Multiple sequence alignment - TraesCS7A01G046200

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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 TraesCS7A01G046200 chr7A 100.000 3694 0 0 1 3694 20966646 20970339 0.000000e+00 6822
1 TraesCS7A01G046200 chr7A 85.662 3020 360 36 25 2997 20911083 20914076 0.000000e+00 3110
2 TraesCS7A01G046200 chr7A 89.016 2440 257 9 1 2435 20483172 20485605 0.000000e+00 3011
3 TraesCS7A01G046200 chr7A 85.168 2353 332 11 1 2349 20980972 20983311 0.000000e+00 2396
4 TraesCS7A01G046200 chr7A 84.179 2484 368 20 1 2471 20676851 20679322 0.000000e+00 2386
5 TraesCS7A01G046200 chr7A 92.077 366 24 3 3017 3382 20914190 20914550 9.150000e-141 510
6 TraesCS7A01G046200 chr7A 87.050 139 16 2 3553 3690 20914823 20914960 4.940000e-34 156
7 TraesCS7A01G046200 chr7D 86.728 3451 339 49 1 3385 20311220 20314617 0.000000e+00 3725
8 TraesCS7A01G046200 chr7D 86.207 2494 317 24 1 2485 20485986 20488461 0.000000e+00 2675
9 TraesCS7A01G046200 chr7D 83.966 2451 385 8 1 2447 89532674 89530228 0.000000e+00 2342
10 TraesCS7A01G046200 chr7D 89.286 112 12 0 3413 3524 20300627 20300516 1.380000e-29 141
11 TraesCS7A01G046200 chr2A 84.644 2416 358 13 14 2422 733088158 733090567 0.000000e+00 2394
12 TraesCS7A01G046200 chr2D 84.167 2438 375 11 6 2437 598814448 598816880 0.000000e+00 2353
13 TraesCS7A01G046200 chr4A 83.483 557 60 16 2645 3176 694364887 694364338 1.190000e-134 490
14 TraesCS7A01G046200 chr5D 80.995 221 24 5 2801 3011 117738935 117739147 3.820000e-35 159


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 TraesCS7A01G046200 chr7A 20966646 20970339 3693 False 6822.000000 6822 100.000 1 3694 1 chr7A.!!$F3 3693
1 TraesCS7A01G046200 chr7A 20483172 20485605 2433 False 3011.000000 3011 89.016 1 2435 1 chr7A.!!$F1 2434
2 TraesCS7A01G046200 chr7A 20980972 20983311 2339 False 2396.000000 2396 85.168 1 2349 1 chr7A.!!$F4 2348
3 TraesCS7A01G046200 chr7A 20676851 20679322 2471 False 2386.000000 2386 84.179 1 2471 1 chr7A.!!$F2 2470
4 TraesCS7A01G046200 chr7A 20911083 20914960 3877 False 1258.666667 3110 88.263 25 3690 3 chr7A.!!$F5 3665
5 TraesCS7A01G046200 chr7D 20311220 20314617 3397 False 3725.000000 3725 86.728 1 3385 1 chr7D.!!$F1 3384
6 TraesCS7A01G046200 chr7D 20485986 20488461 2475 False 2675.000000 2675 86.207 1 2485 1 chr7D.!!$F2 2484
7 TraesCS7A01G046200 chr7D 89530228 89532674 2446 True 2342.000000 2342 83.966 1 2447 1 chr7D.!!$R2 2446
8 TraesCS7A01G046200 chr2A 733088158 733090567 2409 False 2394.000000 2394 84.644 14 2422 1 chr2A.!!$F1 2408
9 TraesCS7A01G046200 chr2D 598814448 598816880 2432 False 2353.000000 2353 84.167 6 2437 1 chr2D.!!$F1 2431
10 TraesCS7A01G046200 chr4A 694364338 694364887 549 True 490.000000 490 83.483 2645 3176 1 chr4A.!!$R1 531

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
