Multiple sequence alignment - TraesCS3A01G339500

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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 TraesCS3A01G339500 chr3A 100.000 4449 0 0 1 4449 586417384 586421832 0.000000e+00 8216.0
1 TraesCS3A01G339500 chr3A 85.366 82 5 4 4214 4288 137914408 137914489 1.330000e-10 78.7
2 TraesCS3A01G339500 chr3B 93.263 3488 169 32 978 4449 583388194 583391631 0.000000e+00 5079.0
3 TraesCS3A01G339500 chr3B 91.146 960 52 25 1 947 583387254 583388193 0.000000e+00 1271.0
4 TraesCS3A01G339500 chr3D 93.351 3038 163 14 2 3032 445032129 445035134 0.000000e+00 4455.0
5 TraesCS3A01G339500 chr3D 90.155 1290 74 19 3192 4449 445035738 445037006 0.000000e+00 1629.0
6 TraesCS3A01G339500 chr3D 94.783 115 6 0 3031 3145 445035249 445035363 3.540000e-41 180.0
7 TraesCS3A01G339500 chr3D 86.905 84 3 5 4211 4286 311668798 311668881 2.200000e-13 87.9
8 TraesCS3A01G339500 chr1D 80.189 106 13 5 4214 4319 253207959 253207862 6.170000e-09 73.1
9 TraesCS3A01G339500 chr1D 94.737 38 2 0 4221 4258 59125545 59125508 4.810000e-05 60.2
10 TraesCS3A01G339500 chr5B 92.857 42 3 0 4219 4260 252322703 252322662 1.340000e-05 62.1


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 TraesCS3A01G339500 chr3A 586417384 586421832 4448 False 8216 8216 100.0000 1 4449 1 chr3A.!!$F2 4448
1 TraesCS3A01G339500 chr3B 583387254 583391631 4377 False 3175 5079 92.2045 1 4449 2 chr3B.!!$F1 4448
2 TraesCS3A01G339500 chr3D 445032129 445037006 4877 False 2088 4455 92.7630 2 4449 3 chr3D.!!$F2 4447

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
860 880 0.099082 GCTCGACTCGAAATCGTCCT 59.901 55.0 15.94 0.0 40.50 3.85 F
901 921 1.314730 GGCGTCCAGGACAAAAAGAA 58.685 50.0 20.13 0.0 32.09 2.52 F
2537 2558 0.105224 TCGGCTTCTGTCGGTTCAAA 59.895 50.0 0.00 0.0 42.24 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1733 0.108756 CTCGAACGGGAACTCCTTCC 60.109 60.0 0.00 0.0 45.04 3.46 R
2727 2750 0.260230 TGGCTTCCTTGACCAAACCA 59.740 50.0 0.00 0.0 0.00 3.67 R
3487 3957 1.026182 TGATTACAAGCAGGCTGGCG 61.026 55.0 17.64 0.0 39.27 5.69 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
42 43 1.298157 CGCTTGGATCAACGCCTTCA 61.298 55.000 0.00 0.00 0.00 3.02
75 76 1.003233 AAAGAGAGCAACGGCCTCC 60.003 57.895 0.00 0.00 42.56 4.30
78 79 3.240134 GAGAGCAACGGCCTCCACA 62.240 63.158 0.00 0.00 42.56 4.17
81 82 3.050275 GCAACGGCCTCCACAGAC 61.050 66.667 0.00 0.00 0.00 3.51
93 94 2.597805 ACAGACCGACAGGAGCGT 60.598 61.111 0.00 0.00 41.02 5.07
