Multiple sequence alignment - TraesCS7B01G428400

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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 TraesCS7B01G428400 chr7B 100.000 3227 0 0 1 3227 697421809 697425035 0.000000e+00 5960.0
1 TraesCS7B01G428400 chr7B 88.700 1885 185 14 1017 2886 695908473 695910344 0.000000e+00 2276.0
2 TraesCS7B01G428400 chr7B 90.142 1765 138 23 1017 2768 697120278 697118537 0.000000e+00 2263.0
3 TraesCS7B01G428400 chr7B 85.618 1780 218 21 998 2755 697615829 697614066 0.000000e+00 1834.0
4 TraesCS7B01G428400 chr7B 87.453 1586 142 27 905 2486 685048463 685049995 0.000000e+00 1773.0
5 TraesCS7B01G428400 chr7B 84.989 1752 231 22 1022 2757 695502309 695500574 0.000000e+00 1749.0
6 TraesCS7B01G428400 chr7B 78.133 1157 217 22 908 2057 697545168 697546295 0.000000e+00 702.0
7 TraesCS7B01G428400 chr7B 81.992 783 130 8 900 1679 685013115 685013889 0.000000e+00 654.0
8 TraesCS7B01G428400 chr7B 93.824 340 19 2 2888 3227 695910667 695911004 7.990000e-141 510.0
9 TraesCS7B01G428400 chr7B 90.549 328 28 3 300 625 685025174 685025500 6.400000e-117 431.0
10 TraesCS7B01G428400 chr7B 95.858 169 5 2 52 219 627652974 627652807 4.100000e-69 272.0
11 TraesCS7B01G428400 chr7B 81.855 248 24 5 2980 3209 697036113 697036357 4.250000e-44 189.0
12 TraesCS7B01G428400 chr7B 82.143 224 33 6 2889 3108 685050854 685051074 5.500000e-43 185.0
13 TraesCS7B01G428400 chr7B 80.100 201 28 8 2925 3119 695355951 695356145 4.340000e-29 139.0
14 TraesCS7B01G428400 chr7B 81.595 163 19 9 904 1061 697401880 697402036 1.220000e-24 124.0
15 TraesCS7B01G428400 chr7D 90.253 2288 149 39 300 2562 608726822 608729060 0.000000e+00 2922.0
16 TraesCS7B01G428400 chr7D 84.244 1720 243 22 1055 2755 610651447 610653157 0.000000e+00 1650.0
17 TraesCS7B01G428400 chr7D 93.064 346 21 2 2884 3227 608724727 608725071 1.340000e-138 503.0
18 TraesCS7B01G428400 chr7D 93.064 346 21 2 2884 3227 608734246 608734590 1.340000e-138 503.0
19 TraesCS7B01G428400 chr7D 89.877 326 28 4 2560 2885 608730565 608730885 6.440000e-112 414.0
20 TraesCS7B01G428400 chr7A 87.507 1745 176 24 814 2539 700160961 700159240 0.000000e+00 1977.0
21 TraesCS7B01G428400 chr7A 91.304 345 29 1 2884 3227 700104761 700105105 1.360000e-128 470.0
22 TraesCS7B01G428400 chr7A 82.022 267 27 6 2980 3226 699926880 699927145 1.170000e-49 207.0
23 TraesCS7B01G428400 chr7A 86.747 166 18 4 2941 3106 700094137 700093976 7.110000e-42 182.0
24 TraesCS7B01G428400 chrUn 85.705 1546 196 13 998 2526 77772805 77774342 0.000000e+00 1607.0
25 TraesCS7B01G428400 chrUn 80.381 683 110 13 1005 1684 77779853 77780514 6.220000e-137 497.0
26 TraesCS7B01G428400 chrUn 95.808 167 6 1 3061 3227 480498818 480498653 5.310000e-68 268.0
27 TraesCS7B01G428400 chr6B 96.988 166 4 1 56 221 719762137 719762301 8.820000e-71 278.0
28 TraesCS7B01G428400 chr6B 95.238 168 6 2 54 221 265686811 265686646 6.860000e-67 265.0
29 TraesCS7B01G428400 chr6B 98.718 78 1 0 222 299 120033952 120033875 4.340000e-29 139.0
30 TraesCS7B01G428400 chr6B 98.718 78 1 0 222 299 307021714 307021791 4.340000e-29 139.0
31 TraesCS7B01G428400 chr1B 97.546 163 3 1 59 221 271215820 271215981 8.820000e-71 278.0
32 TraesCS7B01G428400 chr1B 98.718 78 1 0 222 299 672535160 672535237 4.340000e-29 139.0
33 TraesCS7B01G428400 chr2B 96.429 168 5 1 59 226 177119721 177119555 3.170000e-70 276.0
34 TraesCS7B01G428400 chr2B 95.783 166 6 1 56 221 556218336 556218500 1.910000e-67 267.0
35 TraesCS7B01G428400 chr3B 95.758 165 6 1 59 223 715042556 715042719 6.860000e-67 265.0
36 TraesCS7B01G428400 chr3B 95.181 166 7 1 59 224 457209258 457209094 8.880000e-66 261.0
37 TraesCS7B01G428400 chr3B 94.545 55 3 0 1 55 397953619 397953565 5.740000e-13 86.1
38 TraesCS7B01G428400 chr4A 94.611 167 8 1 56 222 341775490 341775655 1.150000e-64 257.0
39 TraesCS7B01G428400 chr4D 98.718 78 1 0 222 299 123395433 123395510 4.340000e-29 139.0
40 TraesCS7B01G428400 chr4D 98.718 78 1 0 222 299 414810316 414810393 4.340000e-29 139.0
41 TraesCS7B01G428400 chr4B 98.718 78 1 0 222 299 623341268 623341345 4.340000e-29 139.0
42 TraesCS7B01G428400 chr2D 98.718 78 1 0 222 299 55361205 55361128 4.340000e-29 139.0
43 TraesCS7B01G428400 chr1D 98.718 78 1 0 222 299 212451665 212451588 4.340000e-29 139.0
44 TraesCS7B01G428400 chr1A 98.718 78 1 0 222 299 94574127 94574204 4.340000e-29 139.0


