Multiple sequence alignment - TraesCS5D01G162200

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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 TraesCS5D01G162200 chr5D 100.000 4869 0 0 1 4869 253187018 253182150 0.000000e+00 8992.0
1 TraesCS5D01G162200 chr5D 87.500 64 8 0 15 78 529829615 529829678 1.880000e-09 75.0
2 TraesCS5D01G162200 chr5A 92.703 4947 241 42 1 4869 335681426 335676522 0.000000e+00 7025.0
3 TraesCS5D01G162200 chr5B 95.244 3911 104 26 991 4869 285507174 285503314 0.000000e+00 6117.0
4 TraesCS5D01G162200 chr5B 80.861 418 76 4 313 730 285508607 285508194 4.700000e-85 326.0
5 TraesCS5D01G162200 chr5B 99.020 102 0 1 788 889 285507751 285507651 1.080000e-41 182.0
6 TraesCS5D01G162200 chr3B 75.686 510 82 21 231 712 754808855 754808360 2.950000e-52 217.0
7 TraesCS5D01G162200 chr4B 77.843 343 76 0 221 563 40031363 40031705 3.820000e-51 213.0
8 TraesCS5D01G162200 chr4B 82.203 118 18 2 1 115 618071725 618071842 1.120000e-16 99.0
9 TraesCS5D01G162200 chr4B 83.673 98 16 0 504 601 378761163 378761260 5.190000e-15 93.5
10 TraesCS5D01G162200 chr4D 77.054 353 77 4 212 563 27373813 27374162 2.970000e-47 200.0
11 TraesCS5D01G162200 chr2A 78.667 300 55 8 357 653 718719005 718718712 1.790000e-44 191.0
12 TraesCS5D01G162200 chr2A 90.323 62 6 0 17 78 468502977 468502916 1.120000e-11 82.4
13 TraesCS5D01G162200 chr2A 95.556 45 2 0 15 59 564100726 564100770 6.760000e-09 73.1
14 TraesCS5D01G162200 chr2A 85.938 64 9 0 15 78 617725512 617725575 8.740000e-08 69.4
15 TraesCS5D01G162200 chr7A 85.577 104 11 3 1 101 42136395 42136293 6.670000e-19 106.0
16 TraesCS5D01G162200 chr7B 81.553 103 17 2 347 449 670811099 670811199 3.120000e-12 84.2
17 TraesCS5D01G162200 chr2B 87.097 62 8 0 17 78 138786811 138786872 2.430000e-08 71.3
18 TraesCS5D01G162200 chr3D 88.679 53 6 0 24 76 603729126 603729178 1.130000e-06 65.8


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 TraesCS5D01G162200 chr5D 253182150 253187018 4868 True 8992.000000 8992 100.000000 1 4869 1 chr5D.!!$R1 4868
1 TraesCS5D01G162200 chr5A 335676522 335681426 4904 True 7025.000000 7025 92.703000 1 4869 1 chr5A.!!$R1 4868
2 TraesCS5D01G162200 chr5B 285503314 285508607 5293 True 2208.333333 6117 91.708333 313 4869 3 chr5B.!!$R1 4556

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
678 697 0.029834 ACGCGTCCACGGATGTATAC 59.970 55.000 5.58 0.0 40.23 1.47 F
705 724 0.035820 ATTTTAGAGGCCCGCGTTGA 60.036 50.000 4.92 0.0 0.00 3.18 F
1137 1922 0.178958 CGATCCACTAGGGCTAGGGT 60.179 60.000 0.00 0.0 34.83 4.34 F
1247 2033 3.441500 ACATCTTGTCTCTTTTCCCCC 57.558 47.619 0.00 0.0 0.00 5.40 F
1632 2418 3.608316 TTTGCAGTGCTCCTTTTGTTT 57.392 38.095 17.60 0.0 0.00 2.83 F
