Multiple sequence alignment - TraesCS5D01G493700

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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 TraesCS5D01G493700 chr5D 100.000 4850 0 0 1 4850 526296699 526291850 0.000000e+00 8957.0
1 TraesCS5D01G493700 chr5D 73.856 306 74 6 373 675 185211202 185211504 3.070000e-22 117.0
2 TraesCS5D01G493700 chr5D 90.000 60 5 1 701 759 51272284 51272343 5.210000e-10 76.8
3 TraesCS5D01G493700 chr5A 94.229 3760 145 41 1117 4850 653410703 653406990 0.000000e+00 5675.0
4 TraesCS5D01G493700 chr5A 89.015 264 14 5 818 1067 653411236 653410974 3.640000e-81 313.0
5 TraesCS5D01G493700 chr5A 87.313 134 15 1 703 836 653425913 653425782 8.410000e-33 152.0
6 TraesCS5D01G493700 chr5A 93.333 60 3 1 701 759 40526650 40526709 2.400000e-13 87.9
7 TraesCS5D01G493700 chr5B 87.986 2056 152 45 2037 4038 661361255 661359241 0.000000e+00 2340.0
8 TraesCS5D01G493700 chr5B 90.216 1298 67 34 701 1966 661362551 661361282 0.000000e+00 1639.0
9 TraesCS5D01G493700 chr5B 91.360 544 37 1 4307 4850 661358679 661358146 0.000000e+00 736.0
10 TraesCS5D01G493700 chr5B 87.730 326 28 7 4008 4323 661359237 661358914 2.130000e-98 370.0
11 TraesCS5D01G493700 chr5B 74.504 353 84 6 325 674 400771295 400770946 1.090000e-31 148.0
12 TraesCS5D01G493700 chr6A 95.627 686 30 0 1 686 534638505 534637820 0.000000e+00 1101.0
13 TraesCS5D01G493700 chr4A 97.391 575 14 1 109 683 736586406 736586979 0.000000e+00 977.0
14 TraesCS5D01G493700 chr4A 98.221 281 5 0 109 389 734743710 734743990 4.360000e-135 492.0
15 TraesCS5D01G493700 chr4A 96.013 301 12 0 383 683 734747592 734747892 1.570000e-134 490.0
16 TraesCS5D01G493700 chr1B 80.195 308 53 8 367 671 217250428 217250730 1.760000e-54 224.0
17 TraesCS5D01G493700 chr7B 76.291 426 95 4 266 688 204105489 204105911 6.320000e-54 222.0
18 TraesCS5D01G493700 chr7B 78.209 335 61 10 1331 1663 593009013 593009337 2.290000e-48 204.0
19 TraesCS5D01G493700 chr7B 89.474 57 6 0 699 755 658627552 658627608 6.730000e-09 73.1
20 TraesCS5D01G493700 chr7B 89.286 56 6 0 699 754 658499909 658499964 2.420000e-08 71.3
21 TraesCS5D01G493700 chr7B 89.286 56 6 0 699 754 658737909 658737964 2.420000e-08 71.3
22 TraesCS5D01G493700 chr2A 75.435 460 69 27 1454 1903 689715209 689715634 2.980000e-42 183.0
23 TraesCS5D01G493700 chr6D 72.269 357 87 7 322 675 363937208 363937555 3.090000e-17 100.0
24 TraesCS5D01G493700 chr2B 94.340 53 3 0 701 753 749993549 749993497 1.120000e-11 82.4
25 TraesCS5D01G493700 chrUn 89.655 58 6 0 699 756 358028128 358028185 1.870000e-09 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 TraesCS5D01G493700 chr5D 526291850 526296699 4849 True 8957.00 8957 100.000 1 4850 1 chr5D.!!$R1 4849
