Multiple sequence alignment - TraesCS1D01G010500

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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 TraesCS1D01G010500 chr1D 100.000 2207 0 0 1 2207 5451716 5453922 0.000000e+00 4076.0
1 TraesCS1D01G010500 chr1B 85.204 1399 129 40 74 1422 639447418 639448788 0.000000e+00 1365.0
2 TraesCS1D01G010500 chr1B 84.163 1326 125 37 342 1603 8180860 8182164 0.000000e+00 1206.0
3 TraesCS1D01G010500 chr1B 82.054 1042 138 30 1 1011 41002059 41003082 0.000000e+00 843.0
4 TraesCS1D01G010500 chr1B 85.125 679 79 16 350 1011 644621698 644621025 0.000000e+00 675.0
5 TraesCS1D01G010500 chr1B 82.342 521 53 18 1096 1595 17836634 17836132 1.220000e-112 416.0
6 TraesCS1D01G010500 chr1B 87.193 367 22 11 1823 2177 639449846 639450199 5.710000e-106 394.0
7 TraesCS1D01G010500 chr1B 83.503 394 31 13 1834 2207 17833809 17833430 9.760000e-89 337.0
8 TraesCS1D01G010500 chr1B 84.874 357 26 16 1823 2177 8182435 8182765 3.510000e-88 335.0
9 TraesCS1D01G010500 chr1B 89.238 223 23 1 885 1107 17863013 17862792 6.000000e-71 278.0
10 TraesCS1D01G010500 chr1A 89.851 1005 72 17 320 1299 6767242 6766243 0.000000e+00 1264.0
11 TraesCS1D01G010500 chr1A 85.617 737 54 23 901 1603 6765558 6764840 0.000000e+00 726.0
12 TraesCS1D01G010500 chr1A 88.612 562 34 13 1615 2160 6764637 6764090 0.000000e+00 656.0
13 TraesCS1D01G010500 chr1A 83.468 248 21 11 1290 1530 6765830 6765596 1.720000e-51 213.0
14 TraesCS1D01G010500 chr7D 84.615 1040 118 23 1 1011 614264324 614265350 0.000000e+00 996.0
15 TraesCS1D01G010500 chrUn 84.615 1040 117 25 1 1011 187023495 187024520 0.000000e+00 994.0
16 TraesCS1D01G010500 chr5D 84.615 1040 117 25 1 1011 523436822 523437847 0.000000e+00 994.0
17 TraesCS1D01G010500 chr4D 83.942 1040 125 24 1 1011 408289072 408290098 0.000000e+00 957.0
18 TraesCS1D01G010500 chr5B 82.835 1037 134 26 4 1011 548909135 548908114 0.000000e+00 889.0
19 TraesCS1D01G010500 chr7A 90.769 520 23 11 890 1398 692313327 692312822 0.000000e+00 671.0
20 TraesCS1D01G010500 chr7A 91.667 372 25 4 1823 2190 692311969 692311600 5.440000e-141 510.0
21 TraesCS1D01G010500 chr7A 87.778 90 6 3 1706 1795 692312108 692312024 1.390000e-17 100.0
22 TraesCS1D01G010500 chr7A 90.476 63 3 1 1819 1878 692218256 692218194 1.820000e-11 80.5
23 TraesCS1D01G010500 chr2A 82.759 464 54 13 4 451 57438644 57438191 7.390000e-105 390.0