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 TraesCS7B01G428400 chr7B 697421809 697425035 3226 False 5960.0 5960 100.0000 1 3227 1 chr7B.!!$F6 3226
1 TraesCS7B01G428400 chr7B 697118537 697120278 1741 True 2263.0 2263 90.1420 1017 2768 1 chr7B.!!$R3 1751
2 TraesCS7B01G428400 chr7B 697614066 697615829 1763 True 1834.0 1834 85.6180 998 2755 1 chr7B.!!$R4 1757
3 TraesCS7B01G428400 chr7B 695500574 695502309 1735 True 1749.0 1749 84.9890 1022 2757 1 chr7B.!!$R2 1735
4 TraesCS7B01G428400 chr7B 695908473 695911004 2531 False 1393.0 2276 91.2620 1017 3227 2 chr7B.!!$F9 2210
5 TraesCS7B01G428400 chr7B 685048463 685051074 2611 False 979.0 1773 84.7980 905 3108 2 chr7B.!!$F8 2203
6 TraesCS7B01G428400 chr7B 697545168 697546295 1127 False 702.0 702 78.1330 908 2057 1 chr7B.!!$F7 1149
7 TraesCS7B01G428400 chr7B 685013115 685013889 774 False 654.0 654 81.9920 900 1679 1 chr7B.!!$F1 779
8 TraesCS7B01G428400 chr7D 610651447 610653157 1710 False 1650.0 1650 84.2440 1055 2755 1 chr7D.!!$F1 1700
9 TraesCS7B01G428400 chr7D 608724727 608734590 9863 False 1085.5 2922 91.5645 300 3227 4 chr7D.!!$F2 2927
10 TraesCS7B01G428400 chr7A 700159240 700160961 1721 True 1977.0 1977 87.5070 814 2539 1 chr7A.!!$R2 1725
11 TraesCS7B01G428400 chrUn 77772805 77774342 1537 False 1607.0 1607 85.7050 998 2526 1 chrUn.!!$F1 1528
12 TraesCS7B01G428400 chrUn 77779853 77780514 661 False 497.0 497 80.3810 1005 1684 1 chrUn.!!$F2 679

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
84 85 0.179062 GCCACTCATCAGCTGGGTAG 60.179 60.0 15.13 10.88 35.97 3.18 F
214 215 0.957395 AGATTGCAGTTCTGGCACCG 60.957 55.0 0.80 0.00 41.75 4.94 F
1523 3356 0.538057 CAGTGCAAGGCTTTCCTGGA 60.538 55.0 0.00 0.00 43.40 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 3314 0.251916 CTCGCTTACCATGGGGAACA 59.748 55.0 18.09 0.00 38.05 3.18 R
1695 3532 0.911769 GGTGGACCCATGACATCTCA 59.088 55.0 0.00 0.00 0.00 3.27 R
2998 9997 1.039068 TCCACCCAATTTGTGCACAG 58.961 50.0 20.59 9.81 32.30 3.66 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
26 27 7.499232 TCGCCCCTTTTATTTTTGATTTTCAAA 59.501 29.630 0.00 0.00 43.84 2.69
35 36 2.810439 TGATTTTCAAAACGGCCCTG 57.190 45.000 0.00 0.00 0.00 4.45
36 37 1.270041 TGATTTTCAAAACGGCCCTGC 60.270 47.619 0.00 0.00 0.00 4.85
39 40 0.467290 TTTCAAAACGGCCCTGCTCT 60.467 50.000 0.00 0.00 0.00 4.09
41 42 2.358737 AAAACGGCCCTGCTCTCG 60.359 61.111 0.00 0.00 0.00 4.04
42 43 3.178540 AAAACGGCCCTGCTCTCGT 62.179 57.895 0.00 0.00 37.45 4.18
45 46 4.200283 CGGCCCTGCTCTCGTCTC 62.200 72.222 0.00 0.00 0.00 3.36
47 48 2.493973 GCCCTGCTCTCGTCTCTG 59.506 66.667 0.00 0.00 0.00 3.35
51 52 1.311651 CCTGCTCTCGTCTCTGCTGA 61.312 60.000 0.00 0.00 0.00 4.26
52 53 0.179166 CTGCTCTCGTCTCTGCTGAC 60.179 60.000 0.00 0.00 0.00 3.51
60 61 1.354040 GTCTCTGCTGACGACAATGG 58.646 55.000 14.05 0.00 0.00 3.16
61 62 0.390340 TCTCTGCTGACGACAATGGC 60.390 55.000 0.00 0.00 0.00 4.40
62 63 1.690283 CTCTGCTGACGACAATGGCG 61.690 60.000 7.07 7.07 0.00 5.69
63 64 1.737735 CTGCTGACGACAATGGCGA 60.738 57.895 18.23 0.00 0.00 5.54
65 66 1.291184 TGCTGACGACAATGGCGAAG 61.291 55.000 18.23 13.56 0.00 3.79
78 79 4.928398 CGAAGCCACTCATCAGCT 57.072 55.556 0.00 0.00 38.88 4.24
79 80 2.381109 CGAAGCCACTCATCAGCTG 58.619 57.895 7.63 7.63 36.84 4.24
80 81 1.088340 CGAAGCCACTCATCAGCTGG 61.088 60.000 15.13 0.00 36.84 4.85
81 82 0.747283 GAAGCCACTCATCAGCTGGG 60.747 60.000 15.13 6.99 36.84 4.45
82 83 1.495579 AAGCCACTCATCAGCTGGGT 61.496 55.000 15.13 5.36 40.02 4.51
83 84 0.618680 AGCCACTCATCAGCTGGGTA 60.619 55.000 15.13 0.00 35.97 3.69
84 85 0.179062 GCCACTCATCAGCTGGGTAG 60.179 60.000 15.13 10.88 35.97 3.18
86 87 1.137872 CCACTCATCAGCTGGGTAGTC 59.862 57.143 15.13 0.00 35.97 2.59
87 88 1.827344 CACTCATCAGCTGGGTAGTCA 59.173 52.381 15.13 0.00 35.97 3.41
88 89 2.234661 CACTCATCAGCTGGGTAGTCAA 59.765 50.000 15.13 0.00 35.97 3.18
89 90 3.110705 ACTCATCAGCTGGGTAGTCAAT 58.889 45.455 15.13 0.00 36.55 2.57
91 92 3.875727 CTCATCAGCTGGGTAGTCAATTG 59.124 47.826 15.13 0.00 0.00 2.32
92 93 3.519107 TCATCAGCTGGGTAGTCAATTGA 59.481 43.478 15.13 3.38 0.00 2.57
93 94 3.334583 TCAGCTGGGTAGTCAATTGAC 57.665 47.619 27.69 27.69 45.08 3.18
106 107 5.453567 GTCAATTGACTACCCAGCTTTTT 57.546 39.130 27.66 0.00 41.65 1.94
107 108 5.222631 GTCAATTGACTACCCAGCTTTTTG 58.777 41.667 27.66 0.00 41.65 2.44
108 109 5.009610 GTCAATTGACTACCCAGCTTTTTGA 59.990 40.000 27.66 0.00 41.65 2.69
