Multiple sequence alignment - TraesCS5D01G269400

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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 TraesCS5D01G269400 chr5D 100.000 2417 0 0 1 2417 372453297 372455713 0.000000e+00 4464.0
1 TraesCS5D01G269400 chr5D 88.220 382 39 4 1081 1456 372507933 372508314 3.660000e-123 451.0
2 TraesCS5D01G269400 chr5A 86.906 1031 65 27 557 1577 475596203 475597173 0.000000e+00 1092.0
3 TraesCS5D01G269400 chr5A 87.568 555 59 8 893 1442 475599364 475599913 3.390000e-178 634.0
4 TraesCS5D01G269400 chr5A 83.955 268 36 6 1 263 475595587 475595852 1.430000e-62 250.0
5 TraesCS5D01G269400 chr5A 90.909 88 8 0 335 422 475595895 475595982 4.220000e-23 119.0
6 TraesCS5D01G269400 chr5A 91.935 62 4 1 459 520 475596131 475596191 4.280000e-13 86.1
7 TraesCS5D01G269400 chr5B 90.000 720 50 9 882 1590 442821738 442822446 0.000000e+00 911.0
8 TraesCS5D01G269400 chr5B 90.566 636 51 4 954 1589 442851081 442851707 0.000000e+00 833.0
9 TraesCS5D01G269400 chr5B 87.525 497 22 19 337 833 442821269 442821725 2.730000e-149 538.0
10 TraesCS5D01G269400 chr5B 81.663 469 77 7 1951 2416 442822863 442823325 4.880000e-102 381.0
11 TraesCS5D01G269400 chr5B 82.249 338 46 9 862 1198 442853976 442854300 1.830000e-71 279.0
12 TraesCS5D01G269400 chr5B 88.018 217 26 0 1207 1423 442857982 442858198 8.570000e-65 257.0
13 TraesCS5D01G269400 chr5B 86.957 138 15 2 2282 2417 442852639 442852775 4.160000e-33 152.0
14 TraesCS5D01G269400 chr5B 82.558 172 26 4 2219 2389 289740008 289739840 5.380000e-32 148.0
15 TraesCS5D01G269400 chr4D 86.607 112 11 4 15 124 98917045 98917154 1.170000e-23 121.0
16 TraesCS5D01G269400 chr1B 85.455 110 11 3 15 124 632658637 632658741 2.540000e-20 110.0
17 TraesCS5D01G269400 chr1B 82.500 80 11 3 5 83 360602096 360602019 1.550000e-07 67.6
18 TraesCS5D01G269400 chr4A 82.540 126 18 4 1 124 477053351 477053228 9.140000e-20 108.0
19 TraesCS5D01G269400 chr3D 83.036 112 15 4 1 110 504957317 504957426 5.500000e-17 99.0
20 TraesCS5D01G269400 chr3D 78.261 138 19 4 1 127 116048556 116048419 7.160000e-11 78.7
21 TraesCS5D01G269400 chr3B 78.358 134 19 3 1 124 169634867 169634734 7.160000e-11 78.7
22 TraesCS5D01G269400 chr7A 80.808 99 16 3 11 107 734538047 734538144 9.270000e-10 75.0


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 TraesCS5D01G269400 chr5D 372453297 372455713 2416 False 4464.00 4464 100.0000 1 2417 1 chr5D.!!$F1 2416
1 TraesCS5D01G269400 chr5A 475595587 475599913 4326 False 436.22 1092 88.2546 1 1577 5 chr5A.!!$F1 1576
2 TraesCS5D01G269400 chr5B 442821269 442823325 2056 False 610.00 911 86.3960 337 2416 3 chr5B.!!$F1 2079
3 TraesCS5D01G269400 chr5B 442851081 442858198 7117 False 380.25 833 86.9475 862 2417 4 chr5B.!!$F2 1555

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
532 663 0.110464 GCTGCTCGTCTCAAACTTGC 60.11 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2193 0.034756 TCCGGGTTGTCTGTCACATG 59.965 55.0 0.0 0.0 33.9 3.21 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
84 86 5.856126 TTCATGAATCGTGTGGAACTTAC 57.144 39.130 3.38 0.00 38.04 2.34
89 91 7.491372 TCATGAATCGTGTGGAACTTACTTATC 59.509 37.037 2.06 0.00 38.04 1.75
92 94 7.277760 TGAATCGTGTGGAACTTACTTATCATG 59.722 37.037 0.00 0.00 38.04 3.07
96 98 7.015289 CGTGTGGAACTTACTTATCATGTTTG 58.985 38.462 0.00 0.00 38.04 2.93
114 116 5.512473 TGTTTGGTTTTTATACGTGTGCTC 58.488 37.500 0.00 0.00 0.00 4.26
120 122 5.907391 GGTTTTTATACGTGTGCTCATATGC 59.093 40.000 0.00 0.00 0.00 3.14
137 139 7.015226 TCATATGCAGTCAAGTTTATTTCGG 57.985 36.000 0.00 0.00 0.00 4.30
141 143 3.252458 GCAGTCAAGTTTATTTCGGTGGT 59.748 43.478 0.00 0.00 0.00 4.16
142 144 4.453136 GCAGTCAAGTTTATTTCGGTGGTA 59.547 41.667 0.00 0.00 0.00 3.25
143 145 5.049267 GCAGTCAAGTTTATTTCGGTGGTAA 60.049 40.000 0.00 0.00 0.00 2.85
201 203 5.642491 ACTCCACTAAATTTAGAAGTTCGGC 59.358 40.000 27.92 0.00 34.84 5.54
202 204 4.628333 TCCACTAAATTTAGAAGTTCGGCG 59.372 41.667 27.92 0.00 34.84 6.46
203 205 4.201783 CCACTAAATTTAGAAGTTCGGCGG 60.202 45.833 27.92 11.53 34.84 6.13
204 206 4.390909 CACTAAATTTAGAAGTTCGGCGGT 59.609 41.667 27.92 2.83 34.84 5.68
