Multiple sequence alignment - TraesCS2B01G093100

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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 TraesCS2B01G093100 chr2B 100.000 3734 0 0 1 3734 53582138 53585871 0.000000e+00 6896.0
1 TraesCS2B01G093100 chr2B 93.758 817 50 1 2118 2934 53659682 53660497 0.000000e+00 1225.0
2 TraesCS2B01G093100 chr2B 88.241 995 105 3 977 1966 53665682 53666669 0.000000e+00 1179.0
3 TraesCS2B01G093100 chr2B 92.385 696 41 4 3050 3734 704456632 704455938 0.000000e+00 981.0
4 TraesCS2B01G093100 chr2B 89.940 666 60 4 977 1642 53658188 53658846 0.000000e+00 852.0
5 TraesCS2B01G093100 chr2B 90.504 337 32 0 1633 1969 53659325 53659661 2.650000e-121 446.0
6 TraesCS2B01G093100 chrUn 92.138 1132 66 12 856 1969 24900154 24901280 0.000000e+00 1576.0
7 TraesCS2B01G093100 chrUn 90.162 986 88 4 977 1961 24904564 24905541 0.000000e+00 1275.0
8 TraesCS2B01G093100 chrUn 88.600 1000 98 5 977 1966 24910787 24911780 0.000000e+00 1201.0
9 TraesCS2B01G093100 chrUn 89.776 939 81 6 2118 3046 24905570 24906503 0.000000e+00 1188.0
10 TraesCS2B01G093100 chrUn 92.143 700 53 2 2057 2756 24901271 24901968 0.000000e+00 987.0
11 TraesCS2B01G093100 chrUn 82.678 941 146 14 2096 3028 24911775 24912706 0.000000e+00 819.0
12 TraesCS2B01G093100 chrUn 89.712 243 14 7 300 532 24899496 24899737 2.180000e-77 300.0
13 TraesCS2B01G093100 chrUn 90.805 87 4 1 570 652 24899833 24899919 3.050000e-21 113.0
14 TraesCS2B01G093100 chrUn 96.078 51 1 1 1994 2044 4344370 4344321 8.600000e-12 82.4
15 TraesCS2B01G093100 chrUn 96.078 51 1 1 1994 2044 123973498 123973449 8.600000e-12 82.4
16 TraesCS2B01G093100 chrUn 96.078 51 1 1 1994 2044 131820082 131820131 8.600000e-12 82.4
17 TraesCS2B01G093100 chr2A 91.285 1136 73 11 849 1969 35634231 35635355 0.000000e+00 1526.0
18 TraesCS2B01G093100 chr2A 93.078 939 61 3 2118 3055 35650289 35651224 0.000000e+00 1371.0
19 TraesCS2B01G093100 chr2A 90.443 994 86 4 977 1969 35654246 35655231 0.000000e+00 1301.0
20 TraesCS2B01G093100 chr2A 88.609 992 87 14 2057 3046 35635346 35636313 0.000000e+00 1182.0
21 TraesCS2B01G093100 chr2A 92.645 639 47 0 2118 2756 35655252 35655890 0.000000e+00 920.0
22 TraesCS2B01G093100 chr2A 79.794 485 45 27 306 755 35633675 35634141 1.690000e-78 303.0
23 TraesCS2B01G093100 chr2A 86.239 109 10 1 132 240 35633057 35633160 3.050000e-21 113.0
24 TraesCS2B01G093100 chr4A 93.786 692 35 3 3050 3734 665991667 665990977 0.000000e+00 1033.0
25 TraesCS2B01G093100 chr7B 92.909 691 42 3 3050 3734 153173931 153174620 0.000000e+00 998.0
26 TraesCS2B01G093100 chr7B 92.486 692 44 3 3050 3734 420655063 420655753 0.000000e+00 983.0
27 TraesCS2B01G093100 chr7B 95.745 47 1 1 1996 2042 743364689 743364734 1.440000e-09 75.0
28 TraesCS2B01G093100 chr4B 92.319 703 41 7 3040 3734 268547284 268547981 0.000000e+00 987.0
29 TraesCS2B01G093100 chr4B 92.176 703 42 7 3040 3734 268543278 268543975 0.000000e+00 981.0
30 TraesCS2B01G093100 chr4B 95.833 48 1 1 1997 2044 387222106 387222060 4.000000e-10 76.8
31 TraesCS2B01G093100 chr4D 92.486 692 42 4 3050 3734 99929323 99930011 0.000000e+00 981.0
32 TraesCS2B01G093100 chr5B 92.253 697 44 4 3046 3734 711376985 711377679 0.000000e+00 979.0
33 TraesCS2B01G093100 chr5B 97.500 40 0 1 2000 2039 561699401 561699363 2.410000e-07 67.6
34 TraesCS2B01G093100 chr1B 92.352 693 45 4 3049 3734 622060068 622059377 0.000000e+00 979.0
35 TraesCS2B01G093100 chr6A 80.025 801 147 8 1101 1899 121871103 121871892 6.950000e-162 580.0
36 TraesCS2B01G093100 chr6D 78.791 877 160 13 1025 1900 101202226 101203077 1.950000e-157 566.0
37 TraesCS2B01G093100 chr3A 74.479 384 81 15 2255 2631 60472653 60473026 2.320000e-32 150.0
38 TraesCS2B01G093100 chr3A 77.619 210 47 0 2417 2626 48663525 48663316 1.090000e-25 128.0
39 TraesCS2B01G093100 chr3D 71.958 378 92 13 2264 2634 48251104 48250734 8.530000e-17 99.0
40 TraesCS2B01G093100 chr3B 96.078 51 1 1 1994 2044 518932862 518932813 8.600000e-12 82.4


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 TraesCS2B01G093100 chr2B 53582138 53585871 3733 False 6896.000000 6896 100.000000 1 3734 1 chr2B.!!$F1 3733
1 TraesCS2B01G093100 chr2B 53665682 53666669 987 False 1179.000000 1179 88.241000 977 1966 1 chr2B.!!$F2 989
2 TraesCS2B01G093100 chr2B 704455938 704456632 694 True 981.000000 981 92.385000 3050 3734 1 chr2B.!!$R1 684
