Multiple sequence alignment - TraesCS7A01G521100

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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 TraesCS7A01G521100 chr7A 100.000 2438 0 0 1 2438 705216131 705218568 0.000000e+00 4503.0
1 TraesCS7A01G521100 chr7A 94.231 52 3 0 767 818 663949611 663949560 2.010000e-11 80.5
2 TraesCS7A01G521100 chr7B 93.686 1457 69 9 342 1782 704113402 704114851 0.000000e+00 2159.0
3 TraesCS7A01G521100 chr7B 90.877 570 44 6 1863 2432 704114849 704115410 0.000000e+00 758.0
4 TraesCS7A01G521100 chr7B 90.158 569 50 5 1864 2432 704132090 704132652 0.000000e+00 736.0
5 TraesCS7A01G521100 chr7B 90.000 570 51 5 1863 2432 704123153 704123716 0.000000e+00 732.0
6 TraesCS7A01G521100 chr7B 96.241 266 8 2 1 265 704113143 704113407 3.720000e-118 435.0
7 TraesCS7A01G521100 chr7B 91.736 242 9 2 1552 1782 704122914 704123155 2.340000e-85 326.0
8 TraesCS7A01G521100 chr7B 92.050 239 8 2 1552 1779 704131850 704132088 2.340000e-85 326.0
9 TraesCS7A01G521100 chr7B 91.579 95 7 1 1774 1867 483787731 483787825 1.970000e-26 130.0
10 TraesCS7A01G521100 chr7B 97.826 46 1 0 767 812 633676785 633676830 2.010000e-11 80.5
11 TraesCS7A01G521100 chr7B 85.897 78 6 2 748 824 1832815 1832888 7.230000e-11 78.7
12 TraesCS7A01G521100 chr7B 97.222 36 1 0 624 659 704113805 704113840 7.280000e-06 62.1
13 TraesCS7A01G521100 chr1D 77.730 696 139 11 944 1634 9727382 9726698 1.740000e-111 412.0
14 TraesCS7A01G521100 chrUn 77.433 709 141 16 935 1635 2394447 2395144 2.920000e-109 405.0
15 TraesCS7A01G521100 chrUn 87.805 123 11 3 238 357 9840341 9840462 9.090000e-30 141.0
16 TraesCS7A01G521100 chr1B 76.695 708 145 13 935 1635 13898304 13898998 2.290000e-100 375.0
17 TraesCS7A01G521100 chr1B 90.476 105 8 2 244 348 196463127 196463229 1.180000e-28 137.0
18 TraesCS7A01G521100 chr1B 88.991 109 9 3 234 341 470881205 470881311 5.470000e-27 132.0
19 TraesCS7A01G521100 chr1B 86.777 121 9 7 1769 1883 59598401 59598520 7.080000e-26 128.0
20 TraesCS7A01G521100 chr4D 92.233 103 4 4 260 358 62309586 62309484 2.530000e-30 143.0
21 TraesCS7A01G521100 chr3D 98.750 80 1 0 262 341 141424360 141424281 2.530000e-30 143.0
22 TraesCS7A01G521100 chr3D 92.708 96 7 0 1778 1873 475298915 475298820 3.270000e-29 139.0
23 TraesCS7A01G521100 chr3D 93.258 89 6 0 1777 1865 602231941 602232029 5.470000e-27 132.0
24 TraesCS7A01G521100 chr3D 92.727 55 4 0 767 821 315664415 315664361 2.010000e-11 80.5
25 TraesCS7A01G521100 chr3D 89.474 57 5 1 769 825 570500026 570499971 1.210000e-08 71.3
