Multiple sequence alignment - TraesCS1A01G005300

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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 TraesCS1A01G005300 chr1A 100.000 3461 0 0 1 3461 3012341 3015801 0.000000e+00 6392.0
1 TraesCS1A01G005300 chr1A 92.117 1776 124 12 976 2747 2943543 2945306 0.000000e+00 2490.0
2 TraesCS1A01G005300 chr1A 91.370 1715 135 8 990 2695 3532808 3531098 0.000000e+00 2335.0
3 TraesCS1A01G005300 chr1A 98.148 54 1 0 2694 2747 3015085 3015138 1.020000e-15 95.3
4 TraesCS1A01G005300 chr3D 95.539 1771 78 1 977 2747 560024585 560022816 0.000000e+00 2832.0
5 TraesCS1A01G005300 chr3D 82.249 507 57 16 2747 3241 560022866 560022381 1.160000e-109 407.0
6 TraesCS1A01G005300 chr3D 87.634 186 21 2 761 945 560024874 560024690 7.520000e-52 215.0
7 TraesCS1A01G005300 chr1B 94.637 1734 81 4 976 2698 4954156 4952424 0.000000e+00 2676.0
8 TraesCS1A01G005300 chr1B 93.570 1773 96 8 977 2747 4518698 4516942 0.000000e+00 2627.0
9 TraesCS1A01G005300 chr1B 92.494 1692 119 4 990 2679 70233120 70234805 0.000000e+00 2414.0
10 TraesCS1A01G005300 chr1B 91.158 1787 142 10 976 2747 46830035 46828250 0.000000e+00 2410.0
11 TraesCS1A01G005300 chr1B 90.490 1777 147 12 990 2756 4597257 4595493 0.000000e+00 2326.0
12 TraesCS1A01G005300 chr1B 86.230 748 46 24 2745 3461 4146697 4147418 0.000000e+00 758.0
13 TraesCS1A01G005300 chr1B 85.695 748 50 23 2745 3461 4539681 4538960 0.000000e+00 736.0
14 TraesCS1A01G005300 chr1B 85.143 525 56 11 2754 3270 4595545 4595035 5.120000e-143 518.0
15 TraesCS1A01G005300 chr1B 84.499 529 48 9 2754 3270 46828294 46827788 3.100000e-135 492.0
16 TraesCS1A01G005300 chr1B 81.800 500 41 24 181 664 4543635 4543170 1.170000e-99 374.0
17 TraesCS1A01G005300 chr1B 86.452 310 30 9 2754 3057 4798060 4797757 2.580000e-86 329.0
18 TraesCS1A01G005300 chr1B 85.000 300 33 8 2745 3036 4112197 4112492 9.390000e-76 294.0
19 TraesCS1A01G005300 chr1B 87.195 164 16 3 793 955 46691980 46692139 7.630000e-42 182.0
20 TraesCS1A01G005300 chr1B 83.412 211 11 8 227 437 3935659 3935845 1.280000e-39 174.0
21 TraesCS1A01G005300 chr1B 79.921 254 27 12 3094 3336 4516594 4516354 7.680000e-37 165.0
22 TraesCS1A01G005300 chr1B 92.308 91 7 0 457 547 46691778 46691868 2.800000e-26 130.0
23 TraesCS1A01G005300 chr1B 78.414 227 16 8 515 726 70232631 70232839 2.180000e-22 117.0
24 TraesCS1A01G005300 chr1B 80.833 120 16 5 15 127 46690799 46690918 1.710000e-13 87.9
25 TraesCS1A01G005300 chr1B 100.000 43 0 0 79 121 4543679 4543637 2.860000e-11 80.5
26 TraesCS1A01G005300 chr1B 87.097 62 3 2 181 237 3935596 3935657 8.020000e-07 65.8
27 TraesCS1A01G005300 chr6A 90.940 1766 149 8 990 2747 613493934 613495696 0.000000e+00 2364.0
28 TraesCS1A01G005300 chr6A 84.720 517 57 12 2744 3254 613495642 613496142 6.670000e-137 497.0
29 TraesCS1A01G005300 chr6A 84.578 415 42 11 2754 3156 64064193 64063789 3.240000e-105 392.0
30 TraesCS1A01G005300 chr6A 86.667 90 10 1 868 955 64175025 64174936 7.910000e-17 99.0
31 TraesCS1A01G005300 chr1D 87.054 533 52 10 2745 3270 387427 387949 1.380000e-163 586.0
32 TraesCS1A01G005300 chr1D 77.133 293 51 14 386 664 33983984 33984274 4.620000e-34 156.0
33 TraesCS1A01G005300 chr5B 86.639 479 44 13 2754 3221 60823953 60823484 2.380000e-141 512.0
34 TraesCS1A01G005300 chr5B 88.496 113 13 0 3249 3361 60823494 60823382 1.680000e-28 137.0
35 TraesCS1A01G005300 chr6D 85.542 415 35 11 2755 3156 53142814 53142412 8.940000e-111 411.0
36 TraesCS1A01G005300 chr6D 90.385 52 5 0 3196 3247 51076577 51076628 6.200000e-08 69.4
37 TraesCS1A01G005300 chr5D 90.000 260 21 4 2959 3215 57821831 57822088 7.160000e-87 331.0
38 TraesCS1A01G005300 chr5D 89.286 112 12 0 3249 3360 57822084 57822195 1.300000e-29 141.0
39 TraesCS1A01G005300 chrUn 91.441 222 13 3 3243 3461 318171397 318171615 2.020000e-77 300.0
40 TraesCS1A01G005300 chr4B 84.274 248 26 12 2780 3018 630238642 630238885 2.690000e-56 230.0
41 TraesCS1A01G005300 chr7A 87.791 172 16 4 765 935 631984433 631984600 2.730000e-46 196.0
42 TraesCS1A01G005300 chr7A 80.583 103 10 4 515 613 631984181 631984277 1.720000e-08 71.3
43 TraesCS1A01G005300 chr4A 89.286 140 9 4 802 940 666694028 666693894 1.650000e-38 171.0
44 TraesCS1A01G005300 chr7D 83.523 176 23 5 761 935 548231088 548231258 3.580000e-35 159.0
45 TraesCS1A01G005300 chr7D 84.466 103 8 2 515 613 548230833 548230931 1.020000e-15 95.3
46 TraesCS1A01G005300 chr6B 89.286 56 6 0 3195 3250 120592849 120592794 1.720000e-08 71.3


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 TraesCS1A01G005300 chr1A 3012341 3015801 3460 False 3243.650000 6392 99.0740 1 3461 2 chr1A.!!$F2 3460
1 TraesCS1A01G005300 chr1A 2943543 2945306 1763 False 2490.000000 2490 92.1170 976 2747 1 chr1A.!!$F1 1771
2 TraesCS1A01G005300 chr1A 3531098 3532808 1710 True 2335.000000 2335 91.3700 990 2695 1 chr1A.!!$R1 1705
