Multiple sequence alignment - TraesCS3A01G287400

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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 TraesCS3A01G287400 chr3A 100.000 2912 0 0 1 2912 515830022 515827111 0.000000e+00 5378.0
1 TraesCS3A01G287400 chr3A 81.818 242 42 2 2386 2626 143250355 143250595 4.920000e-48 202.0
2 TraesCS3A01G287400 chr3D 93.289 2086 93 18 864 2912 395667464 395665389 0.000000e+00 3033.0
3 TraesCS3A01G287400 chr3D 89.163 609 59 5 1 606 395670758 395670154 0.000000e+00 752.0
4 TraesCS3A01G287400 chr3D 88.406 207 13 6 609 813 395667919 395667722 3.750000e-59 239.0
5 TraesCS3A01G287400 chr3B 95.476 1282 36 8 684 1963 520611954 520610693 0.000000e+00 2026.0
6 TraesCS3A01G287400 chr3B 86.547 223 19 6 2697 2910 520609950 520609730 4.850000e-58 235.0
7 TraesCS3A01G287400 chr3B 84.615 195 10 7 515 692 520613727 520613536 2.980000e-40 176.0
8 TraesCS3A01G287400 chr1A 87.653 899 92 11 1033 1914 537070101 537070997 0.000000e+00 1027.0
9 TraesCS3A01G287400 chr1A 93.750 48 2 1 2305 2352 437726318 437726272 1.450000e-08 71.3
10 TraesCS3A01G287400 chr1D 88.628 853 82 7 1076 1913 441034648 441033796 0.000000e+00 1024.0
11 TraesCS3A01G287400 chr1B 88.277 853 85 7 1076 1913 598702877 598702025 0.000000e+00 1007.0
12 TraesCS3A01G287400 chr1B 78.603 229 37 10 2412 2636 4067674 4067454 1.090000e-29 141.0
13 TraesCS3A01G287400 chr1B 95.238 42 1 1 2316 2356 6453605 6453564 6.740000e-07 65.8
14 TraesCS3A01G287400 chr2A 81.439 264 44 4 2376 2638 780763015 780762756 8.180000e-51 211.0
15 TraesCS3A01G287400 chr2A 77.291 251 45 6 2382 2632 653390879 653391117 1.410000e-28 137.0
16 TraesCS3A01G287400 chr5D 85.279 197 27 2 2409 2604 370360075 370360270 4.920000e-48 202.0
17 TraesCS3A01G287400 chr5D 95.349 43 1 1 2316 2357 543236724 543236682 1.870000e-07 67.6
18 TraesCS3A01G287400 chr2D 80.080 251 42 4 2382 2632 509751326 509751568 2.310000e-41 180.0
19 TraesCS3A01G287400 chr6A 83.957 187 25 3 2410 2596 6585422 6585241 1.070000e-39 174.0
20 TraesCS3A01G287400 chr6A 93.478 46 2 1 2317 2361 609150281 609150236 1.870000e-07 67.6
21 TraesCS3A01G287400 chr5A 80.176 227 39 6 2402 2626 634614947 634615169 6.460000e-37 165.0
22 TraesCS3A01G287400 chr7B 100.000 38 0 0 2316 2353 318026905 318026868 1.450000e-08 71.3
23 TraesCS3A01G287400 chr5B 92.157 51 2 2 2308 2357 398713726 398713677 1.450000e-08 71.3
24 TraesCS3A01G287400 chr4D 97.500 40 1 0 2314 2353 42500117 42500156 5.210000e-08 69.4
25 TraesCS3A01G287400 chr4D 97.297 37 1 0 2316 2352 88513227 88513191 2.420000e-06 63.9


