Multiple sequence alignment - TraesCS2D01G327800

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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 TraesCS2D01G327800 chr2D 100.000 2523 0 0 1 2523 420992075 420989553 0.000000e+00 4660
1 TraesCS2D01G327800 chr2B 88.278 2184 143 53 1 2156 493651792 493649694 0.000000e+00 2510
2 TraesCS2D01G327800 chr2B 92.468 385 17 3 2139 2523 493648345 493647973 7.940000e-150 540
3 TraesCS2D01G327800 chr2A 83.818 2268 159 73 7 2177 566987967 566985811 0.000000e+00 1964
4 TraesCS2D01G327800 chr2A 83.712 1983 156 74 1 1905 547775200 547777093 0.000000e+00 1718
5 TraesCS2D01G327800 chr2A 84.970 499 51 14 650 1132 547271185 547271675 3.770000e-133 484
6 TraesCS2D01G327800 chr2A 85.246 305 18 10 1897 2177 547783795 547784096 3.180000e-74 289
7 TraesCS2D01G327800 chr2A 83.981 206 32 1 3 208 526312299 526312095 1.980000e-46 196
8 TraesCS2D01G327800 chr2A 90.551 127 9 2 2052 2177 547271676 547271800 5.580000e-37 165
9 TraesCS2D01G327800 chr5B 86.905 252 29 4 2273 2523 455518742 455518990 1.910000e-71 279
10 TraesCS2D01G327800 chr1A 85.657 251 31 5 2274 2523 21198747 21198501 2.490000e-65 259
11 TraesCS2D01G327800 chr1A 85.500 200 24 2 1 196 580020934 580021132 1.180000e-48 204
12 TraesCS2D01G327800 chr1A 89.032 155 15 2 1 154 518470429 518470276 9.210000e-45 191
13 TraesCS2D01G327800 chr5A 83.984 256 36 5 2270 2523 480198182 480198434 9.020000e-60 241
14 TraesCS2D01G327800 chr1D 84.878 205 30 1 3 207 291581723 291581520 3.290000e-49 206
15 TraesCS2D01G327800 chr1D 87.342 158 15 2 1 154 417951387 417951543 2.580000e-40 176
16 TraesCS2D01G327800 chr7D 83.163 196 32 1 13 208 4737259 4737065 7.170000e-41 178
17 TraesCS2D01G327800 chr7D 82.915 199 33 1 11 209 96503542 96503345 7.170000e-41 178
18 TraesCS2D01G327800 chr5D 81.193 218 33 6 1 213 510099749 510099535 4.320000e-38 169
19 TraesCS2D01G327800 chr5D 79.661 236 45 3 2273 2507 382938974 382938741 1.550000e-37 167


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 TraesCS2D01G327800 chr2D 420989553 420992075 2522 True 4660.0 4660 100.0000 1 2523 1 chr2D.!!$R1 2522
1 TraesCS2D01G327800 chr2B 493647973 493651792 3819 True 1525.0 2510 90.3730 1 2523 2 chr2B.!!$R1 2522
2 TraesCS2D01G327800 chr2A 566985811 566987967 2156 True 1964.0 1964 83.8180 7 2177 1 chr2A.!!$R2 2170
3 TraesCS2D01G327800 chr2A 547775200 547777093 1893 False 1718.0 1718 83.7120 1 1905 1 chr2A.!!$F1 1904
4 TraesCS2D01G327800 chr2A 547271185 547271800 615 False 324.5 484 87.7605 650 2177 2 chr2A.!!$F3 1527

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
