Multiple sequence alignment - TraesCS3D01G017000

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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 TraesCS3D01G017000 chr3D 100.000 3184 0 0 1 3184 5859004 5855821 0.000000e+00 5880.0
1 TraesCS3D01G017000 chr3D 78.748 687 125 14 1402 2079 5862588 5863262 1.050000e-119 440.0
2 TraesCS3D01G017000 chrUn 91.667 1692 50 20 872 2529 40588511 40590145 0.000000e+00 2259.0
3 TraesCS3D01G017000 chrUn 84.906 318 20 2 2826 3119 40590159 40590472 2.400000e-76 296.0
4 TraesCS3D01G017000 chr3B 92.200 1500 41 23 872 2334 11663643 11665103 0.000000e+00 2052.0
5 TraesCS3D01G017000 chr3B 85.000 520 40 10 2701 3184 11665426 11665943 7.930000e-136 494.0
6 TraesCS3D01G017000 chr3B 79.420 690 125 11 1403 2085 11660042 11659363 3.720000e-129 472.0
7 TraesCS3D01G017000 chr3B 91.667 96 8 0 1564 1659 190848566 190848661 1.990000e-27 134.0
8 TraesCS3D01G017000 chr3B 79.235 183 34 3 1897 2075 7719695 7719513 1.200000e-24 124.0
9 TraesCS3D01G017000 chr3A 90.756 1482 70 27 878 2346 15314724 15316151 0.000000e+00 1916.0
10 TraesCS3D01G017000 chr3A 92.834 628 36 4 1 626 15313104 15313724 0.000000e+00 902.0
11 TraesCS3D01G017000 chr3A 89.873 395 29 3 2425 2815 15317638 15318025 6.130000e-137 497.0
12 TraesCS3D01G017000 chr3A 83.254 418 53 12 1258 1662 313184545 313184132 5.020000e-98 368.0
13 TraesCS3D01G017000 chr3A 84.776 335 24 11 2877 3184 15325805 15326139 8.580000e-81 311.0
14 TraesCS3D01G017000 chr3A 93.407 91 6 0 2485 2575 40858756 40858666 5.540000e-28 135.0
15 TraesCS3D01G017000 chr3A 100.000 28 0 0 2367 2394 15317615 15317642 6.000000e-03 52.8
16 TraesCS3D01G017000 chr7B 78.348 702 120 21 1385 2074 40287317 40286636 2.940000e-115 425.0
17 TraesCS3D01G017000 chr5D 85.821 402 38 13 1238 1625 380295999 380295603 2.960000e-110 409.0
18 TraesCS3D01G017000 chr5D 92.929 99 7 0 1564 1662 30832513 30832415 9.210000e-31 145.0
19 TraesCS3D01G017000 chr4D 92.929 99 7 0 1564 1662 444094288 444094386 9.210000e-31 145.0
20 TraesCS3D01G017000 chr7A 93.750 96 4 2 2485 2580 41451722 41451629 3.310000e-30 143.0
21 TraesCS3D01G017000 chr1B 91.753 97 7 1 1235 1331 298764587 298764682 1.990000e-27 134.0
22 TraesCS3D01G017000 chr1A 85.577 104 10 4 1564 1662 26057202 26057099 1.560000e-18 104.0
23 TraesCS3D01G017000 chr2B 93.939 66 4 0 2510 2575 668571638 668571703 2.020000e-17 100.0


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 TraesCS3D01G017000 chr3D 5855821 5859004 3183 True 5880.00 5880 100.00000 1 3184 1 chr3D.!!$R1 3183
1 TraesCS3D01G017000 chr3D 5862588 5863262 674 False 440.00 440 78.74800 1402 2079 1 chr3D.!!$F1 677
2 TraesCS3D01G017000 chrUn 40588511 40590472 1961 False 1277.50 2259 88.28650 872 3119 2 chrUn.!!$F1 2247
