Multiple sequence alignment - TraesCS2A01G183100

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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 TraesCS2A01G183100 chr2A 100.000 3565 0 0 1 3565 143026378 143029942 0.000000e+00 6584.0
1 TraesCS2A01G183100 chr2A 96.435 589 21 0 1 589 101102538 101101950 0.000000e+00 972.0
2 TraesCS2A01G183100 chr2A 96.265 589 21 1 1 589 751003542 751004129 0.000000e+00 965.0
3 TraesCS2A01G183100 chr2A 81.273 267 25 9 3171 3436 310535641 310535883 3.630000e-45 193.0
4 TraesCS2A01G183100 chr2A 84.375 96 7 3 3345 3439 143029633 143029545 1.760000e-13 87.9
5 TraesCS2A01G183100 chr2D 93.649 2299 85 16 886 3170 134930194 134932445 0.000000e+00 3380.0
6 TraesCS2A01G183100 chr2D 93.898 590 35 1 1 589 634050014 634049425 0.000000e+00 889.0
7 TraesCS2A01G183100 chr2D 85.172 290 18 10 590 858 134929911 134930196 1.260000e-69 274.0
8 TraesCS2A01G183100 chr2D 95.506 89 0 3 3481 3565 134932466 134932554 4.800000e-29 139.0
9 TraesCS2A01G183100 chr2D 77.612 268 27 11 3171 3436 645152724 645152960 8.030000e-27 132.0
10 TraesCS2A01G183100 chr2D 83.673 98 10 4 3341 3438 506452698 506452607 1.760000e-13 87.9
11 TraesCS2A01G183100 chr2D 83.505 97 10 3 3342 3438 83186927 83186837 6.340000e-13 86.1
12 TraesCS2A01G183100 chr2B 93.461 2294 83 21 886 3167 191877739 191879977 0.000000e+00 3343.0
13 TraesCS2A01G183100 chr2B 85.172 290 18 10 590 858 191877456 191877741 1.260000e-69 274.0
14 TraesCS2A01G183100 chr2B 81.716 268 26 4 3169 3436 154494248 154494492 6.030000e-48 202.0
15 TraesCS2A01G183100 chr2B 81.343 268 26 4 3169 3436 154606008 154605765 2.810000e-46 196.0
16 TraesCS2A01G183100 chr2B 93.333 135 5 3 3435 3565 191881149 191881283 2.810000e-46 196.0
17 TraesCS2A01G183100 chr2B 81.343 268 27 6 3169 3436 212273144 212272900 2.810000e-46 196.0
18 TraesCS2A01G183100 chr1A 94.604 593 22 3 1 592 571361956 571361373 0.000000e+00 909.0
19 TraesCS2A01G183100 chr1A 84.701 268 18 9 3171 3438 362683366 362683610 2.750000e-61 246.0
20 TraesCS2A01G183100 chr1A 80.000 270 26 11 3169 3436 90725930 90725687 1.320000e-39 174.0
21 TraesCS2A01G183100 chr7D 94.530 585 32 0 5 589 55576779 55576195 0.000000e+00 904.0
22 TraesCS2A01G183100 chr7D 94.186 86 5 0 3171 3256 299186767 299186682 8.030000e-27 132.0
23 TraesCS2A01G183100 chr5D 93.390 590 35 4 1 590 5689066 5689651 0.000000e+00 870.0
24 TraesCS2A01G183100 chr5D 81.648 267 23 10 3172 3436 449675009 449674767 7.810000e-47 198.0
25 TraesCS2A01G183100 chr5D 83.654 208 14 7 3168 3373 439260233 439260044 1.020000e-40 178.0
26 TraesCS2A01G183100 chrUn 93.220 590 37 2 1 590 365394074 365394660 0.000000e+00 865.0
27 TraesCS2A01G183100 chr1B 93.220 590 37 2 1 590 602526590 602527176 0.000000e+00 865.0
28 TraesCS2A01G183100 chr1B 93.220 590 36 3 1 590 602539524 602540109 0.000000e+00 865.0
29 TraesCS2A01G183100 chr1D 84.387 269 17 6 3169 3436 4974461 4974705 1.280000e-59 241.0
30 TraesCS2A01G183100 chr1D 82.331 266 22 12 3169 3433 381977314 381977073 1.300000e-49 207.0
31 TraesCS2A01G183100 chr1D 85.263 95 8 3 3342 3436 480062544 480062632 3.790000e-15 93.5
32 TraesCS2A01G183100 chr6D 83.636 275 20 8 3169 3441 363386186 363386437 5.950000e-58 235.0
33 TraesCS2A01G183100 chr3D 82.463 268 24 9 3169 3436 611922954 611923198 2.790000e-51 213.0
34 TraesCS2A01G183100 chr7B 83.732 209 17 7 3172 3380 162921275 162921084 7.860000e-42 182.0
35 TraesCS2A01G183100 chr6B 84.277 159 17 4 3279 3436 599807272 599807423 7.970000e-32 148.0
36 TraesCS2A01G183100 chr5B 94.186 86 5 0 3171 3256 521276880 521276795 8.030000e-27 132.0
37 TraesCS2A01G183100 chr4B 84.270 89 6 3 3351 3438 483338719 483338638 2.950000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G183100 chr2A 143026378 143029942 3564 False 6584.000000 6584 100.000000 1 3565 1 chr2A.!!$F1 3564
1 TraesCS2A01G183100 chr2A 101101950 101102538 588 True 972.000000 972 96.435000 1 589 1 chr2A.!!$R1 588
2 TraesCS2A01G183100 chr2A 751003542 751004129 587 False 965.000000 965 96.265000 1 589 1 chr2A.!!$F3 588
3 TraesCS2A01G183100 chr2D 134929911 134932554 2643 False 1264.333333 3380 91.442333 590 3565 3 chr2D.!!$F2 2975
4 TraesCS2A01G183100 chr2D 634049425 634050014 589 True 889.000000 889 93.898000 1 589 1 chr2D.!!$R3 588
5 TraesCS2A01G183100 chr2B 191877456 191881283 3827 False 1271.000000 3343 90.655333 590 3565 3 chr2B.!!$F2 2975
6 TraesCS2A01G183100 chr1A 571361373 571361956 583 True 909.000000 909 94.604000 1 592 1 chr1A.!!$R2 591
7 TraesCS2A01G183100 chr7D 55576195 55576779 584 True 904.000000 904 94.530000 5 589 1 chr7D.!!$R1 584
8 TraesCS2A01G183100 chr5D 5689066 5689651 585 False 870.000000 870 93.390000 1 590 1 chr5D.!!$F1 589
9 TraesCS2A01G183100 chrUn 365394074 365394660 586 False 865.000000 865 93.220000 1 590 1 chrUn.!!$F1 589
10 TraesCS2A01G183100 chr1B 602526590 602527176 586 False 865.000000 865 93.220000 1 590 1 chr1B.!!$F1 589
