Multiple sequence alignment - TraesCS3D01G435300

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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 TraesCS3D01G435300 chr3D 100.000 2873 0 0 1 2873 547620238 547623110 0.000000e+00 5306.0
1 TraesCS3D01G435300 chr3D 82.830 530 59 19 2074 2582 70732936 70732418 2.030000e-121 446.0
2 TraesCS3D01G435300 chr3D 86.477 281 25 9 1 276 547509005 547509277 2.160000e-76 296.0
3 TraesCS3D01G435300 chr3D 86.992 123 16 0 1261 1383 547509583 547509705 3.860000e-29 139.0
4 TraesCS3D01G435300 chr3D 88.525 61 7 0 1823 1883 590046158 590046218 1.100000e-09 75.0
5 TraesCS3D01G435300 chr2D 94.587 1127 21 10 1785 2873 323125387 323126511 0.000000e+00 1707.0
6 TraesCS3D01G435300 chr2D 92.771 166 2 3 1635 1791 323125192 323125356 6.190000e-57 231.0
7 TraesCS3D01G435300 chr2D 82.375 261 37 8 2614 2871 411696582 411696328 4.820000e-53 219.0
8 TraesCS3D01G435300 chr2D 80.399 301 43 13 2585 2873 13225738 13225442 6.230000e-52 215.0
9 TraesCS3D01G435300 chr3A 89.145 1391 79 29 290 1641 684580963 684582320 0.000000e+00 1666.0
10 TraesCS3D01G435300 chr3A 87.532 1171 68 31 508 1641 684582630 684583759 0.000000e+00 1282.0
11 TraesCS3D01G435300 chr3A 83.898 472 43 17 287 726 684512995 684513465 1.230000e-113 420.0
12 TraesCS3D01G435300 chr3A 86.063 287 29 6 1 278 684512665 684512949 6.020000e-77 298.0
13 TraesCS3D01G435300 chr3A 84.116 277 33 8 1 271 684580637 684580908 1.020000e-64 257.0
14 TraesCS3D01G435300 chr3A 73.494 664 111 36 965 1584 684589014 684589656 1.050000e-44 191.0
15 TraesCS3D01G435300 chr3A 85.417 96 14 0 1288 1383 684519343 684519438 1.820000e-17 100.0
16 TraesCS3D01G435300 chr3A 82.353 102 12 5 1785 1883 719801702 719801800 1.830000e-12 84.2
17 TraesCS3D01G435300 chr1B 91.946 1105 47 18 1809 2873 547226319 547227421 0.000000e+00 1509.0
18 TraesCS3D01G435300 chr6A 89.640 1110 64 20 1809 2873 426321114 426322217 0.000000e+00 1365.0
19 TraesCS3D01G435300 chr7D 87.891 991 67 17 1926 2873 622086051 622087031 0.000000e+00 1116.0
20 TraesCS3D01G435300 chr7D 81.887 530 65 20 2074 2582 29063913 29063394 4.430000e-113 418.0
21 TraesCS3D01G435300 chr7D 90.164 61 2 1 1728 1784 622085860 622085920 3.070000e-10 76.8
22 TraesCS3D01G435300 chr5D 86.934 949 49 24 1971 2873 27991421 27990502 0.000000e+00 996.0
23 TraesCS3D01G435300 chr5D 83.712 528 57 17 2074 2582 68209071 68208554 3.350000e-129 472.0
24 TraesCS3D01G435300 chr5D 93.651 189 10 1 1790 1976 27993345 27993157 6.060000e-72 281.0
25 TraesCS3D01G435300 chr5D 89.130 46 3 2 770 813 115744538 115744493 4.000000e-04 56.5
26 TraesCS3D01G435300 chr5D 94.595 37 0 1 769 805 540237886 540237852 4.000000e-04 56.5
27 TraesCS3D01G435300 chr2B 86.957 345 34 9 2242 2582 465796778 465796441 7.510000e-101 377.0
28 TraesCS3D01G435300 chr2B 81.507 292 43 10 2585 2871 514794981 514794696 2.230000e-56 230.0
29 TraesCS3D01G435300 chr2B 79.394 330 41 13 1917 2220 465806811 465806483 1.040000e-49 207.0
30 TraesCS3D01G435300 chr2B 78.333 300 52 13 2581 2873 650152077 650152370 6.320000e-42 182.0
