Multiple sequence alignment - TraesCS4B01G225800

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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 TraesCS4B01G225800 chr4B 100.000 2788 0 0 1 2788 472236460 472239247 0 5149
1 TraesCS4B01G225800 chr4A 91.413 2073 113 28 1 2043 66934083 66936120 0 2782
2 TraesCS4B01G225800 chr4D 94.541 1154 38 9 900 2043 385727335 385728473 0 1759
3 TraesCS4B01G225800 chr4D 88.950 914 57 19 1 897 385726195 385727081 0 1088
4 TraesCS4B01G225800 chr6D 95.604 728 32 0 2061 2788 50572431 50571704 0 1168
5 TraesCS4B01G225800 chr2D 95.467 728 33 0 2061 2788 642480546 642481273 0 1162
6 TraesCS4B01G225800 chr2D 94.391 731 40 1 2059 2788 632622325 632623055 0 1122
7 TraesCS4B01G225800 chr2D 94.490 726 40 0 2059 2784 306547617 306548342 0 1120
8 TraesCS4B01G225800 chr5D 94.932 730 37 0 2059 2788 87177907 87178636 0 1144
9 TraesCS4B01G225800 chr6B 94.376 729 40 1 2060 2788 648795683 648796410 0 1118
10 TraesCS4B01G225800 chr5B 93.434 731 47 1 2059 2788 137291173 137291903 0 1083
11 TraesCS4B01G225800 chr7B 93.352 722 48 0 2067 2788 162330505 162331226 0 1068
12 TraesCS4B01G225800 chr3B 92.339 731 55 1 2059 2788 17588772 17588042 0 1038


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 TraesCS4B01G225800 chr4B 472236460 472239247 2787 False 5149.0 5149 100.0000 1 2788 1 chr4B.!!$F1 2787
1 TraesCS4B01G225800 chr4A 66934083 66936120 2037 False 2782.0 2782 91.4130 1 2043 1 chr4A.!!$F1 2042
2 TraesCS4B01G225800 chr4D 385726195 385728473 2278 False 1423.5 1759 91.7455 1 2043 2 chr4D.!!$F1 2042
3 TraesCS4B01G225800 chr6D 50571704 50572431 727 True 1168.0 1168 95.6040 2061 2788 1 chr6D.!!$R1 727
4 TraesCS4B01G225800 chr2D 642480546 642481273 727 False 1162.0 1162 95.4670 2061 2788 1 chr2D.!!$F3 727
5 TraesCS4B01G225800 chr2D 632622325 632623055 730 False 1122.0 1122 94.3910 2059 2788 1 chr2D.!!$F2 729
6 TraesCS4B01G225800 chr2D 306547617 306548342 725 False 1120.0 1120 94.4900 2059 2784 1 chr2D.!!$F1 725
7 TraesCS4B01G225800 chr5D 87177907 87178636 729 False 1144.0 1144 94.9320 2059 2788 1 chr5D.!!$F1 729
8 TraesCS4B01G225800 chr6B 648795683 648796410 727 False 1118.0 1118 94.3760 2060 2788 1 chr6B.!!$F1 728
9 TraesCS4B01G225800 chr5B 137291173 137291903 730 False 1083.0 1083 93.4340 2059 2788 1 chr5B.!!$F1 729
10 TraesCS4B01G225800 chr7B 162330505 162331226 721 False 1068.0 1068 93.3520 2067 2788 1 chr7B.!!$F1 721
11 TraesCS4B01G225800 chr3B 17588042 17588772 730 True 1038.0 1038 92.3390 2059 2788 1 chr3B.!!$R1 729