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 TraesCS3A01G287400 chr3A 515827111 515830022 2911 True 5378.000000 5378 100.000000 1 2912 1 chr3A.!!$R1 2911
1 TraesCS3A01G287400 chr3D 395665389 395670758 5369 True 1341.333333 3033 90.286000 1 2912 3 chr3D.!!$R1 2911
2 TraesCS3A01G287400 chr3B 520609730 520613727 3997 True 812.333333 2026 88.879333 515 2910 3 chr3B.!!$R1 2395
3 TraesCS3A01G287400 chr1A 537070101 537070997 896 False 1027.000000 1027 87.653000 1033 1914 1 chr1A.!!$F1 881
4 TraesCS3A01G287400 chr1D 441033796 441034648 852 True 1024.000000 1024 88.628000 1076 1913 1 chr1D.!!$R1 837
5 TraesCS3A01G287400 chr1B 598702025 598702877 852 True 1007.000000 1007 88.277000 1076 1913 1 chr1B.!!$R3 837

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
852 4677 0.041535 TTCCCATTCCATTGGCTGCT 59.958 50.0 0.0 0.0 35.29 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 6790 0.032952 GTGACACTGCGGACCTAACA 59.967 55.0 0.0 0.0 0.0 2.41 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
20 21 1.205417 CATTCAGGCGCCTCCAAAATT 59.795 47.619 30.29 4.62 37.29 1.82
24 25 2.506881 GCGCCTCCAAAATTGCCG 60.507 61.111 0.00 0.00 0.00 5.69
37 38 0.323629 ATTGCCGTATATCCACCCCG 59.676 55.000 0.00 0.00 0.00 5.73
38 39 1.049855 TTGCCGTATATCCACCCCGT 61.050 55.000 0.00 0.00 0.00 5.28
85 87 4.742438 TCAACTCGAACATTTAGGCAAC 57.258 40.909 0.00 0.00 0.00 4.17
95 97 3.954258 ACATTTAGGCAACATAGAAGGGC 59.046 43.478 0.00 0.00 41.41 5.19
96 98 2.325583 TTAGGCAACATAGAAGGGCG 57.674 50.000 0.00 0.00 41.41 6.13
111 113 1.305930 GGGCGGGTTGACTAGCAAAG 61.306 60.000 1.86 0.00 38.44 2.77
139 141 0.320374 GGACAATGACCGACAGTCCA 59.680 55.000 0.00 0.00 46.15 4.02
140 142 1.429463 GACAATGACCGACAGTCCAC 58.571 55.000 0.00 0.00 45.68 4.02
141 143 1.000955 GACAATGACCGACAGTCCACT 59.999 52.381 0.00 0.00 45.68 4.00
142 144 1.000955 ACAATGACCGACAGTCCACTC 59.999 52.381 0.00 0.00 45.68 3.51
143 145 1.000843 CAATGACCGACAGTCCACTCA 59.999 52.381 0.00 0.00 45.68 3.41
153 155 4.365723 GACAGTCCACTCAAACGTTTAGA 58.634 43.478 14.20 12.26 0.00 2.10
169 171 4.561734 CGTTTAGAGGAGTTTGAAGAGCCT 60.562 45.833 0.00 0.00 0.00 4.58
170 172 4.543590 TTAGAGGAGTTTGAAGAGCCTG 57.456 45.455 0.00 0.00 0.00 4.85
190 192 5.008118 GCCTGATTGTAAATGCTCTTACCTC 59.992 44.000 6.19 4.63 31.85 3.85
191 193 5.235186 CCTGATTGTAAATGCTCTTACCTCG 59.765 44.000 6.19 0.00 31.85 4.63
201 203 1.068741 CTCTTACCTCGCCGGCTATTT 59.931 52.381 26.68 8.86 35.61 1.40
208 210 1.301009 CGCCGGCTATTTCCCTCTC 60.301 63.158 26.68 0.00 0.00 3.20