619 620 0.250295 TCACAACAAGAGAAGCCCGG 60.250 55.000 0.0 0.0 0.0 5.73 F
949 950 1.482593 AGCTTCATCTACCTCCCAACG 59.517 52.381 0.0 0.0 0.0 4.10 F
1833 1839 1.486211 AGGGAATCTACTGTGGACGG 58.514 55.000 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1769 1.064389 GCCTCAGCTCCCCTAAATGTT 60.064 52.381 0.00 0.0 35.50 2.71 R
2025 2031 1.202486 TGTGACCAACGGAGAGACAAC 60.202 52.381 0.00 0.0 0.00 3.32 R
3548 3874 0.107361 CACATCAGAGCTCCATGCCA 60.107 55.000 18.91 0.0 44.23 4.92 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
319 320 4.024048 GCTTTAGCTGCAAGTGTCTACAAA 60.024 41.667 1.02 0.00 38.21 2.83
442 443 6.369629 AGATACTGCCAGTGTTCTATCTAGT 58.630 40.000 7.83 0.00 0.00 2.57
448 449 6.896883 TGCCAGTGTTCTATCTAGTACTCTA 58.103 40.000 0.00 0.00 30.08 2.43
619 620 0.250295 TCACAACAAGAGAAGCCCGG 60.250 55.000 0.00 0.00 0.00 5.73
669 670 6.588756 CGTATCTTAACACTGGAAGCTTTACA 59.411 38.462 0.00 2.25 37.60 2.41
685 686 4.216257 GCTTTACAAGAAGACAAGGCATGA 59.784 41.667 0.00 0.00 0.00 3.07
738 739 6.996879 AGAGATACAAATCATGAATGTCCCAG 59.003 38.462 17.77 0.00 34.28 4.45
771 772 4.272748 GCCATCGTCCAAGGAAATAGTTAC 59.727 45.833 0.00 0.00 0.00 2.50
784 785 5.243060 GGAAATAGTTACCAAGTGCAAAGGT 59.757 40.000 10.40 10.40 39.41 3.50
899 900 8.470002 GCTGGGAGATAATTAACAATTCAAGTT 58.530 33.333 0.00 0.00 32.38 2.66
949 950 1.482593 AGCTTCATCTACCTCCCAACG 59.517 52.381 0.00 0.00 0.00 4.10
968 969 7.028361 CCCAACGTACTTAAAAAGTTGTTTCA 58.972 34.615 12.21 0.00 42.81 2.69
1090 1091 4.042187 ACATTAGAAGAAGTGGCAGAAGGT 59.958 41.667 0.00 0.00 0.00 3.50
1252 1255 7.516198 ACATATGAGAATAAATGTGAAGGGC 57.484 36.000 10.38 0.00 31.56 5.19
1300 1306 6.554334 TGGTACTGCACAAACTAAAAGATC 57.446 37.500 0.00 0.00 0.00 2.75
1384 1390 6.804677 AGCAAGTCATCATTCACTCTACTAG 58.195 40.000 0.00 0.00 0.00 2.57
1435 1441 5.865085 TGACAGTGCTAGAATTAAGTGGTT 58.135 37.500 0.00 0.00 0.00 3.67
1469 1475 4.637387 AGATTCCAGATGCTATTGGAGG 57.363 45.455 4.31 0.00 43.89 4.30
1557 1563 6.042143 TGAGAAGCTTTCAAATTTGTTGACC 58.958 36.000 17.47 4.68 0.00 4.02
1567 1573 4.670896 AATTTGTTGACCTTGGACCTTG 57.329 40.909 0.00 0.00 0.00 3.61
1587 1593 3.937814 TGGTGGTTCTGACATACATGAC 58.062 45.455 0.00 0.00 0.00 3.06
1654 1660 5.584253 TGCTGAGAGAGTAACTAATCCAC 57.416 43.478 0.00 0.00 0.00 4.02
1697 1703 1.893808 GTGGTATGCGCATCCCCAG 60.894 63.158 31.21 0.00 0.00 4.45
1718 1724 4.214971 CAGTGGTCTTGGAAATCTGACAAG 59.785 45.833 0.00 0.00 42.14 3.16
1740 1746 3.000041 CCTGCAGACGTTACAAGCATTA 59.000 45.455 17.39 0.00 34.35 1.90
1833 1839 1.486211 AGGGAATCTACTGTGGACGG 58.514 55.000 0.00 0.00 0.00 4.79
1838 1844 3.132289 GGAATCTACTGTGGACGGATCAA 59.868 47.826 0.00 0.00 0.00 2.57
1845 1851 1.899142 TGTGGACGGATCAATGAGTCA 59.101 47.619 0.00 0.00 35.49 3.41
