Multiple sequence alignment - TraesCS2A01G482000

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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 TraesCS2A01G482000 chr2A 100.000 2618 0 0 1 2618 718877792 718880409 0.000000e+00 4835.0
1 TraesCS2A01G482000 chr2D 92.638 815 33 13 571 1375 584625555 584626352 0.000000e+00 1147.0
2 TraesCS2A01G482000 chr2D 84.440 482 53 13 1523 1997 584626369 584626835 3.070000e-124 455.0
3 TraesCS2A01G482000 chr2D 86.833 281 23 6 24 303 584624984 584625251 4.230000e-78 302.0
4 TraesCS2A01G482000 chr2D 93.939 165 9 1 311 474 584625293 584625457 5.600000e-62 248.0
5 TraesCS2A01G482000 chr2D 93.506 77 5 0 498 574 584625455 584625531 5.920000e-22 115.0
6 TraesCS2A01G482000 chr2B 87.703 984 69 18 311 1281 704575672 704576616 0.000000e+00 1099.0
7 TraesCS2A01G482000 chr2B 87.420 628 39 8 1374 1997 704576662 704577253 0.000000e+00 686.0
8 TraesCS2A01G482000 chr2B 86.607 448 39 15 2113 2552 704577598 704578032 2.360000e-130 475.0
9 TraesCS2A01G482000 chr2B 88.387 310 21 8 1 306 704575338 704575636 2.480000e-95 359.0
10 TraesCS2A01G482000 chr2B 89.697 165 14 2 709 873 792372659 792372820 9.500000e-50 207.0
11 TraesCS2A01G482000 chr3A 76.705 953 137 51 778 1663 697520867 697521801 3.970000e-123 451.0
12 TraesCS2A01G482000 chr3A 82.645 121 20 1 596 715 700953092 700953212 3.560000e-19 106.0
13 TraesCS2A01G482000 chr7A 76.205 954 143 50 778 1663 674115879 674114942 6.700000e-116 427.0
14 TraesCS2A01G482000 chr7A 76.230 955 140 53 778 1663 672598718 672597782 2.410000e-115 425.0
15 TraesCS2A01G482000 chr7A 94.737 38 1 1 2289 2326 193533310 193533274 1.010000e-04 58.4
16 TraesCS2A01G482000 chr7A 100.000 28 0 0 2289 2316 193059065 193059038 5.000000e-03 52.8
17 TraesCS2A01G482000 chr3D 77.195 763 112 38 596 1339 566132072 566131353 3.160000e-104 388.0
18 TraesCS2A01G482000 chr3D 80.386 311 38 13 1037 1345 566101561 566101272 5.670000e-52 215.0
19 TraesCS2A01G482000 chr3B 77.266 695 96 41 595 1271 755709839 755710489 4.150000e-93 351.0
20 TraesCS2A01G482000 chr3B 75.931 752 112 43 609 1339 754719951 754720654 3.250000e-84 322.0
21 TraesCS2A01G482000 chr3B 89.759 166 13 3 709 873 45147789 45147627 2.640000e-50 209.0
22 TraesCS2A01G482000 chr3B 83.471 121 19 1 596 715 755605031 755605151 7.660000e-21 111.0
23 TraesCS2A01G482000 chr3B 89.130 92 7 3 1256 1345 755710576 755710666 7.660000e-21 111.0
24 TraesCS2A01G482000 chr3B 88.889 45 4 1 2290 2333 187495467 187495423 1.000000e-03 54.7
25 TraesCS2A01G482000 chr5A 77.901 629 88 34 778 1372 609823106 609822495 6.940000e-91 344.0
26 TraesCS2A01G482000 chr5A 86.325 234 31 1 1392 1625 688244227 688244459 1.200000e-63 254.0
27 TraesCS2A01G482000 chr4B 81.544 298 44 7 1369 1660 649492322 649492614 4.360000e-58 235.0
28 TraesCS2A01G482000 chr4B 89.697 165 14 2 709 873 27424412 27424251 9.500000e-50 207.0
29 TraesCS2A01G482000 chr6B 90.854 164 12 2 709 872 632001174 632001014 1.580000e-52 217.0
30 TraesCS2A01G482000 chr7B 89.697 165 14 2 709 873 728065605 728065444 9.500000e-50 207.0
31 TraesCS2A01G482000 chr7B 88.757 169 16 2 709 877 9088817 9088652 1.230000e-48 204.0
32 TraesCS2A01G482000 chr7B 90.909 44 3 1 2287 2329 582619495 582619538 1.010000e-04 58.4
33 TraesCS2A01G482000 chr7B 94.286 35 1 1 2291 2325 327904726 327904693 5.000000e-03 52.8
34 TraesCS2A01G482000 chr4D 82.960 223 38 0 1403 1625 503641746 503641968 4.420000e-48 202.0
35 TraesCS2A01G482000 chr1B 80.952 231 23 17 793 1008 117289897 117289673 2.080000e-36 163.0
36 TraesCS2A01G482000 chr5B 92.105 38 3 0 2290 2327 319897398 319897361 1.000000e-03 54.7


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 TraesCS2A01G482000 chr2A 718877792 718880409 2617 False 4835.00 4835 100.00000 1 2618 1 chr2A.!!$F1 2617
1 TraesCS2A01G482000 chr2D 584624984 584626835 1851 False 453.40 1147 90.27120 24 1997 5 chr2D.!!$F1 1973
2 TraesCS2A01G482000 chr2B 704575338 704578032 2694 False 654.75 1099 87.52925 1 2552 4 chr2B.!!$F2 2551
3 TraesCS2A01G482000 chr3A 697520867 697521801 934 False 451.00 451 76.70500 778 1663 1 chr3A.!!$F1 885
