Multiple sequence alignment - TraesCS3A01G358600

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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 TraesCS3A01G358600 chr3A 100.000 4415 0 0 4392 8806 606670024 606674438 0.000000e+00 8154.0
1 TraesCS3A01G358600 chr3A 100.000 4173 0 0 1 4173 606665633 606669805 0.000000e+00 7707.0
2 TraesCS3A01G358600 chr3A 94.286 105 5 1 839 942 646126932 646126828 9.150000e-35 159.0
3 TraesCS3A01G358600 chr3D 94.981 4284 139 37 4539 8806 463536701 463540924 0.000000e+00 6650.0
4 TraesCS3A01G358600 chr3D 96.057 3145 104 11 939 4076 463533518 463536649 0.000000e+00 5103.0
5 TraesCS3A01G358600 chr3D 90.200 449 36 3 413 856 463533074 463533519 5.930000e-161 579.0
6 TraesCS3A01G358600 chr3D 88.770 187 20 1 32 218 463532297 463532482 2.470000e-55 228.0
7 TraesCS3A01G358600 chr3D 85.714 63 9 0 4460 4522 36979971 36980033 5.710000e-07 67.6
8 TraesCS3A01G358600 chr3D 100.000 28 0 0 4559 4586 463536645 463536672 1.600000e-02 52.8
9 TraesCS3A01G358600 chr3B 94.468 3489 169 12 4508 7984 616892935 616896411 0.000000e+00 5352.0
10 TraesCS3A01G358600 chr3B 88.669 1818 112 26 1035 2808 616889276 616891043 0.000000e+00 2130.0
11 TraesCS3A01G358600 chr3B 90.949 685 37 10 3451 4127 616891700 616892367 0.000000e+00 898.0
12 TraesCS3A01G358600 chr3B 87.348 656 65 13 8092 8745 616898234 616898873 0.000000e+00 736.0
13 TraesCS3A01G358600 chr3B 87.168 452 47 7 413 856 616888796 616889244 3.670000e-138 503.0
14 TraesCS3A01G358600 chr3B 90.274 329 17 4 3094 3407 616891185 616891513 4.920000e-112 416.0
15 TraesCS3A01G358600 chr3B 89.529 191 18 2 29 218 616887138 616887327 3.180000e-59 241.0
16 TraesCS3A01G358600 chr3B 91.250 160 12 2 7981 8139 616898064 616898222 5.350000e-52 217.0
17 TraesCS3A01G358600 chr3B 96.667 120 4 0 2892 3011 616891061 616891180 5.390000e-47 200.0
18 TraesCS3A01G358600 chr3B 93.913 115 6 1 208 322 616887707 616887820 1.180000e-38 172.0
19 TraesCS3A01G358600 chr3B 97.826 46 1 0 4407 4452 616892641 616892686 7.330000e-11 80.5
20 TraesCS3A01G358600 chr5B 90.993 866 61 9 1733 2586 533947279 533946419 0.000000e+00 1151.0
21 TraesCS3A01G358600 chr5D 90.575 870 54 15 1733 2586 560845787 560844930 0.000000e+00 1127.0
22 TraesCS3A01G358600 chr5D 92.683 41 3 0 3015 3055 548029942 548029902 9.550000e-05 60.2
23 TraesCS3A01G358600 chr7D 90.219 869 58 14 1733 2586 143317782 143316926 0.000000e+00 1109.0
24 TraesCS3A01G358600 chr7D 90.115 870 59 14 1733 2586 143350612 143349754 0.000000e+00 1105.0
25 TraesCS3A01G358600 chr7D 87.437 199 19 2 2393 2586 576964041 576963844 3.200000e-54 224.0
26 TraesCS3A01G358600 chr7D 100.000 31 0 0 3015 3045 196134557 196134527 3.430000e-04 58.4
27 TraesCS3A01G358600 chrUn 87.437 199 19 2 2393 2586 361706436 361706633 3.200000e-54 224.0
28 TraesCS3A01G358600 chrUn 95.000 100 4 1 842 941 263385867 263385965 1.180000e-33 156.0
29 TraesCS3A01G358600 chrUn 95.000 100 4 1 842 941 344444673 344444771 1.180000e-33 156.0
30 TraesCS3A01G358600 chr1D 87.437 199 19 2 2393 2586 124376434 124376631 3.200000e-54 224.0
31 TraesCS3A01G358600 chr2B 73.763 465 100 15 5500 5952 429258442 429257988 7.070000e-36 163.0
32 TraesCS3A01G358600 chr2B 96.809 94 2 1 850 942 303097260 303097353 1.180000e-33 156.0
33 TraesCS3A01G358600 chr2B 88.406 69 8 0 4459 4527 406884768 406884700 5.670000e-12 84.2
34 TraesCS3A01G358600 chr2B 100.000 28 0 0 7881 7908 795095972 795095999 1.600000e-02 52.8
35 TraesCS3A01G358600 chr6B 95.918 98 3 1 853 949 678316618 678316521 3.290000e-34 158.0
36 TraesCS3A01G358600 chr6B 95.833 96 3 1 846 941 62471180 62471274 4.260000e-33 154.0
37 TraesCS3A01G358600 chr4D 96.809 94 3 0 847 940 164649448 164649541 3.290000e-34 158.0
38 TraesCS3A01G358600 chr2D 73.742 457 96 16 5500 5943 360302114 360302559 3.290000e-34 158.0
39 TraesCS3A01G358600 chr2A 73.742 457 96 16 5500 5943 485757450 485757895 3.290000e-34 158.0
40 TraesCS3A01G358600 chr2A 91.304 69 6 0 4459 4527 449279179 449279111 2.620000e-15 95.3
41 TraesCS3A01G358600 chr1B 95.000 100 4 1 842 941 58083803 58083705 1.180000e-33 156.0
42 TraesCS3A01G358600 chr1B 95.000 100 4 1 842 941 58109954 58109856 1.180000e-33 156.0
43 TraesCS3A01G358600 chr6A 93.750 48 3 0 3020 3067 8620972 8621019 1.230000e-08 73.1
44 TraesCS3A01G358600 chr6D 83.824 68 11 0 4463 4530 78278110 78278043 2.050000e-06 65.8
45 TraesCS3A01G358600 chr7B 100.000 31 0 0 3015 3045 160475014 160474984 3.430000e-04 58.4
46 TraesCS3A01G358600 chr7B 94.444 36 1 1 7872 7907 51265149 51265183 4.000000e-03 54.7
47 TraesCS3A01G358600 chr7A 89.130 46 4 1 4480 4525 78410264 78410308 1.000000e-03 56.5


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 TraesCS3A01G358600 chr3A 606665633 606674438 8805 False 7930.500000 8154 100.000000 1 8806 2 chr3A.!!$F1 8805
1 TraesCS3A01G358600 chr3D 463532297 463540924 8627 False 2522.560000 6650 94.001600 32 8806 5 chr3D.!!$F2 8774
2 TraesCS3A01G358600 chr3B 616887138 616898873 11735 False 995.045455 5352 91.641909 29 8745 11 chr3B.!!$F1 8716
3 TraesCS3A01G358600 chr5B 533946419 533947279 860 True 1151.000000 1151 90.993000 1733 2586 1 chr5B.!!$R1 853
4 TraesCS3A01G358600 chr5D 560844930 560845787 857 True 1127.000000 1127 90.575000 1733 2586 1 chr5D.!!$R2 853
5 TraesCS3A01G358600 chr7D 143316926 143317782 856 True 1109.000000 1109 90.219000 1733 2586 1 chr7D.!!$R1 853
