Multiple sequence alignment - TraesCS2A01G268100

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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 TraesCS2A01G268100 chr2A 100.000 2634 0 0 1 2634 430483382 430480749 0.000000e+00 4865.0
1 TraesCS2A01G268100 chr2D 94.001 1367 69 10 491 1853 309166334 309167691 0.000000e+00 2058.0
2 TraesCS2A01G268100 chr2D 90.556 540 28 11 1868 2384 309174350 309174889 0.000000e+00 693.0
3 TraesCS2A01G268100 chr2D 92.701 274 19 1 8 281 580268919 580268647 6.830000e-106 394.0
4 TraesCS2A01G268100 chr2D 95.238 189 9 0 2446 2634 309174900 309175088 1.530000e-77 300.0
5 TraesCS2A01G268100 chr2D 89.623 212 21 1 275 486 580268078 580267868 4.320000e-68 268.0
6 TraesCS2A01G268100 chr2B 92.074 1186 64 18 670 1853 359038303 359037146 0.000000e+00 1642.0
7 TraesCS2A01G268100 chr2B 89.171 591 37 12 2056 2634 359036710 359036135 0.000000e+00 712.0
8 TraesCS2A01G268100 chr2B 94.444 144 8 0 1865 2008 359036853 359036710 3.410000e-54 222.0
9 TraesCS2A01G268100 chr2B 100.000 28 0 0 530 557 359039883 359039856 5.000000e-03 52.8
10 TraesCS2A01G268100 chr7A 81.109 487 82 9 3 486 649193790 649194269 5.320000e-102 381.0
11 TraesCS2A01G268100 chr7D 83.562 365 54 5 1 362 72811723 72811362 1.170000e-88 337.0
12 TraesCS2A01G268100 chr7D 79.538 303 45 11 187 487 449076853 449076566 1.600000e-47 200.0


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 TraesCS2A01G268100 chr2A 430480749 430483382 2633 True 4865.0 4865 100.00000 1 2634 1 chr2A.!!$R1 2633
1 TraesCS2A01G268100 chr2D 309166334 309167691 1357 False 2058.0 2058 94.00100 491 1853 1 chr2D.!!$F1 1362
2 TraesCS2A01G268100 chr2D 309174350 309175088 738 False 496.5 693 92.89700 1868 2634 2 chr2D.!!$F2 766
3 TraesCS2A01G268100 chr2D 580267868 580268919 1051 True 331.0 394 91.16200 8 486 2 chr2D.!!$R1 478
4 TraesCS2A01G268100 chr2B 359036135 359039883 3748 True 657.2 1642 93.92225 530 2634 4 chr2B.!!$R1 2104

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
958 3008 0.033503 CCATAGGGGCCGGAAAAACT 60.034 55.0 5.05 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 4800 0.179468 AGTACACCACACCACACCAC 59.821 55.0 0.0 0.0 0.0 4.16 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
63 64 1.605453 GAATCGCCTGGGTGGGTTA 59.395 57.895 0.00 0.00 36.00 2.85
70 71 2.535580 TGGGTGGGTTATGGGGCA 60.536 61.111 0.00 0.00 0.00 5.36
85 86 4.347453 GCACTGGCGTGGGCTTTG 62.347 66.667 10.56 0.00 41.51 2.77
87 88 1.599518 CACTGGCGTGGGCTTTGTA 60.600 57.895 2.23 0.00 39.81 2.41
105 106 4.764050 TGTAGACCACAAGAAACAAGGA 57.236 40.909 0.00 0.00 32.95 3.36