4 TraesCS2A01G482000 chr7A 674114942 674115879 937 True 427.00 427 76.20500 778 1663 1 chr7A.!!$R4 885
5 TraesCS2A01G482000 chr7A 672597782 672598718 936 True 425.00 425 76.23000 778 1663 1 chr7A.!!$R3 885
6 TraesCS2A01G482000 chr3D 566131353 566132072 719 True 388.00 388 77.19500 596 1339 1 chr3D.!!$R2 743
7 TraesCS2A01G482000 chr3B 754719951 754720654 703 False 322.00 322 75.93100 609 1339 1 chr3B.!!$F1 730
8 TraesCS2A01G482000 chr3B 755709839 755710666 827 False 231.00 351 83.19800 595 1345 2 chr3B.!!$F3 750
9 TraesCS2A01G482000 chr5A 609822495 609823106 611 True 344.00 344 77.90100 778 1372 1 chr5A.!!$R1 594

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
439 483 0.037790 AACTGAGCTCGCCTGAACTC 60.038 55.0 9.64 0.0 37.75 3.01 F
631 702 0.042708 CGCGATTCATTCCAAGCTCG 60.043 55.0 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1760 0.097674 AAGCGCGAACTGATTGCATC 59.902 50.0 12.1 0.0 0.0 3.91 R
2031 2316 0.170339 GCCGACTTTCCCCATTTTCG 59.830 55.0 0.0 0.0 0.0 3.46 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
27 28 9.313118 GAGATGAGTTCCTAGATTTTCTTTCTC 57.687 37.037 0.00 0.00 0.00 2.87
43 44 4.857588 TCTTTCTCGCTTCAGTAATCGTTC 59.142 41.667 0.00 0.00 0.00 3.95
77 78 0.041312 CCTCCGTGTGTTTTCTTGCG 60.041 55.000 0.00 0.00 0.00 4.85
81 82 2.032377 TCCGTGTGTTTTCTTGCGAATC 60.032 45.455 0.00 0.00 0.00 2.52
83 84 2.286713 CGTGTGTTTTCTTGCGAATCCA 60.287 45.455 0.00 0.00 0.00 3.41
84 85 3.609175 CGTGTGTTTTCTTGCGAATCCAT 60.609 43.478 0.00 0.00 0.00 3.41
85 86 3.670055 GTGTGTTTTCTTGCGAATCCATG 59.330 43.478 0.00 0.00 0.00 3.66
86 87 3.567585 TGTGTTTTCTTGCGAATCCATGA 59.432 39.130 0.00 0.00 0.00 3.07
87 88 4.161333 GTGTTTTCTTGCGAATCCATGAG 58.839 43.478 0.00 0.00 0.00 2.90
88 89 3.174375 GTTTTCTTGCGAATCCATGAGC 58.826 45.455 0.00 0.00 0.00 4.26
89 90 2.408271 TTCTTGCGAATCCATGAGCT 57.592 45.000 0.00 0.00 0.00 4.09
90 91 1.660167 TCTTGCGAATCCATGAGCTG 58.340 50.000 0.00 0.00 0.00 4.24
118 119 2.265367 TCACTCAAGTAGCATCCCCAA 58.735 47.619 0.00 0.00 0.00 4.12
134 135 3.010472 TCCCCAATGCTTCAAGATCAAGA 59.990 43.478 0.00 0.00 0.00 3.02
221 225 1.676746 AAGCCTAGATGCATGCTGTG 58.323 50.000 20.33 4.65 33.59 3.66
223 227 0.465097 GCCTAGATGCATGCTGTGGT 60.465 55.000 20.33 1.60 0.00 4.16
224 228 1.306148 CCTAGATGCATGCTGTGGTG 58.694 55.000 20.33 4.84 0.00 4.17
226 230 0.253894 TAGATGCATGCTGTGGTGCT 59.746 50.000 20.33 7.80 41.78 4.40
227 231 0.611062 AGATGCATGCTGTGGTGCTT 60.611 50.000 20.33 0.00 41.78 3.91
228 232 0.179145 GATGCATGCTGTGGTGCTTC 60.179 55.000 20.33 0.00 41.78 3.86
229 233 0.896479 ATGCATGCTGTGGTGCTTCA 60.896 50.000 20.33 0.00 41.78 3.02
230 234 0.896479 TGCATGCTGTGGTGCTTCAT 60.896 50.000 20.33 0.00 41.78 2.57
231 235 0.457853 GCATGCTGTGGTGCTTCATG 60.458 55.000 11.37 0.00 38.30 3.07
233 237 0.251474 ATGCTGTGGTGCTTCATGGT 60.251 50.000 0.00 0.00 0.00 3.55
235 239 0.675633 GCTGTGGTGCTTCATGGTTT 59.324 50.000 0.00 0.00 0.00 3.27
236 240 1.069049 GCTGTGGTGCTTCATGGTTTT 59.931 47.619 0.00 0.00 0.00 2.43
237 241 2.295909 GCTGTGGTGCTTCATGGTTTTA 59.704 45.455 0.00 0.00 0.00 1.52
238 242 3.056607 GCTGTGGTGCTTCATGGTTTTAT 60.057 43.478 0.00 0.00 0.00 1.40
242 248 7.055667 TGTGGTGCTTCATGGTTTTATTTTA 57.944 32.000 0.00 0.00 0.00 1.52
249 255 9.213799 TGCTTCATGGTTTTATTTTATTTCCAC 57.786 29.630 0.00 0.00 0.00 4.02
266 272 4.281898 TCCACTCATCATCATGCCATAG 57.718 45.455 0.00 0.00 0.00 2.23
306 312 2.816087 TCTTAGATATACACCGCCGGAC 59.184 50.000 11.71 0.00 0.00 4.79
307 313 1.538047 TAGATATACACCGCCGGACC 58.462 55.000 11.71 0.00 0.00 4.46
308 314 1.080974 GATATACACCGCCGGACCG 60.081 63.158 11.71 6.99 0.00 4.79
381 425 2.173569 AGAAGCAGACCAAAACAGAGGT 59.826 45.455 0.00 0.00 41.83 3.85
389 433 5.180117 CAGACCAAAACAGAGGTGTAGATTG 59.820 44.000 0.00 0.00 38.50 2.67
438 482 0.320247 CAACTGAGCTCGCCTGAACT 60.320 55.000 9.64 0.00 0.00 3.01
439 483 0.037790 AACTGAGCTCGCCTGAACTC 60.038 55.000 9.64 0.00 37.75 3.01
443 487 1.599606 GAGCTCGCCTGAACTCTCCA 61.600 60.000 0.00 0.00 35.01 3.86
479 523 8.325046 ACTTCCTAGATTAGCTGATTTGTCTTT 58.675 33.333 0.00 0.00 0.00 2.52
487 531 2.098117 GCTGATTTGTCTTTCGATGGGG 59.902 50.000 0.00 0.00 0.00 4.96
