Multiple sequence alignment - TraesCS5D01G304400

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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 TraesCS5D01G304400 chr5D 100.000 4037 0 0 1 4037 399621322 399617286 0.000000e+00 7456.0
1 TraesCS5D01G304400 chr5D 100.000 3260 0 0 4312 7571 399617011 399613752 0.000000e+00 6021.0
2 TraesCS5D01G304400 chr5D 100.000 42 0 0 3561 3602 409938916 409938875 2.260000e-10 78.7
3 TraesCS5D01G304400 chr5B 95.252 3307 77 31 4312 7571 479729341 479726068 0.000000e+00 5164.0
4 TraesCS5D01G304400 chr5B 97.287 2875 57 8 1 2865 479733833 479730970 0.000000e+00 4857.0
5 TraesCS5D01G304400 chr5B 97.109 1107 27 3 2914 4020 479730593 479729492 0.000000e+00 1862.0
6 TraesCS5D01G304400 chr5B 93.182 44 3 0 2025 2068 19791260 19791217 1.760000e-06 65.8
7 TraesCS5D01G304400 chr5A 93.722 2644 109 29 1 2615 505024555 505021940 0.000000e+00 3910.0
8 TraesCS5D01G304400 chr5A 91.741 1453 97 13 4822 6255 505020880 505019432 0.000000e+00 1997.0
9 TraesCS5D01G304400 chr5A 89.259 1201 77 23 6294 7486 505019174 505018018 0.000000e+00 1456.0
10 TraesCS5D01G304400 chr5A 91.141 587 40 7 2915 3501 505021448 505020874 0.000000e+00 785.0
11 TraesCS5D01G304400 chr5A 89.899 99 6 1 2771 2865 505021935 505021837 2.870000e-24 124.0
12 TraesCS5D01G304400 chr5A 97.222 36 1 0 2874 2909 505021789 505021754 2.280000e-05 62.1
13 TraesCS5D01G304400 chr3A 95.858 169 4 2 6635 6803 675873017 675873182 3.480000e-68 270.0
14 TraesCS5D01G304400 chr3A 94.012 167 9 1 6638 6804 405691670 405691505 1.260000e-62 252.0
15 TraesCS5D01G304400 chr3A 85.714 119 16 1 2623 2740 690218448 690218566 2.870000e-24 124.0
16 TraesCS5D01G304400 chr3B 94.611 167 9 0 6638 6804 399973281 399973115 7.540000e-65 259.0
17 TraesCS5D01G304400 chr4D 94.048 168 10 0 6639 6806 32019614 32019447 9.750000e-64 255.0
18 TraesCS5D01G304400 chr4D 94.048 168 10 0 6639 6806 32019796 32019629 9.750000e-64 255.0
19 TraesCS5D01G304400 chr3D 94.012 167 10 0 6638 6804 320429812 320429978 3.510000e-63 254.0
20 TraesCS5D01G304400 chr3D 93.023 86 6 0 2673 2758 343451687 343451772 7.980000e-25 126.0
21 TraesCS5D01G304400 chr6A 94.512 164 6 2 6638 6801 47466950 47466790 4.540000e-62 250.0
22 TraesCS5D01G304400 chr7B 90.299 134 12 1 2623 2755 297620696 297620563 2.810000e-39 174.0
23 TraesCS5D01G304400 chr7B 88.073 109 12 1 2642 2749 41294103 41294211 2.220000e-25 128.0
