Multiple sequence alignment - TraesCS2D01G408400

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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 TraesCS2D01G408400 chr2D 100.000 3938 0 0 1 3938 523311468 523307531 0.000000e+00 7273.0
1 TraesCS2D01G408400 chr2D 81.170 701 86 23 1137 1813 523361094 523360416 4.510000e-144 521.0
2 TraesCS2D01G408400 chr2D 89.916 357 27 4 473 828 523393549 523393201 6.000000e-123 451.0
3 TraesCS2D01G408400 chr2D 80.665 331 57 6 1570 1896 523358875 523358548 2.350000e-62 250.0
4 TraesCS2D01G408400 chr2D 77.647 340 64 11 1565 1896 523161953 523162288 3.100000e-46 196.0
5 TraesCS2D01G408400 chr2D 94.355 124 6 1 360 483 523393721 523393599 5.190000e-44 189.0
6 TraesCS2D01G408400 chr2D 97.802 91 2 0 1022 1112 523361480 523361390 1.460000e-34 158.0
7 TraesCS2D01G408400 chr2A 96.951 3149 75 9 361 3496 668925639 668928779 0.000000e+00 5264.0
8 TraesCS2D01G408400 chr2A 97.750 2356 44 3 1150 3496 669106006 669103651 0.000000e+00 4048.0
9 TraesCS2D01G408400 chr2A 94.658 730 27 6 361 1086 669106849 669106128 0.000000e+00 1122.0
10 TraesCS2D01G408400 chr2A 81.650 703 101 11 1137 1813 668920488 668921188 3.440000e-155 558.0
11 TraesCS2D01G408400 chr2A 81.223 703 104 15 1137 1813 669112002 669111302 3.460000e-150 542.0
12 TraesCS2D01G408400 chr2A 94.239 243 10 2 3696 3938 668929831 668930069 6.220000e-98 368.0
13 TraesCS2D01G408400 chr2A 92.181 243 15 3 3696 3938 669102599 669102361 1.360000e-89 340.0
14 TraesCS2D01G408400 chr2A 98.256 172 3 0 3533 3704 668928780 668928951 6.400000e-78 302.0
15 TraesCS2D01G408400 chr2A 97.714 175 4 0 3533 3707 669103650 669103476 6.400000e-78 302.0
16 TraesCS2D01G408400 chr2A 81.600 375 25 24 752 1112 668919473 668919817 1.800000e-68 270.0
17 TraesCS2D01G408400 chr2A 80.577 381 30 20 752 1118 669113017 669112667 1.820000e-63 254.0
18 TraesCS2D01G408400 chr2A 79.758 331 60 6 1570 1896 669109761 669109434 2.370000e-57 233.0
19 TraesCS2D01G408400 chr2A 78.167 371 66 13 1536 1896 668922691 668923056 5.120000e-54 222.0
20 TraesCS2D01G408400 chr2A 78.592 341 59 12 1565 1896 668530943 668530608 3.080000e-51 213.0
21 TraesCS2D01G408400 chr2A 88.415 164 18 1 577 740 669113253 669113091 3.100000e-46 196.0
22 TraesCS2D01G408400 chr2A 90.385 104 6 4 473 573 669114007 669113905 2.470000e-27 134.0
23 TraesCS2D01G408400 chr2A 89.423 104 7 4 473 573 668918483 668918585 1.150000e-25 128.0
24 TraesCS2D01G408400 chr2B 96.182 2567 87 6 360 2924 617529369 617526812 0.000000e+00 4187.0
25 TraesCS2D01G408400 chr2B 94.030 670 38 2 3270 3938 617525616 617524948 0.000000e+00 1014.0
26 TraesCS2D01G408400 chr2B 95.341 279 5 2 3002 3272 617525952 617525674 1.680000e-118 436.0
27 TraesCS2D01G408400 chr2B 80.178 338 58 5 1565 1896 617141906 617142240 1.090000e-60 244.0
28 TraesCS2D01G408400 chr2B 98.148 54 1 0 2923 2976 617526006 617525953 1.160000e-15 95.3
29 TraesCS2D01G408400 chr2B 84.444 90 12 2 461 548 198661458 198661369 1.950000e-13 87.9
30 TraesCS2D01G408400 chr2B 79.487 117 20 4 2036 2150 726226407 726226521 3.260000e-11 80.5
31 TraesCS2D01G408400 chr2B 95.122 41 2 0 2509 2549 203903234 203903194 9.130000e-07 65.8
32 TraesCS2D01G408400 chr6B 80.930 215 27 9 148 359 385113851 385114054 1.460000e-34 158.0
33 TraesCS2D01G408400 chr1D 81.281 203 26 10 161 361 69115043 69114851 1.890000e-33 154.0
