Multiple sequence alignment - TraesCS3B01G098300

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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 TraesCS3B01G098300 chr3B 100.000 2219 0 0 1 2219 65559152 65561370 0.000000e+00 4098.0
1 TraesCS3B01G098300 chr3D 88.545 2200 154 52 3 2164 42089290 42087151 0.000000e+00 2577.0
2 TraesCS3B01G098300 chr3D 95.455 44 2 0 169 212 140199472 140199515 1.100000e-08 71.3
3 TraesCS3B01G098300 chr3A 86.047 2236 148 77 43 2219 53567850 53569980 0.000000e+00 2250.0
4 TraesCS3B01G098300 chr7D 95.455 44 2 0 169 212 541334539 541334582 1.100000e-08 71.3
5 TraesCS3B01G098300 chr6A 92.000 50 4 0 169 218 523164428 523164379 1.100000e-08 71.3
6 TraesCS3B01G098300 chr4B 95.455 44 2 0 169 212 39706696 39706739 1.100000e-08 71.3
7 TraesCS3B01G098300 chr4B 92.000 50 4 0 169 218 75349387 75349338 1.100000e-08 71.3
8 TraesCS3B01G098300 chr2D 92.000 50 4 0 169 218 591895441 591895392 1.100000e-08 71.3
9 TraesCS3B01G098300 chr1D 95.455 44 2 0 169 212 380436647 380436690 1.100000e-08 71.3
10 TraesCS3B01G098300 chr1D 95.455 44 2 0 169 212 383954215 383954258 1.100000e-08 71.3
11 TraesCS3B01G098300 chr1D 95.455 44 2 0 169 212 425364005 425364048 1.100000e-08 71.3
12 TraesCS3B01G098300 chr1D 100.000 28 0 0 60 87 66379405 66379432 4.000000e-03 52.8
13 TraesCS3B01G098300 chr5D 100.000 28 0 0 60 87 216979814 216979787 4.000000e-03 52.8
14 TraesCS3B01G098300 chr4D 100.000 28 0 0 60 87 488483167 488483194 4.000000e-03 52.8


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 TraesCS3B01G098300 chr3B 65559152 65561370 2218 False 4098 4098 100.000 1 2219 1 chr3B.!!$F1 2218
1 TraesCS3B01G098300 chr3D 42087151 42089290 2139 True 2577 2577 88.545 3 2164 1 chr3D.!!$R1 2161
2 TraesCS3B01G098300 chr3A 53567850 53569980 2130 False 2250 2250 86.047 43 2219 1 chr3A.!!$F1 2176

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
277 289 0.237761 CTGCTGCTTGTGCTTCAGTC 59.762 55.0 0.0 0.0 40.48 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1281 0.613853 TAGCTAGCCGGTGGTCTTGT 60.614 55.0 12.13 0.0 0.0 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
24 25 5.712152 AAAATGAGCTCAGGTAACAAAGG 57.288 39.130 22.96 0.00 41.41 3.11
58 69 4.228567 TCGCGGTGCTGTGTTGGA 62.229 61.111 6.13 0.00 0.00 3.53
59 70 4.012895 CGCGGTGCTGTGTTGGAC 62.013 66.667 0.00 0.00 0.00 4.02
100 111 2.106477 AAGCCTGCTTTCTGAGTAGC 57.894 50.000 0.00 6.84 36.83 3.58
106 117 0.995728 GCTTTCTGAGTAGCGAGTGC 59.004 55.000 0.00 0.00 43.24 4.40
151 162 1.244816 TAGGTGAGTGTGACCTCGTG 58.755 55.000 0.00 0.00 43.15 4.35
164 176 2.290641 GACCTCGTGTCAAAAGCAACAT 59.709 45.455 3.51 0.00 43.85 2.71
165 177 3.472652 ACCTCGTGTCAAAAGCAACATA 58.527 40.909 0.00 0.00 0.00 2.29
