Multiple sequence alignment - TraesCS5A01G004000

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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 TraesCS5A01G004000 chr5A 100.000 4550 0 0 1 4550 2866161 2870710 0.000000e+00 8403.0
1 TraesCS5A01G004000 chr5D 91.506 4521 226 63 133 4550 7000526 7004991 0.000000e+00 6076.0
2 TraesCS5A01G004000 chr5D 92.405 158 7 2 3674 3830 549240291 549240444 2.130000e-53 220.0
3 TraesCS5A01G004000 chr5D 91.139 158 9 2 3674 3830 262654193 262654346 4.610000e-50 209.0
4 TraesCS5A01G004000 chr5D 94.203 69 3 1 4 71 7000455 7000523 2.240000e-18 104.0
5 TraesCS5A01G004000 chrUn 95.374 3156 125 6 409 3551 65440497 65437350 0.000000e+00 5000.0
6 TraesCS5A01G004000 chrUn 87.172 1029 46 37 3575 4550 65437287 65436292 0.000000e+00 1090.0
7 TraesCS5A01G004000 chrUn 94.805 308 15 1 99 406 65440891 65440585 3.180000e-131 479.0
8 TraesCS5A01G004000 chrUn 91.139 158 8 3 3674 3830 28596814 28596662 4.610000e-50 209.0
9 TraesCS5A01G004000 chrUn 92.982 114 3 2 404 516 65440554 65440445 1.310000e-35 161.0
10 TraesCS5A01G004000 chr2B 83.180 327 34 11 3596 3914 59916708 59917021 3.470000e-71 279.0
11 TraesCS5A01G004000 chr2D 91.772 158 8 2 3674 3830 336917031 336916878 9.910000e-52 215.0
12 TraesCS5A01G004000 chr2D 91.139 158 7 3 3674 3830 193917240 193917391 1.660000e-49 207.0
13 TraesCS5A01G004000 chr7D 91.139 158 9 2 3674 3830 47173380 47173227 4.610000e-50 209.0
14 TraesCS5A01G004000 chr7D 86.567 67 6 3 68 133 630328420 630328356 2.270000e-08 71.3
15 TraesCS5A01G004000 chr3D 91.139 158 9 2 3674 3830 510785135 510785288 4.610000e-50 209.0
16 TraesCS5A01G004000 chr3B 91.139 158 9 2 3674 3830 165341146 165341299 4.610000e-50 209.0
17 TraesCS5A01G004000 chr6B 86.250 80 7 4 64 141 708111588 708111511 2.920000e-12 84.2
18 TraesCS5A01G004000 chr6B 85.333 75 5 4 72 141 135867648 135867575 6.310000e-09 73.1
19 TraesCS5A01G004000 chr3A 89.394 66 5 2 72 137 571798016 571797953 1.050000e-11 82.4
20 TraesCS5A01G004000 chr4B 88.710 62 4 2 72 133 191228389 191228447 6.310000e-09 73.1
21 TraesCS5A01G004000 chr7A 86.765 68 3 2 70 133 735744298 735744233 2.270000e-08 71.3
22 TraesCS5A01G004000 chr7A 86.765 68 3 2 70 133 735777195 735777130 2.270000e-08 71.3
23 TraesCS5A01G004000 chr5B 85.507 69 4 3 65 133 656470085 656470147 2.940000e-07 67.6


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 TraesCS5A01G004000 chr5A 2866161 2870710 4549 False 8403.0 8403 100.00000 1 4550 1 chr5A.!!$F1 4549
1 TraesCS5A01G004000 chr5D 7000455 7004991 4536 False 3090.0 6076 92.85450 4 4550 2 chr5D.!!$F3 4546