113 114 7.505585 AGACCACAAGAAACAAGGATTTGATAA 59.494 33.333 0.00 0.00 37.73 1.75
115 116 8.482128 ACCACAAGAAACAAGGATTTGATAAAA 58.518 29.630 0.00 0.00 37.73 1.52
119 120 9.415544 CAAGAAACAAGGATTTGATAAAAGGAG 57.584 33.333 0.00 0.00 37.73 3.69
147 148 2.158957 TCAAACACCCGGCTGATCTATC 60.159 50.000 3.11 0.00 0.00 2.08
170 171 6.119536 TCATACAAACTGGTGTCTTTCTTGT 58.880 36.000 0.00 0.00 32.75 3.16
185 186 3.963428 TCTTGTAGCTCTGGAAACCTC 57.037 47.619 0.00 0.00 0.00 3.85
196 197 0.110486 GGAAACCTCTGTCAAGGGCA 59.890 55.000 6.17 0.00 41.04 5.36
218 219 1.374758 GACAGAAGGCACGTGGAGG 60.375 63.158 18.88 0.00 0.00 4.30
250 251 3.560636 AAGGTGTGAGCAAAGTGTACT 57.439 42.857 0.00 0.00 0.00 2.73
254 255 3.458189 GTGTGAGCAAAGTGTACTGAGT 58.542 45.455 0.00 0.00 0.00 3.41
260 261 4.189231 AGCAAAGTGTACTGAGTTTCGTT 58.811 39.130 0.00 0.00 0.00 3.85
293 869 1.079127 GCACCTACGGCATGACACT 60.079 57.895 0.00 0.00 0.00 3.55
308 884 5.423015 CATGACACTTGACTATGCTACCTT 58.577 41.667 0.00 0.00 0.00 3.50
332 908 0.973632 GCCCGATGTTTCCCCTTTTT 59.026 50.000 0.00 0.00 0.00 1.94
334 910 2.243810 CCCGATGTTTCCCCTTTTTGA 58.756 47.619 0.00 0.00 0.00 2.69
335 911 2.029380 CCCGATGTTTCCCCTTTTTGAC 60.029 50.000 0.00 0.00 0.00 3.18
336 912 2.890945 CCGATGTTTCCCCTTTTTGACT 59.109 45.455 0.00 0.00 0.00 3.41
339 915 2.393646 TGTTTCCCCTTTTTGACTGGG 58.606 47.619 0.00 0.00 40.59 4.45
340 916 1.070134 GTTTCCCCTTTTTGACTGGGC 59.930 52.381 0.00 0.00 39.61 5.36
383 959 0.928229 CGGGCTTGTATCGCTTGTAC 59.072 55.000 0.00 0.00 0.00 2.90
386 962 2.351726 GGGCTTGTATCGCTTGTACTTG 59.648 50.000 0.00 0.00 0.00 3.16
389 965 3.863424 GCTTGTATCGCTTGTACTTGCTA 59.137 43.478 8.53 0.00 0.00 3.49
400 976 5.350640 GCTTGTACTTGCTATTCCGTACTTT 59.649 40.000 0.00 0.00 34.75 2.66
403 979 6.225318 TGTACTTGCTATTCCGTACTTTGTT 58.775 36.000 0.00 0.00 34.75 2.83
429 1005 1.523758 ATTTGGTCTGGAACTCGTGC 58.476 50.000 0.00 0.00 0.00 5.34
430 1006 0.534203 TTTGGTCTGGAACTCGTGCC 60.534 55.000 0.00 0.00 0.00 5.01
431 1007 1.691195 TTGGTCTGGAACTCGTGCCA 61.691 55.000 0.00 0.00 0.00 4.92
447 1023 0.548510 GCCAGATCTGTAAGGGCCTT 59.451 55.000 24.44 24.44 38.70 4.35
456 1032 5.202746 TCTGTAAGGGCCTTAGTCTAAGA 57.797 43.478 26.03 18.69 38.02 2.10
466 1042 0.822164 TAGTCTAAGACCGGGCAAGC 59.178 55.000 11.69 2.99 32.18 4.01
467 1043 1.192146 AGTCTAAGACCGGGCAAGCA 61.192 55.000 11.69 0.00 32.18 3.91
477 1053 1.581447 GGGCAAGCACCTCTTTTCG 59.419 57.895 0.00 0.00 31.27 3.46
480 1056 1.335051 GGCAAGCACCTCTTTTCGAAC 60.335 52.381 0.00 0.00 31.27 3.95
486 1062 5.262588 AGCACCTCTTTTCGAACAAAAAT 57.737 34.783 0.00 0.00 0.00 1.82
