Multiple sequence alignment - TraesCS7D01G036500

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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 TraesCS7D01G036500 chr7D 100.000 2877 0 0 1 2877 18630650 18633526 0.000000e+00 5313
1 TraesCS7D01G036500 chr7D 86.556 1205 140 13 747 1949 18589159 18590343 0.000000e+00 1308
2 TraesCS7D01G036500 chr7D 91.656 755 45 8 1 743 18588286 18589034 0.000000e+00 1029
3 TraesCS7D01G036500 chr4A 88.196 1364 128 15 745 2106 714192522 714191190 0.000000e+00 1596
4 TraesCS7D01G036500 chr4A 92.493 746 44 8 1 746 714193375 714192642 0.000000e+00 1057
5 TraesCS7D01G036500 chr7A 85.484 1364 152 22 747 2108 18996252 18997571 0.000000e+00 1380
6 TraesCS7D01G036500 chr7A 91.957 746 42 5 1 734 18995379 18996118 0.000000e+00 1029
7 TraesCS7D01G036500 chr6D 98.456 777 10 2 2103 2877 6277307 6278083 0.000000e+00 1367
8 TraesCS7D01G036500 chr6D 97.927 772 15 1 2107 2877 28099024 28099795 0.000000e+00 1336
9 TraesCS7D01G036500 chr6D 99.200 625 5 0 2107 2731 10967280 10966656 0.000000e+00 1127
10 TraesCS7D01G036500 chr2D 98.701 770 8 2 2109 2877 636770551 636769783 0.000000e+00 1365
11 TraesCS7D01G036500 chr2D 98.452 775 9 3 2105 2877 612821142 612821915 0.000000e+00 1362
12 TraesCS7D01G036500 chr2D 97.674 774 14 2 2108 2877 5614697 5613924 0.000000e+00 1327
13 TraesCS7D01G036500 chr2D 97.671 773 15 3 2106 2877 617940560 617939790 0.000000e+00 1325
14 TraesCS7D01G036500 chr2D 99.201 626 5 0 2106 2731 431423409 431422784 0.000000e+00 1129
15 TraesCS7D01G036500 chr1D 97.290 775 12 4 2105 2877 2193380 2192613 0.000000e+00 1306
16 TraesCS7D01G036500 chr1D 94.043 789 14 4 2109 2877 486238844 486238069 0.000000e+00 1166
17 TraesCS7D01G036500 chr1A 79.385 553 90 15 1413 1959 12404901 12404367 4.530000e-98 368
18 TraesCS7D01G036500 chr1A 84.127 189 26 4 457 643 12834883 12834697 2.280000e-41 180
19 TraesCS7D01G036500 chr1B 82.065 184 26 6 457 635 15659594 15659775 1.790000e-32 150


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 TraesCS7D01G036500 chr7D 18630650 18633526 2876 False 5313.0 5313 100.0000 1 2877 1 chr7D.!!$F1 2876
1 TraesCS7D01G036500 chr7D 18588286 18590343 2057 False 1168.5 1308 89.1060 1 1949 2 chr7D.!!$F2 1948
2 TraesCS7D01G036500 chr4A 714191190 714193375 2185 True 1326.5 1596 90.3445 1 2106 2 chr4A.!!$R1 2105
3 TraesCS7D01G036500 chr7A 18995379 18997571 2192 False 1204.5 1380 88.7205 1 2108 2 chr7A.!!$F1 2107
4 TraesCS7D01G036500 chr6D 6277307 6278083 776 False 1367.0 1367 98.4560 2103 2877 1 chr6D.!!$F1 774
5 TraesCS7D01G036500 chr6D 28099024 28099795 771 False 1336.0 1336 97.9270 2107 2877 1 chr6D.!!$F2 770
6 TraesCS7D01G036500 chr6D 10966656 10967280 624 True 1127.0 1127 99.2000 2107 2731 1 chr6D.!!$R1 624
