Multiple sequence alignment - TraesCS2D01G383400

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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 TraesCS2D01G383400 chr2D 100.000 4632 0 0 1 4632 487935890 487931259 0.000000e+00 8554.0
1 TraesCS2D01G383400 chr2D 84.172 2723 228 83 991 3652 487725380 487722800 0.000000e+00 2453.0
2 TraesCS2D01G383400 chr2D 85.501 2076 181 51 1689 3718 486390982 486392983 0.000000e+00 2056.0
3 TraesCS2D01G383400 chr2D 83.402 1946 194 65 988 2907 487594597 487592755 0.000000e+00 1685.0
4 TraesCS2D01G383400 chr2D 85.372 834 51 34 794 1602 486390121 486390908 0.000000e+00 798.0
5 TraesCS2D01G383400 chr2D 94.382 178 10 0 1 178 201456385 201456562 1.640000e-69 274.0
6 TraesCS2D01G383400 chr2D 94.857 175 9 0 4 178 442966911 442966737 1.640000e-69 274.0
7 TraesCS2D01G383400 chr2D 79.830 352 33 13 987 1320 488059614 488059283 6.030000e-54 222.0
8 TraesCS2D01G383400 chr2D 88.701 177 20 0 1426 1602 488058838 488058662 2.810000e-52 217.0
9 TraesCS2D01G383400 chr2D 76.267 375 40 21 218 586 486389770 486390101 2.230000e-33 154.0
10 TraesCS2D01G383400 chr2D 83.582 67 8 3 149 213 186318031 186318096 5.010000e-05 60.2
11 TraesCS2D01G383400 chr2D 94.737 38 1 1 3938 3975 81313522 81313558 1.800000e-04 58.4
12 TraesCS2D01G383400 chr2B 90.272 2827 169 45 1166 3936 572314291 572311515 0.000000e+00 3600.0
13 TraesCS2D01G383400 chr2B 84.288 2985 289 97 988 3922 572180170 572177316 0.000000e+00 2748.0
14 TraesCS2D01G383400 chr2B 85.444 1690 139 58 794 2453 571345302 571346914 0.000000e+00 1659.0
15 TraesCS2D01G383400 chr2B 86.556 662 31 26 3978 4611 572311341 572310710 0.000000e+00 676.0
16 TraesCS2D01G383400 chr2B 82.313 441 59 10 1908 2347 572324577 572324155 9.470000e-97 364.0
17 TraesCS2D01G383400 chr2B 80.876 502 49 27 269 744 572315137 572314657 7.370000e-93 351.0
18 TraesCS2D01G383400 chr2B 87.719 285 21 8 794 1073 572314564 572314289 2.080000e-83 320.0
19 TraesCS2D01G383400 chr2B 84.228 298 35 6 3485 3771 82961420 82961124 3.530000e-71 279.0
20 TraesCS2D01G383400 chr2B 78.252 492 60 22 3072 3559 572322504 572322056 5.910000e-69 272.0
21 TraesCS2D01G383400 chr2B 84.884 258 27 8 1384 1633 572325289 572325036 2.770000e-62 250.0
22 TraesCS2D01G383400 chr2B 86.452 155 21 0 1687 1841 572324909 572324755 2.220000e-38 171.0
23 TraesCS2D01G383400 chr2B 89.130 138 10 2 4482 4614 572177194 572177057 2.870000e-37 167.0
24 TraesCS2D01G383400 chr2B 97.500 40 1 0 187 226 599206733 599206694 8.320000e-08 69.4
25 TraesCS2D01G383400 chr2A 84.404 3097 288 101 794 3752 631854841 631857880 0.000000e+00 2863.0
26 TraesCS2D01G383400 chr2A 88.458 1906 94 51 543 2384 632590038 632588195 0.000000e+00 2185.0
27 TraesCS2D01G383400 chr2A 91.441 1554 86 20 2388 3918 632588115 632586586 0.000000e+00 2089.0
28 TraesCS2D01G383400 chr2A 85.648 648 73 9 2424 3065 46336674 46337307 0.000000e+00 664.0
29 TraesCS2D01G383400 chr2A 80.000 480 51 25 3073 3535 46337343 46337794 3.480000e-81 313.0
30 TraesCS2D01G383400 chr2A 95.025 201 6 2 3984 4183 632585760 632585563 3.480000e-81 313.0
31 TraesCS2D01G383400 chr2A 92.308 169 4 5 218 377 632590283 632590115 1.000000e-56 231.0
32 TraesCS2D01G383400 chr2A 78.393 361 37 15 987 1320 632596477 632596131 3.660000e-46 196.0
33 TraesCS2D01G383400 chr2A 87.742 155 19 0 1687 1841 632595149 632594995 1.020000e-41 182.0
34 TraesCS2D01G383400 chr2A 76.533 375 42 20 218 586 631854487 631854821 3.710000e-36 163.0
35 TraesCS2D01G383400 chr2A 77.606 259 31 18 4222 4460 632585310 632585059 1.050000e-26 132.0
36 TraesCS2D01G383400 chr2A 94.340 53 3 0 4312 4364 632585239 632585187 1.070000e-11 82.4
37 TraesCS2D01G383400 chr7D 86.883 648 65 8 2424 3065 446551195 446550562 0.000000e+00 708.0
38 TraesCS2D01G383400 chr7D 82.151 437 43 20 1936 2364 446551626 446551217 4.440000e-90 342.0
39 TraesCS2D01G383400 chr7D 78.452 478 72 23 3073 3539 446550526 446550069 2.730000e-72 283.0
40 TraesCS2D01G383400 chr7D 94.318 176 9 1 4 178 402316513 402316338 7.640000e-68 268.0
41 TraesCS2D01G383400 chr7D 90.196 51 3 2 187 237 71621323 71621371 1.080000e-06 65.8
42 TraesCS2D01G383400 chr7A 85.031 648 73 9 2424 3065 321636676 321636047 5.050000e-179 638.0
43 TraesCS2D01G383400 chr7A 94.767 172 9 0 7 178 711960407 711960578 7.640000e-68 268.0
44 TraesCS2D01G383400 chr7A 84.000 150 15 7 3073 3216 321636011 321635865 8.080000e-28 135.0
45 TraesCS2D01G383400 chr3D 86.978 407 38 6 2664 3065 16449279 16449675 1.180000e-120 444.0
46 TraesCS2D01G383400 chr3D 79.079 478 69 22 3073 3539 16449711 16450168 2.710000e-77 300.0
47 TraesCS2D01G383400 chr3D 86.667 60 7 1 162 220 291768074 291768015 1.080000e-06 65.8
48 TraesCS2D01G383400 chr6B 82.517 429 53 14 1936 2362 247035824 247035416 1.580000e-94 357.0
49 TraesCS2D01G383400 chr4B 82.517 429 53 14 1936 2362 16786690 16787098 1.580000e-94 357.0
50 TraesCS2D01G383400 chr4A 82.517 429 53 14 1936 2362 729645110 729644702 1.580000e-94 357.0
51 TraesCS2D01G383400 chr3B 82.284 429 54 14 1936 2362 555551109 555550701 7.370000e-93 351.0
52 TraesCS2D01G383400 chr6A 81.944 432 47 19 3360 3771 226334895 226334475 2.060000e-88 337.0
53 TraesCS2D01G383400 chr6A 87.727 220 22 5 3972 4187 226334308 226334090 7.690000e-63 252.0
54 TraesCS2D01G383400 chr1D 91.892 222 16 2 1 220 366248530 366248751 4.500000e-80 309.0
55 TraesCS2D01G383400 chr1D 76.077 209 30 10 30 223 164858967 164859170 1.770000e-14 91.6
56 TraesCS2D01G383400 chr1D 100.000 30 0 0 3938 3967 68407115 68407086 6.470000e-04 56.5