206 208 1.084289 ATTTAGAAGTTCGGCGGTGC 58.916 50.000 7.21 0.00 0.00 5.01
207 209 0.249953 TTTAGAAGTTCGGCGGTGCA 60.250 50.000 7.21 0.00 0.00 4.57
208 210 0.669318 TTAGAAGTTCGGCGGTGCAG 60.669 55.000 7.21 0.00 0.00 4.41
209 211 1.529152 TAGAAGTTCGGCGGTGCAGA 61.529 55.000 7.21 0.00 0.00 4.26
210 212 2.665185 AAGTTCGGCGGTGCAGAC 60.665 61.111 7.21 0.00 31.79 3.51
211 213 3.454587 AAGTTCGGCGGTGCAGACA 62.455 57.895 7.21 0.00 31.79 3.41
215 217 1.169661 TTCGGCGGTGCAGACAAAAT 61.170 50.000 7.21 0.00 31.79 1.82
216 218 1.169661 TCGGCGGTGCAGACAAAATT 61.170 50.000 7.21 0.00 0.00 1.82
217 219 0.318614 CGGCGGTGCAGACAAAATTT 60.319 50.000 0.00 0.00 0.00 1.82
218 220 1.068885 CGGCGGTGCAGACAAAATTTA 60.069 47.619 0.00 0.00 0.00 1.40
219 221 2.595386 GGCGGTGCAGACAAAATTTAG 58.405 47.619 0.00 0.00 0.00 1.85
220 222 2.030274 GGCGGTGCAGACAAAATTTAGT 60.030 45.455 0.00 0.00 0.00 2.24
221 223 3.189702 GGCGGTGCAGACAAAATTTAGTA 59.810 43.478 0.00 0.00 0.00 1.82
222 224 4.403453 GCGGTGCAGACAAAATTTAGTAG 58.597 43.478 0.00 0.00 0.00 2.57
223 225 4.153475 GCGGTGCAGACAAAATTTAGTAGA 59.847 41.667 0.00 0.00 0.00 2.59
224 226 5.618561 CGGTGCAGACAAAATTTAGTAGAC 58.381 41.667 0.00 0.00 0.00 2.59
225 227 5.408604 CGGTGCAGACAAAATTTAGTAGACT 59.591 40.000 0.00 0.00 0.00 3.24
226 228 6.603095 GGTGCAGACAAAATTTAGTAGACTG 58.397 40.000 0.00 0.00 0.00 3.51
259 263 6.709643 TCACTATAGCTAACTCGACGTTTAC 58.290 40.000 0.00 0.64 37.05 2.01
263 267 2.816087 AGCTAACTCGACGTTTACTCCA 59.184 45.455 5.74 0.00 37.05 3.86
264 268 3.442977 AGCTAACTCGACGTTTACTCCAT 59.557 43.478 5.74 0.00 37.05 3.41
266 270 4.624452 GCTAACTCGACGTTTACTCCATTT 59.376 41.667 5.74 0.00 37.05 2.32
267 271 5.220172 GCTAACTCGACGTTTACTCCATTTC 60.220 44.000 5.74 0.00 37.05 2.17
269 273 4.879598 ACTCGACGTTTACTCCATTTCTT 58.120 39.130 0.00 0.00 0.00 2.52
270 274 4.684703 ACTCGACGTTTACTCCATTTCTTG 59.315 41.667 0.00 0.00 0.00 3.02
271 275 7.719964 AACTCGACGTTTACTCCATTTCTTGG 61.720 42.308 0.00 0.00 38.73 3.61
272 276 3.124636 CGACGTTTACTCCATTTCTTGGG 59.875 47.826 0.00 0.00 46.45 4.12
279 283 2.442236 TCCATTTCTTGGGGATCAGC 57.558 50.000 0.00 0.00 46.45 4.26
280 284 1.925255 TCCATTTCTTGGGGATCAGCT 59.075 47.619 0.00 0.00 46.45 4.24
282 286 2.429610 CCATTTCTTGGGGATCAGCTTG 59.570 50.000 0.00 0.00 42.33 4.01
283 287 3.359033 CATTTCTTGGGGATCAGCTTGA 58.641 45.455 0.00 0.00 0.00 3.02
286 290 2.485659 TCTTGGGGATCAGCTTGAGAT 58.514 47.619 0.00 0.00 0.00 2.75
287 291 2.172082 TCTTGGGGATCAGCTTGAGATG 59.828 50.000 0.00 0.00 0.00 2.90
288 292 0.182061 TGGGGATCAGCTTGAGATGC 59.818 55.000 0.00 0.00 33.63 3.91
289 293 0.473326 GGGGATCAGCTTGAGATGCT 59.527 55.000 4.43 0.00 42.06 3.79
290 294 1.542987 GGGGATCAGCTTGAGATGCTC 60.543 57.143 4.43 0.00 38.92 4.26
291 295 1.417145 GGGATCAGCTTGAGATGCTCT 59.583 52.381 4.43 0.00 38.92 4.09
292 296 2.548493 GGGATCAGCTTGAGATGCTCTC 60.548 54.545 4.43 6.31 43.65 3.20
294 298 3.181463 GGATCAGCTTGAGATGCTCTCTT 60.181 47.826 12.45 0.00 43.73 2.85
295 299 3.977134 TCAGCTTGAGATGCTCTCTTT 57.023 42.857 12.45 0.00 43.73 2.52
297 301 4.649692 TCAGCTTGAGATGCTCTCTTTTT 58.350 39.130 12.45 0.00 43.73 1.94
318 322 5.886960 TTTAGAAAAGGAGCTTGAGATGC 57.113 39.130 0.00 0.00 0.00 3.91
319 323 3.717452 AGAAAAGGAGCTTGAGATGCT 57.283 42.857 0.00 0.00 44.24 3.79
326 330 0.831966 AGCTTGAGATGCTCTGAGGG 59.168 55.000 6.83 0.00 35.67 4.30
327 331 0.814812 GCTTGAGATGCTCTGAGGGC 60.815 60.000 0.00 0.00 0.00 5.19
328 332 0.540454 CTTGAGATGCTCTGAGGGCA 59.460 55.000 10.50 10.50 44.05 5.36
329 333 0.251354 TTGAGATGCTCTGAGGGCAC 59.749 55.000 10.23 3.71 42.69 5.01
330 334 1.227205 GAGATGCTCTGAGGGCACG 60.227 63.158 10.23 0.00 42.69 5.34
331 335 2.202987 GATGCTCTGAGGGCACGG 60.203 66.667 10.23 0.00 42.69 4.94
332 336 2.685017 ATGCTCTGAGGGCACGGA 60.685 61.111 10.23 0.00 42.69 4.69
333 337 2.244117 GATGCTCTGAGGGCACGGAA 62.244 60.000 10.23 0.00 42.69 4.30
441 572 1.415659 CACCAAAAACCATCCTGGCAA 59.584 47.619 0.00 0.00 42.67 4.52
470 601 7.540745 GCGTGAGGTACATTTGTTAATCAATTT 59.459 33.333 0.00 0.00 35.84 1.82
486 617 7.624360 AATCAATTTATAAGGCGTCTGTTGA 57.376 32.000 0.00 0.00 0.00 3.18