110 111 5.649782 ATTGACTACCCAGCTTTTTGATG 57.350 39.130 0.00 0.00 0.00 3.07
111 112 4.365514 TGACTACCCAGCTTTTTGATGA 57.634 40.909 0.00 0.00 33.12 2.92
114 115 5.009610 TGACTACCCAGCTTTTTGATGAAAC 59.990 40.000 0.00 0.00 33.12 2.78
118 119 4.021981 ACCCAGCTTTTTGATGAAACTAGC 60.022 41.667 3.64 3.64 33.12 3.42
121 122 6.127647 CCCAGCTTTTTGATGAAACTAGCATA 60.128 38.462 11.65 0.00 33.97 3.14
122 123 7.417116 CCCAGCTTTTTGATGAAACTAGCATAT 60.417 37.037 11.65 0.00 33.97 1.78
123 124 7.434307 CCAGCTTTTTGATGAAACTAGCATATG 59.566 37.037 11.65 0.00 33.97 1.78
188 189 8.856490 ACTTGACTACACAATTTGAAAATGAC 57.144 30.769 2.79 0.00 0.00 3.06
189 190 8.686334 ACTTGACTACACAATTTGAAAATGACT 58.314 29.630 2.79 0.00 0.00 3.41
192 193 9.114952 TGACTACACAATTTGAAAATGACTACA 57.885 29.630 2.79 0.00 0.00 2.74
193 194 9.382244 GACTACACAATTTGAAAATGACTACAC 57.618 33.333 2.79 0.00 0.00 2.90
194 195 8.898761 ACTACACAATTTGAAAATGACTACACA 58.101 29.630 2.79 0.00 0.00 3.72
196 197 8.633075 ACACAATTTGAAAATGACTACACAAG 57.367 30.769 2.79 0.00 0.00 3.16
197 198 8.465999 ACACAATTTGAAAATGACTACACAAGA 58.534 29.630 2.79 0.00 0.00 3.02
198 199 9.467258 CACAATTTGAAAATGACTACACAAGAT 57.533 29.630 2.79 0.00 0.00 2.40
201 202 7.928908 TTTGAAAATGACTACACAAGATTGC 57.071 32.000 0.00 0.00 0.00 3.56
202 203 6.631971 TGAAAATGACTACACAAGATTGCA 57.368 33.333 0.00 0.00 0.00 4.08
203 204 6.671190 TGAAAATGACTACACAAGATTGCAG 58.329 36.000 0.00 0.00 0.00 4.41
204 205 6.262944 TGAAAATGACTACACAAGATTGCAGT 59.737 34.615 0.00 0.00 0.00 4.40
205 206 6.639632 AAATGACTACACAAGATTGCAGTT 57.360 33.333 0.00 0.00 0.00 3.16
206 207 5.869753 ATGACTACACAAGATTGCAGTTC 57.130 39.130 0.00 0.00 0.00 3.01
208 209 4.751600 TGACTACACAAGATTGCAGTTCTG 59.248 41.667 2.35 0.00 0.00 3.02
209 210 4.067896 ACTACACAAGATTGCAGTTCTGG 58.932 43.478 2.35 2.38 0.00 3.86
210 211 1.610522 ACACAAGATTGCAGTTCTGGC 59.389 47.619 2.35 0.00 0.00 4.85
211 212 1.610038 CACAAGATTGCAGTTCTGGCA 59.390 47.619 2.35 0.00 40.00 4.92
212 213 1.610522 ACAAGATTGCAGTTCTGGCAC 59.389 47.619 2.35 0.00 41.75 5.01
213 214 1.068055 CAAGATTGCAGTTCTGGCACC 60.068 52.381 2.35 0.00 41.75 5.01
214 215 0.957395 AGATTGCAGTTCTGGCACCG 60.957 55.000 0.80 0.00 41.75 4.94
243 244 4.116747 CTGACGAAGCCTTTATCTCTGT 57.883 45.455 0.00 0.00 0.00 3.41
244 245 4.109050 CTGACGAAGCCTTTATCTCTGTC 58.891 47.826 0.00 0.00 0.00 3.51
245 246 3.764434 TGACGAAGCCTTTATCTCTGTCT 59.236 43.478 0.00 0.00 0.00 3.41
246 247 4.142359 TGACGAAGCCTTTATCTCTGTCTC 60.142 45.833 0.00 0.00 0.00 3.36
247 248 4.020543 ACGAAGCCTTTATCTCTGTCTCT 58.979 43.478 0.00 0.00 0.00 3.10
248 249 4.142271 ACGAAGCCTTTATCTCTGTCTCTG 60.142 45.833 0.00 0.00 0.00 3.35
249 250 4.142271 CGAAGCCTTTATCTCTGTCTCTGT 60.142 45.833 0.00 0.00 0.00 3.41
250 251 5.623368 CGAAGCCTTTATCTCTGTCTCTGTT 60.623 44.000 0.00 0.00 0.00 3.16
252 253 7.430760 AAGCCTTTATCTCTGTCTCTGTTAT 57.569 36.000 0.00 0.00 0.00 1.89
254 255 6.041523 AGCCTTTATCTCTGTCTCTGTTATCC 59.958 42.308 0.00 0.00 0.00 2.59
255 256 6.041523 GCCTTTATCTCTGTCTCTGTTATCCT 59.958 42.308 0.00 0.00 0.00 3.24
257 258 6.869315 TTATCTCTGTCTCTGTTATCCTCG 57.131 41.667 0.00 0.00 0.00 4.63
259 260 5.354842 TCTCTGTCTCTGTTATCCTCGTA 57.645 43.478 0.00 0.00 0.00 3.43
260 261 5.117584 TCTCTGTCTCTGTTATCCTCGTAC 58.882 45.833 0.00 0.00 0.00 3.67
262 263 4.080469 TCTGTCTCTGTTATCCTCGTACCT 60.080 45.833 0.00 0.00 0.00 3.08
264 265 2.950309 TCTCTGTTATCCTCGTACCTGC 59.050 50.000 0.00 0.00 0.00 4.85
265 266 2.952978 CTCTGTTATCCTCGTACCTGCT 59.047 50.000 0.00 0.00 0.00 4.24
266 267 2.688446 TCTGTTATCCTCGTACCTGCTG 59.312 50.000 0.00 0.00 0.00 4.41
268 269 3.296854 TGTTATCCTCGTACCTGCTGAT 58.703 45.455 0.00 0.00 0.00 2.90
269 270 3.318275 TGTTATCCTCGTACCTGCTGATC 59.682 47.826 0.00 0.00 0.00 2.92
271 272 1.681538 TCCTCGTACCTGCTGATCTC 58.318 55.000 0.00 0.00 0.00 2.75
272 273 1.213182 TCCTCGTACCTGCTGATCTCT 59.787 52.381 0.00 0.00 0.00 3.10
274 275 2.034053 CCTCGTACCTGCTGATCTCTTC 59.966 54.545 0.00 0.00 0.00 2.87
275 276 1.671328 TCGTACCTGCTGATCTCTTCG 59.329 52.381 0.00 0.00 0.00 3.79
277 278 2.539953 CGTACCTGCTGATCTCTTCGAC 60.540 54.545 0.00 0.00 0.00 4.20
278 279 1.846007 ACCTGCTGATCTCTTCGACT 58.154 50.000 0.00 0.00 0.00 4.18
280 281 3.357203 ACCTGCTGATCTCTTCGACTAA 58.643 45.455 0.00 0.00 0.00 2.24
281 282 3.957497 ACCTGCTGATCTCTTCGACTAAT 59.043 43.478 0.00 0.00 0.00 1.73