488 532 2.091541 TGATTTGTCTTTCGATGGGGC 58.908 47.619 0.00 0.00 0.00 5.80
493 537 1.031571 GTCTTTCGATGGGGCATGCA 61.032 55.000 21.36 0.00 0.00 3.96
502 546 0.605860 TGGGGCATGCATGTTTTTGC 60.606 50.000 26.79 13.66 43.07 3.68
542 586 3.947834 GGATTCATGTTCAGGTAAGGTGG 59.052 47.826 0.00 0.00 0.00 4.61
548 592 2.706723 TGTTCAGGTAAGGTGGTTGCTA 59.293 45.455 0.00 0.00 0.00 3.49
564 608 4.154918 GGTTGCTACTGGAAATTGACTGAG 59.845 45.833 0.00 0.00 0.00 3.35
620 691 3.711814 TTGAGGGGCCGCGATTCA 61.712 61.111 15.00 10.16 0.00 2.57
631 702 0.042708 CGCGATTCATTCCAAGCTCG 60.043 55.000 0.00 0.00 0.00 5.03
643 714 4.537433 AGCTCGATTCCCGGCAGC 62.537 66.667 0.00 0.00 38.10 5.25
788 861 7.393515 ACCTACAGTTTTTCTTCCCATGATAAC 59.606 37.037 0.00 0.00 0.00 1.89
823 901 6.206829 GGATTGTTAAACTTAGGCTCTGTGTT 59.793 38.462 0.00 0.00 0.00 3.32
836 914 2.549754 CTCTGTGTTCCAACATGTGACC 59.450 50.000 0.00 0.00 41.59 4.02
854 937 4.158764 GTGACCTGTCTTGACTGCTAGTAT 59.841 45.833 2.35 0.00 0.00 2.12
856 939 5.357314 TGACCTGTCTTGACTGCTAGTATAC 59.643 44.000 0.00 0.00 0.00 1.47
927 1020 7.038048 TGAGACTATGAACTGCATAAGTCTTG 58.962 38.462 11.55 0.00 42.00 3.02
930 1023 7.547370 AGACTATGAACTGCATAAGTCTTGAAC 59.453 37.037 0.00 0.00 40.74 3.18
977 1076 0.463654 TGCAGGAGCTCGTTGTGTTT 60.464 50.000 6.10 0.00 42.74 2.83
1107 1217 6.782986 TCTGAGGAATGAAAAGGATCTTCAA 58.217 36.000 0.53 0.00 36.43 2.69
1220 1330 1.734117 GAAAGCATGCACCGCAACC 60.734 57.895 21.98 0.00 43.62 3.77
1221 1331 3.556543 AAAGCATGCACCGCAACCG 62.557 57.895 21.98 0.00 43.62 4.44
1224 1334 4.340019 CATGCACCGCAACCGCAA 62.340 61.111 0.00 0.00 43.62 4.85
1225 1335 3.372730 ATGCACCGCAACCGCAAT 61.373 55.556 0.00 0.00 43.62 3.56
1239 1349 3.016736 ACCGCAATAATTGAACCCAGAG 58.983 45.455 0.00 0.00 0.00 3.35
1244 1354 5.345741 CGCAATAATTGAACCCAGAGTTTTG 59.654 40.000 0.00 0.00 39.40 2.44
1252 1362 6.573664 TGAACCCAGAGTTTTGTATCAATG 57.426 37.500 0.00 0.00 39.40 2.82
1273 1485 9.349713 TCAATGTGTTAGTTCTTAGGAAAACAT 57.650 29.630 7.77 3.08 35.78 2.71
1350 1563 8.319057 TGCCTCACTTTAAGAGAATAGGATAA 57.681 34.615 0.00 0.00 35.09 1.75
1351 1564 8.938883 TGCCTCACTTTAAGAGAATAGGATAAT 58.061 33.333 0.00 0.00 35.09 1.28
1514 1760 4.410400 GGGGTTCTCGTGGCTGGG 62.410 72.222 0.00 0.00 0.00 4.45
1515 1761 3.319198 GGGTTCTCGTGGCTGGGA 61.319 66.667 0.00 0.00 0.00 4.37
1542 1788 3.039588 TTCGCGCTTTCGGTCACC 61.040 61.111 5.56 0.00 35.95 4.02
1670 1921 2.413796 CGTCGTGCTAATTGCCAGTTAA 59.586 45.455 0.00 0.00 42.00 2.01
1713 1998 6.398234 TTTAAAGTGCTAATTGCCAGTCAA 57.602 33.333 0.00 0.00 42.00 3.18
1717 2002 3.019564 GTGCTAATTGCCAGTCAAGGAT 58.980 45.455 0.00 0.00 42.00 3.24
1733 2018 6.013379 AGTCAAGGATGGTAAATCAGTTCAGA 60.013 38.462 0.00 0.00 0.00 3.27
1758 2043 1.953559 TGTGCTCAGGACACTTGTTC 58.046 50.000 0.00 0.00 38.86 3.18
1759 2044 1.209261 TGTGCTCAGGACACTTGTTCA 59.791 47.619 0.00 0.00 38.86 3.18
1761 2046 2.481952 GTGCTCAGGACACTTGTTCATC 59.518 50.000 0.00 0.00 35.12 2.92
1762 2047 2.104622 TGCTCAGGACACTTGTTCATCA 59.895 45.455 0.00 0.00 0.00 3.07
1763 2048 2.481952 GCTCAGGACACTTGTTCATCAC 59.518 50.000 0.00 0.00 0.00 3.06
1764 2049 3.070018 CTCAGGACACTTGTTCATCACC 58.930 50.000 0.00 0.00 0.00 4.02
1765 2050 1.800586 CAGGACACTTGTTCATCACCG 59.199 52.381 0.00 0.00 0.00 4.94
1766 2051 1.416401 AGGACACTTGTTCATCACCGT 59.584 47.619 0.00 0.00 0.00 4.83
1767 2052 1.798813 GGACACTTGTTCATCACCGTC 59.201 52.381 0.00 0.00 0.00 4.79
1768 2053 1.455786 GACACTTGTTCATCACCGTCG 59.544 52.381 0.00 0.00 0.00 5.12
1769 2054 0.163788 CACTTGTTCATCACCGTCGC 59.836 55.000 0.00 0.00 0.00 5.19
1770 2055 1.282248 ACTTGTTCATCACCGTCGCG 61.282 55.000 0.00 0.00 0.00 5.87
1771 2056 1.282248 CTTGTTCATCACCGTCGCGT 61.282 55.000 5.77 0.00 0.00 6.01
1772 2057 1.279527 TTGTTCATCACCGTCGCGTC 61.280 55.000 5.77 0.00 0.00 5.19
1773 2058 2.503158 TTCATCACCGTCGCGTCG 60.503 61.111 18.65 18.65 0.00 5.12
1774 2059 3.258070 TTCATCACCGTCGCGTCGT 62.258 57.895 23.01 9.60 0.00 4.34
1775 2060 3.532792 CATCACCGTCGCGTCGTG 61.533 66.667 23.01 19.50 0.00 4.35
1778 2063 4.746951 CACCGTCGCGTCGTGCTA 62.747 66.667 23.01 0.00 43.27 3.49
