Multiple sequence alignment - TraesCS1B01G306900

Loading Multiple Alignment...

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 TraesCS1B01G306900 chr1B 100.000 2327 0 0 1 2327 529997432 529999758 0.000000e+00 4298
1 TraesCS1B01G306900 chr1D 91.253 1955 84 34 1 1899 392698171 392696248 0.000000e+00 2582
2 TraesCS1B01G306900 chr1D 85.468 406 47 9 726 1130 392694593 392694199 1.660000e-111 412
3 TraesCS1B01G306900 chr1D 82.222 405 33 24 1460 1842 392695417 392695804 1.740000e-81 313
4 TraesCS1B01G306900 chr1A 88.409 1967 109 45 1 1899 492651622 492653537 0.000000e+00 2259
5 TraesCS1B01G306900 chr1A 89.252 214 21 2 1460 1673 492654332 492654121 1.370000e-67 267
6 TraesCS1B01G306900 chr1A 90.647 139 13 0 640 778 492654671 492654809 3.950000e-43 185
7 TraesCS1B01G306900 chr1A 85.047 107 6 6 1710 1816 492653924 492653828 1.470000e-17 100
8 TraesCS1B01G306900 chr6B 94.789 403 17 1 1910 2308 208567574 208567172 1.960000e-175 625
9 TraesCS1B01G306900 chr6B 92.593 405 29 1 1906 2309 19441410 19441814 4.310000e-162 580
10 TraesCS1B01G306900 chr6B 92.365 406 29 2 1905 2309 136907703 136907299 5.580000e-161 577
11 TraesCS1B01G306900 chr3B 95.190 395 16 3 1915 2309 283755221 283755612 2.540000e-174 621
12 TraesCS1B01G306900 chr3B 84.854 515 57 11 659 1152 597816760 597816246 1.240000e-137 499
13 TraesCS1B01G306900 chr3B 78.022 273 52 8 802 1070 188877627 188877359 5.140000e-37 165
14 TraesCS1B01G306900 chr2B 96.543 376 10 3 1918 2292 787796475 787796848 9.130000e-174 619
15 TraesCS1B01G306900 chr2B 92.840 405 28 1 1905 2309 324662626 324662223 9.260000e-164 586
16 TraesCS1B01G306900 chr2B 82.274 519 69 16 654 1156 65882949 65883460 5.940000e-116 427
17 TraesCS1B01G306900 chr7B 93.500 400 22 3 1914 2310 8969332 8969730 1.990000e-165 592
18 TraesCS1B01G306900 chr5B 92.840 405 28 1 1905 2309 102439702 102440105 9.260000e-164 586
19 TraesCS1B01G306900 chr4B 91.546 414 31 4 1905 2317 508561084 508561494 3.360000e-158 568
20 TraesCS1B01G306900 chr3D 86.914 512 49 8 659 1152 454904590 454904079 2.020000e-155 558
21 TraesCS1B01G306900 chr3D 77.656 273 53 8 802 1070 132275531 132275263 2.390000e-35 159
22 TraesCS1B01G306900 chr3A 86.719 512 50 8 659 1152 597184829 597184318 9.400000e-154 553
23 TraesCS1B01G306900 chr3A 77.656 273 53 8 802 1070 145667645 145667377 2.390000e-35 159
24 TraesCS1B01G306900 chr2D 82.432 518 70 15 654 1156 37645818 37646329 1.280000e-117 433
25 TraesCS1B01G306900 chr2A 81.731 520 70 16 654 1156 42494693 42495204 5.980000e-111 411


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 TraesCS1B01G306900 chr1B 529997432 529999758 2326 False 4298 4298 100.0000 1 2327 1 chr1B.!!$F1 2326
1 TraesCS1B01G306900 chr1D 392694199 392698171 3972 True 1497 2582 88.3605 1 1899 2 chr1D.!!$R1 1898
2 TraesCS1B01G306900 chr1A 492651622 492654809 3187 False 1222 2259 89.5280 1 1899 2 chr1A.!!$F1 1898
