Multiple sequence alignment - TraesCS1A01G196100

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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 TraesCS1A01G196100 chr1A 100.000 6521 0 0 1 6521 354294106 354300626 0.000000e+00 12043.0
1 TraesCS1A01G196100 chr1D 97.576 6354 116 15 194 6521 282280792 282287133 0.000000e+00 10846.0
2 TraesCS1A01G196100 chr1B 97.646 3228 68 3 2711 5934 383793943 383797166 0.000000e+00 5533.0
3 TraesCS1A01G196100 chr1B 95.664 2260 59 12 235 2474 383791702 383793942 0.000000e+00 3594.0
4 TraesCS1A01G196100 chr1B 92.334 587 37 6 5939 6521 383797217 383797799 0.000000e+00 828.0
5 TraesCS1A01G196100 chr1B 98.477 197 3 0 1 197 661058330 661058134 1.350000e-91 348.0
6 TraesCS1A01G196100 chr1B 79.752 242 38 4 2471 2707 178891255 178891020 1.450000e-36 165.0
7 TraesCS1A01G196100 chr1B 93.878 98 6 0 194 291 144273398 144273495 1.460000e-31 148.0
8 TraesCS1A01G196100 chr1B 98.246 57 1 0 194 250 383791630 383791686 4.160000e-17 100.0
9 TraesCS1A01G196100 chr7D 77.254 954 194 19 3764 4704 14882075 14881132 7.440000e-149 538.0
10 TraesCS1A01G196100 chr7D 89.412 85 6 3 2594 2676 11258137 11258220 3.220000e-18 104.0
11 TraesCS1A01G196100 chr7A 77.044 954 196 19 3764 4704 14191151 14190208 1.610000e-145 527.0
12 TraesCS1A01G196100 chr7A 99.492 197 1 0 1 197 17392413 17392609 6.220000e-95 359.0
13 TraesCS1A01G196100 chr7A 94.898 98 5 0 194 291 113109445 113109348 3.150000e-33 154.0
14 TraesCS1A01G196100 chr4A 76.730 954 199 19 3761 4701 721384195 721385138 1.620000e-140 510.0
15 TraesCS1A01G196100 chr3B 100.000 197 0 0 1 197 144181691 144181887 1.340000e-96 364.0
16 TraesCS1A01G196100 chr3B 87.264 212 21 5 2507 2714 97546219 97546010 3.040000e-58 237.0
17 TraesCS1A01G196100 chr3B 82.927 246 30 4 2469 2711 405231015 405230779 1.840000e-50 211.0
18 TraesCS1A01G196100 chr3B 82.383 193 27 7 4 194 448572310 448572497 1.880000e-35 161.0
19 TraesCS1A01G196100 chr3B 93.878 98 5 1 194 291 799548613 799548709 5.270000e-31 147.0
20 TraesCS1A01G196100 chr3B 94.366 71 4 0 197 267 357046862 357046932 6.910000e-20 110.0
21 TraesCS1A01G196100 chr2B 100.000 197 0 0 1 197 628782 628978 1.340000e-96 364.0
22 TraesCS1A01G196100 chr2B 89.333 75 4 3 2639 2711 90305619 90305691 2.500000e-14 91.6
23 TraesCS1A01G196100 chr2B 88.000 75 5 3 2639 2711 426479175 426479103 1.160000e-12 86.1
24 TraesCS1A01G196100 chr2B 92.500 40 1 2 2471 2509 225571632 225571594 1.000000e-03 56.5
25 TraesCS1A01G196100 chr2D 95.855 193 6 2 6 197 70019029 70018838 1.770000e-80 311.0
26 TraesCS1A01G196100 chr3D 84.677 248 31 5 2469 2711 314620027 314620272 2.350000e-59 241.0
27 TraesCS1A01G196100 chr3D 94.595 37 2 0 2685 2721 85407711 85407675 2.540000e-04 58.4
28 TraesCS1A01G196100 chr7B 89.286 196 14 4 4 195 690261571 690261763 8.450000e-59 239.0
29 TraesCS1A01G196100 chr7B 97.368 38 1 0 2462 2499 302771520 302771557 1.520000e-06 65.8