2 TraesCS5A01G004000 chrUn 65436292 65440891 4599 True 1682.5 5000 92.58325 99 4550 4 chrUn.!!$R2 4451

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
84 85 0.310232 GCATACTACTCCGTCCGTCC 59.69 60.0 0.00 0.0 0.00 4.79 F
1210 1299 0.169672 GCATGTTGCTGGTAGTGCTG 59.83 55.0 0.00 0.0 40.96 4.41 F
2064 2162 0.610232 AGCCAGGGTTCAAGCATGAC 60.61 55.0 2.08 0.0 34.61 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1460 1.000396 ACCAGCTCCTGCAATTCCC 60.000 57.895 0.0 0.0 42.74 3.97 R
2607 2705 1.001974 TGACCAAGAACCTCCATGACG 59.998 52.381 0.0 0.0 0.00 4.35 R
3623 3760 0.399454 ACTGCACCTGTTCATCAGCT 59.601 50.000 0.0 0.0 42.38 4.24 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
32 33 1.165270 ACGCATGCTGGTAAACCTTC 58.835 50.000 17.13 0.00 36.82 3.46
62 63 6.861055 AGTTGCCGACATACATTTTTACTTTG 59.139 34.615 0.00 0.00 0.00 2.77
76 77 9.722056 CATTTTTACTTTGATGCATACTACTCC 57.278 33.333 0.00 0.00 0.00 3.85
77 78 7.534085 TTTTACTTTGATGCATACTACTCCG 57.466 36.000 0.00 0.00 0.00 4.63
78 79 4.737855 ACTTTGATGCATACTACTCCGT 57.262 40.909 0.00 0.00 0.00 4.69
79 80 4.683832 ACTTTGATGCATACTACTCCGTC 58.316 43.478 0.00 0.00 0.00 4.79
80 81 3.728076 TTGATGCATACTACTCCGTCC 57.272 47.619 0.00 0.00 0.00 4.79
81 82 1.607148 TGATGCATACTACTCCGTCCG 59.393 52.381 0.00 0.00 0.00 4.79
82 83 1.607628 GATGCATACTACTCCGTCCGT 59.392 52.381 0.00 0.00 0.00 4.69
83 84 1.019673 TGCATACTACTCCGTCCGTC 58.980 55.000 0.00 0.00 0.00 4.79
84 85 0.310232 GCATACTACTCCGTCCGTCC 59.690 60.000 0.00 0.00 0.00 4.79
85 86 0.950116 CATACTACTCCGTCCGTCCC 59.050 60.000 0.00 0.00 0.00 4.46
86 87 0.548031 ATACTACTCCGTCCGTCCCA 59.452 55.000 0.00 0.00 0.00 4.37
87 88 0.327924 TACTACTCCGTCCGTCCCAA 59.672 55.000 0.00 0.00 0.00 4.12
88 89 0.540365 ACTACTCCGTCCGTCCCAAA 60.540 55.000 0.00 0.00 0.00 3.28
89 90 0.604578 CTACTCCGTCCGTCCCAAAA 59.395 55.000 0.00 0.00 0.00 2.44
90 91 1.206371 CTACTCCGTCCGTCCCAAAAT 59.794 52.381 0.00 0.00 0.00 1.82
91 92 1.269012 ACTCCGTCCGTCCCAAAATA 58.731 50.000 0.00 0.00 0.00 1.40
92 93 1.624813 ACTCCGTCCGTCCCAAAATAA 59.375 47.619 0.00 0.00 0.00 1.40
93 94 2.038820 ACTCCGTCCGTCCCAAAATAAA 59.961 45.455 0.00 0.00 0.00 1.40
94 95 2.417586 CTCCGTCCGTCCCAAAATAAAC 59.582 50.000 0.00 0.00 0.00 2.01
95 96 1.129064 CCGTCCGTCCCAAAATAAACG 59.871 52.381 0.00 0.00 35.01 3.60
96 97 1.799994 CGTCCGTCCCAAAATAAACGT 59.200 47.619 0.00 0.00 33.45 3.99
97 98 2.159801 CGTCCGTCCCAAAATAAACGTC 60.160 50.000 0.00 0.00 33.45 4.34
147 148 9.601217 CGGAGGGAGTATTAAATTATATCCTTG 57.399 37.037 0.00 0.00 0.00 3.61
211 212 7.731054 ACAAAAGATATGACTAGATGAGGGAC 58.269 38.462 0.00 0.00 0.00 4.46