1 TraesCS5D01G493700 chr5A 653406990 653411236 4246 True 2994.00 5675 91.622 818 4850 2 chr5A.!!$R2 4032
2 TraesCS5D01G493700 chr5B 661358146 661362551 4405 True 1271.25 2340 89.323 701 4850 4 chr5B.!!$R2 4149
3 TraesCS5D01G493700 chr6A 534637820 534638505 685 True 1101.00 1101 95.627 1 686 1 chr6A.!!$R1 685
4 TraesCS5D01G493700 chr4A 736586406 736586979 573 False 977.00 977 97.391 109 683 1 chr4A.!!$F1 574
5 TraesCS5D01G493700 chr4A 734743710 734747892 4182 False 491.00 492 97.117 109 683 2 chr4A.!!$F2 574

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
698 4307 1.132689 ACTTGAAGTCAGACCCCCTCT 60.133 52.381 0.00 0.00 0.00 3.69 F
1285 5133 0.327191 TATCCCTTTCGCCCTTCCCT 60.327 55.000 0.00 0.00 0.00 4.20 F
1423 5271 0.917259 GTGCTGATTGCTCGTACGAG 59.083 55.000 35.25 35.25 44.56 4.18 F
3169 7065 0.593773 CTGTTTTTGGTTCCCGTGCG 60.594 55.000 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 5389 1.626321 TCCTCATTGTAAGCGGGAACA 59.374 47.619 0.00 0.00 0.00 3.18 R
3169 7065 0.814812 GAGCCTGCTTCTCCAGATGC 60.815 60.000 7.37 7.37 43.15 3.91 R
3224 7120 5.297776 AGACAAGGAAACAGAATCACAAGTG 59.702 40.000 0.00 0.00 0.00 3.16 R
4364 8580 0.893727 GTGGGTCCTGCGGTTTTGAT 60.894 55.000 0.00 0.00 0.00 2.57 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
236 237 2.292785 AAACTTGTCCCACCGGCCTT 62.293 55.000 0.00 0.00 0.00 4.35
340 341 1.661463 AGAAGGTCTCTCCCATGCAA 58.339 50.000 0.00 0.00 36.75 4.08
620 4229 6.712547 ACCAGAATTTCGAAGAGATTGAAGTT 59.287 34.615 0.00 0.00 41.59 2.66
683 4292 4.924305 AGTGAACGTAGGTACAACTTGA 57.076 40.909 0.00 0.00 0.00 3.02
686 4295 5.045872 GTGAACGTAGGTACAACTTGAAGT 58.954 41.667 0.00 0.00 0.00 3.01
687 4296 5.174579 GTGAACGTAGGTACAACTTGAAGTC 59.825 44.000 0.00 0.00 0.00 3.01
688 4297 4.924305 ACGTAGGTACAACTTGAAGTCA 57.076 40.909 0.00 0.00 0.00 3.41
689 4298 4.868067 ACGTAGGTACAACTTGAAGTCAG 58.132 43.478 0.00 0.00 0.00 3.51
690 4299 4.581824 ACGTAGGTACAACTTGAAGTCAGA 59.418 41.667 0.00 0.00 0.00 3.27
691 4300 4.916249 CGTAGGTACAACTTGAAGTCAGAC 59.084 45.833 0.00 0.00 0.00 3.51
692 4301 4.338379 AGGTACAACTTGAAGTCAGACC 57.662 45.455 12.15 12.15 0.00 3.85
693 4302 3.071167 AGGTACAACTTGAAGTCAGACCC 59.929 47.826 14.98 9.22 0.00 4.46
694 4303 2.640316 ACAACTTGAAGTCAGACCCC 57.360 50.000 0.00 0.00 0.00 4.95
695 4304 1.143073 ACAACTTGAAGTCAGACCCCC 59.857 52.381 0.00 0.00 0.00 5.40
696 4305 1.421646 CAACTTGAAGTCAGACCCCCT 59.578 52.381 0.00 0.00 0.00 4.79
697 4306 1.353091 ACTTGAAGTCAGACCCCCTC 58.647 55.000 0.00 0.00 0.00 4.30
698 4307 1.132689 ACTTGAAGTCAGACCCCCTCT 60.133 52.381 0.00 0.00 0.00 3.69
