Multiple sequence alignment - TraesCS1D01G212300

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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 TraesCS1D01G212300 chr1D 100.000 4617 0 0 1 4617 298010490 298015106 0.000000e+00 8527
1 TraesCS1D01G212300 chr1B 93.182 4620 246 31 39 4617 400665168 400669759 0.000000e+00 6722
2 TraesCS1D01G212300 chr1A 93.106 3191 180 23 12 3181 371083818 371086989 0.000000e+00 4638
3 TraesCS1D01G212300 chr1A 94.387 1443 65 11 3185 4617 371087480 371088916 0.000000e+00 2202
4 TraesCS1D01G212300 chr1A 91.579 95 8 0 3198 3292 371086869 371086963 1.040000e-26 132


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 TraesCS1D01G212300 chr1D 298010490 298015106 4616 False 8527 8527 100.000 1 4617 1 chr1D.!!$F1 4616
1 TraesCS1D01G212300 chr1B 400665168 400669759 4591 False 6722 6722 93.182 39 4617 1 chr1B.!!$F1 4578
2 TraesCS1D01G212300 chr1A 371083818 371088916 5098 False 2324 4638 93.024 12 4617 3 chr1A.!!$F1 4605

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
212 216 0.606604 TTTCACAGTCGTCCCTAGCC 59.393 55.0 0.00 0.00 0.00 3.93 F
1470 1504 0.320374 TTTCATCGCGTGAGGTTCCT 59.680 50.0 10.75 0.00 38.29 3.36 F
2259 2293 0.251253 TTGGCCAGATGCATGTGTCA 60.251 50.0 21.17 15.81 43.89 3.58 F
2689 2723 0.976641 TGAGACCAGTCCATCACCAC 59.023 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2002 0.323360 TCTGGCATTTAGGTGTGGGC 60.323 55.000 0.00 0.0 0.0 5.36 R
2805 2839 0.101759 CCATGGGATGCTTGCTTTCG 59.898 55.000 2.85 0.0 0.0 3.46 R
3307 3830 1.076485 CATGGAAAGGGCAGGGAGG 60.076 63.158 0.00 0.0 0.0 4.30 R
4513 5046 1.187567 AACCCATCTTTGCCTGCACC 61.188 55.000 0.00 0.0 0.0 5.01 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
22 23 5.853572 AGTTGAGGTACTTATTTTGGGGA 57.146 39.130 0.00 0.00 41.55 4.81
23 24 5.816682 AGTTGAGGTACTTATTTTGGGGAG 58.183 41.667 0.00 0.00 41.55 4.30
24 25 5.312443 AGTTGAGGTACTTATTTTGGGGAGT 59.688 40.000 0.00 0.00 41.55 3.85
71 72 1.898574 CTTTTGCCGCCACAGACCT 60.899 57.895 0.00 0.00 0.00 3.85
80 81 3.775654 CACAGACCTCCTCGGGCC 61.776 72.222 0.00 0.00 44.54 5.80
86 87 4.517934 CCTCCTCGGGCCGGTCTA 62.518 72.222 27.98 5.30 0.00 2.59
91 92 2.283388 TCGGGCCGGTCTAACACT 60.283 61.111 27.98 0.00 0.00 3.55
104 106 4.434520 GTCTAACACTGGCCTACAAGATC 58.565 47.826 3.32 0.00 0.00 2.75
109 111 2.027745 CACTGGCCTACAAGATCTGTGT 60.028 50.000 3.32 12.93 39.20 3.72
110 112 2.639839 ACTGGCCTACAAGATCTGTGTT 59.360 45.455 3.32 0.00 39.20 3.32
174 176 3.799420 CGGATTGCTCTTTACACTCTAGC 59.201 47.826 0.00 0.00 0.00 3.42
183 187 4.016851 TCTTTACACTCTAGCTCCCCCTAA 60.017 45.833 0.00 0.00 0.00 2.69
200 204 6.782988 TCCCCCTAACTCTATCTATTTCACAG 59.217 42.308 0.00 0.00 0.00 3.66
212 216 0.606604 TTTCACAGTCGTCCCTAGCC 59.393 55.000 0.00 0.00 0.00 3.93
313 322 3.396911 GATGCGCGAGGACTGACGA 62.397 63.158 12.10 0.00 0.00 4.20
407 416 2.032675 GCATTTCTCGATCCCTTTCTGC 59.967 50.000 0.00 0.00 0.00 4.26
596 626 1.151668 CCTTTTCTGCTGACCTCGTG 58.848 55.000 0.00 0.00 0.00 4.35
