Multiple sequence alignment - TraesCS5A01G275700

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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 TraesCS5A01G275700 chr5A 100.000 1541 0 0 859 2399 484882494 484880954 0.000000e+00 2846
1 TraesCS5A01G275700 chr5A 100.000 542 0 0 1 542 484883352 484882811 0.000000e+00 1002
2 TraesCS5A01G275700 chr5B 94.314 809 37 3 859 1667 460972959 460972160 0.000000e+00 1230
3 TraesCS5A01G275700 chr5B 83.032 554 59 21 1 529 460973547 460973004 1.000000e-128 470
4 TraesCS5A01G275700 chr5B 89.645 338 9 3 1847 2158 460970131 460969794 7.980000e-110 407
5 TraesCS5A01G275700 chr5B 95.506 89 3 1 1770 1857 460972067 460971979 8.940000e-30 141
6 TraesCS5A01G275700 chr4D 87.607 234 19 4 2166 2392 180102894 180103124 1.830000e-66 263
7 TraesCS5A01G275700 chr6D 87.234 235 20 4 2172 2399 25991449 25991680 2.370000e-65 259
8 TraesCS5A01G275700 chr6D 87.446 231 19 3 2172 2395 68074973 68075200 8.510000e-65 257
9 TraesCS5A01G275700 chr6D 86.752 234 21 4 2166 2392 328505273 328505503 3.960000e-63 252
10 TraesCS5A01G275700 chr3A 86.722 241 21 5 2162 2395 121635137 121635373 8.510000e-65 257
11 TraesCS5A01G275700 chr7B 86.307 241 23 5 2166 2399 315032193 315032430 1.100000e-63 254
12 TraesCS5A01G275700 chr7B 87.013 231 20 7 2172 2395 391693970 391693743 3.960000e-63 252
13 TraesCS5A01G275700 chr4A 86.420 243 20 7 2162 2395 101743661 101743423 1.100000e-63 254
14 TraesCS5A01G275700 chr4A 86.008 243 24 5 2164 2399 662450938 662450699 3.960000e-63 252


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 TraesCS5A01G275700 chr5A 484880954 484883352 2398 True 1924 2846 100.00000 1 2399 2 chr5A.!!$R1 2398
1 TraesCS5A01G275700 chr5B 460969794 460973547 3753 True 562 1230 90.62425 1 2158 4 chr5B.!!$R1 2157

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
312 325 0.179142 GACCGCGGTCCTAGTCTTTC 60.179 60.0 41.88 18.2 39.08 2.62 F
1303 1331 0.392998 GGCCATCGAGCTTTTCTGGA 60.393 55.0 0.00 0.0 33.99 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1352 0.729116 AGCACCGCATCGAAGAATTG 59.271 50.00 0.0 0.0 43.58 2.32 R
2186 4113 5.557576 TGGCTTCAGATAATATGCAGAGT 57.442 39.13 0.0 0.0 0.00 3.24 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
42 43 5.189145 AGGAGTCCGGTTGTAATACTTTCAT 59.811 40.000 2.76 0.00 0.00 2.57
49 50 8.141909 TCCGGTTGTAATACTTTCATGATAGAG 58.858 37.037 18.61 9.42 0.00 2.43
106 107 5.936686 ATTTCAATCGTCATCTAGCATGG 57.063 39.130 0.00 0.00 0.00 3.66
114 115 3.739209 CGTCATCTAGCATGGAGAGCAAA 60.739 47.826 0.00 0.00 0.00 3.68
115 116 4.387598 GTCATCTAGCATGGAGAGCAAAT 58.612 43.478 0.00 0.00 0.00 2.32
119 120 2.054232 AGCATGGAGAGCAAATGGAG 57.946 50.000 0.00 0.00 0.00 3.86
129 130 1.142870 AGCAAATGGAGGCGGCTATTA 59.857 47.619 13.24 0.88 32.09 0.98
138 139 3.265791 GAGGCGGCTATTATGATTGGAG 58.734 50.000 13.24 0.00 0.00 3.86
139 140 2.906389 AGGCGGCTATTATGATTGGAGA 59.094 45.455 11.03 0.00 0.00 3.71
153 155 9.904198 TTATGATTGGAGAGATATTTTGTCACA 57.096 29.630 0.00 0.00 0.00 3.58