283 284 5.240623 ACCTGCTGATCTCTTCGACTAATAG 59.759 44.000 0.00 0.00 0.00 1.73
284 285 5.471797 CCTGCTGATCTCTTCGACTAATAGA 59.528 44.000 0.00 0.00 0.00 1.98
285 286 6.348458 CCTGCTGATCTCTTCGACTAATAGAG 60.348 46.154 4.94 4.94 37.37 2.43
286 287 6.058833 TGCTGATCTCTTCGACTAATAGAGT 58.941 40.000 10.14 0.11 42.90 3.24
300 301 7.782897 ACTAATAGAGTCTATGCTATTGGCA 57.217 36.000 13.47 0.00 45.50 4.92
301 302 7.607250 ACTAATAGAGTCTATGCTATTGGCAC 58.393 38.462 13.47 0.00 44.61 5.01
302 303 7.233553 ACTAATAGAGTCTATGCTATTGGCACA 59.766 37.037 13.47 0.00 44.61 4.57
331 2128 6.952773 ATTAAGAGTTTGTACCAAGCAACA 57.047 33.333 0.00 0.00 0.00 3.33
333 2130 2.618709 AGAGTTTGTACCAAGCAACAGC 59.381 45.455 0.00 0.00 0.00 4.40
352 2149 4.079253 CAGCTGTGGTAAATGGTAAGGTT 58.921 43.478 5.25 0.00 0.00 3.50
355 2152 5.013808 AGCTGTGGTAAATGGTAAGGTTACT 59.986 40.000 0.00 0.00 34.16 2.24
374 2172 8.838741 AGGTTACTTGGGTACTCCATATTTTTA 58.161 33.333 4.19 0.00 46.52 1.52
379 2177 9.020731 ACTTGGGTACTCCATATTTTTAAAGTG 57.979 33.333 4.19 0.00 46.52 3.16
415 2213 9.864034 ATAGAGTAATTTCAATGCGTAAAATCG 57.136 29.630 1.00 0.00 0.00 3.34
421 2219 6.667981 TTTCAATGCGTAAAATCGAACAAG 57.332 33.333 0.00 0.00 0.00 3.16
460 2258 2.293170 GGAGCCATCTCTAGCAAAACC 58.707 52.381 0.00 0.00 39.31 3.27
461 2259 2.293170 GAGCCATCTCTAGCAAAACCC 58.707 52.381 0.00 0.00 36.42 4.11
470 2270 4.900054 TCTCTAGCAAAACCCCTATCCTAC 59.100 45.833 0.00 0.00 0.00 3.18
487 2287 9.877178 CCTATCCTACAATCTGAAACATATACC 57.123 37.037 0.00 0.00 0.00 2.73
530 2330 5.403166 TGTTCGAATAGTTACAACGAAGGTG 59.597 40.000 0.00 0.00 42.09 4.00
533 2333 4.328983 CGAATAGTTACAACGAAGGTGCAT 59.671 41.667 0.00 0.00 0.00 3.96
545 2345 1.028330 AGGTGCATGCGACAGGAATG 61.028 55.000 14.09 0.00 0.00 2.67
546 2346 1.308069 GGTGCATGCGACAGGAATGT 61.308 55.000 14.09 0.00 0.00 2.71
565 2365 6.742718 GGAATGTGACAAATGAAGAATACACG 59.257 38.462 0.00 0.00 0.00 4.49
571 2371 5.872635 ACAAATGAAGAATACACGCATCAG 58.127 37.500 0.00 0.00 0.00 2.90
590 2390 5.401531 TCAGAAGGTTCGTAAAGCTGTAT 57.598 39.130 0.00 0.00 42.27 2.29
611 2411 3.121929 AGGAGTCTGGCAGAAATCCTA 57.878 47.619 34.58 8.04 39.56 2.94
612 2412 3.663198 AGGAGTCTGGCAGAAATCCTAT 58.337 45.455 34.58 21.14 39.56 2.57
735 2537 6.594937 TGCAGCTCAAGTTTGAAATTTTCTTT 59.405 30.769 10.33 0.00 36.64 2.52
778 2580 4.965200 TTGGAAAATTTGGGGTGTAAGG 57.035 40.909 0.00 0.00 0.00 2.69
783 2585 5.529430 GGAAAATTTGGGGTGTAAGGTTTTG 59.471 40.000 0.00 0.00 0.00 2.44
786 2588 5.702065 ATTTGGGGTGTAAGGTTTTGTTT 57.298 34.783 0.00 0.00 0.00 2.83
787 2589 5.500546 TTTGGGGTGTAAGGTTTTGTTTT 57.499 34.783 0.00 0.00 0.00 2.43
788 2590 5.500546 TTGGGGTGTAAGGTTTTGTTTTT 57.499 34.783 0.00 0.00 0.00 1.94
807 2610 4.935352 TTTTTGAGACAGATTTGGGGTG 57.065 40.909 0.00 0.00 0.00 4.61
878 2686 4.453892 GGCCCATTCCAGCTGCCT 62.454 66.667 8.66 0.00 39.05 4.75
887 2702 2.434884 CAGCTGCCTACACCCACG 60.435 66.667 0.00 0.00 0.00 4.94
889 2704 4.394712 GCTGCCTACACCCACGCT 62.395 66.667 0.00 0.00 0.00 5.07
893 2708 0.973496 TGCCTACACCCACGCTATCA 60.973 55.000 0.00 0.00 0.00 2.15
897 2712 1.476891 CTACACCCACGCTATCACACT 59.523 52.381 0.00 0.00 0.00 3.55
906 2721 1.428448 GCTATCACACTCGCACACAA 58.572 50.000 0.00 0.00 0.00 3.33
992 2816 4.832608 CCAACCTCGCCGGCCTAC 62.833 72.222 23.46 0.00 35.61 3.18
993 2817 4.077184 CAACCTCGCCGGCCTACA 62.077 66.667 23.46 0.69 35.61 2.74
1215 3042 1.022735 GATTCCTCGACTACGGCAGA 58.977 55.000 0.00 0.00 40.21 4.26
1463 3296 1.452651 CGGTACCTCACGGCCTAGA 60.453 63.158 10.90 0.00 0.00 2.43
1478 3311 2.945398 CTAGACGCCTCGCTTGAGCC 62.945 65.000 0.00 0.00 38.47 4.70
1521 3354 1.530013 CCCAGTGCAAGGCTTTCCTG 61.530 60.000 0.00 3.83 43.40 3.86
1523 3356 0.538057 CAGTGCAAGGCTTTCCTGGA 60.538 55.000 0.00 0.00 43.40 3.86
1612 3445 1.352083 AACTAGTCTGGCTGCCTTCA 58.648 50.000 21.03 0.00 0.00 3.02
1629 3462 4.516698 GCCTTCATCTTCTCTTCAAACACA 59.483 41.667 0.00 0.00 0.00 3.72
1695 3532 3.058160 GGCAAGCACGACATGGCT 61.058 61.111 0.00 0.00 43.46 4.75
1918 3764 4.559153 GATGTTTGGTTTCCATGGTGAAG 58.441 43.478 12.58 0.00 31.53 3.02
1921 3767 3.517296 TTGGTTTCCATGGTGAAGCTA 57.483 42.857 23.32 17.33 31.53 3.32
1955 3801 2.988493 TCTATACCGTTGCACGAAACAC 59.012 45.455 9.75 0.00 46.05 3.32
2107 3959 7.875316 AATGATCGACTTACTGGATATTTCG 57.125 36.000 0.00 0.00 0.00 3.46
2246 4098 8.888579 ATATGAAGTGGTAAAGTTTCTATCGG 57.111 34.615 0.00 0.00 0.00 4.18
