Multiple sequence alignment - TraesCS1D01G317600

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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 TraesCS1D01G317600 chr1D 100.000 3184 0 0 1 3184 412460820 412464003 0.000000e+00 5880.0
1 TraesCS1D01G317600 chr1D 88.124 2442 210 35 1 2385 412227121 412229539 0.000000e+00 2830.0
2 TraesCS1D01G317600 chr1D 88.450 2407 181 40 1 2350 412236250 412238616 0.000000e+00 2815.0
3 TraesCS1D01G317600 chr1D 83.101 645 68 22 2383 2995 412238945 412239580 1.670000e-152 549.0
4 TraesCS1D01G317600 chr1D 84.576 590 45 25 2447 2994 412230392 412230977 7.770000e-151 544.0
5 TraesCS1D01G317600 chr1D 93.525 139 7 1 3016 3152 412239569 412239707 4.160000e-49 206.0
6 TraesCS1D01G317600 chr1D 94.828 58 2 1 2388 2445 412230008 412230064 4.370000e-14 89.8
7 TraesCS1D01G317600 chr1B 86.672 2461 217 65 1 2385 555950438 555952863 0.000000e+00 2625.0
8 TraesCS1D01G317600 chr1B 84.202 633 73 21 2383 2994 555953977 555954603 9.840000e-165 590.0
9 TraesCS1D01G317600 chr1B 90.698 344 26 4 2653 2995 556006105 556006443 1.350000e-123 453.0
10 TraesCS1D01G317600 chr1B 93.023 129 8 1 3013 3140 556006429 556006557 1.510000e-43 187.0
11 TraesCS1D01G317600 chr1B 86.986 146 16 2 2383 2527 556005839 556005982 9.140000e-36 161.0
12 TraesCS1D01G317600 chr1A 90.583 1476 97 17 1 1435 509014260 509015734 0.000000e+00 1917.0
13 TraesCS1D01G317600 chr1A 85.998 957 76 31 1444 2385 509015772 509016685 0.000000e+00 972.0
14 TraesCS1D01G317600 chr1A 86.795 621 49 9 2385 2974 508966267 508966885 0.000000e+00 662.0
15 TraesCS1D01G317600 chr1A 82.134 806 60 38 2383 3133 509017095 509017871 5.840000e-172 614.0
16 TraesCS1D01G317600 chr1A 82.533 687 65 29 1078 1724 508956836 508957507 1.290000e-153 553.0
17 TraesCS1D01G317600 chr1A 85.470 468 44 11 1936 2385 508965192 508965653 1.730000e-127 466.0
18 TraesCS1D01G317600 chr1A 90.303 165 11 1 1774 1933 508964900 508965064 8.950000e-51 211.0
19 TraesCS1D01G317600 chr1A 90.984 122 11 0 32 153 508946859 508946980 7.070000e-37 165.0
20 TraesCS1D01G317600 chr1A 100.000 30 0 0 1544 1573 508957293 508957322 4.440000e-04 56.5
21 TraesCS1D01G317600 chr7D 82.878 403 65 4 16 416 225827397 225827797 3.020000e-95 359.0
22 TraesCS1D01G317600 chrUn 86.992 123 15 1 2412 2533 31647950 31647828 1.540000e-28 137.0


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 TraesCS1D01G317600 chr1D 412460820 412464003 3183 False 5880.000000 5880 100.000000 1 3184 1 chr1D.!!$F1 3183
1 TraesCS1D01G317600 chr1D 412236250 412239707 3457 False 1190.000000 2815 88.358667 1 3152 3 chr1D.!!$F3 3151