3 TraesCS1B01G306900 chr3B 597816246 597816760 514 True 499 499 84.8540 659 1152 1 chr3B.!!$R2 493
4 TraesCS1B01G306900 chr2B 65882949 65883460 511 False 427 427 82.2740 654 1156 1 chr2B.!!$F1 502
5 TraesCS1B01G306900 chr3D 454904079 454904590 511 True 558 558 86.9140 659 1152 1 chr3D.!!$R2 493
6 TraesCS1B01G306900 chr3A 597184318 597184829 511 True 553 553 86.7190 659 1152 1 chr3A.!!$R2 493
7 TraesCS1B01G306900 chr2D 37645818 37646329 511 False 433 433 82.4320 654 1156 1 chr2D.!!$F1 502
8 TraesCS1B01G306900 chr2A 42494693 42495204 511 False 411 411 81.7310 654 1156 1 chr2A.!!$F1 502

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
529 555 0.320247 ATGATCAATCGCCTCCTCGC 60.32 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1612 0.036875 CAACTCTCCCAAGTGACCCC 59.963 60.0 0.0 0.0 0.0 4.95 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
123 132 4.999950 CCAGTTCATCATTAGCTATGGTCC 59.000 45.833 0.00 0.00 34.85 4.46
142 158 1.464395 TTTGGCCACTACCCCTCCA 60.464 57.895 3.88 0.00 0.00 3.86
229 250 8.139350 TGACTATTGTATGTATCCCACTAAACG 58.861 37.037 0.00 0.00 0.00 3.60
249 270 4.087892 CCACCCACTCTGCCCTCG 62.088 72.222 0.00 0.00 0.00 4.63
281 302 4.497300 CCAACTTGGCTGTGGATTTAATG 58.503 43.478 0.00 0.00 0.00 1.90
283 304 5.279406 CCAACTTGGCTGTGGATTTAATGAA 60.279 40.000 0.00 0.00 0.00 2.57
300 322 3.306917 TGAAGACATTTGCATTGCTGG 57.693 42.857 10.49 0.00 0.00 4.85
384 406 5.656549 TTAAGGAGAACAAGGGGAAGAAA 57.343 39.130 0.00 0.00 0.00 2.52
385 407 3.510531 AGGAGAACAAGGGGAAGAAAC 57.489 47.619 0.00 0.00 0.00 2.78
386 408 2.152016 GGAGAACAAGGGGAAGAAACG 58.848 52.381 0.00 0.00 0.00 3.60
387 409 2.486727 GGAGAACAAGGGGAAGAAACGT 60.487 50.000 0.00 0.00 0.00 3.99
388 410 2.548480 GAGAACAAGGGGAAGAAACGTG 59.452 50.000 0.00 0.00 0.00 4.49
389 411 2.171870 AGAACAAGGGGAAGAAACGTGA 59.828 45.455 0.00 0.00 0.00 4.35
438 461 6.154534 TCAGGTAGTAGCACTAACACAATGAT 59.845 38.462 12.07 0.00 40.80 2.45
492 516 4.386954 GGGTAAACGTACACAAGCTAGAAC 59.613 45.833 0.00 0.00 33.44 3.01
529 555 0.320247 ATGATCAATCGCCTCCTCGC 60.320 55.000 0.00 0.00 0.00 5.03
1260 1339 3.961182 CGTGTACGGCATTATACACTCT 58.039 45.455 11.53 0.00 45.92 3.24
1262 1341 3.973135 GTGTACGGCATTATACACTCTCG 59.027 47.826 7.17 0.00 45.08 4.04
1264 1343 1.681793 ACGGCATTATACACTCTCGCT 59.318 47.619 0.00 0.00 0.00 4.93
1265 1344 2.054363 CGGCATTATACACTCTCGCTG 58.946 52.381 0.00 0.00 0.00 5.18
1267 1346 3.304458 CGGCATTATACACTCTCGCTGTA 60.304 47.826 0.00 0.00 0.00 2.74
1282 1361 0.616111 CTGTACCTCACTGCCCCTCT 60.616 60.000 0.00 0.00 0.00 3.69
1336 1415 3.961408 GAGCTTATGGTAGACAAGGGAGA 59.039 47.826 0.00 0.00 0.00 3.71
1385 1470 2.893682 GATGGTCCTTTGGCGAGGGG 62.894 65.000 2.62 0.00 37.41 4.79
1386 1471 4.426313 GGTCCTTTGGCGAGGGGG 62.426 72.222 2.62 0.00 37.41 5.40
