Multiple sequence alignment - TraesCS4A01G201700

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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 TraesCS4A01G201700 chr4A 100.000 3277 0 0 1 3277 491454923 491451647 0.000000e+00 6052.0
1 TraesCS4A01G201700 chr4D 93.278 3228 121 41 74 3277 81667340 81664185 0.000000e+00 4671.0
2 TraesCS4A01G201700 chr4B 92.416 2637 101 44 7 2599 115102438 115099857 0.000000e+00 3670.0
3 TraesCS4A01G201700 chr4B 89.541 392 16 7 2887 3277 115099132 115098765 1.060000e-129 473.0
4 TraesCS4A01G201700 chr4B 92.050 239 9 2 2600 2829 115099371 115099134 8.770000e-86 327.0
5 TraesCS4A01G201700 chr7D 89.583 48 4 1 1180 1227 540369671 540369625 3.530000e-05 60.2
6 TraesCS4A01G201700 chr7B 89.583 48 4 1 1180 1227 583382423 583382469 3.530000e-05 60.2
7 TraesCS4A01G201700 chr7A 89.583 48 4 1 1180 1227 621564751 621564797 3.530000e-05 60.2


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 TraesCS4A01G201700 chr4A 491451647 491454923 3276 True 6052 6052 100.000000 1 3277 1 chr4A.!!$R1 3276
1 TraesCS4A01G201700 chr4D 81664185 81667340 3155 True 4671 4671 93.278000 74 3277 1 chr4D.!!$R1 3203
2 TraesCS4A01G201700 chr4B 115098765 115102438 3673 True 1490 3670 91.335667 7 3277 3 chr4B.!!$R1 3270

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
176 178 0.741221 CGTAGTTGAGGGCTTGAGGC 60.741 60.0 0.00 0.0 40.9 4.70 F
1302 1330 0.036388 TGGGAATTCTCTGTGACGCC 60.036 55.0 6.92 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2076 0.175989 GGAGGATGGAGGTGTCGAAC 59.824 60.0 0.00 0.0 0.0 3.95 R
2332 2372 0.107654 CCAGCTAGCCAACCAGTACC 60.108 60.0 12.13 0.0 0.0 3.34 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
34 35 1.665442 AAAAACAGTCCATGCCGGC 59.335 52.632 22.73 22.73 33.14 6.13
38 39 3.479203 CAGTCCATGCCGGCCCTA 61.479 66.667 26.77 5.45 33.14 3.53
99 101 3.165160 AAAGCGTCTCCCTGCACGT 62.165 57.895 0.00 0.00 38.32 4.49
118 120 5.163854 GCACGTAATTGCTCTGTCATAAAGT 60.164 40.000 0.00 0.00 39.59 2.66
134 136 5.303333 TCATAAAGTCCAGAAACCCCAAAAC 59.697 40.000 0.00 0.00 0.00 2.43
139 141 1.691163 CCAGAAACCCCAAAACCAGGT 60.691 52.381 0.00 0.00 34.60 4.00
166 168 2.390938 TCGCACACTTTCGTAGTTGAG 58.609 47.619 0.00 0.00 33.85 3.02
167 169 1.455786 CGCACACTTTCGTAGTTGAGG 59.544 52.381 0.00 0.00 33.85 3.86
