Multiple sequence alignment - TraesCS4D01G036100

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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 TraesCS4D01G036100 chr4D 100.000 2861 0 0 1 2861 16145493 16148353 0.000000e+00 5284.0
1 TraesCS4D01G036100 chr4D 76.735 533 77 23 1674 2185 16142559 16142053 1.320000e-63 254.0
2 TraesCS4D01G036100 chr4D 86.755 151 16 4 652 799 416425087 416425236 6.340000e-37 165.0
3 TraesCS4D01G036100 chr4A 92.204 1706 67 26 749 2430 584389283 584387620 0.000000e+00 2353.0
4 TraesCS4D01G036100 chr4A 84.464 1371 91 48 1521 2861 584355074 584353796 0.000000e+00 1240.0
5 TraesCS4D01G036100 chr4A 90.608 724 32 18 61 754 584401649 584400932 0.000000e+00 928.0
6 TraesCS4D01G036100 chr4A 90.179 448 35 6 2417 2861 584380509 584380068 2.470000e-160 575.0
7 TraesCS4D01G036100 chr4A 82.741 197 26 3 616 805 626166122 626165927 4.900000e-38 169.0
8 TraesCS4D01G036100 chr4A 89.313 131 11 1 1674 1801 584404467 584404597 8.200000e-36 161.0
9 TraesCS4D01G036100 chr4A 97.436 39 1 0 1474 1512 584355106 584355068 1.840000e-07 67.6
10 TraesCS4D01G036100 chr4B 90.045 1768 86 38 801 2522 27901301 27903024 0.000000e+00 2207.0
11 TraesCS4D01G036100 chr4B 81.882 287 37 8 191 470 47448896 47449174 7.970000e-56 228.0
12 TraesCS4D01G036100 chr4B 83.133 166 8 5 2510 2666 27903346 27903500 1.790000e-27 134.0
13 TraesCS4D01G036100 chr1D 85.279 394 36 12 98 470 95790932 95790540 1.240000e-103 387.0
14 TraesCS4D01G036100 chr6B 85.924 341 35 13 139 471 701424911 701425246 4.540000e-93 351.0
15 TraesCS4D01G036100 chr6B 75.703 391 64 18 99 461 44077591 44077978 1.760000e-37 167.0
16 TraesCS4D01G036100 chr5B 84.142 309 35 9 170 470 416996392 416996694 1.300000e-73 287.0
17 TraesCS4D01G036100 chr7B 78.070 342 50 18 157 479 509734173 509733838 2.910000e-45 193.0
18 TraesCS4D01G036100 chr7B 83.516 182 24 5 281 456 466667233 466667414 6.340000e-37 165.0
19 TraesCS4D01G036100 chr5D 83.838 198 23 4 615 803 443898122 443898319 2.260000e-41 180.0
20 TraesCS4D01G036100 chr2A 82.301 226 22 9 97 309 71369535 71369315 2.260000e-41 180.0
21 TraesCS4D01G036100 chr2A 77.852 298 52 13 170 463 19078158 19077871 3.790000e-39 172.0
22 TraesCS4D01G036100 chr2D 87.662 154 17 2 652 804 22200825 22200977 8.150000e-41 178.0
23 TraesCS4D01G036100 chr2D 87.075 147 17 1 652 798 385383882 385384026 6.340000e-37 165.0
24 TraesCS4D01G036100 chr3D 84.118 170 25 2 628 795 223203936 223203767 2.280000e-36 163.0
25 TraesCS4D01G036100 chr7A 81.683 202 28 8 617 810 654201218 654201018 2.950000e-35 159.0
26 TraesCS4D01G036100 chr3A 83.333 180 23 4 622 795 185592856 185593034 2.950000e-35 159.0


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 TraesCS4D01G036100 chr4D 16145493 16148353 2860 False 5284.0 5284 100.000 1 2861 1 chr4D.!!$F1 2860
1 TraesCS4D01G036100 chr4D 16142053 16142559 506 True 254.0 254 76.735 1674 2185 1 chr4D.!!$R1 511
2 TraesCS4D01G036100 chr4A 584387620 584389283 1663 True 2353.0 2353 92.204 749 2430 1 chr4A.!!$R2 1681
3 TraesCS4D01G036100 chr4A 584400932 584401649 717 True 928.0 928 90.608 61 754 1 chr4A.!!$R3 693
4 TraesCS4D01G036100 chr4A 584353796 584355106 1310 True 653.8 1240 90.950 1474 2861 2 chr4A.!!$R5 1387