166 178 3.250040 ACCTCGTGTCAAAAGCAACATAC 59.750 43.478 0.00 0.00 0.00 2.39
168 180 4.457810 CTCGTGTCAAAAGCAACATACAG 58.542 43.478 0.00 0.00 0.00 2.74
169 181 3.249799 TCGTGTCAAAAGCAACATACAGG 59.750 43.478 0.00 0.00 0.00 4.00
172 184 5.215160 GTGTCAAAAGCAACATACAGGAAG 58.785 41.667 0.00 0.00 0.00 3.46
174 186 5.592282 TGTCAAAAGCAACATACAGGAAGAA 59.408 36.000 0.00 0.00 0.00 2.52
175 187 6.265196 TGTCAAAAGCAACATACAGGAAGAAT 59.735 34.615 0.00 0.00 0.00 2.40
177 189 7.115378 GTCAAAAGCAACATACAGGAAGAATTG 59.885 37.037 0.00 0.00 0.00 2.32
178 190 6.655078 AAAGCAACATACAGGAAGAATTGT 57.345 33.333 0.00 0.00 0.00 2.71
179 191 5.633830 AGCAACATACAGGAAGAATTGTG 57.366 39.130 0.00 0.00 0.00 3.33
185 197 2.146342 ACAGGAAGAATTGTGTGCTCG 58.854 47.619 0.00 0.00 0.00 5.03
186 198 1.466167 CAGGAAGAATTGTGTGCTCGG 59.534 52.381 0.00 0.00 0.00 4.63
188 200 0.804989 GAAGAATTGTGTGCTCGGGG 59.195 55.000 0.00 0.00 0.00 5.73
189 201 0.609131 AAGAATTGTGTGCTCGGGGG 60.609 55.000 0.00 0.00 0.00 5.40
190 202 1.002624 GAATTGTGTGCTCGGGGGA 60.003 57.895 0.00 0.00 0.00 4.81
191 203 1.002134 AATTGTGTGCTCGGGGGAG 60.002 57.895 0.00 0.00 0.00 4.30
202 214 4.677151 GGGGGAGGGGGTGTGTCT 62.677 72.222 0.00 0.00 0.00 3.41
203 215 3.330720 GGGGAGGGGGTGTGTCTG 61.331 72.222 0.00 0.00 0.00 3.51
204 216 2.529389 GGGAGGGGGTGTGTCTGT 60.529 66.667 0.00 0.00 0.00 3.41
205 217 2.750350 GGAGGGGGTGTGTCTGTG 59.250 66.667 0.00 0.00 0.00 3.66
206 218 2.032681 GAGGGGGTGTGTCTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
207 219 3.883744 GAGGGGGTGTGTCTGTGCG 62.884 68.421 0.00 0.00 0.00 5.34
212 224 2.244651 GGTGTGTCTGTGCGGTGTC 61.245 63.158 0.00 0.00 0.00 3.67
214 226 1.067416 TGTGTCTGTGCGGTGTCTC 59.933 57.895 0.00 0.00 0.00 3.36
256 268 3.622166 TTCAGAGAATGATGCAGAGCA 57.378 42.857 0.00 0.00 44.86 4.26
277 289 0.237761 CTGCTGCTTGTGCTTCAGTC 59.762 55.000 0.00 0.00 40.48 3.51
278 290 0.464193 TGCTGCTTGTGCTTCAGTCA 60.464 50.000 0.00 0.00 40.48 3.41
319 343 4.785658 GCAAGTGATTCAGAGAATGATGCG 60.786 45.833 0.00 0.00 37.89 4.73
347 372 0.607112 TCAGTGAAGAGCTGAGCCTG 59.393 55.000 0.00 0.00 37.98 4.85
353 378 0.612744 AAGAGCTGAGCCTGGTCTTC 59.387 55.000 15.57 0.00 43.07 2.87
358 383 1.265236 CTGAGCCTGGTCTTCAGAGT 58.735 55.000 15.40 0.00 46.18 3.24
359 384 1.204467 CTGAGCCTGGTCTTCAGAGTC 59.796 57.143 15.40 0.00 46.18 3.36
363 388 1.067213 GCCTGGTCTTCAGAGTCTCAC 60.067 57.143 1.94 0.00 46.18 3.51
373 398 3.087781 TCAGAGTCTCACAGTGAGGATG 58.912 50.000 27.15 19.71 44.39 3.51
486 511 3.990469 CGTTAAGCTTCTGACAGTGACAT 59.010 43.478 0.00 0.00 0.00 3.06
488 513 5.061064 CGTTAAGCTTCTGACAGTGACATAC 59.939 44.000 0.00 0.00 0.00 2.39
