Multiple sequence alignment - TraesCS5B01G021400

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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 TraesCS5B01G021400 chr5B 100.000 3288 0 0 1 3288 20629495 20626208 0.000000e+00 6072.0
1 TraesCS5B01G021400 chr5B 89.310 449 13 9 2670 3113 20608733 20608315 6.250000e-147 531.0
2 TraesCS5B01G021400 chr5B 91.870 246 18 2 2399 2643 20610199 20609955 3.140000e-90 342.0
3 TraesCS5B01G021400 chr5B 94.915 177 7 1 3112 3288 20606402 20606228 3.230000e-70 276.0
4 TraesCS5B01G021400 chr5B 86.735 98 11 2 1713 1808 547099235 547099332 1.250000e-19 108.0
5 TraesCS5B01G021400 chr5A 91.434 2580 130 33 304 2833 18856624 18859162 0.000000e+00 3456.0
6 TraesCS5B01G021400 chr5A 90.678 472 33 4 2818 3288 18860343 18860804 4.660000e-173 617.0
7 TraesCS5B01G021400 chr5A 91.724 290 13 2 1 290 18849263 18849541 3.080000e-105 392.0
8 TraesCS5B01G021400 chr5D 92.522 1685 105 13 47 1718 27539270 27540946 0.000000e+00 2394.0
9 TraesCS5B01G021400 chr5D 88.355 687 48 17 1940 2617 27540942 27541605 0.000000e+00 797.0
10 TraesCS5B01G021400 chr5D 89.474 57 5 1 2614 2670 27541643 27541698 1.640000e-08 71.3
11 TraesCS5B01G021400 chr3D 83.174 939 114 29 799 1718 109271590 109270677 0.000000e+00 819.0
12 TraesCS5B01G021400 chr3D 81.782 752 109 21 982 1718 108954362 108953624 3.630000e-169 604.0
13 TraesCS5B01G021400 chr3D 89.235 353 38 0 1940 2292 109270681 109270329 3.010000e-120 442.0
14 TraesCS5B01G021400 chr3B 83.031 937 120 27 799 1718 160641077 160640163 0.000000e+00 813.0
15 TraesCS5B01G021400 chr3B 82.195 747 110 17 982 1718 160368048 160367315 3.600000e-174 621.0
16 TraesCS5B01G021400 chr3B 89.459 351 37 0 1940 2290 160640167 160639817 8.370000e-121 444.0
17 TraesCS5B01G021400 chr3B 83.934 361 48 5 1940 2292 160367319 160366961 1.460000e-88 337.0
18 TraesCS5B01G021400 chr3B 85.600 125 14 4 1719 1842 714623084 714622963 9.580000e-26 128.0
19 TraesCS5B01G021400 chr3A 82.703 925 120 24 799 1718 121317269 121318158 0.000000e+00 785.0
20 TraesCS5B01G021400 chr3A 82.651 928 118 25 799 1718 121235541 121236433 0.000000e+00 782.0
21 TraesCS5B01G021400 chr3A 79.623 849 128 23 881 1719 121479398 121480211 4.760000e-158 568.0
22 TraesCS5B01G021400 chr3A 90.141 355 35 0 1940 2294 121318154 121318508 2.310000e-126 462.0
23 TraesCS5B01G021400 chr3A 90.113 354 35 0 1941 2294 121236430 121236783 8.310000e-126 460.0
24 TraesCS5B01G021400 chr3A 84.594 357 45 5 1942 2290 121480208 121480562 2.430000e-91 346.0
25 TraesCS5B01G021400 chr4B 81.058 359 49 9 1940 2290 666255643 666255990 5.410000e-68 268.0
26 TraesCS5B01G021400 chrUn 83.871 248 34 5 1472 1716 30329928 30329684 7.100000e-57 231.0
27 TraesCS5B01G021400 chrUn 83.806 247 36 3 1472 1716 329101071 329100827 7.100000e-57 231.0
28 TraesCS5B01G021400 chr7D 87.200 125 14 2 1719 1842 568271531 568271408 1.230000e-29 141.0
29 TraesCS5B01G021400 chr6A 85.366 123 17 1 1719 1840 578940628 578940506 3.440000e-25 126.0
30 TraesCS5B01G021400 chr6B 84.800 125 17 2 1719 1842 142100589 142100466 1.240000e-24 124.0
31 TraesCS5B01G021400 chr1A 94.118 51 3 0 1719 1769 547259571 547259521 9.780000e-11 78.7