57 TraesCS2D01G383400 chr5D 89.686 223 22 1 1 222 525765464 525765686 2.730000e-72 283.0
58 TraesCS2D01G383400 chr5D 88.696 230 14 5 4 221 410392676 410392447 2.120000e-68 270.0
59 TraesCS2D01G383400 chr5D 100.000 31 0 0 3938 3968 357533757 357533727 1.800000e-04 58.4
60 TraesCS2D01G383400 chr5D 100.000 30 0 0 3938 3967 37884743 37884772 6.470000e-04 56.5
61 TraesCS2D01G383400 chr5A 95.402 174 8 0 4 177 559696380 559696207 1.270000e-70 278.0
62 TraesCS2D01G383400 chr5A 93.820 178 11 0 1 178 32738690 32738867 7.640000e-68 268.0
63 TraesCS2D01G383400 chr5A 100.000 33 0 0 188 220 445551411 445551443 1.390000e-05 62.1
64 TraesCS2D01G383400 chr1B 76.923 234 38 7 5 226 575841963 575841734 8.140000e-23 119.0
65 TraesCS2D01G383400 chr4D 100.000 38 0 0 187 224 499680150 499680113 2.310000e-08 71.3
66 TraesCS2D01G383400 chr4D 100.000 30 0 0 3938 3967 433111226 433111255 6.470000e-04 56.5
67 TraesCS2D01G383400 chrUn 100.000 30 0 0 3938 3967 355919783 355919812 6.470000e-04 56.5
68 TraesCS2D01G383400 chrUn 100.000 30 0 0 3938 3967 362350230 362350259 6.470000e-04 56.5
69 TraesCS2D01G383400 chrUn 100.000 30 0 0 3938 3967 454067043 454067072 6.470000e-04 56.5
70 TraesCS2D01G383400 chr6D 100.000 30 0 0 3938 3967 467421785 467421814 6.470000e-04 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 TraesCS2D01G383400 chr2D 487931259 487935890 4631 True 8554.000000 8554 100.000000 1 4632 1 chr2D.!!$R4 4631
1 TraesCS2D01G383400 chr2D 487722800 487725380 2580 True 2453.000000 2453 84.172000 991 3652 1 chr2D.!!$R3 2661
2 TraesCS2D01G383400 chr2D 487592755 487594597 1842 True 1685.000000 1685 83.402000 988 2907 1 chr2D.!!$R2 1919
3 TraesCS2D01G383400 chr2D 486389770 486392983 3213 False 1002.666667 2056 82.380000 218 3718 3 chr2D.!!$F4 3500
4 TraesCS2D01G383400 chr2D 488058662 488059614 952 True 219.500000 222 84.265500 987 1602 2 chr2D.!!$R5 615
5 TraesCS2D01G383400 chr2B 571345302 571346914 1612 False 1659.000000 1659 85.444000 794 2453 1 chr2B.!!$F1 1659
6 TraesCS2D01G383400 chr2B 572177057 572180170 3113 True 1457.500000 2748 86.709000 988 4614 2 chr2B.!!$R3 3626
7 TraesCS2D01G383400 chr2B 572310710 572315137 4427 True 1236.750000 3600 86.355750 269 4611 4 chr2B.!!$R4 4342
8 TraesCS2D01G383400 chr2B 572322056 572325289 3233 True 264.250000 364 82.975250 1384 3559 4 chr2B.!!$R5 2175
9 TraesCS2D01G383400 chr2A 631854487 631857880 3393 False 1513.000000 2863 80.468500 218 3752 2 chr2A.!!$F2 3534
10 TraesCS2D01G383400 chr2A 632585059 632590283 5224 True 838.733333 2185 89.863000 218 4460 6 chr2A.!!$R1 4242
11 TraesCS2D01G383400 chr2A 46336674 46337794 1120 False 488.500000 664 82.824000 2424 3535 2 chr2A.!!$F1 1111
12 TraesCS2D01G383400 chr7D 446550069 446551626 1557 True 444.333333 708 82.495333 1936 3539 3 chr7D.!!$R2 1603
13 TraesCS2D01G383400 chr7A 321635865 321636676 811 True 386.500000 638 84.515500 2424 3216 2 chr7A.!!$R1 792
14 TraesCS2D01G383400 chr3D 16449279 16450168 889 False 372.000000 444 83.028500 2664 3539 2 chr3D.!!$F1 875
15 TraesCS2D01G383400 chr6A 226334090 226334895 805 True 294.500000 337 84.835500 3360 4187 2 chr6A.!!$R1 827

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
187 188 0.099791 CCAAACAGACGGCGTTTTGT 59.900 50.000 25.21 23.04 34.40 2.83 F
199 200 0.316360 CGTTTTGTCCGTTTGGGTCG 60.316 55.000 0.00 0.00 37.00 4.79 F
284 288 0.324943 AAGTGCATACGCTGTCCCTT 59.675 50.000 0.00 0.00 39.64 3.95 F
737 834 0.388649 AGAAACAGTAGCGTGCGAGG 60.389 55.000 0.00 0.00 0.00 4.63 F
977 1107 0.391661 CGATCACACTTCACCCCCTG 60.392 60.000 0.00 0.00 0.00 4.45 F
1414 1991 1.474478 ACGATTGTTTGTGGTGTTGCA 59.526 42.857 0.00 0.00 0.00 4.08 F
2961 4760 0.250727 TCGGGAAGCTTGTCTTTGGG 60.251 55.000 2.10 0.00 34.56 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1993 0.179119 GGCCTATACGTCGTGCAAGT 60.179 55.0 8.47 0.00 0.00 3.16 R
1726 2435 0.619255 TCCCCAGGAGAACCGCATAA 60.619 55.0 0.00 0.00 41.83 1.90 R
2269 3133 1.899437 GAGGAGGTGGCGTTCCATCA 61.899 60.0 4.83 0.00 46.18 3.07 R
2627 4048 1.442769 TTCTGATGCTTGACTTCGCC 58.557 50.0 0.00 0.00 0.00 5.54 R
2961 4760 1.524008 CCAAAGGCCCCTTGTCGAAC 61.524 60.0 12.85 0.00 36.26 3.95 R
3329 5200 2.101415 CTGCTGCTGCCATGTAGTAGTA 59.899 50.0 13.47 7.98 38.71 1.82 R
4369 7517 0.169009 GTTTCTTCAGCATGTCGGGC 59.831 55.0 0.00 0.00 37.40 6.13 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
17 18 2.658593 CTATCGCCGGCCTTCGTG 60.659 66.667 23.46 5.48 37.11 4.35
18 19 3.133767 CTATCGCCGGCCTTCGTGA 62.134 63.158 23.46 11.83 37.11 4.35
19 20 3.420214 TATCGCCGGCCTTCGTGAC 62.420 63.158 23.46 0.00 37.11 3.67
25 26 4.699522 GGCCTTCGTGACCGGCTT 62.700 66.667 0.00 0.00 43.29 4.35
26 27 2.668550 GCCTTCGTGACCGGCTTT 60.669 61.111 0.00 0.00 40.62 3.51
27 28 2.258726 GCCTTCGTGACCGGCTTTT 61.259 57.895 0.00 0.00 40.62 2.27
28 29 0.952010 GCCTTCGTGACCGGCTTTTA 60.952 55.000 0.00 0.00 40.62 1.52
29 30 1.734163 CCTTCGTGACCGGCTTTTAT 58.266 50.000 0.00 0.00 33.95 1.40
30 31 1.396996 CCTTCGTGACCGGCTTTTATG 59.603 52.381 0.00 0.00 33.95 1.90
31 32 2.073816 CTTCGTGACCGGCTTTTATGT 58.926 47.619 0.00 0.00 33.95 2.29
32 33 2.172851 TCGTGACCGGCTTTTATGTT 57.827 45.000 0.00 0.00 33.95 2.71
33 34 2.496111 TCGTGACCGGCTTTTATGTTT 58.504 42.857 0.00 0.00 33.95 2.83
34 35 3.661944 TCGTGACCGGCTTTTATGTTTA 58.338 40.909 0.00 0.00 33.95 2.01
35 36 4.063689 TCGTGACCGGCTTTTATGTTTAA 58.936 39.130 0.00 0.00 33.95 1.52
36 37 4.696402 TCGTGACCGGCTTTTATGTTTAAT 59.304 37.500 0.00 0.00 33.95 1.40