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
858 886 0.032416 TAGCCCAGTACCAGTCCCTC 60.032 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2510 0.165511 CCGGCGCGTAGTATCTAGTC 59.834 60.0 8.43 0.0 0.0 2.59 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
29 30 2.226674 GCAAACTTCAGGGAGTAGTTGC 59.773 50.000 2.33 2.33 37.82 4.17
65 73 6.289834 ACGCTCTACTGCTCTAGAATTACTA 58.710 40.000 0.00 0.00 0.00 1.82
124 135 7.047891 AGTACTTGAAGACAGAACATGTGAAA 58.952 34.615 0.00 0.00 44.17 2.69
126 137 8.988934 GTACTTGAAGACAGAACATGTGAAATA 58.011 33.333 0.00 0.00 44.17 1.40
134 145 6.920817 ACAGAACATGTGAAATACTCGACTA 58.079 36.000 0.00 0.00 41.91 2.59
148 159 8.978564 AATACTCGACTAATCATCTGCATAAG 57.021 34.615 0.00 0.00 0.00 1.73
225 237 6.971756 CACCATTTGCACGATCATAATTGTTA 59.028 34.615 0.00 0.00 0.00 2.41
227 239 6.140580 CCATTTGCACGATCATAATTGTTACG 59.859 38.462 0.00 0.00 0.00 3.18
334 346 3.445687 CATGGCACGCACATGGCT 61.446 61.111 0.00 0.00 45.16 4.75
354 367 2.317609 CCGCAACCAACCTCTGTCG 61.318 63.158 0.00 0.00 0.00 4.35
397 410 2.290641 TGCGTTGTTTATGATCCACCCT 60.291 45.455 0.00 0.00 0.00 4.34
451 464 4.019501 ACTGCAAATGATCCAACTCTCTCT 60.020 41.667 0.00 0.00 0.00 3.10
457 470 3.102972 TGATCCAACTCTCTCTCCCTTG 58.897 50.000 0.00 0.00 0.00 3.61
460 473 1.338579 CCAACTCTCTCTCCCTTGTGC 60.339 57.143 0.00 0.00 0.00 4.57
472 485 5.299148 TCTCCCTTGTGCAAATTTGAAATG 58.701 37.500 22.31 9.05 0.00 2.32
484 497 2.333688 TTGAAATGTCACACGTCCCA 57.666 45.000 0.00 0.00 31.90 4.37
485 498 2.559698 TGAAATGTCACACGTCCCAT 57.440 45.000 0.00 0.00 0.00 4.00
486 499 2.857483 TGAAATGTCACACGTCCCATT 58.143 42.857 0.00 0.00 0.00 3.16
487 500 3.218453 TGAAATGTCACACGTCCCATTT 58.782 40.909 9.65 9.65 39.51 2.32
511 526 2.993545 TCATTTCAAAACGGAAGCACG 58.006 42.857 0.00 0.00 40.31 5.34
516 531 1.738350 TCAAAACGGAAGCACGAAACA 59.262 42.857 2.50 0.00 37.61 2.83
555 581 4.958897 TCCAACCCCGGGCAAACG 62.959 66.667 17.73 2.88 0.00 3.60
583 610 2.503331 GAGAGCTCGATCAGATCAGGA 58.497 52.381 8.37 0.00 40.33 3.86
591 618 4.124970 TCGATCAGATCAGGAGCAAATTG 58.875 43.478 11.12 0.00 0.00 2.32
696 724 2.391389 GCTCGGTCGCTGGGAAAAG 61.391 63.158 0.00 0.00 0.00 2.27
697 725 1.741770 CTCGGTCGCTGGGAAAAGG 60.742 63.158 0.00 0.00 0.00 3.11
732 760 3.032017 CGAAATGATCGCTGGATAGGT 57.968 47.619 0.00 0.00 45.89 3.08
733 761 4.174411 CGAAATGATCGCTGGATAGGTA 57.826 45.455 0.00 0.00 45.89 3.08
734 762 4.556233 CGAAATGATCGCTGGATAGGTAA 58.444 43.478 0.00 0.00 45.89 2.85
735 763 4.988540 CGAAATGATCGCTGGATAGGTAAA 59.011 41.667 0.00 0.00 45.89 2.01