24 TraesCS1D01G010500 chr2A 81.897 464 58 13 4 451 64992117 64992570 3.460000e-98 368.0
25 TraesCS1D01G010500 chr6A 82.328 464 56 13 4 451 615647408 615646955 1.600000e-101 379.0


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 TraesCS1D01G010500 chr1D 5451716 5453922 2206 False 4076.00 4076 100.000000 1 2207 1 chr1D.!!$F1 2206
1 TraesCS1D01G010500 chr1B 639447418 639450199 2781 False 879.50 1365 86.198500 74 2177 2 chr1B.!!$F3 2103
2 TraesCS1D01G010500 chr1B 41002059 41003082 1023 False 843.00 843 82.054000 1 1011 1 chr1B.!!$F1 1010
3 TraesCS1D01G010500 chr1B 8180860 8182765 1905 False 770.50 1206 84.518500 342 2177 2 chr1B.!!$F2 1835
4 TraesCS1D01G010500 chr1B 644621025 644621698 673 True 675.00 675 85.125000 350 1011 1 chr1B.!!$R2 661
5 TraesCS1D01G010500 chr1B 17833430 17836634 3204 True 376.50 416 82.922500 1096 2207 2 chr1B.!!$R3 1111
6 TraesCS1D01G010500 chr1A 6764090 6767242 3152 True 714.75 1264 86.887000 320 2160 4 chr1A.!!$R1 1840
7 TraesCS1D01G010500 chr7D 614264324 614265350 1026 False 996.00 996 84.615000 1 1011 1 chr7D.!!$F1 1010
8 TraesCS1D01G010500 chrUn 187023495 187024520 1025 False 994.00 994 84.615000 1 1011 1 chrUn.!!$F1 1010
9 TraesCS1D01G010500 chr5D 523436822 523437847 1025 False 994.00 994 84.615000 1 1011 1 chr5D.!!$F1 1010
10 TraesCS1D01G010500 chr4D 408289072 408290098 1026 False 957.00 957 83.942000 1 1011 1 chr4D.!!$F1 1010
11 TraesCS1D01G010500 chr5B 548908114 548909135 1021 True 889.00 889 82.835000 4 1011 1 chr5B.!!$R1 1007
12 TraesCS1D01G010500 chr7A 692311600 692313327 1727 True 427.00 671 90.071333 890 2190 3 chr7A.!!$R2 1300

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
642 684 0.469917 ACTCGCCATTGACCCCTATG 59.53 55.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 5871 0.179148 CGGGCAAAGCGGTAAATTCC 60.179 55.0 0.0 0.0 0.0 3.01 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
38 39 4.583073 TCTGCACAGAGTACAGACACTAAA 59.417 41.667 0.00 0.00 31.83 1.85
95 120 8.783660 ATGAATCTTGTAACCTCTGGATAGTA 57.216 34.615 0.00 0.00 0.00 1.82
96 121 8.008513 TGAATCTTGTAACCTCTGGATAGTAC 57.991 38.462 0.00 0.00 0.00 2.73
97 122 7.839705 TGAATCTTGTAACCTCTGGATAGTACT 59.160 37.037 0.00 0.00 0.00 2.73
98 123 9.352191 GAATCTTGTAACCTCTGGATAGTACTA 57.648 37.037 4.77 4.77 0.00 1.82
99 124 8.927675 ATCTTGTAACCTCTGGATAGTACTAG 57.072 38.462 8.85 0.00 0.00 2.57
100 125 6.771749 TCTTGTAACCTCTGGATAGTACTAGC 59.228 42.308 9.73 9.73 0.00 3.42