278 279 6.094603 CCCATTTATGCACCATATCTAGCTTC 59.905 42.308 0.00 0.00 0.00 3.86
362 363 5.837979 TCATTTGAATGAAAAGGGTCTTCCA 59.162 36.000 4.02 0.00 42.11 3.53
377 378 3.572255 GTCTTCCAAAATGCAACTGGGTA 59.428 43.478 11.06 1.68 0.00 3.69
516 551 1.350071 TCAATTTGGGCCAACTGCAT 58.650 45.000 20.79 6.94 43.89 3.96
525 612 2.435437 GGGCCAACTGCATGGAAAATAT 59.565 45.455 10.63 0.00 43.54 1.28
526 613 3.118298 GGGCCAACTGCATGGAAAATATT 60.118 43.478 10.63 0.00 43.54 1.28
528 615 4.943093 GGCCAACTGCATGGAAAATATTTT 59.057 37.500 13.24 13.24 43.54 1.82
665 752 5.064707 GCGCAGTCTGATTCTTTTATACCAA 59.935 40.000 0.30 0.00 0.00 3.67
705 792 6.148811 CCCTGTTGTCGAACTTGTAAATATGT 59.851 38.462 0.00 0.00 32.79 2.29
757 844 5.863935 TCACGATTGTATCACAGACAAGAAG 59.136 40.000 0.00 0.00 40.01 2.85
759 846 6.146184 CACGATTGTATCACAGACAAGAAGTT 59.854 38.462 0.00 0.00 40.01 2.66
852 939 3.206150 ACTGTTTCTGCGATTCTTGTGT 58.794 40.909 0.00 0.00 0.00 3.72
892 979 4.090354 CCATCGAAACAAATGTTGTCATGC 59.910 41.667 0.00 0.00 44.59 4.06
893 980 4.298744 TCGAAACAAATGTTGTCATGCA 57.701 36.364 0.00 0.00 44.59 3.96
894 981 4.869215 TCGAAACAAATGTTGTCATGCAT 58.131 34.783 0.00 0.00 44.59 3.96
895 982 4.680567 TCGAAACAAATGTTGTCATGCATG 59.319 37.500 21.07 21.07 44.59 4.06
896 983 4.680567 CGAAACAAATGTTGTCATGCATGA 59.319 37.500 25.42 25.42 44.59 3.07
1210 1299 0.169672 GCATGTTGCTGGTAGTGCTG 59.830 55.000 0.00 0.00 40.96 4.41
1371 1460 0.745845 CCAGGGGCATTTCTCAGTCG 60.746 60.000 0.00 0.00 0.00 4.18
1377 1466 2.369394 GGCATTTCTCAGTCGGGAATT 58.631 47.619 0.00 0.00 0.00 2.17
1490 1579 6.419980 CTATTCTAGCAAGCCATTATCTGC 57.580 41.667 0.00 0.00 0.00 4.26
1562 1660 3.118298 GCAAATACCCCTTCCATGCAAAT 60.118 43.478 0.00 0.00 32.80 2.32
1620 1718 3.565905 AAGCCAAAGCAGAATTTCTCG 57.434 42.857 0.00 0.00 43.56 4.04
1650 1748 0.817634 CTGCAGTTTCCGGTTCACCA 60.818 55.000 5.25 0.00 35.14 4.17
1657 1755 2.350057 TTCCGGTTCACCATCACAAA 57.650 45.000 0.00 0.00 35.14 2.83
1709 1807 7.721399 AGGCCACTCAAATTACCATTCTAATAG 59.279 37.037 5.01 0.00 0.00 1.73
1833 1931 5.652452 AGTAGGAACAATAAAAGGTCATGGC 59.348 40.000 0.00 0.00 0.00 4.40
2019 2117 1.193203 CATGACCACAATATCGCGCTC 59.807 52.381 5.56 0.00 0.00 5.03
2031 2129 2.100631 CGCGCTCGGTTTCTTCCAT 61.101 57.895 5.56 0.00 0.00 3.41
2064 2162 0.610232 AGCCAGGGTTCAAGCATGAC 60.610 55.000 2.08 0.00 34.61 3.06
2166 2264 0.673437 GCTTGGTAAACTGCAAGCCA 59.327 50.000 0.00 0.00 42.80 4.75
2169 2267 2.065899 TGGTAAACTGCAAGCCAACT 57.934 45.000 0.00 0.00 37.60 3.16
2220 2318 1.904287 ATGGCCGTGCAAACTTTCTA 58.096 45.000 0.00 0.00 0.00 2.10
2298 2396 2.995939 CGTCACATACTGCACACTGATT 59.004 45.455 0.00 0.00 0.00 2.57