1852 1858 4.748892 ACGGATCAATGAGTCACTAGTTG 58.251 43.478 0.00 0.00 0.00 3.16
1869 1875 6.591448 CACTAGTTGAGATGCAGTATTTGTCA 59.409 38.462 0.00 0.00 0.00 3.58
1876 1882 7.210174 TGAGATGCAGTATTTGTCATACCTAC 58.790 38.462 0.00 0.00 0.00 3.18
1924 1930 3.008485 GGTTCTCCTGTTGAATGTCTCCT 59.992 47.826 0.00 0.00 0.00 3.69
1935 1941 3.073798 TGAATGTCTCCTTGCCAAACCTA 59.926 43.478 0.00 0.00 0.00 3.08
1936 1942 3.806949 ATGTCTCCTTGCCAAACCTAA 57.193 42.857 0.00 0.00 0.00 2.69
2035 2041 6.952743 CATAACTTGCATATGTTGTCTCTCC 58.047 40.000 4.29 0.00 0.00 3.71
2036 2042 3.525537 ACTTGCATATGTTGTCTCTCCG 58.474 45.455 4.29 0.00 0.00 4.63
2068 2074 0.035343 GAGTAAAGACCCCCTGCCAC 60.035 60.000 0.00 0.00 0.00 5.01
2070 2076 2.598787 TAAAGACCCCCTGCCACCG 61.599 63.158 0.00 0.00 0.00 4.94
2136 2142 0.390866 ACAATGGAGAGCAGCTGACG 60.391 55.000 20.43 0.00 0.00 4.35
2142 2148 1.606737 GGAGAGCAGCTGACGTTTCTT 60.607 52.381 20.43 0.00 0.00 2.52
2145 2151 2.035961 AGAGCAGCTGACGTTTCTTACA 59.964 45.455 20.43 0.00 0.00 2.41
2175 2181 2.635915 TCCCAAGCTAAAGGTTCTCGAA 59.364 45.455 0.00 0.00 32.86 3.71
2208 2214 3.834813 TGCCTAATCTGAATCGGCTAGAT 59.165 43.478 9.36 0.00 41.25 1.98
2236 2242 2.352422 GTGCCATGGTGAGCCTGA 59.648 61.111 14.67 0.00 35.27 3.86
2239 2245 2.413142 GCCATGGTGAGCCTGAAGC 61.413 63.158 14.67 0.00 44.25 3.86
2262 2268 5.938125 GCAATTAACCTTAGTCAACCTCAGA 59.062 40.000 0.00 0.00 0.00 3.27
2289 2295 2.191641 GAGGTCCCAGCTGGCATC 59.808 66.667 28.39 14.39 0.00 3.91
2299 2305 0.975040 AGCTGGCATCGAGTTCCTCT 60.975 55.000 0.00 0.00 0.00 3.69
2387 2393 1.019805 GTACTTGAAGGGCAGCGGTC 61.020 60.000 0.00 0.00 0.00 4.79
2461 2473 7.239438 AGGTATGTAAGCTAGGCACTAATCTA 58.761 38.462 0.00 0.00 42.17 1.98
2491 2503 2.108970 CAGTACCACTACTTCCTCCCC 58.891 57.143 0.00 0.00 30.03 4.81
2506 2518 5.434003 TCCTCCCCCATCTCTAATCTTAA 57.566 43.478 0.00 0.00 0.00 1.85
2509 2521 7.192628 TCCTCCCCCATCTCTAATCTTAATAG 58.807 42.308 0.00 0.00 0.00 1.73
2574 2607 0.037512 TTCATTGTTTGGGCCGCATG 60.038 50.000 0.00 0.00 0.00 4.06
2575 2608 2.101835 CATTGTTTGGGCCGCATGC 61.102 57.895 7.91 7.91 40.16 4.06
2792 2871 2.101582 TCGAATTAAGGAGCTCTCTGCC 59.898 50.000 14.64 0.00 44.23 4.85
2837 2923 5.712004 TGATGAACGCATGATTTGTTTCAT 58.288 33.333 0.00 0.47 40.23 2.57
2869 2966 1.303309 GAGTGTGCTTGCTGTGAACT 58.697 50.000 0.00 0.00 0.00 3.01
2881 2978 2.667724 GCTGTGAACTCATTTCAGCTGC 60.668 50.000 9.47 0.00 45.23 5.25
2898 2995 2.921121 GCTGCGGCTGTTAAATAAAACC 59.079 45.455 11.21 0.00 35.22 3.27
2900 2997 4.743493 CTGCGGCTGTTAAATAAAACCAT 58.257 39.130 0.00 0.00 0.00 3.55
2901 2998 5.140747 TGCGGCTGTTAAATAAAACCATT 57.859 34.783 0.00 0.00 0.00 3.16
2902 2999 5.542779 TGCGGCTGTTAAATAAAACCATTT 58.457 33.333 0.00 0.00 32.91 2.32
2903 3000 5.406780 TGCGGCTGTTAAATAAAACCATTTG 59.593 36.000 0.00 0.00 30.84 2.32