2 TraesCS1D01G317600 chr1D 412227121 412230977 3856 False 1154.600000 2830 89.176000 1 2994 3 chr1D.!!$F2 2993
3 TraesCS1D01G317600 chr1B 555950438 555954603 4165 False 1607.500000 2625 85.437000 1 2994 2 chr1B.!!$F1 2993
4 TraesCS1D01G317600 chr1B 556005839 556006557 718 False 267.000000 453 90.235667 2383 3140 3 chr1B.!!$F2 757
5 TraesCS1D01G317600 chr1A 509014260 509017871 3611 False 1167.666667 1917 86.238333 1 3133 3 chr1A.!!$F4 3132
6 TraesCS1D01G317600 chr1A 508964900 508966885 1985 False 446.333333 662 87.522667 1774 2974 3 chr1A.!!$F3 1200
7 TraesCS1D01G317600 chr1A 508956836 508957507 671 False 304.750000 553 91.266500 1078 1724 2 chr1A.!!$F2 646

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
903 923 0.607489 GCTTGGATCACAGTGGCAGT 60.607 55.0 0.00 0.0 0.0 4.40 F
1918 2023 0.038744 AGAAGGCCAACTGACCCATG 59.961 55.0 5.01 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2392 0.391661 ACTGCACCCAAGACGCATAG 60.392 55.000 0.0 0.0 34.63 2.23 R
2825 4890 1.228337 TCCTGGGTTCGTCTCGTCA 60.228 57.895 0.0 0.0 0.00 4.35 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
23 24 3.593942 TCCTTTAACCTCTTGAGTGGGA 58.406 45.455 4.33 0.00 33.22 4.37
52 53 7.633789 TCCCAGAAGAAGTTATAAGCATTTCT 58.366 34.615 0.00 0.00 0.00 2.52
126 127 1.660560 CCACATGTTGGGCAGCTAGC 61.661 60.000 6.62 6.62 42.54 3.42
142 143 5.738208 GCAGCTAGCCAATCTTGCAATAATT 60.738 40.000 16.85 0.07 44.32 1.40
192 193 3.383505 GCAATCCCAAATACCCTTGGTAC 59.616 47.826 0.00 0.00 43.84 3.34
198 199 3.192633 CCAAATACCCTTGGTACTTGTGC 59.807 47.826 12.02 0.00 41.87 4.57
230 231 6.826741 GCAATTCCTACACTTACAAGGGAATA 59.173 38.462 0.00 0.00 41.06 1.75
395 396 1.410850 CCTATCAGGTCCGGTGCCAT 61.411 60.000 17.48 7.83 0.00 4.40
416 417 7.233348 TGCCATATAAGGGGATCTTTTCAAATC 59.767 37.037 0.00 0.00 36.93 2.17
427 428 2.420628 TTTCAAATCCAAGCGCTGTG 57.579 45.000 12.58 11.69 0.00 3.66
501 502 2.699554 ATGCCCATACCCAGCCCA 60.700 61.111 0.00 0.00 0.00 5.36
527 528 1.202348 GCTTGCACGTCACAAACTGC 61.202 55.000 2.47 0.00 34.54 4.40
553 554 4.024048 CACATCTTGGTGTTTACTGTGGTC 60.024 45.833 0.00 0.00 34.09 4.02
618 619 6.934645 TGTTACATTAAGAAGTCAAGAGGTGG 59.065 38.462 0.00 0.00 0.00 4.61
635 636 4.329545 GTGCCCGCCAAGGTCAGA 62.330 66.667 0.00 0.00 38.74 3.27
636 637 4.329545 TGCCCGCCAAGGTCAGAC 62.330 66.667 0.00 0.00 38.74 3.51
650 651 2.039084 GGTCAGACAAACATCCCTGAGT 59.961 50.000 2.17 0.00 36.46 3.41
664 665 3.008375 TCCCTGAGTTGTTTCAGAGGATG 59.992 47.826 4.67 0.00 45.95 3.51
681 682 2.544685 GATGTCATACGCTGAGTTGCT 58.455 47.619 0.00 0.00 33.51 3.91
685 705 2.600867 GTCATACGCTGAGTTGCTTCTC 59.399 50.000 0.00 2.59 33.51 2.87
861 881 4.097437 AGGATTCGACATCGCAAACTAGTA 59.903 41.667 0.00 0.00 39.60 1.82
