Multiple sequence alignment - TraesCS6D01G300800

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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 TraesCS6D01G300800 chr6D 100.000 2291 0 0 1 2291 410174487 410176777 0.000000e+00 4231
1 TraesCS6D01G300800 chr6D 98.592 142 2 0 2150 2291 366688339 366688198 3.780000e-63 252
2 TraesCS6D01G300800 chr6D 84.762 105 16 0 2046 2150 410220243 410220347 3.110000e-19 106
3 TraesCS6D01G300800 chr6B 85.927 2146 158 50 49 2150 617127500 617129545 0.000000e+00 2158
4 TraesCS6D01G300800 chr6A 89.531 1385 83 29 499 1835 555672905 555674275 0.000000e+00 1698
5 TraesCS6D01G300800 chr6A 86.102 295 27 5 1853 2147 555674363 555674643 2.860000e-79 305
6 TraesCS6D01G300800 chr6A 80.043 466 44 21 6 469 555672426 555672844 1.330000e-77 300
7 TraesCS6D01G300800 chr1D 98.592 142 1 1 2151 2291 281409246 281409105 1.360000e-62 250
8 TraesCS6D01G300800 chr4D 98.561 139 2 0 2150 2288 208379973 208380111 1.760000e-61 246
9 TraesCS6D01G300800 chr4D 95.745 141 6 0 2151 2291 420571831 420571691 6.370000e-56 228
10 TraesCS6D01G300800 chr5D 97.163 141 4 0 2151 2291 54715052 54714912 2.940000e-59 239
11 TraesCS6D01G300800 chr7D 88.205 195 22 1 1087 1281 563707857 563708050 4.920000e-57 231
12 TraesCS6D01G300800 chr1B 95.205 146 7 0 2146 2291 583696917 583696772 4.920000e-57 231
13 TraesCS6D01G300800 chr4A 95.775 142 4 1 2152 2291 735534879 735534738 6.370000e-56 228
14 TraesCS6D01G300800 chr3A 96.992 133 4 0 2153 2285 379736906 379737038 8.240000e-55 224
15 TraesCS6D01G300800 chr3A 94.928 138 6 1 2151 2288 269219847 269219983 4.960000e-52 215
16 TraesCS6D01G300800 chr7B 73.904 502 58 31 1121 1617 614229252 614228819 1.430000e-27 134


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 TraesCS6D01G300800 chr6D 410174487 410176777 2290 False 4231.000000 4231 100.000000 1 2291 1 chr6D.!!$F1 2290
1 TraesCS6D01G300800 chr6B 617127500 617129545 2045 False 2158.000000 2158 85.927000 49 2150 1 chr6B.!!$F1 2101
2 TraesCS6D01G300800 chr6A 555672426 555674643 2217 False 767.666667 1698 85.225333 6 2147 3 chr6A.!!$F1 2141

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
603 689 0.038526 AGCAACGCTACAACGCTACT 60.039 50.0 0.0 0.0 36.99 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1804 0.028505 GAGCTGTTGGTGCATATGCG 59.971 55.0 22.21 7.6 45.83 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.684788 CCAACTAAACTTGACATCCTCGG 59.315 47.826 0.00 0.00 0.00 4.63
29 30 4.315803 CAACTAAACTTGACATCCTCGGT 58.684 43.478 0.00 0.00 0.00 4.69
39 40 1.156736 CATCCTCGGTGAACACAACC 58.843 55.000 7.25 0.00 0.00 3.77
45 46 2.993899 CTCGGTGAACACAACCTATCAC 59.006 50.000 7.25 0.00 41.06 3.06
47 48 2.608506 CGGTGAACACAACCTATCACGA 60.609 50.000 7.25 0.00 42.35 4.35
99 100 3.857665 TCTGACGTTCGCTGAATATTCAC 59.142 43.478 14.23 10.25 32.90 3.18
113 114 2.088950 ATTCACGTCCTTACAACGGG 57.911 50.000 0.52 0.00 44.75 5.28
115 116 1.259609 TCACGTCCTTACAACGGGAT 58.740 50.000 0.00 0.00 46.79 3.85
116 117 1.619827 TCACGTCCTTACAACGGGATT 59.380 47.619 0.00 0.00 46.79 3.01
117 118 2.037511 TCACGTCCTTACAACGGGATTT 59.962 45.455 0.00 0.00 46.79 2.17
118 119 2.809696 CACGTCCTTACAACGGGATTTT 59.190 45.455 0.52 0.00 46.27 1.82
119 120 3.069289 ACGTCCTTACAACGGGATTTTC 58.931 45.455 0.52 0.00 44.21 2.29
120 121 3.244318 ACGTCCTTACAACGGGATTTTCT 60.244 43.478 0.52 0.00 44.21 2.52
121 122 3.749609 CGTCCTTACAACGGGATTTTCTT 59.250 43.478 0.00 0.00 36.51 2.52
123 124 5.278120 CGTCCTTACAACGGGATTTTCTTTT 60.278 40.000 0.00 0.00 36.51 2.27
124 125 5.918576 GTCCTTACAACGGGATTTTCTTTTG 59.081 40.000 0.00 0.00 33.89 2.44
207 222 2.964978 GCTGGTTTCGCAATGGCT 59.035 55.556 0.00 0.00 38.10 4.75
227 242 1.729838 GACAGCCGACGTCACAGTC 60.730 63.158 17.16 14.70 37.76 3.51
275 294 2.489938 ACACATGGCGGTATCAACTT 57.510 45.000 0.00 0.00 0.00 2.66
277 296 1.670811 CACATGGCGGTATCAACTTCC 59.329 52.381 0.00 0.00 0.00 3.46
278 297 0.937304 CATGGCGGTATCAACTTCCG 59.063 55.000 0.00 0.00 45.94 4.30
279 298 0.828022 ATGGCGGTATCAACTTCCGA 59.172 50.000 7.01 0.00 46.05 4.55
280 299 0.828022 TGGCGGTATCAACTTCCGAT 59.172 50.000 7.01 0.00 46.05 4.18
282 301 1.129326 GCGGTATCAACTTCCGATCG 58.871 55.000 8.51 8.51 46.05 3.69
294 313 3.118738 ACTTCCGATCGGCTGAAACTATT 60.119 43.478 29.62 3.65 34.68 1.73
338 357 3.492102 ATGGCTAAGCATTGACCGTAT 57.508 42.857 0.00 0.00 0.00 3.06
339 358 3.275617 TGGCTAAGCATTGACCGTATT 57.724 42.857 0.00 0.00 0.00 1.89
366 385 4.040445 CTTCTCGGAAGGAAGCTTAGAG 57.960 50.000 0.00 2.32 33.74 2.43
367 386 1.751924 TCTCGGAAGGAAGCTTAGAGC 59.248 52.381 0.00 0.00 42.84 4.09
368 387 1.478510 CTCGGAAGGAAGCTTAGAGCA 59.521 52.381 0.00 0.00 45.56 4.26