240 241 1.227674 ATTCTTCGCCGGCATCTCC 60.228 57.895 28.98 0.00 0.00 3.71
285 286 1.813753 GCACCCGCACACGACATAT 60.814 57.895 0.00 0.00 43.93 1.78
294 295 1.724082 CACACGACATATGCGTTGACA 59.276 47.619 18.33 0.00 40.44 3.58
303 304 2.357760 GCGTTGACAAGGGCGGTA 60.358 61.111 9.75 0.00 0.00 4.02
764 776 6.263842 ACTTAGAATATGTCATGGTGCAATGG 59.736 38.462 0.00 0.00 0.00 3.16
765 777 4.795469 AGAATATGTCATGGTGCAATGGA 58.205 39.130 0.00 0.00 0.00 3.41
766 778 4.825634 AGAATATGTCATGGTGCAATGGAG 59.174 41.667 0.00 0.00 0.00 3.86
767 779 2.519771 ATGTCATGGTGCAATGGAGT 57.480 45.000 0.00 0.00 0.00 3.85
768 780 1.536940 TGTCATGGTGCAATGGAGTG 58.463 50.000 0.00 0.00 0.00 3.51
769 781 1.073603 TGTCATGGTGCAATGGAGTGA 59.926 47.619 0.00 0.00 0.00 3.41
770 782 1.741706 GTCATGGTGCAATGGAGTGAG 59.258 52.381 0.00 0.00 0.00 3.51
771 783 1.629861 TCATGGTGCAATGGAGTGAGA 59.370 47.619 0.00 0.00 0.00 3.27
772 784 2.014857 CATGGTGCAATGGAGTGAGAG 58.985 52.381 0.00 0.00 0.00 3.20
773 785 1.351076 TGGTGCAATGGAGTGAGAGA 58.649 50.000 0.00 0.00 0.00 3.10
774 786 1.277273 TGGTGCAATGGAGTGAGAGAG 59.723 52.381 0.00 0.00 0.00 3.20
775 787 1.552337 GGTGCAATGGAGTGAGAGAGA 59.448 52.381 0.00 0.00 0.00 3.10
776 788 2.418471 GGTGCAATGGAGTGAGAGAGAG 60.418 54.545 0.00 0.00 0.00 3.20
777 789 2.495270 GTGCAATGGAGTGAGAGAGAGA 59.505 50.000 0.00 0.00 0.00 3.10
778 790 2.759535 TGCAATGGAGTGAGAGAGAGAG 59.240 50.000 0.00 0.00 0.00 3.20
779 791 3.023119 GCAATGGAGTGAGAGAGAGAGA 58.977 50.000 0.00 0.00 0.00 3.10
780 792 3.067180 GCAATGGAGTGAGAGAGAGAGAG 59.933 52.174 0.00 0.00 0.00 3.20
781 793 4.525996 CAATGGAGTGAGAGAGAGAGAGA 58.474 47.826 0.00 0.00 0.00 3.10
844 864 0.325203 AGAGAAGGTGGAGGAGGCTC 60.325 60.000 5.78 5.78 0.00 4.70
860 880 0.099082 GCTCGACTCGAAATCGTCCT 59.901 55.000 15.94 0.00 40.50 3.85
901 921 1.314730 GGCGTCCAGGACAAAAAGAA 58.685 50.000 20.13 0.00 32.09 2.52
906 926 3.642705 GTCCAGGACAAAAAGAATGTGC 58.357 45.455 15.43 0.00 39.17 4.57
986 1007 4.271816 CCGCCCGATCCTCACTCG 62.272 72.222 0.00 0.00 35.92 4.18
1058 1079 4.241555 CGGCCCCGGATTCTCCAG 62.242 72.222 0.73 0.00 35.91 3.86
1466 1487 4.100084 CATCCTCGCCAGGCACCA 62.100 66.667 13.30 0.00 40.12 4.17
1712 1733 2.507992 CCTGCTTCTGTCGAGCGG 60.508 66.667 0.00 0.00 44.32 5.52
1783 1804 1.528776 TGCAACATGGTCTGCAGCA 60.529 52.632 9.47 2.06 43.44 4.41
1784 1805 1.080974 GCAACATGGTCTGCAGCAC 60.081 57.895 9.47 8.27 38.48 4.40
1807 1828 0.900182 GGAGGCCAAGAGGTTTTGGG 60.900 60.000 5.01 0.00 46.23 4.12