11 TraesCS2A01G183100 chr1B 602539524 602540109 585 False 865.000000 865 93.220000 1 590 1 chr1B.!!$F2 589

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
869 908 0.392863 CGATTCCTGGATGTGCACCA 60.393 55.0 15.69 4.11 35.96 4.17 F
1086 1125 0.527565 CATTCCCCGCTTCCACTTTG 59.472 55.0 0.00 0.00 0.00 2.77 F
1833 1877 0.337428 AATTCTCAAGGGGCCTGCAT 59.663 50.0 0.84 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1779 0.440758 CGTGTAAATTTCGGCGAGCA 59.559 50.0 10.46 0.73 0.00 4.26 R
2146 2197 0.710567 CAGATCAGACAACGTGCGAC 59.289 55.0 0.00 0.00 0.00 5.19 R
3172 3233 0.461163 AAAGCCCAAACAAACACGGC 60.461 50.0 0.00 0.00 40.03 5.68 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
170 171 4.215613 GTGGAGGTGACATTAGTGAAAACC 59.784 45.833 0.00 0.00 0.00 3.27
177 178 4.277174 TGACATTAGTGAAAACCGCACATT 59.723 37.500 0.00 0.00 38.70 2.71
245 246 1.472878 TCGACTACTAGGCAGTTGCAG 59.527 52.381 6.43 0.00 44.36 4.41
269 272 5.352643 AAACGAGGTACTAAATTGCACAC 57.647 39.130 0.00 0.00 41.55 3.82
310 316 5.538813 ACATACTCATGCGGGATCTAGTTTA 59.461 40.000 0.00 0.00 35.39 2.01
603 611 7.117241 AGACGCGTCCATGTTTAAATATATG 57.883 36.000 34.08 1.07 0.00 1.78
662 675 4.621068 TCATCTCATGCGAATTTGGTTC 57.379 40.909 0.00 0.00 0.00 3.62
671 684 7.374272 TCATGCGAATTTGGTTCTATGAAAAA 58.626 30.769 0.00 0.00 36.25 1.94
739 772 8.302515 AGCCAAAAACATGAGAAATATCATCT 57.697 30.769 0.00 0.00 37.84 2.90
740 773 8.411683 AGCCAAAAACATGAGAAATATCATCTC 58.588 33.333 0.00 10.22 42.94 2.75
865 904 1.153086 AGGCGATTCCTGGATGTGC 60.153 57.895 0.00 1.42 45.54 4.57
866 905 1.451927 GGCGATTCCTGGATGTGCA 60.452 57.895 14.04 0.00 0.00 4.57
867 906 1.718757 GGCGATTCCTGGATGTGCAC 61.719 60.000 10.75 10.75 0.00 4.57
868 907 1.718757 GCGATTCCTGGATGTGCACC 61.719 60.000 15.69 0.00 0.00 5.01
869 908 0.392863 CGATTCCTGGATGTGCACCA 60.393 55.000 15.69 4.11 35.96 4.17
870 909 1.098050 GATTCCTGGATGTGCACCAC 58.902 55.000 15.69 8.11 33.57 4.16
871 910 0.677731 ATTCCTGGATGTGCACCACG 60.678 55.000 15.69 0.00 37.14 4.94
872 911 2.032528 CCTGGATGTGCACCACGT 59.967 61.111 15.69 0.00 37.14 4.49
873 912 1.600636 CCTGGATGTGCACCACGTT 60.601 57.895 15.69 0.00 37.14 3.99
874 913 1.575922 CTGGATGTGCACCACGTTG 59.424 57.895 15.69 0.00 37.14 4.10
875 914 2.255252 GGATGTGCACCACGTTGC 59.745 61.111 15.69 5.26 43.31 4.17
887 926 4.988598 CGTTGCACGGGAGCACCT 62.989 66.667 0.00 0.00 45.61 4.00
939 978 3.077695 GGGTCCCATTATCCTCTCTCCTA 59.922 52.174 1.78 0.00 0.00 2.94
991 1030 1.229209 GACCTCACTCCCACTCCCA 60.229 63.158 0.00 0.00 0.00 4.37
992 1031 1.536662 ACCTCACTCCCACTCCCAC 60.537 63.158 0.00 0.00 0.00 4.61
993 1032 1.229336 CCTCACTCCCACTCCCACT 60.229 63.158 0.00 0.00 0.00 4.00
994 1033 1.261238 CCTCACTCCCACTCCCACTC 61.261 65.000 0.00 0.00 0.00 3.51
995 1034 1.229209 TCACTCCCACTCCCACTCC 60.229 63.158 0.00 0.00 0.00 3.85
996 1035 2.122954 ACTCCCACTCCCACTCCC 59.877 66.667 0.00 0.00 0.00 4.30
997 1036 2.122729 CTCCCACTCCCACTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
1083 1122 2.677228 CCATTCCCCGCTTCCACT 59.323 61.111 0.00 0.00 0.00 4.00
1086 1125 0.527565 CATTCCCCGCTTCCACTTTG 59.472 55.000 0.00 0.00 0.00 2.77
1156 1195 4.680237 CGCAGCCGTCCACTTCCA 62.680 66.667 0.00 0.00 0.00 3.53
1161 1200 2.358737 CCGTCCACTTCCACTGCC 60.359 66.667 0.00 0.00 0.00 4.85
1361 1400 5.059833 GGAGCTCGTAATCCTCATTCATTT 58.940 41.667 7.83 0.00 32.51 2.32
1434 1473 0.821517 TACGCTGATACTGGTGTGGG 59.178 55.000 0.00 0.00 0.00 4.61
1545 1584 2.100252 CTCGCCGGTGGAGACTAATAAA 59.900 50.000 16.49 0.00 33.27 1.40
1620 1659 2.755650 CTGTTCCTGTACAAGTTCGCT 58.244 47.619 0.00 0.00 0.00 4.93
1622 1661 3.909430 TGTTCCTGTACAAGTTCGCTAG 58.091 45.455 0.00 0.00 0.00 3.42
1702 1742 5.083533 TCCACAATTGTGCTTGTTTCTTT 57.916 34.783 29.42 0.00 44.34 2.52
1711 1751 8.947055 ATTGTGCTTGTTTCTTTCTGTATTTT 57.053 26.923 0.00 0.00 0.00 1.82
1712 1752 7.754069 TGTGCTTGTTTCTTTCTGTATTTTG 57.246 32.000 0.00 0.00 0.00 2.44
1713 1753 7.319646 TGTGCTTGTTTCTTTCTGTATTTTGT 58.680 30.769 0.00 0.00 0.00 2.83
1714 1754 8.462811 TGTGCTTGTTTCTTTCTGTATTTTGTA 58.537 29.630 0.00 0.00 0.00 2.41
1715 1755 8.743099 GTGCTTGTTTCTTTCTGTATTTTGTAC 58.257 33.333 0.00 0.00 0.00 2.90
1736 1776 9.997482 TTGTACTGTATTTCTTTGTTCAAGTTC 57.003 29.630 0.00 0.00 33.66 3.01
1737 1777 9.168451 TGTACTGTATTTCTTTGTTCAAGTTCA 57.832 29.630 0.00 0.00 33.66 3.18
1738 1778 9.651718 GTACTGTATTTCTTTGTTCAAGTTCAG 57.348 33.333 0.00 0.00 33.66 3.02
1739 1779 8.281212 ACTGTATTTCTTTGTTCAAGTTCAGT 57.719 30.769 0.00 0.00 33.66 3.41
1740 1780 8.184192 ACTGTATTTCTTTGTTCAAGTTCAGTG 58.816 33.333 0.00 0.00 33.66 3.66
1741 1781 6.972328 TGTATTTCTTTGTTCAAGTTCAGTGC 59.028 34.615 0.00 0.00 33.66 4.40
1742 1782 5.643379 TTTCTTTGTTCAAGTTCAGTGCT 57.357 34.783 0.00 0.00 33.66 4.40
1743 1783 4.882671 TCTTTGTTCAAGTTCAGTGCTC 57.117 40.909 0.00 0.00 33.66 4.26
1762 1806 3.150731 CTCGCCGAAATTTACACGAAAC 58.849 45.455 9.35 0.00 0.00 2.78
1833 1877 0.337428 AATTCTCAAGGGGCCTGCAT 59.663 50.000 0.84 0.00 0.00 3.96