30 TraesCS1A01G196100 chr4D 81.928 249 36 6 2471 2712 497279389 497279635 1.110000e-47 202.0
31 TraesCS1A01G196100 chr4B 87.719 171 19 2 2507 2675 5526025 5525855 1.430000e-46 198.0
32 TraesCS1A01G196100 chr4B 81.865 193 28 7 4 194 393403795 393403608 8.750000e-34 156.0
33 TraesCS1A01G196100 chr4B 92.308 39 3 0 2471 2509 185164511 185164549 1.000000e-03 56.5
34 TraesCS1A01G196100 chr6B 81.865 193 28 7 4 194 227259327 227259140 8.750000e-34 156.0
35 TraesCS1A01G196100 chr6B 94.898 98 5 0 194 291 708552878 708552781 3.150000e-33 154.0
36 TraesCS1A01G196100 chr5B 93.878 98 6 0 194 291 416465245 416465342 1.460000e-31 148.0
37 TraesCS1A01G196100 chr5B 92.857 98 7 0 194 291 421517666 421517763 6.820000e-30 143.0
38 TraesCS1A01G196100 chr5D 97.436 39 0 1 2461 2499 242650433 242650396 1.520000e-06 65.8
39 TraesCS1A01G196100 chr6D 92.683 41 2 1 2460 2499 347716127 347716087 2.540000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G196100 chr1A 354294106 354300626 6520 False 12043.00 12043 100.0000 1 6521 1 chr1A.!!$F1 6520
1 TraesCS1A01G196100 chr1D 282280792 282287133 6341 False 10846.00 10846 97.5760 194 6521 1 chr1D.!!$F1 6327
2 TraesCS1A01G196100 chr1B 383791630 383797799 6169 False 2513.75 5533 95.9725 194 6521 4 chr1B.!!$F2 6327
3 TraesCS1A01G196100 chr7D 14881132 14882075 943 True 538.00 538 77.2540 3764 4704 1 chr7D.!!$R1 940
4 TraesCS1A01G196100 chr7A 14190208 14191151 943 True 527.00 527 77.0440 3764 4704 1 chr7A.!!$R1 940
5 TraesCS1A01G196100 chr4A 721384195 721385138 943 False 510.00 510 76.7300 3761 4701 1 chr4A.!!$F1 940

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
574 618 0.320683 CGCACCACAACAGATGAGGA 60.321 55.000 0.95 0.00 41.91 3.71 F
577 621 0.326264 ACCACAACAGATGAGGAGGC 59.674 55.000 0.95 0.00 41.91 4.70 F
1968 2025 0.546598 AGTATGCTGGCTTACCCACC 59.453 55.000 12.78 0.00 39.18 4.61 F
3258 3315 0.251165 ACATTGAACCCAGGAACCCG 60.251 55.000 0.00 0.00 0.00 5.28 F
3553 3610 1.523758 GCCCGGTACATGGATTCATC 58.476 55.000 0.00 0.00 0.00 2.92 F
3622 3679 3.614176 ACTGATTTGATGACGATCGTGTG 59.386 43.478 28.12 3.01 0.00 3.82 F
3633 3690 4.034626 TGACGATCGTGTGAACACAATTTT 59.965 37.500 28.12 0.00 46.75 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2443 1.336240 GCAAGTGTGGGATCTTTGCAC 60.336 52.381 2.93 0.00 0.00 4.57 R
2510 2567 7.707624 AATTGATGGTCAAAGCTAAATCTCA 57.292 32.000 0.00 0.00 40.12 3.27 R
3553 3610 0.371301 CGTGCATGATCTTGTGACGG 59.629 55.000 19.01 7.96 0.00 4.79 R
5212 5275 3.033909 TGGTGAGAGGTGGTATCATCAG 58.966 50.000 0.00 0.00 32.35 2.90 R
5475 5538 1.242076 ACTGTTGATTGGCAGCTGTC 58.758 50.000 12.53 12.53 35.55 3.51 R
5476 5539 1.696063 AACTGTTGATTGGCAGCTGT 58.304 45.000 16.64 0.00 40.58 4.40 R
5776 5843 4.461431 AGAATGACATTCAGCTCAAATGCA 59.539 37.500 26.05 14.05 41.71 3.96 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
17 18 2.654877 GTCGACCAGGAAGCCGAA 59.345 61.111 3.51 0.00 32.60 4.30
18 19 1.446272 GTCGACCAGGAAGCCGAAG 60.446 63.158 3.51 0.00 32.60 3.79