2493 2591 1.969589 CACGCCCAACCTGGTTACC 60.970 63.158 12.53 0.00 35.17 2.85
2558 2656 3.462982 ACAATGTCGTGAAGCTGTACAA 58.537 40.909 0.00 0.00 0.00 2.41
2559 2657 3.874543 ACAATGTCGTGAAGCTGTACAAA 59.125 39.130 0.00 0.00 0.00 2.83
2607 2705 4.051922 CCGACAAGATAACCTACAGCATC 58.948 47.826 0.00 0.00 0.00 3.91
2796 2894 0.252375 AGGATGGTTTGCAGCCCAAT 60.252 50.000 10.11 0.00 33.66 3.16
2817 2915 1.306296 GCCCACCTGCAATTCCCTA 59.694 57.895 0.00 0.00 0.00 3.53
2832 2930 2.180276 TCCCTACTCAGTGCTTTCCTC 58.820 52.381 0.00 0.00 0.00 3.71
2847 2945 2.550830 TCCTCAAGCTCAACAGGTTC 57.449 50.000 0.00 0.00 38.33 3.62
2940 3038 2.125229 CTCAGCTGCTGCACCGAT 60.125 61.111 24.38 0.00 42.74 4.18
2994 3092 4.832608 GCGATCACCGGACACCCC 62.833 72.222 9.46 0.00 39.04 4.95
3012 3110 1.210931 CGCCCACATGTTCTTGCTG 59.789 57.895 0.00 0.00 0.00 4.41
3207 3305 0.242825 CGCAGAAGAACGTCTACCCA 59.757 55.000 0.00 0.00 0.00 4.51
3480 3578 3.605664 GGCAACACCGGCTGCTTT 61.606 61.111 19.64 0.31 38.65 3.51
3551 3649 1.596464 GCGCATGCATTTGCTCTAGTC 60.596 52.381 19.57 0.00 40.54 2.59
3594 3731 5.232414 GCTTCTTCTGCTAGGTTACGTTATG 59.768 44.000 0.00 0.00 0.00 1.90
3613 3750 9.042008 ACGTTATGTATCATCAGGAATAAACAC 57.958 33.333 0.00 0.00 0.00 3.32
3614 3751 9.261180 CGTTATGTATCATCAGGAATAAACACT 57.739 33.333 0.00 0.00 0.00 3.55
3622 3759 8.635765 TCATCAGGAATAAACACTTTTTAGCT 57.364 30.769 0.00 0.00 0.00 3.32
3623 3760 9.733556 TCATCAGGAATAAACACTTTTTAGCTA 57.266 29.630 0.00 0.00 0.00 3.32
3624 3761 9.994432 CATCAGGAATAAACACTTTTTAGCTAG 57.006 33.333 0.00 0.00 0.00 3.42
3625 3762 8.040716 TCAGGAATAAACACTTTTTAGCTAGC 57.959 34.615 6.62 6.62 0.00 3.42
3626 3763 7.883311 TCAGGAATAAACACTTTTTAGCTAGCT 59.117 33.333 23.12 23.12 0.00 3.32
3627 3764 7.965107 CAGGAATAAACACTTTTTAGCTAGCTG 59.035 37.037 27.68 12.41 0.00 4.24
3651 3794 2.071778 ACAGGTGCAGTTTTGTGGAT 57.928 45.000 0.00 0.00 0.00 3.41
3705 3850 0.883153 TAGTTTCGTCGCCTGTAGCA 59.117 50.000 0.00 0.00 44.04 3.49
3708 3853 0.037697 TTTCGTCGCCTGTAGCATGT 60.038 50.000 0.00 0.00 44.04 3.21
3729 3874 7.113404 GCATGTGTGTGTTAAGAAAATGTAGTG 59.887 37.037 0.00 0.00 0.00 2.74
3731 3876 7.690228 TGTGTGTGTTAAGAAAATGTAGTGAC 58.310 34.615 0.00 0.00 0.00 3.67
3758 3906 7.979537 GGTTGAGTTCTTATGTTTCCAAACTTT 59.020 33.333 3.92 0.00 39.59 2.66
3822 3970 7.307694 TGTTGCATTCTGAATTAGACAATGAC 58.692 34.615 0.00 0.00 34.43 3.06
3840 3996 4.271696 TGACTTATGTTGCTGTAGCTGT 57.728 40.909 5.38 0.00 42.66 4.40
3852 4008 3.623510 GCTGTAGCTGTAAGTTCCAATCC 59.376 47.826 0.00 0.00 38.21 3.01
3870 4026 2.306847 TCCAACCTTCTGGAAAGCAAC 58.693 47.619 0.00 0.00 42.69 4.17