1455 1540 0.600255 GGTGGTCACTCACAACTCGG 60.600 60.000 0.93 0.00 39.27 4.63
1495 1580 0.595825 GCTGTGGTTGAGCAAGTTGC 60.596 55.000 20.44 20.44 45.46 4.17
1519 1612 5.049818 CAGGTGCAGTTTTCTCAACTTCTAG 60.050 44.000 0.00 0.00 0.00 2.43
1574 1671 0.104672 TCAGTTGGGAGAGTTGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
1591 1688 4.635473 TGGGGATAGTTTTCTCAGGAGAT 58.365 43.478 0.00 0.00 37.29 2.75
1593 1690 5.841237 TGGGGATAGTTTTCTCAGGAGATAG 59.159 44.000 0.00 0.00 37.29 2.08
1596 1693 6.220201 GGATAGTTTTCTCAGGAGATAGCAC 58.780 44.000 0.00 0.00 37.29 4.40
1598 1695 3.118956 AGTTTTCTCAGGAGATAGCACGG 60.119 47.826 0.00 0.00 37.29 4.94
1599 1696 2.437085 TTCTCAGGAGATAGCACGGA 57.563 50.000 0.00 0.00 37.29 4.69
1609 1706 0.107654 ATAGCACGGAGAAAGGTGGC 60.108 55.000 0.00 0.00 34.76 5.01
1612 1709 3.239253 ACGGAGAAAGGTGGCGGT 61.239 61.111 0.00 0.00 0.00 5.68
1613 1710 2.032071 CGGAGAAAGGTGGCGGTT 59.968 61.111 0.00 0.00 0.00 4.44
1617 1714 1.524008 GAGAAAGGTGGCGGTTTGGG 61.524 60.000 0.00 0.00 0.00 4.12
1618 1715 3.220999 GAAAGGTGGCGGTTTGGGC 62.221 63.158 0.00 0.00 0.00 5.36
1627 1724 4.660938 GGTTTGGGCTCCGGTGCT 62.661 66.667 26.25 0.00 0.00 4.40
1630 1727 3.429372 TTTGGGCTCCGGTGCTTGT 62.429 57.895 26.25 0.00 0.00 3.16
1631 1728 2.920076 TTTGGGCTCCGGTGCTTGTT 62.920 55.000 26.25 0.00 0.00 2.83
1632 1729 2.597510 GGGCTCCGGTGCTTGTTT 60.598 61.111 26.25 0.00 0.00 2.83
1634 1731 2.626780 GGCTCCGGTGCTTGTTTCC 61.627 63.158 26.25 5.73 0.00 3.13
1638 1735 2.637025 CGGTGCTTGTTTCCGGTG 59.363 61.111 0.00 0.00 40.49 4.94
1658 1755 2.933834 AAACCAGGGCCGCCTAGT 60.934 61.111 9.86 1.38 0.00 2.57
1674 1772 1.005924 CTAGTTGGGGCTTGGGACATT 59.994 52.381 0.00 0.00 39.30 2.71
1675 1773 0.542702 AGTTGGGGCTTGGGACATTG 60.543 55.000 0.00 0.00 39.30 2.82
1679 1777 2.283821 GGCTTGGGACATTGGGCA 60.284 61.111 0.00 0.00 39.30 5.36
1681 1779 0.396974 GGCTTGGGACATTGGGCATA 60.397 55.000 0.00 0.00 39.30 3.14
1682 1780 1.484038 GCTTGGGACATTGGGCATAA 58.516 50.000 0.00 0.00 39.30 1.90
1683 1781 2.041701 GCTTGGGACATTGGGCATAAT 58.958 47.619 0.00 0.00 39.30 1.28
1684 1782 2.036346 GCTTGGGACATTGGGCATAATC 59.964 50.000 0.00 0.00 39.30 1.75
1775 1898 9.953565 TTGGTTGCTCTTGTTTACTAATACTAT 57.046 29.630 0.00 0.00 0.00 2.12
1776 1899 9.953565 TGGTTGCTCTTGTTTACTAATACTATT 57.046 29.630 0.00 0.00 0.00 1.73
1822 1945 2.038659 ACATGACAACTTTTGTGGGGG 58.961 47.619 0.00 0.00 45.52 5.40
1823 1946 2.038659 CATGACAACTTTTGTGGGGGT 58.961 47.619 0.00 0.00 45.52 4.95
1824 1947 3.226777 CATGACAACTTTTGTGGGGGTA 58.773 45.455 0.00 0.00 45.52 3.69
1825 1948 2.938838 TGACAACTTTTGTGGGGGTAG 58.061 47.619 0.00 0.00 45.52 3.18
1826 1949 2.510382 TGACAACTTTTGTGGGGGTAGA 59.490 45.455 0.00 0.00 45.52 2.59
1876 1999 5.693104 TGTGAGGTTAGATGTAACAAACGAC 59.307 40.000 14.11 4.51 40.46 4.34
1947 2070 6.995511 TGACAAATTTTTCCTACTATCGGG 57.004 37.500 2.00 0.00 0.00 5.14