168 170 1.798813 GCACACTTTCGTAGTTGAGGG 59.201 52.381 0.00 0.00 33.85 4.30
169 171 1.798813 CACACTTTCGTAGTTGAGGGC 59.201 52.381 0.00 0.00 33.85 5.19
170 172 1.692519 ACACTTTCGTAGTTGAGGGCT 59.307 47.619 0.00 0.00 33.85 5.19
171 173 2.104281 ACACTTTCGTAGTTGAGGGCTT 59.896 45.455 0.00 0.00 33.85 4.35
172 174 2.480419 CACTTTCGTAGTTGAGGGCTTG 59.520 50.000 0.00 0.00 33.85 4.01
173 175 2.367567 ACTTTCGTAGTTGAGGGCTTGA 59.632 45.455 0.00 0.00 31.29 3.02
174 176 2.743636 TTCGTAGTTGAGGGCTTGAG 57.256 50.000 0.00 0.00 0.00 3.02
175 177 0.895530 TCGTAGTTGAGGGCTTGAGG 59.104 55.000 0.00 0.00 0.00 3.86
176 178 0.741221 CGTAGTTGAGGGCTTGAGGC 60.741 60.000 0.00 0.00 40.90 4.70
241 248 2.101770 GCCGCAGCAGCAAATCTC 59.898 61.111 0.82 0.00 42.27 2.75
247 254 1.592081 GCAGCAGCAAATCTCTACTCG 59.408 52.381 0.00 0.00 41.58 4.18
253 260 1.535015 GCAAATCTCTACTCGCTCGCT 60.535 52.381 0.00 0.00 0.00 4.93
422 429 2.178235 GCTATTCCCGGAACCGTGC 61.178 63.158 0.73 1.18 37.81 5.34
628 635 1.826385 AATCCTCACTTGGGCTTTCG 58.174 50.000 0.00 0.00 0.00 3.46
644 651 3.181526 GCTTTCGTGCATGTCTTCAGTAG 60.182 47.826 5.68 0.00 0.00 2.57
648 655 3.756963 TCGTGCATGTCTTCAGTAGTACT 59.243 43.478 5.68 0.00 0.00 2.73
650 657 3.614616 GTGCATGTCTTCAGTAGTACTGC 59.385 47.826 23.14 11.76 45.54 4.40
651 658 2.854777 GCATGTCTTCAGTAGTACTGCG 59.145 50.000 23.14 16.49 45.54 5.18
665 672 4.021916 AGTACTGCGGTAAATACTGGTCT 58.978 43.478 7.05 0.00 33.20 3.85
667 674 4.382345 ACTGCGGTAAATACTGGTCTAC 57.618 45.455 0.00 0.00 33.20 2.59
668 675 3.181493 ACTGCGGTAAATACTGGTCTACG 60.181 47.826 0.00 0.00 33.20 3.51
755 770 1.222113 GCAAGACCCTCCTACAGCC 59.778 63.158 0.00 0.00 0.00 4.85
778 806 0.894184 AGTTCATGCTGCTGCTGCTT 60.894 50.000 27.67 20.51 40.48 3.91
787 815 1.351012 GCTGCTGCTTCAGTATGCG 59.649 57.895 8.53 0.00 36.49 4.73
941 969 3.436325 CCTTGATCCTAGCTCTCTCCTCA 60.436 52.174 0.00 0.00 0.00 3.86
960 988 4.252878 CTCAGGCCTTTTCTTTCTCTCTC 58.747 47.826 0.00 0.00 0.00 3.20
1219 1247 2.879462 GCTTCGTCAGGGTACGCG 60.879 66.667 3.53 3.53 42.56 6.01
1244 1272 2.282958 TCTCCCTCGGCAGTTCGT 60.283 61.111 0.00 0.00 0.00 3.85
1246 1274 3.685214 CTCCCTCGGCAGTTCGTCG 62.685 68.421 0.00 0.00 46.75 5.12
1255 1283 0.320160 GCAGTTCGTCGGGGTAAAGT 60.320 55.000 0.00 0.00 0.00 2.66
1258 1286 3.853475 CAGTTCGTCGGGGTAAAGTAAT 58.147 45.455 0.00 0.00 0.00 1.89
