Multiple sequence alignment - TraesCS1B01G265700

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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 TraesCS1B01G265700 chr1B 100.000 2448 0 0 855 3302 466094524 466092077 0.000000e+00 4521.0
1 TraesCS1B01G265700 chr1B 94.627 1340 66 4 1098 2437 682437250 682438583 0.000000e+00 2071.0
2 TraesCS1B01G265700 chr1B 100.000 771 0 0 1 771 466095378 466094608 0.000000e+00 1424.0
3 TraesCS1B01G265700 chr1B 96.711 152 0 1 1 147 466108105 466107954 7.080000e-62 248.0
4 TraesCS1B01G265700 chr1B 94.231 156 3 2 3 152 450423728 450423573 1.980000e-57 233.0
5 TraesCS1B01G265700 chr1B 94.737 152 3 1 1 147 90227220 90227371 7.130000e-57 231.0
6 TraesCS1B01G265700 chr1D 96.246 2451 62 9 855 3302 344590371 344592794 0.000000e+00 3989.0
7 TraesCS1B01G265700 chr1D 91.325 415 16 10 366 771 344590052 344590455 1.730000e-152 549.0
8 TraesCS1B01G265700 chr1D 86.747 166 20 2 203 367 494168465 494168629 2.020000e-42 183.0
9 TraesCS1B01G265700 chr1D 85.965 171 22 2 200 369 452848323 452848492 7.280000e-42 182.0
10 TraesCS1B01G265700 chr1D 94.737 57 3 0 148 204 344589997 344590053 4.540000e-14 89.8
11 TraesCS1B01G265700 chr1A 97.550 1306 32 0 1022 2327 444122300 444123605 0.000000e+00 2235.0
12 TraesCS1B01G265700 chr1A 91.645 383 17 5 362 730 444121634 444122015 1.760000e-142 516.0
13 TraesCS1B01G265700 chr1A 82.414 290 26 13 3029 3302 444124214 444124494 2.560000e-56 230.0
14 TraesCS1B01G265700 chr1A 85.043 234 18 1 2326 2559 444123709 444123925 4.290000e-54 222.0
15 TraesCS1B01G265700 chr1A 94.444 54 3 0 152 205 444121580 444121633 2.110000e-12 84.2
16 TraesCS1B01G265700 chr2A 93.486 568 34 3 2090 2657 476213898 476213334 0.000000e+00 841.0
17 TraesCS1B01G265700 chr2A 97.531 324 8 0 1100 1423 476214251 476213928 3.720000e-154 555.0
18 TraesCS1B01G265700 chr2A 96.012 326 13 0 1098 1423 476212096 476212421 6.270000e-147 531.0
19 TraesCS1B01G265700 chr2A 90.078 383 27 4 2638 3011 476213250 476212870 1.380000e-133 486.0
20 TraesCS1B01G265700 chr2A 90.444 293 21 2 3010 3302 476212831 476212546 2.400000e-101 379.0
21 TraesCS1B01G265700 chr2A 97.143 35 1 0 2587 2621 476213342 476213308 3.560000e-05 60.2
22 TraesCS1B01G265700 chr3D 97.613 377 2 2 1119 1489 284206928 284206553 9.990000e-180 640.0
23 TraesCS1B01G265700 chr3D 95.745 141 0 1 1119 1253 284204286 284204426 4.290000e-54 222.0
24 TraesCS1B01G265700 chr7B 93.664 363 13 2 1112 1473 221893234 221892881 4.850000e-148 534.0
25 TraesCS1B01G265700 chr7B 91.606 274 15 2 1119 1384 29687084 29687357 4.020000e-99 372.0
26 TraesCS1B01G265700 chr7B 98.734 79 1 0 1411 1489 29687351 29687429 1.240000e-29 141.0
27 TraesCS1B01G265700 chr3B 93.611 360 13 2 1112 1470 492742384 492742734 2.260000e-146 529.0
28 TraesCS1B01G265700 chr3B 92.500 360 17 2 1112 1470 622479249 622479599 1.060000e-139 507.0
29 TraesCS1B01G265700 chr3B 86.207 377 23 16 1119 1489 245923633 245923280 6.690000e-102 381.0
30 TraesCS1B01G265700 chr3B 93.631 157 5 1 1 152 606744602 606744758 2.560000e-56 230.0
31 TraesCS1B01G265700 chr2B 93.333 360 14 2 1112 1470 113193319 113193669 1.050000e-144 523.0
32 TraesCS1B01G265700 chr2B 94.904 157 3 1 1 152 441610121 441609965 1.180000e-59 241.0
33 TraesCS1B01G265700 chr2B 94.839 155 3 1 1 150 494351373 494351527 1.530000e-58 237.0
34 TraesCS1B01G265700 chr2B 93.631 157 5 1 1 152 66618059 66617903 2.560000e-56 230.0
35 TraesCS1B01G265700 chr6B 78.000 400 74 13 1068 1460 650928373 650927981 4.260000e-59 239.0
36 TraesCS1B01G265700 chr5B 94.771 153 3 1 1 148 477749169 477749321 1.980000e-57 233.0
37 TraesCS1B01G265700 chr5B 94.737 152 3 1 1 147 7811815 7811664 7.130000e-57 231.0
38 TraesCS1B01G265700 chr5B 88.235 170 17 3 203 370 12846361 12846529 2.010000e-47 200.0
39 TraesCS1B01G265700 chr5B 86.550 171 19 4 200 368 103335825 103335657 5.630000e-43 185.0
40 TraesCS1B01G265700 chr6D 89.506 162 16 1 201 361 6319207 6319368 1.550000e-48 204.0
41 TraesCS1B01G265700 chr7D 87.719 171 19 2 199 368 50710239 50710408 7.230000e-47 198.0
42 TraesCS1B01G265700 chr7D 89.103 156 15 2 213 367 446216463 446216309 3.360000e-45 193.0
43 TraesCS1B01G265700 chr5D 88.125 160 15 4 210 368 396684793 396684949 1.560000e-43 187.0
44 TraesCS1B01G265700 chr5D 87.500 56 7 0 149 204 312433721 312433776 7.650000e-07 65.8
45 TraesCS1B01G265700 chr2D 86.628 172 19 4 202 372 630031348 630031180 1.560000e-43 187.0
46 TraesCS1B01G265700 chrUn 86.826 167 20 2 203 368 108810833 108810998 5.630000e-43 185.0
47 TraesCS1B01G265700 chr5A 85.965 171 20 4 199 367 333434169 333434337 2.620000e-41 180.0