26 TraesCS7A01G521100 chr2B 96.512 86 3 0 256 341 31741624 31741709 2.530000e-30 143.0
27 TraesCS7A01G521100 chr7D 93.617 94 6 0 248 341 545608357 545608450 9.090000e-30 141.0
28 TraesCS7A01G521100 chr7D 91.579 95 7 1 1776 1869 481573844 481573750 1.970000e-26 130.0
29 TraesCS7A01G521100 chr7D 84.615 78 4 5 743 812 485833268 485833345 1.210000e-08 71.3
30 TraesCS7A01G521100 chr5D 92.079 101 7 1 249 348 137915237 137915337 9.090000e-30 141.0
31 TraesCS7A01G521100 chr2D 89.815 108 9 2 242 348 555221207 555221101 1.180000e-28 137.0
32 TraesCS7A01G521100 chr5A 93.478 92 5 1 1774 1865 44801148 44801058 4.230000e-28 135.0
33 TraesCS7A01G521100 chr5A 90.909 55 4 1 769 822 407937768 407937822 3.360000e-09 73.1
34 TraesCS7A01G521100 chr4B 93.407 91 5 1 1781 1871 282886976 282886887 1.520000e-27 134.0
35 TraesCS7A01G521100 chr4B 86.607 112 13 2 1758 1868 166003177 166003067 3.290000e-24 122.0
36 TraesCS7A01G521100 chr6D 92.391 92 7 0 1777 1868 206553865 206553956 5.470000e-27 132.0
37 TraesCS7A01G521100 chr6D 84.337 83 6 3 746 821 406626835 406626753 9.350000e-10 75.0


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 TraesCS7A01G521100 chr7A 705216131 705218568 2437 False 4503.000 4503 100.0000 1 2438 1 chr7A.!!$F1 2437
1 TraesCS7A01G521100 chr7B 704113143 704115410 2267 False 853.525 2159 94.5065 1 2432 4 chr7B.!!$F4 2431
2 TraesCS7A01G521100 chr7B 704131850 704132652 802 False 531.000 736 91.1040 1552 2432 2 chr7B.!!$F6 880
3 TraesCS7A01G521100 chr7B 704122914 704123716 802 False 529.000 732 90.8680 1552 2432 2 chr7B.!!$F5 880
4 TraesCS7A01G521100 chr1D 9726698 9727382 684 True 412.000 412 77.7300 944 1634 1 chr1D.!!$R1 690
5 TraesCS7A01G521100 chrUn 2394447 2395144 697 False 405.000 405 77.4330 935 1635 1 chrUn.!!$F1 700
6 TraesCS7A01G521100 chr1B 13898304 13898998 694 False 375.000 375 76.6950 935 1635 1 chr1B.!!$F1 700

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
600 603 0.033796 ACGGATTAGAGGGACGTGGA 60.034 55.0 0.0 0.0 36.32 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2158 0.251922 AGGGTGTGATTGGCATTGCT 60.252 50.0 8.82 0.0 0.0 3.91 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
28 29 4.035091 TGCTCCGATCATTAATCCAAAACG 59.965 41.667 0.00 0.00 0.00 3.60
37 38 6.904498 TCATTAATCCAAAACGTAACTGTGG 58.096 36.000 0.00 0.00 0.00 4.17
269 271 9.582648 ACACAACAAAAGTAATAAATACTCCCT 57.417 29.630 0.00 0.00 44.22 4.20
271 273 9.239551 ACAACAAAAGTAATAAATACTCCCTCC 57.760 33.333 0.00 0.00 44.22 4.30