369 388 1.899814 TCGGAAGGAAGCTTAGAGCAA 59.100 47.619 0.00 0.00 45.56 3.91
370 389 2.501723 TCGGAAGGAAGCTTAGAGCAAT 59.498 45.455 0.00 0.00 45.56 3.56
371 390 3.704566 TCGGAAGGAAGCTTAGAGCAATA 59.295 43.478 0.00 0.00 45.56 1.90
372 391 4.345257 TCGGAAGGAAGCTTAGAGCAATAT 59.655 41.667 0.00 0.00 45.56 1.28
373 392 5.059833 CGGAAGGAAGCTTAGAGCAATATT 58.940 41.667 0.00 0.00 45.56 1.28
374 393 6.041637 TCGGAAGGAAGCTTAGAGCAATATTA 59.958 38.462 0.00 0.00 45.56 0.98
375 394 6.706270 CGGAAGGAAGCTTAGAGCAATATTAA 59.294 38.462 0.00 0.00 45.56 1.40
376 395 7.226720 CGGAAGGAAGCTTAGAGCAATATTAAA 59.773 37.037 0.00 0.00 45.56 1.52
377 396 8.903820 GGAAGGAAGCTTAGAGCAATATTAAAA 58.096 33.333 0.00 0.00 45.56 1.52
427 447 7.833285 AGAAGTCCCATCTTATCTTCTAGAC 57.167 40.000 0.00 0.00 41.62 2.59
428 448 7.358263 AGAAGTCCCATCTTATCTTCTAGACA 58.642 38.462 0.00 0.00 41.62 3.41
429 449 7.841729 AGAAGTCCCATCTTATCTTCTAGACAA 59.158 37.037 0.00 0.00 41.62 3.18
430 450 7.595819 AGTCCCATCTTATCTTCTAGACAAG 57.404 40.000 0.00 0.00 30.24 3.16
431 451 7.358263 AGTCCCATCTTATCTTCTAGACAAGA 58.642 38.462 0.40 0.40 41.44 3.02
432 452 8.010105 AGTCCCATCTTATCTTCTAGACAAGAT 58.990 37.037 10.94 10.94 46.24 2.40
435 455 9.083422 CCCATCTTATCTTCTAGACAAGATACA 57.917 37.037 11.97 4.89 44.22 2.29
450 470 6.282167 ACAAGATACAGAGAATGCTGATCAG 58.718 40.000 18.84 18.84 39.20 2.90
483 503 7.329471 CACGACTGACAATATGATATAACCCAG 59.671 40.741 0.00 0.00 0.00 4.45
503 523 4.308526 CCTGGCTGGTGTGTCATC 57.691 61.111 1.62 0.00 0.00 2.92
522 588 1.154413 GCCGCATGAGTTCAACACG 60.154 57.895 0.00 0.00 0.00 4.49
525 591 1.061131 CCGCATGAGTTCAACACGATC 59.939 52.381 0.00 0.00 0.00 3.69
545 611 1.405821 CGCTCGGTGGACTAATCTCTT 59.594 52.381 0.00 0.00 0.00 2.85
546 612 2.796383 CGCTCGGTGGACTAATCTCTTG 60.796 54.545 0.00 0.00 0.00 3.02
552 618 4.098654 CGGTGGACTAATCTCTTGTGATCT 59.901 45.833 0.00 0.00 0.00 2.75
553 619 5.394663 CGGTGGACTAATCTCTTGTGATCTT 60.395 44.000 0.00 0.00 0.00 2.40
557 623 8.233190 GTGGACTAATCTCTTGTGATCTTTTTG 58.767 37.037 0.00 0.00 0.00 2.44
558 624 7.094634 TGGACTAATCTCTTGTGATCTTTTTGC 60.095 37.037 0.00 0.00 0.00 3.68
559 625 7.120432 GGACTAATCTCTTGTGATCTTTTTGCT 59.880 37.037 0.00 0.00 0.00 3.91
561 627 8.295288 ACTAATCTCTTGTGATCTTTTTGCTTG 58.705 33.333 0.00 0.00 0.00 4.01
562 628 5.443185 TCTCTTGTGATCTTTTTGCTTGG 57.557 39.130 0.00 0.00 0.00 3.61
563 629 4.889409 TCTCTTGTGATCTTTTTGCTTGGT 59.111 37.500 0.00 0.00 0.00 3.67
564 630 4.935702 TCTTGTGATCTTTTTGCTTGGTG 58.064 39.130 0.00 0.00 0.00 4.17
566 632 3.295093 TGTGATCTTTTTGCTTGGTGGA 58.705 40.909 0.00 0.00 0.00 4.02
567 633 3.068024 TGTGATCTTTTTGCTTGGTGGAC 59.932 43.478 0.00 0.00 0.00 4.02
568 634 2.627699 TGATCTTTTTGCTTGGTGGACC 59.372 45.455 0.00 0.00 0.00 4.46
569 635 2.151502 TCTTTTTGCTTGGTGGACCA 57.848 45.000 0.00 0.00 45.94 4.02
583 669 3.039202 GACCAAGCAATCGGGCACG 62.039 63.158 0.00 0.00 42.74 5.34
598 684 1.127817 CACGAGCAACGCTACAACG 59.872 57.895 0.00 0.00 46.94 4.10
599 685 2.093983 CGAGCAACGCTACAACGC 59.906 61.111 0.00 0.00 39.88 4.84
600 686 2.372690 CGAGCAACGCTACAACGCT 61.373 57.895 0.00 0.00 39.88 5.07
601 687 1.068832 CGAGCAACGCTACAACGCTA 61.069 55.000 0.00 0.00 39.88 4.26
602 688 0.365859 GAGCAACGCTACAACGCTAC 59.634 55.000 0.00 0.00 39.88 3.58
603 689 0.038526 AGCAACGCTACAACGCTACT 60.039 50.000 0.00 0.00 36.99 2.57
604 690 1.200716 AGCAACGCTACAACGCTACTA 59.799 47.619 0.00 0.00 36.99 1.82
605 691 1.319669 GCAACGCTACAACGCTACTAC 59.680 52.381 0.00 0.00 36.19 2.73
771 862 1.332195 TCTGATGATAGACTGGCCGG 58.668 55.000 11.02 11.02 0.00 6.13
774 865 0.394565 GATGATAGACTGGCCGGCTT 59.605 55.000 28.56 11.32 0.00 4.35
797 888 3.938963 TCGAAAAAGCAGCCGATATCTTT 59.061 39.130 0.34 0.00 0.00 2.52
798 889 5.113383 TCGAAAAAGCAGCCGATATCTTTA 58.887 37.500 0.34 0.00 0.00 1.85
852 943 2.943653 CCGAAACGTGAGGCAACC 59.056 61.111 0.00 0.00 37.17 3.77
954 1045 1.203313 GAGCAAACACGTACGCACC 59.797 57.895 16.72 0.00 0.00 5.01
955 1046 2.127906 GCAAACACGTACGCACCG 60.128 61.111 16.72 4.04 0.00 4.94
960 1051 3.467119 CACGTACGCACCGTCTGC 61.467 66.667 16.72 0.00 41.54 4.26
1342 1461 0.823769 TCTCCGATCGGTCCATCAGG 60.824 60.000 32.15 13.46 36.47 3.86
1343 1462 2.029666 CCGATCGGTCCATCAGGC 59.970 66.667 26.35 0.00 33.74 4.85
1345 1464 1.368950 CGATCGGTCCATCAGGCAT 59.631 57.895 7.38 0.00 33.74 4.40
1346 1465 0.668706 CGATCGGTCCATCAGGCATC 60.669 60.000 7.38 0.00 33.74 3.91
1347 1466 0.394192 GATCGGTCCATCAGGCATCA 59.606 55.000 0.00 0.00 33.74 3.07
1348 1467 0.395686 ATCGGTCCATCAGGCATCAG 59.604 55.000 0.00 0.00 33.74 2.90
1349 1468 0.687427 TCGGTCCATCAGGCATCAGA 60.687 55.000 0.00 0.00 33.74 3.27