2922 3738 4.590647 TCATCAAAATGGGCCTGTGTTAAA 59.409 37.500 4.53 0.0 33.42 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2792 0.602905 GGTCGTTGCAGCTACCAAGT 60.603 55.000 17.76 0.0 32.04 3.16 R
2555 3371 4.060900 CTGCAAGCAACAGAAACTCTAGA 58.939 43.478 0.00 0.0 37.32 2.43 R
2822 3638 0.460987 GAAGCATGGGACCACTCTCG 60.461 60.000 0.00 0.0 0.00 4.04 R
3010 3826 3.052944 TGCCCTTACCAAGCCTCATAAAT 60.053 43.478 0.00 0.0 0.00 1.40 R
3585 4405 4.155826 CGGTCTGAATGTCCAAAGCATTTA 59.844 41.667 0.00 0.0 35.03 1.40 R
4757 5598 0.108472 GCAAATGGCCTGCCTTCTTC 60.108 55.000 9.97 0.0 36.11 2.87 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
18 19 3.516578 GCCCGCACCTATCTATGTC 57.483 57.895 0.00 0.00 0.00 3.06
51 52 2.177531 CAGGCGCATGTGCACTTC 59.822 61.111 30.73 14.62 42.21 3.01
55 56 2.076628 GCGCATGTGCACTTCAACG 61.077 57.895 25.87 15.09 42.21 4.10
59 60 1.891919 ATGTGCACTTCAACGCCGT 60.892 52.632 19.41 0.00 0.00 5.68
60 61 0.601576 ATGTGCACTTCAACGCCGTA 60.602 50.000 19.41 0.00 0.00 4.02
75 76 1.154205 CCGTAATGGCGAAGGAGCAG 61.154 60.000 0.00 0.00 39.27 4.24
81 82 2.046892 GCGAAGGAGCAGCCAAGA 60.047 61.111 0.00 0.00 40.02 3.02
86 87 0.969409 AAGGAGCAGCCAAGATTGCC 60.969 55.000 0.00 0.00 41.17 4.52
87 88 2.768492 GGAGCAGCCAAGATTGCCG 61.768 63.158 0.00 0.00 41.17 5.69
88 89 1.746615 GAGCAGCCAAGATTGCCGA 60.747 57.895 0.00 0.00 41.17 5.54
92 93 0.379669 CAGCCAAGATTGCCGATGTC 59.620 55.000 0.00 0.00 0.00 3.06
93 94 1.091771 AGCCAAGATTGCCGATGTCG 61.092 55.000 0.00 0.00 39.44 4.35
94 95 1.089481 GCCAAGATTGCCGATGTCGA 61.089 55.000 3.62 0.00 43.02 4.20
95 96 0.652592 CCAAGATTGCCGATGTCGAC 59.347 55.000 9.11 9.11 43.02 4.20
96 97 0.298707 CAAGATTGCCGATGTCGACG 59.701 55.000 11.62 0.00 43.02 5.12
97 98 0.108804 AAGATTGCCGATGTCGACGT 60.109 50.000 10.75 10.75 43.02 4.34
99 100 0.297820 GATTGCCGATGTCGACGTTC 59.702 55.000 12.40 9.83 43.02 3.95
101 102 3.245315 GCCGATGTCGACGTTCCG 61.245 66.667 12.40 11.53 43.02 4.30
103 104 3.245315 CGATGTCGACGTTCCGGC 61.245 66.667 12.40 0.00 43.02 6.13
115 117 3.659089 TTCCGGCAAGCGTAGGAGC 62.659 63.158 0.00 0.00 33.89 4.70
118 120 2.266055 GGCAAGCGTAGGAGCAGT 59.734 61.111 0.00 0.00 40.15 4.40
119 121 2.103042 GGCAAGCGTAGGAGCAGTG 61.103 63.158 0.00 0.00 40.15 3.66
120 122 2.744768 GCAAGCGTAGGAGCAGTGC 61.745 63.158 7.13 7.13 41.05 4.40
130 132 2.358737 AGCAGTGCCGCTACAACC 60.359 61.111 12.58 0.00 41.55 3.77
133 135 1.293498 CAGTGCCGCTACAACCTCT 59.707 57.895 0.00 0.00 0.00 3.69
161 178 1.817941 CGGAGGGCCAAATGTACGG 60.818 63.158 6.18 0.00 0.00 4.02
169 186 0.368907 CCAAATGTACGGCGAGTTCG 59.631 55.000 16.62 0.00 43.27 3.95
184 201 3.579685 TCGTGAGCGAGGAGACTG 58.420 61.111 0.00 0.00 44.43 3.51
186 203 1.154131 CGTGAGCGAGGAGACTGTG 60.154 63.158 0.00 0.00 44.43 3.66
199 216 0.905357 GACTGTGGTGGCTATGGACT 59.095 55.000 0.00 0.00 0.00 3.85