31 TraesCS3D01G435300 chr7A 93.596 203 12 1 1785 1986 50074301 50074503 4.650000e-78 302.0
32 TraesCS3D01G435300 chr7A 93.596 203 12 1 1785 1986 50097571 50097773 4.650000e-78 302.0
33 TraesCS3D01G435300 chr7A 81.081 74 14 0 1836 1909 566959542 566959615 3.090000e-05 60.2
34 TraesCS3D01G435300 chr2A 86.420 162 19 3 1917 2075 15397039 15397200 1.060000e-39 174.0
35 TraesCS3D01G435300 chr1A 100.000 33 0 0 769 801 121740185 121740153 8.600000e-06 62.1
36 TraesCS3D01G435300 chr1A 89.130 46 3 2 770 813 460054325 460054280 4.000000e-04 56.5
37 TraesCS3D01G435300 chr4B 92.683 41 1 2 770 810 286079545 286079583 1.110000e-04 58.4
38 TraesCS3D01G435300 chr5B 92.500 40 2 1 770 809 530511133 530511171 4.000000e-04 56.5
39 TraesCS3D01G435300 chr4A 89.130 46 3 2 770 813 240544577 240544532 4.000000e-04 56.5
40 TraesCS3D01G435300 chr3B 97.059 34 0 1 770 803 475827839 475827871 4.000000e-04 56.5
41 TraesCS3D01G435300 chr5A 92.105 38 3 0 770 807 451244442 451244405 1.000000e-03 54.7


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 TraesCS3D01G435300 chr3D 547620238 547623110 2872 False 5306.000000 5306 100.0000 1 2873 1 chr3D.!!$F1 2872
1 TraesCS3D01G435300 chr3D 70732418 70732936 518 True 446.000000 446 82.8300 2074 2582 1 chr3D.!!$R1 508
2 TraesCS3D01G435300 chr3D 547509005 547509705 700 False 217.500000 296 86.7345 1 1383 2 chr3D.!!$F3 1382
3 TraesCS3D01G435300 chr2D 323125192 323126511 1319 False 969.000000 1707 93.6790 1635 2873 2 chr2D.!!$F1 1238
4 TraesCS3D01G435300 chr3A 684580637 684583759 3122 False 1068.333333 1666 86.9310 1 1641 3 chr3A.!!$F5 1640
5 TraesCS3D01G435300 chr3A 684512665 684513465 800 False 359.000000 420 84.9805 1 726 2 chr3A.!!$F4 725
6 TraesCS3D01G435300 chr1B 547226319 547227421 1102 False 1509.000000 1509 91.9460 1809 2873 1 chr1B.!!$F1 1064
7 TraesCS3D01G435300 chr6A 426321114 426322217 1103 False 1365.000000 1365 89.6400 1809 2873 1 chr6A.!!$F1 1064
8 TraesCS3D01G435300 chr7D 622085860 622087031 1171 False 596.400000 1116 89.0275 1728 2873 2 chr7D.!!$F1 1145
9 TraesCS3D01G435300 chr7D 29063394 29063913 519 True 418.000000 418 81.8870 2074 2582 1 chr7D.!!$R1 508
10 TraesCS3D01G435300 chr5D 27990502 27993345 2843 True 638.500000 996 90.2925 1790 2873 2 chr5D.!!$R4 1083
11 TraesCS3D01G435300 chr5D 68208554 68209071 517 True 472.000000 472 83.7120 2074 2582 1 chr5D.!!$R1 508

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
214 225 0.035152 AAATCCATGCGGCACAGAGA 60.035 50.0 4.03 0.0 0.0 3.10 F
481 541 0.036388 GGATCGCCTTGACCTTGACA 60.036 55.0 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 1177 0.246910 GGAGGACCACGAAGACCTTC 59.753 60.0 0.00 0.0 35.97 3.46 R
2224 4172 0.037326 GATGATGCCGGCGGAAGATA 60.037 55.0 33.44 10.4 0.00 1.98 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
34 35 2.156917 CCATTGCCATCATCGCATAGT 58.843 47.619 0.00 0.00 35.83 2.12
106 109 1.667236 CTGCACTGAAGTCACCACAA 58.333 50.000 0.00 0.00 0.00 3.33
108 111 0.663153 GCACTGAAGTCACCACAACC 59.337 55.000 0.00 0.00 0.00 3.77