1779 2064 4.029186 ACCGTCGCGTCGTGCTAA 62.029 61.111 23.01 0.00 43.27 3.09
1780 2065 2.578713 CCGTCGCGTCGTGCTAAT 60.579 61.111 23.01 0.00 43.27 1.73
1781 2066 2.156446 CCGTCGCGTCGTGCTAATT 61.156 57.895 23.01 0.00 43.27 1.40
1782 2067 1.014825 CGTCGCGTCGTGCTAATTG 60.015 57.895 17.43 0.00 43.27 2.32
1783 2068 1.295930 GTCGCGTCGTGCTAATTGC 60.296 57.895 5.77 0.00 43.27 3.56
1784 2069 2.021380 CGCGTCGTGCTAATTGCC 59.979 61.111 0.00 0.00 43.27 4.52
1785 2070 2.021380 GCGTCGTGCTAATTGCCG 59.979 61.111 0.00 0.00 42.00 5.69
1808 2093 2.467566 AGATTTCAGTTACCGGCGTT 57.532 45.000 6.01 0.00 0.00 4.84
1858 2143 5.048294 TGTCTGATAGCGTGTCTTCAGTTAA 60.048 40.000 0.00 0.00 37.46 2.01
1885 2170 9.662947 GTGGAATAGTTACTGTTTAGGTAATGT 57.337 33.333 0.00 0.00 32.78 2.71
1886 2171 9.661563 TGGAATAGTTACTGTTTAGGTAATGTG 57.338 33.333 0.00 0.00 32.78 3.21
1887 2172 9.106070 GGAATAGTTACTGTTTAGGTAATGTGG 57.894 37.037 0.00 0.00 32.78 4.17
1888 2173 9.880157 GAATAGTTACTGTTTAGGTAATGTGGA 57.120 33.333 0.00 0.00 32.78 4.02
1890 2175 9.886132 ATAGTTACTGTTTAGGTAATGTGGAAG 57.114 33.333 0.00 0.00 32.78 3.46
1942 2227 2.287849 GCTCCAAGTGGCTTTTGTCTTC 60.288 50.000 0.00 0.00 34.44 2.87
1997 2282 2.619646 GGAGTAGAGTACCAGTAGCAGC 59.380 54.545 0.00 0.00 0.00 5.25
1998 2283 2.619646 GAGTAGAGTACCAGTAGCAGCC 59.380 54.545 0.00 0.00 0.00 4.85
1999 2284 2.242708 AGTAGAGTACCAGTAGCAGCCT 59.757 50.000 0.00 0.00 0.00 4.58
2000 2285 3.458857 AGTAGAGTACCAGTAGCAGCCTA 59.541 47.826 0.00 0.00 0.00 3.93
2001 2286 2.938838 AGAGTACCAGTAGCAGCCTAG 58.061 52.381 0.00 0.00 0.00 3.02
2004 2289 1.067821 GTACCAGTAGCAGCCTAGCAG 59.932 57.143 0.00 0.00 36.85 4.24
2005 2290 1.333636 ACCAGTAGCAGCCTAGCAGG 61.334 60.000 0.00 0.00 38.80 4.85
2006 2291 1.333636 CCAGTAGCAGCCTAGCAGGT 61.334 60.000 4.45 0.00 37.80 4.00
2008 2293 1.339610 CAGTAGCAGCCTAGCAGGTAG 59.660 57.143 0.00 0.00 37.80 3.18
2009 2294 1.063567 AGTAGCAGCCTAGCAGGTAGT 60.064 52.381 5.91 0.00 37.80 2.73
2010 2295 2.175069 AGTAGCAGCCTAGCAGGTAGTA 59.825 50.000 5.91 0.00 37.80 1.82
2011 2296 1.404843 AGCAGCCTAGCAGGTAGTAC 58.595 55.000 5.91 0.00 37.80 2.73
2012 2297 1.112113 GCAGCCTAGCAGGTAGTACA 58.888 55.000 5.91 0.00 37.80 2.90
2013 2298 1.202428 GCAGCCTAGCAGGTAGTACAC 60.202 57.143 5.91 0.00 37.80 2.90
2014 2299 2.100197 CAGCCTAGCAGGTAGTACACA 58.900 52.381 5.91 0.00 37.80 3.72
2015 2300 2.099921 CAGCCTAGCAGGTAGTACACAG 59.900 54.545 5.91 0.00 37.80 3.66
2016 2301 2.025226 AGCCTAGCAGGTAGTACACAGA 60.025 50.000 5.91 0.00 37.80 3.41
2017 2302 2.359531 GCCTAGCAGGTAGTACACAGAG 59.640 54.545 5.91 0.00 37.80 3.35
2018 2303 3.887352 CCTAGCAGGTAGTACACAGAGA 58.113 50.000 5.91 0.00 0.00 3.10
2019 2304 4.270834 CCTAGCAGGTAGTACACAGAGAA 58.729 47.826 5.91 0.00 0.00 2.87
2020 2305 4.096682 CCTAGCAGGTAGTACACAGAGAAC 59.903 50.000 5.91 0.00 0.00 3.01
2021 2306 2.488545 AGCAGGTAGTACACAGAGAACG 59.511 50.000 2.06 0.00 0.00 3.95
2022 2307 2.415625 GCAGGTAGTACACAGAGAACGG 60.416 54.545 2.06 0.00 0.00 4.44
2023 2308 3.079578 CAGGTAGTACACAGAGAACGGA 58.920 50.000 2.06 0.00 0.00 4.69
2024 2309 3.695060 CAGGTAGTACACAGAGAACGGAT 59.305 47.826 2.06 0.00 0.00 4.18
2025 2310 3.946558 AGGTAGTACACAGAGAACGGATC 59.053 47.826 2.06 0.00 0.00 3.36
2026 2311 3.693085 GGTAGTACACAGAGAACGGATCA 59.307 47.826 2.06 0.00 0.00 2.92
2027 2312 4.157289 GGTAGTACACAGAGAACGGATCAA 59.843 45.833 2.06 0.00 0.00 2.57
2028 2313 4.866508 AGTACACAGAGAACGGATCAAA 57.133 40.909 0.00 0.00 0.00 2.69
2029 2314 5.209818 AGTACACAGAGAACGGATCAAAA 57.790 39.130 0.00 0.00 0.00 2.44
2030 2315 5.607477 AGTACACAGAGAACGGATCAAAAA 58.393 37.500 0.00 0.00 0.00 1.94
2031 2316 4.813296 ACACAGAGAACGGATCAAAAAC 57.187 40.909 0.00 0.00 0.00 2.43
2032 2317 3.247648 ACACAGAGAACGGATCAAAAACG 59.752 43.478 0.00 0.00 0.00 3.60
2033 2318 3.493129 CACAGAGAACGGATCAAAAACGA 59.507 43.478 0.00 0.00 0.00 3.85
2034 2319 4.025229 CACAGAGAACGGATCAAAAACGAA 60.025 41.667 0.00 0.00 0.00 3.85
2035 2320 4.573201 ACAGAGAACGGATCAAAAACGAAA 59.427 37.500 0.00 0.00 0.00 3.46
2036 2321 5.065474 ACAGAGAACGGATCAAAAACGAAAA 59.935 36.000 0.00 0.00 0.00 2.29
2037 2322 6.142817 CAGAGAACGGATCAAAAACGAAAAT 58.857 36.000 0.00 0.00 0.00 1.82