3 TraesCS3D01G017000 chr3B 11663643 11665943 2300 False 1273.00 2052 88.60000 872 3184 2 chr3B.!!$F2 2312
4 TraesCS3D01G017000 chr3B 11659363 11660042 679 True 472.00 472 79.42000 1403 2085 1 chr3B.!!$R2 682
5 TraesCS3D01G017000 chr3A 15313104 15318025 4921 False 841.95 1916 93.36575 1 2815 4 chr3A.!!$F2 2814
6 TraesCS3D01G017000 chr7B 40286636 40287317 681 True 425.00 425 78.34800 1385 2074 1 chr7B.!!$R1 689

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
796 1401 0.589223 GCCGTTTGTTTGATCGGACA 59.411 50.0 6.63 0.0 44.86 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2653 5151 0.037734 TCTCAGTCACAGTCCGGCTA 59.962 55.0 0.0 0.0 0.0 3.93 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
73 74 2.972625 TGATCTGGTTAGCACGAAAGG 58.027 47.619 0.00 0.00 0.00 3.11
202 205 3.938334 TCATGTTGGGTACATCATCAACG 59.062 43.478 0.00 0.00 45.71 4.10
208 211 5.365403 TGGGTACATCATCAACGAAAAAC 57.635 39.130 0.00 0.00 0.00 2.43
311 314 3.792401 TGTGGTGTTGATAGGATTAGCG 58.208 45.455 0.00 0.00 0.00 4.26
312 315 3.196901 TGTGGTGTTGATAGGATTAGCGT 59.803 43.478 0.00 0.00 0.00 5.07
313 316 3.555956 GTGGTGTTGATAGGATTAGCGTG 59.444 47.826 0.00 0.00 0.00 5.34
409 412 3.589988 AGTAATGACTCACTCGCAAAGG 58.410 45.455 0.00 0.00 0.00 3.11
416 419 2.301870 ACTCACTCGCAAAGGGTCATTA 59.698 45.455 0.00 0.00 0.00 1.90
440 443 3.518992 TTCCACTAAAGTTGGGAAGGG 57.481 47.619 0.00 0.00 34.63 3.95
445 448 4.017126 CACTAAAGTTGGGAAGGGGATTC 58.983 47.826 0.00 0.00 37.17 2.52
453 456 4.139162 TGGGAAGGGGATTCAAATTGAA 57.861 40.909 11.10 11.10 41.09 2.69
454 457 4.497516 TGGGAAGGGGATTCAAATTGAAA 58.502 39.130 12.75 0.00 40.12 2.69
455 458 4.910304 TGGGAAGGGGATTCAAATTGAAAA 59.090 37.500 12.75 0.00 40.12 2.29
531 534 4.883083 TGAATTATACATGAGGTCGCTCC 58.117 43.478 0.00 0.00 0.00 4.70
535 538 1.663379 TACATGAGGTCGCTCCACGG 61.663 60.000 0.00 0.00 43.89 4.94
545 548 3.654178 GCTCCACGGCGAGTAATTA 57.346 52.632 16.62 0.00 32.11 1.40
575 578 1.846782 CGAATCAAGAGTAACGGCTCG 59.153 52.381 0.00 0.00 40.26 5.03
576 579 2.477357 CGAATCAAGAGTAACGGCTCGA 60.477 50.000 1.50 0.00 40.26 4.04
603 785 5.012893 CCAAAGAGCCATTAACTTTCCTCT 58.987 41.667 0.00 0.00 32.59 3.69
620 802 2.378886 CCTCTAAAGTTGGAAAGGGGGT 59.621 50.000 0.00 0.00 0.00 4.95
627 809 3.664320 AGTTGGAAAGGGGGTTGAAATT 58.336 40.909 0.00 0.00 0.00 1.82
687 1292 3.053896 GGGTAGCAACACGTGGGC 61.054 66.667 21.57 21.95 0.00 5.36
691 1296 1.301401 TAGCAACACGTGGGCTGTC 60.301 57.895 33.60 18.05 38.55 3.51
713 1318 1.289109 GCGTTTCGTCCAGCTAAGCA 61.289 55.000 0.00 0.00 0.00 3.91
716 1321 2.222819 CGTTTCGTCCAGCTAAGCAATC 60.223 50.000 0.00 0.00 0.00 2.67
722 1327 2.799412 GTCCAGCTAAGCAATCGATGAG 59.201 50.000 0.00 0.00 0.00 2.90
725 1330 3.986572 CCAGCTAAGCAATCGATGAGTAG 59.013 47.826 0.00 0.12 0.00 2.57