3 TraesCS2B01G093100 chr2B 53658188 53660497 2309 False 841.000000 1225 91.400667 977 2934 3 chr2B.!!$F3 1957
4 TraesCS2B01G093100 chrUn 24910787 24912706 1919 False 1010.000000 1201 85.639000 977 3028 2 chrUn.!!$F3 2051
5 TraesCS2B01G093100 chrUn 24899496 24906503 7007 False 906.500000 1576 90.789333 300 3046 6 chrUn.!!$F2 2746
6 TraesCS2B01G093100 chr2A 35650289 35655890 5601 False 1197.333333 1371 92.055333 977 3055 3 chr2A.!!$F2 2078
7 TraesCS2B01G093100 chr2A 35633057 35636313 3256 False 781.000000 1526 86.481750 132 3046 4 chr2A.!!$F1 2914
8 TraesCS2B01G093100 chr4A 665990977 665991667 690 True 1033.000000 1033 93.786000 3050 3734 1 chr4A.!!$R1 684
9 TraesCS2B01G093100 chr7B 153173931 153174620 689 False 998.000000 998 92.909000 3050 3734 1 chr7B.!!$F1 684
10 TraesCS2B01G093100 chr7B 420655063 420655753 690 False 983.000000 983 92.486000 3050 3734 1 chr7B.!!$F2 684
11 TraesCS2B01G093100 chr4B 268543278 268547981 4703 False 984.000000 987 92.247500 3040 3734 2 chr4B.!!$F1 694
12 TraesCS2B01G093100 chr4D 99929323 99930011 688 False 981.000000 981 92.486000 3050 3734 1 chr4D.!!$F1 684
13 TraesCS2B01G093100 chr5B 711376985 711377679 694 False 979.000000 979 92.253000 3046 3734 1 chr5B.!!$F1 688
14 TraesCS2B01G093100 chr1B 622059377 622060068 691 True 979.000000 979 92.352000 3049 3734 1 chr1B.!!$R1 685
15 TraesCS2B01G093100 chr6A 121871103 121871892 789 False 580.000000 580 80.025000 1101 1899 1 chr6A.!!$F1 798
16 TraesCS2B01G093100 chr6D 101202226 101203077 851 False 566.000000 566 78.791000 1025 1900 1 chr6D.!!$F1 875

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
779 1346 0.028242 CTCATCCGAGAAGACGACGG 59.972 60.0 0.0 0.0 46.71 4.79 F
928 1538 0.109504 GCTAGAGCCGCCGATCTTAG 60.110 60.0 0.0 0.0 34.31 2.18 F
2016 5505 0.329261 TCTACTCCCTCCGTTTCCGA 59.671 55.0 0.0 0.0 35.63 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 5371 0.251916 TGATGGCTCCCACGGTAAAG 59.748 55.000 0.0 0.0 35.80 1.85 R
2217 5706 1.421382 TGTTACGTACTTCGGCTTGC 58.579 50.000 0.0 0.0 44.69 4.01 R
3036 10775 1.370064 GTAGTGGGTGAACGTGGCT 59.630 57.895 0.0 0.0 0.00 4.75 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
25 26 6.915544 TTCTCACATAAAGAGATGACATGC 57.084 37.500 0.00 0.00 41.42 4.06
26 27 6.231258 TCTCACATAAAGAGATGACATGCT 57.769 37.500 0.00 0.00 37.22 3.79
27 28 7.352079 TCTCACATAAAGAGATGACATGCTA 57.648 36.000 0.00 0.00 37.22 3.49
29 30 6.877236 TCACATAAAGAGATGACATGCTACA 58.123 36.000 0.00 0.00 0.00 2.74
30 31 6.758416 TCACATAAAGAGATGACATGCTACAC 59.242 38.462 0.00 0.00 0.00 2.90
31 32 6.760298 CACATAAAGAGATGACATGCTACACT 59.240 38.462 0.00 0.00 0.00 3.55
32 33 6.983307 ACATAAAGAGATGACATGCTACACTC 59.017 38.462 0.00 0.00 0.00 3.51
33 34 5.411831 AAAGAGATGACATGCTACACTCA 57.588 39.130 0.00 0.00 0.00 3.41
34 35 5.611128 AAGAGATGACATGCTACACTCAT 57.389 39.130 0.00 0.00 0.00 2.90
35 36 4.946445 AGAGATGACATGCTACACTCATG 58.054 43.478 0.00 1.85 44.99 3.07
37 38 2.028420 TGACATGCTACACTCATGCC 57.972 50.000 0.00 0.00 43.71 4.40
38 39 1.303309 GACATGCTACACTCATGCCC 58.697 55.000 0.00 0.00 43.71 5.36
40 41 0.107066 CATGCTACACTCATGCCCCA 60.107 55.000 0.00 0.00 35.48 4.96
41 42 0.107017 ATGCTACACTCATGCCCCAC 60.107 55.000 0.00 0.00 0.00 4.61
42 43 1.299648 GCTACACTCATGCCCCACA 59.700 57.895 0.00 0.00 0.00 4.17
43 44 0.322456 GCTACACTCATGCCCCACAA 60.322 55.000 0.00 0.00 0.00 3.33
45 46 2.726821 CTACACTCATGCCCCACAAAT 58.273 47.619 0.00 0.00 0.00 2.32
49 50 3.245229 ACACTCATGCCCCACAAATTCTA 60.245 43.478 0.00 0.00 0.00 2.10
50 51 3.956199 CACTCATGCCCCACAAATTCTAT 59.044 43.478 0.00 0.00 0.00 1.98
52 53 5.593909 CACTCATGCCCCACAAATTCTATTA 59.406 40.000 0.00 0.00 0.00 0.98
53 54 5.594317 ACTCATGCCCCACAAATTCTATTAC 59.406 40.000 0.00 0.00 0.00 1.89
54 55 5.765510 TCATGCCCCACAAATTCTATTACT 58.234 37.500 0.00 0.00 0.00 2.24
55 56 6.905736 TCATGCCCCACAAATTCTATTACTA 58.094 36.000 0.00 0.00 0.00 1.82
56 57 7.350382 TCATGCCCCACAAATTCTATTACTAA 58.650 34.615 0.00 0.00 0.00 2.24
57 58 7.836685 TCATGCCCCACAAATTCTATTACTAAA 59.163 33.333 0.00 0.00 0.00 1.85
59 60 6.378848 TGCCCCACAAATTCTATTACTAAACC 59.621 38.462 0.00 0.00 0.00 3.27
61 62 7.201794 GCCCCACAAATTCTATTACTAAACCTC 60.202 40.741 0.00 0.00 0.00 3.85
62 63 7.284716 CCCCACAAATTCTATTACTAAACCTCC 59.715 40.741 0.00 0.00 0.00 4.30
63 64 7.832187 CCCACAAATTCTATTACTAAACCTCCA 59.168 37.037 0.00 0.00 0.00 3.86
64 65 8.674607 CCACAAATTCTATTACTAAACCTCCAC 58.325 37.037 0.00 0.00 0.00 4.02