1949 2072 6.373216 TGACAAATTTTTCCTACTATCGGGTG 59.627 38.462 2.00 0.00 0.00 4.61
1951 2074 7.396418 ACAAATTTTTCCTACTATCGGGTGTA 58.604 34.615 0.00 0.00 0.00 2.90
1952 2075 7.551617 ACAAATTTTTCCTACTATCGGGTGTAG 59.448 37.037 0.00 0.00 36.75 2.74
1956 2079 6.699575 TTTCCTACTATCGGGTGTAGTTAC 57.300 41.667 0.00 0.00 35.62 2.50
1958 2081 5.615289 TCCTACTATCGGGTGTAGTTACTC 58.385 45.833 0.00 0.00 35.62 2.59
1959 2082 4.759183 CCTACTATCGGGTGTAGTTACTCC 59.241 50.000 0.00 2.51 38.72 3.85
1968 2091 4.711399 GGTGTAGTTACTCCCACTTTTGT 58.289 43.478 12.62 0.00 34.61 2.83
1971 2094 6.238566 GGTGTAGTTACTCCCACTTTTGTTTC 60.239 42.308 12.62 0.00 34.61 2.78
1972 2095 6.316890 GTGTAGTTACTCCCACTTTTGTTTCA 59.683 38.462 7.55 0.00 0.00 2.69
1973 2096 7.012989 GTGTAGTTACTCCCACTTTTGTTTCAT 59.987 37.037 7.55 0.00 0.00 2.57
1974 2097 8.212312 TGTAGTTACTCCCACTTTTGTTTCATA 58.788 33.333 0.00 0.00 0.00 2.15
1975 2098 7.506328 AGTTACTCCCACTTTTGTTTCATAC 57.494 36.000 0.00 0.00 0.00 2.39
1976 2099 6.204108 AGTTACTCCCACTTTTGTTTCATACG 59.796 38.462 0.00 0.00 0.00 3.06
1977 2100 4.457466 ACTCCCACTTTTGTTTCATACGT 58.543 39.130 0.00 0.00 0.00 3.57
1979 2102 5.008316 ACTCCCACTTTTGTTTCATACGTTC 59.992 40.000 0.00 0.00 0.00 3.95
1980 2103 5.127491 TCCCACTTTTGTTTCATACGTTCT 58.873 37.500 0.00 0.00 0.00 3.01
1981 2104 6.289834 TCCCACTTTTGTTTCATACGTTCTA 58.710 36.000 0.00 0.00 0.00 2.10
1982 2105 6.766944 TCCCACTTTTGTTTCATACGTTCTAA 59.233 34.615 0.00 0.00 0.00 2.10
1983 2106 7.041644 TCCCACTTTTGTTTCATACGTTCTAAG 60.042 37.037 0.00 0.00 0.00 2.18
1987 2110 9.538508 ACTTTTGTTTCATACGTTCTAAGTAGT 57.461 29.630 0.00 0.00 0.00 2.73
2013 2136 8.596271 ATCTATCATATCGGAGAGTATGTACG 57.404 38.462 0.00 0.00 43.63 3.67
2014 2137 4.941325 TCATATCGGAGAGTATGTACGC 57.059 45.455 0.00 0.00 43.63 4.42
2015 2138 3.370061 TCATATCGGAGAGTATGTACGCG 59.630 47.826 3.53 3.53 43.63 6.01
2016 2139 1.590932 ATCGGAGAGTATGTACGCGT 58.409 50.000 19.17 19.17 43.63 6.01
2017 2140 2.223537 TCGGAGAGTATGTACGCGTA 57.776 50.000 16.41 16.41 0.00 4.42
2021 2144 3.677121 CGGAGAGTATGTACGCGTAGTAT 59.323 47.826 21.25 18.64 37.69 2.12
2022 2145 4.433936 CGGAGAGTATGTACGCGTAGTATG 60.434 50.000 21.25 0.37 37.69 2.39
2023 2146 4.450419 GGAGAGTATGTACGCGTAGTATGT 59.550 45.833 21.25 9.14 37.69 2.29
2024 2147 5.635280 GGAGAGTATGTACGCGTAGTATGTA 59.365 44.000 21.25 5.63 37.69 2.29
2025 2148 6.183360 GGAGAGTATGTACGCGTAGTATGTAG 60.183 46.154 21.25 0.00 37.69 2.74
2026 2149 6.219473 AGAGTATGTACGCGTAGTATGTAGT 58.781 40.000 21.25 10.64 37.69 2.73
2027 2150 7.371159 AGAGTATGTACGCGTAGTATGTAGTA 58.629 38.462 21.25 0.00 37.69 1.82
2029 2152 9.290483 GAGTATGTACGCGTAGTATGTAGTATA 57.710 37.037 21.25 4.94 37.69 1.47
2030 2153 9.809096 AGTATGTACGCGTAGTATGTAGTATAT 57.191 33.333 21.25 2.43 37.69 0.86
2034 2157 9.855021 TGTACGCGTAGTATGTAGTATATAAGA 57.145 33.333 21.25 0.00 37.69 2.10