1808 1829 0.178961 GAGGCCAAGAGGTTTTGGGT 60.179 55.000 5.01 0.00 46.23 4.51
1828 1849 2.285592 TCATGGAGCTCAGGGGCA 60.286 61.111 17.19 3.86 34.17 5.36
1857 1878 2.000447 GACGTTGTGTCTTATGGGAGC 59.000 52.381 0.00 0.00 44.58 4.70
1893 1914 3.978571 GAAGGCCGGGAGCTTGGAC 62.979 68.421 2.18 1.71 43.05 4.02
1929 1950 0.618458 TTAACCGCATGAAGGAGGCT 59.382 50.000 13.65 0.00 0.00 4.58
2154 2175 3.944250 AAGGGGGCTGTTGGCATCG 62.944 63.158 0.00 0.00 44.01 3.84
2190 2211 2.810852 TGCATTGTTCGATGTTGCTACA 59.189 40.909 2.82 2.82 38.95 2.74
2220 2241 3.999663 CTGAGGTCTTTGATCTGTTGGAC 59.000 47.826 0.00 0.00 0.00 4.02
2242 2263 3.354948 AGATGAAGGCACTACATTGCA 57.645 42.857 0.00 0.00 44.94 4.08
2364 2385 2.284625 ACCCCTGATCGGAGTGCA 60.285 61.111 2.08 0.00 33.16 4.57
2370 2391 2.611473 CCCTGATCGGAGTGCATACATC 60.611 54.545 2.08 0.00 33.16 3.06
2426 2447 3.728385 AGAGGAGGCTGCAAAGTATTT 57.272 42.857 9.23 0.00 40.26 1.40
2441 2462 7.231317 TGCAAAGTATTTTGAGGAGATGAAAGT 59.769 33.333 14.30 0.00 45.21 2.66
2537 2558 0.105224 TCGGCTTCTGTCGGTTCAAA 59.895 50.000 0.00 0.00 42.24 2.69
2540 2561 1.673920 GGCTTCTGTCGGTTCAAAACA 59.326 47.619 0.00 0.00 0.00 2.83
2547 2568 3.283751 TGTCGGTTCAAAACATGGTTCT 58.716 40.909 0.00 0.00 0.00 3.01
2590 2611 6.316640 TCGTAGAGAGTGGTAAAGATGAAGAG 59.683 42.308 0.00 0.00 0.00 2.85
2597 2618 4.997395 GTGGTAAAGATGAAGAGCACTTGA 59.003 41.667 0.00 0.00 37.34 3.02
2621 2642 9.996554 TGAAAGTGATCTATAGAAAGAAACACA 57.003 29.630 6.52 0.00 38.32 3.72
2623 2644 8.485976 AAGTGATCTATAGAAAGAAACACAGC 57.514 34.615 6.52 0.00 38.32 4.40
2633 2654 5.863935 AGAAAGAAACACAGCTGTTGTTTTC 59.136 36.000 30.41 27.76 39.88 2.29
2643 2664 3.002348 AGCTGTTGTTTTCGAGTAACTGC 59.998 43.478 18.19 18.19 43.68 4.40
2648 2669 5.461078 TGTTGTTTTCGAGTAACTGCTAGAC 59.539 40.000 12.03 0.00 0.00 2.59
2726 2749 6.428159 GTGATCTTCATCTACTTTGTTGTGGT 59.572 38.462 0.00 0.00 0.00 4.16
2727 2750 6.998074 TGATCTTCATCTACTTTGTTGTGGTT 59.002 34.615 0.00 0.00 0.00 3.67
2880 2904 0.972983 AAGAAGGCGCAGAGCTCCTA 60.973 55.000 10.93 0.00 43.49 2.94
2974 2998 3.222603 AGAAAGTGCAACCTAGGGTTTG 58.777 45.455 14.81 10.67 44.33 2.93
2979 3003 1.497286 TGCAACCTAGGGTTTGTCCTT 59.503 47.619 14.81 0.00 44.33 3.36
2982 3006 3.243737 GCAACCTAGGGTTTGTCCTTTTG 60.244 47.826 14.81 5.44 44.33 2.44
3008 3032 4.080356 ACTTGGATAGGCATCACTTTGCTA 60.080 41.667 0.00 0.00 42.38 3.49
3010 3034 4.392047 TGGATAGGCATCACTTTGCTATG 58.608 43.478 0.00 0.00 42.38 2.23
