Multiple sequence alignment - TraesCS1A01G079800

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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 TraesCS1A01G079800 chr1A 100.000 4304 0 0 1 4304 62617746 62613443 0.000000e+00 7949.0
1 TraesCS1A01G079800 chr1D 91.304 4370 235 78 7 4304 63639903 63635607 0.000000e+00 5830.0
2 TraesCS1A01G079800 chr1D 95.455 44 1 1 3628 3671 394488542 394488500 7.720000e-08 69.4
3 TraesCS1A01G079800 chr1B 91.395 3591 194 53 10 3563 104470771 104467259 0.000000e+00 4813.0
4 TraesCS1A01G079800 chr1B 95.503 467 16 2 3841 4304 104466953 104466489 0.000000e+00 741.0
5 TraesCS1A01G079800 chr1B 91.837 49 3 1 3623 3671 12439993 12439946 2.780000e-07 67.6
6 TraesCS1A01G079800 chr7D 97.778 45 1 0 3623 3667 60676557 60676601 1.280000e-10 78.7
7 TraesCS1A01G079800 chr3D 83.750 80 13 0 4184 4263 144291569 144291490 4.620000e-10 76.8
8 TraesCS1A01G079800 chr3D 81.609 87 16 0 4186 4272 192058955 192058869 5.970000e-09 73.1
9 TraesCS1A01G079800 chr3A 80.612 98 19 0 4166 4263 262522695 262522792 4.620000e-10 76.8
10 TraesCS1A01G079800 chr3A 80.899 89 17 0 4184 4272 163924067 163923979 2.150000e-08 71.3
11 TraesCS1A01G079800 chr2B 97.674 43 1 0 3623 3665 136171327 136171369 1.660000e-09 75.0
12 TraesCS1A01G079800 chr6B 95.556 45 2 0 3623 3667 255535421 255535465 5.970000e-09 73.1
13 TraesCS1A01G079800 chr5B 95.556 45 2 0 3623 3667 384594903 384594859 5.970000e-09 73.1
14 TraesCS1A01G079800 chr2D 95.556 45 2 0 3623 3667 391259052 391259008 5.970000e-09 73.1


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 TraesCS1A01G079800 chr1A 62613443 62617746 4303 True 7949 7949 100.000 1 4304 1 chr1A.!!$R1 4303
1 TraesCS1A01G079800 chr1D 63635607 63639903 4296 True 5830 5830 91.304 7 4304 1 chr1D.!!$R1 4297
2 TraesCS1A01G079800 chr1B 104466489 104470771 4282 True 2777 4813 93.449 10 4304 2 chr1B.!!$R2 4294

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
782 816 0.605319 TGAAAGCTACCGGTTGGCTG 60.605 55.0 27.46 10.21 39.70 4.85 F
789 823 0.901114 TACCGGTTGGCTGCTACTGA 60.901 55.0 15.04 0.00 39.70 3.41 F
1428 1463 0.965439 TTTCTCCATTTGGGGTTGCG 59.035 50.0 0.00 0.00 36.89 4.85 F
3156 3231 0.693049 GGGAGAAGAGGGACAAGCAA 59.307 55.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2695 0.179048 TGCTCAGGGATAATGTGGCG 60.179 55.000 0.00 0.0 0.00 5.69 R
2742 2814 4.213270 TGACCTGAACATTTTCGACACATC 59.787 41.667 0.00 0.0 34.04 3.06 R
3270 3345 0.811616 GGACCATCACGACCAGCATC 60.812 60.000 0.00 0.0 0.00 3.91 R
4224 4455 0.662619 CGGCATTGTGCGTCCAATAT 59.337 50.000 2.11 0.0 46.21 1.28 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
