Multiple sequence alignment - TraesCS5D01G506600

Loading Multiple Alignment...

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 TraesCS5D01G506600 chr5D 100.000 3188 0 0 1 3188 532270347 532273534 0.000000e+00 5888.0
1 TraesCS5D01G506600 chr5D 79.229 804 123 32 931 1716 532279000 532278223 1.310000e-143 520.0
2 TraesCS5D01G506600 chr5B 93.689 1949 108 9 962 2899 671706405 671708349 0.000000e+00 2904.0
3 TraesCS5D01G506600 chr5B 77.046 1124 211 32 1026 2130 672474656 672473561 1.270000e-168 603.0
4 TraesCS5D01G506600 chr5B 76.957 1124 208 34 1026 2130 672441624 672440533 7.610000e-166 593.0
5 TraesCS5D01G506600 chr5B 76.408 1119 214 33 1034 2130 671303054 671301964 2.780000e-155 558.0
6 TraesCS5D01G506600 chr5B 82.292 576 94 5 949 1520 676100658 676100087 2.860000e-135 492.0
7 TraesCS5D01G506600 chr5B 72.372 409 97 15 1796 2200 671487804 671488200 7.230000e-22 115.0
8 TraesCS5D01G506600 chr5B 74.882 211 51 1 1981 2191 671713398 671713190 9.410000e-16 95.3
9 TraesCS5D01G506600 chr4A 94.802 1443 69 4 962 2402 640001186 639999748 0.000000e+00 2244.0
10 TraesCS5D01G506600 chr4A 97.264 731 18 2 2459 3188 639999748 639999019 0.000000e+00 1238.0
11 TraesCS5D01G506600 chr4A 86.700 594 62 13 939 1519 639986105 639986694 0.000000e+00 643.0
12 TraesCS5D01G506600 chr4A 92.629 407 23 3 1 403 24204094 24204497 2.130000e-161 579.0
13 TraesCS5D01G506600 chr4A 78.424 774 136 23 996 1749 639993479 639994241 2.880000e-130 475.0
14 TraesCS5D01G506600 chr4A 77.279 691 117 30 1467 2130 636983505 636982828 1.400000e-98 370.0
15 TraesCS5D01G506600 chr4A 75.468 587 116 22 1557 2137 637226015 637225451 8.770000e-66 261.0
16 TraesCS5D01G506600 chr4A 76.559 401 81 8 1801 2200 637200176 637199788 1.160000e-49 207.0
17 TraesCS5D01G506600 chr4A 85.366 205 22 8 2935 3135 639981157 639981357 4.170000e-49 206.0
18 TraesCS5D01G506600 chr4A 74.775 333 84 0 1798 2130 640057062 640057394 1.980000e-32 150.0
19 TraesCS5D01G506600 chr7B 91.088 864 41 17 1 842 685357127 685357976 0.000000e+00 1136.0
20 TraesCS5D01G506600 chr3A 88.027 877 66 13 1 842 64744303 64745175 0.000000e+00 1002.0
21 TraesCS5D01G506600 chr3A 86.842 190 11 6 666 841 64738565 64738754 1.940000e-47 200.0
22 TraesCS5D01G506600 chr3B 89.987 779 57 7 83 842 578404268 578403492 0.000000e+00 987.0
23 TraesCS5D01G506600 chr3B 92.927 410 25 2 1 406 347939705 347940114 7.610000e-166 593.0
24 TraesCS5D01G506600 chr3B 88.350 515 31 11 1 492 599805760 599805252 2.740000e-165 592.0
25 TraesCS5D01G506600 chr3B 93.220 118 8 0 724 841 578585796 578585679 1.180000e-39 174.0
26 TraesCS5D01G506600 chr1A 87.685 877 68 13 1 842 3521830 3520959 0.000000e+00 985.0