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 TraesCS1B01G265700 chr1B 466092077 466095378 3301 True 2972.50 4521 100.000000 1 3302 2 chr1B.!!$R3 3301
1 TraesCS1B01G265700 chr1B 682437250 682438583 1333 False 2071.00 2071 94.627000 1098 2437 1 chr1B.!!$F2 1339
2 TraesCS1B01G265700 chr1D 344589997 344592794 2797 False 1542.60 3989 94.102667 148 3302 3 chr1D.!!$F3 3154
3 TraesCS1B01G265700 chr1A 444121580 444124494 2914 False 657.44 2235 90.219200 152 3302 5 chr1A.!!$F1 3150
4 TraesCS1B01G265700 chr2A 476212546 476214251 1705 True 464.24 841 93.736400 1100 3302 5 chr2A.!!$R1 2202

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
35 36 0.040692 TTCACGGTCGAGTGTCTTCG 60.041 55.0 4.89 0.0 42.4 3.79 F
1682 1878 0.326264 CTGGAGTTTGGGGTCAGGAG 59.674 60.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2104 1.746615 CCCCACGACCATCTTGCTG 60.747 63.158 0.00 0.00 0.00 4.41 R
3195 3662 1.093159 CTTTGCTGCAGAGGATCCAC 58.907 55.000 20.43 8.01 33.66 4.02 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 3.236391 TGGTCGAGTGGTTGGCTT 58.764 55.556 0.00 0.00 0.00 4.35
18 19 1.070786 TGGTCGAGTGGTTGGCTTC 59.929 57.895 0.00 0.00 0.00 3.86
19 20 1.070786 GGTCGAGTGGTTGGCTTCA 59.929 57.895 0.00 0.00 0.00 3.02
20 21 1.228657 GGTCGAGTGGTTGGCTTCAC 61.229 60.000 0.00 0.00 0.00 3.18
21 22 1.300620 TCGAGTGGTTGGCTTCACG 60.301 57.895 0.00 0.00 38.77 4.35
22 23 2.317609 CGAGTGGTTGGCTTCACGG 61.318 63.158 0.00 0.00 38.77 4.94
23 24 1.227853 GAGTGGTTGGCTTCACGGT 60.228 57.895 0.00 0.00 38.77 4.83
24 25 1.227853 AGTGGTTGGCTTCACGGTC 60.228 57.895 0.00 0.00 38.77 4.79
25 26 2.280524 TGGTTGGCTTCACGGTCG 60.281 61.111 0.00 0.00 0.00 4.79
26 27 2.029964 GGTTGGCTTCACGGTCGA 59.970 61.111 0.00 0.00 0.00 4.20
27 28 2.027625 GGTTGGCTTCACGGTCGAG 61.028 63.158 0.00 0.00 0.00 4.04
28 29 1.300697 GTTGGCTTCACGGTCGAGT 60.301 57.895 0.00 0.00 0.00 4.18
29 30 1.300620 TTGGCTTCACGGTCGAGTG 60.301 57.895 0.00 0.00 43.11 3.51
30 31 2.023414 TTGGCTTCACGGTCGAGTGT 62.023 55.000 4.89 0.00 42.40 3.55
31 32 1.733399 GGCTTCACGGTCGAGTGTC 60.733 63.158 4.89 0.00 42.40 3.67
32 33 1.286260 GCTTCACGGTCGAGTGTCT 59.714 57.895 4.89 0.00 42.40 3.41
33 34 0.318784 GCTTCACGGTCGAGTGTCTT 60.319 55.000 4.89 0.00 42.40 3.01
34 35 1.687628 CTTCACGGTCGAGTGTCTTC 58.312 55.000 4.89 0.00 42.40 2.87
35 36 0.040692 TTCACGGTCGAGTGTCTTCG 60.041 55.000 4.89 0.00 42.40 3.79
36 37 0.881600 TCACGGTCGAGTGTCTTCGA 60.882 55.000 4.89 0.00 46.41 3.71
42 43 1.880271 TCGAGTGTCTTCGAGTCTGT 58.120 50.000 0.00 0.00 44.00 3.41
43 44 1.799403 TCGAGTGTCTTCGAGTCTGTC 59.201 52.381 0.00 0.00 44.00 3.51
68 69 3.653344 TGGAACACTTCTGAGTCGATTG 58.347 45.455 0.00 0.00 32.54 2.67
69 70 3.320826 TGGAACACTTCTGAGTCGATTGA 59.679 43.478 0.00 0.00 32.54 2.57
70 71 3.675698 GGAACACTTCTGAGTCGATTGAC 59.324 47.826 4.78 4.78 45.86 3.18
83 84 5.209944 GTCGATTGACAGGTGATTTCTTC 57.790 43.478 8.31 0.00 44.82 2.87
84 85 4.932200 GTCGATTGACAGGTGATTTCTTCT 59.068 41.667 8.31 0.00 44.82 2.85
85 86 6.100004 GTCGATTGACAGGTGATTTCTTCTA 58.900 40.000 8.31 0.00 44.82 2.10
86 87 6.254589 GTCGATTGACAGGTGATTTCTTCTAG 59.745 42.308 8.31 0.00 44.82 2.43
87 88 6.152831 TCGATTGACAGGTGATTTCTTCTAGA 59.847 38.462 0.00 0.00 0.00 2.43
88 89 6.475076 CGATTGACAGGTGATTTCTTCTAGAG 59.525 42.308 0.00 0.00 0.00 2.43
89 90 6.918067 TTGACAGGTGATTTCTTCTAGAGA 57.082 37.500 0.00 0.00 0.00 3.10
90 91 7.487822 TTGACAGGTGATTTCTTCTAGAGAT 57.512 36.000 0.00 0.00 33.49 2.75
91 92 6.871844 TGACAGGTGATTTCTTCTAGAGATG 58.128 40.000 0.00 0.00 33.49 2.90
92 93 6.438741 TGACAGGTGATTTCTTCTAGAGATGT 59.561 38.462 0.00 0.00 33.49 3.06
93 94 6.872920 ACAGGTGATTTCTTCTAGAGATGTC 58.127 40.000 0.00 0.00 33.49 3.06
94 95 6.127196 ACAGGTGATTTCTTCTAGAGATGTCC 60.127 42.308 0.00 0.00 33.49 4.02
95 96 6.098124 CAGGTGATTTCTTCTAGAGATGTCCT 59.902 42.308 0.00 0.00 33.49 3.85
96 97 6.671779 AGGTGATTTCTTCTAGAGATGTCCTT 59.328 38.462 0.00 0.00 33.49 3.36
97 98 6.760770 GGTGATTTCTTCTAGAGATGTCCTTG 59.239 42.308 0.00 0.00 33.49 3.61
98 99 6.760770 GTGATTTCTTCTAGAGATGTCCTTGG 59.239 42.308 0.00 0.00 33.49 3.61
99 100 5.683876 TTTCTTCTAGAGATGTCCTTGGG 57.316 43.478 0.00 0.00 33.49 4.12
100 101 4.338795 TCTTCTAGAGATGTCCTTGGGT 57.661 45.455 0.00 0.00 0.00 4.51
101 102 5.467668 TCTTCTAGAGATGTCCTTGGGTA 57.532 43.478 0.00 0.00 0.00 3.69
102 103 5.202004 TCTTCTAGAGATGTCCTTGGGTAC 58.798 45.833 0.00 0.00 0.00 3.34
103 104 3.552875 TCTAGAGATGTCCTTGGGTACG 58.447 50.000 0.00 0.00 0.00 3.67
104 105 1.486211 AGAGATGTCCTTGGGTACGG 58.514 55.000 0.00 0.00 0.00 4.02
105 106 1.192428 GAGATGTCCTTGGGTACGGT 58.808 55.000 0.00 0.00 0.00 4.83