699 4308 1.552792 CTTGAAGTCAGACCCCCTCTC 59.447 57.143 0.00 0.00 0.00 3.20
709 4318 3.095332 AGACCCCCTCTCGTTTTACTAC 58.905 50.000 0.00 0.00 0.00 2.73
714 4323 3.197116 CCCCTCTCGTTTTACTACCATGT 59.803 47.826 0.00 0.00 0.00 3.21
731 4340 9.553064 ACTACCATGTTTGAAGATGAATAGATC 57.447 33.333 13.82 0.00 31.83 2.75
735 4344 9.731819 CCATGTTTGAAGATGAATAGATCAAAG 57.268 33.333 2.74 0.00 42.54 2.77
744 4353 8.430801 AGATGAATAGATCAAAGGTTTTCTCG 57.569 34.615 0.00 0.00 42.54 4.04
745 4354 6.422776 TGAATAGATCAAAGGTTTTCTCGC 57.577 37.500 0.00 0.00 34.30 5.03
795 4404 4.708177 TCACTGGAGAAAACTTCTGAAGG 58.292 43.478 20.61 4.16 40.87 3.46
890 4513 6.082338 ACGACTATACGAGTAACACACAAAG 58.918 40.000 0.00 0.00 39.06 2.77
1093 4717 2.760385 GCTCCCTCGTACTGCCCT 60.760 66.667 0.00 0.00 0.00 5.19
1110 4741 1.078528 CTTCCCCTCCCAAAACCCC 59.921 63.158 0.00 0.00 0.00 4.95
1112 4743 2.869078 CCCCTCCCAAAACCCCCT 60.869 66.667 0.00 0.00 0.00 4.79
1114 4745 1.857348 CCCTCCCAAAACCCCCTCT 60.857 63.158 0.00 0.00 0.00 3.69
1115 4746 1.384191 CCTCCCAAAACCCCCTCTG 59.616 63.158 0.00 0.00 0.00 3.35
1116 4747 1.304464 CTCCCAAAACCCCCTCTGC 60.304 63.158 0.00 0.00 0.00 4.26
1119 4750 2.283894 CAAAACCCCCTCTGCCCC 60.284 66.667 0.00 0.00 0.00 5.80
1134 4979 4.928520 CCCCCTCCATCCCCTCCC 62.929 77.778 0.00 0.00 0.00 4.30
1250 5098 0.460987 GCATGCACTCGTAAGCCTCT 60.461 55.000 14.21 0.00 37.18 3.69
1262 5110 1.187087 AAGCCTCTTCTGTACTCCCG 58.813 55.000 0.00 0.00 0.00 5.14
1267 5115 3.618351 CCTCTTCTGTACTCCCGTCTTA 58.382 50.000 0.00 0.00 0.00 2.10
1270 5118 4.205587 TCTTCTGTACTCCCGTCTTATCC 58.794 47.826 0.00 0.00 0.00 2.59
1273 5121 3.053095 TCTGTACTCCCGTCTTATCCCTT 60.053 47.826 0.00 0.00 0.00 3.95
1276 5124 1.755380 ACTCCCGTCTTATCCCTTTCG 59.245 52.381 0.00 0.00 0.00 3.46
1277 5125 0.462789 TCCCGTCTTATCCCTTTCGC 59.537 55.000 0.00 0.00 0.00 4.70
1278 5126 0.532196 CCCGTCTTATCCCTTTCGCC 60.532 60.000 0.00 0.00 0.00 5.54
1279 5127 0.532196 CCGTCTTATCCCTTTCGCCC 60.532 60.000 0.00 0.00 0.00 6.13
1280 5128 0.464452 CGTCTTATCCCTTTCGCCCT 59.536 55.000 0.00 0.00 0.00 5.19
1281 5129 1.134491 CGTCTTATCCCTTTCGCCCTT 60.134 52.381 0.00 0.00 0.00 3.95
1282 5130 2.562635 GTCTTATCCCTTTCGCCCTTC 58.437 52.381 0.00 0.00 0.00 3.46
1283 5131 1.489230 TCTTATCCCTTTCGCCCTTCC 59.511 52.381 0.00 0.00 0.00 3.46
1284 5132 0.549469 TTATCCCTTTCGCCCTTCCC 59.451 55.000 0.00 0.00 0.00 3.97
1285 5133 0.327191 TATCCCTTTCGCCCTTCCCT 60.327 55.000 0.00 0.00 0.00 4.20
1286 5134 1.636769 ATCCCTTTCGCCCTTCCCTC 61.637 60.000 0.00 0.00 0.00 4.30
1287 5135 2.301738 CCCTTTCGCCCTTCCCTCT 61.302 63.158 0.00 0.00 0.00 3.69