19 20 2.815647 CGACCAGGAAGCCGAAGC 60.816 66.667 0.00 0.00 40.32 3.86
20 21 2.436824 GACCAGGAAGCCGAAGCC 60.437 66.667 0.00 0.00 41.25 4.35
21 22 3.249189 ACCAGGAAGCCGAAGCCA 61.249 61.111 0.00 0.00 41.25 4.75
22 23 2.437359 CCAGGAAGCCGAAGCCAG 60.437 66.667 0.00 0.00 41.25 4.85
23 24 2.437359 CAGGAAGCCGAAGCCAGG 60.437 66.667 0.00 0.00 41.25 4.45
32 33 4.742201 GAAGCCAGGCGCGTCAGA 62.742 66.667 15.58 0.00 44.49 3.27
33 34 4.087892 AAGCCAGGCGCGTCAGAT 62.088 61.111 15.58 0.00 44.76 2.90
34 35 4.521062 AGCCAGGCGCGTCAGATC 62.521 66.667 15.58 0.00 44.76 2.75
37 38 4.193334 CAGGCGCGTCAGATCGGA 62.193 66.667 15.58 0.00 0.00 4.55
38 39 4.194720 AGGCGCGTCAGATCGGAC 62.195 66.667 15.58 15.18 34.42 4.79
39 40 4.492160 GGCGCGTCAGATCGGACA 62.492 66.667 23.07 0.00 37.66 4.02
40 41 2.951745 GCGCGTCAGATCGGACAG 60.952 66.667 23.07 17.20 37.66 3.51
41 42 2.791927 CGCGTCAGATCGGACAGA 59.208 61.111 23.07 0.00 37.66 3.41
42 43 1.356979 CGCGTCAGATCGGACAGAT 59.643 57.895 23.07 0.00 43.51 2.90
63 64 3.694538 GGCACCAACACCATGGGC 61.695 66.667 18.09 7.55 45.18 5.36
64 65 4.054825 GCACCAACACCATGGGCG 62.055 66.667 18.09 9.42 45.18 6.13
65 66 2.282110 CACCAACACCATGGGCGA 60.282 61.111 18.09 0.00 45.18 5.54
66 67 1.678635 CACCAACACCATGGGCGAT 60.679 57.895 18.09 0.00 45.18 4.58
67 68 1.678635 ACCAACACCATGGGCGATG 60.679 57.895 18.09 11.36 45.18 3.84
68 69 2.491152 CAACACCATGGGCGATGC 59.509 61.111 18.09 0.00 0.00 3.91
69 70 3.133464 AACACCATGGGCGATGCG 61.133 61.111 18.09 0.06 0.00 4.73
81 82 3.869272 GATGCGCAGGCGACCAAG 61.869 66.667 18.32 0.00 44.10 3.61
82 83 4.393155 ATGCGCAGGCGACCAAGA 62.393 61.111 18.32 0.00 44.10 3.02
84 85 4.742201 GCGCAGGCGACCAAGAGA 62.742 66.667 18.96 0.00 42.83 3.10
85 86 2.811317 CGCAGGCGACCAAGAGAC 60.811 66.667 8.15 0.00 42.83 3.36
86 87 2.435059 GCAGGCGACCAAGAGACC 60.435 66.667 0.00 0.00 0.00 3.85
87 88 3.059982 CAGGCGACCAAGAGACCA 58.940 61.111 0.00 0.00 0.00 4.02
88 89 1.374758 CAGGCGACCAAGAGACCAC 60.375 63.158 0.00 0.00 0.00 4.16
89 90 1.534235 AGGCGACCAAGAGACCACT 60.534 57.895 0.00 0.00 0.00 4.00
90 91 1.079750 GGCGACCAAGAGACCACTC 60.080 63.158 0.00 0.00 42.90 3.51
91 92 1.444553 GCGACCAAGAGACCACTCG 60.445 63.158 0.00 0.00 46.64 4.18
92 93 1.444553 CGACCAAGAGACCACTCGC 60.445 63.158 0.00 0.00 46.64 5.03
93 94 1.079750 GACCAAGAGACCACTCGCC 60.080 63.158 0.00 0.00 46.64 5.54
94 95 2.125912 CCAAGAGACCACTCGCCG 60.126 66.667 0.00 0.00 46.64 6.46
95 96 2.651361 CAAGAGACCACTCGCCGT 59.349 61.111 0.00 0.00 46.64 5.68
96 97 1.734477 CAAGAGACCACTCGCCGTG 60.734 63.158 0.00 0.00 46.64 4.94
97 98 2.201022 AAGAGACCACTCGCCGTGT 61.201 57.895 4.40 0.00 46.64 4.49
98 99 2.126424 GAGACCACTCGCCGTGTC 60.126 66.667 0.00 0.00 42.20 3.67
99 100 3.628280 GAGACCACTCGCCGTGTCC 62.628 68.421 0.00 0.00 42.20 4.02
129 130 2.785258 GCGCCAGCGTAGAAAAGG 59.215 61.111 14.22 0.00 42.09 3.11
130 131 2.033194 GCGCCAGCGTAGAAAAGGT 61.033 57.895 14.22 0.00 42.09 3.50
131 132 1.967597 GCGCCAGCGTAGAAAAGGTC 61.968 60.000 14.22 0.00 42.09 3.85