3087 3227 6.946340 TCACAACATATAATGACTGTCCACT 58.054 36.000 5.17 0.00 31.07 4.00
3119 3259 3.952323 CTGGTCCGACTCCTATACTTTCA 59.048 47.826 0.00 0.00 0.00 2.69
3183 3337 9.499479 AGCTCATTTCATATGGTTTGATACTAG 57.501 33.333 2.13 0.00 0.00 2.57
3184 3338 9.277783 GCTCATTTCATATGGTTTGATACTAGT 57.722 33.333 2.13 0.00 0.00 2.57
3231 3700 9.261180 TGTAGCTGTATTCAATATTAGCAGTTC 57.739 33.333 15.19 6.48 33.17 3.01
3245 3714 4.184079 AGCAGTTCCATTTTCATGCTTC 57.816 40.909 0.00 0.00 40.95 3.86
3248 3717 4.622220 GCAGTTCCATTTTCATGCTTCCAT 60.622 41.667 0.00 0.00 0.00 3.41
3249 3718 5.484715 CAGTTCCATTTTCATGCTTCCATT 58.515 37.500 0.00 0.00 0.00 3.16
3250 3719 5.350365 CAGTTCCATTTTCATGCTTCCATTG 59.650 40.000 0.00 0.00 0.00 2.82
3251 3720 5.012354 AGTTCCATTTTCATGCTTCCATTGT 59.988 36.000 0.00 0.00 0.00 2.71
3254 3723 5.701750 TCCATTTTCATGCTTCCATTGTTTG 59.298 36.000 0.00 0.00 0.00 2.93
3257 3726 3.306917 TCATGCTTCCATTGTTTGCAG 57.693 42.857 0.00 0.00 37.07 4.41
3307 3777 3.861840 ACCATTTAGTGACCACTCATCG 58.138 45.455 5.87 0.00 42.54 3.84
3319 3789 1.736126 CACTCATCGCACTGCAGAATT 59.264 47.619 23.35 0.00 0.00 2.17
3335 3805 1.526575 AATTGGCCGCTGTGTGAAGG 61.527 55.000 0.00 0.00 0.00 3.46
3343 3813 1.798813 CGCTGTGTGAAGGTTTAGGTC 59.201 52.381 0.00 0.00 0.00 3.85
3477 3947 1.019673 CACATTGGATCGAAGCTGGG 58.980 55.000 0.00 0.00 0.00 4.45
3569 4039 7.233389 TCCAGTTATATCTGATCAGTTAGGC 57.767 40.000 21.92 11.67 37.61 3.93
3641 4113 5.048573 TGGATTCGATCATACCGACGATAAA 60.049 40.000 0.00 0.00 35.61 1.40
3642 4114 6.034591 GGATTCGATCATACCGACGATAAAT 58.965 40.000 0.00 0.00 35.61 1.40
3643 4115 7.148205 TGGATTCGATCATACCGACGATAAATA 60.148 37.037 0.00 0.00 35.61 1.40
3644 4116 7.861372 GGATTCGATCATACCGACGATAAATAT 59.139 37.037 0.00 0.00 35.61 1.28
3645 4117 9.234384 GATTCGATCATACCGACGATAAATATT 57.766 33.333 0.00 0.00 35.61 1.28
3750 4222 2.205074 AGCTTGTTCTGTCAGTTGTCG 58.795 47.619 0.00 0.00 0.00 4.35
3954 4427 6.695713 CACTGTCAATTTCATGGCATCTTATG 59.304 38.462 0.00 0.00 33.82 1.90
3992 4465 3.969352 GTGTCGCTAACTCATATGACTCG 59.031 47.826 0.00 1.70 0.00 4.18
4104 4577 7.929159 TGTATGCACTGAATGTTACCATTATG 58.071 34.615 0.00 0.00 41.37 1.90
4156 4629 9.030301 CCAAATTCGGATAAACACCAAATATTC 57.970 33.333 0.00 0.00 0.00 1.75
4235 4709 3.632643 TTACCTCCGTCCCAAATTACC 57.367 47.619 0.00 0.00 0.00 2.85
4239 4713 2.629051 CTCCGTCCCAAATTACCTGTC 58.371 52.381 0.00 0.00 0.00 3.51
4241 4715 2.640826 TCCGTCCCAAATTACCTGTCTT 59.359 45.455 0.00 0.00 0.00 3.01