3875 4031 1.135575 CCTTCTGGAAAGCAACGCATC 60.136 52.381 0.00 0.00 34.57 3.91
3955 4128 1.872234 GCTGCTACGATGCGACGAA 60.872 57.895 0.00 0.00 37.03 3.85
3956 4129 1.209275 GCTGCTACGATGCGACGAAT 61.209 55.000 0.00 0.00 37.03 3.34
3957 4130 0.500178 CTGCTACGATGCGACGAATG 59.500 55.000 0.00 0.00 37.03 2.67
3959 4132 0.772926 GCTACGATGCGACGAATGAG 59.227 55.000 0.00 0.00 37.03 2.90
4032 4222 1.996292 TTCATCTGTAGCGAGTGTGC 58.004 50.000 0.00 0.00 0.00 4.57
4054 4244 3.356290 GGACATTTAGGGACTGCATTGT 58.644 45.455 0.00 0.00 41.52 2.71
4179 4374 6.722590 TGTTCTATGTTTCAGTAGACCAGGTA 59.277 38.462 0.00 0.00 0.00 3.08
4285 4500 5.211973 TGCTCAACTAGGATCTTACTCCAT 58.788 41.667 0.00 0.00 37.81 3.41
4286 4501 5.663106 TGCTCAACTAGGATCTTACTCCATT 59.337 40.000 0.00 0.00 37.81 3.16
4287 4502 6.839134 TGCTCAACTAGGATCTTACTCCATTA 59.161 38.462 0.00 0.00 37.81 1.90
4321 4536 4.727655 GCTACAAGACGACGATACAGTTAC 59.272 45.833 0.00 0.00 0.00 2.50
4397 4635 2.828520 AGCAGCTAAGCTACACTCTCAA 59.171 45.455 0.00 0.00 44.50 3.02
4398 4636 3.119173 AGCAGCTAAGCTACACTCTCAAG 60.119 47.826 0.00 0.00 44.50 3.02
4399 4637 3.367910 GCAGCTAAGCTACACTCTCAAGT 60.368 47.826 0.00 0.00 36.40 3.16
4400 4638 4.815269 CAGCTAAGCTACACTCTCAAGTT 58.185 43.478 0.00 0.00 36.40 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.501559 CCAGCATGCGTAAATGAAGAAATG 59.498 41.667 13.01 0.00 31.97 2.32
1 2 4.158394 ACCAGCATGCGTAAATGAAGAAAT 59.842 37.500 13.01 0.00 31.97 2.17
2 3 3.505680 ACCAGCATGCGTAAATGAAGAAA 59.494 39.130 13.01 0.00 31.97 2.52
3 4 3.081061 ACCAGCATGCGTAAATGAAGAA 58.919 40.909 13.01 0.00 31.97 2.52
5 6 4.614555 TTACCAGCATGCGTAAATGAAG 57.385 40.909 13.01 0.00 31.80 3.02
7 8 3.127895 GGTTTACCAGCATGCGTAAATGA 59.872 43.478 24.38 8.47 40.84 2.57
8 9 3.128589 AGGTTTACCAGCATGCGTAAATG 59.871 43.478 24.38 13.56 40.84 2.32
32 33 5.991328 AAATGTATGTCGGCAACTCATAG 57.009 39.130 0.00 0.00 33.83 2.23
73 74 2.389962 TTATTTTGGGACGGACGGAG 57.610 50.000 0.00 0.00 0.00 4.63
74 75 2.425539 GTTTATTTTGGGACGGACGGA 58.574 47.619 0.00 0.00 0.00 4.69
75 76 1.129064 CGTTTATTTTGGGACGGACGG 59.871 52.381 0.00 0.00 32.29 4.79
76 77 1.799994 ACGTTTATTTTGGGACGGACG 59.200 47.619 0.00 0.00 39.63 4.79
77 78 2.807392 TGACGTTTATTTTGGGACGGAC 59.193 45.455 0.00 0.00 39.63 4.79
78 79 3.123157 TGACGTTTATTTTGGGACGGA 57.877 42.857 0.00 0.00 39.63 4.69
79 80 3.900388 TTGACGTTTATTTTGGGACGG 57.100 42.857 0.00 0.00 39.63 4.79
80 81 5.037015 TGATTGACGTTTATTTTGGGACG 57.963 39.130 0.00 0.00 41.00 4.79
81 82 4.857037 GCTGATTGACGTTTATTTTGGGAC 59.143 41.667 0.00 0.00 0.00 4.46