37 38 5.181622 TCGTGACCGGCTTTTATGTTTAATT 59.818 36.000 0.00 0.00 33.95 1.40
38 39 6.370994 TCGTGACCGGCTTTTATGTTTAATTA 59.629 34.615 0.00 0.00 33.95 1.40
39 40 7.022384 CGTGACCGGCTTTTATGTTTAATTAA 58.978 34.615 0.00 0.00 0.00 1.40
40 41 7.537991 CGTGACCGGCTTTTATGTTTAATTAAA 59.462 33.333 0.00 6.54 0.00 1.52
41 42 9.361315 GTGACCGGCTTTTATGTTTAATTAAAT 57.639 29.630 13.54 1.99 0.00 1.40
42 43 9.360093 TGACCGGCTTTTATGTTTAATTAAATG 57.640 29.630 13.54 0.00 0.00 2.32
43 44 8.192068 ACCGGCTTTTATGTTTAATTAAATGC 57.808 30.769 13.54 6.26 37.56 3.56
44 45 7.819900 ACCGGCTTTTATGTTTAATTAAATGCA 59.180 29.630 13.54 8.51 38.87 3.96
45 46 8.825745 CCGGCTTTTATGTTTAATTAAATGCAT 58.174 29.630 13.54 14.28 38.87 3.96
46 47 9.635632 CGGCTTTTATGTTTAATTAAATGCATG 57.364 29.630 13.54 3.94 38.87 4.06
93 94 2.960659 TTTTTGACGCGCCGACGA 60.961 55.556 5.73 0.00 43.93 4.20
94 95 2.523507 TTTTTGACGCGCCGACGAA 61.524 52.632 5.73 1.00 43.93 3.85
95 96 2.033328 TTTTTGACGCGCCGACGAAA 62.033 50.000 5.73 7.36 43.93 3.46
96 97 1.833434 TTTTGACGCGCCGACGAAAT 61.833 50.000 5.73 0.00 43.93 2.17
97 98 2.487443 TTTGACGCGCCGACGAAATG 62.487 55.000 5.73 0.00 43.93 2.32
98 99 4.204891 GACGCGCCGACGAAATGG 62.205 66.667 5.73 0.00 43.93 3.16
101 102 3.861263 GCGCCGACGAAATGGGTC 61.861 66.667 0.00 0.00 43.93 4.46
106 107 2.822701 GACGAAATGGGTCGGGCC 60.823 66.667 0.00 0.00 45.40 5.80
107 108 3.615509 GACGAAATGGGTCGGGCCA 62.616 63.158 4.39 0.00 45.40 5.36
108 109 2.824041 CGAAATGGGTCGGGCCAG 60.824 66.667 4.39 0.00 39.65 4.85
109 110 3.140814 GAAATGGGTCGGGCCAGC 61.141 66.667 4.39 0.00 39.65 4.85
133 134 3.798650 CGCTTGCGCCGATCCAAA 61.799 61.111 4.18 0.00 0.00 3.28
134 135 2.202479 GCTTGCGCCGATCCAAAC 60.202 61.111 4.18 0.00 0.00 2.93
135 136 2.976840 GCTTGCGCCGATCCAAACA 61.977 57.895 4.18 0.00 0.00 2.83
136 137 1.154225 CTTGCGCCGATCCAAACAC 60.154 57.895 4.18 0.00 0.00 3.32
137 138 1.851021 CTTGCGCCGATCCAAACACA 61.851 55.000 4.18 0.00 0.00 3.72
138 139 1.851021 TTGCGCCGATCCAAACACAG 61.851 55.000 4.18 0.00 0.00 3.66
139 140 2.480555 CGCCGATCCAAACACAGC 59.519 61.111 0.00 0.00 0.00 4.40
140 141 2.480555 GCCGATCCAAACACAGCG 59.519 61.111 0.00 0.00 0.00 5.18
141 142 2.480555 CCGATCCAAACACAGCGC 59.519 61.111 0.00 0.00 0.00 5.92
142 143 2.480555 CGATCCAAACACAGCGCC 59.519 61.111 2.29 0.00 0.00 6.53
143 144 2.480555 GATCCAAACACAGCGCCG 59.519 61.111 2.29 0.00 0.00 6.46
144 145 3.039202 GATCCAAACACAGCGCCGG 62.039 63.158 2.29 0.00 0.00 6.13
145 146 3.545124 ATCCAAACACAGCGCCGGA 62.545 57.895 5.05 0.00 0.00 5.14
146 147 4.025401 CCAAACACAGCGCCGGAC 62.025 66.667 5.05 0.00 0.00 4.79
148 149 4.903010 AAACACAGCGCCGGACGT 62.903 61.111 5.05 0.00 46.11 4.34
149 150 4.903010 AACACAGCGCCGGACGTT 62.903 61.111 5.05 3.20 46.11 3.99
150 151 4.903010 ACACAGCGCCGGACGTTT 62.903 61.111 5.05 0.00 46.11 3.60
151 152 4.368808 CACAGCGCCGGACGTTTG 62.369 66.667 5.05 13.47 46.11 2.93
152 153 4.903010 ACAGCGCCGGACGTTTGT 62.903 61.111 5.05 14.09 46.11 2.83
153 154 4.368808 CAGCGCCGGACGTTTGTG 62.369 66.667 5.05 1.98 46.11 3.33
154 155 4.903010 AGCGCCGGACGTTTGTGT 62.903 61.111 5.05 0.00 46.11 3.72
155 156 4.364409 GCGCCGGACGTTTGTGTC 62.364 66.667 5.05 0.00 46.11 3.67
161 162 3.708734 GACGTTTGTGTCCGCCGG 61.709 66.667 0.00 0.00 32.61 6.13
178 179 3.047877 GGCCGACCCAAACAGACG 61.048 66.667 0.00 0.00 0.00 4.18
179 180 3.047877 GCCGACCCAAACAGACGG 61.048 66.667 0.00 0.00 45.26 4.79
180 181 3.047877 CCGACCCAAACAGACGGC 61.048 66.667 0.00 0.00 37.32 5.68
181 182 3.411351 CGACCCAAACAGACGGCG 61.411 66.667 4.80 4.80 0.00 6.46
182 183 2.280592 GACCCAAACAGACGGCGT 60.281 61.111 14.65 14.65 0.00 5.68
183 184 1.890510 GACCCAAACAGACGGCGTT 60.891 57.895 16.19 0.74 0.00 4.84
184 185 1.441732 GACCCAAACAGACGGCGTTT 61.442 55.000 16.19 5.29 37.04 3.60
185 186 1.033202 ACCCAAACAGACGGCGTTTT 61.033 50.000 16.19 8.33 34.40 2.43
186 187 0.593773 CCCAAACAGACGGCGTTTTG 60.594 55.000 22.26 22.26 34.40 2.44
187 188 0.099791 CCAAACAGACGGCGTTTTGT 59.900 50.000 25.21 23.04 34.40 2.83
188 189 1.462791 CAAACAGACGGCGTTTTGTC 58.537 50.000 24.48 9.23 34.40 3.18
189 190 0.379316 AAACAGACGGCGTTTTGTCC 59.621 50.000 24.48 8.56 32.76 4.02
194 195 3.896606 CGGCGTTTTGTCCGTTTG 58.103 55.556 0.00 0.00 40.72 2.93
195 196 1.655959 CGGCGTTTTGTCCGTTTGG 60.656 57.895 0.00 0.00 40.72 3.28
196 197 1.299544 GGCGTTTTGTCCGTTTGGG 60.300 57.895 0.00 0.00 35.24 4.12
197 198 1.434287 GCGTTTTGTCCGTTTGGGT 59.566 52.632 0.00 0.00 37.00 4.51
198 199 0.593008 GCGTTTTGTCCGTTTGGGTC 60.593 55.000 0.00 0.00 37.00 4.46
199 200 0.316360 CGTTTTGTCCGTTTGGGTCG 60.316 55.000 0.00 0.00 37.00 4.79
201 202 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
202 203 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
212 213 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
213 214 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
216 217 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
255 259 1.531578 GAGTCCTTCACGTTTTCAGCC 59.468 52.381 0.00 0.00 0.00 4.85
284 288 0.324943 AAGTGCATACGCTGTCCCTT 59.675 50.000 0.00 0.00 39.64 3.95
288 294 1.065491 TGCATACGCTGTCCCTTTCAT 60.065 47.619 0.00 0.00 39.64 2.57
318 324 8.944029 GTCGCACATTCTACTTATATAGGAGTA 58.056 37.037 0.00 0.00 36.11 2.59
507 541 0.410663 TCCGTACCTCTCCTTTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
533 567 1.597302 CGATGGATGCAGCTGGGAG 60.597 63.158 17.12 0.00 0.00 4.30
534 568 1.228184 GATGGATGCAGCTGGGAGG 60.228 63.158 17.12 0.00 0.00 4.30
535 569 3.432445 ATGGATGCAGCTGGGAGGC 62.432 63.158 17.12 0.00 0.00 4.70