208 225 0.033642 GGCTATGGACTAGAACGCCC 59.966 60.000 0.00 0.00 0.00 6.13
210 227 1.315690 CTATGGACTAGAACGCCCGA 58.684 55.000 0.00 0.00 0.00 5.14
211 228 1.001597 CTATGGACTAGAACGCCCGAC 60.002 57.143 0.00 0.00 0.00 4.79
213 230 1.139095 GGACTAGAACGCCCGACAG 59.861 63.158 0.00 0.00 0.00 3.51
214 231 1.516603 GACTAGAACGCCCGACAGC 60.517 63.158 0.00 0.00 0.00 4.40
215 232 1.935327 GACTAGAACGCCCGACAGCT 61.935 60.000 0.00 0.00 0.00 4.24
216 233 1.517257 CTAGAACGCCCGACAGCTG 60.517 63.158 13.48 13.48 0.00 4.24
217 234 2.214181 CTAGAACGCCCGACAGCTGT 62.214 60.000 21.88 21.88 0.00 4.40
219 236 4.988598 AACGCCCGACAGCTGTGG 62.989 66.667 27.27 23.69 0.00 4.17
225 242 3.414700 CGACAGCTGTGGTTCGCC 61.415 66.667 27.27 6.75 37.92 5.54
249 266 1.080974 CCGCTACGACAACGAGGTT 60.081 57.895 0.00 0.00 42.66 3.50
255 272 3.047877 GACAACGAGGTTGGCCCG 61.048 66.667 12.56 0.00 44.98 6.13
268 285 2.047655 GCCCGTTCACGTCCATCA 60.048 61.111 0.00 0.00 37.74 3.07
269 286 1.449601 GCCCGTTCACGTCCATCAT 60.450 57.895 0.00 0.00 37.74 2.45
283 300 1.206878 CATCATGGACCTCACCTCCA 58.793 55.000 0.00 0.00 42.17 3.86
285 302 0.909610 TCATGGACCTCACCTCCACC 60.910 60.000 0.00 0.00 40.73 4.61
289 306 2.989824 ACCTCACCTCCACCGACG 60.990 66.667 0.00 0.00 0.00 5.12
291 308 2.567049 CTCACCTCCACCGACGAC 59.433 66.667 0.00 0.00 0.00 4.34
295 312 4.112341 CCTCCACCGACGACGTCC 62.112 72.222 21.63 5.01 37.88 4.79
332 349 2.095461 CGAGGAAGAGTGAGACATGGA 58.905 52.381 0.00 0.00 0.00 3.41
337 354 3.506810 GAAGAGTGAGACATGGAAGACG 58.493 50.000 0.00 0.00 0.00 4.18
376 393 0.323178 TCTTACTCTTCCTCGCCGGT 60.323 55.000 1.90 0.00 0.00 5.28
409 427 2.203788 TTCCCAGAGCTCACGGGT 60.204 61.111 30.34 3.99 41.12 5.28
413 431 4.007644 CAGAGCTCACGGGTGGCA 62.008 66.667 17.77 0.00 31.93 4.92
454 472 2.241176 ACAACAAGGACTTGGAGGACAA 59.759 45.455 15.72 0.00 44.45 3.18
471 489 4.511826 AGGACAAACACTGACGAAGATTTC 59.488 41.667 0.00 0.00 0.00 2.17
489 507 8.561738 AAGATTTCGATTAGCTTAACTTCCAA 57.438 30.769 0.00 0.00 0.00 3.53
537 556 8.200120 TGTTGAAAATGTAATGAATGTTGTCCA 58.800 29.630 0.00 0.00 0.00 4.02
573 592 5.725325 TCATCCAGTTTGCATGAAAATCA 57.275 34.783 1.18 0.00 0.00 2.57
578 597 4.380761 CCAGTTTGCATGAAAATCATCCGA 60.381 41.667 1.18 0.00 34.28 4.55
608 627 6.686630 TCAAATTCCGCTTGAAAATGTATGT 58.313 32.000 0.00 0.00 36.33 2.29
635 654 7.285401 GGATATTTGAGGTACATGGTTGAATGT 59.715 37.037 0.00 0.00 43.21 2.71
651 670 1.722034 ATGTCCGGCTCCTGTATCAT 58.278 50.000 0.00 0.00 0.00 2.45
653 672 2.673258 TGTCCGGCTCCTGTATCATTA 58.327 47.619 0.00 0.00 0.00 1.90
658 677 2.492088 CGGCTCCTGTATCATTATCCGA 59.508 50.000 0.00 0.00 36.77 4.55
663 682 2.661675 CCTGTATCATTATCCGAACGCG 59.338 50.000 3.53 3.53 37.24 6.01
678 697 0.029834 ACGCGTCCACGGATGTATAC 59.970 55.000 5.58 0.00 40.23 1.47