106 107 2.024655 AGAGATGTCCTTGGGTACGGTA 60.025 50.000 0.00 0.00 0.00 4.02
107 108 2.361438 GAGATGTCCTTGGGTACGGTAG 59.639 54.545 0.00 0.00 0.00 3.18
108 109 2.105766 GATGTCCTTGGGTACGGTAGT 58.894 52.381 0.00 0.00 0.00 2.73
109 110 2.014010 TGTCCTTGGGTACGGTAGTT 57.986 50.000 0.00 0.00 0.00 2.24
110 111 2.328319 TGTCCTTGGGTACGGTAGTTT 58.672 47.619 0.00 0.00 0.00 2.66
111 112 2.037511 TGTCCTTGGGTACGGTAGTTTG 59.962 50.000 0.00 0.00 0.00 2.93
112 113 1.624813 TCCTTGGGTACGGTAGTTTGG 59.375 52.381 0.00 0.00 0.00 3.28
113 114 1.624813 CCTTGGGTACGGTAGTTTGGA 59.375 52.381 0.00 0.00 0.00 3.53
114 115 2.613725 CCTTGGGTACGGTAGTTTGGAC 60.614 54.545 0.00 0.00 0.00 4.02
115 116 1.714541 TGGGTACGGTAGTTTGGACA 58.285 50.000 0.00 0.00 0.00 4.02
116 117 1.619827 TGGGTACGGTAGTTTGGACAG 59.380 52.381 0.00 0.00 0.00 3.51
117 118 1.066645 GGGTACGGTAGTTTGGACAGG 60.067 57.143 0.00 0.00 0.00 4.00
118 119 1.620323 GGTACGGTAGTTTGGACAGGT 59.380 52.381 0.00 0.00 0.00 4.00
119 120 2.353109 GGTACGGTAGTTTGGACAGGTC 60.353 54.545 0.00 0.00 0.00 3.85
135 136 2.170012 GGTCCATGACCCTAGGTACA 57.830 55.000 8.29 7.79 46.19 2.90
136 137 2.690840 GGTCCATGACCCTAGGTACAT 58.309 52.381 8.29 9.82 46.19 2.29
137 138 3.853207 GGTCCATGACCCTAGGTACATA 58.147 50.000 8.29 0.00 46.19 2.29
138 139 3.833070 GGTCCATGACCCTAGGTACATAG 59.167 52.174 8.29 7.59 46.19 2.23
139 140 3.258622 GTCCATGACCCTAGGTACATAGC 59.741 52.174 9.07 0.00 35.25 2.97
140 141 3.142217 TCCATGACCCTAGGTACATAGCT 59.858 47.826 9.07 0.00 35.25 3.32
141 142 3.904339 CCATGACCCTAGGTACATAGCTT 59.096 47.826 9.07 0.00 35.25 3.74
142 143 4.021016 CCATGACCCTAGGTACATAGCTTC 60.021 50.000 9.07 7.66 35.25 3.86
143 144 4.259933 TGACCCTAGGTACATAGCTTCA 57.740 45.455 9.07 9.95 35.25 3.02
144 145 4.816126 TGACCCTAGGTACATAGCTTCAT 58.184 43.478 9.07 0.00 35.25 2.57
145 146 4.833380 TGACCCTAGGTACATAGCTTCATC 59.167 45.833 9.07 2.79 35.25 2.92
146 147 4.816126 ACCCTAGGTACATAGCTTCATCA 58.184 43.478 9.07 0.00 32.11 3.07
187 188 8.375506 TGATGTAATCTTGAAAGGTTGTACTCT 58.624 33.333 0.00 0.00 45.81 3.24
209 210 9.490083 ACTCTGGGTACAAGTAATATACTCTTT 57.510 33.333 0.00 0.00 38.26 2.52
210 211 9.968870 CTCTGGGTACAAGTAATATACTCTTTC 57.031 37.037 0.00 0.00 38.26 2.62
211 212 9.710818 TCTGGGTACAAGTAATATACTCTTTCT 57.289 33.333 0.00 0.00 38.26 2.52
212 213 9.751542 CTGGGTACAAGTAATATACTCTTTCTG 57.248 37.037 0.00 0.00 38.26 3.02
213 214 9.263446 TGGGTACAAGTAATATACTCTTTCTGT 57.737 33.333 0.00 0.00 38.26 3.41
260 261 9.606631 AGAGATTTCAAATGAACTACCAGATAC 57.393 33.333 0.00 0.00 33.13 2.24
261 262 8.425577 AGATTTCAAATGAACTACCAGATACG 57.574 34.615 0.00 0.00 33.13 3.06
262 263 8.258007 AGATTTCAAATGAACTACCAGATACGA 58.742 33.333 0.00 0.00 33.13 3.43
263 264 8.786826 ATTTCAAATGAACTACCAGATACGAA 57.213 30.769 0.00 0.00 33.13 3.85
264 265 8.786826 TTTCAAATGAACTACCAGATACGAAT 57.213 30.769 0.00 0.00 33.13 3.34
265 266 7.770801 TCAAATGAACTACCAGATACGAATG 57.229 36.000 0.00 0.00 0.00 2.67
266 267 7.327975 TCAAATGAACTACCAGATACGAATGT 58.672 34.615 0.00 0.00 0.00 2.71
267 268 8.471609 TCAAATGAACTACCAGATACGAATGTA 58.528 33.333 0.00 0.00 34.45 2.29
268 269 9.261180 CAAATGAACTACCAGATACGAATGTAT 57.739 33.333 0.00 0.00 43.97 2.29
306 307 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
307 308 8.345724 AGAGTGTAGATTCATTCATTTTGCTT 57.654 30.769 0.00 0.00 0.00 3.91
308 309 8.457261 AGAGTGTAGATTCATTCATTTTGCTTC 58.543 33.333 0.00 0.00 0.00 3.86
309 310 7.246311 AGTGTAGATTCATTCATTTTGCTTCG 58.754 34.615 0.00 0.00 0.00 3.79
310 311 7.119699 AGTGTAGATTCATTCATTTTGCTTCGA 59.880 33.333 0.00 0.00 0.00 3.71
311 312 7.912250 GTGTAGATTCATTCATTTTGCTTCGAT 59.088 33.333 0.00 0.00 0.00 3.59
312 313 7.911727 TGTAGATTCATTCATTTTGCTTCGATG 59.088 33.333 0.00 0.00 0.00 3.84
313 314 6.860080 AGATTCATTCATTTTGCTTCGATGT 58.140 32.000 0.00 0.00 0.00 3.06
314 315 7.988737 AGATTCATTCATTTTGCTTCGATGTA 58.011 30.769 0.00 0.00 0.00 2.29
315 316 8.127327 AGATTCATTCATTTTGCTTCGATGTAG 58.873 33.333 0.00 0.00 0.00 2.74
316 317 6.741992 TCATTCATTTTGCTTCGATGTAGT 57.258 33.333 0.00 0.00 0.00 2.73
317 318 6.775088 TCATTCATTTTGCTTCGATGTAGTC 58.225 36.000 0.00 0.00 0.00 2.59
318 319 6.371271 TCATTCATTTTGCTTCGATGTAGTCA 59.629 34.615 0.00 0.00 0.00 3.41
319 320 5.530519 TCATTTTGCTTCGATGTAGTCAC 57.469 39.130 0.00 0.00 0.00 3.67
320 321 5.237815 TCATTTTGCTTCGATGTAGTCACT 58.762 37.500 0.00 0.00 0.00 3.41
321 322 5.700832 TCATTTTGCTTCGATGTAGTCACTT 59.299 36.000 0.00 0.00 0.00 3.16
322 323 4.990543 TTTGCTTCGATGTAGTCACTTG 57.009 40.909 0.00 0.00 0.00 3.16
323 324 3.660501 TGCTTCGATGTAGTCACTTGT 57.339 42.857 0.00 0.00 0.00 3.16
