Multiple sequence alignment - TraesCS5D01G222500

Loading Multiple Alignment...

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 TraesCS5D01G222500 chr5D 100.000 2690 0 0 1 2690 330077362 330080051 0.000000e+00 4968.0
1 TraesCS5D01G222500 chr5B 91.708 1411 61 19 752 2128 383035548 383036936 0.000000e+00 1906.0
2 TraesCS5D01G222500 chr5B 89.189 444 34 8 2224 2661 383037135 383037570 2.360000e-150 542.0
3 TraesCS5D01G222500 chr5B 91.000 400 21 6 315 710 383035151 383035539 2.370000e-145 525.0
4 TraesCS5D01G222500 chr5B 83.942 274 31 11 9 274 383034751 383035019 1.600000e-62 250.0
5 TraesCS5D01G222500 chr5B 85.714 105 4 2 2128 2221 383036964 383037068 1.700000e-17 100.0
6 TraesCS5D01G222500 chr5B 94.595 37 2 0 2652 2688 383083163 383083199 1.040000e-04 58.4
7 TraesCS5D01G222500 chr5A 94.590 1109 36 12 802 1898 426730885 426729789 0.000000e+00 1694.0
8 TraesCS5D01G222500 chr5A 88.095 420 42 4 2272 2690 426729331 426728919 2.410000e-135 492.0
9 TraesCS5D01G222500 chr5A 89.972 359 18 8 410 757 426731240 426730889 5.280000e-122 448.0
10 TraesCS5D01G222500 chr5A 83.154 279 30 2 142 419 426733375 426733113 3.460000e-59 239.0
11 TraesCS5D01G222500 chr5A 88.889 189 13 5 1947 2128 426729791 426729604 2.690000e-55 226.0
12 TraesCS5D01G222500 chr7D 79.812 213 36 6 1245 1454 529956416 529956208 6.000000e-32 148.0
13 TraesCS5D01G222500 chr7D 74.684 237 41 15 9 232 5318565 5318335 1.330000e-13 87.9
14 TraesCS5D01G222500 chr7D 74.167 240 46 9 3 230 634289713 634289948 4.770000e-13 86.1
15 TraesCS5D01G222500 chr7D 74.009 227 46 12 9 228 510310884 510310664 2.220000e-11 80.5
16 TraesCS5D01G222500 chr7A 80.000 200 33 6 1249 1445 609431477 609431282 1.000000e-29 141.0
17 TraesCS5D01G222500 chr7B 78.873 213 38 6 1245 1454 568107384 568107176 1.300000e-28 137.0
18 TraesCS5D01G222500 chr6A 77.515 169 31 6 1255 1420 85586704 85586540 7.930000e-16 95.3
19 TraesCS5D01G222500 chr3A 78.107 169 23 10 1 159 171541305 171541141 7.930000e-16 95.3
20 TraesCS5D01G222500 chrUn 75.330 227 32 12 3 212 100764478 100764697 1.330000e-13 87.9
21 TraesCS5D01G222500 chr6D 75.843 178 36 6 1245 1419 68098952 68098779 1.720000e-12 84.2
22 TraesCS5D01G222500 chr6B 77.622 143 26 5 1281 1420 143200023 143199884 6.170000e-12 82.4
23 TraesCS5D01G222500 chr1B 84.286 70 8 3 9 78 589774491 589774425 6.220000e-07 65.8
24 TraesCS5D01G222500 chr3B 73.267 202 42 9 3 195 367476076 367476274 2.240000e-06 63.9
25 TraesCS5D01G222500 chr2A 84.375 64 7 2 14 77 539397235 539397175 2.890000e-05 60.2