489 514 4.607293 AAGCTTCTGACAGTGACATACA 57.393 40.909 1.59 0.00 0.00 2.29
495 520 4.498241 TCTGACAGTGACATACAATCTGC 58.502 43.478 1.59 0.00 0.00 4.26
496 521 4.021192 TCTGACAGTGACATACAATCTGCA 60.021 41.667 1.59 0.00 0.00 4.41
502 527 3.498018 GTGACATACAATCTGCACACACA 59.502 43.478 0.00 0.00 0.00 3.72
503 528 3.498018 TGACATACAATCTGCACACACAC 59.502 43.478 0.00 0.00 0.00 3.82
511 536 0.734309 CTGCACACACACACACACAT 59.266 50.000 0.00 0.00 0.00 3.21
527 552 5.120674 CACACACATACATACACCAGTCAAG 59.879 44.000 0.00 0.00 0.00 3.02
529 554 5.120674 CACACATACATACACCAGTCAAGTG 59.879 44.000 0.00 0.00 41.15 3.16
536 561 3.179443 ACACCAGTCAAGTGTACAGTG 57.821 47.619 3.39 5.08 46.37 3.66
539 564 2.504175 ACCAGTCAAGTGTACAGTGGTT 59.496 45.455 3.39 0.00 32.87 3.67
540 565 3.707611 ACCAGTCAAGTGTACAGTGGTTA 59.292 43.478 3.39 0.00 32.87 2.85
541 566 4.202223 ACCAGTCAAGTGTACAGTGGTTAG 60.202 45.833 3.39 0.00 32.87 2.34
543 568 5.357257 CAGTCAAGTGTACAGTGGTTAGTT 58.643 41.667 3.39 0.00 0.00 2.24
544 569 6.461927 CCAGTCAAGTGTACAGTGGTTAGTTA 60.462 42.308 3.39 0.00 0.00 2.24
545 570 6.641314 CAGTCAAGTGTACAGTGGTTAGTTAG 59.359 42.308 3.39 0.00 0.00 2.34
547 572 6.420008 GTCAAGTGTACAGTGGTTAGTTAGTG 59.580 42.308 3.39 0.00 0.00 2.74
549 574 3.992427 GTGTACAGTGGTTAGTTAGTGGC 59.008 47.826 0.00 0.00 0.00 5.01
551 576 4.285003 TGTACAGTGGTTAGTTAGTGGCAT 59.715 41.667 0.00 0.00 0.00 4.40
558 583 4.042311 TGGTTAGTTAGTGGCATCAGGAAA 59.958 41.667 0.00 0.00 0.00 3.13
559 584 4.395231 GGTTAGTTAGTGGCATCAGGAAAC 59.605 45.833 0.00 0.00 0.00 2.78
561 586 3.412386 AGTTAGTGGCATCAGGAAACAC 58.588 45.455 0.00 0.00 0.00 3.32
566 591 2.421424 GTGGCATCAGGAAACACAGATC 59.579 50.000 0.00 0.00 32.58 2.75
583 608 2.039480 AGATCACATGTTCAGCTGGTGT 59.961 45.455 15.13 11.05 0.00 4.16
584 609 3.261643 AGATCACATGTTCAGCTGGTGTA 59.738 43.478 15.13 4.58 0.00 2.90
588 613 3.679980 CACATGTTCAGCTGGTGTAGTAC 59.320 47.826 15.13 0.00 0.00 2.73
589 614 3.323691 ACATGTTCAGCTGGTGTAGTACA 59.676 43.478 15.13 0.00 0.00 2.90
599 624 1.334054 GTGTAGTACACGAGGCAACG 58.666 55.000 17.29 2.85 39.53 4.10
600 625 0.387622 TGTAGTACACGAGGCAACGC 60.388 55.000 0.00 0.00 46.39 4.84
607 632 3.659092 CGAGGCAACGCAAGGCAA 61.659 61.111 0.00 0.00 46.39 4.52
674 702 3.708451 TGCCTAGGTCTCACAAGATGTA 58.292 45.455 11.31 0.00 33.08 2.29
675 703 3.701542 TGCCTAGGTCTCACAAGATGTAG 59.298 47.826 11.31 0.00 33.08 2.74
676 704 3.702045 GCCTAGGTCTCACAAGATGTAGT 59.298 47.826 11.31 0.00 33.08 2.73
677 705 4.440802 GCCTAGGTCTCACAAGATGTAGTG 60.441 50.000 11.31 0.00 37.10 2.74
678 706 4.098654 CCTAGGTCTCACAAGATGTAGTGG 59.901 50.000 0.00 0.00 36.43 4.00
679 707 3.511477 AGGTCTCACAAGATGTAGTGGT 58.489 45.455 0.00 0.00 36.43 4.16