4242 4716 3.839490 TCCGTCCCAAATTACCTGTCTTA 59.161 43.478 0.00 0.00 0.00 2.10
4243 4717 4.081309 TCCGTCCCAAATTACCTGTCTTAG 60.081 45.833 0.00 0.00 0.00 2.18
4244 4718 4.081309 CCGTCCCAAATTACCTGTCTTAGA 60.081 45.833 0.00 0.00 0.00 2.10
4245 4719 5.396436 CCGTCCCAAATTACCTGTCTTAGAT 60.396 44.000 0.00 0.00 0.00 1.98
4247 4721 6.598064 CGTCCCAAATTACCTGTCTTAGATTT 59.402 38.462 0.00 0.00 0.00 2.17
4248 4722 7.120726 CGTCCCAAATTACCTGTCTTAGATTTT 59.879 37.037 0.00 0.00 0.00 1.82
4249 4723 8.803235 GTCCCAAATTACCTGTCTTAGATTTTT 58.197 33.333 0.00 0.00 0.00 1.94
4250 4724 8.802267 TCCCAAATTACCTGTCTTAGATTTTTG 58.198 33.333 0.00 0.00 0.00 2.44
4251 4725 8.585018 CCCAAATTACCTGTCTTAGATTTTTGT 58.415 33.333 0.00 0.00 0.00 2.83
4259 4733 9.877178 ACCTGTCTTAGATTTTTGTAGATACAG 57.123 33.333 0.00 0.00 37.52 2.74
4314 4819 3.393426 AGTAATACTGGACGGAGGGAA 57.607 47.619 0.00 0.00 0.00 3.97
4318 4823 4.891992 AATACTGGACGGAGGGAATATG 57.108 45.455 0.00 0.00 0.00 1.78
4359 4864 6.069789 TCAGATTGATCAAGGGTCAGAAGAAT 60.070 38.462 14.54 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.471904 TGATCCAAGCGAGATAACTGTT 57.528 40.909 0.00 0.00 0.00 3.16
75 76 2.126307 CGCTCCTGTCGGTCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
78 79 2.597805 ACACGCTCCTGTCGGTCT 60.598 61.111 0.00 0.00 0.00 3.85
81 82 1.443872 GTACACACGCTCCTGTCGG 60.444 63.158 0.00 0.00 0.00 4.79
93 94 2.158827 CGGGATGATTGATGGGTACACA 60.159 50.000 0.00 0.00 0.00 3.72
285 286 2.457743 ATACCGCCCTTGTCAACGCA 62.458 55.000 1.86 0.00 0.00 5.24
294 295 1.143183 CTACGTGCATACCGCCCTT 59.857 57.895 0.00 0.00 41.33 3.95
528 529 4.778143 GCCCGCCAGGTGTTCGAT 62.778 66.667 0.00 0.00 38.26 3.59
665 669 3.254024 TTCCCGGCTGACCTCTTGC 62.254 63.158 0.00 0.00 0.00 4.01
764 776 4.646945 TCTCTCTCTCTCTCTCTCTCACTC 59.353 50.000 0.00 0.00 0.00 3.51
765 777 4.614475 TCTCTCTCTCTCTCTCTCTCACT 58.386 47.826 0.00 0.00 0.00 3.41
766 778 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
767 779 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
768 780 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
769 781 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
770 782 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
771 783 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
772 784 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
773 785 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
774 786 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
