Multiple sequence alignment - TraesCS3D01G133300

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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 TraesCS3D01G133300 chr3D 100.000 3234 0 0 1 3234 92815250 92812017 0.000000e+00 5973.0
1 TraesCS3D01G133300 chr3D 82.905 895 127 15 327 1216 92896988 92896115 0.000000e+00 782.0
2 TraesCS3D01G133300 chr3D 86.726 678 78 10 1569 2238 92895859 92895186 0.000000e+00 743.0
3 TraesCS3D01G133300 chr3D 77.746 692 117 20 1575 2248 42679652 42678980 1.090000e-104 390.0
4 TraesCS3D01G133300 chr3D 85.635 181 20 5 1373 1553 92896093 92895919 5.510000e-43 185.0
5 TraesCS3D01G133300 chr3B 91.105 1574 128 9 1 1566 143602859 143604428 0.000000e+00 2121.0
6 TraesCS3D01G133300 chr3B 88.466 1682 162 17 1564 3234 143953605 143955265 0.000000e+00 2002.0
7 TraesCS3D01G133300 chr3B 88.000 1275 109 23 1564 2832 143604468 143605704 0.000000e+00 1467.0
8 TraesCS3D01G133300 chr3B 90.088 797 75 3 773 1566 143952768 143953563 0.000000e+00 1031.0
9 TraesCS3D01G133300 chr3B 88.054 812 85 5 1581 2382 143568175 143568984 0.000000e+00 952.0
10 TraesCS3D01G133300 chr3B 82.960 892 119 24 327 1210 143509037 143509903 0.000000e+00 774.0
11 TraesCS3D01G133300 chr3B 86.880 686 73 13 1569 2238 143510165 143510849 0.000000e+00 752.0
12 TraesCS3D01G133300 chr3B 89.737 419 22 10 2831 3234 143614774 143615186 1.720000e-142 516.0
13 TraesCS3D01G133300 chr3B 76.700 691 116 27 1575 2237 66470553 66469880 3.090000e-90 342.0
14 TraesCS3D01G133300 chr3B 82.094 363 43 9 255 610 143513719 143514066 1.140000e-74 291.0
15 TraesCS3D01G133300 chr3B 93.939 66 4 0 724 789 143522696 143522761 2.050000e-17 100.0
16 TraesCS3D01G133300 chr3A 82.190 904 120 23 323 1216 547181418 547182290 0.000000e+00 739.0
17 TraesCS3D01G133300 chr3A 86.510 682 74 13 1573 2238 547182553 547183232 0.000000e+00 734.0
18 TraesCS3D01G133300 chr3A 76.890 688 114 22 1575 2237 54232681 54232014 6.640000e-92 348.0
19 TraesCS3D01G133300 chr3A 87.273 165 17 4 1405 1566 547182338 547182501 5.510000e-43 185.0
20 TraesCS3D01G133300 chr3A 92.157 51 4 0 2737 2787 738077846 738077796 4.480000e-09 73.1
21 TraesCS3D01G133300 chr2D 89.583 96 10 0 1212 1307 82095178 82095083 4.380000e-24 122.0
22 TraesCS3D01G133300 chr2D 93.750 64 4 0 1 64 385519199 385519136 2.660000e-16 97.1
23 TraesCS3D01G133300 chr7D 93.750 64 4 0 1 64 31180597 31180534 2.660000e-16 97.1
24 TraesCS3D01G133300 chr6A 93.750 64 4 0 1 64 241725543 241725480 2.660000e-16 97.1
25 TraesCS3D01G133300 chr6D 93.750 64 3 1 1 64 153451205 153451143 9.550000e-16 95.3
26 TraesCS3D01G133300 chr4D 94.828 58 3 0 1 58 300084566 300084623 1.240000e-14 91.6