109 134 7.068348 CCTCTGGATAGTACTAGCACAACTTAA 59.932 40.741 19.21 0.00 0.00 1.85
120 145 5.030874 AGCACAACTTAATTTCAGTACGC 57.969 39.130 0.00 0.00 0.00 4.42
121 146 4.755123 AGCACAACTTAATTTCAGTACGCT 59.245 37.500 0.00 0.00 0.00 5.07
172 197 4.201618 GCCAAGAGAAATAAATTGCGTTGC 60.202 41.667 0.00 0.00 0.00 4.17
188 213 2.182014 GTTGCGTGTCTTTCAAACACC 58.818 47.619 1.17 0.00 43.24 4.16
189 214 0.736053 TGCGTGTCTTTCAAACACCC 59.264 50.000 1.17 0.00 43.24 4.61
242 267 6.144402 CCTTTTCAAGTTACATGTGTTGCATC 59.856 38.462 9.11 0.00 35.19 3.91
244 269 3.188254 TCAAGTTACATGTGTTGCATCGG 59.812 43.478 9.11 0.00 35.19 4.18
281 306 0.887836 TGCACTCAGCTCAGGCAAAG 60.888 55.000 0.00 0.00 45.94 2.77
282 307 0.604780 GCACTCAGCTCAGGCAAAGA 60.605 55.000 0.00 0.00 41.70 2.52
286 311 2.620585 ACTCAGCTCAGGCAAAGAAAAC 59.379 45.455 0.00 0.00 41.70 2.43
293 322 4.740334 GCTCAGGCAAAGAAAACAATGGAA 60.740 41.667 0.00 0.00 38.54 3.53
305 334 4.806640 AACAATGGAATTAAGCAGGGTG 57.193 40.909 0.00 0.00 32.46 4.61
308 337 5.329399 ACAATGGAATTAAGCAGGGTGTAA 58.671 37.500 0.00 0.00 32.46 2.41
362 392 3.879295 CCCAACATGTCTCACACATATCC 59.121 47.826 0.00 0.00 44.60 2.59
429 459 4.428294 TTAGCTTGAATGGATCTCCCTG 57.572 45.455 0.00 0.00 35.38 4.45
484 521 1.754745 GACAAGTCCCAGCACCAGA 59.245 57.895 0.00 0.00 0.00 3.86
614 655 8.407457 TGTACAGACAATATTTCGTTCAGATC 57.593 34.615 0.00 0.00 30.68 2.75
642 684 0.469917 ACTCGCCATTGACCCCTATG 59.530 55.000 0.00 0.00 0.00 2.23
645 687 1.283613 TCGCCATTGACCCCTATGTTT 59.716 47.619 0.00 0.00 0.00 2.83
701 743 1.801332 CTGCTGAATGCCAGACTGC 59.199 57.895 0.00 0.00 45.78 4.40
710 752 1.725641 TGCCAGACTGCATAAGAACG 58.274 50.000 0.00 0.00 36.04 3.95
789 833 4.739137 GCAATGCCCAGTTTGAAAGTGTAA 60.739 41.667 11.43 0.00 0.00 2.41
815 859 5.381757 ACTGTATTTTCAAGTGGTGCCTAA 58.618 37.500 0.00 0.00 0.00 2.69
816 860 6.010219 ACTGTATTTTCAAGTGGTGCCTAAT 58.990 36.000 0.00 0.00 0.00 1.73
821 865 6.909550 TTTTCAAGTGGTGCCTAATTGTAT 57.090 33.333 0.00 0.00 0.00 2.29
822 866 8.588290 ATTTTCAAGTGGTGCCTAATTGTATA 57.412 30.769 0.00 0.00 0.00 1.47
850 897 0.895100 TTTCACATCTGTGCCCTGCC 60.895 55.000 5.44 0.00 45.25 4.85
863 911 3.385755 GTGCCCTGCCTTGAATTTGATAT 59.614 43.478 0.00 0.00 0.00 1.63
867 915 5.302823 GCCCTGCCTTGAATTTGATATTAGT 59.697 40.000 0.00 0.00 0.00 2.24
870 918 9.739276 CCCTGCCTTGAATTTGATATTAGTATA 57.261 33.333 0.00 0.00 0.00 1.47