3 TraesCS1A01G005300 chr3D 560022381 560024874 2493 True 1151.333333 2832 88.4740 761 3241 3 chr3D.!!$R1 2480
4 TraesCS1A01G005300 chr1B 4952424 4954156 1732 True 2676.000000 2676 94.6370 976 2698 1 chr1B.!!$R2 1722
5 TraesCS1A01G005300 chr1B 46827788 46830035 2247 True 1451.000000 2410 87.8285 976 3270 2 chr1B.!!$R6 2294
6 TraesCS1A01G005300 chr1B 4595035 4597257 2222 True 1422.000000 2326 87.8165 990 3270 2 chr1B.!!$R5 2280
7 TraesCS1A01G005300 chr1B 4516354 4518698 2344 True 1396.000000 2627 86.7455 977 3336 2 chr1B.!!$R3 2359
8 TraesCS1A01G005300 chr1B 70232631 70234805 2174 False 1265.500000 2414 85.4540 515 2679 2 chr1B.!!$F5 2164
9 TraesCS1A01G005300 chr1B 4146697 4147418 721 False 758.000000 758 86.2300 2745 3461 1 chr1B.!!$F2 716
10 TraesCS1A01G005300 chr1B 4538960 4543679 4719 True 396.833333 736 89.1650 79 3461 3 chr1B.!!$R4 3382
11 TraesCS1A01G005300 chr6A 613493934 613496142 2208 False 1430.500000 2364 87.8300 990 3254 2 chr6A.!!$F1 2264
12 TraesCS1A01G005300 chr1D 387427 387949 522 False 586.000000 586 87.0540 2745 3270 1 chr1D.!!$F1 525
13 TraesCS1A01G005300 chr5B 60823382 60823953 571 True 324.500000 512 87.5675 2754 3361 2 chr5B.!!$R1 607

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
311 315 0.034337 ACCGCCGTTTCTTGCTTCTA 59.966 50.000 0.00 0.0 0.00 2.10 F
340 344 0.106217 CCTGAGAGACTCCTCCCTCC 60.106 65.000 0.00 0.0 40.30 4.30 F
528 541 0.179116 CTCAGCTCATCGTCTGTGGG 60.179 60.000 0.00 0.0 0.00 4.61 F
794 1919 1.068127 CTAATGATTTGGCCTGCCTGC 59.932 52.381 9.97 0.0 36.94 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 2394 0.523072 GGCGCACAATGATGTCAGTT 59.477 50.000 10.83 0.0 37.82 3.16 R
1893 3482 1.251251 GCAGGTTGAGCCAAAGTGAT 58.749 50.000 0.00 0.0 40.61 3.06 R
1956 3545 4.260253 GCGTAAAGGCTGTTATCAGTAAGC 60.260 45.833 2.85 0.0 43.05 3.09 R
2724 4330 0.956633 TCGAAACGGCTACAGACAGT 59.043 50.000 0.00 0.0 0.00 3.55 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
42 43 2.943036 AAAAAGGTGTAGAAGGCCGA 57.057 45.000 0.00 0.00 0.00 5.54
43 44 2.943036 AAAAGGTGTAGAAGGCCGAA 57.057 45.000 0.00 0.00 0.00 4.30
44 45 2.943036 AAAGGTGTAGAAGGCCGAAA 57.057 45.000 0.00 0.00 0.00 3.46
45 46 2.943036 AAGGTGTAGAAGGCCGAAAA 57.057 45.000 0.00 0.00 0.00 2.29
46 47 3.434940 AAGGTGTAGAAGGCCGAAAAT 57.565 42.857 0.00 0.00 0.00 1.82
47 48 4.563140 AAGGTGTAGAAGGCCGAAAATA 57.437 40.909 0.00 0.00 0.00 1.40
48 49 4.138487 AGGTGTAGAAGGCCGAAAATAG 57.862 45.455 0.00 0.00 0.00 1.73
49 50 2.612672 GGTGTAGAAGGCCGAAAATAGC 59.387 50.000 0.00 0.00 0.00 2.97
50 51 2.284417 GTGTAGAAGGCCGAAAATAGCG 59.716 50.000 0.00 0.00 0.00 4.26
51 52 1.260825 GTAGAAGGCCGAAAATAGCGC 59.739 52.381 0.00 0.00 0.00 5.92
52 53 1.095807 AGAAGGCCGAAAATAGCGCC 61.096 55.000 2.29 0.00 0.00 6.53
53 54 2.060004 GAAGGCCGAAAATAGCGCCC 62.060 60.000 2.29 0.00 0.00 6.13
54 55 3.949047 GGCCGAAAATAGCGCCCG 61.949 66.667 2.29 0.00 0.00 6.13
55 56 3.199891 GCCGAAAATAGCGCCCGT 61.200 61.111 2.29 0.00 0.00 5.28
56 57 2.757056 GCCGAAAATAGCGCCCGTT 61.757 57.895 2.29 0.00 0.00 4.44
57 58 1.061887 CCGAAAATAGCGCCCGTTG 59.938 57.895 2.29 0.00 0.00 4.10
58 59 1.061887 CGAAAATAGCGCCCGTTGG 59.938 57.895 2.29 0.00 0.00 3.77
69 70 4.473520 CCGTTGGCCCGCAGAGAT 62.474 66.667 0.00 0.00 0.00 2.75
70 71 2.436646 CGTTGGCCCGCAGAGATT 60.437 61.111 0.00 0.00 0.00 2.40
71 72 2.464459 CGTTGGCCCGCAGAGATTC 61.464 63.158 0.00 0.00 0.00 2.52
72 73 2.115291 GTTGGCCCGCAGAGATTCC 61.115 63.158 0.00 0.00 0.00 3.01
73 74 2.601702 TTGGCCCGCAGAGATTCCA 61.602 57.895 0.00 0.00 0.00 3.53
74 75 2.203126 GGCCCGCAGAGATTCCAG 60.203 66.667 0.00 0.00 0.00 3.86
75 76 2.735772 GGCCCGCAGAGATTCCAGA 61.736 63.158 0.00 0.00 0.00 3.86
76 77 1.227497 GCCCGCAGAGATTCCAGAG 60.227 63.158 0.00 0.00 0.00 3.35
77 78 1.680522 GCCCGCAGAGATTCCAGAGA 61.681 60.000 0.00 0.00 0.00 3.10
119 120 0.179084 CTCCGCTCCGCTGGAAATTA 60.179 55.000 0.00 0.00 32.89 1.40
120 121 0.461339 TCCGCTCCGCTGGAAATTAC 60.461 55.000 0.00 0.00 31.04 1.89
121 122 0.742990 CCGCTCCGCTGGAAATTACA 60.743 55.000 0.00 0.00 0.00 2.41
122 123 0.652592 CGCTCCGCTGGAAATTACAG 59.347 55.000 0.00 0.00 38.95 2.74
123 124 1.739035 CGCTCCGCTGGAAATTACAGA 60.739 52.381 9.83 0.00 38.20 3.41
124 125 1.936547 GCTCCGCTGGAAATTACAGAG 59.063 52.381 9.83 5.59 38.20 3.35
125 126 2.418746 GCTCCGCTGGAAATTACAGAGA 60.419 50.000 9.83 3.90 37.88 3.10
126 127 3.190874 CTCCGCTGGAAATTACAGAGAC 58.809 50.000 9.83 0.00 37.88 3.36
127 128 2.093658 TCCGCTGGAAATTACAGAGACC 60.094 50.000 9.83 0.00 37.88 3.85
128 129 2.354704 CCGCTGGAAATTACAGAGACCA 60.355 50.000 9.83 0.00 37.88 4.02
129 130 3.334691 CGCTGGAAATTACAGAGACCAA 58.665 45.455 9.83 0.00 37.88 3.67
130 131 3.125316 CGCTGGAAATTACAGAGACCAAC 59.875 47.826 9.83 0.00 37.88 3.77
131 132 4.327680 GCTGGAAATTACAGAGACCAACT 58.672 43.478 9.83 0.00 38.20 3.16