2262 4114 6.392625 TCTATCGGTTCCAAGTTATCTCAG 57.607 41.667 0.00 0.00 0.00 3.35
2269 4122 5.179533 GTTCCAAGTTATCTCAGTCCTTCC 58.820 45.833 0.00 0.00 0.00 3.46
2272 4125 5.488919 TCCAAGTTATCTCAGTCCTTCCATT 59.511 40.000 0.00 0.00 0.00 3.16
2274 4127 7.182026 TCCAAGTTATCTCAGTCCTTCCATTTA 59.818 37.037 0.00 0.00 0.00 1.40
2275 4128 7.995488 CCAAGTTATCTCAGTCCTTCCATTTAT 59.005 37.037 0.00 0.00 0.00 1.40
2283 4138 7.993183 TCTCAGTCCTTCCATTTATAATTGACC 59.007 37.037 8.59 0.00 0.00 4.02
2297 4152 8.677148 TTATAATTGACCTGTCTATTGCTTCC 57.323 34.615 14.46 0.00 36.16 3.46
2386 4242 2.096248 ACTAAGAGAGCTCGGGAACAG 58.904 52.381 8.37 4.95 34.09 3.16
2436 4292 5.569355 TGATTGCCACTTTAAGAGAATGGA 58.431 37.500 0.00 0.00 31.69 3.41
2481 4357 4.210120 GTGCACTATGAGTAGCTTATGCAC 59.790 45.833 10.32 9.92 42.74 4.57
2577 6109 9.220767 AGATAAACATAGAAGGAACACAACTTC 57.779 33.333 0.00 0.00 42.56 3.01
2578 6110 5.924475 AACATAGAAGGAACACAACTTCG 57.076 39.130 0.00 0.00 45.83 3.79
2581 6113 6.698380 ACATAGAAGGAACACAACTTCGTAT 58.302 36.000 0.00 0.00 45.83 3.06
2582 6114 6.812160 ACATAGAAGGAACACAACTTCGTATC 59.188 38.462 0.00 0.00 45.83 2.24
2583 6115 4.566987 AGAAGGAACACAACTTCGTATCC 58.433 43.478 0.00 0.00 45.83 2.59
2584 6116 4.039973 AGAAGGAACACAACTTCGTATCCA 59.960 41.667 0.00 0.00 45.83 3.41
2585 6117 3.926616 AGGAACACAACTTCGTATCCAG 58.073 45.455 0.00 0.00 30.23 3.86
2593 6131 5.347907 CACAACTTCGTATCCAGTTTACCTC 59.652 44.000 0.00 0.00 30.48 3.85
2620 6159 7.169813 GGATTGTTTCACCTTGAGAAAATTCAC 59.830 37.037 0.00 0.00 36.80 3.18
2680 6219 6.753913 TTTGATAGATGTAAGGAGGCAGAT 57.246 37.500 0.00 0.00 0.00 2.90
2688 6227 6.385467 AGATGTAAGGAGGCAGATAAGTTCTT 59.615 38.462 0.00 0.00 29.93 2.52
2747 6286 4.455533 TGCGATGCTGTTTTGAGATAAACT 59.544 37.500 0.00 0.00 38.52 2.66
2789 6379 3.763897 GGCAACTGAAATGTTATCCCACT 59.236 43.478 0.00 0.00 0.00 4.00
2790 6380 4.220602 GGCAACTGAAATGTTATCCCACTT 59.779 41.667 0.00 0.00 0.00 3.16
2860 6450 5.726000 TCAGCATGGGCAACTGAAATTGC 62.726 47.826 1.84 1.84 44.59 3.56
2898 9895 7.112984 GTCAATGTCTCCACGTTTCAAATTTAC 59.887 37.037 0.00 0.00 28.40 2.01
2945 9944 4.184629 GCACCTTCCTGTGATACTACTTG 58.815 47.826 0.00 0.00 38.55 3.16
2965 9964 7.741027 ACTTGCCTAAGTACCTTAAAACTTC 57.259 36.000 0.00 0.00 45.07 3.01
3156 10159 2.957402 ACCTTTCAGACAAGATGGCA 57.043 45.000 0.00 0.00 0.00 4.92
3175 10178 4.281435 TGGCACATGACAATGAATTTCACT 59.719 37.500 0.00 0.00 37.24 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.525629 TGAAAATCAAAAATAAAAGGGGCGA 58.474 32.000 0.00 0.00 0.00 5.54
1 2 6.793492 TGAAAATCAAAAATAAAAGGGGCG 57.207 33.333 0.00 0.00 0.00 6.13
14 15 3.462021 CAGGGCCGTTTTGAAAATCAAA 58.538 40.909 0.00 1.57 43.84 2.69
15 16 2.804933 GCAGGGCCGTTTTGAAAATCAA 60.805 45.455 0.00 0.00 34.03 2.57
17 18 1.000843 AGCAGGGCCGTTTTGAAAATC 59.999 47.619 0.00 0.00 0.00 2.17
18 19 1.000843 GAGCAGGGCCGTTTTGAAAAT 59.999 47.619 0.00 0.00 0.00 1.82
19 20 0.387565 GAGCAGGGCCGTTTTGAAAA 59.612 50.000 0.00 0.00 0.00 2.29
20 21 0.467290 AGAGCAGGGCCGTTTTGAAA 60.467 50.000 0.00 0.00 0.00 2.69
21 22 0.889186 GAGAGCAGGGCCGTTTTGAA 60.889 55.000 0.00 0.00 0.00 2.69
26 27 4.070552 GACGAGAGCAGGGCCGTT 62.071 66.667 0.00 0.00 35.22 4.44
28 29 4.200283 GAGACGAGAGCAGGGCCG 62.200 72.222 0.00 0.00 0.00 6.13
29 30 2.757917 AGAGACGAGAGCAGGGCC 60.758 66.667 0.00 0.00 0.00 5.80
30 31 2.493973 CAGAGACGAGAGCAGGGC 59.506 66.667 0.00 0.00 0.00 5.19
31 32 2.051518 AGCAGAGACGAGAGCAGGG 61.052 63.158 0.00 0.00 0.00 4.45
32 33 1.139308 CAGCAGAGACGAGAGCAGG 59.861 63.158 0.00 0.00 0.00 4.85
35 36 4.783903 GTCAGCAGAGACGAGAGC 57.216 61.111 0.00 0.00 0.00 4.09
41 42 1.354040 CCATTGTCGTCAGCAGAGAC 58.646 55.000 0.00 0.00 35.61 3.36
42 43 0.390340 GCCATTGTCGTCAGCAGAGA 60.390 55.000 0.00 0.00 0.00 3.10
44 45 1.737735 CGCCATTGTCGTCAGCAGA 60.738 57.895 0.00 0.00 0.00 4.26
45 46 1.291184 TTCGCCATTGTCGTCAGCAG 61.291 55.000 0.00 0.00 0.00 4.24
47 48 1.421485 CTTCGCCATTGTCGTCAGC 59.579 57.895 0.00 0.00 0.00 4.26
60 61 1.449246 AGCTGATGAGTGGCTTCGC 60.449 57.895 0.00 0.00 31.81 4.70
61 62 1.088340 CCAGCTGATGAGTGGCTTCG 61.088 60.000 17.39 0.00 33.74 3.79
62 63 0.747283 CCCAGCTGATGAGTGGCTTC 60.747 60.000 17.39 0.00 33.74 3.86
63 64 1.302285 CCCAGCTGATGAGTGGCTT 59.698 57.895 17.39 0.00 33.74 4.35
65 66 0.179062 CTACCCAGCTGATGAGTGGC 60.179 60.000 17.39 0.00 0.00 5.01