487 1063 5.043248 AGCACCTCTTTTCGAACAAAAATG 58.957 37.500 0.00 0.00 0.00 2.32
488 1064 4.803613 GCACCTCTTTTCGAACAAAAATGT 59.196 37.500 0.00 0.00 0.00 2.71
489 1065 5.276348 GCACCTCTTTTCGAACAAAAATGTG 60.276 40.000 0.00 1.41 31.80 3.21
490 1066 5.804979 CACCTCTTTTCGAACAAAAATGTGT 59.195 36.000 0.00 0.00 0.00 3.72
491 1067 6.310224 CACCTCTTTTCGAACAAAAATGTGTT 59.690 34.615 0.00 0.00 44.38 3.32
492 1068 7.486551 CACCTCTTTTCGAACAAAAATGTGTTA 59.513 33.333 0.00 0.00 41.78 2.41
493 1069 7.700656 ACCTCTTTTCGAACAAAAATGTGTTAG 59.299 33.333 0.00 0.00 41.78 2.34
494 1070 7.700656 CCTCTTTTCGAACAAAAATGTGTTAGT 59.299 33.333 0.00 0.00 41.78 2.24
495 1071 8.388319 TCTTTTCGAACAAAAATGTGTTAGTG 57.612 30.769 0.00 0.00 41.78 2.74
557 1133 0.809385 TCTTAGCCCAAGTCGAGACG 59.191 55.000 0.00 0.00 35.58 4.18
615 1191 3.243724 AGAGTAAGTGATATGCCCCTCC 58.756 50.000 0.00 0.00 0.00 4.30
632 1208 1.372499 CCGGACACACGAACGACAT 60.372 57.895 0.00 0.00 35.47 3.06
648 1224 3.128068 ACGACATGCACACGAGATACTAA 59.872 43.478 14.19 0.00 0.00 2.24
692 2739 1.973515 TGAATGCACTCCAGAGTCTGT 59.026 47.619 18.74 0.00 40.20 3.41
834 2884 0.343018 TCATCTCATCTCCCCCACCA 59.657 55.000 0.00 0.00 0.00 4.17
858 2908 2.813754 CCACAACATACCACACCAGAAG 59.186 50.000 0.00 0.00 0.00 2.85
881 2931 7.043961 AGTCTTGCTATGAACTCGATATTGA 57.956 36.000 0.00 0.00 0.00 2.57
889 2939 7.148523 GCTATGAACTCGATATTGATGCAATGA 60.149 37.037 0.00 0.00 35.54 2.57
896 2946 4.555313 CGATATTGATGCAATGAAACCGCT 60.555 41.667 0.00 0.00 35.54 5.52
938 2988 3.691609 GCTGGAAGATTCGGATCAGTTTT 59.308 43.478 6.44 0.00 34.07 2.43
941 2991 4.261801 GGAAGATTCGGATCAGTTTTCCA 58.738 43.478 14.63 0.00 34.98 3.53
958 3008 0.033503 CCATAGGGGCCGGAAAAACT 60.034 55.000 5.05 0.00 0.00 2.66
1062 3112 2.015456 TGCCTCTGTTCTTCCTCTCA 57.985 50.000 0.00 0.00 0.00 3.27
1071 3121 2.758423 GTTCTTCCTCTCAGTCCTCCTC 59.242 54.545 0.00 0.00 0.00 3.71
1084 3134 2.204624 TCCTCCTCCTCCCCTCCA 60.205 66.667 0.00 0.00 0.00 3.86
1267 3317 6.094881 GGCAGCAGTAAGGTACAAATAATCAA 59.905 38.462 0.00 0.00 0.00 2.57
1301 3351 2.957402 TGTCTGATGGACCTTTGCTT 57.043 45.000 0.00 0.00 43.89 3.91
1426 3477 1.451936 GCCACCAAGGTGTGAGAGT 59.548 57.895 17.36 0.00 44.02 3.24
1451 3502 1.151221 ATGTCTTGTGGCCACTGCA 59.849 52.632 34.75 25.63 40.13 4.41
1533 3584 2.936829 GATGCGGCGAGTGACATCGA 62.937 60.000 12.98 0.00 45.56 3.59
1557 3608 1.519234 CGATGCTCGCTGCCTACAA 60.519 57.895 0.00 0.00 42.00 2.41
1560 3611 2.512515 GCTCGCTGCCTACAAGGG 60.513 66.667 0.00 0.00 35.37 3.95
1594 3645 3.082548 CTCGGACTACAAACCTCTGAGA 58.917 50.000 6.17 0.00 39.05 3.27
1618 3669 3.055385 GGAAGTGTAGGTGTGGAAGCATA 60.055 47.826 0.00 0.00 0.00 3.14