1905 1954 9.661563 ACATTTGATTGTATGAATCATGCTTTT 57.338 25.926 12.29 0.00 36.63 2.27
2033 2083 4.202441 CAAGATTGTGAGGATTACCAGGG 58.798 47.826 0.00 0.00 38.94 4.45
2189 2245 8.560576 TGATCGAATCTGTTTTTGTTTTTCTC 57.439 30.769 0.00 0.00 0.00 2.87
2248 2304 5.404366 CACAACTTCATCCATTTTCTGCTTG 59.596 40.000 0.00 0.00 0.00 4.01
2253 2312 5.381174 TCATCCATTTTCTGCTTGTTCTG 57.619 39.130 0.00 0.00 0.00 3.02
2262 2321 2.480037 TCTGCTTGTTCTGTGTATTGCG 59.520 45.455 0.00 0.00 0.00 4.85
2297 2356 9.878599 CTTCAGCGAGTCTAATTAAAAGAAAAA 57.121 29.630 0.00 0.00 0.00 1.94
2462 2521 2.923655 CGTAGAGAAAATCAGCGAGCAA 59.076 45.455 0.00 0.00 31.65 3.91
2515 2574 0.885879 AGTGACAGCGTATCGGACAA 59.114 50.000 0.00 0.00 0.00 3.18
2678 2737 4.104776 ACTGTCGTTTTTGAGTGCAAATG 58.895 39.130 0.00 0.00 43.07 2.32
2692 2751 5.585390 AGTGCAAATGCTATGCTAATGAAC 58.415 37.500 6.97 0.00 44.14 3.18
2698 2757 7.043590 GCAAATGCTATGCTAATGAACTTTCAG 60.044 37.037 0.00 0.00 39.49 3.02
2726 2785 7.402862 AGGCTAGTAGTAAAATGTGGTGAAAT 58.597 34.615 0.00 0.00 0.00 2.17
2830 2889 8.772705 TGTTCTACGGTTTGAATAACGTTAATT 58.227 29.630 12.81 7.33 40.38 1.40
2903 2962 3.005791 AGGTACAAATGCTGCTTGGTTTC 59.994 43.478 0.00 0.00 0.00 2.78
3068 3129 2.501723 ACCGATAACCTCAGCAATGTCT 59.498 45.455 0.00 0.00 0.00 3.41
3123 3184 5.489792 AACAGTTTCTTCAGAGCTATCCA 57.510 39.130 0.00 0.00 0.00 3.41
3134 3195 5.869579 TCAGAGCTATCCAAAAGAAACTGT 58.130 37.500 0.00 0.00 0.00 3.55
3139 3200 6.769512 AGCTATCCAAAAGAAACTGTAGTGA 58.230 36.000 0.00 0.00 0.00 3.41
3175 3236 5.945155 GAGAATCTCTAGTGTATAAGGCCG 58.055 45.833 2.45 0.00 0.00 6.13
3176 3237 5.386924 AGAATCTCTAGTGTATAAGGCCGT 58.613 41.667 0.00 0.00 0.00 5.68
3177 3238 5.241949 AGAATCTCTAGTGTATAAGGCCGTG 59.758 44.000 0.00 0.00 0.00 4.94
3178 3239 3.894759 TCTCTAGTGTATAAGGCCGTGT 58.105 45.455 0.00 0.00 0.00 4.49
3179 3240 4.275810 TCTCTAGTGTATAAGGCCGTGTT 58.724 43.478 0.00 0.00 0.00 3.32
3180 3241 4.708421 TCTCTAGTGTATAAGGCCGTGTTT 59.292 41.667 0.00 0.00 0.00 2.83
3181 3242 4.751060 TCTAGTGTATAAGGCCGTGTTTG 58.249 43.478 0.00 0.00 0.00 2.93
3182 3243 3.412237 AGTGTATAAGGCCGTGTTTGT 57.588 42.857 0.00 0.00 0.00 2.83
3183 3244 3.746940 AGTGTATAAGGCCGTGTTTGTT 58.253 40.909 0.00 0.00 0.00 2.83
3184 3245 4.139038 AGTGTATAAGGCCGTGTTTGTTT 58.861 39.130 0.00 0.00 0.00 2.83
3185 3246 4.023536 AGTGTATAAGGCCGTGTTTGTTTG 60.024 41.667 0.00 0.00 0.00 2.93
3186 3247 3.253677 TGTATAAGGCCGTGTTTGTTTGG 59.746 43.478 0.00 0.00 0.00 3.28
3187 3248 1.033574 TAAGGCCGTGTTTGTTTGGG 58.966 50.000 0.00 0.00 0.00 4.12
3188 3249 2.279851 GGCCGTGTTTGTTTGGGC 60.280 61.111 0.00 0.00 43.01 5.36
3189 3250 2.791868 GGCCGTGTTTGTTTGGGCT 61.792 57.895 0.00 0.00 43.27 5.19
3190 3251 1.142965 GCCGTGTTTGTTTGGGCTT 59.857 52.632 0.00 0.00 40.59 4.35
3191 3252 0.461163 GCCGTGTTTGTTTGGGCTTT 60.461 50.000 0.00 0.00 40.59 3.51
3192 3253 2.009542 GCCGTGTTTGTTTGGGCTTTT 61.010 47.619 0.00 0.00 40.59 2.27
3193 3254 1.663135 CCGTGTTTGTTTGGGCTTTTG 59.337 47.619 0.00 0.00 0.00 2.44
3194 3255 1.061857 CGTGTTTGTTTGGGCTTTTGC 59.938 47.619 0.00 0.00 46.64 3.68
3195 3256 2.355197 GTGTTTGTTTGGGCTTTTGCT 58.645 42.857 0.00 0.00 46.54 3.91
3196 3257 2.746904 GTGTTTGTTTGGGCTTTTGCTT 59.253 40.909 0.00 0.00 46.54 3.91
3197 3258 3.006247 TGTTTGTTTGGGCTTTTGCTTC 58.994 40.909 0.00 0.00 46.54 3.86
3198 3259 3.270027 GTTTGTTTGGGCTTTTGCTTCT 58.730 40.909 0.00 0.00 46.54 2.85
3199 3260 3.625649 TTGTTTGGGCTTTTGCTTCTT 57.374 38.095 0.00 0.00 46.54 2.52
3200 3261 3.177997 TGTTTGGGCTTTTGCTTCTTC 57.822 42.857 0.00 0.00 46.54 2.87
3201 3262 2.765699 TGTTTGGGCTTTTGCTTCTTCT 59.234 40.909 0.00 0.00 46.54 2.85
3202 3263 3.197549 TGTTTGGGCTTTTGCTTCTTCTT 59.802 39.130 0.00 0.00 46.54 2.52
3203 3264 4.191544 GTTTGGGCTTTTGCTTCTTCTTT 58.808 39.130 0.00 0.00 46.54 2.52
3204 3265 4.486125 TTGGGCTTTTGCTTCTTCTTTT 57.514 36.364 0.00 0.00 46.54 2.27
3205 3266 3.795877 TGGGCTTTTGCTTCTTCTTTTG 58.204 40.909 0.00 0.00 46.54 2.44
3206 3267 2.545526 GGGCTTTTGCTTCTTCTTTTGC 59.454 45.455 0.00 0.00 46.54 3.68
3207 3268 3.197265 GGCTTTTGCTTCTTCTTTTGCA 58.803 40.909 0.00 0.00 46.54 4.08
3208 3269 3.246936 GGCTTTTGCTTCTTCTTTTGCAG 59.753 43.478 0.00 0.00 46.54 4.41
3209 3270 3.302935 GCTTTTGCTTCTTCTTTTGCAGC 60.303 43.478 0.00 0.00 43.35 5.25
3210 3271 3.806625 TTTGCTTCTTCTTTTGCAGCT 57.193 38.095 0.00 0.00 36.75 4.24
3211 3272 3.806625 TTGCTTCTTCTTTTGCAGCTT 57.193 38.095 0.00 0.00 36.75 3.74
3212 3273 3.806625 TGCTTCTTCTTTTGCAGCTTT 57.193 38.095 0.00 0.00 0.00 3.51
3213 3274 4.127566 TGCTTCTTCTTTTGCAGCTTTT 57.872 36.364 0.00 0.00 0.00 2.27
3214 3275 4.114794 TGCTTCTTCTTTTGCAGCTTTTC 58.885 39.130 0.00 0.00 0.00 2.29
3215 3276 4.142093 TGCTTCTTCTTTTGCAGCTTTTCT 60.142 37.500 0.00 0.00 0.00 2.52
3216 3277 5.067674 TGCTTCTTCTTTTGCAGCTTTTCTA 59.932 36.000 0.00 0.00 0.00 2.10
3217 3278 5.400782 GCTTCTTCTTTTGCAGCTTTTCTAC 59.599 40.000 0.00 0.00 0.00 2.59
3218 3279 6.699575 TTCTTCTTTTGCAGCTTTTCTACT 57.300 33.333 0.00 0.00 0.00 2.57