160 162 7.930325 TGGAGAGATATTTTGTCACAGATCATC 59.070 37.037 0.00 0.00 0.00 2.92
161 163 7.387397 GGAGAGATATTTTGTCACAGATCATCC 59.613 40.741 0.00 0.00 0.00 3.51
162 164 7.799081 AGAGATATTTTGTCACAGATCATCCA 58.201 34.615 0.00 0.00 0.00 3.41
163 165 8.438373 AGAGATATTTTGTCACAGATCATCCAT 58.562 33.333 0.00 0.00 0.00 3.41
167 169 3.548745 TGTCACAGATCATCCATGGTC 57.451 47.619 12.58 1.25 38.20 4.02
170 172 4.019051 TGTCACAGATCATCCATGGTCTTT 60.019 41.667 12.58 0.00 45.59 2.52
174 176 4.135306 CAGATCATCCATGGTCTTTCCTG 58.865 47.826 12.58 9.56 45.59 3.86
190 192 1.001974 TCCTGTGATCAAACGGTCCAG 59.998 52.381 0.00 0.00 0.00 3.86
205 207 3.689161 CGGTCCAGTTTGATGCATCTAAA 59.311 43.478 26.32 20.23 0.00 1.85
206 208 4.437390 CGGTCCAGTTTGATGCATCTAAAC 60.437 45.833 28.50 28.50 35.19 2.01
209 211 3.093574 CAGTTTGATGCATCTAAACGCG 58.906 45.455 28.78 24.03 38.84 6.01
216 229 3.936902 TGCATCTAAACGCGGAATAAC 57.063 42.857 12.47 0.00 0.00 1.89
249 262 3.005554 CTCGTTCAACGGAGGACTACTA 58.994 50.000 10.69 0.00 42.81 1.82
283 296 1.827344 TCTCTGATTGGACGACAGCAT 59.173 47.619 0.00 0.00 0.00 3.79
300 313 3.371097 ATACTGCCACAGACCGCGG 62.371 63.158 26.86 26.86 35.18 6.46
308 321 2.045131 ACAGACCGCGGTCCTAGTC 61.045 63.158 45.66 26.96 45.59 2.59
312 325 0.179142 GACCGCGGTCCTAGTCTTTC 60.179 60.000 41.88 18.20 39.08 2.62
317 330 2.194271 GCGGTCCTAGTCTTTCAATCG 58.806 52.381 0.00 0.00 0.00 3.34
331 344 4.571375 TTCAATCGTACGGTCATTTTCG 57.429 40.909 16.52 0.00 0.00 3.46
336 349 1.701704 GTACGGTCATTTTCGGTCGT 58.298 50.000 0.00 0.00 35.07 4.34
340 353 1.515631 CGGTCATTTTCGGTCGTATCG 59.484 52.381 0.00 0.00 0.00 2.92
358 371 2.359354 AACGGCCGCTGTGCAATA 60.359 55.556 28.58 0.00 0.00 1.90
360 373 1.312371 AACGGCCGCTGTGCAATATT 61.312 50.000 28.58 4.49 0.00 1.28
407 420 3.693085 CCATCTCTTTTGGTCATGGTCTG 59.307 47.826 0.00 0.00 31.01 3.51
422 436 1.929169 GGTCTGACGTATAAAACCGGC 59.071 52.381 0.00 0.00 0.00 6.13
423 437 1.585214 GTCTGACGTATAAAACCGGCG 59.415 52.381 0.00 0.00 33.91 6.46
426 440 1.079266 ACGTATAAAACCGGCGCCA 60.079 52.632 28.98 5.63 0.00 5.69
479 505 4.759205 ACCCCCAATTCGCCCAGC 62.759 66.667 0.00 0.00 0.00 4.85
483 509 2.045045 CCAATTCGCCCAGCTCCA 60.045 61.111 0.00 0.00 0.00 3.86
975 1003 3.861797 ATCACCGTCCGGGGCATC 61.862 66.667 10.91 0.00 41.60 3.91
1009 1037 2.109799 CGCCCCAGATGCTTCGAT 59.890 61.111 0.00 0.00 0.00 3.59
1191 1219 4.468689 GCCTACGCCCTCACCCAC 62.469 72.222 0.00 0.00 0.00 4.61
1262 1290 2.813754 CCGTGGTGAACTTCATGAACAT 59.186 45.455 3.38 0.00 0.00 2.71
1271 1299 5.352293 TGAACTTCATGAACATCTTCATCGG 59.648 40.000 3.38 0.00 44.04 4.18
1303 1331 0.392998 GGCCATCGAGCTTTTCTGGA 60.393 55.000 0.00 0.00 33.99 3.86
1307 1335 2.337583 CATCGAGCTTTTCTGGAACGA 58.662 47.619 0.00 0.00 33.18 3.85
1310 1338 3.199677 TCGAGCTTTTCTGGAACGAAAA 58.800 40.909 0.00 0.00 38.03 2.29
1311 1339 3.623960 TCGAGCTTTTCTGGAACGAAAAA 59.376 39.130 0.00 0.00 39.09 1.94
1315 1343 4.398044 AGCTTTTCTGGAACGAAAAACTCA 59.602 37.500 0.00 0.00 39.09 3.41