225 227 4.974399 CCTCTCCGCTTAGGGAAATAAAT 58.026 43.478 0.00 0.00 41.52 1.40
292 294 0.530288 TCGACCATGAGATGTTCGCA 59.470 50.000 0.00 0.00 43.64 5.10
304 306 5.163632 TGAGATGTTCGCATAAAATGTGCAT 60.164 36.000 0.00 0.00 42.62 3.96
352 354 4.208686 GGAGCGCTCGTGTAGGGG 62.209 72.222 29.81 0.00 38.57 4.79
381 383 6.014327 AGCAACAAAGATTTTACCATGGATGT 60.014 34.615 21.47 0.00 0.00 3.06
432 434 2.386661 AATGGACATGACCACGAGTC 57.613 50.000 19.28 0.00 46.51 3.36
500 503 5.688823 TCTGTTGCAAAAGTGATATTGACG 58.311 37.500 16.28 0.00 0.00 4.35
501 504 4.793071 TGTTGCAAAAGTGATATTGACGG 58.207 39.130 0.00 0.00 0.00 4.79
503 506 2.163412 TGCAAAAGTGATATTGACGGCC 59.837 45.455 0.00 0.00 0.00 6.13
511 514 2.088423 GATATTGACGGCCACAAACCA 58.912 47.619 14.76 5.73 0.00 3.67
541 544 6.491745 TGCTTCTACAACATGGGTCATTTTAA 59.508 34.615 0.00 0.00 0.00 1.52
555 558 7.398618 TGGGTCATTTTAAGATTGCAATAAGGA 59.601 33.333 12.97 7.02 0.00 3.36
564 567 6.461110 AGATTGCAATAAGGATCTTGTTGG 57.539 37.500 12.97 2.58 0.00 3.77
606 609 8.552083 AATAGAAATGCAGATATAATCGCACA 57.448 30.769 0.00 0.00 39.93 4.57
633 2868 0.596083 GACAGCCGGATCTCATGACG 60.596 60.000 5.05 0.00 0.00 4.35
730 4555 3.110178 GTGTGTACGCCAGTCGCC 61.110 66.667 3.51 0.00 43.23 5.54
731 4556 3.607661 TGTGTACGCCAGTCGCCA 61.608 61.111 3.51 0.00 43.23 5.69
732 4557 3.110178 GTGTACGCCAGTCGCCAC 61.110 66.667 0.00 0.00 43.23 5.01
733 4558 4.367023 TGTACGCCAGTCGCCACC 62.367 66.667 0.00 0.00 43.23 4.61
816 4641 0.694196 TGTACCACCTTAGGTTGGGC 59.306 55.000 19.03 13.41 43.08 5.36
835 4660 0.388294 CCCCGGTCGGAGATAAGTTC 59.612 60.000 11.39 0.00 40.67 3.01
852 4677 0.041535 TTCCCATTCCATTGGCTGCT 59.958 50.000 0.00 0.00 35.29 4.24
854 4679 1.682451 CCCATTCCATTGGCTGCTGG 61.682 60.000 0.00 0.00 35.29 4.85
858 4683 4.143333 CCATTGGCTGCTGGCTGC 62.143 66.667 17.87 14.49 41.46 5.25
886 4918 3.941188 ACCCTGGACGTGGCTGTG 61.941 66.667 0.00 0.00 0.00 3.66
942 4974 2.358737 CGGCACCCAAGACTCACC 60.359 66.667 0.00 0.00 0.00 4.02
1635 5673 1.219124 CTCCATCCTCCACCACGTG 59.781 63.158 9.08 9.08 0.00 4.49
1954 6007 1.550976 CACTGTCCTCCTCTGTAACCC 59.449 57.143 0.00 0.00 0.00 4.11
1980 6033 0.249120 CTAATGCCCAGTCACGTCCA 59.751 55.000 0.00 0.00 0.00 4.02
2035 6096 7.891183 TCTTTCTTACTGTAAGATCTGTCTCCT 59.109 37.037 25.99 0.00 43.72 3.69
2056 6143 3.764160 GAGGAGAATGCAGCCCCGG 62.764 68.421 0.00 0.00 0.00 5.73
2073 6160 1.468520 CCGGCAAATGTACTGAACTGG 59.531 52.381 0.00 0.00 0.00 4.00
2098 6185 9.506018 GGAAGTTTACCCTGTAACAGTAATTTA 57.494 33.333 0.00 0.00 0.00 1.40