3219 3280 6.699575 TCTTCTTTTGCAGCTTTTCTACTT 57.300 33.333 0.00 0.00 0.00 2.24
3220 3281 7.100458 TCTTCTTTTGCAGCTTTTCTACTTT 57.900 32.000 0.00 0.00 0.00 2.66
3221 3282 7.547227 TCTTCTTTTGCAGCTTTTCTACTTTT 58.453 30.769 0.00 0.00 0.00 2.27
3222 3283 7.489113 TCTTCTTTTGCAGCTTTTCTACTTTTG 59.511 33.333 0.00 0.00 0.00 2.44
3223 3284 5.519927 TCTTTTGCAGCTTTTCTACTTTTGC 59.480 36.000 0.00 0.00 0.00 3.68
3224 3285 3.369546 TGCAGCTTTTCTACTTTTGCC 57.630 42.857 0.00 0.00 0.00 4.52
3225 3286 2.692557 TGCAGCTTTTCTACTTTTGCCA 59.307 40.909 0.00 0.00 0.00 4.92
3226 3287 3.243501 TGCAGCTTTTCTACTTTTGCCAG 60.244 43.478 0.00 0.00 0.00 4.85
3227 3288 3.004734 GCAGCTTTTCTACTTTTGCCAGA 59.995 43.478 0.00 0.00 0.00 3.86
3228 3289 4.499696 GCAGCTTTTCTACTTTTGCCAGAA 60.500 41.667 0.00 0.00 0.00 3.02
3229 3290 5.591099 CAGCTTTTCTACTTTTGCCAGAAA 58.409 37.500 0.00 0.00 36.70 2.52
3230 3291 5.689068 CAGCTTTTCTACTTTTGCCAGAAAG 59.311 40.000 0.00 3.59 38.95 2.62
3231 3292 4.445718 GCTTTTCTACTTTTGCCAGAAAGC 59.554 41.667 0.00 0.00 38.95 3.51
3232 3293 4.584327 TTTCTACTTTTGCCAGAAAGCC 57.416 40.909 4.74 0.00 39.65 4.35
3233 3294 3.222173 TCTACTTTTGCCAGAAAGCCA 57.778 42.857 4.74 0.00 39.65 4.75
3234 3295 3.766545 TCTACTTTTGCCAGAAAGCCAT 58.233 40.909 4.74 0.00 39.65 4.40
3235 3296 4.917385 TCTACTTTTGCCAGAAAGCCATA 58.083 39.130 4.74 0.00 39.65 2.74
3236 3297 5.321102 TCTACTTTTGCCAGAAAGCCATAA 58.679 37.500 4.74 0.00 39.65 1.90
3237 3298 4.953940 ACTTTTGCCAGAAAGCCATAAA 57.046 36.364 4.74 0.00 39.65 1.40
3238 3299 5.289083 ACTTTTGCCAGAAAGCCATAAAA 57.711 34.783 4.74 0.00 39.65 1.52
3239 3300 5.299949 ACTTTTGCCAGAAAGCCATAAAAG 58.700 37.500 0.00 0.00 39.65 2.27
3240 3301 3.317603 TTGCCAGAAAGCCATAAAAGC 57.682 42.857 0.00 0.00 0.00 3.51
3241 3302 2.528564 TGCCAGAAAGCCATAAAAGCT 58.471 42.857 0.00 0.00 44.19 3.74
3242 3303 2.493278 TGCCAGAAAGCCATAAAAGCTC 59.507 45.455 0.00 0.00 40.49 4.09
3243 3304 2.159184 GCCAGAAAGCCATAAAAGCTCC 60.159 50.000 0.00 0.00 40.49 4.70
3244 3305 3.359950 CCAGAAAGCCATAAAAGCTCCT 58.640 45.455 0.00 0.00 40.49 3.69
3245 3306 4.526970 CCAGAAAGCCATAAAAGCTCCTA 58.473 43.478 0.00 0.00 40.49 2.94
3246 3307 4.949856 CCAGAAAGCCATAAAAGCTCCTAA 59.050 41.667 0.00 0.00 40.49 2.69
3247 3308 5.418840 CCAGAAAGCCATAAAAGCTCCTAAA 59.581 40.000 0.00 0.00 40.49 1.85
3248 3309 6.097412 CCAGAAAGCCATAAAAGCTCCTAAAT 59.903 38.462 0.00 0.00 40.49 1.40
3249 3310 7.285401 CCAGAAAGCCATAAAAGCTCCTAAATA 59.715 37.037 0.00 0.00 40.49 1.40
3250 3311 8.348507 CAGAAAGCCATAAAAGCTCCTAAATAG 58.651 37.037 0.00 0.00 40.49 1.73
3251 3312 7.503902 AGAAAGCCATAAAAGCTCCTAAATAGG 59.496 37.037 0.00 0.00 40.49 2.57
3252 3313 6.267492 AGCCATAAAAGCTCCTAAATAGGT 57.733 37.500 6.39 0.00 44.02 3.08
3253 3314 6.064717 AGCCATAAAAGCTCCTAAATAGGTG 58.935 40.000 6.39 5.41 44.02 4.00
3260 3321 3.118905 CTCCTAAATAGGTGCTGCTCC 57.881 52.381 12.66 12.66 44.02 4.70
3261 3322 2.435805 CTCCTAAATAGGTGCTGCTCCA 59.564 50.000 21.49 9.00 44.02 3.86
3262 3323 2.435805 TCCTAAATAGGTGCTGCTCCAG 59.564 50.000 21.49 10.12 44.02 3.86
3263 3324 2.435805 CCTAAATAGGTGCTGCTCCAGA 59.564 50.000 21.49 10.16 38.69 3.86
3264 3325 3.118261 CCTAAATAGGTGCTGCTCCAGAA 60.118 47.826 21.49 8.00 38.69 3.02
3265 3326 2.706339 AATAGGTGCTGCTCCAGAAG 57.294 50.000 21.49 0.00 32.44 2.85
3279 3340 4.954875 CTCCAGAAGCACCTATTTAGGAG 58.045 47.826 10.61 3.78 46.63 3.69
3280 3341 3.711704 TCCAGAAGCACCTATTTAGGAGG 59.288 47.826 10.61 3.65 46.63 4.30
3288 3349 6.365520 AGCACCTATTTAGGAGGTTTTATGG 58.634 40.000 10.61 0.00 45.40 2.74
3289 3350 5.009710 GCACCTATTTAGGAGGTTTTATGGC 59.990 44.000 10.61 0.00 45.40 4.40
3290 3351 6.365520 CACCTATTTAGGAGGTTTTATGGCT 58.634 40.000 10.61 0.00 45.40 4.75
3291 3352 6.833933 CACCTATTTAGGAGGTTTTATGGCTT 59.166 38.462 10.61 0.00 45.40 4.35
3292 3353 7.342026 CACCTATTTAGGAGGTTTTATGGCTTT 59.658 37.037 10.61 0.00 45.40 3.51
3293 3354 7.899172 ACCTATTTAGGAGGTTTTATGGCTTTT 59.101 33.333 10.61 0.00 45.40 2.27
3294 3355 8.197439 CCTATTTAGGAGGTTTTATGGCTTTTG 58.803 37.037 0.00 0.00 46.63 2.44
3295 3356 5.993748 TTAGGAGGTTTTATGGCTTTTGG 57.006 39.130 0.00 0.00 0.00 3.28
3296 3357 4.126520 AGGAGGTTTTATGGCTTTTGGA 57.873 40.909 0.00 0.00 0.00 3.53
3297 3358 4.089361 AGGAGGTTTTATGGCTTTTGGAG 58.911 43.478 0.00 0.00 0.00 3.86
3314 3375 9.546428 GCTTTTGGAGCCAAATATTGTTATATT 57.454 29.630 14.86 0.00 46.01 1.28
3359 3420 5.240713 CTGCAAAAGCACCTATTTAGGAG 57.759 43.478 10.61 3.78 46.63 3.69
3369 3430 6.319141 CACCTATTTAGGAGCTTTTATGGC 57.681 41.667 10.61 0.00 46.63 4.40
3370 3431 6.064717 CACCTATTTAGGAGCTTTTATGGCT 58.935 40.000 10.61 0.00 46.63 4.75
3371 3432 6.547510 CACCTATTTAGGAGCTTTTATGGCTT 59.452 38.462 10.61 0.00 46.63 4.35
3372 3433 7.068716 CACCTATTTAGGAGCTTTTATGGCTTT 59.931 37.037 10.61 0.00 46.63 3.51
3373 3434 7.619698 ACCTATTTAGGAGCTTTTATGGCTTTT 59.380 33.333 10.61 0.00 46.63 2.27
3374 3435 8.478066 CCTATTTAGGAGCTTTTATGGCTTTTT 58.522 33.333 0.00 0.00 46.63 1.94