891 911 3.988976 ACAGTGTGTGATAGCTTGGAT 57.011 42.857 0.00 0.00 0.00 3.41
903 923 0.607489 GCTTGGATCACAGTGGCAGT 60.607 55.000 0.00 0.00 0.00 4.40
912 932 3.286353 TCACAGTGGCAGTCAATTCAAA 58.714 40.909 0.00 0.00 0.00 2.69
986 1006 1.004440 GCACAGAAGGCGAGTTCCT 60.004 57.895 0.00 0.00 38.31 3.36
1050 1070 1.202698 GCGGAGGCACTGGAATATCTT 60.203 52.381 0.00 0.00 41.55 2.40
1057 1077 4.411540 AGGCACTGGAATATCTTCATCACT 59.588 41.667 0.00 0.00 37.18 3.41
1095 1115 4.804608 TGTTCACTGTGATGTTAAACCG 57.195 40.909 11.86 0.00 0.00 4.44
1163 1183 7.705325 TGACTTCGGACTAGCAAAGATAATTAC 59.295 37.037 0.00 0.00 0.00 1.89
1166 1186 5.068198 TCGGACTAGCAAAGATAATTACGGT 59.932 40.000 0.00 0.00 0.00 4.83
1206 1226 1.536766 CTCGCCAATCAAAGTTGCTCA 59.463 47.619 0.00 0.00 0.00 4.26
1270 1290 3.326747 CTGTTTCCTTCTTACTCCACCG 58.673 50.000 0.00 0.00 0.00 4.94
1301 1344 8.208718 TCAGTAATGGCTTGAAACATATGTAC 57.791 34.615 9.21 7.35 0.00 2.90
1404 1452 4.732784 ACGCATCAACACAATTAATGGAC 58.267 39.130 0.00 0.00 0.00 4.02
1409 1457 6.694411 GCATCAACACAATTAATGGACTGATC 59.306 38.462 0.00 0.00 0.00 2.92
1629 1716 3.047857 TGTATCTTCCATGCCATCCTCA 58.952 45.455 0.00 0.00 0.00 3.86
1641 1728 0.536724 CATCCTCATGTGGTCACCGA 59.463 55.000 13.34 0.00 0.00 4.69
1642 1729 0.537188 ATCCTCATGTGGTCACCGAC 59.463 55.000 13.34 0.00 0.00 4.79
1646 1733 1.205655 CTCATGTGGTCACCGACTCAT 59.794 52.381 0.00 0.00 32.47 2.90
1724 1813 5.066117 TGCCGAGAATACAGTCAACTACTAG 59.934 44.000 0.00 0.00 35.76 2.57
1741 1830 9.367444 CAACTACTAGATGTAAACAACTAAGGG 57.633 37.037 0.00 0.00 32.11 3.95
1801 1900 9.350951 AGTTTATAAGAAAGCTAACACAAACCT 57.649 29.630 0.00 0.00 0.00 3.50
1816 1921 5.955959 ACACAAACCTTTTCCTTCCTTTACT 59.044 36.000 0.00 0.00 0.00 2.24
1849 1954 2.509548 TGGGGACTGAAATATCTGTGGG 59.490 50.000 0.00 0.00 37.80 4.61
1853 1958 3.181450 GGACTGAAATATCTGTGGGAGGG 60.181 52.174 0.00 0.00 37.80 4.30
1918 2023 0.038744 AGAAGGCCAACTGACCCATG 59.961 55.000 5.01 0.00 0.00 3.66
1928 2033 4.549458 CAACTGACCCATGTTTCAATGAC 58.451 43.478 0.00 0.00 0.00 3.06
1933 2163 5.569355 TGACCCATGTTTCAATGACACTAT 58.431 37.500 1.06 0.00 0.00 2.12
1967 2197 0.107508 ATGTTGAGATGGCCTGTCCG 60.108 55.000 3.32 0.00 37.80 4.79
1976 2206 1.335132 TGGCCTGTCCGGGTAATCTC 61.335 60.000 3.32 0.00 37.80 2.75
2078 2308 1.881973 CTTGGTTTAGCTTGCTGCAGA 59.118 47.619 20.43 0.00 45.94 4.26
2162 2392 1.098050 AAATCATGGCCAGCGAGAAC 58.902 50.000 13.05 0.00 0.00 3.01
2195 2431 5.514169 TGGGTGCAGTAATATTGATTGGAA 58.486 37.500 0.00 0.00 0.00 3.53
2277 2534 0.036388 CCATAGCCGACCACACTGTT 60.036 55.000 0.00 0.00 0.00 3.16
2296 2553 8.679056 ACACTGTTTGTATCATACACGACTGTG 61.679 40.741 27.74 27.74 46.23 3.66
