Multiple sequence alignment - TraesCS3D01G306400

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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 TraesCS3D01G306400 chr3D 100.000 3253 0 0 1 3253 420356033 420359285 0.000000e+00 6008
1 TraesCS3D01G306400 chr3D 94.793 3073 128 14 190 3253 416549736 416552785 0.000000e+00 4759
2 TraesCS3D01G306400 chr4D 93.044 3134 145 23 190 3253 222625884 222622754 0.000000e+00 4512
3 TraesCS3D01G306400 chr4D 94.371 2789 133 13 457 3244 236674533 236671768 0.000000e+00 4259
4 TraesCS3D01G306400 chr4D 94.022 368 14 3 2885 3244 125838463 125838096 4.740000e-153 551
5 TraesCS3D01G306400 chr4D 94.493 345 11 2 190 530 225335144 225334804 2.880000e-145 525
6 TraesCS3D01G306400 chr4D 93.773 273 9 2 190 458 196909070 196909338 1.410000e-108 403
7 TraesCS3D01G306400 chr4D 93.548 217 11 3 2 215 372872100 372871884 1.460000e-83 320
8 TraesCS3D01G306400 chr5B 94.279 2954 147 10 236 3172 291683421 291680473 0.000000e+00 4499
9 TraesCS3D01G306400 chr5B 93.959 2963 149 10 236 3172 345113812 345116770 0.000000e+00 4453
10 TraesCS3D01G306400 chr5B 96.552 203 5 2 1 201 125416810 125416608 5.200000e-88 335
11 TraesCS3D01G306400 chr6B 93.860 2964 152 10 236 3172 70649107 70652067 0.000000e+00 4438
12 TraesCS3D01G306400 chr6B 94.047 2923 138 8 283 3172 159278908 159275989 0.000000e+00 4401
13 TraesCS3D01G306400 chr6B 92.142 2698 158 28 190 2850 643318839 643321519 0.000000e+00 3759
14 TraesCS3D01G306400 chr7B 93.309 2989 145 10 236 3172 669513661 669516646 0.000000e+00 4361
15 TraesCS3D01G306400 chr6D 94.312 2690 121 21 559 3244 297173270 297170609 0.000000e+00 4091
16 TraesCS3D01G306400 chr5D 92.743 2825 142 23 458 3244 384514028 384511229 0.000000e+00 4023
17 TraesCS3D01G306400 chr7A 93.683 2612 157 6 245 2850 493522076 493524685 0.000000e+00 3903
18 TraesCS3D01G306400 chr7A 93.578 2616 157 7 245 2853 639855159 639852548 0.000000e+00 3890
19 TraesCS3D01G306400 chr1D 94.750 1619 73 3 1646 3253 417112266 417113883 0.000000e+00 2508
20 TraesCS3D01G306400 chr1D 93.750 368 15 2 2885 3244 463793121 463792754 2.210000e-151 545
21 TraesCS3D01G306400 chr7D 94.293 368 13 3 2885 3244 17927118 17926751 1.020000e-154 556
22 TraesCS3D01G306400 chr7D 97.949 195 2 2 2 194 187739643 187739837 1.450000e-88 337
23 TraesCS3D01G306400 chr7D 95.652 207 6 3 2 206 292884139 292884344 2.420000e-86 329
24 TraesCS3D01G306400 chr4B 98.438 192 2 1 2 193 339923803 339923993 1.450000e-88 337
25 TraesCS3D01G306400 chr2D 95.755 212 4 5 2 211 112212953 112212745 1.450000e-88 337
26 TraesCS3D01G306400 chr2D 96.040 202 7 1 1 201 416334084 416334285 8.700000e-86 327
27 TraesCS3D01G306400 chr1B 93.519 216 10 3 1 216 242887201 242886990 5.240000e-83 318
28 TraesCS3D01G306400 chr5A 92.035 226 12 5 1 224 86797919 86797698 2.440000e-81 313


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 TraesCS3D01G306400 chr3D 420356033 420359285 3252 False 6008 6008 100.000 1 3253 1 chr3D.!!$F2 3252