693 712 7.587629 CGGATGTATACCGTGTCTATTTTAGA 58.412 38.462 0.00 0.00 44.57 2.10
705 724 0.035820 ATTTTAGAGGCCCGCGTTGA 60.036 50.000 4.92 0.00 0.00 3.18
719 738 1.148310 CGTTGAAGATGCGGTGAAGT 58.852 50.000 0.00 0.00 0.00 3.01
730 749 1.818674 GCGGTGAAGTGGGATTGAAAT 59.181 47.619 0.00 0.00 0.00 2.17
744 763 1.271840 TGAAATGGGTCGAGGGGGAG 61.272 60.000 0.00 0.00 0.00 4.30
747 1130 0.327576 AATGGGTCGAGGGGGAGATT 60.328 55.000 0.00 0.00 0.00 2.40
752 1135 2.224548 GGGTCGAGGGGGAGATTAAATG 60.225 54.545 0.00 0.00 0.00 2.32
754 1137 3.135895 GGTCGAGGGGGAGATTAAATGAA 59.864 47.826 0.00 0.00 0.00 2.57
773 1156 8.655935 AAATGAAGTCAAAATCCCTATTGAGT 57.344 30.769 0.00 0.00 40.11 3.41
774 1157 9.753674 AAATGAAGTCAAAATCCCTATTGAGTA 57.246 29.630 0.00 0.00 38.05 2.59
775 1158 9.927081 AATGAAGTCAAAATCCCTATTGAGTAT 57.073 29.630 0.00 0.00 38.05 2.12
777 1160 9.177608 TGAAGTCAAAATCCCTATTGAGTATTG 57.822 33.333 0.00 0.00 38.05 1.90
778 1161 9.396022 GAAGTCAAAATCCCTATTGAGTATTGA 57.604 33.333 0.00 0.00 38.05 2.57
780 1163 9.178758 AGTCAAAATCCCTATTGAGTATTGAAC 57.821 33.333 0.00 0.00 37.42 3.18
781 1164 8.406297 GTCAAAATCCCTATTGAGTATTGAACC 58.594 37.037 0.00 0.00 36.31 3.62
782 1165 7.559897 TCAAAATCCCTATTGAGTATTGAACCC 59.440 37.037 0.00 0.00 32.14 4.11
783 1166 6.848562 AATCCCTATTGAGTATTGAACCCT 57.151 37.500 0.00 0.00 0.00 4.34
784 1167 6.848562 ATCCCTATTGAGTATTGAACCCTT 57.151 37.500 0.00 0.00 0.00 3.95
785 1168 6.248569 TCCCTATTGAGTATTGAACCCTTC 57.751 41.667 0.00 0.00 0.00 3.46
872 1282 0.708802 TAGACGAGAACCCCTCCCTT 59.291 55.000 0.00 0.00 38.71 3.95
1137 1922 0.178958 CGATCCACTAGGGCTAGGGT 60.179 60.000 0.00 0.00 34.83 4.34
1247 2033 3.441500 ACATCTTGTCTCTTTTCCCCC 57.558 47.619 0.00 0.00 0.00 5.40
1304 2090 4.638421 TGTGTGTAGAAAGTTTTGACCCTG 59.362 41.667 0.00 0.00 0.00 4.45
1332 2118 4.101119 CCCCGTTCCTGTTAGATTCACTAT 59.899 45.833 0.00 0.00 0.00 2.12
1334 2120 5.395324 CCCGTTCCTGTTAGATTCACTATGT 60.395 44.000 0.00 0.00 0.00 2.29
1352 2138 8.729756 TCACTATGTGTTTCAAATTCTACATGG 58.270 33.333 0.00 0.00 34.79 3.66
1361 2147 8.925700 GTTTCAAATTCTACATGGAACCATTTC 58.074 33.333 3.35 0.00 33.90 2.17
1362 2148 7.773489 TCAAATTCTACATGGAACCATTTCA 57.227 32.000 3.35 0.00 33.90 2.69
1363 2149 8.365060 TCAAATTCTACATGGAACCATTTCAT 57.635 30.769 3.35 0.00 33.90 2.57
1364 2150 8.469200 TCAAATTCTACATGGAACCATTTCATC 58.531 33.333 3.35 0.00 33.90 2.92
1575 2361 5.051508 GGCATCTTTGTTTGCAATATAAGCG 60.052 40.000 0.00 0.94 40.66 4.68
1603 2389 6.612306 AGCATCAACGGTTTCTCTATTTTTC 58.388 36.000 0.00 0.00 0.00 2.29
1632 2418 3.608316 TTTGCAGTGCTCCTTTTGTTT 57.392 38.095 17.60 0.00 0.00 2.83
1794 2582 6.763715 ATCTACACCCATTGCTTCCTTATA 57.236 37.500 0.00 0.00 0.00 0.98
1886 2674 5.393352 GCTCATTCTGGCACAAAACATCATA 60.393 40.000 0.00 0.00 38.70 2.15
