Multiple sequence alignment - TraesCS4A01G374000

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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 TraesCS4A01G374000 chr4A 100.000 2564 0 0 1 2564 648949305 648951868 0.000000e+00 4735.0
1 TraesCS4A01G374000 chr4A 89.028 319 28 4 2233 2545 556295134 556294817 3.090000e-104 388.0
2 TraesCS4A01G374000 chr4A 82.550 298 52 0 325 622 1133623 1133920 1.960000e-66 263.0
3 TraesCS4A01G374000 chr7D 91.808 1587 110 8 308 1883 41801984 41803561 0.000000e+00 2193.0
4 TraesCS4A01G374000 chr7D 87.240 337 36 4 2233 2564 1412347 1412013 6.700000e-101 377.0
5 TraesCS4A01G374000 chr7D 88.013 317 30 2 1 309 41801730 41802046 4.030000e-98 368.0
6 TraesCS4A01G374000 chr7D 90.580 276 15 5 1885 2159 41803631 41803896 3.140000e-94 355.0
7 TraesCS4A01G374000 chr7D 83.226 155 26 0 107 261 236000806 236000960 2.660000e-30 143.0
8 TraesCS4A01G374000 chr7A 91.081 1323 69 18 585 1883 41454628 41455925 0.000000e+00 1744.0
9 TraesCS4A01G374000 chr7A 92.011 701 29 9 1885 2564 41455998 41456692 0.000000e+00 959.0
10 TraesCS4A01G374000 chr7A 85.804 317 34 4 1 307 41451099 41451414 2.460000e-85 326.0
11 TraesCS4A01G374000 chr7A 85.926 270 38 0 333 602 691054359 691054090 3.230000e-74 289.0
12 TraesCS4A01G374000 chr6D 83.946 299 48 0 325 623 388207605 388207307 1.160000e-73 287.0
13 TraesCS4A01G374000 chr6D 89.796 49 5 0 2235 2283 2902738 2902690 2.130000e-06 63.9
14 TraesCS4A01G374000 chr2D 83.959 293 46 1 325 617 429082105 429081814 1.940000e-71 279.0
15 TraesCS4A01G374000 chr1D 83.959 293 46 1 325 617 447368127 447367836 1.940000e-71 279.0
16 TraesCS4A01G374000 chr1D 83.221 149 24 1 93 240 229179484 229179336 4.450000e-28 135.0
17 TraesCS4A01G374000 chr5B 83.221 298 50 0 325 622 54507869 54508166 9.040000e-70 274.0
18 TraesCS4A01G374000 chr5B 82.530 166 25 4 89 252 637484256 637484093 2.660000e-30 143.0
19 TraesCS4A01G374000 chr1A 82.609 299 51 1 325 623 438651756 438651459 1.960000e-66 263.0
20 TraesCS4A01G374000 chr1A 100.000 36 0 0 2235 2270 140201255 140201220 1.650000e-07 67.6
21 TraesCS4A01G374000 chr3D 81.967 305 55 0 318 622 485230501 485230197 2.530000e-65 259.0
22 TraesCS4A01G374000 chr3D 100.000 36 0 0 2235 2270 31709988 31709953 1.650000e-07 67.6
23 TraesCS4A01G374000 chr3D 94.444 36 2 0 272 307 591965179 591965214 3.560000e-04 56.5
24 TraesCS4A01G374000 chr5A 79.479 307 61 2 318 623 440674867 440675172 1.540000e-52 217.0
25 TraesCS4A01G374000 chr5A 81.871 171 31 0 324 494 269330649 269330479 7.390000e-31 145.0
26 TraesCS4A01G374000 chr5A 80.702 171 33 0 324 494 269333226 269333056 1.600000e-27 134.0
27 TraesCS4A01G374000 chr5A 100.000 36 0 0 272 307 450194052 450194017 1.650000e-07 67.6
28 TraesCS4A01G374000 chr1B 81.726 197 33 3 79 273 31174786 31174981 7.340000e-36 161.0
29 TraesCS4A01G374000 chr1B 76.220 164 34 5 94 252 14529657 14529494 5.880000e-12 82.4