1 TraesCS3D01G306400 chr3D 416549736 416552785 3049 False 4759 4759 94.793 190 3253 1 chr3D.!!$F1 3063
2 TraesCS3D01G306400 chr4D 222622754 222625884 3130 True 4512 4512 93.044 190 3253 1 chr4D.!!$R2 3063
3 TraesCS3D01G306400 chr4D 236671768 236674533 2765 True 4259 4259 94.371 457 3244 1 chr4D.!!$R4 2787
4 TraesCS3D01G306400 chr5B 291680473 291683421 2948 True 4499 4499 94.279 236 3172 1 chr5B.!!$R2 2936
5 TraesCS3D01G306400 chr5B 345113812 345116770 2958 False 4453 4453 93.959 236 3172 1 chr5B.!!$F1 2936
6 TraesCS3D01G306400 chr6B 70649107 70652067 2960 False 4438 4438 93.860 236 3172 1 chr6B.!!$F1 2936
7 TraesCS3D01G306400 chr6B 159275989 159278908 2919 True 4401 4401 94.047 283 3172 1 chr6B.!!$R1 2889
8 TraesCS3D01G306400 chr6B 643318839 643321519 2680 False 3759 3759 92.142 190 2850 1 chr6B.!!$F2 2660
9 TraesCS3D01G306400 chr7B 669513661 669516646 2985 False 4361 4361 93.309 236 3172 1 chr7B.!!$F1 2936
10 TraesCS3D01G306400 chr6D 297170609 297173270 2661 True 4091 4091 94.312 559 3244 1 chr6D.!!$R1 2685
11 TraesCS3D01G306400 chr5D 384511229 384514028 2799 True 4023 4023 92.743 458 3244 1 chr5D.!!$R1 2786
12 TraesCS3D01G306400 chr7A 493522076 493524685 2609 False 3903 3903 93.683 245 2850 1 chr7A.!!$F1 2605
13 TraesCS3D01G306400 chr7A 639852548 639855159 2611 True 3890 3890 93.578 245 2853 1 chr7A.!!$R1 2608
14 TraesCS3D01G306400 chr1D 417112266 417113883 1617 False 2508 2508 94.750 1646 3253 1 chr1D.!!$F1 1607

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
906 995 0.971386 AGAAATGTTTGGCTGGCTGG 59.029 50.0 2.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2401 1.466167 CTGATGGCGTCTGTTCTTTGG 59.534 52.381 8.4 0.0 0.0 3.28 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
24 25 6.661777 TGATTTATCATCATGGAAGTGGACA 58.338 36.000 0.00 0.00 0.00 4.02
25 26 6.543465 TGATTTATCATCATGGAAGTGGACAC 59.457 38.462 0.00 0.00 0.00 3.67
26 27 5.698741 TTATCATCATGGAAGTGGACACT 57.301 39.130 0.00 0.00 44.94 3.55
35 36 3.914984 AGTGGACACTTCCGTGATG 57.085 52.632 0.00 0.00 46.37 3.07
36 37 1.338107 AGTGGACACTTCCGTGATGA 58.662 50.000 0.00 0.00 46.37 2.92
37 38 1.902508 AGTGGACACTTCCGTGATGAT 59.097 47.619 0.00 0.00 46.37 2.45
38 39 3.096852 AGTGGACACTTCCGTGATGATA 58.903 45.455 0.00 0.00 46.37 2.15
39 40 3.513912 AGTGGACACTTCCGTGATGATAA 59.486 43.478 0.00 0.00 46.37 1.75
40 41 4.162320 AGTGGACACTTCCGTGATGATAAT 59.838 41.667 0.00 0.00 46.37 1.28
41 42 4.876107 GTGGACACTTCCGTGATGATAATT 59.124 41.667 0.00 0.00 46.37 1.40
42 43 5.354234 GTGGACACTTCCGTGATGATAATTT 59.646 40.000 0.00 0.00 46.37 1.82
43 44 5.943416 TGGACACTTCCGTGATGATAATTTT 59.057 36.000 0.00 0.00 46.37 1.82
44 45 6.128035 TGGACACTTCCGTGATGATAATTTTG 60.128 38.462 0.00 0.00 46.37 2.44
45 46 6.194796 ACACTTCCGTGATGATAATTTTGG 57.805 37.500 0.00 0.00 43.97 3.28
46 47 5.710099 ACACTTCCGTGATGATAATTTTGGT 59.290 36.000 0.00 0.00 43.97 3.67
47 48 6.882140 ACACTTCCGTGATGATAATTTTGGTA 59.118 34.615 0.00 0.00 43.97 3.25