1892 2680 7.887996 TCTGGCACAAAACATCATATTTTTC 57.112 32.000 0.00 0.00 38.70 2.29
2249 3041 8.986929 AGATATTGGCAGATTTTAGCTTAGTT 57.013 30.769 0.00 0.00 0.00 2.24
2254 3046 7.377766 TGGCAGATTTTAGCTTAGTTAACTG 57.622 36.000 18.56 3.44 0.00 3.16
2307 3099 7.900782 TTACTTAGACTTGTTGCATACCTTC 57.099 36.000 0.00 0.00 0.00 3.46
2801 3617 9.860898 CTAAAGGATTTCTCTAACAAAAATGGG 57.139 33.333 0.00 0.00 40.09 4.00
2922 3738 4.590647 TCATCAAAATGGGCCTGTGTTAAA 59.409 37.500 4.53 0.00 33.42 1.52
3008 3824 6.630444 ATGCATGTCTAGCCATAAGAAAAG 57.370 37.500 0.00 0.00 0.00 2.27
3010 3826 5.126067 GCATGTCTAGCCATAAGAAAAGGA 58.874 41.667 0.00 0.00 0.00 3.36
3068 3885 9.665719 TGTAAACAAGTCTTATGATGCTCAATA 57.334 29.630 0.00 0.00 0.00 1.90
3669 4489 2.260844 ACAACTGGGGATATGATGCG 57.739 50.000 0.00 0.00 0.00 4.73
3678 4498 3.118112 GGGGATATGATGCGGATGATCTT 60.118 47.826 0.00 0.00 0.00 2.40
3834 4664 9.972106 TTTTTGCCTTTGGGATGATAATTTATT 57.028 25.926 0.00 0.00 33.58 1.40
4136 4976 2.038814 TTGTCCACGGCTGCTCAAGA 62.039 55.000 0.00 0.00 0.00 3.02
4543 5384 8.780249 ACACCTTAAACACAAACACTACATATC 58.220 33.333 0.00 0.00 0.00 1.63
4599 5440 3.450817 CCTGAAAGAAAAACACAAGGGGT 59.549 43.478 0.00 0.00 34.07 4.95
4756 5597 4.025858 GCAGGAGCAGCCTCACCA 62.026 66.667 0.00 0.00 46.97 4.17
4757 5598 2.268280 CAGGAGCAGCCTCACCAG 59.732 66.667 0.00 0.00 46.97 4.00
4758 5599 2.121385 AGGAGCAGCCTCACCAGA 59.879 61.111 0.00 0.00 46.97 3.86
4764 5605 0.676151 GCAGCCTCACCAGAAGAAGG 60.676 60.000 0.00 0.00 0.00 3.46
4780 5621 0.395586 AAGGCAGGCCATTTGCGATA 60.396 50.000 13.63 0.00 42.42 2.92
4799 5640 5.728898 GCGATACTTGATTGCTTCTCCTTTG 60.729 44.000 0.00 0.00 41.29 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.035961 TGAAGCCGACATAGATAGGTGC 59.964 50.000 0.00 0.00 0.00 5.01
6 7 2.628657 GGTGAAGCCGACATAGATAGGT 59.371 50.000 0.00 0.00 0.00 3.08
10 11 2.224378 CCATGGTGAAGCCGACATAGAT 60.224 50.000 2.57 0.00 41.21 1.98
18 19 2.046023 TGCTCCATGGTGAAGCCG 60.046 61.111 17.98 0.00 41.21 5.52
59 60 1.153168 GGCTGCTCCTTCGCCATTA 60.153 57.895 0.00 0.00 43.25 1.90
60 61 2.439156 GGCTGCTCCTTCGCCATT 60.439 61.111 0.00 0.00 43.25 3.16
77 78 0.298707 CGTCGACATCGGCAATCTTG 59.701 55.000 17.16 0.00 45.47 3.02
79 80 0.108804 AACGTCGACATCGGCAATCT 60.109 50.000 17.16 0.00 45.47 2.40
80 81 0.297820 GAACGTCGACATCGGCAATC 59.702 55.000 17.16 0.00 45.47 2.67
81 82 1.082117 GGAACGTCGACATCGGCAAT 61.082 55.000 17.16 0.00 45.47 3.56
96 97 1.810030 CTCCTACGCTTGCCGGAAC 60.810 63.158 5.05 0.00 42.52 3.62
97 98 2.577059 CTCCTACGCTTGCCGGAA 59.423 61.111 5.05 0.00 42.52 4.30
99 100 4.451150 TGCTCCTACGCTTGCCGG 62.451 66.667 0.00 0.00 42.52 6.13
101 102 2.103042 CACTGCTCCTACGCTTGCC 61.103 63.158 0.00 0.00 0.00 4.52