1395 1514 1.521457 GGATGCGATTGCTCGTGGA 60.521 57.895 6.47 0.00 46.71 4.02
1396 1515 0.882042 GGATGCGATTGCTCGTGGAT 60.882 55.000 6.47 0.00 46.71 3.41
1397 1516 0.510359 GATGCGATTGCTCGTGGATC 59.490 55.000 6.47 0.00 46.71 3.36
1398 1517 1.217585 ATGCGATTGCTCGTGGATCG 61.218 55.000 6.47 0.00 46.71 3.69
1399 1518 1.878522 GCGATTGCTCGTGGATCGT 60.879 57.895 0.00 0.00 46.71 3.73
1400 1519 1.920051 CGATTGCTCGTGGATCGTG 59.080 57.895 0.00 0.00 40.07 4.35
1401 1520 1.482621 CGATTGCTCGTGGATCGTGG 61.483 60.000 0.00 0.00 40.07 4.94
1492 1616 5.357032 TCTGGACCTGTTTCTTTTTGTTCTC 59.643 40.000 0.00 0.00 0.00 2.87
1509 1633 4.141620 TGTTCTCTCCTGCTTCAGAAGTTT 60.142 41.667 11.94 0.00 32.44 2.66
1510 1634 4.264460 TCTCTCCTGCTTCAGAAGTTTC 57.736 45.455 11.94 0.00 32.44 2.78
1511 1635 3.643320 TCTCTCCTGCTTCAGAAGTTTCA 59.357 43.478 11.94 0.82 32.44 2.69
1512 1636 3.995705 CTCTCCTGCTTCAGAAGTTTCAG 59.004 47.826 11.94 10.01 32.44 3.02
1514 1638 2.157738 CCTGCTTCAGAAGTTTCAGGG 58.842 52.381 20.23 8.31 37.89 4.45
1520 1644 4.021016 GCTTCAGAAGTTTCAGGGTCTCTA 60.021 45.833 11.94 0.00 0.00 2.43
1614 1738 1.481363 TGGAAACGTGGTCTGTGTGTA 59.519 47.619 0.00 0.00 0.00 2.90
1643 1767 1.069513 TGTTTGGAGACGTTGTCCGAT 59.930 47.619 11.98 0.00 40.70 4.18
1677 1804 0.681733 TGTCTGCTGGACTTCCTGAC 59.318 55.000 6.35 5.63 44.74 3.51
1683 1810 1.202580 GCTGGACTTCCTGACGCATAT 60.203 52.381 6.35 0.00 37.15 1.78
1762 1894 9.701355 CAACTTGATAACATGGTTTTTGTTTTC 57.299 29.630 0.00 0.00 38.26 2.29
1784 1916 3.325135 CCTAAGGGAGCGACCTGATTATT 59.675 47.826 2.87 0.00 40.87 1.40
1785 1917 3.933861 AAGGGAGCGACCTGATTATTT 57.066 42.857 2.87 0.00 40.87 1.40
1790 1922 4.201920 GGGAGCGACCTGATTATTTTTGAC 60.202 45.833 0.00 0.00 38.98 3.18
1795 1927 5.106317 GCGACCTGATTATTTTTGACCAAGA 60.106 40.000 0.00 0.00 0.00 3.02
1806 1938 2.178912 TGACCAAGATCAACCGAACC 57.821 50.000 0.00 0.00 0.00 3.62
1809 1941 2.484264 GACCAAGATCAACCGAACCAAG 59.516 50.000 0.00 0.00 0.00 3.61
1813 1945 4.700213 CCAAGATCAACCGAACCAAGTATT 59.300 41.667 0.00 0.00 0.00 1.89
1819 1951 6.642707 TCAACCGAACCAAGTATTTCAAAT 57.357 33.333 0.00 0.00 0.00 2.32
1823 1956 5.470777 ACCGAACCAAGTATTTCAAATCGAA 59.529 36.000 0.00 0.00 0.00 3.71
1824 1957 6.150474 ACCGAACCAAGTATTTCAAATCGAAT 59.850 34.615 0.00 0.00 32.32 3.34
1838 1971 7.270757 TCAAATCGAATGAACTGAAAAAGGA 57.729 32.000 2.10 0.00 0.00 3.36
1839 1972 7.138736 TCAAATCGAATGAACTGAAAAAGGAC 58.861 34.615 2.10 0.00 0.00 3.85
1840 1973 6.633500 AATCGAATGAACTGAAAAAGGACA 57.367 33.333 0.00 0.00 0.00 4.02
1841 1974 6.633500 ATCGAATGAACTGAAAAAGGACAA 57.367 33.333 0.00 0.00 0.00 3.18
1842 1975 6.060028 TCGAATGAACTGAAAAAGGACAAG 57.940 37.500 0.00 0.00 0.00 3.16
1843 1976 5.820423 TCGAATGAACTGAAAAAGGACAAGA 59.180 36.000 0.00 0.00 0.00 3.02
1844 1977 6.317642 TCGAATGAACTGAAAAAGGACAAGAA 59.682 34.615 0.00 0.00 0.00 2.52
1845 1978 6.414987 CGAATGAACTGAAAAAGGACAAGAAC 59.585 38.462 0.00 0.00 0.00 3.01
1848 1981 6.386654 TGAACTGAAAAAGGACAAGAACAAC 58.613 36.000 0.00 0.00 0.00 3.32
1849 1982 4.981794 ACTGAAAAAGGACAAGAACAACG 58.018 39.130 0.00 0.00 0.00 4.10
1850 1983 4.698304 ACTGAAAAAGGACAAGAACAACGA 59.302 37.500 0.00 0.00 0.00 3.85
1857 2060 5.272283 AGGACAAGAACAACGAAAGAGTA 57.728 39.130 0.00 0.00 0.00 2.59
1859 2062 4.210746 GGACAAGAACAACGAAAGAGTACC 59.789 45.833 0.00 0.00 0.00 3.34
1870 2073 4.618489 ACGAAAGAGTACCGATAAAACACG 59.382 41.667 0.00 0.00 0.00 4.49
1877 2080 7.542025 AGAGTACCGATAAAACACGAAGTTAT 58.458 34.615 0.00 0.00 41.61 1.89
1881 2084 7.385668 ACCGATAAAACACGAAGTTATATCG 57.614 36.000 0.00 0.00 41.61 2.92
1887 2090 7.878477 AAAACACGAAGTTATATCGAAGTCA 57.122 32.000 2.65 0.00 41.61 3.41
1916 2120 3.190953 AGTGTCAACTCTAGCTCCGTTAC 59.809 47.826 0.00 0.00 26.77 2.50
1975 2179 6.261826 ACCTATGCACTATGCTCAAAGATTTC 59.738 38.462 2.02 0.00 45.31 2.17
1979 2183 6.384224 TGCACTATGCTCAAAGATTTCAAAG 58.616 36.000 2.02 0.00 45.31 2.77
1980 2184 6.207221 TGCACTATGCTCAAAGATTTCAAAGA 59.793 34.615 2.02 0.00 45.31 2.52
1981 2185 6.746364 GCACTATGCTCAAAGATTTCAAAGAG 59.254 38.462 0.00 0.00 40.96 2.85
1982 2186 7.249147 CACTATGCTCAAAGATTTCAAAGAGG 58.751 38.462 0.00 0.00 0.00 3.69
1983 2187 5.656213 ATGCTCAAAGATTTCAAAGAGGG 57.344 39.130 0.00 0.00 0.00 4.30
1984 2188 4.728772 TGCTCAAAGATTTCAAAGAGGGA 58.271 39.130 0.00 0.00 0.00 4.20
1985 2189 5.327732 TGCTCAAAGATTTCAAAGAGGGAT 58.672 37.500 0.00 0.00 0.00 3.85
1986 2190 6.484288 TGCTCAAAGATTTCAAAGAGGGATA 58.516 36.000 0.00 0.00 0.00 2.59
1987 2191 7.121382 TGCTCAAAGATTTCAAAGAGGGATAT 58.879 34.615 0.00 0.00 0.00 1.63
2056 2260 3.706373 CAGGACAGGACCCACCCG 61.706 72.222 0.00 0.00 40.05 5.28
2060 2264 1.608627 GACAGGACCCACCCGTAGT 60.609 63.158 0.00 0.00 40.05 2.73