597 627 1.151668 CTTTTCTGCTGACCTCGTGG 58.848 55.000 0.99 0.99 39.83 4.94
635 665 0.984230 TGCGAGGGTTCATCCTTTCT 59.016 50.000 0.00 0.00 37.25 2.52
657 687 5.937540 TCTTCGAATGGTTTAGCTGATTCAA 59.062 36.000 0.00 0.00 0.00 2.69
661 691 5.967674 CGAATGGTTTAGCTGATTCAATGAC 59.032 40.000 0.00 0.00 0.00 3.06
666 696 6.433716 TGGTTTAGCTGATTCAATGACAATGA 59.566 34.615 0.00 0.00 0.00 2.57
667 697 7.039853 TGGTTTAGCTGATTCAATGACAATGAA 60.040 33.333 8.35 8.35 40.76 2.57
726 759 6.426937 GCTTTCTTAGTGTTGTCATGTTCCTA 59.573 38.462 0.00 0.00 0.00 2.94
730 763 6.878923 TCTTAGTGTTGTCATGTTCCTATTGG 59.121 38.462 0.00 0.00 0.00 3.16
745 778 6.500589 TCCTATTGGAACTTAGGGATTGAG 57.499 41.667 0.00 0.00 39.87 3.02
758 791 5.456921 AGGGATTGAGGTTGTATGTGAAT 57.543 39.130 0.00 0.00 0.00 2.57
770 803 7.888021 AGGTTGTATGTGAATGAATGGAAACTA 59.112 33.333 0.00 0.00 0.00 2.24
771 804 7.968405 GGTTGTATGTGAATGAATGGAAACTAC 59.032 37.037 0.00 0.00 0.00 2.73
773 806 8.862325 TGTATGTGAATGAATGGAAACTACTT 57.138 30.769 0.00 0.00 0.00 2.24
774 807 8.729756 TGTATGTGAATGAATGGAAACTACTTG 58.270 33.333 0.00 0.00 0.00 3.16
780 813 8.567948 TGAATGAATGGAAACTACTTGTTCTTC 58.432 33.333 0.00 0.00 38.03 2.87
793 826 5.799213 ACTTGTTCTTCTGGAAGTGGATAG 58.201 41.667 9.73 5.81 39.38 2.08
796 829 5.032846 TGTTCTTCTGGAAGTGGATAGGAT 58.967 41.667 9.73 0.00 39.38 3.24
797 830 5.104776 TGTTCTTCTGGAAGTGGATAGGATG 60.105 44.000 9.73 0.00 39.38 3.51
802 835 6.425210 TCTGGAAGTGGATAGGATGTATTG 57.575 41.667 0.00 0.00 33.76 1.90
803 836 5.905331 TCTGGAAGTGGATAGGATGTATTGT 59.095 40.000 0.00 0.00 33.76 2.71
804 837 6.386927 TCTGGAAGTGGATAGGATGTATTGTT 59.613 38.462 0.00 0.00 33.76 2.83
805 838 6.969043 TGGAAGTGGATAGGATGTATTGTTT 58.031 36.000 0.00 0.00 0.00 2.83
806 839 7.410174 TGGAAGTGGATAGGATGTATTGTTTT 58.590 34.615 0.00 0.00 0.00 2.43
807 840 7.556275 TGGAAGTGGATAGGATGTATTGTTTTC 59.444 37.037 0.00 0.00 0.00 2.29
840 873 4.565444 CGGATTTGATGCATAGGATGGGTA 60.565 45.833 0.00 0.00 0.00 3.69
847 880 4.689612 TGCATAGGATGGGTAGAGTTTC 57.310 45.455 0.00 0.00 0.00 2.78
852 885 2.912956 AGGATGGGTAGAGTTTCAAGCA 59.087 45.455 0.00 0.00 0.00 3.91
861 895 5.178809 GGTAGAGTTTCAAGCACGTAAATGT 59.821 40.000 0.00 0.00 0.00 2.71
868 902 3.185594 TCAAGCACGTAAATGTTTCTCCG 59.814 43.478 0.00 0.00 0.00 4.63
872 906 2.478894 CACGTAAATGTTTCTCCGCTGT 59.521 45.455 0.00 0.00 0.00 4.40
886 920 2.165641 TCCGCTGTCGAACTTGATACAT 59.834 45.455 0.00 0.00 38.10 2.29
888 922 4.037565 TCCGCTGTCGAACTTGATACATAT 59.962 41.667 0.00 0.00 38.10 1.78
889 923 5.239963 TCCGCTGTCGAACTTGATACATATA 59.760 40.000 0.00 0.00 38.10 0.86
916 950 9.959721 ATGGTTATGTTGTACTCTATGTTTTCT 57.040 29.630 0.00 0.00 0.00 2.52
917 951 9.431887 TGGTTATGTTGTACTCTATGTTTTCTC 57.568 33.333 0.00 0.00 0.00 2.87
924 958 9.220767 GTTGTACTCTATGTTTTCTCTTGGATT 57.779 33.333 0.00 0.00 0.00 3.01
927 961 9.535878 GTACTCTATGTTTTCTCTTGGATTAGG 57.464 37.037 0.00 0.00 0.00 2.69
954 988 2.224378 TGCCACTGTCCTCTTTTCTCTG 60.224 50.000 0.00 0.00 0.00 3.35
959 993 4.987912 CACTGTCCTCTTTTCTCTGTTCTC 59.012 45.833 0.00 0.00 0.00 2.87