6 TraesCS3A01G358600 chr7D 143349754 143350612 858 True 1105.000000 1105 90.115000 1733 2586 1 chr7D.!!$R2 853

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
597 1943 0.249447 CATTGCAGCCTATCGTCCGA 60.249 55.000 0.00 0.00 0.00 4.55 F
1033 2381 0.031585 GGTTTGGCGTTGGGAAAGAC 59.968 55.000 0.00 0.00 0.00 3.01 F
1444 2818 0.958822 GCGCCTTTTTCCAGGAAGAA 59.041 50.000 1.07 3.32 35.71 2.52 F
1912 3290 0.318445 CGTCGACCGGAGAAAGTTGT 60.318 55.000 9.46 0.00 0.00 3.32 F
3175 4575 0.678048 ATGCAGAGTTTTCGGAGGCC 60.678 55.000 0.00 0.00 0.00 5.19 F
4080 5657 0.184451 GGTCATGGCATCCCAGATGT 59.816 55.000 0.00 0.00 46.24 3.06 F
4544 6328 1.141019 GTGGATGCGGCGAGAACTA 59.859 57.895 12.98 0.00 0.00 2.24 F
4592 6376 1.740296 GGTCGGTGCACATTACGCT 60.740 57.895 20.43 0.00 0.00 5.07 F
4689 6477 2.718062 TGATGGGGTAGGGAGTCGTATA 59.282 50.000 0.00 0.00 0.00 1.47 F
6206 8004 1.136308 CGCACGGTGCAAACGTATAAA 60.136 47.619 30.23 0.00 45.36 1.40 F
6608 8406 1.367659 CTACTGAAGGCAGAAGCAGC 58.632 55.000 0.00 0.00 45.17 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 2789 0.322546 AAAAAGGCGCCCGAGAAGAT 60.323 50.000 26.15 0.00 0.00 2.40 R
1840 3218 2.683362 GGGCTTCTGCACAAATACCTAC 59.317 50.000 0.00 0.00 43.35 3.18 R
3175 4575 2.232208 GCAACTTCCCATTTCCTCCAAG 59.768 50.000 0.00 0.00 0.00 3.61 R
3472 5042 0.108424 AACGCTCAGCTCAGCTTAGG 60.108 55.000 8.35 2.84 36.40 2.69 R
4393 5984 0.039527 GAACAAGCCGCAAAACCGAT 60.040 50.000 0.00 0.00 0.00 4.18 R
5609 7406 0.323725 GGAATTGCCCCTGCTTCAGA 60.324 55.000 0.00 0.00 38.71 3.27 R
5706 7503 1.070134 GTGCCACTCACTGTCAGGTAA 59.930 52.381 4.53 0.00 42.38 2.85 R
5708 7505 1.337384 TGTGCCACTCACTGTCAGGT 61.337 55.000 4.53 0.00 45.81 4.00 R
6608 8406 0.250640 AGGCTTCACTTGTGGAGCTG 60.251 55.000 26.99 0.00 0.00 4.24 R
7438 9236 0.108585 TTTTCTCCGAGTGCTGCCTT 59.891 50.000 0.00 0.00 0.00 4.35 R
8026 11483 0.815615 GAATCGGGTGCTGCCTAAGG 60.816 60.000 0.00 0.00 37.43 2.69 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
34 35 7.280428 CCGGTTTGGTTTTTAAAACTATGGTTT 59.720 33.333 18.31 0.65 46.27 3.27
155 156 3.684788 ACAAACAACGCTCCTAATGCTAG 59.315 43.478 0.00 0.00 0.00 3.42
160 161 3.225177 ACGCTCCTAATGCTAGTCCTA 57.775 47.619 0.00 0.00 0.00 2.94
167 168 7.114095 GCTCCTAATGCTAGTCCTATACTACT 58.886 42.308 0.00 0.00 39.80 2.57
185 186 6.380079 ACTACTCTCTCCACCAAATTTCAT 57.620 37.500 0.00 0.00 0.00 2.57
306 735 0.326927 CGGGGAAAAGTAGGCTCCAA 59.673 55.000 0.00 0.00 0.00 3.53
323 752 0.795085 CAAAGAGAAGAGCAGCGTGG 59.205 55.000 0.00 0.00 0.00 4.94
324 753 0.394565 AAAGAGAAGAGCAGCGTGGT 59.605 50.000 0.00 0.00 0.00 4.16
325 754 0.320247 AAGAGAAGAGCAGCGTGGTG 60.320 55.000 0.00 0.00 0.00 4.17
326 755 1.739562 GAGAAGAGCAGCGTGGTGG 60.740 63.158 0.82 0.00 0.00 4.61
330 1671 4.357947 GAGCAGCGTGGTGGTCGA 62.358 66.667 14.42 0.00 35.38 4.20
333 1674 2.325082 GCAGCGTGGTGGTCGATTT 61.325 57.895 0.82 0.00 0.00 2.17
335 1676 0.999406 CAGCGTGGTGGTCGATTTAG 59.001 55.000 0.00 0.00 0.00 1.85
399 1740 7.793927 GCACATAGCTCTTTACCTATCTTTT 57.206 36.000 0.00 0.00 41.15 2.27
400 1741 8.888579 GCACATAGCTCTTTACCTATCTTTTA 57.111 34.615 0.00 0.00 41.15 1.52
401 1742 9.495572 GCACATAGCTCTTTACCTATCTTTTAT 57.504 33.333 0.00 0.00 41.15 1.40
406 1747 7.920738 AGCTCTTTACCTATCTTTTATTTGCG 58.079 34.615 0.00 0.00 0.00 4.85
407 1748 7.012421 AGCTCTTTACCTATCTTTTATTTGCGG 59.988 37.037 0.00 0.00 0.00 5.69
408 1749 7.562454 TCTTTACCTATCTTTTATTTGCGGG 57.438 36.000 0.00 0.00 0.00 6.13
409 1750 7.114095 TCTTTACCTATCTTTTATTTGCGGGT 58.886 34.615 0.00 0.00 0.00 5.28
410 1751 6.687081 TTACCTATCTTTTATTTGCGGGTG 57.313 37.500 0.00 0.00 0.00 4.61
411 1752 4.595986 ACCTATCTTTTATTTGCGGGTGT 58.404 39.130 0.00 0.00 0.00 4.16
412 1753 4.638865 ACCTATCTTTTATTTGCGGGTGTC 59.361 41.667 0.00 0.00 0.00 3.67
413 1754 4.881850 CCTATCTTTTATTTGCGGGTGTCT 59.118 41.667 0.00 0.00 0.00 3.41
414 1755 5.357032 CCTATCTTTTATTTGCGGGTGTCTT 59.643 40.000 0.00 0.00 0.00 3.01
415 1756 5.722021 ATCTTTTATTTGCGGGTGTCTTT 57.278 34.783 0.00 0.00 0.00 2.52
416 1757 6.827586 ATCTTTTATTTGCGGGTGTCTTTA 57.172 33.333 0.00 0.00 0.00 1.85
417 1758 6.827586 TCTTTTATTTGCGGGTGTCTTTAT 57.172 33.333 0.00 0.00 0.00 1.40
418 1759 6.848451 TCTTTTATTTGCGGGTGTCTTTATC 58.152 36.000 0.00 0.00 0.00 1.75
419 1760 6.657541 TCTTTTATTTGCGGGTGTCTTTATCT 59.342 34.615 0.00 0.00 0.00 1.98
420 1761 7.825270 TCTTTTATTTGCGGGTGTCTTTATCTA 59.175 33.333 0.00 0.00 0.00 1.98
428 1769 5.063564 GCGGGTGTCTTTATCTACTTTTCAG 59.936 44.000 0.00 0.00 0.00 3.02
435 1776 7.705325 TGTCTTTATCTACTTTTCAGCGGATAC 59.295 37.037 0.00 0.00 0.00 2.24
438 1779 9.182933 CTTTATCTACTTTTCAGCGGATACTAC 57.817 37.037 0.00 0.00 0.00 2.73
446 1787 4.929819 TCAGCGGATACTACTTTGCATA 57.070 40.909 0.00 0.00 0.00 3.14
536 1882 4.371624 TCCACACCTTCAATCTTGTGAT 57.628 40.909 2.17 0.00 41.61 3.06
570 1916 5.768164 AGGTTGGTTCATAGTCGTGAAAATT 59.232 36.000 0.00 0.00 39.61 1.82
597 1943 0.249447 CATTGCAGCCTATCGTCCGA 60.249 55.000 0.00 0.00 0.00 4.55
601 1947 1.360551 CAGCCTATCGTCCGAGTGG 59.639 63.158 0.00 1.37 0.00 4.00
614 1960 1.592223 GAGTGGGAGGGAACAGTCG 59.408 63.158 0.00 0.00 0.00 4.18
632 1978 0.461548 CGATGTCCTAGAGCTTGGCA 59.538 55.000 0.00 0.00 0.00 4.92
634 1980 1.208052 GATGTCCTAGAGCTTGGCACA 59.792 52.381 0.00 0.00 0.00 4.57