30 TraesCS4A01G374000 chr1B 100.000 34 0 0 274 307 16200821 16200854 2.130000e-06 63.9
31 TraesCS4A01G374000 chr4D 87.234 141 16 2 113 252 745148 745287 2.640000e-35 159.0
32 TraesCS4A01G374000 chr4D 79.670 182 29 8 88 264 28971076 28971254 9.630000e-25 124.0
33 TraesCS4A01G374000 chr3B 82.659 173 28 2 92 263 759028519 759028690 4.420000e-33 152.0
34 TraesCS4A01G374000 chr7B 83.221 149 25 0 119 267 699362996 699363144 1.240000e-28 137.0
35 TraesCS4A01G374000 chr6A 87.931 58 5 1 2215 2270 440054368 440054311 1.650000e-07 67.6
36 TraesCS4A01G374000 chr2A 91.837 49 3 1 2235 2283 657128 657081 1.650000e-07 67.6
37 TraesCS4A01G374000 chr3A 89.796 49 4 1 2235 2283 10274043 10273996 7.660000e-06 62.1


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 TraesCS4A01G374000 chr4A 648949305 648951868 2563 False 4735.000000 4735 100.000000 1 2564 1 chr4A.!!$F2 2563
1 TraesCS4A01G374000 chr7D 41801730 41803896 2166 False 972.000000 2193 90.133667 1 2159 3 chr7D.!!$F2 2158
2 TraesCS4A01G374000 chr7A 41451099 41456692 5593 False 1009.666667 1744 89.632000 1 2564 3 chr7A.!!$F1 2563

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
360 370 0.036858 GAGTCAGTGTTCCAGGCTCC 60.037 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 4794 0.109319 AACACCGATGGAATTTGCGC 60.109 50.0 0.0 0.0 0.0 6.09 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
20 21 2.386661 TCCACCAAGAGAAGATTCGC 57.613 50.000 0.00 0.00 0.00 4.70
21 22 1.066143 TCCACCAAGAGAAGATTCGCC 60.066 52.381 0.00 0.00 0.00 5.54
24 25 1.275291 ACCAAGAGAAGATTCGCCGAA 59.725 47.619 0.33 0.33 0.00 4.30
148 158 2.058595 CCCCTCGATCTTCACCGGT 61.059 63.158 0.00 0.00 0.00 5.28
149 159 1.141881 CCCTCGATCTTCACCGGTG 59.858 63.158 29.26 29.26 0.00 4.94
152 162 0.811915 CTCGATCTTCACCGGTGAGT 59.188 55.000 34.25 24.57 41.13 3.41
166 176 2.202892 GAGTCCGTGGATTCGCCC 60.203 66.667 0.00 0.00 34.97 6.13
167 177 3.735037 GAGTCCGTGGATTCGCCCC 62.735 68.421 0.00 0.00 34.97 5.80
168 178 3.782443 GTCCGTGGATTCGCCCCT 61.782 66.667 0.00 0.00 34.97 4.79
215 225 1.602237 GCGGTGAGGGGATTTCTGA 59.398 57.895 0.00 0.00 0.00 3.27
242 252 3.768468 GGATCTGGCTAGTAGATACGC 57.232 52.381 0.00 1.63 35.14 4.42
246 256 1.542030 CTGGCTAGTAGATACGCAGGG 59.458 57.143 0.00 0.00 0.00 4.45
247 257 1.133575 TGGCTAGTAGATACGCAGGGT 60.134 52.381 0.00 0.00 0.00 4.34
248 258 1.962100 GGCTAGTAGATACGCAGGGTT 59.038 52.381 0.00 0.00 0.00 4.11
249 259 2.364647 GGCTAGTAGATACGCAGGGTTT 59.635 50.000 0.00 0.00 0.00 3.27
250 260 3.181468 GGCTAGTAGATACGCAGGGTTTT 60.181 47.826 0.00 0.00 0.00 2.43
251 261 4.038402 GGCTAGTAGATACGCAGGGTTTTA 59.962 45.833 0.00 0.00 0.00 1.52
252 262 5.452356 GGCTAGTAGATACGCAGGGTTTTAA 60.452 44.000 0.00 0.00 0.00 1.52
253 263 6.221659 GCTAGTAGATACGCAGGGTTTTAAT 58.778 40.000 0.00 0.00 0.00 1.40
254 264 6.704937 GCTAGTAGATACGCAGGGTTTTAATT 59.295 38.462 0.00 0.00 0.00 1.40