65 66 9.226606 CACAAATTCTATTACTAAACCTCCACA 57.773 33.333 0.00 0.00 0.00 4.17
66 67 9.975218 ACAAATTCTATTACTAAACCTCCACAT 57.025 29.630 0.00 0.00 0.00 3.21
68 69 8.451908 AATTCTATTACTAAACCTCCACATGC 57.548 34.615 0.00 0.00 0.00 4.06
72 73 3.788227 ACTAAACCTCCACATGCTGAA 57.212 42.857 0.00 0.00 0.00 3.02
74 75 2.664402 AAACCTCCACATGCTGAAGT 57.336 45.000 0.00 0.00 0.00 3.01
76 77 1.059098 ACCTCCACATGCTGAAGTGA 58.941 50.000 0.00 0.00 37.97 3.41
77 78 1.632409 ACCTCCACATGCTGAAGTGAT 59.368 47.619 0.00 0.00 37.97 3.06
78 79 2.014857 CCTCCACATGCTGAAGTGATG 58.985 52.381 0.00 0.00 37.97 3.07
80 81 1.170442 CCACATGCTGAAGTGATGCA 58.830 50.000 0.00 0.00 41.13 3.96
81 82 1.749063 CCACATGCTGAAGTGATGCAT 59.251 47.619 0.00 0.00 46.74 3.96
85 86 2.704464 TGCTGAAGTGATGCATAGCT 57.296 45.000 15.82 7.41 32.66 3.32
87 88 4.347360 TGCTGAAGTGATGCATAGCTAT 57.653 40.909 15.82 0.00 32.66 2.97
88 89 4.062991 TGCTGAAGTGATGCATAGCTATG 58.937 43.478 26.42 26.42 36.78 2.23
89 90 4.063689 GCTGAAGTGATGCATAGCTATGT 58.936 43.478 29.62 14.94 36.11 2.29
90 91 4.083961 GCTGAAGTGATGCATAGCTATGTG 60.084 45.833 29.62 12.23 36.11 3.21
92 93 4.101430 TGAAGTGATGCATAGCTATGTGGA 59.899 41.667 29.62 17.12 36.11 4.02
93 94 4.904895 AGTGATGCATAGCTATGTGGAT 57.095 40.909 29.62 20.34 36.11 3.41
96 97 6.169094 AGTGATGCATAGCTATGTGGATAAC 58.831 40.000 29.62 21.55 32.00 1.89
97 98 5.352569 GTGATGCATAGCTATGTGGATAACC 59.647 44.000 29.62 14.21 36.11 2.85
98 99 5.249163 TGATGCATAGCTATGTGGATAACCT 59.751 40.000 29.62 8.70 36.11 3.50
99 100 5.567037 TGCATAGCTATGTGGATAACCTT 57.433 39.130 29.62 0.00 36.11 3.50
100 101 5.308014 TGCATAGCTATGTGGATAACCTTG 58.692 41.667 29.62 6.67 36.11 3.61
101 102 5.163205 TGCATAGCTATGTGGATAACCTTGT 60.163 40.000 29.62 0.00 36.11 3.16
104 105 7.444183 GCATAGCTATGTGGATAACCTTGTAAA 59.556 37.037 29.62 0.00 36.11 2.01
106 107 7.865706 AGCTATGTGGATAACCTTGTAAAAG 57.134 36.000 0.00 0.00 37.04 2.27
153 154 0.877213 AAACACGTACACGGTCTGCC 60.877 55.000 6.72 0.00 44.95 4.85
156 157 1.080093 ACGTACACGGTCTGCCATG 60.080 57.895 6.72 0.00 44.95 3.66
157 158 2.452813 CGTACACGGTCTGCCATGC 61.453 63.158 0.00 0.00 29.60 4.06
158 159 2.106683 GTACACGGTCTGCCATGCC 61.107 63.158 0.00 0.00 29.60 4.40
211 212 6.183360 GGATCATTTCATGTTCATTGCAACAC 60.183 38.462 0.00 0.00 39.09 3.32
216 217 2.200792 TGTTCATTGCAACACCAACG 57.799 45.000 0.00 0.00 31.08 4.10
222 223 0.380378 TTGCAACACCAACGCTTCTC 59.620 50.000 0.00 0.00 0.00 2.87
231 232 0.941542 CAACGCTTCTCCCGTTTTCA 59.058 50.000 0.00 0.00 45.56 2.69
240 241 6.422701 CGCTTCTCCCGTTTTCATACATATAA 59.577 38.462 0.00 0.00 0.00 0.98
259 299 8.750298 ACATATAAGGTGTATGTATGTAGCCTC 58.250 37.037 0.00 0.00 40.11 4.70
260 300 4.585955 AAGGTGTATGTATGTAGCCTCG 57.414 45.455 0.00 0.00 0.00 4.63
262 302 2.316792 GTGTATGTATGTAGCCTCGCG 58.683 52.381 0.00 0.00 0.00 5.87
263 303 1.335597 TGTATGTATGTAGCCTCGCGC 60.336 52.381 0.00 0.00 37.98 6.86
264 304 0.955905 TATGTATGTAGCCTCGCGCA 59.044 50.000 8.75 0.00 41.38 6.09
297 767 7.707774 AAAAAGAAAAACGGGTGTATGAATG 57.292 32.000 0.00 0.00 0.00 2.67
298 768 6.399639 AAAGAAAAACGGGTGTATGAATGT 57.600 33.333 0.00 0.00 0.00 2.71
350 821 4.342092 ACAATTCCCTTGTCCAGTTTTCAG 59.658 41.667 0.00 0.00 44.99 3.02
356 827 4.159506 CCCTTGTCCAGTTTTCAGAAACAA 59.840 41.667 0.00 0.00 46.01 2.83
428 902 0.179004 TTTCACATGGCCCAGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
438 912 2.381589 GCCCAGTCGTTTTCTTTTTCG 58.618 47.619 0.00 0.00 0.00 3.46
482 964 0.312729 GAAAAACAATGCCCGGTCGT 59.687 50.000 0.00 0.00 0.00 4.34
538 1023 3.200593 GCATGCGTCCTGCTGGAG 61.201 66.667 13.36 8.45 44.16 3.86
553 1058 3.157252 GAGGAGCGGCCATGGAGA 61.157 66.667 18.40 0.00 40.02 3.71
568 1073 1.122019 GGAGATGGCCACGGTAGGAT 61.122 60.000 8.16 0.00 0.00 3.24
605 1145 1.716050 CAACGAGACACGATCACACAG 59.284 52.381 0.00 0.00 45.77 3.66
652 1201 4.456222 GGAATCTCGATCCGAATACTCTCA 59.544 45.833 0.00 0.00 34.74 3.27
654 1203 5.559427 ATCTCGATCCGAATACTCTCATG 57.441 43.478 0.00 0.00 34.74 3.07
655 1204 4.642429 TCTCGATCCGAATACTCTCATGA 58.358 43.478 0.00 0.00 34.74 3.07
656 1205 5.249420 TCTCGATCCGAATACTCTCATGAT 58.751 41.667 0.00 0.00 34.74 2.45
658 1207 5.003804 TCGATCCGAATACTCTCATGATGA 58.996 41.667 0.00 0.00 31.06 2.92
659 1208 5.123027 TCGATCCGAATACTCTCATGATGAG 59.877 44.000 16.15 16.15 38.21 2.90
660 1209 7.020461 TCGATCCGAATACTCTCATGATGAGA 61.020 42.308 22.59 22.59 41.14 3.27