48 49 7.392113 ACACTTCCGTGATGATAATTTTGGTAA 59.608 33.333 0.00 0.00 43.97 2.85
49 50 8.405531 CACTTCCGTGATGATAATTTTGGTAAT 58.594 33.333 0.00 0.00 43.97 1.89
50 51 8.405531 ACTTCCGTGATGATAATTTTGGTAATG 58.594 33.333 0.00 0.00 0.00 1.90
51 52 7.873719 TCCGTGATGATAATTTTGGTAATGT 57.126 32.000 0.00 0.00 0.00 2.71
52 53 7.925993 TCCGTGATGATAATTTTGGTAATGTC 58.074 34.615 0.00 0.00 0.00 3.06
53 54 7.554476 TCCGTGATGATAATTTTGGTAATGTCA 59.446 33.333 0.00 0.00 0.00 3.58
54 55 8.352201 CCGTGATGATAATTTTGGTAATGTCAT 58.648 33.333 0.00 0.00 0.00 3.06
55 56 9.172820 CGTGATGATAATTTTGGTAATGTCATG 57.827 33.333 0.00 0.00 0.00 3.07
56 57 9.467258 GTGATGATAATTTTGGTAATGTCATGG 57.533 33.333 0.00 0.00 0.00 3.66
57 58 9.418839 TGATGATAATTTTGGTAATGTCATGGA 57.581 29.630 0.00 0.00 0.00 3.41
73 74 2.433868 TGGAACACTTCTACGACAGC 57.566 50.000 0.00 0.00 0.00 4.40
74 75 1.684450 TGGAACACTTCTACGACAGCA 59.316 47.619 0.00 0.00 0.00 4.41
75 76 2.059541 GGAACACTTCTACGACAGCAC 58.940 52.381 0.00 0.00 0.00 4.40
76 77 2.545113 GGAACACTTCTACGACAGCACA 60.545 50.000 0.00 0.00 0.00 4.57
77 78 2.423926 ACACTTCTACGACAGCACAG 57.576 50.000 0.00 0.00 0.00 3.66
78 79 1.000163 ACACTTCTACGACAGCACAGG 60.000 52.381 0.00 0.00 0.00 4.00
79 80 1.000163 CACTTCTACGACAGCACAGGT 60.000 52.381 0.00 0.00 0.00 4.00
80 81 2.228103 CACTTCTACGACAGCACAGGTA 59.772 50.000 0.00 0.00 0.00 3.08
81 82 3.090037 ACTTCTACGACAGCACAGGTAT 58.910 45.455 0.00 0.00 0.00 2.73
82 83 3.119459 ACTTCTACGACAGCACAGGTATG 60.119 47.826 0.00 0.00 0.00 2.39
83 84 2.718563 TCTACGACAGCACAGGTATGA 58.281 47.619 0.00 0.00 0.00 2.15
84 85 2.422479 TCTACGACAGCACAGGTATGAC 59.578 50.000 0.00 0.00 0.00 3.06
85 86 1.257743 ACGACAGCACAGGTATGACT 58.742 50.000 0.00 0.00 0.00 3.41
86 87 2.443416 ACGACAGCACAGGTATGACTA 58.557 47.619 0.00 0.00 0.00 2.59
87 88 3.024547 ACGACAGCACAGGTATGACTAT 58.975 45.455 0.00 0.00 0.00 2.12
88 89 3.066900 ACGACAGCACAGGTATGACTATC 59.933 47.826 0.00 0.00 0.00 2.08
89 90 3.316588 CGACAGCACAGGTATGACTATCT 59.683 47.826 0.00 0.00 0.00 1.98
90 91 4.202060 CGACAGCACAGGTATGACTATCTT 60.202 45.833 0.00 0.00 0.00 2.40
91 92 5.016051 ACAGCACAGGTATGACTATCTTG 57.984 43.478 0.00 0.00 0.00 3.02
92 93 4.711846 ACAGCACAGGTATGACTATCTTGA 59.288 41.667 0.00 0.00 0.00 3.02
93 94 5.365025 ACAGCACAGGTATGACTATCTTGAT 59.635 40.000 0.00 0.00 0.00 2.57
94 95 6.126940 ACAGCACAGGTATGACTATCTTGATT 60.127 38.462 0.00 0.00 0.00 2.57
95 96 6.423302 CAGCACAGGTATGACTATCTTGATTC 59.577 42.308 0.00 0.00 0.00 2.52
96 97 6.326064 AGCACAGGTATGACTATCTTGATTCT 59.674 38.462 0.00 0.00 0.00 2.40
97 98 6.989169 GCACAGGTATGACTATCTTGATTCTT 59.011 38.462 0.00 0.00 0.00 2.52
98 99 7.497249 GCACAGGTATGACTATCTTGATTCTTT 59.503 37.037 0.00 0.00 0.00 2.52
99 100 9.039870 CACAGGTATGACTATCTTGATTCTTTC 57.960 37.037 0.00 0.00 0.00 2.62
100 101 8.762645 ACAGGTATGACTATCTTGATTCTTTCA 58.237 33.333 0.00 0.00 0.00 2.69
101 102 9.775854 CAGGTATGACTATCTTGATTCTTTCAT 57.224 33.333 0.00 0.00 33.34 2.57