5 TraesCS4D01G036100 chr4B 27901301 27903500 2199 False 1170.5 2207 86.589 801 2666 2 chr4B.!!$F2 1865

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
901 939 0.106918 CCATTTTAGGCCCTGCGGTA 60.107 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2674 3127 0.250166 CCATGGAGCAGATGATCGCA 60.25 55.0 5.56 0.0 0.0 5.1 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
31 32 5.557866 TCTAATACTATAGAGACAGCGGCA 58.442 41.667 6.78 0.00 0.00 5.69
32 33 4.506886 AATACTATAGAGACAGCGGCAC 57.493 45.455 6.78 0.00 0.00 5.01
33 34 2.060050 ACTATAGAGACAGCGGCACT 57.940 50.000 6.78 0.00 0.00 4.40
34 35 2.379972 ACTATAGAGACAGCGGCACTT 58.620 47.619 6.78 0.00 0.00 3.16
35 36 2.359531 ACTATAGAGACAGCGGCACTTC 59.640 50.000 6.78 0.00 0.00 3.01
36 37 1.479709 ATAGAGACAGCGGCACTTCT 58.520 50.000 1.45 0.00 0.00 2.85
37 38 0.528017 TAGAGACAGCGGCACTTCTG 59.472 55.000 1.45 0.00 36.45 3.02
38 39 1.739562 GAGACAGCGGCACTTCTGG 60.740 63.158 1.45 0.00 34.76 3.86
39 40 2.159819 GAGACAGCGGCACTTCTGGA 62.160 60.000 1.45 0.00 34.76 3.86
40 41 1.078848 GACAGCGGCACTTCTGGAT 60.079 57.895 1.45 0.00 34.76 3.41
41 42 1.078848 ACAGCGGCACTTCTGGATC 60.079 57.895 1.45 0.00 34.76 3.36
42 43 1.220206 CAGCGGCACTTCTGGATCT 59.780 57.895 1.45 0.00 0.00 2.75
43 44 0.809241 CAGCGGCACTTCTGGATCTC 60.809 60.000 1.45 0.00 0.00 2.75
44 45 1.880340 GCGGCACTTCTGGATCTCG 60.880 63.158 0.00 0.00 0.00 4.04
45 46 1.513158 CGGCACTTCTGGATCTCGT 59.487 57.895 0.00 0.00 0.00 4.18
46 47 0.738975 CGGCACTTCTGGATCTCGTA 59.261 55.000 0.00 0.00 0.00 3.43
47 48 1.134367 CGGCACTTCTGGATCTCGTAA 59.866 52.381 0.00 0.00 0.00 3.18
48 49 2.416836 CGGCACTTCTGGATCTCGTAAA 60.417 50.000 0.00 0.00 0.00 2.01
49 50 3.596214 GGCACTTCTGGATCTCGTAAAA 58.404 45.455 0.00 0.00 0.00 1.52
50 51 4.192317 GGCACTTCTGGATCTCGTAAAAT 58.808 43.478 0.00 0.00 0.00 1.82
51 52 4.636206 GGCACTTCTGGATCTCGTAAAATT 59.364 41.667 0.00 0.00 0.00 1.82
52 53 5.815740 GGCACTTCTGGATCTCGTAAAATTA 59.184 40.000 0.00 0.00 0.00 1.40
53 54 6.315393 GGCACTTCTGGATCTCGTAAAATTAA 59.685 38.462 0.00 0.00 0.00 1.40
54 55 7.402640 GCACTTCTGGATCTCGTAAAATTAAG 58.597 38.462 0.00 0.00 0.00 1.85
55 56 7.466050 GCACTTCTGGATCTCGTAAAATTAAGG 60.466 40.741 0.00 0.00 0.00 2.69
56 57 6.539103 ACTTCTGGATCTCGTAAAATTAAGGC 59.461 38.462 0.00 0.00 0.00 4.35
57 58 5.365619 TCTGGATCTCGTAAAATTAAGGCC 58.634 41.667 0.00 0.00 0.00 5.19
58 59 4.457466 TGGATCTCGTAAAATTAAGGCCC 58.543 43.478 0.00 0.00 0.00 5.80
59 60 4.080243 TGGATCTCGTAAAATTAAGGCCCA 60.080 41.667 0.00 0.00 0.00 5.36
75 76 3.785887 AGGCCCATATCTAACTTGGTTCA 59.214 43.478 0.00 0.00 0.00 3.18
78 79 4.718961 CCCATATCTAACTTGGTTCAGGG 58.281 47.826 0.00 0.00 0.00 4.45
116 117 8.062065 AGTTTTGAAAGTGTTGTTCTAATCCA 57.938 30.769 0.00 0.00 0.00 3.41
211 215 7.444792 TGACAAATTTTCCATAGCTTGCAAAAT 59.555 29.630 0.00 0.00 0.00 1.82
235 239 3.370672 TCATCGTGAAATGACATTCGTGG 59.629 43.478 0.05 0.00 32.58 4.94
501 507 3.623060 CGGTGTCTTATGGATCTTGTTGG 59.377 47.826 0.00 0.00 0.00 3.77
515 521 1.262417 TGTTGGTGAGCACTCCGATA 58.738 50.000 0.16 0.00 32.93 2.92
527 533 7.387948 GTGAGCACTCCGATACCATAAATAAAT 59.612 37.037 0.00 0.00 0.00 1.40
529 535 9.431887 GAGCACTCCGATACCATAAATAAATAA 57.568 33.333 0.00 0.00 0.00 1.40