736 764 5.119279 CGAAATGATCGCTGGATAGGTAAAG 59.881 44.000 0.00 0.00 45.89 1.85
737 765 5.552870 AATGATCGCTGGATAGGTAAAGT 57.447 39.130 0.00 0.00 31.51 2.66
738 766 6.665992 AATGATCGCTGGATAGGTAAAGTA 57.334 37.500 0.00 0.00 31.51 2.24
739 767 5.707242 TGATCGCTGGATAGGTAAAGTAG 57.293 43.478 0.00 0.00 31.51 2.57
740 768 5.138276 TGATCGCTGGATAGGTAAAGTAGT 58.862 41.667 0.00 0.00 31.51 2.73
741 769 4.913335 TCGCTGGATAGGTAAAGTAGTG 57.087 45.455 0.00 0.00 0.00 2.74
742 770 4.529897 TCGCTGGATAGGTAAAGTAGTGA 58.470 43.478 0.00 0.00 0.00 3.41
743 771 4.579340 TCGCTGGATAGGTAAAGTAGTGAG 59.421 45.833 0.00 0.00 0.00 3.51
744 772 4.338682 CGCTGGATAGGTAAAGTAGTGAGT 59.661 45.833 0.00 0.00 0.00 3.41
745 773 5.530171 CGCTGGATAGGTAAAGTAGTGAGTA 59.470 44.000 0.00 0.00 0.00 2.59
746 774 6.513066 CGCTGGATAGGTAAAGTAGTGAGTAC 60.513 46.154 0.00 0.00 0.00 2.73
747 775 6.238981 GCTGGATAGGTAAAGTAGTGAGTACC 60.239 46.154 0.00 0.00 36.96 3.34
777 805 3.679389 ACTGACCATCCACTGTCAAATC 58.321 45.455 0.00 0.00 40.71 2.17
778 806 3.012518 CTGACCATCCACTGTCAAATCC 58.987 50.000 0.00 0.00 40.71 3.01
779 807 2.009774 GACCATCCACTGTCAAATCCG 58.990 52.381 0.00 0.00 0.00 4.18
780 808 0.734889 CCATCCACTGTCAAATCCGC 59.265 55.000 0.00 0.00 0.00 5.54
789 817 0.101219 GTCAAATCCGCAAGCCCATC 59.899 55.000 0.00 0.00 0.00 3.51
791 819 2.120909 AAATCCGCAAGCCCATCGG 61.121 57.895 0.00 0.00 44.16 4.18
800 828 2.879826 CAAGCCCATCGGTGAATTTTC 58.120 47.619 0.00 0.00 0.00 2.29
839 867 1.303074 CACATGAGCACCAGCCAGT 60.303 57.895 0.00 0.00 43.56 4.00
858 886 0.032416 TAGCCCAGTACCAGTCCCTC 60.032 60.000 0.00 0.00 0.00 4.30
943 1222 1.280421 AGCCTCTTCACCTCATCCAAC 59.720 52.381 0.00 0.00 0.00 3.77
944 1223 1.280421 GCCTCTTCACCTCATCCAACT 59.720 52.381 0.00 0.00 0.00 3.16
945 1224 2.679349 GCCTCTTCACCTCATCCAACTC 60.679 54.545 0.00 0.00 0.00 3.01
946 1225 2.568956 CCTCTTCACCTCATCCAACTCA 59.431 50.000 0.00 0.00 0.00 3.41
947 1226 3.594134 CTCTTCACCTCATCCAACTCAC 58.406 50.000 0.00 0.00 0.00 3.51
949 1228 1.728323 TCACCTCATCCAACTCACCA 58.272 50.000 0.00 0.00 0.00 4.17
950 1229 1.625315 TCACCTCATCCAACTCACCAG 59.375 52.381 0.00 0.00 0.00 4.00
951 1230 1.349026 CACCTCATCCAACTCACCAGT 59.651 52.381 0.00 0.00 0.00 4.00
952 1231 1.349026 ACCTCATCCAACTCACCAGTG 59.651 52.381 0.00 0.00 31.06 3.66
953 1232 1.349026 CCTCATCCAACTCACCAGTGT 59.651 52.381 0.00 0.00 31.06 3.55
1028 1307 1.164041 CGGCTGGTTCTTTTCGGTGT 61.164 55.000 0.00 0.00 0.00 4.16
1044 1323 0.037790 GTGTTCTCGCTCTGCTCCTT 60.038 55.000 0.00 0.00 0.00 3.36
1105 1385 1.598130 GTTGGCTCCGTCAAGTGCT 60.598 57.895 0.00 0.00 0.00 4.40