34 TraesCS2D01G408400 chr1D 78.325 203 29 10 161 359 202313743 202313552 2.490000e-22 117.0
35 TraesCS2D01G408400 chr7B 81.095 201 26 7 161 359 645584560 645584370 2.450000e-32 150.0
36 TraesCS2D01G408400 chr7A 86.047 129 15 3 233 359 546657308 546657435 6.860000e-28 135.0
37 TraesCS2D01G408400 chr7A 78.109 201 33 6 161 360 432713537 432713727 2.490000e-22 117.0
38 TraesCS2D01G408400 chr3A 78.505 214 35 9 148 359 715481251 715481047 3.190000e-26 130.0
39 TraesCS2D01G408400 chr1A 78.744 207 30 9 161 364 341484239 341484044 4.130000e-25 126.0
40 TraesCS2D01G408400 chr4A 82.270 141 21 4 223 360 434084856 434084995 6.910000e-23 119.0


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 TraesCS2D01G408400 chr2D 523307531 523311468 3937 True 7273.000000 7273 100.000000 1 3938 1 chr2D.!!$R1 3937
1 TraesCS2D01G408400 chr2D 523393201 523393721 520 True 320.000000 451 92.135500 360 828 2 chr2D.!!$R3 468
2 TraesCS2D01G408400 chr2D 523358548 523361480 2932 True 309.666667 521 86.545667 1022 1896 3 chr2D.!!$R2 874
3 TraesCS2D01G408400 chr2A 668918483 668930069 11586 False 1016.000000 5264 88.612286 361 3938 7 chr2A.!!$F1 3577
4 TraesCS2D01G408400 chr2A 669102361 669114007 11646 True 796.777778 4048 89.184556 361 3938 9 chr2A.!!$R2 3577
5 TraesCS2D01G408400 chr2B 617524948 617529369 4421 True 1433.075000 4187 95.925250 360 3938 4 chr2B.!!$R3 3578

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
338 339 0.029834 ACACTATAACGGGCGCTACG 59.970 55.0 20.17 20.17 37.36 3.51 F
650 7512 0.468226 TCAGGGAAACAAGCACGACT 59.532 50.0 0.00 0.00 0.00 4.18 F
1406 8542 0.890996 GGTTGTTCAGCAGTCCCTGG 60.891 60.0 0.00 0.00 33.64 4.45 F
2207 9384 2.618816 GGCCATTCTGTTGGATGACTCA 60.619 50.0 0.00 0.00 39.25 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 8776 0.613260 TCAGCATAAGAGGTGCGGTT 59.387 50.000 0.00 0.00 46.86 4.44 R
2351 9535 1.713078 AGGGCCTCATTCTCAGGTTTT 59.287 47.619 0.00 0.00 32.98 2.43 R
2450 9634 2.676839 CTCATCTTCATGTTTCAGCGCT 59.323 45.455 2.64 2.64 0.00 5.92 R
3800 12977 0.951558 GGGCAATGACGTGTTTGAGT 59.048 50.000 10.42 0.00 0.00 3.41 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
83 84 9.713713 TTTTAAGAAAATTTAGGGGGAAAATCG 57.286 29.630 0.00 0.00 0.00 3.34
86 87 6.931838 AGAAAATTTAGGGGGAAAATCGTTC 58.068 36.000 0.00 0.00 0.00 3.95
87 88 5.670792 AAATTTAGGGGGAAAATCGTTCC 57.329 39.130 0.00 0.00 37.86 3.62
88 89 3.810721 TTTAGGGGGAAAATCGTTCCA 57.189 42.857 7.39 0.00 40.32 3.53
89 90 3.810721 TTAGGGGGAAAATCGTTCCAA 57.189 42.857 7.39 0.00 40.32 3.53
92 93 3.310193 AGGGGGAAAATCGTTCCAAAAA 58.690 40.909 7.39 0.00 40.32 1.94
93 94 3.907474 AGGGGGAAAATCGTTCCAAAAAT 59.093 39.130 7.39 0.00 40.32 1.82
95 96 5.186992 AGGGGGAAAATCGTTCCAAAAATAG 59.813 40.000 7.39 0.00 40.32 1.73
96 97 5.186215 GGGGGAAAATCGTTCCAAAAATAGA 59.814 40.000 7.39 0.00 40.32 1.98
97 98 6.295405 GGGGGAAAATCGTTCCAAAAATAGAA 60.295 38.462 7.39 0.00 40.32 2.10
98 99 7.156000 GGGGAAAATCGTTCCAAAAATAGAAA 58.844 34.615 7.39 0.00 40.32 2.52
126 127 4.811969 AAACCCCGAAAAATACCATTCC 57.188 40.909 0.00 0.00 0.00 3.01
128 129 3.361786 ACCCCGAAAAATACCATTCCTG 58.638 45.455 0.00 0.00 0.00 3.86
129 130 2.100749 CCCCGAAAAATACCATTCCTGC 59.899 50.000 0.00 0.00 0.00 4.85
130 131 2.757868 CCCGAAAAATACCATTCCTGCA 59.242 45.455 0.00 0.00 0.00 4.41
131 132 3.194542 CCCGAAAAATACCATTCCTGCAA 59.805 43.478 0.00 0.00 0.00 4.08