1260 1288 4.692155 CAGTTCGTCGGGGTAAAGTAATTT 59.308 41.667 0.00 0.00 0.00 1.82
1261 1289 4.692155 AGTTCGTCGGGGTAAAGTAATTTG 59.308 41.667 0.00 0.00 0.00 2.32
1263 1291 5.398603 TCGTCGGGGTAAAGTAATTTGTA 57.601 39.130 0.00 0.00 0.00 2.41
1265 1293 4.329801 CGTCGGGGTAAAGTAATTTGTACC 59.670 45.833 0.00 0.00 36.12 3.34
1266 1294 4.329801 GTCGGGGTAAAGTAATTTGTACCG 59.670 45.833 15.70 15.70 37.47 4.02
1267 1295 4.020662 TCGGGGTAAAGTAATTTGTACCGT 60.021 41.667 18.90 0.00 37.47 4.83
1270 1298 5.473162 GGGGTAAAGTAATTTGTACCGTGTT 59.527 40.000 0.00 0.00 37.47 3.32
1271 1299 6.372981 GGGTAAAGTAATTTGTACCGTGTTG 58.627 40.000 0.00 0.00 37.47 3.33
1272 1300 6.204495 GGGTAAAGTAATTTGTACCGTGTTGA 59.796 38.462 0.00 0.00 37.47 3.18
1273 1301 7.071414 GGTAAAGTAATTTGTACCGTGTTGAC 58.929 38.462 0.00 0.00 0.00 3.18
1274 1302 4.977741 AGTAATTTGTACCGTGTTGACG 57.022 40.909 0.00 0.00 45.67 4.35
1275 1303 4.370917 AGTAATTTGTACCGTGTTGACGT 58.629 39.130 0.00 0.00 44.54 4.34
1276 1304 5.527951 AGTAATTTGTACCGTGTTGACGTA 58.472 37.500 0.00 0.00 44.54 3.57
1277 1305 5.982516 AGTAATTTGTACCGTGTTGACGTAA 59.017 36.000 0.00 0.00 44.54 3.18
1294 1322 3.782046 CGTAATGACGTGGGAATTCTCT 58.218 45.455 6.92 0.00 44.31 3.10
1295 1323 3.551890 CGTAATGACGTGGGAATTCTCTG 59.448 47.826 6.92 1.71 44.31 3.35
1296 1324 3.703001 AATGACGTGGGAATTCTCTGT 57.297 42.857 6.92 5.18 0.00 3.41
1298 1326 1.967779 TGACGTGGGAATTCTCTGTGA 59.032 47.619 6.92 0.00 0.00 3.58
1299 1327 2.288825 TGACGTGGGAATTCTCTGTGAC 60.289 50.000 6.92 0.00 0.00 3.67
1300 1328 1.336887 ACGTGGGAATTCTCTGTGACG 60.337 52.381 12.82 12.82 0.00 4.35
1301 1329 1.079503 GTGGGAATTCTCTGTGACGC 58.920 55.000 6.92 0.00 0.00 5.19
1302 1330 0.036388 TGGGAATTCTCTGTGACGCC 60.036 55.000 6.92 0.00 0.00 5.68
1303 1331 0.250513 GGGAATTCTCTGTGACGCCT 59.749 55.000 5.23 0.00 0.00 5.52
1304 1332 1.339151 GGGAATTCTCTGTGACGCCTT 60.339 52.381 5.23 0.00 0.00 4.35
1346 1381 2.272146 GCTGATCAAGGGCGGGAA 59.728 61.111 0.00 0.00 0.00 3.97
1500 1535 4.191485 GACGCCGTCGCATTCGTG 62.191 66.667 0.00 0.00 39.84 4.35
1514 1554 2.273370 TTCGTGAGTAACATCCTCGC 57.727 50.000 0.00 0.00 36.37 5.03
1535 1575 3.417224 CGCTGCGCATATCGGCAT 61.417 61.111 12.24 0.00 38.94 4.40
1558 1598 0.717224 CATTTGCATGCGTGGAAAGC 59.283 50.000 26.40 5.06 46.60 3.51