82 83 4.378978 CGCTGATTGACGTTTATTTTGGGA 60.379 41.667 0.00 0.00 0.00 4.37
83 84 3.851403 CGCTGATTGACGTTTATTTTGGG 59.149 43.478 0.00 0.00 0.00 4.12
84 85 4.553429 GTCGCTGATTGACGTTTATTTTGG 59.447 41.667 0.00 0.00 0.00 3.28
85 86 5.058008 GTGTCGCTGATTGACGTTTATTTTG 59.942 40.000 0.00 0.00 39.22 2.44
86 87 5.049680 AGTGTCGCTGATTGACGTTTATTTT 60.050 36.000 0.00 0.00 39.22 1.82
87 88 4.451096 AGTGTCGCTGATTGACGTTTATTT 59.549 37.500 0.00 0.00 39.22 1.40
88 89 3.994392 AGTGTCGCTGATTGACGTTTATT 59.006 39.130 0.00 0.00 39.22 1.40
89 90 3.585862 AGTGTCGCTGATTGACGTTTAT 58.414 40.909 0.00 0.00 39.22 1.40
90 91 3.021269 AGTGTCGCTGATTGACGTTTA 57.979 42.857 0.00 0.00 39.22 2.01
91 92 1.865865 AGTGTCGCTGATTGACGTTT 58.134 45.000 0.00 0.00 39.22 3.60
92 93 1.865865 AAGTGTCGCTGATTGACGTT 58.134 45.000 0.00 0.00 39.22 3.99
93 94 2.717580 TAAGTGTCGCTGATTGACGT 57.282 45.000 0.00 0.00 39.22 4.34
94 95 4.584029 AAATAAGTGTCGCTGATTGACG 57.416 40.909 0.00 0.00 39.22 4.35
95 96 5.088739 CCAAAATAAGTGTCGCTGATTGAC 58.911 41.667 0.00 0.00 36.88 3.18
96 97 4.155826 CCCAAAATAAGTGTCGCTGATTGA 59.844 41.667 0.00 0.00 28.75 2.57
97 98 4.155826 TCCCAAAATAAGTGTCGCTGATTG 59.844 41.667 0.00 0.00 28.75 2.67
147 148 9.767684 CGAGAGAGAATGATATTATGTACTGTC 57.232 37.037 0.00 0.00 0.00 3.51
211 212 2.084610 TGACTCCTTTCATGTGCTCG 57.915 50.000 0.00 0.00 0.00 5.03
325 326 9.932207 TTTCATTCAAATGAGAAGCATAACAAT 57.068 25.926 5.63 0.00 45.35 2.71
326 327 9.761504 TTTTCATTCAAATGAGAAGCATAACAA 57.238 25.926 5.63 0.00 45.35 2.83
350 351 3.711190 AGTTGCATTTTGGAAGACCCTTT 59.289 39.130 0.00 0.00 35.38 3.11
362 363 4.622260 ATTGCTTACCCAGTTGCATTTT 57.378 36.364 0.00 0.00 35.27 1.82
437 471 7.930865 GCAGTTGGCCCAAATTGAATATATAAA 59.069 33.333 12.13 0.00 36.11 1.40
438 472 7.070447 TGCAGTTGGCCCAAATTGAATATATAA 59.930 33.333 12.13 0.00 43.89 0.98
439 473 6.552725 TGCAGTTGGCCCAAATTGAATATATA 59.447 34.615 12.13 0.00 43.89 0.86
440 474 5.366186 TGCAGTTGGCCCAAATTGAATATAT 59.634 36.000 12.13 0.00 43.89 0.86
489 523 6.275335 CAGTTGGCCCAAATTGAATATACAG 58.725 40.000 0.00 0.00 0.00 2.74
593 680 7.280876 CACTGCATAATGACCAAGTAATGTAGT 59.719 37.037 0.00 0.00 39.72 2.73
716 803 4.375272 TCGTGACCGTTAACCAATAAACA 58.625 39.130 0.00 0.00 35.01 2.83
757 844 1.123655 GAACGCAGAAAGCTTGCAAC 58.876 50.000 7.33 0.00 42.61 4.17
759 846 0.029300 GTGAACGCAGAAAGCTTGCA 59.971 50.000 7.33 0.00 42.61 4.08
801 888 6.127619 GCCACAAGGAAAAATAAGCTACAGAT 60.128 38.462 0.00 0.00 36.89 2.90
1172 1261 2.508887 GCGCAGACAGAGGCTGAG 60.509 66.667 0.30 1.08 35.39 3.35
1181 1270 2.948323 CAACATGCTGCGCAGACA 59.052 55.556 40.21 33.22 43.65 3.41