132 133 4.322349 CCCGAAAAATACCATTCCTGCAAA 60.322 41.667 0.00 0.00 0.00 3.68
134 135 5.698545 CCGAAAAATACCATTCCTGCAAAAA 59.301 36.000 0.00 0.00 0.00 1.94
152 153 4.950434 AAAAAGGAAGAAAACGACGTCA 57.050 36.364 17.16 0.00 0.00 4.35
153 154 4.950434 AAAAGGAAGAAAACGACGTCAA 57.050 36.364 17.16 0.00 0.00 3.18
155 156 3.447918 AGGAAGAAAACGACGTCAAGA 57.552 42.857 17.16 0.00 0.00 3.02
156 157 3.121544 AGGAAGAAAACGACGTCAAGAC 58.878 45.455 17.16 2.67 0.00 3.01
157 158 2.861935 GGAAGAAAACGACGTCAAGACA 59.138 45.455 17.16 0.00 0.00 3.41
158 159 3.060473 GGAAGAAAACGACGTCAAGACAG 60.060 47.826 17.16 0.00 0.00 3.51
160 161 3.978687 AGAAAACGACGTCAAGACAGAT 58.021 40.909 17.16 0.00 0.00 2.90
161 162 3.736252 AGAAAACGACGTCAAGACAGATG 59.264 43.478 17.16 0.00 0.00 2.90
162 163 2.065993 AACGACGTCAAGACAGATGG 57.934 50.000 17.16 0.00 0.00 3.51
163 164 0.388649 ACGACGTCAAGACAGATGGC 60.389 55.000 17.16 0.00 0.00 4.40
164 165 0.109086 CGACGTCAAGACAGATGGCT 60.109 55.000 17.16 0.00 30.05 4.75
166 167 0.036952 ACGTCAAGACAGATGGCTGG 60.037 55.000 0.72 0.00 46.60 4.85
168 169 1.609061 CGTCAAGACAGATGGCTGGTT 60.609 52.381 0.72 0.00 46.60 3.67
169 170 1.808945 GTCAAGACAGATGGCTGGTTG 59.191 52.381 0.00 0.00 46.60 3.77
170 171 1.171308 CAAGACAGATGGCTGGTTGG 58.829 55.000 0.00 0.00 46.60 3.77
171 172 0.773644 AAGACAGATGGCTGGTTGGT 59.226 50.000 0.00 0.00 46.60 3.67
172 173 0.773644 AGACAGATGGCTGGTTGGTT 59.226 50.000 0.00 0.00 46.60 3.67
174 175 2.578021 AGACAGATGGCTGGTTGGTTAT 59.422 45.455 0.00 0.00 46.60 1.89
175 176 2.684881 GACAGATGGCTGGTTGGTTATG 59.315 50.000 0.00 0.00 46.60 1.90
177 178 2.684881 CAGATGGCTGGTTGGTTATGTC 59.315 50.000 0.00 0.00 38.51 3.06
179 180 2.666272 TGGCTGGTTGGTTATGTCAA 57.334 45.000 0.00 0.00 0.00 3.18
180 181 2.235016 TGGCTGGTTGGTTATGTCAAC 58.765 47.619 0.00 0.00 42.53 3.18
181 182 1.199097 GGCTGGTTGGTTATGTCAACG 59.801 52.381 0.00 0.00 43.75 4.10
184 185 3.608474 GCTGGTTGGTTATGTCAACGAAC 60.608 47.826 6.50 6.50 43.75 3.95
185 186 2.544686 TGGTTGGTTATGTCAACGAACG 59.455 45.455 8.32 0.00 43.75 3.95
186 187 2.567067 GTTGGTTATGTCAACGAACGC 58.433 47.619 0.00 0.00 35.75 4.84
187 188 2.157834 TGGTTATGTCAACGAACGCT 57.842 45.000 0.00 0.00 0.00 5.07
188 189 1.795872 TGGTTATGTCAACGAACGCTG 59.204 47.619 0.00 0.00 0.00 5.18
190 191 2.477375 GGTTATGTCAACGAACGCTGAA 59.523 45.455 2.00 0.00 0.00 3.02
195 196 0.878523 TCAACGAACGCTGAACCAGG 60.879 55.000 0.00 0.00 31.21 4.45
196 197 0.878523 CAACGAACGCTGAACCAGGA 60.879 55.000 0.00 0.00 31.21 3.86
197 198 0.600255 AACGAACGCTGAACCAGGAG 60.600 55.000 0.00 0.00 31.21 3.69
198 199 1.289066 CGAACGCTGAACCAGGAGA 59.711 57.895 0.00 0.00 31.21 3.71
199 200 0.108615 CGAACGCTGAACCAGGAGAT 60.109 55.000 0.00 0.00 31.21 2.75
200 201 1.646189 GAACGCTGAACCAGGAGATC 58.354 55.000 0.00 0.00 31.21 2.75
201 202 0.108615 AACGCTGAACCAGGAGATCG 60.109 55.000 0.00 0.00 31.21 3.69
202 203 1.880340 CGCTGAACCAGGAGATCGC 60.880 63.158 0.00 0.00 31.21 4.58
203 204 1.522580 GCTGAACCAGGAGATCGCC 60.523 63.158 7.52 7.52 31.21 5.54
204 205 1.965754 GCTGAACCAGGAGATCGCCT 61.966 60.000 12.90 12.90 39.37 5.52
217 218 1.586422 ATCGCCTGTTCGATTCATGG 58.414 50.000 0.00 0.00 45.81 3.66
218 219 0.249120 TCGCCTGTTCGATTCATGGT 59.751 50.000 0.00 0.00 33.02 3.55
219 220 1.478916 TCGCCTGTTCGATTCATGGTA 59.521 47.619 0.00 0.00 33.02 3.25