1571 1611 0.391263 GGAAAGCGGGAACTGATCGT 60.391 55.000 0.00 0.00 36.31 3.73
1576 1616 0.094730 GCGGGAACTGATCGTTTTCG 59.905 55.000 14.83 14.83 40.55 3.46
1753 1793 1.403679 CTCGTCCTCCTCAGCTGTAAG 59.596 57.143 14.67 9.43 0.00 2.34
1804 1844 1.539157 TCCCTCGATCGATCATGGAG 58.461 55.000 26.06 21.69 37.15 3.86
1808 1848 1.201181 CTCGATCGATCATGGAGGACC 59.799 57.143 24.40 0.00 34.46 4.46
1809 1849 0.244994 CGATCGATCATGGAGGACCC 59.755 60.000 24.40 0.00 34.81 4.46
1832 1872 0.394352 TCCCTACCTAACCCGTCGAC 60.394 60.000 5.18 5.18 0.00 4.20
1904 1944 0.970937 TCCAGGACCGGCTCTACAAG 60.971 60.000 0.00 0.00 0.00 3.16
2180 2220 3.078836 TTCGGGCCCTACTTCCGG 61.079 66.667 22.43 0.54 43.54 5.14
2687 3214 6.127730 GGTGTAATTTATGGTCTTGTCTTGGG 60.128 42.308 0.00 0.00 0.00 4.12
2689 3216 7.608761 GTGTAATTTATGGTCTTGTCTTGGGTA 59.391 37.037 0.00 0.00 0.00 3.69
2690 3217 8.164733 TGTAATTTATGGTCTTGTCTTGGGTAA 58.835 33.333 0.00 0.00 0.00 2.85
2705 3241 4.308526 TGGGTAATTATCTGTGCCAACA 57.691 40.909 0.00 0.00 34.34 3.33
2734 3270 4.159321 TGGAAAGAAGTGTCAAATGTTGCA 59.841 37.500 0.00 0.00 0.00 4.08
2755 3291 5.294060 TGCAAAAACAAAATCTTCTTCTGGC 59.706 36.000 0.00 0.00 0.00 4.85
2770 3306 7.666388 TCTTCTTCTGGCATATAGGAGTACTAC 59.334 40.741 0.00 0.00 33.70 2.73
2815 3351 2.113433 GTCGAGGCCGTAGCAGAGA 61.113 63.158 0.00 0.00 42.56 3.10
2817 3353 0.752009 TCGAGGCCGTAGCAGAGATT 60.752 55.000 0.00 0.00 42.56 2.40
2839 3375 3.181485 TGTCGTCGTTGCACCATGATATA 60.181 43.478 0.00 0.00 0.00 0.86
2840 3376 3.987868 GTCGTCGTTGCACCATGATATAT 59.012 43.478 0.00 0.00 0.00 0.86
2847 3383 6.313658 TCGTTGCACCATGATATATTGATAGC 59.686 38.462 0.00 0.00 0.00 2.97
2855 3391 8.845227 ACCATGATATATTGATAGCTCTAGACG 58.155 37.037 0.00 0.00 0.00 4.18
2860 3396 0.859882 TGATAGCTCTAGACGACGCG 59.140 55.000 3.53 3.53 0.00 6.01
2898 3434 1.270414 ATCAGCCACTCAGGGACCTG 61.270 60.000 12.16 12.16 44.86 4.00
2955 3492 6.599638 AGATCCCAAGGAAATCTTTACTTTCG 59.400 38.462 0.00 0.00 39.26 3.46
2956 3493 5.007682 TCCCAAGGAAATCTTTACTTTCGG 58.992 41.667 0.00 1.79 39.26 4.30
3092 3630 0.107703 TGGTAGAATCCAAGCTGCGG 60.108 55.000 0.00 0.00 34.24 5.69
3094 3632 0.107654 GTAGAATCCAAGCTGCGGGT 60.108 55.000 12.09 0.00 0.00 5.28
3128 3666 1.684983 GATGGAGGATGCAAATGGGTG 59.315 52.381 0.00 0.00 42.43 4.61
3169 3708 3.290948 AAAGTGTACTGCCCTGTTGAA 57.709 42.857 0.00 0.00 0.00 2.69