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 TraesCS5B01G021400 chr5B 20626208 20629495 3287 True 6072.000000 6072 100.000000 1 3288 1 chr5B.!!$R1 3287
1 TraesCS5B01G021400 chr5B 20606228 20610199 3971 True 383.000000 531 92.031667 2399 3288 3 chr5B.!!$R2 889
2 TraesCS5B01G021400 chr5A 18856624 18860804 4180 False 2036.500000 3456 91.056000 304 3288 2 chr5A.!!$F2 2984
3 TraesCS5B01G021400 chr5D 27539270 27541698 2428 False 1087.433333 2394 90.117000 47 2670 3 chr5D.!!$F1 2623
4 TraesCS5B01G021400 chr3D 109270329 109271590 1261 True 630.500000 819 86.204500 799 2292 2 chr3D.!!$R2 1493
5 TraesCS5B01G021400 chr3D 108953624 108954362 738 True 604.000000 604 81.782000 982 1718 1 chr3D.!!$R1 736
6 TraesCS5B01G021400 chr3B 160639817 160641077 1260 True 628.500000 813 86.245000 799 2290 2 chr3B.!!$R3 1491
7 TraesCS5B01G021400 chr3B 160366961 160368048 1087 True 479.000000 621 83.064500 982 2292 2 chr3B.!!$R2 1310
8 TraesCS5B01G021400 chr3A 121317269 121318508 1239 False 623.500000 785 86.422000 799 2294 2 chr3A.!!$F2 1495
9 TraesCS5B01G021400 chr3A 121235541 121236783 1242 False 621.000000 782 86.382000 799 2294 2 chr3A.!!$F1 1495
10 TraesCS5B01G021400 chr3A 121479398 121480562 1164 False 457.000000 568 82.108500 881 2290 2 chr3A.!!$F3 1409

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
874 887 0.108520 CATGCATTTCCACACAGCCC 60.109 55.0 0.0 0.0 0.00 5.19 F
1072 1099 0.033011 CCCCGAGGAGAAGGAGAAGA 60.033 60.0 0.0 0.0 33.47 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2122 0.174845 GCTGGCGTCTATGTACACCA 59.825 55.0 0.0 0.0 31.01 4.17 R
2891 5415 0.108138 AGCATCCGCACCTTAGTCAC 60.108 55.0 0.0 0.0 42.27 3.67 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
17 18 3.821995 GGACACGTGGTGCAACTT 58.178 55.556 21.57 0.00 37.84 2.66
18 19 2.103410 GGACACGTGGTGCAACTTT 58.897 52.632 21.57 0.00 37.84 2.66
19 20 0.454196 GGACACGTGGTGCAACTTTT 59.546 50.000 21.57 0.00 37.84 2.27
20 21 1.544686 GACACGTGGTGCAACTTTTG 58.455 50.000 21.57 0.00 36.98 2.44
21 22 0.172352 ACACGTGGTGCAACTTTTGG 59.828 50.000 21.57 0.00 36.98 3.28
22 23 0.527385 CACGTGGTGCAACTTTTGGG 60.527 55.000 7.95 0.00 36.74 4.12
23 24 1.067250 CGTGGTGCAACTTTTGGGG 59.933 57.895 2.04 0.00 36.74 4.96
24 25 1.445518 GTGGTGCAACTTTTGGGGG 59.554 57.895 2.04 0.00 36.74 5.40
25 26 1.045911 GTGGTGCAACTTTTGGGGGA 61.046 55.000 2.04 0.00 36.74 4.81
26 27 0.325671 TGGTGCAACTTTTGGGGGAA 60.326 50.000 2.04 0.00 36.74 3.97
27 28 1.055849 GGTGCAACTTTTGGGGGAAT 58.944 50.000 0.00 0.00 36.74 3.01
28 29 1.270785 GGTGCAACTTTTGGGGGAATG 60.271 52.381 0.00 0.00 36.74 2.67
29 30 1.691434 GTGCAACTTTTGGGGGAATGA 59.309 47.619 0.00 0.00 0.00 2.57
30 31 1.969923 TGCAACTTTTGGGGGAATGAG 59.030 47.619 0.00 0.00 0.00 2.90
31 32 2.247358 GCAACTTTTGGGGGAATGAGA 58.753 47.619 0.00 0.00 0.00 3.27
32 33 2.632512 GCAACTTTTGGGGGAATGAGAA 59.367 45.455 0.00 0.00 0.00 2.87
33 34 3.306294 GCAACTTTTGGGGGAATGAGAAG 60.306 47.826 0.00 0.00 0.00 2.85
34 35 3.897505 CAACTTTTGGGGGAATGAGAAGT 59.102 43.478 0.00 0.00 0.00 3.01
35 36 4.199002 ACTTTTGGGGGAATGAGAAGTT 57.801 40.909 0.00 0.00 0.00 2.66