775 787 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
776 788 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
777 789 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
778 790 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
779 791 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
780 792 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
781 793 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
844 864 1.597445 GCCTAGGACGATTTCGAGTCG 60.597 57.143 14.75 17.33 43.02 4.18
860 880 2.064581 GCGGGAGGGAGAAAGCCTA 61.065 63.158 0.00 0.00 0.00 3.93
890 910 4.571984 AGCAAAAGCACATTCTTTTTGTCC 59.428 37.500 9.72 0.00 42.48 4.02
929 950 0.582005 GTCAACAGAGCAACGTGGTC 59.418 55.000 8.52 8.52 44.62 4.02
932 953 1.290203 ACTGTCAACAGAGCAACGTG 58.710 50.000 16.71 0.00 46.59 4.49
986 1007 0.526524 CAACATCGAGGAGGAGCGAC 60.527 60.000 3.06 0.00 39.56 5.19
1569 1590 1.872234 GATCGCGCTAGCAACGTCA 60.872 57.895 22.11 8.56 45.49 4.35
1633 1654 2.616458 GGAGGCCATGGAACTGGGT 61.616 63.158 18.40 0.00 36.75 4.51
1712 1733 0.108756 CTCGAACGGGAACTCCTTCC 60.109 60.000 0.00 0.00 45.04 3.46
1807 1828 1.142748 CCCTGAGCTCCATGACGAC 59.857 63.158 12.15 0.00 0.00 4.34
1808 1829 2.060383 CCCCTGAGCTCCATGACGA 61.060 63.158 12.15 0.00 0.00 4.20
1828 1849 2.126071 CACAACGTCCCTCGCGAT 60.126 61.111 10.36 0.00 44.19 4.58
1857 1878 2.481903 TCGAGAAGCACGAGATCATG 57.518 50.000 0.00 0.00 34.85 3.07
1893 1914 3.619038 GGTTAAAGAGCTTCATGACCGAG 59.381 47.826 0.00 0.00 0.00 4.63
1941 1962 1.609580 GCATTGTACACCTTCCGGTCA 60.610 52.381 0.00 0.00 43.24 4.02
1992 2013 2.169789 CGCTCTTGCCTCATCCACG 61.170 63.158 0.00 0.00 35.36 4.94
2022 2043 1.893315 CAACCCCCTTCTCCTCCATA 58.107 55.000 0.00 0.00 0.00 2.74
2220 2241 3.441222 TGCAATGTAGTGCCTTCATCTTG 59.559 43.478 1.61 0.00 44.26 3.02
2242 2263 6.506538 AATATAAGTGTCCATCTCTGGCTT 57.493 37.500 0.00 0.00 42.80 4.35
2343 2364 4.364318 CTCCGATCAGGGGTCAGT 57.636 61.111 0.00 0.00 41.52 3.41
2364 2385 6.992123 ACAATCCATGTATGAACACGATGTAT 59.008 34.615 0.00 0.00 41.63 2.29
2370 2391 4.908736 GGAACAATCCATGTATGAACACG 58.091 43.478 0.00 0.00 45.79 4.49
2426 2447 3.909995 TCCCTTGACTTTCATCTCCTCAA 59.090 43.478 0.00 0.00 0.00 3.02
2441 2462 2.986019 TCCTCTGGTGAAAATCCCTTGA 59.014 45.455 0.00 0.00 0.00 3.02
2517 2538 0.320374 TTGAACCGACAGAAGCCGAT 59.680 50.000 0.00 0.00 0.00 4.18
2520 2541 1.673920 TGTTTTGAACCGACAGAAGCC 59.326 47.619 0.00 0.00 0.00 4.35