2113 6201 8.353423 ACAGTAATTTAAGAGATGCAATGGTT 57.647 30.769 0.00 0.00 0.00 3.67
2122 6210 7.559590 AAGAGATGCAATGGTTATTACTCAC 57.440 36.000 0.00 0.00 0.00 3.51
2136 6225 0.109086 ACTCACGTTGCATCCTCGAG 60.109 55.000 5.13 5.13 0.00 4.04
2237 6327 4.637534 CCATCCTCCACAATGTACTGAAAG 59.362 45.833 0.00 0.00 42.29 2.62
2276 6367 5.536161 CCAAATTCCAAAGAGAAGGTGAGAA 59.464 40.000 0.00 0.00 0.00 2.87
2280 6371 6.494666 TTCCAAAGAGAAGGTGAGAACTTA 57.505 37.500 0.00 0.00 0.00 2.24
2296 6387 5.725362 AGAACTTATGTACCTGCTTGTCTC 58.275 41.667 0.00 0.00 0.00 3.36
2297 6388 4.473477 ACTTATGTACCTGCTTGTCTCC 57.527 45.455 0.00 0.00 0.00 3.71
2306 6397 3.525199 ACCTGCTTGTCTCCCTCAATATT 59.475 43.478 0.00 0.00 0.00 1.28
2307 6398 4.721776 ACCTGCTTGTCTCCCTCAATATTA 59.278 41.667 0.00 0.00 0.00 0.98
2309 6400 6.126361 ACCTGCTTGTCTCCCTCAATATTATT 60.126 38.462 0.00 0.00 0.00 1.40
2310 6401 6.774656 CCTGCTTGTCTCCCTCAATATTATTT 59.225 38.462 0.00 0.00 0.00 1.40
2312 6403 9.342308 CTGCTTGTCTCCCTCAATATTATTTAA 57.658 33.333 0.00 0.00 0.00 1.52
2313 6404 9.866655 TGCTTGTCTCCCTCAATATTATTTAAT 57.133 29.630 0.00 0.00 0.00 1.40
2354 6445 4.397348 CTTACCAAGCTGGCCGTT 57.603 55.556 0.00 0.00 42.67 4.44
2382 6476 7.012138 GCTGCATGGTCTCTCAATATATATTGG 59.988 40.741 27.44 20.06 42.46 3.16
2384 6478 8.775151 TGCATGGTCTCTCAATATATATTGGAT 58.225 33.333 27.44 11.14 42.46 3.41
2386 6480 9.775854 CATGGTCTCTCAATATATATTGGATCC 57.224 37.037 27.44 23.84 42.46 3.36
2400 6610 5.965033 ATTGGATCCTGATAAGTGTCACT 57.035 39.130 14.23 0.00 0.00 3.41
2403 6613 2.941453 TCCTGATAAGTGTCACTCGC 57.059 50.000 5.82 0.00 0.00 5.03
2407 6617 1.281899 GATAAGTGTCACTCGCCAGC 58.718 55.000 5.82 0.00 0.00 4.85
2422 6632 1.448365 CAGCTACGAGCACATGGCA 60.448 57.895 8.58 0.00 45.56 4.92
2437 6647 3.749088 ACATGGCAACTTCGATCGTTTTA 59.251 39.130 15.94 0.00 37.61 1.52
2441 6651 5.891084 TGGCAACTTCGATCGTTTTAGACG 61.891 45.833 15.94 6.66 46.09 4.18
2455 6665 5.438117 GTTTTAGACGGCAAGTTTAGTGAC 58.562 41.667 0.00 0.00 0.00 3.67
2459 6669 1.279527 CGGCAAGTTTAGTGACGCGA 61.280 55.000 15.93 0.00 41.30 5.87
2502 6712 1.869342 GCATGCCAACTTTCGTGCTTT 60.869 47.619 6.36 0.00 40.87 3.51
2509 6719 5.009210 TGCCAACTTTCGTGCTTTAGTTTAT 59.991 36.000 0.00 0.00 0.00 1.40
2516 6726 9.016623 ACTTTCGTGCTTTAGTTTATTTTTGAC 57.983 29.630 0.00 0.00 0.00 3.18
2518 6728 8.555166 TTCGTGCTTTAGTTTATTTTTGACAG 57.445 30.769 0.00 0.00 0.00 3.51
2530 6740 3.859411 TTTTGACAGAAACTTGCCGTT 57.141 38.095 0.00 0.00 37.47 4.44
2546 6756 3.119316 TGCCGTTTGTCACTGAAAATTGT 60.119 39.130 0.00 0.00 0.00 2.71
