Multiple sequence alignment - TraesCS7B01G303200

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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 TraesCS7B01G303200 chr7B 100.000 3883 0 0 1 3883 540864654 540868536 0.000000e+00 7171.0
1 TraesCS7B01G303200 chr7B 93.494 1906 100 10 1042 2923 540801052 540802957 0.000000e+00 2811.0
2 TraesCS7B01G303200 chr7B 93.489 814 41 7 242 1047 693728831 693728022 0.000000e+00 1199.0
3 TraesCS7B01G303200 chr7B 89.764 127 9 2 3673 3795 603204105 603204231 4.020000e-35 159.0
4 TraesCS7B01G303200 chr7B 87.770 139 11 3 3663 3795 104049920 104050058 1.440000e-34 158.0
5 TraesCS7B01G303200 chr7D 95.988 2642 80 14 1042 3665 511687668 511690301 0.000000e+00 4268.0
6 TraesCS7B01G303200 chr7D 93.404 1895 112 6 1042 2923 511662146 511664040 0.000000e+00 2795.0
7 TraesCS7B01G303200 chr7D 93.583 187 8 2 3663 3849 511690352 511690534 3.820000e-70 276.0
8 TraesCS7B01G303200 chr7D 88.489 139 10 3 3663 3795 531581398 531581536 3.100000e-36 163.0
9 TraesCS7B01G303200 chr7A 90.554 2255 126 36 1045 3282 584203981 584201797 0.000000e+00 2904.0
10 TraesCS7B01G303200 chr7A 91.667 1992 123 22 1042 3000 584108246 584110227 0.000000e+00 2719.0
11 TraesCS7B01G303200 chr2B 95.388 824 29 7 237 1053 750057079 750056258 0.000000e+00 1303.0
12 TraesCS7B01G303200 chr2B 94.704 812 35 5 241 1047 233588130 233587322 0.000000e+00 1254.0
13 TraesCS7B01G303200 chr2B 94.595 814 34 8 241 1047 750051896 750052706 0.000000e+00 1251.0
14 TraesCS7B01G303200 chr2B 89.552 134 8 4 3668 3795 134692688 134692555 8.630000e-37 165.0
15 TraesCS7B01G303200 chr3B 95.449 813 30 6 240 1047 461613613 461614423 0.000000e+00 1290.0
16 TraesCS7B01G303200 chr3B 94.834 813 34 6 241 1047 689004377 689003567 0.000000e+00 1262.0
17 TraesCS7B01G303200 chr5B 95.226 817 29 6 240 1047 664880868 664881683 0.000000e+00 1284.0
18 TraesCS7B01G303200 chr5B 93.505 816 42 7 241 1047 75208210 75209023 0.000000e+00 1203.0
19 TraesCS7B01G303200 chr5B 74.413 383 45 26 1855 2223 115647264 115646921 8.820000e-22 115.0
20 TraesCS7B01G303200 chrUn 92.953 823 48 7 234 1047 30343702 30344523 0.000000e+00 1190.0
21 TraesCS7B01G303200 chr1D 79.743 1012 140 28 1787 2785 356830200 356829241 0.000000e+00 673.0
22 TraesCS7B01G303200 chr3A 83.577 548 83 4 3123 3665 357114804 357115349 1.240000e-139 507.0
23 TraesCS7B01G303200 chr4B 82.192 584 90 11 3092 3665 572152805 572153384 1.250000e-134 490.0
24 TraesCS7B01G303200 chr3D 83.240 537 87 2 3128 3662 140432221 140432756 1.250000e-134 490.0
25 TraesCS7B01G303200 chr3D 80.218 642 103 16 3030 3665 273479366 273479989 9.830000e-126 460.0
26 TraesCS7B01G303200 chr3D 87.050 139 12 2 3663 3795 313105408 313105546 6.720000e-33 152.0
27 TraesCS7B01G303200 chr3D 90.698 43 3 1 3796 3837 435221901 435221859 5.420000e-04 56.5
28 TraesCS7B01G303200 chr2A 83.730 504 74 7 3165 3664 119077589 119077090 1.630000e-128 470.0
29 TraesCS7B01G303200 chr2A 83.412 211 29 3 2576 2785 175417293 175417088 1.420000e-44 191.0
30 TraesCS7B01G303200 chr2A 96.226 53 2 0 3796 3848 86265129 86265077 1.920000e-13 87.9
31 TraesCS7B01G303200 chr2A 92.593 54 4 0 3796 3849 231890511 231890564 1.160000e-10 78.7
32 TraesCS7B01G303200 chr4A 82.332 549 78 12 3128 3665 629464014 629464554 3.540000e-125 459.0
33 TraesCS7B01G303200 chr5A 81.455 550 84 12 3128 3665 42252633 42252090 5.960000e-118 435.0
34 TraesCS7B01G303200 chr4D 81.495 535 90 6 3128 3660 458046551 458047078 7.710000e-117 431.0
35 TraesCS7B01G303200 chr4D 86.957 138 13 1 3663 3795 397065659 397065522 2.420000e-32 150.0
36 TraesCS7B01G303200 chr1A 75.024 1053 174 42 1742 2786 516234772 516235743 4.670000e-109 405.0
37 TraesCS7B01G303200 chr1A 87.050 139 12 2 3663 3795 486895163 486895025 6.720000e-33 152.0
38 TraesCS7B01G303200 chr2D 87.770 139 11 2 3663 3795 31751695 31751833 1.440000e-34 158.0
39 TraesCS7B01G303200 chr2D 94.444 54 3 0 3796 3849 85733038 85732985 2.490000e-12 84.2


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 TraesCS7B01G303200 chr7B 540864654 540868536 3882 False 7171 7171 100.0000 1 3883 1 chr7B.!!$F3 3882
1 TraesCS7B01G303200 chr7B 540801052 540802957 1905 False 2811 2811 93.4940 1042 2923 1 chr7B.!!$F2 1881
2 TraesCS7B01G303200 chr7B 693728022 693728831 809 True 1199 1199 93.4890 242 1047 1 chr7B.!!$R1 805
3 TraesCS7B01G303200 chr7D 511662146 511664040 1894 False 2795 2795 93.4040 1042 2923 1 chr7D.!!$F1 1881
4 TraesCS7B01G303200 chr7D 511687668 511690534 2866 False 2272 4268 94.7855 1042 3849 2 chr7D.!!$F3 2807
5 TraesCS7B01G303200 chr7A 584201797 584203981 2184 True 2904 2904 90.5540 1045 3282 1 chr7A.!!$R1 2237
6 TraesCS7B01G303200 chr7A 584108246 584110227 1981 False 2719 2719 91.6670 1042 3000 1 chr7A.!!$F1 1958