36 37 4.152647 ACTTTTGGGGGAATGAGAAGTTC 58.847 43.478 0.00 0.00 0.00 3.01
37 38 4.140924 ACTTTTGGGGGAATGAGAAGTTCT 60.141 41.667 4.68 4.68 0.00 3.01
38 39 3.721087 TTGGGGGAATGAGAAGTTCTC 57.279 47.619 23.53 23.53 43.65 2.87
39 40 1.916181 TGGGGGAATGAGAAGTTCTCC 59.084 52.381 26.37 14.08 42.73 3.71
40 41 2.200955 GGGGGAATGAGAAGTTCTCCT 58.799 52.381 26.37 16.33 44.17 3.69
41 42 2.171659 GGGGGAATGAGAAGTTCTCCTC 59.828 54.545 26.37 21.59 44.17 3.71
42 43 3.111484 GGGGAATGAGAAGTTCTCCTCT 58.889 50.000 26.37 12.99 42.73 3.69
43 44 4.290942 GGGGAATGAGAAGTTCTCCTCTA 58.709 47.826 26.37 11.15 42.73 2.43
44 45 4.904853 GGGGAATGAGAAGTTCTCCTCTAT 59.095 45.833 26.37 12.82 42.73 1.98
45 46 6.078664 GGGGAATGAGAAGTTCTCCTCTATA 58.921 44.000 26.37 10.12 42.73 1.31
84 85 1.544724 TGATTGCTTACCAGCCAACC 58.455 50.000 0.00 0.00 46.74 3.77
103 104 5.455326 CCAACCTCTCCCCACTATAGATTTG 60.455 48.000 6.78 0.00 0.00 2.32
114 115 7.321745 CCACTATAGATTTGGGAAAGTTCAC 57.678 40.000 6.78 0.00 0.00 3.18
123 124 2.966309 GAAAGTTCACGCCAGGCCG 61.966 63.158 5.63 3.58 0.00 6.13
133 134 1.452108 GCCAGGCCGAGCATTAAGT 60.452 57.895 14.42 0.00 0.00 2.24
186 187 6.178607 TCAATAGGAGAAATCTGCTGCATA 57.821 37.500 13.93 0.00 44.59 3.14
273 275 8.156165 GGAGACTCTTCATCATCTTTATTGGAT 58.844 37.037 1.74 0.00 0.00 3.41
321 324 7.825270 TCATTAATGATGAAATTTTGCTTGCCT 59.175 29.630 14.23 0.00 41.73 4.75
384 387 6.477253 AGAAATTAGGGGTTCTTCTCTTCAC 58.523 40.000 0.00 0.00 29.67 3.18
462 467 9.722184 AATTTTCAGAACTAAGGTACCTAGTTC 57.278 33.333 31.76 31.76 45.92 3.01
472 477 9.710818 ACTAAGGTACCTAGTTCAATGAGATAA 57.289 33.333 16.67 0.00 0.00 1.75
505 510 5.179045 ACTTTCATGAGCTTTCAGTGTTG 57.821 39.130 0.00 0.00 0.00 3.33
582 590 1.806623 GCCATCCTCGCGACAACTAAT 60.807 52.381 3.71 0.00 0.00 1.73
583 591 2.128035 CCATCCTCGCGACAACTAATC 58.872 52.381 3.71 0.00 0.00 1.75
699 712 2.526432 ACCATCCGACTGAGTACTTGT 58.474 47.619 0.00 0.00 0.00 3.16
703 716 4.307432 CATCCGACTGAGTACTTGTTGTT 58.693 43.478 0.00 0.00 0.00 2.83
708 721 3.454375 ACTGAGTACTTGTTGTTGACCG 58.546 45.455 0.00 0.00 0.00 4.79
716 729 1.222300 TGTTGTTGACCGATTCACCG 58.778 50.000 0.00 0.00 32.26 4.94
729 742 4.115516 CGATTCACCGAGAAACTCATCAT 58.884 43.478 0.00 0.00 40.22 2.45
778 791 6.228616 TCAATTTTGGATCATGTGCATCAT 57.771 33.333 0.00 0.00 37.22 2.45
794 807 1.528129 TCATGTATGCGCCAACAACA 58.472 45.000 14.84 7.74 0.00 3.33
873 886 0.738412 GCATGCATTTCCACACAGCC 60.738 55.000 14.21 0.00 0.00 4.85
874 887 0.108520 CATGCATTTCCACACAGCCC 60.109 55.000 0.00 0.00 0.00 5.19
875 888 0.542467 ATGCATTTCCACACAGCCCA 60.542 50.000 0.00 0.00 0.00 5.36
876 889 0.758310 TGCATTTCCACACAGCCCAA 60.758 50.000 0.00 0.00 0.00 4.12
878 891 1.331214 CATTTCCACACAGCCCAACT 58.669 50.000 0.00 0.00 0.00 3.16
879 892 1.688197 CATTTCCACACAGCCCAACTT 59.312 47.619 0.00 0.00 0.00 2.66
880 893 2.738587 TTTCCACACAGCCCAACTTA 57.261 45.000 0.00 0.00 0.00 2.24
881 894 2.270352 TTCCACACAGCCCAACTTAG 57.730 50.000 0.00 0.00 0.00 2.18
883 896 1.071699 TCCACACAGCCCAACTTAGTC 59.928 52.381 0.00 0.00 0.00 2.59
933 951 1.656587 TGTCCTACTCTTGGGCATGT 58.343 50.000 0.00 0.00 33.83 3.21