2046 2331 5.346181 TCAAAAACGAAAATGGGGAAAGT 57.654 34.783 0.00 0.00 0.00 2.66
2091 2376 3.806949 ACCTGCTTTGGGTTGAAGATA 57.193 42.857 0.00 0.00 32.46 1.98
2096 2381 4.517285 TGCTTTGGGTTGAAGATAGCTAG 58.483 43.478 0.00 0.00 0.00 3.42
2098 2383 4.813697 GCTTTGGGTTGAAGATAGCTAGAG 59.186 45.833 0.00 0.00 0.00 2.43
2114 2399 6.172350 AGCTAGAGGGAGGGATTCATATAA 57.828 41.667 0.00 0.00 0.00 0.98
2115 2400 6.201591 AGCTAGAGGGAGGGATTCATATAAG 58.798 44.000 0.00 0.00 0.00 1.73
2116 2401 5.961421 GCTAGAGGGAGGGATTCATATAAGT 59.039 44.000 0.00 0.00 0.00 2.24
2118 2403 5.020132 AGAGGGAGGGATTCATATAAGTCG 58.980 45.833 0.00 0.00 0.00 4.18
2172 2719 3.618594 CAGGGAATTCCATATATGTCGCG 59.381 47.826 25.67 0.00 38.24 5.87
2231 2778 0.861837 CGAGCGAATGAGTTATGGGC 59.138 55.000 0.00 0.00 0.00 5.36
2256 2803 1.120147 CATTTGTACAACGCGAGCGC 61.120 55.000 15.93 8.99 44.19 5.92
2357 2906 5.163416 CCTGATGTTTCTTCCACTGGTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
2474 3023 9.741647 AAAAATGTTTGTGCTTTTCAAGAAAAA 57.258 22.222 9.05 0.00 39.49 1.94
2490 3039 9.444534 TTCAAGAAAAAGCAAAACTTCAAAAAC 57.555 25.926 0.00 0.00 37.75 2.43
2500 3050 8.691797 AGCAAAACTTCAAAAACTGTTCCTATA 58.308 29.630 0.00 0.00 0.00 1.31
2557 3107 7.964545 AAATCGCGTATTCAAAAAGTATTCC 57.035 32.000 5.77 0.00 0.00 3.01
2558 3108 5.133707 TCGCGTATTCAAAAAGTATTCCG 57.866 39.130 5.77 0.00 0.00 4.30
2559 3109 4.863689 TCGCGTATTCAAAAAGTATTCCGA 59.136 37.500 5.77 0.00 0.00 4.55
2560 3110 5.005012 TCGCGTATTCAAAAAGTATTCCGAG 59.995 40.000 5.77 0.00 0.00 4.63
2561 3111 5.220340 CGCGTATTCAAAAAGTATTCCGAGT 60.220 40.000 0.00 0.00 0.00 4.18
2562 3112 6.020440 CGCGTATTCAAAAAGTATTCCGAGTA 60.020 38.462 0.00 0.00 0.00 2.59
2563 3113 7.306399 CGCGTATTCAAAAAGTATTCCGAGTAT 60.306 37.037 0.00 0.00 0.00 2.12
2564 3114 8.333186 GCGTATTCAAAAAGTATTCCGAGTATT 58.667 33.333 0.00 0.00 0.00 1.89
2565 3115 9.632969 CGTATTCAAAAAGTATTCCGAGTATTG 57.367 33.333 0.00 0.00 0.00 1.90
2566 3116 9.931210 GTATTCAAAAAGTATTCCGAGTATTGG 57.069 33.333 0.00 0.00 42.86 3.16
2575 3125 2.386661 CCGAGTATTGGAACAGCTGT 57.613 50.000 15.25 15.25 45.05 4.40
2576 3126 3.520290 CCGAGTATTGGAACAGCTGTA 57.480 47.619 22.01 4.30 45.05 2.74
2577 3127 3.187700 CCGAGTATTGGAACAGCTGTAC 58.812 50.000 22.01 16.73 45.05 2.90
2578 3128 3.119101 CCGAGTATTGGAACAGCTGTACT 60.119 47.826 22.01 18.40 45.05 2.73
2579 3129 4.106197 CGAGTATTGGAACAGCTGTACTC 58.894 47.826 25.39 25.39 42.39 2.59
2580 3130 4.434520 GAGTATTGGAACAGCTGTACTCC 58.565 47.826 24.90 24.90 42.39 3.85
2581 3131 2.386661 ATTGGAACAGCTGTACTCCG 57.613 50.000 25.51 0.00 42.39 4.63
2582 3132 1.334160 TTGGAACAGCTGTACTCCGA 58.666 50.000 25.51 22.71 42.39 4.55
2583 3133 0.888619 TGGAACAGCTGTACTCCGAG 59.111 55.000 25.51 0.00 29.60 4.63
2584 3134 0.889306 GGAACAGCTGTACTCCGAGT 59.111 55.000 22.01 6.25 0.00 4.18
2585 3135 2.089980 GGAACAGCTGTACTCCGAGTA 58.910 52.381 22.01 4.01 0.00 2.59
2586 3136 6.109280 TTGGAACAGCTGTACTCCGAGTAC 62.109 50.000 25.51 25.77 45.44 2.73
2595 3145 4.808077 GTACTCCGAGTACGAATCATCA 57.192 45.455 20.28 0.00 41.27 3.07
2596 3146 3.694535 ACTCCGAGTACGAATCATCAC 57.305 47.619 0.00 0.00 42.66 3.06
2597 3147 3.280295 ACTCCGAGTACGAATCATCACT 58.720 45.455 0.00 0.00 42.66 3.41
2598 3148 3.695060 ACTCCGAGTACGAATCATCACTT 59.305 43.478 0.00 0.00 42.66 3.16
2599 3149 4.158025 ACTCCGAGTACGAATCATCACTTT 59.842 41.667 0.00 0.00 42.66 2.66
2600 3150 4.421058 TCCGAGTACGAATCATCACTTTG 58.579 43.478 0.00 0.00 42.66 2.77
2601 3151 3.551890 CCGAGTACGAATCATCACTTTGG 59.448 47.826 0.00 0.00 42.66 3.28
2602 3152 4.174009 CGAGTACGAATCATCACTTTGGT 58.826 43.478 0.00 0.00 42.66 3.67
2603 3153 4.031765 CGAGTACGAATCATCACTTTGGTG 59.968 45.833 0.00 0.00 42.18 4.17
2604 3154 3.684788 AGTACGAATCATCACTTTGGTGC 59.315 43.478 0.00 0.00 42.72 5.01
2605 3155 2.503331 ACGAATCATCACTTTGGTGCA 58.497 42.857 0.00 0.00 42.72 4.57
2606 3156 2.485426 ACGAATCATCACTTTGGTGCAG 59.515 45.455 0.00 0.00 42.72 4.41
2607 3157 2.485426 CGAATCATCACTTTGGTGCAGT 59.515 45.455 0.00 0.00 42.72 4.40
2608 3158 3.058016 CGAATCATCACTTTGGTGCAGTT 60.058 43.478 0.00 0.00 42.72 3.16