896 945 3.243569 CCAGTCACTCGTCTCTTGAGTTT 60.244 47.826 0.00 0.00 44.00 2.66
919 968 3.119352 GCCAGAGGACCATTTTTCATGTC 60.119 47.826 0.00 0.00 0.00 3.06
942 991 2.936498 CGCACCTTGGATTGGTAACTAG 59.064 50.000 0.00 0.00 35.80 2.57
989 2150 1.960763 CAGCAGCAGCACAACCGTA 60.961 57.895 3.17 0.00 45.49 4.02
1242 2447 6.128254 CCTTAACTTTGAAACTAGCTACTGCC 60.128 42.308 0.00 0.00 40.80 4.85
1243 2448 4.625607 ACTTTGAAACTAGCTACTGCCT 57.374 40.909 0.00 0.00 40.80 4.75
1244 2449 4.319177 ACTTTGAAACTAGCTACTGCCTG 58.681 43.478 0.00 0.00 40.80 4.85
1246 2451 1.066143 TGAAACTAGCTACTGCCTGCC 60.066 52.381 0.00 0.00 40.80 4.85
1247 2452 1.208293 GAAACTAGCTACTGCCTGCCT 59.792 52.381 0.00 0.00 40.80 4.75
1248 2453 0.827368 AACTAGCTACTGCCTGCCTC 59.173 55.000 0.00 0.00 40.80 4.70
1249 2454 0.032615 ACTAGCTACTGCCTGCCTCT 60.033 55.000 0.00 0.00 40.80 3.69
1275 2486 2.619590 GGACCATGGGTTCGGTTTGTAT 60.620 50.000 18.09 0.00 35.25 2.29
1369 2586 6.586868 TGATGCTTTTTGTTTGTGTGAATC 57.413 33.333 0.00 0.00 0.00 2.52
1375 2592 5.493133 TTTTGTTTGTGTGAATCGTAGCT 57.507 34.783 0.00 0.00 0.00 3.32
1389 2606 0.320421 GTAGCTGCGGTGTCTGGAAA 60.320 55.000 0.00 0.00 0.00 3.13
1403 2862 9.605275 CGGTGTCTGGAAATTATGATATGATAT 57.395 33.333 0.00 0.00 0.00 1.63
1447 2925 2.671070 GCGTATTGTTTTTGCCCCTCAG 60.671 50.000 0.00 0.00 0.00 3.35
1470 2982 7.613022 TCAGAATCAGGCTTTTCTATGTTTGAT 59.387 33.333 8.68 0.00 31.15 2.57
1471 2983 8.248945 CAGAATCAGGCTTTTCTATGTTTGATT 58.751 33.333 8.68 0.52 36.90 2.57
1487 3003 4.572985 TTGATTGACCTCAGTTTTGCAG 57.427 40.909 0.00 0.00 0.00 4.41
1495 3011 1.600636 CAGTTTTGCAGCGGAGGGA 60.601 57.895 0.00 0.00 0.00 4.20
1496 3012 1.302832 AGTTTTGCAGCGGAGGGAG 60.303 57.895 0.00 0.00 0.00 4.30
1497 3013 2.672996 TTTTGCAGCGGAGGGAGC 60.673 61.111 0.00 0.00 0.00 4.70
1508 3024 1.404843 GGAGGGAGCAGTAGTACCTG 58.595 60.000 0.00 0.00 35.49 4.00
1530 3046 2.284995 AGGCAGGGTCCTCTGGTC 60.285 66.667 8.82 0.00 35.43 4.02
1531 3047 2.607750 GGCAGGGTCCTCTGGTCA 60.608 66.667 8.82 0.00 35.43 4.02
1565 3097 2.835895 GCCCGTCCCTCTCTCTCC 60.836 72.222 0.00 0.00 0.00 3.71
1566 3098 2.123640 CCCGTCCCTCTCTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
1568 3100 2.517402 CGTCCCTCTCTCTCCCCG 60.517 72.222 0.00 0.00 0.00 5.73
1586 3118 2.413837 CCGTCAGTTCGGTCTTTTGAT 58.586 47.619 0.00 0.00 44.77 2.57
1587 3119 2.412089 CCGTCAGTTCGGTCTTTTGATC 59.588 50.000 0.00 0.00 44.77 2.92