1128 1408 1.874345 ATTGCTCTCCCGACGACGTT 61.874 55.000 0.13 0.00 37.88 3.99
1177 1457 2.624364 TGGCATCGCTCCTATACGTTTA 59.376 45.455 0.00 0.00 0.00 2.01
1260 1547 1.303561 GCCATCAAGTGCAGGTCCA 60.304 57.895 0.00 0.00 0.00 4.02
1514 1804 0.032952 CCGAGGACACGGTTTTCTCA 59.967 55.000 3.65 0.00 46.70 3.27
1658 1954 0.756070 CCTCCTACGGTCCTCCTTCC 60.756 65.000 0.00 0.00 0.00 3.46
1798 2094 1.422161 AAGAACTGACCTGCCCTGCT 61.422 55.000 0.00 0.00 0.00 4.24
1838 2134 2.456119 CGCTCACTTGCCCATCGAC 61.456 63.158 0.00 0.00 0.00 4.20
1883 2179 1.019278 CAGGCGCTACGACATTTGGT 61.019 55.000 7.64 0.00 37.34 3.67
1900 2196 4.614555 TTGGTGATCGATATGTTTGTGC 57.385 40.909 0.00 0.00 0.00 4.57
1919 2215 3.243643 GTGCTGTTTGTTGATTCAGTTGC 59.756 43.478 0.00 0.00 0.00 4.17
1925 2221 3.646611 TGTTGATTCAGTTGCCATGTG 57.353 42.857 0.00 0.00 0.00 3.21
1926 2222 2.288334 TGTTGATTCAGTTGCCATGTGC 60.288 45.455 0.00 0.00 41.77 4.57
1927 2223 1.913778 TGATTCAGTTGCCATGTGCT 58.086 45.000 7.54 0.00 42.00 4.40
1929 2225 2.029739 TGATTCAGTTGCCATGTGCTTG 60.030 45.455 7.54 4.49 42.00 4.01
1930 2226 1.401761 TTCAGTTGCCATGTGCTTGT 58.598 45.000 7.54 0.00 42.00 3.16
1931 2227 1.401761 TCAGTTGCCATGTGCTTGTT 58.598 45.000 7.54 0.00 42.00 2.83
1932 2228 1.067364 TCAGTTGCCATGTGCTTGTTG 59.933 47.619 7.54 2.59 42.00 3.33
1933 2229 0.390124 AGTTGCCATGTGCTTGTTGG 59.610 50.000 7.54 0.00 42.00 3.77
1934 2230 0.104671 GTTGCCATGTGCTTGTTGGT 59.895 50.000 7.54 0.00 42.00 3.67
1935 2231 0.104487 TTGCCATGTGCTTGTTGGTG 59.896 50.000 7.54 0.00 42.00 4.17
1936 2232 1.665599 GCCATGTGCTTGTTGGTGC 60.666 57.895 0.00 0.00 36.87 5.01
1939 2235 1.202557 CCATGTGCTTGTTGGTGCTTT 60.203 47.619 0.00 0.00 0.00 3.51
1956 2252 7.152645 TGGTGCTTTGTTGTTTTGTTTAGTTA 58.847 30.769 0.00 0.00 0.00 2.24
1964 2260 7.324178 TGTTGTTTTGTTTAGTTACTGCCATT 58.676 30.769 0.00 0.00 0.00 3.16
1985 2281 2.497675 TGTGCTGGCTTTGGTGTTTTAA 59.502 40.909 0.00 0.00 0.00 1.52
1996 2292 2.881513 TGGTGTTTTAATTCGCTGCTCA 59.118 40.909 0.00 0.00 0.00 4.26
2022 2318 8.458843 AGTTCGTGGAATAAAGAAAATGGTATG 58.541 33.333 0.00 0.00 0.00 2.39
2043 2339 3.622612 TGATCTGTGGCATAACATTGTCG 59.377 43.478 0.00 0.00 0.00 4.35
2044 2340 3.052455 TCTGTGGCATAACATTGTCGT 57.948 42.857 0.00 0.00 0.00 4.34
2045 2341 2.741517 TCTGTGGCATAACATTGTCGTG 59.258 45.455 0.00 0.00 0.00 4.35
2046 2342 2.741517 CTGTGGCATAACATTGTCGTGA 59.258 45.455 0.00 0.00 0.00 4.35
2047 2343 3.342719 TGTGGCATAACATTGTCGTGAT 58.657 40.909 0.00 0.00 0.00 3.06
2048 2344 3.755905 TGTGGCATAACATTGTCGTGATT 59.244 39.130 0.00 0.00 0.00 2.57