2609 3159 3.928727 ATCATCACTTTGGTGCAGTTG 57.071 42.857 0.00 0.00 42.72 3.16
2610 3160 2.653726 TCATCACTTTGGTGCAGTTGT 58.346 42.857 0.00 0.00 42.72 3.32
2611 3161 3.814625 TCATCACTTTGGTGCAGTTGTA 58.185 40.909 0.00 0.00 42.72 2.41
2612 3162 3.814842 TCATCACTTTGGTGCAGTTGTAG 59.185 43.478 0.00 0.00 42.72 2.74
2613 3163 3.275617 TCACTTTGGTGCAGTTGTAGT 57.724 42.857 0.00 0.00 42.72 2.73
2614 3164 3.202906 TCACTTTGGTGCAGTTGTAGTC 58.797 45.455 0.00 0.00 42.72 2.59
2615 3165 3.118408 TCACTTTGGTGCAGTTGTAGTCT 60.118 43.478 0.00 0.00 42.72 3.24
2616 3166 3.002656 CACTTTGGTGCAGTTGTAGTCTG 59.997 47.826 0.00 0.00 36.61 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 7.934855 AAGTAACATCTTGATCTTGAAGCAT 57.065 32.000 0.00 0.00 0.00 3.79
134 135 9.965824 CTCTGAATTTTACAACCAAAGTAACAT 57.034 29.630 0.00 0.00 31.67 2.71
221 225 8.664798 GGAAATAAAATAAAACCATGAAGCACC 58.335 33.333 0.00 0.00 0.00 5.01
223 227 9.213799 GTGGAAATAAAATAAAACCATGAAGCA 57.786 29.630 0.00 0.00 0.00 3.91
224 228 9.435688 AGTGGAAATAAAATAAAACCATGAAGC 57.564 29.630 0.00 0.00 0.00 3.86
235 239 9.970395 GCATGATGATGAGTGGAAATAAAATAA 57.030 29.630 0.00 0.00 0.00 1.40
236 240 8.579006 GGCATGATGATGAGTGGAAATAAAATA 58.421 33.333 0.00 0.00 0.00 1.40
237 241 7.070198 TGGCATGATGATGAGTGGAAATAAAAT 59.930 33.333 0.00 0.00 0.00 1.82
238 242 6.380560 TGGCATGATGATGAGTGGAAATAAAA 59.619 34.615 0.00 0.00 0.00 1.52
242 248 3.905968 TGGCATGATGATGAGTGGAAAT 58.094 40.909 0.00 0.00 0.00 2.17
249 255 6.655425 AGTGATTTCTATGGCATGATGATGAG 59.345 38.462 10.98 0.00 0.00 2.90
253 259 4.517832 GCAGTGATTTCTATGGCATGATGA 59.482 41.667 10.98 2.92 0.00 2.92
266 272 8.225603 TCTAAGATAAATTGGGCAGTGATTTC 57.774 34.615 0.00 0.00 0.00 2.17
381 425 8.581253 TCTACTCTTCAAGTGATCAATCTACA 57.419 34.615 0.00 0.00 39.11 2.74
389 433 8.470805 TGTCCTTTATCTACTCTTCAAGTGATC 58.529 37.037 0.00 0.00 39.11 2.92
438 482 3.784178 AGGAAGTGAGACTGAATGGAGA 58.216 45.455 0.00 0.00 0.00 3.71
439 483 4.952957 TCTAGGAAGTGAGACTGAATGGAG 59.047 45.833 0.00 0.00 0.00 3.86
443 487 6.838612 AGCTAATCTAGGAAGTGAGACTGAAT 59.161 38.462 0.00 0.00 0.00 2.57
449 493 7.124901 ACAAATCAGCTAATCTAGGAAGTGAGA 59.875 37.037 0.00 0.00 0.00 3.27
479 523 0.683828 AAACATGCATGCCCCATCGA 60.684 50.000 26.53 0.00 0.00 3.59
493 537 1.270465 GGGCAGCTTCAGCAAAAACAT 60.270 47.619 0.75 0.00 45.16 2.71
502 546 0.393537 CCTTGGTAGGGCAGCTTCAG 60.394 60.000 0.00 0.00 37.94 3.02
542 586 4.997395 TCTCAGTCAATTTCCAGTAGCAAC 59.003 41.667 0.00 0.00 0.00 4.17
548 592 6.774656 AGTTCAATTCTCAGTCAATTTCCAGT 59.225 34.615 0.00 0.00 0.00 4.00
564 608 3.003275 TCACACCAAGCGAAGTTCAATTC 59.997 43.478 3.32 0.00 0.00 2.17
614 685 3.059325 GGAATCGAGCTTGGAATGAATCG 60.059 47.826 0.00 0.00 0.00 3.34
620 691 0.179045 CCGGGAATCGAGCTTGGAAT 60.179 55.000 0.00 0.00 42.43 3.01
631 702 2.830370 CCCTTGCTGCCGGGAATC 60.830 66.667 16.60 0.00 43.44 2.52
823 901 2.437651 TCAAGACAGGTCACATGTTGGA 59.562 45.455 0.00 0.00 0.00 3.53
836 914 5.163744 ACACGTATACTAGCAGTCAAGACAG 60.164 44.000 0.56 0.00 0.00 3.51
854 937 4.710695 CGCTCACCGGCACACGTA 62.711 66.667 0.00 0.00 42.24 3.57
927 1020 4.856664 TCTGAAGAGTAGTCAACACGTTC 58.143 43.478 0.00 0.00 0.00 3.95
930 1023 5.388890 GCAATTCTGAAGAGTAGTCAACACG 60.389 44.000 0.00 0.00 0.00 4.49
977 1076 2.143008 ACACGCGTTAGTTGATGTCA 57.857 45.000 10.22 0.00 0.00 3.58
1220 1330 4.701956 AACTCTGGGTTCAATTATTGCG 57.298 40.909 0.00 0.00 31.69 4.85
1221 1331 6.223120 ACAAAACTCTGGGTTCAATTATTGC 58.777 36.000 0.00 0.00 37.12 3.56
1222 1332 9.573133 GATACAAAACTCTGGGTTCAATTATTG 57.427 33.333 0.00 0.00 37.12 1.90
1223 1333 9.308000 TGATACAAAACTCTGGGTTCAATTATT 57.692 29.630 0.00 0.00 37.12 1.40
1224 1334 8.877864 TGATACAAAACTCTGGGTTCAATTAT 57.122 30.769 0.00 0.00 37.12 1.28
1225 1335 8.698973 TTGATACAAAACTCTGGGTTCAATTA 57.301 30.769 0.00 0.00 37.12 1.40
1273 1485 7.988737 CATGAGTTGCACTTATCCTGAATTTA 58.011 34.615 0.00 0.00 0.00 1.40
1350 1563 6.819397 GGCAACAAGTCTCTTTAAGGTTAT 57.181 37.500 0.00 0.00 0.00 1.89
1379 1592 5.910614 TCACAATGTGATCACTCAGATAGG 58.089 41.667 25.55 9.80 37.67 2.57
1514 1760 0.097674 AAGCGCGAACTGATTGCATC 59.902 50.000 12.10 0.00 0.00 3.91