2101 2224 9.897744 ACCATATTTTATGCATACTTCATTTCG 57.102 29.630 5.74 0.00 0.00 3.46
2102 2225 9.897744 CCATATTTTATGCATACTTCATTTCGT 57.102 29.630 5.74 0.00 0.00 3.85
2106 2229 9.716507 ATTTTATGCATACTTCATTTCGTGTAC 57.283 29.630 5.74 0.00 0.00 2.90
2107 2230 7.835634 TTATGCATACTTCATTTCGTGTACA 57.164 32.000 5.74 0.00 0.00 2.90
2108 2231 6.735678 ATGCATACTTCATTTCGTGTACAA 57.264 33.333 0.00 0.00 0.00 2.41
2109 2232 6.546972 TGCATACTTCATTTCGTGTACAAA 57.453 33.333 0.00 0.00 0.00 2.83
2110 2233 7.139896 TGCATACTTCATTTCGTGTACAAAT 57.860 32.000 0.00 0.00 0.00 2.32
2111 2234 8.257830 TGCATACTTCATTTCGTGTACAAATA 57.742 30.769 0.00 0.00 0.00 1.40
2112 2235 8.888716 TGCATACTTCATTTCGTGTACAAATAT 58.111 29.630 0.00 0.00 0.00 1.28
2113 2236 9.158364 GCATACTTCATTTCGTGTACAAATATG 57.842 33.333 0.00 0.62 0.00 1.78
2155 2278 8.335532 ACAATAAAACTATAAGCTCACTTGCA 57.664 30.769 0.00 0.00 36.57 4.08
2156 2279 8.792633 ACAATAAAACTATAAGCTCACTTGCAA 58.207 29.630 0.00 0.00 36.57 4.08
2157 2280 9.793252 CAATAAAACTATAAGCTCACTTGCAAT 57.207 29.630 0.00 0.00 36.57 3.56
2293 3855 3.523564 ACACCTGGTAGTAGGATGCATTT 59.476 43.478 0.00 0.00 40.42 2.32
2294 3856 4.018415 ACACCTGGTAGTAGGATGCATTTT 60.018 41.667 0.00 0.00 40.42 1.82
2297 3859 4.580580 CCTGGTAGTAGGATGCATTTTTCC 59.419 45.833 0.00 0.00 40.42 3.13
2298 3860 5.440610 CTGGTAGTAGGATGCATTTTTCCT 58.559 41.667 11.26 11.26 44.55 3.36
2300 3862 7.149202 TGGTAGTAGGATGCATTTTTCCTAT 57.851 36.000 15.22 8.44 44.35 2.57
2301 3863 8.270137 TGGTAGTAGGATGCATTTTTCCTATA 57.730 34.615 15.22 7.68 44.35 1.31
2325 3887 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
2326 3888 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 132 1.303282 GGAGGGGTAGTGGCCAAAG 59.697 63.158 7.24 0.00 0.00 2.77
142 158 0.682209 GGAGCTGTGGAACCATGCAT 60.682 55.000 18.17 0.00 34.36 3.96
171 187 6.403418 CCAGTTAAGTTGTACCAAACGAAACA 60.403 38.462 13.75 0.00 34.61 2.83
229 250 2.034221 GGGCAGAGTGGGTGGTTC 59.966 66.667 0.00 0.00 0.00 3.62
281 302 3.308438 ACCAGCAATGCAAATGTCTTC 57.692 42.857 8.35 0.00 0.00 2.87
283 304 3.756933 AAACCAGCAATGCAAATGTCT 57.243 38.095 8.35 0.00 0.00 3.41
300 322 6.019156 TGCAAATCGATCCTTTGTTTGAAAAC 60.019 34.615 10.70 0.00 36.26 2.43
360 382 6.963117 TTCTTCCCCTTGTTCTCCTTAATA 57.037 37.500 0.00 0.00 0.00 0.98
361 383 5.860648 TTCTTCCCCTTGTTCTCCTTAAT 57.139 39.130 0.00 0.00 0.00 1.40
362 384 5.382616 GTTTCTTCCCCTTGTTCTCCTTAA 58.617 41.667 0.00 0.00 0.00 1.85
363 385 4.504340 CGTTTCTTCCCCTTGTTCTCCTTA 60.504 45.833 0.00 0.00 0.00 2.69
376 398 6.249035 TCATAAACATTCACGTTTCTTCCC 57.751 37.500 0.00 0.00 39.70 3.97
384 406 4.825085 ACCCTTGTTCATAAACATTCACGT 59.175 37.500 0.00 0.00 44.59 4.49
385 407 5.371115 ACCCTTGTTCATAAACATTCACG 57.629 39.130 0.00 0.00 44.59 4.35
386 408 7.882179 ACTAACCCTTGTTCATAAACATTCAC 58.118 34.615 0.00 0.00 44.59 3.18