2946 3047 3.631686 TGCTGGGGTATTCATTTTCATCG 59.368 43.478 0.00 0.00 0.00 3.84
2950 3051 4.080015 TGGGGTATTCATTTTCATCGTCCT 60.080 41.667 0.00 0.00 0.00 3.85
2959 3060 2.357327 TTCATCGTCCTGTGGTAACG 57.643 50.000 0.00 0.00 42.51 3.18
2961 3062 2.435422 TCATCGTCCTGTGGTAACGTA 58.565 47.619 0.00 0.00 42.51 3.57
2968 3069 2.093869 TCCTGTGGTAACGTATTGCCTC 60.094 50.000 0.00 0.00 41.03 4.70
2972 3073 3.121544 GTGGTAACGTATTGCCTCTAGC 58.878 50.000 0.00 0.00 41.03 3.42
2978 3079 2.064762 CGTATTGCCTCTAGCTGATGC 58.935 52.381 0.00 1.49 44.23 3.91
3014 3256 1.543642 TGGCTGGGGGAATCCTTGA 60.544 57.895 0.00 0.00 35.33 3.02
3015 3257 1.145900 TGGCTGGGGGAATCCTTGAA 61.146 55.000 0.00 0.00 35.33 2.69
3101 3343 1.982660 TATTTTGGACACGTGGGCAA 58.017 45.000 21.57 1.62 0.00 4.52
3102 3344 1.115467 ATTTTGGACACGTGGGCAAA 58.885 45.000 21.57 12.90 0.00 3.68
3148 3390 1.466360 GCGTTTTCTTGAGCGATGCAT 60.466 47.619 0.00 0.00 0.00 3.96
3149 3391 2.223021 GCGTTTTCTTGAGCGATGCATA 60.223 45.455 0.00 0.00 0.00 3.14
3150 3392 3.345714 CGTTTTCTTGAGCGATGCATAC 58.654 45.455 0.00 0.00 0.00 2.39
3151 3393 3.062639 CGTTTTCTTGAGCGATGCATACT 59.937 43.478 0.00 0.00 0.00 2.12
3155 3403 4.385358 TCTTGAGCGATGCATACTTACA 57.615 40.909 0.00 0.00 0.00 2.41
3164 3412 6.201044 AGCGATGCATACTTACATGTTTACTC 59.799 38.462 2.30 0.00 0.00 2.59
3183 3431 3.826729 ACTCATGGATCATCATGCCAATG 59.173 43.478 6.99 0.00 42.96 2.82
3281 3530 2.978156 AAGATGCAGTTTTCCCAGGA 57.022 45.000 0.00 0.00 0.00 3.86
3304 3553 5.365021 ACCAGTGCTGCTTAGAATCTTAT 57.635 39.130 0.00 0.00 0.00 1.73
3306 3555 6.889198 ACCAGTGCTGCTTAGAATCTTATTA 58.111 36.000 0.00 0.00 0.00 0.98
3308 3557 6.989169 CCAGTGCTGCTTAGAATCTTATTAGT 59.011 38.462 0.00 0.00 0.00 2.24
3311 3560 7.011857 AGTGCTGCTTAGAATCTTATTAGTTGC 59.988 37.037 0.00 0.00 0.00 4.17
3313 3562 7.011763 TGCTGCTTAGAATCTTATTAGTTGCTG 59.988 37.037 0.00 0.00 0.00 4.41
3314 3563 7.011857 GCTGCTTAGAATCTTATTAGTTGCTGT 59.988 37.037 0.00 0.00 0.00 4.40
3315 3564 8.425577 TGCTTAGAATCTTATTAGTTGCTGTC 57.574 34.615 0.00 0.00 0.00 3.51
3316 3565 8.260818 TGCTTAGAATCTTATTAGTTGCTGTCT 58.739 33.333 0.00 0.00 0.00 3.41
3317 3566 9.751542 GCTTAGAATCTTATTAGTTGCTGTCTA 57.248 33.333 0.00 0.00 0.00 2.59
3331 3580 7.879070 AGTTGCTGTCTATTATATGCCATTTG 58.121 34.615 0.00 0.00 0.00 2.32
3338 3587 7.388776 TGTCTATTATATGCCATTTGCTGTCTC 59.611 37.037 0.00 0.00 42.00 3.36
3395 3706 2.752903 GACGGCCATGGTGTTAAGATTT 59.247 45.455 14.67 0.00 0.00 2.17
3396 3707 3.161866 ACGGCCATGGTGTTAAGATTTT 58.838 40.909 14.67 0.00 0.00 1.82
3412 3723 4.504858 AGATTTTATCGACAACCTTCGCT 58.495 39.130 0.00 0.00 38.95 4.93
3427 3738 1.597854 CGCTGTGCCTTTCACTGGA 60.598 57.895 4.56 0.00 45.81 3.86
3431 3742 1.966451 GTGCCTTTCACTGGACCGG 60.966 63.158 0.00 0.00 42.38 5.28
3433 3744 1.122632 TGCCTTTCACTGGACCGGTA 61.123 55.000 7.34 0.00 0.00 4.02