132 133 1.359459 CGCCAGCGTAGAAAAGGTCC 61.359 60.000 3.35 0.00 34.35 4.46
133 134 1.025113 GCCAGCGTAGAAAAGGTCCC 61.025 60.000 0.00 0.00 0.00 4.46
134 135 0.392595 CCAGCGTAGAAAAGGTCCCC 60.393 60.000 0.00 0.00 0.00 4.81
135 136 0.739813 CAGCGTAGAAAAGGTCCCCG 60.740 60.000 0.00 0.00 0.00 5.73
136 137 2.104859 GCGTAGAAAAGGTCCCCGC 61.105 63.158 0.00 0.00 38.28 6.13
137 138 1.449070 CGTAGAAAAGGTCCCCGCC 60.449 63.158 0.00 0.00 0.00 6.13
138 139 1.449070 GTAGAAAAGGTCCCCGCCG 60.449 63.158 0.00 0.00 0.00 6.46
139 140 3.319441 TAGAAAAGGTCCCCGCCGC 62.319 63.158 0.00 0.00 0.00 6.53
246 278 6.823689 ACCAAGTTGCAGTAATAAGGATAGTG 59.176 38.462 0.00 0.00 0.00 2.74
256 288 7.016914 AGTAATAAGGATAGTGGTGGCAGATA 58.983 38.462 0.00 0.00 0.00 1.98
324 364 8.463930 AAGTTATAATTAAGCAAGCAGGCATA 57.536 30.769 2.37 0.00 35.83 3.14
464 507 0.818296 ACCTCTTCGATTCCACTCCG 59.182 55.000 0.00 0.00 0.00 4.63
506 549 2.228545 TTCAAATACAGCCATGGCCA 57.771 45.000 33.14 18.95 43.17 5.36
520 563 3.134127 GCCATGGCCGTGAACCTC 61.134 66.667 27.24 6.01 34.56 3.85
522 565 2.438434 CATGGCCGTGAACCTCCC 60.438 66.667 21.08 0.00 0.00 4.30
523 566 3.728373 ATGGCCGTGAACCTCCCC 61.728 66.667 0.00 0.00 0.00 4.81
525 568 4.410400 GGCCGTGAACCTCCCCAG 62.410 72.222 0.00 0.00 0.00 4.45
526 569 3.637273 GCCGTGAACCTCCCCAGT 61.637 66.667 0.00 0.00 0.00 4.00
527 570 2.288025 GCCGTGAACCTCCCCAGTA 61.288 63.158 0.00 0.00 0.00 2.74
528 571 1.595357 CCGTGAACCTCCCCAGTAC 59.405 63.158 0.00 0.00 0.00 2.73
530 573 0.903454 CGTGAACCTCCCCAGTACCT 60.903 60.000 0.00 0.00 0.00 3.08
533 576 1.982958 TGAACCTCCCCAGTACCTTTC 59.017 52.381 0.00 0.00 0.00 2.62
534 577 2.267192 GAACCTCCCCAGTACCTTTCT 58.733 52.381 0.00 0.00 0.00 2.52
574 618 0.320683 CGCACCACAACAGATGAGGA 60.321 55.000 0.95 0.00 41.91 3.71
577 621 0.326264 ACCACAACAGATGAGGAGGC 59.674 55.000 0.95 0.00 41.91 4.70
602 646 4.414677 AGGTAACCTTCCTTTACTCTCGT 58.585 43.478 0.00 0.00 31.26 4.18
617 661 5.012328 ACTCTCGTTCTACATTCCCAATC 57.988 43.478 0.00 0.00 0.00 2.67
618 662 4.466370 ACTCTCGTTCTACATTCCCAATCA 59.534 41.667 0.00 0.00 0.00 2.57
664 708 9.029368 CCCTCTATGTAATCTACTGATTCATCA 57.971 37.037 0.00 0.00 41.55 3.07
680 724 8.066612 TGATTCATCATTTTCCTTTCCTTACC 57.933 34.615 0.00 0.00 0.00 2.85
798 843 1.139520 CCCAGGCTGCGTTTATTGC 59.860 57.895 9.56 0.00 0.00 3.56
833 878 5.361427 TGCCGATTACGATTTGATTTCCTA 58.639 37.500 0.00 0.00 42.66 2.94
945 1000 3.562973 CAGCCACAAGATAACAGCATAGG 59.437 47.826 0.00 0.00 0.00 2.57
968 1023 3.919216 ACAACATCACGAGGAAGAAGAG 58.081 45.455 0.00 0.00 0.00 2.85
969 1024 3.322254 ACAACATCACGAGGAAGAAGAGT 59.678 43.478 0.00 0.00 0.00 3.24
970 1025 3.859411 ACATCACGAGGAAGAAGAGTC 57.141 47.619 0.00 0.00 0.00 3.36
971 1026 3.157881 ACATCACGAGGAAGAAGAGTCA 58.842 45.455 0.00 0.00 0.00 3.41
972 1027 3.574396 ACATCACGAGGAAGAAGAGTCAA 59.426 43.478 0.00 0.00 0.00 3.18
1116 1173 3.733960 GTCTTTGGGCGGCGAACC 61.734 66.667 12.98 13.13 0.00 3.62
