Multiple sequence alignment - TraesCS3D01G157800

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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 TraesCS3D01G157800 chr3D 100.000 3021 0 0 960 3980 126236365 126233345 0.000000e+00 5579.0
1 TraesCS3D01G157800 chr3D 100.000 754 0 0 1 754 126237324 126236571 0.000000e+00 1393.0
2 TraesCS3D01G157800 chr3D 89.041 365 34 4 3331 3689 306088043 306087679 7.850000e-122 448.0
3 TraesCS3D01G157800 chr3D 92.405 79 6 0 1 79 547514328 547514250 3.250000e-21 113.0
4 TraesCS3D01G157800 chr3A 93.182 1584 59 15 1775 3331 136429066 136427505 0.000000e+00 2281.0
5 TraesCS3D01G157800 chr3A 92.642 530 20 11 960 1479 136429828 136429308 0.000000e+00 745.0
6 TraesCS3D01G157800 chr3A 93.162 468 20 2 299 754 136430326 136429859 0.000000e+00 676.0
7 TraesCS3D01G157800 chr3A 92.070 227 8 6 81 304 136430882 136430663 1.070000e-80 311.0
8 TraesCS3D01G157800 chr3A 93.902 164 8 1 1624 1787 136429245 136429084 3.070000e-61 246.0
9 TraesCS3D01G157800 chr3B 95.022 1125 43 6 1830 2942 180451999 180450876 0.000000e+00 1755.0
10 TraesCS3D01G157800 chr3B 96.513 717 19 4 960 1671 180453158 180452443 0.000000e+00 1181.0
11 TraesCS3D01G157800 chr3B 93.896 557 22 3 208 754 180453743 180453189 0.000000e+00 830.0
12 TraesCS3D01G157800 chr3B 92.132 394 17 5 2941 3330 180450850 180450467 9.730000e-151 544.0
13 TraesCS3D01G157800 chr3B 91.692 325 21 4 3352 3671 446159803 446159480 2.820000e-121 446.0
14 TraesCS3D01G157800 chr6D 90.076 655 28 4 3331 3980 427975519 427974897 0.000000e+00 815.0
15 TraesCS3D01G157800 chr7D 91.688 397 24 5 3332 3723 54149164 54149556 3.500000e-150 542.0
16 TraesCS3D01G157800 chr7D 94.737 57 0 1 3701 3754 535516020 535516076 7.090000e-13 86.1
17 TraesCS3D01G157800 chr1A 88.546 454 43 5 3331 3776 394029126 394029578 3.500000e-150 542.0
18 TraesCS3D01G157800 chr7A 90.347 404 34 3 3332 3730 562903639 562904042 3.520000e-145 525.0
19 TraesCS3D01G157800 chr7A 94.545 55 0 1 3701 3752 618240491 618240437 9.170000e-12 82.4
20 TraesCS3D01G157800 chr4B 87.901 405 36 6 3327 3725 636773028 636773425 7.790000e-127 464.0
21 TraesCS3D01G157800 chr4B 93.333 75 5 0 2 76 89045070 89045144 1.170000e-20 111.0
22 TraesCS3D01G157800 chr4B 90.476 84 8 0 1 84 453256989 453257072 1.170000e-20 111.0
23 TraesCS3D01G157800 chr2A 90.087 343 29 3 3334 3671 285679108 285678766 1.310000e-119 440.0
24 TraesCS3D01G157800 chr2A 89.706 340 27 6 3388 3725 125618362 125618695 1.020000e-115 427.0
25 TraesCS3D01G157800 chr5D 96.203 79 3 0 1 79 353645521 353645443 3.230000e-26 130.0
26 TraesCS3D01G157800 chr5B 94.737 76 4 0 4 79 709365634 709365709 6.990000e-23 119.0
27 TraesCS3D01G157800 chr5B 94.595 37 1 1 3932 3967 283006008 283006044 5.560000e-04 56.5
28 TraesCS3D01G157800 chr7B 91.566 83 6 1 1 82 577286242 577286160 3.250000e-21 113.0
29 TraesCS3D01G157800 chr7B 91.566 83 6 1 1 82 577289171 577289089 3.250000e-21 113.0
30 TraesCS3D01G157800 chr7B 91.566 83 6 1 1 82 577292098 577292016 3.250000e-21 113.0