3170 3709 3.508845 AAGTGTACTGCCCTGTTGAAT 57.491 42.857 0.00 0.00 0.00 2.57
3171 3710 2.783135 AGTGTACTGCCCTGTTGAATG 58.217 47.619 0.00 0.00 0.00 2.67
3172 3711 2.106511 AGTGTACTGCCCTGTTGAATGT 59.893 45.455 0.00 0.00 0.00 2.71
3173 3712 2.884639 GTGTACTGCCCTGTTGAATGTT 59.115 45.455 0.00 0.00 0.00 2.71
3174 3713 2.884012 TGTACTGCCCTGTTGAATGTTG 59.116 45.455 0.00 0.00 0.00 3.33
3175 3714 2.363306 ACTGCCCTGTTGAATGTTGA 57.637 45.000 0.00 0.00 0.00 3.18
3181 3720 3.614870 GCCCTGTTGAATGTTGATGGAAC 60.615 47.826 0.00 0.00 34.84 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.106569 TTGTCCAGGCATGCATAGGG 60.107 55.000 21.36 11.38 0.00 3.53
38 39 0.608856 TTCGTTGTCCAGGCATGCAT 60.609 50.000 21.36 10.32 0.00 3.96
99 101 6.946340 TCTGGACTTTATGACAGAGCAATTA 58.054 36.000 0.00 0.00 35.24 1.40
118 120 1.412361 CCTGGTTTTGGGGTTTCTGGA 60.412 52.381 0.00 0.00 0.00 3.86
134 136 0.946221 GTGTGCGAGTTCTCACCTGG 60.946 60.000 0.00 0.00 31.02 4.45
139 141 1.202371 ACGAAAGTGTGCGAGTTCTCA 60.202 47.619 0.00 0.00 46.97 3.27
166 168 3.521796 GATTGCCGCCTCAAGCCC 61.522 66.667 0.00 0.00 38.78 5.19
167 169 3.521796 GGATTGCCGCCTCAAGCC 61.522 66.667 4.44 4.44 43.99 4.35
208 210 1.813753 GGCATGGCAGCTTTGCATG 60.814 57.895 15.47 12.07 38.12 4.06
209 211 2.582436 GGCATGGCAGCTTTGCAT 59.418 55.556 15.47 0.00 38.12 3.96
210 212 4.058732 CGGCATGGCAGCTTTGCA 62.059 61.111 20.37 0.00 38.12 4.08
241 248 2.161486 GTTGCCAGCGAGCGAGTAG 61.161 63.158 0.00 0.00 34.65 2.57
644 651 4.382345 AGACCAGTATTTACCGCAGTAC 57.618 45.455 0.00 0.00 0.00 2.73
648 655 2.754552 ACGTAGACCAGTATTTACCGCA 59.245 45.455 0.00 0.00 0.00 5.69
649 656 3.427161 ACGTAGACCAGTATTTACCGC 57.573 47.619 0.00 0.00 0.00 5.68
650 657 4.737054 ACAACGTAGACCAGTATTTACCG 58.263 43.478 0.00 0.00 0.00 4.02
651 658 5.928264 ACAACAACGTAGACCAGTATTTACC 59.072 40.000 0.00 0.00 0.00 2.85
665 672 5.005203 ACGTAATTTCACGAACAACAACGTA 59.995 36.000 7.72 0.00 44.69 3.57
667 674 4.265371 ACGTAATTTCACGAACAACAACG 58.735 39.130 7.72 0.00 44.69 4.10
668 675 7.613698 GCAATACGTAATTTCACGAACAACAAC 60.614 37.037 7.72 0.00 44.69 3.32
755 770 1.135660 CAGCAGCAGCATGAACTCTTG 60.136 52.381 3.17 0.00 45.49 3.02
787 815 8.622520 TGCCAAGCATTTAGTGGTACAAAACC 62.623 42.308 0.00 0.00 40.57 3.27
