Multiple sequence alignment - TraesCS6A01G284500

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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 TraesCS6A01G284500 chr6A 100.000 4107 0 0 1 4107 516153717 516157823 0.000000e+00 7585.0
1 TraesCS6A01G284500 chr6D 90.194 979 55 9 2440 3386 374102635 374103604 0.000000e+00 1238.0
2 TraesCS6A01G284500 chr6D 92.509 801 21 22 697 1468 374099966 374100756 0.000000e+00 1110.0
3 TraesCS6A01G284500 chr6D 87.852 568 43 13 3386 3948 374104521 374105067 0.000000e+00 643.0
4 TraesCS6A01G284500 chr6D 95.819 287 6 2 1467 1750 374100839 374101122 3.740000e-125 459.0
5 TraesCS6A01G284500 chr6D 84.345 313 30 10 1117 1424 373800569 373800867 5.190000e-74 289.0
6 TraesCS6A01G284500 chr6D 93.443 183 11 1 2252 2433 374102196 374102378 1.880000e-68 270.0
7 TraesCS6A01G284500 chr6D 95.092 163 8 0 2062 2224 374101124 374101286 1.460000e-64 257.0
8 TraesCS6A01G284500 chr6D 86.813 182 12 5 3934 4103 374105083 374105264 4.190000e-45 193.0
9 TraesCS6A01G284500 chr6D 81.443 194 26 8 2141 2328 373924673 373924862 2.560000e-32 150.0
10 TraesCS6A01G284500 chr7A 93.991 699 39 2 1 699 386804922 386805617 0.000000e+00 1055.0
11 TraesCS6A01G284500 chr7A 94.249 313 16 1 1751 2063 616470000 616469690 1.030000e-130 477.0
12 TraesCS6A01G284500 chr7A 93.968 315 16 2 1751 2064 167863618 167863306 1.340000e-129 473.0
13 TraesCS6A01G284500 chr7A 88.889 108 8 4 1 108 386804826 386804929 3.330000e-26 130.0
14 TraesCS6A01G284500 chr7A 82.000 100 16 2 607 705 7364592 7364494 2.630000e-12 84.2
15 TraesCS6A01G284500 chr6B 91.990 774 28 12 701 1450 561249918 561250681 0.000000e+00 1055.0
16 TraesCS6A01G284500 chr6B 89.819 717 34 11 2491 3171 561251334 561252047 0.000000e+00 883.0
17 TraesCS6A01G284500 chr6B 88.662 441 32 6 276 698 11750941 11751381 4.700000e-144 521.0
18 TraesCS6A01G284500 chr6B 93.949 314 17 1 1751 2064 547713647 547713958 1.340000e-129 473.0
19 TraesCS6A01G284500 chr6B 91.259 286 21 3 1 285 11749739 11750021 1.790000e-103 387.0
20 TraesCS6A01G284500 chr6B 80.124 322 41 15 2141 2460 561250867 561251167 6.910000e-53 219.0
21 TraesCS6A01G284500 chr6B 93.548 62 3 1 1528 1588 561250793 561250854 1.570000e-14 91.6
22 TraesCS6A01G284500 chr6B 86.667 75 10 0 624 698 198212173 198212099 2.630000e-12 84.2
23 TraesCS6A01G284500 chr2A 92.525 709 42 5 1 705 713870860 713871561 0.000000e+00 1005.0
24 TraesCS6A01G284500 chr2A 94.025 318 16 2 1746 2063 597847808 597848122 2.870000e-131 479.0
25 TraesCS6A01G284500 chr2A 93.168 322 19 2 1750 2070 758936711 758937030 1.730000e-128 470.0
26 TraesCS6A01G284500 chr2A 75.578 606 104 28 125 702 15724182 15723593 4.070000e-65 259.0
27 TraesCS6A01G284500 chr2A 87.963 108 7 4 1 108 713870737 713870838 5.580000e-24 122.0
28 TraesCS6A01G284500 chr1B 89.459 702 54 8 1 698 136642763 136643448 0.000000e+00 869.0
29 TraesCS6A01G284500 chr1B 89.016 701 60 5 1 696 18356446 18357134 0.000000e+00 852.0
30 TraesCS6A01G284500 chr3B 88.056 720 60 8 1 696 808631340 808630623 0.000000e+00 830.0
31 TraesCS6A01G284500 chr2B 86.275 714 79 7 1 696 752850689 752849977 0.000000e+00 758.0
32 TraesCS6A01G284500 chr2B 86.047 86 12 0 3187 3272 106447347 106447432 4.370000e-15 93.5
33 TraesCS6A01G284500 chr1A 94.268 314 16 1 1750 2063 499197903 499198214 2.870000e-131 479.0
34 TraesCS6A01G284500 chr5A 94.006 317 15 2 1750 2064 637293534 637293848 1.030000e-130 477.0
35 TraesCS6A01G284500 chr5A 93.949 314 17 2 1750 2063 148832423 148832734 1.340000e-129 473.0
36 TraesCS6A01G284500 chr4A 92.727 330 20 3 1735 2063 57414008 57414334 1.340000e-129 473.0
37 TraesCS6A01G284500 chr3D 87.025 316 24 7 227 535 122568186 122568491 1.410000e-89 340.0
38 TraesCS6A01G284500 chrUn 89.024 82 8 1 3187 3267 377707859 377707940 2.610000e-17 100.0
39 TraesCS6A01G284500 chrUn 87.805 82 9 1 3187 3267 348315117 348315198 1.220000e-15 95.3
40 TraesCS6A01G284500 chrUn 87.805 82 9 1 3187 3267 399203657 399203738 1.220000e-15 95.3
41 TraesCS6A01G284500 chrUn 89.474 76 7 1 3193 3267 427230684 427230609 1.220000e-15 95.3
42 TraesCS6A01G284500 chr7B 89.024 82 8 1 3187 3267 658638708 658638789 2.610000e-17 100.0
43 TraesCS6A01G284500 chr7B 87.805 82 9 1 3187 3267 658512518 658512599 1.220000e-15 95.3
44 TraesCS6A01G284500 chr7B 87.805 82 9 1 3187 3267 658764530 658764611 1.220000e-15 95.3
45 TraesCS6A01G284500 chr2D 91.667 72 6 0 3193 3264 36796290 36796219 2.610000e-17 100.0
46 TraesCS6A01G284500 chr4B 86.420 81 11 0 624 704 586946786 586946706 5.650000e-14 89.8


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 TraesCS6A01G284500 chr6A 516153717 516157823 4106 False 7585.000000 7585 100.000000 1 4107 1 chr6A.!!$F1 4106
1 TraesCS6A01G284500 chr6D 374099966 374105264 5298 False 595.714286 1238 91.674571 697 4103 7 chr6D.!!$F3 3406
2 TraesCS6A01G284500 chr7A 386804826 386805617 791 False 592.500000 1055 91.440000 1 699 2 chr7A.!!$F1 698
3 TraesCS6A01G284500 chr6B 561249918 561252047 2129 False 562.150000 1055 88.870250 701 3171 4 chr6B.!!$F3 2470
4 TraesCS6A01G284500 chr6B 11749739 11751381 1642 False 454.000000 521 89.960500 1 698 2 chr6B.!!$F2 697
5 TraesCS6A01G284500 chr2A 713870737 713871561 824 False 563.500000 1005 90.244000 1 705 2 chr2A.!!$F3 704
6 TraesCS6A01G284500 chr2A 15723593 15724182 589 True 259.000000 259 75.578000 125 702 1 chr2A.!!$R1 577
7 TraesCS6A01G284500 chr1B 136642763 136643448 685 False 869.000000 869 89.459000 1 698 1 chr1B.!!$F2 697