684 2030 1.021390 CGCCAACCTCATGTGTCTCC 61.021 60.000 0.00 0.00 0.00 3.71
688 2034 0.898320 AACCTCATGTGTCTCCTCCG 59.102 55.000 0.00 0.00 0.00 4.63
691 2037 1.177401 CTCATGTGTCTCCTCCGTCA 58.823 55.000 0.00 0.00 0.00 4.35
761 2107 6.303021 ACGAAAAGTAGGTGCGAAAAATAA 57.697 33.333 0.00 0.00 0.00 1.40
859 2207 9.525409 TTACTATTCAGTTTTCGCTTATACTCC 57.475 33.333 0.00 0.00 36.14 3.85
860 2208 6.985059 ACTATTCAGTTTTCGCTTATACTCCC 59.015 38.462 0.00 0.00 0.00 4.30
861 2209 5.416271 TTCAGTTTTCGCTTATACTCCCT 57.584 39.130 0.00 0.00 0.00 4.20
862 2210 5.007385 TCAGTTTTCGCTTATACTCCCTC 57.993 43.478 0.00 0.00 0.00 4.30
863 2211 4.120589 CAGTTTTCGCTTATACTCCCTCC 58.879 47.826 0.00 0.00 0.00 4.30
864 2212 3.121544 GTTTTCGCTTATACTCCCTCCG 58.878 50.000 0.00 0.00 0.00 4.63
865 2213 2.062971 TTCGCTTATACTCCCTCCGT 57.937 50.000 0.00 0.00 0.00 4.69
866 2214 2.062971 TCGCTTATACTCCCTCCGTT 57.937 50.000 0.00 0.00 0.00 4.44
867 2215 1.952296 TCGCTTATACTCCCTCCGTTC 59.048 52.381 0.00 0.00 0.00 3.95
868 2216 1.000496 CGCTTATACTCCCTCCGTTCC 60.000 57.143 0.00 0.00 0.00 3.62
869 2217 2.037144 GCTTATACTCCCTCCGTTCCA 58.963 52.381 0.00 0.00 0.00 3.53
870 2218 2.433239 GCTTATACTCCCTCCGTTCCAA 59.567 50.000 0.00 0.00 0.00 3.53
871 2219 3.118519 GCTTATACTCCCTCCGTTCCAAA 60.119 47.826 0.00 0.00 0.00 3.28
872 2220 4.624604 GCTTATACTCCCTCCGTTCCAAAA 60.625 45.833 0.00 0.00 0.00 2.44
873 2221 5.681639 CTTATACTCCCTCCGTTCCAAAAT 58.318 41.667 0.00 0.00 0.00 1.82
874 2222 6.687139 GCTTATACTCCCTCCGTTCCAAAATA 60.687 42.308 0.00 0.00 0.00 1.40
875 2223 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
876 2224 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
877 2225 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
878 2226 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
879 2227 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
880 2228 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
881 2229 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
882 2230 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
883 2231 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
884 2232 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
885 2233 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
886 2234 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
887 2235 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
888 2236 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
889 2237 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
916 2264 8.482852 ACTAACTTTAGTACTAAGTTGGGTCA 57.517 34.615 26.07 14.61 41.92 4.02
917 2265 9.097946 ACTAACTTTAGTACTAAGTTGGGTCAT 57.902 33.333 26.07 14.32 41.92 3.06
918 2266 9.583765 CTAACTTTAGTACTAAGTTGGGTCATC 57.416 37.037 25.03 0.00 0.00 2.92
919 2267 7.793948 ACTTTAGTACTAAGTTGGGTCATCT 57.206 36.000 14.73 0.00 0.00 2.90
920 2268 8.890410 ACTTTAGTACTAAGTTGGGTCATCTA 57.110 34.615 14.73 0.00 0.00 1.98
921 2269 9.490083 ACTTTAGTACTAAGTTGGGTCATCTAT 57.510 33.333 14.73 0.00 0.00 1.98
926 2274 8.047310 AGTACTAAGTTGGGTCATCTATTTTGG 58.953 37.037 0.00 0.00 0.00 3.28
927 2275 7.027874 ACTAAGTTGGGTCATCTATTTTGGA 57.972 36.000 0.00 0.00 0.00 3.53
928 2276 7.466804 ACTAAGTTGGGTCATCTATTTTGGAA 58.533 34.615 0.00 0.00 0.00 3.53
929 2277 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
930 2278 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
931 2279 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
932 2280 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
933 2281 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
934 2282 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
935 2283 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
936 2284 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
937 2285 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
938 2286 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
939 2287 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
940 2288 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
954 2302 1.471676 GGAGTACAATCGTGAGCCCTG 60.472 57.143 0.00 0.00 0.00 4.45
976 2324 2.476619 CCTGCTGCTATATGTACAACGC 59.523 50.000 0.00 0.79 0.00 4.84
985 2333 0.538516 ATGTACAACGCCCTGCCAAA 60.539 50.000 0.00 0.00 0.00 3.28
990 2338 1.151908 AACGCCCTGCCAAAGGTAA 59.848 52.632 0.00 0.00 45.78 2.85
1007 2355 0.898326 TAAGCGAGCAGGAGTCACCA 60.898 55.000 0.00 0.00 42.04 4.17
1009 2357 2.640302 GCGAGCAGGAGTCACCAGA 61.640 63.158 0.00 0.00 42.04 3.86
1023 2371 2.414750 CCAGACTTTGGTTTGGCGT 58.585 52.632 0.00 0.00 40.14 5.68
1031 2379 0.461961 TTGGTTTGGCGTTGGGAAAG 59.538 50.000 0.00 0.00 0.00 2.62
1032 2380 0.395862 TGGTTTGGCGTTGGGAAAGA 60.396 50.000 0.00 0.00 0.00 2.52
1033 2381 0.031585 GGTTTGGCGTTGGGAAAGAC 59.968 55.000 0.00 0.00 0.00 3.01
1043 2391 2.125633 GGAAAGACGACCCCTCGC 60.126 66.667 0.00 0.00 44.33 5.03
1121 2471 3.736252 CCCGAGAGACAAACATATAAGCG 59.264 47.826 0.00 0.00 0.00 4.68
1415 2789 2.559698 TCTCGCCTGGAAATTTGTGA 57.440 45.000 0.00 0.00 0.00 3.58
1421 2795 3.441572 CGCCTGGAAATTTGTGATCTTCT 59.558 43.478 0.00 0.00 0.00 2.85
1444 2818 0.958822 GCGCCTTTTTCCAGGAAGAA 59.041 50.000 1.07 3.32 35.71 2.52
1536 2914 4.107622 GGAGCCAATCGTCATTTGATTTG 58.892 43.478 0.00 0.00 33.91 2.32
1547 2925 9.740239 ATCGTCATTTGATTTGATTTCAATAGG 57.260 29.630 0.00 0.00 35.55 2.57