3436 3747 1.337823 CCTTTCACTGGACCGGTACAG 60.338 57.143 39.82 39.82 46.90 2.74
3446 3757 2.963782 GGACCGGTACAGTATCTTCCAT 59.036 50.000 13.46 0.00 0.00 3.41
3449 3760 4.539726 ACCGGTACAGTATCTTCCATGTA 58.460 43.478 4.49 0.00 0.00 2.29
3452 3763 5.983720 CCGGTACAGTATCTTCCATGTAAAG 59.016 44.000 0.00 0.00 30.45 1.85
3454 3765 6.475727 CGGTACAGTATCTTCCATGTAAAGTG 59.524 42.308 0.00 0.58 30.45 3.16
3476 3787 4.039488 TGAAGGAAATGCAAAATCAGCTGT 59.961 37.500 14.67 0.00 0.00 4.40
3481 3792 0.599558 TGCAAAATCAGCTGTGAGGC 59.400 50.000 14.67 12.59 35.66 4.70
3484 3795 0.613012 AAAATCAGCTGTGAGGCCCC 60.613 55.000 14.67 0.00 35.66 5.80
3503 3814 4.352893 CCCCACCTCCACAATTTTTCTAT 58.647 43.478 0.00 0.00 0.00 1.98
3526 3852 5.144100 TGGTGTTAAGATTGGAATGGTGTT 58.856 37.500 0.00 0.00 0.00 3.32
3531 3857 1.545582 AGATTGGAATGGTGTTTGCCG 59.454 47.619 0.00 0.00 0.00 5.69
3533 3859 1.467678 TTGGAATGGTGTTTGCCGGG 61.468 55.000 2.18 0.00 0.00 5.73
3538 3864 1.123928 ATGGTGTTTGCCGGGAAAAA 58.876 45.000 23.64 15.81 0.00 1.94
3558 3910 0.610232 AGACTTGGTTGGCATGGAGC 60.610 55.000 0.00 0.00 44.65 4.70
3560 3912 0.610232 ACTTGGTTGGCATGGAGCTC 60.610 55.000 4.71 4.71 44.79 4.09
3563 3915 1.300963 GGTTGGCATGGAGCTCTGA 59.699 57.895 14.64 0.55 44.79 3.27
3566 3918 0.622136 TTGGCATGGAGCTCTGATGT 59.378 50.000 14.64 0.00 44.79 3.06
3583 3935 3.189080 TGATGTGCTCCGTCAAGAATTTG 59.811 43.478 0.00 0.00 36.14 2.32
3591 3943 2.945668 CCGTCAAGAATTTGGGGAGATC 59.054 50.000 0.00 0.00 34.97 2.75
3624 3976 3.187227 GCGCATCTCGATTGACCATATTT 59.813 43.478 0.30 0.00 41.67 1.40
3625 3977 4.319766 GCGCATCTCGATTGACCATATTTT 60.320 41.667 0.30 0.00 41.67 1.82
3645 3998 7.873739 ATTTTGCAGTTTTCCTTTATCTTCG 57.126 32.000 0.00 0.00 0.00 3.79
3646 3999 5.371115 TTGCAGTTTTCCTTTATCTTCGG 57.629 39.130 0.00 0.00 0.00 4.30
3651 4004 5.062308 CAGTTTTCCTTTATCTTCGGACTCG 59.938 44.000 0.00 0.00 37.82 4.18
3657 4010 4.142447 CCTTTATCTTCGGACTCGACTTCA 60.142 45.833 0.00 0.00 45.92 3.02
3667 4020 4.379603 CGGACTCGACTTCAAGACATTACT 60.380 45.833 0.00 0.00 39.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.571605 TCTGAGAGCTATCTGATTCAAACAG 58.428 40.000 13.25 0.00 35.30 3.16
319 320 3.919554 ACTGGAATTTCTCCCTCTCCTTT 59.080 43.478 0.00 0.00 44.69 3.11
407 408 7.425606 ACACTGGCAGTATCTTTAAAAAGTTG 58.574 34.615 21.59 4.44 37.31 3.16
423 424 5.825679 AGAGTACTAGATAGAACACTGGCAG 59.174 44.000 14.16 14.16 0.00 4.85
442 443 5.417266 GCTCATGATGTCCATAGCTAGAGTA 59.583 44.000 0.00 0.00 33.27 2.59
448 449 2.336891 AGGCTCATGATGTCCATAGCT 58.663 47.619 0.00 0.00 34.85 3.32
619 620 1.860484 GAGAGGCAAGTGCAGCAACC 61.860 60.000 0.00 0.00 44.36 3.77
669 670 4.470664 AGAGATCTCATGCCTTGTCTTCTT 59.529 41.667 24.39 0.00 0.00 2.52
685 686 7.175816 GGAAAGGCTTTCTTACAAAAGAGATCT 59.824 37.037 32.28 0.00 42.60 2.75