109 112 1.747206 GCACTGAAGTCACCACAACCT 60.747 52.381 0.00 0.00 0.00 3.50
166 170 1.067516 GCAAGAAAGCACAAGAGGCAA 59.932 47.619 0.00 0.00 0.00 4.52
212 223 1.936436 GCAAATCCATGCGGCACAGA 61.936 55.000 4.03 5.41 36.45 3.41
213 224 0.099968 CAAATCCATGCGGCACAGAG 59.900 55.000 4.03 0.00 0.00 3.35
214 225 0.035152 AAATCCATGCGGCACAGAGA 60.035 50.000 4.03 0.00 0.00 3.10
216 227 0.182061 ATCCATGCGGCACAGAGAAT 59.818 50.000 4.03 0.00 0.00 2.40
217 228 0.035152 TCCATGCGGCACAGAGAATT 60.035 50.000 4.03 0.00 0.00 2.17
218 229 1.209261 TCCATGCGGCACAGAGAATTA 59.791 47.619 4.03 0.00 0.00 1.40
221 232 3.549423 CCATGCGGCACAGAGAATTAATG 60.549 47.826 4.03 0.00 0.00 1.90
224 235 3.947196 TGCGGCACAGAGAATTAATGATT 59.053 39.130 0.00 0.00 0.00 2.57
226 237 5.105797 TGCGGCACAGAGAATTAATGATTTT 60.106 36.000 0.00 0.00 0.00 1.82
228 239 6.020360 GCGGCACAGAGAATTAATGATTTTTC 60.020 38.462 0.00 0.00 0.00 2.29
342 391 1.199789 TCAAACCAACATCATCAGCGC 59.800 47.619 0.00 0.00 0.00 5.92
350 399 1.066645 ACATCATCAGCGCACAGAGAA 60.067 47.619 11.47 0.00 0.00 2.87
364 417 4.502950 GCACAGAGAAGATGCCTAATAGCT 60.503 45.833 0.00 0.00 33.06 3.32
433 486 5.243954 AGAAAGGCTTTCCTAAAACATCCAC 59.756 40.000 30.87 6.86 43.40 4.02
440 493 6.128117 GCTTTCCTAAAACATCCACGACAATA 60.128 38.462 0.00 0.00 0.00 1.90
481 541 0.036388 GGATCGCCTTGACCTTGACA 60.036 55.000 0.00 0.00 0.00 3.58
493 553 3.380004 TGACCTTGACACAAACCATTCAC 59.620 43.478 0.00 0.00 0.00 3.18
497 557 4.202141 CCTTGACACAAACCATTCACATGT 60.202 41.667 0.00 0.00 0.00 3.21
499 559 4.206375 TGACACAAACCATTCACATGTCT 58.794 39.130 0.00 0.00 36.72 3.41
500 560 4.644234 TGACACAAACCATTCACATGTCTT 59.356 37.500 0.00 0.00 36.72 3.01
503 563 4.977963 CACAAACCATTCACATGTCTTGTC 59.022 41.667 0.00 0.00 36.00 3.18
534 613 4.454678 ACTTGAGAACATGAAGAGTGCAA 58.545 39.130 0.00 0.00 0.00 4.08
539 618 1.242076 ACATGAAGAGTGCAACAGCC 58.758 50.000 0.00 0.00 41.43 4.85
561 640 2.209273 GCAAACCCAACAACACCATTC 58.791 47.619 0.00 0.00 0.00 2.67
592 673 2.233922 ACCATGACGAGAACTTGTAGGG 59.766 50.000 0.00 7.97 0.00 3.53
599 680 2.288825 CGAGAACTTGTAGGGCACTTGA 60.289 50.000 0.00 0.00 0.00 3.02
607 688 2.213499 GTAGGGCACTTGAATCCATCG 58.787 52.381 0.00 0.00 0.00 3.84
608 689 0.620556 AGGGCACTTGAATCCATCGT 59.379 50.000 0.00 0.00 0.00 3.73
610 691 1.453155 GGCACTTGAATCCATCGTGT 58.547 50.000 0.00 0.00 0.00 4.49
617 698 5.872617 CACTTGAATCCATCGTGTAACCTTA 59.127 40.000 0.00 0.00 0.00 2.69
621 702 3.235157 TCCATCGTGTAACCTTAACCG 57.765 47.619 0.00 0.00 0.00 4.44
631 712 5.048434 GTGTAACCTTAACCGAGTGTCTAGT 60.048 44.000 0.00 0.00 0.00 2.57
633 714 5.635417 AACCTTAACCGAGTGTCTAGTAC 57.365 43.478 0.00 0.00 0.00 2.73
635 716 4.699257 ACCTTAACCGAGTGTCTAGTACAG 59.301 45.833 0.00 0.00 39.29 2.74
662 743 2.840038 AGTGGCTGATATGTGGACAAGA 59.160 45.455 0.00 0.00 0.00 3.02
664 745 2.205074 GGCTGATATGTGGACAAGACG 58.795 52.381 0.00 0.00 0.00 4.18
676 758 4.301637 GGACAAGACGTGACCAATTTTT 57.698 40.909 0.00 0.00 41.25 1.94
685 767 4.158764 ACGTGACCAATTTTTCCACTTTCA 59.841 37.500 0.00 0.00 0.00 2.69
687 769 4.502645 GTGACCAATTTTTCCACTTTCACG 59.497 41.667 0.00 0.00 0.00 4.35