272 274 8.395633 CAACAAAAGTAATAAATACTCCCTCCG 58.604 37.037 0.00 0.00 44.22 4.63
273 275 7.627311 ACAAAAGTAATAAATACTCCCTCCGT 58.373 34.615 0.00 0.00 44.22 4.69
274 276 8.761689 ACAAAAGTAATAAATACTCCCTCCGTA 58.238 33.333 0.00 0.00 44.22 4.02
275 277 9.603921 CAAAAGTAATAAATACTCCCTCCGTAA 57.396 33.333 0.00 0.00 44.22 3.18
277 279 9.605275 AAAGTAATAAATACTCCCTCCGTAAAC 57.395 33.333 0.00 0.00 44.22 2.01
278 280 8.544687 AGTAATAAATACTCCCTCCGTAAACT 57.455 34.615 0.00 0.00 41.04 2.66
279 281 9.646522 AGTAATAAATACTCCCTCCGTAAACTA 57.353 33.333 0.00 0.00 41.04 2.24
288 290 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
289 291 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
290 292 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
291 293 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
292 294 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
293 295 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
294 296 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
295 297 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
296 298 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
308 310 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
309 311 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
369 371 1.135373 CACTAGTGTGTAGGCAGGTCG 60.135 57.143 15.06 0.00 39.24 4.79
400 403 1.287739 CCCTCCAGCTTTATGGGGAAA 59.712 52.381 0.00 0.00 44.33 3.13
423 426 9.952188 GAAACTAAGAGCAATTTTAACAGAGTT 57.048 29.630 0.00 0.00 0.00 3.01
432 435 8.462016 AGCAATTTTAACAGAGTTGTCATATCC 58.538 33.333 0.00 0.00 36.23 2.59
466 469 6.366877 ACTTGCAATTTCATAAATCTGCACAC 59.633 34.615 0.00 0.00 40.77 3.82
502 505 1.271379 ACAAGGACCTGGAATGAACCG 60.271 52.381 1.72 0.00 0.00 4.44
504 507 0.324943 AGGACCTGGAATGAACCGTG 59.675 55.000 0.00 0.00 0.00 4.94
505 508 0.676782 GGACCTGGAATGAACCGTGG 60.677 60.000 0.00 0.00 34.19 4.94
508 511 0.392998 CCTGGAATGAACCGTGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
519 522 4.410400 GTGGGAGGAAGGGCACGG 62.410 72.222 0.00 0.00 0.00 4.94
525 528 2.232298 GAGGAAGGGCACGGTCTCAG 62.232 65.000 1.57 0.00 0.00 3.35
546 549 3.172106 TCAACACGGCAAGGGGGA 61.172 61.111 0.00 0.00 0.00 4.81
579 582 1.511305 GACTCAATGACCCGAGCGA 59.489 57.895 0.00 0.00 32.21 4.93
595 598 0.311477 GCGAGACGGATTAGAGGGAC 59.689 60.000 0.00 0.00 0.00 4.46
600 603 0.033796 ACGGATTAGAGGGACGTGGA 60.034 55.000 0.00 0.00 36.32 4.02
654 657 4.208047 GTCGCTCAAATGTAGTGCTAGATG 59.792 45.833 0.00 0.00 0.00 2.90