324 325 3.575630 TGCTTCGATGTAGTCACTTGTC 58.424 45.455 0.00 0.00 0.00 3.18
325 326 3.005367 TGCTTCGATGTAGTCACTTGTCA 59.995 43.478 0.00 0.00 0.00 3.58
326 327 3.987868 GCTTCGATGTAGTCACTTGTCAA 59.012 43.478 0.00 0.00 0.00 3.18
327 328 4.447724 GCTTCGATGTAGTCACTTGTCAAA 59.552 41.667 0.00 0.00 0.00 2.69
328 329 5.050363 GCTTCGATGTAGTCACTTGTCAAAA 60.050 40.000 0.00 0.00 0.00 2.44
329 330 6.511121 GCTTCGATGTAGTCACTTGTCAAAAA 60.511 38.462 0.00 0.00 0.00 1.94
330 331 7.490962 TTCGATGTAGTCACTTGTCAAAAAT 57.509 32.000 0.00 0.00 0.00 1.82
331 332 7.490962 TCGATGTAGTCACTTGTCAAAAATT 57.509 32.000 0.00 0.00 0.00 1.82
332 333 7.925993 TCGATGTAGTCACTTGTCAAAAATTT 58.074 30.769 0.00 0.00 0.00 1.82
333 334 8.402472 TCGATGTAGTCACTTGTCAAAAATTTT 58.598 29.630 0.00 0.00 0.00 1.82
334 335 9.658475 CGATGTAGTCACTTGTCAAAAATTTTA 57.342 29.630 3.34 0.00 0.00 1.52
342 343 9.581099 TCACTTGTCAAAAATTTTAGAAAGACC 57.419 29.630 3.34 0.00 0.00 3.85
343 344 9.586435 CACTTGTCAAAAATTTTAGAAAGACCT 57.414 29.630 3.34 0.00 0.00 3.85
417 419 3.121611 CACGTTAAATCGCACGAGGTTTA 59.878 43.478 0.00 0.00 39.76 2.01
432 435 2.445525 AGGTTTACTCCTTTGGGCTCAA 59.554 45.455 0.00 0.00 33.52 3.02
475 481 2.978010 CAACAACCCGAGGCGCTT 60.978 61.111 7.64 0.00 0.00 4.68
488 494 1.603739 GCGCTTTCTTCAACCCCCT 60.604 57.895 0.00 0.00 0.00 4.79
553 559 2.270527 GCACTCTGCTTCCCCTCC 59.729 66.667 0.00 0.00 40.96 4.30
554 560 2.596851 GCACTCTGCTTCCCCTCCA 61.597 63.158 0.00 0.00 40.96 3.86
607 639 0.824759 CAAACCCCTACCTCTCCTCG 59.175 60.000 0.00 0.00 0.00 4.63
608 640 0.976590 AAACCCCTACCTCTCCTCGC 60.977 60.000 0.00 0.00 0.00 5.03
609 641 2.522193 CCCCTACCTCTCCTCGCC 60.522 72.222 0.00 0.00 0.00 5.54
610 642 2.604152 CCCTACCTCTCCTCGCCT 59.396 66.667 0.00 0.00 0.00 5.52
611 643 1.529713 CCCTACCTCTCCTCGCCTC 60.530 68.421 0.00 0.00 0.00 4.70
612 644 1.529713 CCTACCTCTCCTCGCCTCC 60.530 68.421 0.00 0.00 0.00 4.30
613 645 1.529713 CTACCTCTCCTCGCCTCCC 60.530 68.421 0.00 0.00 0.00 4.30
614 646 2.987355 CTACCTCTCCTCGCCTCCCC 62.987 70.000 0.00 0.00 0.00 4.81
689 721 4.038804 CCTCCTCCCCTCCCCCAA 62.039 72.222 0.00 0.00 0.00 4.12
690 722 2.692741 CTCCTCCCCTCCCCCAAC 60.693 72.222 0.00 0.00 0.00 3.77
691 723 4.364686 TCCTCCCCTCCCCCAACC 62.365 72.222 0.00 0.00 0.00 3.77
692 724 4.371231 CCTCCCCTCCCCCAACCT 62.371 72.222 0.00 0.00 0.00 3.50
693 725 2.692741 CTCCCCTCCCCCAACCTC 60.693 72.222 0.00 0.00 0.00 3.85
694 726 4.364686 TCCCCTCCCCCAACCTCC 62.365 72.222 0.00 0.00 0.00 4.30
698 730 4.101448 CTCCCCCAACCTCCGCAG 62.101 72.222 0.00 0.00 0.00 5.18
730 762 4.851214 GCGCCTCCTCCTCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
731 763 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
732 764 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
733 765 3.015332 GCCTCCTCCTCCTCCTCCA 62.015 68.421 0.00 0.00 0.00 3.86
734 766 1.075600 CCTCCTCCTCCTCCTCCAC 60.076 68.421 0.00 0.00 0.00 4.02
735 767 1.075600 CTCCTCCTCCTCCTCCACC 60.076 68.421 0.00 0.00 0.00 4.61
736 768 1.547755 TCCTCCTCCTCCTCCACCT 60.548 63.158 0.00 0.00 0.00 4.00
737 769 1.075600 CCTCCTCCTCCTCCACCTC 60.076 68.421 0.00 0.00 0.00 3.85
738 770 1.454847 CTCCTCCTCCTCCACCTCG 60.455 68.421 0.00 0.00 0.00 4.63
739 771 2.218115 CTCCTCCTCCTCCACCTCGT 62.218 65.000 0.00 0.00 0.00 4.18
740 772 1.755008 CCTCCTCCTCCACCTCGTC 60.755 68.421 0.00 0.00 0.00 4.20
741 773 1.755008 CTCCTCCTCCACCTCGTCC 60.755 68.421 0.00 0.00 0.00 4.79
742 774 2.760385 CCTCCTCCACCTCGTCCC 60.760 72.222 0.00 0.00 0.00 4.46
743 775 3.141488 CTCCTCCACCTCGTCCCG 61.141 72.222 0.00 0.00 0.00 5.14
1533 1729 0.692756 TGCGGGTGGGGAAGATCATA 60.693 55.000 0.00 0.00 0.00 2.15
1682 1878 0.326264 CTGGAGTTTGGGGTCAGGAG 59.674 60.000 0.00 0.00 0.00 3.69
1791 1987 2.158623 TGAGTCCAGCATTTTGGTCAGT 60.159 45.455 0.00 0.00 39.35 3.41
1884 2080 2.550855 GCATGTCAACTTCCTCACAGGA 60.551 50.000 0.00 0.00 44.10 3.86
1908 2104 1.437625 GCTTCTTGCTGTCTCAGGTC 58.562 55.000 0.00 0.00 38.95 3.85
2075 2271 5.598416 TCCACTATAAGATATCGGCATGG 57.402 43.478 0.00 2.73 0.00 3.66
2172 2368 5.064707 GCGTATGAAGTATGACACAATTGGT 59.935 40.000 10.83 4.83 0.00 3.67
2202 2398 8.703378 AAGAAATGGAGGATGATAATTCCTTC 57.297 34.615 0.00 0.00 43.75 3.46
2217 2413 6.986904 AATTCCTTCGACAAAGATAGGTTC 57.013 37.500 0.00 0.00 37.12 3.62
2286 2482 3.666334 GCGATTATGATGAGACTGACGAC 59.334 47.826 0.00 0.00 0.00 4.34
2545 2846 4.150897 TGTAGCATCCATCCTTGTTACC 57.849 45.455 0.00 0.00 31.01 2.85
2546 2847 3.521531 TGTAGCATCCATCCTTGTTACCA 59.478 43.478 0.00 0.00 31.01 3.25
2741 3145 9.793252 AAATTGTGCTGTTATAAATCTGACATC 57.207 29.630 0.00 0.00 0.00 3.06