2553 6763 6.713762 TTGTCACTGAAAATTGTCATCCTT 57.286 33.333 0.00 0.00 0.00 3.36
2554 6764 6.075762 TGTCACTGAAAATTGTCATCCTTG 57.924 37.500 0.00 0.00 0.00 3.61
2559 6769 3.244976 GAAAATTGTCATCCTTGCGTGG 58.755 45.455 0.00 0.00 0.00 4.94
2596 6806 2.561478 AAATGTTAGGTCCGCAGTGT 57.439 45.000 0.00 0.00 0.00 3.55
2603 6813 2.738521 GTCCGCAGTGTCACGCAT 60.739 61.111 16.31 0.00 0.00 4.73
2608 6818 1.080435 CGCAGTGTCACGCATCTGAT 61.080 55.000 16.31 0.00 32.05 2.90
2609 6819 1.798813 CGCAGTGTCACGCATCTGATA 60.799 52.381 16.31 0.00 32.05 2.15
2620 6830 2.222678 CGCATCTGATATGTGGCACTTC 59.777 50.000 19.83 13.09 0.00 3.01
2626 6836 6.484364 TCTGATATGTGGCACTTCTCATTA 57.516 37.500 19.83 9.01 0.00 1.90
2658 6868 4.875544 TCAGAAGTGTCGTTTTCTTTGG 57.124 40.909 0.00 0.00 31.53 3.28
2662 6872 5.064707 CAGAAGTGTCGTTTTCTTTGGAGAA 59.935 40.000 0.00 0.00 40.07 2.87
2685 6895 1.605753 GGGAACACCAAAGTCTCCAC 58.394 55.000 0.00 0.00 39.85 4.02
2731 7101 7.015974 ACAGATCAGGCATGAGATATACTTCAA 59.984 37.037 7.33 0.00 39.29 2.69
2732 7102 7.876582 CAGATCAGGCATGAGATATACTTCAAA 59.123 37.037 7.33 0.00 39.29 2.69
2849 7228 2.169769 GTGATTGGTACGGGATCCTTGA 59.830 50.000 12.58 0.00 0.00 3.02
2855 7234 2.618053 GTACGGGATCCTTGAGTGTTG 58.382 52.381 12.58 0.00 0.00 3.33
2881 7260 4.814771 ACGAAGTGCTAGGTTTTATATGCC 59.185 41.667 0.00 0.00 42.51 4.40
2895 7274 3.963428 ATATGCCTCCTGTATCGGTTC 57.037 47.619 0.00 0.00 0.00 3.62
2901 7280 2.030185 CCTCCTGTATCGGTTCGTATGG 60.030 54.545 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.506881 CGGCAATTTTGGAGGCGC 60.507 61.111 0.00 0.00 44.06 6.53
11 12 4.023193 GGTGGATATACGGCAATTTTGGAG 60.023 45.833 0.00 0.00 0.00 3.86
15 16 3.227614 GGGGTGGATATACGGCAATTTT 58.772 45.455 0.00 0.00 0.00 1.82
20 21 1.049855 AACGGGGTGGATATACGGCA 61.050 55.000 0.00 0.00 0.00 5.69
37 38 1.331214 CCCATGCCCATCCACATAAC 58.669 55.000 0.00 0.00 0.00 1.89
38 39 0.188096 CCCCATGCCCATCCACATAA 59.812 55.000 0.00 0.00 0.00 1.90
85 87 0.541863 AGTCAACCCGCCCTTCTATG 59.458 55.000 0.00 0.00 0.00 2.23
95 97 2.218603 ACAACTTTGCTAGTCAACCCG 58.781 47.619 0.00 0.00 35.54 5.28
96 98 4.023450 GGTAACAACTTTGCTAGTCAACCC 60.023 45.833 0.00 0.00 35.54 4.11
111 113 1.461897 CGGTCATTGTCCGGTAACAAC 59.538 52.381 10.64 0.00 41.65 3.32
131 133 4.365723 TCTAAACGTTTGAGTGGACTGTC 58.634 43.478 23.46 0.00 0.00 3.51
133 135 3.741344 CCTCTAAACGTTTGAGTGGACTG 59.259 47.826 23.46 9.72 0.00 3.51
134 136 3.640029 TCCTCTAAACGTTTGAGTGGACT 59.360 43.478 23.46 0.00 29.99 3.85
135 137 3.986277 TCCTCTAAACGTTTGAGTGGAC 58.014 45.455 23.46 0.00 29.99 4.02