8 TraesCS6A01G284500 chr1B 18356446 18357134 688 False 852.000000 852 89.016000 1 696 1 chr1B.!!$F1 695
9 TraesCS6A01G284500 chr3B 808630623 808631340 717 True 830.000000 830 88.056000 1 696 1 chr3B.!!$R1 695
10 TraesCS6A01G284500 chr2B 752849977 752850689 712 True 758.000000 758 86.275000 1 696 1 chr2B.!!$R1 695

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
764 2008 0.036164 CATCCGGTGGGTCAAACTCA 59.964 55.000 0.0 0.0 33.83 3.41 F
766 2010 0.547075 TCCGGTGGGTCAAACTCAAA 59.453 50.000 0.0 0.0 25.28 2.69 F
767 2011 0.666374 CCGGTGGGTCAAACTCAAAC 59.334 55.000 0.0 0.0 25.28 2.93 F
2360 4641 1.070914 TGTTACAGATGTTGGCACGGA 59.929 47.619 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 4628 0.521735 GGAAGTTCCGTGCCAACATC 59.478 55.000 6.06 0.00 0.00 3.06 R
2749 5438 1.000993 AGGGACAGAGATGGCGTCT 59.999 57.895 9.44 9.44 40.81 4.18 R
2936 5652 3.710722 CGAGAAGGCTGGCCCAGT 61.711 66.667 13.35 0.00 36.58 4.00 R
3905 7549 0.108329 CAACTAACGGGATCGGTGCT 60.108 55.000 0.00 0.00 41.39 4.40 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
60 282 0.952280 TGCAACCGCCGTTCATTTTA 59.048 45.000 0.00 0.00 37.32 1.52
68 290 2.878406 CGCCGTTCATTTTATCTGGGAT 59.122 45.455 0.00 0.00 0.00 3.85
160 384 3.135530 GGAGATGATTTGCTGGGACTAGT 59.864 47.826 0.00 0.00 0.00 2.57
478 1647 0.670546 CAGTGGACATTCGCGGAAGT 60.671 55.000 6.13 0.00 0.00 3.01
488 1657 2.746277 GCGGAAGTTGGGCGTCAT 60.746 61.111 0.00 0.00 0.00 3.06
516 1697 1.078778 TACGACGCATGGCAACCAT 60.079 52.632 0.00 0.00 46.37 3.55
601 1841 2.363680 TGCATGACCCAACGTTTCAAAT 59.636 40.909 0.00 0.00 0.00 2.32
602 1842 3.570125 TGCATGACCCAACGTTTCAAATA 59.430 39.130 0.00 0.00 0.00 1.40
652 1894 6.065976 TGAATCCAACAGATGTAAGTGGAT 57.934 37.500 10.54 10.54 34.56 3.41
702 1944 3.107642 GCAGAGTAGCGCCCTTATTTA 57.892 47.619 2.29 0.00 0.00 1.40
703 1945 3.665190 GCAGAGTAGCGCCCTTATTTAT 58.335 45.455 2.29 0.00 0.00 1.40
704 1946 4.065789 GCAGAGTAGCGCCCTTATTTATT 58.934 43.478 2.29 0.00 0.00 1.40
705 1947 4.515567 GCAGAGTAGCGCCCTTATTTATTT 59.484 41.667 2.29 0.00 0.00 1.40
706 1948 5.560953 GCAGAGTAGCGCCCTTATTTATTTG 60.561 44.000 2.29 0.00 0.00 2.32
707 1949 5.527582 CAGAGTAGCGCCCTTATTTATTTGT 59.472 40.000 2.29 0.00 0.00 2.83
708 1950 6.038271 CAGAGTAGCGCCCTTATTTATTTGTT 59.962 38.462 2.29 0.00 0.00 2.83
709 1951 6.602009 AGAGTAGCGCCCTTATTTATTTGTTT 59.398 34.615 2.29 0.00 0.00 2.83
710 1952 7.771826 AGAGTAGCGCCCTTATTTATTTGTTTA 59.228 33.333 2.29 0.00 0.00 2.01
711 1953 8.459911 AGTAGCGCCCTTATTTATTTGTTTAT 57.540 30.769 2.29 0.00 0.00 1.40
712 1954 9.563748 AGTAGCGCCCTTATTTATTTGTTTATA 57.436 29.630 2.29 0.00 0.00 0.98
745 1989 1.248101 AAATGGTAACTGCGGGTGGC 61.248 55.000 0.00 0.00 43.96 5.01
762 2006 1.303317 GCATCCGGTGGGTCAAACT 60.303 57.895 0.00 0.00 33.83 2.66
763 2007 1.305930 GCATCCGGTGGGTCAAACTC 61.306 60.000 0.00 0.00 33.83 3.01
764 2008 0.036164 CATCCGGTGGGTCAAACTCA 59.964 55.000 0.00 0.00 33.83 3.41
765 2009 0.768622 ATCCGGTGGGTCAAACTCAA 59.231 50.000 0.00 0.00 25.28 3.02
766 2010 0.547075 TCCGGTGGGTCAAACTCAAA 59.453 50.000 0.00 0.00 25.28 2.69
767 2011 0.666374 CCGGTGGGTCAAACTCAAAC 59.334 55.000 0.00 0.00 25.28 2.93
904 2176 5.704515 ACTACACGGCCTAGTACTGTATATG 59.295 44.000 5.39 0.00 0.00 1.78
907 2179 5.471456 ACACGGCCTAGTACTGTATATGTAC 59.529 44.000 5.39 9.59 40.19 2.90
1237 2510 1.364626 CGGCGACTACCTCAGTACGT 61.365 60.000 0.00 0.00 37.72 3.57
1283 2556 4.874970 TCAATTTGCTTCTGCTTCTTTCC 58.125 39.130 0.00 0.00 40.48 3.13
1303 2576 1.800315 CGGTACAGTTCCTGTCGCG 60.800 63.158 0.00 0.00 41.21 5.87
1406 2679 7.906192 TGGGGATCCATAATTCTAGATGTCATA 59.094 37.037 15.23 0.00 38.32 2.15
1552 2948 1.822990 AGGCCATGAAACATGAAGCAG 59.177 47.619 5.01 0.00 0.00 4.24
1666 3065 9.883142 AATAGAATCTTTCTGTAGTGGAAGAAG 57.117 33.333 0.07 0.00 40.94 2.85
1750 3149 7.471679 GCCCCGATTCTAATCTACTAGAAACTT 60.472 40.741 0.00 0.00 40.42 2.66
1751 3150 8.422566 CCCCGATTCTAATCTACTAGAAACTTT 58.577 37.037 0.00 0.00 40.42 2.66
1764 3163 9.425577 CTACTAGAAACTTTAGACCTCTTTTGG 57.574 37.037 0.00 0.00 0.00 3.28
1765 3164 7.803131 ACTAGAAACTTTAGACCTCTTTTGGT 58.197 34.615 0.00 0.00 44.10 3.67
1766 3165 8.272889 ACTAGAAACTTTAGACCTCTTTTGGTT 58.727 33.333 0.00 0.00 41.00 3.67
1767 3166 7.569639 AGAAACTTTAGACCTCTTTTGGTTC 57.430 36.000 0.00 0.00 41.00 3.62
1768 3167 7.116736 AGAAACTTTAGACCTCTTTTGGTTCA 58.883 34.615 0.00 0.00 41.00 3.18
1769 3168 7.780271 AGAAACTTTAGACCTCTTTTGGTTCAT 59.220 33.333 0.00 0.00 41.00 2.57
1770 3169 8.990163 AAACTTTAGACCTCTTTTGGTTCATA 57.010 30.769 0.00 0.00 41.00 2.15
1771 3170 8.622948 AACTTTAGACCTCTTTTGGTTCATAG 57.377 34.615 0.00 0.00 41.00 2.23
1772 3171 7.168905 ACTTTAGACCTCTTTTGGTTCATAGG 58.831 38.462 0.00 0.00 41.00 2.57
1773 3172 6.945636 TTAGACCTCTTTTGGTTCATAGGA 57.054 37.500 0.00 0.00 41.00 2.94
1774 3173 7.510675 TTAGACCTCTTTTGGTTCATAGGAT 57.489 36.000 0.00 0.00 41.00 3.24
1775 3174 8.618240 TTAGACCTCTTTTGGTTCATAGGATA 57.382 34.615 0.00 0.00 41.00 2.59
1776 3175 7.130681 AGACCTCTTTTGGTTCATAGGATAG 57.869 40.000 0.00 0.00 41.00 2.08
1777 3176 6.100424 AGACCTCTTTTGGTTCATAGGATAGG 59.900 42.308 0.00 0.00 41.00 2.57
1778 3177 5.970640 ACCTCTTTTGGTTCATAGGATAGGA 59.029 40.000 0.00 0.00 36.89 2.94
1779 3178 6.621514 ACCTCTTTTGGTTCATAGGATAGGAT 59.378 38.462 0.00 0.00 36.89 3.24
1780 3179 7.129504 ACCTCTTTTGGTTCATAGGATAGGATT 59.870 37.037 0.00 0.00 36.89 3.01