31 TraesCS3D01G157800 chr7B 94.643 56 0 1 3702 3754 577206547 577206602 2.550000e-12 84.2
32 TraesCS3D01G157800 chr1B 91.358 81 7 0 1 81 512454742 512454662 1.170000e-20 111.0
33 TraesCS3D01G157800 chr2B 92.308 65 2 1 3694 3755 78084314 78084250 5.480000e-14 89.8


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 TraesCS3D01G157800 chr3D 126233345 126237324 3979 True 3486.0 5579 100.00000 1 3980 2 chr3D.!!$R3 3979
1 TraesCS3D01G157800 chr3A 136427505 136430882 3377 True 851.8 2281 92.99160 81 3331 5 chr3A.!!$R1 3250
2 TraesCS3D01G157800 chr3B 180450467 180453743 3276 True 1077.5 1755 94.39075 208 3330 4 chr3B.!!$R2 3122
3 TraesCS3D01G157800 chr6D 427974897 427975519 622 True 815.0 815 90.07600 3331 3980 1 chr6D.!!$R1 649

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
21 22 0.174617 AAACACAGGCAACCAAACGG 59.825 50.0 0.0 0.0 37.17 4.44 F
297 306 0.174845 TCGGCAAATACTCCACTCCG 59.825 55.0 0.0 0.0 37.00 4.63 F
1620 1998 0.523519 CTCCGCCTTTGCTTCCTTTC 59.476 55.0 0.0 0.0 34.43 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2125 0.102481 TCCGACGCAAGCCTAATCTC 59.898 55.0 0.0 0.0 45.62 2.75 R
1748 2126 0.535335 TTCCGACGCAAGCCTAATCT 59.465 50.0 0.0 0.0 45.62 2.40 R
3289 4081 0.031721 CGTTCTATACGTGGGGCTCC 59.968 60.0 0.0 0.0 45.14 4.70 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
20 21 2.456010 GTAAACACAGGCAACCAAACG 58.544 47.619 0.00 0.00 37.17 3.60
21 22 0.174617 AAACACAGGCAACCAAACGG 59.825 50.000 0.00 0.00 37.17 4.44
22 23 1.671901 AACACAGGCAACCAAACGGG 61.672 55.000 0.00 0.00 44.81 5.28
36 37 4.231439 CCAAACGGGTAAAATTCTTTCCG 58.769 43.478 0.00 0.00 37.72 4.30
37 38 3.564235 AACGGGTAAAATTCTTTCCGC 57.436 42.857 9.25 0.00 36.06 5.54
38 39 1.465777 ACGGGTAAAATTCTTTCCGCG 59.534 47.619 0.00 0.00 36.06 6.46
39 40 1.792632 CGGGTAAAATTCTTTCCGCGC 60.793 52.381 0.00 0.00 28.65 6.86
40 41 1.530856 GGTAAAATTCTTTCCGCGCG 58.469 50.000 25.67 25.67 0.00 6.86
41 42 1.530856 GTAAAATTCTTTCCGCGCGG 58.469 50.000 42.13 42.13 0.00 6.46
42 43 0.448593 TAAAATTCTTTCCGCGCGGG 59.551 50.000 44.95 30.64 35.59 6.13
43 44 1.520600 AAAATTCTTTCCGCGCGGGT 61.521 50.000 44.95 22.65 37.00 5.28
44 45 1.918868 AAATTCTTTCCGCGCGGGTC 61.919 55.000 44.95 0.00 37.00 4.46
45 46 3.599285 ATTCTTTCCGCGCGGGTCA 62.599 57.895 44.95 28.12 37.00 4.02
46 47 4.735132 TCTTTCCGCGCGGGTCAG 62.735 66.667 44.95 34.76 37.00 3.51
72 73 2.298411 CCATATGCAGGCAACCAAAC 57.702 50.000 0.00 0.00 37.17 2.93
73 74 1.549620 CCATATGCAGGCAACCAAACA 59.450 47.619 0.00 0.00 37.17 2.83
74 75 2.609350 CATATGCAGGCAACCAAACAC 58.391 47.619 0.00 0.00 37.17 3.32
75 76 0.595588 TATGCAGGCAACCAAACACG 59.404 50.000 0.00 0.00 37.17 4.49
76 77 2.658268 GCAGGCAACCAAACACGC 60.658 61.111 0.00 0.00 37.17 5.34
77 78 2.027460 CAGGCAACCAAACACGCC 59.973 61.111 0.00 0.00 45.23 5.68
78 79 3.223589 AGGCAACCAAACACGCCC 61.224 61.111 0.00 0.00 46.08 6.13
79 80 3.532155 GGCAACCAAACACGCCCA 61.532 61.111 0.00 0.00 38.67 5.36
80 81 2.733945 GCAACCAAACACGCCCAT 59.266 55.556 0.00 0.00 0.00 4.00