69 70 3.834489 ATTGACTACCCAGCTGATGAG 57.166 47.619 17.39 11.05 0.00 2.90
70 71 3.519107 TCAATTGACTACCCAGCTGATGA 59.481 43.478 17.39 0.00 0.00 2.92
71 72 3.624861 GTCAATTGACTACCCAGCTGATG 59.375 47.826 27.66 8.57 41.65 3.07
73 74 3.334583 GTCAATTGACTACCCAGCTGA 57.665 47.619 27.66 0.00 41.65 4.26
84 85 5.009610 TCAAAAAGCTGGGTAGTCAATTGAC 59.990 40.000 27.69 27.69 45.08 3.18
86 87 5.452078 TCAAAAAGCTGGGTAGTCAATTG 57.548 39.130 0.00 0.00 0.00 2.32
87 88 5.774690 TCATCAAAAAGCTGGGTAGTCAATT 59.225 36.000 0.00 0.00 0.00 2.32
88 89 5.324409 TCATCAAAAAGCTGGGTAGTCAAT 58.676 37.500 0.00 0.00 0.00 2.57
89 90 4.724399 TCATCAAAAAGCTGGGTAGTCAA 58.276 39.130 0.00 0.00 0.00 3.18
91 92 5.241728 AGTTTCATCAAAAAGCTGGGTAGTC 59.758 40.000 0.00 0.00 0.00 2.59
92 93 5.140454 AGTTTCATCAAAAAGCTGGGTAGT 58.860 37.500 0.00 0.00 0.00 2.73
93 94 5.712152 AGTTTCATCAAAAAGCTGGGTAG 57.288 39.130 0.00 0.00 0.00 3.18
94 95 5.183140 GCTAGTTTCATCAAAAAGCTGGGTA 59.817 40.000 0.00 0.00 33.12 3.69
96 97 4.022068 TGCTAGTTTCATCAAAAAGCTGGG 60.022 41.667 0.00 0.00 35.32 4.45
98 99 7.043590 GCATATGCTAGTTTCATCAAAAAGCTG 60.044 37.037 20.64 0.00 35.32 4.24
99 100 6.976925 GCATATGCTAGTTTCATCAAAAAGCT 59.023 34.615 20.64 0.00 35.32 3.74
163 164 8.686334 AGTCATTTTCAAATTGTGTAGTCAAGT 58.314 29.630 0.00 0.00 0.00 3.16
166 167 9.114952 TGTAGTCATTTTCAAATTGTGTAGTCA 57.885 29.630 0.00 0.00 0.00 3.41
167 168 9.382244 GTGTAGTCATTTTCAAATTGTGTAGTC 57.618 33.333 0.00 0.00 0.00 2.59
168 169 8.898761 TGTGTAGTCATTTTCAAATTGTGTAGT 58.101 29.630 0.00 0.00 0.00 2.73
169 170 9.729023 TTGTGTAGTCATTTTCAAATTGTGTAG 57.271 29.630 0.00 0.00 0.00 2.74
171 172 8.465999 TCTTGTGTAGTCATTTTCAAATTGTGT 58.534 29.630 0.00 0.00 0.00 3.72
172 173 8.854979 TCTTGTGTAGTCATTTTCAAATTGTG 57.145 30.769 0.00 0.00 0.00 3.33
175 176 8.981647 GCAATCTTGTGTAGTCATTTTCAAATT 58.018 29.630 0.00 0.00 0.00 1.82
176 177 8.143193 TGCAATCTTGTGTAGTCATTTTCAAAT 58.857 29.630 0.00 0.00 0.00 2.32
177 178 7.487484 TGCAATCTTGTGTAGTCATTTTCAAA 58.513 30.769 0.00 0.00 0.00 2.69
178 179 7.036996 TGCAATCTTGTGTAGTCATTTTCAA 57.963 32.000 0.00 0.00 0.00 2.69
179 180 6.262944 ACTGCAATCTTGTGTAGTCATTTTCA 59.737 34.615 0.00 0.00 39.94 2.69
180 181 6.672147 ACTGCAATCTTGTGTAGTCATTTTC 58.328 36.000 0.00 0.00 39.94 2.29
181 182 6.639632 ACTGCAATCTTGTGTAGTCATTTT 57.360 33.333 0.00 0.00 39.94 1.82
182 183 6.488006 AGAACTGCAATCTTGTGTAGTCATTT 59.512 34.615 0.00 0.00 42.75 2.32
183 184 6.000219 AGAACTGCAATCTTGTGTAGTCATT 59.000 36.000 0.00 0.00 42.75 2.57
184 185 5.410746 CAGAACTGCAATCTTGTGTAGTCAT 59.589 40.000 0.00 0.00 42.75 3.06
187 188 4.067896 CCAGAACTGCAATCTTGTGTAGT 58.932 43.478 0.00 0.00 45.08 2.73
188 189 3.120060 GCCAGAACTGCAATCTTGTGTAG 60.120 47.826 0.00 0.00 37.27 2.74
189 190 2.813754 GCCAGAACTGCAATCTTGTGTA 59.186 45.455 0.00 0.00 0.00 2.90
190 191 1.610522 GCCAGAACTGCAATCTTGTGT 59.389 47.619 0.00 0.00 0.00 3.72
192 193 1.610522 GTGCCAGAACTGCAATCTTGT 59.389 47.619 0.00 0.00 41.06 3.16
193 194 1.068055 GGTGCCAGAACTGCAATCTTG 60.068 52.381 0.00 0.00 41.06 3.02
194 195 1.251251 GGTGCCAGAACTGCAATCTT 58.749 50.000 0.00 0.00 41.06 2.40
196 197 1.503542 CGGTGCCAGAACTGCAATC 59.496 57.895 0.00 0.00 41.06 2.67
197 198 3.672293 CGGTGCCAGAACTGCAAT 58.328 55.556 0.00 0.00 41.06 3.56
222 223 4.109050 GACAGAGATAAAGGCTTCGTCAG 58.891 47.826 0.00 0.00 0.00 3.51
223 224 3.764434 AGACAGAGATAAAGGCTTCGTCA 59.236 43.478 0.00 0.00 0.00 4.35
224 225 4.097286 AGAGACAGAGATAAAGGCTTCGTC 59.903 45.833 0.00 1.73 0.00 4.20
226 227 4.142271 ACAGAGACAGAGATAAAGGCTTCG 60.142 45.833 0.00 0.00 0.00 3.79
227 228 5.337578 ACAGAGACAGAGATAAAGGCTTC 57.662 43.478 0.00 0.00 0.00 3.86
228 229 5.753721 AACAGAGACAGAGATAAAGGCTT 57.246 39.130 0.00 0.00 0.00 4.35
229 230 6.041523 GGATAACAGAGACAGAGATAAAGGCT 59.958 42.308 0.00 0.00 0.00 4.58
231 232 7.521423 CGAGGATAACAGAGACAGAGATAAAGG 60.521 44.444 0.00 0.00 0.00 3.11
232 233 7.012894 ACGAGGATAACAGAGACAGAGATAAAG 59.987 40.741 0.00 0.00 0.00 1.85
233 234 6.829298 ACGAGGATAACAGAGACAGAGATAAA 59.171 38.462 0.00 0.00 0.00 1.40
236 237 4.787551 ACGAGGATAACAGAGACAGAGAT 58.212 43.478 0.00 0.00 0.00 2.75
238 239 4.273969 GGTACGAGGATAACAGAGACAGAG 59.726 50.000 0.00 0.00 0.00 3.35
239 240 4.080469 AGGTACGAGGATAACAGAGACAGA 60.080 45.833 0.00 0.00 0.00 3.41
241 242 3.945921 CAGGTACGAGGATAACAGAGACA 59.054 47.826 0.00 0.00 0.00 3.41
243 244 2.950309 GCAGGTACGAGGATAACAGAGA 59.050 50.000 0.00 0.00 0.00 3.10