732 1337 4.372656 AGCAATCGATGAGTAGCTAAACC 58.627 43.478 0.00 0.00 0.00 3.27
737 1342 4.789807 TCGATGAGTAGCTAAACCTAGGT 58.210 43.478 9.21 9.21 39.25 3.08
739 1344 4.261656 CGATGAGTAGCTAAACCTAGGTGG 60.262 50.000 17.14 10.16 36.54 4.61
769 1374 1.569653 CCCCTTCCGTTAGAGAACCT 58.430 55.000 0.00 0.00 31.28 3.50
780 1385 1.884235 AGAGAACCTGTTTCTTGCCG 58.116 50.000 0.00 0.00 45.24 5.69
781 1386 1.141053 AGAGAACCTGTTTCTTGCCGT 59.859 47.619 0.00 0.00 45.24 5.68
782 1387 1.947456 GAGAACCTGTTTCTTGCCGTT 59.053 47.619 0.00 0.00 45.24 4.44
783 1388 2.357952 GAGAACCTGTTTCTTGCCGTTT 59.642 45.455 0.00 0.00 45.24 3.60
796 1401 0.589223 GCCGTTTGTTTGATCGGACA 59.411 50.000 6.63 0.00 44.86 4.02
810 1415 1.067213 TCGGACATCGAATGCTCAACA 60.067 47.619 0.00 0.00 45.86 3.33
815 1420 2.738846 ACATCGAATGCTCAACAGTCAC 59.261 45.455 0.00 0.00 43.60 3.67
820 1425 3.061831 CGAATGCTCAACAGTCACATCTC 59.938 47.826 0.00 0.00 43.60 2.75
824 1429 3.999001 TGCTCAACAGTCACATCTCAATC 59.001 43.478 0.00 0.00 0.00 2.67
837 1442 4.159693 ACATCTCAATCGGCGCCTTATATA 59.840 41.667 26.68 8.51 0.00 0.86
862 1602 1.196012 GGGAAGGAGGGAGTACTGTG 58.804 60.000 0.00 0.00 0.00 3.66
871 1611 4.404715 GGAGGGAGTACTGTGCAAGTATAA 59.595 45.833 0.00 0.00 43.30 0.98
872 1612 5.452077 GGAGGGAGTACTGTGCAAGTATAAG 60.452 48.000 0.00 0.00 43.30 1.73
873 1613 5.024118 AGGGAGTACTGTGCAAGTATAAGT 58.976 41.667 0.00 1.79 43.30 2.24
874 1614 6.192773 AGGGAGTACTGTGCAAGTATAAGTA 58.807 40.000 0.00 1.01 43.30 2.24
1361 2157 7.500227 TCTTTCCAGATTATTACAAGGCATGAG 59.500 37.037 0.00 0.00 0.00 2.90
1362 2158 5.065914 TCCAGATTATTACAAGGCATGAGC 58.934 41.667 0.00 0.00 41.10 4.26
1364 2160 5.300034 CCAGATTATTACAAGGCATGAGCAA 59.700 40.000 0.00 0.00 44.61 3.91
1367 2163 7.002879 AGATTATTACAAGGCATGAGCAATCT 58.997 34.615 0.00 2.87 44.61 2.40
1378 2174 4.201783 GCATGAGCAATCTTGGCATTTTTC 60.202 41.667 0.00 0.00 41.58 2.29
2086 2904 3.160748 GCTCCAGCCTCCTCCTCC 61.161 72.222 0.00 0.00 34.31 4.30
2087 2905 2.695597 CTCCAGCCTCCTCCTCCT 59.304 66.667 0.00 0.00 0.00 3.69
2088 2906 1.457455 CTCCAGCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
2089 2907 2.445654 CCAGCCTCCTCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
2090 2908 2.695597 CAGCCTCCTCCTCCTCCT 59.304 66.667 0.00 0.00 0.00 3.69
2091 2909 1.457455 CAGCCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
2092 2910 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
2093 2911 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
2094 2912 1.232792 CCTCCTCCTCCTCCTCCTG 59.767 68.421 0.00 0.00 0.00 3.86
2147 2965 3.589542 CCACCACCACCACCCCAT 61.590 66.667 0.00 0.00 0.00 4.00
2148 2966 2.283101 CACCACCACCACCCCATG 60.283 66.667 0.00 0.00 0.00 3.66
2149 2967 4.299796 ACCACCACCACCCCATGC 62.300 66.667 0.00 0.00 0.00 4.06
