Multiple sequence alignment - TraesCS1D01G081500

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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 TraesCS1D01G081500 chr1D 100.000 4281 0 0 1 4281 63639911 63635631 0.000000e+00 7906.0
1 TraesCS1D01G081500 chr1A 91.293 4353 231 81 4 4280 62617748 62613468 0.000000e+00 5803.0
2 TraesCS1D01G081500 chr1B 91.273 3598 168 51 13 3548 104470771 104467258 0.000000e+00 4771.0
3 TraesCS1D01G081500 chr1B 95.000 440 14 2 3849 4280 104466953 104466514 0.000000e+00 684.0
4 TraesCS1D01G081500 chr3A 81.308 107 20 0 4167 4273 262522695 262522801 2.120000e-13 87.9
5 TraesCS1D01G081500 chr3A 83.146 89 15 0 4185 4273 163924067 163923979 9.870000e-12 82.4
6 TraesCS1D01G081500 chr3D 83.908 87 14 0 4185 4271 144291569 144291483 2.740000e-12 84.2
7 TraesCS1D01G081500 chr3D 83.908 87 14 0 4187 4273 192058955 192058869 2.740000e-12 84.2
8 TraesCS1D01G081500 chr4B 79.646 113 11 6 3595 3697 598457040 598456930 2.140000e-08 71.3
9 TraesCS1D01G081500 chr4A 84.000 75 10 2 3595 3668 681609123 681609196 2.140000e-08 71.3
10 TraesCS1D01G081500 chr5D 100.000 31 0 0 3593 3623 495311482 495311512 1.660000e-04 58.4
11 TraesCS1D01G081500 chr7D 100.000 30 0 0 3597 3626 60676556 60676585 5.980000e-04 56.5
12 TraesCS1D01G081500 chr7D 94.444 36 2 0 3588 3623 101029422 101029457 5.980000e-04 56.5
13 TraesCS1D01G081500 chr7B 97.059 34 0 1 3594 3626 228772977 228772944 5.980000e-04 56.5
14 TraesCS1D01G081500 chr2B 100.000 30 0 0 3597 3626 136171326 136171355 5.980000e-04 56.5
15 TraesCS1D01G081500 chr3B 96.970 33 0 1 3595 3626 753752447 753752415 2.000000e-03 54.7


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 TraesCS1D01G081500 chr1D 63635631 63639911 4280 True 7906.0 7906 100.0000 1 4281 1 chr1D.!!$R1 4280
1 TraesCS1D01G081500 chr1A 62613468 62617748 4280 True 5803.0 5803 91.2930 4 4280 1 chr1A.!!$R1 4276
2 TraesCS1D01G081500 chr1B 104466514 104470771 4257 True 2727.5 4771 93.1365 13 4280 2 chr1B.!!$R1 4267

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
838 865 0.321298 GAGGCGGCTAAGGTGTTTGA 60.321 55.000 13.24 0.0 0.00 2.69 F
1916 1969 0.873054 CAGTGCTTGTCCTTGCTGAG 59.127 55.000 0.00 0.0 0.00 3.35 F
2325 2378 0.732538 GCCTGAAATTGTTTCGCGGG 60.733 55.000 6.13 0.0 42.55 6.13 F
2567 2622 1.061276 GACTTCGATTTCGCTTGCTCC 59.939 52.381 0.00 0.0 39.60 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2376 1.307097 TTGCAGCAAAAACAATGCCC 58.693 45.000 4.99 0.0 44.91 5.36 R