1781 3180 8.660435 CCTCTTTTGGTTCATAGGATAGGATTA 58.340 37.037 0.00 0.00 28.27 1.75
1788 3187 8.914011 TGGTTCATAGGATAGGATTATCATACG 58.086 37.037 0.00 0.00 35.92 3.06
1789 3188 9.132923 GGTTCATAGGATAGGATTATCATACGA 57.867 37.037 0.00 0.00 35.92 3.43
1818 3217 9.857656 AGAAATCTTATAGAAAATGAGATGGCA 57.142 29.630 0.00 0.00 0.00 4.92
1821 3220 9.584008 AATCTTATAGAAAATGAGATGGCATGT 57.416 29.630 3.81 0.00 0.00 3.21
1826 3225 8.789825 ATAGAAAATGAGATGGCATGTATCTC 57.210 34.615 23.83 23.83 46.82 2.75
1835 3234 8.789825 GAGATGGCATGTATCTCAAATTCTAT 57.210 34.615 24.83 0.00 46.22 1.98
1836 3235 8.563123 AGATGGCATGTATCTCAAATTCTATG 57.437 34.615 3.81 0.00 29.05 2.23
1837 3236 8.380867 AGATGGCATGTATCTCAAATTCTATGA 58.619 33.333 3.81 0.00 29.05 2.15
1838 3237 7.974482 TGGCATGTATCTCAAATTCTATGAG 57.026 36.000 0.00 0.00 44.53 2.90
1839 3238 7.512130 TGGCATGTATCTCAAATTCTATGAGT 58.488 34.615 5.71 0.00 43.77 3.41
1840 3239 8.650490 TGGCATGTATCTCAAATTCTATGAGTA 58.350 33.333 5.71 0.00 43.77 2.59
1841 3240 9.149225 GGCATGTATCTCAAATTCTATGAGTAG 57.851 37.037 5.71 0.00 43.77 2.57
1842 3241 9.149225 GCATGTATCTCAAATTCTATGAGTAGG 57.851 37.037 5.71 0.00 43.77 3.18
1849 3248 9.883293 TCTCAAATTCTATGAGTAGGAATAGGA 57.117 33.333 5.71 0.00 43.77 2.94
1856 3255 9.488762 TTCTATGAGTAGGAATAGGAAACAAGA 57.511 33.333 0.00 0.00 0.00 3.02
1857 3256 9.661954 TCTATGAGTAGGAATAGGAAACAAGAT 57.338 33.333 0.00 0.00 0.00 2.40
1858 3257 9.703892 CTATGAGTAGGAATAGGAAACAAGATG 57.296 37.037 0.00 0.00 0.00 2.90
1859 3258 7.496346 TGAGTAGGAATAGGAAACAAGATGT 57.504 36.000 0.00 0.00 0.00 3.06
1860 3259 7.556844 TGAGTAGGAATAGGAAACAAGATGTC 58.443 38.462 0.00 0.00 0.00 3.06
1861 3260 7.180229 TGAGTAGGAATAGGAAACAAGATGTCA 59.820 37.037 0.00 0.00 0.00 3.58
1862 3261 8.095452 AGTAGGAATAGGAAACAAGATGTCAT 57.905 34.615 0.00 0.00 0.00 3.06
1863 3262 8.552296 AGTAGGAATAGGAAACAAGATGTCATT 58.448 33.333 0.00 0.00 0.00 2.57
1864 3263 9.178758 GTAGGAATAGGAAACAAGATGTCATTT 57.821 33.333 0.00 0.00 0.00 2.32
1865 3264 8.059798 AGGAATAGGAAACAAGATGTCATTTG 57.940 34.615 0.00 0.00 0.00 2.32
1866 3265 7.123247 AGGAATAGGAAACAAGATGTCATTTGG 59.877 37.037 10.50 0.00 0.00 3.28
1867 3266 7.093771 GGAATAGGAAACAAGATGTCATTTGGT 60.094 37.037 10.50 3.75 0.00 3.67
1868 3267 7.781324 ATAGGAAACAAGATGTCATTTGGTT 57.219 32.000 9.41 9.41 36.95 3.67
1869 3268 5.846203 AGGAAACAAGATGTCATTTGGTTG 58.154 37.500 12.70 6.32 34.55 3.77
1870 3269 5.598005 AGGAAACAAGATGTCATTTGGTTGA 59.402 36.000 12.70 0.00 34.55 3.18
1871 3270 5.691754 GGAAACAAGATGTCATTTGGTTGAC 59.308 40.000 12.70 0.00 45.05 3.18
1880 3279 5.452078 GTCATTTGGTTGACATCAAAGGA 57.548 39.130 12.16 12.16 44.38 3.36
1881 3280 5.841810 GTCATTTGGTTGACATCAAAGGAA 58.158 37.500 15.68 4.09 42.54 3.36
1882 3281 6.458210 GTCATTTGGTTGACATCAAAGGAAT 58.542 36.000 15.68 0.00 42.54 3.01
1883 3282 6.930722 GTCATTTGGTTGACATCAAAGGAATT 59.069 34.615 15.68 0.00 42.54 2.17
1884 3283 7.442062 GTCATTTGGTTGACATCAAAGGAATTT 59.558 33.333 15.68 0.00 42.54 1.82
1885 3284 7.992033 TCATTTGGTTGACATCAAAGGAATTTT 59.008 29.630 13.20 0.00 39.59 1.82
1886 3285 8.623030 CATTTGGTTGACATCAAAGGAATTTTT 58.377 29.630 9.43 0.00 36.97 1.94
1887 3286 7.784633 TTGGTTGACATCAAAGGAATTTTTC 57.215 32.000 0.00 0.00 37.63 2.29
1902 3301 6.765915 GAATTTTTCCATTGAGTCTAGGCT 57.234 37.500 0.00 0.00 0.00 4.58
1903 3302 6.765915 AATTTTTCCATTGAGTCTAGGCTC 57.234 37.500 17.74 17.74 36.12 4.70
1904 3303 5.505181 TTTTTCCATTGAGTCTAGGCTCT 57.495 39.130 24.20 2.95 36.51 4.09
1905 3304 5.505181 TTTTCCATTGAGTCTAGGCTCTT 57.495 39.130 24.20 9.92 36.51 2.85
1906 3305 5.505181 TTTCCATTGAGTCTAGGCTCTTT 57.495 39.130 24.20 9.56 36.51 2.52
1907 3306 5.505181 TTCCATTGAGTCTAGGCTCTTTT 57.495 39.130 24.20 7.12 36.51 2.27
1908 3307 5.505181 TCCATTGAGTCTAGGCTCTTTTT 57.495 39.130 24.20 4.72 36.51 1.94
1945 3344 9.354673 TGAAATATGAAGGATAGAAACCAATCC 57.645 33.333 0.00 0.00 41.77 3.01
1983 3382 7.751768 GAATCCATTCCTATGAACTAAAGGG 57.248 40.000 0.00 0.00 33.37 3.95
1984 3383 6.848562 ATCCATTCCTATGAACTAAAGGGT 57.151 37.500 0.00 0.00 33.37 4.34
1985 3384 6.652205 TCCATTCCTATGAACTAAAGGGTT 57.348 37.500 0.00 0.00 33.37 4.11
1986 3385 6.659824 TCCATTCCTATGAACTAAAGGGTTC 58.340 40.000 0.00 0.00 43.97 3.62
1987 3386 6.447084 TCCATTCCTATGAACTAAAGGGTTCT 59.553 38.462 8.47 0.00 44.02 3.01
1988 3387 7.626084 TCCATTCCTATGAACTAAAGGGTTCTA 59.374 37.037 8.47 0.00 44.02 2.10
1989 3388 8.272173 CCATTCCTATGAACTAAAGGGTTCTAA 58.728 37.037 8.47 0.00 44.02 2.10
1990 3389 9.681062 CATTCCTATGAACTAAAGGGTTCTAAA 57.319 33.333 8.47 0.00 44.02 1.85
1991 3390 9.907229 ATTCCTATGAACTAAAGGGTTCTAAAG 57.093 33.333 8.47 4.11 44.02 1.85
1992 3391 7.858498 TCCTATGAACTAAAGGGTTCTAAAGG 58.142 38.462 8.47 10.80 44.02 3.11
1993 3392 7.681168 TCCTATGAACTAAAGGGTTCTAAAGGA 59.319 37.037 15.03 15.03 44.02 3.36
1994 3393 8.326529 CCTATGAACTAAAGGGTTCTAAAGGAA 58.673 37.037 8.47 0.00 44.02 3.36
1995 3394 9.734984 CTATGAACTAAAGGGTTCTAAAGGAAA 57.265 33.333 8.47 0.00 44.02 3.13
1997 3396 8.459911 TGAACTAAAGGGTTCTAAAGGAAAAG 57.540 34.615 8.47 0.00 44.02 2.27
1998 3397 8.276477 TGAACTAAAGGGTTCTAAAGGAAAAGA 58.724 33.333 8.47 0.00 44.02 2.52
1999 3398 9.298250 GAACTAAAGGGTTCTAAAGGAAAAGAT 57.702 33.333 0.00 0.00 41.44 2.40
2000 3399 8.865420 ACTAAAGGGTTCTAAAGGAAAAGATC 57.135 34.615 0.00 0.00 35.51 2.75
2031 3430 9.842196 AAGAATCATATCCTCTCTAGAATTCCT 57.158 33.333 0.65 0.00 0.00 3.36
2041 3440 8.875168 TCCTCTCTAGAATTCCTATGAAATTCC 58.125 37.037 0.65 0.00 33.32 3.01