2150 2968 3.983420 CCACCACCACCCCATGCT 61.983 66.667 0.00 0.00 0.00 3.79
2151 2969 2.611505 CCACCACCACCCCATGCTA 61.612 63.158 0.00 0.00 0.00 3.49
2152 2970 1.077501 CACCACCACCCCATGCTAG 60.078 63.158 0.00 0.00 0.00 3.42
2188 3006 1.003233 GGAGGCTCCAGTGACAACC 60.003 63.158 28.55 0.00 36.28 3.77
2231 3049 5.527951 TGATGTTGTGTATGTTTTGGCTTC 58.472 37.500 0.00 0.00 0.00 3.86
2233 3051 5.528043 TGTTGTGTATGTTTTGGCTTCAT 57.472 34.783 0.00 0.00 0.00 2.57
2252 3070 6.742644 GCTTCATATGGCCTGTTATCAGTACT 60.743 42.308 3.32 0.00 39.82 2.73
2292 3110 1.549203 CTAGGGCAAGCATGTTTGGT 58.451 50.000 21.80 0.00 34.30 3.67
2297 3115 1.336240 GGCAAGCATGTTTGGTCTGTC 60.336 52.381 21.80 5.74 31.86 3.51
2309 3127 2.650322 TGGTCTGTCTCCAAAACCAAC 58.350 47.619 0.00 0.00 37.08 3.77
2404 4898 7.114882 GCAAAACATTATTTGTATGCACACA 57.885 32.000 0.00 0.00 44.56 3.72
2405 4899 7.008859 GCAAAACATTATTTGTATGCACACAC 58.991 34.615 0.00 0.00 44.56 3.82
2406 4900 7.307042 GCAAAACATTATTTGTATGCACACACA 60.307 33.333 0.00 0.00 44.56 3.72
2469 4963 1.729284 CCAATCATGGGCAAGCAAAC 58.271 50.000 0.00 0.00 43.51 2.93
2477 4971 1.068895 TGGGCAAGCAAACACATCAAG 59.931 47.619 0.00 0.00 0.00 3.02
2478 4972 1.142474 GGCAAGCAAACACATCAAGC 58.858 50.000 0.00 0.00 0.00 4.01
2507 5001 5.519808 ACCAATCCCCTCCTTTTATTTCTC 58.480 41.667 0.00 0.00 0.00 2.87
2565 5059 7.654022 TGGAATAAAACACCCTATTTCCATC 57.346 36.000 0.00 0.00 0.00 3.51
2571 5065 2.752903 ACACCCTATTTCCATCGCAAAC 59.247 45.455 0.00 0.00 0.00 2.93
2572 5066 2.752354 CACCCTATTTCCATCGCAAACA 59.248 45.455 0.00 0.00 0.00 2.83
2614 5112 2.297033 AGCATTTGGTAGGTGCTGTTTG 59.703 45.455 0.00 0.00 46.60 2.93
2628 5126 0.534412 TGTTTGCACTGGGTGGTTTG 59.466 50.000 0.00 0.00 33.64 2.93
2629 5127 0.820871 GTTTGCACTGGGTGGTTTGA 59.179 50.000 0.00 0.00 33.64 2.69
2637 5135 3.888930 CACTGGGTGGTTTGATAAGTTGT 59.111 43.478 0.00 0.00 0.00 3.32
2643 5141 6.177610 GGGTGGTTTGATAAGTTGTCAGATA 58.822 40.000 2.38 0.00 0.00 1.98
2653 5151 4.833478 AGTTGTCAGATAGCCACTTGAT 57.167 40.909 0.00 0.00 0.00 2.57
2658 5156 2.297315 TCAGATAGCCACTTGATAGCCG 59.703 50.000 0.00 0.00 0.00 5.52
2660 5158 1.618837 GATAGCCACTTGATAGCCGGA 59.381 52.381 5.05 0.00 0.00 5.14
2687 5185 4.021632 TGACTGAGAACTGGAGAACTCATG 60.022 45.833 4.23 0.00 38.43 3.07
2720 5218 5.625150 CTTAATCTTGGATACCTTCTGGGG 58.375 45.833 0.00 0.00 40.03 4.96
2745 5243 0.170561 GAGCTTCAGACGTCGCCTTA 59.829 55.000 10.46 0.00 0.00 2.69
2760 5258 3.066342 TCGCCTTATCTCTGACGTTTAGG 59.934 47.826 0.00 0.00 0.00 2.69
2817 5315 5.444176 TGGATACACAATGTGATATGCCAA 58.556 37.500 21.34 2.75 46.17 4.52
2818 5316 5.299028 TGGATACACAATGTGATATGCCAAC 59.701 40.000 21.34 2.69 46.17 3.77
2819 5317 5.278463 GGATACACAATGTGATATGCCAACC 60.278 44.000 21.34 7.41 36.96 3.77