583 614 9.424659 GCAAATAACAGAAACAAAACAGAAATG 57.575 29.630 0.00 0.00 0.00 2.32
589 620 9.883142 AACAGAAACAAAACAGAAATGGATTTA 57.117 25.926 0.00 0.00 0.00 1.40
693 724 8.641541 ACTTCATCAAGCCTAAAAAGAAAATGA 58.358 29.630 0.00 0.00 32.09 2.57
694 725 9.480053 CTTCATCAAGCCTAAAAAGAAAATGAA 57.520 29.630 0.00 0.00 0.00 2.57
695 726 9.480053 TTCATCAAGCCTAAAAAGAAAATGAAG 57.520 29.630 0.00 0.00 0.00 3.02
696 727 8.859090 TCATCAAGCCTAAAAAGAAAATGAAGA 58.141 29.630 0.00 0.00 0.00 2.87
728 759 1.934589 TATCCACACAAATCTCCGCG 58.065 50.000 0.00 0.00 0.00 6.46
734 765 1.001633 ACACAAATCTCCGCGTAAGGT 59.998 47.619 4.92 0.00 38.28 3.50
901 939 0.106918 CCATTTTAGGCCCTGCGGTA 60.107 55.000 0.00 0.00 0.00 4.02
1830 1872 3.579586 AGACCAACATCAACAATGGCAAT 59.420 39.130 0.00 0.00 39.90 3.56
1831 1873 3.666274 ACCAACATCAACAATGGCAATG 58.334 40.909 0.00 0.00 39.90 2.82
1832 1874 3.004171 CCAACATCAACAATGGCAATGG 58.996 45.455 7.57 0.00 39.90 3.16
1863 1905 0.613777 GGGGGAAATCAGAGTGACGT 59.386 55.000 0.00 0.00 0.00 4.34
1919 1986 1.001181 CCAGGCCTGTTTGATTTGTGG 59.999 52.381 30.63 8.47 0.00 4.17
1997 2068 1.072806 TCAAGATGTTCAGGCAGCAGT 59.927 47.619 0.00 0.00 0.00 4.40
2004 2075 0.674581 TTCAGGCAGCAGTCGAATGG 60.675 55.000 15.48 0.00 0.00 3.16
2036 2111 6.506500 TCTTTGATTGATTCCTCTGCTTTC 57.493 37.500 0.00 0.00 0.00 2.62
2037 2112 5.416952 TCTTTGATTGATTCCTCTGCTTTCC 59.583 40.000 0.00 0.00 0.00 3.13
2038 2113 4.581309 TGATTGATTCCTCTGCTTTCCT 57.419 40.909 0.00 0.00 0.00 3.36
2039 2114 4.927049 TGATTGATTCCTCTGCTTTCCTT 58.073 39.130 0.00 0.00 0.00 3.36
2040 2115 4.946157 TGATTGATTCCTCTGCTTTCCTTC 59.054 41.667 0.00 0.00 0.00 3.46
2041 2116 3.356529 TGATTCCTCTGCTTTCCTTCC 57.643 47.619 0.00 0.00 0.00 3.46
2042 2117 2.284190 GATTCCTCTGCTTTCCTTCCG 58.716 52.381 0.00 0.00 0.00 4.30
2043 2118 1.056660 TTCCTCTGCTTTCCTTCCGT 58.943 50.000 0.00 0.00 0.00 4.69
2044 2119 0.321671 TCCTCTGCTTTCCTTCCGTG 59.678 55.000 0.00 0.00 0.00 4.94
2045 2120 0.321671 CCTCTGCTTTCCTTCCGTGA 59.678 55.000 0.00 0.00 0.00 4.35
2046 2121 1.270839 CCTCTGCTTTCCTTCCGTGAA 60.271 52.381 0.00 0.00 0.00 3.18
2047 2122 2.494059 CTCTGCTTTCCTTCCGTGAAA 58.506 47.619 0.00 0.00 0.00 2.69
2048 2123 2.878406 CTCTGCTTTCCTTCCGTGAAAA 59.122 45.455 0.00 0.00 31.77 2.29
2049 2124 3.283751 TCTGCTTTCCTTCCGTGAAAAA 58.716 40.909 0.00 0.00 31.77 1.94
2089 2181 2.816087 TCTTTGCTTCAGTCTGAATGCC 59.184 45.455 23.00 13.83 35.59 4.40
2130 2222 4.021368 GGCAGTAGGTTCTGTCAAGACTTA 60.021 45.833 1.53 0.00 39.52 2.24
2245 2348 2.981859 ACCAAACCGAGCCTACATAG 57.018 50.000 0.00 0.00 0.00 2.23
2488 2598 1.545582 CATGTCCAAATGGTTTCGCCT 59.454 47.619 0.00 0.00 38.35 5.52
2540 2985 3.060602 GCTAGCTGTTCAAGACGTTCTT 58.939 45.455 7.70 0.00 37.14 2.52
2555 3000 2.159476 CGTTCTTTGCACATCCTCATGG 60.159 50.000 0.00 0.00 33.82 3.66
2556 3001 1.466856 TCTTTGCACATCCTCATGGC 58.533 50.000 0.00 0.00 33.82 4.40
2557 3002 0.458669 CTTTGCACATCCTCATGGCC 59.541 55.000 0.00 0.00 33.82 5.36
2558 3003 0.040058 TTTGCACATCCTCATGGCCT 59.960 50.000 3.32 0.00 33.82 5.19
2559 3004 0.394762 TTGCACATCCTCATGGCCTC 60.395 55.000 3.32 0.00 33.82 4.70
2560 3005 1.225426 GCACATCCTCATGGCCTCA 59.775 57.895 3.32 0.00 33.82 3.86
2561 3006 0.178998 GCACATCCTCATGGCCTCAT 60.179 55.000 3.32 0.00 33.82 2.90