536 570 3.806667 GGATGCAGCTGGGAGGCT 61.807 66.667 17.12 0.00 44.10 4.58
589 639 3.629398 GCTAATTCATGGTGCTAACTGCT 59.371 43.478 0.00 0.00 43.37 4.24
617 671 2.349886 GCAGTTTCTTCGCACATCCTAG 59.650 50.000 0.00 0.00 0.00 3.02
618 672 2.932614 CAGTTTCTTCGCACATCCTAGG 59.067 50.000 0.82 0.82 0.00 3.02
622 676 3.695830 TCTTCGCACATCCTAGGTTTT 57.304 42.857 9.08 0.00 0.00 2.43
623 677 3.596214 TCTTCGCACATCCTAGGTTTTC 58.404 45.455 9.08 0.00 0.00 2.29
624 678 3.007506 TCTTCGCACATCCTAGGTTTTCA 59.992 43.478 9.08 0.00 0.00 2.69
628 682 4.394920 TCGCACATCCTAGGTTTTCATTTC 59.605 41.667 9.08 0.00 0.00 2.17
629 683 4.396166 CGCACATCCTAGGTTTTCATTTCT 59.604 41.667 9.08 0.00 0.00 2.52
630 684 5.584649 CGCACATCCTAGGTTTTCATTTCTA 59.415 40.000 9.08 0.00 0.00 2.10
632 686 6.599638 GCACATCCTAGGTTTTCATTTCTACT 59.400 38.462 9.08 0.00 0.00 2.57
633 687 7.769044 GCACATCCTAGGTTTTCATTTCTACTA 59.231 37.037 9.08 0.00 0.00 1.82
634 688 9.099454 CACATCCTAGGTTTTCATTTCTACTAC 57.901 37.037 9.08 0.00 0.00 2.73
639 693 8.697292 CCTAGGTTTTCATTTCTACTACTAGCT 58.303 37.037 0.00 0.00 0.00 3.32
734 831 1.136690 TGAAGAAACAGTAGCGTGCG 58.863 50.000 0.00 0.00 0.00 5.34
735 832 1.269361 TGAAGAAACAGTAGCGTGCGA 60.269 47.619 0.00 0.00 0.00 5.10
736 833 1.387084 GAAGAAACAGTAGCGTGCGAG 59.613 52.381 0.00 0.00 0.00 5.03
737 834 0.388649 AGAAACAGTAGCGTGCGAGG 60.389 55.000 0.00 0.00 0.00 4.63
738 835 1.352156 GAAACAGTAGCGTGCGAGGG 61.352 60.000 0.00 0.00 0.00 4.30
739 836 2.095978 AAACAGTAGCGTGCGAGGGT 62.096 55.000 0.00 0.00 0.00 4.34
740 837 2.202623 CAGTAGCGTGCGAGGGTC 60.203 66.667 0.00 0.00 0.00 4.46
741 838 2.361357 AGTAGCGTGCGAGGGTCT 60.361 61.111 0.00 0.00 0.00 3.85
742 839 1.077930 AGTAGCGTGCGAGGGTCTA 60.078 57.895 0.00 0.00 0.00 2.59
743 840 1.063811 GTAGCGTGCGAGGGTCTAC 59.936 63.158 0.00 0.00 0.00 2.59
744 841 1.077930 TAGCGTGCGAGGGTCTACT 60.078 57.895 0.00 0.00 0.00 2.57
745 842 1.094073 TAGCGTGCGAGGGTCTACTC 61.094 60.000 0.00 0.00 0.00 2.59
746 843 2.799371 CGTGCGAGGGTCTACTCC 59.201 66.667 0.00 0.00 33.93 3.85
838 953 2.205074 CGAGATCACGGCATTTTAGCT 58.795 47.619 4.47 0.00 34.17 3.32
842 957 4.770795 AGATCACGGCATTTTAGCTAGTT 58.229 39.130 0.00 0.00 34.17 2.24
868 988 3.181476 GGCGGGCATTATCAAGTCAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
972 1102 2.186076 GATCGACGATCACACTTCACC 58.814 52.381 28.48 1.87 38.77 4.02
977 1107 0.391661 CGATCACACTTCACCCCCTG 60.392 60.000 0.00 0.00 0.00 4.45
979 1109 2.469465 ATCACACTTCACCCCCTGCG 62.469 60.000 0.00 0.00 0.00 5.18
980 1110 4.643387 ACACTTCACCCCCTGCGC 62.643 66.667 0.00 0.00 0.00 6.09
1063 1199 2.566724 CACTCTCTGCCTTCTCTTCCTT 59.433 50.000 0.00 0.00 0.00 3.36
1345 1879 3.053455 GTCCTCAATGCAGCTCGTATAC 58.947 50.000 0.00 0.00 0.00 1.47
1358 1892 5.702670 CAGCTCGTATACCATTCATCCATTT 59.297 40.000 0.00 0.00 0.00 2.32
1359 1893 5.934625 AGCTCGTATACCATTCATCCATTTC 59.065 40.000 0.00 0.00 0.00 2.17
1360 1894 5.163953 GCTCGTATACCATTCATCCATTTCG 60.164 44.000 0.00 0.00 0.00 3.46
1413 1990 2.202295 ACGATTGTTTGTGGTGTTGC 57.798 45.000 0.00 0.00 0.00 4.17
1414 1991 1.474478 ACGATTGTTTGTGGTGTTGCA 59.526 42.857 0.00 0.00 0.00 4.08
1415 1992 1.851666 CGATTGTTTGTGGTGTTGCAC 59.148 47.619 0.00 0.00 0.00 4.57
1416 1993 2.733542 CGATTGTTTGTGGTGTTGCACA 60.734 45.455 1.61 0.00 35.86 4.57
1606 2189 4.497291 TGGTGTTCCCAAGGTATACATC 57.503 45.455 5.01 0.00 41.50 3.06
1685 2394 6.917533 ACCAATGACTGATGATCAACTTTTC 58.082 36.000 0.00 0.00 0.00 2.29
1726 2435 3.136626 ACCAGGTCACTGCTAAGAACTTT 59.863 43.478 0.00 0.00 43.53 2.66
1905 2618 7.132694 TGTAGTTCAGCTGATATGTTTTGTG 57.867 36.000 19.04 0.00 0.00 3.33
1915 2750 8.960591 AGCTGATATGTTTTGTGCTATAACTTT 58.039 29.630 0.00 0.00 0.00 2.66
2057 2893 8.638873 TGTATCCTTTCTTTTCTTTTTCCCTTC 58.361 33.333 0.00 0.00 0.00 3.46
2204 3068 2.827921 GAGGGTTTGATGCCACAAGATT 59.172 45.455 0.00 0.00 0.00 2.40
2347 3218 5.014123 TGTTTCTTGGATGGAAGACAGGTAT 59.986 40.000 0.00 0.00 31.53 2.73
2437 3789 2.426522 TGACGCTTGCTTGCTATTCTT 58.573 42.857 0.00 0.00 0.00 2.52
2627 4048 2.481449 CCTCTACCAAGGTTTCGATCCG 60.481 54.545 0.00 0.00 0.00 4.18
2843 4642 6.078202 TCTATCTTCTCGCTTTCAGTATGG 57.922 41.667 0.00 0.00 36.16 2.74
2961 4760 0.250727 TCGGGAAGCTTGTCTTTGGG 60.251 55.000 2.10 0.00 34.56 4.12
2978 4777 1.228459 GGTTCGACAAGGGGCCTTT 60.228 57.895 0.84 0.00 33.42 3.11
3054 4853 2.029918 TCTGAAGACGATGGTGAGTGTG 60.030 50.000 0.00 0.00 0.00 3.82
3124 4995 3.059352 AGTCTGTACTTGATGCCAACC 57.941 47.619 0.00 0.00 29.00 3.77
3278 5149 2.351336 GACGGCTACGACATGGGGAG 62.351 65.000 0.00 0.00 44.60 4.30
3329 5200 2.033141 ATCCGCTTGCAGTGCAGT 59.967 55.556 18.81 0.00 40.61 4.40
3339 5217 4.748892 CTTGCAGTGCAGTACTACTACAT 58.251 43.478 18.81 0.00 40.61 2.29
3340 5218 4.110036 TGCAGTGCAGTACTACTACATG 57.890 45.455 15.37 0.00 37.60 3.21
3341 5219 3.119137 TGCAGTGCAGTACTACTACATGG 60.119 47.826 15.37 0.00 37.60 3.66
3385 5275 2.223745 GAGGTTCCTAGCTAGACCTCG 58.776 57.143 31.00 14.30 46.02 4.63
3389 5279 3.502979 GGTTCCTAGCTAGACCTCGTATG 59.497 52.174 22.70 1.98 0.00 2.39
3464 5365 3.334891 AATGGCGCCCCTGTGGTA 61.335 61.111 26.77 1.65 36.04 3.25
3679 5611 2.299867 ACCAAAACTGATGACCCATTGC 59.700 45.455 0.00 0.00 0.00 3.56
3735 5672 8.421784 CCTACCAAGATCACTTACATAAGCTAA 58.578 37.037 0.00 0.00 36.79 3.09
3753 5695 5.594724 GCTAATGCTGACAAGATGAGATC 57.405 43.478 0.00 0.00 36.03 2.75
3846 5808 1.281899 GCCAGTATGCGAGAACTGAC 58.718 55.000 11.61 0.00 44.79 3.51
3873 5835 2.467880 TCCAGGAGGCAACCTAGTTAG 58.532 52.381 3.10 0.00 38.32 2.34