987 1014 4.077184 CGCCACCGTGGGAGCTTA 62.077 66.667 19.41 0.00 38.19 3.09
1072 1099 0.033011 CCCCGAGGAGAAGGAGAAGA 60.033 60.000 0.00 0.00 33.47 2.87
1116 1143 1.586154 CCAACTCCATCGGCGCTTTT 61.586 55.000 7.64 0.00 0.00 2.27
1131 1158 1.076412 TTTTGCCAGCCAGACCACA 60.076 52.632 0.00 0.00 0.00 4.17
1584 1684 2.031163 GACACCGGAAGCAGCAGT 59.969 61.111 9.46 0.00 0.00 4.40
1730 1830 1.338020 CCACCAGGTTTCACTTTCAGC 59.662 52.381 0.00 0.00 0.00 4.26
1792 1892 5.878669 ACCGGTCACTGAAATATTTACCTTC 59.121 40.000 0.00 0.00 0.00 3.46
1793 1893 6.113411 CCGGTCACTGAAATATTTACCTTCT 58.887 40.000 12.91 0.00 0.00 2.85
1795 1895 6.816640 CGGTCACTGAAATATTTACCTTCTGA 59.183 38.462 12.91 2.55 0.00 3.27
1814 1914 7.820872 CCTTCTGACCAAAATATTTCAGCAATT 59.179 33.333 0.10 0.00 36.26 2.32
1815 1915 8.761575 TTCTGACCAAAATATTTCAGCAATTC 57.238 30.769 0.10 0.00 36.26 2.17
1818 1918 7.622713 TGACCAAAATATTTCAGCAATTCCAT 58.377 30.769 0.10 0.00 0.00 3.41
1819 1919 7.765360 TGACCAAAATATTTCAGCAATTCCATC 59.235 33.333 0.10 0.00 0.00 3.51
1866 1966 9.958234 TTAAATTGAATTCGAGTGAACATTTCA 57.042 25.926 1.10 0.00 36.81 2.69
1888 1988 2.200899 CCTTTTGGCCGAAACACAAAG 58.799 47.619 14.56 3.48 35.74 2.77
1903 2003 4.180844 CACAAAGCGTGTTTTTGATTGG 57.819 40.909 4.87 0.00 38.92 3.16
1905 2005 3.616379 ACAAAGCGTGTTTTTGATTGGTG 59.384 39.130 4.87 0.00 37.01 4.17
1906 2006 1.851658 AGCGTGTTTTTGATTGGTGC 58.148 45.000 0.00 0.00 0.00 5.01
1907 2007 1.408702 AGCGTGTTTTTGATTGGTGCT 59.591 42.857 0.00 0.00 0.00 4.40
1908 2008 1.522258 GCGTGTTTTTGATTGGTGCTG 59.478 47.619 0.00 0.00 0.00 4.41
1909 2009 2.797792 GCGTGTTTTTGATTGGTGCTGA 60.798 45.455 0.00 0.00 0.00 4.26
1910 2010 3.443037 CGTGTTTTTGATTGGTGCTGAA 58.557 40.909 0.00 0.00 0.00 3.02
1911 2011 4.050553 CGTGTTTTTGATTGGTGCTGAAT 58.949 39.130 0.00 0.00 0.00 2.57
1912 2012 4.084952 CGTGTTTTTGATTGGTGCTGAATG 60.085 41.667 0.00 0.00 0.00 2.67
2069 2169 3.055094 GGATTTCCAGTTCTACTCCAGCA 60.055 47.826 0.00 0.00 35.64 4.41
2095 2195 3.263259 AAAGGCCCCTGCTCTGCT 61.263 61.111 0.00 0.00 37.74 4.24
2294 2400 1.525995 CCAACAGCTTGACCCACGT 60.526 57.895 0.00 0.00 0.00 4.49
2405 2524 2.028420 ATGGTCGATGGATGTGTGTG 57.972 50.000 0.00 0.00 0.00 3.82
2406 2525 0.684535 TGGTCGATGGATGTGTGTGT 59.315 50.000 0.00 0.00 0.00 3.72
2407 2526 1.896465 TGGTCGATGGATGTGTGTGTA 59.104 47.619 0.00 0.00 0.00 2.90
2408 2527 2.094234 TGGTCGATGGATGTGTGTGTAG 60.094 50.000 0.00 0.00 0.00 2.74
2409 2528 2.094182 GGTCGATGGATGTGTGTGTAGT 60.094 50.000 0.00 0.00 0.00 2.73
2410 2529 3.129813 GGTCGATGGATGTGTGTGTAGTA 59.870 47.826 0.00 0.00 0.00 1.82
2411 2530 4.103357 GTCGATGGATGTGTGTGTAGTAC 58.897 47.826 0.00 0.00 0.00 2.73
2452 2572 6.464895 ACCGTTGTGATAATGCAAAATTTG 57.535 33.333 0.57 0.57 0.00 2.32
2576 2696 1.927487 AATCAAACATGGAGCCAGCA 58.073 45.000 0.00 0.00 0.00 4.41
2800 4122 1.866483 ATGCCAGTCATCCTTGCCCA 61.866 55.000 0.00 0.00 30.83 5.36
2804 4126 1.548582 CCAGTCATCCTTGCCCAAAGT 60.549 52.381 0.00 0.00 33.66 2.66
2806 4128 1.425066 AGTCATCCTTGCCCAAAGTGA 59.575 47.619 0.00 0.00 33.66 3.41
2808 4130 2.029918 GTCATCCTTGCCCAAAGTGAAC 60.030 50.000 0.00 0.00 33.66 3.18