132 133 5.488341 GCTGGAAATTACAGAGACCAACTA 58.512 41.667 9.83 0.00 38.20 2.24
133 134 5.582665 GCTGGAAATTACAGAGACCAACTAG 59.417 44.000 9.83 0.00 38.20 2.57
134 135 6.574465 GCTGGAAATTACAGAGACCAACTAGA 60.574 42.308 9.83 0.00 38.20 2.43
135 136 7.311092 TGGAAATTACAGAGACCAACTAGAA 57.689 36.000 0.00 0.00 0.00 2.10
136 137 7.741785 TGGAAATTACAGAGACCAACTAGAAA 58.258 34.615 0.00 0.00 0.00 2.52
137 138 8.383175 TGGAAATTACAGAGACCAACTAGAAAT 58.617 33.333 0.00 0.00 0.00 2.17
138 139 8.669243 GGAAATTACAGAGACCAACTAGAAATG 58.331 37.037 0.00 0.00 0.00 2.32
139 140 7.617041 AATTACAGAGACCAACTAGAAATGC 57.383 36.000 0.00 0.00 0.00 3.56
140 141 3.589988 ACAGAGACCAACTAGAAATGCG 58.410 45.455 0.00 0.00 0.00 4.73
141 142 3.258372 ACAGAGACCAACTAGAAATGCGA 59.742 43.478 0.00 0.00 0.00 5.10
142 143 3.862267 CAGAGACCAACTAGAAATGCGAG 59.138 47.826 0.00 0.00 0.00 5.03
151 152 2.880963 AGAAATGCGAGACTAGCTCC 57.119 50.000 9.08 0.00 40.70 4.70
162 163 3.100671 AGACTAGCTCCAGGGTTTACTG 58.899 50.000 0.00 0.00 38.21 2.74
163 164 3.097614 GACTAGCTCCAGGGTTTACTGA 58.902 50.000 0.00 0.00 40.97 3.41
164 165 3.707102 GACTAGCTCCAGGGTTTACTGAT 59.293 47.826 0.00 0.00 40.97 2.90
165 166 3.452627 ACTAGCTCCAGGGTTTACTGATG 59.547 47.826 0.00 0.00 40.97 3.07
166 167 1.065126 AGCTCCAGGGTTTACTGATGC 60.065 52.381 0.00 0.00 40.97 3.91
167 168 1.065126 GCTCCAGGGTTTACTGATGCT 60.065 52.381 0.00 0.00 40.97 3.79
168 169 2.911484 CTCCAGGGTTTACTGATGCTC 58.089 52.381 0.00 0.00 40.97 4.26
169 170 2.237143 CTCCAGGGTTTACTGATGCTCA 59.763 50.000 0.00 0.00 40.97 4.26
170 171 2.642311 TCCAGGGTTTACTGATGCTCAA 59.358 45.455 0.00 0.00 40.97 3.02
171 172 3.073798 TCCAGGGTTTACTGATGCTCAAA 59.926 43.478 0.00 0.00 40.97 2.69
172 173 3.826157 CCAGGGTTTACTGATGCTCAAAA 59.174 43.478 0.00 0.00 40.97 2.44
173 174 4.280677 CCAGGGTTTACTGATGCTCAAAAA 59.719 41.667 0.00 0.00 40.97 1.94
200 201 0.960861 GCTCCAGGGTTTACTGCACC 60.961 60.000 0.00 0.00 37.16 5.01
298 302 1.153628 CTCAAGGAAGGTACCGCCG 60.154 63.158 17.72 7.90 43.70 6.46
311 315 0.034337 ACCGCCGTTTCTTGCTTCTA 59.966 50.000 0.00 0.00 0.00 2.10
324 328 3.011566 TGCTTCTACTCTCCTCTCCTG 57.988 52.381 0.00 0.00 0.00 3.86
325 329 2.578480 TGCTTCTACTCTCCTCTCCTGA 59.422 50.000 0.00 0.00 0.00 3.86
326 330 3.214328 GCTTCTACTCTCCTCTCCTGAG 58.786 54.545 0.00 0.00 39.92 3.35
327 331 3.118038 GCTTCTACTCTCCTCTCCTGAGA 60.118 52.174 0.00 0.00 42.73 3.27
337 341 0.923358 TCTCCTGAGAGACTCCTCCC 59.077 60.000 0.00 0.00 44.42 4.30
338 342 0.926293 CTCCTGAGAGACTCCTCCCT 59.074 60.000 0.00 0.00 43.39 4.20
339 343 0.923358 TCCTGAGAGACTCCTCCCTC 59.077 60.000 0.00 0.00 40.30 4.30
340 344 0.106217 CCTGAGAGACTCCTCCCTCC 60.106 65.000 0.00 0.00 40.30 4.30
341 345 0.926293 CTGAGAGACTCCTCCCTCCT 59.074 60.000 0.00 0.00 40.30 3.69
342 346 1.287739 CTGAGAGACTCCTCCCTCCTT 59.712 57.143 0.00 0.00 40.30 3.36
343 347 1.006519 TGAGAGACTCCTCCCTCCTTG 59.993 57.143 0.00 0.00 40.30 3.61
344 348 0.325203 AGAGACTCCTCCCTCCTTGC 60.325 60.000 0.00 0.00 40.30 4.01
345 349 1.671901 GAGACTCCTCCCTCCTTGCG 61.672 65.000 0.00 0.00 33.30 4.85
346 350 1.985116 GACTCCTCCCTCCTTGCGT 60.985 63.158 0.00 0.00 0.00 5.24
347 351 1.536662 ACTCCTCCCTCCTTGCGTT 60.537 57.895 0.00 0.00 0.00 4.84
348 352 1.078848 CTCCTCCCTCCTTGCGTTG 60.079 63.158 0.00 0.00 0.00 4.10
349 353 2.045926 CCTCCCTCCTTGCGTTGG 60.046 66.667 0.00 0.00 0.00 3.77
350 354 2.750350 CTCCCTCCTTGCGTTGGT 59.250 61.111 0.00 0.00 0.00 3.67
351 355 1.073199 CTCCCTCCTTGCGTTGGTT 59.927 57.895 0.00 0.00 0.00 3.67
352 356 0.955919 CTCCCTCCTTGCGTTGGTTC 60.956 60.000 0.00 0.00 0.00 3.62
353 357 1.971695 CCCTCCTTGCGTTGGTTCC 60.972 63.158 0.00 0.00 0.00 3.62
354 358 1.971695 CCTCCTTGCGTTGGTTCCC 60.972 63.158 0.00 0.00 0.00 3.97
355 359 1.971695 CTCCTTGCGTTGGTTCCCC 60.972 63.158 0.00 0.00 0.00 4.81
356 360 2.115266 CCTTGCGTTGGTTCCCCT 59.885 61.111 0.00 0.00 0.00 4.79
357 361 1.530655 CCTTGCGTTGGTTCCCCTT 60.531 57.895 0.00 0.00 0.00 3.95
358 362 1.112916 CCTTGCGTTGGTTCCCCTTT 61.113 55.000 0.00 0.00 0.00 3.11
359 363 0.313987 CTTGCGTTGGTTCCCCTTTC 59.686 55.000 0.00 0.00 0.00 2.62
368 372 1.280998 GGTTCCCCTTTCCTGATTCGA 59.719 52.381 0.00 0.00 0.00 3.71
376 380 4.096984 CCCTTTCCTGATTCGATTTCTTGG 59.903 45.833 0.00 0.00 0.00 3.61
388 392 7.452880 TTCGATTTCTTGGTCTTGATTGATT 57.547 32.000 0.00 0.00 0.00 2.57
389 393 7.452880 TCGATTTCTTGGTCTTGATTGATTT 57.547 32.000 0.00 0.00 0.00 2.17
391 395 7.174772 TCGATTTCTTGGTCTTGATTGATTTGA 59.825 33.333 0.00 0.00 0.00 2.69
392 396 7.972277 CGATTTCTTGGTCTTGATTGATTTGAT 59.028 33.333 0.00 0.00 0.00 2.57
395 399 7.870509 TCTTGGTCTTGATTGATTTGATAGG 57.129 36.000 0.00 0.00 0.00 2.57
396 400 6.830324 TCTTGGTCTTGATTGATTTGATAGGG 59.170 38.462 0.00 0.00 0.00 3.53
397 401 5.448654 TGGTCTTGATTGATTTGATAGGGG 58.551 41.667 0.00 0.00 0.00 4.79
