Multiple sequence alignment - TraesCS1D01G303300

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 TraesCS1D01G303300 chr1D 100.000 2855 0 0 1 2855 401160020 401162874 0.000000e+00 5273.0
1 TraesCS1D01G303300 chr1B 93.702 1842 96 8 54 1891 539127013 539128838 0.000000e+00 2741.0
2 TraesCS1D01G303300 chr3A 97.826 966 21 0 1890 2855 90374113 90373148 0.000000e+00 1668.0
3 TraesCS1D01G303300 chr3A 97.004 968 27 2 1889 2855 691681932 691680966 0.000000e+00 1626.0
4 TraesCS1D01G303300 chr3A 98.276 58 1 0 1 58 423951526 423951583 5.030000e-18 102.0
5 TraesCS1D01G303300 chr1A 97.622 967 21 2 1890 2855 589497492 589496527 0.000000e+00 1657.0
6 TraesCS1D01G303300 chr1A 97.202 965 27 0 1891 2855 517622888 517623852 0.000000e+00 1633.0
7 TraesCS1D01G303300 chr1A 96.025 805 25 2 55 856 497274589 497275389 0.000000e+00 1303.0
8 TraesCS1D01G303300 chr1A 96.078 306 8 2 1588 1891 497275388 497275691 1.980000e-136 496.0
9 TraesCS1D01G303300 chr2A 97.516 966 24 0 1890 2855 579864226 579865191 0.000000e+00 1652.0
10 TraesCS1D01G303300 chr5A 97.417 968 23 2 1890 2855 222614254 222615221 0.000000e+00 1648.0
11 TraesCS1D01G303300 chr5A 97.208 967 25 2 1890 2855 481674429 481675394 0.000000e+00 1635.0
12 TraesCS1D01G303300 chr7A 97.409 965 25 0 1891 2855 601999839 601998875 0.000000e+00 1644.0
13 TraesCS1D01G303300 chr7A 97.001 967 29 0 1889 2855 96079343 96078377 0.000000e+00 1626.0
14 TraesCS1D01G303300 chr7A 96.552 58 2 0 1 58 292850193 292850250 2.340000e-16 97.1
15 TraesCS1D01G303300 chr3D 98.214 56 1 0 1 56 508385260 508385205 6.510000e-17 99.0
16 TraesCS1D01G303300 chr2B 98.214 56 1 0 1 56 549025559 549025614 6.510000e-17 99.0
17 TraesCS1D01G303300 chr2B 96.552 58 2 0 1 58 215034848 215034791 2.340000e-16 97.1
18 TraesCS1D01G303300 chr7B 96.552 58 2 0 1 58 618673656 618673599 2.340000e-16 97.1
19 TraesCS1D01G303300 chr7B 98.182 55 1 0 2 56 680341340 680341286 2.340000e-16 97.1
20 TraesCS1D01G303300 chr6B 96.552 58 2 0 1 58 246296653 246296710 2.340000e-16 97.1
21 TraesCS1D01G303300 chr4D 98.182 55 1 0 1 55 62100081 62100135 2.340000e-16 97.1


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 TraesCS1D01G303300 chr1D 401160020 401162874 2854 False 5273.0 5273 100.0000 1 2855 1 chr1D.!!$F1 2854
1 TraesCS1D01G303300 chr1B 539127013 539128838 1825 False 2741.0 2741 93.7020 54 1891 1 chr1B.!!$F1 1837
2 TraesCS1D01G303300 chr3A 90373148 90374113 965 True 1668.0 1668 97.8260 1890 2855 1 chr3A.!!$R1 965