2075 2279 3.949754 CCCGTAGTAAGGTCACATGTCTA 59.050 47.826 0.00 0.00 0.00 2.59
2076 2280 4.036498 CCCGTAGTAAGGTCACATGTCTAG 59.964 50.000 0.00 0.00 0.00 2.43
2077 2281 4.639310 CCGTAGTAAGGTCACATGTCTAGT 59.361 45.833 0.00 0.00 0.00 2.57
2094 2298 9.885934 CATGTCTAGTGTCTACTATGTTATCAC 57.114 37.037 0.00 0.00 38.65 3.06
2110 2314 7.581213 TGTTATCACATGGTTGAGAAAAACT 57.419 32.000 0.00 0.00 28.82 2.66
2134 2338 5.665916 TCATGAGCATGAAAGAGTGTAGA 57.334 39.130 10.53 0.00 44.14 2.59
2150 2354 2.361119 TGTAGACGTGAGAACAACTGCT 59.639 45.455 0.00 0.00 0.00 4.24
2151 2355 2.604046 AGACGTGAGAACAACTGCTT 57.396 45.000 0.00 0.00 0.00 3.91
2152 2356 2.906354 AGACGTGAGAACAACTGCTTT 58.094 42.857 0.00 0.00 0.00 3.51
2153 2357 3.270877 AGACGTGAGAACAACTGCTTTT 58.729 40.909 0.00 0.00 0.00 2.27
2154 2358 3.689649 AGACGTGAGAACAACTGCTTTTT 59.310 39.130 0.00 0.00 0.00 1.94
2183 2387 2.935651 GCAAGCTGCGTATCTTTGC 58.064 52.632 6.33 6.33 31.71 3.68
2184 2388 0.168788 GCAAGCTGCGTATCTTTGCA 59.831 50.000 14.64 0.00 39.13 4.08
2185 2389 1.202222 GCAAGCTGCGTATCTTTGCAT 60.202 47.619 14.64 0.00 40.89 3.96
2186 2390 2.733227 GCAAGCTGCGTATCTTTGCATT 60.733 45.455 14.64 0.00 40.89 3.56
2187 2391 2.838386 AGCTGCGTATCTTTGCATTG 57.162 45.000 0.00 0.00 40.89 2.82
2188 2392 2.358957 AGCTGCGTATCTTTGCATTGA 58.641 42.857 0.00 0.00 40.89 2.57
2189 2393 2.947652 AGCTGCGTATCTTTGCATTGAT 59.052 40.909 7.07 7.07 40.89 2.57
2190 2394 4.129380 AGCTGCGTATCTTTGCATTGATA 58.871 39.130 5.41 5.41 40.89 2.15
2191 2395 4.212847 AGCTGCGTATCTTTGCATTGATAG 59.787 41.667 8.77 2.51 40.89 2.08
2192 2396 4.212004 GCTGCGTATCTTTGCATTGATAGA 59.788 41.667 8.77 0.00 40.89 1.98
2193 2397 5.277490 GCTGCGTATCTTTGCATTGATAGAA 60.277 40.000 8.77 0.70 40.89 2.10
2194 2398 6.291067 TGCGTATCTTTGCATTGATAGAAG 57.709 37.500 8.77 0.00 35.90 2.85
2195 2399 6.048509 TGCGTATCTTTGCATTGATAGAAGA 58.951 36.000 8.77 3.80 35.90 2.87
2196 2400 6.538381 TGCGTATCTTTGCATTGATAGAAGAA 59.462 34.615 8.77 0.00 35.90 2.52
2197 2401 7.068341 GCGTATCTTTGCATTGATAGAAGAAG 58.932 38.462 8.77 0.00 30.96 2.85
2198 2402 7.042456 GCGTATCTTTGCATTGATAGAAGAAGA 60.042 37.037 8.77 1.88 30.96 2.87
2199 2403 8.486383 CGTATCTTTGCATTGATAGAAGAAGAG 58.514 37.037 8.77 0.00 30.96 2.85
2200 2404 9.323985 GTATCTTTGCATTGATAGAAGAAGAGT 57.676 33.333 8.77 0.00 30.96 3.24
2201 2405 8.804912 ATCTTTGCATTGATAGAAGAAGAGTT 57.195 30.769 0.00 0.00 30.96 3.01
2202 2406 8.627208 TCTTTGCATTGATAGAAGAAGAGTTT 57.373 30.769 0.00 0.00 0.00 2.66
2203 2407 9.725019 TCTTTGCATTGATAGAAGAAGAGTTTA 57.275 29.630 0.00 0.00 0.00 2.01
2204 2408 9.766277 CTTTGCATTGATAGAAGAAGAGTTTAC 57.234 33.333 0.00 0.00 0.00 2.01
2205 2409 8.846943 TTGCATTGATAGAAGAAGAGTTTACA 57.153 30.769 0.00 0.00 0.00 2.41
2206 2410 8.484641 TGCATTGATAGAAGAAGAGTTTACAG 57.515 34.615 0.00 0.00 0.00 2.74
2207 2411 7.065085 TGCATTGATAGAAGAAGAGTTTACAGC 59.935 37.037 0.00 0.00 0.00 4.40
2208 2412 7.065085 GCATTGATAGAAGAAGAGTTTACAGCA 59.935 37.037 0.00 0.00 0.00 4.41
2209 2413 8.939929 CATTGATAGAAGAAGAGTTTACAGCAA 58.060 33.333 0.00 0.00 0.00 3.91
2210 2414 8.539770 TTGATAGAAGAAGAGTTTACAGCAAG 57.460 34.615 0.00 0.00 0.00 4.01
2211 2415 7.896811 TGATAGAAGAAGAGTTTACAGCAAGA 58.103 34.615 0.00 0.00 0.00 3.02
2212 2416 8.031864 TGATAGAAGAAGAGTTTACAGCAAGAG 58.968 37.037 0.00 0.00 0.00 2.85
2213 2417 5.546526 AGAAGAAGAGTTTACAGCAAGAGG 58.453 41.667 0.00 0.00 0.00 3.69
2214 2418 4.965200 AGAAGAGTTTACAGCAAGAGGT 57.035 40.909 0.00 0.00 0.00 3.85
2215 2419 5.297569 AGAAGAGTTTACAGCAAGAGGTT 57.702 39.130 0.00 0.00 0.00 3.50
2216 2420 6.420913 AGAAGAGTTTACAGCAAGAGGTTA 57.579 37.500 0.00 0.00 0.00 2.85
2217 2421 6.224584 AGAAGAGTTTACAGCAAGAGGTTAC 58.775 40.000 0.00 0.00 0.00 2.50
2218 2422 5.546621 AGAGTTTACAGCAAGAGGTTACA 57.453 39.130 0.00 0.00 0.00 2.41
2219 2423 5.925509 AGAGTTTACAGCAAGAGGTTACAA 58.074 37.500 0.00 0.00 0.00 2.41
2220 2424 5.758784 AGAGTTTACAGCAAGAGGTTACAAC 59.241 40.000 0.00 0.00 0.00 3.32
2231 2435 3.157922 GTTACAACCACACGCAAGC 57.842 52.632 0.00 0.00 45.62 4.01
2232 2436 0.317519 GTTACAACCACACGCAAGCC 60.318 55.000 0.00 0.00 45.62 4.35
2233 2437 0.748367 TTACAACCACACGCAAGCCA 60.748 50.000 0.00 0.00 45.62 4.75
2234 2438 0.536233 TACAACCACACGCAAGCCAT 60.536 50.000 0.00 0.00 45.62 4.40
2235 2439 1.372004 CAACCACACGCAAGCCATG 60.372 57.895 0.00 0.00 45.62 3.66
2236 2440 1.827789 AACCACACGCAAGCCATGT 60.828 52.632 0.00 0.00 45.62 3.21
2237 2441 0.536233 AACCACACGCAAGCCATGTA 60.536 50.000 0.00 0.00 45.62 2.29
2238 2442 1.234615 ACCACACGCAAGCCATGTAC 61.235 55.000 0.00 0.00 45.62 2.90
2239 2443 1.132436 CACACGCAAGCCATGTACG 59.868 57.895 0.00 0.00 45.62 3.67