1515 1761 0.523072 AAAGCGCGAACTGATTGCAT 59.477 45.000 12.10 0.00 0.00 3.96
1542 1788 0.677731 ACCACGTGATGAATGCCAGG 60.678 55.000 19.30 0.00 0.00 4.45
1713 1998 5.128919 GCATCTGAACTGATTTACCATCCT 58.871 41.667 0.00 0.00 0.00 3.24
1717 2002 5.711506 ACATTGCATCTGAACTGATTTACCA 59.288 36.000 3.97 0.00 0.00 3.25
1758 2043 3.532792 CACGACGCGACGGTGATG 61.533 66.667 31.73 18.48 37.61 3.07
1775 2060 4.335594 ACTGAAATCTAACCGGCAATTAGC 59.664 41.667 0.00 0.00 44.65 3.09
1776 2061 6.436843 AACTGAAATCTAACCGGCAATTAG 57.563 37.500 0.00 2.17 0.00 1.73
1777 2062 6.316890 GGTAACTGAAATCTAACCGGCAATTA 59.683 38.462 0.00 0.00 0.00 1.40
1778 2063 5.124936 GGTAACTGAAATCTAACCGGCAATT 59.875 40.000 0.00 0.00 0.00 2.32
1779 2064 4.638865 GGTAACTGAAATCTAACCGGCAAT 59.361 41.667 0.00 0.00 0.00 3.56
1780 2065 4.004982 GGTAACTGAAATCTAACCGGCAA 58.995 43.478 0.00 0.00 0.00 4.52
1781 2066 3.602483 GGTAACTGAAATCTAACCGGCA 58.398 45.455 0.00 0.00 0.00 5.69
1782 2067 2.606272 CGGTAACTGAAATCTAACCGGC 59.394 50.000 0.00 0.00 44.59 6.13
1785 2070 2.606272 CGCCGGTAACTGAAATCTAACC 59.394 50.000 1.90 0.00 0.00 2.85
1808 2093 7.785033 TGCAGTCTATCAATAAGTGATGAAGA 58.215 34.615 0.67 0.00 46.85 2.87
1845 2130 7.964604 AACTATTCCACTTAACTGAAGACAC 57.035 36.000 0.00 0.00 38.65 3.67
1858 2143 9.886132 CATTACCTAAACAGTAACTATTCCACT 57.114 33.333 0.00 0.00 32.77 4.00
1890 2175 3.821033 GCACCCCATATTAGTGATTCCAC 59.179 47.826 0.00 0.00 43.50 4.02
1911 2196 2.565841 CCACTTGGAGCACTAATAGGC 58.434 52.381 0.00 0.00 37.39 3.93
1997 2282 3.887352 TCTCTGTGTACTACCTGCTAGG 58.113 50.000 0.00 1.16 42.49 3.02
1998 2283 4.201832 CGTTCTCTGTGTACTACCTGCTAG 60.202 50.000 0.00 0.00 0.00 3.42
1999 2284 3.688185 CGTTCTCTGTGTACTACCTGCTA 59.312 47.826 0.00 0.00 0.00 3.49
2000 2285 2.488545 CGTTCTCTGTGTACTACCTGCT 59.511 50.000 0.00 0.00 0.00 4.24
2001 2286 2.415625 CCGTTCTCTGTGTACTACCTGC 60.416 54.545 0.00 0.00 0.00 4.85
2004 2289 3.693085 TGATCCGTTCTCTGTGTACTACC 59.307 47.826 0.00 0.00 0.00 3.18
2005 2290 4.959596 TGATCCGTTCTCTGTGTACTAC 57.040 45.455 0.00 0.00 0.00 2.73
2006 2291 5.970317 TTTGATCCGTTCTCTGTGTACTA 57.030 39.130 0.00 0.00 0.00 1.82
2008 2293 5.611844 CGTTTTTGATCCGTTCTCTGTGTAC 60.612 44.000 0.00 0.00 0.00 2.90
2009 2294 4.446385 CGTTTTTGATCCGTTCTCTGTGTA 59.554 41.667 0.00 0.00 0.00 2.90
2010 2295 3.247648 CGTTTTTGATCCGTTCTCTGTGT 59.752 43.478 0.00 0.00 0.00 3.72
2011 2296 3.493129 TCGTTTTTGATCCGTTCTCTGTG 59.507 43.478 0.00 0.00 0.00 3.66
2012 2297 3.724374 TCGTTTTTGATCCGTTCTCTGT 58.276 40.909 0.00 0.00 0.00 3.41
2013 2298 4.725556 TTCGTTTTTGATCCGTTCTCTG 57.274 40.909 0.00 0.00 0.00 3.35
2014 2299 5.744666 TTTTCGTTTTTGATCCGTTCTCT 57.255 34.783 0.00 0.00 0.00 3.10
2015 2300 5.342259 CCATTTTCGTTTTTGATCCGTTCTC 59.658 40.000 0.00 0.00 0.00 2.87
2016 2301 5.219633 CCATTTTCGTTTTTGATCCGTTCT 58.780 37.500 0.00 0.00 0.00 3.01
2017 2302 4.384547 CCCATTTTCGTTTTTGATCCGTTC 59.615 41.667 0.00 0.00 0.00 3.95
2018 2303 4.303282 CCCATTTTCGTTTTTGATCCGTT 58.697 39.130 0.00 0.00 0.00 4.44
2019 2304 3.305744 CCCCATTTTCGTTTTTGATCCGT 60.306 43.478 0.00 0.00 0.00 4.69
2020 2305 3.057174 TCCCCATTTTCGTTTTTGATCCG 60.057 43.478 0.00 0.00 0.00 4.18
2021 2306 4.529109 TCCCCATTTTCGTTTTTGATCC 57.471 40.909 0.00 0.00 0.00 3.36
2022 2307 5.989168 ACTTTCCCCATTTTCGTTTTTGATC 59.011 36.000 0.00 0.00 0.00 2.92
2023 2308 5.924356 ACTTTCCCCATTTTCGTTTTTGAT 58.076 33.333 0.00 0.00 0.00 2.57
2024 2309 5.346181 ACTTTCCCCATTTTCGTTTTTGA 57.654 34.783 0.00 0.00 0.00 2.69
2025 2310 4.208253 CGACTTTCCCCATTTTCGTTTTTG 59.792 41.667 0.00 0.00 0.00 2.44
2026 2311 4.364860 CGACTTTCCCCATTTTCGTTTTT 58.635 39.130 0.00 0.00 0.00 1.94
2027 2312 3.243602 CCGACTTTCCCCATTTTCGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
2028 2313 2.295070 CCGACTTTCCCCATTTTCGTTT 59.705 45.455 0.00 0.00 0.00 3.60
2029 2314 1.883926 CCGACTTTCCCCATTTTCGTT 59.116 47.619 0.00 0.00 0.00 3.85
2030 2315 1.530323 CCGACTTTCCCCATTTTCGT 58.470 50.000 0.00 0.00 0.00 3.85
2031 2316 0.170339 GCCGACTTTCCCCATTTTCG 59.830 55.000 0.00 0.00 0.00 3.46
2032 2317 0.170339 CGCCGACTTTCCCCATTTTC 59.830 55.000 0.00 0.00 0.00 2.29