24 TraesCS5D01G304400 chr7B 92.045 88 7 0 2673 2760 609200105 609200018 2.870000e-24 124.0
25 TraesCS5D01G304400 chr4B 89.781 137 13 1 2623 2758 563993347 563993483 2.810000e-39 174.0
26 TraesCS5D01G304400 chr1A 88.136 118 12 2 2635 2751 582655698 582655582 1.020000e-28 139.0
27 TraesCS5D01G304400 chr2A 85.484 124 15 3 2636 2757 751804848 751804970 7.980000e-25 126.0
28 TraesCS5D01G304400 chr6D 95.349 43 2 0 3561 3603 7532467 7532425 1.360000e-07 69.4


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 TraesCS5D01G304400 chr5D 399613752 399621322 7570 True 6738.500000 7456 100.000000 1 7571 2 chr5D.!!$R2 7570
1 TraesCS5D01G304400 chr5B 479726068 479733833 7765 True 3961.000000 5164 96.549333 1 7571 3 chr5B.!!$R2 7570
2 TraesCS5D01G304400 chr5A 505018018 505024555 6537 True 1389.016667 3910 92.164000 1 7486 6 chr5A.!!$R1 7485

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
246 251 1.003545 CAGCCGCATCCTGTTAATTCG 60.004 52.381 0.00 0.00 0.00 3.34 F
946 953 1.300481 TCTCACAGCCTAGTCGATCG 58.700 55.000 9.36 9.36 0.00 3.69 F
1912 1942 1.717032 TACCTGACCACACTGCTTCT 58.283 50.000 0.00 0.00 0.00 2.85 F
2707 2743 3.818773 TGATGATGTGAATAGGCTGCATG 59.181 43.478 0.50 0.00 0.00 4.06 F
3257 3638 3.430042 ACAGTCCTGTTGCTGATCAAT 57.570 42.857 0.00 0.00 41.83 2.57 F
3609 3990 0.259647 TTGGTAGGCTAGCGGAGGTA 59.740 55.000 18.00 0.00 40.68 3.08 F
4649 5086 2.224402 CCTCCCTTAAGATGCTGCCTAC 60.224 54.545 3.36 0.00 0.00 3.18 F
5969 6422 4.877823 TGAAGATAGGCACAATGTCACATC 59.122 41.667 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1409 1.683917 AGATCAGGGTATGCGTCACTC 59.316 52.381 0.00 0.00 0.00 3.51 R
2630 2666 0.108041 TCTTCATGCGCATGCTCTCA 60.108 50.000 39.11 22.96 43.34 3.27 R
2867 2907 0.176680 GCTGCTTAGCTCTAGCACCA 59.823 55.000 16.95 0.48 45.16 4.17 R
3516 3897 2.749621 GTGATTGTTCGAGCCAAAGGAT 59.250 45.455 0.00 0.00 0.00 3.24 R
4649 5086 7.376336 GTGCTAATACGTATGTGTGAACTCTAG 59.624 40.741 9.24 4.26 0.00 2.43 R
5735 6182 3.483808 TTTTGGCCCCTGATTTTTCAC 57.516 42.857 0.00 0.00 0.00 3.18 R
5927 6380 3.371034 TCAGGTTCGGATCTATGTTGGA 58.629 45.455 0.00 0.00 0.00 3.53 R
7351 8062 0.323178 ATCAGGTACGACACTCCGGT 60.323 55.000 0.00 0.00 0.00 5.28 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
67 72 9.859427 TTCATTTTGCACATTAGAAGAATTAGG 57.141 29.630 0.00 0.00 0.00 2.69
87 92 2.420547 GGCATCCTCACATAGTCAAGCA 60.421 50.000 0.00 0.00 0.00 3.91