1688 3739 6.005823 ACAATCAGGATCACTTCAATTGTGA 58.994 36.000 5.13 2.41 46.58 3.58
1725 3776 5.069914 AGTTGTCCTAAATTGTTTTCCCACC 59.930 40.000 0.00 0.00 0.00 4.61
1731 3784 8.205512 GTCCTAAATTGTTTTCCCACCTTTTTA 58.794 33.333 0.00 0.00 0.00 1.52
1732 3785 8.939932 TCCTAAATTGTTTTCCCACCTTTTTAT 58.060 29.630 0.00 0.00 0.00 1.40
1736 3789 9.693739 AAATTGTTTTCCCACCTTTTTATTCTT 57.306 25.926 0.00 0.00 0.00 2.52
1737 3790 8.902540 ATTGTTTTCCCACCTTTTTATTCTTC 57.097 30.769 0.00 0.00 0.00 2.87
1738 3791 7.669089 TGTTTTCCCACCTTTTTATTCTTCT 57.331 32.000 0.00 0.00 0.00 2.85
1739 3792 8.084985 TGTTTTCCCACCTTTTTATTCTTCTT 57.915 30.769 0.00 0.00 0.00 2.52
1740 3793 8.201464 TGTTTTCCCACCTTTTTATTCTTCTTC 58.799 33.333 0.00 0.00 0.00 2.87
1747 3800 8.300286 CCACCTTTTTATTCTTCTTCTTCTTCC 58.700 37.037 0.00 0.00 0.00 3.46
1757 3810 6.614657 TCTTCTTCTTCTTCCCCTTTTCAAT 58.385 36.000 0.00 0.00 0.00 2.57
1782 3835 1.277557 CTCCAGACCAGAGGTTCAAGG 59.722 57.143 0.00 0.00 35.25 3.61
1783 3836 0.326264 CCAGACCAGAGGTTCAAGGG 59.674 60.000 0.00 0.00 35.25 3.95
1903 4237 2.180017 CATGGGCTCTTGTTGCGC 59.820 61.111 0.00 0.00 42.57 6.09
1932 4266 6.485984 GGACAAACATCTGATCTGCTGAATAT 59.514 38.462 10.03 0.00 0.00 1.28
1959 4293 9.588096 TGTATAAGACATCATCAGGTACTACAT 57.412 33.333 0.00 0.00 30.91 2.29
1971 4305 6.873997 TCAGGTACTACATCAATGTTAGGTG 58.126 40.000 0.20 0.00 41.97 4.00
2002 4336 5.743636 ATCACTGCCACCAAACAAATAAT 57.256 34.783 0.00 0.00 0.00 1.28
2008 4342 7.276218 CACTGCCACCAAACAAATAATGATTAG 59.724 37.037 0.00 0.00 0.00 1.73
2148 4488 3.701205 AGCAACATACCACTGATCACA 57.299 42.857 0.00 0.00 0.00 3.58
2247 4590 2.706190 GGGGATCAGTATTAGCAGTGGT 59.294 50.000 0.00 0.00 0.00 4.16
2248 4591 3.136626 GGGGATCAGTATTAGCAGTGGTT 59.863 47.826 0.00 0.00 0.00 3.67
2265 4608 6.329496 CAGTGGTTGCTTTTCTTTTCTTGTA 58.671 36.000 0.00 0.00 0.00 2.41
2270 4623 7.544217 TGGTTGCTTTTCTTTTCTTGTAAGAAC 59.456 33.333 6.56 0.00 44.18 3.01
2271 4624 7.544217 GGTTGCTTTTCTTTTCTTGTAAGAACA 59.456 33.333 6.56 0.34 44.18 3.18
2300 4653 1.121407 GCTTTGGGGCAGGGAAAAGT 61.121 55.000 0.00 0.00 33.21 2.66
2342 4695 4.459089 GCTGAGGCCGGACCACTC 62.459 72.222 1.76 6.30 43.14 3.51
2354 4707 2.545113 CGGACCACTCGTGAAGAAAAGA 60.545 50.000 0.00 0.00 0.00 2.52
2398 4754 2.439701 CTCGTAGACCGCTCCCCA 60.440 66.667 0.00 0.00 36.19 4.96
2401 4757 1.452651 CGTAGACCGCTCCCCACTA 60.453 63.158 0.00 0.00 0.00 2.74
2402 4758 0.822532 CGTAGACCGCTCCCCACTAT 60.823 60.000 0.00 0.00 0.00 2.12
2412 4768 3.430929 CGCTCCCCACTATATTAGATGCC 60.431 52.174 0.00 0.00 0.00 4.40