103 104 2.103042 GGCACTGCTCCTACGCTTG 61.103 63.158 0.00 0.00 0.00 4.01
104 105 2.266055 GGCACTGCTCCTACGCTT 59.734 61.111 0.00 0.00 0.00 4.68
105 106 4.135153 CGGCACTGCTCCTACGCT 62.135 66.667 0.00 0.00 0.00 5.07
115 117 0.737715 GAGAGGTTGTAGCGGCACTG 60.738 60.000 1.45 0.00 0.00 3.66
118 120 2.656069 GGGAGAGGTTGTAGCGGCA 61.656 63.158 1.45 0.00 0.00 5.69
119 121 1.900545 AAGGGAGAGGTTGTAGCGGC 61.901 60.000 0.00 0.00 0.00 6.53
120 122 0.175989 GAAGGGAGAGGTTGTAGCGG 59.824 60.000 0.00 0.00 0.00 5.52
156 173 2.150837 GCTCACGAACTCGCCGTAC 61.151 63.158 0.00 0.00 44.43 3.67
169 186 1.214062 CCACAGTCTCCTCGCTCAC 59.786 63.158 0.00 0.00 0.00 3.51
181 198 2.111384 CTAGTCCATAGCCACCACAGT 58.889 52.381 0.00 0.00 0.00 3.55
183 200 2.500098 GTTCTAGTCCATAGCCACCACA 59.500 50.000 0.00 0.00 0.00 4.17
184 201 2.481449 CGTTCTAGTCCATAGCCACCAC 60.481 54.545 0.00 0.00 0.00 4.16
186 203 1.538419 GCGTTCTAGTCCATAGCCACC 60.538 57.143 0.00 0.00 0.00 4.61
199 216 2.273179 ACAGCTGTCGGGCGTTCTA 61.273 57.895 15.25 0.00 37.29 2.10
208 225 3.414700 GGCGAACCACAGCTGTCG 61.415 66.667 18.64 18.48 35.26 4.35
210 227 4.643387 GGGGCGAACCACAGCTGT 62.643 66.667 15.25 15.25 40.19 4.40
238 255 3.047877 CGGGCCAACCTCGTTGTC 61.048 66.667 4.39 0.00 41.41 3.18
244 261 3.047877 CGTGAACGGGCCAACCTC 61.048 66.667 4.39 0.00 36.97 3.85
249 266 3.599285 GATGGACGTGAACGGGCCA 62.599 63.158 17.88 17.88 46.33 5.36
268 285 1.990060 CGGTGGAGGTGAGGTCCAT 60.990 63.158 0.00 0.00 45.91 3.41
269 286 2.603473 CGGTGGAGGTGAGGTCCA 60.603 66.667 0.00 0.00 42.06 4.02
285 302 4.129737 ATGGCCTGGACGTCGTCG 62.130 66.667 18.61 6.83 43.34 5.12
295 312 2.187946 GTCGGAGTCCATGGCCTG 59.812 66.667 6.96 4.00 0.00 4.85
309 326 1.157585 TGTCTCACTCTTCCTCGTCG 58.842 55.000 0.00 0.00 0.00 5.12
311 328 1.821753 CCATGTCTCACTCTTCCTCGT 59.178 52.381 0.00 0.00 0.00 4.18
324 341 0.108615 CGCCTTCGTCTTCCATGTCT 60.109 55.000 0.00 0.00 0.00 3.41
337 354 3.684788 AGACATGAAACACATACGCCTTC 59.315 43.478 0.00 0.00 37.46 3.46
345 362 6.773638 AGGAAGAGTAAGACATGAAACACAT 58.226 36.000 0.00 0.00 40.17 3.21
352 369 2.427453 GGCGAGGAAGAGTAAGACATGA 59.573 50.000 0.00 0.00 0.00 3.07
376 393 1.133915 GGGAAGTGAAGTTGTGGGTCA 60.134 52.381 0.00 0.00 0.00 4.02
413 431 1.002069 TCCCCATGTCCAGCATCTTT 58.998 50.000 0.00 0.00 35.19 2.52
422 440 1.203001 TCCTTGTTGTTCCCCATGTCC 60.203 52.381 0.00 0.00 0.00 4.02
471 489 5.879237 TGCATTTGGAAGTTAAGCTAATCG 58.121 37.500 0.00 0.00 0.00 3.34
474 492 7.887996 CAAATGCATTTGGAAGTTAAGCTAA 57.112 32.000 34.70 0.00 42.51 3.09
514 533 9.775854 AATTGGACAACATTCATTACATTTTCA 57.224 25.926 0.00 0.00 0.00 2.69
532 551 9.656040 CTGGATGATTTTCATTTAAATTGGACA 57.344 29.630 0.00 0.00 37.20 4.02
573 592 3.443681 AGCGGAATTTGAACAAATCGGAT 59.556 39.130 12.20 7.38 39.88 4.18