7 TraesCS7D01G036500 chr2D 636769783 636770551 768 True 1365.0 1365 98.7010 2109 2877 1 chr2D.!!$R4 768
8 TraesCS7D01G036500 chr2D 612821142 612821915 773 False 1362.0 1362 98.4520 2105 2877 1 chr2D.!!$F1 772
9 TraesCS7D01G036500 chr2D 5613924 5614697 773 True 1327.0 1327 97.6740 2108 2877 1 chr2D.!!$R1 769
10 TraesCS7D01G036500 chr2D 617939790 617940560 770 True 1325.0 1325 97.6710 2106 2877 1 chr2D.!!$R3 771
11 TraesCS7D01G036500 chr2D 431422784 431423409 625 True 1129.0 1129 99.2010 2106 2731 1 chr2D.!!$R2 625
12 TraesCS7D01G036500 chr1D 2192613 2193380 767 True 1306.0 1306 97.2900 2105 2877 1 chr1D.!!$R1 772
13 TraesCS7D01G036500 chr1D 486238069 486238844 775 True 1166.0 1166 94.0430 2109 2877 1 chr1D.!!$R2 768
14 TraesCS7D01G036500 chr1A 12404367 12404901 534 True 368.0 368 79.3850 1413 1959 1 chr1A.!!$R1 546

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
349 353 0.109153 AAGACAGCAGCATCCACACA 59.891 50.000 0.0 0.0 0.00 3.72 F
886 1026 1.141053 GGTTTGTCTGTGGTCTCACCT 59.859 52.381 0.0 0.0 42.98 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1812 0.527385 GAACAGCTTGTTTTGCGGCA 60.527 50.0 0.00 0.0 41.28 5.69 R
2021 2183 0.606130 TGTCGTCATGCATGGCAAGT 60.606 50.0 29.36 0.0 43.62 3.16 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
25 26 0.952984 GCAGGATGATAAGGCGGCTC 60.953 60.000 13.70 0.00 39.69 4.70
83 84 1.134818 TGCTTCATACGCTGGATTCGT 60.135 47.619 0.00 0.00 43.20 3.85
151 152 2.125310 CACGTTGCCAGCGGGATA 60.125 61.111 7.23 0.00 34.18 2.59
232 233 0.978146 AATACTGCCGACTCCAGCCT 60.978 55.000 0.00 0.00 33.65 4.58
272 276 1.867233 CCTCCTCACTGAACACAAACG 59.133 52.381 0.00 0.00 0.00 3.60
349 353 0.109153 AAGACAGCAGCATCCACACA 59.891 50.000 0.00 0.00 0.00 3.72
382 386 4.730966 AGTCAGAGTTGGAGTACTCAGAA 58.269 43.478 23.91 13.01 45.57 3.02
563 582 4.340381 GCAAAGCCAAATATCCTGTCTCAT 59.660 41.667 0.00 0.00 0.00 2.90
626 645 3.198635 AGGTCATAGTGAATGGTCCACTG 59.801 47.826 0.00 0.00 43.90 3.66
634 653 2.832129 TGAATGGTCCACTGAGGTAGTC 59.168 50.000 0.00 0.00 37.60 2.59
635 654 1.867363 ATGGTCCACTGAGGTAGTCC 58.133 55.000 0.00 0.00 37.60 3.85
646 665 4.892934 ACTGAGGTAGTCCAGAGATCATTC 59.107 45.833 0.00 0.00 33.17 2.67
652 671 1.337071 GTCCAGAGATCATTCGCGGTA 59.663 52.381 6.13 0.00 0.00 4.02
659 678 2.545526 AGATCATTCGCGGTAATGCTTG 59.454 45.455 13.96 0.00 36.89 4.01
690 709 2.435805 TGACTGCCAAGAGAGAAACTGT 59.564 45.455 0.00 0.00 0.00 3.55
691 710 3.641436 TGACTGCCAAGAGAGAAACTGTA 59.359 43.478 0.00 0.00 0.00 2.74
696 715 3.748568 GCCAAGAGAGAAACTGTAACAGG 59.251 47.826 0.00 0.00 35.51 4.00
735 754 5.131642 TGTCAGAGGATAAGGAAGCAATCAT 59.868 40.000 0.00 0.00 0.00 2.45