27 TraesCS3D01G133300 chr4D 94.828 58 3 0 1 58 394924755 394924812 1.240000e-14 91.6
28 TraesCS3D01G133300 chr4B 92.188 64 5 0 1 64 205355904 205355841 1.240000e-14 91.6
29 TraesCS3D01G133300 chr5B 91.935 62 5 0 1 62 633406855 633406916 1.600000e-13 87.9
30 TraesCS3D01G133300 chr4A 91.111 45 4 0 2731 2775 615210111 615210155 9.690000e-06 62.1
31 TraesCS3D01G133300 chrUn 96.875 32 1 0 2742 2773 419686496 419686527 2.000000e-03 54.7
32 TraesCS3D01G133300 chr5A 86.000 50 7 0 2738 2787 556157273 556157224 2.000000e-03 54.7
33 TraesCS3D01G133300 chr2A 96.875 32 1 0 2742 2773 24671058 24671027 2.000000e-03 54.7
34 TraesCS3D01G133300 chr2A 96.875 32 1 0 2742 2773 24684751 24684720 2.000000e-03 54.7
35 TraesCS3D01G133300 chr2A 96.875 32 1 0 2742 2773 24697377 24697346 2.000000e-03 54.7
36 TraesCS3D01G133300 chr2A 96.875 32 1 0 2742 2773 25665962 25665993 2.000000e-03 54.7


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 TraesCS3D01G133300 chr3D 92812017 92815250 3233 True 5973.000000 5973 100.000000 1 3234 1 chr3D.!!$R2 3233
1 TraesCS3D01G133300 chr3D 92895186 92896988 1802 True 570.000000 782 85.088667 327 2238 3 chr3D.!!$R3 1911
2 TraesCS3D01G133300 chr3D 42678980 42679652 672 True 390.000000 390 77.746000 1575 2248 1 chr3D.!!$R1 673
3 TraesCS3D01G133300 chr3B 143602859 143605704 2845 False 1794.000000 2121 89.552500 1 2832 2 chr3B.!!$F5 2831
4 TraesCS3D01G133300 chr3B 143952768 143955265 2497 False 1516.500000 2002 89.277000 773 3234 2 chr3B.!!$F6 2461
5 TraesCS3D01G133300 chr3B 143568175 143568984 809 False 952.000000 952 88.054000 1581 2382 1 chr3B.!!$F2 801
6 TraesCS3D01G133300 chr3B 143509037 143514066 5029 False 605.666667 774 83.978000 255 2238 3 chr3B.!!$F4 1983
7 TraesCS3D01G133300 chr3B 66469880 66470553 673 True 342.000000 342 76.700000 1575 2237 1 chr3B.!!$R1 662
8 TraesCS3D01G133300 chr3A 547181418 547183232 1814 False 552.666667 739 85.324333 323 2238 3 chr3A.!!$F1 1915
9 TraesCS3D01G133300 chr3A 54232014 54232681 667 True 348.000000 348 76.890000 1575 2237 1 chr3A.!!$R1 662

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
226 227 1.144503 GGCTGGAGATGGGATCAACAT 59.855 52.381 2.16 2.16 0.00 2.71 F
1030 1040 2.076863 GTTTTCACCCATGGTCTCTCG 58.923 52.381 11.73 0.00 31.02 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1659 0.17576 AATCCACCTCGTCATGGTCG 59.824 55.0 0.0 0.0 37.27 4.79 R
2635 3218 0.17691 TCAGTGCAACACCGACTTGA 59.823 50.0 0.0 0.0 41.43 3.02 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
35 36 9.118300 AGAGAAATGATAACCATGAATCTTGTC 57.882 33.333 0.00 0.00 35.24 3.18
89 90 9.427821 ACATTTATGAGAAGGTCACTATAGACT 57.572 33.333 6.78 0.00 38.28 3.24
124 125 2.883026 TGAGTTTATTGGGTTGGTGGG 58.117 47.619 0.00 0.00 0.00 4.61
