Multiple sequence alignment - TraesCS2B01G183800

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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 TraesCS2B01G183800 chr2B 100.000 2776 0 0 1 2776 158649388 158652163 0.000000e+00 5127
1 TraesCS2B01G183800 chr2B 96.768 495 16 0 2282 2776 158664356 158664850 0.000000e+00 826
2 TraesCS2B01G183800 chr2B 96.162 495 18 1 2282 2775 424162659 424162165 0.000000e+00 808
3 TraesCS2B01G183800 chr2B 94.175 412 22 1 1873 2282 158775706 158776117 6.530000e-176 627
4 TraesCS2B01G183800 chr2D 93.265 980 28 18 923 1868 109076267 109077242 0.000000e+00 1410
5 TraesCS2B01G183800 chr2D 94.568 810 27 9 1 803 109075419 109076218 0.000000e+00 1236
6 TraesCS2B01G183800 chr2A 85.031 962 56 43 904 1815 104977915 104978838 0.000000e+00 898
7 TraesCS2B01G183800 chr2A 91.262 412 33 2 1873 2282 437056121 437056531 2.410000e-155 558
8 TraesCS2B01G183800 chr2A 93.103 261 9 4 1 259 104977139 104977392 9.390000e-100 374
9 TraesCS2B01G183800 chr2A 94.366 71 4 0 1798 1868 104979044 104979114 2.920000e-20 110
10 TraesCS2B01G183800 chr1B 96.970 495 15 0 2282 2776 609991126 609991620 0.000000e+00 832
11 TraesCS2B01G183800 chr1B 95.808 501 19 2 2275 2773 170191308 170191808 0.000000e+00 808
12 TraesCS2B01G183800 chr1B 95.556 495 20 2 2283 2776 458279731 458280224 0.000000e+00 791
13 TraesCS2B01G183800 chr4B 95.960 495 18 2 2283 2776 63507491 63506998 0.000000e+00 802
14 TraesCS2B01G183800 chr7B 95.547 494 22 0 2283 2776 488852034 488852527 0.000000e+00 791
15 TraesCS2B01G183800 chr6B 95.556 495 21 1 2283 2776 132796187 132795693 0.000000e+00 791
16 TraesCS2B01G183800 chr5D 85.925 746 83 21 1873 2604 522515710 522516447 0.000000e+00 776
17 TraesCS2B01G183800 chr4A 91.566 415 30 4 1872 2282 469429726 469430139 4.010000e-158 568
18 TraesCS2B01G183800 chr6D 91.505 412 30 3 1873 2282 97597059 97597467 1.870000e-156 562
19 TraesCS2B01G183800 chr6D 91.283 413 32 3 1873 2282 403666099 403666510 6.710000e-156 560
20 TraesCS2B01G183800 chr7A 91.422 408 32 2 1878 2282 376875281 376874874 8.690000e-155 556
21 TraesCS2B01G183800 chr5A 91.019 412 34 2 1873 2282 327370702 327370292 1.120000e-153 553
22 TraesCS2B01G183800 chr3A 90.799 413 35 2 1873 2282 644002170 644001758 1.450000e-152 549
23 TraesCS2B01G183800 chr3A 86.120 317 43 1 1149 1465 114544723 114545038 9.520000e-90 340
24 TraesCS2B01G183800 chr3A 81.340 209 37 2 1251 1458 112915888 112915681 4.750000e-38 169
25 TraesCS2B01G183800 chr3D 86.971 307 40 0 1149 1455 96677254 96677560 2.050000e-91 346
26 TraesCS2B01G183800 chr3D 84.211 323 43 6 1205 1523 166966611 166966293 9.660000e-80 307
27 TraesCS2B01G183800 chr3D 83.392 283 47 0 1176 1458 532168644 532168362 2.120000e-66 263
28 TraesCS2B01G183800 chr3B 84.345 313 46 2 1149 1458 704323043 704322731 1.250000e-78 303
29 TraesCS2B01G183800 chr3B 83.108 296 44 2 1149 1438 147776326 147776621 5.900000e-67 265


