.00 3.41
2275 2579 0.596600 TGGAACGAACGTGCTCTGAC 60.597 55.000 5.32 0.00 0.00 3.51
2276 2580 0.318699 CTGGAACGAACGTGCTCTGA 60.319 55.000 5.32 0.00 0.00 3.27
2277 2581 1.891060 GCTGGAACGAACGTGCTCTG 61.891 60.000 5.32 1.97 0.00 3.35
2278 2582 1.664965 GCTGGAACGAACGTGCTCT 60.665 57.895 5.32 0.00 0.00 4.09
2279 2583 2.853914 GCTGGAACGAACGTGCTC 59.146 61.111 5.32 0.00 0.00 4.26
2280 2584 3.036084 CGCTGGAACGAACGTGCT 61.036 61.111 5.32 0.00 34.06 4.40
2281 2585 4.072088 CCGCTGGAACGAACGTGC 62.072 66.667 0.00 0.00 34.06 5.34
2282 2586 0.734942 ATACCGCTGGAACGAACGTG 60.735 55.000 0.00 0.00 34.06 4.49
2283 2587 0.810648 TATACCGCTGGAACGAACGT 59.189 50.000 1.50 0.00 34.06 3.99
2284 2588 2.129823 ATATACCGCTGGAACGAACG 57.870 50.000 1.50 0.00 34.06 3.95
2285 2589 2.798847 GGAATATACCGCTGGAACGAAC 59.201 50.000 1.50 0.00 34.06 3.95
2286 2590 2.544277 CGGAATATACCGCTGGAACGAA 60.544 50.000 0.00 0.00 46.20 3.85
2287 2591 1.001048 CGGAATATACCGCTGGAACGA 60.001 52.381 0.00 0.00 46.20 3.85
2288 2592 1.415374 CGGAATATACCGCTGGAACG 58.585 55.000 0.00 0.00 46.20 3.95


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

AutoCloner maintained by Alex Coulton.