680 708 4.673968 AGGTCTCACAAGATGTAGTGGTA 58.326 43.478 0.00 0.00 36.43 3.25
753 784 1.301716 CGGTCCACCCAACACTGAG 60.302 63.158 0.00 0.00 0.00 3.35
774 805 2.286654 GCTCGCCTGCTAATGACAATTC 60.287 50.000 0.00 0.00 0.00 2.17
886 917 3.186047 GTCATCGTCCCGCCAACG 61.186 66.667 0.00 0.00 41.39 4.10
940 971 4.942852 AGCAGCACTAGCATTAGTAAGAG 58.057 43.478 0.00 0.00 45.49 2.85
941 972 4.404073 AGCAGCACTAGCATTAGTAAGAGT 59.596 41.667 0.00 0.00 45.49 3.24
943 974 5.655488 CAGCACTAGCATTAGTAAGAGTGT 58.345 41.667 13.94 4.23 45.49 3.55
944 975 6.680625 GCAGCACTAGCATTAGTAAGAGTGTA 60.681 42.308 13.94 0.00 45.49 2.90
948 979 7.432838 GCACTAGCATTAGTAAGAGTGTAAGAC 59.567 40.741 13.94 0.00 38.05 3.01
951 982 7.704578 AGCATTAGTAAGAGTGTAAGACAGA 57.295 36.000 0.00 0.00 0.00 3.41
952 983 7.767261 AGCATTAGTAAGAGTGTAAGACAGAG 58.233 38.462 0.00 0.00 0.00 3.35
953 984 7.394923 AGCATTAGTAAGAGTGTAAGACAGAGT 59.605 37.037 0.00 0.00 0.00 3.24
955 986 9.562583 CATTAGTAAGAGTGTAAGACAGAGTTC 57.437 37.037 0.00 0.00 0.00 3.01
956 987 8.921353 TTAGTAAGAGTGTAAGACAGAGTTCT 57.079 34.615 0.00 0.00 0.00 3.01
957 988 7.826918 AGTAAGAGTGTAAGACAGAGTTCTT 57.173 36.000 0.00 0.00 39.28 2.52
958 989 7.653647 AGTAAGAGTGTAAGACAGAGTTCTTG 58.346 38.462 0.00 0.00 36.48 3.02
959 990 6.716934 AAGAGTGTAAGACAGAGTTCTTGA 57.283 37.500 0.00 0.00 36.48 3.02
960 991 6.325919 AGAGTGTAAGACAGAGTTCTTGAG 57.674 41.667 0.00 0.00 36.48 3.02
964 995 5.241949 GTGTAAGACAGAGTTCTTGAGGAGA 59.758 44.000 0.00 0.00 36.48 3.71
1237 1275 2.111043 CCTCCGGCGCCATACATT 59.889 61.111 28.98 0.00 0.00 2.71
1242 1280 0.949105 CCGGCGCCATACATTCTACC 60.949 60.000 28.98 0.00 0.00 3.18
1243 1281 0.249699 CGGCGCCATACATTCTACCA 60.250 55.000 28.98 0.00 0.00 3.25
1254 1292 2.289444 ACATTCTACCACAAGACCACCG 60.289 50.000 0.00 0.00 0.00 4.94
1332 1398 1.338484 TGCTCAGGATTGTCTGTCAGC 60.338 52.381 0.00 0.00 36.25 4.26
1371 1437 3.574284 TTGAATGGTTGATTTGAGCCG 57.426 42.857 0.00 0.00 0.00 5.52
1378 1444 0.034863 TTGATTTGAGCCGTACCCCC 60.035 55.000 0.00 0.00 0.00 5.40
1503 1580 2.715046 GAGACCAGATTGGCATGTTCA 58.285 47.619 0.00 0.00 42.67 3.18
1585 1664 4.500375 CCAGCTTTTGTTCCTTCTTCCTTG 60.500 45.833 0.00 0.00 0.00 3.61
1650 1731 9.661563 AATCATGAGACAACAATTGCATAATTT 57.338 25.926 5.05 0.00 34.34 1.82
1651 1732 8.468720 TCATGAGACAACAATTGCATAATTTG 57.531 30.769 5.05 4.07 34.34 2.32
1707 1788 0.322098 TACCACAAACATCCGGCAGG 60.322 55.000 0.00 0.00 39.46 4.85
1724 1805 0.178068 AGGGAATCAATCACCGGTCG 59.822 55.000 2.59 0.00 28.52 4.79
1852 1933 5.706916 CCCTGAATTCATTCAAAGACACAG 58.293 41.667 8.96 0.00 45.26 3.66
1856 1937 5.978919 TGAATTCATTCAAAGACACAGTTGC 59.021 36.000 3.38 0.00 43.26 4.17
1874 1955 4.060205 GTTGCTTAGTTAAACCGACTCCA 58.940 43.478 0.00 0.00 0.00 3.86