136 138 3.640029 ACTCCTCTAAACGTTTGAGTGGA 59.360 43.478 23.30 23.69 32.22 4.02
137 139 3.991367 ACTCCTCTAAACGTTTGAGTGG 58.009 45.455 23.30 21.80 32.22 4.00
139 141 5.667466 TCAAACTCCTCTAAACGTTTGAGT 58.333 37.500 23.46 21.52 45.81 3.41
142 144 6.598753 TCTTCAAACTCCTCTAAACGTTTG 57.401 37.500 23.46 13.01 44.47 2.93
143 145 5.236695 GCTCTTCAAACTCCTCTAAACGTTT 59.763 40.000 18.90 18.90 0.00 3.60
153 155 3.073650 ACAATCAGGCTCTTCAAACTCCT 59.926 43.478 0.00 0.00 0.00 3.69
165 167 4.884164 GGTAAGAGCATTTACAATCAGGCT 59.116 41.667 11.09 0.00 35.67 4.58
169 171 4.570772 GCGAGGTAAGAGCATTTACAATCA 59.429 41.667 11.09 0.00 35.67 2.57
170 172 4.024809 GGCGAGGTAAGAGCATTTACAATC 60.025 45.833 11.09 8.02 35.67 2.67
185 187 1.744014 GGAAATAGCCGGCGAGGTA 59.256 57.895 23.20 8.40 43.70 3.08
190 192 1.301009 GAGAGGGAAATAGCCGGCG 60.301 63.158 23.20 0.00 0.00 6.46
191 193 1.071642 GGAGAGGGAAATAGCCGGC 59.928 63.158 21.89 21.89 0.00 6.13
208 210 4.037565 GTCCCAATTTATTTCCCTAAGCGG 59.962 45.833 0.00 0.00 0.00 5.52
217 219 9.936759 TTCAATAAAGGTGTCCCAATTTATTTC 57.063 29.630 0.00 0.00 36.28 2.17
247 249 1.887344 GCCATGCCGTGTCCCATTTT 61.887 55.000 0.00 0.00 0.00 1.82
259 261 4.451150 TCGACCACGAGCCATGCC 62.451 66.667 0.00 0.00 43.81 4.40
292 294 5.263599 TGGACCTTGAGATGCACATTTTAT 58.736 37.500 0.00 0.00 0.00 1.40
352 354 4.789784 TGGTAAAATCTTTGTTGCTACGC 58.210 39.130 0.00 0.00 0.00 4.42
355 357 7.178274 ACATCCATGGTAAAATCTTTGTTGCTA 59.822 33.333 12.58 0.00 0.00 3.49
397 399 9.868277 TCATGTCCATTATTATTTTTGTTGTCC 57.132 29.630 0.00 0.00 0.00 4.02
403 405 8.187480 TCGTGGTCATGTCCATTATTATTTTTG 58.813 33.333 14.91 0.00 39.81 2.44
406 408 7.054124 ACTCGTGGTCATGTCCATTATTATTT 58.946 34.615 14.91 0.00 39.81 1.40
409 411 5.597806 GACTCGTGGTCATGTCCATTATTA 58.402 41.667 14.91 0.00 43.94 0.98
412 414 2.159296 CGACTCGTGGTCATGTCCATTA 60.159 50.000 14.91 5.64 44.70 1.90
432 434 2.727798 CCTTGTTGCAAAAGCATCTTCG 59.272 45.455 0.00 0.00 0.00 3.79
449 451 1.228533 GCAATTGCAACAACCCCTTG 58.771 50.000 25.36 1.34 41.59 3.61
500 503 0.681175 AGCATCTTTGGTTTGTGGCC 59.319 50.000 0.00 0.00 0.00 5.36
501 504 2.036346 AGAAGCATCTTTGGTTTGTGGC 59.964 45.455 0.00 0.00 43.35 5.01
503 506 5.437289 TGTAGAAGCATCTTTGGTTTGTG 57.563 39.130 0.00 0.00 43.35 3.33
511 514 4.666512 ACCCATGTTGTAGAAGCATCTTT 58.333 39.130 0.00 0.00 37.10 2.52
541 544 6.189859 TCCAACAAGATCCTTATTGCAATCT 58.810 36.000 16.86 3.39 0.00 2.40
555 558 6.122277 TCTGTTTTTCTCACTCCAACAAGAT 58.878 36.000 0.00 0.00 0.00 2.40