681 1230 6.037500 TGAGAGCAATTTCGGTTCATGATTAG 59.962 38.462 0.00 0.00 0.00 1.73
691 1244 4.941263 CGGTTCATGATTAGTTCTCCCAAA 59.059 41.667 0.00 0.00 0.00 3.28
693 1246 6.238484 CGGTTCATGATTAGTTCTCCCAAATC 60.238 42.308 0.00 0.00 0.00 2.17
756 1309 1.153549 GTGCAGCGACCCTTCCTAG 60.154 63.158 0.00 0.00 0.00 3.02
761 1328 2.588620 CAGCGACCCTTCCTAGTATCT 58.411 52.381 0.00 0.00 0.00 1.98
764 1331 3.158676 GCGACCCTTCCTAGTATCTCAT 58.841 50.000 0.00 0.00 0.00 2.90
779 1346 0.028242 CTCATCCGAGAAGACGACGG 59.972 60.000 0.00 0.00 46.71 4.79
783 1350 2.561885 CGAGAAGACGACGGCACT 59.438 61.111 2.19 1.01 35.09 4.40
784 1351 1.081376 CGAGAAGACGACGGCACTT 60.081 57.895 2.19 3.62 35.09 3.16
785 1352 1.066114 CGAGAAGACGACGGCACTTC 61.066 60.000 14.80 14.80 39.87 3.01
790 1357 0.322277 AGACGACGGCACTTCCTAGA 60.322 55.000 2.19 0.00 0.00 2.43
791 1358 0.739561 GACGACGGCACTTCCTAGAT 59.260 55.000 0.00 0.00 0.00 1.98
793 1360 0.872021 CGACGGCACTTCCTAGATGC 60.872 60.000 0.00 0.00 38.68 3.91
794 1361 0.175760 GACGGCACTTCCTAGATGCA 59.824 55.000 0.00 0.00 41.27 3.96
795 1362 0.833287 ACGGCACTTCCTAGATGCAT 59.167 50.000 0.00 0.00 41.27 3.96
796 1363 1.202580 ACGGCACTTCCTAGATGCATC 60.203 52.381 19.37 19.37 41.27 3.91
829 1412 2.617250 TGCAAACATGCAATCGTCTC 57.383 45.000 0.21 0.00 42.40 3.36
830 1413 1.136000 TGCAAACATGCAATCGTCTCG 60.136 47.619 0.21 0.00 42.40 4.04
831 1414 1.128507 GCAAACATGCAATCGTCTCGA 59.871 47.619 0.00 0.00 36.00 4.04
865 1475 5.008712 TGGCGACATCACTTATACTAGTCAG 59.991 44.000 0.00 0.00 33.40 3.51
894 1504 1.003839 GATGACTTGGTCCGTGCCA 60.004 57.895 0.00 0.00 36.62 4.92
914 1524 4.579340 GCCACTGGCGTATATATAGCTAGA 59.421 45.833 23.35 0.00 41.15 2.43
928 1538 0.109504 GCTAGAGCCGCCGATCTTAG 60.110 60.000 0.00 0.00 34.31 2.18
935 1545 1.854227 CCGCCGATCTTAGAGGAAAC 58.146 55.000 0.00 0.00 0.00 2.78
936 1546 1.478137 CGCCGATCTTAGAGGAAACG 58.522 55.000 0.00 0.00 0.00 3.60
937 1547 1.854227 GCCGATCTTAGAGGAAACGG 58.146 55.000 0.00 0.00 39.85 4.44
938 1548 1.407979 GCCGATCTTAGAGGAAACGGA 59.592 52.381 0.00 0.00 39.54 4.69
942 1552 4.277672 CCGATCTTAGAGGAAACGGACATA 59.722 45.833 0.00 0.00 39.54 2.29
963 1580 0.691078 TGCAGTCTATCCCCACTCCC 60.691 60.000 0.00 0.00 0.00 4.30
1042 4029 0.889638 TCTCGTCTTGGCTCTCGTGT 60.890 55.000 0.00 0.00 0.00 4.49
1048 4035 1.831652 CTTGGCTCTCGTGTTCCCCT 61.832 60.000 0.00 0.00 0.00 4.79
1110 4097 2.281761 CAGAAGTTGCCGCCTGGT 60.282 61.111 0.00 0.00 37.67 4.00
1621 4611 1.353091 GGAAGAGTTCCTGGAGGTGT 58.647 55.000 0.00 0.00 46.57 4.16
1623 4613 2.551071 GGAAGAGTTCCTGGAGGTGTTG 60.551 54.545 0.00 0.00 46.57 3.33
1635 4625 2.730094 GTGTTGCAGCAAGGGGTG 59.270 61.111 8.49 0.00 45.24 4.61
1894 5378 2.048877 ACGACGTGCCCTTTACCG 60.049 61.111 0.00 0.00 0.00 4.02
1930 5414 4.712337 AGTGTCTATTAGTGGTAAGCTGCT 59.288 41.667 0.00 0.00 0.00 4.24
1957 5446 6.027749 CCGGCTAATTGTTTTCATTCACTAC 58.972 40.000 0.00 0.00 0.00 2.73
1977 5466 9.802039 TCACTACCTAATTAATTTGTGTTTCCT 57.198 29.630 5.91 0.00 0.00 3.36
2004 5493 9.476202 AAACAATTTTGCTAAAACATCTACTCC 57.524 29.630 0.00 0.00 32.37 3.85
2005 5494 7.602753 ACAATTTTGCTAAAACATCTACTCCC 58.397 34.615 0.00 0.00 32.37 4.30
2006 5495 7.451566 ACAATTTTGCTAAAACATCTACTCCCT 59.548 33.333 0.00 0.00 32.37 4.20
2007 5496 7.631717 ATTTTGCTAAAACATCTACTCCCTC 57.368 36.000 0.00 0.00 32.37 4.30
2008 5497 4.755266 TGCTAAAACATCTACTCCCTCC 57.245 45.455 0.00 0.00 0.00 4.30
2009 5498 3.132289 TGCTAAAACATCTACTCCCTCCG 59.868 47.826 0.00 0.00 0.00 4.63
2010 5499 3.132467 GCTAAAACATCTACTCCCTCCGT 59.868 47.826 0.00 0.00 0.00 4.69
2011 5500 4.382793 GCTAAAACATCTACTCCCTCCGTT 60.383 45.833 0.00 0.00 0.00 4.44
2012 5501 4.635699 AAAACATCTACTCCCTCCGTTT 57.364 40.909 0.00 0.00 0.00 3.60
2013 5502 3.889520 AACATCTACTCCCTCCGTTTC 57.110 47.619 0.00 0.00 0.00 2.78
2014 5503 2.108970 ACATCTACTCCCTCCGTTTCC 58.891 52.381 0.00 0.00 0.00 3.13
2015 5504 1.067212 CATCTACTCCCTCCGTTTCCG 59.933 57.143 0.00 0.00 0.00 4.30
2016 5505 0.329261 TCTACTCCCTCCGTTTCCGA 59.671 55.000 0.00 0.00 35.63 4.55
2017 5506 1.064166 TCTACTCCCTCCGTTTCCGAT 60.064 52.381 0.00 0.00 35.63 4.18
2018 5507 1.755380 CTACTCCCTCCGTTTCCGATT 59.245 52.381 0.00 0.00 35.63 3.34
2019 5508 0.981943 ACTCCCTCCGTTTCCGATTT 59.018 50.000 0.00 0.00 35.63 2.17
2020 5509 2.181975 ACTCCCTCCGTTTCCGATTTA 58.818 47.619 0.00 0.00 35.63 1.40
2021 5510 2.167900 ACTCCCTCCGTTTCCGATTTAG 59.832 50.000 0.00 0.00 35.63 1.85