3375 3436 9.305925 CTATTTAGGAGCTTTTATGGCTTTTTG 57.694 33.333 0.00 0.00 40.40 2.44
3376 3437 4.541973 AGGAGCTTTTATGGCTTTTTGG 57.458 40.909 0.00 0.00 40.40 3.28
3377 3438 3.903714 AGGAGCTTTTATGGCTTTTTGGT 59.096 39.130 0.00 0.00 40.40 3.67
3378 3439 4.021104 AGGAGCTTTTATGGCTTTTTGGTC 60.021 41.667 0.00 0.00 40.40 4.02
3379 3440 4.262420 GGAGCTTTTATGGCTTTTTGGTCA 60.262 41.667 0.00 0.00 40.40 4.02
3380 3441 5.482006 GAGCTTTTATGGCTTTTTGGTCAT 58.518 37.500 0.00 0.00 40.40 3.06
3381 3442 5.868454 AGCTTTTATGGCTTTTTGGTCATT 58.132 33.333 0.00 0.00 36.56 2.57
3382 3443 5.702209 AGCTTTTATGGCTTTTTGGTCATTG 59.298 36.000 0.00 0.00 36.56 2.82
3383 3444 5.106594 GCTTTTATGGCTTTTTGGTCATTGG 60.107 40.000 0.00 0.00 33.33 3.16
3384 3445 5.559148 TTTATGGCTTTTTGGTCATTGGT 57.441 34.783 0.00 0.00 33.33 3.67
3385 3446 3.683365 ATGGCTTTTTGGTCATTGGTC 57.317 42.857 0.00 0.00 0.00 4.02
3386 3447 2.392662 TGGCTTTTTGGTCATTGGTCA 58.607 42.857 0.00 0.00 0.00 4.02
3387 3448 2.768527 TGGCTTTTTGGTCATTGGTCAA 59.231 40.909 0.00 0.00 0.00 3.18
3388 3449 3.198635 TGGCTTTTTGGTCATTGGTCAAA 59.801 39.130 0.00 0.00 0.00 2.69
3389 3450 3.809279 GGCTTTTTGGTCATTGGTCAAAG 59.191 43.478 0.00 0.00 32.88 2.77
3390 3451 4.442753 GGCTTTTTGGTCATTGGTCAAAGA 60.443 41.667 0.00 0.00 32.88 2.52
3391 3452 5.115480 GCTTTTTGGTCATTGGTCAAAGAA 58.885 37.500 0.00 0.00 32.88 2.52
3392 3453 5.584251 GCTTTTTGGTCATTGGTCAAAGAAA 59.416 36.000 0.00 0.00 32.88 2.52
3393 3454 6.093357 GCTTTTTGGTCATTGGTCAAAGAAAA 59.907 34.615 0.00 0.00 32.88 2.29
3394 3455 7.361628 GCTTTTTGGTCATTGGTCAAAGAAAAA 60.362 33.333 0.00 0.00 32.88 1.94
3418 3479 7.586714 AAGATGCAAAAGCATAAGTAAAAGC 57.413 32.000 2.56 0.00 0.00 3.51
3419 3480 6.101997 AGATGCAAAAGCATAAGTAAAAGCC 58.898 36.000 2.56 0.00 0.00 4.35
3420 3481 4.565022 TGCAAAAGCATAAGTAAAAGCCC 58.435 39.130 0.00 0.00 0.00 5.19
3421 3482 4.039730 TGCAAAAGCATAAGTAAAAGCCCA 59.960 37.500 0.00 0.00 0.00 5.36
3422 3483 4.994217 GCAAAAGCATAAGTAAAAGCCCAA 59.006 37.500 0.00 0.00 0.00 4.12
3423 3484 5.468409 GCAAAAGCATAAGTAAAAGCCCAAA 59.532 36.000 0.00 0.00 0.00 3.28
3424 3485 6.565811 GCAAAAGCATAAGTAAAAGCCCAAAC 60.566 38.462 0.00 0.00 0.00 2.93
3425 3486 5.799827 AAGCATAAGTAAAAGCCCAAACA 57.200 34.783 0.00 0.00 0.00 2.83
3426 3487 5.799827 AGCATAAGTAAAAGCCCAAACAA 57.200 34.783 0.00 0.00 0.00 2.83
3427 3488 6.168270 AGCATAAGTAAAAGCCCAAACAAA 57.832 33.333 0.00 0.00 0.00 2.83
3428 3489 5.989168 AGCATAAGTAAAAGCCCAAACAAAC 59.011 36.000 0.00 0.00 0.00 2.93
3429 3490 5.755861 GCATAAGTAAAAGCCCAAACAAACA 59.244 36.000 0.00 0.00 0.00 2.83
3430 3491 6.073819 GCATAAGTAAAAGCCCAAACAAACAG 60.074 38.462 0.00 0.00 0.00 3.16
3431 3492 4.400529 AGTAAAAGCCCAAACAAACAGG 57.599 40.909 0.00 0.00 0.00 4.00
3432 3493 2.708216 AAAAGCCCAAACAAACAGGG 57.292 45.000 0.00 0.00 45.68 4.45
3450 4678 4.264172 ACAGGGCCTTATTGGTTTATGTGA 60.264 41.667 1.32 0.00 38.35 3.58
3465 4693 9.330063 TGGTTTATGTGATCTTAGCTTATTCTG 57.670 33.333 0.00 0.00 0.00 3.02
3491 4719 8.632906 AGTTCTCTGATGAAAATTCAGTGATT 57.367 30.769 0.00 0.00 41.04 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.094442 CCGCCAACTTTCTATTAGTGGTTC 59.906 45.833 0.00 0.00 0.00 3.62
55 56 1.827789 TGCAACTTTCCGCTTGCCT 60.828 52.632 3.94 0.00 41.83 4.75
170 171 1.813753 CCTACCCCGTGAATGTGCG 60.814 63.158 0.00 0.00 0.00 5.34
177 178 2.604079 TTTCCGCCTACCCCGTGA 60.604 61.111 0.00 0.00 0.00 4.35
245 246 5.849604 GTGTGCAATTTAGTACCTCGTTTTC 59.150 40.000 0.00 0.00 0.00 2.29
292 298 4.893524 TCTTCTAAACTAGATCCCGCATGA 59.106 41.667 0.00 0.00 34.22 3.07
310 316 0.526662 CCCTTACGACGTGCTCTTCT 59.473 55.000 11.56 0.00 0.00 2.85
622 630 9.445878 TGAGATGATATTTCTCATATTTCTGGC 57.554 33.333 12.76 0.00 43.49 4.85
735 768 6.424812 TCATAGAACCAAATACGCATGAGATG 59.575 38.462 2.50 0.00 0.00 2.90
736 769 6.524734 TCATAGAACCAAATACGCATGAGAT 58.475 36.000 2.50 0.00 0.00 2.75
737 770 5.912892 TCATAGAACCAAATACGCATGAGA 58.087 37.500 2.50 0.00 0.00 3.27
738 771 6.791887 ATCATAGAACCAAATACGCATGAG 57.208 37.500 0.00 0.00 0.00 2.90
739 772 8.669946 TTTATCATAGAACCAAATACGCATGA 57.330 30.769 0.00 0.00 0.00 3.07
740 773 9.546909 GATTTATCATAGAACCAAATACGCATG 57.453 33.333 0.00 0.00 0.00 4.06
741 774 9.507329 AGATTTATCATAGAACCAAATACGCAT 57.493 29.630 0.00 0.00 0.00 4.73
742 775 8.902540 AGATTTATCATAGAACCAAATACGCA 57.097 30.769 0.00 0.00 0.00 5.24
858 897 2.255252 GCAACGTGGTGCACATCC 59.745 61.111 20.43 1.27 44.29 3.51
872 911 1.078497 CATAGGTGCTCCCGTGCAA 60.078 57.895 0.00 0.00 45.12 4.08
873 912 2.584064 CATAGGTGCTCCCGTGCA 59.416 61.111 0.00 0.00 41.05 4.57
874 913 2.203070 CCATAGGTGCTCCCGTGC 60.203 66.667 0.00 0.00 38.74 5.34
875 914 3.309582 ACCATAGGTGCTCCCGTG 58.690 61.111 0.00 0.69 38.74 4.94
884 923 2.044492 TCCTCAGTCTTCCACCATAGGT 59.956 50.000 0.00 0.00 35.62 3.08
885 924 2.697751 CTCCTCAGTCTTCCACCATAGG 59.302 54.545 0.00 0.00 0.00 2.57
886 925 2.102252 GCTCCTCAGTCTTCCACCATAG 59.898 54.545 0.00 0.00 0.00 2.23
