Multiple sequence alignment - TraesCS1A01G285400

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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 TraesCS1A01G285400 chr1A 100.000 4726 0 0 1 4726 482772403 482767678 0.000000e+00 8728.0
1 TraesCS1A01G285400 chr1B 92.709 4622 242 60 41 4618 512635019 512630449 0.000000e+00 6580.0
2 TraesCS1A01G285400 chr1B 97.273 110 3 0 4617 4726 512624144 512624035 2.250000e-43 187.0
3 TraesCS1A01G285400 chr1B 100.000 38 0 0 4 41 71997458 71997421 2.360000e-08 71.3
4 TraesCS1A01G285400 chr1D 93.831 4182 190 33 571 4726 382723625 382719486 0.000000e+00 6231.0
5 TraesCS1A01G285400 chr1D 91.870 246 19 1 41 285 382723883 382723638 4.530000e-90 342.0
6 TraesCS1A01G285400 chr4B 89.286 448 36 10 3956 4399 43061687 43061248 6.910000e-153 551.0
7 TraesCS1A01G285400 chrUn 89.333 450 31 9 3963 4399 249353322 249353767 2.490000e-152 549.0
8 TraesCS1A01G285400 chrUn 89.333 450 31 9 3963 4399 249357690 249358135 2.490000e-152 549.0
9 TraesCS1A01G285400 chrUn 89.333 450 31 9 3963 4399 249362058 249362503 2.490000e-152 549.0
10 TraesCS1A01G285400 chrUn 89.333 450 31 10 3963 4399 249943388 249942943 2.490000e-152 549.0
11 TraesCS1A01G285400 chrUn 89.333 450 31 10 3963 4399 249947756 249947311 2.490000e-152 549.0
12 TraesCS1A01G285400 chrUn 89.333 450 31 10 3963 4399 249952124 249951679 2.490000e-152 549.0
13 TraesCS1A01G285400 chr5D 97.368 38 1 0 4 41 236475413 236475376 1.100000e-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 TraesCS1A01G285400 chr1A 482767678 482772403 4725 True 8728.0 8728 100.0000 1 4726 1 chr1A.!!$R1 4725
1 TraesCS1A01G285400 chr1B 512630449 512635019 4570 True 6580.0 6580 92.7090 41 4618 1 chr1B.!!$R3 4577
2 TraesCS1A01G285400 chr1D 382719486 382723883 4397 True 3286.5 6231 92.8505 41 4726 2 chr1D.!!$R1 4685
3 TraesCS1A01G285400 chrUn 249353322 249362503 9181 False 549.0 549 89.3330 3963 4399 3 chrUn.!!$F1 436
4 TraesCS1A01G285400 chrUn 249942943 249952124 9181 True 549.0 549 89.3330 3963 4399 3 chrUn.!!$R1 436

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
934 948 0.314578 GATTTGTCGCGACGATGCAG 60.315 55.0 31.88 0.0 38.42 4.41 F
2454 2474 0.043637 TCCCCCTCAAGTACCGGAAT 59.956 55.0 9.46 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2720 2754 0.107993 TGCTTGATCTTGGAGAGCGG 60.108 55.0 0.0 0.0 32.29 5.52 R
4445 4894 0.470080 GATCATCGTCCTCCTCCCCA 60.470 60.0 0.0 0.0 0.00 4.96 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
17 18 2.279584 TTGTTCGTCTTCGCGCCA 60.280 55.556 0.00 0.00 36.96 5.69