81 82 1.528292 GGCAACCAAACACGCCCATA 61.528 55.000 0.00 0.00 38.67 2.74
82 83 0.315568 GCAACCAAACACGCCCATAA 59.684 50.000 0.00 0.00 0.00 1.90
83 84 1.067213 GCAACCAAACACGCCCATAAT 60.067 47.619 0.00 0.00 0.00 1.28
84 85 2.605030 CAACCAAACACGCCCATAATG 58.395 47.619 0.00 0.00 0.00 1.90
85 86 1.917872 ACCAAACACGCCCATAATGT 58.082 45.000 0.00 0.00 0.00 2.71
86 87 2.243810 ACCAAACACGCCCATAATGTT 58.756 42.857 0.00 0.00 38.18 2.71
87 88 2.029470 ACCAAACACGCCCATAATGTTG 60.029 45.455 0.00 0.00 36.69 3.33
88 89 1.991965 CAAACACGCCCATAATGTTGC 59.008 47.619 0.00 0.00 36.69 4.17
131 132 0.824759 ACATGAAGTACTCCCTCCGC 59.175 55.000 0.00 0.00 0.00 5.54
166 167 5.508200 TTGTTGTGCCTTTAGTTCGAATT 57.492 34.783 0.00 0.00 0.00 2.17
172 173 5.584649 TGTGCCTTTAGTTCGAATTATGGAG 59.415 40.000 18.01 10.04 0.00 3.86
181 182 2.135933 CGAATTATGGAGCGAAGGGAC 58.864 52.381 0.00 0.00 0.00 4.46
185 186 1.996798 TATGGAGCGAAGGGACTAGG 58.003 55.000 0.00 0.00 38.49 3.02
186 187 0.760945 ATGGAGCGAAGGGACTAGGG 60.761 60.000 0.00 0.00 38.49 3.53
297 306 0.174845 TCGGCAAATACTCCACTCCG 59.825 55.000 0.00 0.00 37.00 4.63
320 677 3.095912 TCCACTACACTAGGCTAGCAA 57.904 47.619 21.26 6.21 0.00 3.91
483 846 4.507916 TCTCCTCCTCCTCCCGCG 62.508 72.222 0.00 0.00 0.00 6.46
628 991 3.433319 TCCGTGCGGATAGAGAGC 58.567 61.111 9.48 0.00 39.76 4.09
1289 1652 4.421515 CCAGGTGAGCCAGCCAGG 62.422 72.222 1.45 1.33 41.84 4.45
1318 1681 5.164225 GGAACGTAAAATGTTTCACGCAATC 60.164 40.000 1.30 0.00 37.92 2.67
1325 1692 2.976840 TTTCACGCAATCAGGCCGC 61.977 57.895 0.00 0.00 0.00 6.53
1535 1913 2.206825 GACGGCGTCACTTTACGTGC 62.207 60.000 33.07 2.98 44.64 5.34
1620 1998 0.523519 CTCCGCCTTTGCTTCCTTTC 59.476 55.000 0.00 0.00 34.43 2.62
1622 2000 1.586541 CGCCTTTGCTTCCTTTCCC 59.413 57.895 0.00 0.00 34.43 3.97
1693 2071 1.953559 TCTGGTCTGTGAAGTTGTGC 58.046 50.000 0.00 0.00 0.00 4.57
1713 2091 5.180304 TGTGCTCGACAATAAATGCTGTAAA 59.820 36.000 0.00 0.00 0.00 2.01
1720 2098 7.490079 TCGACAATAAATGCTGTAAAGTACGAT 59.510 33.333 0.00 0.00 0.00 3.73
1747 2125 3.422876 CACATGTTTCATGTTTGCTCGTG 59.577 43.478 11.89 0.00 0.00 4.35
1748 2126 3.314913 ACATGTTTCATGTTTGCTCGTGA 59.685 39.130 9.21 0.00 0.00 4.35
1966 2709 3.432051 GATGTCCACCTCCGAGCCG 62.432 68.421 0.00 0.00 0.00 5.52
2548 3291 3.119709 CTTGGTGCGCAACAACGGT 62.120 57.895 35.69 0.00 39.66 4.83
2616 3359 1.070577 CGAATGCGATTCCATCCGTTC 60.071 52.381 0.00 0.00 40.82 3.95
2672 3415 1.678598 CCGCGGGGTTGTACATAGGA 61.679 60.000 20.10 0.00 0.00 2.94
2674 3417 1.202604 CGCGGGGTTGTACATAGGATT 60.203 52.381 0.00 0.00 0.00 3.01
2675 3418 2.036217 CGCGGGGTTGTACATAGGATTA 59.964 50.000 0.00 0.00 0.00 1.75
2719 3462 3.809832 GGTCGTGGAGATCATACCATTTG 59.190 47.826 8.98 4.33 38.48 2.32
2934 3695 4.223923 AGAATTCTTGTCTGACGGGAGATT 59.776 41.667 0.88 6.62 0.00 2.40
2935 3696 3.319137 TTCTTGTCTGACGGGAGATTG 57.681 47.619 2.98 0.00 0.00 2.67
2942 3703 2.231478 TCTGACGGGAGATTGTGTTCTC 59.769 50.000 0.00 0.00 41.21 2.87