1288 5136 1.222113 CCTTTCGCCCTTCCCTCTC 59.778 63.158 0.00 0.00 0.00 3.20
1289 5137 1.222113 CTTTCGCCCTTCCCTCTCC 59.778 63.158 0.00 0.00 0.00 3.71
1290 5138 2.258748 CTTTCGCCCTTCCCTCTCCC 62.259 65.000 0.00 0.00 0.00 4.30
1388 5236 2.585153 GCCTTCTTCGAGGACCCC 59.415 66.667 0.00 0.00 39.25 4.95
1423 5271 0.917259 GTGCTGATTGCTCGTACGAG 59.083 55.000 35.25 35.25 44.56 4.18
1478 5326 3.189285 GTGTTTGCTCATTTGCTTGTGT 58.811 40.909 0.00 0.00 0.00 3.72
1541 5389 4.092968 GCCGAGAAGTACATTTCGTTGATT 59.907 41.667 9.72 0.00 32.33 2.57
1556 5404 3.119990 CGTTGATTGTTCCCGCTTACAAT 60.120 43.478 0.00 0.00 45.07 2.71
1679 5527 7.356479 ACTGTGCAGTTTATACAACCAGTTGT 61.356 38.462 19.21 19.21 46.44 3.32
1697 5545 5.286320 CAGTTGTCTGTATGTAACTGTAGCG 59.714 44.000 0.00 0.00 42.94 4.26
1699 5547 5.381174 TGTCTGTATGTAACTGTAGCGTT 57.619 39.130 0.00 0.00 0.00 4.84
1785 5636 1.523758 ACCTGAAACAACGCTCATCC 58.476 50.000 0.00 0.00 0.00 3.51
1794 5645 2.813474 CGCTCATCCGCCGACAAA 60.813 61.111 0.00 0.00 0.00 2.83
1835 5686 5.784750 TGTGAGAATCGAACATGTTCATC 57.215 39.130 32.06 25.58 39.46 2.92
1906 5759 4.475944 CAAGCGGAACTAACTTGGATTTG 58.524 43.478 0.00 0.00 37.68 2.32
1953 5820 8.495949 AGTATCACGTTCTTCATTTGTACTTTG 58.504 33.333 0.00 0.00 0.00 2.77
1954 5821 6.671614 TCACGTTCTTCATTTGTACTTTGT 57.328 33.333 0.00 0.00 0.00 2.83
1955 5822 7.079182 TCACGTTCTTCATTTGTACTTTGTT 57.921 32.000 0.00 0.00 0.00 2.83
1956 5823 7.531716 TCACGTTCTTCATTTGTACTTTGTTT 58.468 30.769 0.00 0.00 0.00 2.83
1957 5824 7.483375 TCACGTTCTTCATTTGTACTTTGTTTG 59.517 33.333 0.00 0.00 0.00 2.93
1958 5825 7.272515 CACGTTCTTCATTTGTACTTTGTTTGT 59.727 33.333 0.00 0.00 0.00 2.83
1959 5826 7.810759 ACGTTCTTCATTTGTACTTTGTTTGTT 59.189 29.630 0.00 0.00 0.00 2.83
1960 5827 8.643752 CGTTCTTCATTTGTACTTTGTTTGTTT 58.356 29.630 0.00 0.00 0.00 2.83
1963 5830 9.482627 TCTTCATTTGTACTTTGTTTGTTTTGT 57.517 25.926 0.00 0.00 0.00 2.83
1990 5857 4.718858 TTTGGTCTAAACACGAATGTCG 57.281 40.909 0.00 0.00 46.93 4.35
2028 5895 2.316372 CTGGATACCTATAGCCCCCTCT 59.684 54.545 0.00 0.00 35.86 3.69
2056 5923 4.340097 TCCAGATATGAAAATTGCCTGCAG 59.660 41.667 6.78 6.78 0.00 4.41
2087 5954 7.649533 TTGACCCGATCTTTAGTATAGTGAA 57.350 36.000 0.00 0.00 0.00 3.18
2255 6135 7.577616 GCCCTGACAAAGCTACATAAATTTTCT 60.578 37.037 0.00 0.00 0.00 2.52
2285 6165 8.218256 GCTACTTCGTATTAGCTTCTGAATAC 57.782 38.462 0.00 0.00 38.16 1.89
2475 6355 2.125773 AGAATCTGAGCTGCCTTTGG 57.874 50.000 0.00 0.00 0.00 3.28
2517 6397 4.094090 GGCATACCTATCTACTACACGC 57.906 50.000 0.00 0.00 0.00 5.34
2535 6415 3.780801 CACGCGCTATTTGAAATCTTGTC 59.219 43.478 5.73 0.00 0.00 3.18
2552 6432 6.275494 TCTTGTCATCATTGTCATTTGCAT 57.725 33.333 0.00 0.00 0.00 3.96