438 442 8.915057 ATCATCCTCATCCATAAACTTAGTTG 57.085 34.615 0.00 0.00 0.00 3.16
513 517 1.004044 AGATTGGCCCTGTGAACTCAG 59.996 52.381 0.00 0.00 35.45 3.35
521 525 1.067283 CCTGTGAACTCAGCTCATCGT 60.067 52.381 0.00 0.00 34.47 3.73
528 541 0.179116 CTCAGCTCATCGTCTGTGGG 60.179 60.000 0.00 0.00 0.00 4.61
535 548 2.679837 CTCATCGTCTGTGGGAAAATGG 59.320 50.000 0.00 0.00 0.00 3.16
541 554 4.006989 CGTCTGTGGGAAAATGGTTGATA 58.993 43.478 0.00 0.00 0.00 2.15
627 640 7.814107 GGTTTTCATGTTCAGATTCAGCAATTA 59.186 33.333 0.00 0.00 0.00 1.40
628 641 8.642020 GTTTTCATGTTCAGATTCAGCAATTAC 58.358 33.333 0.00 0.00 0.00 1.89
635 648 9.719355 TGTTCAGATTCAGCAATTACTAGTAAA 57.281 29.630 18.88 1.58 0.00 2.01
664 677 3.490155 TGCAGAATTGTTTGCGTCAATTG 59.510 39.130 14.88 0.00 42.90 2.32
680 714 4.961551 GTCAATTGTTACGTAATCATGGCG 59.038 41.667 11.86 0.00 0.00 5.69
684 718 3.446799 TGTTACGTAATCATGGCGGTAC 58.553 45.455 11.86 0.00 0.00 3.34
690 724 3.243636 CGTAATCATGGCGGTACCTAGTT 60.244 47.826 10.90 0.00 40.22 2.24
691 725 3.926058 AATCATGGCGGTACCTAGTTT 57.074 42.857 10.90 0.00 40.22 2.66
692 726 3.926058 ATCATGGCGGTACCTAGTTTT 57.074 42.857 10.90 0.00 40.22 2.43
694 728 5.562298 ATCATGGCGGTACCTAGTTTTAT 57.438 39.130 10.90 0.00 40.22 1.40
695 729 5.362105 TCATGGCGGTACCTAGTTTTATT 57.638 39.130 10.90 0.00 40.22 1.40
698 732 7.337167 TCATGGCGGTACCTAGTTTTATTTAA 58.663 34.615 10.90 0.00 40.22 1.52
699 733 7.994334 TCATGGCGGTACCTAGTTTTATTTAAT 59.006 33.333 10.90 0.00 40.22 1.40
700 734 7.556733 TGGCGGTACCTAGTTTTATTTAATG 57.443 36.000 10.90 0.00 40.22 1.90
701 735 7.337167 TGGCGGTACCTAGTTTTATTTAATGA 58.663 34.615 10.90 0.00 40.22 2.57
702 736 7.994334 TGGCGGTACCTAGTTTTATTTAATGAT 59.006 33.333 10.90 0.00 40.22 2.45
703 737 8.287503 GGCGGTACCTAGTTTTATTTAATGATG 58.712 37.037 10.90 0.00 34.51 3.07
704 738 8.833493 GCGGTACCTAGTTTTATTTAATGATGT 58.167 33.333 10.90 0.00 0.00 3.06
714 748 6.942532 TTATTTAATGATGTCACCTGGAGC 57.057 37.500 0.00 0.00 0.00 4.70
724 758 2.095718 GTCACCTGGAGCGTCATTTTTC 60.096 50.000 0.00 0.00 0.00 2.29
726 760 2.095567 CACCTGGAGCGTCATTTTTCTG 60.096 50.000 0.00 0.00 0.00 3.02
727 761 2.224523 ACCTGGAGCGTCATTTTTCTGA 60.225 45.455 0.00 0.00 0.00 3.27
729 763 4.191544 CCTGGAGCGTCATTTTTCTGATA 58.808 43.478 0.00 0.00 0.00 2.15
730 764 4.818546 CCTGGAGCGTCATTTTTCTGATAT 59.181 41.667 0.00 0.00 0.00 1.63
733 767 7.173907 CCTGGAGCGTCATTTTTCTGATATTAT 59.826 37.037 0.00 0.00 0.00 1.28
734 768 9.208022 CTGGAGCGTCATTTTTCTGATATTATA 57.792 33.333 0.00 0.00 0.00 0.98
735 769 9.725019 TGGAGCGTCATTTTTCTGATATTATAT 57.275 29.630 0.00 0.00 0.00 0.86
794 1919 1.068127 CTAATGATTTGGCCTGCCTGC 59.932 52.381 9.97 0.00 36.94 4.85
913 2050 6.016276 ACGGATACAGAAAATGCTCAAACTTT 60.016 34.615 0.00 0.00 0.00 2.66
922 2059 7.702348 AGAAAATGCTCAAACTTTGTCAGTAAC 59.298 33.333 1.44 0.84 32.94 2.50
949 2086 5.571784 TCTTCGTAATGATTGTCTACCGT 57.428 39.130 0.00 0.00 0.00 4.83
955 2092 4.801330 AATGATTGTCTACCGTCAGTGA 57.199 40.909 0.00 0.00 0.00 3.41
956 2093 5.344743 AATGATTGTCTACCGTCAGTGAT 57.655 39.130 0.00 0.00 0.00 3.06
959 2096 7.761038 ATGATTGTCTACCGTCAGTGATATA 57.239 36.000 0.00 0.00 0.00 0.86
960 2097 7.761038 TGATTGTCTACCGTCAGTGATATAT 57.239 36.000 0.00 0.00 0.00 0.86
962 2099 8.297426 TGATTGTCTACCGTCAGTGATATATTC 58.703 37.037 0.00 0.00 0.00 1.75
963 2100 7.818997 TTGTCTACCGTCAGTGATATATTCT 57.181 36.000 0.00 0.00 0.00 2.40
964 2101 7.203255 TGTCTACCGTCAGTGATATATTCTG 57.797 40.000 0.00 10.64 0.00 3.02
969 2194 7.761038 ACCGTCAGTGATATATTCTGATGTA 57.239 36.000 23.78 6.91 41.09 2.29
970 2195 8.354711 ACCGTCAGTGATATATTCTGATGTAT 57.645 34.615 23.78 16.06 41.09 2.29
972 2197 7.641802 CCGTCAGTGATATATTCTGATGTATCG 59.358 40.741 23.78 19.12 41.09 2.92
1163 2394 4.556501 CGGTCTTTGCATTGCTACAAAAGA 60.557 41.667 14.46 14.46 35.49 2.52
1684 3273 3.276857 GTGGTCTATGACTCCTCGTACA 58.723 50.000 0.00 0.00 32.47 2.90
1893 3482 4.766891 AGCTGCAGCAACCTTAAAAGAATA 59.233 37.500 38.24 0.00 45.16 1.75
1930 3519 2.550180 CTGCAGCGCTACTCTAGTGATA 59.450 50.000 10.99 0.00 38.55 2.15
1956 3545 0.243907 ATTGTGAGACCAGGACGTCG 59.756 55.000 9.92 0.00 37.85 5.12
1957 3546 2.126424 GTGAGACCAGGACGTCGC 60.126 66.667 9.92 2.53 37.85 5.19
1996 3585 0.247736 CGCTCTAGCCCTCAACTGTT 59.752 55.000 0.00 0.00 37.91 3.16
2696 4302 7.303634 CACCACTTGTGTATTACTATCAACC 57.696 40.000 0.00 0.00 40.26 3.77
2697 4303 6.035650 CACCACTTGTGTATTACTATCAACCG 59.964 42.308 0.00 0.00 40.26 4.44
2698 4304 6.103997 CCACTTGTGTATTACTATCAACCGT 58.896 40.000 0.00 0.00 0.00 4.83
2699 4305 7.093814 ACCACTTGTGTATTACTATCAACCGTA 60.094 37.037 0.00 0.00 0.00 4.02
2700 4306 7.221452 CCACTTGTGTATTACTATCAACCGTAC 59.779 40.741 0.00 0.00 0.00 3.67
2701 4307 7.756272 CACTTGTGTATTACTATCAACCGTACA 59.244 37.037 0.00 0.00 0.00 2.90
2702 4308 8.472413 ACTTGTGTATTACTATCAACCGTACAT 58.528 33.333 0.00 0.00 0.00 2.29