3922 5885 4.060205 GTTTTCAGCGGGTTAGTGACTTA 58.940 43.478 0.00 0.00 0.00 2.24
3923 5886 3.587797 TTCAGCGGGTTAGTGACTTAG 57.412 47.619 0.00 0.00 0.00 2.18
3936 5899 7.040271 GGTTAGTGACTTAGTTCTTCAGACTCT 60.040 40.741 0.00 0.00 0.00 3.24
3937 5900 6.325919 AGTGACTTAGTTCTTCAGACTCTG 57.674 41.667 0.00 0.00 0.00 3.35
3940 5903 5.303078 TGACTTAGTTCTTCAGACTCTGCTT 59.697 40.000 0.62 0.00 0.00 3.91
3942 5905 6.587273 ACTTAGTTCTTCAGACTCTGCTTTT 58.413 36.000 0.62 0.00 0.00 2.27
3943 5906 7.051000 ACTTAGTTCTTCAGACTCTGCTTTTT 58.949 34.615 0.62 0.00 0.00 1.94
3944 5907 5.747951 AGTTCTTCAGACTCTGCTTTTTG 57.252 39.130 0.62 0.00 0.00 2.44
3946 5909 5.295540 AGTTCTTCAGACTCTGCTTTTTGAC 59.704 40.000 0.62 0.00 0.00 3.18
3947 5910 4.769688 TCTTCAGACTCTGCTTTTTGACA 58.230 39.130 0.62 0.00 0.00 3.58
3949 5912 5.295292 TCTTCAGACTCTGCTTTTTGACAAG 59.705 40.000 0.62 0.00 0.00 3.16
3966 5929 3.121030 GCACTCGCTGCGATTGGT 61.121 61.111 33.23 22.65 37.10 3.67
3967 5930 1.809619 GCACTCGCTGCGATTGGTA 60.810 57.895 33.23 10.99 37.10 3.25
4188 7113 6.034363 CAGACGATCGGATTAGAATAAGCATG 59.966 42.308 20.98 0.00 0.00 4.06
4225 7356 1.128136 CAAAGTCAGATGCGCACTCTG 59.872 52.381 28.82 28.82 41.23 3.35
4227 7358 2.125391 TCAGATGCGCACTCTGGC 60.125 61.111 31.32 13.95 40.44 4.85
4228 7359 3.200593 CAGATGCGCACTCTGGCC 61.201 66.667 27.85 0.00 37.15 5.36
4229 7360 4.827087 AGATGCGCACTCTGGCCG 62.827 66.667 14.90 0.00 0.00 6.13
4230 7361 4.819761 GATGCGCACTCTGGCCGA 62.820 66.667 14.90 0.00 0.00 5.54
4231 7362 4.827087 ATGCGCACTCTGGCCGAG 62.827 66.667 14.90 19.02 45.56 4.63
4247 7395 3.526931 CCGAGTGGCTCTTTTCATCTA 57.473 47.619 0.00 0.00 0.00 1.98
4384 7558 0.531532 CTAGGCCCGACATGCTGAAG 60.532 60.000 0.00 0.00 0.00 3.02
4390 7564 1.522668 CCGACATGCTGAAGAAACCA 58.477 50.000 0.00 0.00 0.00 3.67
4440 7623 7.663493 AGTTCTTTGAACCTCTAGATCAAAAGG 59.337 37.037 16.77 6.67 41.14 3.11
4448 7631 5.163395 ACCTCTAGATCAAAAGGTCGAATCC 60.163 44.000 7.01 0.00 37.59 3.01
4449 7632 5.163405 CCTCTAGATCAAAAGGTCGAATCCA 60.163 44.000 0.00 0.00 0.00 3.41
4450 7633 6.463614 CCTCTAGATCAAAAGGTCGAATCCAT 60.464 42.308 0.00 0.00 0.00 3.41
4451 7634 6.283694 TCTAGATCAAAAGGTCGAATCCATG 58.716 40.000 0.00 0.00 0.00 3.66
4452 7635 5.102953 AGATCAAAAGGTCGAATCCATGA 57.897 39.130 0.00 0.00 0.00 3.07
4453 7636 4.878397 AGATCAAAAGGTCGAATCCATGAC 59.122 41.667 0.00 0.00 0.00 3.06
4454 7637 4.014569 TCAAAAGGTCGAATCCATGACA 57.985 40.909 0.00 0.00 36.83 3.58
4455 7638 4.393834 TCAAAAGGTCGAATCCATGACAA 58.606 39.130 0.00 0.00 36.83 3.18
4456 7639 5.009631 TCAAAAGGTCGAATCCATGACAAT 58.990 37.500 0.00 0.00 36.83 2.71
4457 7640 4.970662 AAAGGTCGAATCCATGACAATG 57.029 40.909 0.00 0.00 36.83 2.82
4458 7641 3.634397 AGGTCGAATCCATGACAATGT 57.366 42.857 0.00 0.00 36.83 2.71
4459 7642 3.273434 AGGTCGAATCCATGACAATGTG 58.727 45.455 0.00 0.00 36.83 3.21
4460 7643 3.009723 GGTCGAATCCATGACAATGTGT 58.990 45.455 0.00 0.00 36.83 3.72
4461 7644 3.440173 GGTCGAATCCATGACAATGTGTT 59.560 43.478 0.00 0.00 36.83 3.32
4462 7645 4.437390 GGTCGAATCCATGACAATGTGTTC 60.437 45.833 0.00 0.00 36.83 3.18
4463 7646 4.393062 GTCGAATCCATGACAATGTGTTCT 59.607 41.667 0.00 0.00 35.20 3.01
4464 7647 4.631377 TCGAATCCATGACAATGTGTTCTC 59.369 41.667 0.00 0.00 31.27 2.87
4465 7648 4.493057 CGAATCCATGACAATGTGTTCTCG 60.493 45.833 0.00 0.00 31.27 4.04
4466 7649 2.698803 TCCATGACAATGTGTTCTCGG 58.301 47.619 0.00 0.00 31.27 4.63
4467 7650 2.301583 TCCATGACAATGTGTTCTCGGA 59.698 45.455 0.00 0.00 31.27 4.55
4468 7651 3.073678 CCATGACAATGTGTTCTCGGAA 58.926 45.455 0.00 0.00 31.27 4.30
4469 7652 3.501828 CCATGACAATGTGTTCTCGGAAA 59.498 43.478 0.00 0.00 31.27 3.13
4470 7653 4.023279 CCATGACAATGTGTTCTCGGAAAA 60.023 41.667 0.00 0.00 31.27 2.29
4471 7654 5.507149 CCATGACAATGTGTTCTCGGAAAAA 60.507 40.000 0.00 0.00 31.27 1.94
4498 7681 6.734502 AAATCCATGATAATGTGATGGCAA 57.265 33.333 0.00 0.00 37.20 4.52
4514 7697 1.501169 GCAATCGCCTTTGCTGTTTT 58.499 45.000 10.22 0.00 46.66 2.43
4522 7705 2.986479 GCCTTTGCTGTTTTATTGGACG 59.014 45.455 0.00 0.00 33.53 4.79
4560 7748 3.526534 TGACTTGTTGATGTCACGTCAA 58.473 40.909 8.46 8.46 39.72 3.18
4601 7789 2.159653 GCACTGTTTGTCTCGCCTAATG 60.160 50.000 0.00 0.00 0.00 1.90
4604 7792 3.055094 ACTGTTTGTCTCGCCTAATGGAT 60.055 43.478 0.00 0.00 34.57 3.41
4611 7799 2.029020 TCTCGCCTAATGGATTCCGATG 60.029 50.000 0.00 0.00 34.57 3.84
4614 7802 3.007940 TCGCCTAATGGATTCCGATGATT 59.992 43.478 0.00 0.00 34.57 2.57
4615 7803 4.221924 TCGCCTAATGGATTCCGATGATTA 59.778 41.667 0.00 0.00 34.57 1.75
4616 7804 4.568359 CGCCTAATGGATTCCGATGATTAG 59.432 45.833 11.16 11.16 34.57 1.73
4617 7805 4.333926 GCCTAATGGATTCCGATGATTAGC 59.666 45.833 12.11 6.91 34.57 3.09
4618 7806 5.491070 CCTAATGGATTCCGATGATTAGCA 58.509 41.667 12.11 0.00 34.57 3.49
4619 7807 6.118170 CCTAATGGATTCCGATGATTAGCAT 58.882 40.000 12.11 0.00 36.05 3.79
4620 7808 7.275183 CCTAATGGATTCCGATGATTAGCATA 58.725 38.462 12.11 0.00 34.25 3.14
4621 7809 7.935755 CCTAATGGATTCCGATGATTAGCATAT 59.064 37.037 12.11 0.00 34.25 1.78
4622 7810 7.798596 AATGGATTCCGATGATTAGCATATC 57.201 36.000 0.00 0.00 37.34 1.63
4623 7811 6.550938 TGGATTCCGATGATTAGCATATCT 57.449 37.500 0.00 0.00 37.34 1.98
4624 7812 6.950842 TGGATTCCGATGATTAGCATATCTT 58.049 36.000 0.00 0.00 37.34 2.40
4625 7813 8.078060 TGGATTCCGATGATTAGCATATCTTA 57.922 34.615 0.00 0.00 37.34 2.10
4626 7814 8.200120 TGGATTCCGATGATTAGCATATCTTAG 58.800 37.037 0.00 0.00 37.34 2.18
4627 7815 7.655328 GGATTCCGATGATTAGCATATCTTAGG 59.345 40.741 0.00 0.00 37.34 2.69
4628 7816 6.471233 TCCGATGATTAGCATATCTTAGGG 57.529 41.667 10.70 5.77 37.34 3.53