962 996 6.179906 TGTCCTCTTTTCTCTGTTCTCATT 57.820 37.500 0.00 0.00 0.00 2.57
983 1017 7.639039 TCATTCGAGCAATGTATTATGGTTTC 58.361 34.615 0.00 0.00 42.47 2.78
999 1033 4.219115 TGGTTTCAATGCAGGTTTCCTAA 58.781 39.130 0.00 0.00 29.64 2.69
1035 1069 0.466124 GGCCCAGTGTAGCTAAGGAG 59.534 60.000 0.00 0.00 0.00 3.69
1047 1081 1.473434 GCTAAGGAGACCATGGAACCG 60.473 57.143 21.47 7.10 0.00 4.44
1053 1087 2.280628 GAGACCATGGAACCGATTGAC 58.719 52.381 21.47 0.00 0.00 3.18
1089 1123 1.003355 TAGCAGGGCAGCACAACTC 60.003 57.895 0.00 0.00 36.85 3.01
1329 1363 3.007940 TGTCATTTGGGACTGTCGATTCT 59.992 43.478 1.07 0.00 38.61 2.40
1354 1388 1.209019 CTCAGCCTAGCACAAGTGGAT 59.791 52.381 2.00 0.00 0.00 3.41
1392 1426 0.955428 GGAGCGGTTCATGCAAGTCA 60.955 55.000 0.00 0.00 33.85 3.41
1441 1475 4.591321 TTTAATCAAGATGCCAGGGAGT 57.409 40.909 0.00 0.00 0.00 3.85
1470 1504 0.320374 TTTCATCGCGTGAGGTTCCT 59.680 50.000 10.75 0.00 38.29 3.36
1574 1608 2.012673 GCTCGAAGAAGACAATGCCAT 58.987 47.619 0.00 0.00 34.09 4.40
1581 1615 1.474077 GAAGACAATGCCATGTGTCCC 59.526 52.381 9.81 1.11 44.30 4.46
1642 1676 6.803320 CAGTAGCAAAGGTACAATGTCAAATG 59.197 38.462 8.80 0.00 38.76 2.32
1849 1883 7.056635 GGATCCTTTCATGAAGTCCAAATCTA 58.943 38.462 18.57 0.00 33.06 1.98
1871 1905 0.649992 AGGAATCCCTCCCTCATGGA 59.350 55.000 0.00 0.00 46.81 3.41
1968 2002 5.869344 TGGTATCTCAAGATCTGAACAAACG 59.131 40.000 0.00 0.00 36.05 3.60
2013 2047 2.280186 GAAGCCCGGCCTATCACG 60.280 66.667 5.55 0.00 0.00 4.35
2198 2232 1.127951 CAAACGATCAAGTACGGTGGC 59.872 52.381 0.00 0.00 0.00 5.01
2259 2293 0.251253 TTGGCCAGATGCATGTGTCA 60.251 50.000 21.17 15.81 43.89 3.58
2378 2412 3.119459 TCTGCCGTTGATAGAGTTCAGTC 60.119 47.826 0.00 0.00 0.00 3.51
2598 2632 3.529216 AAAACCCGGTCCCAAGAATTA 57.471 42.857 0.00 0.00 0.00 1.40
2688 2722 1.833630 GATGAGACCAGTCCATCACCA 59.166 52.381 17.30 0.00 37.30 4.17
2689 2723 0.976641 TGAGACCAGTCCATCACCAC 59.023 55.000 0.00 0.00 0.00 4.16
2691 2725 0.979665 AGACCAGTCCATCACCACTG 59.020 55.000 0.00 0.00 39.90 3.66
2727 2761 2.516888 CGGGGGAAGGTGTGACTGT 61.517 63.158 0.00 0.00 0.00 3.55
2805 2839 2.972625 TGGGTCGATTCTGTGATGAAC 58.027 47.619 0.00 0.00 0.00 3.18
2900 2934 3.780804 ACCACCTGTGTGCATTTACTA 57.219 42.857 0.00 0.00 41.35 1.82
2903 2937 3.120338 CCACCTGTGTGCATTTACTAACG 60.120 47.826 0.00 0.00 41.35 3.18
2911 2945 5.061808 GTGTGCATTTACTAACGGTGAGTAG 59.938 44.000 5.53 0.00 31.22 2.57
2929 2963 7.827729 GGTGAGTAGTAATTAACTTGGGTCAAT 59.172 37.037 0.00 0.00 39.80 2.57
2942 2976 5.375354 ACTTGGGTCAATATATGATTCCCCA 59.625 40.000 10.84 0.00 45.46 4.96
2969 3004 8.482429 CAACTTCATTAGCACATCAAAAGAAAC 58.518 33.333 0.00 0.00 0.00 2.78
2973 3008 8.169977 TCATTAGCACATCAAAAGAAACTTCT 57.830 30.769 0.00 0.00 39.74 2.85
3000 3035 5.981088 ATGATGGTTGAAATGCACTGTTA 57.019 34.783 0.00 0.00 0.00 2.41
3016 3051 5.335661 GCACTGTTATTTGGTTCCCACTTAG 60.336 44.000 0.00 0.00 30.78 2.18
3024 3059 4.487714 TGGTTCCCACTTAGAAGCTATG 57.512 45.455 4.58 0.00 41.27 2.23
3049 3084 4.201881 CCCTGTTTTAGTTATACTTGCGCC 60.202 45.833 4.18 0.00 0.00 6.53