2703 4309 9.955208 CTTGTGTATTACTATCAACCGTACATA 57.045 33.333 0.00 0.00 0.00 2.29
2710 4316 9.706691 ATTACTATCAACCGTACATAATTCTGG 57.293 33.333 0.00 0.00 0.00 3.86
2711 4317 7.120923 ACTATCAACCGTACATAATTCTGGT 57.879 36.000 0.00 0.00 0.00 4.00
2712 4318 7.562135 ACTATCAACCGTACATAATTCTGGTT 58.438 34.615 0.00 0.00 40.16 3.67
2713 4319 8.698210 ACTATCAACCGTACATAATTCTGGTTA 58.302 33.333 0.00 0.00 37.60 2.85
2714 4320 7.781548 ATCAACCGTACATAATTCTGGTTAC 57.218 36.000 0.00 0.00 37.60 2.50
2715 4321 6.938507 TCAACCGTACATAATTCTGGTTACT 58.061 36.000 0.00 0.00 37.60 2.24
2716 4322 7.388437 TCAACCGTACATAATTCTGGTTACTT 58.612 34.615 0.00 0.00 37.60 2.24
2717 4323 7.879160 TCAACCGTACATAATTCTGGTTACTTT 59.121 33.333 0.00 0.00 37.60 2.66
2718 4324 9.153721 CAACCGTACATAATTCTGGTTACTTTA 57.846 33.333 0.00 0.00 37.60 1.85
2719 4325 9.895138 AACCGTACATAATTCTGGTTACTTTAT 57.105 29.630 0.00 0.00 37.90 1.40
2720 4326 9.895138 ACCGTACATAATTCTGGTTACTTTATT 57.105 29.630 0.00 0.00 0.00 1.40
2731 4337 9.706691 TTCTGGTTACTTTATTTCTACTGTCTG 57.293 33.333 0.00 0.00 0.00 3.51
2732 4338 8.867097 TCTGGTTACTTTATTTCTACTGTCTGT 58.133 33.333 0.00 0.00 0.00 3.41
2735 4341 9.085250 GGTTACTTTATTTCTACTGTCTGTAGC 57.915 37.037 11.10 0.00 46.15 3.58
2736 4342 9.085250 GTTACTTTATTTCTACTGTCTGTAGCC 57.915 37.037 11.10 0.00 46.15 3.93
2737 4343 6.331061 ACTTTATTTCTACTGTCTGTAGCCG 58.669 40.000 11.10 0.00 46.15 5.52
2738 4344 5.909621 TTATTTCTACTGTCTGTAGCCGT 57.090 39.130 11.10 3.59 46.15 5.68
2739 4345 4.803098 ATTTCTACTGTCTGTAGCCGTT 57.197 40.909 11.10 0.00 46.15 4.44
2740 4346 4.595762 TTTCTACTGTCTGTAGCCGTTT 57.404 40.909 11.10 0.00 46.15 3.60
2741 4347 3.844577 TCTACTGTCTGTAGCCGTTTC 57.155 47.619 11.10 0.00 46.15 2.78
2742 4348 2.161012 TCTACTGTCTGTAGCCGTTTCG 59.839 50.000 11.10 0.00 46.15 3.46
2743 4349 0.956633 ACTGTCTGTAGCCGTTTCGA 59.043 50.000 0.00 0.00 0.00 3.71
2752 4362 2.228138 AGCCGTTTCGAAACTGTACA 57.772 45.000 31.88 0.00 36.77 2.90
2852 4463 2.864097 GCTGTGGAGGCACTATATGACG 60.864 54.545 0.00 0.00 43.63 4.35
2867 4482 7.711772 CACTATATGACGGGTTGGTGTTATTTA 59.288 37.037 0.00 0.00 0.00 1.40
3020 4644 0.719465 GGACATGTACAAAGGCGACG 59.281 55.000 2.19 0.00 0.00 5.12
3021 4645 0.094730 GACATGTACAAAGGCGACGC 59.905 55.000 12.43 12.43 0.00 5.19
3168 4897 4.538746 ACTGAAACTACTGAAGGCCTAC 57.461 45.455 5.16 0.00 0.00 3.18
3223 4962 2.422479 CACATCATGTCTTTGCTCTGGG 59.578 50.000 0.00 0.00 0.00 4.45
3292 5042 9.334947 TGTCTACCTATCAATAGTATATACGGC 57.665 37.037 7.23 0.00 0.00 5.68
3294 5048 6.630444 ACCTATCAATAGTATATACGGCGG 57.370 41.667 13.24 4.05 0.00 6.13
3351 5105 5.825532 TGAGGGATGAGATATCGAGATTCT 58.174 41.667 0.00 0.00 0.00 2.40
3397 5151 7.550906 AGTCTAGTACAAAGATCCTGAAATTGC 59.449 37.037 0.00 0.00 0.00 3.56
3407 5161 7.900782 AGATCCTGAAATTGCAAATCTTTTG 57.099 32.000 1.71 0.00 0.00 2.44
3431 5185 6.979817 TGTTTTAGTAACAAGACAGCTCGTTA 59.020 34.615 0.00 0.00 0.00 3.18
3432 5186 6.998258 TTTAGTAACAAGACAGCTCGTTAC 57.002 37.500 0.00 0.00 42.48 2.50
3433 5187 4.579454 AGTAACAAGACAGCTCGTTACA 57.421 40.909 16.01 0.00 43.86 2.41
3434 5188 5.135508 AGTAACAAGACAGCTCGTTACAT 57.864 39.130 16.01 5.12 43.86 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.943036 TCGGCCTTCTACACCTTTTT 57.057 45.000 0.00 0.00 0.00 1.94
24 25 2.943036 TTCGGCCTTCTACACCTTTT 57.057 45.000 0.00 0.00 0.00 2.27
25 26 2.943036 TTTCGGCCTTCTACACCTTT 57.057 45.000 0.00 0.00 0.00 3.11
26 27 2.943036 TTTTCGGCCTTCTACACCTT 57.057 45.000 0.00 0.00 0.00 3.50
27 28 3.681874 GCTATTTTCGGCCTTCTACACCT 60.682 47.826 0.00 0.00 0.00 4.00
28 29 2.612672 GCTATTTTCGGCCTTCTACACC 59.387 50.000 0.00 0.00 0.00 4.16
29 30 2.284417 CGCTATTTTCGGCCTTCTACAC 59.716 50.000 0.00 0.00 0.00 2.90
30 31 2.546778 CGCTATTTTCGGCCTTCTACA 58.453 47.619 0.00 0.00 0.00 2.74
31 32 1.260825 GCGCTATTTTCGGCCTTCTAC 59.739 52.381 0.00 0.00 0.00 2.59
32 33 1.578583 GCGCTATTTTCGGCCTTCTA 58.421 50.000 0.00 0.00 0.00 2.10
33 34 1.095807 GGCGCTATTTTCGGCCTTCT 61.096 55.000 7.64 0.00 45.13 2.85
34 35 1.355563 GGCGCTATTTTCGGCCTTC 59.644 57.895 7.64 0.00 45.13 3.46
35 36 3.509659 GGCGCTATTTTCGGCCTT 58.490 55.556 7.64 0.00 45.13 4.35
39 40 1.061887 CAACGGGCGCTATTTTCGG 59.938 57.895 7.64 0.00 0.00 4.30
40 41 1.061887 CCAACGGGCGCTATTTTCG 59.938 57.895 7.64 4.88 0.00 3.46
52 53 3.976701 AATCTCTGCGGGCCAACGG 62.977 63.158 4.39 0.00 0.00 4.44
53 54 2.436646 AATCTCTGCGGGCCAACG 60.437 61.111 4.39 0.00 0.00 4.10
54 55 2.115291 GGAATCTCTGCGGGCCAAC 61.115 63.158 4.39 0.00 0.00 3.77
55 56 2.272146 GGAATCTCTGCGGGCCAA 59.728 61.111 4.39 0.00 0.00 4.52
56 57 3.008517 TGGAATCTCTGCGGGCCA 61.009 61.111 4.39 0.00 0.00 5.36
57 58 2.203126 CTGGAATCTCTGCGGGCC 60.203 66.667 0.00 0.00 0.00 5.80
58 59 1.227497 CTCTGGAATCTCTGCGGGC 60.227 63.158 0.00 0.00 0.00 6.13