578 597 6.917217 TTTTCAAGCGGAATTTGAACAAAT 57.083 29.167 6.91 6.91 42.44 2.32
608 627 6.320434 TCAACCATGTACCTCAAATATCCA 57.680 37.500 0.00 0.00 0.00 3.41
635 654 2.832129 GGATAATGATACAGGAGCCGGA 59.168 50.000 5.05 0.00 0.00 5.14
651 670 1.514657 CGTGGACGCGTTCGGATAA 60.515 57.895 15.53 0.00 40.69 1.75
653 672 4.789075 CCGTGGACGCGTTCGGAT 62.789 66.667 31.92 5.04 44.86 4.18
658 677 0.740149 TATACATCCGTGGACGCGTT 59.260 50.000 15.53 0.00 38.18 4.84
678 697 2.802057 CGGGCCTCTAAAATAGACACGG 60.802 54.545 0.84 0.00 27.79 4.94
685 704 1.207570 TCAACGCGGGCCTCTAAAATA 59.792 47.619 12.47 0.00 0.00 1.40
693 712 2.436646 CATCTTCAACGCGGGCCT 60.437 61.111 12.47 0.00 0.00 5.19
705 724 0.620556 ATCCCACTTCACCGCATCTT 59.379 50.000 0.00 0.00 0.00 2.40
713 732 3.165071 ACCCATTTCAATCCCACTTCAC 58.835 45.455 0.00 0.00 0.00 3.18
719 738 1.064758 CCTCGACCCATTTCAATCCCA 60.065 52.381 0.00 0.00 0.00 4.37
730 749 0.340558 TTAATCTCCCCCTCGACCCA 59.659 55.000 0.00 0.00 0.00 4.51
747 1130 9.753674 ACTCAATAGGGATTTTGACTTCATTTA 57.246 29.630 0.00 0.00 0.00 1.40
752 1135 9.396022 TCAATACTCAATAGGGATTTTGACTTC 57.604 33.333 0.00 0.00 0.00 3.01
754 1137 9.178758 GTTCAATACTCAATAGGGATTTTGACT 57.821 33.333 0.00 0.00 0.00 3.41
773 1156 3.009695 ACGGATGTTGGAAGGGTTCAATA 59.990 43.478 0.00 0.00 0.00 1.90
774 1157 2.225017 ACGGATGTTGGAAGGGTTCAAT 60.225 45.455 0.00 0.00 0.00 2.57
775 1158 1.144093 ACGGATGTTGGAAGGGTTCAA 59.856 47.619 0.00 0.00 0.00 2.69
777 1160 1.165270 CACGGATGTTGGAAGGGTTC 58.835 55.000 0.00 0.00 0.00 3.62
778 1161 0.893727 GCACGGATGTTGGAAGGGTT 60.894 55.000 0.00 0.00 0.00 4.11
780 1163 0.680921 ATGCACGGATGTTGGAAGGG 60.681 55.000 0.00 0.00 0.00 3.95
781 1164 0.734889 GATGCACGGATGTTGGAAGG 59.265 55.000 0.00 0.00 0.00 3.46
782 1165 1.667724 GAGATGCACGGATGTTGGAAG 59.332 52.381 0.00 0.00 0.00 3.46
783 1166 1.737838 GAGATGCACGGATGTTGGAA 58.262 50.000 0.00 0.00 0.00 3.53
784 1167 0.460109 CGAGATGCACGGATGTTGGA 60.460 55.000 0.00 0.00 0.00 3.53
785 1168 0.460109 TCGAGATGCACGGATGTTGG 60.460 55.000 0.00 0.00 0.00 3.77
872 1282 1.270907 GGGAAGAAGAGGAGCAGTGA 58.729 55.000 0.00 0.00 0.00 3.41
955 1365 0.916845 GGCCTCCCTCCCTTCTCTTT 60.917 60.000 0.00 0.00 0.00 2.52
987 1397 0.179134 CGTCCATGTCGTCTCTTCCC 60.179 60.000 0.00 0.00 0.00 3.97
1137 1922 1.351683 GAGAGGTAGATCCGCCCTAGA 59.648 57.143 0.00 0.00 41.99 2.43
1247 2033 1.632422 GCGCATTTCAGTTCCAATGG 58.368 50.000 0.30 0.00 31.97 3.16
1332 2118 6.322456 TGGTTCCATGTAGAATTTGAAACACA 59.678 34.615 0.00 0.00 0.00 3.72
1334 2120 6.968263 TGGTTCCATGTAGAATTTGAAACA 57.032 33.333 0.00 0.00 0.00 2.83
1352 2138 6.183360 CCTCCCAAACTATGATGAAATGGTTC 60.183 42.308 0.00 0.00 30.81 3.62
1361 2147 2.509548 TGGACCCTCCCAAACTATGATG 59.490 50.000 0.00 0.00 35.03 3.07