142 143 1.474143 GGGAGCCTAGATTGTGTGCTC 60.474 57.143 6.40 6.40 45.89 4.26
154 155 4.776795 TTGTGTGCTCGTACTTATCTGA 57.223 40.909 0.00 0.00 0.00 3.27
166 167 4.295905 ACTTATCTGATTACCCTCCCCA 57.704 45.455 0.00 0.00 0.00 4.96
167 168 4.235372 ACTTATCTGATTACCCTCCCCAG 58.765 47.826 0.00 0.00 0.00 4.45
168 169 2.897823 ATCTGATTACCCTCCCCAGT 57.102 50.000 0.00 0.00 0.00 4.00
226 227 1.144503 GGCTGGAGATGGGATCAACAT 59.855 52.381 2.16 2.16 0.00 2.71
233 234 6.493166 TGGAGATGGGATCAACATTTAAACT 58.507 36.000 3.96 0.00 0.00 2.66
259 260 7.928873 AGGAGATGAAACTAAGTTAAATGGGA 58.071 34.615 0.00 0.00 0.00 4.37
275 276 8.547894 GTTAAATGGGAATAAAATCAAATCGGC 58.452 33.333 0.00 0.00 0.00 5.54
285 286 8.715191 ATAAAATCAAATCGGCATTTAAAGCA 57.285 26.923 10.45 0.00 30.51 3.91
304 305 7.565323 AAAGCAAGAGATCTGGTGAAATATC 57.435 36.000 0.00 0.00 0.00 1.63
305 306 6.244552 AGCAAGAGATCTGGTGAAATATCA 57.755 37.500 0.00 0.00 0.00 2.15
429 431 9.856162 ATTACCTGAGTTTTCCAACTACTTTTA 57.144 29.630 0.00 0.00 43.79 1.52
431 433 6.544931 ACCTGAGTTTTCCAACTACTTTTACC 59.455 38.462 0.00 0.00 43.79 2.85
486 489 7.662669 AGGGAACAATGAATTCTTCAAATTTGG 59.337 33.333 17.90 3.33 43.95 3.28
487 490 7.661027 GGGAACAATGAATTCTTCAAATTTGGA 59.339 33.333 17.90 8.77 43.95 3.53
555 559 8.276325 CACCATCATTTTAAGATAAGTAGCGAC 58.724 37.037 0.00 0.00 0.00 5.19
556 560 7.985184 ACCATCATTTTAAGATAAGTAGCGACA 59.015 33.333 0.00 0.00 0.00 4.35
807 814 9.378551 ACATTACTTTCTAGTGATTCGCAATTA 57.621 29.630 0.00 0.00 35.78 1.40
935 943 5.186198 GGTCTAATATGTTGAGGCAGTGTT 58.814 41.667 0.00 0.00 0.00 3.32
941 949 3.386768 TGTTGAGGCAGTGTTAGACTC 57.613 47.619 0.00 0.00 41.64 3.36
951 960 4.484236 CAGTGTTAGACTCAGCTCAGAAG 58.516 47.826 0.00 0.00 29.75 2.85
982 991 4.701765 ACAAGATGCACACATAGATCTCC 58.298 43.478 0.00 0.00 36.35 3.71
1014 1024 7.224297 TCCAGTTAGCAATGACTTCTAGTTTT 58.776 34.615 0.00 0.00 0.00 2.43
1017 1027 8.012241 CAGTTAGCAATGACTTCTAGTTTTCAC 58.988 37.037 0.00 0.00 0.00 3.18
1024 1034 4.104102 TGACTTCTAGTTTTCACCCATGGT 59.896 41.667 11.73 0.00 35.62 3.55
1030 1040 2.076863 GTTTTCACCCATGGTCTCTCG 58.923 52.381 11.73 0.00 31.02 4.04
1220 1232 3.643792 GCACCAGATATGGTACTTCCTCT 59.356 47.826 12.63 0.00 40.85 3.69
1233 1245 8.195165 TGGTACTTCCTCTGATCCATAATAAG 57.805 38.462 0.00 0.00 37.07 1.73
1245 1257 5.818136 TCCATAATAAGTGTTGCAGCTTC 57.182 39.130 1.17 0.00 0.00 3.86
1251 1263 2.526304 AGTGTTGCAGCTTCGAACTA 57.474 45.000 1.17 0.00 0.00 2.24
1297 1309 9.515020 TCAAAGTTGTGACACTTTTATTGAATC 57.485 29.630 7.20 0.00 43.17 2.52
1298 1310 9.520204 CAAAGTTGTGACACTTTTATTGAATCT 57.480 29.630 7.20 0.00 43.17 2.40
1341 1353 5.837770 TTCTCCTAAGCATGGATGATCAT 57.162 39.130 8.25 8.25 32.56 2.45
