Multiple sequence alignment - TraesCS5D01G548000

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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 TraesCS5D01G548000 chr5D 100.000 3845 0 0 1 3845 555905766 555909610 0.000000e+00 7101.0
1 TraesCS5D01G548000 chr5D 88.064 3636 338 50 290 3845 555321178 555324797 0.000000e+00 4222.0
2 TraesCS5D01G548000 chr5D 79.631 2872 543 39 991 3845 555635854 555638700 0.000000e+00 2025.0
3 TraesCS5D01G548000 chr5D 79.203 2784 550 27 1077 3845 495551741 495548972 0.000000e+00 1906.0
4 TraesCS5D01G548000 chr5D 79.325 2757 531 35 1109 3845 555555639 555558376 0.000000e+00 1897.0
5 TraesCS5D01G548000 chr5D 77.994 2881 584 46 986 3845 555062237 555065088 0.000000e+00 1762.0
6 TraesCS5D01G548000 chr5D 76.733 2669 570 43 1201 3845 555356797 555359438 0.000000e+00 1441.0
7 TraesCS5D01G548000 chr5D 78.275 1786 361 26 2074 3845 555488291 555490063 0.000000e+00 1123.0
8 TraesCS5D01G548000 chr5D 88.118 951 69 13 1 922 555201031 555201966 0.000000e+00 1090.0
9 TraesCS5D01G548000 chr5D 86.548 617 78 5 1178 1792 555227133 555227746 0.000000e+00 675.0
10 TraesCS5D01G548000 chr5D 83.444 604 92 6 3246 3845 555048252 555048851 4.340000e-154 555.0
11 TraesCS5D01G548000 chr4A 90.514 3036 268 12 819 3845 613744281 613741257 0.000000e+00 3993.0
12 TraesCS5D01G548000 chr4A 80.769 390 39 22 294 662 613744811 613744437 4.890000e-69 272.0
13 TraesCS5D01G548000 chr4A 92.029 138 9 1 652 789 613744415 613744280 3.920000e-45 193.0
14 TraesCS5D01G548000 chr3A 80.079 2796 520 29 1067 3845 44605562 44608337 0.000000e+00 2043.0
15 TraesCS5D01G548000 chr5B 79.840 2743 518 31 1121 3845 695814265 695811540 0.000000e+00 1969.0
16 TraesCS5D01G548000 chr5B 78.517 2872 572 36 993 3845 695493867 695491022 0.000000e+00 1844.0
17 TraesCS5D01G548000 chr5B 80.491 2076 374 30 1787 3845 695695979 695693918 0.000000e+00 1561.0
18 TraesCS5D01G548000 chr5B 76.020 1985 459 17 1077 3052 695724591 695722615 0.000000e+00 1013.0
19 TraesCS5D01G548000 chr5B 76.089 1401 310 22 1078 2467 695894141 695892755 0.000000e+00 708.0
20 TraesCS5D01G548000 chr3D 79.560 2500 469 35 1362 3845 32206644 32209117 0.000000e+00 1748.0
21 TraesCS5D01G548000 chr6A 78.783 1923 381 23 1136 3044 11233977 11235886 0.000000e+00 1266.0
22 TraesCS5D01G548000 chr6A 84.343 792 115 7 3058 3845 11233973 11233187 0.000000e+00 767.0
23 TraesCS5D01G548000 chr6D 83.442 918 141 10 2933 3845 436739061 436738150 0.000000e+00 843.0