63 66 9.189723 GAATCAAGTACTCCCGTACAATATTAC 57.810 37.037 0.00 0.00 46.68 1.89
102 105 5.479306 TGAGTGATTTTTCCGAGGAACTAG 58.521 41.667 3.71 0.00 41.55 2.57
105 108 6.631962 AGTGATTTTTCCGAGGAACTAGTAG 58.368 40.000 3.71 0.00 41.55 2.57
107 110 7.395489 AGTGATTTTTCCGAGGAACTAGTAGTA 59.605 37.037 2.50 0.00 41.55 1.82
108 111 7.487509 GTGATTTTTCCGAGGAACTAGTAGTAC 59.512 40.741 2.50 0.00 41.55 2.73
109 112 7.395489 TGATTTTTCCGAGGAACTAGTAGTACT 59.605 37.037 8.14 8.14 41.55 2.73
110 113 8.814038 ATTTTTCCGAGGAACTAGTAGTACTA 57.186 34.615 9.66 9.66 41.55 1.82
111 114 7.617041 TTTTCCGAGGAACTAGTAGTACTAC 57.383 40.000 23.03 23.03 41.55 2.73
112 115 6.951971 TTTCCGAGGAACTAGTAGTACTACT 58.048 40.000 32.39 32.39 41.55 2.57
144 153 8.244113 GGCAGTATTTAATTGAGCACTTAAAGT 58.756 33.333 10.23 0.00 31.85 2.66
185 194 5.187480 GGAAAATTTGAACGCGTTTGAAAG 58.813 37.500 27.32 0.00 0.00 2.62
188 197 5.369947 AATTTGAACGCGTTTGAAAGTTC 57.630 34.783 27.32 11.25 42.19 3.01
267 277 5.606348 TGCTTTTGTTTTGTCCCAATACT 57.394 34.783 0.00 0.00 0.00 2.12
268 278 5.983540 TGCTTTTGTTTTGTCCCAATACTT 58.016 33.333 0.00 0.00 0.00 2.24
269 279 6.045955 TGCTTTTGTTTTGTCCCAATACTTC 58.954 36.000 0.00 0.00 0.00 3.01
270 280 6.127196 TGCTTTTGTTTTGTCCCAATACTTCT 60.127 34.615 0.00 0.00 0.00 2.85
304 319 9.710900 AATTTCTTTTAAAAGCCTGATACCTTG 57.289 29.630 20.93 0.00 35.99 3.61
341 356 0.973632 TCACATGGCCGTAGAACAGT 59.026 50.000 0.00 0.00 0.00 3.55
349 364 4.940463 TGGCCGTAGAACAGTACAATATC 58.060 43.478 0.00 0.00 0.00 1.63
359 374 4.424626 ACAGTACAATATCGCAGTCAGTG 58.575 43.478 0.00 0.00 0.00 3.66
423 445 3.290710 ACTTGAAGCACCAAGAACATGT 58.709 40.909 20.33 0.00 44.66 3.21
490 513 2.027385 GGAGTTGATCCCTTCATTGGC 58.973 52.381 0.00 0.00 43.01 4.52
508 531 1.165270 GCCGCCATGAACAAGTTACT 58.835 50.000 0.00 0.00 0.00 2.24
509 532 1.539827 GCCGCCATGAACAAGTTACTT 59.460 47.619 0.00 0.00 0.00 2.24
510 533 2.668279 GCCGCCATGAACAAGTTACTTG 60.668 50.000 21.90 21.90 45.85 3.16
554 584 5.695851 ACTTTGCTTCATTTACTGTCCAG 57.304 39.130 0.00 0.00 0.00 3.86
779 813 1.156736 CAGTGAAAGCTACCGGTTGG 58.843 55.000 15.04 7.76 42.84 3.77
782 816 0.605319 TGAAAGCTACCGGTTGGCTG 60.605 55.000 27.46 10.21 39.70 4.85
789 823 0.901114 TACCGGTTGGCTGCTACTGA 60.901 55.000 15.04 0.00 39.70 3.41
868 903 4.013050 AGCTCTCAGTGCCCTTATTTTTC 58.987 43.478 0.00 0.00 0.00 2.29
871 906 4.589908 TCTCAGTGCCCTTATTTTTCTCC 58.410 43.478 0.00 0.00 0.00 3.71
900 935 2.413142 GGATGCTTGCTGTGAGCCC 61.413 63.158 0.00 0.00 41.51 5.19
1077 1112 1.927174 CCGCTGTTGAAGGATCTTACG 59.073 52.381 0.00 0.00 0.00 3.18
1087 1122 4.142138 TGAAGGATCTTACGGAGAAGAAGC 60.142 45.833 0.00 0.00 38.89 3.86