2306 2563 1.229428 CACGACTGTGCCTGTCAATT 58.771 50.000 10.97 0.00 39.67 2.32
2307 2564 2.412870 CACGACTGTGCCTGTCAATTA 58.587 47.619 10.97 0.00 39.67 1.40
2308 2565 3.002791 CACGACTGTGCCTGTCAATTAT 58.997 45.455 10.97 0.00 39.67 1.28
2310 2567 3.261580 CGACTGTGCCTGTCAATTATGA 58.738 45.455 10.97 0.00 33.00 2.15
2312 2569 4.025396 CGACTGTGCCTGTCAATTATGATC 60.025 45.833 10.97 0.00 38.01 2.92
2313 2570 4.847198 ACTGTGCCTGTCAATTATGATCA 58.153 39.130 0.00 0.00 38.01 2.92
2314 2571 4.880120 ACTGTGCCTGTCAATTATGATCAG 59.120 41.667 0.09 0.00 38.01 2.90
2316 2573 5.121105 TGTGCCTGTCAATTATGATCAGAG 58.879 41.667 0.09 0.00 38.01 3.35
2317 2574 5.104817 TGTGCCTGTCAATTATGATCAGAGA 60.105 40.000 0.09 0.00 38.01 3.10
2318 2575 5.819379 GTGCCTGTCAATTATGATCAGAGAA 59.181 40.000 0.09 0.00 38.01 2.87
2319 2576 6.317140 GTGCCTGTCAATTATGATCAGAGAAA 59.683 38.462 0.09 0.00 38.01 2.52
2320 2577 6.541278 TGCCTGTCAATTATGATCAGAGAAAG 59.459 38.462 0.09 0.00 38.01 2.62
2350 2611 1.528586 CGTGAGCTTCTGTTGGTTCAG 59.471 52.381 0.00 0.00 36.85 3.02
2379 2640 9.985730 GAATCAACTATGATCAGAGAAAGATCT 57.014 33.333 23.69 12.39 45.60 2.75
2528 4560 8.988064 ATCGTATATGTAGCCTTGTCTTAATG 57.012 34.615 0.00 0.00 0.00 1.90
2554 4586 3.376859 TCAAATTCGAGCAACAACACAGT 59.623 39.130 0.00 0.00 0.00 3.55
2561 4593 2.618709 GAGCAACAACACAGTAGGCTTT 59.381 45.455 0.00 0.00 33.93 3.51
2572 4604 2.485814 CAGTAGGCTTTGTTCTGCTTCC 59.514 50.000 0.00 0.00 0.00 3.46
2577 4609 3.507622 AGGCTTTGTTCTGCTTCCATTAC 59.492 43.478 0.00 0.00 0.00 1.89
2607 4639 0.108585 TTGGCTTCACACTCACCTCC 59.891 55.000 0.00 0.00 0.00 4.30
2654 4710 4.101114 GGTTTCCCCCTTAACCATCAATT 58.899 43.478 0.00 0.00 42.67 2.32
2668 4724 6.840780 ACCATCAATTCCTCCTTTTGTAAG 57.159 37.500 0.00 0.00 0.00 2.34
2793 4855 0.103937 CTTCAGCTCACCGGATCTCC 59.896 60.000 9.46 0.00 0.00 3.71
2872 4947 1.760086 GCCTCTGGCCTCTCAGCTA 60.760 63.158 3.32 0.00 44.06 3.32
2984 5066 0.179161 CGGAAGACGCGAATCTGAGT 60.179 55.000 15.93 0.00 34.82 3.41
2986 5068 1.656095 GGAAGACGCGAATCTGAGTTG 59.344 52.381 15.93 0.00 0.00 3.16
2987 5069 1.656095 GAAGACGCGAATCTGAGTTGG 59.344 52.381 15.93 0.00 0.00 3.77
2988 5070 0.108615 AGACGCGAATCTGAGTTGGG 60.109 55.000 15.93 7.73 0.00 4.12
2989 5071 0.389948 GACGCGAATCTGAGTTGGGT 60.390 55.000 15.93 13.88 0.00 4.51
2990 5072 0.034896 ACGCGAATCTGAGTTGGGTT 59.965 50.000 15.93 0.00 0.00 4.11
2991 5073 0.721718 CGCGAATCTGAGTTGGGTTC 59.278 55.000 0.00 0.00 0.00 3.62
2992 5074 1.673033 CGCGAATCTGAGTTGGGTTCT 60.673 52.381 0.00 0.00 0.00 3.01
2993 5075 2.427506 GCGAATCTGAGTTGGGTTCTT 58.572 47.619 0.00 0.00 0.00 2.52
2994 5076 2.814336 GCGAATCTGAGTTGGGTTCTTT 59.186 45.455 0.00 0.00 0.00 2.52