255 265 7.869429 GCTAGTAGATACGCAGGGTTTTAATTA 59.131 37.037 0.00 0.00 0.00 1.40
256 266 9.924650 CTAGTAGATACGCAGGGTTTTAATTAT 57.075 33.333 0.00 0.00 0.00 1.28
257 267 8.828688 AGTAGATACGCAGGGTTTTAATTATC 57.171 34.615 0.00 0.00 0.00 1.75
258 268 6.780706 AGATACGCAGGGTTTTAATTATCG 57.219 37.500 0.00 0.00 0.00 2.92
259 269 3.685836 ACGCAGGGTTTTAATTATCGC 57.314 42.857 0.00 0.00 0.00 4.58
260 270 3.011119 ACGCAGGGTTTTAATTATCGCA 58.989 40.909 0.00 0.00 0.00 5.10
261 271 3.064820 ACGCAGGGTTTTAATTATCGCAG 59.935 43.478 0.00 0.00 0.00 5.18
262 272 3.548014 CGCAGGGTTTTAATTATCGCAGG 60.548 47.826 0.00 0.00 0.00 4.85
263 273 3.243401 GCAGGGTTTTAATTATCGCAGGG 60.243 47.826 0.00 0.00 0.00 4.45
264 274 3.317993 CAGGGTTTTAATTATCGCAGGGG 59.682 47.826 0.00 0.00 0.00 4.79
265 275 2.035449 GGGTTTTAATTATCGCAGGGGC 59.965 50.000 0.00 0.00 0.00 5.80
275 285 4.002797 GCAGGGGCGACATTTCTT 57.997 55.556 0.00 0.00 0.00 2.52
276 286 1.803289 GCAGGGGCGACATTTCTTC 59.197 57.895 0.00 0.00 0.00 2.87
277 287 0.678048 GCAGGGGCGACATTTCTTCT 60.678 55.000 0.00 0.00 0.00 2.85
278 288 1.826385 CAGGGGCGACATTTCTTCTT 58.174 50.000 0.00 0.00 0.00 2.52
279 289 1.740025 CAGGGGCGACATTTCTTCTTC 59.260 52.381 0.00 0.00 0.00 2.87
280 290 0.727398 GGGGCGACATTTCTTCTTCG 59.273 55.000 0.00 0.00 34.56 3.79
281 291 1.674817 GGGGCGACATTTCTTCTTCGA 60.675 52.381 0.00 0.00 33.20 3.71
282 292 1.661112 GGGCGACATTTCTTCTTCGAG 59.339 52.381 0.00 0.00 33.20 4.04
283 293 2.338500 GGCGACATTTCTTCTTCGAGT 58.662 47.619 0.00 0.00 33.20 4.18
284 294 2.345942 GGCGACATTTCTTCTTCGAGTC 59.654 50.000 0.00 0.00 33.20 3.36
285 295 2.987149 GCGACATTTCTTCTTCGAGTCA 59.013 45.455 0.00 0.00 33.20 3.41
286 296 3.060098 GCGACATTTCTTCTTCGAGTCAG 59.940 47.826 0.00 0.00 33.20 3.51
287 297 4.230657 CGACATTTCTTCTTCGAGTCAGT 58.769 43.478 0.00 0.00 33.20 3.41
288 298 4.322274 CGACATTTCTTCTTCGAGTCAGTC 59.678 45.833 0.00 0.00 33.20 3.51
289 299 5.461032 ACATTTCTTCTTCGAGTCAGTCT 57.539 39.130 0.00 0.00 0.00 3.24
290 300 5.848406 ACATTTCTTCTTCGAGTCAGTCTT 58.152 37.500 0.00 0.00 0.00 3.01
291 301 5.923684 ACATTTCTTCTTCGAGTCAGTCTTC 59.076 40.000 0.00 0.00 0.00 2.87
292 302 4.506886 TTCTTCTTCGAGTCAGTCTTCC 57.493 45.455 0.00 0.00 0.00 3.46
293 303 3.487372 TCTTCTTCGAGTCAGTCTTCCA 58.513 45.455 0.00 0.00 0.00 3.53
294 304 3.504134 TCTTCTTCGAGTCAGTCTTCCAG 59.496 47.826 0.00 0.00 0.00 3.86
295 305 2.163509 TCTTCGAGTCAGTCTTCCAGG 58.836 52.381 0.00 0.00 0.00 4.45
296 306 0.603569 TTCGAGTCAGTCTTCCAGGC 59.396 55.000 0.00 0.00 0.00 4.85
297 307 0.251386 TCGAGTCAGTCTTCCAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
298 308 0.172352 CGAGTCAGTCTTCCAGGCTC 59.828 60.000 0.00 0.00 0.00 4.70
299 309 0.534873 GAGTCAGTCTTCCAGGCTCC 59.465 60.000 0.00 0.00 0.00 4.70
300 310 1.216710 GTCAGTCTTCCAGGCTCCG 59.783 63.158 0.00 0.00 0.00 4.63
301 311 1.076727 TCAGTCTTCCAGGCTCCGA 59.923 57.895 0.00 0.00 0.00 4.55
302 312 0.324738 TCAGTCTTCCAGGCTCCGAT 60.325 55.000 0.00 0.00 0.00 4.18