738 739 2.632377 TGGACGATGGCTTCAATTCTC 58.368 47.619 0.00 0.00 0.00 2.87
899 900 5.510520 GCAAAACATTCCTTATGTGGTCCAA 60.511 40.000 0.00 0.00 46.75 3.53
968 969 5.102953 TCTGGAAATAAGCTGCAGTACAT 57.897 39.130 16.64 2.90 34.19 2.29
1023 1024 1.207791 CCCCTCTGCTGTCCATAACT 58.792 55.000 0.00 0.00 0.00 2.24
1384 1390 6.545504 TCTTGACTCATTACACAAAAGAGC 57.454 37.500 0.00 0.00 0.00 4.09
1435 1441 4.286707 TCTGGAATCTTCTCGATGGGTAA 58.713 43.478 0.00 0.00 31.20 2.85
1469 1475 5.102313 CCAAATGGCGGAGATTAAAAAGAC 58.898 41.667 0.00 0.00 0.00 3.01
1567 1573 4.207891 AGTCATGTATGTCAGAACCACC 57.792 45.455 0.00 0.00 0.00 4.61
1572 1578 4.558226 AGGCAAGTCATGTATGTCAGAA 57.442 40.909 0.00 0.00 0.00 3.02
1587 1593 2.787473 TCACAATCCCACTAGGCAAG 57.213 50.000 0.00 0.00 34.51 4.01
1654 1660 6.155827 TGCGACATTTAAATTCTTTCCCTTG 58.844 36.000 0.00 0.00 0.00 3.61
1697 1703 3.057946 GCTTGTCAGATTTCCAAGACCAC 60.058 47.826 0.00 0.00 38.23 4.16
1718 1724 1.227999 TGCTTGTAACGTCTGCAGGC 61.228 55.000 15.13 12.04 42.15 4.85
1740 1746 8.097038 TGTTTAATAGACTCATCTTGTGCTTCT 58.903 33.333 0.00 0.00 36.29 2.85
1763 1769 1.064389 GCCTCAGCTCCCCTAAATGTT 60.064 52.381 0.00 0.00 35.50 2.71
1833 1839 6.200665 GCATCTCAACTAGTGACTCATTGATC 59.799 42.308 10.69 0.00 31.13 2.92
1838 1844 4.465660 ACTGCATCTCAACTAGTGACTCAT 59.534 41.667 0.00 0.00 31.13 2.90
1845 1851 6.701340 TGACAAATACTGCATCTCAACTAGT 58.299 36.000 0.00 0.00 0.00 2.57
1852 1858 7.210174 TGTAGGTATGACAAATACTGCATCTC 58.790 38.462 0.00 0.00 0.00 2.75
1869 1875 4.222810 TCACTTGCACTCACATGTAGGTAT 59.777 41.667 0.00 0.00 0.00 2.73
1876 1882 3.332034 TCTCATCACTTGCACTCACATG 58.668 45.455 0.00 0.00 0.00 3.21
1936 1942 4.885325 TCGGCCTCTCAAACTTAACTTTTT 59.115 37.500 0.00 0.00 0.00 1.94
1942 1948 3.368116 GCTAGTCGGCCTCTCAAACTTAA 60.368 47.826 0.00 0.00 0.00 1.85
1986 1992 1.818642 CAACAGCTTGGAAGAGAGGG 58.181 55.000 0.00 0.00 0.00 4.30
2013 2019 5.109210 CGGAGAGACAACATATGCAAGTTA 58.891 41.667 1.58 0.00 0.00 2.24
2023 2029 1.691976 TGACCAACGGAGAGACAACAT 59.308 47.619 0.00 0.00 0.00 2.71
2025 2031 1.202486 TGTGACCAACGGAGAGACAAC 60.202 52.381 0.00 0.00 0.00 3.32
2052 2058 2.598787 CGGTGGCAGGGGGTCTTTA 61.599 63.158 0.00 0.00 0.00 1.85
2053 2059 3.966543 CGGTGGCAGGGGGTCTTT 61.967 66.667 0.00 0.00 0.00 2.52
2070 2076 3.064820 TCAAGTTTGACAACCGAGAAAGC 59.935 43.478 0.00 0.00 32.70 3.51
2095 2101 5.526479 TGTATGCTCTGCTGAATTGAAGATC 59.474 40.000 0.00 0.00 0.00 2.75
2100 2106 4.337274 CCATTGTATGCTCTGCTGAATTGA 59.663 41.667 0.00 0.00 0.00 2.57
2175 2181 6.859112 TTCAGATTAGGCAAGTCTCTTAGT 57.141 37.500 0.00 0.00 0.00 2.24
2208 2214 1.563879 ACCATGGCACCTTGCTGTATA 59.436 47.619 13.04 0.00 44.28 1.47
2236 2242 6.303839 TGAGGTTGACTAAGGTTAATTGCTT 58.696 36.000 0.00 0.00 0.00 3.91
2239 2245 7.361286 GCTTCTGAGGTTGACTAAGGTTAATTG 60.361 40.741 0.00 0.00 0.00 2.32