24 TraesCS5D01G548000 chr1D 95.349 43 2 0 1 43 236175619 236175577 6.890000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G548000 chr5D 555905766 555909610 3844 False 7101 7101 100.000000 1 3845 1 chr5D.!!$F10 3844
1 TraesCS5D01G548000 chr5D 555321178 555324797 3619 False 4222 4222 88.064000 290 3845 1 chr5D.!!$F5 3555
2 TraesCS5D01G548000 chr5D 555635854 555638700 2846 False 2025 2025 79.631000 991 3845 1 chr5D.!!$F9 2854
3 TraesCS5D01G548000 chr5D 495548972 495551741 2769 True 1906 1906 79.203000 1077 3845 1 chr5D.!!$R1 2768
4 TraesCS5D01G548000 chr5D 555555639 555558376 2737 False 1897 1897 79.325000 1109 3845 1 chr5D.!!$F8 2736
5 TraesCS5D01G548000 chr5D 555062237 555065088 2851 False 1762 1762 77.994000 986 3845 1 chr5D.!!$F2 2859
6 TraesCS5D01G548000 chr5D 555356797 555359438 2641 False 1441 1441 76.733000 1201 3845 1 chr5D.!!$F6 2644
7 TraesCS5D01G548000 chr5D 555488291 555490063 1772 False 1123 1123 78.275000 2074 3845 1 chr5D.!!$F7 1771
8 TraesCS5D01G548000 chr5D 555201031 555201966 935 False 1090 1090 88.118000 1 922 1 chr5D.!!$F3 921
9 TraesCS5D01G548000 chr5D 555227133 555227746 613 False 675 675 86.548000 1178 1792 1 chr5D.!!$F4 614
10 TraesCS5D01G548000 chr5D 555048252 555048851 599 False 555 555 83.444000 3246 3845 1 chr5D.!!$F1 599
11 TraesCS5D01G548000 chr4A 613741257 613744811 3554 True 1486 3993 87.770667 294 3845 3 chr4A.!!$R1 3551
12 TraesCS5D01G548000 chr3A 44605562 44608337 2775 False 2043 2043 80.079000 1067 3845 1 chr3A.!!$F1 2778
13 TraesCS5D01G548000 chr5B 695811540 695814265 2725 True 1969 1969 79.840000 1121 3845 1 chr5B.!!$R4 2724
14 TraesCS5D01G548000 chr5B 695491022 695493867 2845 True 1844 1844 78.517000 993 3845 1 chr5B.!!$R1 2852
15 TraesCS5D01G548000 chr5B 695693918 695695979 2061 True 1561 1561 80.491000 1787 3845 1 chr5B.!!$R2 2058
16 TraesCS5D01G548000 chr5B 695722615 695724591 1976 True 1013 1013 76.020000 1077 3052 1 chr5B.!!$R3 1975
17 TraesCS5D01G548000 chr5B 695892755 695894141 1386 True 708 708 76.089000 1078 2467 1 chr5B.!!$R5 1389
18 TraesCS5D01G548000 chr3D 32206644 32209117 2473 False 1748 1748 79.560000 1362 3845 1 chr3D.!!$F1 2483
19 TraesCS5D01G548000 chr6A 11233977 11235886 1909 False 1266 1266 78.783000 1136 3044 1 chr6A.!!$F1 1908
20 TraesCS5D01G548000 chr6A 11233187 11233973 786 True 767 767 84.343000 3058 3845 1 chr6A.!!$R1 787
21 TraesCS5D01G548000 chr6D 436738150 436739061 911 True 843 843 83.442000 2933 3845 1 chr6D.!!$R1 912

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
866 990 0.102663 TACAGAAACCGTGTGCGTCA 59.897 50.000 0.00 0.0 36.15 4.35 F