2537 2558 4.422073 TTGAGAGACACAGAACCATGTT 57.578 40.909 0.00 0.00 0.00 2.71
2540 2561 4.696479 ACTTTGAGAGACACAGAACCAT 57.304 40.909 0.00 0.00 31.52 3.55
2547 2568 4.913335 ACGAGTTACTTTGAGAGACACA 57.087 40.909 0.00 0.00 0.00 3.72
2597 2618 8.940952 GCTGTGTTTCTTTCTATAGATCACTTT 58.059 33.333 2.58 0.00 34.01 2.66
2621 2642 3.002348 GCAGTTACTCGAAAACAACAGCT 59.998 43.478 11.62 0.00 32.57 4.24
2623 2644 4.795970 AGCAGTTACTCGAAAACAACAG 57.204 40.909 11.62 1.20 0.00 3.16
2633 2654 2.747989 TCCAGTGTCTAGCAGTTACTCG 59.252 50.000 0.00 0.00 0.00 4.18
2643 2664 7.069331 ACCAAATAATCTCTCTCCAGTGTCTAG 59.931 40.741 0.00 0.00 0.00 2.43
2648 2669 8.970859 AATAACCAAATAATCTCTCTCCAGTG 57.029 34.615 0.00 0.00 0.00 3.66
2695 2718 8.908786 ACAAAGTAGATGAAGATCACTTGAAA 57.091 30.769 0.00 0.00 36.39 2.69
2696 2719 8.777413 CAACAAAGTAGATGAAGATCACTTGAA 58.223 33.333 0.00 0.00 36.39 2.69
2726 2749 1.342474 TGGCTTCCTTGACCAAACCAA 60.342 47.619 0.00 0.00 0.00 3.67
2727 2750 0.260230 TGGCTTCCTTGACCAAACCA 59.740 50.000 0.00 0.00 0.00 3.67
2880 2904 8.724229 GGTAAACATACTCTTTTCAAATACGGT 58.276 33.333 0.00 0.00 0.00 4.83
2974 2998 4.522789 TGCCTATCCAAGTTTCAAAAGGAC 59.477 41.667 0.00 0.00 0.00 3.85
2979 3003 5.324409 AGTGATGCCTATCCAAGTTTCAAA 58.676 37.500 0.00 0.00 32.09 2.69
2982 3006 5.644644 CAAAGTGATGCCTATCCAAGTTTC 58.355 41.667 0.00 0.00 32.09 2.78
3008 3032 4.640771 TGAGCTACAAAAGAAGGGTCAT 57.359 40.909 0.00 0.00 31.02 3.06
3010 3034 5.735766 ACTATGAGCTACAAAAGAAGGGTC 58.264 41.667 0.00 0.00 0.00 4.46
3087 3227 5.888901 AGGAGTCGGACCAGTATGAATATA 58.111 41.667 4.14 0.00 39.69 0.86
3152 3292 6.317140 TCAAACCATATGAAATGAGCTCTCAC 59.683 38.462 16.19 4.70 43.11 3.51
3187 3341 9.884636 ACAGCTACATATTGAAGTGTGTATTTA 57.115 29.630 0.00 0.00 0.00 1.40
3188 3342 8.792830 ACAGCTACATATTGAAGTGTGTATTT 57.207 30.769 0.00 0.00 0.00 1.40
3191 3345 9.529325 GAATACAGCTACATATTGAAGTGTGTA 57.471 33.333 0.00 0.00 0.00 2.90
3192 3346 8.040727 TGAATACAGCTACATATTGAAGTGTGT 58.959 33.333 0.00 0.00 0.00 3.72
3194 3348 9.618890 ATTGAATACAGCTACATATTGAAGTGT 57.381 29.630 0.00 0.00 0.00 3.55
3231 3700 5.618195 GCAAACAATGGAAGCATGAAAATGG 60.618 40.000 0.00 0.00 0.00 3.16
3245 3714 3.058016 CCAGTACACTCTGCAAACAATGG 60.058 47.826 0.00 0.00 34.47 3.16
3248 3717 1.946768 GCCAGTACACTCTGCAAACAA 59.053 47.619 0.00 0.00 34.47 2.83
3249 3718 1.134250 TGCCAGTACACTCTGCAAACA 60.134 47.619 0.00 0.00 34.47 2.83
3250 3719 1.593196 TGCCAGTACACTCTGCAAAC 58.407 50.000 0.00 0.00 34.47 2.93