113 114 9.992910 TCTTGATTCTTTCATAAAATCGTCATG 57.007 29.630 0.00 0.00 33.34 3.07
114 115 9.229784 CTTGATTCTTTCATAAAATCGTCATGG 57.770 33.333 0.00 0.00 33.34 3.66
115 116 8.504812 TGATTCTTTCATAAAATCGTCATGGA 57.495 30.769 0.00 0.00 33.13 3.41
116 117 9.123902 TGATTCTTTCATAAAATCGTCATGGAT 57.876 29.630 0.00 0.00 33.13 3.41
117 118 9.390795 GATTCTTTCATAAAATCGTCATGGATG 57.609 33.333 0.00 0.00 0.00 3.51
118 119 7.864108 TCTTTCATAAAATCGTCATGGATGT 57.136 32.000 0.00 0.00 0.00 3.06
119 120 8.956533 TCTTTCATAAAATCGTCATGGATGTA 57.043 30.769 0.00 0.00 0.00 2.29
120 121 8.826710 TCTTTCATAAAATCGTCATGGATGTAC 58.173 33.333 0.00 0.00 0.00 2.90
121 122 8.499403 TTTCATAAAATCGTCATGGATGTACA 57.501 30.769 0.00 0.00 0.00 2.90
122 123 8.675705 TTCATAAAATCGTCATGGATGTACAT 57.324 30.769 8.43 8.43 0.00 2.29
124 125 4.818534 AAATCGTCATGGATGTACATGC 57.181 40.909 19.53 19.53 46.02 4.06
125 126 2.977772 TCGTCATGGATGTACATGCA 57.022 45.000 29.03 29.03 46.02 3.96
133 134 5.918426 ATGGATGTACATGCATGACAAAA 57.082 34.783 33.87 18.90 46.05 2.44
134 135 5.718724 TGGATGTACATGCATGACAAAAA 57.281 34.783 32.75 16.53 34.14 1.94
152 153 3.530265 AAAACGTGACCTACTGTGACA 57.470 42.857 0.00 0.00 29.33 3.58
153 154 3.530265 AAACGTGACCTACTGTGACAA 57.470 42.857 0.00 0.00 29.33 3.18
154 155 3.530265 AACGTGACCTACTGTGACAAA 57.470 42.857 0.00 0.00 29.33 2.83
155 156 2.817901 ACGTGACCTACTGTGACAAAC 58.182 47.619 0.00 0.00 29.33 2.93
156 157 2.166870 ACGTGACCTACTGTGACAAACA 59.833 45.455 0.00 0.00 37.22 2.83
169 170 2.990514 TGACAAACACGTATCATCACGG 59.009 45.455 0.00 0.00 46.12 4.94
170 171 3.247442 GACAAACACGTATCATCACGGA 58.753 45.455 0.00 0.00 46.12 4.69
171 172 3.655486 ACAAACACGTATCATCACGGAA 58.345 40.909 0.00 0.00 46.12 4.30
172 173 3.678072 ACAAACACGTATCATCACGGAAG 59.322 43.478 0.00 0.00 46.12 3.46
308 328 5.939764 TGTATCAGTAGCACTTGGAGAAT 57.060 39.130 0.00 0.00 0.00 2.40
387 407 6.491062 TCTCTTCAATTTCCTTCATTGCTTGA 59.509 34.615 0.00 0.00 32.49 3.02
469 521 4.572389 GCTTGCTACTAGTGTACATGCATT 59.428 41.667 18.94 0.00 34.75 3.56
625 696 5.979517 GTGCATCATTTTACTTTATCCCTGC 59.020 40.000 0.00 0.00 0.00 4.85
757 846 8.212312 TCCTTGTGGTTATACTGTCAGTTTTAA 58.788 33.333 11.54 7.31 34.23 1.52
826 915 4.706476 TGAATAAGCTGGCTTAATTGTGCT 59.294 37.500 17.23 0.00 41.21 4.40
833 922 2.692557 TGGCTTAATTGTGCTTGTGTGT 59.307 40.909 4.86 0.00 0.00 3.72
848 937 5.730568 GCTTGTGTGTTGTTAGTCTTCCTTG 60.731 44.000 0.00 0.00 0.00 3.61
906 995 0.971386 AGAAATGTTTGGCTGGCTGG 59.029 50.000 2.00 0.00 0.00 4.85
944 1033 8.836268 AACATTCACCTAATAGTTACGTTTCA 57.164 30.769 0.00 0.00 0.00 2.69
1126 1216 7.556844 TCAAGAAGGTAGTGGAGTTATCAATC 58.443 38.462 0.00 0.00 0.00 2.67
1179 1269 9.267084 GATGAACTTATTAATGGAGAGGAAGTC 57.733 37.037 0.00 0.00 0.00 3.01
1277 1368 3.563808 TGTGTTTCCTTGTGCTCACATAC 59.436 43.478 3.31 0.00 41.52 2.39
1347 1439 6.098124 CACTGAAGGAATCTAGGATGAAGAGT 59.902 42.308 0.00 0.00 0.00 3.24
1365 1457 3.256136 AGAGTCCTGGTGTTAAGAAGACG 59.744 47.826 0.00 0.00 0.00 4.18