2049 2345 4.217334 TGTGGCATAACATTGTCGTGATTT 59.783 37.500 0.00 0.00 0.00 2.17
2050 2346 5.412904 TGTGGCATAACATTGTCGTGATTTA 59.587 36.000 0.00 0.00 0.00 1.40
2051 2347 6.094742 TGTGGCATAACATTGTCGTGATTTAT 59.905 34.615 0.00 0.00 0.00 1.40
2052 2348 6.414694 GTGGCATAACATTGTCGTGATTTATG 59.585 38.462 0.00 2.90 32.45 1.90
2053 2349 5.399301 GGCATAACATTGTCGTGATTTATGC 59.601 40.000 14.64 14.64 45.71 3.14
2054 2350 6.201517 GCATAACATTGTCGTGATTTATGCT 58.798 36.000 15.30 0.00 44.22 3.79
2055 2351 6.141211 GCATAACATTGTCGTGATTTATGCTG 59.859 38.462 15.30 0.00 44.22 4.41
2056 2352 4.621068 ACATTGTCGTGATTTATGCTGG 57.379 40.909 0.00 0.00 0.00 4.85
2057 2353 3.181497 ACATTGTCGTGATTTATGCTGGC 60.181 43.478 0.00 0.00 0.00 4.85
2084 2380 1.060937 CGCGAATACACAAGCTGCC 59.939 57.895 0.00 0.00 0.00 4.85
2089 2385 2.802816 CGAATACACAAGCTGCCTATCC 59.197 50.000 0.00 0.00 0.00 2.59
2155 2451 2.125147 GGCCATGTGCGCACTAGA 60.125 61.111 37.59 21.19 42.61 2.43
2181 2477 0.514691 GAACAAGCGAAGGAGCACAG 59.485 55.000 0.00 0.00 40.15 3.66
2221 2518 1.202952 CCCCACGGCTAGAGACTAGAT 60.203 57.143 9.58 0.00 0.00 1.98
2308 2605 0.729116 CTTGATGGTGTCGGATGTGC 59.271 55.000 0.00 0.00 0.00 4.57
2352 2649 3.667695 CGTCAAAGATGCAAGCATTTCGA 60.668 43.478 9.16 1.83 36.70 3.71
2412 2710 2.687418 ATAGGCCCTTGCGCATGGAG 62.687 60.000 36.41 27.27 38.85 3.86
2489 2787 1.748879 GAAGGCTAATGGGCACGCA 60.749 57.895 0.00 0.00 43.56 5.24
2517 2815 2.768834 GAGGATCTCGTGCCAAACC 58.231 57.895 0.00 0.00 0.00 3.27
2550 2848 3.056313 GCATCCGGCAAGAAGGTGC 62.056 63.158 0.00 0.00 43.97 5.01
2582 2880 2.030027 TCCTCCTGGTCACACAAGAT 57.970 50.000 0.00 0.00 34.23 2.40
2748 3046 4.855340 CTCCAAAGAATAGGGCCTTGTAA 58.145 43.478 13.45 0.00 0.00 2.41
2767 3065 1.293498 CAGGAGCTTGCCGTGTACT 59.707 57.895 0.00 0.00 0.00 2.73
2770 3068 1.067071 AGGAGCTTGCCGTGTACTTAC 60.067 52.381 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.608640 ACGGCAACTACTCCCTGAAG 59.391 55.000 0.00 0.00 0.00 3.02
16 17 0.673644 CCAACGGCAACTACTCCCTG 60.674 60.000 0.00 0.00 0.00 4.45
17 18 1.125711 ACCAACGGCAACTACTCCCT 61.126 55.000 0.00 0.00 0.00 4.20
29 30 2.094854 AGTAGAGCGTAAAGACCAACGG 60.095 50.000 0.00 0.00 39.46 4.44
82 90 1.162698 ACTCGAAGTCGACGGATCAA 58.837 50.000 10.46 0.00 44.22 2.57
124 135 7.363355 CCCTTATGCAGATGATTAGTCGAGTAT 60.363 40.741 0.00 0.00 0.00 2.12
126 137 5.279206 CCCTTATGCAGATGATTAGTCGAGT 60.279 44.000 0.00 0.00 0.00 4.18
134 145 2.498167 GTCGCCCTTATGCAGATGATT 58.502 47.619 0.00 0.00 0.00 2.57
255 267 1.906333 TACCTCTGCGTGGACAGCA 60.906 57.895 4.13 0.00 42.99 4.41