739 758 5.131642 AGAGGATAAGGAAGCAATCATCACA 59.868 40.000 0.00 0.00 33.91 3.58
772 912 8.942338 AATCTTCGTTAATGTTGATAGCAGTA 57.058 30.769 0.00 0.00 0.00 2.74
813 953 4.890088 CAGTTAAAGCACTGGTGGTACTA 58.110 43.478 5.85 0.00 40.60 1.82
874 1014 4.089361 GGAGGAAAATGATGGGTTTGTCT 58.911 43.478 0.00 0.00 0.00 3.41
886 1026 1.141053 GGTTTGTCTGTGGTCTCACCT 59.859 52.381 0.00 0.00 42.98 4.00
904 1044 6.160992 TCTCACCTAAATACTAGTAGGGGACA 59.839 42.308 9.89 0.00 43.59 4.02
920 1060 2.163010 GGGACAATGACACATGCAGAAG 59.837 50.000 0.00 0.00 0.00 2.85
946 1086 2.165845 GCAGCAGAAATTCTGGAGCATT 59.834 45.455 22.73 0.00 44.43 3.56
948 1088 4.174009 CAGCAGAAATTCTGGAGCATTTG 58.826 43.478 22.73 1.96 44.43 2.32
951 1091 3.924686 CAGAAATTCTGGAGCATTTGTGC 59.075 43.478 14.85 0.00 40.71 4.57
954 1094 4.546829 AATTCTGGAGCATTTGTGCATT 57.453 36.364 3.03 0.00 37.25 3.56
977 1117 6.628919 TCATTATGCTGAGAATGGTGAATG 57.371 37.500 0.00 0.00 32.55 2.67
1007 1147 1.848388 ACTCAGGAATGCCATGATGGA 59.152 47.619 17.22 0.43 40.96 3.41
1008 1148 2.445905 ACTCAGGAATGCCATGATGGAT 59.554 45.455 17.22 3.08 40.96 3.41
1085 1226 6.486253 TCTTTCTTTTCATTCCTCGACATG 57.514 37.500 0.00 0.00 0.00 3.21
1096 1237 2.002586 CCTCGACATGTTTACAGCCAG 58.997 52.381 0.00 0.00 0.00 4.85
1097 1238 2.002586 CTCGACATGTTTACAGCCAGG 58.997 52.381 0.00 0.00 0.00 4.45
1110 1251 3.297391 GCCAGGGCGAATTCTCTAG 57.703 57.895 3.52 0.00 0.00 2.43
1119 1260 2.473816 CGAATTCTCTAGCCAATCGCA 58.526 47.619 3.52 0.00 41.38 5.10
1132 1281 3.244345 GCCAATCGCACATTCATTCATTG 59.756 43.478 0.00 0.00 37.47 2.82
1143 1292 5.721000 ACATTCATTCATTGCCCTTTCCTAA 59.279 36.000 0.00 0.00 0.00 2.69
1144 1293 5.659440 TTCATTCATTGCCCTTTCCTAAC 57.341 39.130 0.00 0.00 0.00 2.34
1145 1294 4.671831 TCATTCATTGCCCTTTCCTAACA 58.328 39.130 0.00 0.00 0.00 2.41
1146 1295 5.083122 TCATTCATTGCCCTTTCCTAACAA 58.917 37.500 0.00 0.00 0.00 2.83
1147 1296 4.864704 TTCATTGCCCTTTCCTAACAAC 57.135 40.909 0.00 0.00 0.00 3.32
1148 1297 3.161866 TCATTGCCCTTTCCTAACAACC 58.838 45.455 0.00 0.00 0.00 3.77
1149 1298 2.757894 TTGCCCTTTCCTAACAACCA 57.242 45.000 0.00 0.00 0.00 3.67
1150 1299 2.757894 TGCCCTTTCCTAACAACCAA 57.242 45.000 0.00 0.00 0.00 3.67
1151 1300 3.252554 TGCCCTTTCCTAACAACCAAT 57.747 42.857 0.00 0.00 0.00 3.16
1152 1301 2.896685 TGCCCTTTCCTAACAACCAATG 59.103 45.455 0.00 0.00 0.00 2.82
1153 1302 2.233676 GCCCTTTCCTAACAACCAATGG 59.766 50.000 0.00 0.00 0.00 3.16
1154 1303 2.831526 CCCTTTCCTAACAACCAATGGG 59.168 50.000 3.55 0.00 41.29 4.00
1155 1304 2.233676 CCTTTCCTAACAACCAATGGGC 59.766 50.000 3.55 0.00 37.90 5.36
1156 1305 2.685106 TTCCTAACAACCAATGGGCA 57.315 45.000 3.55 0.00 37.90 5.36
1157 1306 1.917872 TCCTAACAACCAATGGGCAC 58.082 50.000 3.55 0.00 37.90 5.01