2042 3441 8.879227 CCTCTCTAGAATTCCTATGAAATTCCT 58.121 37.037 0.65 0.00 33.32 3.36
2043 3442 9.927668 CTCTCTAGAATTCCTATGAAATTCCTC 57.072 37.037 0.65 0.00 33.32 3.71
2044 3443 9.667607 TCTCTAGAATTCCTATGAAATTCCTCT 57.332 33.333 0.65 0.00 33.32 3.69
2049 3448 9.634021 AGAATTCCTATGAAATTCCTCTAAACC 57.366 33.333 0.65 0.00 33.32 3.27
2050 3449 9.408648 GAATTCCTATGAAATTCCTCTAAACCA 57.591 33.333 0.00 0.00 33.32 3.67
2051 3450 9.768215 AATTCCTATGAAATTCCTCTAAACCAA 57.232 29.630 0.00 0.00 33.32 3.67
2052 3451 9.768215 ATTCCTATGAAATTCCTCTAAACCAAA 57.232 29.630 0.00 0.00 33.32 3.28
2053 3452 8.807948 TCCTATGAAATTCCTCTAAACCAAAG 57.192 34.615 0.00 0.00 0.00 2.77
2054 3453 7.834181 TCCTATGAAATTCCTCTAAACCAAAGG 59.166 37.037 0.00 0.00 0.00 3.11
2055 3454 7.834181 CCTATGAAATTCCTCTAAACCAAAGGA 59.166 37.037 0.00 0.00 37.42 3.36
2056 3455 7.709149 ATGAAATTCCTCTAAACCAAAGGAG 57.291 36.000 0.00 0.00 40.21 3.69
2057 3456 6.010219 TGAAATTCCTCTAAACCAAAGGAGG 58.990 40.000 0.00 0.00 44.69 4.30
2058 3457 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
2059 3458 1.633945 TCCTCTAAACCAAAGGAGGCC 59.366 52.381 0.00 0.00 43.46 5.19
2060 3459 1.636003 CCTCTAAACCAAAGGAGGCCT 59.364 52.381 3.86 3.86 38.82 5.19
2077 3476 5.368989 GAGGCCTTAATGCTACACTACATT 58.631 41.667 6.77 0.00 39.69 2.71
2102 3501 5.690865 AGAAACACAGGTTTAATCAGTGGA 58.309 37.500 5.77 0.00 46.84 4.02
2318 4599 5.633830 TCAATCCTCTCAAGCACAAAATC 57.366 39.130 0.00 0.00 0.00 2.17
2325 4606 6.372659 TCCTCTCAAGCACAAAATCATCTAAC 59.627 38.462 0.00 0.00 0.00 2.34
2358 4639 2.143122 AGTGTTACAGATGTTGGCACG 58.857 47.619 0.00 0.00 35.04 5.34
2360 4641 1.070914 TGTTACAGATGTTGGCACGGA 59.929 47.619 0.00 0.00 0.00 4.69
2373 4654 1.468914 GGCACGGAACTTCCTCAAATC 59.531 52.381 6.25 0.00 33.30 2.17
2414 4700 9.623000 TTAACTTAGGACAGAGCTTAAACTTTT 57.377 29.630 0.00 0.00 0.00 2.27
2519 5203 7.364522 TCACTTAATCACTGATTTGTGTAGC 57.635 36.000 22.88 0.00 37.01 3.58
2588 5277 3.572255 TCAACTAAACCAAACCCATGCTC 59.428 43.478 0.00 0.00 0.00 4.26
2608 5297 5.665459 GCTCATCAGCTACCTTTCTTCTTA 58.335 41.667 0.00 0.00 43.09 2.10
2732 5421 2.777972 ATCTACAGCGGCGGCGTAA 61.778 57.895 32.35 14.23 46.35 3.18
2749 5438 2.831894 TAAGCGGCCTCGAGGAGACA 62.832 60.000 35.69 11.04 39.00 3.41
3183 5902 9.632638 AATTTATATGTAGTCAATGTTCCTGCT 57.367 29.630 0.00 0.00 0.00 4.24
3184 5903 8.437360 TTTATATGTAGTCAATGTTCCTGCTG 57.563 34.615 0.00 0.00 0.00 4.41
3185 5904 3.057969 TGTAGTCAATGTTCCTGCTGG 57.942 47.619 2.58 2.58 0.00 4.85
3186 5905 2.371841 TGTAGTCAATGTTCCTGCTGGT 59.628 45.455 9.73 0.00 34.23 4.00
3187 5906 2.191128 AGTCAATGTTCCTGCTGGTC 57.809 50.000 9.73 5.24 34.23 4.02
3188 5907 1.421268 AGTCAATGTTCCTGCTGGTCA 59.579 47.619 9.73 10.49 34.23 4.02
3203 5922 6.259608 CCTGCTGGTCAGTGAAGAAATATAAG 59.740 42.308 0.51 0.00 41.25 1.73
3206 5925 6.018343 GCTGGTCAGTGAAGAAATATAAGAGC 60.018 42.308 0.00 0.00 0.00 4.09
3209 5928 6.535508 GGTCAGTGAAGAAATATAAGAGCGTT 59.464 38.462 0.00 0.00 0.00 4.84
3352 6076 6.992123 ACAATTTTCGAGGCATATCTATGACA 59.008 34.615 5.86 0.00 44.26 3.58
3364 6088 8.507249 GGCATATCTATGACACAGATTAAAACC 58.493 37.037 0.68 0.00 41.42 3.27
3377 6101 9.463443 CACAGATTAAAACCTTTTCTTTACAGG 57.537 33.333 0.00 0.00 0.00 4.00
3423 7063 8.005466 GCTTAAAAAGTAATAAAAACGGTTGGC 58.995 33.333 0.00 0.00 0.00 4.52
3439 7079 0.618458 TGGCCAACCAACTAGCTAGG 59.382 55.000 24.35 10.67 45.37 3.02
3440 7080 0.107165 GGCCAACCAACTAGCTAGGG 60.107 60.000 24.35 18.25 35.26 3.53
3441 7081 0.909623 GCCAACCAACTAGCTAGGGA 59.090 55.000 24.35 0.00 0.00 4.20
3442 7082 1.134371 GCCAACCAACTAGCTAGGGAG 60.134 57.143 24.35 13.95 0.00 4.30
3458 7098 2.203788 AGCCTCCACCCAGTTCGA 60.204 61.111 0.00 0.00 0.00 3.71
3467 7107 2.093711 CCACCCAGTTCGATATGTCACA 60.094 50.000 0.00 0.00 0.00 3.58
3473 7113 4.108336 CAGTTCGATATGTCACAGAGTGG 58.892 47.826 0.00 0.00 33.87 4.00
3484 7124 2.282040 AGAGTGGCCACTGCAAGC 60.282 61.111 42.40 26.51 42.66 4.01
3485 7125 2.595463 GAGTGGCCACTGCAAGCA 60.595 61.111 42.40 0.00 42.66 3.91
3502 7142 1.139853 AGCATCTAAAAGCGAGGGAGG 59.860 52.381 0.00 0.00 35.48 4.30
3513 7153 1.468914 GCGAGGGAGGAAAACATTCAC 59.531 52.381 0.00 0.00 0.00 3.18
3529 7169 0.956633 TCACCTTACGTCGCTCTTGT 59.043 50.000 0.00 0.00 0.00 3.16
3562 7202 2.824489 GCTCAAACCCTAGCCGCC 60.824 66.667 0.00 0.00 32.40 6.13
3564 7204 1.224592 CTCAAACCCTAGCCGCCAT 59.775 57.895 0.00 0.00 0.00 4.40
3565 7205 0.815615 CTCAAACCCTAGCCGCCATC 60.816 60.000 0.00 0.00 0.00 3.51
3566 7206 2.180204 CAAACCCTAGCCGCCATCG 61.180 63.158 0.00 0.00 0.00 3.84
3593 7233 1.240256 CGGACTCTTCCTCTATCCCG 58.760 60.000 0.00 0.00 40.23 5.14
3594 7234 1.623163 GGACTCTTCCTCTATCCCGG 58.377 60.000 0.00 0.00 39.13 5.73
3595 7235 0.963225 GACTCTTCCTCTATCCCGGC 59.037 60.000 0.00 0.00 0.00 6.13
3597 7237 1.152312 TCTTCCTCTATCCCGGCCC 60.152 63.158 0.00 0.00 0.00 5.80
3599 7239 3.786866 TTCCTCTATCCCGGCCCCC 62.787 68.421 0.00 0.00 0.00 5.40
3600 7240 4.256278 CCTCTATCCCGGCCCCCT 62.256 72.222 0.00 0.00 0.00 4.79
3601 7241 2.604991 CTCTATCCCGGCCCCCTC 60.605 72.222 0.00 0.00 0.00 4.30
3602 7242 3.117648 TCTATCCCGGCCCCCTCT 61.118 66.667 0.00 0.00 0.00 3.69
3603 7243 2.604991 CTATCCCGGCCCCCTCTC 60.605 72.222 0.00 0.00 0.00 3.20
3604 7244 4.250170 TATCCCGGCCCCCTCTCC 62.250 72.222 0.00 0.00 0.00 3.71
3622 7262 1.447838 CCGTAGTCATGTTGCCGCT 60.448 57.895 0.00 0.00 0.00 5.52
3637 7277 1.450312 CGCTGTTGGAGGTGGATCC 60.450 63.158 4.20 4.20 40.03 3.36