1551 2929 8.199449 TCATTTGATTTGATTTCAATAGGAGGC 58.801 33.333 0.00 0.00 35.55 4.70
1572 2950 2.478370 CGATCCGCATGCAAAACTGAAT 60.478 45.455 19.57 0.00 0.00 2.57
1583 2961 7.148373 GCATGCAAAACTGAATTATGGTCATTT 60.148 33.333 14.21 0.00 0.00 2.32
1604 2982 8.724229 TCATTTCTGAGAATTTGTCATGTACTG 58.276 33.333 0.00 0.00 0.00 2.74
1605 2983 8.509690 CATTTCTGAGAATTTGTCATGTACTGT 58.490 33.333 0.00 0.00 0.00 3.55
1627 3005 3.054948 TCTGTCCATGCATCAATCAGTCA 60.055 43.478 0.00 0.00 0.00 3.41
1840 3218 1.266175 CAACTTCTCTGCAGTTGCCTG 59.734 52.381 14.67 2.06 43.48 4.85
1912 3290 0.318445 CGTCGACCGGAGAAAGTTGT 60.318 55.000 9.46 0.00 0.00 3.32
1953 3333 5.642491 AGCCTTTAGACGTAATTTTGACTCC 59.358 40.000 0.00 0.00 0.00 3.85
2137 3518 2.870372 GGGTCGTTGATGCTGCAC 59.130 61.111 3.57 0.00 0.00 4.57
2271 3660 1.546029 GATTCTGGCTTGGGTTGAACC 59.454 52.381 5.62 5.62 37.60 3.62
2490 3886 3.686016 TGAAAGGTATTCTTGGAGTGGC 58.314 45.455 0.00 0.00 35.55 5.01
2602 3998 7.257722 AGTTCACTTTGACACAGGTAAAAATG 58.742 34.615 0.00 0.00 27.95 2.32
2796 4195 6.567769 TCTCTTTTTGTTCAAAAATCACGC 57.432 33.333 19.17 0.00 33.80 5.34
2797 4196 6.096036 TCTCTTTTTGTTCAAAAATCACGCA 58.904 32.000 19.17 1.55 33.80 5.24
2884 4284 4.261489 GCAGGGAACTCATATTCTGCAATG 60.261 45.833 8.05 0.00 44.68 2.82
3034 4434 7.159372 TGTTCTACTCCCTCTGTAAACAAATC 58.841 38.462 0.00 0.00 0.00 2.17
3175 4575 0.678048 ATGCAGAGTTTTCGGAGGCC 60.678 55.000 0.00 0.00 0.00 5.19
3333 4748 7.555087 TGGGTTTTGATGCATTTATAGAAAGG 58.445 34.615 0.00 0.00 0.00 3.11
3420 4848 2.743928 CCTCACCGCAAGCACTCC 60.744 66.667 0.00 0.00 0.00 3.85
3421 4849 2.345244 CTCACCGCAAGCACTCCT 59.655 61.111 0.00 0.00 0.00 3.69
3492 5062 1.674221 CCTAAGCTGAGCTGAGCGTTT 60.674 52.381 19.34 11.64 44.24 3.60
3495 5065 0.250038 AGCTGAGCTGAGCGTTTTCA 60.250 50.000 19.78 0.00 44.24 2.69
3628 5198 3.579302 CCCCTCAGTTGGGTGGCA 61.579 66.667 0.00 0.00 45.70 4.92
3645 5215 1.068753 CAAGCCGCCGATCAGATCT 59.931 57.895 8.82 0.00 0.00 2.75
3774 5348 3.276846 GGCGTCGCACAACAAGGT 61.277 61.111 20.50 0.00 0.00 3.50
3798 5372 2.158559 CCAATGATCCAACAACGGTCA 58.841 47.619 0.00 0.00 0.00 4.02
3814 5388 0.749454 GTCATGGTAGGGCAAGCCAG 60.749 60.000 13.87 0.00 37.98 4.85
3930 5507 1.555075 ACATGTACTGGGCGTCTGAAT 59.445 47.619 0.00 0.00 0.00 2.57
4080 5657 0.184451 GGTCATGGCATCCCAGATGT 59.816 55.000 0.00 0.00 46.24 3.06
4127 5705 4.917385 AGACTAGAGAAGAAGCTCAGACA 58.083 43.478 0.00 0.00 37.37 3.41
4146 5737 1.739562 GAGCGACTGTGGAGCCAAG 60.740 63.158 0.00 0.00 0.00 3.61
4157 5748 1.281925 GGAGCCAAGGATCCTCCCAA 61.282 60.000 16.52 0.00 46.28 4.12
4162 5753 3.272020 AGCCAAGGATCCTCCCAAAATAA 59.728 43.478 16.52 0.00 37.19 1.40
4167 5758 3.117360 AGGATCCTCCCAAAATAAGGCAG 60.117 47.826 9.02 0.00 37.19 4.85
4458 6073 3.113745 GCATTGTGGCCTGGATCG 58.886 61.111 3.32 0.00 0.00 3.69
4477 6092 4.837896 TCGATGTGACATCCTAGCTTAG 57.162 45.455 19.01 3.55 0.00 2.18
4489 6104 8.497910 ACATCCTAGCTTAGAAGGAATGATAA 57.502 34.615 7.05 0.00 44.87 1.75
4491 6106 9.956640 CATCCTAGCTTAGAAGGAATGATAAAT 57.043 33.333 7.05 0.00 44.87 1.40
4493 6108 9.159254 TCCTAGCTTAGAAGGAATGATAAATCA 57.841 33.333 0.14 0.00 38.97 2.57
4534 6318 1.470098 CTTCTTTTCCTGGTGGATGCG 59.530 52.381 0.00 0.00 42.81 4.73
4544 6328 1.141019 GTGGATGCGGCGAGAACTA 59.859 57.895 12.98 0.00 0.00 2.24
4592 6376 1.740296 GGTCGGTGCACATTACGCT 60.740 57.895 20.43 0.00 0.00 5.07
4675 6463 2.936202 CCAGTTGTATTCCTGATGGGG 58.064 52.381 0.00 0.00 35.33 4.96
4689 6477 2.718062 TGATGGGGTAGGGAGTCGTATA 59.282 50.000 0.00 0.00 0.00 1.47
4718 6507 9.326339 GTGTAAGTTTCTAATTTCTTTAAGGCG 57.674 33.333 0.00 0.00 0.00 5.52
5097 6893 5.966853 TCATTCATACAATCACTACCCCA 57.033 39.130 0.00 0.00 0.00 4.96
5158 6954 8.825774 AGGTTTGGCATTTAAAATTTCCTCTAT 58.174 29.630 0.00 0.00 0.00 1.98
5234 7030 8.098912 ACACCTCCACTAATATTCGTTAACTTT 58.901 33.333 3.71 0.00 0.00 2.66
5259 7055 6.496338 ACAAGACCGTAAATCCTCAAATTC 57.504 37.500 0.00 0.00 0.00 2.17
5308 7104 7.016361 ACAGAACAAACATCTCAGTTTACAC 57.984 36.000 0.00 0.00 39.55 2.90
5346 7143 5.462068 GGTATGCCTTTTGTTTTCTTCACAC 59.538 40.000 0.00 0.00 0.00 3.82
5416 7213 7.701924 ACATAACCAACATGATCTTATTTTGCG 59.298 33.333 0.00 0.00 0.00 4.85
5430 7227 7.988737 TCTTATTTTGCGTTCATCATTGAGAT 58.011 30.769 0.00 0.00 37.48 2.75
5609 7406 6.742718 CGTTGTTCATATTTCGCTTGAAATCT 59.257 34.615 6.52 0.00 46.79 2.40
5699 7496 3.956744 ACCCTTTCTCCATAAAGCTGTC 58.043 45.455 0.00 0.00 35.53 3.51
5706 7503 4.922206 TCTCCATAAAGCTGTCCATTGTT 58.078 39.130 0.00 0.00 0.00 2.83
5708 7505 6.480763 TCTCCATAAAGCTGTCCATTGTTTA 58.519 36.000 0.00 0.00 0.00 2.01
5868 7665 1.671379 GTTCACCGGCCTTGAGGAC 60.671 63.158 0.00 0.00 40.84 3.85
6021 7818 1.451387 CCCGGTTTCTATGCGCCTT 60.451 57.895 4.18 0.00 0.00 4.35
6028 7825 3.063588 GGTTTCTATGCGCCTTACACTTC 59.936 47.826 4.18 0.00 0.00 3.01
6161 7959 9.720769 ACAATGTGTAAGTAAGCTAGTTGTAAT 57.279 29.630 0.00 0.00 0.00 1.89
6206 8004 1.136308 CGCACGGTGCAAACGTATAAA 60.136 47.619 30.23 0.00 45.36 1.40
6207 8005 2.474856 CGCACGGTGCAAACGTATAAAT 60.475 45.455 30.23 0.00 45.36 1.40
6208 8006 2.843643 GCACGGTGCAAACGTATAAATG 59.156 45.455 27.10 5.75 44.26 2.32
6209 8007 3.668491 GCACGGTGCAAACGTATAAATGT 60.668 43.478 27.10 0.00 44.26 2.71
6210 8008 4.468643 CACGGTGCAAACGTATAAATGTT 58.531 39.130 16.06 0.00 43.58 2.71
6230 8028 5.981174 TGTTGTTGTTGCTACGATTAGAAC 58.019 37.500 0.00 0.00 0.00 3.01