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 TraesCS2B01G183800 chr2B 158649388 158652163 2775 False 5127.000000 5127 100.000000 1 2776 1 chr2B.!!$F1 2775
1 TraesCS2B01G183800 chr2D 109075419 109077242 1823 False 1323.000000 1410 93.916500 1 1868 2 chr2D.!!$F1 1867
2 TraesCS2B01G183800 chr2A 104977139 104979114 1975 False 460.666667 898 90.833333 1 1868 3 chr2A.!!$F2 1867
3 TraesCS2B01G183800 chr1B 170191308 170191808 500 False 808.000000 808 95.808000 2275 2773 1 chr1B.!!$F1 498
4 TraesCS2B01G183800 chr5D 522515710 522516447 737 False 776.000000 776 85.925000 1873 2604 1 chr5D.!!$F1 731

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
875 1060 0.03438 TAGTCAGCTAGCTCGGTGGT 60.034 55.0 16.15 7.78 33.43 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2494 0.036388 CTTCTTAACGGGCCTGAGCA 60.036 55.0 21.41 0.0 42.56 4.26 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
211 214 3.122150 GCTTTGGGCCGTGAAAATC 57.878 52.632 0.00 0.00 34.27 2.17
222 225 2.609491 CCGTGAAAATCGAGAGGTGTGA 60.609 50.000 0.00 0.00 0.00 3.58
237 242 1.335496 GTGTGAGGGCTTTGCGTAAAA 59.665 47.619 0.00 0.00 0.00 1.52
238 243 1.606668 TGTGAGGGCTTTGCGTAAAAG 59.393 47.619 0.00 4.40 46.90 2.27
281 286 0.106519 GATGGGCCTTGCATAGTGGT 60.107 55.000 4.53 0.00 0.00 4.16
283 288 0.114168 TGGGCCTTGCATAGTGGTTT 59.886 50.000 4.53 0.00 0.00 3.27
284 289 1.266178 GGGCCTTGCATAGTGGTTTT 58.734 50.000 0.84 0.00 0.00 2.43
285 290 1.623311 GGGCCTTGCATAGTGGTTTTT 59.377 47.619 0.84 0.00 0.00 1.94
393 571 2.052104 TGCGATCTTGGAGCTCCGA 61.052 57.895 27.43 24.70 39.43 4.55
564 742 4.742201 ATCTGAAGCGCACGCCGT 62.742 61.111 11.47 0.00 43.17 5.68
660 842 0.744771 GTTCAGATGGGGAAGGCGAC 60.745 60.000 0.00 0.00 0.00 5.19
763 945 3.671971 CGCCGCAAAATTTCATGGTTAGA 60.672 43.478 0.00 0.00 0.00 2.10
787 969 2.438434 GATGTGTGGGCGGAAGGG 60.438 66.667 0.00 0.00 0.00 3.95
803 988 4.011517 GGGACGACGCCAGGGAAA 62.012 66.667 9.90 0.00 0.00 3.13
828 1013 7.703058 AAAATAGTCATCTGGGTTAAGTTGG 57.297 36.000 0.00 0.00 0.00 3.77
829 1014 3.073274 AGTCATCTGGGTTAAGTTGGC 57.927 47.619 0.00 0.00 0.00 4.52
830 1015 1.737793 GTCATCTGGGTTAAGTTGGCG 59.262 52.381 0.00 0.00 0.00 5.69
831 1016 1.094785 CATCTGGGTTAAGTTGGCGG 58.905 55.000 0.00 0.00 0.00 6.13
832 1017 0.988832 ATCTGGGTTAAGTTGGCGGA 59.011 50.000 0.00 0.00 0.00 5.54
833 1018 0.766131 TCTGGGTTAAGTTGGCGGAA 59.234 50.000 0.00 0.00 0.00 4.30
834 1019 1.165270 CTGGGTTAAGTTGGCGGAAG 58.835 55.000 0.00 0.00 0.00 3.46
835 1020 0.250989 TGGGTTAAGTTGGCGGAAGG 60.251 55.000 0.00 0.00 0.00 3.46
836 1021 0.037160 GGGTTAAGTTGGCGGAAGGA 59.963 55.000 0.00 0.00 0.00 3.36
837 1022 1.340697 GGGTTAAGTTGGCGGAAGGAT 60.341 52.381 0.00 0.00 0.00 3.24
838 1023 2.092807 GGGTTAAGTTGGCGGAAGGATA 60.093 50.000 0.00 0.00 0.00 2.59
839 1024 2.941064 GGTTAAGTTGGCGGAAGGATAC 59.059 50.000 0.00 0.00 0.00 2.24
840 1025 2.589798 TAAGTTGGCGGAAGGATACG 57.410 50.000 0.00 0.00 46.39 3.06
841 1026 0.107848 AAGTTGGCGGAAGGATACGG 60.108 55.000 0.00 0.00 46.39 4.02
