Multiple sequence alignment - TraesCS3B01G211700

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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 TraesCS3B01G211700 chr3B 100.000 3428 0 0 1 3428 250820389 250816962 0.000000e+00 6331.0
1 TraesCS3B01G211700 chr3D 96.751 2739 62 12 713 3428 172383511 172380777 0.000000e+00 4540.0
2 TraesCS3B01G211700 chr3A 95.374 2702 75 20 747 3428 210261284 210258613 0.000000e+00 4252.0
3 TraesCS3B01G211700 chr3A 82.157 510 63 19 182 674 100344743 100344245 2.460000e-111 412.0
4 TraesCS3B01G211700 chr3A 83.226 310 34 14 186 487 516837942 516837643 5.640000e-68 268.0
5 TraesCS3B01G211700 chr2B 83.206 524 68 17 203 714 617530402 617529887 2.410000e-126 462.0
6 TraesCS3B01G211700 chr2B 85.600 125 16 2 522 646 631502309 631502187 2.780000e-26 130.0
7 TraesCS3B01G211700 chr6B 82.289 463 51 15 186 643 171464373 171464809 4.180000e-99 372.0
8 TraesCS3B01G211700 chr5D 83.073 384 34 17 189 560 487416224 487415860 1.530000e-83 320.0
9 TraesCS3B01G211700 chr5D 82.445 319 27 16 183 487 9944413 9944716 5.680000e-63 252.0
10 TraesCS3B01G211700 chr6A 84.946 279 28 10 291 560 107513178 107513451 1.570000e-68 270.0
11 TraesCS3B01G211700 chr2D 84.775 289 19 11 186 463 229054029 229053755 2.030000e-67 267.0
12 TraesCS3B01G211700 chr1A 82.792 308 26 11 183 487 186751461 186751744 2.040000e-62 250.0
13 TraesCS3B01G211700 chr6D 83.871 93 10 4 1 89 371523195 371523286 2.190000e-12 84.2
14 TraesCS3B01G211700 chr2A 84.722 72 3 6 275 345 5649616 5649680 7.940000e-07 65.8
15 TraesCS3B01G211700 chr5B 94.872 39 2 0 671 709 503082590 503082628 1.030000e-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 TraesCS3B01G211700 chr3B 250816962 250820389 3427 True 6331 6331 100.000 1 3428 1 chr3B.!!$R1 3427
1 TraesCS3B01G211700 chr3D 172380777 172383511 2734 True 4540 4540 96.751 713 3428 1 chr3D.!!$R1 2715
2 TraesCS3B01G211700 chr3A 210258613 210261284 2671 True 4252 4252 95.374 747 3428 1 chr3A.!!$R2 2681
3 TraesCS3B01G211700 chr2B 617529887 617530402 515 True 462 462 83.206 203 714 1 chr2B.!!$R1 511

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
79 80 0.229753 GCGATGAGTAATTCCGTGCG 59.770 55.0 0.00 0.0 0.00 5.34 F
195 196 0.250727 GTGGGCTACAGCTGGTCAAA 60.251 55.0 19.93 0.0 41.70 2.69 F
201 202 0.250727 TACAGCTGGTCAAACAGGCC 60.251 55.0 19.93 0.0 44.53 5.19 F
1247 1270 0.336737 GAGGAGGTGGAAGAGGAGGA 59.663 60.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1247 1270 0.257616 CTCCTCGACCTCCTCTTCCT 59.742 60.000 0.00 0.0 0.00 3.36 R
1977 2015 0.325933 TCTGGCAGTGCAGCATAACT 59.674 50.000 18.61 0.0 35.83 2.24 R
2108 2146 1.176527 CCCATAACCAGCACCAACAG 58.823 55.000 0.00 0.0 0.00 3.16 R
2440 2478 1.201647 ACAGTTAGGACACATCGACCG 59.798 52.381 0.00 0.0 34.24 4.79 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
28 29 9.875675 GTAGAAACGAATGTATCTAGACGTATT 57.124 33.333 0.00 0.00 33.76 1.89