530 661 1.506493 CTGCTGCTCGTCTCAAACTT 58.494 50.000 0.00 0.00 0.00 2.66
531 662 1.194098 CTGCTGCTCGTCTCAAACTTG 59.806 52.381 0.00 0.00 0.00 3.16
532 663 0.110464 GCTGCTCGTCTCAAACTTGC 60.110 55.000 0.00 0.00 0.00 4.01
533 664 1.220529 CTGCTCGTCTCAAACTTGCA 58.779 50.000 0.00 0.00 34.29 4.08
534 665 1.194098 CTGCTCGTCTCAAACTTGCAG 59.806 52.381 0.00 0.00 41.72 4.41
535 666 0.514691 GCTCGTCTCAAACTTGCAGG 59.485 55.000 0.00 0.00 0.00 4.85
536 667 0.514691 CTCGTCTCAAACTTGCAGGC 59.485 55.000 0.00 0.00 0.00 4.85
537 668 0.884704 TCGTCTCAAACTTGCAGGCC 60.885 55.000 0.00 0.00 0.00 5.19
538 669 1.856265 CGTCTCAAACTTGCAGGCCC 61.856 60.000 0.00 0.00 0.00 5.80
539 670 0.538287 GTCTCAAACTTGCAGGCCCT 60.538 55.000 0.00 0.00 0.00 5.19
540 671 0.250901 TCTCAAACTTGCAGGCCCTC 60.251 55.000 0.00 0.00 0.00 4.30
541 672 1.580845 CTCAAACTTGCAGGCCCTCG 61.581 60.000 0.00 0.00 0.00 4.63
542 673 2.282462 AAACTTGCAGGCCCTCGG 60.282 61.111 0.00 0.00 0.00 4.63
543 674 3.133365 AAACTTGCAGGCCCTCGGT 62.133 57.895 0.00 0.00 0.00 4.69
544 675 3.553095 AACTTGCAGGCCCTCGGTC 62.553 63.158 0.00 0.00 0.00 4.79
551 682 3.782443 GGCCCTCGGTCGGTGAAT 61.782 66.667 0.00 0.00 0.00 2.57
552 683 2.511600 GCCCTCGGTCGGTGAATG 60.512 66.667 0.00 0.00 0.00 2.67
553 684 3.014085 GCCCTCGGTCGGTGAATGA 62.014 63.158 0.00 0.00 0.00 2.57
554 685 1.153628 CCCTCGGTCGGTGAATGAC 60.154 63.158 0.00 0.00 35.60 3.06
594 725 4.301027 CTCTATGGGCGCCCGGTC 62.301 72.222 39.00 17.48 39.42 4.79
596 727 4.910585 CTATGGGCGCCCGGTCAC 62.911 72.222 39.00 16.26 39.42 3.67
643 774 1.429463 GTCGCCACTCTTTGAACGAT 58.571 50.000 0.00 0.00 36.42 3.73
644 775 1.126846 GTCGCCACTCTTTGAACGATG 59.873 52.381 0.00 0.00 36.42 3.84
645 776 1.000394 TCGCCACTCTTTGAACGATGA 60.000 47.619 0.00 0.00 31.17 2.92
646 777 1.126846 CGCCACTCTTTGAACGATGAC 59.873 52.381 0.00 0.00 0.00 3.06
854 986 0.380733 GGCAAGGCAAATACGGTAGC 59.619 55.000 0.00 0.00 0.00 3.58
856 988 1.202143 GCAAGGCAAATACGGTAGCAC 60.202 52.381 0.00 0.00 0.00 4.40
857 989 2.356135 CAAGGCAAATACGGTAGCACT 58.644 47.619 0.00 0.00 0.00 4.40
858 990 3.527533 CAAGGCAAATACGGTAGCACTA 58.472 45.455 0.00 0.00 0.00 2.74
859 991 3.175109 AGGCAAATACGGTAGCACTAC 57.825 47.619 0.00 0.00 35.40 2.73
860 992 2.764572 AGGCAAATACGGTAGCACTACT 59.235 45.455 7.69 0.00 36.36 2.57
861 993 3.121544 GGCAAATACGGTAGCACTACTC 58.878 50.000 7.69 0.00 36.36 2.59
862 994 3.121544 GCAAATACGGTAGCACTACTCC 58.878 50.000 7.69 0.00 36.36 3.85
863 995 3.429822 GCAAATACGGTAGCACTACTCCA 60.430 47.826 7.69 0.00 36.36 3.86
864 996 4.751060 CAAATACGGTAGCACTACTCCAA 58.249 43.478 7.69 0.00 36.36 3.53
865 997 4.382345 AATACGGTAGCACTACTCCAAC 57.618 45.455 7.69 0.00 36.36 3.77
866 998 1.920610 ACGGTAGCACTACTCCAACT 58.079 50.000 7.69 0.00 36.36 3.16
872 1004 1.694150 AGCACTACTCCAACTGAAGCA 59.306 47.619 0.00 0.00 0.00 3.91
877 1009 1.670406 CTCCAACTGAAGCAGCGCT 60.670 57.895 2.64 2.64 42.56 5.92
878 1010 1.909141 CTCCAACTGAAGCAGCGCTG 61.909 60.000 32.83 32.83 39.62 5.18
880 1012 3.360340 AACTGAAGCAGCGCTGGC 61.360 61.111 36.47 27.47 39.62 4.85
905 1037 6.727824 ATAAATAGCTGCCGACACATATTC 57.272 37.500 0.00 0.00 0.00 1.75
906 1038 2.526304 TAGCTGCCGACACATATTCC 57.474 50.000 0.00 0.00 0.00 3.01
907 1039 0.179045 AGCTGCCGACACATATTCCC 60.179 55.000 0.00 0.00 0.00 3.97
911 1043 1.238439 GCCGACACATATTCCCCATG 58.762 55.000 0.00 0.00 0.00 3.66
915 1047 2.158827 CGACACATATTCCCCATGTCCA 60.159 50.000 0.00 0.00 37.05 4.02
923 1055 0.112218 TCCCCATGTCCACAAACCAG 59.888 55.000 0.00 0.00 0.00 4.00
926 1058 0.827089 CCATGTCCACAAACCAGCCA 60.827 55.000 0.00 0.00 0.00 4.75
932 1064 0.523072 CCACAAACCAGCCAAGATCG 59.477 55.000 0.00 0.00 0.00 3.69
939 1080 1.354337 CCAGCCAAGATCGACACACG 61.354 60.000 0.00 0.00 44.09 4.49
979 1121 2.492484 CCTGAAACTAGCGTCAGTAGGT 59.508 50.000 17.59 0.00 39.76 3.08
988 1130 2.011046 GCGTCAGTAGGTACCGAGAGT 61.011 57.143 6.18 0.00 0.00 3.24
1127 1269 4.880537 CGGCCGGCTCTGCTACAG 62.881 72.222 28.56 2.86 0.00 2.74
1158 1300 1.118356 GGGAGATCATGAGCCTCCGT 61.118 60.000 27.26 5.33 45.62 4.69
1188 1330 2.362800 GCACTTCGGTGTCGACGAC 61.363 63.158 20.97 20.97 45.92 4.34