59 60 0.103937 GTCTCTGGAATCTCTGCGGG 59.896 60.000 0.00 0.00 0.00 6.13
60 61 0.248825 CGTCTCTGGAATCTCTGCGG 60.249 60.000 0.00 0.00 0.00 5.69
61 62 0.248825 CCGTCTCTGGAATCTCTGCG 60.249 60.000 0.00 0.00 0.00 5.18
62 63 0.529555 GCCGTCTCTGGAATCTCTGC 60.530 60.000 0.00 0.00 0.00 4.26
63 64 0.248825 CGCCGTCTCTGGAATCTCTG 60.249 60.000 0.00 0.00 0.00 3.35
64 65 2.010582 GCGCCGTCTCTGGAATCTCT 62.011 60.000 0.00 0.00 0.00 3.10
65 66 1.590259 GCGCCGTCTCTGGAATCTC 60.590 63.158 0.00 0.00 0.00 2.75
66 67 2.055042 AGCGCCGTCTCTGGAATCT 61.055 57.895 2.29 0.00 0.00 2.40
67 68 1.880340 CAGCGCCGTCTCTGGAATC 60.880 63.158 2.29 0.00 0.00 2.52
68 69 2.185350 CAGCGCCGTCTCTGGAAT 59.815 61.111 2.29 0.00 0.00 3.01
69 70 4.742201 GCAGCGCCGTCTCTGGAA 62.742 66.667 2.29 0.00 0.00 3.53
119 120 3.258372 TCGCATTTCTAGTTGGTCTCTGT 59.742 43.478 0.00 0.00 0.00 3.41
120 121 3.849911 TCGCATTTCTAGTTGGTCTCTG 58.150 45.455 0.00 0.00 0.00 3.35
121 122 3.764434 TCTCGCATTTCTAGTTGGTCTCT 59.236 43.478 0.00 0.00 0.00 3.10
122 123 3.860536 GTCTCGCATTTCTAGTTGGTCTC 59.139 47.826 0.00 0.00 0.00 3.36
123 124 3.511934 AGTCTCGCATTTCTAGTTGGTCT 59.488 43.478 0.00 0.00 0.00 3.85
124 125 3.851098 AGTCTCGCATTTCTAGTTGGTC 58.149 45.455 0.00 0.00 0.00 4.02
125 126 3.963428 AGTCTCGCATTTCTAGTTGGT 57.037 42.857 0.00 0.00 0.00 3.67
126 127 3.799420 GCTAGTCTCGCATTTCTAGTTGG 59.201 47.826 0.00 0.00 34.28 3.77
127 128 4.677584 AGCTAGTCTCGCATTTCTAGTTG 58.322 43.478 0.00 0.00 34.28 3.16
128 129 4.202070 GGAGCTAGTCTCGCATTTCTAGTT 60.202 45.833 0.00 0.00 42.82 2.24
129 130 3.316868 GGAGCTAGTCTCGCATTTCTAGT 59.683 47.826 0.00 0.00 42.82 2.57
130 131 3.316588 TGGAGCTAGTCTCGCATTTCTAG 59.683 47.826 0.00 0.00 42.82 2.43
131 132 3.288092 TGGAGCTAGTCTCGCATTTCTA 58.712 45.455 0.00 0.00 42.82 2.10
132 133 2.100584 CTGGAGCTAGTCTCGCATTTCT 59.899 50.000 0.00 0.00 42.82 2.52
133 134 2.468831 CTGGAGCTAGTCTCGCATTTC 58.531 52.381 0.00 0.00 42.82 2.17
134 135 1.137872 CCTGGAGCTAGTCTCGCATTT 59.862 52.381 0.00 0.00 42.82 2.32
135 136 0.749649 CCTGGAGCTAGTCTCGCATT 59.250 55.000 0.00 0.00 42.82 3.56
136 137 1.112315 CCCTGGAGCTAGTCTCGCAT 61.112 60.000 0.00 0.00 42.82 4.73
137 138 1.754621 CCCTGGAGCTAGTCTCGCA 60.755 63.158 0.00 6.63 42.82 5.10
138 139 1.324005 AACCCTGGAGCTAGTCTCGC 61.324 60.000 0.00 0.00 42.82 5.03
139 140 1.187087 AAACCCTGGAGCTAGTCTCG 58.813 55.000 0.00 0.00 42.82 4.04
140 141 3.131400 CAGTAAACCCTGGAGCTAGTCTC 59.869 52.174 0.00 5.83 41.15 3.36
141 142 3.100671 CAGTAAACCCTGGAGCTAGTCT 58.899 50.000 0.00 0.00 0.00 3.24
142 143 3.097614 TCAGTAAACCCTGGAGCTAGTC 58.902 50.000 0.00 0.00 33.14 2.59
176 177 2.628178 GCAGTAAACCCTGGAGCTTTTT 59.372 45.455 0.00 0.00 32.92 1.94
177 178 2.239400 GCAGTAAACCCTGGAGCTTTT 58.761 47.619 0.00 0.00 32.92 2.27
178 179 1.144913 TGCAGTAAACCCTGGAGCTTT 59.855 47.619 0.00 0.00 32.92 3.51
179 180 0.771127 TGCAGTAAACCCTGGAGCTT 59.229 50.000 0.00 0.00 32.92 3.74
180 181 0.036875 GTGCAGTAAACCCTGGAGCT 59.963 55.000 0.00 0.00 33.14 4.09
181 182 0.960861 GGTGCAGTAAACCCTGGAGC 60.961 60.000 0.00 0.00 42.58 4.70
182 183 3.249687 GGTGCAGTAAACCCTGGAG 57.750 57.895 0.00 0.00 33.14 3.86
188 189 2.633488 GAGATGAGGGTGCAGTAAACC 58.367 52.381 0.00 0.00 36.94 3.27
189 190 2.237392 AGGAGATGAGGGTGCAGTAAAC 59.763 50.000 0.00 0.00 0.00 2.01
190 191 2.501723 GAGGAGATGAGGGTGCAGTAAA 59.498 50.000 0.00 0.00 0.00 2.01
191 192 2.111384 GAGGAGATGAGGGTGCAGTAA 58.889 52.381 0.00 0.00 0.00 2.24
192 193 1.289231 AGAGGAGATGAGGGTGCAGTA 59.711 52.381 0.00 0.00 0.00 2.74
193 194 0.042431 AGAGGAGATGAGGGTGCAGT 59.958 55.000 0.00 0.00 0.00 4.40
194 195 0.752054 GAGAGGAGATGAGGGTGCAG 59.248 60.000 0.00 0.00 0.00 4.41
195 196 0.689080 GGAGAGGAGATGAGGGTGCA 60.689 60.000 0.00 0.00 0.00 4.57
196 197 1.743321 CGGAGAGGAGATGAGGGTGC 61.743 65.000 0.00 0.00 0.00 5.01
200 201 2.560119 CGCCGGAGAGGAGATGAGG 61.560 68.421 5.05 0.00 43.02 3.86
237 238 4.019141 GGAGGAGATAGAGAATAGACCGGA 60.019 50.000 9.46 0.00 0.00 5.14
238 239 4.266714 GGAGGAGATAGAGAATAGACCGG 58.733 52.174 0.00 0.00 0.00 5.28
298 302 5.400066 AGAGGAGAGTAGAAGCAAGAAAC 57.600 43.478 0.00 0.00 0.00 2.78
325 329 0.325203 GCAAGGAGGGAGGAGTCTCT 60.325 60.000 0.00 0.00 39.86 3.10
326 330 1.671901 CGCAAGGAGGGAGGAGTCTC 61.672 65.000 0.00 0.00 39.25 3.36
327 331 1.684049 CGCAAGGAGGGAGGAGTCT 60.684 63.158 0.00 0.00 0.00 3.24
328 332 1.545706 AACGCAAGGAGGGAGGAGTC 61.546 60.000 0.00 0.00 46.39 3.36
329 333 1.536662 AACGCAAGGAGGGAGGAGT 60.537 57.895 0.00 0.00 46.39 3.85
330 334 1.078848 CAACGCAAGGAGGGAGGAG 60.079 63.158 0.00 0.00 46.39 3.69
333 337 0.955919 GAACCAACGCAAGGAGGGAG 60.956 60.000 0.00 0.00 46.39 4.30
334 338 1.072505 GAACCAACGCAAGGAGGGA 59.927 57.895 0.00 0.00 46.39 4.20
335 339 1.971695 GGAACCAACGCAAGGAGGG 60.972 63.158 0.00 0.00 46.39 4.30
336 340 3.668386 GGAACCAACGCAAGGAGG 58.332 61.111 0.00 0.00 46.39 4.30