18 19 1.883544 TTGTTCGTCTTCGCGCCAA 60.884 52.632 0.00 0.00 36.96 4.52
19 20 1.225376 TTGTTCGTCTTCGCGCCAAT 61.225 50.000 0.00 0.00 36.96 3.16
20 21 1.225376 TGTTCGTCTTCGCGCCAATT 61.225 50.000 0.00 0.00 36.96 2.32
21 22 0.789383 GTTCGTCTTCGCGCCAATTG 60.789 55.000 0.00 0.00 36.96 2.32
32 33 3.055719 CCAATTGGCGCGACAGGT 61.056 61.111 17.30 5.19 0.00 4.00
33 34 2.480555 CAATTGGCGCGACAGGTC 59.519 61.111 17.30 0.00 0.00 3.85
34 35 2.031919 AATTGGCGCGACAGGTCA 59.968 55.556 17.30 0.00 0.00 4.02
35 36 1.377202 AATTGGCGCGACAGGTCAT 60.377 52.632 17.30 1.85 0.00 3.06
37 38 2.244117 ATTGGCGCGACAGGTCATCT 62.244 55.000 17.30 0.00 0.00 2.90
38 39 1.600511 TTGGCGCGACAGGTCATCTA 61.601 55.000 17.30 0.00 0.00 1.98
39 40 1.299468 GGCGCGACAGGTCATCTAG 60.299 63.158 12.10 0.00 0.00 2.43
77 78 7.335171 TGTCAAGGATCATTGTGACTAGAAATG 59.665 37.037 18.78 1.63 40.81 2.32
90 91 3.441572 ACTAGAAATGGTTGCTGATGTGC 59.558 43.478 0.00 0.00 0.00 4.57
116 117 6.161855 AGAGTTCATGCTTACCGATCATTA 57.838 37.500 0.00 0.00 0.00 1.90
138 140 2.105134 ACGGGTGGAGTTTGTCATGTTA 59.895 45.455 0.00 0.00 0.00 2.41
146 148 8.686334 GGTGGAGTTTGTCATGTTAATATCATT 58.314 33.333 0.00 0.00 0.00 2.57
159 161 6.542005 TGTTAATATCATTGCTTCGATGTGGT 59.458 34.615 0.00 0.00 0.00 4.16
245 247 4.067192 CCCGTGATATGAAGATGCAATGA 58.933 43.478 0.00 0.00 0.00 2.57
290 292 4.158384 GTTGTGCTGAATTCGTATGGTTG 58.842 43.478 0.04 0.00 0.00 3.77
314 316 3.866651 ACTCGGAACTGATCCTGAATTG 58.133 45.455 2.33 0.00 46.98 2.32
329 331 5.716228 TCCTGAATTGCAAATGGTGTCTTAT 59.284 36.000 1.71 0.00 0.00 1.73
355 357 1.688884 AGGAAGCTGAGCTCCCTCC 60.689 63.158 6.35 11.22 39.99 4.30
370 374 2.564062 TCCCTCCGATCAGTTTACGTTT 59.436 45.455 0.00 0.00 0.00 3.60
412 416 4.864334 GCGCAGGCAGCCTACCAT 62.864 66.667 15.64 0.00 41.38 3.55
429 433 2.548904 ACCATATCGTCGAGCTCAGTAC 59.451 50.000 15.40 7.62 0.00 2.73
486 490 1.891919 GTTGCGAGCCTGTGACCAA 60.892 57.895 0.00 0.00 0.00 3.67
491 495 1.238439 CGAGCCTGTGACCAAATTGT 58.762 50.000 0.00 0.00 0.00 2.71
492 496 2.422597 CGAGCCTGTGACCAAATTGTA 58.577 47.619 0.00 0.00 0.00 2.41
517 521 1.846124 AGAAAGGGGAGGCGGTCAA 60.846 57.895 0.00 0.00 0.00 3.18
557 562 9.419297 GAAGTTTTAACCTCAGTCTTTTGTTTT 57.581 29.630 0.00 0.00 0.00 2.43
690 704 3.646736 ATTTCAGGCTAAGGGGTACAC 57.353 47.619 0.00 0.00 0.00 2.90
724 738 6.371548 TCATTTTCAGGTGCAACATCTACTAC 59.628 38.462 3.64 0.00 39.98 2.73
824 838 1.020437 GTGGCTGCTTCTATCTTGCC 58.980 55.000 0.00 0.00 40.62 4.52
827 841 1.091771 GCTGCTTCTATCTTGCCGCA 61.092 55.000 0.00 0.00 37.01 5.69