1603 3135 3.260475 TGATCGGACGATGGTTGAATT 57.740 42.857 12.40 0.00 34.60 2.17
1604 3136 3.605634 TGATCGGACGATGGTTGAATTT 58.394 40.909 12.40 0.00 34.60 1.82
1609 3141 3.437395 CGGACGATGGTTGAATTTGGTTA 59.563 43.478 0.00 0.00 0.00 2.85
1611 3143 5.392595 CGGACGATGGTTGAATTTGGTTAAT 60.393 40.000 0.00 0.00 0.00 1.40
1659 5399 3.118038 GGCCATCCACCTGAATAGTTGTA 60.118 47.826 0.00 0.00 0.00 2.41
1662 5402 5.417580 GCCATCCACCTGAATAGTTGTAAAA 59.582 40.000 0.00 0.00 0.00 1.52
1664 5404 7.284489 GCCATCCACCTGAATAGTTGTAAAATA 59.716 37.037 0.00 0.00 0.00 1.40
1699 5847 0.719465 GGGCACACGAATAGTTGTCG 59.281 55.000 0.00 0.00 44.10 4.35
1703 5851 3.466836 GCACACGAATAGTTGTCGAAAC 58.533 45.455 0.18 0.00 41.02 2.78
1705 5853 4.551217 GCACACGAATAGTTGTCGAAACAA 60.551 41.667 11.33 0.23 43.06 2.83
1820 6004 4.750098 GGAAAAAGAGTCTCGTGTGATTGA 59.250 41.667 0.00 0.00 0.00 2.57
1821 6005 5.236478 GGAAAAAGAGTCTCGTGTGATTGAA 59.764 40.000 0.00 0.00 0.00 2.69
1825 6009 4.742417 AGAGTCTCGTGTGATTGAATGAG 58.258 43.478 0.00 0.00 0.00 2.90
1830 6014 4.686091 TCTCGTGTGATTGAATGAGTGAAC 59.314 41.667 0.00 0.00 32.35 3.18
2037 6243 4.803426 GTGCTCGCTCCGGTGAGG 62.803 72.222 18.19 6.09 46.70 3.86
2039 6245 4.500116 GCTCGCTCCGGTGAGGTC 62.500 72.222 18.19 4.28 46.70 3.85
2122 6339 0.037326 GTGAGTTCCCGTGCTCATCA 60.037 55.000 0.00 0.00 42.72 3.07
2123 6340 0.037326 TGAGTTCCCGTGCTCATCAC 60.037 55.000 0.00 0.00 42.23 3.06
2124 6341 0.741221 GAGTTCCCGTGCTCATCACC 60.741 60.000 0.00 0.00 42.69 4.02
2129 6346 2.202797 CGTGCTCATCACCCCTCG 60.203 66.667 0.00 0.00 42.69 4.63
2179 6396 0.965439 GATCTATGGTGCTCTCGGCT 59.035 55.000 0.00 0.00 42.39 5.52
2180 6397 0.965439 ATCTATGGTGCTCTCGGCTC 59.035 55.000 0.00 0.00 42.39 4.70
2181 6398 0.106469 TCTATGGTGCTCTCGGCTCT 60.106 55.000 0.00 0.00 42.39 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.876274 TGTGCAGAACAGGACTAGATC 57.124 47.619 0.00 0.00 33.78 2.75
27 28 2.371841 TCCATGGCTGTTTAGTGTCTGT 59.628 45.455 6.96 0.00 0.00 3.41
64 65 9.213777 TCCAGAGGTTACAAGATTCATAATAGT 57.786 33.333 0.00 0.00 0.00 2.12
95 120 6.128634 GCGTACTGAAATTAAGTTGTGCTAGT 60.129 38.462 0.00 0.00 0.00 2.57
96 121 6.090898 AGCGTACTGAAATTAAGTTGTGCTAG 59.909 38.462 0.00 0.00 30.95 3.42
97 122 5.929992 AGCGTACTGAAATTAAGTTGTGCTA 59.070 36.000 0.00 0.00 30.95 3.49
98 123 4.755123 AGCGTACTGAAATTAAGTTGTGCT 59.245 37.500 0.00 0.00 0.00 4.40