1875 1956 4.546829 TGCTTAGTTAAACCGACTCCAT 57.453 40.909 0.00 0.00 0.00 3.41
1909 1990 0.533308 AAACCGTTGCGCAAGGTAGA 60.533 50.000 33.22 7.61 37.26 2.59
1910 1991 0.949105 AACCGTTGCGCAAGGTAGAG 60.949 55.000 33.22 23.04 37.26 2.43
2034 2115 1.152943 CCATCTGCTCCTGCTGCAT 60.153 57.895 1.31 0.00 39.86 3.96
2065 2146 6.708054 ACAGAAATGTTTCTTCAGTACTGAGG 59.292 38.462 24.99 24.99 44.70 3.86
2106 2188 5.745294 GGCAAATATATTGCAAGTCACAGTG 59.255 40.000 14.34 0.00 46.58 3.66
2195 2277 0.035056 TAAGCTGAGAAAGGGCAGGC 60.035 55.000 0.00 0.00 32.83 4.85
2199 2281 1.845627 CTGAGAAAGGGCAGGCCAGA 61.846 60.000 16.94 0.00 37.98 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.430000 TCCTTTGTTACCTGAGCTCATTTTAC 59.570 38.462 18.63 13.54 0.00 2.01
1 2 6.539173 TCCTTTGTTACCTGAGCTCATTTTA 58.461 36.000 18.63 5.94 0.00 1.52
10 11 3.790089 AACCCTCCTTTGTTACCTGAG 57.210 47.619 0.00 0.00 0.00 3.35
11 12 3.435890 CCAAACCCTCCTTTGTTACCTGA 60.436 47.826 0.00 0.00 30.33 3.86
12 13 2.890945 CCAAACCCTCCTTTGTTACCTG 59.109 50.000 0.00 0.00 30.33 4.00
17 18 2.384828 GACACCAAACCCTCCTTTGTT 58.615 47.619 0.00 0.00 30.33 2.83
24 25 0.666577 CGACTCGACACCAAACCCTC 60.667 60.000 0.00 0.00 0.00 4.30
58 69 2.640184 GCCCCGCTTTGTAGATAAAGT 58.360 47.619 0.00 0.00 39.33 2.66
59 70 1.597663 CGCCCCGCTTTGTAGATAAAG 59.402 52.381 0.00 0.00 39.95 1.85
100 111 0.603707 TTCCTTTCCTGCAGCACTCG 60.604 55.000 8.66 0.00 0.00 4.18
106 117 3.321682 TGGATTTTGTTCCTTTCCTGCAG 59.678 43.478 6.78 6.78 36.68 4.41
151 162 5.689383 TCTTCCTGTATGTTGCTTTTGAC 57.311 39.130 0.00 0.00 0.00 3.18
159 171 5.048504 AGCACACAATTCTTCCTGTATGTTG 60.049 40.000 0.00 0.00 0.00 3.33
164 176 3.325870 CGAGCACACAATTCTTCCTGTA 58.674 45.455 0.00 0.00 0.00 2.74
165 177 2.146342 CGAGCACACAATTCTTCCTGT 58.854 47.619 0.00 0.00 0.00 4.00
166 178 1.466167 CCGAGCACACAATTCTTCCTG 59.534 52.381 0.00 0.00 0.00 3.86
168 180 0.804989 CCCGAGCACACAATTCTTCC 59.195 55.000 0.00 0.00 0.00 3.46
169 181 0.804989 CCCCGAGCACACAATTCTTC 59.195 55.000 0.00 0.00 0.00 2.87
172 184 1.002624 TCCCCCGAGCACACAATTC 60.003 57.895 0.00 0.00 0.00 2.17
174 186 2.671070 CTCCCCCGAGCACACAAT 59.329 61.111 0.00 0.00 0.00 2.71
175 187 3.636231 CCTCCCCCGAGCACACAA 61.636 66.667 0.00 0.00 34.49 3.33
185 197 4.677151 AGACACACCCCCTCCCCC 62.677 72.222 0.00 0.00 0.00 5.40
186 198 3.330720 CAGACACACCCCCTCCCC 61.331 72.222 0.00 0.00 0.00 4.81
188 200 2.750350 CACAGACACACCCCCTCC 59.250 66.667 0.00 0.00 0.00 4.30
189 201 2.032681 GCACAGACACACCCCCTC 59.967 66.667 0.00 0.00 0.00 4.30
190 202 3.941188 CGCACAGACACACCCCCT 61.941 66.667 0.00 0.00 0.00 4.79
194 206 2.203015 ACACCGCACAGACACACC 60.203 61.111 0.00 0.00 0.00 4.16
195 207 1.215655 GAGACACCGCACAGACACAC 61.216 60.000 0.00 0.00 0.00 3.82