846 1031 1.594564 GCGGAAGGATACGGGCTTC 60.595 63.158 0.00 0.00 46.39 3.86
872 1057 5.593679 TTTTTATAGTCAGCTAGCTCGGT 57.406 39.130 16.15 4.28 0.00 4.69
873 1058 4.569761 TTTATAGTCAGCTAGCTCGGTG 57.430 45.455 16.15 10.97 0.00 4.94
874 1059 1.323412 ATAGTCAGCTAGCTCGGTGG 58.677 55.000 16.15 3.09 33.43 4.61
875 1060 0.034380 TAGTCAGCTAGCTCGGTGGT 60.034 55.000 16.15 7.78 33.43 4.16
876 1061 1.153745 GTCAGCTAGCTCGGTGGTG 60.154 63.158 16.15 2.51 33.43 4.17
877 1062 1.606601 TCAGCTAGCTCGGTGGTGT 60.607 57.895 16.15 0.00 33.43 4.16
891 1076 2.073816 GTGGTGTCCGGATAAGTGTTG 58.926 52.381 7.81 0.00 0.00 3.33
893 1078 1.084289 GTGTCCGGATAAGTGTTGGC 58.916 55.000 7.81 0.00 0.00 4.52
894 1079 0.390603 TGTCCGGATAAGTGTTGGCG 60.391 55.000 7.81 0.00 0.00 5.69
895 1080 0.390735 GTCCGGATAAGTGTTGGCGT 60.391 55.000 7.81 0.00 0.00 5.68
897 1082 1.758280 TCCGGATAAGTGTTGGCGTAT 59.242 47.619 0.00 0.00 0.00 3.06
898 1083 2.168936 TCCGGATAAGTGTTGGCGTATT 59.831 45.455 0.00 0.00 0.00 1.89
899 1084 2.286833 CCGGATAAGTGTTGGCGTATTG 59.713 50.000 0.00 0.00 0.00 1.90
900 1085 2.286184 CGGATAAGTGTTGGCGTATTGC 60.286 50.000 0.00 0.00 45.38 3.56
910 1287 3.860125 CGTATTGCACCGCCCGTG 61.860 66.667 0.00 0.00 46.03 4.94
928 1305 3.246699 CCGTGTAGTTGTGTTTGTACCAG 59.753 47.826 0.00 0.00 0.00 4.00
942 1319 3.322466 CCAGGCTGAGTCCGGGTT 61.322 66.667 17.94 0.00 36.81 4.11
997 1376 4.101448 GCTGGTCCGGGTCTGCAT 62.101 66.667 17.05 0.00 0.00 3.96
998 1377 2.124983 CTGGTCCGGGTCTGCATG 60.125 66.667 0.00 0.00 0.00 4.06
999 1378 4.408821 TGGTCCGGGTCTGCATGC 62.409 66.667 11.82 11.82 0.00 4.06
1103 1491 0.947244 AGCTTCCTTTCTTGTGTGCG 59.053 50.000 0.00 0.00 0.00 5.34
1105 1493 1.597937 GCTTCCTTTCTTGTGTGCGTG 60.598 52.381 0.00 0.00 0.00 5.34
1364 1754 2.203294 GCCAAACTCCACCCGTGT 60.203 61.111 0.00 0.00 0.00 4.49
1366 1756 1.147376 CCAAACTCCACCCGTGTCA 59.853 57.895 0.00 0.00 0.00 3.58
1367 1757 1.164041 CCAAACTCCACCCGTGTCAC 61.164 60.000 0.00 0.00 0.00 3.67
1442 1832 2.162608 AGACGAGGACGACTTCAAGATG 59.837 50.000 0.00 0.00 40.95 2.90
1450 1840 2.304761 ACGACTTCAAGATGGGGCTTTA 59.695 45.455 0.00 0.00 0.00 1.85
1513 1907 3.864003 GGAGTGTTGCCTAAGTTCGTATC 59.136 47.826 0.00 0.00 0.00 2.24
1628 2023 4.909894 TCGTCAATCTTCAGATAGACACG 58.090 43.478 0.00 0.00 33.73 4.49
1629 2024 4.395231 TCGTCAATCTTCAGATAGACACGT 59.605 41.667 0.00 0.00 33.73 4.49
1630 2025 4.497251 CGTCAATCTTCAGATAGACACGTG 59.503 45.833 15.48 15.48 33.73 4.49
1631 2026 4.266502 GTCAATCTTCAGATAGACACGTGC 59.733 45.833 17.22 8.74 33.73 5.34
1633 2028 4.662468 ATCTTCAGATAGACACGTGCAT 57.338 40.909 17.22 6.92 32.01 3.96
1634 2029 4.456280 TCTTCAGATAGACACGTGCATT 57.544 40.909 17.22 3.72 0.00 3.56
1635 2030 4.820897 TCTTCAGATAGACACGTGCATTT 58.179 39.130 17.22 0.00 0.00 2.32
1636 2031 4.864806 TCTTCAGATAGACACGTGCATTTC 59.135 41.667 17.22 9.05 0.00 2.17
1637 2032 3.521560 TCAGATAGACACGTGCATTTCC 58.478 45.455 17.22 0.71 0.00 3.13
1639 2034 4.401202 TCAGATAGACACGTGCATTTCCTA 59.599 41.667 17.22 7.98 0.00 2.94