99 124 5.030874 AGCGTACTGAAATTAAGTTGTGC 57.969 39.130 0.00 0.00 0.00 4.57
120 145 2.437281 ACTGGGATTCTGATACAGCCAG 59.563 50.000 15.94 15.94 40.94 4.85
121 146 2.481441 ACTGGGATTCTGATACAGCCA 58.519 47.619 0.00 0.00 32.60 4.75
156 181 3.911964 AGACACGCAACGCAATTTATTTC 59.088 39.130 0.00 0.00 0.00 2.17
172 197 3.817960 CGGGTGTTTGAAAGACACG 57.182 52.632 15.27 15.27 45.17 4.49
188 213 1.852942 ATATACAACGCTCTGCACGG 58.147 50.000 0.08 0.00 34.00 4.94
189 214 2.980476 CCTATATACAACGCTCTGCACG 59.020 50.000 0.00 0.00 0.00 5.34
227 252 2.746904 CCTTCCGATGCAACACATGTAA 59.253 45.455 0.00 0.00 39.84 2.41
281 306 5.639082 CACCCTGCTTAATTCCATTGTTTTC 59.361 40.000 0.00 0.00 0.00 2.29
282 307 5.071653 ACACCCTGCTTAATTCCATTGTTTT 59.928 36.000 0.00 0.00 0.00 2.43
286 311 5.913137 TTACACCCTGCTTAATTCCATTG 57.087 39.130 0.00 0.00 0.00 2.82
293 322 4.022329 GCAACAGTTTACACCCTGCTTAAT 60.022 41.667 0.00 0.00 31.76 1.40
333 363 4.759693 GTGTGAGACATGTTGGGTGATTTA 59.240 41.667 0.00 0.00 0.00 1.40
336 366 2.106338 TGTGTGAGACATGTTGGGTGAT 59.894 45.455 0.00 0.00 0.00 3.06
338 368 1.965935 TGTGTGAGACATGTTGGGTG 58.034 50.000 0.00 0.00 0.00 4.61
345 375 5.239525 TCTCTACGGATATGTGTGAGACATG 59.760 44.000 5.38 0.00 45.43 3.21
362 392 5.316770 GCTGTTGCAAAACTATTCTCTACG 58.683 41.667 0.00 0.00 39.41 3.51
429 459 3.007398 ACTGATCCCAGAAACAGAGACAC 59.993 47.826 0.00 0.00 43.02 3.67
484 521 2.540383 TGTCTCACAAGGCCTGTCTAT 58.460 47.619 5.69 0.00 35.47 1.98
605 646 0.030908 GTAGCCTCCCGATCTGAACG 59.969 60.000 0.00 0.00 0.00 3.95
633 674 3.506067 CACCAACAAGAAACATAGGGGTC 59.494 47.826 0.00 0.00 0.00 4.46
642 684 5.554822 TTACTGTCACACCAACAAGAAAC 57.445 39.130 0.00 0.00 0.00 2.78
645 687 4.055360 CGATTACTGTCACACCAACAAGA 58.945 43.478 0.00 0.00 0.00 3.02
701 743 3.024547 TGACTCCCCTCTCGTTCTTATG 58.975 50.000 0.00 0.00 0.00 1.90
707 749 1.827969 CAATCTGACTCCCCTCTCGTT 59.172 52.381 0.00 0.00 0.00 3.85
710 752 3.637769 ACTACAATCTGACTCCCCTCTC 58.362 50.000 0.00 0.00 0.00 3.20
789 833 4.278419 GGCACCACTTGAAAATACAGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
863 911 6.413052 AGACGAGTGACTGGTTCTATACTAA 58.587 40.000 0.86 0.00 0.00 2.24
867 915 5.100344 AGAGACGAGTGACTGGTTCTATA 57.900 43.478 0.86 0.00 0.00 1.31
870 918 2.279935 AGAGACGAGTGACTGGTTCT 57.720 50.000 0.86 4.48 0.00 3.01
883 931 2.064762 CTCTGGCAAACTCAAGAGACG 58.935 52.381 3.73 0.00 0.00 4.18
896 945 2.673775 TGAAAAATGGTCCTCTGGCA 57.326 45.000 0.00 0.00 0.00 4.92