2553 6433 6.693466 TCTTGTCATCATTGTCATTTGCATT 58.307 32.000 0.00 0.00 0.00 3.56
2554 6434 6.588373 TCTTGTCATCATTGTCATTTGCATTG 59.412 34.615 0.00 0.00 0.00 2.82
2677 6557 5.649782 ATTTGCTTGGTCTTATTCAGGTG 57.350 39.130 0.00 0.00 0.00 4.00
3023 6904 5.105797 GCTCAATCCAATACCATGTTGTTGA 60.106 40.000 1.17 2.06 0.00 3.18
3028 6909 4.458989 TCCAATACCATGTTGTTGAGCTTC 59.541 41.667 1.17 0.00 0.00 3.86
3169 7065 0.593773 CTGTTTTTGGTTCCCGTGCG 60.594 55.000 0.00 0.00 0.00 5.34
3218 7114 3.009143 GGTACATCTCCTGAAACCCAGTT 59.991 47.826 0.00 0.00 41.33 3.16
3229 7125 4.243007 GAAACCCAGTTTCCATCACTTG 57.757 45.455 8.67 0.00 44.04 3.16
3230 7126 3.312736 AACCCAGTTTCCATCACTTGT 57.687 42.857 0.00 0.00 0.00 3.16
3231 7127 2.586425 ACCCAGTTTCCATCACTTGTG 58.414 47.619 0.00 0.00 0.00 3.33
3311 7207 2.766263 ACTGCAGAGGAAATGGTATCGA 59.234 45.455 23.35 0.00 0.00 3.59
3317 7213 5.123979 GCAGAGGAAATGGTATCGAAACTTT 59.876 40.000 0.00 0.00 0.00 2.66
3430 7326 5.456822 GCTGATGATTCCTATTTGCGTTTTC 59.543 40.000 0.00 0.00 0.00 2.29
3459 7357 5.072193 TCTCTGGAGGCATGCTATTTATTCA 59.928 40.000 18.92 4.55 0.00 2.57
3522 7420 0.733909 TGTTCACTCGATCTGCTGCG 60.734 55.000 0.00 0.00 0.00 5.18
3549 7447 9.793259 AGGAAACTCTTTACAAACATCAGATTA 57.207 29.630 0.00 0.00 32.90 1.75
3625 7541 2.225091 TGCAAGGAATGAACATGGAGGT 60.225 45.455 0.00 0.00 0.00 3.85
3642 7559 4.137543 GGAGGTTTGAGTGTTCATTCTGT 58.862 43.478 0.00 0.00 32.27 3.41
3949 7866 7.341445 TGAAACACAGCTACCAAATTAGTTT 57.659 32.000 0.00 0.00 0.00 2.66
4169 8131 2.747396 AGCAGCTTGTCTCTTCAGAG 57.253 50.000 0.00 0.00 43.36 3.35
4206 8168 8.625786 ACTGTAACCTTATTTATCAAAACGGT 57.374 30.769 0.00 0.00 0.00 4.83
4226 8189 3.440228 GTCAGAGAAGATTAGCGTGGTC 58.560 50.000 0.00 0.00 0.00 4.02
4240 8203 2.412847 GCGTGGTCTCTGTGCAAAATAC 60.413 50.000 0.00 0.00 0.00 1.89
4316 8531 0.111089 CTTCGCTTCAGAACGCACAC 60.111 55.000 5.72 0.00 0.00 3.82
4335 8550 1.226888 GTTCGCGCCGTAGAGGAAT 60.227 57.895 0.00 0.00 45.00 3.01
4345 8561 2.166459 CCGTAGAGGAATCAGTTGAGCA 59.834 50.000 0.00 0.00 45.00 4.26
4348 8564 0.723981 GAGGAATCAGTTGAGCACGC 59.276 55.000 0.00 0.00 0.00 5.34
4350 8566 1.014044 GGAATCAGTTGAGCACGCGA 61.014 55.000 15.93 0.00 0.00 5.87
4570 8787 0.107993 CTCGCATTCCTCCTCAAGCA 60.108 55.000 0.00 0.00 0.00 3.91
4574 8791 0.036010 CATTCCTCCTCAAGCACGGT 60.036 55.000 0.00 0.00 0.00 4.83
4611 8828 0.907230 GGTCCTCACCAGGCTCTTCT 60.907 60.000 0.00 0.00 43.17 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.025396 CAGTCAAATCGATGTATCACCTGC 60.025 45.833 0.00 0.00 0.00 4.85
24 25 7.935755 AGATGGAATATTCACAGTCAAATCGAT 59.064 33.333 17.07 0.00 0.00 3.59