655 658 3.060003 CGCTCAAATGTAGTGCTAGATGC 60.060 47.826 0.00 0.00 43.25 3.91
674 677 3.689347 TGCATCCATTTGTTCTAGCACT 58.311 40.909 0.00 0.00 0.00 4.40
718 721 1.072159 GGCTTCTATGCAGGCCGAT 59.928 57.895 0.00 0.00 35.08 4.18
721 724 0.394192 CTTCTATGCAGGCCGATCCA 59.606 55.000 0.00 0.00 37.29 3.41
771 774 3.728845 ACTTGTCGCTCAAATGTAGTGT 58.271 40.909 0.00 0.00 35.48 3.55
783 786 9.967346 GCTCAAATGTAGTGTTAGATACATCTA 57.033 33.333 0.00 0.00 40.78 1.98
848 851 2.224548 GGCCGGTTATGGAATAGCTCTT 60.225 50.000 1.90 0.00 30.01 2.85
850 853 3.498777 GCCGGTTATGGAATAGCTCTTTC 59.501 47.826 1.90 0.00 30.01 2.62
851 854 4.743955 GCCGGTTATGGAATAGCTCTTTCT 60.744 45.833 1.90 0.00 30.01 2.52
957 965 0.107361 ACGTATTTGCAGGGGCTACC 60.107 55.000 0.00 0.00 41.91 3.18
975 983 1.745890 CGAGACCACAGGGAACACA 59.254 57.895 0.00 0.00 38.05 3.72
988 996 4.001248 ACACATTGGCATGGGTCG 57.999 55.556 0.00 0.00 44.41 4.79
1060 1068 0.816018 ACGCGATGTGTTGGGTGAAA 60.816 50.000 15.93 0.00 33.94 2.69
1086 1094 6.804295 GCCGATCTGTCATTACTAATAGTGAG 59.196 42.308 2.68 0.00 28.44 3.51
1109 1117 3.452755 TGGTGAACTCCACTATATGCG 57.547 47.619 0.00 0.00 45.03 4.73
1128 1136 1.347050 CGGATGATCATCAAGGAGGCT 59.653 52.381 31.49 0.00 39.54 4.58
1146 1154 1.065126 GCTCTTAGGTTGCATCCACCT 60.065 52.381 16.12 14.53 37.64 4.00
1162 1170 0.419459 ACCTGGTCCTCTGATTCCCT 59.581 55.000 0.00 0.00 0.00 4.20
1164 1172 1.577736 CTGGTCCTCTGATTCCCTGT 58.422 55.000 0.00 0.00 0.00 4.00
1176 1184 1.965414 TTCCCTGTATGGCCAGAGAA 58.035 50.000 13.05 3.32 34.23 2.87
1179 1187 1.139853 CCCTGTATGGCCAGAGAAGAC 59.860 57.143 13.05 2.67 34.23 3.01
1190 1198 4.021368 GGCCAGAGAAGACTGTACAGTTAA 60.021 45.833 28.49 0.00 42.66 2.01
1324 1332 4.340950 ACAACAATGTGAACTACAAAGGGG 59.659 41.667 0.00 0.00 43.77 4.79
1326 1334 3.157087 CAATGTGAACTACAAAGGGGCT 58.843 45.455 0.00 0.00 43.77 5.19
1333 1341 5.048921 GTGAACTACAAAGGGGCTTACTTTC 60.049 44.000 0.00 0.00 36.09 2.62
1348 1356 5.473504 GCTTACTTTCAGTTCATTCCCTTCA 59.526 40.000 0.00 0.00 0.00 3.02
1350 1358 4.401925 ACTTTCAGTTCATTCCCTTCAGG 58.598 43.478 0.00 0.00 0.00 3.86
1422 1430 5.011943 TGAGATGGCATTAGCAAACCTTTTT 59.988 36.000 0.00 0.00 44.61 1.94
1447 1455 4.556697 TCACTTCCATTAGATGCTCCCTA 58.443 43.478 0.00 0.00 0.00 3.53
1454 1462 4.978099 CATTAGATGCTCCCTAATGGTGT 58.022 43.478 17.66 0.00 44.64 4.16
1475 1483 2.844122 AACCTTGCTTCGTTTGACAC 57.156 45.000 0.00 0.00 0.00 3.67
1610 1621 3.373748 TCAGGTAGCAATGCATGTTTACG 59.626 43.478 8.35 0.00 0.00 3.18
1646 1657 2.993220 GCACGTGTCAATGATGTCACTA 59.007 45.455 18.38 0.00 41.53 2.74