220 221 1.593006 CGCCTGTTCGATTCATGGTAC 59.407 52.381 0.00 0.00 0.00 3.34
221 222 5.235623 TCGCCTGTTCGATTCATGGTACA 62.236 47.826 0.00 0.00 36.61 2.90
241 242 2.353839 CGCTGCACGCTGCTTTTT 60.354 55.556 17.16 0.00 45.31 1.94
267 268 8.568732 TTGCGTCTTTAAACATAAGAAAAAGG 57.431 30.769 0.00 0.00 33.71 3.11
268 269 7.142680 TGCGTCTTTAAACATAAGAAAAAGGG 58.857 34.615 0.00 0.00 33.71 3.95
269 270 7.013464 TGCGTCTTTAAACATAAGAAAAAGGGA 59.987 33.333 0.00 0.00 33.71 4.20
270 271 7.863877 GCGTCTTTAAACATAAGAAAAAGGGAA 59.136 33.333 0.00 0.00 33.71 3.97
312 313 2.836187 AAGGGGTGTGCGCCCTTTA 61.836 57.895 19.00 0.00 44.85 1.85
313 314 2.360439 AAGGGGTGTGCGCCCTTTAA 62.360 55.000 19.00 0.00 44.85 1.52
314 315 2.959372 GGGTGTGCGCCCTTTAAC 59.041 61.111 13.23 0.00 45.22 2.01
315 316 2.559330 GGTGTGCGCCCTTTAACG 59.441 61.111 4.18 0.00 0.00 3.18
316 317 2.255881 GGTGTGCGCCCTTTAACGT 61.256 57.895 4.18 0.00 0.00 3.99
317 318 1.650363 GTGTGCGCCCTTTAACGTT 59.350 52.632 4.18 5.88 0.00 3.99
318 319 0.867086 GTGTGCGCCCTTTAACGTTA 59.133 50.000 4.18 3.29 0.00 3.18
319 320 1.263752 GTGTGCGCCCTTTAACGTTAA 59.736 47.619 16.59 16.59 0.00 2.01
321 322 1.263752 GTGCGCCCTTTAACGTTAACA 59.736 47.619 19.97 10.89 0.00 2.41
322 323 1.263752 TGCGCCCTTTAACGTTAACAC 59.736 47.619 19.97 9.00 0.00 3.32
323 324 1.532437 GCGCCCTTTAACGTTAACACT 59.468 47.619 19.97 0.00 0.00 3.55
324 325 2.736192 GCGCCCTTTAACGTTAACACTA 59.264 45.455 19.97 5.20 0.00 2.74
325 326 3.371898 GCGCCCTTTAACGTTAACACTAT 59.628 43.478 19.97 0.00 0.00 2.12
326 327 4.566360 GCGCCCTTTAACGTTAACACTATA 59.434 41.667 19.97 4.12 0.00 1.31
327 328 5.063312 GCGCCCTTTAACGTTAACACTATAA 59.937 40.000 19.97 3.41 0.00 0.98
335 336 2.543641 GTTAACACTATAACGGGCGCT 58.456 47.619 7.64 0.00 0.00 5.92
336 337 3.705604 GTTAACACTATAACGGGCGCTA 58.294 45.455 7.64 0.00 0.00 4.26
338 339 0.029834 ACACTATAACGGGCGCTACG 59.970 55.000 20.17 20.17 37.36 3.51
340 341 1.080974 CTATAACGGGCGCTACGGG 60.081 63.158 24.06 6.16 35.23 5.28
341 342 3.211564 TATAACGGGCGCTACGGGC 62.212 63.158 24.06 0.39 40.84 6.13
355 356 2.110352 CGGGCGCCGTTTAGGAAAT 61.110 57.895 22.54 0.00 45.00 2.17
356 357 1.431845 GGGCGCCGTTTAGGAAATG 59.568 57.895 22.54 0.00 45.00 2.32
358 359 1.226575 GCGCCGTTTAGGAAATGCC 60.227 57.895 0.00 0.00 45.00 4.40
360 361 1.813859 GCCGTTTAGGAAATGCCCC 59.186 57.895 0.00 0.00 45.00 5.80
363 364 1.615919 CCGTTTAGGAAATGCCCCACT 60.616 52.381 0.00 0.00 45.00 4.00
364 365 1.743394 CGTTTAGGAAATGCCCCACTC 59.257 52.381 0.00 0.00 37.37 3.51
374 7174 1.079336 GCCCCACTCTTCGGTGTAC 60.079 63.158 0.00 0.00 35.63 2.90
390 7190 1.807981 TACCGCGCATCCGAAGTTG 60.808 57.895 8.75 0.00 36.29 3.16
448 7248 2.131405 CCCAGATCGGCATGTCTCT 58.869 57.895 0.00 0.00 0.00 3.10
498 7358 2.725312 CCTAAGCGAGGCTGGCAGA 61.725 63.158 23.60 9.52 39.62 4.26
608 7470 4.748102 CGTCTGATAGTCTCTACACTCCTC 59.252 50.000 0.00 0.00 0.00 3.71
617 7479 5.129155 AGTCTCTACACTCCTCTATACACGT 59.871 44.000 0.00 0.00 0.00 4.49
636 7498 3.198068 CGTCCAATACTCATTGTCAGGG 58.802 50.000 0.00 0.00 40.04 4.45
650 7512 0.468226 TCAGGGAAACAAGCACGACT 59.532 50.000 0.00 0.00 0.00 4.18
652 7514 2.301870 TCAGGGAAACAAGCACGACTAT 59.698 45.455 0.00 0.00 0.00 2.12
843 7706 2.348998 CTGGTTTGCTCGCTCCCT 59.651 61.111 0.00 0.00 0.00 4.20
844 7707 1.743252 CTGGTTTGCTCGCTCCCTC 60.743 63.158 0.00 0.00 0.00 4.30