3 TraesCS1D01G303300 chr3A 691680966 691681932 966 True 1626.0 1626 97.0040 1889 2855 1 chr3A.!!$R2 966
4 TraesCS1D01G303300 chr1A 589496527 589497492 965 True 1657.0 1657 97.6220 1890 2855 1 chr1A.!!$R1 965
5 TraesCS1D01G303300 chr1A 517622888 517623852 964 False 1633.0 1633 97.2020 1891 2855 1 chr1A.!!$F1 964
6 TraesCS1D01G303300 chr1A 497274589 497275691 1102 False 899.5 1303 96.0515 55 1891 2 chr1A.!!$F2 1836
7 TraesCS1D01G303300 chr2A 579864226 579865191 965 False 1652.0 1652 97.5160 1890 2855 1 chr2A.!!$F1 965
8 TraesCS1D01G303300 chr5A 222614254 222615221 967 False 1648.0 1648 97.4170 1890 2855 1 chr5A.!!$F1 965
9 TraesCS1D01G303300 chr5A 481674429 481675394 965 False 1635.0 1635 97.2080 1890 2855 1 chr5A.!!$F2 965
10 TraesCS1D01G303300 chr7A 601998875 601999839 964 True 1644.0 1644 97.4090 1891 2855 1 chr7A.!!$R2 964
11 TraesCS1D01G303300 chr7A 96078377 96079343 966 True 1626.0 1626 97.0010 1889 2855 1 chr7A.!!$R1 966

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
918 922 0.389948 ACATGAACGGCGAGACCTTC 60.39 55.0 16.62 7.12 35.61 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 2564 0.107703 TCCAATGAGATGGTCGGTGC 60.108 55.0 0.0 0.0 41.46 5.01 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
40 41 9.743057 TGGTACAAAGTTGAGTCATTTATTTTG 57.257 29.630 8.80 8.80 31.92 2.44
41 42 9.191995 GGTACAAAGTTGAGTCATTTATTTTGG 57.808 33.333 12.94 0.78 0.00 3.28
42 43 9.959749 GTACAAAGTTGAGTCATTTATTTTGGA 57.040 29.630 12.94 4.81 0.00 3.53
44 45 9.313118 ACAAAGTTGAGTCATTTATTTTGGAAC 57.687 29.630 12.94 0.00 0.00 3.62
45 46 8.479280 CAAAGTTGAGTCATTTATTTTGGAACG 58.521 33.333 0.00 0.00 0.00 3.95
46 47 6.677913 AGTTGAGTCATTTATTTTGGAACGG 58.322 36.000 0.00 0.00 0.00 4.44
47 48 6.488683 AGTTGAGTCATTTATTTTGGAACGGA 59.511 34.615 0.00 0.00 0.00 4.69
48 49 6.494893 TGAGTCATTTATTTTGGAACGGAG 57.505 37.500 0.00 0.00 0.00 4.63
49 50 5.414454 TGAGTCATTTATTTTGGAACGGAGG 59.586 40.000 0.00 0.00 0.00 4.30
50 51 4.705023 AGTCATTTATTTTGGAACGGAGGG 59.295 41.667 0.00 0.00 0.00 4.30
51 52 4.703093 GTCATTTATTTTGGAACGGAGGGA 59.297 41.667 0.00 0.00 0.00 4.20
52 53 4.947388 TCATTTATTTTGGAACGGAGGGAG 59.053 41.667 0.00 0.00 0.00 4.30
58 59 2.134789 TGGAACGGAGGGAGTAGTAC 57.865 55.000 0.00 0.00 0.00 2.73
362 363 8.187913 TGATTTTCTGAAACACCAATTGGATA 57.812 30.769 31.22 8.82 38.94 2.59
459 463 5.049818 AGTGAGCGTTCTCTTCAATCTTTTG 60.050 40.000 0.00 0.00 40.03 2.44
523 527 7.066525 CCATTGTTATAATACCGTCAAACCTGT 59.933 37.037 0.00 0.00 0.00 4.00