1399 1491 6.112927 AGAAGAAGAGCTCAGAAACATCTT 57.887 37.500 17.77 12.44 33.07 2.40
1554 1647 1.737735 TCTGTTGCGCATGGACTCG 60.738 57.895 12.75 2.59 0.00 4.18
1559 1652 1.960040 TTGCGCATGGACTCGGAGAT 61.960 55.000 12.75 0.00 33.89 2.75
1585 1678 1.894466 TGCAAATGGGTGATGAGTTGG 59.106 47.619 0.00 0.00 0.00 3.77
1651 1744 3.387374 CACTGTCTGCCTAGATGAAGGAT 59.613 47.826 0.00 0.00 39.15 3.24
1661 1754 7.241628 TGCCTAGATGAAGGATGAACTATCTA 58.758 38.462 0.00 0.00 39.15 1.98
1721 1814 3.189287 CCTGTTGCACCTTCTATTGACAC 59.811 47.826 0.00 0.00 0.00 3.67
1753 1846 5.180868 GTCATCAATGAAGAAGAACAGCAGT 59.819 40.000 0.00 0.00 38.75 4.40
1758 1851 6.542005 TCAATGAAGAAGAACAGCAGTTTGTA 59.458 34.615 0.00 0.00 38.30 2.41
1770 1863 2.293399 GCAGTTTGTACTTCAACCAGGG 59.707 50.000 0.00 0.00 35.61 4.45
2048 2141 1.350351 AGCTTGCTTCTGAGTGTGGAT 59.650 47.619 0.00 0.00 0.00 3.41
2329 2425 3.340814 AAGAACAGACGCCATCAGATT 57.659 42.857 0.00 0.00 0.00 2.40
2701 2801 8.579006 ACATTTCTGATTCTTGCTGAATAACAA 58.421 29.630 5.70 0.00 44.70 2.83
2923 3043 4.060205 GCCAGCTTTGATGTTGTTTGATT 58.940 39.130 0.00 0.00 0.00 2.57
3092 3255 1.590238 GTTTGATGATCGGCTCACTCG 59.410 52.381 0.00 0.00 36.48 4.18
3122 3286 6.599638 GCCATCTTATATAGAACCACCATTCC 59.400 42.308 0.00 0.00 36.22 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.543465 GTGTCCACTTCCATGATGATAAATCA 59.457 38.462 0.00 0.00 41.70 2.57
2 3 6.666678 AGTGTCCACTTCCATGATGATAAAT 58.333 36.000 0.00 0.00 38.83 1.40
3 4 6.065976 AGTGTCCACTTCCATGATGATAAA 57.934 37.500 0.00 0.00 38.83 1.40
4 5 5.698741 AGTGTCCACTTCCATGATGATAA 57.301 39.130 0.00 0.00 38.83 1.75
25 26 8.405531 ACATTACCAAAATTATCATCACGGAAG 58.594 33.333 0.00 0.00 0.00 3.46
26 27 8.287439 ACATTACCAAAATTATCATCACGGAA 57.713 30.769 0.00 0.00 0.00 4.30
27 28 7.554476 TGACATTACCAAAATTATCATCACGGA 59.446 33.333 0.00 0.00 0.00 4.69
28 29 7.702386 TGACATTACCAAAATTATCATCACGG 58.298 34.615 0.00 0.00 0.00 4.94
29 30 9.172820 CATGACATTACCAAAATTATCATCACG 57.827 33.333 0.00 0.00 0.00 4.35
30 31 9.467258 CCATGACATTACCAAAATTATCATCAC 57.533 33.333 0.00 0.00 0.00 3.06
31 32 9.418839 TCCATGACATTACCAAAATTATCATCA 57.581 29.630 0.00 0.00 0.00 3.07
34 35 9.029368 TGTTCCATGACATTACCAAAATTATCA 57.971 29.630 0.00 0.00 0.00 2.15
35 36 9.301153 GTGTTCCATGACATTACCAAAATTATC 57.699 33.333 0.00 0.00 0.00 1.75
36 37 9.034800 AGTGTTCCATGACATTACCAAAATTAT 57.965 29.630 0.00 0.00 0.00 1.28
37 38 8.415950 AGTGTTCCATGACATTACCAAAATTA 57.584 30.769 0.00 0.00 0.00 1.40
38 39 7.301868 AGTGTTCCATGACATTACCAAAATT 57.698 32.000 0.00 0.00 0.00 1.82
39 40 6.916360 AGTGTTCCATGACATTACCAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
40 41 6.549364 AGAAGTGTTCCATGACATTACCAAAA 59.451 34.615 0.00 0.00 0.00 2.44
41 42 6.068010 AGAAGTGTTCCATGACATTACCAAA 58.932 36.000 0.00 0.00 0.00 3.28
42 43 5.630121 AGAAGTGTTCCATGACATTACCAA 58.370 37.500 0.00 0.00 0.00 3.67
43 44 5.241403 AGAAGTGTTCCATGACATTACCA 57.759 39.130 0.00 0.00 0.00 3.25
44 45 5.291128 CGTAGAAGTGTTCCATGACATTACC 59.709 44.000 0.00 0.00 0.00 2.85