244 245 2.952978 AGCAGGTACGAGGATAACAGAG 59.047 50.000 0.00 0.00 0.00 3.35
245 246 2.688446 CAGCAGGTACGAGGATAACAGA 59.312 50.000 0.00 0.00 0.00 3.41
246 247 2.688446 TCAGCAGGTACGAGGATAACAG 59.312 50.000 0.00 0.00 0.00 3.16
247 248 2.730382 TCAGCAGGTACGAGGATAACA 58.270 47.619 0.00 0.00 0.00 2.41
248 249 3.570550 AGATCAGCAGGTACGAGGATAAC 59.429 47.826 0.00 0.00 0.00 1.89
249 250 3.821600 GAGATCAGCAGGTACGAGGATAA 59.178 47.826 0.00 0.00 0.00 1.75
250 251 3.073209 AGAGATCAGCAGGTACGAGGATA 59.927 47.826 0.00 0.00 0.00 2.59
252 253 1.213182 AGAGATCAGCAGGTACGAGGA 59.787 52.381 0.00 0.00 0.00 3.71
254 255 2.286713 CGAAGAGATCAGCAGGTACGAG 60.287 54.545 0.00 0.00 0.00 4.18
255 256 1.671328 CGAAGAGATCAGCAGGTACGA 59.329 52.381 0.00 0.00 0.00 3.43
257 258 2.685897 AGTCGAAGAGATCAGCAGGTAC 59.314 50.000 0.00 0.00 36.95 3.34
259 260 1.846007 AGTCGAAGAGATCAGCAGGT 58.154 50.000 0.00 0.00 36.95 4.00
260 261 4.582701 ATTAGTCGAAGAGATCAGCAGG 57.417 45.455 0.00 0.00 36.95 4.85
262 263 6.058833 ACTCTATTAGTCGAAGAGATCAGCA 58.941 40.000 16.11 0.00 39.29 4.41
291 292 7.260603 ACTCTTAATTTCATTGTGCCAATAGC 58.739 34.615 0.84 0.00 44.14 2.97
293 294 9.421806 CAAACTCTTAATTTCATTGTGCCAATA 57.578 29.630 0.84 0.00 0.00 1.90
294 295 7.933033 ACAAACTCTTAATTTCATTGTGCCAAT 59.067 29.630 0.00 0.00 0.00 3.16
295 296 7.271511 ACAAACTCTTAATTTCATTGTGCCAA 58.728 30.769 0.00 0.00 0.00 4.52
296 297 6.815089 ACAAACTCTTAATTTCATTGTGCCA 58.185 32.000 0.00 0.00 0.00 4.92
297 298 7.328493 GGTACAAACTCTTAATTTCATTGTGCC 59.672 37.037 7.02 7.02 42.07 5.01
298 299 7.865385 TGGTACAAACTCTTAATTTCATTGTGC 59.135 33.333 0.00 0.00 31.92 4.57
331 2128 4.382386 AACCTTACCATTTACCACAGCT 57.618 40.909 0.00 0.00 0.00 4.24
333 2130 6.150474 CCAAGTAACCTTACCATTTACCACAG 59.850 42.308 0.00 0.00 34.19 3.66
400 2198 5.143660 CACTTGTTCGATTTTACGCATTGA 58.856 37.500 0.00 0.00 0.00 2.57
406 2204 3.185594 TCTGCCACTTGTTCGATTTTACG 59.814 43.478 0.00 0.00 0.00 3.18
415 2213 2.224305 ACTACCACTCTGCCACTTGTTC 60.224 50.000 0.00 0.00 0.00 3.18
421 2219 2.500098 TCCATTACTACCACTCTGCCAC 59.500 50.000 0.00 0.00 0.00 5.01
460 2258 9.877178 GTATATGTTTCAGATTGTAGGATAGGG 57.123 37.037 0.00 0.00 0.00 3.53
461 2259 9.877178 GGTATATGTTTCAGATTGTAGGATAGG 57.123 37.037 0.00 0.00 0.00 2.57
501 2301 5.340403 TCGTTGTAACTATTCGAACAACTCG 59.660 40.000 20.33 12.07 45.97 4.18
513 2313 3.374058 GCATGCACCTTCGTTGTAACTAT 59.626 43.478 14.21 0.00 0.00 2.12
522 2322 2.029288 CTGTCGCATGCACCTTCGT 61.029 57.895 19.57 0.00 0.00 3.85
523 2323 2.743752 CCTGTCGCATGCACCTTCG 61.744 63.158 19.57 0.00 0.00 3.79
530 2330 0.097674 GTCACATTCCTGTCGCATGC 59.902 55.000 7.91 7.91 31.62 4.06
533 2333 1.960417 TTTGTCACATTCCTGTCGCA 58.040 45.000 0.00 0.00 31.62 5.10
545 2345 5.029650 TGCGTGTATTCTTCATTTGTCAC 57.970 39.130 0.00 0.00 0.00 3.67
546 2346 5.411053 TGATGCGTGTATTCTTCATTTGTCA 59.589 36.000 0.00 0.00 0.00 3.58
565 2365 3.003480 AGCTTTACGAACCTTCTGATGC 58.997 45.455 0.00 0.00 0.00 3.91
571 2371 5.899299 TCCTATACAGCTTTACGAACCTTC 58.101 41.667 0.00 0.00 0.00 3.46
590 2390 3.121929 AGGATTTCTGCCAGACTCCTA 57.878 47.619 18.93 0.00 35.80 2.94
697 2498 4.859304 TGAGCTGCAATTTTCACTCAAT 57.141 36.364 1.02 0.00 31.60 2.57
757 2559 4.299485 ACCTTACACCCCAAATTTTCCAA 58.701 39.130 0.00 0.00 0.00 3.53
758 2560 3.930035 ACCTTACACCCCAAATTTTCCA 58.070 40.909 0.00 0.00 0.00 3.53
786 2588 4.285863 ACACCCCAAATCTGTCTCAAAAA 58.714 39.130 0.00 0.00 0.00 1.94
787 2589 3.909732 ACACCCCAAATCTGTCTCAAAA 58.090 40.909 0.00 0.00 0.00 2.44
788 2590 3.593442 ACACCCCAAATCTGTCTCAAA 57.407 42.857 0.00 0.00 0.00 2.69
789 2591 4.506625 CCTTACACCCCAAATCTGTCTCAA 60.507 45.833 0.00 0.00 0.00 3.02
790 2592 3.009033 CCTTACACCCCAAATCTGTCTCA 59.991 47.826 0.00 0.00 0.00 3.27
791 2593 3.009143 ACCTTACACCCCAAATCTGTCTC 59.991 47.826 0.00 0.00 0.00 3.36
793 2595 3.081804 CACCTTACACCCCAAATCTGTC 58.918 50.000 0.00 0.00 0.00 3.51
794 2596 2.225017 CCACCTTACACCCCAAATCTGT 60.225 50.000 0.00 0.00 0.00 3.41
795 2597 2.225017 ACCACCTTACACCCCAAATCTG 60.225 50.000 0.00 0.00 0.00 2.90
797 2599 2.597578 ACCACCTTACACCCCAAATC 57.402 50.000 0.00 0.00 0.00 2.17
805 2608 3.828451 TGGTACAGACTACCACCTTACAC 59.172 47.826 0.00 0.00 42.21 2.90
878 2686 1.475280 GAGTGTGATAGCGTGGGTGTA 59.525 52.381 0.00 0.00 0.00 2.90
887 2702 1.126846 GTTGTGTGCGAGTGTGATAGC 59.873 52.381 0.00 0.00 0.00 2.97