2439 4795 0.330604 AGCATGAATCTGGCTGGTGT 59.669 50.000 0.00 0.00 36.34 4.16
2442 4798 0.700564 ATGAATCTGGCTGGTGTGGT 59.299 50.000 0.00 0.00 0.00 4.16
2443 4799 0.250858 TGAATCTGGCTGGTGTGGTG 60.251 55.000 0.00 0.00 0.00 4.17
2444 4800 0.962356 GAATCTGGCTGGTGTGGTGG 60.962 60.000 0.00 0.00 0.00 4.61
2461 4817 1.272554 TGGTGGTGTGGTGTGGTGTA 61.273 55.000 0.00 0.00 0.00 2.90
2475 4831 4.222145 GTGTGGTGTACTCTCCCTTTCATA 59.778 45.833 0.00 0.00 0.00 2.15
2525 4881 0.677731 GTCCTGCATGCAAGCCACTA 60.678 55.000 22.88 0.00 0.00 2.74
2578 4934 0.542467 AGACCACCATTGCAATGCCA 60.542 50.000 30.15 0.00 35.08 4.92
2588 4944 2.964174 CAATGCCATGTGCCGTGT 59.036 55.556 4.07 0.00 40.16 4.49
2619 4975 6.684686 CATGATAATTTGAATCGGAATGGCT 58.315 36.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.808755 GGCCAACCGGTAGAAATGTG 59.191 55.000 8.00 0.00 33.28 3.21
1 2 0.402504 TGGCCAACCGGTAGAAATGT 59.597 50.000 8.00 0.00 39.70 2.71
2 3 1.094785 CTGGCCAACCGGTAGAAATG 58.905 55.000 8.00 0.73 39.70 2.32
3 4 0.034477 CCTGGCCAACCGGTAGAAAT 60.034 55.000 8.00 0.00 41.25 2.17
6 7 3.006728 CCCTGGCCAACCGGTAGA 61.007 66.667 8.00 0.00 41.25 2.59
37 38 0.673985 CCCAGGCGATTCGTCTATCA 59.326 55.000 13.57 0.00 40.90 2.15
49 50 2.124320 CCATAACCCACCCAGGCG 60.124 66.667 0.00 0.00 35.39 5.52
70 71 1.302511 CTACAAAGCCCACGCCAGT 60.303 57.895 0.00 0.00 34.57 4.00
83 84 5.105567 TCCTTGTTTCTTGTGGTCTACAA 57.894 39.130 1.48 1.48 46.62 2.41
85 86 6.262273 TCAAATCCTTGTTTCTTGTGGTCTAC 59.738 38.462 0.00 0.00 33.94 2.59
87 88 5.200483 TCAAATCCTTGTTTCTTGTGGTCT 58.800 37.500 0.00 0.00 33.94 3.85
113 114 5.183228 CGGGTGTTTGATGTATACTCCTTT 58.817 41.667 4.17 0.00 0.00 3.11
115 116 3.134081 CCGGGTGTTTGATGTATACTCCT 59.866 47.826 4.17 0.00 0.00 3.69
119 120 2.612212 CAGCCGGGTGTTTGATGTATAC 59.388 50.000 25.51 0.00 0.00 1.47
147 148 6.377327 ACAAGAAAGACACCAGTTTGTATG 57.623 37.500 0.00 0.00 0.00 2.39
170 171 2.889512 TGACAGAGGTTTCCAGAGCTA 58.110 47.619 0.00 0.00 0.00 3.32
185 186 1.233019 CTGTCTTGTGCCCTTGACAG 58.767 55.000 7.44 7.44 46.45 3.51
196 197 0.532862 CCACGTGCCTTCTGTCTTGT 60.533 55.000 10.91 0.00 0.00 3.16
218 219 3.741476 CACCTTTGCTGCGAGCCC 61.741 66.667 5.82 0.00 41.51 5.19
250 251 2.351455 TGTGTTGCTCAACGAAACTCA 58.649 42.857 8.07 0.00 43.94 3.41
254 255 1.403679 CCCTTGTGTTGCTCAACGAAA 59.596 47.619 8.07 4.56 43.94 3.46
260 261 1.827789 GTGCCCCTTGTGTTGCTCA 60.828 57.895 0.00 0.00 0.00 4.26
281 857 2.621338 CATAGTCAAGTGTCATGCCGT 58.379 47.619 0.00 0.00 0.00 5.68
293 869 3.133003 GGCTCTCAAGGTAGCATAGTCAA 59.867 47.826 0.00 0.00 40.61 3.18
308 884 1.602237 GGGAAACATCGGGCTCTCA 59.398 57.895 0.00 0.00 0.00 3.27