260 272 1.884075 ATTGCGTACCTCTGCGTGGA 61.884 55.000 4.13 0.00 0.00 4.02
334 346 2.594303 CAGAGGTTGGTTGCGGCA 60.594 61.111 0.00 0.00 0.00 5.69
354 367 3.625764 ACGGTGCATGGTTTATGTATGAC 59.374 43.478 0.00 0.00 39.08 3.06
383 396 4.721274 TCATCTGTCAGGGTGGATCATAAA 59.279 41.667 0.00 0.00 0.00 1.40
397 410 1.140652 TGTGGTGTGCTTCATCTGTCA 59.859 47.619 0.00 0.00 0.00 3.58
430 443 4.511527 GAGAGAGAGTTGGATCATTTGCA 58.488 43.478 0.00 0.00 0.00 4.08
451 464 5.033589 ACATTTCAAATTTGCACAAGGGA 57.966 34.783 13.54 0.00 0.00 4.20
457 470 4.267452 ACGTGTGACATTTCAAATTTGCAC 59.733 37.500 13.54 13.81 31.90 4.57
460 473 4.444056 GGGACGTGTGACATTTCAAATTTG 59.556 41.667 12.15 12.15 31.90 2.32
487 500 5.220303 CGTGCTTCCGTTTTGAAATGAAAAA 60.220 36.000 0.00 0.00 0.00 1.94
511 526 2.808543 GGACAGACCAGTCATGTGTTTC 59.191 50.000 0.00 0.00 40.29 2.78
540 562 2.272447 AATCGTTTGCCCGGGGTTG 61.272 57.895 25.28 0.00 0.00 3.77
583 610 5.688621 CGCTATATCATTTGTGCAATTTGCT 59.311 36.000 21.19 2.19 45.31 3.91
591 618 5.075448 CGATGAACGCTATATCATTTGTGC 58.925 41.667 0.00 0.00 36.45 4.57
596 623 5.134202 TGTCCGATGAACGCTATATCATT 57.866 39.130 0.00 0.00 41.07 2.57
604 631 2.125512 GCCTGTCCGATGAACGCT 60.126 61.111 0.00 0.00 41.07 5.07
696 724 0.819582 TTCGTCCGTGATTCTACCCC 59.180 55.000 0.00 0.00 0.00 4.95
697 725 2.660189 TTTCGTCCGTGATTCTACCC 57.340 50.000 0.00 0.00 0.00 3.69
723 751 7.061688 AGGTACTCACTACTTTACCTATCCAG 58.938 42.308 0.00 0.00 42.12 3.86
728 756 8.150827 TCAGTAGGTACTCACTACTTTACCTA 57.849 38.462 7.37 2.81 46.63 3.08
729 757 7.025520 TCAGTAGGTACTCACTACTTTACCT 57.974 40.000 7.37 4.64 46.63 3.08
730 758 6.883756 ACTCAGTAGGTACTCACTACTTTACC 59.116 42.308 7.37 0.00 46.63 2.85
732 760 8.820831 AGTACTCAGTAGGTACTCACTACTTTA 58.179 37.037 7.37 0.77 46.63 1.85
733 761 7.607223 CAGTACTCAGTAGGTACTCACTACTTT 59.393 40.741 7.37 0.54 46.63 2.66
734 762 7.038445 TCAGTACTCAGTAGGTACTCACTACTT 60.038 40.741 7.37 0.00 46.63 2.24
736 764 6.534793 GTCAGTACTCAGTAGGTACTCACTAC 59.465 46.154 0.00 0.00 45.27 2.73
737 765 6.351711 GGTCAGTACTCAGTAGGTACTCACTA 60.352 46.154 7.66 0.00 45.27 2.74
738 766 5.490159 GTCAGTACTCAGTAGGTACTCACT 58.510 45.833 0.00 0.00 45.27 3.41
739 767 4.635324 GGTCAGTACTCAGTAGGTACTCAC 59.365 50.000 0.00 2.21 45.27 3.51
740 768 4.287845 TGGTCAGTACTCAGTAGGTACTCA 59.712 45.833 0.00 0.00 45.27 3.41
741 769 4.841422 TGGTCAGTACTCAGTAGGTACTC 58.159 47.826 0.00 0.00 45.27 2.59
743 771 4.579753 GGATGGTCAGTACTCAGTAGGTAC 59.420 50.000 0.00 0.00 39.60 3.34