2773 3178 7.015098 TCAGAATTGAGATATGAACCTCCTCTC 59.985 40.741 0.00 0.00 34.33 3.20
2837 3251 3.541632 TGGTGTCACCTTGTCTCTTTTC 58.458 45.455 22.56 0.00 39.58 2.29
2851 3265 7.356089 TGTCTCTTTTCTAGTTGACCTTGTA 57.644 36.000 0.00 0.00 31.99 2.41
2958 3372 6.509199 GCATCAAGATTCTGACTATGTTGTCG 60.509 42.308 0.00 0.00 39.64 4.35
3179 3646 3.249917 CGTTTGGTTTGGAATATGGTGC 58.750 45.455 0.00 0.00 0.00 5.01
3219 3697 3.181489 GGATCCTCTGCAGCAAAGAATTG 60.181 47.826 9.47 0.00 39.65 2.32
3223 3701 1.000060 TCTGCAGCAAAGAATTGTGCC 60.000 47.619 9.47 0.00 41.88 5.01
3249 3727 3.679389 ACATTTCAGTTCCAGTAGCCAG 58.321 45.455 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.070786 GAAGCCAACCACTCGACCA 59.929 57.895 0.00 0.00 0.00 4.02
1 2 1.070786 TGAAGCCAACCACTCGACC 59.929 57.895 0.00 0.00 0.00 4.79
2 3 1.557443 CGTGAAGCCAACCACTCGAC 61.557 60.000 0.00 0.00 0.00 4.20
3 4 1.300620 CGTGAAGCCAACCACTCGA 60.301 57.895 0.00 0.00 0.00 4.04
4 5 2.317609 CCGTGAAGCCAACCACTCG 61.318 63.158 0.00 0.00 0.00 4.18
5 6 1.227853 ACCGTGAAGCCAACCACTC 60.228 57.895 0.00 0.00 0.00 3.51
6 7 1.227853 GACCGTGAAGCCAACCACT 60.228 57.895 0.00 0.00 0.00 4.00
7 8 2.604174 CGACCGTGAAGCCAACCAC 61.604 63.158 0.00 0.00 0.00 4.16
8 9 2.280524 CGACCGTGAAGCCAACCA 60.281 61.111 0.00 0.00 0.00 3.67
9 10 2.027625 CTCGACCGTGAAGCCAACC 61.028 63.158 0.00 0.00 0.00 3.77
10 11 1.300697 ACTCGACCGTGAAGCCAAC 60.301 57.895 0.00 0.00 0.00 3.77
11 12 1.300620 CACTCGACCGTGAAGCCAA 60.301 57.895 0.00 0.00 37.06 4.52
12 13 2.338620 CACTCGACCGTGAAGCCA 59.661 61.111 0.00 0.00 37.06 4.75
13 14 1.733399 GACACTCGACCGTGAAGCC 60.733 63.158 11.39 0.00 38.27 4.35
14 15 0.318784 AAGACACTCGACCGTGAAGC 60.319 55.000 11.39 1.60 38.27 3.86
15 16 1.687628 GAAGACACTCGACCGTGAAG 58.312 55.000 11.39 0.00 38.27 3.02
16 17 0.040692 CGAAGACACTCGACCGTGAA 60.041 55.000 11.39 0.00 41.44 3.18
17 18 0.881600 TCGAAGACACTCGACCGTGA 60.882 55.000 11.39 0.00 42.69 4.35
18 19 0.452950 CTCGAAGACACTCGACCGTG 60.453 60.000 3.43 3.43 42.69 4.94
19 20 0.883814 ACTCGAAGACACTCGACCGT 60.884 55.000 0.00 0.00 42.69 4.83
20 21 0.179220 GACTCGAAGACACTCGACCG 60.179 60.000 0.00 0.00 42.69 4.79
21 22 1.135916 CAGACTCGAAGACACTCGACC 60.136 57.143 0.00 0.00 42.69 4.79
22 23 1.532007 ACAGACTCGAAGACACTCGAC 59.468 52.381 0.00 0.00 42.69 4.20
23 24 1.799403 GACAGACTCGAAGACACTCGA 59.201 52.381 0.00 0.00 45.22 4.04
24 25 1.462705 CGACAGACTCGAAGACACTCG 60.463 57.143 0.00 0.00 46.14 4.18
25 26 2.235238 CGACAGACTCGAAGACACTC 57.765 55.000 0.00 0.00 46.14 3.51
34 35 0.591659 TGTTCCACTCGACAGACTCG 59.408 55.000 0.00 0.00 44.44 4.18
35 36 1.609555 AGTGTTCCACTCGACAGACTC 59.390 52.381 0.00 0.00 41.21 3.36
36 37 1.693627 AGTGTTCCACTCGACAGACT 58.306 50.000 0.00 0.00 41.21 3.24
37 38 2.034812 AGAAGTGTTCCACTCGACAGAC 59.965 50.000 0.00 0.00 44.62 3.51
38 39 2.034685 CAGAAGTGTTCCACTCGACAGA 59.965 50.000 0.00 0.00 44.62 3.41
39 40 2.034685 TCAGAAGTGTTCCACTCGACAG 59.965 50.000 0.00 0.00 44.62 3.51
40 41 2.028876 TCAGAAGTGTTCCACTCGACA 58.971 47.619 0.00 0.00 44.62 4.35
41 42 2.034812 ACTCAGAAGTGTTCCACTCGAC 59.965 50.000 0.00 0.00 44.62 4.20
42 43 2.293677 GACTCAGAAGTGTTCCACTCGA 59.706 50.000 0.00 0.00 44.62 4.04
43 44 2.667137 GACTCAGAAGTGTTCCACTCG 58.333 52.381 0.00 0.00 44.62 4.18
44 45 2.293677 TCGACTCAGAAGTGTTCCACTC 59.706 50.000 0.00 0.00 44.62 3.51
45 46 8.880410 GTCAATCGACTCAGAAGTGTTCCACT 62.880 46.154 0.00 0.00 41.78 4.00
46 47 2.795175 TCGACTCAGAAGTGTTCCAC 57.205 50.000 0.00 0.00 35.28 4.02
47 48 3.320826 TCAATCGACTCAGAAGTGTTCCA 59.679 43.478 0.00 0.00 35.28 3.53
48 49 3.675698 GTCAATCGACTCAGAAGTGTTCC 59.324 47.826 0.00 0.00 39.22 3.62
49 50 4.299155 TGTCAATCGACTCAGAAGTGTTC 58.701 43.478 0.00 0.00 43.06 3.18
50 51 4.302455 CTGTCAATCGACTCAGAAGTGTT 58.698 43.478 0.00 0.00 43.06 3.32
51 52 3.305676 CCTGTCAATCGACTCAGAAGTGT 60.306 47.826 8.77 0.00 43.06 3.55
52 53 3.249091 CCTGTCAATCGACTCAGAAGTG 58.751 50.000 8.77 0.00 43.06 3.16
53 54 2.894126 ACCTGTCAATCGACTCAGAAGT 59.106 45.455 8.77 0.00 43.06 3.01
54 55 3.057245 TCACCTGTCAATCGACTCAGAAG 60.057 47.826 8.77 3.14 43.06 2.85
55 56 2.890945 TCACCTGTCAATCGACTCAGAA 59.109 45.455 8.77 0.00 43.06 3.02
56 57 2.514803 TCACCTGTCAATCGACTCAGA 58.485 47.619 8.77 0.00 43.06 3.27
57 58 3.516981 ATCACCTGTCAATCGACTCAG 57.483 47.619 0.00 0.00 43.06 3.35
58 59 3.961480 AATCACCTGTCAATCGACTCA 57.039 42.857 0.00 0.00 43.06 3.41
59 60 4.499183 AGAAATCACCTGTCAATCGACTC 58.501 43.478 0.00 0.00 43.06 3.36
60 61 4.543590 AGAAATCACCTGTCAATCGACT 57.456 40.909 0.00 0.00 43.06 4.18