1324 1352 0.875059 CGAAAAACTCACTGGCCCTC 59.125 55.000 0.00 0.00 0.00 4.30
1347 1375 1.522355 CTTCGATGCGGTGCTGGAT 60.522 57.895 0.00 0.00 0.00 3.41
1397 1425 2.786854 CGTGGACTACATTCGTCTCTG 58.213 52.381 0.00 0.00 0.00 3.35
1401 1429 4.079970 TGGACTACATTCGTCTCTGAAGT 58.920 43.478 0.00 0.00 0.00 3.01
1598 1626 3.243035 TGTTGGAACGAAATCAAGTGCTG 60.243 43.478 0.00 0.00 0.00 4.41
1607 1635 6.603095 ACGAAATCAAGTGCTGAATTTAGTC 58.397 36.000 0.00 0.00 37.67 2.59
1613 1641 3.960571 AGTGCTGAATTTAGTCTGCCAT 58.039 40.909 6.60 0.00 40.63 4.40
1614 1642 4.338879 AGTGCTGAATTTAGTCTGCCATT 58.661 39.130 6.60 0.00 40.63 3.16
1615 1643 4.768968 AGTGCTGAATTTAGTCTGCCATTT 59.231 37.500 6.60 0.00 40.63 2.32
1616 1644 5.098211 GTGCTGAATTTAGTCTGCCATTTC 58.902 41.667 6.60 0.00 40.63 2.17
1617 1645 4.142622 TGCTGAATTTAGTCTGCCATTTCG 60.143 41.667 6.60 0.00 40.63 3.46
1667 1695 3.117512 CCAGTGGGGCTTCCTTATGTTAT 60.118 47.826 0.00 0.00 36.20 1.89
1668 1696 4.104102 CCAGTGGGGCTTCCTTATGTTATA 59.896 45.833 0.00 0.00 36.20 0.98
1669 1697 5.222130 CCAGTGGGGCTTCCTTATGTTATAT 60.222 44.000 0.00 0.00 36.20 0.86
1670 1698 5.940470 CAGTGGGGCTTCCTTATGTTATATC 59.060 44.000 0.00 0.00 36.20 1.63
1671 1699 5.014228 AGTGGGGCTTCCTTATGTTATATCC 59.986 44.000 0.00 0.00 36.20 2.59
1672 1700 4.019681 TGGGGCTTCCTTATGTTATATCCG 60.020 45.833 0.00 0.00 36.20 4.18
1673 1701 4.224370 GGGGCTTCCTTATGTTATATCCGA 59.776 45.833 0.00 0.00 0.00 4.55
1674 1702 5.176592 GGGCTTCCTTATGTTATATCCGAC 58.823 45.833 0.00 0.00 0.00 4.79
1675 1703 4.863131 GGCTTCCTTATGTTATATCCGACG 59.137 45.833 0.00 0.00 0.00 5.12
1676 1704 4.863131 GCTTCCTTATGTTATATCCGACGG 59.137 45.833 7.84 7.84 0.00 4.79
1677 1705 4.445452 TCCTTATGTTATATCCGACGGC 57.555 45.455 9.66 0.00 0.00 5.68
1678 1706 4.084287 TCCTTATGTTATATCCGACGGCT 58.916 43.478 9.66 1.10 0.00 5.52
1679 1707 4.082408 TCCTTATGTTATATCCGACGGCTG 60.082 45.833 9.66 0.00 0.00 4.85
1680 1708 2.080286 ATGTTATATCCGACGGCTGC 57.920 50.000 9.66 0.00 0.00 5.25
1681 1709 0.318360 TGTTATATCCGACGGCTGCG 60.318 55.000 9.66 0.00 0.00 5.18
1682 1710 1.372499 TTATATCCGACGGCTGCGC 60.372 57.895 9.66 0.00 0.00 6.09
1683 1711 2.077821 TTATATCCGACGGCTGCGCA 62.078 55.000 10.98 10.98 0.00 6.09
1684 1712 2.472232 TATATCCGACGGCTGCGCAG 62.472 60.000 32.83 32.83 0.00 5.18
1688 1716 3.109547 CGACGGCTGCGCAGTTTA 61.110 61.111 35.80 0.93 37.05 2.01
1689 1717 2.452813 CGACGGCTGCGCAGTTTAT 61.453 57.895 35.80 20.41 37.05 1.40
1701 1729 2.541556 GCAGTTTATCTCCCTCACGTC 58.458 52.381 0.00 0.00 0.00 4.34
1719 1747 2.437413 GTCCCTTTTCCAGCGAAAGAT 58.563 47.619 0.00 0.00 39.14 2.40
1720 1748 2.820197 GTCCCTTTTCCAGCGAAAGATT 59.180 45.455 0.00 0.00 39.14 2.40
1721 1749 3.255888 GTCCCTTTTCCAGCGAAAGATTT 59.744 43.478 0.00 0.00 39.14 2.17
1722 1750 3.895041 TCCCTTTTCCAGCGAAAGATTTT 59.105 39.130 0.00 0.00 39.14 1.82
1723 1751 4.343814 TCCCTTTTCCAGCGAAAGATTTTT 59.656 37.500 0.00 0.00 39.14 1.94
1748 1776 7.485418 TTTTTACAAACAGCTCGTATTCTCA 57.515 32.000 0.00 0.00 0.00 3.27