3107 3191 0.547712 TCCCTCTTCTCCCCCAACTG 60.548 60.000 0.00 0.0 0.00 3.16 R
3139 3223 1.417145 GCCATCTGATCCTTGAGCTCT 59.583 52.381 16.19 0.0 0.00 4.09 R
3716 3900 3.374988 CGCATAATGGACTCAAGAAGCAA 59.625 43.478 0.00 0.0 0.00 3.91 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
52 53 4.935808 ACAATCCACGGAAATCAAGTACTC 59.064 41.667 0.00 0.00 0.00 2.59
69 74 5.131594 GTACTCCCCGTACAATATTCCTC 57.868 47.826 0.00 0.00 46.21 3.71
111 116 6.645790 TTTTTCGAGGAACTACTACTCTGT 57.354 37.500 0.00 0.00 41.55 3.41
112 117 5.624344 TTTCGAGGAACTACTACTCTGTG 57.376 43.478 0.00 0.00 41.55 3.66
113 118 3.008330 TCGAGGAACTACTACTCTGTGC 58.992 50.000 0.00 0.00 41.55 4.57
114 119 2.097791 CGAGGAACTACTACTCTGTGCC 59.902 54.545 0.00 0.00 41.55 5.01
115 120 3.358118 GAGGAACTACTACTCTGTGCCT 58.642 50.000 0.00 0.00 42.16 4.75
254 260 3.135348 TGGAATCTCGATTGGAAGATGCT 59.865 43.478 0.00 0.00 0.00 3.79
275 281 6.173339 TGCTTTTTGTTTTGTCCCAATACAA 58.827 32.000 8.31 8.31 37.58 2.41
348 357 2.294791 TTGTTTTTCACATGGCCGTAGG 59.705 45.455 0.00 0.00 44.06 3.18
369 378 4.009675 GGACAGGACAATATTGCAGTCAA 58.990 43.478 15.48 0.00 36.51 3.18
421 437 0.928229 ACGCGTGAGTTGACTTGAAC 59.072 50.000 12.93 0.00 0.00 3.18
468 484 1.529865 GTAGTGTCCGCAAAGTTGACC 59.470 52.381 0.00 0.00 0.00 4.02
554 577 9.476202 ACATTTTCTTACTTTGCTTCATTTACC 57.524 29.630 0.00 0.00 0.00 2.85
556 579 9.696917 ATTTTCTTACTTTGCTTCATTTACCAG 57.303 29.630 0.00 0.00 0.00 4.00
572 595 8.664992 TCATTTACCAGCCATCCATTACTAATA 58.335 33.333 0.00 0.00 0.00 0.98
573 596 8.730680 CATTTACCAGCCATCCATTACTAATAC 58.269 37.037 0.00 0.00 0.00 1.89
574 597 4.894784 ACCAGCCATCCATTACTAATACG 58.105 43.478 0.00 0.00 0.00 3.06
575 598 4.347000 ACCAGCCATCCATTACTAATACGT 59.653 41.667 0.00 0.00 0.00 3.57
576 599 5.541101 ACCAGCCATCCATTACTAATACGTA 59.459 40.000 0.00 0.00 0.00 3.57
596 619 5.393124 CGTAGTACAAAACTATGTCGACCA 58.607 41.667 14.12 1.26 42.63 4.02
702 728 3.970205 GGCCAGTAACTTAAGGGCA 57.030 52.632 17.93 0.00 46.37 5.36
800 827 1.134560 CGGTTGACTACTACTGGCCTC 59.865 57.143 3.32 0.00 0.00 4.70
827 854 0.603975 GAGAAGTTTGTGAGGCGGCT 60.604 55.000 13.09 13.09 0.00 5.52
829 856 1.071699 AGAAGTTTGTGAGGCGGCTAA 59.928 47.619 13.24 0.00 0.00 3.09
838 865 0.321298 GAGGCGGCTAAGGTGTTTGA 60.321 55.000 13.24 0.00 0.00 2.69
859 887 2.732412 TTGTCAAAGAGGAGCTCTCG 57.268 50.000 14.64 0.00 46.82 4.04
881 909 4.306600 GGTGCCCTTATTTTTGTCTTGTG 58.693 43.478 0.00 0.00 0.00 3.33