157 162 6.304624 TCTGGTTATACGATGTCATAGTCCT 58.695 40.000 1.44 0.00 0.00 3.85
246 251 1.003545 CAGCCGCATCCTGTTAATTCG 60.004 52.381 0.00 0.00 0.00 3.34
370 375 2.348666 CCTGCGAATACTTTTCCACTCG 59.651 50.000 0.00 0.00 0.00 4.18
382 387 1.913762 CCACTCGAGGGTGAAGGGT 60.914 63.158 18.41 0.00 39.34 4.34
493 500 9.808808 CATTCTGATGTTGATCGAAATATTCTC 57.191 33.333 0.00 0.00 30.36 2.87
618 625 6.753744 GGCTAATTCTTGGAGCTTTAAACATG 59.246 38.462 0.00 0.00 36.43 3.21
865 872 7.062749 TGCCTCACTCCTATAAATTTACGAT 57.937 36.000 0.00 0.00 0.00 3.73
944 951 3.739519 GCATTTCTCACAGCCTAGTCGAT 60.740 47.826 0.00 0.00 0.00 3.59
946 953 1.300481 TCTCACAGCCTAGTCGATCG 58.700 55.000 9.36 9.36 0.00 3.69
1243 1252 8.244802 AGCTCTACATACTTGTAAGTAACACAG 58.755 37.037 8.41 4.78 44.03 3.66
1406 1423 3.710326 TCATAGTGAGTGACGCATACC 57.290 47.619 0.00 0.00 0.00 2.73
1421 1438 5.077564 ACGCATACCCTGATCTATACAAGA 58.922 41.667 0.00 0.00 39.02 3.02
1443 1460 3.921677 TCCTTACTCAAAGCAACCTACG 58.078 45.455 0.00 0.00 33.49 3.51
1754 1772 4.329462 AGTTCGAGTTTGAAGCTCTCTT 57.671 40.909 7.44 0.00 34.68 2.85
1805 1824 6.759272 TGCTATGAACATCCTCTACATAACC 58.241 40.000 0.00 0.00 0.00 2.85
1880 1910 7.309621 CCTGAACCCGCTAGCTATATAAAAGTA 60.310 40.741 13.93 0.00 0.00 2.24
1912 1942 1.717032 TACCTGACCACACTGCTTCT 58.283 50.000 0.00 0.00 0.00 2.85
2223 2254 7.747690 TGTTTATAGTTCAAGAACCCCTTACA 58.252 34.615 9.20 6.54 42.06 2.41
2625 2661 4.765813 CCTTAATAAGGTTCCGGGAGAA 57.234 45.455 10.83 0.00 43.95 2.87
2630 2666 5.970501 AATAAGGTTCCGGGAGAATTACT 57.029 39.130 0.00 0.00 36.69 2.24
2707 2743 3.818773 TGATGATGTGAATAGGCTGCATG 59.181 43.478 0.50 0.00 0.00 4.06
2823 2863 6.086785 TGACATCAACATGAAAAGCATCAA 57.913 33.333 0.00 0.00 34.15 2.57
2869 2909 9.667107 TCAATAGTACTGTTAGAGGAAAAATGG 57.333 33.333 5.39 0.00 0.00 3.16
2870 2910 9.449719 CAATAGTACTGTTAGAGGAAAAATGGT 57.550 33.333 5.39 0.00 0.00 3.55
2871 2911 9.449719 AATAGTACTGTTAGAGGAAAAATGGTG 57.550 33.333 5.39 0.00 0.00 4.17
2872 2912 5.705905 AGTACTGTTAGAGGAAAAATGGTGC 59.294 40.000 0.00 0.00 0.00 5.01
3224 3605 9.672673 AGGCATAGGTTTATGTAGCTTATATTG 57.327 33.333 0.00 0.00 39.12 1.90
3257 3638 3.430042 ACAGTCCTGTTGCTGATCAAT 57.570 42.857 0.00 0.00 41.83 2.57
3470 3851 7.231317 TGGGTATCAATATCTTTCCTCAATTGC 59.769 37.037 0.00 0.00 0.00 3.56
3475 3856 7.064866 TCAATATCTTTCCTCAATTGCTCCAT 58.935 34.615 0.00 0.00 0.00 3.41