2606 3051 7.552687 CAGGAGCACCAACACTTTATTATCTAA 59.447 37.037 2.07 0.00 38.94 2.10
2613 3058 9.367444 ACCAACACTTTATTATCTAAGAGAACG 57.633 33.333 0.00 0.00 0.00 3.95
2616 3061 9.583765 AACACTTTATTATCTAAGAGAACGACC 57.416 33.333 0.00 0.00 0.00 4.79
2626 3079 3.372660 AGAGAACGACCAAACTCTCAC 57.627 47.619 0.00 0.00 37.39 3.51
2642 3095 3.871485 TCTCACGGACTCTAGTTCCTAC 58.129 50.000 10.31 0.00 0.00 3.18
2643 3096 3.518705 TCTCACGGACTCTAGTTCCTACT 59.481 47.826 10.31 0.00 38.44 2.57
2644 3097 4.713814 TCTCACGGACTCTAGTTCCTACTA 59.286 45.833 10.31 0.00 35.78 1.82
2654 3107 0.940047 GTTCCTACTATGAGCGCCGC 60.940 60.000 2.29 0.00 0.00 6.53
2659 3112 1.792118 TACTATGAGCGCCGCGTGAT 61.792 55.000 15.34 6.59 0.00 3.06
2667 3120 2.802667 CGCCGCGTGATTCTCTTGG 61.803 63.158 4.92 0.00 0.00 3.61
2669 3122 2.464459 CCGCGTGATTCTCTTGGCC 61.464 63.158 4.92 0.00 0.00 5.36
2670 3123 1.741401 CGCGTGATTCTCTTGGCCA 60.741 57.895 0.00 0.00 0.00 5.36
2672 3125 1.372087 GCGTGATTCTCTTGGCCAGG 61.372 60.000 8.96 8.96 0.00 4.45
2674 3127 1.134280 CGTGATTCTCTTGGCCAGGAT 60.134 52.381 19.14 3.17 0.00 3.24
2675 3128 2.295885 GTGATTCTCTTGGCCAGGATG 58.704 52.381 19.14 12.39 0.00 3.51
2676 3129 1.316651 GATTCTCTTGGCCAGGATGC 58.683 55.000 19.14 4.46 31.97 3.91
2677 3130 0.465097 ATTCTCTTGGCCAGGATGCG 60.465 55.000 19.14 7.15 31.97 4.73
2678 3131 1.552799 TTCTCTTGGCCAGGATGCGA 61.553 55.000 19.14 9.62 31.97 5.10
2679 3132 1.147824 CTCTTGGCCAGGATGCGAT 59.852 57.895 19.14 0.00 31.97 4.58
2680 3133 0.883814 CTCTTGGCCAGGATGCGATC 60.884 60.000 19.14 0.00 31.97 3.69
2681 3134 1.153107 CTTGGCCAGGATGCGATCA 60.153 57.895 9.80 0.00 31.97 2.92
2682 3135 0.536687 CTTGGCCAGGATGCGATCAT 60.537 55.000 9.80 0.00 35.17 2.45
2683 3136 0.535780 TTGGCCAGGATGCGATCATC 60.536 55.000 5.11 0.00 46.46 2.92
2684 3137 1.374190 GGCCAGGATGCGATCATCT 59.626 57.895 0.00 0.00 46.41 2.90
2685 3138 0.954449 GGCCAGGATGCGATCATCTG 60.954 60.000 0.00 0.00 46.41 2.90
2686 3139 1.575576 GCCAGGATGCGATCATCTGC 61.576 60.000 0.00 0.00 46.41 4.26
2687 3140 0.035036 CCAGGATGCGATCATCTGCT 59.965 55.000 5.41 0.00 46.41 4.24
2688 3141 1.430479 CAGGATGCGATCATCTGCTC 58.570 55.000 5.41 0.17 46.41 4.26
2689 3142 0.321021 AGGATGCGATCATCTGCTCC 59.679 55.000 5.41 7.18 46.41 4.70
2690 3143 0.034476 GGATGCGATCATCTGCTCCA 59.966 55.000 5.41 0.00 46.41 3.86
2691 3144 1.338864 GGATGCGATCATCTGCTCCAT 60.339 52.381 5.41 0.00 46.41 3.41
2692 3145 1.732809 GATGCGATCATCTGCTCCATG 59.267 52.381 0.00 0.00 44.38 3.66
2709 3162 5.414454 GCTCCATGGTTGTTTGACATACTTA 59.586 40.000 12.58 0.00 0.00 2.24
2714 3167 7.822334 CCATGGTTGTTTGACATACTTAGTAGA 59.178 37.037 2.57 0.00 0.00 2.59
2717 3170 7.870954 TGGTTGTTTGACATACTTAGTAGACAG 59.129 37.037 0.00 0.00 0.00 3.51
2721 3174 8.297426 TGTTTGACATACTTAGTAGACAGTCAG 58.703 37.037 2.66 0.00 36.31 3.51
2724 3177 4.335874 ACATACTTAGTAGACAGTCAGCGG 59.664 45.833 2.66 0.00 0.00 5.52
2725 3178 2.792878 ACTTAGTAGACAGTCAGCGGT 58.207 47.619 2.66 0.00 0.00 5.68
2726 3179 3.155501 ACTTAGTAGACAGTCAGCGGTT 58.844 45.455 2.66 0.00 0.00 4.44
2727 3180 3.190953 ACTTAGTAGACAGTCAGCGGTTC 59.809 47.826 2.66 0.00 0.00 3.62
2728 3181 0.889306 AGTAGACAGTCAGCGGTTCC 59.111 55.000 2.66 0.00 0.00 3.62