2022 5511 2.167900 CTCCCTCCGTTTCCGATTTAGT 59.832 50.000 0.00 0.00 35.63 2.24
2023 5512 2.167075 TCCCTCCGTTTCCGATTTAGTC 59.833 50.000 0.00 0.00 35.63 2.59
2036 5525 5.109815 CGATTTAGTCGTCGTGGTTTTAG 57.890 43.478 0.00 0.00 45.19 1.85
2037 5526 4.618489 CGATTTAGTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 45.19 2.24
2038 5527 5.117592 CGATTTAGTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 45.19 2.24
2039 5528 5.888412 TTTAGTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
2040 5529 3.441496 AGTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2041 5530 3.784338 AGTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2042 5531 4.183101 AGTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2043 5532 4.812626 AGTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2044 5533 4.901881 GTCGTCGTGGTTTTAGTTCAAATG 59.098 41.667 0.00 0.00 0.00 2.32
2045 5534 4.571580 TCGTCGTGGTTTTAGTTCAAATGT 59.428 37.500 0.00 0.00 0.00 2.71
2046 5535 5.064962 TCGTCGTGGTTTTAGTTCAAATGTT 59.935 36.000 0.00 0.00 0.00 2.71
2047 5536 6.257411 TCGTCGTGGTTTTAGTTCAAATGTTA 59.743 34.615 0.00 0.00 0.00 2.41
2048 5537 7.041916 TCGTCGTGGTTTTAGTTCAAATGTTAT 60.042 33.333 0.00 0.00 0.00 1.89
2049 5538 7.267600 CGTCGTGGTTTTAGTTCAAATGTTATC 59.732 37.037 0.00 0.00 0.00 1.75
2050 5539 7.536281 GTCGTGGTTTTAGTTCAAATGTTATCC 59.464 37.037 0.00 0.00 0.00 2.59
2051 5540 7.228906 TCGTGGTTTTAGTTCAAATGTTATCCA 59.771 33.333 0.00 0.00 0.00 3.41
2052 5541 7.863375 CGTGGTTTTAGTTCAAATGTTATCCAA 59.137 33.333 0.00 0.00 0.00 3.53
2053 5542 9.535878 GTGGTTTTAGTTCAAATGTTATCCAAA 57.464 29.630 0.00 0.00 0.00 3.28
2142 5631 1.347707 CAGGACCTGTTTAGTGCTGGA 59.652 52.381 13.84 0.00 46.45 3.86
2217 5706 0.945265 CAACCACCATGGCAAAAGCG 60.945 55.000 13.04 0.00 42.67 4.68
2328 5817 3.670637 GACGCTCAGGCTGCATCCA 62.671 63.158 10.34 0.00 36.09 3.41
2340 5829 2.111878 CATCCATCGGTGCCCCTC 59.888 66.667 0.00 0.00 0.00 4.30
2470 5959 1.529309 GATGCCCCTGAGGAGTTCC 59.471 63.158 0.00 0.00 38.24 3.62
2635 10364 2.303022 CACTTTGACTGGGAGCTTCCTA 59.697 50.000 13.68 0.12 36.57 2.94
2825 10563 3.077229 TGCACACAAATTCCTTGAACG 57.923 42.857 0.00 0.00 38.50 3.95
2841 10579 4.148128 TGAACGTTTTGTTACCAGGGTA 57.852 40.909 0.46 0.00 42.09 3.69
2843 10581 4.515944 TGAACGTTTTGTTACCAGGGTATG 59.484 41.667 0.46 0.00 42.09 2.39
2845 10583 4.067192 ACGTTTTGTTACCAGGGTATGAC 58.933 43.478 0.00 0.00 0.00 3.06
2851 10589 0.688418 TACCAGGGTATGACGGTGGG 60.688 60.000 0.00 0.00 32.81 4.61
2955 10694 3.332187 TGTGGTTTCCCATCACCAATCTA 59.668 43.478 0.00 0.00 44.86 1.98
2962 10701 6.449635 TTCCCATCACCAATCTAATTTTCG 57.550 37.500 0.00 0.00 0.00 3.46
3022 10761 3.845860 TCTACTCCTTGTGTGAACTCCT 58.154 45.455 0.00 0.00 0.00 3.69
3027 10766 4.654262 ACTCCTTGTGTGAACTCCTTTCTA 59.346 41.667 0.00 0.00 34.97 2.10
3036 10775 7.147794 TGTGTGAACTCCTTTCTAGTACTTTCA 60.148 37.037 0.00 0.00 34.97 2.69
3046 10785 2.902705 AGTACTTTCAGCCACGTTCA 57.097 45.000 0.00 0.00 0.00 3.18
3047 10786 2.480845 AGTACTTTCAGCCACGTTCAC 58.519 47.619 0.00 0.00 0.00 3.18
3095 10834 2.303022 GACCTTCTGTCAATGACCCTGA 59.697 50.000 11.24 4.03 43.85 3.86
3144 10890 5.119931 CCAATTGGTCAAAATCTGTTCGA 57.880 39.130 16.90 0.00 0.00 3.71
3167 10913 2.100197 GGCTCCAAACCCTAAACCATC 58.900 52.381 0.00 0.00 0.00 3.51
3212 10958 6.652062 AGGTCGTAATTTCCTTACACGAAATT 59.348 34.615 11.86 11.86 46.48 1.82
3253 10999 2.237643 TGGTCCGCTGCCTTATTTCTAA 59.762 45.455 0.00 0.00 0.00 2.10
3359 11109 2.769893 TGTGTCATGTCCATGTGTCAG 58.230 47.619 7.13 0.00 39.72 3.51
3397 11147 6.985188 TGTGAAGCAACCTATATTTCTGTC 57.015 37.500 0.00 0.00 0.00 3.51
3401 11151 8.462016 GTGAAGCAACCTATATTTCTGTCATTT 58.538 33.333 0.00 0.00 0.00 2.32
3417 11167 8.977267 TCTGTCATTTCAAAAATTCCCAAAAT 57.023 26.923 0.00 0.00 0.00 1.82
3634 11385 0.958091 CCAAAACTCACGCCCATTGA 59.042 50.000 0.00 0.00 0.00 2.57
3671 15428 3.430895 CGTACCGCTAATCAAACACTTGT 59.569 43.478 0.00 0.00 33.94 3.16
3678 15435 5.622378 GCTAATCAAACACTTGTCTGCTAC 58.378 41.667 0.00 0.00 33.94 3.58
3695 15452 6.092670 GTCTGCTACTTCATGTTTGAGCATAA 59.907 38.462 12.97 5.24 37.22 1.90
3710 15467 3.220110 AGCATAATTCGGTCTCCTCGTA 58.780 45.455 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.982724 TGAGTGTAGCATGTCATCTCTTTATG 59.017 38.462 0.00 0.00 0.00 1.90
10 11 6.530019 TGAGTGTAGCATGTCATCTCTTTA 57.470 37.500 0.00 0.00 0.00 1.85
11 12 5.411831 TGAGTGTAGCATGTCATCTCTTT 57.588 39.130 0.00 0.00 0.00 2.52