925 939 1.789464 GATAGGCTGAGATTTGTCGCG 59.211 52.381 0.00 0.00 0.00 5.87
926 940 0.815095 TAGGCTGAGATTTGTCGCGA 59.185 50.000 3.71 3.71 0.00 5.87
931 945 1.253800 CTGAGATTTGTCGCGACGATG 59.746 52.381 31.88 13.67 38.42 3.84
934 948 0.314578 GATTTGTCGCGACGATGCAG 60.315 55.000 31.88 0.00 38.42 4.41
973 987 6.757897 AAACATATTTCGGAGCTGATTTCA 57.242 33.333 0.00 0.00 0.00 2.69
1090 1104 0.321671 TCCTTTTCCTCTGTCGCTGG 59.678 55.000 0.00 0.00 0.00 4.85
1301 1315 0.400213 ACGAGAACAAGAATGGGCCA 59.600 50.000 9.61 9.61 0.00 5.36
1307 1321 3.903090 AGAACAAGAATGGGCCAATTTCA 59.097 39.130 19.27 0.00 0.00 2.69
1356 1370 2.016318 TCACAACTGTTGGTGCTGAAG 58.984 47.619 23.15 4.40 35.04 3.02
1505 1519 7.655490 AGAAATTCCTGATTTTCTGAACACAG 58.345 34.615 13.41 9.30 38.69 3.66
1616 1630 3.648545 ACTACCTTCCAGCCTCCATTATC 59.351 47.826 0.00 0.00 0.00 1.75
1756 1771 3.969976 AGCTATGCTTGGACTATCAAGGA 59.030 43.478 6.71 4.29 46.23 3.36
1848 1863 8.958506 TGATGAACAATGTCAATGTCAATATCA 58.041 29.630 0.00 0.00 0.00 2.15
1882 1898 7.743400 CGATATACTGCATTTTCATGTAGCAAG 59.257 37.037 0.72 0.00 44.76 4.01
2015 2035 2.028930 AGATGACGAGAAGGGTGACAAC 60.029 50.000 0.00 0.00 0.00 3.32
2159 2179 1.001268 CCTATGATGTCTCCGGTCACG 60.001 57.143 0.00 0.00 40.55 4.35
2385 2405 1.471684 GCAAAGACCATCCTTGCTCTG 59.528 52.381 5.15 0.00 0.00 3.35
2454 2474 0.043637 TCCCCCTCAAGTACCGGAAT 59.956 55.000 9.46 0.00 0.00 3.01
2466 2486 2.499205 CGGAATGGAGGCGTGCTA 59.501 61.111 0.00 0.00 0.00 3.49
2520 2540 2.822255 GTCGCATTGGCCGGCTTA 60.822 61.111 28.56 15.26 36.38 3.09
2582 2602 1.026182 GGCTCGATGGCATCAACACA 61.026 55.000 25.88 4.40 41.37 3.72
2684 2704 6.569179 GGTGAAGCCTTTGTGAACTTATTA 57.431 37.500 0.00 0.00 0.00 0.98
2720 2754 8.547967 TCTGATTTGGATAGTACTGTTTGAAC 57.452 34.615 5.39 0.00 0.00 3.18
2722 2756 6.370442 TGATTTGGATAGTACTGTTTGAACCG 59.630 38.462 5.39 0.00 0.00 4.44
2754 2788 9.797556 CAAGATCAAGCAGATAAATGAAATGAA 57.202 29.630 0.00 0.00 37.00 2.57
2760 2794 9.361315 CAAGCAGATAAATGAAATGAAATGTGA 57.639 29.630 0.00 0.00 0.00 3.58
2799 2834 3.203040 ACATCCTCCAGATACCCCTTTTG 59.797 47.826 0.00 0.00 32.37 2.44
2814 2852 6.187682 ACCCCTTTTGATACGATCTCATTTT 58.812 36.000 0.00 0.00 0.00 1.82
2815 2853 6.318900 ACCCCTTTTGATACGATCTCATTTTC 59.681 38.462 0.00 0.00 0.00 2.29
2817 2855 6.422223 CCTTTTGATACGATCTCATTTTCGG 58.578 40.000 0.00 0.00 39.61 4.30
2818 2856 6.037172 CCTTTTGATACGATCTCATTTTCGGT 59.963 38.462 0.00 0.00 39.61 4.69
2858 2896 3.055021 GGTACAGGAGGAAAAGGGAGAAG 60.055 52.174 0.00 0.00 0.00 2.85
2868 2906 1.376649 AAGGGAGAAGCTGGTGGAAT 58.623 50.000 0.00 0.00 0.00 3.01