2729 3182 0.108756 GTAGACAGTCAGCGGTTCCC 60.109 60.000 2.66 0.00 0.00 3.97
2730 3183 0.541063 TAGACAGTCAGCGGTTCCCA 60.541 55.000 2.66 0.00 0.00 4.37
2731 3184 1.668151 GACAGTCAGCGGTTCCCAC 60.668 63.158 0.00 0.00 0.00 4.61
2732 3185 2.377628 GACAGTCAGCGGTTCCCACA 62.378 60.000 0.00 0.00 0.00 4.17
2733 3186 1.003355 CAGTCAGCGGTTCCCACAT 60.003 57.895 0.00 0.00 0.00 3.21
2734 3187 1.003355 AGTCAGCGGTTCCCACATG 60.003 57.895 0.00 0.00 0.00 3.21
2735 3188 2.040544 GTCAGCGGTTCCCACATGG 61.041 63.158 0.00 0.00 0.00 3.66
2736 3189 2.034066 CAGCGGTTCCCACATGGT 59.966 61.111 0.00 0.00 34.77 3.55
2737 3190 1.603455 CAGCGGTTCCCACATGGTT 60.603 57.895 0.00 0.00 34.77 3.67
2743 3196 2.024414 GGTTCCCACATGGTTCTATGC 58.976 52.381 0.00 0.00 34.77 3.14
2770 3223 2.277084 GTGTCACACGATCCCCATAAC 58.723 52.381 0.00 0.00 0.00 1.89
2839 3292 4.638421 CGCCCTGATATCTTTTGTTACCAA 59.362 41.667 3.98 0.00 0.00 3.67
2850 3303 7.324354 TCTTTTGTTACCAAGACAACTAACC 57.676 36.000 0.00 0.00 36.79 2.85
2851 3304 6.885376 TCTTTTGTTACCAAGACAACTAACCA 59.115 34.615 0.00 0.00 36.79 3.67
2852 3305 6.439675 TTTGTTACCAAGACAACTAACCAC 57.560 37.500 0.00 0.00 36.79 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.644206 TGCCGCTGTCTCTATAGTATTAGAG 59.356 44.000 0.00 2.72 44.37 2.43
8 9 5.411977 GTGCCGCTGTCTCTATAGTATTAGA 59.588 44.000 0.00 0.00 0.00 2.10
9 10 5.413213 AGTGCCGCTGTCTCTATAGTATTAG 59.587 44.000 0.00 0.00 0.00 1.73
10 11 5.314529 AGTGCCGCTGTCTCTATAGTATTA 58.685 41.667 0.00 0.00 0.00 0.98
11 12 4.145807 AGTGCCGCTGTCTCTATAGTATT 58.854 43.478 0.00 0.00 0.00 1.89
12 13 3.757270 AGTGCCGCTGTCTCTATAGTAT 58.243 45.455 0.00 0.00 0.00 2.12
13 14 3.210232 AGTGCCGCTGTCTCTATAGTA 57.790 47.619 0.00 0.00 0.00 1.82
14 15 2.060050 AGTGCCGCTGTCTCTATAGT 57.940 50.000 0.00 0.00 0.00 2.12
15 16 2.621055 AGAAGTGCCGCTGTCTCTATAG 59.379 50.000 0.00 0.00 0.00 1.31
16 17 2.359214 CAGAAGTGCCGCTGTCTCTATA 59.641 50.000 0.00 0.00 0.00 1.31
17 18 1.135915 CAGAAGTGCCGCTGTCTCTAT 59.864 52.381 0.00 0.00 0.00 1.98
18 19 0.528017 CAGAAGTGCCGCTGTCTCTA 59.472 55.000 0.00 0.00 0.00 2.43
19 20 1.291588 CAGAAGTGCCGCTGTCTCT 59.708 57.895 0.00 0.00 0.00 3.10
20 21 1.739562 CCAGAAGTGCCGCTGTCTC 60.740 63.158 0.00 0.00 0.00 3.36
21 22 1.548357 ATCCAGAAGTGCCGCTGTCT 61.548 55.000 0.00 0.00 0.00 3.41
22 23 1.078848 ATCCAGAAGTGCCGCTGTC 60.079 57.895 0.00 0.00 0.00 3.51
23 24 1.078848 GATCCAGAAGTGCCGCTGT 60.079 57.895 0.00 0.00 0.00 4.40
24 25 0.809241 GAGATCCAGAAGTGCCGCTG 60.809 60.000 0.00 0.00 0.00 5.18
25 26 1.519719 GAGATCCAGAAGTGCCGCT 59.480 57.895 0.00 0.00 0.00 5.52
26 27 1.880340 CGAGATCCAGAAGTGCCGC 60.880 63.158 0.00 0.00 0.00 6.53
27 28 0.738975 TACGAGATCCAGAAGTGCCG 59.261 55.000 0.00 0.00 0.00 5.69
28 29 2.961526 TTACGAGATCCAGAAGTGCC 57.038 50.000 0.00 0.00 0.00 5.01
29 30 5.803020 AATTTTACGAGATCCAGAAGTGC 57.197 39.130 0.00 0.00 0.00 4.40
30 31 7.466050 GCCTTAATTTTACGAGATCCAGAAGTG 60.466 40.741 0.00 0.00 0.00 3.16
31 32 6.539103 GCCTTAATTTTACGAGATCCAGAAGT 59.461 38.462 0.00 0.00 0.00 3.01
32 33 6.017852 GGCCTTAATTTTACGAGATCCAGAAG 60.018 42.308 0.00 0.00 0.00 2.85
33 34 5.820947 GGCCTTAATTTTACGAGATCCAGAA 59.179 40.000 0.00 0.00 0.00 3.02
34 35 5.365619 GGCCTTAATTTTACGAGATCCAGA 58.634 41.667 0.00 0.00 0.00 3.86