196 208 1.067416 GAGACACCGCACAGACACA 59.933 57.895 0.00 0.00 0.00 3.72
197 209 0.941463 CAGAGACACCGCACAGACAC 60.941 60.000 0.00 0.00 0.00 3.67
198 210 1.363807 CAGAGACACCGCACAGACA 59.636 57.895 0.00 0.00 0.00 3.41
201 213 2.148916 TTTACAGAGACACCGCACAG 57.851 50.000 0.00 0.00 0.00 3.66
202 214 2.805671 CAATTTACAGAGACACCGCACA 59.194 45.455 0.00 0.00 0.00 4.57
203 215 2.159627 CCAATTTACAGAGACACCGCAC 59.840 50.000 0.00 0.00 0.00 5.34
204 216 2.224426 ACCAATTTACAGAGACACCGCA 60.224 45.455 0.00 0.00 0.00 5.69
205 217 2.415512 GACCAATTTACAGAGACACCGC 59.584 50.000 0.00 0.00 0.00 5.68
206 218 3.679980 CAGACCAATTTACAGAGACACCG 59.320 47.826 0.00 0.00 0.00 4.94
207 219 4.894784 TCAGACCAATTTACAGAGACACC 58.105 43.478 0.00 0.00 0.00 4.16
212 224 7.678947 ATCACTTTCAGACCAATTTACAGAG 57.321 36.000 0.00 0.00 0.00 3.35
214 226 7.874940 TGAATCACTTTCAGACCAATTTACAG 58.125 34.615 0.00 0.00 39.44 2.74
278 290 0.822164 GCAGCCTGAATGCAAGGATT 59.178 50.000 7.13 0.00 43.31 3.01
319 343 1.724429 CTCTTCACTGAAGCAGCTCC 58.276 55.000 13.24 0.00 39.29 4.70
347 372 2.887783 TCACTGTGAGACTCTGAAGACC 59.112 50.000 6.36 0.00 0.00 3.85
359 384 1.338484 CCACCACATCCTCACTGTGAG 60.338 57.143 26.94 26.94 45.44 3.51
363 388 0.390340 CGTCCACCACATCCTCACTG 60.390 60.000 0.00 0.00 0.00 3.66
373 398 1.300697 GACAGACACCGTCCACCAC 60.301 63.158 0.00 0.00 32.18 4.16
410 435 1.361668 GCTACACATCAGGCACACCG 61.362 60.000 0.00 0.00 42.76 4.94
421 446 0.034756 TTGTCAGCACGGCTACACAT 59.965 50.000 9.27 0.00 36.40 3.21
449 474 2.779951 TAACGACGCAGCCTGCATGT 62.780 55.000 18.21 7.26 45.36 3.21
486 511 2.611751 GTGTGTGTGTGTGCAGATTGTA 59.388 45.455 0.00 0.00 0.00 2.41
488 513 1.401199 TGTGTGTGTGTGTGCAGATTG 59.599 47.619 0.00 0.00 0.00 2.67
489 514 1.401552 GTGTGTGTGTGTGTGCAGATT 59.598 47.619 0.00 0.00 0.00 2.40
495 520 4.509600 TGTATGTATGTGTGTGTGTGTGTG 59.490 41.667 0.00 0.00 0.00 3.82
496 521 4.509970 GTGTATGTATGTGTGTGTGTGTGT 59.490 41.667 0.00 0.00 0.00 3.72
502 527 4.039852 TGACTGGTGTATGTATGTGTGTGT 59.960 41.667 0.00 0.00 0.00 3.72
503 528 4.565022 TGACTGGTGTATGTATGTGTGTG 58.435 43.478 0.00 0.00 0.00 3.82
511 536 5.537295 ACTGTACACTTGACTGGTGTATGTA 59.463 40.000 9.40 0.00 46.97 2.29
527 552 3.992427 GCCACTAACTAACCACTGTACAC 59.008 47.826 0.00 0.00 0.00 2.90
529 554 4.261578 TGCCACTAACTAACCACTGTAC 57.738 45.455 0.00 0.00 0.00 2.90
536 561 3.906720 TCCTGATGCCACTAACTAACC 57.093 47.619 0.00 0.00 0.00 2.85
539 564 4.041075 TGTGTTTCCTGATGCCACTAACTA 59.959 41.667 0.00 0.00 0.00 2.24
540 565 3.181445 TGTGTTTCCTGATGCCACTAACT 60.181 43.478 0.00 0.00 0.00 2.24
541 566 3.146066 TGTGTTTCCTGATGCCACTAAC 58.854 45.455 0.00 0.00 0.00 2.34