1217 1252 9.096160 GGAGGTTAGTAAATTTCTACTACTTGC 57.904 37.037 0.00 0.00 34.76 4.01
1400 1435 2.698803 CATCACCGAACATGTGAGGAA 58.301 47.619 22.22 12.31 44.84 3.36
1428 1463 0.965439 TTTCTCCATTTGGGGTTGCG 59.035 50.000 0.00 0.00 36.89 4.85
1473 1509 7.663827 TCCATTTCTATTCCATGATGAATTGC 58.336 34.615 0.00 0.00 36.41 3.56
1523 1576 9.815306 TTCTAAGCATACTACTCTAGATTCCAT 57.185 33.333 0.00 0.00 0.00 3.41
1529 1582 8.961634 GCATACTACTCTAGATTCCATACATGA 58.038 37.037 0.00 0.00 0.00 3.07
1568 1622 2.715046 CAGTGCAACATAGTGGGTGAT 58.285 47.619 0.00 0.00 41.43 3.06
1569 1623 2.421073 CAGTGCAACATAGTGGGTGATG 59.579 50.000 0.00 0.00 41.43 3.07
1608 1662 9.702726 GTAAAATTGCTTTCCTTTGTTTCTTTC 57.297 29.630 0.00 0.00 0.00 2.62
1617 1672 5.505780 TCCTTTGTTTCTTTCCTGAACTGA 58.494 37.500 0.00 0.00 0.00 3.41
1652 1707 4.824479 TTGCTGAACTGATGGTGATCTA 57.176 40.909 0.00 0.00 0.00 1.98
1658 1713 4.223700 TGAACTGATGGTGATCTAAGCACT 59.776 41.667 0.00 0.00 36.53 4.40
1718 1777 6.662414 TCGAAAAATCTTCTTATGCGTGAT 57.338 33.333 0.00 0.00 0.00 3.06
1764 1823 5.598754 TCCCAACCCTAATGATTCCATTTT 58.401 37.500 0.00 0.00 42.56 1.82
1776 1835 8.624367 AATGATTCCATTTTGCTTCAAATTGA 57.376 26.923 12.84 0.00 39.86 2.57
1918 1977 2.974148 CAGGCGCAGTGCTTGTCA 60.974 61.111 14.33 0.00 45.05 3.58
1952 2011 1.751351 TGAATGAGAAGGATCGCTCGT 59.249 47.619 4.94 2.33 33.89 4.18
2074 2133 7.461749 AGGATGAAGTTTTAAGGATTGAGACA 58.538 34.615 0.00 0.00 0.00 3.41
2140 2199 5.153950 ACGAGCTTCTGAAGGTTTTATCT 57.846 39.130 21.62 7.27 39.77 1.98
2171 2230 8.607441 TTCACCAAGGAATATCGAGAATATTG 57.393 34.615 0.00 0.00 40.03 1.90
2313 2372 7.718753 TCCTTGCATCCACAAAATAACAAAATT 59.281 29.630 0.00 0.00 0.00 1.82
2354 2413 3.737266 CAGACATTGTTTTCGCTGCAATT 59.263 39.130 0.00 0.00 31.31 2.32
2355 2414 4.209703 CAGACATTGTTTTCGCTGCAATTT 59.790 37.500 0.00 0.00 31.31 1.82
2361 2420 2.917343 GTTTTCGCTGCAATTTAGCTCC 59.083 45.455 0.00 0.00 39.00 4.70
2427 2489 2.342279 CGCAGAACCGACCAGGAA 59.658 61.111 0.00 0.00 45.00 3.36
2475 2537 3.401033 TTCTGCCTTCAAGAATCACGA 57.599 42.857 0.00 0.00 0.00 4.35
2514 2576 7.450124 ACTTCAGAGGGTATGTACATATACG 57.550 40.000 18.27 5.38 34.97 3.06
2523 2585 7.666804 AGGGTATGTACATATACGTGTGTATCA 59.333 37.037 18.27 6.78 41.50 2.15
2568 2630 3.417185 GAAACATGACTTCGATTTCGCC 58.583 45.455 0.00 0.00 39.60 5.54
2630 2701 6.038161 CCTTCTTGAATTGAATATACGCCACA 59.962 38.462 0.00 0.00 0.00 4.17
2646 2717 2.420642 CCACATTATCCCTGAGCATCG 58.579 52.381 0.00 0.00 38.61 3.84
2647 2718 2.224378 CCACATTATCCCTGAGCATCGT 60.224 50.000 0.00 0.00 38.61 3.73
2648 2719 3.006859 CCACATTATCCCTGAGCATCGTA 59.993 47.826 0.00 0.00 38.61 3.43