1649 1660 5.553721 CACGTGTCAATGATGTCACTATTG 58.446 41.667 7.58 5.06 41.53 1.90
1665 1676 4.217334 CACTATTGTGGTGCATGGTTGTAA 59.783 41.667 0.00 0.00 40.33 2.41
1702 1713 7.920151 GCAAACATTATGGTATTGCATCTACAA 59.080 33.333 19.86 0.00 44.29 2.41
1787 1808 9.790297 ATCATATAGGACATAATTGTACTCCCT 57.210 33.333 0.00 0.00 44.06 4.20
1788 1809 9.256228 TCATATAGGACATAATTGTACTCCCTC 57.744 37.037 0.00 0.00 44.06 4.30
1789 1810 9.261035 CATATAGGACATAATTGTACTCCCTCT 57.739 37.037 0.00 0.00 44.06 3.69
1790 1811 5.878406 AGGACATAATTGTACTCCCTCTG 57.122 43.478 0.00 0.00 44.06 3.35
1791 1812 5.281314 AGGACATAATTGTACTCCCTCTGT 58.719 41.667 0.00 0.00 44.06 3.41
1792 1813 6.441222 AGGACATAATTGTACTCCCTCTGTA 58.559 40.000 0.00 0.00 44.06 2.74
1793 1814 6.901300 AGGACATAATTGTACTCCCTCTGTAA 59.099 38.462 0.00 0.00 44.06 2.41
1794 1815 7.402071 AGGACATAATTGTACTCCCTCTGTAAA 59.598 37.037 0.00 0.00 44.06 2.01
1795 1816 7.494952 GGACATAATTGTACTCCCTCTGTAAAC 59.505 40.741 0.00 0.00 35.79 2.01
1796 1817 8.147244 ACATAATTGTACTCCCTCTGTAAACT 57.853 34.615 0.00 0.00 33.16 2.66
1797 1818 9.263446 ACATAATTGTACTCCCTCTGTAAACTA 57.737 33.333 0.00 0.00 33.16 2.24
1861 1882 9.584008 ACGATCTTATATTAGTTTACAGAGGGA 57.416 33.333 0.00 0.00 0.00 4.20
1951 1972 8.984764 ACAATTGATTTGTGATCAGAAACATTG 58.015 29.630 26.09 26.09 46.80 2.82
1953 1974 7.933728 TTGATTTGTGATCAGAAACATTGTG 57.066 32.000 19.22 0.00 0.00 3.33
1954 1975 7.041635 TGATTTGTGATCAGAAACATTGTGT 57.958 32.000 19.22 2.84 0.00 3.72
1956 1977 8.628280 TGATTTGTGATCAGAAACATTGTGTTA 58.372 29.630 19.22 0.00 40.14 2.41
1957 1978 9.462174 GATTTGTGATCAGAAACATTGTGTTAA 57.538 29.630 19.22 0.00 40.14 2.01
1958 1979 9.985730 ATTTGTGATCAGAAACATTGTGTTAAT 57.014 25.926 19.22 0.00 40.14 1.40
1959 1980 8.800231 TTGTGATCAGAAACATTGTGTTAATG 57.200 30.769 2.20 0.00 40.14 1.90
2009 2030 2.727392 CCCGTTATGGCCACTCCGA 61.727 63.158 8.16 0.00 37.80 4.55
2061 2082 2.175499 TGCTAATCCTAGGCCATTGCTT 59.825 45.455 5.01 0.00 37.74 3.91
2062 2083 2.555757 GCTAATCCTAGGCCATTGCTTG 59.444 50.000 5.01 0.00 37.74 4.01
2079 2100 2.985847 GCCACCTGCCACCTTCAC 60.986 66.667 0.00 0.00 0.00 3.18
2137 2158 3.047280 GGCATCAACGTCGTGGCA 61.047 61.111 13.84 0.00 38.21 4.92
2141 2162 1.596752 ATCAACGTCGTGGCAGCAA 60.597 52.632 0.00 0.00 0.00 3.91
2158 2179 0.452987 CAATGCCAATCACACCCTCG 59.547 55.000 0.00 0.00 0.00 4.63
2190 2211 4.823442 TCCATGCATAACTTCTAGCAATGG 59.177 41.667 0.00 0.00 40.76 3.16
2200 2221 7.944729 AACTTCTAGCAATGGTTAATCATGT 57.055 32.000 0.96 0.00 0.00 3.21