1234 1403 0.172578 CGGTGTCTCATGTAGCCGAA 59.827 55.000 9.87 0.0 41.45 4.30 F
1269 1438 2.811317 GCTCTGTCGTTGCCGGAG 60.811 66.667 5.05 0.0 33.95 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2334 0.323725 TGCCAAGGGAAGCTGGAATC 60.324 55.0 0.00 0.00 34.35 2.52 R
2811 2983 0.395724 TCAGATGGTAGCGCTCCAGA 60.396 55.0 25.57 17.79 38.42 3.86 R
2969 3143 1.519408 TTAGCTTTTCGAGTGTGCCC 58.481 50.0 0.00 0.00 0.00 5.36 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
115 117 7.697352 TTATCAAACAATGTTGCAAGTGAAG 57.303 32.000 0.00 0.00 0.00 3.02
128 130 6.012658 TGCAAGTGAAGTGGATTTCAATAC 57.987 37.500 0.00 0.00 38.69 1.89
137 139 9.699410 TGAAGTGGATTTCAATACTTATCCAAT 57.301 29.630 0.00 0.00 45.84 3.16
200 227 7.986320 TCCAACAAAATATTTCTAATGGCCATG 59.014 33.333 21.63 8.02 0.00 3.66
204 231 5.733620 AATATTTCTAATGGCCATGGCAG 57.266 39.130 36.56 25.00 42.43 4.85
220 247 0.305922 GCAGCGCATGGACATTCTAC 59.694 55.000 11.47 0.00 0.00 2.59
243 270 4.111375 AGTGCGATAAATTGACGAGACT 57.889 40.909 0.00 0.00 0.00 3.24
245 272 5.035443 AGTGCGATAAATTGACGAGACTAC 58.965 41.667 0.00 0.00 0.00 2.73
256 283 9.590088 AAATTGACGAGACTACGAAATTTAAAC 57.410 29.630 0.00 0.00 39.05 2.01
383 411 4.158394 TGGGCTAGAAATTCTGAAATGCAC 59.842 41.667 5.64 4.30 0.00 4.57
394 422 6.647334 TTCTGAAATGCACTTTCACCATAA 57.353 33.333 15.74 8.64 46.45 1.90
400 428 7.814107 TGAAATGCACTTTCACCATAAAGATTC 59.186 33.333 15.74 0.00 46.45 2.52
478 511 8.986477 ACATTATTTGACTCAAATTTGTAGGC 57.014 30.769 19.72 15.17 40.60 3.93
558 596 1.075542 TGAAATGATCGCCACGACAC 58.924 50.000 0.00 0.00 39.18 3.67
559 597 1.337728 TGAAATGATCGCCACGACACT 60.338 47.619 0.00 0.00 39.18 3.55
560 598 1.732259 GAAATGATCGCCACGACACTT 59.268 47.619 0.00 0.00 39.18 3.16
640 699 1.000955 CAGCCGGTTCACACTAGAACT 59.999 52.381 1.90 0.00 45.52 3.01
688 779 6.363357 GCATGTCCACAGCTAAACTTTAAAAG 59.637 38.462 0.00 0.00 0.00 2.27
690 781 6.123651 TGTCCACAGCTAAACTTTAAAAGGA 58.876 36.000 0.00 0.00 0.00 3.36
703 794 8.757164 AACTTTAAAAGGAAGTCAGTTTTGTG 57.243 30.769 0.00 0.00 36.38 3.33
710 801 6.174720 AGGAAGTCAGTTTTGTGATGTAGA 57.825 37.500 0.00 0.00 0.00 2.59
732 828 5.634020 AGAAGTACGTGTATGAAAGCAGTTC 59.366 40.000 0.00 0.00 36.70 3.01
766 866 0.537188 ACTTCCTACCTGCCGTGATG 59.463 55.000 0.00 0.00 0.00 3.07
768 868 0.535335 TTCCTACCTGCCGTGATGAC 59.465 55.000 0.00 0.00 0.00 3.06
805 929 1.954362 TTTTGGCTGCAGCGTTGGTT 61.954 50.000 31.19 0.00 43.26 3.67
806 930 2.625973 TTTGGCTGCAGCGTTGGTTG 62.626 55.000 31.19 0.00 43.26 3.77