1232 1374 2.809601 CGCAAAGCTCTACCGCGT 60.810 61.111 4.92 0.00 40.99 6.01
1248 1390 2.202058 GTTCTGTTCGCGCGCTTC 60.202 61.111 30.48 18.60 0.00 3.86
1429 1571 1.734465 CTGCCTGACCGATTCTGTTTC 59.266 52.381 0.00 0.00 0.00 2.78
1440 1588 5.877012 ACCGATTCTGTTTCTACTACTACGA 59.123 40.000 0.00 0.00 0.00 3.43
1548 1700 3.917329 CCTCAATGGCATTCAGCTATG 57.083 47.619 10.36 0.00 44.46 2.23
1576 1732 7.502177 ACGTAATTGTGTATTTACAGAGACG 57.498 36.000 12.90 12.90 37.62 4.18
1584 1740 7.094631 TGTGTATTTACAGAGACGTTTATGCT 58.905 34.615 0.00 0.00 36.78 3.79
1590 1746 4.831741 CAGAGACGTTTATGCTCTGTTC 57.168 45.455 18.37 0.00 46.51 3.18
1595 1751 4.081420 AGACGTTTATGCTCTGTTCAGGAT 60.081 41.667 0.00 0.00 0.00 3.24
1598 1754 5.122396 ACGTTTATGCTCTGTTCAGGATTTC 59.878 40.000 0.00 0.00 0.00 2.17
1599 1755 5.122239 CGTTTATGCTCTGTTCAGGATTTCA 59.878 40.000 0.00 0.00 0.00 2.69
1602 1758 4.564782 TGCTCTGTTCAGGATTTCATCT 57.435 40.909 0.00 0.00 0.00 2.90
1639 1795 9.933723 TTAATTTACCGATTAATCCCTACTAGC 57.066 33.333 9.87 0.00 0.00 3.42
1651 1807 3.954904 TCCCTACTAGCAGAGTCATTGAC 59.045 47.826 8.82 8.82 39.81 3.18
1658 1814 1.565305 CAGAGTCATTGACTAGCCGC 58.435 55.000 19.00 6.80 43.53 6.53
1659 1815 1.134995 CAGAGTCATTGACTAGCCGCA 60.135 52.381 19.00 0.00 43.53 5.69
1660 1816 1.759445 AGAGTCATTGACTAGCCGCAT 59.241 47.619 19.00 0.00 43.53 4.73
1661 1817 2.169352 AGAGTCATTGACTAGCCGCATT 59.831 45.455 19.00 0.00 43.53 3.56
1663 1819 3.722147 AGTCATTGACTAGCCGCATTAG 58.278 45.455 17.63 0.00 41.51 1.73
1670 1855 7.661437 TCATTGACTAGCCGCATTAGATTAATT 59.339 33.333 0.00 0.00 0.00 1.40
1672 1857 5.700832 TGACTAGCCGCATTAGATTAATTGG 59.299 40.000 0.00 0.00 0.00 3.16
1682 1867 9.248291 CGCATTAGATTAATTGGTTAATTTGCT 57.752 29.630 0.00 0.00 39.88 3.91
1728 1928 3.680937 CGCCTACCAGTTAACGATTTTCA 59.319 43.478 0.00 0.00 0.00 2.69
1729 1929 4.331717 CGCCTACCAGTTAACGATTTTCAT 59.668 41.667 0.00 0.00 0.00 2.57
1731 1931 6.036300 CGCCTACCAGTTAACGATTTTCATAA 59.964 38.462 0.00 0.00 0.00 1.90
1737 1937 8.788806 ACCAGTTAACGATTTTCATAACAATGA 58.211 29.630 0.00 0.00 32.10 2.57
1762 1962 7.960793 AGTTTGTGTACTATTTTCATACGAGC 58.039 34.615 0.00 0.00 0.00 5.03
1806 2032 4.040706 AGAACCATCACATTTGTGCCAAAT 59.959 37.500 5.81 7.18 45.25 2.32
1833 2059 5.723672 TCTCCATCGTTTACTCTCAAACT 57.276 39.130 0.00 0.00 36.46 2.66
1844 2070 4.825546 ACTCTCAAACTGTCTGCATTTG 57.174 40.909 3.78 3.78 35.15 2.32
1847 2074 5.173774 TCTCAAACTGTCTGCATTTGTTC 57.826 39.130 9.01 0.00 35.33 3.18
1858 2085 2.029470 TGCATTTGTTCGGACCCATTTC 60.029 45.455 0.00 0.00 0.00 2.17
1870 2097 3.768757 GGACCCATTTCACCATTCAATGA 59.231 43.478 0.00 0.00 30.66 2.57
1892 2153 5.270967 GAGGTATCTCATCAAACCGAAGGC 61.271 50.000 0.00 0.00 46.04 4.35
1904 2165 1.247567 CCGAAGGCAAACCAATGAGT 58.752 50.000 0.00 0.00 46.14 3.41
1965 2226 1.901464 CCGGACCCACCCAAAACTG 60.901 63.158 0.00 0.00 34.64 3.16
1980 2241 4.020617 CTGTCTCCCTTGCCCGCA 62.021 66.667 0.00 0.00 0.00 5.69
1992 2253 1.901464 GCCCGCACCCTTTCTCAAA 60.901 57.895 0.00 0.00 0.00 2.69
1993 2254 1.250840 GCCCGCACCCTTTCTCAAAT 61.251 55.000 0.00 0.00 0.00 2.32
2000 2261 3.056322 GCACCCTTTCTCAAATGAAGCAT 60.056 43.478 0.00 0.00 0.00 3.79
2011 2272 3.581024 AATGAAGCATTTGACACGCAT 57.419 38.095 0.00 0.00 28.76 4.73
2012 2273 3.581024 ATGAAGCATTTGACACGCATT 57.419 38.095 0.00 0.00 0.00 3.56
2015 2276 0.599558 AGCATTTGACACGCATTGCT 59.400 45.000 7.12 0.00 39.87 3.91
2016 2277 1.000060 AGCATTTGACACGCATTGCTT 60.000 42.857 7.12 0.00 41.07 3.91
2034 2295 0.319900 TTCTTCAGAGTGTCAGCGCC 60.320 55.000 2.29 0.00 0.00 6.53
2035 2296 1.005748 CTTCAGAGTGTCAGCGCCA 60.006 57.895 2.29 0.00 0.00 5.69
2040 2301 0.250467 AGAGTGTCAGCGCCACATTT 60.250 50.000 16.02 7.25 35.24 2.32
2044 2305 1.468520 GTGTCAGCGCCACATTTATGT 59.531 47.619 12.56 0.00 42.84 2.29
2056 2317 2.283298 CATTTATGTCGGCACAGAGCT 58.717 47.619 0.00 0.00 44.79 4.09
2077 2338 2.626780 CGCGACCTCTCACTGGTGA 61.627 63.158 0.00 3.34 38.03 4.02
2078 2339 1.893786 GCGACCTCTCACTGGTGAT 59.106 57.895 3.80 0.00 39.13 3.06
2085 2346 3.092301 CCTCTCACTGGTGATGACACTA 58.908 50.000 3.80 0.00 45.32 2.74
2086 2347 3.119316 CCTCTCACTGGTGATGACACTAC 60.119 52.174 3.80 0.00 45.32 2.73