1640 2035 5.069119 TCAGATAGACACGTGCATTTCCTAT 59.931 40.000 17.22 12.14 0.00 2.57
1643 2038 4.737855 AGACACGTGCATTTCCTATACT 57.262 40.909 17.22 0.00 0.00 2.12
1644 2039 4.683832 AGACACGTGCATTTCCTATACTC 58.316 43.478 17.22 0.25 0.00 2.59
1645 2040 4.402793 AGACACGTGCATTTCCTATACTCT 59.597 41.667 17.22 2.90 0.00 3.24
1646 2041 5.593095 AGACACGTGCATTTCCTATACTCTA 59.407 40.000 17.22 0.00 0.00 2.43
1649 2065 5.915758 CACGTGCATTTCCTATACTCTACTC 59.084 44.000 0.82 0.00 0.00 2.59
1703 2130 7.768120 TGCAACAAACTGTTTTCATTTTATCCT 59.232 29.630 2.41 0.00 38.77 3.24
1759 2186 6.625532 AATTTAGATTGCATCCCACCTTTT 57.374 33.333 0.00 0.00 0.00 2.27
1767 2194 2.302733 GCATCCCACCTTTTTGTCCAAT 59.697 45.455 0.00 0.00 0.00 3.16
1799 2226 2.604046 AACTTGGATTCTCCGGATCG 57.396 50.000 3.57 0.00 40.17 3.69
1844 2494 1.201429 AGGAATGGAGAAGCACGGGT 61.201 55.000 0.00 0.00 0.00 5.28
1868 2518 0.546988 AGGCCCGTTAAGAAGGAGGT 60.547 55.000 0.00 0.00 0.00 3.85
1869 2519 0.107800 GGCCCGTTAAGAAGGAGGTC 60.108 60.000 0.00 0.00 0.00 3.85
1870 2520 0.459759 GCCCGTTAAGAAGGAGGTCG 60.460 60.000 0.00 0.00 0.00 4.79
1871 2521 0.893447 CCCGTTAAGAAGGAGGTCGT 59.107 55.000 0.00 0.00 0.00 4.34
1876 2526 3.551454 CGTTAAGAAGGAGGTCGTTGTCA 60.551 47.826 0.00 0.00 0.00 3.58
1890 2540 1.741145 GTTGTCAGTGTCAAAACCGGT 59.259 47.619 0.00 0.00 0.00 5.28
1891 2541 2.937799 GTTGTCAGTGTCAAAACCGGTA 59.062 45.455 8.00 0.00 0.00 4.02
1894 2544 2.798847 GTCAGTGTCAAAACCGGTAGAC 59.201 50.000 21.37 21.37 0.00 2.59
1897 2547 2.436911 AGTGTCAAAACCGGTAGACCTT 59.563 45.455 23.75 13.72 0.00 3.50
1901 2551 1.072648 CAAAACCGGTAGACCTTGGGA 59.927 52.381 8.00 0.00 0.00 4.37
1948 2598 2.223525 GGATCGAAGGTAACAGGAGACG 60.224 54.545 0.00 0.00 41.41 4.18
1958 2608 0.252284 ACAGGAGACGAAGGGGACAT 60.252 55.000 0.00 0.00 0.00 3.06
1978 2628 1.979308 TGATGTTTACCCAGGTTCGGA 59.021 47.619 0.00 0.00 0.00 4.55
2019 2669 2.578021 ACCCTACATCCTGCTTGATTGT 59.422 45.455 0.00 0.00 0.00 2.71
2020 2670 3.780294 ACCCTACATCCTGCTTGATTGTA 59.220 43.478 0.00 0.00 0.00 2.41
2021 2671 4.413520 ACCCTACATCCTGCTTGATTGTAT 59.586 41.667 0.00 0.00 0.00 2.29
2027 2677 6.802608 ACATCCTGCTTGATTGTATTTGATG 58.197 36.000 0.00 0.00 33.80 3.07
2028 2678 5.840243 TCCTGCTTGATTGTATTTGATGG 57.160 39.130 0.00 0.00 0.00 3.51
2092 2742 3.007074 GGCTAAACCCTAGATGTCTAGCC 59.993 52.174 16.28 16.28 43.47 3.93
2093 2743 3.305471 GCTAAACCCTAGATGTCTAGCCG 60.305 52.174 10.84 6.28 43.47 5.52
2134 2784 2.886382 CGGACTAAACCCTCCGGTA 58.114 57.895 0.00 0.00 43.71 4.02
2139 2789 4.397417 CGGACTAAACCCTCCGGTATATAG 59.603 50.000 0.00 0.95 43.71 1.31
2140 2790 5.574188 GGACTAAACCCTCCGGTATATAGA 58.426 45.833 0.00 0.00 43.71 1.98
2141 2791 5.417266 GGACTAAACCCTCCGGTATATAGAC 59.583 48.000 0.00 0.00 43.71 2.59
2144 2794 3.166560 ACCCTCCGGTATATAGACACC 57.833 52.381 0.00 0.00 42.18 4.16
2181 2832 6.350445 GGGTTGTATAGAGTCGGTTTACAGAA 60.350 42.308 0.00 0.00 0.00 3.02