2649 2720 4.503123 CCACATTATCCCTGAGCATCGTAA 60.503 45.833 0.00 0.00 38.61 3.18
2656 2727 3.197766 TCCCTGAGCATCGTAACAAGATT 59.802 43.478 0.00 0.00 38.61 2.40
2749 2821 3.489738 GCAGTTGGCCATAATGATGTGTC 60.490 47.826 6.09 0.00 36.11 3.67
2758 2830 6.035843 GCCATAATGATGTGTCGAAAATGTT 58.964 36.000 0.00 0.00 0.00 2.71
2780 2852 5.034852 TCAGGTCAAAGTCAAACAGATCA 57.965 39.130 0.00 0.00 0.00 2.92
2797 2869 5.045872 CAGATCACTGATTCATGCGTTCTA 58.954 41.667 0.00 0.00 46.03 2.10
2799 2871 4.718940 TCACTGATTCATGCGTTCTAGA 57.281 40.909 0.00 0.00 0.00 2.43
2811 2883 6.315393 TCATGCGTTCTAGAAAAACCCTATTC 59.685 38.462 6.78 0.00 0.00 1.75
2954 3026 8.570488 TGATGCCTGCAATAAAATATACTGAAG 58.430 33.333 0.00 0.00 0.00 3.02
2958 3030 7.168135 GCCTGCAATAAAATATACTGAAGCAAC 59.832 37.037 0.00 0.00 0.00 4.17
2968 3040 1.800586 ACTGAAGCAACGCATACACTG 59.199 47.619 0.00 0.00 0.00 3.66
2992 3064 4.177165 TGTGATAGCCATGTTTTTGCAG 57.823 40.909 0.00 0.00 0.00 4.41
2993 3065 2.925563 GTGATAGCCATGTTTTTGCAGC 59.074 45.455 0.00 0.00 0.00 5.25
2994 3066 2.561858 TGATAGCCATGTTTTTGCAGCA 59.438 40.909 0.00 0.00 0.00 4.41
3000 3072 2.937799 CCATGTTTTTGCAGCAAACTGT 59.062 40.909 20.49 4.41 46.30 3.55
3001 3073 3.374678 CCATGTTTTTGCAGCAAACTGTT 59.625 39.130 20.49 3.60 46.30 3.16
3002 3074 4.336101 CATGTTTTTGCAGCAAACTGTTG 58.664 39.130 20.49 11.85 46.30 3.33
3003 3075 3.657634 TGTTTTTGCAGCAAACTGTTGA 58.342 36.364 20.49 1.60 46.30 3.18
3004 3076 4.060900 TGTTTTTGCAGCAAACTGTTGAA 58.939 34.783 20.49 8.12 46.30 2.69
3042 3114 3.972502 GGCAACTAAACACATGTCGAAAC 59.027 43.478 0.00 0.00 0.00 2.78
3069 3141 3.760684 AGAAGATTTTCATGGTGCTCACC 59.239 43.478 11.95 11.95 42.56 4.02
3090 3162 3.136763 CGATCAGTTGGGATCATTGAGG 58.863 50.000 0.00 0.00 43.07 3.86
3156 3231 0.693049 GGGAGAAGAGGGACAAGCAA 59.307 55.000 0.00 0.00 0.00 3.91
3255 3330 5.556915 TGGGAGAATGATACGTTCAAGTTT 58.443 37.500 0.00 0.00 38.03 2.66
3270 3345 3.418913 TTTGTCGCCGGCATGTCG 61.419 61.111 28.98 13.99 0.00 4.35
3333 3408 6.037098 GCGTCATCTTGTGTAGAGAAGTTAT 58.963 40.000 0.00 0.00 36.02 1.89
3377 3463 4.998033 GCTCTGTAGTTTTAAGAAGCCAGT 59.002 41.667 0.00 0.00 0.00 4.00
3462 3548 1.130749 AGAGACCAGAATTCGTCGACG 59.869 52.381 31.30 31.30 41.45 5.12
3516 3602 1.664659 GCTCAGCTGCTAGTTCATGTG 59.335 52.381 9.47 0.00 0.00 3.21
3619 3792 7.120051 AGAGGTTTAGTACTCTTCAGCATCTA 58.880 38.462 0.00 0.00 41.05 1.98
3620 3793 7.067737 AGAGGTTTAGTACTCTTCAGCATCTAC 59.932 40.741 0.00 0.00 41.05 2.59
3621 3794 6.097129 AGGTTTAGTACTCTTCAGCATCTACC 59.903 42.308 0.00 0.00 0.00 3.18
3708 3914 9.289782 AGATCATTAAAGTACATGGCTAATTCC 57.710 33.333 0.00 0.00 0.00 3.01