35 36 4.515567 GGGCCTTAATTTTACGAGATCCAG 59.484 45.833 0.84 0.00 0.00 3.86
36 37 4.080243 TGGGCCTTAATTTTACGAGATCCA 60.080 41.667 4.53 0.00 0.00 3.41
37 38 4.457466 TGGGCCTTAATTTTACGAGATCC 58.543 43.478 4.53 0.00 0.00 3.36
38 39 7.824779 AGATATGGGCCTTAATTTTACGAGATC 59.175 37.037 4.53 0.00 0.00 2.75
39 40 7.690256 AGATATGGGCCTTAATTTTACGAGAT 58.310 34.615 4.53 0.00 0.00 2.75
40 41 7.074653 AGATATGGGCCTTAATTTTACGAGA 57.925 36.000 4.53 0.00 0.00 4.04
41 42 8.718734 GTTAGATATGGGCCTTAATTTTACGAG 58.281 37.037 4.53 0.00 0.00 4.18
42 43 8.434392 AGTTAGATATGGGCCTTAATTTTACGA 58.566 33.333 4.53 0.00 0.00 3.43
43 44 8.617290 AGTTAGATATGGGCCTTAATTTTACG 57.383 34.615 4.53 0.00 0.00 3.18
45 46 9.362151 CCAAGTTAGATATGGGCCTTAATTTTA 57.638 33.333 4.53 0.00 0.00 1.52
46 47 7.844269 ACCAAGTTAGATATGGGCCTTAATTTT 59.156 33.333 4.53 0.00 38.58 1.82
47 48 7.362234 ACCAAGTTAGATATGGGCCTTAATTT 58.638 34.615 4.53 0.00 38.58 1.82
48 49 6.922540 ACCAAGTTAGATATGGGCCTTAATT 58.077 36.000 4.53 0.00 38.58 1.40
49 50 6.530601 ACCAAGTTAGATATGGGCCTTAAT 57.469 37.500 4.53 0.00 38.58 1.40
50 51 5.987019 ACCAAGTTAGATATGGGCCTTAA 57.013 39.130 4.53 0.00 38.58 1.85
51 52 5.430417 TGAACCAAGTTAGATATGGGCCTTA 59.570 40.000 4.53 2.64 38.58 2.69
52 53 4.229582 TGAACCAAGTTAGATATGGGCCTT 59.770 41.667 4.53 0.00 38.58 4.35
53 54 3.785887 TGAACCAAGTTAGATATGGGCCT 59.214 43.478 4.53 0.00 38.58 5.19
54 55 4.137543 CTGAACCAAGTTAGATATGGGCC 58.862 47.826 0.00 0.00 38.58 5.80
55 56 4.137543 CCTGAACCAAGTTAGATATGGGC 58.862 47.826 0.00 0.00 38.58 5.36
56 57 4.412199 TCCCTGAACCAAGTTAGATATGGG 59.588 45.833 0.00 0.00 38.58 4.00
57 58 5.366768 TCTCCCTGAACCAAGTTAGATATGG 59.633 44.000 0.00 0.00 40.16 2.74
58 59 6.485830 TCTCCCTGAACCAAGTTAGATATG 57.514 41.667 0.00 0.00 0.00 1.78
59 60 6.408662 GCTTCTCCCTGAACCAAGTTAGATAT 60.409 42.308 0.00 0.00 0.00 1.63
75 76 5.880901 TCAAAACTTAATGAGCTTCTCCCT 58.119 37.500 0.00 0.00 0.00 4.20
78 79 8.131731 ACACTTTCAAAACTTAATGAGCTTCTC 58.868 33.333 0.00 0.00 0.00 2.87
163 164 9.734620 TGTCAATGTTTCATAGAAAAACTTCAG 57.265 29.630 0.00 0.00 37.48 3.02
180 183 7.095102 GCAAGCTATGGAAAATTTGTCAATGTT 60.095 33.333 0.00 0.00 0.00 2.71
327 332 8.721478 GCTTGTAAAATATCATCACCATACGAT 58.279 33.333 0.00 0.00 0.00 3.73
501 507 3.728076 TTATGGTATCGGAGTGCTCAC 57.272 47.619 1.41 0.00 0.00 3.51
569 575 9.065798 CCCAAATAAATCCATTTCTGTTTTGTT 57.934 29.630 0.00 0.00 0.00 2.83
571 577 7.882271 TCCCCAAATAAATCCATTTCTGTTTTG 59.118 33.333 0.00 0.00 0.00 2.44
572 578 7.983363 TCCCCAAATAAATCCATTTCTGTTTT 58.017 30.769 0.00 0.00 0.00 2.43
576 582 7.422465 TCTTCCCCAAATAAATCCATTTCTG 57.578 36.000 0.00 0.00 0.00 3.02
615 646 3.332485 TGCCCTAGACACACCCTATTTTT 59.668 43.478 0.00 0.00 0.00 1.94
616 647 2.916934 TGCCCTAGACACACCCTATTTT 59.083 45.455 0.00 0.00 0.00 1.82
620 651 0.115547 TGTGCCCTAGACACACCCTA 59.884 55.000 12.81 0.00 42.88 3.53
709 740 1.206132 ACGCGGAGATTTGTGTGGATA 59.794 47.619 12.47 0.00 0.00 2.59
710 741 0.036388 ACGCGGAGATTTGTGTGGAT 60.036 50.000 12.47 0.00 0.00 3.41
711 742 0.604073 TACGCGGAGATTTGTGTGGA 59.396 50.000 12.47 0.00 0.00 4.02
712 743 1.393539 CTTACGCGGAGATTTGTGTGG 59.606 52.381 12.47 0.00 0.00 4.17
715 746 1.659098 GACCTTACGCGGAGATTTGTG 59.341 52.381 12.47 0.00 0.00 3.33