61 62 4.932200 AGAAGAAATCACCTGTCAATCGAC 59.068 41.667 0.00 0.00 42.93 4.20
62 63 5.152623 AGAAGAAATCACCTGTCAATCGA 57.847 39.130 0.00 0.00 0.00 3.59
63 64 6.333416 TCTAGAAGAAATCACCTGTCAATCG 58.667 40.000 0.00 0.00 0.00 3.34
64 65 7.551585 TCTCTAGAAGAAATCACCTGTCAATC 58.448 38.462 0.00 0.00 0.00 2.67
65 66 7.487822 TCTCTAGAAGAAATCACCTGTCAAT 57.512 36.000 0.00 0.00 0.00 2.57
66 67 6.918067 TCTCTAGAAGAAATCACCTGTCAA 57.082 37.500 0.00 0.00 0.00 3.18
67 68 6.438741 ACATCTCTAGAAGAAATCACCTGTCA 59.561 38.462 0.00 0.00 37.61 3.58
68 69 6.872920 ACATCTCTAGAAGAAATCACCTGTC 58.127 40.000 0.00 0.00 37.61 3.51
69 70 6.127196 GGACATCTCTAGAAGAAATCACCTGT 60.127 42.308 0.00 0.00 37.61 4.00
70 71 6.098124 AGGACATCTCTAGAAGAAATCACCTG 59.902 42.308 0.00 0.00 37.61 4.00
71 72 6.201591 AGGACATCTCTAGAAGAAATCACCT 58.798 40.000 0.00 0.00 37.61 4.00
72 73 6.478512 AGGACATCTCTAGAAGAAATCACC 57.521 41.667 0.00 0.00 37.61 4.02
73 74 6.760770 CCAAGGACATCTCTAGAAGAAATCAC 59.239 42.308 0.00 0.00 37.61 3.06
74 75 6.126940 CCCAAGGACATCTCTAGAAGAAATCA 60.127 42.308 0.00 0.00 37.61 2.57
75 76 6.126911 ACCCAAGGACATCTCTAGAAGAAATC 60.127 42.308 0.00 0.00 37.61 2.17
76 77 5.728741 ACCCAAGGACATCTCTAGAAGAAAT 59.271 40.000 0.00 0.00 37.61 2.17
77 78 5.094387 ACCCAAGGACATCTCTAGAAGAAA 58.906 41.667 0.00 0.00 37.61 2.52
78 79 4.689062 ACCCAAGGACATCTCTAGAAGAA 58.311 43.478 0.00 0.00 37.61 2.52
79 80 4.338795 ACCCAAGGACATCTCTAGAAGA 57.661 45.455 0.00 0.00 38.72 2.87
80 81 4.036971 CGTACCCAAGGACATCTCTAGAAG 59.963 50.000 0.00 0.00 0.00 2.85
81 82 3.952323 CGTACCCAAGGACATCTCTAGAA 59.048 47.826 0.00 0.00 0.00 2.10
82 83 3.552875 CGTACCCAAGGACATCTCTAGA 58.447 50.000 0.00 0.00 0.00 2.43
83 84 2.623889 CCGTACCCAAGGACATCTCTAG 59.376 54.545 0.00 0.00 0.00 2.43
84 85 2.024655 ACCGTACCCAAGGACATCTCTA 60.025 50.000 0.00 0.00 0.00 2.43
85 86 1.273098 ACCGTACCCAAGGACATCTCT 60.273 52.381 0.00 0.00 0.00 3.10
86 87 1.192428 ACCGTACCCAAGGACATCTC 58.808 55.000 0.00 0.00 0.00 2.75
87 88 2.292061 ACTACCGTACCCAAGGACATCT 60.292 50.000 0.00 0.00 0.00 2.90
88 89 2.105766 ACTACCGTACCCAAGGACATC 58.894 52.381 0.00 0.00 0.00 3.06
89 90 2.242882 ACTACCGTACCCAAGGACAT 57.757 50.000 0.00 0.00 0.00 3.06
90 91 2.014010 AACTACCGTACCCAAGGACA 57.986 50.000 0.00 0.00 0.00 4.02
91 92 2.613725 CCAAACTACCGTACCCAAGGAC 60.614 54.545 0.00 0.00 0.00 3.85
92 93 1.624813 CCAAACTACCGTACCCAAGGA 59.375 52.381 0.00 0.00 0.00 3.36
93 94 1.624813 TCCAAACTACCGTACCCAAGG 59.375 52.381 0.00 0.00 0.00 3.61
94 95 2.037511 TGTCCAAACTACCGTACCCAAG 59.962 50.000 0.00 0.00 0.00 3.61
95 96 2.037511 CTGTCCAAACTACCGTACCCAA 59.962 50.000 0.00 0.00 0.00 4.12
96 97 1.619827 CTGTCCAAACTACCGTACCCA 59.380 52.381 0.00 0.00 0.00 4.51
97 98 1.066645 CCTGTCCAAACTACCGTACCC 60.067 57.143 0.00 0.00 0.00 3.69
98 99 1.620323 ACCTGTCCAAACTACCGTACC 59.380 52.381 0.00 0.00 0.00 3.34
99 100 2.951726 GACCTGTCCAAACTACCGTAC 58.048 52.381 0.00 0.00 0.00 3.67
117 118 3.258622 GCTATGTACCTAGGGTCATGGAC 59.741 52.174 24.70 16.34 37.09 4.02
118 119 3.142217 AGCTATGTACCTAGGGTCATGGA 59.858 47.826 24.70 11.07 37.09 3.41
119 120 3.511477 AGCTATGTACCTAGGGTCATGG 58.489 50.000 22.73 21.18 37.09 3.66
120 121 4.588951 TGAAGCTATGTACCTAGGGTCATG 59.411 45.833 22.73 16.05 37.09 3.07
121 122 4.816126 TGAAGCTATGTACCTAGGGTCAT 58.184 43.478 14.81 17.90 37.09 3.06
122 123 4.259933 TGAAGCTATGTACCTAGGGTCA 57.740 45.455 14.81 11.96 37.09 4.02
123 124 4.833380 TGATGAAGCTATGTACCTAGGGTC 59.167 45.833 14.81 6.12 37.09 4.46
124 125 4.589374 GTGATGAAGCTATGTACCTAGGGT 59.411 45.833 14.81 1.17 40.16 4.34
125 126 4.021016 GGTGATGAAGCTATGTACCTAGGG 60.021 50.000 14.81 0.00 0.00 3.53
126 127 4.588951 TGGTGATGAAGCTATGTACCTAGG 59.411 45.833 7.41 7.41 0.00 3.02
127 128 5.509840 GGTGGTGATGAAGCTATGTACCTAG 60.510 48.000 1.10 1.10 0.00 3.02
128 129 4.344102 GGTGGTGATGAAGCTATGTACCTA 59.656 45.833 0.00 0.00 0.00 3.08
129 130 3.134804 GGTGGTGATGAAGCTATGTACCT 59.865 47.826 0.00 0.00 0.00 3.08
130 131 3.134804 AGGTGGTGATGAAGCTATGTACC 59.865 47.826 0.00 0.00 0.00 3.34
131 132 4.408182 AGGTGGTGATGAAGCTATGTAC 57.592 45.455 0.00 0.00 0.00 2.90
132 133 5.208890 ACTAGGTGGTGATGAAGCTATGTA 58.791 41.667 0.00 0.00 0.00 2.29
133 134 4.033709 ACTAGGTGGTGATGAAGCTATGT 58.966 43.478 0.00 0.00 0.00 2.29
134 135 4.679373 ACTAGGTGGTGATGAAGCTATG 57.321 45.455 0.00 0.00 0.00 2.23
135 136 7.730784 AGTTATACTAGGTGGTGATGAAGCTAT 59.269 37.037 0.00 0.00 0.00 2.97
136 137 7.014326 CAGTTATACTAGGTGGTGATGAAGCTA 59.986 40.741 0.00 0.00 0.00 3.32
137 138 5.900123 AGTTATACTAGGTGGTGATGAAGCT 59.100 40.000 0.00 0.00 0.00 3.74
138 139 5.986135 CAGTTATACTAGGTGGTGATGAAGC 59.014 44.000 0.00 0.00 0.00 3.86