1753 1781 5.934625 ACAAACAGCTCGTATTCTCAGAAAT 59.065 36.000 0.00 0.00 0.00 2.17
1764 1792 9.047371 TCGTATTCTCAGAAATAACAACAACAA 57.953 29.630 0.00 0.00 0.00 2.83
1765 1793 9.103048 CGTATTCTCAGAAATAACAACAACAAC 57.897 33.333 0.00 0.00 0.00 3.32
1767 1795 8.856490 ATTCTCAGAAATAACAACAACAACAC 57.144 30.769 0.00 0.00 0.00 3.32
1768 1796 6.482835 TCTCAGAAATAACAACAACAACACG 58.517 36.000 0.00 0.00 0.00 4.49
1780 1822 3.749088 ACAACAACACGAACTTGACTTGA 59.251 39.130 0.00 0.00 0.00 3.02
1836 1878 4.098654 TCTGGATTAGACTGCAGCTTCTAC 59.901 45.833 15.27 3.79 34.84 2.59
1991 3892 2.319136 TGTAGGCGTCAACACTGTTT 57.681 45.000 0.00 0.00 0.00 2.83
1993 3894 3.125316 TGTAGGCGTCAACACTGTTTAC 58.875 45.455 0.00 0.00 0.00 2.01
2029 3953 7.920151 CAGTGATTAATTTGTTTTGTCCTCACA 59.080 33.333 0.00 0.00 33.49 3.58
2038 3962 7.397892 TTGTTTTGTCCTCACATAACTGAAA 57.602 32.000 9.04 0.00 42.11 2.69
2069 3993 3.865745 AGATCATTAAGAACCAAGTCGCG 59.134 43.478 0.00 0.00 0.00 5.87
2123 4050 1.913419 AGGAATACCGAGAAGGCCAAA 59.087 47.619 5.01 0.00 46.52 3.28
2136 4063 3.990959 AGGCCAAAAGAAACCAAAACA 57.009 38.095 5.01 0.00 0.00 2.83
2158 4085 5.827797 ACAAGCAAAAGAGACCATTAACTGA 59.172 36.000 0.00 0.00 0.00 3.41
2159 4086 6.321181 ACAAGCAAAAGAGACCATTAACTGAA 59.679 34.615 0.00 0.00 0.00 3.02
2160 4087 6.959639 AGCAAAAGAGACCATTAACTGAAA 57.040 33.333 0.00 0.00 0.00 2.69
2161 4088 6.974965 AGCAAAAGAGACCATTAACTGAAAG 58.025 36.000 0.00 0.00 42.29 2.62
2162 4089 6.772716 AGCAAAAGAGACCATTAACTGAAAGA 59.227 34.615 0.00 0.00 37.43 2.52
2163 4090 7.449704 AGCAAAAGAGACCATTAACTGAAAGAT 59.550 33.333 0.00 0.00 37.43 2.40
2164 4091 8.730680 GCAAAAGAGACCATTAACTGAAAGATA 58.269 33.333 0.00 0.00 37.43 1.98
2192 4119 8.100508 AGTTCCTCTGTTTTTATTTACTCTGC 57.899 34.615 0.00 0.00 0.00 4.26
2193 4120 7.719633 AGTTCCTCTGTTTTTATTTACTCTGCA 59.280 33.333 0.00 0.00 0.00 4.41
2194 4121 8.515414 GTTCCTCTGTTTTTATTTACTCTGCAT 58.485 33.333 0.00 0.00 0.00 3.96
2195 4122 9.733556 TTCCTCTGTTTTTATTTACTCTGCATA 57.266 29.630 0.00 0.00 0.00 3.14
2196 4123 9.905713 TCCTCTGTTTTTATTTACTCTGCATAT 57.094 29.630 0.00 0.00 0.00 1.78
2207 4134 7.969536 TTTACTCTGCATATTATCTGAAGCC 57.030 36.000 0.00 0.00 0.00 4.35
2208 4135 5.557576 ACTCTGCATATTATCTGAAGCCA 57.442 39.130 0.00 0.00 0.00 4.75
2209 4136 5.933617 ACTCTGCATATTATCTGAAGCCAA 58.066 37.500 0.00 0.00 0.00 4.52
2210 4137 6.359804 ACTCTGCATATTATCTGAAGCCAAA 58.640 36.000 0.00 0.00 0.00 3.28
2211 4138 6.261826 ACTCTGCATATTATCTGAAGCCAAAC 59.738 38.462 0.00 0.00 0.00 2.93
2212 4139 6.359804 TCTGCATATTATCTGAAGCCAAACT 58.640 36.000 0.00 0.00 0.00 2.66
2213 4140 6.830324 TCTGCATATTATCTGAAGCCAAACTT 59.170 34.615 0.00 0.00 42.98 2.66
2214 4141 6.798482 TGCATATTATCTGAAGCCAAACTTG 58.202 36.000 0.00 0.00 39.29 3.16
2215 4142 6.602803 TGCATATTATCTGAAGCCAAACTTGA 59.397 34.615 0.00 0.00 39.29 3.02
2216 4143 7.286087 TGCATATTATCTGAAGCCAAACTTGAT 59.714 33.333 0.00 0.00 39.29 2.57
2217 4144 8.786898 GCATATTATCTGAAGCCAAACTTGATA 58.213 33.333 0.00 0.00 39.29 2.15