887 926 2.111384 GCTCCTCAGTCTTCCACCATA 58.889 52.381 0.00 0.00 0.00 2.74
961 1000 1.677966 TGAGGTCGGGAGGTCTTCG 60.678 63.158 0.00 0.00 0.00 3.79
991 1030 1.635817 ATTAGCGGCATGGTGGGAGT 61.636 55.000 1.45 0.00 0.00 3.85
992 1031 0.886490 GATTAGCGGCATGGTGGGAG 60.886 60.000 1.45 0.00 0.00 4.30
993 1032 1.148273 GATTAGCGGCATGGTGGGA 59.852 57.895 1.45 0.00 0.00 4.37
994 1033 1.898574 GGATTAGCGGCATGGTGGG 60.899 63.158 1.45 0.00 0.00 4.61
995 1034 0.751277 TTGGATTAGCGGCATGGTGG 60.751 55.000 1.45 0.00 0.00 4.61
996 1035 1.001048 CATTGGATTAGCGGCATGGTG 60.001 52.381 1.45 0.00 0.00 4.17
997 1036 1.321474 CATTGGATTAGCGGCATGGT 58.679 50.000 1.45 0.00 0.00 3.55
1172 1211 2.874780 CGCTGTCGTCGTAGGTGC 60.875 66.667 0.00 0.00 0.00 5.01
1361 1400 2.682494 GCGGTGGTGGGAGGTAGA 60.682 66.667 0.00 0.00 0.00 2.59
1434 1473 1.589716 GCACCCTCTGCACCAATCAC 61.590 60.000 0.00 0.00 46.29 3.06
1468 1507 0.695347 CTCAGGTTCCTGGGCTTCTT 59.305 55.000 17.37 0.00 35.01 2.52
1602 1641 2.666994 GCTAGCGAACTTGTACAGGAAC 59.333 50.000 12.54 4.30 0.00 3.62
1620 1659 3.138798 GAGGCCTCGACGGTGCTA 61.139 66.667 19.06 0.00 34.25 3.49
1711 1751 9.168451 TGAACTTGAACAAAGAAATACAGTACA 57.832 29.630 0.00 0.00 39.38 2.90
1712 1752 9.651718 CTGAACTTGAACAAAGAAATACAGTAC 57.348 33.333 0.00 0.00 39.38 2.73
1713 1753 9.391006 ACTGAACTTGAACAAAGAAATACAGTA 57.609 29.630 0.00 0.00 39.38 2.74
1714 1754 8.184192 CACTGAACTTGAACAAAGAAATACAGT 58.816 33.333 0.00 0.00 39.38 3.55
1715 1755 7.166473 GCACTGAACTTGAACAAAGAAATACAG 59.834 37.037 0.00 0.00 39.38 2.74
1736 1776 1.463056 TGTAAATTTCGGCGAGCACTG 59.537 47.619 10.46 0.00 0.00 3.66
1737 1777 1.463444 GTGTAAATTTCGGCGAGCACT 59.537 47.619 10.46 0.00 0.00 4.40
1738 1778 1.785518 CGTGTAAATTTCGGCGAGCAC 60.786 52.381 10.46 12.06 0.00 4.40
1739 1779 0.440758 CGTGTAAATTTCGGCGAGCA 59.559 50.000 10.46 0.73 0.00 4.26
1740 1780 0.717224 TCGTGTAAATTTCGGCGAGC 59.283 50.000 10.46 0.00 0.00 5.03
1741 1781 3.150731 GTTTCGTGTAAATTTCGGCGAG 58.849 45.455 10.46 0.00 0.00 5.03
1742 1782 2.410006 CGTTTCGTGTAAATTTCGGCGA 60.410 45.455 4.99 4.99 0.00 5.54
1743 1783 1.893689 CGTTTCGTGTAAATTTCGGCG 59.106 47.619 0.00 0.00 0.00 6.46
1762 1806 4.783242 ACTGCTATTGTAAAACAACTGCG 58.217 39.130 11.52 9.59 41.40 5.18
1905 1954 8.751242 GCCTATGTATTTTGGGGTTAAAACTTA 58.249 33.333 0.00 0.00 32.86 2.24
1906 1955 7.235812 TGCCTATGTATTTTGGGGTTAAAACTT 59.764 33.333 0.00 0.00 32.86 2.66
1907 1956 6.726764 TGCCTATGTATTTTGGGGTTAAAACT 59.273 34.615 0.00 0.00 32.86 2.66
1908 1957 6.937392 TGCCTATGTATTTTGGGGTTAAAAC 58.063 36.000 0.00 0.00 32.86 2.43
2047 2097 6.206634 CAGCACTACTAACCAGGAATCAAAAA 59.793 38.462 0.00 0.00 0.00 1.94
2146 2197 0.710567 CAGATCAGACAACGTGCGAC 59.289 55.000 0.00 0.00 0.00 5.19
2189 2245 1.066143 ACTGTTATCTGGCGAACCTGG 60.066 52.381 0.00 0.00 35.65 4.45
2248 2304 5.121768 AGGATAACAACGCAATACACAGAAC 59.878 40.000 0.00 0.00 0.00 3.01
2253 2312 5.539582 TGAAGGATAACAACGCAATACAC 57.460 39.130 0.00 0.00 0.00 2.90
2262 2321 3.851098 AGACTCGCTGAAGGATAACAAC 58.149 45.455 0.00 0.00 0.00 3.32
2297 2356 4.090761 TGTTCTGCAGAGGAAAGTCAAT 57.909 40.909 17.43 0.00 0.00 2.57
2301 2360 8.635765 TTTATAATTGTTCTGCAGAGGAAAGT 57.364 30.769 17.43 13.61 0.00 2.66
2462 2521 2.029623 GATGAAGCCATTGTGCTGGAT 58.970 47.619 0.00 0.00 41.80 3.41
2515 2574 3.490590 CGAGATCTGCTGCAAGTCACTAT 60.491 47.826 0.00 0.00 35.30 2.12
2692 2751 9.654663 ACATTTTACTACTAGCCTAACTGAAAG 57.345 33.333 0.00 0.00 42.29 2.62
2698 2757 7.325694 TCACCACATTTTACTACTAGCCTAAC 58.674 38.462 0.00 0.00 0.00 2.34
2726 2785 9.770097 TGTATTTTTGCAGTTCAATCCAAAATA 57.230 25.926 4.02 4.02 37.13 1.40
2903 2962 3.206964 TGGCATGCAAAATATTGGCATG 58.793 40.909 31.54 31.54 44.64 4.06
2939 2998 6.105657 CCAACTTTTGGTTTGTCAAATGTC 57.894 37.500 0.40 0.00 45.93 3.06
3068 3129 2.393646 ACCAAAAAGCACTTGCCCTTA 58.606 42.857 0.00 0.00 43.38 2.69
3123 3184 9.952188 GAGCTTATTTTCACTACAGTTTCTTTT 57.048 29.630 0.00 0.00 0.00 2.27
3170 3231 2.791868 GCCCAAACAAACACGGCCT 61.792 57.895 0.00 0.00 33.30 5.19
3171 3232 2.279851 GCCCAAACAAACACGGCC 60.280 61.111 0.00 0.00 33.30 6.13
3172 3233 0.461163 AAAGCCCAAACAAACACGGC 60.461 50.000 0.00 0.00 40.03 5.68
3173 3234 1.663135 CAAAAGCCCAAACAAACACGG 59.337 47.619 0.00 0.00 0.00 4.94
3174 3235 1.061857 GCAAAAGCCCAAACAAACACG 59.938 47.619 0.00 0.00 0.00 4.49
3175 3236 2.355197 AGCAAAAGCCCAAACAAACAC 58.645 42.857 0.00 0.00 0.00 3.32
3176 3237 2.777832 AGCAAAAGCCCAAACAAACA 57.222 40.000 0.00 0.00 0.00 2.83
3177 3238 3.270027 AGAAGCAAAAGCCCAAACAAAC 58.730 40.909 0.00 0.00 0.00 2.93
3178 3239 3.625649 AGAAGCAAAAGCCCAAACAAA 57.374 38.095 0.00 0.00 0.00 2.83
3179 3240 3.197549 AGAAGAAGCAAAAGCCCAAACAA 59.802 39.130 0.00 0.00 0.00 2.83
3180 3241 2.765699 AGAAGAAGCAAAAGCCCAAACA 59.234 40.909 0.00 0.00 0.00 2.83
3181 3242 3.459232 AGAAGAAGCAAAAGCCCAAAC 57.541 42.857 0.00 0.00 0.00 2.93
3182 3243 4.486125 AAAGAAGAAGCAAAAGCCCAAA 57.514 36.364 0.00 0.00 0.00 3.28
3183 3244 4.190772 CAAAAGAAGAAGCAAAAGCCCAA 58.809 39.130 0.00 0.00 0.00 4.12