139 140 7.348080 TCAGTTATACTAGGTGGTGATGAAG 57.652 40.000 0.00 0.00 0.00 3.02
140 141 7.344612 ACATCAGTTATACTAGGTGGTGATGAA 59.655 37.037 20.05 0.00 41.61 2.57
141 142 6.839134 ACATCAGTTATACTAGGTGGTGATGA 59.161 38.462 20.05 7.32 41.61 2.92
142 143 7.055667 ACATCAGTTATACTAGGTGGTGATG 57.944 40.000 15.10 15.10 43.64 3.07
143 144 8.777578 TTACATCAGTTATACTAGGTGGTGAT 57.222 34.615 0.00 0.00 0.00 3.06
144 145 8.777578 ATTACATCAGTTATACTAGGTGGTGA 57.222 34.615 0.00 0.00 0.00 4.02
145 146 8.861086 AGATTACATCAGTTATACTAGGTGGTG 58.139 37.037 0.00 0.00 0.00 4.17
146 147 9.435570 AAGATTACATCAGTTATACTAGGTGGT 57.564 33.333 0.00 0.00 0.00 4.16
187 188 9.263446 ACAGAAAGAGTATATTACTTGTACCCA 57.737 33.333 0.00 0.00 39.59 4.51
234 235 9.606631 GTATCTGGTAGTTCATTTGAAATCTCT 57.393 33.333 0.00 0.00 35.58 3.10
235 236 8.543774 CGTATCTGGTAGTTCATTTGAAATCTC 58.456 37.037 0.00 0.00 35.58 2.75
236 237 8.258007 TCGTATCTGGTAGTTCATTTGAAATCT 58.742 33.333 0.00 0.00 35.58 2.40
237 238 8.420374 TCGTATCTGGTAGTTCATTTGAAATC 57.580 34.615 0.00 0.00 35.58 2.17
238 239 8.786826 TTCGTATCTGGTAGTTCATTTGAAAT 57.213 30.769 0.00 0.00 35.58 2.17
239 240 8.664798 CATTCGTATCTGGTAGTTCATTTGAAA 58.335 33.333 0.00 0.00 35.58 2.69
240 241 7.822334 ACATTCGTATCTGGTAGTTCATTTGAA 59.178 33.333 0.00 0.00 0.00 2.69
241 242 7.327975 ACATTCGTATCTGGTAGTTCATTTGA 58.672 34.615 0.00 0.00 0.00 2.69
242 243 7.539712 ACATTCGTATCTGGTAGTTCATTTG 57.460 36.000 0.00 0.00 0.00 2.32
280 281 9.624373 AGCAAAATGAATGAATCTACACTCTAT 57.376 29.630 0.00 0.00 0.00 1.98
281 282 9.453572 AAGCAAAATGAATGAATCTACACTCTA 57.546 29.630 0.00 0.00 0.00 2.43
282 283 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
283 284 7.427606 CGAAGCAAAATGAATGAATCTACACTC 59.572 37.037 0.00 0.00 0.00 3.51
284 285 7.119699 TCGAAGCAAAATGAATGAATCTACACT 59.880 33.333 0.00 0.00 0.00 3.55
285 286 7.243487 TCGAAGCAAAATGAATGAATCTACAC 58.757 34.615 0.00 0.00 0.00 2.90
286 287 7.376435 TCGAAGCAAAATGAATGAATCTACA 57.624 32.000 0.00 0.00 0.00 2.74
287 288 7.912250 ACATCGAAGCAAAATGAATGAATCTAC 59.088 33.333 0.00 0.00 0.00 2.59
288 289 7.988737 ACATCGAAGCAAAATGAATGAATCTA 58.011 30.769 0.00 0.00 0.00 1.98
289 290 6.860080 ACATCGAAGCAAAATGAATGAATCT 58.140 32.000 0.00 0.00 0.00 2.40
290 291 7.912250 ACTACATCGAAGCAAAATGAATGAATC 59.088 33.333 0.00 0.00 0.00 2.52
291 292 7.765307 ACTACATCGAAGCAAAATGAATGAAT 58.235 30.769 0.00 0.00 0.00 2.57
292 293 7.094848 TGACTACATCGAAGCAAAATGAATGAA 60.095 33.333 0.00 0.00 0.00 2.57
293 294 6.371271 TGACTACATCGAAGCAAAATGAATGA 59.629 34.615 0.00 0.00 0.00 2.57
294 295 6.467047 GTGACTACATCGAAGCAAAATGAATG 59.533 38.462 0.00 0.00 0.00 2.67
295 296 6.372659 AGTGACTACATCGAAGCAAAATGAAT 59.627 34.615 0.00 0.00 0.00 2.57
296 297 5.700832 AGTGACTACATCGAAGCAAAATGAA 59.299 36.000 0.00 0.00 0.00 2.57
297 298 5.237815 AGTGACTACATCGAAGCAAAATGA 58.762 37.500 0.00 0.00 0.00 2.57
298 299 5.536554 AGTGACTACATCGAAGCAAAATG 57.463 39.130 0.00 0.00 0.00 2.32
299 300 5.470098 ACAAGTGACTACATCGAAGCAAAAT 59.530 36.000 0.00 0.00 0.00 1.82
300 301 4.814234 ACAAGTGACTACATCGAAGCAAAA 59.186 37.500 0.00 0.00 0.00 2.44
301 302 4.377021 ACAAGTGACTACATCGAAGCAAA 58.623 39.130 0.00 0.00 0.00 3.68
302 303 3.987868 GACAAGTGACTACATCGAAGCAA 59.012 43.478 0.00 0.00 0.00 3.91
303 304 3.005367 TGACAAGTGACTACATCGAAGCA 59.995 43.478 0.00 0.00 0.00 3.91
304 305 3.575630 TGACAAGTGACTACATCGAAGC 58.424 45.455 0.00 0.00 0.00 3.86
305 306 6.525121 TTTTGACAAGTGACTACATCGAAG 57.475 37.500 0.00 0.00 0.00 3.79
306 307 6.912203 TTTTTGACAAGTGACTACATCGAA 57.088 33.333 0.00 0.00 0.00 3.71
307 308 7.490962 AATTTTTGACAAGTGACTACATCGA 57.509 32.000 0.00 0.00 0.00 3.59
308 309 8.560576 AAAATTTTTGACAAGTGACTACATCG 57.439 30.769 0.00 0.00 0.00 3.84
316 317 9.581099 GGTCTTTCTAAAATTTTTGACAAGTGA 57.419 29.630 13.53 6.32 0.00 3.41
317 318 9.586435 AGGTCTTTCTAAAATTTTTGACAAGTG 57.414 29.630 13.53 4.52 0.00 3.16
342 343 6.607004 ACTCCCATCCGTTCCTAAATATAG 57.393 41.667 0.00 0.00 0.00 1.31
343 344 9.772605 TTATACTCCCATCCGTTCCTAAATATA 57.227 33.333 0.00 0.00 0.00 0.86
344 345 8.674925 TTATACTCCCATCCGTTCCTAAATAT 57.325 34.615 0.00 0.00 0.00 1.28
345 346 8.495160 TTTATACTCCCATCCGTTCCTAAATA 57.505 34.615 0.00 0.00 0.00 1.40
346 347 7.383156 TTTATACTCCCATCCGTTCCTAAAT 57.617 36.000 0.00 0.00 0.00 1.40
347 348 6.811634 TTTATACTCCCATCCGTTCCTAAA 57.188 37.500 0.00 0.00 0.00 1.85
348 349 6.384886 AGTTTTATACTCCCATCCGTTCCTAA 59.615 38.462 0.00 0.00 28.23 2.69
349 350 5.901276 AGTTTTATACTCCCATCCGTTCCTA 59.099 40.000 0.00 0.00 28.23 2.94
350 351 4.720273 AGTTTTATACTCCCATCCGTTCCT 59.280 41.667 0.00 0.00 28.23 3.36