2221 4148 8.635765 TTATCTGAAGCCAAACTTGATAAAGT 57.364 30.769 0.00 0.00 39.29 2.66
2222 4149 6.959639 TCTGAAGCCAAACTTGATAAAGTT 57.040 33.333 1.96 1.96 44.25 2.66
2385 4312 9.495572 AAAGTTTACAAAGTTTGATTTGACCAA 57.504 25.926 22.23 0.69 41.71 3.67
2386 4313 9.495572 AAGTTTACAAAGTTTGATTTGACCAAA 57.504 25.926 22.23 0.00 41.71 3.28
2387 4314 9.495572 AGTTTACAAAGTTTGATTTGACCAAAA 57.504 25.926 22.23 5.53 41.71 2.44
2388 4315 9.536558 GTTTACAAAGTTTGATTTGACCAAAAC 57.463 29.630 22.23 12.10 41.71 2.43
2389 4316 9.495572 TTTACAAAGTTTGATTTGACCAAAACT 57.504 25.926 22.23 0.00 41.71 2.66
2392 4319 9.665719 ACAAAGTTTGATTTGACCAAAACTAAT 57.334 25.926 22.23 0.00 41.71 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.208431 GGACTCCTCAAATGCTCATCG 58.792 52.381 0.00 0.00 0.00 3.84
6 7 2.208431 CGGACTCCTCAAATGCTCATC 58.792 52.381 0.00 0.00 0.00 2.92
7 8 1.134280 CCGGACTCCTCAAATGCTCAT 60.134 52.381 0.00 0.00 0.00 2.90
10 11 0.693049 AACCGGACTCCTCAAATGCT 59.307 50.000 9.46 0.00 0.00 3.79
80 81 9.322773 CCATGCTAGATGACGATTGAAATATAT 57.677 33.333 0.00 0.00 0.00 0.86
81 82 8.531146 TCCATGCTAGATGACGATTGAAATATA 58.469 33.333 0.00 0.00 0.00 0.86
82 83 7.389232 TCCATGCTAGATGACGATTGAAATAT 58.611 34.615 0.00 0.00 0.00 1.28
83 84 6.758254 TCCATGCTAGATGACGATTGAAATA 58.242 36.000 0.00 0.00 0.00 1.40
86 87 4.342092 TCTCCATGCTAGATGACGATTGAA 59.658 41.667 0.00 0.00 0.00 2.69
97 98 2.773661 TCCATTTGCTCTCCATGCTAGA 59.226 45.455 0.00 0.00 0.00 2.43
98 99 3.139850 CTCCATTTGCTCTCCATGCTAG 58.860 50.000 0.00 0.00 0.00 3.42
106 107 2.476320 GCCGCCTCCATTTGCTCTC 61.476 63.158 0.00 0.00 0.00 3.20
114 115 3.614092 CAATCATAATAGCCGCCTCCAT 58.386 45.455 0.00 0.00 0.00 3.41
115 116 2.290260 CCAATCATAATAGCCGCCTCCA 60.290 50.000 0.00 0.00 0.00 3.86
119 120 3.055819 TCTCTCCAATCATAATAGCCGCC 60.056 47.826 0.00 0.00 0.00 6.13
129 130 8.270030 TCTGTGACAAAATATCTCTCCAATCAT 58.730 33.333 0.00 0.00 0.00 2.45
138 139 8.504815 CATGGATGATCTGTGACAAAATATCTC 58.495 37.037 0.00 0.00 0.00 2.75
139 140 7.447545 CCATGGATGATCTGTGACAAAATATCT 59.552 37.037 5.56 0.00 0.00 1.98
148 150 3.834489 AGACCATGGATGATCTGTGAC 57.166 47.619 21.47 0.00 0.00 3.67
149 151 4.384537 GGAAAGACCATGGATGATCTGTGA 60.385 45.833 21.47 0.00 38.79 3.58
153 155 3.784763 ACAGGAAAGACCATGGATGATCT 59.215 43.478 21.47 7.88 42.04 2.75
160 162 3.354948 TGATCACAGGAAAGACCATGG 57.645 47.619 11.19 11.19 42.04 3.66
161 163 4.378770 CGTTTGATCACAGGAAAGACCATG 60.379 45.833 0.00 0.00 42.04 3.66
162 164 3.753272 CGTTTGATCACAGGAAAGACCAT 59.247 43.478 0.00 0.00 42.04 3.55
163 165 3.138304 CGTTTGATCACAGGAAAGACCA 58.862 45.455 0.00 0.00 42.04 4.02
167 169 2.484264 GGACCGTTTGATCACAGGAAAG 59.516 50.000 14.96 1.46 0.00 2.62
170 172 1.001974 CTGGACCGTTTGATCACAGGA 59.998 52.381 14.96 0.00 0.00 3.86
190 192 2.095213 TCCGCGTTTAGATGCATCAAAC 59.905 45.455 27.81 27.45 37.67 2.93
197 199 2.870411 AGGTTATTCCGCGTTTAGATGC 59.130 45.455 4.92 0.00 41.99 3.91
209 211 1.761198 AGTAGGCACGGAGGTTATTCC 59.239 52.381 0.00 0.00 0.00 3.01