7 TraesCS7B01G303200 chr2B 750056258 750057079 821 True 1303 1303 95.3880 237 1053 1 chr2B.!!$R3 816
8 TraesCS7B01G303200 chr2B 233587322 233588130 808 True 1254 1254 94.7040 241 1047 1 chr2B.!!$R2 806
9 TraesCS7B01G303200 chr2B 750051896 750052706 810 False 1251 1251 94.5950 241 1047 1 chr2B.!!$F1 806
10 TraesCS7B01G303200 chr3B 461613613 461614423 810 False 1290 1290 95.4490 240 1047 1 chr3B.!!$F1 807
11 TraesCS7B01G303200 chr3B 689003567 689004377 810 True 1262 1262 94.8340 241 1047 1 chr3B.!!$R1 806
12 TraesCS7B01G303200 chr5B 664880868 664881683 815 False 1284 1284 95.2260 240 1047 1 chr5B.!!$F2 807
13 TraesCS7B01G303200 chr5B 75208210 75209023 813 False 1203 1203 93.5050 241 1047 1 chr5B.!!$F1 806
14 TraesCS7B01G303200 chrUn 30343702 30344523 821 False 1190 1190 92.9530 234 1047 1 chrUn.!!$F1 813
15 TraesCS7B01G303200 chr1D 356829241 356830200 959 True 673 673 79.7430 1787 2785 1 chr1D.!!$R1 998
16 TraesCS7B01G303200 chr3A 357114804 357115349 545 False 507 507 83.5770 3123 3665 1 chr3A.!!$F1 542
17 TraesCS7B01G303200 chr4B 572152805 572153384 579 False 490 490 82.1920 3092 3665 1 chr4B.!!$F1 573
18 TraesCS7B01G303200 chr3D 140432221 140432756 535 False 490 490 83.2400 3128 3662 1 chr3D.!!$F1 534
19 TraesCS7B01G303200 chr3D 273479366 273479989 623 False 460 460 80.2180 3030 3665 1 chr3D.!!$F2 635
20 TraesCS7B01G303200 chr4A 629464014 629464554 540 False 459 459 82.3320 3128 3665 1 chr4A.!!$F1 537
21 TraesCS7B01G303200 chr5A 42252090 42252633 543 True 435 435 81.4550 3128 3665 1 chr5A.!!$R1 537
22 TraesCS7B01G303200 chr4D 458046551 458047078 527 False 431 431 81.4950 3128 3660 1 chr4D.!!$F1 532
23 TraesCS7B01G303200 chr1A 516234772 516235743 971 False 405 405 75.0240 1742 2786 1 chr1A.!!$F1 1044

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
153 154 0.037605 AAATCACGTCCAGACCGTCC 60.038 55.0 0.0 0.0 36.17 4.79 F
226 227 0.103208 ACGGTCGATCTTGGAGATGC 59.897 55.0 0.0 0.0 34.53 3.91 F
228 229 0.250081 GGTCGATCTTGGAGATGCCC 60.250 60.0 0.0 0.0 34.53 5.36 F
231 232 0.467384 CGATCTTGGAGATGCCCTGT 59.533 55.0 0.0 0.0 34.53 4.00 F
1240 1267 0.806102 CATCCTGTACGCCTTGACCG 60.806 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1035 1.772063 AAAGAAGACGCACCACACGC 61.772 55.000 0.00 0.0 0.0 5.34 R
1263 1290 2.040884 AATGGGCTAGGCGGGAGA 60.041 61.111 10.58 0.0 0.0 3.71 R
1825 1852 2.353607 CGCGCCGATGTAGTCCTC 60.354 66.667 0.00 0.0 0.0 3.71 R
2797 2860 3.762247 CCCCTAAACCCGACGCGA 61.762 66.667 15.93 0.0 0.0 5.87 R
3675 3879 0.382515 CGGAGAGGTTCGAGGACATC 59.617 60.000 0.00 0.0 0.0 3.06 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
20 21 3.362870 AAGGAAGAGAAGGGCAGAATG 57.637 47.619 0.00 0.00 40.87 2.67
21 22 1.563410 AGGAAGAGAAGGGCAGAATGG 59.437 52.381 0.00 0.00 35.86 3.16
22 23 1.561542 GGAAGAGAAGGGCAGAATGGA 59.438 52.381 0.00 0.00 35.86 3.41
23 24 2.025887 GGAAGAGAAGGGCAGAATGGAA 60.026 50.000 0.00 0.00 35.86 3.53
24 25 3.277715 GAAGAGAAGGGCAGAATGGAAG 58.722 50.000 0.00 0.00 35.86 3.46
25 26 2.555664 AGAGAAGGGCAGAATGGAAGA 58.444 47.619 0.00 0.00 35.86 2.87
26 27 2.915604 AGAGAAGGGCAGAATGGAAGAA 59.084 45.455 0.00 0.00 35.86 2.52
27 28 3.331889 AGAGAAGGGCAGAATGGAAGAAA 59.668 43.478 0.00 0.00 35.86 2.52
28 29 4.082125 GAGAAGGGCAGAATGGAAGAAAA 58.918 43.478 0.00 0.00 35.86 2.29
29 30 4.681484 AGAAGGGCAGAATGGAAGAAAAT 58.319 39.130 0.00 0.00 35.86 1.82
30 31 5.831103 AGAAGGGCAGAATGGAAGAAAATA 58.169 37.500 0.00 0.00 35.86 1.40
31 32 5.890419 AGAAGGGCAGAATGGAAGAAAATAG 59.110 40.000 0.00 0.00 35.86 1.73
32 33 4.540715 AGGGCAGAATGGAAGAAAATAGG 58.459 43.478 0.00 0.00 35.86 2.57
33 34 4.230502 AGGGCAGAATGGAAGAAAATAGGA 59.769 41.667 0.00 0.00 35.86 2.94
34 35 4.339530 GGGCAGAATGGAAGAAAATAGGAC 59.660 45.833 0.00 0.00 35.86 3.85
35 36 4.339530 GGCAGAATGGAAGAAAATAGGACC 59.660 45.833 0.00 0.00 35.86 4.46
36 37 4.949856 GCAGAATGGAAGAAAATAGGACCA 59.050 41.667 0.00 0.00 35.86 4.02
37 38 5.067023 GCAGAATGGAAGAAAATAGGACCAG 59.933 44.000 0.00 0.00 35.86 4.00
38 39 5.591877 CAGAATGGAAGAAAATAGGACCAGG 59.408 44.000 0.00 0.00 0.00 4.45
39 40 5.492524 AGAATGGAAGAAAATAGGACCAGGA 59.507 40.000 0.00 0.00 0.00 3.86
40 41 4.844349 TGGAAGAAAATAGGACCAGGAG 57.156 45.455 0.00 0.00 0.00 3.69
41 42 3.523564 TGGAAGAAAATAGGACCAGGAGG 59.476 47.826 0.00 0.00 42.21 4.30
42 43 3.117851 GGAAGAAAATAGGACCAGGAGGG 60.118 52.174 0.00 0.00 44.81 4.30
43 44 2.493091 AGAAAATAGGACCAGGAGGGG 58.507 52.381 0.00 0.00 42.91 4.79
49 50 2.190578 GACCAGGAGGGGCGATTG 59.809 66.667 0.00 0.00 42.91 2.67
50 51 3.406595 GACCAGGAGGGGCGATTGG 62.407 68.421 0.00 0.00 42.91 3.16
51 52 4.195334 CCAGGAGGGGCGATTGGG 62.195 72.222 0.00 0.00 0.00 4.12
52 53 3.411517 CAGGAGGGGCGATTGGGT 61.412 66.667 0.00 0.00 0.00 4.51