387 409 9.747898 ATACTAACCCTTGTTCATAAACATTCA 57.252 29.630 0.00 0.00 44.59 2.57
389 411 9.747898 TGATACTAACCCTTGTTCATAAACATT 57.252 29.630 0.00 0.00 44.59 2.71
415 438 5.995565 TCATTGTGTTAGTGCTACTACCT 57.004 39.130 0.00 0.00 28.93 3.08
438 461 9.360093 CCATTTTTGACTACACAAAGTACAAAA 57.640 29.630 0.00 0.00 40.15 2.44
492 516 1.865340 CATGATCAGATCAGCGTGTGG 59.135 52.381 18.13 0.00 43.53 4.17
529 555 1.561643 TCCTGACTAGTTGCCTCCAG 58.438 55.000 0.00 0.00 0.00 3.86
586 625 1.497722 CGCGTGCCCTTTTTCTCTC 59.502 57.895 0.00 0.00 0.00 3.20
825 901 0.978146 AGCACCGCCTCTCCAACTAT 60.978 55.000 0.00 0.00 0.00 2.12
1258 1337 1.595993 GGCAGTGAGGTACAGCGAGA 61.596 60.000 0.00 0.00 42.21 4.04
1260 1339 2.646175 GGGCAGTGAGGTACAGCGA 61.646 63.158 0.00 0.00 42.21 4.93
1262 1341 2.245438 GAGGGGCAGTGAGGTACAGC 62.245 65.000 0.00 0.00 40.72 4.40
1264 1343 0.614979 GAGAGGGGCAGTGAGGTACA 60.615 60.000 0.00 0.00 0.00 2.90
1265 1344 1.331399 GGAGAGGGGCAGTGAGGTAC 61.331 65.000 0.00 0.00 0.00 3.34
1267 1346 2.284995 GGAGAGGGGCAGTGAGGT 60.285 66.667 0.00 0.00 0.00 3.85
1300 1379 0.687354 AAGCTCGGAAGAAGAAGCCA 59.313 50.000 0.00 0.00 41.32 4.75
1304 1383 4.954202 TCTACCATAAGCTCGGAAGAAGAA 59.046 41.667 3.92 0.00 41.32 2.52
1336 1415 2.158928 CCAGCTAGCTCTCTCTGCAAAT 60.159 50.000 16.15 0.00 0.00 2.32
1398 1483 0.179258 GGTGTATAATAAGCGCGCGC 60.179 55.000 45.10 45.10 42.33 6.86
1399 1484 1.124297 CAGGTGTATAATAAGCGCGCG 59.876 52.381 28.44 28.44 0.00 6.86
1400 1485 1.459592 CCAGGTGTATAATAAGCGCGC 59.540 52.381 26.66 26.66 0.00 6.86
1401 1486 2.066262 CCCAGGTGTATAATAAGCGCG 58.934 52.381 0.00 0.00 0.00 6.86
1455 1540 1.615392 AGACAAATGGCCAAGTTGCTC 59.385 47.619 25.09 20.91 0.00 4.26
1495 1580 3.629398 AGAAGTTGAGAAAACTGCACCTG 59.371 43.478 0.00 0.00 0.00 4.00
1519 1612 0.036875 CAACTCTCCCAAGTGACCCC 59.963 60.000 0.00 0.00 0.00 4.95
1574 1671 5.221342 CCGTGCTATCTCCTGAGAAAACTAT 60.221 44.000 0.20 0.00 41.36 2.12
1591 1688 1.295423 GCCACCTTTCTCCGTGCTA 59.705 57.895 0.00 0.00 0.00 3.49
1593 1690 3.423154 CGCCACCTTTCTCCGTGC 61.423 66.667 0.00 0.00 0.00 5.34
1596 1693 1.599797 AAACCGCCACCTTTCTCCG 60.600 57.895 0.00 0.00 0.00 4.63
1598 1695 1.524008 CCCAAACCGCCACCTTTCTC 61.524 60.000 0.00 0.00 0.00 2.87
1599 1696 1.530655 CCCAAACCGCCACCTTTCT 60.531 57.895 0.00 0.00 0.00 2.52
1612 1709 2.597217 CAAGCACCGGAGCCCAAA 60.597 61.111 20.91 0.00 34.23 3.28
1613 1710 2.920076 AAACAAGCACCGGAGCCCAA 62.920 55.000 20.91 0.00 34.23 4.12
1617 1714 2.954611 GGAAACAAGCACCGGAGC 59.045 61.111 16.88 16.88 0.00 4.70
1618 1715 3.253955 CGGAAACAAGCACCGGAG 58.746 61.111 9.46 0.00 42.48 4.63
1653 1750 1.303282 GTCCCAAGCCCCAACTAGG 59.697 63.158 0.00 0.00 37.03 3.02
1654 1751 0.625849 ATGTCCCAAGCCCCAACTAG 59.374 55.000 0.00 0.00 0.00 2.57
1658 1755 1.229145 CCAATGTCCCAAGCCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