3717 3923 3.950395 ACATGGCTAATTCCTGCTTCTTC 59.050 43.478 0.00 0.00 0.00 2.87
3735 3941 2.890808 TCAGTCCATTATGCGACTCC 57.109 50.000 11.51 0.00 37.23 3.85
3739 3945 3.941483 CAGTCCATTATGCGACTCCTTTT 59.059 43.478 11.51 0.00 37.23 2.27
3808 4014 4.764823 CCTGTTCCAAACAAGGCTATACAA 59.235 41.667 0.00 0.00 41.61 2.41
3812 4018 6.547880 TGTTCCAAACAAGGCTATACAAAGAA 59.452 34.615 0.00 0.00 38.72 2.52
3863 4091 2.290514 TGGAATCTGGACTTGGAAGCAG 60.291 50.000 0.00 0.00 0.00 4.24
3908 4136 9.561270 GCAGTGTTTATTATCTTCCTTTTTCTC 57.439 33.333 0.00 0.00 0.00 2.87
3915 4143 9.892130 TTATTATCTTCCTTTTTCTCTCTGTCC 57.108 33.333 0.00 0.00 0.00 4.02
4119 4350 0.696501 ATACAAAAGGCCGGAGTGGT 59.303 50.000 5.05 0.00 41.21 4.16
4281 4512 3.673746 TTCAAACAACACGCAGAAGAG 57.326 42.857 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.115095 CGTGGATTGCGAGGTTAAAATTAAAAA 59.885 33.333 0.00 0.00 0.00 1.94
11 12 6.583050 CGTGGATTGCGAGGTTAAAATTAAAA 59.417 34.615 0.00 0.00 0.00 1.52
12 13 6.087522 CGTGGATTGCGAGGTTAAAATTAAA 58.912 36.000 0.00 0.00 0.00 1.52
13 14 5.392165 CCGTGGATTGCGAGGTTAAAATTAA 60.392 40.000 0.00 0.00 0.00 1.40
14 15 4.095185 CCGTGGATTGCGAGGTTAAAATTA 59.905 41.667 0.00 0.00 0.00 1.40
15 16 3.119637 CCGTGGATTGCGAGGTTAAAATT 60.120 43.478 0.00 0.00 0.00 1.82
22 23 0.462047 GATTCCGTGGATTGCGAGGT 60.462 55.000 0.00 0.00 0.00 3.85
25 26 1.338674 ACTTGATTCCGTGGATTGCGA 60.339 47.619 0.00 0.00 0.00 5.10
27 28 3.270877 AGTACTTGATTCCGTGGATTGC 58.729 45.455 0.00 0.00 0.00 3.56
75 78 6.940298 AGTTCCTCGGAAAAATCACTCATTTA 59.060 34.615 0.00 0.00 33.16 1.40
91 94 5.984926 CAGAGTAGTACTACTAGTTCCTCGG 59.015 48.000 30.80 15.92 45.63 4.63
144 153 6.458232 TTTTCCAAAGAATCCGACAGAAAA 57.542 33.333 0.00 0.00 31.54 2.29
270 280 9.965824 CAGGCTTTTAAAAGAAATTACTGAAGA 57.034 29.630 28.11 0.00 38.28 2.87
288 300 9.920946 TCTTTTATATCAAGGTATCAGGCTTTT 57.079 29.630 0.00 0.00 0.00 2.27
304 319 9.455847 GCCATGTGAGAAACAATCTTTTATATC 57.544 33.333 0.00 0.00 43.61 1.63
311 326 2.489329 CGGCCATGTGAGAAACAATCTT 59.511 45.455 2.24 0.00 43.61 2.40
321 336 1.066858 ACTGTTCTACGGCCATGTGAG 60.067 52.381 2.24 0.00 0.00 3.51
341 356 6.918022 CAGAATACACTGACTGCGATATTGTA 59.082 38.462 0.00 0.00 39.94 2.41
349 364 5.839262 TTTTACAGAATACACTGACTGCG 57.161 39.130 0.00 0.00 40.63 5.18
359 374 9.977762 CGGTACAGGTTAATTTTTACAGAATAC 57.022 33.333 0.00 0.00 0.00 1.89
423 445 3.343617 GGACACTAGGCTGCAAACATAA 58.656 45.455 0.50 0.00 0.00 1.90
436 458 2.755650 AGTCAACTTTGCGGACACTAG 58.244 47.619 0.00 0.00 34.04 2.57
484 507 0.458889 CTTGTTCATGGCGGCCAATG 60.459 55.000 27.70 22.43 36.95 2.82