2150 2411 1.943968 GCTCGCACCTGTTCAATACCA 60.944 52.381 0.00 0.00 0.00 3.25
2173 2434 1.765230 AGATGTGACTAGACGGGACC 58.235 55.000 0.00 0.00 0.00 4.46
2175 2436 1.035932 ATGTGACTAGACGGGACCGG 61.036 60.000 15.92 0.00 44.69 5.28
2178 2439 0.107508 TGACTAGACGGGACCGGTAG 60.108 60.000 7.34 16.17 44.69 3.18
2181 2442 1.559682 ACTAGACGGGACCGGTAGTTA 59.440 52.381 7.34 3.58 44.69 2.24
2235 2496 4.914312 ACCGTCATTAAACATACACACG 57.086 40.909 0.00 0.00 0.00 4.49
2236 2497 3.123959 ACCGTCATTAAACATACACACGC 59.876 43.478 0.00 0.00 0.00 5.34
2237 2498 3.369756 CCGTCATTAAACATACACACGCT 59.630 43.478 0.00 0.00 0.00 5.07
2242 2503 1.313772 AAACATACACACGCTGGCAA 58.686 45.000 0.00 0.00 0.00 4.52
2255 2516 2.738321 CGCTGGCAAAGAAACCAACTTT 60.738 45.455 0.00 0.00 37.96 2.66
2256 2517 3.490078 CGCTGGCAAAGAAACCAACTTTA 60.490 43.478 0.00 0.00 36.09 1.85
2258 2519 4.441495 GCTGGCAAAGAAACCAACTTTAGT 60.441 41.667 0.00 0.00 36.09 2.24
2263 2524 5.393678 GCAAAGAAACCAACTTTAGTGTCCA 60.394 40.000 0.00 0.00 36.09 4.02
2280 2541 1.896183 CACATTGACACACCCCGCA 60.896 57.895 0.00 0.00 0.00 5.69
2333 2766 2.477176 GCCACGCCTGACACAAACA 61.477 57.895 0.00 0.00 0.00 2.83
2334 2767 1.795170 GCCACGCCTGACACAAACAT 61.795 55.000 0.00 0.00 0.00 2.71
2366 2799 2.166459 CGTCTTGCTTCACATCCTCCTA 59.834 50.000 0.00 0.00 0.00 2.94
2370 2803 4.962362 TCTTGCTTCACATCCTCCTATGTA 59.038 41.667 0.00 0.00 38.01 2.29
2373 2806 4.655649 TGCTTCACATCCTCCTATGTACAT 59.344 41.667 13.93 13.93 38.01 2.29
2376 2809 6.519721 GCTTCACATCCTCCTATGTACATCAT 60.520 42.308 12.68 0.00 38.01 2.45
2389 2823 3.708121 TGTACATCATCTCTGCCATGACT 59.292 43.478 0.00 0.00 33.04 3.41
2394 2828 4.824479 TCATCTCTGCCATGACTACAAA 57.176 40.909 0.00 0.00 0.00 2.83
2396 2830 2.977914 TCTCTGCCATGACTACAAAGC 58.022 47.619 0.00 0.00 0.00 3.51
2397 2831 2.568956 TCTCTGCCATGACTACAAAGCT 59.431 45.455 0.00 0.00 0.00 3.74
2398 2832 2.676839 CTCTGCCATGACTACAAAGCTG 59.323 50.000 0.00 0.00 0.00 4.24
2399 2833 2.038952 TCTGCCATGACTACAAAGCTGT 59.961 45.455 0.00 0.00 39.75 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.099266 TCAAATTCAAACACACTGAATGAGT 57.901 32.000 0.00 0.00 41.56 3.41
6 7 7.990541 TTCAAATTCAAACACACTGAATGAG 57.009 32.000 0.00 0.00 41.56 2.90
55 56 9.996554 AGTTCCACACGATTCATGAATATTATA 57.003 29.630 20.75 1.69 0.00 0.98
56 57 8.908786 AGTTCCACACGATTCATGAATATTAT 57.091 30.769 20.75 5.07 0.00 1.28
64 66 5.862924 AAGTAAGTTCCACACGATTCATG 57.137 39.130 0.00 0.00 0.00 3.07
71 73 6.721571 AACATGATAAGTAAGTTCCACACG 57.278 37.500 0.00 0.00 0.00 4.49
84 86 9.834628 ACACGTATAAAAACCAAACATGATAAG 57.165 29.630 0.00 0.00 0.00 1.73
89 91 5.918011 AGCACACGTATAAAAACCAAACATG 59.082 36.000 0.00 0.00 0.00 3.21
92 94 5.512473 TGAGCACACGTATAAAAACCAAAC 58.488 37.500 0.00 0.00 0.00 2.93
96 98 5.907391 GCATATGAGCACACGTATAAAAACC 59.093 40.000 6.97 0.00 0.00 3.27
106 108 1.643880 TGACTGCATATGAGCACACG 58.356 50.000 6.97 0.00 40.11 4.49
114 116 6.688385 CACCGAAATAAACTTGACTGCATATG 59.312 38.462 0.00 0.00 0.00 1.78
120 122 6.548441 TTACCACCGAAATAAACTTGACTG 57.452 37.500 0.00 0.00 0.00 3.51
187 189 1.084289 GCACCGCCGAACTTCTAAAT 58.916 50.000 0.00 0.00 0.00 1.40
195 197 2.054140 TTTTGTCTGCACCGCCGAAC 62.054 55.000 0.00 0.00 0.00 3.95
201 203 5.408604 AGTCTACTAAATTTTGTCTGCACCG 59.591 40.000 8.57 0.00 0.00 4.94
202 204 6.426937 TCAGTCTACTAAATTTTGTCTGCACC 59.573 38.462 8.57 0.00 0.00 5.01
203 205 7.421530 TCAGTCTACTAAATTTTGTCTGCAC 57.578 36.000 8.57 2.78 0.00 4.57
204 206 8.621532 ATTCAGTCTACTAAATTTTGTCTGCA 57.378 30.769 8.57 2.41 0.00 4.41
225 227 9.731819 CGAGTTAGCTATAGTGAAGTAAATTCA 57.268 33.333 0.84 0.00 45.79 2.57
226 228 9.947669 TCGAGTTAGCTATAGTGAAGTAAATTC 57.052 33.333 0.84 0.00 38.50 2.17
232 236 4.874966 ACGTCGAGTTAGCTATAGTGAAGT 59.125 41.667 0.00 0.00 0.00 3.01
235 239 5.808042 AAACGTCGAGTTAGCTATAGTGA 57.192 39.130 0.00 0.00 43.37 3.41
240 244 4.637534 TGGAGTAAACGTCGAGTTAGCTAT 59.362 41.667 0.00 0.00 43.37 2.97
263 267 3.267812 TCTCAAGCTGATCCCCAAGAAAT 59.732 43.478 0.00 0.00 0.00 2.17
264 268 2.644299 TCTCAAGCTGATCCCCAAGAAA 59.356 45.455 0.00 0.00 0.00 2.52