30 31 9.798994 AGAAACGAATGTATCTAGACGTATTTT 57.201 29.630 0.00 0.00 33.76 1.82
61 62 9.407380 TCTAGATCCATTTCTCTCTATCTATGC 57.593 37.037 0.00 0.00 0.00 3.14
62 63 7.099266 AGATCCATTTCTCTCTATCTATGCG 57.901 40.000 0.00 0.00 0.00 4.73
63 64 6.889177 AGATCCATTTCTCTCTATCTATGCGA 59.111 38.462 0.00 0.00 0.00 5.10
64 65 7.560991 AGATCCATTTCTCTCTATCTATGCGAT 59.439 37.037 0.00 0.00 36.11 4.58
65 66 6.861144 TCCATTTCTCTCTATCTATGCGATG 58.139 40.000 0.00 0.00 33.48 3.84
66 67 6.660949 TCCATTTCTCTCTATCTATGCGATGA 59.339 38.462 0.00 0.00 33.48 2.92
67 68 6.974048 CCATTTCTCTCTATCTATGCGATGAG 59.026 42.308 0.00 0.00 33.48 2.90
68 69 7.362834 CCATTTCTCTCTATCTATGCGATGAGT 60.363 40.741 0.00 0.00 33.15 3.41
69 70 8.672815 CATTTCTCTCTATCTATGCGATGAGTA 58.327 37.037 0.00 0.00 33.15 2.59
70 71 8.622948 TTTCTCTCTATCTATGCGATGAGTAA 57.377 34.615 0.00 0.00 33.15 2.24
71 72 8.800370 TTCTCTCTATCTATGCGATGAGTAAT 57.200 34.615 0.00 0.00 33.15 1.89
72 73 8.800370 TCTCTCTATCTATGCGATGAGTAATT 57.200 34.615 0.00 0.00 33.15 1.40
73 74 8.888716 TCTCTCTATCTATGCGATGAGTAATTC 58.111 37.037 0.00 0.00 33.15 2.17
74 75 7.990917 TCTCTATCTATGCGATGAGTAATTCC 58.009 38.462 0.00 0.00 33.15 3.01
75 76 6.786207 TCTATCTATGCGATGAGTAATTCCG 58.214 40.000 0.00 0.00 33.48 4.30
76 77 4.848562 TCTATGCGATGAGTAATTCCGT 57.151 40.909 0.00 0.00 0.00 4.69
77 78 4.546570 TCTATGCGATGAGTAATTCCGTG 58.453 43.478 0.00 0.00 0.00 4.94
78 79 1.286501 TGCGATGAGTAATTCCGTGC 58.713 50.000 0.00 0.00 0.00 5.34
79 80 0.229753 GCGATGAGTAATTCCGTGCG 59.770 55.000 0.00 0.00 0.00 5.34
80 81 1.835121 CGATGAGTAATTCCGTGCGA 58.165 50.000 0.00 0.00 0.00 5.10
81 82 2.190161 CGATGAGTAATTCCGTGCGAA 58.810 47.619 0.00 0.00 34.14 4.70
82 83 2.216488 CGATGAGTAATTCCGTGCGAAG 59.784 50.000 0.00 0.00 32.78 3.79
83 84 2.004583 TGAGTAATTCCGTGCGAAGG 57.995 50.000 0.00 0.00 32.78 3.46
84 85 1.287425 GAGTAATTCCGTGCGAAGGG 58.713 55.000 0.00 0.00 32.78 3.95
85 86 0.899720 AGTAATTCCGTGCGAAGGGA 59.100 50.000 0.00 0.00 32.78 4.20
86 87 1.134788 AGTAATTCCGTGCGAAGGGAG 60.135 52.381 4.72 0.00 32.78 4.30
87 88 0.899720 TAATTCCGTGCGAAGGGAGT 59.100 50.000 4.72 0.00 32.78 3.85
88 89 0.899720 AATTCCGTGCGAAGGGAGTA 59.100 50.000 4.72 0.00 32.78 2.59
89 90 0.460311 ATTCCGTGCGAAGGGAGTAG 59.540 55.000 4.72 0.00 32.78 2.57
90 91 0.896940 TTCCGTGCGAAGGGAGTAGT 60.897 55.000 4.72 0.00 33.01 2.73
91 92 0.896940 TCCGTGCGAAGGGAGTAGTT 60.897 55.000 0.00 0.00 0.00 2.24
92 93 0.736325 CCGTGCGAAGGGAGTAGTTG 60.736 60.000 0.00 0.00 0.00 3.16
93 94 1.352156 CGTGCGAAGGGAGTAGTTGC 61.352 60.000 0.00 0.00 0.00 4.17
94 95 0.320421 GTGCGAAGGGAGTAGTTGCA 60.320 55.000 0.00 0.00 0.00 4.08
95 96 0.394938 TGCGAAGGGAGTAGTTGCAA 59.605 50.000 0.00 0.00 0.00 4.08
96 97 1.202710 TGCGAAGGGAGTAGTTGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
97 98 1.877443 GCGAAGGGAGTAGTTGCAAAA 59.123 47.619 0.00 0.00 0.00 2.44
98 99 2.095718 GCGAAGGGAGTAGTTGCAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