6254 8052 8.237811 ACAATATTCACCTTGGTGATATTTCC 57.762 34.615 21.39 0.00 32.91 3.13
6256 8054 4.666412 TTCACCTTGGTGATATTTCCCA 57.334 40.909 21.39 3.23 32.91 4.37
6478 8276 6.014647 TCCTAGCCGTGTCCATATTTATAGT 58.985 40.000 0.00 0.00 0.00 2.12
6506 8304 6.238593 GGACAAACAGACCTATACTACTACCG 60.239 46.154 0.00 0.00 0.00 4.02
6608 8406 1.367659 CTACTGAAGGCAGAAGCAGC 58.632 55.000 0.00 0.00 45.17 5.25
7111 8909 2.834638 ATCCCCCAAAATCAGTGAGG 57.165 50.000 0.00 0.00 0.00 3.86
7579 9377 6.480763 ACAACCATCATCTATTGTTGTACCA 58.519 36.000 4.66 0.00 46.89 3.25
7658 9456 9.116067 TGATGTAATTAGTGGTGTATTTTAGGC 57.884 33.333 0.00 0.00 0.00 3.93
7706 9504 4.836125 AGCGTTTGTCTTGTGAAATGAT 57.164 36.364 0.00 0.00 0.00 2.45
7771 9571 4.457257 GCAGTTCTTTGTATCTCTTGGCTT 59.543 41.667 0.00 0.00 0.00 4.35
7806 9606 7.872483 ACATTTTGCACTAGTTTTTAGATTGGG 59.128 33.333 0.00 0.00 0.00 4.12
7854 9654 5.046529 CCTCACTATTTCTTCAGATCCACG 58.953 45.833 0.00 0.00 0.00 4.94
7961 9761 8.698973 ATGCTAAGTGTAGACATAGTGAGTAT 57.301 34.615 4.46 0.00 0.00 2.12
8026 11483 0.386838 GAGCATGTTATTGCAGGGCC 59.613 55.000 0.00 0.00 45.23 5.80
8233 11749 2.185004 TAAGGCTGAGTTGTCTTGCC 57.815 50.000 0.00 0.00 40.88 4.52
8270 11786 2.159142 ACCCGCGAGTTTAGTTCATAGG 60.159 50.000 8.23 0.00 0.00 2.57
8329 11846 4.524316 TTCTCACAAGGCAATTTCATGG 57.476 40.909 0.00 0.00 0.00 3.66
8342 11859 3.749665 TTTCATGGAGTTTTTGCCCAG 57.250 42.857 0.00 0.00 32.90 4.45
8377 11894 5.034152 GGCAAATGTGTGTACCATTAATCG 58.966 41.667 0.00 0.00 32.40 3.34
8524 12042 4.127171 GGTAATCTTGTGTATGCCATCGT 58.873 43.478 0.00 0.00 0.00 3.73
8533 12051 1.116536 TATGCCATCGTCGCCCCTAA 61.117 55.000 0.00 0.00 0.00 2.69
8535 12053 3.090219 GCCATCGTCGCCCCTAACT 62.090 63.158 0.00 0.00 0.00 2.24
8542 12060 1.202336 CGTCGCCCCTAACTTATCGTT 60.202 52.381 0.00 0.00 39.64 3.85
8616 12134 1.006832 CGATGTCGGTAAGGCCTTTG 58.993 55.000 26.08 14.30 35.37 2.77
8636 12155 2.030412 ACTGTTGCGCATCACCGA 59.970 55.556 16.92 0.00 0.00 4.69
8677 12196 1.805945 ATCGTCAAAGTCGAGCGCC 60.806 57.895 2.29 0.00 40.57 6.53
8703 12222 0.257039 ACCACCATCAATCCTCAGGC 59.743 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.581076 AACCATAGTTTTAAAAACCAAACCGGT 60.581 33.333 0.00 0.00 41.66 5.28
8 9 6.282167 ACCATAGTTTTAAAAACCAAACCGG 58.718 36.000 0.00 0.00 42.50 5.28
9 10 7.773864 AACCATAGTTTTAAAAACCAAACCG 57.226 32.000 1.31 0.00 29.61 4.44
10 11 9.163899 TGAAACCATAGTTTTAAAAACCAAACC 57.836 29.630 1.31 0.00 46.25 3.27
11 12 9.976255 GTGAAACCATAGTTTTAAAAACCAAAC 57.024 29.630 1.31 0.00 46.25 2.93
34 35 2.845659 ACATATCTCAGGGGTTGGTGA 58.154 47.619 0.00 0.00 0.00 4.02
72 73 3.826729 TGGCACGTATCACTGCTATAGAT 59.173 43.478 3.21 0.00 33.63 1.98
74 75 3.309388 GTGGCACGTATCACTGCTATAG 58.691 50.000 0.00 0.00 33.63 1.31
80 81 1.518325 TTTGGTGGCACGTATCACTG 58.482 50.000 12.17 0.00 34.57 3.66
155 156 5.307544 TGGTGGAGAGAGTAGTATAGGAC 57.692 47.826 0.00 0.00 0.00 3.85
160 161 7.496346 TGAAATTTGGTGGAGAGAGTAGTAT 57.504 36.000 0.00 0.00 0.00 2.12
167 168 6.975196 TTTTCATGAAATTTGGTGGAGAGA 57.025 33.333 21.10 0.00 0.00 3.10
194 195 9.326413 GCACTTTTCTATGGCTTACTATCTTTA 57.674 33.333 0.00 0.00 0.00 1.85
197 198 6.292150 GGCACTTTTCTATGGCTTACTATCT 58.708 40.000 0.00 0.00 38.32 1.98
198 199 6.546972 GGCACTTTTCTATGGCTTACTATC 57.453 41.667 0.00 0.00 38.32 2.08
206 207 2.924421 AGCTAGGCACTTTTCTATGGC 58.076 47.619 0.00 0.00 41.75 4.40
235 664 1.295792 AAGCGTTCTTTGCGACTCAA 58.704 45.000 0.00 0.00 37.44 3.02
288 717 2.041216 TCTTTGGAGCCTACTTTTCCCC 59.959 50.000 0.00 0.00 0.00 4.81
306 735 0.320247 CACCACGCTGCTCTTCTCTT 60.320 55.000 0.00 0.00 0.00 2.85
317 746 0.108329 CCTAAATCGACCACCACGCT 60.108 55.000 0.00 0.00 0.00 5.07
384 1725 7.066525 CACCCGCAAATAAAAGATAGGTAAAGA 59.933 37.037 0.00 0.00 0.00 2.52
394 1735 6.657541 AGATAAAGACACCCGCAAATAAAAGA 59.342 34.615 0.00 0.00 0.00 2.52
395 1736 6.852664 AGATAAAGACACCCGCAAATAAAAG 58.147 36.000 0.00 0.00 0.00 2.27
396 1737 6.827586 AGATAAAGACACCCGCAAATAAAA 57.172 33.333 0.00 0.00 0.00 1.52
397 1738 7.107542 AGTAGATAAAGACACCCGCAAATAAA 58.892 34.615 0.00 0.00 0.00 1.40
398 1739 6.646267 AGTAGATAAAGACACCCGCAAATAA 58.354 36.000 0.00 0.00 0.00 1.40
399 1740 6.229936 AGTAGATAAAGACACCCGCAAATA 57.770 37.500 0.00 0.00 0.00 1.40
400 1741 5.099042 AGTAGATAAAGACACCCGCAAAT 57.901 39.130 0.00 0.00 0.00 2.32
401 1742 4.546829 AGTAGATAAAGACACCCGCAAA 57.453 40.909 0.00 0.00 0.00 3.68
402 1743 4.546829 AAGTAGATAAAGACACCCGCAA 57.453 40.909 0.00 0.00 0.00 4.85
403 1744 4.546829 AAAGTAGATAAAGACACCCGCA 57.453 40.909 0.00 0.00 0.00 5.69
404 1745 4.933400 TGAAAAGTAGATAAAGACACCCGC 59.067 41.667 0.00 0.00 0.00 6.13
405 1746 5.063564 GCTGAAAAGTAGATAAAGACACCCG 59.936 44.000 0.00 0.00 0.00 5.28
406 1747 5.063564 CGCTGAAAAGTAGATAAAGACACCC 59.936 44.000 0.00 0.00 0.00 4.61
407 1748 5.063564 CCGCTGAAAAGTAGATAAAGACACC 59.936 44.000 0.00 0.00 0.00 4.16
408 1749 5.867716 TCCGCTGAAAAGTAGATAAAGACAC 59.132 40.000 0.00 0.00 0.00 3.67
409 1750 6.032956 TCCGCTGAAAAGTAGATAAAGACA 57.967 37.500 0.00 0.00 0.00 3.41
410 1751 7.921745 AGTATCCGCTGAAAAGTAGATAAAGAC 59.078 37.037 0.00 0.00 0.00 3.01
411 1752 8.008513 AGTATCCGCTGAAAAGTAGATAAAGA 57.991 34.615 0.00 0.00 0.00 2.52
412 1753 9.182933 GTAGTATCCGCTGAAAAGTAGATAAAG 57.817 37.037 0.00 0.00 0.00 1.85