216 229 1.139095 GAACGAGTAGGCACGGAGG 59.861 63.158 0.00 0.00 33.08 4.30
283 296 4.063967 CCGCGGTCTGTGGCAGTA 62.064 66.667 19.50 0.00 42.37 2.74
292 305 0.611340 AAAGACTAGGACCGCGGTCT 60.611 55.000 46.25 35.47 44.04 3.85
295 308 0.245539 TTGAAAGACTAGGACCGCGG 59.754 55.000 26.86 26.86 0.00 6.46
300 313 4.142513 ACCGTACGATTGAAAGACTAGGAC 60.143 45.833 18.76 0.00 0.00 3.85
308 321 5.013236 CGAAAATGACCGTACGATTGAAAG 58.987 41.667 18.76 0.00 0.00 2.62
312 325 2.669434 ACCGAAAATGACCGTACGATTG 59.331 45.455 18.76 2.16 0.00 2.67
317 330 1.701704 ACGACCGAAAATGACCGTAC 58.298 50.000 0.00 0.00 0.00 3.67
336 349 2.202690 CACAGCGGCCGTTCGATA 60.203 61.111 28.70 0.00 0.00 2.92
340 353 1.714899 ATATTGCACAGCGGCCGTTC 61.715 55.000 28.70 11.34 0.00 3.95
378 391 2.043953 AAAAGAGATGGGCGGGGC 60.044 61.111 0.00 0.00 0.00 5.80
387 400 4.916041 TCAGACCATGACCAAAAGAGAT 57.084 40.909 0.00 0.00 31.12 2.75
407 420 1.083242 TGGCGCCGGTTTTATACGTC 61.083 55.000 23.90 0.00 0.00 4.34
410 424 0.099259 GGTTGGCGCCGGTTTTATAC 59.901 55.000 23.90 8.85 0.00 1.47
496 522 2.036572 GGCGAATTTGGGGGTGGA 59.963 61.111 0.00 0.00 0.00 4.02
504 530 1.508088 GTGGAGCTGGGCGAATTTG 59.492 57.895 0.00 0.00 0.00 2.32
505 531 1.678970 GGTGGAGCTGGGCGAATTT 60.679 57.895 0.00 0.00 0.00 1.82
913 941 4.175489 GTCGAGCGCGGTGAGCTA 62.175 66.667 18.92 0.00 46.13 3.32
988 1016 4.408821 AAGCATCTGGGGCGCGAA 62.409 61.111 12.10 0.00 36.08 4.70
1037 1065 0.580104 GTCCTTGTTGTTGACGACGG 59.420 55.000 0.00 0.00 32.90 4.79
1082 1110 0.508641 CGTGTCAGCAACTAGTGTGC 59.491 55.000 17.19 17.19 0.00 4.57
1089 1117 1.301244 CTGCCTCGTGTCAGCAACT 60.301 57.895 0.00 0.00 35.79 3.16
1191 1219 3.353836 CCAACACCGTTGCCGAGG 61.354 66.667 1.26 0.00 35.63 4.63
1262 1290 3.289704 TTGACGCGCCCGATGAAGA 62.290 57.895 5.73 0.00 38.29 2.87
1303 1331 1.029681 GGGCCAGTGAGTTTTTCGTT 58.970 50.000 4.39 0.00 0.00 3.85
1307 1335 2.452600 TTGAGGGCCAGTGAGTTTTT 57.547 45.000 6.18 0.00 0.00 1.94
1310 1338 1.707427 AGAATTGAGGGCCAGTGAGTT 59.293 47.619 6.18 0.00 0.00 3.01
1311 1339 1.366319 AGAATTGAGGGCCAGTGAGT 58.634 50.000 6.18 0.00 0.00 3.41
1315 1343 0.984230 TCGAAGAATTGAGGGCCAGT 59.016 50.000 6.18 0.00 0.00 4.00
1324 1352 0.729116 AGCACCGCATCGAAGAATTG 59.271 50.000 0.00 0.00 43.58 2.32
1356 1384 1.754234 GGCCCTGATGCCGACAATT 60.754 57.895 0.00 0.00 42.54 2.32
1397 1425 3.254892 GCTAGCAGTACTTCCACACTTC 58.745 50.000 10.63 0.00 0.00 3.01
1401 1429 3.981071 AATGCTAGCAGTACTTCCACA 57.019 42.857 23.89 0.00 0.00 4.17
1495 1523 7.505585 CCCCATTACATAACTCAACACCATAAT 59.494 37.037 0.00 0.00 0.00 1.28
1558 1586 5.124297 TCCAACAGATAACTCAACATGCATG 59.876 40.000 25.09 25.09 0.00 4.06
1559 1587 5.255687 TCCAACAGATAACTCAACATGCAT 58.744 37.500 0.00 0.00 0.00 3.96
1560 1588 4.650734 TCCAACAGATAACTCAACATGCA 58.349 39.130 0.00 0.00 0.00 3.96
1561 1589 5.393962 GTTCCAACAGATAACTCAACATGC 58.606 41.667 0.00 0.00 0.00 4.06
1562 1590 5.408299 TCGTTCCAACAGATAACTCAACATG 59.592 40.000 0.00 0.00 0.00 3.21
1563 1591 5.547465 TCGTTCCAACAGATAACTCAACAT 58.453 37.500 0.00 0.00 0.00 2.71