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 TraesCS5D01G222500 chr5D 330077362 330080051 2689 False 4968.0 4968 100.0000 1 2690 1 chr5D.!!$F1 2689
1 TraesCS5D01G222500 chr5B 383034751 383037570 2819 False 664.6 1906 88.3106 9 2661 5 chr5B.!!$F2 2652
2 TraesCS5D01G222500 chr5A 426728919 426733375 4456 True 619.8 1694 88.9400 142 2690 5 chr5A.!!$R1 2548

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
134 143 0.106519 ATTTCCTTCCCTGCCATCGG 60.107 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 4151 1.202758 ACAAGCGACAGTGGAAATGGA 60.203 47.619 0.0 0.0 35.33 3.41 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
40 41 4.149046 CGGAAGACAAACTCGAAGAAGAAG 59.851 45.833 0.00 0.00 34.09 2.85
46 47 4.271291 ACAAACTCGAAGAAGAAGAAGTGC 59.729 41.667 0.00 0.00 34.09 4.40
47 48 3.735237 ACTCGAAGAAGAAGAAGTGCA 57.265 42.857 0.00 0.00 34.09 4.57
49 50 2.408050 TCGAAGAAGAAGAAGTGCAGC 58.592 47.619 0.00 0.00 0.00 5.25
55 56 2.110901 AGAAGAAGTGCAGCCATCTG 57.889 50.000 0.00 0.00 43.16 2.90
57 58 1.736681 GAAGAAGTGCAGCCATCTGTC 59.263 52.381 0.00 0.00 42.29 3.51
58 59 0.689055 AGAAGTGCAGCCATCTGTCA 59.311 50.000 0.00 0.00 42.29 3.58
59 60 1.085091 GAAGTGCAGCCATCTGTCAG 58.915 55.000 0.00 0.00 42.29 3.51
63 64 2.172372 GCAGCCATCTGTCAGAGCG 61.172 63.158 8.82 2.06 42.29 5.03
98 107 8.957466 GCCAGAATTGAAACCTAAACTACTAAT 58.043 33.333 0.00 0.00 0.00 1.73
105 114 8.922058 TGAAACCTAAACTACTAATTAGAGCG 57.078 34.615 19.38 8.77 32.10 5.03
134 143 0.106519 ATTTCCTTCCCTGCCATCGG 60.107 55.000 0.00 0.00 0.00 4.18
155 164 2.523902 CCAGGGTGGCAGGCAAAA 60.524 61.111 0.00 0.00 0.00 2.44
162 171 3.385384 GGCAGGCAAAAGGGAGGC 61.385 66.667 0.00 0.00 0.00 4.70
171 180 1.969923 CAAAAGGGAGGCAAATCCACA 59.030 47.619 4.47 0.00 41.52 4.17
178 187 2.354259 GAGGCAAATCCACAGACTCAG 58.646 52.381 0.00 0.00 37.29 3.35
195 204 2.032681 GCGGCAAAGTCTGGAGGT 59.967 61.111 0.00 0.00 0.00 3.85
198 207 0.250295 CGGCAAAGTCTGGAGGTGAA 60.250 55.000 0.00 0.00 0.00 3.18
276 287 9.823602 CCAACTTTGGTACTACTTCGGCTAAGT 62.824 44.444 9.50 9.50 45.60 2.24
284 295 5.718146 ACTACTTCGGCTAAGTTAGGTTTC 58.282 41.667 9.85 0.00 46.61 2.78
285 296 4.612264 ACTTCGGCTAAGTTAGGTTTCA 57.388 40.909 11.84 0.00 46.61 2.69
286 297 4.566987 ACTTCGGCTAAGTTAGGTTTCAG 58.433 43.478 11.84 0.00 46.61 3.02
287 298 4.040095 ACTTCGGCTAAGTTAGGTTTCAGT 59.960 41.667 11.84 0.00 46.61 3.41
293 304 6.612306 GGCTAAGTTAGGTTTCAGTTTCATG 58.388 40.000 11.84 0.00 0.00 3.07
296 307 6.715347 AAGTTAGGTTTCAGTTTCATGCTT 57.285 33.333 0.00 0.00 0.00 3.91
343 459 1.968050 GCCCTACTCGCTGGCCTAAA 61.968 60.000 3.32 0.00 39.30 1.85