702 784 3.955771 TTCACGTGTTCTTTTACAGCC 57.044 42.857 16.51 0.00 0.00 4.85
734 816 3.917985 GTGTTTCCACAAGTTTGTCACAC 59.082 43.478 8.18 8.61 39.91 3.82
736 818 4.165779 GTTTCCACAAGTTTGTCACACTG 58.834 43.478 0.00 0.00 39.91 3.66
742 824 3.315191 ACAAGTTTGTCACACTGCCATAC 59.685 43.478 0.00 0.00 36.50 2.39
743 825 3.207265 AGTTTGTCACACTGCCATACA 57.793 42.857 0.00 0.00 0.00 2.29
744 826 3.550820 AGTTTGTCACACTGCCATACAA 58.449 40.909 0.00 0.00 0.00 2.41
748 830 5.528043 TTGTCACACTGCCATACAAAAAT 57.472 34.783 0.00 0.00 0.00 1.82
750 832 6.252967 TGTCACACTGCCATACAAAAATAG 57.747 37.500 0.00 0.00 0.00 1.73
758 840 5.719173 TGCCATACAAAAATAGGTTTGCTC 58.281 37.500 0.00 0.00 41.33 4.26
761 843 6.476706 GCCATACAAAAATAGGTTTGCTCATC 59.523 38.462 0.00 0.00 41.33 2.92
770 852 8.457238 AAATAGGTTTGCTCATCCTTTCTATC 57.543 34.615 0.00 0.00 33.34 2.08
771 853 5.441718 AGGTTTGCTCATCCTTTCTATCA 57.558 39.130 0.00 0.00 0.00 2.15
774 856 6.060788 GGTTTGCTCATCCTTTCTATCATCT 58.939 40.000 0.00 0.00 0.00 2.90
775 857 7.071698 AGGTTTGCTCATCCTTTCTATCATCTA 59.928 37.037 0.00 0.00 0.00 1.98
776 858 7.882271 GGTTTGCTCATCCTTTCTATCATCTAT 59.118 37.037 0.00 0.00 0.00 1.98
777 859 9.282569 GTTTGCTCATCCTTTCTATCATCTATT 57.717 33.333 0.00 0.00 0.00 1.73
778 860 9.857656 TTTGCTCATCCTTTCTATCATCTATTT 57.142 29.630 0.00 0.00 0.00 1.40
779 861 9.857656 TTGCTCATCCTTTCTATCATCTATTTT 57.142 29.630 0.00 0.00 0.00 1.82
780 862 9.281371 TGCTCATCCTTTCTATCATCTATTTTG 57.719 33.333 0.00 0.00 0.00 2.44
781 863 8.728833 GCTCATCCTTTCTATCATCTATTTTGG 58.271 37.037 0.00 0.00 0.00 3.28
785 867 8.662781 TCCTTTCTATCATCTATTTTGGAACG 57.337 34.615 0.00 0.00 0.00 3.95
786 868 7.715249 TCCTTTCTATCATCTATTTTGGAACGG 59.285 37.037 0.00 0.00 0.00 4.44
787 869 7.715249 CCTTTCTATCATCTATTTTGGAACGGA 59.285 37.037 0.00 0.00 0.00 4.69
788 870 8.662781 TTTCTATCATCTATTTTGGAACGGAG 57.337 34.615 0.00 0.00 0.00 4.63
789 871 6.759272 TCTATCATCTATTTTGGAACGGAGG 58.241 40.000 0.00 0.00 0.00 4.30
790 872 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
791 873 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
792 874 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
793 875 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
794 876 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
795 877 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
834 916 7.212976 TCATACAAAAATTGGTTTGCTTAGCA 58.787 30.769 1.39 1.39 41.33 3.49
850 932 5.047164 TGCTTAGCATGTCCATTTTCACATT 60.047 36.000 1.39 0.00 31.71 2.71
863 945 7.717436 TCCATTTTCACATTGTCAGTTACACTA 59.283 33.333 0.00 0.00 38.00 2.74
892 974 6.633856 ACAAAAATCTATTTGCTTAGCCTGG 58.366 36.000 0.29 0.00 42.68 4.45
893 975 6.437162 ACAAAAATCTATTTGCTTAGCCTGGA 59.563 34.615 0.29 0.00 42.68 3.86
894 976 7.039082 ACAAAAATCTATTTGCTTAGCCTGGAA 60.039 33.333 0.29 0.00 42.68 3.53
895 977 6.705863 AAATCTATTTGCTTAGCCTGGAAG 57.294 37.500 0.29 0.00 0.00 3.46
899 981 4.232310 GCTTAGCCTGGAAGCCTG 57.768 61.111 8.54 0.00 42.90 4.85
900 982 1.452833 GCTTAGCCTGGAAGCCTGG 60.453 63.158 8.54 5.13 42.90 4.45