894 963 0.472161 TGTTTAAACCCTTGGCCCCC 60.472 55.0 15.59 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 1995 0.032912 AGATGGTTCATGGCATGGCA 60.033 50.0 25.52 25.52 0.0 4.92 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
74 75 4.008933 GGCCTCCGTGTGCTCTGT 62.009 66.667 0.00 0.00 0.00 3.41
77 78 2.341543 CTCCGTGTGCTCTGTGCT 59.658 61.111 3.20 0.00 43.37 4.40
124 125 1.803289 GTGCATCGGAAGGAAAGCC 59.197 57.895 0.00 0.00 0.00 4.35
133 134 2.216782 GAAGGAAAGCCTGGGAGGGG 62.217 65.000 0.00 0.00 46.28 4.79
152 153 1.716826 GGCGGGTGACGTGTTTTTGA 61.717 55.000 0.00 0.00 46.52 2.69
157 158 3.304391 CGGGTGACGTGTTTTTGATTGAT 60.304 43.478 0.00 0.00 37.93 2.57
175 177 6.650390 TGATTGATCAAAACAGTCAGAATCGA 59.350 34.615 13.09 0.00 33.08 3.59
176 178 7.335171 TGATTGATCAAAACAGTCAGAATCGAT 59.665 33.333 13.09 0.00 33.08 3.59
178 180 6.165577 TGATCAAAACAGTCAGAATCGATCA 58.834 36.000 0.00 0.00 35.59 2.92
208 210 2.029560 GTCCGGACTTTCGTAAACCTCT 60.030 50.000 27.64 0.00 0.00 3.69
210 212 2.991866 CCGGACTTTCGTAAACCTCTTC 59.008 50.000 0.00 0.00 0.00 2.87
211 213 3.553508 CCGGACTTTCGTAAACCTCTTCA 60.554 47.826 0.00 0.00 0.00 3.02
212 214 3.427863 CGGACTTTCGTAAACCTCTTCAC 59.572 47.826 0.00 0.00 0.00 3.18
216 234 3.713858 TTCGTAAACCTCTTCACGTGA 57.286 42.857 15.76 15.76 35.91 4.35
225 243 4.703897 ACCTCTTCACGTGAAAGAAATCA 58.296 39.130 29.32 7.27 33.07 2.57
229 247 6.293626 CCTCTTCACGTGAAAGAAATCATGTT 60.294 38.462 29.32 0.00 45.00 2.71
242 260 2.226602 TCATGTTCGAACCGTGTTGA 57.773 45.000 24.78 15.82 0.00 3.18
256 274 5.702865 ACCGTGTTGAATGATTTTCATGAG 58.297 37.500 0.00 0.00 37.15 2.90
257 275 4.560035 CCGTGTTGAATGATTTTCATGAGC 59.440 41.667 0.00 0.00 37.15 4.26
293 316 1.144057 GGATCGGCGTTGGAGATGT 59.856 57.895 6.85 0.00 0.00 3.06
294 317 1.154205 GGATCGGCGTTGGAGATGTG 61.154 60.000 6.85 0.00 0.00 3.21
295 318 1.766143 GATCGGCGTTGGAGATGTGC 61.766 60.000 6.85 0.00 0.00 4.57
296 319 2.244117 ATCGGCGTTGGAGATGTGCT 62.244 55.000 6.85 0.00 0.00 4.40
304 327 4.142600 GCGTTGGAGATGTGCTAAAAGATT 60.143 41.667 0.00 0.00 0.00 2.40
513 540 1.048724 TCTGCTCCCCCGTCCTATTG 61.049 60.000 0.00 0.00 0.00 1.90
601 628 1.699634 CTTGACAGGAGGAGGACCAAA 59.300 52.381 0.00 0.00 38.94 3.28
602 629 2.044793 TGACAGGAGGAGGACCAAAT 57.955 50.000 0.00 0.00 38.94 2.32
603 630 2.348472 TGACAGGAGGAGGACCAAATT 58.652 47.619 0.00 0.00 38.94 1.82
604 631 2.716424 TGACAGGAGGAGGACCAAATTT 59.284 45.455 0.00 0.00 38.94 1.82
605 632 3.244911 TGACAGGAGGAGGACCAAATTTC 60.245 47.826 0.00 0.00 38.94 2.17
606 633 2.041755 ACAGGAGGAGGACCAAATTTCC 59.958 50.000 0.00 0.00 38.94 3.13
607 634 2.041620 CAGGAGGAGGACCAAATTTCCA 59.958 50.000 0.00 0.00 38.94 3.53