2820 5318 3.429492 ACACAATGTGATATGCCAACCA 58.571 40.909 21.34 0.00 36.96 3.67
2821 5319 3.444742 ACACAATGTGATATGCCAACCAG 59.555 43.478 21.34 0.00 36.96 4.00
2823 5321 4.340097 CACAATGTGATATGCCAACCAGAT 59.660 41.667 7.78 0.00 35.23 2.90
2824 5322 4.340097 ACAATGTGATATGCCAACCAGATG 59.660 41.667 0.00 0.00 0.00 2.90
2888 5407 5.063817 TGCGCATGTATGTAAGCATATCATC 59.936 40.000 5.66 0.00 39.49 2.92
2944 5463 2.095567 CCACCTGTTTGATTCAAGCGAG 60.096 50.000 8.46 5.14 0.00 5.03
2963 5482 7.527084 AGCGAGATGAGTTATTTACAAAGTC 57.473 36.000 0.00 0.00 0.00 3.01
3028 5571 2.559668 AGCATATCATTTGGCCAATCCG 59.440 45.455 21.26 10.95 37.80 4.18
3079 5622 4.324402 GCAGTAAACATTTGATTCAAGCGG 59.676 41.667 0.00 0.00 0.00 5.52
3164 5707 2.183858 GACGAGGCGTTTTTGCTCCC 62.184 60.000 0.00 0.00 41.37 4.30
3165 5708 2.962569 GAGGCGTTTTTGCTCCCC 59.037 61.111 0.00 0.00 34.52 4.81
3166 5709 2.978018 GAGGCGTTTTTGCTCCCCG 61.978 63.158 0.00 0.00 34.52 5.73
3170 5713 2.650778 GTTTTTGCTCCCCGGCTG 59.349 61.111 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.836577 TTAAAGTTTGTATTTGCAAGGTGC 57.163 33.333 0.00 0.00 45.29 5.01
47 48 7.201732 CCTTTCGTGCTAACCAGATCAAATTAT 60.202 37.037 0.00 0.00 0.00 1.28
99 102 5.927689 CAGCAAAAATGAAACTCCTATTGCA 59.072 36.000 9.46 0.00 43.12 4.08
114 117 6.592607 CCAAGCAGAATATTGTCAGCAAAAAT 59.407 34.615 0.00 0.00 38.21 1.82
119 122 3.954200 TCCAAGCAGAATATTGTCAGCA 58.046 40.909 0.00 0.00 32.78 4.41
208 211 5.864474 ACGCTTCAGAACATTCAACTAGTAG 59.136 40.000 0.00 0.00 0.00 2.57
283 286 6.708885 ATCCTATCAACACCACATGGATAT 57.291 37.500 4.53 0.00 38.94 1.63
284 287 6.514012 AATCCTATCAACACCACATGGATA 57.486 37.500 4.53 0.00 38.94 2.59
285 288 5.393068 AATCCTATCAACACCACATGGAT 57.607 39.130 4.53 0.00 38.94 3.41
286 289 4.860802 AATCCTATCAACACCACATGGA 57.139 40.909 4.53 0.00 38.94 3.41
287 290 4.516698 GCTAATCCTATCAACACCACATGG 59.483 45.833 0.00 0.00 42.17 3.66
288 291 4.212004 CGCTAATCCTATCAACACCACATG 59.788 45.833 0.00 0.00 0.00 3.21
289 292 4.141711 ACGCTAATCCTATCAACACCACAT 60.142 41.667 0.00 0.00 0.00 3.21
313 316 9.357652 AGATAAAAACATGTTGATATGCACAAC 57.642 29.630 12.82 10.81 45.07 3.32
352 355 5.810074 CGGTCTGATATTACACATTGTGTCA 59.190 40.000 24.92 15.54 43.92 3.58
465 468 3.547054 TTTGTCCTACCACGACACTTT 57.453 42.857 0.00 0.00 39.89 2.66
506 509 6.073548 GGAGCGACCTCATGTATAATTCAAAG 60.074 42.308 0.00 0.00 39.96 2.77
531 534 1.326548 GGCAAGTAATTACTCGCCGTG 59.673 52.381 27.36 17.84 45.40 4.94
535 538 3.554324 TCGATTGGCAAGTAATTACTCGC 59.446 43.478 18.42 18.42 35.56 5.03
545 548 3.679389 ACTCTTGATTCGATTGGCAAGT 58.321 40.909 5.96 0.00 38.95 3.16
555 558 1.846782 CGAGCCGTTACTCTTGATTCG 59.153 52.381 0.00 0.00 34.35 3.34
575 578 1.094785 TTAATGGCTCTTTGGCGCTC 58.905 50.000 7.64 0.00 45.14 5.03