2185 2836 8.752766 TGTATAGAGTCGGTTTACAGAAAAAG 57.247 34.615 0.00 0.00 0.00 2.27
2190 2841 6.600427 AGAGTCGGTTTACAGAAAAAGGAAAA 59.400 34.615 0.00 0.00 0.00 2.29
2191 2842 7.284716 AGAGTCGGTTTACAGAAAAAGGAAAAT 59.715 33.333 0.00 0.00 0.00 1.82
2192 2843 8.454570 AGTCGGTTTACAGAAAAAGGAAAATA 57.545 30.769 0.00 0.00 0.00 1.40
2193 2844 8.347771 AGTCGGTTTACAGAAAAAGGAAAATAC 58.652 33.333 0.00 0.00 0.00 1.89
2196 2847 7.380333 CGGTTTACAGAAAAAGGAAAATACACC 59.620 37.037 0.00 0.00 0.00 4.16
2203 2854 3.345508 AAGGAAAATACACCTCCGGAC 57.654 47.619 0.00 0.00 35.25 4.79
2204 2855 2.262637 AGGAAAATACACCTCCGGACA 58.737 47.619 0.00 0.00 34.22 4.02
2205 2856 2.844348 AGGAAAATACACCTCCGGACAT 59.156 45.455 0.00 0.00 34.22 3.06
2206 2857 3.265995 AGGAAAATACACCTCCGGACATT 59.734 43.478 0.00 0.00 34.22 2.71
2223 2874 2.030007 ACATTCAAACTTGCCATCCACG 60.030 45.455 0.00 0.00 0.00 4.94
2236 2887 0.250513 ATCCACGCAAAGGAGAGTCC 59.749 55.000 0.00 0.00 38.83 3.85
2240 2891 1.207089 CACGCAAAGGAGAGTCCCATA 59.793 52.381 1.17 0.00 37.19 2.74
2263 2914 3.330720 ACGGGGGAAGGCCTTCTG 61.331 66.667 37.72 27.45 39.45 3.02
2264 2915 4.803908 CGGGGGAAGGCCTTCTGC 62.804 72.222 37.72 25.12 39.45 4.26
2277 2928 3.549794 GCCTTCTGCCTTGTATCTTCAT 58.450 45.455 0.00 0.00 0.00 2.57
2278 2929 3.314635 GCCTTCTGCCTTGTATCTTCATG 59.685 47.826 0.00 0.00 0.00 3.07
2386 3037 0.898789 GGGACAAGGGACACGAGAGA 60.899 60.000 0.00 0.00 0.00 3.10
2396 3047 6.880942 AGGGACACGAGAGATTTATACTAC 57.119 41.667 0.00 0.00 0.00 2.73
2411 3062 0.323725 ACTACTTCGGCCCCTTACGA 60.324 55.000 0.00 0.00 37.33 3.43
2454 3110 7.007723 TCTAGTTGGGTTGGTATTGATGTTTT 58.992 34.615 0.00 0.00 0.00 2.43
2574 3231 1.040646 CTGCGGCTTATAGAGTCCCA 58.959 55.000 0.00 0.00 0.00 4.37
2576 3235 1.041437 GCGGCTTATAGAGTCCCAGT 58.959 55.000 0.00 0.00 0.00 4.00
2643 3302 6.263842 ACCTTATGATACAAGTCATGCCATTG 59.736 38.462 0.00 0.00 39.13 2.82
2644 3303 4.579454 ATGATACAAGTCATGCCATTGC 57.421 40.909 4.80 0.00 37.44 3.56
2660 3319 0.248539 TTGCGGCGGTTTGTTACAAC 60.249 50.000 9.78 0.00 0.00 3.32
2719 3378 0.035152 ACCGCCATCTTCATGCTTGA 60.035 50.000 0.00 0.00 0.00 3.02
2739 3398 2.276732 TCTTGGGCTTCTTTCTGGTG 57.723 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 214 0.671781 CAAAGCCCTCACACCTCTCG 60.672 60.000 0.00 0.00 0.00 4.04
222 225 3.219281 TCTTTCTTTTACGCAAAGCCCT 58.781 40.909 3.31 0.00 41.72 5.19
237 242 3.412386 CCGTGGTTTTCCTCATCTTTCT 58.588 45.455 0.00 0.00 41.38 2.52
238 243 2.488153 CCCGTGGTTTTCCTCATCTTTC 59.512 50.000 0.00 0.00 41.38 2.62
239 244 2.514803 CCCGTGGTTTTCCTCATCTTT 58.485 47.619 0.00 0.00 41.38 2.52
240 245 1.886655 GCCCGTGGTTTTCCTCATCTT 60.887 52.381 0.00 0.00 41.38 2.40
284 289 7.432252 GCTGTCGAATTTTCAGAAGAAGAAAAA 59.568 33.333 4.30 0.00 45.02 1.94
285 290 6.912591 GCTGTCGAATTTTCAGAAGAAGAAAA 59.087 34.615 4.30 3.89 45.68 2.29
286 291 6.430451 GCTGTCGAATTTTCAGAAGAAGAAA 58.570 36.000 4.30 0.00 34.71 2.52
287 292 5.049405 GGCTGTCGAATTTTCAGAAGAAGAA 60.049 40.000 4.30 0.00 34.71 2.52