608 635 2.721906 AGGAGGAGGACCAAATTTCCAA 59.278 45.455 0.00 0.00 38.94 3.53
618 645 4.713553 ACCAAATTTCCAATTTCCACACC 58.286 39.130 0.00 0.00 0.00 4.16
630 663 4.919653 CACACCATCGTGGAGAGG 57.080 61.111 10.46 0.00 44.86 3.69
697 744 4.634004 TGTGTTTATCTGTAATCAAGGGCG 59.366 41.667 0.00 0.00 0.00 6.13
732 781 0.669318 CGTGAGCAGGGCGAGTTAAA 60.669 55.000 0.00 0.00 0.00 1.52
733 782 1.519408 GTGAGCAGGGCGAGTTAAAA 58.481 50.000 0.00 0.00 0.00 1.52
750 799 6.075315 AGTTAAAAGCCCATTTACTCCACTT 58.925 36.000 0.00 0.00 0.00 3.16
894 963 0.472161 TGTTTAAACCCTTGGCCCCC 60.472 55.000 15.59 0.00 0.00 5.40
917 986 4.271049 CGCTCTATTTAACCATCACACAGG 59.729 45.833 0.00 0.00 0.00 4.00
930 999 4.008933 ACAGGCTGACTCCGGCAC 62.009 66.667 23.66 0.00 46.41 5.01
1107 1176 4.733850 TGTCTAACTACTCAATGCGACAG 58.266 43.478 0.00 0.00 0.00 3.51
1120 1198 2.809446 TGCGACAGTGCATGATAGTAC 58.191 47.619 0.00 0.00 40.62 2.73
1122 1200 2.794981 GCGACAGTGCATGATAGTACGT 60.795 50.000 0.00 0.00 34.15 3.57
1128 1206 7.448748 ACAGTGCATGATAGTACGTATGATA 57.551 36.000 0.00 0.00 0.00 2.15
1141 1219 5.654603 ACGTATGATACTCCAACTCACAA 57.345 39.130 0.66 0.00 0.00 3.33
1142 1220 6.222038 ACGTATGATACTCCAACTCACAAT 57.778 37.500 0.66 0.00 0.00 2.71
1164 1247 2.026822 GCTGATTTTCTCCTCTGGGTGA 60.027 50.000 0.00 0.00 33.83 4.02
1266 1349 7.574021 AAGGTATCAAATCTGCCCTATGATA 57.426 36.000 0.00 0.00 33.17 2.15
1268 1351 6.962311 AGGTATCAAATCTGCCCTATGATAGA 59.038 38.462 0.00 0.00 34.61 1.98
1269 1352 7.626890 AGGTATCAAATCTGCCCTATGATAGAT 59.373 37.037 0.00 0.00 34.61 1.98
1270 1353 8.928448 GGTATCAAATCTGCCCTATGATAGATA 58.072 37.037 0.00 0.00 34.61 1.98
1271 1354 9.979578 GTATCAAATCTGCCCTATGATAGATAG 57.020 37.037 0.00 0.00 34.61 2.08
1272 1355 7.429374 TCAAATCTGCCCTATGATAGATAGG 57.571 40.000 0.00 0.00 40.59 2.57
1273 1356 7.191918 TCAAATCTGCCCTATGATAGATAGGA 58.808 38.462 8.99 0.00 42.90 2.94
1290 1373 9.699410 ATAGATAGGAGTATTTCAGATGAGAGG 57.301 37.037 0.00 0.00 0.00 3.69
1299 1382 0.942962 CAGATGAGAGGAAATGCGCC 59.057 55.000 4.18 0.00 0.00 6.53
1321 1404 1.902938 TTCATTCCATGGCGTGTGAA 58.097 45.000 6.96 11.26 0.00 3.18
1322 1405 2.127271 TCATTCCATGGCGTGTGAAT 57.873 45.000 6.96 14.04 31.84 2.57
1323 1406 1.744522 TCATTCCATGGCGTGTGAATG 59.255 47.619 27.39 27.39 41.64 2.67
1523 1606 0.607489 CAAGACCAAGTGCCCCTGAG 60.607 60.000 0.00 0.00 0.00 3.35
1524 1607 2.360475 GACCAAGTGCCCCTGAGC 60.360 66.667 0.00 0.00 0.00 4.26
1525 1608 3.927481 GACCAAGTGCCCCTGAGCC 62.927 68.421 0.00 0.00 0.00 4.70
1527 1610 3.655211 CAAGTGCCCCTGAGCCCT 61.655 66.667 0.00 0.00 0.00 5.19
1528 1611 3.655211 AAGTGCCCCTGAGCCCTG 61.655 66.667 0.00 0.00 0.00 4.45