99 100 3.399330 CGAAGGGAGTAGTTGCAAAAGA 58.601 45.455 0.00 0.00 0.00 2.52
100 101 3.813166 CGAAGGGAGTAGTTGCAAAAGAA 59.187 43.478 0.00 0.00 0.00 2.52
101 102 4.274950 CGAAGGGAGTAGTTGCAAAAGAAA 59.725 41.667 0.00 0.00 0.00 2.52
102 103 5.220970 CGAAGGGAGTAGTTGCAAAAGAAAA 60.221 40.000 0.00 0.00 0.00 2.29
103 104 6.538945 AAGGGAGTAGTTGCAAAAGAAAAA 57.461 33.333 0.00 0.00 0.00 1.94
104 105 5.902681 AGGGAGTAGTTGCAAAAGAAAAAC 58.097 37.500 0.00 0.00 0.00 2.43
105 106 5.420739 AGGGAGTAGTTGCAAAAGAAAAACA 59.579 36.000 0.00 0.00 0.00 2.83
106 107 5.518847 GGGAGTAGTTGCAAAAGAAAAACAC 59.481 40.000 0.00 0.00 0.00 3.32
107 108 5.518847 GGAGTAGTTGCAAAAGAAAAACACC 59.481 40.000 0.00 0.00 0.00 4.16
108 109 5.416083 AGTAGTTGCAAAAGAAAAACACCC 58.584 37.500 0.00 0.00 0.00 4.61
109 110 4.551702 AGTTGCAAAAGAAAAACACCCT 57.448 36.364 0.00 0.00 0.00 4.34
110 111 5.669164 AGTTGCAAAAGAAAAACACCCTA 57.331 34.783 0.00 0.00 0.00 3.53
111 112 6.043854 AGTTGCAAAAGAAAAACACCCTAA 57.956 33.333 0.00 0.00 0.00 2.69
112 113 6.649155 AGTTGCAAAAGAAAAACACCCTAAT 58.351 32.000 0.00 0.00 0.00 1.73
113 114 7.109501 AGTTGCAAAAGAAAAACACCCTAATT 58.890 30.769 0.00 0.00 0.00 1.40
114 115 6.917217 TGCAAAAGAAAAACACCCTAATTG 57.083 33.333 0.00 0.00 0.00 2.32
115 116 5.295540 TGCAAAAGAAAAACACCCTAATTGC 59.704 36.000 0.00 0.00 39.72 3.56
116 117 5.295540 GCAAAAGAAAAACACCCTAATTGCA 59.704 36.000 0.00 0.00 39.25 4.08
117 118 6.183360 GCAAAAGAAAAACACCCTAATTGCAA 60.183 34.615 0.00 0.00 39.25 4.08
118 119 7.468494 GCAAAAGAAAAACACCCTAATTGCAAT 60.468 33.333 5.99 5.99 39.25 3.56
119 120 9.050601 CAAAAGAAAAACACCCTAATTGCAATA 57.949 29.630 13.39 0.54 0.00 1.90
120 121 9.620259 AAAAGAAAAACACCCTAATTGCAATAA 57.380 25.926 13.39 0.00 0.00 1.40
121 122 9.620259 AAAGAAAAACACCCTAATTGCAATAAA 57.380 25.926 13.39 3.23 0.00 1.40
122 123 9.620259 AAGAAAAACACCCTAATTGCAATAAAA 57.380 25.926 13.39 0.56 0.00 1.52
123 124 9.791801 AGAAAAACACCCTAATTGCAATAAAAT 57.208 25.926 13.39 0.00 0.00 1.82
178 179 2.359975 GGAAGGGTCCTTGCCGTG 60.360 66.667 7.03 0.00 41.24 4.94
179 180 2.359975 GAAGGGTCCTTGCCGTGG 60.360 66.667 7.03 0.00 36.26 4.94
180 181 3.920093 GAAGGGTCCTTGCCGTGGG 62.920 68.421 7.03 0.00 36.26 4.61
191 192 3.706373 CCGTGGGCTACAGCTGGT 61.706 66.667 19.93 6.35 41.70 4.00
192 193 2.125512 CGTGGGCTACAGCTGGTC 60.126 66.667 19.93 1.79 41.70 4.02
193 194 2.942796 CGTGGGCTACAGCTGGTCA 61.943 63.158 19.93 5.69 41.70 4.02
194 195 1.374947 GTGGGCTACAGCTGGTCAA 59.625 57.895 19.93 0.00 41.70 3.18
195 196 0.250727 GTGGGCTACAGCTGGTCAAA 60.251 55.000 19.93 0.00 41.70 2.69
196 197 0.250727 TGGGCTACAGCTGGTCAAAC 60.251 55.000 19.93 4.18 41.70 2.93
197 198 0.250727 GGGCTACAGCTGGTCAAACA 60.251 55.000 19.93 0.00 41.70 2.83
198 199 1.160137 GGCTACAGCTGGTCAAACAG 58.840 55.000 19.93 4.33 41.70 3.16
199 200 1.160137 GCTACAGCTGGTCAAACAGG 58.840 55.000 19.93 0.00 38.90 4.00