53 54 3.411517 AGGAGGGGCGATTGGGTG 61.412 66.667 0.00 0.00 0.00 4.61
54 55 4.506255 GGAGGGGCGATTGGGTGG 62.506 72.222 0.00 0.00 0.00 4.61
55 56 3.407967 GAGGGGCGATTGGGTGGA 61.408 66.667 0.00 0.00 0.00 4.02
56 57 3.699134 GAGGGGCGATTGGGTGGAC 62.699 68.421 0.00 0.00 0.00 4.02
57 58 4.815108 GGGGCGATTGGGTGGACC 62.815 72.222 0.00 0.00 40.81 4.46
61 62 4.483243 CGATTGGGTGGACCGGGG 62.483 72.222 6.32 0.00 44.64 5.73
62 63 4.123545 GATTGGGTGGACCGGGGG 62.124 72.222 6.32 0.00 44.64 5.40
74 75 3.633116 CGGGGGTGTCGGAAACCT 61.633 66.667 16.75 0.00 37.85 3.50
75 76 2.285024 CGGGGGTGTCGGAAACCTA 61.285 63.158 16.75 0.00 37.85 3.08
76 77 1.297689 GGGGGTGTCGGAAACCTAC 59.702 63.158 16.75 10.08 37.85 3.18
77 78 1.482748 GGGGGTGTCGGAAACCTACA 61.483 60.000 16.75 0.00 37.85 2.74
78 79 0.616891 GGGGTGTCGGAAACCTACAT 59.383 55.000 16.75 0.00 37.85 2.29
79 80 1.003928 GGGGTGTCGGAAACCTACATT 59.996 52.381 16.75 0.00 37.85 2.71
80 81 2.553685 GGGGTGTCGGAAACCTACATTT 60.554 50.000 16.75 0.00 37.85 2.32
81 82 2.745821 GGGTGTCGGAAACCTACATTTC 59.254 50.000 16.75 0.00 37.85 2.17
82 83 2.414138 GGTGTCGGAAACCTACATTTCG 59.586 50.000 10.23 0.00 39.13 3.46
83 84 2.414138 GTGTCGGAAACCTACATTTCGG 59.586 50.000 0.00 0.00 39.13 4.30
84 85 2.004733 GTCGGAAACCTACATTTCGGG 58.995 52.381 6.12 0.00 39.13 5.14
85 86 1.624813 TCGGAAACCTACATTTCGGGT 59.375 47.619 6.12 0.00 39.13 5.28
86 87 1.735571 CGGAAACCTACATTTCGGGTG 59.264 52.381 0.00 0.00 39.13 4.61
87 88 2.786777 GGAAACCTACATTTCGGGTGT 58.213 47.619 0.00 0.00 39.13 4.16
88 89 2.745821 GGAAACCTACATTTCGGGTGTC 59.254 50.000 0.00 0.00 39.13 3.67
89 90 2.484742 AACCTACATTTCGGGTGTCC 57.515 50.000 0.00 0.00 33.20 4.02
90 91 1.354101 ACCTACATTTCGGGTGTCCA 58.646 50.000 0.00 0.00 31.48 4.02
91 92 1.278127 ACCTACATTTCGGGTGTCCAG 59.722 52.381 0.00 0.00 31.48 3.86
92 93 1.553248 CCTACATTTCGGGTGTCCAGA 59.447 52.381 0.00 0.00 0.00 3.86
93 94 2.618053 CTACATTTCGGGTGTCCAGAC 58.382 52.381 0.00 0.00 0.00 3.51
94 95 1.056660 ACATTTCGGGTGTCCAGACT 58.943 50.000 0.00 0.00 0.00 3.24
95 96 1.002087 ACATTTCGGGTGTCCAGACTC 59.998 52.381 0.00 0.00 0.00 3.36
96 97 0.613777 ATTTCGGGTGTCCAGACTCC 59.386 55.000 9.87 9.87 42.56 3.85
100 101 4.083862 GGTGTCCAGACTCCCGCC 62.084 72.222 7.52 0.00 38.63 6.13
101 102 3.311110 GTGTCCAGACTCCCGCCA 61.311 66.667 0.00 0.00 0.00 5.69
102 103 2.525629 TGTCCAGACTCCCGCCAA 60.526 61.111 0.00 0.00 0.00 4.52
103 104 2.047179 GTCCAGACTCCCGCCAAC 60.047 66.667 0.00 0.00 0.00 3.77
104 105 3.319198 TCCAGACTCCCGCCAACC 61.319 66.667 0.00 0.00 0.00 3.77
105 106 3.322466 CCAGACTCCCGCCAACCT 61.322 66.667 0.00 0.00 0.00 3.50
106 107 2.266055 CAGACTCCCGCCAACCTC 59.734 66.667 0.00 0.00 0.00 3.85
107 108 3.382832 AGACTCCCGCCAACCTCG 61.383 66.667 0.00 0.00 0.00 4.63
115 116 2.597510 GCCAACCTCGCCCACTTT 60.598 61.111 0.00 0.00 0.00 2.66
116 117 2.919494 GCCAACCTCGCCCACTTTG 61.919 63.158 0.00 0.00 0.00 2.77
117 118 1.528309 CCAACCTCGCCCACTTTGT 60.528 57.895 0.00 0.00 0.00 2.83
118 119 1.106944 CCAACCTCGCCCACTTTGTT 61.107 55.000 0.00 0.00 0.00 2.83
119 120 0.744281 CAACCTCGCCCACTTTGTTT 59.256 50.000 0.00 0.00 0.00 2.83
120 121 1.029681 AACCTCGCCCACTTTGTTTC 58.970 50.000 0.00 0.00 0.00 2.78
121 122 0.822121 ACCTCGCCCACTTTGTTTCC 60.822 55.000 0.00 0.00 0.00 3.13
122 123 0.821711 CCTCGCCCACTTTGTTTCCA 60.822 55.000 0.00 0.00 0.00 3.53
123 124 1.028905 CTCGCCCACTTTGTTTCCAA 58.971 50.000 0.00 0.00 0.00 3.53
124 125 1.613437 CTCGCCCACTTTGTTTCCAAT 59.387 47.619 0.00 0.00 0.00 3.16
125 126 2.035632 TCGCCCACTTTGTTTCCAATT 58.964 42.857 0.00 0.00 0.00 2.32
126 127 2.432510 TCGCCCACTTTGTTTCCAATTT 59.567 40.909 0.00 0.00 0.00 1.82
127 128 3.637229 TCGCCCACTTTGTTTCCAATTTA 59.363 39.130 0.00 0.00 0.00 1.40
128 129 4.099573 TCGCCCACTTTGTTTCCAATTTAA 59.900 37.500 0.00 0.00 0.00 1.52
129 130 4.447389 CGCCCACTTTGTTTCCAATTTAAG 59.553 41.667 0.00 0.00 0.00 1.85
130 131 4.754618 GCCCACTTTGTTTCCAATTTAAGG 59.245 41.667 0.00 0.00 0.00 2.69
131 132 5.304778 CCCACTTTGTTTCCAATTTAAGGG 58.695 41.667 0.00 0.00 0.00 3.95
132 133 5.071115 CCCACTTTGTTTCCAATTTAAGGGA 59.929 40.000 0.00 0.00 30.39 4.20
133 134 6.223120 CCACTTTGTTTCCAATTTAAGGGAG 58.777 40.000 0.00 0.00 34.02 4.30
134 135 6.041523 CCACTTTGTTTCCAATTTAAGGGAGA 59.958 38.462 0.00 0.00 34.02 3.71
135 136 7.418483 CCACTTTGTTTCCAATTTAAGGGAGAA 60.418 37.037 0.00 0.00 34.02 2.87
136 137 7.984617 CACTTTGTTTCCAATTTAAGGGAGAAA 59.015 33.333 0.00 0.00 34.02 2.52
137 138 8.713971 ACTTTGTTTCCAATTTAAGGGAGAAAT 58.286 29.630 0.00 0.00 34.02 2.17
138 139 9.208022 CTTTGTTTCCAATTTAAGGGAGAAATC 57.792 33.333 0.00 0.00 34.02 2.17
139 140 7.847711 TGTTTCCAATTTAAGGGAGAAATCA 57.152 32.000 0.00 0.00 34.02 2.57
140 141 7.666623 TGTTTCCAATTTAAGGGAGAAATCAC 58.333 34.615 0.00 0.00 34.02 3.06