1148 8284 1.522092 GATCATCGAGGCACCACCA 59.478 57.895 0.00 0.00 43.14 4.17
1406 8542 0.890996 GGTTGTTCAGCAGTCCCTGG 60.891 60.000 0.00 0.00 33.64 4.45
1613 8776 3.183754 CACTTCACACACAGTACAACGA 58.816 45.455 0.00 0.00 0.00 3.85
1907 9072 6.149474 AGCATGTAGTTAAGTTGGCAACTAAG 59.851 38.462 31.34 13.14 41.91 2.18
2207 9384 2.618816 GGCCATTCTGTTGGATGACTCA 60.619 50.000 0.00 0.00 39.25 3.41
2351 9535 3.772619 GGCACATTCTAAGCCCGTA 57.227 52.632 0.00 0.00 42.58 4.02
2368 9552 2.678336 CCGTAAAACCTGAGAATGAGGC 59.322 50.000 0.00 0.00 46.92 4.70
2394 9578 5.121105 TGCTACAAGATCAAGTGATGGATG 58.879 41.667 0.00 0.00 34.37 3.51
2450 9634 1.069978 TGTGTTGGCGACAGATCTTCA 59.930 47.619 8.08 0.00 44.54 3.02
2811 9995 5.534654 ACAGTTAGCCATTTAAAGCTGTCAA 59.465 36.000 11.19 0.00 40.28 3.18
2885 10069 6.246420 AGTGTATTTGCTGTCAGTGATTTC 57.754 37.500 0.00 0.00 0.00 2.17
3141 11362 6.128902 GGCGTGAGATTGATTAGTTTATACCG 60.129 42.308 0.00 0.00 0.00 4.02
3293 11581 5.469479 ACCTTACGAAGCATTTTTGGATTG 58.531 37.500 0.00 0.00 0.00 2.67
3330 11618 2.111384 GAGGACCTCTGCAGAATGGTA 58.889 52.381 23.61 0.00 35.86 3.25
3364 11652 1.263484 GCATGCCATCAACGAGATCAG 59.737 52.381 6.36 0.00 33.72 2.90
3505 11793 4.371975 GCTGGTGCGGTAACAGAA 57.628 55.556 15.63 0.00 34.21 3.02
3800 12977 3.014085 GCGGGAGACGGATGGACAA 62.014 63.158 0.00 0.00 44.51 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.713713 CGATTTTCCCCCTAAATTTTCTTAAAA 57.286 29.630 0.00 0.00 34.41 1.52
59 60 8.425237 ACGATTTTCCCCCTAAATTTTCTTAA 57.575 30.769 0.00 0.00 0.00 1.85
60 61 8.425237 AACGATTTTCCCCCTAAATTTTCTTA 57.575 30.769 0.00 0.00 0.00 2.10
62 63 6.070995 GGAACGATTTTCCCCCTAAATTTTCT 60.071 38.462 0.00 0.00 32.48 2.52
63 64 6.103997 GGAACGATTTTCCCCCTAAATTTTC 58.896 40.000 0.00 0.00 32.48 2.29
65 66 5.088026 TGGAACGATTTTCCCCCTAAATTT 58.912 37.500 0.00 0.00 37.79 1.82
66 67 4.679331 TGGAACGATTTTCCCCCTAAATT 58.321 39.130 0.60 0.00 37.79 1.82
68 69 3.810721 TGGAACGATTTTCCCCCTAAA 57.189 42.857 0.60 0.00 37.79 1.85
69 70 3.810721 TTGGAACGATTTTCCCCCTAA 57.189 42.857 0.60 0.00 37.79 2.69
70 71 3.810721 TTTGGAACGATTTTCCCCCTA 57.189 42.857 0.60 0.00 37.79 3.53
71 72 2.687003 TTTGGAACGATTTTCCCCCT 57.313 45.000 0.60 0.00 37.79 4.79
72 73 3.755112 TTTTTGGAACGATTTTCCCCC 57.245 42.857 0.60 0.00 37.79 5.40
73 74 6.275494 TCTATTTTTGGAACGATTTTCCCC 57.725 37.500 0.60 0.00 37.79 4.81
104 105 4.841813 AGGAATGGTATTTTTCGGGGTTTT 59.158 37.500 0.00 0.00 0.00 2.43
106 107 3.767131 CAGGAATGGTATTTTTCGGGGTT 59.233 43.478 0.00 0.00 0.00 4.11
107 108 3.361786 CAGGAATGGTATTTTTCGGGGT 58.638 45.455 0.00 0.00 0.00 4.95
108 109 2.100749 GCAGGAATGGTATTTTTCGGGG 59.899 50.000 0.00 0.00 0.00 5.73
109 110 2.757868 TGCAGGAATGGTATTTTTCGGG 59.242 45.455 0.00 0.00 0.00 5.14
111 112 6.777526 TTTTTGCAGGAATGGTATTTTTCG 57.222 33.333 0.00 0.00 0.00 3.46
131 132 4.950434 TGACGTCGTTTTCTTCCTTTTT 57.050 36.364 11.62 0.00 0.00 1.94
132 133 4.632688 TCTTGACGTCGTTTTCTTCCTTTT 59.367 37.500 11.62 0.00 0.00 2.27
134 135 3.554731 GTCTTGACGTCGTTTTCTTCCTT 59.445 43.478 11.62 0.00 0.00 3.36
135 136 3.121544 GTCTTGACGTCGTTTTCTTCCT 58.878 45.455 11.62 0.00 0.00 3.36
136 137 2.861935 TGTCTTGACGTCGTTTTCTTCC 59.138 45.455 11.62 0.00 0.00 3.46
137 138 3.795101 TCTGTCTTGACGTCGTTTTCTTC 59.205 43.478 11.62 0.00 0.00 2.87
138 139 3.777478 TCTGTCTTGACGTCGTTTTCTT 58.223 40.909 11.62 0.00 0.00 2.52