1537 1549 4.940463 TGTAACGGCCTTCTATGTATGTC 58.060 43.478 0.00 0.00 0.00 3.06
1557 1570 9.914131 GTATGTCTTGACACATCTTATATGCTA 57.086 33.333 5.53 0.00 38.07 3.49
1561 1574 7.439356 GTCTTGACACATCTTATATGCTAAGCA 59.561 37.037 0.00 0.00 44.86 3.91
1690 1749 0.549902 TCTTCCTCAATGGCCAGGGA 60.550 55.000 13.05 13.23 35.26 4.20
1837 1920 5.783111 ACTCAGCATATATATCACGTGCAA 58.217 37.500 11.67 0.72 38.23 4.08
1839 1922 5.537188 TCAGCATATATATCACGTGCAACA 58.463 37.500 11.67 0.00 38.23 3.33
1894 1985 0.615850 GGGTGCTCAAGAACCTAGCT 59.384 55.000 7.12 0.00 43.60 3.32
1901 1992 1.078759 CAAGAACCTAGCTGGACGCG 61.079 60.000 3.53 3.53 45.59 6.01
2213 2304 0.727398 GTTCAACTACCATCTGCCGC 59.273 55.000 0.00 0.00 0.00 6.53
2258 2349 0.320771 AGCTTTCTGTGTGGCCGTAG 60.321 55.000 0.00 0.00 0.00 3.51
2260 2351 1.876416 GCTTTCTGTGTGGCCGTAGAA 60.876 52.381 0.00 2.35 0.00 2.10
2322 2413 5.831525 TCTACTTCAACCGATCCTAGCAATA 59.168 40.000 0.00 0.00 0.00 1.90
2323 2414 5.552870 ACTTCAACCGATCCTAGCAATAT 57.447 39.130 0.00 0.00 0.00 1.28
2324 2415 6.665992 ACTTCAACCGATCCTAGCAATATA 57.334 37.500 0.00 0.00 0.00 0.86
2325 2416 6.456501 ACTTCAACCGATCCTAGCAATATAC 58.543 40.000 0.00 0.00 0.00 1.47
2326 2417 6.041637 ACTTCAACCGATCCTAGCAATATACA 59.958 38.462 0.00 0.00 0.00 2.29
2327 2418 6.413783 TCAACCGATCCTAGCAATATACAA 57.586 37.500 0.00 0.00 0.00 2.41
2344 2462 7.925703 ATATACAACGGTTGAAGTAGATTCG 57.074 36.000 26.39 0.00 41.14 3.34
2466 2602 8.893563 TTTTCAACAAAGGATCCATATAAGGT 57.106 30.769 15.82 0.00 0.00 3.50
2490 2626 9.654663 GGTTCAGTAGTTCATTAACTCTATTGT 57.345 33.333 0.00 0.00 42.42 2.71
2529 2667 3.193267 GTCCATTGACAATTGGCTTGCTA 59.807 43.478 13.62 0.00 41.37 3.49
2532 2670 4.558178 CATTGACAATTGGCTTGCTAACA 58.442 39.130 13.62 0.00 38.50 2.41
2561 2699 4.906618 ACTTCAGGTGGTTTACGATGAAT 58.093 39.130 0.00 0.00 36.04 2.57
2605 3179 7.759489 TTATTAGCACACAACCTCTTGATTT 57.241 32.000 0.00 0.00 0.00 2.17
2620 3203 7.174253 ACCTCTTGATTTTGCGAAGTATTTACA 59.826 33.333 0.00 0.00 0.00 2.41
2622 3205 9.393249 CTCTTGATTTTGCGAAGTATTTACAAA 57.607 29.630 0.00 0.00 33.33 2.83
2630 3213 9.464714 TTTGCGAAGTATTTACAAAAATTAGCA 57.535 25.926 0.00 0.00 36.67 3.49
2718 3301 8.810652 TTCAACTAATCTTGTTGCATAAAACC 57.189 30.769 0.00 0.00 43.00 3.27
2735 3318 9.209175 GCATAAAACCACCAACAACATTTAATA 57.791 29.630 0.00 0.00 0.00 0.98
2792 3375 1.271488 GGAACCCACCCGTCAATGTTA 60.271 52.381 0.00 0.00 0.00 2.41
2868 3451 1.393539 CACGTTAGCATCAACCTTCCG 59.606 52.381 0.00 0.00 0.00 4.30
2876 3459 0.909610 ATCAACCTTCCGCCTCCTCA 60.910 55.000 0.00 0.00 0.00 3.86
2909 3494 2.238521 TGGCATTTCCTCAAACACCTC 58.761 47.619 0.00 0.00 35.26 3.85