27 TraesCS5D01G506600 chr1A 85.864 573 40 14 298 839 566474566 566475128 3.570000e-159 571.0
28 TraesCS5D01G506600 chr1A 96.154 52 2 0 784 835 566468776 566468827 5.670000e-13 86.1
29 TraesCS5D01G506600 chr6B 86.773 877 63 17 1 843 340076434 340075577 0.000000e+00 928.0
30 TraesCS5D01G506600 chr2B 93.171 410 24 2 1 406 296063928 296064337 1.640000e-167 599.0
31 TraesCS5D01G506600 chr2B 84.492 187 14 7 669 841 103474193 103474008 1.520000e-38 171.0
32 TraesCS5D01G506600 chr2A 88.270 503 32 17 1 492 192246839 192247325 7.670000e-161 577.0
33 TraesCS5D01G506600 chr4D 88.072 503 32 15 1 492 10683326 10683811 3.570000e-159 571.0
34 TraesCS5D01G506600 chr2D 92.157 408 26 4 1 404 589682266 589682671 3.570000e-159 571.0
35 TraesCS5D01G506600 chr3D 86.146 563 37 14 176 717 136768163 136768705 1.280000e-158 569.0
36 TraesCS5D01G506600 chr4B 92.893 394 20 3 1324 1709 14506411 14506804 1.660000e-157 566.0
37 TraesCS5D01G506600 chr4B 94.483 290 12 2 1324 1610 14503811 14504099 8.110000e-121 444.0
38 TraesCS5D01G506600 chr4B 93.448 290 15 2 1324 1610 14505978 14506266 8.170000e-116 427.0
39 TraesCS5D01G506600 chr4B 92.759 290 17 2 1324 1610 14504245 14504533 1.770000e-112 416.0
40 TraesCS5D01G506600 chr4B 92.414 290 17 3 1324 1610 14505545 14505832 2.960000e-110 409.0
41 TraesCS5D01G506600 chr4B 92.096 291 18 3 1324 1610 14504678 14504967 3.830000e-109 405.0
42 TraesCS5D01G506600 chr4B 96.087 230 9 0 2946 3175 15415994 15416223 3.000000e-100 375.0
43 TraesCS5D01G506600 chr4B 95.964 223 9 0 2953 3175 14528594 14528816 2.340000e-96 363.0
44 TraesCS5D01G506600 chr4B 92.857 196 10 2 2732 2923 14527761 14527956 6.730000e-72 281.0
45 TraesCS5D01G506600 chr4B 89.796 196 7 7 2182 2373 14507125 14507311 4.110000e-59 239.0
46 TraesCS5D01G506600 chr4B 88.679 159 3 5 2449 2592 14527598 14527756 2.530000e-41 180.0
47 TraesCS5D01G506600 chr4B 85.906 149 17 1 1705 1849 14506918 14507066 4.260000e-34 156.0
48 TraesCS5D01G506600 chr7D 76.818 729 157 10 1032 1754 636779015 636778293 1.780000e-107 399.0
49 TraesCS5D01G506600 chr7D 90.000 240 18 2 462 698 448927758 448927994 4.000000e-79 305.0
50 TraesCS5D01G506600 chr7D 86.000 200 13 7 657 841 448872344 448872543 1.940000e-47 200.0
51 TraesCS5D01G506600 chr1B 79.466 599 96 22 931 1519 22108684 22109265 1.780000e-107 399.0
52 TraesCS5D01G506600 chrUn 76.279 215 49 2 1917 2130 67294377 67294164 2.600000e-21 113.0


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 TraesCS5D01G506600 chr5D 532270347 532273534 3187 False 5888.000000 5888 100.000000 1 3188 1 chr5D.!!$F1 3187
1 TraesCS5D01G506600 chr5D 532278223 532279000 777 True 520.000000 520 79.229000 931 1716 1 chr5D.!!$R1 785