303 313 0.103937 CAGTCTTCCAGGCTCCGATC 59.896 60.000 0.00 0.00 0.00 3.69
304 314 1.045911 AGTCTTCCAGGCTCCGATCC 61.046 60.000 0.00 0.00 0.00 3.36
305 315 1.045911 GTCTTCCAGGCTCCGATCCT 61.046 60.000 0.00 0.00 0.00 3.24
306 316 0.757188 TCTTCCAGGCTCCGATCCTC 60.757 60.000 0.00 0.00 0.00 3.71
316 326 3.492829 GGCTCCGATCCTCGTTTTAATCT 60.493 47.826 0.00 0.00 38.40 2.40
349 359 2.154007 GCGTTTCTTCTTCGAGTCAGTG 59.846 50.000 0.00 0.00 0.00 3.66
360 370 0.036858 GAGTCAGTGTTCCAGGCTCC 60.037 60.000 0.00 0.00 0.00 4.70
388 398 2.674357 CGTAAAATTCGTCCGTTGGGAT 59.326 45.455 0.00 0.00 46.14 3.85
399 409 2.841266 TCCGTTGGGATGGATTAGACAA 59.159 45.455 0.00 0.00 37.43 3.18
401 411 4.013728 CCGTTGGGATGGATTAGACAAAA 58.986 43.478 0.00 0.00 33.44 2.44
405 415 6.294508 CGTTGGGATGGATTAGACAAAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
406 416 6.588719 TGGGATGGATTAGACAAAACTTTG 57.411 37.500 0.60 0.60 43.62 2.77
432 442 3.905153 TTCCTGCCAGCTCCTCGGA 62.905 63.158 0.00 0.00 0.00 4.55
460 471 1.066136 GTTAGGGTTTCTCGTCGTGC 58.934 55.000 0.00 0.00 0.00 5.34
486 497 3.694734 GCAATGACGATATTTGGTGTGG 58.305 45.455 0.00 0.00 0.00 4.17
494 505 4.019141 ACGATATTTGGTGTGGGGTTCTTA 60.019 41.667 0.00 0.00 0.00 2.10
496 507 5.065988 CGATATTTGGTGTGGGGTTCTTAAG 59.934 44.000 0.00 0.00 0.00 1.85
526 537 3.678056 AGGATTCAACAGCGACAACTA 57.322 42.857 0.00 0.00 0.00 2.24
572 583 1.151668 GCACATGCACGAAGACTTCT 58.848 50.000 13.22 0.00 41.59 2.85
580 591 1.199327 CACGAAGACTTCTCGGCTGTA 59.801 52.381 13.22 0.00 0.00 2.74
589 3597 4.385825 ACTTCTCGGCTGTAATTGACAAA 58.614 39.130 0.00 0.00 37.70 2.83
592 3600 4.385825 TCTCGGCTGTAATTGACAAAGTT 58.614 39.130 0.00 0.00 37.70 2.66
596 3604 4.454504 CGGCTGTAATTGACAAAGTTAGGT 59.545 41.667 0.00 0.00 37.70 3.08
603 3611 3.202829 TGACAAAGTTAGGTCGGCTTT 57.797 42.857 0.00 0.00 36.83 3.51
605 3613 3.135994 GACAAAGTTAGGTCGGCTTTGA 58.864 45.455 19.01 0.00 46.98 2.69
644 3652 4.815040 ATACGACGGTGAGAAGATGTAG 57.185 45.455 0.00 0.00 0.00 2.74
686 3694 3.304721 GCACATGGCCTGCAACCA 61.305 61.111 10.43 10.38 42.61 3.67
720 3733 1.073897 GCAGTCAAGCAGAAGGGGT 59.926 57.895 0.00 0.00 0.00 4.95
748 3761 3.670377 GACGGTTGCACAAGGGCC 61.670 66.667 0.00 0.00 0.00 5.80
749 3762 4.204028 ACGGTTGCACAAGGGCCT 62.204 61.111 0.00 0.00 0.00 5.19
751 3764 2.203480 GGTTGCACAAGGGCCTGA 60.203 61.111 6.92 0.00 0.00 3.86
759 3772 0.982852 ACAAGGGCCTGATCGGATCA 60.983 55.000 18.96 18.96 37.76 2.92
835 3848 1.404181 CGACTCACACGATCCATGGTT 60.404 52.381 12.58 2.52 0.00 3.67
845 3858 1.856597 GATCCATGGTTACACGTACGC 59.143 52.381 16.72 0.00 0.00 4.42
846 3859 0.456482 TCCATGGTTACACGTACGCG 60.456 55.000 16.72 8.78 44.93 6.01
916 3929 1.918800 CTCCCCAAGTCGAACCCCT 60.919 63.158 0.00 0.00 0.00 4.79
1080 4097 2.982130 GCCTCCGTCACCATGTCT 59.018 61.111 0.00 0.00 0.00 3.41
1104 4127 1.228367 CAGCAACAACAGCCTCCCT 60.228 57.895 0.00 0.00 0.00 4.20