576 579 0.811281 GTTAATGGCTCTTTGGCGCT 59.189 50.000 7.64 0.00 45.14 5.92
603 785 3.975479 TCAACCCCCTTTCCAACTTTA 57.025 42.857 0.00 0.00 0.00 1.85
607 789 3.389656 TCAATTTCAACCCCCTTTCCAAC 59.610 43.478 0.00 0.00 0.00 3.77
610 792 4.908601 ATTCAATTTCAACCCCCTTTCC 57.091 40.909 0.00 0.00 0.00 3.13
612 794 4.802583 GCGAATTCAATTTCAACCCCCTTT 60.803 41.667 6.22 0.00 0.00 3.11
644 1249 3.995705 CCGTTCGGGTTTGTAATAAGACA 59.004 43.478 3.04 0.00 0.00 3.41
651 1256 0.035176 CCCTCCGTTCGGGTTTGTAA 59.965 55.000 11.37 0.00 36.91 2.41
652 1257 1.672898 CCCTCCGTTCGGGTTTGTA 59.327 57.895 11.37 0.00 36.91 2.41
653 1258 2.428622 CCCTCCGTTCGGGTTTGT 59.571 61.111 11.37 0.00 36.91 2.83
662 1267 1.844289 TGTTGCTACCCCCTCCGTT 60.844 57.895 0.00 0.00 0.00 4.44
671 1276 2.032071 AGCCCACGTGTTGCTACC 59.968 61.111 23.50 1.56 32.56 3.18
687 1292 3.110178 GGACGAAACGCGGGACAG 61.110 66.667 12.47 0.00 46.49 3.51
691 1296 3.636313 TAGCTGGACGAAACGCGGG 62.636 63.158 12.47 0.00 46.49 6.13
713 1318 5.834204 ACCTAGGTTTAGCTACTCATCGATT 59.166 40.000 9.21 0.00 0.00 3.34
716 1321 4.261656 CCACCTAGGTTTAGCTACTCATCG 60.262 50.000 13.15 0.00 0.00 3.84
732 1337 0.759346 GGGGCTGTGATACCACCTAG 59.241 60.000 0.00 0.00 42.53 3.02
749 1354 0.540454 GGTTCTCTAACGGAAGGGGG 59.460 60.000 0.00 0.00 36.39 5.40
762 1367 1.594331 ACGGCAAGAAACAGGTTCTC 58.406 50.000 0.00 0.00 46.36 2.87
769 1374 3.577649 TCAAACAAACGGCAAGAAACA 57.422 38.095 0.00 0.00 0.00 2.83
796 1401 3.044235 TGTGACTGTTGAGCATTCGAT 57.956 42.857 0.00 0.00 30.34 3.59
800 1405 4.011966 TGAGATGTGACTGTTGAGCATT 57.988 40.909 0.00 0.00 0.00 3.56
807 1412 2.350522 GCCGATTGAGATGTGACTGTT 58.649 47.619 0.00 0.00 0.00 3.16
810 1415 0.807667 GCGCCGATTGAGATGTGACT 60.808 55.000 0.00 0.00 0.00 3.41
815 1420 1.800805 ATAAGGCGCCGATTGAGATG 58.199 50.000 23.20 0.00 0.00 2.90
820 1425 5.799936 CCAAAAATATATAAGGCGCCGATTG 59.200 40.000 23.20 11.93 0.00 2.67
824 1429 3.754323 TCCCAAAAATATATAAGGCGCCG 59.246 43.478 23.20 0.81 0.00 6.46
837 1442 3.923425 AGTACTCCCTCCTTCCCAAAAAT 59.077 43.478 0.00 0.00 0.00 1.82
862 1602 4.088213 GCGTCGTGCTATACTTATACTTGC 59.912 45.833 0.00 0.00 41.73 4.01
871 1611 2.619177 AGAGATTGCGTCGTGCTATACT 59.381 45.455 0.00 3.33 46.63 2.12
872 1612 2.974536 GAGAGATTGCGTCGTGCTATAC 59.025 50.000 0.00 1.51 46.63 1.47
873 1613 2.349532 CGAGAGATTGCGTCGTGCTATA 60.350 50.000 0.00 0.00 46.63 1.31
874 1614 1.598183 CGAGAGATTGCGTCGTGCTAT 60.598 52.381 0.00 2.09 46.63 2.97
1284 2067 4.682714 AGGGGGAGGAAGCAGGCA 62.683 66.667 0.00 0.00 0.00 4.75
1361 2157 2.001872 CGGGAAAAATGCCAAGATTGC 58.998 47.619 0.00 0.00 0.00 3.56
1362 2158 3.253230 GTCGGGAAAAATGCCAAGATTG 58.747 45.455 0.00 0.00 0.00 2.67
1364 2160 1.472480 CGTCGGGAAAAATGCCAAGAT 59.528 47.619 0.00 0.00 0.00 2.40