2809 4131 2.158475 TCATCCTTGCCCAAAGTGAACT 60.158 45.455 0.00 0.00 33.66 3.01
2810 4132 1.981256 TCCTTGCCCAAAGTGAACTC 58.019 50.000 0.00 0.00 33.66 3.01
2865 5389 2.592512 TCCTCCTAATCCTCCTCCAGTT 59.407 50.000 0.00 0.00 0.00 3.16
2866 5390 2.969262 CCTCCTAATCCTCCTCCAGTTC 59.031 54.545 0.00 0.00 0.00 3.01
2901 5425 4.386867 CATGACGTATGGTGACTAAGGT 57.613 45.455 0.00 0.00 32.95 3.50
2902 5426 3.861276 TGACGTATGGTGACTAAGGTG 57.139 47.619 0.00 0.00 0.00 4.00
2903 5427 2.094390 TGACGTATGGTGACTAAGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
2904 5428 1.135199 ACGTATGGTGACTAAGGTGCG 60.135 52.381 0.00 0.00 0.00 5.34
2905 5429 1.801395 CGTATGGTGACTAAGGTGCGG 60.801 57.143 0.00 0.00 0.00 5.69
2906 5430 1.479323 GTATGGTGACTAAGGTGCGGA 59.521 52.381 0.00 0.00 0.00 5.54
2907 5431 1.204146 ATGGTGACTAAGGTGCGGAT 58.796 50.000 0.00 0.00 0.00 4.18
2908 5432 0.249120 TGGTGACTAAGGTGCGGATG 59.751 55.000 0.00 0.00 0.00 3.51
2909 5433 1.090052 GGTGACTAAGGTGCGGATGC 61.090 60.000 0.00 0.00 43.20 3.91
2910 5434 0.108138 GTGACTAAGGTGCGGATGCT 60.108 55.000 0.00 0.00 43.34 3.79
2911 5435 0.108186 TGACTAAGGTGCGGATGCTG 60.108 55.000 0.00 0.00 43.34 4.41
2912 5436 0.108138 GACTAAGGTGCGGATGCTGT 60.108 55.000 0.00 0.00 43.34 4.40
2919 5463 1.227645 TGCGGATGCTGTGGATAGC 60.228 57.895 0.00 0.00 43.34 2.97
3106 5650 6.073548 CGGCAAGAGTCTTCCATGATAATAAC 60.074 42.308 1.26 0.00 0.00 1.89
3225 7683 2.447408 TCAGCCACCGAGAATAGGTA 57.553 50.000 0.00 0.00 44.64 3.08
3261 7719 2.052690 GGCTCACTCGACTAGGCCA 61.053 63.158 5.01 0.00 39.38 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.172352 CCAAAAGTTGCACCACGTGT 59.828 50.000 15.65 0.00 35.75 4.49
3 4 0.527385 CCCAAAAGTTGCACCACGTG 60.527 55.000 9.08 9.08 36.51 4.49
5 6 1.067250 CCCCAAAAGTTGCACCACG 59.933 57.895 0.00 0.00 0.00 4.94
6 7 1.045911 TCCCCCAAAAGTTGCACCAC 61.046 55.000 0.00 0.00 0.00 4.16
7 8 0.325671 TTCCCCCAAAAGTTGCACCA 60.326 50.000 0.00 0.00 0.00 4.17
8 9 1.055849 ATTCCCCCAAAAGTTGCACC 58.944 50.000 0.00 0.00 0.00 5.01
9 10 1.691434 TCATTCCCCCAAAAGTTGCAC 59.309 47.619 0.00 0.00 0.00 4.57
10 11 1.969923 CTCATTCCCCCAAAAGTTGCA 59.030 47.619 0.00 0.00 0.00 4.08
11 12 2.247358 TCTCATTCCCCCAAAAGTTGC 58.753 47.619 0.00 0.00 0.00 4.17
12 13 3.897505 ACTTCTCATTCCCCCAAAAGTTG 59.102 43.478 0.00 0.00 0.00 3.16
13 14 4.199002 ACTTCTCATTCCCCCAAAAGTT 57.801 40.909 0.00 0.00 0.00 2.66
14 15 3.903530 ACTTCTCATTCCCCCAAAAGT 57.096 42.857 0.00 0.00 0.00 2.66
15 16 4.411013 AGAACTTCTCATTCCCCCAAAAG 58.589 43.478 0.00 0.00 0.00 2.27
16 17 4.407365 GAGAACTTCTCATTCCCCCAAAA 58.593 43.478 13.12 0.00 42.90 2.44
17 18 3.245264 GGAGAACTTCTCATTCCCCCAAA 60.245 47.826 18.56 0.00 45.12 3.28
18 19 2.308866 GGAGAACTTCTCATTCCCCCAA 59.691 50.000 18.56 0.00 45.12 4.12
19 20 1.916181 GGAGAACTTCTCATTCCCCCA 59.084 52.381 18.56 0.00 45.12 4.96
20 21 2.171659 GAGGAGAACTTCTCATTCCCCC 59.828 54.545 18.56 2.38 45.12 5.40
21 22 3.111484 AGAGGAGAACTTCTCATTCCCC 58.889 50.000 18.56 3.03 45.12 4.81
22 23 7.604657 TTATAGAGGAGAACTTCTCATTCCC 57.395 40.000 18.56 3.68 45.12 3.97
23 24 9.541143 CTTTTATAGAGGAGAACTTCTCATTCC 57.459 37.037 18.56 4.26 45.12 3.01