934 962 2.982488 AGAAAGAAAAGGCCTGAGGAGA 59.018 45.455 5.69 0.00 0.00 3.71
935 963 3.008923 AGAGAAAGAAAAGGCCTGAGGAG 59.991 47.826 5.69 0.00 0.00 3.69
941 969 4.167319 AGAGAGAGAGAAAGAAAAGGCCT 58.833 43.478 0.00 0.00 0.00 5.19
1185 1213 2.029844 GCAGTCGTGGAACTGGAGC 61.030 63.158 6.21 0.00 45.52 4.70
1239 1267 4.452114 ACAAATTACTTTACCCCGACGAAC 59.548 41.667 0.00 0.00 0.00 3.95
1244 1272 4.020662 ACGGTACAAATTACTTTACCCCGA 60.021 41.667 12.66 0.00 34.00 5.14
1246 1274 5.003160 ACACGGTACAAATTACTTTACCCC 58.997 41.667 0.00 0.00 0.00 4.95
1274 1302 4.330074 CACAGAGAATTCCCACGTCATTAC 59.670 45.833 0.65 0.00 0.00 1.89
1275 1303 4.221924 TCACAGAGAATTCCCACGTCATTA 59.778 41.667 0.65 0.00 0.00 1.90
1276 1304 3.007940 TCACAGAGAATTCCCACGTCATT 59.992 43.478 0.65 0.00 0.00 2.57
1277 1305 2.567169 TCACAGAGAATTCCCACGTCAT 59.433 45.455 0.65 0.00 0.00 3.06
1292 1320 0.884514 CTGAGAGAAGGCGTCACAGA 59.115 55.000 13.35 0.00 0.00 3.41
1294 1322 1.536073 CCCTGAGAGAAGGCGTCACA 61.536 60.000 2.69 0.00 35.85 3.58
1295 1323 1.216710 CCCTGAGAGAAGGCGTCAC 59.783 63.158 2.69 0.00 35.85 3.67
1296 1324 1.984570 CCCCTGAGAGAAGGCGTCA 60.985 63.158 2.69 0.00 35.85 4.35
1298 1326 2.120718 ACCCCTGAGAGAAGGCGT 59.879 61.111 0.00 0.00 35.85 5.68
1299 1327 2.581354 CACCCCTGAGAGAAGGCG 59.419 66.667 0.00 0.00 35.85 5.52
1300 1328 2.270527 GCACCCCTGAGAGAAGGC 59.729 66.667 0.00 0.00 35.85 4.35
1301 1329 1.984570 TCGCACCCCTGAGAGAAGG 60.985 63.158 0.00 0.00 37.05 3.46
1302 1330 1.216710 GTCGCACCCCTGAGAGAAG 59.783 63.158 0.00 0.00 0.00 2.85
1303 1331 2.636412 CGTCGCACCCCTGAGAGAA 61.636 63.158 0.00 0.00 0.00 2.87
1304 1332 3.062466 CGTCGCACCCCTGAGAGA 61.062 66.667 0.00 0.00 0.00 3.10
1346 1381 2.590575 CCACCTCCGCGTTGTTGT 60.591 61.111 4.92 0.00 0.00 3.32
1500 1535 2.577785 GCGCGCGAGGATGTTACTC 61.578 63.158 37.18 6.98 0.00 2.59
1539 1579 0.717224 GCTTTCCACGCATGCAAATG 59.283 50.000 19.57 12.27 0.00 2.32
1542 1582 2.254951 CGCTTTCCACGCATGCAA 59.745 55.556 19.57 0.58 0.00 4.08
1543 1583 3.736100 CCGCTTTCCACGCATGCA 61.736 61.111 19.57 0.00 0.00 3.96
1544 1584 4.481112 CCCGCTTTCCACGCATGC 62.481 66.667 7.91 7.91 0.00 4.06
1545 1585 2.331893 TTCCCGCTTTCCACGCATG 61.332 57.895 0.00 0.00 0.00 4.06
1546 1586 2.033448 TTCCCGCTTTCCACGCAT 59.967 55.556 0.00 0.00 0.00 4.73
1547 1587 2.975799 GTTCCCGCTTTCCACGCA 60.976 61.111 0.00 0.00 0.00 5.24