1215 1272 2.591753 CACATCCCCATGACGCCT 59.408 61.111 0.00 0.00 33.72 5.52
1260 1317 3.936203 ACCAAGGCCGACGAGCAA 61.936 61.111 0.00 0.00 0.00 3.91
1910 1967 1.014352 GCCATTACTGTTACCTGCCG 58.986 55.000 0.00 0.00 0.00 5.69
1968 2025 0.546598 AGTATGCTGGCTTACCCACC 59.453 55.000 12.78 0.00 39.18 4.61
2089 2146 6.547880 TGGTGTTAAAAAGTGATTAGAGCCAA 59.452 34.615 0.00 0.00 0.00 4.52
2247 2304 7.966812 TCAGCCAAAGATCATAGTATGTGTAT 58.033 34.615 9.94 0.00 0.00 2.29
2270 2327 4.130118 AGACTAGTCAAAAAGTGTGCCTG 58.870 43.478 24.44 0.00 0.00 4.85
2355 2412 7.877003 TGTGTTCTCTGTCACAAAACTTTAAA 58.123 30.769 0.00 0.00 40.81 1.52
2386 2443 8.044060 TCCACATATAGCAGTTGAAAAGAAAG 57.956 34.615 0.00 0.00 0.00 2.62
2675 2732 9.810545 TTTATGGTCAAACTTAAACCTCAAAAG 57.189 29.630 0.00 0.00 34.05 2.27
2721 2778 2.301870 TGGAGGGAGTACATGACAACAC 59.698 50.000 0.00 0.00 0.00 3.32
3258 3315 0.251165 ACATTGAACCCAGGAACCCG 60.251 55.000 0.00 0.00 0.00 5.28
3309 3366 5.012893 CCTTTCAAGAATAAGGTGAAGGCT 58.987 41.667 0.00 0.00 36.88 4.58
3351 3408 4.343526 AGAAGGATCAAGCGTGAGTATGAT 59.656 41.667 8.63 0.00 37.14 2.45
3553 3610 1.523758 GCCCGGTACATGGATTCATC 58.476 55.000 0.00 0.00 0.00 2.92
3619 3676 4.098044 AGGTACTGATTTGATGACGATCGT 59.902 41.667 22.97 22.97 37.18 3.73
3622 3679 3.614176 ACTGATTTGATGACGATCGTGTG 59.386 43.478 28.12 3.01 0.00 3.82
3633 3690 4.034626 TGACGATCGTGTGAACACAATTTT 59.965 37.500 28.12 0.00 46.75 1.82
5212 5275 6.514705 ACTCTACGAAGTAAAGTGGACTTCAC 60.515 42.308 14.09 0.00 43.39 3.18
5476 5539 3.280197 TTGCAATCAATCCTCCATCGA 57.720 42.857 0.00 0.00 0.00 3.59
6120 6239 8.600625 TGCATAGTTCAAACTTATGTAACGATC 58.399 33.333 0.00 0.00 40.37 3.69
6205 6324 8.092687 GTGGAGAAACAACTAAAGTATACCTGA 58.907 37.037 0.00 0.00 0.00 3.86
6389 6508 3.529533 CTGCATCTGAGTAGAACCCAAG 58.470 50.000 0.00 0.00 36.32 3.61
6400 6519 6.849697 TGAGTAGAACCCAAGGTTATGGATAT 59.150 38.462 3.94 0.00 46.95 1.63
6504 6623 1.877637 AATTTTTGTTGGGCGCTTCC 58.122 45.000 7.64 0.33 0.00 3.46
6506 6625 0.537188 TTTTTGTTGGGCGCTTCCAA 59.463 45.000 13.35 13.35 43.82 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.446272 CTTCGGCTTCCTGGTCGAC 60.446 63.158 7.13 7.13 43.09 4.20
1 2 2.970639 CTTCGGCTTCCTGGTCGA 59.029 61.111 0.00 0.00 41.67 4.20
2 3 2.815647 GCTTCGGCTTCCTGGTCG 60.816 66.667 0.00 0.00 38.08 4.79
3 4 2.436824 GGCTTCGGCTTCCTGGTC 60.437 66.667 0.00 0.00 41.44 4.02
4 5 3.249189 TGGCTTCGGCTTCCTGGT 61.249 61.111 0.00 0.00 41.44 4.00
5 6 2.437359 CTGGCTTCGGCTTCCTGG 60.437 66.667 0.00 0.00 41.44 4.45
6 7 2.437359 CCTGGCTTCGGCTTCCTG 60.437 66.667 0.00 0.00 41.44 3.86
7 8 4.416738 GCCTGGCTTCGGCTTCCT 62.417 66.667 12.43 0.00 44.17 3.36
15 16 4.742201 TCTGACGCGCCTGGCTTC 62.742 66.667 17.92 10.66 40.16 3.86
16 17 4.087892 ATCTGACGCGCCTGGCTT 62.088 61.111 17.92 0.00 40.44 4.35
17 18 4.521062 GATCTGACGCGCCTGGCT 62.521 66.667 17.92 0.00 40.44 4.75
20 21 4.193334 TCCGATCTGACGCGCCTG 62.193 66.667 5.73 0.00 0.00 4.85
21 22 4.194720 GTCCGATCTGACGCGCCT 62.195 66.667 5.73 0.00 0.00 5.52