3537 3918 2.151202 TCCTTTGGCTCGAACAATCAC 58.849 47.619 3.39 0.00 0.00 3.06
3579 3960 7.472334 TGAACTACTACCTCCGTTCTAAAAT 57.528 36.000 0.00 0.00 37.31 1.82
3609 3990 0.259647 TTGGTAGGCTAGCGGAGGTA 59.740 55.000 18.00 0.00 40.68 3.08
3835 4216 8.428063 AGGCTAATATACCATATGCTGAGATTC 58.572 37.037 0.00 0.00 0.00 2.52
3870 4251 8.838649 AATTAGGCATTTTTGTTCTATACCCT 57.161 30.769 0.00 0.00 0.00 4.34
4499 4936 4.338964 TGTGGCCAGCATAAATACAAGATG 59.661 41.667 5.11 0.00 0.00 2.90
4569 5006 5.278512 GGAACTTCCATTTCCAAGTGAAGAC 60.279 44.000 2.62 0.00 42.04 3.01
4608 5045 7.500892 TGCCACTTAGAACACTAATCTGAAAAA 59.499 33.333 0.00 0.00 0.00 1.94
4624 5061 7.441890 TCTGAAAAATTATCACGGTGCTTTA 57.558 32.000 2.51 0.00 0.00 1.85
4649 5086 2.224402 CCTCCCTTAAGATGCTGCCTAC 60.224 54.545 3.36 0.00 0.00 3.18
5969 6422 4.877823 TGAAGATAGGCACAATGTCACATC 59.122 41.667 0.00 0.00 0.00 3.06
6054 6509 6.885376 CCAGTTGAGAAGTACTAGACTAGGAA 59.115 42.308 14.03 0.00 37.44 3.36
6310 7006 9.727627 CTTACTAACTACCTTACAATACTTCGG 57.272 37.037 0.00 0.00 0.00 4.30
6473 7169 5.016245 ACACCATCCCTATTTAATATGGGGG 59.984 44.000 10.41 11.56 43.98 5.40
6478 7174 7.737149 CCATCCCTATTTAATATGGGGGAAAAA 59.263 37.037 12.54 0.00 44.75 1.94
6883 7581 4.019411 TCCAGTAGTCCAGCAATTGATTCA 60.019 41.667 10.34 0.00 0.00 2.57
7086 7791 9.127277 GTGAGATTACTACCAGTATCTCTCTTT 57.873 37.037 17.98 0.00 38.87 2.52
7123 7833 2.478292 TCCCATTAAGACTGGTCCTCC 58.522 52.381 0.00 0.00 31.44 4.30
7124 7834 2.045885 TCCCATTAAGACTGGTCCTCCT 59.954 50.000 0.00 0.00 31.44 3.69
7125 7835 2.436173 CCCATTAAGACTGGTCCTCCTC 59.564 54.545 0.00 0.00 31.44 3.71
7126 7836 3.379452 CCATTAAGACTGGTCCTCCTCT 58.621 50.000 0.00 0.00 34.23 3.69
7127 7837 3.133721 CCATTAAGACTGGTCCTCCTCTG 59.866 52.174 0.00 0.00 34.23 3.35
7131 7841 1.711375 AGACTGGTCCTCCTCTGTGTA 59.289 52.381 0.00 0.00 34.23 2.90
7140 7850 2.352814 CCTCCTCTGTGTAAACTGGACG 60.353 54.545 0.00 0.00 0.00 4.79
7141 7851 2.557056 CTCCTCTGTGTAAACTGGACGA 59.443 50.000 0.00 0.00 0.00 4.20
7142 7852 2.557056 TCCTCTGTGTAAACTGGACGAG 59.443 50.000 0.00 0.00 0.00 4.18
7148 7858 0.606604 GTAAACTGGACGAGGCTCCA 59.393 55.000 9.32 0.83 38.05 3.86
7178 7888 5.400066 TGATCAGATCACTCGGTTGTTAA 57.600 39.130 9.21 0.00 33.59 2.01
7190 7900 4.328536 TCGGTTGTTAATGCAAGTGGTAT 58.671 39.130 0.00 0.00 0.00 2.73
7252 7963 0.392706 ACGGCAACACTCATGTCTGA 59.607 50.000 0.00 0.00 38.45 3.27