1222 1311 4.397417 AGGAATGACATTAACAGCTTGAGC 59.603 41.667 0.00 0.00 42.49 4.26
1371 1460 1.000396 ACCAGCTCCTGCAATTCCC 60.000 57.895 0.00 0.00 42.74 3.97
1377 1466 1.567357 TATACACACCAGCTCCTGCA 58.433 50.000 0.00 0.00 42.74 4.41
1490 1579 4.878397 CCTTGTTATTAGAAGACTGGCCAG 59.122 45.833 31.60 31.60 0.00 4.85
1650 1748 6.855763 TGCCTTTGATTCCTTATTTGTGAT 57.144 33.333 0.00 0.00 0.00 3.06
1657 1755 7.529555 TGATTAGGATGCCTTTGATTCCTTAT 58.470 34.615 0.00 0.00 39.33 1.73
1709 1807 3.209410 CTGCCATCTGAATTGGGACTAC 58.791 50.000 0.00 0.00 34.66 2.73
1851 1949 5.122239 CCGCAATGACTTCAGTGATCTTAAA 59.878 40.000 10.74 0.00 43.86 1.52
2019 2117 3.857010 GCTTCAACCAATGGAAGAAACCG 60.857 47.826 6.16 0.00 42.39 4.44
2031 2129 3.294493 GGCTGCCGCTTCAACCAA 61.294 61.111 1.35 0.00 36.09 3.67
2064 2162 1.145377 GGTGGTGTAGGTATGGCCG 59.855 63.158 0.00 0.00 43.70 6.13
2166 2264 4.415881 TCTGTTGTATGTCACCACAGTT 57.584 40.909 8.06 0.00 46.27 3.16
2169 2267 8.097662 TGTATTATTCTGTTGTATGTCACCACA 58.902 33.333 0.00 0.00 36.78 4.17
2220 2318 3.056465 CGAAGACCTTAACAGCCTCTCTT 60.056 47.826 0.00 0.00 0.00 2.85
2298 2396 4.234550 ACCCTGACTTAGCATGGATATCA 58.765 43.478 4.83 0.00 0.00 2.15
2493 2591 4.754618 TGCAGGGCGATTATTATGTTGTAG 59.245 41.667 0.00 0.00 0.00 2.74
2607 2705 1.001974 TGACCAAGAACCTCCATGACG 59.998 52.381 0.00 0.00 0.00 4.35
2736 2834 1.393539 CCTAACGCCTTGTCGACATTG 59.606 52.381 20.80 14.36 0.00 2.82
2796 2894 1.907807 GGAATTGCAGGTGGGCACA 60.908 57.895 0.00 0.00 44.86 4.57
2832 2930 1.202806 TCCTGGAACCTGTTGAGCTTG 60.203 52.381 0.00 0.00 0.00 4.01
2940 3038 2.515290 CCCATCTGCGCATGAGCA 60.515 61.111 23.08 23.08 45.96 4.26
2946 3044 2.111669 CATAGCCCCATCTGCGCA 59.888 61.111 10.98 10.98 0.00 6.09
2994 3092 1.210931 CAGCAAGAACATGTGGGCG 59.789 57.895 0.00 0.00 0.00 6.13
3332 3430 2.937959 GATCCTCTCGGGGCAGGAGT 62.938 65.000 0.00 0.00 42.28 3.85
3551 3649 3.891049 AGCAGGCCCTAATTAAGAACTG 58.109 45.455 0.00 0.00 0.00 3.16
3613 3750 5.645497 ACCTGTTCATCAGCTAGCTAAAAAG 59.355 40.000 18.86 12.99 42.38 2.27
3614 3751 5.412594 CACCTGTTCATCAGCTAGCTAAAAA 59.587 40.000 18.86 6.91 42.38 1.94
3618 3755 2.159043 GCACCTGTTCATCAGCTAGCTA 60.159 50.000 18.86 6.64 42.38 3.32
3619 3756 1.406614 GCACCTGTTCATCAGCTAGCT 60.407 52.381 12.68 12.68 42.38 3.32
3620 3757 1.012841 GCACCTGTTCATCAGCTAGC 58.987 55.000 6.62 6.62 42.38 3.42
3621 3758 2.277969 CTGCACCTGTTCATCAGCTAG 58.722 52.381 0.00 0.00 42.38 3.42
3622 3759 1.625315 ACTGCACCTGTTCATCAGCTA 59.375 47.619 0.00 0.00 42.38 3.32
3623 3760 0.399454 ACTGCACCTGTTCATCAGCT 59.601 50.000 0.00 0.00 42.38 4.24
3624 3761 1.242076 AACTGCACCTGTTCATCAGC 58.758 50.000 0.00 0.00 42.38 4.26