2906 2944 2.199927 TGCCTACTAAATGGGGCCTA 57.800 50.000 0.84 0.00 43.50 3.93
2973 3012 2.499197 TCGCTGTTGCAAAGGTAATGA 58.501 42.857 0.00 0.00 39.64 2.57
3006 3045 4.202111 TGTGTTTCTCTGACAGAACGATCA 60.202 41.667 6.61 2.26 41.13 2.92
3051 3090 3.543494 CGTTTGATTGTGCGATTCAATCC 59.457 43.478 17.97 7.92 45.88 3.01
3054 3093 2.023673 GATTGTGCGATTCAATCCCCA 58.976 47.619 13.04 0.00 42.79 4.96
3065 3104 4.437682 TTCAATCCCCAGCGATCTTTAT 57.562 40.909 0.00 0.00 0.00 1.40
3066 3105 4.008074 TCAATCCCCAGCGATCTTTATC 57.992 45.455 0.00 0.00 0.00 1.75
3083 3133 4.576216 TTATCGTTTGTGGCAAATGTGT 57.424 36.364 11.90 6.67 0.00 3.72
3088 3138 2.364002 GTTTGTGGCAAATGTGTAGGGT 59.636 45.455 0.00 0.00 0.00 4.34
3094 3144 4.644685 GTGGCAAATGTGTAGGGTGATATT 59.355 41.667 0.00 0.00 0.00 1.28
3221 3271 2.759973 TGATCGAGAAGGCCGGCT 60.760 61.111 28.56 7.30 0.00 5.52
3241 3291 2.108514 CGGCGTCCTCGTGTACCTA 61.109 63.158 0.00 0.00 39.49 3.08
3400 3453 3.933332 CCCAGGTTCGTACTTGAATTCTC 59.067 47.826 7.05 0.00 33.45 2.87
3465 3518 6.211587 TGATGATTGATGGTGGTGAATTTC 57.788 37.500 0.00 0.00 0.00 2.17
3485 3538 1.656095 CGCTGTCCGTTTCAGATTCTC 59.344 52.381 0.00 0.00 35.20 2.87
3536 3589 2.124236 ACGAACAACCCGGCCAAA 60.124 55.556 2.24 0.00 0.00 3.28
3542 3595 1.080839 CAACCCGGCCAAATTCGTG 60.081 57.895 2.24 0.00 0.00 4.35
3668 3721 2.188161 CCTCTACGGCTCCGACCTC 61.188 68.421 15.95 0.00 42.83 3.85
3805 3858 5.676953 TCTGATATACAACGATCGAACGAG 58.323 41.667 24.34 15.12 37.03 4.18
3931 3984 1.550065 AGACGATCATCAAACGCGAG 58.450 50.000 15.93 1.66 0.00 5.03
3943 3996 1.363145 AACGCGAGGAGACGAGAGAG 61.363 60.000 15.93 0.00 36.92 3.20
3945 3998 1.084935 CGCGAGGAGACGAGAGAGAA 61.085 60.000 0.00 0.00 35.31 2.87
4272 4682 0.321671 TCTTGGCCTTCTTGTCCGAG 59.678 55.000 3.32 0.00 33.58 4.63
4273 4683 1.301677 CTTGGCCTTCTTGTCCGAGC 61.302 60.000 3.32 0.00 0.00 5.03
4274 4684 2.436824 GGCCTTCTTGTCCGAGCC 60.437 66.667 0.00 0.00 0.00 4.70
4438 4887 4.463879 CGAGAGGTGGCTGGCTGG 62.464 72.222 2.00 0.00 0.00 4.85
4439 4888 3.325753 GAGAGGTGGCTGGCTGGT 61.326 66.667 2.00 0.00 0.00 4.00
4440 4889 2.856000 AGAGGTGGCTGGCTGGTT 60.856 61.111 2.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.225376 AATTGGCGCGAAGACGAACA 61.225 50.000 12.10 0.00 42.66 3.18
2 3 0.789383 CAATTGGCGCGAAGACGAAC 60.789 55.000 12.10 0.00 42.66 3.95
3 4 1.495509 CAATTGGCGCGAAGACGAA 59.504 52.632 12.10 0.00 42.66 3.85
4 5 2.387445 CCAATTGGCGCGAAGACGA 61.387 57.895 12.10 0.00 42.66 4.20
5 6 2.098298 CCAATTGGCGCGAAGACG 59.902 61.111 12.10 1.29 42.93 4.18