368 488 2.486203 TGGATCAAACACACCGTATTGC 59.514 45.455 0.00 0.00 0.00 3.56
432 2434 4.273148 ACTAATCGGCAGTTGACTCTTT 57.727 40.909 0.00 0.00 0.00 2.52
433 2435 5.401531 ACTAATCGGCAGTTGACTCTTTA 57.598 39.130 0.00 0.00 0.00 1.85
434 2436 5.978814 ACTAATCGGCAGTTGACTCTTTAT 58.021 37.500 0.00 0.00 0.00 1.40
435 2437 6.407202 ACTAATCGGCAGTTGACTCTTTATT 58.593 36.000 0.00 0.00 0.00 1.40
467 2469 5.937540 TCTTTCAGAAATTCACGCCTGATAA 59.062 36.000 0.00 0.00 35.82 1.75
529 2535 3.979495 GCACAATGCAGAAGAAAAGAGTG 59.021 43.478 0.00 0.00 44.26 3.51
587 2593 4.657039 TCCTCACTACTTGGTTTACTTGGT 59.343 41.667 0.00 0.00 0.00 3.67
589 2595 6.327104 TCCTCACTACTTGGTTTACTTGGTAA 59.673 38.462 0.00 0.00 0.00 2.85
648 2654 1.153756 CCCAACACAAGCTTCCCCT 59.846 57.895 0.00 0.00 0.00 4.79
649 2655 1.181098 CCCAACACAAGCTTCCCCTG 61.181 60.000 0.00 0.00 0.00 4.45
650 2656 1.662044 CAACACAAGCTTCCCCTGC 59.338 57.895 0.00 0.00 0.00 4.85
651 2657 1.108727 CAACACAAGCTTCCCCTGCA 61.109 55.000 0.00 0.00 0.00 4.41
744 2757 3.849145 CGCTAGATATCGCTAAGCAAGAC 59.151 47.826 16.97 0.00 0.00 3.01
746 2759 4.321304 GCTAGATATCGCTAAGCAAGACCA 60.321 45.833 13.88 0.00 0.00 4.02
760 2773 5.831997 AGCAAGACCATTTTAATAATCGGC 58.168 37.500 0.00 0.00 0.00 5.54
774 2787 8.870160 TTAATAATCGGCAATGGAATCTTTTG 57.130 30.769 0.00 0.00 0.00 2.44
775 2788 2.652941 TCGGCAATGGAATCTTTTGC 57.347 45.000 10.64 10.64 0.00 3.68
776 2789 2.170166 TCGGCAATGGAATCTTTTGCT 58.830 42.857 15.96 0.00 0.00 3.91
777 2790 2.562298 TCGGCAATGGAATCTTTTGCTT 59.438 40.909 15.96 0.00 0.00 3.91
822 2835 2.492418 CATGGCGCCATGTTACCTT 58.508 52.632 46.57 23.60 46.20 3.50
823 2836 1.674359 CATGGCGCCATGTTACCTTA 58.326 50.000 46.57 19.00 46.20 2.69
824 2837 1.333619 CATGGCGCCATGTTACCTTAC 59.666 52.381 46.57 12.52 46.20 2.34
825 2838 0.393267 TGGCGCCATGTTACCTTACC 60.393 55.000 29.03 0.00 0.00 2.85
826 2839 0.107361 GGCGCCATGTTACCTTACCT 60.107 55.000 24.80 0.00 0.00 3.08
827 2840 1.296727 GCGCCATGTTACCTTACCTC 58.703 55.000 0.00 0.00 0.00 3.85
828 2841 1.134491 GCGCCATGTTACCTTACCTCT 60.134 52.381 0.00 0.00 0.00 3.69
911 2924 4.785453 CTTCCAGCTCCCGGCCAC 62.785 72.222 2.24 0.00 43.05 5.01
920 2933 2.834505 CCCGGCCACCATCCATTG 60.835 66.667 2.24 0.00 0.00 2.82
944 2957 3.055240 CAGCCTCTCAAGATCCAAGAAGT 60.055 47.826 0.00 0.00 0.00 3.01
945 2958 3.197549 AGCCTCTCAAGATCCAAGAAGTC 59.802 47.826 0.00 0.00 0.00 3.01
946 2959 3.681313 GCCTCTCAAGATCCAAGAAGTCC 60.681 52.174 0.00 0.00 0.00 3.85
987 3002 2.476821 GTGCCGTGTGTGTAGTAAGTT 58.523 47.619 0.00 0.00 0.00 2.66