807 931 4.347453 GGCTGCAGCGTTGGTTGG 62.347 66.667 31.19 0.00 43.26 3.77
808 932 3.595758 GCTGCAGCGTTGGTTGGT 61.596 61.111 25.23 0.00 0.00 3.67
862 986 2.206750 TGACTTACAGAAACCGTGTGC 58.793 47.619 0.00 0.00 0.00 4.57
866 990 0.102663 TACAGAAACCGTGTGCGTCA 59.897 50.000 0.00 0.00 36.15 4.35
882 1006 1.135257 CGTCAGGTCAAGCGAGATTCT 60.135 52.381 0.00 0.00 0.00 2.40
894 1018 2.551459 GCGAGATTCTATTGCCAGCAAT 59.449 45.455 20.66 20.66 46.85 3.56
895 1019 3.004106 GCGAGATTCTATTGCCAGCAATT 59.996 43.478 21.87 5.14 43.32 2.32
896 1020 4.214119 GCGAGATTCTATTGCCAGCAATTA 59.786 41.667 21.87 9.18 43.32 1.40
897 1021 5.277974 GCGAGATTCTATTGCCAGCAATTAA 60.278 40.000 21.87 16.40 43.32 1.40
900 1024 7.325338 CGAGATTCTATTGCCAGCAATTAAATG 59.675 37.037 21.87 8.76 43.32 2.32
907 1031 5.601583 TGCCAGCAATTAAATGTCATCAT 57.398 34.783 0.00 0.00 35.59 2.45
922 1046 4.158949 TGTCATCATTGCCTTTGATGGAAG 59.841 41.667 16.15 0.00 46.75 3.46
923 1047 4.400251 GTCATCATTGCCTTTGATGGAAGA 59.600 41.667 16.15 0.52 46.75 2.87
928 1052 2.459644 TGCCTTTGATGGAAGAATGGG 58.540 47.619 0.00 0.00 0.00 4.00
930 1054 2.428530 GCCTTTGATGGAAGAATGGGAC 59.571 50.000 0.00 0.00 0.00 4.46
931 1055 3.879321 GCCTTTGATGGAAGAATGGGACT 60.879 47.826 0.00 0.00 0.00 3.85
933 1057 4.884164 CCTTTGATGGAAGAATGGGACTAC 59.116 45.833 0.00 0.00 0.00 2.73
938 1070 7.206789 TGATGGAAGAATGGGACTACAAATA 57.793 36.000 0.00 0.00 0.00 1.40
962 1094 0.520404 TCGCTACACTCCTTGTCGAC 59.480 55.000 9.11 9.11 39.91 4.20
963 1095 0.522180 CGCTACACTCCTTGTCGACT 59.478 55.000 17.92 0.00 39.91 4.18
974 1106 2.095161 CCTTGTCGACTCACACTACTCC 60.095 54.545 17.92 0.00 0.00 3.85
976 1108 1.202842 TGTCGACTCACACTACTCCCA 60.203 52.381 17.92 0.00 0.00 4.37
979 1111 2.303890 TCGACTCACACTACTCCCACTA 59.696 50.000 0.00 0.00 0.00 2.74
994 1148 1.074471 ACTATCCCATCCGCACCCT 60.074 57.895 0.00 0.00 0.00 4.34
1005 1159 2.362120 GCACCCTGCTCAATGGCT 60.362 61.111 0.00 0.00 40.96 4.75
1015 1169 2.105993 TGCTCAATGGCTGCTCTATCAT 59.894 45.455 0.00 0.00 0.00 2.45
1063 1217 4.959723 ACTCATACTACTACTCTCCGTCC 58.040 47.826 0.00 0.00 0.00 4.79
1068 1234 3.106054 ACTACTACTCTCCGTCCTCTCA 58.894 50.000 0.00 0.00 0.00 3.27
1071 1237 2.506231 ACTACTCTCCGTCCTCTCATCA 59.494 50.000 0.00 0.00 0.00 3.07
1116 1285 1.014044 ACAGTAATGGCAGCGACACG 61.014 55.000 0.00 0.00 0.00 4.49
1168 1337 3.358076 CTTGCCGACCCTCTCCGTC 62.358 68.421 0.00 0.00 0.00 4.79
1234 1403 0.172578 CGGTGTCTCATGTAGCCGAA 59.827 55.000 9.87 0.00 41.45 4.30
1269 1438 2.811317 GCTCTGTCGTTGCCGGAG 60.811 66.667 5.05 0.00 33.95 4.63