1158 1307 1.145945 TCCTAACAACCAATGGGCACA 59.854 47.619 3.55 0.00 37.90 4.57
1159 1308 2.178580 CCTAACAACCAATGGGCACAT 58.821 47.619 3.55 0.00 39.54 3.21
1161 1310 3.007831 CCTAACAACCAATGGGCACATTT 59.992 43.478 12.63 0.00 44.69 2.32
1162 1311 2.837532 ACAACCAATGGGCACATTTC 57.162 45.000 12.63 0.00 44.69 2.17
1163 1312 1.347378 ACAACCAATGGGCACATTTCC 59.653 47.619 12.63 0.00 44.69 3.13
1164 1313 1.624813 CAACCAATGGGCACATTTCCT 59.375 47.619 12.63 0.00 44.69 3.36
1165 1314 2.028561 ACCAATGGGCACATTTCCTT 57.971 45.000 12.63 0.00 44.69 3.36
1252 1401 5.932619 ATACACTATTGTCACCACTGCTA 57.067 39.130 0.00 0.00 37.15 3.49
1253 1402 4.826274 ACACTATTGTCACCACTGCTAT 57.174 40.909 0.00 0.00 0.00 2.97
1280 1429 5.288952 GTGCTCGAAGAAATACTACTTGGTC 59.711 44.000 0.00 0.00 34.09 4.02
1296 1445 1.746517 GTCGTGAGTCAACAGGGGT 59.253 57.895 0.00 0.00 0.00 4.95
1324 1473 5.952947 AGGAATTCCCGAATATACGAGATCT 59.047 40.000 21.22 0.00 40.87 2.75
1331 1480 4.379603 CCGAATATACGAGATCTGGTGGTC 60.380 50.000 19.53 10.18 35.09 4.02
1344 1493 1.305930 GGTGGTCATGTCGAAAGCCC 61.306 60.000 0.00 0.00 0.00 5.19
1352 1501 3.055458 TCATGTCGAAAGCCCAGTCATTA 60.055 43.478 0.00 0.00 0.00 1.90
1409 1558 3.393941 CTCCCATCCTAGGCAGAAGAAAT 59.606 47.826 2.96 0.00 0.00 2.17
1423 1572 3.503748 AGAAGAAATACCACAAGCTGCAC 59.496 43.478 1.02 0.00 0.00 4.57
1477 1626 6.174720 TGTGACAAACTAGACCTTGATCTT 57.825 37.500 0.00 0.00 0.00 2.40
1480 1629 6.876257 GTGACAAACTAGACCTTGATCTTGAT 59.124 38.462 0.00 0.00 0.00 2.57
1483 1632 5.690464 AACTAGACCTTGATCTTGATGCT 57.310 39.130 0.00 0.00 0.00 3.79
1489 1638 6.656902 AGACCTTGATCTTGATGCTATTTCA 58.343 36.000 0.00 0.00 0.00 2.69
1551 1700 3.118149 TGTGTCATGATCAGCCTTGCTAT 60.118 43.478 0.00 0.00 36.40 2.97
1557 1706 3.801698 TGATCAGCCTTGCTATGAAGAC 58.198 45.455 0.00 0.00 36.40 3.01
1558 1707 3.198417 TGATCAGCCTTGCTATGAAGACA 59.802 43.478 0.00 0.00 36.40 3.41
1579 1728 3.438087 CAGTGCAGTTAAACAGGGATCTG 59.562 47.826 0.00 0.00 46.10 2.90
1663 1812 2.226962 AACTCAAGAGCCATGGCAAT 57.773 45.000 37.18 22.78 44.88 3.56
1835 1984 2.672651 CACGGCAACTCCATGGCA 60.673 61.111 6.96 0.00 45.50 4.92
1843 1992 4.516323 GGCAACTCCATGGCAAAATTAAT 58.484 39.130 6.96 0.00 44.66 1.40
1846 1995 5.732633 CAACTCCATGGCAAAATTAATGGA 58.267 37.500 6.96 3.89 44.90 3.41
1855 2004 5.095490 GGCAAAATTAATGGACAAGACTCG 58.905 41.667 0.00 0.00 0.00 4.18
1876 2025 4.760715 TCGGAAATAGTACCAGCTAGCTAG 59.239 45.833 18.86 16.84 0.00 3.42
1934 2087 7.383029 TGCAACAGATTTGCTTCAGATTTTTAG 59.617 33.333 10.15 0.00 45.13 1.85
1937 2090 9.468532 AACAGATTTGCTTCAGATTTTTAGTTC 57.531 29.630 0.00 0.00 0.00 3.01
1960 2113 2.128035 GATAGGGATTTGCGTCTGTCG 58.872 52.381 0.00 0.00 43.12 4.35