45 46 6.034683 GTCGTAGAAGTGTTCCATGACATTAC 59.965 42.308 0.00 0.00 39.69 1.89
46 47 6.097356 GTCGTAGAAGTGTTCCATGACATTA 58.903 40.000 0.00 0.00 39.69 1.90
47 48 4.929808 GTCGTAGAAGTGTTCCATGACATT 59.070 41.667 0.00 0.00 39.69 2.71
48 49 4.021456 TGTCGTAGAAGTGTTCCATGACAT 60.021 41.667 6.17 0.00 40.63 3.06
49 50 3.319689 TGTCGTAGAAGTGTTCCATGACA 59.680 43.478 6.17 6.17 42.33 3.58
50 51 3.909430 TGTCGTAGAAGTGTTCCATGAC 58.091 45.455 0.00 1.80 39.69 3.06
51 52 3.614150 GCTGTCGTAGAAGTGTTCCATGA 60.614 47.826 0.00 0.00 39.69 3.07
52 53 2.668457 GCTGTCGTAGAAGTGTTCCATG 59.332 50.000 0.00 0.00 39.69 3.66
53 54 2.299013 TGCTGTCGTAGAAGTGTTCCAT 59.701 45.455 0.00 0.00 39.69 3.41
54 55 1.684450 TGCTGTCGTAGAAGTGTTCCA 59.316 47.619 0.00 0.00 39.69 3.53
55 56 2.059541 GTGCTGTCGTAGAAGTGTTCC 58.940 52.381 0.00 0.00 39.69 3.62
56 57 2.726760 CTGTGCTGTCGTAGAAGTGTTC 59.273 50.000 0.00 0.00 39.69 3.18
57 58 2.545952 CCTGTGCTGTCGTAGAAGTGTT 60.546 50.000 0.00 0.00 39.69 3.32
58 59 1.000163 CCTGTGCTGTCGTAGAAGTGT 60.000 52.381 0.00 0.00 39.69 3.55
59 60 1.000163 ACCTGTGCTGTCGTAGAAGTG 60.000 52.381 0.00 0.00 39.69 3.16
60 61 1.329256 ACCTGTGCTGTCGTAGAAGT 58.671 50.000 0.00 0.00 39.69 3.01
61 62 3.128764 TCATACCTGTGCTGTCGTAGAAG 59.871 47.826 0.00 0.00 39.69 2.85
62 63 3.086282 TCATACCTGTGCTGTCGTAGAA 58.914 45.455 0.00 0.00 39.69 2.10
63 64 2.422479 GTCATACCTGTGCTGTCGTAGA 59.578 50.000 0.00 0.00 0.00 2.59
64 65 2.423892 AGTCATACCTGTGCTGTCGTAG 59.576 50.000 0.00 0.00 0.00 3.51
65 66 2.443416 AGTCATACCTGTGCTGTCGTA 58.557 47.619 0.00 0.00 0.00 3.43
66 67 1.257743 AGTCATACCTGTGCTGTCGT 58.742 50.000 0.00 0.00 0.00 4.34
67 68 3.316588 AGATAGTCATACCTGTGCTGTCG 59.683 47.826 0.00 0.00 0.00 4.35
68 69 4.927978 AGATAGTCATACCTGTGCTGTC 57.072 45.455 0.00 0.00 0.00 3.51
69 70 4.711846 TCAAGATAGTCATACCTGTGCTGT 59.288 41.667 0.00 0.00 0.00 4.40
70 71 5.268118 TCAAGATAGTCATACCTGTGCTG 57.732 43.478 0.00 0.00 0.00 4.41
71 72 6.326064 AGAATCAAGATAGTCATACCTGTGCT 59.674 38.462 0.00 0.00 0.00 4.40
72 73 6.520272 AGAATCAAGATAGTCATACCTGTGC 58.480 40.000 0.00 0.00 0.00 4.57
73 74 8.954950 AAAGAATCAAGATAGTCATACCTGTG 57.045 34.615 0.00 0.00 0.00 3.66
74 75 8.762645 TGAAAGAATCAAGATAGTCATACCTGT 58.237 33.333 0.00 0.00 34.30 4.00
75 76 9.775854 ATGAAAGAATCAAGATAGTCATACCTG 57.224 33.333 0.00 0.00 42.54 4.00
87 88 9.992910 CATGACGATTTTATGAAAGAATCAAGA 57.007 29.630 0.00 0.00 42.54 3.02
88 89 9.229784 CCATGACGATTTTATGAAAGAATCAAG 57.770 33.333 0.00 0.00 42.54 3.02
89 90 8.955388 TCCATGACGATTTTATGAAAGAATCAA 58.045 29.630 0.00 0.00 42.54 2.57
90 91 8.504812 TCCATGACGATTTTATGAAAGAATCA 57.495 30.769 0.00 0.00 43.67 2.57
91 92 9.390795 CATCCATGACGATTTTATGAAAGAATC 57.609 33.333 0.00 0.00 0.00 2.52
92 93 8.906867 ACATCCATGACGATTTTATGAAAGAAT 58.093 29.630 0.00 0.00 0.00 2.40
93 94 8.279970 ACATCCATGACGATTTTATGAAAGAA 57.720 30.769 0.00 0.00 0.00 2.52
94 95 7.864108 ACATCCATGACGATTTTATGAAAGA 57.136 32.000 0.00 0.00 0.00 2.52