910 992 1.601759 GAAGCCTGGAAGCAGCACA 60.602 57.895 0.00 0.00 34.23 4.57
914 996 0.319405 GCCTGGAAGCAGCACAAAAT 59.681 50.000 0.00 0.00 0.00 1.82
954 1036 0.464373 AATGTATGCTGCCACGAGGG 60.464 55.000 0.00 0.00 40.85 4.30
955 1037 1.337384 ATGTATGCTGCCACGAGGGA 61.337 55.000 0.00 0.00 40.01 4.20
979 1061 6.638021 AATACTCCTATATAACAAGCCCCC 57.362 41.667 0.00 0.00 0.00 5.40
997 1079 0.105913 CCCTCCCCTCTCCTCTACAC 60.106 65.000 0.00 0.00 0.00 2.90
1000 1082 0.854039 TCCCCTCTCCTCTACACCCA 60.854 60.000 0.00 0.00 0.00 4.51
1014 1096 6.027025 TCTACACCCATCTACCATAGAACT 57.973 41.667 0.00 0.00 38.50 3.01
1021 1103 4.021544 CCATCTACCATAGAACTCAGCTCC 60.022 50.000 0.00 0.00 38.50 4.70
1115 1210 2.508887 CTCCTGCTGCTGCTCGTC 60.509 66.667 17.00 0.00 40.48 4.20
1149 1244 9.116067 GTATGTATACATGCCTACCTTTGAAAA 57.884 33.333 25.48 0.00 37.15 2.29
1159 1254 8.133024 TGCCTACCTTTGAAAATATTTGACAT 57.867 30.769 0.39 0.00 0.00 3.06
1216 1311 4.397481 TGTGTGAGATGATGACTGATCC 57.603 45.455 0.00 0.00 0.00 3.36
1428 1523 4.666412 AGGACTGCTAGATGCCTAGATA 57.334 45.455 0.00 0.00 44.00 1.98
1432 1527 2.430332 CTGCTAGATGCCTAGATAGCCC 59.570 54.545 0.00 0.00 44.00 5.19
1579 1674 6.811634 TTGCATGAATGAATAAGGGGAATT 57.188 33.333 0.00 0.00 0.00 2.17
1580 1675 6.164417 TGCATGAATGAATAAGGGGAATTG 57.836 37.500 0.00 0.00 0.00 2.32
1599 1694 2.353323 TGCATCATCTTGTGAGTGAGC 58.647 47.619 0.00 0.00 40.92 4.26
1608 1703 1.413118 TGTGAGTGAGCTCTGTTCCA 58.587 50.000 16.19 3.65 42.13 3.53
1797 1974 4.849310 GGGCGGCGCATGGAGTAA 62.849 66.667 34.36 0.00 0.00 2.24
2036 3957 3.074412 CTGTCCAGCGGAAATTAAGTGT 58.926 45.455 0.00 0.00 31.38 3.55
2125 4073 5.755375 ACATGCTACTAAAATCAGACGGATG 59.245 40.000 0.00 0.00 36.02 3.51
2233 4181 9.744468 ACCAAAATATGTTAAATTATCTTCCGC 57.256 29.630 0.00 0.00 0.00 5.54
2235 4183 8.901748 CAAAATATGTTAAATTATCTTCCGCCG 58.098 33.333 0.00 0.00 0.00 6.46
2236 4184 6.737254 ATATGTTAAATTATCTTCCGCCGG 57.263 37.500 0.00 0.00 0.00 6.13
2237 4185 2.614983 TGTTAAATTATCTTCCGCCGGC 59.385 45.455 19.07 19.07 0.00 6.13
2238 4186 2.614983 GTTAAATTATCTTCCGCCGGCA 59.385 45.455 28.98 6.55 0.00 5.69
2329 4470 6.989796 TCAACACAATGAAATCATGTTTCG 57.010 33.333 12.83 5.23 33.52 3.46
2497 4702 8.075761 TCCATGAGATAGATACATGATTCCAG 57.924 38.462 0.00 0.00 42.41 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.016318 CATCCTTGCGGCTATGTCAAA 58.984 47.619 0.00 0.00 0.00 2.69
106 109 6.375455 CCTTCAGCTATATGTCAACAAAAGGT 59.625 38.462 0.00 0.00 0.00 3.50
108 111 7.119699 TGACCTTCAGCTATATGTCAACAAAAG 59.880 37.037 6.01 0.00 30.44 2.27
109 112 6.939730 TGACCTTCAGCTATATGTCAACAAAA 59.060 34.615 6.01 0.00 30.44 2.44
191 201 1.226773 GTGCCGCATGGATTTGCTC 60.227 57.895 0.00 0.00 40.54 4.26
194 204 0.099968 CTCTGTGCCGCATGGATTTG 59.900 55.000 0.00 0.00 37.49 2.32
209 220 8.297470 TCCCAGGAAAAATCATTAATTCTCTG 57.703 34.615 0.00 0.00 0.00 3.35
217 228 9.880254 TCATGATTATCCCAGGAAAAATCATTA 57.120 29.630 24.35 18.74 42.27 1.90
218 229 8.645110 GTCATGATTATCCCAGGAAAAATCATT 58.355 33.333 24.35 14.59 42.27 2.57