25 26 7.275183 AGATGGAATATTCACAGTCAAATCGA 58.725 34.615 17.07 0.00 0.00 3.59
340 341 7.597743 CGGCTTCATATACCTTTCGTAGTATTT 59.402 37.037 0.00 0.00 31.73 1.40
557 4166 3.404899 TGAACGGAAAGTACATTGGGTC 58.595 45.455 0.00 0.00 0.00 4.46
620 4229 3.490933 CGAAGAAGATGTGCGGGAATCTA 60.491 47.826 0.00 0.00 32.79 1.98
683 4292 0.178929 AACGAGAGGGGGTCTGACTT 60.179 55.000 7.85 0.00 34.71 3.01
686 4295 1.897802 GTAAAACGAGAGGGGGTCTGA 59.102 52.381 0.00 0.00 34.71 3.27
687 4296 1.900486 AGTAAAACGAGAGGGGGTCTG 59.100 52.381 0.00 0.00 34.71 3.51
688 4297 2.322339 AGTAAAACGAGAGGGGGTCT 57.678 50.000 0.00 0.00 38.71 3.85
689 4298 2.167281 GGTAGTAAAACGAGAGGGGGTC 59.833 54.545 0.00 0.00 0.00 4.46
690 4299 2.182827 GGTAGTAAAACGAGAGGGGGT 58.817 52.381 0.00 0.00 0.00 4.95
691 4300 2.181975 TGGTAGTAAAACGAGAGGGGG 58.818 52.381 0.00 0.00 0.00 5.40
692 4301 3.197116 ACATGGTAGTAAAACGAGAGGGG 59.803 47.826 0.00 0.00 0.00 4.79
693 4302 4.467198 ACATGGTAGTAAAACGAGAGGG 57.533 45.455 0.00 0.00 0.00 4.30
694 4303 5.929992 TCAAACATGGTAGTAAAACGAGAGG 59.070 40.000 0.00 0.00 0.00 3.69
695 4304 7.384115 TCTTCAAACATGGTAGTAAAACGAGAG 59.616 37.037 0.00 0.00 0.00 3.20
696 4305 7.211573 TCTTCAAACATGGTAGTAAAACGAGA 58.788 34.615 0.00 0.00 0.00 4.04
697 4306 7.416154 TCTTCAAACATGGTAGTAAAACGAG 57.584 36.000 0.00 0.00 0.00 4.18
698 4307 7.658167 TCATCTTCAAACATGGTAGTAAAACGA 59.342 33.333 0.00 0.00 0.00 3.85
699 4308 7.802738 TCATCTTCAAACATGGTAGTAAAACG 58.197 34.615 0.00 0.00 0.00 3.60
709 4318 9.731819 CTTTGATCTATTCATCTTCAAACATGG 57.268 33.333 0.00 0.00 33.89 3.66
753 4362 7.389053 CCAGTGAGTTAGCTGATTTAAGAGTTT 59.611 37.037 0.00 0.00 34.87 2.66
1093 4717 2.484286 GGGGGTTTTGGGAGGGGAA 61.484 63.158 0.00 0.00 0.00 3.97
1262 5110 2.562635 GAAGGGCGAAAGGGATAAGAC 58.437 52.381 0.00 0.00 0.00 3.01
1267 5115 1.619669 AGGGAAGGGCGAAAGGGAT 60.620 57.895 0.00 0.00 0.00 3.85
1270 5118 1.222113 GAGAGGGAAGGGCGAAAGG 59.778 63.158 0.00 0.00 0.00 3.11
1273 5121 2.687566 GGGAGAGGGAAGGGCGAA 60.688 66.667 0.00 0.00 0.00 4.70
1278 5126 2.840102 ATCGCGGGAGAGGGAAGG 60.840 66.667 6.13 0.00 36.66 3.46
1279 5127 1.830408 AGATCGCGGGAGAGGGAAG 60.830 63.158 6.13 0.00 36.66 3.46
1280 5128 2.127869 CAGATCGCGGGAGAGGGAA 61.128 63.158 6.13 0.00 36.66 3.97
1281 5129 2.519541 CAGATCGCGGGAGAGGGA 60.520 66.667 6.13 0.00 37.49 4.20
1282 5130 3.610669 CCAGATCGCGGGAGAGGG 61.611 72.222 6.13 5.06 0.00 4.30
1283 5131 4.292178 GCCAGATCGCGGGAGAGG 62.292 72.222 6.13 10.43 0.00 3.69
1284 5132 4.292178 GGCCAGATCGCGGGAGAG 62.292 72.222 6.13 0.00 0.00 3.20
1292 5140 4.457496 AGGTGCACGGCCAGATCG 62.457 66.667 11.45 0.00 0.00 3.69
1304 5152 1.668151 GGACCAGTCAACGAGGTGC 60.668 63.158 5.27 4.73 35.36 5.01