1529 1612 4.664267 AGTGCCCCTGAGCCCTGA 62.664 66.667 0.00 0.00 0.00 3.86
1530 1613 4.416738 GTGCCCCTGAGCCCTGAC 62.417 72.222 0.00 0.00 0.00 3.51
1532 1615 4.106925 GCCCCTGAGCCCTGACTG 62.107 72.222 0.00 0.00 0.00 3.51
1533 1616 4.106925 CCCCTGAGCCCTGACTGC 62.107 72.222 0.00 0.00 0.00 4.40
1536 1619 2.583520 CTGAGCCCTGACTGCCTC 59.416 66.667 0.00 0.00 0.00 4.70
1538 1621 2.686835 GAGCCCTGACTGCCTCCT 60.687 66.667 0.00 0.00 0.00 3.69
1539 1622 2.686835 AGCCCTGACTGCCTCCTC 60.687 66.667 0.00 0.00 0.00 3.71
1540 1623 3.005539 GCCCTGACTGCCTCCTCA 61.006 66.667 0.00 0.00 0.00 3.86
1541 1624 2.373707 GCCCTGACTGCCTCCTCAT 61.374 63.158 0.00 0.00 0.00 2.90
1542 1625 1.525923 CCCTGACTGCCTCCTCATG 59.474 63.158 0.00 0.00 0.00 3.07
1543 1626 1.270414 CCCTGACTGCCTCCTCATGT 61.270 60.000 0.00 0.00 0.00 3.21
1544 1627 0.177604 CCTGACTGCCTCCTCATGTC 59.822 60.000 0.00 0.00 0.00 3.06
1545 1628 1.193323 CTGACTGCCTCCTCATGTCT 58.807 55.000 0.00 0.00 0.00 3.41
1546 1629 1.554160 CTGACTGCCTCCTCATGTCTT 59.446 52.381 0.00 0.00 0.00 3.01
1547 1630 1.552337 TGACTGCCTCCTCATGTCTTC 59.448 52.381 0.00 0.00 0.00 2.87
1548 1631 0.534412 ACTGCCTCCTCATGTCTTCG 59.466 55.000 0.00 0.00 0.00 3.79
1549 1632 0.809241 CTGCCTCCTCATGTCTTCGC 60.809 60.000 0.00 0.00 0.00 4.70
1550 1633 1.522580 GCCTCCTCATGTCTTCGCC 60.523 63.158 0.00 0.00 0.00 5.54
1551 1634 1.965754 GCCTCCTCATGTCTTCGCCT 61.966 60.000 0.00 0.00 0.00 5.52
1552 1635 0.103937 CCTCCTCATGTCTTCGCCTC 59.896 60.000 0.00 0.00 0.00 4.70
1553 1636 0.248825 CTCCTCATGTCTTCGCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
1554 1637 1.880340 CCTCATGTCTTCGCCTCGC 60.880 63.158 0.00 0.00 0.00 5.03
1664 1752 1.339097 AGGAACGGTGTTGACTAGCT 58.661 50.000 0.00 0.00 0.00 3.32
1665 1753 1.000955 AGGAACGGTGTTGACTAGCTG 59.999 52.381 0.00 0.00 0.00 4.24
1739 1835 3.753294 CGTAGGTGGGCATATTTCTCT 57.247 47.619 0.00 0.00 0.00 3.10
1832 1929 0.881118 TTGAGATGAAAGTTGGCGCC 59.119 50.000 22.73 22.73 0.00 6.53
1862 1963 0.034337 CCCTCGTCCCTCGTTCAAAA 59.966 55.000 0.00 0.00 40.80 2.44
1894 1995 3.389329 AGTTCTTATCCATCGCAGTCCAT 59.611 43.478 0.00 0.00 0.00 3.41
1917 2019 1.337071 CATGCCATGAACCATCTGCTC 59.663 52.381 0.00 0.00 0.00 4.26
1968 2077 2.639286 GCTGTCGTGTTGCAAGGG 59.361 61.111 0.00 0.00 0.00 3.95
2008 2117 2.431260 GGTTGTGCATGCAAGCGG 60.431 61.111 24.58 0.00 37.17 5.52
2032 2154 0.454600 CGGTACTGCCTCGAGCTAAA 59.545 55.000 6.99 0.00 44.23 1.85
2037 2159 1.272781 CTGCCTCGAGCTAAAAGACG 58.727 55.000 6.99 0.00 44.23 4.18
2038 2160 0.736325 TGCCTCGAGCTAAAAGACGC 60.736 55.000 6.99 2.01 44.23 5.19
2044 2166 2.672874 TCGAGCTAAAAGACGCGTACTA 59.327 45.455 13.97 0.00 0.00 1.82