2201 2222 7.559590 ACTTCTAGCAATGGTTAATCATGTC 57.440 36.000 0.96 0.00 0.00 3.06
2203 2224 8.486210 ACTTCTAGCAATGGTTAATCATGTCTA 58.514 33.333 0.96 6.09 0.00 2.59
2249 2270 3.056250 AGACAGCAGACCAACTCATACAG 60.056 47.826 0.00 0.00 0.00 2.74
2260 2281 5.106157 ACCAACTCATACAGCATTAAAGTGC 60.106 40.000 0.00 0.00 45.38 4.40
2271 2292 3.236816 CATTAAAGTGCGCTTGAGTTGG 58.763 45.455 14.36 0.00 34.71 3.77
2413 2436 2.911509 ATGGTGTGGCAAAGCGCA 60.912 55.556 11.47 0.00 45.17 6.09
2435 2458 6.889301 CATTATTCATGCTAGTGTTCCCAT 57.111 37.500 0.00 0.00 0.00 4.00
2436 2459 7.984422 CATTATTCATGCTAGTGTTCCCATA 57.016 36.000 0.00 0.00 0.00 2.74
2437 2460 8.571461 CATTATTCATGCTAGTGTTCCCATAT 57.429 34.615 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.277974 CGTTTTGGATTAATGATCGGAGCAT 60.278 40.000 2.30 2.30 35.49 3.79
11 12 7.696453 CCACAGTTACGTTTTGGATTAATGATC 59.304 37.037 0.00 0.00 0.00 2.92
28 29 2.032290 GTGCGGTTCTTTCCACAGTTAC 60.032 50.000 0.00 0.00 0.00 2.50
246 248 8.395633 CGGAGGGAGTATTTATTACTTTTGTTG 58.604 37.037 0.00 0.00 41.35 3.33
262 264 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
263 265 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
264 266 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
265 267 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
266 268 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
267 269 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
268 270 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
269 271 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
270 272 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
282 284 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
283 285 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
284 286 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
285 287 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
329 331 9.347240 ACTAGTGTGTACTTTCTCTGTAAACTA 57.653 33.333 0.00 0.00 38.36 2.24
330 332 8.136165 CACTAGTGTGTACTTTCTCTGTAAACT 58.864 37.037 15.06 0.00 39.24 2.66
331 333 8.283340 CACTAGTGTGTACTTTCTCTGTAAAC 57.717 38.462 15.06 0.00 39.24 2.01
369 371 2.692368 TGGAGGGAGTGGATGCCC 60.692 66.667 0.00 0.00 41.30 5.36
400 403 8.451908 ACAACTCTGTTAAAATTGCTCTTAGT 57.548 30.769 0.00 0.00 28.57 2.24
423 426 2.677914 AGTGATCCGGTGGATATGACA 58.322 47.619 0.00 0.00 43.27 3.58
432 435 2.228582 TGAAATTGCAAGTGATCCGGTG 59.771 45.455 4.94 0.00 0.00 4.94
502 505 4.410400 CCGTGCCCTTCCTCCCAC 62.410 72.222 0.00 0.00 0.00 4.61