2 TraesCS5D01G506600 chr5B 671706405 671708349 1944 False 2904.000000 2904 93.689000 962 2899 1 chr5B.!!$F2 1937
3 TraesCS5D01G506600 chr5B 672473561 672474656 1095 True 603.000000 603 77.046000 1026 2130 1 chr5B.!!$R4 1104
4 TraesCS5D01G506600 chr5B 672440533 672441624 1091 True 593.000000 593 76.957000 1026 2130 1 chr5B.!!$R3 1104
5 TraesCS5D01G506600 chr5B 671301964 671303054 1090 True 558.000000 558 76.408000 1034 2130 1 chr5B.!!$R1 1096
6 TraesCS5D01G506600 chr5B 676100087 676100658 571 True 492.000000 492 82.292000 949 1520 1 chr5B.!!$R5 571
7 TraesCS5D01G506600 chr4A 639999019 640001186 2167 True 1741.000000 2244 96.033000 962 3188 2 chr4A.!!$R4 2226
8 TraesCS5D01G506600 chr4A 639986105 639986694 589 False 643.000000 643 86.700000 939 1519 1 chr4A.!!$F3 580
9 TraesCS5D01G506600 chr4A 639993479 639994241 762 False 475.000000 475 78.424000 996 1749 1 chr4A.!!$F4 753
10 TraesCS5D01G506600 chr4A 636982828 636983505 677 True 370.000000 370 77.279000 1467 2130 1 chr4A.!!$R1 663
11 TraesCS5D01G506600 chr4A 637225451 637226015 564 True 261.000000 261 75.468000 1557 2137 1 chr4A.!!$R3 580
12 TraesCS5D01G506600 chr7B 685357127 685357976 849 False 1136.000000 1136 91.088000 1 842 1 chr7B.!!$F1 841
13 TraesCS5D01G506600 chr3A 64744303 64745175 872 False 1002.000000 1002 88.027000 1 842 1 chr3A.!!$F2 841
14 TraesCS5D01G506600 chr3B 578403492 578404268 776 True 987.000000 987 89.987000 83 842 1 chr3B.!!$R1 759
15 TraesCS5D01G506600 chr3B 599805252 599805760 508 True 592.000000 592 88.350000 1 492 1 chr3B.!!$R3 491
16 TraesCS5D01G506600 chr1A 3520959 3521830 871 True 985.000000 985 87.685000 1 842 1 chr1A.!!$R1 841
17 TraesCS5D01G506600 chr1A 566474566 566475128 562 False 571.000000 571 85.864000 298 839 1 chr1A.!!$F2 541
18 TraesCS5D01G506600 chr6B 340075577 340076434 857 True 928.000000 928 86.773000 1 843 1 chr6B.!!$R1 842
19 TraesCS5D01G506600 chr3D 136768163 136768705 542 False 569.000000 569 86.146000 176 717 1 chr3D.!!$F1 541
20 TraesCS5D01G506600 chr4B 14503811 14507311 3500 False 382.750000 566 91.724375 1324 2373 8 chr4B.!!$F2 1049
21 TraesCS5D01G506600 chr4B 14527598 14528816 1218 False 274.666667 363 92.500000 2449 3175 3 chr4B.!!$F3 726
22 TraesCS5D01G506600 chr7D 636778293 636779015 722 True 399.000000 399 76.818000 1032 1754 1 chr7D.!!$R1 722
23 TraesCS5D01G506600 chr1B 22108684 22109265 581 False 399.000000 399 79.466000 931 1519 1 chr1B.!!$F1 588

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
960 1017 0.107654 GAACCATTCCACCCTCTCCG 60.108 60.0 0.0 0.0 0.00 4.63 F