4629 7817 6.194967 TCCGATGATTAGCATATCTTAGGGA 58.805 40.000 10.70 7.27 37.34 4.20
4630 7818 6.841229 TCCGATGATTAGCATATCTTAGGGAT 59.159 38.462 10.70 0.00 37.34 3.85
4631 7819 8.004801 TCCGATGATTAGCATATCTTAGGGATA 58.995 37.037 10.70 0.00 40.69 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.658593 CACGAAGGCCGGCGATAG 60.659 66.667 22.54 14.31 43.93 2.08
2 3 4.814294 GTCACGAAGGCCGGCGAT 62.814 66.667 22.54 12.00 43.93 4.58
10 11 1.396996 CATAAAAGCCGGTCACGAAGG 59.603 52.381 1.90 0.00 44.60 3.46
11 12 2.073816 ACATAAAAGCCGGTCACGAAG 58.926 47.619 1.90 0.00 44.60 3.79
12 13 2.172851 ACATAAAAGCCGGTCACGAA 57.827 45.000 1.90 0.00 44.60 3.85
13 14 2.172851 AACATAAAAGCCGGTCACGA 57.827 45.000 1.90 0.00 44.60 4.35
14 15 2.981400 AAACATAAAAGCCGGTCACG 57.019 45.000 1.90 0.00 40.55 4.35
15 16 8.745464 TTTAATTAAACATAAAAGCCGGTCAC 57.255 30.769 6.54 0.00 0.00 3.67
16 17 9.360093 CATTTAATTAAACATAAAAGCCGGTCA 57.640 29.630 12.74 0.00 0.00 4.02
17 18 8.325282 GCATTTAATTAAACATAAAAGCCGGTC 58.675 33.333 12.74 0.00 32.48 4.79
18 19 7.819900 TGCATTTAATTAAACATAAAAGCCGGT 59.180 29.630 12.74 0.00 35.80 5.28
19 20 8.190888 TGCATTTAATTAAACATAAAAGCCGG 57.809 30.769 12.74 0.00 35.80 6.13
20 21 9.635632 CATGCATTTAATTAAACATAAAAGCCG 57.364 29.630 12.74 0.00 35.80 5.52
76 77 2.033328 TTTCGTCGGCGCGTCAAAAA 62.033 50.000 12.89 11.86 38.14 1.94
77 78 1.833434 ATTTCGTCGGCGCGTCAAAA 61.833 50.000 12.89 14.32 38.14 2.44
78 79 2.311701 ATTTCGTCGGCGCGTCAAA 61.312 52.632 12.89 3.58 38.14 2.69
79 80 2.735478 ATTTCGTCGGCGCGTCAA 60.735 55.556 12.89 14.84 38.14 3.18
80 81 3.474904 CATTTCGTCGGCGCGTCA 61.475 61.111 12.89 10.46 38.14 4.35
81 82 4.204891 CCATTTCGTCGGCGCGTC 62.205 66.667 19.58 3.30 38.14 5.19
84 85 3.861263 GACCCATTTCGTCGGCGC 61.861 66.667 3.52 0.00 38.14 6.53
89 90 2.822701 GGCCCGACCCATTTCGTC 60.823 66.667 0.00 0.00 37.29 4.20
90 91 3.622060 CTGGCCCGACCCATTTCGT 62.622 63.158 0.00 0.00 37.29 3.85
91 92 2.824041 CTGGCCCGACCCATTTCG 60.824 66.667 0.00 0.00 37.83 3.46
92 93 3.140814 GCTGGCCCGACCCATTTC 61.141 66.667 0.00 0.00 37.83 2.17
118 119 1.154225 GTGTTTGGATCGGCGCAAG 60.154 57.895 10.83 1.95 43.44 4.01
119 120 1.851021 CTGTGTTTGGATCGGCGCAA 61.851 55.000 10.83 0.00 0.00 4.85
120 121 2.281139 TGTGTTTGGATCGGCGCA 60.281 55.556 10.83 0.00 0.00 6.09
121 122 2.480555 CTGTGTTTGGATCGGCGC 59.519 61.111 0.00 0.00 0.00 6.53
122 123 2.480555 GCTGTGTTTGGATCGGCG 59.519 61.111 0.00 0.00 0.00 6.46
123 124 2.480555 CGCTGTGTTTGGATCGGC 59.519 61.111 0.00 0.00 0.00 5.54
124 125 2.480555 GCGCTGTGTTTGGATCGG 59.519 61.111 0.00 0.00 0.00 4.18
125 126 2.480555 GGCGCTGTGTTTGGATCG 59.519 61.111 7.64 0.00 0.00 3.69
126 127 2.480555 CGGCGCTGTGTTTGGATC 59.519 61.111 8.45 0.00 0.00 3.36
127 128 3.055719 CCGGCGCTGTGTTTGGAT 61.056 61.111 16.49 0.00 0.00 3.41
128 129 4.243008 TCCGGCGCTGTGTTTGGA 62.243 61.111 16.49 0.42 0.00 3.53
129 130 4.025401 GTCCGGCGCTGTGTTTGG 62.025 66.667 16.49 0.00 0.00 3.28
130 131 4.368808 CGTCCGGCGCTGTGTTTG 62.369 66.667 16.49 0.00 0.00 2.93
131 132 4.903010 ACGTCCGGCGCTGTGTTT 62.903 61.111 16.49 0.00 46.11 2.83
132 133 4.903010 AACGTCCGGCGCTGTGTT 62.903 61.111 16.49 13.60 46.11 3.32
133 134 4.903010 AAACGTCCGGCGCTGTGT 62.903 61.111 16.49 7.84 46.11 3.72
134 135 4.368808 CAAACGTCCGGCGCTGTG 62.369 66.667 16.49 6.93 46.11 3.66
135 136 4.903010 ACAAACGTCCGGCGCTGT 62.903 61.111 16.49 16.04 46.11 4.40
136 137 4.368808 CACAAACGTCCGGCGCTG 62.369 66.667 9.96 9.96 46.11 5.18
137 138 4.903010 ACACAAACGTCCGGCGCT 62.903 61.111 16.48 3.50 46.11 5.92
138 139 4.364409 GACACAAACGTCCGGCGC 62.364 66.667 16.48 0.00 46.11 6.53
139 140 3.708734 GGACACAAACGTCCGGCG 61.709 66.667 15.25 15.25 45.77 6.46
144 145 3.708734 CCGGCGGACACAAACGTC 61.709 66.667 24.41 0.00 35.03 4.34
161 162 3.047877 CGTCTGTTTGGGTCGGCC 61.048 66.667 0.00 0.00 0.00 6.13
162 163 3.047877 CCGTCTGTTTGGGTCGGC 61.048 66.667 0.00 0.00 35.01 5.54
163 164 3.047877 GCCGTCTGTTTGGGTCGG 61.048 66.667 0.00 0.00 43.37 4.79
164 165 3.411351 CGCCGTCTGTTTGGGTCG 61.411 66.667 0.00 0.00 0.00 4.79
165 166 1.441732 AAACGCCGTCTGTTTGGGTC 61.442 55.000 0.00 0.00 38.08 4.46
166 167 1.033202 AAAACGCCGTCTGTTTGGGT 61.033 50.000 0.00 0.00 39.36 4.51
167 168 0.593773 CAAAACGCCGTCTGTTTGGG 60.594 55.000 5.25 0.00 39.36 4.12
168 169 0.099791 ACAAAACGCCGTCTGTTTGG 59.900 50.000 15.02 0.00 39.36 3.28
169 170 1.462791 GACAAAACGCCGTCTGTTTG 58.537 50.000 10.42 10.42 39.36 2.93
170 171 0.379316 GGACAAAACGCCGTCTGTTT 59.621 50.000 6.41 0.00 41.07 2.83
171 172 1.768112 CGGACAAAACGCCGTCTGTT 61.768 55.000 6.41 0.00 42.49 3.16
172 173 2.241880 CGGACAAAACGCCGTCTGT 61.242 57.895 4.78 4.78 42.49 3.41
173 174 2.549282 CGGACAAAACGCCGTCTG 59.451 61.111 0.00 0.00 42.49 3.51
178 179 1.299544 CCCAAACGGACAAAACGCC 60.300 57.895 0.00 0.00 34.00 5.68
179 180 0.593008 GACCCAAACGGACAAAACGC 60.593 55.000 0.00 0.00 34.64 4.84
180 181 0.316360 CGACCCAAACGGACAAAACG 60.316 55.000 0.00 0.00 34.64 3.60
181 182 3.537471 CGACCCAAACGGACAAAAC 57.463 52.632 0.00 0.00 34.64 2.43
195 196 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
196 197 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
199 200 2.180159 TAGAGCAACTCCAACGGGCC 62.180 60.000 0.00 0.00 0.00 5.80
200 201 0.321298 TTAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
201 202 1.676014 CCTTAGAGCAACTCCAACGGG 60.676 57.143 0.00 0.00 0.00 5.28
202 203 1.275291 TCCTTAGAGCAACTCCAACGG 59.725 52.381 0.00 0.00 0.00 4.44
203 204 2.743636 TCCTTAGAGCAACTCCAACG 57.256 50.000 0.00 0.00 0.00 4.10