2911 3496 2.151202 GCATTTCCTCAAACACCTCGA 58.849 47.619 0.00 0.00 0.00 4.04
2912 3497 2.160417 GCATTTCCTCAAACACCTCGAG 59.840 50.000 5.13 5.13 0.00 4.04
2913 3498 3.403038 CATTTCCTCAAACACCTCGAGT 58.597 45.455 12.31 0.00 0.00 4.18
2921 3506 2.981302 CACCTCGAGTGCATGGGA 59.019 61.111 12.31 0.00 40.28 4.37
2922 3507 1.153489 CACCTCGAGTGCATGGGAG 60.153 63.158 12.31 0.00 40.28 4.30
2923 3508 2.503061 CCTCGAGTGCATGGGAGG 59.497 66.667 12.31 13.35 40.05 4.30
2924 3509 2.503061 CTCGAGTGCATGGGAGGG 59.497 66.667 3.62 0.00 0.00 4.30
2925 3510 2.038813 TCGAGTGCATGGGAGGGA 59.961 61.111 0.00 0.00 0.00 4.20
2929 3514 2.825836 GTGCATGGGAGGGAAGCG 60.826 66.667 0.00 0.00 0.00 4.68
2965 3550 0.603065 GCACAACTGAACATTCCCCC 59.397 55.000 0.00 0.00 0.00 5.40
2966 3551 0.881118 CACAACTGAACATTCCCCCG 59.119 55.000 0.00 0.00 0.00 5.73
2968 3553 0.609131 CAACTGAACATTCCCCCGCT 60.609 55.000 0.00 0.00 0.00 5.52
2969 3554 0.322546 AACTGAACATTCCCCCGCTC 60.323 55.000 0.00 0.00 0.00 5.03
2970 3555 1.201429 ACTGAACATTCCCCCGCTCT 61.201 55.000 0.00 0.00 0.00 4.09
2972 3557 0.322456 TGAACATTCCCCCGCTCTTG 60.322 55.000 0.00 0.00 0.00 3.02
2973 3558 0.035439 GAACATTCCCCCGCTCTTGA 60.035 55.000 0.00 0.00 0.00 3.02
3069 4966 1.847818 TCAACGACAAGAAGGACGTG 58.152 50.000 0.00 0.00 38.92 4.49
3089 4986 1.302752 TGAGCCGTCTTTGCTGCAT 60.303 52.632 1.84 0.00 39.69 3.96
3104 5001 2.526993 GCATGCTGCTCGCTCTCTG 61.527 63.158 11.37 0.00 40.96 3.35
3105 5002 2.202905 ATGCTGCTCGCTCTCTGC 60.203 61.111 0.00 0.00 40.11 4.26
3114 5011 2.496817 GCTCTCTGCGTTCCCGAT 59.503 61.111 0.00 0.00 35.63 4.18
3128 5025 2.944557 CGATCGAGTGGACGTGCG 60.945 66.667 10.26 0.00 34.70 5.34
3157 5054 1.164411 TAAGTGGTTTCTGCATGCCG 58.836 50.000 16.68 9.39 0.00 5.69
3164 5061 1.368345 TTTCTGCATGCCGTCGATGG 61.368 55.000 19.87 19.87 0.00 3.51
3184 5081 4.742201 CACCAGTGTCCGGGAGCG 62.742 72.222 0.00 0.00 0.00 5.03
3225 5122 3.059884 CGCCAAGCTCAACGATGTATAT 58.940 45.455 0.00 0.00 0.00 0.86
3226 5123 3.120889 CGCCAAGCTCAACGATGTATATG 60.121 47.826 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.192642 TGATGACAAGATTCATGGTTATCATTT 57.807 29.630 0.00 0.00 36.30 2.32
56 57 8.328758 AGTGACCTTCTCATAAATGTAATGGAA 58.671 33.333 0.00 0.00 0.00 3.53
76 77 6.216046 AGGAGGGAGTATAGTCTATAGTGACC 59.784 46.154 11.30 12.26 37.66 4.02
124 125 1.134965 ACGAGCACACAATCTAGGCTC 60.135 52.381 0.00 0.00 45.61 4.70
142 143 4.220163 GGGGAGGGTAATCAGATAAGTACG 59.780 50.000 0.00 0.00 0.00 3.67
154 155 6.858792 ATTAATTACACTGGGGAGGGTAAT 57.141 37.500 4.23 4.23 37.88 1.89
190 191 4.269183 TCCAGCCAATCGTTTATGTTGAT 58.731 39.130 0.00 0.00 0.00 2.57
198 199 1.683011 CCCATCTCCAGCCAATCGTTT 60.683 52.381 0.00 0.00 0.00 3.60