559 562 5.097742 TCTCTGTTTTTCTCACTCCAACA 57.902 39.130 0.00 0.00 0.00 3.33
606 609 3.153919 GAGATCCGGCTGTCTAATCTCT 58.846 50.000 16.07 0.00 39.37 3.10
648 2883 2.103432 TCGGCCGGCTTATCTATTGAAA 59.897 45.455 28.56 0.00 0.00 2.69
649 2884 1.689813 TCGGCCGGCTTATCTATTGAA 59.310 47.619 28.56 0.00 0.00 2.69
654 2889 3.036577 CGTCGGCCGGCTTATCTA 58.963 61.111 29.47 0.34 0.00 1.98
665 2900 1.349259 AATGAGTGTTACGCGTCGGC 61.349 55.000 18.63 7.95 0.00 5.54
730 4555 2.280797 CACGACTGGGTGTGGGTG 60.281 66.667 0.00 0.00 33.24 4.61
736 4561 3.991051 AGGCGACACGACTGGGTG 61.991 66.667 0.00 0.38 46.62 4.61
816 4641 0.388294 GAACTTATCTCCGACCGGGG 59.612 60.000 6.32 5.14 37.02 5.73
835 4660 1.682451 CCAGCAGCCAATGGAATGGG 61.682 60.000 2.05 0.00 41.90 4.00
871 4901 4.320456 AGCACAGCCACGTCCAGG 62.320 66.667 0.00 0.00 0.00 4.45
895 4927 3.952628 GATGTATAGGCGCGGGGGC 62.953 68.421 8.83 10.77 42.69 5.80
1761 5799 3.682292 GATGAGCACCACCGACCCC 62.682 68.421 0.00 0.00 0.00 4.95
1932 5985 2.249139 GTTACAGAGGAGGACAGTGGT 58.751 52.381 0.00 0.00 0.00 4.16
1954 6007 2.287915 GTGACTGGGCATTAGTATTGCG 59.712 50.000 10.14 1.26 41.07 4.85
2035 6096 0.767375 GGGGCTGCATTCTCCTCATA 59.233 55.000 0.50 0.00 0.00 2.15
2046 6107 3.575703 TACATTTGCCGGGGCTGCA 62.576 57.895 11.55 0.00 42.51 4.41
2050 6137 0.963355 TTCAGTACATTTGCCGGGGC 60.963 55.000 2.18 1.86 42.35 5.80
2056 6143 5.438761 AACTTCCAGTTCAGTACATTTGC 57.561 39.130 0.00 0.00 31.77 3.68
2088 6175 7.944729 ACCATTGCATCTCTTAAATTACTGT 57.055 32.000 0.00 0.00 0.00 3.55
2098 6185 6.258727 CGTGAGTAATAACCATTGCATCTCTT 59.741 38.462 0.00 0.00 0.00 2.85
2099 6186 5.755375 CGTGAGTAATAACCATTGCATCTCT 59.245 40.000 0.00 0.00 0.00 3.10
2113 6201 7.445569 CCTCGAGGATGCAACGTGAGTAATA 62.446 48.000 28.21 0.00 40.30 0.98
2122 6210 2.859273 AAGCCCTCGAGGATGCAACG 62.859 60.000 33.39 14.91 38.24 4.10
2136 6225 4.124238 TGTATGCGAGTATTACAAAGCCC 58.876 43.478 0.00 0.00 0.00 5.19
2210 6300 4.102210 CAGTACATTGTGGAGGATGGAGAT 59.898 45.833 0.00 0.00 0.00 2.75
2237 6327 5.990996 TGGAATTTGGAATTGCAGAAAGAAC 59.009 36.000 0.00 0.00 0.00 3.01
2276 6367 3.197983 GGGAGACAAGCAGGTACATAAGT 59.802 47.826 0.00 0.00 0.00 2.24
2280 6371 1.834263 GAGGGAGACAAGCAGGTACAT 59.166 52.381 0.00 0.00 0.00 2.29
2354 6445 0.622136 ATTGAGAGACCATGCAGCCA 59.378 50.000 0.00 0.00 0.00 4.75
2356 6447 7.012138 CCAATATATATTGAGAGACCATGCAGC 59.988 40.741 29.23 0.00 44.40 5.25
2357 6448 8.262933 TCCAATATATATTGAGAGACCATGCAG 58.737 37.037 29.23 12.74 44.40 4.41
2358 6449 8.149631 TCCAATATATATTGAGAGACCATGCA 57.850 34.615 29.23 0.00 44.40 3.96