2944 3705 2.029020 TGACGGGAGATTGTGTTCTCAG 60.029 50.000 4.07 0.56 43.28 3.35
2945 3706 1.338200 ACGGGAGATTGTGTTCTCAGC 60.338 52.381 4.07 0.00 43.28 4.26
2947 3708 1.003580 GGGAGATTGTGTTCTCAGCCA 59.996 52.381 4.07 0.00 43.28 4.75
2948 3709 2.356535 GGGAGATTGTGTTCTCAGCCAT 60.357 50.000 4.07 0.00 43.28 4.40
2950 3711 2.681848 GAGATTGTGTTCTCAGCCATGG 59.318 50.000 7.63 7.63 41.51 3.66
3013 3802 5.046529 CAGAGTCATGAATTCCCTCGTAAG 58.953 45.833 2.27 0.00 0.00 2.34
3221 4013 1.133513 AGCCAAACAGGTGTGATTCCA 60.134 47.619 0.00 0.00 40.61 3.53
3249 4041 2.715749 TGGGATCACGCTGATTTGAT 57.284 45.000 0.00 0.00 37.20 2.57
3250 4042 2.291365 TGGGATCACGCTGATTTGATG 58.709 47.619 0.00 0.00 37.20 3.07
3261 4053 3.019564 CTGATTTGATGTTGAGGTCCCC 58.980 50.000 0.00 0.00 0.00 4.81
3278 4070 3.130227 CGTCTCCCGGATCCCTTC 58.870 66.667 0.73 0.00 0.00 3.46
3279 4071 2.499827 CGTCTCCCGGATCCCTTCC 61.500 68.421 0.73 0.00 41.59 3.46
3280 4072 1.075151 GTCTCCCGGATCCCTTCCT 60.075 63.158 0.73 0.00 42.99 3.36
3281 4073 0.187851 GTCTCCCGGATCCCTTCCTA 59.812 60.000 0.73 0.00 42.99 2.94
3292 4084 0.189822 CCCTTCCTAGGAGAGGGGAG 59.810 65.000 32.03 19.55 46.70 4.30
3361 4154 0.323957 GTTAGTTTCTCCACCGGCCT 59.676 55.000 0.00 0.00 0.00 5.19
3363 4156 0.543410 TAGTTTCTCCACCGGCCTGA 60.543 55.000 0.00 0.00 0.00 3.86
3405 4201 0.767375 GGAGCAGGGCATGGATAAGA 59.233 55.000 0.00 0.00 0.00 2.10
3432 4229 5.568620 ACAGGGTCAAAAAGTAGATGACT 57.431 39.130 5.27 0.00 42.36 3.41
3452 4249 1.636148 AGTTGATTGGTTGCCTGCAT 58.364 45.000 0.00 0.00 0.00 3.96
3470 4267 2.099098 GCATTAGGGGTTTTGTCATCGG 59.901 50.000 0.00 0.00 0.00 4.18
3475 4272 0.455815 GGGTTTTGTCATCGGGATGC 59.544 55.000 3.77 0.87 38.65 3.91
3485 4282 2.426738 TCATCGGGATGCAATTTTCACC 59.573 45.455 3.77 0.00 38.65 4.02
3490 4287 0.246086 GATGCAATTTTCACCCGGCA 59.754 50.000 0.00 0.00 35.54 5.69
3656 4453 4.803426 GCTCGCCACCTGGACTCG 62.803 72.222 0.00 0.02 37.39 4.18
3739 4536 2.686816 CCGCCCCGTGATGTTGTTC 61.687 63.158 0.00 0.00 0.00 3.18
3741 4538 1.875963 GCCCCGTGATGTTGTTCTG 59.124 57.895 0.00 0.00 0.00 3.02
3745 4542 0.110056 CCGTGATGTTGTTCTGCAGC 60.110 55.000 9.47 0.00 0.00 5.25
3746 4543 0.587768 CGTGATGTTGTTCTGCAGCA 59.412 50.000 9.47 0.33 42.38 4.41
3747 4544 1.399343 CGTGATGTTGTTCTGCAGCAG 60.399 52.381 17.10 17.10 41.51 4.24
3748 4545 0.594602 TGATGTTGTTCTGCAGCAGC 59.405 50.000 18.43 5.26 43.50 5.25
3749 4546 0.109412 GATGTTGTTCTGCAGCAGCC 60.109 55.000 18.43 10.96 41.51 4.85
3750 4547 0.538977 ATGTTGTTCTGCAGCAGCCT 60.539 50.000 18.43 0.00 41.51 4.58
3751 4548 1.285023 GTTGTTCTGCAGCAGCCTG 59.715 57.895 18.43 0.00 41.13 4.85
3752 4549 1.148949 TTGTTCTGCAGCAGCCTGA 59.851 52.632 18.43 0.00 41.77 3.86
3753 4550 0.466007 TTGTTCTGCAGCAGCCTGAA 60.466 50.000 18.43 4.01 41.77 3.02
3754 4551 0.887836 TGTTCTGCAGCAGCCTGAAG 60.888 55.000 18.43 0.00 44.87 3.02
3755 4552 1.970114 TTCTGCAGCAGCCTGAAGC 60.970 57.895 18.43 0.00 43.43 3.86
3756 4553 3.441290 CTGCAGCAGCCTGAAGCC 61.441 66.667 10.14 0.00 45.47 4.35