956 986 3.055094 GTGCTCCCAGGATCTGAGTTTTA 60.055 47.826 0.00 0.00 32.44 1.52
984 1018 6.478512 TTGGGCTTAAATCTTGTCTGTTTT 57.521 33.333 0.00 0.00 0.00 2.43
1014 1048 2.113860 TGGCTATGGCAGTTTCAGAC 57.886 50.000 2.58 0.00 40.87 3.51
1095 1129 7.096551 ATCTTACAGAGAAGAAGTTGAGCTTC 58.903 38.462 0.36 0.36 43.68 3.86
1215 1249 9.199645 AGGGAGGTTAGTAAATTTCTACTACTC 57.800 37.037 0.00 2.71 34.76 2.59
1380 1414 1.667724 CAGCTAAATGCAACGAGAGGG 59.332 52.381 0.00 0.00 45.94 4.30
1431 1465 2.178580 TCTCCATTTGGGGTTGCATTC 58.821 47.619 0.00 0.00 36.89 2.67
1584 1634 8.654230 TGTATTTGCTTGTAAAATTGCTTTCA 57.346 26.923 0.00 0.00 0.00 2.69
1603 1653 6.074142 GCTTTCATTCGTTTCTTTTGCTGAAT 60.074 34.615 0.00 0.00 0.00 2.57
1641 1691 2.981898 TGCTGAACTGATGGTGATCTG 58.018 47.619 0.00 0.00 34.51 2.90
1664 1714 3.261137 AGCACCTGGAAAAGAGTAGTACC 59.739 47.826 0.00 0.00 0.00 3.34
1684 1734 8.498054 AGTACCATTTCACATCTTCATACTTG 57.502 34.615 0.00 0.00 0.00 3.16
1757 1808 4.225717 CCCAACCCAAATGATTCCATTTCT 59.774 41.667 0.00 0.00 46.83 2.52
1916 1969 0.873054 CAGTGCTTGTCCTTGCTGAG 59.127 55.000 0.00 0.00 0.00 3.35
1935 1988 3.446873 TGAGAGAGCTGAATGAGAAGGAC 59.553 47.826 0.00 0.00 0.00 3.85
2117 2170 6.207928 GGTCTAGTAAAGATAACGAGCTTCC 58.792 44.000 0.00 0.00 36.36 3.46
2196 2249 8.484214 TGAATACTAAGGATACAGAGATTGCT 57.516 34.615 0.00 0.00 41.41 3.91
2262 2315 5.986004 ACAAAACAAAGGAACTAGAGTCG 57.014 39.130 0.00 0.00 38.49 4.18
2285 2338 5.499139 CAAGTAAGTTGTCTTCCTTGCAA 57.501 39.130 0.00 0.00 39.46 4.08
2298 2351 3.971150 TCCTTGCAACCACAAAATAACG 58.029 40.909 0.00 0.00 0.00 3.18
2323 2376 1.451651 GTTGCCTGAAATTGTTTCGCG 59.548 47.619 0.00 0.00 42.55 5.87
2325 2378 0.732538 GCCTGAAATTGTTTCGCGGG 60.733 55.000 6.13 0.00 42.55 6.13
2335 2388 1.213491 GTTTCGCGGGCATTGTTTTT 58.787 45.000 6.13 0.00 0.00 1.94
2350 2403 3.533547 TGTTTTTGCTGCAATGAAGCTT 58.466 36.364 16.77 0.00 41.42 3.74
2364 2417 7.138736 GCAATGAAGCTTTGTAAGTTTACTCA 58.861 34.615 0.00 0.00 31.74 3.41
2411 2466 3.223423 CTAGAGAAGCAGCGAAGAACA 57.777 47.619 0.00 0.00 0.00 3.18
2429 2484 2.856222 ACAGACCAGGAGCTGAAAAAG 58.144 47.619 17.45 0.00 36.07 2.27
2438 2493 3.910627 AGGAGCTGAAAAAGAGGGTTCTA 59.089 43.478 0.00 0.00 31.96 2.10
2468 2523 2.839486 TCTGCCTTCAAGAATCACGT 57.161 45.000 0.00 0.00 0.00 4.49
2478 2533 6.073058 CCTTCAAGAATCACGTTCTCAAATCA 60.073 38.462 0.00 0.00 46.39 2.57
2567 2622 1.061276 GACTTCGATTTCGCTTGCTCC 59.939 52.381 0.00 0.00 39.60 4.70