289 294 4.667668 CGGCTGTCGAATTTTCAGAAGAAG 60.668 45.833 0.00 0.00 42.43 2.85
290 295 3.186409 CGGCTGTCGAATTTTCAGAAGAA 59.814 43.478 0.00 0.00 42.43 2.52
291 296 2.736721 CGGCTGTCGAATTTTCAGAAGA 59.263 45.455 0.00 0.00 42.43 2.87
292 297 2.736721 TCGGCTGTCGAATTTTCAGAAG 59.263 45.455 0.03 0.00 45.86 2.85
294 299 2.448926 TCGGCTGTCGAATTTTCAGA 57.551 45.000 0.03 0.00 45.86 3.27
594 776 2.260743 GTCGTCCGGTGAGGTTCC 59.739 66.667 0.00 0.00 41.99 3.62
648 830 2.047213 AAAAGTCGTCGCCTTCCCCA 62.047 55.000 0.00 0.00 0.00 4.96
711 893 2.515523 CCCATGGAGGCGCTCTTG 60.516 66.667 15.22 6.15 35.39 3.02
763 945 1.526887 CGCCCACACATCCTACCAT 59.473 57.895 0.00 0.00 0.00 3.55
787 969 1.598685 TTTTTCCCTGGCGTCGTCC 60.599 57.895 0.00 0.00 0.00 4.79
803 988 7.309805 GCCAACTTAACCCAGATGACTATTTTT 60.310 37.037 0.00 0.00 0.00 1.94
808 993 3.369052 CGCCAACTTAACCCAGATGACTA 60.369 47.826 0.00 0.00 0.00 2.59
810 995 1.737793 CGCCAACTTAACCCAGATGAC 59.262 52.381 0.00 0.00 0.00 3.06
817 1002 0.037160 TCCTTCCGCCAACTTAACCC 59.963 55.000 0.00 0.00 0.00 4.11
818 1003 2.124277 ATCCTTCCGCCAACTTAACC 57.876 50.000 0.00 0.00 0.00 2.85
821 1006 1.137479 CCGTATCCTTCCGCCAACTTA 59.863 52.381 0.00 0.00 0.00 2.24
822 1007 0.107848 CCGTATCCTTCCGCCAACTT 60.108 55.000 0.00 0.00 0.00 2.66
823 1008 1.520666 CCGTATCCTTCCGCCAACT 59.479 57.895 0.00 0.00 0.00 3.16
824 1009 1.523032 CCCGTATCCTTCCGCCAAC 60.523 63.158 0.00 0.00 0.00 3.77
825 1010 2.904905 CCCGTATCCTTCCGCCAA 59.095 61.111 0.00 0.00 0.00 4.52
826 1011 3.857038 GCCCGTATCCTTCCGCCA 61.857 66.667 0.00 0.00 0.00 5.69
827 1012 2.990830 GAAGCCCGTATCCTTCCGCC 62.991 65.000 0.00 0.00 33.13 6.13
828 1013 1.594564 GAAGCCCGTATCCTTCCGC 60.595 63.158 0.00 0.00 33.13 5.54
829 1014 1.299926 CGAAGCCCGTATCCTTCCG 60.300 63.158 0.00 0.00 35.23 4.30
830 1015 1.069258 CCGAAGCCCGTATCCTTCC 59.931 63.158 0.00 0.00 35.23 3.46
831 1016 0.177373 AACCGAAGCCCGTATCCTTC 59.823 55.000 0.00 0.00 36.31 3.46
832 1017 0.616891 AAACCGAAGCCCGTATCCTT 59.383 50.000 0.00 0.00 36.31 3.36
833 1018 0.616891 AAAACCGAAGCCCGTATCCT 59.383 50.000 0.00 0.00 36.31 3.24
834 1019 1.456296 AAAAACCGAAGCCCGTATCC 58.544 50.000 0.00 0.00 36.31 2.59
870 1055 0.611714 ACACTTATCCGGACACCACC 59.388 55.000 6.12 0.00 0.00 4.61
871 1056 2.073816 CAACACTTATCCGGACACCAC 58.926 52.381 6.12 0.00 0.00 4.16
872 1057 1.002659 CCAACACTTATCCGGACACCA 59.997 52.381 6.12 0.00 0.00 4.17
873 1058 1.734163 CCAACACTTATCCGGACACC 58.266 55.000 6.12 0.00 0.00 4.16
874 1059 1.084289 GCCAACACTTATCCGGACAC 58.916 55.000 6.12 0.00 0.00 3.67
875 1060 0.390603 CGCCAACACTTATCCGGACA 60.391 55.000 6.12 0.00 0.00 4.02
876 1061 0.390735 ACGCCAACACTTATCCGGAC 60.391 55.000 6.12 0.00 0.00 4.79
877 1062 1.184431 TACGCCAACACTTATCCGGA 58.816 50.000 6.61 6.61 0.00 5.14
893 1078 3.860125 CACGGGCGGTGCAATACG 61.860 66.667 12.41 0.00 40.33 3.06
901 1086 2.029964 CACAACTACACGGGCGGT 59.970 61.111 0.00 0.00 0.00 5.68
902 1087 1.161563 AAACACAACTACACGGGCGG 61.162 55.000 0.00 0.00 0.00 6.13