2995 5077 3.253432 GCGAATCTGAGTTGGGTTCTTTT 59.747 43.478 0.00 0.00 0.00 2.27
2996 5078 4.261614 GCGAATCTGAGTTGGGTTCTTTTT 60.262 41.667 0.00 0.00 0.00 1.94
3072 5154 5.127845 ACGGAGCAGAGAAGAAGATGATAAA 59.872 40.000 0.00 0.00 0.00 1.40
3099 5182 3.432326 CCTTATGGGCTGTAGTGGAAGTC 60.432 52.174 0.00 0.00 0.00 3.01
3133 5216 6.110707 CCGGGTACTAAAAGAATTTCTGCTA 58.889 40.000 0.00 0.00 37.28 3.49
3173 5258 8.697507 AGAACTGGGAAATGATATAAATCACC 57.302 34.615 0.00 0.00 44.79 4.02
3174 5259 8.506083 AGAACTGGGAAATGATATAAATCACCT 58.494 33.333 0.00 0.00 44.79 4.00
3175 5260 8.469309 AACTGGGAAATGATATAAATCACCTG 57.531 34.615 0.00 0.00 44.79 4.00
3176 5261 7.006509 ACTGGGAAATGATATAAATCACCTGG 58.993 38.462 0.00 0.00 44.79 4.45
3177 5262 7.147141 ACTGGGAAATGATATAAATCACCTGGA 60.147 37.037 0.00 0.00 44.79 3.86
3178 5263 7.768643 TGGGAAATGATATAAATCACCTGGAT 58.231 34.615 0.00 0.00 44.79 3.41
3179 5264 7.890127 TGGGAAATGATATAAATCACCTGGATC 59.110 37.037 0.00 0.00 44.79 3.36
3180 5265 7.066284 GGGAAATGATATAAATCACCTGGATCG 59.934 40.741 0.00 0.00 44.79 3.69
3181 5266 7.607991 GGAAATGATATAAATCACCTGGATCGT 59.392 37.037 0.00 0.00 44.79 3.73
3182 5267 9.653287 GAAATGATATAAATCACCTGGATCGTA 57.347 33.333 0.00 0.00 44.79 3.43
3183 5268 9.658799 AAATGATATAAATCACCTGGATCGTAG 57.341 33.333 0.00 0.00 44.79 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.829373 ATGCTTATAACTTCTTCTGGGATTTT 57.171 30.769 0.00 0.00 0.00 1.82
43 44 1.203100 ACAGCCAGGGAAGAAATGCTT 60.203 47.619 0.00 0.00 40.25 3.91
52 53 4.228210 AGATTGAGAAATACAGCCAGGGAA 59.772 41.667 0.00 0.00 0.00 3.97
126 127 8.936070 TGAGAAATCAATTATTGCAAGATTGG 57.064 30.769 25.73 10.17 32.91 3.16
142 143 9.166173 CCTGATAACTTGTTACATGAGAAATCA 57.834 33.333 0.00 5.85 0.00 2.57
153 154 5.163652 GGGATTGCACCTGATAACTTGTTAC 60.164 44.000 0.00 0.00 0.00 2.50
154 155 4.947388 GGGATTGCACCTGATAACTTGTTA 59.053 41.667 0.00 0.00 0.00 2.41
198 199 7.144722 TGTAAGTGTAGGAATTGCAATTCTG 57.855 36.000 37.77 0.00 43.33 3.02
395 396 7.287696 GCTTGGATTTGAAAAGATCCCCTTATA 59.712 37.037 0.00 0.00 40.92 0.98
416 417 1.005748 TGAGAGACACAGCGCTTGG 60.006 57.895 7.50 5.11 0.00 3.61
427 428 3.064545 GCATGCCATTACTTGTGAGAGAC 59.935 47.826 6.36 0.00 0.00 3.36
501 502 2.698803 TGTGACGTGCAAGCTTATCAT 58.301 42.857 0.00 0.00 0.00 2.45
527 528 5.277974 CCACAGTAAACACCAAGATGTGAAG 60.278 44.000 4.11 0.00 39.03 3.02
553 554 2.158986 ACAGAGAAGGATGAATGCTCCG 60.159 50.000 0.00 0.00 37.88 4.63
618 619 4.329545 TCTGACCTTGGCGGGCAC 62.330 66.667 2.73 0.00 46.57 5.01
635 636 4.277476 TGAAACAACTCAGGGATGTTTGT 58.723 39.130 13.13 0.00 44.72 2.83
636 637 4.580167 TCTGAAACAACTCAGGGATGTTTG 59.420 41.667 13.13 0.90 44.72 2.93