221 232 7.587037 TGTCATGATTATCCCAGGAAAAATC 57.413 36.000 0.00 14.07 34.21 2.17
224 235 5.356751 CGTTGTCATGATTATCCCAGGAAAA 59.643 40.000 0.00 0.00 0.00 2.29
226 237 4.163268 TCGTTGTCATGATTATCCCAGGAA 59.837 41.667 0.00 0.00 0.00 3.36
228 239 4.071961 TCGTTGTCATGATTATCCCAGG 57.928 45.455 0.00 0.00 0.00 4.45
242 253 2.241722 CCGCAACATTGATTCGTTGTC 58.758 47.619 0.00 0.00 43.52 3.18
276 289 3.253188 CGACACCACCATCACAATCTTTT 59.747 43.478 0.00 0.00 0.00 2.27
279 292 1.623311 TCGACACCACCATCACAATCT 59.377 47.619 0.00 0.00 0.00 2.40
280 293 2.093306 TCGACACCACCATCACAATC 57.907 50.000 0.00 0.00 0.00 2.67
281 294 2.237143 AGATCGACACCACCATCACAAT 59.763 45.455 0.00 0.00 0.00 2.71
283 296 1.204704 GAGATCGACACCACCATCACA 59.795 52.381 0.00 0.00 0.00 3.58
284 297 1.799181 CGAGATCGACACCACCATCAC 60.799 57.143 0.00 0.00 43.02 3.06
285 298 0.455815 CGAGATCGACACCACCATCA 59.544 55.000 0.00 0.00 43.02 3.07
342 391 5.212532 AGCTATTAGGCATCTTCTCTGTG 57.787 43.478 0.00 0.00 34.17 3.66
350 399 2.502295 GCAGCAAGCTATTAGGCATCT 58.498 47.619 0.00 0.00 41.15 2.90
364 417 2.689785 CGGCCTTTCATCGCAGCAA 61.690 57.895 0.00 0.00 0.00 3.91
433 486 9.976511 TCTACCCTCTATTATTTGTTATTGTCG 57.023 33.333 0.00 0.00 0.00 4.35
440 493 6.458784 TCCCCTCTACCCTCTATTATTTGTT 58.541 40.000 0.00 0.00 0.00 2.83
481 541 4.889409 AGACAAGACATGTGAATGGTTTGT 59.111 37.500 1.15 2.48 44.12 2.83
493 553 5.930569 TCAAGTTCTCATCAGACAAGACATG 59.069 40.000 0.00 0.00 0.00 3.21
497 557 6.183360 TGTTCTCAAGTTCTCATCAGACAAGA 60.183 38.462 0.00 0.00 0.00 3.02
499 559 5.917462 TGTTCTCAAGTTCTCATCAGACAA 58.083 37.500 0.00 0.00 0.00 3.18
500 560 5.535753 TGTTCTCAAGTTCTCATCAGACA 57.464 39.130 0.00 0.00 0.00 3.41
503 563 6.872547 TCTTCATGTTCTCAAGTTCTCATCAG 59.127 38.462 0.00 0.00 0.00 2.90
534 613 0.975040 TTGTTGGGTTTGCAGGCTGT 60.975 50.000 17.16 0.00 0.00 4.40
539 618 0.534412 TGGTGTTGTTGGGTTTGCAG 59.466 50.000 0.00 0.00 0.00 4.41
561 640 0.601576 TCGTCATGGTTTGGGTGTCG 60.602 55.000 0.00 0.00 0.00 4.35
592 673 3.181510 GGTTACACGATGGATTCAAGTGC 60.182 47.826 11.57 0.00 38.36 4.40
599 680 4.081531 TCGGTTAAGGTTACACGATGGATT 60.082 41.667 0.00 0.00 0.00 3.01
607 688 4.248691 AGACACTCGGTTAAGGTTACAC 57.751 45.455 0.00 0.00 0.00 2.90
608 689 5.072741 ACTAGACACTCGGTTAAGGTTACA 58.927 41.667 0.00 0.00 0.00 2.41
610 691 6.237901 TGTACTAGACACTCGGTTAAGGTTA 58.762 40.000 0.00 0.00 31.20 2.85
617 698 3.484407 ACACTGTACTAGACACTCGGTT 58.516 45.455 0.00 0.00 33.31 4.44
621 702 5.106634 CCACTGTACACTGTACTAGACACTC 60.107 48.000 18.16 0.00 33.31 3.51
631 712 4.709886 ACATATCAGCCACTGTACACTGTA 59.290 41.667 10.11 4.46 32.61 2.74
633 714 3.867493 CACATATCAGCCACTGTACACTG 59.133 47.826 5.13 5.13 32.61 3.66
635 716 3.118775 TCCACATATCAGCCACTGTACAC 60.119 47.826 0.00 0.00 32.61 2.90
662 743 4.158764 TGAAAGTGGAAAAATTGGTCACGT 59.841 37.500 0.00 0.00 33.98 4.49
664 745 4.502645 CGTGAAAGTGGAAAAATTGGTCAC 59.497 41.667 0.00 0.00 0.00 3.67
671 752 5.576447 AGAACACGTGAAAGTGGAAAAAT 57.424 34.783 25.01 0.00 45.80 1.82
676 758 4.936411 TGTAAAAGAACACGTGAAAGTGGA 59.064 37.500 25.01 0.00 45.80 4.02