2240 2444 2.098298 CACGCAAGCCATGTACGC 59.902 61.111 0.00 0.00 45.62 4.42
2241 2445 2.047274 ACGCAAGCCATGTACGCT 60.047 55.556 0.00 0.00 45.62 5.07
2242 2446 1.081556 CACGCAAGCCATGTACGCTA 61.082 55.000 0.00 0.00 45.62 4.26
2243 2447 0.806102 ACGCAAGCCATGTACGCTAG 60.806 55.000 0.00 0.00 45.62 3.42
2244 2448 0.527600 CGCAAGCCATGTACGCTAGA 60.528 55.000 0.00 0.00 34.84 2.43
2245 2449 1.212616 GCAAGCCATGTACGCTAGAG 58.787 55.000 0.00 0.00 34.84 2.43
2246 2450 1.858091 CAAGCCATGTACGCTAGAGG 58.142 55.000 0.00 0.00 34.84 3.69
2247 2451 0.105039 AAGCCATGTACGCTAGAGGC 59.895 55.000 0.00 0.00 42.31 4.70
2248 2452 1.043116 AGCCATGTACGCTAGAGGCA 61.043 55.000 10.74 0.00 44.34 4.75
2249 2453 0.034059 GCCATGTACGCTAGAGGCAT 59.966 55.000 0.00 0.00 41.63 4.40
2250 2454 1.788258 CCATGTACGCTAGAGGCATG 58.212 55.000 18.96 18.96 41.91 4.06
2251 2455 1.341209 CCATGTACGCTAGAGGCATGA 59.659 52.381 23.96 0.00 41.91 3.07
2252 2456 2.028658 CCATGTACGCTAGAGGCATGAT 60.029 50.000 23.96 0.00 41.91 2.45
2253 2457 3.249091 CATGTACGCTAGAGGCATGATC 58.751 50.000 20.30 0.00 41.91 2.92
2254 2458 1.266989 TGTACGCTAGAGGCATGATCG 59.733 52.381 0.00 0.00 41.91 3.69
2255 2459 0.241213 TACGCTAGAGGCATGATCGC 59.759 55.000 0.00 0.00 41.91 4.58
2256 2460 2.085262 CGCTAGAGGCATGATCGCG 61.085 63.158 0.00 0.00 41.91 5.87
2257 2461 1.735920 GCTAGAGGCATGATCGCGG 60.736 63.158 6.13 0.00 41.35 6.46
2258 2462 1.080230 CTAGAGGCATGATCGCGGG 60.080 63.158 6.13 0.00 0.00 6.13
2259 2463 3.226429 TAGAGGCATGATCGCGGGC 62.226 63.158 6.13 1.14 0.00 6.13
2273 2477 4.767255 GGGCGGTGGAGCAGACAG 62.767 72.222 0.00 0.00 39.27 3.51
2274 2478 3.695606 GGCGGTGGAGCAGACAGA 61.696 66.667 0.00 0.00 39.27 3.41
2275 2479 2.343758 GCGGTGGAGCAGACAGAA 59.656 61.111 0.00 0.00 37.05 3.02
2276 2480 2.029844 GCGGTGGAGCAGACAGAAC 61.030 63.158 0.00 0.00 37.05 3.01
2277 2481 1.367471 CGGTGGAGCAGACAGAACA 59.633 57.895 0.00 0.00 0.00 3.18
2278 2482 0.249868 CGGTGGAGCAGACAGAACAA 60.250 55.000 0.00 0.00 0.00 2.83
2279 2483 1.517242 GGTGGAGCAGACAGAACAAG 58.483 55.000 0.00 0.00 0.00 3.16
2280 2484 1.517242 GTGGAGCAGACAGAACAAGG 58.483 55.000 0.00 0.00 0.00 3.61
2281 2485 0.397941 TGGAGCAGACAGAACAAGGG 59.602 55.000 0.00 0.00 0.00 3.95
2282 2486 0.322008 GGAGCAGACAGAACAAGGGG 60.322 60.000 0.00 0.00 0.00 4.79
2283 2487 0.957888 GAGCAGACAGAACAAGGGGC 60.958 60.000 0.00 0.00 0.00 5.80
2284 2488 1.073897 GCAGACAGAACAAGGGGCT 59.926 57.895 0.00 0.00 0.00 5.19
2285 2489 1.239968 GCAGACAGAACAAGGGGCTG 61.240 60.000 0.00 0.00 35.81 4.85
2286 2490 1.073897 AGACAGAACAAGGGGCTGC 59.926 57.895 0.00 0.00 33.03 5.25
2287 2491 1.073897 GACAGAACAAGGGGCTGCT 59.926 57.895 0.00 0.00 33.03 4.24
2288 2492 0.324943 GACAGAACAAGGGGCTGCTA 59.675 55.000 0.00 0.00 33.03 3.49
2289 2493 0.771127 ACAGAACAAGGGGCTGCTAA 59.229 50.000 0.00 0.00 33.03 3.09
2290 2494 1.355720 ACAGAACAAGGGGCTGCTAAT 59.644 47.619 0.00 0.00 33.03 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.954989 TGTCAAGTTTAGTTGGCATGCA 59.045 40.909 21.36 2.54 37.12 3.96
1 2 3.641437 TGTCAAGTTTAGTTGGCATGC 57.359 42.857 9.90 9.90 37.12 4.06
4 5 4.072131 GAGGATGTCAAGTTTAGTTGGCA 58.928 43.478 7.02 7.02 45.70 4.92
14 15 1.691976 TGTTCACCGAGGATGTCAAGT 59.308 47.619 0.00 0.00 0.00 3.16
19 20 1.542547 GGTTGTGTTCACCGAGGATGT 60.543 52.381 0.00 0.00 0.00 3.06
28 29 5.412526 TTTTCGTGATAGGTTGTGTTCAC 57.587 39.130 0.00 0.00 36.09 3.18
67 68 2.415512 GCGAACGTCAGATTTTTAGGCT 59.584 45.455 0.00 0.00 0.00 4.58
99 100 3.332034 AGAAAATCCCGTTGTAAGGACG 58.668 45.455 0.00 0.00 40.05 4.79
138 142 2.466982 CCATCGCGCTGCAAGACAT 61.467 57.895 5.56 0.00 34.07 3.06
207 222 0.887836 ACTGTGACGTCGGCTGTCTA 60.888 55.000 11.62 0.00 37.26 2.59
215 230 1.315497 CACGTAAGACTGTGACGTCG 58.685 55.000 11.62 0.00 46.19 5.12
275 294 2.429250 TCAATAGTTTCAGCCGATCGGA 59.571 45.455 37.64 14.67 37.50 4.55
277 296 3.243877 CAGTCAATAGTTTCAGCCGATCG 59.756 47.826 8.51 8.51 0.00 3.69
278 297 4.268884 GTCAGTCAATAGTTTCAGCCGATC 59.731 45.833 0.00 0.00 0.00 3.69
279 298 4.184629 GTCAGTCAATAGTTTCAGCCGAT 58.815 43.478 0.00 0.00 0.00 4.18
280 299 3.585862 GTCAGTCAATAGTTTCAGCCGA 58.414 45.455 0.00 0.00 0.00 5.54
282 301 2.094417 GCGTCAGTCAATAGTTTCAGCC 59.906 50.000 0.00 0.00 0.00 4.85
338 357 2.631160 TCCTTCCGAGAAGCAACAAA 57.369 45.000 7.82 0.00 0.00 2.83
339 358 2.494059 CTTCCTTCCGAGAAGCAACAA 58.506 47.619 7.82 0.00 34.77 2.83
427 447 5.697178 CCTGATCAGCATTCTCTGTATCTTG 59.303 44.000 17.76 0.00 35.63 3.02
428 448 5.366186 ACCTGATCAGCATTCTCTGTATCTT 59.634 40.000 17.76 0.00 35.63 2.40
429 449 4.900652 ACCTGATCAGCATTCTCTGTATCT 59.099 41.667 17.76 0.00 35.63 1.98
430 450 5.212532 ACCTGATCAGCATTCTCTGTATC 57.787 43.478 17.76 0.00 35.63 2.24