12 13 5.358090 CATGAGTGTAGCATGTCATCTCTT 58.642 41.667 0.00 0.00 38.59 2.85
13 14 4.740034 GCATGAGTGTAGCATGTCATCTCT 60.740 45.833 0.00 0.00 43.79 3.10
14 15 3.493877 GCATGAGTGTAGCATGTCATCTC 59.506 47.826 0.00 0.00 43.79 2.75
15 16 3.464907 GCATGAGTGTAGCATGTCATCT 58.535 45.455 0.00 0.00 43.79 2.90
16 17 2.547211 GGCATGAGTGTAGCATGTCATC 59.453 50.000 0.00 0.00 45.23 2.92
18 19 2.028420 GGCATGAGTGTAGCATGTCA 57.972 50.000 0.00 0.00 45.23 3.58
19 20 1.303309 GGGCATGAGTGTAGCATGTC 58.697 55.000 0.00 0.00 45.18 3.06
20 21 0.107017 GGGGCATGAGTGTAGCATGT 60.107 55.000 0.00 0.00 43.79 3.21
22 23 0.107017 GTGGGGCATGAGTGTAGCAT 60.107 55.000 0.00 0.00 0.00 3.79
23 24 1.299648 GTGGGGCATGAGTGTAGCA 59.700 57.895 0.00 0.00 0.00 3.49
25 26 2.198827 TTTGTGGGGCATGAGTGTAG 57.801 50.000 0.00 0.00 0.00 2.74
26 27 2.897271 ATTTGTGGGGCATGAGTGTA 57.103 45.000 0.00 0.00 0.00 2.90
27 28 1.895131 GAATTTGTGGGGCATGAGTGT 59.105 47.619 0.00 0.00 0.00 3.55
29 30 2.610438 AGAATTTGTGGGGCATGAGT 57.390 45.000 0.00 0.00 0.00 3.41
30 31 5.829924 AGTAATAGAATTTGTGGGGCATGAG 59.170 40.000 0.00 0.00 0.00 2.90
31 32 5.765510 AGTAATAGAATTTGTGGGGCATGA 58.234 37.500 0.00 0.00 0.00 3.07
32 33 7.581213 TTAGTAATAGAATTTGTGGGGCATG 57.419 36.000 0.00 0.00 0.00 4.06
33 34 7.069455 GGTTTAGTAATAGAATTTGTGGGGCAT 59.931 37.037 0.00 0.00 0.00 4.40
34 35 6.378848 GGTTTAGTAATAGAATTTGTGGGGCA 59.621 38.462 0.00 0.00 0.00 5.36
35 36 6.605995 AGGTTTAGTAATAGAATTTGTGGGGC 59.394 38.462 0.00 0.00 0.00 5.80
37 38 7.832187 TGGAGGTTTAGTAATAGAATTTGTGGG 59.168 37.037 0.00 0.00 0.00 4.61
38 39 8.674607 GTGGAGGTTTAGTAATAGAATTTGTGG 58.325 37.037 0.00 0.00 0.00 4.17
40 41 9.975218 ATGTGGAGGTTTAGTAATAGAATTTGT 57.025 29.630 0.00 0.00 0.00 2.83
42 43 8.903820 GCATGTGGAGGTTTAGTAATAGAATTT 58.096 33.333 0.00 0.00 0.00 1.82
43 44 8.275040 AGCATGTGGAGGTTTAGTAATAGAATT 58.725 33.333 0.00 0.00 0.00 2.17
45 46 7.047891 CAGCATGTGGAGGTTTAGTAATAGAA 58.952 38.462 0.00 0.00 0.00 2.10
49 50 5.435686 TCAGCATGTGGAGGTTTAGTAAT 57.564 39.130 0.00 0.00 37.40 1.89
50 51 4.901197 TCAGCATGTGGAGGTTTAGTAA 57.099 40.909 0.00 0.00 37.40 2.24
52 53 3.073062 ACTTCAGCATGTGGAGGTTTAGT 59.927 43.478 8.03 0.00 37.40 2.24
53 54 3.438087 CACTTCAGCATGTGGAGGTTTAG 59.562 47.826 8.03 0.00 37.40 1.85
54 55 3.072330 TCACTTCAGCATGTGGAGGTTTA 59.928 43.478 8.03 0.00 37.40 2.01
55 56 2.158623 TCACTTCAGCATGTGGAGGTTT 60.159 45.455 8.03 0.00 37.40 3.27
56 57 1.421268 TCACTTCAGCATGTGGAGGTT 59.579 47.619 8.03 0.00 37.40 3.50
57 58 1.059098 TCACTTCAGCATGTGGAGGT 58.941 50.000 8.03 3.85 37.40 3.85
59 60 1.400846 GCATCACTTCAGCATGTGGAG 59.599 52.381 0.00 0.00 37.40 3.86
61 62 1.170442 TGCATCACTTCAGCATGTGG 58.830 50.000 0.00 0.00 37.40 4.17
66 67 2.704464 AGCTATGCATCACTTCAGCA 57.296 45.000 16.92 0.00 43.14 4.41
68 69 4.451435 CCACATAGCTATGCATCACTTCAG 59.549 45.833 29.60 5.78 37.19 3.02
72 73 4.904895 ATCCACATAGCTATGCATCACT 57.095 40.909 29.60 9.75 37.19 3.41
74 75 5.249163 AGGTTATCCACATAGCTATGCATCA 59.751 40.000 29.60 14.10 37.19 3.07
76 77 5.768980 AGGTTATCCACATAGCTATGCAT 57.231 39.130 29.60 21.15 37.19 3.96
77 78 5.163205 ACAAGGTTATCCACATAGCTATGCA 60.163 40.000 29.60 16.39 37.19 3.96
78 79 5.308825 ACAAGGTTATCCACATAGCTATGC 58.691 41.667 29.60 13.73 37.19 3.14
80 81 9.561069 CTTTTACAAGGTTATCCACATAGCTAT 57.439 33.333 0.00 0.00 35.89 2.97
81 82 7.990886 CCTTTTACAAGGTTATCCACATAGCTA 59.009 37.037 0.00 0.00 44.46 3.32
159 160 0.737219 ATTTCTCGCATGCCTTCTGC 59.263 50.000 13.15 0.00 41.77 4.26
160 161 3.003068 CCTTATTTCTCGCATGCCTTCTG 59.997 47.826 13.15 0.00 0.00 3.02
211 212 0.237498 GAAAACGGGAGAAGCGTTGG 59.763 55.000 0.00 0.00 0.00 3.77
216 217 7.095187 CCTTATATGTATGAAAACGGGAGAAGC 60.095 40.741 0.00 0.00 0.00 3.86
222 223 8.842358 ATACACCTTATATGTATGAAAACGGG 57.158 34.615 0.00 0.00 40.85 5.28
240 241 2.296471 GCGAGGCTACATACATACACCT 59.704 50.000 0.00 0.00 0.00 4.00
251 291 4.050955 TTTTTGCGCGAGGCTACA 57.949 50.000 12.10 0.00 44.05 2.74
274 744 6.811954 ACATTCATACACCCGTTTTTCTTTT 58.188 32.000 0.00 0.00 0.00 2.27
284 754 6.426633 TCAATAATGCTACATTCATACACCCG 59.573 38.462 0.00 0.00 0.00 5.28
285 755 7.228507 TGTCAATAATGCTACATTCATACACCC 59.771 37.037 0.00 0.00 0.00 4.61
286 756 8.153479 TGTCAATAATGCTACATTCATACACC 57.847 34.615 0.00 0.00 0.00 4.16
291 761 9.128404 AGACAATGTCAATAATGCTACATTCAT 57.872 29.630 16.38 0.00 39.80 2.57
292 762 8.510243 AGACAATGTCAATAATGCTACATTCA 57.490 30.769 16.38 0.00 39.80 2.57