340 916 1.555538 GAAGATAAGCGACGCAGCG 59.444 57.895 23.70 14.82 43.00 5.18
383 959 6.812160 AGTAGAACAAAGTACGGAATAGCAAG 59.188 38.462 0.00 0.00 0.00 4.01
386 962 8.868635 ATAAGTAGAACAAAGTACGGAATAGC 57.131 34.615 0.00 0.00 0.00 2.97
389 965 8.943002 CCAAATAAGTAGAACAAAGTACGGAAT 58.057 33.333 0.00 0.00 0.00 3.01
400 976 7.074653 AGTTCCAGACCAAATAAGTAGAACA 57.925 36.000 0.00 0.00 0.00 3.18
403 979 5.479375 ACGAGTTCCAGACCAAATAAGTAGA 59.521 40.000 0.00 0.00 0.00 2.59
413 989 2.137528 TGGCACGAGTTCCAGACCA 61.138 57.895 0.00 0.00 0.00 4.02
429 1005 3.041946 ACTAAGGCCCTTACAGATCTGG 58.958 50.000 26.08 9.59 34.19 3.86
430 1006 3.964031 AGACTAAGGCCCTTACAGATCTG 59.036 47.826 21.37 21.37 0.00 2.90
431 1007 4.273300 AGACTAAGGCCCTTACAGATCT 57.727 45.455 0.00 0.00 0.00 2.75
447 1023 0.822164 GCTTGCCCGGTCTTAGACTA 59.178 55.000 12.41 0.00 32.47 2.59
456 1032 2.640581 AAAAGAGGTGCTTGCCCGGT 62.641 55.000 0.00 0.00 36.80 5.28
466 1042 5.804979 ACACATTTTTGTTCGAAAAGAGGTG 59.195 36.000 13.24 13.24 36.34 4.00
467 1043 5.961272 ACACATTTTTGTTCGAAAAGAGGT 58.039 33.333 0.00 0.00 32.54 3.85
477 1053 5.575019 ACGTCCACTAACACATTTTTGTTC 58.425 37.500 0.00 0.00 40.29 3.18
480 1056 7.960738 CCTTATACGTCCACTAACACATTTTTG 59.039 37.037 0.00 0.00 0.00 2.44
486 1062 5.243507 TCAACCTTATACGTCCACTAACACA 59.756 40.000 0.00 0.00 0.00 3.72
487 1063 5.713025 TCAACCTTATACGTCCACTAACAC 58.287 41.667 0.00 0.00 0.00 3.32
488 1064 5.981088 TCAACCTTATACGTCCACTAACA 57.019 39.130 0.00 0.00 0.00 2.41
489 1065 7.838771 ATTTCAACCTTATACGTCCACTAAC 57.161 36.000 0.00 0.00 0.00 2.34
492 1068 9.457436 AAATAATTTCAACCTTATACGTCCACT 57.543 29.630 0.00 0.00 0.00 4.00
493 1069 9.712359 GAAATAATTTCAACCTTATACGTCCAC 57.288 33.333 0.00 0.00 39.45 4.02
494 1070 9.451002 TGAAATAATTTCAACCTTATACGTCCA 57.549 29.630 0.00 0.00 45.94 4.02
524 1100 3.370527 GGGCTAAGAGCATTCTACAACCA 60.371 47.826 0.21 0.00 44.75 3.67
557 1133 7.821359 TGCATATCATTTACCTAGCTCATCTTC 59.179 37.037 0.00 0.00 0.00 2.87
595 1171 2.028930 CGGAGGGGCATATCACTTACTC 60.029 54.545 0.00 0.00 0.00 2.59
615 1191 1.772882 CATGTCGTTCGTGTGTCCG 59.227 57.895 0.00 0.00 0.00 4.79
625 1201 2.094700 AGTATCTCGTGTGCATGTCGTT 60.095 45.455 0.00 0.00 0.00 3.85
632 1208 4.482386 GTGAGTTTAGTATCTCGTGTGCA 58.518 43.478 0.00 0.00 33.88 4.57
648 1224 2.930826 AATCTTGTCGGTGGTGAGTT 57.069 45.000 0.00 0.00 0.00 3.01
692 2739 5.484290 GGGATTAGCTAGCTATTTCCAGGTA 59.516 44.000 33.66 17.96 35.03 3.08
758 2807 4.603610 AGGATAGAATATTTGGGACTGGGG 59.396 45.833 0.00 0.00 0.00 4.96
765 2814 9.965902 AGTGCTAAATAGGATAGAATATTTGGG 57.034 33.333 0.00 0.00 34.36 4.12