650 651 3.932710 GCGTATGACATCCTCTGAAACAA 59.067 43.478 0.00 0.00 0.00 2.83
664 665 2.600867 GAGAAGCAACTCAGCGTATGAC 59.399 50.000 5.50 0.00 40.15 3.06
681 682 3.070878 GGCCAACCAAATTTTCCAGAGAA 59.929 43.478 0.00 0.00 35.26 2.87
685 705 1.069978 ACGGCCAACCAAATTTTCCAG 59.930 47.619 2.24 0.00 34.57 3.86
891 911 2.636647 TGAATTGACTGCCACTGTGA 57.363 45.000 9.86 0.00 0.00 3.58
986 1006 1.142667 TCTGCATCAGGTTTGGTGTCA 59.857 47.619 0.00 0.00 37.75 3.58
1050 1070 7.147320 ACAATTGGAGGGTCAATATAGTGATGA 60.147 37.037 10.83 0.00 36.45 2.92
1057 1077 6.828273 CAGTGAACAATTGGAGGGTCAATATA 59.172 38.462 10.83 0.00 36.45 0.86
1065 1085 2.862541 TCACAGTGAACAATTGGAGGG 58.137 47.619 10.83 0.00 0.00 4.30
1163 1183 1.808411 TTGCCTGCTTTCTTCTACCG 58.192 50.000 0.00 0.00 0.00 4.02
1166 1186 4.256920 GAGTGATTGCCTGCTTTCTTCTA 58.743 43.478 0.00 0.00 0.00 2.10
1192 1212 2.867624 TCCAGCTGAGCAACTTTGATT 58.132 42.857 17.39 0.00 0.00 2.57
1206 1226 1.999648 TTGTGCCTTTGATTCCAGCT 58.000 45.000 0.00 0.00 0.00 4.24
1270 1290 5.695816 TGTTTCAAGCCATTACTGAAAATGC 59.304 36.000 0.00 0.00 35.85 3.56
1301 1344 7.546358 TGATGCAGGTTACCATTTCTTTTATG 58.454 34.615 3.51 0.00 0.00 1.90
1377 1425 5.950758 TTAATTGTGTTGATGCGTACCTT 57.049 34.783 0.00 0.00 0.00 3.50
1404 1452 4.330250 AGGAACAAACATGAGGTGATCAG 58.670 43.478 0.00 0.00 42.53 2.90
1409 1457 3.077359 GGAGAGGAACAAACATGAGGTG 58.923 50.000 0.00 0.00 0.00 4.00
1439 1487 0.324943 AATGTACGCTGGAGCCAAGT 59.675 50.000 0.00 0.00 37.91 3.16
1450 1526 4.835199 AGTCGACAATAACAATGTACGC 57.165 40.909 19.50 0.00 0.00 4.42
1507 1584 9.305925 GAATCATGAACAATTATTGAGGGAAAC 57.694 33.333 12.28 0.00 0.00 2.78
1540 1622 9.561069 TGGAGGCTTAAAGCTTCTTATAATTAG 57.439 33.333 0.00 0.00 45.44 1.73
1629 1716 0.173481 CGATGAGTCGGTGACCACAT 59.827 55.000 1.11 1.34 44.00 3.21
1641 1728 7.720442 TCAGATTCTCATTTGATACGATGAGT 58.280 34.615 11.72 0.00 45.93 3.41
1642 1729 8.585189 TTCAGATTCTCATTTGATACGATGAG 57.415 34.615 6.95 6.95 46.73 2.90
1682 1771 3.728718 CGGCACAACAAATTACTGTGAAC 59.271 43.478 15.13 8.23 42.48 3.18
1685 1774 3.249799 TCTCGGCACAACAAATTACTGTG 59.750 43.478 9.15 9.15 42.70 3.66
1689 1778 5.933790 TGTATTCTCGGCACAACAAATTAC 58.066 37.500 0.00 0.00 0.00 1.89
1724 1813 7.807907 CACACAAATCCCTTAGTTGTTTACATC 59.192 37.037 0.00 0.00 43.55 3.06
1801 1900 7.037873 TGCCATACTCTAGTAAAGGAAGGAAAA 60.038 37.037 13.29 0.00 33.95 2.29
1816 1921 2.090775 TCAGTCCCCATGCCATACTCTA 60.091 50.000 0.00 0.00 0.00 2.43
1849 1954 1.067212 CATAGCTGTACACGTCCCCTC 59.933 57.143 0.00 0.00 0.00 4.30
1853 1958 1.203994 ACACCATAGCTGTACACGTCC 59.796 52.381 0.00 0.00 0.00 4.79