1324 1493 6.607004 TCGGTAATCTTTCTTTTCTCTCCT 57.393 37.500 0.00 0.00 0.00 3.69
1325 1494 7.713734 TCGGTAATCTTTCTTTTCTCTCCTA 57.286 36.000 0.00 0.00 0.00 2.94
1335 1504 4.884744 TCTTTTCTCTCCTACCTCGATCTG 59.115 45.833 0.00 0.00 0.00 2.90
1401 1570 4.039730 AGGCTACGTCGTCTTAGGTATCTA 59.960 45.833 0.00 0.00 0.00 1.98
1439 1608 4.579869 AGCTTGTCAAACACCATACCTAG 58.420 43.478 0.00 0.00 0.00 3.02
1503 1672 4.687219 GCTTATAACCAACTCTCAGGCCAT 60.687 45.833 5.01 0.00 0.00 4.40
1656 1826 7.939588 GGAAATAATAGCTTGTCAGGTCCTATT 59.060 37.037 0.00 0.00 34.27 1.73
1691 1861 3.877559 CACACCTATCCATGCTTGAGAA 58.122 45.455 0.22 0.00 0.00 2.87
1697 1867 6.264744 CACCTATCCATGCTTGAGAAATTCAT 59.735 38.462 0.22 0.00 35.27 2.57
1743 1913 5.277857 GTCTAGTACCACAAGCCATGTAT 57.722 43.478 0.00 0.00 41.46 2.29
1761 1931 4.006989 TGTATAACATGTCCAGGTTGCAC 58.993 43.478 0.00 5.84 35.94 4.57
1845 2016 4.787551 ACCTCCCAATGTTGCGATTTATA 58.212 39.130 0.00 0.00 0.00 0.98
1946 2117 4.058124 GGTGAAAATTCTTTTGAGGGCAC 58.942 43.478 0.00 0.00 31.94 5.01
2163 2334 6.776744 TGGATCCAATCAATTGATAGGAGAG 58.223 40.000 21.00 7.06 40.14 3.20
2221 2392 9.290988 TGTCTGTTCTAATTTTGGCAAATAGTA 57.709 29.630 14.29 4.81 31.89 1.82
2385 2556 5.940470 AGAAGATAATTCTTTCACTGGCGTT 59.060 36.000 0.00 0.00 42.34 4.84
2436 2607 6.072112 TCAAAACTAGTCACTTTCATTGCC 57.928 37.500 0.00 0.00 0.00 4.52
2598 2769 3.588955 TCTCTCCAACAATGACATGTCG 58.411 45.455 20.54 9.32 31.81 4.35
2784 2955 7.337942 AGCATTTTCCACCTAGATAAACTTCTG 59.662 37.037 0.00 0.00 0.00 3.02
2819 2991 5.818136 TCAAATATTCCTTTTCTGGAGCG 57.182 39.130 0.00 0.00 37.43 5.03
2837 3009 1.599542 GCGCTACCATCTGATGTTTCC 59.400 52.381 15.95 2.08 0.00 3.13
2969 3143 5.959618 ACTCCTTCAAAGGTTTTATTCCG 57.040 39.130 8.60 0.00 46.54 4.30
3278 3452 1.526887 CTCACACTAGTTGTTGGTGCG 59.473 52.381 0.00 0.00 41.61 5.34
3322 3497 9.892130 CCTATGGTCTAGAAAGAAACTTAACAT 57.108 33.333 0.00 0.00 32.16 2.71
3332 3507 8.579863 AGAAAGAAACTTAACATGGGAAATGAG 58.420 33.333 0.00 0.00 0.00 2.90
3338 3513 7.553881 ACTTAACATGGGAAATGAGATAACG 57.446 36.000 0.00 0.00 0.00 3.18
3566 3741 1.600356 TCAAGTGCTTCGCATGGCA 60.600 52.632 0.00 0.00 41.91 4.92
3572 3747 2.753966 GCTTCGCATGGCACGACAT 61.754 57.895 0.00 0.00 39.67 3.06
3680 3856 0.171455 CGCTCCTACACCAGTCTGAC 59.829 60.000 0.00 0.00 0.00 3.51
3695 3871 1.421268 TCTGACAGTTCATGGCACCTT 59.579 47.619 1.59 0.00 44.15 3.50
3716 3892 2.111972 TGGGTTCCTTGAGAGACTAGGT 59.888 50.000 0.00 0.00 41.16 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 8.355913 TGCAACATTGTTTGATAATCTGTTACA 58.644 29.630 0.00 0.00 0.00 2.41