3066 3101 1.333619 CGCCACTTAACAGTTGCACTT 59.666 47.619 0.00 0.00 40.96 3.16
3074 3109 7.491048 CCACTTAACAGTTGCACTTGTTAAAAT 59.509 33.333 24.13 17.06 34.53 1.82
3084 3119 9.060547 GTTGCACTTGTTAAAATTTCTTTTTGG 57.939 29.630 0.00 0.00 38.03 3.28
3096 3131 4.576216 TTCTTTTTGGCGAATGCACTAA 57.424 36.364 0.00 0.00 45.35 2.24
3103 3138 5.378292 TTGGCGAATGCACTAATTAACAA 57.622 34.783 0.00 0.00 45.35 2.83
3107 3142 7.138081 TGGCGAATGCACTAATTAACAATATG 58.862 34.615 0.00 0.00 45.35 1.78
3160 3195 4.108699 TCCAACTGTTGAAGCAAACAAG 57.891 40.909 21.49 1.35 39.47 3.16
3241 3764 9.979578 TTTTTGATGAATGCACTAGTTAACATT 57.020 25.926 8.61 12.93 35.52 2.71
3287 3810 4.036262 TCATTTGTGTACTCCAACTGTTGC 59.964 41.667 14.94 1.87 0.00 4.17
3331 3854 2.291540 CCCTGCCCTTTCCATGAAAGTA 60.292 50.000 13.75 2.10 45.12 2.24
3334 3857 3.686016 TGCCCTTTCCATGAAAGTAGAC 58.314 45.455 13.75 3.35 45.12 2.59
3344 3867 4.564821 CCATGAAAGTAGACGGGAAAGGAA 60.565 45.833 0.00 0.00 0.00 3.36
3412 3935 4.691175 TCTCAGTCTGCATATCTTTGCTC 58.309 43.478 0.00 0.00 43.18 4.26
3464 3987 7.168219 TGGTATAGAGAAATTCAAGCACAAGT 58.832 34.615 0.00 0.00 0.00 3.16
3514 4037 5.490139 TCAAAGAAGAAGTGAAGCAGTTG 57.510 39.130 0.00 0.00 0.00 3.16
3517 4040 5.938438 AAGAAGAAGTGAAGCAGTTGATC 57.062 39.130 0.00 0.00 0.00 2.92
3564 4087 4.014569 AGAAAGTGAAGAGGAGGAAAGC 57.985 45.455 0.00 0.00 0.00 3.51
3649 4172 2.286008 CCATCATGTTCATCGTTCAGCG 60.286 50.000 0.00 0.00 43.01 5.18
3693 4216 4.839668 TGTTTTGTAAGATCAAACGGGG 57.160 40.909 0.00 0.00 37.10 5.73
3712 4235 8.866970 AACGGGGATACTTTTTATCTTGTTTA 57.133 30.769 0.00 0.00 0.00 2.01
3944 4468 1.470632 CGGATCTTGACCACTGCTCTC 60.471 57.143 0.00 0.00 0.00 3.20
3947 4471 0.315251 TCTTGACCACTGCTCTCGTG 59.685 55.000 0.00 0.00 0.00 4.35
4034 4561 8.329502 AGTACAGGTAGAAGCAAATATTCCTTT 58.670 33.333 0.00 0.00 0.00 3.11
4079 4606 2.498885 GCTTCCCTCCAGCAATTTTGAT 59.501 45.455 0.00 0.00 37.22 2.57
4108 4637 7.703197 TGATGCATGCTTTTGAACTACATAATG 59.297 33.333 20.33 0.00 0.00 1.90
4132 4661 5.536161 GGGCAACATATATCATGACCAAACT 59.464 40.000 12.46 0.00 40.86 2.66
4151 4680 4.123497 ACTGCGCATATGTAGTTTCAGA 57.877 40.909 12.24 0.00 0.00 3.27
4207 4736 4.754372 CATCTGCTGCAAGTTCAAGTTA 57.246 40.909 3.02 0.00 35.30 2.24
4214 4743 4.695455 GCTGCAAGTTCAAGTTATAGGTGA 59.305 41.667 0.00 0.00 35.30 4.02
4374 4906 5.557891 AGATATGCTCAAAGTTGTCAAGC 57.442 39.130 0.00 0.00 0.00 4.01
4408 4941 7.756395 AGACATGTTGAATTTTGATCTCAGT 57.244 32.000 0.00 0.00 0.00 3.41
4431 4964 5.006358 GTCTGACTTTTCTTGTAAGCACGAA 59.994 40.000 0.00 0.00 32.13 3.85
4438 4971 2.823747 TCTTGTAAGCACGAAGAGGCTA 59.176 45.455 0.00 0.00 40.24 3.93
4501 5034 0.321034 GTGGCTGTCATCTGCTCACA 60.321 55.000 0.00 0.00 38.35 3.58
4580 5113 2.716424 CCCATCCCTAGGCCATTTTCTA 59.284 50.000 5.01 0.00 0.00 2.10
4593 5126 7.573710 AGGCCATTTTCTATGTGTATTCTGTA 58.426 34.615 5.01 0.00 0.00 2.74
4603 5136 6.668541 ATGTGTATTCTGTAAGTGTCATGC 57.331 37.500 0.00 0.00 33.76 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.312443 ACTCCCCAAAATAAGTACCTCAACT 59.688 40.000 0.00 0.00 0.00 3.16