834 2884 2.955660 CTGGTGTGGTATGTTGTGGTTT 59.044 45.455 0.00 0.00 0.00 3.27
858 2908 7.621013 GCATCAATATCGAGTTCATAGCAAGAC 60.621 40.741 0.00 0.00 0.00 3.01
881 2931 3.544684 TCTATCAGCGGTTTCATTGCAT 58.455 40.909 0.00 0.00 0.00 3.96
889 2939 2.362717 GCTAGACCTCTATCAGCGGTTT 59.637 50.000 0.00 0.00 32.59 3.27
896 2946 2.876485 GCGGCTAGCTAGACCTCTATCA 60.876 54.545 25.15 0.00 44.04 2.15
938 2988 0.033894 GTTTTTCCGGCCCCTATGGA 60.034 55.000 0.00 0.00 35.39 3.41
941 2991 0.996583 TCAGTTTTTCCGGCCCCTAT 59.003 50.000 0.00 0.00 0.00 2.57
958 3008 9.959721 ACCTTCTTAATTAAACTAGCTCAATCA 57.040 29.630 0.00 0.00 0.00 2.57
1035 3085 3.585862 GAAGAACAGAGGCAACGACATA 58.414 45.455 0.00 0.00 46.39 2.29
1062 3112 2.329399 GGGGAGGAGGAGGAGGACT 61.329 68.421 0.00 0.00 0.00 3.85
1071 3121 1.461075 CTCCATGGAGGGGAGGAGG 60.461 68.421 31.14 5.66 46.65 4.30
1084 3134 3.542648 CATCTGAATGTGCTGACTCCAT 58.457 45.455 0.00 0.00 0.00 3.41
1107 3157 3.451402 TGAGCACTAGAGGTCTTACCA 57.549 47.619 18.19 0.00 41.95 3.25
1206 3256 1.136329 AGTGGCAACCTCCCTGTGAT 61.136 55.000 0.00 0.00 0.00 3.06
1267 3317 5.048504 CCATCAGACAATAGCAACAACTTGT 60.049 40.000 0.00 0.00 34.68 3.16
1330 3380 5.549619 CCCCTTCTCCTCCTATGACATTAAT 59.450 44.000 0.00 0.00 0.00 1.40
1359 3410 3.411454 TCTTCATCATCTCCCCTCTGT 57.589 47.619 0.00 0.00 0.00 3.41
1426 3477 1.454572 GGCCACAAGACATGCACACA 61.455 55.000 0.00 0.00 0.00 3.72
1557 3608 1.076485 GAGATGCCACCATTGCCCT 60.076 57.895 0.00 0.00 0.00 5.19
1560 3611 1.451927 TCCGAGATGCCACCATTGC 60.452 57.895 0.00 0.00 0.00 3.56
1576 3627 3.769844 TCCATCTCAGAGGTTTGTAGTCC 59.230 47.826 0.00 0.00 0.00 3.85
1594 3645 2.290323 GCTTCCACACCTACACTTCCAT 60.290 50.000 0.00 0.00 0.00 3.41
1645 3696 8.370493 TGATTGTTGAGTTGAGAACTTTAGAG 57.630 34.615 0.00 0.00 43.03 2.43
1649 3700 6.122277 TCCTGATTGTTGAGTTGAGAACTTT 58.878 36.000 0.00 0.00 43.03 2.66
1703 3754 5.212745 AGGTGGGAAAACAATTTAGGACAA 58.787 37.500 0.00 0.00 0.00 3.18
1710 3761 9.693739 AAGAATAAAAAGGTGGGAAAACAATTT 57.306 25.926 0.00 0.00 0.00 1.82
1715 3766 8.421784 AGAAGAAGAATAAAAAGGTGGGAAAAC 58.578 33.333 0.00 0.00 0.00 2.43
1725 3776 8.642935 AGGGGAAGAAGAAGAAGAATAAAAAG 57.357 34.615 0.00 0.00 0.00 2.27
1731 3784 6.614657 TGAAAAGGGGAAGAAGAAGAAGAAT 58.385 36.000 0.00 0.00 0.00 2.40
1732 3785 6.013554 TGAAAAGGGGAAGAAGAAGAAGAA 57.986 37.500 0.00 0.00 0.00 2.52
1734 3787 6.907853 ATTGAAAAGGGGAAGAAGAAGAAG 57.092 37.500 0.00 0.00 0.00 2.85
1736 3789 7.202001 GGAAAATTGAAAAGGGGAAGAAGAAGA 60.202 37.037 0.00 0.00 0.00 2.87
1737 3790 6.931281 GGAAAATTGAAAAGGGGAAGAAGAAG 59.069 38.462 0.00 0.00 0.00 2.85