413 1754 8.910944 AGTAGTATCCGCTGAAAAGTAGATAAA 58.089 33.333 0.00 0.00 0.00 1.40
414 1755 8.461249 AGTAGTATCCGCTGAAAAGTAGATAA 57.539 34.615 0.00 0.00 0.00 1.75
415 1756 8.461249 AAGTAGTATCCGCTGAAAAGTAGATA 57.539 34.615 0.00 0.00 0.00 1.98
416 1757 6.963083 AGTAGTATCCGCTGAAAAGTAGAT 57.037 37.500 0.00 0.00 0.00 1.98
417 1758 6.770746 AAGTAGTATCCGCTGAAAAGTAGA 57.229 37.500 0.00 0.00 0.00 2.59
418 1759 6.237861 GCAAAGTAGTATCCGCTGAAAAGTAG 60.238 42.308 0.00 0.00 0.00 2.57
419 1760 5.579511 GCAAAGTAGTATCCGCTGAAAAGTA 59.420 40.000 0.00 0.00 0.00 2.24
420 1761 4.392138 GCAAAGTAGTATCCGCTGAAAAGT 59.608 41.667 0.00 0.00 0.00 2.66
531 1877 2.296752 CCAACCTGCATCAAACATCACA 59.703 45.455 0.00 0.00 0.00 3.58
536 1882 2.382882 TGAACCAACCTGCATCAAACA 58.617 42.857 0.00 0.00 0.00 2.83
588 1934 1.152819 CCCTCCCACTCGGACGATA 60.153 63.158 0.00 0.00 34.86 2.92
597 1943 0.252284 ATCGACTGTTCCCTCCCACT 60.252 55.000 0.00 0.00 0.00 4.00
601 1947 0.175989 GGACATCGACTGTTCCCTCC 59.824 60.000 0.00 0.00 38.54 4.30
608 1954 2.425312 CAAGCTCTAGGACATCGACTGT 59.575 50.000 0.00 0.00 42.15 3.55
609 1955 2.223688 CCAAGCTCTAGGACATCGACTG 60.224 54.545 0.00 0.00 0.00 3.51
614 1960 1.208052 TGTGCCAAGCTCTAGGACATC 59.792 52.381 4.15 0.00 0.00 3.06
632 1978 1.405872 TGTCGACCTACACACCTTGT 58.594 50.000 14.12 0.00 42.84 3.16
669 2015 0.898320 CGGAGGAGACACATGAGGTT 59.102 55.000 0.00 0.00 0.00 3.50
684 2030 1.635663 GGGAAATGCACGTGACGGAG 61.636 60.000 22.23 2.22 0.00 4.63
688 2034 2.686816 CCCGGGAAATGCACGTGAC 61.687 63.158 22.23 11.46 43.44 3.67
691 2037 1.910580 ATCTCCCGGGAAATGCACGT 61.911 55.000 26.68 1.16 43.44 4.49
761 2107 6.385759 ACCCTGTAAATTTTGTTTCTCCCTTT 59.614 34.615 0.00 0.00 0.00 3.11
844 2192 2.762327 ACGGAGGGAGTATAAGCGAAAA 59.238 45.455 0.00 0.00 0.00 2.29
856 2204 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
857 2205 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
858 2206 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
859 2207 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
860 2208 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
861 2209 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
862 2210 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
863 2211 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
890 2238 9.586732 TGACCCAACTTAGTACTAAAGTTAGTA 57.413 33.333 15.95 6.81 43.36 1.82
891 2239 8.482852 TGACCCAACTTAGTACTAAAGTTAGT 57.517 34.615 15.95 18.05 45.39 2.24
892 2240 9.583765 GATGACCCAACTTAGTACTAAAGTTAG 57.416 37.037 15.95 15.88 36.82 2.34
893 2241 9.317827 AGATGACCCAACTTAGTACTAAAGTTA 57.682 33.333 15.95 7.83 0.00 2.24
894 2242 8.203681 AGATGACCCAACTTAGTACTAAAGTT 57.796 34.615 15.95 16.90 0.00 2.66
895 2243 7.793948 AGATGACCCAACTTAGTACTAAAGT 57.206 36.000 15.95 12.68 0.00 2.66
900 2248 8.047310 CCAAAATAGATGACCCAACTTAGTACT 58.953 37.037 0.00 0.00 0.00 2.73
901 2249 8.044908 TCCAAAATAGATGACCCAACTTAGTAC 58.955 37.037 0.00 0.00 0.00 2.73
902 2250 8.153221 TCCAAAATAGATGACCCAACTTAGTA 57.847 34.615 0.00 0.00 0.00 1.82
903 2251 7.027874 TCCAAAATAGATGACCCAACTTAGT 57.972 36.000 0.00 0.00 0.00 2.24
904 2252 7.414098 CGTTCCAAAATAGATGACCCAACTTAG 60.414 40.741 0.00 0.00 0.00 2.18
905 2253 6.373216 CGTTCCAAAATAGATGACCCAACTTA 59.627 38.462 0.00 0.00 0.00 2.24
906 2254 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
907 2255 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
908 2256 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
909 2257 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
910 2258 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
911 2259 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
912 2260 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
913 2261 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
914 2262 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
915 2263 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
916 2264 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
917 2265 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
918 2266 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
919 2267 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
920 2268 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
921 2269 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
922 2270 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
923 2271 1.719529 TTGTACTCCCTCCGTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
924 2272 1.829222 GATTGTACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
925 2273 1.202382 CGATTGTACTCCCTCCGTTCC 60.202 57.143 0.00 0.00 0.00 3.62
926 2274 1.475682 ACGATTGTACTCCCTCCGTTC 59.524 52.381 0.00 0.00 0.00 3.95
927 2275 1.203994 CACGATTGTACTCCCTCCGTT 59.796 52.381 0.00 0.00 0.00 4.44
928 2276 0.815734 CACGATTGTACTCCCTCCGT 59.184 55.000 0.00 0.00 0.00 4.69
929 2277 1.065701 CTCACGATTGTACTCCCTCCG 59.934 57.143 0.00 0.00 0.00 4.63
930 2278 1.202428 GCTCACGATTGTACTCCCTCC 60.202 57.143 0.00 0.00 0.00 4.30
931 2279 1.202428 GGCTCACGATTGTACTCCCTC 60.202 57.143 0.00 0.00 0.00 4.30
932 2280 0.824759 GGCTCACGATTGTACTCCCT 59.175 55.000 0.00 0.00 0.00 4.20
933 2281 0.179081 GGGCTCACGATTGTACTCCC 60.179 60.000 0.00 1.29 0.00 4.30
934 2282 0.824759 AGGGCTCACGATTGTACTCC 59.175 55.000 0.00 0.00 0.00 3.85
935 2283 1.927895 CAGGGCTCACGATTGTACTC 58.072 55.000 0.00 0.00 0.00 2.59