1962 2115 0.389948 AGGGATTTGCGTCTGTCGAC 60.390 55.000 9.11 9.11 42.86 4.20
1964 2117 0.716108 GGATTTGCGTCTGTCGACTG 59.284 55.000 17.92 16.72 42.86 3.51
1965 2118 1.419374 GATTTGCGTCTGTCGACTGT 58.581 50.000 17.92 0.00 42.86 3.55
1967 2120 0.933047 TTTGCGTCTGTCGACTGTCG 60.933 55.000 27.91 27.91 42.86 4.35
1968 2121 2.055310 TTGCGTCTGTCGACTGTCGT 62.055 55.000 30.37 0.00 41.35 4.34
1969 2122 1.370172 GCGTCTGTCGACTGTCGTT 60.370 57.895 30.37 0.00 41.35 3.85
1970 2123 1.328685 GCGTCTGTCGACTGTCGTTC 61.329 60.000 30.37 20.93 41.35 3.95
1971 2124 0.041576 CGTCTGTCGACTGTCGTTCA 60.042 55.000 27.16 23.64 41.35 3.18
1972 2125 1.396644 GTCTGTCGACTGTCGTTCAC 58.603 55.000 27.16 19.16 41.35 3.18
1973 2126 0.309922 TCTGTCGACTGTCGTTCACC 59.690 55.000 27.16 12.95 41.35 4.02
1974 2127 0.311165 CTGTCGACTGTCGTTCACCT 59.689 55.000 27.16 0.00 41.35 4.00
1975 2128 0.309922 TGTCGACTGTCGTTCACCTC 59.690 55.000 27.16 11.85 41.35 3.85
1976 2129 0.725118 GTCGACTGTCGTTCACCTCG 60.725 60.000 27.16 1.84 41.35 4.63
1977 2130 1.162181 TCGACTGTCGTTCACCTCGT 61.162 55.000 27.16 0.00 41.35 4.18
1978 2131 0.317603 CGACTGTCGTTCACCTCGTT 60.318 55.000 21.30 0.00 34.72 3.85
1979 2132 1.406447 GACTGTCGTTCACCTCGTTC 58.594 55.000 0.00 0.00 0.00 3.95
1980 2133 1.001597 GACTGTCGTTCACCTCGTTCT 60.002 52.381 0.00 0.00 0.00 3.01
1981 2134 2.224606 ACTGTCGTTCACCTCGTTCTA 58.775 47.619 0.00 0.00 0.00 2.10
1990 2152 3.008330 TCACCTCGTTCTACTCTACTGC 58.992 50.000 0.00 0.00 0.00 4.40
2021 2183 9.857957 TGTCGTATTGTATTACTATGTTTCACA 57.142 29.630 1.64 0.00 0.00 3.58
2435 2619 5.337330 CCCTTCACTATAAAAGACGTGGTCT 60.337 44.000 0.00 0.00 45.64 3.85
2560 2744 5.006746 CGGACTTGCATCTTAAGGTATGAAC 59.993 44.000 1.85 0.00 0.00 3.18
2732 2916 4.340617 TCTTGCGGGGAATTAAACTTGAT 58.659 39.130 0.00 0.00 0.00 2.57
2734 2918 5.946972 TCTTGCGGGGAATTAAACTTGATTA 59.053 36.000 0.00 0.00 0.00 1.75
2735 2919 6.434652 TCTTGCGGGGAATTAAACTTGATTAA 59.565 34.615 0.00 0.00 0.00 1.40
2739 2923 8.097662 TGCGGGGAATTAAACTTGATTAAATTT 58.902 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.899239 GAGGCTGCGGACCCGATG 62.899 72.222 13.24 4.81 42.83 3.84
83 84 1.365633 GTTTGTCAAATGGGCGCCA 59.634 52.632 30.85 15.30 38.19 5.69
151 152 0.464916 GTGGGAACTGGACCAAACGT 60.465 55.000 0.00 0.00 38.73 3.99
232 233 4.336280 AGGAGGATGACGATGATCGATAA 58.664 43.478 22.88 6.59 43.74 1.75
272 276 2.231721 GTGGAGTCCTTGTAGTGTCTCC 59.768 54.545 11.33 0.00 41.00 3.71
349 353 2.208132 ACTCTGACTCCAGTGTCGAT 57.792 50.000 0.00 0.00 41.68 3.59
382 386 5.508567 TCTGATTCTGACTCTGACTCTGAT 58.491 41.667 8.02 0.00 0.00 2.90
563 582 1.270305 GCTAACAGGCGCCATGATCTA 60.270 52.381 31.54 15.22 0.00 1.98
626 645 3.305064 GCGAATGATCTCTGGACTACCTC 60.305 52.174 0.00 0.00 37.04 3.85