2572 2627 1.221414 GATTTCGCTTGCTCCGCTAT 58.779 50.000 0.00 0.00 0.00 2.97
2620 2684 5.713861 GGCCTTCTTGGATTGAATATATGCT 59.286 40.000 0.00 0.00 38.35 3.79
2631 2695 8.494433 GGATTGAATATATGCTACCTTATCCCA 58.506 37.037 0.00 0.00 0.00 4.37
2642 2706 2.158900 ACCTTATCCCAGAGCATCAACG 60.159 50.000 0.00 0.00 37.82 4.10
2704 2776 1.752498 TGCCATGTGAATGAAGCATCC 59.248 47.619 0.00 0.00 0.00 3.51
2744 2816 5.750067 GCCATAATCATGTGTGGAAAATGTC 59.250 40.000 3.60 0.00 33.53 3.06
2777 2849 4.093998 GTCAAACAGATCGCTGATTCATGT 59.906 41.667 0.00 0.00 45.17 3.21
2912 2985 1.683938 CCTGGCCTCTGCATTGATTGA 60.684 52.381 3.32 0.00 40.13 2.57
2933 3006 8.771920 ATTGATGATGCCTGCAATAAAATATG 57.228 30.769 0.00 0.00 0.00 1.78
2943 3016 7.011669 GCCTGCAATAAAATATGCTGAAACAAT 59.988 33.333 6.26 0.00 42.12 2.71
2954 3027 4.074259 TGCTGAAACAATGCATACACTCT 58.926 39.130 0.00 0.00 0.00 3.24
2957 3030 5.570589 GCTGAAACAATGCATACACTCTTTC 59.429 40.000 0.00 2.20 0.00 2.62
2972 3050 3.122297 CTCTTTCGCCATGTTTTTGCAA 58.878 40.909 0.00 0.00 0.00 4.08
2973 3051 3.726607 TCTTTCGCCATGTTTTTGCAAT 58.273 36.364 0.00 0.00 0.00 3.56
2974 3052 3.493877 TCTTTCGCCATGTTTTTGCAATG 59.506 39.130 0.00 0.00 0.00 2.82
2985 3069 6.791887 TGTTTTTGCAATGAACTGTTGAAA 57.208 29.167 20.28 5.07 0.00 2.69
3139 3223 0.767375 AGAGGGACAAGCAGCTCAAA 59.233 50.000 0.00 0.00 0.00 2.69
3309 3393 4.090642 GCGTGATCTTGTGTAGAGAAGTTG 59.909 45.833 0.00 0.00 36.02 3.16
3310 3394 4.623167 CGTGATCTTGTGTAGAGAAGTTGG 59.377 45.833 0.00 0.00 36.02 3.77
3311 3395 5.564848 CGTGATCTTGTGTAGAGAAGTTGGA 60.565 44.000 0.00 0.00 36.02 3.53
3312 3396 5.866633 GTGATCTTGTGTAGAGAAGTTGGAG 59.133 44.000 0.00 0.00 36.02 3.86
3313 3397 5.775195 TGATCTTGTGTAGAGAAGTTGGAGA 59.225 40.000 0.00 0.00 36.02 3.71
3314 3398 5.455056 TCTTGTGTAGAGAAGTTGGAGAC 57.545 43.478 0.00 0.00 0.00 3.36
3315 3399 5.141182 TCTTGTGTAGAGAAGTTGGAGACT 58.859 41.667 0.00 0.00 41.47 3.24
3316 3400 5.241949 TCTTGTGTAGAGAAGTTGGAGACTC 59.758 44.000 0.00 0.00 37.72 3.36
3317 3401 4.730966 TGTGTAGAGAAGTTGGAGACTCT 58.269 43.478 1.74 0.00 37.72 3.24
3318 3402 5.877491 TGTGTAGAGAAGTTGGAGACTCTA 58.123 41.667 1.74 0.00 37.72 2.43
3319 3403 5.941058 TGTGTAGAGAAGTTGGAGACTCTAG 59.059 44.000 1.74 0.00 40.87 2.43
3320 3404 6.174760 GTGTAGAGAAGTTGGAGACTCTAGA 58.825 44.000 1.74 0.00 40.87 2.43
3321 3405 6.093082 GTGTAGAGAAGTTGGAGACTCTAGAC 59.907 46.154 0.00 0.00 43.44 2.59