685 767 6.628919 ATTAAAGGCTGTAAAAGAACACGT 57.371 33.333 0.32 0.00 0.00 4.49
687 769 7.704899 ACACAATTAAAGGCTGTAAAAGAACAC 59.295 33.333 0.32 0.00 0.00 3.32
734 816 5.723295 AGCAAACCTATTTTTGTATGGCAG 58.277 37.500 0.00 0.00 38.51 4.85
736 818 5.719173 TGAGCAAACCTATTTTTGTATGGC 58.281 37.500 0.00 0.00 38.51 4.40
742 824 7.381323 AGAAAGGATGAGCAAACCTATTTTTG 58.619 34.615 0.00 0.00 39.15 2.44
743 825 7.544804 AGAAAGGATGAGCAAACCTATTTTT 57.455 32.000 0.00 0.00 33.34 1.94
744 826 8.829373 ATAGAAAGGATGAGCAAACCTATTTT 57.171 30.769 0.00 0.00 33.34 1.82
748 830 6.560003 TGATAGAAAGGATGAGCAAACCTA 57.440 37.500 0.00 0.00 33.34 3.08
750 832 6.060788 AGATGATAGAAAGGATGAGCAAACC 58.939 40.000 0.00 0.00 0.00 3.27
761 843 7.715249 TCCGTTCCAAAATAGATGATAGAAAGG 59.285 37.037 0.00 0.00 34.31 3.11
770 852 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
771 853 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
774 856 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
775 857 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
776 858 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
777 859 2.235402 GACATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
778 860 1.829222 GACATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
779 861 1.272816 TGACATACTCCCTCCGTTCCA 60.273 52.381 0.00 0.00 0.00 3.53
780 862 1.409427 CTGACATACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
781 863 2.100989 ACTGACATACTCCCTCCGTTC 58.899 52.381 0.00 0.00 0.00 3.95
782 864 2.233305 ACTGACATACTCCCTCCGTT 57.767 50.000 0.00 0.00 0.00 4.44
783 865 2.233305 AACTGACATACTCCCTCCGT 57.767 50.000 0.00 0.00 0.00 4.69
784 866 3.021695 TGTAACTGACATACTCCCTCCG 58.978 50.000 0.00 0.00 31.20 4.63
785 867 4.388378 GTGTAACTGACATACTCCCTCC 57.612 50.000 0.00 0.00 41.14 4.30
834 916 6.409524 AACTGACAATGTGAAAATGGACAT 57.590 33.333 0.00 0.00 34.16 3.06
863 945 5.722021 AAGCAAATAGATTTTTGTCGGGT 57.278 34.783 0.00 0.00 38.55 5.28
892 974 1.174712 TTGTGCTGCTTCCAGGCTTC 61.175 55.000 0.00 0.00 39.54 3.86
893 975 0.756442 TTTGTGCTGCTTCCAGGCTT 60.756 50.000 0.00 0.00 39.54 4.35
894 976 0.756442 TTTTGTGCTGCTTCCAGGCT 60.756 50.000 0.00 0.00 39.54 4.58
895 977 0.319405 ATTTTGTGCTGCTTCCAGGC 59.681 50.000 0.00 0.00 39.54 4.85
896 978 2.825861 AATTTTGTGCTGCTTCCAGG 57.174 45.000 0.00 0.00 39.54 4.45
897 979 4.092383 GCATTAATTTTGTGCTGCTTCCAG 59.908 41.667 0.00 0.00 42.13 3.86
898 980 3.995705 GCATTAATTTTGTGCTGCTTCCA 59.004 39.130 0.00 0.00 36.02 3.53
899 981 4.248058 AGCATTAATTTTGTGCTGCTTCC 58.752 39.130 10.06 0.00 46.60 3.46
939 1021 0.546122 ATTTCCCTCGTGGCAGCATA 59.454 50.000 0.00 0.00 0.00 3.14
940 1022 0.546122 TATTTCCCTCGTGGCAGCAT 59.454 50.000 0.00 0.00 0.00 3.79
954 1036 7.110810 GGGGGCTTGTTATATAGGAGTATTTC 58.889 42.308 0.00 0.00 0.00 2.17
955 1037 7.029053 GGGGGCTTGTTATATAGGAGTATTT 57.971 40.000 0.00 0.00 0.00 1.40
979 1061 0.105913 GGTGTAGAGGAGAGGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
986 1068 2.856864 TGGTAGATGGGTGTAGAGGAGA 59.143 50.000 0.00 0.00 0.00 3.71
992 1074 5.833667 TGAGTTCTATGGTAGATGGGTGTAG 59.166 44.000 0.00 0.00 34.22 2.74