293 763 9.793252 AAAGACAATGTCAATAATGCTACATTC 57.207 29.630 16.38 0.00 39.80 2.67
332 803 3.943671 TTCTGAAAACTGGACAAGGGA 57.056 42.857 0.00 0.00 0.00 4.20
343 814 6.468000 CCGACTGTTTACTTGTTTCTGAAAAC 59.532 38.462 4.09 0.00 44.18 2.43
350 821 4.870221 ACACCGACTGTTTACTTGTTTC 57.130 40.909 0.00 0.00 0.00 2.78
356 827 5.529800 AGCAATTTTACACCGACTGTTTACT 59.470 36.000 0.00 0.00 33.91 2.24
428 902 6.319399 GTCCTTTGACTGAACGAAAAAGAAA 58.681 36.000 0.00 0.00 38.53 2.52
538 1023 2.281345 CATCTCCATGGCCGCTCC 60.281 66.667 6.96 0.00 0.00 4.70
553 1058 3.117663 ACATTAAATCCTACCGTGGCCAT 60.118 43.478 9.72 0.00 0.00 4.40
568 1073 4.366586 TCGTTGTACGTCCACACATTAAA 58.633 39.130 0.00 0.00 43.14 1.52
605 1145 0.107703 TTCAGGTGATCGGTGATGGC 60.108 55.000 0.00 0.00 0.00 4.40
652 1201 4.264253 TGAACCGAAATTGCTCTCATCAT 58.736 39.130 0.00 0.00 0.00 2.45
654 1203 4.333649 TCATGAACCGAAATTGCTCTCATC 59.666 41.667 0.00 0.00 0.00 2.92
655 1204 4.264253 TCATGAACCGAAATTGCTCTCAT 58.736 39.130 0.00 0.00 0.00 2.90
656 1205 3.673902 TCATGAACCGAAATTGCTCTCA 58.326 40.909 0.00 0.00 0.00 3.27
658 1207 5.882557 ACTAATCATGAACCGAAATTGCTCT 59.117 36.000 0.00 0.00 0.00 4.09
659 1208 6.124088 ACTAATCATGAACCGAAATTGCTC 57.876 37.500 0.00 0.00 0.00 4.26
660 1209 6.375455 AGAACTAATCATGAACCGAAATTGCT 59.625 34.615 0.00 0.00 0.00 3.91
661 1210 6.555315 AGAACTAATCATGAACCGAAATTGC 58.445 36.000 0.00 0.00 0.00 3.56
663 1212 6.318900 GGGAGAACTAATCATGAACCGAAATT 59.681 38.462 0.00 0.00 0.00 1.82
664 1213 5.823045 GGGAGAACTAATCATGAACCGAAAT 59.177 40.000 0.00 0.00 0.00 2.17
665 1214 5.183228 GGGAGAACTAATCATGAACCGAAA 58.817 41.667 0.00 0.00 0.00 3.46
666 1215 4.224147 TGGGAGAACTAATCATGAACCGAA 59.776 41.667 0.00 0.00 0.00 4.30
667 1216 3.772572 TGGGAGAACTAATCATGAACCGA 59.227 43.478 0.00 0.00 0.00 4.69
668 1217 4.137116 TGGGAGAACTAATCATGAACCG 57.863 45.455 0.00 0.00 0.00 4.44
669 1218 6.830838 AGATTTGGGAGAACTAATCATGAACC 59.169 38.462 0.00 0.00 31.12 3.62
681 1230 3.188667 GGAAACGTCAGATTTGGGAGAAC 59.811 47.826 0.00 0.00 0.00 3.01
691 1244 2.404215 CGTCAACAGGAAACGTCAGAT 58.596 47.619 0.00 0.00 0.00 2.90
693 1246 0.859232 CCGTCAACAGGAAACGTCAG 59.141 55.000 0.00 0.00 34.71 3.51
761 1328 1.989966 GCCGTCGTCTTCTCGGATGA 61.990 60.000 7.01 0.00 46.05 2.92
764 1331 2.670592 TGCCGTCGTCTTCTCGGA 60.671 61.111 7.01 0.00 46.05 4.55
779 1346 1.872313 GCTGATGCATCTAGGAAGTGC 59.128 52.381 26.32 13.33 39.41 4.40
859 1469 1.374343 ATCGTTCGCTCGGCTGACTA 61.374 55.000 0.00 0.00 0.00 2.59
865 1475 1.805945 AAGTCATCGTTCGCTCGGC 60.806 57.895 0.00 0.00 0.00 5.54
894 1504 4.822896 GGCTCTAGCTATATATACGCCAGT 59.177 45.833 1.39 0.00 41.70 4.00
900 1510 4.063689 TCGGCGGCTCTAGCTATATATAC 58.936 47.826 7.21 0.00 41.70 1.47
908 1518 0.537600 TAAGATCGGCGGCTCTAGCT 60.538 55.000 7.21 0.00 41.70 3.32
910 1520 1.466950 CTCTAAGATCGGCGGCTCTAG 59.533 57.143 7.21 9.49 0.00 2.43
914 1524 0.755698 TTCCTCTAAGATCGGCGGCT 60.756 55.000 7.21 1.56 0.00 5.52
928 1538 2.271800 CTGCACTATGTCCGTTTCCTC 58.728 52.381 0.00 0.00 0.00 3.71
935 1545 2.029828 GGGATAGACTGCACTATGTCCG 60.030 54.545 1.78 0.00 33.85 4.79
936 1546 2.300437 GGGGATAGACTGCACTATGTCC 59.700 54.545 1.78 0.00 33.85 4.02
937 1547 2.965831 TGGGGATAGACTGCACTATGTC 59.034 50.000 1.78 0.00 33.85 3.06
938 1548 2.700897 GTGGGGATAGACTGCACTATGT 59.299 50.000 1.78 0.00 33.85 2.29
942 1552 1.490574 GAGTGGGGATAGACTGCACT 58.509 55.000 0.00 0.00 0.00 4.40
972 1595 3.368236 CGTGTTACTTTCTTGAGCTAGCC 59.632 47.826 12.13 3.49 0.00 3.93
1042 4029 2.834113 CTTGAGGAGTAGGAAGGGGAA 58.166 52.381 0.00 0.00 0.00 3.97
1048 4035 3.703556 CTGATGAGCTTGAGGAGTAGGAA 59.296 47.826 0.00 0.00 0.00 3.36
1515 4505 1.375908 GCTGATGTTGACGGGCTCA 60.376 57.895 0.00 0.00 0.00 4.26
1584 4574 2.031012 CGCCTGCTGAACCTGTCA 59.969 61.111 0.00 0.00 34.17 3.58
1621 4611 1.792757 ATCCTCACCCCTTGCTGCAA 61.793 55.000 15.16 15.16 0.00 4.08
1623 4613 1.452833 GATCCTCACCCCTTGCTGC 60.453 63.158 0.00 0.00 0.00 5.25
1816 5294 2.445654 CTCCTGCTCCCCCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
1887 5371 0.251916 TGATGGCTCCCACGGTAAAG 59.748 55.000 0.00 0.00 35.80 1.85
1894 5378 2.859992 GACACTTGATGGCTCCCAC 58.140 57.895 0.00 0.00 35.80 4.61
1930 5414 1.621992 TGAAAACAATTAGCCGGGCA 58.378 45.000 23.09 0.60 0.00 5.36
1978 5467 9.476202 GGAGTAGATGTTTTAGCAAAATTGTTT 57.524 29.630 0.00 0.00 32.22 2.83