1548 1588 2.668550 AGTTCCCGCTTTCCACGC 60.669 61.111 0.00 0.00 0.00 5.34
1549 1589 0.673644 ATCAGTTCCCGCTTTCCACG 60.674 55.000 0.00 0.00 0.00 4.94
1550 1590 1.087501 GATCAGTTCCCGCTTTCCAC 58.912 55.000 0.00 0.00 0.00 4.02
1551 1591 0.391130 CGATCAGTTCCCGCTTTCCA 60.391 55.000 0.00 0.00 0.00 3.53
1552 1592 0.391263 ACGATCAGTTCCCGCTTTCC 60.391 55.000 0.00 0.00 0.00 3.13
1553 1593 1.439679 AACGATCAGTTCCCGCTTTC 58.560 50.000 0.00 0.00 39.16 2.62
1554 1594 1.892209 AAACGATCAGTTCCCGCTTT 58.108 45.000 0.00 0.00 43.37 3.51
1558 1598 1.425412 ACGAAAACGATCAGTTCCCG 58.575 50.000 15.37 15.37 43.37 5.14
1564 1604 1.262950 TGCACCAACGAAAACGATCAG 59.737 47.619 0.00 0.00 0.00 2.90
1571 1611 1.440938 CCGGTCTGCACCAACGAAAA 61.441 55.000 0.00 0.00 44.02 2.29
1753 1793 1.227527 GGTGGGTTGGTTTGCTTGC 60.228 57.895 0.00 0.00 0.00 4.01
1805 1845 1.767088 GGTTAGGTAGGGACATGGGTC 59.233 57.143 0.00 0.00 43.55 4.46
1806 1846 1.627195 GGGTTAGGTAGGGACATGGGT 60.627 57.143 0.00 0.00 0.00 4.51
1808 1848 0.756903 CGGGTTAGGTAGGGACATGG 59.243 60.000 0.00 0.00 0.00 3.66
1809 1849 1.411612 GACGGGTTAGGTAGGGACATG 59.588 57.143 0.00 0.00 0.00 3.21
1810 1850 1.785647 GACGGGTTAGGTAGGGACAT 58.214 55.000 0.00 0.00 0.00 3.06
1811 1851 0.680921 CGACGGGTTAGGTAGGGACA 60.681 60.000 0.00 0.00 0.00 4.02
1812 1852 0.394352 TCGACGGGTTAGGTAGGGAC 60.394 60.000 0.00 0.00 0.00 4.46
1813 1853 0.394352 GTCGACGGGTTAGGTAGGGA 60.394 60.000 0.00 0.00 0.00 4.20
1814 1854 1.718757 CGTCGACGGGTTAGGTAGGG 61.719 65.000 29.70 0.00 35.37 3.53
1815 1855 1.723870 CGTCGACGGGTTAGGTAGG 59.276 63.158 29.70 0.00 35.37 3.18
1868 1908 1.298859 GGATGAAGAAGCACGCCGTT 61.299 55.000 0.00 0.00 0.00 4.44
1991 2031 4.719369 ACGCGCGAGTTGGAGTCC 62.719 66.667 39.36 0.73 0.00 3.85
2036 2076 0.175989 GGAGGATGGAGGTGTCGAAC 59.824 60.000 0.00 0.00 0.00 3.95
2180 2220 2.507324 GAGTCCGCGAAGTCCTGC 60.507 66.667 8.23 0.00 0.00 4.85
2327 2367 2.418334 GCTAGCCAACCAGTACCAGTAC 60.418 54.545 2.29 0.00 36.35 2.73
2328 2368 1.829222 GCTAGCCAACCAGTACCAGTA 59.171 52.381 2.29 0.00 0.00 2.74
2329 2369 0.613777 GCTAGCCAACCAGTACCAGT 59.386 55.000 2.29 0.00 0.00 4.00
2330 2370 0.905357 AGCTAGCCAACCAGTACCAG 59.095 55.000 12.13 0.00 0.00 4.00
2331 2371 0.613260 CAGCTAGCCAACCAGTACCA 59.387 55.000 12.13 0.00 0.00 3.25