2246 2252 3.685139 TGCTTCTGAGGTTGACTAAGG 57.315 47.619 0.00 0.00 0.00 2.69
2262 2268 1.903877 CTGGGACCTCCGTCATGCTT 61.904 60.000 0.00 0.00 41.13 3.91
2299 2305 3.056080 AGCTTAGATATTGGAGGGGCAA 58.944 45.455 0.00 0.00 0.00 4.52
2363 2369 2.079925 GCTGCCCTTCAAGTACAGAAG 58.920 52.381 16.77 16.77 41.61 2.85
2461 2473 2.025636 AGTGGTACTGGCTAGTTGGT 57.974 50.000 8.46 0.00 38.36 3.67
2506 2518 8.612619 CCTGCGTAATCAACATCTTAAAACTAT 58.387 33.333 0.00 0.00 0.00 2.12
2509 2521 6.608610 ACCTGCGTAATCAACATCTTAAAAC 58.391 36.000 0.00 0.00 0.00 2.43
2574 2607 5.446473 CCTTCACTCACTGAATTGAATACGC 60.446 44.000 4.07 0.00 38.26 4.42
2575 2608 5.063944 CCCTTCACTCACTGAATTGAATACG 59.936 44.000 4.07 0.00 38.26 3.06
2792 2871 7.938140 TCAGTTTCTGAAATAAACATAGGGG 57.062 36.000 6.06 0.00 37.57 4.79
2837 2923 5.177511 GCAAGCACACTCGCAAATATATAGA 59.822 40.000 0.00 0.00 0.00 1.98
2881 2978 7.414814 AACAAATGGTTTTATTTAACAGCCG 57.585 32.000 0.00 0.00 35.82 5.52
2907 3004 6.610830 ACCCCAGCAATAATTATGAAATCACA 59.389 34.615 0.00 0.00 0.00 3.58
2946 3047 2.004733 GGCAATACGTTACCACAGGAC 58.995 52.381 0.00 0.00 0.00 3.85
2950 3051 3.429822 GCTAGAGGCAATACGTTACCACA 60.430 47.826 0.00 0.00 41.35 4.17
2972 3073 6.580041 CAGCAAGTAAGTTAAAACAGCATCAG 59.420 38.462 0.00 0.00 0.00 2.90
2978 3079 5.215160 CAGCCAGCAAGTAAGTTAAAACAG 58.785 41.667 0.00 0.00 0.00 3.16
2983 3084 2.554344 CCCCAGCCAGCAAGTAAGTTAA 60.554 50.000 0.00 0.00 0.00 2.01
3036 3278 1.376812 TGCAGAGCAGACAGGCATG 60.377 57.895 0.00 0.00 33.32 4.06
3148 3390 9.764363 GATGATCCATGAGTAAACATGTAAGTA 57.236 33.333 0.00 0.00 44.00 2.24
3149 3391 8.267183 TGATGATCCATGAGTAAACATGTAAGT 58.733 33.333 0.00 0.00 44.00 2.24
3150 3392 8.667076 TGATGATCCATGAGTAAACATGTAAG 57.333 34.615 0.00 0.00 44.00 2.34
3151 3393 9.059260 CATGATGATCCATGAGTAAACATGTAA 57.941 33.333 0.00 0.00 44.98 2.41
3155 3403 5.475909 GGCATGATGATCCATGAGTAAACAT 59.524 40.000 14.10 0.00 44.98 2.71
3164 3412 2.562738 AGCATTGGCATGATGATCCATG 59.437 45.455 0.00 7.40 44.97 3.66
3200 3448 8.630054 TTAATGACATAAGTACACTGGCTTTT 57.370 30.769 0.00 0.00 0.00 2.27
3240 3489 0.672401 TTGAACCCGTCGATTGCCTC 60.672 55.000 0.00 0.00 0.00 4.70
3304 3553 9.573166 AAATGGCATATAATAGACAGCAACTAA 57.427 29.630 0.00 0.00 0.00 2.24
3306 3555 7.522725 GCAAATGGCATATAATAGACAGCAACT 60.523 37.037 0.00 0.00 43.97 3.16
3308 3557 6.680810 GCAAATGGCATATAATAGACAGCAA 58.319 36.000 0.00 0.00 43.97 3.91
3331 3580 2.667724 GCAACTGAAGCATTGAGACAGC 60.668 50.000 0.00 0.00 31.17 4.40
3338 3587 4.022935 TGGTCTTTAGCAACTGAAGCATTG 60.023 41.667 0.00 0.00 28.95 2.82
3378 3627 6.183360 TGTCGATAAAATCTTAACACCATGGC 60.183 38.462 13.04 0.00 0.00 4.40
3395 3706 2.333926 CACAGCGAAGGTTGTCGATAA 58.666 47.619 0.00 0.00 43.86 1.75
3396 3707 1.990799 CACAGCGAAGGTTGTCGATA 58.009 50.000 0.00 0.00 43.86 2.92