634 653 2.509052 TTACCGCGAATGATCTCTGG 57.491 50.000 8.23 0.00 0.00 3.86
635 654 2.156504 GCATTACCGCGAATGATCTCTG 59.843 50.000 20.88 0.00 38.83 3.35
646 665 1.092921 TTAGGCCAAGCATTACCGCG 61.093 55.000 5.01 0.00 36.85 6.46
652 671 3.194116 CAGTCACAATTAGGCCAAGCATT 59.806 43.478 5.01 0.00 0.00 3.56
659 678 1.474077 CTTGGCAGTCACAATTAGGCC 59.526 52.381 0.00 0.00 41.70 5.19
690 709 1.419762 TCTGTTGAAGCAGGCCTGTTA 59.580 47.619 32.81 11.49 37.12 2.41
691 710 0.183492 TCTGTTGAAGCAGGCCTGTT 59.817 50.000 32.81 25.91 37.12 3.16
696 715 1.467734 CTGACATCTGTTGAAGCAGGC 59.532 52.381 0.00 0.00 37.12 4.85
735 754 7.390440 ACATTAACGAAGATTCTTCCATTGTGA 59.610 33.333 18.46 3.59 0.00 3.58
739 758 8.335532 TCAACATTAACGAAGATTCTTCCATT 57.664 30.769 18.46 15.23 0.00 3.16
772 912 4.929479 ACTGTAGTCTCTCTGATGGAGTT 58.071 43.478 0.00 0.00 42.40 3.01
874 1014 6.832384 CCTACTAGTATTTAGGTGAGACCACA 59.168 42.308 2.33 0.00 44.93 4.17
886 1026 7.620491 TGTGTCATTGTCCCCTACTAGTATTTA 59.380 37.037 2.33 0.00 0.00 1.40
904 1044 3.057736 GCACTTCTTCTGCATGTGTCATT 60.058 43.478 0.00 0.00 34.56 2.57
920 1060 2.816087 TCCAGAATTTCTGCTGCACTTC 59.184 45.455 19.04 0.01 42.98 3.01
951 1091 6.628919 TCACCATTCTCAGCATAATGAATG 57.371 37.500 0.00 0.00 42.93 2.67
954 1094 6.038936 CACATTCACCATTCTCAGCATAATGA 59.961 38.462 0.00 0.00 35.53 2.57
992 1132 2.589720 TCACATCCATCATGGCATTCC 58.410 47.619 0.00 0.00 37.47 3.01
1007 1147 4.207165 GGTACATACCTTTGGCATCACAT 58.793 43.478 0.49 0.00 43.10 3.21
1008 1148 3.616219 GGTACATACCTTTGGCATCACA 58.384 45.455 0.49 0.00 43.10 3.58
1085 1226 1.132453 GAATTCGCCCTGGCTGTAAAC 59.868 52.381 6.60 0.00 39.32 2.01
1096 1237 2.147150 GATTGGCTAGAGAATTCGCCC 58.853 52.381 16.52 7.59 41.80 6.13
1097 1238 1.795286 CGATTGGCTAGAGAATTCGCC 59.205 52.381 13.43 13.43 42.78 5.54
1110 1251 2.565210 TGAATGAATGTGCGATTGGC 57.435 45.000 0.00 0.00 43.96 4.52
1112 1253 3.244345 GGCAATGAATGAATGTGCGATTG 59.756 43.478 0.00 0.00 36.04 2.67
1119 1260 4.098894 AGGAAAGGGCAATGAATGAATGT 58.901 39.130 0.00 0.00 0.00 2.71
1132 1281 2.233676 CCATTGGTTGTTAGGAAAGGGC 59.766 50.000 0.00 0.00 0.00 5.19
1143 1292 1.347378 GGAAATGTGCCCATTGGTTGT 59.653 47.619 1.20 0.00 40.42 3.32
1144 1293 1.624813 AGGAAATGTGCCCATTGGTTG 59.375 47.619 1.20 0.00 40.42 3.77
1145 1294 2.028561 AGGAAATGTGCCCATTGGTT 57.971 45.000 1.20 0.00 40.42 3.67
1146 1295 2.028561 AAGGAAATGTGCCCATTGGT 57.971 45.000 1.20 0.00 40.42 3.67
1147 1296 3.099141 AGTAAGGAAATGTGCCCATTGG 58.901 45.455 0.00 0.00 40.42 3.16
1148 1297 4.806640 AAGTAAGGAAATGTGCCCATTG 57.193 40.909 0.00 0.00 40.42 2.82
1149 1298 4.592778 ACAAAGTAAGGAAATGTGCCCATT 59.407 37.500 0.00 0.00 43.14 3.16
1150 1299 4.021192 CACAAAGTAAGGAAATGTGCCCAT 60.021 41.667 0.00 0.00 35.50 4.00