2045 2167 2.775149 CGAGCTAAAAGACGCGTACTAC 59.225 50.000 13.97 0.00 0.00 2.73
2059 2181 6.171921 ACGCGTACTACCATAGAGAAGATAT 58.828 40.000 11.67 0.00 0.00 1.63
2142 3634 2.813726 CCACCGAGTTGTGTCCCCA 61.814 63.158 0.00 0.00 34.35 4.96
2177 3670 0.308993 GGCCAAGATTGCGCATACTC 59.691 55.000 12.75 9.08 0.00 2.59
2179 3672 1.672881 GCCAAGATTGCGCATACTCTT 59.327 47.619 12.75 16.97 0.00 2.85
2180 3673 2.098117 GCCAAGATTGCGCATACTCTTT 59.902 45.455 21.05 9.41 0.00 2.52
2181 3674 3.428045 GCCAAGATTGCGCATACTCTTTT 60.428 43.478 21.05 5.84 0.00 2.27
2182 3675 4.737054 CCAAGATTGCGCATACTCTTTTT 58.263 39.130 21.05 5.28 0.00 1.94
2218 3711 5.633601 GCAAGATTGCGCATACTATGTACTA 59.366 40.000 12.75 0.00 45.11 1.82
2287 3780 6.398095 AGGTGGTTCTTTTTCTTGAAACAAG 58.602 36.000 5.29 5.29 40.89 3.16
2324 3817 9.787532 TCGCCATTTTTATTGAATAAGAAGAAG 57.212 29.630 6.96 0.90 0.00 2.85
2325 3818 9.787532 CGCCATTTTTATTGAATAAGAAGAAGA 57.212 29.630 6.96 0.00 0.00 2.87
2366 3859 1.204704 GGCCAAATTACAAGCCTCACC 59.795 52.381 0.00 0.00 42.34 4.02
2369 3862 2.755103 CCAAATTACAAGCCTCACCCTC 59.245 50.000 0.00 0.00 0.00 4.30
2380 3873 0.317160 CTCACCCTCGCGGCATAATA 59.683 55.000 6.13 0.00 33.26 0.98
2432 3925 5.299279 CACCACAAAGAAGCTTCCTCTTTAA 59.701 40.000 22.81 0.00 33.05 1.52
2435 3928 7.087007 CCACAAAGAAGCTTCCTCTTTAATTC 58.913 38.462 22.81 0.00 33.05 2.17
2456 3949 1.065551 GAGCAACAAGAACACCCACAC 59.934 52.381 0.00 0.00 0.00 3.82
2459 3952 1.330521 CAACAAGAACACCCACACGAG 59.669 52.381 0.00 0.00 0.00 4.18
2474 3967 1.795872 CACGAGTTGCATTGTTACGGA 59.204 47.619 0.00 0.00 0.00 4.69
2507 4000 8.137745 TGCATTTCTCTTTTTCCATATTTCCT 57.862 30.769 0.00 0.00 0.00 3.36
2509 4002 9.521503 GCATTTCTCTTTTTCCATATTTCCTAC 57.478 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 1.298788 CAAAAACACGTCACCCGCC 60.299 57.895 0.00 0.00 41.42 6.13
152 153 7.335171 TGATCGATTCTGACTGTTTTGATCAAT 59.665 33.333 9.40 0.00 37.38 2.57
157 158 8.034804 TCTTATGATCGATTCTGACTGTTTTGA 58.965 33.333 0.00 0.00 0.00 2.69
175 177 2.877866 AGTCCGGACCGATCTTATGAT 58.122 47.619 30.82 4.74 35.26 2.45
176 178 2.359981 AGTCCGGACCGATCTTATGA 57.640 50.000 30.82 0.00 0.00 2.15
178 180 2.034305 CGAAAGTCCGGACCGATCTTAT 59.966 50.000 30.82 6.96 0.00 1.73
208 210 5.235401 TCGAACATGATTTCTTTCACGTGAA 59.765 36.000 26.53 26.53 0.00 3.18
210 212 5.017484 TCGAACATGATTTCTTTCACGTG 57.983 39.130 9.94 9.94 0.00 4.49
211 213 5.440685 GTTCGAACATGATTTCTTTCACGT 58.559 37.500 23.12 0.00 0.00 4.49
212 214 4.846137 GGTTCGAACATGATTTCTTTCACG 59.154 41.667 28.24 0.00 0.00 4.35
216 234 4.274950 ACACGGTTCGAACATGATTTCTTT 59.725 37.500 28.52 9.73 0.00 2.52