3251 3720 2.566833 ATGCCAGTACACTCTGCAAA 57.433 45.000 7.07 0.00 34.47 3.68
3254 3723 6.483307 TGAATAAATATGCCAGTACACTCTGC 59.517 38.462 0.00 0.00 34.47 4.26
3257 3726 7.786178 TGTGAATAAATATGCCAGTACACTC 57.214 36.000 0.00 0.00 0.00 3.51
3307 3777 2.180017 CGGCCAATTCTGCAGTGC 59.820 61.111 14.67 8.58 0.00 4.40
3319 3789 2.902423 AAACCTTCACACAGCGGCCA 62.902 55.000 2.24 0.00 0.00 5.36
3375 3845 1.604593 GGCTGGCTGGCAGAAAGAA 60.605 57.895 32.31 0.00 41.37 2.52
3487 3957 1.026182 TGATTACAAGCAGGCTGGCG 61.026 55.000 17.64 0.00 39.27 5.69
3569 4039 5.235186 CCACAGGATAGCAGAGAAAATAACG 59.765 44.000 0.00 0.00 0.00 3.18
3641 4113 9.997482 AAGATAAATTTTTGACGCGTACAATAT 57.003 25.926 13.97 11.90 0.00 1.28
3642 4114 9.480538 GAAGATAAATTTTTGACGCGTACAATA 57.519 29.630 13.97 10.78 0.00 1.90
3643 4115 7.215568 CGAAGATAAATTTTTGACGCGTACAAT 59.784 33.333 13.97 5.24 0.00 2.71
3644 4116 6.517034 CGAAGATAAATTTTTGACGCGTACAA 59.483 34.615 13.97 15.66 0.00 2.41
3645 4117 6.010675 CGAAGATAAATTTTTGACGCGTACA 58.989 36.000 13.97 9.74 0.00 2.90
3750 4222 9.964303 CATAACAGAGATCAGGATATATGTAGC 57.036 37.037 4.80 0.00 33.92 3.58
3877 4350 4.202315 TGGCTGTAGCTTGTACAGAGAAAA 60.202 41.667 17.47 0.00 45.69 2.29
3927 4400 2.874014 TGCCATGAAATTGACAGTGGA 58.126 42.857 0.00 0.00 0.00 4.02
3992 4465 4.183865 TGCACTATGTTAGTCTGCATCAC 58.816 43.478 0.00 0.00 36.76 3.06
4104 4577 5.186198 ACAGTGGGTTCAGATATTAACAGC 58.814 41.667 0.00 0.00 0.00 4.40
4235 4709 9.593134 AGCTGTATCTACAAAAATCTAAGACAG 57.407 33.333 0.00 0.00 35.50 3.51
4247 4721 9.991906 AGTTTTAGTGTTAGCTGTATCTACAAA 57.008 29.630 0.00 0.00 35.50 2.83
4248 4722 9.419297 CAGTTTTAGTGTTAGCTGTATCTACAA 57.581 33.333 0.00 0.00 35.50 2.41
4249 4723 8.582437 ACAGTTTTAGTGTTAGCTGTATCTACA 58.418 33.333 0.00 0.00 35.71 2.74
4250 4724 8.983307 ACAGTTTTAGTGTTAGCTGTATCTAC 57.017 34.615 0.00 0.00 35.71 2.59
4251 4725 9.021807 AGACAGTTTTAGTGTTAGCTGTATCTA 57.978 33.333 0.00 0.00 37.32 1.98
4256 4730 7.286215 TCTAGACAGTTTTAGTGTTAGCTGT 57.714 36.000 0.00 0.00 39.51 4.40
4257 4731 9.291664 GTATCTAGACAGTTTTAGTGTTAGCTG 57.708 37.037 0.00 0.00 30.64 4.24
4259 4733 9.804758 ATGTATCTAGACAGTTTTAGTGTTAGC 57.195 33.333 0.00 0.00 30.64 3.09
4302 4807 1.874129 ACACATATTCCCTCCGTCCA 58.126 50.000 0.00 0.00 0.00 4.02
4318 4823 8.807667 ATCAATCTGAAACAAATCTGAAACAC 57.192 30.769 0.00 0.00 32.11 3.32
4359 4864 8.974060 AATCTCAAGTCTAAACACCAAACTTA 57.026 30.769 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.