139 140 3.431922 TCTGTCTTGACGTCGTTTTCT 57.568 42.857 11.62 0.00 0.00 2.52
140 141 3.120991 CCATCTGTCTTGACGTCGTTTTC 60.121 47.826 11.62 1.11 0.00 2.29
142 143 2.404215 CCATCTGTCTTGACGTCGTTT 58.596 47.619 11.62 0.00 0.00 3.60
143 144 1.935300 GCCATCTGTCTTGACGTCGTT 60.935 52.381 11.62 0.00 0.00 3.85
144 145 0.388649 GCCATCTGTCTTGACGTCGT 60.389 55.000 11.62 0.00 0.00 4.34
145 146 0.109086 AGCCATCTGTCTTGACGTCG 60.109 55.000 11.62 0.00 0.00 5.12
146 147 1.354040 CAGCCATCTGTCTTGACGTC 58.646 55.000 9.11 9.11 35.61 4.34
148 149 0.036952 ACCAGCCATCTGTCTTGACG 60.037 55.000 0.00 0.00 38.66 4.35
149 150 1.808945 CAACCAGCCATCTGTCTTGAC 59.191 52.381 0.00 0.00 38.66 3.18
150 151 1.271543 CCAACCAGCCATCTGTCTTGA 60.272 52.381 0.00 0.00 38.66 3.02
151 152 1.171308 CCAACCAGCCATCTGTCTTG 58.829 55.000 0.00 0.00 38.66 3.02
152 153 0.773644 ACCAACCAGCCATCTGTCTT 59.226 50.000 0.00 0.00 38.66 3.01
153 154 0.773644 AACCAACCAGCCATCTGTCT 59.226 50.000 0.00 0.00 38.66 3.41
155 156 2.041620 ACATAACCAACCAGCCATCTGT 59.958 45.455 0.00 0.00 38.66 3.41
156 157 2.684881 GACATAACCAACCAGCCATCTG 59.315 50.000 0.00 0.00 40.02 2.90
157 158 2.308570 TGACATAACCAACCAGCCATCT 59.691 45.455 0.00 0.00 0.00 2.90
158 159 2.722094 TGACATAACCAACCAGCCATC 58.278 47.619 0.00 0.00 0.00 3.51
160 161 2.235016 GTTGACATAACCAACCAGCCA 58.765 47.619 0.00 0.00 38.28 4.75
161 162 1.199097 CGTTGACATAACCAACCAGCC 59.801 52.381 0.00 0.00 40.40 4.85
162 163 2.147958 TCGTTGACATAACCAACCAGC 58.852 47.619 0.00 0.00 40.40 4.85
163 164 3.363575 CGTTCGTTGACATAACCAACCAG 60.364 47.826 0.00 0.00 40.40 4.00
164 165 2.544686 CGTTCGTTGACATAACCAACCA 59.455 45.455 0.00 0.00 40.40 3.67
165 166 2.663606 GCGTTCGTTGACATAACCAACC 60.664 50.000 0.00 0.00 40.40 3.77
166 167 2.222445 AGCGTTCGTTGACATAACCAAC 59.778 45.455 0.00 0.00 40.19 3.77
168 169 1.795872 CAGCGTTCGTTGACATAACCA 59.204 47.619 3.13 0.00 0.00 3.67
169 170 2.063266 TCAGCGTTCGTTGACATAACC 58.937 47.619 7.58 0.00 0.00 2.85
170 171 3.466836 GTTCAGCGTTCGTTGACATAAC 58.533 45.455 10.85 4.07 0.00 1.89
171 172 2.477375 GGTTCAGCGTTCGTTGACATAA 59.523 45.455 10.85 0.00 0.00 1.90
172 173 2.063266 GGTTCAGCGTTCGTTGACATA 58.937 47.619 10.85 0.00 0.00 2.29
174 175 0.460459 TGGTTCAGCGTTCGTTGACA 60.460 50.000 10.85 5.06 0.00 3.58
175 176 0.232303 CTGGTTCAGCGTTCGTTGAC 59.768 55.000 10.85 7.04 0.00 3.18
177 178 0.878523 TCCTGGTTCAGCGTTCGTTG 60.879 55.000 2.86 2.86 0.00 4.10
179 180 1.006102 CTCCTGGTTCAGCGTTCGT 60.006 57.895 0.00 0.00 0.00 3.85
180 181 0.108615 ATCTCCTGGTTCAGCGTTCG 60.109 55.000 0.00 0.00 0.00 3.95
181 182 1.646189 GATCTCCTGGTTCAGCGTTC 58.354 55.000 0.00 0.00 0.00 3.95
184 185 1.880340 GCGATCTCCTGGTTCAGCG 60.880 63.158 0.00 0.00 0.00 5.18
185 186 1.522580 GGCGATCTCCTGGTTCAGC 60.523 63.158 0.00 0.00 0.00 4.26
186 187 2.206635 AGGCGATCTCCTGGTTCAG 58.793 57.895 2.67 0.00 34.56 3.02
187 188 4.461119 AGGCGATCTCCTGGTTCA 57.539 55.556 2.67 0.00 34.56 3.18
199 200 0.249120 ACCATGAATCGAACAGGCGA 59.751 50.000 0.00 0.00 45.22 5.54
200 201 1.593006 GTACCATGAATCGAACAGGCG 59.407 52.381 0.00 0.00 0.00 5.52
201 202 2.351726 GTGTACCATGAATCGAACAGGC 59.648 50.000 0.00 0.00 0.00 4.85
202 203 3.370978 GTGTGTACCATGAATCGAACAGG 59.629 47.826 0.00 0.00 0.00 4.00
203 204 3.060761 CGTGTGTACCATGAATCGAACAG 59.939 47.826 0.00 0.00 31.20 3.16
204 205 2.990514 CGTGTGTACCATGAATCGAACA 59.009 45.455 0.00 0.00 31.20 3.18