22 23 4.492160 TGTCCGATCTGACGCGCC 62.492 66.667 5.73 0.00 38.11 6.53
23 24 2.669808 ATCTGTCCGATCTGACGCGC 62.670 60.000 5.73 0.00 38.11 6.86
24 25 0.658829 GATCTGTCCGATCTGACGCG 60.659 60.000 3.53 3.53 44.21 6.01
25 26 0.318275 GGATCTGTCCGATCTGACGC 60.318 60.000 11.98 2.71 46.33 5.19
26 27 3.855630 GGATCTGTCCGATCTGACG 57.144 57.895 11.98 7.54 46.33 4.35
35 36 2.966732 TTGGTGCCCGGATCTGTCC 61.967 63.158 0.73 0.00 41.40 4.02
36 37 1.745489 GTTGGTGCCCGGATCTGTC 60.745 63.158 0.73 0.00 0.00 3.51
37 38 2.351276 GTTGGTGCCCGGATCTGT 59.649 61.111 0.73 0.00 0.00 3.41
38 39 2.040544 GTGTTGGTGCCCGGATCTG 61.041 63.158 0.73 0.00 0.00 2.90
39 40 2.351276 GTGTTGGTGCCCGGATCT 59.649 61.111 0.73 0.00 0.00 2.75
40 41 2.750237 GGTGTTGGTGCCCGGATC 60.750 66.667 0.73 0.00 0.00 3.36
41 42 2.917897 ATGGTGTTGGTGCCCGGAT 61.918 57.895 0.73 0.00 0.00 4.18
42 43 3.575247 ATGGTGTTGGTGCCCGGA 61.575 61.111 0.73 0.00 0.00 5.14
43 44 3.372730 CATGGTGTTGGTGCCCGG 61.373 66.667 0.00 0.00 0.00 5.73
44 45 3.372730 CCATGGTGTTGGTGCCCG 61.373 66.667 2.57 0.00 31.74 6.13
45 46 2.996734 CCCATGGTGTTGGTGCCC 60.997 66.667 11.73 0.00 34.77 5.36
46 47 3.694538 GCCCATGGTGTTGGTGCC 61.695 66.667 11.73 0.00 34.77 5.01
47 48 4.054825 CGCCCATGGTGTTGGTGC 62.055 66.667 11.73 3.79 34.77 5.01
48 49 1.678635 ATCGCCCATGGTGTTGGTG 60.679 57.895 11.73 1.29 34.77 4.17
49 50 1.678635 CATCGCCCATGGTGTTGGT 60.679 57.895 11.73 0.00 34.77 3.67
50 51 3.067480 GCATCGCCCATGGTGTTGG 62.067 63.158 11.73 0.00 34.56 3.77
51 52 2.491152 GCATCGCCCATGGTGTTG 59.509 61.111 11.73 9.17 36.37 3.33
52 53 3.133464 CGCATCGCCCATGGTGTT 61.133 61.111 11.73 0.00 34.40 3.32
64 65 3.869272 CTTGGTCGCCTGCGCATC 61.869 66.667 12.24 4.95 39.59 3.91
65 66 4.393155 TCTTGGTCGCCTGCGCAT 62.393 61.111 12.24 0.00 39.59 4.73
67 68 4.742201 TCTCTTGGTCGCCTGCGC 62.742 66.667 6.67 0.00 39.59 6.09
68 69 2.811317 GTCTCTTGGTCGCCTGCG 60.811 66.667 4.92 4.92 41.35 5.18
69 70 2.435059 GGTCTCTTGGTCGCCTGC 60.435 66.667 0.00 0.00 0.00 4.85
70 71 1.374758 GTGGTCTCTTGGTCGCCTG 60.375 63.158 0.00 0.00 0.00 4.85
71 72 1.534235 AGTGGTCTCTTGGTCGCCT 60.534 57.895 0.00 0.00 0.00 5.52
72 73 1.079750 GAGTGGTCTCTTGGTCGCC 60.080 63.158 0.00 0.00 37.68 5.54
73 74 1.444553 CGAGTGGTCTCTTGGTCGC 60.445 63.158 0.00 0.00 38.45 5.19
74 75 1.444553 GCGAGTGGTCTCTTGGTCG 60.445 63.158 0.00 0.00 38.45 4.79
75 76 1.079750 GGCGAGTGGTCTCTTGGTC 60.080 63.158 0.00 0.00 38.45 4.02
76 77 2.932234 CGGCGAGTGGTCTCTTGGT 61.932 63.158 0.00 0.00 38.45 3.67
77 78 2.125912 CGGCGAGTGGTCTCTTGG 60.126 66.667 0.00 0.00 38.45 3.61
78 79 1.734477 CACGGCGAGTGGTCTCTTG 60.734 63.158 16.62 0.00 46.77 3.02
79 80 2.651361 CACGGCGAGTGGTCTCTT 59.349 61.111 16.62 0.00 46.77 2.85
87 88 3.432588 CTCTCGGACACGGCGAGT 61.433 66.667 16.62 13.28 41.39 4.18
88 89 4.838486 GCTCTCGGACACGGCGAG 62.838 72.222 16.62 8.85 41.39 5.03
108 109 3.950794 TTTCTACGCTGGCGCTGGG 62.951 63.158 15.04 11.78 44.19 4.45