225 243 3.135225 TCATTCAACACGGTTCGAACAT 58.865 40.909 28.24 14.01 0.00 2.71
228 246 4.822036 AAATCATTCAACACGGTTCGAA 57.178 36.364 0.00 0.00 0.00 3.71
229 247 4.273724 TGAAAATCATTCAACACGGTTCGA 59.726 37.500 0.00 0.00 0.00 3.71
242 260 2.355756 CGTCCGGCTCATGAAAATCATT 59.644 45.455 0.00 0.00 34.28 2.57
257 275 4.215742 TTATCCGCAGCCGTCCGG 62.216 66.667 0.24 0.24 45.64 5.14
265 283 1.734477 CGCCGATCCTTATCCGCAG 60.734 63.158 0.00 0.00 36.49 5.18
272 290 1.068588 CATCTCCAACGCCGATCCTTA 59.931 52.381 0.00 0.00 0.00 2.69
273 291 0.179073 CATCTCCAACGCCGATCCTT 60.179 55.000 0.00 0.00 0.00 3.36
294 317 9.295214 GCTCAAATTCTCCTAAAATCTTTTAGC 57.705 33.333 14.29 1.37 45.11 3.09
304 327 7.094205 GGATTTGTCTGCTCAAATTCTCCTAAA 60.094 37.037 13.16 0.00 44.62 1.85
308 331 4.704057 AGGATTTGTCTGCTCAAATTCTCC 59.296 41.667 13.55 11.72 45.19 3.71
319 342 0.255890 TGCCCCTAGGATTTGTCTGC 59.744 55.000 11.48 0.29 33.47 4.26
485 512 2.125188 GGGAGCAGAGCAGAGTGC 60.125 66.667 0.00 0.00 45.46 4.40
513 540 2.811317 CGGTGAGCGAGACAAGGC 60.811 66.667 0.00 0.00 0.00 4.35
601 628 3.831911 ACGATGGTGTGGAAATTGGAAAT 59.168 39.130 0.00 0.00 0.00 2.17
602 629 3.005261 CACGATGGTGTGGAAATTGGAAA 59.995 43.478 0.00 0.00 39.38 3.13
603 630 2.556189 CACGATGGTGTGGAAATTGGAA 59.444 45.455 0.00 0.00 39.38 3.53
604 631 2.158559 CACGATGGTGTGGAAATTGGA 58.841 47.619 0.00 0.00 39.38 3.53
605 632 2.634982 CACGATGGTGTGGAAATTGG 57.365 50.000 0.00 0.00 39.38 3.16
630 663 3.418995 TCCGTATAGCACACCTAGGATC 58.581 50.000 17.98 0.90 0.00 3.36
669 702 3.936453 TGATTACAGATAAACACACGGGC 59.064 43.478 0.00 0.00 0.00 6.13
670 703 5.064707 CCTTGATTACAGATAAACACACGGG 59.935 44.000 0.00 0.00 0.00 5.28
671 704 5.064707 CCCTTGATTACAGATAAACACACGG 59.935 44.000 0.00 0.00 0.00 4.94
727 776 5.977489 AGTGGAGTAAATGGGCTTTTAAC 57.023 39.130 0.00 0.00 0.00 2.01
732 781 3.621558 GCTAAGTGGAGTAAATGGGCTT 58.378 45.455 0.00 0.00 0.00 4.35
733 782 2.092375 GGCTAAGTGGAGTAAATGGGCT 60.092 50.000 0.00 0.00 0.00 5.19
894 963 4.271049 CCTGTGTGATGGTTAAATAGAGCG 59.729 45.833 0.00 0.00 0.00 5.03
917 986 3.965539 ATGCAGTGCCGGAGTCAGC 62.966 63.158 13.72 1.93 0.00 4.26
940 1009 1.456705 TGGTGTCTTTGGGTTGGGC 60.457 57.895 0.00 0.00 0.00 5.36
976 1045 3.169099 CTCCTTCCTCTGGAGTCTGAAA 58.831 50.000 0.00 0.00 44.42 2.69
1039 1108 4.173924 GCTGAGCAGGAGGAGGGC 62.174 72.222 0.00 0.00 0.00 5.19
1041 1110 2.583520 GTGCTGAGCAGGAGGAGG 59.416 66.667 7.71 0.00 40.08 4.30
1068 1137 3.613494 GACAGAAGGTCCCCTTAACTC 57.387 52.381 0.00 0.00 44.82 3.01
1092 1161 1.713597 TGCACTGTCGCATTGAGTAG 58.286 50.000 1.65 0.00 36.86 2.57
1107 1176 6.967767 GGAGTATCATACGTACTATCATGCAC 59.032 42.308 0.00 0.00 36.25 4.57