504 507 4.097361 GACCGTGCCCTTCCTCCC 62.097 72.222 0.00 0.00 0.00 4.30
505 508 3.003763 AGACCGTGCCCTTCCTCC 61.004 66.667 0.00 0.00 0.00 4.30
508 511 2.113243 AACTGAGACCGTGCCCTTCC 62.113 60.000 0.00 0.00 0.00 3.46
519 522 1.140816 GCCGTGTTGAGAACTGAGAC 58.859 55.000 0.00 0.00 0.00 3.36
525 528 1.515521 CCCCTTGCCGTGTTGAGAAC 61.516 60.000 0.00 0.00 0.00 3.01
546 549 2.424557 TGAGTCGCTACGAGAAACTCT 58.575 47.619 0.00 0.00 36.23 3.24
579 582 1.390565 CACGTCCCTCTAATCCGTCT 58.609 55.000 0.00 0.00 0.00 4.18
585 588 1.887198 CGCTATCCACGTCCCTCTAAT 59.113 52.381 0.00 0.00 0.00 1.73
595 598 1.063806 GCTTCTATGCGCTATCCACG 58.936 55.000 9.73 0.00 0.00 4.94
600 603 3.634448 AGATATCGGCTTCTATGCGCTAT 59.366 43.478 9.73 3.00 0.00 2.97
654 657 6.382869 AATAGTGCTAGAACAAATGGATGC 57.617 37.500 3.00 0.00 0.00 3.91
655 658 9.941664 CTAAAATAGTGCTAGAACAAATGGATG 57.058 33.333 3.00 0.00 0.00 3.51
718 721 9.362151 AGGACAAAATATTTTTCTACAACTGGA 57.638 29.630 10.77 0.00 0.00 3.86
771 774 8.414003 ACTTGTCGCTCAAATAGATGTATCTAA 58.586 33.333 5.75 0.00 36.26 2.10
783 786 3.374058 CCGGAATTACTTGTCGCTCAAAT 59.626 43.478 0.00 0.00 35.48 2.32
784 787 2.739913 CCGGAATTACTTGTCGCTCAAA 59.260 45.455 0.00 0.00 35.48 2.69
785 788 2.028839 TCCGGAATTACTTGTCGCTCAA 60.029 45.455 0.00 0.00 34.61 3.02
786 789 1.546923 TCCGGAATTACTTGTCGCTCA 59.453 47.619 0.00 0.00 0.00 4.26
860 863 8.138074 GTGCATATTATGTCTTCTCTCTGTGTA 58.862 37.037 5.60 0.00 0.00 2.90
957 965 0.321671 ATGTGTTCCCTGTGGTCTCG 59.678 55.000 0.00 0.00 0.00 4.04
975 983 1.768275 TCTGATACGACCCATGCCAAT 59.232 47.619 0.00 0.00 0.00 3.16
988 996 3.561725 GGGTTGTGCATAAGCTCTGATAC 59.438 47.826 22.15 3.09 42.74 2.24
1060 1068 6.490381 TCACTATTAGTAATGACAGATCGGCT 59.510 38.462 5.61 0.00 0.00 5.52
1109 1117 2.638855 AGAGCCTCCTTGATGATCATCC 59.361 50.000 28.61 13.92 37.02 3.51
1128 1136 1.281867 CCAGGTGGATGCAACCTAAGA 59.718 52.381 14.77 0.00 46.58 2.10
1146 1154 2.940514 TACAGGGAATCAGAGGACCA 57.059 50.000 0.00 0.00 0.00 4.02
1162 1170 2.540383 ACAGTCTTCTCTGGCCATACA 58.460 47.619 5.51 0.00 39.48 2.29
1164 1172 3.701542 CTGTACAGTCTTCTCTGGCCATA 59.298 47.826 15.06 0.00 39.48 2.74
1176 1184 7.735326 ATCATAACCCTTAACTGTACAGTCT 57.265 36.000 28.04 19.28 41.58 3.24
1179 1187 8.095169 GGGATATCATAACCCTTAACTGTACAG 58.905 40.741 21.44 21.44 40.39 2.74
1324 1332 9.175755 CCTGAAGGGAATGAACTGAAAGTAAGC 62.176 44.444 0.00 0.00 42.59 3.09
1326 1334 6.003950 CCTGAAGGGAATGAACTGAAAGTAA 58.996 40.000 0.00 0.00 42.59 2.24