3644 7285 0.325203 TGGAGGTGGATCCGACATGA 60.325 55.000 7.39 0.00 42.77 3.07
3651 7292 1.757118 TGGATCCGACATGAGGTTCTC 59.243 52.381 7.39 2.30 0.00 2.87
3652 7293 2.035632 GGATCCGACATGAGGTTCTCT 58.964 52.381 0.00 0.00 0.00 3.10
3675 7316 0.685097 AAGCTTGGCAGACCGTTAGA 59.315 50.000 0.00 0.00 39.70 2.10
3681 7322 2.029623 TGGCAGACCGTTAGATAGGAC 58.970 52.381 0.00 0.00 39.70 3.85
3702 7343 7.395617 AGGACTATTCTTTACCCACTTTCTTC 58.604 38.462 0.00 0.00 0.00 2.87
3709 7350 1.972872 ACCCACTTTCTTCACTGCTG 58.027 50.000 0.00 0.00 0.00 4.41
3730 7371 0.179936 GGGCACTGATGGAGAGAAGG 59.820 60.000 0.00 0.00 0.00 3.46
3731 7372 0.908198 GGCACTGATGGAGAGAAGGT 59.092 55.000 0.00 0.00 0.00 3.50
3732 7373 1.406614 GGCACTGATGGAGAGAAGGTG 60.407 57.143 0.00 0.00 0.00 4.00
3733 7374 1.406614 GCACTGATGGAGAGAAGGTGG 60.407 57.143 0.00 0.00 0.00 4.61
3734 7375 1.905215 CACTGATGGAGAGAAGGTGGT 59.095 52.381 0.00 0.00 0.00 4.16
3748 7389 3.282135 AGGTGGTAGATCTATGGCCAT 57.718 47.619 24.45 24.45 0.00 4.40
3762 7403 2.661718 TGGCCATCACACTCGTATCTA 58.338 47.619 0.00 0.00 0.00 1.98
3775 7416 2.092592 TCGTATCTAGTGCTCTGTGGGA 60.093 50.000 0.00 0.00 0.00 4.37
3798 7442 0.524862 AAAGCTCGCTTGGATGCTTG 59.475 50.000 4.73 0.00 43.80 4.01
3813 7457 1.374947 CTTGGTCTTCCTTCGCCCA 59.625 57.895 0.00 0.00 34.23 5.36
3815 7459 0.404040 TTGGTCTTCCTTCGCCCATT 59.596 50.000 0.00 0.00 34.23 3.16
3834 7478 3.378861 TTGGCCACCATATCAACATCA 57.621 42.857 3.88 0.00 31.53 3.07
3840 7484 3.742882 CCACCATATCAACATCAGCTACG 59.257 47.826 0.00 0.00 0.00 3.51
3888 7532 4.647853 AGTCTTCGGTATGCCACTACATTA 59.352 41.667 0.00 0.00 34.09 1.90
3892 7536 4.146564 TCGGTATGCCACTACATTAGCTA 58.853 43.478 0.00 0.00 34.09 3.32
3905 7549 3.973973 ACATTAGCTAGGGTTGATGCCTA 59.026 43.478 0.00 0.00 0.00 3.93
3969 7643 1.693640 CACTCTTCCCCTTGCCCAT 59.306 57.895 0.00 0.00 0.00 4.00
3973 7647 0.625849 TCTTCCCCTTGCCCATCTTC 59.374 55.000 0.00 0.00 0.00 2.87
3991 7665 0.391927 TCGGCAAAGTTATGGTCGGG 60.392 55.000 0.00 0.00 0.00 5.14
4030 7704 3.830178 TCTCTCAAGACCGGATTGTGTTA 59.170 43.478 9.46 4.22 0.00 2.41
4031 7705 4.466370 TCTCTCAAGACCGGATTGTGTTAT 59.534 41.667 9.46 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 262 0.318614 AAAATGAACGGCGGTTGCAG 60.319 50.000 15.03 0.00 45.35 4.41
44 266 2.422127 CCAGATAAAATGAACGGCGGTT 59.578 45.455 13.24 9.69 39.63 4.44
49 271 4.023707 GCTGATCCCAGATAAAATGAACGG 60.024 45.833 0.00 0.00 43.02 4.44
60 282 5.482878 ACAAAAATTCTTGCTGATCCCAGAT 59.517 36.000 0.00 0.00 43.02 2.90
68 290 4.332268 GGTTGCAACAAAAATTCTTGCTGA 59.668 37.500 29.55 0.00 40.81 4.26
160 384 1.305201 GGTTGCAGTTTTCCGTCTCA 58.695 50.000 0.00 0.00 0.00 3.27
385 1550 1.663379 CGCAGGTACTCCGTCATCCA 61.663 60.000 0.00 0.00 34.60 3.41
478 1647 0.881118 GCTTTTCTCATGACGCCCAA 59.119 50.000 0.00 0.00 0.00 4.12
488 1657 1.992667 CATGCGTCGTAGCTTTTCTCA 59.007 47.619 0.00 0.00 38.13 3.27
535 1725 2.113131 AAAACGAGCCCGCTTTGTCG 62.113 55.000 0.00 0.00 39.95 4.35
601 1841 6.560003 TCCTGAAACATTGGATCTAGCTTA 57.440 37.500 0.00 0.00 0.00 3.09
602 1842 5.441718 TCCTGAAACATTGGATCTAGCTT 57.558 39.130 0.00 0.00 0.00 3.74
629 1871 5.497464 TCCACTTACATCTGTTGGATTCA 57.503 39.130 0.00 0.00 31.27 2.57
639 1881 0.389391 CCGCCGATCCACTTACATCT 59.611 55.000 0.00 0.00 0.00 2.90
644 1886 1.140161 CGTTCCGCCGATCCACTTA 59.860 57.895 0.00 0.00 0.00 2.24
702 1944 9.474313 TTTCTCTGCCACCTATTATAAACAAAT 57.526 29.630 0.00 0.00 0.00 2.32
703 1945 8.871629 TTTCTCTGCCACCTATTATAAACAAA 57.128 30.769 0.00 0.00 0.00 2.83
704 1946 8.902806 CATTTCTCTGCCACCTATTATAAACAA 58.097 33.333 0.00 0.00 0.00 2.83
705 1947 7.502226 CCATTTCTCTGCCACCTATTATAAACA 59.498 37.037 0.00 0.00 0.00 2.83
706 1948 7.502561 ACCATTTCTCTGCCACCTATTATAAAC 59.497 37.037 0.00 0.00 0.00 2.01
707 1949 7.582719 ACCATTTCTCTGCCACCTATTATAAA 58.417 34.615 0.00 0.00 0.00 1.40
708 1950 7.149202 ACCATTTCTCTGCCACCTATTATAA 57.851 36.000 0.00 0.00 0.00 0.98
709 1951 6.763715 ACCATTTCTCTGCCACCTATTATA 57.236 37.500 0.00 0.00 0.00 0.98
710 1952 5.653255 ACCATTTCTCTGCCACCTATTAT 57.347 39.130 0.00 0.00 0.00 1.28
711 1953 6.157994 AGTTACCATTTCTCTGCCACCTATTA 59.842 38.462 0.00 0.00 0.00 0.98
712 1954 5.044846 AGTTACCATTTCTCTGCCACCTATT 60.045 40.000 0.00 0.00 0.00 1.73
713 1955 4.475016 AGTTACCATTTCTCTGCCACCTAT 59.525 41.667 0.00 0.00 0.00 2.57
721 1965 2.009774 CCCGCAGTTACCATTTCTCTG 58.990 52.381 0.00 0.00 0.00 3.35
745 1989 0.036164 TGAGTTTGACCCACCGGATG 59.964 55.000 9.46 2.15 0.00 3.51
762 2006 6.631971 TGTGCATCTTTGAGTAATGTTTGA 57.368 33.333 0.00 0.00 0.00 2.69
763 2007 7.061441 GTCATGTGCATCTTTGAGTAATGTTTG 59.939 37.037 0.00 0.00 0.00 2.93
764 2008 7.086376 GTCATGTGCATCTTTGAGTAATGTTT 58.914 34.615 0.00 0.00 0.00 2.83
765 2009 6.207221 TGTCATGTGCATCTTTGAGTAATGTT 59.793 34.615 0.00 0.00 0.00 2.71
766 2010 5.706833 TGTCATGTGCATCTTTGAGTAATGT 59.293 36.000 0.00 0.00 0.00 2.71
767 2011 6.185852 TGTCATGTGCATCTTTGAGTAATG 57.814 37.500 0.00 0.00 0.00 1.90
904 2176 9.485206 TCTTGTGTTAAGAGTAATCCAAAGTAC 57.515 33.333 0.00 0.00 0.00 2.73
907 2179 7.173218 TGCTCTTGTGTTAAGAGTAATCCAAAG 59.827 37.037 15.64 0.00 44.22 2.77
920 2192 3.118408 AGTGTCCTGTGCTCTTGTGTTAA 60.118 43.478 0.00 0.00 0.00 2.01
926 2198 3.883830 ATCTAGTGTCCTGTGCTCTTG 57.116 47.619 0.00 0.00 0.00 3.02
1237 2510 3.306472 AGCAGTTGGTTTAGGTTGGAA 57.694 42.857 0.00 0.00 0.00 3.53
1303 2576 0.946528 TCACACTCACTGCACATTGC 59.053 50.000 0.00 0.00 45.29 3.56