1933 2163 9.613428 CCATCTCAACATACTTTGGTAGATTTA 57.387 33.333 0.00 0.00 0.00 1.40
1967 2197 5.125578 GTCCATTGTTTCCAAGAGATTACCC 59.874 44.000 0.00 0.00 33.17 3.69
1976 2206 3.980646 TTGACGTCCATTGTTTCCAAG 57.019 42.857 14.12 0.00 33.17 3.61
2143 2373 1.098050 GTTCTCGCTGGCCATGATTT 58.902 50.000 5.51 0.00 0.00 2.17
2157 2387 2.271800 CACCCAAGACGCATAGTTCTC 58.728 52.381 0.00 0.00 0.00 2.87
2162 2392 0.391661 ACTGCACCCAAGACGCATAG 60.392 55.000 0.00 0.00 34.63 2.23
2195 2431 3.008049 ACAGAAATAGAACAAGCCGTCCT 59.992 43.478 0.00 0.00 0.00 3.85
2245 2496 7.389607 GTGGTCGGCTATGGTAAAATACATAAT 59.610 37.037 0.00 0.00 0.00 1.28
2247 2498 6.183360 TGTGGTCGGCTATGGTAAAATACATA 60.183 38.462 0.00 0.00 0.00 2.29
2277 2534 3.194755 AGGCACAGTCGTGTATGATACAA 59.805 43.478 6.89 0.00 45.50 2.41
2296 2553 6.765036 TCTTTCTCTGATCATAATTGACAGGC 59.235 38.462 0.00 0.00 34.50 4.85
2306 2563 6.875726 CGCCCAATAATCTTTCTCTGATCATA 59.124 38.462 0.00 0.00 0.00 2.15
2307 2564 5.704515 CGCCCAATAATCTTTCTCTGATCAT 59.295 40.000 0.00 0.00 0.00 2.45
2308 2565 5.059161 CGCCCAATAATCTTTCTCTGATCA 58.941 41.667 0.00 0.00 0.00 2.92
2310 2567 4.818546 CACGCCCAATAATCTTTCTCTGAT 59.181 41.667 0.00 0.00 0.00 2.90
2312 2569 4.191544 TCACGCCCAATAATCTTTCTCTG 58.808 43.478 0.00 0.00 0.00 3.35
2313 2570 4.446371 CTCACGCCCAATAATCTTTCTCT 58.554 43.478 0.00 0.00 0.00 3.10
2314 2571 3.002759 GCTCACGCCCAATAATCTTTCTC 59.997 47.826 0.00 0.00 0.00 2.87
2316 2573 2.945668 AGCTCACGCCCAATAATCTTTC 59.054 45.455 0.00 0.00 36.60 2.62
2317 2574 3.004752 AGCTCACGCCCAATAATCTTT 57.995 42.857 0.00 0.00 36.60 2.52
2318 2575 2.717639 AGCTCACGCCCAATAATCTT 57.282 45.000 0.00 0.00 36.60 2.40
2319 2576 2.171448 AGAAGCTCACGCCCAATAATCT 59.829 45.455 0.00 0.00 36.60 2.40
2320 2577 2.289002 CAGAAGCTCACGCCCAATAATC 59.711 50.000 0.00 0.00 36.60 1.75
2350 2611 5.815233 TCTCTGATCATAGTTGATTCCCC 57.185 43.478 7.87 0.00 42.73 4.81
2379 2640 5.580998 AGGATAGGAGCCGATCATAGTTTA 58.419 41.667 11.02 0.00 31.14 2.01
2385 2646 1.277557 GCAAGGATAGGAGCCGATCAT 59.722 52.381 11.02 1.89 31.14 2.45
2386 2647 0.681733 GCAAGGATAGGAGCCGATCA 59.318 55.000 11.02 0.00 31.14 2.92
2391 4043 1.301322 GAGCGCAAGGATAGGAGCC 60.301 63.158 11.47 0.00 38.28 4.70
2528 4560 4.848299 GTGTTGTTGCTCGAATTTGAGATC 59.152 41.667 24.41 13.78 38.28 2.75
2554 4586 2.949177 TGGAAGCAGAACAAAGCCTA 57.051 45.000 0.00 0.00 0.00 3.93
2561 4593 3.820467 CCAACAGTAATGGAAGCAGAACA 59.180 43.478 0.00 0.00 40.56 3.18
2572 4604 4.320608 AGCCAACAAACCAACAGTAATG 57.679 40.909 0.00 0.00 0.00 1.90
2577 4609 2.094286 TGTGAAGCCAACAAACCAACAG 60.094 45.455 0.00 0.00 0.00 3.16
2607 4639 7.277098 CCATTGATGCATCTTACAAAAGAAAGG 59.723 37.037 26.32 11.82 44.75 3.11