1265 4288 1.068741 GACCGTGCCTTCCCATACTAG 59.931 57.143 0.00 0.00 0.00 2.57
1271 4294 2.249139 GCCTTCCCATACTAGGACGAT 58.751 52.381 0.00 0.00 31.50 3.73
1293 4316 5.468540 TGATGAAGACGGAAGAAGAAGAA 57.531 39.130 0.00 0.00 0.00 2.52
1584 4607 4.805719 TGATCAACAGATCGGATTTTCTCG 59.194 41.667 0.00 0.00 40.83 4.04
1661 4690 0.233848 GCTTTTCCCGTGTACGTGTG 59.766 55.000 0.00 0.00 37.74 3.82
1662 4691 1.574134 CTTTTCCCGTGTACGTGTGT 58.426 50.000 0.00 0.00 37.74 3.72
1676 4705 4.841443 ACGTGTGTAATGTCTCTGTACA 57.159 40.909 0.00 0.00 0.00 2.90
1703 4732 4.500603 AGATCGACAACCACGGTATATC 57.499 45.455 0.00 0.00 0.00 1.63
1767 4796 8.712341 TTATGAATAACATCGATTTGATTGCG 57.288 30.769 0.00 0.00 40.07 4.85
1776 4805 2.922387 CGATTTGATTGCGCAAATTCCA 59.078 40.909 28.81 18.69 45.63 3.53
1783 4812 1.240641 TGCGCAAATTCCATCGGTGT 61.241 50.000 8.16 0.00 0.00 4.16
1803 4832 6.984474 CGGTGTTGTAATGTTGTATAGGATCT 59.016 38.462 0.00 0.00 0.00 2.75
1816 4845 6.948353 TGTATAGGATCTACACGTACGTTTC 58.052 40.000 20.23 10.36 0.00 2.78
1853 4885 5.107109 TGTCGTTTTTCCTGATGATGTTG 57.893 39.130 0.00 0.00 0.00 3.33
1883 4915 4.798907 AGCACATTGAGACGAAATACTACG 59.201 41.667 0.00 0.00 0.00 3.51
1910 5013 3.737774 GCTCTGTTTTTGTTTCTGCATCC 59.262 43.478 0.00 0.00 0.00 3.51
1990 5094 8.325787 ACCTGTCATAACATACCTTTCATTGTA 58.674 33.333 0.00 0.00 34.13 2.41
1998 5102 3.764237 ACCTTTCATTGTACAGTCGGT 57.236 42.857 0.00 0.00 0.00 4.69
2009 5113 4.758688 TGTACAGTCGGTCTCGTCTATAA 58.241 43.478 0.00 0.00 33.79 0.98
2019 5123 4.136051 GTCTCGTCTATAACTAGCCCTGT 58.864 47.826 0.00 0.00 0.00 4.00
2108 5219 1.491563 CAAAGAGGCGTGCACGTAC 59.508 57.895 36.80 29.18 42.22 3.67
2109 5220 2.019951 AAAGAGGCGTGCACGTACG 61.020 57.895 36.80 15.01 46.28 3.67
2110 5221 2.688526 AAAGAGGCGTGCACGTACGT 62.689 55.000 36.80 23.77 45.36 3.57
2111 5222 1.855213 AAGAGGCGTGCACGTACGTA 61.855 55.000 36.80 3.16 45.36 3.57
2179 5297 5.670485 CATAGCCCTACACACTTATGAACA 58.330 41.667 0.00 0.00 0.00 3.18
2224 5342 5.016985 GCACGAAGACGCGAAAAATATTTA 58.983 37.500 15.93 0.00 43.96 1.40
2231 5349 9.646336 GAAGACGCGAAAAATATTTATACACAT 57.354 29.630 15.93 0.00 0.00 3.21
2242 5360 0.756294 TATACACATGCCCGGTCCTG 59.244 55.000 0.00 0.00 0.00 3.86
2251 5369 0.035439 GCCCGGTCCTGAGATTTTGA 60.035 55.000 0.00 0.00 0.00 2.69
2261 5379 2.442087 GATTTTGAGGGCCCGGGG 60.442 66.667 25.28 9.31 0.00 5.73
2275 5393 1.520666 CGGGGCGAAACTAGGACAT 59.479 57.895 0.00 0.00 0.00 3.06
2282 5401 1.077716 AAACTAGGACATGGGCGCC 60.078 57.895 21.18 21.18 0.00 6.53
2296 5415 1.153369 GCGCCAGCATTCCTAGACA 60.153 57.895 0.00 0.00 44.35 3.41
2458 5577 4.033129 CCAAATTGCATTTACCATCAAGCG 59.967 41.667 0.00 0.00 0.00 4.68
2509 5632 4.759693 GGATGTTGGACTGTTTGATGTACA 59.240 41.667 0.00 0.00 0.00 2.90
2527 5650 5.763088 TGTACAAAAATGATAGCGTGCAAA 58.237 33.333 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.958822 ACTTGTGGGAATTGTTCGGC 59.041 50.000 0.00 0.00 0.00 5.54