997 1079 3.900601 AGCTGAGTTCTATGGTAGATGGG 59.099 47.826 0.00 0.00 34.22 4.00
1000 1082 5.073437 AGGAGCTGAGTTCTATGGTAGAT 57.927 43.478 0.00 0.00 34.22 1.98
1014 1096 2.820178 TGGTAGAATGTGAGGAGCTGA 58.180 47.619 0.00 0.00 0.00 4.26
1021 1103 7.060383 AGAGGATTGTATGGTAGAATGTGAG 57.940 40.000 0.00 0.00 0.00 3.51
1060 1155 1.745489 GACAGACCCATGGCGGTTC 60.745 63.158 6.09 0.00 35.79 3.62
1082 1177 0.246910 GGAGGACCACGAAGACCTTC 59.753 60.000 0.00 0.00 35.97 3.46
1115 1210 2.333926 CATGTATACATACCCGTGGCG 58.666 52.381 17.86 0.00 34.26 5.69
1149 1244 8.737175 GGATGCATCATCAGTTATGTCAAATAT 58.263 33.333 27.25 0.00 42.13 1.28
1159 1254 7.381323 CAGTATGTAGGATGCATCATCAGTTA 58.619 38.462 27.25 8.70 41.75 2.24
1216 1311 1.189884 CCAAAATCAACAAAGCGTGCG 59.810 47.619 0.00 0.00 0.00 5.34
1258 1353 3.005539 AGAGCCACCTGCACCGAT 61.006 61.111 0.00 0.00 44.83 4.18
1432 1527 0.716108 CGCGAGAACAAACTAGCCAG 59.284 55.000 0.00 0.00 35.66 4.85
1477 1572 7.710676 ATAGATCTACCATCGTTCAGCTAAT 57.289 36.000 4.10 0.00 0.00 1.73
1515 1610 1.366494 GATCAACGCACGCATACGC 60.366 57.895 0.00 0.00 45.53 4.42
1518 1613 1.751536 CGCAGATCAACGCACGCATA 61.752 55.000 0.00 0.00 0.00 3.14
1519 1614 2.787249 GCAGATCAACGCACGCAT 59.213 55.556 0.00 0.00 0.00 4.73
1524 1619 2.382746 GCACTCGCAGATCAACGCA 61.383 57.895 0.00 0.00 38.36 5.24
1579 1674 2.027469 AGCTCACTCACAAGATGATGCA 60.027 45.455 0.00 0.00 36.48 3.96
1580 1675 2.608546 GAGCTCACTCACAAGATGATGC 59.391 50.000 9.40 0.00 42.93 3.91
1608 1703 4.700700 TGATCGATGATCTCACAAAGCAT 58.299 39.130 0.54 0.00 39.56 3.79
1797 1974 5.256474 CCATAAGGTCTGGTGTTCAAATCT 58.744 41.667 0.00 0.00 0.00 2.40
2036 3957 3.266510 ACTCGCATGATTTTAGGAGCA 57.733 42.857 0.00 0.00 0.00 4.26
2125 4073 2.614983 TGCCGGCGGAAGATAATTTAAC 59.385 45.455 33.44 7.31 0.00 2.01
2215 4163 3.252458 GCCGGCGGAAGATAATTTAACAT 59.748 43.478 33.44 0.00 0.00 2.71
2220 4168 1.880027 GATGCCGGCGGAAGATAATTT 59.120 47.619 33.44 0.28 0.00 1.82
2221 4169 1.202758 TGATGCCGGCGGAAGATAATT 60.203 47.619 33.44 1.28 0.00 1.40
2224 4172 0.037326 GATGATGCCGGCGGAAGATA 60.037 55.000 33.44 10.40 0.00 1.98
2225 4173 1.302033 GATGATGCCGGCGGAAGAT 60.302 57.895 33.44 16.19 0.00 2.40
2227 4175 1.958205 GAGATGATGCCGGCGGAAG 60.958 63.158 33.44 3.04 0.00 3.46
2228 4176 2.108976 GAGATGATGCCGGCGGAA 59.891 61.111 33.44 23.28 0.00 4.30
2229 4177 4.284860 CGAGATGATGCCGGCGGA 62.285 66.667 33.44 15.74 0.00 5.54
2230 4178 3.790334 TTCGAGATGATGCCGGCGG 62.790 63.158 24.35 24.35 0.00 6.13
2233 4181 1.951130 CCGTTCGAGATGATGCCGG 60.951 63.158 0.00 0.00 0.00 6.13
2235 4183 1.595382 CCCCGTTCGAGATGATGCC 60.595 63.158 0.00 0.00 0.00 4.40
2236 4184 0.179084 TTCCCCGTTCGAGATGATGC 60.179 55.000 0.00 0.00 0.00 3.91
2237 4185 2.533266 ATTCCCCGTTCGAGATGATG 57.467 50.000 0.00 0.00 0.00 3.07
2238 4186 3.206150 CAAATTCCCCGTTCGAGATGAT 58.794 45.455 0.00 0.00 0.00 2.45
2329 4470 5.294552 CCAGGAGTAAATTCTCGAATTGACC 59.705 44.000 13.71 10.61 41.16 4.02


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

AutoCloner maintained by Alex Coulton.