1 2 5.414765 CACTCCCCAAAATAAGTACCTCAAC 59.585 44.000 0.00 0.00 0.00 3.18
2 3 5.311121 TCACTCCCCAAAATAAGTACCTCAA 59.689 40.000 0.00 0.00 0.00 3.02
4 5 5.045797 ACTCACTCCCCAAAATAAGTACCTC 60.046 44.000 0.00 0.00 0.00 3.85
5 6 4.850386 ACTCACTCCCCAAAATAAGTACCT 59.150 41.667 0.00 0.00 0.00 3.08
6 7 5.175388 ACTCACTCCCCAAAATAAGTACC 57.825 43.478 0.00 0.00 0.00 3.34
8 9 7.989947 ATCTACTCACTCCCCAAAATAAGTA 57.010 36.000 0.00 0.00 0.00 2.24
9 10 6.893020 ATCTACTCACTCCCCAAAATAAGT 57.107 37.500 0.00 0.00 0.00 2.24
10 11 8.251383 TCTATCTACTCACTCCCCAAAATAAG 57.749 38.462 0.00 0.00 0.00 1.73
11 12 8.618240 TTCTATCTACTCACTCCCCAAAATAA 57.382 34.615 0.00 0.00 0.00 1.40
12 13 8.065627 TCTTCTATCTACTCACTCCCCAAAATA 58.934 37.037 0.00 0.00 0.00 1.40
13 14 6.903534 TCTTCTATCTACTCACTCCCCAAAAT 59.096 38.462 0.00 0.00 0.00 1.82
14 15 6.261435 TCTTCTATCTACTCACTCCCCAAAA 58.739 40.000 0.00 0.00 0.00 2.44
15 16 5.838955 TCTTCTATCTACTCACTCCCCAAA 58.161 41.667 0.00 0.00 0.00 3.28
16 17 5.193930 TCTCTTCTATCTACTCACTCCCCAA 59.806 44.000 0.00 0.00 0.00 4.12
17 18 4.727332 TCTCTTCTATCTACTCACTCCCCA 59.273 45.833 0.00 0.00 0.00 4.96
18 19 5.313280 TCTCTTCTATCTACTCACTCCCC 57.687 47.826 0.00 0.00 0.00 4.81
19 20 5.710099 CCATCTCTTCTATCTACTCACTCCC 59.290 48.000 0.00 0.00 0.00 4.30
20 21 6.303839 ACCATCTCTTCTATCTACTCACTCC 58.696 44.000 0.00 0.00 0.00 3.85
21 22 7.934665 TGTACCATCTCTTCTATCTACTCACTC 59.065 40.741 0.00 0.00 0.00 3.51
22 23 7.807198 TGTACCATCTCTTCTATCTACTCACT 58.193 38.462 0.00 0.00 0.00 3.41
23 24 8.511321 CATGTACCATCTCTTCTATCTACTCAC 58.489 40.741 0.00 0.00 0.00 3.51
24 25 7.667635 CCATGTACCATCTCTTCTATCTACTCA 59.332 40.741 0.00 0.00 0.00 3.41
71 72 2.757099 GTTAGACCGGCCCGAGGA 60.757 66.667 3.71 0.00 0.00 3.71
80 81 0.892755 TGTAGGCCAGTGTTAGACCG 59.107 55.000 5.01 0.00 0.00 4.79
86 87 2.639839 ACAGATCTTGTAGGCCAGTGTT 59.360 45.455 5.01 0.00 38.56 3.32
91 92 3.055385 GGTAACACAGATCTTGTAGGCCA 60.055 47.826 5.01 0.00 38.16 5.36
104 106 2.746277 GCTGGGCCGGTAACACAG 60.746 66.667 15.16 4.08 0.00 3.66
157 159 2.761208 GGGAGCTAGAGTGTAAAGAGCA 59.239 50.000 0.00 0.00 35.55 4.26
174 176 6.782988 TGTGAAATAGATAGAGTTAGGGGGAG 59.217 42.308 0.00 0.00 0.00 4.30
183 187 5.299782 GGGACGACTGTGAAATAGATAGAGT 59.700 44.000 0.00 0.00 0.00 3.24
313 322 1.774856 AGGCAGTGGACTTTACTGGTT 59.225 47.619 7.19 0.00 44.36 3.67
407 416 1.202533 AGGACCGCCGTATGAATCAAG 60.203 52.381 0.00 0.00 39.96 3.02
635 665 6.374053 TCATTGAATCAGCTAAACCATTCGAA 59.626 34.615 0.00 0.00 0.00 3.71
657 687 3.686241 CGGATCACACAGTTCATTGTCAT 59.314 43.478 0.00 0.00 0.00 3.06
661 691 3.588955 TCTCGGATCACACAGTTCATTG 58.411 45.455 0.00 0.00 0.00 2.82
666 696 3.687125 TCTACTCTCGGATCACACAGTT 58.313 45.455 0.00 0.00 0.00 3.16
667 697 3.351794 TCTACTCTCGGATCACACAGT 57.648 47.619 0.00 0.00 0.00 3.55
702 735 6.867662 AGGAACATGACAACACTAAGAAAG 57.132 37.500 0.00 0.00 0.00 2.62
704 737 7.390440 CCAATAGGAACATGACAACACTAAGAA 59.610 37.037 0.00 0.00 36.89 2.52