1674 1772 2.358582 CGCATCACTTTGATTATGCCCA 59.641 45.455 0.00 0.00 41.29 5.36
1675 1773 2.859806 GCGCATCACTTTGATTATGCCC 60.860 50.000 0.30 0.00 41.29 5.36
1679 1777 2.620115 CTGGGCGCATCACTTTGATTAT 59.380 45.455 10.83 0.00 34.28 1.28
1681 1779 0.813184 CTGGGCGCATCACTTTGATT 59.187 50.000 10.83 0.00 34.28 2.57
1682 1780 0.322816 ACTGGGCGCATCACTTTGAT 60.323 50.000 10.83 0.00 37.65 2.57
1683 1781 0.537143 AACTGGGCGCATCACTTTGA 60.537 50.000 10.83 0.00 0.00 2.69
1684 1782 0.387622 CAACTGGGCGCATCACTTTG 60.388 55.000 10.83 7.36 0.00 2.77
1735 1858 4.754322 AGCAACCAACCTTAACAACAAAG 58.246 39.130 0.00 0.00 0.00 2.77
1775 1898 3.140325 CTCAAAAGGAGGCACTGGTAA 57.860 47.619 0.00 0.00 41.55 2.85
1776 1899 2.859165 CTCAAAAGGAGGCACTGGTA 57.141 50.000 0.00 0.00 41.55 3.25
1777 1900 3.733709 CTCAAAAGGAGGCACTGGT 57.266 52.632 0.00 0.00 41.55 4.00
1837 1960 4.842574 ACCTCACAACCTTTTTGCAAAAT 58.157 34.783 24.39 8.04 0.00 1.82
1921 2044 9.284968 CCCGATAGTAGGAAAAATTTGTCATAT 57.715 33.333 10.53 3.26 0.00 1.78
1923 2046 7.067008 CACCCGATAGTAGGAAAAATTTGTCAT 59.933 37.037 10.53 5.73 0.00 3.06
1925 2048 6.373495 ACACCCGATAGTAGGAAAAATTTGTC 59.627 38.462 0.00 0.00 0.00 3.18
1927 2050 6.753107 ACACCCGATAGTAGGAAAAATTTG 57.247 37.500 0.00 0.00 0.00 2.32
1928 2051 7.627311 ACTACACCCGATAGTAGGAAAAATTT 58.373 34.615 11.12 0.00 41.49 1.82
1929 2052 7.191593 ACTACACCCGATAGTAGGAAAAATT 57.808 36.000 11.12 0.00 41.49 1.82
1932 2055 6.891908 AGTAACTACACCCGATAGTAGGAAAA 59.108 38.462 11.12 0.00 41.49 2.29
1933 2056 6.426587 AGTAACTACACCCGATAGTAGGAAA 58.573 40.000 11.12 0.00 41.49 3.13
1934 2057 6.006275 AGTAACTACACCCGATAGTAGGAA 57.994 41.667 11.12 0.00 41.49 3.36
1935 2058 5.455326 GGAGTAACTACACCCGATAGTAGGA 60.455 48.000 11.12 0.00 41.49 2.94
1936 2059 4.759183 GGAGTAACTACACCCGATAGTAGG 59.241 50.000 11.12 0.00 41.49 3.18
1937 2060 4.759183 GGGAGTAACTACACCCGATAGTAG 59.241 50.000 6.62 0.00 45.03 2.57
1939 2062 3.560105 GGGAGTAACTACACCCGATAGT 58.440 50.000 6.62 0.00 45.03 2.12
1947 2070 6.316890 TGAAACAAAAGTGGGAGTAACTACAC 59.683 38.462 0.00 0.00 0.00 2.90
1949 2072 6.930667 TGAAACAAAAGTGGGAGTAACTAC 57.069 37.500 0.00 0.00 0.00 2.73
1951 2074 6.204108 CGTATGAAACAAAAGTGGGAGTAACT 59.796 38.462 0.00 0.00 0.00 2.24
1952 2075 6.017687 ACGTATGAAACAAAAGTGGGAGTAAC 60.018 38.462 0.00 0.00 0.00 2.50
1956 2079 5.238650 AGAACGTATGAAACAAAAGTGGGAG 59.761 40.000 0.00 0.00 0.00 4.30
1958 2081 5.432885 AGAACGTATGAAACAAAAGTGGG 57.567 39.130 0.00 0.00 0.00 4.61
1959 2082 7.636326 ACTTAGAACGTATGAAACAAAAGTGG 58.364 34.615 0.00 0.00 0.00 4.00
1960 2083 9.793245 CTACTTAGAACGTATGAAACAAAAGTG 57.207 33.333 0.00 0.00 0.00 3.16
1961 2084 9.538508 ACTACTTAGAACGTATGAAACAAAAGT 57.461 29.630 0.00 0.00 0.00 2.66
1987 2110 9.694137 CGTACATACTCTCCGATATGATAGATA 57.306 37.037 0.00 0.00 33.73 1.98