489 512 1.165270 AGTAACTTGTTCATGGCGGC 58.835 50.000 0.00 0.00 0.00 6.53
490 513 3.201726 CAAGTAACTTGTTCATGGCGG 57.798 47.619 0.00 0.00 36.79 6.13
512 535 9.463443 GCAAAGTAAGATAATGTTGTTCAAACT 57.537 29.630 0.00 0.00 0.00 2.66
513 536 9.463443 AGCAAAGTAAGATAATGTTGTTCAAAC 57.537 29.630 0.00 0.00 0.00 2.93
548 578 6.056090 TGTACAATTAGTAATGGCTGGACA 57.944 37.500 6.91 6.91 33.72 4.02
549 579 6.995511 TTGTACAATTAGTAATGGCTGGAC 57.004 37.500 3.59 0.00 33.72 4.02
708 742 3.428532 AGAAAGATGGTGATGCTTGCTT 58.571 40.909 0.00 0.00 0.00 3.91
779 813 2.072298 CTTTCACAGGTCAGTAGCAGC 58.928 52.381 0.00 0.00 0.00 5.25
782 816 3.508012 TCTCTCTTTCACAGGTCAGTAGC 59.492 47.826 0.00 0.00 0.00 3.58
789 823 4.878397 CACAAACTTCTCTCTTTCACAGGT 59.122 41.667 0.00 0.00 0.00 4.00
868 903 4.321718 CAAGCATCCCATGTATACAGGAG 58.678 47.826 18.73 5.87 0.00 3.69
871 906 3.501062 CAGCAAGCATCCCATGTATACAG 59.499 47.826 11.91 3.82 0.00 2.74
900 935 1.593196 TCTCCAAGAACAAACAGCGG 58.407 50.000 0.00 0.00 0.00 5.52
968 1003 3.315191 CCGAACCAAACAGACAAGATTGT 59.685 43.478 0.00 0.00 45.65 2.71
969 1004 3.304659 CCCGAACCAAACAGACAAGATTG 60.305 47.826 0.00 0.00 0.00 2.67
970 1005 2.884639 CCCGAACCAAACAGACAAGATT 59.115 45.455 0.00 0.00 0.00 2.40
971 1006 2.504367 CCCGAACCAAACAGACAAGAT 58.496 47.619 0.00 0.00 0.00 2.40
1087 1122 3.120511 GCCACGTTTCTTCTAAAGCTCAG 60.121 47.826 0.00 0.00 0.00 3.35
1217 1252 5.128919 AGCCATGCTGAAGGTAGAAATTAG 58.871 41.667 0.00 0.00 37.57 1.73
1259 1294 0.741915 CGTTCTCTCCCTAGTCAGGC 59.258 60.000 0.00 0.00 41.08 4.85
1260 1295 2.131776 ACGTTCTCTCCCTAGTCAGG 57.868 55.000 0.00 0.00 42.22 3.86
1290 1325 1.448717 GCTCCTTGCCTTCGTCTCC 60.449 63.158 0.00 0.00 35.15 3.71
1400 1435 2.310052 CCAAATGGAGAAAGGAGGGAGT 59.690 50.000 0.00 0.00 37.39 3.85
1409 1444 0.965439 CGCAACCCCAAATGGAGAAA 59.035 50.000 0.00 0.00 37.39 2.52
1444 1479 9.650714 ATTCATCATGGAATAGAAATGGAGAAA 57.349 29.630 0.00 0.00 35.79 2.52
1495 1532 9.292195 GGAATCTAGAGTAGTATGCTTAGAAGT 57.708 37.037 0.00 0.00 29.91 3.01
1496 1533 9.290988 TGGAATCTAGAGTAGTATGCTTAGAAG 57.709 37.037 0.00 0.00 29.91 2.85
1497 1534 9.815306 ATGGAATCTAGAGTAGTATGCTTAGAA 57.185 33.333 0.00 0.00 29.91 2.10
1501 1538 8.941995 TGTATGGAATCTAGAGTAGTATGCTT 57.058 34.615 0.00 0.00 0.00 3.91
1502 1539 8.965819 CATGTATGGAATCTAGAGTAGTATGCT 58.034 37.037 0.00 0.00 0.00 3.79
1503 1540 8.961634 TCATGTATGGAATCTAGAGTAGTATGC 58.038 37.037 0.00 0.00 0.00 3.14
1529 1582 6.930164 TGCACTGCATTCAACTCATTTTAAAT 59.070 30.769 0.00 0.00 31.71 1.40
1568 1622 8.830201 AAGCAATTTTACAAGCAAATACATCA 57.170 26.923 0.00 0.00 0.00 3.07
1569 1623 9.745323 GAAAGCAATTTTACAAGCAAATACATC 57.255 29.630 0.00 0.00 0.00 3.06