663 667 9.546909 GACAGTGAACAACATATTGAGTTATTG 57.453 33.333 0.00 0.00 39.30 1.90
687 691 4.559862 AGAGGAAACAACCCAGATACTG 57.440 45.455 0.00 0.00 0.00 2.74
805 809 1.702957 CTCCCCTGTACAAGGTGGAAA 59.297 52.381 9.67 0.00 45.78 3.13
839 843 1.004918 CCGACGACCCTTCTTTGCT 60.005 57.895 0.00 0.00 0.00 3.91
898 902 2.100252 CGAGCCCGTAATCTGGAAACTA 59.900 50.000 0.00 0.00 0.00 2.24
904 908 5.424757 CCCGTAATCTGGAAACTAACATGA 58.575 41.667 0.00 0.00 0.00 3.07
905 909 5.878116 CCCGTAATCTGGAAACTAACATGAA 59.122 40.000 0.00 0.00 0.00 2.57
910 914 1.801771 TGGAAACTAACATGAACGGCG 59.198 47.619 4.80 4.80 0.00 6.46
918 922 0.389948 ACATGAACGGCGAGACCTTC 60.390 55.000 16.62 7.12 35.61 3.46
1066 1070 3.445687 CGGTCGTCGGGGACATGA 61.446 66.667 0.00 0.00 38.70 3.07
1093 1097 0.035056 CCTCACATCAACCCCTGACC 60.035 60.000 0.00 0.00 36.69 4.02
1096 1100 0.955428 CACATCAACCCCTGACCACG 60.955 60.000 0.00 0.00 36.69 4.94
1110 1114 0.818040 ACCACGTTCAAGAGCCCAAC 60.818 55.000 0.00 0.00 0.00 3.77
1113 1117 1.264288 CACGTTCAAGAGCCCAACTTC 59.736 52.381 0.00 0.00 0.00 3.01
1119 1123 2.281484 GAGCCCAACTTCGTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
1121 1125 1.228552 AGCCCAACTTCGTGCCATT 60.229 52.632 0.00 0.00 0.00 3.16
1125 1129 1.068434 CCCAACTTCGTGCCATTGTTT 59.932 47.619 0.00 0.00 0.00 2.83
1138 1142 2.939103 CCATTGTTTGAGGTCCTCGATC 59.061 50.000 14.34 11.70 32.35 3.69
1140 1144 3.594603 TTGTTTGAGGTCCTCGATCTC 57.405 47.619 14.34 6.90 39.98 2.75
1157 1161 1.949847 CTCTCCAAGCCGGACGTCAT 61.950 60.000 18.91 0.00 39.64 3.06
1158 1162 1.519455 CTCCAAGCCGGACGTCATC 60.519 63.158 18.91 5.36 39.64 2.92
1164 1168 2.762234 GCCGGACGTCATCGAGACT 61.762 63.158 18.91 0.00 45.32 3.24
1205 1209 2.347490 GGACACGTGCACCTGGAT 59.653 61.111 17.22 0.29 0.00 3.41
1206 1210 2.034879 GGACACGTGCACCTGGATG 61.035 63.158 17.22 8.92 0.00 3.51
1210 1214 2.438975 CGTGCACCTGGATGCCAT 60.439 61.111 12.15 0.00 45.50 4.40
1234 1238 1.612442 TACCCGCTCTGCTTCCCTT 60.612 57.895 0.00 0.00 0.00 3.95
1238 1242 1.968017 CGCTCTGCTTCCCTTGCAA 60.968 57.895 0.00 0.00 40.13 4.08
1247 1251 2.677875 CCCTTGCAAGCTCACCCC 60.678 66.667 21.43 0.00 0.00 4.95
1277 1281 2.263741 GCAGGCCGCCCATGATAAG 61.264 63.158 5.55 0.00 32.94 1.73
1278 1282 1.149174 CAGGCCGCCCATGATAAGT 59.851 57.895 5.55 0.00 0.00 2.24
1282 1286 1.498865 GCCGCCCATGATAAGTGTCG 61.499 60.000 0.00 0.00 0.00 4.35
1290 1294 0.454600 TGATAAGTGTCGCGTCCTCC 59.545 55.000 5.77 0.00 0.00 4.30
1305 1309 4.988716 TCCGTGGTGGTCGAGCCT 62.989 66.667 12.85 0.00 39.52 4.58