726 759 5.222337 ACAACCTCAATCCCTAAGTTCCAAT 60.222 40.000 0.00 0.00 0.00 3.16
730 763 6.316390 CACATACAACCTCAATCCCTAAGTTC 59.684 42.308 0.00 0.00 0.00 3.01
739 772 7.067372 TCCATTCATTCACATACAACCTCAATC 59.933 37.037 0.00 0.00 0.00 2.67
745 778 6.924111 AGTTTCCATTCATTCACATACAACC 58.076 36.000 0.00 0.00 0.00 3.77
758 791 6.486657 CCAGAAGAACAAGTAGTTTCCATTCA 59.513 38.462 0.00 0.00 41.51 2.57
770 803 4.713792 ATCCACTTCCAGAAGAACAAGT 57.286 40.909 14.19 0.00 40.79 3.16
771 804 5.046304 TCCTATCCACTTCCAGAAGAACAAG 60.046 44.000 14.19 4.95 40.79 3.16
773 806 4.425772 TCCTATCCACTTCCAGAAGAACA 58.574 43.478 14.19 0.00 40.79 3.18
774 807 5.104735 ACATCCTATCCACTTCCAGAAGAAC 60.105 44.000 14.19 0.00 40.79 3.01
780 813 6.179906 ACAATACATCCTATCCACTTCCAG 57.820 41.667 0.00 0.00 0.00 3.86
793 826 6.801862 CGTCCAAGAAAGAAAACAATACATCC 59.198 38.462 0.00 0.00 0.00 3.51
796 829 5.823570 TCCGTCCAAGAAAGAAAACAATACA 59.176 36.000 0.00 0.00 0.00 2.29
797 830 6.308371 TCCGTCCAAGAAAGAAAACAATAC 57.692 37.500 0.00 0.00 0.00 1.89
802 835 5.827666 TCAAATCCGTCCAAGAAAGAAAAC 58.172 37.500 0.00 0.00 0.00 2.43
803 836 6.446318 CATCAAATCCGTCCAAGAAAGAAAA 58.554 36.000 0.00 0.00 0.00 2.29
804 837 5.564651 GCATCAAATCCGTCCAAGAAAGAAA 60.565 40.000 0.00 0.00 0.00 2.52
805 838 4.082787 GCATCAAATCCGTCCAAGAAAGAA 60.083 41.667 0.00 0.00 0.00 2.52
806 839 3.440173 GCATCAAATCCGTCCAAGAAAGA 59.560 43.478 0.00 0.00 0.00 2.52
807 840 3.191162 TGCATCAAATCCGTCCAAGAAAG 59.809 43.478 0.00 0.00 0.00 2.62
840 873 5.751243 AACATTTACGTGCTTGAAACTCT 57.249 34.783 0.00 0.00 0.00 3.24
847 880 3.479006 CGGAGAAACATTTACGTGCTTG 58.521 45.455 0.00 0.00 0.00 4.01
852 885 2.735134 GACAGCGGAGAAACATTTACGT 59.265 45.455 0.00 0.00 0.00 3.57
861 895 1.067974 TCAAGTTCGACAGCGGAGAAA 59.932 47.619 0.00 0.00 38.28 2.52
868 902 7.385205 ACCATTATATGTATCAAGTTCGACAGC 59.615 37.037 0.00 0.00 0.00 4.40
901 935 9.535878 CCTAATCCAAGAGAAAACATAGAGTAC 57.464 37.037 0.00 0.00 0.00 2.73
903 937 7.569240 CCCTAATCCAAGAGAAAACATAGAGT 58.431 38.462 0.00 0.00 0.00 3.24
904 938 6.484977 GCCCTAATCCAAGAGAAAACATAGAG 59.515 42.308 0.00 0.00 0.00 2.43
906 940 6.261826 CAGCCCTAATCCAAGAGAAAACATAG 59.738 42.308 0.00 0.00 0.00 2.23
908 942 4.952335 CAGCCCTAATCCAAGAGAAAACAT 59.048 41.667 0.00 0.00 0.00 2.71
909 943 4.042809 TCAGCCCTAATCCAAGAGAAAACA 59.957 41.667 0.00 0.00 0.00 2.83
910 944 4.589908 TCAGCCCTAATCCAAGAGAAAAC 58.410 43.478 0.00 0.00 0.00 2.43
911 945 4.927267 TCAGCCCTAATCCAAGAGAAAA 57.073 40.909 0.00 0.00 0.00 2.29
912 946 4.785301 CATCAGCCCTAATCCAAGAGAAA 58.215 43.478 0.00 0.00 0.00 2.52
913 947 3.434167 GCATCAGCCCTAATCCAAGAGAA 60.434 47.826 0.00 0.00 33.58 2.87
914 948 2.105477 GCATCAGCCCTAATCCAAGAGA 59.895 50.000 0.00 0.00 33.58 3.10
915 949 2.502295 GCATCAGCCCTAATCCAAGAG 58.498 52.381 0.00 0.00 33.58 2.85
916 950 2.645838 GCATCAGCCCTAATCCAAGA 57.354 50.000 0.00 0.00 33.58 3.02
936 970 4.954875 AGAACAGAGAAAAGAGGACAGTG 58.045 43.478 0.00 0.00 0.00 3.66
943 977 5.062058 GCTCGAATGAGAACAGAGAAAAGAG 59.938 44.000 0.00 0.00 45.57 2.85