1608 1662 1.808945 GACAGGCACAATCAGTTCAGG 59.191 52.381 0.00 0.00 0.00 3.86
1617 1672 2.309613 TCAGCAAAAGACAGGCACAAT 58.690 42.857 0.00 0.00 0.00 2.71
1652 1707 4.989168 CGTACTACTCTTTTCCAAGTGCTT 59.011 41.667 0.00 0.00 0.00 3.91
1658 1713 9.798994 GAAGATAATCGTACTACTCTTTTCCAA 57.201 33.333 0.00 0.00 0.00 3.53
1697 1756 7.640240 GGTACATCACGCATAAGAAGATTTTTC 59.360 37.037 0.00 0.00 0.00 2.29
1718 1777 7.506114 GGAAACCAGTATCATAATGAGGTACA 58.494 38.462 0.00 0.00 0.00 2.90
1764 1823 7.980662 TGACAAAGAGAATTTCAATTTGAAGCA 59.019 29.630 22.65 16.70 37.70 3.91
1796 1855 6.874664 TCGAGGTACTGCACATAATTACAAAA 59.125 34.615 0.00 0.00 41.55 2.44
1797 1856 6.399743 TCGAGGTACTGCACATAATTACAAA 58.600 36.000 0.00 0.00 41.55 2.83
1798 1857 5.968254 TCGAGGTACTGCACATAATTACAA 58.032 37.500 0.00 0.00 41.55 2.41
1855 1914 2.421619 GCTTCTGCTGTAGCTTGAGTT 58.578 47.619 13.75 0.00 42.66 3.01
2074 2133 3.202818 TGGAAACTGCACCCATGATATCT 59.797 43.478 3.98 0.00 0.00 1.98
2140 2199 5.739959 TCGATATTCCTTGGTGAAACATCA 58.260 37.500 0.00 0.00 39.98 3.07
2171 2230 5.835113 TCCTTAGTATTCAAATGCTTGCC 57.165 39.130 0.00 0.00 33.32 4.52
2313 2372 3.122297 CTGCGAAACAATTTCAGGCAAA 58.878 40.909 2.50 0.00 39.63 3.68
2354 2413 4.937620 TCTCGAGTAAACTTACGGAGCTAA 59.062 41.667 13.13 0.00 38.16 3.09
2355 2414 4.507710 TCTCGAGTAAACTTACGGAGCTA 58.492 43.478 13.13 0.00 38.16 3.32
2388 2447 1.276415 GCTTCTCTAGCTGTTCAGCG 58.724 55.000 17.28 6.31 46.77 5.18
2475 2537 5.645497 CCTCTGAAGTTTTCGGATTTGAGAT 59.355 40.000 1.14 0.00 43.68 2.75
2514 2576 9.180678 CACTTGTTAAAGGAAAATGATACACAC 57.819 33.333 0.00 0.00 37.76 3.82
2624 2695 0.179048 TGCTCAGGGATAATGTGGCG 60.179 55.000 0.00 0.00 0.00 5.69
2630 2701 4.955811 TGTTACGATGCTCAGGGATAAT 57.044 40.909 0.00 0.00 0.00 1.28
2742 2814 4.213270 TGACCTGAACATTTTCGACACATC 59.787 41.667 0.00 0.00 34.04 3.06
2749 2821 5.168526 TGACTTTGACCTGAACATTTTCG 57.831 39.130 0.00 0.00 34.04 3.46
2758 2830 4.816385 GTGATCTGTTTGACTTTGACCTGA 59.184 41.667 0.00 0.00 0.00 3.86
2780 2852 6.348540 GGTTTTTCTAGAACGCATGAATCAGT 60.349 38.462 4.18 0.00 0.00 3.41
2811 2883 9.897744 GAGAAGATGAGATCACTGATACTAAAG 57.102 37.037 0.00 0.00 0.00 1.85
2823 2895 4.871822 TGGTACCAGAGAAGATGAGATCA 58.128 43.478 11.60 0.00 0.00 2.92
2825 2897 3.640967 GCTGGTACCAGAGAAGATGAGAT 59.359 47.826 40.26 0.00 46.30 2.75
2874 2946 8.774586 CGATTTCTTCCTCAAGTTTTCTAAAGA 58.225 33.333 0.00 0.00 0.00 2.52
2877 2949 8.557029 GTTCGATTTCTTCCTCAAGTTTTCTAA 58.443 33.333 0.00 0.00 0.00 2.10
2968 3040 3.368843 GCAAAAACATGGCTATCACAAGC 59.631 43.478 0.00 0.00 41.99 4.01