3625 3762 3.067180 ACAAAACTGCACCTGTTCATCAG 59.933 43.478 0.00 0.00 43.27 2.90
3626 3763 3.023119 ACAAAACTGCACCTGTTCATCA 58.977 40.909 0.00 0.00 0.00 3.07
3627 3764 3.374745 CACAAAACTGCACCTGTTCATC 58.625 45.455 0.00 0.00 0.00 2.92
3651 3794 5.879763 TCCTTCATCAAAGAGAATGGTTGA 58.120 37.500 0.00 0.00 37.12 3.18
3705 3850 8.342634 GTCACTACATTTTCTTAACACACACAT 58.657 33.333 0.00 0.00 0.00 3.21
3708 3853 6.018588 CCGTCACTACATTTTCTTAACACACA 60.019 38.462 0.00 0.00 0.00 3.72
3729 3874 4.753107 TGGAAACATAAGAACTCAACCGTC 59.247 41.667 0.00 0.00 33.40 4.79
3731 3876 5.682943 TTGGAAACATAAGAACTCAACCG 57.317 39.130 0.00 0.00 42.32 4.44
3758 3906 8.797350 ATGTTCTCATCACATCACAGATAAAA 57.203 30.769 0.00 0.00 27.99 1.52
3822 3970 6.183360 GGAACTTACAGCTACAGCAACATAAG 60.183 42.308 3.70 7.80 45.16 1.73
3840 3996 4.352595 TCCAGAAGGTTGGATTGGAACTTA 59.647 41.667 0.00 0.00 42.24 2.24
3852 4008 1.600413 GCGTTGCTTTCCAGAAGGTTG 60.600 52.381 0.00 0.00 35.89 3.77
3870 4026 1.645034 ACAATCAGAAGACCGATGCG 58.355 50.000 0.00 0.00 0.00 4.73
3875 4031 3.659786 TGGTGTAACAATCAGAAGACCG 58.340 45.455 0.00 0.00 39.98 4.79
3955 4128 5.886474 TCAGAAAGGTACATCGACTACTCAT 59.114 40.000 0.00 0.00 0.00 2.90
3956 4129 5.250982 TCAGAAAGGTACATCGACTACTCA 58.749 41.667 0.00 0.00 0.00 3.41
3957 4130 5.814764 TCAGAAAGGTACATCGACTACTC 57.185 43.478 0.00 0.00 0.00 2.59
3959 4132 6.797454 AGATTCAGAAAGGTACATCGACTAC 58.203 40.000 0.00 0.00 0.00 2.73
4032 4222 2.332063 ATGCAGTCCCTAAATGTCCG 57.668 50.000 0.00 0.00 0.00 4.79
4179 4374 3.423539 TTGCATTTCCTGAGCTACAGT 57.576 42.857 10.86 0.00 44.40 3.55
4213 4428 9.935241 GGCAGTAAGAATCAGAAGATCAATATA 57.065 33.333 0.00 0.00 31.90 0.86
4285 4500 5.462729 TCGTCTTGTAGCGACAATTTTGTAA 59.537 36.000 12.99 0.00 44.53 2.41
4286 4501 4.983538 TCGTCTTGTAGCGACAATTTTGTA 59.016 37.500 12.99 0.00 44.53 2.41
4287 4502 3.805422 TCGTCTTGTAGCGACAATTTTGT 59.195 39.130 12.99 0.00 44.53 2.83
4321 4536 7.404985 CAAAGATAACCAAGATTCACATCGAG 58.595 38.462 0.00 0.00 34.17 4.04
4397 4635 6.602009 ACTGGCTGAGTAACTTTGTAAAAACT 59.398 34.615 0.00 0.00 30.86 2.66
4398 4636 6.792326 ACTGGCTGAGTAACTTTGTAAAAAC 58.208 36.000 0.00 0.00 30.86 2.43
4399 4637 8.508883 TTACTGGCTGAGTAACTTTGTAAAAA 57.491 30.769 0.00 0.00 41.42 1.94
4400 4638 7.988599 TCTTACTGGCTGAGTAACTTTGTAAAA 59.011 33.333 0.00 0.00 41.42 1.52
4412 4652 6.351456 GGATTCTTAGTTCTTACTGGCTGAGT 60.351 42.308 0.00 0.00 38.88 3.41
4413 4653 6.045955 GGATTCTTAGTTCTTACTGGCTGAG 58.954 44.000 0.00 0.00 35.78 3.35


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

AutoCloner maintained by Alex Coulton.