1119 1197 5.654603 TTGTGAGTTGGAGTATCATACGT 57.345 39.130 0.00 0.00 36.25 3.57
1120 1198 5.050769 GCATTGTGAGTTGGAGTATCATACG 60.051 44.000 0.00 0.00 36.25 3.06
1122 1200 6.051074 CAGCATTGTGAGTTGGAGTATCATA 58.949 40.000 0.00 0.00 36.25 2.15
1128 1206 2.936919 TCAGCATTGTGAGTTGGAGT 57.063 45.000 0.00 0.00 0.00 3.85
1141 1219 2.579860 ACCCAGAGGAGAAAATCAGCAT 59.420 45.455 0.00 0.00 36.73 3.79
1142 1220 1.988107 ACCCAGAGGAGAAAATCAGCA 59.012 47.619 0.00 0.00 36.73 4.41
1164 1247 2.442272 AGTCGGCAGCCTATCGGT 60.442 61.111 10.54 0.00 0.00 4.69
1266 1349 7.764617 TCCTCTCATCTGAAATACTCCTATCT 58.235 38.462 0.00 0.00 0.00 1.98
1268 1351 8.789767 TTTCCTCTCATCTGAAATACTCCTAT 57.210 34.615 0.00 0.00 0.00 2.57
1269 1352 8.646004 CATTTCCTCTCATCTGAAATACTCCTA 58.354 37.037 0.00 0.00 36.77 2.94
1270 1353 7.507829 CATTTCCTCTCATCTGAAATACTCCT 58.492 38.462 0.00 0.00 36.77 3.69
1271 1354 6.204495 GCATTTCCTCTCATCTGAAATACTCC 59.796 42.308 0.00 0.00 36.77 3.85
1272 1355 6.073873 CGCATTTCCTCTCATCTGAAATACTC 60.074 42.308 0.00 0.00 36.77 2.59
1273 1356 5.757320 CGCATTTCCTCTCATCTGAAATACT 59.243 40.000 0.00 0.00 36.77 2.12
1290 1373 1.136695 TGGAATGAATGGGCGCATTTC 59.863 47.619 27.38 20.58 35.05 2.17
1321 1404 2.941064 GCAGTCTGCATACATCACACAT 59.059 45.455 20.16 0.00 44.26 3.21
1322 1405 2.349590 GCAGTCTGCATACATCACACA 58.650 47.619 20.16 0.00 44.26 3.72
1323 1406 1.325640 CGCAGTCTGCATACATCACAC 59.674 52.381 24.13 0.00 45.36 3.82
1523 1606 2.373707 ATGAGGAGGCAGTCAGGGC 61.374 63.158 0.00 0.00 0.00 5.19
1524 1607 1.270414 ACATGAGGAGGCAGTCAGGG 61.270 60.000 0.00 0.00 0.00 4.45
1525 1608 0.177604 GACATGAGGAGGCAGTCAGG 59.822 60.000 0.00 0.00 0.00 3.86
1527 1610 1.552337 GAAGACATGAGGAGGCAGTCA 59.448 52.381 0.00 0.00 0.00 3.41
1528 1611 1.470632 CGAAGACATGAGGAGGCAGTC 60.471 57.143 0.00 0.00 0.00 3.51
1529 1612 0.534412 CGAAGACATGAGGAGGCAGT 59.466 55.000 0.00 0.00 0.00 4.40
1530 1613 0.809241 GCGAAGACATGAGGAGGCAG 60.809 60.000 0.00 0.00 0.00 4.85
1532 1615 1.522580 GGCGAAGACATGAGGAGGC 60.523 63.158 0.00 0.00 31.66 4.70
1533 1616 0.103937 GAGGCGAAGACATGAGGAGG 59.896 60.000 0.00 0.00 39.87 4.30
1536 1619 1.880340 GCGAGGCGAAGACATGAGG 60.880 63.158 0.00 0.00 39.87 3.86
1548 1631 1.956620 GATATTTAGGCGCGCGAGGC 61.957 60.000 37.18 28.22 38.69 4.70
1549 1632 0.388649 AGATATTTAGGCGCGCGAGG 60.389 55.000 37.18 4.86 0.00 4.63
1550 1633 1.419374 AAGATATTTAGGCGCGCGAG 58.581 50.000 37.18 8.39 0.00 5.03
1551 1634 2.030540 ACTAAGATATTTAGGCGCGCGA 60.031 45.455 37.18 13.36 0.00 5.87
1552 1635 2.325761 ACTAAGATATTTAGGCGCGCG 58.674 47.619 28.44 28.44 0.00 6.86
1553 1636 4.730657 TCTACTAAGATATTTAGGCGCGC 58.269 43.478 25.94 25.94 0.00 6.86