266 270 1.956869 TCTCAAGCTGATCCCCAAGA 58.043 50.000 0.00 0.00 0.00 3.02
267 271 2.573369 CATCTCAAGCTGATCCCCAAG 58.427 52.381 0.00 0.00 0.00 3.61
269 273 0.182061 GCATCTCAAGCTGATCCCCA 59.818 55.000 0.00 0.00 0.00 4.96
270 274 0.473326 AGCATCTCAAGCTGATCCCC 59.527 55.000 0.00 0.00 41.61 4.81
271 275 1.881591 GAGCATCTCAAGCTGATCCC 58.118 55.000 0.00 0.00 43.58 3.85
294 298 6.491403 AGCATCTCAAGCTCCTTTTCTAAAAA 59.509 34.615 0.00 0.00 38.01 1.94
295 299 6.006449 AGCATCTCAAGCTCCTTTTCTAAAA 58.994 36.000 0.00 0.00 38.01 1.52
297 301 5.171339 AGCATCTCAAGCTCCTTTTCTAA 57.829 39.130 0.00 0.00 38.01 2.10
314 318 2.202987 CCGTGCCCTCAGAGCATC 60.203 66.667 0.00 0.00 43.29 3.91
315 319 1.841302 TTTCCGTGCCCTCAGAGCAT 61.841 55.000 0.00 0.00 43.29 3.79
316 320 2.515979 TTTCCGTGCCCTCAGAGCA 61.516 57.895 0.00 0.00 38.08 4.26
317 321 2.035442 GTTTCCGTGCCCTCAGAGC 61.035 63.158 0.00 0.00 0.00 4.09
318 322 1.738099 CGTTTCCGTGCCCTCAGAG 60.738 63.158 0.00 0.00 0.00 3.35
319 323 1.750341 TTCGTTTCCGTGCCCTCAGA 61.750 55.000 0.00 0.00 35.01 3.27
320 324 0.882927 TTTCGTTTCCGTGCCCTCAG 60.883 55.000 0.00 0.00 35.01 3.35
321 325 1.146485 TTTCGTTTCCGTGCCCTCA 59.854 52.632 0.00 0.00 35.01 3.86
322 326 1.572941 GTTTCGTTTCCGTGCCCTC 59.427 57.895 0.00 0.00 35.01 4.30
323 327 2.248835 CGTTTCGTTTCCGTGCCCT 61.249 57.895 0.00 0.00 35.01 5.19
324 328 2.166584 CTCGTTTCGTTTCCGTGCCC 62.167 60.000 0.00 0.00 35.01 5.36
325 329 1.203313 CTCGTTTCGTTTCCGTGCC 59.797 57.895 0.00 0.00 35.01 5.01
326 330 0.161024 CTCTCGTTTCGTTTCCGTGC 59.839 55.000 0.00 0.00 35.01 5.34
327 331 0.782384 CCTCTCGTTTCGTTTCCGTG 59.218 55.000 0.00 0.00 35.01 4.94
328 332 0.670162 TCCTCTCGTTTCGTTTCCGT 59.330 50.000 0.00 0.00 35.01 4.69
329 333 1.068748 TCTCCTCTCGTTTCGTTTCCG 60.069 52.381 0.00 0.00 0.00 4.30
330 334 2.719426 TCTCCTCTCGTTTCGTTTCC 57.281 50.000 0.00 0.00 0.00 3.13
331 335 2.409041 GCTTCTCCTCTCGTTTCGTTTC 59.591 50.000 0.00 0.00 0.00 2.78
332 336 2.036089 AGCTTCTCCTCTCGTTTCGTTT 59.964 45.455 0.00 0.00 0.00 3.60
333 337 1.614413 AGCTTCTCCTCTCGTTTCGTT 59.386 47.619 0.00 0.00 0.00 3.85
363 367 0.529773 TCGTCGATTGGTGGCTATGC 60.530 55.000 0.00 0.00 0.00 3.14
364 368 2.154854 ATCGTCGATTGGTGGCTATG 57.845 50.000 0.75 0.00 0.00 2.23
441 572 6.205853 TGATTAACAAATGTACCTCACGCTTT 59.794 34.615 0.00 0.00 0.00 3.51
470 601 3.676172 CGTGTTTCAACAGACGCCTTATA 59.324 43.478 0.00 0.00 40.05 0.98
471 602 2.478894 CGTGTTTCAACAGACGCCTTAT 59.521 45.455 0.00 0.00 40.05 1.73
486 617 1.264826 GTTTGGATGGTACGCGTGTTT 59.735 47.619 24.59 3.47 0.00 2.83
520 651 0.538287 AGGGCCTGCAAGTTTGAGAC 60.538 55.000 4.50 0.00 0.00 3.36
522 653 1.580845 CGAGGGCCTGCAAGTTTGAG 61.581 60.000 12.95 0.00 0.00 3.02
523 654 1.600636 CGAGGGCCTGCAAGTTTGA 60.601 57.895 12.95 0.00 0.00 2.69
524 655 2.629656 CCGAGGGCCTGCAAGTTTG 61.630 63.158 12.95 0.00 0.00 2.93
525 656 2.282462 CCGAGGGCCTGCAAGTTT 60.282 61.111 12.95 0.00 0.00 2.66
526 657 3.553095 GACCGAGGGCCTGCAAGTT 62.553 63.158 12.95 0.00 0.00 2.66
534 665 3.782443 ATTCACCGACCGAGGGCC 61.782 66.667 0.00 0.00 35.02 5.80
535 666 2.511600 CATTCACCGACCGAGGGC 60.512 66.667 0.00 0.00 35.02 5.19
536 667 1.153628 GTCATTCACCGACCGAGGG 60.154 63.158 0.00 0.00 35.02 4.30
537 668 0.037697 TTGTCATTCACCGACCGAGG 60.038 55.000 0.00 0.00 32.15 4.63
538 669 1.790755 TTTGTCATTCACCGACCGAG 58.209 50.000 0.00 0.00 32.15 4.63
539 670 1.868498 GTTTTGTCATTCACCGACCGA 59.132 47.619 0.00 0.00 32.15 4.69
540 671 1.600013 TGTTTTGTCATTCACCGACCG 59.400 47.619 0.00 0.00 32.15 4.79
541 672 3.181495 TGTTGTTTTGTCATTCACCGACC 60.181 43.478 0.00 0.00 32.15 4.79
542 673 4.022464 TGTTGTTTTGTCATTCACCGAC 57.978 40.909 0.00 0.00 0.00 4.79
543 674 3.066064 CCTGTTGTTTTGTCATTCACCGA 59.934 43.478 0.00 0.00 0.00 4.69
544 675 3.066064 TCCTGTTGTTTTGTCATTCACCG 59.934 43.478 0.00 0.00 0.00 4.94
545 676 4.499696 CCTCCTGTTGTTTTGTCATTCACC 60.500 45.833 0.00 0.00 0.00 4.02
546 677 4.097892 ACCTCCTGTTGTTTTGTCATTCAC 59.902 41.667 0.00 0.00 0.00 3.18
547 678 4.097741 CACCTCCTGTTGTTTTGTCATTCA 59.902 41.667 0.00 0.00 0.00 2.57
548 679 4.097892 ACACCTCCTGTTGTTTTGTCATTC 59.902 41.667 0.00 0.00 0.00 2.67
549 680 4.023291 ACACCTCCTGTTGTTTTGTCATT 58.977 39.130 0.00 0.00 0.00 2.57