1988 2111 7.171848 GCGTACATACTCTCCGATATGATAGAT 59.828 40.741 0.00 0.00 33.73 1.98
1989 2112 6.479331 GCGTACATACTCTCCGATATGATAGA 59.521 42.308 0.00 0.00 33.73 1.98
1990 2113 6.562455 CGCGTACATACTCTCCGATATGATAG 60.562 46.154 0.00 0.00 33.73 2.08
1991 2114 5.233689 CGCGTACATACTCTCCGATATGATA 59.766 44.000 0.00 0.00 33.73 2.15
1992 2115 4.034163 CGCGTACATACTCTCCGATATGAT 59.966 45.833 0.00 0.00 33.73 2.45
1993 2116 3.370061 CGCGTACATACTCTCCGATATGA 59.630 47.826 0.00 0.00 33.73 2.15
1995 2118 3.332919 ACGCGTACATACTCTCCGATAT 58.667 45.455 11.67 0.00 0.00 1.63
1996 2119 2.759191 ACGCGTACATACTCTCCGATA 58.241 47.619 11.67 0.00 0.00 2.92
2000 2123 4.450419 ACATACTACGCGTACATACTCTCC 59.550 45.833 16.41 0.00 0.00 3.71
2001 2124 5.588568 ACATACTACGCGTACATACTCTC 57.411 43.478 16.41 0.00 0.00 3.20
2002 2125 6.219473 ACTACATACTACGCGTACATACTCT 58.781 40.000 16.41 0.00 0.00 3.24
2003 2126 6.459257 ACTACATACTACGCGTACATACTC 57.541 41.667 16.41 0.00 0.00 2.59
2075 2198 9.897744 CGAAATGAAGTATGCATAAAATATGGT 57.102 29.630 8.28 0.00 27.94 3.55
2076 2199 9.897744 ACGAAATGAAGTATGCATAAAATATGG 57.102 29.630 8.28 0.00 27.94 2.74
2080 2203 9.716507 GTACACGAAATGAAGTATGCATAAAAT 57.283 29.630 8.28 0.00 27.94 1.82
2081 2204 8.722394 TGTACACGAAATGAAGTATGCATAAAA 58.278 29.630 8.28 0.00 27.94 1.52
2082 2205 8.257830 TGTACACGAAATGAAGTATGCATAAA 57.742 30.769 8.28 0.00 27.94 1.40
2083 2206 7.835634 TGTACACGAAATGAAGTATGCATAA 57.164 32.000 8.28 0.00 27.94 1.90
2084 2207 7.835634 TTGTACACGAAATGAAGTATGCATA 57.164 32.000 1.16 1.16 27.94 3.14
2085 2208 6.735678 TTGTACACGAAATGAAGTATGCAT 57.264 33.333 3.79 3.79 33.97 3.96
2086 2209 6.546972 TTTGTACACGAAATGAAGTATGCA 57.453 33.333 0.00 0.00 0.00 3.96
2087 2210 9.158364 CATATTTGTACACGAAATGAAGTATGC 57.842 33.333 0.00 0.00 0.00 3.14
2129 2252 9.443323 TGCAAGTGAGCTTATAGTTTTATTGTA 57.557 29.630 0.00 0.00 32.87 2.41
2130 2253 8.335532 TGCAAGTGAGCTTATAGTTTTATTGT 57.664 30.769 0.00 0.00 32.87 2.71
2131 2254 9.793252 ATTGCAAGTGAGCTTATAGTTTTATTG 57.207 29.630 4.94 0.00 32.87 1.90
2135 2258 9.546428 AAAAATTGCAAGTGAGCTTATAGTTTT 57.454 25.926 4.94 0.00 32.87 2.43
2238 2377 9.166222 ACCCATTTCTTATATACTACCATGTGA 57.834 33.333 0.00 0.00 0.00 3.58
2240 2379 8.945193 ACACCCATTTCTTATATACTACCATGT 58.055 33.333 0.00 0.00 0.00 3.21
2244 2383 8.813951 AGCTACACCCATTTCTTATATACTACC 58.186 37.037 0.00 0.00 0.00 3.18
2247 2386 9.375974 TGTAGCTACACCCATTTCTTATATACT 57.624 33.333 22.67 0.00 0.00 2.12
2272 3834 3.845781 AATGCATCCTACTACCAGGTG 57.154 47.619 0.76 0.00 36.99 4.00
2274 3836 4.580580 GGAAAAATGCATCCTACTACCAGG 59.419 45.833 0.00 0.00 37.00 4.45
2276 3838 5.450818 AGGAAAAATGCATCCTACTACCA 57.549 39.130 4.72 0.00 44.24 3.25
2300 3862 8.254508 ACACACACACACACACACATATATATA 58.745 33.333 0.00 0.00 0.00 0.86
2301 3863 7.102993 ACACACACACACACACACATATATAT 58.897 34.615 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.