1367 2163 1.470890 GATCGTCGGGAAAAATGCCAA 59.529 47.619 0.00 0.00 0.00 4.52
1378 2174 2.125673 AACGGCAAGATCGTCGGG 60.126 61.111 0.00 0.00 40.18 5.14
2086 2904 1.078567 GTGGAAGCAGCAGGAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
2087 2905 1.537397 AGTGGAAGCAGCAGGAGGA 60.537 57.895 0.00 0.00 0.00 3.71
2088 2906 1.376942 CAGTGGAAGCAGCAGGAGG 60.377 63.158 0.00 0.00 0.00 4.30
2089 2907 2.039405 GCAGTGGAAGCAGCAGGAG 61.039 63.158 0.00 0.00 0.00 3.69
2090 2908 2.033141 GCAGTGGAAGCAGCAGGA 59.967 61.111 0.00 0.00 0.00 3.86
2091 2909 2.033757 AGCAGTGGAAGCAGCAGG 59.966 61.111 0.00 0.00 0.00 4.85
2092 2910 1.575576 GACAGCAGTGGAAGCAGCAG 61.576 60.000 0.00 0.00 0.00 4.24
2093 2911 1.598962 GACAGCAGTGGAAGCAGCA 60.599 57.895 0.00 0.00 0.00 4.41
2094 2912 2.675056 CGACAGCAGTGGAAGCAGC 61.675 63.158 0.00 0.00 0.00 5.25
2147 2965 2.289444 GGTTGTTGTCCTAGCACTAGCA 60.289 50.000 0.00 0.00 45.49 3.49
2148 2966 2.289444 TGGTTGTTGTCCTAGCACTAGC 60.289 50.000 0.00 0.00 42.56 3.42
2149 2967 3.589988 CTGGTTGTTGTCCTAGCACTAG 58.410 50.000 0.00 0.00 0.00 2.57
2150 2968 2.301870 CCTGGTTGTTGTCCTAGCACTA 59.698 50.000 0.00 0.00 0.00 2.74
2151 2969 1.072331 CCTGGTTGTTGTCCTAGCACT 59.928 52.381 0.00 0.00 0.00 4.40
2152 2970 1.071699 TCCTGGTTGTTGTCCTAGCAC 59.928 52.381 0.00 0.00 0.00 4.40
2188 3006 4.829968 TCATCAAGAAGAAGAAGAGCAGG 58.170 43.478 0.00 0.00 0.00 4.85
2252 3070 1.444836 GGCCTACACAAACGCATACA 58.555 50.000 0.00 0.00 0.00 2.29
2281 3099 1.421268 TGGAGACAGACCAAACATGCT 59.579 47.619 0.00 0.00 34.25 3.79
2282 3100 1.896220 TGGAGACAGACCAAACATGC 58.104 50.000 0.00 0.00 34.25 4.06
2292 3110 3.221771 CATGGTTGGTTTTGGAGACAGA 58.778 45.455 0.00 0.00 44.54 3.41
2297 3115 4.399004 TTTGACATGGTTGGTTTTGGAG 57.601 40.909 0.00 0.00 0.00 3.86
2357 3408 9.688091 TTGCAACCATCCAAATAATAAGTAGTA 57.312 29.630 0.00 0.00 0.00 1.82
2359 3410 9.868277 TTTTGCAACCATCCAAATAATAAGTAG 57.132 29.630 0.00 0.00 31.71 2.57
2360 3411 9.646427 GTTTTGCAACCATCCAAATAATAAGTA 57.354 29.630 0.00 0.00 31.71 2.24
2361 3412 8.153550 TGTTTTGCAACCATCCAAATAATAAGT 58.846 29.630 0.00 0.00 31.71 2.24
2362 3413 8.545229 TGTTTTGCAACCATCCAAATAATAAG 57.455 30.769 0.00 0.00 31.71 1.73
2363 3414 9.512588 AATGTTTTGCAACCATCCAAATAATAA 57.487 25.926 0.00 0.00 31.71 1.40
2365 3416 7.999450 AATGTTTTGCAACCATCCAAATAAT 57.001 28.000 0.00 0.00 31.71 1.28
2403 4897 1.588082 GAGGGCAAGTTGGCATGTG 59.412 57.895 28.33 0.00 45.76 3.21
2404 4898 1.607467 GGAGGGCAAGTTGGCATGT 60.607 57.895 28.33 13.88 45.76 3.21
2405 4899 0.974010 ATGGAGGGCAAGTTGGCATG 60.974 55.000 28.33 0.00 45.76 4.06
2406 4900 0.630673 TATGGAGGGCAAGTTGGCAT 59.369 50.000 28.33 23.33 45.76 4.40
2468 4962 4.218417 GGATTGGTACTTTGCTTGATGTGT 59.782 41.667 0.00 0.00 0.00 3.72
2469 4963 4.380867 GGGATTGGTACTTTGCTTGATGTG 60.381 45.833 0.00 0.00 0.00 3.21