27 28 9.756571 ACTACTTTTATAGAGGAGAACTTCTCA 57.243 33.333 18.56 0.76 45.12 3.27
103 104 2.626780 GCCTGGCGTGAACTTTCCC 61.627 63.158 1.35 0.00 0.00 3.97
106 107 2.978010 CGGCCTGGCGTGAACTTT 60.978 61.111 13.40 0.00 0.00 2.66
114 115 2.513666 TTAATGCTCGGCCTGGCG 60.514 61.111 13.40 6.79 0.00 5.69
123 124 4.697352 TGGCAAGAAGAAGACTTAATGCTC 59.303 41.667 14.35 8.67 42.35 4.26
133 134 6.533730 TCATTAAGAACTGGCAAGAAGAAGA 58.466 36.000 0.00 0.00 0.00 2.87
170 171 6.674694 TTCTTTCTATGCAGCAGATTTCTC 57.325 37.500 0.00 0.00 0.00 2.87
171 172 7.642082 AATTCTTTCTATGCAGCAGATTTCT 57.358 32.000 0.00 0.00 0.00 2.52
296 298 7.981142 AGGCAAGCAAAATTTCATCATTAATG 58.019 30.769 9.29 9.29 36.65 1.90
321 324 2.821969 GCTTGATTCCTGCCTCTTTGAA 59.178 45.455 0.00 0.00 0.00 2.69
377 380 6.073873 GCAAGAATGATTATCTCCGTGAAGAG 60.074 42.308 0.00 0.00 35.04 2.85
384 387 4.063689 AGCTGCAAGAATGATTATCTCCG 58.936 43.478 1.02 0.00 34.07 4.63
472 477 8.667076 AAAGCTCATGAAAGTAAATTTGCTTT 57.333 26.923 27.58 27.58 44.07 3.51
525 530 1.812571 GGCAAATCCTTGTCACGTGAT 59.187 47.619 23.12 0.52 37.11 3.06
527 532 0.110238 CGGCAAATCCTTGTCACGTG 60.110 55.000 9.94 9.94 36.95 4.49
530 535 0.387239 GCACGGCAAATCCTTGTCAC 60.387 55.000 0.00 0.00 36.95 3.67
699 712 1.341852 TCTCGGTGAATCGGTCAACAA 59.658 47.619 5.99 0.00 45.06 2.83
703 716 1.616865 AGTTTCTCGGTGAATCGGTCA 59.383 47.619 0.00 0.00 34.24 4.02
708 721 6.019479 GTGTATGATGAGTTTCTCGGTGAATC 60.019 42.308 0.00 0.00 34.24 2.52
716 729 7.010923 GTCATGAAGGTGTATGATGAGTTTCTC 59.989 40.741 0.00 0.00 35.91 2.87
729 742 3.650942 AGACTTTGGGTCATGAAGGTGTA 59.349 43.478 0.00 0.00 46.72 2.90
778 791 1.068679 CATGTGTTGTTGGCGCATACA 60.069 47.619 10.83 10.00 35.58 2.29
779 792 1.198867 TCATGTGTTGTTGGCGCATAC 59.801 47.619 10.83 6.99 35.58 2.39
780 793 1.198867 GTCATGTGTTGTTGGCGCATA 59.801 47.619 10.83 0.00 35.58 3.14
781 794 0.039256 GTCATGTGTTGTTGGCGCAT 60.039 50.000 10.83 0.00 37.53 4.73
794 807 1.075542 CGTGGTTATGCACGTCATGT 58.924 50.000 9.77 0.00 39.64 3.21
873 886 3.305335 GCCATGTTGGTTGACTAAGTTGG 60.305 47.826 0.00 4.83 40.46 3.77
874 887 3.569701 AGCCATGTTGGTTGACTAAGTTG 59.430 43.478 0.00 0.00 40.46 3.16
875 888 3.832527 AGCCATGTTGGTTGACTAAGTT 58.167 40.909 0.00 0.00 40.46 2.66
876 889 3.508845 AGCCATGTTGGTTGACTAAGT 57.491 42.857 0.00 0.00 40.46 2.24
878 891 4.098914 AGAAGCCATGTTGGTTGACTAA 57.901 40.909 0.00 0.00 40.46 2.24
879 892 3.788227 AGAAGCCATGTTGGTTGACTA 57.212 42.857 0.00 0.00 40.46 2.59
880 893 2.664402 AGAAGCCATGTTGGTTGACT 57.336 45.000 0.00 0.00 40.46 3.41
881 894 2.029918 GGAAGAAGCCATGTTGGTTGAC 60.030 50.000 0.00 0.00 40.46 3.18
883 896 1.962807 TGGAAGAAGCCATGTTGGTTG 59.037 47.619 0.00 0.00 40.46 3.77
1072 1099 2.909006 TCTGCTTGAAGATCTGGAACCT 59.091 45.455 0.00 0.00 0.00 3.50
1116 1143 3.170672 ACTGTGGTCTGGCTGGCA 61.171 61.111 3.18 3.18 0.00 4.92
1152 1179 0.920763 TGATGGTCTGGGGCCTGAAT 60.921 55.000 0.84 0.00 0.00 2.57
1156 1183 3.017581 GGTGATGGTCTGGGGCCT 61.018 66.667 0.84 0.00 0.00 5.19
1730 1830 9.708222 AATTCAGTAAATTTCATCGAAATCTCG 57.292 29.630 0.00 0.00 40.77 4.04
1762 1862 6.834168 AATATTTCAGTGACCGGTGAAATT 57.166 33.333 26.45 13.97 46.49 1.82