1535 3559 1.378124 GACTAGCTCCCGAGACGCTT 61.378 60.000 0.00 0.00 35.33 4.68
1540 3564 1.880340 CTCCCGAGACGCTTGCATC 60.880 63.158 0.00 0.00 0.00 3.91
1552 3576 2.208431 GCTTGCATCCTACAGTAGCAG 58.792 52.381 1.50 0.00 36.47 4.24
1678 3702 2.365068 CCAGCGTCGTCAGTTCGTG 61.365 63.158 0.00 0.00 0.00 4.35
1705 3729 6.750501 TGTTTCGTAGATAGTGTCTGTAATGC 59.249 38.462 0.00 0.00 37.83 3.56
1720 3744 8.311109 TGTCTGTAATGCTGTAATTTCTGTCTA 58.689 33.333 0.00 0.00 0.00 2.59
1721 3745 9.319143 GTCTGTAATGCTGTAATTTCTGTCTAT 57.681 33.333 0.00 0.00 0.00 1.98
1850 3880 3.255642 GGTAATTGTTCTGGCTTTGCTGA 59.744 43.478 0.00 0.00 0.00 4.26
1934 3967 2.109799 CGATCTGCGGCCTCCATT 59.890 61.111 0.00 0.00 36.03 3.16
1938 3971 3.830192 CTGCGGCCTCCATTTGCC 61.830 66.667 0.00 0.00 44.41 4.52
1990 4046 6.940298 TCTGGTTTCCTCTTTTGATTTATCGT 59.060 34.615 0.00 0.00 0.00 3.73
2026 4082 2.017782 GTCTCTGGCTATGACTGACGA 58.982 52.381 0.00 0.00 0.00 4.20
2033 4089 2.599082 GGCTATGACTGACGAGAAAACG 59.401 50.000 0.00 0.00 39.31 3.60
2035 4091 4.409570 GCTATGACTGACGAGAAAACGTA 58.590 43.478 0.00 0.00 46.52 3.57
2057 4113 5.078411 AGAAAACAGATACGCATGTCTCT 57.922 39.130 0.00 0.00 32.22 3.10
2092 4155 7.550196 ACTTATTTAACGTATCAACCGTTCCAT 59.450 33.333 1.07 0.00 44.56 3.41
2114 4177 1.301244 CACTGTCGCTTGTCAGCCT 60.301 57.895 0.00 0.00 44.06 4.58
2167 4262 3.324117 GTTACTTCCCGTTTGACCTCTC 58.676 50.000 0.00 0.00 0.00 3.20
2200 4302 4.432712 CCCAGTTTTGTTTTGGAACAGAG 58.567 43.478 0.00 0.00 45.80 3.35
2217 4319 1.372087 GAGAAATGTCCTGCCCTGCG 61.372 60.000 0.00 0.00 0.00 5.18
2234 4404 2.990479 GGTGGTTCCGATCAGCCT 59.010 61.111 0.00 0.00 0.00 4.58
2236 4406 1.519455 GTGGTTCCGATCAGCCTCG 60.519 63.158 0.00 0.00 38.37 4.63
2245 4415 1.035923 GATCAGCCTCGTCCATCTCA 58.964 55.000 0.00 0.00 0.00 3.27
2253 4423 0.248498 TCGTCCATCTCATCGCGAAC 60.248 55.000 15.24 2.52 0.00 3.95
2291 4497 2.147433 CTCTCCCTTTGGCTTGCCCT 62.147 60.000 9.35 0.00 0.00 5.19
2333 4539 1.646540 CAAACCAGAGCGCGTTCAA 59.353 52.632 24.99 0.00 0.00 2.69
2334 4540 0.238289 CAAACCAGAGCGCGTTCAAT 59.762 50.000 24.99 6.76 0.00 2.57
2335 4541 0.238289 AAACCAGAGCGCGTTCAATG 59.762 50.000 24.99 14.72 0.00 2.82
2336 4542 0.884704 AACCAGAGCGCGTTCAATGT 60.885 50.000 24.99 14.84 0.00 2.71
2337 4543 0.884704 ACCAGAGCGCGTTCAATGTT 60.885 50.000 24.99 0.82 0.00 2.71
2338 4544 0.179215 CCAGAGCGCGTTCAATGTTC 60.179 55.000 24.99 0.00 0.00 3.18
2339 4545 0.792640 CAGAGCGCGTTCAATGTTCT 59.207 50.000 24.99 0.72 0.00 3.01
2362 4568 1.596203 CGGACGCAGCATCCATGAT 60.596 57.895 8.54 0.00 35.83 2.45