3322 3406 5.514500 AGAGAAGTTGGAGACTCTAGACT 57.486 43.478 1.74 1.72 37.72 3.24
3351 3435 1.833860 CAACTAGCTCGCTCTGTAGC 58.166 55.000 0.00 0.00 45.86 3.58
3371 3455 3.498927 CTTTAAGAAGCCAGCCATGTG 57.501 47.619 0.00 0.00 0.00 3.21
3407 3491 5.265989 TGTAAAATTAGGTTTAGGCCTGGG 58.734 41.667 17.99 0.00 39.60 4.45
3640 3824 7.726033 ATAAGACATTCTACTGTTCCTCTGT 57.274 36.000 0.00 0.00 0.00 3.41
3641 3825 8.824756 ATAAGACATTCTACTGTTCCTCTGTA 57.175 34.615 0.00 0.00 0.00 2.74
3642 3826 7.540474 AAGACATTCTACTGTTCCTCTGTAA 57.460 36.000 0.00 0.00 31.83 2.41
3643 3827 7.540474 AGACATTCTACTGTTCCTCTGTAAA 57.460 36.000 0.00 0.00 31.83 2.01
3644 3828 7.379750 AGACATTCTACTGTTCCTCTGTAAAC 58.620 38.462 0.00 0.00 31.83 2.01
3645 3829 7.233757 AGACATTCTACTGTTCCTCTGTAAACT 59.766 37.037 0.00 0.00 31.83 2.66
3646 3830 8.418597 ACATTCTACTGTTCCTCTGTAAACTA 57.581 34.615 0.00 0.00 31.83 2.24
3647 3831 8.867097 ACATTCTACTGTTCCTCTGTAAACTAA 58.133 33.333 0.00 0.00 31.83 2.24
3648 3832 9.877178 CATTCTACTGTTCCTCTGTAAACTAAT 57.123 33.333 0.00 0.00 31.83 1.73
3697 3881 9.988815 AGTACATATAAGATGTTTGAGATCACC 57.011 33.333 0.00 0.00 33.76 4.02
3707 3891 7.667219 AGATGTTTGAGATCACCAAAGTACATT 59.333 33.333 11.88 0.00 34.59 2.71
3709 3893 6.545666 TGTTTGAGATCACCAAAGTACATTGT 59.454 34.615 9.76 0.00 34.59 2.71
3716 3900 9.520515 AGATCACCAAAGTACATTGTTAATTCT 57.479 29.630 9.76 3.34 0.00 2.40
3725 3909 9.683069 AAGTACATTGTTAATTCTTGCTTCTTG 57.317 29.630 0.00 0.00 0.00 3.02
3740 3924 3.812053 GCTTCTTGAGTCCATTATGCGAT 59.188 43.478 0.00 0.00 0.00 4.58
3816 4000 4.396166 CCTGTTCCAAACAAGGCTATACAG 59.604 45.833 0.00 0.00 41.61 2.74
3820 4004 5.957771 TCCAAACAAGGCTATACAGAGAT 57.042 39.130 0.00 0.00 0.00 2.75
3875 4081 3.507162 TCTGGACTTGGAAGCAAATGA 57.493 42.857 0.00 0.00 0.00 2.57
4264 4480 0.929824 CGACGGCTGCAAACTGTTTG 60.930 55.000 24.98 24.98 43.44 2.93
4273 4489 4.084118 GCTGCAAACTGTTTGAAACAACAA 60.084 37.500 31.35 8.95 43.26 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.738830 TTCGAGGAATATTGTACGGGG 57.261 47.619 0.00 0.00 0.00 5.73
66 67 8.579682 AAAAATCACTCATTTCTTTTTCGAGG 57.420 30.769 0.00 0.00 33.16 4.63
323 332 2.988493 CGGCCATGTGAAAAACAATCTG 59.012 45.455 2.24 0.00 43.61 2.90
348 357 5.824904 ATTGACTGCAATATTGTCCTGTC 57.175 39.130 16.61 17.51 42.73 3.51
468 484 4.825422 TCAACTCCTGAAGCATCTACTTG 58.175 43.478 0.00 0.00 0.00 3.16
519 535 7.010460 AGCAAAGTAAGAAAATGTTGTTCAAGC 59.990 33.333 0.00 0.00 0.00 4.01