3184 3245 3.795877 CAAAAGAAGAAGCAAAAGCCCA 58.204 40.909 0.00 0.00 0.00 5.36
3185 3246 2.545526 GCAAAAGAAGAAGCAAAAGCCC 59.454 45.455 0.00 0.00 0.00 5.19
3186 3247 3.197265 TGCAAAAGAAGAAGCAAAAGCC 58.803 40.909 0.00 0.00 33.48 4.35
3187 3248 3.302935 GCTGCAAAAGAAGAAGCAAAAGC 60.303 43.478 0.00 0.00 37.60 3.51
3188 3249 4.117685 AGCTGCAAAAGAAGAAGCAAAAG 58.882 39.130 1.02 0.00 40.27 2.27
3189 3250 4.127566 AGCTGCAAAAGAAGAAGCAAAA 57.872 36.364 1.02 0.00 40.27 2.44
3190 3251 3.806625 AGCTGCAAAAGAAGAAGCAAA 57.193 38.095 1.02 0.00 40.27 3.68
3191 3252 3.806625 AAGCTGCAAAAGAAGAAGCAA 57.193 38.095 1.02 0.00 40.27 3.91
3192 3253 3.806625 AAAGCTGCAAAAGAAGAAGCA 57.193 38.095 1.02 0.00 40.27 3.91
3193 3254 4.366586 AGAAAAGCTGCAAAAGAAGAAGC 58.633 39.130 1.02 0.00 37.96 3.86
3194 3255 6.733145 AGTAGAAAAGCTGCAAAAGAAGAAG 58.267 36.000 1.02 0.00 0.00 2.85
3195 3256 6.699575 AGTAGAAAAGCTGCAAAAGAAGAA 57.300 33.333 1.02 0.00 0.00 2.52
3196 3257 6.699575 AAGTAGAAAAGCTGCAAAAGAAGA 57.300 33.333 1.02 0.00 0.00 2.87
3197 3258 7.615790 CAAAAGTAGAAAAGCTGCAAAAGAAG 58.384 34.615 1.02 0.00 0.00 2.85
3198 3259 6.035975 GCAAAAGTAGAAAAGCTGCAAAAGAA 59.964 34.615 1.02 0.00 0.00 2.52
3199 3260 5.519927 GCAAAAGTAGAAAAGCTGCAAAAGA 59.480 36.000 1.02 0.00 0.00 2.52
3200 3261 5.277011 GGCAAAAGTAGAAAAGCTGCAAAAG 60.277 40.000 1.02 0.00 0.00 2.27
3201 3262 4.570369 GGCAAAAGTAGAAAAGCTGCAAAA 59.430 37.500 1.02 0.00 0.00 2.44
3202 3263 4.119136 GGCAAAAGTAGAAAAGCTGCAAA 58.881 39.130 1.02 0.00 0.00 3.68
3203 3264 3.131933 TGGCAAAAGTAGAAAAGCTGCAA 59.868 39.130 1.02 0.00 0.00 4.08
3204 3265 2.692557 TGGCAAAAGTAGAAAAGCTGCA 59.307 40.909 1.02 0.00 0.00 4.41
3205 3266 3.004734 TCTGGCAAAAGTAGAAAAGCTGC 59.995 43.478 0.00 0.00 0.00 5.25
3206 3267 4.836125 TCTGGCAAAAGTAGAAAAGCTG 57.164 40.909 0.00 0.00 0.00 4.24
3207 3268 5.737349 GCTTTCTGGCAAAAGTAGAAAAGCT 60.737 40.000 17.39 0.00 39.23 3.74
3208 3269 4.445718 GCTTTCTGGCAAAAGTAGAAAAGC 59.554 41.667 17.39 0.00 39.23 3.51
3209 3270 4.984785 GGCTTTCTGGCAAAAGTAGAAAAG 59.015 41.667 17.39 0.00 39.23 2.27
3210 3271 4.944048 GGCTTTCTGGCAAAAGTAGAAAA 58.056 39.130 17.39 0.00 39.23 2.29
3211 3272 4.584327 GGCTTTCTGGCAAAAGTAGAAA 57.416 40.909 17.39 9.45 38.30 2.52
3222 3283 2.159184 GGAGCTTTTATGGCTTTCTGGC 60.159 50.000 0.00 0.00 40.40 4.85
3223 3284 3.359950 AGGAGCTTTTATGGCTTTCTGG 58.640 45.455 0.00 0.00 40.40 3.86
3224 3285 6.515272 TTTAGGAGCTTTTATGGCTTTCTG 57.485 37.500 0.00 0.00 40.40 3.02
3225 3286 7.503902 CCTATTTAGGAGCTTTTATGGCTTTCT 59.496 37.037 0.00 0.00 46.63 2.52
3226 3287 7.285629 ACCTATTTAGGAGCTTTTATGGCTTTC 59.714 37.037 10.61 0.00 46.63 2.62
3227 3288 7.068716 CACCTATTTAGGAGCTTTTATGGCTTT 59.931 37.037 10.61 0.00 46.63 3.51
3228 3289 6.547510 CACCTATTTAGGAGCTTTTATGGCTT 59.452 38.462 10.61 0.00 46.63 4.35
3229 3290 6.064717 CACCTATTTAGGAGCTTTTATGGCT 58.935 40.000 10.61 0.00 46.63 4.75
3230 3291 6.319141 CACCTATTTAGGAGCTTTTATGGC 57.681 41.667 10.61 0.00 46.63 4.40
3240 3301 2.435805 TGGAGCAGCACCTATTTAGGAG 59.564 50.000 10.54 3.78 46.63 3.69
3241 3302 2.435805 CTGGAGCAGCACCTATTTAGGA 59.564 50.000 10.54 0.00 46.63 2.94
3243 3304 3.827008 TCTGGAGCAGCACCTATTTAG 57.173 47.619 10.54 0.00 0.00 1.85
3244 3305 4.142609 CTTCTGGAGCAGCACCTATTTA 57.857 45.455 10.54 0.00 0.00 1.40
3245 3306 2.996631 CTTCTGGAGCAGCACCTATTT 58.003 47.619 10.54 0.00 0.00 1.40
3246 3307 2.706339 CTTCTGGAGCAGCACCTATT 57.294 50.000 10.54 0.00 0.00 1.73
3256 3317 3.134804 TCCTAAATAGGTGCTTCTGGAGC 59.865 47.826 0.00 0.00 45.81 4.70
3257 3318 4.202305 CCTCCTAAATAGGTGCTTCTGGAG 60.202 50.000 6.39 0.00 44.02 3.86
3258 3319 3.711704 CCTCCTAAATAGGTGCTTCTGGA 59.288 47.826 6.39 0.00 44.02 3.86
3259 3320 3.456277 ACCTCCTAAATAGGTGCTTCTGG 59.544 47.826 6.39 2.62 45.78 3.86
3260 3321 4.762289 ACCTCCTAAATAGGTGCTTCTG 57.238 45.455 6.39 0.00 45.78 3.02
3261 3322 5.780958 AAACCTCCTAAATAGGTGCTTCT 57.219 39.130 6.39 0.00 46.85 2.85
3262 3323 7.013369 CCATAAAACCTCCTAAATAGGTGCTTC 59.987 40.741 6.39 0.00 46.85 3.86
3263 3324 6.833933 CCATAAAACCTCCTAAATAGGTGCTT 59.166 38.462 6.39 0.00 46.85 3.91
3264 3325 6.365520 CCATAAAACCTCCTAAATAGGTGCT 58.634 40.000 6.39 0.00 46.85 4.40
3265 3326 5.009710 GCCATAAAACCTCCTAAATAGGTGC 59.990 44.000 6.39 0.00 46.85 5.01
3266 3327 6.365520 AGCCATAAAACCTCCTAAATAGGTG 58.634 40.000 6.39 4.21 46.85 4.00
3268 3329 7.898014 AAAGCCATAAAACCTCCTAAATAGG 57.102 36.000 0.00 0.00 45.02 2.57
3269 3330 8.197439 CCAAAAGCCATAAAACCTCCTAAATAG 58.803 37.037 0.00 0.00 0.00 1.73
3270 3331 7.896496 TCCAAAAGCCATAAAACCTCCTAAATA 59.104 33.333 0.00 0.00 0.00 1.40
3271 3332 6.728632 TCCAAAAGCCATAAAACCTCCTAAAT 59.271 34.615 0.00 0.00 0.00 1.40
3272 3333 6.078664 TCCAAAAGCCATAAAACCTCCTAAA 58.921 36.000 0.00 0.00 0.00 1.85
3273 3334 5.646215 TCCAAAAGCCATAAAACCTCCTAA 58.354 37.500 0.00 0.00 0.00 2.69
3274 3335 5.261216 CTCCAAAAGCCATAAAACCTCCTA 58.739 41.667 0.00 0.00 0.00 2.94