1554 1637 5.940595 ACTCTACTAAGATATTTAGGCGCG 58.059 41.667 0.00 0.00 0.00 6.86
1555 1638 6.968335 GCTACTCTACTAAGATATTTAGGCGC 59.032 42.308 0.00 0.00 0.00 6.53
1556 1639 8.178964 CAGCTACTCTACTAAGATATTTAGGCG 58.821 40.741 0.00 0.00 0.00 5.52
1664 1752 1.152118 ACCAGGTCCACCAGCTACA 60.152 57.895 0.00 0.00 38.89 2.74
1665 1753 1.296715 CACCAGGTCCACCAGCTAC 59.703 63.158 0.00 0.00 38.89 3.58
1675 1767 1.670811 CACAAGAACACACACCAGGTC 59.329 52.381 0.00 0.00 0.00 3.85
1730 1826 9.301897 GGATGGGCTTTATTACAAGAGAAATAT 57.698 33.333 0.00 0.00 0.00 1.28
1739 1835 3.434453 CCTCCGGATGGGCTTTATTACAA 60.434 47.826 3.57 0.00 35.24 2.41
1868 1969 3.068873 ACTGCGATGGATAAGAACTCTCC 59.931 47.826 0.00 0.00 0.00 3.71
1894 1995 0.032912 AGATGGTTCATGGCATGGCA 60.033 50.000 25.52 25.52 0.00 4.92
1917 2019 2.672478 CGGAGTAAAGAGTGGCAGACAG 60.672 54.545 0.00 0.00 0.00 3.51
1952 2061 2.639286 GCCCTTGCAACACGACAG 59.361 61.111 0.00 0.00 37.47 3.51
1985 2094 2.400399 CTTGCATGCACAACCAAGAAG 58.600 47.619 22.58 7.94 37.46 2.85
2021 2130 0.456312 ACGCGTCTTTTAGCTCGAGG 60.456 55.000 15.58 0.00 0.00 4.63
2032 2154 3.801698 TCTCTATGGTAGTACGCGTCTT 58.198 45.455 18.63 8.01 0.00 3.01
2037 2159 6.787225 CCATATCTTCTCTATGGTAGTACGC 58.213 44.000 1.91 0.00 40.44 4.42
2059 2181 2.102252 TGCGTGCTATGATCACATACCA 59.898 45.455 0.00 0.00 37.87 3.25
2095 2217 0.699151 GTGTTACTGTCACGTACGCG 59.301 55.000 16.72 3.53 44.93 6.01
2096 2218 1.055338 GGTGTTACTGTCACGTACGC 58.945 55.000 16.72 0.00 36.76 4.42
2299 3792 9.787532 TCTTCTTCTTATTCAATAAAAATGGCG 57.212 29.630 0.00 0.00 0.00 5.69
2323 3816 5.221541 CCGATGGCCTAGACTCTAAAAATCT 60.222 44.000 3.32 0.00 0.00 2.40
2324 3817 4.991687 CCGATGGCCTAGACTCTAAAAATC 59.008 45.833 3.32 0.00 0.00 2.17
2325 3818 4.743955 GCCGATGGCCTAGACTCTAAAAAT 60.744 45.833 3.32 0.00 44.06 1.82
2350 3843 2.711542 CGAGGGTGAGGCTTGTAATTT 58.288 47.619 0.00 0.00 0.00 1.82
2366 3859 7.201609 ATATTTGTGTAATATTATGCCGCGAGG 60.202 37.037 8.23 0.00 44.36 4.63
2369 3862 8.667987 AAATATTTGTGTAATATTATGCCGCG 57.332 30.769 0.00 0.00 44.74 6.46
2380 3873 4.202111 GCCTGGGCGAAATATTTGTGTAAT 60.202 41.667 5.17 0.00 0.00 1.89
2432 3925 1.880027 GGGTGTTCTTGTTGCTCGAAT 59.120 47.619 0.00 0.00 0.00 3.34
2435 3928 0.307760 GTGGGTGTTCTTGTTGCTCG 59.692 55.000 0.00 0.00 0.00 5.03
2456 3949 3.740044 ATTCCGTAACAATGCAACTCG 57.260 42.857 0.00 0.00 0.00 4.18
2459 3952 5.037015 TGTGTATTCCGTAACAATGCAAC 57.963 39.130 0.00 0.00 29.07 4.17
2474 3967 7.669427 TGGAAAAAGAGAAATGCATGTGTATT 58.331 30.769 0.00 0.00 31.67 1.89


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

AutoCloner maintained by Alex Coulton.