543 568 2.637382 TCTGTGTTTCCTGATGCCACTA 59.363 45.455 0.00 0.00 0.00 2.74
544 569 1.421268 TCTGTGTTTCCTGATGCCACT 59.579 47.619 0.00 0.00 0.00 4.00
545 570 1.896220 TCTGTGTTTCCTGATGCCAC 58.104 50.000 0.00 0.00 0.00 5.01
547 572 2.421424 GTGATCTGTGTTTCCTGATGCC 59.579 50.000 0.00 0.00 0.00 4.40
549 574 4.698780 ACATGTGATCTGTGTTTCCTGATG 59.301 41.667 0.00 0.00 0.00 3.07
551 576 4.356405 ACATGTGATCTGTGTTTCCTGA 57.644 40.909 0.00 0.00 0.00 3.86
558 583 3.072211 CAGCTGAACATGTGATCTGTGT 58.928 45.455 8.42 0.00 0.00 3.72
559 584 2.418976 CCAGCTGAACATGTGATCTGTG 59.581 50.000 17.39 0.63 0.00 3.66
561 586 2.418976 CACCAGCTGAACATGTGATCTG 59.581 50.000 17.39 4.98 0.00 2.90
566 591 2.771089 ACTACACCAGCTGAACATGTG 58.229 47.619 17.39 16.39 0.00 3.21
583 608 0.314618 TTGCGTTGCCTCGTGTACTA 59.685 50.000 0.00 0.00 0.00 1.82
584 609 0.944311 CTTGCGTTGCCTCGTGTACT 60.944 55.000 0.00 0.00 0.00 2.73
588 613 4.389576 GCCTTGCGTTGCCTCGTG 62.390 66.667 0.15 0.00 0.00 4.35
589 614 4.927782 TGCCTTGCGTTGCCTCGT 62.928 61.111 0.15 0.00 0.00 4.18
590 615 3.599792 CTTGCCTTGCGTTGCCTCG 62.600 63.158 0.00 0.00 0.00 4.63
591 616 1.589716 ATCTTGCCTTGCGTTGCCTC 61.590 55.000 0.00 0.00 0.00 4.70
593 618 1.444895 CATCTTGCCTTGCGTTGCC 60.445 57.895 0.00 0.00 0.00 4.52
595 620 1.469703 TCATCATCTTGCCTTGCGTTG 59.530 47.619 0.00 0.00 0.00 4.10
596 621 1.741706 CTCATCATCTTGCCTTGCGTT 59.258 47.619 0.00 0.00 0.00 4.84
597 622 1.065926 TCTCATCATCTTGCCTTGCGT 60.066 47.619 0.00 0.00 0.00 5.24
599 624 2.613133 GTCTCTCATCATCTTGCCTTGC 59.387 50.000 0.00 0.00 0.00 4.01
600 625 3.622163 GTGTCTCTCATCATCTTGCCTTG 59.378 47.826 0.00 0.00 0.00 3.61
607 632 5.657745 AGATCACTTGTGTCTCTCATCATCT 59.342 40.000 0.00 0.00 0.00 2.90
655 683 4.098654 CCACTACATCTTGTGAGACCTAGG 59.901 50.000 7.41 7.41 36.38 3.02
674 702 0.475828 AGACCCCAAAGGCTACCACT 60.476 55.000 0.00 0.00 40.58 4.00
675 703 0.035343 GAGACCCCAAAGGCTACCAC 60.035 60.000 0.00 0.00 40.58 4.16
676 704 0.474854 TGAGACCCCAAAGGCTACCA 60.475 55.000 0.00 0.00 40.58 3.25
677 705 0.253327 CTGAGACCCCAAAGGCTACC 59.747 60.000 0.00 0.00 40.58 3.18
678 706 1.276622 TCTGAGACCCCAAAGGCTAC 58.723 55.000 0.00 0.00 40.58 3.58
679 707 1.909302 CTTCTGAGACCCCAAAGGCTA 59.091 52.381 0.00 0.00 40.58 3.93
680 708 0.695347 CTTCTGAGACCCCAAAGGCT 59.305 55.000 0.00 0.00 40.58 4.58
753 784 1.303309 ATTGTCATTAGCAGGCGAGC 58.697 50.000 0.00 0.00 0.00 5.03
940 971 5.241949 TCTCCTCAAGAACTCTGTCTTACAC 59.758 44.000 0.00 0.00 35.63 2.90
941 972 5.386060 TCTCCTCAAGAACTCTGTCTTACA 58.614 41.667 0.00 0.00 35.63 2.41
943 974 5.882040 TCTCTCCTCAAGAACTCTGTCTTA 58.118 41.667 0.00 0.00 35.63 2.10
944 975 4.735369 TCTCTCCTCAAGAACTCTGTCTT 58.265 43.478 0.00 0.00 38.41 3.01