141 142 6.509418 TTCCAATTTAAGGGAGAAATCACG 57.491 37.500 0.00 0.00 34.02 4.35
142 143 5.566469 TCCAATTTAAGGGAGAAATCACGT 58.434 37.500 0.00 0.00 0.00 4.49
143 144 5.646360 TCCAATTTAAGGGAGAAATCACGTC 59.354 40.000 0.00 0.00 0.00 4.34
144 145 5.163652 CCAATTTAAGGGAGAAATCACGTCC 60.164 44.000 0.00 0.00 0.00 4.79
145 146 4.627284 TTTAAGGGAGAAATCACGTCCA 57.373 40.909 0.00 0.00 31.31 4.02
146 147 2.770164 AAGGGAGAAATCACGTCCAG 57.230 50.000 0.00 0.00 31.31 3.86
147 148 1.938585 AGGGAGAAATCACGTCCAGA 58.061 50.000 0.00 0.00 31.31 3.86
148 149 1.550976 AGGGAGAAATCACGTCCAGAC 59.449 52.381 0.00 0.00 31.31 3.51
149 150 1.405661 GGGAGAAATCACGTCCAGACC 60.406 57.143 0.00 0.00 31.31 3.85
150 151 1.630148 GAGAAATCACGTCCAGACCG 58.370 55.000 0.00 0.00 0.00 4.79
151 152 0.966920 AGAAATCACGTCCAGACCGT 59.033 50.000 0.00 0.00 39.52 4.83
152 153 1.067776 AGAAATCACGTCCAGACCGTC 60.068 52.381 0.00 0.00 36.17 4.79
153 154 0.037605 AAATCACGTCCAGACCGTCC 60.038 55.000 0.00 0.00 36.17 4.79
154 155 1.885163 AATCACGTCCAGACCGTCCC 61.885 60.000 0.00 0.00 36.17 4.46
155 156 4.415332 CACGTCCAGACCGTCCCG 62.415 72.222 0.00 0.00 36.17 5.14
188 189 5.914085 GCTAAGCGATACAGATCAATGTT 57.086 39.130 0.00 0.00 34.56 2.71
189 190 5.674008 GCTAAGCGATACAGATCAATGTTG 58.326 41.667 0.00 0.00 34.56 3.33
190 191 5.333645 GCTAAGCGATACAGATCAATGTTGG 60.334 44.000 0.00 0.00 34.56 3.77
191 192 4.406648 AGCGATACAGATCAATGTTGGA 57.593 40.909 0.00 0.00 34.56 3.53
192 193 4.965814 AGCGATACAGATCAATGTTGGAT 58.034 39.130 0.00 0.00 34.56 3.41
193 194 4.753610 AGCGATACAGATCAATGTTGGATG 59.246 41.667 0.00 0.00 34.56 3.51
194 195 4.083643 GCGATACAGATCAATGTTGGATGG 60.084 45.833 0.00 0.00 34.56 3.51
195 196 4.083643 CGATACAGATCAATGTTGGATGGC 60.084 45.833 0.00 0.00 34.56 4.40
196 197 2.381911 ACAGATCAATGTTGGATGGCC 58.618 47.619 0.00 0.00 0.00 5.36
197 198 2.024655 ACAGATCAATGTTGGATGGCCT 60.025 45.455 3.32 0.00 34.31 5.19
198 199 2.621998 CAGATCAATGTTGGATGGCCTC 59.378 50.000 3.32 0.00 34.31 4.70
199 200 1.959282 GATCAATGTTGGATGGCCTCC 59.041 52.381 3.32 9.38 45.19 4.30
206 207 2.355115 GGATGGCCTCCGTGGTTT 59.645 61.111 3.32 0.00 38.35 3.27
207 208 1.605453 GGATGGCCTCCGTGGTTTA 59.395 57.895 3.32 0.00 38.35 2.01
208 209 0.746923 GGATGGCCTCCGTGGTTTAC 60.747 60.000 3.32 0.00 38.35 2.01
220 221 1.997606 GTGGTTTACGGTCGATCTTGG 59.002 52.381 0.00 0.00 0.00 3.61
221 222 1.894466 TGGTTTACGGTCGATCTTGGA 59.106 47.619 0.00 0.00 0.00 3.53
222 223 2.094390 TGGTTTACGGTCGATCTTGGAG 60.094 50.000 0.00 0.00 0.00 3.86
223 224 2.165030 GGTTTACGGTCGATCTTGGAGA 59.835 50.000 0.00 0.00 0.00 3.71
224 225 3.181478 GGTTTACGGTCGATCTTGGAGAT 60.181 47.826 0.00 0.00 37.73 2.75
225 226 3.710326 TTACGGTCGATCTTGGAGATG 57.290 47.619 0.00 0.00 34.53 2.90
226 227 0.103208 ACGGTCGATCTTGGAGATGC 59.897 55.000 0.00 0.00 34.53 3.91
227 228 0.598680 CGGTCGATCTTGGAGATGCC 60.599 60.000 0.00 0.00 34.53 4.40
228 229 0.250081 GGTCGATCTTGGAGATGCCC 60.250 60.000 0.00 0.00 34.53 5.36
229 230 0.755686 GTCGATCTTGGAGATGCCCT 59.244 55.000 0.00 0.00 34.53 5.19
230 231 0.755079 TCGATCTTGGAGATGCCCTG 59.245 55.000 0.00 0.00 34.53 4.45
231 232 0.467384 CGATCTTGGAGATGCCCTGT 59.533 55.000 0.00 0.00 34.53 4.00
232 233 1.134280 CGATCTTGGAGATGCCCTGTT 60.134 52.381 0.00 0.00 34.53 3.16
251 252 7.599171 CCCTGTTAAGAAAACGGAAATGTTAT 58.401 34.615 0.00 0.00 0.00 1.89
260 261 1.946768 CGGAAATGTTATCGCCCACAT 59.053 47.619 0.00 0.00 35.00 3.21
281 282 2.031919 TGGGCGTTTGCAGATCGT 59.968 55.556 8.51 0.00 45.35 3.73
412 414 5.397240 CGAACTAAAAATCCGTTTTCACCAC 59.603 40.000 0.00 0.00 40.07 4.16
519 523 6.978343 TGATGTTTACACTATAGTTGCCAC 57.022 37.500 1.56 0.00 0.00 5.01
569 573 7.009540 GTGGCAATTTTAGTTTGTAGATCATGC 59.990 37.037 0.00 0.00 0.00 4.06
617 622 6.350445 GCAATTCCAGTACTTTGACCATGAAT 60.350 38.462 8.83 0.00 0.00 2.57
618 623 7.605449 CAATTCCAGTACTTTGACCATGAATT 58.395 34.615 0.00 0.00 31.97 2.17
685 692 6.105333 GGCAATTTTAGTTTATGGTGCATGA 58.895 36.000 0.00 0.00 32.41 3.07
823 833 4.764308 TGTGCAATAGACATGGCAACTTTA 59.236 37.500 0.00 0.00 42.87 1.85
879 899 3.026630 AGTTTTGAAGATCTCGTCGCA 57.973 42.857 0.00 0.00 0.00 5.10
1013 1035 7.653713 ACGTGGCAATCTATTTACATTAGAGAG 59.346 37.037 0.00 0.00 0.00 3.20
1105 1127 4.541705 AGCTAGAACCAGCAGATCTAAGA 58.458 43.478 0.00 0.00 44.35 2.10
1106 1128 4.584325 AGCTAGAACCAGCAGATCTAAGAG 59.416 45.833 0.00 0.00 44.35 2.85
1136 1163 2.887568 CCGCTCCATCGTCAGCAC 60.888 66.667 0.00 0.00 35.15 4.40
1234 1261 3.849951 CCGCCATCCTGTACGCCT 61.850 66.667 0.00 0.00 0.00 5.52
1240 1267 0.806102 CATCCTGTACGCCTTGACCG 60.806 60.000 0.00 0.00 0.00 4.79
1374 1401 3.227276 CACGGCCCGCTCCTCTAT 61.227 66.667 1.23 0.00 0.00 1.98
1450 1477 1.666011 GTGCTCAAGACCCACGAGA 59.334 57.895 0.00 0.00 0.00 4.04