2332 2372 0.107654 CCAGCTAGCCAACCAGTACC 60.108 60.000 12.13 0.00 0.00 3.34
2586 2628 9.937876 AAGCACATCTTATATATACCCTAGCTA 57.062 33.333 0.00 0.00 32.10 3.32
2587 2629 8.846423 AAGCACATCTTATATATACCCTAGCT 57.154 34.615 0.00 0.00 32.10 3.32
2705 3241 5.596836 TTTGACACTTCTTTCCAATTGCT 57.403 34.783 0.00 0.00 0.00 3.91
2790 3326 0.456312 CTACGGCCTCGACACTTGAC 60.456 60.000 0.00 0.00 40.11 3.18
2815 3351 0.516877 CATGGTGCAACGACGACAAT 59.483 50.000 0.00 0.00 38.12 2.71
2817 3353 0.320334 ATCATGGTGCAACGACGACA 60.320 50.000 0.00 0.00 38.12 4.35
2839 3375 2.096169 CGCGTCGTCTAGAGCTATCAAT 60.096 50.000 0.00 0.00 0.00 2.57
2840 3376 1.260825 CGCGTCGTCTAGAGCTATCAA 59.739 52.381 0.00 0.00 0.00 2.57
2847 3383 1.823260 ATCTCGCGCGTCGTCTAGAG 61.823 60.000 30.98 17.01 39.67 2.43
2875 3411 2.519013 GTCCCTGAGTGGCTGATTTTT 58.481 47.619 0.00 0.00 0.00 1.94
2876 3412 1.272147 GGTCCCTGAGTGGCTGATTTT 60.272 52.381 0.00 0.00 0.00 1.82
2877 3413 0.329596 GGTCCCTGAGTGGCTGATTT 59.670 55.000 0.00 0.00 0.00 2.17
2878 3414 0.548682 AGGTCCCTGAGTGGCTGATT 60.549 55.000 0.00 0.00 0.00 2.57
2879 3415 1.081833 AGGTCCCTGAGTGGCTGAT 59.918 57.895 0.00 0.00 0.00 2.90
2898 3434 0.326927 TTTGGTCCTCGACAATCCCC 59.673 55.000 0.00 0.00 33.68 4.81
2932 3468 5.652452 CCGAAAGTAAAGATTTCCTTGGGAT 59.348 40.000 0.00 0.00 34.79 3.85
2955 3492 0.618458 TACAGTTCCATGCACCTCCC 59.382 55.000 0.00 0.00 0.00 4.30
2956 3493 2.359900 CTTACAGTTCCATGCACCTCC 58.640 52.381 0.00 0.00 0.00 4.30
3109 3647 1.690209 CCACCCATTTGCATCCTCCAT 60.690 52.381 0.00 0.00 0.00 3.41
3128 3666 7.538678 CACTTTTACTCAATATGTGTTTCAGCC 59.461 37.037 0.00 0.00 0.00 4.85
3169 3708 1.545582 CAAAGGCCGTTCCATCAACAT 59.454 47.619 0.00 0.00 37.29 2.71
3170 3709 0.958091 CAAAGGCCGTTCCATCAACA 59.042 50.000 0.00 0.00 37.29 3.33
3171 3710 0.388520 GCAAAGGCCGTTCCATCAAC 60.389 55.000 0.00 0.00 37.29 3.18
3172 3711 0.539438 AGCAAAGGCCGTTCCATCAA 60.539 50.000 0.00 0.00 42.56 2.57
3173 3712 0.539438 AAGCAAAGGCCGTTCCATCA 60.539 50.000 0.00 0.00 42.56 3.07
3174 3713 0.171231 GAAGCAAAGGCCGTTCCATC 59.829 55.000 0.00 0.00 42.56 3.51
3175 3714 0.251341 AGAAGCAAAGGCCGTTCCAT 60.251 50.000 0.00 0.00 42.56 3.41
3181 3720 0.659957 GAGCATAGAAGCAAAGGCCG 59.340 55.000 0.00 0.00 42.56 6.13


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

AutoCloner maintained by Alex Coulton.