7273 7984 6.042093 TCTGAGACACAAACTAAACAGATCCT 59.958 38.462 0.00 0.00 0.00 3.24
7278 7989 5.765182 ACACAAACTAAACAGATCCTTGAGG 59.235 40.000 0.00 0.00 0.00 3.86
7279 7990 5.765182 CACAAACTAAACAGATCCTTGAGGT 59.235 40.000 0.00 0.00 36.34 3.85
7325 8036 1.067565 TGCTTGAGCTCACTAAGACCG 60.068 52.381 18.03 0.00 42.66 4.79
7351 8062 7.487829 GCAAAGAACAAATCTGAACAACTTACA 59.512 33.333 0.00 0.00 38.79 2.41
7384 8095 5.994054 TCGTACCTGATCTAGTAATAAGCGT 59.006 40.000 0.00 0.00 0.00 5.07
7385 8096 6.146837 TCGTACCTGATCTAGTAATAAGCGTC 59.853 42.308 0.00 0.00 0.00 5.19
7391 8102 7.204496 TGATCTAGTAATAAGCGTCTTCCTC 57.796 40.000 0.00 0.00 0.00 3.71
7392 8103 6.207025 TGATCTAGTAATAAGCGTCTTCCTCC 59.793 42.308 0.00 0.00 0.00 4.30
7443 8154 1.393603 TGACATTGCGTGGTCCAAAA 58.606 45.000 0.00 0.00 33.09 2.44
7454 8165 3.057596 CGTGGTCCAAAACATGCATACTT 60.058 43.478 0.00 0.00 0.00 2.24
7466 8177 4.937620 ACATGCATACTTGAATCGAACAGT 59.062 37.500 0.00 0.00 0.00 3.55
7475 8186 2.927477 TGAATCGAACAGTACCATTCGC 59.073 45.455 19.28 9.84 45.68 4.70
7476 8187 1.556564 ATCGAACAGTACCATTCGCG 58.443 50.000 19.28 0.00 45.68 5.87
7477 8188 0.522626 TCGAACAGTACCATTCGCGA 59.477 50.000 19.28 3.71 45.68 5.87
7480 8191 0.319083 AACAGTACCATTCGCGACCA 59.681 50.000 9.15 0.00 0.00 4.02
7488 8206 1.659098 CCATTCGCGACCAACTAAGTC 59.341 52.381 9.15 0.00 0.00 3.01
7489 8207 2.333926 CATTCGCGACCAACTAAGTCA 58.666 47.619 9.15 0.00 33.70 3.41
7505 8223 0.470341 GTCAGATTACTCCAGCCCCC 59.530 60.000 0.00 0.00 0.00 5.40
7506 8224 0.044092 TCAGATTACTCCAGCCCCCA 59.956 55.000 0.00 0.00 0.00 4.96
7507 8225 0.471617 CAGATTACTCCAGCCCCCAG 59.528 60.000 0.00 0.00 0.00 4.45
7508 8226 0.695803 AGATTACTCCAGCCCCCAGG 60.696 60.000 0.00 0.00 0.00 4.45
7526 8244 1.701847 AGGCAGAGTTGGTGTCTCATT 59.298 47.619 0.00 0.00 34.73 2.57
7539 8259 1.135859 GTCTCATTTCAGCAACTGCCG 60.136 52.381 0.00 0.00 43.38 5.69
7542 8262 1.005294 CATTTCAGCAACTGCCGCAC 61.005 55.000 0.00 0.00 43.38 5.34
7559 8279 0.799917 CACTGAGCGACGATCTGTGG 60.800 60.000 32.56 20.05 41.67 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 72 2.871022 CTGCTTGACTATGTGAGGATGC 59.129 50.000 0.00 0.00 0.00 3.91
87 92 3.181402 ACCTGGATATCATGAGGTAGCCT 60.181 47.826 15.32 0.00 37.04 4.58
157 162 4.038763 TCAGCGAACTCAGACTTCCTTTTA 59.961 41.667 0.00 0.00 0.00 1.52
175 180 6.955963 GTGTCTTATTGTGATTACTTTCAGCG 59.044 38.462 0.00 0.00 0.00 5.18