1825 1852 1.603455 ATGGGCACGTTCAACCTGG 60.603 57.895 0.00 0.00 0.00 4.45
2515 2572 2.757099 GTTCCGGCCGGAGAGGTA 60.757 66.667 42.70 28.11 46.06 3.08
2797 2860 3.715097 GCTGCCCTGAGGAGCTGT 61.715 66.667 0.00 0.00 34.98 4.40
2986 3084 7.120579 TGTCGCTTCACTAATTGGTTTGAATAT 59.879 33.333 0.00 0.00 0.00 1.28
2987 3085 8.609176 GTCGCTTCACTAATTGGTTTGAATATA 58.391 33.333 0.00 0.00 0.00 0.86
3045 3145 2.678336 GTTTTAGGGCATCTCCAACGAG 59.322 50.000 0.00 0.00 37.48 4.18
3090 3201 0.179018 GTTAGCGGCCATGGGAGATT 60.179 55.000 15.13 0.00 0.00 2.40
3111 3222 1.271379 AGTCAGCGGACACGAATGTAA 59.729 47.619 19.33 0.00 46.80 2.41
3301 3430 4.753516 ATAACATCAGTCCGACAATCCA 57.246 40.909 0.40 0.00 0.00 3.41
3351 3485 2.234143 CCAGTCATCTGCTCCTCGATA 58.766 52.381 0.00 0.00 40.09 2.92
3363 3497 0.463833 CCTCGATAAAGGTGGTGCCC 60.464 60.000 0.00 0.00 38.26 5.36
3385 3530 3.884350 CGCCGCGTAGACTGCCTA 61.884 66.667 4.92 0.00 0.00 3.93
3475 3626 0.323302 TGCAACATCTGGTAGCGGAA 59.677 50.000 7.68 0.00 0.00 4.30
3476 3627 1.271108 TGCAACATCTGGTAGCGGAAA 60.271 47.619 7.68 0.00 0.00 3.13
3572 3723 1.281899 CGGCGATCTTCACCTTCTTC 58.718 55.000 0.00 0.00 0.00 2.87
3607 3758 2.036992 CCTTCCTCTCTTCGATCATGGG 59.963 54.545 0.00 0.00 0.00 4.00
3669 3873 7.814587 CCTCCATCAATAGTTTGAACCTTTTTC 59.185 37.037 0.00 0.00 44.70 2.29
3675 3879 3.780902 AGTTTGAACCTTTTTCGCCAAG 58.219 40.909 0.00 0.00 0.00 3.61
3694 3898 0.382515 GATGTCCTCGAACCTCTCCG 59.617 60.000 0.00 0.00 0.00 4.63
3695 3899 0.323542 ATGTCCTCGAACCTCTCCGT 60.324 55.000 0.00 0.00 0.00 4.69
3700 3904 1.303398 TCGAACCTCTCCGTCAGCT 60.303 57.895 0.00 0.00 0.00 4.24
3736 3940 0.691078 TCGCTTTGCCCTATCCTCCT 60.691 55.000 0.00 0.00 0.00 3.69
3737 3941 0.250081 CGCTTTGCCCTATCCTCCTC 60.250 60.000 0.00 0.00 0.00 3.71
3738 3942 0.109532 GCTTTGCCCTATCCTCCTCC 59.890 60.000 0.00 0.00 0.00 4.30
3779 3983 1.640917 ACCTTCTTCAGCGGTCCTTA 58.359 50.000 0.00 0.00 0.00 2.69
3817 4021 1.992557 TGACACCCTAGATTTTGCCCT 59.007 47.619 0.00 0.00 0.00 5.19
3849 4053 9.844257 TTTTTCTTGGATTTGTTGGATATTTGT 57.156 25.926 0.00 0.00 0.00 2.83
3850 4054 9.487790 TTTTCTTGGATTTGTTGGATATTTGTC 57.512 29.630 0.00 0.00 0.00 3.18
3851 4055 7.773489 TCTTGGATTTGTTGGATATTTGTCA 57.227 32.000 0.00 0.00 0.00 3.58
3852 4056 8.187913 TCTTGGATTTGTTGGATATTTGTCAA 57.812 30.769 0.00 0.00 0.00 3.18
3853 4057 8.087750 TCTTGGATTTGTTGGATATTTGTCAAC 58.912 33.333 0.00 0.00 40.59 3.18
3854 4058 7.537596 TGGATTTGTTGGATATTTGTCAACT 57.462 32.000 0.00 0.00 40.75 3.16
3855 4059 7.601856 TGGATTTGTTGGATATTTGTCAACTC 58.398 34.615 0.00 0.00 40.75 3.01
3856 4060 7.451255 TGGATTTGTTGGATATTTGTCAACTCT 59.549 33.333 0.00 0.00 40.75 3.24
3857 4061 8.306761 GGATTTGTTGGATATTTGTCAACTCTT 58.693 33.333 0.00 0.00 40.75 2.85
3858 4062 9.696917 GATTTGTTGGATATTTGTCAACTCTTT 57.303 29.630 0.00 0.00 40.75 2.52
3861 4065 9.567776 TTGTTGGATATTTGTCAACTCTTTAGA 57.432 29.630 0.00 0.00 40.75 2.10
3862 4066 8.999431 TGTTGGATATTTGTCAACTCTTTAGAC 58.001 33.333 0.00 0.00 40.75 2.59
3863 4067 9.220767 GTTGGATATTTGTCAACTCTTTAGACT 57.779 33.333 0.00 0.00 38.10 3.24
3864 4068 9.793259 TTGGATATTTGTCAACTCTTTAGACTT 57.207 29.630 0.00 0.00 33.56 3.01
3865 4069 9.219603 TGGATATTTGTCAACTCTTTAGACTTG 57.780 33.333 0.00 0.00 33.56 3.16
3866 4070 8.178313 GGATATTTGTCAACTCTTTAGACTTGC 58.822 37.037 0.00 0.00 33.56 4.01
3867 4071 8.854614 ATATTTGTCAACTCTTTAGACTTGCT 57.145 30.769 0.00 0.00 33.56 3.91
3868 4072 5.991328 TTGTCAACTCTTTAGACTTGCTG 57.009 39.130 0.00 0.00 33.56 4.41
3869 4073 5.023533 TGTCAACTCTTTAGACTTGCTGT 57.976 39.130 0.00 0.00 33.56 4.40
3870 4074 5.050490 TGTCAACTCTTTAGACTTGCTGTC 58.950 41.667 2.86 2.86 45.67 3.51
3880 4084 2.695359 GACTTGCTGTCGGGTTTATGA 58.305 47.619 0.00 0.00 35.81 2.15
3881 4085 3.270877 GACTTGCTGTCGGGTTTATGAT 58.729 45.455 0.00 0.00 35.81 2.45
3882 4086 4.439057 GACTTGCTGTCGGGTTTATGATA 58.561 43.478 0.00 0.00 35.81 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.563410 CCATTCTGCCCTTCTCTTCCT 59.437 52.381 0.00 0.00 0.00 3.36
2 3 1.561542 TCCATTCTGCCCTTCTCTTCC 59.438 52.381 0.00 0.00 0.00 3.46
3 4 3.054802 TCTTCCATTCTGCCCTTCTCTTC 60.055 47.826 0.00 0.00 0.00 2.87
4 5 2.915604 TCTTCCATTCTGCCCTTCTCTT 59.084 45.455 0.00 0.00 0.00 2.85
5 6 2.555664 TCTTCCATTCTGCCCTTCTCT 58.444 47.619 0.00 0.00 0.00 3.10
6 7 3.356529 TTCTTCCATTCTGCCCTTCTC 57.643 47.619 0.00 0.00 0.00 2.87
7 8 3.814504 TTTCTTCCATTCTGCCCTTCT 57.185 42.857 0.00 0.00 0.00 2.85
8 9 5.068329 CCTATTTTCTTCCATTCTGCCCTTC 59.932 44.000 0.00 0.00 0.00 3.46
9 10 4.958581 CCTATTTTCTTCCATTCTGCCCTT 59.041 41.667 0.00 0.00 0.00 3.95
10 11 4.230502 TCCTATTTTCTTCCATTCTGCCCT 59.769 41.667 0.00 0.00 0.00 5.19
11 12 4.339530 GTCCTATTTTCTTCCATTCTGCCC 59.660 45.833 0.00 0.00 0.00 5.36