1998 4849 0.746659 AAGTGTTGGGCTTTGCTCAC 59.253 50.0 0.0 0.0 39.49 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 5033 0.038744 CCTGAGTTGGGTTCAGCCAT 59.961 55.0 0.0 0.0 40.54 4.40 R
2952 6440 0.751643 GGTCAACCCACAGCACAGTT 60.752 55.0 0.0 0.0 0.00 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
26 27 3.333804 TGCAAGTCAAATCATGCGACTA 58.666 40.909 7.16 0.00 39.04 2.59
263 274 2.243736 ACTTTCTGTTTTCCCCACAGGA 59.756 45.455 0.40 0.00 45.68 3.86
408 437 5.887754 TGGGTTTGAAGGAGTTTTAGCTAT 58.112 37.500 0.00 0.00 0.00 2.97
430 459 2.847449 TCCTCATATTTTTCCCACGGGA 59.153 45.455 0.00 0.00 43.52 5.14
442 471 1.549037 CCCACGGGATTTTTGGAGGAA 60.549 52.381 0.00 0.00 37.50 3.36
477 506 5.022282 TGATGGATTCTTATGACAAGCGA 57.978 39.130 0.00 0.00 0.00 4.93
591 623 9.874205 ATCAAGTTTTCATGAAGAACTTTTTGA 57.126 25.926 27.65 24.64 40.54 2.69
621 656 7.569111 AGAATCTTTTAAGATAGCCCTACCTGA 59.431 37.037 5.47 0.00 44.67 3.86
651 686 6.038936 TCGTGAGACGATTCTATATGGTCAAA 59.961 38.462 0.00 0.00 46.73 2.69
716 752 2.145397 GGAAATCTCCCCTTCCCAAC 57.855 55.000 0.00 0.00 35.95 3.77
718 754 0.331616 AAATCTCCCCTTCCCAACCG 59.668 55.000 0.00 0.00 0.00 4.44
719 755 2.211468 AATCTCCCCTTCCCAACCGC 62.211 60.000 0.00 0.00 0.00 5.68
744 794 2.187946 GGACGCATCTGGTCTGGG 59.812 66.667 0.00 0.00 34.82 4.45
778 828 1.738432 GAACCGTCGTATCCCTCCC 59.262 63.158 0.00 0.00 0.00 4.30
843 893 6.437928 TCAATCACTTTGATTCGAAACAAGG 58.562 36.000 22.88 22.88 43.03 3.61
844 894 6.262049 TCAATCACTTTGATTCGAAACAAGGA 59.738 34.615 28.63 21.78 43.03 3.36
845 895 5.673337 TCACTTTGATTCGAAACAAGGAG 57.327 39.130 28.63 22.70 0.00 3.69
846 896 4.515191 TCACTTTGATTCGAAACAAGGAGG 59.485 41.667 28.63 21.07 0.00 4.30
847 897 4.515191 CACTTTGATTCGAAACAAGGAGGA 59.485 41.667 28.63 11.81 0.00 3.71
848 898 4.757149 ACTTTGATTCGAAACAAGGAGGAG 59.243 41.667 28.63 20.41 0.00 3.69
849 899 2.699954 TGATTCGAAACAAGGAGGAGC 58.300 47.619 5.55 0.00 0.00 4.70
850 900 2.010497 GATTCGAAACAAGGAGGAGCC 58.990 52.381 0.00 0.00 0.00 4.70
851 901 0.762418 TTCGAAACAAGGAGGAGCCA 59.238 50.000 0.00 0.00 40.02 4.75
852 902 0.321671 TCGAAACAAGGAGGAGCCAG 59.678 55.000 0.00 0.00 40.02 4.85
853 903 0.674895 CGAAACAAGGAGGAGCCAGG 60.675 60.000 0.00 0.00 40.02 4.45
854 904 0.693049 GAAACAAGGAGGAGCCAGGA 59.307 55.000 0.00 0.00 40.02 3.86
855 905 1.283321 GAAACAAGGAGGAGCCAGGAT 59.717 52.381 0.00 0.00 40.02 3.24
856 906 1.376649 AACAAGGAGGAGCCAGGATT 58.623 50.000 0.00 0.00 40.02 3.01
857 907 0.622665 ACAAGGAGGAGCCAGGATTG 59.377 55.000 0.00 0.00 40.02 2.67
858 908 0.914644 CAAGGAGGAGCCAGGATTGA 59.085 55.000 0.00 0.00 40.02 2.57
859 909 1.134159 CAAGGAGGAGCCAGGATTGAG 60.134 57.143 0.00 0.00 40.02 3.02