246 251 5.163884 GCTGAAGACCTTAAATCGTGGTAAC 60.164 44.000 0.00 0.00 33.74 2.50
370 375 2.258109 AGTACTTCACCCTTCACCCTC 58.742 52.381 0.00 0.00 0.00 4.30
382 387 7.560262 ACAGCAATGGTAGTATCTAGTACTTCA 59.440 37.037 0.00 9.05 40.80 3.02
546 553 3.614870 GCTAGGACAAAGGTTTGCAATGG 60.615 47.826 0.00 0.00 41.79 3.16
618 625 0.625849 TTCCCCAAAGATCTGGAGGC 59.374 55.000 0.00 0.00 38.96 4.70
865 872 7.586515 TCTGTGTGGAAGAACAGAGTAGTTCA 61.587 42.308 9.21 0.00 45.97 3.18
933 940 1.671845 GACACTTCGATCGACTAGGCT 59.328 52.381 19.26 2.85 0.00 4.58
944 951 5.723672 AGAGGATTTTACTGACACTTCGA 57.276 39.130 0.00 0.00 0.00 3.71
946 953 6.483640 ACACAAGAGGATTTTACTGACACTTC 59.516 38.462 0.00 0.00 0.00 3.01
1265 1274 6.648879 ACACAATAAACCTGCAAACTACAT 57.351 33.333 0.00 0.00 0.00 2.29
1393 1409 1.683917 AGATCAGGGTATGCGTCACTC 59.316 52.381 0.00 0.00 0.00 3.51
1421 1438 4.020485 ACGTAGGTTGCTTTGAGTAAGGAT 60.020 41.667 0.00 0.00 33.89 3.24
1443 1460 6.206829 AGACTTGTGCATAAGGGTTTCTAAAC 59.793 38.462 24.73 0.00 38.17 2.01
1716 1734 4.515191 TCGAACTTTAAGCAAAGCAGACAT 59.485 37.500 0.00 0.00 44.27 3.06
1805 1824 7.429636 TTTTCTGGGTAGTTTTGTCTATTCG 57.570 36.000 0.00 0.00 0.00 3.34
1880 1910 8.993424 AGTGTGGTCAGGTATCTTCTTTTATAT 58.007 33.333 0.00 0.00 0.00 0.86
1912 1942 6.985117 AGCAAAAAGAAGAATGCAATAGTGA 58.015 32.000 0.00 0.00 41.18 3.41
2015 2045 6.043938 TCCACCATAACCTTATAAGATGGGAC 59.956 42.308 24.78 0.00 41.21 4.46
2223 2254 5.912149 TTCCAATCCTGCAGGTTATCTAT 57.088 39.130 31.58 14.42 36.34 1.98
2621 2657 2.220593 GCGCATGCTCTCAGTAATTCTC 59.779 50.000 17.13 0.00 38.39 2.87
2622 2658 2.208431 GCGCATGCTCTCAGTAATTCT 58.792 47.619 17.13 0.00 38.39 2.40
2623 2659 1.935873 TGCGCATGCTCTCAGTAATTC 59.064 47.619 17.13 0.00 43.34 2.17
2624 2660 2.028420 TGCGCATGCTCTCAGTAATT 57.972 45.000 17.13 0.00 43.34 1.40
2625 2661 1.871676 CATGCGCATGCTCTCAGTAAT 59.128 47.619 35.08 0.70 43.34 1.89
2630 2666 0.108041 TCTTCATGCGCATGCTCTCA 60.108 50.000 39.11 22.96 43.34 3.27
2740 2776 7.785028 CCAGCTCACCATATCCTATATACCTAA 59.215 40.741 0.00 0.00 0.00 2.69
2833 2873 8.695456 TCTAACAGTACTATTGAGATTGCATCA 58.305 33.333 0.00 0.00 0.00 3.07
2865 2905 2.744494 GCTGCTTAGCTCTAGCACCATT 60.744 50.000 16.95 0.00 45.16 3.16
2867 2907 0.176680 GCTGCTTAGCTCTAGCACCA 59.823 55.000 16.95 0.48 45.16 4.17
2868 2908 0.463620 AGCTGCTTAGCTCTAGCACC 59.536 55.000 16.95 12.08 42.12 5.01