1406 2679 0.678950 CGCCAAGACCCAACCATTTT 59.321 50.000 0.00 0.00 0.00 1.82
1459 2732 6.736123 AGTTTGTACTCGCATATAGTACTGG 58.264 40.000 5.39 0.00 46.21 4.00
1468 2741 4.311606 TGAAGCAAGTTTGTACTCGCATA 58.688 39.130 0.00 0.00 36.76 3.14
1513 2909 5.112686 GGCCTCTGTTACATACTTCTTCAG 58.887 45.833 0.00 0.00 0.00 3.02
1521 2917 4.941263 TGTTTCATGGCCTCTGTTACATAC 59.059 41.667 3.32 0.00 0.00 2.39
1552 2948 5.882557 TGGATCTAAGTTCTGAATTCTTGGC 59.117 40.000 7.05 0.00 0.00 4.52
1750 3149 6.945636 TCCTATGAACCAAAAGAGGTCTAA 57.054 37.500 0.00 0.00 42.25 2.10
1751 3150 7.290248 CCTATCCTATGAACCAAAAGAGGTCTA 59.710 40.741 0.00 0.00 42.25 2.59
1752 3151 6.100424 CCTATCCTATGAACCAAAAGAGGTCT 59.900 42.308 0.00 0.00 42.25 3.85
1753 3152 6.099845 TCCTATCCTATGAACCAAAAGAGGTC 59.900 42.308 0.00 0.00 42.25 3.85
1754 3153 5.970640 TCCTATCCTATGAACCAAAAGAGGT 59.029 40.000 0.00 0.00 45.91 3.85
1755 3154 6.500589 TCCTATCCTATGAACCAAAAGAGG 57.499 41.667 0.00 0.00 0.00 3.69
1762 3161 8.914011 CGTATGATAATCCTATCCTATGAACCA 58.086 37.037 0.00 0.00 34.10 3.67
1763 3162 9.132923 TCGTATGATAATCCTATCCTATGAACC 57.867 37.037 0.00 0.00 32.29 3.62
1792 3191 9.857656 TGCCATCTCATTTTCTATAAGATTTCT 57.142 29.630 0.00 0.00 0.00 2.52
1795 3194 9.584008 ACATGCCATCTCATTTTCTATAAGATT 57.416 29.630 0.00 0.00 0.00 2.40
1800 3199 9.881649 GAGATACATGCCATCTCATTTTCTATA 57.118 33.333 23.49 0.00 45.17 1.31
1801 3200 8.789825 GAGATACATGCCATCTCATTTTCTAT 57.210 34.615 23.49 0.00 45.17 1.98
1810 3209 8.666573 CATAGAATTTGAGATACATGCCATCTC 58.333 37.037 22.40 22.40 45.76 2.75
1811 3210 8.380867 TCATAGAATTTGAGATACATGCCATCT 58.619 33.333 9.57 9.57 35.43 2.90
1812 3211 8.557592 TCATAGAATTTGAGATACATGCCATC 57.442 34.615 0.00 0.00 0.00 3.51
1813 3212 8.162085 ACTCATAGAATTTGAGATACATGCCAT 58.838 33.333 11.68 0.00 42.63 4.40
1814 3213 7.512130 ACTCATAGAATTTGAGATACATGCCA 58.488 34.615 11.68 0.00 42.63 4.92
1815 3214 7.976135 ACTCATAGAATTTGAGATACATGCC 57.024 36.000 11.68 0.00 42.63 4.40
1816 3215 9.149225 CCTACTCATAGAATTTGAGATACATGC 57.851 37.037 11.68 0.00 42.63 4.06
1823 3222 9.883293 TCCTATTCCTACTCATAGAATTTGAGA 57.117 33.333 11.68 0.00 42.63 3.27
1830 3229 9.488762 TCTTGTTTCCTATTCCTACTCATAGAA 57.511 33.333 0.00 0.00 0.00 2.10
1831 3230 9.661954 ATCTTGTTTCCTATTCCTACTCATAGA 57.338 33.333 0.00 0.00 0.00 1.98
1832 3231 9.703892 CATCTTGTTTCCTATTCCTACTCATAG 57.296 37.037 0.00 0.00 0.00 2.23
1833 3232 9.213777 ACATCTTGTTTCCTATTCCTACTCATA 57.786 33.333 0.00 0.00 0.00 2.15
1834 3233 8.095452 ACATCTTGTTTCCTATTCCTACTCAT 57.905 34.615 0.00 0.00 0.00 2.90
1835 3234 7.180229 TGACATCTTGTTTCCTATTCCTACTCA 59.820 37.037 0.00 0.00 0.00 3.41
1836 3235 7.556844 TGACATCTTGTTTCCTATTCCTACTC 58.443 38.462 0.00 0.00 0.00 2.59
1837 3236 7.496346 TGACATCTTGTTTCCTATTCCTACT 57.504 36.000 0.00 0.00 0.00 2.57
1838 3237 8.738645 AATGACATCTTGTTTCCTATTCCTAC 57.261 34.615 0.00 0.00 0.00 3.18
1839 3238 9.177608 CAAATGACATCTTGTTTCCTATTCCTA 57.822 33.333 0.00 0.00 0.00 2.94
1840 3239 7.123247 CCAAATGACATCTTGTTTCCTATTCCT 59.877 37.037 0.00 0.00 0.00 3.36
1841 3240 7.093771 ACCAAATGACATCTTGTTTCCTATTCC 60.094 37.037 0.00 0.00 0.00 3.01
1842 3241 7.830739 ACCAAATGACATCTTGTTTCCTATTC 58.169 34.615 0.00 0.00 0.00 1.75
1843 3242 7.781324 ACCAAATGACATCTTGTTTCCTATT 57.219 32.000 0.00 0.00 0.00 1.73
1844 3243 7.451255 TCAACCAAATGACATCTTGTTTCCTAT 59.549 33.333 0.00 0.00 0.00 2.57
1845 3244 6.775142 TCAACCAAATGACATCTTGTTTCCTA 59.225 34.615 0.00 0.00 0.00 2.94
1846 3245 5.598005 TCAACCAAATGACATCTTGTTTCCT 59.402 36.000 0.00 0.00 0.00 3.36
1847 3246 5.841810 TCAACCAAATGACATCTTGTTTCC 58.158 37.500 0.00 0.00 0.00 3.13
1859 3258 6.669125 ATTCCTTTGATGTCAACCAAATGA 57.331 33.333 0.00 5.19 35.28 2.57
1860 3259 7.733402 AAATTCCTTTGATGTCAACCAAATG 57.267 32.000 0.00 3.42 35.28 2.32
1861 3260 8.750515 AAAAATTCCTTTGATGTCAACCAAAT 57.249 26.923 0.00 0.00 35.28 2.32
1862 3261 7.281999 GGAAAAATTCCTTTGATGTCAACCAAA 59.718 33.333 1.86 4.41 46.57 3.28
1863 3262 6.765512 GGAAAAATTCCTTTGATGTCAACCAA 59.234 34.615 1.86 0.00 46.57 3.67
1864 3263 6.287525 GGAAAAATTCCTTTGATGTCAACCA 58.712 36.000 1.86 0.00 46.57 3.67
1865 3264 6.785488 GGAAAAATTCCTTTGATGTCAACC 57.215 37.500 1.86 0.00 46.57 3.77
1877 3276 8.285329 GAGCCTAGACTCAATGGAAAAATTCCT 61.285 40.741 10.28 0.00 42.21 3.36
1878 3277 6.183360 GAGCCTAGACTCAATGGAAAAATTCC 60.183 42.308 0.51 2.12 42.14 3.01
1879 3278 6.601217 AGAGCCTAGACTCAATGGAAAAATTC 59.399 38.462 8.89 0.00 39.26 2.17
1880 3279 6.488715 AGAGCCTAGACTCAATGGAAAAATT 58.511 36.000 8.89 0.00 39.26 1.82
1881 3280 6.072199 AGAGCCTAGACTCAATGGAAAAAT 57.928 37.500 8.89 0.00 39.26 1.82
1882 3281 5.505181 AGAGCCTAGACTCAATGGAAAAA 57.495 39.130 8.89 0.00 39.26 1.94
1883 3282 5.505181 AAGAGCCTAGACTCAATGGAAAA 57.495 39.130 8.89 0.00 39.26 2.29
1884 3283 5.505181 AAAGAGCCTAGACTCAATGGAAA 57.495 39.130 8.89 0.00 39.26 3.13
1885 3284 5.505181 AAAAGAGCCTAGACTCAATGGAA 57.495 39.130 8.89 0.00 39.26 3.53
1886 3285 5.505181 AAAAAGAGCCTAGACTCAATGGA 57.495 39.130 8.89 0.00 39.26 3.41
1919 3318 9.354673 GGATTGGTTTCTATCCTTCATATTTCA 57.645 33.333 0.00 0.00 40.55 2.69
1934 3333 9.225682 TCCTATTTCTACATAGGATTGGTTTCT 57.774 33.333 5.49 0.00 46.83 2.52
1959 3358 7.290813 ACCCTTTAGTTCATAGGAATGGATTC 58.709 38.462 0.00 0.00 35.05 2.52
1960 3359 7.226059 ACCCTTTAGTTCATAGGAATGGATT 57.774 36.000 0.00 0.00 35.05 3.01
1961 3360 6.848562 ACCCTTTAGTTCATAGGAATGGAT 57.151 37.500 0.00 0.00 35.05 3.41
1962 3361 6.652205 AACCCTTTAGTTCATAGGAATGGA 57.348 37.500 0.00 0.00 35.05 3.41