199 200 0.107017 CCCATCTCCAGCCAATCGTT 60.107 55.000 0.00 0.00 0.00 3.85
233 234 9.053472 TCCCATTTAACTTAGTTTCATCTCCTA 57.947 33.333 1.94 0.00 0.00 2.94
253 254 6.232581 TGCCGATTTGATTTTATTCCCATT 57.767 33.333 0.00 0.00 0.00 3.16
254 255 5.867903 TGCCGATTTGATTTTATTCCCAT 57.132 34.783 0.00 0.00 0.00 4.00
259 260 9.160496 TGCTTTAAATGCCGATTTGATTTTATT 57.840 25.926 7.04 0.00 33.63 1.40
268 269 5.643379 TCTCTTGCTTTAAATGCCGATTT 57.357 34.783 7.04 0.00 35.83 2.17
275 276 6.748333 TCACCAGATCTCTTGCTTTAAATG 57.252 37.500 0.00 0.00 0.00 2.32
283 284 6.297694 GTGATATTTCACCAGATCTCTTGC 57.702 41.667 5.07 0.00 45.45 4.01
323 325 3.305720 AGGGACCATGATTACTAAGCGA 58.694 45.455 0.00 0.00 0.00 4.93
330 332 3.741388 CGAGACCAAGGGACCATGATTAC 60.741 52.174 0.00 0.00 0.00 1.89
402 404 9.856162 AAAAGTAGTTGGAAAACTCAGGTAATA 57.144 29.630 0.00 0.00 34.37 0.98
404 406 9.112725 GTAAAAGTAGTTGGAAAACTCAGGTAA 57.887 33.333 0.00 0.00 34.37 2.85
409 411 6.347696 TCGGTAAAAGTAGTTGGAAAACTCA 58.652 36.000 0.00 0.00 34.37 3.41
429 431 8.114102 TGATAATACCTACTATCTCCATTCGGT 58.886 37.037 0.00 0.00 0.00 4.69
431 433 8.957466 TGTGATAATACCTACTATCTCCATTCG 58.043 37.037 0.00 0.00 0.00 3.34
492 496 9.696917 GAAATTACCATTTCAATCTTGTCTTGT 57.303 29.630 3.32 0.00 45.45 3.16
595 601 5.511202 CCCCATTGCTTTTGTATGAAGTTGT 60.511 40.000 0.00 0.00 0.00 3.32
713 720 9.968870 AGTCTTTTGTTATTTTTGGCGTATTAA 57.031 25.926 0.00 0.00 0.00 1.40
719 726 8.568732 TTAGAAGTCTTTTGTTATTTTTGGCG 57.431 30.769 0.00 0.00 0.00 5.69
910 918 5.104360 ACACTGCCTCAACATATTAGACCAT 60.104 40.000 0.00 0.00 0.00 3.55
927 935 1.273606 TGAGCTGAGTCTAACACTGCC 59.726 52.381 0.00 0.00 35.07 4.85
935 943 3.501349 ACCAACTTCTGAGCTGAGTCTA 58.499 45.455 0.00 0.00 0.00 2.59
941 949 5.296780 TCTTGTTTAACCAACTTCTGAGCTG 59.703 40.000 0.00 0.00 36.21 4.24
951 960 4.677584 TGTGTGCATCTTGTTTAACCAAC 58.322 39.130 0.00 0.00 35.71 3.77
982 991 5.431765 AGTCATTGCTAACTGGATTGGTAG 58.568 41.667 0.00 0.00 0.00 3.18
1014 1024 0.970937 GGACGAGAGACCATGGGTGA 60.971 60.000 18.09 0.00 45.48 4.02
1017 1027 2.509549 ACAAGGACGAGAGACCATGGG 61.510 57.143 18.09 0.00 46.15 4.00
1024 1034 0.699399 AGGAGGACAAGGACGAGAGA 59.301 55.000 0.00 0.00 0.00 3.10
1030 1040 1.480789 GAGAGGAGGAGGACAAGGAC 58.519 60.000 0.00 0.00 0.00 3.85
1116 1126 3.469008 TTGGCTAGGTGATAACCATCG 57.531 47.619 0.85 0.00 29.65 3.84
1143 1153 3.192001 CCATGATGAGGGAAACTTGTGTG 59.808 47.826 0.00 0.00 0.00 3.82
1204 1216 6.865834 ATGGATCAGAGGAAGTACCATATC 57.134 41.667 0.00 0.00 42.04 1.63
1210 1222 8.643324 ACACTTATTATGGATCAGAGGAAGTAC 58.357 37.037 0.00 0.00 0.00 2.73
1220 1232 5.439721 AGCTGCAACACTTATTATGGATCA 58.560 37.500 1.02 0.00 0.00 2.92