200 201 1.160137 CTACAGCTGGTCAAACAGGC 58.840 55.000 19.93 0.00 38.90 4.85
201 202 0.250727 TACAGCTGGTCAAACAGGCC 60.251 55.000 19.93 0.00 44.53 5.19
206 207 2.594592 GGTCAAACAGGCCGTGCT 60.595 61.111 0.00 0.00 28.17 4.40
214 215 2.928396 AGGCCGTGCTAACTGGGT 60.928 61.111 0.00 0.00 0.00 4.51
359 370 1.010419 GCACGACACGACCCGTTTAT 61.010 55.000 0.00 0.00 38.32 1.40
449 460 4.335082 TTGTAGTGCATGCGTACATTTC 57.665 40.909 25.21 8.07 32.87 2.17
466 477 9.464714 CGTACATTTCTAGTGCTCTAATATGTT 57.535 33.333 15.96 6.88 0.00 2.71
528 544 5.888691 TTTTGCCTTTTTCCCTTTTTGAC 57.111 34.783 0.00 0.00 0.00 3.18
537 553 6.466885 TTTTCCCTTTTTGACGGTATTTCA 57.533 33.333 0.00 0.00 0.00 2.69
538 554 6.658188 TTTCCCTTTTTGACGGTATTTCAT 57.342 33.333 0.00 0.00 0.00 2.57
545 563 9.685828 CCTTTTTGACGGTATTTCATAGAAAAA 57.314 29.630 0.00 0.00 0.00 1.94
576 594 0.741574 CACATACCGGCGTGCCTAAA 60.742 55.000 9.55 0.00 0.00 1.85
584 602 2.686816 GCGTGCCTAAACGTGCCAT 61.687 57.895 0.00 0.00 45.32 4.40
606 624 2.598787 CCGGCCCACTTAACTCCCA 61.599 63.158 0.00 0.00 0.00 4.37
666 684 4.699522 GCCCGGCCCGGCTATTAG 62.700 72.222 25.94 2.47 46.86 1.73
674 692 1.440060 CCGGCTATTAGTCGTGCCA 59.560 57.895 15.87 0.00 42.67 4.92
675 693 0.597637 CCGGCTATTAGTCGTGCCAG 60.598 60.000 15.87 0.00 42.67 4.85
677 695 0.880718 GGCTATTAGTCGTGCCAGGC 60.881 60.000 3.66 3.66 44.34 4.85
679 697 0.753262 CTATTAGTCGTGCCAGGCCT 59.247 55.000 9.64 0.00 0.00 5.19
681 699 1.553690 ATTAGTCGTGCCAGGCCTGT 61.554 55.000 30.63 13.32 0.00 4.00
682 700 1.764571 TTAGTCGTGCCAGGCCTGTT 61.765 55.000 30.63 9.75 0.00 3.16
683 701 1.764571 TAGTCGTGCCAGGCCTGTTT 61.765 55.000 30.63 10.42 0.00 2.83
684 702 1.302192 GTCGTGCCAGGCCTGTTTA 60.302 57.895 30.63 13.94 0.00 2.01
687 705 1.656818 CGTGCCAGGCCTGTTTATGG 61.657 60.000 30.63 16.80 35.84 2.74
714 732 3.741476 CCGTTTGGCCAGCTCTGC 61.741 66.667 5.11 0.00 0.00 4.26
737 755 3.119849 CCTGGGCGTTCTTCTAACAATTG 60.120 47.826 3.24 3.24 0.00 2.32
744 762 4.693566 CGTTCTTCTAACAATTGTAGGCCA 59.306 41.667 12.39 0.00 0.00 5.36
752 770 2.375174 ACAATTGTAGGCCAAGGAGACA 59.625 45.455 9.97 0.00 36.25 3.41
770 792 1.355720 ACAACAGGGATTGCTTAGCCT 59.644 47.619 0.29 0.00 32.47 4.58
775 797 2.373169 CAGGGATTGCTTAGCCTATCCA 59.627 50.000 25.95 0.00 39.16 3.41
816 838 7.039722 AGGAAAGGAAAACACCCATATAAGA 57.960 36.000 0.00 0.00 0.00 2.10
818 840 8.122481 AGGAAAGGAAAACACCCATATAAGATT 58.878 33.333 0.00 0.00 0.00 2.40
876 898 2.033194 GTGCCGTGAACTAGCCACC 61.033 63.158 9.46 0.00 0.00 4.61
1247 1270 0.336737 GAGGAGGTGGAAGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
1284 1322 2.338785 GGAAGAACAGCAGCAGGCC 61.339 63.158 0.00 0.00 46.50 5.19
1890 1928 2.342279 CTCGACAAGGCAACCGGA 59.658 61.111 9.46 0.00 37.17 5.14
1977 2015 1.522668 CGCACAAGTCATTTGAGGGA 58.477 50.000 0.00 0.00 40.91 4.20
2086 2124 2.478890 GCTGCTGGCTATGGTGCTG 61.479 63.158 0.00 0.00 38.06 4.41