83 84 8.741101 TGCAACATTGTTTGATAATCTGTTAC 57.259 30.769 0.00 0.00 0.00 2.50
84 85 9.409312 CTTGCAACATTGTTTGATAATCTGTTA 57.591 29.630 0.00 0.00 0.00 2.41
85 86 7.927629 ACTTGCAACATTGTTTGATAATCTGTT 59.072 29.630 0.00 0.00 0.00 3.16
86 87 7.383029 CACTTGCAACATTGTTTGATAATCTGT 59.617 33.333 0.00 0.00 0.00 3.41
87 88 7.595875 TCACTTGCAACATTGTTTGATAATCTG 59.404 33.333 0.00 0.00 0.00 2.90
88 89 7.660112 TCACTTGCAACATTGTTTGATAATCT 58.340 30.769 0.00 0.00 0.00 2.40
89 90 7.872163 TCACTTGCAACATTGTTTGATAATC 57.128 32.000 0.00 0.00 0.00 1.75
90 91 7.927629 ACTTCACTTGCAACATTGTTTGATAAT 59.072 29.630 0.00 0.00 0.00 1.28
93 94 5.521010 CACTTCACTTGCAACATTGTTTGAT 59.479 36.000 0.00 0.00 0.00 2.57
94 95 4.863689 CACTTCACTTGCAACATTGTTTGA 59.136 37.500 0.00 0.00 0.00 2.69
171 198 8.691797 GGCCATTAGAAATATTTTGTTGGAGTA 58.308 33.333 17.58 0.00 0.00 2.59
189 216 3.036577 CGCTGCCATGGCCATTAG 58.963 61.111 33.44 23.95 41.09 1.73
200 227 0.815213 TAGAATGTCCATGCGCTGCC 60.815 55.000 9.73 0.00 0.00 4.85
204 231 2.797156 CACTAGTAGAATGTCCATGCGC 59.203 50.000 0.00 0.00 0.00 6.09
209 236 6.459670 TTTATCGCACTAGTAGAATGTCCA 57.540 37.500 3.59 0.00 0.00 4.02
210 237 7.652105 TCAATTTATCGCACTAGTAGAATGTCC 59.348 37.037 3.59 0.00 0.00 4.02
220 247 5.274718 AGTCTCGTCAATTTATCGCACTAG 58.725 41.667 0.00 0.00 0.00 2.57
243 270 4.510711 TGGAGCACACGTTTAAATTTCGTA 59.489 37.500 3.43 0.00 36.05 3.43
245 272 3.662186 GTGGAGCACACGTTTAAATTTCG 59.338 43.478 0.00 0.00 40.85 3.46
383 411 9.454859 AGTTTAGGAGAATCTTTATGGTGAAAG 57.545 33.333 0.00 0.00 37.70 2.62
500 533 4.989279 AAGATGATACAACCATGGCAAC 57.011 40.909 13.04 0.00 0.00 4.17
558 596 2.730069 CATGCTCTCTCGCAGACTAAG 58.270 52.381 0.00 0.00 44.10 2.18
559 597 1.202348 GCATGCTCTCTCGCAGACTAA 60.202 52.381 11.37 0.00 44.10 2.24
560 598 0.383590 GCATGCTCTCTCGCAGACTA 59.616 55.000 11.37 0.00 44.10 2.59
640 699 5.124776 GCATGTGTAAGCAATTTACCTACCA 59.875 40.000 0.00 0.00 40.80 3.25
688 779 6.483640 ACTTCTACATCACAAAACTGACTTCC 59.516 38.462 0.00 0.00 0.00 3.46
690 781 7.169308 CGTACTTCTACATCACAAAACTGACTT 59.831 37.037 0.00 0.00 0.00 3.01
703 794 6.750501 TGCTTTCATACACGTACTTCTACATC 59.249 38.462 0.00 0.00 0.00 3.06
710 801 4.384846 CGAACTGCTTTCATACACGTACTT 59.615 41.667 0.00 0.00 33.24 2.24
761 861 3.118629 TGTCCCTCAGCATTAGTCATCAC 60.119 47.826 0.00 0.00 0.00 3.06
766 866 3.618690 ACTTGTCCCTCAGCATTAGTC 57.381 47.619 0.00 0.00 0.00 2.59