109 110 1.970917 CTTTTCTACGCTGGCGCTGG 61.971 60.000 15.04 0.93 44.19 4.85
110 111 1.421485 CTTTTCTACGCTGGCGCTG 59.579 57.895 15.04 8.03 44.19 5.18
111 112 1.741770 CCTTTTCTACGCTGGCGCT 60.742 57.895 15.04 5.25 44.19 5.92
112 113 1.967597 GACCTTTTCTACGCTGGCGC 61.968 60.000 15.04 0.00 44.19 6.53
113 114 1.359459 GGACCTTTTCTACGCTGGCG 61.359 60.000 13.56 13.56 46.03 5.69
114 115 1.025113 GGGACCTTTTCTACGCTGGC 61.025 60.000 0.00 0.00 0.00 4.85
115 116 3.154589 GGGACCTTTTCTACGCTGG 57.845 57.895 0.00 0.00 0.00 4.85
178 179 4.131088 GTCCTCTCCGTCGCCACC 62.131 72.222 0.00 0.00 0.00 4.61
179 180 2.615262 GATGTCCTCTCCGTCGCCAC 62.615 65.000 0.00 0.00 0.00 5.01
180 181 2.362503 ATGTCCTCTCCGTCGCCA 60.363 61.111 0.00 0.00 0.00 5.69
181 182 1.739338 ATGATGTCCTCTCCGTCGCC 61.739 60.000 0.00 0.00 0.00 5.54
182 183 0.103208 AATGATGTCCTCTCCGTCGC 59.897 55.000 0.00 0.00 0.00 5.19
183 184 1.405463 TCAATGATGTCCTCTCCGTCG 59.595 52.381 0.00 0.00 0.00 5.12
184 185 2.428890 AGTCAATGATGTCCTCTCCGTC 59.571 50.000 0.00 0.00 0.00 4.79
185 186 2.167281 CAGTCAATGATGTCCTCTCCGT 59.833 50.000 0.00 0.00 0.00 4.69
186 187 2.428530 TCAGTCAATGATGTCCTCTCCG 59.571 50.000 0.00 0.00 31.12 4.63
324 364 1.136305 CAGTCCCGTTCATACCGATGT 59.864 52.381 0.00 0.00 34.41 3.06
363 403 8.598924 GCATGATGCATACATTCATACTACTAC 58.401 37.037 13.36 0.00 44.26 2.73
464 507 1.478105 GTTCCATCCAATCAGCCAACC 59.522 52.381 0.00 0.00 0.00 3.77
506 549 3.728373 GGGGAGGTTCACGGCCAT 61.728 66.667 2.24 0.00 0.00 4.40
510 553 1.595357 GTACTGGGGAGGTTCACGG 59.405 63.158 0.00 0.00 0.00 4.94
513 556 1.982958 GAAAGGTACTGGGGAGGTTCA 59.017 52.381 0.00 0.00 40.86 3.18
515 558 2.435203 AGAAAGGTACTGGGGAGGTT 57.565 50.000 0.00 0.00 40.86 3.50
516 559 2.267192 GAAGAAAGGTACTGGGGAGGT 58.733 52.381 0.00 0.00 40.86 3.85
517 560 1.560146 GGAAGAAAGGTACTGGGGAGG 59.440 57.143 0.00 0.00 40.86 4.30
519 562 1.132332 TGGGAAGAAAGGTACTGGGGA 60.132 52.381 0.00 0.00 40.86 4.81
520 563 1.368374 TGGGAAGAAAGGTACTGGGG 58.632 55.000 0.00 0.00 40.86 4.96
522 565 3.010138 TGGAATGGGAAGAAAGGTACTGG 59.990 47.826 0.00 0.00 40.86 4.00
523 566 4.301072 TGGAATGGGAAGAAAGGTACTG 57.699 45.455 0.00 0.00 40.86 2.74
525 568 3.877508 CGATGGAATGGGAAGAAAGGTAC 59.122 47.826 0.00 0.00 0.00 3.34
526 569 3.684413 GCGATGGAATGGGAAGAAAGGTA 60.684 47.826 0.00 0.00 0.00 3.08
527 570 2.945890 GCGATGGAATGGGAAGAAAGGT 60.946 50.000 0.00 0.00 0.00 3.50
528 571 1.678101 GCGATGGAATGGGAAGAAAGG 59.322 52.381 0.00 0.00 0.00 3.11
530 573 1.005332 TGGCGATGGAATGGGAAGAAA 59.995 47.619 0.00 0.00 0.00 2.52
533 576 1.338973 CAATGGCGATGGAATGGGAAG 59.661 52.381 0.00 0.00 0.00 3.46
534 577 1.401761 CAATGGCGATGGAATGGGAA 58.598 50.000 0.00 0.00 0.00 3.97
600 644 2.614057 GGCTGATTGGGAATGTAGAACG 59.386 50.000 0.00 0.00 0.00 3.95
602 646 4.526970 GAAGGCTGATTGGGAATGTAGAA 58.473 43.478 0.00 0.00 0.00 2.10
617 661 0.102481 GCATGCAATCAGGAAGGCTG 59.898 55.000 14.21 0.00 0.00 4.85
618 662 0.323999 TGCATGCAATCAGGAAGGCT 60.324 50.000 20.30 0.00 0.00 4.58