860 910 1.148048 GGAGGAGCCAGGATTGAGC 59.852 63.158 0.00 0.00 36.34 4.26
861 911 1.227497 GAGGAGCCAGGATTGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
862 912 1.680522 GAGGAGCCAGGATTGAGCGA 61.681 60.000 0.00 0.00 0.00 4.93
863 913 1.227497 GGAGCCAGGATTGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
864 914 1.886777 GAGCCAGGATTGAGCGAGC 60.887 63.158 0.00 0.00 0.00 5.03
865 915 3.267860 GCCAGGATTGAGCGAGCG 61.268 66.667 0.00 0.00 0.00 5.03
866 916 2.496341 CCAGGATTGAGCGAGCGA 59.504 61.111 0.00 0.00 0.00 4.93
867 917 1.591059 CCAGGATTGAGCGAGCGAG 60.591 63.158 0.00 0.00 0.00 5.03
868 918 2.105930 AGGATTGAGCGAGCGAGC 59.894 61.111 0.00 0.00 37.41 5.03
869 919 2.202797 GGATTGAGCGAGCGAGCA 60.203 61.111 9.01 0.00 40.15 4.26
870 920 2.236382 GGATTGAGCGAGCGAGCAG 61.236 63.158 9.01 0.00 40.15 4.24
881 931 2.398429 CGAGCAGCTCGCATGTTG 59.602 61.111 30.85 4.30 46.75 3.33
882 932 2.789917 GAGCAGCTCGCATGTTGG 59.210 61.111 6.67 0.00 46.13 3.77
883 933 2.749044 AGCAGCTCGCATGTTGGG 60.749 61.111 10.16 0.00 46.13 4.12
884 934 4.487412 GCAGCTCGCATGTTGGGC 62.487 66.667 4.00 4.00 41.79 5.36
885 935 3.818787 CAGCTCGCATGTTGGGCC 61.819 66.667 8.14 0.00 0.00 5.80
914 964 4.006532 GTCAAGTGTGACGCGTGA 57.993 55.556 20.70 4.74 44.58 4.35
915 965 1.846648 GTCAAGTGTGACGCGTGAG 59.153 57.895 20.70 0.00 44.58 3.51
960 1017 0.107654 GAACCATTCCACCCTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
1119 1189 2.685380 CTCCTCCGTGCCTCCCTT 60.685 66.667 0.00 0.00 0.00 3.95
1275 1351 1.517832 CGCATCGTCCTTCTCCCTT 59.482 57.895 0.00 0.00 0.00 3.95
1915 4760 5.163205 ACTGATGCAATATGGGTACTTAGCA 60.163 40.000 0.00 0.00 35.03 3.49
1967 4812 1.134310 TGATGCTCTCGTGGATGCAAT 60.134 47.619 0.00 0.00 38.96 3.56
1998 4849 0.746659 AAGTGTTGGGCTTTGCTCAC 59.253 50.000 0.00 0.00 39.49 3.51
2019 4870 3.805422 ACGAAGCAAATGTCACTTTCGTA 59.195 39.130 8.13 0.00 30.83 3.43
2139 4992 2.052782 TCTACACTCCGCATGCTAGA 57.947 50.000 17.13 11.73 0.00 2.43
2158 5011 1.672356 CTCAAAGCACTCGTGGGGG 60.672 63.158 0.00 0.00 0.00 5.40
2159 5012 2.111999 CTCAAAGCACTCGTGGGGGA 62.112 60.000 0.00 0.00 0.00 4.81
2161 5014 1.228154 AAAGCACTCGTGGGGGAAC 60.228 57.895 0.00 0.00 0.00 3.62
2164 5017 2.032071 CACTCGTGGGGGAACACC 59.968 66.667 0.00 0.00 38.11 4.16
2375 5235 6.543465 TGTTCCCTCAATGCTTGATACTTATG 59.457 38.462 0.08 0.00 39.30 1.90
2396 5256 4.922206 TGTGTTGAATAGAAGGCTGGAAT 58.078 39.130 0.00 0.00 0.00 3.01
2866 5744 4.764050 TGTTCACCTGTTTGGAGACTAA 57.236 40.909 0.00 0.00 35.17 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.037758 AGATGATAGAGACTTCGTGAACAAATT 58.962 33.333 0.00 0.00 0.00 1.82
232 242 5.885912 GGGAAAACAGAAAGTATGGCATAGA 59.114 40.000 7.61 0.00 0.00 1.98