3761 4558 4.096003 GCAGCCTGAAGCCCCGTA 62.096 66.667 0.00 0.00 45.47 4.02
3762 4559 2.125106 CAGCCTGAAGCCCCGTAC 60.125 66.667 0.00 0.00 45.47 3.67
3763 4560 2.606519 AGCCTGAAGCCCCGTACA 60.607 61.111 0.00 0.00 45.47 2.90
3764 4561 2.436115 GCCTGAAGCCCCGTACAC 60.436 66.667 0.00 0.00 34.35 2.90
3765 4562 2.955881 GCCTGAAGCCCCGTACACT 61.956 63.158 0.00 0.00 34.35 3.55
3766 4563 1.677552 CCTGAAGCCCCGTACACTT 59.322 57.895 0.00 0.00 0.00 3.16
3767 4564 0.391263 CCTGAAGCCCCGTACACTTC 60.391 60.000 7.59 7.59 40.17 3.01
3768 4565 0.320374 CTGAAGCCCCGTACACTTCA 59.680 55.000 13.67 13.67 45.56 3.02
3769 4566 0.320374 TGAAGCCCCGTACACTTCAG 59.680 55.000 11.46 0.00 43.55 3.02
3770 4567 0.606604 GAAGCCCCGTACACTTCAGA 59.393 55.000 9.03 0.00 39.66 3.27
3771 4568 0.608640 AAGCCCCGTACACTTCAGAG 59.391 55.000 0.00 0.00 0.00 3.35
3772 4569 0.542232 AGCCCCGTACACTTCAGAGT 60.542 55.000 0.00 0.00 36.25 3.24
3773 4570 0.320697 GCCCCGTACACTTCAGAGTT 59.679 55.000 0.00 0.00 32.54 3.01
3774 4571 1.672145 GCCCCGTACACTTCAGAGTTC 60.672 57.143 0.00 0.00 32.54 3.01
3775 4572 1.616865 CCCCGTACACTTCAGAGTTCA 59.383 52.381 0.00 0.00 32.54 3.18
3776 4573 2.233922 CCCCGTACACTTCAGAGTTCAT 59.766 50.000 0.00 0.00 32.54 2.57
3843 4640 1.143305 CCGTGCACTTCAGAGTTCAG 58.857 55.000 16.19 0.00 29.60 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.456010 CGTTTGGTTGCCTGTGTTTAC 58.544 47.619 0.00 0.00 0.00 2.01
4 5 2.124693 CCCGTTTGGTTGCCTGTGT 61.125 57.895 0.00 0.00 0.00 3.72
5 6 2.727544 CCCGTTTGGTTGCCTGTG 59.272 61.111 0.00 0.00 0.00 3.66
8 9 9.980084 GAAAGAATTTTACCCGTTTGGTTGCCT 62.980 40.741 0.00 0.00 41.95 4.75
9 10 7.934578 GAAAGAATTTTACCCGTTTGGTTGCC 61.935 42.308 0.00 0.00 41.95 4.52
10 11 5.050634 GAAAGAATTTTACCCGTTTGGTTGC 60.051 40.000 0.00 0.00 41.95 4.17
11 12 5.464057 GGAAAGAATTTTACCCGTTTGGTTG 59.536 40.000 0.00 0.00 41.95 3.77
12 13 5.603596 GGAAAGAATTTTACCCGTTTGGTT 58.396 37.500 0.00 0.00 41.95 3.67
13 14 4.261698 CGGAAAGAATTTTACCCGTTTGGT 60.262 41.667 0.00 0.00 45.53 3.67
14 15 4.231439 CGGAAAGAATTTTACCCGTTTGG 58.769 43.478 0.00 0.00 39.27 3.28
15 16 3.671459 GCGGAAAGAATTTTACCCGTTTG 59.329 43.478 0.00 0.00 39.27 2.93
16 17 3.609879 CGCGGAAAGAATTTTACCCGTTT 60.610 43.478 0.00 0.00 39.27 3.60
17 18 2.095617 CGCGGAAAGAATTTTACCCGTT 60.096 45.455 0.00 0.00 39.27 4.44
18 19 1.465777 CGCGGAAAGAATTTTACCCGT 59.534 47.619 0.00 0.00 39.27 5.28
19 20 1.792632 GCGCGGAAAGAATTTTACCCG 60.793 52.381 8.83 0.00 39.27 5.28
20 21 1.792632 CGCGCGGAAAGAATTTTACCC 60.793 52.381 24.84 0.00 39.27 3.69
21 22 1.530856 CGCGCGGAAAGAATTTTACC 58.469 50.000 24.84 0.00 39.27 2.85
22 23 1.530856 CCGCGCGGAAAGAATTTTAC 58.469 50.000 44.86 0.00 39.27 2.01
23 24 3.980136 CCGCGCGGAAAGAATTTTA 57.020 47.368 44.86 0.00 39.27 1.52
24 25 4.859784 CCGCGCGGAAAGAATTTT 57.140 50.000 44.86 0.00 39.27 1.82
47 48 3.300765 GCCTGCATATGGCCCAGC 61.301 66.667 0.00 0.00 44.32 4.85
53 54 1.549620 TGTTTGGTTGCCTGCATATGG 59.450 47.619 4.56 0.00 0.00 2.74
54 55 2.609350 GTGTTTGGTTGCCTGCATATG 58.391 47.619 0.00 0.00 0.00 1.78