1770 1870 6.816640 TCAGAAGGTAAATATTTCAGTGACCG 59.183 38.462 3.39 0.00 0.00 4.79
1792 1892 7.098477 TGGAATTGCTGAAATATTTTGGTCAG 58.902 34.615 1.43 6.35 40.40 3.51
1793 1893 7.002250 TGGAATTGCTGAAATATTTTGGTCA 57.998 32.000 1.43 0.00 0.00 4.02
1795 1895 7.622713 TGATGGAATTGCTGAAATATTTTGGT 58.377 30.769 1.43 0.00 0.00 3.67
1846 1946 4.083324 GGCTGAAATGTTCACTCGAATTCA 60.083 41.667 6.22 0.00 35.46 2.57
1866 1966 1.040339 TGTGTTTCGGCCAAAAGGCT 61.040 50.000 2.24 0.00 39.43 4.58
1888 1988 1.522258 CAGCACCAATCAAAAACACGC 59.478 47.619 0.00 0.00 0.00 5.34
1894 1994 5.754406 CAGAAACATTCAGCACCAATCAAAA 59.246 36.000 0.00 0.00 0.00 2.44
1895 1995 5.068855 TCAGAAACATTCAGCACCAATCAAA 59.931 36.000 0.00 0.00 0.00 2.69
1897 1997 4.143543 TCAGAAACATTCAGCACCAATCA 58.856 39.130 0.00 0.00 0.00 2.57
1898 1998 4.771590 TCAGAAACATTCAGCACCAATC 57.228 40.909 0.00 0.00 0.00 2.67
1899 1999 5.069516 AGTTTCAGAAACATTCAGCACCAAT 59.930 36.000 24.85 0.01 43.79 3.16
1900 2000 4.402155 AGTTTCAGAAACATTCAGCACCAA 59.598 37.500 24.85 0.00 43.79 3.67
1901 2001 3.953612 AGTTTCAGAAACATTCAGCACCA 59.046 39.130 24.85 0.00 43.79 4.17
1902 2002 4.036734 TCAGTTTCAGAAACATTCAGCACC 59.963 41.667 24.85 0.00 43.79 5.01
1903 2003 5.173774 TCAGTTTCAGAAACATTCAGCAC 57.826 39.130 24.85 0.00 43.79 4.40
1905 2005 6.197842 CACTTTCAGTTTCAGAAACATTCAGC 59.802 38.462 24.85 0.00 43.79 4.26
1906 2006 7.475015 TCACTTTCAGTTTCAGAAACATTCAG 58.525 34.615 24.85 17.18 43.79 3.02
1907 2007 7.389803 TCACTTTCAGTTTCAGAAACATTCA 57.610 32.000 24.85 7.97 43.79 2.57
1908 2008 8.687824 TTTCACTTTCAGTTTCAGAAACATTC 57.312 30.769 24.85 1.31 43.79 2.67
1909 2009 8.925700 GTTTTCACTTTCAGTTTCAGAAACATT 58.074 29.630 24.85 5.48 43.79 2.71
1910 2010 8.306761 AGTTTTCACTTTCAGTTTCAGAAACAT 58.693 29.630 24.85 9.78 43.79 2.71
1911 2011 7.657336 AGTTTTCACTTTCAGTTTCAGAAACA 58.343 30.769 24.85 5.48 43.79 2.83
1912 2012 8.520835 AAGTTTTCACTTTCAGTTTCAGAAAC 57.479 30.769 17.11 17.11 40.66 2.78
1936 2036 2.029964 GTGACGGACGCCTGGAAA 59.970 61.111 0.00 0.00 0.00 3.13
2022 2122 0.174845 GCTGGCGTCTATGTACACCA 59.825 55.000 0.00 0.00 31.01 4.17
2069 2169 0.257039 CAGGGGCCTTTGTAGATGCT 59.743 55.000 0.84 0.00 0.00 3.79
2095 2195 4.649705 TTCACCCTCCCGGCCTCA 62.650 66.667 0.00 0.00 33.26 3.86
2122 2222 1.589196 GCAGTAGCCGACGATGGTC 60.589 63.158 0.00 0.00 39.89 4.02
2294 2400 3.792736 GTAGGCATGGCGGTGGGA 61.793 66.667 14.30 0.00 0.00 4.37
2405 2524 9.755804 GGTACCATAAGGAAACAATAGTACTAC 57.244 37.037 7.15 0.00 38.69 2.73
2406 2525 8.632679 CGGTACCATAAGGAAACAATAGTACTA 58.367 37.037 13.54 4.77 38.69 1.82
2407 2526 7.124750 ACGGTACCATAAGGAAACAATAGTACT 59.875 37.037 13.54 0.00 38.69 2.73
2408 2527 7.267857 ACGGTACCATAAGGAAACAATAGTAC 58.732 38.462 13.54 0.00 38.69 2.73
2409 2528 7.422465 ACGGTACCATAAGGAAACAATAGTA 57.578 36.000 13.54 0.00 38.69 1.82
2410 2529 6.303903 ACGGTACCATAAGGAAACAATAGT 57.696 37.500 13.54 0.00 38.69 2.12
2411 2530 6.596497 ACAACGGTACCATAAGGAAACAATAG 59.404 38.462 13.54 0.00 38.69 1.73
2452 2572 7.042456 ACGAGCAATCACATTATTGAGTACATC 60.042 37.037 0.00 0.00 38.84 3.06