349 353 2.781681 TCGAATCAGGAAAGGGGAAC 57.218 50.000 0.00 0.00 0.00 3.62
350 354 4.018415 AGAAATCGAATCAGGAAAGGGGAA 60.018 41.667 0.00 0.00 0.00 3.97
351 355 3.523564 AGAAATCGAATCAGGAAAGGGGA 59.476 43.478 0.00 0.00 0.00 4.81
352 356 3.891049 AGAAATCGAATCAGGAAAGGGG 58.109 45.455 0.00 0.00 0.00 4.79
353 357 4.096984 CCAAGAAATCGAATCAGGAAAGGG 59.903 45.833 0.00 0.00 0.00 3.95
354 358 4.702131 ACCAAGAAATCGAATCAGGAAAGG 59.298 41.667 15.30 3.05 0.00 3.11
355 359 5.645497 AGACCAAGAAATCGAATCAGGAAAG 59.355 40.000 15.30 0.00 0.00 2.62
356 360 5.560724 AGACCAAGAAATCGAATCAGGAAA 58.439 37.500 15.30 0.00 0.00 3.13
357 361 5.165961 AGACCAAGAAATCGAATCAGGAA 57.834 39.130 15.30 0.00 0.00 3.36
358 362 4.826274 AGACCAAGAAATCGAATCAGGA 57.174 40.909 15.30 0.00 0.00 3.86
359 363 4.937620 TCAAGACCAAGAAATCGAATCAGG 59.062 41.667 0.00 0.44 0.00 3.86
376 380 6.039829 GGTTCCCCTATCAAATCAATCAAGAC 59.960 42.308 0.00 0.00 0.00 3.01
388 392 1.004979 CCGGTTTGGTTCCCCTATCAA 59.995 52.381 0.00 0.00 0.00 2.57
389 393 0.621609 CCGGTTTGGTTCCCCTATCA 59.378 55.000 0.00 0.00 0.00 2.15
466 470 9.914834 ATCTGTTCAACTAGAGAATACTAGAGT 57.085 33.333 9.28 0.00 41.42 3.24
474 478 7.930865 GCCAATCTATCTGTTCAACTAGAGAAT 59.069 37.037 0.00 0.00 0.00 2.40
476 480 6.183360 GGCCAATCTATCTGTTCAACTAGAGA 60.183 42.308 0.00 0.00 0.00 3.10
478 482 5.163301 GGGCCAATCTATCTGTTCAACTAGA 60.163 44.000 4.39 0.00 0.00 2.43
480 484 4.721776 AGGGCCAATCTATCTGTTCAACTA 59.278 41.667 6.18 0.00 0.00 2.24
481 485 3.525199 AGGGCCAATCTATCTGTTCAACT 59.475 43.478 6.18 0.00 0.00 3.16
482 486 3.629398 CAGGGCCAATCTATCTGTTCAAC 59.371 47.826 6.18 0.00 0.00 3.18
484 488 2.846206 ACAGGGCCAATCTATCTGTTCA 59.154 45.455 6.18 0.00 35.44 3.18
485 489 3.118261 TCACAGGGCCAATCTATCTGTTC 60.118 47.826 6.18 0.00 36.66 3.18
486 490 2.846206 TCACAGGGCCAATCTATCTGTT 59.154 45.455 6.18 0.00 36.66 3.16
487 491 2.481441 TCACAGGGCCAATCTATCTGT 58.519 47.619 6.18 3.56 38.99 3.41
488 492 3.118112 AGTTCACAGGGCCAATCTATCTG 60.118 47.826 6.18 2.81 0.00 2.90
489 493 3.118531 AGTTCACAGGGCCAATCTATCT 58.881 45.455 6.18 0.00 0.00 1.98
490 494 3.118261 TGAGTTCACAGGGCCAATCTATC 60.118 47.826 6.18 0.00 0.00 2.08
491 495 2.846206 TGAGTTCACAGGGCCAATCTAT 59.154 45.455 6.18 0.00 0.00 1.98
496 500 1.228245 GCTGAGTTCACAGGGCCAA 60.228 57.895 6.18 0.00 38.22 4.52
513 517 1.808411 TTTTCCCACAGACGATGAGC 58.192 50.000 0.00 0.00 0.00 4.26
521 525 5.200483 GGATATCAACCATTTTCCCACAGA 58.800 41.667 4.83 0.00 0.00 3.41
528 541 8.753497 AGAAAGTAGGGATATCAACCATTTTC 57.247 34.615 4.83 8.67 0.00 2.29
535 548 7.201741 GGCAAGAAAGAAAGTAGGGATATCAAC 60.202 40.741 4.83 0.00 0.00 3.18
541 554 3.333680 TGGGCAAGAAAGAAAGTAGGGAT 59.666 43.478 0.00 0.00 0.00 3.85
664 677 2.796593 GGTACCGCCATGATTACGTAAC 59.203 50.000 10.81 5.62 37.17 2.50
690 724 6.038161 CGCTCCAGGTGACATCATTAAATAAA 59.962 38.462 0.00 0.00 0.00 1.40
691 725 5.527214 CGCTCCAGGTGACATCATTAAATAA 59.473 40.000 0.00 0.00 0.00 1.40
692 726 5.056480 CGCTCCAGGTGACATCATTAAATA 58.944 41.667 0.00 0.00 0.00 1.40
694 728 3.270027 CGCTCCAGGTGACATCATTAAA 58.730 45.455 0.00 0.00 0.00 1.52
695 729 2.236146 ACGCTCCAGGTGACATCATTAA 59.764 45.455 0.00 0.00 0.00 1.40
698 732 0.176680 GACGCTCCAGGTGACATCAT 59.823 55.000 0.00 0.00 0.00 2.45
699 733 1.184970 TGACGCTCCAGGTGACATCA 61.185 55.000 0.00 0.00 0.00 3.07
700 734 0.176680 ATGACGCTCCAGGTGACATC 59.823 55.000 0.00 0.00 36.44 3.06
701 735 0.615331 AATGACGCTCCAGGTGACAT 59.385 50.000 0.00 0.00 41.08 3.06
702 736 0.396435 AAATGACGCTCCAGGTGACA 59.604 50.000 0.00 0.00 35.03 3.58
703 737 1.523758 AAAATGACGCTCCAGGTGAC 58.476 50.000 0.00 0.00 0.00 3.67
704 738 2.151202 GAAAAATGACGCTCCAGGTGA 58.849 47.619 0.00 0.00 0.00 4.02
705 739 2.095567 CAGAAAAATGACGCTCCAGGTG 60.096 50.000 0.00 0.00 0.00 4.00
706 740 2.154462 CAGAAAAATGACGCTCCAGGT 58.846 47.619 0.00 0.00 0.00 4.00
734 768 9.107177 CTGATGAACTTTGAGCACTTCTATTAT 57.893 33.333 0.00 0.00 0.00 1.28
735 769 8.097038 ACTGATGAACTTTGAGCACTTCTATTA 58.903 33.333 0.00 0.00 0.00 0.98
737 771 6.471146 ACTGATGAACTTTGAGCACTTCTAT 58.529 36.000 0.00 0.00 0.00 1.98
738 772 5.858381 ACTGATGAACTTTGAGCACTTCTA 58.142 37.500 0.00 0.00 0.00 2.10
739 773 4.712476 ACTGATGAACTTTGAGCACTTCT 58.288 39.130 0.00 0.00 0.00 2.85
740 774 5.390356 GCTACTGATGAACTTTGAGCACTTC 60.390 44.000 0.00 0.00 0.00 3.01
774 1899 1.068127 GCAGGCAGGCCAAATCATTAG 59.932 52.381 13.63 0.00 38.92 1.73
821 1946 5.144100 AGCTAGCACCTTATCTGTGTCTAT 58.856 41.667 18.83 0.00 36.11 1.98
922 2059 8.639428 CGGTAGACAATCATTACGAAGAATATG 58.361 37.037 0.00 0.00 0.00 1.78
939 2076 7.501225 TCAGAATATATCACTGACGGTAGACAA 59.499 37.037 14.53 0.00 36.04 3.18
945 2082 6.656632 ACATCAGAATATATCACTGACGGT 57.343 37.500 18.44 16.70 42.18 4.83
946 2083 7.641802 CGATACATCAGAATATATCACTGACGG 59.358 40.741 18.44 16.28 42.18 4.79