533 556 6.294508 GGCTGGTAAATGAAGCAAAGTAAGAA 60.295 38.462 0.00 0.00 38.73 2.52
554 577 6.688578 ACTACGTATTAGTAATGGATGGCTG 58.311 40.000 5.61 0.00 39.45 4.85
556 579 7.596494 TGTACTACGTATTAGTAATGGATGGC 58.404 38.462 5.61 0.00 43.59 4.40
572 595 5.048782 TGGTCGACATAGTTTTGTACTACGT 60.049 40.000 18.91 0.00 41.99 3.57
573 596 5.284660 GTGGTCGACATAGTTTTGTACTACG 59.715 44.000 18.91 0.00 41.99 3.51
574 597 6.307318 CAGTGGTCGACATAGTTTTGTACTAC 59.693 42.308 18.91 0.00 41.99 2.73
575 598 6.207221 TCAGTGGTCGACATAGTTTTGTACTA 59.793 38.462 18.91 0.00 43.29 1.82
576 599 5.010314 TCAGTGGTCGACATAGTTTTGTACT 59.990 40.000 18.91 2.76 41.04 2.73
596 619 3.609853 TGACAGAAGTGTTGCTTTCAGT 58.390 40.909 0.00 0.00 36.88 3.41
800 827 4.213059 GCCTCACAAACTTCTCTCTTTCAG 59.787 45.833 0.00 0.00 0.00 3.02
838 865 3.594134 CGAGAGCTCCTCTTTGACAAAT 58.406 45.455 10.93 0.00 41.35 2.32
906 936 6.490040 TCCTATTTTCTCCAAGAACAAACAGG 59.510 38.462 0.00 0.00 33.26 4.00
984 1018 1.077787 CATAGCCAAGCCCCGAACA 60.078 57.895 0.00 0.00 0.00 3.18
1014 1048 2.461110 GCATGGTCGTACCGCCTTG 61.461 63.158 0.00 10.19 42.58 3.61
1095 1129 2.414481 CAGAGATGCCACGTTTCTTCTG 59.586 50.000 6.86 3.13 0.00 3.02
1119 1153 3.181456 GCCTCACATCCTTTAGCTCAGAT 60.181 47.826 0.00 0.00 0.00 2.90
1215 1249 4.273480 CCATGCTGAAGGTAGAAATTACCG 59.727 45.833 0.00 0.00 42.26 4.02
1380 1414 2.544685 CTCCTCACATGTTCGGTGATC 58.455 52.381 0.00 0.00 43.72 2.92
1584 1634 5.600696 ACCAATTCAGCAAAAGAAACGAAT 58.399 33.333 0.00 0.00 0.00 3.34
1587 1637 4.566360 ACAACCAATTCAGCAAAAGAAACG 59.434 37.500 0.00 0.00 0.00 3.60
1603 1653 1.134848 GCAAAAGACAGGCACAACCAA 60.135 47.619 0.00 0.00 43.14 3.67
1641 1691 3.686916 ACTACTCTTTTCCAGGTGCTC 57.313 47.619 0.00 0.00 0.00 4.26
1647 1697 6.934645 TGTGAAATGGTACTACTCTTTTCCAG 59.065 38.462 0.00 0.00 0.00 3.86
1684 1734 9.851043 GTCACGCATAAGAAGATTTTAGATTAC 57.149 33.333 0.00 0.00 0.00 1.89
1690 1740 6.254157 GGTACGTCACGCATAAGAAGATTTTA 59.746 38.462 0.00 0.00 0.00 1.52
1757 1808 8.236585 TGACAAAGAGAATTCCAATTTGAAGA 57.763 30.769 23.68 11.13 35.40 2.87
1916 1969 2.481104 CGGTCCTTCTCATTCAGCTCTC 60.481 54.545 0.00 0.00 0.00 3.20
2117 2170 5.321516 GTGAAACATCGGATAAAACCTTCG 58.678 41.667 0.00 0.00 36.32 3.79
2196 2249 8.907829 ATATCCTAATTTCATCTCTCAGCCTA 57.092 34.615 0.00 0.00 0.00 3.93
2285 2338 4.747605 GGCAACATTTCGTTATTTTGTGGT 59.252 37.500 0.00 0.00 35.52 4.16
2298 2351 5.669122 CGAAACAATTTCAGGCAACATTTC 58.331 37.500 2.50 0.00 39.63 2.17