2108 2146 3.915575 CCATTCTCTGCCTGGCAC 58.084 61.111 19.30 0.00 33.79 5.01
2440 2478 5.751586 TGGGTCATTAGGTAAGATTTGGTC 58.248 41.667 0.00 0.00 0.00 4.02
2588 2626 8.630054 TTTACACTGGTATTAGTCTTGCATTT 57.370 30.769 0.00 0.00 0.00 2.32
2836 2875 7.609056 TGTAGGTCATCTGTTAAGTAAGGAAC 58.391 38.462 0.00 0.00 0.00 3.62
2993 3033 8.785184 AATAGTAATAGGTTGAGGCTAGAAGT 57.215 34.615 0.00 0.00 0.00 3.01
3039 3080 8.023128 GCTCTGTTTTAGTTTAATGATGCTTGA 58.977 33.333 0.00 0.00 0.00 3.02
3117 3158 0.753111 GGCCTTGCAGTATCCTTGGG 60.753 60.000 0.00 0.00 0.00 4.12
3175 3216 3.891422 TTTGGCAGGCCTTATCATTTG 57.109 42.857 0.00 0.00 36.94 2.32
3251 3292 3.221771 TGCAGGTTTCAGTGCTTACATT 58.778 40.909 0.00 0.00 40.54 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.407380 GCATAGATAGAGAGAAATGGATCTAGA 57.593 37.037 0.00 0.00 31.37 2.43
36 37 8.344831 CGCATAGATAGAGAGAAATGGATCTAG 58.655 40.741 0.00 0.00 31.37 2.43
37 38 8.049721 TCGCATAGATAGAGAGAAATGGATCTA 58.950 37.037 0.00 0.00 32.15 1.98
38 39 6.889177 TCGCATAGATAGAGAGAAATGGATCT 59.111 38.462 0.00 0.00 0.00 2.75
39 40 7.094508 TCGCATAGATAGAGAGAAATGGATC 57.905 40.000 0.00 0.00 0.00 3.36
40 41 7.341512 TCATCGCATAGATAGAGAGAAATGGAT 59.658 37.037 0.00 0.00 37.52 3.41
41 42 6.660949 TCATCGCATAGATAGAGAGAAATGGA 59.339 38.462 0.00 0.00 37.52 3.41
42 43 6.861144 TCATCGCATAGATAGAGAGAAATGG 58.139 40.000 0.00 0.00 37.52 3.16
43 44 7.537715 ACTCATCGCATAGATAGAGAGAAATG 58.462 38.462 0.00 0.00 37.52 2.32
44 45 7.701539 ACTCATCGCATAGATAGAGAGAAAT 57.298 36.000 0.00 0.00 37.52 2.17
45 46 8.622948 TTACTCATCGCATAGATAGAGAGAAA 57.377 34.615 0.00 0.00 37.52 2.52
46 47 8.800370 ATTACTCATCGCATAGATAGAGAGAA 57.200 34.615 0.00 0.00 37.52 2.87
47 48 8.800370 AATTACTCATCGCATAGATAGAGAGA 57.200 34.615 0.00 0.00 37.52 3.10
48 49 8.128582 GGAATTACTCATCGCATAGATAGAGAG 58.871 40.741 0.00 0.00 37.52 3.20
49 50 7.201652 CGGAATTACTCATCGCATAGATAGAGA 60.202 40.741 0.00 0.00 37.52 3.10
50 51 6.909895 CGGAATTACTCATCGCATAGATAGAG 59.090 42.308 0.00 0.00 37.52 2.43
51 52 6.374613 ACGGAATTACTCATCGCATAGATAGA 59.625 38.462 0.00 0.00 37.52 1.98
52 53 6.470556 CACGGAATTACTCATCGCATAGATAG 59.529 42.308 0.00 0.00 37.52 2.08
53 54 6.322491 CACGGAATTACTCATCGCATAGATA 58.678 40.000 0.00 0.00 37.52 1.98
54 55 5.164233 CACGGAATTACTCATCGCATAGAT 58.836 41.667 0.00 0.00 41.01 1.98
55 56 4.546570 CACGGAATTACTCATCGCATAGA 58.453 43.478 0.00 0.00 0.00 1.98
56 57 3.121944 GCACGGAATTACTCATCGCATAG 59.878 47.826 0.00 0.00 0.00 2.23
57 58 3.057019 GCACGGAATTACTCATCGCATA 58.943 45.455 0.00 0.00 0.00 3.14
58 59 1.867233 GCACGGAATTACTCATCGCAT 59.133 47.619 0.00 0.00 0.00 4.73
59 60 1.286501 GCACGGAATTACTCATCGCA 58.713 50.000 0.00 0.00 0.00 5.10
60 61 0.229753 CGCACGGAATTACTCATCGC 59.770 55.000 0.00 0.00 0.00 4.58
61 62 1.835121 TCGCACGGAATTACTCATCG 58.165 50.000 0.00 0.00 0.00 3.84
62 63 2.540101 CCTTCGCACGGAATTACTCATC 59.460 50.000 0.00 0.00 33.26 2.92
63 64 2.550978 CCTTCGCACGGAATTACTCAT 58.449 47.619 0.00 0.00 33.26 2.90