2477 4971 1.285078 AGGAGGGGATTGGTACTTTGC 59.715 52.381 0.00 0.00 0.00 3.68
2478 4972 3.739401 AAGGAGGGGATTGGTACTTTG 57.261 47.619 0.00 0.00 0.00 2.77
2507 5001 7.542130 GGAATTACAATCCTTAGCAACAAGTTG 59.458 37.037 8.53 8.53 37.52 3.16
2565 5059 5.106791 TGCCCATGATTTTTATTTGTTTGCG 60.107 36.000 0.00 0.00 0.00 4.85
2571 5065 6.316640 TGCTCATTGCCCATGATTTTTATTTG 59.683 34.615 0.00 0.00 41.35 2.32
2572 5066 6.416415 TGCTCATTGCCCATGATTTTTATTT 58.584 32.000 0.00 0.00 41.35 1.40
2595 5093 2.676076 GCAAACAGCACCTACCAAATG 58.324 47.619 0.00 0.00 44.79 2.32
2614 5112 2.514803 ACTTATCAAACCACCCAGTGC 58.485 47.619 0.00 0.00 31.34 4.40
2623 5121 5.880332 TGGCTATCTGACAACTTATCAAACC 59.120 40.000 0.00 0.00 0.00 3.27
2628 5126 6.341316 TCAAGTGGCTATCTGACAACTTATC 58.659 40.000 0.00 0.00 34.07 1.75
2629 5127 6.299805 TCAAGTGGCTATCTGACAACTTAT 57.700 37.500 0.00 0.00 34.07 1.73
2637 5135 2.297315 CGGCTATCAAGTGGCTATCTGA 59.703 50.000 0.00 0.00 34.25 3.27
2643 5141 0.978146 AGTCCGGCTATCAAGTGGCT 60.978 55.000 0.00 0.00 34.25 4.75
2653 5151 0.037734 TCTCAGTCACAGTCCGGCTA 59.962 55.000 0.00 0.00 0.00 3.93
2658 5156 1.964223 TCCAGTTCTCAGTCACAGTCC 59.036 52.381 0.00 0.00 0.00 3.85
2660 5158 2.950781 TCTCCAGTTCTCAGTCACAGT 58.049 47.619 0.00 0.00 0.00 3.55
2687 5185 7.051000 GGTATCCAAGATTAAGCATATCTCCC 58.949 42.308 0.00 0.00 31.28 4.30
2720 5218 1.704070 GACGTCTGAAGCTCAAGTCC 58.296 55.000 8.70 0.00 0.00 3.85
2745 5243 4.699257 ACGAGTAACCTAAACGTCAGAGAT 59.301 41.667 0.00 0.00 31.69 2.75
2760 5258 7.010830 GTCATCCATTTTTACCCTACGAGTAAC 59.989 40.741 0.00 0.00 29.63 2.50
2788 5286 1.737236 CACATTGTGTATCCACCGGTG 59.263 52.381 28.26 28.26 41.09 4.94
2792 5290 4.216257 GGCATATCACATTGTGTATCCACC 59.784 45.833 16.06 8.70 41.09 4.61
2815 5313 2.756840 TGAGTCTGCTCATCTGGTTG 57.243 50.000 0.00 0.00 45.94 3.77
2824 5322 6.553524 ACTTACTACGTATTTGAGTCTGCTC 58.446 40.000 0.00 0.00 41.97 4.26
2844 5363 5.334569 GCGCAAAAATGTTGACTCCTACTTA 60.335 40.000 0.30 0.00 0.00 2.24
2846 5365 3.058224 GCGCAAAAATGTTGACTCCTACT 60.058 43.478 0.30 0.00 0.00 2.57
2847 5366 3.234386 GCGCAAAAATGTTGACTCCTAC 58.766 45.455 0.30 0.00 0.00 3.18
2854 5373 4.554292 ACATACATGCGCAAAAATGTTGA 58.446 34.783 17.11 0.00 38.05 3.18
2860 5379 4.166187 TGCTTACATACATGCGCAAAAA 57.834 36.364 17.11 2.05 0.00 1.94
2888 5407 3.885484 ATCTTATTTCGCCATCGCAAG 57.115 42.857 0.00 0.00 35.26 4.01
2944 5463 9.922305 GCATACAGACTTTGTAAATAACTCATC 57.078 33.333 0.00 0.00 45.00 2.92
2963 5482 7.429636 TCATATGATGATGTTGTGCATACAG 57.570 36.000 0.00 0.00 38.06 2.74
3028 5571 0.889186 AGACCAAACGTGCCATCACC 60.889 55.000 0.00 0.00 40.04 4.02
3079 5622 6.299266 GTCGAAACTTTGTAAATAACTCGTGC 59.701 38.462 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.