1323 1327 5.107453 CGAGCCTTACATTTTGATATCGGTC 60.107 44.000 0.00 0.00 0.00 4.79
1340 1344 0.319297 GTCAGTCGCCCGTACAACTT 60.319 55.000 0.00 0.00 0.00 2.66
1341 1345 0.390124 TCAGTCGCCCGTACAACTTT 59.610 50.000 0.00 0.00 0.00 2.66
1344 1348 1.615392 AGTCGCCCGTACAACTTTACT 59.385 47.619 0.00 0.00 0.00 2.24
1347 1351 4.082026 AGTCGCCCGTACAACTTTACTTAT 60.082 41.667 0.00 0.00 0.00 1.73
1356 1360 7.480542 CCGTACAACTTTACTTATGCATTTGAC 59.519 37.037 3.54 1.15 0.00 3.18
1366 1370 1.241165 TGCATTTGACACCAGCTCAG 58.759 50.000 0.00 0.00 0.00 3.35
1378 1382 0.179078 CAGCTCAGGAGAGTGGCATC 60.179 60.000 0.00 0.00 44.00 3.91
1404 1408 3.660111 GGCGAGCAACTGCCGTTT 61.660 61.111 12.11 0.00 42.22 3.60
1405 1409 2.427410 GCGAGCAACTGCCGTTTG 60.427 61.111 12.11 0.00 43.38 2.93
1407 1411 1.355210 CGAGCAACTGCCGTTTGTT 59.645 52.632 0.00 0.00 43.38 2.83
1480 1485 0.394352 CGGCCCCATCAAAGCTTACT 60.394 55.000 0.00 0.00 0.00 2.24
1497 1502 0.969149 ACTGCATCCGAGTCTCAACA 59.031 50.000 0.00 0.00 0.00 3.33
1503 1508 0.532573 TCCGAGTCTCAACATCTGGC 59.467 55.000 0.00 0.00 0.00 4.85
1576 1581 4.458989 AGGAGCATGAAGAAATTAACGCAA 59.541 37.500 0.00 0.00 0.00 4.85
1581 1586 2.230266 TGAAGAAATTAACGCAAGGGGC 59.770 45.455 0.00 0.00 46.39 5.80
1821 1826 1.153289 CCCTGGGTTCTCTGATGCG 60.153 63.158 3.97 0.00 0.00 4.73
1848 1853 7.050377 CCATCGCCTTCACTTTATCCATATAT 58.950 38.462 0.00 0.00 0.00 0.86
1849 1854 8.204160 CCATCGCCTTCACTTTATCCATATATA 58.796 37.037 0.00 0.00 0.00 0.86
1876 1883 8.721019 ATAATGCCATTGGACACTTTTATTTG 57.279 30.769 6.95 0.00 0.00 2.32
1950 1957 8.225603 ACTTTCTTATTTCAGCTCAGAAACAA 57.774 30.769 1.61 0.00 40.03 2.83
2294 2301 0.729116 CATAGCTGTTTGGCCACTCG 59.271 55.000 3.88 0.00 0.00 4.18
2660 2667 7.659390 AGCAGTGTTAATATGATAAGGAAGAGC 59.341 37.037 0.00 0.00 0.00 4.09
2662 2669 9.202273 CAGTGTTAATATGATAAGGAAGAGCTC 57.798 37.037 5.27 5.27 0.00 4.09
2676 2683 6.635030 GGAAGAGCTCTTTTCCTACAAAAA 57.365 37.500 29.02 0.00 39.78 1.94
2742 2749 4.018960 AGAATGTTGGGTAGAGAAGCATGT 60.019 41.667 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.429493 ACTCAACTTTGTACCAACTTTAGTAC 57.571 34.615 0.00 0.00 39.44 2.73
6 7 7.107542 TGACTCAACTTTGTACCAACTTTAGT 58.892 34.615 0.00 0.00 0.00 2.24
7 8 7.548196 TGACTCAACTTTGTACCAACTTTAG 57.452 36.000 0.00 0.00 0.00 1.85
8 9 8.514330 AATGACTCAACTTTGTACCAACTTTA 57.486 30.769 0.00 0.00 0.00 1.85
9 10 7.404671 AATGACTCAACTTTGTACCAACTTT 57.595 32.000 0.00 0.00 0.00 2.66
10 11 7.404671 AAATGACTCAACTTTGTACCAACTT 57.595 32.000 0.00 0.00 0.00 2.66