205 206 2.222729 GCGTGTGTACCATGAATCGAAC 60.223 50.000 0.00 0.00 31.20 3.95
206 207 1.996898 GCGTGTGTACCATGAATCGAA 59.003 47.619 0.00 0.00 31.20 3.71
207 208 1.203758 AGCGTGTGTACCATGAATCGA 59.796 47.619 0.00 0.00 31.20 3.59
209 210 1.062587 GCAGCGTGTGTACCATGAATC 59.937 52.381 0.00 0.00 31.20 2.52
211 212 0.250081 TGCAGCGTGTGTACCATGAA 60.250 50.000 0.00 0.00 31.20 2.57
212 213 0.948623 GTGCAGCGTGTGTACCATGA 60.949 55.000 0.00 0.00 35.82 3.07
213 214 1.497278 GTGCAGCGTGTGTACCATG 59.503 57.895 0.00 0.00 35.82 3.66
215 216 2.660224 CGTGCAGCGTGTGTACCA 60.660 61.111 0.00 0.00 38.49 3.25
241 242 9.026074 CCTTTTTCTTATGTTTAAAGACGCAAA 57.974 29.630 0.00 0.00 32.81 3.68
242 243 7.650104 CCCTTTTTCTTATGTTTAAAGACGCAA 59.350 33.333 0.00 0.00 32.81 4.85
243 244 7.013464 TCCCTTTTTCTTATGTTTAAAGACGCA 59.987 33.333 0.00 0.00 32.81 5.24
244 245 7.364970 TCCCTTTTTCTTATGTTTAAAGACGC 58.635 34.615 0.00 0.00 32.81 5.19
245 246 9.177304 GTTCCCTTTTTCTTATGTTTAAAGACG 57.823 33.333 0.00 0.00 32.81 4.18
249 250 9.825109 CCAAGTTCCCTTTTTCTTATGTTTAAA 57.175 29.630 0.00 0.00 0.00 1.52
250 251 8.425703 CCCAAGTTCCCTTTTTCTTATGTTTAA 58.574 33.333 0.00 0.00 0.00 1.52
251 252 7.472240 GCCCAAGTTCCCTTTTTCTTATGTTTA 60.472 37.037 0.00 0.00 0.00 2.01
252 253 6.687901 GCCCAAGTTCCCTTTTTCTTATGTTT 60.688 38.462 0.00 0.00 0.00 2.83
254 255 4.283467 GCCCAAGTTCCCTTTTTCTTATGT 59.717 41.667 0.00 0.00 0.00 2.29
258 259 2.047061 GGCCCAAGTTCCCTTTTTCTT 58.953 47.619 0.00 0.00 0.00 2.52
259 260 1.062505 TGGCCCAAGTTCCCTTTTTCT 60.063 47.619 0.00 0.00 0.00 2.52
260 261 1.344438 CTGGCCCAAGTTCCCTTTTTC 59.656 52.381 0.00 0.00 0.00 2.29
261 262 1.423584 CTGGCCCAAGTTCCCTTTTT 58.576 50.000 0.00 0.00 0.00 1.94
262 263 1.121407 GCTGGCCCAAGTTCCCTTTT 61.121 55.000 0.00 0.00 0.00 2.27
263 264 1.533994 GCTGGCCCAAGTTCCCTTT 60.534 57.895 0.00 0.00 0.00 3.11
264 265 2.118294 GCTGGCCCAAGTTCCCTT 59.882 61.111 0.00 0.00 0.00 3.95
265 266 3.984732 GGCTGGCCCAAGTTCCCT 61.985 66.667 0.00 0.00 0.00 4.20
298 299 1.788067 AACGTTAAAGGGCGCACACC 61.788 55.000 14.57 1.74 0.00 4.16
300 301 1.263752 GTTAACGTTAAAGGGCGCACA 59.736 47.619 21.67 0.00 0.00 4.57
301 302 1.263752 TGTTAACGTTAAAGGGCGCAC 59.736 47.619 21.67 5.15 0.00 5.34
302 303 1.263752 GTGTTAACGTTAAAGGGCGCA 59.736 47.619 21.67 11.76 0.00 6.09
304 305 6.469322 GTTATAGTGTTAACGTTAAAGGGCG 58.531 40.000 21.67 0.00 0.00 6.13
305 306 6.469322 CGTTATAGTGTTAACGTTAAAGGGC 58.531 40.000 21.67 10.39 45.75 5.19
315 316 2.543641 AGCGCCCGTTATAGTGTTAAC 58.456 47.619 2.29 0.00 0.00 2.01
316 317 2.965572 AGCGCCCGTTATAGTGTTAA 57.034 45.000 2.29 0.00 0.00 2.01
317 318 2.286950 CGTAGCGCCCGTTATAGTGTTA 60.287 50.000 2.29 0.00 0.00 2.41
318 319 1.534595 CGTAGCGCCCGTTATAGTGTT 60.535 52.381 2.29 0.00 0.00 3.32
319 320 0.029834 CGTAGCGCCCGTTATAGTGT 59.970 55.000 2.29 0.00 0.00 3.55
321 322 1.656441 CCGTAGCGCCCGTTATAGT 59.344 57.895 14.85 0.00 0.00 2.12
322 323 1.080974 CCCGTAGCGCCCGTTATAG 60.081 63.158 14.85 0.81 0.00 1.31
323 324 3.041701 CCCGTAGCGCCCGTTATA 58.958 61.111 14.85 0.00 0.00 0.98
324 325 4.597215 GCCCGTAGCGCCCGTTAT 62.597 66.667 14.85 0.00 0.00 1.89
338 339 1.431845 CATTTCCTAAACGGCGCCC 59.568 57.895 23.46 2.84 0.00 6.13
340 341 1.226575 GGCATTTCCTAAACGGCGC 60.227 57.895 6.90 0.00 0.00 6.53
341 342 1.431845 GGGCATTTCCTAAACGGCG 59.568 57.895 4.80 4.80 34.39 6.46