936 2284 0.108138 GCAGGGCTCACGATTGTACT 60.108 55.000 0.00 0.00 0.00 2.73
937 2285 1.090052 GGCAGGGCTCACGATTGTAC 61.090 60.000 0.00 0.00 0.00 2.90
938 2286 1.220749 GGCAGGGCTCACGATTGTA 59.779 57.895 0.00 0.00 0.00 2.41
939 2287 2.045926 GGCAGGGCTCACGATTGT 60.046 61.111 0.00 0.00 0.00 2.71
940 2288 2.110967 CAGGCAGGGCTCACGATTG 61.111 63.158 0.00 0.00 0.00 2.67
954 2302 2.476619 CGTTGTACATATAGCAGCAGGC 59.523 50.000 0.00 0.00 45.30 4.85
985 2333 0.612174 TGACTCCTGCTCGCTTACCT 60.612 55.000 0.00 0.00 0.00 3.08
990 2338 2.601666 TGGTGACTCCTGCTCGCT 60.602 61.111 0.00 0.00 37.07 4.93
1007 2355 0.744281 CCAACGCCAAACCAAAGTCT 59.256 50.000 0.00 0.00 0.00 3.24
1009 2357 0.684805 TCCCAACGCCAAACCAAAGT 60.685 50.000 0.00 0.00 0.00 2.66
1023 2371 1.823169 CGAGGGGTCGTCTTTCCCAA 61.823 60.000 0.00 0.00 45.06 4.12
1031 2379 4.176851 GACTCGCGAGGGGTCGTC 62.177 72.222 36.93 22.39 34.16 4.20
1033 2381 4.180946 CTGACTCGCGAGGGGTCG 62.181 72.222 36.93 18.95 37.17 4.79
1043 2391 0.172803 CGGGGTAGGAAACTGACTCG 59.827 60.000 0.00 0.00 43.88 4.18
1121 2471 7.928908 GATCAGTCTCTGTATTGATCAAGAC 57.071 40.000 23.22 23.22 43.30 3.01
1314 2687 0.253327 AAAAGGGCGGATGAGGAGAC 59.747 55.000 0.00 0.00 0.00 3.36
1415 2789 0.322546 AAAAAGGCGCCCGAGAAGAT 60.323 50.000 26.15 0.00 0.00 2.40
1421 2795 2.671619 CTGGAAAAAGGCGCCCGA 60.672 61.111 26.15 3.08 0.00 5.14
1444 2818 7.560991 TGATGATAACAAATAAGAACAGCCCAT 59.439 33.333 0.00 0.00 0.00 4.00
1481 2859 9.525409 CCAGGCTCATTGAGAAAATAAAAATAG 57.475 33.333 17.87 0.00 0.00 1.73
1536 2914 2.996621 CGGATCGCCTCCTATTGAAATC 59.003 50.000 2.89 0.00 42.47 2.17
1551 2929 0.447406 TCAGTTTTGCATGCGGATCG 59.553 50.000 14.09 0.00 0.00 3.69
1572 2950 8.634335 TGACAAATTCTCAGAAATGACCATAA 57.366 30.769 9.85 0.00 0.00 1.90
1583 2961 6.870439 CAGACAGTACATGACAAATTCTCAGA 59.130 38.462 0.00 0.00 0.00 3.27
1604 2982 3.276857 ACTGATTGATGCATGGACAGAC 58.723 45.455 2.46 0.00 0.00 3.51
1605 2983 3.054948 TGACTGATTGATGCATGGACAGA 60.055 43.478 2.46 0.00 0.00 3.41
1840 3218 2.683362 GGGCTTCTGCACAAATACCTAC 59.317 50.000 0.00 0.00 43.35 3.18
1953 3333 7.811236 AGATAATGCACTCTGTGTTGAAATTTG 59.189 33.333 0.00 0.00 35.75 2.32
2137 3518 4.799678 AGATTATGTCTATTCAGCGTCCG 58.200 43.478 0.00 0.00 34.69 4.79
2271 3660 5.890110 AATCATAACTTCACTATGACGCG 57.110 39.130 3.53 3.53 38.32 6.01
2490 3886 6.849085 AGATACCTATGCCAGATAACTGAG 57.151 41.667 0.79 0.00 46.03 3.35
2602 3998 6.773638 AGATATGGTTGGATCACATTAGTCC 58.226 40.000 0.00 0.00 0.00 3.85
2777 4176 6.304208 GCTTTTGCGTGATTTTTGAACAAAAA 59.696 30.769 21.84 21.84 43.42 1.94
2778 4177 5.792468 GCTTTTGCGTGATTTTTGAACAAAA 59.208 32.000 8.37 8.37 35.62 2.44
2796 4195 4.443315 CCAGCAATAAATAGGGGGCTTTTG 60.443 45.833 0.00 0.00 0.00 2.44
2797 4196 3.711190 CCAGCAATAAATAGGGGGCTTTT 59.289 43.478 0.00 0.00 0.00 2.27
2884 4284 9.740239 ATGTATTTCAGTATCACAAAATGCATC 57.260 29.630 0.00 0.00 38.94 3.91
3034 4434 8.510505 ACTACTTAGTGACCTAAAACGTCTTAG 58.489 37.037 1.45 1.45 34.72 2.18
3104 4504 4.731961 GCATCGACAAACAAGCTATCAATG 59.268 41.667 0.00 0.00 0.00 2.82
3175 4575 2.232208 GCAACTTCCCATTTCCTCCAAG 59.768 50.000 0.00 0.00 0.00 3.61
3298 4713 3.524541 CATCAAAACCCAAGGCTTATGC 58.475 45.455 0.00 0.00 38.76 3.14
3333 4748 6.094186 CCTTCTTAGGGCTTGTACAAATTCTC 59.906 42.308 10.03 2.10 37.94 2.87
3436 4864 7.093322 ACATGATTAAGTCAGAGGAAAATGC 57.907 36.000 0.00 0.00 40.92 3.56
3472 5042 0.108424 AACGCTCAGCTCAGCTTAGG 60.108 55.000 8.35 2.84 36.40 2.69
3492 5062 4.024133 CACCACAACACGATCATCTTTGAA 60.024 41.667 0.00 0.00 34.96 2.69
3495 5065 2.226437 GCACCACAACACGATCATCTTT 59.774 45.455 0.00 0.00 0.00 2.52
3628 5198 0.600557 CTAGATCTGATCGGCGGCTT 59.399 55.000 7.21 0.00 0.00 4.35
3634 5204 2.487762 GTGCTCTCCTAGATCTGATCGG 59.512 54.545 11.73 8.37 0.00 4.18
3645 5215 1.381872 GGCCTGAGGTGCTCTCCTA 60.382 63.158 0.00 0.00 41.76 2.94
3677 5247 4.699925 TCTCCTCTCTAGCTACTCCTTC 57.300 50.000 0.00 0.00 0.00 3.46
3774 5348 1.811965 CGTTGTTGGATCATTGGAGCA 59.188 47.619 0.00 0.00 0.00 4.26
3778 5352 2.158559 TGACCGTTGTTGGATCATTGG 58.841 47.619 0.00 0.00 0.00 3.16
3798 5372 0.184451 CATCTGGCTTGCCCTACCAT 59.816 55.000 9.35 0.00 31.79 3.55
3814 5388 5.588648 TGTTCCGAGGGTCAATTTATTCATC 59.411 40.000 0.00 0.00 0.00 2.92
3869 5443 4.065789 CCCTTTTCCAGTGAGTTGTCTAC 58.934 47.826 0.00 0.00 0.00 2.59
3870 5444 3.714798 ACCCTTTTCCAGTGAGTTGTCTA 59.285 43.478 0.00 0.00 0.00 2.59
3872 5446 2.618709 CACCCTTTTCCAGTGAGTTGTC 59.381 50.000 0.00 0.00 33.21 3.18
3873 5447 2.025321 ACACCCTTTTCCAGTGAGTTGT 60.025 45.455 0.00 0.00 35.47 3.32
3874 5448 2.618709 GACACCCTTTTCCAGTGAGTTG 59.381 50.000 0.00 0.00 35.47 3.16
3875 5449 2.745152 CGACACCCTTTTCCAGTGAGTT 60.745 50.000 0.00 0.00 35.47 3.01
3930 5507 2.037251 GCGTCCTCCTATAGCATTGGAA 59.963 50.000 0.00 0.00 33.85 3.53
4080 5657 2.577059 CACTAGGAAGCGGCGGAA 59.423 61.111 9.78 0.00 0.00 4.30
4127 5705 2.164865 CTTGGCTCCACAGTCGCTCT 62.165 60.000 0.00 0.00 0.00 4.09
4391 5982 1.444212 CAAGCCGCAAAACCGATGG 60.444 57.895 0.00 0.00 0.00 3.51
4392 5983 0.318614 AACAAGCCGCAAAACCGATG 60.319 50.000 0.00 0.00 0.00 3.84
4393 5984 0.039527 GAACAAGCCGCAAAACCGAT 60.040 50.000 0.00 0.00 0.00 4.18
4394 5985 1.357334 GAACAAGCCGCAAAACCGA 59.643 52.632 0.00 0.00 0.00 4.69
4395 5986 0.526524 TTGAACAAGCCGCAAAACCG 60.527 50.000 0.00 0.00 0.00 4.44