2467 2587 3.318017 AGTACACTCAACGAGCAATCAC 58.682 45.455 0.00 0.00 32.04 3.06
2576 2696 0.694771 TGCTTCCCACTTGAGCTGAT 59.305 50.000 0.00 0.00 37.32 2.90
2612 2732 9.692749 AGGCCGTTCATATAACATATATATTCG 57.307 33.333 0.00 0.00 0.00 3.34
2709 4026 4.379394 CCATCGTCATTCGGTTGAAAATGT 60.379 41.667 0.00 0.00 37.71 2.71
2800 4122 1.132365 AGGGGAGGAGGAGTTCACTTT 60.132 52.381 0.00 0.00 0.00 2.66
2804 4126 0.338814 GGTAGGGGAGGAGGAGTTCA 59.661 60.000 0.00 0.00 0.00 3.18
2806 4128 1.219824 TCGGTAGGGGAGGAGGAGTT 61.220 60.000 0.00 0.00 0.00 3.01
2808 4130 0.468400 CTTCGGTAGGGGAGGAGGAG 60.468 65.000 0.00 0.00 0.00 3.69
2809 4131 1.219824 ACTTCGGTAGGGGAGGAGGA 61.220 60.000 0.00 0.00 0.00 3.71
2810 4132 0.325390 AACTTCGGTAGGGGAGGAGG 60.325 60.000 0.00 0.00 0.00 4.30
2865 5389 0.963225 TCATGGAGGACGACAAACGA 59.037 50.000 0.00 0.00 45.77 3.85
2886 5410 1.479323 TCCGCACCTTAGTCACCATAC 59.521 52.381 0.00 0.00 0.00 2.39
2887 5411 1.855295 TCCGCACCTTAGTCACCATA 58.145 50.000 0.00 0.00 0.00 2.74
2888 5412 1.134401 CATCCGCACCTTAGTCACCAT 60.134 52.381 0.00 0.00 0.00 3.55
2889 5413 0.249120 CATCCGCACCTTAGTCACCA 59.751 55.000 0.00 0.00 0.00 4.17
2890 5414 1.090052 GCATCCGCACCTTAGTCACC 61.090 60.000 0.00 0.00 38.36 4.02
2891 5415 0.108138 AGCATCCGCACCTTAGTCAC 60.108 55.000 0.00 0.00 42.27 3.67
2892 5416 0.108186 CAGCATCCGCACCTTAGTCA 60.108 55.000 0.00 0.00 42.27 3.41
2893 5417 0.108138 ACAGCATCCGCACCTTAGTC 60.108 55.000 0.00 0.00 42.27 2.59
2894 5418 0.391661 CACAGCATCCGCACCTTAGT 60.392 55.000 0.00 0.00 42.27 2.24
2895 5419 1.091771 CCACAGCATCCGCACCTTAG 61.092 60.000 0.00 0.00 42.27 2.18
2896 5420 1.078497 CCACAGCATCCGCACCTTA 60.078 57.895 0.00 0.00 42.27 2.69
2897 5421 2.202236 ATCCACAGCATCCGCACCTT 62.202 55.000 0.00 0.00 42.27 3.50
2898 5422 1.337384 TATCCACAGCATCCGCACCT 61.337 55.000 0.00 0.00 42.27 4.00
2899 5423 0.882042 CTATCCACAGCATCCGCACC 60.882 60.000 0.00 0.00 42.27 5.01
2900 5424 1.502163 GCTATCCACAGCATCCGCAC 61.502 60.000 0.00 0.00 41.40 5.34
2901 5425 1.227645 GCTATCCACAGCATCCGCA 60.228 57.895 0.00 0.00 41.40 5.69
2902 5426 2.313172 CGCTATCCACAGCATCCGC 61.313 63.158 0.00 0.00 41.88 5.54
2903 5427 1.665916 CCGCTATCCACAGCATCCG 60.666 63.158 0.00 0.00 41.88 4.18
2904 5428 0.322975 ATCCGCTATCCACAGCATCC 59.677 55.000 0.00 0.00 41.88 3.51
2905 5429 1.270518 ACATCCGCTATCCACAGCATC 60.271 52.381 0.00 0.00 41.88 3.91
2906 5430 0.761187 ACATCCGCTATCCACAGCAT 59.239 50.000 0.00 0.00 41.88 3.79
2907 5431 1.068588 GTACATCCGCTATCCACAGCA 59.931 52.381 0.00 0.00 41.88 4.41
2908 5432 1.341531 AGTACATCCGCTATCCACAGC 59.658 52.381 0.00 0.00 38.23 4.40
2909 5433 2.887783 AGAGTACATCCGCTATCCACAG 59.112 50.000 0.00 0.00 0.00 3.66
2910 5434 2.623416 CAGAGTACATCCGCTATCCACA 59.377 50.000 0.00 0.00 0.00 4.17
2911 5435 2.029828 CCAGAGTACATCCGCTATCCAC 60.030 54.545 0.00 0.00 0.00 4.02
2912 5436 2.239400 CCAGAGTACATCCGCTATCCA 58.761 52.381 0.00 0.00 0.00 3.41
2919 5463 0.179100 CAGCACCCAGAGTACATCCG 60.179 60.000 0.00 0.00 0.00 4.18
3225 7683 1.202510 GCCGTCTCTGATCAATGCTCT 60.203 52.381 0.00 0.00 0.00 4.09
3261 7719 4.652881 TGTAGACATTCAGCCATCTCAGAT 59.347 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.