12 13 4.339530 GGTCCTATTTTCTTCCATTCTGCC 59.660 45.833 0.00 0.00 0.00 4.85
13 14 4.949856 TGGTCCTATTTTCTTCCATTCTGC 59.050 41.667 0.00 0.00 0.00 4.26
14 15 5.591877 CCTGGTCCTATTTTCTTCCATTCTG 59.408 44.000 0.00 0.00 0.00 3.02
15 16 5.492524 TCCTGGTCCTATTTTCTTCCATTCT 59.507 40.000 0.00 0.00 0.00 2.40
16 17 5.755849 TCCTGGTCCTATTTTCTTCCATTC 58.244 41.667 0.00 0.00 0.00 2.67
17 18 5.340360 CCTCCTGGTCCTATTTTCTTCCATT 60.340 44.000 0.00 0.00 0.00 3.16
18 19 4.166919 CCTCCTGGTCCTATTTTCTTCCAT 59.833 45.833 0.00 0.00 0.00 3.41
19 20 3.523564 CCTCCTGGTCCTATTTTCTTCCA 59.476 47.826 0.00 0.00 0.00 3.53
20 21 3.117851 CCCTCCTGGTCCTATTTTCTTCC 60.118 52.174 0.00 0.00 0.00 3.46
21 22 3.117851 CCCCTCCTGGTCCTATTTTCTTC 60.118 52.174 0.00 0.00 0.00 2.87
22 23 2.853077 CCCCTCCTGGTCCTATTTTCTT 59.147 50.000 0.00 0.00 0.00 2.52
23 24 2.493091 CCCCTCCTGGTCCTATTTTCT 58.507 52.381 0.00 0.00 0.00 2.52
24 25 1.133761 GCCCCTCCTGGTCCTATTTTC 60.134 57.143 0.00 0.00 0.00 2.29
25 26 0.927029 GCCCCTCCTGGTCCTATTTT 59.073 55.000 0.00 0.00 0.00 1.82
26 27 1.345715 CGCCCCTCCTGGTCCTATTT 61.346 60.000 0.00 0.00 0.00 1.40
27 28 1.766461 CGCCCCTCCTGGTCCTATT 60.766 63.158 0.00 0.00 0.00 1.73
28 29 2.037304 ATCGCCCCTCCTGGTCCTAT 62.037 60.000 0.00 0.00 0.00 2.57
29 30 2.252012 AATCGCCCCTCCTGGTCCTA 62.252 60.000 0.00 0.00 0.00 2.94
30 31 3.642741 AATCGCCCCTCCTGGTCCT 62.643 63.158 0.00 0.00 0.00 3.85
31 32 3.090532 AATCGCCCCTCCTGGTCC 61.091 66.667 0.00 0.00 0.00 4.46
32 33 2.190578 CAATCGCCCCTCCTGGTC 59.809 66.667 0.00 0.00 0.00 4.02
33 34 3.411517 CCAATCGCCCCTCCTGGT 61.412 66.667 0.00 0.00 0.00 4.00
34 35 4.195334 CCCAATCGCCCCTCCTGG 62.195 72.222 0.00 0.00 0.00 4.45
35 36 3.411517 ACCCAATCGCCCCTCCTG 61.412 66.667 0.00 0.00 0.00 3.86
36 37 3.411517 CACCCAATCGCCCCTCCT 61.412 66.667 0.00 0.00 0.00 3.69
37 38 4.506255 CCACCCAATCGCCCCTCC 62.506 72.222 0.00 0.00 0.00 4.30
38 39 3.407967 TCCACCCAATCGCCCCTC 61.408 66.667 0.00 0.00 0.00 4.30
39 40 3.728373 GTCCACCCAATCGCCCCT 61.728 66.667 0.00 0.00 0.00 4.79
40 41 4.815108 GGTCCACCCAATCGCCCC 62.815 72.222 0.00 0.00 0.00 5.80
44 45 4.483243 CCCCGGTCCACCCAATCG 62.483 72.222 0.00 0.00 0.00 3.34
45 46 4.123545 CCCCCGGTCCACCCAATC 62.124 72.222 0.00 0.00 0.00 2.67
54 55 3.628982 TTTCCGACACCCCCGGTC 61.629 66.667 0.00 0.00 46.53 4.79
55 56 3.944945 GTTTCCGACACCCCCGGT 61.945 66.667 0.00 0.00 46.53 5.28
57 58 2.285024 TAGGTTTCCGACACCCCCG 61.285 63.158 0.00 0.00 34.44 5.73
58 59 1.297689 GTAGGTTTCCGACACCCCC 59.702 63.158 0.00 0.00 34.44 5.40
59 60 0.616891 ATGTAGGTTTCCGACACCCC 59.383 55.000 4.06 0.00 41.53 4.95
60 61 2.484742 AATGTAGGTTTCCGACACCC 57.515 50.000 4.06 0.00 41.53 4.61
61 62 2.414138 CGAAATGTAGGTTTCCGACACC 59.586 50.000 4.06 0.00 41.53 4.16
62 63 2.414138 CCGAAATGTAGGTTTCCGACAC 59.586 50.000 4.06 0.00 41.53 3.67
63 64 2.613474 CCCGAAATGTAGGTTTCCGACA 60.613 50.000 4.42 4.42 42.78 4.35
64 65 2.004733 CCCGAAATGTAGGTTTCCGAC 58.995 52.381 0.00 0.00 35.23 4.79
65 66 1.624813 ACCCGAAATGTAGGTTTCCGA 59.375 47.619 0.00 0.00 35.23 4.55
66 67 1.735571 CACCCGAAATGTAGGTTTCCG 59.264 52.381 0.00 0.00 35.23 4.30
67 68 2.745821 GACACCCGAAATGTAGGTTTCC 59.254 50.000 0.00 0.00 35.23 3.13
68 69 2.745821 GGACACCCGAAATGTAGGTTTC 59.254 50.000 0.00 0.00 35.31 2.78
69 70 2.106857 TGGACACCCGAAATGTAGGTTT 59.893 45.455 0.00 0.00 34.29 3.27
70 71 1.700739 TGGACACCCGAAATGTAGGTT 59.299 47.619 0.00 0.00 34.29 3.50
71 72 1.278127 CTGGACACCCGAAATGTAGGT 59.722 52.381 0.00 0.00 34.29 3.08
72 73 1.553248 TCTGGACACCCGAAATGTAGG 59.447 52.381 0.00 0.00 34.29 3.18
73 74 2.233922 AGTCTGGACACCCGAAATGTAG 59.766 50.000 3.51 0.00 34.29 2.74
74 75 2.232941 GAGTCTGGACACCCGAAATGTA 59.767 50.000 3.51 0.00 34.29 2.29
75 76 1.002087 GAGTCTGGACACCCGAAATGT 59.998 52.381 3.51 0.00 34.29 2.71
76 77 1.676014 GGAGTCTGGACACCCGAAATG 60.676 57.143 6.02 0.00 36.27 2.32
77 78 0.613777 GGAGTCTGGACACCCGAAAT 59.386 55.000 6.02 0.00 36.27 2.17
78 79 2.055299 GGAGTCTGGACACCCGAAA 58.945 57.895 6.02 0.00 36.27 3.46
79 80 3.787394 GGAGTCTGGACACCCGAA 58.213 61.111 6.02 0.00 36.27 4.30
83 84 4.083862 GGCGGGAGTCTGGACACC 62.084 72.222 8.36 8.36 40.68 4.16
84 85 2.879233 TTGGCGGGAGTCTGGACAC 61.879 63.158 3.51 0.00 33.91 3.67
85 86 2.525629 TTGGCGGGAGTCTGGACA 60.526 61.111 3.51 0.00 33.91 4.02
86 87 2.047179 GTTGGCGGGAGTCTGGAC 60.047 66.667 0.00 0.00 33.91 4.02
87 88 3.319198 GGTTGGCGGGAGTCTGGA 61.319 66.667 0.00 0.00 33.91 3.86
88 89 3.316573 GAGGTTGGCGGGAGTCTGG 62.317 68.421 0.00 0.00 33.91 3.86
89 90 2.266055 GAGGTTGGCGGGAGTCTG 59.734 66.667 0.00 0.00 33.91 3.51
90 91 3.382832 CGAGGTTGGCGGGAGTCT 61.383 66.667 0.00 0.00 33.91 3.24
98 99 2.597510 AAAGTGGGCGAGGTTGGC 60.598 61.111 0.00 0.00 0.00 4.52
99 100 1.106944 AACAAAGTGGGCGAGGTTGG 61.107 55.000 0.00 0.00 0.00 3.77