15 16 3.039202 GACCTGTCGCGCCAATTGG 62.039 63.158 20.81 20.81 38.53 3.16
17 18 1.369091 GATGACCTGTCGCGCCAATT 61.369 55.000 0.00 0.00 0.00 2.32
18 19 1.815421 GATGACCTGTCGCGCCAAT 60.815 57.895 0.00 0.00 0.00 3.16
19 20 1.600511 TAGATGACCTGTCGCGCCAA 61.601 55.000 0.00 0.00 0.00 4.52
20 21 2.004808 CTAGATGACCTGTCGCGCCA 62.005 60.000 0.00 0.00 0.00 5.69
21 22 1.299468 CTAGATGACCTGTCGCGCC 60.299 63.158 0.00 0.00 0.00 6.53
23 24 1.018148 AGACTAGATGACCTGTCGCG 58.982 55.000 0.00 0.00 34.92 5.87
24 25 6.503589 AATATAGACTAGATGACCTGTCGC 57.496 41.667 0.00 0.00 34.92 5.19
77 78 2.704572 ACTCTTAGCACATCAGCAACC 58.295 47.619 0.00 0.00 36.85 3.77
90 91 5.592054 TGATCGGTAAGCATGAACTCTTAG 58.408 41.667 0.00 0.00 0.00 2.18
116 117 1.133915 ACATGACAAACTCCACCCGTT 60.134 47.619 0.00 0.00 0.00 4.44
138 140 5.125356 TGACCACATCGAAGCAATGATATT 58.875 37.500 0.00 0.00 0.00 1.28
146 148 1.805943 CAACATGACCACATCGAAGCA 59.194 47.619 0.00 0.00 34.15 3.91
192 194 0.551377 TTTCAGGATACCCAGGGGCA 60.551 55.000 11.37 0.00 39.32 5.36
197 199 4.301072 TGGAAAGTTTCAGGATACCCAG 57.699 45.455 17.16 0.00 33.88 4.45
314 316 4.811024 TCGAGATCATAAGACACCATTTGC 59.189 41.667 0.00 0.00 0.00 3.68
329 331 0.743688 GCTCAGCTTCCTCGAGATCA 59.256 55.000 15.71 0.00 0.00 2.92
370 374 0.112412 GGGTGGCTGAAGGGAGAAAA 59.888 55.000 0.00 0.00 0.00 2.29
412 416 1.140452 AGGGTACTGAGCTCGACGATA 59.860 52.381 9.64 0.00 0.00 2.92
429 433 9.681062 TTTACTGAATAAGAAGGTAAATGAGGG 57.319 33.333 0.00 0.00 30.62 4.30
469 473 0.537143 ATTTGGTCACAGGCTCGCAA 60.537 50.000 0.00 0.00 0.00 4.85
486 490 5.132816 CCTCCCCTTTCTGAGGTATACAATT 59.867 44.000 5.01 0.00 44.71 2.32
517 521 8.040727 AGGTTAAAACTTCTTCAGTTGCAAAAT 58.959 29.630 0.00 0.00 45.77 1.82
544 548 4.440112 GGTGTCCCAGAAAACAAAAGACTG 60.440 45.833 0.00 0.00 0.00 3.51
557 562 0.191064 AGAGGTTCAGGTGTCCCAGA 59.809 55.000 0.00 0.00 0.00 3.86
724 738 5.809051 GGTCTAGTTAAGGGTCAAATGTACG 59.191 44.000 0.00 0.00 0.00 3.67
824 838 1.081242 GGCCACATGTTTCTGTGCG 60.081 57.895 0.00 0.00 44.16 5.34
827 841 1.143684 AGACTGGCCACATGTTTCTGT 59.856 47.619 0.00 0.00 0.00 3.41
917 931 2.379634 CCTGCATCGTCGCGACAAA 61.380 57.895 35.71 24.47 39.18 2.83
925 939 0.387878 CCTCTATCGCCTGCATCGTC 60.388 60.000 8.11 0.00 0.00 4.20
926 940 1.109920 ACCTCTATCGCCTGCATCGT 61.110 55.000 8.11 0.44 0.00 3.73
931 945 5.962433 TGTTTATATACCTCTATCGCCTGC 58.038 41.667 0.00 0.00 0.00 4.85
960 974 2.793790 CGATCTTCTGAAATCAGCTCCG 59.206 50.000 5.53 1.95 43.46 4.63
973 987 1.856629 TCCCCGTTAACCGATCTTCT 58.143 50.000 0.00 0.00 39.56 2.85
1090 1104 0.108329 TTCGTTCCCGGCAAGATCTC 60.108 55.000 0.00 0.00 33.95 2.75