889 2704 2.609491 GGAGTTGTGTGCGAGTGTGATA 60.609 50.000 0.00 0.00 0.00 2.15
893 2708 0.249489 GAGGAGTTGTGTGCGAGTGT 60.249 55.000 0.00 0.00 0.00 3.55
897 2712 1.691195 TTGGGAGGAGTTGTGTGCGA 61.691 55.000 0.00 0.00 0.00 5.10
906 2721 1.226311 GATGGGGAATTGGGAGGAGT 58.774 55.000 0.00 0.00 0.00 3.85
977 2801 3.315949 TTGTAGGCCGGCGAGGTT 61.316 61.111 22.54 5.79 43.70 3.50
978 2802 4.078516 GTTGTAGGCCGGCGAGGT 62.079 66.667 22.54 7.45 43.70 3.85
987 2811 2.489751 GCCATTGGCGTTGTAGGC 59.510 61.111 12.82 0.00 39.62 3.93
1481 3314 0.251916 CTCGCTTACCATGGGGAACA 59.748 55.000 18.09 0.00 38.05 3.18
1521 3354 4.916314 TCCTCGCCGAGGGGATCC 62.916 72.222 31.34 1.92 46.85 3.36
1543 3376 1.756950 TTGTCTCTCCCGCCGCTAT 60.757 57.895 0.00 0.00 0.00 2.97
1612 3445 5.296151 TGTCCTGTGTTTGAAGAGAAGAT 57.704 39.130 0.00 0.00 0.00 2.40
1629 3462 3.064324 GCGGCTTGCCATTGTCCT 61.064 61.111 12.45 0.00 37.76 3.85
1695 3532 0.911769 GGTGGACCCATGACATCTCA 59.088 55.000 0.00 0.00 0.00 3.27
1918 3764 6.127591 ACGGTATAGATGAGATTGGATGTAGC 60.128 42.308 0.00 0.00 0.00 3.58
1921 3767 6.459066 CAACGGTATAGATGAGATTGGATGT 58.541 40.000 0.00 0.00 0.00 3.06
1955 3801 2.045536 GCCTGGGACTCTTGCCTG 60.046 66.667 0.00 0.00 33.27 4.85
1993 3839 7.989947 ATTTGTACCCAGAATCTAGTAGGAA 57.010 36.000 0.00 0.00 0.00 3.36
2107 3959 2.855180 CAACGTCTTGACATCCATTGC 58.145 47.619 0.00 0.00 0.00 3.56
2244 4096 3.195825 AGGACTGAGATAACTTGGAACCG 59.804 47.826 0.00 0.00 0.00 4.44
2246 4098 5.179533 GGAAGGACTGAGATAACTTGGAAC 58.820 45.833 0.00 0.00 0.00 3.62
2262 4114 7.775561 AGACAGGTCAATTATAAATGGAAGGAC 59.224 37.037 1.84 0.00 0.00 3.85
2272 4125 8.494433 AGGAAGCAATAGACAGGTCAATTATAA 58.506 33.333 1.84 0.00 0.00 0.98
2274 4127 6.769822 CAGGAAGCAATAGACAGGTCAATTAT 59.230 38.462 1.84 0.00 0.00 1.28
2275 4128 6.115446 CAGGAAGCAATAGACAGGTCAATTA 58.885 40.000 1.84 0.00 0.00 1.40
2276 4129 4.946157 CAGGAAGCAATAGACAGGTCAATT 59.054 41.667 1.84 0.00 0.00 2.32
2277 4130 4.018960 ACAGGAAGCAATAGACAGGTCAAT 60.019 41.667 1.84 0.00 0.00 2.57
2278 4131 3.327757 ACAGGAAGCAATAGACAGGTCAA 59.672 43.478 1.84 0.00 0.00 3.18
2283 4138 7.255035 CCATAATGAACAGGAAGCAATAGACAG 60.255 40.741 0.00 0.00 0.00 3.51
2297 4152 8.199449 AGAAATACCAATTGCCATAATGAACAG 58.801 33.333 0.00 0.00 0.00 3.16
2336 4191 7.703621 CCCATGAGCATAAGAAATTAAACACTG 59.296 37.037 0.00 0.00 0.00 3.66
2386 4242 8.515473 AACAAACAAGAAAAGAAACACAGTAC 57.485 30.769 0.00 0.00 0.00 2.73
2436 4292 9.944376 TGCACAAGATTATTTCTCTTACTAACT 57.056 29.630 0.00 0.00 31.78 2.24
2481 4357 4.655762 TTAGTGATTCCATCAGGACTCG 57.344 45.455 0.00 0.00 45.73 4.18
2544 4568 7.606456 TGTTCCTTCTATGTTTATCTTGACCAC 59.394 37.037 0.00 0.00 0.00 4.16
2577 6109 4.049186 CAATCCGAGGTAAACTGGATACG 58.951 47.826 0.00 0.00 36.63 3.06
2578 6110 5.019785 ACAATCCGAGGTAAACTGGATAC 57.980 43.478 0.00 0.00 36.63 2.24
2581 6113 4.202377 TGAAACAATCCGAGGTAAACTGGA 60.202 41.667 0.00 0.00 33.10 3.86
2582 6114 4.069304 TGAAACAATCCGAGGTAAACTGG 58.931 43.478 0.00 0.00 0.00 4.00
2583 6115 4.083484 GGTGAAACAATCCGAGGTAAACTG 60.083 45.833 0.00 0.00 39.98 3.16
2584 6116 4.070009 GGTGAAACAATCCGAGGTAAACT 58.930 43.478 0.00 0.00 39.98 2.66
2585 6117 4.070009 AGGTGAAACAATCCGAGGTAAAC 58.930 43.478 0.00 0.00 39.98 2.01
2593 6131 4.829064 TTTCTCAAGGTGAAACAATCCG 57.171 40.909 0.00 0.00 39.98 4.18
2620 6159 5.686159 AAATGAGCTGTCTTTGACTTGAG 57.314 39.130 0.00 0.00 33.15 3.02
2710 6249 6.430451 ACAGCATCGCAAGCTAAAATTATAC 58.570 36.000 0.00 0.00 41.14 1.47
2789 6379 9.906660 GAGGTTGATTCACATAAAACAACATAA 57.093 29.630 0.00 0.00 41.22 1.90
2790 6380 9.072375 TGAGGTTGATTCACATAAAACAACATA 57.928 29.630 0.00 0.00 41.22 2.29
2803 6393 4.686972 TCGATCTCATGAGGTTGATTCAC 58.313 43.478 20.26 0.46 27.18 3.18
2860 6450 5.645067 TGGAGACATTGACAGCAATAAAGAG 59.355 40.000 0.00 0.00 42.66 2.85
2871 6461 3.186702 TGAAACGTGGAGACATTGACA 57.813 42.857 0.00 0.00 46.14 3.58
2965 9964 9.803315 AAGAGTTTTACAAGCTTAAAAGGAAAG 57.197 29.630 7.27 0.00 32.77 2.62
2998 9997 1.039068 TCCACCCAATTTGTGCACAG 58.961 50.000 20.59 9.81 32.30 3.66
3000 9999 2.611225 TTTCCACCCAATTTGTGCAC 57.389 45.000 10.75 10.75 32.30 4.57
3156 10159 5.221481 TGCCAAGTGAAATTCATTGTCATGT 60.221 36.000 0.00 0.00 0.00 3.21
3175 10178 8.922931 ATCAACATATACATGACTATTGCCAA 57.077 30.769 0.00 0.00 35.96 4.52


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

AutoCloner maintained by Alex Coulton.