100 101 0.744281 AAACAAAGTGGGCGAGGTTG 59.256 50.000 0.00 0.00 0.00 3.77
101 102 1.029681 GAAACAAAGTGGGCGAGGTT 58.970 50.000 0.00 0.00 0.00 3.50
102 103 0.822121 GGAAACAAAGTGGGCGAGGT 60.822 55.000 0.00 0.00 0.00 3.85
103 104 0.821711 TGGAAACAAAGTGGGCGAGG 60.822 55.000 0.00 0.00 37.44 4.63
104 105 2.714259 TGGAAACAAAGTGGGCGAG 58.286 52.632 0.00 0.00 37.44 5.03
105 106 4.988744 TGGAAACAAAGTGGGCGA 57.011 50.000 0.00 0.00 37.44 5.54
115 116 7.523052 CGTGATTTCTCCCTTAAATTGGAAACA 60.523 37.037 0.00 0.00 39.83 2.83
116 117 6.806739 CGTGATTTCTCCCTTAAATTGGAAAC 59.193 38.462 0.00 0.00 0.00 2.78
117 118 6.492087 ACGTGATTTCTCCCTTAAATTGGAAA 59.508 34.615 0.00 0.00 0.00 3.13
118 119 6.007703 ACGTGATTTCTCCCTTAAATTGGAA 58.992 36.000 0.00 0.00 0.00 3.53
119 120 5.566469 ACGTGATTTCTCCCTTAAATTGGA 58.434 37.500 0.00 0.00 0.00 3.53
120 121 5.163652 GGACGTGATTTCTCCCTTAAATTGG 60.164 44.000 0.00 0.00 0.00 3.16
121 122 5.414454 TGGACGTGATTTCTCCCTTAAATTG 59.586 40.000 0.00 0.00 0.00 2.32
122 123 5.566469 TGGACGTGATTTCTCCCTTAAATT 58.434 37.500 0.00 0.00 0.00 1.82
123 124 5.045869 TCTGGACGTGATTTCTCCCTTAAAT 60.046 40.000 0.00 0.00 0.00 1.40
124 125 4.285003 TCTGGACGTGATTTCTCCCTTAAA 59.715 41.667 0.00 0.00 0.00 1.52
125 126 3.835978 TCTGGACGTGATTTCTCCCTTAA 59.164 43.478 0.00 0.00 0.00 1.85
126 127 3.194968 GTCTGGACGTGATTTCTCCCTTA 59.805 47.826 0.00 0.00 0.00 2.69
127 128 2.028020 GTCTGGACGTGATTTCTCCCTT 60.028 50.000 0.00 0.00 0.00 3.95
128 129 1.550976 GTCTGGACGTGATTTCTCCCT 59.449 52.381 0.00 0.00 0.00 4.20
129 130 1.405661 GGTCTGGACGTGATTTCTCCC 60.406 57.143 0.00 0.00 0.00 4.30
130 131 1.736032 CGGTCTGGACGTGATTTCTCC 60.736 57.143 0.00 0.00 0.00 3.71
131 132 1.067776 ACGGTCTGGACGTGATTTCTC 60.068 52.381 0.00 0.00 43.78 2.87
132 133 0.966920 ACGGTCTGGACGTGATTTCT 59.033 50.000 0.00 0.00 43.78 2.52
133 134 1.347320 GACGGTCTGGACGTGATTTC 58.653 55.000 0.00 0.00 45.68 2.17
134 135 0.037605 GGACGGTCTGGACGTGATTT 60.038 55.000 8.23 0.00 45.68 2.17
135 136 1.590147 GGACGGTCTGGACGTGATT 59.410 57.895 8.23 0.00 45.68 2.57
136 137 2.348888 GGGACGGTCTGGACGTGAT 61.349 63.158 8.23 0.00 45.68 3.06
137 138 2.987547 GGGACGGTCTGGACGTGA 60.988 66.667 8.23 0.00 45.68 4.35
166 167 5.333645 CCAACATTGATCTGTATCGCTTAGC 60.334 44.000 0.00 0.00 34.60 3.09
167 168 5.985530 TCCAACATTGATCTGTATCGCTTAG 59.014 40.000 0.00 0.00 34.60 2.18
168 169 5.912892 TCCAACATTGATCTGTATCGCTTA 58.087 37.500 0.00 0.00 34.60 3.09
169 170 4.769688 TCCAACATTGATCTGTATCGCTT 58.230 39.130 0.00 0.00 34.60 4.68
170 171 4.406648 TCCAACATTGATCTGTATCGCT 57.593 40.909 0.00 0.00 34.60 4.93
171 172 4.083643 CCATCCAACATTGATCTGTATCGC 60.084 45.833 0.00 0.00 34.60 4.58
172 173 4.083643 GCCATCCAACATTGATCTGTATCG 60.084 45.833 0.00 0.00 34.60 2.92
173 174 4.217118 GGCCATCCAACATTGATCTGTATC 59.783 45.833 0.00 0.00 0.00 2.24
174 175 4.141088 AGGCCATCCAACATTGATCTGTAT 60.141 41.667 5.01 0.00 33.74 2.29
175 176 3.202818 AGGCCATCCAACATTGATCTGTA 59.797 43.478 5.01 0.00 33.74 2.74
176 177 2.024655 AGGCCATCCAACATTGATCTGT 60.025 45.455 5.01 0.00 33.74 3.41
177 178 2.621998 GAGGCCATCCAACATTGATCTG 59.378 50.000 5.01 0.00 33.74 2.90
178 179 2.941480 GAGGCCATCCAACATTGATCT 58.059 47.619 5.01 0.00 33.74 2.75
189 190 0.746923 GTAAACCACGGAGGCCATCC 60.747 60.000 5.01 8.43 45.64 3.51
190 191 2.776659 GTAAACCACGGAGGCCATC 58.223 57.895 5.01 0.00 43.14 3.51
200 201 1.997606 CCAAGATCGACCGTAAACCAC 59.002 52.381 0.00 0.00 0.00 4.16
201 202 1.894466 TCCAAGATCGACCGTAAACCA 59.106 47.619 0.00 0.00 0.00 3.67
202 203 2.165030 TCTCCAAGATCGACCGTAAACC 59.835 50.000 0.00 0.00 0.00 3.27
203 204 3.498927 TCTCCAAGATCGACCGTAAAC 57.501 47.619 0.00 0.00 0.00 2.01
204 205 3.737047 GCATCTCCAAGATCGACCGTAAA 60.737 47.826 0.00 0.00 31.32 2.01
205 206 2.223735 GCATCTCCAAGATCGACCGTAA 60.224 50.000 0.00 0.00 31.32 3.18
206 207 1.337071 GCATCTCCAAGATCGACCGTA 59.663 52.381 0.00 0.00 31.32 4.02
207 208 0.103208 GCATCTCCAAGATCGACCGT 59.897 55.000 0.00 0.00 31.32 4.83
208 209 0.598680 GGCATCTCCAAGATCGACCG 60.599 60.000 0.00 0.00 31.32 4.79
209 210 0.250081 GGGCATCTCCAAGATCGACC 60.250 60.000 0.00 0.00 31.32 4.79
210 211 0.755686 AGGGCATCTCCAAGATCGAC 59.244 55.000 0.00 0.00 31.32 4.20
211 212 0.755079 CAGGGCATCTCCAAGATCGA 59.245 55.000 0.00 0.00 31.32 3.59
212 213 0.467384 ACAGGGCATCTCCAAGATCG 59.533 55.000 0.00 0.00 31.32 3.69
213 214 2.725221 AACAGGGCATCTCCAAGATC 57.275 50.000 0.00 0.00 31.32 2.75
214 215 3.782523 TCTTAACAGGGCATCTCCAAGAT 59.217 43.478 0.00 0.00 34.74 2.40
215 216 3.181329 TCTTAACAGGGCATCTCCAAGA 58.819 45.455 0.00 0.00 36.21 3.02
216 217 3.634397 TCTTAACAGGGCATCTCCAAG 57.366 47.619 0.00 0.00 36.21 3.61
217 218 4.380843 TTTCTTAACAGGGCATCTCCAA 57.619 40.909 0.00 0.00 36.21 3.53