2033 2318 1.248101 CCGCCGACTTTCCCCATTTT 61.248 55.000 0.00 0.00 0.00 1.82
2034 2319 1.677633 CCGCCGACTTTCCCCATTT 60.678 57.895 0.00 0.00 0.00 2.32
2035 2320 2.045340 CCGCCGACTTTCCCCATT 60.045 61.111 0.00 0.00 0.00 3.16
2036 2321 3.327404 ACCGCCGACTTTCCCCAT 61.327 61.111 0.00 0.00 0.00 4.00
2037 2322 4.323477 CACCGCCGACTTTCCCCA 62.323 66.667 0.00 0.00 0.00 4.96
2065 2350 1.699730 AACCCAAAGCAGGTTGTACC 58.300 50.000 0.00 0.00 45.93 3.34
2074 2359 3.439857 AGCTATCTTCAACCCAAAGCA 57.560 42.857 0.00 0.00 0.00 3.91
2091 2376 4.708420 ATATGAATCCCTCCCTCTAGCT 57.292 45.455 0.00 0.00 0.00 3.32
2096 2381 4.773149 ACGACTTATATGAATCCCTCCCTC 59.227 45.833 0.00 0.00 0.00 4.30
2098 2383 6.793505 ATACGACTTATATGAATCCCTCCC 57.206 41.667 0.00 0.00 0.00 4.30
2114 2399 5.220586 CGCCATTTTGTCACATAATACGACT 60.221 40.000 8.84 0.00 0.00 4.18
2115 2400 4.961551 CGCCATTTTGTCACATAATACGAC 59.038 41.667 8.84 0.00 0.00 4.34
2116 2401 4.870991 TCGCCATTTTGTCACATAATACGA 59.129 37.500 11.65 11.65 0.00 3.43
2118 2403 5.874831 TGTCGCCATTTTGTCACATAATAC 58.125 37.500 0.00 0.00 0.00 1.89
2172 2719 0.237235 TCGCCATTTTGTCGCAGAAC 59.763 50.000 0.00 0.00 39.69 3.01
2231 2778 1.511043 CGTTGTACAAATGCGCCGG 60.511 57.895 10.51 0.00 0.00 6.13
2256 2803 0.368907 CCAAAACGGATCGCGTACTG 59.631 55.000 5.77 9.24 36.56 2.74
2318 2866 3.823304 ACATCAGGAAAGAGAAAACCAGC 59.177 43.478 0.00 0.00 0.00 4.85
2449 2998 9.396938 CTTTTTCTTGAAAAGCACAAACATTTT 57.603 25.926 8.29 0.00 45.43 1.82
2464 3013 9.444534 GTTTTTGAAGTTTTGCTTTTTCTTGAA 57.555 25.926 0.00 0.00 37.59 2.69
2465 3014 8.835439 AGTTTTTGAAGTTTTGCTTTTTCTTGA 58.165 25.926 0.00 0.00 37.59 3.02
2466 3015 8.894864 CAGTTTTTGAAGTTTTGCTTTTTCTTG 58.105 29.630 0.00 0.00 37.59 3.02
2469 3018 8.781067 AACAGTTTTTGAAGTTTTGCTTTTTC 57.219 26.923 0.00 0.00 37.59 2.29
2471 3020 7.228507 AGGAACAGTTTTTGAAGTTTTGCTTTT 59.771 29.630 0.00 0.00 37.59 2.27
2472 3021 6.710295 AGGAACAGTTTTTGAAGTTTTGCTTT 59.290 30.769 0.00 0.00 37.59 3.51
2473 3022 6.230472 AGGAACAGTTTTTGAAGTTTTGCTT 58.770 32.000 0.00 0.00 40.76 3.91
2474 3023 5.793817 AGGAACAGTTTTTGAAGTTTTGCT 58.206 33.333 0.00 0.00 0.00 3.91
2534 3084 6.036300 TCGGAATACTTTTTGAATACGCGATT 59.964 34.615 15.93 8.44 0.00 3.34
2544 3094 7.662258 TGTTCCAATACTCGGAATACTTTTTGA 59.338 33.333 0.00 0.00 44.18 2.69
2552 3102 4.161565 ACAGCTGTTCCAATACTCGGAATA 59.838 41.667 15.25 0.00 44.18 1.75
2553 3103 3.055094 ACAGCTGTTCCAATACTCGGAAT 60.055 43.478 15.25 0.00 44.18 3.01
2554 3104 2.301870 ACAGCTGTTCCAATACTCGGAA 59.698 45.455 15.25 0.00 40.26 4.30
2555 3105 1.899814 ACAGCTGTTCCAATACTCGGA 59.100 47.619 15.25 0.00 0.00 4.55
2556 3106 2.386661 ACAGCTGTTCCAATACTCGG 57.613 50.000 15.25 0.00 0.00 4.63
2557 3107 4.106197 GAGTACAGCTGTTCCAATACTCG 58.894 47.826 27.06 0.00 31.92 4.18
2558 3108 4.434520 GGAGTACAGCTGTTCCAATACTC 58.565 47.826 27.06 26.71 38.42 2.59
2559 3109 3.119101 CGGAGTACAGCTGTTCCAATACT 60.119 47.826 28.72 22.89 0.00 2.12
2560 3110 3.119245 TCGGAGTACAGCTGTTCCAATAC 60.119 47.826 28.72 19.20 0.00 1.89
2561 3111 3.093814 TCGGAGTACAGCTGTTCCAATA 58.906 45.455 28.72 15.66 0.00 1.90
2562 3112 1.899814 TCGGAGTACAGCTGTTCCAAT 59.100 47.619 28.72 12.31 0.00 3.16
2563 3113 1.272490 CTCGGAGTACAGCTGTTCCAA 59.728 52.381 28.72 15.94 0.00 3.53
2564 3114 0.888619 CTCGGAGTACAGCTGTTCCA 59.111 55.000 28.72 18.21 0.00 3.53
2565 3115 0.889306 ACTCGGAGTACAGCTGTTCC 59.111 55.000 27.06 24.48 0.00 3.62
2574 3124 4.272991 AGTGATGATTCGTACTCGGAGTAC 59.727 45.833 29.78 29.78 45.71 2.73
2575 3125 4.449131 AGTGATGATTCGTACTCGGAGTA 58.551 43.478 13.70 13.70 37.69 2.59
2576 3126 3.280295 AGTGATGATTCGTACTCGGAGT 58.720 45.455 15.95 15.95 37.69 3.85
2577 3127 3.972950 AGTGATGATTCGTACTCGGAG 57.027 47.619 2.83 2.83 37.69 4.63
2578 3128 4.421058 CAAAGTGATGATTCGTACTCGGA 58.579 43.478 0.00 0.00 37.69 4.55
2579 3129 3.551890 CCAAAGTGATGATTCGTACTCGG 59.448 47.826 0.00 0.00 37.69 4.63
2580 3130 4.174009 ACCAAAGTGATGATTCGTACTCG 58.826 43.478 0.00 0.00 38.55 4.18
2595 3145 3.206150 CAGACTACAACTGCACCAAAGT 58.794 45.455 0.00 0.00 0.00 2.66
2596 3146 3.885484 CAGACTACAACTGCACCAAAG 57.115 47.619 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.