2869 2909 3.444703 TTAGCTGCTTAGCTCTAGCAC 57.555 47.619 16.95 13.94 45.00 4.40
2870 2910 3.987547 CATTAGCTGCTTAGCTCTAGCA 58.012 45.455 19.02 19.02 45.00 3.49
3224 3605 4.194640 ACAGGACTGTTCATACATGATGC 58.805 43.478 0.00 0.00 41.83 3.91
3257 3638 5.530915 CCAACAAGACAACACCTTTAGATCA 59.469 40.000 0.00 0.00 0.00 2.92
3516 3897 2.749621 GTGATTGTTCGAGCCAAAGGAT 59.250 45.455 0.00 0.00 0.00 3.24
3537 3918 5.057149 AGTTCATTAAGTAGCGGGCTTATG 58.943 41.667 0.00 0.00 0.00 1.90
3579 3960 6.163476 CGCTAGCCTACCAAAACATCATATA 58.837 40.000 9.66 0.00 0.00 0.86
3633 4014 7.590689 CGCTTGCAAATTTTATTTTGTTGGAAT 59.409 29.630 0.00 0.00 38.55 3.01
3721 4102 4.704540 ACGATGGCTTGAATTAACCATTGA 59.295 37.500 13.70 0.00 43.92 2.57
3820 4201 6.939132 AAGACAAAGAATCTCAGCATATGG 57.061 37.500 4.56 0.00 0.00 2.74
4569 5006 8.946085 TGTTCTAAGTGGCATTCTAGTATTTTG 58.054 33.333 0.00 0.00 0.00 2.44
4649 5086 7.376336 GTGCTAATACGTATGTGTGAACTCTAG 59.624 40.741 9.24 4.26 0.00 2.43
5735 6182 3.483808 TTTTGGCCCCTGATTTTTCAC 57.516 42.857 0.00 0.00 0.00 3.18
5927 6380 3.371034 TCAGGTTCGGATCTATGTTGGA 58.629 45.455 0.00 0.00 0.00 3.53
5969 6422 3.717294 CACCCCTCCCTGGTTCCG 61.717 72.222 0.00 0.00 32.46 4.30
6310 7006 9.436957 TCTACCATATCACTTCTTTCTTGAAAC 57.563 33.333 0.00 0.00 0.00 2.78
6343 7039 5.160386 AGGAGAACACCCTAACCTTCTTTA 58.840 41.667 0.00 0.00 30.92 1.85
6478 7174 7.195374 TGTCCTAGAAATAACATGCCTAGTT 57.805 36.000 0.00 0.00 0.00 2.24
6479 7175 6.808321 TGTCCTAGAAATAACATGCCTAGT 57.192 37.500 0.00 0.00 0.00 2.57
6480 7176 9.429359 CTATTGTCCTAGAAATAACATGCCTAG 57.571 37.037 0.00 0.00 0.00 3.02
6481 7177 7.878127 GCTATTGTCCTAGAAATAACATGCCTA 59.122 37.037 0.00 0.00 0.00 3.93
7074 7779 9.372369 GCAAAGTATGTACAAAAGAGAGATACT 57.628 33.333 0.00 0.00 0.00 2.12
7086 7791 6.849085 AATGGGATTGCAAAGTATGTACAA 57.151 33.333 1.71 0.00 0.00 2.41
7123 7833 2.927014 GCCTCGTCCAGTTTACACAGAG 60.927 54.545 0.00 0.00 0.00 3.35
7124 7834 1.000506 GCCTCGTCCAGTTTACACAGA 59.999 52.381 0.00 0.00 0.00 3.41
7125 7835 1.000955 AGCCTCGTCCAGTTTACACAG 59.999 52.381 0.00 0.00 0.00 3.66
7126 7836 1.000506 GAGCCTCGTCCAGTTTACACA 59.999 52.381 0.00 0.00 0.00 3.72
7127 7837 1.672145 GGAGCCTCGTCCAGTTTACAC 60.672 57.143 0.00 0.00 36.51 2.90
7131 7841 3.885814 TGGAGCCTCGTCCAGTTT 58.114 55.556 0.00 0.00 41.99 2.66
7161 7871 3.937814 TGCATTAACAACCGAGTGATCT 58.062 40.909 0.00 0.00 0.00 2.75