95 96 8.611757 TGTACATCCATGACGATTTTATGAAAG 58.388 33.333 0.00 0.00 0.00 2.62
96 97 8.499403 TGTACATCCATGACGATTTTATGAAA 57.501 30.769 0.00 0.00 0.00 2.69
97 98 8.558700 CATGTACATCCATGACGATTTTATGAA 58.441 33.333 5.07 0.00 43.99 2.57
98 99 7.307930 GCATGTACATCCATGACGATTTTATGA 60.308 37.037 5.07 0.00 43.99 2.15
99 100 6.798476 GCATGTACATCCATGACGATTTTATG 59.202 38.462 5.07 0.00 43.99 1.90
100 101 6.486320 TGCATGTACATCCATGACGATTTTAT 59.514 34.615 5.07 0.00 43.99 1.40
101 102 5.819901 TGCATGTACATCCATGACGATTTTA 59.180 36.000 5.07 0.00 43.99 1.52
102 103 4.639755 TGCATGTACATCCATGACGATTTT 59.360 37.500 5.07 0.00 43.99 1.82
103 104 4.198530 TGCATGTACATCCATGACGATTT 58.801 39.130 5.07 0.00 43.99 2.17
104 105 3.807553 TGCATGTACATCCATGACGATT 58.192 40.909 5.07 0.00 43.99 3.34
105 106 3.473923 TGCATGTACATCCATGACGAT 57.526 42.857 5.07 0.00 43.99 3.73
106 107 2.977772 TGCATGTACATCCATGACGA 57.022 45.000 5.07 0.00 43.99 4.20
107 108 3.132925 TCATGCATGTACATCCATGACG 58.867 45.455 30.25 12.42 43.99 4.35
109 110 4.153673 TGTCATGCATGTACATCCATGA 57.846 40.909 30.25 30.25 43.99 3.07
110 111 4.904253 TTGTCATGCATGTACATCCATG 57.096 40.909 27.23 27.23 44.07 3.66
111 112 5.918426 TTTTGTCATGCATGTACATCCAT 57.082 34.783 25.43 6.44 0.00 3.41
112 113 5.718724 TTTTTGTCATGCATGTACATCCA 57.281 34.783 25.43 2.99 0.00 3.41
131 132 3.864243 TGTCACAGTAGGTCACGTTTTT 58.136 40.909 0.00 0.00 0.00 1.94
132 133 3.530265 TGTCACAGTAGGTCACGTTTT 57.470 42.857 0.00 0.00 0.00 2.43
133 134 3.530265 TTGTCACAGTAGGTCACGTTT 57.470 42.857 0.00 0.00 0.00 3.60
134 135 3.192466 GTTTGTCACAGTAGGTCACGTT 58.808 45.455 0.00 0.00 0.00 3.99
135 136 2.166870 TGTTTGTCACAGTAGGTCACGT 59.833 45.455 0.00 0.00 0.00 4.49
136 137 2.538449 GTGTTTGTCACAGTAGGTCACG 59.462 50.000 0.00 0.00 45.51 4.35
137 138 2.538449 CGTGTTTGTCACAGTAGGTCAC 59.462 50.000 0.00 0.00 46.44 3.67
138 139 2.166870 ACGTGTTTGTCACAGTAGGTCA 59.833 45.455 0.00 0.00 46.44 4.02
139 140 2.817901 ACGTGTTTGTCACAGTAGGTC 58.182 47.619 0.00 0.00 46.44 3.85
140 141 2.973694 ACGTGTTTGTCACAGTAGGT 57.026 45.000 0.00 0.00 46.44 3.08
141 142 4.552355 TGATACGTGTTTGTCACAGTAGG 58.448 43.478 0.00 0.00 46.44 3.18
142 143 5.861787 TGATGATACGTGTTTGTCACAGTAG 59.138 40.000 0.00 0.00 46.44 2.57
143 144 5.631929 GTGATGATACGTGTTTGTCACAGTA 59.368 40.000 15.50 0.00 46.44 2.74
144 145 4.447724 GTGATGATACGTGTTTGTCACAGT 59.552 41.667 15.50 0.00 46.44 3.55
145 146 4.432892 CGTGATGATACGTGTTTGTCACAG 60.433 45.833 18.33 11.29 46.44 3.66
146 147 3.427193 CGTGATGATACGTGTTTGTCACA 59.573 43.478 18.33 0.60 46.44 3.58
147 148 3.181534 CCGTGATGATACGTGTTTGTCAC 60.182 47.826 0.00 6.93 42.24 3.67
148 149 2.990514 CCGTGATGATACGTGTTTGTCA 59.009 45.455 0.00 0.00 42.24 3.58
149 150 3.247442 TCCGTGATGATACGTGTTTGTC 58.753 45.455 0.00 0.00 42.24 3.18
150 151 3.306917 TCCGTGATGATACGTGTTTGT 57.693 42.857 0.00 0.00 42.24 2.83
151 152 3.678072 ACTTCCGTGATGATACGTGTTTG 59.322 43.478 0.00 0.00 42.24 2.93