1305 5153 1.372997 CGGACCAGTCAACGAGGTG 60.373 63.158 5.27 0.00 35.36 4.00
1306 5154 3.048602 CGGACCAGTCAACGAGGT 58.951 61.111 0.00 0.79 38.63 3.85
1308 5156 2.432628 GGCGGACCAGTCAACGAG 60.433 66.667 0.00 0.00 35.26 4.18
1367 5215 1.596895 GGTCCTCGAAGAAGGCGTCT 61.597 60.000 0.00 0.00 38.69 4.18
1388 5236 2.097038 CACCTTCTTGAGCGAGCCG 61.097 63.158 0.00 0.00 0.00 5.52
1496 5344 0.594110 GGTCAAAAATCGACGGGCAA 59.406 50.000 0.00 0.00 34.04 4.52
1541 5389 1.626321 TCCTCATTGTAAGCGGGAACA 59.374 47.619 0.00 0.00 0.00 3.18
1556 5404 3.377656 GGAAGCCGACACTCCTCA 58.622 61.111 0.00 0.00 0.00 3.86
1679 5527 7.281549 TCAGATAACGCTACAGTTACATACAGA 59.718 37.037 0.00 0.00 39.13 3.41
1697 5545 4.991056 TCAAGCAATCGCCTATCAGATAAC 59.009 41.667 0.00 0.00 39.83 1.89
1699 5547 4.871933 TCAAGCAATCGCCTATCAGATA 57.128 40.909 0.00 0.00 39.83 1.98
1785 5636 6.043327 TCATAAGTAAATGATTTGTCGGCG 57.957 37.500 0.00 0.00 30.92 6.46
1953 5820 9.717892 TTTAGACCAAAACAAAACAAAACAAAC 57.282 25.926 0.00 0.00 0.00 2.93
1954 5821 9.717892 GTTTAGACCAAAACAAAACAAAACAAA 57.282 25.926 0.00 0.00 38.85 2.83
1955 5822 8.889717 TGTTTAGACCAAAACAAAACAAAACAA 58.110 25.926 0.00 0.00 44.23 2.83
1956 5823 8.433421 TGTTTAGACCAAAACAAAACAAAACA 57.567 26.923 0.00 0.00 44.23 2.83
1990 5857 3.606687 TCCAGAATTTAGGAGCGGAAAC 58.393 45.455 0.00 0.00 0.00 2.78
2028 5895 5.133322 AGGCAATTTTCATATCTGGAGAGGA 59.867 40.000 0.00 0.00 0.00 3.71
2056 5923 2.474410 AAGATCGGGTCAAACTCCAC 57.526 50.000 0.00 0.00 0.00 4.02
2160 6034 6.893020 AGATCCAGGTCTTTAGTTTGGTAT 57.107 37.500 0.00 0.00 0.00 2.73
2161 6035 6.383147 CCTAGATCCAGGTCTTTAGTTTGGTA 59.617 42.308 0.00 0.00 0.00 3.25
2285 6165 9.416794 GACAATACATATAGGACAAGTGATGAG 57.583 37.037 0.00 0.00 0.00 2.90
2413 6293 3.056628 CTGGATTCAGTGAGGCGTC 57.943 57.895 0.00 0.00 36.30 5.19
2475 6355 3.128242 CCTGACTGAATTCTGCACCATTC 59.872 47.826 11.86 6.26 0.00 2.67
2517 6397 7.699391 ACAATGATGACAAGATTTCAAATAGCG 59.301 33.333 0.00 0.00 0.00 4.26
2535 6415 4.860352 ACGACAATGCAAATGACAATGATG 59.140 37.500 9.59 0.00 0.00 3.07
2552 6432 4.453136 GCCTAGGTCAATACAAAACGACAA 59.547 41.667 11.31 0.00 0.00 3.18
2553 6433 3.998341 GCCTAGGTCAATACAAAACGACA 59.002 43.478 11.31 0.00 0.00 4.35
2554 6434 4.092968 CAGCCTAGGTCAATACAAAACGAC 59.907 45.833 11.31 0.00 0.00 4.34
2585 6465 2.020720 AGACGTTGTGCCACAAAATGA 58.979 42.857 12.63 0.00 40.15 2.57
2677 6557 5.812642 AGTACTTCCATCATCGACAATCAAC 59.187 40.000 0.00 0.00 0.00 3.18
2862 6743 5.649557 TCCACAAATAATTGGAAAGCATCG 58.350 37.500 0.00 0.00 39.04 3.84
3023 6904 4.521639 TGCTCATCACAATCAAAAGAAGCT 59.478 37.500 0.00 0.00 0.00 3.74