233 243 5.067805 GGGGAAAACAGAAAGTATGGCATAG 59.932 44.000 7.61 0.00 0.00 2.23
263 274 5.883673 TGCCGCATATACTTTCCTAAAAACT 59.116 36.000 0.00 0.00 0.00 2.66
381 393 3.662759 AAACTCCTTCAAACCCAGTGA 57.337 42.857 0.00 0.00 0.00 3.41
408 437 3.267291 TCCCGTGGGAAAAATATGAGGAA 59.733 43.478 4.80 0.00 42.05 3.36
430 459 9.933723 CATCTTGATTAAGTTTCCTCCAAAAAT 57.066 29.630 0.00 0.00 35.38 1.82
477 506 8.285891 TCTTAAGAAGAGACTCCTCCTAATCAT 58.714 37.037 1.68 0.00 40.30 2.45
558 590 8.348507 GTTCTTCATGAAAACTTGATGAGAACT 58.651 33.333 16.71 0.00 36.30 3.01
591 623 9.839817 GTAGGGCTATCTTAAAAGATTCTTCTT 57.160 33.333 10.32 0.17 42.96 2.52
642 677 7.341256 ACTTCCTCTAATCTACGTTTGACCATA 59.659 37.037 0.00 0.00 0.00 2.74
651 686 9.939802 AATTTTAACACTTCCTCTAATCTACGT 57.060 29.630 0.00 0.00 0.00 3.57
744 794 0.096108 GTTCGGACTAGACGTCGGTC 59.904 60.000 25.59 25.59 43.79 4.79
796 846 5.852282 TTGATCTCATCGATGGTTACAGA 57.148 39.130 24.61 18.82 30.84 3.41
843 893 1.227497 CGCTCAATCCTGGCTCCTC 60.227 63.158 0.00 0.00 0.00 3.71
844 894 1.684386 CTCGCTCAATCCTGGCTCCT 61.684 60.000 0.00 0.00 0.00 3.69
845 895 1.227497 CTCGCTCAATCCTGGCTCC 60.227 63.158 0.00 0.00 0.00 4.70
846 896 1.886777 GCTCGCTCAATCCTGGCTC 60.887 63.158 0.00 0.00 0.00 4.70
847 897 2.188994 GCTCGCTCAATCCTGGCT 59.811 61.111 0.00 0.00 0.00 4.75
848 898 3.267860 CGCTCGCTCAATCCTGGC 61.268 66.667 0.00 0.00 0.00 4.85
849 899 1.591059 CTCGCTCGCTCAATCCTGG 60.591 63.158 0.00 0.00 0.00 4.45
850 900 2.236382 GCTCGCTCGCTCAATCCTG 61.236 63.158 0.00 0.00 0.00 3.86
851 901 2.105930 GCTCGCTCGCTCAATCCT 59.894 61.111 0.00 0.00 0.00 3.24
852 902 2.202797 TGCTCGCTCGCTCAATCC 60.203 61.111 0.00 0.00 0.00 3.01
853 903 2.869256 GCTGCTCGCTCGCTCAATC 61.869 63.158 0.00 0.00 35.14 2.67
854 904 2.889503 GCTGCTCGCTCGCTCAAT 60.890 61.111 0.00 0.00 35.14 2.57
865 915 2.758089 CCCAACATGCGAGCTGCTC 61.758 63.158 19.53 19.53 46.63 4.26
866 916 2.749044 CCCAACATGCGAGCTGCT 60.749 61.111 0.00 0.00 46.63 4.24
867 917 4.487412 GCCCAACATGCGAGCTGC 62.487 66.667 0.00 0.00 46.70 5.25
868 918 3.818787 GGCCCAACATGCGAGCTG 61.819 66.667 0.00 0.00 0.00 4.24
886 936 4.681978 ACTTGACTCGCGTGGGCC 62.682 66.667 13.32 0.00 35.02 5.80
887 937 3.414700 CACTTGACTCGCGTGGGC 61.415 66.667 13.32 6.93 0.00 5.36
888 938 2.029073 ACACTTGACTCGCGTGGG 59.971 61.111 13.32 0.00 33.13 4.61
889 939 1.299850 TCACACTTGACTCGCGTGG 60.300 57.895 13.32 6.71 33.13 4.94
890 940 4.319249 TCACACTTGACTCGCGTG 57.681 55.556 5.77 6.24 34.92 5.34
898 948 1.949133 GCTCACGCGTCACACTTGA 60.949 57.895 9.86 0.00 0.00 3.02
899 949 2.546321 GCTCACGCGTCACACTTG 59.454 61.111 9.86 0.00 0.00 3.16