55 56 1.202114 CGTGTTTGGTTGCCTGCATAT 59.798 47.619 0.00 0.00 0.00 1.78
56 57 0.595588 CGTGTTTGGTTGCCTGCATA 59.404 50.000 0.00 0.00 0.00 3.14
57 58 1.363443 CGTGTTTGGTTGCCTGCAT 59.637 52.632 0.00 0.00 0.00 3.96
58 59 2.804167 CGTGTTTGGTTGCCTGCA 59.196 55.556 0.00 0.00 0.00 4.41
59 60 2.658268 GCGTGTTTGGTTGCCTGC 60.658 61.111 0.00 0.00 0.00 4.85
60 61 2.027460 GGCGTGTTTGGTTGCCTG 59.973 61.111 0.00 0.00 44.16 4.85
61 62 3.223589 GGGCGTGTTTGGTTGCCT 61.224 61.111 1.77 0.00 46.72 4.75
62 63 1.528292 TATGGGCGTGTTTGGTTGCC 61.528 55.000 0.00 0.00 46.82 4.52
63 64 0.315568 TTATGGGCGTGTTTGGTTGC 59.684 50.000 0.00 0.00 0.00 4.17
64 65 2.029470 ACATTATGGGCGTGTTTGGTTG 60.029 45.455 0.00 0.00 0.00 3.77
65 66 2.243810 ACATTATGGGCGTGTTTGGTT 58.756 42.857 0.00 0.00 0.00 3.67
66 67 1.917872 ACATTATGGGCGTGTTTGGT 58.082 45.000 0.00 0.00 0.00 3.67
67 68 2.605030 CAACATTATGGGCGTGTTTGG 58.395 47.619 0.00 0.00 34.09 3.28
68 69 1.991965 GCAACATTATGGGCGTGTTTG 59.008 47.619 0.00 0.00 34.09 2.93
69 70 1.892474 AGCAACATTATGGGCGTGTTT 59.108 42.857 0.00 0.00 34.09 2.83
70 71 1.472480 GAGCAACATTATGGGCGTGTT 59.528 47.619 0.00 0.00 36.57 3.32
71 72 1.094785 GAGCAACATTATGGGCGTGT 58.905 50.000 0.00 0.00 0.00 4.49
72 73 1.093972 TGAGCAACATTATGGGCGTG 58.906 50.000 0.00 0.00 0.00 5.34
73 74 1.832883 TTGAGCAACATTATGGGCGT 58.167 45.000 0.00 0.00 0.00 5.68
74 75 3.565482 AGTATTGAGCAACATTATGGGCG 59.435 43.478 0.00 0.00 0.00 6.13
75 76 6.430925 TGATAGTATTGAGCAACATTATGGGC 59.569 38.462 0.00 0.00 0.00 5.36
76 77 7.984422 TGATAGTATTGAGCAACATTATGGG 57.016 36.000 0.00 0.00 0.00 4.00
77 78 8.839343 TGTTGATAGTATTGAGCAACATTATGG 58.161 33.333 9.80 0.00 42.49 2.74
82 83 9.577110 CATTTTGTTGATAGTATTGAGCAACAT 57.423 29.630 13.10 2.54 45.43 2.71
83 84 7.541783 GCATTTTGTTGATAGTATTGAGCAACA 59.458 33.333 9.80 9.80 44.74 3.33
84 85 7.541783 TGCATTTTGTTGATAGTATTGAGCAAC 59.458 33.333 0.00 0.00 39.29 4.17
85 86 7.600960 TGCATTTTGTTGATAGTATTGAGCAA 58.399 30.769 0.00 0.00 0.00 3.91
86 87 7.155655 TGCATTTTGTTGATAGTATTGAGCA 57.844 32.000 0.00 0.00 0.00 4.26
87 88 8.375465 GTTTGCATTTTGTTGATAGTATTGAGC 58.625 33.333 0.00 0.00 0.00 4.26
88 89 9.409312 TGTTTGCATTTTGTTGATAGTATTGAG 57.591 29.630 0.00 0.00 0.00 3.02
153 154 6.292381 CCTTCGCTCCATAATTCGAACTAAAG 60.292 42.308 0.00 0.00 36.24 1.85
166 167 1.480683 CCCTAGTCCCTTCGCTCCATA 60.481 57.143 0.00 0.00 0.00 2.74
172 173 0.611714 TTGTTCCCTAGTCCCTTCGC 59.388 55.000 0.00 0.00 0.00 4.70
181 182 2.519013 AGCCTGCTTTTTGTTCCCTAG 58.481 47.619 0.00 0.00 0.00 3.02
185 186 3.942130 ATGTAGCCTGCTTTTTGTTCC 57.058 42.857 0.00 0.00 0.00 3.62
186 187 5.126396 AGAATGTAGCCTGCTTTTTGTTC 57.874 39.130 0.00 0.00 0.00 3.18
297 306 2.223852 GCTAGCCTAGTGTAGTGGAAGC 60.224 54.545 2.29 0.00 0.00 3.86
320 677 1.734465 GAATACGTTGCTGCTCTGCTT 59.266 47.619 0.00 0.00 0.00 3.91
428 785 2.311841 TGAGGACATGTACTGGGAGAGA 59.688 50.000 17.47 0.00 0.00 3.10
529 892 2.746277 GCGGTGGGTGAAGCGAAT 60.746 61.111 0.00 0.00 43.52 3.34