431 451 5.366460 CAACCTGATCAGCATTCTCTGTAT 58.634 41.667 17.76 0.00 35.63 2.29
432 452 4.383444 CCAACCTGATCAGCATTCTCTGTA 60.383 45.833 17.76 0.00 35.63 2.74
435 455 2.575279 ACCAACCTGATCAGCATTCTCT 59.425 45.455 17.76 0.00 0.00 3.10
491 511 3.490759 GCGGCGATGACACACCAG 61.491 66.667 12.98 0.00 0.00 4.00
492 512 3.604129 ATGCGGCGATGACACACCA 62.604 57.895 12.98 0.00 0.00 4.17
493 513 2.819595 ATGCGGCGATGACACACC 60.820 61.111 12.98 0.00 0.00 4.16
494 514 2.028766 CTCATGCGGCGATGACACAC 62.029 60.000 12.98 0.00 0.00 3.82
503 523 1.154413 GTGTTGAACTCATGCGGCG 60.154 57.895 0.51 0.51 0.00 6.46
522 588 1.609555 AGATTAGTCCACCGAGCGATC 59.390 52.381 0.00 0.00 0.00 3.69
525 591 1.025812 AGAGATTAGTCCACCGAGCG 58.974 55.000 0.00 0.00 0.00 5.03
545 611 3.068024 GTCCACCAAGCAAAAAGATCACA 59.932 43.478 0.00 0.00 0.00 3.58
546 612 3.552890 GGTCCACCAAGCAAAAAGATCAC 60.553 47.826 0.00 0.00 35.64 3.06
561 627 2.046285 CCCGATTGCTTGGTCCACC 61.046 63.158 0.00 0.00 0.00 4.61
562 628 2.700773 GCCCGATTGCTTGGTCCAC 61.701 63.158 0.00 0.00 0.00 4.02
563 629 2.361104 GCCCGATTGCTTGGTCCA 60.361 61.111 0.00 0.00 0.00 4.02
564 630 2.361104 TGCCCGATTGCTTGGTCC 60.361 61.111 0.00 0.00 0.00 4.46
566 632 3.055719 CGTGCCCGATTGCTTGGT 61.056 61.111 0.00 0.00 35.63 3.67
567 633 2.745884 TCGTGCCCGATTGCTTGG 60.746 61.111 0.00 0.00 38.40 3.61
568 634 2.787249 CTCGTGCCCGATTGCTTG 59.213 61.111 0.00 0.00 43.27 4.01
569 635 3.127533 GCTCGTGCCCGATTGCTT 61.128 61.111 0.00 0.00 43.27 3.91
573 654 3.118454 CGTTGCTCGTGCCCGATT 61.118 61.111 7.05 0.00 43.27 3.34
583 669 0.365859 GTAGCGTTGTAGCGTTGCTC 59.634 55.000 0.00 0.00 40.44 4.26
590 676 6.536731 TCTATACTGTAGTAGCGTTGTAGC 57.463 41.667 0.00 0.00 33.52 3.58
598 684 9.562583 GCAGTGATTATTCTATACTGTAGTAGC 57.437 37.037 0.00 0.00 40.52 3.58
601 687 9.920133 CATGCAGTGATTATTCTATACTGTAGT 57.080 33.333 0.00 0.00 40.52 2.73
602 688 8.867935 GCATGCAGTGATTATTCTATACTGTAG 58.132 37.037 14.21 0.00 40.52 2.74
603 689 7.542130 CGCATGCAGTGATTATTCTATACTGTA 59.458 37.037 19.57 0.00 40.52 2.74
604 690 6.367149 CGCATGCAGTGATTATTCTATACTGT 59.633 38.462 19.57 0.00 40.52 3.55
605 691 6.367149 ACGCATGCAGTGATTATTCTATACTG 59.633 38.462 19.57 0.00 41.15 2.74
774 865 3.531538 AGATATCGGCTGCTTTTTCGAA 58.468 40.909 0.00 0.00 35.25 3.71
863 954 4.498323 GGTAACTACGTCTACATGCTTTCG 59.502 45.833 0.00 0.00 0.00 3.46
974 1065 6.350612 CCTCCTCGATCTTTCTACTCTGTTTT 60.351 42.308 0.00 0.00 0.00 2.43
975 1066 5.126384 CCTCCTCGATCTTTCTACTCTGTTT 59.874 44.000 0.00 0.00 0.00 2.83
977 1068 4.080243 TCCTCCTCGATCTTTCTACTCTGT 60.080 45.833 0.00 0.00 0.00 3.41
978 1069 4.456535 TCCTCCTCGATCTTTCTACTCTG 58.543 47.826 0.00 0.00 0.00 3.35
979 1070 4.781775 TCCTCCTCGATCTTTCTACTCT 57.218 45.455 0.00 0.00 0.00 3.24
980 1071 4.217550 CCATCCTCCTCGATCTTTCTACTC 59.782 50.000 0.00 0.00 0.00 2.59
982 1073 3.305744 GCCATCCTCCTCGATCTTTCTAC 60.306 52.174 0.00 0.00 0.00 2.59
983 1074 2.894126 GCCATCCTCCTCGATCTTTCTA 59.106 50.000 0.00 0.00 0.00 2.10
984 1075 1.691434 GCCATCCTCCTCGATCTTTCT 59.309 52.381 0.00 0.00 0.00 2.52
985 1076 1.604185 CGCCATCCTCCTCGATCTTTC 60.604 57.143 0.00 0.00 0.00 2.62
1140 1246 2.358737 CAGGCGAACCACAGGTCC 60.359 66.667 0.00 0.00 39.06 4.46
1342 1461 3.497640 AGGAGTACGTACGTATCTGATGC 59.502 47.826 29.05 17.52 32.82 3.91
1343 1462 5.925397 AGTAGGAGTACGTACGTATCTGATG 59.075 44.000 29.05 0.00 40.77 3.07
1345 1464 5.521906 AGTAGGAGTACGTACGTATCTGA 57.478 43.478 29.05 7.60 40.77 3.27
1346 1465 5.344665 GCTAGTAGGAGTACGTACGTATCTG 59.655 48.000 29.05 15.45 40.77 2.90
1347 1466 5.242838 AGCTAGTAGGAGTACGTACGTATCT 59.757 44.000 29.05 25.01 40.77 1.98
1348 1467 5.344665 CAGCTAGTAGGAGTACGTACGTATC 59.655 48.000 29.05 23.81 40.77 2.24
1349 1468 5.226396 CAGCTAGTAGGAGTACGTACGTAT 58.774 45.833 29.05 18.23 40.77 3.06
1395 1514 0.038166 ACCAATCAACCAGCCACGAT 59.962 50.000 0.00 0.00 0.00 3.73
1396 1515 0.687920 TACCAATCAACCAGCCACGA 59.312 50.000 0.00 0.00 0.00 4.35
1397 1516 1.750193 ATACCAATCAACCAGCCACG 58.250 50.000 0.00 0.00 0.00 4.94
1398 1517 3.632145 CCTAATACCAATCAACCAGCCAC 59.368 47.826 0.00 0.00 0.00 5.01
1399 1518 3.268334 ACCTAATACCAATCAACCAGCCA 59.732 43.478 0.00 0.00 0.00 4.75
1400 1519 3.898482 ACCTAATACCAATCAACCAGCC 58.102 45.455 0.00 0.00 0.00 4.85
1401 1520 4.705023 ACAACCTAATACCAATCAACCAGC 59.295 41.667 0.00 0.00 0.00 4.85
1492 1616 3.072944 CCTGAAACTTCTGAAGCAGGAG 58.927 50.000 25.85 14.59 44.27 3.69
1554 1678 4.815308 GGTTCTGATCACTGAAGATGGATG 59.185 45.833 0.00 0.00 35.33 3.51
1555 1679 4.472470 TGGTTCTGATCACTGAAGATGGAT 59.528 41.667 0.00 0.00 35.33 3.41
1556 1680 3.840078 TGGTTCTGATCACTGAAGATGGA 59.160 43.478 0.00 0.00 35.33 3.41