915 965 0.108945 ACCAGTTAACGAGCCTACGC 60.109 55.000 0.00 0.00 36.70 4.42
916 966 1.990563 CAACCAGTTAACGAGCCTACG 59.009 52.381 0.00 0.00 39.31 3.51
917 967 3.251571 CTCAACCAGTTAACGAGCCTAC 58.748 50.000 0.00 0.00 0.00 3.18
918 968 2.353406 GCTCAACCAGTTAACGAGCCTA 60.353 50.000 16.95 0.00 42.57 3.93
919 969 1.608283 GCTCAACCAGTTAACGAGCCT 60.608 52.381 16.95 0.00 42.57 4.58
920 970 0.796927 GCTCAACCAGTTAACGAGCC 59.203 55.000 16.95 4.54 42.57 4.70
921 971 0.796927 GGCTCAACCAGTTAACGAGC 59.203 55.000 18.63 18.63 46.58 5.03
922 972 1.068474 CGGCTCAACCAGTTAACGAG 58.932 55.000 0.00 1.73 39.03 4.18
923 973 0.675083 TCGGCTCAACCAGTTAACGA 59.325 50.000 0.00 0.00 39.03 3.85
924 974 1.193874 GTTCGGCTCAACCAGTTAACG 59.806 52.381 0.00 0.00 39.03 3.18
925 975 1.534163 GGTTCGGCTCAACCAGTTAAC 59.466 52.381 11.26 0.00 44.79 2.01
926 976 1.886886 GGTTCGGCTCAACCAGTTAA 58.113 50.000 11.26 0.00 44.79 2.01
927 977 3.618171 GGTTCGGCTCAACCAGTTA 57.382 52.632 11.26 0.00 44.79 2.24
928 978 4.475527 GGTTCGGCTCAACCAGTT 57.524 55.556 11.26 0.00 44.79 3.16
960 1017 0.806868 CTGGATGTGATGTGTGTGCC 59.193 55.000 0.00 0.00 0.00 5.01
1066 1136 4.005978 TGGGAGGCGGAGGAGGAA 62.006 66.667 0.00 0.00 0.00 3.36
1119 1189 2.752358 CTCCAGGCCTTGCAGACA 59.248 61.111 0.00 0.00 0.00 3.41
1496 3757 1.346722 AGACGAAGACCACCCGAAAAT 59.653 47.619 0.00 0.00 0.00 1.82
1606 4304 2.887568 CTCACCGTGCATCGAGGC 60.888 66.667 16.46 16.46 42.86 4.70
1915 4760 6.438425 AGCAAAATATTCAAGTTGATGACCCT 59.562 34.615 6.36 0.00 0.00 4.34
1967 4812 3.243704 GCCCAACACTTGCACTGAATTTA 60.244 43.478 0.00 0.00 0.00 1.40
1998 4849 3.253371 ACGAAAGTGACATTTGCTTCG 57.747 42.857 0.00 0.00 46.97 3.79
2019 4870 3.537206 GAGGCCAGCAACCGTCACT 62.537 63.158 5.01 0.00 0.00 3.41
2139 4992 1.071471 CCCCACGAGTGCTTTGAGT 59.929 57.895 0.00 0.00 0.00 3.41
2158 5011 1.304134 GGTGGGTCATGGGGTGTTC 60.304 63.158 0.00 0.00 0.00 3.18
2159 5012 2.851045 GGTGGGTCATGGGGTGTT 59.149 61.111 0.00 0.00 0.00 3.32
2164 5017 4.127744 ATGGCGGTGGGTCATGGG 62.128 66.667 0.00 0.00 40.15 4.00
2180 5033 0.038744 CCTGAGTTGGGTTCAGCCAT 59.961 55.000 0.00 0.00 40.54 4.40
2375 5235 5.904362 AATTCCAGCCTTCTATTCAACAC 57.096 39.130 0.00 0.00 0.00 3.32
2384 5244 3.011032 AGGACATCAAATTCCAGCCTTCT 59.989 43.478 0.00 0.00 33.92 2.85
2561 5436 6.639563 AGCAAATACGCCTCCAATTTTAAAT 58.360 32.000 0.00 0.00 0.00 1.40
2808 5686 6.935240 ATAGGCTGGCACATACTATAGAAA 57.065 37.500 6.78 0.00 36.08 2.52
2850 5728 7.290813 AGAAGAAAATTAGTCTCCAAACAGGT 58.709 34.615 0.00 0.00 39.02 4.00
2911 5790 6.589830 ATGTAATTCAGATACGTTGCAGAC 57.410 37.500 0.00 0.00 0.00 3.51
2952 6440 0.751643 GGTCAACCCACAGCACAGTT 60.752 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.