1350 1358 2.825836 CATTGCCGTCTCCCAGCC 60.826 66.667 0.00 0.00 0.00 4.85
1422 1430 5.608437 AGGGAGCATCTAATGGAAGTGATAA 59.392 40.000 0.00 0.00 33.73 1.75
1432 1440 4.978099 ACACCATTAGGGAGCATCTAATG 58.022 43.478 18.60 18.60 46.61 1.90
1436 1444 4.385310 GGTTAACACCATTAGGGAGCATCT 60.385 45.833 8.10 0.00 43.61 2.90
1454 1462 4.281525 GTGTCAAACGAAGCAAGGTTAA 57.718 40.909 0.00 0.00 0.00 2.01
1475 1483 2.920647 GCAAACCCAAATTTCTCGGACG 60.921 50.000 3.11 0.00 0.00 4.79
1610 1621 0.512952 CGTGCTGAAAGTGCAGGTAC 59.487 55.000 0.00 0.00 41.41 3.34
1646 1657 3.230134 AGTTACAACCATGCACCACAAT 58.770 40.909 0.00 0.00 0.00 2.71
1649 1660 3.726291 AAAGTTACAACCATGCACCAC 57.274 42.857 0.00 0.00 0.00 4.16
1665 1676 6.700352 ACCATAATGTTTGCTTGCATAAAGT 58.300 32.000 0.00 0.00 38.25 2.66
1835 1856 9.584008 TCCCTCTGTAAACTAATATAAGATCGT 57.416 33.333 0.00 0.00 0.00 3.73
1848 1869 9.939424 AGTAGAATAATACTCCCTCTGTAAACT 57.061 33.333 0.00 0.00 29.89 2.66
1895 1916 6.127619 ACTGAAATCCAGCAAGTTATAAAGGC 60.128 38.462 0.00 0.00 46.81 4.35
1987 2008 1.628846 GGAGTGGCCATAACGGGATAT 59.371 52.381 9.72 0.00 36.34 1.63
2009 2030 0.965363 GGTCGATGGGGCAAACACAT 60.965 55.000 0.00 0.00 0.00 3.21
2062 2083 2.124507 TAGTGAAGGTGGCAGGTGGC 62.125 60.000 0.00 0.00 43.74 5.01
2067 2088 2.086869 CATGGTTAGTGAAGGTGGCAG 58.913 52.381 0.00 0.00 0.00 4.85
2079 2100 2.784596 CACGCGCCACATGGTTAG 59.215 61.111 5.73 0.00 37.57 2.34
2102 2123 1.401018 GCCACCTACACAATTTGTCGC 60.401 52.381 0.00 0.00 39.91 5.19
2108 2129 2.487762 CGTTGATGCCACCTACACAATT 59.512 45.455 0.00 0.00 0.00 2.32
2137 2158 0.251922 AGGGTGTGATTGGCATTGCT 60.252 50.000 8.82 0.00 0.00 3.91
2141 2162 0.548031 ATCGAGGGTGTGATTGGCAT 59.452 50.000 0.00 0.00 0.00 4.40
2158 2179 3.484407 AGTTATGCATGGAAGCCTCATC 58.516 45.455 10.16 0.00 0.00 2.92
2166 2187 5.300034 CCATTGCTAGAAGTTATGCATGGAA 59.700 40.000 10.16 0.00 36.83 3.53
2211 2232 8.599774 GTCTGCTGTCTTTTATAGTGAAAGATC 58.400 37.037 3.01 0.00 42.95 2.75
2214 2235 6.650807 TGGTCTGCTGTCTTTTATAGTGAAAG 59.349 38.462 0.00 0.00 35.85 2.62
2249 2270 2.619013 ACTCAAGCGCACTTTAATGC 57.381 45.000 11.47 0.00 42.48 3.56
2260 2281 0.318441 TCCTCTGTCCAACTCAAGCG 59.682 55.000 0.00 0.00 0.00 4.68
2334 2357 2.093783 CCAAGGTTATTTGTCGCTCGTC 59.906 50.000 0.00 0.00 0.00 4.20
2338 2361 3.950397 TCATCCAAGGTTATTTGTCGCT 58.050 40.909 0.00 0.00 0.00 4.93
2339 2362 4.900635 ATCATCCAAGGTTATTTGTCGC 57.099 40.909 0.00 0.00 0.00 5.19
2381 2404 2.644299 ACACCATGGAGATTTGAGGACA 59.356 45.455 21.47 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.