2418 4624 3.904800 TCACAACCTGAAAGTCTCACA 57.095 42.857 0.00 0.00 0.00 3.58
2423 4629 2.498167 ACCTGAAAGTCTCACACATGC 58.502 47.619 0.00 0.00 0.00 4.06
2428 4634 2.267174 AAGTCTCACACATGCTGCTT 57.733 45.000 0.00 0.00 0.00 3.91
2448 4654 0.331278 AAGATTGACATTGCCCGGGA 59.669 50.000 29.31 3.75 0.00 5.14
2488 4694 7.881751 TCATGGCTATTCCTTCTTCATATTCTG 59.118 37.037 0.00 0.00 35.26 3.02
2498 4704 5.028549 TCTTCATATTCTGAGCCACCTTC 57.971 43.478 0.00 0.00 34.68 3.46
2516 4723 3.423154 GTTTGGCCTCGCTGACGG 61.423 66.667 3.32 0.00 40.63 4.79
2632 4841 2.794941 GCGACATGCTCTCTCGATC 58.205 57.895 6.83 0.00 41.73 3.69
2650 4859 3.675225 CGATCTTGTTCACTCACGACATT 59.325 43.478 0.00 0.00 0.00 2.71
2653 4862 4.631131 TCTTGTTCACTCACGACATTGAT 58.369 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009829 CCGGGCTTCGATTCTTCTTG 58.990 55.000 0.00 0.00 42.43 3.02
1 2 0.902531 TCCGGGCTTCGATTCTTCTT 59.097 50.000 0.00 0.00 42.43 2.52
2 3 0.902531 TTCCGGGCTTCGATTCTTCT 59.097 50.000 0.00 0.00 42.43 2.85
3 4 1.134788 TCTTCCGGGCTTCGATTCTTC 60.135 52.381 0.00 0.00 42.43 2.87
4 5 0.902531 TCTTCCGGGCTTCGATTCTT 59.097 50.000 0.00 0.00 42.43 2.52
5 6 0.175989 GTCTTCCGGGCTTCGATTCT 59.824 55.000 0.00 0.00 42.43 2.40
6 7 0.108329 TGTCTTCCGGGCTTCGATTC 60.108 55.000 0.00 0.00 42.43 2.52
7 8 0.323629 TTGTCTTCCGGGCTTCGATT 59.676 50.000 0.00 0.00 42.43 3.34
12 13 0.602905 CGAGTTTGTCTTCCGGGCTT 60.603 55.000 0.00 0.00 0.00 4.35
17 18 3.639538 TCTTCTTCGAGTTTGTCTTCCG 58.360 45.455 0.00 0.00 0.00 4.30
18 19 5.290386 TCTTCTTCTTCGAGTTTGTCTTCC 58.710 41.667 0.00 0.00 0.00 3.46
40 41 1.085091 CTGACAGATGGCTGCACTTC 58.915 55.000 0.50 0.00 46.26 3.01
47 48 2.186384 GCGCTCTGACAGATGGCT 59.814 61.111 16.51 0.00 0.00 4.75
49 50 2.584418 CGGCGCTCTGACAGATGG 60.584 66.667 7.64 2.14 0.00 3.51
63 64 3.064324 AATTCTGGCAGGTGCGGC 61.064 61.111 15.73 0.00 43.26 6.53
99 108 4.853142 ATCCCGGTGCCCGCTCTA 62.853 66.667 0.00 0.00 46.86 2.43
101 110 4.796495 AAATCCCGGTGCCCGCTC 62.796 66.667 0.00 0.00 46.86 5.03
102 111 4.796495 GAAATCCCGGTGCCCGCT 62.796 66.667 0.00 0.00 46.86 5.52
105 114 1.753078 GAAGGAAATCCCGGTGCCC 60.753 63.158 0.00 0.00 40.87 5.36
117 126 2.998097 CCGATGGCAGGGAAGGAA 59.002 61.111 1.27 0.00 0.00 3.36
140 149 2.203684 CCTTTTGCCTGCCACCCT 60.204 61.111 0.00 0.00 0.00 4.34
153 162 1.428912 TCTGTGGATTTGCCTCCCTTT 59.571 47.619 0.00 0.00 37.63 3.11
155 164 0.329596 GTCTGTGGATTTGCCTCCCT 59.670 55.000 0.00 0.00 37.63 4.20
162 171 1.081892 CCGCTGAGTCTGTGGATTTG 58.918 55.000 21.61 0.00 35.45 2.32
171 180 2.053618 AGACTTTGCCGCTGAGTCT 58.946 52.632 17.94 17.94 43.84 3.24