152 153 3.678072 CACTTCCGTGATGATACGTGTTT 59.322 43.478 0.00 0.00 43.97 2.83
153 154 3.250744 CACTTCCGTGATGATACGTGTT 58.749 45.455 0.00 0.00 43.97 3.32
154 155 2.230508 ACACTTCCGTGATGATACGTGT 59.769 45.455 0.00 0.00 43.97 4.49
155 156 2.876091 ACACTTCCGTGATGATACGTG 58.124 47.619 0.00 0.00 43.97 4.49
156 157 3.587797 AACACTTCCGTGATGATACGT 57.412 42.857 0.00 0.00 43.97 3.57
157 158 4.921470 AAAACACTTCCGTGATGATACG 57.079 40.909 0.00 0.00 43.97 3.06
387 407 6.846350 GCAAAGTGCTACTGATAGAAACAAT 58.154 36.000 0.00 0.00 40.96 2.71
443 495 4.391830 GCATGTACACTAGTAGCAAGCAAA 59.608 41.667 0.00 0.00 32.00 3.68
469 521 6.935741 AACATGTAAGTGCACTAAACAAGA 57.064 33.333 29.34 14.87 0.00 3.02
778 867 7.756272 CAGATTGCAGCAATACATTTCACTTAA 59.244 33.333 20.90 0.00 33.90 1.85
826 915 4.095782 GCAAGGAAGACTAACAACACACAA 59.904 41.667 0.00 0.00 0.00 3.33
833 922 4.431416 TTCAGGCAAGGAAGACTAACAA 57.569 40.909 0.00 0.00 0.00 2.83
878 967 6.501781 CCAGCCAAACATTTCTTATGAGATC 58.498 40.000 0.00 0.00 0.00 2.75
906 995 2.674357 GTGAATGTTTGGAATGCATGGC 59.326 45.455 0.00 0.00 0.00 4.40
944 1033 6.127793 AGAGGCTCTTCTTTGCATGATAAAT 58.872 36.000 12.24 0.00 0.00 1.40
1126 1216 5.453903 CCTTAGGATTGTACTCTGGGTCATG 60.454 48.000 0.00 0.00 0.00 3.07
1159 1249 7.661968 TCATCGACTTCCTCTCCATTAATAAG 58.338 38.462 0.00 0.00 0.00 1.73
1179 1269 6.034363 CAGTCTTCTTCACTACAACATCATCG 59.966 42.308 0.00 0.00 0.00 3.84
1347 1439 2.298163 GACCGTCTTCTTAACACCAGGA 59.702 50.000 0.00 0.00 0.00 3.86
1365 1457 2.741517 GCTCTTCTTCTTCTTGCTGACC 59.258 50.000 0.00 0.00 0.00 4.02
1399 1491 1.839994 CCTTCCTGGAGGCATTGTAGA 59.160 52.381 0.00 0.00 38.35 2.59
1554 1647 1.303309 CCATTTGCACCGAGATCTCC 58.697 55.000 17.13 3.53 0.00 3.71
1559 1652 0.327924 ATCACCCATTTGCACCGAGA 59.672 50.000 0.00 0.00 0.00 4.04
1585 1678 1.453745 TTCCTTCATCCATGGGCGC 60.454 57.895 13.02 0.00 0.00 6.53
1651 1744 7.524532 GCCTGCTTCATCTATGTAGATAGTTCA 60.525 40.741 6.78 0.20 40.91 3.18
1661 1754 2.238144 ACAGTGCCTGCTTCATCTATGT 59.762 45.455 2.50 0.00 34.37 2.29
1721 1814 7.242914 TCTTCTTCATTGATGACATCATTCG 57.757 36.000 18.62 10.25 39.39 3.34
1770 1863 3.005155 AGAGCATTGCAAAGGTCAACTTC 59.995 43.478 29.01 7.99 38.85 3.01
1885 1978 6.094464 TGGTAGTCATTGCATCTGAAAATGAG 59.906 38.462 11.67 0.00 40.11 2.90
2048 2141 1.536766 CAGATGGCTTCTTGCAACGAA 59.463 47.619 0.00 3.14 45.15 3.85
2108 2201 6.485830 TCCCAATGTAGTTCTCCAATAGAG 57.514 41.667 0.00 0.00 44.75 2.43
2306 2401 1.466167 CTGATGGCGTCTGTTCTTTGG 59.534 52.381 8.40 0.00 0.00 3.28
2329 2425 9.525409 GCTACGGTATCAAAATACTTCTTCTTA 57.475 33.333 0.00 0.00 38.27 2.10
2538 2634 2.138320 CATCTTGTTCGACACACAGCT 58.862 47.619 0.00 0.00 33.98 4.24
2539 2635 2.135139 TCATCTTGTTCGACACACAGC 58.865 47.619 0.00 0.00 33.98 4.40
2923 3043 5.562696 GCTCCGAATCAAACAACATCAAAGA 60.563 40.000 0.00 0.00 0.00 2.52
3092 3255 6.174049 GTGGTTCTATATAAGATGGCTTCCC 58.826 44.000 0.00 0.00 35.56 3.97


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

AutoCloner maintained by Alex Coulton.