4396 5987 1.208259 CTTGAACAAGCCGCAAAACC 58.792 50.000 1.60 0.00 0.00 3.27
4445 6036 1.221566 CACATCGATCCAGGCCACA 59.778 57.895 5.01 0.00 0.00 4.17
4452 6043 2.297315 GCTAGGATGTCACATCGATCCA 59.703 50.000 11.76 0.00 38.55 3.41
4453 6044 2.560542 AGCTAGGATGTCACATCGATCC 59.439 50.000 11.76 0.00 36.63 3.36
4458 6073 5.303078 TCCTTCTAAGCTAGGATGTCACATC 59.697 44.000 9.53 9.53 35.66 3.06
4489 6104 5.255687 TGCACCTTGTTGATATGAGTGATT 58.744 37.500 0.00 0.00 0.00 2.57
4491 6106 4.284829 TGCACCTTGTTGATATGAGTGA 57.715 40.909 0.00 0.00 0.00 3.41
4492 6107 4.880120 AGATGCACCTTGTTGATATGAGTG 59.120 41.667 0.00 0.00 0.00 3.51
4493 6108 5.108187 AGATGCACCTTGTTGATATGAGT 57.892 39.130 0.00 0.00 0.00 3.41
4534 6318 0.806492 CTCGGCCTTTAGTTCTCGCC 60.806 60.000 0.00 0.00 36.21 5.54
4544 6328 3.009714 GGAGGGGTCTCGGCCTTT 61.010 66.667 0.00 0.00 40.85 3.11
4592 6376 2.560981 TGCACACTTTATCCTCACTCGA 59.439 45.455 0.00 0.00 0.00 4.04
4718 6507 5.005394 GCACAATCAATGCATGAAAGATCAC 59.995 40.000 0.00 0.00 42.54 3.06
4731 6520 6.317140 ACCTGAACTATGTAGCACAATCAATG 59.683 38.462 0.00 0.00 0.00 2.82
5097 6893 3.069443 GCTCCTTGAGAAGAGATTCCGAT 59.931 47.826 0.00 0.00 0.00 4.18
5158 6954 4.330620 GTGTATCGAATTGCGGAAAGGTTA 59.669 41.667 0.00 0.00 41.33 2.85
5234 7030 7.148540 CGAATTTGAGGATTTACGGTCTTGTAA 60.149 37.037 0.00 0.00 32.70 2.41
5259 7055 3.130633 TGACAGATGTTTCCTGTGAACG 58.869 45.455 0.00 0.00 44.14 3.95
5299 7095 6.760770 ACCATGTCAAAAATTGGTGTAAACTG 59.239 34.615 0.00 0.00 40.87 3.16
5308 7104 5.088680 AGGCATACCATGTCAAAAATTGG 57.911 39.130 0.00 0.00 37.34 3.16
5346 7143 2.159282 GGTGCTTCATTTCCTGCATCAG 60.159 50.000 0.00 0.00 36.64 2.90
5416 7213 9.825972 TTTAAAAGACGAATCTCAATGATGAAC 57.174 29.630 0.00 0.00 34.49 3.18
5430 7227 8.728833 TGAAAAGGTAACACTTTAAAAGACGAA 58.271 29.630 0.00 0.00 39.63 3.85
5609 7406 0.323725 GGAATTGCCCCTGCTTCAGA 60.324 55.000 0.00 0.00 38.71 3.27
5699 7496 4.214119 CACTCACTGTCAGGTAAACAATGG 59.786 45.833 4.53 0.00 0.00 3.16
5706 7503 1.070134 GTGCCACTCACTGTCAGGTAA 59.930 52.381 4.53 0.00 42.38 2.85
5708 7505 1.337384 TGTGCCACTCACTGTCAGGT 61.337 55.000 4.53 0.00 45.81 4.00
5868 7665 3.376234 AGCCATCGTTGTCAGATTCATTG 59.624 43.478 0.00 0.00 0.00 2.82
6021 7818 2.299013 AGCGACATTGTGGAGAAGTGTA 59.701 45.455 2.68 0.00 0.00 2.90
6028 7825 1.364626 GAGGCAGCGACATTGTGGAG 61.365 60.000 2.68 0.00 0.00 3.86
6081 7878 8.938801 ATTAATATCAGGAATACATTGGCACA 57.061 30.769 0.00 0.00 0.00 4.57
6090 7888 8.129211 GCGGCCAAATATTAATATCAGGAATAC 58.871 37.037 21.55 11.71 0.00 1.89
6161 7959 7.767198 CGGTTGGAGATTAACCTAACTCAAATA 59.233 37.037 0.00 0.00 44.24 1.40
6190 7988 4.468643 ACAACATTTATACGTTTGCACCG 58.531 39.130 0.00 3.55 0.00 4.94
6206 8004 6.203915 TGTTCTAATCGTAGCAACAACAACAT 59.796 34.615 0.00 0.00 30.83 2.71
6207 8005 5.524281 TGTTCTAATCGTAGCAACAACAACA 59.476 36.000 0.00 0.00 30.83 3.33
6208 8006 5.981174 TGTTCTAATCGTAGCAACAACAAC 58.019 37.500 0.00 0.00 30.83 3.32
6209 8007 6.606234 TTGTTCTAATCGTAGCAACAACAA 57.394 33.333 0.00 0.00 35.17 2.83
6210 8008 6.795098 ATTGTTCTAATCGTAGCAACAACA 57.205 33.333 0.00 0.00 38.59 3.33
6336 8134 6.108687 TCCAACTGTACATAGAAAGCAGATG 58.891 40.000 0.00 0.00 32.28 2.90
6478 8276 6.491383 AGTAGTATAGGTCTGTTTGTCCAGA 58.509 40.000 0.00 0.00 39.11 3.86
6506 8304 6.147328 ACAGAACGATCTTTAAGCTGGTAAAC 59.853 38.462 0.00 0.00 32.03 2.01
6608 8406 0.250640 AGGCTTCACTTGTGGAGCTG 60.251 55.000 26.99 0.00 0.00 4.24
6806 8604 1.063174 CTGCAGCGCCATCTTTACTTC 59.937 52.381 2.29 0.00 0.00 3.01
7111 8909 0.817229 GGCCTAGGCAGCTCATGAAC 60.817 60.000 34.09 9.77 44.11 3.18
7435 9233 0.973632 TCTCCGAGTGCTGCCTTTAA 59.026 50.000 0.00 0.00 0.00 1.52
7438 9236 0.108585 TTTTCTCCGAGTGCTGCCTT 59.891 50.000 0.00 0.00 0.00 4.35
7579 9377 4.348168 AGGTAGTTGTCACAAGGATTCTGT 59.652 41.667 0.00 0.00 0.00 3.41
7684 9482 5.940192 ATCATTTCACAAGACAAACGCTA 57.060 34.783 0.00 0.00 0.00 4.26
7785 9585 5.048083 CAGCCCAATCTAAAAACTAGTGCAA 60.048 40.000 0.00 0.00 0.00 4.08
7804 9604 2.224305 ACTCAGAGTACACAAACAGCCC 60.224 50.000 0.00 0.00 0.00 5.19
7806 9606 4.811557 AGAAACTCAGAGTACACAAACAGC 59.188 41.667 2.64 0.00 0.00 4.40
7854 9654 4.680171 AACATAGAGGCTTTGCGTTAAC 57.320 40.909 0.00 0.00 0.00 2.01
8026 11483 0.815615 GAATCGGGTGCTGCCTAAGG 60.816 60.000 0.00 0.00 37.43 2.69
8198 11714 1.602311 CTTATCCTGCCTCATGGTGC 58.398 55.000 0.00 0.00 35.27 5.01
8209 11725 3.902881 AGACAACTCAGCCTTATCCTG 57.097 47.619 0.00 0.00 0.00 3.86
8233 11749 5.051816 TCGCGGGTATAATTTAGTCCAAAG 58.948 41.667 6.13 0.00 0.00 2.77
8377 11894 5.164158 CGTTCATTGTATTCTGCTTGTTTGC 60.164 40.000 0.00 0.00 0.00 3.68
8533 12051 1.955080 CCTCCGAGCCTAACGATAAGT 59.045 52.381 0.00 0.00 0.00 2.24
8535 12053 2.158711 TCTCCTCCGAGCCTAACGATAA 60.159 50.000 0.00 0.00 35.94 1.75
8565 12083 5.831525 TCATAGACTCGCAACTCCCTTATTA 59.168 40.000 0.00 0.00 0.00 0.98
8612 12130 1.005294 GATGCGCAACAGTGGCAAAG 61.005 55.000 17.11 0.00 40.49 2.77
8616 12134 2.126734 GTGATGCGCAACAGTGGC 60.127 61.111 21.54 5.39 0.00 5.01
8620 12138 2.743752 CCTCGGTGATGCGCAACAG 61.744 63.158 21.54 13.20 32.14 3.16
8624 12142 4.819761 GCTCCTCGGTGATGCGCA 62.820 66.667 14.96 14.96 0.00 6.09
8677 12196 5.439721 TGAGGATTGATGGTGGTAAATCTG 58.560 41.667 0.00 0.00 31.20 2.90
8703 12222 2.648059 GATGGTGGTTTGAGATCTGGG 58.352 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.