1233 1245 3.002348 ACTTTAGTTCGAAGCTGCAACAC 59.998 43.478 0.00 0.00 0.00 3.32
1282 1294 6.784031 ACTCCCTCAGATTCAATAAAAGTGT 58.216 36.000 0.00 0.00 0.00 3.55
1297 1309 2.894126 AGTGTGTGAAGTACTCCCTCAG 59.106 50.000 0.00 0.00 0.00 3.35
1298 1310 2.958818 AGTGTGTGAAGTACTCCCTCA 58.041 47.619 0.00 0.00 0.00 3.86
1537 1549 7.719778 TGCTTAGCATATAAGATGTGTCAAG 57.280 36.000 1.39 0.00 31.71 3.02
1557 1570 5.872070 GTGAGCTAGAGTACAAGAAATGCTT 59.128 40.000 0.00 0.00 37.29 3.91
1561 1574 5.183331 TGTCGTGAGCTAGAGTACAAGAAAT 59.817 40.000 0.00 0.00 0.00 2.17
1562 1575 4.517832 TGTCGTGAGCTAGAGTACAAGAAA 59.482 41.667 0.00 0.00 0.00 2.52
1600 1659 0.175760 AATCCACCTCGTCATGGTCG 59.824 55.000 0.00 0.00 37.27 4.79
1690 1749 5.515106 AGGTAGAACTTCTGCTCTCTGTAT 58.485 41.667 6.81 0.00 29.49 2.29
1772 1831 3.949754 ACCCGATCGATGACTTACACTAA 59.050 43.478 18.66 0.00 0.00 2.24
1837 1920 1.476891 ACAAGCATCCTACGATCGTGT 59.523 47.619 30.23 13.29 0.00 4.49
1839 1922 1.268589 CGACAAGCATCCTACGATCGT 60.269 52.381 25.94 25.94 0.00 3.73
2213 2304 7.818642 ACTAGTTAGTTGTAACTGCACTCTAG 58.181 38.462 7.50 11.96 46.91 2.43
2313 2404 5.815740 ACTTCAACCGTTGTATATTGCTAGG 59.184 40.000 11.01 0.00 0.00 3.02
2322 2413 5.717119 ACGAATCTACTTCAACCGTTGTAT 58.283 37.500 11.01 1.34 33.10 2.29
2323 2414 5.048504 AGACGAATCTACTTCAACCGTTGTA 60.049 40.000 11.01 0.79 31.46 2.41
2324 2415 3.985925 GACGAATCTACTTCAACCGTTGT 59.014 43.478 11.01 0.00 33.10 3.32
2325 2416 4.235360 AGACGAATCTACTTCAACCGTTG 58.765 43.478 4.78 4.78 31.46 4.10
2326 2417 4.516365 AGACGAATCTACTTCAACCGTT 57.484 40.909 0.00 0.00 31.46 4.44
2327 2418 5.633830 TTAGACGAATCTACTTCAACCGT 57.366 39.130 0.00 0.00 37.15 4.83
2344 2462 4.715713 ACAGTTTGGGAAGAGGTTTAGAC 58.284 43.478 0.00 0.00 0.00 2.59
2466 2602 9.151471 GCACAATAGAGTTAATGAACTACTGAA 57.849 33.333 0.00 0.00 46.23 3.02
2597 3171 9.737427 TTTTGTAAATACTTCGCAAAATCAAGA 57.263 25.926 0.00 0.00 35.13 3.02
2605 3179 9.632807 ATGCTAATTTTTGTAAATACTTCGCAA 57.367 25.926 0.00 0.00 32.85 4.85
2620 3203 6.420604 CACCGACTTGAAACATGCTAATTTTT 59.579 34.615 0.00 0.00 0.00 1.94
2622 3205 5.009610 ACACCGACTTGAAACATGCTAATTT 59.990 36.000 0.00 0.00 0.00 1.82
2624 3207 4.072131 ACACCGACTTGAAACATGCTAAT 58.928 39.130 0.00 0.00 0.00 1.73
2627 3210 1.967319 ACACCGACTTGAAACATGCT 58.033 45.000 0.00 0.00 0.00 3.79
2628 3211 2.384382 CAACACCGACTTGAAACATGC 58.616 47.619 0.00 0.00 0.00 4.06
2629 3212 2.223456 TGCAACACCGACTTGAAACATG 60.223 45.455 0.00 0.00 0.00 3.21
2630 3213 2.020720 TGCAACACCGACTTGAAACAT 58.979 42.857 0.00 0.00 0.00 2.71
2635 3218 0.176910 TCAGTGCAACACCGACTTGA 59.823 50.000 0.00 0.00 41.43 3.02
2636 3219 1.013596 TTCAGTGCAACACCGACTTG 58.986 50.000 0.00 0.00 41.43 3.16