550 681 3.631250 ACACCTCCTGTTGTTTTGTCAT 58.369 40.909 0.00 0.00 0.00 3.06
551 682 3.080300 ACACCTCCTGTTGTTTTGTCA 57.920 42.857 0.00 0.00 0.00 3.58
552 683 3.442273 TGAACACCTCCTGTTGTTTTGTC 59.558 43.478 0.00 0.00 43.60 3.18
553 684 3.426615 TGAACACCTCCTGTTGTTTTGT 58.573 40.909 0.00 0.00 43.60 2.83
554 685 3.181487 CCTGAACACCTCCTGTTGTTTTG 60.181 47.826 0.00 0.00 43.60 2.44
643 774 1.214589 GCTAAAGCGAGACCGGTCA 59.785 57.895 35.00 12.73 46.74 4.02
644 775 0.802607 CTGCTAAAGCGAGACCGGTC 60.803 60.000 27.67 27.67 46.74 4.79
646 777 0.802607 GACTGCTAAAGCGAGACCGG 60.803 60.000 0.00 0.00 45.83 5.28
736 867 2.557298 GCGGCGGCGAGTTTTAAA 59.443 55.556 36.87 0.00 0.00 1.52
840 972 3.121544 GAGTAGTGCTACCGTATTTGCC 58.878 50.000 5.80 0.00 36.75 4.52
841 973 3.121544 GGAGTAGTGCTACCGTATTTGC 58.878 50.000 5.80 0.00 36.75 3.68
854 986 2.072298 GCTGCTTCAGTTGGAGTAGTG 58.928 52.381 7.27 0.00 33.43 2.74
856 988 1.354040 CGCTGCTTCAGTTGGAGTAG 58.646 55.000 1.53 1.53 33.43 2.57
857 989 0.670546 GCGCTGCTTCAGTTGGAGTA 60.671 55.000 0.00 0.00 33.43 2.59
858 990 1.963338 GCGCTGCTTCAGTTGGAGT 60.963 57.895 0.00 0.00 33.43 3.85
859 991 1.670406 AGCGCTGCTTCAGTTGGAG 60.670 57.895 10.39 0.00 33.89 3.86
860 992 1.962822 CAGCGCTGCTTCAGTTGGA 60.963 57.895 26.68 0.00 36.40 3.53
861 993 2.559840 CAGCGCTGCTTCAGTTGG 59.440 61.111 26.68 0.00 36.40 3.77
862 994 2.559840 CCAGCGCTGCTTCAGTTG 59.440 61.111 31.96 11.77 36.40 3.16
863 995 3.360340 GCCAGCGCTGCTTCAGTT 61.360 61.111 31.96 0.00 36.40 3.16
864 996 4.326507 AGCCAGCGCTGCTTCAGT 62.327 61.111 31.96 8.62 46.19 3.41
880 1012 7.010552 GGAATATGTGTCGGCAGCTATTTATAG 59.989 40.741 0.00 0.00 0.00 1.31
890 1022 0.180171 TGGGGAATATGTGTCGGCAG 59.820 55.000 0.00 0.00 0.00 4.85
895 1027 3.214328 GTGGACATGGGGAATATGTGTC 58.786 50.000 0.00 0.00 38.78 3.67
902 1034 1.148867 TGGTTTGTGGACATGGGGAAT 59.851 47.619 0.00 0.00 0.00 3.01
905 1037 1.535204 GCTGGTTTGTGGACATGGGG 61.535 60.000 0.00 0.00 0.00 4.96
906 1038 1.535204 GGCTGGTTTGTGGACATGGG 61.535 60.000 0.00 0.00 0.00 4.00
907 1039 0.827089 TGGCTGGTTTGTGGACATGG 60.827 55.000 0.00 0.00 0.00 3.66
911 1043 1.541588 GATCTTGGCTGGTTTGTGGAC 59.458 52.381 0.00 0.00 0.00 4.02
915 1047 1.202758 TGTCGATCTTGGCTGGTTTGT 60.203 47.619 0.00 0.00 0.00 2.83
923 1055 4.571250 TCGTGTGTCGATCTTGGC 57.429 55.556 0.00 0.00 44.01 4.52
932 1064 0.799152 TGTGTCGTGTGTCGTGTGTC 60.799 55.000 0.00 0.00 40.80 3.67
939 1080 2.676342 AGGAGTTTTTGTGTCGTGTGTC 59.324 45.455 0.00 0.00 0.00 3.67
943 1084 4.095610 GTTTCAGGAGTTTTTGTGTCGTG 58.904 43.478 0.00 0.00 0.00 4.35
979 1121 5.710567 TCATCTTCAGAAGAAACTCTCGGTA 59.289 40.000 17.00 0.00 41.63 4.02
988 1130 3.006859 TCCACGCTCATCTTCAGAAGAAA 59.993 43.478 17.00 7.58 41.63 2.52
1115 1257 0.597118 CATCTCGCTGTAGCAGAGCC 60.597 60.000 15.79 0.00 42.21 4.70
1116 1258 0.597118 CCATCTCGCTGTAGCAGAGC 60.597 60.000 15.79 0.00 42.21 4.09
1121 1263 2.659897 CGGCCATCTCGCTGTAGC 60.660 66.667 2.24 0.00 37.78 3.58
1232 1374 3.762992 CGAAGCGCGCGAACAGAA 61.763 61.111 37.18 0.00 0.00 3.02
1268 1410 2.181445 GAACTCTTCCCGGTCCACCC 62.181 65.000 0.00 0.00 0.00 4.61
1429 1571 8.640091 TCTGTAACATACACTCGTAGTAGTAG 57.360 38.462 0.00 0.00 34.46 2.57
1440 1588 3.832490 TGCCTCACTCTGTAACATACACT 59.168 43.478 0.00 0.00 34.46 3.55
1488 1640 9.849166 ACTCACTTCTCGTTTTGAAAATAAAAA 57.151 25.926 0.00 0.00 31.92 1.94
1548 1700 9.778993 TCTCTGTAAATACACAATTACGTAGAC 57.221 33.333 0.00 0.00 35.30 2.59
1576 1732 6.500684 TGAAATCCTGAACAGAGCATAAAC 57.499 37.500 3.19 0.00 0.00 2.01
1620 1776 4.737578 TCTGCTAGTAGGGATTAATCGGT 58.262 43.478 8.07 1.80 0.00 4.69
1621 1777 4.767928 ACTCTGCTAGTAGGGATTAATCGG 59.232 45.833 15.37 0.00 36.36 4.18
1639 1795 1.134995 TGCGGCTAGTCAATGACTCTG 60.135 52.381 20.25 14.48 42.40 3.35
1651 1807 6.560253 AACCAATTAATCTAATGCGGCTAG 57.440 37.500 0.00 0.00 0.00 3.42
1693 1878 6.334102 ACTGGTAGGCGAATAGAAGATTAG 57.666 41.667 0.00 0.00 0.00 1.73
1704 1889 3.598019 AATCGTTAACTGGTAGGCGAA 57.402 42.857 3.71 0.00 32.15 4.70
1737 1937 7.817962 AGCTCGTATGAAAATAGTACACAAACT 59.182 33.333 0.00 0.00 0.00 2.66