204 205 4.187694 CAGATCCTTAGAGCAACTCCAAC 58.812 47.826 0.00 0.00 0.00 3.77
205 206 3.198635 CCAGATCCTTAGAGCAACTCCAA 59.801 47.826 0.00 0.00 0.00 3.53
206 207 2.768527 CCAGATCCTTAGAGCAACTCCA 59.231 50.000 0.00 0.00 0.00 3.86
207 208 3.034635 TCCAGATCCTTAGAGCAACTCC 58.965 50.000 0.00 0.00 0.00 3.85
208 209 3.704061 AGTCCAGATCCTTAGAGCAACTC 59.296 47.826 0.00 0.00 0.00 3.01
209 210 3.718723 AGTCCAGATCCTTAGAGCAACT 58.281 45.455 0.00 0.00 0.00 3.16
210 211 4.038642 CCTAGTCCAGATCCTTAGAGCAAC 59.961 50.000 0.00 0.00 0.00 4.17
211 212 4.219115 CCTAGTCCAGATCCTTAGAGCAA 58.781 47.826 0.00 0.00 0.00 3.91
212 213 3.838565 CCTAGTCCAGATCCTTAGAGCA 58.161 50.000 0.00 0.00 0.00 4.26
213 214 2.560981 GCCTAGTCCAGATCCTTAGAGC 59.439 54.545 0.00 0.00 0.00 4.09
214 215 2.817258 CGCCTAGTCCAGATCCTTAGAG 59.183 54.545 0.00 0.00 0.00 2.43
215 216 2.442126 TCGCCTAGTCCAGATCCTTAGA 59.558 50.000 0.00 0.00 0.00 2.10
216 217 2.817258 CTCGCCTAGTCCAGATCCTTAG 59.183 54.545 0.00 0.00 0.00 2.18
255 259 0.025513 GTATGCACTTCTTCGCTGCG 59.974 55.000 17.25 17.25 33.35 5.18
318 324 8.846211 TGAACCGACTTTTTGAAGAAGAAATAT 58.154 29.630 2.21 0.00 0.00 1.28
416 438 2.845019 GCTTCCTGCAAAAATGGCC 58.155 52.632 0.00 0.00 42.31 5.36
507 541 1.153188 TGCATCCATCGCACGGAAT 60.153 52.632 0.00 0.00 35.77 3.01
541 575 2.672996 CAGCTCCGTGGTTTGGGG 60.673 66.667 0.00 0.00 0.00 4.96
589 639 0.884704 GCGAAGAAACTGCCCACTCA 60.885 55.000 0.00 0.00 0.00 3.41
602 652 3.007506 TGAAAACCTAGGATGTGCGAAGA 59.992 43.478 17.98 0.00 0.00 2.87
617 671 8.251721 TCTCAGCTAGTAGTAGAAATGAAAACC 58.748 37.037 8.87 0.00 0.00 3.27
618 672 9.640963 TTCTCAGCTAGTAGTAGAAATGAAAAC 57.359 33.333 8.87 0.00 0.00 2.43
622 676 7.283580 GGACTTCTCAGCTAGTAGTAGAAATGA 59.716 40.741 8.87 7.81 36.10 2.57
623 677 7.422399 GGACTTCTCAGCTAGTAGTAGAAATG 58.578 42.308 8.87 4.07 36.10 2.32
624 678 6.261381 CGGACTTCTCAGCTAGTAGTAGAAAT 59.739 42.308 8.87 0.00 36.10 2.17
628 682 4.444536 ACGGACTTCTCAGCTAGTAGTAG 58.555 47.826 0.00 0.00 36.10 2.57
629 683 4.440880 GACGGACTTCTCAGCTAGTAGTA 58.559 47.826 0.00 0.00 36.10 1.82
630 684 3.272581 GACGGACTTCTCAGCTAGTAGT 58.727 50.000 0.00 0.00 38.44 2.73
632 686 2.641305 GGACGGACTTCTCAGCTAGTA 58.359 52.381 0.00 0.00 0.00 1.82
633 687 1.465794 GGACGGACTTCTCAGCTAGT 58.534 55.000 0.00 0.00 0.00 2.57
634 688 0.378962 CGGACGGACTTCTCAGCTAG 59.621 60.000 0.00 0.00 0.00 3.42
639 693 2.974489 GACGCGGACGGACTTCTCA 61.974 63.158 12.47 0.00 46.04 3.27
737 834 1.832366 GAAAGGACAGGGGAGTAGACC 59.168 57.143 0.00 0.00 0.00 3.85
738 835 1.832366 GGAAAGGACAGGGGAGTAGAC 59.168 57.143 0.00 0.00 0.00 2.59
739 836 1.722851 AGGAAAGGACAGGGGAGTAGA 59.277 52.381 0.00 0.00 0.00 2.59
740 837 2.112190 GAGGAAAGGACAGGGGAGTAG 58.888 57.143 0.00 0.00 0.00 2.57
741 838 1.722851 AGAGGAAAGGACAGGGGAGTA 59.277 52.381 0.00 0.00 0.00 2.59
742 839 0.494095 AGAGGAAAGGACAGGGGAGT 59.506 55.000 0.00 0.00 0.00 3.85
743 840 1.662686 AAGAGGAAAGGACAGGGGAG 58.337 55.000 0.00 0.00 0.00 4.30
744 841 3.246350 TGATAAGAGGAAAGGACAGGGGA 60.246 47.826 0.00 0.00 0.00 4.81
745 842 3.115390 TGATAAGAGGAAAGGACAGGGG 58.885 50.000 0.00 0.00 0.00 4.79
746 843 4.502259 CGATGATAAGAGGAAAGGACAGGG 60.502 50.000 0.00 0.00 0.00 4.45
747 844 4.100189 ACGATGATAAGAGGAAAGGACAGG 59.900 45.833 0.00 0.00 0.00 4.00
748 845 5.269505 ACGATGATAAGAGGAAAGGACAG 57.730 43.478 0.00 0.00 0.00 3.51
749 846 4.099573 GGACGATGATAAGAGGAAAGGACA 59.900 45.833 0.00 0.00 0.00 4.02
750 847 4.623002 GGACGATGATAAGAGGAAAGGAC 58.377 47.826 0.00 0.00 0.00 3.85
751 848 3.318275 CGGACGATGATAAGAGGAAAGGA 59.682 47.826 0.00 0.00 0.00 3.36
838 953 4.425180 TGATAATGCCCGCCTAAAACTA 57.575 40.909 0.00 0.00 0.00 2.24
842 957 3.211045 GACTTGATAATGCCCGCCTAAA 58.789 45.455 0.00 0.00 0.00 1.85
868 988 1.365633 GGCGTGCACAATTTCCCAA 59.634 52.632 18.64 0.00 0.00 4.12
894 1022 0.179009 CCTCCGTATCCGTAGTGGGA 60.179 60.000 0.00 0.00 41.17 4.37
1063 1199 0.456221 GCGTGTGCTAGAGCCTAGAA 59.544 55.000 11.96 0.49 41.18 2.10
1156 1325 2.269241 GGCTCCGAGTTCCCCTTG 59.731 66.667 0.00 0.00 0.00 3.61
1345 1879 9.701098 ATTTTCATATTCGAAATGGATGAATGG 57.299 29.630 19.85 0.00 36.64 3.16
1358 1892 7.438160 ACACGCTATCAGAATTTTCATATTCGA 59.562 33.333 0.00 0.00 39.09 3.71
1359 1893 7.528516 CACACGCTATCAGAATTTTCATATTCG 59.471 37.037 0.00 0.00 39.09 3.34
1360 1894 7.322222 GCACACGCTATCAGAATTTTCATATTC 59.678 37.037 0.00 0.00 33.59 1.75
1413 1990 1.917955 CCTATACGTCGTGCAAGTGTG 59.082 52.381 8.47 0.00 0.00 3.82
1414 1991 1.734707 GCCTATACGTCGTGCAAGTGT 60.735 52.381 8.47 2.73 0.00 3.55
1415 1992 0.921347 GCCTATACGTCGTGCAAGTG 59.079 55.000 8.47 0.00 0.00 3.16
1416 1993 0.179119 GGCCTATACGTCGTGCAAGT 60.179 55.000 8.47 0.00 0.00 3.16
1417 1994 1.206745 CGGCCTATACGTCGTGCAAG 61.207 60.000 8.47 2.44 0.00 4.01
1419 1996 1.449726 ATCGGCCTATACGTCGTGCA 61.450 55.000 8.47 0.00 0.00 4.57
1474 2057 4.702131 ACCACAATGTTCTCATCCTTTAGC 59.298 41.667 0.00 0.00 32.56 3.09
1685 2394 2.492484 GGTCACCAGTGTAGTCCTGTAG 59.508 54.545 0.00 0.00 0.00 2.74
1726 2435 0.619255 TCCCCAGGAGAACCGCATAA 60.619 55.000 0.00 0.00 41.83 1.90
2204 3068 7.442666 TGATGCCGCTGTAACATAAATATTGTA 59.557 33.333 0.00 0.00 0.00 2.41
2269 3133 1.899437 GAGGAGGTGGCGTTCCATCA 61.899 60.000 4.83 0.00 46.18 3.07
2437 3789 7.284261 TGCAAATTAATCAGGATCGAATGGTTA 59.716 33.333 0.00 0.00 0.00 2.85
2474 3831 7.084486 GCTTGATGGTTTCGTTCTTTAGATTT 58.916 34.615 0.00 0.00 0.00 2.17
2627 4048 1.442769 TTCTGATGCTTGACTTCGCC 58.557 50.000 0.00 0.00 0.00 5.54