1557 1681 4.212143 TGGTTCTGATCACTGAAGATGG 57.788 45.455 0.00 0.00 35.33 3.51
1614 1738 7.214467 ACAACGTCTCCAAACATCATTATTT 57.786 32.000 0.00 0.00 0.00 1.40
1659 1786 0.389166 CGTCAGGAAGTCCAGCAGAC 60.389 60.000 0.00 0.00 46.71 3.51
1677 1804 0.028505 GAGCTGTTGGTGCATATGCG 59.971 55.000 22.21 7.60 45.83 4.73
1683 1810 1.675714 CGATTAGGAGCTGTTGGTGCA 60.676 52.381 0.00 0.00 34.40 4.57
1762 1894 1.123928 AATCAGGTCGCTCCCTTAGG 58.876 55.000 0.00 0.00 36.75 2.69
1784 1916 3.316868 GGTTCGGTTGATCTTGGTCAAAA 59.683 43.478 0.00 0.00 39.61 2.44
1785 1917 2.882137 GGTTCGGTTGATCTTGGTCAAA 59.118 45.455 0.00 0.00 39.61 2.69
1790 1922 2.504367 ACTTGGTTCGGTTGATCTTGG 58.496 47.619 0.00 0.00 0.00 3.61
1795 1927 6.642707 TTTGAAATACTTGGTTCGGTTGAT 57.357 33.333 0.00 0.00 0.00 2.57
1806 1938 9.611284 TTCAGTTCATTCGATTTGAAATACTTG 57.389 29.630 11.57 7.14 40.71 3.16
1813 1945 7.647715 GTCCTTTTTCAGTTCATTCGATTTGAA 59.352 33.333 7.10 7.10 41.81 2.69
1819 1951 5.820423 TCTTGTCCTTTTTCAGTTCATTCGA 59.180 36.000 0.00 0.00 0.00 3.71
1823 1956 6.773976 TGTTCTTGTCCTTTTTCAGTTCAT 57.226 33.333 0.00 0.00 0.00 2.57
1824 1957 6.386654 GTTGTTCTTGTCCTTTTTCAGTTCA 58.613 36.000 0.00 0.00 0.00 3.18
1835 1968 4.138487 ACTCTTTCGTTGTTCTTGTCCT 57.862 40.909 0.00 0.00 0.00 3.85
1838 1971 3.800506 CGGTACTCTTTCGTTGTTCTTGT 59.199 43.478 0.00 0.00 0.00 3.16
1839 1972 4.046462 TCGGTACTCTTTCGTTGTTCTTG 58.954 43.478 0.00 0.00 0.00 3.02
1840 1973 4.311816 TCGGTACTCTTTCGTTGTTCTT 57.688 40.909 0.00 0.00 0.00 2.52
1841 1974 3.996150 TCGGTACTCTTTCGTTGTTCT 57.004 42.857 0.00 0.00 0.00 3.01
1842 1975 6.695292 TTTATCGGTACTCTTTCGTTGTTC 57.305 37.500 0.00 0.00 0.00 3.18
1843 1976 6.479660 TGTTTTATCGGTACTCTTTCGTTGTT 59.520 34.615 0.00 0.00 0.00 2.83
1844 1977 5.984926 TGTTTTATCGGTACTCTTTCGTTGT 59.015 36.000 0.00 0.00 0.00 3.32
1845 1978 6.294363 GTGTTTTATCGGTACTCTTTCGTTG 58.706 40.000 0.00 0.00 0.00 4.10
1848 1981 4.853196 TCGTGTTTTATCGGTACTCTTTCG 59.147 41.667 0.00 0.00 0.00 3.46
1849 1982 6.364435 ACTTCGTGTTTTATCGGTACTCTTTC 59.636 38.462 0.00 0.00 0.00 2.62
1850 1983 6.218746 ACTTCGTGTTTTATCGGTACTCTTT 58.781 36.000 0.00 0.00 0.00 2.52
1881 2084 4.551388 AGTTGACACTCTCGAATGACTTC 58.449 43.478 0.00 0.00 0.00 3.01
1895 2098 2.726832 AACGGAGCTAGAGTTGACAC 57.273 50.000 0.00 0.00 0.00 3.67
1926 2130 9.974980 GGTTTTGTATTCTACATTTTTCAGGAA 57.025 29.630 0.00 0.00 38.68 3.36
1975 2179 7.151308 GTGTATGAGACTCATATCCCTCTTTG 58.849 42.308 24.44 0.00 40.97 2.77
1979 2183 6.656632 TTGTGTATGAGACTCATATCCCTC 57.343 41.667 24.44 13.70 40.97 4.30
1980 2184 8.727100 TTATTGTGTATGAGACTCATATCCCT 57.273 34.615 24.44 12.99 40.97 4.20
1981 2185 8.589338 ACTTATTGTGTATGAGACTCATATCCC 58.411 37.037 24.44 16.30 40.97 3.85
1982 2186 9.416794 CACTTATTGTGTATGAGACTCATATCC 57.583 37.037 24.44 18.28 40.97 2.59
1985 2189 9.408648 TCTCACTTATTGTGTATGAGACTCATA 57.591 33.333 19.24 19.24 46.27 2.15
1986 2190 8.298729 TCTCACTTATTGTGTATGAGACTCAT 57.701 34.615 21.31 21.31 46.27 2.90
1987 2191 7.703058 TCTCACTTATTGTGTATGAGACTCA 57.297 36.000 7.80 7.80 46.27 3.41
2056 2260 6.374894 AGACACTAGACATGTGACCTTACTAC 59.625 42.308 1.15 0.00 38.65 2.73
2060 2264 6.482524 AGTAGACACTAGACATGTGACCTTA 58.517 40.000 1.15 0.00 38.65 2.69
2075 2279 7.661536 ACCATGTGATAACATAGTAGACACT 57.338 36.000 0.00 0.00 38.91 3.55
2076 2280 7.979537 TCAACCATGTGATAACATAGTAGACAC 59.020 37.037 0.00 0.00 0.00 3.67
2077 2281 8.073467 TCAACCATGTGATAACATAGTAGACA 57.927 34.615 0.00 0.00 0.00 3.41
2094 2298 6.971184 GCTCATGATAGTTTTTCTCAACCATG 59.029 38.462 0.00 0.00 0.00 3.66
2110 2314 7.205992 GTCTACACTCTTTCATGCTCATGATA 58.794 38.462 12.72 7.87 46.12 2.15
2165 2369 0.168788 TGCAAAGATACGCAGCTTGC 59.831 50.000 7.64 7.64 40.69 4.01
2166 2370 2.838386 ATGCAAAGATACGCAGCTTG 57.162 45.000 0.00 0.00 42.37 4.01
2167 2371 2.749076 TCAATGCAAAGATACGCAGCTT 59.251 40.909 0.00 0.00 42.37 3.74
2168 2372 2.358957 TCAATGCAAAGATACGCAGCT 58.641 42.857 0.00 0.00 42.37 4.24
2169 2373 2.830772 TCAATGCAAAGATACGCAGC 57.169 45.000 0.00 0.00 42.37 5.25
2170 2374 5.912360 TCTATCAATGCAAAGATACGCAG 57.088 39.130 7.22 1.65 42.37 5.18
2171 2375 6.048509 TCTTCTATCAATGCAAAGATACGCA 58.951 36.000 7.22 0.00 43.45 5.24
2172 2376 6.530913 TCTTCTATCAATGCAAAGATACGC 57.469 37.500 7.22 0.00 0.00 4.42
2173 2377 8.357796 TCTTCTTCTATCAATGCAAAGATACG 57.642 34.615 7.22 5.25 0.00 3.06
2174 2378 9.323985 ACTCTTCTTCTATCAATGCAAAGATAC 57.676 33.333 7.22 0.00 0.00 2.24
2175 2379 9.896645 AACTCTTCTTCTATCAATGCAAAGATA 57.103 29.630 10.07 10.07 0.00 1.98
2176 2380 8.804912 AACTCTTCTTCTATCAATGCAAAGAT 57.195 30.769 8.96 8.96 0.00 2.40
2177 2381 8.627208 AAACTCTTCTTCTATCAATGCAAAGA 57.373 30.769 0.00 0.00 0.00 2.52