1577 1605 3.003275 TCAGCACTTGATTTCGTTCCAAC 59.997 43.478 0.00 0.00 0.00 3.77
1598 1626 8.911247 AATAAACGAAATGGCAGACTAAATTC 57.089 30.769 0.00 0.00 0.00 2.17
1646 1674 2.514458 AACATAAGGAAGCCCCACTG 57.486 50.000 0.00 0.00 37.41 3.66
1677 1705 1.134699 TGAGGGAGATAAACTGCGCAG 60.135 52.381 34.89 34.89 37.85 5.18
1678 1706 0.901827 TGAGGGAGATAAACTGCGCA 59.098 50.000 10.98 10.98 37.85 6.09
1679 1707 1.291132 GTGAGGGAGATAAACTGCGC 58.709 55.000 0.00 0.00 37.85 6.09
1680 1708 1.135083 ACGTGAGGGAGATAAACTGCG 60.135 52.381 0.00 0.00 37.85 5.18
1681 1709 2.541556 GACGTGAGGGAGATAAACTGC 58.458 52.381 0.00 0.00 36.20 4.40
1682 1710 2.159085 GGGACGTGAGGGAGATAAACTG 60.159 54.545 0.00 0.00 0.00 3.16
1683 1711 2.108970 GGGACGTGAGGGAGATAAACT 58.891 52.381 0.00 0.00 0.00 2.66
1684 1712 2.108970 AGGGACGTGAGGGAGATAAAC 58.891 52.381 0.00 0.00 0.00 2.01
1685 1713 2.544844 AGGGACGTGAGGGAGATAAA 57.455 50.000 0.00 0.00 0.00 1.40
1686 1714 2.544844 AAGGGACGTGAGGGAGATAA 57.455 50.000 0.00 0.00 0.00 1.75
1687 1715 2.544844 AAAGGGACGTGAGGGAGATA 57.455 50.000 0.00 0.00 0.00 1.98
1688 1716 1.555533 GAAAAGGGACGTGAGGGAGAT 59.444 52.381 0.00 0.00 0.00 2.75
1689 1717 0.974383 GAAAAGGGACGTGAGGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
1701 1729 3.942130 AAATCTTTCGCTGGAAAAGGG 57.058 42.857 0.00 0.00 41.38 3.95
1724 1752 7.439955 TCTGAGAATACGAGCTGTTTGTAAAAA 59.560 33.333 0.00 0.00 0.00 1.94
1725 1753 6.926826 TCTGAGAATACGAGCTGTTTGTAAAA 59.073 34.615 0.00 0.00 0.00 1.52
1727 1755 6.020971 TCTGAGAATACGAGCTGTTTGTAA 57.979 37.500 0.00 0.00 0.00 2.41
1728 1756 5.638596 TCTGAGAATACGAGCTGTTTGTA 57.361 39.130 0.00 0.00 0.00 2.41
1730 1758 5.845985 TTTCTGAGAATACGAGCTGTTTG 57.154 39.130 0.00 0.00 0.00 2.93
1735 1763 7.097192 TGTTGTTATTTCTGAGAATACGAGCT 58.903 34.615 0.00 0.00 0.00 4.09
1736 1764 7.290857 TGTTGTTATTTCTGAGAATACGAGC 57.709 36.000 0.00 0.00 0.00 5.03
1737 1765 8.708742 TGTTGTTGTTATTTCTGAGAATACGAG 58.291 33.333 0.00 0.00 0.00 4.18
1738 1766 8.596271 TGTTGTTGTTATTTCTGAGAATACGA 57.404 30.769 0.00 0.00 0.00 3.43
1739 1767 9.103048 GTTGTTGTTGTTATTTCTGAGAATACG 57.897 33.333 0.00 0.00 0.00 3.06
1740 1768 9.944663 TGTTGTTGTTGTTATTTCTGAGAATAC 57.055 29.630 0.00 0.00 0.00 1.89
1742 1770 7.643764 CGTGTTGTTGTTGTTATTTCTGAGAAT 59.356 33.333 0.00 0.00 0.00 2.40
1743 1771 6.964370 CGTGTTGTTGTTGTTATTTCTGAGAA 59.036 34.615 0.00 0.00 0.00 2.87
1748 1776 6.848451 AGTTCGTGTTGTTGTTGTTATTTCT 58.152 32.000 0.00 0.00 0.00 2.52
1753 1781 5.179742 AGTCAAGTTCGTGTTGTTGTTGTTA 59.820 36.000 0.00 0.00 0.00 2.41
1764 1792 1.940613 GCCTTCAAGTCAAGTTCGTGT 59.059 47.619 0.00 0.00 0.00 4.49
1765 1793 1.939934 TGCCTTCAAGTCAAGTTCGTG 59.060 47.619 0.00 0.00 0.00 4.35
1767 1795 2.599848 CGTTGCCTTCAAGTCAAGTTCG 60.600 50.000 0.00 0.00 31.93 3.95
1768 1796 2.612212 TCGTTGCCTTCAAGTCAAGTTC 59.388 45.455 0.00 0.00 31.93 3.01
1780 1822 5.359576 TGAAATATAAATGCCTCGTTGCCTT 59.640 36.000 0.00 0.00 0.00 4.35