905 1282 2.545106 GGTACAAACACAACTACACGGG 59.455 50.000 0.00 0.00 0.00 5.28
910 1287 3.250040 CAGCCTGGTACAAACACAACTAC 59.750 47.826 0.00 0.00 38.70 2.73
928 1305 0.831307 AATCTAACCCGGACTCAGCC 59.169 55.000 0.73 0.00 0.00 4.85
942 1319 6.645827 CGGACTCGTAGATGAACTCTAATCTA 59.354 42.308 0.00 0.00 38.20 1.98
997 1376 3.676291 TTCGCTGCACATATATAGGCA 57.324 42.857 0.00 9.39 34.66 4.75
998 1377 3.557595 GGATTCGCTGCACATATATAGGC 59.442 47.826 0.00 1.78 0.00 3.93
999 1378 5.016051 AGGATTCGCTGCACATATATAGG 57.984 43.478 0.00 0.00 0.00 2.57
1000 1379 5.654497 TGAGGATTCGCTGCACATATATAG 58.346 41.667 0.00 0.00 0.00 1.31
1082 1470 2.223572 CGCACACAAGAAAGGAAGCTTT 60.224 45.455 0.00 0.00 0.00 3.51
1103 1491 6.355638 CGATAGTCAAGTCAGTCAAAAACAC 58.644 40.000 0.00 0.00 0.00 3.32
1105 1493 5.465724 ACCGATAGTCAAGTCAGTCAAAAAC 59.534 40.000 0.00 0.00 0.00 2.43
1364 1754 1.186917 CCATTTGCTTGCCCCAGTGA 61.187 55.000 0.00 0.00 0.00 3.41
1366 1756 1.152269 ACCATTTGCTTGCCCCAGT 60.152 52.632 0.00 0.00 0.00 4.00
1367 1757 1.593265 GACCATTTGCTTGCCCCAG 59.407 57.895 0.00 0.00 0.00 4.45
1442 1832 8.956426 TCATCGATTAATAATGAATAAAGCCCC 58.044 33.333 0.00 0.00 0.00 5.80
1513 1907 4.060038 ACCGGCTAAACATATCTGACAG 57.940 45.455 0.00 0.00 0.00 3.51
1628 2023 7.045126 ACAGAGTAGAGTATAGGAAATGCAC 57.955 40.000 0.00 0.00 0.00 4.57
1629 2024 7.661536 AACAGAGTAGAGTATAGGAAATGCA 57.338 36.000 0.00 0.00 0.00 3.96
1630 2025 8.417884 AGAAACAGAGTAGAGTATAGGAAATGC 58.582 37.037 0.00 0.00 0.00 3.56
1663 2079 1.265568 GTTGCAATCAAGCATCGCTG 58.734 50.000 0.59 0.00 45.19 5.18
1665 2081 1.700523 TTGTTGCAATCAAGCATCGC 58.299 45.000 0.59 0.00 45.19 4.58
1670 2095 4.863152 AAACAGTTTGTTGCAATCAAGC 57.137 36.364 0.59 10.91 40.14 4.01
1718 2145 5.975693 AAATTTAGCAGAATCGGTGGAAA 57.024 34.783 0.00 0.00 0.00 3.13
1799 2226 2.166254 CTCTTCTCCACTCTCTTCTGCC 59.834 54.545 0.00 0.00 0.00 4.85
1844 2494 0.036388 CTTCTTAACGGGCCTGAGCA 60.036 55.000 21.41 0.00 42.56 4.26
1852 2502 0.893447 ACGACCTCCTTCTTAACGGG 59.107 55.000 0.00 0.00 0.00 5.28
1868 2518 1.661617 CGGTTTTGACACTGACAACGA 59.338 47.619 0.00 0.00 0.00 3.85
1869 2519 1.267832 CCGGTTTTGACACTGACAACG 60.268 52.381 0.00 0.00 0.00 4.10
1870 2520 1.741145 ACCGGTTTTGACACTGACAAC 59.259 47.619 0.00 0.00 0.00 3.32
1871 2521 2.116827 ACCGGTTTTGACACTGACAA 57.883 45.000 0.00 0.00 0.00 3.18
1876 2526 2.044758 AGGTCTACCGGTTTTGACACT 58.955 47.619 25.56 19.58 42.08 3.55
1894 2544 3.282374 CGGAACCCCCTTCCCAAGG 62.282 68.421 0.00 0.00 45.50 3.61
1897 2547 2.121872 TTCGGAACCCCCTTCCCA 60.122 61.111 0.00 0.00 45.50 4.37
1901 2551 1.454539 CACAGTTCGGAACCCCCTT 59.545 57.895 16.84 0.00 0.00 3.95
1909 2559 1.285950 CTCAGACGCACAGTTCGGA 59.714 57.895 0.00 0.00 0.00 4.55
1948 2598 3.288092 GGGTAAACATCATGTCCCCTTC 58.712 50.000 11.31 0.00 32.86 3.46
1958 2608 1.979308 TCCGAACCTGGGTAAACATCA 59.021 47.619 0.00 0.00 0.00 3.07
1981 2631 3.701664 AGGGTTTTGCCTCCATTAAGAG 58.298 45.455 0.00 0.00 37.43 2.85