954 988 7.041780 ACCATAATACATTGCTCGAATGAGAAC 60.042 37.037 2.65 0.00 45.57 3.01
959 993 7.416817 TGAAACCATAATACATTGCTCGAATG 58.583 34.615 0.00 0.00 46.20 2.67
962 996 6.993786 TTGAAACCATAATACATTGCTCGA 57.006 33.333 0.00 0.00 0.00 4.04
983 1017 3.118665 CCCCATTTAGGAAACCTGCATTG 60.119 47.826 0.00 0.00 41.22 2.82
1035 1069 1.006832 CGTCAATCGGTTCCATGGTC 58.993 55.000 12.58 6.39 35.71 4.02
1047 1081 4.170256 GACTCTCTGTTTCCTCGTCAATC 58.830 47.826 0.00 0.00 0.00 2.67
1053 1087 2.098443 GCTAGGACTCTCTGTTTCCTCG 59.902 54.545 0.00 0.00 40.42 4.63
1089 1123 2.223112 CGAGTTTCCATCCGAGCATTTG 60.223 50.000 0.00 0.00 0.00 2.32
1096 1130 2.582436 GCCCGAGTTTCCATCCGA 59.418 61.111 0.00 0.00 0.00 4.55
1131 1165 5.993441 ACTCTTGCAATGAAAATTTGGGAAG 59.007 36.000 0.00 0.00 0.00 3.46
1329 1363 1.552337 CTTGTGCTAGGCTGAGAGGAA 59.448 52.381 0.00 0.00 0.00 3.36
1354 1388 1.504359 CGTTGCGGAACCAAGTAAGA 58.496 50.000 14.56 0.00 0.00 2.10
1392 1426 7.036220 CACGAGTTATGTTCATAGAAGACCTT 58.964 38.462 0.00 0.00 0.00 3.50
1441 1475 4.438148 TCACGCGATGAAATATCCAGAAA 58.562 39.130 15.93 0.00 33.02 2.52
1470 1504 2.703536 TCCAAGCCTCAAGTTGTCACTA 59.296 45.455 2.11 0.00 30.68 2.74
1532 1566 2.034436 TAACCCCGGGAAACTCTCTT 57.966 50.000 26.32 2.08 0.00 2.85
1536 1570 0.812811 GCGATAACCCCGGGAAACTC 60.813 60.000 26.32 12.45 0.00 3.01
1587 1621 1.749634 AGCAAATGAGGAGCAGCATTC 59.250 47.619 0.00 0.00 33.87 2.67
1685 1719 6.987386 AGATTACTCACCGAATCTATTCTGG 58.013 40.000 10.19 10.19 39.96 3.86
1865 1899 5.741962 TTTTGCATCTTCCATTTCCATGA 57.258 34.783 0.00 0.00 31.07 3.07
1871 1905 5.231702 ACCACATTTTGCATCTTCCATTT 57.768 34.783 0.00 0.00 0.00 2.32
1968 2002 0.323360 TCTGGCATTTAGGTGTGGGC 60.323 55.000 0.00 0.00 0.00 5.36
2013 2047 1.135199 TGAGTCGGCGATGAAGTAACC 60.135 52.381 14.79 0.00 0.00 2.85
2175 2209 0.368907 CCGTACTTGATCGTTTGCCG 59.631 55.000 0.00 0.00 38.13 5.69
2193 2227 1.303643 CTTGGAGGTCCTTGCCACC 60.304 63.158 0.00 0.00 39.35 4.61
2198 2232 1.141858 GCCTATCCTTGGAGGTCCTTG 59.858 57.143 0.00 0.00 36.53 3.61
2259 2293 7.836685 TCTTCAACTTCAGAGTACAGATAGGAT 59.163 37.037 0.00 0.00 34.21 3.24
2361 2395 6.424176 TCTGTAGACTGAACTCTATCAACG 57.576 41.667 0.00 0.00 0.00 4.10
2378 2412 3.007940 TGGTGGTTGAGTGGAATCTGTAG 59.992 47.826 0.00 0.00 0.00 2.74
2598 2632 4.118168 ACCAGGTGATGATCCAGTTTTT 57.882 40.909 0.00 0.00 0.00 1.94
2688 2722 3.586892 GCTCTTTAGACGGTTAAGCAGT 58.413 45.455 5.38 3.81 0.00 4.40
2689 2723 2.599082 CGCTCTTTAGACGGTTAAGCAG 59.401 50.000 5.38 0.52 0.00 4.24
2691 2725 1.925185 CCGCTCTTTAGACGGTTAAGC 59.075 52.381 10.59 0.00 42.01 3.09
2727 2761 1.004628 CAAGACATGTCCCATCCACCA 59.995 52.381 22.21 0.00 0.00 4.17
2805 2839 0.101759 CCATGGGATGCTTGCTTTCG 59.898 55.000 2.85 0.00 0.00 3.46
2865 2899 6.152661 ACACAGGTGGTAATAATCAAACATGG 59.847 38.462 4.24 0.00 34.19 3.66
2867 2901 6.350110 GCACACAGGTGGTAATAATCAAACAT 60.350 38.462 4.24 0.00 45.38 2.71
2900 2934 6.168389 CCCAAGTTAATTACTACTCACCGTT 58.832 40.000 0.00 0.00 35.54 4.44