744 772 4.228895 TGGATGGTCAGTACTCAGTAGGTA 59.771 45.833 0.00 0.00 0.00 3.08
745 773 3.011369 TGGATGGTCAGTACTCAGTAGGT 59.989 47.826 0.00 0.00 0.00 3.08
746 774 3.381908 GTGGATGGTCAGTACTCAGTAGG 59.618 52.174 0.00 0.00 0.00 3.18
747 775 4.097135 CAGTGGATGGTCAGTACTCAGTAG 59.903 50.000 0.00 0.00 0.00 2.57
778 806 1.656818 AATTCACCGATGGGCTTGCG 61.657 55.000 0.00 0.00 36.48 4.85
779 807 0.532115 AAATTCACCGATGGGCTTGC 59.468 50.000 0.00 0.00 36.48 4.01
780 808 2.417243 GGAAAATTCACCGATGGGCTTG 60.417 50.000 0.00 0.00 36.48 4.01
789 817 2.092323 GGGAAGAGGGAAAATTCACCG 58.908 52.381 0.00 0.00 0.00 4.94
791 819 1.472878 GCGGGAAGAGGGAAAATTCAC 59.527 52.381 0.00 0.00 0.00 3.18
839 867 0.032416 GAGGGACTGGTACTGGGCTA 60.032 60.000 0.00 0.00 41.55 3.93
858 886 1.869767 GTCGGCTCTTGATATTGCAGG 59.130 52.381 0.00 0.00 0.00 4.85
890 918 2.941453 ATATATAGGGCGCTGTGACG 57.059 50.000 14.51 0.00 0.00 4.35
897 925 2.104111 TGCATGGGTATATATAGGGCGC 59.896 50.000 0.00 0.00 0.00 6.53
943 1222 4.950050 AGAAGAAACACTACACTGGTGAG 58.050 43.478 7.78 3.72 38.01 3.51
944 1223 5.597182 AGTAGAAGAAACACTACACTGGTGA 59.403 40.000 7.78 0.00 40.68 4.02
945 1224 5.692204 CAGTAGAAGAAACACTACACTGGTG 59.308 44.000 0.00 0.00 40.68 4.17
946 1225 5.739358 GCAGTAGAAGAAACACTACACTGGT 60.739 44.000 0.00 0.00 40.68 4.00
947 1226 4.686554 GCAGTAGAAGAAACACTACACTGG 59.313 45.833 0.00 0.00 40.68 4.00
949 1228 5.302059 TCTGCAGTAGAAGAAACACTACACT 59.698 40.000 14.67 0.00 40.68 3.55
950 1229 5.529791 TCTGCAGTAGAAGAAACACTACAC 58.470 41.667 14.67 0.00 40.68 2.90
951 1230 5.279006 CCTCTGCAGTAGAAGAAACACTACA 60.279 44.000 14.67 0.00 40.68 2.74
952 1231 5.164954 CCTCTGCAGTAGAAGAAACACTAC 58.835 45.833 14.67 0.00 39.15 2.73
953 1232 4.322049 GCCTCTGCAGTAGAAGAAACACTA 60.322 45.833 14.67 0.00 34.32 2.74
1028 1307 1.079543 GCAAGGAGCAGAGCGAGAA 60.080 57.895 0.00 0.00 44.79 2.87
1105 1385 1.218047 CGTCGGGAGAGCAATCCAA 59.782 57.895 9.22 0.00 41.52 3.53
1838 2134 1.386533 CCTCCTTGCTGTAATGCCAG 58.613 55.000 0.00 0.00 35.49 4.85
1883 2179 5.181056 ACAAACAGCACAAACATATCGATCA 59.819 36.000 0.00 0.00 0.00 2.92
1900 2196 4.044336 TGGCAACTGAATCAACAAACAG 57.956 40.909 0.00 0.00 36.58 3.16
1919 2215 0.390124 AAGCACCAACAAGCACATGG 59.610 50.000 0.00 0.00 40.16 3.66
1925 2221 2.008752 ACAACAAAGCACCAACAAGC 57.991 45.000 0.00 0.00 0.00 4.01
1926 2222 4.213059 ACAAAACAACAAAGCACCAACAAG 59.787 37.500 0.00 0.00 0.00 3.16
1927 2223 4.130118 ACAAAACAACAAAGCACCAACAA 58.870 34.783 0.00 0.00 0.00 2.83
1929 2225 4.740741 AACAAAACAACAAAGCACCAAC 57.259 36.364 0.00 0.00 0.00 3.77