1994 2644 3.420893 TCAAGCAGGATGTAGGGTTTTG 58.579 45.455 0.00 0.00 39.31 2.44
1997 2647 3.010584 ACAATCAAGCAGGATGTAGGGTT 59.989 43.478 0.00 0.00 39.31 4.11
2005 2655 5.303589 CCCATCAAATACAATCAAGCAGGAT 59.696 40.000 0.00 0.00 0.00 3.24
2019 2669 7.573238 TCTTGTAACCCCTATACCCATCAAATA 59.427 37.037 0.00 0.00 0.00 1.40
2020 2670 6.391649 TCTTGTAACCCCTATACCCATCAAAT 59.608 38.462 0.00 0.00 0.00 2.32
2021 2671 5.732170 TCTTGTAACCCCTATACCCATCAAA 59.268 40.000 0.00 0.00 0.00 2.69
2027 2677 4.718276 TCAACTCTTGTAACCCCTATACCC 59.282 45.833 0.00 0.00 0.00 3.69
2028 2678 5.945144 TCAACTCTTGTAACCCCTATACC 57.055 43.478 0.00 0.00 0.00 2.73
2092 2742 6.909895 CGTAGAGGCTATCAGAATTCATATCG 59.090 42.308 8.44 0.00 0.00 2.92
2093 2743 7.067615 TCCGTAGAGGCTATCAGAATTCATATC 59.932 40.741 8.44 0.00 40.77 1.63
2134 2784 0.544595 GGCCCCTCCGGTGTCTATAT 60.545 60.000 0.00 0.00 0.00 0.86
2139 2789 3.155167 CTAGGCCCCTCCGGTGTC 61.155 72.222 0.00 0.00 40.77 3.67
2140 2790 4.798682 CCTAGGCCCCTCCGGTGT 62.799 72.222 0.00 0.00 40.77 4.16
2144 2794 2.884179 TACAACCCTAGGCCCCTCCG 62.884 65.000 2.05 0.00 40.77 4.63
2145 2795 0.401541 ATACAACCCTAGGCCCCTCC 60.402 60.000 2.05 0.00 0.00 4.30
2196 2847 1.200020 GGCAAGTTTGAATGTCCGGAG 59.800 52.381 3.06 0.00 0.00 4.63
2203 2854 2.598589 CGTGGATGGCAAGTTTGAATG 58.401 47.619 0.00 0.00 0.00 2.67
2204 2855 1.067635 GCGTGGATGGCAAGTTTGAAT 60.068 47.619 0.00 0.00 0.00 2.57
2205 2856 0.313672 GCGTGGATGGCAAGTTTGAA 59.686 50.000 0.00 0.00 0.00 2.69
2206 2857 0.821301 TGCGTGGATGGCAAGTTTGA 60.821 50.000 0.00 0.00 37.49 2.69
2223 2874 1.473434 CCGTATGGGACTCTCCTTTGC 60.473 57.143 0.00 0.00 38.47 3.68
2236 2887 2.306255 CTTCCCCCGTGTCCGTATGG 62.306 65.000 0.00 0.00 0.00 2.74
2264 2915 3.209410 GACAGGCCATGAAGATACAAGG 58.791 50.000 5.01 0.00 0.00 3.61
2277 2928 0.605319 GACAATTCCACGACAGGCCA 60.605 55.000 5.01 0.00 0.00 5.36
2278 2929 0.605319 TGACAATTCCACGACAGGCC 60.605 55.000 0.00 0.00 0.00 5.19
2386 3037 5.279156 CGTAAGGGGCCGAAGTAGTATAAAT 60.279 44.000 0.00 0.00 0.00 1.40
2396 3047 0.177141 TTCATCGTAAGGGGCCGAAG 59.823 55.000 0.00 0.00 36.57 3.79
2454 3110 0.397675 ATCTCGCTCCCTGGTCATCA 60.398 55.000 0.00 0.00 0.00 3.07
2565 3222 2.750141 ATAAGCCGACTGGGACTCTA 57.250 50.000 0.00 0.00 38.47 2.43
2574 3231 3.675228 CGGACACTGTTTATAAGCCGACT 60.675 47.826 0.00 0.00 39.85 4.18
2576 3235 2.417651 CCGGACACTGTTTATAAGCCGA 60.418 50.000 0.00 0.00 39.85 5.54
2643 3302 1.723197 CGTTGTAACAAACCGCCGC 60.723 57.895 0.00 0.00 0.00 6.53
2644 3303 1.082627 CCGTTGTAACAAACCGCCG 60.083 57.895 0.00 0.00 0.00 6.46
2653 3312 1.728425 CGACTTAAGGCCCGTTGTAAC 59.272 52.381 7.53 0.00 0.00 2.50
2654 3313 1.940752 GCGACTTAAGGCCCGTTGTAA 60.941 52.381 7.53 0.00 0.00 2.41
2719 3378 2.376518 TCACCAGAAAGAAGCCCAAGAT 59.623 45.455 0.00 0.00 0.00 2.40
2739 3398 1.725164 CGGGTTACGCAAAGAAGACTC 59.275 52.381 0.00 0.00 34.82 3.36


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

AutoCloner maintained by Alex Coulton.