2323 2376 1.307097 TTGCAGCAAAAACAATGCCC 58.693 45.000 4.99 0.00 44.91 5.36
2325 2378 3.881780 TCATTGCAGCAAAAACAATGC 57.118 38.095 12.97 0.00 46.50 3.56
2335 2388 3.318839 ACTTACAAAGCTTCATTGCAGCA 59.681 39.130 10.88 0.00 39.99 4.41
2405 2460 1.722034 TCAGCTCCTGGTCTGTTCTT 58.278 50.000 14.78 0.00 31.51 2.52
2411 2466 2.039613 CCTCTTTTTCAGCTCCTGGTCT 59.960 50.000 0.00 0.00 31.51 3.85
2429 2484 6.382608 GCAGAATTCAAGTTTTAGAACCCTC 58.617 40.000 8.44 0.00 36.39 4.30
2468 2523 6.488006 CCCTCTGAAGTTTTCTGATTTGAGAA 59.512 38.462 0.00 0.00 37.08 2.87
2478 2533 6.681729 TGTACATACCCTCTGAAGTTTTCT 57.318 37.500 0.00 0.00 0.00 2.52
2567 2622 5.422145 TGGATATGGACAATGATGATAGCG 58.578 41.667 0.00 0.00 0.00 4.26
2606 2670 9.553064 CTGGGATAAGGTAGCATATATTCAATC 57.447 37.037 0.00 0.00 0.00 2.67
2620 2684 3.069586 CGTTGATGCTCTGGGATAAGGTA 59.930 47.826 0.00 0.00 0.00 3.08
2631 2695 2.168106 AGAGATCTTGCGTTGATGCTCT 59.832 45.455 0.00 0.00 35.36 4.09
2642 2706 9.548208 GTTAATTTTAACTGTCAGAGATCTTGC 57.452 33.333 6.91 0.00 39.82 4.01
2744 2816 3.187227 CGATCTGTTTGACTTTGACCTGG 59.813 47.826 0.00 0.00 0.00 4.45
2777 2849 7.064229 ACTAAACAATAGGGTTTTCCAGAACA 58.936 34.615 0.00 0.00 41.07 3.18
2859 2932 8.384365 CGATTTCTTCCTAAAGTTTTCTAGAGC 58.616 37.037 0.00 0.00 33.95 4.09
2873 2946 4.081642 CCAGGAGTGTTCGATTTCTTCCTA 60.082 45.833 5.91 0.00 0.00 2.94
2912 2985 6.014925 TCAGCATATTTTATTGCAGGCATCAT 60.015 34.615 0.00 0.00 41.35 2.45
2933 3006 4.691860 AGAGTGTATGCATTGTTTCAGC 57.308 40.909 3.54 0.00 0.00 4.26
2943 3016 2.009051 CATGGCGAAAGAGTGTATGCA 58.991 47.619 0.00 0.00 0.00 3.96
2954 3027 3.461061 TCATTGCAAAAACATGGCGAAA 58.539 36.364 1.71 0.00 0.00 3.46
2957 3030 2.801679 AGTTCATTGCAAAAACATGGCG 59.198 40.909 22.60 0.00 0.00 5.69
2973 3051 9.462174 GTTGACATTGATTATTTCAACAGTTCA 57.538 29.630 10.34 0.00 46.24 3.18
2990 3074 5.984627 TCGACATGTGTTTAGTTGACATTG 58.015 37.500 1.15 0.00 0.00 2.82
2995 3079 7.225734 TCAAGATTTCGACATGTGTTTAGTTGA 59.774 33.333 1.15 1.58 0.00 3.18
3035 3119 1.193323 CCCAGCTGATCAGTGAGAGT 58.807 55.000 23.38 0.00 0.00 3.24
3036 3120 1.482954 TCCCAGCTGATCAGTGAGAG 58.517 55.000 23.38 9.57 0.00 3.20
3037 3121 2.037901 GATCCCAGCTGATCAGTGAGA 58.962 52.381 23.38 15.92 40.71 3.27
3105 3189 1.492133 CCTCTTCTCCCCCAACTGCA 61.492 60.000 0.00 0.00 0.00 4.41
3106 3190 1.301293 CCTCTTCTCCCCCAACTGC 59.699 63.158 0.00 0.00 0.00 4.40
3107 3191 0.547712 TCCCTCTTCTCCCCCAACTG 60.548 60.000 0.00 0.00 0.00 3.16