20 21 3.188460 CACTACTTGTGGGAATTGTTCGG 59.812 47.826 0.00 0.00 42.68 4.30
21 22 4.404507 CACTACTTGTGGGAATTGTTCG 57.595 45.455 0.00 0.00 42.68 3.95
42 43 1.468914 GAATTGAACGTCTTGCCTCCC 59.531 52.381 0.00 0.00 0.00 4.30
148 158 2.577059 GGCGAATCCACGGACTCA 59.423 61.111 0.00 0.00 34.01 3.41
149 159 2.202892 GGGCGAATCCACGGACTC 60.203 66.667 0.00 0.00 36.21 3.36
152 162 3.006728 AAGGGGCGAATCCACGGA 61.007 61.111 0.00 0.00 45.34 4.69
201 211 2.486013 CGATGCATCAGAAATCCCCTCA 60.486 50.000 25.70 0.00 0.00 3.86
215 225 1.346062 ACTAGCCAGATCCGATGCAT 58.654 50.000 0.00 0.00 0.00 3.96
242 252 3.317993 CCCCTGCGATAATTAAAACCCTG 59.682 47.826 0.00 0.00 0.00 4.45
258 268 0.678048 AGAAGAAATGTCGCCCCTGC 60.678 55.000 0.00 0.00 0.00 4.85
259 269 1.740025 GAAGAAGAAATGTCGCCCCTG 59.260 52.381 0.00 0.00 0.00 4.45
260 270 1.676014 CGAAGAAGAAATGTCGCCCCT 60.676 52.381 0.00 0.00 0.00 4.79
261 271 0.727398 CGAAGAAGAAATGTCGCCCC 59.273 55.000 0.00 0.00 0.00 5.80
262 272 1.661112 CTCGAAGAAGAAATGTCGCCC 59.339 52.381 0.00 0.00 34.09 6.13
263 273 2.338500 ACTCGAAGAAGAAATGTCGCC 58.662 47.619 0.00 0.00 34.09 5.54
264 274 2.987149 TGACTCGAAGAAGAAATGTCGC 59.013 45.455 0.00 0.00 34.09 5.19
265 275 4.230657 ACTGACTCGAAGAAGAAATGTCG 58.769 43.478 0.00 0.00 34.09 4.35
266 276 5.465935 AGACTGACTCGAAGAAGAAATGTC 58.534 41.667 0.00 0.00 34.09 3.06
267 277 5.461032 AGACTGACTCGAAGAAGAAATGT 57.539 39.130 0.00 0.00 34.09 2.71
268 278 5.347364 GGAAGACTGACTCGAAGAAGAAATG 59.653 44.000 0.00 0.00 34.09 2.32
269 279 5.011125 TGGAAGACTGACTCGAAGAAGAAAT 59.989 40.000 0.00 0.00 34.09 2.17
270 280 4.341235 TGGAAGACTGACTCGAAGAAGAAA 59.659 41.667 0.00 0.00 34.09 2.52
271 281 3.889538 TGGAAGACTGACTCGAAGAAGAA 59.110 43.478 0.00 0.00 34.09 2.52
272 282 3.487372 TGGAAGACTGACTCGAAGAAGA 58.513 45.455 0.00 0.00 34.09 2.87
273 283 3.366883 CCTGGAAGACTGACTCGAAGAAG 60.367 52.174 0.00 0.00 34.07 2.85
274 284 2.558795 CCTGGAAGACTGACTCGAAGAA 59.441 50.000 0.00 0.00 34.07 2.52
275 285 2.163509 CCTGGAAGACTGACTCGAAGA 58.836 52.381 0.00 0.00 34.07 2.87
276 286 1.403514 GCCTGGAAGACTGACTCGAAG 60.404 57.143 0.00 0.00 34.07 3.79
277 287 0.603569 GCCTGGAAGACTGACTCGAA 59.396 55.000 0.00 0.00 34.07 3.71
278 288 0.251386 AGCCTGGAAGACTGACTCGA 60.251 55.000 0.00 0.00 34.07 4.04
279 289 0.172352 GAGCCTGGAAGACTGACTCG 59.828 60.000 0.00 0.00 34.07 4.18
280 290 0.534873 GGAGCCTGGAAGACTGACTC 59.465 60.000 0.00 0.00 34.07 3.36
281 291 1.254284 CGGAGCCTGGAAGACTGACT 61.254 60.000 0.00 0.00 34.07 3.41
282 292 1.216710 CGGAGCCTGGAAGACTGAC 59.783 63.158 0.00 0.00 34.07 3.51
283 293 0.324738 ATCGGAGCCTGGAAGACTGA 60.325 55.000 0.00 0.00 34.07 3.41
284 294 0.103937 GATCGGAGCCTGGAAGACTG 59.896 60.000 0.00 0.00 34.07 3.51
285 295 1.045911 GGATCGGAGCCTGGAAGACT 61.046 60.000 4.74 0.00 34.07 3.24
286 296 1.045911 AGGATCGGAGCCTGGAAGAC 61.046 60.000 15.14 0.00 34.07 3.01
287 297 0.757188 GAGGATCGGAGCCTGGAAGA 60.757 60.000 21.29 0.00 35.44 2.87