2814 4879 4.680237 CTCGTCACGGCTGGGCAA 62.680 66.667 0.00 0.00 0.00 4.52
2825 4890 1.228337 TCCTGGGTTCGTCTCGTCA 60.228 57.895 0.00 0.00 0.00 4.35
2994 5076 8.934825 CCAACTGTTCTCAAATCAAAAAGAAAA 58.065 29.630 0.00 0.00 30.10 2.29
2995 5077 7.548780 CCCAACTGTTCTCAAATCAAAAAGAAA 59.451 33.333 0.00 0.00 30.10 2.52
2996 5078 7.041107 CCCAACTGTTCTCAAATCAAAAAGAA 58.959 34.615 0.00 0.00 0.00 2.52
2997 5079 6.154363 ACCCAACTGTTCTCAAATCAAAAAGA 59.846 34.615 0.00 0.00 0.00 2.52
2998 5080 6.340522 ACCCAACTGTTCTCAAATCAAAAAG 58.659 36.000 0.00 0.00 0.00 2.27
2999 5081 6.154363 AGACCCAACTGTTCTCAAATCAAAAA 59.846 34.615 0.00 0.00 0.00 1.94
3000 5082 5.656416 AGACCCAACTGTTCTCAAATCAAAA 59.344 36.000 0.00 0.00 0.00 2.44
3001 5083 5.200483 AGACCCAACTGTTCTCAAATCAAA 58.800 37.500 0.00 0.00 0.00 2.69
3002 5084 4.792068 AGACCCAACTGTTCTCAAATCAA 58.208 39.130 0.00 0.00 0.00 2.57
3003 5085 4.437682 AGACCCAACTGTTCTCAAATCA 57.562 40.909 0.00 0.00 0.00 2.57
3004 5086 5.067805 ACAAAGACCCAACTGTTCTCAAATC 59.932 40.000 0.00 0.00 0.00 2.17
3005 5087 4.956075 ACAAAGACCCAACTGTTCTCAAAT 59.044 37.500 0.00 0.00 0.00 2.32
3006 5088 4.157656 CACAAAGACCCAACTGTTCTCAAA 59.842 41.667 0.00 0.00 0.00 2.69
3007 5089 3.694072 CACAAAGACCCAACTGTTCTCAA 59.306 43.478 0.00 0.00 0.00 3.02
3008 5090 3.278574 CACAAAGACCCAACTGTTCTCA 58.721 45.455 0.00 0.00 0.00 3.27
3009 5091 3.065371 CACACAAAGACCCAACTGTTCTC 59.935 47.826 0.00 0.00 0.00 2.87
3010 5092 3.016736 CACACAAAGACCCAACTGTTCT 58.983 45.455 0.00 0.00 0.00 3.01
3011 5093 2.752903 ACACACAAAGACCCAACTGTTC 59.247 45.455 0.00 0.00 0.00 3.18
3012 5094 2.752903 GACACACAAAGACCCAACTGTT 59.247 45.455 0.00 0.00 0.00 3.16
3013 5095 2.365582 GACACACAAAGACCCAACTGT 58.634 47.619 0.00 0.00 0.00 3.55
3014 5096 1.330521 CGACACACAAAGACCCAACTG 59.669 52.381 0.00 0.00 0.00 3.16
3050 5132 6.427547 CCATTTATCATCTTCTTCTCTGCTCC 59.572 42.308 0.00 0.00 0.00 4.70
3062 5144 5.336102 CCCATAAGGCCCATTTATCATCTT 58.664 41.667 0.00 0.00 0.00 2.40
3099 5182 8.776376 TTCTTTTAGTACCCGGTATTAACAAG 57.224 34.615 11.14 15.08 0.00 3.16
3152 5237 7.233632 TCCAGGTGATTTATATCATTTCCCAG 58.766 38.462 0.00 0.00 42.49 4.45
3153 5238 7.160457 TCCAGGTGATTTATATCATTTCCCA 57.840 36.000 0.00 0.00 42.49 4.37
3154 5239 7.066284 CGATCCAGGTGATTTATATCATTTCCC 59.934 40.741 0.00 0.00 42.49 3.97
3155 5240 7.607991 ACGATCCAGGTGATTTATATCATTTCC 59.392 37.037 0.00 0.00 42.49 3.13
3156 5241 8.553459 ACGATCCAGGTGATTTATATCATTTC 57.447 34.615 0.00 0.00 42.49 2.17
3157 5242 9.658799 CTACGATCCAGGTGATTTATATCATTT 57.341 33.333 0.00 0.00 42.49 2.32


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

AutoCloner maintained by Alex Coulton.