3139 3223 1.417145 GCCATCTGATCCTTGAGCTCT 59.583 52.381 16.19 0.00 0.00 4.09
3277 3361 2.802247 CACAAGATCACGCTGTTCTCAA 59.198 45.455 0.00 0.00 0.00 3.02
3290 3374 6.071616 AGTCTCCAACTTCTCTACACAAGATC 60.072 42.308 0.00 0.00 33.03 2.75
3309 3393 4.337274 GCTCACCTAAAGTCTAGAGTCTCC 59.663 50.000 0.00 0.00 0.00 3.71
3310 3394 4.944930 TGCTCACCTAAAGTCTAGAGTCTC 59.055 45.833 0.00 0.00 0.00 3.36
3311 3395 4.924625 TGCTCACCTAAAGTCTAGAGTCT 58.075 43.478 0.00 0.00 0.00 3.24
3312 3396 5.184287 AGTTGCTCACCTAAAGTCTAGAGTC 59.816 44.000 0.00 0.00 0.00 3.36
3313 3397 5.081032 AGTTGCTCACCTAAAGTCTAGAGT 58.919 41.667 0.00 0.00 0.00 3.24
3314 3398 5.652994 AGTTGCTCACCTAAAGTCTAGAG 57.347 43.478 0.00 0.00 0.00 2.43
3315 3399 5.125739 GCTAGTTGCTCACCTAAAGTCTAGA 59.874 44.000 0.00 0.00 38.95 2.43
3316 3400 5.344884 GCTAGTTGCTCACCTAAAGTCTAG 58.655 45.833 0.00 0.00 38.95 2.43
3317 3401 5.326200 GCTAGTTGCTCACCTAAAGTCTA 57.674 43.478 0.00 0.00 38.95 2.59
3318 3402 4.195225 GCTAGTTGCTCACCTAAAGTCT 57.805 45.455 0.00 0.00 38.95 3.24
3351 3435 2.416431 GCACATGGCTGGCTTCTTAAAG 60.416 50.000 2.00 0.00 40.25 1.85
3575 3719 8.723942 AAGTAGATGCTAAAGAGTACCAAATG 57.276 34.615 0.00 0.00 0.00 2.32
3576 3720 7.988028 GGAAGTAGATGCTAAAGAGTACCAAAT 59.012 37.037 0.00 0.00 0.00 2.32
3580 3761 6.548251 AGAGGAAGTAGATGCTAAAGAGTACC 59.452 42.308 0.00 0.00 0.00 3.34
3650 3834 9.926158 TGTACTTTGGTGATCTAAAACGTATTA 57.074 29.630 0.00 0.00 0.00 0.98
3651 3835 8.836268 TGTACTTTGGTGATCTAAAACGTATT 57.164 30.769 0.00 0.00 0.00 1.89
3678 3862 9.167311 GTACTTTGGTGATCTCAAACATCTTAT 57.833 33.333 9.61 0.00 31.71 1.73
3682 3866 6.801539 TGTACTTTGGTGATCTCAAACATC 57.198 37.500 9.61 0.00 31.71 3.06
3689 3873 9.774742 GAATTAACAATGTACTTTGGTGATCTC 57.225 33.333 19.38 13.09 0.00 2.75
3696 3880 8.816640 AAGCAAGAATTAACAATGTACTTTGG 57.183 30.769 21.54 7.59 0.00 3.28
3697 3881 9.683069 AGAAGCAAGAATTAACAATGTACTTTG 57.317 29.630 17.42 17.42 0.00 2.77
3707 3891 6.061441 TGGACTCAAGAAGCAAGAATTAACA 58.939 36.000 0.00 0.00 0.00 2.41
3709 3893 7.765695 AATGGACTCAAGAAGCAAGAATTAA 57.234 32.000 0.00 0.00 0.00 1.40
3716 3900 3.374988 CGCATAATGGACTCAAGAAGCAA 59.625 43.478 0.00 0.00 0.00 3.91
3725 3909 5.278022 GGGAAAAGAATCGCATAATGGACTC 60.278 44.000 0.00 0.00 32.88 3.36
3740 3924 4.867086 ACAGAAACAGAAGGGGAAAAGAA 58.133 39.130 0.00 0.00 0.00 2.52
3816 4000 9.912634 TTTCTCATTTTGTGTTGGATTTATCTC 57.087 29.630 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.