768 868 4.082571 CCAAAACTTGTCCCTCAGCATTAG 60.083 45.833 0.00 0.00 0.00 1.73
805 929 3.090210 TCCAGGAATCACGTAGTACCA 57.910 47.619 0.00 0.00 41.61 3.25
806 930 4.667519 ATTCCAGGAATCACGTAGTACC 57.332 45.455 9.12 0.00 41.61 3.34
807 931 6.746120 ACATATTCCAGGAATCACGTAGTAC 58.254 40.000 18.67 0.00 34.12 2.73
808 932 6.971726 ACATATTCCAGGAATCACGTAGTA 57.028 37.500 18.67 0.00 34.12 1.82
861 985 0.737715 AATCTCGCTTGACCTGACGC 60.738 55.000 0.00 0.00 0.00 5.19
862 986 1.135257 AGAATCTCGCTTGACCTGACG 60.135 52.381 0.00 0.00 0.00 4.35
866 990 3.462021 GCAATAGAATCTCGCTTGACCT 58.538 45.455 0.00 0.00 0.00 3.85
882 1006 7.110043 TGATGACATTTAATTGCTGGCAATA 57.890 32.000 19.16 6.49 44.86 1.90
907 1031 2.833338 CCCATTCTTCCATCAAAGGCAA 59.167 45.455 0.00 0.00 0.00 4.52
922 1046 5.122396 GCGATGGATATTTGTAGTCCCATTC 59.878 44.000 0.00 0.00 34.83 2.67
923 1047 5.003804 GCGATGGATATTTGTAGTCCCATT 58.996 41.667 0.00 0.00 34.83 3.16
928 1052 6.448006 AGTGTAGCGATGGATATTTGTAGTC 58.552 40.000 0.00 0.00 0.00 2.59
930 1054 5.864474 GGAGTGTAGCGATGGATATTTGTAG 59.136 44.000 0.00 0.00 0.00 2.74
931 1055 5.538813 AGGAGTGTAGCGATGGATATTTGTA 59.461 40.000 0.00 0.00 0.00 2.41
933 1057 4.887748 AGGAGTGTAGCGATGGATATTTG 58.112 43.478 0.00 0.00 0.00 2.32
938 1070 2.101582 GACAAGGAGTGTAGCGATGGAT 59.898 50.000 0.00 0.00 41.96 3.41
962 1094 2.959707 GGGATAGTGGGAGTAGTGTGAG 59.040 54.545 0.00 0.00 0.00 3.51
963 1095 2.313643 TGGGATAGTGGGAGTAGTGTGA 59.686 50.000 0.00 0.00 0.00 3.58
974 1106 1.071471 GGTGCGGATGGGATAGTGG 59.929 63.158 0.00 0.00 0.00 4.00
976 1108 1.074471 AGGGTGCGGATGGGATAGT 60.074 57.895 0.00 0.00 0.00 2.12
979 1111 4.195334 GCAGGGTGCGGATGGGAT 62.195 66.667 0.00 0.00 31.71 3.85
994 1148 1.487558 TGATAGAGCAGCCATTGAGCA 59.512 47.619 0.00 0.00 34.23 4.26
1005 1159 1.627329 GGGATGGAGCATGATAGAGCA 59.373 52.381 0.00 0.00 0.00 4.26
1015 1169 0.925720 AAGGGAATGGGGATGGAGCA 60.926 55.000 0.00 0.00 0.00 4.26
1063 1217 7.864379 GCTAGAAGAAGAAGAAGATGATGAGAG 59.136 40.741 0.00 0.00 0.00 3.20
1068 1234 6.610830 TCAGGCTAGAAGAAGAAGAAGATGAT 59.389 38.462 0.00 0.00 0.00 2.45
1071 1237 5.128663 GGTCAGGCTAGAAGAAGAAGAAGAT 59.871 44.000 0.00 0.00 0.00 2.40
1125 1294 2.626088 CTTTGAAAGCTAGCAGTGCC 57.374 50.000 18.83 0.00 0.00 5.01
1168 1337 3.677527 CCAGTTGCTGGCAAGGAG 58.322 61.111 8.34 2.06 45.13 3.69
1234 1403 2.031163 GGTGACTCGTTGCCTGCT 59.969 61.111 0.00 0.00 0.00 4.24
1269 1438 1.153349 GGATCCAACCAGAGGCGTC 60.153 63.158 6.95 0.00 0.00 5.19
1278 1447 2.750237 GGTGCCACGGATCCAACC 60.750 66.667 13.41 7.14 0.00 3.77