959 2096 9.424319 GTACCATTCATTACGATACATCAGAAT 57.576 33.333 0.00 0.00 0.00 2.40
960 2097 8.417884 TGTACCATTCATTACGATACATCAGAA 58.582 33.333 0.00 0.00 0.00 3.02
962 2099 7.148738 GCTGTACCATTCATTACGATACATCAG 60.149 40.741 0.00 0.00 0.00 2.90
963 2100 6.645003 GCTGTACCATTCATTACGATACATCA 59.355 38.462 0.00 0.00 0.00 3.07
964 2101 6.868864 AGCTGTACCATTCATTACGATACATC 59.131 38.462 0.00 0.00 0.00 3.06
969 2194 5.276461 TCAGCTGTACCATTCATTACGAT 57.724 39.130 14.67 0.00 0.00 3.73
970 2195 4.729227 TCAGCTGTACCATTCATTACGA 57.271 40.909 14.67 0.00 0.00 3.43
972 2197 7.088589 ACAATTCAGCTGTACCATTCATTAC 57.911 36.000 14.67 0.00 0.00 1.89
974 2199 6.594788 AACAATTCAGCTGTACCATTCATT 57.405 33.333 14.67 3.14 0.00 2.57
979 2204 3.937814 TCGAACAATTCAGCTGTACCAT 58.062 40.909 14.67 0.00 0.00 3.55
1163 2394 0.523072 GGCGCACAATGATGTCAGTT 59.477 50.000 10.83 0.00 37.82 3.16
1200 2431 7.703058 ACCAGAGTAATCGATTTCCAATTTT 57.297 32.000 17.19 0.00 0.00 1.82
1893 3482 1.251251 GCAGGTTGAGCCAAAGTGAT 58.749 50.000 0.00 0.00 40.61 3.06
1930 3519 4.382040 CGTCCTGGTCTCACAATAGTTGAT 60.382 45.833 0.00 0.00 0.00 2.57
1956 3545 4.260253 GCGTAAAGGCTGTTATCAGTAAGC 60.260 45.833 2.85 0.00 43.05 3.09
1957 3546 5.109903 AGCGTAAAGGCTGTTATCAGTAAG 58.890 41.667 2.85 0.00 42.86 2.34
1996 3585 5.835280 TGAGGTCTATCATCTGAAGCATACA 59.165 40.000 0.00 0.00 0.00 2.29
2620 4216 4.450419 GCCGTCCAAAGATCATCATTAGAG 59.550 45.833 0.00 0.00 0.00 2.43
2693 4299 9.895138 ATAAAGTAACCAGAATTATGTACGGTT 57.105 29.630 0.00 0.00 39.87 4.44
2694 4300 9.895138 AATAAAGTAACCAGAATTATGTACGGT 57.105 29.630 0.00 0.00 0.00 4.83
2705 4311 9.706691 CAGACAGTAGAAATAAAGTAACCAGAA 57.293 33.333 0.00 0.00 0.00 3.02
2706 4312 8.867097 ACAGACAGTAGAAATAAAGTAACCAGA 58.133 33.333 0.00 0.00 0.00 3.86
2722 4328 8.912916 AGTTTCGAAACGGCTACAGACAGTAG 62.913 46.154 29.72 0.80 46.11 2.57
2723 4329 2.153645 TCGAAACGGCTACAGACAGTA 58.846 47.619 0.00 0.00 0.00 2.74
2724 4330 0.956633 TCGAAACGGCTACAGACAGT 59.043 50.000 0.00 0.00 0.00 3.55
2725 4331 2.060326 TTCGAAACGGCTACAGACAG 57.940 50.000 0.00 0.00 0.00 3.51
2726 4332 2.129607 GTTTCGAAACGGCTACAGACA 58.870 47.619 24.02 0.00 0.00 3.41
2727 4333 2.155155 CAGTTTCGAAACGGCTACAGAC 59.845 50.000 29.72 8.12 43.51 3.51
2728 4334 2.223876 ACAGTTTCGAAACGGCTACAGA 60.224 45.455 32.06 0.00 43.51 3.41
2729 4335 2.132762 ACAGTTTCGAAACGGCTACAG 58.867 47.619 32.06 19.75 43.51 2.74
2730 4336 2.228138 ACAGTTTCGAAACGGCTACA 57.772 45.000 32.06 0.00 43.51 2.74
2731 4337 3.052036 TGTACAGTTTCGAAACGGCTAC 58.948 45.455 32.06 28.83 43.51 3.58
2732 4338 3.367992 TGTACAGTTTCGAAACGGCTA 57.632 42.857 32.06 22.38 43.51 3.93
2733 4339 2.228138 TGTACAGTTTCGAAACGGCT 57.772 45.000 32.06 23.18 43.51 5.52
2734 4340 4.650545 TTATGTACAGTTTCGAAACGGC 57.349 40.909 32.06 22.89 43.51 5.68
2735 4341 6.953743 CAGAATTATGTACAGTTTCGAAACGG 59.046 38.462 31.00 31.00 43.51 4.44
2736 4342 6.953743 CCAGAATTATGTACAGTTTCGAAACG 59.046 38.462 29.72 25.66 43.51 3.60
2737 4343 7.803724 ACCAGAATTATGTACAGTTTCGAAAC 58.196 34.615 29.36 29.36 39.17 2.78
2738 4344 7.972832 ACCAGAATTATGTACAGTTTCGAAA 57.027 32.000 6.47 6.47 0.00 3.46
2739 4345 7.972832 AACCAGAATTATGTACAGTTTCGAA 57.027 32.000 0.33 0.00 0.00 3.71
2740 4346 8.308931 AGTAACCAGAATTATGTACAGTTTCGA 58.691 33.333 0.33 0.00 0.00 3.71
2741 4347 8.475331 AGTAACCAGAATTATGTACAGTTTCG 57.525 34.615 0.33 2.06 0.00 3.46
2778 4388 1.458445 GGTTTCGAAACGGCTACAGAC 59.542 52.381 29.23 12.39 39.77 3.51
2867 4482 8.470002 GGTCCAGAACATTTGCTTAAATAAGAT 58.530 33.333 4.39 0.00 35.33 2.40
2886 4501 4.148838 CACAATAAAACAAGGGGTCCAGA 58.851 43.478 0.00 0.00 0.00 3.86
3020 4644 1.447938 CGATGTCAACAAAACAAGCGC 59.552 47.619 0.00 0.00 0.00 5.92
3021 4645 2.713976 GTCGATGTCAACAAAACAAGCG 59.286 45.455 0.00 0.00 32.93 4.68
3168 4897 7.094805 ACCTGTAATTAGCACACAGTTATGTTG 60.095 37.037 4.95 0.00 37.65 3.33
3223 4962 1.279840 GTTGTTGAGTGCTGGACGC 59.720 57.895 0.00 0.00 39.77 5.19
3266 5005 9.334947 GCCGTATATACTATTGATAGGTAGACA 57.665 37.037 11.05 0.00 34.69 3.41
3269 5019 7.094890 CCCGCCGTATATACTATTGATAGGTAG 60.095 44.444 11.05 2.05 34.69 3.18
3289 5039 1.263217 GCTATTTTCATACACCCGCCG 59.737 52.381 0.00 0.00 0.00 6.46
3292 5042 5.811399 TTTCTGCTATTTTCATACACCCG 57.189 39.130 0.00 0.00 0.00 5.28
3321 5075 5.047021 TCGATATCTCATCCCTCAAATGGTC 60.047 44.000 0.34 0.00 0.00 4.02
3351 5105 3.446873 ACTGATGAACCAAGCAAACACAA 59.553 39.130 0.00 0.00 0.00 3.33
3407 5161 5.902051 ACGAGCTGTCTTGTTACTAAAAC 57.098 39.130 0.00 0.00 33.10 2.43
3431 5185 3.181482 CCTACGAGCTGAACTGATGATGT 60.181 47.826 0.00 0.00 0.00 3.06
3432 5186 3.067320 TCCTACGAGCTGAACTGATGATG 59.933 47.826 0.00 0.00 0.00 3.07
3433 5187 3.291584 TCCTACGAGCTGAACTGATGAT 58.708 45.455 0.00 0.00 0.00 2.45
3434 5188 2.723273 TCCTACGAGCTGAACTGATGA 58.277 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.