716 747 1.274167 TGACCTTACGCGGAGATTTGT 59.726 47.619 12.47 1.04 0.00 2.83
717 748 2.004583 TGACCTTACGCGGAGATTTG 57.995 50.000 12.47 0.00 0.00 2.32
718 749 2.754946 TTGACCTTACGCGGAGATTT 57.245 45.000 12.47 0.00 0.00 2.17
728 759 8.135382 TCTAAGGCCTATATCATTGACCTTAC 57.865 38.462 5.16 0.00 37.27 2.34
734 765 5.664457 CGCATCTAAGGCCTATATCATTGA 58.336 41.667 5.16 0.00 0.00 2.57
821 853 2.044946 GATGGGCCGCCTTGACTT 60.045 61.111 9.86 0.00 0.00 3.01
901 939 6.352137 GGCAAAATGATAAGAAATTCCCACCT 60.352 38.462 0.00 0.00 0.00 4.00
956 995 3.864686 CGCCGGCGAATTGACCTG 61.865 66.667 44.86 10.04 42.83 4.00
1722 1764 3.432759 GTTGAAGACGGCGTTGAAC 57.567 52.632 16.19 6.10 0.00 3.18
1830 1872 2.687932 CCCCCATTGCCATTGCCA 60.688 61.111 0.00 0.00 36.33 4.92
1863 1905 8.662255 TGTAATCTAAAAAGAAGTCCCCTTGTA 58.338 33.333 0.00 0.00 0.00 2.41
1919 1986 1.275856 TGGAAGGCCAATGCATTTCAC 59.724 47.619 9.83 2.50 41.61 3.18
1989 2060 1.660560 ATTGCCATTCGACTGCTGCC 61.661 55.000 0.00 0.00 0.00 4.85
1997 2068 4.198530 TCAAAGATGCTATTGCCATTCGA 58.801 39.130 0.00 0.00 38.71 3.71
2004 2075 6.746120 AGGAATCAATCAAAGATGCTATTGC 58.254 36.000 0.00 0.00 40.20 3.56
2046 2121 5.998363 AGATTAGGAACTCGCAGAAGTTTTT 59.002 36.000 0.00 0.00 41.75 1.94
2047 2122 5.552178 AGATTAGGAACTCGCAGAAGTTTT 58.448 37.500 0.00 0.00 41.75 2.43
2048 2123 5.153950 AGATTAGGAACTCGCAGAAGTTT 57.846 39.130 0.00 0.00 41.75 2.66
2049 2124 4.810191 AGATTAGGAACTCGCAGAAGTT 57.190 40.909 0.00 0.00 41.75 2.66
2050 2125 4.810191 AAGATTAGGAACTCGCAGAAGT 57.190 40.909 0.00 0.00 41.75 3.01
2064 2149 6.256686 GCATTCAGACTGAAGCAAAGATTAG 58.743 40.000 21.78 4.52 40.05 1.73
2089 2181 2.874086 TGCCATCGCTGAATCTACATTG 59.126 45.455 0.00 0.00 35.36 2.82
2202 2297 8.122952 GGTTCAACTTAGTACACATGAATATGC 58.877 37.037 0.00 0.00 37.85 3.14
2333 2440 7.388437 TCACCGTCATTACCAGTAGTTTTAAT 58.612 34.615 0.00 0.00 0.00 1.40
2334 2441 6.757237 TCACCGTCATTACCAGTAGTTTTAA 58.243 36.000 0.00 0.00 0.00 1.52
2335 2442 6.343716 TCACCGTCATTACCAGTAGTTTTA 57.656 37.500 0.00 0.00 0.00 1.52
2340 2447 3.555956 GCAATCACCGTCATTACCAGTAG 59.444 47.826 0.00 0.00 0.00 2.57
2351 2458 7.012044 ACCTATATTTTGTAAGCAATCACCGTC 59.988 37.037 0.00 0.00 34.18 4.79
2430 2538 9.832445 TGTATTAACTTAAGATTCAGATGGGAC 57.168 33.333 10.09 0.00 0.00 4.46
2488 2598 6.311690 TCGACTTAACAATTGCGATGATTGTA 59.688 34.615 5.05 0.00 44.55 2.41
2540 2985 0.394762 GAGGCCATGAGGATGTGCAA 60.395 55.000 5.01 0.00 36.89 4.08
2555 3000 2.308722 TTCCTGACCCCCATGAGGC 61.309 63.158 0.00 0.00 0.00 4.70
2556 3001 1.609783 GTTCCTGACCCCCATGAGG 59.390 63.158 0.00 0.00 0.00 3.86
2557 3002 1.609783 GGTTCCTGACCCCCATGAG 59.390 63.158 0.00 0.00 43.06 2.90
2558 3003 3.835134 GGTTCCTGACCCCCATGA 58.165 61.111 0.00 0.00 43.06 3.07
2606 3051 2.287668 CGTGAGAGTTTGGTCGTTCTCT 60.288 50.000 0.00 0.00 39.54 3.10
2613 3058 1.614413 AGAGTCCGTGAGAGTTTGGTC 59.386 52.381 0.00 0.00 0.00 4.02
2616 3061 4.477780 GAACTAGAGTCCGTGAGAGTTTG 58.522 47.826 0.00 0.00 0.00 2.93
2626 3079 4.453136 GCTCATAGTAGGAACTAGAGTCCG 59.547 50.000 0.00 0.00 44.14 4.79
2642 3095 1.880601 GAATCACGCGGCGCTCATAG 61.881 60.000 30.54 16.27 0.00 2.23
2643 3096 1.949133 GAATCACGCGGCGCTCATA 60.949 57.895 30.54 12.80 0.00 2.15