1151 1300 3.320541 CACAAAGTAAGGAAATGTGCCCA 59.679 43.478 0.00 0.00 35.50 5.36
1152 1301 3.320826 ACACAAAGTAAGGAAATGTGCCC 59.679 43.478 4.27 0.00 43.89 5.36
1153 1302 4.584327 ACACAAAGTAAGGAAATGTGCC 57.416 40.909 4.27 0.00 43.89 5.01
1154 1303 6.039616 TCAAACACAAAGTAAGGAAATGTGC 58.960 36.000 4.27 0.00 43.89 4.57
1155 1304 8.647143 AATCAAACACAAAGTAAGGAAATGTG 57.353 30.769 2.90 2.90 45.18 3.21
1156 1305 9.097257 CAAATCAAACACAAAGTAAGGAAATGT 57.903 29.630 0.00 0.00 0.00 2.71
1157 1306 9.097257 ACAAATCAAACACAAAGTAAGGAAATG 57.903 29.630 0.00 0.00 0.00 2.32
1186 1335 5.486526 AGAATGTTTGCAACCACTTCAAAA 58.513 33.333 15.82 0.00 32.36 2.44
1195 1344 9.369904 ACATAAATATTGAGAATGTTTGCAACC 57.630 29.630 0.00 0.00 34.60 3.77
1245 1394 2.359214 TCTTCGAGCACCTATAGCAGTG 59.641 50.000 5.12 5.12 37.05 3.66
1252 1401 6.963083 AGTAGTATTTCTTCGAGCACCTAT 57.037 37.500 0.00 0.00 0.00 2.57
1253 1402 6.405508 CCAAGTAGTATTTCTTCGAGCACCTA 60.406 42.308 0.00 0.00 0.00 3.08
1280 1429 1.254026 TCTACCCCTGTTGACTCACG 58.746 55.000 0.00 0.00 0.00 4.35
1296 1445 6.944290 TCTCGTATATTCGGGAATTCCTTCTA 59.056 38.462 23.63 10.86 37.38 2.10
1324 1473 0.605319 GGCTTTCGACATGACCACCA 60.605 55.000 0.00 0.00 0.00 4.17
1331 1480 1.742761 ATGACTGGGCTTTCGACATG 58.257 50.000 0.00 0.00 0.00 3.21
1344 1493 5.337554 TCTTATCGTTGTCCGTAATGACTG 58.662 41.667 0.00 0.00 36.21 3.51
1352 1501 4.247267 TGTTCTTCTTATCGTTGTCCGT 57.753 40.909 0.00 0.00 37.94 4.69
1409 1558 1.781025 GCAACGTGCAGCTTGTGGTA 61.781 55.000 0.00 0.00 44.26 3.25
1423 1572 0.749649 AGAGGGATAGCAGAGCAACG 59.250 55.000 0.00 0.00 0.00 4.10
1477 1626 4.384537 CCTTCTCCCAGTGAAATAGCATCA 60.385 45.833 0.00 0.00 0.00 3.07
1480 1629 3.181329 TCCTTCTCCCAGTGAAATAGCA 58.819 45.455 0.00 0.00 0.00 3.49
1483 1632 5.342017 TCTCTTCCTTCTCCCAGTGAAATA 58.658 41.667 0.00 0.00 0.00 1.40
1489 1638 3.481559 TGATCTCTTCCTTCTCCCAGT 57.518 47.619 0.00 0.00 0.00 4.00
1551 1700 3.876914 CCTGTTTAACTGCACTGTCTTCA 59.123 43.478 0.00 0.00 0.00 3.02
1557 1706 3.438087 CAGATCCCTGTTTAACTGCACTG 59.562 47.826 0.00 0.00 35.70 3.66
1558 1707 3.679389 CAGATCCCTGTTTAACTGCACT 58.321 45.455 0.00 0.00 35.70 4.40
1663 1812 0.527385 GAACAGCTTGTTTTGCGGCA 60.527 50.000 0.00 0.00 41.28 5.69
1782 1931 0.745845 ATCGAGGGTGTCAGCAATGC 60.746 55.000 0.00 0.00 0.00 3.56
1835 1984 7.519032 TTTCCGAGTCTTGTCCATTAATTTT 57.481 32.000 0.00 0.00 0.00 1.82
1843 1992 4.159135 GGTACTATTTCCGAGTCTTGTCCA 59.841 45.833 0.00 0.00 0.00 4.02
1846 1995 4.381718 GCTGGTACTATTTCCGAGTCTTGT 60.382 45.833 0.00 0.00 0.00 3.16
1855 2004 4.811908 GCTAGCTAGCTGGTACTATTTCC 58.188 47.826 33.71 4.21 45.62 3.13
1876 2025 2.079158 TGTTTGCATGAGACAGCTAGC 58.921 47.619 6.62 6.62 0.00 3.42