1979 5468 8.088365 GGGAGTAGATGTTTTAGCAAAATTGTT 58.912 33.333 0.00 0.00 32.22 2.83
1980 5469 7.451566 AGGGAGTAGATGTTTTAGCAAAATTGT 59.548 33.333 0.00 0.00 32.22 2.71
1981 5470 7.830739 AGGGAGTAGATGTTTTAGCAAAATTG 58.169 34.615 0.00 0.00 32.22 2.32
1982 5471 7.122799 GGAGGGAGTAGATGTTTTAGCAAAATT 59.877 37.037 0.00 0.00 32.22 1.82
1983 5472 6.603599 GGAGGGAGTAGATGTTTTAGCAAAAT 59.396 38.462 0.00 0.00 32.22 1.82
1984 5473 5.944007 GGAGGGAGTAGATGTTTTAGCAAAA 59.056 40.000 0.00 0.00 0.00 2.44
1985 5474 5.497474 GGAGGGAGTAGATGTTTTAGCAAA 58.503 41.667 0.00 0.00 0.00 3.68
1986 5475 4.382685 CGGAGGGAGTAGATGTTTTAGCAA 60.383 45.833 0.00 0.00 0.00 3.91
1987 5476 3.132289 CGGAGGGAGTAGATGTTTTAGCA 59.868 47.826 0.00 0.00 0.00 3.49
1988 5477 3.132467 ACGGAGGGAGTAGATGTTTTAGC 59.868 47.826 0.00 0.00 0.00 3.09
1989 5478 5.340439 AACGGAGGGAGTAGATGTTTTAG 57.660 43.478 0.00 0.00 0.00 1.85
1990 5479 5.337813 GGAAACGGAGGGAGTAGATGTTTTA 60.338 44.000 0.00 0.00 0.00 1.52
1991 5480 4.565028 GGAAACGGAGGGAGTAGATGTTTT 60.565 45.833 0.00 0.00 0.00 2.43
1992 5481 3.055312 GGAAACGGAGGGAGTAGATGTTT 60.055 47.826 0.00 0.00 0.00 2.83
1993 5482 2.500504 GGAAACGGAGGGAGTAGATGTT 59.499 50.000 0.00 0.00 0.00 2.71
1994 5483 2.108970 GGAAACGGAGGGAGTAGATGT 58.891 52.381 0.00 0.00 0.00 3.06
1995 5484 2.892784 GGAAACGGAGGGAGTAGATG 57.107 55.000 0.00 0.00 0.00 2.90
2015 5504 6.144402 TGAACTAAAACCACGACGACTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
2016 5505 5.984926 TGAACTAAAACCACGACGACTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
2017 5506 5.347342 TGAACTAAAACCACGACGACTAAA 58.653 37.500 0.00 0.00 0.00 1.85
2018 5507 4.930963 TGAACTAAAACCACGACGACTAA 58.069 39.130 0.00 0.00 0.00 2.24
2019 5508 4.566545 TGAACTAAAACCACGACGACTA 57.433 40.909 0.00 0.00 0.00 2.59
2020 5509 3.441496 TGAACTAAAACCACGACGACT 57.559 42.857 0.00 0.00 0.00 4.18
2021 5510 4.519191 TTTGAACTAAAACCACGACGAC 57.481 40.909 0.00 0.00 0.00 4.34
2022 5511 4.571580 ACATTTGAACTAAAACCACGACGA 59.428 37.500 0.00 0.00 0.00 4.20
2023 5512 4.839796 ACATTTGAACTAAAACCACGACG 58.160 39.130 0.00 0.00 0.00 5.12
2024 5513 7.536281 GGATAACATTTGAACTAAAACCACGAC 59.464 37.037 0.00 0.00 0.00 4.34
2025 5514 7.228906 TGGATAACATTTGAACTAAAACCACGA 59.771 33.333 0.00 0.00 0.00 4.35
2026 5515 7.364200 TGGATAACATTTGAACTAAAACCACG 58.636 34.615 0.00 0.00 0.00 4.94
2027 5516 9.535878 TTTGGATAACATTTGAACTAAAACCAC 57.464 29.630 0.00 0.00 0.00 4.16
2103 5592 5.707764 GTCCTGCAGATTAAAAGAGAAGGTT 59.292 40.000 17.39 0.00 0.00 3.50
2142 5631 1.515088 CGTCGCTGATGTCTCGCTT 60.515 57.895 0.00 0.00 0.00 4.68
2217 5706 1.421382 TGTTACGTACTTCGGCTTGC 58.579 50.000 0.00 0.00 44.69 4.01
2360 5849 4.373116 GGACCTTGCACGCCTCGA 62.373 66.667 0.00 0.00 0.00 4.04
2460 5949 4.689549 TCCGGCCGGAACTCCTCA 62.690 66.667 43.93 19.95 42.05 3.86
2635 10364 2.606826 GTCCAACTCCCCTCCGGT 60.607 66.667 0.00 0.00 0.00 5.28
2699 10428 3.375299 CACAAGGACTTTAGCATGTAGGC 59.625 47.826 0.00 0.00 0.00 3.93
2841 10579 5.306937 TCATTACTATGATTCCCACCGTCAT 59.693 40.000 0.00 0.00 35.87 3.06
2843 10581 5.209818 TCATTACTATGATTCCCACCGTC 57.790 43.478 0.00 0.00 35.87 4.79
2962 10701 7.905031 GCTTGAGCTCATAATATCAAACAAC 57.095 36.000 19.04 0.00 38.21 3.32
2988 10727 7.391833 ACACAAGGAGTAGATCTTGGAAAATTC 59.608 37.037 0.00 0.00 43.20 2.17
3022 10761 4.595762 ACGTGGCTGAAAGTACTAGAAA 57.404 40.909 0.00 0.00 35.30 2.52
3027 10766 2.480845 GTGAACGTGGCTGAAAGTACT 58.519 47.619 0.00 0.00 35.30 2.73
3036 10775 1.370064 GTAGTGGGTGAACGTGGCT 59.630 57.895 0.00 0.00 0.00 4.75
3046 10785 6.779860 AGTTGACATATTTCTTGTAGTGGGT 58.220 36.000 0.00 0.00 0.00 4.51
3047 10786 8.041323 ACTAGTTGACATATTTCTTGTAGTGGG 58.959 37.037 0.00 0.00 0.00 4.61
3212 10958 3.549827 CCAGCGTTGTTTGCTTTATGACA 60.550 43.478 0.00 0.00 41.72 3.58
3359 11109 3.798889 GCTTCACAACCTAGGGCAAAAAC 60.799 47.826 14.81 0.00 0.00 2.43
3417 11167 8.750515 TGTGATCCAAGCAATTTATGAGAATA 57.249 30.769 0.00 0.00 0.00 1.75
3432 11182 8.847196 ACATATTTGATGAAGATGTGATCCAAG 58.153 33.333 0.00 0.00 45.70 3.61
3465 11215 3.876309 TTTGAACTAGGCAAGGAAGGT 57.124 42.857 0.00 0.00 0.00 3.50
3634 11385 1.459450 GTACGGGAAATGCACATGGT 58.541 50.000 0.00 0.00 0.00 3.55
3671 15428 4.006780 TGCTCAAACATGAAGTAGCAGA 57.993 40.909 0.00 0.00 35.11 4.26
3678 15435 5.883661 ACCGAATTATGCTCAAACATGAAG 58.116 37.500 0.00 0.00 0.00 3.02
3695 15452 4.208746 AGATTCTTACGAGGAGACCGAAT 58.791 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.