2903 2937 6.704310 TGACCCAAGTTAATTACTACTCACC 58.296 40.000 0.00 0.00 35.54 4.02
2919 2953 5.711976 GTGGGGAATCATATATTGACCCAAG 59.288 44.000 0.00 0.00 45.15 3.61
2929 2963 7.665559 GCTAATGAAGTTGTGGGGAATCATATA 59.334 37.037 0.00 0.00 0.00 0.86
2942 2976 7.275888 TCTTTTGATGTGCTAATGAAGTTGT 57.724 32.000 0.00 0.00 0.00 3.32
2969 3004 8.288208 GTGCATTTCAACCATCATATAGAGAAG 58.712 37.037 0.00 0.00 0.00 2.85
2973 3008 7.056006 ACAGTGCATTTCAACCATCATATAGA 58.944 34.615 0.00 0.00 0.00 1.98
2983 3018 5.296748 ACCAAATAACAGTGCATTTCAACC 58.703 37.500 0.00 0.00 0.00 3.77
2984 3019 6.073819 GGAACCAAATAACAGTGCATTTCAAC 60.074 38.462 0.00 0.00 0.00 3.18
3016 3051 9.043079 GTATAACTAAAACAGGGACATAGCTTC 57.957 37.037 0.00 0.00 0.00 3.86
3024 3059 5.446875 GCGCAAGTATAACTAAAACAGGGAC 60.447 44.000 0.30 0.00 41.68 4.46
3066 3101 7.128976 GCATTCGCCAAAAAGAAATTTTAACA 58.871 30.769 0.00 0.00 39.20 2.41
3074 3109 3.451141 AGTGCATTCGCCAAAAAGAAA 57.549 38.095 0.00 0.00 37.32 2.52
3084 3119 8.560576 AACATATTGTTAATTAGTGCATTCGC 57.439 30.769 0.00 0.00 39.09 4.70
3181 3216 6.677913 ACTAGTGCATTGTTGTTGAAATACC 58.322 36.000 0.00 0.00 0.00 2.73
3254 3777 8.542497 TGGAGTACACAAATGAAATACTACAC 57.458 34.615 0.00 0.00 32.85 2.90
3287 3810 2.427506 GACTTCTTGGTTACCCTGCTG 58.572 52.381 0.00 0.00 0.00 4.41
3307 3830 1.076485 CATGGAAAGGGCAGGGAGG 60.076 63.158 0.00 0.00 0.00 4.30
3331 3854 4.202472 ACTGAGAAATTTCCTTTCCCGTCT 60.202 41.667 14.61 0.00 43.66 4.18
3334 3857 3.191371 CCACTGAGAAATTTCCTTTCCCG 59.809 47.826 14.61 3.42 43.66 5.14
3412 3935 2.224378 TGGAGAAGCTTCAGAACAGTGG 60.224 50.000 27.57 0.00 0.00 4.00
3464 3987 7.669427 AGCATTTTCATTGAACTGGAATACAA 58.331 30.769 0.00 0.00 0.00 2.41
3514 4037 4.099573 TCTTTCCCTGTTACTGATCCGATC 59.900 45.833 1.01 1.01 0.00 3.69
3517 4040 3.447586 TCTCTTTCCCTGTTACTGATCCG 59.552 47.826 0.00 0.00 0.00 4.18
3564 4087 1.268335 CGTTGACCACCGGAGTTTTTG 60.268 52.381 9.46 0.00 0.00 2.44
3649 4172 2.134789 AGAGCATGATCAACCCCAAC 57.865 50.000 14.38 0.00 0.00 3.77
3731 4254 4.207891 TCCTTATGGACAAGACAGCTTC 57.792 45.455 0.00 0.00 37.46 3.86
3947 4471 2.061740 AAAGGAGAGCGACGTTGTAC 57.938 50.000 4.37 0.00 0.00 2.90
4034 4561 6.430925 GCAATGGATTATTCAGGTACATGCTA 59.569 38.462 1.79 0.00 0.00 3.49
4079 4606 4.859304 AGTTCAAAAGCATGCATCAAGA 57.141 36.364 21.98 8.09 0.00 3.02
4108 4637 5.536161 AGTTTGGTCATGATATATGTTGCCC 59.464 40.000 0.00 0.00 0.00 5.36
4132 4661 4.123497 ACTCTGAAACTACATATGCGCA 57.877 40.909 14.96 14.96 0.00 6.09
4151 4680 8.567948 CACCAACAAATATACAGAAACTGAACT 58.432 33.333 5.76 0.00 35.18 3.01
4287 4816 3.565307 AGCACCCAAGATTTGACTGAAA 58.435 40.909 0.00 0.00 0.00 2.69
4374 4906 8.629986 CAAAATTCAACATGTCTACGCTAAAAG 58.370 33.333 0.00 0.00 0.00 2.27
4408 4941 4.689071 TCGTGCTTACAAGAAAAGTCAGA 58.311 39.130 0.00 0.00 30.94 3.27
4438 4971 3.749981 CCACAAGTTCGGCAGCTT 58.250 55.556 0.00 0.00 0.00 3.74
4513 5046 1.187567 AACCCATCTTTGCCTGCACC 61.188 55.000 0.00 0.00 0.00 5.01
4580 5113 5.291858 CGCATGACACTTACAGAATACACAT 59.708 40.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.