1818 1860 5.598005 AGATCTGTAGAAGCTGCAGTCTAAT 59.402 40.000 16.64 6.21 43.08 1.73
1836 1878 2.172082 TCTCCCAATGCCTGAAGATCTG 59.828 50.000 0.00 0.00 0.00 2.90
1888 3789 2.594541 GCAGGTATACTCTGCGCAC 58.405 57.895 22.33 0.00 46.33 5.34
1991 3892 0.973632 AATCACTGCCAGGTCACGTA 59.026 50.000 0.00 0.00 0.00 3.57
1993 3894 2.093306 TTAATCACTGCCAGGTCACG 57.907 50.000 0.00 0.00 0.00 4.35
2069 3993 1.301322 GGCGAGCTGCTAAGGATCC 60.301 63.158 2.48 2.48 45.43 3.36
2102 4029 1.120530 TGGCCTTCTCGGTATTCCTC 58.879 55.000 3.32 0.00 34.25 3.71
2123 4050 6.368791 GTCTCTTTTGCTTGTTTTGGTTTCTT 59.631 34.615 0.00 0.00 0.00 2.52
2136 4063 6.959639 TTCAGTTAATGGTCTCTTTTGCTT 57.040 33.333 0.00 0.00 0.00 3.91
2166 4093 9.216117 GCAGAGTAAATAAAAACAGAGGAACTA 57.784 33.333 0.00 0.00 41.55 2.24
2168 4095 7.871853 TGCAGAGTAAATAAAAACAGAGGAAC 58.128 34.615 0.00 0.00 0.00 3.62
2169 4096 8.635765 ATGCAGAGTAAATAAAAACAGAGGAA 57.364 30.769 0.00 0.00 0.00 3.36
2170 4097 9.905713 ATATGCAGAGTAAATAAAAACAGAGGA 57.094 29.630 0.00 0.00 0.00 3.71
2181 4108 9.658799 GGCTTCAGATAATATGCAGAGTAAATA 57.341 33.333 0.00 0.00 0.00 1.40
2182 4109 8.159447 TGGCTTCAGATAATATGCAGAGTAAAT 58.841 33.333 0.00 0.00 0.00 1.40
2183 4110 7.508687 TGGCTTCAGATAATATGCAGAGTAAA 58.491 34.615 0.00 0.00 0.00 2.01
2184 4111 7.066307 TGGCTTCAGATAATATGCAGAGTAA 57.934 36.000 0.00 0.00 0.00 2.24
2185 4112 6.670695 TGGCTTCAGATAATATGCAGAGTA 57.329 37.500 0.00 0.00 0.00 2.59
2186 4113 5.557576 TGGCTTCAGATAATATGCAGAGT 57.442 39.130 0.00 0.00 0.00 3.24
2187 4114 6.485984 AGTTTGGCTTCAGATAATATGCAGAG 59.514 38.462 0.00 0.00 0.00 3.35
2188 4115 6.359804 AGTTTGGCTTCAGATAATATGCAGA 58.640 36.000 0.00 0.00 0.00 4.26
2189 4116 6.630444 AGTTTGGCTTCAGATAATATGCAG 57.370 37.500 0.00 0.00 0.00 4.41
2190 4117 6.602803 TCAAGTTTGGCTTCAGATAATATGCA 59.397 34.615 0.00 0.00 34.69 3.96
2191 4118 7.031226 TCAAGTTTGGCTTCAGATAATATGC 57.969 36.000 0.00 0.00 34.69 3.14
2195 4122 9.247861 ACTTTATCAAGTTTGGCTTCAGATAAT 57.752 29.630 0.00 0.00 40.66 1.28
2196 4123 8.635765 ACTTTATCAAGTTTGGCTTCAGATAA 57.364 30.769 0.00 0.00 40.66 1.75
2355 4282 9.698309 TCAAATCAAACTTTGTAAACTTTGACA 57.302 25.926 11.61 0.00 35.26 3.58
2356 4283 9.952341 GTCAAATCAAACTTTGTAAACTTTGAC 57.048 29.630 19.07 19.07 41.19 3.18
2357 4284 9.145865 GGTCAAATCAAACTTTGTAAACTTTGA 57.854 29.630 11.71 11.71 36.16 2.69
2358 4285 8.930760 TGGTCAAATCAAACTTTGTAAACTTTG 58.069 29.630 1.44 5.95 37.39 2.77
2359 4286 9.495572 TTGGTCAAATCAAACTTTGTAAACTTT 57.504 25.926 1.44 0.00 37.39 2.66
2360 4287 9.495572 TTTGGTCAAATCAAACTTTGTAAACTT 57.504 25.926 1.44 0.00 37.39 2.66
2361 4288 9.495572 TTTTGGTCAAATCAAACTTTGTAAACT 57.504 25.926 1.44 0.00 37.39 2.66
2362 4289 9.536558 GTTTTGGTCAAATCAAACTTTGTAAAC 57.463 29.630 1.44 0.00 37.39 2.01
2363 4290 9.495572 AGTTTTGGTCAAATCAAACTTTGTAAA 57.504 25.926 1.44 0.00 37.39 2.01
2366 4293 9.665719 ATTAGTTTTGGTCAAATCAAACTTTGT 57.334 25.926 1.75 0.00 37.39 2.83


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

AutoCloner maintained by Alex Coulton.