704 1067 3.438216 TGGACCGGATCGTATATACCA 57.562 47.619 9.46 0.00 0.00 3.25
1289 1652 7.299053 CGTGAAACATTTTACGTTCCTAAAC 57.701 36.000 12.10 0.00 42.75 2.01
1495 1873 6.264292 CCGTCCTATATGATAGCTAGCTCATT 59.736 42.308 23.26 7.55 34.14 2.57
1535 1913 9.959775 GAGAAACAAATGATCTTTTCGTAGTAG 57.040 33.333 3.70 0.00 33.92 2.57
1620 1998 2.514013 GCGACGCAACGATACAGGG 61.514 63.158 16.42 0.00 35.09 4.45
1622 2000 2.608204 CGCGACGCAACGATACAG 59.392 61.111 21.35 0.00 35.09 2.74
1693 2071 7.008901 TCGTACTTTACAGCATTTATTGTCGAG 59.991 37.037 0.00 0.00 0.00 4.04
1713 2091 4.252878 TGAAACATGTGCATCATCGTACT 58.747 39.130 0.00 0.00 34.09 2.73
1720 2098 3.741856 GCAAACATGAAACATGTGCATCA 59.258 39.130 16.29 5.38 31.80 3.07
1747 2125 0.102481 TCCGACGCAAGCCTAATCTC 59.898 55.000 0.00 0.00 45.62 2.75
1748 2126 0.535335 TTCCGACGCAAGCCTAATCT 59.465 50.000 0.00 0.00 45.62 2.40
1824 2265 1.954146 AGCACACGCACTGTTACGG 60.954 57.895 5.16 0.00 42.27 4.02
1825 2266 1.201578 CAGCACACGCACTGTTACG 59.798 57.895 0.00 0.00 42.27 3.18
1826 2267 1.493772 TACAGCACACGCACTGTTAC 58.506 50.000 0.45 0.00 44.59 2.50
1836 2569 5.122239 TGATTCTACTGCAAATACAGCACAC 59.878 40.000 0.00 0.00 41.60 3.82
1966 2709 1.741770 CACGCTTGTGTAGGAGGGC 60.742 63.158 0.00 0.00 38.84 5.19
2106 2849 2.762043 TCCGCATGATGTCCCGGA 60.762 61.111 0.73 8.30 46.50 5.14
2269 3012 2.509336 CCGGACACGAGCATGGTC 60.509 66.667 15.01 15.01 44.60 4.02
2527 3270 0.317770 CGTTGTTGCGCACCAAGAAT 60.318 50.000 21.41 0.00 38.71 2.40
2605 3348 0.676466 ATTGCTGCGAACGGATGGAA 60.676 50.000 0.00 0.00 0.00 3.53
2672 3415 6.579042 CGATTCCCAGTCCCATGGATTATAAT 60.579 42.308 15.22 0.00 43.57 1.28
2674 3417 4.225042 CGATTCCCAGTCCCATGGATTATA 59.775 45.833 15.22 0.00 43.57 0.98
2675 3418 3.009473 CGATTCCCAGTCCCATGGATTAT 59.991 47.826 15.22 0.00 43.57 1.28
2719 3462 0.312102 GCTCTGAAAACCACACCTGC 59.688 55.000 0.00 0.00 0.00 4.85
2865 3626 4.141756 ACCTGGTCATTGACTCATGATCTC 60.142 45.833 16.02 0.00 32.47 2.75
2934 3695 0.994247 ATCCCATGGCTGAGAACACA 59.006 50.000 6.09 0.00 0.00 3.72
2935 3696 1.673168 GATCCCATGGCTGAGAACAC 58.327 55.000 6.09 0.00 0.00 3.32
2950 3711 2.555757 GAGCAAAGCATACATGGGATCC 59.444 50.000 1.92 1.92 0.00 3.36
3191 3982 2.028130 CCTGTTTGGCTGTGGTAAACA 58.972 47.619 0.00 0.00 40.73 2.83
3261 4053 2.499827 GGAAGGGATCCGGGAGACG 61.500 68.421 5.45 0.00 38.79 4.18
3278 4070 2.202899 GGGCTCCCCTCTCCTAGG 59.797 72.222 0.82 0.82 46.09 3.02
3289 4081 0.031721 CGTTCTATACGTGGGGCTCC 59.968 60.000 0.00 0.00 45.14 4.70
3361 4154 4.256920 GCTCATTTTTGCTCTCCTAGTCA 58.743 43.478 0.00 0.00 0.00 3.41
3363 4156 3.009473 TGGCTCATTTTTGCTCTCCTAGT 59.991 43.478 0.00 0.00 0.00 2.57
3370 4163 1.135170 GCTCCTGGCTCATTTTTGCTC 60.135 52.381 0.00 0.00 38.06 4.26
3416 4212 9.219603 CCAATCAACTAGTCATCTACTTTTTGA 57.780 33.333 0.00 0.00 39.86 2.69
3432 4229 2.284754 TGCAGGCAACCAATCAACTA 57.715 45.000 0.00 0.00 37.17 2.24
3452 4249 1.986631 TCCCGATGACAAAACCCCTAA 59.013 47.619 0.00 0.00 0.00 2.69
3460 4257 4.021632 TGAAAATTGCATCCCGATGACAAA 60.022 37.500 8.89 0.53 41.20 2.83