1963 3362 6.944234 GAACCCTTTAGTTCATAGGAATGG 57.056 41.667 0.00 0.00 44.55 3.16
1973 3372 8.687292 TCTTTTCCTTTAGAACCCTTTAGTTC 57.313 34.615 0.00 0.00 45.34 3.01
1974 3373 9.298250 GATCTTTTCCTTTAGAACCCTTTAGTT 57.702 33.333 0.00 0.00 32.95 2.24
1975 3374 7.889073 GGATCTTTTCCTTTAGAACCCTTTAGT 59.111 37.037 0.00 0.00 41.78 2.24
1976 3375 8.282455 GGATCTTTTCCTTTAGAACCCTTTAG 57.718 38.462 0.00 0.00 41.78 1.85
2005 3404 9.842196 AGGAATTCTAGAGAGGATATGATTCTT 57.158 33.333 5.23 0.00 0.00 2.52
2015 3414 8.875168 GGAATTTCATAGGAATTCTAGAGAGGA 58.125 37.037 5.23 0.00 31.93 3.71
2016 3415 8.879227 AGGAATTTCATAGGAATTCTAGAGAGG 58.121 37.037 5.23 0.00 31.93 3.69
2017 3416 9.927668 GAGGAATTTCATAGGAATTCTAGAGAG 57.072 37.037 5.23 0.00 31.93 3.20
2018 3417 9.667607 AGAGGAATTTCATAGGAATTCTAGAGA 57.332 33.333 5.23 0.00 31.93 3.10
2023 3422 9.634021 GGTTTAGAGGAATTTCATAGGAATTCT 57.366 33.333 5.23 0.00 31.93 2.40
2024 3423 9.408648 TGGTTTAGAGGAATTTCATAGGAATTC 57.591 33.333 0.00 0.00 31.93 2.17
2025 3424 9.768215 TTGGTTTAGAGGAATTTCATAGGAATT 57.232 29.630 0.00 0.00 31.93 2.17
2026 3425 9.768215 TTTGGTTTAGAGGAATTTCATAGGAAT 57.232 29.630 0.00 0.00 31.93 3.01
2027 3426 9.243105 CTTTGGTTTAGAGGAATTTCATAGGAA 57.757 33.333 0.00 0.00 0.00 3.36
2028 3427 7.834181 CCTTTGGTTTAGAGGAATTTCATAGGA 59.166 37.037 0.00 0.00 32.11 2.94
2029 3428 7.834181 TCCTTTGGTTTAGAGGAATTTCATAGG 59.166 37.037 0.00 0.00 36.67 2.57
2030 3429 8.807948 TCCTTTGGTTTAGAGGAATTTCATAG 57.192 34.615 0.00 0.00 36.67 2.23
2031 3430 8.807948 CTCCTTTGGTTTAGAGGAATTTCATA 57.192 34.615 0.00 0.00 39.00 2.15
2032 3431 7.709149 CTCCTTTGGTTTAGAGGAATTTCAT 57.291 36.000 0.00 0.00 39.00 2.57
2040 3439 2.041755 AAGGCCTCCTTTGGTTTAGAGG 59.958 50.000 5.23 0.43 41.69 3.69
2041 3440 3.441500 AAGGCCTCCTTTGGTTTAGAG 57.558 47.619 5.23 0.00 41.69 2.43
2042 3441 5.261216 CATTAAGGCCTCCTTTGGTTTAGA 58.739 41.667 5.23 0.00 41.69 2.10
2043 3442 4.142160 GCATTAAGGCCTCCTTTGGTTTAG 60.142 45.833 5.23 0.00 41.69 1.85
2044 3443 3.767131 GCATTAAGGCCTCCTTTGGTTTA 59.233 43.478 5.23 0.00 41.69 2.01
2045 3444 2.567169 GCATTAAGGCCTCCTTTGGTTT 59.433 45.455 5.23 0.00 41.69 3.27
2046 3445 2.179427 GCATTAAGGCCTCCTTTGGTT 58.821 47.619 5.23 0.00 41.69 3.67
2047 3446 1.359130 AGCATTAAGGCCTCCTTTGGT 59.641 47.619 5.23 4.67 41.69 3.67
2048 3447 2.149973 AGCATTAAGGCCTCCTTTGG 57.850 50.000 5.23 0.00 41.69 3.28
2049 3448 3.378427 GTGTAGCATTAAGGCCTCCTTTG 59.622 47.826 5.23 2.88 41.69 2.77
2050 3449 3.267031 AGTGTAGCATTAAGGCCTCCTTT 59.733 43.478 5.23 0.00 41.69 3.11
2051 3450 2.846827 AGTGTAGCATTAAGGCCTCCTT 59.153 45.455 5.23 3.40 46.63 3.36
2052 3451 2.482494 AGTGTAGCATTAAGGCCTCCT 58.518 47.619 5.23 0.00 33.87 3.69
2053 3452 3.134081 TGTAGTGTAGCATTAAGGCCTCC 59.866 47.826 5.23 0.00 0.00 4.30
2054 3453 4.402056 TGTAGTGTAGCATTAAGGCCTC 57.598 45.455 5.23 2.91 0.00 4.70
2055 3454 5.104527 TCAATGTAGTGTAGCATTAAGGCCT 60.105 40.000 8.77 0.00 34.01 5.19
2056 3455 5.123227 TCAATGTAGTGTAGCATTAAGGCC 58.877 41.667 8.77 0.00 34.01 5.19
2057 3456 6.049149 TCTCAATGTAGTGTAGCATTAAGGC 58.951 40.000 3.37 3.37 34.01 4.35
2058 3457 8.391106 GTTTCTCAATGTAGTGTAGCATTAAGG 58.609 37.037 0.00 0.00 34.01 2.69
2059 3458 8.935844 TGTTTCTCAATGTAGTGTAGCATTAAG 58.064 33.333 0.00 0.00 34.01 1.85
2060 3459 8.717821 GTGTTTCTCAATGTAGTGTAGCATTAA 58.282 33.333 0.00 0.00 34.01 1.40
2077 3476 5.530915 CCACTGATTAAACCTGTGTTTCTCA 59.469 40.000 13.28 0.00 43.50 3.27
2102 3501 2.108952 AGGGCAAAACAGAGGTGAAGAT 59.891 45.455 0.00 0.00 0.00 2.40
2236 3635 2.258748 GAGGCTAAGGGAGGTGCACC 62.259 65.000 29.22 29.22 0.00 5.01
2237 3636 1.222113 GAGGCTAAGGGAGGTGCAC 59.778 63.158 8.80 8.80 0.00 4.57
2238 3637 1.995626 GGAGGCTAAGGGAGGTGCA 60.996 63.158 0.00 0.00 0.00 4.57
2239 3638 2.911928 GGAGGCTAAGGGAGGTGC 59.088 66.667 0.00 0.00 0.00 5.01
2347 4628 0.521735 GGAAGTTCCGTGCCAACATC 59.478 55.000 6.06 0.00 0.00 3.06
2358 4639 9.764363 ATTTTAAGTTTGATTTGAGGAAGTTCC 57.236 29.630 14.54 14.54 36.58 3.62
2438 4977 9.790344 ACTTAATTGCTGATGCTAGAGAAATAT 57.210 29.630 0.00 0.00 40.48 1.28
2519 5203 8.338259 AGCTGTACGATGCAAAGAAAAATATAG 58.662 33.333 0.00 0.00 0.00 1.31
2588 5277 6.981559 GGTAGTAAGAAGAAAGGTAGCTGATG 59.018 42.308 0.00 0.00 0.00 3.07
2600 5289 8.242053 CGTCTTGAATACTGGTAGTAAGAAGAA 58.758 37.037 0.00 0.00 33.89 2.52
2602 5291 7.759465 TCGTCTTGAATACTGGTAGTAAGAAG 58.241 38.462 0.00 0.00 33.89 2.85
2608 5297 4.456911 TCGTTCGTCTTGAATACTGGTAGT 59.543 41.667 0.00 0.00 39.21 2.73
2732 5421 4.742649 TGTCTCCTCGAGGCCGCT 62.743 66.667 27.39 0.00 32.68 5.52
2749 5438 1.000993 AGGGACAGAGATGGCGTCT 59.999 57.895 9.44 9.44 40.81 4.18
2936 5652 3.710722 CGAGAAGGCTGGCCCAGT 61.711 66.667 13.35 0.00 36.58 4.00
2942 5658 2.492090 CGAGACCGAGAAGGCTGG 59.508 66.667 0.00 0.00 46.52 4.85
3112 5828 2.734723 CGACACAGCGTGACCCTG 60.735 66.667 14.18 0.00 36.96 4.45
3181 5900 6.018343 GCTCTTATATTTCTTCACTGACCAGC 60.018 42.308 0.00 0.00 0.00 4.85
3183 5902 6.042777 CGCTCTTATATTTCTTCACTGACCA 58.957 40.000 0.00 0.00 0.00 4.02
3184 5903 6.043411 ACGCTCTTATATTTCTTCACTGACC 58.957 40.000 0.00 0.00 0.00 4.02
3185 5904 7.527084 AACGCTCTTATATTTCTTCACTGAC 57.473 36.000 0.00 0.00 0.00 3.51
3186 5905 9.302345 CTAAACGCTCTTATATTTCTTCACTGA 57.698 33.333 0.00 0.00 0.00 3.41
3187 5906 9.302345 TCTAAACGCTCTTATATTTCTTCACTG 57.698 33.333 0.00 0.00 0.00 3.66
3313 6037 9.243637 CCTCGAAAATTGTAAACTTTTCATGAA 57.756 29.630 3.38 3.38 39.98 2.57