342 343 0.968393 TGGGGCATTTCCTAAACGGC 60.968 55.000 0.00 0.00 34.39 5.68
343 344 0.815095 GTGGGGCATTTCCTAAACGG 59.185 55.000 0.00 0.00 34.39 4.44
345 346 3.087370 AGAGTGGGGCATTTCCTAAAC 57.913 47.619 0.00 0.00 34.39 2.01
346 347 3.697166 GAAGAGTGGGGCATTTCCTAAA 58.303 45.455 0.00 0.00 34.39 1.85
347 348 2.355716 CGAAGAGTGGGGCATTTCCTAA 60.356 50.000 0.00 0.00 34.39 2.69
348 349 1.209504 CGAAGAGTGGGGCATTTCCTA 59.790 52.381 0.00 0.00 34.39 2.94
350 351 1.032114 CCGAAGAGTGGGGCATTTCC 61.032 60.000 0.00 0.00 0.00 3.13
351 352 0.322546 ACCGAAGAGTGGGGCATTTC 60.323 55.000 0.00 0.00 0.00 2.17
352 353 0.609131 CACCGAAGAGTGGGGCATTT 60.609 55.000 0.00 0.00 33.95 2.32
353 354 1.002134 CACCGAAGAGTGGGGCATT 60.002 57.895 0.00 0.00 33.95 3.56
355 356 1.534476 TACACCGAAGAGTGGGGCA 60.534 57.895 0.00 0.00 42.28 5.36
356 357 1.079336 GTACACCGAAGAGTGGGGC 60.079 63.158 0.00 0.00 42.28 5.80
374 7174 2.094126 GATCAACTTCGGATGCGCGG 62.094 60.000 8.83 0.00 0.00 6.46
390 7190 1.069978 GGCTAGTGGGCTGAAGAGATC 59.930 57.143 0.00 0.00 37.53 2.75
586 7448 5.925509 AGAGGAGTGTAGAGACTATCAGAC 58.074 45.833 0.00 0.00 0.00 3.51
608 7470 7.200455 TGACAATGAGTATTGGACGTGTATAG 58.800 38.462 0.00 0.00 46.33 1.31
617 7479 5.222027 TGTTTCCCTGACAATGAGTATTGGA 60.222 40.000 5.17 0.00 46.33 3.53
636 7498 4.725556 TGTCAATAGTCGTGCTTGTTTC 57.274 40.909 0.00 0.00 0.00 2.78
691 7553 6.811253 CAACTAGTTTGGTTGCCTACATTA 57.189 37.500 5.07 0.00 37.76 1.90
726 7588 4.142049 CGGGCCCTTCAAATATAAGCAAAA 60.142 41.667 22.43 0.00 0.00 2.44
727 7589 3.383185 CGGGCCCTTCAAATATAAGCAAA 59.617 43.478 22.43 0.00 0.00 3.68
728 7590 2.955660 CGGGCCCTTCAAATATAAGCAA 59.044 45.455 22.43 0.00 0.00 3.91
729 7591 2.582052 CGGGCCCTTCAAATATAAGCA 58.418 47.619 22.43 0.00 0.00 3.91
843 7706 2.738521 GCCGCGTGCTTCAAGAGA 60.739 61.111 4.92 0.00 36.87 3.10
844 7707 3.020026 CTGCCGCGTGCTTCAAGAG 62.020 63.158 18.14 4.95 42.00 2.85
1148 8284 1.138568 CAGCCTCCATGGAGATCCTT 58.861 55.000 38.37 17.88 44.53 3.36
1406 8542 5.120830 ACATGTTTACTCACTCGCATCTTTC 59.879 40.000 0.00 0.00 0.00 2.62
1613 8776 0.613260 TCAGCATAAGAGGTGCGGTT 59.387 50.000 0.00 0.00 46.86 4.44
2207 9384 3.058293 CACACCGTAACACAATTCTGCAT 60.058 43.478 0.00 0.00 0.00 3.96
2351 9535 1.713078 AGGGCCTCATTCTCAGGTTTT 59.287 47.619 0.00 0.00 32.98 2.43
2368 9552 3.616956 TCACTTGATCTTGTAGCAGGG 57.383 47.619 0.00 0.00 0.00 4.45
2394 9578 7.040409 ACCTTCAAAGTAACCATCTGAAATGTC 60.040 37.037 0.00 0.00 0.00 3.06
2450 9634 2.676839 CTCATCTTCATGTTTCAGCGCT 59.323 45.455 2.64 2.64 0.00 5.92
2811 9995 4.406003 AGCCGTTAAGACAATGGATAGAGT 59.594 41.667 0.00 0.00 0.00 3.24
2885 10069 7.063074 CGAAGGGTGTAGTAGACAATTTAAGTG 59.937 40.741 0.00 0.00 40.66 3.16
2968 11188 5.371115 ACAAAACATTACCTCCGTTCATG 57.629 39.130 0.00 0.00 0.00 3.07
3034 11255 8.557450 ACCCATGTAGTATTCAGGAGTAAAAAT 58.443 33.333 0.00 0.00 0.00 1.82
3141 11362 4.024048 CACGGATGTCAATTAGGCATTACC 60.024 45.833 0.00 0.00 44.12 2.85
3364 11652 4.678509 TTGTCTGTTTGATATCGGCAAC 57.321 40.909 0.00 2.21 0.00 4.17
3496 11784 4.403734 TCAATTGGGACCTTTCTGTTACC 58.596 43.478 5.42 0.00 0.00 2.85
3505 11793 4.568592 GGAGTGATTCTCAATTGGGACCTT 60.569 45.833 7.75 0.00 44.40 3.50
3588 11876 3.012518 GCTCATGCAGTCTACCAAACAT 58.987 45.455 0.00 0.00 39.41 2.71
3800 12977 0.951558 GGGCAATGACGTGTTTGAGT 59.048 50.000 10.42 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.