2178 2382 9.766277 GTAAACTCTTCTTCTATCAATGCAAAG 57.234 33.333 0.00 0.00 0.00 2.77
2179 2383 9.283768 TGTAAACTCTTCTTCTATCAATGCAAA 57.716 29.630 0.00 0.00 0.00 3.68
2180 2384 8.846943 TGTAAACTCTTCTTCTATCAATGCAA 57.153 30.769 0.00 0.00 0.00 4.08
2181 2385 7.065085 GCTGTAAACTCTTCTTCTATCAATGCA 59.935 37.037 0.00 0.00 0.00 3.96
2182 2386 7.065085 TGCTGTAAACTCTTCTTCTATCAATGC 59.935 37.037 0.00 0.00 0.00 3.56
2183 2387 8.484641 TGCTGTAAACTCTTCTTCTATCAATG 57.515 34.615 0.00 0.00 0.00 2.82
2184 2388 9.160496 CTTGCTGTAAACTCTTCTTCTATCAAT 57.840 33.333 0.00 0.00 0.00 2.57
2185 2389 8.367911 TCTTGCTGTAAACTCTTCTTCTATCAA 58.632 33.333 0.00 0.00 0.00 2.57
2186 2390 7.896811 TCTTGCTGTAAACTCTTCTTCTATCA 58.103 34.615 0.00 0.00 0.00 2.15
2187 2391 7.491048 CCTCTTGCTGTAAACTCTTCTTCTATC 59.509 40.741 0.00 0.00 0.00 2.08
2188 2392 7.038658 ACCTCTTGCTGTAAACTCTTCTTCTAT 60.039 37.037 0.00 0.00 0.00 1.98
2189 2393 6.267928 ACCTCTTGCTGTAAACTCTTCTTCTA 59.732 38.462 0.00 0.00 0.00 2.10
2190 2394 5.071115 ACCTCTTGCTGTAAACTCTTCTTCT 59.929 40.000 0.00 0.00 0.00 2.85
2191 2395 5.301555 ACCTCTTGCTGTAAACTCTTCTTC 58.698 41.667 0.00 0.00 0.00 2.87
2192 2396 5.297569 ACCTCTTGCTGTAAACTCTTCTT 57.702 39.130 0.00 0.00 0.00 2.52
2193 2397 4.965200 ACCTCTTGCTGTAAACTCTTCT 57.035 40.909 0.00 0.00 0.00 2.85
2194 2398 5.989777 TGTAACCTCTTGCTGTAAACTCTTC 59.010 40.000 0.00 0.00 0.00 2.87
2195 2399 5.925509 TGTAACCTCTTGCTGTAAACTCTT 58.074 37.500 0.00 0.00 0.00 2.85
2196 2400 5.546621 TGTAACCTCTTGCTGTAAACTCT 57.453 39.130 0.00 0.00 0.00 3.24
2197 2401 5.049612 GGTTGTAACCTCTTGCTGTAAACTC 60.050 44.000 6.54 0.00 45.75 3.01
2198 2402 4.820173 GGTTGTAACCTCTTGCTGTAAACT 59.180 41.667 6.54 0.00 45.75 2.66
2199 2403 5.104562 GGTTGTAACCTCTTGCTGTAAAC 57.895 43.478 6.54 0.00 45.75 2.01
2213 2417 0.317519 GGCTTGCGTGTGGTTGTAAC 60.318 55.000 0.00 0.00 0.00 2.50
2214 2418 0.748367 TGGCTTGCGTGTGGTTGTAA 60.748 50.000 0.00 0.00 0.00 2.41
2215 2419 0.536233 ATGGCTTGCGTGTGGTTGTA 60.536 50.000 0.00 0.00 0.00 2.41
2216 2420 1.827789 ATGGCTTGCGTGTGGTTGT 60.828 52.632 0.00 0.00 0.00 3.32
2217 2421 1.372004 CATGGCTTGCGTGTGGTTG 60.372 57.895 0.00 0.00 0.00 3.77
2218 2422 0.536233 TACATGGCTTGCGTGTGGTT 60.536 50.000 0.00 0.00 0.00 3.67
2219 2423 1.072332 TACATGGCTTGCGTGTGGT 59.928 52.632 0.00 0.00 0.00 4.16
2220 2424 1.501741 GTACATGGCTTGCGTGTGG 59.498 57.895 0.00 0.00 0.00 4.17
2221 2425 1.132436 CGTACATGGCTTGCGTGTG 59.868 57.895 0.00 2.08 0.00 3.82
2222 2426 2.677003 GCGTACATGGCTTGCGTGT 61.677 57.895 0.00 7.27 0.00 4.49
2223 2427 1.081556 TAGCGTACATGGCTTGCGTG 61.082 55.000 0.00 0.00 41.80 5.34
2224 2428 0.806102 CTAGCGTACATGGCTTGCGT 60.806 55.000 0.00 0.00 41.80 5.24
2225 2429 0.527600 TCTAGCGTACATGGCTTGCG 60.528 55.000 0.00 0.00 41.80 4.85
2226 2430 1.212616 CTCTAGCGTACATGGCTTGC 58.787 55.000 0.00 0.00 41.80 4.01
2227 2431 1.858091 CCTCTAGCGTACATGGCTTG 58.142 55.000 0.00 0.00 41.80 4.01
2228 2432 0.105039 GCCTCTAGCGTACATGGCTT 59.895 55.000 0.00 0.00 41.80 4.35
2229 2433 1.742768 GCCTCTAGCGTACATGGCT 59.257 57.895 0.00 0.00 44.35 4.75
2230 2434 4.345337 GCCTCTAGCGTACATGGC 57.655 61.111 0.00 0.00 0.00 4.40
2239 2443 1.735920 CCGCGATCATGCCTCTAGC 60.736 63.158 8.23 0.00 44.14 3.42
2240 2444 1.080230 CCCGCGATCATGCCTCTAG 60.080 63.158 8.23 0.00 0.00 2.43
2241 2445 3.051210 CCCGCGATCATGCCTCTA 58.949 61.111 8.23 0.00 0.00 2.43
2242 2446 4.615815 GCCCGCGATCATGCCTCT 62.616 66.667 8.23 0.00 0.00 3.69
2256 2460 4.767255 CTGTCTGCTCCACCGCCC 62.767 72.222 0.00 0.00 0.00 6.13
2257 2461 3.240134 TTCTGTCTGCTCCACCGCC 62.240 63.158 0.00 0.00 0.00 6.13
2258 2462 2.029844 GTTCTGTCTGCTCCACCGC 61.030 63.158 0.00 0.00 0.00 5.68
2259 2463 0.249868 TTGTTCTGTCTGCTCCACCG 60.250 55.000 0.00 0.00 0.00 4.94
2260 2464 1.517242 CTTGTTCTGTCTGCTCCACC 58.483 55.000 0.00 0.00 0.00 4.61
2261 2465 1.517242 CCTTGTTCTGTCTGCTCCAC 58.483 55.000 0.00 0.00 0.00 4.02
2262 2466 0.397941 CCCTTGTTCTGTCTGCTCCA 59.602 55.000 0.00 0.00 0.00 3.86
2263 2467 0.322008 CCCCTTGTTCTGTCTGCTCC 60.322 60.000 0.00 0.00 0.00 4.70
2264 2468 0.957888 GCCCCTTGTTCTGTCTGCTC 60.958 60.000 0.00 0.00 0.00 4.26
2265 2469 1.073897 GCCCCTTGTTCTGTCTGCT 59.926 57.895 0.00 0.00 0.00 4.24
2266 2470 1.073897 AGCCCCTTGTTCTGTCTGC 59.926 57.895 0.00 0.00 0.00 4.26
2267 2471 1.239968 GCAGCCCCTTGTTCTGTCTG 61.240 60.000 0.00 0.00 0.00 3.51
2268 2472 1.073897 GCAGCCCCTTGTTCTGTCT 59.926 57.895 0.00 0.00 0.00 3.41
2269 2473 0.324943 TAGCAGCCCCTTGTTCTGTC 59.675 55.000 0.00 0.00 0.00 3.51
2270 2474 0.771127 TTAGCAGCCCCTTGTTCTGT 59.229 50.000 0.00 0.00 0.00 3.41
2271 2475 2.134789 ATTAGCAGCCCCTTGTTCTG 57.865 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.