3169 7065 0.814812 GAGCCTGCTTCTCCAGATGC 60.815 60.000 7.37 7.37 43.15 3.91
3224 7120 5.297776 AGACAAGGAAACAGAATCACAAGTG 59.702 40.000 0.00 0.00 0.00 3.16
3226 7122 5.762218 AGAGACAAGGAAACAGAATCACAAG 59.238 40.000 0.00 0.00 0.00 3.16
3227 7123 5.684704 AGAGACAAGGAAACAGAATCACAA 58.315 37.500 0.00 0.00 0.00 3.33
3229 7125 6.370166 CCTAAGAGACAAGGAAACAGAATCAC 59.630 42.308 0.00 0.00 34.58 3.06
3230 7126 6.043243 ACCTAAGAGACAAGGAAACAGAATCA 59.957 38.462 0.00 0.00 36.66 2.57
3231 7127 6.468543 ACCTAAGAGACAAGGAAACAGAATC 58.531 40.000 0.00 0.00 36.66 2.52
3317 7213 5.701224 ACCAAGTGGAAACCTTTCATAAGA 58.299 37.500 3.83 0.00 38.92 2.10
3430 7326 2.444421 AGCATGCCTCCAGAGAAAAAG 58.556 47.619 15.66 0.00 0.00 2.27
3522 7420 7.730364 TCTGATGTTTGTAAAGAGTTTCCTC 57.270 36.000 0.00 0.00 38.04 3.71
3595 7511 8.415553 CCATGTTCATTCCTTGCAAGATTATTA 58.584 33.333 28.05 6.61 0.00 0.98
3614 7530 3.882888 TGAACACTCAAACCTCCATGTTC 59.117 43.478 7.75 7.75 43.90 3.18
3618 7534 4.763793 CAGAATGAACACTCAAACCTCCAT 59.236 41.667 0.00 0.00 39.69 3.41
3625 7541 8.397906 CAAAGTAGAACAGAATGAACACTCAAA 58.602 33.333 0.00 0.00 39.69 2.69
3642 7559 3.181445 ACCTGGTCATGCACAAAGTAGAA 60.181 43.478 0.00 0.00 0.00 2.10
3949 7866 8.908903 TCTCAAAAAGTTTTACAATGCTCCTTA 58.091 29.630 0.24 0.00 0.00 2.69
4120 8079 5.641636 TCAGTTAAGAGAAACATGCGCAATA 59.358 36.000 17.11 0.00 0.00 1.90
4126 8085 7.114106 GCTTTTCTTCAGTTAAGAGAAACATGC 59.886 37.037 0.00 0.00 44.95 4.06
4169 8131 3.477530 AGGTTACAGTTTTGTCAGCCTC 58.522 45.455 0.00 0.00 38.76 4.70
4172 8134 9.556030 GATAAATAAGGTTACAGTTTTGTCAGC 57.444 33.333 0.00 0.00 38.76 4.26
4182 8144 8.723311 TGACCGTTTTGATAAATAAGGTTACAG 58.277 33.333 0.00 0.00 32.41 2.74
4204 8166 2.166664 ACCACGCTAATCTTCTCTGACC 59.833 50.000 0.00 0.00 0.00 4.02
4206 8168 3.357203 AGACCACGCTAATCTTCTCTGA 58.643 45.455 0.00 0.00 0.00 3.27
4245 8208 4.592485 TTGGAAATTTAGCCAAGCGAAA 57.408 36.364 7.15 0.00 39.14 3.46
4251 8214 4.141620 TGGCAACTTTGGAAATTTAGCCAA 60.142 37.500 7.15 7.15 45.60 4.52
4316 8531 2.931713 ATTCCTCTACGGCGCGAACG 62.932 60.000 12.10 16.89 44.07 3.95
4320 8535 1.658717 CTGATTCCTCTACGGCGCG 60.659 63.158 6.90 0.00 0.00 6.86
4335 8550 1.227118 TGTTCGCGTGCTCAACTGA 60.227 52.632 5.77 0.00 0.00 3.41
4348 8564 1.341802 GATCTTCGCTGCGTGTTCG 59.658 57.895 22.48 7.13 40.37 3.95
4350 8566 1.225855 TTTGATCTTCGCTGCGTGTT 58.774 45.000 22.48 10.92 0.00 3.32
4364 8580 0.893727 GTGGGTCCTGCGGTTTTGAT 60.894 55.000 0.00 0.00 0.00 2.57
4570 8787 2.214920 GGGTTGGAGTGGAGACCGT 61.215 63.158 0.00 0.00 32.91 4.83
4574 8791 2.203788 AGCGGGTTGGAGTGGAGA 60.204 61.111 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.