178 187 2.032681 ACCTCCAGACTTTGCCGC 59.967 61.111 0.00 0.00 0.00 6.53
221 230 3.374762 CCTCTTCCTCAACTCCTCCCTAT 60.375 52.174 0.00 0.00 0.00 2.57
276 287 5.183140 GGCTAAGCATGAAACTGAAACCTAA 59.817 40.000 0.00 0.00 0.00 2.69
284 295 0.099436 GCCGGCTAAGCATGAAACTG 59.901 55.000 22.15 0.00 0.00 3.16
285 296 0.322456 TGCCGGCTAAGCATGAAACT 60.322 50.000 29.70 0.00 34.69 2.66
286 297 0.525761 TTGCCGGCTAAGCATGAAAC 59.474 50.000 29.70 0.00 40.59 2.78
287 298 1.067915 GTTTGCCGGCTAAGCATGAAA 60.068 47.619 29.70 14.14 40.59 2.69
293 304 1.080772 GTTGGTTTGCCGGCTAAGC 60.081 57.895 35.37 35.37 37.67 3.09
296 307 3.358707 GCGTTGGTTTGCCGGCTA 61.359 61.111 29.70 19.10 37.67 3.93
343 459 3.140325 ACGGTGTGTTTGATCCATCTT 57.860 42.857 0.00 0.00 0.00 2.40
406 526 6.228258 AGAGTCAACTGCCGATTAGTTAAAA 58.772 36.000 0.00 0.00 36.29 1.52
412 2414 6.910536 AATAAAGAGTCAACTGCCGATTAG 57.089 37.500 0.00 0.00 0.00 1.73
458 2460 9.329913 GTGCTACATATTTTTAATTATCAGGCG 57.670 33.333 0.00 0.00 0.00 5.52
467 2469 5.896678 TGGCCAGGTGCTACATATTTTTAAT 59.103 36.000 0.00 0.00 40.92 1.40
529 2535 4.984161 TGGTTCTAGTTTTGTACGCTACAC 59.016 41.667 0.00 0.00 38.63 2.90
649 2655 0.952010 CTTTGGTGGCAAAGGCATGC 60.952 55.000 9.90 9.90 45.67 4.06
650 2656 0.680618 TCTTTGGTGGCAAAGGCATG 59.319 50.000 0.00 0.00 43.71 4.06
651 2657 1.422531 TTCTTTGGTGGCAAAGGCAT 58.577 45.000 0.00 0.00 43.71 4.40
672 2678 3.976701 TTAGGCCAGCTTGCTCGGC 62.977 63.158 20.07 20.07 45.47 5.54
744 2757 8.090214 AGATTCCATTGCCGATTATTAAAATGG 58.910 33.333 9.24 9.24 43.47 3.16
774 2787 7.467131 GCATCCAGAGAGAGAAGAAAAATAAGC 60.467 40.741 0.00 0.00 0.00 3.09
775 2788 7.012232 GGCATCCAGAGAGAGAAGAAAAATAAG 59.988 40.741 0.00 0.00 0.00 1.73
776 2789 6.825721 GGCATCCAGAGAGAGAAGAAAAATAA 59.174 38.462 0.00 0.00 0.00 1.40
777 2790 6.352516 GGCATCCAGAGAGAGAAGAAAAATA 58.647 40.000 0.00 0.00 0.00 1.40
822 2835 4.124351 CCGGACGCGCAAGAGGTA 62.124 66.667 5.73 0.00 43.56 3.08
911 2924 1.211212 TGAGAGGCTGACAATGGATGG 59.789 52.381 0.00 0.00 0.00 3.51
920 2933 2.499289 TCTTGGATCTTGAGAGGCTGAC 59.501 50.000 0.00 0.00 0.00 3.51
944 2957 3.097293 ACCGCTAGTGAGGGAGGA 58.903 61.111 4.44 0.00 37.85 3.71
980 2993 4.379813 CCATCACGTACGTACCAACTTACT 60.380 45.833 22.34 0.00 30.23 2.24
981 2994 3.853671 CCATCACGTACGTACCAACTTAC 59.146 47.826 22.34 0.00 0.00 2.34
987 3002 1.512230 GCCCATCACGTACGTACCA 59.488 57.895 22.34 8.49 0.00 3.25
1197 3221 2.908940 ACCGTCACCGTCCTCGTT 60.909 61.111 0.00 0.00 35.01 3.85
1535 3559 2.034878 CCTCTGCTACTGTAGGATGCA 58.965 52.381 16.09 7.94 0.00 3.96