1930 2226 5.992217 ACTAAACAAAACAACAAAGCACCAA 59.008 32.000 0.00 0.00 0.00 3.67
1931 2227 5.542779 ACTAAACAAAACAACAAAGCACCA 58.457 33.333 0.00 0.00 0.00 4.17
1932 2228 6.474819 AACTAAACAAAACAACAAAGCACC 57.525 33.333 0.00 0.00 0.00 5.01
1933 2229 8.159709 CAGTAACTAAACAAAACAACAAAGCAC 58.840 33.333 0.00 0.00 0.00 4.40
1934 2230 7.148722 GCAGTAACTAAACAAAACAACAAAGCA 60.149 33.333 0.00 0.00 0.00 3.91
1935 2231 7.170773 GCAGTAACTAAACAAAACAACAAAGC 58.829 34.615 0.00 0.00 0.00 3.51
1936 2232 7.329717 TGGCAGTAACTAAACAAAACAACAAAG 59.670 33.333 0.00 0.00 0.00 2.77
1939 2235 6.268825 TGGCAGTAACTAAACAAAACAACA 57.731 33.333 0.00 0.00 0.00 3.33
1964 2260 0.901124 AAAACACCAAAGCCAGCACA 59.099 45.000 0.00 0.00 0.00 4.57
1973 2269 4.202060 TGAGCAGCGAATTAAAACACCAAA 60.202 37.500 0.00 0.00 0.00 3.28
1985 2281 1.016130 CCACGAACTGAGCAGCGAAT 61.016 55.000 0.00 0.00 0.00 3.34
1996 2292 6.894339 ACCATTTTCTTTATTCCACGAACT 57.106 33.333 0.00 0.00 0.00 3.01
2022 2318 3.623060 ACGACAATGTTATGCCACAGATC 59.377 43.478 0.00 0.00 0.00 2.75
2075 2371 4.080356 TCAATACAAGGATAGGCAGCTTGT 60.080 41.667 0.00 0.00 40.67 3.16
2084 2380 9.308000 ACTCTCCTTCTATCAATACAAGGATAG 57.692 37.037 13.33 13.33 42.81 2.08
2089 2385 9.743057 CTTGTACTCTCCTTCTATCAATACAAG 57.257 37.037 0.00 0.00 40.03 3.16
2155 2451 1.202758 TCCTTCGCTTGTTCACCATGT 60.203 47.619 0.00 0.00 0.00 3.21
2181 2477 1.338579 GCTGAGCATACCCCTATCTGC 60.339 57.143 0.00 0.00 34.85 4.26
2214 2510 0.165511 CCGGCGCGTAGTATCTAGTC 59.834 60.000 8.43 0.00 0.00 2.59
2221 2518 0.895100 ATTATCCCCGGCGCGTAGTA 60.895 55.000 8.43 0.00 0.00 1.82
2288 2585 1.675714 GCACATCCGACACCATCAAGA 60.676 52.381 0.00 0.00 0.00 3.02
2308 2605 1.498865 GCCACGCCATCGATTACCTG 61.499 60.000 0.00 0.00 39.41 4.00
2352 2649 1.856629 CCTGGTGGATTTGGAAGCAT 58.143 50.000 0.00 0.00 34.57 3.79
2412 2710 4.436998 CTCGACCTCACGCCCACC 62.437 72.222 0.00 0.00 0.00 4.61
2420 2718 1.107114 GCAATCCTCTCTCGACCTCA 58.893 55.000 0.00 0.00 0.00 3.86
2472 2770 1.076777 ATGCGTGCCCATTAGCCTT 60.077 52.632 0.00 0.00 0.00 4.35
2489 2787 1.832912 GAGATCCTCGGTTGGGCAT 59.167 57.895 0.00 0.00 0.00 4.40
2517 2815 1.569708 GATGCTCTTTCTCTCGCCAG 58.430 55.000 0.00 0.00 0.00 4.85
2550 2848 1.129917 AGGAGGATGAGACCATGCAG 58.870 55.000 0.00 0.00 42.72 4.41
2748 3046 1.004918 GTACACGGCAAGCTCCTGT 60.005 57.895 0.00 0.00 0.00 4.00
2767 3065 1.263356 CGTTGGACCTCCTCTGGTAA 58.737 55.000 0.00 0.00 41.00 2.85
2770 3068 2.266055 GCGTTGGACCTCCTCTGG 59.734 66.667 0.00 0.00 36.82 3.86


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

AutoCloner maintained by Alex Coulton.