7190 7900 5.885912 ACTCACTAACAGAAAGGAAAAGCAA 59.114 36.000 0.00 0.00 0.00 3.91
7252 7963 6.591935 TCAAGGATCTGTTTAGTTTGTGTCT 58.408 36.000 0.00 0.00 0.00 3.41
7273 7984 3.184628 ACCTCTTCATGGATGACCTCAA 58.815 45.455 0.00 0.00 36.36 3.02
7278 7989 4.583871 AGTTTGACCTCTTCATGGATGAC 58.416 43.478 0.00 0.00 36.36 3.06
7279 7990 4.916041 AGTTTGACCTCTTCATGGATGA 57.084 40.909 0.00 0.00 32.84 2.92
7325 8036 6.892310 AAGTTGTTCAGATTTGTTCTTTGC 57.108 33.333 0.00 0.00 29.93 3.68
7351 8062 0.323178 ATCAGGTACGACACTCCGGT 60.323 55.000 0.00 0.00 0.00 5.28
7366 8077 7.209471 AGGAAGACGCTTATTACTAGATCAG 57.791 40.000 0.00 0.00 0.00 2.90
7391 8102 2.653953 ATAATTCACGCCCCCGTCGG 62.654 60.000 3.60 3.60 46.39 4.79
7392 8103 1.219522 GATAATTCACGCCCCCGTCG 61.220 60.000 0.00 0.00 46.39 5.12
7407 8118 7.334171 CGCAATGTCATCTGGTTATATGGATAA 59.666 37.037 0.00 0.00 0.00 1.75
7430 8141 1.361993 GCATGTTTTGGACCACGCA 59.638 52.632 0.00 0.00 0.00 5.24
7443 8154 4.937620 ACTGTTCGATTCAAGTATGCATGT 59.062 37.500 10.16 0.00 0.00 3.21
7454 8165 2.927477 GCGAATGGTACTGTTCGATTCA 59.073 45.455 26.03 2.08 44.91 2.57
7466 8177 2.231964 ACTTAGTTGGTCGCGAATGGTA 59.768 45.455 12.06 0.00 0.00 3.25
7475 8186 5.105877 TGGAGTAATCTGACTTAGTTGGTCG 60.106 44.000 0.00 0.00 36.58 4.79
7476 8187 6.282199 TGGAGTAATCTGACTTAGTTGGTC 57.718 41.667 0.00 0.00 0.00 4.02
7477 8188 5.337652 GCTGGAGTAATCTGACTTAGTTGGT 60.338 44.000 0.00 0.00 0.00 3.67
7480 8191 4.162509 GGGCTGGAGTAATCTGACTTAGTT 59.837 45.833 0.00 0.00 0.00 2.24
7488 8206 0.471617 CTGGGGGCTGGAGTAATCTG 59.528 60.000 0.00 0.00 0.00 2.90
7489 8207 0.695803 CCTGGGGGCTGGAGTAATCT 60.696 60.000 0.00 0.00 0.00 2.40
7505 8223 0.394192 TGAGACACCAACTCTGCCTG 59.606 55.000 0.00 0.00 35.66 4.85
7506 8224 1.356124 ATGAGACACCAACTCTGCCT 58.644 50.000 0.00 0.00 35.66 4.75
7507 8225 2.191128 AATGAGACACCAACTCTGCC 57.809 50.000 0.00 0.00 35.66 4.85
7508 8226 3.141398 TGAAATGAGACACCAACTCTGC 58.859 45.455 0.00 0.00 35.66 4.26
7509 8227 3.188048 GCTGAAATGAGACACCAACTCTG 59.812 47.826 0.00 0.00 35.66 3.35
7510 8228 3.181451 TGCTGAAATGAGACACCAACTCT 60.181 43.478 0.00 0.00 35.66 3.24
7511 8229 3.141398 TGCTGAAATGAGACACCAACTC 58.859 45.455 0.00 0.00 35.26 3.01
7539 8259 1.153939 ACAGATCGTCGCTCAGTGC 60.154 57.895 0.00 0.00 38.57 4.40
7542 8262 1.875813 GCCACAGATCGTCGCTCAG 60.876 63.158 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.