2969 3041 4.558178 TGCAAAAACATGGCTATCACAAG 58.442 39.130 0.00 0.00 0.00 3.16
2992 3064 7.755582 AATTAGTTCAACTTCAACAGTTTGC 57.244 32.000 0.00 0.00 43.89 3.68
2999 3071 8.699749 GTTGCCATTAATTAGTTCAACTTCAAC 58.300 33.333 0.00 0.00 32.19 3.18
3000 3072 8.637986 AGTTGCCATTAATTAGTTCAACTTCAA 58.362 29.630 14.44 0.00 39.40 2.69
3001 3073 8.177119 AGTTGCCATTAATTAGTTCAACTTCA 57.823 30.769 14.44 0.00 39.40 3.02
3004 3076 9.908152 GTTTAGTTGCCATTAATTAGTTCAACT 57.092 29.630 19.78 19.78 43.20 3.16
3042 3114 4.461781 AGCACCATGAAAATCTTCTCAAGG 59.538 41.667 0.00 0.00 36.66 3.61
3069 3141 3.136763 CCTCAATGATCCCAACTGATCG 58.863 50.000 0.00 0.00 43.34 3.69
3076 3148 2.777114 TCGGATTCCTCAATGATCCCAA 59.223 45.455 0.30 0.00 0.00 4.12
3090 3162 2.426381 AGTTAGTCTCGGGTTCGGATTC 59.574 50.000 0.00 0.00 36.95 2.52
3156 3231 2.500910 CTGATCCTTGAGCTCCTTGAGT 59.499 50.000 12.15 0.00 31.39 3.41
3255 3330 4.141965 ATCGACATGCCGGCGACA 62.142 61.111 23.90 1.91 36.83 4.35
3270 3345 0.811616 GGACCATCACGACCAGCATC 60.812 60.000 0.00 0.00 0.00 3.91
3377 3463 2.823747 ACAACGCTACTCCAGTACATGA 59.176 45.455 0.00 0.00 0.00 3.07
3462 3548 3.700539 GGTCTAGAGGACTAAACCTGGAC 59.299 52.174 0.00 0.00 43.97 4.02
3516 3602 7.834803 AGTACAGGATTACAGTTAACTACCAC 58.165 38.462 8.04 0.00 0.00 4.16
3591 3727 7.534723 TGCTGAAGAGTACTAAACCTCTTAA 57.465 36.000 0.00 0.00 36.44 1.85
3597 3733 6.127423 TGGTAGATGCTGAAGAGTACTAAACC 60.127 42.308 0.00 0.00 0.00 3.27
3611 3784 2.499289 ACAGAGGAAGTGGTAGATGCTG 59.501 50.000 0.00 0.00 0.00 4.41
3688 3894 6.423182 AGCAGGAATTAGCCATGTACTTTAA 58.577 36.000 0.00 0.00 0.00 1.52
3689 3895 6.001449 AGCAGGAATTAGCCATGTACTTTA 57.999 37.500 0.00 0.00 0.00 1.85
3699 3905 3.615155 ACTGAAGAAGCAGGAATTAGCC 58.385 45.455 0.00 0.00 40.20 3.93
3701 3907 4.836825 TGGACTGAAGAAGCAGGAATTAG 58.163 43.478 0.00 0.00 40.20 1.73
3708 3914 3.002042 CGCATAATGGACTGAAGAAGCAG 59.998 47.826 0.00 0.00 41.63 4.24
3717 3923 2.898729 AGGAGTCGCATAATGGACTG 57.101 50.000 6.38 0.00 43.23 3.51
3735 3941 6.095440 TCTCAAACAGAAACAGAAGGGAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
3739 3945 4.771114 TCTCAAACAGAAACAGAAGGGA 57.229 40.909 0.00 0.00 0.00 4.20
3808 4014 9.447157 TTTCTCATTTTGTGTTGGATTTTTCTT 57.553 25.926 0.00 0.00 0.00 2.52
3894 4122 4.528596 TCGGACAGAGAGAAAAAGGAAGAT 59.471 41.667 0.00 0.00 0.00 2.40
3915 4143 5.312120 AGTACCTAGAACACTTGTCATCG 57.688 43.478 0.00 0.00 0.00 3.84
4119 4350 2.511373 CATGCCGGACGCTAAGCA 60.511 61.111 5.05 0.00 40.00 3.91
4224 4455 0.662619 CGGCATTGTGCGTCCAATAT 59.337 50.000 2.11 0.00 46.21 1.28
4281 4512 2.890945 AGCCACTTGTAACACCATTTCC 59.109 45.455 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.