948 979 2.760092 CCCTCTCTCCTCAAGAACTCTG 59.240 54.545 0.00 0.00 32.23 3.35
951 982 1.899438 GCCCCTCTCTCCTCAAGAACT 60.899 57.143 0.00 0.00 32.23 3.01
952 983 0.539518 GCCCCTCTCTCCTCAAGAAC 59.460 60.000 0.00 0.00 32.23 3.01
953 984 0.972983 CGCCCCTCTCTCCTCAAGAA 60.973 60.000 0.00 0.00 32.23 2.52
955 986 2.430610 CCGCCCCTCTCTCCTCAAG 61.431 68.421 0.00 0.00 0.00 3.02
956 987 2.364317 CCGCCCCTCTCTCCTCAA 60.364 66.667 0.00 0.00 0.00 3.02
992 1030 3.822192 CGCCCGACATGGAGACGA 61.822 66.667 0.00 0.00 42.00 4.20
993 1031 3.822192 TCGCCCGACATGGAGACG 61.822 66.667 0.00 0.00 42.00 4.18
994 1032 2.202756 GTCGCCCGACATGGAGAC 60.203 66.667 15.22 0.71 45.79 3.36
995 1033 2.362503 AGTCGCCCGACATGGAGA 60.363 61.111 21.14 0.00 46.76 3.71
996 1034 2.202797 CAGTCGCCCGACATGGAG 60.203 66.667 21.14 3.84 46.76 3.86
1237 1275 1.823169 GCCGGTGGTCTTGTGGTAGA 61.823 60.000 1.90 0.00 0.00 2.59
1242 1280 1.741770 GCTAGCCGGTGGTCTTGTG 60.742 63.158 2.29 0.00 0.00 3.33
1243 1281 0.613853 TAGCTAGCCGGTGGTCTTGT 60.614 55.000 12.13 0.00 0.00 3.16
1254 1292 2.194271 GAACACACACGATAGCTAGCC 58.806 52.381 12.13 0.00 42.67 3.93
1306 1372 6.461640 TGACAGACAATCCTGAGCATATATG 58.538 40.000 8.45 8.45 37.59 1.78
1332 1398 7.919091 CCATTCAATAAATCACAGGTTGATGAG 59.081 37.037 0.00 0.00 44.86 2.90
1395 1461 3.417101 TGGTGATACCGAATTGCACTTT 58.583 40.909 0.00 0.00 42.58 2.66
1407 1473 2.681097 GCCCTCTTTGACTGGTGATACC 60.681 54.545 0.00 0.00 39.22 2.73
1411 1477 2.024176 TAGCCCTCTTTGACTGGTGA 57.976 50.000 0.00 0.00 0.00 4.02
1482 1548 1.667724 GAACATGCCAATCTGGTCTCG 59.332 52.381 0.00 0.00 40.46 4.04
1585 1664 2.147150 GAAGCTCTGTTGGTTCCACTC 58.853 52.381 0.00 0.00 38.18 3.51
1707 1788 2.690326 CCGACCGGTGATTGATTCC 58.310 57.895 14.63 0.00 0.00 3.01
1852 1933 4.060205 TGGAGTCGGTTTAACTAAGCAAC 58.940 43.478 0.00 0.00 33.83 4.17
1874 1955 2.359900 GGTTTGCCATGAGAACTCGAT 58.640 47.619 0.00 0.00 34.09 3.59
1875 1956 1.808411 GGTTTGCCATGAGAACTCGA 58.192 50.000 0.00 0.00 34.09 4.04
1900 1981 1.995626 TGGCCTCCCTCTACCTTGC 60.996 63.158 3.32 0.00 0.00 4.01
1909 1990 2.608988 CCTGTGAGTGGCCTCCCT 60.609 66.667 3.32 0.00 36.86 4.20
1910 1991 1.566298 ATTCCTGTGAGTGGCCTCCC 61.566 60.000 3.32 0.00 36.86 4.30
2075 2156 9.935241 TGACTTGCAATATATTTGCCTTTTAAA 57.065 25.926 0.00 0.00 44.32 1.52
2076 2157 9.364989 GTGACTTGCAATATATTTGCCTTTTAA 57.635 29.630 0.00 6.32 44.32 1.52
2077 2158 8.526978 TGTGACTTGCAATATATTTGCCTTTTA 58.473 29.630 0.00 0.49 44.32 1.52
2175 2257 1.409381 GCCTGCCCTTTCTCAGCTTAT 60.409 52.381 0.00 0.00 0.00 1.73
2195 2277 2.357009 GAGTGCAATGCCTGTAATCTGG 59.643 50.000 1.53 0.00 32.69 3.86
2199 2281 1.767759 GGGAGTGCAATGCCTGTAAT 58.232 50.000 18.18 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.