1362 2148 2.780010 CTGGACCCTCCCAAACTATGAT 59.220 50.000 0.00 0.00 35.03 2.45
1363 2149 2.196595 CTGGACCCTCCCAAACTATGA 58.803 52.381 0.00 0.00 35.03 2.15
1364 2150 1.408822 GCTGGACCCTCCCAAACTATG 60.409 57.143 0.00 0.00 35.03 2.23
1575 2361 6.663944 ATAGAGAAACCGTTGATGCTTAAC 57.336 37.500 0.00 0.00 0.00 2.01
1603 2389 8.437742 CAAAAGGAGCACTGCAAAAATAATAAG 58.562 33.333 3.30 0.00 0.00 1.73
1615 2401 3.553105 CAGAAAAACAAAAGGAGCACTGC 59.447 43.478 0.00 0.00 0.00 4.40
1632 2418 6.934645 CCAACTGTTCTATGTCCTTACAGAAA 59.065 38.462 0.00 0.00 39.49 2.52
1794 2582 6.262273 CGTTGAACATGGCCTAGGTTTAATAT 59.738 38.462 11.31 0.00 32.44 1.28
1816 2604 3.986277 ACGGAAGTGTGTAGATTTCGTT 58.014 40.909 0.00 0.00 46.97 3.85
2003 2792 0.602905 GGTCGTTGCAGCTACCAAGT 60.603 55.000 17.76 0.00 32.04 3.16
2184 2975 7.734924 ATTATCATGCAATACAGTGTCGATT 57.265 32.000 0.00 0.00 0.00 3.34
2307 3099 6.309712 TCAGAAGTGCAGAAGAAAATGAAG 57.690 37.500 0.00 0.00 0.00 3.02
2555 3371 4.060900 CTGCAAGCAACAGAAACTCTAGA 58.939 43.478 0.00 0.00 37.32 2.43
2722 3538 3.674997 ACAGTACAAGGCACATTAGTGG 58.325 45.455 0.00 0.00 45.98 4.00
2801 3617 2.588989 CTCCTGCTCCCTTCAGCC 59.411 66.667 0.00 0.00 38.80 4.85
2822 3638 0.460987 GAAGCATGGGACCACTCTCG 60.461 60.000 0.00 0.00 0.00 4.04
2922 3738 6.288941 TCAAGAAATGTGCCATTCATCAAT 57.711 33.333 1.57 0.00 0.00 2.57
3008 3824 4.145052 CCCTTACCAAGCCTCATAAATCC 58.855 47.826 0.00 0.00 0.00 3.01
3010 3826 3.052944 TGCCCTTACCAAGCCTCATAAAT 60.053 43.478 0.00 0.00 0.00 1.40
3068 3885 7.624077 ACTTCCTTACACAGTTAGGATATCCTT 59.376 37.037 29.06 12.01 46.09 3.36
3107 3924 7.907389 TGTAACTTCTACACTGAGATCCAAAT 58.093 34.615 0.00 0.00 0.00 2.32
3580 4400 8.650714 GTCTGAATGTCCAAAGCATTTATTTTC 58.349 33.333 0.00 0.00 35.03 2.29
3585 4405 4.155826 CGGTCTGAATGTCCAAAGCATTTA 59.844 41.667 0.00 0.00 35.03 1.40
3669 4489 3.828875 ACTTCCTCCGAAAGATCATCC 57.171 47.619 0.00 0.00 0.00 3.51
3678 4498 2.492881 TGTACGCAATACTTCCTCCGAA 59.507 45.455 0.00 0.00 34.56 4.30
3808 4628 9.972106 AATAAATTATCATCCCAAAGGCAAAAA 57.028 25.926 0.00 0.00 0.00 1.94
4483 5324 5.960113 ACTGCATTCAACAAACACAAGTAA 58.040 33.333 0.00 0.00 0.00 2.24
4599 5440 3.202818 ACAGCCACCTCCATGAATTCATA 59.797 43.478 20.32 5.71 34.26 2.15
4756 5597 1.553706 CAAATGGCCTGCCTTCTTCT 58.446 50.000 9.97 0.00 36.94 2.85
4757 5598 0.108472 GCAAATGGCCTGCCTTCTTC 60.108 55.000 9.97 0.00 36.11 2.87
4758 5599 1.880819 CGCAAATGGCCTGCCTTCTT 61.881 55.000 9.97 0.00 40.31 2.52
4764 5605 0.740737 AAGTATCGCAAATGGCCTGC 59.259 50.000 3.32 4.54 40.31 4.85
4780 5621 3.160269 CCCAAAGGAGAAGCAATCAAGT 58.840 45.455 0.00 0.00 33.47 3.16
4799 5640 5.122519 TGTTTGAAATTTCCTTTTCAGCCC 58.877 37.500 15.48 0.00 44.12 5.19


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

AutoCloner maintained by Alex Coulton.