3427 3738 3.371965 ACATGGAAGATACTGTACCGGT 58.628 45.455 13.98 13.98 0.00 5.28
3431 3742 8.997621 TTCACTTTACATGGAAGATACTGTAC 57.002 34.615 15.44 0.00 0.00 2.90
3433 3744 7.038302 TCCTTCACTTTACATGGAAGATACTGT 60.038 37.037 15.44 0.00 39.20 3.55
3436 3747 8.561738 TTTCCTTCACTTTACATGGAAGATAC 57.438 34.615 15.44 0.00 39.20 2.24
3441 3752 5.538053 TGCATTTCCTTCACTTTACATGGAA 59.462 36.000 0.00 0.00 32.54 3.53
3442 3753 5.076182 TGCATTTCCTTCACTTTACATGGA 58.924 37.500 0.00 0.00 0.00 3.41
3446 3757 7.495901 TGATTTTGCATTTCCTTCACTTTACA 58.504 30.769 0.00 0.00 0.00 2.41
3449 3760 5.467735 GCTGATTTTGCATTTCCTTCACTTT 59.532 36.000 0.00 0.00 0.00 2.66
3452 3763 4.387862 CAGCTGATTTTGCATTTCCTTCAC 59.612 41.667 8.42 0.00 0.00 3.18
3454 3765 4.387862 CACAGCTGATTTTGCATTTCCTTC 59.612 41.667 23.35 0.00 0.00 3.46
3481 3792 2.608623 AGAAAAATTGTGGAGGTGGGG 58.391 47.619 0.00 0.00 0.00 4.96
3484 3795 5.243730 ACACCATAGAAAAATTGTGGAGGTG 59.756 40.000 0.00 0.00 46.06 4.00
3503 3814 4.735369 ACACCATTCCAATCTTAACACCA 58.265 39.130 0.00 0.00 0.00 4.17
3538 3864 1.915141 CTCCATGCCAACCAAGTCTT 58.085 50.000 0.00 0.00 0.00 3.01
3540 3866 0.610232 AGCTCCATGCCAACCAAGTC 60.610 55.000 0.00 0.00 44.23 3.01
3542 3868 0.323178 AGAGCTCCATGCCAACCAAG 60.323 55.000 10.93 0.00 44.23 3.61
3543 3869 0.609957 CAGAGCTCCATGCCAACCAA 60.610 55.000 10.93 0.00 44.23 3.67
3544 3870 1.001764 CAGAGCTCCATGCCAACCA 60.002 57.895 10.93 0.00 44.23 3.67
3546 3872 1.022735 CATCAGAGCTCCATGCCAAC 58.977 55.000 10.93 0.00 44.23 3.77
3548 3874 0.107361 CACATCAGAGCTCCATGCCA 60.107 55.000 18.91 0.00 44.23 4.92
3550 3876 0.464013 AGCACATCAGAGCTCCATGC 60.464 55.000 18.91 16.50 37.03 4.06
3551 3877 3.782632 AGCACATCAGAGCTCCATG 57.217 52.632 17.84 17.84 37.03 3.66
3558 3910 1.203287 TCTTGACGGAGCACATCAGAG 59.797 52.381 0.00 0.00 0.00 3.35
3560 3912 2.084610 TTCTTGACGGAGCACATCAG 57.915 50.000 0.00 0.00 0.00 2.90
3563 3915 2.489329 CCAAATTCTTGACGGAGCACAT 59.511 45.455 0.00 0.00 34.14 3.21
3566 3918 1.533625 CCCAAATTCTTGACGGAGCA 58.466 50.000 0.00 0.00 34.14 4.26
3571 3923 2.609459 CGATCTCCCCAAATTCTTGACG 59.391 50.000 0.00 0.00 34.14 4.35
3583 3935 0.462759 CCTTGCAAGTCGATCTCCCC 60.463 60.000 24.35 0.00 0.00 4.81
3624 3976 5.048991 GTCCGAAGATAAAGGAAAACTGCAA 60.049 40.000 0.00 0.00 35.60 4.08
3625 3977 4.454504 GTCCGAAGATAAAGGAAAACTGCA 59.545 41.667 0.00 0.00 35.60 4.41
3645 3998 4.859798 CAGTAATGTCTTGAAGTCGAGTCC 59.140 45.833 0.00 0.00 0.00 3.85
3646 3999 5.462405 ACAGTAATGTCTTGAAGTCGAGTC 58.538 41.667 0.00 0.00 0.00 3.36
3651 4004 8.488764 GTTAAGTGACAGTAATGTCTTGAAGTC 58.511 37.037 22.54 6.12 39.41 3.01
3657 4010 9.998106 AATAGTGTTAAGTGACAGTAATGTCTT 57.002 29.630 22.54 12.78 38.53 3.01


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

AutoCloner maintained by Alex Coulton.