919 968 0.322997 TTACCAATCCAAGGTGCGGG 60.323 55.000 0.00 0.00 40.26 6.13
942 991 7.542130 GGACAGAAATGTGGAAAATGTTACATC 59.458 37.037 0.00 0.00 27.62 3.06
982 2143 1.492873 TCGACGACGACTACGGTTG 59.507 57.895 5.75 0.00 43.81 3.77
983 2144 3.951332 TCGACGACGACTACGGTT 58.049 55.556 5.75 0.00 43.81 4.44
1174 2371 3.706373 GGTGGAGGAGCTTGCGGA 61.706 66.667 0.00 0.00 0.00 5.54
1242 2447 1.692042 ATGGTCCTGGGAGAGGCAG 60.692 63.158 0.00 0.00 42.47 4.85
1243 2448 1.997311 CATGGTCCTGGGAGAGGCA 60.997 63.158 0.00 0.00 42.47 4.75
1244 2449 2.750657 CCATGGTCCTGGGAGAGGC 61.751 68.421 2.57 0.00 42.47 4.70
1266 2477 7.381139 GCACCCATTATTATCAAATACAAACCG 59.619 37.037 0.00 0.00 0.00 4.44
1275 2486 8.588290 AACTAACAGCACCCATTATTATCAAA 57.412 30.769 0.00 0.00 0.00 2.69
1369 2586 2.486636 TTCCAGACACCGCAGCTACG 62.487 60.000 0.00 0.00 0.00 3.51
1375 2592 3.342377 TCATAATTTCCAGACACCGCA 57.658 42.857 0.00 0.00 0.00 5.69
1389 2606 6.835174 AGCGGAGGCAATATCATATCATAAT 58.165 36.000 0.00 0.00 43.41 1.28
1403 2862 4.338118 CCTTATATTTTGAAGCGGAGGCAA 59.662 41.667 0.00 0.00 43.41 4.52
1447 2925 8.246180 TCAATCAAACATAGAAAAGCCTGATTC 58.754 33.333 0.00 0.00 31.62 2.52
1470 2982 0.662619 CGCTGCAAAACTGAGGTCAA 59.337 50.000 0.00 0.00 0.00 3.18
1471 2983 1.165907 CCGCTGCAAAACTGAGGTCA 61.166 55.000 0.00 0.00 33.33 4.02
1487 3003 1.734748 GTACTACTGCTCCCTCCGC 59.265 63.158 0.00 0.00 0.00 5.54
1495 3011 2.180276 CCTCCAACAGGTACTACTGCT 58.820 52.381 0.00 0.00 42.21 4.24
1496 3012 1.405661 GCCTCCAACAGGTACTACTGC 60.406 57.143 0.00 0.00 45.61 4.40
1497 3013 1.899814 TGCCTCCAACAGGTACTACTG 59.100 52.381 0.00 0.00 45.61 2.74
1530 3046 3.727673 CGGGCAACATATTTCAACGACTG 60.728 47.826 0.00 0.00 39.74 3.51
1531 3047 2.418628 CGGGCAACATATTTCAACGACT 59.581 45.455 0.00 0.00 39.74 4.18
1568 3100 2.412089 CCGATCAAAAGACCGAACTGAC 59.588 50.000 0.00 0.00 0.00 3.51
1586 3118 2.080693 CCAAATTCAACCATCGTCCGA 58.919 47.619 0.00 0.00 0.00 4.55
1587 3119 1.810151 ACCAAATTCAACCATCGTCCG 59.190 47.619 0.00 0.00 0.00 4.79
1603 3135 4.456222 TCGGCTTTCGATTGAATTAACCAA 59.544 37.500 0.00 0.00 43.74 3.67
1604 3136 4.004314 TCGGCTTTCGATTGAATTAACCA 58.996 39.130 0.00 0.00 43.74 3.67
1618 5358 2.001872 CCATTTGGCAAATCGGCTTTC 58.998 47.619 22.02 0.00 41.89 2.62
1664 5404 8.113173 TCGTGTGCCCTAAACTTAAATTATTT 57.887 30.769 0.00 0.00 0.00 1.40
1666 5406 7.690952 TTCGTGTGCCCTAAACTTAAATTAT 57.309 32.000 0.00 0.00 0.00 1.28