2796 4584 9.289782 AGATTAGCAGACAAATTAGTCAAAACT 57.710 29.630 0.00 0.00 40.98 2.66
2843 4642 2.242196 TCTGATCCCCCATTCAACTTCC 59.758 50.000 0.00 0.00 0.00 3.46
2961 4760 1.524008 CCAAAGGCCCCTTGTCGAAC 61.524 60.000 12.85 0.00 36.26 3.95
3054 4853 4.877282 AGAGTGCAGAGTAAGAAACTGTC 58.123 43.478 0.00 0.00 39.07 3.51
3124 4995 2.365068 CGAACACTCGCACCTGACG 61.365 63.158 0.00 0.00 38.45 4.35
3278 5149 2.671963 GAACCAACGGGCTCCACC 60.672 66.667 0.00 0.00 37.90 4.61
3329 5200 2.101415 CTGCTGCTGCCATGTAGTAGTA 59.899 50.000 13.47 7.98 38.71 1.82
3389 5279 6.480981 GGTATACCAATGTGTGTATGTACACC 59.519 42.308 17.44 11.15 44.54 4.16
3401 5301 9.135843 CTTGTATGTATACGGTATACCAATGTG 57.864 37.037 27.04 14.39 40.18 3.21
3412 5312 9.148104 GTTTCTTCTTTCTTGTATGTATACGGT 57.852 33.333 0.00 0.00 36.06 4.83
3413 5313 8.601476 GGTTTCTTCTTTCTTGTATGTATACGG 58.399 37.037 0.00 0.00 36.06 4.02
3414 5314 8.318876 CGGTTTCTTCTTTCTTGTATGTATACG 58.681 37.037 0.00 0.00 36.06 3.06
3464 5365 7.208064 ACCATACACTACTGATTAACCCAAT 57.792 36.000 0.00 0.00 0.00 3.16
3559 5476 2.984471 GCACTGTCATGCAAAGACATTG 59.016 45.455 25.45 25.45 44.27 2.82
3593 5516 0.179032 ACTGCCAACCATTGTCACGA 60.179 50.000 0.00 0.00 0.00 4.35
3594 5517 0.040157 CACTGCCAACCATTGTCACG 60.040 55.000 0.00 0.00 0.00 4.35
3608 5531 1.180029 ACCAAATCAGATGGCACTGC 58.820 50.000 10.87 0.00 41.89 4.40
3679 5611 2.741145 AGGAGGAGCACTACCTTACTG 58.259 52.381 0.00 0.00 37.93 2.74
3735 5672 5.354842 TCTTGATCTCATCTTGTCAGCAT 57.645 39.130 0.00 0.00 0.00 3.79
3753 5695 3.683802 AGGGAGCTTCACAAAGATCTTG 58.316 45.455 9.17 6.08 45.28 3.02
3846 5808 0.955919 GTTGCCTCCTGGAAGAACCG 60.956 60.000 0.00 0.00 42.61 4.44
3873 5835 8.629158 TGGTGTATCAATGCAGGTTAATTAATC 58.371 33.333 0.31 0.03 0.00 1.75
3922 5885 5.295540 GTCAAAAAGCAGAGTCTGAAGAACT 59.704 40.000 24.55 7.84 32.44 3.01
3923 5886 5.065218 TGTCAAAAAGCAGAGTCTGAAGAAC 59.935 40.000 24.55 11.32 32.44 3.01
3951 5914 0.246635 ACTTACCAATCGCAGCGAGT 59.753 50.000 24.08 18.90 39.91 4.18
3952 5915 2.203800 TACTTACCAATCGCAGCGAG 57.796 50.000 24.08 12.29 39.91 5.03
3953 5916 2.882927 ATACTTACCAATCGCAGCGA 57.117 45.000 22.06 22.06 41.13 4.93
3954 5917 6.887376 ATATTATACTTACCAATCGCAGCG 57.113 37.500 9.06 9.06 0.00 5.18
3955 5918 9.582431 TTCTATATTATACTTACCAATCGCAGC 57.418 33.333 0.00 0.00 0.00 5.25
3958 5921 9.530633 CCCTTCTATATTATACTTACCAATCGC 57.469 37.037 0.00 0.00 0.00 4.58
3959 5922 9.530633 GCCCTTCTATATTATACTTACCAATCG 57.469 37.037 0.00 0.00 0.00 3.34
3999 6921 6.496338 AACTTTCTCTTGTTTTCAGTTCGT 57.504 33.333 0.00 0.00 0.00 3.85
4188 7113 9.429359 TCTGACTTTGTACTAGTACTACTGTAC 57.571 37.037 28.56 18.75 46.89 2.90
4201 7126 2.069273 GTGCGCATCTGACTTTGTACT 58.931 47.619 15.91 0.00 0.00 2.73
4210 7337 2.125391 GCCAGAGTGCGCATCTGA 60.125 61.111 32.83 5.91 45.80 3.27
4211 7338 3.200593 GGCCAGAGTGCGCATCTG 61.201 66.667 28.24 28.24 43.15 2.90
4227 7358 2.393271 AGATGAAAAGAGCCACTCGG 57.607 50.000 0.00 0.00 35.36 4.63
4228 7359 4.116747 ACTAGATGAAAAGAGCCACTCG 57.883 45.455 0.00 0.00 35.36 4.18
4229 7360 7.043059 CGATAAACTAGATGAAAAGAGCCACTC 60.043 40.741 0.00 0.00 0.00 3.51
4230 7361 6.758886 CGATAAACTAGATGAAAAGAGCCACT 59.241 38.462 0.00 0.00 0.00 4.00
4231 7362 6.018669 CCGATAAACTAGATGAAAAGAGCCAC 60.019 42.308 0.00 0.00 0.00 5.01
4232 7363 6.049149 CCGATAAACTAGATGAAAAGAGCCA 58.951 40.000 0.00 0.00 0.00 4.75
4233 7364 5.467063 CCCGATAAACTAGATGAAAAGAGCC 59.533 44.000 0.00 0.00 0.00 4.70
4234 7365 6.281405 TCCCGATAAACTAGATGAAAAGAGC 58.719 40.000 0.00 0.00 0.00 4.09
4364 7512 1.971505 TTCAGCATGTCGGGCCTAGG 61.972 60.000 3.67 3.67 37.40 3.02
4366 7514 0.975556 TCTTCAGCATGTCGGGCCTA 60.976 55.000 0.84 0.00 37.40 3.93
4367 7515 1.841302 TTCTTCAGCATGTCGGGCCT 61.841 55.000 0.84 0.00 37.40 5.19
4368 7516 0.960364 TTTCTTCAGCATGTCGGGCC 60.960 55.000 0.00 0.00 37.40 5.80
4369 7517 0.169009 GTTTCTTCAGCATGTCGGGC 59.831 55.000 0.00 0.00 37.40 6.13
4375 7549 2.096069 CGACACTGGTTTCTTCAGCATG 60.096 50.000 0.00 0.00 35.78 4.06
4384 7558 1.064952 CCACCAAACGACACTGGTTTC 59.935 52.381 0.00 0.00 43.62 2.78
4390 7564 0.889186 GATGGCCACCAAACGACACT 60.889 55.000 8.16 0.00 36.95 3.55
4440 7623 4.393062 AGAACACATTGTCATGGATTCGAC 59.607 41.667 0.00 0.00 35.21 4.20
4448 7631 4.747540 TTTCCGAGAACACATTGTCATG 57.252 40.909 0.00 0.00 36.34 3.07
4449 7632 5.766150 TTTTTCCGAGAACACATTGTCAT 57.234 34.783 0.00 0.00 0.00 3.06
4473 7656 7.127012 TGCCATCACATTATCATGGATTTTT 57.873 32.000 1.21 0.00 39.73 1.94
4474 7657 6.734502 TGCCATCACATTATCATGGATTTT 57.265 33.333 1.21 0.00 39.73 1.82
4475 7658 6.734502 TTGCCATCACATTATCATGGATTT 57.265 33.333 1.21 0.00 39.73 2.17
4476 7659 6.349860 CGATTGCCATCACATTATCATGGATT 60.350 38.462 1.21 0.00 39.73 3.01
4477 7660 5.124936 CGATTGCCATCACATTATCATGGAT 59.875 40.000 1.21 0.00 39.73 3.41
4478 7661 4.456566 CGATTGCCATCACATTATCATGGA 59.543 41.667 1.21 0.00 39.73 3.41
4479 7662 4.729595 CGATTGCCATCACATTATCATGG 58.270 43.478 0.00 0.00 40.24 3.66
4480 7663 4.163552 GCGATTGCCATCACATTATCATG 58.836 43.478 0.00 0.00 33.74 3.07
4508 7691 6.727824 ATGTTCTCTCGTCCAATAAAACAG 57.272 37.500 0.00 0.00 0.00 3.16
4514 7697 7.524717 TGATGATATGTTCTCTCGTCCAATA 57.475 36.000 0.00 0.00 0.00 1.90
4522 7705 8.549548 CAACAAGTCATGATGATATGTTCTCTC 58.450 37.037 19.34 0.00 36.53 3.20
4601 7789 7.655328 CCTAAGATATGCTAATCATCGGAATCC 59.345 40.741 0.00 0.00 36.63 3.01
4604 7792 6.667848 TCCCTAAGATATGCTAATCATCGGAA 59.332 38.462 2.39 0.00 36.63 4.30


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

AutoCloner maintained by Alex Coulton.