64 65 1.404986 CCCTTCGCACGGAATTACTCA 60.405 52.381 0.00 0.00 33.26 3.41
65 66 1.134907 TCCCTTCGCACGGAATTACTC 60.135 52.381 0.00 0.00 33.26 2.59
66 67 0.899720 TCCCTTCGCACGGAATTACT 59.100 50.000 0.00 0.00 33.26 2.24
67 68 1.287425 CTCCCTTCGCACGGAATTAC 58.713 55.000 0.00 0.00 33.26 1.89
68 69 0.899720 ACTCCCTTCGCACGGAATTA 59.100 50.000 0.00 0.00 33.26 1.40
69 70 0.899720 TACTCCCTTCGCACGGAATT 59.100 50.000 0.00 0.00 33.26 2.17
70 71 0.460311 CTACTCCCTTCGCACGGAAT 59.540 55.000 0.00 0.00 33.26 3.01
71 72 0.896940 ACTACTCCCTTCGCACGGAA 60.897 55.000 0.00 0.00 0.00 4.30
72 73 0.896940 AACTACTCCCTTCGCACGGA 60.897 55.000 0.00 0.00 0.00 4.69
73 74 0.736325 CAACTACTCCCTTCGCACGG 60.736 60.000 0.00 0.00 0.00 4.94
74 75 1.352156 GCAACTACTCCCTTCGCACG 61.352 60.000 0.00 0.00 0.00 5.34
75 76 0.320421 TGCAACTACTCCCTTCGCAC 60.320 55.000 0.00 0.00 0.00 5.34
76 77 0.394938 TTGCAACTACTCCCTTCGCA 59.605 50.000 0.00 0.00 0.00 5.10
77 78 1.519408 TTTGCAACTACTCCCTTCGC 58.481 50.000 0.00 0.00 0.00 4.70
78 79 3.399330 TCTTTTGCAACTACTCCCTTCG 58.601 45.455 0.00 0.00 0.00 3.79
79 80 5.767816 TTTCTTTTGCAACTACTCCCTTC 57.232 39.130 0.00 0.00 0.00 3.46
80 81 6.071051 TGTTTTTCTTTTGCAACTACTCCCTT 60.071 34.615 0.00 0.00 0.00 3.95
81 82 5.420739 TGTTTTTCTTTTGCAACTACTCCCT 59.579 36.000 0.00 0.00 0.00 4.20
82 83 5.518847 GTGTTTTTCTTTTGCAACTACTCCC 59.481 40.000 0.00 0.00 0.00 4.30
83 84 5.518847 GGTGTTTTTCTTTTGCAACTACTCC 59.481 40.000 0.00 0.00 0.00 3.85
84 85 5.518847 GGGTGTTTTTCTTTTGCAACTACTC 59.481 40.000 0.00 0.00 0.00 2.59
85 86 5.186992 AGGGTGTTTTTCTTTTGCAACTACT 59.813 36.000 0.00 0.00 0.00 2.57
86 87 5.416083 AGGGTGTTTTTCTTTTGCAACTAC 58.584 37.500 0.00 0.00 0.00 2.73
87 88 5.669164 AGGGTGTTTTTCTTTTGCAACTA 57.331 34.783 0.00 0.00 0.00 2.24
88 89 4.551702 AGGGTGTTTTTCTTTTGCAACT 57.448 36.364 0.00 0.00 0.00 3.16
89 90 6.918892 ATTAGGGTGTTTTTCTTTTGCAAC 57.081 33.333 0.00 0.00 0.00 4.17
90 91 6.183360 GCAATTAGGGTGTTTTTCTTTTGCAA 60.183 34.615 0.00 0.00 36.61 4.08
91 92 5.295540 GCAATTAGGGTGTTTTTCTTTTGCA 59.704 36.000 0.00 0.00 36.61 4.08
92 93 5.295540 TGCAATTAGGGTGTTTTTCTTTTGC 59.704 36.000 0.00 0.00 37.00 3.68
93 94 6.917217 TGCAATTAGGGTGTTTTTCTTTTG 57.083 33.333 0.00 0.00 0.00 2.44
94 95 9.620259 TTATTGCAATTAGGGTGTTTTTCTTTT 57.380 25.926 18.75 0.00 0.00 2.27
95 96 9.620259 TTTATTGCAATTAGGGTGTTTTTCTTT 57.380 25.926 18.75 0.00 0.00 2.52
96 97 9.620259 TTTTATTGCAATTAGGGTGTTTTTCTT 57.380 25.926 18.75 0.00 0.00 2.52
97 98 9.791801 ATTTTATTGCAATTAGGGTGTTTTTCT 57.208 25.926 18.75 0.00 0.00 2.52
161 162 2.359975 CACGGCAAGGACCCTTCC 60.360 66.667 0.00 3.31 43.22 3.46
162 163 2.359975 CCACGGCAAGGACCCTTC 60.360 66.667 0.00 0.00 33.42 3.46
163 164 3.966543 CCCACGGCAAGGACCCTT 61.967 66.667 0.00 0.00 36.60 3.95
174 175 3.665675 GACCAGCTGTAGCCCACGG 62.666 68.421 13.81 0.00 43.38 4.94
175 176 2.125512 GACCAGCTGTAGCCCACG 60.126 66.667 13.81 0.00 43.38 4.94