1324 1493 1.822990 GGTGTTGGTCAGATCGAGGTA 59.177 52.381 0.00 0.00 0.00 3.08
1325 1494 0.608640 GGTGTTGGTCAGATCGAGGT 59.391 55.000 0.00 0.00 0.00 3.85
1335 1504 1.156736 CCGTGAGATTGGTGTTGGTC 58.843 55.000 0.00 0.00 0.00 4.02
1409 1578 6.403866 TGGTGTTTGACAAGCTATTTTCAT 57.596 33.333 3.59 0.00 0.00 2.57
1410 1579 5.843673 TGGTGTTTGACAAGCTATTTTCA 57.156 34.783 3.59 0.00 0.00 2.69
1439 1608 1.896122 CGTGAGGTTCCCCAGGGTAC 61.896 65.000 4.22 4.43 35.23 3.34
1503 1672 4.708177 GCAGTAGCATCTCAAAAGGGATA 58.292 43.478 0.00 0.00 41.58 2.59
1656 1826 4.840005 TGTGCAACGGCGTGTGGA 62.840 61.111 15.70 12.71 45.35 4.02
1691 1861 6.653989 AGTTGATTAACCTCGAGGATGAATT 58.346 36.000 37.69 22.30 37.52 2.17
1697 1867 4.399618 CAGAGAGTTGATTAACCTCGAGGA 59.600 45.833 37.69 16.59 38.27 3.71
1743 1913 2.647683 TGTGCAACCTGGACATGTTA 57.352 45.000 0.00 0.00 43.78 2.41
1761 1931 4.439153 CCATTACTTGCAAGTGCCATAGTG 60.439 45.833 36.50 23.51 40.07 2.74
1863 2034 1.868109 GCTGGAAACTGGCCGAAAAAC 60.868 52.381 0.00 0.00 0.00 2.43
2019 2190 1.491668 TGCTAAGAGCGGTTGGGATA 58.508 50.000 0.00 0.00 46.26 2.59
2163 2334 0.323725 TGCCAAGGGAAGCTGGAATC 60.324 55.000 0.00 0.00 34.35 2.52
2436 2607 5.242838 TCCACCTATTAACTGGTTTTTGCTG 59.757 40.000 0.00 0.00 33.75 4.41
2476 2647 4.403453 CGTACAAGGCTTCTTATGTTTGC 58.597 43.478 0.00 0.00 0.00 3.68
2487 2658 5.834204 ACTAAGATCTATCCGTACAAGGCTT 59.166 40.000 0.00 0.00 0.00 4.35
2598 2769 4.324267 CAATTTGTATCGGGATAGGACCC 58.676 47.826 0.00 0.00 45.92 4.46
2811 2983 0.395724 TCAGATGGTAGCGCTCCAGA 60.396 55.000 25.57 17.79 38.42 3.86
2819 2991 3.873952 GACTGGAAACATCAGATGGTAGC 59.126 47.826 15.13 4.20 41.51 3.58
2969 3143 1.519408 TTAGCTTTTCGAGTGTGCCC 58.481 50.000 0.00 0.00 0.00 5.36
3249 3423 3.391296 ACAACTAGTGTGAGTGTTGGGAT 59.609 43.478 0.00 0.00 42.61 3.85
3278 3452 6.153340 ACCATAGGTATATGCAAATGGCAATC 59.847 38.462 17.85 0.00 46.05 2.67
3322 3497 4.561500 TCAACCGTTATCTCATTTCCCA 57.438 40.909 0.00 0.00 0.00 4.37
3332 3507 8.612619 ACATTTGTTAGATCATCAACCGTTATC 58.387 33.333 0.00 0.00 0.00 1.75
3338 3513 5.126061 AGCCACATTTGTTAGATCATCAACC 59.874 40.000 0.00 0.00 0.00 3.77
3566 3741 2.665649 TGATTAGGTTGCGATGTCGT 57.334 45.000 4.20 0.00 42.22 4.34
3572 3747 5.592104 TGAGTATCTTGATTAGGTTGCGA 57.408 39.130 0.00 0.00 34.92 5.10
3680 3856 0.540365 ACCCAAGGTGCCATGAACTG 60.540 55.000 0.00 0.00 32.98 3.16
3695 3871 2.111972 ACCTAGTCTCTCAAGGAACCCA 59.888 50.000 0.00 0.00 34.34 4.51


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

AutoCloner maintained by Alex Coulton.