1742 1942 8.753175 CCTTTAGCTCGTATGAAAATAGTACAC 58.247 37.037 0.00 0.00 0.00 2.90
1817 2043 4.049186 GCAGACAGTTTGAGAGTAAACGA 58.951 43.478 0.00 0.00 43.51 3.85
1833 2059 1.234821 GGTCCGAACAAATGCAGACA 58.765 50.000 0.00 0.00 0.00 3.41
1844 2070 1.834188 ATGGTGAAATGGGTCCGAAC 58.166 50.000 0.00 0.00 0.00 3.95
1847 2074 1.832883 TGAATGGTGAAATGGGTCCG 58.167 50.000 0.00 0.00 0.00 4.79
1870 2097 3.432326 GCCTTCGGTTTGATGAGATACCT 60.432 47.826 0.00 0.00 0.00 3.08
1884 2111 1.247567 CTCATTGGTTTGCCTTCGGT 58.752 50.000 0.00 0.00 35.27 4.69
1886 2113 3.369546 AAACTCATTGGTTTGCCTTCG 57.630 42.857 3.44 0.00 37.91 3.79
1892 2153 7.113404 CGAATGTTCACTAAACTCATTGGTTTG 59.887 37.037 11.28 6.29 39.39 2.93
1900 2161 4.312443 GGTCCGAATGTTCACTAAACTCA 58.688 43.478 0.00 0.00 38.76 3.41
1902 2163 3.243975 ACGGTCCGAATGTTCACTAAACT 60.244 43.478 20.51 0.00 38.76 2.66
1904 2165 3.389925 ACGGTCCGAATGTTCACTAAA 57.610 42.857 20.51 0.00 0.00 1.85
1932 2193 0.034756 TCCGGGTTGTCTGTCACATG 59.965 55.000 0.00 0.00 33.90 3.21
1980 2241 5.813513 AAATGCTTCATTTGAGAAAGGGT 57.186 34.783 4.20 0.00 41.70 4.34
1992 2253 3.247442 CAATGCGTGTCAAATGCTTCAT 58.753 40.909 0.00 0.00 41.76 2.57
1993 2254 2.663808 CAATGCGTGTCAAATGCTTCA 58.336 42.857 0.00 0.00 41.76 3.02
2000 2261 2.357323 TGAAGAAGCAATGCGTGTCAAA 59.643 40.909 0.00 0.00 0.00 2.69
2004 2265 1.802960 CTCTGAAGAAGCAATGCGTGT 59.197 47.619 0.00 0.00 0.00 4.49
2011 2272 2.487934 GCTGACACTCTGAAGAAGCAA 58.512 47.619 0.00 0.00 0.00 3.91
2012 2273 1.603931 CGCTGACACTCTGAAGAAGCA 60.604 52.381 2.79 0.00 0.00 3.91
2015 2276 0.319900 GGCGCTGACACTCTGAAGAA 60.320 55.000 7.64 0.00 0.00 2.52
2016 2277 1.290324 GGCGCTGACACTCTGAAGA 59.710 57.895 7.64 0.00 0.00 2.87
2034 2295 2.223112 GCTCTGTGCCGACATAAATGTG 60.223 50.000 0.00 0.00 37.07 3.21
2035 2296 2.009774 GCTCTGTGCCGACATAAATGT 58.990 47.619 0.00 0.00 38.71 2.71
2040 2301 0.173481 GTCAGCTCTGTGCCGACATA 59.827 55.000 11.90 0.00 45.67 2.29
2044 2305 4.724602 GCGTCAGCTCTGTGCCGA 62.725 66.667 0.00 0.00 44.23 5.54
2056 2317 2.626780 CCAGTGAGAGGTCGCGTCA 61.627 63.158 5.77 0.00 38.32 4.35
2077 2338 1.446099 CGCACCGCTGTAGTGTCAT 60.446 57.895 0.00 0.00 37.56 3.06
2078 2339 2.049526 CGCACCGCTGTAGTGTCA 60.050 61.111 0.00 0.00 37.56 3.58
2132 2393 2.552599 TTGGTATTGAACAGGTGCGA 57.447 45.000 0.00 0.00 0.00 5.10
2150 2411 4.341520 GGTCCCGTCTAGTCACATCTATTT 59.658 45.833 0.00 0.00 0.00 1.40
2175 2436 4.337274 AGCCCATTTAAATGCGGTAACTAC 59.663 41.667 24.59 13.96 35.08 2.73
2178 2439 3.443976 CAGCCCATTTAAATGCGGTAAC 58.556 45.455 24.59 14.89 35.08 2.50
2181 2442 0.175531 GCAGCCCATTTAAATGCGGT 59.824 50.000 24.59 19.01 35.08 5.68
2235 2496 2.602257 AAGTTGGTTTCTTTGCCAGC 57.398 45.000 0.00 0.00 36.00 4.85
2236 2497 5.043248 CACTAAAGTTGGTTTCTTTGCCAG 58.957 41.667 0.00 0.00 36.65 4.85
2237 2498 4.464597 ACACTAAAGTTGGTTTCTTTGCCA 59.535 37.500 0.00 0.00 36.65 4.92
2242 2503 5.258051 TGTGGACACTAAAGTTGGTTTCTT 58.742 37.500 3.91 0.00 0.00 2.52
2258 2519 0.179004 GGGGTGTGTCAATGTGGACA 60.179 55.000 0.00 0.00 45.06 4.02
2263 2524 1.600636 CTGCGGGGTGTGTCAATGT 60.601 57.895 0.00 0.00 0.00 2.71
2323 2756 4.377021 GAGGTGTAGTGATGTTTGTGTCA 58.623 43.478 0.00 0.00 0.00 3.58
2325 2758 3.181469 ACGAGGTGTAGTGATGTTTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
2333 2766 2.171840 AGCAAGACGAGGTGTAGTGAT 58.828 47.619 0.00 0.00 0.00 3.06
2334 2767 1.617322 AGCAAGACGAGGTGTAGTGA 58.383 50.000 0.00 0.00 0.00 3.41
2366 2799 4.347292 AGTCATGGCAGAGATGATGTACAT 59.653 41.667 8.43 8.43 42.47 2.29
2370 2803 3.708121 TGTAGTCATGGCAGAGATGATGT 59.292 43.478 0.00 0.00 32.53 3.06
2373 2806 4.763073 CTTTGTAGTCATGGCAGAGATGA 58.237 43.478 0.00 0.00 0.00 2.92
2376 2809 2.568956 AGCTTTGTAGTCATGGCAGAGA 59.431 45.455 0.00 0.00 0.00 3.10
2394 2828 1.185618 TCTCCCACAACGCTACAGCT 61.186 55.000 0.00 0.00 39.32 4.24
2396 2830 0.737715 GCTCTCCCACAACGCTACAG 60.738 60.000 0.00 0.00 0.00 2.74
2397 2831 1.292223 GCTCTCCCACAACGCTACA 59.708 57.895 0.00 0.00 0.00 2.74
2398 2832 1.448013 GGCTCTCCCACAACGCTAC 60.448 63.158 0.00 0.00 0.00 3.58
2399 2833 2.978824 GGCTCTCCCACAACGCTA 59.021 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.