664 708 6.493189 TTTGCTTGGTAAGGAAAGGAAAAT 57.507 33.333 4.46 0.00 42.74 1.82
798 843 4.982295 TCGTAATCGGCAGATCATAACAAG 59.018 41.667 0.00 0.00 35.74 3.16
833 878 6.548622 AGACATATTTGGAAAGCACAGCATAT 59.451 34.615 0.00 0.00 0.00 1.78
945 1000 4.307432 TCTTCTTCCTCGTGATGTTGTTC 58.693 43.478 0.00 0.00 0.00 3.18
968 1023 3.121944 CGTATGTGCTCTTCACTGTTGAC 59.878 47.826 0.00 0.00 45.81 3.18
969 1024 3.317150 CGTATGTGCTCTTCACTGTTGA 58.683 45.455 0.00 0.00 45.81 3.18
970 1025 2.413112 CCGTATGTGCTCTTCACTGTTG 59.587 50.000 0.00 0.00 45.81 3.33
971 1026 2.299013 TCCGTATGTGCTCTTCACTGTT 59.701 45.455 0.00 0.00 45.81 3.16
972 1027 1.893137 TCCGTATGTGCTCTTCACTGT 59.107 47.619 0.00 0.00 45.81 3.55
986 1043 1.843376 CCCATGGCCTCCTCCGTAT 60.843 63.158 6.09 0.00 0.00 3.06
1116 1173 1.880340 GATGAAGCGCCCAGACTCG 60.880 63.158 2.29 0.00 0.00 4.18
1215 1272 1.379916 CTCCATGGGCTGGTTGTCA 59.620 57.895 13.02 0.00 46.08 3.58
1260 1317 0.464735 AGAGCGAGCTGGAGACGTAT 60.465 55.000 0.84 0.00 0.00 3.06
2089 2146 7.951591 ACATTTACTTGAAGGTTAACAGCATT 58.048 30.769 8.10 0.00 0.00 3.56
2247 2304 5.163343 ACAGGCACACTTTTTGACTAGTCTA 60.163 40.000 23.01 13.60 0.00 2.59
2256 2313 5.493133 TTACTGTACAGGCACACTTTTTG 57.507 39.130 26.12 0.00 0.00 2.44
2270 2327 6.582672 GGAAGAAAATTGCAAGCTTACTGTAC 59.417 38.462 4.94 0.00 0.00 2.90
2386 2443 1.336240 GCAAGTGTGGGATCTTTGCAC 60.336 52.381 2.93 0.00 0.00 4.57
2510 2567 7.707624 AATTGATGGTCAAAGCTAAATCTCA 57.292 32.000 0.00 0.00 40.12 3.27
2667 2724 2.668212 TCCGCACGCCTTTTGAGG 60.668 61.111 0.00 0.00 35.38 3.86
2675 2732 1.145803 GAATATAAGGTCCGCACGCC 58.854 55.000 0.00 0.00 0.00 5.68
2736 2793 6.430925 CAGACAAGAGGATGGTATCACAAAAA 59.569 38.462 0.00 0.00 0.00 1.94
3258 3315 3.330267 CTTCAGGTTGAAGTAGCTGTCC 58.670 50.000 10.00 0.00 46.50 4.02
3309 3366 5.454755 CCTTCTCCTGTCCTTTACAAAGTCA 60.455 44.000 1.32 0.41 37.74 3.41
3351 3408 0.675083 TAACGCGGACCTTGAACTCA 59.325 50.000 12.47 0.00 0.00 3.41
3553 3610 0.371301 CGTGCATGATCTTGTGACGG 59.629 55.000 19.01 7.96 0.00 4.79
3607 3664 2.324860 GTGTTCACACGATCGTCATCA 58.675 47.619 19.84 10.48 37.10 3.07
3619 3676 6.791303 GTCTAGACCAAAAATTGTGTTCACA 58.209 36.000 12.13 1.23 0.00 3.58
3746 3803 4.333926 GCATTGGAAGTCTTGTATCCACTC 59.666 45.833 0.00 0.00 42.71 3.51
4805 4868 5.106673 GCAATCCTTTGTAGTACCTGTGAAC 60.107 44.000 0.00 0.00 35.17 3.18
5212 5275 3.033909 TGGTGAGAGGTGGTATCATCAG 58.966 50.000 0.00 0.00 32.35 2.90
5475 5538 1.242076 ACTGTTGATTGGCAGCTGTC 58.758 50.000 12.53 12.53 35.55 3.51
5476 5539 1.696063 AACTGTTGATTGGCAGCTGT 58.304 45.000 16.64 0.00 40.58 4.40
5776 5843 4.461431 AGAATGACATTCAGCTCAAATGCA 59.539 37.500 26.05 14.05 41.71 3.96
5976 6089 5.856126 TTTCTGTATCCGTTTTAGCACTG 57.144 39.130 0.00 0.00 0.00 3.66
6205 6324 8.534496 CCCATGGACTAGATTTGAAAGAAATTT 58.466 33.333 15.22 0.00 0.00 1.82
6419 6538 7.287696 ACCTTTTGAATATCATCCCACCATTAC 59.712 37.037 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.