11 12 8.691661 ATAAATGACTCAACTTTGTACCAACT 57.308 30.769 0.00 0.00 0.00 3.16
12 13 9.744468 AAATAAATGACTCAACTTTGTACCAAC 57.256 29.630 0.00 0.00 0.00 3.77
14 15 9.743057 CAAAATAAATGACTCAACTTTGTACCA 57.257 29.630 0.00 0.00 0.00 3.25
15 16 9.191995 CCAAAATAAATGACTCAACTTTGTACC 57.808 33.333 0.00 0.00 0.00 3.34
16 17 9.959749 TCCAAAATAAATGACTCAACTTTGTAC 57.040 29.630 0.00 0.00 0.00 2.90
18 19 9.313118 GTTCCAAAATAAATGACTCAACTTTGT 57.687 29.630 0.00 0.00 0.00 2.83
19 20 8.479280 CGTTCCAAAATAAATGACTCAACTTTG 58.521 33.333 0.00 0.00 0.00 2.77
20 21 7.651704 CCGTTCCAAAATAAATGACTCAACTTT 59.348 33.333 0.00 0.00 0.00 2.66
21 22 7.013846 TCCGTTCCAAAATAAATGACTCAACTT 59.986 33.333 0.00 0.00 0.00 2.66
22 23 6.488683 TCCGTTCCAAAATAAATGACTCAACT 59.511 34.615 0.00 0.00 0.00 3.16
23 24 6.674066 TCCGTTCCAAAATAAATGACTCAAC 58.326 36.000 0.00 0.00 0.00 3.18
24 25 6.072175 CCTCCGTTCCAAAATAAATGACTCAA 60.072 38.462 0.00 0.00 0.00 3.02
25 26 5.414454 CCTCCGTTCCAAAATAAATGACTCA 59.586 40.000 0.00 0.00 0.00 3.41
26 27 5.163652 CCCTCCGTTCCAAAATAAATGACTC 60.164 44.000 0.00 0.00 0.00 3.36
27 28 4.705023 CCCTCCGTTCCAAAATAAATGACT 59.295 41.667 0.00 0.00 0.00 3.41
28 29 4.703093 TCCCTCCGTTCCAAAATAAATGAC 59.297 41.667 0.00 0.00 0.00 3.06
29 30 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
30 31 4.705023 ACTCCCTCCGTTCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
31 32 4.930696 ACTCCCTCCGTTCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
32 33 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
33 34 4.533311 ACTACTCCCTCCGTTCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
34 35 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
35 36 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
36 37 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
37 38 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
38 39 2.450476 GTACTACTCCCTCCGTTCCAA 58.550 52.381 0.00 0.00 0.00 3.53
39 40 1.679944 CGTACTACTCCCTCCGTTCCA 60.680 57.143 0.00 0.00 0.00 3.53
40 41 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
41 42 0.380024 GCGTACTACTCCCTCCGTTC 59.620 60.000 0.00 0.00 0.00 3.95
42 43 0.322816 TGCGTACTACTCCCTCCGTT 60.323 55.000 0.00 0.00 0.00 4.44
43 44 0.322816 TTGCGTACTACTCCCTCCGT 60.323 55.000 0.00 0.00 0.00 4.69
44 45 0.381089 CTTGCGTACTACTCCCTCCG 59.619 60.000 0.00 0.00 0.00 4.63
45 46 1.472188 ACTTGCGTACTACTCCCTCC 58.528 55.000 0.00 0.00 0.00 4.30