2718 3301 7.701809 AAACGGTTATTAAATGTTGTTGGTG 57.298 32.000 0.00 0.00 0.00 4.17
2758 3341 3.942748 GTGGGTTCCGCTTATCATAAACA 59.057 43.478 0.00 0.00 0.00 2.83
2792 3375 4.402155 TGGCTTTGACTTTTCTGTCATGTT 59.598 37.500 0.00 0.00 45.03 2.71
2849 3432 1.722011 CGGAAGGTTGATGCTAACGT 58.278 50.000 0.00 0.00 0.00 3.99
2850 3433 0.373716 GCGGAAGGTTGATGCTAACG 59.626 55.000 0.00 0.00 0.00 3.18
2893 3478 3.403038 CACTCGAGGTGTTTGAGGAAAT 58.597 45.455 18.41 0.00 41.04 2.17
2909 3494 1.153289 CTTCCCTCCCATGCACTCG 60.153 63.158 0.00 0.00 0.00 4.18
2911 3496 2.679716 GCTTCCCTCCCATGCACT 59.320 61.111 0.00 0.00 0.00 4.40
2912 3497 2.825836 CGCTTCCCTCCCATGCAC 60.826 66.667 0.00 0.00 0.00 4.57
2913 3498 4.113815 CCGCTTCCCTCCCATGCA 62.114 66.667 0.00 0.00 0.00 3.96
2914 3499 4.883354 CCCGCTTCCCTCCCATGC 62.883 72.222 0.00 0.00 0.00 4.06
2915 3500 3.411517 ACCCGCTTCCCTCCCATG 61.412 66.667 0.00 0.00 0.00 3.66
2916 3501 3.411517 CACCCGCTTCCCTCCCAT 61.412 66.667 0.00 0.00 0.00 4.00
2917 3502 4.649705 TCACCCGCTTCCCTCCCA 62.650 66.667 0.00 0.00 0.00 4.37
2920 3505 1.079057 GAGTTCACCCGCTTCCCTC 60.079 63.158 0.00 0.00 0.00 4.30
2921 3506 2.593956 GGAGTTCACCCGCTTCCCT 61.594 63.158 0.00 0.00 0.00 4.20
2922 3507 2.046217 GGAGTTCACCCGCTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
2923 3508 2.434359 CGGAGTTCACCCGCTTCC 60.434 66.667 0.00 0.00 40.54 3.46
2924 3509 1.737008 GTCGGAGTTCACCCGCTTC 60.737 63.158 0.00 0.00 46.10 3.86
2925 3510 2.035237 TTGTCGGAGTTCACCCGCTT 62.035 55.000 0.00 0.00 46.10 4.68
2929 3514 2.315386 GCGTTGTCGGAGTTCACCC 61.315 63.158 0.00 0.00 37.56 4.61
2965 3550 1.554392 CACTTCCTCGATCAAGAGCG 58.446 55.000 9.82 0.65 42.20 5.03
2966 3551 1.478510 TCCACTTCCTCGATCAAGAGC 59.521 52.381 9.82 0.00 36.95 4.09
2968 3553 1.472878 CGTCCACTTCCTCGATCAAGA 59.527 52.381 9.82 0.00 0.00 3.02
2969 3554 1.469940 CCGTCCACTTCCTCGATCAAG 60.470 57.143 0.00 2.66 0.00 3.02
2970 3555 0.530744 CCGTCCACTTCCTCGATCAA 59.469 55.000 0.00 0.00 0.00 2.57
2972 3557 0.179134 CACCGTCCACTTCCTCGATC 60.179 60.000 0.00 0.00 0.00 3.69
2973 3558 0.611062 TCACCGTCCACTTCCTCGAT 60.611 55.000 0.00 0.00 0.00 3.59
3069 4966 2.970974 GCAGCAAAGACGGCTCACC 61.971 63.158 0.00 0.00 40.23 4.02
3111 5008 2.944557 CGCACGTCCACTCGATCG 60.945 66.667 9.36 9.36 34.70 3.69
3128 5025 0.939419 AAACCACTTAACACGACGGC 59.061 50.000 0.00 0.00 0.00 5.68
3134 5031 3.308530 GCATGCAGAAACCACTTAACAC 58.691 45.455 14.21 0.00 0.00 3.32
3137 5034 1.539388 CGGCATGCAGAAACCACTTAA 59.461 47.619 21.36 0.00 0.00 1.85
3157 5054 3.490759 CACTGGTGCGCCATCGAC 61.491 66.667 21.54 0.00 45.05 4.20
3205 5102 3.364366 GCATATACATCGTTGAGCTTGGC 60.364 47.826 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.