3470 4267 0.460109 GCCGGGTGAAAATTGCATCC 60.460 55.000 2.18 0.00 33.08 3.51
3475 4272 2.075338 CCAAATGCCGGGTGAAAATTG 58.925 47.619 2.18 0.00 0.00 2.32
3485 4282 0.529833 TGTATGCAACCAAATGCCGG 59.470 50.000 0.00 0.00 45.83 6.13
3525 4322 2.428890 TGGTGGGTGTTAAGCTTTGTTG 59.571 45.455 3.20 0.00 0.00 3.33
3739 4536 3.441290 GGCTTCAGGCTGCTGCAG 61.441 66.667 24.80 24.80 41.91 4.41
3745 4542 2.125106 GTACGGGGCTTCAGGCTG 60.125 66.667 8.58 8.58 41.46 4.85
3746 4543 2.606519 TGTACGGGGCTTCAGGCT 60.607 61.111 0.00 0.00 41.46 4.58
3747 4544 2.436115 GTGTACGGGGCTTCAGGC 60.436 66.667 0.00 0.00 40.90 4.85
3748 4545 0.391263 GAAGTGTACGGGGCTTCAGG 60.391 60.000 11.72 0.00 38.65 3.86
3749 4546 0.320374 TGAAGTGTACGGGGCTTCAG 59.680 55.000 13.99 0.00 42.24 3.02
3750 4547 0.320374 CTGAAGTGTACGGGGCTTCA 59.680 55.000 15.89 15.89 44.08 3.02
3751 4548 0.606604 TCTGAAGTGTACGGGGCTTC 59.393 55.000 10.42 10.42 39.09 3.86
3752 4549 0.608640 CTCTGAAGTGTACGGGGCTT 59.391 55.000 0.00 0.00 0.00 4.35
3753 4550 0.542232 ACTCTGAAGTGTACGGGGCT 60.542 55.000 0.00 0.00 33.32 5.19
3754 4551 0.320697 AACTCTGAAGTGTACGGGGC 59.679 55.000 0.00 0.00 35.36 5.80
3755 4552 1.616865 TGAACTCTGAAGTGTACGGGG 59.383 52.381 0.00 0.00 35.36 5.73
3756 4553 3.594603 ATGAACTCTGAAGTGTACGGG 57.405 47.619 0.00 0.00 35.36 5.28
3757 4554 5.562506 TCTATGAACTCTGAAGTGTACGG 57.437 43.478 0.00 0.00 35.36 4.02
3758 4555 5.031578 GCTCTATGAACTCTGAAGTGTACG 58.968 45.833 0.00 0.00 35.36 3.67
3759 4556 5.802956 GTGCTCTATGAACTCTGAAGTGTAC 59.197 44.000 0.00 0.00 35.36 2.90
3760 4557 5.476945 TGTGCTCTATGAACTCTGAAGTGTA 59.523 40.000 0.00 0.00 35.36 2.90
3761 4558 4.281941 TGTGCTCTATGAACTCTGAAGTGT 59.718 41.667 0.00 0.00 35.36 3.55
3762 4559 4.624882 GTGTGCTCTATGAACTCTGAAGTG 59.375 45.833 0.00 0.00 35.36 3.16
3763 4560 4.281941 TGTGTGCTCTATGAACTCTGAAGT 59.718 41.667 0.00 0.00 37.32 3.01
3764 4561 4.814147 TGTGTGCTCTATGAACTCTGAAG 58.186 43.478 0.00 0.00 0.00 3.02
3765 4562 4.871933 TGTGTGCTCTATGAACTCTGAA 57.128 40.909 0.00 0.00 0.00 3.02
3766 4563 4.814147 CTTGTGTGCTCTATGAACTCTGA 58.186 43.478 0.00 0.00 0.00 3.27
3767 4564 3.370366 GCTTGTGTGCTCTATGAACTCTG 59.630 47.826 0.00 0.00 0.00 3.35
3768 4565 3.007290 TGCTTGTGTGCTCTATGAACTCT 59.993 43.478 0.00 0.00 0.00 3.24
3769 4566 3.329386 TGCTTGTGTGCTCTATGAACTC 58.671 45.455 0.00 0.00 0.00 3.01
3770 4567 3.407424 TGCTTGTGTGCTCTATGAACT 57.593 42.857 0.00 0.00 0.00 3.01
3771 4568 3.669023 GCTTGCTTGTGTGCTCTATGAAC 60.669 47.826 0.00 0.00 0.00 3.18
3772 4569 2.485426 GCTTGCTTGTGTGCTCTATGAA 59.515 45.455 0.00 0.00 0.00 2.57
3773 4570 2.079158 GCTTGCTTGTGTGCTCTATGA 58.921 47.619 0.00 0.00 0.00 2.15
3774 4571 1.808343 TGCTTGCTTGTGTGCTCTATG 59.192 47.619 0.00 0.00 0.00 2.23
3775 4572 2.189594 TGCTTGCTTGTGTGCTCTAT 57.810 45.000 0.00 0.00 0.00 1.98
3776 4573 1.875514 CTTGCTTGCTTGTGTGCTCTA 59.124 47.619 0.00 0.00 0.00 2.43
3843 4640 5.523916 TCTTCTTGCTTACTTGTGTGTTCTC 59.476 40.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.