1877 2026 3.750130 AGTTGTTTGCATGAGACAGCTAG 59.250 43.478 0.00 0.00 33.88 3.42
1878 2027 3.743521 AGTTGTTTGCATGAGACAGCTA 58.256 40.909 0.00 0.00 33.88 3.32
1879 2028 2.579873 AGTTGTTTGCATGAGACAGCT 58.420 42.857 0.00 1.99 31.30 4.24
1934 2087 4.034510 CAGACGCAAATCCCTATCTTGAAC 59.965 45.833 0.00 0.00 0.00 3.18
1937 2090 3.535561 ACAGACGCAAATCCCTATCTTG 58.464 45.455 0.00 0.00 0.00 3.02
1960 2113 1.001597 AGAACGAGGTGAACGACAGTC 60.002 52.381 0.00 0.00 34.70 3.51
1962 2115 2.225963 AGTAGAACGAGGTGAACGACAG 59.774 50.000 0.00 0.00 34.70 3.51
1964 2117 2.483491 AGAGTAGAACGAGGTGAACGAC 59.517 50.000 0.00 0.00 34.70 4.34
1965 2118 2.775890 AGAGTAGAACGAGGTGAACGA 58.224 47.619 0.00 0.00 34.70 3.85
1967 2120 4.672283 GCAGTAGAGTAGAACGAGGTGAAC 60.672 50.000 0.00 0.00 0.00 3.18
1968 2121 3.439476 GCAGTAGAGTAGAACGAGGTGAA 59.561 47.826 0.00 0.00 0.00 3.18
1969 2122 3.008330 GCAGTAGAGTAGAACGAGGTGA 58.992 50.000 0.00 0.00 0.00 4.02
1970 2123 2.747989 TGCAGTAGAGTAGAACGAGGTG 59.252 50.000 0.00 0.00 0.00 4.00
1971 2124 2.748532 GTGCAGTAGAGTAGAACGAGGT 59.251 50.000 0.00 0.00 0.00 3.85
1972 2125 3.011119 AGTGCAGTAGAGTAGAACGAGG 58.989 50.000 0.00 0.00 0.00 4.63
1973 2126 5.294799 ACATAGTGCAGTAGAGTAGAACGAG 59.705 44.000 7.45 0.00 0.00 4.18
1974 2127 5.183969 ACATAGTGCAGTAGAGTAGAACGA 58.816 41.667 7.45 0.00 0.00 3.85
1975 2128 5.487153 ACATAGTGCAGTAGAGTAGAACG 57.513 43.478 7.45 0.00 0.00 3.95
1976 2129 5.064962 ACGACATAGTGCAGTAGAGTAGAAC 59.935 44.000 17.78 4.63 0.00 3.01
1977 2130 5.183969 ACGACATAGTGCAGTAGAGTAGAA 58.816 41.667 17.78 0.00 0.00 2.10
1978 2131 4.767478 ACGACATAGTGCAGTAGAGTAGA 58.233 43.478 17.78 0.00 0.00 2.59
1979 2132 6.788684 ATACGACATAGTGCAGTAGAGTAG 57.211 41.667 7.45 10.52 0.00 2.57
1980 2133 6.541278 ACAATACGACATAGTGCAGTAGAGTA 59.459 38.462 7.45 8.56 31.83 2.59
1981 2134 5.357314 ACAATACGACATAGTGCAGTAGAGT 59.643 40.000 7.45 8.14 31.83 3.24
2021 2183 0.606130 TGTCGTCATGCATGGCAAGT 60.606 50.000 29.36 0.00 43.62 3.16
2025 2187 0.734309 TTGATGTCGTCATGCATGGC 59.266 50.000 25.97 23.81 36.54 4.40
2026 2188 1.738908 TGTTGATGTCGTCATGCATGG 59.261 47.619 25.97 11.53 36.54 3.66
2435 2619 2.632377 CTTATTCTTCTTCCTGCCGCA 58.368 47.619 0.00 0.00 0.00 5.69
2560 2744 3.252974 AGTAAGTTGAGATTCAGGCGG 57.747 47.619 0.00 0.00 0.00 6.13
2732 2916 9.288576 CCTAGCATGGATGATGACTAAATTTAA 57.711 33.333 0.00 0.00 33.31 1.52
2734 2918 7.520798 TCCTAGCATGGATGATGACTAAATTT 58.479 34.615 0.00 0.00 33.31 1.82
2735 2919 7.083062 TCCTAGCATGGATGATGACTAAATT 57.917 36.000 0.00 0.00 33.31 1.82
2739 2923 6.497640 ACTATCCTAGCATGGATGATGACTA 58.502 40.000 17.41 0.00 45.58 2.59


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

AutoCloner maintained by Alex Coulton.