3314 6038 7.381139 GCCTCGAAAATTGTAAACTTTTCATGA 59.619 33.333 8.65 0.00 39.98 3.07
3335 6059 4.773323 TCTGTGTCATAGATATGCCTCG 57.227 45.455 0.00 0.00 33.76 4.63
3336 6060 9.494271 TTTTAATCTGTGTCATAGATATGCCTC 57.506 33.333 12.03 0.00 33.92 4.70
3352 6076 9.197306 ACCTGTAAAGAAAAGGTTTTAATCTGT 57.803 29.630 0.00 0.00 41.65 3.41
3392 6116 9.465985 CCGTTTTTATTACTTTTTAAGCAAGGA 57.534 29.630 0.00 0.00 0.00 3.36
3393 6117 9.251792 ACCGTTTTTATTACTTTTTAAGCAAGG 57.748 29.630 0.00 0.00 0.00 3.61
3397 6121 8.005466 GCCAACCGTTTTTATTACTTTTTAAGC 58.995 33.333 0.00 0.00 0.00 3.09
3399 6123 7.983484 TGGCCAACCGTTTTTATTACTTTTTAA 59.017 29.630 0.61 0.00 39.70 1.52
3400 6124 7.495055 TGGCCAACCGTTTTTATTACTTTTTA 58.505 30.769 0.61 0.00 39.70 1.52
3405 7045 4.873817 GTTGGCCAACCGTTTTTATTACT 58.126 39.130 34.36 0.00 39.70 2.24
3423 7063 1.134371 GCTCCCTAGCTAGTTGGTTGG 60.134 57.143 19.31 11.89 45.85 3.77
3435 7075 1.764054 CTGGGTGGAGGCTCCCTAG 60.764 68.421 30.03 18.36 43.74 3.02
3436 7076 2.119847 AACTGGGTGGAGGCTCCCTA 62.120 60.000 30.03 12.96 43.74 3.53
3439 7079 2.671682 GAACTGGGTGGAGGCTCC 59.328 66.667 26.95 26.95 36.96 4.70
3440 7080 1.617947 ATCGAACTGGGTGGAGGCTC 61.618 60.000 5.78 5.78 0.00 4.70
3441 7081 0.325296 TATCGAACTGGGTGGAGGCT 60.325 55.000 0.00 0.00 0.00 4.58
3442 7082 0.759346 ATATCGAACTGGGTGGAGGC 59.241 55.000 0.00 0.00 0.00 4.70
3443 7083 1.762957 ACATATCGAACTGGGTGGAGG 59.237 52.381 0.00 0.00 0.00 4.30
3449 7089 3.131223 ACTCTGTGACATATCGAACTGGG 59.869 47.826 0.00 0.00 0.00 4.45
3458 7098 2.093288 CAGTGGCCACTCTGTGACATAT 60.093 50.000 35.79 7.82 40.20 1.78
3467 7107 2.282040 GCTTGCAGTGGCCACTCT 60.282 61.111 35.79 14.37 40.20 3.24
3473 7113 2.872370 CTTTTAGATGCTTGCAGTGGC 58.128 47.619 0.87 0.00 41.68 5.01
3484 7124 3.543680 TTCCTCCCTCGCTTTTAGATG 57.456 47.619 0.00 0.00 0.00 2.90
3485 7125 4.262617 GTTTTCCTCCCTCGCTTTTAGAT 58.737 43.478 0.00 0.00 0.00 1.98
3502 7142 3.185797 AGCGACGTAAGGTGAATGTTTTC 59.814 43.478 0.00 0.00 46.39 2.29
3513 7153 1.060713 CACACAAGAGCGACGTAAGG 58.939 55.000 0.00 0.00 46.39 2.69
3545 7185 2.824489 GGCGGCTAGGGTTTGAGC 60.824 66.667 0.00 0.00 38.00 4.26
3566 7206 2.495809 GGAAGAGTCCGGAGAGTCC 58.504 63.158 3.06 5.97 42.60 3.85
3582 7222 4.250170 GGGGGCCGGGATAGAGGA 62.250 72.222 2.18 0.00 0.00 3.71
3593 7233 4.477119 ACTACGGGAGAGGGGGCC 62.477 72.222 0.00 0.00 0.00 5.80
3594 7234 2.838693 GACTACGGGAGAGGGGGC 60.839 72.222 0.00 0.00 0.00 5.80
3595 7235 1.115930 CATGACTACGGGAGAGGGGG 61.116 65.000 0.00 0.00 0.00 5.40
3597 7237 1.137086 CAACATGACTACGGGAGAGGG 59.863 57.143 0.00 0.00 0.00 4.30
3599 7239 1.471676 GGCAACATGACTACGGGAGAG 60.472 57.143 0.00 0.00 0.00 3.20
3600 7240 0.535335 GGCAACATGACTACGGGAGA 59.465 55.000 0.00 0.00 0.00 3.71
3601 7241 0.806102 CGGCAACATGACTACGGGAG 60.806 60.000 0.00 0.00 0.00 4.30
3602 7242 1.216977 CGGCAACATGACTACGGGA 59.783 57.895 0.00 0.00 0.00 5.14
3603 7243 2.461110 GCGGCAACATGACTACGGG 61.461 63.158 0.00 0.00 0.00 5.28
3604 7244 1.447838 AGCGGCAACATGACTACGG 60.448 57.895 0.00 0.00 0.00 4.02
3605 7245 1.014044 ACAGCGGCAACATGACTACG 61.014 55.000 0.00 0.00 0.00 3.51
3622 7262 0.834261 TGTCGGATCCACCTCCAACA 60.834 55.000 13.41 1.24 34.78 3.33
3637 7277 5.837437 AGCTTATTAGAGAACCTCATGTCG 58.163 41.667 0.00 0.00 32.06 4.35
3644 7285 4.471386 TCTGCCAAGCTTATTAGAGAACCT 59.529 41.667 0.00 0.00 0.00 3.50
3651 7292 2.906354 ACGGTCTGCCAAGCTTATTAG 58.094 47.619 0.00 0.00 34.09 1.73
3652 7293 3.343941 AACGGTCTGCCAAGCTTATTA 57.656 42.857 0.00 0.00 34.09 0.98
3675 7316 8.625467 AGAAAGTGGGTAAAGAATAGTCCTAT 57.375 34.615 0.00 0.00 0.00 2.57
3681 7322 7.361286 GCAGTGAAGAAAGTGGGTAAAGAATAG 60.361 40.741 0.00 0.00 0.00 1.73
3709 7350 0.615331 TTCTCTCCATCAGTGCCCAC 59.385 55.000 0.00 0.00 0.00 4.61
3730 7371 3.324846 TGTGATGGCCATAGATCTACCAC 59.675 47.826 20.84 19.25 32.13 4.16
3731 7372 3.324846 GTGTGATGGCCATAGATCTACCA 59.675 47.826 20.84 11.79 34.28 3.25
3732 7373 3.580458 AGTGTGATGGCCATAGATCTACC 59.420 47.826 20.84 3.78 0.00 3.18
3733 7374 4.617067 CGAGTGTGATGGCCATAGATCTAC 60.617 50.000 20.84 11.97 0.00 2.59
3734 7375 3.507622 CGAGTGTGATGGCCATAGATCTA 59.492 47.826 20.84 4.57 0.00 1.98
3748 7389 3.623510 CAGAGCACTAGATACGAGTGTGA 59.376 47.826 12.00 0.00 45.09 3.58
3762 7403 3.713764 AGCTTTATATCCCACAGAGCACT 59.286 43.478 0.00 0.00 0.00 4.40
3775 7416 4.013267 AGCATCCAAGCGAGCTTTATAT 57.987 40.909 7.70 0.00 40.15 0.86
3798 7442 1.032114 CCAATGGGCGAAGGAAGACC 61.032 60.000 0.00 0.00 37.28 3.85
3813 7457 3.893200 CTGATGTTGATATGGTGGCCAAT 59.107 43.478 7.24 0.00 36.95 3.16
3815 7459 2.934887 CTGATGTTGATATGGTGGCCA 58.065 47.619 0.00 0.00 38.19 5.36
3834 7478 0.179108 GATCTTCAACCGCCGTAGCT 60.179 55.000 0.00 0.00 36.60 3.32
3892 7536 1.609783 GGTGCTAGGCATCAACCCT 59.390 57.895 0.00 0.00 41.91 4.34
3905 7549 0.108329 CAACTAACGGGATCGGTGCT 60.108 55.000 0.00 0.00 41.39 4.40
3908 7552 1.219935 GGCAACTAACGGGATCGGT 59.780 57.895 0.00 0.00 41.39 4.69
3937 7581 1.661463 AGAGTGCCTCCCTTGATTGA 58.339 50.000 0.00 0.00 0.00 2.57
3969 7643 2.343101 CGACCATAACTTTGCCGAAGA 58.657 47.619 0.00 0.00 38.77 2.87
3973 7647 1.373590 CCCCGACCATAACTTTGCCG 61.374 60.000 0.00 0.00 0.00 5.69
3995 7669 3.684693 GAGAGAAGCTCAGGATGCC 57.315 57.895 0.00 0.00 43.38 4.40
4030 7704 9.394767 TGTACATGCTCTAAATATGACACAAAT 57.605 29.630 0.00 0.00 0.00 2.32
4031 7705 8.785329 TGTACATGCTCTAAATATGACACAAA 57.215 30.769 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.