1540 3564 2.950781 TCCATCCTCTGCTACTGTAGG 58.049 52.381 16.09 2.16 0.00 3.18
1552 3576 4.273480 CACACGGTTAAATGATCCATCCTC 59.727 45.833 0.00 0.00 0.00 3.71
1649 3673 1.518133 GACGCTGGCTCTAGCACAG 60.518 63.158 13.09 13.09 43.87 3.66
1678 3702 8.959058 CATTACAGACACTATCTACGAAACATC 58.041 37.037 0.00 0.00 35.15 3.06
1938 3971 1.866853 GAGAAGGTTGCCAAAGCCCG 61.867 60.000 0.00 0.00 38.69 6.13
1990 4046 4.503910 CAGAGACATGTTAATGAACCGGA 58.496 43.478 9.46 0.00 37.24 5.14
2026 4082 5.693104 TGCGTATCTGTTTTCTACGTTTTCT 59.307 36.000 0.00 0.00 40.16 2.52
2033 4089 6.037098 AGAGACATGCGTATCTGTTTTCTAC 58.963 40.000 0.00 0.00 42.10 2.59
2035 4091 5.078411 AGAGACATGCGTATCTGTTTTCT 57.922 39.130 0.00 0.00 42.10 2.52
2057 4113 2.548904 ACGTTAAATAAGTGCCACGCAA 59.451 40.909 0.00 0.00 41.47 4.85
2061 4117 6.253013 GGTTGATACGTTAAATAAGTGCCAC 58.747 40.000 0.00 0.00 0.00 5.01
2064 4120 6.098367 ACGGTTGATACGTTAAATAAGTGC 57.902 37.500 0.00 0.00 42.70 4.40
2088 4151 1.202758 ACAAGCGACAGTGGAAATGGA 60.203 47.619 0.00 0.00 35.33 3.41
2092 4155 1.581934 CTGACAAGCGACAGTGGAAA 58.418 50.000 0.00 0.00 31.32 3.13
2114 4177 5.848138 ATCATTTCTGATGGCGAGACGCA 62.848 47.826 17.28 4.87 45.34 5.24
2167 4262 4.284829 ACAAAACTGGGGGCATTTTATG 57.715 40.909 0.00 0.00 0.00 1.90
2200 4302 3.190878 CGCAGGGCAGGACATTTC 58.809 61.111 0.00 0.00 0.00 2.17
2217 4319 1.153349 GAGGCTGATCGGAACCACC 60.153 63.158 5.48 0.00 0.00 4.61
2234 4404 0.248498 GTTCGCGATGAGATGGACGA 60.248 55.000 10.88 0.00 0.00 4.20
2236 4406 0.103208 AGGTTCGCGATGAGATGGAC 59.897 55.000 10.88 1.44 0.00 4.02
2291 4497 2.280524 CCGTGTCACCAAGCCGAA 60.281 61.111 0.00 0.00 0.00 4.30
2316 4522 0.238289 CATTGAACGCGCTCTGGTTT 59.762 50.000 5.73 0.00 0.00 3.27
2333 4539 2.813908 GCGTCCGGCGAAGAACAT 60.814 61.111 20.06 0.00 44.77 2.71
2418 4624 5.647589 CAATGTCAATCTTAAGCAGCATGT 58.352 37.500 0.00 0.00 39.31 3.21
2423 4629 3.488047 CGGGCAATGTCAATCTTAAGCAG 60.488 47.826 0.00 0.00 0.00 4.24
2428 4634 1.562008 TCCCGGGCAATGTCAATCTTA 59.438 47.619 18.49 0.00 0.00 2.10
2448 4654 2.636893 AGCCATGAGACTGAGTTGAACT 59.363 45.455 0.00 0.00 0.00 3.01
2498 4704 3.777925 CGTCAGCGAGGCCAAACG 61.778 66.667 5.01 9.21 41.33 3.60
2627 4835 2.292292 TGTCGTGAGTGAACAAGATCGA 59.708 45.455 0.00 0.00 31.97 3.59
2632 4841 4.212004 ACATCAATGTCGTGAGTGAACAAG 59.788 41.667 0.00 0.00 35.87 3.16
2650 4859 5.508567 TGGATCAAAGCATTTAGGACATCA 58.491 37.500 0.00 0.00 35.03 3.07
2653 4862 3.696051 GCTGGATCAAAGCATTTAGGACA 59.304 43.478 13.25 0.00 35.03 4.02


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

AutoCloner maintained by Alex Coulton.