46 47 2.033174 GCTACTTGCGTACTACTCCCTC 59.967 54.545 0.00 0.00 0.00 4.30
47 48 2.022934 GCTACTTGCGTACTACTCCCT 58.977 52.381 0.00 0.00 0.00 4.20
48 49 2.488639 GCTACTTGCGTACTACTCCC 57.511 55.000 0.00 0.00 0.00 4.30
84 85 8.077991 CACAACACTCTGAAACATGACAATATT 58.922 33.333 0.00 0.00 0.00 1.28
85 86 7.587629 CACAACACTCTGAAACATGACAATAT 58.412 34.615 0.00 0.00 0.00 1.28
86 87 6.513230 GCACAACACTCTGAAACATGACAATA 60.513 38.462 0.00 0.00 0.00 1.90
87 88 5.734220 GCACAACACTCTGAAACATGACAAT 60.734 40.000 0.00 0.00 0.00 2.71
279 280 3.489059 CCGATGCGGCTTTTGAACAATAT 60.489 43.478 0.00 0.00 41.17 1.28
303 304 2.216898 GTTTATCTGCAGCTGCTAGGG 58.783 52.381 36.61 23.29 42.66 3.53
362 363 5.756833 CGTTCTTGACTAGTAAACAAGGGTT 59.243 40.000 17.93 0.00 40.60 4.11
484 488 0.901114 ACAATGGCAATGGCTCTGCA 60.901 50.000 8.59 0.00 41.78 4.41
485 489 0.248289 AACAATGGCAATGGCTCTGC 59.752 50.000 8.59 3.17 40.87 4.26
523 527 7.606073 TGCACACTGCTAATGAGTTCTAAAATA 59.394 33.333 0.00 0.00 45.31 1.40
614 618 5.951148 TCCCTGCATCATCATAAAAAGTCAA 59.049 36.000 0.00 0.00 0.00 3.18
663 667 1.981256 TCTGGGTTGTTTCCTCTTGC 58.019 50.000 0.00 0.00 0.00 4.01
687 691 1.654023 CGCCGATCCCCTTTTGGTTC 61.654 60.000 0.00 0.00 38.10 3.62
805 809 0.918983 TCGGAATTGGAGAGGGCAAT 59.081 50.000 0.00 0.00 0.00 3.56
898 902 0.034896 AAGGTCTCGCCGTTCATGTT 59.965 50.000 0.00 0.00 43.70 2.71
918 922 1.202582 CACCCTGACTACAAGGAGACG 59.797 57.143 0.00 0.00 32.39 4.18
928 932 1.753141 GCCGACTATCCACCCTGACTA 60.753 57.143 0.00 0.00 0.00 2.59
1050 1054 1.067582 GATCATGTCCCCGACGACC 59.932 63.158 0.00 0.00 34.95 4.79
1056 1060 3.540211 GGCATAGATCATGTCCCCG 57.460 57.895 0.00 0.00 36.95 5.73
1064 1068 3.181451 GGTTGATGTGAGGGCATAGATCA 60.181 47.826 0.00 0.00 0.00 2.92
1066 1070 2.107204 GGGTTGATGTGAGGGCATAGAT 59.893 50.000 0.00 0.00 0.00 1.98
1093 1097 1.264288 GAAGTTGGGCTCTTGAACGTG 59.736 52.381 0.00 0.00 0.00 4.49
1096 1100 1.264288 CACGAAGTTGGGCTCTTGAAC 59.736 52.381 0.00 0.00 41.61 3.18
1110 1114 1.608590 ACCTCAAACAATGGCACGAAG 59.391 47.619 0.00 0.00 0.00 3.79
1113 1117 0.240945 GGACCTCAAACAATGGCACG 59.759 55.000 0.00 0.00 0.00 5.34
1119 1123 3.772025 AGAGATCGAGGACCTCAAACAAT 59.228 43.478 21.49 6.22 0.00 2.71
1121 1125 2.755655 GAGAGATCGAGGACCTCAAACA 59.244 50.000 21.49 2.27 0.00 2.83
1125 1129 0.919710 TGGAGAGATCGAGGACCTCA 59.080 55.000 21.49 8.99 0.00 3.86
1188 1192 2.034879 CATCCAGGTGCACGTGTCC 61.035 63.158 31.20 18.87 0.00 4.02
1234 1238 4.680237 CGTCGGGGTGAGCTTGCA 62.680 66.667 0.00 0.00 0.00 4.08