176 177 0.250727 TTTGACCAGCTGTAGCCCAC 60.251 55.000 13.81 0.00 43.38 4.61
177 178 0.250727 GTTTGACCAGCTGTAGCCCA 60.251 55.000 13.81 0.00 43.38 5.36
178 179 0.250727 TGTTTGACCAGCTGTAGCCC 60.251 55.000 13.81 0.00 43.38 5.19
179 180 1.160137 CTGTTTGACCAGCTGTAGCC 58.840 55.000 13.81 0.00 43.38 3.93
180 181 1.160137 CCTGTTTGACCAGCTGTAGC 58.840 55.000 13.81 1.74 42.49 3.58
181 182 1.160137 GCCTGTTTGACCAGCTGTAG 58.840 55.000 13.81 0.00 0.00 2.74
182 183 0.250727 GGCCTGTTTGACCAGCTGTA 60.251 55.000 13.81 0.00 0.00 2.74
183 184 1.529244 GGCCTGTTTGACCAGCTGT 60.529 57.895 13.81 0.11 0.00 4.40
184 185 2.620112 CGGCCTGTTTGACCAGCTG 61.620 63.158 6.78 6.78 0.00 4.24
185 186 2.281761 CGGCCTGTTTGACCAGCT 60.282 61.111 0.00 0.00 0.00 4.24
186 187 2.594592 ACGGCCTGTTTGACCAGC 60.595 61.111 0.00 0.00 0.00 4.85
187 188 2.908073 GCACGGCCTGTTTGACCAG 61.908 63.158 0.00 0.00 0.00 4.00
188 189 2.046009 TAGCACGGCCTGTTTGACCA 62.046 55.000 0.00 0.00 0.00 4.02
189 190 0.887387 TTAGCACGGCCTGTTTGACC 60.887 55.000 0.00 0.00 0.00 4.02
190 191 0.237498 GTTAGCACGGCCTGTTTGAC 59.763 55.000 0.00 0.00 0.00 3.18
191 192 0.107831 AGTTAGCACGGCCTGTTTGA 59.892 50.000 0.00 0.00 0.00 2.69
192 193 0.238289 CAGTTAGCACGGCCTGTTTG 59.762 55.000 0.00 0.00 0.00 2.93
193 194 0.889186 CCAGTTAGCACGGCCTGTTT 60.889 55.000 0.00 0.00 0.00 2.83
194 195 1.302511 CCAGTTAGCACGGCCTGTT 60.303 57.895 0.00 0.00 0.00 3.16
195 196 2.347490 CCAGTTAGCACGGCCTGT 59.653 61.111 0.00 0.00 0.00 4.00
196 197 2.436646 CCCAGTTAGCACGGCCTG 60.437 66.667 0.00 0.00 0.00 4.85
197 198 2.928396 ACCCAGTTAGCACGGCCT 60.928 61.111 0.00 0.00 0.00 5.19
198 199 2.436115 GACCCAGTTAGCACGGCC 60.436 66.667 0.00 0.00 0.00 6.13
199 200 2.813908 CGACCCAGTTAGCACGGC 60.814 66.667 0.00 0.00 0.00 5.68
200 201 2.125673 CCGACCCAGTTAGCACGG 60.126 66.667 0.00 0.00 34.77 4.94
201 202 2.813908 GCCGACCCAGTTAGCACG 60.814 66.667 0.00 0.00 0.00 5.34
202 203 2.436115 GGCCGACCCAGTTAGCAC 60.436 66.667 0.00 0.00 0.00 4.40
220 221 3.179265 CGTTCCTGCGTGCTACCG 61.179 66.667 0.00 0.00 0.00 4.02
254 255 3.440415 GTGCCTGGCCCGTTTAGC 61.440 66.667 17.53 0.00 0.00 3.09
283 294 4.097863 GTGCCGTGCCGTTTAGCC 62.098 66.667 0.00 0.00 0.00 3.93
284 295 4.439472 CGTGCCGTGCCGTTTAGC 62.439 66.667 0.00 0.00 0.00 3.09
285 296 2.726691 CTCGTGCCGTGCCGTTTAG 61.727 63.158 6.64 0.00 0.00 1.85
286 297 2.735478 CTCGTGCCGTGCCGTTTA 60.735 61.111 6.64 0.00 0.00 2.01
297 308 3.434319 CCATGGTGTGCCTCGTGC 61.434 66.667 2.57 0.00 41.77 5.34
304 315 4.365111 TCCAGGGCCATGGTGTGC 62.365 66.667 34.18 0.00 41.43 4.57
340 351 1.010419 ATAAACGGGTCGTGTCGTGC 61.010 55.000 0.00 0.00 39.99 5.34
420 431 7.975750 TGTACGCATGCACTACAAAATTATTA 58.024 30.769 19.57 0.00 0.00 0.98
511 525 3.812156 ACCGTCAAAAAGGGAAAAAGG 57.188 42.857 0.00 0.00 36.70 3.11
516 530 7.169591 TCTATGAAATACCGTCAAAAAGGGAA 58.830 34.615 0.00 0.00 36.70 3.97