2644 3097 3.264897 GAATCACGCGGCGCTCAT 61.265 61.111 30.54 15.36 0.00 2.90
2654 3107 0.250234 TCCTGGCCAAGAGAATCACG 59.750 55.000 7.01 0.00 37.82 4.35
2659 3112 1.078214 CGCATCCTGGCCAAGAGAA 60.078 57.895 10.43 0.00 0.00 2.87
2674 3127 0.250166 CCATGGAGCAGATGATCGCA 60.250 55.000 5.56 0.00 0.00 5.10
2675 3128 0.250209 ACCATGGAGCAGATGATCGC 60.250 55.000 21.47 1.93 0.00 4.58
2676 3129 1.871676 CAACCATGGAGCAGATGATCG 59.128 52.381 21.47 0.00 0.00 3.69
2677 3130 2.928334 ACAACCATGGAGCAGATGATC 58.072 47.619 21.47 0.00 0.00 2.92
2678 3131 3.377253 AACAACCATGGAGCAGATGAT 57.623 42.857 21.47 0.00 0.00 2.45
2679 3132 2.821378 CAAACAACCATGGAGCAGATGA 59.179 45.455 21.47 0.00 0.00 2.92
2680 3133 2.821378 TCAAACAACCATGGAGCAGATG 59.179 45.455 21.47 10.04 0.00 2.90
2681 3134 2.821969 GTCAAACAACCATGGAGCAGAT 59.178 45.455 21.47 0.00 0.00 2.90
2682 3135 2.229792 GTCAAACAACCATGGAGCAGA 58.770 47.619 21.47 5.53 0.00 4.26
2683 3136 1.955778 TGTCAAACAACCATGGAGCAG 59.044 47.619 21.47 7.34 0.00 4.24
2684 3137 2.064434 TGTCAAACAACCATGGAGCA 57.936 45.000 21.47 2.22 0.00 4.26
2685 3138 3.758554 AGTATGTCAAACAACCATGGAGC 59.241 43.478 21.47 0.00 0.00 4.70
2686 3139 5.964958 AAGTATGTCAAACAACCATGGAG 57.035 39.130 21.47 13.13 0.00 3.86
2687 3140 6.539173 ACTAAGTATGTCAAACAACCATGGA 58.461 36.000 21.47 0.00 0.00 3.41
2688 3141 6.817765 ACTAAGTATGTCAAACAACCATGG 57.182 37.500 11.19 11.19 0.00 3.66
2689 3142 8.656849 GTCTACTAAGTATGTCAAACAACCATG 58.343 37.037 0.00 0.00 0.00 3.66
2690 3143 8.372459 TGTCTACTAAGTATGTCAAACAACCAT 58.628 33.333 0.00 0.00 0.00 3.55
2691 3144 7.728148 TGTCTACTAAGTATGTCAAACAACCA 58.272 34.615 0.00 0.00 0.00 3.67
2692 3145 7.871463 ACTGTCTACTAAGTATGTCAAACAACC 59.129 37.037 0.00 0.00 0.00 3.77
2709 3162 0.889306 GGAACCGCTGACTGTCTACT 59.111 55.000 9.51 0.00 0.00 2.57
2724 3177 2.024414 GGCATAGAACCATGTGGGAAC 58.976 52.381 3.77 0.00 41.15 3.62
2725 3178 1.064017 GGGCATAGAACCATGTGGGAA 60.064 52.381 3.77 0.00 41.15 3.97
2726 3179 0.550914 GGGCATAGAACCATGTGGGA 59.449 55.000 3.77 0.00 41.15 4.37
2727 3180 0.552848 AGGGCATAGAACCATGTGGG 59.447 55.000 3.77 0.00 44.81 4.61
2728 3181 2.439507 ACTAGGGCATAGAACCATGTGG 59.560 50.000 13.87 0.00 36.90 4.17
2729 3182 3.118261 ACACTAGGGCATAGAACCATGTG 60.118 47.826 13.87 2.14 37.84 3.21
2730 3183 3.115390 ACACTAGGGCATAGAACCATGT 58.885 45.455 13.87 3.39 35.30 3.21
2731 3184 3.118261 ACACACTAGGGCATAGAACCATG 60.118 47.826 13.87 2.72 35.30 3.66
2732 3185 3.115390 ACACACTAGGGCATAGAACCAT 58.885 45.455 13.87 0.00 35.30 3.55
2733 3186 2.500098 GACACACTAGGGCATAGAACCA 59.500 50.000 13.87 0.00 35.30 3.67
2734 3187 2.500098 TGACACACTAGGGCATAGAACC 59.500 50.000 13.87 0.00 35.30 3.62
2735 3188 3.056107 TGTGACACACTAGGGCATAGAAC 60.056 47.826 13.87 2.33 35.11 3.01
2736 3189 3.056107 GTGTGACACACTAGGGCATAGAA 60.056 47.826 27.73 0.00 45.27 2.10
2737 3190 2.496070 GTGTGACACACTAGGGCATAGA 59.504 50.000 27.73 0.00 45.27 1.98
2743 3196 1.135083 GGATCGTGTGACACACTAGGG 60.135 57.143 30.51 18.12 46.46 3.53
2758 3211 4.564041 CATCTCAAGAGTTATGGGGATCG 58.436 47.826 0.00 0.00 0.00 3.69
2770 3223 3.567164 ACCAGTGTTTTGCATCTCAAGAG 59.433 43.478 0.00 0.00 35.84 2.85


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

AutoCloner maintained by Alex Coulton.