1667 5407 7.690952 ATTCGTGTGCCCTAAACTTAAATTA 57.309 32.000 0.00 0.00 0.00 1.40
1669 5409 6.882678 ACTATTCGTGTGCCCTAAACTTAAAT 59.117 34.615 0.00 0.00 0.00 1.40
1670 5410 6.232692 ACTATTCGTGTGCCCTAAACTTAAA 58.767 36.000 0.00 0.00 0.00 1.52
1671 5411 5.797051 ACTATTCGTGTGCCCTAAACTTAA 58.203 37.500 0.00 0.00 0.00 1.85
1672 5412 5.410355 ACTATTCGTGTGCCCTAAACTTA 57.590 39.130 0.00 0.00 0.00 2.24
1705 5853 9.938280 GTAAATTCCATAAGCCCTTAACTTTTT 57.062 29.630 0.00 0.00 0.00 1.94
1711 5859 4.581409 GCGGTAAATTCCATAAGCCCTTAA 59.419 41.667 0.00 0.00 0.00 1.85
1712 5860 4.139038 GCGGTAAATTCCATAAGCCCTTA 58.861 43.478 0.00 0.00 0.00 2.69
1713 5861 2.956333 GCGGTAAATTCCATAAGCCCTT 59.044 45.455 0.00 0.00 0.00 3.95
1714 5862 2.174854 AGCGGTAAATTCCATAAGCCCT 59.825 45.455 0.00 0.00 0.00 5.19
1716 5864 4.359706 CAAAGCGGTAAATTCCATAAGCC 58.640 43.478 0.00 0.00 0.00 4.35
1718 5866 4.359706 GGCAAAGCGGTAAATTCCATAAG 58.640 43.478 0.00 0.00 0.00 1.73
1719 5867 3.131400 GGGCAAAGCGGTAAATTCCATAA 59.869 43.478 0.00 0.00 0.00 1.90
1720 5868 2.691011 GGGCAAAGCGGTAAATTCCATA 59.309 45.455 0.00 0.00 0.00 2.74
1723 5871 0.179148 CGGGCAAAGCGGTAAATTCC 60.179 55.000 0.00 0.00 0.00 3.01
1724 5872 0.524414 ACGGGCAAAGCGGTAAATTC 59.476 50.000 0.00 0.00 0.00 2.17
1796 5975 3.107642 TCACACGAGACTCTTTTTCCC 57.892 47.619 0.03 0.00 0.00 3.97
1797 5976 4.750098 TCAATCACACGAGACTCTTTTTCC 59.250 41.667 0.03 0.00 0.00 3.13
1798 5977 5.907197 TCAATCACACGAGACTCTTTTTC 57.093 39.130 0.03 0.00 0.00 2.29
1800 5979 5.991606 TCATTCAATCACACGAGACTCTTTT 59.008 36.000 0.03 0.00 0.00 2.27
1803 5987 4.219507 ACTCATTCAATCACACGAGACTCT 59.780 41.667 0.03 0.00 0.00 3.24
1820 6004 8.290325 GGATTTAGTTTCTTTCGTTCACTCATT 58.710 33.333 0.00 0.00 0.00 2.57
1821 6005 7.444183 TGGATTTAGTTTCTTTCGTTCACTCAT 59.556 33.333 0.00 0.00 0.00 2.90
1825 6009 6.356190 CGTTGGATTTAGTTTCTTTCGTTCAC 59.644 38.462 0.00 0.00 0.00 3.18
1830 6014 6.462073 TCTCGTTGGATTTAGTTTCTTTCG 57.538 37.500 0.00 0.00 0.00 3.46
2008 6214 2.105930 GAGCACCGGAGCTAGCAG 59.894 66.667 26.96 7.69 46.75 4.24
2031 6237 4.717313 GGGCAACGGGACCTCACC 62.717 72.222 0.00 0.00 43.78 4.02
2076 6286 4.147322 GCACGACGGCGATGTTGG 62.147 66.667 22.49 0.00 41.64 3.77
2124 6341 4.452733 GTGGACCGAAGCCGAGGG 62.453 72.222 0.00 0.00 38.22 4.30
2129 6346 1.689273 AGATAGATGTGGACCGAAGCC 59.311 52.381 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.