1301 1315 5.009310 GGACCCGTTTAGTTCTTGTGAAATT 59.991 40.000 0.00 0.00 33.52 1.82
1307 1321 2.436911 ACTGGACCCGTTTAGTTCTTGT 59.563 45.455 0.00 0.00 0.00 3.16
1356 1370 5.994668 AGAAATCTCCTGTTTCTTGAGTGAC 59.005 40.000 0.00 0.00 41.75 3.67
1406 1420 1.269012 AACCCTCCGTCGGTTTATCA 58.731 50.000 11.88 0.00 40.84 2.15
1568 1582 2.846193 TCGGCATATCTTTAAGCACCC 58.154 47.619 0.00 0.00 0.00 4.61
1697 1712 9.653287 CTTTACATGAAGGTACTCAATTACTCA 57.347 33.333 0.00 0.00 38.49 3.41
1781 1796 0.957395 CACCTTGCTCACTGGCGATT 60.957 55.000 0.00 0.00 34.52 3.34
1882 1898 3.062042 CCTGGATTTTGAAGCAAGCAAC 58.938 45.455 0.00 0.00 0.00 4.17
1899 1919 4.650588 TGATAATTCATTTGAAGGCCCTGG 59.349 41.667 0.00 0.00 37.48 4.45
2015 2035 2.038952 TGCCATGATAAGATCCCCTTCG 59.961 50.000 0.00 0.00 36.34 3.79
2159 2179 4.240096 CAGCTGAAATGTCACCAATTTCC 58.760 43.478 8.42 0.00 34.40 3.13
2168 2188 2.294233 GGAAGCAACAGCTGAAATGTCA 59.706 45.455 23.35 0.00 38.93 3.58
2182 2202 1.667236 CACTGTCACTGTGGAAGCAA 58.333 50.000 8.11 0.00 31.27 3.91
2309 2329 5.167121 CCACTCTCGCATCCTAAATAGATG 58.833 45.833 0.00 0.00 43.31 2.90
2385 2405 2.610859 TTGGAGTCAGGGGAGGCC 60.611 66.667 0.00 0.00 0.00 5.19
2454 2474 1.808411 CTCTTTTTAGCACGCCTCCA 58.192 50.000 0.00 0.00 0.00 3.86
2466 2486 2.200337 GGTGTGCCCGGCTCTTTTT 61.200 57.895 11.61 0.00 0.00 1.94
2490 2510 0.460284 ATGCGACAAGATCCACCGAC 60.460 55.000 0.00 0.00 0.00 4.79
2520 2540 1.207329 GAAAGGACAGATACAGGGCGT 59.793 52.381 0.00 0.00 0.00 5.68
2526 2546 5.497464 TGATGGTTGAAAGGACAGATACA 57.503 39.130 0.00 0.00 0.00 2.29
2532 2552 3.334691 GTCGATGATGGTTGAAAGGACA 58.665 45.455 0.00 0.00 0.00 4.02
2565 2585 1.202110 GCTTGTGTTGATGCCATCGAG 60.202 52.381 0.00 0.00 0.00 4.04
2582 2602 0.607489 AGCCATCTGTTTCAGCGCTT 60.607 50.000 7.50 0.00 28.85 4.68
2704 2724 4.745649 AGAGCGGTTCAAACAGTACTATC 58.254 43.478 0.00 0.00 0.00 2.08
2714 2748 2.038426 TGATCTTGGAGAGCGGTTCAAA 59.962 45.455 0.00 0.00 32.29 2.69
2720 2754 0.107993 TGCTTGATCTTGGAGAGCGG 60.108 55.000 0.00 0.00 32.29 5.52
2722 2756 2.687700 TCTGCTTGATCTTGGAGAGC 57.312 50.000 5.86 0.00 0.00 4.09
2781 2816 4.503296 CGTATCAAAAGGGGTATCTGGAGG 60.503 50.000 0.00 0.00 0.00 4.30
2782 2817 4.344102 TCGTATCAAAAGGGGTATCTGGAG 59.656 45.833 0.00 0.00 0.00 3.86
2784 2819 4.682778 TCGTATCAAAAGGGGTATCTGG 57.317 45.455 0.00 0.00 0.00 3.86
2791 2826 6.511767 CGAAAATGAGATCGTATCAAAAGGGG 60.512 42.308 0.00 0.00 34.48 4.79
2792 2827 6.422223 CGAAAATGAGATCGTATCAAAAGGG 58.578 40.000 0.00 0.00 34.48 3.95