3275 3336 4.089361 CTCCAAAAGCCATAAAACCTCCT 58.911 43.478 0.00 0.00 0.00 3.69
3276 3337 3.368427 GCTCCAAAAGCCATAAAACCTCC 60.368 47.826 0.00 0.00 45.92 4.30
3277 3338 3.849911 GCTCCAAAAGCCATAAAACCTC 58.150 45.455 0.00 0.00 45.92 3.85
3278 3339 3.961480 GCTCCAAAAGCCATAAAACCT 57.039 42.857 0.00 0.00 45.92 3.50
3346 3407 6.064717 AGCCATAAAAGCTCCTAAATAGGTG 58.935 40.000 6.39 5.41 44.02 4.00
3347 3408 6.267492 AGCCATAAAAGCTCCTAAATAGGT 57.733 37.500 6.39 0.00 44.02 3.08
3348 3409 7.588497 AAAGCCATAAAAGCTCCTAAATAGG 57.412 36.000 0.00 0.00 40.49 2.57
3349 3410 9.305925 CAAAAAGCCATAAAAGCTCCTAAATAG 57.694 33.333 0.00 0.00 40.49 1.73
3350 3411 8.257306 CCAAAAAGCCATAAAAGCTCCTAAATA 58.743 33.333 0.00 0.00 40.49 1.40
3351 3412 7.105588 CCAAAAAGCCATAAAAGCTCCTAAAT 58.894 34.615 0.00 0.00 40.49 1.40
3352 3413 6.042666 ACCAAAAAGCCATAAAAGCTCCTAAA 59.957 34.615 0.00 0.00 40.49 1.85
3353 3414 5.542251 ACCAAAAAGCCATAAAAGCTCCTAA 59.458 36.000 0.00 0.00 40.49 2.69
3354 3415 5.083821 ACCAAAAAGCCATAAAAGCTCCTA 58.916 37.500 0.00 0.00 40.49 2.94
3355 3416 3.903714 ACCAAAAAGCCATAAAAGCTCCT 59.096 39.130 0.00 0.00 40.49 3.69
3356 3417 4.245660 GACCAAAAAGCCATAAAAGCTCC 58.754 43.478 0.00 0.00 40.49 4.70
3357 3418 4.881920 TGACCAAAAAGCCATAAAAGCTC 58.118 39.130 0.00 0.00 40.49 4.09
3358 3419 4.953940 TGACCAAAAAGCCATAAAAGCT 57.046 36.364 0.00 0.00 44.19 3.74
3359 3420 5.106594 CCAATGACCAAAAAGCCATAAAAGC 60.107 40.000 0.00 0.00 0.00 3.51
3360 3421 5.997129 ACCAATGACCAAAAAGCCATAAAAG 59.003 36.000 0.00 0.00 0.00 2.27
3361 3422 5.934781 ACCAATGACCAAAAAGCCATAAAA 58.065 33.333 0.00 0.00 0.00 1.52
3362 3423 5.070981 TGACCAATGACCAAAAAGCCATAAA 59.929 36.000 0.00 0.00 0.00 1.40
3363 3424 4.590647 TGACCAATGACCAAAAAGCCATAA 59.409 37.500 0.00 0.00 0.00 1.90
3364 3425 4.155709 TGACCAATGACCAAAAAGCCATA 58.844 39.130 0.00 0.00 0.00 2.74
3365 3426 2.971330 TGACCAATGACCAAAAAGCCAT 59.029 40.909 0.00 0.00 0.00 4.40
3366 3427 2.392662 TGACCAATGACCAAAAAGCCA 58.607 42.857 0.00 0.00 0.00 4.75
3367 3428 3.467374 TTGACCAATGACCAAAAAGCC 57.533 42.857 0.00 0.00 0.00 4.35
3368 3429 4.692228 TCTTTGACCAATGACCAAAAAGC 58.308 39.130 0.00 0.00 30.56 3.51
3369 3430 7.608308 TTTTCTTTGACCAATGACCAAAAAG 57.392 32.000 0.00 0.00 30.56 2.27
3370 3431 7.986085 TTTTTCTTTGACCAATGACCAAAAA 57.014 28.000 0.00 2.01 30.56 1.94
3400 3461 6.481644 TGTTTGGGCTTTTACTTATGCTTTTG 59.518 34.615 0.00 0.00 0.00 2.44
3401 3462 6.587273 TGTTTGGGCTTTTACTTATGCTTTT 58.413 32.000 0.00 0.00 0.00 2.27
3402 3463 6.168270 TGTTTGGGCTTTTACTTATGCTTT 57.832 33.333 0.00 0.00 0.00 3.51
3403 3464 5.799827 TGTTTGGGCTTTTACTTATGCTT 57.200 34.783 0.00 0.00 0.00 3.91
3404 3465 5.799827 TTGTTTGGGCTTTTACTTATGCT 57.200 34.783 0.00 0.00 0.00 3.79
3405 3466 5.755861 TGTTTGTTTGGGCTTTTACTTATGC 59.244 36.000 0.00 0.00 0.00 3.14
3406 3467 6.423604 CCTGTTTGTTTGGGCTTTTACTTATG 59.576 38.462 0.00 0.00 0.00 1.90
3407 3468 6.463755 CCCTGTTTGTTTGGGCTTTTACTTAT 60.464 38.462 0.00 0.00 33.88 1.73
3408 3469 5.163395 CCCTGTTTGTTTGGGCTTTTACTTA 60.163 40.000 0.00 0.00 33.88 2.24
3409 3470 4.383661 CCCTGTTTGTTTGGGCTTTTACTT 60.384 41.667 0.00 0.00 33.88 2.24
3410 3471 3.133901 CCCTGTTTGTTTGGGCTTTTACT 59.866 43.478 0.00 0.00 33.88 2.24
3411 3472 3.462982 CCCTGTTTGTTTGGGCTTTTAC 58.537 45.455 0.00 0.00 33.88 2.01
3412 3473 3.828875 CCCTGTTTGTTTGGGCTTTTA 57.171 42.857 0.00 0.00 33.88 1.52
3413 3474 2.708216 CCCTGTTTGTTTGGGCTTTT 57.292 45.000 0.00 0.00 33.88 2.27
3418 3479 1.710816 TAAGGCCCTGTTTGTTTGGG 58.289 50.000 0.00 0.00 43.62 4.12
3419 3480 3.556843 CCAATAAGGCCCTGTTTGTTTGG 60.557 47.826 0.00 2.10 0.00 3.28
3420 3481 3.070878 ACCAATAAGGCCCTGTTTGTTTG 59.929 43.478 0.00 0.00 43.14 2.93
3421 3482 3.313791 ACCAATAAGGCCCTGTTTGTTT 58.686 40.909 0.00 0.00 43.14 2.83
3422 3483 2.970987 ACCAATAAGGCCCTGTTTGTT 58.029 42.857 0.00 0.00 43.14 2.83
3423 3484 2.694616 ACCAATAAGGCCCTGTTTGT 57.305 45.000 0.00 0.00 43.14 2.83
3424 3485 5.046663 ACATAAACCAATAAGGCCCTGTTTG 60.047 40.000 0.00 3.32 43.14 2.93
3425 3486 5.046663 CACATAAACCAATAAGGCCCTGTTT 60.047 40.000 0.00 3.20 43.14 2.83
3426 3487 4.466015 CACATAAACCAATAAGGCCCTGTT 59.534 41.667 0.00 0.00 43.14 3.16
3427 3488 4.023291 CACATAAACCAATAAGGCCCTGT 58.977 43.478 0.00 0.00 43.14 4.00
3428 3489 4.277476 TCACATAAACCAATAAGGCCCTG 58.723 43.478 0.00 0.00 43.14 4.45
3429 3490 4.601406 TCACATAAACCAATAAGGCCCT 57.399 40.909 0.00 0.00 43.14 5.19
3430 3491 5.140454 AGATCACATAAACCAATAAGGCCC 58.860 41.667 0.00 0.00 43.14 5.80
3431 3492 6.715347 AAGATCACATAAACCAATAAGGCC 57.285 37.500 0.00 0.00 43.14 5.19
3432 3493 7.229506 AGCTAAGATCACATAAACCAATAAGGC 59.770 37.037 0.00 0.00 43.14 4.35
3433 3494 8.682936 AGCTAAGATCACATAAACCAATAAGG 57.317 34.615 0.00 0.00 45.67 2.69
3450 4678 8.532186 TCAGAGAACTCAGAATAAGCTAAGAT 57.468 34.615 4.64 0.00 0.00 2.40
3465 4693 7.664082 TCACTGAATTTTCATCAGAGAACTC 57.336 36.000 10.27 0.00 45.74 3.01


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

AutoCloner maintained by Alex Coulton.