517 531 6.713276 TCTATGAAATACCGTCAAAAAGGGA 58.287 36.000 0.00 0.00 36.70 4.20
545 563 2.745281 CCGGTATGTGTCGGTTTGATTT 59.255 45.455 0.00 0.00 41.23 2.17
560 578 1.519898 CGTTTAGGCACGCCGGTAT 60.520 57.895 1.90 0.00 41.95 2.73
561 579 2.125991 CGTTTAGGCACGCCGGTA 60.126 61.111 1.90 0.00 41.95 4.02
562 580 4.303993 ACGTTTAGGCACGCCGGT 62.304 61.111 1.90 0.00 44.37 5.28
564 582 4.439472 GCACGTTTAGGCACGCCG 62.439 66.667 1.61 0.00 44.37 6.46
588 606 1.921869 ATGGGAGTTAAGTGGGCCGG 61.922 60.000 0.00 0.00 0.00 6.13
652 670 2.049433 CGACTAATAGCCGGGCCG 60.049 66.667 21.46 21.46 0.00 6.13
654 672 1.954651 GCACGACTAATAGCCGGGC 60.955 63.158 12.11 12.11 44.37 6.13
659 677 0.880718 GGCCTGGCACGACTAATAGC 60.881 60.000 22.05 0.00 0.00 2.97
666 684 0.676782 ATAAACAGGCCTGGCACGAC 60.677 55.000 35.42 2.38 34.19 4.34
677 695 3.209097 CGGCCCGCCATAAACAGG 61.209 66.667 6.52 0.00 35.37 4.00
714 732 0.323629 TGTTAGAAGAACGCCCAGGG 59.676 55.000 0.00 0.00 0.00 4.45
715 733 2.178912 TTGTTAGAAGAACGCCCAGG 57.821 50.000 0.00 0.00 0.00 4.45
716 734 3.502211 ACAATTGTTAGAAGAACGCCCAG 59.498 43.478 4.92 0.00 0.00 4.45
717 735 3.482436 ACAATTGTTAGAAGAACGCCCA 58.518 40.909 4.92 0.00 0.00 5.36
720 738 4.436986 GGCCTACAATTGTTAGAAGAACGC 60.437 45.833 17.78 6.81 0.00 4.84
737 755 1.339151 CCTGTTGTCTCCTTGGCCTAC 60.339 57.143 3.32 0.00 0.00 3.18
744 762 1.707427 AGCAATCCCTGTTGTCTCCTT 59.293 47.619 0.00 0.00 0.00 3.36
752 770 3.181439 GGATAGGCTAAGCAATCCCTGTT 60.181 47.826 0.00 0.00 36.95 3.16
770 792 5.408880 TTTATTATGGGCGACGATGGATA 57.591 39.130 0.00 0.00 0.00 2.59
775 797 4.345859 TTCCTTTATTATGGGCGACGAT 57.654 40.909 0.00 0.00 0.00 3.73
834 856 7.306205 CCGTTATATCGGTGTTTTCCTTTTA 57.694 36.000 13.14 0.00 44.77 1.52
835 857 6.185852 CCGTTATATCGGTGTTTTCCTTTT 57.814 37.500 13.14 0.00 44.77 2.27
836 858 5.806366 CCGTTATATCGGTGTTTTCCTTT 57.194 39.130 13.14 0.00 44.77 3.11
1247 1270 0.257616 CTCCTCGACCTCCTCTTCCT 59.742 60.000 0.00 0.00 0.00 3.36
1890 1928 0.758734 GAGCAAAACCCTTGGGCTTT 59.241 50.000 5.46 3.29 34.44 3.51
1977 2015 0.325933 TCTGGCAGTGCAGCATAACT 59.674 50.000 18.61 0.00 35.83 2.24
2108 2146 1.176527 CCCATAACCAGCACCAACAG 58.823 55.000 0.00 0.00 0.00 3.16
2440 2478 1.201647 ACAGTTAGGACACATCGACCG 59.798 52.381 0.00 0.00 34.24 4.79
2836 2875 2.161609 GCAATTTGTCGGGAAGTACTGG 59.838 50.000 0.00 0.00 0.00 4.00
2993 3033 5.132648 AGAGCCCATATATTCAACACCTTCA 59.867 40.000 0.00 0.00 0.00 3.02
3039 3080 9.651913 ATCGAATAAGGCAAACAAAACATAAAT 57.348 25.926 0.00 0.00 0.00 1.40
3175 3216 6.197096 GTGAAACAATGTTTGTGAGATGACAC 59.803 38.462 16.78 10.32 44.59 3.67
3220 3261 4.003648 ACTGAAACCTGCATACAAGCTAC 58.996 43.478 0.00 0.00 34.99 3.58
3279 3321 2.170166 CTCATAGCTTGGGGTTTGCAA 58.830 47.619 0.00 0.00 0.00 4.08
3292 3334 9.552114 CTGCTAAATAAATGCATAACTCATAGC 57.448 33.333 16.89 16.89 36.07 2.97


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

AutoCloner maintained by Alex Coulton.