2361 6452 9.741198 AGGATCCAATATATATTGAGAGACCAT 57.259 33.333 29.23 10.37 44.40 3.55
2382 6476 3.376540 GCGAGTGACACTTATCAGGATC 58.623 50.000 10.01 0.00 0.00 3.36
2384 6478 1.476891 GGCGAGTGACACTTATCAGGA 59.523 52.381 10.01 0.00 0.00 3.86
2386 6480 2.534298 CTGGCGAGTGACACTTATCAG 58.466 52.381 10.01 12.76 0.00 2.90
2400 6610 2.710902 ATGTGCTCGTAGCTGGCGA 61.711 57.895 13.22 13.22 42.97 5.54
2403 6613 2.176273 GCCATGTGCTCGTAGCTGG 61.176 63.158 0.00 8.23 42.97 4.85
2407 6617 1.394917 GAAGTTGCCATGTGCTCGTAG 59.605 52.381 7.54 0.00 42.00 3.51
2437 6647 1.779569 CGTCACTAAACTTGCCGTCT 58.220 50.000 0.00 0.00 0.00 4.18
2441 6651 0.438830 CTCGCGTCACTAAACTTGCC 59.561 55.000 5.77 0.00 0.00 4.52
2455 6665 2.607187 ACTAAAGTTGTCATCCTCGCG 58.393 47.619 0.00 0.00 0.00 5.87
2480 6690 0.318955 GCACGAAAGTTGGCATGCTT 60.319 50.000 18.92 2.78 46.40 3.91
2487 6697 7.924103 AAATAAACTAAAGCACGAAAGTTGG 57.076 32.000 0.00 0.00 46.40 3.77
2495 6705 8.555166 TTCTGTCAAAAATAAACTAAAGCACG 57.445 30.769 0.00 0.00 0.00 5.34
2502 6712 7.646130 CGGCAAGTTTCTGTCAAAAATAAACTA 59.354 33.333 0.00 0.00 38.95 2.24
2509 6719 3.859411 ACGGCAAGTTTCTGTCAAAAA 57.141 38.095 0.00 0.00 0.00 1.94
2530 6740 6.506147 CAAGGATGACAATTTTCAGTGACAA 58.494 36.000 0.23 0.00 0.00 3.18
2580 6790 0.032952 GTGACACTGCGGACCTAACA 59.967 55.000 0.00 0.00 0.00 2.41
2591 6801 3.244579 CACATATCAGATGCGTGACACTG 59.755 47.826 3.68 0.00 0.00 3.66
2596 6806 1.138661 TGCCACATATCAGATGCGTGA 59.861 47.619 13.20 0.00 0.00 4.35
2603 6813 5.363562 AATGAGAAGTGCCACATATCAGA 57.636 39.130 3.69 0.00 0.00 3.27
2608 6818 5.435686 ACCTTAATGAGAAGTGCCACATA 57.564 39.130 0.00 0.00 0.00 2.29
2609 6819 4.307032 ACCTTAATGAGAAGTGCCACAT 57.693 40.909 0.00 0.00 0.00 3.21
2626 6836 8.617290 AAACGACACTTCTGAAAATATACCTT 57.383 30.769 0.00 0.00 0.00 3.50
2668 6878 2.614057 CTGTGTGGAGACTTTGGTGTTC 59.386 50.000 0.00 0.00 0.00 3.18
2695 6905 4.355543 TGCCTGATCTGTTTTATTTCGC 57.644 40.909 0.00 0.00 0.00 4.70
2731 7101 5.337652 CCACCTACTAGCTGCTAGTTTTCTT 60.338 44.000 38.22 20.39 43.82 2.52
2732 7102 4.160626 CCACCTACTAGCTGCTAGTTTTCT 59.839 45.833 38.22 21.02 43.82 2.52
2796 7166 8.708742 GGATTAACTAAAACCATGTGCTTTTTC 58.291 33.333 0.00 0.00 0.00 2.29
2849 7228 2.545952 CCTAGCACTTCGTGTCAACACT 60.546 50.000 11.23 0.00 44.34 3.55
2855 7234 6.509677 GCATATAAAACCTAGCACTTCGTGTC 60.510 42.308 0.00 0.00 35.75 3.67
2881 7260 2.621998 ACCATACGAACCGATACAGGAG 59.378 50.000 0.00 0.00 34.73 3.69


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

AutoCloner maintained by Alex Coulton.