2799 2834 7.169308 ACAACATACCGAAAATGAGATCGTATC 59.831 37.037 0.00 0.00 37.36 2.24
2814 2852 5.998981 ACCTGAATTTACAACAACATACCGA 59.001 36.000 0.00 0.00 0.00 4.69
2815 2853 6.249035 ACCTGAATTTACAACAACATACCG 57.751 37.500 0.00 0.00 0.00 4.02
2817 2855 8.234546 CCTGTACCTGAATTTACAACAACATAC 58.765 37.037 0.00 0.00 0.00 2.39
2818 2856 8.158132 TCCTGTACCTGAATTTACAACAACATA 58.842 33.333 0.00 0.00 0.00 2.29
2858 2896 0.379669 CAGCGATCAATTCCACCAGC 59.620 55.000 0.00 0.00 0.00 4.85
2868 2906 2.603110 GCAAACGAGATACAGCGATCAA 59.397 45.455 0.00 0.00 0.00 2.57
2973 3012 7.121168 TCTGTCAGAGAAACACAACAAGAATTT 59.879 33.333 0.00 0.00 0.00 1.82
3006 3045 0.036022 GGCTCACTGGTTTCTGCTCT 59.964 55.000 0.00 0.00 0.00 4.09
3065 3104 2.292016 CCTACACATTTGCCACAAACGA 59.708 45.455 0.00 0.00 0.00 3.85
3066 3105 2.606795 CCCTACACATTTGCCACAAACG 60.607 50.000 0.00 0.00 0.00 3.60
3072 3122 2.897271 ATCACCCTACACATTTGCCA 57.103 45.000 0.00 0.00 0.00 4.92
3083 3133 2.567169 CTCCATCGCCAATATCACCCTA 59.433 50.000 0.00 0.00 0.00 3.53
3088 3138 3.552890 CGTCTTCTCCATCGCCAATATCA 60.553 47.826 0.00 0.00 0.00 2.15
3094 3144 1.215382 CACGTCTTCTCCATCGCCA 59.785 57.895 0.00 0.00 0.00 5.69
3221 3271 4.409218 GTACACGAGGACGCCGCA 62.409 66.667 0.00 0.00 43.96 5.69
3400 3453 4.362279 CAAGAATGTTAAATCCGCCATGG 58.638 43.478 7.63 7.63 40.09 3.66
3465 3518 1.656095 GAGAATCTGAAACGGACAGCG 59.344 52.381 0.00 0.00 35.61 5.18
3485 3538 3.803082 CGCACGCCAATGTCCCTG 61.803 66.667 0.00 0.00 0.00 4.45
3536 3589 2.677228 CCCTTGAGCCCCACGAAT 59.323 61.111 0.00 0.00 0.00 3.34
3542 3595 3.793888 CCGTACCCCTTGAGCCCC 61.794 72.222 0.00 0.00 0.00 5.80
3602 3655 4.530946 TCGAGGTATTTCTGGTTCTCCTTT 59.469 41.667 0.00 0.00 34.23 3.11
3750 3803 9.710900 ATGAAGTTAAAAGAAACCAAATGATCC 57.289 29.630 0.00 0.00 0.00 3.36
3789 3842 4.725359 TCAATTCTCGTTCGATCGTTGTA 58.275 39.130 15.94 5.01 0.00 2.41
3790 3843 3.571571 TCAATTCTCGTTCGATCGTTGT 58.428 40.909 15.94 0.00 0.00 3.32
3805 3858 6.321717 TGGTTGCAATATTTCGTCTCAATTC 58.678 36.000 0.59 0.00 0.00 2.17
3931 3984 1.720694 CGCCCTTCTCTCTCGTCTCC 61.721 65.000 0.00 0.00 0.00 3.71
4438 4887 4.410400 CCTCCTCCCCACCGCAAC 62.410 72.222 0.00 0.00 0.00 4.17
4439 4888 4.649705 TCCTCCTCCCCACCGCAA 62.650 66.667 0.00 0.00 0.00 4.85
4445 4894 0.470080 GATCATCGTCCTCCTCCCCA 60.470 60.000 0.00 0.00 0.00 4.96
4447 4896 1.528292 CCGATCATCGTCCTCCTCCC 61.528 65.000 6.25 0.00 38.40 4.30
4457 4906 2.256764 CGCCCTCTCCGATCATCG 59.743 66.667 0.00 0.00 40.07 3.84
4481 4930 0.680921 CTCATCCCACCGCAAACCAT 60.681 55.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.