288 298 1.745264 GAGGATCGGAGCCTGGAAG 59.255 63.158 21.29 0.00 35.44 3.46
289 299 3.956377 GAGGATCGGAGCCTGGAA 58.044 61.111 21.29 0.00 35.44 3.53
300 310 4.025647 CCTGCGAAGATTAAAACGAGGATC 60.026 45.833 0.00 0.00 0.00 3.36
301 311 3.871594 CCTGCGAAGATTAAAACGAGGAT 59.128 43.478 0.00 0.00 0.00 3.24
302 312 3.259064 CCTGCGAAGATTAAAACGAGGA 58.741 45.455 0.00 0.00 0.00 3.71
303 313 2.351726 CCCTGCGAAGATTAAAACGAGG 59.648 50.000 0.00 0.00 0.00 4.63
304 314 2.351726 CCCCTGCGAAGATTAAAACGAG 59.648 50.000 0.00 0.00 0.00 4.18
305 315 2.352388 CCCCTGCGAAGATTAAAACGA 58.648 47.619 0.00 0.00 0.00 3.85
306 316 1.202143 GCCCCTGCGAAGATTAAAACG 60.202 52.381 0.00 0.00 0.00 3.60
349 359 1.443828 GAGGATCGGAGCCTGGAAC 59.556 63.158 21.29 0.69 35.44 3.62
388 398 6.316640 TCAACGTCAAAGTTTTGTCTAATCCA 59.683 34.615 4.67 0.00 39.18 3.41
399 409 3.243401 GGCAGGAATCAACGTCAAAGTTT 60.243 43.478 0.00 0.00 30.96 2.66
401 411 1.880027 GGCAGGAATCAACGTCAAAGT 59.120 47.619 0.00 0.00 0.00 2.66
405 415 0.955428 GCTGGCAGGAATCAACGTCA 60.955 55.000 17.64 0.00 0.00 4.35
406 416 0.674895 AGCTGGCAGGAATCAACGTC 60.675 55.000 17.64 0.00 0.00 4.34
432 442 2.517484 GAAACCCTAACCTCGCCGCT 62.517 60.000 0.00 0.00 0.00 5.52
460 471 3.244345 ACCAAATATCGTCATTGCGTACG 59.756 43.478 11.84 11.84 40.40 3.67
471 482 2.307686 AGAACCCCACACCAAATATCGT 59.692 45.455 0.00 0.00 0.00 3.73
486 497 5.671493 TCCTTGAATCGATCTTAAGAACCC 58.329 41.667 9.71 1.31 0.00 4.11
494 505 5.065731 GCTGTTGAATCCTTGAATCGATCTT 59.934 40.000 0.00 0.00 0.00 2.40
496 507 4.551603 CGCTGTTGAATCCTTGAATCGATC 60.552 45.833 0.00 0.00 0.00 3.69
572 583 4.693566 CCTAACTTTGTCAATTACAGCCGA 59.306 41.667 0.00 0.00 39.87 5.54
580 591 3.751518 AGCCGACCTAACTTTGTCAATT 58.248 40.909 0.00 0.00 0.00 2.32
589 3597 4.649674 TCTCATATCAAAGCCGACCTAACT 59.350 41.667 0.00 0.00 0.00 2.24
592 3600 3.005897 GCTCTCATATCAAAGCCGACCTA 59.994 47.826 0.00 0.00 0.00 3.08
596 3604 1.269778 CCGCTCTCATATCAAAGCCGA 60.270 52.381 0.00 0.00 0.00 5.54
603 3611 0.744281 TTGTCGCCGCTCTCATATCA 59.256 50.000 0.00 0.00 0.00 2.15
605 3613 2.533266 ATTTGTCGCCGCTCTCATAT 57.467 45.000 0.00 0.00 0.00 1.78
672 3680 2.601067 TGGTGGTTGCAGGCCATG 60.601 61.111 5.01 0.97 38.40 3.66
699 3712 1.093159 CCCTTCTGCTTGACTGCATC 58.907 55.000 0.00 0.00 42.48 3.91
706 3719 2.538141 CCCCACCCCTTCTGCTTGA 61.538 63.158 0.00 0.00 0.00 3.02
748 3761 2.806818 CCTCAAGCAATGATCCGATCAG 59.193 50.000 16.07 5.41 43.53 2.90
749 3762 2.435437 TCCTCAAGCAATGATCCGATCA 59.565 45.455 13.46 13.46 44.55 2.92
751 3764 3.135348 TCTTCCTCAAGCAATGATCCGAT 59.865 43.478 0.00 0.00 37.44 4.18
759 3772 6.128172 CGTTCATTACTTCTTCCTCAAGCAAT 60.128 38.462 0.00 0.00 0.00 3.56
813 3826 0.173481 CATGGATCGTGTGAGTCGGT 59.827 55.000 0.00 0.00 0.00 4.69
846 3859 0.817229 AGCTAGGGAGGCGTACGTAC 60.817 60.000 17.90 15.90 34.52 3.67
847 3860 0.758734 TAGCTAGGGAGGCGTACGTA 59.241 55.000 17.90 0.00 34.52 3.57