218 219 4.079253 GTTTTCTTAACAGGGCATCTCCA 58.921 43.478 0.00 0.00 36.21 3.86
219 220 3.127030 CGTTTTCTTAACAGGGCATCTCC 59.873 47.826 0.00 0.00 0.00 3.71
220 221 3.127030 CCGTTTTCTTAACAGGGCATCTC 59.873 47.826 0.00 0.00 0.00 2.75
221 222 3.081804 CCGTTTTCTTAACAGGGCATCT 58.918 45.455 0.00 0.00 0.00 2.90
222 223 3.078837 TCCGTTTTCTTAACAGGGCATC 58.921 45.455 0.00 0.00 0.00 3.91
223 224 3.149005 TCCGTTTTCTTAACAGGGCAT 57.851 42.857 0.00 0.00 0.00 4.40
224 225 2.642154 TCCGTTTTCTTAACAGGGCA 57.358 45.000 0.00 0.00 0.00 5.36
225 226 3.994204 TTTCCGTTTTCTTAACAGGGC 57.006 42.857 0.00 0.00 0.00 5.19
226 227 5.447624 ACATTTCCGTTTTCTTAACAGGG 57.552 39.130 0.00 0.00 0.00 4.45
227 228 7.480542 CGATAACATTTCCGTTTTCTTAACAGG 59.519 37.037 0.00 0.00 0.00 4.00
228 229 7.007099 GCGATAACATTTCCGTTTTCTTAACAG 59.993 37.037 0.00 0.00 0.00 3.16
229 230 6.797995 GCGATAACATTTCCGTTTTCTTAACA 59.202 34.615 0.00 0.00 0.00 2.41
230 231 6.249893 GGCGATAACATTTCCGTTTTCTTAAC 59.750 38.462 0.00 0.00 0.00 2.01
231 232 6.316319 GGCGATAACATTTCCGTTTTCTTAA 58.684 36.000 0.00 0.00 0.00 1.85
232 233 5.163733 GGGCGATAACATTTCCGTTTTCTTA 60.164 40.000 0.00 0.00 0.00 2.10
260 261 1.514678 GATCTGCAAACGCCCACACA 61.515 55.000 0.00 0.00 0.00 3.72
281 282 3.936203 GTGGTGGAGGCGTGTGGA 61.936 66.667 0.00 0.00 0.00 4.02
519 523 5.181690 TGGCAACTTTAGTTTAAGCACTG 57.818 39.130 5.98 0.00 35.83 3.66
633 640 5.149973 ACATGCACTTAAAATTGCCATGA 57.850 34.783 16.50 0.00 38.00 3.07
756 764 8.297470 ACACTGAAGTTGCCATGATATATTTT 57.703 30.769 0.00 0.00 0.00 1.82
879 899 5.081032 TCCGTTTTCACCATTAAATCCCTT 58.919 37.500 0.00 0.00 0.00 3.95
1013 1035 1.772063 AAAGAAGACGCACCACACGC 61.772 55.000 0.00 0.00 0.00 5.34
1105 1127 4.021925 GCGGAGTTGACTGCCCCT 62.022 66.667 0.00 0.00 36.30 4.79
1106 1128 3.959991 GAGCGGAGTTGACTGCCCC 62.960 68.421 0.00 0.00 42.44 5.80
1234 1261 4.329545 GCTCCTGTGCCCGGTCAA 62.330 66.667 0.00 0.00 0.00 3.18
1263 1290 2.040884 AATGGGCTAGGCGGGAGA 60.041 61.111 10.58 0.00 0.00 3.71
1825 1852 2.353607 CGCGCCGATGTAGTCCTC 60.354 66.667 0.00 0.00 0.00 3.71
2797 2860 3.762247 CCCCTAAACCCGACGCGA 61.762 66.667 15.93 0.00 0.00 5.87
2839 2903 3.576078 TCCCAGCTCTGACTTTTTGAA 57.424 42.857 0.00 0.00 0.00 2.69
2986 3084 5.046878 TGGATCGGAGAAGTAGCTGTTTTTA 60.047 40.000 0.00 0.00 43.58 1.52
2987 3085 4.254492 GGATCGGAGAAGTAGCTGTTTTT 58.746 43.478 0.00 0.00 43.58 1.94
3079 3190 1.270518 CCGCTGACTAATCTCCCATGG 60.271 57.143 4.14 4.14 0.00 3.66
3082 3193 1.112113 GTCCGCTGACTAATCTCCCA 58.888 55.000 0.37 0.00 38.53 4.37
3085 3196 1.400846 TCGTGTCCGCTGACTAATCTC 59.599 52.381 9.79 0.00 42.28 2.75
3090 3201 0.885879 ACATTCGTGTCCGCTGACTA 59.114 50.000 9.79 0.00 42.28 2.59
3111 3222 1.152881 GATCTTGGATGGCGGCCTT 60.153 57.895 21.46 14.55 0.00 4.35
3262 3391 7.554476 TGATGTTATTTTGGATTCGGACATGTA 59.446 33.333 0.00 0.00 0.00 2.29
3301 3430 1.039233 CCGGCAGGGCAGAAATTCAT 61.039 55.000 0.00 0.00 0.00 2.57
3380 3514 4.221422 GACGCGGAGGCATAGGCA 62.221 66.667 12.47 0.00 43.71 4.75
3500 3651 6.656693 CCTTGAATGTGGACTCTTTGAATACT 59.343 38.462 0.00 0.00 0.00 2.12
3669 3873 1.084370 GGTTCGAGGACATCTTGGCG 61.084 60.000 0.00 0.00 0.00 5.69
3675 3879 0.382515 CGGAGAGGTTCGAGGACATC 59.617 60.000 0.00 0.00 0.00 3.06
3700 3904 3.842925 GAGAAGGTGTGGCGGCCAA 62.843 63.158 25.70 11.51 34.18 4.52
3709 3913 1.600916 GGGCAAAGCGAGAAGGTGT 60.601 57.895 0.00 0.00 0.00 4.16
3736 3940 2.133858 AGAAAGGGGAAGAAGTGGGA 57.866 50.000 0.00 0.00 0.00 4.37
3737 3941 2.376855 AGAAGAAAGGGGAAGAAGTGGG 59.623 50.000 0.00 0.00 0.00 4.61
3738 3942 3.797559 AGAAGAAAGGGGAAGAAGTGG 57.202 47.619 0.00 0.00 0.00 4.00
3779 3983 1.152183 ACACCTACCGACCCAACCT 60.152 57.895 0.00 0.00 0.00 3.50
3806 4010 7.067372 CCAAGAAAAAGAAAAAGGGCAAAATCT 59.933 33.333 0.00 0.00 0.00 2.40
3817 4021 8.854614 TCCAACAAATCCAAGAAAAAGAAAAA 57.145 26.923 0.00 0.00 0.00 1.94
3851 4055 3.555168 CCCGACAGCAAGTCTAAAGAGTT 60.555 47.826 7.58 0.00 45.32 3.01
3852 4056 2.028930 CCCGACAGCAAGTCTAAAGAGT 60.029 50.000 7.58 0.00 45.32 3.24
3853 4057 2.028930 ACCCGACAGCAAGTCTAAAGAG 60.029 50.000 7.58 0.00 45.32 2.85
3854 4058 1.968493 ACCCGACAGCAAGTCTAAAGA 59.032 47.619 7.58 0.00 45.32 2.52
3855 4059 2.457366 ACCCGACAGCAAGTCTAAAG 57.543 50.000 7.58 0.00 45.32 1.85
3856 4060 2.922740 AACCCGACAGCAAGTCTAAA 57.077 45.000 7.58 0.00 45.32 1.85
3857 4061 2.922740 AAACCCGACAGCAAGTCTAA 57.077 45.000 7.58 0.00 45.32 2.10
3858 4062 3.512329 TCATAAACCCGACAGCAAGTCTA 59.488 43.478 7.58 0.00 45.32 2.59
3859 4063 2.301870 TCATAAACCCGACAGCAAGTCT 59.698 45.455 7.58 0.00 45.32 3.24
3860 4064 2.695359 TCATAAACCCGACAGCAAGTC 58.305 47.619 0.00 0.00 44.02 3.01
3861 4065 2.851263 TCATAAACCCGACAGCAAGT 57.149 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.