1238 1242 4.680537 AGTCCGTCGGGGTGAGCT 62.681 66.667 12.29 0.00 37.00 4.09
1260 1264 1.149174 ACTTATCATGGGCGGCCTG 59.851 57.895 29.87 22.81 0.00 4.85
1262 1266 1.152963 ACACTTATCATGGGCGGCC 60.153 57.895 23.42 23.42 0.00 6.13
1266 1270 0.810031 ACGCGACACTTATCATGGGC 60.810 55.000 15.93 0.00 0.00 5.36
1271 1275 0.454600 GGAGGACGCGACACTTATCA 59.545 55.000 15.93 0.00 0.00 2.15
1290 1294 1.445582 GTAAGGCTCGACCACCACG 60.446 63.158 6.78 0.00 43.14 4.94
1305 1309 5.233476 GCGACTGACCGATATCAAAATGTAA 59.767 40.000 3.12 0.00 0.00 2.41
1323 1327 1.723003 GTAAAGTTGTACGGGCGACTG 59.277 52.381 0.00 0.00 44.60 3.51
1340 1344 5.009631 AGCTGGTGTCAAATGCATAAGTAA 58.990 37.500 0.00 0.00 0.00 2.24
1341 1345 4.588899 AGCTGGTGTCAAATGCATAAGTA 58.411 39.130 0.00 0.00 0.00 2.24
1344 1348 3.419943 TGAGCTGGTGTCAAATGCATAA 58.580 40.909 0.00 0.00 0.00 1.90
1347 1351 1.241165 CTGAGCTGGTGTCAAATGCA 58.759 50.000 0.00 0.00 0.00 3.96
1356 1360 1.595882 CCACTCTCCTGAGCTGGTG 59.404 63.158 0.00 0.00 43.85 4.17
1366 1370 1.142748 CGACCTGATGCCACTCTCC 59.857 63.158 0.00 0.00 0.00 3.71
1378 1382 4.069232 TTGCTCGCCCTCGACCTG 62.069 66.667 0.00 0.00 40.21 4.00
1480 1485 1.827344 AGATGTTGAGACTCGGATGCA 59.173 47.619 0.00 0.00 0.00 3.96
1497 1502 1.207488 TAGCACCACCCTTGCCAGAT 61.207 55.000 0.00 0.00 41.18 2.90
1503 1508 2.489329 CAACTCAATAGCACCACCCTTG 59.511 50.000 0.00 0.00 0.00 3.61
1704 1709 3.449737 TCCCAGTTCGATAGGTAACCAAG 59.550 47.826 0.00 0.00 37.17 3.61
1821 1826 1.604278 GATAAAGTGAAGGCGATGGGC 59.396 52.381 0.00 0.00 42.51 5.36
1849 1854 9.737844 AAATAAAAGTGTCCAATGGCATTATTT 57.262 25.926 13.23 8.20 0.00 1.40
1950 1957 4.142687 GGCTTTGTAATTCATGCTGTACGT 60.143 41.667 0.00 0.00 0.00 3.57
2223 2230 1.971167 GTCTTTGGCGTCATGGGCA 60.971 57.895 11.01 3.36 41.13 5.36
2294 2301 2.176792 CGCTTCTTTTGGCGGCTC 59.823 61.111 11.43 0.00 46.42 4.70
2500 2507 6.819146 GGGAAAACGATTAAGTCTGATCTTCT 59.181 38.462 0.00 0.00 0.00 2.85
2557 2564 0.107703 TCCAATGAGATGGTCGGTGC 60.108 55.000 0.00 0.00 41.46 5.01
2602 2609 4.695455 CCTGTGTAATGAACTCGGTGATTT 59.305 41.667 0.00 0.00 0.00 2.17
2608 2615 1.066143 AGCCCTGTGTAATGAACTCGG 60.066 52.381 0.00 0.00 0.00 4.63
2676 2683 9.129532 CTTTGGAAAGCTAGGAATGATTATCTT 57.870 33.333 0.00 0.00 0.00 2.40
2678 2685 8.563732 GTCTTTGGAAAGCTAGGAATGATTATC 58.436 37.037 0.00 0.00 35.99 1.75
2742 2749 9.227777 CTTGCTCTGATTAATATGAATCATCCA 57.772 33.333 14.77 9.87 43.22 3.41


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

AutoCloner maintained by Alex Coulton.