1738 3791 6.615316 AGGAAAATTGAAAAGGGGAAGAAGAA 59.385 34.615 0.00 0.00 0.00 2.52
1739 3792 6.143206 AGGAAAATTGAAAAGGGGAAGAAGA 58.857 36.000 0.00 0.00 0.00 2.87
1740 3793 6.425210 AGGAAAATTGAAAAGGGGAAGAAG 57.575 37.500 0.00 0.00 0.00 2.85
1747 3800 4.021104 GGTCTGGAGGAAAATTGAAAAGGG 60.021 45.833 0.00 0.00 0.00 3.95
1782 3835 0.254178 TTGCAGCTCATTCTCCCTCC 59.746 55.000 0.00 0.00 0.00 4.30
1783 3836 2.119801 TTTGCAGCTCATTCTCCCTC 57.880 50.000 0.00 0.00 0.00 4.30
1861 3914 8.481314 TGGCCAAATTGAAATAAATGCATAGTA 58.519 29.630 0.61 0.00 0.00 1.82
1903 4237 4.125703 GCAGATCAGATGTTTGTCCCTAG 58.874 47.826 0.00 0.00 0.00 3.02
1932 4266 9.416284 TGTAGTACCTGATGATGTCTTATACAA 57.584 33.333 0.00 0.00 42.70 2.41
1944 4278 7.344612 ACCTAACATTGATGTAGTACCTGATGA 59.655 37.037 0.00 0.00 40.80 2.92
1959 4293 1.072266 AGTGGCCCACCTAACATTGA 58.928 50.000 11.06 0.00 34.49 2.57
1971 4305 1.032114 GTGGCAGTGATAAGTGGCCC 61.032 60.000 8.95 0.00 43.96 5.80
2041 4375 9.542462 CGACATTCAGGTTTTATTATTCCTCTA 57.458 33.333 0.00 0.00 0.00 2.43
2265 4608 2.983725 AAGCTGCGGCCCTTGTTCTT 62.984 55.000 15.55 0.00 39.73 2.52
2270 4623 4.060038 CCAAAGCTGCGGCCCTTG 62.060 66.667 15.55 17.52 39.73 3.61
2290 4643 5.067674 TCAAGTCATCACAAACTTTTCCCTG 59.932 40.000 0.00 0.00 33.53 4.45
2291 4644 5.067805 GTCAAGTCATCACAAACTTTTCCCT 59.932 40.000 0.00 0.00 33.53 4.20
2292 4645 5.163561 TGTCAAGTCATCACAAACTTTTCCC 60.164 40.000 0.00 0.00 33.53 3.97
2300 4653 5.067544 TGCAGAAATGTCAAGTCATCACAAA 59.932 36.000 0.00 0.00 0.00 2.83
2342 4695 5.229921 TGGTCAAGTTTCTTTTCTTCACG 57.770 39.130 0.00 0.00 0.00 4.35
2354 4707 4.284234 CCATCCATTTCCTTGGTCAAGTTT 59.716 41.667 9.51 0.00 38.01 2.66
2398 4754 4.046938 CCGCATCGGCATCTAATATAGT 57.953 45.455 0.00 0.00 41.17 2.12
2423 4779 0.700564 ACCACACCAGCCAGATTCAT 59.299 50.000 0.00 0.00 0.00 2.57
2430 4786 4.202574 CCACCACCACACCAGCCA 62.203 66.667 0.00 0.00 0.00 4.75
2439 4795 2.273776 CACACCACACCACCACCA 59.726 61.111 0.00 0.00 0.00 4.17
2442 4798 1.272554 TACACCACACCACACCACCA 61.273 55.000 0.00 0.00 0.00 4.17
2443 4799 0.816421 GTACACCACACCACACCACC 60.816 60.000 0.00 0.00 0.00 4.61
2444 4800 0.179468 AGTACACCACACCACACCAC 59.821 55.000 0.00 0.00 0.00 4.16
2461 4817 2.103263 GCCGTGATATGAAAGGGAGAGT 59.897 50.000 0.00 0.00 0.00 3.24
2475 4831 4.479993 GCTCCAGCCAGCCGTGAT 62.480 66.667 0.00 0.00 32.76 3.06
2541 4897 4.147449 CGCCAGATCTGTGCCCGA 62.147 66.667 21.11 0.00 0.00 5.14
2588 4944 5.692654 CCGATTCAAATTATCATGCATGCAA 59.307 36.000 26.68 17.33 0.00 4.08


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

AutoCloner maintained by Alex Coulton.