848 3861 0.817229 GTAGCTAGGGAGGCGTACGT 60.817 60.000 17.90 0.00 34.52 3.57
888 3901 0.320697 ACTTGGGGAGAAGCGTACAC 59.679 55.000 0.00 0.00 0.00 2.90
916 3929 2.375845 CTCTATAGGGGGAGTCCGAGAA 59.624 54.545 2.26 0.00 36.01 2.87
1080 4097 3.121934 CTGTTGTTGCTGCTGCCA 58.878 55.556 13.47 0.00 38.71 4.92
1143 4166 1.860641 TCTTCATCTCCGGGCTTGTA 58.139 50.000 0.00 0.00 0.00 2.41
1146 4169 0.471617 CCATCTTCATCTCCGGGCTT 59.528 55.000 0.00 0.00 0.00 4.35
1265 4288 2.099263 TCTTCCGTCTTCATCATCGTCC 59.901 50.000 0.00 0.00 0.00 4.79
1271 4294 5.230942 GTTCTTCTTCTTCCGTCTTCATCA 58.769 41.667 0.00 0.00 0.00 3.07
1402 4425 3.760035 CACCGAGCGGCAGTACCT 61.760 66.667 9.14 0.00 39.32 3.08
1548 4571 0.948623 TTGATCACGCCAGAACCACG 60.949 55.000 0.00 0.00 0.00 4.94
1584 4607 2.362397 TCCTGCTGAATCCTACATCGAC 59.638 50.000 0.00 0.00 0.00 4.20
1676 4705 4.142790 ACCGTGGTTGTCGATCTAGATAT 58.857 43.478 4.89 0.00 0.00 1.63
1703 4732 1.135803 CCAAAAAGGCACGACGGTATG 60.136 52.381 0.00 0.00 0.00 2.39
1715 4744 8.306761 AGTGAATAGTTAAATCAGCCAAAAAGG 58.693 33.333 0.00 0.00 41.84 3.11
1765 4794 0.109319 AACACCGATGGAATTTGCGC 60.109 50.000 0.00 0.00 0.00 6.09
1767 4796 2.723124 ACAACACCGATGGAATTTGC 57.277 45.000 0.00 0.00 0.00 3.68
1776 4805 6.880484 TCCTATACAACATTACAACACCGAT 58.120 36.000 0.00 0.00 0.00 4.18
1783 4812 8.689061 ACGTGTAGATCCTATACAACATTACAA 58.311 33.333 0.00 0.00 35.04 2.41
1803 4832 3.847457 CGATCACATGAAACGTACGTGTA 59.153 43.478 23.57 11.69 36.01 2.90
1816 4845 4.783959 AACGACATCAATCGATCACATG 57.216 40.909 0.00 4.07 45.13 3.21
1853 4885 3.002791 TCGTCTCAATGTGCTGGAAATC 58.997 45.455 0.00 0.00 0.00 2.17
1883 4915 2.033424 AGAAACAAAAACAGAGCCGAGC 59.967 45.455 0.00 0.00 0.00 5.03
1910 5013 1.595093 GGTGGCCAAACCTTGATCCG 61.595 60.000 7.24 0.00 40.22 4.18
1990 5094 3.871485 AGTTATAGACGAGACCGACTGT 58.129 45.455 0.00 0.00 40.63 3.55
1998 5102 4.141551 TGACAGGGCTAGTTATAGACGAGA 60.142 45.833 0.00 0.00 38.00 4.04
2040 5144 0.250234 CCAGATGAAGAGCGGTCCAA 59.750 55.000 11.73 0.00 0.00 3.53
2179 5297 6.484643 GTGCATACATACATGGATCAAAGAGT 59.515 38.462 0.00 0.00 0.00 3.24
2224 5342 0.980754 TCAGGACCGGGCATGTGTAT 60.981 55.000 23.49 0.00 0.00 2.29
2231 5349 0.322456 CAAAATCTCAGGACCGGGCA 60.322 55.000 11.00 0.00 0.00 5.36
2242 5360 1.453928 CCCGGGCCCTCAAAATCTC 60.454 63.158 22.43 0.00 0.00 2.75
2261 5379 1.429148 CGCCCATGTCCTAGTTTCGC 61.429 60.000 0.00 0.00 0.00 4.70
2275 5393 3.405093 CTAGGAATGCTGGCGCCCA 62.405 63.158 26.77 16.76 34.43 5.36
2282 5401 3.057969 TGGTTGTGTCTAGGAATGCTG 57.942 47.619 0.00 0.00 0.00 4.41
2314 5433 5.355596 GTTGAGATGACACCTCTCCTAATG 58.644 45.833 0.00 0.00 38.70 1.90
2370 5489 3.207474 ACGCTTGATTTCTTGTGCATC 57.793 42.857 0.00 0.00 0.00 3.91
2491 5610 7.776107 TCATTTTTGTACATCAAACAGTCCAA 58.224 30.769 0.00 0.00 44.39 3.53


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

AutoCloner maintained by Alex Coulton.