351 352 5.032327 AGTTTTATACTCCCATCCGTTCC 57.968 43.478 0.00 0.00 28.23 3.62
394 396 0.368907 CCTCGTGCGATTTAACGTGG 59.631 55.000 0.00 2.42 44.13 4.94
417 419 1.620323 GCAAATTGAGCCCAAAGGAGT 59.380 47.619 0.00 0.00 35.67 3.85
466 472 1.497722 GGTTGAAGAAAGCGCCTCG 59.502 57.895 2.29 0.00 0.00 4.63
475 481 3.245122 GGTACAATCAGGGGGTTGAAGAA 60.245 47.826 0.00 0.00 0.00 2.52
488 494 2.270850 GCCGCTGGGGTACAATCA 59.729 61.111 12.70 0.00 38.44 2.57
551 557 1.675936 GGGGTAGGGAGAGGGATGGA 61.676 65.000 0.00 0.00 0.00 3.41
552 558 1.152008 GGGGTAGGGAGAGGGATGG 60.152 68.421 0.00 0.00 0.00 3.51
553 559 1.534235 CGGGGTAGGGAGAGGGATG 60.534 68.421 0.00 0.00 0.00 3.51
554 560 1.301913 TTCGGGGTAGGGAGAGGGAT 61.302 60.000 0.00 0.00 0.00 3.85
612 644 3.723922 ATTTCCGGTCGGGGTGGG 61.724 66.667 9.68 0.00 36.01 4.61
613 645 2.265467 ATCATTTCCGGTCGGGGTGG 62.265 60.000 9.68 0.00 36.01 4.61
614 646 1.095228 CATCATTTCCGGTCGGGGTG 61.095 60.000 9.68 6.44 36.01 4.61
685 717 4.785453 GAGCCTGCGGAGGTTGGG 62.785 72.222 24.99 0.00 42.15 4.12
686 718 4.785453 GGAGCCTGCGGAGGTTGG 62.785 72.222 24.99 0.00 42.15 3.77
687 719 3.672295 GAGGAGCCTGCGGAGGTTG 62.672 68.421 24.99 0.00 42.15 3.77
688 720 3.394836 GAGGAGCCTGCGGAGGTT 61.395 66.667 24.99 19.66 42.15 3.50
689 721 4.390556 AGAGGAGCCTGCGGAGGT 62.391 66.667 24.99 11.27 42.15 3.85
690 722 3.847602 CAGAGGAGCCTGCGGAGG 61.848 72.222 20.23 20.23 43.19 4.30
713 745 4.851214 AGGAGGAGGAGGAGGCGC 62.851 72.222 0.00 0.00 0.00 6.53
714 746 2.520741 GAGGAGGAGGAGGAGGCG 60.521 72.222 0.00 0.00 0.00 5.52
715 747 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
716 748 1.075600 GTGGAGGAGGAGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
717 749 1.075600 GGTGGAGGAGGAGGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
718 750 1.547755 AGGTGGAGGAGGAGGAGGA 60.548 63.158 0.00 0.00 0.00 3.71
719 751 1.075600 GAGGTGGAGGAGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
720 752 1.454847 CGAGGTGGAGGAGGAGGAG 60.455 68.421 0.00 0.00 0.00 3.69
721 753 2.212794 GACGAGGTGGAGGAGGAGGA 62.213 65.000 0.00 0.00 0.00 3.71
722 754 1.755008 GACGAGGTGGAGGAGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
723 755 1.755008 GGACGAGGTGGAGGAGGAG 60.755 68.421 0.00 0.00 0.00 3.69
724 756 2.359404 GGACGAGGTGGAGGAGGA 59.641 66.667 0.00 0.00 0.00 3.71
725 757 2.760385 GGGACGAGGTGGAGGAGG 60.760 72.222 0.00 0.00 0.00 4.30
1386 1582 2.203509 CCGAGGAGCTCCGGGTAT 60.204 66.667 28.32 13.54 41.89 2.73
1533 1729 2.635714 AGGTGTTCGACGAAAGGTTTT 58.364 42.857 12.67 0.00 0.00 2.43
1791 1987 3.260632 TGACTCTTCCGAAATCATCACCA 59.739 43.478 0.00 0.00 0.00 4.17
1908 2104 1.746615 CCCCACGACCATCTTGCTG 60.747 63.158 0.00 0.00 0.00 4.41
1941 2137 6.712095 TCTTCATTATATCCATGTTCAGTGCC 59.288 38.462 0.00 0.00 0.00 5.01
2075 2271 2.536066 ACCCCTTTTTAGCCACAATCC 58.464 47.619 0.00 0.00 0.00 3.01
2172 2368 8.827832 AATTATCATCCTCCATTTCTTCAACA 57.172 30.769 0.00 0.00 0.00 3.33
2202 2398 3.179830 CTCCACGAACCTATCTTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
2217 2413 2.926200 CTCATCTTGTACTTGCTCCACG 59.074 50.000 0.00 0.00 0.00 4.94
2545 2846 6.183360 CCCATATGAAAATGCCAAATGTGTTG 60.183 38.462 3.65 0.00 0.00 3.33
2546 2847 5.881443 CCCATATGAAAATGCCAAATGTGTT 59.119 36.000 3.65 0.00 0.00 3.32
2650 2951 4.408993 TGCAGATTCACATTCAGAAACG 57.591 40.909 0.00 0.00 0.00 3.60
2666 3070 1.281577 TGCAGTGGGTCATAATGCAGA 59.718 47.619 0.00 0.00 41.65 4.26
2699 3103 5.425398 CACAATTTGTTCATTGTTTGCTCG 58.575 37.500 0.00 0.00 43.54 5.03
2723 3127 6.595682 ACTGGGGATGTCAGATTTATAACAG 58.404 40.000 0.00 0.00 36.22 3.16
2741 3145 5.557576 TCATATCTCAATTCTGACTGGGG 57.442 43.478 0.00 0.00 0.00 4.96
2810 3215 4.956075 AGAGACAAGGTGACACCAAAAATT 59.044 37.500 26.30 8.75 41.95 1.82
2944 3358 5.048153 TCAGTTCTCGACAACATAGTCAG 57.952 43.478 6.33 0.00 38.43 3.51
2958 3372 5.826586 TCTCTGCGATCTTTATCAGTTCTC 58.173 41.667 0.00 0.00 31.93 2.87
3095 3557 3.380004 CACTATCTGGAGACTGGAGTGAC 59.620 52.174 0.00 0.00 41.61 3.67
3096 3558 3.625853 CACTATCTGGAGACTGGAGTGA 58.374 50.000 0.00 0.00 41.61 3.41
3179 3646 1.265635 TCCACTTTTGCGATGGAAACG 59.734 47.619 0.00 0.00 39.60 3.60
3195 3662 1.093159 CTTTGCTGCAGAGGATCCAC 58.907 55.000 20.43 8.01 33.66 4.02
3219 3697 2.607038 GGAACTGAAATGTTTCCGGCAC 60.607 50.000 0.00 0.00 36.36 5.01
3223 3701 4.378459 GCTACTGGAACTGAAATGTTTCCG 60.378 45.833 3.26 0.00 36.36 4.30
3249 3727 2.098770 GCAGCAATTTCTCCAGATGGAC 59.901 50.000 0.00 0.00 39.78 4.02


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

AutoCloner maintained by Alex Coulton.